Multiple sequence alignment - TraesCS7D01G034400

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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 TraesCS7D01G034400 chr7D 100.000 3943 0 0 1 3943 17785134 17781192 0.000000e+00 7282.0
1 TraesCS7D01G034400 chr7D 90.217 92 5 4 1 90 100673661 100673572 2.490000e-22 117.0
2 TraesCS7D01G034400 chr4A 95.813 2221 77 9 889 3106 715901848 715904055 0.000000e+00 3572.0
3 TraesCS7D01G034400 chr4A 96.124 903 29 3 2205 3106 715906808 715907705 0.000000e+00 1469.0
4 TraesCS7D01G034400 chr4A 83.990 812 75 28 88 881 715900972 715901746 0.000000e+00 728.0
5 TraesCS7D01G034400 chr6A 94.013 618 36 1 3325 3942 13856427 13855811 0.000000e+00 935.0
6 TraesCS7D01G034400 chr1B 81.329 1189 179 33 1853 3024 517087096 517088258 0.000000e+00 926.0
7 TraesCS7D01G034400 chr1B 81.602 674 93 14 1165 1838 517078716 517079358 2.700000e-146 529.0
8 TraesCS7D01G034400 chr7A 92.926 622 30 11 3325 3943 624192872 624193482 0.000000e+00 893.0
9 TraesCS7D01G034400 chr7A 92.915 621 31 11 3325 3943 692577911 692578520 0.000000e+00 891.0
10 TraesCS7D01G034400 chr7A 90.698 43 4 0 3316 3358 465346551 465346593 1.530000e-04 58.4
11 TraesCS7D01G034400 chr6B 91.276 619 37 7 3325 3943 1497977 1497376 0.000000e+00 828.0
12 TraesCS7D01G034400 chr1A 91.011 89 6 2 1 87 496644218 496644306 6.920000e-23 119.0
13 TraesCS7D01G034400 chr2A 92.593 81 5 1 8 87 31757800 31757720 8.950000e-22 115.0
14 TraesCS7D01G034400 chr1D 90.588 85 6 2 4 87 398122705 398122788 1.160000e-20 111.0
15 TraesCS7D01G034400 chr7B 91.139 79 6 1 10 87 578433875 578433953 5.390000e-19 106.0
16 TraesCS7D01G034400 chr3A 88.462 52 2 3 3104 3154 57018593 57018545 4.260000e-05 60.2


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 TraesCS7D01G034400 chr7D 17781192 17785134 3942 True 7282 7282 100.000000 1 3943 1 chr7D.!!$R1 3942
1 TraesCS7D01G034400 chr4A 715900972 715907705 6733 False 1923 3572 91.975667 88 3106 3 chr4A.!!$F1 3018
2 TraesCS7D01G034400 chr6A 13855811 13856427 616 True 935 935 94.013000 3325 3942 1 chr6A.!!$R1 617
3 TraesCS7D01G034400 chr1B 517087096 517088258 1162 False 926 926 81.329000 1853 3024 1 chr1B.!!$F2 1171
4 TraesCS7D01G034400 chr1B 517078716 517079358 642 False 529 529 81.602000 1165 1838 1 chr1B.!!$F1 673
5 TraesCS7D01G034400 chr7A 624192872 624193482 610 False 893 893 92.926000 3325 3943 1 chr7A.!!$F2 618
6 TraesCS7D01G034400 chr7A 692577911 692578520 609 False 891 891 92.915000 3325 3943 1 chr7A.!!$F3 618
7 TraesCS7D01G034400 chr6B 1497376 1497977 601 True 828 828 91.276000 3325 3943 1 chr6B.!!$R1 618

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
736 761 0.107456 CTCCCGCCAGAGCATGTAAT 59.893 55.0 0.00 0.0 39.83 1.89 F
863 888 0.178068 TTCCAATCTCCTGGCGCTAC 59.822 55.0 7.64 0.0 36.32 3.58 F
1544 1663 0.668535 AAGAAGCTTGGACGTTTGGC 59.331 50.0 2.10 0.0 0.00 4.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2471 2600 0.517316 GCACCAGAAAGGCGTTGTAG 59.483 55.000 0.0 0.0 43.14 2.74 R
2721 2850 1.601903 CACAAAGCTAAGCACGACCAA 59.398 47.619 0.0 0.0 0.00 3.67 R
3123 3259 0.096976 CCAATACTTCCGCAGCAACG 59.903 55.000 0.0 0.0 0.00 4.10 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
22 23 5.936686 GGGCCGTCCTAATTAACTAAATC 57.063 43.478 0.00 0.00 0.00 2.17
23 24 5.370679 GGGCCGTCCTAATTAACTAAATCA 58.629 41.667 0.00 0.00 0.00 2.57
24 25 5.237996 GGGCCGTCCTAATTAACTAAATCAC 59.762 44.000 0.00 0.00 0.00 3.06
25 26 5.818857 GGCCGTCCTAATTAACTAAATCACA 59.181 40.000 0.00 0.00 0.00 3.58
26 27 6.018180 GGCCGTCCTAATTAACTAAATCACAG 60.018 42.308 0.00 0.00 0.00 3.66
27 28 6.511282 GCCGTCCTAATTAACTAAATCACAGC 60.511 42.308 0.00 0.00 0.00 4.40
28 29 6.018180 CCGTCCTAATTAACTAAATCACAGCC 60.018 42.308 0.00 0.00 0.00 4.85
29 30 6.537301 CGTCCTAATTAACTAAATCACAGCCA 59.463 38.462 0.00 0.00 0.00 4.75
30 31 7.226720 CGTCCTAATTAACTAAATCACAGCCAT 59.773 37.037 0.00 0.00 0.00 4.40
31 32 8.903820 GTCCTAATTAACTAAATCACAGCCATT 58.096 33.333 0.00 0.00 0.00 3.16
39 40 8.579850 AACTAAATCACAGCCATTAATCTTCA 57.420 30.769 0.00 0.00 0.00 3.02
40 41 8.579850 ACTAAATCACAGCCATTAATCTTCAA 57.420 30.769 0.00 0.00 0.00 2.69
41 42 9.193806 ACTAAATCACAGCCATTAATCTTCAAT 57.806 29.630 0.00 0.00 0.00 2.57
45 46 7.031226 TCACAGCCATTAATCTTCAATTAGC 57.969 36.000 0.00 0.00 0.00 3.09
46 47 6.039717 TCACAGCCATTAATCTTCAATTAGCC 59.960 38.462 0.00 0.00 0.00 3.93
47 48 5.302823 ACAGCCATTAATCTTCAATTAGCCC 59.697 40.000 0.00 0.00 0.00 5.19
48 49 4.520492 AGCCATTAATCTTCAATTAGCCCG 59.480 41.667 0.00 0.00 0.00 6.13
49 50 4.278419 GCCATTAATCTTCAATTAGCCCGT 59.722 41.667 0.00 0.00 0.00 5.28
50 51 5.472137 GCCATTAATCTTCAATTAGCCCGTA 59.528 40.000 0.00 0.00 0.00 4.02
51 52 6.016610 GCCATTAATCTTCAATTAGCCCGTAA 60.017 38.462 0.00 0.00 0.00 3.18
52 53 7.469456 GCCATTAATCTTCAATTAGCCCGTAAA 60.469 37.037 0.00 0.00 0.00 2.01
53 54 8.410141 CCATTAATCTTCAATTAGCCCGTAAAA 58.590 33.333 0.00 0.00 0.00 1.52
54 55 9.233232 CATTAATCTTCAATTAGCCCGTAAAAC 57.767 33.333 0.00 0.00 0.00 2.43
55 56 5.830000 ATCTTCAATTAGCCCGTAAAACC 57.170 39.130 0.00 0.00 0.00 3.27
56 57 4.913784 TCTTCAATTAGCCCGTAAAACCT 58.086 39.130 0.00 0.00 0.00 3.50
57 58 4.939439 TCTTCAATTAGCCCGTAAAACCTC 59.061 41.667 0.00 0.00 0.00 3.85
58 59 4.563140 TCAATTAGCCCGTAAAACCTCT 57.437 40.909 0.00 0.00 0.00 3.69
