Multiple sequence alignment - TraesCS2B01G501100

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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 TraesCS2B01G501100 chr2B 100.000 5405 0 0 1 5405 696292443 696287039 0.000000e+00 9982
1 TraesCS2B01G501100 chr2B 82.596 1741 267 26 2680 4407 696675268 696673551 0.000000e+00 1504
2 TraesCS2B01G501100 chr2B 79.944 1795 318 30 2650 4420 695842921 695841145 0.000000e+00 1282
3 TraesCS2B01G501100 chr2B 96.244 213 8 0 2441 2653 696289898 696289686 3.100000e-92 350
4 TraesCS2B01G501100 chr2B 96.244 213 8 0 2546 2758 696290003 696289791 3.100000e-92 350
5 TraesCS2B01G501100 chr2B 97.196 107 3 0 2442 2548 696289792 696289686 1.200000e-41 182
6 TraesCS2B01G501100 chr2B 97.196 107 3 0 2652 2758 696290002 696289896 1.200000e-41 182
7 TraesCS2B01G501100 chr2B 88.660 97 11 0 2446 2542 73977700 73977604 9.510000e-23 119
8 TraesCS2B01G501100 chr2B 86.598 97 13 0 2551 2647 73977700 73977604 2.060000e-19 108
9 TraesCS2B01G501100 chr2D 93.841 4741 190 41 629 5314 579189759 579185066 0.000000e+00 7044
10 TraesCS2B01G501100 chr2D 82.075 1735 289 14 2680 4407 579391517 579389798 0.000000e+00 1461
11 TraesCS2B01G501100 chr2D 80.334 1734 303 28 2707 4421 578931468 578929754 0.000000e+00 1279
12 TraesCS2B01G501100 chr2D 95.775 213 9 0 2546 2758 579187946 579187734 1.440000e-90 344
13 TraesCS2B01G501100 chr2D 94.836 213 11 0 2441 2653 579187841 579187629 3.120000e-87 333
14 TraesCS2B01G501100 chr2D 98.131 107 2 0 2442 2548 579187735 579187629 2.570000e-43 187
15 TraesCS2B01G501100 chr2D 97.196 107 3 0 2652 2758 579187945 579187839 1.200000e-41 182
16 TraesCS2B01G501100 chr2D 94.792 96 5 0 5310 5405 579176441 579176346 3.370000e-32 150
17 TraesCS2B01G501100 chr2D 93.976 83 5 0 2446 2528 220628000 220627918 5.680000e-25 126
18 TraesCS2B01G501100 chr2D 91.566 83 7 0 2551 2633 220628000 220627918 1.230000e-21 115
19 TraesCS2B01G501100 chr2A 95.757 2781 95 10 2546 5314 716897813 716895044 0.000000e+00 4460
20 TraesCS2B01G501100 chr2A 93.383 1995 97 23 683 2653 716899584 716897601 0.000000e+00 2920
21 TraesCS2B01G501100 chr2A 94.134 1398 65 9 3929 5314 716839959 716838567 0.000000e+00 2111
22 TraesCS2B01G501100 chr2A 82.574 1733 281 13 2680 4407 717142340 717140624 0.000000e+00 1507
23 TraesCS2B01G501100 chr2A 80.277 1734 304 28 2707 4421 716458617 716456903 0.000000e+00 1273
24 TraesCS2B01G501100 chr2A 96.698 212 7 0 3722 3933 716880557 716880346 2.390000e-93 353
25 TraesCS2B01G501100 chr2A 99.074 108 1 0 2441 2548 716897708 716897601 1.540000e-45 195
26 TraesCS2B01G501100 chr2A 93.458 107 7 0 2652 2758 716897812 716897706 5.600000e-35 159
27 TraesCS2B01G501100 chr2A 95.000 100 1 1 634 733 716899659 716899564 2.610000e-33 154
28 TraesCS2B01G501100 chr1A 90.461 629 59 1 1 629 20806657 20807284 0.000000e+00 828
29 TraesCS2B01G501100 chr1A 90.431 627 59 1 1 627 20789543 20790168 0.000000e+00 824
30 TraesCS2B01G501100 chrUn 81.775 631 112 3 4 633 227956600 227955972 4.800000e-145 525
31 TraesCS2B01G501100 chrUn 92.857 98 5 1 5310 5405 11730194 11730097 2.030000e-29 141
32 TraesCS2B01G501100 chr3D 81.111 630 117 2 4 632 85765784 85765156 2.250000e-138 503
33 TraesCS2B01G501100 chr3D 80.727 633 117 4 4 632 581979736 581979105 6.290000e-134 488
34 TraesCS2B01G501100 chr4D 80.952 630 118 2 4 632 18732739 18732111 1.050000e-136 497
35 TraesCS2B01G501100 chr5D 80.800 625 118 2 4 627 448601094 448601717 6.290000e-134 488
36 TraesCS2B01G501100 chr3B 89.841 315 29 2 4 316 828341149 828340836 8.430000e-108 401


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 TraesCS2B01G501100 chr2B 696287039 696292443 5404 True 2209.2 9982 97.3760 1 5405 5 chr2B.!!$R4 5404
1 TraesCS2B01G501100 chr2B 696673551 696675268 1717 True 1504.0 1504 82.5960 2680 4407 1 chr2B.!!$R2 1727
2 TraesCS2B01G501100 chr2B 695841145 695842921 1776 True 1282.0 1282 79.9440 2650 4420 1 chr2B.!!$R1 1770
3 TraesCS2B01G501100 chr2D 579185066 579189759 4693 True 1618.0 7044 95.9558 629 5314 5 chr2D.!!$R5 4685
4 TraesCS2B01G501100 chr2D 579389798 579391517 1719 True 1461.0 1461 82.0750 2680 4407 1 chr2D.!!$R3 1727
5 TraesCS2B01G501100 chr2D 578929754 578931468 1714 True 1279.0 1279 80.3340 2707 4421 1 chr2D.!!$R1 1714
6 TraesCS2B01G501100 chr2A 716838567 716839959 1392 True 2111.0 2111 94.1340 3929 5314 1 chr2A.!!$R2 1385
7 TraesCS2B01G501100 chr2A 716895044 716899659 4615 True 1577.6 4460 95.3344 634 5314 5 chr2A.!!$R5 4680
8 TraesCS2B01G501100 chr2A 717140624 717142340 1716 True 1507.0 1507 82.5740 2680 4407 1 chr2A.!!$R4 1727
