Multiple sequence alignment - TraesCS2D01G578500

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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 TraesCS2D01G578500 chr2D 100.000 3862 0 0 3255 7116 641233596 641229735 0.000000e+00 7132.0
1 TraesCS2D01G578500 chr2D 100.000 2808 0 0 1 2808 641236850 641234043 0.000000e+00 5186.0
2 TraesCS2D01G578500 chr2D 94.068 236 13 1 3255 3489 641233500 641233265 2.440000e-94 357.0
3 TraesCS2D01G578500 chr2D 94.068 236 13 1 3351 3586 641233596 641233362 2.440000e-94 357.0
4 TraesCS2D01G578500 chr2D 88.129 278 33 0 2480 2757 641234320 641234043 1.480000e-86 331.0
5 TraesCS2D01G578500 chr2D 88.129 278 33 0 2531 2808 641234371 641234094 1.480000e-86 331.0
6 TraesCS2D01G578500 chr2D 92.647 136 10 0 3255 3390 641233404 641233269 5.630000e-46 196.0
7 TraesCS2D01G578500 chr2D 92.647 136 10 0 3447 3582 641233596 641233461 5.630000e-46 196.0
8 TraesCS2D01G578500 chr2A 92.819 2799 124 17 44 2808 766470615 766467860 0.000000e+00 3984.0
9 TraesCS2D01G578500 chr2A 95.448 1999 65 9 3263 5253 766467318 766465338 0.000000e+00 3164.0
10 TraesCS2D01G578500 chr2A 85.452 1849 114 67 5314 7056 766465315 766463516 0.000000e+00 1781.0
11 TraesCS2D01G578500 chr2A 92.241 232 12 1 3255 3486 766467230 766467005 2.480000e-84 324.0
12 TraesCS2D01G578500 chr2A 91.667 228 12 2 3359 3586 766467318 766467098 6.930000e-80 309.0
13 TraesCS2D01G578500 chr2A 92.481 133 10 0 3258 3390 766467137 766467005 2.620000e-44 191.0
14 TraesCS2D01G578500 chr2A 92.188 128 10 0 3455 3582 766467318 766467191 1.580000e-41 182.0
15 TraesCS2D01G578500 chr2A 81.461 178 33 0 2631 2808 766468190 766468013 5.750000e-31 147.0
16 TraesCS2D01G578500 chr2A 91.045 67 1 2 7055 7116 766463268 766463202 1.270000e-12 86.1
17 TraesCS2D01G578500 chr2A 97.143 35 1 0 1 35 766470677 766470643 7.710000e-05 60.2
18 TraesCS2D01G578500 chr2B 92.305 2690 127 27 167 2808 800119090 800121747 0.000000e+00 3747.0
19 TraesCS2D01G578500 chr2B 92.902 1423 60 16 3841 5253 800122635 800124026 0.000000e+00 2030.0
20 TraesCS2D01G578500 chr2B 95.874 509 21 0 3277 3785 800122128 800122636 0.000000e+00 824.0
21 TraesCS2D01G578500 chr2B 89.338 544 21 22 5985 6519 800124652 800125167 0.000000e+00 649.0
22 TraesCS2D01G578500 chr2B 90.423 355 17 9 5635 5986 800124286 800124626 1.090000e-122 451.0
23 TraesCS2D01G578500 chr2B 94.492 236 12 1 3255 3489 800122202 800122437 5.250000e-96 363.0
24 TraesCS2D01G578500 chr2B 90.421 261 20 3 58 313 800118372 800118632 8.840000e-89 339.0
25 TraesCS2D01G578500 chr2B 85.479 303 41 1 2478 2780 800121471 800121770 5.360000e-81 313.0
26 TraesCS2D01G578500 chr2B 92.093 215 16 1 3372 3586 800122127 800122340 1.160000e-77 302.0
27 TraesCS2D01G578500 chr2B 85.714 280 27 8 6096 6364 800126388 800126665 4.200000e-72 283.0
28 TraesCS2D01G578500 chr2B 84.116 277 41 1 2532 2808 800121423 800121696 1.520000e-66 265.0
29 TraesCS2D01G578500 chr2B 94.776 134 6 1 181 313 800118954 800119087 2.600000e-49 207.0
30 TraesCS2D01G578500 chr2B 94.118 136 8 0 3255 3390 800122298 800122433 2.600000e-49 207.0
31 TraesCS2D01G578500 chr2B 81.890 254 31 12 5302 5553 800124036 800124276 4.350000e-47 200.0
32 TraesCS2D01G578500 chr2B 93.277 119 7 1 3468 3586 800122127 800122244 2.640000e-39 174.0
33 TraesCS2D01G578500 chr2B 82.941 170 29 0 2638 2807 800121427 800121596 3.440000e-33 154.0
34 TraesCS2D01G578500 chr2B 94.118 51 2 1 6829 6879 800127101 800127150 7.650000e-10 76.8
35 TraesCS2D01G578500 chr2B 100.000 37 0 0 1 37 800118299 800118335 1.280000e-07 69.4
36 TraesCS2D01G578500 chr7D 89.062 256 26 2 4859 5114 596062748 596063001 4.140000e-82 316.0
37 TraesCS2D01G578500 chr7D 86.184 152 18 3 5121 5270 596063040 596063190 2.050000e-35 161.0


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 TraesCS2D01G578500 chr2D 641229735 641236850 7115 True 1760.75 7132 93.711000 1 7116 8 chr2D.!!$R1 7115
1 TraesCS2D01G578500 chr2A 766463202 766470677 7475 True 1022.83 3984 91.194500 1 7116 10 chr2A.!!$R1 7115
2 TraesCS2D01G578500 chr2B 800118299 800127150 8851 False 591.90 3747 90.793167 1 6879 18 chr2B.!!$F1 6878

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
93 113 0.036164 CCTCCGACAACAATCCCACA 59.964 55.000 0.00 0.00 0.00 4.17 F
333 961 0.464036 TGAAGATGCGCTCCGGTAAT 59.536 50.000 9.73 0.00 0.00 1.89 F
598 1227 0.748450 TGACGGTGATTATCGGTCCC 59.252 55.000 0.00 0.00 33.84 4.46 F
2139 2829 0.467474 ATGATGGTGCCAGGCATGAG 60.467 55.000 19.75 0.00 41.91 2.90 F
