Multiple sequence alignment - TraesCS3B01G548800

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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 TraesCS3B01G548800 chr3B 100.000 3243 0 0 2587 5829 784434074 784430832 0.000000e+00 5989.0
1 TraesCS3B01G548800 chr3B 100.000 2148 0 0 1 2148 784436660 784434513 0.000000e+00 3967.0
2 TraesCS3B01G548800 chr3B 100.000 194 0 0 6112 6305 784430549 784430356 6.010000e-95 359.0
3 TraesCS3B01G548800 chr3D 89.840 3258 271 40 2587 5828 587381246 587378033 0.000000e+00 4128.0
4 TraesCS3B01G548800 chr3D 84.476 2873 360 46 2927 5783 603426790 603429592 0.000000e+00 2756.0
5 TraesCS3B01G548800 chr3D 91.161 1154 76 12 1 1146 587383326 587382191 0.000000e+00 1543.0
6 TraesCS3B01G548800 chr3D 92.258 930 52 9 1222 2148 587382198 587381286 0.000000e+00 1301.0
7 TraesCS3B01G548800 chr3D 81.787 862 116 26 318 1153 603424498 603425344 0.000000e+00 684.0
8 TraesCS3B01G548800 chr3D 81.699 612 79 18 1487 2088 603425810 603426398 4.420000e-131 479.0
9 TraesCS3B01G548800 chr3D 74.902 769 153 36 4613 5361 585982695 585983443 1.320000e-81 315.0
10 TraesCS3B01G548800 chr3D 89.100 211 20 3 1186 1395 603425587 603425795 6.270000e-65 259.0
11 TraesCS3B01G548800 chr3D 85.340 191 27 1 6115 6305 587378001 587377812 4.990000e-46 196.0
12 TraesCS3B01G548800 chr3D 81.356 118 21 1 6124 6241 358840383 358840499 1.870000e-15 95.3
13 TraesCS3B01G548800 chr3A 83.896 2813 354 49 2987 5783 732641217 732638488 0.000000e+00 2593.0
14 TraesCS3B01G548800 chr3A 82.699 1104 142 35 318 1395 732644904 732643824 0.000000e+00 935.0
15 TraesCS3B01G548800 chr3A 81.549 607 79 18 1487 2083 732643809 732643226 2.660000e-128 470.0
16 TraesCS3B01G548800 chr6B 79.231 390 73 8 4949 5335 664822256 664821872 1.350000e-66 265.0
17 TraesCS3B01G548800 chr7D 81.746 126 22 1 6115 6240 600895696 600895820 3.110000e-18 104.0
18 TraesCS3B01G548800 chr7D 82.051 117 20 1 6122 6238 54941409 54941294 1.450000e-16 99.0
19 TraesCS3B01G548800 chrUn 81.356 118 21 1 6124 6241 229153877 229153993 1.870000e-15 95.3
20 TraesCS3B01G548800 chr7A 79.070 129 26 1 6112 6240 692891673 692891800 3.130000e-13 87.9
21 TraesCS3B01G548800 chr7A 80.342 117 19 4 6124 6240 13795500 13795388 1.130000e-12 86.1
22 TraesCS3B01G548800 chr4A 80.342 117 22 1 6124 6240 682002097 682001982 3.130000e-13 87.9
23 TraesCS3B01G548800 chr1B 80.180 111 21 1 6125 6235 176472525 176472634 1.460000e-11 82.4
24 TraesCS3B01G548800 chr2B 93.750 48 3 0 3244 3291 379951711 379951664 8.770000e-09 73.1


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 TraesCS3B01G548800 chr3B 784430356 784436660 6304 True 3438.333333 5989 100.000000 1 6305 3 chr3B.!!$R1 6304
1 TraesCS3B01G548800 chr3D 587377812 587383326 5514 True 1792.000000 4128 89.649750 1 6305 4 chr3D.!!$R1 6304
2 TraesCS3B01G548800 chr3D 603424498 603429592 5094 False 1044.500000 2756 84.265500 318 5783 4 chr3D.!!$F3 5465
3 TraesCS3B01G548800 chr3D 585982695 585983443 748 False 315.000000 315 74.902000 4613 5361 1 chr3D.!!$F2 748
4 TraesCS3B01G548800 chr3A 732638488 732644904 6416 True 1332.666667 2593 82.714667 318 5783 3 chr3A.!!$R1 5465

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
635 674 0.032403 CTACCGTCCAAACACGACCA 59.968 55.000 0.0 0.0 42.69 4.02 F
636 675 0.032403 TACCGTCCAAACACGACCAG 59.968 55.000 0.0 0.0 42.69 4.00 F
641 680 1.010125 CCAAACACGACCAGTTGCG 60.010 57.895 0.0 0.0 0.00 4.85 F
2665 2951 0.544697 GGCCCGAGGAGTTGGATTTA 59.455 55.000 0.0 0.0 0.00 1.40 F
2891 3178 0.032515 TCAGTCATTCCCCTCCGCTA 60.033 55.000 0.0 0.0 0.00 4.26 F
3703 5557 0.178068 GATGGCTCTCTAAACCGGCA 59.822 55.000 0.0 0.0 36.36 5.69 F
3709 5563 1.152963 CTCTAAACCGGCATGGGGG 60.153 63.158 0.0 0.0 44.64 5.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1847 2109 0.447801 CTTGCTCGGTAATGTGTGCC 59.552 55.000 0.00 0.0 0.00 5.01 R
2609 2895 0.882042 AGCGCGGATCCATCATTGTC 60.882 55.000 13.41 0.0 0.00 3.18 R
2680 2966 2.169769 CGGGGCCGGTATACAATGATAT 59.830 50.000 1.90 0.0 35.56 1.63 R
3703 5557 0.398381 AACATATTTGCGGCCCCCAT 60.398 50.000 0.00 0.0 0.00 4.00 R
4077 5934 1.204941 CTACACCTTCTTCCTGACCCG 59.795 57.143 0.00 0.0 0.00 5.28 R
5036 6904 1.550072 CAAAACCGCCCCAGAATGAAT 59.450 47.619 0.00 0.0 39.69 2.57 R
5576 7445 1.890489 GAACTTTGTACCCGCCCAAAT 59.110 47.619 0.00 0.0 30.76 2.32 R

All possible primers

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

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
32 33 8.808529 CGTTACGATCAAGAATGTTTAATCTCT 58.191 33.333 0.00 0.00 0.00 3.10
33 34 9.907576 GTTACGATCAAGAATGTTTAATCTCTG 57.092 33.333 0.00 0.00 0.00 3.35
