Multiple sequence alignment - TraesCS3D01G010500

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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 TraesCS3D01G010500 chr3D 100.000 4911 0 0 1 4911 3826695 3821785 0.000000e+00 9070.0
1 TraesCS3D01G010500 chr3D 82.075 106 17 2 1639 1743 417163379 417163275 6.770000e-14 89.8
2 TraesCS3D01G010500 chr3B 91.321 3860 188 60 932 4730 663206 666979 0.000000e+00 5136.0
3 TraesCS3D01G010500 chr3B 80.144 831 70 43 101 873 662389 663182 2.600000e-147 532.0
4 TraesCS3D01G010500 chr3B 93.478 138 6 3 4753 4888 667034 667170 8.340000e-48 202.0
5 TraesCS3D01G010500 chr3B 82.075 106 17 2 1639 1743 543470290 543470186 6.770000e-14 89.8
6 TraesCS3D01G010500 chr3B 92.157 51 2 2 2440 2489 178267939 178267890 2.450000e-08 71.3
7 TraesCS3D01G010500 chr3B 100.000 31 0 0 1875 1905 30520847 30520817 1.910000e-04 58.4
8 TraesCS3D01G010500 chr3B 97.143 35 0 1 1870 1904 477652791 477652758 1.910000e-04 58.4
9 TraesCS3D01G010500 chrUn 94.055 1968 71 13 2968 4911 31932354 31934299 0.000000e+00 2944.0
10 TraesCS3D01G010500 chrUn 91.242 1941 88 31 320 2248 31929826 31931696 0.000000e+00 2567.0
11 TraesCS3D01G010500 chrUn 87.129 606 37 26 2285 2859 31931699 31932294 0.000000e+00 649.0
12 TraesCS3D01G010500 chrUn 92.647 68 2 2 428 495 31929966 31930030 1.460000e-15 95.3
13 TraesCS3D01G010500 chrUn 91.837 49 3 1 2440 2488 10247989 10248036 3.170000e-07 67.6
14 TraesCS3D01G010500 chrUn 100.000 30 0 0 1875 1904 42486826 42486855 6.870000e-04 56.5
15 TraesCS3D01G010500 chr1D 81.646 316 58 0 3209 3524 424730679 424730994 3.770000e-66 263.0
16 TraesCS3D01G010500 chr1D 95.000 40 1 1 2443 2482 483382977 483383015 1.480000e-05 62.1
17 TraesCS3D01G010500 chr1B 81.013 316 58 2 3210 3524 573861286 573861600 2.930000e-62 250.0
18 TraesCS3D01G010500 chr3A 81.731 104 17 2 1639 1741 533659110 533659212 8.760000e-13 86.1
19 TraesCS3D01G010500 chr3A 97.436 39 1 0 2861 2899 695773465 695773503 3.170000e-07 67.6
20 TraesCS3D01G010500 chr4D 92.157 51 3 1 2438 2487 420142683 420142733 2.450000e-08 71.3
21 TraesCS3D01G010500 chr4D 100.000 31 0 0 1875 1905 133481815 133481785 1.910000e-04 58.4
22 TraesCS3D01G010500 chr5D 95.455 44 1 1 2443 2486 423232440 423232482 8.820000e-08 69.4
23 TraesCS3D01G010500 chr5D 96.970 33 0 1 1870 1902 135643153 135643122 2.000000e-03 54.7
24 TraesCS3D01G010500 chr5B 93.478 46 3 0 2443 2488 611540087 611540132 8.820000e-08 69.4
25 TraesCS3D01G010500 chr2A 87.931 58 4 3 2443 2500 107315265 107315211 1.140000e-06 65.8
26 TraesCS3D01G010500 chr1A 91.667 48 2 2 2442 2489 563809216 563809261 1.140000e-06 65.8
27 TraesCS3D01G010500 chr5A 82.278 79 9 4 228 306 491212576 491212503 4.100000e-06 63.9
28 TraesCS3D01G010500 chr5A 96.970 33 0 1 1870 1902 169310207 169310238 2.000000e-03 54.7
29 TraesCS3D01G010500 chr4B 93.023 43 1 1 2443 2485 63793756 63793716 1.480000e-05 62.1
30 TraesCS3D01G010500 chr6D 100.000 30 0 0 1875 1904 430014785 430014756 6.870000e-04 56.5


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS3D01G010500 chr3D 3821785 3826695 4910 True 9070.000000 9070 100.000000 1 4911 1 chr3D.!!$R1 4910
1 TraesCS3D01G010500 chr3B 662389 667170 4781 False 1956.666667 5136 88.314333 101 4888 3 chr3B.!!$F1 4787
2 TraesCS3D01G010500 chrUn 31929826 31934299 4473 False 1563.825000 2944 91.268250 320 4911 4 chrUn.!!$F3 4591

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
883 954 0.036732 TCACTAACCAGCTGGGCTTG 59.963 55.0 35.42 24.52 42.05 4.01 F
1486 1566 0.036294 CCACCTTCCGGAGAACCTTC 60.036 60.0 3.34 0.00 0.00 3.46 F
2423 2534 0.037590 ATTTGGCCGTTGACCTAGCA 59.962 50.0 0.00 0.00 0.00 3.49 F
3475 3629 0.179032 AGTTCAACGCCATGGTGTCA 60.179 50.0 30.36 17.57 37.94 3.58 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2194 2289 1.774217 TGGGTTGGGCTGGAAGTCT 60.774 57.895 0.00 0.0 39.67 3.24 R
3138 3292 0.542805 TCTCTATGTGCCAGCATGCA 59.457 50.000 21.98 0.0 39.37 3.96 R
3691 3845 0.539051 CCAGTGATGTGACCTCCTCC 59.461 60.000 0.00 0.0 0.00 4.30 R
4638 4799 1.283029 TCCTCCTTGGGCATCTCTTTG 59.717 52.381 0.00 0.0 36.20 2.77 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