2615 3317 0.319728 GAGGCTCTGCAGAGTGAACA 59.680 55.000 37.25 7.21 43.85 3.18 F
2699 3401 1.340889 TCAAGTTGCAGGTGAAATGGC 59.659 47.619 0.00 0.00 0.00 4.40 F
3767 4562 1.015109 CTGAGCCAGCAAGCATACTG 58.985 55.000 0.55 0.00 34.23 2.74 F
4026 4821 0.252479 AGCAGGTGGAGAATGAGCAG 59.748 55.000 0.00 0.00 0.00 4.24 F
5366 6169 0.036105 CCACATGGACTACAGCAGCA 60.036 55.000 0.00 0.00 37.39 4.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2090 2780 1.376543 CACCGCAGCTTCATCTTCAT 58.623 50.000 0.00 0.00 0.00 2.57 R
2133 2823 1.140452 TCTGCCTCTTCATCCTCATGC 59.860 52.381 0.00 0.00 0.00 4.06 R
2429 3131 1.026584 TTCAATCAGGCATGCATCCG 58.973 50.000 21.36 0.98 0.00 4.18 R
3421 4210 0.250467 TCACTTTGCAGAGCCTCCAC 60.250 55.000 3.74 0.00 0.00 4.02 R
3748 4543 1.015109 CAGTATGCTTGCTGGCTCAG 58.985 55.000 9.47 0.00 32.45 3.35 R
3929 4724 1.546323 CCAGCTGTTGATCACCCTGTT 60.546 52.381 13.81 0.00 0.00 3.16 R
5281 6084 0.478942 TCCTATAGCCCTCGACTGCT 59.521 55.000 8.79 8.79 41.57 4.24 R
5910 6730 0.840617 TGGCACAGGTAACACTGGAA 59.159 50.000 0.00 0.00 42.75 3.53 R
6928 9460 0.108472 TGCCTCGCATCAGTTCAGAG 60.108 55.000 0.00 0.00 31.71 3.35 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
83 103 4.697756 CAAGGGCGCCTCCGACAA 62.698 66.667 28.56 0.00 46.86 3.18
93 113 0.036164 CCTCCGACAACAATCCCACA 59.964 55.000 0.00 0.00 0.00 4.17
123 143 3.243068 GGCGTTACCCAAGCATTTATCAG 60.243 47.826 0.00 0.00 0.00 2.90
172 192 3.432252 CGCGTCAAGACCAACTTCTAAAT 59.568 43.478 0.00 0.00 36.61 1.40
210 382 4.751098 GGCGATACGTTACCAATTTATCCA 59.249 41.667 0.00 0.00 0.00 3.41
333 961 0.464036 TGAAGATGCGCTCCGGTAAT 59.536 50.000 9.73 0.00 0.00 1.89
368 996 2.436417 CGAGCATCTTTTCCCCTTCAA 58.564 47.619 0.00 0.00 0.00 2.69
597 1226 2.589798 TTGACGGTGATTATCGGTCC 57.410 50.000 0.00 1.29 33.84 4.46
598 1227 0.748450 TGACGGTGATTATCGGTCCC 59.252 55.000 0.00 0.00 33.84 4.46
633 1262 4.063967 CGCACGGGGTCTGCAGTA 62.064 66.667 14.67 0.00 34.00 2.74
634 1263 2.345991 GCACGGGGTCTGCAGTAA 59.654 61.111 14.67 0.00 34.56 2.24
635 1264 1.302192 GCACGGGGTCTGCAGTAAA 60.302 57.895 14.67 0.00 34.56 2.01
636 1265 0.887387 GCACGGGGTCTGCAGTAAAA 60.887 55.000 14.67 0.00 34.56 1.52
637 1266 1.600023 CACGGGGTCTGCAGTAAAAA 58.400 50.000 14.67 0.00 0.00 1.94
685 1314 2.174835 CGGGCCGCAGTAAAAACG 59.825 61.111 15.42 0.00 0.00 3.60
688 1317 0.952010 GGGCCGCAGTAAAAACGAGA 60.952 55.000 0.00 0.00 0.00 4.04
853 1497 4.647615 ACGCAAGCAGACGACGCT 62.648 61.111 0.00 0.00 42.98 5.07
967 1611 0.966370 CGTCGGAGGAAAGGAGGAGT 60.966 60.000 0.00 0.00 0.00 3.85
980 1624 2.125633 GGAGTCTTTCCCGTCCGC 60.126 66.667 0.00 0.00 40.37 5.54
1534 2206 0.961358 CAAGAGGGACGAGGACGACT 60.961 60.000 0.00 0.00 42.66 4.18
1560 2232 4.530857 CTAGCCCGGGCCAAGTCG 62.531 72.222 41.72 19.28 43.17 4.18
1713 2385 1.107114 CCATGTCACGCTCCTACTCT 58.893 55.000 0.00 0.00 0.00 3.24
1800 2475 4.436998 GACCGCAGACTGGACCGG 62.437 72.222 15.79 15.79 45.80 5.28
1819 2494 3.322318 AAGCGGAGGAGCAGAAGCC 62.322 63.158 0.00 0.00 43.56 4.35
1969 2659 3.745803 GCAAGGTGCCAGCAGAGC 61.746 66.667 0.00 0.00 37.42 4.09
2044 2734 2.429610 CTGCCAAGGGATCCAAAGATTG 59.570 50.000 15.23 9.57 30.90 2.67
2045 2735 2.225343 TGCCAAGGGATCCAAAGATTGT 60.225 45.455 15.23 0.00 30.90 2.71
2090 2780 2.359850 GAATGACGGTGCCAGCCA 60.360 61.111 0.00 0.00 0.00 4.75
2133 2823 1.101635 CAGAGCATGATGGTGCCAGG 61.102 60.000 0.12 0.00 46.19 4.45
2139 2829 0.467474 ATGATGGTGCCAGGCATGAG 60.467 55.000 19.75 0.00 41.91 2.90
2166 2856 5.893824 TGAAGAGGCAGAGTATGAGTATGAA 59.106 40.000 0.00 0.00 0.00 2.57
2292 2994 1.067425 GTTGCTGGCTTGAATGATGCA 60.067 47.619 0.00 0.00 0.00 3.96
2462 3164 1.808945 GATTGAACCAGTGGCTGACAG 59.191 52.381 9.78 0.00 32.44 3.51
2529 3231 4.636206 AGTCAACCTGAAACTGAACTTCAC 59.364 41.667 0.00 0.00 0.00 3.18
2537 3239 5.898174 TGAAACTGAACTTCACGTTAGAGA 58.102 37.500 1.64 0.00 35.56 3.10
2552 3254 4.384940 GTTAGAGATGAAATGGAGGCTCC 58.615 47.826 26.95 26.95 36.96 4.70
2615 3317 0.319728 GAGGCTCTGCAGAGTGAACA 59.680 55.000 37.25 7.21 43.85 3.18
2637 3339 5.105797 ACATGAAACTGAACTTCAAGTTGCA 60.106 36.000 7.75 13.09 38.80 4.08
2665 3367 2.507992 CGGCTCCGCAGAGTGAAG 60.508 66.667 0.00 0.00 42.59 3.02
2675 3377 2.032549 CGCAGAGTGAAGTTGAAACTGG 60.033 50.000 0.00 0.00 39.66 4.00
2688 3390 3.351740 TGAAACTGGACTTCAAGTTGCA 58.648 40.909 3.29 3.29 29.93 4.08
2690 3392 1.972872 ACTGGACTTCAAGTTGCAGG 58.027 50.000 7.45 0.00 0.00 4.85
2699 3401 1.340889 TCAAGTTGCAGGTGAAATGGC 59.659 47.619 0.00 0.00 0.00 4.40