88 89 0.038892 CATGCAAGTGTCCAGTTGGC 60.039 55.000 14.81 8.82 40.99 4.52
89 90 1.181098 ATGCAAGTGTCCAGTTGGCC 61.181 55.000 14.81 0.00 40.99 5.36
112 113 5.278660 CCTGAAAAAGGTCAATGGAGACAAG 60.279 44.000 0.00 0.00 42.64 3.16
156 157 4.072131 GAGAAGTGGCAAACTACCAATGA 58.928 43.478 0.00 0.00 38.56 2.57
158 159 3.508845 AGTGGCAAACTACCAATGACT 57.491 42.857 0.00 0.00 39.39 3.41
164 165 6.428771 GTGGCAAACTACCAATGACTAAGTTA 59.571 38.462 0.00 0.00 39.39 2.24
200 201 2.537633 ACCCGGATAACTCCAGTACA 57.462 50.000 0.73 0.00 42.19 2.90
201 202 2.823959 ACCCGGATAACTCCAGTACAA 58.176 47.619 0.73 0.00 42.19 2.41
247 251 1.068748 GGATGATGCCGTGATGAATGC 60.069 52.381 0.00 0.00 0.00 3.56
258 262 3.842428 CGTGATGAATGCAACGAAGAAAG 59.158 43.478 0.06 0.00 0.00 2.62
369 375 4.225208 GCTAACTCCGTATCGACCATTAC 58.775 47.826 0.00 0.00 0.00 1.89
437 445 9.214953 TGCGCAAAGTTGTTAATTTTTATTTTG 57.785 25.926 8.16 0.00 0.00 2.44
468 476 6.014669 TGCTCTGCAACCTTTTTATTACCATT 60.015 34.615 0.00 0.00 34.76 3.16
477 485 8.148807 ACCTTTTTATTACCATTGTTGTTTGC 57.851 30.769 0.00 0.00 0.00 3.68
484 492 4.255833 ACCATTGTTGTTTGCTACATGG 57.744 40.909 0.00 7.78 36.44 3.66
493 525 8.065473 TGTTGTTTGCTACATGGATATGAATT 57.935 30.769 0.00 0.00 36.44 2.17
498 530 7.894753 TTGCTACATGGATATGAATTTCCAA 57.105 32.000 6.57 0.00 44.83 3.53
508 540 7.720957 TGGATATGAATTTCCAAGTGTATCCTG 59.279 37.037 0.00 0.00 39.05 3.86
587 626 1.697394 ATGGGTGGCCAGGCTCATA 60.697 57.895 5.11 0.00 0.00 2.15
631 670 0.038526 AGCTCTACCGTCCAAACACG 60.039 55.000 0.00 0.00 39.61 4.49
632 671 0.038892 GCTCTACCGTCCAAACACGA 60.039 55.000 0.00 0.00 42.69 4.35
635 674 0.032403 CTACCGTCCAAACACGACCA 59.968 55.000 0.00 0.00 42.69 4.02
636 675 0.032403 TACCGTCCAAACACGACCAG 59.968 55.000 0.00 0.00 42.69 4.00
641 680 1.010125 CCAAACACGACCAGTTGCG 60.010 57.895 0.00 0.00 0.00 4.85
656 695 2.435805 AGTTGCGATCCCTATGTGATGT 59.564 45.455 0.00 0.00 0.00 3.06
676 715 8.616076 GTGATGTGTGATTAGATAAAAGGAAGG 58.384 37.037 0.00 0.00 0.00 3.46
678 717 7.265599 TGTGTGATTAGATAAAAGGAAGGGA 57.734 36.000 0.00 0.00 0.00 4.20
696 735 1.189752 GATGAGTGGGTGAGAGAGCA 58.810 55.000 0.00 0.00 0.00 4.26
701 740 2.235898 GAGTGGGTGAGAGAGCAAGAAT 59.764 50.000 0.00 0.00 0.00 2.40
910 954 5.916883 CGATCTTTGGGACATTAATTGCATC 59.083 40.000 0.00 0.00 39.30 3.91
941 985 8.976353 ACAACCATTAAACTATTGATATGCCAA 58.024 29.630 0.00 0.00 0.00 4.52
989 1033 7.701539 TGCAGTATGAAAGTTAACCATTCAT 57.298 32.000 27.07 27.07 43.91 2.57
1011 1055 7.563906 TCATGGTTTCCAAAATGAAAGAAAGT 58.436 30.769 0.00 0.00 36.95 2.66
1043 1087 2.360801 GAGCGCTCCTTCTACTCTCATT 59.639 50.000 27.22 0.00 0.00 2.57
1055 1099 7.491048 CCTTCTACTCTCATTTCTTGTTCTAGC 59.509 40.741 0.00 0.00 0.00 3.42
1074 1118 4.592485 AGCAACCAGAGGAATAGATACG 57.408 45.455 0.00 0.00 0.00 3.06
1084 1128 7.309177 CAGAGGAATAGATACGACTACAATGG 58.691 42.308 0.00 0.00 0.00 3.16
1133 1178 7.763985 CCTTGCCCATCGAAAAGTTAATAAAAT 59.236 33.333 0.00 0.00 0.00 1.82
1134 1179 9.150348 CTTGCCCATCGAAAAGTTAATAAAATT 57.850 29.630 0.00 0.00 0.00 1.82
1265 1520 4.443913 TTGCATTGATGTGAATGTCCAG 57.556 40.909 0.00 0.00 35.98 3.86
1370 1626 2.222819 GCTCAAATGGACGTCGATTCAC 60.223 50.000 23.51 11.29 0.00 3.18
1437 1693 8.984891 TGAATGTTAGTTAGCCATCAAATTTG 57.015 30.769 12.15 12.15 0.00 2.32
1438 1694 8.801299 TGAATGTTAGTTAGCCATCAAATTTGA 58.199 29.630 22.52 22.52 42.14 2.69
1460 1716 9.896645 TTTGAGGGAATAGATCATCTATTATGC 57.103 33.333 18.30 7.73 46.46 3.14
1464 1720 9.593565 AGGGAATAGATCATCTATTATGCGATA 57.406 33.333 18.30 0.00 46.46 2.92
1528 1784 9.807921 TTGTTCTACTCCCTTTAGATTCAAATT 57.192 29.630 0.00 0.00 0.00 1.82
1571 1832 6.870971 ATACGTGTACAAACAATGGAAGTT 57.129 33.333 0.00 0.00 37.36 2.66
1577 1838 2.698274 ACAAACAATGGAAGTTGGGGTC 59.302 45.455 0.00 0.00 33.40 4.46
1580 1841 3.258722 ACAATGGAAGTTGGGGTCAAT 57.741 42.857 0.00 0.00 35.10 2.57
1585 1846 6.100424 ACAATGGAAGTTGGGGTCAATTAAAA 59.900 34.615 0.00 0.00 35.10 1.52
1727 1989 5.163088 ACAGATGGAACCAAGTTCTTTACCT 60.163 40.000 7.36 0.00 41.70 3.08
1784 2046 4.211389 GTGTTTTACAAGCACATCTGTCG 58.789 43.478 0.00 0.00 33.70 4.35
1787 2049 5.107104 TGTTTTACAAGCACATCTGTCGATC 60.107 40.000 0.00 0.00 0.00 3.69
1801 2063 2.657484 TCGATCGTCGAATGCCCGAC 62.657 60.000 15.94 11.72 46.90 4.79
1847 2109 3.914426 AATAGAAGGGGCCATATAGCG 57.086 47.619 4.39 0.00 0.00 4.26
1905 2167 7.732025 TGAACAACTAGAGGTGAGTTTTCATA 58.268 34.615 0.53 0.00 34.90 2.15
1961 2226 5.086104 AGTAATTGAGCGACTAACACCAT 57.914 39.130 0.00 0.00 0.00 3.55
2665 2951 0.544697 GGCCCGAGGAGTTGGATTTA 59.455 55.000 0.00 0.00 0.00 1.40