46 47 7.730364 CAAGTATTGTAGTCCTGTGAAAAGT 57.270 36.000 0.00 0.00 42.34 2.66
47 48 8.154649 CAAGTATTGTAGTCCTGTGAAAAGTT 57.845 34.615 0.00 0.00 42.34 2.66
48 49 8.621286 CAAGTATTGTAGTCCTGTGAAAAGTTT 58.379 33.333 0.00 0.00 42.34 2.66
49 50 8.379457 AGTATTGTAGTCCTGTGAAAAGTTTC 57.621 34.615 0.00 0.00 37.69 2.78
50 51 8.211629 AGTATTGTAGTCCTGTGAAAAGTTTCT 58.788 33.333 5.45 0.00 38.02 2.52
51 52 6.920569 TTGTAGTCCTGTGAAAAGTTTCTC 57.079 37.500 5.45 2.65 38.02 2.87
52 53 5.365619 TGTAGTCCTGTGAAAAGTTTCTCC 58.634 41.667 5.45 0.00 38.02 3.71
53 54 4.503714 AGTCCTGTGAAAAGTTTCTCCA 57.496 40.909 5.45 2.08 38.02 3.86
54 55 4.855340 AGTCCTGTGAAAAGTTTCTCCAA 58.145 39.130 5.45 0.00 38.02 3.53
55 56 4.884164 AGTCCTGTGAAAAGTTTCTCCAAG 59.116 41.667 5.45 0.00 38.02 3.61
56 57 4.881850 GTCCTGTGAAAAGTTTCTCCAAGA 59.118 41.667 5.45 0.09 38.02 3.02
57 58 5.357032 GTCCTGTGAAAAGTTTCTCCAAGAA 59.643 40.000 5.45 0.00 38.02 2.52
58 59 5.949354 TCCTGTGAAAAGTTTCTCCAAGAAA 59.051 36.000 5.45 0.00 41.51 2.52
70 71 7.703058 TTTCTCCAAGAAACAGAAACTCTTT 57.297 32.000 0.00 0.00 39.13 2.52
71 72 6.927294 TCTCCAAGAAACAGAAACTCTTTC 57.073 37.500 0.00 0.00 39.96 2.62
72 73 6.414732 TCTCCAAGAAACAGAAACTCTTTCA 58.585 36.000 0.00 0.00 42.10 2.69
73 74 6.540189 TCTCCAAGAAACAGAAACTCTTTCAG 59.460 38.462 0.00 0.00 42.10 3.02
74 75 6.414732 TCCAAGAAACAGAAACTCTTTCAGA 58.585 36.000 0.00 0.00 42.10 3.27
75 76 6.884295 TCCAAGAAACAGAAACTCTTTCAGAA 59.116 34.615 0.00 0.00 42.10 3.02
76 77 7.393234 TCCAAGAAACAGAAACTCTTTCAGAAA 59.607 33.333 0.00 0.00 42.10 2.52
77 78 8.028938 CCAAGAAACAGAAACTCTTTCAGAAAA 58.971 33.333 0.00 0.00 42.10 2.29
78 79 9.410556 CAAGAAACAGAAACTCTTTCAGAAAAA 57.589 29.630 0.00 0.00 42.10 1.94
102 103 8.459911 AAAAGGAAACTCTTTCGGAAATTAGA 57.540 30.769 15.76 5.52 42.68 2.10
103 104 8.459911 AAAGGAAACTCTTTCGGAAATTAGAA 57.540 30.769 15.76 0.00 42.68 2.10
104 105 8.459911 AAGGAAACTCTTTCGGAAATTAGAAA 57.540 30.769 15.76 4.38 42.68 2.52
105 106 8.459911 AGGAAACTCTTTCGGAAATTAGAAAA 57.540 30.769 15.76 0.00 40.57 2.29
106 107 8.568794 AGGAAACTCTTTCGGAAATTAGAAAAG 58.431 33.333 15.76 0.00 40.57 2.27
111 112 7.937394 ACTCTTTCGGAAATTAGAAAAGAAGGA 59.063 33.333 15.76 1.66 36.14 3.36
113 114 9.297037 TCTTTCGGAAATTAGAAAAGAAGGAAT 57.703 29.630 3.24 0.00 36.14 3.01
278 279 5.828299 TTTACTTTGTGCATATAGGGTGC 57.172 39.130 5.93 0.00 42.81 5.01
279 280 2.288666 ACTTTGTGCATATAGGGTGCG 58.711 47.619 5.93 0.00 45.37 5.34
280 281 2.288666 CTTTGTGCATATAGGGTGCGT 58.711 47.619 0.00 0.00 45.37 5.24
281 282 2.411628 TTGTGCATATAGGGTGCGTT 57.588 45.000 0.00 0.00 45.37 4.84
282 283 1.662517 TGTGCATATAGGGTGCGTTG 58.337 50.000 0.00 0.00 45.37 4.10
283 284 0.944386 GTGCATATAGGGTGCGTTGG 59.056 55.000 0.00 0.00 45.37 3.77
284 285 0.817634 TGCATATAGGGTGCGTTGGC 60.818 55.000 0.00 0.00 45.37 4.52
297 298 1.822186 GTTGGCACCCGTGTTCACT 60.822 57.895 0.00 0.00 0.00 3.41
309 310 5.105837 ACCCGTGTTCACTAGAGTATTTCTC 60.106 44.000 0.00 0.00 43.05 2.87
310 311 5.105877 CCCGTGTTCACTAGAGTATTTCTCA 60.106 44.000 0.00 0.00 44.98 3.27
311 312 5.800941 CCGTGTTCACTAGAGTATTTCTCAC 59.199 44.000 0.00 0.00 44.98 3.51
316 317 8.246871 TGTTCACTAGAGTATTTCTCACTGATG 58.753 37.037 0.00 0.00 44.98 3.07
317 318 7.946381 TCACTAGAGTATTTCTCACTGATGT 57.054 36.000 0.00 0.00 44.98 3.06
318 319 9.462606 TTCACTAGAGTATTTCTCACTGATGTA 57.537 33.333 0.00 0.00 44.98 2.29
354 355 2.035066 GTGTTGCATCTCAAACTTGGCT 59.965 45.455 0.00 0.00 36.26 4.75
356 357 4.081406 TGTTGCATCTCAAACTTGGCTAT 58.919 39.130 0.00 0.00 36.26 2.97
357 358 4.156556 TGTTGCATCTCAAACTTGGCTATC 59.843 41.667 0.00 0.00 36.26 2.08
469 502 4.566545 CAGCTCCACTGTATCTCTACTG 57.433 50.000 0.00 0.00 41.86 2.74
470 503 4.203226 CAGCTCCACTGTATCTCTACTGA 58.797 47.826 0.00 0.00 41.86 3.41
471 504 4.642437 CAGCTCCACTGTATCTCTACTGAA 59.358 45.833 0.00 0.00 41.86 3.02
472 505 5.301551 CAGCTCCACTGTATCTCTACTGAAT 59.698 44.000 0.00 0.00 41.86 2.57
532 565 2.125753 GAGCCACTCAGGTGAGCG 60.126 66.667 6.91 0.00 45.79 5.03
533 566 3.655810 GAGCCACTCAGGTGAGCGG 62.656 68.421 9.34 9.34 45.79 5.52
534 567 3.695606 GCCACTCAGGTGAGCGGA 61.696 66.667 16.67 0.00 44.94 5.54
535 568 3.023949 GCCACTCAGGTGAGCGGAT 62.024 63.158 16.67 0.00 44.94 4.18
