Multiple sequence alignment - TraesCS1B01G251900

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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 TraesCS1B01G251900 chr1B 100.000 3709 0 0 1 3709 444685817 444689525 0.000000e+00 6850
1 TraesCS1B01G251900 chr1D 91.174 2436 119 38 865 3257 329729984 329732366 0.000000e+00 3219
2 TraesCS1B01G251900 chr1D 86.507 667 48 15 36 685 329728648 329729289 0.000000e+00 695
3 TraesCS1B01G251900 chr1D 95.437 263 6 4 3452 3709 329732679 329732940 7.410000e-112 414
4 TraesCS1B01G251900 chr1D 94.845 194 6 2 3256 3449 329732443 329732632 2.170000e-77 300
5 TraesCS1B01G251900 chr1A 90.967 1417 66 25 1369 2750 426887233 426888622 0.000000e+00 1851
6 TraesCS1B01G251900 chr1A 84.098 654 46 16 36 669 426885763 426886378 2.480000e-161 579
7 TraesCS1B01G251900 chr1A 90.160 437 31 9 2732 3161 426888648 426889079 3.240000e-155 558
8 TraesCS1B01G251900 chr1A 91.268 355 17 7 865 1205 426886849 426887203 4.340000e-129 472
9 TraesCS1B01G251900 chr1A 93.916 263 14 2 3447 3709 426889433 426889693 2.680000e-106 396
10 TraesCS1B01G251900 chr1A 82.482 274 20 8 3178 3450 426889145 426889391 8.070000e-52 215
11 TraesCS1B01G251900 chr1A 91.753 97 5 2 524 620 576619360 576619453 8.360000e-27 132
12 TraesCS1B01G251900 chr5A 96.341 82 3 0 518 599 585434558 585434639 6.460000e-28 135
13 TraesCS1B01G251900 chr4B 98.684 76 1 0 524 599 488694120 488694045 6.460000e-28 135
14 TraesCS1B01G251900 chr4A 98.684 76 1 0 524 599 78250216 78250141 6.460000e-28 135
15 TraesCS1B01G251900 chr4D 95.181 83 4 0 520 602 7905070 7904988 8.360000e-27 132
16 TraesCS1B01G251900 chr6A 94.118 85 3 2 523 607 602912712 602912794 1.080000e-25 128
17 TraesCS1B01G251900 chr5B 94.186 86 2 3 519 603 687215899 687215982 1.080000e-25 128


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 TraesCS1B01G251900 chr1B 444685817 444689525 3708 False 6850.0 6850 100.000000 1 3709 1 chr1B.!!$F1 3708
1 TraesCS1B01G251900 chr1D 329728648 329732940 4292 False 1157.0 3219 91.990750 36 3709 4 chr1D.!!$F1 3673
2 TraesCS1B01G251900 chr1A 426885763 426889693 3930 False 678.5 1851 88.815167 36 3709 6 chr1A.!!$F2 3673

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
749 1037 0.103937 CACTCTCCGCCATCTTCTCC 59.896 60.0 0.0 0.0 0.0 3.71 F
753 1041 0.179062 CTCCGCCATCTTCTCCAAGG 60.179 60.0 0.0 0.0 0.0 3.61 F
2018 2701 0.094730 GTTGAGCGTTCGTGTATGGC 59.905 55.0 0.0 0.0 0.0 4.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2000 2679 0.037697 AGCCATACACGAACGCTCAA 60.038 50.0 0.00 0.0 0.0 3.02 R
2338 3022 0.179070 GATTCCCCTCGAGAACCTGC 60.179 60.0 15.71 0.0 0.0 4.85 R
3129 3871 0.108186 TCCGTGCAGATGGTGTGATC 60.108 55.0 0.00 0.0 0.0 2.92 R

All possible primers

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

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
24 25 2.637521 TGCTCTTCCAAGCAGCTTG 58.362 52.632 26.03 26.03 47.00 4.01
25 26 1.212229 GCTCTTCCAAGCAGCTTGC 59.788 57.895 27.32 12.84 45.46 4.01
32 33 2.097464 TCCAAGCAGCTTGCATTGGAA 61.097 47.619 27.32 4.25 46.89 3.53
33 34 4.233013 TCCAAGCAGCTTGCATTGGAAC 62.233 50.000 27.32 0.00 46.89 3.62
34 35 4.157817 GCAGCTTGCATTGGAACG 57.842 55.556 0.00 0.00 44.26 3.95
103 104 3.004629 TGTGAAATGTGGCATGTTCTCAC 59.995 43.478 10.76 10.76 34.03 3.51
104 105 3.254166 GTGAAATGTGGCATGTTCTCACT 59.746 43.478 0.00 0.00 33.04 3.41
106 107 4.022935 TGAAATGTGGCATGTTCTCACTTC 60.023 41.667 0.00 1.74 33.04 3.01
109 110 2.104622 TGTGGCATGTTCTCACTTCTCA 59.895 45.455 0.00 0.00 33.04 3.27
110 111 2.740981 GTGGCATGTTCTCACTTCTCAG 59.259 50.000 0.00 0.00 0.00 3.35
111 112 1.736681 GGCATGTTCTCACTTCTCAGC 59.263 52.381 0.00 0.00 0.00 4.26
112 113 2.614987 GGCATGTTCTCACTTCTCAGCT 60.615 50.000 0.00 0.00 0.00 4.24
113 114 3.072944 GCATGTTCTCACTTCTCAGCTT 58.927 45.455 0.00 0.00 0.00 3.74
114 115 3.501445 GCATGTTCTCACTTCTCAGCTTT 59.499 43.478 0.00 0.00 0.00 3.51
115 116 4.023365 GCATGTTCTCACTTCTCAGCTTTT 60.023 41.667 0.00 0.00 0.00 2.27
116 117 5.450171 CATGTTCTCACTTCTCAGCTTTTG 58.550 41.667 0.00 0.00 0.00 2.44
