Multiple sequence alignment - TraesCS4B01G194600

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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 TraesCS4B01G194600 chr4B 100.000 9467 0 0 1 9467 418353429 418343963 0.000000e+00 17483.0
1 TraesCS4B01G194600 chr4B 97.647 85 2 0 7020 7104 418346329 418346245 7.660000e-31 147.0
2 TraesCS4B01G194600 chr4B 97.647 85 2 0 7101 7185 418346410 418346326 7.660000e-31 147.0
3 TraesCS4B01G194600 chr4D 96.395 8489 205 43 50 8483 339043248 339034806 0.000000e+00 13887.0
4 TraesCS4B01G194600 chr4D 87.313 536 55 10 8939 9467 339034145 339033616 1.360000e-167 601.0
5 TraesCS4B01G194600 chr4D 82.663 398 29 20 8570 8940 339034786 339034402 5.520000e-82 316.0
6 TraesCS4B01G194600 chr4D 98.824 85 1 0 7101 7185 339036261 339036177 1.650000e-32 152.0
7 TraesCS4B01G194600 chr4D 97.647 85 2 0 7020 7104 339036180 339036096 7.660000e-31 147.0
8 TraesCS4B01G194600 chr4A 94.665 4705 189 30 401 5070 133056709 133061386 0.000000e+00 7241.0
9 TraesCS4B01G194600 chr4A 95.797 2665 78 19 5844 8482 133062689 133065345 0.000000e+00 4270.0
10 TraesCS4B01G194600 chr4A 97.665 771 17 1 5077 5847 133061489 133062258 0.000000e+00 1323.0
11 TraesCS4B01G194600 chr4A 94.404 554 28 3 8916 9467 133065620 133066172 0.000000e+00 848.0
12 TraesCS4B01G194600 chr4A 91.544 272 16 5 8554 8824 133065351 133065616 1.500000e-97 368.0
13 TraesCS4B01G194600 chr4A 93.289 149 7 2 258 404 133056531 133056678 5.760000e-52 217.0
14 TraesCS4B01G194600 chr4A 83.796 216 24 8 50 261 133052992 133053200 2.700000e-45 195.0
15 TraesCS4B01G194600 chr4A 100.000 84 0 0 7102 7185 133063888 133063971 1.270000e-33 156.0
16 TraesCS4B01G194600 chr4A 95.294 85 4 0 7020 7104 133063968 133064052 1.660000e-27 135.0
17 TraesCS4B01G194600 chr4A 91.139 79 7 0 8482 8560 82849186 82849264 3.620000e-19 108.0
18 TraesCS4B01G194600 chr7D 80.490 1225 182 26 2219 3420 503335971 503334781 0.000000e+00 885.0
19 TraesCS4B01G194600 chr7D 80.457 875 120 24 2219 3093 503733881 503733058 1.040000e-173 621.0
20 TraesCS4B01G194600 chr7D 84.802 454 66 2 3432 3885 503705383 503704933 4.030000e-123 453.0
21 TraesCS4B01G194600 chr7D 80.148 539 76 18 2315 2843 503030012 503029495 3.230000e-99 374.0
22 TraesCS4B01G194600 chr7D 79.017 529 74 21 2315 2836 503293918 503293420 2.550000e-85 327.0
23 TraesCS4B01G194600 chr7D 92.424 66 5 0 3014 3079 503029471 503029406 2.810000e-15 95.3
24 TraesCS4B01G194600 chr7D 86.765 68 9 0 2122 2189 503030080 503030013 1.020000e-09 76.8
25 TraesCS4B01G194600 chr7A 80.908 1079 150 30 2206 3261 570147733 570146688 0.000000e+00 800.0
26 TraesCS4B01G194600 chr7A 81.839 446 60 13 2315 2752 570139884 570139452 1.170000e-93 355.0
27 TraesCS4B01G194600 chr7B 81.310 519 62 16 2122 2639 531808888 531808404 1.150000e-103 388.0
28 TraesCS4B01G194600 chr7B 80.078 512 72 17 2315 2815 531761091 531760599 4.210000e-93 353.0
29 TraesCS4B01G194600 chr7B 92.424 66 5 0 3014 3079 531760549 531760484 2.810000e-15 95.3
30 TraesCS4B01G194600 chr7B 94.231 52 2 1 4007 4058 531813226 531813176 2.830000e-10 78.7
31 TraesCS4B01G194600 chr1B 92.405 79 6 0 8482 8560 662158863 662158785 7.770000e-21 113.0
32 TraesCS4B01G194600 chr1B 92.405 79 6 0 8482 8560 662161416 662161338 7.770000e-21 113.0
33 TraesCS4B01G194600 chr3A 89.535 86 7 2 8477 8560 303756785 303756870 3.620000e-19 108.0
34 TraesCS4B01G194600 chr3A 89.286 84 9 0 8477 8560 35768032 35768115 1.300000e-18 106.0
35 TraesCS4B01G194600 chr3A 92.424 66 5 0 8482 8547 161458278 161458343 2.810000e-15 95.3
36 TraesCS4B01G194600 chr1A 87.640 89 9 2 8473 8560 527694950 527694863 1.680000e-17 102.0
37 TraesCS4B01G194600 chr2A 87.356 87 11 0 8474 8560 31043411 31043325 6.050000e-17 100.0
38 TraesCS4B01G194600 chr6B 87.500 80 10 0 8481 8560 38772957 38772878 1.010000e-14 93.5


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 TraesCS4B01G194600 chr4B 418343963 418353429 9466 True 17483.000000 17483 100.000000 1 9467 1 chr4B.!!$R1 9466
1 TraesCS4B01G194600 chr4D 339033616 339043248 9632 True 4934.666667 13887 88.790333 50 9467 3 chr4D.!!$R1 9417
2 TraesCS4B01G194600 chr4A 133052992 133066172 13180 False 1639.222222 7241 94.050444 50 9467 9 chr4A.!!$F2 9417
3 TraesCS4B01G194600 chr7D 503334781 503335971 1190 True 885.000000 885 80.490000 2219 3420 1 chr7D.!!$R2 1201
4 TraesCS4B01G194600 chr7D 503733058 503733881 823 True 621.000000 621 80.457000 2219 3093 1 chr7D.!!$R4 874
5 TraesCS4B01G194600 chr7A 570146688 570147733 1045 True 800.000000 800 80.908000 2206 3261 1 chr7A.!!$R2 1055
6 TraesCS4B01G194600 chr7B 531760484 531761091 607 True 224.150000 353 86.251000 2315 3079 2 chr7B.!!$R3 764

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
