Multiple sequence alignment - TraesCS5B01G502100

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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 TraesCS5B01G502100 chr5B 100.000 3228 0 0 1 3228 669307562 669304335 0.000000e+00 5962.0
1 TraesCS5B01G502100 chr5D 84.875 1600 114 61 1268 2794 530073512 530071968 0.000000e+00 1496.0
2 TraesCS5B01G502100 chr5D 94.982 817 41 0 1 817 199005264 199004448 0.000000e+00 1282.0
3 TraesCS5B01G502100 chr5D 89.648 454 33 6 815 1257 530073928 530073478 1.680000e-157 566.0
4 TraesCS5B01G502100 chr3D 95.471 817 37 0 1 817 179919101 179918285 0.000000e+00 1304.0
5 TraesCS5B01G502100 chr3D 84.615 65 7 3 838 900 554781312 554781249 9.670000e-06 62.1
6 TraesCS5B01G502100 chr3A 95.104 817 40 0 1 817 489306366 489307182 0.000000e+00 1288.0
7 TraesCS5B01G502100 chr6B 94.859 817 42 0 1 817 712053155 712053971 0.000000e+00 1277.0
8 TraesCS5B01G502100 chr6B 95.556 45 1 1 831 874 256481581 256481537 1.610000e-08 71.3
9 TraesCS5B01G502100 chr6B 100.000 30 0 0 844 873 214058111 214058140 4.500000e-04 56.5
10 TraesCS5B01G502100 chr3B 94.614 817 44 0 1 817 605292034 605291218 0.000000e+00 1266.0
11 TraesCS5B01G502100 chr3B 94.370 817 46 0 1 817 739219194 739218378 0.000000e+00 1254.0
12 TraesCS5B01G502100 chr7A 94.492 817 45 0 1 817 33526825 33527641 0.000000e+00 1260.0
13 TraesCS5B01G502100 chr6D 94.010 818 48 1 1 817 423164946 423165763 0.000000e+00 1238.0
14 TraesCS5B01G502100 chr1B 93.865 815 49 1 1 815 428617927 428617114 0.000000e+00 1227.0
15 TraesCS5B01G502100 chr5A 88.127 977 87 15 1268 2231 657998097 657997137 0.000000e+00 1134.0
16 TraesCS5B01G502100 chr5A 84.923 325 19 17 964 1261 657998380 657998059 5.230000e-78 302.0
17 TraesCS5B01G502100 chr2B 86.667 75 7 3 831 903 707634007 707633934 2.670000e-11 80.5
18 TraesCS5B01G502100 chr2B 93.750 48 1 2 831 876 41109636 41109589 1.610000e-08 71.3
19 TraesCS5B01G502100 chr2B 91.111 45 1 3 831 872 68335615 68335659 1.250000e-04 58.4


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 TraesCS5B01G502100 chr5B 669304335 669307562 3227 True 5962 5962 100.0000 1 3228 1 chr5B.!!$R1 3227
1 TraesCS5B01G502100 chr5D 199004448 199005264 816 True 1282 1282 94.9820 1 817 1 chr5D.!!$R1 816
2 TraesCS5B01G502100 chr5D 530071968 530073928 1960 True 1031 1496 87.2615 815 2794 2 chr5D.!!$R2 1979
3 TraesCS5B01G502100 chr3D 179918285 179919101 816 True 1304 1304 95.4710 1 817 1 chr3D.!!$R1 816
4 TraesCS5B01G502100 chr3A 489306366 489307182 816 False 1288 1288 95.1040 1 817 1 chr3A.!!$F1 816
5 TraesCS5B01G502100 chr6B 712053155 712053971 816 False 1277 1277 94.8590 1 817 1 chr6B.!!$F2 816
6 TraesCS5B01G502100 chr3B 605291218 605292034 816 True 1266 1266 94.6140 1 817 1 chr3B.!!$R1 816
7 TraesCS5B01G502100 chr3B 739218378 739219194 816 True 1254 1254 94.3700 1 817 1 chr3B.!!$R2 816
8 TraesCS5B01G502100 chr7A 33526825 33527641 816 False 1260 1260 94.4920 1 817 1 chr7A.!!$F1 816
9 TraesCS5B01G502100 chr6D 423164946 423165763 817 False 1238 1238 94.0100 1 817 1 chr6D.!!$F1 816
10 TraesCS5B01G502100 chr1B 428617114 428617927 813 True 1227 1227 93.8650 1 815 1 chr1B.!!$R1 814
11 TraesCS5B01G502100 chr5A 657997137 657998380 1243 True 718 1134 86.5250 964 2231 2 chr5A.!!$R1 1267

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
394 395 0.323629 CCTACAAGAAGGGTTCGGCA 59.676 55.0 0.0 0.0 32.55 5.69 F
820 822 0.481567 CAGACCGACCCCCTCCTATA 59.518 60.0 0.0 0.0 0.00 1.31 F
1513 1561 0.025898 TCGTCGTCATCGTCATCGTC 59.974 55.0 0.0 0.0 38.33 4.20 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1303 1342 0.236711 GTCGTCGTCGTCCAAGAAGA 59.763 55.0 1.33 0.0 38.33 2.87 R
1989 2040 0.532862 CACCTCTCCACGTGTGCTTT 60.533 55.0 15.65 0.0 0.00 3.51 R
2868 2983 0.107945 GCGGAGAATGGAGTTGAGCT 60.108 55.0 0.00 0.0 0.00 4.09 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
170 171 0.687757 TAGGATGAAGCACCGCTCCT 60.688 55.000 0.00 0.00 38.25 3.69
212 213 4.344865 ACCAATCCGCCGCCAAGT 62.345 61.111 0.00 0.00 0.00 3.16
215 216 1.309499 CCAATCCGCCGCCAAGTAAA 61.309 55.000 0.00 0.00 0.00 2.01
279 280 4.047059 GAAGGTGACGACGCCCGA 62.047 66.667 13.87 0.00 46.81 5.14
301 302 2.125552 CCGCTGTCGCTTGATCCA 60.126 61.111 0.00 0.00 0.00 3.41
321 322 0.603065 GCAAGGATTTGGGCTTTCGT 59.397 50.000 0.00 0.00 34.79 3.85
389 390 1.002502 GGCGCCTACAAGAAGGGTT 60.003 57.895 22.15 0.00 37.11 4.11
394 395 0.323629 CCTACAAGAAGGGTTCGGCA 59.676 55.000 0.00 0.00 32.55 5.69
544 545 1.065126 GCAGCCCTGGTTGAAGTAGAT 60.065 52.381 4.01 0.00 0.00 1.98
591 592 4.552365 CCGAGATGCCCGCACCAT 62.552 66.667 0.00 0.00 0.00 3.55
652 654 2.902423 AAGAACGGCCAGCACCAACA 62.902 55.000 2.24 0.00 0.00 3.33
660 662 3.595758 AGCACCAACAAGCACCGC 61.596 61.111 0.00 0.00 0.00 5.68
817 819 4.400251 CCAGACCGACCCCCTCCT 62.400 72.222 0.00 0.00 0.00 3.69
818 820 2.687902 CAGACCGACCCCCTCCTA 59.312 66.667 0.00 0.00 0.00 2.94
819 821 1.233369 CAGACCGACCCCCTCCTAT 59.767 63.158 0.00 0.00 0.00 2.57
820 822 0.481567 CAGACCGACCCCCTCCTATA 59.518 60.000 0.00 0.00 0.00 1.31
827 829 3.244457 CCGACCCCCTCCTATATTTGTTC 60.244 52.174 0.00 0.00 0.00 3.18
846 848 4.387559 TGTTCGATGTAATTCTGACCGTTG 59.612 41.667 0.00 0.00 0.00 4.10
849 851 4.803613 TCGATGTAATTCTGACCGTTGATG 59.196 41.667 0.00 0.00 0.00 3.07