117 118 4.769688 TGTTCTCACTTCTCAGCTTTTGA 58.230 39.130 0.00 0.00 0.00 2.69
118 119 5.185454 TGTTCTCACTTCTCAGCTTTTGAA 58.815 37.500 0.00 0.00 34.81 2.69
119 120 5.065218 TGTTCTCACTTCTCAGCTTTTGAAC 59.935 40.000 0.00 0.00 34.81 3.18
120 121 4.130118 TCTCACTTCTCAGCTTTTGAACC 58.870 43.478 0.00 0.00 34.81 3.62
121 122 2.872245 TCACTTCTCAGCTTTTGAACCG 59.128 45.455 0.00 0.00 34.81 4.44
157 159 2.922335 GCAAGCATGTCCTCCGTTTTTC 60.922 50.000 0.00 0.00 0.00 2.29
158 160 1.534729 AGCATGTCCTCCGTTTTTCC 58.465 50.000 0.00 0.00 0.00 3.13
184 186 5.505181 AGGCTCTTCAGTTTATCTTGGAA 57.495 39.130 0.00 0.00 0.00 3.53
199 201 1.271856 TGGAACCCATGACGCTTCTA 58.728 50.000 0.00 0.00 0.00 2.10
212 214 7.225538 CCATGACGCTTCTAGTTCTAAATGAAT 59.774 37.037 0.00 0.00 36.99 2.57
332 347 3.319755 CAATGCCATGTGTTTCCAAGAC 58.680 45.455 0.00 0.00 0.00 3.01
334 349 2.665165 TGCCATGTGTTTCCAAGACTT 58.335 42.857 0.00 0.00 0.00 3.01
338 353 3.383761 CATGTGTTTCCAAGACTTTGCC 58.616 45.455 0.00 0.00 32.79 4.52
358 373 2.169978 CCTCCAGCATGAGAATGTCTGA 59.830 50.000 0.00 0.00 39.69 3.27
367 382 6.866770 AGCATGAGAATGTCTGATTTTGTTTG 59.133 34.615 0.00 0.00 0.00 2.93
368 383 6.643770 GCATGAGAATGTCTGATTTTGTTTGT 59.356 34.615 0.00 0.00 0.00 2.83
369 384 7.809331 GCATGAGAATGTCTGATTTTGTTTGTA 59.191 33.333 0.00 0.00 0.00 2.41
424 439 1.862201 CCTTTGTTGTTGCACATGCTG 59.138 47.619 5.31 0.00 42.66 4.41
425 440 2.481622 CCTTTGTTGTTGCACATGCTGA 60.482 45.455 5.31 0.00 42.66 4.26
426 441 2.495409 TTGTTGTTGCACATGCTGAG 57.505 45.000 5.31 0.00 42.66 3.35
427 442 1.677942 TGTTGTTGCACATGCTGAGA 58.322 45.000 5.31 0.00 42.66 3.27
428 443 2.232399 TGTTGTTGCACATGCTGAGAT 58.768 42.857 5.31 0.00 42.66 2.75
429 444 3.410508 TGTTGTTGCACATGCTGAGATA 58.589 40.909 5.31 0.00 42.66 1.98
430 445 4.011698 TGTTGTTGCACATGCTGAGATAT 58.988 39.130 5.31 0.00 42.66 1.63
441 456 4.886496 TGCTGAGATATCATCTTCCCAG 57.114 45.455 5.32 2.18 40.38 4.45
449 464 6.809428 AGATATCATCTTCCCAGATAGTGGA 58.191 40.000 5.32 0.00 42.71 4.02
458 473 1.115467 CAGATAGTGGAGGGCGAGTT 58.885 55.000 0.00 0.00 0.00 3.01
463 478 3.706373 TGGAGGGCGAGTTGGAGC 61.706 66.667 0.00 0.00 0.00 4.70
469 484 1.598130 GGCGAGTTGGAGCAACAGT 60.598 57.895 0.00 0.00 45.66 3.55
482 497 6.116806 TGGAGCAACAGTTAGTTTGAAACTA 58.883 36.000 13.39 13.39 42.81 2.24
603 618 3.124921 CCTACCTGGCGCGGTTTG 61.125 66.667 12.38 6.30 38.49 2.93
617 632 3.546020 CGCGGTTTGCCTCATAGTATTTG 60.546 47.826 0.00 0.00 42.08 2.32
623 642 6.806739 GGTTTGCCTCATAGTATTTGTTGTTC 59.193 38.462 0.00 0.00 0.00 3.18
638 657 4.920376 TGTTGTTCTCTTTTGTGCTTAGC 58.080 39.130 0.00 0.00 0.00 3.09
695 731 5.105392 TCAAGAGGAGAAGATCTGAAGAAGC 60.105 44.000 0.00 0.00 0.00 3.86
726 1014 3.886324 AAAAAGGGTGTCACGGTGA 57.114 47.368 6.76 6.76 0.00 4.02
727 1015 2.358322 AAAAAGGGTGTCACGGTGAT 57.642 45.000 14.78 0.00 0.00 3.06
729 1017 3.495434 AAAAGGGTGTCACGGTGATAA 57.505 42.857 14.78 3.22 0.00 1.75
730 1018 2.467566 AAGGGTGTCACGGTGATAAC 57.532 50.000 14.78 14.26 0.00 1.89
731 1019 1.344065 AGGGTGTCACGGTGATAACA 58.656 50.000 21.93 10.58 25.54 2.41
732 1020 1.001633 AGGGTGTCACGGTGATAACAC 59.998 52.381 21.93 19.93 45.27 3.32
733 1021 1.001633 GGGTGTCACGGTGATAACACT 59.998 52.381 21.93 0.00 45.32 3.55
736 1024 3.243336 GTGTCACGGTGATAACACTCTC 58.757 50.000 14.78 0.00 45.32 3.20
739 1027 2.959275 CGGTGATAACACTCTCCGC 58.041 57.895 2.93 0.00 43.00 5.54
740 1028 0.527817 CGGTGATAACACTCTCCGCC 60.528 60.000 2.93 0.00 43.00 6.13
741 1029 0.535335 GGTGATAACACTCTCCGCCA 59.465 55.000 2.93 0.00 45.32 5.69
743 1031 2.474816 GTGATAACACTCTCCGCCATC 58.525 52.381 0.00 0.00 42.99 3.51
746 1034 2.961526 TAACACTCTCCGCCATCTTC 57.038 50.000 0.00 0.00 0.00 2.87
748 1036 0.820871 ACACTCTCCGCCATCTTCTC 59.179 55.000 0.00 0.00 0.00 2.87
749 1037 0.103937 CACTCTCCGCCATCTTCTCC 59.896 60.000 0.00 0.00 0.00 3.71
750 1038 0.324738 ACTCTCCGCCATCTTCTCCA 60.325 55.000 0.00 0.00 0.00 3.86
751 1039 0.826715 CTCTCCGCCATCTTCTCCAA 59.173 55.000 0.00 0.00 0.00 3.53
752 1040 0.826715 TCTCCGCCATCTTCTCCAAG 59.173 55.000 0.00 0.00 0.00 3.61
