Multiple sequence alignment - TraesCS7B01G445000

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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 TraesCS7B01G445000 chr7B 100.000 3805 0 0 1 3805 709096547 709092743 0.000000e+00 7027.0
1 TraesCS7B01G445000 chr7B 89.835 1456 107 24 1197 2636 709047977 709049407 0.000000e+00 1831.0
2 TraesCS7B01G445000 chr7D 92.205 2104 111 23 1112 3172 616009734 616007641 0.000000e+00 2928.0
3 TraesCS7B01G445000 chr7D 88.889 1476 122 28 1197 2657 615942051 615943499 0.000000e+00 1779.0
4 TraesCS7B01G445000 chr7D 87.591 411 24 13 3239 3627 616007467 616007062 5.800000e-123 451.0
5 TraesCS7B01G445000 chr7D 84.615 273 32 4 366 628 616010175 616009903 2.910000e-66 263.0
6 TraesCS7B01G445000 chr7D 96.226 53 1 1 964 1015 616009835 616009783 6.770000e-13 86.1
7 TraesCS7B01G445000 chr7A 87.351 2103 144 54 1105 3149 708785118 708783080 0.000000e+00 2298.0
8 TraesCS7B01G445000 chr7A 89.485 1455 102 27 1197 2636 708708261 708709679 0.000000e+00 1792.0
9 TraesCS7B01G445000 chr7A 85.809 303 30 4 321 622 708785883 708785593 3.690000e-80 309.0
10 TraesCS7B01G445000 chr7A 81.972 355 38 19 3239 3572 708781126 708780777 1.040000e-70 278.0
11 TraesCS7B01G445000 chr7A 84.100 239 25 6 18 255 708788437 708788211 6.400000e-53 219.0
12 TraesCS7B01G445000 chr7A 90.909 77 7 0 95 171 708805686 708805610 1.870000e-18 104.0
13 TraesCS7B01G445000 chr6D 84.615 91 12 2 3669 3758 434464374 434464285 5.240000e-14 89.8
14 TraesCS7B01G445000 chr6D 80.899 89 11 5 3674 3758 38894960 38895046 8.820000e-07 65.8
15 TraesCS7B01G445000 chr2D 83.908 87 13 1 3674 3759 201091969 201092055 8.760000e-12 82.4
16 TraesCS7B01G445000 chr6B 83.721 86 13 1 3674 3758 23449393 23449478 3.150000e-11 80.5
17 TraesCS7B01G445000 chr6B 80.233 86 16 1 3674 3758 6629453 6629368 3.170000e-06 63.9
18 TraesCS7B01G445000 chr2B 92.727 55 4 0 1788 1842 487211816 487211762 3.150000e-11 80.5
19 TraesCS7B01G445000 chr5D 94.118 51 3 0 2540 2590 406199405 406199455 1.130000e-10 78.7
20 TraesCS7B01G445000 chr2A 83.529 85 13 1 3674 3758 196518415 196518332 1.130000e-10 78.7
21 TraesCS7B01G445000 chr1D 84.146 82 11 2 3687 3766 233893316 233893235 1.130000e-10 78.7
22 TraesCS7B01G445000 chr4A 84.416 77 10 2 3679 3754 642955512 642955437 1.470000e-09 75.0
23 TraesCS7B01G445000 chr3D 82.353 85 14 1 3674 3758 415532814 415532731 5.270000e-09 73.1
24 TraesCS7B01G445000 chr5B 93.617 47 3 0 2540 2586 486897299 486897345 1.900000e-08 71.3
25 TraesCS7B01G445000 chr5A 96.970 33 1 0 1786 1818 624111471 624111503 5.310000e-04 56.5
26 TraesCS7B01G445000 chr4B 100.000 30 0 0 1787 1816 567002505 567002476 5.310000e-04 56.5


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 TraesCS7B01G445000 chr7B 709092743 709096547 3804 True 7027.000 7027 100.00000 1 3805 1 chr7B.!!$R1 3804
1 TraesCS7B01G445000 chr7B 709047977 709049407 1430 False 1831.000 1831 89.83500 1197 2636 1 chr7B.!!$F1 1439
2 TraesCS7B01G445000 chr7D 615942051 615943499 1448 False 1779.000 1779 88.88900 1197 2657 1 chr7D.!!$F1 1460
3 TraesCS7B01G445000 chr7D 616007062 616010175 3113 True 932.025 2928 90.15925 366 3627 4 chr7D.!!$R1 3261
4 TraesCS7B01G445000 chr7A 708708261 708709679 1418 False 1792.000 1792 89.48500 1197 2636 1 chr7A.!!$F1 1439
5 TraesCS7B01G445000 chr7A 708780777 708788437 7660 True 776.000 2298 84.80800 18 3572 4 chr7A.!!$R2 3554

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
76 77 0.108945 GAAGGAAGGCATTGTGCTGC 60.109 55.0 1.64 0.0 44.28 5.25 F
1026 3456 0.106819 TGCCGTAGTAGGAGGACCTC 60.107 60.0 13.60 13.6 46.43 3.85 F
2048 4519 0.099082 CCTTCTCGTACTGCCTCGTC 59.901 60.0 0.00 0.0 0.00 4.20 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1104 3534 0.324614 TTCGCCATGGCTGAGAAAGA 59.675 50.0 33.07 18.61 39.32 2.52 R
2155 4638 0.100146 GTAGTAGAAGGTGTCCGCCG 59.900 60.0 0.00 0.00 0.00 6.46 R
3713 8145 0.111878 CACGAACACACGCAACTACG 60.112 55.0 0.00 0.00 36.70 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
17 18 3.429141 TCGTCGACGAGGGCTCAC 61.429 66.667 34.97 0.00 44.22 3.51
18 19 4.477975 CGTCGACGAGGGCTCACC 62.478 72.222 33.35 0.00 43.02 4.02
27 28 4.436998 GGGCTCACCTGGACGTCG 62.437 72.222 9.92 0.00 35.85 5.12
30 31 4.778415 CTCACCTGGACGTCGCCG 62.778 72.222 9.92 1.00 40.83 6.46
63 64 4.157120 GCTAGCGGGCGGAAGGAA 62.157 66.667 0.00 0.00 0.00 3.36
64 65 2.107141 CTAGCGGGCGGAAGGAAG 59.893 66.667 0.00 0.00 0.00 3.46
65 66 3.447025 CTAGCGGGCGGAAGGAAGG 62.447 68.421 0.00 0.00 0.00 3.46
72 73 1.508088 GCGGAAGGAAGGCATTGTG 59.492 57.895 0.00 0.00 0.00 3.33
75 76 0.529378 GGAAGGAAGGCATTGTGCTG 59.471 55.000 1.64 0.00 44.28 4.41
76 77 0.108945 GAAGGAAGGCATTGTGCTGC 60.109 55.000 1.64 0.00 44.28 5.25
133 134 1.639298 CCAAAGGAAGAAGAGCCGCG 61.639 60.000 0.00 0.00 0.00 6.46
135 136 3.959991 AAGGAAGAAGAGCCGCGGC 62.960 63.158 42.34 42.34 42.33 6.53
166 167 3.135056 GATCGGACGACGGAAGGGG 62.135 68.421 0.00 0.00 44.45 4.79
170 171 1.143401 GGACGACGGAAGGGGATTC 59.857 63.158 0.00 0.00 37.17 2.52
171 172 1.610554 GGACGACGGAAGGGGATTCA 61.611 60.000 0.00 0.00 39.91 2.57
174 175 1.280998 ACGACGGAAGGGGATTCAATT 59.719 47.619 0.00 0.00 39.91 2.32
175 176 2.290705 ACGACGGAAGGGGATTCAATTT 60.291 45.455 0.00 0.00 39.91 1.82
176 177 3.054948 ACGACGGAAGGGGATTCAATTTA 60.055 43.478 0.00 0.00 39.91 1.40