867 870 7.223777 CCGTTGATGGTTTTGTTAATTCAAAGT 59.776 33.333 0.00 0.00 38.32 2.66
868 871 8.265998 CGTTGATGGTTTTGTTAATTCAAAGTC 58.734 33.333 0.00 0.00 38.32 3.01
874 877 4.759516 TTGTTAATTCAAAGTCGGGCTC 57.240 40.909 0.00 0.00 0.00 4.70
879 882 2.457366 TTCAAAGTCGGGCTCTCTTC 57.543 50.000 0.00 0.00 0.00 2.87
883 886 1.343069 AAGTCGGGCTCTCTTCAACT 58.657 50.000 0.00 0.00 0.00 3.16
885 888 1.273886 AGTCGGGCTCTCTTCAACTTC 59.726 52.381 0.00 0.00 0.00 3.01
890 893 2.495084 GGCTCTCTTCAACTTCCGTTT 58.505 47.619 0.00 0.00 0.00 3.60
892 895 3.315470 GGCTCTCTTCAACTTCCGTTTTT 59.685 43.478 0.00 0.00 0.00 1.94
893 896 4.514066 GGCTCTCTTCAACTTCCGTTTTTA 59.486 41.667 0.00 0.00 0.00 1.52
894 897 5.008316 GGCTCTCTTCAACTTCCGTTTTTAA 59.992 40.000 0.00 0.00 0.00 1.52
895 898 6.459161 GGCTCTCTTCAACTTCCGTTTTTAAA 60.459 38.462 0.00 0.00 0.00 1.52
896 899 6.970613 GCTCTCTTCAACTTCCGTTTTTAAAA 59.029 34.615 0.00 0.00 0.00 1.52
951 955 2.829741 TTTTTGTTGCCCCTGTATGC 57.170 45.000 0.00 0.00 0.00 3.14
1250 1289 3.368571 GGGCTGCAGCACCTTCAC 61.369 66.667 37.63 19.48 44.36 3.18
1251 1290 3.730761 GGCTGCAGCACCTTCACG 61.731 66.667 37.63 0.00 44.36 4.35
1252 1291 3.730761 GCTGCAGCACCTTCACGG 61.731 66.667 33.36 0.00 41.59 4.94
1253 1292 3.052082 CTGCAGCACCTTCACGGG 61.052 66.667 0.00 0.00 36.97 5.28
1256 1295 3.357079 CAGCACCTTCACGGGCAC 61.357 66.667 0.00 0.00 36.97 5.01
1304 1343 2.815647 CTCCTTCGCGGGCACTTC 60.816 66.667 6.13 0.00 0.00 3.01
1305 1344 3.302347 CTCCTTCGCGGGCACTTCT 62.302 63.158 6.13 0.00 0.00 2.85
1306 1345 2.358737 CCTTCGCGGGCACTTCTT 60.359 61.111 6.13 0.00 0.00 2.52
1307 1346 2.391389 CCTTCGCGGGCACTTCTTC 61.391 63.158 6.13 0.00 0.00 2.87
1308 1347 1.374758 CTTCGCGGGCACTTCTTCT 60.375 57.895 6.13 0.00 0.00 2.85
1309 1348 0.951040 CTTCGCGGGCACTTCTTCTT 60.951 55.000 6.13 0.00 0.00 2.52
1310 1349 1.227999 TTCGCGGGCACTTCTTCTTG 61.228 55.000 6.13 0.00 0.00 3.02
1311 1350 2.680913 CGCGGGCACTTCTTCTTGG 61.681 63.158 0.00 0.00 0.00 3.61
1366 1414 0.326264 AAAGCCTCGGCAGAGTCATT 59.674 50.000 13.02 0.00 42.86 2.57
1367 1415 0.392193 AAGCCTCGGCAGAGTCATTG 60.392 55.000 13.02 0.00 42.86 2.82
1508 1556 0.672711 AGGAGTCGTCGTCATCGTCA 60.673 55.000 0.00 0.00 38.33 4.35
1509 1557 0.377554 GGAGTCGTCGTCATCGTCAT 59.622 55.000 0.00 0.00 38.33 3.06
1510 1558 1.595003 GGAGTCGTCGTCATCGTCATC 60.595 57.143 0.00 0.00 38.33 2.92
1511 1559 0.026414 AGTCGTCGTCATCGTCATCG 59.974 55.000 0.00 0.00 38.33 3.84
1512 1560 0.247576 GTCGTCGTCATCGTCATCGT 60.248 55.000 0.00 0.00 38.33 3.73
1513 1561 0.025898 TCGTCGTCATCGTCATCGTC 59.974 55.000 0.00 0.00 38.33 4.20
1516 1564 2.451132 GTCGTCATCGTCATCGTCATT 58.549 47.619 0.00 0.00 38.33 2.57
1538 1586 3.452024 GACGACTCTAGACGCGGCC 62.452 68.421 9.25 0.00 36.73 6.13
1649 1700 4.077184 TGGTGGGACCGCATCGAC 62.077 66.667 4.09 0.00 42.58 4.20
1664 1715 2.390599 CGACGGCACCAACATCCTG 61.391 63.158 0.00 0.00 0.00 3.86
1776 1827 1.282248 CGTGCCCAAGTCACTGTACG 61.282 60.000 0.00 0.00 32.54 3.67
1790 1841 6.420008 AGTCACTGTACGTTAAACACAAGATC 59.580 38.462 0.00 0.00 0.00 2.75
1853 1904 2.970639 CAGAAGGACCTCCGCGAA 59.029 61.111 8.23 0.00 42.08 4.70
1891 1942 3.755628 CGTCGCGGAGAAAGGGGA 61.756 66.667 6.13 0.00 0.00 4.81
1893 1944 1.221021 GTCGCGGAGAAAGGGGAAT 59.779 57.895 6.13 0.00 0.00 3.01
1896 1947 1.523938 GCGGAGAAAGGGGAATCGG 60.524 63.158 0.00 0.00 0.00 4.18
1959 2010 0.613260 GGTGATGTGCTACCTGGTGA 59.387 55.000 10.23 0.00 34.11 4.02
1980 2031 2.727392 TACAAGGGGATGACGGCGG 61.727 63.158 13.24 0.00 0.00 6.13
2004 2055 4.336581 CGAAAGCACACGTGGAGA 57.663 55.556 21.57 0.00 0.00 3.71
2071 2122 1.203523 CCAGGACTTCGAGGACTTCTG 59.796 57.143 0.00 0.00 0.00 3.02
2107 2158 1.004440 GCTCGGAGTGAAGCCAACT 60.004 57.895 6.90 0.00 0.00 3.16
2131 2182 1.293924 CAACTCTGCGGATGGATCAC 58.706 55.000 0.00 0.00 0.00 3.06
2138 2189 2.106938 GGATGGATCACGCGAGCA 59.893 61.111 15.93 0.00 0.00 4.26
2153 2204 2.799371 GCACGACGCTAGCTAGGT 59.201 61.111 22.10 17.06 37.77 3.08
2155 2206 0.458025 GCACGACGCTAGCTAGGTTT 60.458 55.000 22.10 7.12 37.77 3.27
2157 2208 1.654105 CACGACGCTAGCTAGGTTTTG 59.346 52.381 22.10 13.64 0.00 2.44
2159 2210 1.654105 CGACGCTAGCTAGGTTTTGTG 59.346 52.381 22.10 5.22 0.00 3.33
2190 2248 2.740055 CAGGTGCTGGACGTGAGC 60.740 66.667 15.57 8.87 42.10 4.26
2227 2285 8.851541 AACACTGTTCCGTTATTCCTAATAAA 57.148 30.769 0.00 0.00 35.29 1.40
2228 2286 8.488651 ACACTGTTCCGTTATTCCTAATAAAG 57.511 34.615 0.00 0.00 35.29 1.85
2229 2287 8.098912 ACACTGTTCCGTTATTCCTAATAAAGT 58.901 33.333 0.00 0.00 35.29 2.66
2230 2288 9.590451 CACTGTTCCGTTATTCCTAATAAAGTA 57.410 33.333 0.00 0.00 35.29 2.24
2283 2350 5.989168 TGCCAGGTGTACGATATTATTTCAG 59.011 40.000 0.00 0.00 0.00 3.02
2288 2355 4.694037 GTGTACGATATTATTTCAGGGCCC 59.306 45.833 16.46 16.46 0.00 5.80
2289 2356 4.595781 TGTACGATATTATTTCAGGGCCCT 59.404 41.667 22.28 22.28 0.00 5.19
2290 2357 4.287766 ACGATATTATTTCAGGGCCCTC 57.712 45.455 25.77 5.69 0.00 4.30
2303 2370 1.550524 GGGCCCTCTTTGAATTTCCAC 59.449 52.381 17.04 0.00 0.00 4.02
2307 2374 4.263025 GGCCCTCTTTGAATTTCCACAAAT 60.263 41.667 0.00 0.00 35.84 2.32
2308 2375 5.308014 GCCCTCTTTGAATTTCCACAAATT 58.692 37.500 0.00 0.00 43.64 1.82
2309 2376 5.764686 GCCCTCTTTGAATTTCCACAAATTT 59.235 36.000 0.00 0.00 41.47 1.82
