Multiple sequence alignment - TraesCS2A01G040700

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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 TraesCS2A01G040700 chr2A 100.000 2906 0 0 1 2906 16623568 16620663 0.000000e+00 5367.0
1 TraesCS2A01G040700 chr2A 89.474 2014 138 42 1 1968 16609019 16607034 0.000000e+00 2477.0
2 TraesCS2A01G040700 chr2A 94.948 871 19 8 1969 2833 16607108 16606257 0.000000e+00 1341.0
3 TraesCS2A01G040700 chr2D 90.548 1333 71 17 657 1957 14379815 14381124 0.000000e+00 1712.0
4 TraesCS2A01G040700 chr2D 85.484 186 21 4 1969 2148 14381063 14381248 3.820000e-44 189.0
5 TraesCS2A01G040700 chr2D 84.444 135 18 2 482 616 289157301 289157170 2.350000e-26 130.0
6 TraesCS2A01G040700 chr2D 91.667 84 5 1 2285 2366 106857105 106857188 6.580000e-22 115.0
7 TraesCS2A01G040700 chr2D 100.000 28 0 0 2681 2708 54178498 54178471 5.000000e-03 52.8
8 TraesCS2A01G040700 chr2B 95.277 974 46 0 972 1945 26135613 26136586 0.000000e+00 1544.0
9 TraesCS2A01G040700 chr2B 91.363 822 45 11 1167 1966 26201391 26202208 0.000000e+00 1101.0
10 TraesCS2A01G040700 chr2B 83.577 274 13 13 691 954 26135306 26135557 8.100000e-56 228.0
11 TraesCS2A01G040700 chr2B 82.840 169 21 5 478 640 755622278 755622444 8.390000e-31 145.0
12 TraesCS2A01G040700 chr2B 87.097 124 13 2 2525 2646 26138119 26138241 1.400000e-28 137.0
13 TraesCS2A01G040700 chr1A 79.004 562 81 23 1097 1632 536974478 536975028 1.660000e-92 350.0
14 TraesCS2A01G040700 chr1A 94.286 70 4 0 2365 2434 100084879 100084810 1.100000e-19 108.0
15 TraesCS2A01G040700 chr1A 88.889 63 6 1 2832 2893 16938543 16938605 3.110000e-10 76.8
16 TraesCS2A01G040700 chr1B 78.832 548 93 13 1100 1628 598844454 598843911 5.960000e-92 348.0
17 TraesCS2A01G040700 chr1B 94.286 70 4 0 2365 2434 472046198 472046129 1.100000e-19 108.0
18 TraesCS2A01G040700 chr1B 75.926 162 29 4 2743 2902 653806934 653807087 1.120000e-09 75.0
19 TraesCS2A01G040700 chr1B 76.978 139 22 4 2766 2902 653806540 653806670 1.440000e-08 71.3
20 TraesCS2A01G040700 chr1B 76.978 139 22 4 2766 2902 653807374 653807504 1.440000e-08 71.3
21 TraesCS2A01G040700 chr1B 76.978 139 22 4 2766 2902 653807791 653807921 1.440000e-08 71.3
22 TraesCS2A01G040700 chr1B 76.978 139 22 4 2766 2902 653808208 653808338 1.440000e-08 71.3
23 TraesCS2A01G040700 chr5B 76.740 546 108 15 1091 1628 504775470 504776004 1.320000e-73 287.0
24 TraesCS2A01G040700 chr5B 83.824 136 19 2 478 613 129721948 129721816 3.040000e-25 126.0
25 TraesCS2A01G040700 chr5D 76.471 544 113 11 1091 1628 417607967 417608501 6.130000e-72 281.0
26 TraesCS2A01G040700 chr5D 86.585 82 9 2 2285 2364 435926775 435926856 3.990000e-14 89.8
27 TraesCS2A01G040700 chr6B 82.143 168 21 6 481 642 216574556 216574392 5.050000e-28 135.0
28 TraesCS2A01G040700 chr6B 85.714 84 9 3 2285 2366 253447305 253447387 5.160000e-13 86.1
29 TraesCS2A01G040700 chr1D 85.496 131 16 2 478 607 471764868 471764740 1.820000e-27 134.0
30 TraesCS2A01G040700 chr1D 84.444 135 19 1 478 612 3690246 3690114 6.530000e-27 132.0
31 TraesCS2A01G040700 chr1D 94.286 70 4 0 2365 2434 62800308 62800377 1.100000e-19 108.0
32 TraesCS2A01G040700 chr1D 92.857 70 5 0 2365 2434 45499747 45499816 5.120000e-18 102.0
33 TraesCS2A01G040700 chr1D 86.885 61 7 1 2834 2893 16358075 16358015 1.870000e-07 67.6
34 TraesCS2A01G040700 chr6D 86.555 119 15 1 474 592 337026531 337026414 2.350000e-26 130.0
35 TraesCS2A01G040700 chr6D 94.286 70 4 0 2365 2434 255009514 255009583 1.100000e-19 108.0
36 TraesCS2A01G040700 chr4A 79.412 170 24 6 479 639 56208489 56208656 3.060000e-20 110.0
37 TraesCS2A01G040700 chr7D 94.286 70 4 0 2365 2434 51464245 51464176 1.100000e-19 108.0
38 TraesCS2A01G040700 chr7D 89.706 68 7 0 2838 2905 484991232 484991165 1.430000e-13 87.9
39 TraesCS2A01G040700 chr5A 94.286 70 4 0 2365 2434 9566573 9566642 1.100000e-19 108.0
40 TraesCS2A01G040700 chr3B 94.286 70 4 0 2365 2434 43339554 43339623 1.100000e-19 108.0
41 TraesCS2A01G040700 chr3D 88.095 84 8 1 2285 2366 598117231 598117314 6.630000e-17 99.0
42 TraesCS2A01G040700 chr7A 86.905 84 8 3 2285 2366 610198631 610198713 1.110000e-14 91.6
43 TraesCS2A01G040700 chr7B 91.935 62 4 1 2833 2893 85790888 85790827 5.160000e-13 86.1


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 TraesCS2A01G040700 chr2A 16620663 16623568 2905 True 5367.000000 5367 100.000000 1 2906 1 chr2A.!!$R1 2905
1 TraesCS2A01G040700 chr2A 16606257 16609019 2762 True 1909.000000 2477 92.211000 1 2833 2 chr2A.!!$R2 2832
2 TraesCS2A01G040700 chr2D 14379815 14381248 1433 False 950.500000 1712 88.016000 657 2148 2 chr2D.!!$F2 1491
3 TraesCS2A01G040700 chr2B 26201391 26202208 817 False 1101.000000 1101 91.363000 1167 1966 1 chr2B.!!$F1 799
4 TraesCS2A01G040700 chr2B 26135306 26138241 2935 False 636.333333 1544 88.650333 691 2646 3 chr2B.!!$F3 1955