2667 2953 2.495084 GCCCGAGGAGTTGGATTTATC 58.505 52.381 0.00 0.00 0.00 1.75
2672 2958 4.383118 CCGAGGAGTTGGATTTATCACTGT 60.383 45.833 0.00 0.00 0.00 3.55
2674 2960 6.338146 CGAGGAGTTGGATTTATCACTGTTA 58.662 40.000 0.00 0.00 0.00 2.41
2677 2963 6.215636 AGGAGTTGGATTTATCACTGTTACCT 59.784 38.462 0.00 0.00 0.00 3.08
2678 2964 7.402071 AGGAGTTGGATTTATCACTGTTACCTA 59.598 37.037 0.00 0.00 0.00 3.08
2679 2965 8.211629 GGAGTTGGATTTATCACTGTTACCTAT 58.788 37.037 0.00 0.00 0.00 2.57
2704 2990 1.049855 ATTGTATACCGGCCCCGTGA 61.050 55.000 0.00 0.00 37.81 4.35
2715 3001 1.301623 CCCCGTGATTTAGCCCACA 59.698 57.895 0.00 0.00 33.13 4.17
2738 3024 1.152819 CAGCATAGCCCAGGCACAT 60.153 57.895 12.03 0.46 44.88 3.21
2752 3038 3.873952 CAGGCACATAAAGACTCTAAGCC 59.126 47.826 0.00 0.00 39.82 4.35
2775 3061 5.449553 CAGCTACCTAAATCCCTTCCAATT 58.550 41.667 0.00 0.00 0.00 2.32
2796 3082 3.505386 TGGCAATTATGTCCCAAACTGT 58.495 40.909 0.00 0.00 0.00 3.55
2801 3087 5.359576 GCAATTATGTCCCAAACTGTATCCA 59.640 40.000 0.00 0.00 0.00 3.41
2803 3089 7.483307 CAATTATGTCCCAAACTGTATCCAAG 58.517 38.462 0.00 0.00 0.00 3.61
2855 3142 1.490910 GCTTTCCCAGCTACCCACTAT 59.509 52.381 0.00 0.00 46.27 2.12
2857 3144 1.410004 TTCCCAGCTACCCACTATCG 58.590 55.000 0.00 0.00 0.00 2.92
2891 3178 0.032515 TCAGTCATTCCCCTCCGCTA 60.033 55.000 0.00 0.00 0.00 4.26
2900 3187 2.518825 CCTCCGCTACTACGCCCT 60.519 66.667 0.00 0.00 0.00 5.19
2903 3190 4.587189 CCGCTACTACGCCCTGGC 62.587 72.222 0.00 0.00 37.85 4.85
2915 3202 4.785453 CCTGGCGGCTCCACCTTC 62.785 72.222 11.43 0.00 40.72 3.46
2916 3203 4.020617 CTGGCGGCTCCACCTTCA 62.021 66.667 11.43 0.00 40.72 3.02
2918 3205 4.021925 GGCGGCTCCACCTTCACT 62.022 66.667 0.00 0.00 35.61 3.41
2919 3206 2.743928 GCGGCTCCACCTTCACTG 60.744 66.667 0.00 0.00 35.61 3.66
2920 3207 2.046892 CGGCTCCACCTTCACTGG 60.047 66.667 0.00 0.00 35.61 4.00
2921 3208 2.883828 CGGCTCCACCTTCACTGGT 61.884 63.158 0.00 0.00 41.77 4.00
2931 3223 2.233271 CCTTCACTGGTGTCTGCAAAT 58.767 47.619 0.53 0.00 0.00 2.32
2938 3230 0.445436 GGTGTCTGCAAATCAGCTCG 59.555 55.000 0.00 0.00 42.56 5.03
2944 3236 1.802960 CTGCAAATCAGCTCGAGTGTT 59.197 47.619 15.13 3.79 35.78 3.32
2958 3250 2.416296 CGAGTGTTACATCCCGCACTAA 60.416 50.000 0.00 0.00 41.59 2.24
2959 3251 2.928116 GAGTGTTACATCCCGCACTAAC 59.072 50.000 0.00 0.00 41.59 2.34
2963 3256 1.405872 TACATCCCGCACTAACCGAT 58.594 50.000 0.00 0.00 0.00 4.18
2973 4816 0.253044 ACTAACCGATGTGCTGCCAT 59.747 50.000 0.00 0.00 0.00 4.40
3013 4859 4.846779 TTCCAGCATTAGGTTGTTGTTC 57.153 40.909 0.00 0.00 0.00 3.18
3036 4882 7.913674 TCTTTGTATACACAATGTGCATGTA 57.086 32.000 14.01 0.00 44.01 2.29
3051 4898 9.955208 AATGTGCATGTATACATTTTGTGATAG 57.045 29.630 15.85 2.98 43.00 2.08
3072 4919 8.999895 TGATAGTTTTAGGAAGTTATTAGGGCT 58.000 33.333 0.00 0.00 0.00 5.19
3127 4974 5.875359 CAGAGTTTACTTTAATTCCGGCTCT 59.125 40.000 0.00 0.00 0.00 4.09
3151 4998 2.726912 GCGCATGCACACACACAC 60.727 61.111 19.57 0.00 42.15 3.82
3152 4999 2.714387 CGCATGCACACACACACA 59.286 55.556 19.57 0.00 0.00 3.72
3153 5000 1.655046 CGCATGCACACACACACAC 60.655 57.895 19.57 0.00 0.00 3.82
3222 5069 8.206325 AGTAGTTAGCATTGAATTCATCACAG 57.794 34.615 9.40 0.00 37.92 3.66
3227 5074 5.950883 AGCATTGAATTCATCACAGAGTTG 58.049 37.500 9.40 0.00 37.92 3.16
3323 5171 6.660722 TGTGGAACATCGTACAAAATAACAC 58.339 36.000 0.00 0.00 45.67 3.32
3335 5185 5.510671 ACAAAATAACACTCAGCAAAGTCG 58.489 37.500 0.00 0.00 0.00 4.18
3338 5188 1.166531 AACACTCAGCAAAGTCGCCC 61.167 55.000 0.00 0.00 0.00 6.13
3351 5201 0.390860 GTCGCCCTATGCATCACTCT 59.609 55.000 0.19 0.00 41.33 3.24
3355 5205 3.062763 CGCCCTATGCATCACTCTAAAG 58.937 50.000 0.19 0.00 41.33 1.85
3361 5211 3.423539 TGCATCACTCTAAAGCCAACT 57.576 42.857 0.00 0.00 0.00 3.16
3384 5235 1.284785 TGCGAGGGAGGGAAATTTCAT 59.715 47.619 19.49 7.63 0.00 2.57
3387 5238 3.891049 CGAGGGAGGGAAATTTCATCTT 58.109 45.455 19.49 9.34 0.00 2.40
3403 5254 6.773976 TTCATCTTCTTCTTCCTCTCTCTC 57.226 41.667 0.00 0.00 0.00 3.20
3413 5264 2.408565 TCCTCTCTCTCCCTCTCTCTC 58.591 57.143 0.00 0.00 0.00 3.20
3438 5289 3.441572 CCTCTCTTTTGTGCCCATACAAG 59.558 47.826 0.00 0.00 41.18 3.16
3441 5292 5.815581 TCTCTTTTGTGCCCATACAAGTAT 58.184 37.500 0.00 0.00 41.18 2.12
3472 5323 0.679960 GCCCCATTAGGAAACGTGCT 60.680 55.000 0.00 0.00 38.24 4.40
3479 5330 5.740809 CCATTAGGAAACGTGCTCCTTAGC 61.741 50.000 21.15 0.00 40.61 3.09
3529 5382 5.499139 GTCTTTGTGACTCATTTTCCACA 57.501 39.130 0.00 0.00 42.21 4.17
3641 5495 1.243902 GGAGACACATTTTTGGCGGA 58.756 50.000 0.00 0.00 0.00 5.54
3653 5507 2.081425 TTGGCGGATGTGTGTTTGCC 62.081 55.000 0.00 0.00 42.76 4.52
