Multiple sequence alignment - TraesCS4B01G079500

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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 TraesCS4B01G079500 chr4B 100.000 2772 0 0 1 2772 77304780 77302009 0.000000e+00 5120
1 TraesCS4B01G079500 chr4D 90.896 2790 186 26 1 2766 52626030 52623285 0.000000e+00 3683
2 TraesCS4B01G079500 chrUn 84.146 164 13 8 2616 2766 54298401 54298564 2.220000e-31 147
3 TraesCS4B01G079500 chr4A 85.185 135 10 4 2117 2246 527008330 527008459 2.240000e-26 130


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 TraesCS4B01G079500 chr4B 77302009 77304780 2771 True 5120 5120 100.000 1 2772 1 chr4B.!!$R1 2771
1 TraesCS4B01G079500 chr4D 52623285 52626030 2745 True 3683 3683 90.896 1 2766 1 chr4D.!!$R1 2765

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
737 745 0.040425 AGCGTTCAAAATGGCGTCAC 60.04 50.0 0.0 0.0 0.0 3.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2583 2607 0.463833 GGGGGAAACGAGTATGCCAG 60.464 60.0 0.0 0.0 0.0 4.85 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
79 80 0.394565 AGAACCAGGCGAGCCATATC 59.605 55.000 17.18 8.69 38.92 1.63
81 82 0.107456 AACCAGGCGAGCCATATCTG 59.893 55.000 17.18 5.15 38.92 2.90
140 142 0.895100 TGAGCACATTGCCAGGAACC 60.895 55.000 0.00 0.00 46.52 3.62
180 182 1.485895 TGATGATGGTGAGCGGATTGA 59.514 47.619 0.00 0.00 0.00 2.57
225 230 5.722021 AAAGCACGAGGAAATTTTATGGT 57.278 34.783 0.00 0.00 0.00 3.55
249 254 2.299993 TCATGAGTCATGAACGCTCC 57.700 50.000 29.39 0.00 46.17 4.70
257 262 0.647410 CATGAACGCTCCGTGTCATC 59.353 55.000 10.30 0.00 39.99 2.92
259 264 0.109272 TGAACGCTCCGTGTCATCTC 60.109 55.000 0.00 0.00 39.99 2.75
262 267 1.875813 CGCTCCGTGTCATCTCTGC 60.876 63.158 0.00 0.00 0.00 4.26
275 280 1.078848 CTCTGCCTTTAGTGCGCCT 60.079 57.895 4.18 3.99 0.00 5.52
290 295 2.622942 TGCGCCTAATCCAATGATTTCC 59.377 45.455 4.18 0.00 41.44 3.13
346 352 3.862642 GCTCATGGGAATCGATACACTCC 60.863 52.174 0.00 1.19 0.00 3.85
356 362 3.139850 TCGATACACTCCTGCTAGCTAC 58.860 50.000 17.23 0.00 0.00 3.58
361 367 2.014857 CACTCCTGCTAGCTACGTGTA 58.985 52.381 17.23 0.00 0.00 2.90
372 378 4.481368 AGCTACGTGTATGATTTTGGGA 57.519 40.909 0.00 0.00 0.00 4.37
441 447 6.995511 TTTACTTCTCATTACCCGAATTGG 57.004 37.500 0.00 0.00 37.55 3.16
474 481 1.795768 GCCTGCTTTGGCCTAAAAAC 58.204 50.000 3.32 0.00 46.82 2.43
476 483 1.691434 CCTGCTTTGGCCTAAAAACCA 59.309 47.619 3.32 0.00 37.74 3.67
477 484 2.547855 CCTGCTTTGGCCTAAAAACCAC 60.548 50.000 3.32 0.00 35.10 4.16
478 485 1.067821 TGCTTTGGCCTAAAAACCACG 59.932 47.619 3.32 0.00 35.10 4.94
479 486 1.604438 GCTTTGGCCTAAAAACCACGG 60.604 52.381 3.32 0.00 35.10 4.94
584 592 8.966194 CCAAACATTTCAAATAATTTTGCAACC 58.034 29.630 0.00 0.00 41.66 3.77
593 601 9.474920 TCAAATAATTTTGCAACCAAAGAGTAG 57.525 29.630 0.00 0.00 41.58 2.57
627 635 8.725148 ACTCTAACTTTTGATGCACTTCTATTG 58.275 33.333 0.00 0.00 0.00 1.90
680 688 6.849085 ACAAAACCAATAGGCATGTATCAA 57.151 33.333 0.00 0.00 39.06 2.57
681 689 6.630071 ACAAAACCAATAGGCATGTATCAAC 58.370 36.000 0.00 0.00 39.06 3.18
682 690 5.852282 AAACCAATAGGCATGTATCAACC 57.148 39.130 0.00 0.00 39.06 3.77
683 691 4.518278 ACCAATAGGCATGTATCAACCA 57.482 40.909 0.00 0.00 39.06 3.67
684 692 4.865905 ACCAATAGGCATGTATCAACCAA 58.134 39.130 0.00 0.00 39.06 3.67
685 693 5.457686 ACCAATAGGCATGTATCAACCAAT 58.542 37.500 0.00 0.00 39.06 3.16
686 694 6.609876 ACCAATAGGCATGTATCAACCAATA 58.390 36.000 0.00 0.00 39.06 1.90
687 695 6.716628 ACCAATAGGCATGTATCAACCAATAG 59.283 38.462 0.00 0.00 39.06 1.73
688 696 6.151648 CCAATAGGCATGTATCAACCAATAGG 59.848 42.308 0.00 0.00 42.21 2.57
689 697 3.490348 AGGCATGTATCAACCAATAGGC 58.510 45.455 0.00 0.00 39.06 3.93
690 698 3.117550 AGGCATGTATCAACCAATAGGCA 60.118 43.478 0.00 0.00 39.06 4.75
691 699 3.828451 GGCATGTATCAACCAATAGGCAT 59.172 43.478 0.00 0.00 39.06 4.40
692 700 4.321452 GGCATGTATCAACCAATAGGCATG 60.321 45.833 0.00 0.00 39.06 4.06