9 TraesCS2B01G501100 chr2A 716456903 716458617 1714 True 1273.0 1273 80.2770 2707 4421 1 chr2A.!!$R1 1714
10 TraesCS2B01G501100 chr1A 20806657 20807284 627 False 828.0 828 90.4610 1 629 1 chr1A.!!$F2 628
11 TraesCS2B01G501100 chr1A 20789543 20790168 625 False 824.0 824 90.4310 1 627 1 chr1A.!!$F1 626
12 TraesCS2B01G501100 chrUn 227955972 227956600 628 True 525.0 525 81.7750 4 633 1 chrUn.!!$R2 629
13 TraesCS2B01G501100 chr3D 85765156 85765784 628 True 503.0 503 81.1110 4 632 1 chr3D.!!$R1 628
14 TraesCS2B01G501100 chr3D 581979105 581979736 631 True 488.0 488 80.7270 4 632 1 chr3D.!!$R2 628
15 TraesCS2B01G501100 chr4D 18732111 18732739 628 True 497.0 497 80.9520 4 632 1 chr4D.!!$R1 628
16 TraesCS2B01G501100 chr5D 448601094 448601717 623 False 488.0 488 80.8000 4 627 1 chr5D.!!$F1 623

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
226 229 0.179000 GAATGACGCCATGAGTCCCT 59.821 55.000 15.45 5.71 37.80 4.20 F
803 838 0.608035 TTGAATCCAGGCCGAACCAC 60.608 55.000 0.00 0.00 43.14 4.16 F
1986 2068 1.000506 TGGTGTCCAGTCGACTTTAGC 59.999 52.381 17.26 12.12 42.49 3.09 F
2702 2889 0.618680 AGCTCCAGTGGCATCACCTA 60.619 55.000 3.51 0.00 44.64 3.08 F
4266 4475 2.113986 GCTGCTATTGCCCGGGAT 59.886 61.111 29.31 13.09 38.71 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1587 1642 0.392461 GCGCCACCTTGGACTGATTA 60.392 55.0 0.00 0.00 40.96 1.75 R
2418 2500 0.185901 TTTGAGCTTTCCTGGCAGGT 59.814 50.0 31.60 13.59 36.53 4.00 R
3363 3559 0.329261 TGATGGGAAGGCACCTCTTG 59.671 55.0 0.00 0.00 0.00 3.02 R
4341 4550 0.108945 CGATGCTCAGTGTGCTCTGA 60.109 55.0 17.38 4.26 41.40 3.27 R
5323 5543 0.036732 AATCTCAACGGCTGGCTTCA 59.963 50.0 0.00 0.00 0.00 3.02 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
50 51 1.239296 CCAGCCATATCGCCCACATG 61.239 60.000 0.00 0.00 0.00 3.21
75 76 3.015327 ACTACCATCGTCACCAGACTAC 58.985 50.000 0.00 0.00 42.73 2.73
190 191 0.529992 GCCCATACACACCTAGCGAC 60.530 60.000 0.00 0.00 0.00 5.19
226 229 0.179000 GAATGACGCCATGAGTCCCT 59.821 55.000 15.45 5.71 37.80 4.20
253 256 2.223641 CGCACAGCTGGCATTTATCATT 60.224 45.455 19.93 0.00 0.00 2.57
275 278 4.606457 ATCTGACATTTTTCTAGCGTGC 57.394 40.909 0.00 0.00 0.00 5.34
286 289 5.546621 TTTCTAGCGTGCCTTATATCCTT 57.453 39.130 0.00 0.00 0.00 3.36
287 290 4.785511 TCTAGCGTGCCTTATATCCTTC 57.214 45.455 0.00 0.00 0.00 3.46
293 296 2.295349 GTGCCTTATATCCTTCGTCGGA 59.705 50.000 0.00 0.00 37.50 4.55
353 356 1.358152 TCCCGGGAACTTTGACAGAT 58.642 50.000 24.50 0.00 0.00 2.90
364 367 6.876257 GGAACTTTGACAGATCATAGAGTTGT 59.124 38.462 0.00 0.00 37.35 3.32
392 396 4.862902 TTTGGCTTCCGATTCAAAATCA 57.137 36.364 1.07 0.00 0.00 2.57
398 402 4.396166 GCTTCCGATTCAAAATCAGAGGAA 59.604 41.667 1.07 4.60 35.52 3.36
416 420 5.660864 AGAGGAACCTGATCTTCCTTCTAAG 59.339 44.000 14.20 0.00 46.39 2.18
433 437 1.673767 AAGCATTCCTCCCTTCTCCA 58.326 50.000 0.00 0.00 0.00 3.86
479 483 7.540400 CGGTATGCAGATCTTACTGAGAATAAG 59.460 40.741 6.14 0.00 39.94 1.73
480 484 8.364142 GGTATGCAGATCTTACTGAGAATAAGT 58.636 37.037 0.00 0.00 39.94 2.24
481 485 9.757227 GTATGCAGATCTTACTGAGAATAAGTT 57.243 33.333 0.00 0.00 39.94 2.66
494 498 7.993183 ACTGAGAATAAGTTGTTCCTCTCAAAA 59.007 33.333 8.58 0.00 38.94 2.44
509 513 3.261390 TCTCAAAATTCCAAGCCCAATGG 59.739 43.478 0.00 0.00 39.41 3.16
512 516 1.571955 AATTCCAAGCCCAATGGTCC 58.428 50.000 0.00 0.00 39.09 4.46
545 549 5.070047 CCTAGTACAGTTCGGGATGGTTAAT 59.930 44.000 0.00 0.00 0.00 1.40
591 595 4.628963 AAATTTGCATCAAGGGCTTCTT 57.371 36.364 0.00 0.00 35.79 2.52
753 788 6.733145 AGCTGAAATCAAAAGAAGACAGAAC 58.267 36.000 0.00 0.00 0.00 3.01
762 797 6.931281 TCAAAAGAAGACAGAACGAGATTGAT 59.069 34.615 0.00 0.00 0.00 2.57
783 818 2.715880 TCCAATATAAGCCCATCCAGCA 59.284 45.455 0.00 0.00 0.00 4.41
803 838 0.608035 TTGAATCCAGGCCGAACCAC 60.608 55.000 0.00 0.00 43.14 4.16
804 839 1.749258 GAATCCAGGCCGAACCACC 60.749 63.158 0.00 0.00 43.14 4.61
805 840 2.478335 GAATCCAGGCCGAACCACCA 62.478 60.000 0.00 0.00 43.14 4.17
1130 1175 4.109766 GTGCTGTGCTACATTACATACGA 58.890 43.478 0.00 0.00 0.00 3.43
1152 1198 3.118905 GCAAAGGTGCCATTTTTGGTA 57.881 42.857 6.17 0.00 45.68 3.25
1153 1199 2.805671 GCAAAGGTGCCATTTTTGGTAC 59.194 45.455 4.84 4.84 45.68 3.34
1158 1204 3.709141 AGGTGCCATTTTTGGTACAGTTT 59.291 39.130 13.92 0.00 44.75 2.66
1174 1220 3.128589 ACAGTTTTGTGACATTTCGTGCT 59.871 39.130 0.00 0.00 35.83 4.40
1185 1231 3.251004 ACATTTCGTGCTTGGAAGAAGTC 59.749 43.478 0.00 0.00 0.00 3.01
1247 1294 1.081376 CGCGCTCGGTAATCTAGGG 60.081 63.158 5.56 0.00 0.00 3.53
1332 1385 3.808728 AGCATATGTATGTGTGTGTCCC 58.191 45.455 4.29 0.00 36.11 4.46
1358 1412 9.799106 CTATGGTCTTAAATTATGGAGGATGTT 57.201 33.333 0.00 0.00 0.00 2.71