2706 3408 2.044946 GGTGAAATGGCGGCTCCT 60.045 61.111 11.43 0.00 35.26 3.69
2715 3417 1.743252 GGCGGCTCCTCAAAGTGAG 60.743 63.158 0.00 0.00 43.91 3.51
2722 3424 2.697654 CTCCTCAAAGTGAGCCTGAAG 58.302 52.381 0.00 0.00 42.98 3.02
3296 4085 7.818930 GGAAAATCCACAAATAGAAATTGAGCA 59.181 33.333 0.00 0.00 36.28 4.26
3443 4232 1.544314 GGAGGCTCTGCAAAGTGAACT 60.544 52.381 15.23 0.00 0.00 3.01
3444 4233 2.225467 GAGGCTCTGCAAAGTGAACTT 58.775 47.619 7.40 0.00 37.91 2.66
3445 4234 1.952296 AGGCTCTGCAAAGTGAACTTG 59.048 47.619 0.00 0.00 36.12 3.16
3446 4235 1.949525 GGCTCTGCAAAGTGAACTTGA 59.050 47.619 0.00 0.00 36.12 3.02
3447 4236 2.358898 GGCTCTGCAAAGTGAACTTGAA 59.641 45.455 0.00 0.00 36.12 2.69
3448 4237 3.181487 GGCTCTGCAAAGTGAACTTGAAA 60.181 43.478 0.00 0.00 36.12 2.69
3564 4359 3.812156 TCTGAACTTGTCGAGGAAACA 57.188 42.857 0.00 0.00 0.00 2.83
3565 4360 4.131649 TCTGAACTTGTCGAGGAAACAA 57.868 40.909 0.00 0.00 35.44 2.83
3594 4389 2.094390 TGAAATTGAAGCTGCTGATGGC 60.094 45.455 1.35 0.00 42.22 4.40
3719 4514 3.340814 TCCTCCTGAAGAACATGCTTC 57.659 47.619 6.22 6.22 43.53 3.86
3748 4543 2.421424 CTGCCTGATTTAGTTGGTCAGC 59.579 50.000 0.00 0.00 38.38 4.26
3767 4562 1.015109 CTGAGCCAGCAAGCATACTG 58.985 55.000 0.55 0.00 34.23 2.74
3787 4582 4.648762 ACTGTGATCCTCCAGATACTCAAG 59.351 45.833 10.17 0.00 34.42 3.02
3929 4724 2.242043 TCAGATAGCCGATGAGCATGA 58.758 47.619 0.00 0.00 34.23 3.07
3963 4758 1.153168 GCTGGAGGGCGAGCAAATA 60.153 57.895 0.00 0.00 44.27 1.40
3964 4759 0.748005 GCTGGAGGGCGAGCAAATAA 60.748 55.000 0.00 0.00 44.27 1.40
3971 4766 5.163561 TGGAGGGCGAGCAAATAATTTTAAG 60.164 40.000 0.00 0.00 0.00 1.85
3980 4775 7.043192 CGAGCAAATAATTTTAAGCAATGAGGG 60.043 37.037 0.00 0.00 0.00 4.30
3982 4777 7.983484 AGCAAATAATTTTAAGCAATGAGGGAG 59.017 33.333 0.00 0.00 0.00 4.30
4026 4821 0.252479 AGCAGGTGGAGAATGAGCAG 59.748 55.000 0.00 0.00 0.00 4.24
4045 4840 2.100197 AGTTGCTACCTGATCGTGCTA 58.900 47.619 0.00 0.00 0.00 3.49
4074 4869 5.986135 CGTTAATCACCAGATAAAGGAGGAG 59.014 44.000 0.00 0.00 33.08 3.69
4335 5130 0.545309 AGCAGCCTGGTACCAGAGAA 60.545 55.000 38.35 6.06 46.30 2.87
4344 5139 5.452636 GCCTGGTACCAGAGAATTCTTAGAG 60.453 48.000 38.35 19.72 46.30 2.43
4359 5154 5.242795 TCTTAGAGCCCAAGTAAGCTTTT 57.757 39.130 3.20 0.00 40.11 2.27
4712 5508 4.514066 GGGGAACTGTTACTGTACAACTTG 59.486 45.833 2.26 0.00 0.00 3.16
4727 5523 7.682628 TGTACAACTTGCTTTAATACTAGGGT 58.317 34.615 0.00 0.00 0.00 4.34
4729 5525 7.683437 ACAACTTGCTTTAATACTAGGGTTC 57.317 36.000 0.00 0.00 0.00 3.62
4730 5526 6.657966 ACAACTTGCTTTAATACTAGGGTTCC 59.342 38.462 0.00 0.00 0.00 3.62
4731 5527 6.382919 ACTTGCTTTAATACTAGGGTTCCA 57.617 37.500 0.00 0.00 0.00 3.53
4774 5571 4.202398 CCATATAGTCACATGCTCAAGGGT 60.202 45.833 0.00 0.00 0.00 4.34
4797 5594 8.336801 GGTTAATTACCAAATCAGTCTGTTCT 57.663 34.615 0.00 0.00 46.92 3.01
4819 5616 5.243507 TCTTGCTCTTATTGGCATTTGTCAA 59.756 36.000 0.00 0.00 44.39 3.18
4851 5649 4.923871 TCGTCATTGTTCTTCTCTAACTGC 59.076 41.667 0.00 0.00 0.00 4.40
5111 5914 8.364142 CCTGGTTTGTCTCAAATTTTTACCATA 58.636 33.333 0.00 0.00 33.15 2.74
5112 5915 9.927668 CTGGTTTGTCTCAAATTTTTACCATAT 57.072 29.630 0.00 0.00 33.15 1.78
5157 5960 8.904099 AAGCTTGTGTAGATTAGTTAACTTGT 57.096 30.769 14.49 2.64 28.77 3.16
5230 6033 3.778265 ACTTTTGGACCAAGCCACATAT 58.222 40.909 7.07 0.00 37.75 1.78
5253 6056 0.538746 TGATAGCTGGCATGCATGGG 60.539 55.000 27.34 4.09 34.99 4.00
5254 6057 1.874345 GATAGCTGGCATGCATGGGC 61.874 60.000 27.34 19.51 41.68 5.36
5270 6073 4.094684 GCACTAGCTGCCTGTACG 57.905 61.111 0.00 0.00 40.42 3.67
5271 6074 1.519455 GCACTAGCTGCCTGTACGG 60.519 63.158 0.00 0.00 40.42 4.02
5283 6086 4.808649 GTACGGCTGTACCAGAGC 57.191 61.111 23.00 0.00 44.25 4.09
5284 6087 1.888018 GTACGGCTGTACCAGAGCA 59.112 57.895 23.00 0.00 44.25 4.26
5285 6088 0.179134 GTACGGCTGTACCAGAGCAG 60.179 60.000 23.00 4.47 44.25 4.24
5286 6089 0.611062 TACGGCTGTACCAGAGCAGT 60.611 55.000 12.66 12.66 45.25 4.40
5287 6090 1.153745 CGGCTGTACCAGAGCAGTC 60.154 63.158 6.08 0.00 38.27 3.51
5288 6091 1.153745 GGCTGTACCAGAGCAGTCG 60.154 63.158 6.08 0.00 38.27 4.18
5289 6092 1.595993 GGCTGTACCAGAGCAGTCGA 61.596 60.000 6.08 0.00 38.27 4.20
5290 6093 0.179150 GCTGTACCAGAGCAGTCGAG 60.179 60.000 0.00 0.00 36.40 4.04
5291 6094 0.453793 CTGTACCAGAGCAGTCGAGG 59.546 60.000 0.00 0.00 32.44 4.63
5292 6095 0.965866 TGTACCAGAGCAGTCGAGGG 60.966 60.000 0.00 0.00 0.00 4.30
5293 6096 2.052690 TACCAGAGCAGTCGAGGGC 61.053 63.158 0.06 0.06 0.00 5.19
5294 6097 2.500815 TACCAGAGCAGTCGAGGGCT 62.501 60.000 10.30 10.30 44.48 5.19