177 178 3.560068 CGACGGAAGGGGATTCAATTTAG 59.440 47.826 0.00 0.00 39.91 1.85
178 179 3.883489 GACGGAAGGGGATTCAATTTAGG 59.117 47.826 0.00 0.00 39.91 2.69
179 180 3.526019 ACGGAAGGGGATTCAATTTAGGA 59.474 43.478 0.00 0.00 39.91 2.94
185 186 6.361304 AGGGGATTCAATTTAGGAAGGAAT 57.639 37.500 0.00 0.00 0.00 3.01
187 188 6.068260 AGGGGATTCAATTTAGGAAGGAATGA 60.068 38.462 0.00 0.00 0.00 2.57
188 189 6.611236 GGGGATTCAATTTAGGAAGGAATGAA 59.389 38.462 0.00 0.00 0.00 2.57
248 249 2.029073 CGTCCTGACTTGGCGTGT 59.971 61.111 0.00 0.00 0.00 4.49
299 2588 4.016790 TGCCCTGCTCCTCCTCCT 62.017 66.667 0.00 0.00 0.00 3.69
300 2589 3.160748 GCCCTGCTCCTCCTCCTC 61.161 72.222 0.00 0.00 0.00 3.71
301 2590 2.445654 CCCTGCTCCTCCTCCTCC 60.446 72.222 0.00 0.00 0.00 4.30
302 2591 2.445654 CCTGCTCCTCCTCCTCCC 60.446 72.222 0.00 0.00 0.00 4.30
303 2592 2.837291 CTGCTCCTCCTCCTCCCG 60.837 72.222 0.00 0.00 0.00 5.14
304 2593 4.465446 TGCTCCTCCTCCTCCCGG 62.465 72.222 0.00 0.00 0.00 5.73
307 2596 4.124943 TCCTCCTCCTCCCGGTCG 62.125 72.222 0.00 0.00 0.00 4.79
334 2623 2.851805 GGCATCCGAAATCCTTGAAC 57.148 50.000 0.00 0.00 0.00 3.18
335 2624 1.405463 GGCATCCGAAATCCTTGAACC 59.595 52.381 0.00 0.00 0.00 3.62
336 2625 2.369394 GCATCCGAAATCCTTGAACCT 58.631 47.619 0.00 0.00 0.00 3.50
342 2631 2.084546 GAAATCCTTGAACCTGACGGG 58.915 52.381 0.00 0.00 41.89 5.28
361 2650 3.174573 GCGCACGCAGCAAATTCC 61.175 61.111 10.65 0.00 46.13 3.01
473 2766 1.246056 TATATTCCTCCGGCCGGTCG 61.246 60.000 41.57 31.48 36.47 4.79
487 2780 0.448990 CGGTCGACGGTGATAGACAA 59.551 55.000 14.48 0.00 39.42 3.18
494 2787 2.915463 GACGGTGATAGACAAAGACGTG 59.085 50.000 0.00 0.00 33.09 4.49
498 2791 2.341760 GTGATAGACAAAGACGTGCGAC 59.658 50.000 0.00 0.00 0.00 5.19
539 2832 3.002348 CGTTTCGAGCTGTCTTTTCCTTT 59.998 43.478 0.00 0.00 0.00 3.11
545 2838 6.492254 TCGAGCTGTCTTTTCCTTTAAAAAC 58.508 36.000 0.00 0.00 36.64 2.43
547 2840 7.496591 TCGAGCTGTCTTTTCCTTTAAAAACTA 59.503 33.333 0.00 0.00 36.64 2.24
568 2867 2.567169 ACAGTTTGACTCGATCCATCCA 59.433 45.455 0.00 0.00 0.00 3.41
576 2875 0.839277 TCGATCCATCCATGCTTGGT 59.161 50.000 17.54 3.55 44.06 3.67
649 3031 0.796927 GCGTGCAAGTCTTTCCTACC 59.203 55.000 0.59 0.00 0.00 3.18
655 3037 2.673368 GCAAGTCTTTCCTACCATGACG 59.327 50.000 0.00 0.00 33.40 4.35
684 3067 4.579384 CCACGGGGTTGGTGCTGT 62.579 66.667 0.00 0.00 34.08 4.40
691 3074 2.345991 GTTGGTGCTGTCCGGCTA 59.654 61.111 0.00 0.00 0.00 3.93
694 3077 2.125512 GGTGCTGTCCGGCTAGTG 60.126 66.667 0.00 0.00 0.00 2.74
709 3092 0.457853 TAGTGAAGCCGCACGTCATC 60.458 55.000 0.00 0.00 43.42 2.92
717 3100 2.430146 CGCACGTCATCGCGTTACA 61.430 57.895 5.77 0.00 46.23 2.41
727 3110 3.107661 GCGTTACACCACGTCCCG 61.108 66.667 0.00 0.00 42.43 5.14
728 3111 2.431260 CGTTACACCACGTCCCGG 60.431 66.667 0.00 0.00 35.34 5.73
751 3134 0.385473 CGCAAATGGGTCGTCAACAC 60.385 55.000 0.00 0.00 0.00 3.32
773 3156 4.102996 ACCCAGGTCAAATGCTTTCAAAAT 59.897 37.500 0.00 0.00 0.00 1.82
774 3157 5.306678 ACCCAGGTCAAATGCTTTCAAAATA 59.693 36.000 0.00 0.00 0.00 1.40
775 3158 6.013466 ACCCAGGTCAAATGCTTTCAAAATAT 60.013 34.615 0.00 0.00 0.00 1.28
776 3159 6.880529 CCCAGGTCAAATGCTTTCAAAATATT 59.119 34.615 0.00 0.00 0.00 1.28
777 3160 7.064966 CCCAGGTCAAATGCTTTCAAAATATTC 59.935 37.037 0.00 0.00 0.00 1.75
778 3161 7.820872 CCAGGTCAAATGCTTTCAAAATATTCT 59.179 33.333 0.00 0.00 0.00 2.40
779 3162 8.653338 CAGGTCAAATGCTTTCAAAATATTCTG 58.347 33.333 0.00 0.00 0.00 3.02
780 3163 8.587608 AGGTCAAATGCTTTCAAAATATTCTGA 58.412 29.630 0.00 0.00 0.00 3.27
781 3164 9.206870 GGTCAAATGCTTTCAAAATATTCTGAA 57.793 29.630 0.00 0.00 0.00 3.02
809 3192 1.212935 ACTGTGCTCCCTTTGTTGAGT 59.787 47.619 0.00 0.00 0.00 3.41
815 3198 5.362430 TGTGCTCCCTTTGTTGAGTAAAAAT 59.638 36.000 0.00 0.00 0.00 1.82
816 3199 6.547880 TGTGCTCCCTTTGTTGAGTAAAAATA 59.452 34.615 0.00 0.00 0.00 1.40
819 3202 7.923878 TGCTCCCTTTGTTGAGTAAAAATAAAC 59.076 33.333 0.00 0.00 0.00 2.01
820 3203 8.141909 GCTCCCTTTGTTGAGTAAAAATAAACT 58.858 33.333 0.00 0.00 0.00 2.66
822 3205 8.973182 TCCCTTTGTTGAGTAAAAATAAACTGT 58.027 29.630 0.00 0.00 0.00 3.55
823 3206 9.030301 CCCTTTGTTGAGTAAAAATAAACTGTG 57.970 33.333 0.00 0.00 0.00 3.66
824 3207 9.581099 CCTTTGTTGAGTAAAAATAAACTGTGT 57.419 29.630 0.00 0.00 0.00 3.72
866 3249 5.499139 TTTTCCTCACTTTGTTGCTGTAG 57.501 39.130 0.00 0.00 0.00 2.74
868 3251 3.466836 TCCTCACTTTGTTGCTGTAGTG 58.533 45.455 0.00 0.00 39.41 2.74
909 3338 3.468007 CGCTCTCGCTGGTCAAAG 58.532 61.111 0.00 0.00 0.00 2.77
910 3339 2.734673 CGCTCTCGCTGGTCAAAGC 61.735 63.158 0.00 0.00 39.94 3.51
911 3340 1.669115 GCTCTCGCTGGTCAAAGCA 60.669 57.895 0.00 0.00 43.73 3.91
912 3341 1.633852 GCTCTCGCTGGTCAAAGCAG 61.634 60.000 1.88 1.88 45.86 4.24
933 3362 0.249911 AGAAGCTCTCCGCGTTGTTT 60.250 50.000 4.92 0.00 45.59 2.83
936 3365 0.249911 AGCTCTCCGCGTTGTTTCTT 60.250 50.000 4.92 0.00 45.59 2.52
937 3366 0.586802 GCTCTCCGCGTTGTTTCTTT 59.413 50.000 4.92 0.00 0.00 2.52
938 3367 1.398578 GCTCTCCGCGTTGTTTCTTTC 60.399 52.381 4.92 0.00 0.00 2.62
939 3368 2.135933 CTCTCCGCGTTGTTTCTTTCT 58.864 47.619 4.92 0.00 0.00 2.52
940 3369 2.132762 TCTCCGCGTTGTTTCTTTCTC 58.867 47.619 4.92 0.00 0.00 2.87
941 3370 1.194772 CTCCGCGTTGTTTCTTTCTCC 59.805 52.381 4.92 0.00 0.00 3.71
942 3371 0.941542 CCGCGTTGTTTCTTTCTCCA 59.058 50.000 4.92 0.00 0.00 3.86
