Multiple sequence alignment - TraesCS5B01G412400

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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 TraesCS5B01G412400 chr5B 100.000 5618 0 0 1 5618 587339783 587345400 0.000000e+00 10375.0
1 TraesCS5B01G412400 chr5B 91.765 85 7 0 40 124 137697726 137697810 9.890000e-23 119.0
2 TraesCS5B01G412400 chr5B 88.889 45 5 0 4157 4201 685566334 685566290 7.860000e-04 56.5
3 TraesCS5B01G412400 chr5D 93.775 3550 139 33 214 3699 479578946 479582477 0.000000e+00 5256.0
4 TraesCS5B01G412400 chr5D 86.114 1786 147 53 3838 5603 479582755 479584459 0.000000e+00 1831.0
5 TraesCS5B01G412400 chr5D 87.719 57 6 1 175 231 384339639 384339584 1.310000e-06 65.8
6 TraesCS5B01G412400 chr5A 95.340 2940 99 13 799 3713 598241680 598244606 0.000000e+00 4636.0
7 TraesCS5B01G412400 chr5A 83.344 1597 147 56 3758 5294 598244774 598246311 0.000000e+00 1365.0
8 TraesCS5B01G412400 chr5A 82.979 846 60 40 4516 5296 598271972 598272798 0.000000e+00 688.0
9 TraesCS5B01G412400 chr5A 84.586 266 16 9 5339 5603 598246315 598246556 2.020000e-59 241.0
10 TraesCS5B01G412400 chr5A 86.341 205 12 7 5339 5533 598272800 598272998 5.700000e-50 209.0
11 TraesCS5B01G412400 chr5A 78.539 219 27 14 545 757 598241477 598241681 5.910000e-25 126.0
12 TraesCS5B01G412400 chr5A 97.561 41 1 0 1 41 598240956 598240996 2.810000e-08 71.3
13 TraesCS5B01G412400 chr7D 72.890 948 227 27 1432 2362 618486696 618487630 3.290000e-77 300.0
14 TraesCS5B01G412400 chr1B 92.135 89 7 0 40 128 345500242 345500330 5.910000e-25 126.0
15 TraesCS5B01G412400 chr2B 90.526 95 7 2 39 132 703710559 703710652 2.130000e-24 124.0
16 TraesCS5B01G412400 chr2B 88.660 97 11 0 39 135 77775741 77775645 9.890000e-23 119.0
17 TraesCS5B01G412400 chr2B 90.196 51 4 1 175 224 90192303 90192253 1.310000e-06 65.8
18 TraesCS5B01G412400 chr2B 100.000 35 0 0 175 209 97394872 97394906 1.310000e-06 65.8
19 TraesCS5B01G412400 chrUn 92.045 88 5 2 39 125 55795794 55795708 7.640000e-24 122.0
20 TraesCS5B01G412400 chrUn 100.000 35 0 0 175 209 33028216 33028182 1.310000e-06 65.8
21 TraesCS5B01G412400 chr4B 91.954 87 7 0 39 125 595701806 595701720 7.640000e-24 122.0
22 TraesCS5B01G412400 chr4B 85.849 106 14 1 40 144 163901608 163901503 1.650000e-20 111.0
23 TraesCS5B01G412400 chr4B 90.909 44 4 0 4157 4200 377938595 377938552 6.080000e-05 60.2
24 TraesCS5B01G412400 chr3B 91.954 87 7 0 40 126 822768200 822768114 7.640000e-24 122.0
25 TraesCS5B01G412400 chr3B 95.238 42 2 0 4157 4198 76433069 76433028 3.630000e-07 67.6
26 TraesCS5B01G412400 chr3B 90.385 52 3 2 175 224 86636811 86636862 3.630000e-07 67.6
27 TraesCS5B01G412400 chr2A 90.217 92 9 0 37 128 422563297 422563206 2.750000e-23 121.0
28 TraesCS5B01G412400 chr4A 90.741 54 5 0 4157 4210 668094127 668094074 7.810000e-09 73.1
29 TraesCS5B01G412400 chr4A 100.000 30 0 0 4157 4186 625488098 625488127 7.860000e-04 56.5
30 TraesCS5B01G412400 chr7B 97.500 40 1 0 175 214 78554413 78554452 1.010000e-07 69.4
31 TraesCS5B01G412400 chr7B 89.796 49 3 2 175 221 660672395 660672347 1.690000e-05 62.1
32 TraesCS5B01G412400 chr3D 95.238 42 2 0 175 216 489175844 489175803 3.630000e-07 67.6
33 TraesCS5B01G412400 chr3D 100.000 29 0 0 4157 4185 445638704 445638732 3.000000e-03 54.7
34 TraesCS5B01G412400 chr3A 100.000 35 0 0 175 209 734138394 734138428 1.310000e-06 65.8
35 TraesCS5B01G412400 chr4D 90.909 44 4 0 4157 4200 303518797 303518754 6.080000e-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 TraesCS5B01G412400 chr5B 587339783 587345400 5617 False 10375.00 10375 100.0000 1 5618 1 chr5B.!!$F2 5617
1 TraesCS5B01G412400 chr5D 479578946 479584459 5513 False 3543.50 5256 89.9445 214 5603 2 chr5D.!!$F1 5389
2 TraesCS5B01G412400 chr5A 598240956 598246556 5600 False 1287.86 4636 87.8740 1 5603 5 chr5A.!!$F1 5602
3 TraesCS5B01G412400 chr5A 598271972 598272998 1026 False 448.50 688 84.6600 4516 5533 2 chr5A.!!$F2 1017
4 TraesCS5B01G412400 chr7D 618486696 618487630 934 False 300.00 300 72.8900 1432 2362 1 chr7D.!!$F1 930

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
428 445 0.108472 TCACAGATTCTCGCAGGCAG 60.108 55.000 0.00 0.00 0.00 4.85 F
663 797 1.079612 GCAGCCATTGGGTCAAAGC 60.080 57.895 3.93 1.62 36.17 3.51 F
988 1142 1.743252 CCCGAGAGAGCCAAGCAAC 60.743 63.158 0.00 0.00 0.00 4.17 F
2608 2780 1.443802 GCTGCTCACTTACTTGGACC 58.556 55.000 0.00 0.00 0.00 4.46 F
4073 4568 1.651138 CTAGCTGCGAAAGAACGTCAG 59.349 52.381 0.00 0.00 38.93 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1573 1745 4.129737 GAGGTACTGCAGCCGCGA 62.130 66.667 15.27 0.00 41.55 5.87 R
2463 2635 2.329379 GAGAACGAGTTGCGATCAAGT 58.671 47.619 0.00 0.00 43.37 3.16 R
2985 3157 2.517450 CGACCGCGCCTTCAGAATC 61.517 63.158 0.00 0.00 0.00 2.52 R
4113 4608 0.107508 ATTCTGGACAGCCACGGATG 60.108 55.000 0.00 0.00 39.92 3.51 R
5237 5817 0.526739 GGGCAAAGCGTCGTTTGTTT 60.527 50.000 16.28 1.87 39.27 2.83 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
37 38 6.640499 CGAGCATGTTTATCAAAAACAGGAAA 59.360 34.615 16.66 0.00 42.48 3.13