3660 5514 1.747325 ATGTGTGTTTGCCCACAGCC 61.747 55.000 1.64 0.00 45.45 4.85
3663 5517 0.975040 TGTGTTTGCCCACAGCCTTT 60.975 50.000 0.00 0.00 40.30 3.11
3703 5557 0.178068 GATGGCTCTCTAAACCGGCA 59.822 55.000 0.00 0.00 36.36 5.69
3709 5563 1.152963 CTCTAAACCGGCATGGGGG 60.153 63.158 0.00 0.00 44.64 5.40
3732 5586 4.972440 GCCGCAAATATGTTGAATCTTCTC 59.028 41.667 2.91 0.00 0.00 2.87
3752 5606 4.517832 TCTCGAGTTGCTCTAAGTTGTGTA 59.482 41.667 13.13 0.00 0.00 2.90
3796 5650 8.780846 TGTGTAGTAATTCCATATTTTCACGT 57.219 30.769 0.00 0.00 0.00 4.49
3856 5710 5.470047 TTGGTCTCTCTAACTCCAAGTTC 57.530 43.478 0.00 0.00 39.51 3.01
3900 5754 9.725019 TCATTGATGTTATATGGTATTGGACTC 57.275 33.333 0.00 0.00 0.00 3.36
3936 5790 8.387813 TGGTTAATATAGTTATCCCATTGACCC 58.612 37.037 0.00 0.00 35.49 4.46
4077 5934 7.773690 AGGTGTACTAATTGATAATGGACCAAC 59.226 37.037 0.00 0.00 0.00 3.77
4157 6014 4.935352 AGCTTTGCAAGGTTTCATGTTA 57.065 36.364 10.54 0.00 35.27 2.41
4390 6248 7.784470 AAGAGTACTTCCTGTTTCAGTCTAT 57.216 36.000 0.00 0.00 0.00 1.98
4436 6294 8.029642 AGACATTTACATTTTCAAGGTACTCG 57.970 34.615 0.00 0.00 38.49 4.18
4550 6408 5.794894 ACCAATTTAGGTAGCTCGATATGG 58.205 41.667 0.00 5.02 40.98 2.74
4553 6411 6.812160 CCAATTTAGGTAGCTCGATATGGTAC 59.188 42.308 0.00 4.43 37.58 3.34
4560 6418 3.403038 AGCTCGATATGGTACCAATTGC 58.597 45.455 20.76 16.36 0.00 3.56
4561 6419 3.138304 GCTCGATATGGTACCAATTGCA 58.862 45.455 20.76 2.28 0.00 4.08
4578 6436 6.342906 CAATTGCATAATTCTGGAACACCAT 58.657 36.000 0.00 0.00 34.34 3.55
4584 6442 7.043565 GCATAATTCTGGAACACCATCATTTT 58.956 34.615 0.00 0.00 32.90 1.82
4637 6496 9.447040 CATACTATCTTTTGACATGCATTTGAG 57.553 33.333 0.00 0.00 0.00 3.02
4654 6513 9.577110 TGCATTTGAGAAATTATCAAGAACATC 57.423 29.630 3.22 0.00 37.91 3.06
4674 6533 8.920509 AACATCGCCTAAAATAAAATTACCAC 57.079 30.769 0.00 0.00 0.00 4.16
4726 6585 7.649533 TCAGCAAAAAGTATCAATCATGGAT 57.350 32.000 0.00 0.00 0.00 3.41
4731 6590 9.585099 GCAAAAAGTATCAATCATGGATAACAA 57.415 29.630 0.00 0.00 0.00 2.83
4749 6610 8.355913 GGATAACAATTGATCTTCAAGGATTCC 58.644 37.037 13.59 0.00 40.05 3.01
4891 6758 5.806654 ACATTGAGTGTTTTATGCCCTTT 57.193 34.783 0.00 0.00 38.01 3.11
4893 6760 5.990996 ACATTGAGTGTTTTATGCCCTTTTG 59.009 36.000 0.00 0.00 38.01 2.44
4943 6811 6.160483 TGATTTACCTTAGGACCCCAAAAT 57.840 37.500 4.77 1.29 0.00 1.82
4947 6815 2.923629 ACCTTAGGACCCCAAAATAGCA 59.076 45.455 4.77 0.00 0.00 3.49
5147 7015 6.017400 TGGAAAAGCAGCTTTTATGAGAAG 57.983 37.500 29.18 0.00 42.72 2.85
5166 7034 4.828939 AGAAGCATCCAGATTGTTGACAAA 59.171 37.500 0.10 0.00 39.55 2.83
5169 7037 6.105397 AGCATCCAGATTGTTGACAAAAAT 57.895 33.333 3.10 3.10 39.55 1.82
5193 7061 4.718961 ACAAGCTTGTCACTCCAAATAGT 58.281 39.130 26.36 0.00 36.50 2.12
5216 7084 4.879545 TCACAAAGACCTTGTTGGAACTAC 59.120 41.667 0.00 0.00 46.49 2.73
5353 7221 8.506168 AAATTGTGAACAGACTTCTTGAGTTA 57.494 30.769 0.00 0.00 39.19 2.24
5354 7222 6.903883 TTGTGAACAGACTTCTTGAGTTAC 57.096 37.500 0.00 0.00 39.19 2.50
5389 7257 5.862678 TTATCGGGAGTTGTCATACATCA 57.137 39.130 0.00 0.00 0.00 3.07
5396 7264 5.122396 GGGAGTTGTCATACATCAAAGTGTC 59.878 44.000 0.00 0.00 33.62 3.67
5404 7272 6.978659 GTCATACATCAAAGTGTCTATTCCGA 59.021 38.462 0.00 0.00 33.62 4.55
5428 7296 7.116948 CGATGAGTAGTTTATCAATCCCATCAC 59.883 40.741 0.00 0.00 0.00 3.06
5476 7345 7.088589 ACATGAATAGAAATTTTGAGGGACG 57.911 36.000 0.00 0.00 0.00 4.79
5495 7364 6.537660 AGGGACGCACTGTAATATTTTAGTTC 59.462 38.462 0.00 0.00 0.00 3.01
5522 7391 7.622713 TCATGGATAATTGCTTGGATTTGTTT 58.377 30.769 0.00 0.00 0.00 2.83
5523 7392 7.549842 TCATGGATAATTGCTTGGATTTGTTTG 59.450 33.333 0.00 0.00 0.00 2.93
5547 7416 5.810074 GCGCAAAACAAATTCCCATACTTAT 59.190 36.000 0.30 0.00 0.00 1.73
5595 7464 2.003937 ATTTGGGCGGGTACAAAGTT 57.996 45.000 0.00 0.00 39.63 2.66
5681 7550 6.151144 ACAATAGAGCATTGACCTTGTAAACC 59.849 38.462 4.10 0.00 45.99 3.27
5789 7658 8.531146 GTTCAAATTCAAAATCTCCTCCCAATA 58.469 33.333 0.00 0.00 0.00 1.90
5790 7659 8.843308 TCAAATTCAAAATCTCCTCCCAATAT 57.157 30.769 0.00 0.00 0.00 1.28
5793 7662 5.128033 TCAAAATCTCCTCCCAATATGCA 57.872 39.130 0.00 0.00 0.00 3.96
5814 7683 8.729805 ATGCATTTTCCTTGTTTTTCTTTACA 57.270 26.923 0.00 0.00 0.00 2.41
6167 8036 0.307760 AAAAACGCTCTCTGCAACGG 59.692 50.000 0.00 0.00 43.06 4.44
6168 8037 0.814010 AAAACGCTCTCTGCAACGGT 60.814 50.000 0.00 0.00 43.06 4.83
6169 8038 1.222115 AAACGCTCTCTGCAACGGTC 61.222 55.000 0.00 0.00 43.06 4.79
6171 8040 2.811317 GCTCTCTGCAACGGTCGG 60.811 66.667 0.00 0.00 42.31 4.79
6172 8041 2.651361 CTCTCTGCAACGGTCGGT 59.349 61.111 0.00 0.00 0.00 4.69
