Multiple sequence alignment - TraesCS2A01G074500

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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 TraesCS2A01G074500 chr2A 100.000 5776 0 0 1 5776 32915115 32920890 0.000000e+00 10667.0
1 TraesCS2A01G074500 chr2A 89.441 2112 150 36 2190 4292 33008052 33006005 0.000000e+00 2597.0
2 TraesCS2A01G074500 chr2A 91.197 1295 96 9 3493 4783 33023467 33022187 0.000000e+00 1744.0
3 TraesCS2A01G074500 chr2A 85.669 628 77 9 4290 4908 33005971 33005348 0.000000e+00 649.0
4 TraesCS2A01G074500 chr2A 76.253 998 131 51 4830 5776 33022183 33021241 3.200000e-117 433.0
5 TraesCS2A01G074500 chr2A 75.852 998 127 63 884 1869 33009133 33008238 2.510000e-108 403.0
6 TraesCS2A01G074500 chr2A 87.805 164 18 2 1387 1548 655311454 655311291 2.120000e-44 191.0
7 TraesCS2A01G074500 chr2A 95.000 80 4 0 3381 3460 33023546 33023467 6.080000e-25 126.0
8 TraesCS2A01G074500 chr2A 82.192 146 24 1 4681 4824 760506920 760507065 2.190000e-24 124.0
9 TraesCS2A01G074500 chr2A 86.364 110 12 2 1645 1754 108028337 108028231 3.660000e-22 117.0
10 TraesCS2A01G074500 chr2D 93.657 3169 148 26 2190 5338 30656916 30660051 0.000000e+00 4689.0
11 TraesCS2A01G074500 chr2D 84.185 1214 66 33 884 2062 30655888 30657010 0.000000e+00 1062.0
12 TraesCS2A01G074500 chr2D 82.048 830 113 25 3471 4292 630088399 630089200 0.000000e+00 675.0
13 TraesCS2A01G074500 chr2D 87.661 543 59 7 3471 4008 630635299 630634760 4.910000e-175 625.0
14 TraesCS2A01G074500 chr2D 85.841 339 19 14 5466 5776 30660176 30660513 3.340000e-87 333.0
15 TraesCS2A01G074500 chr2D 88.636 88 6 2 2089 2176 30657122 30657205 2.850000e-18 104.0
16 TraesCS2A01G074500 chr2B 91.782 3176 189 30 2418 5553 43801501 43804644 0.000000e+00 4353.0
17 TraesCS2A01G074500 chr2B 89.396 2433 160 34 3408 5776 50486958 50484560 0.000000e+00 2974.0
18 TraesCS2A01G074500 chr2B 90.052 2111 158 18 2190 4292 50627225 50629291 0.000000e+00 2687.0
19 TraesCS2A01G074500 chr2B 96.077 1198 38 6 2089 3284 50488171 50486981 0.000000e+00 1943.0
20 TraesCS2A01G074500 chr2B 82.101 1190 98 42 894 2052 50489408 50488303 0.000000e+00 911.0
21 TraesCS2A01G074500 chr2B 82.264 1060 118 33 4290 5326 50629325 50630337 0.000000e+00 852.0
22 TraesCS2A01G074500 chr2B 85.162 647 53 26 1423 2051 43800777 43801398 1.770000e-174 623.0
23 TraesCS2A01G074500 chr2B 85.413 569 69 7 3471 4035 773734832 773734274 3.880000e-161 579.0
24 TraesCS2A01G074500 chr2B 77.764 832 94 44 1061 1869 50626276 50627039 1.490000e-115 427.0
25 TraesCS2A01G074500 chr2B 79.534 386 28 23 971 1323 43799954 43800321 1.620000e-55 228.0
26 TraesCS2A01G074500 chr2B 86.979 192 14 2 2190 2380 43801314 43801495 7.590000e-49 206.0
27 TraesCS2A01G074500 chr2B 94.737 95 5 0 1968 2062 50488074 50487980 1.300000e-31 148.0
28 TraesCS2A01G074500 chr2B 80.137 146 27 1 4681 4824 773734279 773734134 2.200000e-19 108.0
29 TraesCS2A01G074500 chr1A 96.625 889 25 5 1 884 570045310 570046198 0.000000e+00 1471.0
30 TraesCS2A01G074500 chrUn 96.175 889 29 5 1 884 1715852 1716740 0.000000e+00 1448.0
31 TraesCS2A01G074500 chrUn 96.063 889 30 5 1 884 189302739 189303627 0.000000e+00 1443.0
32 TraesCS2A01G074500 chrUn 95.608 888 35 4 1 884 255003172 255002285 0.000000e+00 1421.0
33 TraesCS2A01G074500 chrUn 95.506 890 36 4 1 886 82679574 82680463 0.000000e+00 1419.0
34 TraesCS2A01G074500 chr5A 95.969 893 29 7 1 887 616364089 616364980 0.000000e+00 1443.0
35 TraesCS2A01G074500 chr5A 95.843 890 31 6 1 884 211619651 211620540 0.000000e+00 1434.0
36 TraesCS2A01G074500 chr3A 95.726 889 32 6 1 884 698713178 698712291 0.000000e+00 1426.0
37 TraesCS2A01G074500 chr3A 95.613 889 34 5 1 884 713896948 713896060 0.000000e+00 1421.0
38 TraesCS2A01G074500 chr6D 86.803 538 47 11 2198 2732 447021189 447020673 3.880000e-161 579.0
39 TraesCS2A01G074500 chr3B 85.793 542 55 10 2198 2736 697171596 697171074 6.540000e-154 555.0
40 TraesCS2A01G074500 chr3B 82.407 108 11 5 1624 1726 697171758 697171654 2.870000e-13 87.9
41 TraesCS2A01G074500 chr6B 86.747 166 21 1 1384 1548 485756897 485757062 3.550000e-42 183.0
42 TraesCS2A01G074500 chr7A 75.448 391 57 30 1395 1754 565752935 565752553 2.790000e-33 154.0


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 TraesCS2A01G074500 chr2A 32915115 32920890 5775 False 10667.000000 10667 100.000000 1 5776 1 chr2A.!!$F1 5775
1 TraesCS2A01G074500 chr2A 33005348 33009133 3785 True 1216.333333 2597 83.654000 884 4908 3 chr2A.!!$R3 4024
2 TraesCS2A01G074500 chr2A 33021241 33023546 2305 True 767.666667 1744 87.483333 3381 5776 3 chr2A.!!$R4 2395
3 TraesCS2A01G074500 chr2D 30655888 30660513 4625 False 1547.000000 4689 88.079750 884 5776 4 chr2D.!!$F2 4892
4 TraesCS2A01G074500 chr2D 630088399 630089200 801 False 675.000000 675 82.048000 3471 4292 1 chr2D.!!$F1 821
5 TraesCS2A01G074500 chr2D 630634760 630635299 539 True 625.000000 625 87.661000 3471 4008 1 chr2D.!!$R1 537
6 TraesCS2A01G074500 chr2B 50484560 50489408 4848 True 1494.000000 2974 90.577750 894 5776 4 chr2B.!!$R1 4882
7 TraesCS2A01G074500 chr2B 43799954 43804644 4690 False 1352.500000 4353 85.864250 971 5553 4 chr2B.!!$F1 4582
8 TraesCS2A01G074500 chr2B 50626276 50630337 4061 False 1322.000000 2687 83.360000 1061 5326 3 chr2B.!!$F2 4265