5 TraesCS2A01G040700 chr1A 536974478 536975028 550 False 350.000000 350 79.004000 1097 1632 1 chr1A.!!$F2 535
6 TraesCS2A01G040700 chr1B 598843911 598844454 543 True 348.000000 348 78.832000 1100 1628 1 chr1B.!!$R2 528
7 TraesCS2A01G040700 chr5B 504775470 504776004 534 False 287.000000 287 76.740000 1091 1628 1 chr5B.!!$F1 537
8 TraesCS2A01G040700 chr5D 417607967 417608501 534 False 281.000000 281 76.471000 1091 1628 1 chr5D.!!$F1 537

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
639 644 0.466555 CTCAGGGACGGAGGGAGTAG 60.467 65.0 0.0 0.0 46.65 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2279 3733 1.134491 GGTTACATTGGCTAGACCGCT 60.134 52.381 0.0 0.0 43.94 5.52 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 38 1.673920 GACCTCGTCTCTAGCAGGAAG 59.326 57.143 0.00 0.00 0.00 3.46
45 46 2.695666 TCTCTAGCAGGAAGTACCATGC 59.304 50.000 1.15 1.15 42.04 4.06
120 121 8.335356 CAATTTACATTAATGACCTACAGACGG 58.665 37.037 22.16 0.00 0.00 4.79
199 200 2.746279 TCAGGGGCAACAAGAGAAAA 57.254 45.000 0.00 0.00 39.74 2.29
225 228 7.759489 AAATACGCCATAATATTGGATGTGT 57.241 32.000 0.00 0.14 39.25 3.72
227 230 8.856153 AATACGCCATAATATTGGATGTGTAA 57.144 30.769 0.00 0.00 39.25 2.41
232 235 8.914654 CGCCATAATATTGGATGTGTAAAATTG 58.085 33.333 0.00 0.00 39.25 2.32
244 247 7.171337 GGATGTGTAAAATTGTTGACAAATGCT 59.829 33.333 0.10 0.00 39.55 3.79
255 258 5.472137 TGTTGACAAATGCTAGTTTAGGACC 59.528 40.000 0.00 0.00 0.00 4.46
276 279 5.869579 ACCATATATCCACAGTTCACATCC 58.130 41.667 0.00 0.00 0.00 3.51
279 282 7.237471 ACCATATATCCACAGTTCACATCCATA 59.763 37.037 0.00 0.00 0.00 2.74
287 290 7.015098 TCCACAGTTCACATCCATAATTTTTGT 59.985 33.333 0.00 0.00 0.00 2.83
300 303 2.350899 TTTTTGTGGATGCATGCTCG 57.649 45.000 20.33 0.00 0.00 5.03
306 309 3.643978 GATGCATGCTCGTCGGCC 61.644 66.667 20.33 0.00 0.00 6.13
308 311 3.974835 ATGCATGCTCGTCGGCCAA 62.975 57.895 20.33 0.00 0.00 4.52
383 386 1.071041 CGCGACGACGACATAGATGTA 60.071 52.381 12.29 0.00 41.95 2.29
388 391 4.288531 GACGACGACATAGATGTAAAGGG 58.711 47.826 0.00 0.00 41.95 3.95
397 400 2.871453 AGATGTAAAGGGTTGGCGTTT 58.129 42.857 0.00 0.00 0.00 3.60
398 401 4.023726 AGATGTAAAGGGTTGGCGTTTA 57.976 40.909 0.00 0.00 0.00 2.01
399 402 4.007659 AGATGTAAAGGGTTGGCGTTTAG 58.992 43.478 0.00 0.00 0.00 1.85
401 404 3.553904 TGTAAAGGGTTGGCGTTTAGTT 58.446 40.909 0.00 0.00 0.00 2.24
402 405 4.712476 TGTAAAGGGTTGGCGTTTAGTTA 58.288 39.130 0.00 0.00 0.00 2.24
403 406 4.756135 TGTAAAGGGTTGGCGTTTAGTTAG 59.244 41.667 0.00 0.00 0.00 2.34
404 407 3.497103 AAGGGTTGGCGTTTAGTTAGT 57.503 42.857 0.00 0.00 0.00 2.24
405 408 2.774687 AGGGTTGGCGTTTAGTTAGTG 58.225 47.619 0.00 0.00 0.00 2.74
406 409 1.198408 GGGTTGGCGTTTAGTTAGTGC 59.802 52.381 0.00 0.00 0.00 4.40
407 410 1.136169 GGTTGGCGTTTAGTTAGTGCG 60.136 52.381 0.00 0.00 0.00 5.34
413 417 2.413634 GCGTTTAGTTAGTGCGCCAAAT 60.414 45.455 4.18 0.00 41.93 2.32
490 494 1.442148 GCGTGGATGTACTCCCTCC 59.558 63.158 8.36 3.94 44.23 4.30
491 495 1.327690 GCGTGGATGTACTCCCTCCA 61.328 60.000 8.36 6.09 44.23 3.86
542 547 9.445786 GATTTTATTGTAAACCACATACGGATG 57.554 33.333 5.94 5.94 36.90 3.51
545 550 6.913873 ATTGTAAACCACATACGGATGTAC 57.086 37.500 14.23 8.34 44.82 2.90
570 575 9.731819 ACGTAGATACATTTTACAGTGTAGATG 57.268 33.333 19.31 19.31 34.60 2.90
571 576 9.731819 CGTAGATACATTTTACAGTGTAGATGT 57.268 33.333 25.14 25.14 34.60 3.06
583 588 9.938280 TTACAGTGTAGATGTACTTATTTTGCT 57.062 29.630 2.68 0.00 33.01 3.91
584 589 8.480643 ACAGTGTAGATGTACTTATTTTGCTC 57.519 34.615 0.00 0.00 0.00 4.26
586 591 6.757010 AGTGTAGATGTACTTATTTTGCTCCG 59.243 38.462 1.30 0.00 0.00 4.63
587 592 6.534079 GTGTAGATGTACTTATTTTGCTCCGT 59.466 38.462 1.30 0.00 0.00 4.69
588 593 7.703621 GTGTAGATGTACTTATTTTGCTCCGTA 59.296 37.037 1.30 0.00 0.00 4.02
597 602 8.813643 ACTTATTTTGCTCCGTATATGTAGTC 57.186 34.615 0.00 0.00 0.00 2.59
625 630 7.639113 AGTGAAATCTCTAGACTTACTCAGG 57.361 40.000 0.00 0.00 0.00 3.86
626 631 6.605594 AGTGAAATCTCTAGACTTACTCAGGG 59.394 42.308 0.00 0.00 0.00 4.45
627 632 6.603997 GTGAAATCTCTAGACTTACTCAGGGA 59.396 42.308 0.00 0.00 0.00 4.20
628 633 6.603997 TGAAATCTCTAGACTTACTCAGGGAC 59.396 42.308 0.00 0.00 0.00 4.46
629 634 4.139859 TCTCTAGACTTACTCAGGGACG 57.860 50.000 0.00 0.00 0.00 4.79
630 635 3.118334 TCTCTAGACTTACTCAGGGACGG 60.118 52.174 0.00 0.00 0.00 4.79
638 643 1.613610 CTCAGGGACGGAGGGAGTA 59.386 63.158 0.00 0.00 46.65 2.59
639 644 0.466555 CTCAGGGACGGAGGGAGTAG 60.467 65.000 0.00 0.00 46.65 2.57
640 645 1.212934 TCAGGGACGGAGGGAGTAGT 61.213 60.000 0.00 0.00 0.00 2.73
641 646 0.549950 CAGGGACGGAGGGAGTAGTA 59.450 60.000 0.00 0.00 0.00 1.82
687 705 1.959226 ACGTTTGAGCGTCCGCATT 60.959 52.632 14.70 0.00 41.71 3.56
729 757 4.221422 GCGGCGCCTAGACATGGA 62.221 66.667 26.68 0.00 0.00 3.41
824 854 1.652329 CGCAGCCGATCGAAATTGC 60.652 57.895 18.66 17.76 36.29 3.56