693 701 4.279169 GCATGTATCAACCAATAGGCATGT 59.721 41.667 0.00 0.00 39.06 3.21
694 702 5.473162 GCATGTATCAACCAATAGGCATGTA 59.527 40.000 0.00 0.00 39.06 2.29
695 703 6.151648 GCATGTATCAACCAATAGGCATGTAT 59.848 38.462 0.00 0.00 39.06 2.29
696 704 7.627088 GCATGTATCAACCAATAGGCATGTATC 60.627 40.741 0.00 0.00 39.06 2.24
697 705 6.836242 TGTATCAACCAATAGGCATGTATCA 58.164 36.000 0.00 0.00 39.06 2.15
698 706 6.710295 TGTATCAACCAATAGGCATGTATCAC 59.290 38.462 0.00 0.00 39.06 3.06
729 737 4.917415 GCTCAATGTTACAGCGTTCAAAAT 59.083 37.500 0.00 0.00 0.00 1.82
734 742 1.231221 TACAGCGTTCAAAATGGCGT 58.769 45.000 0.00 0.00 0.00 5.68
736 744 0.040514 CAGCGTTCAAAATGGCGTCA 60.041 50.000 0.00 0.00 0.00 4.35
737 745 0.040425 AGCGTTCAAAATGGCGTCAC 60.040 50.000 0.00 0.00 0.00 3.67
738 746 1.001745 GCGTTCAAAATGGCGTCACC 61.002 55.000 0.00 0.00 39.84 4.02
756 764 1.903404 CCCCCAACCTTGCTGACAC 60.903 63.158 0.00 0.00 0.00 3.67
775 783 1.428912 ACAAAAGAGGATCCCAAGCCA 59.571 47.619 8.55 0.00 33.66 4.75
848 856 3.053991 TGTTTGGACCAACTTCCTTGAGA 60.054 43.478 6.36 0.00 36.51 3.27
857 865 6.129179 ACCAACTTCCTTGAGAAAAATGAGA 58.871 36.000 0.00 0.00 32.88 3.27
859 867 7.124147 ACCAACTTCCTTGAGAAAAATGAGAAA 59.876 33.333 0.00 0.00 32.88 2.52
862 870 6.040955 ACTTCCTTGAGAAAAATGAGAAACCC 59.959 38.462 0.00 0.00 32.88 4.11
879 887 4.510167 AACCCAAGTCAGATAATGAGGG 57.490 45.455 0.00 0.00 43.55 4.30
881 889 4.310740 ACCCAAGTCAGATAATGAGGGAT 58.689 43.478 0.00 0.00 41.48 3.85
919 927 3.194968 CCATTGAGCTGCAGGAAAAATCT 59.805 43.478 17.12 1.07 0.00 2.40
933 941 5.049129 AGGAAAAATCTGAGCAGAAGAAACG 60.049 40.000 4.06 0.00 41.36 3.60
940 948 3.067106 TGAGCAGAAGAAACGAATGGAC 58.933 45.455 0.00 0.00 0.00 4.02
947 955 4.039973 AGAAGAAACGAATGGACCTGTACA 59.960 41.667 0.00 0.00 0.00 2.90
993 1002 3.562635 CTTCGTTGGAAGGACGGC 58.437 61.111 0.00 0.00 44.83 5.68
1005 1014 1.568504 AGGACGGCCTTGAGATGTTA 58.431 50.000 2.12 0.00 43.90 2.41
1012 1021 4.835615 ACGGCCTTGAGATGTTAGATAGAT 59.164 41.667 0.00 0.00 0.00 1.98
1024 1033 9.307121 AGATGTTAGATAGATTGAACAAGAACG 57.693 33.333 0.00 0.00 35.56 3.95
1027 1036 7.272731 TGTTAGATAGATTGAACAAGAACGACG 59.727 37.037 0.00 0.00 0.00 5.12
1044 1053 2.490991 GACGCCAGACTAACACCTTTT 58.509 47.619 0.00 0.00 0.00 2.27
1046 1055 1.069227 CGCCAGACTAACACCTTTTGC 60.069 52.381 0.00 0.00 0.00 3.68
1053 1062 3.813166 GACTAACACCTTTTGCTGCAGTA 59.187 43.478 16.64 8.31 0.00 2.74
1059 1068 4.827284 ACACCTTTTGCTGCAGTATACTTT 59.173 37.500 16.64 0.00 0.00 2.66
1064 1073 3.829886 TGCTGCAGTATACTTTTGTGC 57.170 42.857 16.64 4.87 34.62 4.57
1068 1077 3.411446 TGCAGTATACTTTTGTGCTGCT 58.589 40.909 14.61 0.00 45.21 4.24
1074 1083 2.755836 ACTTTTGTGCTGCTGTTACG 57.244 45.000 0.00 0.00 0.00 3.18
1077 1086 2.111932 TTTGTGCTGCTGTTACGGCG 62.112 55.000 11.80 4.80 45.31 6.46
1081 1090 1.809619 GCTGCTGTTACGGCGATGA 60.810 57.895 16.62 0.00 38.82 2.92
1084 1093 1.258982 CTGCTGTTACGGCGATGATTC 59.741 52.381 16.62 0.00 38.82 2.52
1095 1104 1.876156 GCGATGATTCTGGGAATGGTC 59.124 52.381 0.00 0.00 0.00 4.02
1098 1107 0.911769 TGATTCTGGGAATGGTCGCT 59.088 50.000 0.00 0.00 37.59 4.93
1112 1121 1.074775 TCGCTTGCAAGTTCCCCAT 59.925 52.632 26.55 0.00 0.00 4.00
1119 1128 0.895100 GCAAGTTCCCCATGTCAGCA 60.895 55.000 0.00 0.00 0.00 4.41
1124 1133 1.064758 GTTCCCCATGTCAGCACCATA 60.065 52.381 0.00 0.00 0.00 2.74
1167 1176 0.524816 GAGCATTCCACGCATTGCTG 60.525 55.000 7.12 4.31 44.98 4.41
1174 1183 0.241749 CCACGCATTGCTGTTCATGT 59.758 50.000 7.12 0.00 0.00 3.21
1188 1197 1.896220 TCATGTTGCTGGGACTTCAC 58.104 50.000 0.00 0.00 0.00 3.18
1189 1198 1.421268 TCATGTTGCTGGGACTTCACT 59.579 47.619 0.00 0.00 0.00 3.41
1191 1200 1.967319 TGTTGCTGGGACTTCACTTC 58.033 50.000 0.00 0.00 0.00 3.01
1197 1206 0.391597 TGGGACTTCACTTCGACACC 59.608 55.000 0.00 0.00 0.00 4.16
1199 1208 1.891150 GGGACTTCACTTCGACACCTA 59.109 52.381 0.00 0.00 0.00 3.08
