Multiple sequence alignment - TraesCS1D01G064700

Loading Multiple Alignment...

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 TraesCS1D01G064700 chr1D 100.000 5813 0 0 1 5813 46186725 46180913 0.000000e+00 10735
1 TraesCS1D01G064700 chr1B 91.301 5012 215 97 168 5050 65551902 65546983 0.000000e+00 6636
2 TraesCS1D01G064700 chr1B 89.905 525 32 12 5307 5813 65546403 65545882 0.000000e+00 656
3 TraesCS1D01G064700 chr1B 87.317 205 12 6 5118 5310 65546773 65546571 7.580000e-54 222
4 TraesCS1D01G064700 chr1A 91.969 4719 184 85 488 5104 45793425 45798050 0.000000e+00 6434
5 TraesCS1D01G064700 chr1A 92.269 401 17 6 5424 5813 45798370 45798767 1.830000e-154 556
6 TraesCS1D01G064700 chr1A 87.826 460 43 8 1 451 45792973 45793428 1.430000e-145 527
7 TraesCS1D01G064700 chr1A 87.407 270 15 5 5117 5370 45798107 45798373 5.700000e-75 292


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 TraesCS1D01G064700 chr1D 46180913 46186725 5812 True 10735.000000 10735 100.000000 1 5813 1 chr1D.!!$R1 5812
1 TraesCS1D01G064700 chr1B 65545882 65551902 6020 True 2504.666667 6636 89.507667 168 5813 3 chr1B.!!$R1 5645
2 TraesCS1D01G064700 chr1A 45792973 45798767 5794 False 1952.250000 6434 89.867750 1 5813 4 chr1A.!!$F1 5812

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
441 465 0.305922 CGCTTGCTGCTAGTTATGCC 59.694 55.000 12.43 0.0 40.11 4.40 F
711 740 0.389025 CAAGCTGTCCAACCCCAAAC 59.611 55.000 0.00 0.0 0.00 2.93 F
1261 1338 0.104304 CGGTGGTATTCTCCTTCCCG 59.896 60.000 0.00 0.0 0.00 5.14 F
1289 1366 0.884704 GCGAGTGTTTGCTGGGAGAA 60.885 55.000 0.00 0.0 0.00 2.87 F
3179 3319 0.819582 TGGTCGAGGGTAATTCGGTC 59.180 55.000 0.00 0.0 38.54 4.79 F
3700 3841 1.475213 GGTAGGCCTTCCCGATTCTTG 60.475 57.143 17.50 0.0 39.21 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1242 1315 0.104304 CGGGAAGGAGAATACCACCG 59.896 60.0 0.00 0.0 37.52 4.94 R
2449 2578 0.179156 GCATGTTCAGGCATGTTCGG 60.179 55.0 0.00 0.0 45.75 4.30 R
2482 2611 0.537371 AGTTTTGAGGAAGGCCACCG 60.537 55.0 5.01 0.0 36.29 4.94 R
3194 3334 2.776312 GCATACAGCGCAGAGTACTA 57.224 50.0 11.47 0.0 0.00 1.82 R
4041 4184 0.030909 TACAAGGGGATAGCCGGGAA 60.031 55.0 2.18 0.0 33.83 3.97 R
5059 5349 0.109597 CGGCACTTCCAATTGCACTC 60.110 55.0 0.00 0.0 40.75 3.51 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
26 27 7.524912 AGCGAGTTTGCATTCATCATATTATC 58.475 34.615 0.00 0.00 37.31 1.75
56 57 4.642429 ACACTCTCTAAAGCCAAATTCGT 58.358 39.130 0.00 0.00 0.00 3.85
84 88 3.354131 GATGGACTCGACTCTTGCC 57.646 57.895 0.00 0.00 0.00 4.52
92 96 0.809385 TCGACTCTTGCCGGAACTAG 59.191 55.000 5.05 0.00 0.00 2.57
166 171 9.981114 AAACCATAATTCAACTACAAGAAAAGG 57.019 29.630 0.00 0.00 0.00 3.11
173 178 4.885325 TCAACTACAAGAAAAGGACAACCC 59.115 41.667 0.00 0.00 36.73 4.11
181 186 3.920817 AGGACAACCCTCCATGCA 58.079 55.556 0.00 0.00 43.31 3.96
188 193 1.068333 CAACCCTCCATGCAAAAGTCG 60.068 52.381 0.00 0.00 0.00 4.18
191 196 1.672881 CCCTCCATGCAAAAGTCGATC 59.327 52.381 0.00 0.00 0.00 3.69
219 227 9.554395 CCCAAAATAAATAAATAACATGGACCC 57.446 33.333 0.00 0.00 0.00 4.46
294 311 9.410556 AGACAAAATACCGAAATGAAAGAAATG 57.589 29.630 0.00 0.00 0.00 2.32
349 366 8.420222 AGAATCGAGAGTCAGAAATATGTTGAT 58.580 33.333 3.38 0.00 0.00 2.57
359 376 6.541278 TCAGAAATATGTTGATTGGAGCTGAG 59.459 38.462 0.00 0.00 0.00 3.35
410 433 1.139256 TCCGTAGAAGTGTTTGCACCA 59.861 47.619 0.00 0.00 46.35 4.17
417 440 4.183101 AGAAGTGTTTGCACCAACATTTG 58.817 39.130 14.50 0.00 46.35 2.32
423 446 3.557577 TTGCACCAACATTTGAGATCG 57.442 42.857 0.00 0.00 0.00 3.69
440 464 1.290203 TCGCTTGCTGCTAGTTATGC 58.710 50.000 12.43 0.00 40.11 3.14
441 465 0.305922 CGCTTGCTGCTAGTTATGCC 59.694 55.000 12.43 0.00 40.11 4.40
445 469 3.367292 GCTTGCTGCTAGTTATGCCAAAA 60.367 43.478 12.43 0.00 38.95 2.44
446 470 4.678840 GCTTGCTGCTAGTTATGCCAAAAT 60.679 41.667 12.43 0.00 38.95 1.82
447 471 5.450412 GCTTGCTGCTAGTTATGCCAAAATA 60.450 40.000 12.43 0.00 38.95 1.40
448 472 6.522625 TTGCTGCTAGTTATGCCAAAATAA 57.477 33.333 0.00 0.00 0.00 1.40