865 899 2.502510 CACGCGCGTACGTACCTT 60.503 61.111 37.24 6.52 46.34 3.50
866 900 2.502510 ACGCGCGTACGTACCTTG 60.503 61.111 37.08 10.60 46.19 3.61
867 901 2.502510 CGCGCGTACGTACCTTGT 60.503 61.111 24.19 0.00 42.83 3.16
868 902 2.770925 CGCGCGTACGTACCTTGTG 61.771 63.158 24.19 13.14 42.83 3.33
869 903 1.442520 GCGCGTACGTACCTTGTGA 60.443 57.895 19.67 0.00 42.83 3.58
870 904 1.003262 GCGCGTACGTACCTTGTGAA 61.003 55.000 19.67 0.00 42.83 3.18
871 905 0.704551 CGCGTACGTACCTTGTGAAC 59.295 55.000 19.67 0.00 33.53 3.18
872 906 1.769733 GCGTACGTACCTTGTGAACA 58.230 50.000 19.67 0.00 0.00 3.18
873 907 2.126467 GCGTACGTACCTTGTGAACAA 58.874 47.619 19.67 0.00 0.00 2.83
874 908 2.539274 GCGTACGTACCTTGTGAACAAA 59.461 45.455 19.67 0.00 35.15 2.83
881 915 3.733443 ACCTTGTGAACAAATGCCTTC 57.267 42.857 0.00 0.00 35.15 3.46
899 933 3.435169 CCTTCCTTCCTTGCCTATTACCC 60.435 52.174 0.00 0.00 0.00 3.69
900 934 3.145559 TCCTTCCTTGCCTATTACCCT 57.854 47.619 0.00 0.00 0.00 4.34
901 935 4.289837 TCCTTCCTTGCCTATTACCCTA 57.710 45.455 0.00 0.00 0.00 3.53
902 936 3.971971 TCCTTCCTTGCCTATTACCCTAC 59.028 47.826 0.00 0.00 0.00 3.18
903 937 3.072622 CCTTCCTTGCCTATTACCCTACC 59.927 52.174 0.00 0.00 0.00 3.18
969 1029 6.018425 GCCATGATCATCACTGTAACTAACTG 60.018 42.308 4.86 0.00 0.00 3.16
970 1030 6.018425 CCATGATCATCACTGTAACTAACTGC 60.018 42.308 4.86 0.00 0.00 4.40
989 1067 5.923204 ACTGCAAGAAGAAGAAGAAGAAGA 58.077 37.500 0.00 0.00 37.43 2.87
992 1070 5.238214 TGCAAGAAGAAGAAGAAGAAGAAGC 59.762 40.000 0.00 0.00 0.00 3.86
993 1071 5.238214 GCAAGAAGAAGAAGAAGAAGAAGCA 59.762 40.000 0.00 0.00 0.00 3.91
994 1072 6.566376 GCAAGAAGAAGAAGAAGAAGAAGCAG 60.566 42.308 0.00 0.00 0.00 4.24
995 1073 6.173427 AGAAGAAGAAGAAGAAGAAGCAGT 57.827 37.500 0.00 0.00 0.00 4.40
1027 1105 1.082117 CCGACGCCCTTCATGTGTAC 61.082 60.000 0.00 0.00 0.00 2.90
1037 1115 5.202004 CCCTTCATGTGTACTACTAGGAGT 58.798 45.833 13.42 13.42 0.00 3.85
1326 1410 2.285442 ACCCAGTACTCCCTGCCC 60.285 66.667 0.00 0.00 0.00 5.36
1717 1813 4.484872 GGTACCCCCGGAGCAAGC 62.485 72.222 0.73 0.00 0.00 4.01
1858 1968 3.271250 TGGGACAGGTACTACGACC 57.729 57.895 0.00 0.00 36.02 4.79
1872 1982 0.755698 ACGACCAGCAGACCGGATAT 60.756 55.000 9.46 0.00 0.00 1.63
1899 2009 0.739813 AACTCTACAACGGCGGCATC 60.740 55.000 13.24 0.00 0.00 3.91
1900 2010 1.153647 CTCTACAACGGCGGCATCA 60.154 57.895 13.24 0.00 0.00 3.07
1901 2011 0.739462 CTCTACAACGGCGGCATCAA 60.739 55.000 13.24 0.00 0.00 2.57
1902 2012 1.017177 TCTACAACGGCGGCATCAAC 61.017 55.000 13.24 0.00 0.00 3.18
1903 2013 1.004320 TACAACGGCGGCATCAACT 60.004 52.632 13.24 0.00 0.00 3.16
1904 2014 0.246910 TACAACGGCGGCATCAACTA 59.753 50.000 13.24 0.00 0.00 2.24
1905 2015 0.604243 ACAACGGCGGCATCAACTAA 60.604 50.000 13.24 0.00 0.00 2.24
1906 2016 0.732571 CAACGGCGGCATCAACTAAT 59.267 50.000 13.24 0.00 0.00 1.73
1907 2017 1.937223 CAACGGCGGCATCAACTAATA 59.063 47.619 13.24 0.00 0.00 0.98
1908 2018 2.319136 ACGGCGGCATCAACTAATAA 57.681 45.000 13.24 0.00 0.00 1.40
1909 2019 2.846193 ACGGCGGCATCAACTAATAAT 58.154 42.857 13.24 0.00 0.00 1.28
1910 2020 2.806244 ACGGCGGCATCAACTAATAATC 59.194 45.455 13.24 0.00 0.00 1.75
1911 2021 3.067106 CGGCGGCATCAACTAATAATCT 58.933 45.455 10.53 0.00 0.00 2.40
1912 2022 4.242475 CGGCGGCATCAACTAATAATCTA 58.758 43.478 10.53 0.00 0.00 1.98
1913 2023 4.091509 CGGCGGCATCAACTAATAATCTAC 59.908 45.833 10.53 0.00 0.00 2.59
1914 2024 4.994852 GGCGGCATCAACTAATAATCTACA 59.005 41.667 3.07 0.00 0.00 2.74
1915 2025 5.107065 GGCGGCATCAACTAATAATCTACAC 60.107 44.000 3.07 0.00 0.00 2.90
1916 2026 5.388475 GCGGCATCAACTAATAATCTACACG 60.388 44.000 0.00 0.00 0.00 4.49
1917 2027 5.388475 CGGCATCAACTAATAATCTACACGC 60.388 44.000 0.00 0.00 0.00 5.34
1918 2028 5.465390 GGCATCAACTAATAATCTACACGCA 59.535 40.000 0.00 0.00 0.00 5.24
1919 2029 6.147821 GGCATCAACTAATAATCTACACGCAT 59.852 38.462 0.00 0.00 0.00 4.73
1920 2030 7.011773 GCATCAACTAATAATCTACACGCATG 58.988 38.462 0.00 0.00 0.00 4.06
1921 2031 6.525121 TCAACTAATAATCTACACGCATGC 57.475 37.500 7.91 7.91 0.00 4.06
1922 2032 6.045955 TCAACTAATAATCTACACGCATGCA 58.954 36.000 19.57 0.00 0.00 3.96
1923 2033 6.705825 TCAACTAATAATCTACACGCATGCAT 59.294 34.615 19.57 0.00 0.00 3.96
1924 2034 6.471976 ACTAATAATCTACACGCATGCATG 57.528 37.500 22.70 22.70 0.00 4.06
1943 2053 5.177725 CATGCATGCATTATAGTGTGTGT 57.822 39.130 30.32 2.79 33.90 3.72
1944 2054 4.619437 TGCATGCATTATAGTGTGTGTG 57.381 40.909 18.46 0.00 0.00 3.82
1945 2055 3.377798 TGCATGCATTATAGTGTGTGTGG 59.622 43.478 18.46 0.00 0.00 4.17
1946 2056 3.243168 GCATGCATTATAGTGTGTGTGGG 60.243 47.826 14.21 0.00 0.00 4.61
1947 2057 2.997980 TGCATTATAGTGTGTGTGGGG 58.002 47.619 0.00 0.00 0.00 4.96
1948 2058 1.676006 GCATTATAGTGTGTGTGGGGC 59.324 52.381 0.00 0.00 0.00 5.80
1949 2059 2.943646 GCATTATAGTGTGTGTGGGGCA 60.944 50.000 0.00 0.00 0.00 5.36
1950 2060 3.351740 CATTATAGTGTGTGTGGGGCAA 58.648 45.455 0.00 0.00 0.00 4.52