59 60 4.258543 TCAATTAGCCCGTAAAACCTCTG 58.741 43.478 0.00 0.00 0.00 3.35
60 61 3.994931 ATTAGCCCGTAAAACCTCTGT 57.005 42.857 0.00 0.00 0.00 3.41
61 62 2.754946 TAGCCCGTAAAACCTCTGTG 57.245 50.000 0.00 0.00 0.00 3.66
62 63 1.053424 AGCCCGTAAAACCTCTGTGA 58.947 50.000 0.00 0.00 0.00 3.58
63 64 1.418637 AGCCCGTAAAACCTCTGTGAA 59.581 47.619 0.00 0.00 0.00 3.18
64 65 2.039879 AGCCCGTAAAACCTCTGTGAAT 59.960 45.455 0.00 0.00 0.00 2.57
65 66 2.418976 GCCCGTAAAACCTCTGTGAATC 59.581 50.000 0.00 0.00 0.00 2.52
66 67 3.007635 CCCGTAAAACCTCTGTGAATCC 58.992 50.000 0.00 0.00 0.00 3.01
67 68 3.007635 CCGTAAAACCTCTGTGAATCCC 58.992 50.000 0.00 0.00 0.00 3.85
68 69 3.007635 CGTAAAACCTCTGTGAATCCCC 58.992 50.000 0.00 0.00 0.00 4.81
69 70 2.604912 AAAACCTCTGTGAATCCCCC 57.395 50.000 0.00 0.00 0.00 5.40
70 71 1.760405 AAACCTCTGTGAATCCCCCT 58.240 50.000 0.00 0.00 0.00 4.79
71 72 0.995024 AACCTCTGTGAATCCCCCTG 59.005 55.000 0.00 0.00 0.00 4.45
72 73 0.178861 ACCTCTGTGAATCCCCCTGT 60.179 55.000 0.00 0.00 0.00 4.00
73 74 0.254178 CCTCTGTGAATCCCCCTGTG 59.746 60.000 0.00 0.00 0.00 3.66
74 75 0.987294 CTCTGTGAATCCCCCTGTGT 59.013 55.000 0.00 0.00 0.00 3.72
75 76 0.692476 TCTGTGAATCCCCCTGTGTG 59.308 55.000 0.00 0.00 0.00 3.82
76 77 0.401738 CTGTGAATCCCCCTGTGTGT 59.598 55.000 0.00 0.00 0.00 3.72
77 78 1.628340 CTGTGAATCCCCCTGTGTGTA 59.372 52.381 0.00 0.00 0.00 2.90
78 79 1.628340 TGTGAATCCCCCTGTGTGTAG 59.372 52.381 0.00 0.00 0.00 2.74
79 80 0.618458 TGAATCCCCCTGTGTGTAGC 59.382 55.000 0.00 0.00 0.00 3.58
80 81 0.618458 GAATCCCCCTGTGTGTAGCA 59.382 55.000 0.00 0.00 0.00 3.49
81 82 1.212935 GAATCCCCCTGTGTGTAGCAT 59.787 52.381 0.00 0.00 0.00 3.79
82 83 1.298953 ATCCCCCTGTGTGTAGCATT 58.701 50.000 0.00 0.00 0.00 3.56
83 84 1.959710 TCCCCCTGTGTGTAGCATTA 58.040 50.000 0.00 0.00 0.00 1.90
84 85 1.557832 TCCCCCTGTGTGTAGCATTAC 59.442 52.381 0.00 0.00 0.00 1.89
85 86 1.559682 CCCCCTGTGTGTAGCATTACT 59.440 52.381 0.00 0.00 0.00 2.24
86 87 2.420129 CCCCCTGTGTGTAGCATTACTC 60.420 54.545 0.00 0.00 0.00 2.59
90 91 4.393062 CCCTGTGTGTAGCATTACTCTTTG 59.607 45.833 0.00 0.00 0.00 2.77
120 121 1.401018 GCAGTACCCAACGAAATGCAC 60.401 52.381 0.00 0.00 32.58 4.57
135 136 1.368850 GCACTCGTCAAACAACCGC 60.369 57.895 0.00 0.00 0.00 5.68
151 152 4.098807 ACAACCGCCATTAGACAAAGTTTT 59.901 37.500 0.00 0.00 0.00 2.43
152 153 4.237349 ACCGCCATTAGACAAAGTTTTG 57.763 40.909 3.17 3.17 43.62 2.44
153 154 3.005367 ACCGCCATTAGACAAAGTTTTGG 59.995 43.478 9.22 0.00 42.34 3.28
154 155 3.574614 CGCCATTAGACAAAGTTTTGGG 58.425 45.455 9.22 1.33 42.34 4.12
172 173 0.603975 GGTTCCAGTGGTGAGCACTC 60.604 60.000 15.19 3.45 0.00 3.51
185 186 3.251972 GTGAGCACTCTTTTGGAGAAAGG 59.748 47.826 0.00 0.00 44.45 3.11
191 192 5.067805 GCACTCTTTTGGAGAAAGGAAAAGA 59.932 40.000 0.00 0.00 44.45 2.52
192 193 6.405842 GCACTCTTTTGGAGAAAGGAAAAGAA 60.406 38.462 0.00 0.00 42.32 2.52
194 195 8.034804 CACTCTTTTGGAGAAAGGAAAAGAAAA 58.965 33.333 0.00 0.00 42.32 2.29
197 198 8.034804 TCTTTTGGAGAAAGGAAAAGAAAAGTG 58.965 33.333 0.00 0.00 40.83 3.16
199 200 6.699575 TGGAGAAAGGAAAAGAAAAGTGAG 57.300 37.500 0.00 0.00 0.00 3.51
200 201 5.594317 TGGAGAAAGGAAAAGAAAAGTGAGG 59.406 40.000 0.00 0.00 0.00 3.86
201 202 5.828328 GGAGAAAGGAAAAGAAAAGTGAGGA 59.172 40.000 0.00 0.00 0.00 3.71
202 203 6.016693 GGAGAAAGGAAAAGAAAAGTGAGGAG 60.017 42.308 0.00 0.00 0.00 3.69
204 205 7.293828 AGAAAGGAAAAGAAAAGTGAGGAGAT 58.706 34.615 0.00 0.00 0.00 2.75
205 206 7.446931 AGAAAGGAAAAGAAAAGTGAGGAGATC 59.553 37.037 0.00 0.00 0.00 2.75
207 208 6.788218 AGGAAAAGAAAAGTGAGGAGATCAT 58.212 36.000 0.00 0.00 40.92 2.45
208 209 6.883756 AGGAAAAGAAAAGTGAGGAGATCATC 59.116 38.462 0.00 0.00 40.92 2.92
209 210 6.183360 GGAAAAGAAAAGTGAGGAGATCATCG 60.183 42.308 0.00 0.00 40.92 3.84
210 211 5.413309 AAGAAAAGTGAGGAGATCATCGT 57.587 39.130 0.00 0.00 40.92 3.73
211 212 6.531503 AAGAAAAGTGAGGAGATCATCGTA 57.468 37.500 0.00 0.00 40.92 3.43
212 213 6.723298 AGAAAAGTGAGGAGATCATCGTAT 57.277 37.500 0.00 0.00 40.92 3.06
223 224 5.175856 GGAGATCATCGTATTCCGTTTCTTG 59.824 44.000 0.00 0.00 37.94 3.02
342 348 4.021719 CCCGACTCCAACAAGTCTTAGTTA 60.022 45.833 2.89 0.00 42.90 2.24
343 349 5.510179 CCCGACTCCAACAAGTCTTAGTTAA 60.510 44.000 2.89 0.00 42.90 2.01
344 350 6.164176 CCGACTCCAACAAGTCTTAGTTAAT 58.836 40.000 2.89 0.00 42.90 1.40
345 351 6.310711 CCGACTCCAACAAGTCTTAGTTAATC 59.689 42.308 2.89 0.00 42.90 1.75
346 352 6.310711 CGACTCCAACAAGTCTTAGTTAATCC 59.689 42.308 2.89 0.00 42.90 3.01
347 353 6.164176 ACTCCAACAAGTCTTAGTTAATCCG 58.836 40.000 0.00 0.00 0.00 4.18
348 354 4.933400 TCCAACAAGTCTTAGTTAATCCGC 59.067 41.667 0.00 0.00 0.00 5.54
349 355 4.935808 CCAACAAGTCTTAGTTAATCCGCT 59.064 41.667 0.00 0.00 0.00 5.52
350 356 5.411669 CCAACAAGTCTTAGTTAATCCGCTT 59.588 40.000 0.00 0.00 0.00 4.68
381 399 7.598493 AGTTTGAAGAAGAAGAAGAAGATCGAG 59.402 37.037 0.00 0.00 0.00 4.04
396 418 2.983402 TCGAGTCTAGGACGTTTGTG 57.017 50.000 0.00 0.00 37.67 3.33
424 448 5.455899 CCCAAGGAGGAAAAGAGATATGGAG 60.456 48.000 0.00 0.00 41.22 3.86
441 465 2.766263 TGGAGCTGATTATTGAGGACGT 59.234 45.455 0.00 0.00 0.00 4.34
443 467 4.404394 TGGAGCTGATTATTGAGGACGTTA 59.596 41.667 0.00 0.00 0.00 3.18
457 481 2.544267 GGACGTTATGATAAGTGGCAGC 59.456 50.000 0.00 0.00 0.00 5.25
492 516 2.030562 CGAAGACCTGGTTGCCGT 59.969 61.111 0.00 0.00 0.00 5.68