39 40 8.907222 AGCATGTTTATCAAAAACAGGAAAAT 57.093 26.923 16.66 0.19 42.48 1.82
40 41 9.995003 AGCATGTTTATCAAAAACAGGAAAATA 57.005 25.926 16.66 0.00 42.48 1.40
48 49 7.284919 TCAAAAACAGGAAAATACTTCCTCC 57.715 36.000 2.99 0.00 45.32 4.30
49 50 5.959618 AAAACAGGAAAATACTTCCTCCG 57.040 39.130 2.99 0.00 45.32 4.63
50 51 4.635699 AACAGGAAAATACTTCCTCCGT 57.364 40.909 2.99 0.00 45.32 4.69
51 52 4.635699 ACAGGAAAATACTTCCTCCGTT 57.364 40.909 2.99 0.00 45.32 4.44
52 53 4.981812 ACAGGAAAATACTTCCTCCGTTT 58.018 39.130 2.99 0.00 45.32 3.60
53 54 5.001874 ACAGGAAAATACTTCCTCCGTTTC 58.998 41.667 2.99 0.00 45.32 2.78
54 55 5.001232 CAGGAAAATACTTCCTCCGTTTCA 58.999 41.667 2.99 0.00 45.32 2.69
55 56 5.472137 CAGGAAAATACTTCCTCCGTTTCAA 59.528 40.000 2.99 0.00 45.32 2.69
56 57 6.016610 CAGGAAAATACTTCCTCCGTTTCAAA 60.017 38.462 2.99 0.00 45.32 2.69
57 58 6.548251 AGGAAAATACTTCCTCCGTTTCAAAA 59.452 34.615 0.00 0.00 45.32 2.44
58 59 7.232737 AGGAAAATACTTCCTCCGTTTCAAAAT 59.767 33.333 0.00 0.00 45.32 1.82
59 60 8.517056 GGAAAATACTTCCTCCGTTTCAAAATA 58.483 33.333 0.00 0.00 35.73 1.40
60 61 9.556030 GAAAATACTTCCTCCGTTTCAAAATAG 57.444 33.333 0.00 0.00 0.00 1.73
61 62 8.857694 AAATACTTCCTCCGTTTCAAAATAGA 57.142 30.769 0.00 0.00 0.00 1.98
62 63 9.462606 AAATACTTCCTCCGTTTCAAAATAGAT 57.537 29.630 0.00 0.00 0.00 1.98
63 64 6.743575 ACTTCCTCCGTTTCAAAATAGATG 57.256 37.500 0.00 0.00 0.00 2.90
64 65 6.472887 ACTTCCTCCGTTTCAAAATAGATGA 58.527 36.000 0.00 0.00 0.00 2.92
65 66 6.371825 ACTTCCTCCGTTTCAAAATAGATGAC 59.628 38.462 0.00 0.00 0.00 3.06
66 67 6.049955 TCCTCCGTTTCAAAATAGATGACT 57.950 37.500 0.00 0.00 0.00 3.41
67 68 6.106673 TCCTCCGTTTCAAAATAGATGACTC 58.893 40.000 0.00 0.00 0.00 3.36
68 69 5.874810 CCTCCGTTTCAAAATAGATGACTCA 59.125 40.000 0.00 0.00 0.00 3.41
69 70 6.371548 CCTCCGTTTCAAAATAGATGACTCAA 59.628 38.462 0.00 0.00 0.00 3.02
70 71 7.129109 TCCGTTTCAAAATAGATGACTCAAC 57.871 36.000 0.00 0.00 0.00 3.18
71 72 6.934645 TCCGTTTCAAAATAGATGACTCAACT 59.065 34.615 0.00 0.00 0.00 3.16
72 73 7.117812 TCCGTTTCAAAATAGATGACTCAACTC 59.882 37.037 0.00 0.00 0.00 3.01
73 74 7.118390 CCGTTTCAAAATAGATGACTCAACTCT 59.882 37.037 0.00 0.00 0.00 3.24
74 75 9.140286 CGTTTCAAAATAGATGACTCAACTCTA 57.860 33.333 0.00 0.00 0.00 2.43
116 117 7.502120 AATTGGATCATCTATTTTGAGACGG 57.498 36.000 0.00 0.00 0.00 4.79
117 118 5.869649 TGGATCATCTATTTTGAGACGGA 57.130 39.130 0.00 0.00 0.00 4.69
118 119 5.847304 TGGATCATCTATTTTGAGACGGAG 58.153 41.667 0.00 0.00 0.00 4.63
119 120 5.221521 TGGATCATCTATTTTGAGACGGAGG 60.222 44.000 0.00 0.00 0.00 4.30
120 121 4.672587 TCATCTATTTTGAGACGGAGGG 57.327 45.455 0.00 0.00 0.00 4.30
121 122 4.286707 TCATCTATTTTGAGACGGAGGGA 58.713 43.478 0.00 0.00 0.00 4.20
122 123 4.342378 TCATCTATTTTGAGACGGAGGGAG 59.658 45.833 0.00 0.00 0.00 4.30
130 131 0.927767 AGACGGAGGGAGTAGGTGAT 59.072 55.000 0.00 0.00 0.00 3.06
134 135 2.445905 ACGGAGGGAGTAGGTGATATCA 59.554 50.000 0.00 0.00 0.00 2.15
140 141 7.256190 CGGAGGGAGTAGGTGATATCATTTTAA 60.256 40.741 9.02 0.00 0.00 1.52
177 178 7.774625 AGAAGAAGAAGAATGAGGGAAATCATC 59.225 37.037 0.00 0.00 39.00 2.92
190 191 2.533266 AATCATCCATTCCTCCGACG 57.467 50.000 0.00 0.00 0.00 5.12
191 192 1.704641 ATCATCCATTCCTCCGACGA 58.295 50.000 0.00 0.00 0.00 4.20
192 193 1.032794 TCATCCATTCCTCCGACGAG 58.967 55.000 0.00 0.00 35.72 4.18
193 194 0.747255 CATCCATTCCTCCGACGAGT 59.253 55.000 0.00 0.00 33.93 4.18
194 195 1.954382 CATCCATTCCTCCGACGAGTA 59.046 52.381 0.00 0.00 33.93 2.59
195 196 2.359981 TCCATTCCTCCGACGAGTAT 57.640 50.000 0.00 0.00 33.93 2.12
196 197 2.662866 TCCATTCCTCCGACGAGTATT 58.337 47.619 0.00 0.00 33.93 1.89
197 198 3.028850 TCCATTCCTCCGACGAGTATTT 58.971 45.455 0.00 0.00 33.93 1.40
198 199 3.449737 TCCATTCCTCCGACGAGTATTTT 59.550 43.478 0.00 0.00 33.93 1.82
199 200 3.802685 CCATTCCTCCGACGAGTATTTTC 59.197 47.826 0.00 0.00 33.93 2.29
200 201 2.838386 TCCTCCGACGAGTATTTTCG 57.162 50.000 0.00 0.00 45.70 3.46
205 206 1.186030 CGACGAGTATTTTCGGACGG 58.814 55.000 0.00 0.00 44.57 4.79
206 207 1.202065 CGACGAGTATTTTCGGACGGA 60.202 52.381 0.00 0.00 44.57 4.69
207 208 2.448219 GACGAGTATTTTCGGACGGAG 58.552 52.381 0.00 0.00 44.57 4.63
208 209 1.133790 ACGAGTATTTTCGGACGGAGG 59.866 52.381 0.00 0.00 44.57 4.30
209 210 1.402968 CGAGTATTTTCGGACGGAGGA 59.597 52.381 0.00 0.00 36.95 3.71
210 211 2.159338 CGAGTATTTTCGGACGGAGGAA 60.159 50.000 0.00 0.00 36.95 3.36
211 212 3.674138 CGAGTATTTTCGGACGGAGGAAA 60.674 47.826 0.00 0.00 36.95 3.13
212 213 4.439968 GAGTATTTTCGGACGGAGGAAAT 58.560 43.478 0.00 0.00 32.67 2.17
222 223 9.563748 TTTCGGACGGAGGAAATATAAAATTAT 57.436 29.630 0.00 0.00 0.00 1.28
328 341 3.053693 TCATGGATCGATTTGAAACCCCT 60.054 43.478 0.00 0.00 0.00 4.79
332 345 5.326069 TGGATCGATTTGAAACCCCTAAAA 58.674 37.500 0.00 0.00 0.00 1.52
381 394 5.413523 AGTTACCGGAAACCATTGTAATGTC 59.586 40.000 9.46 0.00 34.60 3.06
423 440 1.474478 GTCTCCTCACAGATTCTCGCA 59.526 52.381 0.00 0.00 0.00 5.10
426 443 0.809241 CCTCACAGATTCTCGCAGGC 60.809 60.000 0.00 0.00 0.00 4.85