9 TraesCS2A01G074500 chr2B 773734134 773734832 698 True 343.500000 579 82.775000 3471 4824 2 chr2B.!!$R2 1353
10 TraesCS2A01G074500 chr1A 570045310 570046198 888 False 1471.000000 1471 96.625000 1 884 1 chr1A.!!$F1 883
11 TraesCS2A01G074500 chrUn 1715852 1716740 888 False 1448.000000 1448 96.175000 1 884 1 chrUn.!!$F1 883
12 TraesCS2A01G074500 chrUn 189302739 189303627 888 False 1443.000000 1443 96.063000 1 884 1 chrUn.!!$F3 883
13 TraesCS2A01G074500 chrUn 255002285 255003172 887 True 1421.000000 1421 95.608000 1 884 1 chrUn.!!$R1 883
14 TraesCS2A01G074500 chrUn 82679574 82680463 889 False 1419.000000 1419 95.506000 1 886 1 chrUn.!!$F2 885
15 TraesCS2A01G074500 chr5A 616364089 616364980 891 False 1443.000000 1443 95.969000 1 887 1 chr5A.!!$F2 886
16 TraesCS2A01G074500 chr5A 211619651 211620540 889 False 1434.000000 1434 95.843000 1 884 1 chr5A.!!$F1 883
17 TraesCS2A01G074500 chr3A 698712291 698713178 887 True 1426.000000 1426 95.726000 1 884 1 chr3A.!!$R1 883
18 TraesCS2A01G074500 chr3A 713896060 713896948 888 True 1421.000000 1421 95.613000 1 884 1 chr3A.!!$R2 883
19 TraesCS2A01G074500 chr6D 447020673 447021189 516 True 579.000000 579 86.803000 2198 2732 1 chr6D.!!$R1 534
20 TraesCS2A01G074500 chr3B 697171074 697171758 684 True 321.450000 555 84.100000 1624 2736 2 chr3B.!!$R1 1112

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
925 933 0.958091 CCCTGAGAGGAGCGATACAG 59.042 60.000 0.0 0.0 37.67 2.74 F
1336 1430 0.032615 TTCTTGCCCCCAGTTTGTGT 60.033 50.000 0.0 0.0 0.00 3.72 F
1337 1431 0.032615 TCTTGCCCCCAGTTTGTGTT 60.033 50.000 0.0 0.0 0.00 3.32 F
2122 2750 0.106918 TGCCCCAGTCGTTCTTTGTT 60.107 50.000 0.0 0.0 0.00 2.83 F
2123 2751 1.029681 GCCCCAGTCGTTCTTTGTTT 58.970 50.000 0.0 0.0 0.00 2.83 F
2124 2752 1.269051 GCCCCAGTCGTTCTTTGTTTG 60.269 52.381 0.0 0.0 0.00 2.93 F
2126 2754 1.676006 CCCAGTCGTTCTTTGTTTGCT 59.324 47.619 0.0 0.0 0.00 3.91 F
2127 2755 2.099098 CCCAGTCGTTCTTTGTTTGCTT 59.901 45.455 0.0 0.0 0.00 3.91 F
2304 3251 2.158856 CCTCCCAAACGTCCTATTACCC 60.159 54.545 0.0 0.0 0.00 3.69 F
3599 4567 2.352388 TCGCTTAATTGTGGGCACTAC 58.648 47.619 0.0 0.0 41.48 2.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2103 2731 0.106918 AACAAAGAACGACTGGGGCA 60.107 50.000 0.00 0.0 0.00 5.36 R
2397 3346 0.249398 ACATAACGACTGGGGCACTC 59.751 55.000 0.00 0.0 0.00 3.51 R
3092 4055 5.599999 AGCATTCCATAAGACGAGTAACT 57.400 39.130 0.00 0.0 0.00 2.24 R
3366 4333 2.872732 AGGTTAACAGTCTGACGAGGA 58.127 47.619 6.91 0.0 0.00 3.71 R
3599 4567 5.859114 CACTTATAGCTGTTAGATAGTGGCG 59.141 44.000 3.32 0.0 0.00 5.69 R
4204 5187 6.622427 TGATATCTGAGGATAGTACGAGGA 57.378 41.667 3.98 0.0 37.78 3.71 R
4298 5323 7.624549 TCTGAGCTAAAATGTTTATCCAGAGT 58.375 34.615 0.00 0.0 0.00 3.24 R
4315 5340 6.003950 AGTGGCAAACTTTATTTCTGAGCTA 58.996 36.000 0.00 0.0 34.57 3.32 R
4317 5342 5.126396 AGTGGCAAACTTTATTTCTGAGC 57.874 39.130 0.00 0.0 34.57 4.26 R
4884 5920 0.599204 CAGTAGTCGCGGGTTGTTGT 60.599 55.000 6.13 0.0 0.00 3.32 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
889 896 3.728385 GGCTGGAGATGCCCTAAATAT 57.272 47.619 0.00 0.00 44.32 1.28
890 897 3.350833 GGCTGGAGATGCCCTAAATATG 58.649 50.000 0.00 0.00 44.32 1.78
891 898 3.350833 GCTGGAGATGCCCTAAATATGG 58.649 50.000 0.00 0.00 34.97 2.74
925 933 0.958091 CCCTGAGAGGAGCGATACAG 59.042 60.000 0.00 0.00 37.67 2.74
928 936 2.890311 CCTGAGAGGAGCGATACAGAAT 59.110 50.000 0.00 0.00 37.67 2.40
932 940 4.646945 TGAGAGGAGCGATACAGAATTTCT 59.353 41.667 0.00 0.00 0.00 2.52
934 942 6.491745 TGAGAGGAGCGATACAGAATTTCTAT 59.508 38.462 0.00 0.00 0.00 1.98
949 957 3.565764 TTCTATACGAGACGAGGGGAA 57.434 47.619 0.00 0.00 32.31 3.97
963 978 3.348119 GAGGGGAAAAGCGAGAAAATCT 58.652 45.455 0.00 0.00 0.00 2.40
964 979 3.348119 AGGGGAAAAGCGAGAAAATCTC 58.652 45.455 0.00 0.00 40.06 2.75
966 981 3.127721 GGGGAAAAGCGAGAAAATCTCTG 59.872 47.826 5.88 1.47 41.26 3.35
967 982 4.003648 GGGAAAAGCGAGAAAATCTCTGA 58.996 43.478 5.88 0.00 41.26 3.27
968 983 4.094146 GGGAAAAGCGAGAAAATCTCTGAG 59.906 45.833 0.00 0.00 41.26 3.35
969 984 4.094146 GGAAAAGCGAGAAAATCTCTGAGG 59.906 45.833 4.59 0.00 41.26 3.86
1157 1199 4.379243 CAGACGGCGCTTCCCACT 62.379 66.667 6.90 0.00 0.00 4.00
1161 1203 3.121030 CGGCGCTTCCCACTTCAG 61.121 66.667 7.64 0.00 0.00 3.02
1210 1273 4.580835 GGTGAGTTCTCAGCGTCC 57.419 61.111 14.62 4.31 0.00 4.79
1213 1276 0.598562 GTGAGTTCTCAGCGTCCTGA 59.401 55.000 2.53 0.00 45.54 3.86
1222 1285 1.005340 CAGCGTCCTGAAGCATCTTC 58.995 55.000 7.76 0.00 41.77 2.87
1224 1287 0.458543 GCGTCCTGAAGCATCTTCGA 60.459 55.000 0.06 0.00 35.86 3.71
1239 1303 2.279451 CGATGGCGATTGCTCGGA 60.279 61.111 4.59 0.00 45.15 4.55
1299 1363 1.021968 GTGCGTCTGGGTGTTCTTTT 58.978 50.000 0.00 0.00 0.00 2.27
1335 1429 1.118838 TTTCTTGCCCCCAGTTTGTG 58.881 50.000 0.00 0.00 0.00 3.33
1336 1430 0.032615 TTCTTGCCCCCAGTTTGTGT 60.033 50.000 0.00 0.00 0.00 3.72
1337 1431 0.032615 TCTTGCCCCCAGTTTGTGTT 60.033 50.000 0.00 0.00 0.00 3.32
1338 1432 0.829990 CTTGCCCCCAGTTTGTGTTT 59.170 50.000 0.00 0.00 0.00 2.83
1339 1433 0.539051 TTGCCCCCAGTTTGTGTTTG 59.461 50.000 0.00 0.00 0.00 2.93
1340 1434 0.616111 TGCCCCCAGTTTGTGTTTGT 60.616 50.000 0.00 0.00 0.00 2.83
1344 1438 0.463620 CCCAGTTTGTGTTTGTGGGG 59.536 55.000 0.00 0.00 43.76 4.96