542 566 2.856222 CGAGGTTCCTACTACGGGTAT 58.144 52.381 0.00 0.00 0.00 2.73
568 592 1.101635 TTCCTCGAGATGACCGCGAT 61.102 55.000 15.71 0.00 45.51 4.58
621 646 1.301795 TGCCCAACGCACGTTCATA 60.302 52.632 5.28 0.00 44.64 2.15
627 652 1.701545 AACGCACGTTCATATGCCCG 61.702 55.000 1.93 10.95 38.69 6.13
650 675 3.950794 TTCATCGCGCGGCCTTCTT 62.951 57.895 31.69 3.29 0.00 2.52
683 708 1.857217 CGATCTGCATCGTCTTCTTGG 59.143 52.381 1.50 0.00 45.90 3.61
686 711 2.171003 TCTGCATCGTCTTCTTGGAGA 58.829 47.619 0.00 0.00 35.78 3.71
687 712 2.094494 TCTGCATCGTCTTCTTGGAGAC 60.094 50.000 0.00 0.00 42.05 3.36
698 723 2.457598 TCTTGGAGACGCAGGTAGAAT 58.542 47.619 0.00 0.00 0.00 2.40
701 726 3.695830 TGGAGACGCAGGTAGAATTTT 57.304 42.857 0.00 0.00 0.00 1.82
723 748 3.735237 TGAACTATGATTCTCTCCCGC 57.265 47.619 0.00 0.00 0.00 6.13
724 749 2.365617 TGAACTATGATTCTCTCCCGCC 59.634 50.000 0.00 0.00 0.00 6.13
725 750 2.088104 ACTATGATTCTCTCCCGCCA 57.912 50.000 0.00 0.00 0.00 5.69
728 753 1.047002 ATGATTCTCTCCCGCCAGAG 58.953 55.000 3.06 3.06 41.35 3.35
733 758 2.685017 TCTCCCGCCAGAGCATGT 60.685 61.111 0.00 0.00 39.83 3.21
735 760 0.975556 TCTCCCGCCAGAGCATGTAA 60.976 55.000 0.00 0.00 39.83 2.41
736 761 0.107456 CTCCCGCCAGAGCATGTAAT 59.893 55.000 0.00 0.00 39.83 1.89
750 775 6.823689 AGAGCATGTAATTATTTTCACCGTCT 59.176 34.615 0.00 0.00 0.00 4.18
751 776 7.336931 AGAGCATGTAATTATTTTCACCGTCTT 59.663 33.333 0.00 0.00 0.00 3.01
752 777 7.472543 AGCATGTAATTATTTTCACCGTCTTC 58.527 34.615 0.00 0.00 0.00 2.87
753 778 7.336931 AGCATGTAATTATTTTCACCGTCTTCT 59.663 33.333 0.00 0.00 0.00 2.85
789 814 2.728690 TGCAATGAAGCAAAATCGCT 57.271 40.000 0.00 0.00 46.67 4.93
822 847 6.613679 TCTCACTATAATTGGGTGTGGACATA 59.386 38.462 0.00 0.00 33.30 2.29
831 856 8.635765 AATTGGGTGTGGACATACATATATTC 57.364 34.615 1.73 0.00 32.43 1.75
856 881 4.141181 TGGATAACCCATTCCAATCTCCTG 60.141 45.833 0.00 0.00 40.82 3.86
863 888 0.178068 TTCCAATCTCCTGGCGCTAC 59.822 55.000 7.64 0.00 36.32 3.58
864 889 0.975556 TCCAATCTCCTGGCGCTACA 60.976 55.000 7.64 0.00 36.32 2.74
867 892 0.905357 AATCTCCTGGCGCTACAACT 59.095 50.000 7.64 0.00 0.00 3.16
872 897 3.895656 TCTCCTGGCGCTACAACTTATAT 59.104 43.478 7.64 0.00 0.00 0.86
877 902 6.434965 TCCTGGCGCTACAACTTATATATACA 59.565 38.462 7.64 0.00 0.00 2.29
881 906 8.741841 TGGCGCTACAACTTATATATACATACA 58.258 33.333 7.64 0.00 0.00 2.29
882 907 9.234384 GGCGCTACAACTTATATATACATACAG 57.766 37.037 7.64 0.00 0.00 2.74
883 908 9.999009 GCGCTACAACTTATATATACATACAGA 57.001 33.333 0.00 0.00 0.00 3.41
950 1069 3.737663 GTGTCTCACAGCTGAGGATCATC 60.738 52.174 23.35 0.00 43.87 2.92
1065 1184 0.739112 CTGGTGAGAAGGCTCTTCGC 60.739 60.000 10.32 10.32 41.84 4.70
1248 1367 2.683933 GAGGAACAGCCGAGGGGA 60.684 66.667 0.00 0.00 43.43 4.81
1249 1368 3.003763 AGGAACAGCCGAGGGGAC 61.004 66.667 0.00 0.00 43.43 4.46
1250 1369 3.319198 GGAACAGCCGAGGGGACA 61.319 66.667 0.00 0.00 34.06 4.02
1251 1370 2.047179 GAACAGCCGAGGGGACAC 60.047 66.667 0.00 0.00 34.06 3.67
1252 1371 3.934391 GAACAGCCGAGGGGACACG 62.934 68.421 0.00 0.00 44.43 4.49
1384 1503 0.955178 CCTCTATCTCGCCGTGTCAT 59.045 55.000 0.00 0.00 0.00 3.06
1393 1512 4.794439 CCGTGTCATGCCGCTCGA 62.794 66.667 0.00 0.00 0.00 4.04
1544 1663 0.668535 AAGAAGCTTGGACGTTTGGC 59.331 50.000 2.10 0.00 0.00 4.52
1594 1713 5.278266 CGGACCTCTTTTGCAGAAATTACAA 60.278 40.000 0.00 0.00 0.00 2.41
1597 1716 7.112452 ACCTCTTTTGCAGAAATTACAAGTT 57.888 32.000 0.00 0.00 0.00 2.66
1918 2037 2.634982 AAAATACGTCGTCGGTAGCA 57.365 45.000 0.00 0.00 41.85 3.49
2107 2226 1.098050 CAGCTTCTTGCCCATGGTAC 58.902 55.000 11.73 2.72 44.23 3.34
2137 2256 9.660180 AAAAACCCATATTGCGTTAATTAATGT 57.340 25.926 16.79 2.58 0.00 2.71
2139 2258 9.959749 AAACCCATATTGCGTTAATTAATGTAG 57.040 29.630 16.79 4.55 0.00 2.74
2140 2259 7.590279 ACCCATATTGCGTTAATTAATGTAGC 58.410 34.615 16.79 12.77 0.00 3.58
2471 2600 2.435410 CTGCGGGGTACGTTTCCC 60.435 66.667 16.97 16.97 46.52 3.97
2555 2684 1.457643 CATCTACGGGAGGGGAGCA 60.458 63.158 0.00 0.00 0.00 4.26
2608 2737 1.564348 GGCCCTCATCTTCCTTTGGTA 59.436 52.381 0.00 0.00 0.00 3.25
2721 2850 1.668151 GCGTTGCCGTTCTTCTCCT 60.668 57.895 0.00 0.00 36.15 3.69
2753 2882 3.198236 CTTTGTGTGGGCAGCACCG 62.198 63.158 0.00 0.00 40.62 4.94
2799 2928 1.234615 ACTGTTCCGTGCCCAAATCG 61.235 55.000 0.00 0.00 0.00 3.34
2900 3029 5.692115 TGTTCTGGTTCCTCAATGCTATA 57.308 39.130 0.00 0.00 0.00 1.31
2948 3077 4.510571 TCATGATCACAGTCTGATTGTGG 58.489 43.478 26.43 14.14 44.63 4.17
2953 3082 0.767375 ACAGTCTGATTGTGGCTGGT 59.233 50.000 6.91 0.00 0.00 4.00
3072 3208 3.256879 CGTACTCTGTATGATGAGGCCAT 59.743 47.826 5.01 0.00 34.84 4.40
3075 3211 4.226384 ACTCTGTATGATGAGGCCATGTA 58.774 43.478 5.01 0.00 34.84 2.29
3082 3218 5.573380 ATGATGAGGCCATGTATGTACTT 57.427 39.130 5.01 0.00 32.09 2.24
3120 3256 9.991906 TTATTAAAGAAACTAGATGATACCCCG 57.008 33.333 0.00 0.00 0.00 5.73
3121 3257 7.664552 TTAAAGAAACTAGATGATACCCCGA 57.335 36.000 0.00 0.00 0.00 5.14
3122 3258 5.793030 AAGAAACTAGATGATACCCCGAG 57.207 43.478 0.00 0.00 0.00 4.63
3123 3259 3.574826 AGAAACTAGATGATACCCCGAGC 59.425 47.826 0.00 0.00 0.00 5.03
3124 3260 1.535833 ACTAGATGATACCCCGAGCG 58.464 55.000 0.00 0.00 0.00 5.03
3126 3262 1.887198 CTAGATGATACCCCGAGCGTT 59.113 52.381 0.00 0.00 0.00 4.84
3129 3265 1.686325 ATGATACCCCGAGCGTTGCT 61.686 55.000 0.00 0.00 43.88 3.91