1200 1209 2.496470 GGGACTTCACTTCGACACCTAT 59.504 50.000 0.00 0.00 0.00 2.57
1202 1211 4.341520 GGGACTTCACTTCGACACCTATAT 59.658 45.833 0.00 0.00 0.00 0.86
1206 1215 7.175293 GGACTTCACTTCGACACCTATATCTAT 59.825 40.741 0.00 0.00 0.00 1.98
1214 1223 6.856895 TCGACACCTATATCTATCATGCAAG 58.143 40.000 0.00 0.00 0.00 4.01
1219 1228 6.877855 CACCTATATCTATCATGCAAGTGCTT 59.122 38.462 4.69 0.00 42.66 3.91
1221 1230 7.941238 ACCTATATCTATCATGCAAGTGCTTTT 59.059 33.333 4.69 0.00 42.66 2.27
1247 1256 0.752054 ATTGGGTGTGCTTGTGTTGG 59.248 50.000 0.00 0.00 0.00 3.77
1254 1263 1.476085 TGTGCTTGTGTTGGAGGTTTG 59.524 47.619 0.00 0.00 0.00 2.93
1260 1269 0.746659 GTGTTGGAGGTTTGCTGCTT 59.253 50.000 0.00 0.00 0.00 3.91
1261 1270 1.032014 TGTTGGAGGTTTGCTGCTTC 58.968 50.000 0.00 0.00 0.00 3.86
1262 1271 1.322442 GTTGGAGGTTTGCTGCTTCT 58.678 50.000 0.00 0.00 0.00 2.85
1278 1287 1.072331 CTTCTTGTGTACTGGGGCTGT 59.928 52.381 0.00 0.00 0.00 4.40
1281 1290 1.623811 CTTGTGTACTGGGGCTGTAGT 59.376 52.381 0.00 0.00 0.00 2.73
1284 1293 2.225192 TGTGTACTGGGGCTGTAGTACT 60.225 50.000 19.30 0.00 45.88 2.73
1287 1296 1.853963 ACTGGGGCTGTAGTACTGAG 58.146 55.000 5.39 2.41 0.00 3.35
1290 1299 1.291033 TGGGGCTGTAGTACTGAGGAT 59.709 52.381 5.39 0.00 0.00 3.24
1293 1302 1.964933 GGCTGTAGTACTGAGGATCCC 59.035 57.143 8.55 0.11 0.00 3.85
1296 1305 3.006323 GCTGTAGTACTGAGGATCCCATG 59.994 52.174 8.55 0.68 0.00 3.66
1302 1311 5.977533 AGTACTGAGGATCCCATGGTAATA 58.022 41.667 11.73 0.00 0.00 0.98
1352 1361 6.396450 ACCAATTTCTTCTACGAGTCTAACC 58.604 40.000 0.00 0.00 0.00 2.85
1375 1388 8.629821 ACCATTATATATGCAGGTTATCTCCT 57.370 34.615 0.00 0.00 38.51 3.69
1377 1390 9.553064 CCATTATATATGCAGGTTATCTCCTTC 57.447 37.037 0.00 0.00 35.37 3.46
1381 1394 3.616956 TGCAGGTTATCTCCTTCTGTG 57.383 47.619 0.00 0.00 35.37 3.66
1387 1400 3.935828 GGTTATCTCCTTCTGTGTCAAGC 59.064 47.826 0.00 0.00 0.00 4.01
1398 1411 0.725784 GTGTCAAGCACGCCAAATCG 60.726 55.000 0.00 0.00 38.45 3.34
1411 1424 1.462616 CAAATCGGCAGGTTCATGGA 58.537 50.000 0.00 0.00 0.00 3.41
1413 1426 3.213506 CAAATCGGCAGGTTCATGGATA 58.786 45.455 0.00 0.00 0.00 2.59
1416 1429 0.877071 CGGCAGGTTCATGGATATGC 59.123 55.000 5.09 5.09 34.21 3.14
1420 1433 3.418995 GCAGGTTCATGGATATGCTCAT 58.581 45.455 6.21 0.00 34.21 2.90
1423 1436 5.474532 GCAGGTTCATGGATATGCTCATTTA 59.525 40.000 6.21 0.00 34.21 1.40
1438 1451 4.678840 GCTCATTTATTTGGTGGGCTCTTG 60.679 45.833 0.00 0.00 36.44 3.02
1523 1536 2.549754 ACAATTTTGTCAGCTCCTCGTG 59.450 45.455 0.00 0.00 36.50 4.35
1524 1537 1.813513 ATTTTGTCAGCTCCTCGTGG 58.186 50.000 0.00 0.00 0.00 4.94
1527 1540 2.680352 GTCAGCTCCTCGTGGGGA 60.680 66.667 7.79 0.94 35.23 4.81
1534 1547 0.461961 CTCCTCGTGGGGAAAGCTAG 59.538 60.000 0.00 0.00 35.23 3.42
1545 1558 4.103469 TGGGGAAAGCTAGTCAACAAACTA 59.897 41.667 0.00 0.00 0.00 2.24
1555 1568 8.311836 AGCTAGTCAACAAACTACAAAGCTATA 58.688 33.333 0.00 0.00 34.76 1.31
1559 1572 7.603024 AGTCAACAAACTACAAAGCTATAGGAC 59.397 37.037 1.04 0.00 0.00 3.85
1565 1578 1.343681 ACAAAGCTATAGGACCCGGGA 60.344 52.381 32.02 4.18 0.00 5.14
1567 1580 0.471401 AAGCTATAGGACCCGGGACC 60.471 60.000 31.99 31.99 0.00 4.46
1571 1584 2.668106 TATAGGACCCGGGACCCTGC 62.668 65.000 34.22 18.35 0.00 4.85
1578 1591 2.354729 CGGGACCCTGCCAATGAA 59.645 61.111 9.41 0.00 0.00 2.57
1622 1644 4.291783 GAGAGGTCGGTAAAATCATCTCG 58.708 47.826 0.00 0.00 30.46 4.04
1628 1650 5.278858 GGTCGGTAAAATCATCTCGGTCTAT 60.279 44.000 0.00 0.00 0.00 1.98
1693 1715 9.729281 ATTTTGGATAATTTTGCATCTTCTGTT 57.271 25.926 0.00 0.00 0.00 3.16
1704 1726 3.618351 CATCTTCTGTTCCTTGGCATCT 58.382 45.455 0.00 0.00 0.00 2.90
1705 1727 3.063510 TCTTCTGTTCCTTGGCATCTG 57.936 47.619 0.00 0.00 0.00 2.90
1706 1728 2.639347 TCTTCTGTTCCTTGGCATCTGA 59.361 45.455 0.00 0.00 0.00 3.27
1707 1729 3.265221 TCTTCTGTTCCTTGGCATCTGAT 59.735 43.478 0.00 0.00 0.00 2.90