1951 2061 3.730215 TTATAGTGTGTGTGGGGCAAT 57.270 42.857 0.00 0.00 0.00 3.56
1952 2062 4.846168 TTATAGTGTGTGTGGGGCAATA 57.154 40.909 0.00 0.00 0.00 1.90
1953 2063 3.730215 ATAGTGTGTGTGGGGCAATAA 57.270 42.857 0.00 0.00 0.00 1.40
1954 2064 2.603075 AGTGTGTGTGGGGCAATAAT 57.397 45.000 0.00 0.00 0.00 1.28
1955 2065 3.730215 AGTGTGTGTGGGGCAATAATA 57.270 42.857 0.00 0.00 0.00 0.98
1956 2066 4.040936 AGTGTGTGTGGGGCAATAATAA 57.959 40.909 0.00 0.00 0.00 1.40
1957 2067 4.609301 AGTGTGTGTGGGGCAATAATAAT 58.391 39.130 0.00 0.00 0.00 1.28
1958 2068 5.022787 AGTGTGTGTGGGGCAATAATAATT 58.977 37.500 0.00 0.00 0.00 1.40
1959 2069 5.483583 AGTGTGTGTGGGGCAATAATAATTT 59.516 36.000 0.00 0.00 0.00 1.82
1960 2070 6.665680 AGTGTGTGTGGGGCAATAATAATTTA 59.334 34.615 0.00 0.00 0.00 1.40
1961 2071 7.179338 AGTGTGTGTGGGGCAATAATAATTTAA 59.821 33.333 0.00 0.00 0.00 1.52
1962 2072 7.819900 GTGTGTGTGGGGCAATAATAATTTAAA 59.180 33.333 0.00 0.00 0.00 1.52
1963 2073 7.819900 TGTGTGTGGGGCAATAATAATTTAAAC 59.180 33.333 0.00 0.00 0.00 2.01
1964 2074 7.819900 GTGTGTGGGGCAATAATAATTTAAACA 59.180 33.333 0.00 0.00 0.00 2.83
1965 2075 7.819900 TGTGTGGGGCAATAATAATTTAAACAC 59.180 33.333 0.00 0.00 33.93 3.32
1966 2076 7.819900 GTGTGGGGCAATAATAATTTAAACACA 59.180 33.333 0.00 0.00 33.62 3.72
1967 2077 7.819900 TGTGGGGCAATAATAATTTAAACACAC 59.180 33.333 0.00 0.00 0.00 3.82
1968 2078 7.009723 GTGGGGCAATAATAATTTAAACACACG 59.990 37.037 0.00 0.00 0.00 4.49
1969 2079 6.019398 GGGGCAATAATAATTTAAACACACGC 60.019 38.462 0.00 0.00 0.00 5.34
1970 2080 6.531948 GGGCAATAATAATTTAAACACACGCA 59.468 34.615 0.00 0.00 0.00 5.24
1971 2081 7.223777 GGGCAATAATAATTTAAACACACGCAT 59.776 33.333 0.00 0.00 0.00 4.73
1987 2104 7.265673 ACACACGCATCAACTAATAATCTACT 58.734 34.615 0.00 0.00 0.00 2.57
2014 2135 3.181498 TGCATGCATTATAGTGTGTGTGC 60.181 43.478 18.46 0.00 0.00 4.57
2016 2137 1.396648 TGCATTATAGTGTGTGTGCGC 59.603 47.619 0.00 0.00 35.46 6.09
2272 3726 3.494045 TGAGATGACTGTAGAAGTGCG 57.506 47.619 0.00 0.00 40.07 5.34
2278 3732 0.962489 ACTGTAGAAGTGCGTGCTCT 59.038 50.000 0.00 0.00 37.88 4.09
2279 3733 2.160205 ACTGTAGAAGTGCGTGCTCTA 58.840 47.619 0.00 0.00 37.88 2.43
2280 3734 2.162608 ACTGTAGAAGTGCGTGCTCTAG 59.837 50.000 0.00 0.00 37.88 2.43
2281 3735 1.135373 TGTAGAAGTGCGTGCTCTAGC 60.135 52.381 0.00 0.00 42.50 3.42
2282 3736 0.098905 TAGAAGTGCGTGCTCTAGCG 59.901 55.000 0.00 0.00 45.83 4.26
2283 3737 2.125912 AAGTGCGTGCTCTAGCGG 60.126 61.111 0.00 0.00 45.83 5.52
2284 3738 2.820767 GAAGTGCGTGCTCTAGCGGT 62.821 60.000 0.00 0.00 45.83 5.68
2285 3739 2.820767 AAGTGCGTGCTCTAGCGGTC 62.821 60.000 0.00 0.00 45.83 4.79
2669 4123 8.178132 TCCTATTCTCCTCCTAATTAACTAGGG 58.822 40.741 10.02 1.53 39.26 3.53
2670 4124 7.400627 CCTATTCTCCTCCTAATTAACTAGGGG 59.599 44.444 10.02 6.52 39.05 4.79
2671 4125 4.490706 TCTCCTCCTAATTAACTAGGGGC 58.509 47.826 10.02 0.00 38.12 5.80
2672 4126 4.078219 TCTCCTCCTAATTAACTAGGGGCA 60.078 45.833 10.02 0.00 38.12 5.36
2673 4127 4.637600 TCCTCCTAATTAACTAGGGGCAA 58.362 43.478 10.02 0.00 38.12 4.52
2674 4128 5.041015 TCCTCCTAATTAACTAGGGGCAAA 58.959 41.667 10.02 0.00 38.12 3.68
2675 4129 5.674958 TCCTCCTAATTAACTAGGGGCAAAT 59.325 40.000 10.02 0.00 38.12 2.32
2676 4130 5.770162 CCTCCTAATTAACTAGGGGCAAATG 59.230 44.000 10.02 0.00 38.12 2.32
2677 4131 5.701224 TCCTAATTAACTAGGGGCAAATGG 58.299 41.667 10.02 0.00 39.26 3.16
2687 4141 0.752658 GGGCAAATGGTAAGGGCATC 59.247 55.000 0.00 0.00 0.00 3.91
2699 4153 1.831580 AGGGCATCTTCAAAGCTGAC 58.168 50.000 0.00 0.00 29.44 3.51
2711 4165 1.506493 AAGCTGACTCTCAAACTGCG 58.494 50.000 0.00 0.00 34.59 5.18
2714 4168 1.858091 CTGACTCTCAAACTGCGTGT 58.142 50.000 0.00 0.00 0.00 4.49
2721 4175 3.472652 TCTCAAACTGCGTGTAACCATT 58.527 40.909 0.00 0.00 0.00 3.16
2776 4230 1.019278 AGCAGGCGTGTATCGGTTTG 61.019 55.000 8.40 0.00 40.26 2.93
2784 4238 1.850441 GTGTATCGGTTTGTCGATCGG 59.150 52.381 16.41 0.00 45.43 4.18
2791 4245 0.179119 GTTTGTCGATCGGTCCGGAT 60.179 55.000 16.41 3.60 0.00 4.18
2796 4250 1.033202 TCGATCGGTCCGGATGTGAA 61.033 55.000 16.41 0.00 0.00 3.18
2822 4276 1.068434 CCACAAACCGGAAACATGCTT 59.932 47.619 9.46 0.00 0.00 3.91
2848 4302 4.062032 GGGGGCTTTGGGGAGTCC 62.062 72.222 0.00 0.00 40.79 3.85
2849 4303 4.426313 GGGGCTTTGGGGAGTCCG 62.426 72.222 2.26 0.00 42.49 4.79
2850 4304 4.426313 GGGCTTTGGGGAGTCCGG 62.426 72.222 2.26 0.00 38.76 5.14
2851 4305 3.327404 GGCTTTGGGGAGTCCGGA 61.327 66.667 0.00 0.00 38.76 5.14
2852 4306 2.046217 GCTTTGGGGAGTCCGGAC 60.046 66.667 27.67 27.67 38.76 4.79
2853 4307 2.669240 CTTTGGGGAGTCCGGACC 59.331 66.667 30.82 21.02 38.76 4.46
2854 4308 3.310860 CTTTGGGGAGTCCGGACCG 62.311 68.421 30.82 6.99 38.76 4.79
2855 4309 4.626402 TTGGGGAGTCCGGACCGT 62.626 66.667 30.82 14.09 38.76 4.83
2856 4310 4.626402 TGGGGAGTCCGGACCGTT 62.626 66.667 30.82 13.25 38.76 4.44
