Multiple sequence alignment - TraesCS2A01G060600

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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 TraesCS2A01G060600 chr2A 100.000 5096 0 0 1 5096 27327385 27332480 0.000000e+00 9411
1 TraesCS2A01G060600 chr2A 90.445 607 58 0 1995 2601 27341250 27341856 0.000000e+00 800
2 TraesCS2A01G060600 chr2A 87.354 601 52 17 3010 3592 27342249 27342843 0.000000e+00 667
3 TraesCS2A01G060600 chr2A 84.560 557 71 10 1214 1765 27340246 27340792 5.810000e-149 538
4 TraesCS2A01G060600 chr2A 84.882 549 55 10 3718 4242 27343059 27343603 3.490000e-146 529
5 TraesCS2A01G060600 chr2A 88.140 371 29 8 2599 2965 27341893 27342252 1.310000e-115 427
6 TraesCS2A01G060600 chr2A 79.052 401 63 15 679 1072 27339748 27340134 6.550000e-64 255
7 TraesCS2A01G060600 chr2A 86.036 222 23 6 4876 5093 688245467 688245250 1.100000e-56 231
8 TraesCS2A01G060600 chr2A 87.204 211 16 7 68 277 27338900 27339100 3.970000e-56 230
9 TraesCS2A01G060600 chr2A 80.201 298 29 20 139 425 27339116 27339394 4.030000e-46 196
10 TraesCS2A01G060600 chr2A 84.409 186 15 9 4252 4425 27343644 27343827 2.440000e-38 171
11 TraesCS2A01G060600 chr2D 94.060 2946 135 22 668 3598 24705663 24702743 0.000000e+00 4434
12 TraesCS2A01G060600 chr2D 93.086 781 29 3 3698 4471 24702522 24701760 0.000000e+00 1120
13 TraesCS2A01G060600 chr2D 90.656 610 57 0 1995 2604 24561301 24560692 0.000000e+00 811
14 TraesCS2A01G060600 chr2D 87.372 586 51 16 3013 3582 24560299 24559721 0.000000e+00 651
15 TraesCS2A01G060600 chr2D 85.971 556 64 7 1214 1765 24562304 24561759 2.640000e-162 582
16 TraesCS2A01G060600 chr2D 85.841 565 52 10 3707 4246 24559490 24558929 4.430000e-160 575
17 TraesCS2A01G060600 chr2D 95.210 334 15 1 4539 4872 24701744 24701412 1.260000e-145 527
18 TraesCS2A01G060600 chr2D 86.713 429 32 12 1 420 24706660 24706248 2.160000e-123 453
19 TraesCS2A01G060600 chr2D 88.949 371 26 7 2599 2965 24560658 24560299 1.300000e-120 444
20 TraesCS2A01G060600 chr2D 87.429 350 31 11 51 398 24563339 24563001 1.720000e-104 390
21 TraesCS2A01G060600 chr2D 88.797 241 24 2 1764 2004 24561700 24561463 4.990000e-75 292
22 TraesCS2A01G060600 chr2D 96.190 105 4 0 3599 3703 24702705 24702601 6.780000e-39 172
23 TraesCS2A01G060600 chr2B 93.896 1409 78 3 1084 2492 40067091 40068491 0.000000e+00 2119
24 TraesCS2A01G060600 chr2B 94.345 1061 45 9 2542 3592 40068490 40069545 0.000000e+00 1613
25 TraesCS2A01G060600 chr2B 90.977 1075 70 15 67 1130 40066046 40067104 0.000000e+00 1423
26 TraesCS2A01G060600 chr2B 88.889 1089 67 19 3698 4774 40069797 40070843 0.000000e+00 1291
27 TraesCS2A01G060600 chr2B 91.104 607 54 0 1995 2601 40276608 40277214 0.000000e+00 822
28 TraesCS2A01G060600 chr2B 87.146 529 45 17 3010 3521 40277614 40278136 3.420000e-161 579
29 TraesCS2A01G060600 chr2B 83.158 570 62 18 3707 4246 40278416 40278981 1.650000e-134 490
30 TraesCS2A01G060600 chr2B 89.247 372 30 5 2599 2965 40277251 40277617 1.670000e-124 457
31 TraesCS2A01G060600 chr2B 84.807 441 54 10 1331 1765 40275717 40276150 1.010000e-116 431
32 TraesCS2A01G060600 chr2B 85.714 336 28 16 64 389 40274780 40275105 2.270000e-88 337
33 TraesCS2A01G060600 chr2B 87.552 241 27 2 1764 2004 40276209 40276446 5.030000e-70 276
34 TraesCS2A01G060600 chr2B 92.727 110 7 1 3599 3708 40069589 40069697 1.900000e-34 158
35 TraesCS2A01G060600 chr2B 86.325 117 16 0 1104 1220 445669127 445669011 1.490000e-25 128
36 TraesCS2A01G060600 chr1D 86.996 223 22 5 4876 5095 302913201 302912983 1.420000e-60 244
37 TraesCS2A01G060600 chr1D 84.305 223 28 4 4877 5095 484445702 484445921 1.440000e-50 211
38 TraesCS2A01G060600 chr3D 86.026 229 19 8 4876 5095 467488544 467488768 3.070000e-57 233
39 TraesCS2A01G060600 chr3D 85.650 223 24 6 4876 5093 146136076 146135857 1.430000e-55 228
40 TraesCS2A01G060600 chr7A 85.650 223 23 6 4876 5093 526863049 526862831 5.130000e-55 226
41 TraesCS2A01G060600 chr7A 84.956 226 25 6 4876 5096 470291116 470290895 2.390000e-53 220
42 TraesCS2A01G060600 chr1A 84.375 224 28 5 4876 5095 124010223 124010443 4.000000e-51 213
43 TraesCS2A01G060600 chrUn 83.700 227 27 9 4875 5095 392321057 392320835 6.690000e-49 206
44 TraesCS2A01G060600 chr5B 77.536 276 25 17 4119 4363 49007511 49007242 1.150000e-26 132


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 TraesCS2A01G060600 chr2A 27327385 27332480 5095 False 9411.000000 9411 100.000000 1 5096 1 chr2A.!!$F1 5095
1 TraesCS2A01G060600 chr2A 27338900 27343827 4927 False 423.666667 800 85.138556 68 4425 9 chr2A.!!$F2 4357
2 TraesCS2A01G060600 chr2D 24701412 24706660 5248 True 1341.200000 4434 93.051800 1 4872 5 chr2D.!!$R2 4871
3 TraesCS2A01G060600 chr2D 24558929 24563339 4410 True 535.000000 811 87.859286 51 4246 7 chr2D.!!$R1 4195
4 TraesCS2A01G060600 chr2B 40066046 40070843 4797 False 1320.800000 2119 92.166800 67 4774 5 chr2B.!!$F1 4707