753 1041 0.179062 CTCCGCCATCTTCTCCAAGG 60.179 60.000 0.00 0.00 0.00 3.61
754 1042 1.153086 CCGCCATCTTCTCCAAGGG 60.153 63.158 0.00 0.00 0.00 3.95
755 1043 1.626356 CCGCCATCTTCTCCAAGGGA 61.626 60.000 0.00 0.00 0.00 4.20
765 1053 1.783071 CTCCAAGGGAGGGAGTACTC 58.217 60.000 14.87 14.87 45.43 2.59
766 1054 1.007238 CTCCAAGGGAGGGAGTACTCA 59.993 57.143 23.91 0.00 45.43 3.41
767 1055 1.651770 TCCAAGGGAGGGAGTACTCAT 59.348 52.381 23.91 12.09 39.27 2.90
768 1056 2.045885 TCCAAGGGAGGGAGTACTCATT 59.954 50.000 23.91 11.33 39.27 2.57
769 1057 2.846827 CCAAGGGAGGGAGTACTCATTT 59.153 50.000 23.91 8.80 39.27 2.32
770 1058 3.267031 CCAAGGGAGGGAGTACTCATTTT 59.733 47.826 23.91 6.32 39.27 1.82
771 1059 4.518249 CAAGGGAGGGAGTACTCATTTTC 58.482 47.826 23.91 14.05 39.27 2.29
772 1060 3.116174 AGGGAGGGAGTACTCATTTTCC 58.884 50.000 23.91 20.68 39.27 3.13
783 1104 7.086685 AGTACTCATTTTCCTTAACTCCCAA 57.913 36.000 0.00 0.00 0.00 4.12
787 1108 6.839134 ACTCATTTTCCTTAACTCCCAAGTTT 59.161 34.615 0.00 0.00 43.28 2.66
791 1112 6.459670 TTTCCTTAACTCCCAAGTTTCAAC 57.540 37.500 0.00 0.00 43.28 3.18
797 1118 5.993748 AACTCCCAAGTTTCAACAAGAAA 57.006 34.783 0.00 0.00 43.28 2.52
813 1134 5.449553 ACAAGAAAATGGTGAGGAGAAGTT 58.550 37.500 0.00 0.00 0.00 2.66
819 1140 6.396829 AAATGGTGAGGAGAAGTTTGAAAG 57.603 37.500 0.00 0.00 0.00 2.62
821 1142 4.199310 TGGTGAGGAGAAGTTTGAAAGTG 58.801 43.478 0.00 0.00 0.00 3.16
843 1164 8.224620 AGTGCCCCAAGATCTAAATAAGATAT 57.775 34.615 0.00 0.00 45.35 1.63
901 1517 5.528870 ACCTAAAATGAGCCAAGAAAAACG 58.471 37.500 0.00 0.00 0.00 3.60
913 1529 5.556947 GCCAAGAAAAACGCAATCAAAAGAG 60.557 40.000 0.00 0.00 0.00 2.85
952 1570 6.152831 ACGAGGAAATAATTAGGCAAAAAGCT 59.847 34.615 0.00 0.00 44.79 3.74
954 1572 6.564328 AGGAAATAATTAGGCAAAAAGCTCG 58.436 36.000 0.00 0.00 44.79 5.03
1098 1725 4.078516 CCACGGACGGGAAGGGAC 62.079 72.222 0.00 0.00 0.00 4.46
1110 1740 1.229209 AAGGGACGGAGAAGGAGCA 60.229 57.895 0.00 0.00 0.00 4.26
1181 1811 0.250234 CCAACCGAGGATGCAGAGAA 59.750 55.000 0.00 0.00 0.00 2.87
1188 1818 3.388308 CGAGGATGCAGAGAACATAAGG 58.612 50.000 0.00 0.00 0.00 2.69
1197 1827 5.178797 GCAGAGAACATAAGGAAAGCAGTA 58.821 41.667 0.00 0.00 0.00 2.74
1208 1838 4.386711 AGGAAAGCAGTACAAGGTACAAC 58.613 43.478 9.01 1.01 0.00 3.32
1209 1847 4.131596 GGAAAGCAGTACAAGGTACAACA 58.868 43.478 9.01 0.00 0.00 3.33
1249 1888 3.740115 GTTTTTGTAGCTCTCCTGGTCA 58.260 45.455 0.00 0.00 0.00 4.02
1254 1893 2.501723 TGTAGCTCTCCTGGTCAATTCC 59.498 50.000 0.00 0.00 0.00 3.01
1259 1898 3.812167 GCTCTCCTGGTCAATTCCTTTGT 60.812 47.826 0.00 0.00 36.65 2.83
1269 1908 1.915141 ATTCCTTTGTGAGGTGGCTG 58.085 50.000 0.00 0.00 46.39 4.85
1270 1909 0.823356 TTCCTTTGTGAGGTGGCTGC 60.823 55.000 0.00 0.00 46.39 5.25
1271 1910 1.228367 CCTTTGTGAGGTGGCTGCT 60.228 57.895 0.00 0.00 40.95 4.24
1272 1911 1.521450 CCTTTGTGAGGTGGCTGCTG 61.521 60.000 0.00 0.00 40.95 4.41
1273 1912 0.820891 CTTTGTGAGGTGGCTGCTGT 60.821 55.000 0.00 0.00 0.00 4.40
1274 1913 0.395586 TTTGTGAGGTGGCTGCTGTT 60.396 50.000 0.00 0.00 0.00 3.16
1275 1914 0.819259 TTGTGAGGTGGCTGCTGTTC 60.819 55.000 0.00 0.00 0.00 3.18
1276 1915 1.227943 GTGAGGTGGCTGCTGTTCA 60.228 57.895 0.00 0.00 0.00 3.18
1300 1939 8.300286 TCAAGTCTGTTTTGTTGTTGTCATTTA 58.700 29.630 0.00 0.00 0.00 1.40
1347 1994 3.826157 GGGACAATGATTGTTCTTGGTGA 59.174 43.478 15.67 0.00 45.52 4.02
1377 2024 2.171237 TGCCAGTAGGAGTCCATTGATG 59.829 50.000 12.86 2.58 36.89 3.07
1428 2077 7.187480 CGAGAAGAATCTGTACTGAAATCGTA 58.813 38.462 6.54 0.00 35.54 3.43
1562 2211 4.069232 CTCCTCCGCACGCTCCAA 62.069 66.667 0.00 0.00 0.00 3.53
1612 2264 9.058925 GGTAATATACACCTTCACCTCCATGGT 62.059 44.444 12.58 0.00 40.42 3.55
1674 2340 1.737735 CTCCATGTCTGCGCGTTGA 60.738 57.895 8.43 3.17 0.00 3.18
1682 2348 1.446792 CTGCGCGTTGATCTGGTCT 60.447 57.895 8.43 0.00 0.00 3.85
1862 2530 2.210711 GGCCTACTGCTCCGCCTAT 61.211 63.158 0.00 0.00 40.92 2.57
1910 2578 1.142748 CTGCCCGCTCTACAAGGAG 59.857 63.158 0.00 0.00 36.50 3.69
1955 2623 2.158842 CCGATCTTGGCATTCTCCTTCT 60.159 50.000 0.00 0.00 0.00 2.85
