Multiple sequence alignment - TraesCS1B01G474900

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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 TraesCS1B01G474900 chr1B 100.000 3378 0 0 1 3378 683470423 683473800 0.000000e+00 6239.0
1 TraesCS1B01G474900 chr1B 96.599 147 5 0 2232 2378 683476010 683476156 9.360000e-61 244.0
2 TraesCS1B01G474900 chr1B 90.805 87 7 1 509 595 683470886 683470971 7.660000e-22 115.0
3 TraesCS1B01G474900 chr1B 90.805 87 7 1 464 549 683470931 683471017 7.660000e-22 115.0
4 TraesCS1B01G474900 chr1B 90.323 62 6 0 34 95 683478814 683478875 7.770000e-12 82.4
5 TraesCS1B01G474900 chr1D 85.502 2021 100 67 1 1931 491039179 491041096 0.000000e+00 1930.0
6 TraesCS1B01G474900 chr1D 87.815 755 40 22 1954 2695 491041157 491041872 0.000000e+00 837.0
7 TraesCS1B01G474900 chr1D 90.182 275 20 5 2731 3005 491042092 491042359 5.360000e-93 351.0
8 TraesCS1B01G474900 chr1D 87.973 291 25 4 3088 3378 491042704 491042984 5.400000e-88 335.0
9 TraesCS1B01G474900 chr1D 80.851 235 15 16 2467 2697 491045480 491045688 1.250000e-34 158.0
10 TraesCS1B01G474900 chr1D 96.250 80 3 0 509 588 491039654 491039733 7.610000e-27 132.0
11 TraesCS1B01G474900 chr1D 93.103 87 5 1 464 549 491039699 491039785 3.540000e-25 126.0
12 TraesCS1B01G474900 chr1D 91.176 68 6 0 34 101 491047704 491047771 3.590000e-15 93.5
13 TraesCS1B01G474900 chr1D 94.286 35 2 0 554 588 491039654 491039688 2.000000e-03 54.7
14 TraesCS1B01G474900 chr1A 93.577 685 41 1 1 685 589032456 589033137 0.000000e+00 1018.0
15 TraesCS1B01G474900 chr1A 88.735 648 49 14 2731 3378 589039892 589040515 0.000000e+00 771.0
16 TraesCS1B01G474900 chr1A 86.104 734 41 29 1682 2378 589038757 589039466 0.000000e+00 734.0
17 TraesCS1B01G474900 chr1A 78.723 517 34 34 1205 1689 589033652 589034124 3.320000e-70 276.0
18 TraesCS1B01G474900 chr1A 91.124 169 10 5 1008 1173 589033416 589033582 1.220000e-54 224.0
19 TraesCS1B01G474900 chr1A 82.796 186 19 6 2485 2666 589039545 589039721 1.620000e-33 154.0
20 TraesCS1B01G474900 chr1A 92.857 84 5 1 467 549 589032964 589033047 1.650000e-23 121.0
21 TraesCS1B01G474900 chr1A 90.698 86 8 0 509 594 589032916 589033001 7.660000e-22 115.0
22 TraesCS1B01G474900 chr1A 82.963 135 4 10 2467 2596 589042927 589043047 1.660000e-18 104.0
23 TraesCS1B01G474900 chr6A 90.816 98 9 0 2220 2317 159242937 159242840 7.610000e-27 132.0


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 TraesCS1B01G474900 chr1B 683470423 683473800 3377 False 2156.333333 6239 93.8700 1 3378 3 chr1B.!!$F1 3377
1 TraesCS1B01G474900 chr1D 491039179 491047771 8592 False 446.355556 1930 89.6820 1 3378 9 chr1D.!!$F1 3377
2 TraesCS1B01G474900 chr1A 589038757 589043047 4290 False 440.750000 771 85.1495 1682 3378 4 chr1A.!!$F2 1696
3 TraesCS1B01G474900 chr1A 589032456 589034124 1668 False 350.800000 1018 89.3958 1 1689 5 chr1A.!!$F1 1688

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
412 425 0.098200 CACATCGACGTCTAAGCCGA 59.902 55.0 14.7 5.55 35.43 5.54 F
1198 1292 0.105709 GAGGAGGAAGGAGGAGGAGG 60.106 65.0 0.0 0.00 0.00 4.30 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1593 1767 0.108945 GCATCTGCCAAGCCAAAGAC 60.109 55.0 0.0 0.0 34.31 3.01 R
2613 2859 0.106519 AAGCAACAAGACCAGCCTGT 60.107 50.0 0.0 0.0 0.00 4.00 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
24 25 0.251698 TGATGCAACATGGGCAAGGA 60.252 50.000 16.70 3.25 45.60 3.36
25 26 0.174162 GATGCAACATGGGCAAGGAC 59.826 55.000 16.70 6.94 45.60 3.85
46 47 1.217882 CTCGGCTGGTAATAAAGCGG 58.782 55.000 0.00 0.00 40.46 5.52
96 97 6.036517 GGAATCAACATAAGCTATATGCCTCG 59.963 42.308 12.84 0.00 44.23 4.63
129 130 4.141574 CCTCCAAATATCGGTAACCAAGGA 60.142 45.833 0.00 0.00 0.00 3.36
203 204 0.178068 CATTCCAGGTACCCGGTGAG 59.822 60.000 14.08 1.55 0.00 3.51
412 425 0.098200 CACATCGACGTCTAAGCCGA 59.902 55.000 14.70 5.55 35.43 5.54
415 428 0.235144 ATCGACGTCTAAGCCGATCG 59.765 55.000 14.70 8.51 37.18 3.69
434 447 0.252239 GGCTCCCCCAAGGACAATTT 60.252 55.000 0.00 0.00 40.93 1.82
461 474 2.293399 GGAACGAAACTTCAGTGCCATT 59.707 45.455 0.00 0.00 32.88 3.16
475 488 1.271108 TGCCATTGTCGTCTAGCCAAA 60.271 47.619 0.00 0.00 0.00 3.28
505 518 2.490903 CAGAGGCAAATTTCAGGTGGAG 59.509 50.000 0.00 0.00 0.00 3.86
