Multiple sequence alignment - TraesCS4D01G068100

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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 TraesCS4D01G068100 chr4D 100.000 3256 0 0 1 3256 43299207 43302462 0.000000e+00 6013.0
1 TraesCS4D01G068100 chr4D 100.000 2804 0 0 3628 6431 43302834 43305637 0.000000e+00 5179.0
2 TraesCS4D01G068100 chr4D 90.230 174 14 3 6260 6431 437153373 437153201 2.330000e-54 224.0
3 TraesCS4D01G068100 chr4B 93.537 2646 107 27 3630 6237 62970029 62972648 0.000000e+00 3880.0
4 TraesCS4D01G068100 chr4B 92.201 2513 108 25 795 3256 62967150 62969625 0.000000e+00 3474.0
5 TraesCS4D01G068100 chr4A 92.746 2688 124 32 595 3256 556756821 556754179 0.000000e+00 3818.0
6 TraesCS4D01G068100 chr4A 90.552 2519 124 41 3628 6115 556754138 556751703 0.000000e+00 3229.0
7 TraesCS4D01G068100 chr4A 95.292 531 20 5 38 566 556757464 556756937 0.000000e+00 837.0
8 TraesCS4D01G068100 chr4A 81.481 756 78 25 1003 1720 528540849 528541580 1.210000e-156 564.0
9 TraesCS4D01G068100 chr4A 96.053 76 2 1 6162 6237 556750516 556750442 8.760000e-24 122.0
10 TraesCS4D01G068100 chr7A 83.181 767 68 30 1003 1725 648928117 648928866 0.000000e+00 645.0
11 TraesCS4D01G068100 chr7A 86.885 183 17 5 6256 6431 507594137 507593955 1.410000e-46 198.0
12 TraesCS4D01G068100 chr5D 88.462 182 17 3 6254 6431 419267449 419267630 3.900000e-52 217.0
13 TraesCS4D01G068100 chr3D 87.958 191 13 7 6249 6431 430313122 430313310 3.900000e-52 217.0
14 TraesCS4D01G068100 chr3D 87.640 178 15 5 6256 6431 341890592 341890420 3.930000e-47 200.0
15 TraesCS4D01G068100 chr7D 84.574 188 17 5 6251 6431 254775 254957 6.630000e-40 176.0
16 TraesCS4D01G068100 chr7D 87.963 108 11 2 6250 6356 566993190 566993296 6.770000e-25 126.0
17 TraesCS4D01G068100 chr5B 84.746 177 17 6 6262 6429 88253854 88253679 1.110000e-37 169.0
18 TraesCS4D01G068100 chr5B 100.000 29 0 0 6235 6263 553464634 553464662 3.000000e-03 54.7
19 TraesCS4D01G068100 chr2B 78.431 204 33 8 6238 6431 163137265 163137063 8.760000e-24 122.0
20 TraesCS4D01G068100 chr2D 85.246 122 10 7 6239 6356 521417726 521417609 1.130000e-22 119.0
21 TraesCS4D01G068100 chr2A 80.000 105 14 4 6327 6431 623794173 623794270 3.220000e-08 71.3


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 TraesCS4D01G068100 chr4D 43299207 43305637 6430 False 5596.0 6013 100.00000 1 6431 2 chr4D.!!$F1 6430
1 TraesCS4D01G068100 chr4B 62967150 62972648 5498 False 3677.0 3880 92.86900 795 6237 2 chr4B.!!$F1 5442
2 TraesCS4D01G068100 chr4A 556750442 556757464 7022 True 2001.5 3818 93.66075 38 6237 4 chr4A.!!$R1 6199
3 TraesCS4D01G068100 chr4A 528540849 528541580 731 False 564.0 564 81.48100 1003 1720 1 chr4A.!!$F1 717
4 TraesCS4D01G068100 chr7A 648928117 648928866 749 False 645.0 645 83.18100 1003 1725 1 chr7A.!!$F1 722

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
849 941 0.120377 AGGGGTTGGTGAGGGTGATA 59.880 55.0 0.00 0.0 0.00 2.15 F
1675 1857 1.192428 GCCCTCGTTCCTTCCTTCTA 58.808 55.0 0.00 0.0 0.00 2.10 F
2509 2701 1.106285 GTGGACATCTTTCCCATGGC 58.894 55.0 6.09 0.0 34.33 4.40 F
3717 3942 0.036388 GGCTAGTTGCTGCTGGTGTA 60.036 55.0 0.00 0.0 42.39 2.90 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2140 2332 1.348064 CCTACTGTGGACTTGACCCA 58.652 55.000 0.00 0.00 0.00 4.51 R
2738 2930 1.358787 AGAACCATTGAGCCATGGGAA 59.641 47.619 15.13 0.00 42.10 3.97 R