37 38 0.098728 AAAGCAACGTGTGAGTGTGC 59.901 50.000 0.00 0.0 0.00 4.57 F
177 183 0.521291 CCACATTGGCAATTCGTCGT 59.479 50.000 10.65 1.9 0.00 4.34 F
1913 5331 0.039074 CCAGTCGTCTCTGTTTCGCT 60.039 55.000 0.00 0.0 34.02 4.93 F
3272 6725 0.396139 TTCCCCACCTATAGCGTCGT 60.396 55.000 0.00 0.0 0.00 4.34 F
3853 7306 1.203052 CTGTTGGCAGCATGTAAAGGG 59.797 52.381 3.98 0.0 39.31 3.95 F
4402 7855 1.999648 AGCCCAAAGAATCACTGCAA 58.000 45.000 0.00 0.0 0.00 4.08 F
5046 8507 3.431912 TGTATTGTGATCAGTGTGAACGC 59.568 43.478 0.00 0.0 31.45 4.84 F
6382 10383 2.235650 TCTCCAGAAAGATGGTGAGCTG 59.764 50.000 0.00 0.0 41.43 4.24 F
7855 11868 1.673920 TGACAAGAAAAACCAGCGACC 59.326 47.619 0.00 0.0 0.00 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1894 5312 0.039074 AGCGAAACAGAGACGACTGG 60.039 55.000 0.00 0.00 41.59 4.00 R
1968 5388 1.143073 GCCGTGGGGAGGAGATTTTAT 59.857 52.381 0.00 0.00 34.06 1.40 R
3586 7039 1.202915 TCCCTTGAAACTGCTGCATCA 60.203 47.619 1.31 0.84 0.00 3.07 R
4911 8372 1.305930 CCGGAGTGGCCTACAAAAGC 61.306 60.000 3.32 0.00 0.00 3.51 R
5710 9267 2.027377 ACAAGACTGCAGAGATGAAGGG 60.027 50.000 23.35 2.22 0.00 3.95 R
6382 10383 4.694339 ACCTAAAAGTGCCGACAGATATC 58.306 43.478 0.00 0.00 0.00 1.63 R
6840 10853 3.072915 TGCCAATTCAAACCTCTGAGAGA 59.927 43.478 11.82 0.00 0.00 3.10 R
8214 12230 0.322546 AAGCCTCGTGGATCCAAACC 60.323 55.000 18.20 2.99 34.57 3.27 R
8909 12955 1.444553 GACGGAAGCAGTCAGGTCG 60.445 63.158 0.00 0.00 38.42 4.79 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
36 37 2.542766 AAAAGCAACGTGTGAGTGTG 57.457 45.000 0.00 0.00 0.00 3.82
37 38 0.098728 AAAGCAACGTGTGAGTGTGC 59.901 50.000 0.00 0.00 0.00 4.57
38 39 2.035617 AAGCAACGTGTGAGTGTGCG 62.036 55.000 0.00 0.00 0.00 5.34
39 40 2.625906 CAACGTGTGAGTGTGCGG 59.374 61.111 0.00 0.00 0.00 5.69
40 41 3.269347 AACGTGTGAGTGTGCGGC 61.269 61.111 0.00 0.00 0.00 6.53
43 44 3.349006 GTGTGAGTGTGCGGCCAG 61.349 66.667 2.24 0.00 0.00 4.85
62 63 4.099170 CCGACCGCGTTCGAGTCT 62.099 66.667 28.08 0.00 41.78 3.24
69 70 2.095252 GCGTTCGAGTCTTGGCTCC 61.095 63.158 0.00 0.00 32.11 4.70
71 72 1.446272 GTTCGAGTCTTGGCTCCCG 60.446 63.158 0.00 0.00 32.11 5.14
76 77 2.825836 GTCTTGGCTCCCGCATGG 60.826 66.667 0.00 0.00 38.10 3.66
84 85 1.452651 CTCCCGCATGGTGCTCAAT 60.453 57.895 0.00 0.00 42.25 2.57
89 90 1.621107 CGCATGGTGCTCAATGTTTC 58.379 50.000 5.10 0.00 42.25 2.78
90 91 1.733389 CGCATGGTGCTCAATGTTTCC 60.733 52.381 5.10 0.00 42.25 3.13
91 92 1.547372 GCATGGTGCTCAATGTTTCCT 59.453 47.619 5.10 0.00 40.96 3.36
92 93 2.416431 GCATGGTGCTCAATGTTTCCTC 60.416 50.000 5.10 0.00 40.96 3.71
93 94 2.957402 TGGTGCTCAATGTTTCCTCT 57.043 45.000 0.00 0.00 0.00 3.69
95 96 3.149196 TGGTGCTCAATGTTTCCTCTTC 58.851 45.455 0.00 0.00 0.00 2.87
96 97 3.181440 TGGTGCTCAATGTTTCCTCTTCT 60.181 43.478 0.00 0.00 0.00 2.85
97 98 3.190118 GGTGCTCAATGTTTCCTCTTCTG 59.810 47.826 0.00 0.00 0.00 3.02
98 99 3.817647 GTGCTCAATGTTTCCTCTTCTGT 59.182 43.478 0.00 0.00 0.00 3.41
103 109 7.080724 GCTCAATGTTTCCTCTTCTGTTTTAG 58.919 38.462 0.00 0.00 0.00 1.85
133 139 8.956617 AAATGACTTCTTTTATTCTCTTTCGC 57.043 30.769 0.00 0.00 0.00 4.70
156 162 2.710377 TGTTCCCCGATGAAGTTCATG 58.290 47.619 22.93 14.04 37.20 3.07
161 167 0.734889 CCGATGAAGTTCATGGCCAC 59.265 55.000 22.93 7.21 37.20 5.01
166 172 1.894466 TGAAGTTCATGGCCACATTGG 59.106 47.619 8.16 0.00 41.55 3.16
176 182 3.311080 CCACATTGGCAATTCGTCG 57.689 52.632 10.65 1.20 0.00 5.12
177 183 0.521291 CCACATTGGCAATTCGTCGT 59.479 50.000 10.65 1.90 0.00 4.34
280 3620 4.483950 TCCTCTCTCTCTCTGTCCAAAAA 58.516 43.478 0.00 0.00 0.00 1.94
366 3708 4.993584 CACCTGCATATCTTTAGCGATTCT 59.006 41.667 0.00 0.00 0.00 2.40
367 3709 5.119898 CACCTGCATATCTTTAGCGATTCTC 59.880 44.000 0.00 0.00 0.00 2.87
379 3721 4.537135 AGCGATTCTCCAAGTAAAGACA 57.463 40.909 0.00 0.00 0.00 3.41
444 3825 5.218139 CGCAGCTCATTTCTTTTCTTTTCT 58.782 37.500 0.00 0.00 0.00 2.52
453 3834 3.909732 TCTTTTCTTTTCTCCCAAGGCA 58.090 40.909 0.00 0.00 0.00 4.75
459 3840 0.700564 TTTCTCCCAAGGCAGATGCT 59.299 50.000 4.59 0.00 41.70 3.79
472 3853 3.144506 GCAGATGCTATATTGGCTGTGT 58.855 45.455 0.00 0.00 38.21 3.72
481 3862 2.116983 ATTGGCTGTGTCTCACGCCT 62.117 55.000 23.76 11.38 46.11 5.52
593 3981 2.568090 CATTCACACGCCCTTGCC 59.432 61.111 0.00 0.00 0.00 4.52
611 4002 2.281484 GCAGTGGCGGGACAAAGA 60.281 61.111 0.00 0.00 0.00 2.52
613 4004 1.227823 CAGTGGCGGGACAAAGACA 60.228 57.895 0.00 0.00 0.00 3.41
656 4053 0.891904 GGCGACCTTAAACCCTTGCA 60.892 55.000 0.00 0.00 0.00 4.08
734 4132 4.755123 CCGAGATCAAAACACAGTAAAGGT 59.245 41.667 0.00 0.00 0.00 3.50
767 4165 1.310904 CCAAAACGGAAGGAAACGGA 58.689 50.000 0.00 0.00 36.56 4.69
777 4175 4.142315 CGGAAGGAAACGGAATCACTACTA 60.142 45.833 0.00 0.00 0.00 1.82
783 4181 1.404391 ACGGAATCACTACTACCGCTG 59.596 52.381 0.00 0.00 46.18 5.18