6173 8042 1.734477 CTCTCTGCAACGGTCGGTG 60.734 63.158 3.80 3.80 35.59 4.94
6174 8043 2.142357 CTCTCTGCAACGGTCGGTGA 62.142 60.000 12.92 0.00 34.08 4.02
6175 8044 1.079819 CTCTGCAACGGTCGGTGAT 60.080 57.895 12.92 0.00 34.08 3.06
6176 8045 0.172578 CTCTGCAACGGTCGGTGATA 59.827 55.000 12.92 0.00 34.08 2.15
6178 8047 1.001068 TCTGCAACGGTCGGTGATAAA 59.999 47.619 12.92 0.00 34.08 1.40
6179 8048 1.801771 CTGCAACGGTCGGTGATAAAA 59.198 47.619 12.92 0.00 34.08 1.52
6220 8089 1.031235 CAGGACATGTTTGGCACACA 58.969 50.000 9.17 9.17 39.29 3.72
6241 8110 4.766891 ACAAAATTGTGATAGTGGTGGGAG 59.233 41.667 1.62 0.00 40.49 4.30
6271 8140 1.211949 CGGGCTATCTTTTTCCCTCCA 59.788 52.381 0.00 0.00 36.61 3.86
6274 8143 2.242452 GGCTATCTTTTTCCCTCCAGGT 59.758 50.000 0.00 0.00 36.75 4.00
6276 8145 3.201045 GCTATCTTTTTCCCTCCAGGTCT 59.799 47.826 0.00 0.00 36.75 3.85
6285 8154 0.399091 CCTCCAGGTCTGCCTCCATA 60.399 60.000 0.00 0.00 44.97 2.74
6291 8160 1.674057 GTCTGCCTCCATATCGGGG 59.326 63.158 0.00 0.00 34.36 5.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 9.907576 CAGAGATTAAACATTCTTGATCGTAAC 57.092 33.333 0.00 0.00 0.00 2.50
89 90 5.278660 CCTTGTCTCCATTGACCTTTTTCAG 60.279 44.000 0.00 0.00 36.21 3.02
100 101 4.034285 ACTTTACCCCTTGTCTCCATTG 57.966 45.455 0.00 0.00 0.00 2.82
112 113 4.221482 TCGAGAAGAGGTAAACTTTACCCC 59.779 45.833 22.27 13.97 38.33 4.95
140 141 4.980573 ACTTAGTCATTGGTAGTTTGCCA 58.019 39.130 0.00 0.00 0.00 4.92
187 188 3.244284 TGTTGCCGTTGTACTGGAGTTAT 60.244 43.478 0.00 0.00 0.00 1.89
224 228 2.174363 TCATCACGGCATCATCCATC 57.826 50.000 0.00 0.00 0.00 3.51
284 290 3.260884 ACCGGTTCTCTAGATTCTTTGCA 59.739 43.478 0.00 0.00 0.00 4.08
312 318 4.805947 GACCCATGTCCATCTGTGTAACAA 60.806 45.833 0.00 0.00 40.41 2.83
437 445 4.708726 AAAAGGTTGCAGAGCATCATAC 57.291 40.909 0.00 0.00 38.76 2.39
447 455 7.440856 ACAACAATGGTAATAAAAAGGTTGCAG 59.559 33.333 0.00 0.00 37.26 4.41
450 458 9.928236 CAAACAACAATGGTAATAAAAAGGTTG 57.072 29.630 0.00 0.00 39.07 3.77
468 476 7.643569 ATTCATATCCATGTAGCAAACAACA 57.356 32.000 0.00 0.00 42.70 3.33
477 485 8.455903 ACACTTGGAAATTCATATCCATGTAG 57.544 34.615 12.59 10.46 46.47 2.74
484 492 7.721399 ACCAGGATACACTTGGAAATTCATATC 59.279 37.037 5.08 0.00 46.90 1.63
493 525 6.270000 CCAGATATACCAGGATACACTTGGAA 59.730 42.308 5.08 0.00 46.90 3.53
498 530 8.796684 AGATATCCAGATATACCAGGATACACT 58.203 37.037 0.37 1.93 43.68 3.55
508 540 9.344772 CTACACCACTAGATATCCAGATATACC 57.655 40.741 5.08 0.00 34.36 2.73
608 647 4.060205 GTGTTTGGACGGTAGAGCTAAAA 58.940 43.478 0.00 0.00 0.00 1.52
631 670 1.139058 ACATAGGGATCGCAACTGGTC 59.861 52.381 12.83 0.00 0.00 4.02
632 671 1.134401 CACATAGGGATCGCAACTGGT 60.134 52.381 12.83 0.12 0.00 4.00
635 674 2.435805 ACATCACATAGGGATCGCAACT 59.564 45.455 12.83 0.00 0.00 3.16
636 675 2.545526 CACATCACATAGGGATCGCAAC 59.454 50.000 12.83 0.00 0.00 4.17
641 680 6.997655 TCTAATCACACATCACATAGGGATC 58.002 40.000 0.00 0.00 0.00 3.36
656 695 8.101309 TCATCCCTTCCTTTTATCTAATCACA 57.899 34.615 0.00 0.00 0.00 3.58
671 710 0.543749 CTCACCCACTCATCCCTTCC 59.456 60.000 0.00 0.00 0.00 3.46
676 715 0.463620 GCTCTCTCACCCACTCATCC 59.536 60.000 0.00 0.00 0.00 3.51
678 717 1.554160 CTTGCTCTCTCACCCACTCAT 59.446 52.381 0.00 0.00 0.00 2.90
696 735 7.720957 TCCGGATATTCAAATGTGATCATTCTT 59.279 33.333 0.00 0.00 42.60 2.52
701 740 8.916628 TTATTCCGGATATTCAAATGTGATCA 57.083 30.769 4.15 0.00 32.48 2.92
871 914 8.567948 TCCCAAAGATCGAATTCTTTTATATGC 58.432 33.333 10.59 0.00 41.95 3.14
877 920 6.840780 ATGTCCCAAAGATCGAATTCTTTT 57.159 33.333 10.59 0.00 41.95 2.27
989 1033 6.940739 TGACTTTCTTTCATTTTGGAAACCA 58.059 32.000 0.00 0.00 33.48 3.67
1043 1087 3.646162 TCCTCTGGTTGCTAGAACAAGAA 59.354 43.478 11.13 0.00 30.39 2.52
1055 1099 5.776173 AGTCGTATCTATTCCTCTGGTTG 57.224 43.478 0.00 0.00 0.00 3.77
1074 1118 6.834168 TCATTTTCCCTTTCCATTGTAGTC 57.166 37.500 0.00 0.00 0.00 2.59
1084 1128 5.242615 GGATCTGGCTATCATTTTCCCTTTC 59.757 44.000 0.00 0.00 0.00 2.62
1133 1178 8.862325 ATGAGTAATTGTTCTTACCATGACAA 57.138 30.769 0.00 0.00 33.02 3.18
1134 1179 8.100164 TGATGAGTAATTGTTCTTACCATGACA 58.900 33.333 0.00 0.00 33.02 3.58
1168 1213 8.729756 GCCAATGAAACCAAAAAGCTTATAAAT 58.270 29.630 0.00 0.00 0.00 1.40
1169 1214 7.936301 AGCCAATGAAACCAAAAAGCTTATAAA 59.064 29.630 0.00 0.00 0.00 1.40
1171 1216 7.003402 AGCCAATGAAACCAAAAAGCTTATA 57.997 32.000 0.00 0.00 0.00 0.98
1172 1217 5.868454 AGCCAATGAAACCAAAAAGCTTAT 58.132 33.333 0.00 0.00 0.00 1.73
1173 1218 5.289083 AGCCAATGAAACCAAAAAGCTTA 57.711 34.783 0.00 0.00 0.00 3.09
1174 1219 4.155063 AGCCAATGAAACCAAAAAGCTT 57.845 36.364 0.00 0.00 0.00 3.74