1384 1438 5.421056 TGTACTCAGATCGATGTAGGGTTTT 59.579 40.000 0.54 0.00 0.00 2.43
1414 1468 9.847224 TTGGAACTATATGGATTTCTTCTTACC 57.153 33.333 0.00 0.00 0.00 2.85
1425 1479 8.772250 TGGATTTCTTCTTACCATACTTCTGAT 58.228 33.333 0.00 0.00 0.00 2.90
1459 1513 7.372260 AGCTATCTTCTTGGACTGATATGTT 57.628 36.000 0.00 0.00 0.00 2.71
1511 1566 2.625639 AGCTATGGGGAATCCTGGTAG 58.374 52.381 0.00 0.55 36.20 3.18
1515 1570 1.279025 TGGGGAATCCTGGTAGGCAC 61.279 60.000 0.00 0.00 34.61 5.01
1527 1582 1.112113 GTAGGCACGAGAAGGATGGA 58.888 55.000 0.00 0.00 0.00 3.41
1574 1629 1.153289 GTGCTCACATCTCGCCCAT 60.153 57.895 0.00 0.00 0.00 4.00
1762 1838 3.373565 GCCCAGCCAAACCGGAAG 61.374 66.667 9.46 0.00 36.56 3.46
1845 1921 6.610075 ATGTTCATTTTTGCCTATTCAGGT 57.390 33.333 0.00 0.00 44.68 4.00
1877 1954 2.706190 ACCTTCTACTTGGCTCAGTGTT 59.294 45.455 0.70 0.00 0.00 3.32
1882 1959 6.360370 TTCTACTTGGCTCAGTGTTTAGAT 57.640 37.500 0.70 0.00 0.00 1.98
1883 1960 5.724328 TCTACTTGGCTCAGTGTTTAGATG 58.276 41.667 0.70 0.00 0.00 2.90
1884 1961 3.679389 ACTTGGCTCAGTGTTTAGATGG 58.321 45.455 0.00 0.00 0.00 3.51
1892 1969 5.181245 GCTCAGTGTTTAGATGGCACTTTAA 59.819 40.000 0.00 0.00 40.99 1.52
1893 1970 6.127897 GCTCAGTGTTTAGATGGCACTTTAAT 60.128 38.462 0.00 0.00 40.99 1.40
1894 1971 7.065803 GCTCAGTGTTTAGATGGCACTTTAATA 59.934 37.037 0.00 0.00 40.99 0.98
1895 1972 8.263940 TCAGTGTTTAGATGGCACTTTAATAC 57.736 34.615 0.00 0.00 40.99 1.89
1896 1973 8.100791 TCAGTGTTTAGATGGCACTTTAATACT 58.899 33.333 0.00 0.00 40.99 2.12
1905 1982 8.198109 AGATGGCACTTTAATACTGTAGTAGTG 58.802 37.037 11.75 11.75 40.65 2.74
1906 1983 7.470935 TGGCACTTTAATACTGTAGTAGTGA 57.529 36.000 17.58 0.00 40.65 3.41
1907 1984 7.544622 TGGCACTTTAATACTGTAGTAGTGAG 58.455 38.462 17.58 9.98 40.65 3.51
1911 1988 9.275231 CACTTTAATACTGTAGTAGTGAGTTCG 57.725 37.037 10.96 0.00 40.65 3.95
1926 2003 3.071892 TGAGTTCGTAGTTCCCAAATGGT 59.928 43.478 0.00 0.00 34.77 3.55
1932 2009 3.554324 CGTAGTTCCCAAATGGTATGTCG 59.446 47.826 0.00 0.00 34.77 4.35
1933 2010 3.713826 AGTTCCCAAATGGTATGTCGT 57.286 42.857 0.00 0.00 34.77 4.34
1935 2012 4.007659 AGTTCCCAAATGGTATGTCGTTC 58.992 43.478 0.00 0.00 34.77 3.95
1938 2015 5.423704 TCCCAAATGGTATGTCGTTCTTA 57.576 39.130 0.00 0.00 34.77 2.10
1939 2016 5.996644 TCCCAAATGGTATGTCGTTCTTAT 58.003 37.500 0.00 0.00 34.77 1.73
1940 2017 6.419791 TCCCAAATGGTATGTCGTTCTTATT 58.580 36.000 0.00 0.00 34.77 1.40
1964 2046 1.678101 GTTCCATGCATTACCTGGCTC 59.322 52.381 0.00 0.00 0.00 4.70
1966 2048 1.496001 TCCATGCATTACCTGGCTCAT 59.504 47.619 0.00 0.00 0.00 2.90
1978 2060 1.448540 GGCTCATGGTGTCCAGTCG 60.449 63.158 0.00 0.00 36.75 4.18
1985 2067 3.056821 TCATGGTGTCCAGTCGACTTTAG 60.057 47.826 17.26 8.03 42.49 1.85
1986 2068 1.000506 TGGTGTCCAGTCGACTTTAGC 59.999 52.381 17.26 12.12 42.49 3.09
1994 2076 3.502920 CAGTCGACTTTAGCAGTAGTGG 58.497 50.000 17.26 0.00 35.01 4.00
2001 2083 5.007332 CGACTTTAGCAGTAGTGGTTTGTTT 59.993 40.000 7.71 0.00 35.01 2.83
2021 2103 7.007313 TGTTTGTTAGCAGTGTGTAGTTTAC 57.993 36.000 0.00 0.00 0.00 2.01
2077 2159 7.665559 AGATAATTGAACTCTGGCACAAAGTAA 59.334 33.333 0.00 0.00 38.70 2.24
2090 2172 5.963586 GGCACAAAGTAACTATTCGTATTGC 59.036 40.000 0.00 0.00 0.00 3.56
2096 2178 9.210426 CAAAGTAACTATTCGTATTGCATTCAC 57.790 33.333 0.00 0.00 0.00 3.18
2165 2247 4.975502 TGATGAAATTTTTGCAGTGACGAC 59.024 37.500 0.00 0.00 0.00 4.34
2191 2273 3.381908 CGACATAAGCTCAGTAAGTCCCT 59.618 47.826 0.00 0.00 0.00 4.20
2205 2287 4.317530 AAGTCCCTTAAAATGGAGGTCC 57.682 45.455 0.00 0.00 0.00 4.46
2245 2327 4.963878 CCATCTTCGTTGAGGGGG 57.036 61.111 3.85 0.00 34.59 5.40
2418 2500 1.579932 GGTGCGAGACGAGTCTTCA 59.420 57.895 7.23 6.19 40.61 3.02
2565 2752 5.570641 TGGTACAAAATGCTCTAGCAAGCTA 60.571 40.000 9.01 1.37 46.93 3.32
2610 2797 1.208706 TCACCTATCGGCCCATTCAA 58.791 50.000 0.00 0.00 0.00 2.69
2611 2798 1.562008 TCACCTATCGGCCCATTCAAA 59.438 47.619 0.00 0.00 0.00 2.69
2612 2799 2.174639 TCACCTATCGGCCCATTCAAAT 59.825 45.455 0.00 0.00 0.00 2.32
2613 2800 2.294233 CACCTATCGGCCCATTCAAATG 59.706 50.000 0.00 0.00 36.17 2.32
2627 2814 6.694877 CATTCAAATGGTGTCAGATCATCT 57.305 37.500 0.00 0.00 32.78 2.90
2628 2815 7.797038 CATTCAAATGGTGTCAGATCATCTA 57.203 36.000 0.00 0.00 32.78 1.98
2629 2816 8.392372 CATTCAAATGGTGTCAGATCATCTAT 57.608 34.615 0.00 0.00 32.78 1.98
2630 2817 8.504815 CATTCAAATGGTGTCAGATCATCTATC 58.495 37.037 0.00 0.00 32.78 2.08
2631 2818 6.528321 TCAAATGGTGTCAGATCATCTATCC 58.472 40.000 0.00 0.00 34.90 2.59
2632 2819 5.495926 AATGGTGTCAGATCATCTATCCC 57.504 43.478 0.00 0.00 34.90 3.85