1708 1730 3.726557 TCTGTTCCTTGGCATCTGATT 57.273 42.857 0.00 0.00 0.00 2.57
1709 1731 4.842531 TCTGTTCCTTGGCATCTGATTA 57.157 40.909 0.00 0.00 0.00 1.75
1710 1732 5.178096 TCTGTTCCTTGGCATCTGATTAA 57.822 39.130 0.00 0.00 0.00 1.40
1711 1733 5.188434 TCTGTTCCTTGGCATCTGATTAAG 58.812 41.667 0.00 0.00 0.00 1.85
1712 1734 4.922206 TGTTCCTTGGCATCTGATTAAGT 58.078 39.130 0.00 0.00 0.00 2.24
1713 1735 5.324409 TGTTCCTTGGCATCTGATTAAGTT 58.676 37.500 0.00 0.00 0.00 2.66
1714 1736 5.774690 TGTTCCTTGGCATCTGATTAAGTTT 59.225 36.000 0.00 0.00 0.00 2.66
1715 1737 5.902613 TCCTTGGCATCTGATTAAGTTTG 57.097 39.130 0.00 0.00 0.00 2.93
1730 1752 7.541783 TGATTAAGTTTGTATTGAACAGCATGC 59.458 33.333 10.51 10.51 42.53 4.06
1731 1753 4.852134 AGTTTGTATTGAACAGCATGCA 57.148 36.364 21.98 0.00 42.53 3.96
1737 1759 1.612676 TTGAACAGCATGCAGAAGCT 58.387 45.000 21.98 5.37 42.53 3.74
1752 1774 3.564644 CAGAAGCTGCTGATTAAGGATGG 59.435 47.826 17.72 0.00 38.14 3.51
1753 1775 3.201708 AGAAGCTGCTGATTAAGGATGGT 59.798 43.478 1.35 0.00 0.00 3.55
1754 1776 2.928334 AGCTGCTGATTAAGGATGGTG 58.072 47.619 0.00 0.00 0.00 4.17
1756 1778 2.357009 GCTGCTGATTAAGGATGGTGTG 59.643 50.000 0.00 0.00 0.00 3.82
1757 1779 2.357009 CTGCTGATTAAGGATGGTGTGC 59.643 50.000 0.00 0.00 0.00 4.57
1758 1780 1.678101 GCTGATTAAGGATGGTGTGCC 59.322 52.381 0.00 0.00 0.00 5.01
1769 1791 2.347490 GTGTGCCACCCGATGTCT 59.653 61.111 0.00 0.00 0.00 3.41
1770 1792 2.034879 GTGTGCCACCCGATGTCTG 61.035 63.158 0.00 0.00 0.00 3.51
1771 1793 2.213513 TGTGCCACCCGATGTCTGA 61.214 57.895 0.00 0.00 0.00 3.27
1772 1794 1.741770 GTGCCACCCGATGTCTGAC 60.742 63.158 0.00 0.00 0.00 3.51
1773 1795 2.125106 GCCACCCGATGTCTGACC 60.125 66.667 5.17 0.00 0.00 4.02
1774 1796 2.660064 GCCACCCGATGTCTGACCT 61.660 63.158 5.17 0.00 0.00 3.85
1775 1797 1.517832 CCACCCGATGTCTGACCTC 59.482 63.158 5.17 4.15 0.00 3.85
1776 1798 1.257750 CCACCCGATGTCTGACCTCA 61.258 60.000 12.51 0.00 0.00 3.86
1777 1799 0.826715 CACCCGATGTCTGACCTCAT 59.173 55.000 12.51 0.00 0.00 2.90
1778 1800 2.031870 CACCCGATGTCTGACCTCATA 58.968 52.381 12.51 0.00 0.00 2.15
1779 1801 2.035193 CACCCGATGTCTGACCTCATAG 59.965 54.545 12.51 3.96 0.00 2.23
1800 1822 2.472695 TCCACTTAAAGATGCAGCGT 57.527 45.000 0.00 0.00 0.00 5.07
1801 1823 2.076100 TCCACTTAAAGATGCAGCGTG 58.924 47.619 0.00 0.00 0.00 5.34
1803 1825 1.131126 CACTTAAAGATGCAGCGTGGG 59.869 52.381 0.00 0.00 0.00 4.61
1810 1832 1.696336 AGATGCAGCGTGGGAGATAAT 59.304 47.619 0.00 0.00 0.00 1.28
1824 1846 4.016444 GGAGATAATTCAAACAGTGGGCA 58.984 43.478 0.00 0.00 0.00 5.36
1829 1851 0.550914 TTCAAACAGTGGGCAGGAGT 59.449 50.000 0.00 0.00 0.00 3.85
1830 1852 0.179020 TCAAACAGTGGGCAGGAGTG 60.179 55.000 0.00 0.00 0.00 3.51
1832 1854 0.258774 AAACAGTGGGCAGGAGTGTT 59.741 50.000 0.00 0.00 38.38 3.32
1834 1856 1.136828 ACAGTGGGCAGGAGTGTTAA 58.863 50.000 0.00 0.00 0.00 2.01
1843 1865 4.323562 GGGCAGGAGTGTTAATACAGTTCT 60.324 45.833 5.08 0.00 43.12 3.01
1851 1873 3.770933 TGTTAATACAGTTCTAGCCCGGT 59.229 43.478 0.00 0.00 0.00 5.28
1857 1879 0.321653 AGTTCTAGCCCGGTTTGCAG 60.322 55.000 0.00 0.00 0.00 4.41
1929 1951 0.394488 TTGGTGGCAACGTTCAGGAA 60.394 50.000 0.00 0.00 42.51 3.36
2010 2032 6.042781 TGGGTGGTTCCTCTGATAATATACAC 59.957 42.308 0.00 0.00 36.25 2.90
2052 2074 2.558380 GATCTGGTGCTCCCAACCCC 62.558 65.000 1.59 0.00 44.65 4.95
2061 2083 2.040144 GCTCCCAACCCCAGCTAGATA 61.040 57.143 0.00 0.00 0.00 1.98
2067 2091 4.223953 CCAACCCCAGCTAGATACTCTTA 58.776 47.826 0.00 0.00 0.00 2.10
2070 2094 5.340891 ACCCCAGCTAGATACTCTTATCA 57.659 43.478 0.00 0.00 37.20 2.15
2126 2150 0.764890 AGCAAGTGTAAGCACCCTGA 59.235 50.000 0.00 0.00 46.35 3.86
2165 2189 5.486775 AGGATTCTGAATCTTCCTCTGTGAA 59.513 40.000 24.96 0.00 33.22 3.18
2223 2247 6.560253 TCCACTTCAGTTTTGCTAGAATTC 57.440 37.500 0.00 0.00 0.00 2.17
2229 2253 9.301897 ACTTCAGTTTTGCTAGAATTCCTAAAT 57.698 29.630 0.65 0.00 0.00 1.40
2290 2314 4.024048 GGGTATTTATCACTCGTGGCAATG 60.024 45.833 0.00 0.00 0.00 2.82