2857 4311 4.078516 GGGGAGTCCGGACCGTTG 62.079 72.222 30.82 0.00 0.00 4.10
2858 4312 3.308705 GGGAGTCCGGACCGTTGT 61.309 66.667 30.82 12.40 0.00 3.32
2859 4313 2.260743 GGAGTCCGGACCGTTGTC 59.739 66.667 30.82 20.32 40.98 3.18
2860 4314 2.567497 GGAGTCCGGACCGTTGTCA 61.567 63.158 30.82 0.00 43.65 3.58
2861 4315 1.372623 GAGTCCGGACCGTTGTCAC 60.373 63.158 30.82 3.19 43.65 3.67
2862 4316 2.732094 GTCCGGACCGTTGTCACG 60.732 66.667 24.75 0.00 46.71 4.35
2863 4317 3.218470 TCCGGACCGTTGTCACGT 61.218 61.111 13.94 0.00 45.62 4.49
2864 4318 2.732094 CCGGACCGTTGTCACGTC 60.732 66.667 13.94 0.00 45.62 4.34
2865 4319 2.732094 CGGACCGTTGTCACGTCC 60.732 66.667 5.48 0.00 45.62 4.79
2866 4320 2.732094 GGACCGTTGTCACGTCCG 60.732 66.667 0.00 0.00 45.62 4.79
2867 4321 3.400590 GACCGTTGTCACGTCCGC 61.401 66.667 0.00 0.00 45.62 5.54
2868 4322 3.836176 GACCGTTGTCACGTCCGCT 62.836 63.158 0.00 0.00 45.62 5.52
2869 4323 2.660552 CCGTTGTCACGTCCGCTT 60.661 61.111 0.00 0.00 45.62 4.68
2870 4324 2.654912 CCGTTGTCACGTCCGCTTC 61.655 63.158 0.00 0.00 45.62 3.86
2871 4325 1.660575 CGTTGTCACGTCCGCTTCT 60.661 57.895 0.00 0.00 41.84 2.85
2872 4326 1.853319 GTTGTCACGTCCGCTTCTG 59.147 57.895 0.00 0.00 0.00 3.02
2873 4327 0.596600 GTTGTCACGTCCGCTTCTGA 60.597 55.000 0.00 0.00 0.00 3.27
2874 4328 0.596600 TTGTCACGTCCGCTTCTGAC 60.597 55.000 0.00 2.36 34.74 3.51
2875 4329 1.286260 GTCACGTCCGCTTCTGACT 59.714 57.895 0.00 0.00 31.99 3.41
2876 4330 1.004277 GTCACGTCCGCTTCTGACTG 61.004 60.000 0.00 0.00 31.99 3.51
2877 4331 2.049063 ACGTCCGCTTCTGACTGC 60.049 61.111 0.00 0.00 0.00 4.40
2878 4332 2.811317 CGTCCGCTTCTGACTGCC 60.811 66.667 0.00 0.00 0.00 4.85
2879 4333 2.435059 GTCCGCTTCTGACTGCCC 60.435 66.667 0.00 0.00 0.00 5.36
2880 4334 2.604686 TCCGCTTCTGACTGCCCT 60.605 61.111 0.00 0.00 0.00 5.19
2881 4335 2.435586 CCGCTTCTGACTGCCCTG 60.436 66.667 0.00 0.00 0.00 4.45
2882 4336 2.659016 CGCTTCTGACTGCCCTGA 59.341 61.111 0.00 0.00 0.00 3.86
2883 4337 1.739562 CGCTTCTGACTGCCCTGAC 60.740 63.158 0.00 0.00 0.00 3.51
2884 4338 1.376553 GCTTCTGACTGCCCTGACC 60.377 63.158 0.00 0.00 0.00 4.02
2885 4339 1.298014 CTTCTGACTGCCCTGACCC 59.702 63.158 0.00 0.00 0.00 4.46
2886 4340 1.461268 TTCTGACTGCCCTGACCCA 60.461 57.895 0.00 0.00 0.00 4.51
2887 4341 1.768684 TTCTGACTGCCCTGACCCAC 61.769 60.000 0.00 0.00 0.00 4.61
2888 4342 3.249189 TGACTGCCCTGACCCACC 61.249 66.667 0.00 0.00 0.00 4.61
2889 4343 4.035102 GACTGCCCTGACCCACCC 62.035 72.222 0.00 0.00 0.00 4.61
2890 4344 4.918360 ACTGCCCTGACCCACCCA 62.918 66.667 0.00 0.00 0.00 4.51
2891 4345 3.579302 CTGCCCTGACCCACCCAA 61.579 66.667 0.00 0.00 0.00 4.12
2892 4346 3.106609 TGCCCTGACCCACCCAAA 61.107 61.111 0.00 0.00 0.00 3.28
2893 4347 2.200092 GCCCTGACCCACCCAAAA 59.800 61.111 0.00 0.00 0.00 2.44
2894 4348 1.458588 GCCCTGACCCACCCAAAAA 60.459 57.895 0.00 0.00 0.00 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
13 14 1.353804 GCTAGAGACGAGGTCTGCG 59.646 63.158 2.51 0.00 43.53 5.18
19 20 1.757682 ACTTCCTGCTAGAGACGAGG 58.242 55.000 0.00 0.00 0.00 4.63
20 21 2.614983 GGTACTTCCTGCTAGAGACGAG 59.385 54.545 0.00 0.00 0.00 4.18
110 111 4.508124 GCAATAATCTTGACCGTCTGTAGG 59.492 45.833 0.00 0.00 0.00 3.18
120 121 6.321717 TCATTTCAACCGCAATAATCTTGAC 58.678 36.000 0.00 0.00 0.00 3.18
199 200 8.637986 ACACATCCAATATTATGGCGTATTTTT 58.362 29.630 3.80 0.00 40.46 1.94
227 230 8.637986 TCCTAAACTAGCATTTGTCAACAATTT 58.362 29.630 0.00 0.00 35.55 1.82
232 235 5.472137 TGGTCCTAAACTAGCATTTGTCAAC 59.528 40.000 0.00 0.00 0.00 3.18
244 247 8.792830 AACTGTGGATATATGGTCCTAAACTA 57.207 34.615 9.56 0.00 36.68 2.24
255 258 9.676861 ATTATGGATGTGAACTGTGGATATATG 57.323 33.333 0.00 0.00 0.00 1.78
276 279 5.051307 CGAGCATGCATCCACAAAAATTATG 60.051 40.000 21.98 0.00 0.00 1.90
279 282 3.255725 CGAGCATGCATCCACAAAAATT 58.744 40.909 21.98 0.00 0.00 1.82
287 290 2.202919 CCGACGAGCATGCATCCA 60.203 61.111 21.98 0.00 0.00 3.41
290 293 3.974835 TTGGCCGACGAGCATGCAT 62.975 57.895 21.98 4.40 0.00 3.96
300 303 0.669318 TCGTCATCAACTTGGCCGAC 60.669 55.000 0.00 0.00 0.00 4.79
306 309 1.139989 ACACGCTCGTCATCAACTTG 58.860 50.000 0.00 0.00 0.00 3.16
308 311 1.732732 GCTACACGCTCGTCATCAACT 60.733 52.381 0.00 0.00 35.14 3.16
329 332 1.885887 GCCACAACCATGTAAAGCTCA 59.114 47.619 0.00 0.00 37.82 4.26
362 365 0.992263 CATCTATGTCGTCGTCGCGG 60.992 60.000 6.13 0.00 36.96 6.46
363 366 0.315951 ACATCTATGTCGTCGTCGCG 60.316 55.000 0.00 0.00 35.87 5.87
369 372 4.809426 CCAACCCTTTACATCTATGTCGTC 59.191 45.833 0.00 0.00 41.97 4.20
372 375 3.560068 CGCCAACCCTTTACATCTATGTC 59.440 47.826 0.00 0.00 41.97 3.06
383 386 3.566742 CACTAACTAAACGCCAACCCTTT 59.433 43.478 0.00 0.00 0.00 3.11
388 391 1.723701 GCGCACTAACTAAACGCCAAC 60.724 52.381 0.30 0.00 43.58 3.77
397 400 3.129113 TCGTCTATTTGGCGCACTAACTA 59.871 43.478 10.83 0.00 44.46 2.24
398 401 2.094390 TCGTCTATTTGGCGCACTAACT 60.094 45.455 10.83 0.00 44.46 2.24