944 3373 1.656429 CGCGTTGTTTCTTTCTCCACG 60.656 52.381 0.00 0.00 0.00 4.94
945 3374 1.333791 GCGTTGTTTCTTTCTCCACGG 60.334 52.381 0.00 0.00 0.00 4.94
946 3375 1.333791 CGTTGTTTCTTTCTCCACGGC 60.334 52.381 0.00 0.00 0.00 5.68
947 3376 1.673920 GTTGTTTCTTTCTCCACGGCA 59.326 47.619 0.00 0.00 0.00 5.69
948 3377 1.305201 TGTTTCTTTCTCCACGGCAC 58.695 50.000 0.00 0.00 0.00 5.01
1020 3450 2.722487 CGGCTGCCGTAGTAGGAG 59.278 66.667 31.72 1.11 42.73 3.69
1021 3451 2.846652 CGGCTGCCGTAGTAGGAGG 61.847 68.421 31.72 0.30 42.73 4.30
1022 3452 1.455217 GGCTGCCGTAGTAGGAGGA 60.455 63.158 1.35 0.00 0.00 3.71
1023 3453 1.734748 GCTGCCGTAGTAGGAGGAC 59.265 63.158 0.00 0.00 0.00 3.85
1024 3454 1.736365 GCTGCCGTAGTAGGAGGACC 61.736 65.000 0.00 0.00 0.00 4.46
1026 3456 0.106819 TGCCGTAGTAGGAGGACCTC 60.107 60.000 13.60 13.60 46.43 3.85
1027 3457 0.183252 GCCGTAGTAGGAGGACCTCT 59.817 60.000 20.97 9.69 46.43 3.69
1028 3458 1.970092 CCGTAGTAGGAGGACCTCTG 58.030 60.000 20.97 3.18 46.43 3.35
1029 3459 1.310904 CGTAGTAGGAGGACCTCTGC 58.689 60.000 20.97 10.51 46.43 4.26
1030 3460 1.134037 CGTAGTAGGAGGACCTCTGCT 60.134 57.143 20.97 16.38 46.43 4.24
1031 3461 2.578786 GTAGTAGGAGGACCTCTGCTC 58.421 57.143 20.97 4.44 46.43 4.26
1032 3462 1.003646 AGTAGGAGGACCTCTGCTCA 58.996 55.000 20.97 0.00 46.43 4.26
1033 3463 1.064017 AGTAGGAGGACCTCTGCTCAG 60.064 57.143 20.97 0.00 46.43 3.35
1034 3464 0.396417 TAGGAGGACCTCTGCTCAGC 60.396 60.000 20.97 2.59 46.43 4.26
1035 3465 1.685421 GGAGGACCTCTGCTCAGCT 60.685 63.158 20.97 0.00 36.59 4.24
1036 3466 1.675720 GGAGGACCTCTGCTCAGCTC 61.676 65.000 20.97 0.00 36.59 4.09
1037 3467 0.969917 GAGGACCTCTGCTCAGCTCA 60.970 60.000 14.72 0.00 34.98 4.26
1038 3468 1.217779 GGACCTCTGCTCAGCTCAC 59.782 63.158 0.00 0.00 0.00 3.51
1039 3469 1.217779 GACCTCTGCTCAGCTCACC 59.782 63.158 0.00 0.00 0.00 4.02
1040 3470 2.183811 CCTCTGCTCAGCTCACCG 59.816 66.667 0.00 0.00 0.00 4.94
1082 3512 3.756783 CGTCCTCCCTCCCTCCCT 61.757 72.222 0.00 0.00 0.00 4.20
1083 3513 2.284151 GTCCTCCCTCCCTCCCTC 59.716 72.222 0.00 0.00 0.00 4.30
1084 3514 2.133201 TCCTCCCTCCCTCCCTCT 59.867 66.667 0.00 0.00 0.00 3.69
1085 3515 2.015726 TCCTCCCTCCCTCCCTCTC 61.016 68.421 0.00 0.00 0.00 3.20
1086 3516 2.018086 CCTCCCTCCCTCCCTCTCT 61.018 68.421 0.00 0.00 0.00 3.10
1087 3517 1.541672 CTCCCTCCCTCCCTCTCTC 59.458 68.421 0.00 0.00 0.00 3.20
1088 3518 0.998945 CTCCCTCCCTCCCTCTCTCT 60.999 65.000 0.00 0.00 0.00 3.10
1089 3519 0.996762 TCCCTCCCTCCCTCTCTCTC 60.997 65.000 0.00 0.00 0.00 3.20
1090 3520 0.998945 CCCTCCCTCCCTCTCTCTCT 60.999 65.000 0.00 0.00 0.00 3.10
1091 3521 0.478507 CCTCCCTCCCTCTCTCTCTC 59.521 65.000 0.00 0.00 0.00 3.20
1092 3522 1.522900 CTCCCTCCCTCTCTCTCTCT 58.477 60.000 0.00 0.00 0.00 3.10
1093 3523 1.421646 CTCCCTCCCTCTCTCTCTCTC 59.578 61.905 0.00 0.00 0.00 3.20
1094 3524 1.010793 TCCCTCCCTCTCTCTCTCTCT 59.989 57.143 0.00 0.00 0.00 3.10
1095 3525 1.421646 CCCTCCCTCTCTCTCTCTCTC 59.578 61.905 0.00 0.00 0.00 3.20
1096 3526 2.412591 CCTCCCTCTCTCTCTCTCTCT 58.587 57.143 0.00 0.00 0.00 3.10
1097 3527 2.370189 CCTCCCTCTCTCTCTCTCTCTC 59.630 59.091 0.00 0.00 0.00 3.20
1098 3528 3.312890 CTCCCTCTCTCTCTCTCTCTCT 58.687 54.545 0.00 0.00 0.00 3.10
1099 3529 3.309296 TCCCTCTCTCTCTCTCTCTCTC 58.691 54.545 0.00 0.00 0.00 3.20
1100 3530 3.051803 TCCCTCTCTCTCTCTCTCTCTCT 60.052 52.174 0.00 0.00 0.00 3.10
1101 3531 3.323403 CCCTCTCTCTCTCTCTCTCTCTC 59.677 56.522 0.00 0.00 0.00 3.20
1102 3532 4.222336 CCTCTCTCTCTCTCTCTCTCTCT 58.778 52.174 0.00 0.00 0.00 3.10
1103 3533 5.389520 CCTCTCTCTCTCTCTCTCTCTCTA 58.610 50.000 0.00 0.00 0.00 2.43
1104 3534 6.015918 CCTCTCTCTCTCTCTCTCTCTCTAT 58.984 48.000 0.00 0.00 0.00 1.98
1105 3535 6.152661 CCTCTCTCTCTCTCTCTCTCTCTATC 59.847 50.000 0.00 0.00 0.00 2.08
1106 3536 6.857848 TCTCTCTCTCTCTCTCTCTCTATCT 58.142 44.000 0.00 0.00 0.00 1.98
1107 3537 7.301420 TCTCTCTCTCTCTCTCTCTCTATCTT 58.699 42.308 0.00 0.00 0.00 2.40
1138 3570 3.663176 GAAGCAGCTTGCCGTGCA 61.663 61.111 13.91 0.00 46.52 4.57
1145 3583 3.782244 CTTGCCGTGCACGCTCTC 61.782 66.667 33.17 20.22 38.71 3.20
1153 3591 4.385405 GCACGCTCTCCTGCTGGT 62.385 66.667 9.73 0.00 34.23 4.00
1154 3592 2.433838 CACGCTCTCCTGCTGGTG 60.434 66.667 9.73 7.45 34.23 4.17
1181 3619 4.462417 CTCGCGCTCTCGTCCGTT 62.462 66.667 5.56 0.00 38.14 4.44
1182 3620 4.456253 TCGCGCTCTCGTCCGTTC 62.456 66.667 5.56 0.00 38.14 3.95
1183 3621 4.753877 CGCGCTCTCGTCCGTTCA 62.754 66.667 5.56 0.00 38.14 3.18
1625 4090 4.943252 AACTGGCTGCAGTGCGCT 62.943 61.111 24.07 0.00 43.06 5.92
2048 4519 0.099082 CCTTCTCGTACTGCCTCGTC 59.901 60.000 0.00 0.00 0.00 4.20
2051 4522 1.060622 CTCGTACTGCCTCGTCGAC 59.939 63.158 5.18 5.18 0.00 4.20
2648 5146 1.406539 GACGTCTAATTAGTCCGGCCA 59.593 52.381 22.13 0.00 0.00 5.36
2682 5184 5.875224 TGACTTACTGATTGGGTTGATTGA 58.125 37.500 0.00 0.00 0.00 2.57
2698 5200 3.118775 TGATTGATTGACCGGTAGGAGTG 60.119 47.826 7.34 0.00 41.02 3.51
2724 5226 1.196766 TGGCTCTGCTGACTGGATGT 61.197 55.000 0.00 0.00 0.00 3.06
2801 5303 6.293135 GGATTGACAAACAAACAGAGTCTCTC 60.293 42.308 0.00 0.00 42.03 3.20
2802 5304 5.344743 TGACAAACAAACAGAGTCTCTCT 57.655 39.130 0.00 0.00 42.11 3.10
2805 5307 6.980978 TGACAAACAAACAGAGTCTCTCTAAG 59.019 38.462 0.00 0.00 38.99 2.18
2897 5400 4.859798 TGCTTGATTTTCGTTTCGTTTTGT 59.140 33.333 0.00 0.00 0.00 2.83
