Multiple sequence alignment - TraesCS6D01G307700

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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 TraesCS6D01G307700 chr6D 100.000 4842 0 0 1 4842 418743598 418738757 0.000000e+00 8942.0
1 TraesCS6D01G307700 chr6D 90.476 63 3 3 1957 2018 451106515 451106575 4.020000e-11 80.5
2 TraesCS6D01G307700 chr6A 86.236 1998 140 65 1 1958 562378843 562376941 0.000000e+00 2041.0
3 TraesCS6D01G307700 chr6A 91.447 912 66 5 2009 2914 562376740 562375835 0.000000e+00 1242.0
4 TraesCS6D01G307700 chr6A 86.622 1039 78 25 3068 4078 562375742 562374737 0.000000e+00 1092.0
5 TraesCS6D01G307700 chr6A 85.487 503 30 23 4346 4842 562297722 562297257 7.290000e-133 484.0
6 TraesCS6D01G307700 chr6A 92.704 233 12 4 4610 4840 562373856 562374085 1.000000e-86 331.0
7 TraesCS6D01G307700 chr6A 95.732 164 7 0 4437 4600 562374265 562374102 1.030000e-66 265.0
8 TraesCS6D01G307700 chr6A 89.855 138 6 6 4338 4470 562374399 562374265 2.320000e-38 171.0
9 TraesCS6D01G307700 chr6A 91.262 103 7 1 4161 4263 562297862 562297762 6.530000e-29 139.0
10 TraesCS6D01G307700 chr6A 88.060 67 8 0 2941 3007 224661923 224661989 4.020000e-11 80.5
11 TraesCS6D01G307700 chr6A 85.246 61 6 3 1954 2013 218349504 218349446 5.230000e-05 60.2
12 TraesCS6D01G307700 chr6B 90.994 1077 39 25 906 1958 631203611 631202569 0.000000e+00 1399.0
13 TraesCS6D01G307700 chr6B 89.516 1116 78 17 2190 3304 631202447 631201370 0.000000e+00 1376.0
14 TraesCS6D01G307700 chr6B 92.622 881 43 8 3291 4154 631201311 631200436 0.000000e+00 1247.0
15 TraesCS6D01G307700 chr6B 94.318 792 20 11 906 1697 630846785 630847551 0.000000e+00 1190.0
16 TraesCS6D01G307700 chr6B 85.664 1137 103 25 3166 4282 630849055 630850151 0.000000e+00 1142.0
17 TraesCS6D01G307700 chr6B 90.358 726 56 6 2192 2911 630848083 630848800 0.000000e+00 941.0
18 TraesCS6D01G307700 chr6B 91.943 422 25 5 4423 4841 631199336 631198921 2.510000e-162 582.0
19 TraesCS6D01G307700 chr6B 94.942 257 13 0 4287 4543 630858206 630858462 2.100000e-108 403.0
20 TraesCS6D01G307700 chr6B 87.658 316 16 6 4536 4842 630865113 630865414 3.590000e-91 346.0
21 TraesCS6D01G307700 chr6B 85.942 313 25 11 554 851 630846463 630846771 2.810000e-82 316.0
22 TraesCS6D01G307700 chr6B 92.233 206 6 5 653 851 631203827 631203625 2.850000e-72 283.0
23 TraesCS6D01G307700 chr6B 78.866 388 65 16 445 827 630777647 630778022 3.740000e-61 246.0
24 TraesCS6D01G307700 chr6B 81.533 287 44 6 89 368 162610863 162611147 1.360000e-55 228.0
25 TraesCS6D01G307700 chr7D 86.066 610 85 0 1065 1674 120321665 120322274 0.000000e+00 656.0
26 TraesCS6D01G307700 chr7D 92.593 135 10 0 2052 2186 190386537 190386403 1.380000e-45 195.0
27 TraesCS6D01G307700 chr7D 88.406 69 6 2 2939 3007 518096721 518096655 1.120000e-11 82.4
28 TraesCS6D01G307700 chr7D 95.556 45 2 0 1964 2008 414373043 414373087 6.720000e-09 73.1
29 TraesCS6D01G307700 chr7A 86.088 611 83 2 1065 1674 125262870 125263479 0.000000e+00 656.0
30 TraesCS6D01G307700 chr7A 93.333 45 3 0 1964 2008 47504449 47504405 3.130000e-07 67.6
31 TraesCS6D01G307700 chr7B 85.574 610 88 0 1065 1674 81691136 81691745 1.470000e-179 640.0
32 TraesCS6D01G307700 chr5D 83.972 287 39 5 89 368 512212063 512211777 7.990000e-68 268.0
33 TraesCS6D01G307700 chr5D 87.963 216 20 3 89 298 499229775 499229990 2.890000e-62 250.0
34 TraesCS6D01G307700 chr5D 91.935 62 5 0 2942 3003 23070930 23070991 2.400000e-13 87.9
35 TraesCS6D01G307700 chr5D 88.406 69 4 3 2941 3007 349376264 349376330 4.020000e-11 80.5
36 TraesCS6D01G307700 chr5D 92.157 51 1 3 1964 2013 137478870 137478822 8.700000e-08 69.4
37 TraesCS6D01G307700 chr5D 93.333 45 3 0 1964 2008 527501709 527501753 3.130000e-07 67.6
38 TraesCS6D01G307700 chr4B 83.860 285 31 13 89 362 572208766 572209046 1.730000e-64 257.0
39 TraesCS6D01G307700 chr4B 90.566 53 4 1 1961 2013 255388171 255388222 8.700000e-08 69.4
40 TraesCS6D01G307700 chr4B 88.679 53 5 1 1956 2007 518879505 518879453 4.050000e-06 63.9
41 TraesCS6D01G307700 chr2A 86.111 216 24 3 89 298 199712253 199712468 1.360000e-55 228.0
42 TraesCS6D01G307700 chr2A 81.206 282 47 4 89 364 618263781 618263500 6.310000e-54 222.0
43 TraesCS6D01G307700 chr1B 81.469 286 44 6 89 368 411575404 411575122 4.880000e-55 226.0
44 TraesCS6D01G307700 chr5A 82.197 264 40 5 91 348 667308869 667308607 2.270000e-53 220.0
45 TraesCS6D01G307700 chr5B 84.685 222 27 4 92 307 84660820 84660600 1.060000e-51 215.0
46 TraesCS6D01G307700 chr3A 92.063 63 5 0 2124 2186 496376459 496376397 6.670000e-14 89.8
47 TraesCS6D01G307700 chr3A 90.909 66 6 0 2942 3007 506377725 506377790 6.670000e-14 89.8
48 TraesCS6D01G307700 chr3A 89.394 66 7 0 2942 3007 332036594 332036659 3.110000e-12 84.2
49 TraesCS6D01G307700 chr2B 89.855 69 4 2 2941 3006 634975357 634975425 8.630000e-13 86.1
50 TraesCS6D01G307700 chr1D 87.671 73 6 2 2938 3008 221880981 221881052 1.120000e-11 82.4