546 559 2.791170 GCAGAGGCAGATTTCAGGG 58.209 57.895 0.00 0.00 40.72 4.45
550 563 0.625849 GAGGCAGATTTCAGGGGGAA 59.374 55.000 0.00 0.00 0.00 3.97
624 637 2.048603 GCATGGACAAGAGGTGGGC 61.049 63.158 0.00 0.00 0.00 5.36
686 699 1.523032 CTCCGCATCATCAGCAGCA 60.523 57.895 0.00 0.00 0.00 4.41
687 700 1.499688 CTCCGCATCATCAGCAGCAG 61.500 60.000 0.00 0.00 0.00 4.24
688 701 2.328289 CGCATCATCAGCAGCAGC 59.672 61.111 0.00 0.00 42.56 5.25
689 702 2.722487 GCATCATCAGCAGCAGCC 59.278 61.111 0.00 0.00 43.56 4.85
690 703 3.023118 CATCATCAGCAGCAGCCG 58.977 61.111 0.00 0.00 43.56 5.52
691 704 2.900838 ATCATCAGCAGCAGCCGC 60.901 61.111 0.00 0.00 43.56 6.53
692 705 3.692370 ATCATCAGCAGCAGCCGCA 62.692 57.895 2.79 0.00 43.56 5.69
693 706 3.877357 CATCAGCAGCAGCCGCAG 61.877 66.667 2.79 0.00 43.56 5.18
699 712 3.877357 CAGCAGCCGCAGCATCAG 61.877 66.667 10.66 0.00 43.56 2.90
812 825 2.595754 GCCGGGCTGATGGAATCC 60.596 66.667 12.87 0.00 44.73 3.01
868 882 6.150140 CCCTTGTCTCTGAAATCCAAAGTTAG 59.850 42.308 0.00 0.00 0.00 2.34
882 896 3.582714 AAGTTAGTGTACAGGTACGCC 57.417 47.619 16.99 5.50 45.06 5.68
897 935 1.377229 CGCCCTTGTTTCCCTACCA 59.623 57.895 0.00 0.00 0.00 3.25
903 941 3.562182 CCTTGTTTCCCTACCAACTTGT 58.438 45.455 0.00 0.00 0.00 3.16
904 942 3.317993 CCTTGTTTCCCTACCAACTTGTG 59.682 47.826 0.00 0.00 0.00 3.33
905 943 3.655615 TGTTTCCCTACCAACTTGTGT 57.344 42.857 0.00 0.00 0.00 3.72
906 944 3.970842 TGTTTCCCTACCAACTTGTGTT 58.029 40.909 0.00 0.00 36.75 3.32
907 945 4.345854 TGTTTCCCTACCAACTTGTGTTT 58.654 39.130 0.00 0.00 33.52 2.83
909 947 5.950549 TGTTTCCCTACCAACTTGTGTTTAA 59.049 36.000 0.00 0.00 33.52 1.52
911 949 7.124448 TGTTTCCCTACCAACTTGTGTTTAAAT 59.876 33.333 0.00 0.00 33.52 1.40
912 950 7.663043 TTCCCTACCAACTTGTGTTTAAATT 57.337 32.000 0.00 0.00 33.52 1.82
916 954 7.168469 CCCTACCAACTTGTGTTTAAATTTTCG 59.832 37.037 0.00 0.00 33.52 3.46
917 955 7.703197 CCTACCAACTTGTGTTTAAATTTTCGT 59.297 33.333 0.00 0.00 33.52 3.85
918 956 7.284518 ACCAACTTGTGTTTAAATTTTCGTG 57.715 32.000 0.00 0.00 33.52 4.35
919 957 6.181944 CCAACTTGTGTTTAAATTTTCGTGC 58.818 36.000 0.00 0.00 33.52 5.34
920 958 6.035542 CCAACTTGTGTTTAAATTTTCGTGCT 59.964 34.615 0.00 0.00 33.52 4.40
921 959 6.567769 ACTTGTGTTTAAATTTTCGTGCTG 57.432 33.333 0.00 0.00 0.00 4.41
922 960 6.326375 ACTTGTGTTTAAATTTTCGTGCTGA 58.674 32.000 0.00 0.00 0.00 4.26
923 961 6.252655 ACTTGTGTTTAAATTTTCGTGCTGAC 59.747 34.615 0.00 0.00 0.00 3.51
924 962 5.885881 TGTGTTTAAATTTTCGTGCTGACT 58.114 33.333 0.00 0.00 0.00 3.41
925 963 7.017498 TGTGTTTAAATTTTCGTGCTGACTA 57.983 32.000 0.00 0.00 0.00 2.59
926 964 7.644490 TGTGTTTAAATTTTCGTGCTGACTAT 58.356 30.769 0.00 0.00 0.00 2.12
927 965 8.132362 TGTGTTTAAATTTTCGTGCTGACTATT 58.868 29.630 0.00 0.00 0.00 1.73
938 1001 7.946655 TCGTGCTGACTATTTATTATCTTGG 57.053 36.000 0.00 0.00 0.00 3.61
969 1032 2.999507 TTGACGTTTGCTGTGTGTTT 57.000 40.000 0.00 0.00 0.00 2.83
992 1055 3.267900 GGTGTCGGACCGATGTATG 57.732 57.895 21.53 0.00 38.42 2.39
993 1056 0.249322 GGTGTCGGACCGATGTATGG 60.249 60.000 21.53 0.00 38.42 2.74
994 1057 0.742505 GTGTCGGACCGATGTATGGA 59.257 55.000 21.53 0.00 38.42 3.41
995 1058 1.135527 GTGTCGGACCGATGTATGGAA 59.864 52.381 21.53 0.00 38.42 3.53
996 1059 2.036387 TGTCGGACCGATGTATGGAAT 58.964 47.619 21.53 0.00 38.42 3.01
997 1060 2.223947 TGTCGGACCGATGTATGGAATG 60.224 50.000 21.53 0.00 38.42 2.67
998 1061 1.343142 TCGGACCGATGTATGGAATGG 59.657 52.381 13.88 0.00 0.00 3.16
999 1062 1.343142 CGGACCGATGTATGGAATGGA 59.657 52.381 8.64 0.00 0.00 3.41
1000 1063 2.224185 CGGACCGATGTATGGAATGGAA 60.224 50.000 8.64 0.00 0.00 3.53
1001 1064 3.557054 CGGACCGATGTATGGAATGGAAT 60.557 47.826 8.64 0.00 0.00 3.01
1002 1065 3.753272 GGACCGATGTATGGAATGGAATG 59.247 47.826 0.00 0.00 0.00 2.67
1003 1066 3.753272 GACCGATGTATGGAATGGAATGG 59.247 47.826 0.00 0.00 0.00 3.16
1004 1067 3.394274 ACCGATGTATGGAATGGAATGGA 59.606 43.478 0.00 0.00 0.00 3.41
1005 1068 4.141274 ACCGATGTATGGAATGGAATGGAA 60.141 41.667 0.00 0.00 0.00 3.53
1006 1069 4.216257 CCGATGTATGGAATGGAATGGAAC 59.784 45.833 0.00 0.00 0.00 3.62
1139 1207 0.821711 TTTGAGGTTTGGTCGGCTGG 60.822 55.000 0.00 0.00 0.00 4.85
1140 1208 1.990160 TTGAGGTTTGGTCGGCTGGT 61.990 55.000 0.00 0.00 0.00 4.00