399 402 2.264813 TCGTCTATTTGGCGCACTAAC 58.735 47.619 10.83 0.00 44.46 2.34
401 404 2.159156 ACATCGTCTATTTGGCGCACTA 60.159 45.455 10.83 0.00 44.46 2.74
402 405 1.290203 CATCGTCTATTTGGCGCACT 58.710 50.000 10.83 0.00 44.46 4.40
403 406 1.006832 ACATCGTCTATTTGGCGCAC 58.993 50.000 10.83 0.00 44.46 5.34
404 407 2.588027 TACATCGTCTATTTGGCGCA 57.412 45.000 10.83 0.00 44.46 6.09
405 408 2.800544 ACATACATCGTCTATTTGGCGC 59.199 45.455 0.00 0.00 44.46 6.53
406 409 7.700656 TGATATACATACATCGTCTATTTGGCG 59.299 37.037 0.00 0.00 46.47 5.69
407 410 8.926715 TGATATACATACATCGTCTATTTGGC 57.073 34.615 0.00 0.00 0.00 4.52
413 417 8.893727 CACCTCATGATATACATACATCGTCTA 58.106 37.037 0.00 0.00 37.46 2.59
514 519 8.885722 TCCGTATGTGGTTTACAATAAAATCTC 58.114 33.333 0.00 0.00 43.77 2.75
521 526 6.696583 CGTACATCCGTATGTGGTTTACAATA 59.303 38.462 3.56 0.00 45.99 1.90
523 528 4.863689 CGTACATCCGTATGTGGTTTACAA 59.136 41.667 3.56 0.00 45.99 2.41
525 530 4.423732 ACGTACATCCGTATGTGGTTTAC 58.576 43.478 3.56 0.00 45.99 2.01
527 532 3.598019 ACGTACATCCGTATGTGGTTT 57.402 42.857 3.56 0.00 45.99 3.27
528 533 3.947196 TCTACGTACATCCGTATGTGGTT 59.053 43.478 3.56 0.00 45.45 3.67
533 538 8.738199 AAAATGTATCTACGTACATCCGTATG 57.262 34.615 2.31 0.00 42.79 2.39
545 550 9.731819 ACATCTACACTGTAAAATGTATCTACG 57.268 33.333 12.22 0.00 31.10 3.51
560 565 7.254117 CGGAGCAAAATAAGTACATCTACACTG 60.254 40.741 0.00 0.00 0.00 3.66
570 575 9.688592 ACTACATATACGGAGCAAAATAAGTAC 57.311 33.333 0.00 0.00 0.00 2.73
571 576 9.903682 GACTACATATACGGAGCAAAATAAGTA 57.096 33.333 0.00 0.00 0.00 2.24
572 577 8.639761 AGACTACATATACGGAGCAAAATAAGT 58.360 33.333 0.00 0.00 0.00 2.24
581 586 8.489990 TTCACTATAGACTACATATACGGAGC 57.510 38.462 6.78 0.00 0.00 4.70
614 619 1.104630 CCTCCGTCCCTGAGTAAGTC 58.895 60.000 0.00 0.00 0.00 3.01
616 621 0.033405 TCCCTCCGTCCCTGAGTAAG 60.033 60.000 0.00 0.00 0.00 2.34
618 623 1.212934 ACTCCCTCCGTCCCTGAGTA 61.213 60.000 0.00 0.00 34.68 2.59
619 624 1.212934 TACTCCCTCCGTCCCTGAGT 61.213 60.000 0.00 0.00 39.47 3.41
620 625 0.466555 CTACTCCCTCCGTCCCTGAG 60.467 65.000 0.00 0.00 0.00 3.35
621 626 1.212934 ACTACTCCCTCCGTCCCTGA 61.213 60.000 0.00 0.00 0.00 3.86
622 627 0.549950 TACTACTCCCTCCGTCCCTG 59.450 60.000 0.00 0.00 0.00 4.45
623 628 0.845337 CTACTACTCCCTCCGTCCCT 59.155 60.000 0.00 0.00 0.00 4.20
624 629 0.178995 CCTACTACTCCCTCCGTCCC 60.179 65.000 0.00 0.00 0.00 4.46
625 630 0.842635 TCCTACTACTCCCTCCGTCC 59.157 60.000 0.00 0.00 0.00 4.79
626 631 1.476652 GGTCCTACTACTCCCTCCGTC 60.477 61.905 0.00 0.00 0.00 4.79
627 632 0.550432 GGTCCTACTACTCCCTCCGT 59.450 60.000 0.00 0.00 0.00 4.69
628 633 0.549950 TGGTCCTACTACTCCCTCCG 59.450 60.000 0.00 0.00 0.00 4.63
629 634 2.842645 TTGGTCCTACTACTCCCTCC 57.157 55.000 0.00 0.00 0.00 4.30
630 635 3.119209 CGTTTTGGTCCTACTACTCCCTC 60.119 52.174 0.00 0.00 0.00 4.30
632 637 2.676176 GCGTTTTGGTCCTACTACTCCC 60.676 54.545 0.00 0.00 0.00 4.30
633 638 2.614779 GCGTTTTGGTCCTACTACTCC 58.385 52.381 0.00 0.00 0.00 3.85
635 640 1.670967 GCGCGTTTTGGTCCTACTACT 60.671 52.381 8.43 0.00 0.00 2.57
636 641 0.717784 GCGCGTTTTGGTCCTACTAC 59.282 55.000 8.43 0.00 0.00 2.73
638 643 2.025418 CGCGCGTTTTGGTCCTACT 61.025 57.895 24.19 0.00 0.00 2.57
639 644 2.472934 CGCGCGTTTTGGTCCTAC 59.527 61.111 24.19 0.00 0.00 3.18
640 645 3.416382 GCGCGCGTTTTGGTCCTA 61.416 61.111 32.35 0.00 0.00 2.94
682 700 4.023707 GGAGAAGACCCATTGATTAATGCG 60.024 45.833 4.71 0.00 41.87 4.73
684 702 6.548622 ACATGGAGAAGACCCATTGATTAATG 59.451 38.462 3.26 3.26 42.18 1.90
685 703 6.548622 CACATGGAGAAGACCCATTGATTAAT 59.451 38.462 0.00 0.00 42.18 1.40
687 705 5.439721 CACATGGAGAAGACCCATTGATTA 58.560 41.667 0.00 0.00 42.18 1.75
720 748 3.627395 AAACGGCAGATTCCATGTCTA 57.373 42.857 0.00 0.00 0.00 2.59
724 752 3.855689 AAGAAAACGGCAGATTCCATG 57.144 42.857 0.00 0.00 0.00 3.66
727 755 4.435651 CGTAGAAAGAAAACGGCAGATTCC 60.436 45.833 0.00 0.00 33.13 3.01
729 757 3.120304 GCGTAGAAAGAAAACGGCAGATT 60.120 43.478 0.00 0.00 37.12 2.40
813 843 2.352343 GCCGGCGCAATTTCGATC 60.352 61.111 12.58 0.00 34.03 3.69
824 854 1.442520 CATTTCTTGTGTGCCGGCG 60.443 57.895 23.90 6.13 0.00 6.46
865 899 2.627699 GGAAGGAAGGCATTTGTTCACA 59.372 45.455 8.17 0.00 0.00 3.58
866 900 2.893489 AGGAAGGAAGGCATTTGTTCAC 59.107 45.455 8.17 0.33 0.00 3.18
867 901 3.243359 AGGAAGGAAGGCATTTGTTCA 57.757 42.857 8.17 0.00 0.00 3.18
868 902 3.862264 GCAAGGAAGGAAGGCATTTGTTC 60.862 47.826 0.00 0.00 0.00 3.18
869 903 2.037641 GCAAGGAAGGAAGGCATTTGTT 59.962 45.455 0.00 0.00 0.00 2.83
870 904 1.620323 GCAAGGAAGGAAGGCATTTGT 59.380 47.619 0.00 0.00 0.00 2.83
871 905 1.066645 GGCAAGGAAGGAAGGCATTTG 60.067 52.381 0.00 0.00 0.00 2.32
872 906 1.203225 AGGCAAGGAAGGAAGGCATTT 60.203 47.619 0.00 0.00 0.00 2.32
873 907 0.411058 AGGCAAGGAAGGAAGGCATT 59.589 50.000 0.00 0.00 0.00 3.56