2907 5410 8.702408 TTTCGTTTCGTTTTGTTGTATAGATG 57.298 30.769 0.00 0.00 0.00 2.90
2908 5411 6.823531 TCGTTTCGTTTTGTTGTATAGATGG 58.176 36.000 0.00 0.00 0.00 3.51
2910 5413 6.735063 CGTTTCGTTTTGTTGTATAGATGGAC 59.265 38.462 0.00 0.00 0.00 4.02
2918 5426 4.142249 TGTTGTATAGATGGACGGACTGTG 60.142 45.833 0.00 0.00 0.00 3.66
2942 5450 9.626045 GTGATGACATGATAAATGTATCTCGTA 57.374 33.333 0.00 0.00 37.58 3.43
2970 5485 0.541998 TCTCTTGGTGCTCCTTCGGA 60.542 55.000 6.34 0.00 34.23 4.55
2988 5503 2.980476 CGGATATGTGTGAGCGTGATAC 59.020 50.000 0.00 0.00 0.00 2.24
3030 5549 0.730155 GTCCGTCGATGTGTGCGTTA 60.730 55.000 3.52 0.00 0.00 3.18
3031 5550 0.171679 TCCGTCGATGTGTGCGTTAT 59.828 50.000 3.52 0.00 0.00 1.89
3045 5571 2.511373 TTATGGACGGCAGCTGCG 60.511 61.111 31.19 26.56 43.26 5.18
3046 5572 3.012859 TTATGGACGGCAGCTGCGA 62.013 57.895 31.19 13.35 43.26 5.10
3172 5765 2.568090 CCGGTGTGGAAGCAATGC 59.432 61.111 0.00 0.00 42.00 3.56
3173 5766 1.973281 CCGGTGTGGAAGCAATGCT 60.973 57.895 0.00 0.00 42.56 3.79
3175 5768 1.503542 GGTGTGGAAGCAATGCTCG 59.496 57.895 8.71 0.00 38.25 5.03
3179 6072 1.065491 TGTGGAAGCAATGCTCGGTAT 60.065 47.619 8.71 0.00 38.25 2.73
3181 6074 1.230324 GGAAGCAATGCTCGGTATCC 58.770 55.000 8.71 7.76 38.25 2.59
3202 6095 4.394712 CACCTCACGGGCCAGTCC 62.395 72.222 5.20 0.00 39.10 3.85
3217 6110 1.982938 GTCCTGGTAGGAGCACGGT 60.983 63.158 0.00 0.00 46.90 4.83
3279 7678 3.474570 CCCGCTCCTCCCTCCTTG 61.475 72.222 0.00 0.00 0.00 3.61
3335 7757 4.803426 GCACCGACCCGAGCAGAG 62.803 72.222 0.00 0.00 0.00 3.35
3336 7758 4.803426 CACCGACCCGAGCAGAGC 62.803 72.222 0.00 0.00 0.00 4.09
3359 7781 3.241059 GCTACGACGTGCTCTGCG 61.241 66.667 11.56 0.00 0.00 5.18
3412 7834 3.589881 GCGCCCATCACATGCTCC 61.590 66.667 0.00 0.00 0.00 4.70
3423 7845 1.301558 CATGCTCCTGCCTCGATCC 60.302 63.158 0.00 0.00 38.71 3.36
3450 7872 5.106357 CGCATCAGCAGAGAGTACATACTAT 60.106 44.000 0.00 0.00 42.27 2.12
3453 7875 7.094592 GCATCAGCAGAGAGTACATACTATACA 60.095 40.741 0.00 0.00 41.58 2.29
3525 7957 2.165301 GTGCACCGGAGTATGTCGC 61.165 63.158 9.46 0.00 0.00 5.19
3577 8009 3.057033 TCTCTAGCGGTACCAAACTGTTC 60.057 47.826 13.54 0.00 36.77 3.18
3580 8012 2.927028 AGCGGTACCAAACTGTTCTTT 58.073 42.857 13.54 0.00 36.77 2.52
3582 8014 3.314357 AGCGGTACCAAACTGTTCTTTTC 59.686 43.478 13.54 0.00 36.77 2.29
3585 8017 5.507974 CGGTACCAAACTGTTCTTTTCTTC 58.492 41.667 13.54 0.00 0.00 2.87
3588 8020 6.769341 GGTACCAAACTGTTCTTTTCTTCCTA 59.231 38.462 7.15 0.00 0.00 2.94
3608 8040 5.067674 TCCTAAAATGATAAGTGCCACATGC 59.932 40.000 0.00 0.00 41.77 4.06
3684 8116 8.061125 TGATGTAGAAAATATTGTCATCGTCG 57.939 34.615 8.36 0.00 34.75 5.12
3685 8117 7.918562 TGATGTAGAAAATATTGTCATCGTCGA 59.081 33.333 8.36 0.00 34.75 4.20
3686 8118 7.679659 TGTAGAAAATATTGTCATCGTCGAG 57.320 36.000 8.36 0.00 0.00 4.04
3687 8119 7.255569 TGTAGAAAATATTGTCATCGTCGAGT 58.744 34.615 8.36 0.00 0.00 4.18
3688 8120 6.814076 AGAAAATATTGTCATCGTCGAGTC 57.186 37.500 8.36 0.00 0.00 3.36
3689 8121 6.330278 AGAAAATATTGTCATCGTCGAGTCA 58.670 36.000 8.36 0.00 0.00 3.41
3690 8122 5.950965 AAATATTGTCATCGTCGAGTCAC 57.049 39.130 0.00 0.00 0.00 3.67
3691 8123 4.902443 ATATTGTCATCGTCGAGTCACT 57.098 40.909 0.00 0.00 0.00 3.41
3692 8124 6.373186 AATATTGTCATCGTCGAGTCACTA 57.627 37.500 0.00 0.00 0.00 2.74
3693 8125 4.696899 ATTGTCATCGTCGAGTCACTAA 57.303 40.909 0.00 0.00 0.00 2.24
3694 8126 4.492791 TTGTCATCGTCGAGTCACTAAA 57.507 40.909 0.00 0.00 0.00 1.85
3695 8127 4.696899 TGTCATCGTCGAGTCACTAAAT 57.303 40.909 0.00 0.00 0.00 1.40
3696 8128 5.055642 TGTCATCGTCGAGTCACTAAATT 57.944 39.130 0.00 0.00 0.00 1.82
3697 8129 5.466819 TGTCATCGTCGAGTCACTAAATTT 58.533 37.500 0.00 0.00 0.00 1.82
3698 8130 6.614160 TGTCATCGTCGAGTCACTAAATTTA 58.386 36.000 0.00 0.00 0.00 1.40
3699 8131 7.255569 TGTCATCGTCGAGTCACTAAATTTAT 58.744 34.615 0.00 0.00 0.00 1.40
3700 8132 7.431376 TGTCATCGTCGAGTCACTAAATTTATC 59.569 37.037 0.00 0.00 0.00 1.75
3701 8133 6.631636 TCATCGTCGAGTCACTAAATTTATCG 59.368 38.462 10.49 10.49 0.00 2.92
3702 8134 5.872635 TCGTCGAGTCACTAAATTTATCGT 58.127 37.500 14.48 2.17 0.00 3.73
3703 8135 7.003939 TCGTCGAGTCACTAAATTTATCGTA 57.996 36.000 14.48 3.56 0.00 3.43
3704 8136 7.463544 TCGTCGAGTCACTAAATTTATCGTAA 58.536 34.615 14.48 3.49 0.00 3.18
3705 8137 7.962373 TCGTCGAGTCACTAAATTTATCGTAAA 59.038 33.333 14.48 3.23 0.00 2.01
3706 8138 8.577939 CGTCGAGTCACTAAATTTATCGTAAAA 58.422 33.333 14.48 0.00 0.00 1.52
3709 8141 9.469239 CGAGTCACTAAATTTATCGTAAAAACC 57.531 33.333 9.10 0.00 0.00 3.27
3720 8152 9.815936 ATTTATCGTAAAAACCTTTCGTAGTTG 57.184 29.630 0.00 0.00 0.00 3.16
3721 8153 5.081888 TCGTAAAAACCTTTCGTAGTTGC 57.918 39.130 0.00 0.00 0.00 4.17
3722 8154 3.896030 CGTAAAAACCTTTCGTAGTTGCG 59.104 43.478 0.00 0.00 0.00 4.85
3723 8155 4.550639 CGTAAAAACCTTTCGTAGTTGCGT 60.551 41.667 0.00 0.00 0.00 5.24
3724 8156 3.328237 AAAACCTTTCGTAGTTGCGTG 57.672 42.857 0.00 0.00 0.00 5.34
3725 8157 1.944032 AACCTTTCGTAGTTGCGTGT 58.056 45.000 0.00 0.00 0.00 4.49
3726 8158 1.214367 ACCTTTCGTAGTTGCGTGTG 58.786 50.000 0.00 0.00 0.00 3.82
3727 8159 1.214367 CCTTTCGTAGTTGCGTGTGT 58.786 50.000 0.00 0.00 0.00 3.72
3728 8160 1.595794 CCTTTCGTAGTTGCGTGTGTT 59.404 47.619 0.00 0.00 0.00 3.32
3729 8161 2.348218 CCTTTCGTAGTTGCGTGTGTTC 60.348 50.000 0.00 0.00 0.00 3.18