536 569 1.142748 CCACTCAGGTGAGCGGATC 59.857 63.158 8.14 0.00 44.94 3.36
549 582 2.586792 GGATCTGAAGCACGGCCT 59.413 61.111 0.00 0.00 0.00 5.19
559 592 1.039856 AGCACGGCCTCAATTTGTTT 58.960 45.000 0.00 0.00 0.00 2.83
739 808 0.620556 AATCCAAGGGACGCATCACT 59.379 50.000 0.00 0.00 41.93 3.41
740 809 1.496060 ATCCAAGGGACGCATCACTA 58.504 50.000 0.00 0.00 37.75 2.74
741 810 0.824109 TCCAAGGGACGCATCACTAG 59.176 55.000 0.00 0.00 37.75 2.57
742 811 0.811616 CCAAGGGACGCATCACTAGC 60.812 60.000 0.00 0.00 37.75 3.42
743 812 0.176680 CAAGGGACGCATCACTAGCT 59.823 55.000 0.00 0.00 37.75 3.32
744 813 1.409064 CAAGGGACGCATCACTAGCTA 59.591 52.381 0.00 0.00 37.75 3.32
745 814 1.323412 AGGGACGCATCACTAGCTAG 58.677 55.000 19.44 19.44 36.55 3.42
746 815 0.319125 GGGACGCATCACTAGCTAGC 60.319 60.000 20.91 6.62 0.00 3.42
747 816 0.319125 GGACGCATCACTAGCTAGCC 60.319 60.000 20.91 7.31 0.00 3.93
748 817 0.319125 GACGCATCACTAGCTAGCCC 60.319 60.000 20.91 3.95 0.00 5.19
873 944 5.654603 AGAACACATCGTATCACTAACCA 57.345 39.130 0.00 0.00 0.00 3.67
874 945 5.651530 AGAACACATCGTATCACTAACCAG 58.348 41.667 0.00 0.00 0.00 4.00
875 946 3.782046 ACACATCGTATCACTAACCAGC 58.218 45.455 0.00 0.00 0.00 4.85
882 953 0.995024 ATCACTAACCAGCTGGGCTT 59.005 50.000 35.42 23.65 42.05 4.35
883 954 0.036732 TCACTAACCAGCTGGGCTTG 59.963 55.000 35.42 24.52 42.05 4.01
884 955 0.036732 CACTAACCAGCTGGGCTTGA 59.963 55.000 35.42 14.84 42.05 3.02
896 967 1.521681 GGCTTGACTTCCCGATCCG 60.522 63.158 0.00 0.00 0.00 4.18
938 1009 0.598419 CACGCACTGACTGAGCTGAA 60.598 55.000 0.00 0.00 0.00 3.02
939 1010 0.104855 ACGCACTGACTGAGCTGAAA 59.895 50.000 0.00 0.00 0.00 2.69
1041 1121 3.241530 AAGGAGGAGCACGGCACA 61.242 61.111 0.00 0.00 0.00 4.57
1053 1133 3.591835 GGCACACCGGTGGTTGTG 61.592 66.667 36.47 25.98 45.38 3.33
1377 1457 4.208686 GAGACGGCCGCCTACCTG 62.209 72.222 28.58 0.00 0.00 4.00
1398 1478 1.498176 AAGGGTGGCACTACTTCCCC 61.498 60.000 18.45 8.35 38.97 4.81
1473 1553 4.021925 GAGCACCTCCGCCACCTT 62.022 66.667 0.00 0.00 0.00 3.50
1485 1565 2.067197 CCACCTTCCGGAGAACCTT 58.933 57.895 3.34 0.00 0.00 3.50
1486 1566 0.036294 CCACCTTCCGGAGAACCTTC 60.036 60.000 3.34 0.00 0.00 3.46
1487 1567 0.389948 CACCTTCCGGAGAACCTTCG 60.390 60.000 3.34 0.00 31.34 3.79
1491 1571 2.434359 CCGGAGAACCTTCGGCAC 60.434 66.667 0.00 0.00 46.15 5.01
1492 1572 2.434359 CGGAGAACCTTCGGCACC 60.434 66.667 0.00 0.00 0.00 5.01
1493 1573 2.943978 CGGAGAACCTTCGGCACCT 61.944 63.158 0.00 0.00 0.00 4.00
1494 1574 1.375326 GGAGAACCTTCGGCACCTT 59.625 57.895 0.00 0.00 0.00 3.50
1495 1575 0.673956 GGAGAACCTTCGGCACCTTC 60.674 60.000 0.00 0.00 0.00 3.46
1496 1576 0.673956 GAGAACCTTCGGCACCTTCC 60.674 60.000 0.00 0.00 0.00 3.46
1503 1583 2.434359 CGGCACCTTCCGGAGAAC 60.434 66.667 3.34 0.00 45.38 3.01
1504 1584 2.046217 GGCACCTTCCGGAGAACC 60.046 66.667 3.34 0.00 0.00 3.62
1505 1585 2.593956 GGCACCTTCCGGAGAACCT 61.594 63.158 3.34 0.00 0.00 3.50
1587 1667 2.717485 GCATACGTGGCATGGCTG 59.283 61.111 21.08 14.91 0.00 4.85
1770 1850 2.403586 GGCAGCAAATACGCCGAC 59.596 61.111 0.00 0.00 35.79 4.79
1774 1854 2.156446 AGCAAATACGCCGACGACG 61.156 57.895 0.85 0.85 43.93 5.12
1984 2079 4.193334 CAGATCGACTGGCCGCGA 62.193 66.667 8.23 15.91 42.39 5.87
2194 2289 2.506217 GTCGCCATCTTCGACGCA 60.506 61.111 0.00 0.00 45.19 5.24
2252 2347 3.488553 CGTCCCACACTTCAAGGTTTTTC 60.489 47.826 0.00 0.00 0.00 2.29
2253 2348 3.699538 GTCCCACACTTCAAGGTTTTTCT 59.300 43.478 0.00 0.00 0.00 2.52
2254 2349 3.951680 TCCCACACTTCAAGGTTTTTCTC 59.048 43.478 0.00 0.00 0.00 2.87
2255 2350 3.954258 CCCACACTTCAAGGTTTTTCTCT 59.046 43.478 0.00 0.00 0.00 3.10
2256 2351 4.402474 CCCACACTTCAAGGTTTTTCTCTT 59.598 41.667 0.00 0.00 0.00 2.85
2257 2352 5.105351 CCCACACTTCAAGGTTTTTCTCTTT 60.105 40.000 0.00 0.00 0.00 2.52
2361 2457 8.032451 GCATGATAAAAGAGAGATCTACTACCC 58.968 40.741 0.00 0.00 0.00 3.69
2368 2464 5.159637 AGAGAGATCTACTACCCAGCTAGA 58.840 45.833 0.00 0.00 0.00 2.43
2381 2477 4.162509 ACCCAGCTAGATGGACTAACTTTC 59.837 45.833 28.60 0.00 43.57 2.62
2383 2479 5.355596 CCAGCTAGATGGACTAACTTTCAG 58.644 45.833 22.93 0.00 43.57 3.02
2384 2480 4.808364 CAGCTAGATGGACTAACTTTCAGC 59.192 45.833 0.00 0.00 0.00 4.26