2633 2820 4.204792 TGGTGTCAGATCATCTATCCCT 57.795 45.455 0.00 0.00 34.90 4.20
2634 2821 5.339423 TGGTGTCAGATCATCTATCCCTA 57.661 43.478 0.00 0.00 34.90 3.53
2635 2822 5.080337 TGGTGTCAGATCATCTATCCCTAC 58.920 45.833 0.00 0.00 34.90 3.18
2636 2823 4.464597 GGTGTCAGATCATCTATCCCTACC 59.535 50.000 0.00 0.00 34.90 3.18
2637 2824 5.080337 GTGTCAGATCATCTATCCCTACCA 58.920 45.833 0.00 0.00 34.90 3.25
2638 2825 5.184864 GTGTCAGATCATCTATCCCTACCAG 59.815 48.000 0.00 0.00 34.90 4.00
2639 2826 4.159506 GTCAGATCATCTATCCCTACCAGC 59.840 50.000 0.00 0.00 34.90 4.85
2640 2827 4.092279 CAGATCATCTATCCCTACCAGCA 58.908 47.826 0.00 0.00 34.90 4.41
2641 2828 4.081752 CAGATCATCTATCCCTACCAGCAC 60.082 50.000 0.00 0.00 34.90 4.40
2642 2829 2.609747 TCATCTATCCCTACCAGCACC 58.390 52.381 0.00 0.00 0.00 5.01
2643 2830 2.090775 TCATCTATCCCTACCAGCACCA 60.091 50.000 0.00 0.00 0.00 4.17
2644 2831 2.088104 TCTATCCCTACCAGCACCAG 57.912 55.000 0.00 0.00 0.00 4.00
2645 2832 1.573857 TCTATCCCTACCAGCACCAGA 59.426 52.381 0.00 0.00 0.00 3.86
2646 2833 2.180086 TCTATCCCTACCAGCACCAGAT 59.820 50.000 0.00 0.00 0.00 2.90
2647 2834 1.135094 ATCCCTACCAGCACCAGATG 58.865 55.000 0.00 0.00 0.00 2.90
2663 2850 5.496133 CCAGATGGTTCAAAATGCTCTAG 57.504 43.478 0.00 0.00 0.00 2.43
2696 2883 1.525923 CTAGCAGCTCCAGTGGCAT 59.474 57.895 3.51 0.00 0.00 4.40
2701 2888 1.922369 AGCTCCAGTGGCATCACCT 60.922 57.895 3.51 0.00 44.64 4.00
2702 2889 0.618680 AGCTCCAGTGGCATCACCTA 60.619 55.000 3.51 0.00 44.64 3.08
2709 2902 2.828868 GGCATCACCTATCGGCCA 59.171 61.111 2.24 0.00 44.01 5.36
3298 3494 4.074970 TCTTGACCAGAAGATTTTGAGCC 58.925 43.478 0.00 0.00 0.00 4.70
3363 3559 4.450053 AGCTCAAGGAGATGCTCATAAAC 58.550 43.478 0.00 0.00 31.08 2.01
3823 4020 4.318332 AGAAGAAGCATCAAACGATCACA 58.682 39.130 0.00 0.00 0.00 3.58
4036 4233 5.910166 CAGGAACTCTTCGATGAATACTACG 59.090 44.000 2.36 0.00 34.60 3.51
4158 4367 3.683822 GCCAGATGTCTTCAGAACTTGAG 59.316 47.826 0.00 0.00 37.07 3.02
4266 4475 2.113986 GCTGCTATTGCCCGGGAT 59.886 61.111 29.31 13.09 38.71 3.85
4341 4550 2.110578 GGGCCAGTAATTCCAAAGCAT 58.889 47.619 4.39 0.00 0.00 3.79
4451 4660 2.175931 ACCTCTCCGTCCTATGATCACT 59.824 50.000 0.00 0.00 0.00 3.41
4452 4661 2.556189 CCTCTCCGTCCTATGATCACTG 59.444 54.545 0.00 0.00 0.00 3.66
4517 4726 5.011586 TGATTGGCAGAATTGATCTTCACA 58.988 37.500 0.00 0.00 35.73 3.58
4542 4751 1.734117 GCTTGTGGGAACAATGCGC 60.734 57.895 0.00 0.00 46.06 6.09
4698 4907 3.103738 GCTGCTTAATCTCATGTTTGCG 58.896 45.455 0.00 0.00 0.00 4.85
4848 5057 9.996554 TTCATTATCACATCGTTGGTTATAGAT 57.003 29.630 0.00 0.00 0.00 1.98
4946 5155 3.067833 CTCGTTTCAAAGAGAAGGGGAC 58.932 50.000 0.00 0.00 36.77 4.46
4967 5176 1.059584 TGTTCCCCTGCTGAACTGGA 61.060 55.000 4.94 0.00 42.04 3.86
5003 5212 2.162408 GCCTGTGTGTTCCTGAAATAGC 59.838 50.000 0.00 0.00 0.00 2.97
5004 5213 2.749621 CCTGTGTGTTCCTGAAATAGCC 59.250 50.000 0.00 0.00 0.00 3.93
5045 5254 1.098712 GGACAAACAGGCGTTGGTGA 61.099 55.000 6.91 0.00 39.50 4.02
5052 5261 1.675641 AGGCGTTGGTGAATGGAGC 60.676 57.895 0.00 0.00 0.00 4.70
5110 5322 3.820777 GCGTCAAGCTCTGAGAAAATT 57.179 42.857 9.28 0.00 44.04 1.82
5113 5325 4.668686 GCGTCAAGCTCTGAGAAAATTCAG 60.669 45.833 9.28 0.00 44.04 3.02
5114 5326 4.142945 CGTCAAGCTCTGAGAAAATTCAGG 60.143 45.833 9.28 0.00 43.78 3.86
5117 5329 5.704515 TCAAGCTCTGAGAAAATTCAGGAAG 59.295 40.000 9.28 0.00 43.78 3.46
5148 5368 1.888436 ATCGCCAGTCGCCTGAAGAA 61.888 55.000 0.00 0.00 41.50 2.52
5234 5454 1.520342 CTGAGCGAGGGTTGCTAGC 60.520 63.158 8.10 8.10 44.18 3.42
5245 5465 2.538141 TTGCTAGCTTGGGGGCTGT 61.538 57.895 17.23 0.00 43.01 4.40
5248 5468 1.685224 CTAGCTTGGGGGCTGTTGA 59.315 57.895 0.00 0.00 43.01 3.18
5268 5488 2.594303 TGGCCTGCCAACGTTCTG 60.594 61.111 8.75 0.00 44.12 3.02
5269 5489 2.594592 GGCCTGCCAACGTTCTGT 60.595 61.111 0.00 0.00 35.81 3.41
5314 5534 1.748122 GGTGCTCCTCATGCTGGTG 60.748 63.158 0.00 4.05 0.00 4.17
5315 5535 1.748122 GTGCTCCTCATGCTGGTGG 60.748 63.158 4.83 0.00 0.00 4.61
5316 5536 2.124403 GCTCCTCATGCTGGTGGG 60.124 66.667 4.83 0.00 0.00 4.61
5317 5537 2.673200 GCTCCTCATGCTGGTGGGA 61.673 63.158 4.83 0.00 0.00 4.37
5318 5538 1.222936 CTCCTCATGCTGGTGGGAC 59.777 63.158 4.83 0.00 0.00 4.46
5319 5539 2.124983 CCTCATGCTGGTGGGACG 60.125 66.667 0.00 0.00 0.00 4.79
5320 5540 2.665000 CTCATGCTGGTGGGACGT 59.335 61.111 0.00 0.00 0.00 4.34
5321 5541 1.003355 CTCATGCTGGTGGGACGTT 60.003 57.895 0.00 0.00 0.00 3.99
5322 5542 0.249120 CTCATGCTGGTGGGACGTTA 59.751 55.000 0.00 0.00 0.00 3.18
5323 5543 0.908910 TCATGCTGGTGGGACGTTAT 59.091 50.000 0.00 0.00 0.00 1.89
5324 5544 1.016627 CATGCTGGTGGGACGTTATG 58.983 55.000 0.00 0.00 0.00 1.90