3730 8162 0.847670 TTCGTAGTTGCGTGTGTTCG 59.152 50.000 0.00 0.00 0.00 3.95
3731 8163 0.248580 TCGTAGTTGCGTGTGTTCGT 60.249 50.000 0.00 0.00 0.00 3.85
3732 8164 0.111878 CGTAGTTGCGTGTGTTCGTG 60.112 55.000 0.00 0.00 0.00 4.35
3733 8165 0.382636 GTAGTTGCGTGTGTTCGTGC 60.383 55.000 0.00 0.00 0.00 5.34
3734 8166 1.492319 TAGTTGCGTGTGTTCGTGCC 61.492 55.000 0.00 0.00 0.00 5.01
3735 8167 2.820037 TTGCGTGTGTTCGTGCCA 60.820 55.556 0.00 0.00 0.00 4.92
3736 8168 3.102107 TTGCGTGTGTTCGTGCCAC 62.102 57.895 0.00 0.00 0.00 5.01
3737 8169 3.568743 GCGTGTGTTCGTGCCACA 61.569 61.111 0.00 0.00 40.35 4.17
3755 8187 3.026630 ACACGTGTGACACTTATCAGG 57.973 47.619 22.71 0.00 31.34 3.86
3756 8188 2.288825 ACACGTGTGACACTTATCAGGG 60.289 50.000 22.71 0.29 31.34 4.45
3757 8189 1.968493 ACGTGTGACACTTATCAGGGT 59.032 47.619 14.42 0.00 40.51 4.34
3758 8190 2.367567 ACGTGTGACACTTATCAGGGTT 59.632 45.455 14.42 0.00 36.47 4.11
3759 8191 3.181458 ACGTGTGACACTTATCAGGGTTT 60.181 43.478 14.42 0.00 36.47 3.27
3760 8192 3.813166 CGTGTGACACTTATCAGGGTTTT 59.187 43.478 14.42 0.00 36.47 2.43
3761 8193 4.274950 CGTGTGACACTTATCAGGGTTTTT 59.725 41.667 14.42 0.00 36.47 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 3.063084 AGGTGAGCCCTCGTCGAC 61.063 66.667 5.18 5.18 40.71 4.20
3 4 3.062466 CAGGTGAGCCCTCGTCGA 61.062 66.667 0.00 0.00 43.86 4.20
4 5 4.135153 CCAGGTGAGCCCTCGTCG 62.135 72.222 0.00 0.00 43.86 5.12
5 6 2.680352 TCCAGGTGAGCCCTCGTC 60.680 66.667 0.00 0.00 43.86 4.20
6 7 2.997897 GTCCAGGTGAGCCCTCGT 60.998 66.667 0.00 0.00 43.86 4.18
8 9 2.997897 ACGTCCAGGTGAGCCCTC 60.998 66.667 0.00 0.00 43.86 4.30
10 11 4.436998 CGACGTCCAGGTGAGCCC 62.437 72.222 10.58 0.00 34.57 5.19
62 63 1.530013 GGTCAGCAGCACAATGCCTT 61.530 55.000 0.00 0.00 46.52 4.35
63 64 1.975407 GGTCAGCAGCACAATGCCT 60.975 57.895 0.00 0.00 46.52 4.75
64 65 2.570181 GGTCAGCAGCACAATGCC 59.430 61.111 0.00 0.00 46.52 4.40
65 66 2.177531 CGGTCAGCAGCACAATGC 59.822 61.111 0.00 0.00 46.88 3.56
76 77 4.421479 ACTTCGAGCGGCGGTCAG 62.421 66.667 34.25 27.05 41.33 3.51
137 138 2.106131 TCCGATCCGCATCCAACG 59.894 61.111 0.00 0.00 0.00 4.10
145 146 4.183686 TTCCGTCGTCCGATCCGC 62.184 66.667 0.00 0.00 39.56 5.54
147 148 2.412112 CCTTCCGTCGTCCGATCC 59.588 66.667 0.00 0.00 39.56 3.36
151 152 2.624437 GAATCCCCTTCCGTCGTCCG 62.624 65.000 0.00 0.00 0.00 4.79
267 2556 4.500116 GCACGTCCCTCTCGGCTC 62.500 72.222 0.00 0.00 0.00 4.70
280 2569 4.154347 GAGGAGGAGCAGGGCACG 62.154 72.222 0.00 0.00 0.00 5.34
316 2605 2.098117 CAGGTTCAAGGATTTCGGATGC 59.902 50.000 0.00 0.00 0.00 3.91
317 2606 3.375299 GTCAGGTTCAAGGATTTCGGATG 59.625 47.826 0.00 0.00 0.00 3.51
318 2607 3.610911 GTCAGGTTCAAGGATTTCGGAT 58.389 45.455 0.00 0.00 0.00 4.18
319 2608 2.611971 CGTCAGGTTCAAGGATTTCGGA 60.612 50.000 0.00 0.00 0.00 4.55
320 2609 1.732259 CGTCAGGTTCAAGGATTTCGG 59.268 52.381 0.00 0.00 0.00 4.30
321 2610 1.732259 CCGTCAGGTTCAAGGATTTCG 59.268 52.381 0.00 0.00 0.00 3.46
322 2611 2.084546 CCCGTCAGGTTCAAGGATTTC 58.915 52.381 0.00 0.00 35.12 2.17
323 2612 1.271926 CCCCGTCAGGTTCAAGGATTT 60.272 52.381 0.00 0.00 35.12 2.17
324 2613 0.328258 CCCCGTCAGGTTCAAGGATT 59.672 55.000 0.00 0.00 35.12 3.01
325 2614 1.562672 CCCCCGTCAGGTTCAAGGAT 61.563 60.000 0.00 0.00 35.12 3.24
326 2615 2.221299 CCCCCGTCAGGTTCAAGGA 61.221 63.158 0.00 0.00 35.12 3.36
327 2616 2.351276 CCCCCGTCAGGTTCAAGG 59.649 66.667 0.00 0.00 35.12 3.61
328 2617 2.359975 GCCCCCGTCAGGTTCAAG 60.360 66.667 0.00 0.00 35.12 3.02
329 2618 4.323477 CGCCCCCGTCAGGTTCAA 62.323 66.667 0.00 0.00 35.12 2.69
342 2631 4.722855 AATTTGCTGCGTGCGCCC 62.723 61.111 14.16 5.82 46.63 6.13
469 2762 2.163010 TCTTTGTCTATCACCGTCGACC 59.837 50.000 10.58 0.00 0.00 4.79
473 2766 2.915463 CACGTCTTTGTCTATCACCGTC 59.085 50.000 0.00 0.00 0.00 4.79
498 2791 2.320339 GAACCTAGGAGTCGTCGCGG 62.320 65.000 17.98 0.00 0.00 6.46
502 2795 2.727298 CGAAACGAACCTAGGAGTCGTC 60.727 54.545 31.32 22.98 35.93 4.20
505 2798 2.731654 GCTCGAAACGAACCTAGGAGTC 60.732 54.545 17.98 11.33 34.74 3.36
539 2832 7.211573 TGGATCGAGTCAAACTGTAGTTTTTA 58.788 34.615 7.25 0.00 45.07 1.52
545 2838 4.142160 TGGATGGATCGAGTCAAACTGTAG 60.142 45.833 0.00 0.00 0.00 2.74
547 2840 2.567169 TGGATGGATCGAGTCAAACTGT 59.433 45.455 0.00 0.00 0.00 3.55
576 2875 7.195374 AGTACTGTATAATTTCCTGGAAGCA 57.805 36.000 9.42 0.00 0.00 3.91
610 2909 1.538512 CATGACTTGTGACCTGGCAAG 59.461 52.381 9.99 9.99 45.33 4.01
667 3049 4.579384 ACAGCACCAACCCCGTGG 62.579 66.667 0.00 0.00 44.92 4.94
674 3057 1.741770 CTAGCCGGACAGCACCAAC 60.742 63.158 5.05 0.00 34.23 3.77
691 3074 1.738099 GATGACGTGCGGCTTCACT 60.738 57.895 8.21 0.00 34.92 3.41
694 3077 4.210304 GCGATGACGTGCGGCTTC 62.210 66.667 0.00 0.98 41.98 3.86
727 3110 1.964373 ACGACCCATTTGCGTCACC 60.964 57.895 0.00 0.00 31.98 4.02
728 3111 3.650369 ACGACCCATTTGCGTCAC 58.350 55.556 0.00 0.00 31.98 3.67
740 3123 1.301479 GACCTGGGTGTTGACGACC 60.301 63.158 0.00 0.00 0.00 4.79
751 3134 3.749665 TTTGAAAGCATTTGACCTGGG 57.250 42.857 0.00 0.00 39.27 4.45
754 3137 8.587608 TCAGAATATTTTGAAAGCATTTGACCT 58.412 29.630 6.23 0.00 39.27 3.85
773 3156 8.585881 GGGAGCACAGTAGTATATTTCAGAATA 58.414 37.037 0.00 0.00 32.56 1.75
774 3157 7.291182 AGGGAGCACAGTAGTATATTTCAGAAT 59.709 37.037 0.00 0.00 0.00 2.40
775 3158 6.611642 AGGGAGCACAGTAGTATATTTCAGAA 59.388 38.462 0.00 0.00 0.00 3.02