5 TraesCS2A01G060600 chr2B 40274780 40278981 4201 False 484.571429 822 86.961143 64 4246 7 chr2B.!!$F2 4182

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
425 604 0.608640 CCGTGGCTAGGACTCTTGTT 59.391 55.0 0.00 0.0 0.00 2.83 F
1212 1840 0.598562 ATTCTCGCAGTGTGTCTCGT 59.401 50.0 3.13 0.0 0.00 4.18 F
1895 2596 0.364180 CAAAGCGCATTTGCATGACG 59.636 50.0 11.47 0.0 41.77 4.35 F
2694 3602 0.687354 TCCCAGAGAAAGGTCTGCAC 59.313 55.0 0.00 0.0 42.40 4.57 F
3482 4463 0.322975 TTCCCTGTCAGCTGCTTCTC 59.677 55.0 9.47 0.0 0.00 2.87 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1858 2559 0.955428 TGGCGTCAGAAACATCTGGC 60.955 55.000 6.04 3.32 38.85 4.85 R
2335 3204 1.342819 GGTGAGCTCAGAGTCACAACT 59.657 52.381 18.89 4.63 44.17 3.16 R
3466 4447 2.181954 AAAGAGAAGCAGCTGACAGG 57.818 50.000 20.43 0.00 0.00 4.00 R
3968 5156 0.749091 CCTCGGCAATTCTGGATGCA 60.749 55.000 0.00 0.00 44.32 3.96 R
4964 6212 0.106369 TCCGGATGTACACTCGGGAT 60.106 55.000 27.66 1.12 42.44 3.85 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
17 18 4.157607 CAGCGAACACCAAACCCT 57.842 55.556 0.00 0.00 0.00 4.34
19 20 1.228154 AGCGAACACCAAACCCTCC 60.228 57.895 0.00 0.00 0.00 4.30
80 86 4.324099 GCCAAGCATCCTCCTCATACATAT 60.324 45.833 0.00 0.00 0.00 1.78
99 105 0.952280 TGCCGATATCCAGAGTCGAC 59.048 55.000 7.70 7.70 37.55 4.20
243 406 2.981560 GAGTTCGACACCGGCCGTA 61.982 63.158 26.12 0.00 36.24 4.02
244 407 2.806621 GTTCGACACCGGCCGTAC 60.807 66.667 26.12 10.99 36.24 3.67
245 408 2.985282 TTCGACACCGGCCGTACT 60.985 61.111 26.12 4.66 36.24 2.73
267 430 1.722082 GCGGCCTTTTCCTCGATTC 59.278 57.895 0.00 0.00 0.00 2.52
301 465 2.290134 GGTTCTTCAGGTTCAGGTACCC 60.290 54.545 8.74 0.00 39.08 3.69
302 466 1.652947 TCTTCAGGTTCAGGTACCCC 58.347 55.000 8.74 2.05 39.08 4.95
339 508 6.602179 TCTGTGTTTATTTTTCGCATCTCAG 58.398 36.000 0.00 0.00 0.00 3.35
340 509 5.698832 TGTGTTTATTTTTCGCATCTCAGG 58.301 37.500 0.00 0.00 0.00 3.86
384 563 3.697045 AGGACTAGTAGATCTGTGTGTGC 59.303 47.826 5.18 4.97 0.00 4.57
425 604 0.608640 CCGTGGCTAGGACTCTTGTT 59.391 55.000 0.00 0.00 0.00 2.83
500 717 2.436109 GCAGGGGGCTTGTTGAGA 59.564 61.111 0.00 0.00 40.25 3.27
533 781 7.920151 TGATTATTGATAACAAATTTGAGGGCG 59.080 33.333 24.64 0.00 39.54 6.13
551 800 1.080705 GTCCCTCTTCACGACCACG 60.081 63.158 0.00 0.00 45.75 4.94
571 822 3.142951 CGGGATGTGGTTTTGTCAGTAA 58.857 45.455 0.00 0.00 0.00 2.24
588 839 6.867816 TGTCAGTAATAAAAGGCTGCAATTTG 59.132 34.615 0.50 0.00 0.00 2.32
589 840 5.868801 TCAGTAATAAAAGGCTGCAATTTGC 59.131 36.000 14.49 14.49 45.29 3.68
650 903 2.067932 CTCCCCCACTGGAAGCACAA 62.068 60.000 0.00 0.00 37.60 3.33
819 1385 9.856488 AAAGATGCTTGCATGAATATCATAATC 57.144 29.630 13.18 0.00 34.28 1.75
844 1410 5.448496 CGGTGTCTGTTTTTGAAAGATGACA 60.448 40.000 0.00 0.00 0.00 3.58
862 1428 8.890124 AGATGACATCATTTCTAGTGAAGATG 57.110 34.615 17.57 12.85 39.12 2.90
895 1462 9.727403 CTTATACGCGACATTTACTTGATTATG 57.273 33.333 15.93 0.00 0.00 1.90
925 1493 3.438216 TTTTCATGTCTGCAGGGATCA 57.562 42.857 15.13 8.88 0.00 2.92
956 1524 6.495181 ACCTTCACTTCTCTGAGTAGATTTGA 59.505 38.462 16.85 8.26 31.21 2.69
964 1532 9.134734 CTTCTCTGAGTAGATTTGACTACAAAC 57.865 37.037 5.46 0.00 46.56 2.93
972 1540 3.684103 TTTGACTACAAACAAGGCACG 57.316 42.857 0.00 0.00 40.47 5.34
992 1560 4.032217 CACGCAATCTGTAGACTGTCATTC 59.968 45.833 10.88 0.68 0.00 2.67
1017 1585 3.129287 CCACAATGTCTGTAGATTTGGCC 59.871 47.826 0.00 0.00 36.10 5.36
1088 1665 8.443160 CACCCGTGTAATATACAATGATGATTC 58.557 37.037 0.00 0.00 40.93 2.52
1117 1745 9.972106 AAGAAGATTCCAAGACTGAGATAATTT 57.028 29.630 0.00 0.00 0.00 1.82
1153 1781 2.260822 CCTCTCCTTCACCCTCAGAAA 58.739 52.381 0.00 0.00 0.00 2.52
1174 1802 9.844790 CAGAAATTAATGTTGCTTCTGTTGATA 57.155 29.630 14.64 0.00 38.66 2.15
1189 1817 6.103997 TCTGTTGATAATAACTCCGGTGAAC 58.896 40.000 11.17 2.23 0.00 3.18
1212 1840 0.598562 ATTCTCGCAGTGTGTCTCGT 59.401 50.000 3.13 0.00 0.00 4.18
1254 1882 7.011202 CGGTCTAAAGTTAAGAATAAGAAGGCC 59.989 40.741 0.00 0.00 0.00 5.19
1270 1898 4.772624 AGAAGGCCCCAAAAACTATTTCTC 59.227 41.667 0.00 0.00 0.00 2.87
1326 1954 2.084546 GGTCTTGGGGTTGAAAGATCG 58.915 52.381 0.00 0.00 35.03 3.69
1413 2041 5.279006 CCCTTCTAAGGCAAAAAGAAAGACC 60.279 44.000 3.03 0.00 45.10 3.85
1415 2043 3.818773 TCTAAGGCAAAAAGAAAGACCGG 59.181 43.478 0.00 0.00 0.00 5.28
1535 2169 3.733337 ACTTAGTGACACAGAAGCTTGG 58.267 45.455 2.10 0.00 0.00 3.61
1794 2495 2.493278 ACCATTTATCTGTTGTGCTGCC 59.507 45.455 0.00 0.00 0.00 4.85
1825 2526 4.456911 CCCATCGAAGATAATGAATGTGGG 59.543 45.833 0.00 0.00 45.12 4.61
1858 2559 2.566833 TCATCACCCAACCAACTGAG 57.433 50.000 0.00 0.00 0.00 3.35
1895 2596 0.364180 CAAAGCGCATTTGCATGACG 59.636 50.000 11.47 0.00 41.77 4.35
2049 2918 2.422479 CTGATTCATGTGGAAGCACAGG 59.578 50.000 0.00 0.00 46.28 4.00
2054 2923 2.674380 GTGGAAGCACAGGCAGGG 60.674 66.667 0.00 0.00 44.61 4.45
2078 2947 2.436417 GCAGTTTGCATGAGGAGGTTA 58.564 47.619 0.00 0.00 44.26 2.85
2199 3068 7.062605 CACAGGCTACAATTTTGCTTTTGATAG 59.937 37.037 0.00 0.00 0.00 2.08