2560 2584 7.815068 GGCTCCTGTAATACATAGATAACACTG 59.185 40.741 6.99 0.00 0.00 3.66
2590 2614 1.828081 CTGCTCAGCTCCTGGCATA 59.172 57.895 0.00 0.00 44.79 3.14
2598 2622 1.134670 AGCTCCTGGCATACTCGTTTC 60.135 52.381 0.00 0.00 44.79 2.78
2633 2657 9.474313 AGAAGGCCATATACTGTTGATTTAAAA 57.526 29.630 5.01 0.00 0.00 1.52
2637 2661 7.978975 GGCCATATACTGTTGATTTAAAAAGCA 59.021 33.333 0.00 0.00 31.66 3.91
2638 2662 9.023967 GCCATATACTGTTGATTTAAAAAGCAG 57.976 33.333 13.23 13.23 35.54 4.24
2657 2681 9.988350 AAAAGCAGATAATTACAAACACTATCG 57.012 29.630 0.00 0.00 0.00 2.92
2680 2704 4.002982 GTGTTACCATCATCTGCTGTCAA 58.997 43.478 0.00 0.00 0.00 3.18
2692 2716 4.260985 TCTGCTGTCAAGTCAAAAAGTCA 58.739 39.130 0.00 0.00 0.00 3.41
2695 2719 3.181497 GCTGTCAAGTCAAAAAGTCAGCA 60.181 43.478 0.00 0.00 43.99 4.41
2766 2790 8.239038 TCTAACAGAAGGAGGTTATCTATGTG 57.761 38.462 0.00 0.00 0.00 3.21
2767 2791 6.875972 AACAGAAGGAGGTTATCTATGTGT 57.124 37.500 0.00 0.00 0.00 3.72
2768 2792 6.227298 ACAGAAGGAGGTTATCTATGTGTG 57.773 41.667 0.00 0.00 0.00 3.82
2769 2793 5.721960 ACAGAAGGAGGTTATCTATGTGTGT 59.278 40.000 0.00 0.00 0.00 3.72
2770 2794 6.045318 CAGAAGGAGGTTATCTATGTGTGTG 58.955 44.000 0.00 0.00 0.00 3.82
2771 2795 5.721960 AGAAGGAGGTTATCTATGTGTGTGT 59.278 40.000 0.00 0.00 0.00 3.72
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 4.921470 ATTCGGTTCATAGACAAACACG 57.079 40.909 0.00 0.00 0.00 4.49
79 80 1.393539 CGTATTGTTTCTGACGGCCAG 59.606 52.381 2.24 0.00 44.27 4.85
81 82 0.096454 GCGTATTGTTTCTGACGGCC 59.904 55.000 0.00 0.00 35.87 6.13
180 182 0.744414 CATCAGGCCCGAAACGTGAT 60.744 55.000 0.00 0.00 41.86 3.06
206 211 4.412207 GACACCATAAAATTTCCTCGTGC 58.588 43.478 0.00 0.00 0.00 5.34
208 213 4.918588 AGGACACCATAAAATTTCCTCGT 58.081 39.130 0.00 0.00 0.00 4.18
233 238 0.388520 CACGGAGCGTTCATGACTCA 60.389 55.000 12.41 0.00 38.32 3.41
248 253 2.093973 ACTAAAGGCAGAGATGACACGG 60.094 50.000 0.00 0.00 0.00 4.94
249 254 2.926200 CACTAAAGGCAGAGATGACACG 59.074 50.000 0.00 0.00 0.00 4.49
257 262 0.175760 TAGGCGCACTAAAGGCAGAG 59.824 55.000 10.83 0.00 35.18 3.35
259 264 1.599542 GATTAGGCGCACTAAAGGCAG 59.400 52.381 18.16 0.00 44.39 4.85
262 267 2.325583 TGGATTAGGCGCACTAAAGG 57.674 50.000 18.16 0.00 44.39 3.11
275 280 7.292713 CATCACCATGGAAATCATTGGATTA 57.707 36.000 21.47 0.00 42.87 1.75
290 295 4.512484 TGTACATACACACCATCACCATG 58.488 43.478 0.00 0.00 0.00 3.66
346 352 5.050769 CCAAAATCATACACGTAGCTAGCAG 60.051 44.000 18.83 10.33 0.00 4.24
356 362 4.414852 CAAAGCTCCCAAAATCATACACG 58.585 43.478 0.00 0.00 0.00 4.49
372 378 7.168905 AGTGTTATAAAAGTAGGAGCAAAGCT 58.831 34.615 0.00 0.00 43.88 3.74
441 447 3.760580 AGCAGGCACTCTATACCAATC 57.239 47.619 0.00 0.00 34.60 2.67
474 481 2.228582 TCAAACAAGAATCATGCCGTGG 59.771 45.455 0.00 0.00 0.00 4.94
476 483 4.218200 TCAATCAAACAAGAATCATGCCGT 59.782 37.500 0.00 0.00 0.00 5.68
477 484 4.735985 TCAATCAAACAAGAATCATGCCG 58.264 39.130 0.00 0.00 0.00 5.69
478 485 7.223387 GGTTATCAATCAAACAAGAATCATGCC 59.777 37.037 0.00 0.00 0.00 4.40
479 486 7.977853 AGGTTATCAATCAAACAAGAATCATGC 59.022 33.333 0.00 0.00 0.00 4.06
584 592 9.868277 AAGTTAGAGTTCATCATCTACTCTTTG 57.132 33.333 9.03 0.00 44.58 2.77
593 601 7.695618 GTGCATCAAAAGTTAGAGTTCATCATC 59.304 37.037 0.00 0.00 0.00 2.92
627 635 4.251268 AGGAACGTTGTAGCAAATAGTCC 58.749 43.478 5.00 0.00 0.00 3.85
658 666 6.042143 GGTTGATACATGCCTATTGGTTTTG 58.958 40.000 0.00 0.00 35.27 2.44
680 688 4.828939 CCAATGTGATACATGCCTATTGGT 59.171 41.667 0.00 0.00 37.97 3.67
681 689 4.828939 ACCAATGTGATACATGCCTATTGG 59.171 41.667 16.56 16.56 45.21 3.16
682 690 6.210796 CAACCAATGTGATACATGCCTATTG 58.789 40.000 0.00 0.00 37.97 1.90
683 691 5.221303 GCAACCAATGTGATACATGCCTATT 60.221 40.000 0.00 0.00 37.97 1.73
684 692 4.279169 GCAACCAATGTGATACATGCCTAT 59.721 41.667 0.00 0.00 37.97 2.57