428 445 0.108472 TCACAGATTCTCGCAGGCAG 60.108 55.000 0.00 0.00 0.00 4.85
445 492 2.293170 GCAGAAGAGGGCTGTAAATCC 58.707 52.381 0.00 0.00 35.81 3.01
447 494 3.274288 CAGAAGAGGGCTGTAAATCCAC 58.726 50.000 0.00 0.00 0.00 4.02
456 503 1.654105 CTGTAAATCCACTCGACACGC 59.346 52.381 0.00 0.00 0.00 5.34
460 507 1.532604 AATCCACTCGACACGCTGGA 61.533 55.000 10.89 10.89 37.64 3.86
464 513 2.202362 CTCGACACGCTGGACTCG 60.202 66.667 0.00 0.00 0.00 4.18
468 517 1.606350 CGACACGCTGGACTCGAAAC 61.606 60.000 0.00 0.00 0.00 2.78
476 528 2.864968 CTGGACTCGAAACTCTTACCG 58.135 52.381 0.00 0.00 0.00 4.02
496 548 2.795389 GCTCGCCGCGTTTCAAAC 60.795 61.111 13.39 0.00 0.00 2.93
508 560 3.059800 GCGTTTCAAACAGGAGTAGTGTC 60.060 47.826 0.22 0.00 0.00 3.67
509 561 3.493503 CGTTTCAAACAGGAGTAGTGTCC 59.506 47.826 0.22 0.00 36.79 4.02
518 570 1.664321 GAGTAGTGTCCGCCCATCGT 61.664 60.000 0.00 0.00 36.19 3.73
663 797 1.079612 GCAGCCATTGGGTCAAAGC 60.080 57.895 3.93 1.62 36.17 3.51
788 928 3.814906 CACACCCCACCCCACACA 61.815 66.667 0.00 0.00 0.00 3.72
789 929 3.816090 ACACCCCACCCCACACAC 61.816 66.667 0.00 0.00 0.00 3.82
873 1025 2.281484 GTGTCCAAAGCCAGGCGA 60.281 61.111 5.55 0.00 0.00 5.54
882 1034 4.838486 GCCAGGCGAGACGAGACG 62.838 72.222 0.00 0.00 0.00 4.18
884 1036 2.401592 CAGGCGAGACGAGACGAG 59.598 66.667 0.00 0.00 0.00 4.18
885 1037 2.101233 CAGGCGAGACGAGACGAGA 61.101 63.158 0.00 0.00 0.00 4.04
886 1038 2.101835 AGGCGAGACGAGACGAGAC 61.102 63.158 0.00 0.00 0.00 3.36
988 1142 1.743252 CCCGAGAGAGCCAAGCAAC 60.743 63.158 0.00 0.00 0.00 4.17
1004 1158 2.272447 AACCCGAAACCCCAATGCG 61.272 57.895 0.00 0.00 0.00 4.73
1254 1423 4.821589 GGCGGGCTCAACCTCTCG 62.822 72.222 0.00 0.00 39.10 4.04
1260 1429 3.764466 CTCAACCTCTCGGGCGCT 61.764 66.667 7.64 0.00 39.10 5.92
1683 1855 2.465860 ACATTGGCTACTACAACGCA 57.534 45.000 0.00 0.00 0.00 5.24
2463 2635 2.462456 CTGGTGTTCAGAAGCTGCTA 57.538 50.000 0.90 0.00 46.18 3.49
2489 2661 2.049433 CAACTCGTTCTCCGGCGT 60.049 61.111 6.01 0.00 37.11 5.68
2532 2704 2.338785 GCAGGAGCTGTCAAAGGCC 61.339 63.158 0.00 0.00 37.91 5.19
2608 2780 1.443802 GCTGCTCACTTACTTGGACC 58.556 55.000 0.00 0.00 0.00 4.46
2769 2941 6.154445 GGTCGACTTCTCATACAACAACTTA 58.846 40.000 16.46 0.00 0.00 2.24
2922 3094 2.922162 CCATGGAGGGCTGTCTAGT 58.078 57.895 5.56 0.00 0.00 2.57
2976 3148 5.693555 GCTTCTTTGCTCCATTATATTTGCC 59.306 40.000 0.00 0.00 0.00 4.52
3081 3253 2.391616 TCACCTGTGATGATGTGCTC 57.608 50.000 0.00 0.00 34.14 4.26
3225 3397 3.146847 GCATGATCATGGATTCTCAGCA 58.853 45.455 31.62 0.00 39.16 4.41
3339 3511 5.606749 TGAGTATATGCCCAATGGTAGTCTT 59.393 40.000 0.00 0.00 0.00 3.01
3402 3574 2.000447 GACACTCGGTACAAGATTGCC 59.000 52.381 0.00 0.00 0.00 4.52
3450 3622 1.887854 CTGCACCATGATTGTTCACCA 59.112 47.619 0.00 0.00 33.85 4.17
3541 3713 1.993369 CTTCGGGCTGGCGAAATTCC 61.993 60.000 9.03 0.00 0.00 3.01
3650 3822 8.262933 TCCTTTAGTTAAATTCAGGTAGCCTAC 58.737 37.037 0.00 0.00 29.64 3.18
3654 3826 6.879400 AGTTAAATTCAGGTAGCCTACTCTG 58.121 40.000 11.80 11.80 29.64 3.35
3659 3831 5.407407 TTCAGGTAGCCTACTCTGAAAAG 57.593 43.478 22.58 2.67 40.09 2.27
3660 3832 4.673968 TCAGGTAGCCTACTCTGAAAAGA 58.326 43.478 16.06 0.16 34.95 2.52
3661 3833 5.273208 TCAGGTAGCCTACTCTGAAAAGAT 58.727 41.667 16.06 0.00 34.95 2.40
3662 3834 5.127845 TCAGGTAGCCTACTCTGAAAAGATG 59.872 44.000 16.06 0.00 34.95 2.90
3665 3837 3.604582 AGCCTACTCTGAAAAGATGCAC 58.395 45.455 0.00 0.00 0.00 4.57
3667 3839 3.753272 GCCTACTCTGAAAAGATGCACAA 59.247 43.478 0.00 0.00 0.00 3.33
3668 3840 4.397417 GCCTACTCTGAAAAGATGCACAAT 59.603 41.667 0.00 0.00 0.00 2.71
3670 3842 6.457528 GCCTACTCTGAAAAGATGCACAATAC 60.458 42.308 0.00 0.00 0.00 1.89
3671 3843 6.820656 CCTACTCTGAAAAGATGCACAATACT 59.179 38.462 0.00 0.00 0.00 2.12
3672 3844 6.492007 ACTCTGAAAAGATGCACAATACTG 57.508 37.500 0.00 0.00 0.00 2.74
3673 3845 6.233434 ACTCTGAAAAGATGCACAATACTGA 58.767 36.000 0.00 0.00 0.00 3.41
3675 3850 7.080353 TCTGAAAAGATGCACAATACTGATG 57.920 36.000 0.00 0.00 0.00 3.07
3713 4000 6.830324 TGATTCTTATTGCAGAGGCTTGTTAT 59.170 34.615 0.00 0.00 41.91 1.89
3716 4003 7.553881 TCTTATTGCAGAGGCTTGTTATAAC 57.446 36.000 8.75 8.75 41.91 1.89
3718 4005 7.775093 TCTTATTGCAGAGGCTTGTTATAACAT 59.225 33.333 18.69 4.15 41.91 2.71
3722 4009 5.106197 TGCAGAGGCTTGTTATAACATTGTG 60.106 40.000 18.69 13.46 41.91 3.33
3724 4011 5.124457 CAGAGGCTTGTTATAACATTGTGCT 59.876 40.000 18.69 10.99 38.95 4.40
3725 4012 5.124457 AGAGGCTTGTTATAACATTGTGCTG 59.876 40.000 18.69 5.44 38.95 4.41
3727 4014 5.943416 AGGCTTGTTATAACATTGTGCTGTA 59.057 36.000 18.69 0.31 38.95 2.74
3728 4015 6.603201 AGGCTTGTTATAACATTGTGCTGTAT 59.397 34.615 18.69 6.97 38.95 2.29
3729 4016 6.692681 GGCTTGTTATAACATTGTGCTGTATG 59.307 38.462 18.69 0.00 38.95 2.39
3730 4017 7.250569 GCTTGTTATAACATTGTGCTGTATGT 58.749 34.615 18.69 0.00 38.95 2.29
3731 4018 8.394877 GCTTGTTATAACATTGTGCTGTATGTA 58.605 33.333 18.69 0.00 38.95 2.29
3732 4019 9.920826 CTTGTTATAACATTGTGCTGTATGTAG 57.079 33.333 18.69 4.72 38.95 2.74
3744 4031 7.327975 TGTGCTGTATGTAGTACTTAGCAATT 58.672 34.615 16.87 0.00 41.32 2.32