789 4187 2.636830 TCACTACTACCGCTGACCTAC 58.363 52.381 0.00 0.00 0.00 3.18
798 4210 1.265905 CCGCTGACCTACAACCAAAAC 59.734 52.381 0.00 0.00 0.00 2.43
807 4219 3.449377 CCTACAACCAAAACCACCACTTT 59.551 43.478 0.00 0.00 0.00 2.66
808 4220 3.326836 ACAACCAAAACCACCACTTTG 57.673 42.857 0.00 0.00 33.25 2.77
1063 4481 3.339093 CCCTCCCCCAACCACCTC 61.339 72.222 0.00 0.00 0.00 3.85
1064 4482 3.339093 CCTCCCCCAACCACCTCC 61.339 72.222 0.00 0.00 0.00 4.30
1065 4483 3.717294 CTCCCCCAACCACCTCCG 61.717 72.222 0.00 0.00 0.00 4.63
1103 4521 2.735772 GCTCTCCAATCCGAGGCCA 61.736 63.158 5.01 0.00 0.00 5.36
1368 4786 3.177884 AGGCCCACTGCACCTTCA 61.178 61.111 0.00 0.00 43.89 3.02
1478 4896 5.504665 CGATTGAGTTGGCATCCATCTAAAC 60.505 44.000 0.00 0.00 34.15 2.01
1548 4966 4.159321 TGAAGTTCTTGTCAAACAATGGCA 59.841 37.500 4.17 0.00 43.31 4.92
1673 5091 3.826729 AGATCTTTGCTTTGTTGGTACCC 59.173 43.478 10.07 0.00 0.00 3.69
1674 5092 3.306472 TCTTTGCTTTGTTGGTACCCT 57.694 42.857 10.07 0.00 0.00 4.34
1689 5107 4.717280 TGGTACCCTTGTGGAAAATTGTTT 59.283 37.500 10.07 0.00 38.00 2.83
1713 5131 4.340617 GAATCATGGGTTCTTGGTTGGTA 58.659 43.478 0.00 0.00 0.00 3.25
1720 5138 2.036862 GGTTCTTGGTTGGTACTCGACT 59.963 50.000 0.00 0.00 0.00 4.18
1748 5166 7.446625 ACTGAATGTTATTATTGGCCTCTCATC 59.553 37.037 3.32 0.00 0.00 2.92
1749 5167 6.716628 TGAATGTTATTATTGGCCTCTCATCC 59.283 38.462 3.32 0.00 0.00 3.51
1758 5176 1.677217 GGCCTCTCATCCAAGTGTCAC 60.677 57.143 0.00 0.00 0.00 3.67
1807 5225 1.720894 CTGTCTTGCGCACACACAA 59.279 52.632 11.12 0.00 0.00 3.33
1858 5276 5.833406 TGGAATGTGTAGCATTGTATTGG 57.167 39.130 0.00 0.00 46.90 3.16
1859 5277 5.260424 TGGAATGTGTAGCATTGTATTGGT 58.740 37.500 0.00 0.00 46.90 3.67
1871 5289 7.172342 AGCATTGTATTGGTTTAGTAGGAACA 58.828 34.615 0.00 0.00 0.00 3.18
1894 5312 7.203218 ACACAAAAGAAAAATAGGAAGTGAGC 58.797 34.615 0.00 0.00 0.00 4.26
1898 5316 5.248380 AGAAAAATAGGAAGTGAGCCAGT 57.752 39.130 0.00 0.00 0.00 4.00
1913 5331 0.039074 CCAGTCGTCTCTGTTTCGCT 60.039 55.000 0.00 0.00 34.02 4.93
1968 5388 3.053768 TGGTCAACCAATGGCATCATCTA 60.054 43.478 0.00 0.00 44.35 1.98
1983 5403 6.118852 GCATCATCTATAAAATCTCCTCCCC 58.881 44.000 0.00 0.00 0.00 4.81
2036 5456 2.981805 CTGATGCGTGTTGGAAATGTTG 59.018 45.455 0.00 0.00 0.00 3.33
2211 5631 5.105310 ACAACTTCCGCTCTGTAAGATACAT 60.105 40.000 0.00 0.00 45.62 2.29
2229 5649 9.850628 AAGATACATTGATTTTGTTGATGACAG 57.149 29.630 0.00 0.00 39.94 3.51
2407 5828 3.928754 TGCACTAGTGGAAGGATCCTAT 58.071 45.455 23.95 5.35 46.70 2.57
2559 5986 1.892209 ACATGGAAACCACGAGGAAC 58.108 50.000 5.68 0.00 35.80 3.62
2757 6185 3.462483 ACGGTCTGTATGTGACAAACA 57.538 42.857 0.00 0.00 44.79 2.83
2843 6271 7.382218 CAGCCTTTCAAAATAAAAATGTCGAGT 59.618 33.333 0.00 0.00 0.00 4.18
3272 6725 0.396139 TTCCCCACCTATAGCGTCGT 60.396 55.000 0.00 0.00 0.00 4.34
3325 6778 6.603940 TTTTCCCAGGGACAAATTAATGAG 57.396 37.500 8.12 0.00 0.00 2.90
3381 6834 4.335594 GGCATTAGGTTGGAGTATTGTGTC 59.664 45.833 0.00 0.00 0.00 3.67
3571 7024 1.647346 ATTGCAATCATTTGGCAGCG 58.353 45.000 5.99 0.00 33.22 5.18
3586 7039 1.734465 GCAGCGCACAGAGTAAATCTT 59.266 47.619 11.47 0.00 35.47 2.40
3812 7265 3.007398 GGAGCTTCGGTATCATTCTCCAT 59.993 47.826 0.00 0.00 38.69 3.41
3836 7289 3.181445 TGGCAAGTCCTACAAATGTCTGT 60.181 43.478 0.00 0.00 35.26 3.41
3853 7306 1.203052 CTGTTGGCAGCATGTAAAGGG 59.797 52.381 3.98 0.00 39.31 3.95
4135 7588 3.429207 GTGCTAAAACCGTTCTGTCTCTC 59.571 47.826 0.00 0.00 0.00 3.20
4402 7855 1.999648 AGCCCAAAGAATCACTGCAA 58.000 45.000 0.00 0.00 0.00 4.08
4589 8042 9.801873 TTTCATCCAGAGTTTTTAACTTTTCAG 57.198 29.630 0.00 0.00 43.03 3.02
4692 8150 7.219484 ACTTTTCTTATTTGATCACCAGTGG 57.781 36.000 7.91 7.91 0.00 4.00
4714 8172 5.834742 TGGTTCATTGGATATTTCCCATCAG 59.165 40.000 0.00 0.00 41.83 2.90
4763 8221 5.448654 AGCACTTGGAATGCCTATTCAATA 58.551 37.500 0.00 0.00 44.53 1.90
4784 8242 8.628280 TCAATATCTGTTTTGAACAATGTGACA 58.372 29.630 0.00 0.00 41.61 3.58
4911 8372 3.463944 TCTGACATGCAGTATGATGCTG 58.536 45.455 6.14 6.14 46.63 4.41
5046 8507 3.431912 TGTATTGTGATCAGTGTGAACGC 59.568 43.478 0.00 0.00 31.45 4.84
5550 9107 5.344665 CACACGAAGAGATCTTTCTGAAGAC 59.655 44.000 0.00 0.00 44.27 3.01
5710 9267 4.946784 ACCTTCGTTTCACAATATCTGC 57.053 40.909 0.00 0.00 0.00 4.26
5914 9905 9.880157 GAAACACAGGGAGTACTATATTACAAA 57.120 33.333 0.00 0.00 0.00 2.83
5915 9906 9.662947 AAACACAGGGAGTACTATATTACAAAC 57.337 33.333 0.00 0.00 0.00 2.93
5916 9907 8.370266 ACACAGGGAGTACTATATTACAAACA 57.630 34.615 0.00 0.00 0.00 2.83
6044 10038 5.504994 CGCTCACTTAGTTCTAGGATGACTC 60.505 48.000 0.00 0.00 0.00 3.36
6187 10186 9.112725 CTGATCAATCCACATATACTTCAACAA 57.887 33.333 0.00 0.00 0.00 2.83