1175 1220 3.843893 AGCCAATGAAACCAAAAAGCT 57.156 38.095 0.00 0.00 0.00 3.74
1176 1221 4.813697 TGTTAGCCAATGAAACCAAAAAGC 59.186 37.500 0.00 0.00 0.00 3.51
1177 1222 6.511605 GCTTGTTAGCCAATGAAACCAAAAAG 60.512 38.462 0.00 0.00 41.74 2.27
1178 1223 5.295540 GCTTGTTAGCCAATGAAACCAAAAA 59.704 36.000 0.00 0.00 41.74 1.94
1179 1224 4.813697 GCTTGTTAGCCAATGAAACCAAAA 59.186 37.500 0.00 0.00 41.74 2.44
1180 1225 4.376146 GCTTGTTAGCCAATGAAACCAAA 58.624 39.130 0.00 0.00 41.74 3.28
1181 1226 3.988819 GCTTGTTAGCCAATGAAACCAA 58.011 40.909 0.00 0.00 41.74 3.67
1182 1227 3.658757 GCTTGTTAGCCAATGAAACCA 57.341 42.857 0.00 0.00 41.74 3.67
1183 1228 9.605684 TTCATCTGCTTGTTAGCCAATGAAACC 62.606 40.741 15.75 0.00 44.99 3.27
1184 1229 6.791028 TTCATCTGCTTGTTAGCCAATGAAAC 60.791 38.462 15.75 0.00 44.99 2.78
1348 1604 1.999735 GAATCGACGTCCATTTGAGCA 59.000 47.619 9.82 0.00 0.00 4.26
1370 1626 7.464830 AACTATTCATTTATGTCTTCCGTCG 57.535 36.000 0.00 0.00 0.00 5.12
1414 1670 8.253113 CCTCAAATTTGATGGCTAACTAACATT 58.747 33.333 20.76 0.00 36.46 2.71
1437 1693 7.946207 TCGCATAATAGATGATCTATTCCCTC 58.054 38.462 26.12 14.94 44.03 4.30
1438 1694 7.904558 TCGCATAATAGATGATCTATTCCCT 57.095 36.000 26.12 12.87 44.03 4.20
1495 1751 7.848128 TCTAAAGGGAGTAGAACAAACTATGG 58.152 38.462 0.00 0.00 0.00 2.74
1552 1813 4.500716 CCCCAACTTCCATTGTTTGTACAC 60.501 45.833 0.00 0.00 32.98 2.90
1554 1815 3.639561 ACCCCAACTTCCATTGTTTGTAC 59.360 43.478 0.00 0.00 0.00 2.90
1668 1930 8.895141 AAACTTTAAAGCCTTATTAGTCCCAT 57.105 30.769 15.24 0.00 0.00 4.00
1727 1989 5.339200 GGGAGATTTTATCCTCTGTCCAACA 60.339 44.000 0.00 0.00 37.01 3.33
1739 2001 4.835056 CCATTTGGGGAGGGAGATTTTATC 59.165 45.833 0.00 0.00 0.00 1.75
1801 2063 3.071479 CGTATAATTGGAACCATCCCCG 58.929 50.000 0.00 0.00 45.95 5.73
1847 2109 0.447801 CTTGCTCGGTAATGTGTGCC 59.552 55.000 0.00 0.00 0.00 5.01
1929 2194 7.291411 AGTCGCTCAATTACTATGATACCTT 57.709 36.000 0.00 0.00 0.00 3.50
1947 2212 3.003275 CACAAAACATGGTGTTAGTCGCT 59.997 43.478 0.00 0.00 40.14 4.93
1961 2226 5.590530 ACATTTTCTAGGCACACAAAACA 57.409 34.783 0.00 0.00 0.00 2.83
2024 2290 8.675705 TGCATCGGAATTATCTTTGAGAATTA 57.324 30.769 0.96 0.00 34.28 1.40
2044 2310 8.715088 AGCATTCAATTAAAAAGACTTTGCATC 58.285 29.630 0.06 0.00 0.00 3.91
2609 2895 0.882042 AGCGCGGATCCATCATTGTC 60.882 55.000 13.41 0.00 0.00 3.18
2672 2958 8.863086 GGCCGGTATACAATGATATATAGGTAA 58.137 37.037 1.90 0.00 0.00 2.85
2674 2960 6.269307 GGGCCGGTATACAATGATATATAGGT 59.731 42.308 1.90 0.00 0.00 3.08
2677 2963 5.244402 CGGGGCCGGTATACAATGATATATA 59.756 44.000 1.90 0.00 35.56 0.86
2678 2964 4.039973 CGGGGCCGGTATACAATGATATAT 59.960 45.833 1.90 0.00 35.56 0.86
2679 2965 3.385433 CGGGGCCGGTATACAATGATATA 59.615 47.826 1.90 0.00 35.56 0.86
2680 2966 2.169769 CGGGGCCGGTATACAATGATAT 59.830 50.000 1.90 0.00 35.56 1.63
2681 2967 1.551430 CGGGGCCGGTATACAATGATA 59.449 52.381 1.90 0.00 35.56 2.15
2682 2968 0.323629 CGGGGCCGGTATACAATGAT 59.676 55.000 1.90 0.00 35.56 2.45
2683 2969 1.049855 ACGGGGCCGGTATACAATGA 61.050 55.000 15.91 0.00 44.69 2.57
2694 2980 2.900337 GGCTAAATCACGGGGCCG 60.900 66.667 0.00 0.00 46.03 6.13
2704 2990 0.972471 GCTGGGCTTGTGGGCTAAAT 60.972 55.000 0.00 0.00 40.65 1.40
2715 3001 2.599597 CTGGGCTATGCTGGGCTT 59.400 61.111 0.00 0.00 0.00 4.35
2738 3024 4.611367 AGGTAGCTGGCTTAGAGTCTTTA 58.389 43.478 0.00 0.00 0.00 1.85
2752 3038 4.503714 TTGGAAGGGATTTAGGTAGCTG 57.496 45.455 4.27 0.00 0.00 4.24
2775 3061 3.505386 ACAGTTTGGGACATAATTGCCA 58.495 40.909 0.00 0.00 39.30 4.92
2796 3082 0.758734 CATGGTCCCGAGCTTGGATA 59.241 55.000 22.68 6.23 33.65 2.59
2801 3087 2.671070 CCACATGGTCCCGAGCTT 59.329 61.111 0.00 0.00 0.00 3.74
2857 3144 1.291877 ACTGATTGGCTCGTTGCGAC 61.292 55.000 0.00 0.00 44.05 5.19
2872 3159 0.032515 TAGCGGAGGGGAATGACTGA 60.033 55.000 0.00 0.00 0.00 3.41
2903 3190 2.046892 CCAGTGAAGGTGGAGCCG 60.047 66.667 0.00 0.00 43.70 5.52
2904 3191 3.161557 ACCAGTGAAGGTGGAGCC 58.838 61.111 0.00 0.00 41.30 4.70
2910 3197 0.546122 TTGCAGACACCAGTGAAGGT 59.454 50.000 4.48 0.00 44.48 3.50
2911 3198 1.679139 TTTGCAGACACCAGTGAAGG 58.321 50.000 4.48 0.00 0.00 3.46
2912 3199 2.880268 TGATTTGCAGACACCAGTGAAG 59.120 45.455 4.48 0.00 0.00 3.02
2913 3200 2.929641 TGATTTGCAGACACCAGTGAA 58.070 42.857 4.48 0.00 0.00 3.18
2914 3201 2.636647 TGATTTGCAGACACCAGTGA 57.363 45.000 4.48 0.00 0.00 3.41
2931 3223 1.476891 GGGATGTAACACTCGAGCTGA 59.523 52.381 13.61 0.00 0.00 4.26
2938 3230 2.928116 GTTAGTGCGGGATGTAACACTC 59.072 50.000 0.00 0.00 42.19 3.51
2944 3236 1.067974 CATCGGTTAGTGCGGGATGTA 59.932 52.381 0.00 0.00 32.02 2.29