2385 2481 4.714308 AGCTAGATGGACTAACTTTCAGCT 59.286 41.667 0.00 0.00 0.00 4.24
2386 2482 5.047188 GCTAGATGGACTAACTTTCAGCTC 58.953 45.833 0.00 0.00 0.00 4.09
2387 2483 5.394663 GCTAGATGGACTAACTTTCAGCTCA 60.395 44.000 0.00 0.00 0.00 4.26
2389 2485 5.486526 AGATGGACTAACTTTCAGCTCAAG 58.513 41.667 1.23 1.23 0.00 3.02
2411 2522 2.224378 TGGATCGATCTCAGATTTGGCC 60.224 50.000 23.96 0.00 0.00 5.36
2423 2534 0.037590 ATTTGGCCGTTGACCTAGCA 59.962 50.000 0.00 0.00 0.00 3.49
2442 2588 4.849111 GCAAGTAGCTAGTTTGCTAGTG 57.151 45.455 25.02 11.13 45.34 2.74
2447 2593 6.197364 AGTAGCTAGTTTGCTAGTGTAGTG 57.803 41.667 0.00 0.00 44.65 2.74
2449 2595 5.923733 AGCTAGTTTGCTAGTGTAGTGAT 57.076 39.130 0.00 0.00 44.93 3.06
2450 2596 5.897050 AGCTAGTTTGCTAGTGTAGTGATC 58.103 41.667 0.00 0.00 44.93 2.92
2451 2597 5.654650 AGCTAGTTTGCTAGTGTAGTGATCT 59.345 40.000 0.00 0.00 44.93 2.75
2452 2598 6.829298 AGCTAGTTTGCTAGTGTAGTGATCTA 59.171 38.462 0.00 0.00 44.93 1.98
2453 2599 7.339721 AGCTAGTTTGCTAGTGTAGTGATCTAA 59.660 37.037 0.00 0.00 44.93 2.10
2456 2602 6.807230 AGTTTGCTAGTGTAGTGATCTAAACG 59.193 38.462 0.00 0.00 38.89 3.60
2457 2603 4.669318 TGCTAGTGTAGTGATCTAAACGC 58.331 43.478 0.00 0.00 38.89 4.84
2458 2604 4.398358 TGCTAGTGTAGTGATCTAAACGCT 59.602 41.667 11.06 11.06 38.89 5.07
2459 2605 4.971220 GCTAGTGTAGTGATCTAAACGCTC 59.029 45.833 10.02 0.00 38.89 5.03
2460 2606 5.220892 GCTAGTGTAGTGATCTAAACGCTCT 60.221 44.000 10.02 2.19 38.89 4.09
2461 2607 5.646577 AGTGTAGTGATCTAAACGCTCTT 57.353 39.130 0.00 0.00 38.89 2.85
2463 2609 7.336161 AGTGTAGTGATCTAAACGCTCTTAT 57.664 36.000 0.00 0.00 38.89 1.73
2464 2610 8.447924 AGTGTAGTGATCTAAACGCTCTTATA 57.552 34.615 0.00 0.00 38.89 0.98
2466 2612 9.680315 GTGTAGTGATCTAAACGCTCTTATATT 57.320 33.333 0.00 0.00 0.00 1.28
2479 2625 8.649973 ACGCTCTTATATTTTTCTTACAGAGG 57.350 34.615 0.00 0.00 0.00 3.69
2480 2626 7.711339 ACGCTCTTATATTTTTCTTACAGAGGG 59.289 37.037 8.01 8.01 42.67 4.30
2481 2627 7.926555 CGCTCTTATATTTTTCTTACAGAGGGA 59.073 37.037 0.00 0.00 40.65 4.20
2482 2628 9.047371 GCTCTTATATTTTTCTTACAGAGGGAC 57.953 37.037 0.00 0.00 0.00 4.46
2490 2636 6.939132 TTTCTTACAGAGGGACTACTATCG 57.061 41.667 0.00 0.00 41.55 2.92
2491 2637 5.627182 TCTTACAGAGGGACTACTATCGT 57.373 43.478 0.00 0.00 41.55 3.73
2492 2638 6.737720 TCTTACAGAGGGACTACTATCGTA 57.262 41.667 0.00 0.00 41.55 3.43
2493 2639 7.313740 TCTTACAGAGGGACTACTATCGTAT 57.686 40.000 0.00 0.00 41.55 3.06
2494 2640 8.427902 TCTTACAGAGGGACTACTATCGTATA 57.572 38.462 0.00 0.00 41.55 1.47
2495 2641 9.044646 TCTTACAGAGGGACTACTATCGTATAT 57.955 37.037 0.00 0.00 41.55 0.86
2499 2645 8.824783 ACAGAGGGACTACTATCGTATATAAGT 58.175 37.037 0.00 0.00 41.55 2.24
2532 2678 8.449251 ACAAATTGGCTTTGAATTTACATGTT 57.551 26.923 2.30 0.00 45.96 2.71
2680 2834 1.078848 GGTCGAGCAGCAGGTCAAT 60.079 57.895 10.30 0.00 42.32 2.57
2852 3006 4.954202 TCTACCTCAACGATGTCAAGGTAT 59.046 41.667 10.82 0.00 40.75 2.73
2871 3025 9.026121 CAAGGTATATTATACTACTGCCTCTGT 57.974 37.037 12.41 0.00 0.00 3.41
2892 3046 6.315393 TCTGTCCCAAAATATAAGAGCGTTTC 59.685 38.462 0.00 0.00 0.00 2.78
2899 3053 5.950965 AATATAAGAGCGTTTCTGACACG 57.049 39.130 11.70 11.70 40.75 4.49
2904 3058 4.017380 AGAGCGTTTCTGACACGTATAG 57.983 45.455 16.55 0.00 39.92 1.31
2909 3063 6.425504 AGCGTTTCTGACACGTATAGTATAC 58.574 40.000 16.55 9.88 39.92 1.47
2997 3151 3.334691 TGTATTTGTGTAGGTGCTCTGC 58.665 45.455 0.00 0.00 0.00 4.26
3113 3267 7.630242 TCATCAAGTCCAAGGTGATTTTATC 57.370 36.000 0.00 0.00 29.49 1.75
3136 3290 6.701937 TCGATTAATTAACAGTCACAATCGC 58.298 36.000 0.00 0.00 41.64 4.58
3137 3291 6.311690 TCGATTAATTAACAGTCACAATCGCA 59.688 34.615 0.00 0.00 41.64 5.10
3138 3292 7.011016 TCGATTAATTAACAGTCACAATCGCAT 59.989 33.333 0.00 0.00 41.64 4.73
3139 3293 7.110628 CGATTAATTAACAGTCACAATCGCATG 59.889 37.037 0.00 0.00 37.53 4.06
3140 3294 3.469899 TTAACAGTCACAATCGCATGC 57.530 42.857 7.91 7.91 0.00 4.06
3141 3295 1.237533 AACAGTCACAATCGCATGCA 58.762 45.000 19.57 5.34 0.00 3.96
3142 3296 1.456296 ACAGTCACAATCGCATGCAT 58.544 45.000 19.57 7.64 0.00 3.96
3143 3297 1.131693 ACAGTCACAATCGCATGCATG 59.868 47.619 22.70 22.70 0.00 4.06
3253 3407 2.612285 TGCTCTTCTTCCTCCTCAGA 57.388 50.000 0.00 0.00 0.00 3.27