450 474 7.111247 TGCTGCTAGTTATGCCAAAATAAAT 57.889 32.000 0.00 0.00 0.00 1.40
453 477 9.528018 GCTGCTAGTTATGCCAAAATAAATAAA 57.472 29.630 0.00 0.00 0.00 1.40
482 506 5.923684 TGAACCTGAAAATAAAACCATTCGC 59.076 36.000 0.00 0.00 0.00 4.70
485 509 4.323336 CCTGAAAATAAAACCATTCGCACG 59.677 41.667 0.00 0.00 0.00 5.34
486 510 5.109662 TGAAAATAAAACCATTCGCACGA 57.890 34.783 0.00 0.00 0.00 4.35
498 523 4.204978 CCATTCGCACGAAAAATAGCAATC 59.795 41.667 9.80 0.00 37.69 2.67
504 529 3.126171 CACGAAAAATAGCAATCCCGTGA 59.874 43.478 0.00 0.00 45.93 4.35
518 543 1.201414 CCCGTGAAAGTATTTGCACCC 59.799 52.381 3.63 0.00 39.27 4.61
526 551 6.643360 GTGAAAGTATTTGCACCCGTATTTTT 59.357 34.615 0.00 0.00 39.27 1.94
609 634 4.463891 AGTGCATCCAAGAATACCCAAAAG 59.536 41.667 0.00 0.00 0.00 2.27
621 650 1.402107 CCCAAAAGCACCCAAGCACT 61.402 55.000 0.00 0.00 36.85 4.40
625 654 0.746659 AAAGCACCCAAGCACTCAAC 59.253 50.000 0.00 0.00 36.85 3.18
711 740 0.389025 CAAGCTGTCCAACCCCAAAC 59.611 55.000 0.00 0.00 0.00 2.93
712 741 0.759060 AAGCTGTCCAACCCCAAACC 60.759 55.000 0.00 0.00 0.00 3.27
713 742 2.207229 GCTGTCCAACCCCAAACCC 61.207 63.158 0.00 0.00 0.00 4.11
714 743 1.231641 CTGTCCAACCCCAAACCCA 59.768 57.895 0.00 0.00 0.00 4.51
715 744 1.075896 TGTCCAACCCCAAACCCAC 60.076 57.895 0.00 0.00 0.00 4.61
717 746 0.688087 GTCCAACCCCAAACCCACAA 60.688 55.000 0.00 0.00 0.00 3.33
718 747 0.688087 TCCAACCCCAAACCCACAAC 60.688 55.000 0.00 0.00 0.00 3.32
719 748 1.691195 CCAACCCCAAACCCACAACC 61.691 60.000 0.00 0.00 0.00 3.77
720 749 1.383386 AACCCCAAACCCACAACCC 60.383 57.895 0.00 0.00 0.00 4.11
721 750 2.182858 AACCCCAAACCCACAACCCA 62.183 55.000 0.00 0.00 0.00 4.51
722 751 1.383248 CCCCAAACCCACAACCCAA 60.383 57.895 0.00 0.00 0.00 4.12
734 763 2.746362 CACAACCCAAAGAGAGAGCATC 59.254 50.000 0.00 0.00 0.00 3.91
735 764 2.290577 ACAACCCAAAGAGAGAGCATCC 60.291 50.000 0.00 0.00 33.66 3.51
736 765 0.915364 ACCCAAAGAGAGAGCATCCC 59.085 55.000 0.00 0.00 33.66 3.85
737 766 0.914644 CCCAAAGAGAGAGCATCCCA 59.085 55.000 0.00 0.00 33.66 4.37
738 767 1.493871 CCCAAAGAGAGAGCATCCCAT 59.506 52.381 0.00 0.00 33.66 4.00
799 837 1.079266 CTCACCACTCCAGCAGCTC 60.079 63.158 0.00 0.00 0.00 4.09
844 882 1.038130 CCCTCCTGTCAGTCCTACCG 61.038 65.000 0.00 0.00 0.00 4.02
847 885 1.982395 CCTGTCAGTCCTACCGCCA 60.982 63.158 0.00 0.00 0.00 5.69
951 1004 3.566130 AGCAATTCAGCTGTCCTCC 57.434 52.632 14.67 1.04 44.66 4.30
952 1005 0.990374 AGCAATTCAGCTGTCCTCCT 59.010 50.000 14.67 3.48 44.66 3.69
953 1006 1.065564 AGCAATTCAGCTGTCCTCCTC 60.066 52.381 14.67 0.00 44.66 3.71
975 1028 1.961277 CGCCAACCTGACACACCTC 60.961 63.158 0.00 0.00 0.00 3.85
976 1029 1.600916 GCCAACCTGACACACCTCC 60.601 63.158 0.00 0.00 0.00 4.30
977 1030 1.073199 CCAACCTGACACACCTCCC 59.927 63.158 0.00 0.00 0.00 4.30
978 1031 1.073199 CAACCTGACACACCTCCCC 59.927 63.158 0.00 0.00 0.00 4.81
979 1032 1.073706 AACCTGACACACCTCCCCT 60.074 57.895 0.00 0.00 0.00 4.79
980 1033 0.697854 AACCTGACACACCTCCCCTT 60.698 55.000 0.00 0.00 0.00 3.95
981 1034 1.128188 ACCTGACACACCTCCCCTTC 61.128 60.000 0.00 0.00 0.00 3.46
982 1035 1.679898 CTGACACACCTCCCCTTCC 59.320 63.158 0.00 0.00 0.00 3.46
983 1036 1.842381 CTGACACACCTCCCCTTCCC 61.842 65.000 0.00 0.00 0.00 3.97
984 1037 1.846124 GACACACCTCCCCTTCCCA 60.846 63.158 0.00 0.00 0.00 4.37
989 1042 2.378522 CCTCCCCTTCCCATCCCT 59.621 66.667 0.00 0.00 0.00 4.20
1055 1119 4.680237 CACCGCACCGCAAGAGGA 62.680 66.667 0.00 0.00 43.02 3.71
1056 1120 3.936203 ACCGCACCGCAAGAGGAA 61.936 61.111 0.00 0.00 43.02 3.36
1057 1121 3.121030 CCGCACCGCAAGAGGAAG 61.121 66.667 0.00 0.00 43.02 3.46
1058 1122 3.121030 CGCACCGCAAGAGGAAGG 61.121 66.667 0.00 0.00 43.02 3.46
1059 1123 2.747855 GCACCGCAAGAGGAAGGG 60.748 66.667 0.00 0.00 43.02 3.95
1060 1124 2.747855 CACCGCAAGAGGAAGGGC 60.748 66.667 0.00 0.00 43.02 5.19
1061 1125 3.249189 ACCGCAAGAGGAAGGGCA 61.249 61.111 0.00 0.00 43.02 5.36
1062 1126 2.747855 CCGCAAGAGGAAGGGCAC 60.748 66.667 0.00 0.00 43.02 5.01