2249 3118 1.296715 GACACTCAAGATGGGCGGT 59.703 57.895 0.00 0.00 0.00 5.68
2329 3198 5.016831 ACAAAAACTTCTGTTGGAGTTCCT 58.983 37.500 0.00 0.00 36.39 3.36
2333 3202 4.713792 ACTTCTGTTGGAGTTCCTGATT 57.286 40.909 0.00 0.00 36.82 2.57
2335 3204 4.103153 ACTTCTGTTGGAGTTCCTGATTCA 59.897 41.667 0.00 0.00 36.82 2.57
2358 3227 1.973515 TGTGACTCTGAGCTCACCAAT 59.026 47.619 24.38 0.00 36.70 3.16
2451 3320 4.994852 TCAGTTAAGTGGTACAGTGAATGC 59.005 41.667 10.39 0.00 43.84 3.56
2570 3439 5.485620 GACATGCAATATCAGATAGCTCCA 58.514 41.667 0.00 0.00 0.00 3.86
2694 3602 0.687354 TCCCAGAGAAAGGTCTGCAC 59.313 55.000 0.00 0.00 42.40 4.57
2875 3791 6.741992 TCTATGCCATCTGTAGTGTTTTTG 57.258 37.500 0.00 0.00 0.00 2.44
2973 3890 9.798994 AAAGATTAATCTTGAAGATTGTGATGC 57.201 29.630 27.25 11.83 45.83 3.91
2974 3891 8.515695 AGATTAATCTTGAAGATTGTGATGCA 57.484 30.769 26.11 5.58 44.14 3.96
2975 3892 8.963725 AGATTAATCTTGAAGATTGTGATGCAA 58.036 29.630 26.11 13.35 44.14 4.08
2976 3893 9.234384 GATTAATCTTGAAGATTGTGATGCAAG 57.766 33.333 26.11 3.13 44.14 4.01
2977 3894 6.585695 AATCTTGAAGATTGTGATGCAAGT 57.414 33.333 18.83 0.00 42.90 3.16
2978 3895 7.692460 AATCTTGAAGATTGTGATGCAAGTA 57.308 32.000 18.83 0.00 42.90 2.24
2979 3896 7.692460 ATCTTGAAGATTGTGATGCAAGTAA 57.308 32.000 0.97 0.00 40.86 2.24
2980 3897 7.692460 TCTTGAAGATTGTGATGCAAGTAAT 57.308 32.000 0.00 0.00 40.86 1.89
2981 3898 7.755591 TCTTGAAGATTGTGATGCAAGTAATC 58.244 34.615 0.00 0.00 40.86 1.75
2982 3899 7.391275 TCTTGAAGATTGTGATGCAAGTAATCA 59.609 33.333 14.59 1.84 40.86 2.57
2983 3900 7.451501 TGAAGATTGTGATGCAAGTAATCAA 57.548 32.000 14.59 6.07 40.86 2.57
2984 3901 7.532571 TGAAGATTGTGATGCAAGTAATCAAG 58.467 34.615 14.59 0.00 40.86 3.02
2985 3902 5.888105 AGATTGTGATGCAAGTAATCAAGC 58.112 37.500 14.59 7.77 40.86 4.01
2986 3903 5.416639 AGATTGTGATGCAAGTAATCAAGCA 59.583 36.000 14.59 0.00 40.86 3.91
2988 3905 5.648178 TGTGATGCAAGTAATCAAGCATT 57.352 34.783 0.00 0.00 46.71 3.56
2989 3906 6.756299 TGTGATGCAAGTAATCAAGCATTA 57.244 33.333 0.00 0.00 46.71 1.90
2990 3907 6.554419 TGTGATGCAAGTAATCAAGCATTAC 58.446 36.000 12.38 12.38 46.71 1.89
2991 3908 5.973565 GTGATGCAAGTAATCAAGCATTACC 59.026 40.000 9.21 0.00 46.71 2.85
2992 3909 5.887598 TGATGCAAGTAATCAAGCATTACCT 59.112 36.000 0.00 0.00 46.71 3.08
2993 3910 5.818136 TGCAAGTAATCAAGCATTACCTC 57.182 39.130 2.65 0.00 45.83 3.85
2994 3911 5.252547 TGCAAGTAATCAAGCATTACCTCA 58.747 37.500 2.65 0.00 45.83 3.86
2995 3912 5.355071 TGCAAGTAATCAAGCATTACCTCAG 59.645 40.000 2.65 0.00 45.83 3.35
2996 3913 5.586243 GCAAGTAATCAAGCATTACCTCAGA 59.414 40.000 2.65 0.00 45.83 3.27
2997 3914 6.457528 GCAAGTAATCAAGCATTACCTCAGAC 60.458 42.308 2.65 0.00 45.83 3.51
2998 3915 6.299805 AGTAATCAAGCATTACCTCAGACA 57.700 37.500 2.65 0.00 45.83 3.41
2999 3916 6.711277 AGTAATCAAGCATTACCTCAGACAA 58.289 36.000 2.65 0.00 45.83 3.18
3000 3917 5.886960 AATCAAGCATTACCTCAGACAAC 57.113 39.130 0.00 0.00 0.00 3.32
3001 3918 4.350368 TCAAGCATTACCTCAGACAACA 57.650 40.909 0.00 0.00 0.00 3.33
3002 3919 4.713553 TCAAGCATTACCTCAGACAACAA 58.286 39.130 0.00 0.00 0.00 2.83
3003 3920 5.129634 TCAAGCATTACCTCAGACAACAAA 58.870 37.500 0.00 0.00 0.00 2.83
3004 3921 5.008613 TCAAGCATTACCTCAGACAACAAAC 59.991 40.000 0.00 0.00 0.00 2.93
3005 3922 4.460263 AGCATTACCTCAGACAACAAACA 58.540 39.130 0.00 0.00 0.00 2.83
3006 3923 4.887071 AGCATTACCTCAGACAACAAACAA 59.113 37.500 0.00 0.00 0.00 2.83
3007 3924 5.009010 AGCATTACCTCAGACAACAAACAAG 59.991 40.000 0.00 0.00 0.00 3.16
3008 3925 4.893424 TTACCTCAGACAACAAACAAGC 57.107 40.909 0.00 0.00 0.00 4.01
3009 3926 2.722094 ACCTCAGACAACAAACAAGCA 58.278 42.857 0.00 0.00 0.00 3.91
3010 3927 3.088532 ACCTCAGACAACAAACAAGCAA 58.911 40.909 0.00 0.00 0.00 3.91
3011 3928 3.701040 ACCTCAGACAACAAACAAGCAAT 59.299 39.130 0.00 0.00 0.00 3.56
3241 4206 5.171339 AGCACATGAGAAGTTTAGTGGAT 57.829 39.130 0.00 0.00 0.00 3.41
3426 4405 1.949525 TGACTCTGGAGCACAAAAAGC 59.050 47.619 0.00 0.00 0.00 3.51
3482 4463 0.322975 TTCCCTGTCAGCTGCTTCTC 59.677 55.000 9.47 0.00 0.00 2.87
3537 4518 8.035984 AGCTCCTTCTGTTACTAGTAATTTGAC 58.964 37.037 18.03 6.66 0.00 3.18
3621 4644 7.566760 TGATCACACGCCTTATCAATTATTT 57.433 32.000 0.00 0.00 0.00 1.40
3769 4925 8.789825 ATAATTATCATTCACAGATGAGAGCC 57.210 34.615 0.00 0.00 39.26 4.70
3931 5119 8.898761 TGAACTCTCAGCTTACATTGTTAAAAA 58.101 29.630 0.00 0.00 0.00 1.94
3968 5156 5.532779 CACTAGAAGGAAAGAAGGCTGTTTT 59.467 40.000 0.00 0.00 0.00 2.43
4101 5289 5.250200 TGCGAGGGTGAGTTATAAACATTT 58.750 37.500 0.00 0.00 0.00 2.32
4144 5332 8.863049 CAGGCAATTTTGTCATAATAAGTTGAC 58.137 33.333 0.00 0.00 42.05 3.18
4357 5602 6.808829 ACAAGAATCAACTTCTGCAATTTGA 58.191 32.000 0.00 0.00 43.60 2.69
4358 5603 7.439381 ACAAGAATCAACTTCTGCAATTTGAT 58.561 30.769 0.00 6.11 43.60 2.57
4359 5604 7.929785 ACAAGAATCAACTTCTGCAATTTGATT 59.070 29.630 17.70 17.70 46.61 2.57
4360 5605 7.884816 AGAATCAACTTCTGCAATTTGATTG 57.115 32.000 20.60 8.30 45.19 2.67