874 908 1.298953 TAGGCAAGGAAGGAAGGCAT 58.701 50.000 0.00 0.00 0.00 4.40
881 915 3.072622 GGTAGGGTAATAGGCAAGGAAGG 59.927 52.174 0.00 0.00 0.00 3.46
899 933 2.949678 CGCGCGTGCAGTAGGTAG 60.950 66.667 24.19 0.00 42.97 3.18
969 1029 5.238214 TGCTTCTTCTTCTTCTTCTTCTTGC 59.762 40.000 0.00 0.00 0.00 4.01
970 1030 6.482973 ACTGCTTCTTCTTCTTCTTCTTCTTG 59.517 38.462 0.00 0.00 0.00 3.02
1027 1105 2.801679 CGGCGAGAAGTACTCCTAGTAG 59.198 54.545 0.00 0.00 42.18 2.57
1037 1115 1.093159 GAAGGAGACGGCGAGAAGTA 58.907 55.000 16.62 0.00 0.00 2.24
1821 1931 3.379865 GAGCATGACCCCGCCGTAA 62.380 63.158 0.00 0.00 0.00 3.18
1858 1968 1.302033 GGCCATATCCGGTCTGCTG 60.302 63.158 0.00 0.00 0.00 4.41
1872 1982 1.373748 GTTGTAGAGTTCGCGGCCA 60.374 57.895 6.13 0.00 0.00 5.36
1899 2009 6.285790 TGCATGCGTGTAGATTATTAGTTG 57.714 37.500 14.09 0.00 0.00 3.16
1900 2010 6.566564 GCATGCATGCGTGTAGATTATTAGTT 60.567 38.462 33.99 0.00 44.67 2.24
1901 2011 5.106948 GCATGCATGCGTGTAGATTATTAGT 60.107 40.000 33.99 0.00 44.67 2.24
1902 2012 5.319139 GCATGCATGCGTGTAGATTATTAG 58.681 41.667 33.99 10.77 44.67 1.73
1903 2013 5.281693 GCATGCATGCGTGTAGATTATTA 57.718 39.130 33.99 4.90 44.67 0.98
1904 2014 4.151258 GCATGCATGCGTGTAGATTATT 57.849 40.909 33.99 0.00 44.67 1.40
1905 2015 3.818961 GCATGCATGCGTGTAGATTAT 57.181 42.857 33.99 8.53 44.67 1.28
1921 2031 4.973663 CACACACACTATAATGCATGCATG 59.026 41.667 32.79 22.59 36.68 4.06
1922 2032 4.037089 CCACACACACTATAATGCATGCAT 59.963 41.667 27.46 27.46 38.46 3.96
1923 2033 3.377798 CCACACACACTATAATGCATGCA 59.622 43.478 25.04 25.04 0.00 3.96
1924 2034 3.243168 CCCACACACACTATAATGCATGC 60.243 47.826 11.82 11.82 0.00 4.06
1925 2035 3.316029 CCCCACACACACTATAATGCATG 59.684 47.826 0.00 0.00 0.00 4.06
1926 2036 3.554934 CCCCACACACACTATAATGCAT 58.445 45.455 0.00 0.00 0.00 3.96
1927 2037 2.943646 GCCCCACACACACTATAATGCA 60.944 50.000 0.00 0.00 0.00 3.96
1928 2038 1.676006 GCCCCACACACACTATAATGC 59.324 52.381 0.00 0.00 0.00 3.56
1929 2039 2.997980 TGCCCCACACACACTATAATG 58.002 47.619 0.00 0.00 0.00 1.90
1930 2040 3.730215 TTGCCCCACACACACTATAAT 57.270 42.857 0.00 0.00 0.00 1.28
1931 2041 3.730215 ATTGCCCCACACACACTATAA 57.270 42.857 0.00 0.00 0.00 0.98
1932 2042 4.846168 TTATTGCCCCACACACACTATA 57.154 40.909 0.00 0.00 0.00 1.31
1933 2043 3.730215 TTATTGCCCCACACACACTAT 57.270 42.857 0.00 0.00 0.00 2.12
1934 2044 3.730215 ATTATTGCCCCACACACACTA 57.270 42.857 0.00 0.00 0.00 2.74
1935 2045 2.603075 ATTATTGCCCCACACACACT 57.397 45.000 0.00 0.00 0.00 3.55
1936 2046 5.337578 AATTATTATTGCCCCACACACAC 57.662 39.130 0.00 0.00 0.00 3.82
1937 2047 7.482169 TTAAATTATTATTGCCCCACACACA 57.518 32.000 0.00 0.00 0.00 3.72
1938 2048 7.819900 TGTTTAAATTATTATTGCCCCACACAC 59.180 33.333 0.00 0.00 0.00 3.82
1939 2049 7.819900 GTGTTTAAATTATTATTGCCCCACACA 59.180 33.333 0.00 0.00 0.00 3.72
1940 2050 7.819900 TGTGTTTAAATTATTATTGCCCCACAC 59.180 33.333 0.00 0.00 0.00 3.82
1941 2051 7.819900 GTGTGTTTAAATTATTATTGCCCCACA 59.180 33.333 0.00 0.00 0.00 4.17
1942 2052 7.009723 CGTGTGTTTAAATTATTATTGCCCCAC 59.990 37.037 0.00 0.00 0.00 4.61
1943 2053 7.036220 CGTGTGTTTAAATTATTATTGCCCCA 58.964 34.615 0.00 0.00 0.00 4.96
1944 2054 6.019398 GCGTGTGTTTAAATTATTATTGCCCC 60.019 38.462 0.00 0.00 0.00 5.80
1945 2055 6.531948 TGCGTGTGTTTAAATTATTATTGCCC 59.468 34.615 0.00 0.00 0.00 5.36
1946 2056 7.513190 TGCGTGTGTTTAAATTATTATTGCC 57.487 32.000 0.00 0.00 0.00 4.52
1947 2057 8.802856 TGATGCGTGTGTTTAAATTATTATTGC 58.197 29.630 0.00 0.00 0.00 3.56
1952 2062 9.900710 TTAGTTGATGCGTGTGTTTAAATTATT 57.099 25.926 0.00 0.00 0.00 1.40
1955 2065 9.900710 TTATTAGTTGATGCGTGTGTTTAAATT 57.099 25.926 0.00 0.00 0.00 1.82
1957 2067 9.549509 GATTATTAGTTGATGCGTGTGTTTAAA 57.450 29.630 0.00 0.00 0.00 1.52
1958 2068 8.941977 AGATTATTAGTTGATGCGTGTGTTTAA 58.058 29.630 0.00 0.00 0.00 1.52
1959 2069 8.487313 AGATTATTAGTTGATGCGTGTGTTTA 57.513 30.769 0.00 0.00 0.00 2.01
1960 2070 7.377766 AGATTATTAGTTGATGCGTGTGTTT 57.622 32.000 0.00 0.00 0.00 2.83
1961 2071 6.985188 AGATTATTAGTTGATGCGTGTGTT 57.015 33.333 0.00 0.00 0.00 3.32
1962 2072 7.265673 AGTAGATTATTAGTTGATGCGTGTGT 58.734 34.615 0.00 0.00 0.00 3.72
1963 2073 7.357613 CGAGTAGATTATTAGTTGATGCGTGTG 60.358 40.741 0.00 0.00 0.00 3.82
1964 2074 6.637254 CGAGTAGATTATTAGTTGATGCGTGT 59.363 38.462 0.00 0.00 0.00 4.49
1965 2075 6.399039 GCGAGTAGATTATTAGTTGATGCGTG 60.399 42.308 0.00 0.00 0.00 5.34
1966 2076 5.629849 GCGAGTAGATTATTAGTTGATGCGT 59.370 40.000 0.00 0.00 0.00 5.24
1967 2077 5.629435 TGCGAGTAGATTATTAGTTGATGCG 59.371 40.000 0.00 0.00 0.00 4.73
1968 2078 7.451429 CATGCGAGTAGATTATTAGTTGATGC 58.549 38.462 0.00 0.00 0.00 3.91
1969 2079 7.116805 TGCATGCGAGTAGATTATTAGTTGATG 59.883 37.037 14.09 0.00 0.00 3.07
1970 2080 7.154656 TGCATGCGAGTAGATTATTAGTTGAT 58.845 34.615 14.09 0.00 0.00 2.57
1971 2081 6.512297 TGCATGCGAGTAGATTATTAGTTGA 58.488 36.000 14.09 0.00 0.00 3.18