1350 1444 4.283212 CAGTTTGTGTTTGTGGGGGATATT 59.717 41.667 0.00 0.00 0.00 1.28
1357 1451 5.949952 GTGTTTGTGGGGGATATTAGTTCTT 59.050 40.000 0.00 0.00 0.00 2.52
1358 1452 5.949354 TGTTTGTGGGGGATATTAGTTCTTG 59.051 40.000 0.00 0.00 0.00 3.02
1380 1474 4.241555 GCTGTCGGATCGGGGCAT 62.242 66.667 0.00 0.00 0.00 4.40
1381 1475 2.029666 CTGTCGGATCGGGGCATC 59.970 66.667 0.00 0.00 0.00 3.91
1419 1514 1.285962 CATGGGGGATGAGTTCTTGGT 59.714 52.381 0.00 0.00 33.31 3.67
1509 2005 0.951040 CTTGCAGTTCGTGGGGAGAC 60.951 60.000 0.00 0.00 0.00 3.36
1556 2061 6.405731 CCCAAAATTGTGTTCTGAACTTCTGA 60.406 38.462 20.18 8.14 0.00 3.27
1557 2062 7.205297 CCAAAATTGTGTTCTGAACTTCTGAT 58.795 34.615 20.18 9.63 0.00 2.90
1558 2063 8.352201 CCAAAATTGTGTTCTGAACTTCTGATA 58.648 33.333 20.18 0.00 0.00 2.15
1559 2064 9.390795 CAAAATTGTGTTCTGAACTTCTGATAG 57.609 33.333 20.18 3.31 0.00 2.08
1560 2065 8.682936 AAATTGTGTTCTGAACTTCTGATAGT 57.317 30.769 20.18 0.00 0.00 2.12
1561 2066 8.682936 AATTGTGTTCTGAACTTCTGATAGTT 57.317 30.769 20.18 5.36 40.92 2.24
1626 2159 4.841813 TGTTCTGGTATTCCCTGTTCACTA 59.158 41.667 0.00 0.00 33.97 2.74
1637 2170 3.189287 CCCTGTTCACTACATTTGTGCTC 59.811 47.826 0.00 0.00 35.85 4.26
1668 2206 7.069986 TCCTCTTATACAAGGAATACTCTGCT 58.930 38.462 0.61 0.00 38.74 4.24
1700 2238 2.124942 GCTGGAAGAAGGGGAGCG 60.125 66.667 0.00 0.00 34.07 5.03
1762 2300 1.448069 GATTCGGAAGGGGAGCTCC 59.552 63.158 25.59 25.59 0.00 4.70
1763 2301 1.306997 ATTCGGAAGGGGAGCTCCA 60.307 57.895 33.29 11.44 37.91 3.86
1796 2334 4.087182 CCTGGTAACTTCCTCTCTACACA 58.913 47.826 0.00 0.00 37.61 3.72
2057 2685 1.629043 TCAGACCACCTGAGTGTACC 58.371 55.000 0.00 0.00 46.38 3.34
2058 2686 1.147191 TCAGACCACCTGAGTGTACCT 59.853 52.381 0.00 0.00 46.38 3.08
2059 2687 1.273606 CAGACCACCTGAGTGTACCTG 59.726 57.143 0.00 0.00 45.78 4.00
2060 2688 1.147191 AGACCACCTGAGTGTACCTGA 59.853 52.381 0.00 0.00 42.88 3.86
2061 2689 1.272769 GACCACCTGAGTGTACCTGAC 59.727 57.143 0.00 0.00 42.88 3.51
2062 2690 0.243907 CCACCTGAGTGTACCTGACG 59.756 60.000 0.00 0.00 42.88 4.35
2063 2691 0.243907 CACCTGAGTGTACCTGACGG 59.756 60.000 0.00 0.00 39.30 4.79
2064 2692 1.215647 CCTGAGTGTACCTGACGGC 59.784 63.158 0.00 0.00 0.00 5.68
2065 2693 1.215647 CTGAGTGTACCTGACGGCC 59.784 63.158 0.00 0.00 0.00 6.13
2066 2694 2.227089 CTGAGTGTACCTGACGGCCC 62.227 65.000 0.00 0.00 0.00 5.80
2067 2695 3.352338 GAGTGTACCTGACGGCCCG 62.352 68.421 0.00 0.00 0.00 6.13
2068 2696 3.376078 GTGTACCTGACGGCCCGA 61.376 66.667 11.71 0.00 0.00 5.14
2069 2697 2.601067 TGTACCTGACGGCCCGAA 60.601 61.111 11.71 0.00 0.00 4.30
2070 2698 1.985662 TGTACCTGACGGCCCGAAT 60.986 57.895 11.71 0.00 0.00 3.34
2071 2699 1.520787 GTACCTGACGGCCCGAATG 60.521 63.158 11.71 0.00 0.00 2.67
2072 2700 1.985662 TACCTGACGGCCCGAATGT 60.986 57.895 11.71 3.74 0.00 2.71
2073 2701 1.952102 TACCTGACGGCCCGAATGTC 61.952 60.000 11.71 0.00 0.00 3.06
2074 2702 2.579201 CTGACGGCCCGAATGTCT 59.421 61.111 11.71 0.00 33.81 3.41
2075 2703 1.079127 CTGACGGCCCGAATGTCTT 60.079 57.895 11.71 0.00 33.81 3.01
2076 2704 0.174845 CTGACGGCCCGAATGTCTTA 59.825 55.000 11.71 0.00 33.81 2.10
2077 2705 0.108520 TGACGGCCCGAATGTCTTAC 60.109 55.000 11.71 0.00 33.81 2.34
2078 2706 0.175073 GACGGCCCGAATGTCTTACT 59.825 55.000 11.71 0.00 0.00 2.24
2079 2707 1.406539 GACGGCCCGAATGTCTTACTA 59.593 52.381 11.71 0.00 0.00 1.82
2080 2708 2.035576 GACGGCCCGAATGTCTTACTAT 59.964 50.000 11.71 0.00 0.00 2.12
2081 2709 3.225104 ACGGCCCGAATGTCTTACTATA 58.775 45.455 11.71 0.00 0.00 1.31
2082 2710 3.830755 ACGGCCCGAATGTCTTACTATAT 59.169 43.478 11.71 0.00 0.00 0.86
2083 2711 5.012239 ACGGCCCGAATGTCTTACTATATA 58.988 41.667 11.71 0.00 0.00 0.86
2084 2712 5.477984 ACGGCCCGAATGTCTTACTATATAA 59.522 40.000 11.71 0.00 0.00 0.98
2085 2713 6.154021 ACGGCCCGAATGTCTTACTATATAAT 59.846 38.462 11.71 0.00 0.00 1.28
2086 2714 6.475727 CGGCCCGAATGTCTTACTATATAATG 59.524 42.308 0.00 0.00 0.00 1.90
2087 2715 6.761714 GGCCCGAATGTCTTACTATATAATGG 59.238 42.308 0.00 0.00 0.00 3.16
2088 2716 7.364408 GGCCCGAATGTCTTACTATATAATGGA 60.364 40.741 0.00 0.00 0.00 3.41
2089 2717 7.707035 GCCCGAATGTCTTACTATATAATGGAG 59.293 40.741 0.00 0.00 0.00 3.86
2090 2718 8.750298 CCCGAATGTCTTACTATATAATGGAGT 58.250 37.037 0.00 0.00 0.00 3.85
2105 2733 5.438761 AATGGAGTAAACTTGTTCAGTGC 57.561 39.130 0.00 0.00 35.12 4.40
2106 2734 3.211045 TGGAGTAAACTTGTTCAGTGCC 58.789 45.455 0.00 0.00 35.12 5.01
2107 2735 2.552743 GGAGTAAACTTGTTCAGTGCCC 59.447 50.000 0.00 0.00 35.12 5.36
2108 2736 2.552743 GAGTAAACTTGTTCAGTGCCCC 59.447 50.000 0.00 0.00 35.12 5.80
2109 2737 2.092103 AGTAAACTTGTTCAGTGCCCCA 60.092 45.455 0.00 0.00 35.12 4.96
2110 2738 1.402787 AAACTTGTTCAGTGCCCCAG 58.597 50.000 0.00 0.00 35.12 4.45
2111 2739 0.258774 AACTTGTTCAGTGCCCCAGT 59.741 50.000 0.00 0.00 35.12 4.00
2112 2740 0.179018 ACTTGTTCAGTGCCCCAGTC 60.179 55.000 0.00 0.00 32.83 3.51
2113 2741 1.227823 TTGTTCAGTGCCCCAGTCG 60.228 57.895 0.00 0.00 0.00 4.18
2114 2742 1.978455 TTGTTCAGTGCCCCAGTCGT 61.978 55.000 0.00 0.00 0.00 4.34
2115 2743 1.227853 GTTCAGTGCCCCAGTCGTT 60.228 57.895 0.00 0.00 0.00 3.85
2116 2744 1.070786 TTCAGTGCCCCAGTCGTTC 59.929 57.895 0.00 0.00 0.00 3.95
2117 2745 1.407656 TTCAGTGCCCCAGTCGTTCT 61.408 55.000 0.00 0.00 0.00 3.01