1995 2663 3.501950 GTTAATTTCTTGCTCTTGCCGG 58.498 45.455 0.00 0.00 38.71 6.13
1997 2665 1.168714 ATTTCTTGCTCTTGCCGGTC 58.831 50.000 1.90 0.00 38.71 4.79
2000 2679 1.302033 CTTGCTCTTGCCGGTCAGT 60.302 57.895 1.90 0.00 38.71 3.41
2017 2700 1.390123 CAGTTGAGCGTTCGTGTATGG 59.610 52.381 0.00 0.00 0.00 2.74
2018 2701 0.094730 GTTGAGCGTTCGTGTATGGC 59.905 55.000 0.00 0.00 0.00 4.40
2056 2739 4.111016 TGGTGAGCTCGTACCGCG 62.111 66.667 16.22 0.00 39.87 6.46
2253 2936 3.875727 CCATCGACGAGGTCTACTTTCTA 59.124 47.826 8.86 0.00 0.00 2.10
2278 2961 5.407502 GGCGCCATTATTTTTCTACAGTTT 58.592 37.500 24.80 0.00 0.00 2.66
2301 2985 4.897025 AAAAACCCGAACACACGAAATA 57.103 36.364 0.00 0.00 35.09 1.40
2309 2993 5.121142 CCCGAACACACGAAATAAACACTAT 59.879 40.000 0.00 0.00 35.09 2.12
2338 3022 1.263776 TTTTATGCGCCGCAAATTCG 58.736 45.000 18.69 0.00 43.62 3.34
2353 3037 1.961180 ATTCGCAGGTTCTCGAGGGG 61.961 60.000 13.56 4.46 36.02 4.79
2442 3126 0.032130 TTCGCAGAGGTGACACTCAC 59.968 55.000 5.39 0.00 46.23 3.51
2466 3150 1.377333 GACTCCGCCTTTTCCAGGG 60.377 63.158 0.00 0.00 44.16 4.45
2481 3165 1.517242 CAGGGTGCTTCTGTTCTGAC 58.483 55.000 0.00 0.00 0.00 3.51
2487 3171 2.473235 GTGCTTCTGTTCTGACGTTCTC 59.527 50.000 0.00 0.00 0.00 2.87
2522 3206 2.060383 CCAGGTGATCCGGAGCTCA 61.060 63.158 22.18 12.75 39.05 4.26
2746 3430 1.134699 CAAGCTCGGAGGATGCAGTTA 60.135 52.381 7.20 0.00 0.00 2.24
2775 3506 3.059051 GCTACTTAGACCGTTCGATCGAT 60.059 47.826 20.18 3.14 0.00 3.59
2786 3517 1.102978 TCGATCGATCAGAGTGGCAA 58.897 50.000 24.40 0.00 0.00 4.52
2791 3522 1.827344 TCGATCAGAGTGGCAATGTCT 59.173 47.619 0.00 0.00 0.00 3.41
2816 3553 8.631480 TTGTGTACAATCTAGAGAGTGAAGTA 57.369 34.615 13.53 0.00 42.16 2.24
2817 3554 8.041829 TGTGTACAATCTAGAGAGTGAAGTAC 57.958 38.462 13.53 6.63 42.16 2.73
2826 3563 5.615925 AGAGAGTGAAGTACTTGGTGTTT 57.384 39.130 14.14 0.00 40.53 2.83
2840 3577 4.839668 TGGTGTTTTGAAATAAGACCCG 57.160 40.909 0.00 0.00 37.95 5.28
2864 3601 7.279090 CCGTGACAGTTCATTTATTGGTGTATA 59.721 37.037 0.00 0.00 33.11 1.47
2884 3621 6.866770 TGTATACAGCACTAGTTTGAGACAAC 59.133 38.462 0.08 0.00 0.00 3.32
2896 3636 5.011329 AGTTTGAGACAACGGTACTTCCATA 59.989 40.000 0.00 0.00 35.57 2.74
2919 3661 9.533983 CATAACGATTTGATTTATCCGAAGATG 57.466 33.333 0.00 0.00 33.67 2.90
2984 3726 2.540361 GCGGCGATTCGACTCTAAGTAA 60.540 50.000 12.98 0.00 29.68 2.24
2996 3738 5.116680 CGACTCTAAGTAAAACACAGAACGG 59.883 44.000 0.00 0.00 0.00 4.44
3008 3750 0.455633 CAGAACGGACGGTAGAACGG 60.456 60.000 0.00 0.00 38.39 4.44
3034 3776 5.181245 AGAACCAAACACACATCCTATTTCG 59.819 40.000 0.00 0.00 0.00 3.46
3051 3793 2.904866 GTCAACAGGCGGGTGCAA 60.905 61.111 0.00 0.00 45.35 4.08
3090 3832 4.783621 GCAGCTGCGATCCCACCA 62.784 66.667 25.23 0.00 0.00 4.17
3105 3847 2.159000 CCCACCAACGATAAGTCCTACC 60.159 54.545 0.00 0.00 0.00 3.18
3153 3895 0.603707 CACCATCTGCACGGAACAGT 60.604 55.000 0.00 0.00 36.50 3.55
3166 3908 3.068307 ACGGAACAGTGCTATCAGTATCC 59.932 47.826 0.00 0.00 32.01 2.59
3237 4029 0.588252 GCGCACTGTTGTCACTTCAT 59.412 50.000 0.30 0.00 0.00 2.57
3283 4153 7.912056 TTTCTACTGAGAATTGAGGAACATG 57.088 36.000 0.00 0.00 41.40 3.21
3332 4202 9.408069 GAATCGTAGAAAAGTATGGTCGATTAT 57.592 33.333 8.92 0.00 43.38 1.28
3465 4390 7.230712 GGGGAATTTATGTTCAACTAGTATGGG 59.769 40.741 0.00 0.00 0.00 4.00
3492 4417 5.983333 AAAGATGATGGTCCCAGATTACT 57.017 39.130 0.00 0.00 0.00 2.24
3532 4457 8.417273 AAAACATATGCACTTATATTACCCCC 57.583 34.615 1.58 0.00 0.00 5.40
3642 4572 1.959985 ACATGTCCGGCACAAAAATGA 59.040 42.857 10.17 0.00 38.97 2.57
3655 4585 6.654582 GGCACAAAAATGATACTTGGGAATTT 59.345 34.615 0.00 0.00 0.00 1.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 1.212229 GCAAGCTGCTTGGAAGAGC 59.788 57.895 35.43 21.03 41.31 4.09
8 9 1.174783 ATGCAAGCTGCTTGGAAGAG 58.825 50.000 34.40 14.57 44.25 2.85
9 10 1.271379 CAATGCAAGCTGCTTGGAAGA 59.729 47.619 34.40 9.80 44.25 2.87
10 11 1.671850 CCAATGCAAGCTGCTTGGAAG 60.672 52.381 34.40 28.10 45.71 3.46
11 12 0.319083 CCAATGCAAGCTGCTTGGAA 59.681 50.000 34.40 15.98 45.71 3.53