2014 2135 7.971168 TCAGGTGTGTTTAAATTATTATTGGCG 59.029 33.333 0.00 0.00 0.00 5.69
2260 3714 2.791567 CTAGAGCACGCACTTCTACAG 58.208 52.381 0.00 0.00 0.00 2.74
2272 3726 1.360911 GGCTAGACCGCTAGAGCAC 59.639 63.158 1.89 0.00 45.71 4.40
2278 3732 2.101917 GGTTACATTGGCTAGACCGCTA 59.898 50.000 0.00 0.00 43.94 4.26
2279 3733 1.134491 GGTTACATTGGCTAGACCGCT 60.134 52.381 0.00 0.00 43.94 5.52
2280 3734 1.296727 GGTTACATTGGCTAGACCGC 58.703 55.000 0.00 0.00 43.94 5.68
2281 3735 2.684001 TGGTTACATTGGCTAGACCG 57.316 50.000 0.00 0.00 43.94 4.79
2282 3736 5.715434 TTTTTGGTTACATTGGCTAGACC 57.285 39.130 0.00 0.00 39.84 3.85
2669 4123 1.780503 AGATGCCCTTACCATTTGCC 58.219 50.000 0.00 0.00 0.00 4.52
2670 4124 2.760092 TGAAGATGCCCTTACCATTTGC 59.240 45.455 0.00 0.00 34.68 3.68
2671 4125 5.404466 TTTGAAGATGCCCTTACCATTTG 57.596 39.130 0.00 0.00 34.68 2.32
2672 4126 4.081476 GCTTTGAAGATGCCCTTACCATTT 60.081 41.667 0.00 0.00 34.68 2.32
2673 4127 3.448660 GCTTTGAAGATGCCCTTACCATT 59.551 43.478 0.00 0.00 34.68 3.16
2674 4128 3.026694 GCTTTGAAGATGCCCTTACCAT 58.973 45.455 0.00 0.00 34.68 3.55
2675 4129 2.041620 AGCTTTGAAGATGCCCTTACCA 59.958 45.455 0.00 0.00 34.68 3.25
2676 4130 2.424956 CAGCTTTGAAGATGCCCTTACC 59.575 50.000 0.00 0.00 35.47 2.85
2677 4131 3.127721 GTCAGCTTTGAAGATGCCCTTAC 59.872 47.826 4.20 0.00 41.94 2.34
2687 4141 4.554330 GCAGTTTGAGAGTCAGCTTTGAAG 60.554 45.833 0.00 0.00 0.00 3.02
2699 4153 2.479837 TGGTTACACGCAGTTTGAGAG 58.520 47.619 0.00 0.00 41.61 3.20
2711 4165 3.128589 ACATGCAATCCGAATGGTTACAC 59.871 43.478 0.00 0.00 36.30 2.90
2714 4168 4.096231 CAGAACATGCAATCCGAATGGTTA 59.904 41.667 0.00 0.00 36.30 2.85
2721 4175 1.678728 GGTCCAGAACATGCAATCCGA 60.679 52.381 0.00 0.00 0.00 4.55
2776 4230 1.299165 CACATCCGGACCGATCGAC 60.299 63.158 18.66 10.14 0.00 4.20
2784 4238 3.254657 TGTGGAAAAATTCACATCCGGAC 59.745 43.478 6.12 0.00 38.75 4.79
2791 4245 3.447586 TCCGGTTTGTGGAAAAATTCACA 59.552 39.130 0.00 0.00 41.47 3.58
2832 4286 4.426313 CGGACTCCCCAAAGCCCC 62.426 72.222 0.00 0.00 34.14 5.80
2833 4287 4.426313 CCGGACTCCCCAAAGCCC 62.426 72.222 0.00 0.00 34.14 5.19
2834 4288 3.327404 TCCGGACTCCCCAAAGCC 61.327 66.667 0.00 0.00 34.14 4.35
2835 4289 2.046217 GTCCGGACTCCCCAAAGC 60.046 66.667 27.64 0.00 34.14 3.51
2836 4290 2.669240 GGTCCGGACTCCCCAAAG 59.331 66.667 32.52 0.00 34.14 2.77
2837 4291 3.315949 CGGTCCGGACTCCCCAAA 61.316 66.667 32.52 0.00 34.14 3.28
2838 4292 4.626402 ACGGTCCGGACTCCCCAA 62.626 66.667 32.52 0.00 34.14 4.12
2839 4293 4.626402 AACGGTCCGGACTCCCCA 62.626 66.667 32.52 0.00 34.14 4.96
2840 4294 4.078516 CAACGGTCCGGACTCCCC 62.079 72.222 32.52 16.40 0.00 4.81
2841 4295 3.292500 GACAACGGTCCGGACTCCC 62.293 68.421 32.52 16.79 38.12 4.30
2842 4296 2.260743 GACAACGGTCCGGACTCC 59.739 66.667 32.52 17.56 38.12 3.85
2843 4297 1.372623 GTGACAACGGTCCGGACTC 60.373 63.158 32.52 22.00 43.65 3.36
2844 4298 2.732658 GTGACAACGGTCCGGACT 59.267 61.111 32.52 14.04 43.65 3.85
2845 4299 2.732094 CGTGACAACGGTCCGGAC 60.732 66.667 27.04 27.04 46.25 4.79
2854 4308 0.596600 TCAGAAGCGGACGTGACAAC 60.597 55.000 0.00 0.00 0.00 3.32
2855 4309 0.596600 GTCAGAAGCGGACGTGACAA 60.597 55.000 0.00 0.00 39.33 3.18
2856 4310 1.007734 GTCAGAAGCGGACGTGACA 60.008 57.895 0.00 0.00 39.33 3.58
2857 4311 1.004277 CAGTCAGAAGCGGACGTGAC 61.004 60.000 0.00 5.40 40.20 3.67
2858 4312 1.285950 CAGTCAGAAGCGGACGTGA 59.714 57.895 0.00 0.00 40.20 4.35
2859 4313 2.375766 GCAGTCAGAAGCGGACGTG 61.376 63.158 0.00 0.00 40.20 4.49
2860 4314 2.049063 GCAGTCAGAAGCGGACGT 60.049 61.111 0.00 0.00 40.20 4.34
2861 4315 2.811317 GGCAGTCAGAAGCGGACG 60.811 66.667 0.00 0.00 40.20 4.79
2862 4316 2.435059 GGGCAGTCAGAAGCGGAC 60.435 66.667 0.00 0.00 35.50 4.79
2863 4317 2.604686 AGGGCAGTCAGAAGCGGA 60.605 61.111 0.00 0.00 0.00 5.54
2864 4318 2.435586 CAGGGCAGTCAGAAGCGG 60.436 66.667 0.00 0.00 0.00 5.52
2865 4319 1.739562 GTCAGGGCAGTCAGAAGCG 60.740 63.158 0.00 0.00 0.00 4.68
2866 4320 1.376553 GGTCAGGGCAGTCAGAAGC 60.377 63.158 0.00 0.00 0.00 3.86
2867 4321 1.298014 GGGTCAGGGCAGTCAGAAG 59.702 63.158 0.00 0.00 0.00 2.85
2868 4322 1.461268 TGGGTCAGGGCAGTCAGAA 60.461 57.895 0.00 0.00 0.00 3.02
2869 4323 2.204034 TGGGTCAGGGCAGTCAGA 59.796 61.111 0.00 0.00 0.00 3.27
2870 4324 2.348998 GTGGGTCAGGGCAGTCAG 59.651 66.667 0.00 0.00 0.00 3.51
2871 4325 3.249189 GGTGGGTCAGGGCAGTCA 61.249 66.667 0.00 0.00 0.00 3.41
2872 4326 4.035102 GGGTGGGTCAGGGCAGTC 62.035 72.222 0.00 0.00 0.00 3.51
2873 4327 4.918360 TGGGTGGGTCAGGGCAGT 62.918 66.667 0.00 0.00 0.00 4.40
2874 4328 2.655077 TTTTGGGTGGGTCAGGGCAG 62.655 60.000 0.00 0.00 0.00 4.85
2875 4329 2.243774 TTTTTGGGTGGGTCAGGGCA 62.244 55.000 0.00 0.00 0.00 5.36
2876 4330 1.458588 TTTTTGGGTGGGTCAGGGC 60.459 57.895 0.00 0.00 0.00 5.19


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

AutoCloner maintained by Alex Coulton.