2118 2746 1.071471 CAGTGCCCCAGTCGTTCTT 59.929 57.895 0.00 0.00 0.00 2.52
2119 2747 0.535102 CAGTGCCCCAGTCGTTCTTT 60.535 55.000 0.00 0.00 0.00 2.52
2120 2748 0.535102 AGTGCCCCAGTCGTTCTTTG 60.535 55.000 0.00 0.00 0.00 2.77
2121 2749 0.818040 GTGCCCCAGTCGTTCTTTGT 60.818 55.000 0.00 0.00 0.00 2.83
2122 2750 0.106918 TGCCCCAGTCGTTCTTTGTT 60.107 50.000 0.00 0.00 0.00 2.83
2123 2751 1.029681 GCCCCAGTCGTTCTTTGTTT 58.970 50.000 0.00 0.00 0.00 2.83
2124 2752 1.269051 GCCCCAGTCGTTCTTTGTTTG 60.269 52.381 0.00 0.00 0.00 2.93
2125 2753 1.269051 CCCCAGTCGTTCTTTGTTTGC 60.269 52.381 0.00 0.00 0.00 3.68
2126 2754 1.676006 CCCAGTCGTTCTTTGTTTGCT 59.324 47.619 0.00 0.00 0.00 3.91
2127 2755 2.099098 CCCAGTCGTTCTTTGTTTGCTT 59.901 45.455 0.00 0.00 0.00 3.91
2128 2756 3.314080 CCCAGTCGTTCTTTGTTTGCTTA 59.686 43.478 0.00 0.00 0.00 3.09
2129 2757 4.279659 CCAGTCGTTCTTTGTTTGCTTAC 58.720 43.478 0.00 0.00 0.00 2.34
2130 2758 4.035208 CCAGTCGTTCTTTGTTTGCTTACT 59.965 41.667 0.00 0.00 0.00 2.24
2131 2759 4.963953 CAGTCGTTCTTTGTTTGCTTACTG 59.036 41.667 0.00 0.00 0.00 2.74
2132 2760 4.634443 AGTCGTTCTTTGTTTGCTTACTGT 59.366 37.500 0.00 0.00 0.00 3.55
2133 2761 5.123344 AGTCGTTCTTTGTTTGCTTACTGTT 59.877 36.000 0.00 0.00 0.00 3.16
2134 2762 5.798434 GTCGTTCTTTGTTTGCTTACTGTTT 59.202 36.000 0.00 0.00 0.00 2.83
2135 2763 6.307077 GTCGTTCTTTGTTTGCTTACTGTTTT 59.693 34.615 0.00 0.00 0.00 2.43
2136 2764 7.482428 GTCGTTCTTTGTTTGCTTACTGTTTTA 59.518 33.333 0.00 0.00 0.00 1.52
2137 2765 8.185505 TCGTTCTTTGTTTGCTTACTGTTTTAT 58.814 29.630 0.00 0.00 0.00 1.40
2138 2766 8.259194 CGTTCTTTGTTTGCTTACTGTTTTATG 58.741 33.333 0.00 0.00 0.00 1.90
2139 2767 9.083080 GTTCTTTGTTTGCTTACTGTTTTATGT 57.917 29.630 0.00 0.00 0.00 2.29
2173 2801 7.468922 TCTTAGATGTTGTATTGAGCAATCG 57.531 36.000 0.00 0.00 32.50 3.34
2174 2802 4.542662 AGATGTTGTATTGAGCAATCGC 57.457 40.909 0.00 0.00 38.99 4.58
2175 2803 3.940852 AGATGTTGTATTGAGCAATCGCA 59.059 39.130 0.00 0.00 42.27 5.10
2176 2804 4.395854 AGATGTTGTATTGAGCAATCGCAA 59.604 37.500 0.00 4.44 42.27 4.85
2177 2805 4.700268 TGTTGTATTGAGCAATCGCAAT 57.300 36.364 12.74 0.00 43.49 3.56
2178 2806 4.661125 TGTTGTATTGAGCAATCGCAATC 58.339 39.130 12.74 9.18 40.93 2.67
2179 2807 4.395854 TGTTGTATTGAGCAATCGCAATCT 59.604 37.500 12.74 0.00 40.93 2.40
2180 2808 5.106197 TGTTGTATTGAGCAATCGCAATCTT 60.106 36.000 12.74 0.00 40.93 2.40
2181 2809 6.093357 TGTTGTATTGAGCAATCGCAATCTTA 59.907 34.615 12.74 3.32 40.93 2.10
2182 2810 6.291067 TGTATTGAGCAATCGCAATCTTAG 57.709 37.500 0.00 0.00 40.93 2.18
2183 2811 6.048509 TGTATTGAGCAATCGCAATCTTAGA 58.951 36.000 0.00 0.00 40.93 2.10
2184 2812 6.707608 TGTATTGAGCAATCGCAATCTTAGAT 59.292 34.615 0.00 0.00 40.93 1.98
2185 2813 5.413969 TTGAGCAATCGCAATCTTAGATG 57.586 39.130 0.00 0.00 42.27 2.90
2186 2814 4.696455 TGAGCAATCGCAATCTTAGATGA 58.304 39.130 0.00 0.00 42.27 2.92
2187 2815 5.303165 TGAGCAATCGCAATCTTAGATGAT 58.697 37.500 0.00 0.00 42.27 2.45
2188 2816 5.178809 TGAGCAATCGCAATCTTAGATGATG 59.821 40.000 0.00 0.00 42.27 3.07
2189 2817 5.061853 AGCAATCGCAATCTTAGATGATGT 58.938 37.500 0.00 0.00 42.27 3.06
2190 2818 6.226052 AGCAATCGCAATCTTAGATGATGTA 58.774 36.000 0.00 0.00 42.27 2.29
2191 2819 6.707608 AGCAATCGCAATCTTAGATGATGTAA 59.292 34.615 0.00 0.00 42.27 2.41
2192 2820 7.014115 GCAATCGCAATCTTAGATGATGTAAG 58.986 38.462 3.15 3.15 38.36 2.34
2193 2821 6.718454 ATCGCAATCTTAGATGATGTAAGC 57.282 37.500 4.60 0.00 0.00 3.09
2194 2822 5.847304 TCGCAATCTTAGATGATGTAAGCT 58.153 37.500 4.60 0.00 0.00 3.74
2195 2823 5.923114 TCGCAATCTTAGATGATGTAAGCTC 59.077 40.000 4.60 0.00 0.00 4.09
2196 2824 5.925397 CGCAATCTTAGATGATGTAAGCTCT 59.075 40.000 4.60 0.00 0.00 4.09
2229 3168 6.203530 TGAAGTGAATGAACTCTGTAAAGCAG 59.796 38.462 0.00 0.00 46.34 4.24
2232 3171 6.870965 AGTGAATGAACTCTGTAAAGCAGTAG 59.129 38.462 0.00 0.00 45.23 2.57
2304 3251 2.158856 CCTCCCAAACGTCCTATTACCC 60.159 54.545 0.00 0.00 0.00 3.69
2365 3314 7.716560 TGACTATCACATGATATTTGGGAGTTG 59.283 37.037 0.00 0.00 36.53 3.16
2397 3346 5.437289 TCATTTCCACAGTAAGCTTGTTG 57.563 39.130 9.86 9.74 0.00 3.33
2509 3458 5.125356 TGATGTCGGCAGATGTTAAATGAT 58.875 37.500 0.00 0.00 0.00 2.45
2599 3552 5.997746 TCTTACCATGAAGTCCTCAGTTTTG 59.002 40.000 0.00 0.00 37.52 2.44
2677 3635 8.843262 CAAATCCATGCTCAAGTTAGATGAATA 58.157 33.333 0.00 0.00 0.00 1.75
3092 4055 5.474532 ACAGATGCAAGATAAACAAGCTGAA 59.525 36.000 0.00 0.00 0.00 3.02
3113 4076 5.810587 TGAAGTTACTCGTCTTATGGAATGC 59.189 40.000 0.00 0.00 0.00 3.56
3170 4133 3.997021 AGTGGAACAAAGCATACTTCTCG 59.003 43.478 0.00 0.00 44.16 4.04
3179 4142 5.866633 CAAAGCATACTTCTCGATAGATCCC 59.133 44.000 2.06 0.00 39.16 3.85
3366 4333 8.169977 TCTGAAAAATAACTGAACTCATGCTT 57.830 30.769 0.00 0.00 0.00 3.91
3462 4429 7.512130 ACAAATGGATAAGATGATGCAGAGTA 58.488 34.615 0.00 0.00 30.02 2.59
3547 4514 4.749099 TCAGTTTGCCATGTTTTATGTTGC 59.251 37.500 0.00 0.00 0.00 4.17
3599 4567 2.352388 TCGCTTAATTGTGGGCACTAC 58.648 47.619 0.00 0.00 41.48 2.73
3624 4592 6.515200 CGCCACTATCTAACAGCTATAAGTGT 60.515 42.308 0.00 0.00 0.00 3.55
4204 5187 2.556114 CCTCCAGGTGGAATTTCTGCTT 60.556 50.000 0.55 0.00 44.91 3.91
4220 5203 3.118000 TCTGCTTCCTCGTACTATCCTCA 60.118 47.826 0.00 0.00 0.00 3.86
4298 5323 7.630082 AGACTTGGCATACTAATTACCTTTCA 58.370 34.615 0.00 0.00 0.00 2.69