12 13 1.969085 CCAATGCAAGCTGCTTGGA 59.031 52.632 35.43 34.39 45.71 3.53
13 14 0.319083 TTCCAATGCAAGCTGCTTGG 59.681 50.000 35.43 23.73 44.98 3.61
14 15 1.425412 GTTCCAATGCAAGCTGCTTG 58.575 50.000 32.35 32.35 45.31 4.01
15 16 0.038892 CGTTCCAATGCAAGCTGCTT 60.039 50.000 9.53 9.53 45.31 3.91
16 17 0.890542 TCGTTCCAATGCAAGCTGCT 60.891 50.000 0.00 0.00 45.31 4.24
17 18 0.039256 TTCGTTCCAATGCAAGCTGC 60.039 50.000 0.00 0.00 45.29 5.25
18 19 1.267806 ACTTCGTTCCAATGCAAGCTG 59.732 47.619 0.00 0.00 0.00 4.24
19 20 1.267806 CACTTCGTTCCAATGCAAGCT 59.732 47.619 0.00 0.00 0.00 3.74
20 21 1.001378 ACACTTCGTTCCAATGCAAGC 60.001 47.619 0.00 0.00 0.00 4.01
21 22 2.605338 CCACACTTCGTTCCAATGCAAG 60.605 50.000 0.00 0.00 0.00 4.01
22 23 1.336440 CCACACTTCGTTCCAATGCAA 59.664 47.619 0.00 0.00 0.00 4.08
23 24 0.950836 CCACACTTCGTTCCAATGCA 59.049 50.000 0.00 0.00 0.00 3.96
24 25 0.240945 CCCACACTTCGTTCCAATGC 59.759 55.000 0.00 0.00 0.00 3.56
25 26 1.604604 ACCCACACTTCGTTCCAATG 58.395 50.000 0.00 0.00 0.00 2.82
26 27 2.358322 AACCCACACTTCGTTCCAAT 57.642 45.000 0.00 0.00 0.00 3.16
27 28 2.018515 GAAACCCACACTTCGTTCCAA 58.981 47.619 0.00 0.00 0.00 3.53
28 29 1.065345 TGAAACCCACACTTCGTTCCA 60.065 47.619 0.00 0.00 0.00 3.53
29 30 1.332686 GTGAAACCCACACTTCGTTCC 59.667 52.381 0.00 0.00 45.03 3.62
30 31 1.004292 CGTGAAACCCACACTTCGTTC 60.004 52.381 0.00 0.00 45.98 3.95
31 32 1.011333 CGTGAAACCCACACTTCGTT 58.989 50.000 0.00 0.00 45.98 3.85
32 33 0.812412 CCGTGAAACCCACACTTCGT 60.812 55.000 0.00 0.00 45.98 3.85
33 34 0.531090 TCCGTGAAACCCACACTTCG 60.531 55.000 0.00 0.00 45.98 3.79
34 35 1.202604 TCTCCGTGAAACCCACACTTC 60.203 52.381 0.00 0.00 45.98 3.01
61 62 5.647225 TCACAAAGCATTTCAAAGCCTTTTT 59.353 32.000 0.00 0.00 35.03 1.94
83 84 3.489355 AGTGAGAACATGCCACATTTCA 58.511 40.909 0.00 0.00 33.53 2.69
103 104 1.537202 CCCGGTTCAAAAGCTGAGAAG 59.463 52.381 0.00 0.00 34.81 2.85
104 105 1.604604 CCCGGTTCAAAAGCTGAGAA 58.395 50.000 0.00 0.00 34.81 2.87
106 107 1.581447 GCCCGGTTCAAAAGCTGAG 59.419 57.895 0.00 0.00 34.81 3.35
109 110 3.670377 GCGCCCGGTTCAAAAGCT 61.670 61.111 0.00 0.00 0.00 3.74
110 111 3.281359 ATGCGCCCGGTTCAAAAGC 62.281 57.895 4.18 0.00 0.00 3.51
111 112 1.444212 CATGCGCCCGGTTCAAAAG 60.444 57.895 4.18 0.00 0.00 2.27
112 113 2.647875 CATGCGCCCGGTTCAAAA 59.352 55.556 4.18 0.00 0.00 2.44
113 114 3.369400 CCATGCGCCCGGTTCAAA 61.369 61.111 4.18 0.00 0.00 2.69
114 115 3.851897 TTCCATGCGCCCGGTTCAA 62.852 57.895 4.18 0.00 0.00 2.69
115 116 4.337177 TTCCATGCGCCCGGTTCA 62.337 61.111 4.18 0.00 0.00 3.18
116 117 3.810896 GTTCCATGCGCCCGGTTC 61.811 66.667 4.18 0.00 0.00 3.62
157 159 4.508662 AGATAAACTGAAGAGCCTTTCGG 58.491 43.478 5.35 5.35 38.99 4.30
158 160 5.163814 CCAAGATAAACTGAAGAGCCTTTCG 60.164 44.000 0.00 0.00 0.00 3.46
184 186 2.180276 AGAACTAGAAGCGTCATGGGT 58.820 47.619 1.61 0.00 0.00 4.51
212 214 4.491676 CTCACGCTTTACTACTTTAGCCA 58.508 43.478 0.00 0.00 0.00 4.75
338 353 3.538634 TCAGACATTCTCATGCTGGAG 57.461 47.619 0.00 0.00 36.22 3.86
424 439 6.894654 TCCACTATCTGGGAAGATGATATCTC 59.105 42.308 3.98 0.00 41.06 2.75
425 440 6.809428 TCCACTATCTGGGAAGATGATATCT 58.191 40.000 3.98 0.00 41.06 1.98
426 441 6.098124 CCTCCACTATCTGGGAAGATGATATC 59.902 46.154 0.00 0.00 41.06 1.63
427 442 5.963253 CCTCCACTATCTGGGAAGATGATAT 59.037 44.000 0.00 0.00 41.06 1.63
428 443 5.336945 CCTCCACTATCTGGGAAGATGATA 58.663 45.833 0.00 0.00 41.06 2.15
429 444 4.166539 CCTCCACTATCTGGGAAGATGAT 58.833 47.826 0.00 0.00 41.06 2.45
430 445 3.581101 CCTCCACTATCTGGGAAGATGA 58.419 50.000 0.00 0.00 41.06 2.92
441 456 0.105039 CCAACTCGCCCTCCACTATC 59.895 60.000 0.00 0.00 0.00 2.08
449 464 2.032681 GTTGCTCCAACTCGCCCT 59.967 61.111 1.09 0.00 40.73 5.19
453 468 2.755650 ACTAACTGTTGCTCCAACTCG 58.244 47.619 2.69 3.81 43.85 4.18
458 473 4.947388 AGTTTCAAACTAACTGTTGCTCCA 59.053 37.500 0.00 0.00 40.69 3.86
482 497 8.235230 TCCTCTACACTATCTATTCCCATCTTT 58.765 37.037 0.00 0.00 0.00 2.52
483 498 7.770662 TCCTCTACACTATCTATTCCCATCTT 58.229 38.462 0.00 0.00 0.00 2.40
487 502 6.781857 TCTCCTCTACACTATCTATTCCCA 57.218 41.667 0.00 0.00 0.00 4.37