3292 3446 1.333177 ACTCCTTCACGCTCTTCTGT 58.667 50.000 0.00 0.00 0.00 3.41
3409 3563 4.035102 GCGCCCAAGTCCTTCCCT 62.035 66.667 0.00 0.00 0.00 4.20
3475 3629 0.179032 AGTTCAACGCCATGGTGTCA 60.179 50.000 30.36 17.57 37.94 3.58
3532 3686 3.311110 ACGAAGAAGGCCGGCAGA 61.311 61.111 30.85 0.00 0.00 4.26
3559 3713 3.532896 GGAGTCCGACATCTTTGCA 57.467 52.632 0.40 0.00 0.00 4.08
3686 3840 1.973812 GACCTGCAACTGAAGGCCC 60.974 63.158 3.38 0.00 45.26 5.80
3691 3845 3.058160 CAACTGAAGGCCCAGGCG 61.058 66.667 12.93 0.74 43.06 5.52
3715 3869 1.002868 GGTCACATCACTGGCAGCT 60.003 57.895 15.89 0.00 0.00 4.24
3775 3929 0.326264 TCTTCAAGAAGGAGCTGGCC 59.674 55.000 9.73 0.00 38.88 5.36
3880 4034 2.033141 ACCTTCCTCGTCGTCGGA 59.967 61.111 1.55 2.60 37.69 4.55
4321 4477 7.414540 GCCTATATGCATCCGAATTAGAAAAGG 60.415 40.741 0.19 0.00 0.00 3.11
4375 4531 6.162079 GGAGTAGTATTTAATTCGGTAGCCC 58.838 44.000 0.00 0.00 0.00 5.19
4474 4630 2.092882 GTGCGGTCTCGTGCTAACC 61.093 63.158 0.00 0.00 38.89 2.85
4478 4634 1.218316 GGTCTCGTGCTAACCAGGG 59.782 63.158 0.00 0.00 33.11 4.45
4482 4638 0.321653 CTCGTGCTAACCAGGGCTTT 60.322 55.000 0.00 0.00 0.00 3.51
4491 4647 4.628959 GCTAACCAGGGCTTTTAGAAGGAT 60.629 45.833 0.00 0.00 33.34 3.24
4549 4708 0.973632 AGAGGGTACATCGTGTTGCA 59.026 50.000 0.00 0.00 0.00 4.08
4581 4742 2.223641 TGGGCATCGTATGAGTTCGTAC 60.224 50.000 2.13 2.13 35.54 3.67
4679 4854 2.612212 AGAACACATGACACCAACGAAC 59.388 45.455 0.00 0.00 0.00 3.95
4753 4952 7.631717 AAATTCAGGGAGTGAGCTTAATTAC 57.368 36.000 0.00 0.00 36.21 1.89
4754 4953 5.755409 TTCAGGGAGTGAGCTTAATTACA 57.245 39.130 0.00 0.00 36.21 2.41
4755 4954 5.957771 TCAGGGAGTGAGCTTAATTACAT 57.042 39.130 0.00 0.00 0.00 2.29
4836 5046 1.004595 TGGACTCGATCGACGTACAG 58.995 55.000 21.31 11.89 43.13 2.74
4898 5108 4.168014 TCGCACCACACTACTTAATTACG 58.832 43.478 0.00 0.00 0.00 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 9.725019 ACAATACTTGATCACATTTGACTCTAA 57.275 29.630 0.00 0.00 33.38 2.10
7 8 9.376075 CTACAATACTTGATCACATTTGACTCT 57.624 33.333 0.00 0.00 33.38 3.24
8 9 9.155975 ACTACAATACTTGATCACATTTGACTC 57.844 33.333 0.00 0.00 33.38 3.36
9 10 9.155975 GACTACAATACTTGATCACATTTGACT 57.844 33.333 0.00 0.00 33.38 3.41
10 11 8.391106 GGACTACAATACTTGATCACATTTGAC 58.609 37.037 0.00 0.00 33.38 3.18
11 12 8.321353 AGGACTACAATACTTGATCACATTTGA 58.679 33.333 0.00 0.00 35.73 2.69
12 13 8.393366 CAGGACTACAATACTTGATCACATTTG 58.607 37.037 0.00 0.17 0.00 2.32
13 14 8.103305 ACAGGACTACAATACTTGATCACATTT 58.897 33.333 0.00 0.00 0.00 2.32
14 15 7.550551 CACAGGACTACAATACTTGATCACATT 59.449 37.037 0.00 0.00 0.00 2.71
15 16 7.044181 CACAGGACTACAATACTTGATCACAT 58.956 38.462 0.00 0.00 0.00 3.21
16 17 6.210584 TCACAGGACTACAATACTTGATCACA 59.789 38.462 0.00 0.00 0.00 3.58
17 18 6.631016 TCACAGGACTACAATACTTGATCAC 58.369 40.000 0.00 0.00 0.00 3.06
18 19 6.850752 TCACAGGACTACAATACTTGATCA 57.149 37.500 0.00 0.00 0.00 2.92
19 20 8.547967 TTTTCACAGGACTACAATACTTGATC 57.452 34.615 0.00 0.00 0.00 2.92
20 21 8.157476 ACTTTTCACAGGACTACAATACTTGAT 58.843 33.333 0.00 0.00 0.00 2.57
21 22 7.506114 ACTTTTCACAGGACTACAATACTTGA 58.494 34.615 0.00 0.00 0.00 3.02
22 23 7.730364 ACTTTTCACAGGACTACAATACTTG 57.270 36.000 0.00 0.00 0.00 3.16
23 24 8.747538 AAACTTTTCACAGGACTACAATACTT 57.252 30.769 0.00 0.00 0.00 2.24
24 25 8.211629 AGAAACTTTTCACAGGACTACAATACT 58.788 33.333 4.58 0.00 39.61 2.12
25 26 8.379457 AGAAACTTTTCACAGGACTACAATAC 57.621 34.615 4.58 0.00 39.61 1.89
26 27 7.660208 GGAGAAACTTTTCACAGGACTACAATA 59.340 37.037 4.58 0.00 39.61 1.90
27 28 6.486993 GGAGAAACTTTTCACAGGACTACAAT 59.513 38.462 4.58 0.00 39.61 2.71
28 29 5.820947 GGAGAAACTTTTCACAGGACTACAA 59.179 40.000 4.58 0.00 39.61 2.41
29 30 5.104693 TGGAGAAACTTTTCACAGGACTACA 60.105 40.000 4.58 0.00 39.61 2.74
30 31 5.365619 TGGAGAAACTTTTCACAGGACTAC 58.634 41.667 4.58 0.00 39.61 2.73
31 32 5.623956 TGGAGAAACTTTTCACAGGACTA 57.376 39.130 4.58 0.00 39.61 2.59
32 33 4.503714 TGGAGAAACTTTTCACAGGACT 57.496 40.909 4.58 0.00 39.61 3.85
33 34 4.881850 TCTTGGAGAAACTTTTCACAGGAC 59.118 41.667 4.58 0.00 39.61 3.85
34 35 5.110814 TCTTGGAGAAACTTTTCACAGGA 57.889 39.130 4.58 5.99 39.61 3.86
35 36 5.835113 TTCTTGGAGAAACTTTTCACAGG 57.165 39.130 4.58 4.01 39.61 4.00