6231 10230 8.546244 CACAGTAATTCATCTATGTACAGCTTG 58.454 37.037 0.33 0.00 0.00 4.01
6382 10383 2.235650 TCTCCAGAAAGATGGTGAGCTG 59.764 50.000 0.00 0.00 41.43 4.24
6722 10726 5.105797 CCTGGCATTTTGTAGCACTATTCAA 60.106 40.000 0.00 0.00 0.00 2.69
6840 10853 4.734398 TTGGTTTCACAGCAATGTCTTT 57.266 36.364 0.00 0.00 37.98 2.52
6923 10936 3.623060 TCAGAAGATTTTAGATGCCACGC 59.377 43.478 0.00 0.00 0.00 5.34
6967 10980 4.931571 GCATCCAGTTGGTGGTTAATGCA 61.932 47.826 12.67 0.00 46.47 3.96
7288 11301 4.934356 AGTTGAATGGTCTCTCTCTCTCT 58.066 43.478 0.00 0.00 0.00 3.10
7289 11302 4.949856 AGTTGAATGGTCTCTCTCTCTCTC 59.050 45.833 0.00 0.00 0.00 3.20
7290 11303 4.860802 TGAATGGTCTCTCTCTCTCTCT 57.139 45.455 0.00 0.00 0.00 3.10
7291 11304 4.780815 TGAATGGTCTCTCTCTCTCTCTC 58.219 47.826 0.00 0.00 0.00 3.20
7365 11378 8.719645 TGGAATCCTAAAAAGGAAAGATGAAA 57.280 30.769 0.00 0.00 41.90 2.69
7419 11432 9.584008 AATTGATGCTACCTCTGAATATGAATT 57.416 29.630 0.00 0.00 0.00 2.17
7855 11868 1.673920 TGACAAGAAAAACCAGCGACC 59.326 47.619 0.00 0.00 0.00 4.79
7910 11923 4.980573 ACAACCTTGTTTACCAGCTATGA 58.019 39.130 0.00 0.00 38.47 2.15
7927 11940 6.534436 CAGCTATGACCAGTATCTTATGATGC 59.466 42.308 1.45 0.29 35.87 3.91
8113 12129 5.104109 TCCAGGATCCAAATACAAGGGTAAG 60.104 44.000 15.82 0.00 32.19 2.34
8167 12183 3.418684 AGGAAACTAGAAATGCACGGT 57.581 42.857 0.00 0.00 40.61 4.83
8170 12186 4.694037 AGGAAACTAGAAATGCACGGTTAC 59.306 41.667 0.00 0.00 40.61 2.50
8214 12230 2.597455 ACTGGGTTCATTCCACCAAAG 58.403 47.619 0.00 0.00 35.80 2.77
8375 12394 8.682936 AAGAAAAATGTTGTATCAGTCTCTGT 57.317 30.769 0.00 0.00 32.61 3.41
8376 12395 8.092521 AGAAAAATGTTGTATCAGTCTCTGTG 57.907 34.615 0.00 0.00 32.61 3.66
8393 12412 3.118075 TCTGTGGATGTTTTCACACCTGA 60.118 43.478 0.00 0.00 38.75 3.86
8394 12413 3.822735 CTGTGGATGTTTTCACACCTGAT 59.177 43.478 0.00 0.00 38.75 2.90
8489 12508 9.768662 TCACCCGTTTTTATTATATACTCCTTC 57.231 33.333 0.00 0.00 0.00 3.46
8490 12509 8.996271 CACCCGTTTTTATTATATACTCCTTCC 58.004 37.037 0.00 0.00 0.00 3.46
8492 12511 7.874528 CCCGTTTTTATTATATACTCCTTCCGT 59.125 37.037 0.00 0.00 0.00 4.69
8507 12526 8.999220 ACTCCTTCCGTAAACTTTTATAAGAG 57.001 34.615 1.56 1.56 35.30 2.85
8508 12527 7.548427 ACTCCTTCCGTAAACTTTTATAAGAGC 59.452 37.037 3.00 0.00 35.30 4.09
8509 12528 6.532657 TCCTTCCGTAAACTTTTATAAGAGCG 59.467 38.462 3.00 0.00 35.30 5.03
8510 12529 6.312180 CCTTCCGTAAACTTTTATAAGAGCGT 59.688 38.462 3.00 0.00 35.30 5.07
8511 12530 7.148523 CCTTCCGTAAACTTTTATAAGAGCGTT 60.149 37.037 3.00 1.38 35.30 4.84
8512 12531 7.656707 TCCGTAAACTTTTATAAGAGCGTTT 57.343 32.000 3.00 6.02 35.30 3.60
8513 12532 8.755696 TCCGTAAACTTTTATAAGAGCGTTTA 57.244 30.769 3.00 5.24 35.30 2.01
8514 12533 8.863049 TCCGTAAACTTTTATAAGAGCGTTTAG 58.137 33.333 3.00 3.49 35.30 1.85
8515 12534 8.863049 CCGTAAACTTTTATAAGAGCGTTTAGA 58.137 33.333 3.00 0.00 35.30 2.10
8520 12539 9.654663 AACTTTTATAAGAGCGTTTAGATCACT 57.345 29.630 3.00 0.00 37.82 3.41
8524 12543 9.947669 TTTATAAGAGCGTTTAGATCACTAGAC 57.052 33.333 0.00 0.00 37.82 2.59
8525 12544 7.811117 ATAAGAGCGTTTAGATCACTAGACT 57.189 36.000 0.00 0.00 37.82 3.24
8526 12545 8.905660 ATAAGAGCGTTTAGATCACTAGACTA 57.094 34.615 0.00 0.00 37.82 2.59
8527 12546 6.854496 AGAGCGTTTAGATCACTAGACTAG 57.146 41.667 8.00 8.00 37.82 2.57
8528 12547 6.350906 AGAGCGTTTAGATCACTAGACTAGT 58.649 40.000 9.45 9.45 37.82 2.57
8529 12548 7.499292 AGAGCGTTTAGATCACTAGACTAGTA 58.501 38.462 14.79 4.82 37.82 1.82
8530 12549 7.986320 AGAGCGTTTAGATCACTAGACTAGTAA 59.014 37.037 14.79 0.76 37.82 2.24
8531 12550 8.680039 AGCGTTTAGATCACTAGACTAGTAAT 57.320 34.615 14.79 6.39 37.23 1.89
8532 12551 8.776470 AGCGTTTAGATCACTAGACTAGTAATC 58.224 37.037 15.56 15.56 37.23 1.75
8533 12552 8.776470 GCGTTTAGATCACTAGACTAGTAATCT 58.224 37.037 25.23 25.23 44.17 2.40
8539 12558 8.776470 AGATCACTAGACTAGTAATCTAAACGC 58.224 37.037 22.12 0.00 41.03 4.84
8540 12559 8.680039 ATCACTAGACTAGTAATCTAAACGCT 57.320 34.615 14.79 0.00 37.23 5.07
8541 12560 8.140677 TCACTAGACTAGTAATCTAAACGCTC 57.859 38.462 14.79 0.00 37.23 5.03
8542 12561 7.986320 TCACTAGACTAGTAATCTAAACGCTCT 59.014 37.037 14.79 0.00 37.23 4.09
8543 12562 8.614346 CACTAGACTAGTAATCTAAACGCTCTT 58.386 37.037 14.79 0.00 37.23 2.85
8544 12563 9.829507 ACTAGACTAGTAATCTAAACGCTCTTA 57.170 33.333 13.63 0.00 37.23 2.10
8552 12571 9.962783 AGTAATCTAAACGCTCTTATATTTCGT 57.037 29.630 0.00 0.00 34.63 3.85
8556 12575 9.740239 ATCTAAACGCTCTTATATTTCGTTACA 57.260 29.630 0.00 0.00 41.67 2.41
8557 12576 9.229784 TCTAAACGCTCTTATATTTCGTTACAG 57.770 33.333 0.00 0.00 41.67 2.74
8558 12577 9.229784 CTAAACGCTCTTATATTTCGTTACAGA 57.770 33.333 0.00 0.00 41.67 3.41
8559 12578 7.681125 AACGCTCTTATATTTCGTTACAGAG 57.319 36.000 0.00 0.00 40.88 3.35
8560 12579 7.024340 ACGCTCTTATATTTCGTTACAGAGA 57.976 36.000 0.00 0.00 0.00 3.10