776 3159 6.136857 AGGGAGCACAGTAGTATATTTCAGA 58.863 40.000 0.00 0.00 0.00 3.27
777 3160 6.412362 AGGGAGCACAGTAGTATATTTCAG 57.588 41.667 0.00 0.00 0.00 3.02
778 3161 6.808321 AAGGGAGCACAGTAGTATATTTCA 57.192 37.500 0.00 0.00 0.00 2.69
779 3162 7.048512 ACAAAGGGAGCACAGTAGTATATTTC 58.951 38.462 0.00 0.00 0.00 2.17
780 3163 6.958767 ACAAAGGGAGCACAGTAGTATATTT 58.041 36.000 0.00 0.00 0.00 1.40
781 3164 6.561519 ACAAAGGGAGCACAGTAGTATATT 57.438 37.500 0.00 0.00 0.00 1.28
782 3165 6.156256 TCAACAAAGGGAGCACAGTAGTATAT 59.844 38.462 0.00 0.00 0.00 0.86
783 3166 5.482526 TCAACAAAGGGAGCACAGTAGTATA 59.517 40.000 0.00 0.00 0.00 1.47
794 3177 8.141909 AGTTTATTTTTACTCAACAAAGGGAGC 58.858 33.333 0.00 0.00 34.48 4.70
833 3216 9.498176 AACAAAGTGAGGAAAATTATACGTACT 57.502 29.630 0.00 0.00 0.00 2.73
834 3217 9.537848 CAACAAAGTGAGGAAAATTATACGTAC 57.462 33.333 0.00 0.00 0.00 3.67
835 3218 8.231837 GCAACAAAGTGAGGAAAATTATACGTA 58.768 33.333 0.00 0.00 0.00 3.57
836 3219 7.040686 AGCAACAAAGTGAGGAAAATTATACGT 60.041 33.333 0.00 0.00 0.00 3.57
837 3220 7.271223 CAGCAACAAAGTGAGGAAAATTATACG 59.729 37.037 0.00 0.00 0.00 3.06
848 3231 2.549754 CCACTACAGCAACAAAGTGAGG 59.450 50.000 3.00 0.00 41.47 3.86
896 3325 2.866028 GCTGCTTTGACCAGCGAG 59.134 61.111 0.00 0.00 45.20 5.03
900 3329 0.240411 GCTTCTGCTGCTTTGACCAG 59.760 55.000 0.00 0.00 36.03 4.00
901 3330 2.334307 GCTTCTGCTGCTTTGACCA 58.666 52.632 0.00 0.00 36.03 4.02
913 3342 0.946221 AACAACGCGGAGAGCTTCTG 60.946 55.000 12.47 0.00 45.59 3.02
918 3347 0.586802 AAAGAAACAACGCGGAGAGC 59.413 50.000 12.47 0.00 43.95 4.09
933 3362 1.006571 GACGTGCCGTGGAGAAAGA 60.007 57.895 4.94 0.00 41.37 2.52
936 3365 4.351938 CCGACGTGCCGTGGAGAA 62.352 66.667 10.39 0.00 41.37 2.87
952 3381 2.340328 GGAATGGTTGTCGGGTGCC 61.340 63.158 0.00 0.00 0.00 5.01
953 3382 1.175983 TTGGAATGGTTGTCGGGTGC 61.176 55.000 0.00 0.00 0.00 5.01
954 3383 0.596082 GTTGGAATGGTTGTCGGGTG 59.404 55.000 0.00 0.00 0.00 4.61
955 3384 0.538746 GGTTGGAATGGTTGTCGGGT 60.539 55.000 0.00 0.00 0.00 5.28
1015 3445 0.396417 GCTGAGCAGAGGTCCTCCTA 60.396 60.000 15.72 0.00 45.24 2.94
1017 3447 1.675720 GAGCTGAGCAGAGGTCCTCC 61.676 65.000 15.72 0.93 34.91 4.30
1018 3448 0.969917 TGAGCTGAGCAGAGGTCCTC 60.970 60.000 11.31 11.31 39.33 3.71
1019 3449 1.078166 TGAGCTGAGCAGAGGTCCT 59.922 57.895 7.39 0.00 39.33 3.85
1020 3450 1.217779 GTGAGCTGAGCAGAGGTCC 59.782 63.158 7.39 0.00 39.33 4.46
1021 3451 1.217779 GGTGAGCTGAGCAGAGGTC 59.782 63.158 7.39 7.13 40.29 3.85
1022 3452 2.644212 CGGTGAGCTGAGCAGAGGT 61.644 63.158 7.39 0.00 0.00 3.85
1023 3453 2.183811 CGGTGAGCTGAGCAGAGG 59.816 66.667 7.39 0.00 0.00 3.69
1024 3454 1.153862 GACGGTGAGCTGAGCAGAG 60.154 63.158 7.39 0.00 0.00 3.35
1025 3455 1.903404 TGACGGTGAGCTGAGCAGA 60.903 57.895 7.39 0.00 0.00 4.26
1026 3456 1.735920 GTGACGGTGAGCTGAGCAG 60.736 63.158 7.39 0.00 0.00 4.24
1027 3457 2.340078 GTGACGGTGAGCTGAGCA 59.660 61.111 7.39 0.00 0.00 4.26
1028 3458 2.433318 GGTGACGGTGAGCTGAGC 60.433 66.667 0.00 0.00 0.00 4.26
1029 3459 1.214062 GAGGTGACGGTGAGCTGAG 59.786 63.158 3.54 0.00 0.00 3.35
1030 3460 2.276116 GGAGGTGACGGTGAGCTGA 61.276 63.158 3.54 0.00 0.00 4.26
1031 3461 2.262915 GGAGGTGACGGTGAGCTG 59.737 66.667 3.54 0.00 0.00 4.24
1032 3462 2.997897 GGGAGGTGACGGTGAGCT 60.998 66.667 0.00 0.00 0.00 4.09
1033 3463 4.083862 GGGGAGGTGACGGTGAGC 62.084 72.222 0.00 0.00 0.00 4.26
1034 3464 3.391382 GGGGGAGGTGACGGTGAG 61.391 72.222 0.00 0.00 0.00 3.51
1076 3506 2.370189 GAGAGAGAGAGAGAGAGGGAGG 59.630 59.091 0.00 0.00 0.00 4.30
1078 3508 3.051803 AGAGAGAGAGAGAGAGAGAGGGA 60.052 52.174 0.00 0.00 0.00 4.20
1079 3509 3.312890 AGAGAGAGAGAGAGAGAGAGGG 58.687 54.545 0.00 0.00 0.00 4.30
1080 3510 4.222336 AGAGAGAGAGAGAGAGAGAGAGG 58.778 52.174 0.00 0.00 0.00 3.69
1081 3511 6.947733 AGATAGAGAGAGAGAGAGAGAGAGAG 59.052 46.154 0.00 0.00 0.00 3.20
1082 3512 6.857848 AGATAGAGAGAGAGAGAGAGAGAGA 58.142 44.000 0.00 0.00 0.00 3.10
1083 3513 7.537596 AAGATAGAGAGAGAGAGAGAGAGAG 57.462 44.000 0.00 0.00 0.00 3.20
1084 3514 7.786943 AGAAAGATAGAGAGAGAGAGAGAGAGA 59.213 40.741 0.00 0.00 0.00 3.10
1085 3515 7.961351 AGAAAGATAGAGAGAGAGAGAGAGAG 58.039 42.308 0.00 0.00 0.00 3.20
1086 3516 7.565029 TGAGAAAGATAGAGAGAGAGAGAGAGA 59.435 40.741 0.00 0.00 0.00 3.10
1087 3517 7.730084 TGAGAAAGATAGAGAGAGAGAGAGAG 58.270 42.308 0.00 0.00 0.00 3.20
1088 3518 7.675161 TGAGAAAGATAGAGAGAGAGAGAGA 57.325 40.000 0.00 0.00 0.00 3.10
1089 3519 6.426328 GCTGAGAAAGATAGAGAGAGAGAGAG 59.574 46.154 0.00 0.00 0.00 3.20
1090 3520 6.291377 GCTGAGAAAGATAGAGAGAGAGAGA 58.709 44.000 0.00 0.00 0.00 3.10
1091 3521 5.471456 GGCTGAGAAAGATAGAGAGAGAGAG 59.529 48.000 0.00 0.00 0.00 3.20
1092 3522 5.104151 TGGCTGAGAAAGATAGAGAGAGAGA 60.104 44.000 0.00 0.00 0.00 3.10
1093 3523 5.132502 TGGCTGAGAAAGATAGAGAGAGAG 58.867 45.833 0.00 0.00 0.00 3.20
1094 3524 5.122707 TGGCTGAGAAAGATAGAGAGAGA 57.877 43.478 0.00 0.00 0.00 3.10
1095 3525 5.279106 CCATGGCTGAGAAAGATAGAGAGAG 60.279 48.000 0.00 0.00 0.00 3.20
1096 3526 4.588106 CCATGGCTGAGAAAGATAGAGAGA 59.412 45.833 0.00 0.00 0.00 3.10
1097 3527 4.800249 GCCATGGCTGAGAAAGATAGAGAG 60.800 50.000 29.98 0.00 38.26 3.20
1098 3528 3.070734 GCCATGGCTGAGAAAGATAGAGA 59.929 47.826 29.98 0.00 38.26 3.10