1141 1209 1.228154 GAGGTTTGGTCGGCTGGTT 60.228 57.895 0.00 0.00 0.00 3.67
1142 1210 1.515521 GAGGTTTGGTCGGCTGGTTG 61.516 60.000 0.00 0.00 0.00 3.77
1156 1224 3.118592 GGCTGGTTGCAGTCTAGATAAGT 60.119 47.826 0.00 0.00 45.15 2.24
1196 1290 0.855855 TGGAGGAGGAAGGAGGAGGA 60.856 60.000 0.00 0.00 0.00 3.71
1198 1292 0.105709 GAGGAGGAAGGAGGAGGAGG 60.106 65.000 0.00 0.00 0.00 4.30
1199 1293 0.556380 AGGAGGAAGGAGGAGGAGGA 60.556 60.000 0.00 0.00 0.00 3.71
1200 1294 0.105709 GGAGGAAGGAGGAGGAGGAG 60.106 65.000 0.00 0.00 0.00 3.69
1222 1337 3.095738 GTGTTTTGTTTTCCGTGTCTCG 58.904 45.455 0.00 0.00 39.52 4.04
1223 1338 2.743126 TGTTTTGTTTTCCGTGTCTCGT 59.257 40.909 0.00 0.00 37.94 4.18
1224 1339 3.181518 TGTTTTGTTTTCCGTGTCTCGTC 60.182 43.478 0.00 0.00 37.94 4.20
1225 1340 1.202203 TTGTTTTCCGTGTCTCGTCG 58.798 50.000 0.00 0.00 37.94 5.12
1226 1341 0.595567 TGTTTTCCGTGTCTCGTCGG 60.596 55.000 0.00 0.00 46.93 4.79
1271 1386 1.338960 TGTACATGCTGCTGCTGCTTA 60.339 47.619 27.67 15.52 40.48 3.09
1272 1387 1.945394 GTACATGCTGCTGCTGCTTAT 59.055 47.619 27.67 16.21 40.48 1.73
1273 1388 0.738975 ACATGCTGCTGCTGCTTATG 59.261 50.000 27.67 24.41 40.48 1.90
1274 1389 0.595053 CATGCTGCTGCTGCTTATGC 60.595 55.000 27.67 14.65 40.48 3.14
1275 1390 0.752009 ATGCTGCTGCTGCTTATGCT 60.752 50.000 27.67 7.12 40.48 3.79
1276 1391 0.963856 TGCTGCTGCTGCTTATGCTT 60.964 50.000 27.67 0.00 40.48 3.91
1277 1392 0.525668 GCTGCTGCTGCTTATGCTTG 60.526 55.000 22.10 0.00 40.48 4.01
1278 1393 0.809385 CTGCTGCTGCTTATGCTTGT 59.191 50.000 17.00 0.00 40.48 3.16
1279 1394 1.201647 CTGCTGCTGCTTATGCTTGTT 59.798 47.619 17.00 0.00 40.48 2.83
1298 1413 2.367567 GTTGGTTGGTGGTAGAGTCAGA 59.632 50.000 0.00 0.00 0.00 3.27
1301 1416 2.028930 GGTTGGTGGTAGAGTCAGAGTG 60.029 54.545 0.00 0.00 0.00 3.51
1305 1420 2.750712 GGTGGTAGAGTCAGAGTGTCTC 59.249 54.545 0.00 0.00 33.68 3.36
1306 1421 3.560453 GGTGGTAGAGTCAGAGTGTCTCT 60.560 52.174 8.42 8.42 43.38 3.10
1307 1422 4.076394 GTGGTAGAGTCAGAGTGTCTCTT 58.924 47.826 8.63 0.00 39.26 2.85
1308 1423 4.075682 TGGTAGAGTCAGAGTGTCTCTTG 58.924 47.826 8.63 0.00 39.26 3.02
1372 1498 7.114811 CAGTGGTACAACAAGTTGATTAAATGC 59.885 37.037 18.90 0.06 44.16 3.56
1380 1506 5.238432 ACAAGTTGATTAAATGCGACAGTGA 59.762 36.000 10.54 0.00 0.00 3.41
1383 1511 6.317088 AGTTGATTAAATGCGACAGTGAATG 58.683 36.000 0.00 0.00 0.00 2.67
1395 1523 4.273480 CGACAGTGAATGGTTGAAAGAGTT 59.727 41.667 0.00 0.00 0.00 3.01
1397 1525 5.192927 ACAGTGAATGGTTGAAAGAGTTCA 58.807 37.500 0.00 0.00 42.12 3.18
1398 1526 5.829924 ACAGTGAATGGTTGAAAGAGTTCAT 59.170 36.000 0.00 0.00 43.29 2.57
1417 1546 5.219343 TCATCGTTGCATTGGATCTATCT 57.781 39.130 0.00 0.00 0.00 1.98
1455 1610 0.953471 CATTCGTCCCAGCAAACGGA 60.953 55.000 0.00 0.00 39.31 4.69
1456 1611 0.250553 ATTCGTCCCAGCAAACGGAA 60.251 50.000 0.00 0.00 39.31 4.30
1457 1612 0.464013 TTCGTCCCAGCAAACGGAAA 60.464 50.000 0.00 0.00 39.31 3.13
1515 1680 0.824109 TAGGCCATCCAGTTCAGTCG 59.176 55.000 5.01 0.00 33.74 4.18
1542 1713 3.181493 GCTCAGCGGTGAAAATGAATGAT 60.181 43.478 19.16 0.00 30.14 2.45
1584 1758 1.830477 CAGATAGATAGGGGAGCTGGC 59.170 57.143 0.00 0.00 0.00 4.85
1586 1760 1.830477 GATAGATAGGGGAGCTGGCTG 59.170 57.143 0.00 0.00 0.00 4.85
1587 1761 0.178921 TAGATAGGGGAGCTGGCTGG 60.179 60.000 0.00 0.00 0.00 4.85
1588 1762 1.460305 GATAGGGGAGCTGGCTGGA 60.460 63.158 0.00 0.00 0.00 3.86
1589 1763 0.839853 GATAGGGGAGCTGGCTGGAT 60.840 60.000 0.00 0.00 0.00 3.41
1590 1764 0.493639 ATAGGGGAGCTGGCTGGATA 59.506 55.000 0.00 0.00 0.00 2.59
1591 1765 0.178921 TAGGGGAGCTGGCTGGATAG 60.179 60.000 0.00 0.00 0.00 2.08
1592 1766 1.460305 GGGGAGCTGGCTGGATAGA 60.460 63.158 0.00 0.00 0.00 1.98
1593 1767 1.479368 GGGGAGCTGGCTGGATAGAG 61.479 65.000 0.00 0.00 0.00 2.43
1594 1768 0.762461 GGGAGCTGGCTGGATAGAGT 60.762 60.000 0.00 0.00 0.00 3.24
1595 1769 0.678950 GGAGCTGGCTGGATAGAGTC 59.321 60.000 0.00 0.00 0.00 3.36
1596 1770 1.703411 GAGCTGGCTGGATAGAGTCT 58.297 55.000 0.00 0.00 0.00 3.24
1597 1771 2.038659 GAGCTGGCTGGATAGAGTCTT 58.961 52.381 0.00 0.00 0.00 3.01
1659 1837 3.482436 AGGAAAGCGATATCTCGTCTCT 58.518 45.455 0.34 0.00 46.71 3.10
1660 1838 3.500680 AGGAAAGCGATATCTCGTCTCTC 59.499 47.826 0.34 0.00 46.71 3.20
1661 1839 3.475242 GAAAGCGATATCTCGTCTCTCG 58.525 50.000 0.34 0.00 46.71 4.04