8561 12580 7.649973 ACGCTCTTATATTTCGTTACAGAGAT 58.350 34.615 0.00 0.00 0.00 2.75
8649 12668 1.202065 ACAACATAAATCGCGCTGCAG 60.202 47.619 10.11 10.11 0.00 4.41
8661 12680 2.005537 GCTGCAGAAACAACGCACG 61.006 57.895 20.43 0.00 0.00 5.34
8682 12701 4.817464 ACGGTAGCACTAAAAACAACATGA 59.183 37.500 0.00 0.00 0.00 3.07
8685 12704 6.142817 GGTAGCACTAAAAACAACATGACTG 58.857 40.000 0.00 0.00 0.00 3.51
8696 12715 4.450976 ACAACATGACTGCTTCACACTTA 58.549 39.130 0.00 0.00 36.92 2.24
8790 12809 3.623510 TGATGAGTACTGTACGAGCTCAG 59.376 47.826 15.40 6.57 39.20 3.35
8834 12879 3.139077 GGTTGACTCAAGGGTACAAGTG 58.861 50.000 0.00 0.00 0.00 3.16
8859 12904 8.383318 GTGCCAAACACTAGATATTATGACAT 57.617 34.615 0.00 0.00 46.41 3.06
8860 12905 9.489084 GTGCCAAACACTAGATATTATGACATA 57.511 33.333 0.00 0.00 46.41 2.29
8881 12927 9.167311 GACATAGTCCTTGAATGACATTACTTT 57.833 33.333 0.00 0.00 35.15 2.66
8889 12935 2.987413 TGACATTACTTTGGCTTGCG 57.013 45.000 0.00 0.00 0.00 4.85
8893 12939 0.958091 ATTACTTTGGCTTGCGTGCA 59.042 45.000 3.25 0.00 34.04 4.57
8900 12946 2.644418 GCTTGCGTGCAATGGTGA 59.356 55.556 7.85 0.00 35.20 4.02
8909 12955 2.012673 GTGCAATGGTGAGAGTGGATC 58.987 52.381 0.00 0.00 0.00 3.36
8912 12958 2.544685 CAATGGTGAGAGTGGATCGAC 58.455 52.381 0.00 0.00 0.00 4.20
8913 12959 1.115467 ATGGTGAGAGTGGATCGACC 58.885 55.000 4.00 0.00 36.40 4.79
9007 13312 3.714798 ACAGGAGGGAAAGAAGTGTTGTA 59.285 43.478 0.00 0.00 0.00 2.41
9014 13319 4.097286 GGGAAAGAAGTGTTGTACAAAGCA 59.903 41.667 10.51 2.02 0.00 3.91
9052 13357 6.254281 ACCAGTGTTTGCAATGTTAGTATC 57.746 37.500 0.00 0.00 38.86 2.24
9127 13434 0.179048 GATGCACCGGATGTCATGGA 60.179 55.000 9.46 0.00 0.00 3.41
9205 13512 8.807948 ATGTTTTAACCATGTTAGCTAGACAT 57.192 30.769 12.81 12.81 38.21 3.06
9247 13559 5.453567 AATTAACTTTGTGCCTCTGTTCC 57.546 39.130 0.00 0.00 0.00 3.62
9259 13571 3.539604 CCTCTGTTCCTAGAGCCAAATG 58.460 50.000 0.00 0.00 42.26 2.32
9316 13628 6.464892 CCAAAGAAGGGCTCATCTATGACATA 60.465 42.308 0.00 0.00 32.50 2.29
9394 13706 8.854614 ATAGGAGATGGATTGCAAGTTAATAC 57.145 34.615 4.94 0.00 0.00 1.89
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
16 17 2.862512 CACACTCACACGTTGCTTTTT 58.137 42.857 0.00 0.00 0.00 1.94
18 19 0.098728 GCACACTCACACGTTGCTTT 59.901 50.000 0.00 0.00 0.00 3.51
19 20 1.721487 GCACACTCACACGTTGCTT 59.279 52.632 0.00 0.00 0.00 3.91
20 21 2.525248 CGCACACTCACACGTTGCT 61.525 57.895 4.78 0.00 0.00 3.91
21 22 2.053116 CGCACACTCACACGTTGC 60.053 61.111 0.00 0.00 0.00 4.17
22 23 2.625906 CCGCACACTCACACGTTG 59.374 61.111 0.00 0.00 0.00 4.10
23 24 3.269347 GCCGCACACTCACACGTT 61.269 61.111 0.00 0.00 0.00 3.99
26 27 3.349006 CTGGCCGCACACTCACAC 61.349 66.667 0.00 0.00 0.00 3.82
45 46 3.606065 AAGACTCGAACGCGGTCGG 62.606 63.158 41.95 33.29 41.43 4.79
46 47 2.126965 AAGACTCGAACGCGGTCG 60.127 61.111 38.93 38.93 40.36 4.79
47 48 2.087009 CCAAGACTCGAACGCGGTC 61.087 63.158 15.81 15.81 37.72 4.79
48 49 2.049433 CCAAGACTCGAACGCGGT 60.049 61.111 12.47 1.91 38.28 5.68
71 72 1.547372 AGGAAACATTGAGCACCATGC 59.453 47.619 0.00 0.00 45.46 4.06
76 77 3.817647 ACAGAAGAGGAAACATTGAGCAC 59.182 43.478 0.00 0.00 0.00 4.40
110 116 6.655003 TGGCGAAAGAGAATAAAAGAAGTCAT 59.345 34.615 0.00 0.00 0.00 3.06
111 117 5.995282 TGGCGAAAGAGAATAAAAGAAGTCA 59.005 36.000 0.00 0.00 0.00 3.41
112 118 6.481954 TGGCGAAAGAGAATAAAAGAAGTC 57.518 37.500 0.00 0.00 0.00 3.01
115 121 6.817765 ACATGGCGAAAGAGAATAAAAGAA 57.182 33.333 0.00 0.00 0.00 2.52
117 123 6.030228 GGAACATGGCGAAAGAGAATAAAAG 58.970 40.000 0.00 0.00 0.00 2.27
126 132 1.376683 CGGGGAACATGGCGAAAGA 60.377 57.895 0.00 0.00 0.00 2.52
132 138 0.394352 ACTTCATCGGGGAACATGGC 60.394 55.000 0.00 0.00 0.00 4.40
133 139 2.017049 GAACTTCATCGGGGAACATGG 58.983 52.381 0.00 0.00 0.00 3.66
161 167 2.670905 TGTCTACGACGAATTGCCAATG 59.329 45.455 0.00 0.00 34.95 2.82
166 172 3.102276 CTCTCTGTCTACGACGAATTGC 58.898 50.000 0.00 0.00 34.95 3.56
169 175 3.199677 CTCCTCTCTGTCTACGACGAAT 58.800 50.000 0.00 0.00 34.95 3.34
173 179 0.653636 CGCTCCTCTCTGTCTACGAC 59.346 60.000 0.00 0.00 0.00 4.34
176 182 0.661020 GCTCGCTCCTCTCTGTCTAC 59.339 60.000 0.00 0.00 0.00 2.59
177 183 0.544223 AGCTCGCTCCTCTCTGTCTA 59.456 55.000 0.00 0.00 0.00 2.59
184 190 2.284754 TCATATCAGCTCGCTCCTCT 57.715 50.000 0.00 0.00 0.00 3.69
191 197 2.746997 CGGGCATCATATCAGCTCG 58.253 57.895 0.00 0.00 46.40 5.03
357 3699 5.654603 TGTCTTTACTTGGAGAATCGCTA 57.345 39.130 0.00 0.00 34.37 4.26
358 3700 4.537135 TGTCTTTACTTGGAGAATCGCT 57.463 40.909 0.00 0.00 34.37 4.93
366 3708 2.158682 TGCAGCCTTGTCTTTACTTGGA 60.159 45.455 0.00 0.00 0.00 3.53
367 3709 2.227388 CTGCAGCCTTGTCTTTACTTGG 59.773 50.000 0.00 0.00 0.00 3.61
379 3721 1.134159 CCTGATCTTAGCTGCAGCCTT 60.134 52.381 34.39 20.12 43.38 4.35