1063 1127 2.348998 CGCAAGAGGAAGGGCACT 59.651 61.111 0.00 0.00 43.02 4.40
1064 1128 1.743252 CGCAAGAGGAAGGGCACTC 60.743 63.158 0.00 0.00 43.02 3.51
1242 1315 2.107953 GGAGGCGCAGATCTGACC 59.892 66.667 27.04 23.97 0.00 4.02
1244 1317 3.781770 GAGGCGCAGATCTGACCGG 62.782 68.421 27.04 12.27 34.66 5.28
1245 1318 4.148825 GGCGCAGATCTGACCGGT 62.149 66.667 27.04 6.92 0.00 5.28
1246 1319 2.887568 GCGCAGATCTGACCGGTG 60.888 66.667 27.04 6.55 0.00 4.94
1248 1321 2.982130 GCAGATCTGACCGGTGGT 59.018 61.111 27.04 0.00 39.44 4.16
1249 1322 1.663379 CGCAGATCTGACCGGTGGTA 61.663 60.000 27.04 0.00 35.25 3.25
1250 1323 0.753262 GCAGATCTGACCGGTGGTAT 59.247 55.000 27.04 0.83 35.25 2.73
1251 1324 1.139058 GCAGATCTGACCGGTGGTATT 59.861 52.381 27.04 0.00 35.25 1.89
1252 1325 2.803492 GCAGATCTGACCGGTGGTATTC 60.803 54.545 27.04 2.02 35.25 1.75
1254 1327 2.959707 AGATCTGACCGGTGGTATTCTC 59.040 50.000 14.63 0.00 35.25 2.87
1255 1328 1.481871 TCTGACCGGTGGTATTCTCC 58.518 55.000 14.63 0.00 35.25 3.71
1257 1330 1.831736 CTGACCGGTGGTATTCTCCTT 59.168 52.381 14.63 0.00 35.25 3.36
1261 1338 0.104304 CGGTGGTATTCTCCTTCCCG 59.896 60.000 0.00 0.00 0.00 5.14
1281 1358 4.072088 CCGTCGGCGAGTGTTTGC 62.072 66.667 12.93 0.00 41.33 3.68
1289 1366 0.884704 GCGAGTGTTTGCTGGGAGAA 60.885 55.000 0.00 0.00 0.00 2.87
1397 1474 8.566109 AGGAGGAGGTAATAATTAATTTGTGGT 58.434 33.333 5.91 0.00 0.00 4.16
1398 1475 9.856162 GGAGGAGGTAATAATTAATTTGTGGTA 57.144 33.333 5.91 0.00 0.00 3.25
1409 1490 8.816640 AATTAATTTGTGGTAACTCTTGCTTG 57.183 30.769 0.00 0.00 37.61 4.01
1412 1493 1.771854 TGTGGTAACTCTTGCTTGGGA 59.228 47.619 0.00 0.00 37.61 4.37
1482 1565 8.669946 ATTTCCTTAGATTTTACTGCTAGCTC 57.330 34.615 17.23 2.85 0.00 4.09
1483 1566 7.425224 TTCCTTAGATTTTACTGCTAGCTCT 57.575 36.000 17.23 10.72 0.00 4.09
1528 1611 1.428912 AGGATTTGGCTGTTTCCTCCA 59.571 47.619 0.00 0.00 33.22 3.86
1529 1612 2.043526 AGGATTTGGCTGTTTCCTCCAT 59.956 45.455 0.00 0.00 33.22 3.41
1530 1613 2.167075 GGATTTGGCTGTTTCCTCCATG 59.833 50.000 0.00 0.00 0.00 3.66
1562 1646 2.557924 TGCAAACAGTCAGCTTATTGGG 59.442 45.455 0.00 0.00 0.00 4.12
1563 1647 2.819608 GCAAACAGTCAGCTTATTGGGA 59.180 45.455 0.00 0.00 0.00 4.37
1564 1648 3.255642 GCAAACAGTCAGCTTATTGGGAA 59.744 43.478 0.00 0.00 0.00 3.97
1574 1671 5.043248 CAGCTTATTGGGAATTTTTAGGCG 58.957 41.667 0.00 0.00 0.00 5.52
1605 1702 8.851541 ATCTTGAAATTGGCATATTGTTTTGT 57.148 26.923 0.00 0.00 0.00 2.83
1606 1703 8.674263 TCTTGAAATTGGCATATTGTTTTGTT 57.326 26.923 0.00 0.00 0.00 2.83
1607 1704 8.772705 TCTTGAAATTGGCATATTGTTTTGTTC 58.227 29.630 0.00 0.00 0.00 3.18
1608 1705 8.442632 TTGAAATTGGCATATTGTTTTGTTCA 57.557 26.923 0.00 0.00 0.00 3.18
1609 1706 7.859598 TGAAATTGGCATATTGTTTTGTTCAC 58.140 30.769 0.00 0.00 0.00 3.18
1717 1819 1.686052 GGGCTGTCATGTTTGGACAAA 59.314 47.619 0.00 0.00 44.04 2.83
2167 2296 1.507974 TATCGAGGGAAGAGCTCGCG 61.508 60.000 8.37 0.00 41.82 5.87
2262 2391 3.747529 GCCATTTGGAATGTTTTGTGAGG 59.252 43.478 0.00 0.00 37.39 3.86
2421 2550 7.899178 TTTTCAACTTTGGAAGAAAAACTCC 57.101 32.000 0.00 0.00 37.12 3.85
2477 2606 1.730064 GCCTGAACATGCAAGCAAATG 59.270 47.619 0.00 0.00 0.00 2.32
2478 2607 2.868839 GCCTGAACATGCAAGCAAATGT 60.869 45.455 0.00 0.00 38.66 2.71
2482 2611 2.074547 ACATGCAAGCAAATGTCTGC 57.925 45.000 0.00 2.98 42.97 4.26
2510 2639 5.048643 GGCCTTCCTCAAAACTTTCTCTTAC 60.049 44.000 0.00 0.00 0.00 2.34
2576 2705 9.248291 GTCAGTTGCTTTTAATTTGAATTGAGA 57.752 29.630 0.00 0.00 0.00 3.27
2610 2740 9.425577 GTGAAATTCTTAGCTACTTACAGTTCT 57.574 33.333 0.00 0.00 0.00 3.01
2700 2830 4.550076 ACCAGAATCCTCTGTTCTTCTG 57.450 45.455 4.56 4.56 46.71 3.02
2745 2875 7.004555 TCTTACTCCTTAAAAGCACTCATCA 57.995 36.000 0.00 0.00 0.00 3.07
2759 2889 5.132648 AGCACTCATCACCCCTTATGATTTA 59.867 40.000 0.00 0.00 34.49 1.40
2813 2943 3.888930 TGTTGAAGAGGGCCTACAAAAAG 59.111 43.478 5.73 0.00 0.00 2.27
2815 2945 4.657814 TGAAGAGGGCCTACAAAAAGAT 57.342 40.909 5.73 0.00 0.00 2.40