46 47 7.393234 TGAAAGAGTTTCTGTTTCTTGGAGAAA 59.607 33.333 16.26 0.00 42.03 2.52
47 48 6.884295 TGAAAGAGTTTCTGTTTCTTGGAGAA 59.116 34.615 16.26 0.00 42.03 2.87
48 49 6.414732 TGAAAGAGTTTCTGTTTCTTGGAGA 58.585 36.000 16.26 0.00 42.03 3.71
49 50 6.540189 TCTGAAAGAGTTTCTGTTTCTTGGAG 59.460 38.462 16.26 8.53 42.03 3.86
50 51 6.414732 TCTGAAAGAGTTTCTGTTTCTTGGA 58.585 36.000 16.26 10.85 42.03 3.53
51 52 6.683974 TCTGAAAGAGTTTCTGTTTCTTGG 57.316 37.500 16.26 9.38 42.03 3.61
76 77 8.909923 TCTAATTTCCGAAAGAGTTTCCTTTTT 58.090 29.630 0.00 0.00 36.58 1.94
77 78 8.459911 TCTAATTTCCGAAAGAGTTTCCTTTT 57.540 30.769 0.00 0.00 36.58 2.27
78 79 8.459911 TTCTAATTTCCGAAAGAGTTTCCTTT 57.540 30.769 0.00 0.00 38.92 3.11
79 80 8.459911 TTTCTAATTTCCGAAAGAGTTTCCTT 57.540 30.769 0.00 0.00 36.30 3.36
80 81 8.459911 TTTTCTAATTTCCGAAAGAGTTTCCT 57.540 30.769 0.00 0.00 36.30 3.36
81 82 8.565416 TCTTTTCTAATTTCCGAAAGAGTTTCC 58.435 33.333 0.00 0.00 36.30 3.13
82 83 9.946165 TTCTTTTCTAATTTCCGAAAGAGTTTC 57.054 29.630 0.00 0.00 36.32 2.78
83 84 9.952188 CTTCTTTTCTAATTTCCGAAAGAGTTT 57.048 29.630 0.00 0.00 31.52 2.66
84 85 8.568794 CCTTCTTTTCTAATTTCCGAAAGAGTT 58.431 33.333 0.00 0.00 31.52 3.01
85 86 7.937394 TCCTTCTTTTCTAATTTCCGAAAGAGT 59.063 33.333 0.00 0.00 31.52 3.24
86 87 8.324163 TCCTTCTTTTCTAATTTCCGAAAGAG 57.676 34.615 0.00 0.20 31.52 2.85
87 88 8.685838 TTCCTTCTTTTCTAATTTCCGAAAGA 57.314 30.769 0.00 0.00 31.52 2.52
88 89 9.561270 GATTCCTTCTTTTCTAATTTCCGAAAG 57.439 33.333 0.00 0.00 31.52 2.62
89 90 9.297037 AGATTCCTTCTTTTCTAATTTCCGAAA 57.703 29.630 0.00 0.00 0.00 3.46
90 91 8.863872 AGATTCCTTCTTTTCTAATTTCCGAA 57.136 30.769 0.00 0.00 0.00 4.30
91 92 8.322091 AGAGATTCCTTCTTTTCTAATTTCCGA 58.678 33.333 0.00 0.00 33.74 4.55
92 93 8.499403 AGAGATTCCTTCTTTTCTAATTTCCG 57.501 34.615 0.00 0.00 33.74 4.30
175 176 9.197306 ACATGATTAAGTACTGTACCTGTATGA 57.803 33.333 14.05 0.00 0.00 2.15
182 183 7.773149 AGTCAGACATGATTAAGTACTGTACC 58.227 38.462 14.05 0.00 37.87 3.34
252 253 8.576442 GCACCCTATATGCACAAAGTAAATTAT 58.424 33.333 0.00 0.00 42.88 1.28
260 261 2.288666 ACGCACCCTATATGCACAAAG 58.711 47.619 0.00 0.00 43.57 2.77
278 279 2.897846 TGAACACGGGTGCCAACG 60.898 61.111 0.00 0.00 0.00 4.10
279 280 0.533308 TAGTGAACACGGGTGCCAAC 60.533 55.000 0.00 0.00 36.20 3.77
280 281 0.250124 CTAGTGAACACGGGTGCCAA 60.250 55.000 0.00 0.00 36.20 4.52
281 282 1.116536 TCTAGTGAACACGGGTGCCA 61.117 55.000 0.00 0.00 36.20 4.92
282 283 0.389948 CTCTAGTGAACACGGGTGCC 60.390 60.000 0.00 0.00 36.20 5.01
283 284 0.317479 ACTCTAGTGAACACGGGTGC 59.683 55.000 0.00 0.00 36.20 5.01
284 285 4.451629 AATACTCTAGTGAACACGGGTG 57.548 45.455 0.00 0.00 36.20 4.61
285 286 4.771054 AGAAATACTCTAGTGAACACGGGT 59.229 41.667 0.00 0.00 36.20 5.28
286 287 5.105877 TGAGAAATACTCTAGTGAACACGGG 60.106 44.000 0.00 0.00 45.13 5.28
287 288 5.800941 GTGAGAAATACTCTAGTGAACACGG 59.199 44.000 0.00 0.00 45.13 4.94
288 289 6.524933 CAGTGAGAAATACTCTAGTGAACACG 59.475 42.308 0.00 0.00 45.13 4.49
289 290 7.594714 TCAGTGAGAAATACTCTAGTGAACAC 58.405 38.462 0.00 0.00 45.13 3.32
290 291 7.761038 TCAGTGAGAAATACTCTAGTGAACA 57.239 36.000 0.00 0.00 45.13 3.18
309 310 8.864024 CACTCATTAACAAGTACTACATCAGTG 58.136 37.037 0.00 0.00 38.24 3.66
310 311 8.585881 ACACTCATTAACAAGTACTACATCAGT 58.414 33.333 0.00 0.00 41.62 3.41
311 312 8.988064 ACACTCATTAACAAGTACTACATCAG 57.012 34.615 0.00 0.00 0.00 2.90
316 317 7.416154 TGCAACACTCATTAACAAGTACTAC 57.584 36.000 0.00 0.00 0.00 2.73
317 318 8.094548 AGATGCAACACTCATTAACAAGTACTA 58.905 33.333 0.00 0.00 0.00 1.82
318 319 6.936900 AGATGCAACACTCATTAACAAGTACT 59.063 34.615 0.00 0.00 0.00 2.73
354 355 6.329197 CCCACTTGGAGGGTTTTATAGAGATA 59.671 42.308 0.00 0.00 41.61 1.98
356 357 4.473559 CCCACTTGGAGGGTTTTATAGAGA 59.526 45.833 0.00 0.00 41.61 3.10
357 358 4.781934 CCCACTTGGAGGGTTTTATAGAG 58.218 47.826 0.00 0.00 41.61 2.43
467 500 3.257469 TGAGTGGCTAGCTTGATTCAG 57.743 47.619 15.72 0.00 0.00 3.02
468 501 3.008375 ACTTGAGTGGCTAGCTTGATTCA 59.992 43.478 15.72 8.61 0.00 2.57
469 502 3.373439 CACTTGAGTGGCTAGCTTGATTC 59.627 47.826 15.72 6.14 42.10 2.52
470 503 3.008375 TCACTTGAGTGGCTAGCTTGATT 59.992 43.478 15.72 0.00 45.65 2.57