1662 1840 3.283712 GCGATATCTCGTCTCTCGC 57.716 57.895 0.34 0.00 46.71 5.03
1666 1844 4.431894 CGATATCTCGTCTCTCGCTATC 57.568 50.000 0.34 0.00 40.07 2.08
1667 1845 4.109766 CGATATCTCGTCTCTCGCTATCT 58.890 47.826 0.34 0.00 40.07 1.98
1668 1846 4.206404 CGATATCTCGTCTCTCGCTATCTC 59.794 50.000 0.34 0.00 40.07 2.75
1669 1847 3.678056 ATCTCGTCTCTCGCTATCTCT 57.322 47.619 0.00 0.00 39.67 3.10
1670 1848 3.021269 TCTCGTCTCTCGCTATCTCTC 57.979 52.381 0.00 0.00 39.67 3.20
1671 1849 2.626266 TCTCGTCTCTCGCTATCTCTCT 59.374 50.000 0.00 0.00 39.67 3.10
1709 1887 4.598036 ATTCCACATCCACCATTCTTCT 57.402 40.909 0.00 0.00 0.00 2.85
1735 1913 4.240096 GCCCTGATTGATTGTTTCTTGTG 58.760 43.478 0.00 0.00 0.00 3.33
1898 2076 4.052229 CCTTCGTCGGCGGTCAGT 62.052 66.667 10.62 0.00 38.89 3.41
1900 2078 1.513586 CTTCGTCGGCGGTCAGTAC 60.514 63.158 10.62 0.00 38.89 2.73
1924 2102 1.158904 ATCCCGATCTCACTCCCCTA 58.841 55.000 0.00 0.00 0.00 3.53
1931 2109 2.438800 TCTCACTCCCCTACTGCTAC 57.561 55.000 0.00 0.00 0.00 3.58
1932 2110 1.923850 TCTCACTCCCCTACTGCTACT 59.076 52.381 0.00 0.00 0.00 2.57
1934 2112 1.063867 TCACTCCCCTACTGCTACTCC 60.064 57.143 0.00 0.00 0.00 3.85
1949 2160 0.609681 ACTCCGCCTTCTTCTCTCGT 60.610 55.000 0.00 0.00 0.00 4.18
1966 2182 1.964223 TCGTAGAGATCCAAGATGCCC 59.036 52.381 0.00 0.00 0.00 5.36
2003 2220 3.517602 CACTGTTGCAATCCATCCATTG 58.482 45.455 0.59 0.00 36.91 2.82
2008 2229 3.227273 CAATCCATCCATTGCCCCA 57.773 52.632 0.00 0.00 0.00 4.96
2009 2230 0.754472 CAATCCATCCATTGCCCCAC 59.246 55.000 0.00 0.00 0.00 4.61
2131 2367 2.992114 AAGACCGCCGACTCTGCT 60.992 61.111 0.00 0.00 0.00 4.24
2134 2370 3.991536 GACCGCCGACTCTGCTTCC 62.992 68.421 0.00 0.00 0.00 3.46
2155 2391 4.539083 ACTGCAACGGCGTCCACA 62.539 61.111 15.17 11.25 45.35 4.17
2156 2392 3.049674 CTGCAACGGCGTCCACAT 61.050 61.111 15.17 0.00 45.35 3.21
2165 2401 2.880879 CGTCCACATCGTCTGCCG 60.881 66.667 0.00 0.00 38.13 5.69
2387 2629 1.520342 GTGCTCTGAGACCGGATGC 60.520 63.158 9.46 1.68 0.00 3.91
2388 2630 2.279120 GCTCTGAGACCGGATGCG 60.279 66.667 9.46 0.00 0.00 4.73
2389 2631 3.069980 GCTCTGAGACCGGATGCGT 62.070 63.158 9.46 0.00 0.00 5.24
2390 2632 1.226802 CTCTGAGACCGGATGCGTG 60.227 63.158 9.46 0.00 0.00 5.34
2391 2633 2.202797 CTGAGACCGGATGCGTGG 60.203 66.667 9.46 0.00 0.00 4.94
2393 2635 2.021068 CTGAGACCGGATGCGTGGAT 62.021 60.000 9.46 0.00 0.00 3.41
2394 2636 1.592669 GAGACCGGATGCGTGGATG 60.593 63.158 9.46 0.00 0.00 3.51
2395 2637 2.588877 GACCGGATGCGTGGATGG 60.589 66.667 9.46 0.00 0.00 3.51
2396 2638 4.175337 ACCGGATGCGTGGATGGG 62.175 66.667 9.46 0.00 0.00 4.00
2400 2642 2.589540 GATGCGTGGATGGGTGGA 59.410 61.111 0.00 0.00 0.00 4.02
2412 2654 4.208632 GGTGGATGAAGCTCACCG 57.791 61.111 5.83 0.00 41.03 4.94
2434 2676 2.286831 CCAGATTGATCGATGTTGCTGC 60.287 50.000 0.54 0.00 0.00 5.25
2467 2709 2.105006 TGCTTTGCCTCATGTCTCTC 57.895 50.000 0.00 0.00 0.00 3.20
2468 2710 1.627329 TGCTTTGCCTCATGTCTCTCT 59.373 47.619 0.00 0.00 0.00 3.10
2527 2769 0.944386 AGTTGATTGTGTCGTGTGGC 59.056 50.000 0.00 0.00 0.00 5.01
2539 2781 3.930229 TGTCGTGTGGCACTGTTATTATC 59.070 43.478 19.83 0.95 31.34 1.75
2588 2834 2.364842 AGGCCCATCTCGAGCTGT 60.365 61.111 14.70 0.00 0.00 4.40
2596 2842 4.142381 GCCCATCTCGAGCTGTTTTATTTT 60.142 41.667 14.70 0.00 0.00 1.82
2597 2843 5.065988 GCCCATCTCGAGCTGTTTTATTTTA 59.934 40.000 14.70 0.00 0.00 1.52
2598 2844 6.719365 CCCATCTCGAGCTGTTTTATTTTAG 58.281 40.000 14.70 0.00 0.00 1.85
2599 2845 6.316390 CCCATCTCGAGCTGTTTTATTTTAGT 59.684 38.462 14.70 0.00 0.00 2.24
2600 2846 7.148239 CCCATCTCGAGCTGTTTTATTTTAGTT 60.148 37.037 14.70 0.00 0.00 2.24
2601 2847 7.693951 CCATCTCGAGCTGTTTTATTTTAGTTG 59.306 37.037 14.70 0.00 0.00 3.16
2613 2859 7.517614 TTTATTTTAGTTGTGTGGATGCAGA 57.482 32.000 0.00 0.00 0.00 4.26
2617 2863 0.877071 GTTGTGTGGATGCAGACAGG 59.123 55.000 16.51 0.00 30.00 4.00
2640 2886 1.559831 GTCTTGTTGCTTGTGTTGCC 58.440 50.000 0.00 0.00 0.00 4.52
2643 2889 0.175302 TTGTTGCTTGTGTTGCCCTG 59.825 50.000 0.00 0.00 0.00 4.45
2655 2901 1.615392 GTTGCCCTGTGCTTCTTCAAT 59.385 47.619 0.00 0.00 42.00 2.57
2667 2913 8.806429 TGTGCTTCTTCAATATAAGGATTTGA 57.194 30.769 0.00 0.00 0.00 2.69
2676 2922 9.830975 TTCAATATAAGGATTTGATTCGTCTCA 57.169 29.630 0.00 0.00 0.00 3.27