51 TraesCS6D01G307700 chr4A 86.207 58 5 3 1957 2013 262745812 262745867 5.230000e-05 60.2


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 TraesCS6D01G307700 chr6D 418738757 418743598 4841 True 8942.00 8942 100.0000 1 4842 1 chr6D.!!$R1 4841
1 TraesCS6D01G307700 chr6A 562374102 562378843 4741 True 962.20 2041 89.9784 1 4600 5 chr6A.!!$R3 4599
2 TraesCS6D01G307700 chr6A 562297257 562297862 605 True 311.50 484 88.3745 4161 4842 2 chr6A.!!$R2 681
3 TraesCS6D01G307700 chr6B 631198921 631203827 4906 True 977.40 1399 91.4616 653 4841 5 chr6B.!!$R1 4188
4 TraesCS6D01G307700 chr6B 630846463 630850151 3688 False 897.25 1190 89.0705 554 4282 4 chr6B.!!$F5 3728
5 TraesCS6D01G307700 chr7D 120321665 120322274 609 False 656.00 656 86.0660 1065 1674 1 chr7D.!!$F1 609
6 TraesCS6D01G307700 chr7A 125262870 125263479 609 False 656.00 656 86.0880 1065 1674 1 chr7A.!!$F1 609
7 TraesCS6D01G307700 chr7B 81691136 81691745 609 False 640.00 640 85.5740 1065 1674 1 chr7B.!!$F1 609

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
300 306 0.034337 GTCCCGCGGGCAAATATAGA 59.966 55.0 39.89 16.56 34.68 1.98 F
444 455 0.109597 GTTGCTTGCCGGACATCAAG 60.110 55.0 5.05 10.65 41.79 3.02 F
2246 2608 0.035439 CCGACCCCACAGCTTAACAT 60.035 55.0 0.00 0.00 0.00 2.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1744 1801 0.673985 TGACCGAGAACACTGACAGG 59.326 55.0 7.51 0.00 0.00 4.00 R
2354 2716 0.321919 GCAGTCCATGGTCTGAAGCA 60.322 55.0 34.31 2.19 34.14 3.91 R
4201 5912 0.179062 GATCTGCGCCTCTTGATGGT 60.179 55.0 4.18 0.00 0.00 3.55 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
41 42 8.496916 TGGAAAGATTGGATTCTCATCTTATCA 58.503 33.333 9.78 8.83 32.01 2.15
42 43 9.001542 GGAAAGATTGGATTCTCATCTTATCAG 57.998 37.037 9.78 0.00 32.01 2.90
49 50 8.162878 TGGATTCTCATCTTATCAGAAAATGC 57.837 34.615 0.00 0.00 30.76 3.56
50 51 7.776500 TGGATTCTCATCTTATCAGAAAATGCA 59.224 33.333 0.00 0.00 30.76 3.96
54 55 8.320396 TCTCATCTTATCAGAAAATGCATAGC 57.680 34.615 0.00 0.00 30.76 2.97
68 69 1.741732 GCATAGCAGCTATCCGGATGG 60.742 57.143 27.55 25.03 0.00 3.51
70 71 1.257743 TAGCAGCTATCCGGATGGTC 58.742 55.000 27.55 18.73 35.05 4.02
83 84 1.212616 GATGGTCGCATACAGAGTGC 58.787 55.000 0.00 0.00 39.18 4.40
95 96 1.002134 AGAGTGCCCGGTGATTTGG 60.002 57.895 0.00 0.00 0.00 3.28
101 102 1.883021 CCCGGTGATTTGGTTGAGC 59.117 57.895 0.00 0.00 0.00 4.26
105 106 2.097466 CCGGTGATTTGGTTGAGCATAC 59.903 50.000 0.00 0.00 0.00 2.39
106 107 2.223021 CGGTGATTTGGTTGAGCATACG 60.223 50.000 0.00 0.00 0.00 3.06
110 111 2.552599 TTTGGTTGAGCATACGTGGA 57.447 45.000 0.00 0.00 0.00 4.02
111 112 1.803334 TTGGTTGAGCATACGTGGAC 58.197 50.000 0.00 0.00 0.00 4.02
121 122 1.665679 CATACGTGGACTCATGTTGGC 59.334 52.381 0.00 0.00 42.56 4.52
125 126 0.238289 GTGGACTCATGTTGGCAACG 59.762 55.000 24.03 12.89 42.51 4.10
126 127 0.107643 TGGACTCATGTTGGCAACGA 59.892 50.000 24.03 15.36 42.51 3.85
127 128 1.234821 GGACTCATGTTGGCAACGAA 58.765 50.000 24.03 9.32 42.51 3.85
273 279 6.128769 TGTGTATATTTGTTGAGAAACGACGG 60.129 38.462 0.00 0.00 35.76 4.79
298 304 1.071814 GGTCCCGCGGGCAAATATA 59.928 57.895 39.89 18.28 34.68 0.86
300 306 0.034337 GTCCCGCGGGCAAATATAGA 59.966 55.000 39.89 16.56 34.68 1.98
301 307 0.759959 TCCCGCGGGCAAATATAGAA 59.240 50.000 39.89 15.70 34.68 2.10
303 309 1.588674 CCGCGGGCAAATATAGAACA 58.411 50.000 20.10 0.00 0.00 3.18
311 317 4.577283 GGGCAAATATAGAACAGCGGTTTA 59.423 41.667 3.10 0.00 37.36 2.01
312 318 5.066764 GGGCAAATATAGAACAGCGGTTTAA 59.933 40.000 3.10 0.00 37.36 1.52
323 334 1.131826 CGGTTTAAACGCTCTGCCG 59.868 57.895 12.07 4.66 0.00 5.69
325 336 1.084289 GGTTTAAACGCTCTGCCGAT 58.916 50.000 12.07 0.00 0.00 4.18
331 342 0.392998 AACGCTCTGCCGATCCAAAT 60.393 50.000 0.00 0.00 0.00 2.32
333 344 1.134521 ACGCTCTGCCGATCCAAATAA 60.135 47.619 0.00 0.00 0.00 1.40
335 346 2.354510 CGCTCTGCCGATCCAAATAAAA 59.645 45.455 0.00 0.00 0.00 1.52
336 347 3.181501 CGCTCTGCCGATCCAAATAAAAA 60.182 43.478 0.00 0.00 0.00 1.94
411 422 3.244875 TGGAGTTGCTCTTAGGATGCAAA 60.245 43.478 11.36 0.00 46.22 3.68
412 423 3.376546 GGAGTTGCTCTTAGGATGCAAAG 59.623 47.826 11.36 0.00 46.22 2.77
437 448 1.531739 GGATTTGGTTGCTTGCCGGA 61.532 55.000 5.05 0.00 0.00 5.14
438 449 0.388520 GATTTGGTTGCTTGCCGGAC 60.389 55.000 5.05 0.00 0.00 4.79
439 450 1.112315 ATTTGGTTGCTTGCCGGACA 61.112 50.000 5.05 0.00 0.00 4.02
440 451 1.112315 TTTGGTTGCTTGCCGGACAT 61.112 50.000 5.05 0.00 0.00 3.06
441 452 1.523154 TTGGTTGCTTGCCGGACATC 61.523 55.000 5.05 0.00 0.00 3.06
442 453 1.971167 GGTTGCTTGCCGGACATCA 60.971 57.895 5.05 1.50 0.00 3.07
443 454 1.523154 GGTTGCTTGCCGGACATCAA 61.523 55.000 5.05 7.69 0.00 2.57
444 455 0.109597 GTTGCTTGCCGGACATCAAG 60.110 55.000 5.05 10.65 41.79 3.02
445 456 0.537143 TTGCTTGCCGGACATCAAGT 60.537 50.000 17.43 0.00 41.15 3.16
446 457 1.236616 TGCTTGCCGGACATCAAGTG 61.237 55.000 17.43 0.00 41.15 3.16