4361 5606 7.439381 AGAATCAACTTCTGCAATTTGATTGT 58.561 30.769 20.60 16.42 45.19 2.71
4362 5607 7.929785 AGAATCAACTTCTGCAATTTGATTGTT 59.070 29.630 20.60 11.26 45.19 2.83
4363 5608 7.647907 ATCAACTTCTGCAATTTGATTGTTC 57.352 32.000 0.00 0.00 38.22 3.18
4364 5609 6.808829 TCAACTTCTGCAATTTGATTGTTCT 58.191 32.000 0.00 0.00 42.20 3.01
4365 5610 6.698329 TCAACTTCTGCAATTTGATTGTTCTG 59.302 34.615 0.00 0.00 42.20 3.02
4366 5611 5.535333 ACTTCTGCAATTTGATTGTTCTGG 58.465 37.500 0.00 0.00 42.20 3.86
4367 5612 3.916761 TCTGCAATTTGATTGTTCTGGC 58.083 40.909 0.00 0.00 42.20 4.85
4368 5613 2.664568 CTGCAATTTGATTGTTCTGGCG 59.335 45.455 0.00 0.00 42.20 5.69
4369 5614 2.295629 TGCAATTTGATTGTTCTGGCGA 59.704 40.909 0.00 0.00 42.20 5.54
4370 5615 3.056678 TGCAATTTGATTGTTCTGGCGAT 60.057 39.130 0.00 0.00 42.20 4.58
4371 5616 3.928375 GCAATTTGATTGTTCTGGCGATT 59.072 39.130 0.00 0.00 42.20 3.34
4372 5617 4.389687 GCAATTTGATTGTTCTGGCGATTT 59.610 37.500 0.00 0.00 42.20 2.17
4373 5618 5.445010 GCAATTTGATTGTTCTGGCGATTTC 60.445 40.000 0.00 0.00 42.20 2.17
4435 5680 4.963276 TTAGCCATGACACTATGTTTGC 57.037 40.909 0.00 0.00 0.00 3.68
4448 5693 1.522668 TGTTTGCGGATTCCTCTGTG 58.477 50.000 0.30 0.00 0.00 3.66
4489 5734 2.241941 TGATCAAGCAATTAGAGGGGCA 59.758 45.455 0.00 0.00 0.00 5.36
4490 5735 2.425143 TCAAGCAATTAGAGGGGCAG 57.575 50.000 0.00 0.00 0.00 4.85
4564 5809 2.287915 GGGGTCAATCGTTCATCATTCG 59.712 50.000 0.00 0.00 0.00 3.34
4598 5843 5.128008 GTCTTGGGCTGAGAGTAGAAATACT 59.872 44.000 0.00 0.00 0.00 2.12
4698 5946 4.098914 AGGCACTTCATAAAGTTGTGGA 57.901 40.909 0.00 0.00 43.28 4.02
4734 5982 2.812613 CGCCAGTGGTTAGAGGGAAAAA 60.813 50.000 11.74 0.00 0.00 1.94
4872 6120 9.927668 ATTCACCCATGTAAATGTAAAAGAAAG 57.072 29.630 0.00 0.00 0.00 2.62
4873 6121 7.375053 TCACCCATGTAAATGTAAAAGAAAGC 58.625 34.615 0.00 0.00 0.00 3.51
4874 6122 7.014711 TCACCCATGTAAATGTAAAAGAAAGCA 59.985 33.333 0.00 0.00 0.00 3.91
4875 6123 7.655328 CACCCATGTAAATGTAAAAGAAAGCAA 59.345 33.333 0.00 0.00 0.00 3.91
4876 6124 7.872483 ACCCATGTAAATGTAAAAGAAAGCAAG 59.128 33.333 0.00 0.00 0.00 4.01
4877 6125 8.087750 CCCATGTAAATGTAAAAGAAAGCAAGA 58.912 33.333 0.00 0.00 0.00 3.02
4878 6126 9.132521 CCATGTAAATGTAAAAGAAAGCAAGAG 57.867 33.333 0.00 0.00 0.00 2.85
4879 6127 9.683069 CATGTAAATGTAAAAGAAAGCAAGAGT 57.317 29.630 0.00 0.00 0.00 3.24
4880 6128 9.683069 ATGTAAATGTAAAAGAAAGCAAGAGTG 57.317 29.630 0.00 0.00 0.00 3.51
4881 6129 8.898761 TGTAAATGTAAAAGAAAGCAAGAGTGA 58.101 29.630 0.00 0.00 0.00 3.41
4882 6130 9.170584 GTAAATGTAAAAGAAAGCAAGAGTGAC 57.829 33.333 0.00 0.00 0.00 3.67
4883 6131 5.403897 TGTAAAAGAAAGCAAGAGTGACG 57.596 39.130 0.00 0.00 0.00 4.35
4884 6132 4.873827 TGTAAAAGAAAGCAAGAGTGACGT 59.126 37.500 0.00 0.00 0.00 4.34
4885 6133 4.965119 AAAAGAAAGCAAGAGTGACGTT 57.035 36.364 0.00 0.00 0.00 3.99
4886 6134 4.965119 AAAGAAAGCAAGAGTGACGTTT 57.035 36.364 0.00 0.00 0.00 3.60
4887 6135 4.965119 AAGAAAGCAAGAGTGACGTTTT 57.035 36.364 0.00 0.00 0.00 2.43
4888 6136 4.278678 AGAAAGCAAGAGTGACGTTTTG 57.721 40.909 0.00 0.00 0.00 2.44
4889 6137 3.065371 AGAAAGCAAGAGTGACGTTTTGG 59.935 43.478 0.00 0.00 0.00 3.28
4890 6138 0.663153 AGCAAGAGTGACGTTTTGGC 59.337 50.000 0.00 0.00 0.00 4.52
4891 6139 0.663153 GCAAGAGTGACGTTTTGGCT 59.337 50.000 0.00 0.00 0.00 4.75
4892 6140 1.334149 GCAAGAGTGACGTTTTGGCTC 60.334 52.381 0.00 0.00 0.00 4.70
4893 6141 1.264288 CAAGAGTGACGTTTTGGCTCC 59.736 52.381 0.00 0.00 0.00 4.70
4894 6142 0.759346 AGAGTGACGTTTTGGCTCCT 59.241 50.000 0.00 0.00 0.00 3.69
4895 6143 1.968493 AGAGTGACGTTTTGGCTCCTA 59.032 47.619 0.00 0.00 0.00 2.94
4896 6144 2.028930 AGAGTGACGTTTTGGCTCCTAG 60.029 50.000 0.00 0.00 0.00 3.02
4897 6145 1.002087 AGTGACGTTTTGGCTCCTAGG 59.998 52.381 0.82 0.82 0.00 3.02
4898 6146 1.053424 TGACGTTTTGGCTCCTAGGT 58.947 50.000 9.08 0.00 0.00 3.08
4899 6147 1.270625 TGACGTTTTGGCTCCTAGGTG 60.271 52.381 9.08 7.68 0.00 4.00
4900 6148 0.763035 ACGTTTTGGCTCCTAGGTGT 59.237 50.000 9.08 0.00 0.00 4.16
4901 6149 1.972795 ACGTTTTGGCTCCTAGGTGTA 59.027 47.619 9.08 0.00 0.00 2.90
4902 6150 2.028385 ACGTTTTGGCTCCTAGGTGTAG 60.028 50.000 9.08 0.00 0.00 2.74
4903 6151 2.232941 CGTTTTGGCTCCTAGGTGTAGA 59.767 50.000 9.08 0.00 0.00 2.59
4904 6152 3.118738 CGTTTTGGCTCCTAGGTGTAGAT 60.119 47.826 9.08 0.00 0.00 1.98
4905 6153 4.098960 CGTTTTGGCTCCTAGGTGTAGATA 59.901 45.833 9.08 0.00 0.00 1.98
4906 6154 5.358090 GTTTTGGCTCCTAGGTGTAGATAC 58.642 45.833 9.08 0.85 0.00 2.24
4907 6155 3.965470 TGGCTCCTAGGTGTAGATACA 57.035 47.619 9.08 0.00 0.00 2.29
4981 6229 2.596904 AAATCCCGAGTGTACATCCG 57.403 50.000 0.00 5.85 0.00 4.18
4982 6230 0.750850 AATCCCGAGTGTACATCCGG 59.249 55.000 23.69 23.69 41.47 5.14
4983 6231 0.106369 ATCCCGAGTGTACATCCGGA 60.106 55.000 28.96 20.87 44.29 5.14
4984 6232 1.033746 TCCCGAGTGTACATCCGGAC 61.034 60.000 28.96 5.76 44.29 4.79
4985 6233 1.317431 CCCGAGTGTACATCCGGACA 61.317 60.000 28.96 0.00 44.29 4.02