444 3825 3.245016 CCAATATAGCATCTGCCTTGGGA 60.245 47.826 12.19 0.00 43.38 4.37
453 3834 4.346127 TGAGACACAGCCAATATAGCATCT 59.654 41.667 0.94 0.00 0.00 2.90
459 3840 2.483013 GGCGTGAGACACAGCCAATATA 60.483 50.000 22.10 0.00 45.66 0.86
472 3853 3.066190 CCGTGGGTAGGCGTGAGA 61.066 66.667 0.00 0.00 0.00 3.27
481 3862 3.841845 AGCAATAATATAGGCCGTGGGTA 59.158 43.478 0.00 0.00 0.00 3.69
548 3932 4.019950 TGATGGAGCTCACAAGATCTCAAA 60.020 41.667 17.19 0.00 38.47 2.69
611 4002 1.021968 GTCCTTGCGTTTCCACTTGT 58.978 50.000 0.00 0.00 0.00 3.16
613 4004 1.164041 CCGTCCTTGCGTTTCCACTT 61.164 55.000 0.00 0.00 0.00 3.16
656 4053 1.165270 GTGATGTTTACTGCGGCCTT 58.835 50.000 0.00 0.00 0.00 4.35
734 4132 2.354704 CGTTTTGGCAGGTAGATGAGGA 60.355 50.000 0.00 0.00 0.00 3.71
767 4165 2.736347 AGGTCAGCGGTAGTAGTGATT 58.264 47.619 0.00 0.00 0.00 2.57
777 4175 0.470766 TTTGGTTGTAGGTCAGCGGT 59.529 50.000 0.00 0.00 0.00 5.68
783 4181 2.359848 GTGGTGGTTTTGGTTGTAGGTC 59.640 50.000 0.00 0.00 0.00 3.85
789 4187 3.326836 ACAAAGTGGTGGTTTTGGTTG 57.673 42.857 2.54 0.00 38.33 3.77
798 4210 1.480137 TGCCAGAAAACAAAGTGGTGG 59.520 47.619 0.00 0.00 32.20 4.61
807 4219 7.446931 TGAGAATGTAATACTTGCCAGAAAACA 59.553 33.333 0.00 0.00 0.00 2.83
808 4220 7.750903 GTGAGAATGTAATACTTGCCAGAAAAC 59.249 37.037 0.00 0.00 0.00 2.43
1079 4497 4.570874 GGATTGGAGAGCCGGGCC 62.571 72.222 17.02 7.43 36.79 5.80
1087 4505 1.410850 GGATGGCCTCGGATTGGAGA 61.411 60.000 3.32 0.00 36.08 3.71
1091 4509 1.595382 GACGGATGGCCTCGGATTG 60.595 63.158 3.32 0.00 0.00 2.67
1353 4771 1.303561 TGATGAAGGTGCAGTGGGC 60.304 57.895 0.00 0.00 45.13 5.36
1368 4786 4.880120 CCACATTAGCACAAGTCATCTGAT 59.120 41.667 0.00 0.00 0.00 2.90
1478 4896 1.671328 TCTGCCGACAGTCTTAGATCG 59.329 52.381 0.00 0.00 44.77 3.69
1583 5001 2.596904 GGCAGACTAATTAGGCGACA 57.403 50.000 16.73 0.00 36.12 4.35
1636 5054 6.072286 AGCAAAGATCTTTTACCATGTCACTG 60.072 38.462 18.16 4.43 0.00 3.66
1640 5058 7.147976 ACAAAGCAAAGATCTTTTACCATGTC 58.852 34.615 18.16 3.97 31.94 3.06
1673 5091 7.308109 CCATGATTCCAAACAATTTTCCACAAG 60.308 37.037 0.00 0.00 0.00 3.16
1674 5092 6.485984 CCATGATTCCAAACAATTTTCCACAA 59.514 34.615 0.00 0.00 0.00 3.33
1689 5107 3.164268 CAACCAAGAACCCATGATTCCA 58.836 45.455 0.00 0.00 0.00 3.53
1713 5131 7.492669 CCAATAATAACATTCAGTCAGTCGAGT 59.507 37.037 0.00 0.00 0.00 4.18
1720 5138 6.662755 AGAGGCCAATAATAACATTCAGTCA 58.337 36.000 5.01 0.00 0.00 3.41
1748 5166 2.031682 GCTACTGCAAAGTGACACTTGG 60.032 50.000 21.24 19.11 38.66 3.61
1749 5167 3.259207 GCTACTGCAAAGTGACACTTG 57.741 47.619 21.24 15.38 38.66 3.16
1807 5225 4.666512 AGCACTCAACAATGAAGGGTAAT 58.333 39.130 0.00 0.00 34.49 1.89
1871 5289 6.323739 TGGCTCACTTCCTATTTTTCTTTTGT 59.676 34.615 0.00 0.00 0.00 2.83
1894 5312 0.039074 AGCGAAACAGAGACGACTGG 60.039 55.000 0.00 0.00 41.59 4.00
1898 5316 1.442184 GCGAGCGAAACAGAGACGA 60.442 57.895 0.00 0.00 0.00 4.20
1913 5331 4.890088 ACAAGTAAACTCATTAGGTGCGA 58.110 39.130 0.00 0.00 0.00 5.10
1968 5388 1.143073 GCCGTGGGGAGGAGATTTTAT 59.857 52.381 0.00 0.00 34.06 1.40
1983 5403 7.376866 GTGATAAATGATAACAATGAAGCCGTG 59.623 37.037 0.00 0.00 0.00 4.94
2066 5486 7.004086 TCCCATTCACAAGTATGAGAGTTTTT 58.996 34.615 0.00 0.00 0.00 1.94
2211 5631 5.850557 ACCACTGTCATCAACAAAATCAA 57.149 34.783 0.00 0.00 37.45 2.57
2229 5649 1.542187 AAGAGGTGACCCGCTACCAC 61.542 60.000 0.00 0.00 40.39 4.16
2407 5828 1.144708 TCAGCAATGACACCTTCCCAA 59.855 47.619 0.00 0.00 0.00 4.12
2476 5903 1.599071 ACTGCCATAATGCGTTCATCG 59.401 47.619 0.00 0.00 43.12 3.84
2559 5986 2.629617 AGCATTTGGAGAAACAACCAGG 59.370 45.455 0.00 0.00 37.48 4.45
2757 6185 7.825709 TCCTATTTGATTTCCATCTTGGGTAT 58.174 34.615 0.00 0.00 38.32 2.73
2843 6271 3.450817 TCCAGCTTATCCGAGACAATTGA 59.549 43.478 13.59 0.00 0.00 2.57
3325 6778 2.996249 TCAGCTTCATCCTCATGGTC 57.004 50.000 0.00 0.00 34.23 4.02
3571 7024 4.730035 GCTGCATCAAGATTTACTCTGTGC 60.730 45.833 0.00 0.00 33.29 4.57
3586 7039 1.202915 TCCCTTGAAACTGCTGCATCA 60.203 47.619 1.31 0.84 0.00 3.07
3812 7265 5.185454 CAGACATTTGTAGGACTTGCCATA 58.815 41.667 0.00 0.00 40.02 2.74
3836 7289 2.041081 AGTACCCTTTACATGCTGCCAA 59.959 45.455 0.00 0.00 0.00 4.52
3853 7306 8.204836 TCCTTTTGATATCCTTGCTCTAAGTAC 58.795 37.037 0.00 0.00 34.45 2.73
3974 7427 6.112734 ACGTGCCATCATGTCTATCTAAAAA 58.887 36.000 0.00 0.00 37.94 1.94
4402 7855 2.358898 ACAATTTGTCTTCAAGCGCACT 59.641 40.909 11.47 0.00 34.88 4.40
4589 8042 3.487544 GGAGACTTGCGAAAACATATGCC 60.488 47.826 1.58 0.00 0.00 4.40
4763 8221 5.750067 GCTTGTCACATTGTTCAAAACAGAT 59.250 36.000 5.92 0.00 43.27 2.90
4784 8242 5.711976 AGTATGAAGCTAAAACCACATGCTT 59.288 36.000 0.00 0.00 45.15 3.91
4911 8372 1.305930 CCGGAGTGGCCTACAAAAGC 61.306 60.000 3.32 0.00 0.00 3.51