3753 4040 9.938280 ATGTAGTACTTAGCAATTGTTTACTGA 57.062 29.630 12.71 3.51 0.00 3.41
3802 4280 5.186198 AGTATTCCAATGCTTACTGACACC 58.814 41.667 0.00 0.00 0.00 4.16
3850 4341 2.598565 AGCCCGCTATCAAGATGTAGA 58.401 47.619 0.00 0.00 0.00 2.59
3852 4343 3.580458 AGCCCGCTATCAAGATGTAGATT 59.420 43.478 0.00 0.00 0.00 2.40
3859 4350 9.261180 CCGCTATCAAGATGTAGATTCTAAAAA 57.739 33.333 0.00 0.00 0.00 1.94
3896 4387 8.705048 AGTCGTTCTTTTATTAGTCCTGAATC 57.295 34.615 0.00 0.00 0.00 2.52
3909 4400 6.114187 AGTCCTGAATCACATCTGTAAACA 57.886 37.500 0.00 0.00 0.00 2.83
3912 4403 7.984050 AGTCCTGAATCACATCTGTAAACATAG 59.016 37.037 0.00 0.00 0.00 2.23
3918 4409 5.102313 TCACATCTGTAAACATAGCGTCTG 58.898 41.667 0.00 0.00 0.00 3.51
3939 4430 4.832248 TGCTTCTTAGTACCACCTCATTG 58.168 43.478 0.00 0.00 0.00 2.82
3942 4433 4.901197 TCTTAGTACCACCTCATTGCAA 57.099 40.909 0.00 0.00 0.00 4.08
3945 4436 6.953101 TCTTAGTACCACCTCATTGCAATTA 58.047 36.000 9.83 0.23 0.00 1.40
3947 4438 8.052748 TCTTAGTACCACCTCATTGCAATTAAT 58.947 33.333 9.83 0.00 0.00 1.40
3950 4441 4.997565 ACCACCTCATTGCAATTAATTCG 58.002 39.130 9.83 0.00 0.00 3.34
3951 4442 4.462483 ACCACCTCATTGCAATTAATTCGT 59.538 37.500 9.83 0.00 0.00 3.85
3952 4443 5.650266 ACCACCTCATTGCAATTAATTCGTA 59.350 36.000 9.83 0.00 0.00 3.43
3953 4444 6.151985 ACCACCTCATTGCAATTAATTCGTAA 59.848 34.615 9.83 1.34 0.00 3.18
3954 4445 6.472163 CCACCTCATTGCAATTAATTCGTAAC 59.528 38.462 9.83 0.00 0.00 2.50
3955 4446 7.250569 CACCTCATTGCAATTAATTCGTAACT 58.749 34.615 9.83 0.00 0.00 2.24
3956 4447 7.429340 CACCTCATTGCAATTAATTCGTAACTC 59.571 37.037 9.83 0.00 0.00 3.01
3957 4448 6.628856 CCTCATTGCAATTAATTCGTAACTCG 59.371 38.462 9.83 0.00 41.41 4.18
4032 4527 9.226345 GTTCAGTTACTTCAATTCTTTGTCTTG 57.774 33.333 0.00 0.00 34.32 3.02
4046 4541 8.644318 TTCTTTGTCTTGTACTCTAACTTGAC 57.356 34.615 0.00 0.00 0.00 3.18
4047 4542 7.778083 TCTTTGTCTTGTACTCTAACTTGACA 58.222 34.615 0.00 0.00 33.72 3.58
4061 4556 3.257393 ACTTGACATTTCTCTAGCTGCG 58.743 45.455 0.00 0.00 0.00 5.18
4069 4564 2.264109 TCTCTAGCTGCGAAAGAACG 57.736 50.000 0.00 0.00 0.00 3.95
4071 4566 1.914700 CTCTAGCTGCGAAAGAACGTC 59.085 52.381 0.00 0.00 35.59 4.34
4073 4568 1.651138 CTAGCTGCGAAAGAACGTCAG 59.349 52.381 0.00 0.00 38.93 3.51
4079 4574 2.984471 TGCGAAAGAACGTCAGTGTATC 59.016 45.455 0.00 0.00 35.59 2.24
4106 4601 9.515226 ACTTTCTAACTAACCAATCTTGCATTA 57.485 29.630 0.00 0.00 0.00 1.90
4113 4608 8.986477 ACTAACCAATCTTGCATTATTTTGTC 57.014 30.769 0.00 0.00 0.00 3.18
4117 4612 7.043565 ACCAATCTTGCATTATTTTGTCATCC 58.956 34.615 0.00 0.00 0.00 3.51
4124 4619 4.353737 CATTATTTTGTCATCCGTGGCTG 58.646 43.478 0.00 0.00 0.00 4.85
4182 4677 1.868251 CGACGTCTACAGCTTCGGC 60.868 63.158 14.70 0.00 42.17 5.54
4350 4845 1.445410 GCACGAGGTCATGCACGTA 60.445 57.895 0.00 0.00 41.65 3.57
4457 4952 2.598394 GCCAGCTGCCAACCAAGA 60.598 61.111 8.66 0.00 0.00 3.02
4460 4955 1.601419 CCAGCTGCCAACCAAGATGG 61.601 60.000 8.66 0.00 45.02 3.51
4461 4956 0.609957 CAGCTGCCAACCAAGATGGA 60.610 55.000 0.00 0.00 40.96 3.41
4523 5021 1.497309 CCTCCTGCCCCAACCAGTTA 61.497 60.000 0.00 0.00 0.00 2.24
4530 5028 0.321298 CCCCAACCAGTTACACCGAG 60.321 60.000 0.00 0.00 0.00 4.63
4536 5034 1.369692 CAGTTACACCGAGGCACCA 59.630 57.895 0.00 0.00 0.00 4.17
4537 5035 0.670546 CAGTTACACCGAGGCACCAG 60.671 60.000 0.00 0.00 0.00 4.00
4628 5132 5.306160 TCATCAGCATCTGATCATCCAAGTA 59.694 40.000 6.37 0.00 46.83 2.24
4632 5136 3.657634 CATCTGATCATCCAAGTACCCG 58.342 50.000 0.00 0.00 0.00 5.28
4656 5160 4.728102 TCGCCGTCCGTCGCAAAT 62.728 61.111 0.00 0.00 38.35 2.32
4658 5162 2.235016 CGCCGTCCGTCGCAAATAT 61.235 57.895 0.00 0.00 38.35 1.28
4659 5163 1.275657 GCCGTCCGTCGCAAATATG 59.724 57.895 0.00 0.00 38.35 1.78
4661 5165 1.003851 CCGTCCGTCGCAAATATGTT 58.996 50.000 0.00 0.00 38.35 2.71
4662 5166 1.267334 CCGTCCGTCGCAAATATGTTG 60.267 52.381 0.00 0.00 38.35 3.33
4669 5173 1.748493 TCGCAAATATGTTGGGGCTTC 59.252 47.619 11.76 0.00 33.77 3.86
4673 5177 3.055167 GCAAATATGTTGGGGCTTCCTTT 60.055 43.478 0.00 0.00 36.20 3.11
4686 5190 1.808945 CTTCCTTTGATCGTGCAAGCT 59.191 47.619 0.00 0.00 0.00 3.74
4700 5208 1.674962 GCAAGCTTAGGCCTGAATCTG 59.325 52.381 17.99 8.56 39.73 2.90
4728 5236 2.618709 GTTGGGTGAGAGACTTTGTTGG 59.381 50.000 0.00 0.00 0.00 3.77
4768 5276 2.601367 CTGCTTTGGTGGTGGGGG 60.601 66.667 0.00 0.00 0.00 5.40
4798 5306 1.476488 GCTTCCAGTTTGGTGTGTGTT 59.524 47.619 0.00 0.00 39.03 3.32
4801 5309 1.203523 TCCAGTTTGGTGTGTGTTTGC 59.796 47.619 0.00 0.00 39.03 3.68
4802 5310 1.639280 CAGTTTGGTGTGTGTTTGCC 58.361 50.000 0.00 0.00 0.00 4.52
5041 5587 4.634012 AATGTTTGCAGTAGGAGTACCA 57.366 40.909 0.00 0.00 38.94 3.25
5052 5598 2.902608 AGGAGTACCACTTCATCACCA 58.097 47.619 0.00 0.00 38.94 4.17
5060 5606 3.244875 ACCACTTCATCACCAATGCTGTA 60.245 43.478 0.00 0.00 35.17 2.74
5061 5607 3.376234 CCACTTCATCACCAATGCTGTAG 59.624 47.826 0.00 0.00 35.17 2.74
5064 5633 5.063944 CACTTCATCACCAATGCTGTAGTAC 59.936 44.000 0.00 0.00 32.27 2.73
5067 5636 4.019771 TCATCACCAATGCTGTAGTACCAA 60.020 41.667 0.00 0.00 35.17 3.67