4986 6234 0.744874 CCGAGTGTACATCCGGACAT 59.255 55.000 25.39 0.00 44.29 3.06
4987 6235 1.269102 CCGAGTGTACATCCGGACATC 60.269 57.143 25.39 0.00 44.29 3.06
4988 6236 1.269102 CGAGTGTACATCCGGACATCC 60.269 57.143 6.12 0.00 0.00 3.51
4989 6237 2.032620 GAGTGTACATCCGGACATCCT 58.967 52.381 6.12 0.00 0.00 3.24
4990 6238 3.220110 GAGTGTACATCCGGACATCCTA 58.780 50.000 6.12 0.00 0.00 2.94
4991 6239 3.827302 GAGTGTACATCCGGACATCCTAT 59.173 47.826 6.12 0.00 0.00 2.57
4992 6240 3.574396 AGTGTACATCCGGACATCCTATG 59.426 47.826 6.12 0.79 34.87 2.23
4994 6242 3.964688 TGTACATCCGGACATCCTATGTT 59.035 43.478 6.12 0.00 45.03 2.71
4995 6243 4.407621 TGTACATCCGGACATCCTATGTTT 59.592 41.667 6.12 0.00 45.03 2.83
4996 6244 3.808728 ACATCCGGACATCCTATGTTTG 58.191 45.455 6.12 0.00 45.03 2.93
4997 6245 2.325583 TCCGGACATCCTATGTTTGC 57.674 50.000 0.00 0.00 45.03 3.68
4998 6246 1.557371 TCCGGACATCCTATGTTTGCA 59.443 47.619 0.00 0.00 45.03 4.08
4999 6247 1.670811 CCGGACATCCTATGTTTGCAC 59.329 52.381 0.00 0.00 45.03 4.57
5000 6248 2.355197 CGGACATCCTATGTTTGCACA 58.645 47.619 0.00 0.00 45.03 4.57
5001 6249 2.746904 CGGACATCCTATGTTTGCACAA 59.253 45.455 0.00 0.00 45.03 3.33
5002 6250 3.190327 CGGACATCCTATGTTTGCACAAA 59.810 43.478 0.00 0.00 45.03 2.83
5003 6251 4.142403 CGGACATCCTATGTTTGCACAAAT 60.142 41.667 0.00 0.00 45.03 2.32
5004 6252 5.622007 CGGACATCCTATGTTTGCACAAATT 60.622 40.000 0.00 0.00 45.03 1.82
5005 6253 6.165577 GGACATCCTATGTTTGCACAAATTT 58.834 36.000 0.00 0.00 45.03 1.82
5006 6254 6.650390 GGACATCCTATGTTTGCACAAATTTT 59.350 34.615 0.00 0.00 45.03 1.82
5007 6255 7.173047 GGACATCCTATGTTTGCACAAATTTTT 59.827 33.333 0.00 0.00 45.03 1.94
5076 6324 6.893958 AAAATGTCTCGTGAATAGCAGTAG 57.106 37.500 0.00 0.00 0.00 2.57
5077 6325 5.584253 AATGTCTCGTGAATAGCAGTAGT 57.416 39.130 0.00 0.00 0.00 2.73
5078 6326 4.617808 TGTCTCGTGAATAGCAGTAGTC 57.382 45.455 0.00 0.00 0.00 2.59
5079 6327 4.007659 TGTCTCGTGAATAGCAGTAGTCA 58.992 43.478 0.00 0.00 30.85 3.41
5080 6328 4.457949 TGTCTCGTGAATAGCAGTAGTCAA 59.542 41.667 0.00 0.00 35.12 3.18
5081 6329 5.031578 GTCTCGTGAATAGCAGTAGTCAAG 58.968 45.833 0.00 0.00 35.12 3.02
5082 6330 3.770666 TCGTGAATAGCAGTAGTCAAGC 58.229 45.455 0.00 0.00 35.12 4.01
5083 6331 3.192633 TCGTGAATAGCAGTAGTCAAGCA 59.807 43.478 0.00 0.00 35.12 3.91
5084 6332 4.115516 CGTGAATAGCAGTAGTCAAGCAT 58.884 43.478 0.00 0.00 35.12 3.79
5085 6333 4.208047 CGTGAATAGCAGTAGTCAAGCATC 59.792 45.833 0.00 0.00 35.12 3.91
5086 6334 4.208047 GTGAATAGCAGTAGTCAAGCATCG 59.792 45.833 0.00 0.00 35.12 3.84
5087 6335 4.097892 TGAATAGCAGTAGTCAAGCATCGA 59.902 41.667 0.00 0.00 30.39 3.59
5088 6336 4.655762 ATAGCAGTAGTCAAGCATCGAA 57.344 40.909 0.00 0.00 0.00 3.71
5089 6337 3.319137 AGCAGTAGTCAAGCATCGAAA 57.681 42.857 0.00 0.00 0.00 3.46
5090 6338 3.664107 AGCAGTAGTCAAGCATCGAAAA 58.336 40.909 0.00 0.00 0.00 2.29
5091 6339 4.256920 AGCAGTAGTCAAGCATCGAAAAT 58.743 39.130 0.00 0.00 0.00 1.82
5092 6340 4.697352 AGCAGTAGTCAAGCATCGAAAATT 59.303 37.500 0.00 0.00 0.00 1.82
5093 6341 4.790140 GCAGTAGTCAAGCATCGAAAATTG 59.210 41.667 0.00 0.00 0.00 2.32
5094 6342 5.617751 GCAGTAGTCAAGCATCGAAAATTGT 60.618 40.000 0.00 0.00 0.00 2.71
5095 6343 6.373779 CAGTAGTCAAGCATCGAAAATTGTT 58.626 36.000 0.00 0.00 0.00 2.83
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 3.894547 GAAAGTTGGCGCGGAGGGA 62.895 63.158 8.83 0.00 46.37 4.20
19 20 3.431725 GGAAAGTTGGCGCGGAGG 61.432 66.667 8.83 0.00 0.00 4.30
61 67 3.199508 GGCATATGTATGAGGAGGATGCT 59.800 47.826 4.29 0.00 42.52 3.79
80 86 0.952280 GTCGACTCTGGATATCGGCA 59.048 55.000 8.70 0.00 40.14 5.69
99 105 1.625818 AGTGGAACCCTACTCTGCTTG 59.374 52.381 0.00 0.00 37.80 4.01
151 299 1.258676 GACTGAAAGACGGAGGGAGT 58.741 55.000 0.00 0.00 37.43 3.85
243 406 4.717313 GGAAAAGGCCGCGGGAGT 62.717 66.667 29.38 0.00 0.00 3.85
244 407 4.410400 AGGAAAAGGCCGCGGGAG 62.410 66.667 29.38 0.83 0.00 4.30
245 408 4.404098 GAGGAAAAGGCCGCGGGA 62.404 66.667 29.38 0.00 0.00 5.14
254 417 1.369625 CCGGGTGAATCGAGGAAAAG 58.630 55.000 0.00 0.00 0.00 2.27
301 465 0.387202 CACAGATCTAGACCCTGCGG 59.613 60.000 18.73 10.85 0.00 5.69
302 466 1.107114 ACACAGATCTAGACCCTGCG 58.893 55.000 18.73 14.00 0.00 5.18
339 508 1.035139 ATTCATTTCATCGGCCTGCC 58.965 50.000 0.00 0.00 0.00 4.85
340 509 2.159198 ACAATTCATTTCATCGGCCTGC 60.159 45.455 0.00 0.00 0.00 4.85
384 563 2.061773 AGATTCAGAGTCAACGCAACG 58.938 47.619 0.00 0.00 0.00 4.10
433 612 2.934932 TGTCAGGCCTGGGATGCA 60.935 61.111 32.23 19.12 0.00 3.96
533 781 1.080705 CGTGGTCGTGAAGAGGGAC 60.081 63.158 0.00 0.00 0.00 4.46
551 800 6.827586 TTATTACTGACAAAACCACATCCC 57.172 37.500 0.00 0.00 0.00 3.85
554 803 7.015195 AGCCTTTTATTACTGACAAAACCACAT 59.985 33.333 0.00 0.00 0.00 3.21
555 804 6.322712 AGCCTTTTATTACTGACAAAACCACA 59.677 34.615 0.00 0.00 0.00 4.17
556 805 6.640907 CAGCCTTTTATTACTGACAAAACCAC 59.359 38.462 0.00 0.00 31.67 4.16
557 806 6.737346 GCAGCCTTTTATTACTGACAAAACCA 60.737 38.462 0.00 0.00 31.67 3.67