2816 2946 4.589908 TGAAGAGGGCCTACAAAAAGATC 58.410 43.478 5.73 0.00 0.00 2.75
2817 2947 4.289672 TGAAGAGGGCCTACAAAAAGATCT 59.710 41.667 5.73 0.00 0.00 2.75
2825 2965 5.106515 GGCCTACAAAAAGATCTTCACAGAC 60.107 44.000 8.78 0.00 0.00 3.51
2951 3091 6.037610 CCTTGATACAAAGGTAGCATGTCTTC 59.962 42.308 6.65 6.69 44.59 2.87
2996 3136 5.746284 TCCAAAAACACGATACCATATCCA 58.254 37.500 0.00 0.00 0.00 3.41
3084 3224 6.655003 CCGAACCAGGATTGCTATACATATTT 59.345 38.462 0.00 0.00 0.00 1.40
3091 3231 9.499479 CAGGATTGCTATACATATTTTGAGAGT 57.501 33.333 0.00 0.00 0.00 3.24
3092 3232 9.717942 AGGATTGCTATACATATTTTGAGAGTC 57.282 33.333 0.00 0.00 0.00 3.36
3093 3233 9.494271 GGATTGCTATACATATTTTGAGAGTCA 57.506 33.333 0.00 0.00 0.00 3.41
3179 3319 0.819582 TGGTCGAGGGTAATTCGGTC 59.180 55.000 0.00 0.00 38.54 4.79
3278 3418 3.513119 TGAAGATGTCTGAGGAGAACCAG 59.487 47.826 0.00 0.00 38.94 4.00
3465 3605 4.579869 TGAGTACTCCAATTTCCAGAAGC 58.420 43.478 20.11 0.00 0.00 3.86
3617 3758 3.119173 AGGAGAAGATCGAAGCAAGTCTG 60.119 47.826 0.00 0.00 0.00 3.51
3700 3841 1.475213 GGTAGGCCTTCCCGATTCTTG 60.475 57.143 17.50 0.00 39.21 3.02
3757 3900 6.535150 TCGACTATGTCTCTTAAAATGCTTGG 59.465 38.462 0.00 0.00 0.00 3.61
4058 4201 1.451936 CTTCCCGGCTATCCCCTTG 59.548 63.158 0.00 0.00 0.00 3.61
4110 4253 6.529220 AGTTGTGAAGAAGAAATCTGCTACT 58.471 36.000 0.00 0.00 38.79 2.57
4170 4313 1.300465 CGTGCTCAGTGTGCAGTCT 60.300 57.895 19.61 0.00 41.41 3.24
4239 4382 2.578128 AGCCTCGCAAGCTCTCTG 59.422 61.111 0.00 0.00 34.91 3.35
4468 4611 1.522569 GTGAAGGACATCCCCGAGG 59.477 63.158 0.00 0.00 36.42 4.63
4522 4665 4.556942 TGAGACAAACAAGCAACTCATG 57.443 40.909 0.00 0.00 31.02 3.07
4553 4699 3.239449 ACGGGACTATGGATTATGCAGA 58.761 45.455 0.00 0.00 0.00 4.26
4554 4700 3.840666 ACGGGACTATGGATTATGCAGAT 59.159 43.478 0.00 0.00 0.00 2.90
4681 4829 0.250381 ACTCTCGGTGTCGTCTGTCT 60.250 55.000 0.00 0.00 37.69 3.41
4699 4847 4.619973 TGTCTGTCCATTTCATTTGTTGC 58.380 39.130 0.00 0.00 0.00 4.17
4700 4848 4.341806 TGTCTGTCCATTTCATTTGTTGCT 59.658 37.500 0.00 0.00 0.00 3.91
4701 4849 5.163426 TGTCTGTCCATTTCATTTGTTGCTT 60.163 36.000 0.00 0.00 0.00 3.91
4702 4850 5.176223 GTCTGTCCATTTCATTTGTTGCTTG 59.824 40.000 0.00 0.00 0.00 4.01
4783 4931 5.335113 GCGAGCAATATATTTCTTCCATGCA 60.335 40.000 0.00 0.00 35.11 3.96
4785 4933 6.745907 CGAGCAATATATTTCTTCCATGCATG 59.254 38.462 20.19 20.19 35.11 4.06
4787 4935 5.579511 GCAATATATTTCTTCCATGCATGCC 59.420 40.000 21.69 0.00 33.00 4.40
4804 4967 2.238521 TGCCTTCCCAATGAACTTGTC 58.761 47.619 0.00 0.00 32.61 3.18
4810 4973 4.852134 TCCCAATGAACTTGTCAATGTG 57.148 40.909 0.00 0.00 40.50 3.21
4848 5011 7.686434 TGCCCCAATAAGTATCCTATCTTTAC 58.314 38.462 0.00 0.00 0.00 2.01
4850 5021 9.043548 GCCCCAATAAGTATCCTATCTTTACTA 57.956 37.037 0.00 0.00 0.00 1.82
4942 5115 2.821366 GTGGTGGCCATGCTCTCG 60.821 66.667 9.72 0.00 35.28 4.04
4952 5125 2.117156 ATGCTCTCGCCATGGTTGC 61.117 57.895 14.67 11.02 34.43 4.17
4967 5140 1.078497 TTGCTGTCGGCCATGGTAG 60.078 57.895 14.67 7.95 40.92 3.18
4968 5141 2.897350 GCTGTCGGCCATGGTAGC 60.897 66.667 14.67 11.73 34.27 3.58
4969 5142 2.903357 CTGTCGGCCATGGTAGCT 59.097 61.111 14.67 0.00 0.00 3.32
4970 5143 1.522355 CTGTCGGCCATGGTAGCTG 60.522 63.158 14.67 4.14 38.00 4.24
4971 5144 1.960040 CTGTCGGCCATGGTAGCTGA 61.960 60.000 14.67 6.74 43.28 4.26
4972 5145 2.900273 TCGGCCATGGTAGCTGAC 59.100 61.111 14.67 0.00 40.67 3.51
4973 5146 1.685765 TCGGCCATGGTAGCTGACT 60.686 57.895 14.67 0.00 40.67 3.41
4974 5147 0.396556 TCGGCCATGGTAGCTGACTA 60.397 55.000 14.67 0.00 40.67 2.59
4975 5148 0.032678 CGGCCATGGTAGCTGACTAG 59.967 60.000 14.67 0.00 39.03 2.57
5034 5207 0.961019 TTGCCCAGCATTCAGTTGAC 59.039 50.000 0.00 0.00 38.76 3.18
5185 5536 8.632906 ATTATGCAAAATTTTGTTCATTGGGA 57.367 26.923 27.13 9.27 40.24 4.37
5216 5567 9.150348 CACAAAAGTAAAATGAAAAGGTTGTCT 57.850 29.630 0.00 0.00 0.00 3.41
5260 5613 5.722021 AATTTTGTTCTCCGCAAATACCT 57.278 34.783 0.00 0.00 35.99 3.08
5292 5645 5.221891 GTCAGAACGACAATACTACCGTA 57.778 43.478 0.00 0.00 44.69 4.02