4046 4289 0.035458 AGACCTGCTTAAGCGCAACT 59.965 50.000 21.97 15.16 45.83 3.16 R
5558 5815 1.009389 GGACTGGAGCAAACGAGACG 61.009 60.000 0.00 0.00 0.00 4.18 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 4.852388 GCCTTGCCCTCTCCTTTT 57.148 55.556 0.00 0.00 0.00 2.27
18 19 3.057749 GCCTTGCCCTCTCCTTTTT 57.942 52.632 0.00 0.00 0.00 1.94
39 40 4.953940 TTTTTCTGGCCTGCTGTTATTT 57.046 36.364 3.32 0.00 0.00 1.40
40 41 4.519540 TTTTCTGGCCTGCTGTTATTTC 57.480 40.909 3.32 0.00 0.00 2.17
41 42 2.877097 TCTGGCCTGCTGTTATTTCA 57.123 45.000 3.32 0.00 0.00 2.69
42 43 2.436417 TCTGGCCTGCTGTTATTTCAC 58.564 47.619 3.32 0.00 0.00 3.18
43 44 1.131126 CTGGCCTGCTGTTATTTCACG 59.869 52.381 3.32 0.00 0.00 4.35
44 45 0.179163 GGCCTGCTGTTATTTCACGC 60.179 55.000 0.00 0.00 0.00 5.34
45 46 0.804989 GCCTGCTGTTATTTCACGCT 59.195 50.000 0.00 0.00 0.00 5.07
46 47 1.466360 GCCTGCTGTTATTTCACGCTG 60.466 52.381 0.00 0.00 0.00 5.18
47 48 1.806542 CCTGCTGTTATTTCACGCTGT 59.193 47.619 0.00 0.00 0.00 4.40
48 49 2.226437 CCTGCTGTTATTTCACGCTGTT 59.774 45.455 0.00 0.00 0.00 3.16
49 50 3.435327 CCTGCTGTTATTTCACGCTGTTA 59.565 43.478 0.00 0.00 0.00 2.41
50 51 4.094887 CCTGCTGTTATTTCACGCTGTTAT 59.905 41.667 0.00 0.00 0.00 1.89
79 80 5.182190 TCTCGTGCTTTTTGTATGGCAATAA 59.818 36.000 0.00 0.00 36.89 1.40
87 88 9.150348 GCTTTTTGTATGGCAATAAAAGTATGT 57.850 29.630 18.89 0.00 37.30 2.29
127 128 6.697395 AGTATATAGGCGTGTGCATCATTTA 58.303 36.000 0.00 0.00 45.35 1.40
237 239 5.066893 CCATTTGTTAGGTGATGGATGACAG 59.933 44.000 0.00 0.00 41.20 3.51
257 259 4.009675 CAGTGCTGGTGCTATTTCCTTTA 58.990 43.478 0.00 0.00 40.48 1.85
275 277 2.851263 TACGATTTGGTGTCCTGCTT 57.149 45.000 0.00 0.00 0.00 3.91
327 329 3.650950 TGCAACCTCTGGGCCTCC 61.651 66.667 4.53 0.00 35.63 4.30
328 330 3.650950 GCAACCTCTGGGCCTCCA 61.651 66.667 4.53 0.00 41.58 3.86
355 358 6.701400 GCACAAGATTTGTTTGGTTCAATACT 59.299 34.615 0.00 0.00 43.23 2.12
356 359 7.224557 GCACAAGATTTGTTTGGTTCAATACTT 59.775 33.333 0.00 0.00 43.23 2.24
446 449 5.100259 GCTAACACACTCGCATAAACTAGA 58.900 41.667 0.00 0.00 0.00 2.43
476 479 2.515901 GGGATGCCCGGCTTATGT 59.484 61.111 11.61 0.00 32.13 2.29
492 495 2.604046 ATGTGATCAACGTCCCTAGC 57.396 50.000 0.00 0.00 0.00 3.42
548 551 5.021033 ACATGTTTTCTGTTTGCATGGAA 57.979 34.783 0.00 0.00 40.63 3.53
555 558 6.899393 TTTCTGTTTGCATGGAATAGTTCT 57.101 33.333 0.00 0.00 0.00 3.01
566 569 8.843262 TGCATGGAATAGTTCTCTTCAATTATG 58.157 33.333 0.00 0.00 0.00 1.90
576 579 9.082313 AGTTCTCTTCAATTATGAAAACATGGT 57.918 29.630 0.00 0.00 44.64 3.55
625 715 2.656947 AGTGCAGGCTAAGTTCCAAA 57.343 45.000 0.00 0.00 0.00 3.28
635 725 5.250774 AGGCTAAGTTCCAAAGATAACCAGA 59.749 40.000 0.00 0.00 0.00 3.86
652 742 8.801715 ATAACCAGATAAATTAATTGCTTGCG 57.198 30.769 0.39 0.00 0.00 4.85
655 745 7.319646 ACCAGATAAATTAATTGCTTGCGAAA 58.680 30.769 0.39 0.00 0.00 3.46
804 895 4.662278 TGAAACCGAGGGAAAATGAAGAT 58.338 39.130 0.00 0.00 0.00 2.40
807 898 6.889722 TGAAACCGAGGGAAAATGAAGATAAT 59.110 34.615 0.00 0.00 0.00 1.28
814 905 8.352942 CGAGGGAAAATGAAGATAATAAAAGGG 58.647 37.037 0.00 0.00 0.00 3.95
849 941 0.120377 AGGGGTTGGTGAGGGTGATA 59.880 55.000 0.00 0.00 0.00 2.15
1112 1222 3.798511 CCGCTCTCCCCCTTTCCC 61.799 72.222 0.00 0.00 0.00 3.97
1120 1230 1.283321 CTCCCCCTTTCCCTCTTCTTG 59.717 57.143 0.00 0.00 0.00 3.02