5297 6100 1.610363 CAGAGCAGTCGAGGGCTATA 58.390 55.000 10.47 0.00 41.22 1.31
5298 6101 1.539388 CAGAGCAGTCGAGGGCTATAG 59.461 57.143 10.47 0.00 41.22 1.31
5300 6103 0.478942 AGCAGTCGAGGGCTATAGGA 59.521 55.000 8.88 0.00 38.90 2.94
5303 6106 3.090037 GCAGTCGAGGGCTATAGGATTA 58.910 50.000 1.04 0.00 0.00 1.75
5306 6109 5.337652 GCAGTCGAGGGCTATAGGATTATTT 60.338 44.000 1.04 0.00 0.00 1.40
5310 6113 7.181125 AGTCGAGGGCTATAGGATTATTTGAAT 59.819 37.037 1.04 0.00 0.00 2.57
5364 6167 0.745845 GCCCACATGGACTACAGCAG 60.746 60.000 0.00 0.00 37.39 4.24
5366 6169 0.036105 CCACATGGACTACAGCAGCA 60.036 55.000 0.00 0.00 37.39 4.41
5369 6172 1.556451 ACATGGACTACAGCAGCATCA 59.444 47.619 0.00 0.00 0.00 3.07
5372 6175 1.556451 TGGACTACAGCAGCATCATGT 59.444 47.619 0.00 0.00 0.00 3.21
5395 6211 4.690748 TCATTTAGTGATATAAGCGCAGGC 59.309 41.667 11.47 0.00 40.37 4.85
5416 6232 3.007635 CCATTTCTTTAGGTGGACCGAC 58.992 50.000 0.00 0.00 42.08 4.79
5553 6372 7.412455 GCTCTTTTTCTGCTTAGTCTGTATGTC 60.412 40.741 0.00 0.00 0.00 3.06
5569 6388 3.882102 ATGTCTTATAATGGGGCTGCA 57.118 42.857 0.50 0.00 0.00 4.41
5597 6416 8.600668 CATATCCCCCATTCGATGATCTATATT 58.399 37.037 0.00 0.00 0.00 1.28
5600 6419 7.698912 TCCCCCATTCGATGATCTATATTTTT 58.301 34.615 0.00 0.00 0.00 1.94
5601 6420 7.829211 TCCCCCATTCGATGATCTATATTTTTC 59.171 37.037 0.00 0.00 0.00 2.29
5628 6447 1.435256 ACCTGGTGACTAGTTTGCCT 58.565 50.000 0.00 0.00 0.00 4.75
5667 6486 1.346722 CTTCCTGGGTTCCTGTACGTT 59.653 52.381 0.00 0.00 0.00 3.99
5672 6491 1.000731 TGGGTTCCTGTACGTTTACCG 59.999 52.381 0.00 0.00 44.03 4.02
5748 6567 7.361713 GCATGCTATGTTTAACTGAACTTACCA 60.362 37.037 11.37 0.00 0.00 3.25
5771 6590 2.158943 GGGATGCGGTAGCTAGTTTCTT 60.159 50.000 0.00 0.00 45.42 2.52
5826 6645 5.708736 TGTTATCTCCTATTTTCAGGCCA 57.291 39.130 5.01 0.00 35.49 5.36
5892 6712 4.960938 TGCTCTGTGACTAGTTTGTCAAT 58.039 39.130 0.00 0.00 46.77 2.57
5903 6723 8.724229 TGACTAGTTTGTCAATCATGAATCTTG 58.276 33.333 0.00 0.00 43.08 3.02
5904 6724 8.048534 ACTAGTTTGTCAATCATGAATCTTGG 57.951 34.615 0.00 0.00 37.30 3.61
5905 6725 5.717119 AGTTTGTCAATCATGAATCTTGGC 58.283 37.500 0.00 1.96 37.30 4.52
5908 6728 5.988310 TGTCAATCATGAATCTTGGCTTT 57.012 34.783 12.10 0.00 37.30 3.51
5909 6729 5.957798 TGTCAATCATGAATCTTGGCTTTC 58.042 37.500 12.10 0.00 37.30 2.62
5910 6730 5.713389 TGTCAATCATGAATCTTGGCTTTCT 59.287 36.000 12.10 0.00 37.30 2.52
5911 6731 6.209986 TGTCAATCATGAATCTTGGCTTTCTT 59.790 34.615 12.10 0.00 37.30 2.52
5912 6732 6.750963 GTCAATCATGAATCTTGGCTTTCTTC 59.249 38.462 0.00 0.00 37.30 2.87
5913 6733 5.848833 ATCATGAATCTTGGCTTTCTTCC 57.151 39.130 0.00 0.00 0.00 3.46
5914 6734 4.665451 TCATGAATCTTGGCTTTCTTCCA 58.335 39.130 0.00 0.00 0.00 3.53
5915 6735 4.703575 TCATGAATCTTGGCTTTCTTCCAG 59.296 41.667 0.00 0.00 34.66 3.86
5916 6736 4.104383 TGAATCTTGGCTTTCTTCCAGT 57.896 40.909 0.00 0.00 34.66 4.00
5917 6737 3.822735 TGAATCTTGGCTTTCTTCCAGTG 59.177 43.478 0.00 0.00 34.66 3.66
5918 6738 3.515602 ATCTTGGCTTTCTTCCAGTGT 57.484 42.857 0.00 0.00 34.66 3.55
5931 6751 0.951558 CCAGTGTTACCTGTGCCAAC 59.048 55.000 0.00 0.00 0.00 3.77
5932 6752 1.674359 CAGTGTTACCTGTGCCAACA 58.326 50.000 0.00 0.00 34.34 3.33
5959 6781 6.529125 CACATATGCTTGTTCATTTCTTGTCC 59.471 38.462 1.58 0.00 0.00 4.02
5992 6828 4.039973 TCAACTGAACCGAACCTACAGATT 59.960 41.667 0.00 0.00 33.53 2.40
6026 6891 5.358160 GCTAGTTATTTCAGGCCATGTCTTT 59.642 40.000 5.01 0.00 0.00 2.52
6091 6958 1.228521 CAATGTGTGGGACCTGCCA 60.229 57.895 0.00 0.00 38.95 4.92
6120 6987 1.213926 GCTGGGGAAATCCTGATGAGT 59.786 52.381 0.00 0.00 35.95 3.41
6138 7010 1.608590 AGTTGCCATGCTGTGTTGTAC 59.391 47.619 0.00 0.00 0.00 2.90
6139 7011 0.590682 TTGCCATGCTGTGTTGTACG 59.409 50.000 0.00 0.00 0.00 3.67
6141 7013 0.110238 GCCATGCTGTGTTGTACGTG 60.110 55.000 0.00 0.00 0.00 4.49
6142 7014 0.110238 CCATGCTGTGTTGTACGTGC 60.110 55.000 0.00 0.00 33.71 5.34
6143 7015 0.450972 CATGCTGTGTTGTACGTGCG 60.451 55.000 0.00 0.00 35.17 5.34
6144 7016 0.878523 ATGCTGTGTTGTACGTGCGT 60.879 50.000 0.00 2.05 35.17 5.24
6145 7017 1.083657 GCTGTGTTGTACGTGCGTG 60.084 57.895 7.55 0.00 0.00 5.34
6146 7018 1.083657 CTGTGTTGTACGTGCGTGC 60.084 57.895 7.55 6.68 0.00 5.34
6147 7019 2.128274 GTGTTGTACGTGCGTGCG 60.128 61.111 7.55 0.00 33.40 5.34
6148 7020 3.990806 TGTTGTACGTGCGTGCGC 61.991 61.111 9.85 9.85 42.35 6.09
6192 7068 4.025396 CAGCTTACTGTCTGTCTGTTGTTG 60.025 45.833 0.00 0.00 39.22 3.33
6199 7075 4.055360 TGTCTGTCTGTTGTTGGTTATCG 58.945 43.478 0.00 0.00 0.00 2.92