5325 5545 0.908910 ATGCTGGTGGGACGTTATGA 59.091 50.000 0.00 0.00 0.00 2.15
5326 5546 0.687920 TGCTGGTGGGACGTTATGAA 59.312 50.000 0.00 0.00 0.00 2.57
5327 5547 1.338674 TGCTGGTGGGACGTTATGAAG 60.339 52.381 0.00 0.00 0.00 3.02
5328 5548 1.369625 CTGGTGGGACGTTATGAAGC 58.630 55.000 0.00 0.00 0.00 3.86
5329 5549 0.035820 TGGTGGGACGTTATGAAGCC 60.036 55.000 0.00 0.00 0.00 4.35
5330 5550 0.035820 GGTGGGACGTTATGAAGCCA 60.036 55.000 0.00 0.00 0.00 4.75
5331 5551 1.369625 GTGGGACGTTATGAAGCCAG 58.630 55.000 0.00 0.00 0.00 4.85
5332 5552 0.392461 TGGGACGTTATGAAGCCAGC 60.392 55.000 0.00 0.00 0.00 4.85
5333 5553 1.095807 GGGACGTTATGAAGCCAGCC 61.096 60.000 0.00 0.00 0.00 4.85
5334 5554 1.429148 GGACGTTATGAAGCCAGCCG 61.429 60.000 0.00 0.00 0.00 5.52
5335 5555 0.739813 GACGTTATGAAGCCAGCCGT 60.740 55.000 0.00 0.00 0.00 5.68
5336 5556 0.321298 ACGTTATGAAGCCAGCCGTT 60.321 50.000 0.00 0.00 0.00 4.44
5337 5557 0.096976 CGTTATGAAGCCAGCCGTTG 59.903 55.000 0.00 0.00 0.00 4.10
5338 5558 1.448985 GTTATGAAGCCAGCCGTTGA 58.551 50.000 0.00 0.00 0.00 3.18
5339 5559 1.398390 GTTATGAAGCCAGCCGTTGAG 59.602 52.381 0.00 0.00 0.00 3.02
5340 5560 0.901827 TATGAAGCCAGCCGTTGAGA 59.098 50.000 0.00 0.00 0.00 3.27
5341 5561 0.254178 ATGAAGCCAGCCGTTGAGAT 59.746 50.000 0.00 0.00 0.00 2.75
5342 5562 0.036732 TGAAGCCAGCCGTTGAGATT 59.963 50.000 0.00 0.00 0.00 2.40
5343 5563 1.168714 GAAGCCAGCCGTTGAGATTT 58.831 50.000 0.00 0.00 0.00 2.17
5344 5564 0.883833 AAGCCAGCCGTTGAGATTTG 59.116 50.000 0.00 0.00 0.00 2.32
5345 5565 0.962356 AGCCAGCCGTTGAGATTTGG 60.962 55.000 0.00 0.00 0.00 3.28
5350 5570 2.544480 GCCGTTGAGATTTGGCTAAC 57.456 50.000 0.00 0.00 44.16 2.34
5351 5571 2.084546 GCCGTTGAGATTTGGCTAACT 58.915 47.619 0.00 0.00 44.16 2.24
5352 5572 2.488153 GCCGTTGAGATTTGGCTAACTT 59.512 45.455 0.00 0.00 44.16 2.66
5353 5573 3.057526 GCCGTTGAGATTTGGCTAACTTT 60.058 43.478 0.00 0.00 44.16 2.66
5354 5574 4.155280 GCCGTTGAGATTTGGCTAACTTTA 59.845 41.667 0.00 0.00 44.16 1.85
5355 5575 5.163652 GCCGTTGAGATTTGGCTAACTTTAT 60.164 40.000 0.00 0.00 44.16 1.40
5356 5576 6.625081 GCCGTTGAGATTTGGCTAACTTTATT 60.625 38.462 0.00 0.00 44.16 1.40
5357 5577 7.312899 CCGTTGAGATTTGGCTAACTTTATTT 58.687 34.615 0.00 0.00 0.00 1.40
5358 5578 7.812669 CCGTTGAGATTTGGCTAACTTTATTTT 59.187 33.333 0.00 0.00 0.00 1.82
5359 5579 8.850452 CGTTGAGATTTGGCTAACTTTATTTTC 58.150 33.333 0.00 0.00 0.00 2.29
5360 5580 9.914131 GTTGAGATTTGGCTAACTTTATTTTCT 57.086 29.630 0.00 0.00 0.00 2.52
5384 5604 9.188588 TCTACAATAACAACACTAGTTTCTTCG 57.811 33.333 0.00 0.00 35.28 3.79
5385 5605 7.781548 ACAATAACAACACTAGTTTCTTCGT 57.218 32.000 0.00 0.00 35.28 3.85
5386 5606 7.627340 ACAATAACAACACTAGTTTCTTCGTG 58.373 34.615 0.00 0.00 35.28 4.35
5387 5607 7.279313 ACAATAACAACACTAGTTTCTTCGTGT 59.721 33.333 0.00 0.00 41.92 4.49
5388 5608 8.757789 CAATAACAACACTAGTTTCTTCGTGTA 58.242 33.333 0.00 0.00 39.47 2.90
5389 5609 8.876275 ATAACAACACTAGTTTCTTCGTGTAA 57.124 30.769 0.00 0.00 39.47 2.41
5390 5610 6.579491 ACAACACTAGTTTCTTCGTGTAAC 57.421 37.500 0.00 0.00 39.47 2.50
5391 5611 6.101332 ACAACACTAGTTTCTTCGTGTAACA 58.899 36.000 0.00 0.00 39.47 2.41
5392 5612 6.591062 ACAACACTAGTTTCTTCGTGTAACAA 59.409 34.615 0.00 0.00 39.47 2.83
5393 5613 7.118101 ACAACACTAGTTTCTTCGTGTAACAAA 59.882 33.333 0.00 0.00 39.47 2.83
5394 5614 7.599630 ACACTAGTTTCTTCGTGTAACAAAA 57.400 32.000 0.00 0.00 38.69 2.44
5395 5615 8.031848 ACACTAGTTTCTTCGTGTAACAAAAA 57.968 30.769 0.00 0.00 38.69 1.94
5396 5616 8.671028 ACACTAGTTTCTTCGTGTAACAAAAAT 58.329 29.630 0.00 0.00 38.69 1.82
5397 5617 9.155053 CACTAGTTTCTTCGTGTAACAAAAATC 57.845 33.333 0.00 0.00 35.74 2.17
5398 5618 8.340443 ACTAGTTTCTTCGTGTAACAAAAATCC 58.660 33.333 0.00 0.00 35.74 3.01
5399 5619 7.090953 AGTTTCTTCGTGTAACAAAAATCCA 57.909 32.000 0.00 0.00 35.74 3.41
5400 5620 6.970613 AGTTTCTTCGTGTAACAAAAATCCAC 59.029 34.615 0.00 0.00 35.74 4.02
5401 5621 6.438259 TTCTTCGTGTAACAAAAATCCACA 57.562 33.333 0.00 0.00 35.74 4.17
5402 5622 6.055231 TCTTCGTGTAACAAAAATCCACAG 57.945 37.500 0.00 0.00 35.74 3.66
5403 5623 4.822036 TCGTGTAACAAAAATCCACAGG 57.178 40.909 0.00 0.00 35.74 4.00
5404 5624 3.566322 TCGTGTAACAAAAATCCACAGGG 59.434 43.478 0.00 0.00 35.74 4.45
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
19 20 3.491652 GGCTGGCTCGTCGAAAGC 61.492 66.667 11.63 11.63 39.09 3.51
33 34 1.073722 CCATGTGGGCGATATGGCT 59.926 57.895 12.01 0.00 44.11 4.75
34 35 1.228245 ACCATGTGGGCGATATGGC 60.228 57.895 22.02 0.27 45.26 4.40
50 51 0.892755 TGGTGACGATGGTAGTGACC 59.107 55.000 0.00 0.00 44.43 4.02
89 90 7.630082 AGGTGTGGTTATTTTCAGCTATAGAA 58.370 34.615 3.21 0.00 36.98 2.10