3130 3266 1.883084 GATACCCCGAGCGTTGCTG 60.883 63.158 0.00 0.00 39.88 4.41
3136 3272 4.139420 CGAGCGTTGCTGCGGAAG 62.139 66.667 0.00 0.00 39.88 3.46
3138 3274 1.736645 GAGCGTTGCTGCGGAAGTA 60.737 57.895 0.00 0.00 39.88 2.24
3139 3275 1.079127 AGCGTTGCTGCGGAAGTAT 60.079 52.632 0.00 0.00 37.57 2.12
3140 3276 0.673644 AGCGTTGCTGCGGAAGTATT 60.674 50.000 0.00 0.00 37.57 1.89
3141 3277 0.521242 GCGTTGCTGCGGAAGTATTG 60.521 55.000 0.00 0.00 0.00 1.90
3142 3278 0.096976 CGTTGCTGCGGAAGTATTGG 59.903 55.000 0.00 0.00 0.00 3.16
3143 3279 1.165270 GTTGCTGCGGAAGTATTGGT 58.835 50.000 0.00 0.00 0.00 3.67
3144 3280 2.352388 GTTGCTGCGGAAGTATTGGTA 58.648 47.619 0.00 0.00 0.00 3.25
3145 3281 2.745281 GTTGCTGCGGAAGTATTGGTAA 59.255 45.455 0.00 0.00 0.00 2.85
3147 3283 1.330829 GCTGCGGAAGTATTGGTAAGC 59.669 52.381 0.00 0.00 0.00 3.09
3148 3284 2.627945 CTGCGGAAGTATTGGTAAGCA 58.372 47.619 0.00 0.00 0.00 3.91
3150 3286 3.616219 TGCGGAAGTATTGGTAAGCAAT 58.384 40.909 0.00 0.00 0.00 3.56
3151 3287 4.013728 TGCGGAAGTATTGGTAAGCAATT 58.986 39.130 0.00 0.00 0.00 2.32
3152 3288 5.186942 TGCGGAAGTATTGGTAAGCAATTA 58.813 37.500 0.00 0.00 0.00 1.40
3154 3290 6.142817 GCGGAAGTATTGGTAAGCAATTATG 58.857 40.000 0.00 0.00 0.00 1.90
3155 3291 6.238648 GCGGAAGTATTGGTAAGCAATTATGT 60.239 38.462 0.00 0.00 0.00 2.29
3156 3292 7.681065 GCGGAAGTATTGGTAAGCAATTATGTT 60.681 37.037 0.00 0.00 0.00 2.71
3157 3293 8.188139 CGGAAGTATTGGTAAGCAATTATGTTT 58.812 33.333 0.00 0.00 34.16 2.83
3158 3294 9.301153 GGAAGTATTGGTAAGCAATTATGTTTG 57.699 33.333 0.00 0.00 31.90 2.93
3164 3300 8.984891 TTGGTAAGCAATTATGTTTGAAGATG 57.015 30.769 0.00 0.00 31.90 2.90
3165 3301 8.347004 TGGTAAGCAATTATGTTTGAAGATGA 57.653 30.769 0.00 0.00 31.90 2.92
3197 3333 8.801715 TTTTTAGCAAACATGAAGAGATGAAC 57.198 30.769 0.00 0.00 0.00 3.18
3198 3334 6.500684 TTAGCAAACATGAAGAGATGAACC 57.499 37.500 0.00 0.00 0.00 3.62
3199 3335 4.660168 AGCAAACATGAAGAGATGAACCT 58.340 39.130 0.00 0.00 0.00 3.50
3200 3336 4.458295 AGCAAACATGAAGAGATGAACCTG 59.542 41.667 0.00 0.00 0.00 4.00
3201 3337 4.456911 GCAAACATGAAGAGATGAACCTGA 59.543 41.667 0.00 0.00 0.00 3.86
3202 3338 5.618640 GCAAACATGAAGAGATGAACCTGAC 60.619 44.000 0.00 0.00 0.00 3.51
3203 3339 4.213564 ACATGAAGAGATGAACCTGACC 57.786 45.455 0.00 0.00 0.00 4.02
3204 3340 3.584406 ACATGAAGAGATGAACCTGACCA 59.416 43.478 0.00 0.00 0.00 4.02
3205 3341 4.042062 ACATGAAGAGATGAACCTGACCAA 59.958 41.667 0.00 0.00 0.00 3.67
3206 3342 4.705110 TGAAGAGATGAACCTGACCAAA 57.295 40.909 0.00 0.00 0.00 3.28
3207 3343 5.246981 TGAAGAGATGAACCTGACCAAAT 57.753 39.130 0.00 0.00 0.00 2.32
3208 3344 6.373005 TGAAGAGATGAACCTGACCAAATA 57.627 37.500 0.00 0.00 0.00 1.40
3209 3345 6.409704 TGAAGAGATGAACCTGACCAAATAG 58.590 40.000 0.00 0.00 0.00 1.73
3210 3346 6.213397 TGAAGAGATGAACCTGACCAAATAGA 59.787 38.462 0.00 0.00 0.00 1.98
3211 3347 6.821616 AGAGATGAACCTGACCAAATAGAT 57.178 37.500 0.00 0.00 0.00 1.98
3212 3348 7.921041 AGAGATGAACCTGACCAAATAGATA 57.079 36.000 0.00 0.00 0.00 1.98
3213 3349 8.503428 AGAGATGAACCTGACCAAATAGATAT 57.497 34.615 0.00 0.00 0.00 1.63
3214 3350 9.607333 AGAGATGAACCTGACCAAATAGATATA 57.393 33.333 0.00 0.00 0.00 0.86
3215 3351 9.646427 GAGATGAACCTGACCAAATAGATATAC 57.354 37.037 0.00 0.00 0.00 1.47
3216 3352 9.159254 AGATGAACCTGACCAAATAGATATACA 57.841 33.333 0.00 0.00 0.00 2.29
3217 3353 9.950496 GATGAACCTGACCAAATAGATATACAT 57.050 33.333 0.00 0.00 0.00 2.29
3218 3354 9.950496 ATGAACCTGACCAAATAGATATACATC 57.050 33.333 0.00 0.00 0.00 3.06
3219 3355 9.159254 TGAACCTGACCAAATAGATATACATCT 57.841 33.333 0.00 0.00 44.04 2.90
3245 3381 8.737168 TTCAGTGAAAGATAATCATGGGTTAG 57.263 34.615 2.20 0.00 0.00 2.34
3246 3382 8.089625 TCAGTGAAAGATAATCATGGGTTAGA 57.910 34.615 0.00 0.00 0.00 2.10
3247 3383 8.717717 TCAGTGAAAGATAATCATGGGTTAGAT 58.282 33.333 0.00 0.00 0.00 1.98
3248 3384 8.781196 CAGTGAAAGATAATCATGGGTTAGATG 58.219 37.037 0.00 0.00 0.00 2.90
3249 3385 7.941238 AGTGAAAGATAATCATGGGTTAGATGG 59.059 37.037 0.00 0.00 0.00 3.51
3250 3386 7.939039 GTGAAAGATAATCATGGGTTAGATGGA 59.061 37.037 0.00 0.00 0.00 3.41
3251 3387 8.501904 TGAAAGATAATCATGGGTTAGATGGAA 58.498 33.333 0.00 0.00 0.00 3.53
3252 3388 8.697507 AAAGATAATCATGGGTTAGATGGAAC 57.302 34.615 0.00 0.00 0.00 3.62
3263 3399 5.954335 GGTTAGATGGAACCAAACTCAATG 58.046 41.667 0.00 0.00 46.97 2.82
3264 3400 5.710099 GGTTAGATGGAACCAAACTCAATGA 59.290 40.000 0.00 0.00 46.97 2.57
3265 3401 6.208599 GGTTAGATGGAACCAAACTCAATGAA 59.791 38.462 0.00 0.00 46.97 2.57
3266 3402 7.093771 GGTTAGATGGAACCAAACTCAATGAAT 60.094 37.037 0.00 0.00 46.97 2.57
3267 3403 8.956426 GTTAGATGGAACCAAACTCAATGAATA 58.044 33.333 0.00 0.00 0.00 1.75
3268 3404 9.527157 TTAGATGGAACCAAACTCAATGAATAA 57.473 29.630 0.00 0.00 0.00 1.40
3269 3405 8.599624 AGATGGAACCAAACTCAATGAATAAT 57.400 30.769 0.00 0.00 0.00 1.28
3270 3406 9.039165 AGATGGAACCAAACTCAATGAATAATT 57.961 29.630 0.00 0.00 0.00 1.40
3271 3407 9.657419 GATGGAACCAAACTCAATGAATAATTT 57.343 29.630 0.00 0.00 0.00 1.82
3272 3408 9.657419 ATGGAACCAAACTCAATGAATAATTTC 57.343 29.630 0.00 0.00 0.00 2.17
3273 3409 8.869109 TGGAACCAAACTCAATGAATAATTTCT 58.131 29.630 0.00 0.00 32.78 2.52
3274 3410 9.710900 GGAACCAAACTCAATGAATAATTTCTT 57.289 29.630 0.00 0.00 32.78 2.52
3276 3412 9.492973 AACCAAACTCAATGAATAATTTCTTGG 57.507 29.630 0.00 0.00 32.78 3.61