1099 3529 3.401182 GCCATGGCTGAGAAAGATAGAG 58.599 50.000 29.98 0.00 38.26 2.43
1100 3530 2.224137 CGCCATGGCTGAGAAAGATAGA 60.224 50.000 33.07 0.00 39.32 1.98
1101 3531 2.141517 CGCCATGGCTGAGAAAGATAG 58.858 52.381 33.07 10.20 39.32 2.08
1102 3532 1.762370 TCGCCATGGCTGAGAAAGATA 59.238 47.619 33.07 6.69 39.32 1.98
1103 3533 0.543277 TCGCCATGGCTGAGAAAGAT 59.457 50.000 33.07 0.00 39.32 2.40
1104 3534 0.324614 TTCGCCATGGCTGAGAAAGA 59.675 50.000 33.07 18.61 39.32 2.52
1105 3535 0.731417 CTTCGCCATGGCTGAGAAAG 59.269 55.000 33.07 21.99 39.32 2.62
1106 3536 1.308069 GCTTCGCCATGGCTGAGAAA 61.308 55.000 33.07 17.53 39.32 2.52
1107 3537 1.746615 GCTTCGCCATGGCTGAGAA 60.747 57.895 33.07 25.84 39.32 2.87
1128 3560 3.782244 GAGAGCGTGCACGGCAAG 61.782 66.667 37.47 12.79 41.47 4.01
1138 3570 3.699894 CCACCAGCAGGAGAGCGT 61.700 66.667 0.35 0.00 40.15 5.07
1145 3583 1.673665 GAGCAAGACCACCAGCAGG 60.674 63.158 0.00 0.00 42.21 4.85
1179 3617 2.050985 GTTGCTGCCAGCGTGAAC 60.051 61.111 12.80 7.41 46.26 3.18
1181 3619 2.666190 GAGTTGCTGCCAGCGTGA 60.666 61.111 12.80 0.00 46.26 4.35
1182 3620 4.081030 CGAGTTGCTGCCAGCGTG 62.081 66.667 12.80 0.00 46.26 5.34
1183 3621 4.299547 TCGAGTTGCTGCCAGCGT 62.300 61.111 12.80 0.00 46.26 5.07
1312 3762 3.334054 GCTTGAGGGAGGGTGGCT 61.334 66.667 0.00 0.00 0.00 4.75
1314 3764 2.674220 GGAGCTTGAGGGAGGGTGG 61.674 68.421 0.00 0.00 0.00 4.61
1375 3825 0.736053 CGAGTCGAGGAAGAAGGAGG 59.264 60.000 6.73 0.00 0.00 4.30
1625 4090 2.604686 AAGCAGTCGAGGCAGGGA 60.605 61.111 11.19 0.00 0.00 4.20
2036 4507 1.154073 GTGGTCGACGAGGCAGTAC 60.154 63.158 9.92 0.00 0.00 2.73
2153 4636 4.124351 TAGAAGGTGTCCGCCGCG 62.124 66.667 5.59 5.59 0.00 6.46
2154 4637 1.660560 TAGTAGAAGGTGTCCGCCGC 61.661 60.000 0.00 0.00 0.00 6.53
2155 4638 0.100146 GTAGTAGAAGGTGTCCGCCG 59.900 60.000 0.00 0.00 0.00 6.46
2156 4639 0.459078 GGTAGTAGAAGGTGTCCGCC 59.541 60.000 0.00 0.00 0.00 6.13
2157 4640 1.404748 GAGGTAGTAGAAGGTGTCCGC 59.595 57.143 0.00 0.00 0.00 5.54
2158 4641 2.022934 GGAGGTAGTAGAAGGTGTCCG 58.977 57.143 0.00 0.00 0.00 4.79
2648 5146 4.345859 TCAGTAAGTCAAAATGGACGGT 57.654 40.909 0.00 0.00 42.62 4.83
2682 5184 1.640917 ACACACTCCTACCGGTCAAT 58.359 50.000 12.40 0.00 0.00 2.57
2698 5200 0.390472 GTCAGCAGAGCCACCTACAC 60.390 60.000 0.00 0.00 0.00 2.90
2724 5226 6.094048 CCAGTTTCTTCACTGTTTCTTCTTCA 59.906 38.462 0.44 0.00 42.45 3.02
2753 5255 4.513406 AACCCAGTTTCTTTCTACACCA 57.487 40.909 0.00 0.00 0.00 4.17
2801 5303 6.102897 TCACCAAAACCTCTCTCTTCTTAG 57.897 41.667 0.00 0.00 0.00 2.18
2802 5304 6.099845 AGTTCACCAAAACCTCTCTCTTCTTA 59.900 38.462 0.00 0.00 0.00 2.10
2805 5307 4.709250 AGTTCACCAAAACCTCTCTCTTC 58.291 43.478 0.00 0.00 0.00 2.87
2821 5323 3.049912 GCCGAATTGGTCAAAAGTTCAC 58.950 45.455 0.00 0.00 41.21 3.18
2871 5374 4.287238 ACGAAACGAAAATCAAGCAAGT 57.713 36.364 0.00 0.00 0.00 3.16
2876 5379 6.747344 ACAACAAAACGAAACGAAAATCAAG 58.253 32.000 0.00 0.00 0.00 3.02
2882 5385 7.799447 CCATCTATACAACAAAACGAAACGAAA 59.201 33.333 0.00 0.00 0.00 3.46
2883 5386 7.171167 TCCATCTATACAACAAAACGAAACGAA 59.829 33.333 0.00 0.00 0.00 3.85
2884 5387 6.645827 TCCATCTATACAACAAAACGAAACGA 59.354 34.615 0.00 0.00 0.00 3.85
2885 5388 6.735063 GTCCATCTATACAACAAAACGAAACG 59.265 38.462 0.00 0.00 0.00 3.60
2886 5389 6.735063 CGTCCATCTATACAACAAAACGAAAC 59.265 38.462 0.00 0.00 0.00 2.78
2897 5400 4.274978 TCACAGTCCGTCCATCTATACAA 58.725 43.478 0.00 0.00 0.00 2.41
2907 5410 1.204704 TCATGTCATCACAGTCCGTCC 59.795 52.381 0.00 0.00 35.41 4.79
2908 5411 2.654749 TCATGTCATCACAGTCCGTC 57.345 50.000 0.00 0.00 35.41 4.79
2910 5413 5.525012 ACATTTATCATGTCATCACAGTCCG 59.475 40.000 0.00 0.00 35.41 4.79
2942 5450 1.701847 AGCACCAAGAGAGACACCAAT 59.298 47.619 0.00 0.00 0.00 3.16
2970 5485 3.492656 GGTGGTATCACGCTCACACATAT 60.493 47.826 0.00 0.00 44.50 1.78
2988 5503 1.135689 CGCAAAGGAAGAAATCGGTGG 60.136 52.381 0.00 0.00 0.00 4.61
3046 5572 1.151777 CGTCTGTGCGACAAAGGTGT 61.152 55.000 0.00 0.00 42.98 4.16
3051 5577 3.625232 GCTCGTCTGTGCGACAAA 58.375 55.556 0.00 0.00 42.98 2.83
3085 5615 2.544590 AATCAATACGGCCGGCACCA 62.545 55.000 31.76 12.58 0.00 4.17
3086 5616 1.822186 AATCAATACGGCCGGCACC 60.822 57.895 31.76 11.20 0.00 5.01
3091 5621 1.153046 ACCCCAATCAATACGGCCG 60.153 57.895 26.86 26.86 0.00 6.13
3175 5768 1.065928 CGTGAGGTGAGCGGATACC 59.934 63.158 0.00 0.00 37.23 2.73
3202 6095 2.267681 GACGACCGTGCTCCTACCAG 62.268 65.000 0.00 0.00 0.00 4.00
3207 6100 4.057428 GCTGACGACCGTGCTCCT 62.057 66.667 0.00 0.00 0.00 3.69
3229 6122 5.593095 TCCACTTGAGAATATAGCACGTACT 59.407 40.000 0.00 0.00 0.00 2.73
3273 7668 3.382803 CTGGAGGCGAGCCAAGGAG 62.383 68.421 17.18 2.77 38.92 3.69
3274 7669 3.393970 CTGGAGGCGAGCCAAGGA 61.394 66.667 17.18 0.00 38.92 3.36
3275 7670 3.393970 TCTGGAGGCGAGCCAAGG 61.394 66.667 17.18 3.76 38.92 3.61
3276 7671 2.125350 GTCTGGAGGCGAGCCAAG 60.125 66.667 17.18 10.52 38.92 3.61
3335 7757 3.241059 CACGTCGTAGCGCTCTGC 61.241 66.667 16.34 4.61 46.98 4.26
3336 7758 3.241059 GCACGTCGTAGCGCTCTG 61.241 66.667 16.34 8.05 34.88 3.35
3337 7759 3.384014 GAGCACGTCGTAGCGCTCT 62.384 63.158 16.34 0.63 45.86 4.09
3359 7781 1.703438 CTCACCGATGAAGCAGCAGC 61.703 60.000 0.00 0.00 42.56 5.25
3423 7845 0.378610 TACTCTCTGCTGATGCGTCG 59.621 55.000 0.58 0.00 43.34 5.12
3450 7872 8.405531 GGTAGGTACGAGTTGTTGTATATTGTA 58.594 37.037 0.00 0.00 0.00 2.41