4315 5340 7.839680 ACCTTTCACTCTGGATAAACATTTT 57.160 32.000 0.00 0.00 0.00 1.82
4317 5342 9.014297 ACCTTTCACTCTGGATAAACATTTTAG 57.986 33.333 0.00 0.00 0.00 1.85
4351 5376 5.453567 AGTTTGCCACTAGTCAATTTTCC 57.546 39.130 0.00 0.00 31.97 3.13
4352 5377 4.280929 AGTTTGCCACTAGTCAATTTTCCC 59.719 41.667 0.00 0.00 31.97 3.97
4360 5385 7.628580 GCCACTAGTCAATTTTCCCTGATTTAC 60.629 40.741 0.00 0.00 0.00 2.01
4361 5386 7.393234 CCACTAGTCAATTTTCCCTGATTTACA 59.607 37.037 0.00 0.00 0.00 2.41
4393 5420 8.937634 AAGATAACCAGTACTACATTTTACCG 57.062 34.615 0.00 0.00 0.00 4.02
4407 5434 5.880332 ACATTTTACCGCTGACAGATTACAT 59.120 36.000 6.65 0.00 0.00 2.29
4409 5436 6.811253 TTTTACCGCTGACAGATTACATTT 57.189 33.333 6.65 0.00 0.00 2.32
4410 5437 6.811253 TTTACCGCTGACAGATTACATTTT 57.189 33.333 6.65 0.00 0.00 1.82
4411 5438 7.908827 TTTACCGCTGACAGATTACATTTTA 57.091 32.000 6.65 0.00 0.00 1.52
4412 5439 7.908827 TTACCGCTGACAGATTACATTTTAA 57.091 32.000 6.65 0.00 0.00 1.52
4454 5481 6.430451 GTTGTGATAACAGTTCTGTTGGAAG 58.570 40.000 23.14 0.00 34.23 3.46
4603 5630 3.274288 GCCTCGATTTCTTCCATGAGTT 58.726 45.455 0.00 0.00 0.00 3.01
4608 5635 3.926527 CGATTTCTTCCATGAGTTCGACA 59.073 43.478 0.00 0.00 0.00 4.35
4693 5720 0.179000 AAGCAGGGAAGCTACGATGG 59.821 55.000 0.00 0.00 45.89 3.51
4828 5858 4.357918 AACTTCCTCCGGGATGATTATG 57.642 45.455 0.00 0.00 41.87 1.90
4884 5920 1.300620 CGTTTGTCGGTCTGCTCCA 60.301 57.895 0.00 0.00 35.71 3.86
4885 5921 1.557443 CGTTTGTCGGTCTGCTCCAC 61.557 60.000 0.00 0.00 35.71 4.02
4895 5931 2.904866 TGCTCCACAACAACCCGC 60.905 61.111 0.00 0.00 0.00 6.13
4906 5967 2.094659 CAACCCGCGACTACTGCTG 61.095 63.158 8.23 0.00 0.00 4.41
4908 5969 4.435436 CCCGCGACTACTGCTGCA 62.435 66.667 8.23 0.88 0.00 4.41
5081 6155 4.025040 AGATTTGCAACATCAGACCTGA 57.975 40.909 17.89 1.83 44.59 3.86
5082 6156 4.401022 AGATTTGCAACATCAGACCTGAA 58.599 39.130 17.89 0.00 43.58 3.02
5132 6226 6.018425 ACAATTTCTATATGAGCTTGACTGCG 60.018 38.462 0.00 0.00 38.13 5.18
5207 6301 9.452287 TGAATAGAACATTGAATGTGAATCTGA 57.548 29.630 12.09 1.95 44.07 3.27
5211 6305 8.577048 AGAACATTGAATGTGAATCTGAATCT 57.423 30.769 12.09 4.69 44.07 2.40
5217 6311 7.137490 TGAATGTGAATCTGAATCTTGTGTC 57.863 36.000 0.00 0.00 0.00 3.67
5254 6348 2.501723 TGTCTTCACTGGCCTCTTATCC 59.498 50.000 3.32 0.00 0.00 2.59
5280 6376 5.582550 TCACACATAAGCGAGAGTGAATAG 58.417 41.667 8.91 0.00 33.55 1.73
5283 6379 4.979197 CACATAAGCGAGAGTGAATAGACC 59.021 45.833 0.00 0.00 33.99 3.85
5322 6418 1.685820 GCAGTGGGTTTCTAGGGCT 59.314 57.895 0.00 0.00 0.00 5.19
5349 6476 8.450964 TGAAATTCTGACTGAAATATCGAAACC 58.549 33.333 0.00 0.00 38.29 3.27
5353 6480 3.938963 TGACTGAAATATCGAAACCTGCC 59.061 43.478 0.00 0.00 0.00 4.85
5357 6484 4.340617 TGAAATATCGAAACCTGCCCTTT 58.659 39.130 0.00 0.00 0.00 3.11
5359 6486 3.933861 ATATCGAAACCTGCCCTTTCT 57.066 42.857 0.00 0.00 0.00 2.52
5361 6488 0.036306 TCGAAACCTGCCCTTTCTCC 59.964 55.000 0.00 0.00 0.00 3.71
5362 6489 0.250727 CGAAACCTGCCCTTTCTCCA 60.251 55.000 0.00 0.00 0.00 3.86
5364 6491 0.853530 AAACCTGCCCTTTCTCCAGT 59.146 50.000 0.00 0.00 0.00 4.00
5365 6492 0.111253 AACCTGCCCTTTCTCCAGTG 59.889 55.000 0.00 0.00 0.00 3.66
5366 6493 0.768221 ACCTGCCCTTTCTCCAGTGA 60.768 55.000 0.00 0.00 0.00 3.41
5367 6494 0.401738 CCTGCCCTTTCTCCAGTGAA 59.598 55.000 0.00 0.00 0.00 3.18
5368 6495 1.202927 CCTGCCCTTTCTCCAGTGAAA 60.203 52.381 0.00 0.00 35.07 2.69
5369 6496 2.586425 CTGCCCTTTCTCCAGTGAAAA 58.414 47.619 0.00 0.00 35.79 2.29
5370 6497 2.294512 CTGCCCTTTCTCCAGTGAAAAC 59.705 50.000 0.00 0.00 35.79 2.43
5371 6498 2.091885 TGCCCTTTCTCCAGTGAAAACT 60.092 45.455 0.00 0.00 35.79 2.66
5372 6499 2.959030 GCCCTTTCTCCAGTGAAAACTT 59.041 45.455 0.00 0.00 35.79 2.66
5373 6500 4.142038 GCCCTTTCTCCAGTGAAAACTTA 58.858 43.478 0.00 0.00 35.79 2.24
5374 6501 4.583073 GCCCTTTCTCCAGTGAAAACTTAA 59.417 41.667 0.00 0.00 35.79 1.85
5375 6502 5.068591 GCCCTTTCTCCAGTGAAAACTTAAA 59.931 40.000 0.00 0.00 35.79 1.52
5376 6503 6.735968 GCCCTTTCTCCAGTGAAAACTTAAAG 60.736 42.308 0.00 0.00 35.79 1.85
5377 6504 6.239036 CCCTTTCTCCAGTGAAAACTTAAAGG 60.239 42.308 0.00 0.00 39.94 3.11
5378 6505 5.767816 TTCTCCAGTGAAAACTTAAAGGC 57.232 39.130 0.00 0.00 0.00 4.35
5379 6506 5.048846 TCTCCAGTGAAAACTTAAAGGCT 57.951 39.130 0.00 0.00 0.00 4.58
5380 6507 6.182507 TCTCCAGTGAAAACTTAAAGGCTA 57.817 37.500 0.00 0.00 0.00 3.93
5381 6508 5.995897 TCTCCAGTGAAAACTTAAAGGCTAC 59.004 40.000 0.00 0.00 0.00 3.58
5382 6509 5.937111 TCCAGTGAAAACTTAAAGGCTACT 58.063 37.500 0.00 0.00 0.00 2.57
5383 6510 6.362248 TCCAGTGAAAACTTAAAGGCTACTT 58.638 36.000 0.00 0.00 38.99 2.24
5384 6511 7.511268 TCCAGTGAAAACTTAAAGGCTACTTA 58.489 34.615 0.00 0.00 35.41 2.24
5385 6512 8.161425 TCCAGTGAAAACTTAAAGGCTACTTAT 58.839 33.333 0.00 0.00 35.41 1.73
5386 6513 9.444600 CCAGTGAAAACTTAAAGGCTACTTATA 57.555 33.333 0.00 0.00 35.41 0.98
5442 6569 3.055094 TCTTAGGGAAGTGAACCATCTGC 60.055 47.826 0.00 0.00 34.03 4.26
5534 6676 4.460034 CCATTGATGTCTTGATGGTTGTCA 59.540 41.667 0.00 0.00 35.43 3.58
5617 6784 5.415701 TCAAAACTGAAGCCATCTATTGACC 59.584 40.000 0.00 0.00 0.00 4.02
5626 6793 6.959606 AGCCATCTATTGACCCTAACATAT 57.040 37.500 0.00 0.00 0.00 1.78
5657 6845 0.593128 CAACTCAAGGGCCTGAAACG 59.407 55.000 6.92 0.00 0.00 3.60