2804 3237 0.940126 GCAAGTGTGGTCAGTGTCTG 59.060 55.000 0.00 0.00 0.00 3.51
2820 3253 5.698089 CAGTGTCTGTATGAGTGTGAATGTT 59.302 40.000 0.00 0.00 0.00 2.71
2869 3302 0.453390 GCCAAAATTGAGCTCCTCCG 59.547 55.000 12.15 0.00 0.00 4.63
2917 3350 4.406648 CTACAGATAGCCACACATCCAA 57.593 45.455 0.00 0.00 0.00 3.53
2925 3358 0.896940 CCACACATCCAAAGCTGCCT 60.897 55.000 0.00 0.00 0.00 4.75
2926 3359 0.524862 CACACATCCAAAGCTGCCTC 59.475 55.000 0.00 0.00 0.00 4.70
2927 3360 0.111061 ACACATCCAAAGCTGCCTCA 59.889 50.000 0.00 0.00 0.00 3.86
2946 3379 5.674525 CCTCAAATAACATCCACTAGCTCA 58.325 41.667 0.00 0.00 0.00 4.26
2969 3402 1.237163 CTGCTCCTCCTCCCCCATA 59.763 63.158 0.00 0.00 0.00 2.74
2998 3431 1.101331 CAGAATTGGAGGGCTTCTGC 58.899 55.000 0.00 0.00 39.40 4.26
3021 3454 2.334946 GCATCAGGCAGGCGTTCAA 61.335 57.895 0.00 0.00 43.97 2.69
3054 3487 1.068753 AGCATCCGAATCTCAGGCG 59.931 57.895 0.00 0.00 0.00 5.52
3062 3495 1.601663 CGAATCTCAGGCGAGTCATCC 60.602 57.143 6.32 0.00 40.44 3.51
3063 3496 0.755686 AATCTCAGGCGAGTCATCCC 59.244 55.000 6.32 0.00 40.44 3.85
3148 3855 0.884704 GTTGTGCTGGAGGCGAGAAA 60.885 55.000 0.00 0.00 45.43 2.52
3149 3856 0.036732 TTGTGCTGGAGGCGAGAAAT 59.963 50.000 0.00 0.00 45.43 2.17
3193 3900 1.792301 CTGTGCAGACATTCAGCCG 59.208 57.895 0.00 0.00 0.00 5.52
3225 3932 1.610522 CCCACTCTTCTTGCAAGGTTG 59.389 52.381 25.73 15.50 0.00 3.77
3267 3974 4.928020 CACTCTACTTTTCCCGTTACTTCC 59.072 45.833 0.00 0.00 0.00 3.46
3268 3975 4.590222 ACTCTACTTTTCCCGTTACTTCCA 59.410 41.667 0.00 0.00 0.00 3.53
3269 3976 5.247792 ACTCTACTTTTCCCGTTACTTCCAT 59.752 40.000 0.00 0.00 0.00 3.41
3270 3977 5.727434 TCTACTTTTCCCGTTACTTCCATC 58.273 41.667 0.00 0.00 0.00 3.51
3271 3978 3.332034 ACTTTTCCCGTTACTTCCATCG 58.668 45.455 0.00 0.00 0.00 3.84
3283 3990 1.734465 CTTCCATCGCACTTCCTGTTC 59.266 52.381 0.00 0.00 0.00 3.18
3295 4002 2.273370 TCCTGTTCGCTAATGTCGTC 57.727 50.000 0.00 0.00 0.00 4.20
3296 4003 0.914551 CCTGTTCGCTAATGTCGTCG 59.085 55.000 0.00 0.00 0.00 5.12
3297 4004 1.614385 CTGTTCGCTAATGTCGTCGT 58.386 50.000 0.00 0.00 0.00 4.34
3301 4008 2.289890 TCGCTAATGTCGTCGTATCG 57.710 50.000 0.00 0.00 0.00 2.92
3327 4034 4.780815 TGGATGCAGTTAATGTAGGGAAG 58.219 43.478 0.00 0.00 0.00 3.46
3357 4064 1.090052 GCGGAGACATAGGGCAACAC 61.090 60.000 0.00 0.00 39.74 3.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
24 25 1.134189 GCTTTATTACCAGCCGAGGGT 60.134 52.381 0.00 0.00 42.48 4.34
25 26 1.594331 GCTTTATTACCAGCCGAGGG 58.406 55.000 0.00 0.00 0.00 4.30
30 31 1.099689 TTGCCGCTTTATTACCAGCC 58.900 50.000 0.00 0.00 31.82 4.85
46 47 2.224314 GCTGAGGTGTAACTGAAGTTGC 59.776 50.000 5.95 5.21 40.37 4.17
96 97 0.680921 TATTTGGAGGCTGCTGCACC 60.681 55.000 17.89 18.43 41.91 5.01
129 130 1.542375 AGGAGGACCCTGCACCAAT 60.542 57.895 10.21 0.00 45.61 3.16
224 225 2.229792 GGATGTTGTTCTGTGCTGGAA 58.770 47.619 0.00 0.00 0.00 3.53
306 319 2.045926 GGAATCGCCTGGCTGTGT 60.046 61.111 17.92 0.00 0.00 3.72
412 425 3.090532 GTCCTTGGGGGAGCCGAT 61.091 66.667 0.00 0.00 46.10 4.18
415 428 0.252239 AAATTGTCCTTGGGGGAGCC 60.252 55.000 0.00 0.00 46.10 4.70
434 447 0.464013 TGAAGTTTCGTTCCCGGCAA 60.464 50.000 0.00 0.00 33.95 4.52
461 474 1.725641 CATGCTTTGGCTAGACGACA 58.274 50.000 0.00 0.00 39.59 4.35
505 518 1.113517 ATGCCTTGGCTGGATGATGC 61.114 55.000 13.18 0.00 0.00 3.91
546 559 1.396653 CTTGGCTGGATGATGTTCCC 58.603 55.000 0.00 0.00 34.67 3.97
550 563 0.260816 ATGCCTTGGCTGGATGATGT 59.739 50.000 13.18 0.00 0.00 3.06
693 706 0.810823 GTCTCTGCTGGAGCTGATGC 60.811 60.000 8.47 0.00 45.61 3.91
694 707 0.179078 GGTCTCTGCTGGAGCTGATG 60.179 60.000 8.47 4.35 45.61 3.07
695 708 0.616964 TGGTCTCTGCTGGAGCTGAT 60.617 55.000 8.47 0.00 45.61 2.90
696 709 1.228988 TGGTCTCTGCTGGAGCTGA 60.229 57.895 7.84 7.84 44.81 4.26
697 710 1.218585 CTGGTCTCTGCTGGAGCTG 59.781 63.158 0.00 0.00 41.60 4.24
698 711 0.835543 AACTGGTCTCTGCTGGAGCT 60.836 55.000 0.00 0.00 41.60 4.09
699 712 0.673022 CAACTGGTCTCTGCTGGAGC 60.673 60.000 0.00 0.00 41.60 4.70
700 713 0.036577 CCAACTGGTCTCTGCTGGAG 60.037 60.000 0.00 0.00 43.12 3.86
882 896 3.317993 CACAAGTTGGTAGGGAAACAAGG 59.682 47.826 7.96 0.00 0.00 3.61
897 935 6.809196 TCAGCACGAAAATTTAAACACAAGTT 59.191 30.769 0.00 0.00 40.40 2.66