1188 1299 1.464189 GCTCTTCCGAAACAATCACGC 60.464 52.381 0.00 0.00 0.00 5.34
1312 1452 4.231439 GTCCGTTTGTCTGTTTGTTTGTT 58.769 39.130 0.00 0.00 0.00 2.83
1313 1453 4.682401 GTCCGTTTGTCTGTTTGTTTGTTT 59.318 37.500 0.00 0.00 0.00 2.83
1314 1454 4.681942 TCCGTTTGTCTGTTTGTTTGTTTG 59.318 37.500 0.00 0.00 0.00 2.93
1315 1455 4.446051 CCGTTTGTCTGTTTGTTTGTTTGT 59.554 37.500 0.00 0.00 0.00 2.83
1471 1651 3.374988 CACCATGATTCGCTGTATTGTGT 59.625 43.478 0.00 0.00 0.00 3.72
1472 1652 3.623060 ACCATGATTCGCTGTATTGTGTC 59.377 43.478 0.00 0.00 0.00 3.67
1473 1653 3.873361 CCATGATTCGCTGTATTGTGTCT 59.127 43.478 0.00 0.00 0.00 3.41
1675 1857 1.192428 GCCCTCGTTCCTTCCTTCTA 58.808 55.000 0.00 0.00 0.00 2.10
1732 1916 2.163810 AATGGATGTGGGGGTCAATG 57.836 50.000 0.00 0.00 0.00 2.82
1745 1931 2.440409 GGTCAATGATGTGAACTGGCT 58.560 47.619 0.00 0.00 32.14 4.75
1863 2049 3.954258 GTGGGGAGGTAAAATCTTGATGG 59.046 47.826 0.00 0.00 0.00 3.51
1905 2091 4.401519 CCTTATTAGGTTCTCTCGTGTCCA 59.598 45.833 0.00 0.00 36.74 4.02
1928 2114 7.889073 TCCAGTAGAACTAACTAATGACTCTGT 59.111 37.037 0.00 0.00 39.71 3.41
2084 2276 1.412079 ATGCTCCACAGTTGGCAAAA 58.588 45.000 0.00 0.00 43.56 2.44
2130 2322 8.529476 GGGTAATCTTCTAAAGTAGTCAAGTCA 58.471 37.037 0.00 0.00 0.00 3.41
2166 2358 5.471257 GTCAAGTCCACAGTAGGTTCTTAG 58.529 45.833 0.00 0.00 0.00 2.18
2168 2360 5.243283 TCAAGTCCACAGTAGGTTCTTAGTC 59.757 44.000 0.00 0.00 0.00 2.59
2172 2364 3.258372 CCACAGTAGGTTCTTAGTCTGCA 59.742 47.826 0.00 0.00 0.00 4.41
2183 2375 8.734386 AGGTTCTTAGTCTGCATAAGAAATTTG 58.266 33.333 18.14 0.00 45.81 2.32
2212 2404 4.272504 GCATATGTGCGTACACCATTTACT 59.727 41.667 8.99 0.00 46.86 2.24
2213 2405 5.737353 CATATGTGCGTACACCATTTACTG 58.263 41.667 8.99 0.00 46.86 2.74
2220 2412 4.612033 GCGTACACCATTTACTGACCAAAC 60.612 45.833 0.00 0.00 0.00 2.93
2224 2416 7.201496 CGTACACCATTTACTGACCAAACTATC 60.201 40.741 0.00 0.00 0.00 2.08
2272 2464 3.430929 GGTACACAGCTGGGATTAGACAG 60.431 52.174 26.06 0.00 37.76 3.51
2359 2551 3.784573 CACCAAATTGGGGGCGAA 58.215 55.556 17.27 0.00 43.37 4.70
2509 2701 1.106285 GTGGACATCTTTCCCATGGC 58.894 55.000 6.09 0.00 34.33 4.40
2635 2827 7.618502 TCTGTGTAGTTTGCTGTTTCTTTTA 57.381 32.000 0.00 0.00 0.00 1.52
2918 3110 3.593328 TCATGGAAGTTTTGGGATCTCCT 59.407 43.478 0.00 0.00 36.20 3.69
2971 3163 3.059188 CGTGAAGTGGAAAAAGTGCGTAT 60.059 43.478 0.00 0.00 0.00 3.06
3120 3313 6.798482 TCATATGTTGCTAAGCTTCATTTGG 58.202 36.000 0.00 0.00 30.60 3.28
3717 3942 0.036388 GGCTAGTTGCTGCTGGTGTA 60.036 55.000 0.00 0.00 42.39 2.90
3947 4190 6.264067 AGAATGCAAAGGCCTAACAATCTATC 59.736 38.462 5.16 0.00 40.13 2.08
4005 4248 1.073897 GCTGCTGTCTTCCCAGGTT 59.926 57.895 0.00 0.00 32.92 3.50
4046 4289 2.371841 CCATACTATTACTGGCCTGGCA 59.628 50.000 22.05 3.71 0.00 4.92
4091 4334 6.317391 GCAGCACTTCTGTTCCTTAATATTCT 59.683 38.462 0.00 0.00 44.66 2.40
4092 4335 7.495934 GCAGCACTTCTGTTCCTTAATATTCTA 59.504 37.037 0.00 0.00 44.66 2.10
4129 4372 9.478768 TGTATTTTATACAGTTTGTCGTTCTGA 57.521 29.630 0.00 0.00 33.93 3.27
4144 4387 5.006746 GTCGTTCTGATTAACTAATGCCCTG 59.993 44.000 0.00 0.00 0.00 4.45
4159 4402 2.295909 TGCCCTGATGTGCTGTTTAAAC 59.704 45.455 11.54 11.54 0.00 2.01
4209 4452 5.526846 AGCTTATCAAGAGCAAGTTATGAGC 59.473 40.000 0.00 0.00 42.56 4.26
4436 4679 8.250332 AGAACTTACTTCAAATTGCTTTGTTGA 58.750 29.630 0.00 0.00 42.02 3.18