5388 5914 4.284490 TGACAAGCCTCAGAAACATACTCT 59.716 41.667 0.00 0.00 0.00 3.24
5389 5915 4.826556 ACAAGCCTCAGAAACATACTCTC 58.173 43.478 0.00 0.00 0.00 3.20
5390 5916 4.187694 CAAGCCTCAGAAACATACTCTCC 58.812 47.826 0.00 0.00 0.00 3.71
5391 5917 3.445008 AGCCTCAGAAACATACTCTCCA 58.555 45.455 0.00 0.00 0.00 3.86
5392 5918 3.196685 AGCCTCAGAAACATACTCTCCAC 59.803 47.826 0.00 0.00 0.00 4.02
5394 5920 4.323104 GCCTCAGAAACATACTCTCCACTT 60.323 45.833 0.00 0.00 0.00 3.16
5410 5938 7.494952 ACTCTCCACTTCTTAAACAACTAACAC 59.505 37.037 0.00 0.00 0.00 3.32
5412 5940 6.416415 TCCACTTCTTAAACAACTAACACCA 58.584 36.000 0.00 0.00 0.00 4.17
5438 5966 7.603024 AGTTTTAGATAGACAGTAACAGCCAAC 59.397 37.037 0.00 0.00 0.00 3.77
5482 6010 7.407393 TCACTAATCATGGCAATTGATCAAA 57.593 32.000 13.09 0.00 32.72 2.69
5502 6030 0.099968 CATTCATGGCCGAAGCACAG 59.900 55.000 0.00 0.00 42.56 3.66
5597 6138 1.975680 GGTTGGGTGTCTCAACTCCTA 59.024 52.381 11.43 0.00 42.76 2.94
5742 6292 2.354704 CCTTCTGGTTGATCGGCAGTTA 60.355 50.000 0.00 0.00 0.00 2.24
5754 6304 1.461127 CGGCAGTTACTTGCAGAGAAC 59.539 52.381 8.51 1.59 45.86 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
26 27 6.801539 TGGCTTTAGAGAGTGTATGTTTTG 57.198 37.500 0.00 0.00 0.00 2.44
84 88 6.295039 TCTTTTTGTTAGTTGCTAGTTCCG 57.705 37.500 0.00 0.00 0.00 4.30
165 170 1.273327 CTTTTGCATGGAGGGTTGTCC 59.727 52.381 0.00 0.00 37.10 4.02
166 171 1.963515 ACTTTTGCATGGAGGGTTGTC 59.036 47.619 0.00 0.00 0.00 3.18
173 178 2.096496 GGTGATCGACTTTTGCATGGAG 59.904 50.000 0.00 0.00 0.00 3.86
219 227 5.160607 TGGACATTCTAGTGGGTAGTTTG 57.839 43.478 0.00 0.00 0.00 2.93
262 279 8.568676 TTCATTTCGGTATTTTGTCTAATGGA 57.431 30.769 0.00 0.00 0.00 3.41
327 344 6.758416 CCAATCAACATATTTCTGACTCTCGA 59.242 38.462 0.00 0.00 0.00 4.04
349 366 6.429692 TCGAATTGTTTTATTCTCAGCTCCAA 59.570 34.615 0.00 0.00 33.34 3.53
401 424 3.670055 CGATCTCAAATGTTGGTGCAAAC 59.330 43.478 0.00 0.00 0.00 2.93
410 433 2.415090 GCAGCAAGCGATCTCAAATGTT 60.415 45.455 0.00 0.00 0.00 2.71
423 446 1.382522 TGGCATAACTAGCAGCAAGC 58.617 50.000 0.00 0.00 46.19 4.01
455 479 9.632807 CGAATGGTTTTATTTTCAGGTTCAATA 57.367 29.630 0.00 0.00 0.00 1.90
459 483 5.923684 TGCGAATGGTTTTATTTTCAGGTTC 59.076 36.000 0.00 0.00 0.00 3.62
466 490 6.830114 TTTTCGTGCGAATGGTTTTATTTT 57.170 29.167 7.87 0.00 33.79 1.82
475 499 3.129852 TGCTATTTTTCGTGCGAATGG 57.870 42.857 7.87 0.00 33.79 3.16
477 501 4.351192 GGATTGCTATTTTTCGTGCGAAT 58.649 39.130 7.87 0.00 33.79 3.34
478 502 3.426963 GGGATTGCTATTTTTCGTGCGAA 60.427 43.478 2.65 2.65 0.00 4.70
480 504 2.450160 GGGATTGCTATTTTTCGTGCG 58.550 47.619 0.00 0.00 0.00 5.34
482 506 3.126171 TCACGGGATTGCTATTTTTCGTG 59.874 43.478 14.60 14.60 45.15 4.35
485 509 5.709966 ACTTTCACGGGATTGCTATTTTTC 58.290 37.500 0.00 0.00 0.00 2.29
486 510 5.722021 ACTTTCACGGGATTGCTATTTTT 57.278 34.783 0.00 0.00 0.00 1.94
498 523 1.201414 GGGTGCAAATACTTTCACGGG 59.799 52.381 0.00 0.00 0.00 5.28
504 529 6.750148 TCAAAAATACGGGTGCAAATACTTT 58.250 32.000 0.00 0.00 0.00 2.66
518 543 3.786048 GCCGCAAGAGATTCAAAAATACG 59.214 43.478 0.00 0.00 43.02 3.06
526 551 3.334583 AAACTAGCCGCAAGAGATTCA 57.665 42.857 0.00 0.00 43.02 2.57
609 634 2.564721 GGGTTGAGTGCTTGGGTGC 61.565 63.158 0.00 0.00 0.00 5.01
621 650 5.420409 GTGTTGTTTATGTTTTGGGGTTGA 58.580 37.500 0.00 0.00 0.00 3.18
625 654 4.408182 TGGTGTTGTTTATGTTTTGGGG 57.592 40.909 0.00 0.00 0.00 4.96
663 692 5.466728 CAGAAGAGGAAACGAATTGAAGTGA 59.533 40.000 0.00 0.00 0.00 3.41
711 740 1.884067 GCTCTCTCTTTGGGTTGTGGG 60.884 57.143 0.00 0.00 0.00 4.61
712 741 1.202806 TGCTCTCTCTTTGGGTTGTGG 60.203 52.381 0.00 0.00 0.00 4.17
713 742 2.260844 TGCTCTCTCTTTGGGTTGTG 57.739 50.000 0.00 0.00 0.00 3.33
714 743 2.290577 GGATGCTCTCTCTTTGGGTTGT 60.291 50.000 0.00 0.00 0.00 3.32
715 744 2.363683 GGATGCTCTCTCTTTGGGTTG 58.636 52.381 0.00 0.00 0.00 3.77
717 746 0.915364 GGGATGCTCTCTCTTTGGGT 59.085 55.000 0.00 0.00 0.00 4.51