488 503 8.658840 ATTTCTCCTCTACACTATCTATTCCC 57.341 38.462 0.00 0.00 0.00 3.97
502 517 7.523873 CGCCTTGATGTACATATTTCTCCTCTA 60.524 40.741 8.71 0.00 0.00 2.43
515 530 0.899019 TACAGGCGCCTTGATGTACA 59.101 50.000 30.60 5.48 0.00 2.90
516 531 1.571919 CTACAGGCGCCTTGATGTAC 58.428 55.000 30.60 0.00 0.00 2.90
518 533 1.450312 GCTACAGGCGCCTTGATGT 60.450 57.895 30.60 24.90 0.00 3.06
599 614 7.593825 AGAACAACAAATACTATGAGGCAAAC 58.406 34.615 0.00 0.00 0.00 2.93
603 618 7.617041 AAGAGAACAACAAATACTATGAGGC 57.383 36.000 0.00 0.00 0.00 4.70
608 623 8.850156 AGCACAAAAGAGAACAACAAATACTAT 58.150 29.630 0.00 0.00 0.00 2.12
609 624 8.220755 AGCACAAAAGAGAACAACAAATACTA 57.779 30.769 0.00 0.00 0.00 1.82
610 625 7.100458 AGCACAAAAGAGAACAACAAATACT 57.900 32.000 0.00 0.00 0.00 2.12
617 632 4.972440 CAGCTAAGCACAAAAGAGAACAAC 59.028 41.667 0.00 0.00 0.00 3.32
623 642 2.351157 GCACCAGCTAAGCACAAAAGAG 60.351 50.000 0.00 0.00 37.91 2.85
638 657 2.426738 TCCTTCAAAAACAGTGCACCAG 59.573 45.455 14.63 9.45 0.00 4.00
670 690 6.528537 TTCTTCAGATCTTCTCCTCTTGAG 57.471 41.667 0.00 0.00 42.90 3.02
672 692 5.111293 GCTTCTTCAGATCTTCTCCTCTTG 58.889 45.833 0.00 0.00 0.00 3.02
673 693 4.776837 TGCTTCTTCAGATCTTCTCCTCTT 59.223 41.667 0.00 0.00 0.00 2.85
677 713 5.021033 TCATGCTTCTTCAGATCTTCTCC 57.979 43.478 0.00 0.00 0.00 3.71
682 718 5.944599 ACATGTTTCATGCTTCTTCAGATCT 59.055 36.000 9.27 0.00 0.00 2.75
684 720 7.692460 TTACATGTTTCATGCTTCTTCAGAT 57.308 32.000 2.30 0.00 0.00 2.90
686 722 8.578308 TTTTTACATGTTTCATGCTTCTTCAG 57.422 30.769 2.30 0.00 0.00 3.02
713 1001 1.001633 AGTGTTATCACCGTGACACCC 59.998 52.381 14.98 3.59 44.83 4.61
714 1002 2.029290 AGAGTGTTATCACCGTGACACC 60.029 50.000 14.98 9.08 44.83 4.16
715 1003 3.243336 GAGAGTGTTATCACCGTGACAC 58.757 50.000 2.57 8.49 44.83 3.67
716 1004 2.230508 GGAGAGTGTTATCACCGTGACA 59.769 50.000 2.57 0.00 44.83 3.58
719 1007 1.909376 CGGAGAGTGTTATCACCGTG 58.091 55.000 4.70 0.00 45.04 4.94
722 1010 0.535335 TGGCGGAGAGTGTTATCACC 59.465 55.000 0.18 0.00 44.83 4.02
723 1011 2.101582 AGATGGCGGAGAGTGTTATCAC 59.898 50.000 0.00 0.00 44.15 3.06
724 1012 2.388735 AGATGGCGGAGAGTGTTATCA 58.611 47.619 0.00 0.00 0.00 2.15
725 1013 3.068873 AGAAGATGGCGGAGAGTGTTATC 59.931 47.826 0.00 0.00 0.00 1.75
726 1014 3.034635 AGAAGATGGCGGAGAGTGTTAT 58.965 45.455 0.00 0.00 0.00 1.89
727 1015 2.427453 GAGAAGATGGCGGAGAGTGTTA 59.573 50.000 0.00 0.00 0.00 2.41
729 1017 0.820871 GAGAAGATGGCGGAGAGTGT 59.179 55.000 0.00 0.00 0.00 3.55
730 1018 0.103937 GGAGAAGATGGCGGAGAGTG 59.896 60.000 0.00 0.00 0.00 3.51
731 1019 0.324738 TGGAGAAGATGGCGGAGAGT 60.325 55.000 0.00 0.00 0.00 3.24
732 1020 0.826715 TTGGAGAAGATGGCGGAGAG 59.173 55.000 0.00 0.00 0.00 3.20
733 1021 0.826715 CTTGGAGAAGATGGCGGAGA 59.173 55.000 0.00 0.00 0.00 3.71
736 1024 1.153086 CCCTTGGAGAAGATGGCGG 60.153 63.158 0.00 0.00 0.00 6.13
748 1036 2.182516 ATGAGTACTCCCTCCCTTGG 57.817 55.000 20.11 0.00 0.00 3.61
749 1037 4.518249 GAAAATGAGTACTCCCTCCCTTG 58.482 47.826 20.11 0.00 0.00 3.61
750 1038 3.523972 GGAAAATGAGTACTCCCTCCCTT 59.476 47.826 20.11 5.14 0.00 3.95
751 1039 3.116174 GGAAAATGAGTACTCCCTCCCT 58.884 50.000 20.11 0.00 0.00 4.20
752 1040 3.116174 AGGAAAATGAGTACTCCCTCCC 58.884 50.000 20.11 13.74 0.00 4.30
753 1041 4.846168 AAGGAAAATGAGTACTCCCTCC 57.154 45.455 20.11 17.82 0.00 4.30
754 1042 6.948589 AGTTAAGGAAAATGAGTACTCCCTC 58.051 40.000 20.11 10.48 0.00 4.30
755 1043 6.070136 GGAGTTAAGGAAAATGAGTACTCCCT 60.070 42.308 20.11 15.02 42.81 4.20
756 1044 6.114089 GGAGTTAAGGAAAATGAGTACTCCC 58.886 44.000 20.11 13.01 42.81 4.30
757 1045 6.114089 GGGAGTTAAGGAAAATGAGTACTCC 58.886 44.000 20.11 0.00 46.08 3.85
758 1046 6.708285 TGGGAGTTAAGGAAAATGAGTACTC 58.292 40.000 16.32 16.32 0.00 2.59
759 1047 6.697641 TGGGAGTTAAGGAAAATGAGTACT 57.302 37.500 0.00 0.00 0.00 2.73
760 1048 6.940867 ACTTGGGAGTTAAGGAAAATGAGTAC 59.059 38.462 0.00 0.00 29.87 2.73
761 1049 7.086685 ACTTGGGAGTTAAGGAAAATGAGTA 57.913 36.000 0.00 0.00 29.87 2.59
762 1050 5.953571 ACTTGGGAGTTAAGGAAAATGAGT 58.046 37.500 0.00 0.00 29.87 3.41