558 807 5.633601 GCAGCCTTTTATTACTGACAAAACC 59.366 40.000 0.00 0.00 31.67 3.27
588 839 6.058183 ACAGACAATTTGTATAGAGATGGGC 58.942 40.000 1.15 0.00 0.00 5.36
589 840 7.770433 TGAACAGACAATTTGTATAGAGATGGG 59.230 37.037 1.15 0.00 0.00 4.00
723 1273 2.680339 GTGTTCTTCATAAGAGGGCAGC 59.320 50.000 0.00 0.00 39.03 5.25
728 1278 4.999950 AGCTTGTGTGTTCTTCATAAGAGG 59.000 41.667 6.60 0.00 39.03 3.69
819 1385 4.036262 TCATCTTTCAAAAACAGACACCGG 59.964 41.667 0.00 0.00 0.00 5.28
844 1410 7.774157 AGCATCAACATCTTCACTAGAAATGAT 59.226 33.333 0.00 0.00 36.22 2.45
862 1428 4.452890 AATGTCGCGTATAAGCATCAAC 57.547 40.909 5.77 4.02 36.85 3.18
925 1493 8.871125 TCTACTCAGAGAAGTGAAGGTTAAAAT 58.129 33.333 3.79 0.00 0.00 1.82
956 1524 1.384525 TTGCGTGCCTTGTTTGTAGT 58.615 45.000 0.00 0.00 0.00 2.73
964 1532 1.394917 GTCTACAGATTGCGTGCCTTG 59.605 52.381 0.00 0.00 0.00 3.61
972 1540 3.553511 CCGAATGACAGTCTACAGATTGC 59.446 47.826 1.31 0.00 35.49 3.56
992 1560 2.315925 ATCTACAGACATTGTGGCCG 57.684 50.000 0.00 0.00 41.10 6.13
1017 1585 5.926542 TCTGAGAGTCGAAACTATTTTGTGG 59.073 40.000 0.00 0.00 35.28 4.17
1088 1665 6.035368 TCTCAGTCTTGGAATCTTCTTCAG 57.965 41.667 0.00 0.00 0.00 3.02
1174 1802 5.805728 AGAATCTTGTTCACCGGAGTTATT 58.194 37.500 9.46 0.00 0.00 1.40
1178 1806 2.352814 CGAGAATCTTGTTCACCGGAGT 60.353 50.000 9.46 0.00 0.00 3.85
1179 1807 2.263077 CGAGAATCTTGTTCACCGGAG 58.737 52.381 9.46 0.00 0.00 4.63
1189 1817 2.665537 GAGACACACTGCGAGAATCTTG 59.334 50.000 0.00 0.00 0.00 3.02
1232 1860 7.116736 TGGGGCCTTCTTATTCTTAACTTTAG 58.883 38.462 0.84 0.00 0.00 1.85
1254 1882 7.363268 CCAGATCCTTGAGAAATAGTTTTTGGG 60.363 40.741 0.00 0.00 0.00 4.12
1270 1898 3.135348 TGATCCTTAGTGCCAGATCCTTG 59.865 47.826 0.00 0.00 35.34 3.61
1326 1954 6.238429 GCTCATCAAGATCAACTTCCTCATTC 60.238 42.308 0.00 0.00 36.61 2.67
1413 2041 1.293924 GTGGAGAAGATGATGCACCG 58.706 55.000 0.00 0.00 32.20 4.94
1415 2043 2.033049 GCATGTGGAGAAGATGATGCAC 59.967 50.000 0.00 0.00 36.91 4.57
1535 2169 5.043248 GCTCTTGATCTACAGCTCTTCTTC 58.957 45.833 0.00 0.00 0.00 2.87
1794 2495 6.283694 TCATTATCTTCGATGGGAAACTGAG 58.716 40.000 0.00 0.00 33.34 3.35
1825 2526 1.246056 TGATGAAACCAGGCTGCTGC 61.246 55.000 9.56 7.10 38.76 5.25
1858 2559 0.955428 TGGCGTCAGAAACATCTGGC 60.955 55.000 6.04 3.32 38.85 4.85
1983 2684 7.826744 TGCACCTCACATCTGTGTAATTAATTA 59.173 33.333 9.96 3.71 45.76 1.40
1986 2687 5.411361 GTGCACCTCACATCTGTGTAATTAA 59.589 40.000 5.22 0.00 45.76 1.40
2061 2930 3.427161 GCATAACCTCCTCATGCAAAC 57.573 47.619 0.00 0.00 43.59 2.93
2078 2947 2.191375 CTCCACCGGCATCTGCAT 59.809 61.111 0.00 0.00 44.36 3.96
2199 3068 4.574013 CAGTATGAGCCAAATCAAGAGTCC 59.426 45.833 0.00 0.00 39.69 3.85
2329 3198 3.323115 AGCTCAGAGTCACAACTGAATCA 59.677 43.478 0.00 0.00 42.83 2.57
2333 3202 2.035193 GTGAGCTCAGAGTCACAACTGA 59.965 50.000 18.89 4.95 42.31 3.41
2335 3204 1.342819 GGTGAGCTCAGAGTCACAACT 59.657 52.381 18.89 4.63 44.17 3.16
2570 3439 8.697507 ATTTCTTGTGTTTCTTCAGGATTAGT 57.302 30.769 0.00 0.00 0.00 2.24
2694 3602 9.520204 TTCTTTGAAACTTGATTTAAAGAGCTG 57.480 29.630 0.00 0.00 34.72 4.24
2781 3690 4.900635 TTGCAAAACTTCTCCTGAGAAC 57.099 40.909 5.50 0.00 42.06 3.01
2964 3881 5.648178 TGCTTGATTACTTGCATCACAAT 57.352 34.783 0.00 0.00 37.72 2.71
2965 3882 5.648178 ATGCTTGATTACTTGCATCACAA 57.352 34.783 0.00 0.00 41.60 3.33
2966 3883 5.648178 AATGCTTGATTACTTGCATCACA 57.352 34.783 0.00 0.00 44.15 3.58
2967 3884 5.973565 GGTAATGCTTGATTACTTGCATCAC 59.026 40.000 0.00 0.00 44.20 3.06
2968 3885 5.887598 AGGTAATGCTTGATTACTTGCATCA 59.112 36.000 0.00 0.00 44.20 3.07
2969 3886 6.038603 TGAGGTAATGCTTGATTACTTGCATC 59.961 38.462 0.00 0.00 44.20 3.91
2970 3887 5.887598 TGAGGTAATGCTTGATTACTTGCAT 59.112 36.000 0.00 0.00 44.20 3.96
2971 3888 5.252547 TGAGGTAATGCTTGATTACTTGCA 58.747 37.500 0.00 0.00 44.20 4.08
2972 3889 5.586243 TCTGAGGTAATGCTTGATTACTTGC 59.414 40.000 0.00 0.00 44.20 4.01
2973 3890 6.595326 TGTCTGAGGTAATGCTTGATTACTTG 59.405 38.462 0.00 0.00 44.20 3.16
2974 3891 6.711277 TGTCTGAGGTAATGCTTGATTACTT 58.289 36.000 0.00 0.00 44.20 2.24
2975 3892 6.299805 TGTCTGAGGTAATGCTTGATTACT 57.700 37.500 0.00 0.00 44.20 2.24
2976 3893 6.371548 TGTTGTCTGAGGTAATGCTTGATTAC 59.628 38.462 0.00 0.00 44.08 1.89
2977 3894 6.472016 TGTTGTCTGAGGTAATGCTTGATTA 58.528 36.000 0.00 0.00 0.00 1.75
2978 3895 5.316167 TGTTGTCTGAGGTAATGCTTGATT 58.684 37.500 0.00 0.00 0.00 2.57
2979 3896 4.910195 TGTTGTCTGAGGTAATGCTTGAT 58.090 39.130 0.00 0.00 0.00 2.57
2980 3897 4.350368 TGTTGTCTGAGGTAATGCTTGA 57.650 40.909 0.00 0.00 0.00 3.02
2981 3898 5.215160 GTTTGTTGTCTGAGGTAATGCTTG 58.785 41.667 0.00 0.00 0.00 4.01
2982 3899 4.887071 TGTTTGTTGTCTGAGGTAATGCTT 59.113 37.500 0.00 0.00 0.00 3.91
2983 3900 4.460263 TGTTTGTTGTCTGAGGTAATGCT 58.540 39.130 0.00 0.00 0.00 3.79
2984 3901 4.829064 TGTTTGTTGTCTGAGGTAATGC 57.171 40.909 0.00 0.00 0.00 3.56
2985 3902 5.215160 GCTTGTTTGTTGTCTGAGGTAATG 58.785 41.667 0.00 0.00 0.00 1.90