718 747 0.914644 TGGGATGCTCTCTCTTTGGG 59.085 55.000 0.00 0.00 0.00 4.12
719 748 2.486907 GGATGGGATGCTCTCTCTTTGG 60.487 54.545 0.00 0.00 0.00 3.28
720 749 2.486907 GGGATGGGATGCTCTCTCTTTG 60.487 54.545 0.00 0.00 0.00 2.77
721 750 1.773653 GGGATGGGATGCTCTCTCTTT 59.226 52.381 0.00 0.00 0.00 2.52
722 751 1.344803 TGGGATGGGATGCTCTCTCTT 60.345 52.381 0.00 0.00 0.00 2.85
734 763 0.112218 TTGGTGTCTGTTGGGATGGG 59.888 55.000 0.00 0.00 0.00 4.00
735 764 1.538047 CTTGGTGTCTGTTGGGATGG 58.462 55.000 0.00 0.00 0.00 3.51
736 765 0.883833 GCTTGGTGTCTGTTGGGATG 59.116 55.000 0.00 0.00 0.00 3.51
737 766 0.478072 TGCTTGGTGTCTGTTGGGAT 59.522 50.000 0.00 0.00 0.00 3.85
738 767 0.257328 TTGCTTGGTGTCTGTTGGGA 59.743 50.000 0.00 0.00 0.00 4.37
844 882 3.397613 CTAGCTGGCTGGAGGTGGC 62.398 68.421 5.25 0.00 0.00 5.01
847 885 0.041238 TGTACTAGCTGGCTGGAGGT 59.959 55.000 12.65 5.54 0.00 3.85
860 902 3.039011 GGAGGAGCTGGGAATTGTACTA 58.961 50.000 0.00 0.00 0.00 1.82
951 1004 0.946221 GTGTCAGGTTGGCGTGAGAG 60.946 60.000 0.00 0.00 39.76 3.20
952 1005 1.069090 GTGTCAGGTTGGCGTGAGA 59.931 57.895 0.00 0.00 39.76 3.27
953 1006 1.227527 TGTGTCAGGTTGGCGTGAG 60.228 57.895 0.00 0.00 39.76 3.51
975 1028 2.395353 GGGAAGGGATGGGAAGGGG 61.395 68.421 0.00 0.00 0.00 4.79
976 1029 0.926220 AAGGGAAGGGATGGGAAGGG 60.926 60.000 0.00 0.00 0.00 3.95
977 1030 0.553333 GAAGGGAAGGGATGGGAAGG 59.447 60.000 0.00 0.00 0.00 3.46
978 1031 0.553333 GGAAGGGAAGGGATGGGAAG 59.447 60.000 0.00 0.00 0.00 3.46
979 1032 0.123266 AGGAAGGGAAGGGATGGGAA 59.877 55.000 0.00 0.00 0.00 3.97
980 1033 0.123266 AAGGAAGGGAAGGGATGGGA 59.877 55.000 0.00 0.00 0.00 4.37
981 1034 0.553333 GAAGGAAGGGAAGGGATGGG 59.447 60.000 0.00 0.00 0.00 4.00
982 1035 0.553333 GGAAGGAAGGGAAGGGATGG 59.447 60.000 0.00 0.00 0.00 3.51
983 1036 0.553333 GGGAAGGAAGGGAAGGGATG 59.447 60.000 0.00 0.00 0.00 3.51
984 1037 0.988678 CGGGAAGGAAGGGAAGGGAT 60.989 60.000 0.00 0.00 0.00 3.85
989 1042 2.034436 ACTAACGGGAAGGAAGGGAA 57.966 50.000 0.00 0.00 0.00 3.97
1040 1104 3.121030 CTTCCTCTTGCGGTGCGG 61.121 66.667 0.00 0.00 0.00 5.69
1041 1105 3.121030 CCTTCCTCTTGCGGTGCG 61.121 66.667 0.00 0.00 0.00 5.34
1043 1107 2.747855 GCCCTTCCTCTTGCGGTG 60.748 66.667 0.00 0.00 0.00 4.94
1044 1108 3.249189 TGCCCTTCCTCTTGCGGT 61.249 61.111 0.00 0.00 0.00 5.68
1045 1109 2.747855 GTGCCCTTCCTCTTGCGG 60.748 66.667 0.00 0.00 0.00 5.69
1047 1111 1.743252 CGAGTGCCCTTCCTCTTGC 60.743 63.158 0.00 0.00 0.00 4.01
1049 1113 2.665603 GCGAGTGCCCTTCCTCTT 59.334 61.111 0.00 0.00 33.98 2.85
1148 1216 2.515057 ACACACAAAAGGGCGCGA 60.515 55.556 12.10 0.00 0.00 5.87
1242 1315 0.104304 CGGGAAGGAGAATACCACCG 59.896 60.000 0.00 0.00 37.52 4.94
1244 1317 1.138464 GGACGGGAAGGAGAATACCAC 59.862 57.143 0.00 0.00 0.00 4.16
1245 1318 1.492764 GGACGGGAAGGAGAATACCA 58.507 55.000 0.00 0.00 0.00 3.25
1246 1319 0.757512 GGGACGGGAAGGAGAATACC 59.242 60.000 0.00 0.00 0.00 2.73
1261 1338 3.853597 AAACACTCGCCGACGGGAC 62.854 63.158 17.22 0.00 44.96 4.46
1271 1348 1.593196 TTTCTCCCAGCAAACACTCG 58.407 50.000 0.00 0.00 0.00 4.18
1281 1358 2.289631 GCCCCAACAAATTTTCTCCCAG 60.290 50.000 0.00 0.00 0.00 4.45
1289 1366 0.697658 CCCATGGCCCCAACAAATTT 59.302 50.000 6.09 0.00 0.00 1.82
1397 1474 5.249393 AGAGAAGAATCCCAAGCAAGAGTTA 59.751 40.000 0.00 0.00 0.00 2.24
1398 1475 4.042684 AGAGAAGAATCCCAAGCAAGAGTT 59.957 41.667 0.00 0.00 0.00 3.01
1399 1476 3.586618 AGAGAAGAATCCCAAGCAAGAGT 59.413 43.478 0.00 0.00 0.00 3.24
1438 1520 2.857186 TCCAGCACAAGAACTGCATA 57.143 45.000 0.00 0.00 37.08 3.14
1439 1521 2.211250 ATCCAGCACAAGAACTGCAT 57.789 45.000 0.00 0.00 37.08 3.96
1440 1522 1.985473 AATCCAGCACAAGAACTGCA 58.015 45.000 0.00 0.00 37.08 4.41
1441 1523 2.352127 GGAAATCCAGCACAAGAACTGC 60.352 50.000 0.00 0.00 35.64 4.40
1442 1524 3.152341 AGGAAATCCAGCACAAGAACTG 58.848 45.455 1.67 0.00 38.89 3.16
1482 1565 1.970114 CCCACAGCAGGCTCACAAG 60.970 63.158 0.00 0.00 0.00 3.16
1483 1566 2.113774 CCCACAGCAGGCTCACAA 59.886 61.111 0.00 0.00 0.00 3.33