5103 5672 3.692257 TTCTTTCTGCCCTCTGAGAAG 57.308 47.619 6.17 0.83 30.03 2.85
5123 5692 4.644103 AGAATGATAATTGCAAAGCGCT 57.356 36.364 2.64 2.64 43.06 5.92
5195 5775 3.203161 TGACGTTCAGAGACGATCAAG 57.797 47.619 4.29 0.00 45.47 3.02
5200 5780 3.794028 CGTTCAGAGACGATCAAGGAATC 59.206 47.826 0.00 0.00 45.47 2.52
5236 5816 2.690778 AAGCCGGCTTGCGAATGTC 61.691 57.895 39.85 0.00 34.60 3.06
5237 5817 3.430862 GCCGGCTTGCGAATGTCA 61.431 61.111 22.15 0.00 0.00 3.58
5238 5818 2.976840 GCCGGCTTGCGAATGTCAA 61.977 57.895 22.15 0.00 0.00 3.18
5239 5819 1.578926 CCGGCTTGCGAATGTCAAA 59.421 52.632 0.00 0.00 0.00 2.69
5247 5827 2.710760 TGCGAATGTCAAACAAACGAC 58.289 42.857 11.36 0.00 34.50 4.34
5283 5863 4.189188 CGCCAAGCAGCAGCATCC 62.189 66.667 3.17 0.00 45.49 3.51
5284 5864 4.189188 GCCAAGCAGCAGCATCCG 62.189 66.667 3.17 0.00 45.49 4.18
5285 5865 2.437180 CCAAGCAGCAGCATCCGA 60.437 61.111 3.17 0.00 45.49 4.55
5286 5866 2.042259 CCAAGCAGCAGCATCCGAA 61.042 57.895 3.17 0.00 45.49 4.30
5287 5867 1.381928 CCAAGCAGCAGCATCCGAAT 61.382 55.000 3.17 0.00 45.49 3.34
5288 5868 0.248498 CAAGCAGCAGCATCCGAATG 60.248 55.000 3.17 0.00 45.49 2.67
5325 5907 2.094494 CACTAGTGAGTGCACCAGTAGG 60.094 54.545 31.69 23.53 43.59 3.18
5380 5963 1.739750 CCTGAGGCCCCATCTAATCT 58.260 55.000 0.00 0.00 0.00 2.40
5384 5967 4.080638 CCTGAGGCCCCATCTAATCTAATC 60.081 50.000 0.00 0.00 0.00 1.75
5385 5968 4.767908 TGAGGCCCCATCTAATCTAATCT 58.232 43.478 0.00 0.00 0.00 2.40
5447 6039 2.608368 CTGTGGGGACGGGGGTTA 60.608 66.667 0.00 0.00 0.00 2.85
5448 6040 2.122054 TGTGGGGACGGGGGTTAA 60.122 61.111 0.00 0.00 0.00 2.01
5449 6041 1.773391 TGTGGGGACGGGGGTTAAA 60.773 57.895 0.00 0.00 0.00 1.52
5584 6185 1.454847 CCCTCTCCCTCGTCTCCTG 60.455 68.421 0.00 0.00 0.00 3.86
5591 6192 2.043450 CTCGTCTCCTGGCTCCCT 60.043 66.667 0.00 0.00 0.00 4.20
5603 6204 2.438763 CTGGCTCCCTTGATCTGATCTT 59.561 50.000 17.82 0.00 0.00 2.40
5604 6205 3.645212 CTGGCTCCCTTGATCTGATCTTA 59.355 47.826 17.82 6.13 0.00 2.10
5605 6206 3.389329 TGGCTCCCTTGATCTGATCTTAC 59.611 47.826 17.82 2.09 0.00 2.34
5606 6207 3.244387 GGCTCCCTTGATCTGATCTTACC 60.244 52.174 17.82 6.87 0.00 2.85
5607 6208 3.645687 GCTCCCTTGATCTGATCTTACCT 59.354 47.826 17.82 0.00 0.00 3.08
5608 6209 4.835615 GCTCCCTTGATCTGATCTTACCTA 59.164 45.833 17.82 0.00 0.00 3.08
5609 6210 5.279256 GCTCCCTTGATCTGATCTTACCTAC 60.279 48.000 17.82 1.08 0.00 3.18
5610 6211 5.148502 TCCCTTGATCTGATCTTACCTACC 58.851 45.833 17.82 0.00 0.00 3.18
5611 6212 4.284746 CCCTTGATCTGATCTTACCTACCC 59.715 50.000 17.82 0.00 0.00 3.69
5612 6213 5.151454 CCTTGATCTGATCTTACCTACCCT 58.849 45.833 17.82 0.00 0.00 4.34
5613 6214 5.011533 CCTTGATCTGATCTTACCTACCCTG 59.988 48.000 17.82 0.00 0.00 4.45
5614 6215 3.898123 TGATCTGATCTTACCTACCCTGC 59.102 47.826 17.82 0.00 0.00 4.85
5615 6216 3.689872 TCTGATCTTACCTACCCTGCT 57.310 47.619 0.00 0.00 0.00 4.24
5616 6217 3.995636 TCTGATCTTACCTACCCTGCTT 58.004 45.455 0.00 0.00 0.00 3.91
5617 6218 4.362677 TCTGATCTTACCTACCCTGCTTT 58.637 43.478 0.00 0.00 0.00 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
37 38 8.893727 CATCTATTTTGAAACGGAGGAAGTATT 58.106 33.333 0.00 0.00 0.00 1.89
39 40 7.548075 GTCATCTATTTTGAAACGGAGGAAGTA 59.452 37.037 0.00 0.00 0.00 2.24
40 41 6.371825 GTCATCTATTTTGAAACGGAGGAAGT 59.628 38.462 0.00 0.00 0.00 3.01
41 42 6.595716 AGTCATCTATTTTGAAACGGAGGAAG 59.404 38.462 0.00 0.00 0.00 3.46
42 43 6.472887 AGTCATCTATTTTGAAACGGAGGAA 58.527 36.000 0.00 0.00 0.00 3.36
43 44 6.049955 AGTCATCTATTTTGAAACGGAGGA 57.950 37.500 0.00 0.00 0.00 3.71
44 45 5.874810 TGAGTCATCTATTTTGAAACGGAGG 59.125 40.000 0.00 0.00 0.00 4.30
45 46 6.968131 TGAGTCATCTATTTTGAAACGGAG 57.032 37.500 0.00 0.00 0.00 4.63
46 47 6.934645 AGTTGAGTCATCTATTTTGAAACGGA 59.065 34.615 1.70 0.00 0.00 4.69
47 48 7.118390 AGAGTTGAGTCATCTATTTTGAAACGG 59.882 37.037 3.66 0.00 0.00 4.44
48 49 8.023050 AGAGTTGAGTCATCTATTTTGAAACG 57.977 34.615 3.66 0.00 0.00 3.60
90 91 8.408601 CCGTCTCAAAATAGATGATCCAATTTT 58.591 33.333 9.17 9.17 34.94 1.82
91 92 7.775093 TCCGTCTCAAAATAGATGATCCAATTT 59.225 33.333 0.00 0.00 34.94 1.82
92 93 7.282585 TCCGTCTCAAAATAGATGATCCAATT 58.717 34.615 0.00 0.00 34.94 2.32
93 94 6.830912 TCCGTCTCAAAATAGATGATCCAAT 58.169 36.000 0.00 0.00 34.94 3.16
94 95 6.233905 TCCGTCTCAAAATAGATGATCCAA 57.766 37.500 0.00 0.00 34.94 3.53
95 96 5.221521 CCTCCGTCTCAAAATAGATGATCCA 60.222 44.000 0.00 0.00 34.94 3.41
96 97 5.233988 CCTCCGTCTCAAAATAGATGATCC 58.766 45.833 0.00 0.00 34.94 3.36
97 98 5.011125 TCCCTCCGTCTCAAAATAGATGATC 59.989 44.000 0.00 0.00 34.94 2.92
98 99 4.901849 TCCCTCCGTCTCAAAATAGATGAT 59.098 41.667 0.00 0.00 34.94 2.45
99 100 4.286707 TCCCTCCGTCTCAAAATAGATGA 58.713 43.478 0.00 0.00 34.94 2.92
100 101 4.100189 ACTCCCTCCGTCTCAAAATAGATG 59.900 45.833 0.00 0.00 33.12 2.90
101 102 4.290942 ACTCCCTCCGTCTCAAAATAGAT 58.709 43.478 0.00 0.00 0.00 1.98
102 103 3.709587 ACTCCCTCCGTCTCAAAATAGA 58.290 45.455 0.00 0.00 0.00 1.98
103 104 4.038162 CCTACTCCCTCCGTCTCAAAATAG 59.962 50.000 0.00 0.00 0.00 1.73