912 950 8.826710 CCAAGATAATAAATAGTCAGCACGAAA 58.173 33.333 0.00 0.00 0.00 3.46
916 954 9.937175 GTTTCCAAGATAATAAATAGTCAGCAC 57.063 33.333 0.00 0.00 0.00 4.40
917 955 9.905713 AGTTTCCAAGATAATAAATAGTCAGCA 57.094 29.630 0.00 0.00 0.00 4.41
936 999 4.974368 AACGTCAAAACATCAGTTTCCA 57.026 36.364 0.00 0.00 46.79 3.53
938 1001 4.798387 AGCAAACGTCAAAACATCAGTTTC 59.202 37.500 0.00 0.00 46.79 2.78
969 1032 1.605451 ATCGGTCCGACACCTGACA 60.605 57.895 18.08 0.00 44.21 3.58
988 1051 3.815809 TCCGTTCCATTCCATTCCATAC 58.184 45.455 0.00 0.00 0.00 2.39
989 1052 4.204012 GTTCCGTTCCATTCCATTCCATA 58.796 43.478 0.00 0.00 0.00 2.74
990 1053 3.023832 GTTCCGTTCCATTCCATTCCAT 58.976 45.455 0.00 0.00 0.00 3.41
991 1054 2.442413 GTTCCGTTCCATTCCATTCCA 58.558 47.619 0.00 0.00 0.00 3.53
992 1055 1.400494 CGTTCCGTTCCATTCCATTCC 59.600 52.381 0.00 0.00 0.00 3.01
993 1056 1.400494 CCGTTCCGTTCCATTCCATTC 59.600 52.381 0.00 0.00 0.00 2.67
994 1057 1.003812 TCCGTTCCGTTCCATTCCATT 59.996 47.619 0.00 0.00 0.00 3.16
995 1058 0.616371 TCCGTTCCGTTCCATTCCAT 59.384 50.000 0.00 0.00 0.00 3.41
996 1059 0.397187 TTCCGTTCCGTTCCATTCCA 59.603 50.000 0.00 0.00 0.00 3.53
997 1060 0.800631 GTTCCGTTCCGTTCCATTCC 59.199 55.000 0.00 0.00 0.00 3.01
998 1061 0.441145 CGTTCCGTTCCGTTCCATTC 59.559 55.000 0.00 0.00 0.00 2.67
999 1062 0.033781 TCGTTCCGTTCCGTTCCATT 59.966 50.000 0.00 0.00 0.00 3.16
1000 1063 0.033781 TTCGTTCCGTTCCGTTCCAT 59.966 50.000 0.00 0.00 0.00 3.41
1001 1064 0.179089 TTTCGTTCCGTTCCGTTCCA 60.179 50.000 0.00 0.00 0.00 3.53
1002 1065 0.509929 CTTTCGTTCCGTTCCGTTCC 59.490 55.000 0.00 0.00 0.00 3.62
1003 1066 1.190984 GACTTTCGTTCCGTTCCGTTC 59.809 52.381 0.00 0.00 0.00 3.95
1004 1067 1.211743 GACTTTCGTTCCGTTCCGTT 58.788 50.000 0.00 0.00 0.00 4.44
1005 1068 0.936297 CGACTTTCGTTCCGTTCCGT 60.936 55.000 0.00 0.00 34.72 4.69
1006 1069 1.771044 CGACTTTCGTTCCGTTCCG 59.229 57.895 0.00 0.00 34.72 4.30
1016 1083 1.071239 CACTGTCAGCAACGACTTTCG 60.071 52.381 0.00 0.00 46.93 3.46
1018 1085 1.299541 CCACTGTCAGCAACGACTTT 58.700 50.000 0.00 0.00 36.82 2.66
1129 1197 3.825160 GACTGCAACCAGCCGACCA 62.825 63.158 0.00 0.00 43.02 4.02
1139 1207 8.160521 TCTATCTCACTTATCTAGACTGCAAC 57.839 38.462 0.00 0.00 0.00 4.17
1140 1208 8.932434 ATCTATCTCACTTATCTAGACTGCAA 57.068 34.615 0.00 0.00 0.00 4.08
1141 1209 8.791675 CAATCTATCTCACTTATCTAGACTGCA 58.208 37.037 0.00 0.00 0.00 4.41
1142 1210 9.008965 TCAATCTATCTCACTTATCTAGACTGC 57.991 37.037 0.00 0.00 0.00 4.40
1156 1224 8.925338 CCTCCATCATCATATCAATCTATCTCA 58.075 37.037 0.00 0.00 0.00 3.27
1196 1290 2.425668 CACGGAAAACAAAACACCTCCT 59.574 45.455 0.00 0.00 0.00 3.69
1198 1292 3.128068 AGACACGGAAAACAAAACACCTC 59.872 43.478 0.00 0.00 0.00 3.85
1199 1293 3.086282 AGACACGGAAAACAAAACACCT 58.914 40.909 0.00 0.00 0.00 4.00
1200 1294 3.431856 GAGACACGGAAAACAAAACACC 58.568 45.455 0.00 0.00 0.00 4.16
1222 1337 3.600388 GGTTATCATCCATCCATCCGAC 58.400 50.000 0.00 0.00 0.00 4.79
1223 1338 2.233676 CGGTTATCATCCATCCATCCGA 59.766 50.000 0.00 0.00 38.03 4.55
1224 1339 2.621338 CGGTTATCATCCATCCATCCG 58.379 52.381 0.00 0.00 0.00 4.18
1225 1340 2.571653 TCCGGTTATCATCCATCCATCC 59.428 50.000 0.00 0.00 0.00 3.51
1226 1341 3.981071 TCCGGTTATCATCCATCCATC 57.019 47.619 0.00 0.00 0.00 3.51
1227 1342 3.009473 CCTTCCGGTTATCATCCATCCAT 59.991 47.826 0.00 0.00 0.00 3.41
1228 1343 2.371841 CCTTCCGGTTATCATCCATCCA 59.628 50.000 0.00 0.00 0.00 3.41
1271 1386 2.158534 TCTACCACCAACCAACAAGCAT 60.159 45.455 0.00 0.00 0.00 3.79
1272 1387 1.213182 TCTACCACCAACCAACAAGCA 59.787 47.619 0.00 0.00 0.00 3.91
1273 1388 1.880027 CTCTACCACCAACCAACAAGC 59.120 52.381 0.00 0.00 0.00 4.01
1274 1389 3.139077 GACTCTACCACCAACCAACAAG 58.861 50.000 0.00 0.00 0.00 3.16
1275 1390 2.506231 TGACTCTACCACCAACCAACAA 59.494 45.455 0.00 0.00 0.00 2.83
1276 1391 2.104111 CTGACTCTACCACCAACCAACA 59.896 50.000 0.00 0.00 0.00 3.33
1277 1392 2.367567 TCTGACTCTACCACCAACCAAC 59.632 50.000 0.00 0.00 0.00 3.77
1278 1393 2.632996 CTCTGACTCTACCACCAACCAA 59.367 50.000 0.00 0.00 0.00 3.67
1279 1394 2.248248 CTCTGACTCTACCACCAACCA 58.752 52.381 0.00 0.00 0.00 3.67
1298 1413 7.526142 TTTATACAGTCACTCAAGAGACACT 57.474 36.000 3.73 2.39 37.97 3.55
1301 1416 9.209175 ACAAATTTATACAGTCACTCAAGAGAC 57.791 33.333 3.73 0.00 36.17 3.36