685 693 3.631686 GCAACCAATGTGATACATGCCTA 59.368 43.478 0.00 0.00 37.97 3.93
686 694 2.428171 GCAACCAATGTGATACATGCCT 59.572 45.455 0.00 0.00 37.97 4.75
687 695 2.428171 AGCAACCAATGTGATACATGCC 59.572 45.455 0.00 0.00 37.97 4.40
688 696 3.129113 TGAGCAACCAATGTGATACATGC 59.871 43.478 0.00 0.00 37.97 4.06
689 697 4.968812 TGAGCAACCAATGTGATACATG 57.031 40.909 0.00 0.00 37.97 3.21
690 698 5.898174 CATTGAGCAACCAATGTGATACAT 58.102 37.500 14.47 0.00 44.97 2.29
691 699 5.313520 CATTGAGCAACCAATGTGATACA 57.686 39.130 14.47 0.00 44.97 2.29
738 746 1.903404 GTGTCAGCAAGGTTGGGGG 60.903 63.158 0.00 0.00 0.00 5.40
754 762 1.821136 GGCTTGGGATCCTCTTTTGTG 59.179 52.381 12.58 0.00 0.00 3.33
756 764 2.097825 CTGGCTTGGGATCCTCTTTTG 58.902 52.381 12.58 0.00 0.00 2.44
819 827 3.312736 AGTTGGTCCAAACATGAGGTT 57.687 42.857 5.69 0.00 42.98 3.50
848 856 6.983906 ATCTGACTTGGGTTTCTCATTTTT 57.016 33.333 0.00 0.00 0.00 1.94
857 865 4.540099 TCCCTCATTATCTGACTTGGGTTT 59.460 41.667 0.00 0.00 37.86 3.27
859 867 3.736094 TCCCTCATTATCTGACTTGGGT 58.264 45.455 0.00 0.00 37.86 4.51
879 887 8.715088 GCTCAATGGGAAATGCAATTAATAATC 58.285 33.333 0.00 0.00 33.67 1.75
881 889 7.711772 CAGCTCAATGGGAAATGCAATTAATAA 59.288 33.333 0.00 0.00 33.67 1.40
919 927 3.067106 GTCCATTCGTTTCTTCTGCTCA 58.933 45.455 0.00 0.00 0.00 4.26
940 948 3.535561 GGTGATCAGACCATTGTACAGG 58.464 50.000 0.00 0.00 35.88 4.00
947 955 1.153369 CCGCGGTGATCAGACCATT 60.153 57.895 19.50 0.00 35.50 3.16
992 1001 7.712639 TGTTCAATCTATCTAACATCTCAAGGC 59.287 37.037 0.00 0.00 0.00 4.35
993 1002 9.605275 TTGTTCAATCTATCTAACATCTCAAGG 57.395 33.333 0.00 0.00 32.31 3.61
1005 1014 4.563184 GCGTCGTTCTTGTTCAATCTATCT 59.437 41.667 0.00 0.00 0.00 1.98
1012 1021 0.934496 CTGGCGTCGTTCTTGTTCAA 59.066 50.000 0.00 0.00 0.00 2.69
1022 1031 1.177256 AGGTGTTAGTCTGGCGTCGT 61.177 55.000 0.00 0.00 0.00 4.34
1024 1033 2.165319 AAAGGTGTTAGTCTGGCGTC 57.835 50.000 0.00 0.00 0.00 5.19
1027 1036 2.030805 CAGCAAAAGGTGTTAGTCTGGC 60.031 50.000 0.00 0.00 0.00 4.85
1044 1053 3.189080 CAGCACAAAAGTATACTGCAGCA 59.811 43.478 15.27 0.00 0.00 4.41
1053 1062 3.188460 CCGTAACAGCAGCACAAAAGTAT 59.812 43.478 0.00 0.00 0.00 2.12
1059 1068 2.603247 CGCCGTAACAGCAGCACAA 61.603 57.895 0.00 0.00 0.00 3.33
1064 1073 1.258982 GAATCATCGCCGTAACAGCAG 59.741 52.381 0.00 0.00 0.00 4.24
1068 1077 1.472552 CCCAGAATCATCGCCGTAACA 60.473 52.381 0.00 0.00 0.00 2.41
1074 1083 1.242076 CCATTCCCAGAATCATCGCC 58.758 55.000 0.00 0.00 0.00 5.54
1077 1086 1.876156 GCGACCATTCCCAGAATCATC 59.124 52.381 0.00 0.00 0.00 2.92
1081 1090 1.755179 CAAGCGACCATTCCCAGAAT 58.245 50.000 0.00 0.00 0.00 2.40
1084 1093 1.243342 TTGCAAGCGACCATTCCCAG 61.243 55.000 0.00 0.00 0.00 4.45
1095 1104 1.213537 CATGGGGAACTTGCAAGCG 59.786 57.895 26.27 5.15 0.00 4.68
1098 1107 1.619654 CTGACATGGGGAACTTGCAA 58.380 50.000 0.00 0.00 0.00 4.08
1112 1121 2.099405 TCATCGAGTATGGTGCTGACA 58.901 47.619 0.00 0.00 36.15 3.58
1158 1167 0.711670 GCAACATGAACAGCAATGCG 59.288 50.000 0.00 0.00 0.00 4.73
1161 1170 1.274167 CCCAGCAACATGAACAGCAAT 59.726 47.619 0.00 0.00 0.00 3.56
1162 1171 0.675083 CCCAGCAACATGAACAGCAA 59.325 50.000 0.00 0.00 0.00 3.91
1167 1176 2.030805 GTGAAGTCCCAGCAACATGAAC 60.031 50.000 0.00 0.00 0.00 3.18
1174 1183 0.756294 TCGAAGTGAAGTCCCAGCAA 59.244 50.000 0.00 0.00 0.00 3.91
1188 1197 6.856895 TGCATGATAGATATAGGTGTCGAAG 58.143 40.000 0.00 0.00 0.00 3.79
1189 1198 6.834168 TGCATGATAGATATAGGTGTCGAA 57.166 37.500 0.00 0.00 0.00 3.71
1191 1200 6.529477 CACTTGCATGATAGATATAGGTGTCG 59.471 42.308 6.60 0.00 0.00 4.35
1219 1228 2.324541 AGCACACCCAATAGCCAAAAA 58.675 42.857 0.00 0.00 0.00 1.94
1221 1230 1.617850 CAAGCACACCCAATAGCCAAA 59.382 47.619 0.00 0.00 0.00 3.28
1223 1232 0.112218 ACAAGCACACCCAATAGCCA 59.888 50.000 0.00 0.00 0.00 4.75
1230 1239 0.751277 CTCCAACACAAGCACACCCA 60.751 55.000 0.00 0.00 0.00 4.51
1233 1242 1.102978 AACCTCCAACACAAGCACAC 58.897 50.000 0.00 0.00 0.00 3.82