104 105 3.958798 CCTACTCCCTCCGTCTCAAAATA 59.041 47.826 0.00 0.00 0.00 1.40
105 106 2.766828 CCTACTCCCTCCGTCTCAAAAT 59.233 50.000 0.00 0.00 0.00 1.82
106 107 2.176889 CCTACTCCCTCCGTCTCAAAA 58.823 52.381 0.00 0.00 0.00 2.44
107 108 1.076677 ACCTACTCCCTCCGTCTCAAA 59.923 52.381 0.00 0.00 0.00 2.69
108 109 0.702902 ACCTACTCCCTCCGTCTCAA 59.297 55.000 0.00 0.00 0.00 3.02
109 110 0.034380 CACCTACTCCCTCCGTCTCA 60.034 60.000 0.00 0.00 0.00 3.27
110 111 0.255318 TCACCTACTCCCTCCGTCTC 59.745 60.000 0.00 0.00 0.00 3.36
111 112 0.927767 ATCACCTACTCCCTCCGTCT 59.072 55.000 0.00 0.00 0.00 4.18
112 113 2.653234 TATCACCTACTCCCTCCGTC 57.347 55.000 0.00 0.00 0.00 4.79
113 114 2.445905 TGATATCACCTACTCCCTCCGT 59.554 50.000 0.00 0.00 0.00 4.69
114 115 3.156288 TGATATCACCTACTCCCTCCG 57.844 52.381 0.00 0.00 0.00 4.63
115 116 6.441088 AAAATGATATCACCTACTCCCTCC 57.559 41.667 7.78 0.00 0.00 4.30
116 117 9.847224 TTTTAAAATGATATCACCTACTCCCTC 57.153 33.333 7.78 0.00 0.00 4.30
140 141 9.408648 TCATTCTTCTTCTTCTTACTTGGTTTT 57.591 29.630 0.00 0.00 0.00 2.43
144 145 6.597280 CCCTCATTCTTCTTCTTCTTACTTGG 59.403 42.308 0.00 0.00 0.00 3.61
152 153 7.013178 GGATGATTTCCCTCATTCTTCTTCTTC 59.987 40.741 0.00 0.00 38.75 2.87
160 161 5.135705 AGGAATGGATGATTTCCCTCATTCT 59.864 40.000 11.82 0.00 44.77 2.40
177 178 3.454371 AAATACTCGTCGGAGGAATGG 57.546 47.619 1.73 0.00 44.93 3.16
181 182 2.838386 CGAAAATACTCGTCGGAGGA 57.162 50.000 0.00 0.00 44.93 3.71
186 187 1.186030 CCGTCCGAAAATACTCGTCG 58.814 55.000 0.00 0.00 37.11 5.12
187 188 2.448219 CTCCGTCCGAAAATACTCGTC 58.552 52.381 0.00 0.00 37.11 4.20
188 189 1.133790 CCTCCGTCCGAAAATACTCGT 59.866 52.381 0.00 0.00 37.11 4.18
189 190 1.402968 TCCTCCGTCCGAAAATACTCG 59.597 52.381 0.00 0.00 38.58 4.18
190 191 3.515330 TTCCTCCGTCCGAAAATACTC 57.485 47.619 0.00 0.00 0.00 2.59
191 192 3.967332 TTTCCTCCGTCCGAAAATACT 57.033 42.857 0.00 0.00 0.00 2.12
192 193 7.951530 TTATATTTCCTCCGTCCGAAAATAC 57.048 36.000 0.00 0.00 32.08 1.89
193 194 8.961294 TTTTATATTTCCTCCGTCCGAAAATA 57.039 30.769 0.00 0.00 32.08 1.40
194 195 7.868906 TTTTATATTTCCTCCGTCCGAAAAT 57.131 32.000 0.00 0.00 32.08 1.82
195 196 7.868906 ATTTTATATTTCCTCCGTCCGAAAA 57.131 32.000 0.00 0.00 32.08 2.29
196 197 7.868906 AATTTTATATTTCCTCCGTCCGAAA 57.131 32.000 0.00 0.00 32.82 3.46
197 198 9.563748 AATAATTTTATATTTCCTCCGTCCGAA 57.436 29.630 0.00 0.00 0.00 4.30
198 199 8.995220 CAATAATTTTATATTTCCTCCGTCCGA 58.005 33.333 0.00 0.00 0.00 4.55
199 200 8.995220 TCAATAATTTTATATTTCCTCCGTCCG 58.005 33.333 0.00 0.00 0.00 4.79
201 202 9.807386 CGTCAATAATTTTATATTTCCTCCGTC 57.193 33.333 0.00 0.00 0.00 4.79
202 203 9.333724 ACGTCAATAATTTTATATTTCCTCCGT 57.666 29.630 0.00 0.00 0.00 4.69
206 207 9.659830 GCGAACGTCAATAATTTTATATTTCCT 57.340 29.630 0.00 0.00 0.00 3.36
207 208 9.440784 TGCGAACGTCAATAATTTTATATTTCC 57.559 29.630 0.00 0.00 0.00 3.13
222 223 6.469139 TTTATGTATTCTTGCGAACGTCAA 57.531 33.333 0.00 0.00 30.67 3.18
296 309 8.696043 TCAAATCGATCCATGAAATCCTATTT 57.304 30.769 0.00 3.00 0.00 1.40
304 317 4.159506 GGGGTTTCAAATCGATCCATGAAA 59.840 41.667 20.85 20.85 38.92 2.69
381 394 9.604626 GAGACTAAACATCTGATTTTGTTCTTG 57.395 33.333 0.00 0.00 35.09 3.02
423 440 1.362224 TTTACAGCCCTCTTCTGCCT 58.638 50.000 0.00 0.00 35.04 4.75
426 443 3.054802 AGTGGATTTACAGCCCTCTTCTG 60.055 47.826 0.00 0.00 37.56 3.02
428 445 3.536570 GAGTGGATTTACAGCCCTCTTC 58.463 50.000 0.00 0.00 0.00 2.87
445 492 1.442857 GAGTCCAGCGTGTCGAGTG 60.443 63.158 0.00 0.00 0.00 3.51
447 494 2.183858 TTCGAGTCCAGCGTGTCGAG 62.184 60.000 0.00 0.00 42.03 4.04
456 503 2.415625 CCGGTAAGAGTTTCGAGTCCAG 60.416 54.545 0.00 0.00 0.00 3.86
460 507 0.893447 CCCCGGTAAGAGTTTCGAGT 59.107 55.000 0.00 0.00 0.00 4.18
464 513 0.459759 CGAGCCCCGGTAAGAGTTTC 60.460 60.000 0.00 0.00 33.91 2.78
468 517 4.222847 GGCGAGCCCCGGTAAGAG 62.223 72.222 1.97 0.00 39.04 2.85
496 548 1.330655 ATGGGCGGACACTACTCCTG 61.331 60.000 0.00 0.00 0.00 3.86
508 560 1.531149 GATGTCATTTACGATGGGCGG 59.469 52.381 0.00 0.00 46.49 6.13
518 570 3.315470 CCGAGACCGAGAGATGTCATTTA 59.685 47.826 0.00 0.00 38.22 1.40
873 1025 1.674980 GGGTGGTCTCGTCTCGTCT 60.675 63.158 0.00 0.00 0.00 4.18
882 1034 2.037527 AGACGGGAGGGTGGTCTC 59.962 66.667 0.00 0.00 36.32 3.36
884 1036 2.283676 TGAGACGGGAGGGTGGTC 60.284 66.667 0.00 0.00 0.00 4.02
885 1037 2.603776 GTGAGACGGGAGGGTGGT 60.604 66.667 0.00 0.00 0.00 4.16
886 1038 2.603473 TGTGAGACGGGAGGGTGG 60.603 66.667 0.00 0.00 0.00 4.61
968 1120 3.394836 GCTTGGCTCTCTCGGGGT 61.395 66.667 0.00 0.00 0.00 4.95
981 1135 1.395826 TTGGGGTTTCGGGTTGCTTG 61.396 55.000 0.00 0.00 0.00 4.01
988 1142 2.675075 ACGCATTGGGGTTTCGGG 60.675 61.111 5.65 0.00 36.72 5.14
1027 1181 2.387772 CGAGGAGGAGGAGGAGGGA 61.388 68.421 0.00 0.00 0.00 4.20
1028 1182 2.197324 CGAGGAGGAGGAGGAGGG 59.803 72.222 0.00 0.00 0.00 4.30
1573 1745 4.129737 GAGGTACTGCAGCCGCGA 62.130 66.667 15.27 0.00 41.55 5.87
2463 2635 2.329379 GAGAACGAGTTGCGATCAAGT 58.671 47.619 0.00 0.00 43.37 3.16
2489 2661 2.594303 CAACCTCGGCAGGCAACA 60.594 61.111 0.00 0.00 45.05 3.33