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
101 102 2.050350 CGACGCCCAACTCTCCCTA 61.050 63.158 0.00 0.00 0.00 3.53
132 133 1.863662 GAGGAAGTCGAGGTCGTGCA 61.864 60.000 0.00 0.00 40.80 4.57
415 417 1.856920 CTCCCTCTCCCTACCTCTCTT 59.143 57.143 0.00 0.00 0.00 2.85
416 418 1.529744 CTCCCTCTCCCTACCTCTCT 58.470 60.000 0.00 0.00 0.00 3.10
515 518 2.506217 CCTCGCACGCGTACACAT 60.506 61.111 13.44 0.00 40.74 3.21
852 857 2.348888 CCGCGTCCCAGTAAGGTCT 61.349 63.158 4.92 0.00 34.66 3.85
853 858 2.183555 CCGCGTCCCAGTAAGGTC 59.816 66.667 4.92 0.00 34.66 3.85
854 859 4.078516 GCCGCGTCCCAGTAAGGT 62.079 66.667 4.92 0.00 34.66 3.50
855 860 3.771160 AGCCGCGTCCCAGTAAGG 61.771 66.667 4.92 0.00 37.03 2.69
857 862 4.077184 CCAGCCGCGTCCCAGTAA 62.077 66.667 4.92 0.00 0.00 2.24
887 894 2.438254 CCCAACTGCTGCGCCATA 60.438 61.111 4.18 0.00 0.00 2.74
888 895 4.666253 ACCCAACTGCTGCGCCAT 62.666 61.111 4.18 0.00 0.00 4.40
892 899 4.335647 AGGGACCCAACTGCTGCG 62.336 66.667 14.60 0.00 0.00 5.18
925 933 4.518211 TCCCCTCGTCTCGTATAGAAATTC 59.482 45.833 0.00 0.00 35.47 2.17
928 936 3.565764 TCCCCTCGTCTCGTATAGAAA 57.434 47.619 0.00 0.00 35.47 2.52
932 940 2.360165 GCTTTTCCCCTCGTCTCGTATA 59.640 50.000 0.00 0.00 0.00 1.47
934 942 0.529378 GCTTTTCCCCTCGTCTCGTA 59.471 55.000 0.00 0.00 0.00 3.43
963 978 1.005924 GCCCATTTCTTTCCCCTCAGA 59.994 52.381 0.00 0.00 0.00 3.27
964 979 1.478631 GCCCATTTCTTTCCCCTCAG 58.521 55.000 0.00 0.00 0.00 3.35
966 981 0.687757 GGGCCCATTTCTTTCCCCTC 60.688 60.000 19.95 0.00 0.00 4.30
967 982 1.392131 GGGCCCATTTCTTTCCCCT 59.608 57.895 19.95 0.00 0.00 4.79
968 983 2.058001 CGGGCCCATTTCTTTCCCC 61.058 63.158 24.92 0.00 33.43 4.81
969 984 0.613572 TTCGGGCCCATTTCTTTCCC 60.614 55.000 24.92 0.00 0.00 3.97
1073 1088 2.805546 GTCGGTCTAGCATCGCCA 59.194 61.111 0.00 0.00 0.00 5.69
1129 1171 3.432588 CCGTCTGGTCGCGAGAGT 61.433 66.667 10.24 0.00 43.49 3.24
1210 1273 0.580578 CGCCATCGAAGATGCTTCAG 59.419 55.000 7.81 1.57 45.12 3.02
1222 1285 2.279451 TCCGAGCAATCGCCATCG 60.279 61.111 0.00 0.00 39.83 3.84
1224 1287 0.969149 TATCTCCGAGCAATCGCCAT 59.031 50.000 0.00 0.00 39.83 4.40
1239 1303 7.869800 GGAAGATGATTCTTGCGAAAATATCT 58.130 34.615 0.00 0.00 42.34 1.98
1258 1322 2.747446 CAAATTTCACCGACCGGAAGAT 59.253 45.455 16.07 1.19 38.96 2.40
1259 1323 2.147958 CAAATTTCACCGACCGGAAGA 58.852 47.619 16.07 9.55 38.96 2.87
1260 1324 1.199097 CCAAATTTCACCGACCGGAAG 59.801 52.381 16.07 7.33 38.96 3.46
1261 1325 1.240256 CCAAATTTCACCGACCGGAA 58.760 50.000 16.07 0.00 38.96 4.30
1299 1363 1.673920 GAAACAGGCCAAGAACGACAA 59.326 47.619 5.01 0.00 0.00 3.18
1335 1429 5.359860 CCAAGAACTAATATCCCCCACAAAC 59.640 44.000 0.00 0.00 0.00 2.93
1336 1430 5.515106 CCAAGAACTAATATCCCCCACAAA 58.485 41.667 0.00 0.00 0.00 2.83
1337 1431 4.630184 GCCAAGAACTAATATCCCCCACAA 60.630 45.833 0.00 0.00 0.00 3.33
1338 1432 3.117663 GCCAAGAACTAATATCCCCCACA 60.118 47.826 0.00 0.00 0.00 4.17
1339 1433 3.138468 AGCCAAGAACTAATATCCCCCAC 59.862 47.826 0.00 0.00 0.00 4.61
1340 1434 3.138283 CAGCCAAGAACTAATATCCCCCA 59.862 47.826 0.00 0.00 0.00 4.96
1344 1438 3.817647 CAGCCAGCCAAGAACTAATATCC 59.182 47.826 0.00 0.00 0.00 2.59
1350 1444 0.037326 CGACAGCCAGCCAAGAACTA 60.037 55.000 0.00 0.00 0.00 2.24
1357 1451 4.147449 CGATCCGACAGCCAGCCA 62.147 66.667 0.00 0.00 0.00 4.75
1358 1452 4.899239 CCGATCCGACAGCCAGCC 62.899 72.222 0.00 0.00 0.00 4.85
1467 1961 1.609635 TTGCAGAAGGGTCCGCGATA 61.610 55.000 8.23 0.00 0.00 2.92
1468 1962 2.859273 CTTGCAGAAGGGTCCGCGAT 62.859 60.000 8.23 0.00 0.00 4.58
1509 2005 4.142249 GGTCAAATTAGAAAATCCCACCCG 60.142 45.833 0.00 0.00 0.00 5.28
1556 2061 6.372659 CAGCTGATTGTACCAAGAACAACTAT 59.627 38.462 8.42 0.00 39.51 2.12
1557 2062 5.700832 CAGCTGATTGTACCAAGAACAACTA 59.299 40.000 8.42 0.00 39.51 2.24
1558 2063 4.516698 CAGCTGATTGTACCAAGAACAACT 59.483 41.667 8.42 0.00 39.51 3.16
1559 2064 4.515191 TCAGCTGATTGTACCAAGAACAAC 59.485 41.667 13.74 0.00 39.51 3.32
1560 2065 4.713553 TCAGCTGATTGTACCAAGAACAA 58.286 39.130 13.74 0.00 40.85 2.83
1561 2066 4.350368 TCAGCTGATTGTACCAAGAACA 57.650 40.909 13.74 0.00 0.00 3.18
1626 2159 4.074970 AGAGGAATTTCGAGCACAAATGT 58.925 39.130 0.00 0.00 0.00 2.71
1661 2199 4.141824 GCTCCACCTAGAAAATAGCAGAGT 60.142 45.833 0.00 0.00 0.00 3.24
1666 2204 3.134804 TCCAGCTCCACCTAGAAAATAGC 59.865 47.826 0.00 0.00 0.00 2.97
1668 2206 5.030147 TCTTCCAGCTCCACCTAGAAAATA 58.970 41.667 0.00 0.00 0.00 1.40
1700 2238 4.262981 CCCCTGAATCTTCATCATCTCCTC 60.263 50.000 0.00 0.00 36.46 3.71
1763 2301 1.132495 AGTTACCAGGAAGTGACCCCT 60.132 52.381 0.00 0.00 0.00 4.79
1796 2334 2.739943 TCCTCGGATCACTCATGAAGT 58.260 47.619 0.00 0.00 38.69 3.01
1811 2349 6.691508 TGATATCATCTGGTATGTTTCCTCG 58.308 40.000 0.00 0.00 0.00 4.63
2051 2679 2.234913 ATTCGGGCCGTCAGGTACAC 62.235 60.000 27.32 0.00 40.50 2.90
2056 2684 2.511600 GACATTCGGGCCGTCAGG 60.512 66.667 27.32 17.67 41.62 3.86
2057 2685 0.174845 TAAGACATTCGGGCCGTCAG 59.825 55.000 27.32 18.15 31.92 3.51
2058 2686 0.108520 GTAAGACATTCGGGCCGTCA 60.109 55.000 27.32 14.63 31.92 4.35
2059 2687 0.175073 AGTAAGACATTCGGGCCGTC 59.825 55.000 27.32 16.16 0.00 4.79
2060 2688 1.477553 TAGTAAGACATTCGGGCCGT 58.522 50.000 27.32 6.05 0.00 5.68