1247 1256 1.678101 ACACAAGAAGCAGCAAACCTC 59.322 47.619 0.00 0.00 0.00 3.85
1254 1263 1.160137 CCCAGTACACAAGAAGCAGC 58.840 55.000 0.00 0.00 0.00 5.25
1260 1269 1.899814 CTACAGCCCCAGTACACAAGA 59.100 52.381 0.00 0.00 0.00 3.02
1261 1270 1.623811 ACTACAGCCCCAGTACACAAG 59.376 52.381 0.00 0.00 0.00 3.16
1262 1271 1.724545 ACTACAGCCCCAGTACACAA 58.275 50.000 0.00 0.00 0.00 3.33
1278 1287 3.993658 ACCATGGGATCCTCAGTACTA 57.006 47.619 18.09 0.00 0.00 1.82
1281 1290 6.849697 AGTTTATTACCATGGGATCCTCAGTA 59.150 38.462 18.09 6.08 0.00 2.74
1284 1293 5.669904 TCAGTTTATTACCATGGGATCCTCA 59.330 40.000 18.09 8.57 0.00 3.86
1287 1296 6.187727 TCTCAGTTTATTACCATGGGATCC 57.812 41.667 18.09 1.92 0.00 3.36
1290 1299 6.558775 AGCTATCTCAGTTTATTACCATGGGA 59.441 38.462 18.09 3.85 0.00 4.37
1381 1394 1.154225 CCGATTTGGCGTGCTTGAC 60.154 57.895 0.00 0.00 0.00 3.18
1391 1404 0.457035 CCATGAACCTGCCGATTTGG 59.543 55.000 0.00 0.00 42.50 3.28
1393 1406 2.442236 ATCCATGAACCTGCCGATTT 57.558 45.000 0.00 0.00 0.00 2.17
1394 1407 3.415212 CATATCCATGAACCTGCCGATT 58.585 45.455 0.00 0.00 33.67 3.34
1398 1411 2.157738 GAGCATATCCATGAACCTGCC 58.842 52.381 0.00 0.00 33.67 4.85
1411 1424 5.149976 AGCCCACCAAATAAATGAGCATAT 58.850 37.500 0.00 0.00 0.00 1.78
1413 1426 3.377573 AGCCCACCAAATAAATGAGCAT 58.622 40.909 0.00 0.00 0.00 3.79
1416 1429 4.706476 TCAAGAGCCCACCAAATAAATGAG 59.294 41.667 0.00 0.00 0.00 2.90
1420 1433 4.706476 CAGATCAAGAGCCCACCAAATAAA 59.294 41.667 0.00 0.00 0.00 1.40
1423 1436 2.042162 ACAGATCAAGAGCCCACCAAAT 59.958 45.455 0.00 0.00 0.00 2.32
1518 1531 0.895530 TGACTAGCTTTCCCCACGAG 59.104 55.000 0.00 0.00 0.00 4.18
1519 1532 1.001633 GTTGACTAGCTTTCCCCACGA 59.998 52.381 0.00 0.00 0.00 4.35
1521 1534 2.561478 TGTTGACTAGCTTTCCCCAC 57.439 50.000 0.00 0.00 0.00 4.61
1523 1536 3.487372 AGTTTGTTGACTAGCTTTCCCC 58.513 45.455 0.00 0.00 0.00 4.81
1524 1537 5.061179 TGTAGTTTGTTGACTAGCTTTCCC 58.939 41.667 0.00 0.00 33.04 3.97
1527 1540 6.318900 AGCTTTGTAGTTTGTTGACTAGCTTT 59.681 34.615 0.00 0.00 33.04 3.51
1534 1547 7.148457 GGTCCTATAGCTTTGTAGTTTGTTGAC 60.148 40.741 0.00 0.00 0.00 3.18
1545 1558 1.129058 CCCGGGTCCTATAGCTTTGT 58.871 55.000 14.18 0.00 0.00 2.83
1559 1572 4.820744 CATTGGCAGGGTCCCGGG 62.821 72.222 16.85 16.85 0.00 5.73
1565 1578 2.969821 TGTAGTTTCATTGGCAGGGT 57.030 45.000 0.00 0.00 0.00 4.34
1567 1580 4.942852 TGTTTTGTAGTTTCATTGGCAGG 58.057 39.130 0.00 0.00 0.00 4.85
1571 1584 6.040391 TCCTTCCTGTTTTGTAGTTTCATTGG 59.960 38.462 0.00 0.00 0.00 3.16
1578 1591 3.881089 CGGTTCCTTCCTGTTTTGTAGTT 59.119 43.478 0.00 0.00 0.00 2.24
1622 1644 2.200373 ACAACAGCCAACCATAGACC 57.800 50.000 0.00 0.00 0.00 3.85
1628 1650 2.435372 AAGAGAACAACAGCCAACCA 57.565 45.000 0.00 0.00 0.00 3.67
1693 1715 5.324409 ACAAACTTAATCAGATGCCAAGGA 58.676 37.500 0.00 0.00 0.00 3.36
1704 1726 7.541783 GCATGCTGTTCAATACAAACTTAATCA 59.458 33.333 11.37 0.00 36.02 2.57
1705 1727 7.541783 TGCATGCTGTTCAATACAAACTTAATC 59.458 33.333 20.33 0.00 36.02 1.75
1706 1728 7.377398 TGCATGCTGTTCAATACAAACTTAAT 58.623 30.769 20.33 0.00 36.02 1.40
1707 1729 6.743110 TGCATGCTGTTCAATACAAACTTAA 58.257 32.000 20.33 0.00 36.02 1.85
1708 1730 6.206438 TCTGCATGCTGTTCAATACAAACTTA 59.794 34.615 20.33 0.00 36.02 2.24
1709 1731 5.009911 TCTGCATGCTGTTCAATACAAACTT 59.990 36.000 20.33 0.00 36.02 2.66
1710 1732 4.520111 TCTGCATGCTGTTCAATACAAACT 59.480 37.500 20.33 0.00 36.02 2.66
1711 1733 4.797471 TCTGCATGCTGTTCAATACAAAC 58.203 39.130 20.33 0.00 36.02 2.93
1712 1734 5.450592 TTCTGCATGCTGTTCAATACAAA 57.549 34.783 20.33 2.49 36.02 2.83
1713 1735 4.616604 GCTTCTGCATGCTGTTCAATACAA 60.617 41.667 20.33 5.19 36.25 2.41
1714 1736 3.119743 GCTTCTGCATGCTGTTCAATACA 60.120 43.478 20.33 0.00 39.41 2.29
1715 1737 3.128242 AGCTTCTGCATGCTGTTCAATAC 59.872 43.478 20.33 5.94 42.74 1.89
1730 1752 3.564644 CCATCCTTAATCAGCAGCTTCTG 59.435 47.826 7.08 7.08 35.46 3.02