471 504 2.568956 TCACTTGAGTGGCTAGCTTGAT 59.431 45.455 15.72 0.00 45.65 2.57
472 505 1.970640 TCACTTGAGTGGCTAGCTTGA 59.029 47.619 15.72 2.26 45.65 3.02
525 558 1.086634 GTGCTTCAGATCCGCTCACC 61.087 60.000 0.00 0.00 0.00 4.02
532 565 1.522580 GAGGCCGTGCTTCAGATCC 60.523 63.158 0.00 0.00 34.72 3.36
533 566 0.391661 TTGAGGCCGTGCTTCAGATC 60.392 55.000 9.82 0.00 44.84 2.75
534 567 0.254178 ATTGAGGCCGTGCTTCAGAT 59.746 50.000 9.82 5.75 44.84 2.90
535 568 0.036732 AATTGAGGCCGTGCTTCAGA 59.963 50.000 9.82 4.13 44.84 3.27
536 569 0.883833 AAATTGAGGCCGTGCTTCAG 59.116 50.000 9.82 0.00 44.84 3.02
549 582 8.231692 TGTAACCTGATGAGAAAACAAATTGA 57.768 30.769 0.00 0.00 0.00 2.57
559 592 4.525487 ACGTACCTTGTAACCTGATGAGAA 59.475 41.667 0.00 0.00 0.00 2.87
637 694 8.784043 ACATTTAGTTTCTAAGAATTTGTCGCT 58.216 29.630 0.00 0.00 0.00 4.93
748 817 0.536006 GCCCCCGATCCAAGATCTTG 60.536 60.000 25.75 25.75 40.13 3.02
791 860 2.839486 TGTGAGGTAGGTTGCTTCAG 57.161 50.000 0.00 0.00 0.00 3.02
873 944 2.759795 GGGAAGTCAAGCCCAGCT 59.240 61.111 0.00 0.00 44.07 4.24
874 945 2.543067 ATCGGGAAGTCAAGCCCAGC 62.543 60.000 0.00 0.00 44.94 4.85
875 946 0.462759 GATCGGGAAGTCAAGCCCAG 60.463 60.000 0.00 0.00 44.94 4.45
882 953 1.945354 GCTGACGGATCGGGAAGTCA 61.945 60.000 5.18 5.97 40.77 3.41
883 954 1.227002 GCTGACGGATCGGGAAGTC 60.227 63.158 5.18 1.82 0.00 3.01
884 955 1.982395 TGCTGACGGATCGGGAAGT 60.982 57.895 5.18 0.00 0.00 3.01
896 967 1.260561 CACGTTGGTAACTGTGCTGAC 59.739 52.381 0.00 0.00 32.44 3.51
938 1009 2.809665 GCTTGCTCGATGGATGGATCTT 60.810 50.000 0.00 0.00 0.00 2.40
939 1010 1.270732 GCTTGCTCGATGGATGGATCT 60.271 52.381 0.00 0.00 0.00 2.75
972 1047 3.309961 TGCTCAGATCACTCAGTGAAC 57.690 47.619 12.63 9.58 45.96 3.18
1041 1121 0.250727 CCATCTTCACAACCACCGGT 60.251 55.000 0.00 0.00 37.65 5.28
1050 1130 1.444933 AGGGGTTGTCCATCTTCACA 58.555 50.000 0.00 0.00 37.22 3.58
1053 1133 2.170817 GGAGTAGGGGTTGTCCATCTTC 59.829 54.545 0.00 0.00 37.22 2.87
1377 1457 1.613520 GGGAAGTAGTGCCACCCTTTC 60.614 57.143 0.00 0.00 37.76 2.62
1497 1577 3.003763 AGGTGGCGGAGGTTCTCC 61.004 66.667 3.96 3.96 46.44 3.71
1498 1578 2.266055 CAGGTGGCGGAGGTTCTC 59.734 66.667 0.00 0.00 0.00 2.87
1499 1579 4.021925 GCAGGTGGCGGAGGTTCT 62.022 66.667 0.00 0.00 0.00 3.01
1572 1652 2.516930 GCCAGCCATGCCACGTAT 60.517 61.111 0.00 0.00 0.00 3.06
1581 1661 4.133373 ATGCGGAAGGCCAGCCAT 62.133 61.111 12.03 0.00 42.61 4.40
1587 1667 1.591863 GTAGTCGATGCGGAAGGCC 60.592 63.158 0.00 0.00 42.61 5.19
1737 1817 2.103143 CCACGTTTGTTTGCGGCA 59.897 55.556 0.00 0.00 0.00 5.69
1774 1854 2.413765 GCCGTCCTCGAGGTCATC 59.586 66.667 30.17 15.07 39.71 2.92
2194 2289 1.774217 TGGGTTGGGCTGGAAGTCT 60.774 57.895 0.00 0.00 39.67 3.24
2361 2457 4.808364 GCTGAAAGTTAGTCCATCTAGCTG 59.192 45.833 0.00 0.00 39.52 4.24
2368 2464 4.999950 CACTTGAGCTGAAAGTTAGTCCAT 59.000 41.667 8.37 0.00 35.70 3.41
2381 2477 2.100418 TGAGATCGATCCACTTGAGCTG 59.900 50.000 21.66 0.00 34.04 4.24
2383 2479 2.360483 TCTGAGATCGATCCACTTGAGC 59.640 50.000 21.66 2.64 0.00 4.26
2384 2480 4.852134 ATCTGAGATCGATCCACTTGAG 57.148 45.455 21.66 7.12 0.00 3.02
2385 2481 5.354767 CAAATCTGAGATCGATCCACTTGA 58.645 41.667 21.66 16.43 0.00 3.02
2386 2482 4.510711 CCAAATCTGAGATCGATCCACTTG 59.489 45.833 21.66 14.96 0.00 3.16
2387 2483 4.701765 CCAAATCTGAGATCGATCCACTT 58.298 43.478 21.66 2.94 0.00 3.16
2389 2485 2.805099 GCCAAATCTGAGATCGATCCAC 59.195 50.000 21.66 15.98 0.00 4.02
2453 2599 9.099454 CCTCTGTAAGAAAAATATAAGAGCGTT 57.901 33.333 0.00 0.00 46.34 4.84
2456 2602 9.047371 GTCCCTCTGTAAGAAAAATATAAGAGC 57.953 37.037 0.00 0.00 46.34 4.09
2464 2610 8.414778 CGATAGTAGTCCCTCTGTAAGAAAAAT 58.585 37.037 0.00 0.00 46.34 1.82
2466 2612 7.330900 CGATAGTAGTCCCTCTGTAAGAAAA 57.669 40.000 0.00 0.00 46.34 2.29
2467 2613 6.939132 CGATAGTAGTCCCTCTGTAAGAAA 57.061 41.667 0.00 0.00 46.34 2.52
2496 2642 9.606631 TTCAAAGCCAATTTGTTTTGTATACTT 57.393 25.926 15.34 0.00 46.96 2.24
2497 2643 9.777297 ATTCAAAGCCAATTTGTTTTGTATACT 57.223 25.926 15.34 0.00 46.96 2.12
2502 2648 8.734386 TGTAAATTCAAAGCCAATTTGTTTTGT 58.266 25.926 15.34 3.10 46.96 2.83
2503 2649 9.733219 ATGTAAATTCAAAGCCAATTTGTTTTG 57.267 25.926 11.22 11.22 46.96 2.44