763 1051 6.901081 AACTTGGGAGTTAAGGAAAATGAG 57.099 37.500 0.00 0.00 44.13 2.90
764 1052 6.836527 TGAAACTTGGGAGTTAAGGAAAATGA 59.163 34.615 0.00 0.00 45.18 2.57
765 1053 7.049799 TGAAACTTGGGAGTTAAGGAAAATG 57.950 36.000 0.00 0.00 45.18 2.32
766 1054 7.125053 TGTTGAAACTTGGGAGTTAAGGAAAAT 59.875 33.333 0.00 0.00 45.18 1.82
767 1055 6.437793 TGTTGAAACTTGGGAGTTAAGGAAAA 59.562 34.615 0.00 0.00 45.18 2.29
768 1056 5.952947 TGTTGAAACTTGGGAGTTAAGGAAA 59.047 36.000 0.00 0.00 45.18 3.13
769 1057 5.511363 TGTTGAAACTTGGGAGTTAAGGAA 58.489 37.500 0.00 0.00 45.18 3.36
770 1058 5.118729 TGTTGAAACTTGGGAGTTAAGGA 57.881 39.130 0.00 0.00 45.18 3.36
771 1059 5.592688 TCTTGTTGAAACTTGGGAGTTAAGG 59.407 40.000 0.00 0.00 45.18 2.69
772 1060 6.693315 TCTTGTTGAAACTTGGGAGTTAAG 57.307 37.500 0.00 0.00 45.18 1.85
783 1104 5.656416 TCCTCACCATTTTCTTGTTGAAACT 59.344 36.000 0.00 0.00 43.55 2.66
787 1108 5.047566 TCTCCTCACCATTTTCTTGTTGA 57.952 39.130 0.00 0.00 0.00 3.18
791 1112 6.039717 TCAAACTTCTCCTCACCATTTTCTTG 59.960 38.462 0.00 0.00 0.00 3.02
797 1118 5.300286 CACTTTCAAACTTCTCCTCACCATT 59.700 40.000 0.00 0.00 0.00 3.16
813 1134 2.978156 AGATCTTGGGGCACTTTCAA 57.022 45.000 0.00 0.00 0.00 2.69
819 1140 8.734386 CAATATCTTATTTAGATCTTGGGGCAC 58.266 37.037 0.00 0.00 42.69 5.01
821 1142 8.870075 ACAATATCTTATTTAGATCTTGGGGC 57.130 34.615 0.00 0.00 45.11 5.80
846 1167 8.890718 GTCATGAGTCACTGTACTTATGTAGTA 58.109 37.037 0.00 0.00 41.68 1.82
848 1169 7.990917 AGTCATGAGTCACTGTACTTATGTAG 58.009 38.462 0.00 0.00 41.68 2.74
849 1170 7.939784 AGTCATGAGTCACTGTACTTATGTA 57.060 36.000 0.00 0.00 41.68 2.29
850 1171 6.842437 AGTCATGAGTCACTGTACTTATGT 57.158 37.500 0.00 0.00 41.68 2.29
851 1172 8.678199 TCTTAGTCATGAGTCACTGTACTTATG 58.322 37.037 6.25 11.98 42.09 1.90
852 1173 8.809468 TCTTAGTCATGAGTCACTGTACTTAT 57.191 34.615 6.25 0.00 0.00 1.73
901 1517 1.067199 CGCGTGCCTCTTTTGATTGC 61.067 55.000 0.00 0.00 0.00 3.56
954 1572 2.126850 GAAAGCTTCGCCGGCAAC 60.127 61.111 28.98 12.23 0.00 4.17
1098 1725 1.446272 GGTTCGTGCTCCTTCTCCG 60.446 63.158 0.00 0.00 0.00 4.63
1110 1740 2.610859 ATGGGGCTGAGGGTTCGT 60.611 61.111 0.00 0.00 0.00 3.85
1156 1786 1.910580 GCATCCTCGGTTGGGGAAGA 61.911 60.000 0.00 0.00 35.08 2.87
1181 1811 5.242795 ACCTTGTACTGCTTTCCTTATGT 57.757 39.130 0.00 0.00 0.00 2.29
1188 1818 5.744666 TTGTTGTACCTTGTACTGCTTTC 57.255 39.130 6.02 0.00 0.00 2.62
1197 1827 7.346751 ACTTGATTGAATTGTTGTACCTTGT 57.653 32.000 0.00 0.00 0.00 3.16
1225 1863 3.181458 ACCAGGAGAGCTACAAAAACGAA 60.181 43.478 0.00 0.00 0.00 3.85
1254 1893 0.820891 ACAGCAGCCACCTCACAAAG 60.821 55.000 0.00 0.00 0.00 2.77
1259 1898 0.535780 CTTGAACAGCAGCCACCTCA 60.536 55.000 0.00 0.00 0.00 3.86
1263 1902 0.590195 CAGACTTGAACAGCAGCCAC 59.410 55.000 0.00 0.00 0.00 5.01
1269 1908 4.485163 ACAACAAAACAGACTTGAACAGC 58.515 39.130 0.00 0.00 0.00 4.40
1270 1909 5.920273 ACAACAACAAAACAGACTTGAACAG 59.080 36.000 0.00 0.00 0.00 3.16
1271 1910 5.837437 ACAACAACAAAACAGACTTGAACA 58.163 33.333 0.00 0.00 0.00 3.18
1272 1911 5.918011 TGACAACAACAAAACAGACTTGAAC 59.082 36.000 0.00 0.00 0.00 3.18
1273 1912 6.078202 TGACAACAACAAAACAGACTTGAA 57.922 33.333 0.00 0.00 0.00 2.69
1274 1913 5.697473 TGACAACAACAAAACAGACTTGA 57.303 34.783 0.00 0.00 0.00 3.02
1275 1914 6.949578 AATGACAACAACAAAACAGACTTG 57.050 33.333 0.00 0.00 0.00 3.16
1276 1915 9.482627 TTTAAATGACAACAACAAAACAGACTT 57.517 25.926 0.00 0.00 0.00 3.01
1307 1946 2.524440 TCCCAATCTCTCTACCCTCCAT 59.476 50.000 0.00 0.00 0.00 3.41
1315 1954 6.566079 ACAATCATTGTCCCAATCTCTCTA 57.434 37.500 0.00 0.00 40.56 2.43
1318 1957 5.824421 AGAACAATCATTGTCCCAATCTCT 58.176 37.500 2.74 0.00 44.59 3.10
1322 1969 4.840115 ACCAAGAACAATCATTGTCCCAAT 59.160 37.500 2.74 0.00 44.59 3.16
1347 1994 2.639839 ACTCCTACTGGCAATCACTTGT 59.360 45.455 0.00 0.00 34.69 3.16
1377 2024 4.180057 TGGAGCAAAAACAACAACATCAC 58.820 39.130 0.00 0.00 0.00 3.06
1428 2077 1.079073 CCCACCCTGCCCATTTCTT 59.921 57.895 0.00 0.00 0.00 2.52
1562 2211 2.036414 TGGCTGGAGAGCTCGTCT 59.964 61.111 8.37 0.00 45.44 4.18