6208 7084 1.070445 TGTTGGTTATCGTGGACCGTT 59.930 47.619 0.00 0.00 38.81 4.44
6278 7160 6.611785 ACTATGTGGTCTTATGCTAGGTAGA 58.388 40.000 0.00 0.00 0.00 2.59
6279 7161 6.717540 ACTATGTGGTCTTATGCTAGGTAGAG 59.282 42.308 0.00 0.00 0.00 2.43
6408 7290 2.770164 AAGCACTACCCTGTAGCTTG 57.230 50.000 0.00 0.00 43.25 4.01
6496 7378 4.673534 GGTCTAACCAACCGTTATGTTG 57.326 45.455 8.06 0.00 44.12 3.33
6533 7415 1.251251 GATTCACCTTGCCAAGTGCT 58.749 50.000 3.37 0.00 42.00 4.40
6583 7480 3.264998 ACAGTTTTGGCTGCAAAATGT 57.735 38.095 11.24 11.24 39.96 2.71
6586 7483 4.141959 ACAGTTTTGGCTGCAAAATGTAGT 60.142 37.500 14.25 4.75 39.96 2.73
6587 7484 5.068460 ACAGTTTTGGCTGCAAAATGTAGTA 59.932 36.000 14.25 0.00 39.96 1.82
6588 7485 5.630680 CAGTTTTGGCTGCAAAATGTAGTAG 59.369 40.000 2.51 0.00 36.58 2.57
6593 8974 3.623510 GGCTGCAAAATGTAGTAGGAGTC 59.376 47.826 0.50 0.00 32.42 3.36
6599 8980 6.426937 TGCAAAATGTAGTAGGAGTCTTGTTC 59.573 38.462 0.00 0.00 0.00 3.18
6600 8981 6.426937 GCAAAATGTAGTAGGAGTCTTGTTCA 59.573 38.462 0.00 0.00 0.00 3.18
6601 8982 7.119846 GCAAAATGTAGTAGGAGTCTTGTTCAT 59.880 37.037 0.00 0.00 0.00 2.57
6604 8985 8.824756 AATGTAGTAGGAGTCTTGTTCATCTA 57.175 34.615 0.00 0.00 0.00 1.98
6605 8986 8.824756 ATGTAGTAGGAGTCTTGTTCATCTAA 57.175 34.615 0.00 0.00 0.00 2.10
6623 9004 0.610232 AACCTCCTGATGCACCTTGC 60.610 55.000 0.00 0.00 45.29 4.01
6637 9033 3.340953 CTTGCGAACCGGGCCATTG 62.341 63.158 6.32 0.00 0.00 2.82
6675 9071 1.666054 CTCCTCCTGATTCAGCTTGC 58.334 55.000 8.23 0.00 0.00 4.01
6676 9072 0.254178 TCCTCCTGATTCAGCTTGCC 59.746 55.000 8.23 0.00 0.00 4.52
6688 9084 0.540923 AGCTTGCCAAGTGCCAAAAA 59.459 45.000 6.28 0.00 40.16 1.94
6788 9200 4.397103 GGCAATGAATGAATGAGTGAGTGA 59.603 41.667 0.00 0.00 0.00 3.41
6842 9373 2.418628 ACAAGATAACATTTGTCGGGCG 59.581 45.455 0.00 0.00 32.32 6.13
6881 9413 3.008485 GTCCCTGATTTGAGAGGAACAGT 59.992 47.826 0.00 0.00 0.00 3.55
6904 9436 3.794270 GCTGCTGCAATGCCATTG 58.206 55.556 13.11 13.11 43.06 2.82
6984 9516 1.625818 AGGGTAAGAAGGTCTGCTGTG 59.374 52.381 0.00 0.00 0.00 3.66
6985 9517 1.443802 GGTAAGAAGGTCTGCTGTGC 58.556 55.000 0.00 0.00 0.00 4.57
6986 9518 1.002544 GGTAAGAAGGTCTGCTGTGCT 59.997 52.381 0.00 0.00 0.00 4.40
7051 9592 5.699001 GGACCAAAACCAAACCAAATCATAC 59.301 40.000 0.00 0.00 0.00 2.39
7052 9593 5.616270 ACCAAAACCAAACCAAATCATACC 58.384 37.500 0.00 0.00 0.00 2.73
7053 9594 5.368230 ACCAAAACCAAACCAAATCATACCT 59.632 36.000 0.00 0.00 0.00 3.08
7109 9906 1.466167 TGAGACTACCGTGTTAGCGAC 59.534 52.381 0.00 0.00 0.00 5.19
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
37 38 3.194272 GAACTGTGTTGGTGCGCCC 62.194 63.158 15.15 6.44 0.00 6.13
38 39 2.331451 GAACTGTGTTGGTGCGCC 59.669 61.111 10.11 10.11 0.00 6.53
41 42 2.331451 GCGGAACTGTGTTGGTGC 59.669 61.111 0.00 0.00 0.00 5.01
67 87 4.699522 GTTGTCGGAGGCGCCCTT 62.700 66.667 26.15 4.93 31.76 3.95
83 103 2.158900 CGCCTCTTATCTGTGGGATTGT 60.159 50.000 0.00 0.00 35.98 2.71
93 113 2.158943 GCTTGGGTAACGCCTCTTATCT 60.159 50.000 0.00 0.00 37.43 1.98
123 143 1.792006 CCGGTAGGAATTATGGCGTC 58.208 55.000 0.00 0.00 41.02 5.19
210 382 7.210873 GTCTAGTTCGTCCATCCAGATATTTT 58.789 38.462 0.00 0.00 0.00 1.82
318 946 0.814010 AACCATTACCGGAGCGCATC 60.814 55.000 9.46 4.01 0.00 3.91
424 1052 4.272504 TGCCGTCTCCGAATATTTTCAATC 59.727 41.667 0.00 0.00 35.63 2.67
427 1055 3.254470 TGCCGTCTCCGAATATTTTCA 57.746 42.857 0.00 0.00 35.63 2.69
450 1078 1.551452 CTCCCTCATAGATCCGGGTC 58.449 60.000 6.61 6.61 37.92 4.46
452 1080 0.616111 CCCTCCCTCATAGATCCGGG 60.616 65.000 0.00 0.00 38.07 5.73
505 1134 3.057596 AGTTAACAACAATGGCGATGTGG 60.058 43.478 8.61 0.00 0.00 4.17
570 1199 6.479001 ACCGATAATCACCGTCAAAATTAGAG 59.521 38.462 0.00 0.00 0.00 2.43
572 1201 6.292703 GGACCGATAATCACCGTCAAAATTAG 60.293 42.308 0.00 0.00 0.00 1.73
597 1226 4.093850 GTGCGTGGTAAACTGGTAATAAGG 59.906 45.833 0.00 0.00 0.00 2.69
598 1227 4.201647 CGTGCGTGGTAAACTGGTAATAAG 60.202 45.833 0.00 0.00 0.00 1.73
635 1264 7.428282 TGCCGTTTTCTTTTTCTTTCTTTTT 57.572 28.000 0.00 0.00 0.00 1.94
636 1265 7.172532 AGTTGCCGTTTTCTTTTTCTTTCTTTT 59.827 29.630 0.00 0.00 0.00 2.27
637 1266 6.649141 AGTTGCCGTTTTCTTTTTCTTTCTTT 59.351 30.769 0.00 0.00 0.00 2.52
638 1267 6.163476 AGTTGCCGTTTTCTTTTTCTTTCTT 58.837 32.000 0.00 0.00 0.00 2.52
639 1268 5.720202 AGTTGCCGTTTTCTTTTTCTTTCT 58.280 33.333 0.00 0.00 0.00 2.52
640 1269 6.528774 TGTAGTTGCCGTTTTCTTTTTCTTTC 59.471 34.615 0.00 0.00 0.00 2.62
641 1270 6.309494 GTGTAGTTGCCGTTTTCTTTTTCTTT 59.691 34.615 0.00 0.00 0.00 2.52