2504 2650 9.733219 CATGTAAATTCAAAGCCAATTTGTTTT 57.267 25.926 0.74 5.28 46.96 2.43
2514 2660 8.250332 TCCATCTAAACATGTAAATTCAAAGCC 58.750 33.333 0.00 0.00 0.00 4.35
2680 2834 3.368427 CGAAGAAGTTGAGGTAGATGCCA 60.368 47.826 0.00 0.00 0.00 4.92
2758 2912 3.127533 GTGGTGCGCTCCATCCAC 61.128 66.667 31.67 23.39 39.81 4.02
2852 3006 5.960704 TGGGACAGAGGCAGTAGTATAATA 58.039 41.667 0.00 0.00 0.00 0.98
2864 3018 4.517075 GCTCTTATATTTTGGGACAGAGGC 59.483 45.833 0.00 0.00 42.39 4.70
2871 3025 6.315393 GTCAGAAACGCTCTTATATTTTGGGA 59.685 38.462 0.00 0.00 29.07 4.37
2892 3046 5.673068 GCATCCGGTATACTATACGTGTCAG 60.673 48.000 0.00 0.00 0.00 3.51
2899 3053 7.013464 AGCTAGATTGCATCCGGTATACTATAC 59.987 40.741 0.00 0.00 34.99 1.47
2904 3058 4.457834 AGCTAGATTGCATCCGGTATAC 57.542 45.455 0.00 0.00 34.99 1.47
2909 3063 3.257393 GACATAGCTAGATTGCATCCGG 58.743 50.000 0.00 0.00 34.99 5.14
2968 3122 9.923143 GAGCACCTACACAAATACATATGTATA 57.077 33.333 25.07 10.36 40.10 1.47
2969 3123 8.651389 AGAGCACCTACACAAATACATATGTAT 58.349 33.333 20.49 20.49 42.60 2.29
2970 3124 7.926018 CAGAGCACCTACACAAATACATATGTA 59.074 37.037 17.65 17.65 34.67 2.29
2971 3125 6.763135 CAGAGCACCTACACAAATACATATGT 59.237 38.462 13.93 13.93 0.00 2.29
2975 3129 3.941483 GCAGAGCACCTACACAAATACAT 59.059 43.478 0.00 0.00 0.00 2.29
2997 3151 1.944676 GTACGATTCCGGCAGCTCG 60.945 63.158 0.00 4.86 40.78 5.03
3113 3267 6.474364 TGCGATTGTGACTGTTAATTAATCG 58.526 36.000 16.31 16.31 44.63 3.34
3124 3278 1.822581 CATGCATGCGATTGTGACTG 58.177 50.000 14.93 0.00 0.00 3.51
3136 3290 1.266989 CTCTATGTGCCAGCATGCATG 59.733 52.381 22.70 22.70 44.30 4.06
3137 3291 1.142262 TCTCTATGTGCCAGCATGCAT 59.858 47.619 21.98 5.78 44.30 3.96
3138 3292 0.542805 TCTCTATGTGCCAGCATGCA 59.457 50.000 21.98 0.00 39.37 3.96
3139 3293 1.805345 GATCTCTATGTGCCAGCATGC 59.195 52.381 10.51 10.51 31.97 4.06
3140 3294 3.067833 CAGATCTCTATGTGCCAGCATG 58.932 50.000 0.00 0.00 0.00 4.06
3141 3295 2.550423 GCAGATCTCTATGTGCCAGCAT 60.550 50.000 0.00 0.00 44.54 3.79
3142 3296 1.202615 GCAGATCTCTATGTGCCAGCA 60.203 52.381 0.00 0.00 44.54 4.41
3143 3297 1.510776 GCAGATCTCTATGTGCCAGC 58.489 55.000 0.00 0.00 44.54 4.85
3148 3302 3.068448 AGTCAGCAGCAGATCTCTATGTG 59.932 47.826 0.00 0.00 0.00 3.21
3149 3303 3.298619 AGTCAGCAGCAGATCTCTATGT 58.701 45.455 0.00 0.00 0.00 2.29
3200 3354 2.500098 CCTTCTTCCACAACGGGATCTA 59.500 50.000 0.00 0.00 36.67 1.98
3253 3407 0.998145 AGAAGGGCAGGATGAGCTTT 59.002 50.000 0.00 0.00 39.69 3.51
3409 3563 4.111577 AGAGGAGGTATGGGATGACAAAA 58.888 43.478 0.00 0.00 0.00 2.44
3541 3695 1.808411 TTGCAAAGATGTCGGACTCC 58.192 50.000 9.88 1.21 0.00 3.85
3556 3710 2.268920 GTCTCCTCGGCCATTGCA 59.731 61.111 2.24 0.00 40.13 4.08
3559 3713 2.363795 TCGGTCTCCTCGGCCATT 60.364 61.111 2.24 0.00 0.00 3.16
3686 3840 2.303549 GATGTGACCTCCTCCGCCTG 62.304 65.000 0.00 0.00 0.00 4.85
3691 3845 0.539051 CCAGTGATGTGACCTCCTCC 59.461 60.000 0.00 0.00 0.00 4.30
3715 3869 3.368427 CCTTACTGGTCTTCTTGATCGCA 60.368 47.826 0.00 0.00 0.00 5.10
3745 3899 3.245052 CCTTCTTGAAGATCCTGTTGGGT 60.245 47.826 11.53 0.00 36.25 4.51
3775 3929 0.911525 TGAGGAGGAGAAAGGCCAGG 60.912 60.000 5.01 0.00 0.00 4.45
3784 3938 3.219928 GCGGCGATGAGGAGGAGA 61.220 66.667 12.98 0.00 0.00 3.71
3962 4116 3.047877 GCAGCCTTGGCGTACGTT 61.048 61.111 17.90 0.00 0.00 3.99
3963 4117 2.233605 TATGCAGCCTTGGCGTACGT 62.234 55.000 17.90 0.00 0.00 3.57
4085 4239 7.865707 ACAGTTCATGTAACATTGAGTCTTTC 58.134 34.615 9.64 0.00 41.60 2.62
4251 4405 6.716934 ACTCATTCAATCCGTATGTAGTCT 57.283 37.500 0.00 0.00 0.00 3.24
4474 4630 3.282885 GTCCATCCTTCTAAAAGCCCTG 58.717 50.000 0.00 0.00 0.00 4.45
4478 4634 3.863041 AGACGTCCATCCTTCTAAAAGC 58.137 45.455 13.01 0.00 0.00 3.51
4482 4638 4.098044 CAGCTTAGACGTCCATCCTTCTAA 59.902 45.833 13.01 0.70 0.00 2.10
4491 4647 2.571757 CCGCAGCTTAGACGTCCA 59.428 61.111 13.01 0.00 0.00 4.02
4549 4708 5.425217 TCATACGATGCCCATTACATATCCT 59.575 40.000 0.00 0.00 0.00 3.24
4581 4742 1.671850 GGGTCATACGATGCCCATACG 60.672 57.143 15.50 0.00 42.51 3.06
4638 4799 1.283029 TCCTCCTTGGGCATCTCTTTG 59.717 52.381 0.00 0.00 36.20 2.77


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

AutoCloner maintained by Alex Coulton.