2061 2689 2.814280 ATAGTAAGACATTCGGGCCG 57.186 50.000 22.51 22.51 0.00 6.13
2062 2690 6.761714 CCATTATATAGTAAGACATTCGGGCC 59.238 42.308 0.00 0.00 0.00 5.80
2063 2691 7.553334 TCCATTATATAGTAAGACATTCGGGC 58.447 38.462 0.00 0.00 0.00 6.13
2064 2692 8.750298 ACTCCATTATATAGTAAGACATTCGGG 58.250 37.037 0.00 0.00 0.00 5.14
2079 2707 8.893727 GCACTGAACAAGTTTACTCCATTATAT 58.106 33.333 0.00 0.00 36.83 0.86
2080 2708 7.335924 GGCACTGAACAAGTTTACTCCATTATA 59.664 37.037 0.00 0.00 36.83 0.98
2081 2709 6.151144 GGCACTGAACAAGTTTACTCCATTAT 59.849 38.462 0.00 0.00 36.83 1.28
2082 2710 5.472137 GGCACTGAACAAGTTTACTCCATTA 59.528 40.000 0.00 0.00 36.83 1.90
2083 2711 4.278419 GGCACTGAACAAGTTTACTCCATT 59.722 41.667 0.00 0.00 36.83 3.16
2084 2712 3.821033 GGCACTGAACAAGTTTACTCCAT 59.179 43.478 0.00 0.00 36.83 3.41
2085 2713 3.211045 GGCACTGAACAAGTTTACTCCA 58.789 45.455 0.00 0.00 36.83 3.86
2086 2714 2.552743 GGGCACTGAACAAGTTTACTCC 59.447 50.000 0.00 0.00 36.83 3.85
2087 2715 2.552743 GGGGCACTGAACAAGTTTACTC 59.447 50.000 0.00 0.00 36.83 2.59
2088 2716 2.092103 TGGGGCACTGAACAAGTTTACT 60.092 45.455 0.00 0.00 36.83 2.24
2089 2717 2.293399 CTGGGGCACTGAACAAGTTTAC 59.707 50.000 0.00 0.00 36.83 2.01
2090 2718 2.092103 ACTGGGGCACTGAACAAGTTTA 60.092 45.455 0.00 0.00 36.83 2.01
2091 2719 1.341976 ACTGGGGCACTGAACAAGTTT 60.342 47.619 0.00 0.00 36.83 2.66
2092 2720 0.258774 ACTGGGGCACTGAACAAGTT 59.741 50.000 0.00 0.00 36.83 2.66
2093 2721 0.179018 GACTGGGGCACTGAACAAGT 60.179 55.000 0.00 0.00 40.93 3.16
2094 2722 1.230635 CGACTGGGGCACTGAACAAG 61.231 60.000 0.00 0.00 0.00 3.16
2095 2723 1.227823 CGACTGGGGCACTGAACAA 60.228 57.895 0.00 0.00 0.00 2.83
2096 2724 1.978455 AACGACTGGGGCACTGAACA 61.978 55.000 0.00 0.00 0.00 3.18
2097 2725 1.227853 AACGACTGGGGCACTGAAC 60.228 57.895 0.00 0.00 0.00 3.18
2098 2726 1.070786 GAACGACTGGGGCACTGAA 59.929 57.895 0.00 0.00 0.00 3.02
2099 2727 1.407656 AAGAACGACTGGGGCACTGA 61.408 55.000 0.00 0.00 0.00 3.41
2100 2728 0.535102 AAAGAACGACTGGGGCACTG 60.535 55.000 0.00 0.00 0.00 3.66
2101 2729 0.535102 CAAAGAACGACTGGGGCACT 60.535 55.000 0.00 0.00 0.00 4.40
2102 2730 0.818040 ACAAAGAACGACTGGGGCAC 60.818 55.000 0.00 0.00 0.00 5.01
2103 2731 0.106918 AACAAAGAACGACTGGGGCA 60.107 50.000 0.00 0.00 0.00 5.36
2104 2732 1.029681 AAACAAAGAACGACTGGGGC 58.970 50.000 0.00 0.00 0.00 5.80
2105 2733 1.269051 GCAAACAAAGAACGACTGGGG 60.269 52.381 0.00 0.00 0.00 4.96
2106 2734 1.676006 AGCAAACAAAGAACGACTGGG 59.324 47.619 0.00 0.00 0.00 4.45
2107 2735 3.420839 AAGCAAACAAAGAACGACTGG 57.579 42.857 0.00 0.00 0.00 4.00
2108 2736 4.963953 CAGTAAGCAAACAAAGAACGACTG 59.036 41.667 0.00 0.00 0.00 3.51
2109 2737 4.634443 ACAGTAAGCAAACAAAGAACGACT 59.366 37.500 0.00 0.00 0.00 4.18
2110 2738 4.905269 ACAGTAAGCAAACAAAGAACGAC 58.095 39.130 0.00 0.00 0.00 4.34
2111 2739 5.554822 AACAGTAAGCAAACAAAGAACGA 57.445 34.783 0.00 0.00 0.00 3.85
2112 2740 6.626199 AAAACAGTAAGCAAACAAAGAACG 57.374 33.333 0.00 0.00 0.00 3.95
2113 2741 9.083080 ACATAAAACAGTAAGCAAACAAAGAAC 57.917 29.630 0.00 0.00 0.00 3.01
2147 2775 8.554528 CGATTGCTCAATACAACATCTAAGATT 58.445 33.333 0.00 0.00 0.00 2.40
2148 2776 7.307632 GCGATTGCTCAATACAACATCTAAGAT 60.308 37.037 0.00 0.00 38.39 2.40
2149 2777 6.018751 GCGATTGCTCAATACAACATCTAAGA 60.019 38.462 0.00 0.00 38.39 2.10
2150 2778 6.132056 GCGATTGCTCAATACAACATCTAAG 58.868 40.000 0.00 0.00 38.39 2.18
2151 2779 5.584251 TGCGATTGCTCAATACAACATCTAA 59.416 36.000 6.47 0.00 43.34 2.10
2152 2780 5.115480 TGCGATTGCTCAATACAACATCTA 58.885 37.500 6.47 0.00 43.34 1.98
2153 2781 3.940852 TGCGATTGCTCAATACAACATCT 59.059 39.130 6.47 0.00 43.34 2.90
2154 2782 4.277257 TGCGATTGCTCAATACAACATC 57.723 40.909 6.47 0.00 43.34 3.06
2155 2783 4.700268 TTGCGATTGCTCAATACAACAT 57.300 36.364 6.47 0.00 43.34 2.71
2156 2784 4.395854 AGATTGCGATTGCTCAATACAACA 59.604 37.500 6.47 0.01 43.34 3.33
2157 2785 4.913376 AGATTGCGATTGCTCAATACAAC 58.087 39.130 6.47 7.13 43.34 3.32
2158 2786 5.565592 AAGATTGCGATTGCTCAATACAA 57.434 34.783 6.47 10.83 43.34 2.41
2159 2787 6.048509 TCTAAGATTGCGATTGCTCAATACA 58.951 36.000 6.47 0.00 43.34 2.29
2160 2788 6.530913 TCTAAGATTGCGATTGCTCAATAC 57.469 37.500 6.47 0.00 43.34 1.89
2161 2789 6.930722 TCATCTAAGATTGCGATTGCTCAATA 59.069 34.615 6.47 0.00 43.34 1.90
2162 2790 5.761726 TCATCTAAGATTGCGATTGCTCAAT 59.238 36.000 6.47 0.00 43.34 2.57
2163 2791 5.118286 TCATCTAAGATTGCGATTGCTCAA 58.882 37.500 6.47 0.00 43.34 3.02
2164 2792 4.696455 TCATCTAAGATTGCGATTGCTCA 58.304 39.130 6.47 0.00 43.34 4.26
2165 2793 5.178996 ACATCATCTAAGATTGCGATTGCTC 59.821 40.000 6.47 0.00 43.34 4.26
2166 2794 5.061853 ACATCATCTAAGATTGCGATTGCT 58.938 37.500 6.47 0.00 43.34 3.91
2167 2795 5.354054 ACATCATCTAAGATTGCGATTGC 57.646 39.130 0.00 0.00 43.20 3.56
2168 2796 7.014115 GCTTACATCATCTAAGATTGCGATTG 58.986 38.462 0.00 0.00 0.00 2.67
2169 2797 6.933521 AGCTTACATCATCTAAGATTGCGATT 59.066 34.615 0.00 0.00 0.00 3.34
2170 2798 6.462500 AGCTTACATCATCTAAGATTGCGAT 58.538 36.000 0.00 0.00 0.00 4.58
2171 2799 5.847304 AGCTTACATCATCTAAGATTGCGA 58.153 37.500 0.00 0.00 0.00 5.10
2172 2800 5.925397 AGAGCTTACATCATCTAAGATTGCG 59.075 40.000 0.00 0.00 0.00 4.85
2173 2801 7.440556 TGAAGAGCTTACATCATCTAAGATTGC 59.559 37.037 0.00 0.00 0.00 3.56
2174 2802 8.883954 TGAAGAGCTTACATCATCTAAGATTG 57.116 34.615 0.00 0.00 0.00 2.67