4545 4797 7.894376 TGTACTTTACTTTTAAGGATGTCCG 57.106 36.000 0.00 0.00 42.08 4.79
4597 4849 5.246307 AGCTTAACTTCAAAAGGCTACGAT 58.754 37.500 0.00 0.00 0.00 3.73
4603 4855 7.448748 AACTTCAAAAGGCTACGATATTGTT 57.551 32.000 0.00 0.00 0.00 2.83
4656 4908 5.358725 TGGTGAACCTCAAGAAAAAGGTAAC 59.641 40.000 0.37 0.00 45.21 2.50
4666 4918 9.110502 CTCAAGAAAAAGGTAACAGAGTACTTT 57.889 33.333 0.00 0.00 41.41 2.66
4829 5082 9.710900 GGACACTTATCATTCCTTTCAAATTTT 57.289 29.630 0.00 0.00 0.00 1.82
5239 5495 6.623979 TTTGTATGCCCTTACCTACTACAA 57.376 37.500 0.00 0.00 0.00 2.41
5439 5695 6.701841 TGAAGTACAAGAACTAAGAACTGCTG 59.298 38.462 0.00 0.00 0.00 4.41
5471 5727 2.154462 CAAAGGTGTGCTCCGAGAAAT 58.846 47.619 0.00 0.00 0.00 2.17
5479 5735 6.828785 AGGTGTGCTCCGAGAAATAAATTATT 59.171 34.615 0.00 0.00 0.00 1.40
5507 5763 7.331026 TCATCCAGTCCTTAAGAAACACATAG 58.669 38.462 3.36 0.00 0.00 2.23
5509 5765 5.783360 TCCAGTCCTTAAGAAACACATAGGA 59.217 40.000 3.36 0.00 0.00 2.94
5510 5766 6.070767 TCCAGTCCTTAAGAAACACATAGGAG 60.071 42.308 3.36 0.00 0.00 3.69
5511 5767 6.295916 CCAGTCCTTAAGAAACACATAGGAGT 60.296 42.308 3.36 0.00 0.00 3.85
5512 5768 7.093465 CCAGTCCTTAAGAAACACATAGGAGTA 60.093 40.741 3.36 0.00 0.00 2.59
5513 5769 7.760340 CAGTCCTTAAGAAACACATAGGAGTAC 59.240 40.741 3.36 0.00 0.00 2.73
5514 5770 7.453752 AGTCCTTAAGAAACACATAGGAGTACA 59.546 37.037 3.36 0.00 0.00 2.90
5590 5847 0.537371 CCAGTCCTGGGTTGTTCACC 60.537 60.000 5.37 0.00 46.81 4.02
5604 5861 5.449304 GTTGTTCACCGTTTTAGATCTTGG 58.551 41.667 0.00 0.00 0.00 3.61
5623 5880 2.012673 GGACCAAGCTTACATCTGCAG 58.987 52.381 7.63 7.63 0.00 4.41
5627 5884 3.261897 ACCAAGCTTACATCTGCAGTAGT 59.738 43.478 14.67 15.38 0.00 2.73
5628 5885 4.256920 CCAAGCTTACATCTGCAGTAGTT 58.743 43.478 14.67 0.00 0.00 2.24
5702 5959 1.790481 GCTGCTTTTCGCGTAATCACC 60.790 52.381 5.77 0.00 43.27 4.02
5903 6164 5.809562 GCTTCGCTGATATGCTATATGAACT 59.190 40.000 0.00 0.00 0.00 3.01
5942 6203 9.991388 GGATAAACATTTACTTACACGCATTTA 57.009 29.630 0.00 0.00 0.00 1.40
6016 6278 1.132453 TCGTGAGCTCATGTAGGAACG 59.868 52.381 30.22 20.88 34.59 3.95
6066 6332 1.519751 CCCAACCACGATTCGGCAAA 61.520 55.000 11.29 0.00 0.00 3.68
6067 6333 0.312416 CCAACCACGATTCGGCAAAA 59.688 50.000 11.29 0.00 0.00 2.44
6068 6334 1.067915 CCAACCACGATTCGGCAAAAT 60.068 47.619 11.29 0.00 0.00 1.82
6076 6342 2.369394 GATTCGGCAAAATCTGTCCCT 58.631 47.619 3.69 0.00 33.67 4.20
6080 6346 3.820595 GCAAAATCTGTCCCTTGCC 57.179 52.632 0.00 0.00 38.56 4.52
6115 6381 1.951510 CAGGCAGTGTTCAATGCGT 59.048 52.632 16.70 14.96 43.49 5.24
6116 6382 1.155889 CAGGCAGTGTTCAATGCGTA 58.844 50.000 17.25 0.00 43.49 4.42
6118 6384 1.001974 AGGCAGTGTTCAATGCGTAGA 59.998 47.619 16.43 0.00 43.49 2.59
6119 6385 1.804151 GGCAGTGTTCAATGCGTAGAA 59.196 47.619 16.70 0.00 43.49 2.10
6120 6386 2.420022 GGCAGTGTTCAATGCGTAGAAT 59.580 45.455 16.70 0.00 43.49 2.40
6121 6387 3.419915 GCAGTGTTCAATGCGTAGAATG 58.580 45.455 9.31 0.00 31.87 2.67
6123 6389 4.641954 CAGTGTTCAATGCGTAGAATGTC 58.358 43.478 0.00 0.00 0.00 3.06
6124 6390 3.367932 AGTGTTCAATGCGTAGAATGTCG 59.632 43.478 0.00 0.00 0.00 4.35
6168 7591 4.109675 CCTGGGTGGGTAAGGGCG 62.110 72.222 0.00 0.00 0.00 6.13
6172 7595 2.676265 GGGTGGGTAAGGGCGACAT 61.676 63.158 0.00 0.00 0.00 3.06
6237 7660 3.331889 ACCAAATGTCTGGACCTTCATCT 59.668 43.478 0.00 0.00 38.96 2.90
6238 7661 4.536090 ACCAAATGTCTGGACCTTCATCTA 59.464 41.667 0.00 0.00 38.96 1.98