3277 3413 8.869109 ACCAAACTCAATGAATAATTTCTTGGA 58.131 29.630 0.00 0.00 32.78 3.53
3278 3414 9.709495 CCAAACTCAATGAATAATTTCTTGGAA 57.291 29.630 0.00 0.00 32.78 3.53
3302 3438 6.543430 AAAAGCAATATTCCCTAACATGCA 57.457 33.333 0.00 0.00 34.89 3.96
3303 3439 5.779529 AAGCAATATTCCCTAACATGCAG 57.220 39.130 0.00 0.00 34.89 4.41
3304 3440 5.052693 AGCAATATTCCCTAACATGCAGA 57.947 39.130 0.00 0.00 34.89 4.26
3306 3442 5.893255 AGCAATATTCCCTAACATGCAGAAA 59.107 36.000 0.00 0.00 34.89 2.52
3307 3443 6.380846 AGCAATATTCCCTAACATGCAGAAAA 59.619 34.615 0.00 0.00 34.89 2.29
3309 3445 7.416664 GCAATATTCCCTAACATGCAGAAAAGA 60.417 37.037 0.00 0.00 32.80 2.52
3310 3446 8.469200 CAATATTCCCTAACATGCAGAAAAGAA 58.531 33.333 0.00 0.00 0.00 2.52
3313 3449 4.518970 TCCCTAACATGCAGAAAAGAACAC 59.481 41.667 0.00 0.00 0.00 3.32
3314 3450 4.278170 CCCTAACATGCAGAAAAGAACACA 59.722 41.667 0.00 0.00 0.00 3.72
3316 3452 6.449698 CCTAACATGCAGAAAAGAACACAAT 58.550 36.000 0.00 0.00 0.00 2.71
3317 3453 6.925165 CCTAACATGCAGAAAAGAACACAATT 59.075 34.615 0.00 0.00 0.00 2.32
3319 3455 9.630098 CTAACATGCAGAAAAGAACACAATTAT 57.370 29.630 0.00 0.00 0.00 1.28
3320 3456 8.891671 AACATGCAGAAAAGAACACAATTATT 57.108 26.923 0.00 0.00 0.00 1.40
3347 3483 2.962786 CGTCAACCCGTGCGTTCA 60.963 61.111 0.00 0.00 0.00 3.18
3732 6522 5.895636 ATCTGCATCGGTTTAATGACAAA 57.104 34.783 0.00 0.00 0.00 2.83
3750 6540 3.069729 ACAAAGACTACTCGGAGCACTTT 59.930 43.478 4.58 8.75 31.23 2.66
3931 7122 7.012610 CACACATGAGCATTCATAATCTTACCA 59.987 37.037 0.00 0.00 42.12 3.25
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 5.237996 GTGATTTAGTTAATTAGGACGGCCC 59.762 44.000 1.76 0.00 33.31 5.80
1 2 5.818857 TGTGATTTAGTTAATTAGGACGGCC 59.181 40.000 0.00 0.00 0.00 6.13
2 3 6.511282 GCTGTGATTTAGTTAATTAGGACGGC 60.511 42.308 0.00 0.00 0.00 5.68
3 4 6.018180 GGCTGTGATTTAGTTAATTAGGACGG 60.018 42.308 0.00 0.00 0.00 4.79
4 5 6.537301 TGGCTGTGATTTAGTTAATTAGGACG 59.463 38.462 0.00 0.00 0.00 4.79
5 6 7.859325 TGGCTGTGATTTAGTTAATTAGGAC 57.141 36.000 0.00 0.00 0.00 3.85
13 14 9.679661 TGAAGATTAATGGCTGTGATTTAGTTA 57.320 29.630 0.00 0.00 0.00 2.24
14 15 8.579850 TGAAGATTAATGGCTGTGATTTAGTT 57.420 30.769 0.00 0.00 0.00 2.24
15 16 8.579850 TTGAAGATTAATGGCTGTGATTTAGT 57.420 30.769 0.00 0.00 0.00 2.24
19 20 8.139989 GCTAATTGAAGATTAATGGCTGTGATT 58.860 33.333 0.00 0.00 0.00 2.57
20 21 7.255730 GGCTAATTGAAGATTAATGGCTGTGAT 60.256 37.037 0.00 0.00 0.00 3.06
21 22 6.039717 GGCTAATTGAAGATTAATGGCTGTGA 59.960 38.462 0.00 0.00 0.00 3.58
22 23 6.211515 GGCTAATTGAAGATTAATGGCTGTG 58.788 40.000 0.00 0.00 0.00 3.66
23 24 5.302823 GGGCTAATTGAAGATTAATGGCTGT 59.697 40.000 0.00 0.00 0.00 4.40
24 25 5.563475 CGGGCTAATTGAAGATTAATGGCTG 60.563 44.000 0.00 0.00 0.00 4.85
25 26 4.520492 CGGGCTAATTGAAGATTAATGGCT 59.480 41.667 0.00 0.00 0.00 4.75
26 27 4.278419 ACGGGCTAATTGAAGATTAATGGC 59.722 41.667 0.00 0.00 0.00 4.40
27 28 7.504924 TTACGGGCTAATTGAAGATTAATGG 57.495 36.000 0.00 0.00 0.00 3.16
28 29 9.233232 GTTTTACGGGCTAATTGAAGATTAATG 57.767 33.333 0.00 0.00 0.00 1.90
29 30 8.410912 GGTTTTACGGGCTAATTGAAGATTAAT 58.589 33.333 0.00 0.00 0.00 1.40
30 31 7.612633 AGGTTTTACGGGCTAATTGAAGATTAA 59.387 33.333 0.00 0.00 0.00 1.40
31 32 7.114095 AGGTTTTACGGGCTAATTGAAGATTA 58.886 34.615 0.00 0.00 0.00 1.75
32 33 5.949952 AGGTTTTACGGGCTAATTGAAGATT 59.050 36.000 0.00 0.00 0.00 2.40
33 34 5.506708 AGGTTTTACGGGCTAATTGAAGAT 58.493 37.500 0.00 0.00 0.00 2.40
34 35 4.913784 AGGTTTTACGGGCTAATTGAAGA 58.086 39.130 0.00 0.00 0.00 2.87
35 36 4.941873 AGAGGTTTTACGGGCTAATTGAAG 59.058 41.667 0.00 0.00 0.00 3.02
36 37 4.698304 CAGAGGTTTTACGGGCTAATTGAA 59.302 41.667 0.00 0.00 0.00 2.69
37 38 4.258543 CAGAGGTTTTACGGGCTAATTGA 58.741 43.478 0.00 0.00 0.00 2.57
38 39 4.007659 ACAGAGGTTTTACGGGCTAATTG 58.992 43.478 0.00 0.00 0.00 2.32
39 40 4.007659 CACAGAGGTTTTACGGGCTAATT 58.992 43.478 0.00 0.00 0.00 1.40
40 41 3.262405 TCACAGAGGTTTTACGGGCTAAT 59.738 43.478 0.00 0.00 0.00 1.73
41 42 2.633967 TCACAGAGGTTTTACGGGCTAA 59.366 45.455 0.00 0.00 0.00 3.09
42 43 2.250031 TCACAGAGGTTTTACGGGCTA 58.750 47.619 0.00 0.00 0.00 3.93
43 44 1.053424 TCACAGAGGTTTTACGGGCT 58.947 50.000 0.00 0.00 0.00 5.19
44 45 1.886886 TTCACAGAGGTTTTACGGGC 58.113 50.000 0.00 0.00 0.00 6.13
45 46 3.007635 GGATTCACAGAGGTTTTACGGG 58.992 50.000 0.00 0.00 0.00 5.28
46 47 3.007635 GGGATTCACAGAGGTTTTACGG 58.992 50.000 0.00 0.00 0.00 4.02
47 48 3.007635 GGGGATTCACAGAGGTTTTACG 58.992 50.000 0.00 0.00 0.00 3.18
48 49 3.010250 AGGGGGATTCACAGAGGTTTTAC 59.990 47.826 0.00 0.00 0.00 2.01
49 50 3.010138 CAGGGGGATTCACAGAGGTTTTA 59.990 47.826 0.00 0.00 0.00 1.52
50 51 2.073776 AGGGGGATTCACAGAGGTTTT 58.926 47.619 0.00 0.00 0.00 2.43
51 52 1.355720 CAGGGGGATTCACAGAGGTTT 59.644 52.381 0.00 0.00 0.00 3.27
52 53 0.995024 CAGGGGGATTCACAGAGGTT 59.005 55.000 0.00 0.00 0.00 3.50
53 54 0.178861 ACAGGGGGATTCACAGAGGT 60.179 55.000 0.00 0.00 0.00 3.85
54 55 0.254178 CACAGGGGGATTCACAGAGG 59.746 60.000 0.00 0.00 0.00 3.69
55 56 0.987294 ACACAGGGGGATTCACAGAG 59.013 55.000 0.00 0.00 0.00 3.35
56 57 0.692476 CACACAGGGGGATTCACAGA 59.308 55.000 0.00 0.00 0.00 3.41
57 58 0.401738 ACACACAGGGGGATTCACAG 59.598 55.000 0.00 0.00 0.00 3.66
58 59 1.628340 CTACACACAGGGGGATTCACA 59.372 52.381 0.00 0.00 0.00 3.58
59 60 1.679032 GCTACACACAGGGGGATTCAC 60.679 57.143 0.00 0.00 0.00 3.18