447 458 1.503542 CTTGCCGGACATCAAGTGC 59.496 57.895 5.05 0.00 36.01 4.40
448 459 1.926511 CTTGCCGGACATCAAGTGCC 61.927 60.000 5.05 0.00 36.01 5.01
449 460 2.359850 GCCGGACATCAAGTGCCA 60.360 61.111 5.05 0.00 34.68 4.92
450 461 2.690778 GCCGGACATCAAGTGCCAC 61.691 63.158 5.05 0.00 34.68 5.01
451 462 2.040544 CCGGACATCAAGTGCCACC 61.041 63.158 0.00 0.00 34.68 4.61
452 463 2.390599 CGGACATCAAGTGCCACCG 61.391 63.158 0.00 0.00 34.68 4.94
453 464 2.040544 GGACATCAAGTGCCACCGG 61.041 63.158 0.00 0.00 31.47 5.28
493 504 1.804326 CTCCGCTACCGAACCGTTG 60.804 63.158 0.00 0.00 36.29 4.10
629 641 1.215382 GGATCCAAACGGCAAAGCC 59.785 57.895 6.95 0.00 46.75 4.35
737 763 2.679349 GCCAAAAGCAAACAAACTCCCA 60.679 45.455 0.00 0.00 42.97 4.37
741 767 3.733443 AAGCAAACAAACTCCCATGAC 57.267 42.857 0.00 0.00 0.00 3.06
762 788 0.527817 CTCCCGCCATTACTCACGAC 60.528 60.000 0.00 0.00 0.00 4.34
808 834 4.410225 CTGACAAGCAGGCCATGT 57.590 55.556 5.01 4.09 41.07 3.21
819 845 1.620323 CAGGCCATGTCTCCATCGATA 59.380 52.381 5.01 0.00 0.00 2.92
821 847 2.909006 AGGCCATGTCTCCATCGATATT 59.091 45.455 5.01 0.00 0.00 1.28
822 848 3.005554 GGCCATGTCTCCATCGATATTG 58.994 50.000 0.00 0.00 0.00 1.90
823 849 2.417933 GCCATGTCTCCATCGATATTGC 59.582 50.000 0.00 0.00 0.00 3.56
824 850 3.867600 GCCATGTCTCCATCGATATTGCT 60.868 47.826 0.00 0.00 0.00 3.91
825 851 3.931468 CCATGTCTCCATCGATATTGCTC 59.069 47.826 0.00 0.00 0.00 4.26
826 852 4.322574 CCATGTCTCCATCGATATTGCTCT 60.323 45.833 0.00 0.00 0.00 4.09
827 853 5.105595 CCATGTCTCCATCGATATTGCTCTA 60.106 44.000 0.00 0.00 0.00 2.43
828 854 5.635417 TGTCTCCATCGATATTGCTCTAG 57.365 43.478 0.00 0.00 0.00 2.43
888 914 1.830279 ACTTACACATGCATGCTGCT 58.170 45.000 26.53 14.87 45.31 4.24
896 922 1.531578 CATGCATGCTGCTGCTACTAG 59.468 52.381 20.33 3.49 45.31 2.57
903 929 1.683917 GCTGCTGCTACTAGGCTTCTA 59.316 52.381 8.53 0.00 36.03 2.10
904 930 2.288152 GCTGCTGCTACTAGGCTTCTAG 60.288 54.545 8.53 0.00 40.08 2.43
912 938 0.313672 CTAGGCTTCTAGCTCGCAGG 59.686 60.000 0.00 0.00 41.99 4.85
934 960 2.356313 CGAGCCGCACAGTTCACT 60.356 61.111 0.00 0.00 0.00 3.41
942 968 0.233332 GCACAGTTCACTTCAGTCGC 59.767 55.000 0.00 0.00 0.00 5.19
956 982 3.695606 TCGCCAGTGAGCTCCACC 61.696 66.667 12.15 0.00 46.87 4.61
959 985 4.767255 CCAGTGAGCTCCACCGCC 62.767 72.222 12.15 0.00 46.87 6.13
960 986 4.767255 CAGTGAGCTCCACCGCCC 62.767 72.222 12.15 0.00 46.87 6.13
978 1004 4.222847 GGCCCCCGACGAAGCTAG 62.223 72.222 0.00 0.00 0.00 3.42
979 1005 4.893601 GCCCCCGACGAAGCTAGC 62.894 72.222 6.62 6.62 0.00 3.42
1048 1085 1.226575 GTGATGGTCGCGATCGTCA 60.227 57.895 34.36 34.36 35.26 4.35
1058 1095 2.230940 CGATCGTCATGGTGGCGTC 61.231 63.158 7.03 1.13 46.84 5.19
1059 1096 2.202743 ATCGTCATGGTGGCGTCG 60.203 61.111 3.78 0.00 46.84 5.12
1551 1588 4.367023 TACGTGGTGCAGGTCGGC 62.367 66.667 0.00 0.00 34.30 5.54
1709 1746 3.947196 TCAAACTGCTGCTCTTTTCTTCA 59.053 39.130 0.00 0.00 0.00 3.02
1720 1757 2.216940 TCTTTTCTTCAACGTACGTGCG 59.783 45.455 23.57 24.57 37.94 5.34
1739 1796 4.782156 TGCGACACACATTTTACATTCAG 58.218 39.130 0.00 0.00 0.00 3.02
1744 1801 6.254281 ACACACATTTTACATTCAGTAGGC 57.746 37.500 0.00 0.00 33.43 3.93
1754 1811 1.717032 TTCAGTAGGCCTGTCAGTGT 58.283 50.000 17.99 0.00 42.19 3.55
1790 1856 2.203401 TGTGCTGCATTGCTTTGAAAC 58.797 42.857 5.27 1.12 0.00 2.78
1801 1873 4.481930 TGCTTTGAAACGGAATGTAGTG 57.518 40.909 0.00 0.00 0.00 2.74
1802 1874 3.880490 TGCTTTGAAACGGAATGTAGTGT 59.120 39.130 0.00 0.00 0.00 3.55
1803 1875 4.219033 GCTTTGAAACGGAATGTAGTGTG 58.781 43.478 0.00 0.00 0.00 3.82
1804 1876 4.024387 GCTTTGAAACGGAATGTAGTGTGA 60.024 41.667 0.00 0.00 0.00 3.58
1805 1877 5.504994 GCTTTGAAACGGAATGTAGTGTGAA 60.505 40.000 0.00 0.00 0.00 3.18
1806 1878 5.412526 TTGAAACGGAATGTAGTGTGAAC 57.587 39.130 0.00 0.00 0.00 3.18
1807 1879 4.699637 TGAAACGGAATGTAGTGTGAACT 58.300 39.130 0.00 0.00 0.00 3.01
1812 1884 4.750098 ACGGAATGTAGTGTGAACTTGAAG 59.250 41.667 0.00 0.00 0.00 3.02
1827 1899 4.218312 ACTTGAAGTGGCCTCAATTTTCT 58.782 39.130 3.32 0.00 30.76 2.52
1828 1900 5.385198 ACTTGAAGTGGCCTCAATTTTCTA 58.615 37.500 3.32 0.00 30.76 2.10
1829 1901 5.474876 ACTTGAAGTGGCCTCAATTTTCTAG 59.525 40.000 3.32 9.04 30.76 2.43
1875 1956 3.390135 CGAAGTTCTGTTAAGGCACTGA 58.610 45.455 0.56 0.00 40.86 3.41
1974 2086 8.939929 CGAATTGTATACTATTACTACCTCCGA 58.060 37.037 11.74 0.00 0.00 4.55
1990 2102 5.529791 ACCTCCGATTCATATTACTTGTCG 58.470 41.667 0.00 0.00 0.00 4.35
1991 2103 4.386049 CCTCCGATTCATATTACTTGTCGC 59.614 45.833 0.00 0.00 0.00 5.19
1993 2105 5.220381 TCCGATTCATATTACTTGTCGCTC 58.780 41.667 0.00 0.00 0.00 5.03
1994 2106 4.982295 CCGATTCATATTACTTGTCGCTCA 59.018 41.667 0.00 0.00 0.00 4.26
1996 2108 6.019075 CCGATTCATATTACTTGTCGCTCAAA 60.019 38.462 0.00 0.00 35.48 2.69
1999 2111 6.603237 TCATATTACTTGTCGCTCAAATGG 57.397 37.500 0.00 0.00 35.48 3.16
2000 2112 6.345298 TCATATTACTTGTCGCTCAAATGGA 58.655 36.000 0.00 0.00 35.48 3.41