6239 7662 5.192522 ACCAAATGTCTGGACCTTCATCTAT 59.807 40.000 0.00 0.00 38.96 1.98
6240 7663 6.386927 ACCAAATGTCTGGACCTTCATCTATA 59.613 38.462 0.00 0.00 38.96 1.31
6241 7664 7.072961 ACCAAATGTCTGGACCTTCATCTATAT 59.927 37.037 0.00 0.00 38.96 0.86
6242 7665 7.605691 CCAAATGTCTGGACCTTCATCTATATC 59.394 40.741 0.00 0.00 38.96 1.63
6243 7666 8.373981 CAAATGTCTGGACCTTCATCTATATCT 58.626 37.037 0.00 0.00 0.00 1.98
6244 7667 9.607333 AAATGTCTGGACCTTCATCTATATCTA 57.393 33.333 0.00 0.00 0.00 1.98
6245 7668 9.781425 AATGTCTGGACCTTCATCTATATCTAT 57.219 33.333 0.00 0.00 0.00 1.98
6283 7706 6.839820 ATACCTACTAATAAAGCAACGTGC 57.160 37.500 0.00 0.00 45.46 5.34
6292 7715 4.987419 GCAACGTGCGTTTCTTCA 57.013 50.000 7.27 0.00 36.00 3.02
6293 7716 3.228085 GCAACGTGCGTTTCTTCAA 57.772 47.368 7.27 0.00 36.00 2.69
6294 7717 1.753956 GCAACGTGCGTTTCTTCAAT 58.246 45.000 7.27 0.00 36.00 2.57
6295 7718 2.116366 GCAACGTGCGTTTCTTCAATT 58.884 42.857 7.27 0.00 36.00 2.32
6296 7719 2.533942 GCAACGTGCGTTTCTTCAATTT 59.466 40.909 7.27 0.00 36.00 1.82
6297 7720 3.000177 GCAACGTGCGTTTCTTCAATTTT 60.000 39.130 7.27 0.00 36.00 1.82
6298 7721 4.491763 GCAACGTGCGTTTCTTCAATTTTT 60.492 37.500 7.27 0.00 36.00 1.94
6315 7738 2.835580 TTTTATCCGTTCACCACCGA 57.164 45.000 0.00 0.00 0.00 4.69
6316 7739 2.835580 TTTATCCGTTCACCACCGAA 57.164 45.000 0.00 0.00 0.00 4.30
6317 7740 2.835580 TTATCCGTTCACCACCGAAA 57.164 45.000 0.00 0.00 0.00 3.46
6318 7741 2.835580 TATCCGTTCACCACCGAAAA 57.164 45.000 0.00 0.00 0.00 2.29
6319 7742 2.194201 ATCCGTTCACCACCGAAAAT 57.806 45.000 0.00 0.00 0.00 1.82
6320 7743 2.835580 TCCGTTCACCACCGAAAATA 57.164 45.000 0.00 0.00 0.00 1.40
6321 7744 3.337694 TCCGTTCACCACCGAAAATAT 57.662 42.857 0.00 0.00 0.00 1.28
6322 7745 3.677190 TCCGTTCACCACCGAAAATATT 58.323 40.909 0.00 0.00 0.00 1.28
6323 7746 4.073549 TCCGTTCACCACCGAAAATATTT 58.926 39.130 0.00 0.00 0.00 1.40
6324 7747 4.519730 TCCGTTCACCACCGAAAATATTTT 59.480 37.500 13.24 13.24 0.00 1.82
6325 7748 5.009811 TCCGTTCACCACCGAAAATATTTTT 59.990 36.000 14.45 0.00 0.00 1.94
6354 7777 7.712204 ATCCGAGGTGGTATTAAAATTTTGT 57.288 32.000 13.76 4.96 39.52 2.83
6355 7778 6.915349 TCCGAGGTGGTATTAAAATTTTGTG 58.085 36.000 13.76 0.00 39.52 3.33
6356 7779 6.715718 TCCGAGGTGGTATTAAAATTTTGTGA 59.284 34.615 13.76 0.24 39.52 3.58
6357 7780 7.394923 TCCGAGGTGGTATTAAAATTTTGTGAT 59.605 33.333 13.76 7.42 39.52 3.06
6358 7781 7.700656 CCGAGGTGGTATTAAAATTTTGTGATC 59.299 37.037 13.76 0.00 0.00 2.92
6359 7782 7.700656 CGAGGTGGTATTAAAATTTTGTGATCC 59.299 37.037 13.76 9.56 0.00 3.36
6360 7783 8.429237 AGGTGGTATTAAAATTTTGTGATCCA 57.571 30.769 13.76 11.69 0.00 3.41
6361 7784 9.045745 AGGTGGTATTAAAATTTTGTGATCCAT 57.954 29.630 13.76 0.59 0.00 3.41
6362 7785 9.313118 GGTGGTATTAAAATTTTGTGATCCATC 57.687 33.333 13.76 11.18 0.00 3.51
6365 7788 9.034544 GGTATTAAAATTTTGTGATCCATCTGC 57.965 33.333 13.76 0.00 0.00 4.26
6366 7789 9.807649 GTATTAAAATTTTGTGATCCATCTGCT 57.192 29.630 13.76 0.00 0.00 4.24
6369 7792 7.707624 AAAATTTTGTGATCCATCTGCTAGA 57.292 32.000 1.75 0.00 0.00 2.43
6370 7793 7.707624 AAATTTTGTGATCCATCTGCTAGAA 57.292 32.000 0.00 0.00 0.00 2.10
6371 7794 7.707624 AATTTTGTGATCCATCTGCTAGAAA 57.292 32.000 0.00 0.00 0.00 2.52
6372 7795 7.707624 ATTTTGTGATCCATCTGCTAGAAAA 57.292 32.000 0.00 0.00 0.00 2.29