642 1271 5.803461 GTGTAGTTGCCGTTTTCTTTTTCTT 59.197 36.000 0.00 0.00 0.00 2.52
643 1272 5.106078 TGTGTAGTTGCCGTTTTCTTTTTCT 60.106 36.000 0.00 0.00 0.00 2.52
644 1273 5.004061 GTGTGTAGTTGCCGTTTTCTTTTTC 59.996 40.000 0.00 0.00 0.00 2.29
650 1279 1.333435 CCGTGTGTAGTTGCCGTTTTC 60.333 52.381 0.00 0.00 0.00 2.29
685 1314 1.071471 CACACCCACACACCCTCTC 59.929 63.158 0.00 0.00 0.00 3.20
688 1317 2.313427 AACCACACCCACACACCCT 61.313 57.895 0.00 0.00 0.00 4.34
825 1469 2.257371 CTTGCGTCCTTCGTCGGA 59.743 61.111 0.00 0.00 42.13 4.55
835 1479 4.122515 GCGTCGTCTGCTTGCGTC 62.123 66.667 0.00 0.00 0.00 5.19
1800 2475 1.813337 GCTTCTGCTCCTCCGCTTC 60.813 63.158 0.00 0.00 36.03 3.86
1819 2494 2.413765 GCTCCGGCTTCTACTCCG 59.586 66.667 0.00 0.00 44.89 4.63
2044 2734 2.227089 ATCACCACCTCCGAGCGAAC 62.227 60.000 0.00 0.00 0.00 3.95
2045 2735 1.982395 ATCACCACCTCCGAGCGAA 60.982 57.895 0.00 0.00 0.00 4.70
2090 2780 1.376543 CACCGCAGCTTCATCTTCAT 58.623 50.000 0.00 0.00 0.00 2.57
2133 2823 1.140452 TCTGCCTCTTCATCCTCATGC 59.860 52.381 0.00 0.00 0.00 4.06
2139 2829 3.640967 ACTCATACTCTGCCTCTTCATCC 59.359 47.826 0.00 0.00 0.00 3.51
2166 2856 2.837947 TCATCTGATTCCACCACCTCT 58.162 47.619 0.00 0.00 0.00 3.69
2292 2994 3.702548 TGGCATTTATTTCAGCAGCATCT 59.297 39.130 0.00 0.00 0.00 2.90
2429 3131 1.026584 TTCAATCAGGCATGCATCCG 58.973 50.000 21.36 0.98 0.00 4.18
2462 3164 4.127171 TCTAACTTCAGAACAACCACTGC 58.873 43.478 0.00 0.00 34.57 4.40
2529 3231 4.054671 GAGCCTCCATTTCATCTCTAACG 58.945 47.826 0.00 0.00 0.00 3.18
2559 3261 4.332819 ACTTGAAGTTCAGTTCCAAGTTCG 59.667 41.667 5.56 0.00 36.39 3.95
2615 3317 5.450965 CCTGCAACTTGAAGTTCAGTTTCAT 60.451 40.000 23.20 0.00 36.03 2.57
2637 3339 2.044946 GGAGCCGCCATTTCACCT 60.045 61.111 0.00 0.00 36.34 4.00
2665 3367 4.105486 GCAACTTGAAGTCCAGTTTCAAC 58.895 43.478 0.00 0.00 39.05 3.18
2675 3377 4.293415 CATTTCACCTGCAACTTGAAGTC 58.707 43.478 0.00 0.00 31.11 3.01
2688 3390 2.044946 GGAGCCGCCATTTCACCT 60.045 61.111 0.00 0.00 36.34 4.00
2690 3392 0.960364 TTGAGGAGCCGCCATTTCAC 60.960 55.000 0.00 0.00 40.02 3.18
2722 3424 1.678101 ACCTGCAACTTGAAGTTCAGC 59.322 47.619 21.47 17.42 36.03 4.26
3254 3956 5.008712 GGATTTTCCTCGACAAGTTCAGTTT 59.991 40.000 0.00 0.00 32.53 2.66
3255 3957 4.515567 GGATTTTCCTCGACAAGTTCAGTT 59.484 41.667 0.00 0.00 32.53 3.16
3256 3958 4.065789 GGATTTTCCTCGACAAGTTCAGT 58.934 43.478 0.00 0.00 32.53 3.41
3257 3959 4.065088 TGGATTTTCCTCGACAAGTTCAG 58.935 43.478 0.00 0.00 37.46 3.02
3258 3960 3.813166 GTGGATTTTCCTCGACAAGTTCA 59.187 43.478 0.00 0.00 37.46 3.18
3259 3961 3.813166 TGTGGATTTTCCTCGACAAGTTC 59.187 43.478 0.00 0.00 37.46 3.01
3260 3962 3.815809 TGTGGATTTTCCTCGACAAGTT 58.184 40.909 0.00 0.00 37.46 2.66
3261 3963 3.485463 TGTGGATTTTCCTCGACAAGT 57.515 42.857 0.00 0.00 37.46 3.16
3275 4064 6.608405 TCCATGCTCAATTTCTATTTGTGGAT 59.392 34.615 0.00 0.00 31.57 3.41
3296 4085 2.887152 GCCACTTGAAGTTCAGTTCCAT 59.113 45.455 5.56 0.00 0.00 3.41
3421 4210 0.250467 TCACTTTGCAGAGCCTCCAC 60.250 55.000 3.74 0.00 0.00 4.02
3443 4232 4.131649 TCCTCGACAAGTTCAGTTTCAA 57.868 40.909 0.00 0.00 0.00 2.69
3444 4233 3.812156 TCCTCGACAAGTTCAGTTTCA 57.188 42.857 0.00 0.00 0.00 2.69
3445 4234 4.571176 AGTTTCCTCGACAAGTTCAGTTTC 59.429 41.667 0.00 0.00 0.00 2.78
3446 4235 4.514401 AGTTTCCTCGACAAGTTCAGTTT 58.486 39.130 0.00 0.00 0.00 2.66
3447 4236 4.120589 GAGTTTCCTCGACAAGTTCAGTT 58.879 43.478 0.00 0.00 0.00 3.16
3448 4237 3.492829 GGAGTTTCCTCGACAAGTTCAGT 60.493 47.826 0.00 0.00 38.70 3.41
3564 4359 5.818857 AGCAGCTTCAATTTCAATTTGTGTT 59.181 32.000 0.00 0.00 0.00 3.32
3565 4360 5.235616 CAGCAGCTTCAATTTCAATTTGTGT 59.764 36.000 0.00 0.00 0.00 3.72
3594 4389 6.128282 GCTCTTCTTCATCTCTAGTAGGATCG 60.128 46.154 0.00 0.00 0.00 3.69
3719 4514 5.296283 CCAACTAAATCAGGCAGAGAATCAG 59.704 44.000 0.00 0.00 37.82 2.90
3748 4543 1.015109 CAGTATGCTTGCTGGCTCAG 58.985 55.000 9.47 0.00 32.45 3.35
3767 4562 5.127845 TGAACTTGAGTATCTGGAGGATCAC 59.872 44.000 0.00 0.00 35.98 3.06
3787 4582 5.530519 TCATCTGCACGTTTATCTTGAAC 57.469 39.130 0.00 0.00 0.00 3.18
3929 4724 1.546323 CCAGCTGTTGATCACCCTGTT 60.546 52.381 13.81 0.00 0.00 3.16
3963 4758 5.743636 TTGCTCCCTCATTGCTTAAAATT 57.256 34.783 0.00 0.00 0.00 1.82
3964 4759 5.667466 CATTGCTCCCTCATTGCTTAAAAT 58.333 37.500 0.00 0.00 0.00 1.82
3971 4766 1.683943 TAGCATTGCTCCCTCATTGC 58.316 50.000 15.81 0.00 40.44 3.56
4026 4821 2.194271 GTAGCACGATCAGGTAGCAAC 58.806 52.381 0.00 0.00 0.00 4.17