2361 2432 9.770097 TTCCTATGTTTATTGTTTGATTTGCAA 57.230 25.926 0.00 0.00 33.88 4.08
2362 2433 9.421806 TCCTATGTTTATTGTTTGATTTGCAAG 57.578 29.630 0.00 0.00 37.87 4.01
2401 2490 8.261492 AGAAGTTCATTGCACTACATTTAGAG 57.739 34.615 5.50 0.00 0.00 2.43
2404 2493 8.261492 AGTTCATTGCACTACATTTAGAGAAG 57.739 34.615 0.00 0.00 0.00 2.85
2405 2494 8.097038 AGTTCATTGCACTACATTTAGAGAAGA 58.903 33.333 0.00 0.00 0.00 2.87
2406 2495 8.721478 GTTCATTGCACTACATTTAGAGAAGAA 58.279 33.333 0.00 0.00 0.00 2.52
2407 2496 8.484641 TCATTGCACTACATTTAGAGAAGAAG 57.515 34.615 0.00 0.00 0.00 2.85
2432 2521 5.534207 AAATCCACTCAAACATCTTGCAA 57.466 34.783 0.00 0.00 0.00 4.08
2433 2522 5.534207 AATCCACTCAAACATCTTGCAAA 57.466 34.783 0.00 0.00 0.00 3.68
2456 2545 9.868389 CAAAGAATTCTTTTACTTTTCCATTGC 57.132 29.630 27.08 0.00 43.07 3.56
2497 2586 6.593807 TGGTACAAAACAAACTAGAGGCTAA 58.406 36.000 0.00 0.00 31.92 3.09
2503 2592 1.654105 CAAACTAGAGGCTAACGTGCG 59.346 52.381 0.00 0.00 0.00 5.34
2534 2623 0.685097 TTCTTCACTCACGGGAAGGG 59.315 55.000 4.67 0.00 40.65 3.95
2535 2624 1.192146 TCTTCACTCACGGGAAGGGG 61.192 60.000 4.67 0.00 40.65 4.79
2581 2670 7.106439 TCTTTCTTCCAAACAAGTTATTGCA 57.894 32.000 0.00 0.00 40.27 4.08
2588 2677 4.499019 CCAAACAAGTTATTGCAGTCGGTT 60.499 41.667 0.00 0.00 40.27 4.44
2606 2695 5.118510 GTCGGTTGCATCATTTTGGTTTTAG 59.881 40.000 0.00 0.00 0.00 1.85
2607 2696 4.987912 CGGTTGCATCATTTTGGTTTTAGT 59.012 37.500 0.00 0.00 0.00 2.24
2612 2701 7.593875 TGCATCATTTTGGTTTTAGTTATGC 57.406 32.000 0.00 0.00 37.19 3.14
2628 2742 2.939460 ATGCTATGGCGGTGTTTTTC 57.061 45.000 0.00 0.00 42.25 2.29
2629 2743 0.885196 TGCTATGGCGGTGTTTTTCC 59.115 50.000 0.00 0.00 42.25 3.13
2630 2744 1.173913 GCTATGGCGGTGTTTTTCCT 58.826 50.000 0.00 0.00 0.00 3.36
2631 2745 1.132453 GCTATGGCGGTGTTTTTCCTC 59.868 52.381 0.00 0.00 0.00 3.71
2632 2746 2.432444 CTATGGCGGTGTTTTTCCTCA 58.568 47.619 0.00 0.00 0.00 3.86
2633 2747 1.923356 ATGGCGGTGTTTTTCCTCAT 58.077 45.000 0.00 0.00 0.00 2.90
2634 2748 1.698506 TGGCGGTGTTTTTCCTCATT 58.301 45.000 0.00 0.00 0.00 2.57
2635 2749 2.865079 TGGCGGTGTTTTTCCTCATTA 58.135 42.857 0.00 0.00 0.00 1.90
2654 2768 8.289618 CCTCATTAATTTGTATATCGTGTTGGG 58.710 37.037 0.00 0.00 0.00 4.12
2676 2790 5.299949 GGCTGTTGTTGGAGATGAATTTTT 58.700 37.500 0.00 0.00 0.00 1.94
2677 2791 5.406477 GGCTGTTGTTGGAGATGAATTTTTC 59.594 40.000 0.00 0.00 0.00 2.29
2691 2806 8.738106 AGATGAATTTTTCAAGCCTAGAAGAAG 58.262 33.333 0.00 0.00 43.95 2.85
2724 2839 8.348983 TGTTTAGAGAAGAGTTAACTTGTTCG 57.651 34.615 10.02 0.00 0.00 3.95
2741 2856 3.058570 TGTTCGGTGCATGTTGTAATGTC 60.059 43.478 0.00 0.00 0.00 3.06
2742 2857 2.080693 TCGGTGCATGTTGTAATGTCC 58.919 47.619 0.00 0.00 0.00 4.02
2743 2858 2.083774 CGGTGCATGTTGTAATGTCCT 58.916 47.619 0.00 0.00 0.00 3.85
2744 2859 2.487762 CGGTGCATGTTGTAATGTCCTT 59.512 45.455 0.00 0.00 0.00 3.36
2745 2860 3.670359 CGGTGCATGTTGTAATGTCCTTG 60.670 47.826 0.00 0.00 0.00 3.61
2746 2861 3.244976 GTGCATGTTGTAATGTCCTTGC 58.755 45.455 0.00 0.00 0.00 4.01
2747 2862 2.889678 TGCATGTTGTAATGTCCTTGCA 59.110 40.909 0.00 0.00 36.15 4.08
2748 2863 3.510753 TGCATGTTGTAATGTCCTTGCAT 59.489 39.130 0.00 0.00 34.36 3.96
2749 2864 3.861113 GCATGTTGTAATGTCCTTGCATG 59.139 43.478 0.00 0.00 36.51 4.06
2754 2869 5.301551 TGTTGTAATGTCCTTGCATGTTTCT 59.698 36.000 0.00 0.00 29.03 2.52
2755 2870 5.375417 TGTAATGTCCTTGCATGTTTCTG 57.625 39.130 0.00 0.00 0.00 3.02
2760 2875 1.888512 TCCTTGCATGTTTCTGCTTCC 59.111 47.619 0.00 0.00 42.75 3.46
2762 2877 1.536766 CTTGCATGTTTCTGCTTCCGA 59.463 47.619 0.00 0.00 42.75 4.55
2766 2881 1.391485 CATGTTTCTGCTTCCGAGTCG 59.609 52.381 5.29 5.29 0.00 4.18
2781 2896 1.145377 GTCGGCCGGTGGTGATTAT 59.855 57.895 27.83 0.00 0.00 1.28
2794 2909 2.609459 GGTGATTATCGTGAGCCAGTTG 59.391 50.000 0.00 0.00 0.00 3.16
2795 2910 2.609459 GTGATTATCGTGAGCCAGTTGG 59.391 50.000 0.00 0.00 38.53 3.77
2796 2911 2.499693 TGATTATCGTGAGCCAGTTGGA 59.500 45.455 1.45 0.00 37.39 3.53
2797 2912 3.055458 TGATTATCGTGAGCCAGTTGGAA 60.055 43.478 1.45 0.00 37.39 3.53
2798 2913 2.672961 TATCGTGAGCCAGTTGGAAG 57.327 50.000 1.45 0.00 37.39 3.46
2799 2914 0.674895 ATCGTGAGCCAGTTGGAAGC 60.675 55.000 1.45 0.00 37.39 3.86
2800 2915 1.302033 CGTGAGCCAGTTGGAAGCT 60.302 57.895 1.45 0.00 40.24 3.74
2806 2921 3.728385 AGCCAGTTGGAAGCTCTTATT 57.272 42.857 1.45 0.00 37.39 1.40
2807 2922 3.615155 AGCCAGTTGGAAGCTCTTATTC 58.385 45.455 1.45 0.00 37.39 1.75
2808 2923 2.685388 GCCAGTTGGAAGCTCTTATTCC 59.315 50.000 1.45 0.00 45.45 3.01
2816 2931 4.786425 GGAAGCTCTTATTCCATGGAAGT 58.214 43.478 29.98 20.14 44.74 3.01
2817 2932 4.578105 GGAAGCTCTTATTCCATGGAAGTG 59.422 45.833 29.98 21.32 44.74 3.16
2818 2933 3.549794 AGCTCTTATTCCATGGAAGTGC 58.450 45.455 29.98 25.91 39.05 4.40
2819 2934 3.201708 AGCTCTTATTCCATGGAAGTGCT 59.798 43.478 29.98 27.41 42.28 4.40
2820 2935 3.563390 GCTCTTATTCCATGGAAGTGCTC 59.437 47.826 29.98 14.56 36.96 4.26
2821 2936 4.133078 CTCTTATTCCATGGAAGTGCTCC 58.867 47.826 29.98 0.00 45.64 4.70
2822 2937 3.782523 TCTTATTCCATGGAAGTGCTCCT 59.217 43.478 29.98 15.35 45.64 3.69
2823 2938 4.968719 TCTTATTCCATGGAAGTGCTCCTA 59.031 41.667 29.98 14.36 45.64 2.94
2824 2939 5.608437 TCTTATTCCATGGAAGTGCTCCTAT 59.392 40.000 29.98 13.97 45.64 2.57