1305 1420 9.599322 GACAACAAATTTATACAGTCACTCAAG 57.401 33.333 0.00 0.00 0.00 3.02
1306 1421 8.279800 CGACAACAAATTTATACAGTCACTCAA 58.720 33.333 0.00 0.00 0.00 3.02
1307 1422 7.439955 ACGACAACAAATTTATACAGTCACTCA 59.560 33.333 0.00 0.00 0.00 3.41
1308 1423 7.793902 ACGACAACAAATTTATACAGTCACTC 58.206 34.615 0.00 0.00 0.00 3.51
1344 1470 5.751243 AATCAACTTGTTGTACCACTGTC 57.249 39.130 12.44 0.00 0.00 3.51
1372 1498 3.809832 ACTCTTTCAACCATTCACTGTCG 59.190 43.478 0.00 0.00 0.00 4.35
1380 1506 5.762045 CAACGATGAACTCTTTCAACCATT 58.238 37.500 0.00 0.00 45.01 3.16
1383 1511 3.003275 TGCAACGATGAACTCTTTCAACC 59.997 43.478 0.00 0.00 45.01 3.77
1395 1523 5.219343 AGATAGATCCAATGCAACGATGA 57.781 39.130 0.00 0.00 0.00 2.92
1397 1525 7.180322 AGATAGATAGATCCAATGCAACGAT 57.820 36.000 0.00 0.00 0.00 3.73
1398 1526 6.596309 AGATAGATAGATCCAATGCAACGA 57.404 37.500 0.00 0.00 0.00 3.85
1417 1546 9.217278 GACGAATGAGGTACAAGTAGATAGATA 57.783 37.037 0.00 0.00 0.00 1.98
1438 1593 0.464013 TTTCCGTTTGCTGGGACGAA 60.464 50.000 0.00 0.00 41.53 3.85
1439 1594 0.250553 ATTTCCGTTTGCTGGGACGA 60.251 50.000 0.00 0.00 41.53 4.20
1455 1610 1.748122 CCAGCCGCTCAGCTCATTT 60.748 57.895 0.00 0.00 42.61 2.32
1456 1611 2.124819 CCAGCCGCTCAGCTCATT 60.125 61.111 0.00 0.00 42.61 2.57
1457 1612 4.853050 GCCAGCCGCTCAGCTCAT 62.853 66.667 0.00 0.00 42.61 2.90
1515 1680 1.442769 TTTTCACCGCTGAGCATCTC 58.557 50.000 4.88 0.00 34.92 2.75
1542 1713 4.401202 TGTCTGTACAGATATCGCTTTCCA 59.599 41.667 27.54 13.99 39.97 3.53
1584 1758 3.539604 CCAAGCCAAAGACTCTATCCAG 58.460 50.000 0.00 0.00 0.00 3.86
1586 1760 2.293170 GCCAAGCCAAAGACTCTATCC 58.707 52.381 0.00 0.00 0.00 2.59
1587 1761 2.941720 CTGCCAAGCCAAAGACTCTATC 59.058 50.000 0.00 0.00 0.00 2.08
1588 1762 2.573462 TCTGCCAAGCCAAAGACTCTAT 59.427 45.455 0.00 0.00 0.00 1.98
1589 1763 1.977854 TCTGCCAAGCCAAAGACTCTA 59.022 47.619 0.00 0.00 0.00 2.43
1590 1764 0.767375 TCTGCCAAGCCAAAGACTCT 59.233 50.000 0.00 0.00 0.00 3.24
1591 1765 1.471684 CATCTGCCAAGCCAAAGACTC 59.528 52.381 0.00 0.00 0.00 3.36
1592 1766 1.542492 CATCTGCCAAGCCAAAGACT 58.458 50.000 0.00 0.00 0.00 3.24
1593 1767 0.108945 GCATCTGCCAAGCCAAAGAC 60.109 55.000 0.00 0.00 34.31 3.01
1594 1768 1.588824 CGCATCTGCCAAGCCAAAGA 61.589 55.000 0.00 0.00 37.91 2.52
1595 1769 1.153901 CGCATCTGCCAAGCCAAAG 60.154 57.895 0.00 0.00 37.91 2.77
1596 1770 2.964174 CGCATCTGCCAAGCCAAA 59.036 55.556 0.00 0.00 37.91 3.28
1597 1771 3.751246 GCGCATCTGCCAAGCCAA 61.751 61.111 0.30 0.00 37.91 4.52
1659 1837 1.595466 GTTCGGGAGAGAGATAGCGA 58.405 55.000 0.00 0.00 41.75 4.93
1660 1838 0.594110 GGTTCGGGAGAGAGATAGCG 59.406 60.000 0.00 0.00 41.75 4.26
1661 1839 0.963225 GGGTTCGGGAGAGAGATAGC 59.037 60.000 0.00 0.00 41.75 2.97
1662 1840 1.623163 GGGGTTCGGGAGAGAGATAG 58.377 60.000 0.00 0.00 41.75 2.08
1663 1841 0.187851 GGGGGTTCGGGAGAGAGATA 59.812 60.000 0.00 0.00 41.75 1.98
1664 1842 1.075151 GGGGGTTCGGGAGAGAGAT 60.075 63.158 0.00 0.00 41.75 2.75
1665 1843 2.363361 GGGGGTTCGGGAGAGAGA 59.637 66.667 0.00 0.00 41.75 3.10
1666 1844 2.038975 TGGGGGTTCGGGAGAGAG 59.961 66.667 0.00 0.00 41.75 3.20
1667 1845 2.284405 GTGGGGGTTCGGGAGAGA 60.284 66.667 0.00 0.00 41.75 3.10
1668 1846 3.400054 GGTGGGGGTTCGGGAGAG 61.400 72.222 0.00 0.00 41.75 3.20
1669 1847 3.795977 TTGGTGGGGGTTCGGGAGA 62.796 63.158 0.00 0.00 0.00 3.71
1670 1848 2.150014 ATTTGGTGGGGGTTCGGGAG 62.150 60.000 0.00 0.00 0.00 4.30
1671 1849 1.731324 AATTTGGTGGGGGTTCGGGA 61.731 55.000 0.00 0.00 0.00 5.14
1709 1887 3.896888 AGAAACAATCAATCAGGGCAACA 59.103 39.130 0.00 0.00 39.74 3.33
1898 2076 0.471211 GTGAGATCGGGATGGGGGTA 60.471 60.000 0.00 0.00 0.00 3.69
1900 2078 1.460305 AGTGAGATCGGGATGGGGG 60.460 63.158 0.00 0.00 0.00 5.40
1924 2102 0.533032 GAAGAAGGCGGAGTAGCAGT 59.467 55.000 0.00 0.00 39.27 4.40
1931 2109 1.332375 CTACGAGAGAAGAAGGCGGAG 59.668 57.143 0.00 0.00 0.00 4.63
1932 2110 1.065636 TCTACGAGAGAAGAAGGCGGA 60.066 52.381 0.00 0.00 0.00 5.54
1934 2112 2.748461 CTCTACGAGAGAAGAAGGCG 57.252 55.000 6.13 0.00 45.07 5.52
1949 2160 1.342074 CCGGGCATCTTGGATCTCTA 58.658 55.000 0.00 0.00 0.00 2.43
2008 2229 2.159179 AGAAACAAGCAAACCCCAGT 57.841 45.000 0.00 0.00 0.00 4.00
2009 2230 3.197265 CAAAGAAACAAGCAAACCCCAG 58.803 45.455 0.00 0.00 0.00 4.45