6373 7796 7.523293 TTTTGTGATCCATCTGCTAGAAAAA 57.477 32.000 0.00 0.00 0.00 1.94
6394 7817 5.372343 AAAAAGGAGTTTTGCCCAGAATT 57.628 34.783 0.00 0.00 38.04 2.17
6395 7818 5.372343 AAAAGGAGTTTTGCCCAGAATTT 57.628 34.783 0.00 0.00 34.44 1.82
6396 7819 4.607293 AAGGAGTTTTGCCCAGAATTTC 57.393 40.909 0.00 0.00 0.00 2.17
6397 7820 2.558359 AGGAGTTTTGCCCAGAATTTCG 59.442 45.455 0.00 0.00 0.00 3.46
6398 7821 2.296190 GGAGTTTTGCCCAGAATTTCGT 59.704 45.455 0.00 0.00 0.00 3.85
6399 7822 3.504520 GGAGTTTTGCCCAGAATTTCGTA 59.495 43.478 0.00 0.00 0.00 3.43
6400 7823 4.473199 GAGTTTTGCCCAGAATTTCGTAC 58.527 43.478 0.00 0.00 0.00 3.67
6401 7824 3.058501 AGTTTTGCCCAGAATTTCGTACG 60.059 43.478 9.53 9.53 0.00 3.67
6402 7825 2.172851 TTGCCCAGAATTTCGTACGT 57.827 45.000 16.05 0.00 0.00 3.57
6403 7826 1.434555 TGCCCAGAATTTCGTACGTG 58.565 50.000 16.05 4.70 0.00 4.49
6404 7827 0.725117 GCCCAGAATTTCGTACGTGG 59.275 55.000 16.05 13.80 0.00 4.94
6405 7828 1.365699 CCCAGAATTTCGTACGTGGG 58.634 55.000 20.84 20.84 38.85 4.61
6406 7829 0.725117 CCAGAATTTCGTACGTGGGC 59.275 55.000 16.05 2.70 0.00 5.36
6407 7830 0.725117 CAGAATTTCGTACGTGGGCC 59.275 55.000 16.05 0.00 0.00 5.80
6408 7831 0.738412 AGAATTTCGTACGTGGGCCG 60.738 55.000 16.05 0.00 44.03 6.13
6409 7832 2.300597 GAATTTCGTACGTGGGCCGC 62.301 60.000 16.05 7.12 41.42 6.53
6410 7833 3.592856 ATTTCGTACGTGGGCCGCA 62.593 57.895 18.64 0.00 41.42 5.69
6426 7849 4.077184 CACGCGGTAAGGCCCAGA 62.077 66.667 12.47 0.00 0.00 3.86
6427 7850 3.315949 ACGCGGTAAGGCCCAGAA 61.316 61.111 12.47 0.00 0.00 3.02
6428 7851 2.046700 CGCGGTAAGGCCCAGAAA 60.047 61.111 0.00 0.00 0.00 2.52
6429 7852 1.673009 CGCGGTAAGGCCCAGAAAA 60.673 57.895 0.00 0.00 0.00 2.29
6430 7853 1.644786 CGCGGTAAGGCCCAGAAAAG 61.645 60.000 0.00 0.00 0.00 2.27
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.057749 AAAAAGGAGAGGGCAAGGC 57.942 52.632 0.00 0.00 0.00 4.35
18 19 4.343526 TGAAATAACAGCAGGCCAGAAAAA 59.656 37.500 5.01 0.00 0.00 1.94
19 20 3.894427 TGAAATAACAGCAGGCCAGAAAA 59.106 39.130 5.01 0.00 0.00 2.29
20 21 3.255642 GTGAAATAACAGCAGGCCAGAAA 59.744 43.478 5.01 0.00 0.00 2.52
21 22 2.819608 GTGAAATAACAGCAGGCCAGAA 59.180 45.455 5.01 0.00 0.00 3.02
22 23 2.436417 GTGAAATAACAGCAGGCCAGA 58.564 47.619 5.01 0.00 0.00 3.86
23 24 1.131126 CGTGAAATAACAGCAGGCCAG 59.869 52.381 5.01 0.00 0.00 4.85
24 25 1.164411 CGTGAAATAACAGCAGGCCA 58.836 50.000 5.01 0.00 0.00 5.36
25 26 0.179163 GCGTGAAATAACAGCAGGCC 60.179 55.000 0.00 0.00 37.43 5.19
26 27 0.804989 AGCGTGAAATAACAGCAGGC 59.195 50.000 0.00 0.00 42.02 4.85
27 28 1.806542 ACAGCGTGAAATAACAGCAGG 59.193 47.619 0.00 0.00 0.00 4.85
28 29 3.542712 AACAGCGTGAAATAACAGCAG 57.457 42.857 0.00 0.00 0.00 4.24
29 30 5.621197 AATAACAGCGTGAAATAACAGCA 57.379 34.783 0.00 0.00 0.00 4.41
30 31 6.927933 AAAATAACAGCGTGAAATAACAGC 57.072 33.333 0.00 0.00 0.00 4.40
79 80 8.639761 ACTAGATATTTACCGAGCACATACTTT 58.360 33.333 0.00 0.00 0.00 2.66
87 88 9.064706 GCCTATATACTAGATATTTACCGAGCA 57.935 37.037 0.00 0.00 0.00 4.26
203 205 3.886505 ACCTAACAAATGGAAAGCGACAA 59.113 39.130 0.00 0.00 0.00 3.18
237 239 3.181510 CGTAAAGGAAATAGCACCAGCAC 60.182 47.826 0.00 0.00 45.49 4.40
257 259 1.880027 GAAAGCAGGACACCAAATCGT 59.120 47.619 0.00 0.00 0.00 3.73
275 277 6.371548 GTGATGTGGTTAACTGCTAATCAGAA 59.628 38.462 5.42 0.00 45.72 3.02
291 293 6.350110 GGTTGCACATATAAAAGTGATGTGGT 60.350 38.462 14.21 0.00 46.85 4.16