2825 2940 6.787458 TCTTATTCCATGGAAGTGCTCCTATA 59.213 38.462 29.98 12.99 45.64 1.31
2826 2941 5.912149 ATTCCATGGAAGTGCTCCTATAA 57.088 39.130 29.98 4.85 45.64 0.98
2827 2942 4.689612 TCCATGGAAGTGCTCCTATAAC 57.310 45.455 13.46 0.00 45.64 1.89
2828 2943 4.298626 TCCATGGAAGTGCTCCTATAACT 58.701 43.478 13.46 0.00 45.64 2.24
2829 2944 4.345257 TCCATGGAAGTGCTCCTATAACTC 59.655 45.833 13.46 0.00 45.64 3.01
2830 2945 4.101585 CCATGGAAGTGCTCCTATAACTCA 59.898 45.833 5.56 0.00 45.64 3.41
2831 2946 4.737855 TGGAAGTGCTCCTATAACTCAC 57.262 45.455 0.00 0.00 45.64 3.51
2832 2947 4.093743 TGGAAGTGCTCCTATAACTCACA 58.906 43.478 0.00 0.00 45.64 3.58
2833 2948 4.716784 TGGAAGTGCTCCTATAACTCACAT 59.283 41.667 0.00 0.00 45.64 3.21
2834 2949 5.053145 GGAAGTGCTCCTATAACTCACATG 58.947 45.833 0.00 0.00 41.61 3.21
2835 2950 4.679373 AGTGCTCCTATAACTCACATGG 57.321 45.455 0.00 0.00 0.00 3.66
2836 2951 4.290093 AGTGCTCCTATAACTCACATGGA 58.710 43.478 0.00 0.00 0.00 3.41
2837 2952 4.100189 AGTGCTCCTATAACTCACATGGAC 59.900 45.833 0.00 0.00 0.00 4.02
2838 2953 3.388024 TGCTCCTATAACTCACATGGACC 59.612 47.826 0.00 0.00 0.00 4.46
2839 2954 3.553096 GCTCCTATAACTCACATGGACCG 60.553 52.174 0.00 0.00 0.00 4.79
2840 2955 2.963101 TCCTATAACTCACATGGACCGG 59.037 50.000 0.00 0.00 0.00 5.28
2841 2956 2.548067 CCTATAACTCACATGGACCGGC 60.548 54.545 0.00 0.00 0.00 6.13
2842 2957 0.180406 ATAACTCACATGGACCGGCC 59.820 55.000 0.00 4.32 37.10 6.13
2850 2965 2.192443 TGGACCGGCCAACGAAAA 59.808 55.556 14.27 0.00 45.87 2.29
2851 2966 1.228306 TGGACCGGCCAACGAAAAT 60.228 52.632 14.27 0.00 45.87 1.82
2852 2967 1.238625 TGGACCGGCCAACGAAAATC 61.239 55.000 14.27 0.00 45.87 2.17
2853 2968 3.599978 TGGACCGGCCAACGAAAATCT 62.600 52.381 14.27 0.00 45.87 2.40
2858 2973 2.902065 GGCCAACGAAAATCTCACTC 57.098 50.000 0.00 0.00 0.00 3.51
2859 2974 1.128692 GGCCAACGAAAATCTCACTCG 59.871 52.381 0.00 0.00 38.53 4.18
2860 2975 1.464189 GCCAACGAAAATCTCACTCGC 60.464 52.381 0.00 0.00 36.03 5.03
2861 2976 2.069273 CCAACGAAAATCTCACTCGCT 58.931 47.619 0.00 0.00 36.03 4.93
2862 2977 2.092838 CCAACGAAAATCTCACTCGCTC 59.907 50.000 0.00 0.00 36.03 5.03
2863 2978 2.724977 ACGAAAATCTCACTCGCTCA 57.275 45.000 0.00 0.00 36.03 4.26
2864 2979 2.600731 ACGAAAATCTCACTCGCTCAG 58.399 47.619 0.00 0.00 36.03 3.35
2865 2980 1.322936 CGAAAATCTCACTCGCTCAGC 59.677 52.381 0.00 0.00 0.00 4.26
2866 2981 2.615869 GAAAATCTCACTCGCTCAGCT 58.384 47.619 0.00 0.00 0.00 4.24
2867 2982 2.292103 AAATCTCACTCGCTCAGCTC 57.708 50.000 0.00 0.00 0.00 4.09
2868 2983 1.180907 AATCTCACTCGCTCAGCTCA 58.819 50.000 0.00 0.00 0.00 4.26
2869 2984 0.740149 ATCTCACTCGCTCAGCTCAG 59.260 55.000 0.00 0.00 0.00 3.35
2870 2985 1.516821 CTCACTCGCTCAGCTCAGC 60.517 63.158 0.00 0.00 35.90 4.26
2871 2986 1.936436 CTCACTCGCTCAGCTCAGCT 61.936 60.000 8.35 0.00 40.77 4.24
2872 2987 1.516821 CACTCGCTCAGCTCAGCTC 60.517 63.158 8.35 0.00 36.40 4.09
2873 2988 1.975940 ACTCGCTCAGCTCAGCTCA 60.976 57.895 8.35 0.00 36.40 4.26
2874 2989 1.214853 CTCGCTCAGCTCAGCTCAA 59.785 57.895 8.35 0.00 36.40 3.02
2875 2990 1.077645 CTCGCTCAGCTCAGCTCAAC 61.078 60.000 8.35 0.00 36.40 3.18
2876 2991 1.079956 CGCTCAGCTCAGCTCAACT 60.080 57.895 8.35 0.00 36.40 3.16
2877 2992 1.077645 CGCTCAGCTCAGCTCAACTC 61.078 60.000 8.35 0.00 36.40 3.01
2878 2993 0.740516 GCTCAGCTCAGCTCAACTCC 60.741 60.000 0.67 0.00 36.40 3.85
2879 2994 0.607112 CTCAGCTCAGCTCAACTCCA 59.393 55.000 0.00 0.00 36.40 3.86
2880 2995 1.207570 CTCAGCTCAGCTCAACTCCAT 59.792 52.381 0.00 0.00 36.40 3.41
2881 2996 1.627329 TCAGCTCAGCTCAACTCCATT 59.373 47.619 0.00 0.00 36.40 3.16
2882 2997 2.008329 CAGCTCAGCTCAACTCCATTC 58.992 52.381 0.00 0.00 36.40 2.67
2883 2998 1.907936 AGCTCAGCTCAACTCCATTCT 59.092 47.619 0.00 0.00 30.62 2.40
2884 2999 2.093553 AGCTCAGCTCAACTCCATTCTC 60.094 50.000 0.00 0.00 30.62 2.87
2885 3000 2.903798 CTCAGCTCAACTCCATTCTCC 58.096 52.381 0.00 0.00 0.00 3.71
2886 3001 1.205655 TCAGCTCAACTCCATTCTCCG 59.794 52.381 0.00 0.00 0.00 4.63
2887 3002 0.107945 AGCTCAACTCCATTCTCCGC 60.108 55.000 0.00 0.00 0.00 5.54
2888 3003 0.107945 GCTCAACTCCATTCTCCGCT 60.108 55.000 0.00 0.00 0.00 5.52
2889 3004 1.677217 GCTCAACTCCATTCTCCGCTT 60.677 52.381 0.00 0.00 0.00 4.68
2890 3005 2.418746 GCTCAACTCCATTCTCCGCTTA 60.419 50.000 0.00 0.00 0.00 3.09
2891 3006 3.190874 CTCAACTCCATTCTCCGCTTAC 58.809 50.000 0.00 0.00 0.00 2.34
2892 3007 2.832129 TCAACTCCATTCTCCGCTTACT 59.168 45.455 0.00 0.00 0.00 2.24
2893 3008 3.119101 TCAACTCCATTCTCCGCTTACTC 60.119 47.826 0.00 0.00 0.00 2.59
2894 3009 2.457598 ACTCCATTCTCCGCTTACTCA 58.542 47.619 0.00 0.00 0.00 3.41
2895 3010 2.428890 ACTCCATTCTCCGCTTACTCAG 59.571 50.000 0.00 0.00 0.00 3.35
2896 3011 2.690497 CTCCATTCTCCGCTTACTCAGA 59.310 50.000 0.00 0.00 0.00 3.27
2897 3012 3.300388 TCCATTCTCCGCTTACTCAGAT 58.700 45.455 0.00 0.00 0.00 2.90
2898 3013 3.706594 TCCATTCTCCGCTTACTCAGATT 59.293 43.478 0.00 0.00 0.00 2.40
2899 3014 4.162320 TCCATTCTCCGCTTACTCAGATTT 59.838 41.667 0.00 0.00 0.00 2.17
2900 3015 4.878397 CCATTCTCCGCTTACTCAGATTTT 59.122 41.667 0.00 0.00 0.00 1.82
2901 3016 5.355350 CCATTCTCCGCTTACTCAGATTTTT 59.645 40.000 0.00 0.00 0.00 1.94
2997 3112 7.031226 AGAAATATTCATGACAATGTTCGGG 57.969 36.000 0.00 0.00 35.15 5.14