2001 2113 6.992123 TCATATTACTTGTCGCTCAAATGGAT 59.008 34.615 0.00 0.00 35.48 3.41
2002 2114 8.147704 TCATATTACTTGTCGCTCAAATGGATA 58.852 33.333 0.00 0.00 35.48 2.59
2003 2115 8.939929 CATATTACTTGTCGCTCAAATGGATAT 58.060 33.333 0.00 0.00 35.48 1.63
2006 2118 8.534333 TTACTTGTCGCTCAAATGGATATATC 57.466 34.615 3.96 3.96 35.48 1.63
2007 2119 6.763355 ACTTGTCGCTCAAATGGATATATCT 58.237 36.000 12.42 0.00 35.48 1.98
2014 2245 6.815641 CGCTCAAATGGATATATCTTAGCAGT 59.184 38.462 12.42 0.00 0.00 4.40
2220 2582 6.538742 TGTATGCTCTGCTTTTGTCTATTACC 59.461 38.462 0.00 0.00 0.00 2.85
2232 2594 5.272283 TGTCTATTACCAATTCTCCGACC 57.728 43.478 0.00 0.00 0.00 4.79
2241 2603 1.201429 ATTCTCCGACCCCACAGCTT 61.201 55.000 0.00 0.00 0.00 3.74
2246 2608 0.035439 CCGACCCCACAGCTTAACAT 60.035 55.000 0.00 0.00 0.00 2.71
2354 2716 4.768448 TGTGCATCATCATTTCCAAAGACT 59.232 37.500 0.00 0.00 0.00 3.24
2375 2737 1.612726 GCTTCAGACCATGGACTGCTT 60.613 52.381 31.66 4.61 37.70 3.91
2453 2815 2.415491 GCCGGGCAATCTCAAGTAAAAC 60.415 50.000 15.62 0.00 0.00 2.43
2462 2824 7.308589 GGCAATCTCAAGTAAAACTCAGCTTAA 60.309 37.037 0.00 0.00 0.00 1.85
2535 2903 5.546621 TCATAACCCCTATCTTTCCTTCG 57.453 43.478 0.00 0.00 0.00 3.79
2558 2926 2.291865 TGCCAGTTTATATTGCACCCCA 60.292 45.455 0.00 0.00 0.00 4.96
2570 2938 1.302832 CACCCCAGCTTCACTGTCC 60.303 63.158 0.00 0.00 45.68 4.02
2571 2939 1.770110 ACCCCAGCTTCACTGTCCA 60.770 57.895 0.00 0.00 45.68 4.02
2660 3028 3.959975 GCGGGCTGCAACGTTTCA 61.960 61.111 14.74 0.00 45.45 2.69
2663 3031 1.154225 GGGCTGCAACGTTTCATCG 60.154 57.895 0.00 0.00 0.00 3.84
2684 3052 2.095059 GTGCAGCTATGGAGGTTTTGTG 60.095 50.000 0.00 0.00 0.00 3.33
2721 3089 4.732285 ACTCTGTAAGCAATGTGTTTCG 57.268 40.909 0.00 0.00 0.00 3.46
2726 3094 3.628032 TGTAAGCAATGTGTTTCGGAACA 59.372 39.130 4.79 4.79 43.23 3.18
2727 3095 3.354089 AAGCAATGTGTTTCGGAACAG 57.646 42.857 10.23 0.00 45.86 3.16
2732 3100 4.259770 GCAATGTGTTTCGGAACAGTTTTG 60.260 41.667 10.23 14.25 45.86 2.44
2873 3243 0.038744 ATTCAGACCCAAGGCTGTGG 59.961 55.000 8.28 8.28 38.51 4.17
2911 3281 1.798813 CTTGTAGACTCCGCACAAACC 59.201 52.381 0.00 0.00 32.16 3.27
2919 3289 2.050691 CTCCGCACAAACCATTTTTCG 58.949 47.619 0.00 0.00 0.00 3.46
2934 3304 5.327091 CATTTTTCGAATGTAGGAGCACTG 58.673 41.667 0.00 0.00 0.00 3.66
2957 3327 4.211374 GCGCACAAACTCTCTTCTTCTTAA 59.789 41.667 0.30 0.00 0.00 1.85
2986 3356 4.142293 GGATGAGACAAATCTTTTGCCTCC 60.142 45.833 11.94 3.74 34.34 4.30
3154 3525 3.181489 CCGTGTCACCAGAATCTACCTAC 60.181 52.174 0.00 0.00 0.00 3.18
3321 3827 9.599322 CATTGAAATAGCCGACATTATACTTTC 57.401 33.333 0.00 0.00 0.00 2.62
3382 3890 7.391554 TGAATGAAGTTCAGAATCCTAAACAGG 59.608 37.037 11.91 0.00 41.79 4.00
3403 3911 2.357952 GACACCTGAAAACCCACAAGAC 59.642 50.000 0.00 0.00 0.00 3.01
3436 3947 4.561735 AACACCGGAAACAATACACTTG 57.438 40.909 9.46 0.00 0.00 3.16
3437 3948 3.547746 ACACCGGAAACAATACACTTGT 58.452 40.909 9.46 0.00 0.00 3.16
3438 3949 3.949113 ACACCGGAAACAATACACTTGTT 59.051 39.130 9.46 0.00 43.72 2.83
3457 3968 7.066163 CACTTGTTTGATCTATGTTCCATGCTA 59.934 37.037 0.00 0.00 0.00 3.49
3502 4013 1.209261 TCATTCGGTCAGCATAGCCAA 59.791 47.619 0.00 0.00 0.00 4.52
3517 4028 9.999009 CAGCATAGCCAATATTACTTTGATATG 57.001 33.333 10.41 6.95 32.51 1.78
3766 4277 1.966451 CGTCTCAAAGGCACCACCC 60.966 63.158 0.00 0.00 40.58 4.61
3943 4472 5.127194 TGAGGTAAGTGGACAGTATGATGAC 59.873 44.000 0.00 0.00 39.69 3.06
4083 4618 2.427095 AGGATATGTTTTGCGGCCTTTC 59.573 45.455 0.00 0.00 0.00 2.62
4122 4660 4.159506 CCACCGGGTAATGATCATGTTTTT 59.840 41.667 9.46 0.00 0.00 1.94
4141 4680 0.951558 TTTGCCAAGGAAACGAGAGC 59.048 50.000 0.00 0.00 0.00 4.09
4190 5901 1.584724 CCCAAGGAGGAGGTACATGT 58.415 55.000 2.69 2.69 41.22 3.21
4201 5912 3.118408 GGAGGTACATGTATGCACTTGGA 60.118 47.826 9.18 0.00 34.84 3.53
4248 5963 3.077484 ACCCCATGAAGATCACACTTG 57.923 47.619 0.00 0.00 0.00 3.16
4249 5964 2.376518 ACCCCATGAAGATCACACTTGT 59.623 45.455 0.00 0.00 0.00 3.16
4250 5965 3.181429 ACCCCATGAAGATCACACTTGTT 60.181 43.478 0.00 0.00 0.00 2.83
4251 5966 3.828451 CCCCATGAAGATCACACTTGTTT 59.172 43.478 0.00 0.00 0.00 2.83
4252 5967 4.082571 CCCCATGAAGATCACACTTGTTTC 60.083 45.833 0.00 0.00 0.00 2.78
4253 5968 4.763793 CCCATGAAGATCACACTTGTTTCT 59.236 41.667 0.00 0.00 0.00 2.52
4254 5969 5.939883 CCCATGAAGATCACACTTGTTTCTA 59.060 40.000 0.00 0.00 0.00 2.10
4255 5970 6.093219 CCCATGAAGATCACACTTGTTTCTAG 59.907 42.308 0.00 0.00 0.00 2.43
4256 5971 6.875726 CCATGAAGATCACACTTGTTTCTAGA 59.124 38.462 0.00 0.00 0.00 2.43
4257 5972 7.551974 CCATGAAGATCACACTTGTTTCTAGAT 59.448 37.037 0.00 0.00 0.00 1.98
4258 5973 8.602328 CATGAAGATCACACTTGTTTCTAGATC 58.398 37.037 0.00 0.00 0.00 2.75
4259 5974 6.808704 TGAAGATCACACTTGTTTCTAGATCG 59.191 38.462 0.00 0.00 36.45 3.69
4260 5975 6.516739 AGATCACACTTGTTTCTAGATCGA 57.483 37.500 0.00 0.00 36.45 3.59