327 329 3.457610 ACCAAACAAATCTTGTGCCTG 57.542 42.857 0.00 0.00 44.59 4.85
328 330 3.450457 TGAACCAAACAAATCTTGTGCCT 59.550 39.130 0.00 0.00 44.59 4.75
356 359 4.123506 GCAAAATTCTTCACCGGGAAAAA 58.876 39.130 6.32 0.00 34.44 1.94
362 365 1.669795 GCAGGCAAAATTCTTCACCGG 60.670 52.381 0.00 0.00 0.00 5.28
364 367 2.036346 ACAGCAGGCAAAATTCTTCACC 59.964 45.455 0.00 0.00 0.00 4.02
374 377 1.381056 ACCAACCACAGCAGGCAAA 60.381 52.632 0.00 0.00 0.00 3.68
446 449 3.365472 GGGCATCCCTACAATTTTCACT 58.635 45.455 0.00 0.00 41.34 3.41
451 454 0.755327 GCCGGGCATCCCTACAATTT 60.755 55.000 15.62 0.00 42.67 1.82
476 479 1.672854 CGGGCTAGGGACGTTGATCA 61.673 60.000 0.00 0.00 0.00 2.92
492 495 3.680642 CATTCAGATGCTGTTAACGGG 57.319 47.619 16.13 5.39 32.61 5.28
569 572 9.762381 TCCCTTTTTGTTAGATTATACCATGTT 57.238 29.630 0.00 0.00 0.00 2.71
570 573 9.408648 CTCCCTTTTTGTTAGATTATACCATGT 57.591 33.333 0.00 0.00 0.00 3.21
571 574 8.352942 GCTCCCTTTTTGTTAGATTATACCATG 58.647 37.037 0.00 0.00 0.00 3.66
572 575 8.058847 TGCTCCCTTTTTGTTAGATTATACCAT 58.941 33.333 0.00 0.00 0.00 3.55
574 577 7.875327 TGCTCCCTTTTTGTTAGATTATACC 57.125 36.000 0.00 0.00 0.00 2.73
575 578 9.343539 AGATGCTCCCTTTTTGTTAGATTATAC 57.656 33.333 0.00 0.00 0.00 1.47
576 579 9.920946 AAGATGCTCCCTTTTTGTTAGATTATA 57.079 29.630 0.00 0.00 0.00 0.98
577 580 8.689972 CAAGATGCTCCCTTTTTGTTAGATTAT 58.310 33.333 0.00 0.00 0.00 1.28
578 581 7.362920 GCAAGATGCTCCCTTTTTGTTAGATTA 60.363 37.037 0.00 0.00 40.96 1.75
579 582 6.573094 GCAAGATGCTCCCTTTTTGTTAGATT 60.573 38.462 0.00 0.00 40.96 2.40
580 583 5.105595 GCAAGATGCTCCCTTTTTGTTAGAT 60.106 40.000 0.00 0.00 40.96 1.98
582 585 4.488879 GCAAGATGCTCCCTTTTTGTTAG 58.511 43.478 0.00 0.00 40.96 2.34
583 586 4.519540 GCAAGATGCTCCCTTTTTGTTA 57.480 40.909 0.00 0.00 40.96 2.41
584 587 3.391506 GCAAGATGCTCCCTTTTTGTT 57.608 42.857 0.00 0.00 40.96 2.83
625 715 9.971922 GCAAGCAATTAATTTATCTGGTTATCT 57.028 29.630 0.00 0.00 0.00 1.98
655 745 4.279982 TGGTTACCTCGTTTTCCCTTTTT 58.720 39.130 2.07 0.00 0.00 1.94
660 750 2.845363 TCTGGTTACCTCGTTTTCCC 57.155 50.000 2.07 0.00 0.00 3.97
718 809 7.433537 TTTGGGGTGGTTAGTTTATGAAAAA 57.566 32.000 0.00 0.00 0.00 1.94
719 810 7.433537 TTTTGGGGTGGTTAGTTTATGAAAA 57.566 32.000 0.00 0.00 0.00 2.29
720 811 7.433537 TTTTTGGGGTGGTTAGTTTATGAAA 57.566 32.000 0.00 0.00 0.00 2.69
758 849 8.927411 TCAGAAAAGAGAAAAATGGGAGATTTT 58.073 29.630 0.00 0.00 33.12 1.82
804 895 8.820831 TCAATCCAAGCATTTTCCCTTTTATTA 58.179 29.630 0.00 0.00 0.00 0.98
807 898 6.295802 CCTCAATCCAAGCATTTTCCCTTTTA 60.296 38.462 0.00 0.00 0.00 1.52
814 905 2.833943 ACCCCTCAATCCAAGCATTTTC 59.166 45.455 0.00 0.00 0.00 2.29
817 908 2.181975 CAACCCCTCAATCCAAGCATT 58.818 47.619 0.00 0.00 0.00 3.56
818 909 1.620524 CCAACCCCTCAATCCAAGCAT 60.621 52.381 0.00 0.00 0.00 3.79
819 910 0.251742 CCAACCCCTCAATCCAAGCA 60.252 55.000 0.00 0.00 0.00 3.91
820 911 0.251787 ACCAACCCCTCAATCCAAGC 60.252 55.000 0.00 0.00 0.00 4.01
821 912 1.075374 TCACCAACCCCTCAATCCAAG 59.925 52.381 0.00 0.00 0.00 3.61
849 941 0.176680 GATCAGCATCCACCAGACGT 59.823 55.000 0.00 0.00 0.00 4.34
1112 1222 6.308766 CCGCCAAAAATGATTTACAAGAAGAG 59.691 38.462 0.00 0.00 0.00 2.85
1120 1230 1.923864 CCGCCGCCAAAAATGATTTAC 59.076 47.619 0.00 0.00 0.00 2.01
1188 1299 8.500773 CAAATCAAACAAGGAAAAATGGATGAG 58.499 33.333 0.00 0.00 0.00 2.90