2998 3113 6.828273 AGAAATATTCATGACAATGTTCGGGA 59.172 34.615 0.00 0.00 35.15 5.14
2999 3114 7.339212 AGAAATATTCATGACAATGTTCGGGAA 59.661 33.333 0.00 0.00 35.15 3.97
3000 3115 7.587037 AATATTCATGACAATGTTCGGGAAT 57.413 32.000 0.00 0.00 35.15 3.01
3001 3116 5.920193 ATTCATGACAATGTTCGGGAATT 57.080 34.783 0.00 0.00 35.15 2.17
3002 3117 5.720371 TTCATGACAATGTTCGGGAATTT 57.280 34.783 0.00 0.00 35.15 1.82
3003 3118 5.309323 TCATGACAATGTTCGGGAATTTC 57.691 39.130 0.00 0.00 35.15 2.17
3004 3119 4.764308 TCATGACAATGTTCGGGAATTTCA 59.236 37.500 0.00 0.00 35.15 2.69
3005 3120 5.242615 TCATGACAATGTTCGGGAATTTCAA 59.757 36.000 0.00 0.00 35.15 2.69
3006 3121 5.521906 TGACAATGTTCGGGAATTTCAAA 57.478 34.783 0.00 0.00 0.00 2.69
3007 3122 5.907207 TGACAATGTTCGGGAATTTCAAAA 58.093 33.333 0.00 0.00 0.00 2.44
3008 3123 6.341316 TGACAATGTTCGGGAATTTCAAAAA 58.659 32.000 0.00 0.00 0.00 1.94
3059 3174 9.979578 TTGCATACTTAAAAATGTTCATGAACT 57.020 25.926 32.57 18.44 41.67 3.01
3060 3175 9.979578 TGCATACTTAAAAATGTTCATGAACTT 57.020 25.926 32.57 25.75 41.67 2.66
3150 3265 9.667989 TGTTCTTTTACTTTTAACGAAATAGCC 57.332 29.630 0.00 0.00 0.00 3.93
3151 3266 9.667989 GTTCTTTTACTTTTAACGAAATAGCCA 57.332 29.630 0.00 0.00 0.00 4.75
3153 3268 9.834628 TCTTTTACTTTTAACGAAATAGCCATG 57.165 29.630 0.00 0.00 0.00 3.66
3154 3269 9.620660 CTTTTACTTTTAACGAAATAGCCATGT 57.379 29.630 0.00 0.00 0.00 3.21
3193 3308 9.651913 AAGATAAAAGAAAGAAAAACAAGCACA 57.348 25.926 0.00 0.00 0.00 4.57
3194 3309 9.651913 AGATAAAAGAAAGAAAAACAAGCACAA 57.348 25.926 0.00 0.00 0.00 3.33
3198 3313 9.964303 AAAAGAAAGAAAAACAAGCACAAAAAT 57.036 22.222 0.00 0.00 0.00 1.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
212 213 3.509575 GGGTGGATGTGATGCTTTGTTTA 59.490 43.478 0.00 0.00 0.00 2.01
215 216 1.549203 GGGTGGATGTGATGCTTTGT 58.451 50.000 0.00 0.00 0.00 2.83
301 302 0.890683 CGAAAGCCCAAATCCTTGCT 59.109 50.000 0.00 0.00 35.08 3.91
321 322 3.536917 CCCAGCTCGTATGCCGGA 61.537 66.667 5.05 0.00 32.49 5.14
470 471 1.519408 CGGAGTTGTACCTGTTTGGG 58.481 55.000 0.00 0.00 41.11 4.12
544 545 0.043183 TCCAGATCTGAAGGCCTCCA 59.957 55.000 24.62 0.00 0.00 3.86
652 654 1.799258 CTTTGGCTTGAGCGGTGCTT 61.799 55.000 0.00 0.00 39.88 3.91
660 662 1.462670 GCGAGACTTCTTTGGCTTGAG 59.537 52.381 0.00 0.00 0.00 3.02
817 819 8.974408 CGGTCAGAATTACATCGAACAAATATA 58.026 33.333 0.00 0.00 0.00 0.86
818 820 7.494625 ACGGTCAGAATTACATCGAACAAATAT 59.505 33.333 0.00 0.00 0.00 1.28
819 821 6.814644 ACGGTCAGAATTACATCGAACAAATA 59.185 34.615 0.00 0.00 0.00 1.40
820 822 5.642063 ACGGTCAGAATTACATCGAACAAAT 59.358 36.000 0.00 0.00 0.00 2.32
827 829 4.025730 CCATCAACGGTCAGAATTACATCG 60.026 45.833 0.00 0.00 0.00 3.84
839 841 6.210078 TGAATTAACAAAACCATCAACGGTC 58.790 36.000 0.00 0.00 38.76 4.79
840 842 6.150396 TGAATTAACAAAACCATCAACGGT 57.850 33.333 0.00 0.00 42.71 4.83
842 844 8.125728 ACTTTGAATTAACAAAACCATCAACG 57.874 30.769 0.00 0.00 38.90 4.10
846 848 6.364976 CCCGACTTTGAATTAACAAAACCATC 59.635 38.462 0.00 0.00 38.90 3.51
849 851 4.446385 GCCCGACTTTGAATTAACAAAACC 59.554 41.667 0.00 0.00 38.90 3.27
851 853 5.300792 AGAGCCCGACTTTGAATTAACAAAA 59.699 36.000 0.00 0.00 38.90 2.44
867 870 0.608640 GGAAGTTGAAGAGAGCCCGA 59.391 55.000 0.00 0.00 0.00 5.14
868 871 0.737715 CGGAAGTTGAAGAGAGCCCG 60.738 60.000 0.00 0.00 0.00 6.13
905 908 2.653742 CGTGCTCATCTACCACACG 58.346 57.895 0.00 0.00 46.57 4.49
937 940 3.876198 CGCGCATACAGGGGCAAC 61.876 66.667 8.75 0.00 46.02 4.17
951 955 2.154198 TGAAACAGTTAATCGTCACGCG 59.846 45.455 3.53 3.53 43.01 6.01
1181 1220 0.248825 AGCGCATCTCTGATCGTGAC 60.249 55.000 11.47 0.00 0.00 3.67
1230 1269 4.982701 AAGGTGCTGCAGCCCCAC 62.983 66.667 36.78 26.95 41.27 4.61
1231 1270 4.666253 GAAGGTGCTGCAGCCCCA 62.666 66.667 36.78 17.73 41.27 4.96
1232 1271 4.666253 TGAAGGTGCTGCAGCCCC 62.666 66.667 34.64 32.57 41.18 5.80
1233 1272 3.368571 GTGAAGGTGCTGCAGCCC 61.369 66.667 34.64 31.29 41.18 5.19
1234 1273 3.730761 CGTGAAGGTGCTGCAGCC 61.731 66.667 34.64 24.64 41.18 4.85
1235 1274 3.730761 CCGTGAAGGTGCTGCAGC 61.731 66.667 31.89 31.89 42.50 5.25
1236 1275 3.052082 CCCGTGAAGGTGCTGCAG 61.052 66.667 10.11 10.11 38.74 4.41
1239 1278 3.357079 GTGCCCGTGAAGGTGCTG 61.357 66.667 0.64 0.00 38.74 4.41
1240 1279 4.988598 CGTGCCCGTGAAGGTGCT 62.989 66.667 0.64 0.00 38.74 4.40
1250 1289 2.584143 GGGTTATCGACGTGCCCG 60.584 66.667 0.00 0.00 40.83 6.13
1251 1290 2.202974 GGGGTTATCGACGTGCCC 60.203 66.667 0.00 7.43 38.61 5.36
1252 1291 2.584143 CGGGGTTATCGACGTGCC 60.584 66.667 0.00 0.00 0.00 5.01
1253 1292 1.875364 GTCGGGGTTATCGACGTGC 60.875 63.158 0.00 0.00 45.53 5.34
1254 1293 4.389772 GTCGGGGTTATCGACGTG 57.610 61.111 0.00 0.00 45.53 4.49
1258 1297 1.077501 ACTCCGTCGGGGTTATCGA 60.078 57.895 12.17 0.00 37.00 3.59
1259 1298 1.065273 CACTCCGTCGGGGTTATCG 59.935 63.158 15.99 0.00 37.00 2.92
1260 1299 1.039233 TCCACTCCGTCGGGGTTATC 61.039 60.000 15.99 0.00 37.00 1.75
1261 1300 1.000739 TCCACTCCGTCGGGGTTAT 59.999 57.895 15.99 0.00 37.00 1.89
1262 1301 1.679977 CTCCACTCCGTCGGGGTTA 60.680 63.158 15.99 4.86 37.00 2.85
1263 1302 2.995574 CTCCACTCCGTCGGGGTT 60.996 66.667 15.99 0.00 37.00 4.11
1266 1305 4.135153 CAGCTCCACTCCGTCGGG 62.135 72.222 12.29 4.77 0.00 5.14
1290 1329 0.951040 AAGAAGAAGTGCCCGCGAAG 60.951 55.000 8.23 0.00 0.00 3.79