4261 5976 7.106439 AGATCACACTTGTTTCTAGATCGAT 57.894 36.000 0.00 0.00 36.45 3.59
4262 5977 6.977502 AGATCACACTTGTTTCTAGATCGATG 59.022 38.462 0.54 0.00 36.45 3.84
4263 5978 6.025749 TCACACTTGTTTCTAGATCGATGT 57.974 37.500 0.54 0.00 0.00 3.06
4264 5979 7.153217 TCACACTTGTTTCTAGATCGATGTA 57.847 36.000 0.54 1.36 0.00 2.29
4265 5980 7.027760 TCACACTTGTTTCTAGATCGATGTAC 58.972 38.462 0.54 0.00 0.00 2.90
4266 5981 7.030165 CACACTTGTTTCTAGATCGATGTACT 58.970 38.462 0.54 0.00 0.00 2.73
4267 5982 8.182227 CACACTTGTTTCTAGATCGATGTACTA 58.818 37.037 0.54 0.00 0.00 1.82
4268 5983 8.182881 ACACTTGTTTCTAGATCGATGTACTAC 58.817 37.037 0.54 0.08 0.00 2.73
4269 5984 8.399425 CACTTGTTTCTAGATCGATGTACTACT 58.601 37.037 0.54 0.00 0.00 2.57
4270 5985 9.610705 ACTTGTTTCTAGATCGATGTACTACTA 57.389 33.333 0.54 0.00 0.00 1.82
4272 5987 8.085720 TGTTTCTAGATCGATGTACTACTAGC 57.914 38.462 0.54 0.00 0.00 3.42
4273 5988 7.713942 TGTTTCTAGATCGATGTACTACTAGCA 59.286 37.037 0.54 0.00 0.00 3.49
4274 5989 7.892778 TTCTAGATCGATGTACTACTAGCAG 57.107 40.000 0.54 0.00 0.00 4.24
4275 5990 5.870433 TCTAGATCGATGTACTACTAGCAGC 59.130 44.000 0.54 0.00 0.00 5.25
4276 5991 3.754323 AGATCGATGTACTACTAGCAGCC 59.246 47.826 0.54 0.00 0.00 4.85
4277 5992 2.927028 TCGATGTACTACTAGCAGCCA 58.073 47.619 0.00 0.00 0.00 4.75
4278 5993 3.487372 TCGATGTACTACTAGCAGCCAT 58.513 45.455 0.00 0.00 0.00 4.40
4279 5994 3.253432 TCGATGTACTACTAGCAGCCATG 59.747 47.826 0.00 0.00 0.00 3.66
4306 6021 2.044650 ATGCATGGGCGTGCTTCT 60.045 55.556 13.47 0.00 45.27 2.85
4307 6022 1.679977 ATGCATGGGCGTGCTTCTT 60.680 52.632 13.47 0.00 45.27 2.52
4308 6023 1.252904 ATGCATGGGCGTGCTTCTTT 61.253 50.000 13.47 0.00 45.27 2.52
4309 6024 1.290009 GCATGGGCGTGCTTCTTTT 59.710 52.632 6.28 0.00 41.82 2.27
4310 6025 0.733909 GCATGGGCGTGCTTCTTTTC 60.734 55.000 6.28 0.00 41.82 2.29
4311 6026 0.454957 CATGGGCGTGCTTCTTTTCG 60.455 55.000 0.00 0.00 0.00 3.46
4312 6027 0.889186 ATGGGCGTGCTTCTTTTCGT 60.889 50.000 0.00 0.00 0.00 3.85
4313 6028 1.082104 GGGCGTGCTTCTTTTCGTG 60.082 57.895 0.00 0.00 0.00 4.35
4314 6029 1.082104 GGCGTGCTTCTTTTCGTGG 60.082 57.895 0.00 0.00 0.00 4.94
4315 6030 1.082104 GCGTGCTTCTTTTCGTGGG 60.082 57.895 0.00 0.00 0.00 4.61
4316 6031 1.574428 CGTGCTTCTTTTCGTGGGG 59.426 57.895 0.00 0.00 0.00 4.96
4317 6032 1.285950 GTGCTTCTTTTCGTGGGGC 59.714 57.895 0.00 0.00 0.00 5.80
4318 6033 2.258013 TGCTTCTTTTCGTGGGGCG 61.258 57.895 0.00 0.00 43.01 6.13
4319 6034 2.978018 GCTTCTTTTCGTGGGGCGG 61.978 63.158 0.00 0.00 41.72 6.13
4320 6035 2.978018 CTTCTTTTCGTGGGGCGGC 61.978 63.158 0.00 0.00 41.72 6.53
4396 6160 1.207593 GCGCCACTACAAAGCAGTG 59.792 57.895 0.00 0.00 42.52 3.66
4440 6204 3.254166 TGCTGTTTGCTTTCTTGATCTCC 59.746 43.478 0.00 0.00 43.37 3.71
4516 6323 3.683518 GCCAAATCCCCCACCCCT 61.684 66.667 0.00 0.00 0.00 4.79
4587 6394 5.716094 CTGAGCACATTTTCATCATGGAAA 58.284 37.500 0.00 0.00 35.11 3.13
4765 6575 3.637926 GACCACCTCGCCACCGTAC 62.638 68.421 0.00 0.00 35.54 3.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
41 42 3.750130 CGGATAGCTGCTATGCATTTTCT 59.250 43.478 31.44 7.53 38.13 2.52
42 43 3.120060 CCGGATAGCTGCTATGCATTTTC 60.120 47.826 31.44 16.01 38.13 2.29
44 45 2.038952 TCCGGATAGCTGCTATGCATTT 59.961 45.455 31.44 9.57 38.13 2.32
46 47 1.269958 TCCGGATAGCTGCTATGCAT 58.730 50.000 31.44 11.56 38.13 3.96
47 48 1.066645 CATCCGGATAGCTGCTATGCA 60.067 52.381 31.44 18.89 35.05 3.96
48 49 1.649664 CATCCGGATAGCTGCTATGC 58.350 55.000 25.75 25.71 32.61 3.14
49 50 1.552337 ACCATCCGGATAGCTGCTATG 59.448 52.381 25.75 13.11 35.59 2.23
50 51 1.827969 GACCATCCGGATAGCTGCTAT 59.172 52.381 21.44 21.44 35.59 2.97
52 53 1.810606 CGACCATCCGGATAGCTGCT 61.811 60.000 18.63 7.57 35.59 4.24
53 54 1.373497 CGACCATCCGGATAGCTGC 60.373 63.158 18.63 2.26 35.59 5.25
54 55 1.373497 GCGACCATCCGGATAGCTG 60.373 63.158 18.63 6.17 35.59 4.24
68 69 1.878522 CGGGCACTCTGTATGCGAC 60.879 63.158 0.00 0.00 44.37 5.19
70 71 2.586079 CCGGGCACTCTGTATGCG 60.586 66.667 0.00 0.00 44.37 4.73
83 84 0.893270 TGCTCAACCAAATCACCGGG 60.893 55.000 6.32 0.00 0.00 5.73
95 96 2.363788 TGAGTCCACGTATGCTCAAC 57.636 50.000 11.16 0.00 35.36 3.18
101 102 1.665679 GCCAACATGAGTCCACGTATG 59.334 52.381 0.00 0.00 0.00 2.39
105 106 0.238289 GTTGCCAACATGAGTCCACG 59.762 55.000 1.91 0.00 0.00 4.94
106 107 0.238289 CGTTGCCAACATGAGTCCAC 59.762 55.000 8.51 0.00 0.00 4.02
110 111 3.937814 TCTATTCGTTGCCAACATGAGT 58.062 40.909 8.51 0.00 0.00 3.41
111 112 4.333649 ACATCTATTCGTTGCCAACATGAG 59.666 41.667 8.51 0.00 0.00 2.90
213 218 9.816354 ATAGTTTCACAAGCAAACAAAAATAGT 57.184 25.926 0.19 0.00 36.38 2.12
217 222 8.988064 TGTATAGTTTCACAAGCAAACAAAAA 57.012 26.923 0.19 0.00 36.38 1.94
247 253 7.412563 CCGTCGTTTCTCAACAAATATACACAT 60.413 37.037 0.00 0.00 32.54 3.21
249 255 6.238508 CCGTCGTTTCTCAACAAATATACAC 58.761 40.000 0.00 0.00 32.54 2.90
262 268 2.861006 GGCTTGCCGTCGTTTCTC 59.139 61.111 0.00 0.00 0.00 2.87