2958 3250 1.303561 AACATGGCAGCACATCGGT 60.304 52.632 0.00 0.00 0.00 4.69
2959 3251 1.138036 CAACATGGCAGCACATCGG 59.862 57.895 0.00 0.00 0.00 4.18
2963 3256 0.036590 TAGAGCAACATGGCAGCACA 59.963 50.000 0.00 0.00 35.83 4.57
3051 4898 9.458727 AGTTTAGCCCTAATAACTTCCTAAAAC 57.541 33.333 0.00 0.00 0.00 2.43
3066 4913 3.761752 GCAACATGGAAAGTTTAGCCCTA 59.238 43.478 0.00 0.00 0.00 3.53
3111 4958 2.618053 CGACAGAGCCGGAATTAAAGT 58.382 47.619 5.05 0.00 0.00 2.66
3147 4994 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
3148 4995 1.598882 TTGTGTGTGTGTGTGTGTGT 58.401 45.000 0.00 0.00 0.00 3.72
3149 4996 2.287248 TGTTTGTGTGTGTGTGTGTGTG 60.287 45.455 0.00 0.00 0.00 3.82
3150 4997 1.950216 TGTTTGTGTGTGTGTGTGTGT 59.050 42.857 0.00 0.00 0.00 3.72
3151 4998 2.695613 TGTTTGTGTGTGTGTGTGTG 57.304 45.000 0.00 0.00 0.00 3.82
3152 4999 5.378292 TTTATGTTTGTGTGTGTGTGTGT 57.622 34.783 0.00 0.00 0.00 3.72
3153 5000 4.797868 CCTTTATGTTTGTGTGTGTGTGTG 59.202 41.667 0.00 0.00 0.00 3.82
3195 5042 7.823799 TGTGATGAATTCAATGCTAACTACTCA 59.176 33.333 13.09 4.13 35.70 3.41
3206 5053 7.863877 TGAAACAACTCTGTGATGAATTCAATG 59.136 33.333 13.09 1.64 35.70 2.82
3227 5074 8.560374 AGACTTGCTCTTACTATTTGTTGAAAC 58.440 33.333 0.00 0.00 0.00 2.78
3323 5171 1.293924 CATAGGGCGACTTTGCTGAG 58.706 55.000 0.00 0.00 34.52 3.35
3335 5185 2.810852 GCTTTAGAGTGATGCATAGGGC 59.189 50.000 0.00 0.00 45.13 5.19
3338 5188 5.007430 CAGTTGGCTTTAGAGTGATGCATAG 59.993 44.000 0.00 0.00 0.00 2.23
3351 5201 1.234821 CCTCGCAACAGTTGGCTTTA 58.765 50.000 15.28 0.00 0.00 1.85
3355 5205 2.281484 TCCCTCGCAACAGTTGGC 60.281 61.111 15.28 6.54 0.00 4.52
3361 5211 0.404040 AATTTCCCTCCCTCGCAACA 59.596 50.000 0.00 0.00 0.00 3.33
3384 5235 3.596046 AGGGAGAGAGAGGAAGAAGAAGA 59.404 47.826 0.00 0.00 0.00 2.87
3387 5238 3.197983 AGAGGGAGAGAGAGGAAGAAGA 58.802 50.000 0.00 0.00 0.00 2.87
3403 5254 1.522900 AGAGAGGGAGAGAGAGAGGG 58.477 60.000 0.00 0.00 0.00 4.30
3413 5264 0.401738 TGGGCACAAAAGAGAGGGAG 59.598 55.000 0.00 0.00 0.00 4.30
3641 5495 1.741525 GCTGTGGGCAAACACACAT 59.258 52.632 0.98 0.00 45.70 3.21
3653 5507 1.662044 GAGGTTGCAAAGGCTGTGG 59.338 57.895 6.84 0.00 41.91 4.17
3679 5533 1.559682 GGTTTAGAGAGCCATCCACCA 59.440 52.381 0.00 0.00 0.00 4.17
3703 5557 0.398381 AACATATTTGCGGCCCCCAT 60.398 50.000 0.00 0.00 0.00 4.00
3709 5563 4.925068 AGAAGATTCAACATATTTGCGGC 58.075 39.130 0.00 0.00 0.00 6.53
3732 5586 5.900339 TTTACACAACTTAGAGCAACTCG 57.100 39.130 0.00 0.00 35.36 4.18
3821 5675 5.999044 AGAGAGACCAATGCATATCAAACT 58.001 37.500 0.00 0.00 0.00 2.66
3947 5803 5.491070 TGAATATCTAATTCCCGCCATCTG 58.509 41.667 0.00 0.00 0.00 2.90
4077 5934 1.204941 CTACACCTTCTTCCTGACCCG 59.795 57.143 0.00 0.00 0.00 5.28
4084 5941 2.224548 ACAAGCACCTACACCTTCTTCC 60.225 50.000 0.00 0.00 0.00 3.46
4525 6383 7.015877 ACCATATCGAGCTACCTAAATTGGTTA 59.984 37.037 0.00 0.00 41.22 2.85
4550 6408 6.751888 GTGTTCCAGAATTATGCAATTGGTAC 59.248 38.462 7.72 0.00 34.44 3.34
4553 6411 5.111293 GGTGTTCCAGAATTATGCAATTGG 58.889 41.667 7.72 0.00 34.44 3.16
4595 6453 2.026262 AGTATGTGGGTGTGGAATGACC 60.026 50.000 0.00 0.00 39.54 4.02
4603 6461 5.937540 TGTCAAAAGATAGTATGTGGGTGTG 59.062 40.000 0.00 0.00 0.00 3.82
4637 6496 9.736023 ATTTTAGGCGATGTTCTTGATAATTTC 57.264 29.630 0.00 0.00 0.00 2.17
4654 6513 6.970613 GGTGAGTGGTAATTTTATTTTAGGCG 59.029 38.462 0.00 0.00 0.00 5.52
4726 6585 7.181361 TGGGAATCCTTGAAGATCAATTGTTA 58.819 34.615 5.13 0.00 35.59 2.41
4731 6590 8.672329 TGTATATGGGAATCCTTGAAGATCAAT 58.328 33.333 0.00 0.00 35.59 2.57
4760 6621 9.784531 CTTGTAATAAGGGATGTACATCAAGAT 57.215 33.333 31.51 18.13 39.54 2.40
4783 6648 7.591057 TGCATTTCTTCTCATAACGTTTTCTTG 59.409 33.333 5.91 0.00 0.00 3.02
4784 6649 7.648142 TGCATTTCTTCTCATAACGTTTTCTT 58.352 30.769 5.91 0.00 0.00 2.52
4785 6650 7.202016 TGCATTTCTTCTCATAACGTTTTCT 57.798 32.000 5.91 0.00 0.00 2.52
4833 6698 2.914695 AGTGTGCATGCCATTGTTTT 57.085 40.000 16.68 0.00 0.00 2.43
4841 6706 4.318332 TGCTAATATCTAGTGTGCATGCC 58.682 43.478 16.68 7.25 0.00 4.40
4878 6745 3.727726 AGCACACAAAAGGGCATAAAAC 58.272 40.909 0.00 0.00 0.00 2.43
4886 6753 4.074970 AGATTACTGAGCACACAAAAGGG 58.925 43.478 0.00 0.00 0.00 3.95
4891 6758 5.335113 GCATGAAAGATTACTGAGCACACAA 60.335 40.000 0.00 0.00 0.00 3.33
4893 6760 4.154737 TGCATGAAAGATTACTGAGCACAC 59.845 41.667 0.00 0.00 0.00 3.82
4943 6811 3.168035 ACATCACCCACCAATTTGCTA 57.832 42.857 0.00 0.00 0.00 3.49
4947 6815 3.768757 CACCATACATCACCCACCAATTT 59.231 43.478 0.00 0.00 0.00 1.82
5036 6904 1.550072 CAAAACCGCCCCAGAATGAAT 59.450 47.619 0.00 0.00 39.69 2.57
5147 7015 7.384660 TGTTATTTTTGTCAACAATCTGGATGC 59.615 33.333 0.21 0.00 35.55 3.91