1294 1333 1.302511 TCCAAGAAGAAGTGCCCGC 60.303 57.895 0.00 0.00 0.00 6.13
1302 1341 0.946528 TCGTCGTCGTCCAAGAAGAA 59.053 50.000 1.33 0.00 38.33 2.52
1303 1342 0.236711 GTCGTCGTCGTCCAAGAAGA 59.763 55.000 1.33 0.00 38.33 2.87
1304 1343 1.058590 CGTCGTCGTCGTCCAAGAAG 61.059 60.000 3.67 0.00 38.33 2.85
1305 1344 1.082561 CGTCGTCGTCGTCCAAGAA 60.083 57.895 3.67 0.00 38.33 2.52
1306 1345 2.552768 CGTCGTCGTCGTCCAAGA 59.447 61.111 3.67 0.00 38.33 3.02
1307 1346 2.501222 CCGTCGTCGTCGTCCAAG 60.501 66.667 10.76 0.00 38.33 3.61
1308 1347 4.688419 GCCGTCGTCGTCGTCCAA 62.688 66.667 10.76 0.00 38.33 3.53
1347 1395 0.326264 AATGACTCTGCCGAGGCTTT 59.674 50.000 12.62 9.29 46.01 3.51
1478 1526 1.153745 CGACTCCTCCGAGGCTTTG 60.154 63.158 9.87 2.76 42.67 2.77
1511 1559 1.400846 TCTAGAGTCGTCGCCAATGAC 59.599 52.381 0.00 0.00 43.19 3.06
1512 1560 1.400846 GTCTAGAGTCGTCGCCAATGA 59.599 52.381 0.00 0.00 0.00 2.57
1513 1561 1.828832 GTCTAGAGTCGTCGCCAATG 58.171 55.000 0.00 0.00 0.00 2.82
1516 1564 2.747822 GCGTCTAGAGTCGTCGCCA 61.748 63.158 12.30 0.00 40.83 5.69
1608 1656 4.176851 GTCGGACGAGAGGCGGTC 62.177 72.222 0.00 0.00 46.49 4.79
1642 1693 2.309764 GATGTTGGTGCCGTCGATGC 62.310 60.000 0.00 0.54 0.00 3.91
1649 1700 2.360350 AGCAGGATGTTGGTGCCG 60.360 61.111 0.00 0.00 39.31 5.69
1769 1820 5.522456 TCGATCTTGTGTTTAACGTACAGT 58.478 37.500 0.00 0.00 0.00 3.55
1776 1827 5.107065 CCAGGTTCTCGATCTTGTGTTTAAC 60.107 44.000 0.00 0.00 0.00 2.01
1790 1841 2.743928 GGCAGCACCAGGTTCTCG 60.744 66.667 0.00 0.00 38.86 4.04
1875 1926 0.810426 GATTCCCCTTTCTCCGCGAC 60.810 60.000 8.23 0.00 0.00 5.19
1876 1927 1.520666 GATTCCCCTTTCTCCGCGA 59.479 57.895 8.23 0.00 0.00 5.87
1879 1930 1.523938 GCCGATTCCCCTTTCTCCG 60.524 63.158 0.00 0.00 0.00 4.63
1884 1935 1.153509 CGTACGCCGATTCCCCTTT 60.154 57.895 0.52 0.00 39.56 3.11
1885 1936 2.353610 ACGTACGCCGATTCCCCTT 61.354 57.895 16.72 0.00 40.70 3.95
1890 1941 1.804326 AGTGCACGTACGCCGATTC 60.804 57.895 16.72 1.50 40.70 2.52
1891 1942 2.092291 CAGTGCACGTACGCCGATT 61.092 57.895 16.72 0.00 40.70 3.34
1896 1947 2.170985 CTTGCAGTGCACGTACGC 59.829 61.111 19.58 13.33 38.71 4.42
1959 2010 1.623542 GCCGTCATCCCCTTGTACCT 61.624 60.000 0.00 0.00 0.00 3.08
1980 2031 2.383527 CGTGTGCTTTCGCCTCCTC 61.384 63.158 0.00 0.00 34.43 3.71
1989 2040 0.532862 CACCTCTCCACGTGTGCTTT 60.533 55.000 15.65 0.00 0.00 3.51
1991 2042 2.737180 CACCTCTCCACGTGTGCT 59.263 61.111 15.65 0.00 0.00 4.40
1993 2044 2.357517 GGCACCTCTCCACGTGTG 60.358 66.667 15.65 6.00 32.40 3.82
1994 2045 3.991051 CGGCACCTCTCCACGTGT 61.991 66.667 15.65 0.00 32.40 4.49
2107 2158 1.078918 CATCCGCAGAGTTGGAGCA 60.079 57.895 0.00 0.00 37.76 4.26
2138 2189 1.271656 ACAAAACCTAGCTAGCGTCGT 59.728 47.619 15.74 4.91 0.00 4.34
2148 2199 7.985184 TGTGGAAGCTATATACACAAAACCTAG 59.015 37.037 0.00 0.00 38.91 3.02
2150 2201 6.717289 TGTGGAAGCTATATACACAAAACCT 58.283 36.000 0.00 0.00 38.91 3.50
2151 2202 6.038271 CCTGTGGAAGCTATATACACAAAACC 59.962 42.308 3.59 0.00 41.00 3.27
2152 2203 6.598064 ACCTGTGGAAGCTATATACACAAAAC 59.402 38.462 3.59 0.00 41.00 2.43
2153 2204 6.597672 CACCTGTGGAAGCTATATACACAAAA 59.402 38.462 3.59 0.00 41.00 2.44
2155 2206 5.670485 CACCTGTGGAAGCTATATACACAA 58.330 41.667 3.59 0.00 41.00 3.33
2157 2208 4.058817 GCACCTGTGGAAGCTATATACAC 58.941 47.826 0.00 0.00 0.00 2.90
2159 2210 4.310769 CAGCACCTGTGGAAGCTATATAC 58.689 47.826 0.00 0.00 36.32 1.47
2190 2248 4.466828 GGAACAGTGTTCGAACATTGATG 58.533 43.478 42.24 32.10 45.97 3.07
2264 2331 4.694037 GGCCCTGAAATAATATCGTACACC 59.306 45.833 0.00 0.00 0.00 4.16
2283 2350 1.550524 GTGGAAATTCAAAGAGGGCCC 59.449 52.381 16.46 16.46 0.00 5.80
2288 2355 8.337532 GTCCAAAATTTGTGGAAATTCAAAGAG 58.662 33.333 9.97 0.00 46.66 2.85
2289 2356 7.010923 CGTCCAAAATTTGTGGAAATTCAAAGA 59.989 33.333 9.97 0.00 46.66 2.52
2290 2357 7.010923 TCGTCCAAAATTTGTGGAAATTCAAAG 59.989 33.333 9.97 0.00 46.66 2.77
2303 2370 8.863049 CCAAAAGATTAGATCGTCCAAAATTTG 58.137 33.333 0.00 0.00 0.00 2.32
2307 2374 7.753309 TTCCAAAAGATTAGATCGTCCAAAA 57.247 32.000 0.00 0.00 0.00 2.44
2308 2375 7.938140 ATTCCAAAAGATTAGATCGTCCAAA 57.062 32.000 0.00 0.00 0.00 3.28
2309 2376 7.938140 AATTCCAAAAGATTAGATCGTCCAA 57.062 32.000 0.00 0.00 0.00 3.53
2352 2423 5.083122 TGGGGAAGATTAACTTGCAAATCA 58.917 37.500 10.62 0.00 46.41 2.57
2353 2424 5.659440 TGGGGAAGATTAACTTGCAAATC 57.341 39.130 0.00 0.17 46.41 2.17
2354 2425 5.779771 TCTTGGGGAAGATTAACTTGCAAAT 59.220 36.000 0.00 0.00 46.41 2.32
2357 2428 4.380843 TCTTGGGGAAGATTAACTTGCA 57.619 40.909 0.00 0.00 46.41 4.08
2369 2440 2.627699 GTGCAATGAACTTCTTGGGGAA 59.372 45.455 0.00 0.00 0.00 3.97
2401 2490 8.355913 AGATGTTTGAGTGGATTTTTCTTCTTC 58.644 33.333 0.00 0.00 0.00 2.87
2404 2493 7.095899 GCAAGATGTTTGAGTGGATTTTTCTTC 60.096 37.037 0.00 0.00 0.00 2.87
2405 2494 6.703165 GCAAGATGTTTGAGTGGATTTTTCTT 59.297 34.615 0.00 0.00 0.00 2.52
2406 2495 6.183360 TGCAAGATGTTTGAGTGGATTTTTCT 60.183 34.615 0.00 0.00 0.00 2.52
2407 2496 5.984926 TGCAAGATGTTTGAGTGGATTTTTC 59.015 36.000 0.00 0.00 0.00 2.29
2432 2521 9.836864 AAGCAATGGAAAAGTAAAAGAATTCTT 57.163 25.926 15.11 15.11 37.91 2.52
2444 2533 6.420604 CGTGTTTGATTAAGCAATGGAAAAGT 59.579 34.615 7.03 0.00 0.00 2.66