2055 2276 3.131155 CTGCAGGTTGCCAAGCAA 58.869 55.556 5.57 0.00 46.80 3.91
2078 2314 1.401199 GTAGTAGGTCCTGACGAGCAC 59.599 57.143 0.00 0.00 41.71 4.40
2387 2629 1.097547 GCTTCATCCACCCATCCACG 61.098 60.000 0.00 0.00 0.00 4.94
2388 2630 0.257039 AGCTTCATCCACCCATCCAC 59.743 55.000 0.00 0.00 0.00 4.02
2389 2631 0.548031 GAGCTTCATCCACCCATCCA 59.452 55.000 0.00 0.00 0.00 3.41
2390 2632 0.548031 TGAGCTTCATCCACCCATCC 59.452 55.000 0.00 0.00 0.00 3.51
2391 2633 1.673168 GTGAGCTTCATCCACCCATC 58.327 55.000 0.00 0.00 0.00 3.51
2393 2635 1.685224 GGTGAGCTTCATCCACCCA 59.315 57.895 9.83 0.00 43.32 4.51
2394 2636 1.450312 CGGTGAGCTTCATCCACCC 60.450 63.158 14.17 0.11 45.58 4.61
2395 2637 2.109126 GCGGTGAGCTTCATCCACC 61.109 63.158 10.74 10.74 45.07 4.61
2396 2638 3.490890 GCGGTGAGCTTCATCCAC 58.509 61.111 0.00 0.00 44.04 4.02
2412 2654 1.945394 AGCAACATCGATCAATCTGGC 59.055 47.619 0.00 0.00 0.00 4.85
2492 2734 8.499162 CACAATCAACTAACTAAAGAGTCCAAG 58.501 37.037 0.00 0.00 33.58 3.61
2588 2834 7.865385 GTCTGCATCCACACAACTAAAATAAAA 59.135 33.333 0.00 0.00 0.00 1.52
2596 2842 2.289631 CCTGTCTGCATCCACACAACTA 60.290 50.000 0.00 0.00 0.00 2.24
2597 2843 1.544093 CCTGTCTGCATCCACACAACT 60.544 52.381 0.00 0.00 0.00 3.16
2598 2844 0.877071 CCTGTCTGCATCCACACAAC 59.123 55.000 0.00 0.00 0.00 3.32
2599 2845 0.890542 GCCTGTCTGCATCCACACAA 60.891 55.000 0.00 0.00 0.00 3.33
2600 2846 1.302752 GCCTGTCTGCATCCACACA 60.303 57.895 0.00 0.00 0.00 3.72
2601 2847 1.002868 AGCCTGTCTGCATCCACAC 60.003 57.895 0.00 0.00 0.00 3.82
2613 2859 0.106519 AAGCAACAAGACCAGCCTGT 60.107 50.000 0.00 0.00 0.00 4.00
2617 2863 0.740737 ACACAAGCAACAAGACCAGC 59.259 50.000 0.00 0.00 0.00 4.85
2640 2886 7.814264 AATCCTTATATTGAAGAAGCACAGG 57.186 36.000 0.00 0.00 0.00 4.00
2676 2922 9.612620 GAAAACAATCAGTTGAATATCTCGTTT 57.387 29.630 0.00 0.00 41.19 3.60
2680 2926 9.552114 CACAGAAAACAATCAGTTGAATATCTC 57.448 33.333 0.00 0.00 41.19 2.75
2804 3237 4.997395 ACAGACCAACATTCACACTCATAC 59.003 41.667 0.00 0.00 0.00 2.39
2820 3253 2.247358 TGCTATCACAGTCACAGACCA 58.753 47.619 0.00 0.00 32.18 4.02
2896 3329 4.406648 TTGGATGTGTGGCTATCTGTAG 57.593 45.455 0.00 0.00 0.00 2.74
2917 3350 3.445096 GTGGATGTTATTTGAGGCAGCTT 59.555 43.478 0.00 0.00 0.00 3.74
2925 3358 5.104776 AGCTGAGCTAGTGGATGTTATTTGA 60.105 40.000 4.49 0.00 36.99 2.69
2926 3359 5.007430 CAGCTGAGCTAGTGGATGTTATTTG 59.993 44.000 8.42 0.00 36.40 2.32
2927 3360 5.121811 CAGCTGAGCTAGTGGATGTTATTT 58.878 41.667 8.42 0.00 36.40 1.40
2962 3395 2.694397 TCTGATCTTGGAGTATGGGGG 58.306 52.381 0.00 0.00 0.00 5.40
3006 3439 1.153066 TTGTTGAACGCCTGCCTGA 60.153 52.632 0.00 0.00 0.00 3.86
3014 3447 1.154225 CGGCATCCTTGTTGAACGC 60.154 57.895 0.00 0.00 0.00 4.84
3017 3450 1.976474 GCCCGGCATCCTTGTTGAA 60.976 57.895 3.91 0.00 0.00 2.69
3062 3495 2.773525 ATCAGAAGAGAGAGAGGGGG 57.226 55.000 0.00 0.00 0.00 5.40
3063 3496 3.432046 GCAAATCAGAAGAGAGAGAGGGG 60.432 52.174 0.00 0.00 0.00 4.79
3067 3500 7.180322 AGTATTGCAAATCAGAAGAGAGAGA 57.820 36.000 1.71 0.00 0.00 3.10
3078 3511 9.995003 AGTTTTGGATAAAAGTATTGCAAATCA 57.005 25.926 1.71 0.00 37.60 2.57
3163 3870 2.283351 GTCTGCACAGCAAAAGCAAAAG 59.717 45.455 0.00 0.00 38.41 2.27
3205 3912 1.610522 CAACCTTGCAAGAAGAGTGGG 59.389 52.381 28.05 11.67 0.00 4.61
3225 3932 4.775236 AGTGAAATCAGAGGATAGCAACC 58.225 43.478 0.00 0.00 32.09 3.77
3230 3937 9.528018 GAAAAGTAGAGTGAAATCAGAGGATAG 57.472 37.037 0.00 0.00 32.09 2.08
3232 3939 7.334858 GGAAAAGTAGAGTGAAATCAGAGGAT 58.665 38.462 0.00 0.00 34.43 3.24
3235 3942 5.578727 CGGGAAAAGTAGAGTGAAATCAGAG 59.421 44.000 0.00 0.00 0.00 3.35
3271 3978 2.076863 ACATTAGCGAACAGGAAGTGC 58.923 47.619 0.00 0.00 0.00 4.40
3283 3990 2.014641 ACGATACGACGACATTAGCG 57.985 50.000 0.00 0.00 37.03 4.26
3295 4002 3.740044 AACTGCATCCAAAACGATACG 57.260 42.857 0.00 0.00 0.00 3.06
3296 4003 6.551736 ACATTAACTGCATCCAAAACGATAC 58.448 36.000 0.00 0.00 0.00 2.24
3297 4004 6.751514 ACATTAACTGCATCCAAAACGATA 57.248 33.333 0.00 0.00 0.00 2.92
3301 4008 5.417580 TCCCTACATTAACTGCATCCAAAAC 59.582 40.000 0.00 0.00 0.00 2.43
3327 4034 3.512033 ATGTCTCCGCTGTACTCTTTC 57.488 47.619 0.00 0.00 0.00 2.62


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

AutoCloner maintained by Alex Coulton.