1731 1753 3.201708 ACCATCCTTAATCAGCAGCTTCT 59.798 43.478 0.00 0.00 0.00 2.85
1737 1759 2.368439 GCACACCATCCTTAATCAGCA 58.632 47.619 0.00 0.00 0.00 4.41
1739 1761 3.003394 TGGCACACCATCCTTAATCAG 57.997 47.619 0.00 0.00 42.67 2.90
1753 1775 2.213513 TCAGACATCGGGTGGCACA 61.214 57.895 20.82 0.00 38.81 4.57
1754 1776 1.741770 GTCAGACATCGGGTGGCAC 60.742 63.158 9.70 9.70 38.81 5.01
1756 1778 2.125106 GGTCAGACATCGGGTGGC 60.125 66.667 2.17 0.00 35.41 5.01
1757 1779 1.257750 TGAGGTCAGACATCGGGTGG 61.258 60.000 10.54 0.00 30.36 4.61
1758 1780 0.826715 ATGAGGTCAGACATCGGGTG 59.173 55.000 10.54 0.00 30.36 4.61
1760 1782 2.587522 TCTATGAGGTCAGACATCGGG 58.412 52.381 10.54 3.65 30.36 5.14
1761 1783 3.192422 GGATCTATGAGGTCAGACATCGG 59.808 52.174 10.54 3.97 30.36 4.18
1762 1784 3.823304 TGGATCTATGAGGTCAGACATCG 59.177 47.826 10.54 0.00 30.36 3.84
1765 1787 4.256983 AGTGGATCTATGAGGTCAGACA 57.743 45.455 2.17 0.00 0.00 3.41
1766 1788 6.716934 TTAAGTGGATCTATGAGGTCAGAC 57.283 41.667 0.00 0.00 0.00 3.51
1768 1790 7.353414 TCTTTAAGTGGATCTATGAGGTCAG 57.647 40.000 0.00 0.00 0.00 3.51
1769 1791 7.687837 GCATCTTTAAGTGGATCTATGAGGTCA 60.688 40.741 0.00 0.00 0.00 4.02
1770 1792 6.648725 GCATCTTTAAGTGGATCTATGAGGTC 59.351 42.308 0.00 0.00 0.00 3.85
1771 1793 6.100279 TGCATCTTTAAGTGGATCTATGAGGT 59.900 38.462 0.00 0.00 0.00 3.85
1772 1794 6.528321 TGCATCTTTAAGTGGATCTATGAGG 58.472 40.000 0.00 0.00 0.00 3.86
1773 1795 6.147492 GCTGCATCTTTAAGTGGATCTATGAG 59.853 42.308 0.00 0.00 0.00 2.90
1774 1796 5.994054 GCTGCATCTTTAAGTGGATCTATGA 59.006 40.000 0.00 0.00 0.00 2.15
1775 1797 5.107182 CGCTGCATCTTTAAGTGGATCTATG 60.107 44.000 0.00 0.00 0.00 2.23
1776 1798 4.993584 CGCTGCATCTTTAAGTGGATCTAT 59.006 41.667 0.00 0.00 0.00 1.98
1777 1799 4.141937 ACGCTGCATCTTTAAGTGGATCTA 60.142 41.667 0.00 0.00 0.00 1.98
1778 1800 3.201290 CGCTGCATCTTTAAGTGGATCT 58.799 45.455 0.00 0.00 0.00 2.75
1779 1801 2.939103 ACGCTGCATCTTTAAGTGGATC 59.061 45.455 0.00 0.00 0.00 3.36
1800 1822 4.599041 CCCACTGTTTGAATTATCTCCCA 58.401 43.478 0.00 0.00 0.00 4.37
1801 1823 3.381590 GCCCACTGTTTGAATTATCTCCC 59.618 47.826 0.00 0.00 0.00 4.30
1803 1825 4.096984 CCTGCCCACTGTTTGAATTATCTC 59.903 45.833 0.00 0.00 0.00 2.75
1810 1832 0.550914 ACTCCTGCCCACTGTTTGAA 59.449 50.000 0.00 0.00 0.00 2.69
1824 1846 5.128991 GGGCTAGAACTGTATTAACACTCCT 59.871 44.000 0.00 0.00 0.00 3.69
1829 1851 3.770933 ACCGGGCTAGAACTGTATTAACA 59.229 43.478 6.32 0.00 0.00 2.41
1830 1852 4.397481 ACCGGGCTAGAACTGTATTAAC 57.603 45.455 6.32 0.00 0.00 2.01
1832 1854 4.761975 CAAACCGGGCTAGAACTGTATTA 58.238 43.478 6.32 0.00 0.00 0.98
1834 1856 2.679930 GCAAACCGGGCTAGAACTGTAT 60.680 50.000 6.32 0.00 0.00 2.29
1851 1873 2.594303 CCACTCACGGCCTGCAAA 60.594 61.111 0.00 0.00 0.00 3.68
1874 1896 7.430760 AGAGGAAAACTATTACAGAGCTCAT 57.569 36.000 17.77 6.09 0.00 2.90
2010 2032 6.726230 TCGAAGGAATCAAGACGAACTATAG 58.274 40.000 0.00 0.00 0.00 1.31
2061 2083 9.656040 GAATATCAGCAGATCAATGATAAGAGT 57.344 33.333 14.64 5.29 38.89 3.24
2067 2091 7.160049 ACGAAGAATATCAGCAGATCAATGAT 58.840 34.615 0.00 0.00 37.44 2.45
2070 2094 6.519382 TGACGAAGAATATCAGCAGATCAAT 58.481 36.000 0.00 0.00 35.67 2.57
2223 2247 5.709164 GGAACATCATCCATCCTGATTTAGG 59.291 44.000 0.00 0.00 42.55 2.69
2290 2314 6.016860 TGGTAATCATGTGAGATTATTGCAGC 60.017 38.462 0.00 0.00 41.17 5.25
2560 2584 2.222007 CTGAGCAGCTGTGGACTATC 57.778 55.000 16.64 3.39 0.00 2.08
2583 2607 0.463833 GGGGGAAACGAGTATGCCAG 60.464 60.000 0.00 0.00 0.00 4.85
2590 2614 0.541296 TCTTCGAGGGGGAAACGAGT 60.541 55.000 0.00 0.00 37.36 4.18
2598 2622 1.054406 TATGGCCTTCTTCGAGGGGG 61.054 60.000 3.32 0.00 37.29 5.40
2633 2657 7.769044 ACCGATAGTGTTTGTAATTATCTGCTT 59.231 33.333 0.00 0.00 0.00 3.91
2680 2704 5.008415 CAGAAGACATGCTGACTTTTTGACT 59.992 40.000 0.00 0.00 32.89 3.41


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

AutoCloner maintained by Alex Coulton.