60 61 0.618458 GCTACACACAGGGGGATTCA 59.382 55.000 0.00 0.00 0.00 2.57
61 62 0.618458 TGCTACACACAGGGGGATTC 59.382 55.000 0.00 0.00 0.00 2.52
62 63 1.298953 ATGCTACACACAGGGGGATT 58.701 50.000 0.00 0.00 0.00 3.01
63 64 1.298953 AATGCTACACACAGGGGGAT 58.701 50.000 0.00 0.00 0.00 3.85
64 65 1.557832 GTAATGCTACACACAGGGGGA 59.442 52.381 0.00 0.00 0.00 4.81
65 66 1.559682 AGTAATGCTACACACAGGGGG 59.440 52.381 0.00 0.00 0.00 5.40
66 67 2.501723 AGAGTAATGCTACACACAGGGG 59.498 50.000 0.00 0.00 0.00 4.79
67 68 3.895232 AGAGTAATGCTACACACAGGG 57.105 47.619 0.00 0.00 0.00 4.45
68 69 4.142816 GCAAAGAGTAATGCTACACACAGG 60.143 45.833 0.00 0.00 39.46 4.00
69 70 4.142816 GGCAAAGAGTAATGCTACACACAG 60.143 45.833 0.00 0.00 42.20 3.66
70 71 3.751175 GGCAAAGAGTAATGCTACACACA 59.249 43.478 0.00 0.00 42.20 3.72
71 72 4.003648 AGGCAAAGAGTAATGCTACACAC 58.996 43.478 0.00 0.00 42.20 3.82
72 73 4.286297 AGGCAAAGAGTAATGCTACACA 57.714 40.909 0.00 0.00 42.20 3.72
73 74 4.271291 GCTAGGCAAAGAGTAATGCTACAC 59.729 45.833 0.00 0.00 42.20 2.90
74 75 4.081142 TGCTAGGCAAAGAGTAATGCTACA 60.081 41.667 0.00 0.00 42.20 2.74
75 76 4.271291 GTGCTAGGCAAAGAGTAATGCTAC 59.729 45.833 0.00 0.00 41.47 3.58
76 77 4.442706 GTGCTAGGCAAAGAGTAATGCTA 58.557 43.478 0.00 0.00 41.47 3.49
77 78 3.274288 GTGCTAGGCAAAGAGTAATGCT 58.726 45.455 0.00 0.00 41.47 3.79
78 79 2.030946 CGTGCTAGGCAAAGAGTAATGC 59.969 50.000 0.00 0.00 41.47 3.56
79 80 2.609459 CCGTGCTAGGCAAAGAGTAATG 59.391 50.000 0.00 0.00 41.47 1.90
80 81 2.906354 CCGTGCTAGGCAAAGAGTAAT 58.094 47.619 0.00 0.00 41.47 1.89
81 82 2.380084 CCGTGCTAGGCAAAGAGTAA 57.620 50.000 0.00 0.00 41.47 2.24
120 121 0.591170 AATGGCGGTTGTTTGACGAG 59.409 50.000 0.00 0.00 0.00 4.18
127 128 3.219281 ACTTTGTCTAATGGCGGTTGTT 58.781 40.909 0.00 0.00 0.00 2.83
135 136 5.069781 TGGAACCCAAAACTTTGTCTAATGG 59.930 40.000 1.76 0.00 36.45 3.16
151 152 2.075566 TGCTCACCACTGGAACCCA 61.076 57.895 0.71 0.00 0.00 4.51
152 153 1.600916 GTGCTCACCACTGGAACCC 60.601 63.158 0.71 0.00 41.35 4.11
153 154 4.065110 GTGCTCACCACTGGAACC 57.935 61.111 0.71 0.00 41.35 3.62
172 173 8.034804 TCACTTTTCTTTTCCTTTCTCCAAAAG 58.965 33.333 0.00 0.00 38.12 2.27
185 186 6.370166 ACGATGATCTCCTCACTTTTCTTTTC 59.630 38.462 0.00 0.00 36.48 2.29
191 192 6.284459 GGAATACGATGATCTCCTCACTTTT 58.716 40.000 0.00 0.00 36.48 2.27
192 193 5.848406 GGAATACGATGATCTCCTCACTTT 58.152 41.667 0.00 0.00 36.48 2.66
209 210 4.226761 CAAGCCAACAAGAAACGGAATAC 58.773 43.478 0.00 0.00 0.00 1.89
210 211 3.886505 ACAAGCCAACAAGAAACGGAATA 59.113 39.130 0.00 0.00 0.00 1.75
211 212 2.693074 ACAAGCCAACAAGAAACGGAAT 59.307 40.909 0.00 0.00 0.00 3.01
212 213 2.096248 ACAAGCCAACAAGAAACGGAA 58.904 42.857 0.00 0.00 0.00 4.30
223 224 0.387239 GCATGTTCGGACAAGCCAAC 60.387 55.000 13.09 0.00 42.92 3.77
253 254 7.713507 GGCCACAACTATTACAATCACATAGTA 59.286 37.037 0.00 0.00 33.44 1.82
342 348 8.561738 TCTTCTTCAAACTAATAAAGCGGATT 57.438 30.769 0.00 0.00 0.00 3.01
343 349 8.561738 TTCTTCTTCAAACTAATAAAGCGGAT 57.438 30.769 0.00 0.00 0.00 4.18
344 350 7.876068 TCTTCTTCTTCAAACTAATAAAGCGGA 59.124 33.333 0.00 0.00 0.00 5.54
345 351 8.029642 TCTTCTTCTTCAAACTAATAAAGCGG 57.970 34.615 0.00 0.00 0.00 5.52
346 352 9.535270 CTTCTTCTTCTTCAAACTAATAAAGCG 57.465 33.333 0.00 0.00 0.00 4.68
374 380 3.127203 CACAAACGTCCTAGACTCGATCT 59.873 47.826 0.00 0.00 41.95 2.75
381 399 3.194116 TGGGTATCACAAACGTCCTAGAC 59.806 47.826 0.00 0.00 0.00 2.59
396 418 5.638530 ATCTCTTTTCCTCCTTGGGTATC 57.361 43.478 0.00 0.00 36.20 2.24
424 448 8.534333 TTATCATAACGTCCTCAATAATCAGC 57.466 34.615 0.00 0.00 0.00 4.26
441 465 1.217001 CGCGCTGCCACTTATCATAA 58.783 50.000 5.56 0.00 0.00 1.90
443 467 2.537560 GCGCGCTGCCACTTATCAT 61.538 57.895 26.67 0.00 37.76 2.45
471 495 1.300697 GCAACCAGGTCTTCGTCGT 60.301 57.895 0.00 0.00 0.00 4.34
478 502 1.525995 CAACACGGCAACCAGGTCT 60.526 57.895 0.00 0.00 0.00 3.85
492 516 4.641645 CCCTGGCACGGCTCAACA 62.642 66.667 0.00 0.00 0.00 3.33
519 543 1.354506 CGTAGTAGGAACCTCGCGG 59.645 63.158 6.13 0.00 0.00 6.46
542 566 1.153568 CATCTCGAGGAAGCGGCAA 60.154 57.895 13.56 0.00 0.00 4.52
614 639 0.532862 AAGCTCCGGGCATATGAACG 60.533 55.000 15.92 9.58 44.79 3.95
621 646 2.109799 CGATGAAGCTCCGGGCAT 59.890 61.111 15.92 5.13 44.79 4.40
650 675 3.059386 GATCGTTTGCCGCCCCAA 61.059 61.111 0.00 0.00 36.19 4.12
701 726 4.442706 GCGGGAGAGAATCATAGTTCAAA 58.557 43.478 0.00 0.00 37.82 2.69
703 728 2.365617 GGCGGGAGAGAATCATAGTTCA 59.634 50.000 0.00 0.00 37.82 3.18
704 729 2.365617 TGGCGGGAGAGAATCATAGTTC 59.634 50.000 0.00 0.00 37.82 3.01
705 730 2.366916 CTGGCGGGAGAGAATCATAGTT 59.633 50.000 0.00 0.00 37.82 2.24
706 731 1.967066 CTGGCGGGAGAGAATCATAGT 59.033 52.381 0.00 0.00 37.82 2.12
707 732 2.230992 CTCTGGCGGGAGAGAATCATAG 59.769 54.545 0.00 0.00 41.95 2.23
708 733 2.242926 CTCTGGCGGGAGAGAATCATA 58.757 52.381 0.00 0.00 41.95 2.15
709 734 1.047002 CTCTGGCGGGAGAGAATCAT 58.953 55.000 0.00 0.00 41.95 2.45
710 735 1.680522 GCTCTGGCGGGAGAGAATCA 61.681 60.000 10.74 0.00 41.95 2.57
711 736 1.068921 GCTCTGGCGGGAGAGAATC 59.931 63.158 10.74 0.00 41.95 2.52
712 737 1.053264 ATGCTCTGGCGGGAGAGAAT 61.053 55.000 10.74 2.66 41.95 2.40
713 738 1.687146 ATGCTCTGGCGGGAGAGAA 60.687 57.895 10.74 0.45 41.95 2.87
714 739 2.042537 ATGCTCTGGCGGGAGAGA 60.043 61.111 10.74 0.00 41.95 3.10