264 270 4.084888 CCGGCTTGCCGTCGTTTC 62.085 66.667 28.61 0.00 39.61 2.78
284 290 1.531149 CTGTTCTATATTTGCCCGCGG 59.469 52.381 21.04 21.04 0.00 6.46
286 292 1.069906 CGCTGTTCTATATTTGCCCGC 60.070 52.381 0.00 0.00 0.00 6.13
288 294 2.572290 ACCGCTGTTCTATATTTGCCC 58.428 47.619 0.00 0.00 0.00 5.36
311 317 0.605319 TTTGGATCGGCAGAGCGTTT 60.605 50.000 0.00 0.00 32.66 3.60
312 318 0.392998 ATTTGGATCGGCAGAGCGTT 60.393 50.000 0.00 0.00 32.66 4.84
335 346 0.848305 CGTTCGACGTCCGTCTTTTT 59.152 50.000 16.76 0.00 42.54 1.94
336 347 0.936297 CCGTTCGACGTCCGTCTTTT 60.936 55.000 16.76 0.00 42.54 2.27
361 372 1.350193 CTCAAACAGATCGTGGGTCG 58.650 55.000 0.00 0.00 41.41 4.79
362 373 1.079503 GCTCAAACAGATCGTGGGTC 58.920 55.000 0.00 0.00 0.00 4.46
363 374 0.670546 CGCTCAAACAGATCGTGGGT 60.671 55.000 0.00 0.00 31.57 4.51
364 375 1.361668 CCGCTCAAACAGATCGTGGG 61.362 60.000 0.00 0.00 34.21 4.61
365 376 1.970917 GCCGCTCAAACAGATCGTGG 61.971 60.000 0.00 0.00 34.21 4.94
366 377 1.421485 GCCGCTCAAACAGATCGTG 59.579 57.895 0.00 0.00 34.21 4.35
367 378 2.094659 CGCCGCTCAAACAGATCGT 61.095 57.895 0.00 0.00 34.21 3.73
368 379 2.697425 CGCCGCTCAAACAGATCG 59.303 61.111 0.00 0.00 35.73 3.69
369 380 2.401195 GCGCCGCTCAAACAGATC 59.599 61.111 0.00 0.00 0.00 2.75
370 381 3.490759 CGCGCCGCTCAAACAGAT 61.491 61.111 7.78 0.00 0.00 2.90
411 422 1.039856 AGCAACCAAATCCGCAAACT 58.960 45.000 0.00 0.00 0.00 2.66
412 423 1.526464 CAAGCAACCAAATCCGCAAAC 59.474 47.619 0.00 0.00 0.00 2.93
467 478 0.395311 TCGGTAGCGGAGAGAATGGT 60.395 55.000 15.23 0.00 0.00 3.55
493 504 4.079253 TGAAAAGGAAGAGGTAACCATGC 58.921 43.478 0.00 0.00 37.17 4.06
737 763 0.694444 AGTAATGGCGGGAGGGTCAT 60.694 55.000 0.00 0.00 32.62 3.06
741 767 1.146263 GTGAGTAATGGCGGGAGGG 59.854 63.158 0.00 0.00 0.00 4.30
806 832 7.066233 GCCTAGAGCAATATCGATGGAGACA 62.066 48.000 8.54 0.00 44.14 3.41
808 834 3.445450 GCCTAGAGCAATATCGATGGAGA 59.555 47.826 8.54 0.00 42.97 3.71
819 845 1.422531 CCAGGAGAGCCTAGAGCAAT 58.577 55.000 6.07 0.00 44.80 3.56
821 847 1.760086 GCCAGGAGAGCCTAGAGCA 60.760 63.158 0.00 0.00 44.80 4.26
822 848 3.137687 GCCAGGAGAGCCTAGAGC 58.862 66.667 0.00 0.00 44.80 4.09
853 879 5.049336 TGTGTAAGTATAAGCTGCGCAAAAA 60.049 36.000 13.05 0.00 0.00 1.94
854 880 4.452795 TGTGTAAGTATAAGCTGCGCAAAA 59.547 37.500 13.05 0.00 0.00 2.44
855 881 3.997681 TGTGTAAGTATAAGCTGCGCAAA 59.002 39.130 13.05 0.00 0.00 3.68
856 882 3.591023 TGTGTAAGTATAAGCTGCGCAA 58.409 40.909 13.05 0.00 0.00 4.85
857 883 3.239587 TGTGTAAGTATAAGCTGCGCA 57.760 42.857 10.98 10.98 0.00 6.09
858 884 3.604772 GCATGTGTAAGTATAAGCTGCGC 60.605 47.826 0.00 0.00 0.00 6.09
859 885 3.555547 TGCATGTGTAAGTATAAGCTGCG 59.444 43.478 0.00 0.00 0.00 5.18
860 886 5.446709 CATGCATGTGTAAGTATAAGCTGC 58.553 41.667 18.91 0.00 0.00 5.25
861 887 5.237996 AGCATGCATGTGTAAGTATAAGCTG 59.762 40.000 26.79 0.00 0.00 4.24
862 888 5.237996 CAGCATGCATGTGTAAGTATAAGCT 59.762 40.000 26.79 10.71 0.00 3.74
863 889 5.446709 CAGCATGCATGTGTAAGTATAAGC 58.553 41.667 26.79 8.51 0.00 3.09
888 914 2.222886 CGAGCTAGAAGCCTAGTAGCA 58.777 52.381 10.83 0.00 43.77 3.49
896 922 2.107953 CCCTGCGAGCTAGAAGCC 59.892 66.667 0.00 0.00 43.77 4.35
903 929 3.753434 CTCGTGACCCTGCGAGCT 61.753 66.667 1.06 0.00 46.01 4.09
912 938 4.664677 ACTGTGCGGCTCGTGACC 62.665 66.667 0.00 0.00 0.00 4.02
934 960 1.290324 GAGCTCACTGGCGACTGAA 59.710 57.895 9.40 0.00 37.29 3.02
961 987 4.222847 CTAGCTTCGTCGGGGGCC 62.223 72.222 0.00 0.00 0.00 5.80
962 988 4.893601 GCTAGCTTCGTCGGGGGC 62.894 72.222 7.70 0.00 0.00 5.80
963 989 3.432051 CTGCTAGCTTCGTCGGGGG 62.432 68.421 17.23 0.00 0.00 5.40
964 990 2.105128 CTGCTAGCTTCGTCGGGG 59.895 66.667 17.23 0.00 0.00 5.73
977 1003 1.519719 GTTCCCGAGAGATGCTGCT 59.480 57.895 0.00 0.00 0.00 4.24
978 1004 1.880340 CGTTCCCGAGAGATGCTGC 60.880 63.158 0.00 0.00 35.63 5.25
979 1005 0.526524 GTCGTTCCCGAGAGATGCTG 60.527 60.000 0.00 0.00 45.26 4.41
1389 1426 4.570663 CGGATCTGGTCGGCGGAC 62.571 72.222 15.59 15.59 42.66 4.79
1600 1637 1.398041 CATGGCGTTCACGTTCATGAT 59.602 47.619 21.97 0.32 45.78 2.45
1709 1746 3.604400 GTGTGTCGCACGTACGTT 58.396 55.556 20.23 0.76 38.45 3.99
1720 1757 6.314784 GCCTACTGAATGTAAAATGTGTGTC 58.685 40.000 0.00 0.00 0.00 3.67
1739 1796 1.402984 CGAGAACACTGACAGGCCTAC 60.403 57.143 3.98 3.09 0.00 3.18
1744 1801 0.673985 TGACCGAGAACACTGACAGG 59.326 55.000 7.51 0.00 0.00 4.00
1754 1811 1.668919 GCACAACGATCTGACCGAGAA 60.669 52.381 0.00 0.00 33.12 2.87
1790 1856 4.750098 ACTTCAAGTTCACACTACATTCCG 59.250 41.667 0.00 0.00 30.68 4.30
1801 1873 1.967319 TGAGGCCACTTCAAGTTCAC 58.033 50.000 5.01 0.00 0.00 3.18
1802 1874 2.727123 TTGAGGCCACTTCAAGTTCA 57.273 45.000 5.01 0.00 0.00 3.18
1803 1875 4.590850 AAATTGAGGCCACTTCAAGTTC 57.409 40.909 11.77 0.00 27.47 3.01
1804 1876 4.651045 AGAAAATTGAGGCCACTTCAAGTT 59.349 37.500 11.77 11.77 33.90 2.66
1805 1877 4.218312 AGAAAATTGAGGCCACTTCAAGT 58.782 39.130 5.01 2.39 0.00 3.16