190 191 5.084722 GTCATTCACTTTTCGAATGCTCAG 58.915 41.667 0.00 0.00 46.10 3.35
226 229 2.747460 GCCAGCTGTGCGGAATGA 60.747 61.111 13.81 0.00 0.00 2.57
233 236 3.447918 AATGATAAATGCCAGCTGTGC 57.552 42.857 13.81 15.86 0.00 4.57
253 256 4.570772 GGCACGCTAGAAAAATGTCAGATA 59.429 41.667 0.00 0.00 0.00 1.98
275 278 4.155462 TCGATTCCGACGAAGGATATAAGG 59.845 45.833 0.00 0.00 40.30 2.69
286 289 1.625616 GAAGCTTTCGATTCCGACGA 58.374 50.000 0.00 0.00 45.50 4.20
305 308 3.369147 GTCATTTCATGTGGAGACTGTCG 59.631 47.826 1.52 0.00 0.00 4.35
398 402 5.397334 GGAATGCTTAGAAGGAAGATCAGGT 60.397 44.000 0.00 0.00 0.00 4.00
416 420 2.744352 AATGGAGAAGGGAGGAATGC 57.256 50.000 0.00 0.00 0.00 3.56
433 437 2.758009 GCATGTTGGCTGACACAAAAT 58.242 42.857 0.00 0.00 31.30 1.82
479 483 4.984785 GCTTGGAATTTTGAGAGGAACAAC 59.015 41.667 0.00 0.00 0.00 3.32
480 484 4.039124 GGCTTGGAATTTTGAGAGGAACAA 59.961 41.667 0.00 0.00 0.00 2.83
481 485 3.573967 GGCTTGGAATTTTGAGAGGAACA 59.426 43.478 0.00 0.00 0.00 3.18
494 498 0.712380 AGGACCATTGGGCTTGGAAT 59.288 50.000 8.83 0.00 37.69 3.01
509 513 2.166664 CTGTACTAGGCAGTTGGAGGAC 59.833 54.545 8.02 0.00 36.14 3.85
531 535 4.171878 TGGCAATATTAACCATCCCGAA 57.828 40.909 5.48 0.00 0.00 4.30
545 549 1.879380 GCGGCTGATACAATGGCAATA 59.121 47.619 0.00 0.00 0.00 1.90
591 595 5.107109 GCACATAATGCGACATGGAATAA 57.893 39.130 0.00 0.00 46.55 1.40
710 716 4.874966 CAGCTCTTATTCTGTCCTTCCAAG 59.125 45.833 0.00 0.00 0.00 3.61
712 718 4.096681 TCAGCTCTTATTCTGTCCTTCCA 58.903 43.478 0.00 0.00 0.00 3.53
753 788 5.491070 TGGGCTTATATTGGATCAATCTCG 58.509 41.667 0.00 0.00 35.54 4.04
762 797 2.715880 TGCTGGATGGGCTTATATTGGA 59.284 45.455 0.00 0.00 0.00 3.53
783 818 0.331278 TGGTTCGGCCTGGATTCAAT 59.669 50.000 0.00 0.00 38.35 2.57
803 838 7.175641 CCTGCTAAAACCCAGATAATCTATTGG 59.824 40.741 0.00 0.00 0.00 3.16
804 839 7.175641 CCCTGCTAAAACCCAGATAATCTATTG 59.824 40.741 0.00 0.00 0.00 1.90
805 840 7.234355 CCCTGCTAAAACCCAGATAATCTATT 58.766 38.462 0.00 0.00 0.00 1.73
1113 1158 5.712217 TTGCTTCGTATGTAATGTAGCAC 57.288 39.130 0.00 0.00 44.36 4.40
1152 1198 3.128589 AGCACGAAATGTCACAAAACTGT 59.871 39.130 0.00 0.00 0.00 3.55
1153 1199 3.694734 AGCACGAAATGTCACAAAACTG 58.305 40.909 0.00 0.00 0.00 3.16
1158 1204 2.293170 TCCAAGCACGAAATGTCACAA 58.707 42.857 0.00 0.00 0.00 3.33
1309 1356 4.035558 GGGACACACACATACATATGCTTG 59.964 45.833 1.58 3.29 37.19 4.01
1332 1385 9.799106 AACATCCTCCATAATTTAAGACCATAG 57.201 33.333 0.00 0.00 0.00 2.23
1358 1412 5.877491 ACCCTACATCGATCTGAGTACATA 58.123 41.667 0.00 0.00 0.00 2.29
1463 1518 6.318648 ACAGCAACTCAGTCAAGTATGAAAAA 59.681 34.615 0.00 0.00 37.30 1.94
1511 1566 1.092345 GCTTCCATCCTTCTCGTGCC 61.092 60.000 0.00 0.00 0.00 5.01
1515 1570 2.609427 TCATGCTTCCATCCTTCTCG 57.391 50.000 0.00 0.00 0.00 4.04
1527 1582 2.418368 TAACCATCGCCTTCATGCTT 57.582 45.000 0.00 0.00 0.00 3.91
1574 1629 7.309744 CCTTGGACTGATTATTGTGCCTTTTTA 60.310 37.037 0.00 0.00 0.00 1.52
1583 1638 3.356290 GCCACCTTGGACTGATTATTGT 58.644 45.455 0.00 0.00 40.96 2.71
1587 1642 0.392461 GCGCCACCTTGGACTGATTA 60.392 55.000 0.00 0.00 40.96 1.75
1623 1678 1.272704 GGCTGGAACTCCTCCCAAATT 60.273 52.381 0.00 0.00 44.69 1.82
1845 1921 5.192927 CCAAGTAGAAGGTAATGCATGGAA 58.807 41.667 0.00 0.00 0.00 3.53
1882 1959 7.177921 ACTCACTACTACAGTATTAAAGTGCCA 59.822 37.037 4.92 0.00 34.98 4.92
1883 1960 7.545489 ACTCACTACTACAGTATTAAAGTGCC 58.455 38.462 4.92 0.00 34.98 5.01
1884 1961 8.983307 AACTCACTACTACAGTATTAAAGTGC 57.017 34.615 4.92 0.00 34.98 4.40
1892 1969 7.279758 GGAACTACGAACTCACTACTACAGTAT 59.720 40.741 0.00 0.00 34.98 2.12
1893 1970 6.591834 GGAACTACGAACTCACTACTACAGTA 59.408 42.308 0.00 0.00 34.98 2.74
1894 1971 5.411053 GGAACTACGAACTCACTACTACAGT 59.589 44.000 0.00 0.00 38.32 3.55
1895 1972 5.163774 GGGAACTACGAACTCACTACTACAG 60.164 48.000 0.00 0.00 0.00 2.74
1896 1973 4.697352 GGGAACTACGAACTCACTACTACA 59.303 45.833 0.00 0.00 0.00 2.74
1905 1982 3.671716 ACCATTTGGGAACTACGAACTC 58.328 45.455 0.96 0.00 41.15 3.01
1906 1983 3.782656 ACCATTTGGGAACTACGAACT 57.217 42.857 0.96 0.00 41.15 3.01
1907 1984 4.939439 ACATACCATTTGGGAACTACGAAC 59.061 41.667 0.96 0.00 41.15 3.95
1911 1988 4.510571 ACGACATACCATTTGGGAACTAC 58.489 43.478 0.96 0.00 41.15 2.73
1914 1991 4.007659 AGAACGACATACCATTTGGGAAC 58.992 43.478 0.96 0.00 41.15 3.62
1926 2003 6.288941 TGGAACCTGAATAAGAACGACATA 57.711 37.500 0.00 0.00 0.00 2.29
1932 2009 5.841957 ATGCATGGAACCTGAATAAGAAC 57.158 39.130 0.00 0.00 0.00 3.01
1933 2010 6.321181 GGTAATGCATGGAACCTGAATAAGAA 59.679 38.462 15.50 0.00 0.00 2.52
1935 2012 5.829924 AGGTAATGCATGGAACCTGAATAAG 59.170 40.000 21.69 0.00 40.83 1.73