5166 7034 6.463995 TTTGGAGTGACAAGCTTGTTATTT 57.536 33.333 31.58 19.64 42.43 1.40
5169 7037 6.296026 ACTATTTGGAGTGACAAGCTTGTTA 58.704 36.000 31.58 25.44 42.43 2.41
5335 7203 7.484035 AATGTGTAACTCAAGAAGTCTGTTC 57.516 36.000 0.00 0.00 37.17 3.18
5353 7221 8.836413 CAACTCCCGATAATTATGTAAATGTGT 58.164 33.333 1.78 0.00 0.00 3.72
5354 7222 8.836413 ACAACTCCCGATAATTATGTAAATGTG 58.164 33.333 1.78 0.00 0.00 3.21
5371 7239 4.093408 CACTTTGATGTATGACAACTCCCG 59.907 45.833 0.00 0.00 0.00 5.14
5389 7257 6.777213 ACTACTCATCGGAATAGACACTTT 57.223 37.500 0.00 0.00 0.00 2.66
5396 7264 9.360093 GGATTGATAAACTACTCATCGGAATAG 57.640 37.037 0.00 0.00 0.00 1.73
5404 7272 6.931281 CGTGATGGGATTGATAAACTACTCAT 59.069 38.462 0.00 0.00 0.00 2.90
5476 7345 9.669353 CCATGATGAACTAAAATATTACAGTGC 57.331 33.333 0.00 2.56 0.00 4.40
5495 7364 7.214381 ACAAATCCAAGCAATTATCCATGATG 58.786 34.615 0.00 0.00 0.00 3.07
5522 7391 2.540265 ATGGGAATTTGTTTTGCGCA 57.460 40.000 5.66 5.66 0.00 6.09
5523 7392 3.584834 AGTATGGGAATTTGTTTTGCGC 58.415 40.909 0.00 0.00 0.00 6.09
5551 7420 9.905713 ATTGTACCACTAGAAACACATCAATAT 57.094 29.630 0.00 0.00 0.00 1.28
5576 7445 1.890489 GAACTTTGTACCCGCCCAAAT 59.110 47.619 0.00 0.00 30.76 2.32
5612 7481 9.836864 TCAAATGTATGTGTCTAATAGCAGATT 57.163 29.630 0.00 0.00 0.00 2.40
5650 7519 5.848406 AGGTCAATGCTCTATTGTAGTAGC 58.152 41.667 0.00 0.00 45.17 3.58
5656 7525 6.151144 GGTTTACAAGGTCAATGCTCTATTGT 59.849 38.462 0.00 0.00 45.17 2.71
5757 7626 9.317936 GAGGAGATTTTGAATTTGAACTGTTTT 57.682 29.630 0.00 0.00 0.00 2.43
5789 7658 8.729805 TGTAAAGAAAAACAAGGAAAATGCAT 57.270 26.923 0.00 0.00 0.00 3.96
5790 7659 8.553459 TTGTAAAGAAAAACAAGGAAAATGCA 57.447 26.923 0.00 0.00 32.11 3.96
6111 7980 6.535150 TCAATTATCTTTCCTGCTACTTCACG 59.465 38.462 0.00 0.00 0.00 4.35
6112 7981 7.849804 TCAATTATCTTTCCTGCTACTTCAC 57.150 36.000 0.00 0.00 0.00 3.18
6113 7982 8.049117 ACATCAATTATCTTTCCTGCTACTTCA 58.951 33.333 0.00 0.00 0.00 3.02
6118 7987 6.767902 GGACACATCAATTATCTTTCCTGCTA 59.232 38.462 0.00 0.00 0.00 3.49
6120 7989 5.357878 TGGACACATCAATTATCTTTCCTGC 59.642 40.000 0.00 0.00 0.00 4.85
6154 8023 2.811317 CCGACCGTTGCAGAGAGC 60.811 66.667 0.00 0.00 45.96 4.09
6155 8024 1.734477 CACCGACCGTTGCAGAGAG 60.734 63.158 0.00 0.00 0.00 3.20
6156 8025 1.532604 ATCACCGACCGTTGCAGAGA 61.533 55.000 0.00 0.00 0.00 3.10
6157 8026 0.172578 TATCACCGACCGTTGCAGAG 59.827 55.000 0.00 0.00 0.00 3.35
6160 8029 1.532007 GTTTTATCACCGACCGTTGCA 59.468 47.619 0.00 0.00 0.00 4.08
6161 8030 1.532007 TGTTTTATCACCGACCGTTGC 59.468 47.619 0.00 0.00 0.00 4.17
6162 8031 3.364565 CCTTGTTTTATCACCGACCGTTG 60.365 47.826 0.00 0.00 0.00 4.10
6164 8033 2.037511 TCCTTGTTTTATCACCGACCGT 59.962 45.455 0.00 0.00 0.00 4.83
6165 8034 2.671396 CTCCTTGTTTTATCACCGACCG 59.329 50.000 0.00 0.00 0.00 4.79
6167 8036 4.514066 ACAACTCCTTGTTTTATCACCGAC 59.486 41.667 0.00 0.00 37.31 4.79
6168 8037 4.710324 ACAACTCCTTGTTTTATCACCGA 58.290 39.130 0.00 0.00 37.31 4.69
6169 8038 5.212194 CAACAACTCCTTGTTTTATCACCG 58.788 41.667 0.00 0.00 46.55 4.94
6171 8040 7.027778 AGACAACAACTCCTTGTTTTATCAC 57.972 36.000 0.00 0.00 46.55 3.06
6172 8041 7.556275 AGAAGACAACAACTCCTTGTTTTATCA 59.444 33.333 0.00 0.00 46.55 2.15
6173 8042 7.931275 AGAAGACAACAACTCCTTGTTTTATC 58.069 34.615 0.00 0.00 46.55 1.75
6174 8043 7.556275 TGAGAAGACAACAACTCCTTGTTTTAT 59.444 33.333 0.00 0.00 46.55 1.40
6175 8044 6.882140 TGAGAAGACAACAACTCCTTGTTTTA 59.118 34.615 0.00 0.00 46.55 1.52
6176 8045 5.710099 TGAGAAGACAACAACTCCTTGTTTT 59.290 36.000 0.00 0.00 46.55 2.43
6179 8048 4.192317 GTGAGAAGACAACAACTCCTTGT 58.808 43.478 0.00 0.00 42.81 3.16
6191 8060 4.129380 CAAACATGTCCTGTGAGAAGACA 58.871 43.478 0.00 0.00 44.11 3.41
6194 8063 2.227388 GCCAAACATGTCCTGTGAGAAG 59.773 50.000 0.00 0.00 38.39 2.85
6220 8089 3.763897 GCTCCCACCACTATCACAATTTT 59.236 43.478 0.00 0.00 0.00 1.82
6225 8094 0.613260 GTGCTCCCACCACTATCACA 59.387 55.000 0.00 0.00 35.92 3.58
6226 8095 3.460648 GTGCTCCCACCACTATCAC 57.539 57.895 0.00 0.00 35.92 3.06
6253 8122 2.242452 ACCTGGAGGGAAAAAGATAGCC 59.758 50.000 0.00 0.00 40.27 3.93
6256 8125 3.054361 GCAGACCTGGAGGGAAAAAGATA 60.054 47.826 0.00 0.00 40.27 1.98
6257 8126 2.291217 GCAGACCTGGAGGGAAAAAGAT 60.291 50.000 0.00 0.00 40.27 2.40
6274 8143 0.399949 AACCCCGATATGGAGGCAGA 60.400 55.000 0.00 0.00 42.00 4.26
6276 8145 0.986019 ACAACCCCGATATGGAGGCA 60.986 55.000 0.00 0.00 42.00 4.75
6285 8154 4.740822 GGCAGCCACAACCCCGAT 62.741 66.667 6.55 0.00 0.00 4.18


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

AutoCloner maintained by Alex Coulton.