2532 2704 2.709475 GCATTGCCGCTAAGGTCG 59.291 61.111 0.00 0.00 43.70 4.79
2922 3094 3.011818 CACAATGAGCAGCTTGATGGTA 58.988 45.455 0.00 0.00 0.00 3.25
2976 3148 2.802667 CTTCAGAATCGCCGCGGTG 61.803 63.158 32.48 32.48 0.00 4.94
2985 3157 2.517450 CGACCGCGCCTTCAGAATC 61.517 63.158 0.00 0.00 0.00 2.52
3081 3253 3.055819 TGTTCTCCTCTTTCAGGGAATCG 60.056 47.826 0.00 0.00 43.67 3.34
3225 3397 4.168101 TCCTCCCAAGTGTTTGTATCTCT 58.832 43.478 0.00 0.00 32.21 3.10
3402 3574 1.895238 CCCCTTGGCAGCTTCAATG 59.105 57.895 0.00 0.00 0.00 2.82
3450 3622 3.509967 TGACATCACGGTGAAGTATCAGT 59.490 43.478 17.86 7.16 35.88 3.41
3573 3745 2.033372 CCATATGAACCAGCAATGGCA 58.967 47.619 3.65 0.00 44.61 4.92
3631 3803 6.875076 TCAGAGTAGGCTACCTGAATTTAAC 58.125 40.000 28.39 5.68 34.95 2.01
3636 3808 5.721960 TCTTTTCAGAGTAGGCTACCTGAAT 59.278 40.000 34.00 17.06 41.31 2.57
3642 3814 4.568760 GTGCATCTTTTCAGAGTAGGCTAC 59.431 45.833 16.93 16.93 30.36 3.58
3643 3815 4.222810 TGTGCATCTTTTCAGAGTAGGCTA 59.777 41.667 0.00 0.00 30.36 3.93
3644 3816 3.008375 TGTGCATCTTTTCAGAGTAGGCT 59.992 43.478 0.00 0.00 30.36 4.58
3646 3818 6.820656 AGTATTGTGCATCTTTTCAGAGTAGG 59.179 38.462 0.00 0.00 30.36 3.18
3650 3822 6.732531 TCAGTATTGTGCATCTTTTCAGAG 57.267 37.500 0.00 0.00 30.36 3.35
3654 3826 6.845302 TGACATCAGTATTGTGCATCTTTTC 58.155 36.000 0.00 0.00 0.00 2.29
3659 3831 9.817365 GTATTTATGACATCAGTATTGTGCATC 57.183 33.333 0.00 0.00 0.00 3.91
3660 3832 9.565090 AGTATTTATGACATCAGTATTGTGCAT 57.435 29.630 0.00 0.00 0.00 3.96
3661 3833 8.962884 AGTATTTATGACATCAGTATTGTGCA 57.037 30.769 0.00 0.00 0.00 4.57
3689 3976 5.573337 AACAAGCCTCTGCAATAAGAATC 57.427 39.130 0.00 0.00 41.13 2.52
3692 3979 7.109501 TGTTATAACAAGCCTCTGCAATAAGA 58.890 34.615 15.92 0.00 35.13 2.10
3702 3989 5.106157 ACAGCACAATGTTATAACAAGCCTC 60.106 40.000 21.57 11.25 43.03 4.70
3713 4000 9.797556 CTAAGTACTACATACAGCACAATGTTA 57.202 33.333 0.00 0.00 37.50 2.41
3716 4003 6.756542 TGCTAAGTACTACATACAGCACAATG 59.243 38.462 0.00 0.00 37.70 2.82
3718 4005 6.275494 TGCTAAGTACTACATACAGCACAA 57.725 37.500 0.00 0.00 37.70 3.33
3722 4009 7.772332 ACAATTGCTAAGTACTACATACAGC 57.228 36.000 5.05 0.00 36.09 4.40
3727 4014 9.938280 TCAGTAAACAATTGCTAAGTACTACAT 57.062 29.630 5.05 0.00 29.66 2.29
3728 4015 9.938280 ATCAGTAAACAATTGCTAAGTACTACA 57.062 29.630 5.05 0.00 29.66 2.74
3762 4049 8.079211 TGGAATACTCATCAAAACTACTAGCT 57.921 34.615 0.00 0.00 0.00 3.32
3763 4050 8.718102 TTGGAATACTCATCAAAACTACTAGC 57.282 34.615 0.00 0.00 0.00 3.42
3785 4263 1.086696 CCGGTGTCAGTAAGCATTGG 58.913 55.000 0.00 0.00 0.00 3.16
3802 4280 6.313164 GGAAGGAAACTCTTATAACTTGACCG 59.687 42.308 0.00 0.00 42.68 4.79
3850 4341 9.003658 ACGACTCAATGTCTCAATTTTTAGAAT 57.996 29.630 0.00 0.00 43.25 2.40
3852 4343 7.962964 ACGACTCAATGTCTCAATTTTTAGA 57.037 32.000 0.00 0.00 43.25 2.10
3859 4350 6.867662 AAAAGAACGACTCAATGTCTCAAT 57.132 33.333 0.00 0.00 43.25 2.57
3864 4355 8.381387 GGACTAATAAAAGAACGACTCAATGTC 58.619 37.037 0.00 0.00 42.06 3.06
3873 4364 8.092068 TGTGATTCAGGACTAATAAAAGAACGA 58.908 33.333 0.00 0.00 0.00 3.85
3896 4387 4.259970 GCAGACGCTATGTTTACAGATGTG 60.260 45.833 0.00 0.00 34.30 3.21
3912 4403 2.260481 GTGGTACTAAGAAGCAGACGC 58.740 52.381 0.00 0.00 38.99 5.19
3918 4409 3.623510 GCAATGAGGTGGTACTAAGAAGC 59.376 47.826 0.00 0.00 0.00 3.86
3922 4413 7.624360 TTAATTGCAATGAGGTGGTACTAAG 57.376 36.000 13.82 0.00 0.00 2.18
3927 4418 5.650266 ACGAATTAATTGCAATGAGGTGGTA 59.350 36.000 13.82 0.00 0.00 3.25
3939 4430 7.009907 ACCTCTTACGAGTTACGAATTAATTGC 59.990 37.037 5.17 0.00 45.77 3.56
3942 4433 8.992835 AAACCTCTTACGAGTTACGAATTAAT 57.007 30.769 0.00 0.00 45.77 1.40
3945 4436 7.439056 TCAAAAACCTCTTACGAGTTACGAATT 59.561 33.333 0.00 0.00 45.77 2.17
3947 4438 6.272318 TCAAAAACCTCTTACGAGTTACGAA 58.728 36.000 0.00 0.00 45.77 3.85
3952 4443 9.333724 TCTTAAATCAAAAACCTCTTACGAGTT 57.666 29.630 0.00 0.00 35.43 3.01
3953 4444 8.897872 TCTTAAATCAAAAACCTCTTACGAGT 57.102 30.769 0.00 0.00 35.43 4.18
3956 4447 8.902735 GCTTTCTTAAATCAAAAACCTCTTACG 58.097 33.333 0.00 0.00 0.00 3.18
3957 4448 9.744468 TGCTTTCTTAAATCAAAAACCTCTTAC 57.256 29.630 0.00 0.00 0.00 2.34
3965 4456 6.581712 AGTGCCTGCTTTCTTAAATCAAAAA 58.418 32.000 0.00 0.00 0.00 1.94
3974 4465 1.003580 CAGGGAGTGCCTGCTTTCTTA 59.996 52.381 18.64 0.00 0.00 2.10
3976 4467 1.377994 CAGGGAGTGCCTGCTTTCT 59.622 57.895 18.64 0.00 0.00 2.52
4001 4496 9.665264 CAAAGAATTGAAGTAACTGAACCTAAC 57.335 33.333 0.00 0.00 38.94 2.34
4025 4520 8.958119 AAATGTCAAGTTAGAGTACAAGACAA 57.042 30.769 0.00 0.00 37.50 3.18
4032 4527 8.463607 AGCTAGAGAAATGTCAAGTTAGAGTAC 58.536 37.037 0.00 0.00 0.00 2.73
4046 4541 4.491602 CGTTCTTTCGCAGCTAGAGAAATG 60.492 45.833 12.65 8.94 43.54 2.32
4047 4542 3.614616 CGTTCTTTCGCAGCTAGAGAAAT 59.385 43.478 12.65 0.00 43.54 2.17
4061 4556 6.421202 AGAAAGTGATACACTGACGTTCTTTC 59.579 38.462 5.17 0.00 44.62 2.62
4069 4564 8.086522 TGGTTAGTTAGAAAGTGATACACTGAC 58.913 37.037 5.17 3.50 44.62 3.51
4071 4566 8.827177 TTGGTTAGTTAGAAAGTGATACACTG 57.173 34.615 5.17 0.00 44.62 3.66