5046 8507 4.210537 AGTGTTCAGAAAACCGTACATTCG 59.789 41.667 0.00 0.00 0.00 3.34
5087 8644 6.033966 GGAAATCAGCGGTTTTCGAAATATT 58.966 36.000 12.12 1.38 42.43 1.28
5550 9107 9.429359 AGTTCTTACTCTCTATTGAACACAATG 57.571 33.333 0.00 0.00 37.03 2.82
5710 9267 2.027377 ACAAGACTGCAGAGATGAAGGG 60.027 50.000 23.35 2.22 0.00 3.95
6044 10038 4.778534 TGTTAAGAGGGAGTTACTGACG 57.221 45.455 0.00 0.00 0.00 4.35
6382 10383 4.694339 ACCTAAAAGTGCCGACAGATATC 58.306 43.478 0.00 0.00 0.00 1.63
6722 10726 9.869757 AAGTAACTGCAAAGTACAAAAAGAAAT 57.130 25.926 0.00 0.00 0.00 2.17
6732 10745 4.515567 AGCCAGAAAGTAACTGCAAAGTAC 59.484 41.667 0.00 0.00 34.47 2.73
6840 10853 3.072915 TGCCAATTCAAACCTCTGAGAGA 59.927 43.478 11.82 0.00 0.00 3.10
6923 10936 8.966069 ATGCTCATATCTCTTGGATTATGATG 57.034 34.615 0.00 0.00 35.98 3.07
6959 10972 6.587608 CCCAACTCAATTTCTTCTGCATTAAC 59.412 38.462 0.00 0.00 0.00 2.01
6967 10980 5.324832 TCTTCCCCAACTCAATTTCTTCT 57.675 39.130 0.00 0.00 0.00 2.85
7097 11110 1.870402 CACAACCGTGTCACATGCTAA 59.130 47.619 3.42 0.00 38.41 3.09
7234 11247 5.398169 TGGCTAAATGCATTACTTGAAACG 58.602 37.500 13.39 0.00 45.15 3.60
7288 11301 2.085320 GTACCAAGTGAGCGAGAGAGA 58.915 52.381 0.00 0.00 0.00 3.10
7289 11302 2.088423 AGTACCAAGTGAGCGAGAGAG 58.912 52.381 0.00 0.00 0.00 3.20
7290 11303 2.201921 AGTACCAAGTGAGCGAGAGA 57.798 50.000 0.00 0.00 0.00 3.10
7291 11304 2.600731 CAAGTACCAAGTGAGCGAGAG 58.399 52.381 0.00 0.00 0.00 3.20
7331 11344 6.715264 TCCTTTTTAGGATTCCAGAAACTGAC 59.285 38.462 5.29 0.00 30.65 3.51
7419 11432 2.805671 CTGTGCGGACATAGACAACAAA 59.194 45.455 11.16 0.00 37.20 2.83
7470 11483 3.928375 GGCATGTTTGAAGCAACCTATTG 59.072 43.478 0.00 0.00 38.99 1.90
7618 11631 6.500684 TTCTTGACTATCACTTTCCAATGC 57.499 37.500 0.00 0.00 0.00 3.56
7855 11868 8.183830 GAGAATCTGTCAACAAGAATCACTAG 57.816 38.462 0.00 0.00 0.00 2.57
7910 11923 8.654997 AGAAATACAGCATCATAAGATACTGGT 58.345 33.333 11.78 2.31 45.85 4.00
7927 11940 5.237815 TCTGCACCAACACTAGAAATACAG 58.762 41.667 0.00 0.00 0.00 2.74
7987 12003 1.621814 AGCATACGTACCACAACAGGT 59.378 47.619 0.00 0.00 45.72 4.00
7995 12011 3.389221 CATGTATGCAGCATACGTACCA 58.611 45.455 31.25 18.93 46.69 3.25
8113 12129 2.320367 CATCTATTCCGCTCGTAGCAC 58.680 52.381 7.47 0.00 42.58 4.40
8167 12183 2.372504 TCATTTTGTGGAGACCCCGTAA 59.627 45.455 0.00 0.00 37.93 3.18
8170 12186 1.165270 GTCATTTTGTGGAGACCCCG 58.835 55.000 0.00 0.00 37.93 5.73
8214 12230 0.322546 AAGCCTCGTGGATCCAAACC 60.323 55.000 18.20 2.99 34.57 3.27
8375 12394 5.867903 AAAATCAGGTGTGAAAACATCCA 57.132 34.783 0.00 0.00 35.88 3.41
8376 12395 6.279882 TGAAAAATCAGGTGTGAAAACATCC 58.720 36.000 0.00 0.00 35.88 3.51
8394 12413 9.224267 TGAGAACCAACAATTTGAATTGAAAAA 57.776 25.926 20.04 0.00 46.72 1.94
8483 12502 7.254017 CGCTCTTATAAAAGTTTACGGAAGGAG 60.254 40.741 0.00 0.00 34.13 3.69
8485 12504 6.312180 ACGCTCTTATAAAAGTTTACGGAAGG 59.688 38.462 0.00 0.00 34.13 3.46
8486 12505 7.287050 ACGCTCTTATAAAAGTTTACGGAAG 57.713 36.000 0.00 0.00 34.13 3.46
8488 12507 7.656707 AAACGCTCTTATAAAAGTTTACGGA 57.343 32.000 0.00 0.00 34.13 4.69
8489 12508 8.863049 TCTAAACGCTCTTATAAAAGTTTACGG 58.137 33.333 0.00 4.28 34.29 4.02
8494 12513 9.654663 AGTGATCTAAACGCTCTTATAAAAGTT 57.345 29.630 0.00 0.00 34.13 2.66
8498 12517 9.947669 GTCTAGTGATCTAAACGCTCTTATAAA 57.052 33.333 0.00 0.00 0.00 1.40
8499 12518 9.339850 AGTCTAGTGATCTAAACGCTCTTATAA 57.660 33.333 0.00 0.00 0.00 0.98
8500 12519 8.905660 AGTCTAGTGATCTAAACGCTCTTATA 57.094 34.615 0.00 0.00 0.00 0.98
8502 12521 7.986320 ACTAGTCTAGTGATCTAAACGCTCTTA 59.014 37.037 11.88 0.00 37.69 2.10
8503 12522 6.824704 ACTAGTCTAGTGATCTAAACGCTCTT 59.175 38.462 11.88 0.00 37.69 2.85
8504 12523 6.350906 ACTAGTCTAGTGATCTAAACGCTCT 58.649 40.000 11.88 0.00 37.69 4.09
8505 12524 6.607735 ACTAGTCTAGTGATCTAAACGCTC 57.392 41.667 11.88 0.00 37.69 5.03
8506 12525 8.680039 ATTACTAGTCTAGTGATCTAAACGCT 57.320 34.615 20.78 0.00 39.81 5.07
8507 12526 8.938047 GATTACTAGTCTAGTGATCTAAACGC 57.062 38.462 26.38 8.69 44.10 4.84
8514 12533 8.776470 AGCGTTTAGATTACTAGTCTAGTGATC 58.224 37.037 26.37 26.37 46.38 2.92
8515 12534 8.680039 AGCGTTTAGATTACTAGTCTAGTGAT 57.320 34.615 20.78 17.96 39.81 3.06
8516 12535 7.986320 AGAGCGTTTAGATTACTAGTCTAGTGA 59.014 37.037 20.78 14.08 39.81 3.41
8517 12536 8.145316 AGAGCGTTTAGATTACTAGTCTAGTG 57.855 38.462 20.78 3.77 39.81 2.74
8518 12537 8.735692 AAGAGCGTTTAGATTACTAGTCTAGT 57.264 34.615 16.65 16.65 42.68 2.57
8526 12545 9.962783 ACGAAATATAAGAGCGTTTAGATTACT 57.037 29.630 0.00 0.00 0.00 2.24
8530 12549 9.740239 TGTAACGAAATATAAGAGCGTTTAGAT 57.260 29.630 0.00 0.00 41.74 1.98
8531 12550 9.229784 CTGTAACGAAATATAAGAGCGTTTAGA 57.770 33.333 0.00 0.00 41.74 2.10
8532 12551 9.229784 TCTGTAACGAAATATAAGAGCGTTTAG 57.770 33.333 0.00 0.00 41.74 1.85