1612 2264 1.898154 GAAGCTAGGAGGTCGCCAA 59.102 57.895 0.00 0.00 0.00 4.52
1613 2265 2.415608 CGAAGCTAGGAGGTCGCCA 61.416 63.158 0.00 0.00 0.00 5.69
1618 2270 0.896226 GGACAACGAAGCTAGGAGGT 59.104 55.000 0.00 0.00 0.00 3.85
1674 2340 0.911525 CCCTGACCACCAGACCAGAT 60.912 60.000 0.00 0.00 45.78 2.90
1754 2422 2.124942 CCGCCCTTCTTCCTGAGC 60.125 66.667 0.00 0.00 0.00 4.26
1910 2578 3.066814 CTTGCCTGCTTGAGGGGC 61.067 66.667 0.00 0.00 43.07 5.80
1977 2645 1.541588 GACCGGCAAGAGCAAGAAATT 59.458 47.619 0.00 0.00 44.61 1.82
1995 2663 1.762419 TACACGAACGCTCAACTGAC 58.238 50.000 0.00 0.00 0.00 3.51
1997 2665 1.390123 CCATACACGAACGCTCAACTG 59.610 52.381 0.00 0.00 0.00 3.16
2000 2679 0.037697 AGCCATACACGAACGCTCAA 60.038 50.000 0.00 0.00 0.00 3.02
2017 2700 1.008079 GCACCAAGAACTGCACAGC 60.008 57.895 0.00 0.00 33.31 4.40
2018 2701 1.280746 CGCACCAAGAACTGCACAG 59.719 57.895 0.00 0.00 32.57 3.66
2253 2936 3.011119 TGTAGAAAAATAATGGCGCCGT 58.989 40.909 23.90 20.88 0.00 5.68
2287 2971 7.946043 ACTATAGTGTTTATTTCGTGTGTTCG 58.054 34.615 4.10 0.00 0.00 3.95
2309 2993 3.246699 GCGGCGCATAAAAACAGATACTA 59.753 43.478 29.21 0.00 0.00 1.82
2317 3001 2.531998 CGAATTTGCGGCGCATAAAAAC 60.532 45.455 36.69 21.65 38.76 2.43
2338 3022 0.179070 GATTCCCCTCGAGAACCTGC 60.179 60.000 15.71 0.00 0.00 4.85
2353 3037 1.059835 GAGAGCTTGTCGTTGCGATTC 59.940 52.381 0.00 0.00 38.42 2.52
2442 3126 0.875059 GAAAAGGCGGAGTCCACTTG 59.125 55.000 14.86 0.00 0.00 3.16
2447 3131 1.377333 CCTGGAAAAGGCGGAGTCC 60.377 63.158 0.00 0.00 39.93 3.85
2448 3132 1.377333 CCCTGGAAAAGGCGGAGTC 60.377 63.158 0.00 0.00 45.89 3.36
2449 3133 2.154074 ACCCTGGAAAAGGCGGAGT 61.154 57.895 0.00 0.00 45.89 3.85
2453 3137 1.866853 GAAGCACCCTGGAAAAGGCG 61.867 60.000 0.00 0.00 45.89 5.52
2454 3138 0.540597 AGAAGCACCCTGGAAAAGGC 60.541 55.000 0.00 0.00 45.89 4.35
2466 3150 2.473235 GAGAACGTCAGAACAGAAGCAC 59.527 50.000 0.00 0.00 0.00 4.40
2481 3165 3.805267 GCAGAGCCATGGAGAACG 58.195 61.111 18.40 0.00 0.00 3.95
2522 3206 2.203070 GTGCCGAGCCCGATGATT 60.203 61.111 0.00 0.00 38.22 2.57
2746 3430 4.387862 CGAACGGTCTAAGTAGCAAACATT 59.612 41.667 0.00 0.00 0.00 2.71
2775 3506 2.158769 ACACAAGACATTGCCACTCTGA 60.159 45.455 0.00 0.00 40.27 3.27
2786 3517 7.394641 TCACTCTCTAGATTGTACACAAGACAT 59.605 37.037 0.00 0.00 39.47 3.06
2791 3522 7.526142 ACTTCACTCTCTAGATTGTACACAA 57.474 36.000 0.00 0.00 40.51 3.33
2816 3553 5.221165 CGGGTCTTATTTCAAAACACCAAGT 60.221 40.000 0.00 0.00 0.00 3.16
2817 3554 5.219633 CGGGTCTTATTTCAAAACACCAAG 58.780 41.667 0.00 0.00 0.00 3.61
2826 3563 4.345859 ACTGTCACGGGTCTTATTTCAA 57.654 40.909 0.00 0.00 0.00 2.69
2840 3577 8.941977 TGTATACACCAATAAATGAACTGTCAC 58.058 33.333 0.08 0.00 36.31 3.67
2864 3601 3.123804 CGTTGTCTCAAACTAGTGCTGT 58.876 45.455 0.00 0.00 0.00 4.40
2884 3621 6.598753 AATCAAATCGTTATGGAAGTACCG 57.401 37.500 0.00 0.00 42.61 4.02
2896 3636 6.038161 TGCATCTTCGGATAAATCAAATCGTT 59.962 34.615 0.00 0.00 32.70 3.85
2919 3661 0.819259 ATGATACCATGGCACCGTGC 60.819 55.000 15.50 15.50 44.08 5.34
2984 3726 1.682854 TCTACCGTCCGTTCTGTGTTT 59.317 47.619 0.00 0.00 0.00 2.83
2996 3738 1.812571 TGGTTCTACCGTTCTACCGTC 59.187 52.381 0.00 0.00 42.58 4.79
3008 3750 7.448748 AAATAGGATGTGTGTTTGGTTCTAC 57.551 36.000 0.00 0.00 0.00 2.59
3034 3776 2.200170 GATTGCACCCGCCTGTTGAC 62.200 60.000 0.00 0.00 37.32 3.18
3051 3793 4.577875 CTCTTGCAAGGAAGAAGTGAGAT 58.422 43.478 25.73 0.00 31.52 2.75
3090 3832 2.097825 ACTGCGGTAGGACTTATCGTT 58.902 47.619 0.00 0.00 38.17 3.85
3129 3871 0.108186 TCCGTGCAGATGGTGTGATC 60.108 55.000 0.00 0.00 0.00 2.92
3153 3895 2.820197 CTGGCTACGGATACTGATAGCA 59.180 50.000 4.65 0.00 41.52 3.49
3465 4390 9.606631 GTAATCTGGGACCATCATCTTTATATC 57.393 37.037 0.00 0.00 0.00 1.63
3492 4417 8.417106 TGCATATGTTTTTCAACTGTTTAAGGA 58.583 29.630 4.29 0.00 33.58 3.36
3642 4572 3.448660 GCTTGAGCCAAATTCCCAAGTAT 59.551 43.478 0.00 0.00 37.23 2.12
3675 4605 4.320494 CCTTGTGTGCTACTCCATTTCAAC 60.320 45.833 0.00 0.00 0.00 3.18


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

AutoCloner maintained by Alex Coulton.