2456 2545 5.753744 TGTACCAAAGCGTGTTTGATTAAG 58.246 37.500 12.37 0.87 0.00 1.85
2503 2592 2.253758 TGAAGAACAGTGCGGCAGC 61.254 57.895 1.18 0.31 45.41 5.25
2554 2643 7.379797 GCAATAACTTGTTTGGAAGAAAGAGTC 59.620 37.037 0.00 0.00 34.69 3.36
2569 2658 2.031157 GCAACCGACTGCAATAACTTGT 60.031 45.455 4.07 0.00 42.17 3.16
2570 2659 2.584791 GCAACCGACTGCAATAACTTG 58.415 47.619 4.07 0.00 42.17 3.16
2581 2670 2.238521 ACCAAAATGATGCAACCGACT 58.761 42.857 0.00 0.00 0.00 4.18
2588 2677 7.385267 AGCATAACTAAAACCAAAATGATGCA 58.615 30.769 0.00 0.00 38.69 3.96
2594 2683 6.978080 CGCCATAGCATAACTAAAACCAAAAT 59.022 34.615 0.00 0.00 39.83 1.82
2606 2695 3.775661 AAAACACCGCCATAGCATAAC 57.224 42.857 0.00 0.00 39.83 1.89
2607 2696 3.129638 GGAAAAACACCGCCATAGCATAA 59.870 43.478 0.00 0.00 39.83 1.90
2612 2701 2.432444 TGAGGAAAAACACCGCCATAG 58.568 47.619 0.00 0.00 0.00 2.23
2628 2742 8.289618 CCCAACACGATATACAAATTAATGAGG 58.710 37.037 0.00 0.00 0.00 3.86
2629 2743 7.803189 GCCCAACACGATATACAAATTAATGAG 59.197 37.037 0.00 0.00 0.00 2.90
2630 2744 7.500892 AGCCCAACACGATATACAAATTAATGA 59.499 33.333 0.00 0.00 0.00 2.57
2631 2745 7.591057 CAGCCCAACACGATATACAAATTAATG 59.409 37.037 0.00 0.00 0.00 1.90
2632 2746 7.284489 ACAGCCCAACACGATATACAAATTAAT 59.716 33.333 0.00 0.00 0.00 1.40
2633 2747 6.600032 ACAGCCCAACACGATATACAAATTAA 59.400 34.615 0.00 0.00 0.00 1.40
2634 2748 6.116806 ACAGCCCAACACGATATACAAATTA 58.883 36.000 0.00 0.00 0.00 1.40
2635 2749 4.947388 ACAGCCCAACACGATATACAAATT 59.053 37.500 0.00 0.00 0.00 1.82
2646 2760 1.065600 CCAACAACAGCCCAACACG 59.934 57.895 0.00 0.00 0.00 4.49
2654 2768 5.984926 TGAAAAATTCATCTCCAACAACAGC 59.015 36.000 0.00 0.00 34.08 4.40
2676 2790 5.683876 AATACTGCTTCTTCTAGGCTTGA 57.316 39.130 0.00 0.00 0.00 3.02
2677 2791 5.645497 ACAAATACTGCTTCTTCTAGGCTTG 59.355 40.000 0.00 0.00 0.00 4.01
2723 2838 2.083774 AGGACATTACAACATGCACCG 58.916 47.619 0.00 0.00 32.44 4.94
2724 2839 3.836949 CAAGGACATTACAACATGCACC 58.163 45.455 0.00 0.00 0.00 5.01
2745 2860 1.129437 GACTCGGAAGCAGAAACATGC 59.871 52.381 0.00 0.00 46.88 4.06
2746 2861 1.391485 CGACTCGGAAGCAGAAACATG 59.609 52.381 0.00 0.00 0.00 3.21
2747 2862 1.714794 CGACTCGGAAGCAGAAACAT 58.285 50.000 0.00 0.00 0.00 2.71
2748 2863 3.195041 CGACTCGGAAGCAGAAACA 57.805 52.632 0.00 0.00 0.00 2.83
2762 2877 1.335132 ATAATCACCACCGGCCGACT 61.335 55.000 30.73 8.37 0.00 4.18
2766 2881 1.145377 ACGATAATCACCACCGGCC 59.855 57.895 0.00 0.00 0.00 6.13
2770 2885 1.134521 TGGCTCACGATAATCACCACC 60.135 52.381 0.00 0.00 0.00 4.61
2774 2889 2.609459 CCAACTGGCTCACGATAATCAC 59.391 50.000 0.00 0.00 0.00 3.06
2781 2896 1.301716 GCTTCCAACTGGCTCACGA 60.302 57.895 0.00 0.00 34.44 4.35
2794 2909 4.578105 CACTTCCATGGAATAAGAGCTTCC 59.422 45.833 27.20 0.00 42.15 3.46
2795 2910 4.036144 GCACTTCCATGGAATAAGAGCTTC 59.964 45.833 27.20 4.79 35.02 3.86
2796 2911 3.950395 GCACTTCCATGGAATAAGAGCTT 59.050 43.478 27.20 0.00 35.02 3.74
2797 2912 3.201708 AGCACTTCCATGGAATAAGAGCT 59.798 43.478 27.20 24.99 40.71 4.09
2798 2913 3.549794 AGCACTTCCATGGAATAAGAGC 58.450 45.455 27.20 23.32 37.17 4.09
2799 2914 4.133078 GGAGCACTTCCATGGAATAAGAG 58.867 47.826 27.20 17.37 46.01 2.85
2800 2915 4.156455 GGAGCACTTCCATGGAATAAGA 57.844 45.455 27.20 5.19 46.01 2.10
2812 2927 5.053145 CCATGTGAGTTATAGGAGCACTTC 58.947 45.833 0.00 0.00 0.00 3.01
2813 2928 4.716784 TCCATGTGAGTTATAGGAGCACTT 59.283 41.667 0.00 0.00 0.00 3.16
2814 2929 4.100189 GTCCATGTGAGTTATAGGAGCACT 59.900 45.833 0.00 0.00 0.00 4.40
2815 2930 4.372656 GTCCATGTGAGTTATAGGAGCAC 58.627 47.826 0.00 0.00 0.00 4.40
2816 2931 3.388024 GGTCCATGTGAGTTATAGGAGCA 59.612 47.826 0.00 0.00 41.80 4.26
2817 2932 3.553096 CGGTCCATGTGAGTTATAGGAGC 60.553 52.174 0.00 0.00 39.55 4.70
2818 2933 3.005897 CCGGTCCATGTGAGTTATAGGAG 59.994 52.174 0.00 0.00 0.00 3.69
2819 2934 2.963101 CCGGTCCATGTGAGTTATAGGA 59.037 50.000 0.00 0.00 0.00 2.94
2820 2935 2.548067 GCCGGTCCATGTGAGTTATAGG 60.548 54.545 1.90 0.00 0.00 2.57
2821 2936 2.548067 GGCCGGTCCATGTGAGTTATAG 60.548 54.545 1.90 0.00 34.01 1.31
2822 2937 1.414919 GGCCGGTCCATGTGAGTTATA 59.585 52.381 1.90 0.00 34.01 0.98
2823 2938 0.180406 GGCCGGTCCATGTGAGTTAT 59.820 55.000 1.90 0.00 34.01 1.89
2824 2939 1.195442 TGGCCGGTCCATGTGAGTTA 61.195 55.000 12.86 0.00 40.72 2.24
2825 2940 2.063015 TTGGCCGGTCCATGTGAGTT 62.063 55.000 16.81 0.00 46.04 3.01
2826 2941 2.525124 TTGGCCGGTCCATGTGAGT 61.525 57.895 16.81 0.00 46.04 3.41
2827 2942 2.040544 GTTGGCCGGTCCATGTGAG 61.041 63.158 16.81 0.00 46.04 3.51
2828 2943 2.033448 GTTGGCCGGTCCATGTGA 59.967 61.111 16.81 1.32 46.04 3.58
2829 2944 3.430862 CGTTGGCCGGTCCATGTG 61.431 66.667 16.81 7.53 46.04 3.21
2830 2945 2.684192 TTTCGTTGGCCGGTCCATGT 62.684 55.000 16.81 0.00 46.04 3.21
2831 2946 1.519751 TTTTCGTTGGCCGGTCCATG 61.520 55.000 16.81 5.71 46.04 3.66
2832 2947 0.610785 ATTTTCGTTGGCCGGTCCAT 60.611 50.000 16.81 0.00 46.04 3.41
2833 2948 1.228306 ATTTTCGTTGGCCGGTCCA 60.228 52.632 12.86 12.86 44.85 4.02
2834 2949 0.958876 AGATTTTCGTTGGCCGGTCC 60.959 55.000 2.12 5.67 37.11 4.46
2835 2950 0.446616 GAGATTTTCGTTGGCCGGTC 59.553 55.000 0.00 0.00 37.11 4.79
2836 2951 0.250553 TGAGATTTTCGTTGGCCGGT 60.251 50.000 1.90 0.00 37.11 5.28
2837 2952 0.168128 GTGAGATTTTCGTTGGCCGG 59.832 55.000 0.00 0.00 37.11 6.13