1938 2015 4.255510 AGGTAATGCATGGAACCTGAAT 57.744 40.909 21.69 4.49 40.83 2.57
1939 2016 3.737559 AGGTAATGCATGGAACCTGAA 57.262 42.857 21.69 0.00 40.83 3.02
1960 2042 1.448540 CGACTGGACACCATGAGCC 60.449 63.158 0.00 0.00 30.82 4.70
1978 2060 6.183360 ACAAACAAACCACTACTGCTAAAGTC 60.183 38.462 0.00 0.00 40.56 3.01
1985 2067 4.201970 TGCTAACAAACAAACCACTACTGC 60.202 41.667 0.00 0.00 0.00 4.40
1986 2068 5.065988 ACTGCTAACAAACAAACCACTACTG 59.934 40.000 0.00 0.00 0.00 2.74
1994 2076 5.875930 ACTACACACTGCTAACAAACAAAC 58.124 37.500 0.00 0.00 0.00 2.93
2001 2083 5.185668 TCGTAAACTACACACTGCTAACA 57.814 39.130 0.00 0.00 0.00 2.41
2021 2103 6.522625 AGGAATATCTGTGTATCCAGATCG 57.477 41.667 6.93 0.00 46.70 3.69
2077 2159 4.439057 ACCGTGAATGCAATACGAATAGT 58.561 39.130 18.41 7.94 40.01 2.12
2096 2178 6.870965 TGGATTAATTTGATTCACCAAAACCG 59.129 34.615 0.00 0.00 39.20 4.44
2165 2247 3.181499 ACTTACTGAGCTTATGTCGTCGG 60.181 47.826 0.00 0.00 0.00 4.79
2205 2287 4.081697 GGTGTGAAACCCTCCCATATTTTG 60.082 45.833 0.00 0.00 44.02 2.44
2325 2407 1.959985 TGCCCATGTCGTTTTGAACAT 59.040 42.857 0.00 0.00 0.00 2.71
2418 2500 0.185901 TTTGAGCTTTCCTGGCAGGT 59.814 50.000 31.60 13.59 36.53 4.00
2565 2752 4.154347 GAGCTGCTAGCCCTGCGT 62.154 66.667 13.29 4.51 43.77 5.24
2610 2797 5.161135 AGGGATAGATGATCTGACACCATT 58.839 41.667 4.96 0.00 34.66 3.16
2611 2798 4.761086 AGGGATAGATGATCTGACACCAT 58.239 43.478 4.96 0.00 34.66 3.55
2612 2799 4.204792 AGGGATAGATGATCTGACACCA 57.795 45.455 4.96 0.00 34.66 4.17
2613 2800 4.464597 GGTAGGGATAGATGATCTGACACC 59.535 50.000 4.96 2.48 34.66 4.16
2614 2801 5.080337 TGGTAGGGATAGATGATCTGACAC 58.920 45.833 4.96 0.09 34.66 3.67
2615 2802 5.328565 CTGGTAGGGATAGATGATCTGACA 58.671 45.833 4.96 0.00 34.66 3.58
2616 2803 4.159506 GCTGGTAGGGATAGATGATCTGAC 59.840 50.000 4.96 0.00 34.66 3.51
2617 2804 4.202716 TGCTGGTAGGGATAGATGATCTGA 60.203 45.833 4.96 0.00 34.66 3.27
2618 2805 4.081752 GTGCTGGTAGGGATAGATGATCTG 60.082 50.000 4.96 0.00 34.66 2.90
2619 2806 4.093011 GTGCTGGTAGGGATAGATGATCT 58.907 47.826 0.00 0.00 34.66 2.75
2620 2807 3.196685 GGTGCTGGTAGGGATAGATGATC 59.803 52.174 0.00 0.00 0.00 2.92
2621 2808 3.177228 GGTGCTGGTAGGGATAGATGAT 58.823 50.000 0.00 0.00 0.00 2.45
2622 2809 2.090775 TGGTGCTGGTAGGGATAGATGA 60.091 50.000 0.00 0.00 0.00 2.92
2623 2810 2.301296 CTGGTGCTGGTAGGGATAGATG 59.699 54.545 0.00 0.00 0.00 2.90
2624 2811 2.180086 TCTGGTGCTGGTAGGGATAGAT 59.820 50.000 0.00 0.00 0.00 1.98
2625 2812 1.573857 TCTGGTGCTGGTAGGGATAGA 59.426 52.381 0.00 0.00 0.00 1.98
2626 2813 2.088104 TCTGGTGCTGGTAGGGATAG 57.912 55.000 0.00 0.00 0.00 2.08
2627 2814 2.329267 CATCTGGTGCTGGTAGGGATA 58.671 52.381 0.00 0.00 0.00 2.59
2628 2815 1.135094 CATCTGGTGCTGGTAGGGAT 58.865 55.000 0.00 0.00 0.00 3.85
2629 2816 0.982852 CCATCTGGTGCTGGTAGGGA 60.983 60.000 0.00 0.00 0.00 4.20
2630 2817 1.528824 CCATCTGGTGCTGGTAGGG 59.471 63.158 0.00 0.00 0.00 3.53
2639 2826 8.545478 GCTAGAGCATTTTGAACCATCTGGTG 62.545 46.154 1.88 0.00 44.15 4.17
2640 2827 6.608924 GCTAGAGCATTTTGAACCATCTGGT 61.609 44.000 0.00 0.00 45.76 4.00
2641 2828 4.201990 GCTAGAGCATTTTGAACCATCTGG 60.202 45.833 0.00 0.00 41.59 3.86
2642 2829 4.918037 GCTAGAGCATTTTGAACCATCTG 58.082 43.478 0.00 0.00 41.59 2.90
2672 2859 3.753806 CTGGAGCTGCTAGCCCTGC 62.754 68.421 13.29 13.99 43.77 4.85
2677 2864 2.513435 GCCACTGGAGCTGCTAGC 60.513 66.667 8.10 8.10 42.84 3.42
2701 2888 2.364632 CACCACTTGAATTGGCCGATA 58.635 47.619 5.71 0.00 37.69 2.92
2702 2889 1.176527 CACCACTTGAATTGGCCGAT 58.823 50.000 0.00 0.00 37.69 4.18
2709 2902 3.159213 TGATCTGCCACCACTTGAATT 57.841 42.857 0.00 0.00 0.00 2.17
3363 3559 0.329261 TGATGGGAAGGCACCTCTTG 59.671 55.000 0.00 0.00 0.00 3.02
4233 4442 1.523758 CAGCAAGTGTGGGGTACTTC 58.476 55.000 0.00 0.00 36.29 3.01
4266 4475 2.202878 GCCGGCATCGCTAAGACA 60.203 61.111 24.80 0.00 34.56 3.41
4341 4550 0.108945 CGATGCTCAGTGTGCTCTGA 60.109 55.000 17.38 4.26 41.40 3.27
4451 4660 2.494445 CATCGCGCTACTGGGTCA 59.506 61.111 5.56 0.00 0.00 4.02
4452 4661 2.962253 GCATCGCGCTACTGGGTC 60.962 66.667 5.56 0.00 37.77 4.46
4517 4726 1.846007 TGTTCCCACAAGCAAACAGT 58.154 45.000 0.00 0.00 0.00 3.55
4542 4751 2.944129 TCCAAAACCAAGGAAGTCCAG 58.056 47.619 0.00 0.00 38.89 3.86
4803 5012 4.713553 TGAAAGTACCAGAATGTGAAGCA 58.286 39.130 0.00 0.00 0.00 3.91
4933 5142 3.510531 GGAACAAGTCCCCTTCTCTTT 57.489 47.619 0.00 0.00 41.10 2.52
4946 5155 1.242076 CAGTTCAGCAGGGGAACAAG 58.758 55.000 7.87 0.00 45.45 3.16
4948 5157 1.059584 TCCAGTTCAGCAGGGGAACA 61.060 55.000 7.87 0.00 45.45 3.18
4967 5176 4.076394 ACACAGGCCGTATAACAAACATT 58.924 39.130 0.00 0.00 0.00 2.71