2175 2803 9.323985 GTTGAAGAGCTTACATCATCTAAGATT 57.676 33.333 0.00 0.00 0.00 2.40
2176 2804 7.930865 GGTTGAAGAGCTTACATCATCTAAGAT 59.069 37.037 0.00 0.00 0.00 2.40
2177 2805 7.093333 TGGTTGAAGAGCTTACATCATCTAAGA 60.093 37.037 0.00 0.00 0.00 2.10
2178 2806 7.044181 TGGTTGAAGAGCTTACATCATCTAAG 58.956 38.462 0.00 0.00 0.00 2.18
2179 2807 6.946340 TGGTTGAAGAGCTTACATCATCTAA 58.054 36.000 0.00 0.00 0.00 2.10
2180 2808 6.544928 TGGTTGAAGAGCTTACATCATCTA 57.455 37.500 0.00 0.00 0.00 1.98
2181 2809 5.426689 TGGTTGAAGAGCTTACATCATCT 57.573 39.130 0.00 0.00 0.00 2.90
2182 2810 5.819379 TCATGGTTGAAGAGCTTACATCATC 59.181 40.000 0.00 0.00 0.00 2.92
2183 2811 5.748402 TCATGGTTGAAGAGCTTACATCAT 58.252 37.500 0.00 0.00 0.00 2.45
2184 2812 5.164620 TCATGGTTGAAGAGCTTACATCA 57.835 39.130 0.00 0.00 0.00 3.07
2196 2824 6.016860 CAGAGTTCATTCACTTCATGGTTGAA 60.017 38.462 6.91 6.91 39.54 2.69
2229 3168 4.031878 CCGAGCACGAAAAAGAGAATCTAC 59.968 45.833 4.70 0.00 44.06 2.59
2232 3171 2.737252 ACCGAGCACGAAAAAGAGAATC 59.263 45.455 4.70 0.00 42.66 2.52
2365 3314 5.320549 ACTGTGGAAATGATTGAGAATGC 57.679 39.130 0.00 0.00 0.00 3.56
2397 3346 0.249398 ACATAACGACTGGGGCACTC 59.751 55.000 0.00 0.00 0.00 3.51
2599 3552 7.278868 TGTTTTTATGGTTTTCACACATGGAAC 59.721 33.333 0.00 0.00 0.00 3.62
2677 3635 9.931698 ATTAAGGTATGATGGATGATATGCAAT 57.068 29.630 0.00 0.00 33.18 3.56
3092 4055 5.599999 AGCATTCCATAAGACGAGTAACT 57.400 39.130 0.00 0.00 0.00 2.24
3366 4333 2.872732 AGGTTAACAGTCTGACGAGGA 58.127 47.619 6.91 0.00 0.00 3.71
3547 4514 8.659491 TGAAATCGAAACTACAATCATCAAGAG 58.341 33.333 0.00 0.00 0.00 2.85
3599 4567 5.859114 CACTTATAGCTGTTAGATAGTGGCG 59.141 44.000 3.32 0.00 0.00 5.69
4204 5187 6.622427 TGATATCTGAGGATAGTACGAGGA 57.378 41.667 3.98 0.00 37.78 3.71
4298 5323 7.624549 TCTGAGCTAAAATGTTTATCCAGAGT 58.375 34.615 0.00 0.00 0.00 3.24
4315 5340 6.003950 AGTGGCAAACTTTATTTCTGAGCTA 58.996 36.000 0.00 0.00 34.57 3.32
4317 5342 5.126396 AGTGGCAAACTTTATTTCTGAGC 57.874 39.130 0.00 0.00 34.57 4.26
4378 5405 5.404946 TCTGTCAGCGGTAAAATGTAGTAC 58.595 41.667 0.00 0.00 0.00 2.73
4385 5412 7.391148 AAATGTAATCTGTCAGCGGTAAAAT 57.609 32.000 0.00 0.00 0.00 1.82
4526 5553 1.484227 CCACGACTTCGACACGCAAA 61.484 55.000 5.47 0.00 43.02 3.68
4603 5630 2.367202 GGGCCCTTCTCCATGTCGA 61.367 63.158 17.04 0.00 0.00 4.20
4608 5635 1.385206 GGAGAGGGCCCTTCTCCAT 60.385 63.158 39.10 21.32 46.82 3.41
4663 5690 0.750850 TCCCTGCTTCAGCGGTATAC 59.249 55.000 6.87 0.00 45.66 1.47
4693 5720 2.735663 CCATCAGATGATAGCAAGTCGC 59.264 50.000 12.41 0.00 34.70 5.19
4828 5858 2.107726 AGGACTGTTACAAGGTTTCCCC 59.892 50.000 0.00 0.00 0.00 4.81
4838 5868 6.008331 ACACACACTATAGAGGACTGTTACA 58.992 40.000 6.78 0.00 0.00 2.41
4848 5878 1.476891 ACGGCCACACACACTATAGAG 59.523 52.381 6.78 0.31 0.00 2.43
4850 5880 2.380084 AACGGCCACACACACTATAG 57.620 50.000 2.24 0.00 0.00 1.31
4884 5920 0.599204 CAGTAGTCGCGGGTTGTTGT 60.599 55.000 6.13 0.00 0.00 3.32
4885 5921 1.897398 GCAGTAGTCGCGGGTTGTTG 61.897 60.000 6.13 0.00 0.00 3.33
4895 5931 1.512926 AAACCTTGCAGCAGTAGTCG 58.487 50.000 0.00 0.00 0.00 4.18
4908 5969 6.068010 TGACATGTCATTCAAGGTAAACCTT 58.932 36.000 24.56 8.63 45.00 3.50
4930 5991 0.694771 AACCAAGGAGCAGAGCATGA 59.305 50.000 0.00 0.00 0.00 3.07
5033 6095 6.680378 GCACACAACAGTATCCCAATAATTCC 60.680 42.308 0.00 0.00 0.00 3.01
5105 6199 8.830580 GCAGTCAAGCTCATATAGAAATTGTTA 58.169 33.333 0.00 0.00 0.00 2.41
5106 6200 7.466455 CGCAGTCAAGCTCATATAGAAATTGTT 60.466 37.037 0.00 0.00 0.00 2.83
5107 6201 6.018425 CGCAGTCAAGCTCATATAGAAATTGT 60.018 38.462 0.00 0.00 0.00 2.71
5115 6209 3.742882 GCATTCGCAGTCAAGCTCATATA 59.257 43.478 0.00 0.00 38.36 0.86
5193 6287 6.711645 TGACACAAGATTCAGATTCACATTCA 59.288 34.615 0.00 0.00 0.00 2.57
5234 6328 2.158885 GGGATAAGAGGCCAGTGAAGAC 60.159 54.545 5.01 0.00 0.00 3.01
5254 6348 2.926200 CACTCTCGCTTATGTGTGAAGG 59.074 50.000 0.00 0.00 31.69 3.46
5296 6392 0.820871 GAAACCCACTGCCACAAACA 59.179 50.000 0.00 0.00 0.00 2.83
5322 6418 9.825972 GTTTCGATATTTCAGTCAGAATTTCAA 57.174 29.630 0.00 0.00 35.83 2.69
5349 6476 2.276732 TTTCACTGGAGAAAGGGCAG 57.723 50.000 0.00 0.00 32.88 4.85
5353 6480 6.735968 GCCTTTAAGTTTTCACTGGAGAAAGG 60.736 42.308 0.00 0.00 39.58 3.11
5357 6484 5.048846 AGCCTTTAAGTTTTCACTGGAGA 57.951 39.130 0.00 0.00 31.60 3.71
5359 6486 5.937111 AGTAGCCTTTAAGTTTTCACTGGA 58.063 37.500 0.00 0.00 31.60 3.86
5373 6500 9.740710 AGTTTCAAGAACATATAAGTAGCCTTT 57.259 29.630 0.00 0.00 31.89 3.11
5374 6501 9.740710 AAGTTTCAAGAACATATAAGTAGCCTT 57.259 29.630 0.00 0.00 34.56 4.35
5384 6511 9.740710 AGTAGCCTTTAAGTTTCAAGAACATAT 57.259 29.630 0.00 0.00 0.00 1.78
5385 6512 9.569122 AAGTAGCCTTTAAGTTTCAAGAACATA 57.431 29.630 0.00 0.00 0.00 2.29
5386 6513 8.465273 AAGTAGCCTTTAAGTTTCAAGAACAT 57.535 30.769 0.00 0.00 0.00 2.71
5387 6514 7.875327 AAGTAGCCTTTAAGTTTCAAGAACA 57.125 32.000 0.00 0.00 0.00 3.18
5512 6654 5.632244 TGACAACCATCAAGACATCAATG 57.368 39.130 0.00 0.00 0.00 2.82
5534 6676 8.997621 TTTACTATAGTGCGAAACTCATCTTT 57.002 30.769 15.90 0.00 40.56 2.52
5657 6845 5.527582 ACCTACGATTGCCAAATTATCTGTC 59.472 40.000 0.00 0.00 0.00 3.51


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

AutoCloner maintained by Alex Coulton.