715 740 1.395045 TACATGCTCTGGCGGGAGAG 61.395 60.000 10.74 3.99 42.24 3.20
716 741 0.975556 TTACATGCTCTGGCGGGAGA 60.976 55.000 10.74 0.00 42.25 3.71
717 742 0.107456 ATTACATGCTCTGGCGGGAG 59.893 55.000 0.00 0.00 42.25 4.30
723 748 6.183360 ACGGTGAAAATAATTACATGCTCTGG 60.183 38.462 0.00 0.00 0.00 3.86
724 749 6.785191 ACGGTGAAAATAATTACATGCTCTG 58.215 36.000 0.00 0.00 0.00 3.35
725 750 6.823689 AGACGGTGAAAATAATTACATGCTCT 59.176 34.615 0.00 0.00 0.00 4.09
728 753 7.472543 AGAAGACGGTGAAAATAATTACATGC 58.527 34.615 0.00 0.00 0.00 4.06
797 822 4.780554 TGTCCACACCCAATTATAGTGAGA 59.219 41.667 8.26 3.24 35.47 3.27
801 826 6.569127 TGTATGTCCACACCCAATTATAGT 57.431 37.500 0.00 0.00 0.00 2.12
805 830 9.733556 GAATATATGTATGTCCACACCCAATTA 57.266 33.333 0.00 0.00 0.00 1.40
807 832 6.878923 CGAATATATGTATGTCCACACCCAAT 59.121 38.462 0.00 0.00 0.00 3.16
809 834 5.305902 ACGAATATATGTATGTCCACACCCA 59.694 40.000 0.00 0.00 0.00 4.51
811 836 5.637810 CCACGAATATATGTATGTCCACACC 59.362 44.000 0.00 0.00 0.00 4.16
812 837 6.452242 TCCACGAATATATGTATGTCCACAC 58.548 40.000 0.00 0.00 0.00 3.82
813 838 6.658188 TCCACGAATATATGTATGTCCACA 57.342 37.500 0.00 0.00 0.00 4.17
814 839 9.084164 GTTATCCACGAATATATGTATGTCCAC 57.916 37.037 0.00 0.00 0.00 4.02
856 881 9.234384 CTGTATGTATATATAAGTTGTAGCGCC 57.766 37.037 2.29 0.00 0.00 6.53
885 910 9.330063 CACTACCATTACAATTCAGATGTATGT 57.670 33.333 0.00 0.00 33.55 2.29
886 911 8.285394 GCACTACCATTACAATTCAGATGTATG 58.715 37.037 0.00 0.00 33.55 2.39
887 912 8.213679 AGCACTACCATTACAATTCAGATGTAT 58.786 33.333 0.00 0.00 33.55 2.29
941 1060 3.118482 TGTGCTCTTCCTTGATGATCCTC 60.118 47.826 0.00 0.00 0.00 3.71
950 1069 1.284982 CCGTCGTGTGCTCTTCCTTG 61.285 60.000 0.00 0.00 0.00 3.61
1103 1222 0.246910 GTCTCGGACTTGGAGTTCCC 59.753 60.000 0.00 0.00 34.29 3.97
1230 1349 4.148825 CCCCTCGGCTGTTCCTCG 62.149 72.222 0.00 0.00 0.00 4.63
1254 1373 4.326766 ACATGCAACGCCGTGTGC 62.327 61.111 14.54 14.54 0.00 4.57
1255 1374 2.427245 CACATGCAACGCCGTGTG 60.427 61.111 1.75 1.75 37.63 3.82
1332 1451 2.656007 TCGTTCACACCGCACGAC 60.656 61.111 0.00 0.00 38.00 4.34
1365 1484 0.955178 ATGACACGGCGAGATAGAGG 59.045 55.000 16.62 0.00 0.00 3.69
1392 1511 0.723981 GAGCTTTCACGATGCCTGTC 59.276 55.000 0.00 0.00 0.00 3.51
1393 1512 0.322975 AGAGCTTTCACGATGCCTGT 59.677 50.000 0.00 0.00 0.00 4.00
1544 1663 5.923733 ATTAGTACTCTGTCCAAGTCCAG 57.076 43.478 0.00 0.00 0.00 3.86
1594 1713 4.946157 CAGGCTCCATCTCAAAACATAACT 59.054 41.667 0.00 0.00 0.00 2.24
1597 1716 3.523157 TCCAGGCTCCATCTCAAAACATA 59.477 43.478 0.00 0.00 0.00 2.29
1685 1804 2.279120 GCTGGCTGACGATCTCCG 60.279 66.667 0.00 0.00 45.44 4.63
1899 2018 2.253603 GTGCTACCGACGACGTATTTT 58.746 47.619 0.00 0.00 37.88 1.82
2119 2238 9.988350 GCTATGCTACATTAATTAACGCAATAT 57.012 29.630 13.67 4.29 0.00 1.28
2138 2257 8.906867 ACATAACTATTTTTCACATGCTATGCT 58.093 29.630 0.00 0.00 0.00 3.79
2139 2258 8.961092 CACATAACTATTTTTCACATGCTATGC 58.039 33.333 0.00 0.00 0.00 3.14
2140 2259 8.961092 GCACATAACTATTTTTCACATGCTATG 58.039 33.333 0.00 0.00 0.00 2.23
2154 2275 8.359642 AGAACAAACATTGTGCACATAACTATT 58.640 29.630 22.39 10.11 44.59 1.73
2471 2600 0.517316 GCACCAGAAAGGCGTTGTAG 59.483 55.000 0.00 0.00 43.14 2.74
2608 2737 4.471908 TCATGCCCATGAGCGCGT 62.472 61.111 8.43 0.00 42.42 6.01
2721 2850 1.601903 CACAAAGCTAAGCACGACCAA 59.398 47.619 0.00 0.00 0.00 3.67
2753 2882 2.639327 GCTGGTGATGGTTGGTGCC 61.639 63.158 0.00 0.00 0.00 5.01
2759 2888 1.602237 CCCTACGCTGGTGATGGTT 59.398 57.895 0.00 0.00 0.00 3.67
2799 2928 3.567797 GCGCATGCGGTCTTCTCC 61.568 66.667 38.22 17.45 40.19 3.71
2900 3029 2.026641 TGCAGAGTGAAAGCAAAAGCT 58.973 42.857 0.00 0.00 34.97 3.74
2948 3077 2.766828 AGGTGAAGTATGACCTACCAGC 59.233 50.000 0.00 0.00 41.01 4.85
2991 3125 8.620116 ACATTTTGGAAATAGGTGAAAAATGG 57.380 30.769 17.86 5.61 43.90 3.16
3047 3183 4.320348 GGCCTCATCATACAGAGTACGTAC 60.320 50.000 18.10 18.10 0.00 3.67
3048 3184 3.819337 GGCCTCATCATACAGAGTACGTA 59.181 47.826 0.00 0.00 0.00 3.57
3049 3185 2.623889 GGCCTCATCATACAGAGTACGT 59.376 50.000 0.00 0.00 0.00 3.57
3050 3186 2.623416 TGGCCTCATCATACAGAGTACG 59.377 50.000 3.32 0.00 0.00 3.67
3106 3242 1.535833 ACGCTCGGGGTATCATCTAG 58.464 55.000 0.00 0.00 0.00 2.43
3107 3243 1.611977 CAACGCTCGGGGTATCATCTA 59.388 52.381 0.00 0.00 0.00 1.98
3109 3245 1.222115 GCAACGCTCGGGGTATCATC 61.222 60.000 0.00 0.00 0.00 2.92
3111 3247 2.185867 GCAACGCTCGGGGTATCA 59.814 61.111 0.00 0.00 0.00 2.15
3112 3248 1.883084 CAGCAACGCTCGGGGTATC 60.883 63.158 0.00 0.00 36.40 2.24
3120 3256 1.084370 ATACTTCCGCAGCAACGCTC 61.084 55.000 0.00 0.00 36.40 5.03
3121 3257 0.673644 AATACTTCCGCAGCAACGCT 60.674 50.000 0.00 0.00 40.77 5.07
3122 3258 0.521242 CAATACTTCCGCAGCAACGC 60.521 55.000 0.00 0.00 0.00 4.84
3123 3259 0.096976 CCAATACTTCCGCAGCAACG 59.903 55.000 0.00 0.00 0.00 4.10
3124 3260 1.165270 ACCAATACTTCCGCAGCAAC 58.835 50.000 0.00 0.00 0.00 4.17
3126 3262 2.627945 CTTACCAATACTTCCGCAGCA 58.372 47.619 0.00 0.00 0.00 4.41
3129 3265 2.772077 TGCTTACCAATACTTCCGCA 57.228 45.000 0.00 0.00 0.00 5.69
3130 3266 4.632538 AATTGCTTACCAATACTTCCGC 57.367 40.909 0.00 0.00 43.22 5.54
3132 3268 9.301153 CAAACATAATTGCTTACCAATACTTCC 57.699 33.333 0.00 0.00 43.22 3.46
3138 3274 9.590451 CATCTTCAAACATAATTGCTTACCAAT 57.410 29.630 0.00 0.00 45.90 3.16