1491 1574 1.833630 TCCTGATTAGACCCACAGCAG 59.166 52.381 0.00 0.00 0.00 4.24
1504 1587 3.766051 GAGGAAACAGCCAAATCCTGATT 59.234 43.478 3.67 0.00 42.28 2.57
1528 1611 7.277098 GCTGACTGTTTGCAATTAATTCATCAT 59.723 33.333 0.00 0.00 0.00 2.45
1529 1612 6.587226 GCTGACTGTTTGCAATTAATTCATCA 59.413 34.615 0.00 0.00 0.00 3.07
1530 1613 6.810182 AGCTGACTGTTTGCAATTAATTCATC 59.190 34.615 0.00 0.00 0.00 2.92
1562 1646 4.639135 AGATTCTGCCGCCTAAAAATTC 57.361 40.909 0.00 0.00 0.00 2.17
1563 1647 4.462483 TCAAGATTCTGCCGCCTAAAAATT 59.538 37.500 0.00 0.00 0.00 1.82
1564 1648 4.016444 TCAAGATTCTGCCGCCTAAAAAT 58.984 39.130 0.00 0.00 0.00 1.82
1574 1671 3.598019 TGCCAATTTCAAGATTCTGCC 57.402 42.857 0.00 0.00 0.00 4.85
1605 1702 1.317613 AATTGCTGGCGTGAAGTGAA 58.682 45.000 0.00 0.00 0.00 3.18
1606 1703 1.317613 AAATTGCTGGCGTGAAGTGA 58.682 45.000 0.00 0.00 0.00 3.41
1607 1704 2.987413 TAAATTGCTGGCGTGAAGTG 57.013 45.000 0.00 0.00 0.00 3.16
1608 1705 3.836949 CAATAAATTGCTGGCGTGAAGT 58.163 40.909 0.00 0.00 0.00 3.01
1646 1748 6.126565 TGGACAGGCTATCAGAACTAGTACTA 60.127 42.308 1.89 1.89 0.00 1.82
1647 1749 5.134661 GGACAGGCTATCAGAACTAGTACT 58.865 45.833 0.00 0.00 0.00 2.73
1657 1759 3.109044 CATGAGTGGACAGGCTATCAG 57.891 52.381 0.00 0.00 0.00 2.90
1717 1819 7.288810 TGGCAAGTAAGAAATGAAAAGATGT 57.711 32.000 0.00 0.00 0.00 3.06
1815 1929 6.417635 ACACAATCGCAAAGACAATAGTTTTG 59.582 34.615 0.00 0.00 35.47 2.44
2167 2296 1.303309 CGGTCTGGATCTTGATTGCC 58.697 55.000 0.00 0.00 0.00 4.52
2216 2345 7.198390 GCATGAAATTGCTAATTCAAGAGCTA 58.802 34.615 2.79 0.00 39.54 3.32
2346 2475 6.760298 TCAGAAAATAAAACACTGCATGCAAA 59.240 30.769 22.88 0.00 0.00 3.68
2449 2578 0.179156 GCATGTTCAGGCATGTTCGG 60.179 55.000 0.00 0.00 45.75 4.30
2477 2606 3.959991 GAGGAAGGCCACCGCAGAC 62.960 68.421 5.01 0.00 36.38 3.51
2478 2607 3.706373 GAGGAAGGCCACCGCAGA 61.706 66.667 5.01 0.00 36.38 4.26
2482 2611 0.537371 AGTTTTGAGGAAGGCCACCG 60.537 55.000 5.01 0.00 36.29 4.94
2610 2740 6.162079 TGCAAAATTTGTGAACAGAACAGAA 58.838 32.000 7.60 0.00 0.00 3.02
2700 2830 4.515567 AGAGAGGATTGGTTTGTCGAAAAC 59.484 41.667 12.10 12.10 0.00 2.43
2745 2875 8.557450 ACATTAGTGAGTTAAATCATAAGGGGT 58.443 33.333 9.08 1.74 0.00 4.95
2790 2920 3.806949 TTTGTAGGCCCTCTTCAACAT 57.193 42.857 0.00 0.00 33.46 2.71
2813 2943 5.236047 GTGCATGGATTAGTCTGTGAAGATC 59.764 44.000 0.00 0.00 0.00 2.75
2815 2945 4.020307 TGTGCATGGATTAGTCTGTGAAGA 60.020 41.667 0.00 0.00 0.00 2.87
2816 2946 4.256110 TGTGCATGGATTAGTCTGTGAAG 58.744 43.478 0.00 0.00 0.00 3.02
2817 2947 4.284829 TGTGCATGGATTAGTCTGTGAA 57.715 40.909 0.00 0.00 0.00 3.18
2825 2965 4.449131 ACTGACAGATGTGCATGGATTAG 58.551 43.478 10.08 0.00 0.00 1.73
2951 3091 6.039270 TGGAATGGAACTACAAAGTCAAGTTG 59.961 38.462 0.00 0.00 33.75 3.16
3084 3224 8.735692 TGCATTATTACAATGATGACTCTCAA 57.264 30.769 10.05 0.00 35.17 3.02
3091 3231 6.239092 CCTTGCCTGCATTATTACAATGATGA 60.239 38.462 10.05 0.00 35.17 2.92
3092 3232 5.924254 CCTTGCCTGCATTATTACAATGATG 59.076 40.000 1.26 3.09 35.99 3.07
3093 3233 5.834742 TCCTTGCCTGCATTATTACAATGAT 59.165 36.000 1.26 0.00 0.00 2.45
3194 3334 2.776312 GCATACAGCGCAGAGTACTA 57.224 50.000 11.47 0.00 0.00 1.82
3465 3605 2.030893 TGGAGCAAAACAGAAAGCGATG 60.031 45.455 0.00 0.00 0.00 3.84
3476 3616 2.030805 ACTGCGAGATTTGGAGCAAAAC 60.031 45.455 0.00 0.00 39.26 2.43
3617 3758 1.307097 CAGCCTCTTGCCTGCTTATC 58.693 55.000 0.00 0.00 42.71 1.75
3700 3841 7.250569 TGAAACGAAGATTGGCATCTATTTTC 58.749 34.615 0.00 4.93 39.00 2.29
3960 4103 4.579869 GGTTGAAGGCTTTAGTGATCTCA 58.420 43.478 0.00 0.00 0.00 3.27
4014 4157 0.250338 GGGTCAGCTTTGGAGTCGTT 60.250 55.000 0.00 0.00 0.00 3.85
4041 4184 0.030909 TACAAGGGGATAGCCGGGAA 60.031 55.000 2.18 0.00 33.83 3.97
4058 4201 3.414486 ACTTTGGCAGTGGGTGTAC 57.586 52.632 0.00 0.00 32.83 2.90
4238 4381 1.278985 CCATGTAGCTTGGGACTGACA 59.721 52.381 0.00 0.00 0.00 3.58
4239 4382 2.014068 GCCATGTAGCTTGGGACTGAC 61.014 57.143 5.09 0.00 34.66 3.51
4522 4665 1.623542 ATAGTCCCGTCCCCACTTGC 61.624 60.000 0.00 0.00 0.00 4.01