3453 7875 6.095440 ACGGTAGGTACGAGTTGTTGTATATT 59.905 38.462 0.00 0.00 34.93 1.28
3549 7981 1.681793 TGGTACCGCTAGAGATTGCTC 59.318 52.381 7.57 0.00 41.62 4.26
3577 8009 8.522830 TGGCACTTATCATTTTAGGAAGAAAAG 58.477 33.333 0.00 0.00 32.06 2.27
3580 8012 6.945435 TGTGGCACTTATCATTTTAGGAAGAA 59.055 34.615 19.83 0.00 0.00 2.52
3582 8014 6.757897 TGTGGCACTTATCATTTTAGGAAG 57.242 37.500 19.83 0.00 0.00 3.46
3585 8017 5.284079 GCATGTGGCACTTATCATTTTAGG 58.716 41.667 19.83 0.00 43.97 2.69
3588 8020 3.193267 ACGCATGTGGCACTTATCATTTT 59.807 39.130 19.83 0.00 45.17 1.82
3658 8090 8.539674 CGACGATGACAATATTTTCTACATCAA 58.460 33.333 0.00 0.00 34.34 2.57
3659 8091 7.918562 TCGACGATGACAATATTTTCTACATCA 59.081 33.333 0.00 0.00 34.34 3.07
3660 8092 8.282124 TCGACGATGACAATATTTTCTACATC 57.718 34.615 0.00 0.00 0.00 3.06
3661 8093 7.921214 ACTCGACGATGACAATATTTTCTACAT 59.079 33.333 0.00 0.00 0.00 2.29
3662 8094 7.255569 ACTCGACGATGACAATATTTTCTACA 58.744 34.615 0.00 0.00 0.00 2.74
3663 8095 7.431376 TGACTCGACGATGACAATATTTTCTAC 59.569 37.037 0.00 0.00 0.00 2.59
3664 8096 7.431376 GTGACTCGACGATGACAATATTTTCTA 59.569 37.037 0.00 0.00 0.00 2.10
3665 8097 6.253727 GTGACTCGACGATGACAATATTTTCT 59.746 38.462 0.00 0.00 0.00 2.52
3666 8098 6.253727 AGTGACTCGACGATGACAATATTTTC 59.746 38.462 0.00 0.00 0.00 2.29
3667 8099 6.100004 AGTGACTCGACGATGACAATATTTT 58.900 36.000 0.00 0.00 0.00 1.82
3668 8100 5.651530 AGTGACTCGACGATGACAATATTT 58.348 37.500 0.00 0.00 0.00 1.40
3669 8101 5.250235 AGTGACTCGACGATGACAATATT 57.750 39.130 0.00 0.00 0.00 1.28
3670 8102 4.902443 AGTGACTCGACGATGACAATAT 57.098 40.909 0.00 0.00 0.00 1.28
3671 8103 5.806366 TTAGTGACTCGACGATGACAATA 57.194 39.130 0.00 0.44 0.00 1.90
3672 8104 4.696899 TTAGTGACTCGACGATGACAAT 57.303 40.909 0.00 1.40 0.00 2.71
3673 8105 4.492791 TTTAGTGACTCGACGATGACAA 57.507 40.909 0.00 0.00 0.00 3.18
3674 8106 4.696899 ATTTAGTGACTCGACGATGACA 57.303 40.909 0.00 0.00 0.00 3.58
3675 8107 7.356557 CGATAAATTTAGTGACTCGACGATGAC 60.357 40.741 11.06 0.00 0.00 3.06
3676 8108 6.631636 CGATAAATTTAGTGACTCGACGATGA 59.368 38.462 11.06 0.00 0.00 2.92
3677 8109 6.414109 ACGATAAATTTAGTGACTCGACGATG 59.586 38.462 19.61 0.00 0.00 3.84
3678 8110 6.493116 ACGATAAATTTAGTGACTCGACGAT 58.507 36.000 19.61 1.00 0.00 3.73
3679 8111 5.872635 ACGATAAATTTAGTGACTCGACGA 58.127 37.500 19.61 0.00 0.00 4.20
3680 8112 7.654963 TTACGATAAATTTAGTGACTCGACG 57.345 36.000 19.61 9.50 0.00 5.12
3683 8115 9.469239 GGTTTTTACGATAAATTTAGTGACTCG 57.531 33.333 13.78 13.78 0.00 4.18
3694 8126 9.815936 CAACTACGAAAGGTTTTTACGATAAAT 57.184 29.630 0.00 0.00 0.00 1.40
3695 8127 7.798052 GCAACTACGAAAGGTTTTTACGATAAA 59.202 33.333 0.00 0.00 0.00 1.40
3696 8128 7.290118 GCAACTACGAAAGGTTTTTACGATAA 58.710 34.615 0.00 0.00 0.00 1.75
3697 8129 6.399880 CGCAACTACGAAAGGTTTTTACGATA 60.400 38.462 0.00 0.00 34.06 2.92
3698 8130 5.613142 CGCAACTACGAAAGGTTTTTACGAT 60.613 40.000 0.00 0.00 34.06 3.73
3699 8131 4.317980 CGCAACTACGAAAGGTTTTTACGA 60.318 41.667 0.00 0.00 34.06 3.43
3700 8132 3.896030 CGCAACTACGAAAGGTTTTTACG 59.104 43.478 0.00 0.00 34.06 3.18
3701 8133 4.667504 CACGCAACTACGAAAGGTTTTTAC 59.332 41.667 0.00 0.00 36.70 2.01
3702 8134 4.332268 ACACGCAACTACGAAAGGTTTTTA 59.668 37.500 0.00 0.00 36.70 1.52
3703 8135 3.127376 ACACGCAACTACGAAAGGTTTTT 59.873 39.130 0.00 0.00 36.70 1.94
3704 8136 2.679336 ACACGCAACTACGAAAGGTTTT 59.321 40.909 0.00 0.00 36.70 2.43
3705 8137 2.031191 CACACGCAACTACGAAAGGTTT 59.969 45.455 0.00 0.00 36.70 3.27
3706 8138 1.595794 CACACGCAACTACGAAAGGTT 59.404 47.619 0.00 0.00 36.70 3.50
3707 8139 1.214367 CACACGCAACTACGAAAGGT 58.786 50.000 0.00 0.00 36.70 3.50
3708 8140 1.214367 ACACACGCAACTACGAAAGG 58.786 50.000 0.00 0.00 36.70 3.11
3709 8141 2.655577 CGAACACACGCAACTACGAAAG 60.656 50.000 0.00 0.00 36.70 2.62
3710 8142 1.255859 CGAACACACGCAACTACGAAA 59.744 47.619 0.00 0.00 36.70 3.46
3711 8143 0.847670 CGAACACACGCAACTACGAA 59.152 50.000 0.00 0.00 36.70 3.85
3712 8144 0.248580 ACGAACACACGCAACTACGA 60.249 50.000 0.00 0.00 36.70 3.43
3713 8145 0.111878 CACGAACACACGCAACTACG 60.112 55.000 0.00 0.00 36.70 3.51
3714 8146 0.382636 GCACGAACACACGCAACTAC 60.383 55.000 0.00 0.00 36.70 2.73
3715 8147 1.492319 GGCACGAACACACGCAACTA 61.492 55.000 0.00 0.00 36.70 2.24
3716 8148 2.707039 GCACGAACACACGCAACT 59.293 55.556 0.00 0.00 36.70 3.16
3717 8149 2.351888 GGCACGAACACACGCAAC 60.352 61.111 0.00 0.00 36.70 4.17
3718 8150 2.820037 TGGCACGAACACACGCAA 60.820 55.556 0.00 0.00 36.70 4.85
3719 8151 3.568743 GTGGCACGAACACACGCA 61.569 61.111 0.00 0.00 38.67 5.24
3720 8152 3.568743 TGTGGCACGAACACACGC 61.569 61.111 13.77 0.00 43.35 5.34
3733 8165 2.731451 CTGATAAGTGTCACACGTGTGG 59.269 50.000 39.88 25.18 45.65 4.17
3734 8166 2.731451 CCTGATAAGTGTCACACGTGTG 59.269 50.000 37.04 37.04 46.91 3.82
3735 8167 2.288825 CCCTGATAAGTGTCACACGTGT 60.289 50.000 17.22 17.22 39.64 4.49
3736 8168 2.288825 ACCCTGATAAGTGTCACACGTG 60.289 50.000 15.48 15.48 39.64 4.49
3737 8169 1.968493 ACCCTGATAAGTGTCACACGT 59.032 47.619 1.22 1.06 39.64 4.49
3738 8170 2.743636 ACCCTGATAAGTGTCACACG 57.256 50.000 1.22 0.00 39.64 4.49
3739 8171 5.767816 AAAAACCCTGATAAGTGTCACAC 57.232 39.130 0.00 0.00 34.10 3.82


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

AutoCloner maintained by Alex Coulton.