4073 4568 9.654663 AGATTGGTTAGTTAGAAAGTGATACAC 57.345 33.333 0.00 0.00 34.10 2.90
4079 4574 7.202016 TGCAAGATTGGTTAGTTAGAAAGTG 57.798 36.000 0.00 0.00 0.00 3.16
4100 4595 3.428725 GCCACGGATGACAAAATAATGCA 60.429 43.478 0.00 0.00 0.00 3.96
4106 4601 1.812571 GACAGCCACGGATGACAAAAT 59.187 47.619 8.61 0.00 35.26 1.82
4107 4602 1.234821 GACAGCCACGGATGACAAAA 58.765 50.000 8.61 0.00 35.26 2.44
4109 4604 1.003839 GGACAGCCACGGATGACAA 60.004 57.895 8.61 0.00 35.26 3.18
4113 4608 0.107508 ATTCTGGACAGCCACGGATG 60.108 55.000 0.00 0.00 39.92 3.51
4117 4612 0.940126 GCATATTCTGGACAGCCACG 59.060 55.000 0.00 0.00 39.92 4.94
4124 4619 4.202357 TGAGGGTGTATGCATATTCTGGAC 60.202 45.833 10.16 0.00 0.00 4.02
4155 4650 1.732809 CTGTAGACGTCGCTCTTCTCA 59.267 52.381 10.46 1.61 0.00 3.27
4167 4662 2.152699 CACGCCGAAGCTGTAGACG 61.153 63.158 0.00 0.00 36.60 4.18
4212 4707 1.146152 CCAAACTCCCCCACAGGTTTA 59.854 52.381 0.00 0.00 31.80 2.01
4350 4845 1.141881 CAGCAGGGCGACGTAGAAT 59.858 57.895 0.00 0.00 0.00 2.40
4362 4857 3.947132 CTCCTCGGTGCACAGCAGG 62.947 68.421 20.43 20.78 40.08 4.85
4363 4858 2.433838 CTCCTCGGTGCACAGCAG 60.434 66.667 20.43 13.27 40.08 4.24
4483 4981 0.690192 TTGGATTCAGGTCCTTCGCA 59.310 50.000 0.00 0.00 39.12 5.10
4632 5136 4.814294 ACGGACGGCGATGCTTCC 62.814 66.667 16.62 8.91 0.00 3.46
4648 5152 1.102978 AGCCCCAACATATTTGCGAC 58.897 50.000 0.00 0.00 0.00 5.19
4653 5157 4.424842 TCAAAGGAAGCCCCAACATATTT 58.575 39.130 0.00 0.00 37.41 1.40
4656 5160 3.631250 GATCAAAGGAAGCCCCAACATA 58.369 45.455 0.00 0.00 37.41 2.29
4658 5162 1.886222 CGATCAAAGGAAGCCCCAACA 60.886 52.381 0.00 0.00 37.41 3.33
4659 5163 0.811281 CGATCAAAGGAAGCCCCAAC 59.189 55.000 0.00 0.00 37.41 3.77
4661 5165 0.322456 CACGATCAAAGGAAGCCCCA 60.322 55.000 0.00 0.00 37.41 4.96
4662 5166 1.657751 GCACGATCAAAGGAAGCCCC 61.658 60.000 0.00 0.00 0.00 5.80
4669 5173 2.096496 CCTAAGCTTGCACGATCAAAGG 59.904 50.000 9.86 0.00 0.00 3.11
4673 5177 0.744414 GGCCTAAGCTTGCACGATCA 60.744 55.000 9.86 0.00 39.73 2.92
4686 5190 1.564348 GAACCCCAGATTCAGGCCTAA 59.436 52.381 3.98 0.30 0.00 2.69
4700 5208 1.003718 CTCTCACCCAACGAACCCC 60.004 63.158 0.00 0.00 0.00 4.95
4728 5236 4.437390 GCTTGGATATGTACAGCACAACAC 60.437 45.833 0.33 0.00 41.55 3.32
4768 5276 2.262423 AACTGGAAGCTCTTGGACAC 57.738 50.000 0.00 0.00 37.60 3.67
4798 5306 2.383855 AGCAAAGTACCAAACAGGCAA 58.616 42.857 0.00 0.00 43.14 4.52
4801 5309 3.123050 GCAAAGCAAAGTACCAAACAGG 58.877 45.455 0.00 0.00 45.67 4.00
4802 5310 3.798337 CAGCAAAGCAAAGTACCAAACAG 59.202 43.478 0.00 0.00 0.00 3.16
4919 5449 1.377333 GGACCGGAAAGGAGCTTGG 60.377 63.158 9.46 0.00 45.00 3.61
5041 5587 4.292186 ACTACAGCATTGGTGATGAAGT 57.708 40.909 21.85 14.79 44.34 3.01
5052 5598 7.817418 TTTCTTTCTTTGGTACTACAGCATT 57.183 32.000 0.00 0.00 33.85 3.56
5060 5606 3.883489 AGCGCTTTTCTTTCTTTGGTACT 59.117 39.130 2.64 0.00 0.00 2.73
5061 5607 4.224715 AGCGCTTTTCTTTCTTTGGTAC 57.775 40.909 2.64 0.00 0.00 3.34
5064 5633 4.698947 GAAAGCGCTTTTCTTTCTTTGG 57.301 40.909 34.01 0.00 43.55 3.28
5195 5775 1.542108 CCTCGGATCAGCAAGGATTCC 60.542 57.143 0.00 0.00 0.00 3.01
5200 5780 2.203126 GGCCTCGGATCAGCAAGG 60.203 66.667 0.00 0.00 0.00 3.61
5225 5805 3.177643 GTCGTTTGTTTGACATTCGCAAG 59.822 43.478 0.00 0.00 35.20 4.01
5227 5807 2.710760 GTCGTTTGTTTGACATTCGCA 58.289 42.857 0.00 0.00 35.20 5.10
5236 5816 0.570272 GGCAAAGCGTCGTTTGTTTG 59.430 50.000 16.28 11.81 39.27 2.93
5237 5817 0.526739 GGGCAAAGCGTCGTTTGTTT 60.527 50.000 16.28 1.87 39.27 2.83
5238 5818 1.065109 GGGCAAAGCGTCGTTTGTT 59.935 52.632 16.28 0.00 39.27 2.83
5239 5819 1.782028 GAGGGCAAAGCGTCGTTTGT 61.782 55.000 16.28 3.42 39.27 2.83
5283 5863 2.221286 GCTGCTGATCTGATCACATTCG 59.779 50.000 16.06 7.72 35.06 3.34
5284 5864 3.002451 GTGCTGCTGATCTGATCACATTC 59.998 47.826 16.06 12.87 35.06 2.67
5285 5865 2.943690 GTGCTGCTGATCTGATCACATT 59.056 45.455 16.06 0.00 35.06 2.71
5286 5866 2.170817 AGTGCTGCTGATCTGATCACAT 59.829 45.455 16.06 3.14 35.06 3.21
5287 5867 1.553704 AGTGCTGCTGATCTGATCACA 59.446 47.619 16.06 16.33 35.06 3.58
5288 5868 2.312722 AGTGCTGCTGATCTGATCAC 57.687 50.000 16.06 13.08 35.06 3.06
5325 5907 7.682501 GCCTGACATTAGTCTAGAGTTTAGACC 60.683 44.444 15.38 2.43 45.20 3.85
5384 5967 7.567771 CGCATCATCATCATCGATCATCATTAG 60.568 40.741 0.00 0.00 0.00 1.73
5385 5968 6.200286 CGCATCATCATCATCGATCATCATTA 59.800 38.462 0.00 0.00 0.00 1.90
5439 6031 2.227865 CGGCATGATTATTTAACCCCCG 59.772 50.000 0.00 0.00 0.00 5.73
5445 6037 2.292016 CCGGTGCGGCATGATTATTTAA 59.708 45.455 5.72 0.00 41.17 1.52
5447 6039 0.667993 CCGGTGCGGCATGATTATTT 59.332 50.000 5.72 0.00 41.17 1.40
5448 6040 2.330254 CCGGTGCGGCATGATTATT 58.670 52.632 5.72 0.00 41.17 1.40
5449 6041 4.063529 CCGGTGCGGCATGATTAT 57.936 55.556 5.72 0.00 41.17 1.28
5584 6185 3.244387 GGTAAGATCAGATCAAGGGAGCC 60.244 52.174 13.14 1.69 0.00 4.70
5591 6192 4.345257 GCAGGGTAGGTAAGATCAGATCAA 59.655 45.833 13.14 0.00 0.00 2.57


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

AutoCloner maintained by Alex Coulton.