8533 12552 9.229784 CTCTGTAACGAAATATAAGAGCGTTTA 57.770 33.333 0.00 0.00 41.74 2.01
8534 12553 7.972277 TCTCTGTAACGAAATATAAGAGCGTTT 59.028 33.333 0.00 0.00 41.74 3.60
8535 12554 7.478322 TCTCTGTAACGAAATATAAGAGCGTT 58.522 34.615 0.00 0.00 45.62 4.84
8536 12555 7.024340 TCTCTGTAACGAAATATAAGAGCGT 57.976 36.000 0.00 0.00 36.68 5.07
8537 12556 7.803659 TGATCTCTGTAACGAAATATAAGAGCG 59.196 37.037 0.00 0.00 0.00 5.03
8538 12557 8.907685 GTGATCTCTGTAACGAAATATAAGAGC 58.092 37.037 0.00 0.00 0.00 4.09
8539 12558 9.108449 CGTGATCTCTGTAACGAAATATAAGAG 57.892 37.037 0.00 0.00 38.27 2.85
8540 12559 8.074370 CCGTGATCTCTGTAACGAAATATAAGA 58.926 37.037 2.86 0.00 38.27 2.10
8541 12560 7.148950 GCCGTGATCTCTGTAACGAAATATAAG 60.149 40.741 2.86 0.00 38.27 1.73
8542 12561 6.639686 GCCGTGATCTCTGTAACGAAATATAA 59.360 38.462 2.86 0.00 38.27 0.98
8543 12562 6.016527 AGCCGTGATCTCTGTAACGAAATATA 60.017 38.462 2.86 0.00 38.27 0.86
8544 12563 4.982916 GCCGTGATCTCTGTAACGAAATAT 59.017 41.667 2.86 0.00 38.27 1.28
8545 12564 4.097437 AGCCGTGATCTCTGTAACGAAATA 59.903 41.667 2.86 0.00 38.27 1.40
8546 12565 3.119101 AGCCGTGATCTCTGTAACGAAAT 60.119 43.478 2.86 0.00 38.27 2.17
8547 12566 2.230508 AGCCGTGATCTCTGTAACGAAA 59.769 45.455 2.86 0.00 38.27 3.46
8548 12567 1.816835 AGCCGTGATCTCTGTAACGAA 59.183 47.619 2.86 0.00 38.27 3.85
8549 12568 1.132453 CAGCCGTGATCTCTGTAACGA 59.868 52.381 2.86 0.00 38.27 3.85
8550 12569 1.132453 TCAGCCGTGATCTCTGTAACG 59.868 52.381 0.00 0.00 35.85 3.18
8551 12570 2.924290 GTTCAGCCGTGATCTCTGTAAC 59.076 50.000 0.00 1.10 30.85 2.50
8552 12571 2.415491 CGTTCAGCCGTGATCTCTGTAA 60.415 50.000 0.00 0.00 30.85 2.41
8553 12572 1.132453 CGTTCAGCCGTGATCTCTGTA 59.868 52.381 0.00 0.00 30.85 2.74
8554 12573 0.109086 CGTTCAGCCGTGATCTCTGT 60.109 55.000 0.00 0.00 30.85 3.41
8555 12574 0.171231 TCGTTCAGCCGTGATCTCTG 59.829 55.000 0.00 0.00 30.85 3.35
8556 12575 1.107114 ATCGTTCAGCCGTGATCTCT 58.893 50.000 0.00 0.00 30.85 3.10
8557 12576 2.776312 TATCGTTCAGCCGTGATCTC 57.224 50.000 0.00 0.00 30.85 2.75
8558 12577 4.321304 CCTTATATCGTTCAGCCGTGATCT 60.321 45.833 0.00 0.00 30.85 2.75
8559 12578 3.921021 CCTTATATCGTTCAGCCGTGATC 59.079 47.826 0.00 0.00 30.85 2.92
8560 12579 3.321111 ACCTTATATCGTTCAGCCGTGAT 59.679 43.478 0.00 0.00 30.85 3.06
8561 12580 2.691526 ACCTTATATCGTTCAGCCGTGA 59.308 45.455 0.00 0.00 0.00 4.35
8599 12618 7.554835 ACTGTTTGTTTGATCTGGTTGTAAGTA 59.445 33.333 0.00 0.00 0.00 2.24
8649 12668 0.383860 GTGCTACCGTGCGTTGTTTC 60.384 55.000 0.00 0.00 35.36 2.78
8661 12680 6.142817 CAGTCATGTTGTTTTTAGTGCTACC 58.857 40.000 0.00 0.00 0.00 3.18
8682 12701 6.374333 TCTTCAAAAAGTAAGTGTGAAGCAGT 59.626 34.615 6.80 0.00 43.10 4.40
8685 12704 7.377131 GTCATCTTCAAAAAGTAAGTGTGAAGC 59.623 37.037 6.80 0.00 43.10 3.86
8696 12715 7.389053 AGAATAAGCGAGTCATCTTCAAAAAGT 59.611 33.333 0.00 0.00 33.95 2.66
8801 12820 4.585955 TGAGTCAACCTCAGTGTTAGTC 57.414 45.455 0.00 0.00 45.34 2.59
8859 12904 6.374333 GCCAAAGTAATGTCATTCAAGGACTA 59.626 38.462 3.48 0.00 36.26 2.59
8860 12905 5.183904 GCCAAAGTAATGTCATTCAAGGACT 59.816 40.000 3.48 0.00 36.26 3.85
8864 12909 5.346822 GCAAGCCAAAGTAATGTCATTCAAG 59.653 40.000 0.07 0.00 0.00 3.02
8881 12927 2.911509 ACCATTGCACGCAAGCCA 60.912 55.556 10.60 0.00 45.62 4.75
8889 12935 2.012673 GATCCACTCTCACCATTGCAC 58.987 52.381 0.00 0.00 0.00 4.57
8893 12939 1.482593 GGTCGATCCACTCTCACCATT 59.517 52.381 0.00 0.00 35.97 3.16
8900 12946 1.468985 CAGTCAGGTCGATCCACTCT 58.531 55.000 0.00 0.00 39.02 3.24
8909 12955 1.444553 GACGGAAGCAGTCAGGTCG 60.445 63.158 0.00 0.00 38.42 4.79
9014 13319 2.501723 CACTGGTATGGACTAAGCCACT 59.498 50.000 0.00 0.00 41.56 4.00
9069 13375 7.295672 TGTCATTTCCTAGATCCCCTTAATGAT 59.704 37.037 11.13 0.00 0.00 2.45
9115 13422 6.624352 ACATAATTTTCTCCATGACATCCG 57.376 37.500 0.00 0.00 0.00 4.18
9201 13508 5.374921 AGGTTCATCCATCAATCTCATGTC 58.625 41.667 0.00 0.00 39.02 3.06
9205 13512 9.342308 GTTAATTAGGTTCATCCATCAATCTCA 57.658 33.333 0.00 0.00 39.02 3.27
9259 13571 5.482908 TCAACAGATTTCCTTCTGAGTAGC 58.517 41.667 8.36 0.00 44.88 3.58
9263 13575 5.182570 TGCATTCAACAGATTTCCTTCTGAG 59.817 40.000 8.36 1.47 44.88 3.35
9266 13578 4.828939 TGTGCATTCAACAGATTTCCTTCT 59.171 37.500 0.00 0.00 0.00 2.85
9316 13628 4.210331 CAAGCCTGGAATAATACCTTGCT 58.790 43.478 0.00 0.00 36.87 3.91
9358 13670 2.750166 CCATCTCCTATACGCGAGACAT 59.250 50.000 15.93 2.58 37.94 3.06
9394 13706 4.796606 AGGAACCCAGTTATCATTCCATG 58.203 43.478 4.28 0.00 41.15 3.66
9406 13718 1.460699 GGGCTCAAAGGAACCCAGT 59.539 57.895 0.00 0.00 46.87 4.00
9407 13719 4.423231 GGGCTCAAAGGAACCCAG 57.577 61.111 0.00 0.00 46.87 4.45


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

AutoCloner maintained by Alex Coulton.