2986 3903 4.887071 TGCTTGTTTGTTGTCTGAGGTAAT 59.113 37.500 0.00 0.00 0.00 1.89
2987 3904 4.265893 TGCTTGTTTGTTGTCTGAGGTAA 58.734 39.130 0.00 0.00 0.00 2.85
2988 3905 3.879998 TGCTTGTTTGTTGTCTGAGGTA 58.120 40.909 0.00 0.00 0.00 3.08
2989 3906 2.722094 TGCTTGTTTGTTGTCTGAGGT 58.278 42.857 0.00 0.00 0.00 3.85
2990 3907 3.781079 TTGCTTGTTTGTTGTCTGAGG 57.219 42.857 0.00 0.00 0.00 3.86
2991 3908 5.215160 GGTATTGCTTGTTTGTTGTCTGAG 58.785 41.667 0.00 0.00 0.00 3.35
2992 3909 4.260990 CGGTATTGCTTGTTTGTTGTCTGA 60.261 41.667 0.00 0.00 0.00 3.27
2993 3910 3.974401 CGGTATTGCTTGTTTGTTGTCTG 59.026 43.478 0.00 0.00 0.00 3.51
2994 3911 3.880490 TCGGTATTGCTTGTTTGTTGTCT 59.120 39.130 0.00 0.00 0.00 3.41
2995 3912 4.217754 TCGGTATTGCTTGTTTGTTGTC 57.782 40.909 0.00 0.00 0.00 3.18
2996 3913 4.518970 AGATCGGTATTGCTTGTTTGTTGT 59.481 37.500 0.00 0.00 0.00 3.32
2997 3914 4.853196 CAGATCGGTATTGCTTGTTTGTTG 59.147 41.667 0.00 0.00 0.00 3.33
2998 3915 4.518970 ACAGATCGGTATTGCTTGTTTGTT 59.481 37.500 0.00 0.00 0.00 2.83
2999 3916 4.072131 ACAGATCGGTATTGCTTGTTTGT 58.928 39.130 0.00 0.00 0.00 2.83
3000 3917 4.083324 ACACAGATCGGTATTGCTTGTTTG 60.083 41.667 0.00 0.00 0.00 2.93
3001 3918 4.072131 ACACAGATCGGTATTGCTTGTTT 58.928 39.130 0.00 0.00 0.00 2.83
3002 3919 3.674997 ACACAGATCGGTATTGCTTGTT 58.325 40.909 0.00 0.00 0.00 2.83
3003 3920 3.334583 ACACAGATCGGTATTGCTTGT 57.665 42.857 0.00 0.00 0.00 3.16
3004 3921 5.447279 GGTTAACACAGATCGGTATTGCTTG 60.447 44.000 8.10 0.00 0.00 4.01
3005 3922 4.634443 GGTTAACACAGATCGGTATTGCTT 59.366 41.667 8.10 0.00 0.00 3.91
3006 3923 4.189231 GGTTAACACAGATCGGTATTGCT 58.811 43.478 8.10 0.00 0.00 3.91
3007 3924 3.936453 TGGTTAACACAGATCGGTATTGC 59.064 43.478 8.10 0.00 0.00 3.56
3080 4045 6.139679 TGGGGATTCTGTTGACTTAAGAAT 57.860 37.500 10.09 0.00 42.03 2.40
3241 4206 4.037327 TGTGCTTCCGATGACAAATTTTCA 59.963 37.500 5.81 5.81 0.00 2.69
3389 4368 8.768397 TCCAGAGTCAATATATGGTGTAACTTT 58.232 33.333 0.00 0.00 36.74 2.66
3411 4390 4.510038 AATACAGCTTTTTGTGCTCCAG 57.490 40.909 0.00 0.00 38.92 3.86
3466 4447 2.181954 AAAGAGAAGCAGCTGACAGG 57.818 50.000 20.43 0.00 0.00 4.00
3537 4518 7.757097 AACTAACTTTGTACAGATCATAGCG 57.243 36.000 0.00 0.00 0.00 4.26
3588 4573 7.931407 TGATAAGGCGTGTGATCAATAGTAATT 59.069 33.333 0.00 0.00 0.00 1.40
3592 4577 5.276461 TGATAAGGCGTGTGATCAATAGT 57.724 39.130 0.00 0.00 0.00 2.12
3593 4578 6.791887 ATTGATAAGGCGTGTGATCAATAG 57.208 37.500 16.64 0.00 43.72 1.73
3594 4579 8.846943 ATAATTGATAAGGCGTGTGATCAATA 57.153 30.769 17.70 10.83 44.39 1.90
3637 4660 3.681897 CACAGACAGGAGAAAGCACATAC 59.318 47.826 0.00 0.00 0.00 2.39
3931 5119 7.540474 TTCCTTCTAGTGTCTGTCATTAAGT 57.460 36.000 0.00 0.00 0.00 2.24
3951 5139 2.387757 TGCAAAACAGCCTTCTTTCCT 58.612 42.857 0.00 0.00 0.00 3.36
3968 5156 0.749091 CCTCGGCAATTCTGGATGCA 60.749 55.000 0.00 0.00 44.32 3.96
4117 5305 7.545265 TCAACTTATTATGACAAAATTGCCTGC 59.455 33.333 0.00 0.00 0.00 4.85
4144 5332 9.304731 TCTTGTTTGATTCTTCATTGTCAAAAG 57.695 29.630 1.46 0.00 40.85 2.27
4253 5479 7.418337 TGGACTCTAGCATCTAAACATACAA 57.582 36.000 0.00 0.00 0.00 2.41
4357 5602 4.789012 ACAATGAAATCGCCAGAACAAT 57.211 36.364 0.00 0.00 0.00 2.71
4358 5603 4.517075 TGTACAATGAAATCGCCAGAACAA 59.483 37.500 0.00 0.00 0.00 2.83
4359 5604 4.068599 TGTACAATGAAATCGCCAGAACA 58.931 39.130 0.00 0.00 0.00 3.18
4360 5605 4.678509 TGTACAATGAAATCGCCAGAAC 57.321 40.909 0.00 0.00 0.00 3.01
4361 5606 4.759693 AGTTGTACAATGAAATCGCCAGAA 59.240 37.500 12.26 0.00 0.00 3.02
4362 5607 4.154015 CAGTTGTACAATGAAATCGCCAGA 59.846 41.667 12.26 0.00 0.00 3.86
4363 5608 4.154015 TCAGTTGTACAATGAAATCGCCAG 59.846 41.667 12.26 0.00 0.00 4.85
4364 5609 4.068599 TCAGTTGTACAATGAAATCGCCA 58.931 39.130 12.26 0.00 0.00 5.69
4365 5610 4.678509 TCAGTTGTACAATGAAATCGCC 57.321 40.909 12.26 0.00 0.00 5.54
4366 5611 6.086222 ACAATCAGTTGTACAATGAAATCGC 58.914 36.000 12.26 0.00 46.37 4.58
4435 5680 1.207089 TGGCTAACACAGAGGAATCCG 59.793 52.381 0.00 0.00 0.00 4.18
4448 5693 5.181690 TCAAAAACAGTGTCATGGCTAAC 57.818 39.130 0.00 0.00 0.00 2.34
4512 5757 1.994916 CAAACGGATGGTGAATTGCC 58.005 50.000 0.00 0.00 0.00 4.52
4522 5767 3.312421 CCCTGTATTACAGCAAACGGATG 59.688 47.826 16.85 2.05 44.63 3.51
4525 5770 2.014128 CCCCTGTATTACAGCAAACGG 58.986 52.381 16.85 12.16 44.63 4.44
4526 5771 2.014128 CCCCCTGTATTACAGCAAACG 58.986 52.381 16.85 4.57 44.63 3.60
4598 5843 1.302192 GTTACGGCCTGAGCAACCA 60.302 57.895 0.00 0.00 42.56 3.67
4651 5899 4.511454 TGAATTCAACGAACCAGTCTGAAG 59.489 41.667 5.45 0.00 30.76 3.02
4655 5903 5.221048 CCTTTTGAATTCAACGAACCAGTCT 60.221 40.000 20.35 0.00 35.28 3.24
4660 5908 3.489416 GTGCCTTTTGAATTCAACGAACC 59.511 43.478 20.35 8.78 35.28 3.62
4698 5946 2.038557 ACTGGCGGTCACAATTTAGACT 59.961 45.455 0.00 0.00 35.18 3.24
4734 5982 7.497595 TCTGGTTAATTAGCGATAACTCATGT 58.502 34.615 0.00 0.00 0.00 3.21
4805 6053 8.562892 GCACAGTTAGTTATCATCAGCAATAAT 58.437 33.333 0.00 0.00 0.00 1.28