4530 4673 2.301870 TGCATAATCCATAGTCCCGTCC 59.698 50.000 0.00 0.00 0.00 4.79
4681 4829 3.808726 GCAAGCAACAAATGAAATGGACA 59.191 39.130 0.00 0.00 0.00 4.02
4699 4847 5.410067 CCCATATGGTTTTACACAAGCAAG 58.590 41.667 20.46 0.00 37.68 4.01
4700 4848 4.221703 CCCCATATGGTTTTACACAAGCAA 59.778 41.667 20.46 0.00 37.68 3.91
4701 4849 3.766591 CCCCATATGGTTTTACACAAGCA 59.233 43.478 20.46 0.00 38.48 3.91
4702 4850 3.767131 ACCCCATATGGTTTTACACAAGC 59.233 43.478 20.46 0.00 33.91 4.01
4783 4931 2.827921 GACAAGTTCATTGGGAAGGCAT 59.172 45.455 0.00 0.00 43.68 4.40
4785 4933 2.238521 TGACAAGTTCATTGGGAAGGC 58.761 47.619 0.00 0.00 43.68 4.35
4787 4935 5.009911 TCACATTGACAAGTTCATTGGGAAG 59.990 40.000 0.00 0.00 42.46 3.46
4804 4967 3.181503 GGCAGAGTGCTACATTCACATTG 60.182 47.826 0.00 0.00 44.28 2.82
4810 4973 0.253044 TGGGGCAGAGTGCTACATTC 59.747 55.000 0.00 0.00 44.28 2.67
4872 5043 4.345854 ACCCAGTGAACAAAACCACTAAA 58.654 39.130 0.00 0.00 41.26 1.85
4913 5086 0.467804 GCCACCACCAACCATTGTTT 59.532 50.000 0.00 0.00 30.42 2.83
4942 5115 4.120331 GCCGACAGCAACCATGGC 62.120 66.667 13.04 0.00 42.97 4.40
4952 5125 1.522355 CAGCTACCATGGCCGACAG 60.522 63.158 13.04 2.59 0.00 3.51
4968 5141 4.824537 TGATTAGAGGTAGCAGCTAGTCAG 59.175 45.833 1.02 0.00 30.56 3.51
4969 5142 4.793201 TGATTAGAGGTAGCAGCTAGTCA 58.207 43.478 1.02 12.64 31.26 3.41
4970 5143 5.242838 ACATGATTAGAGGTAGCAGCTAGTC 59.757 44.000 1.02 2.94 0.00 2.59
4971 5144 5.144100 ACATGATTAGAGGTAGCAGCTAGT 58.856 41.667 1.02 0.00 0.00 2.57
4972 5145 5.720371 ACATGATTAGAGGTAGCAGCTAG 57.280 43.478 1.02 0.00 0.00 3.42
4973 5146 5.740224 GCAACATGATTAGAGGTAGCAGCTA 60.740 44.000 0.00 0.00 0.00 3.32
4974 5147 4.701765 CAACATGATTAGAGGTAGCAGCT 58.298 43.478 0.00 0.00 0.00 4.24
4975 5148 3.249559 GCAACATGATTAGAGGTAGCAGC 59.750 47.826 0.00 0.00 0.00 5.25
4976 5149 3.812053 GGCAACATGATTAGAGGTAGCAG 59.188 47.826 0.00 0.00 0.00 4.24
4977 5150 3.455910 AGGCAACATGATTAGAGGTAGCA 59.544 43.478 0.00 0.00 41.41 3.49
5053 5227 4.737352 GCACTTCCAATTGCACTCTTGAAA 60.737 41.667 0.00 0.00 38.68 2.69
5059 5349 0.109597 CGGCACTTCCAATTGCACTC 60.110 55.000 0.00 0.00 40.75 3.51
5066 5356 2.496899 ATGTCTTCGGCACTTCCAAT 57.503 45.000 0.00 0.00 34.01 3.16
5076 5366 4.946478 AGATAAGGGAGAATGTCTTCGG 57.054 45.455 0.00 0.00 36.45 4.30
5125 5463 7.646548 TTCCACATAGATAAGGGAGATATCG 57.353 40.000 0.00 0.00 35.40 2.92
5173 5524 1.327303 GTGCAGGTCCCAATGAACAA 58.673 50.000 0.00 0.00 30.86 2.83
5185 5536 6.538381 CCTTTTCATTTTACTTTTGTGCAGGT 59.462 34.615 0.00 0.00 0.00 4.00
5260 5613 2.971660 TCGTTCTGACACCAGTTTCA 57.028 45.000 0.00 0.00 41.16 2.69
5388 5914 6.416415 TGGTGTTAGTTGTTTAAGAAGTGGA 58.584 36.000 0.00 0.00 0.00 4.02
5389 5915 6.317893 ACTGGTGTTAGTTGTTTAAGAAGTGG 59.682 38.462 0.00 0.00 0.00 4.00
5390 5916 7.316544 ACTGGTGTTAGTTGTTTAAGAAGTG 57.683 36.000 0.00 0.00 0.00 3.16
5391 5917 7.933215 AACTGGTGTTAGTTGTTTAAGAAGT 57.067 32.000 0.00 0.00 39.33 3.01
5394 5920 9.669887 TCTAAAACTGGTGTTAGTTGTTTAAGA 57.330 29.630 9.63 0.00 40.58 2.10
5410 5938 6.535508 GGCTGTTACTGTCTATCTAAAACTGG 59.464 42.308 0.00 0.00 0.00 4.00
5412 5940 7.241042 TGGCTGTTACTGTCTATCTAAAACT 57.759 36.000 0.00 0.00 0.00 2.66
5438 5966 1.608055 TGGAACTGTGCTTGGATGTG 58.392 50.000 0.00 0.00 0.00 3.21
5482 6010 0.608856 TGTGCTTCGGCCATGAATGT 60.609 50.000 2.24 0.00 40.91 2.71
5578 6119 2.289506 GGTAGGAGTTGAGACACCCAAC 60.290 54.545 0.00 0.00 42.97 3.77
5580 6121 1.132977 TGGTAGGAGTTGAGACACCCA 60.133 52.381 0.00 0.00 37.24 4.51
5597 6138 4.759782 CTTCTGAACATAGACGGAATGGT 58.240 43.478 0.00 0.00 32.18 3.55
5678 6226 0.244994 TCTCCTGAAGACTGAAGCGC 59.755 55.000 0.00 0.00 0.00 5.92
5720 6270 3.502572 GCCGATCAACCAGAAGGC 58.497 61.111 0.00 0.00 43.53 4.35
5742 6292 2.550830 ACAATCCGTTCTCTGCAAGT 57.449 45.000 0.00 0.00 33.76 3.16
5754 6304 9.413048 GAGAGAAGGTATATTTTCTACAATCCG 57.587 37.037 2.70 0.00 33.97 4.18


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

AutoCloner maintained by Alex Coulton.