4045 4840 6.070995 TCCTTTATCTGGTGATTAACGTCTGT 60.071 38.462 0.00 0.00 34.32 3.41
4074 4869 7.019774 TGTAACATGATCTAGAAGCATTTGC 57.980 36.000 0.00 0.00 42.49 3.68
4335 5130 5.443230 AAGCTTACTTGGGCTCTAAGAAT 57.557 39.130 0.00 0.00 37.87 2.40
4395 5191 4.522789 TCAAATGTAAAAGGTTGCCCTCTC 59.477 41.667 0.00 0.00 41.56 3.20
4405 5201 6.748132 AGTGGACATGTTCAAATGTAAAAGG 58.252 36.000 8.85 0.00 40.87 3.11
4630 5426 4.895668 ATGAACAAAAATGAGGGCACAT 57.104 36.364 0.00 0.00 0.00 3.21
4712 5508 6.651086 AGAAGTGGAACCCTAGTATTAAAGC 58.349 40.000 0.00 0.00 37.80 3.51
4727 5523 4.022068 GCAAATCATTGGTGAGAAGTGGAA 60.022 41.667 0.00 0.00 37.87 3.53
4729 5525 3.367703 GGCAAATCATTGGTGAGAAGTGG 60.368 47.826 0.00 0.00 37.87 4.00
4730 5526 3.367703 GGGCAAATCATTGGTGAGAAGTG 60.368 47.826 0.00 0.00 37.87 3.16
4731 5527 2.827921 GGGCAAATCATTGGTGAGAAGT 59.172 45.455 0.00 0.00 37.87 3.01
4774 5571 8.296713 GCAAGAACAGACTGATTTGGTAATTAA 58.703 33.333 10.08 0.00 0.00 1.40
4797 5594 5.465532 TTGACAAATGCCAATAAGAGCAA 57.534 34.783 0.00 0.00 43.36 3.91
4819 5616 4.537135 AGAACAATGACGAGTGTGGTAT 57.463 40.909 0.00 0.00 28.82 2.73
5157 5960 2.283101 GCCAGGAATGTGCACCCA 60.283 61.111 15.69 0.00 0.00 4.51
5254 6057 4.814900 CCGTACAGGCAGCTAGTG 57.185 61.111 0.00 0.00 0.00 2.74
5273 6076 0.965866 CCCTCGACTGCTCTGGTACA 60.966 60.000 0.00 0.00 0.00 2.90
5274 6077 1.810532 CCCTCGACTGCTCTGGTAC 59.189 63.158 0.00 0.00 0.00 3.34
5275 6078 2.052690 GCCCTCGACTGCTCTGGTA 61.053 63.158 0.00 0.00 0.00 3.25
5276 6079 2.500815 TAGCCCTCGACTGCTCTGGT 62.501 60.000 7.18 0.00 39.00 4.00
5277 6080 1.112315 ATAGCCCTCGACTGCTCTGG 61.112 60.000 7.18 0.00 39.00 3.86
5278 6081 1.539388 CTATAGCCCTCGACTGCTCTG 59.461 57.143 7.18 0.00 39.00 3.35
5279 6082 1.546773 CCTATAGCCCTCGACTGCTCT 60.547 57.143 7.18 1.56 39.00 4.09
5280 6083 0.885196 CCTATAGCCCTCGACTGCTC 59.115 60.000 7.18 0.00 39.00 4.26
5281 6084 0.478942 TCCTATAGCCCTCGACTGCT 59.521 55.000 8.79 8.79 41.57 4.24
5282 6085 1.551452 ATCCTATAGCCCTCGACTGC 58.449 55.000 0.00 0.00 0.00 4.40
5283 6086 5.923733 AATAATCCTATAGCCCTCGACTG 57.076 43.478 0.00 0.00 0.00 3.51
5284 6087 6.017192 TCAAATAATCCTATAGCCCTCGACT 58.983 40.000 0.00 0.00 0.00 4.18
5285 6088 6.282199 TCAAATAATCCTATAGCCCTCGAC 57.718 41.667 0.00 0.00 0.00 4.20
5286 6089 6.928348 TTCAAATAATCCTATAGCCCTCGA 57.072 37.500 0.00 0.00 0.00 4.04
5287 6090 9.838339 AATATTCAAATAATCCTATAGCCCTCG 57.162 33.333 0.00 0.00 0.00 4.63
5326 6129 1.820519 GCATGCAAATGACTCTGGGAA 59.179 47.619 14.21 0.00 0.00 3.97
5330 6133 1.135199 GTGGGCATGCAAATGACTCTG 60.135 52.381 21.36 0.00 0.00 3.35
5331 6134 1.180029 GTGGGCATGCAAATGACTCT 58.820 50.000 21.36 0.00 0.00 3.24
5356 6159 4.895224 AAATGACATGATGCTGCTGTAG 57.105 40.909 0.00 0.00 0.00 2.74
5364 6167 7.901889 CGCTTATATCACTAAATGACATGATGC 59.098 37.037 0.00 0.00 41.24 3.91
5366 6169 7.603784 TGCGCTTATATCACTAAATGACATGAT 59.396 33.333 9.73 0.00 41.24 2.45
5369 6172 6.369890 CCTGCGCTTATATCACTAAATGACAT 59.630 38.462 9.73 0.00 41.24 3.06
5372 6175 4.690748 GCCTGCGCTTATATCACTAAATGA 59.309 41.667 9.73 0.00 43.13 2.57
5395 6211 3.007635 GTCGGTCCACCTAAAGAAATGG 58.992 50.000 0.00 0.00 0.00 3.16
5553 6372 2.363306 TGGTGCAGCCCCATTATAAG 57.637 50.000 14.36 0.00 36.04 1.73
5561 6380 2.116125 GGGATATGGTGCAGCCCC 59.884 66.667 14.36 12.75 36.04 5.80
5569 6388 2.631384 TCATCGAATGGGGGATATGGT 58.369 47.619 0.00 0.00 0.00 3.55
5628 6447 4.495422 GAAGAAAGCCAAGACTGACGATA 58.505 43.478 0.00 0.00 0.00 2.92
5667 6486 1.693062 TCAGTAAGTTGGCACCGGTAA 59.307 47.619 6.87 0.00 0.00 2.85
5672 6491 3.380320 AGTTGTTTCAGTAAGTTGGCACC 59.620 43.478 0.00 0.00 0.00 5.01
5748 6567 1.424638 AACTAGCTACCGCATCCCAT 58.575 50.000 0.00 0.00 39.10 4.00
5771 6590 2.892852 CCCTGGCAGAAACAAGATTTGA 59.107 45.455 17.94 0.00 0.00 2.69
5826 6645 5.529800 AGTTGTTTCAGTAAGCGGTAAACAT 59.470 36.000 12.00 0.00 39.15 2.71
5892 6712 4.665451 TGGAAGAAAGCCAAGATTCATGA 58.335 39.130 0.00 0.00 31.13 3.07
5903 6723 2.814336 CAGGTAACACTGGAAGAAAGCC 59.186 50.000 0.00 0.00 37.43 4.35
5904 6724 3.251004 CACAGGTAACACTGGAAGAAAGC 59.749 47.826 0.00 0.00 42.75 3.51
5905 6725 3.251004 GCACAGGTAACACTGGAAGAAAG 59.749 47.826 0.00 0.00 42.75 2.62
5908 6728 1.071699 GGCACAGGTAACACTGGAAGA 59.928 52.381 0.00 0.00 42.75 2.87
5909 6729 1.202758 TGGCACAGGTAACACTGGAAG 60.203 52.381 0.00 0.00 42.75 3.46
5910 6730 0.840617 TGGCACAGGTAACACTGGAA 59.159 50.000 0.00 0.00 42.75 3.53
5911 6731 0.840617 TTGGCACAGGTAACACTGGA 59.159 50.000 0.00 0.00 42.39 3.86