4806 6054 7.552330 TGCACAGTTAGTTATCATCAGCAATAA 59.448 33.333 0.00 0.00 0.00 1.40
4812 6060 4.813161 CCCTGCACAGTTAGTTATCATCAG 59.187 45.833 0.00 0.00 0.00 2.90
4872 6120 0.663153 AGCCAAAACGTCACTCTTGC 59.337 50.000 0.00 0.00 0.00 4.01
4873 6121 1.264288 GGAGCCAAAACGTCACTCTTG 59.736 52.381 0.00 0.00 0.00 3.02
4874 6122 1.141053 AGGAGCCAAAACGTCACTCTT 59.859 47.619 0.00 0.00 0.00 2.85
4875 6123 0.759346 AGGAGCCAAAACGTCACTCT 59.241 50.000 0.00 0.00 0.00 3.24
4876 6124 2.338500 CTAGGAGCCAAAACGTCACTC 58.662 52.381 0.00 0.00 0.00 3.51
4877 6125 1.002087 CCTAGGAGCCAAAACGTCACT 59.998 52.381 1.05 0.00 0.00 3.41
4878 6126 1.270678 ACCTAGGAGCCAAAACGTCAC 60.271 52.381 17.98 0.00 0.00 3.67
4879 6127 1.053424 ACCTAGGAGCCAAAACGTCA 58.947 50.000 17.98 0.00 0.00 4.35
4880 6128 1.270678 ACACCTAGGAGCCAAAACGTC 60.271 52.381 17.98 0.00 0.00 4.34
4881 6129 0.763035 ACACCTAGGAGCCAAAACGT 59.237 50.000 17.98 0.00 0.00 3.99
4882 6130 2.232941 TCTACACCTAGGAGCCAAAACG 59.767 50.000 17.98 0.00 0.00 3.60
4883 6131 3.975168 TCTACACCTAGGAGCCAAAAC 57.025 47.619 17.98 0.00 0.00 2.43
4884 6132 5.027460 TGTATCTACACCTAGGAGCCAAAA 58.973 41.667 17.98 0.00 0.00 2.44
4885 6133 4.616553 TGTATCTACACCTAGGAGCCAAA 58.383 43.478 17.98 0.00 0.00 3.28
4886 6134 4.259933 TGTATCTACACCTAGGAGCCAA 57.740 45.455 17.98 0.00 0.00 4.52
4887 6135 3.965470 TGTATCTACACCTAGGAGCCA 57.035 47.619 17.98 0.00 0.00 4.75
4960 6208 3.267483 CGGATGTACACTCGGGATTTTT 58.733 45.455 0.00 0.00 0.00 1.94
4961 6209 2.419574 CCGGATGTACACTCGGGATTTT 60.420 50.000 23.42 0.00 38.93 1.82
4962 6210 1.138266 CCGGATGTACACTCGGGATTT 59.862 52.381 23.42 0.00 38.93 2.17
4963 6211 0.750850 CCGGATGTACACTCGGGATT 59.249 55.000 23.42 0.00 38.93 3.01
4964 6212 0.106369 TCCGGATGTACACTCGGGAT 60.106 55.000 27.66 1.12 42.44 3.85
4965 6213 1.033746 GTCCGGATGTACACTCGGGA 61.034 60.000 27.66 23.88 42.44 5.14
4966 6214 1.317431 TGTCCGGATGTACACTCGGG 61.317 60.000 27.66 22.57 42.44 5.14
4967 6215 0.744874 ATGTCCGGATGTACACTCGG 59.255 55.000 24.54 24.54 43.42 4.63
4968 6216 1.269102 GGATGTCCGGATGTACACTCG 60.269 57.143 7.81 5.14 0.00 4.18
4969 6217 2.032620 AGGATGTCCGGATGTACACTC 58.967 52.381 7.81 1.56 42.08 3.51
4970 6218 2.160721 AGGATGTCCGGATGTACACT 57.839 50.000 7.81 0.00 42.08 3.55
4971 6219 3.321111 ACATAGGATGTCCGGATGTACAC 59.679 47.826 7.81 0.00 42.08 2.90
4972 6220 3.572642 ACATAGGATGTCCGGATGTACA 58.427 45.455 7.81 0.55 42.08 2.90
4973 6221 4.602340 AACATAGGATGTCCGGATGTAC 57.398 45.455 7.81 0.00 44.07 2.90
4974 6222 4.742440 GCAAACATAGGATGTCCGGATGTA 60.742 45.833 7.81 0.00 44.07 2.29
4975 6223 3.808728 CAAACATAGGATGTCCGGATGT 58.191 45.455 7.81 2.42 44.07 3.06
4976 6224 2.549754 GCAAACATAGGATGTCCGGATG 59.450 50.000 7.81 1.63 44.07 3.51
4977 6225 2.172505 TGCAAACATAGGATGTCCGGAT 59.827 45.455 7.81 0.00 44.07 4.18
4978 6226 1.557371 TGCAAACATAGGATGTCCGGA 59.443 47.619 0.00 0.00 44.07 5.14
4979 6227 1.670811 GTGCAAACATAGGATGTCCGG 59.329 52.381 0.00 0.00 44.07 5.14
4980 6228 2.355197 TGTGCAAACATAGGATGTCCG 58.645 47.619 0.00 0.00 44.07 4.79
4981 6229 4.782019 TTTGTGCAAACATAGGATGTCC 57.218 40.909 0.00 0.00 44.07 4.02
4982 6230 7.656707 AAAATTTGTGCAAACATAGGATGTC 57.343 32.000 0.00 0.00 44.07 3.06
5052 6300 6.874134 ACTACTGCTATTCACGAGACATTTTT 59.126 34.615 0.00 0.00 0.00 1.94
5053 6301 6.398918 ACTACTGCTATTCACGAGACATTTT 58.601 36.000 0.00 0.00 0.00 1.82
5054 6302 5.967088 ACTACTGCTATTCACGAGACATTT 58.033 37.500 0.00 0.00 0.00 2.32
5055 6303 5.125578 TGACTACTGCTATTCACGAGACATT 59.874 40.000 0.00 0.00 0.00 2.71
5056 6304 4.640647 TGACTACTGCTATTCACGAGACAT 59.359 41.667 0.00 0.00 0.00 3.06
5057 6305 4.007659 TGACTACTGCTATTCACGAGACA 58.992 43.478 0.00 0.00 0.00 3.41
5058 6306 4.617808 TGACTACTGCTATTCACGAGAC 57.382 45.455 0.00 0.00 0.00 3.36
5059 6307 4.438880 GCTTGACTACTGCTATTCACGAGA 60.439 45.833 0.00 0.00 0.00 4.04
5060 6308 3.794028 GCTTGACTACTGCTATTCACGAG 59.206 47.826 0.00 0.00 0.00 4.18
5061 6309 3.192633 TGCTTGACTACTGCTATTCACGA 59.807 43.478 0.00 0.00 0.00 4.35
5062 6310 3.511699 TGCTTGACTACTGCTATTCACG 58.488 45.455 0.00 0.00 0.00 4.35
5063 6311 4.208047 CGATGCTTGACTACTGCTATTCAC 59.792 45.833 0.00 0.00 0.00 3.18
5064 6312 4.097892 TCGATGCTTGACTACTGCTATTCA 59.902 41.667 0.00 0.00 0.00 2.57
5065 6313 4.611943 TCGATGCTTGACTACTGCTATTC 58.388 43.478 0.00 0.00 0.00 1.75
5066 6314 4.655762 TCGATGCTTGACTACTGCTATT 57.344 40.909 0.00 0.00 0.00 1.73
5067 6315 4.655762 TTCGATGCTTGACTACTGCTAT 57.344 40.909 0.00 0.00 0.00 2.97
5068 6316 4.450082 TTTCGATGCTTGACTACTGCTA 57.550 40.909 0.00 0.00 0.00 3.49
5069 6317 3.319137 TTTCGATGCTTGACTACTGCT 57.681 42.857 0.00 0.00 0.00 4.24
5070 6318 4.606457 ATTTTCGATGCTTGACTACTGC 57.394 40.909 0.00 0.00 0.00 4.40
5071 6319 5.931532 ACAATTTTCGATGCTTGACTACTG 58.068 37.500 7.97 0.00 0.00 2.74
5072 6320 6.560253 AACAATTTTCGATGCTTGACTACT 57.440 33.333 7.97 0.00 0.00 2.57


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

AutoCloner maintained by Alex Coulton.