2838 2953 1.128692 GAGTGAGATTTTCGTTGGCCG 59.871 52.381 0.00 0.00 38.13 6.13
2839 2954 1.128692 CGAGTGAGATTTTCGTTGGCC 59.871 52.381 0.00 0.00 0.00 5.36
2840 2955 1.464189 GCGAGTGAGATTTTCGTTGGC 60.464 52.381 0.00 0.00 36.74 4.52
2841 2956 2.069273 AGCGAGTGAGATTTTCGTTGG 58.931 47.619 0.00 0.00 36.74 3.77
2842 2957 2.731451 TGAGCGAGTGAGATTTTCGTTG 59.269 45.455 0.00 0.00 36.74 4.10
2843 2958 2.989840 CTGAGCGAGTGAGATTTTCGTT 59.010 45.455 0.00 0.00 36.74 3.85
2844 2959 2.600731 CTGAGCGAGTGAGATTTTCGT 58.399 47.619 0.00 0.00 36.74 3.85
2845 2960 1.322936 GCTGAGCGAGTGAGATTTTCG 59.677 52.381 0.00 0.00 37.40 3.46
2846 2961 2.602660 GAGCTGAGCGAGTGAGATTTTC 59.397 50.000 0.00 0.00 0.00 2.29
2847 2962 2.028658 TGAGCTGAGCGAGTGAGATTTT 60.029 45.455 0.00 0.00 0.00 1.82
2848 2963 1.547820 TGAGCTGAGCGAGTGAGATTT 59.452 47.619 0.00 0.00 0.00 2.17
2849 2964 1.134753 CTGAGCTGAGCGAGTGAGATT 59.865 52.381 0.00 0.00 0.00 2.40
2850 2965 0.740149 CTGAGCTGAGCGAGTGAGAT 59.260 55.000 0.00 0.00 0.00 2.75
2851 2966 1.932011 GCTGAGCTGAGCGAGTGAGA 61.932 60.000 10.09 0.00 0.00 3.27
2852 2967 1.516821 GCTGAGCTGAGCGAGTGAG 60.517 63.158 10.09 0.00 0.00 3.51
2853 2968 1.932011 GAGCTGAGCTGAGCGAGTGA 61.932 60.000 19.78 0.00 44.24 3.41
2854 2969 1.516821 GAGCTGAGCTGAGCGAGTG 60.517 63.158 19.78 0.00 44.24 3.51
2855 2970 1.530876 TTGAGCTGAGCTGAGCGAGT 61.531 55.000 19.78 1.78 44.24 4.18
2856 2971 1.077645 GTTGAGCTGAGCTGAGCGAG 61.078 60.000 19.78 0.00 44.24 5.03
2857 2972 1.080230 GTTGAGCTGAGCTGAGCGA 60.080 57.895 19.78 7.69 44.24 4.93
2858 2973 1.077645 GAGTTGAGCTGAGCTGAGCG 61.078 60.000 19.78 0.00 44.24 5.03
2859 2974 0.740516 GGAGTTGAGCTGAGCTGAGC 60.741 60.000 18.32 18.32 39.88 4.26
2860 2975 0.607112 TGGAGTTGAGCTGAGCTGAG 59.393 55.000 13.71 0.00 39.88 3.35
2861 2976 1.273759 ATGGAGTTGAGCTGAGCTGA 58.726 50.000 13.71 0.00 39.88 4.26
2862 2977 2.008329 GAATGGAGTTGAGCTGAGCTG 58.992 52.381 13.71 0.00 39.88 4.24
2863 2978 1.907936 AGAATGGAGTTGAGCTGAGCT 59.092 47.619 6.69 6.69 43.88 4.09
2864 2979 2.278854 GAGAATGGAGTTGAGCTGAGC 58.721 52.381 0.00 0.00 0.00 4.26
2865 2980 2.738000 CGGAGAATGGAGTTGAGCTGAG 60.738 54.545 0.00 0.00 0.00 3.35
2866 2981 1.205655 CGGAGAATGGAGTTGAGCTGA 59.794 52.381 0.00 0.00 0.00 4.26
2867 2982 1.649664 CGGAGAATGGAGTTGAGCTG 58.350 55.000 0.00 0.00 0.00 4.24
2868 2983 0.107945 GCGGAGAATGGAGTTGAGCT 60.108 55.000 0.00 0.00 0.00 4.09
2869 2984 0.107945 AGCGGAGAATGGAGTTGAGC 60.108 55.000 0.00 0.00 0.00 4.26
2870 2985 2.393271 AAGCGGAGAATGGAGTTGAG 57.607 50.000 0.00 0.00 0.00 3.02
2871 2986 2.832129 AGTAAGCGGAGAATGGAGTTGA 59.168 45.455 0.00 0.00 0.00 3.18
2872 2987 3.190874 GAGTAAGCGGAGAATGGAGTTG 58.809 50.000 0.00 0.00 0.00 3.16
2873 2988 2.832129 TGAGTAAGCGGAGAATGGAGTT 59.168 45.455 0.00 0.00 0.00 3.01
2874 2989 2.428890 CTGAGTAAGCGGAGAATGGAGT 59.571 50.000 0.00 0.00 0.00 3.85
2875 2990 2.690497 TCTGAGTAAGCGGAGAATGGAG 59.310 50.000 0.00 0.00 0.00 3.86
2876 2991 2.735151 TCTGAGTAAGCGGAGAATGGA 58.265 47.619 0.00 0.00 0.00 3.41
2877 2992 3.742433 ATCTGAGTAAGCGGAGAATGG 57.258 47.619 0.00 0.00 0.00 3.16
2878 2993 6.428385 AAAAATCTGAGTAAGCGGAGAATG 57.572 37.500 0.00 0.00 0.00 2.67
2971 3086 8.620416 CCCGAACATTGTCATGAATATTTCTAA 58.380 33.333 0.00 0.00 34.11 2.10
2972 3087 7.990314 TCCCGAACATTGTCATGAATATTTCTA 59.010 33.333 0.00 0.00 34.11 2.10
2973 3088 6.828273 TCCCGAACATTGTCATGAATATTTCT 59.172 34.615 0.00 0.00 34.11 2.52
2974 3089 7.026631 TCCCGAACATTGTCATGAATATTTC 57.973 36.000 0.00 0.00 34.11 2.17
2975 3090 7.403312 TTCCCGAACATTGTCATGAATATTT 57.597 32.000 0.00 0.00 34.11 1.40
2976 3091 7.587037 ATTCCCGAACATTGTCATGAATATT 57.413 32.000 0.00 0.00 34.11 1.28
2977 3092 7.587037 AATTCCCGAACATTGTCATGAATAT 57.413 32.000 0.00 0.00 34.11 1.28
2978 3093 7.121907 TGAAATTCCCGAACATTGTCATGAATA 59.878 33.333 0.00 0.00 34.11 1.75
2979 3094 5.920193 AATTCCCGAACATTGTCATGAAT 57.080 34.783 0.00 0.00 34.11 2.57
2980 3095 5.242615 TGAAATTCCCGAACATTGTCATGAA 59.757 36.000 0.00 0.00 34.11 2.57
2981 3096 4.764308 TGAAATTCCCGAACATTGTCATGA 59.236 37.500 0.00 0.00 34.11 3.07
2982 3097 5.058149 TGAAATTCCCGAACATTGTCATG 57.942 39.130 0.00 0.00 36.34 3.07
2983 3098 5.720371 TTGAAATTCCCGAACATTGTCAT 57.280 34.783 0.00 0.00 0.00 3.06
2984 3099 5.521906 TTTGAAATTCCCGAACATTGTCA 57.478 34.783 0.00 0.00 0.00 3.58
2985 3100 6.836577 TTTTTGAAATTCCCGAACATTGTC 57.163 33.333 0.00 0.00 0.00 3.18
3033 3148 9.979578 AGTTCATGAACATTTTTAAGTATGCAA 57.020 25.926 33.92 0.00 43.47 4.08
3034 3149 9.979578 AAGTTCATGAACATTTTTAAGTATGCA 57.020 25.926 33.92 0.00 43.47 3.96
3124 3239 9.667989 GGCTATTTCGTTAAAAGTAAAAGAACA 57.332 29.630 0.00 0.00 0.00 3.18
3125 3240 9.667989 TGGCTATTTCGTTAAAAGTAAAAGAAC 57.332 29.630 0.00 0.00 0.00 3.01
3127 3242 9.834628 CATGGCTATTTCGTTAAAAGTAAAAGA 57.165 29.630 0.00 0.00 0.00 2.52
3128 3243 9.620660 ACATGGCTATTTCGTTAAAAGTAAAAG 57.379 29.630 0.00 0.00 0.00 2.27
3167 3282 9.651913 TGTGCTTGTTTTTCTTTCTTTTATCTT 57.348 25.926 0.00 0.00 0.00 2.40
3168 3283 9.651913 TTGTGCTTGTTTTTCTTTCTTTTATCT 57.348 25.926 0.00 0.00 0.00 1.98
3172 3287 9.964303 ATTTTTGTGCTTGTTTTTCTTTCTTTT 57.036 22.222 0.00 0.00 0.00 2.27


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

AutoCloner maintained by Alex Coulton.