5912 6732 0.951558 GTTGGCACAGGTAACACTGG 59.048 55.000 0.00 0.00 42.39 4.00
5913 6733 1.603802 CTGTTGGCACAGGTAACACTG 59.396 52.381 8.60 0.00 46.10 3.66
5914 6734 1.967319 CTGTTGGCACAGGTAACACT 58.033 50.000 8.60 0.00 46.10 3.55
5934 6754 6.529125 GGACAAGAAATGAACAAGCATATGTG 59.471 38.462 4.29 0.00 32.81 3.21
5959 6781 5.295431 TCGGTTCAGTTGAATAAAGCATG 57.705 39.130 0.00 0.00 36.33 4.06
5992 6828 5.335897 CCTGAAATAACTAGCAGCAAAGCAA 60.336 40.000 0.00 0.00 36.85 3.91
6091 6958 0.625849 ATTTCCCCAGCTCCGTTGAT 59.374 50.000 0.00 0.00 0.00 2.57
6120 6987 0.590682 CGTACAACACAGCATGGCAA 59.409 50.000 0.00 0.00 43.62 4.52
6149 7021 4.451652 GCCAAAGCGAGCGCACTC 62.452 66.667 17.68 0.00 44.88 3.51
6150 7022 4.996434 AGCCAAAGCGAGCGCACT 62.996 61.111 17.68 0.00 46.67 4.40
6151 7023 4.451652 GAGCCAAAGCGAGCGCAC 62.452 66.667 17.68 0.96 46.67 5.34
6154 7026 3.494336 CTGGAGCCAAAGCGAGCG 61.494 66.667 0.00 0.00 46.67 5.03
6155 7027 3.808656 GCTGGAGCCAAAGCGAGC 61.809 66.667 0.00 0.00 46.67 5.03
6156 7028 0.391661 TAAGCTGGAGCCAAAGCGAG 60.392 55.000 0.00 0.00 46.67 5.03
6157 7029 0.673644 GTAAGCTGGAGCCAAAGCGA 60.674 55.000 0.00 0.00 46.67 4.93
6158 7030 0.674895 AGTAAGCTGGAGCCAAAGCG 60.675 55.000 0.00 0.00 46.67 4.68
6159 7031 0.807496 CAGTAAGCTGGAGCCAAAGC 59.193 55.000 0.00 0.00 43.38 3.51
6160 7032 2.079925 GACAGTAAGCTGGAGCCAAAG 58.920 52.381 0.00 0.00 46.62 2.77
6161 7033 1.699634 AGACAGTAAGCTGGAGCCAAA 59.300 47.619 0.00 0.00 46.62 3.28
6162 7034 1.002430 CAGACAGTAAGCTGGAGCCAA 59.998 52.381 0.00 0.00 46.62 4.52
6163 7035 0.610174 CAGACAGTAAGCTGGAGCCA 59.390 55.000 0.00 0.00 46.62 4.75
6164 7036 0.610687 ACAGACAGTAAGCTGGAGCC 59.389 55.000 0.00 0.00 46.62 4.70
6199 7075 3.047877 CGGCCTTCAACGGTCCAC 61.048 66.667 0.00 0.00 0.00 4.02
6278 7160 8.958119 TCATCTAACAACAAGACAACTAAACT 57.042 30.769 0.00 0.00 0.00 2.66
6279 7161 9.813080 GATCATCTAACAACAAGACAACTAAAC 57.187 33.333 0.00 0.00 0.00 2.01
6432 7314 3.135712 TGCAGTCAAAACTTGTAGGAGGA 59.864 43.478 0.00 0.00 31.71 3.71
6433 7315 3.476552 TGCAGTCAAAACTTGTAGGAGG 58.523 45.455 0.00 0.00 31.71 4.30
6434 7316 5.499139 TTTGCAGTCAAAACTTGTAGGAG 57.501 39.130 0.00 0.00 39.08 3.69
6496 7378 1.739562 CAGGAGGAGAGCAACACGC 60.740 63.158 0.00 0.00 42.91 5.34
6533 7415 4.257654 TCCGGTGCCCTTTTCGCA 62.258 61.111 0.00 0.00 0.00 5.10
6583 7480 7.411808 AGGTTAGATGAACAAGACTCCTACTA 58.588 38.462 0.00 0.00 40.09 1.82
6586 7483 5.657302 GGAGGTTAGATGAACAAGACTCCTA 59.343 44.000 0.00 0.00 38.64 2.94
6587 7484 4.468153 GGAGGTTAGATGAACAAGACTCCT 59.532 45.833 0.00 0.00 38.64 3.69
6588 7485 4.468153 AGGAGGTTAGATGAACAAGACTCC 59.532 45.833 0.00 0.00 40.46 3.85
6593 8974 4.574013 GCATCAGGAGGTTAGATGAACAAG 59.426 45.833 5.88 0.00 41.18 3.16
6599 8980 2.437281 AGGTGCATCAGGAGGTTAGATG 59.563 50.000 0.00 0.00 41.50 2.90
6600 8981 2.769209 AGGTGCATCAGGAGGTTAGAT 58.231 47.619 0.00 0.00 0.00 1.98
6601 8982 2.237143 CAAGGTGCATCAGGAGGTTAGA 59.763 50.000 0.00 0.00 0.00 2.10
6604 8985 0.610232 GCAAGGTGCATCAGGAGGTT 60.610 55.000 0.00 0.00 44.26 3.50
6605 8986 1.001641 GCAAGGTGCATCAGGAGGT 60.002 57.895 0.00 0.00 44.26 3.85
6623 9004 3.439540 CACCAATGGCCCGGTTCG 61.440 66.667 0.00 0.00 31.41 3.95
6627 9008 2.751436 CTCACACCAATGGCCCGG 60.751 66.667 0.00 0.00 0.00 5.73
6628 9009 1.746615 CTCTCACACCAATGGCCCG 60.747 63.158 0.00 0.00 0.00 6.13
6629 9010 1.379044 CCTCTCACACCAATGGCCC 60.379 63.158 0.00 0.00 0.00 5.80
6637 9033 1.277557 AGCTCATGAACCTCTCACACC 59.722 52.381 0.00 0.00 36.69 4.16
6688 9084 1.004440 GGTCTCCAGCACGCTTCTT 60.004 57.895 0.00 0.00 0.00 2.52
6788 9200 4.561326 GCTGGAACACACCAAGCAAATTAT 60.561 41.667 0.00 0.00 39.59 1.28
6842 9373 1.613925 GGACAGGGAGCAAGGAAAAAC 59.386 52.381 0.00 0.00 0.00 2.43
6928 9460 0.108472 TGCCTCGCATCAGTTCAGAG 60.108 55.000 0.00 0.00 31.71 3.35
6935 9467 1.063616 CAACATCTTGCCTCGCATCAG 59.936 52.381 0.00 0.00 38.76 2.90
6985 9517 4.820897 TCAGACAGTTGGTTGCTATACAG 58.179 43.478 0.00 0.00 0.00 2.74
6986 9518 4.882842 TCAGACAGTTGGTTGCTATACA 57.117 40.909 0.00 0.00 0.00 2.29
7002 9539 8.116753 CCAACACGATTCAGTAATAATTCAGAC 58.883 37.037 0.00 0.00 0.00 3.51
7003 9540 8.038351 TCCAACACGATTCAGTAATAATTCAGA 58.962 33.333 0.00 0.00 0.00 3.27
7051 9592 2.041620 TCCCTGTGAATTCCCAAGAAGG 59.958 50.000 2.27 1.24 34.86 3.46
7052 9593 3.439857 TCCCTGTGAATTCCCAAGAAG 57.560 47.619 2.27 0.00 34.86 2.85
7053 9594 4.202663 TGAATCCCTGTGAATTCCCAAGAA 60.203 41.667 2.27 0.00 36.15 2.52


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

AutoCloner maintained by Alex Coulton.