1806 1878 4.861102 AGAAAATTGAGGCCACTTCAAG 57.139 40.909 5.01 0.00 0.00 3.02
1807 1879 5.385198 ACTAGAAAATTGAGGCCACTTCAA 58.615 37.500 5.01 6.99 0.00 2.69
1812 1884 7.769044 TCATAGTTACTAGAAAATTGAGGCCAC 59.231 37.037 5.01 0.00 0.00 5.01
1827 1899 5.302059 GGGCACATGACTCTCATAGTTACTA 59.698 44.000 0.00 0.00 39.07 1.82
1828 1900 4.100189 GGGCACATGACTCTCATAGTTACT 59.900 45.833 0.00 0.00 39.07 2.24
1829 1901 4.141937 TGGGCACATGACTCTCATAGTTAC 60.142 45.833 0.00 0.00 39.07 2.50
1875 1956 3.448660 TCTGCTCTACTGTATGTGTGCAT 59.551 43.478 0.00 0.00 39.03 3.96
1974 2086 7.498900 TCCATTTGAGCGACAAGTAATATGAAT 59.501 33.333 0.00 0.00 39.77 2.57
1975 2087 6.821160 TCCATTTGAGCGACAAGTAATATGAA 59.179 34.615 0.00 0.00 39.77 2.57
1990 2102 8.449397 CAACTGCTAAGATATATCCATTTGAGC 58.551 37.037 9.18 5.73 0.00 4.26
1991 2103 9.716531 TCAACTGCTAAGATATATCCATTTGAG 57.283 33.333 9.18 2.18 0.00 3.02
2000 2112 9.809096 CCGTATCAATCAACTGCTAAGATATAT 57.191 33.333 0.00 0.00 0.00 0.86
2001 2113 9.020731 TCCGTATCAATCAACTGCTAAGATATA 57.979 33.333 0.00 0.00 0.00 0.86
2002 2114 7.815068 GTCCGTATCAATCAACTGCTAAGATAT 59.185 37.037 0.00 0.00 0.00 1.63
2003 2115 7.145985 GTCCGTATCAATCAACTGCTAAGATA 58.854 38.462 0.00 0.00 0.00 1.98
2004 2116 5.986135 GTCCGTATCAATCAACTGCTAAGAT 59.014 40.000 0.00 0.00 0.00 2.40
2005 2117 5.348986 GTCCGTATCAATCAACTGCTAAGA 58.651 41.667 0.00 0.00 0.00 2.10
2006 2118 4.508124 GGTCCGTATCAATCAACTGCTAAG 59.492 45.833 0.00 0.00 0.00 2.18
2007 2119 4.161565 AGGTCCGTATCAATCAACTGCTAA 59.838 41.667 0.00 0.00 0.00 3.09
2014 2245 3.737047 GCTCGAAGGTCCGTATCAATCAA 60.737 47.826 0.00 0.00 0.00 2.57
2041 2272 8.798859 AACAATGTGCTAGTGAATCTCTTATT 57.201 30.769 0.00 0.00 0.00 1.40
2048 2279 5.869753 ACTGAACAATGTGCTAGTGAATC 57.130 39.130 0.00 0.00 0.00 2.52
2220 2582 1.026718 GCTGTGGGGTCGGAGAATTG 61.027 60.000 0.00 0.00 39.69 2.32
2232 2594 5.705609 ACAAAGTTATGTTAAGCTGTGGG 57.294 39.130 0.00 0.00 0.00 4.61
2241 2603 9.515020 CAGAAAAGAGCAAACAAAGTTATGTTA 57.485 29.630 4.55 0.00 42.49 2.41
2246 2608 7.598278 TGTTCAGAAAAGAGCAAACAAAGTTA 58.402 30.769 0.00 0.00 0.00 2.24
2354 2716 0.321919 GCAGTCCATGGTCTGAAGCA 60.322 55.000 34.31 2.19 34.14 3.91
2375 2737 1.824230 GCATAGGTTCCATTTGCCACA 59.176 47.619 0.00 0.00 0.00 4.17
2470 2832 6.917477 CAGTAATGCTGCTTTTTGTGAACTAA 59.083 34.615 6.08 0.00 38.52 2.24
2471 2833 6.262049 TCAGTAATGCTGCTTTTTGTGAACTA 59.738 34.615 6.08 0.00 44.66 2.24
2472 2834 5.067674 TCAGTAATGCTGCTTTTTGTGAACT 59.932 36.000 6.08 0.41 44.66 3.01
2473 2835 5.280945 TCAGTAATGCTGCTTTTTGTGAAC 58.719 37.500 6.08 0.00 44.66 3.18
2475 2837 5.241285 TCATCAGTAATGCTGCTTTTTGTGA 59.759 36.000 6.08 7.49 44.66 3.58
2476 2838 5.463286 TCATCAGTAATGCTGCTTTTTGTG 58.537 37.500 6.08 2.80 44.66 3.33
2477 2839 5.710513 TCATCAGTAATGCTGCTTTTTGT 57.289 34.783 6.08 0.00 44.66 2.83
2506 2868 7.914407 AGGAAAGATAGGGGTTATGATCCATAT 59.086 37.037 0.00 0.00 33.36 1.78
2558 2926 2.680221 GCATGATCTGGACAGTGAAGCT 60.680 50.000 0.00 0.00 0.00 3.74
2654 3022 1.004610 CCATAGCTGCACGATGAAACG 60.005 52.381 1.02 0.00 33.53 3.60
2657 3025 1.202568 CCTCCATAGCTGCACGATGAA 60.203 52.381 1.02 0.00 33.53 2.57
2660 3028 0.833287 AACCTCCATAGCTGCACGAT 59.167 50.000 1.02 0.00 0.00 3.73
2663 3031 2.095059 CACAAAACCTCCATAGCTGCAC 60.095 50.000 1.02 0.00 0.00 4.57
2684 3052 7.224949 GCTTACAGAGTTGTAATAGTCCCATTC 59.775 40.741 1.08 0.00 45.90 2.67
2721 3089 4.749598 CAGCAATAAACCCAAAACTGTTCC 59.250 41.667 0.00 0.00 0.00 3.62
2726 3094 6.538381 CAGAAAACAGCAATAAACCCAAAACT 59.462 34.615 0.00 0.00 0.00 2.66
2727 3095 6.714492 CAGAAAACAGCAATAAACCCAAAAC 58.286 36.000 0.00 0.00 0.00 2.43
2732 3100 3.988819 TGCAGAAAACAGCAATAAACCC 58.011 40.909 0.00 0.00 37.90 4.11
2783 3151 0.037232 GACCAGTGTCCAGCCTGTAC 60.037 60.000 0.00 0.00 35.34 2.90
2785 3153 1.056700 AAGACCAGTGTCCAGCCTGT 61.057 55.000 0.00 0.00 42.81 4.00
2873 3243 1.700955 AGGGATGAATGGATTGCTGC 58.299 50.000 0.00 0.00 0.00 5.25
2879 3249 4.349342 GGAGTCTACAAGGGATGAATGGAT 59.651 45.833 0.00 0.00 0.00 3.41
2911 3281 5.327091 CAGTGCTCCTACATTCGAAAAATG 58.673 41.667 0.00 0.00 0.00 2.32
2919 3289 0.740868 TGCGCAGTGCTCCTACATTC 60.741 55.000 5.66 0.00 46.63 2.67
2934 3304 2.139118 AGAAGAAGAGAGTTTGTGCGC 58.861 47.619 0.00 0.00 0.00 6.09
2957 3327 7.983484 GGCAAAAGATTTGTCTCATCCATTTAT 59.017 33.333 4.90 0.00 0.00 1.40
2971 3341 3.976169 TGAAACGGAGGCAAAAGATTTG 58.024 40.909 0.00 0.00 0.00 2.32
2998 3368 7.319646 AGTCTTGCCAAATTGCGATTTATTTA 58.680 30.769 11.64 0.00 33.78 1.40
3002 3372 4.782019 AGTCTTGCCAAATTGCGATTTA 57.218 36.364 11.64 0.00 33.78 1.40
3003 3373 3.665745 AGTCTTGCCAAATTGCGATTT 57.334 38.095 6.06 6.06 35.90 2.17
3004 3374 3.319755 CAAGTCTTGCCAAATTGCGATT 58.680 40.909 0.00 0.00 0.00 3.34
3005 3375 2.950433 CAAGTCTTGCCAAATTGCGAT 58.050 42.857 0.00 0.00 0.00 4.58
3046 3417 4.858965 ATGAAGAATGGAAGCCTTCTCT 57.141 40.909 4.15 0.00 37.69 3.10