3139 3275 8.801299 TCATCTTCAAACATAATTGCTTACCAA 58.199 29.630 0.00 0.00 37.94 3.67
3140 3276 8.347004 TCATCTTCAAACATAATTGCTTACCA 57.653 30.769 0.00 0.00 0.00 3.25
3141 3277 8.677300 TCTCATCTTCAAACATAATTGCTTACC 58.323 33.333 0.00 0.00 0.00 2.85
3172 3308 7.867403 GGTTCATCTCTTCATGTTTGCTAAAAA 59.133 33.333 0.00 0.00 0.00 1.94
3173 3309 7.231317 AGGTTCATCTCTTCATGTTTGCTAAAA 59.769 33.333 0.00 0.00 0.00 1.52
3174 3310 6.716628 AGGTTCATCTCTTCATGTTTGCTAAA 59.283 34.615 0.00 0.00 0.00 1.85
3175 3311 6.149973 CAGGTTCATCTCTTCATGTTTGCTAA 59.850 38.462 0.00 0.00 0.00 3.09
3176 3312 5.645067 CAGGTTCATCTCTTCATGTTTGCTA 59.355 40.000 0.00 0.00 0.00 3.49
3177 3313 4.458295 CAGGTTCATCTCTTCATGTTTGCT 59.542 41.667 0.00 0.00 0.00 3.91
3178 3314 4.456911 TCAGGTTCATCTCTTCATGTTTGC 59.543 41.667 0.00 0.00 0.00 3.68
3179 3315 5.106396 GGTCAGGTTCATCTCTTCATGTTTG 60.106 44.000 0.00 0.00 0.00 2.93
3180 3316 5.006386 GGTCAGGTTCATCTCTTCATGTTT 58.994 41.667 0.00 0.00 0.00 2.83
3181 3317 4.042062 TGGTCAGGTTCATCTCTTCATGTT 59.958 41.667 0.00 0.00 0.00 2.71
3182 3318 3.584406 TGGTCAGGTTCATCTCTTCATGT 59.416 43.478 0.00 0.00 0.00 3.21
3183 3319 4.212143 TGGTCAGGTTCATCTCTTCATG 57.788 45.455 0.00 0.00 0.00 3.07
3184 3320 4.916041 TTGGTCAGGTTCATCTCTTCAT 57.084 40.909 0.00 0.00 0.00 2.57
3185 3321 4.705110 TTTGGTCAGGTTCATCTCTTCA 57.295 40.909 0.00 0.00 0.00 3.02
3186 3322 6.644347 TCTATTTGGTCAGGTTCATCTCTTC 58.356 40.000 0.00 0.00 0.00 2.87
3187 3323 6.627087 TCTATTTGGTCAGGTTCATCTCTT 57.373 37.500 0.00 0.00 0.00 2.85
3188 3324 6.821616 ATCTATTTGGTCAGGTTCATCTCT 57.178 37.500 0.00 0.00 0.00 3.10
3189 3325 9.646427 GTATATCTATTTGGTCAGGTTCATCTC 57.354 37.037 0.00 0.00 0.00 2.75
3190 3326 9.159254 TGTATATCTATTTGGTCAGGTTCATCT 57.841 33.333 0.00 0.00 0.00 2.90
3191 3327 9.950496 ATGTATATCTATTTGGTCAGGTTCATC 57.050 33.333 0.00 0.00 0.00 2.92
3192 3328 9.950496 GATGTATATCTATTTGGTCAGGTTCAT 57.050 33.333 0.00 0.00 0.00 2.57
3193 3329 9.159254 AGATGTATATCTATTTGGTCAGGTTCA 57.841 33.333 0.00 0.00 41.82 3.18
3219 3355 9.177608 CTAACCCATGATTATCTTTCACTGAAA 57.822 33.333 4.16 4.16 0.00 2.69
3220 3356 8.548025 TCTAACCCATGATTATCTTTCACTGAA 58.452 33.333 0.00 0.00 0.00 3.02
3221 3357 8.089625 TCTAACCCATGATTATCTTTCACTGA 57.910 34.615 0.00 0.00 0.00 3.41
3222 3358 8.781196 CATCTAACCCATGATTATCTTTCACTG 58.219 37.037 0.00 0.00 0.00 3.66
3223 3359 7.941238 CCATCTAACCCATGATTATCTTTCACT 59.059 37.037 0.00 0.00 0.00 3.41
3224 3360 7.939039 TCCATCTAACCCATGATTATCTTTCAC 59.061 37.037 0.00 0.00 0.00 3.18
3225 3361 8.044574 TCCATCTAACCCATGATTATCTTTCA 57.955 34.615 0.00 0.00 0.00 2.69
3226 3362 8.787852 GTTCCATCTAACCCATGATTATCTTTC 58.212 37.037 0.00 0.00 0.00 2.62
3227 3363 7.725844 GGTTCCATCTAACCCATGATTATCTTT 59.274 37.037 0.00 0.00 42.68 2.52
3228 3364 7.234355 GGTTCCATCTAACCCATGATTATCTT 58.766 38.462 0.00 0.00 42.68 2.40
3229 3365 6.784031 GGTTCCATCTAACCCATGATTATCT 58.216 40.000 0.00 0.00 42.68 1.98
3241 3377 6.817765 TCATTGAGTTTGGTTCCATCTAAC 57.182 37.500 0.00 0.00 0.00 2.34
3242 3378 9.527157 TTATTCATTGAGTTTGGTTCCATCTAA 57.473 29.630 0.00 0.00 0.00 2.10
3243 3379 9.699410 ATTATTCATTGAGTTTGGTTCCATCTA 57.301 29.630 0.00 0.00 0.00 1.98
3244 3380 8.599624 ATTATTCATTGAGTTTGGTTCCATCT 57.400 30.769 0.00 0.00 0.00 2.90
3245 3381 9.657419 AAATTATTCATTGAGTTTGGTTCCATC 57.343 29.630 0.00 0.00 0.00 3.51
3246 3382 9.657419 GAAATTATTCATTGAGTTTGGTTCCAT 57.343 29.630 0.00 0.00 35.54 3.41
3247 3383 8.869109 AGAAATTATTCATTGAGTTTGGTTCCA 58.131 29.630 0.00 0.00 38.06 3.53
3248 3384 9.710900 AAGAAATTATTCATTGAGTTTGGTTCC 57.289 29.630 0.00 0.00 38.06 3.62
3250 3386 9.492973 CCAAGAAATTATTCATTGAGTTTGGTT 57.507 29.630 4.35 0.00 38.06 3.67
3251 3387 8.869109 TCCAAGAAATTATTCATTGAGTTTGGT 58.131 29.630 7.51 0.00 38.06 3.67
3252 3388 9.709495 TTCCAAGAAATTATTCATTGAGTTTGG 57.291 29.630 4.35 3.05 38.06 3.28
3278 3414 6.945218 TGCATGTTAGGGAATATTGCTTTTT 58.055 32.000 6.93 0.00 0.00 1.94
3279 3415 6.380846 TCTGCATGTTAGGGAATATTGCTTTT 59.619 34.615 6.93 0.00 0.00 2.27
3280 3416 5.893255 TCTGCATGTTAGGGAATATTGCTTT 59.107 36.000 6.93 0.00 0.00 3.51
3286 3422 7.615365 TGTTCTTTTCTGCATGTTAGGGAATAT 59.385 33.333 0.00 0.00 0.00 1.28
3292 3428 5.437289 TGTGTTCTTTTCTGCATGTTAGG 57.563 39.130 0.00 0.00 0.00 2.69
3296 3432 8.891671 AAATAATTGTGTTCTTTTCTGCATGT 57.108 26.923 0.00 0.00 0.00 3.21
3313 3449 7.901377 CGGGTTGACGACTAGTTTAAATAATTG 59.099 37.037 0.00 0.00 35.47 2.32
3314 3450 7.603784 ACGGGTTGACGACTAGTTTAAATAATT 59.396 33.333 0.00 0.00 37.61 1.40
3316 3452 6.365789 CACGGGTTGACGACTAGTTTAAATAA 59.634 38.462 0.00 0.00 37.61 1.40
3317 3453 5.863397 CACGGGTTGACGACTAGTTTAAATA 59.137 40.000 0.00 0.00 37.61 1.40
3319 3455 4.050553 CACGGGTTGACGACTAGTTTAAA 58.949 43.478 0.00 0.00 37.61 1.52
3320 3456 3.641648 CACGGGTTGACGACTAGTTTAA 58.358 45.455 0.00 0.00 37.61 1.52
3347 3483 7.990886 TCAAATAGAATATTTTCTAGCCCGTGT 59.009 33.333 10.74 0.00 45.29 4.49
3713 6503 4.759693 AGTCTTTGTCATTAAACCGATGCA 59.240 37.500 0.00 0.00 0.00 3.96
3732 6522 4.096682 GTGATAAAGTGCTCCGAGTAGTCT 59.903 45.833 0.00 0.00 0.00 3.24
3829 7020 6.835819 ATTCAATCTATTCCATCCATGCAG 57.164 37.500 0.00 0.00 0.00 4.41
3903 7094 3.678915 TTATGAATGCTCATGTGTGCG 57.321 42.857 0.00 0.00 42.48 5.34


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

AutoCloner maintained by Alex Coulton.