5003 5212 1.090052 GGCGAATGAAGACCTTCCGG 61.090 60.000 0.00 0.00 38.77 5.14
5004 5213 1.421410 CGGCGAATGAAGACCTTCCG 61.421 60.000 0.00 5.24 38.77 4.30
5052 5261 0.530211 CGCAGCCTGGAGAATCTCAG 60.530 60.000 12.79 7.53 34.50 3.35
5104 5316 2.043115 AGGTCCCCCTTCCTGAATTTTC 59.957 50.000 0.00 0.00 38.13 2.29
5105 5317 2.081855 AGGTCCCCCTTCCTGAATTTT 58.918 47.619 0.00 0.00 38.13 1.82
5107 5319 3.540354 AGGTCCCCCTTCCTGAATT 57.460 52.632 0.00 0.00 38.13 2.17
5113 5325 3.023735 ATGCCAGGTCCCCCTTCC 61.024 66.667 0.00 0.00 39.89 3.46
5114 5326 2.597903 GATGCCAGGTCCCCCTTC 59.402 66.667 0.00 0.00 39.89 3.46
5148 5368 0.955428 TTTCAAGAGCCGCGCAGATT 60.955 50.000 8.75 0.00 0.00 2.40
5201 5421 0.662619 CTCAGGCGCAAAACAGAACA 59.337 50.000 10.83 0.00 0.00 3.18
5234 5454 1.252904 CCACATCAACAGCCCCCAAG 61.253 60.000 0.00 0.00 0.00 3.61
5276 5496 3.165071 CCCAACAGGCTAGAACCAAAAT 58.835 45.455 0.00 0.00 0.00 1.82
5292 5512 1.001641 AGCATGAGGAGCACCCAAC 60.002 57.895 0.00 0.00 37.41 3.77
5314 5534 1.095807 GGCTGGCTTCATAACGTCCC 61.096 60.000 0.00 0.00 0.00 4.46
5315 5535 1.429148 CGGCTGGCTTCATAACGTCC 61.429 60.000 0.00 0.00 0.00 4.79
5316 5536 0.739813 ACGGCTGGCTTCATAACGTC 60.740 55.000 0.00 0.00 0.00 4.34
5317 5537 0.321298 AACGGCTGGCTTCATAACGT 60.321 50.000 0.00 0.00 34.25 3.99
5318 5538 0.096976 CAACGGCTGGCTTCATAACG 59.903 55.000 0.00 0.00 0.00 3.18
5319 5539 1.398390 CTCAACGGCTGGCTTCATAAC 59.602 52.381 0.00 0.00 0.00 1.89
5320 5540 1.277842 TCTCAACGGCTGGCTTCATAA 59.722 47.619 0.00 0.00 0.00 1.90
5321 5541 0.901827 TCTCAACGGCTGGCTTCATA 59.098 50.000 0.00 0.00 0.00 2.15
5322 5542 0.254178 ATCTCAACGGCTGGCTTCAT 59.746 50.000 0.00 0.00 0.00 2.57
5323 5543 0.036732 AATCTCAACGGCTGGCTTCA 59.963 50.000 0.00 0.00 0.00 3.02
5324 5544 1.135575 CAAATCTCAACGGCTGGCTTC 60.136 52.381 0.00 0.00 0.00 3.86
5325 5545 0.883833 CAAATCTCAACGGCTGGCTT 59.116 50.000 0.00 0.00 0.00 4.35
5326 5546 0.962356 CCAAATCTCAACGGCTGGCT 60.962 55.000 0.00 0.00 0.00 4.75
5327 5547 1.508088 CCAAATCTCAACGGCTGGC 59.492 57.895 0.00 0.00 0.00 4.85
5328 5548 1.508088 GCCAAATCTCAACGGCTGG 59.492 57.895 0.00 0.00 41.50 4.85
5331 5551 2.084546 AGTTAGCCAAATCTCAACGGC 58.915 47.619 0.00 0.00 45.23 5.68
5332 5552 4.766404 AAAGTTAGCCAAATCTCAACGG 57.234 40.909 0.00 0.00 0.00 4.44
5333 5553 8.742554 AAAATAAAGTTAGCCAAATCTCAACG 57.257 30.769 0.00 0.00 0.00 4.10
5334 5554 9.914131 AGAAAATAAAGTTAGCCAAATCTCAAC 57.086 29.630 0.00 0.00 0.00 3.18
5358 5578 9.188588 CGAAGAAACTAGTGTTGTTATTGTAGA 57.811 33.333 0.00 0.00 36.39 2.59
5359 5579 8.975439 ACGAAGAAACTAGTGTTGTTATTGTAG 58.025 33.333 0.00 0.00 36.39 2.74
5360 5580 8.757789 CACGAAGAAACTAGTGTTGTTATTGTA 58.242 33.333 0.00 0.00 36.39 2.41
5361 5581 7.279313 ACACGAAGAAACTAGTGTTGTTATTGT 59.721 33.333 0.00 2.95 44.32 2.71
5362 5582 7.627340 ACACGAAGAAACTAGTGTTGTTATTG 58.373 34.615 0.00 2.42 44.32 1.90
5363 5583 7.781548 ACACGAAGAAACTAGTGTTGTTATT 57.218 32.000 0.00 0.00 44.32 1.40
5364 5584 8.758715 GTTACACGAAGAAACTAGTGTTGTTAT 58.241 33.333 14.31 0.00 44.32 1.89
5365 5585 7.758980 TGTTACACGAAGAAACTAGTGTTGTTA 59.241 33.333 14.31 0.00 44.32 2.41
5366 5586 6.591062 TGTTACACGAAGAAACTAGTGTTGTT 59.409 34.615 14.31 0.00 44.32 2.83
5367 5587 6.101332 TGTTACACGAAGAAACTAGTGTTGT 58.899 36.000 14.31 0.00 44.32 3.32
5368 5588 6.578020 TGTTACACGAAGAAACTAGTGTTG 57.422 37.500 14.31 0.00 44.32 3.33
5369 5589 7.599630 TTTGTTACACGAAGAAACTAGTGTT 57.400 32.000 14.31 0.00 44.32 3.32
5371 5591 9.155053 GATTTTTGTTACACGAAGAAACTAGTG 57.845 33.333 0.00 0.00 40.17 2.74
5372 5592 8.340443 GGATTTTTGTTACACGAAGAAACTAGT 58.660 33.333 0.00 0.00 30.47 2.57
5373 5593 8.339714 TGGATTTTTGTTACACGAAGAAACTAG 58.660 33.333 0.00 0.00 30.47 2.57
5374 5594 8.124199 GTGGATTTTTGTTACACGAAGAAACTA 58.876 33.333 0.00 0.00 30.47 2.24
5375 5595 6.970613 GTGGATTTTTGTTACACGAAGAAACT 59.029 34.615 0.00 0.00 30.47 2.66
5376 5596 6.748198 TGTGGATTTTTGTTACACGAAGAAAC 59.252 34.615 0.00 0.00 30.47 2.78
5377 5597 6.853720 TGTGGATTTTTGTTACACGAAGAAA 58.146 32.000 0.00 0.00 34.93 2.52
5378 5598 6.438259 TGTGGATTTTTGTTACACGAAGAA 57.562 33.333 0.00 0.00 34.93 2.52
5379 5599 5.008217 CCTGTGGATTTTTGTTACACGAAGA 59.992 40.000 0.00 0.00 34.93 2.87
5380 5600 5.212194 CCTGTGGATTTTTGTTACACGAAG 58.788 41.667 0.00 0.00 34.93 3.79
5381 5601 4.036971 CCCTGTGGATTTTTGTTACACGAA 59.963 41.667 0.00 0.00 34.93 3.85
5382 5602 3.566322 CCCTGTGGATTTTTGTTACACGA 59.434 43.478 0.00 0.00 34.93 4.35
5383 5603 3.896122 CCCTGTGGATTTTTGTTACACG 58.104 45.455 0.00 0.00 34.93 4.49


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

AutoCloner maintained by Alex Coulton.