3048 3419 4.948621 CAGAATGAAGAATGGAAGCCTTCT 59.051 41.667 4.15 0.00 39.69 2.85
3049 3420 4.946157 TCAGAATGAAGAATGGAAGCCTTC 59.054 41.667 0.00 0.00 45.97 3.46
3133 3504 3.442625 TGTAGGTAGATTCTGGTGACACG 59.557 47.826 0.00 0.00 35.60 4.49
3154 3525 9.208022 TGTGAAGTTTTCTGTATCTATTGACTG 57.792 33.333 0.00 0.00 0.00 3.51
3169 3540 6.701400 ACTGCCATACAAATTGTGAAGTTTTC 59.299 34.615 9.15 0.00 0.00 2.29
3251 3682 2.752903 TCAGTGTGCGACAGAAGCTATA 59.247 45.455 0.00 0.00 35.28 1.31
3382 3890 2.357952 GTCTTGTGGGTTTTCAGGTGTC 59.642 50.000 0.00 0.00 0.00 3.67
3395 3903 4.157656 TGTTTCAGTTTGAAGGTCTTGTGG 59.842 41.667 0.00 0.00 37.70 4.17
3403 3911 2.294074 TCCGGTGTTTCAGTTTGAAGG 58.706 47.619 0.00 0.00 37.70 3.46
3475 3986 1.281899 GCTGACCGAATGAGCTACAC 58.718 55.000 0.00 0.00 0.00 2.90
3766 4277 1.815421 CGGTTTGCTCATCGGAGGG 60.815 63.158 0.00 0.00 41.67 4.30
3943 4472 0.949588 TGCATGCAAAAACATGGCCG 60.950 50.000 20.30 0.00 46.14 6.13
4122 4660 0.951558 GCTCTCGTTTCCTTGGCAAA 59.048 50.000 0.00 0.00 0.00 3.68
4123 4661 1.227999 CGCTCTCGTTTCCTTGGCAA 61.228 55.000 0.00 0.00 0.00 4.52
4141 4680 8.920665 TGGTTAATCAATCAAAACAATAAAGCG 58.079 29.630 0.00 0.00 0.00 4.68
4190 5901 3.370846 CCTCTTGATGGTCCAAGTGCATA 60.371 47.826 0.00 0.00 42.95 3.14
4201 5912 0.179062 GATCTGCGCCTCTTGATGGT 60.179 55.000 4.18 0.00 0.00 3.55
4248 5963 8.085720 TGCTAGTAGTACATCGATCTAGAAAC 57.914 38.462 16.60 3.80 0.00 2.78
4249 5964 7.095144 GCTGCTAGTAGTACATCGATCTAGAAA 60.095 40.741 16.60 6.53 0.00 2.52
4250 5965 6.369340 GCTGCTAGTAGTACATCGATCTAGAA 59.631 42.308 16.60 8.33 0.00 2.10
4251 5966 5.870433 GCTGCTAGTAGTACATCGATCTAGA 59.130 44.000 16.60 0.00 0.00 2.43
4252 5967 5.064198 GGCTGCTAGTAGTACATCGATCTAG 59.936 48.000 9.73 10.66 0.00 2.43
4253 5968 4.936411 GGCTGCTAGTAGTACATCGATCTA 59.064 45.833 9.73 0.00 0.00 1.98
4254 5969 3.754323 GGCTGCTAGTAGTACATCGATCT 59.246 47.826 9.73 0.00 0.00 2.75
4255 5970 3.502595 TGGCTGCTAGTAGTACATCGATC 59.497 47.826 9.73 0.00 0.00 3.69
4256 5971 3.487372 TGGCTGCTAGTAGTACATCGAT 58.513 45.455 9.73 0.00 0.00 3.59
4257 5972 2.927028 TGGCTGCTAGTAGTACATCGA 58.073 47.619 9.73 0.00 0.00 3.59
4258 5973 3.569548 CATGGCTGCTAGTAGTACATCG 58.430 50.000 9.73 6.32 0.00 3.84
4259 5974 3.321497 GCATGGCTGCTAGTAGTACATC 58.679 50.000 9.73 5.83 45.32 3.06
4260 5975 3.393089 GCATGGCTGCTAGTAGTACAT 57.607 47.619 9.73 11.11 45.32 2.29
4261 5976 2.890808 GCATGGCTGCTAGTAGTACA 57.109 50.000 9.73 9.36 45.32 2.90
4291 6006 0.733909 GAAAAGAAGCACGCCCATGC 60.734 55.000 0.00 0.00 46.50 4.06
4292 6007 0.454957 CGAAAAGAAGCACGCCCATG 60.455 55.000 0.00 0.00 0.00 3.66
4293 6008 0.889186 ACGAAAAGAAGCACGCCCAT 60.889 50.000 0.00 0.00 0.00 4.00
4294 6009 1.525077 ACGAAAAGAAGCACGCCCA 60.525 52.632 0.00 0.00 0.00 5.36
4295 6010 1.082104 CACGAAAAGAAGCACGCCC 60.082 57.895 0.00 0.00 0.00 6.13
4296 6011 1.082104 CCACGAAAAGAAGCACGCC 60.082 57.895 0.00 0.00 0.00 5.68
4297 6012 1.082104 CCCACGAAAAGAAGCACGC 60.082 57.895 0.00 0.00 0.00 5.34
4298 6013 1.574428 CCCCACGAAAAGAAGCACG 59.426 57.895 0.00 0.00 0.00 5.34
4299 6014 1.285950 GCCCCACGAAAAGAAGCAC 59.714 57.895 0.00 0.00 0.00 4.40
4300 6015 3.758172 GCCCCACGAAAAGAAGCA 58.242 55.556 0.00 0.00 0.00 3.91
4325 6040 1.502163 GATGAAGCCGGCGAAGATGG 61.502 60.000 23.20 0.00 0.00 3.51
4326 6041 0.811219 TGATGAAGCCGGCGAAGATG 60.811 55.000 23.20 0.00 0.00 2.90
4327 6042 0.531532 CTGATGAAGCCGGCGAAGAT 60.532 55.000 23.20 11.99 0.00 2.40
4328 6043 1.153568 CTGATGAAGCCGGCGAAGA 60.154 57.895 23.20 6.89 0.00 2.87
4329 6044 0.740868 TTCTGATGAAGCCGGCGAAG 60.741 55.000 23.20 13.22 0.00 3.79
4330 6045 0.321210 TTTCTGATGAAGCCGGCGAA 60.321 50.000 23.20 13.78 33.28 4.70
4331 6046 0.321210 TTTTCTGATGAAGCCGGCGA 60.321 50.000 23.20 9.85 33.28 5.54
4332 6047 0.097674 CTTTTCTGATGAAGCCGGCG 59.902 55.000 23.20 4.58 33.28 6.46
4333 6048 1.453155 TCTTTTCTGATGAAGCCGGC 58.547 50.000 21.89 21.89 33.28 6.13
4334 6049 5.818136 TTTATCTTTTCTGATGAAGCCGG 57.182 39.130 0.00 0.00 33.28 6.13
4335 6050 7.701445 AGAATTTATCTTTTCTGATGAAGCCG 58.299 34.615 0.00 0.00 33.39 5.52
4336 6051 8.680903 TGAGAATTTATCTTTTCTGATGAAGCC 58.319 33.333 0.00 0.00 38.96 4.35
4396 6160 3.133721 ACATGCATGACTCCTCTAGAACC 59.866 47.826 32.75 0.00 0.00 3.62
4397 6161 4.118410 CACATGCATGACTCCTCTAGAAC 58.882 47.826 32.75 0.00 0.00 3.01
4398 6162 3.431346 GCACATGCATGACTCCTCTAGAA 60.431 47.826 32.75 0.00 41.59 2.10
4440 6204 7.340122 AGGAGAAGAAGAAAAACAAAAGAGG 57.660 36.000 0.00 0.00 0.00 3.69
4516 6323 1.202663 AGCTCGATCCGCTAGACAGTA 60.203 52.381 2.53 0.00 35.63 2.74
4587 6394 5.394883 CCAGTACATCCATTTGGTACTACGT 60.395 44.000 0.00 0.00 44.23 3.57
4756 6566 2.513897 GCCTGATGGTACGGTGGC 60.514 66.667 0.00 0.00 35.27 5.01
4822 6632 0.321653 GATGTTTGGCCTGGAGACGT 60.322 55.000 3.32 0.00 0.00 4.34


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

AutoCloner maintained by Alex Coulton.