1312 1452 1.103803 TAAGCACGGGCAACAAACAA 58.896 45.000 14.57 0.00 44.61 2.83
1313 1453 1.268352 GATAAGCACGGGCAACAAACA 59.732 47.619 14.57 0.00 44.61 2.83
1314 1454 1.539827 AGATAAGCACGGGCAACAAAC 59.460 47.619 14.57 0.00 44.61 2.93
1315 1455 1.904287 AGATAAGCACGGGCAACAAA 58.096 45.000 14.57 0.00 44.61 2.83
1472 1652 0.322008 GTCCTGGAGAAAGCACCCAG 60.322 60.000 0.00 0.00 45.28 4.45
1473 1653 1.059584 TGTCCTGGAGAAAGCACCCA 61.060 55.000 0.00 0.00 0.00 4.51
1732 1916 1.512926 AACGACAGCCAGTTCACATC 58.487 50.000 0.00 0.00 0.00 3.06
1745 1931 1.919918 CAAGCAAAGCCAAAACGACA 58.080 45.000 0.00 0.00 0.00 4.35
1888 2074 2.581216 ACTGGACACGAGAGAACCTA 57.419 50.000 0.00 0.00 0.00 3.08
1988 2179 3.076621 TGCATCACCAAAAGCAGTAGAG 58.923 45.455 0.00 0.00 32.48 2.43
2084 2276 9.951866 ATTACCCTATTTCCCATCAAGTAAAAT 57.048 29.630 0.00 0.00 0.00 1.82
2125 2317 7.393515 GGACTTGACCCATTAACTTTATGACTT 59.606 37.037 0.00 0.00 0.00 3.01
2130 2322 6.548321 TGTGGACTTGACCCATTAACTTTAT 58.452 36.000 0.00 0.00 35.91 1.40
2137 2329 3.517901 CCTACTGTGGACTTGACCCATTA 59.482 47.826 0.00 0.00 35.91 1.90
2140 2332 1.348064 CCTACTGTGGACTTGACCCA 58.652 55.000 0.00 0.00 0.00 4.51
2166 2358 5.119125 GCCAACACAAATTTCTTATGCAGAC 59.881 40.000 0.00 0.00 0.00 3.51
2168 2360 4.989797 TGCCAACACAAATTTCTTATGCAG 59.010 37.500 0.00 0.00 0.00 4.41
2172 2364 7.278424 GCACATATGCCAACACAAATTTCTTAT 59.722 33.333 1.58 0.00 46.97 1.73
2199 2391 7.822822 AGATAGTTTGGTCAGTAAATGGTGTAC 59.177 37.037 0.00 0.00 0.00 2.90
2297 2489 7.849804 AGAACATAGTGGTTAGCAATGTAAG 57.150 36.000 2.72 0.00 30.85 2.34
2300 2492 5.415701 CCAAGAACATAGTGGTTAGCAATGT 59.584 40.000 0.00 0.00 32.32 2.71
2359 2551 5.127682 GGCAGAAATTGGTCATCCAGTTAAT 59.872 40.000 0.00 0.00 45.22 1.40
2509 2701 5.772672 AGAAGCAGATAGATGTACCTGGTAG 59.227 44.000 6.84 0.00 36.49 3.18
2723 2915 5.413499 CCATGGGAATTTCTCAAACATCAC 58.587 41.667 2.85 0.00 26.19 3.06
2738 2930 1.358787 AGAACCATTGAGCCATGGGAA 59.641 47.619 15.13 0.00 42.10 3.97
3002 3195 5.010922 AGACAATGCAGCAAGAAACCATTTA 59.989 36.000 0.00 0.00 0.00 1.40
3015 3208 6.624352 TGAAAATATCCTAGACAATGCAGC 57.376 37.500 0.00 0.00 0.00 5.25
3120 3313 4.816925 ACTTTTCTCCAACTGCAGAAGTAC 59.183 41.667 23.35 0.00 38.56 2.73
3675 3900 1.878088 CTGATATGTGCCATGTCTGCC 59.122 52.381 11.28 0.00 0.00 4.85
3813 4038 8.073467 TCCCTTGTTTGTTTATTTCTTTCACT 57.927 30.769 0.00 0.00 0.00 3.41
4005 4248 0.780637 TTATGGGGTCCACCTTGCAA 59.219 50.000 0.00 0.00 35.80 4.08
4046 4289 0.035458 AGACCTGCTTAAGCGCAACT 59.965 50.000 21.97 15.16 45.83 3.16
4121 4364 5.105106 TCAGGGCATTAGTTAATCAGAACGA 60.105 40.000 0.00 0.00 34.36 3.85
4129 4372 4.581824 CAGCACATCAGGGCATTAGTTAAT 59.418 41.667 0.00 0.00 0.00 1.40
4130 4373 3.947196 CAGCACATCAGGGCATTAGTTAA 59.053 43.478 0.00 0.00 0.00 2.01
4134 4377 2.048444 ACAGCACATCAGGGCATTAG 57.952 50.000 0.00 0.00 0.00 1.73
4144 4387 4.229876 GCCTGAAGTTTAAACAGCACATC 58.770 43.478 20.06 8.64 0.00 3.06
4159 4402 2.564947 ACTCCTGAGTAGTTGCCTGAAG 59.435 50.000 0.00 0.00 40.43 3.02
4436 4679 5.638133 TGTTGGTACTCAGTACTCCTACTT 58.362 41.667 14.75 0.00 38.85 2.24
4438 4681 6.527057 AATGTTGGTACTCAGTACTCCTAC 57.473 41.667 14.75 6.97 38.85 3.18
4530 4782 7.417612 CCATCAAATACGGACATCCTTAAAAG 58.582 38.462 0.00 0.00 0.00 2.27
4537 4789 2.571212 TGCCATCAAATACGGACATCC 58.429 47.619 0.00 0.00 0.00 3.51
4538 4790 4.836125 ATTGCCATCAAATACGGACATC 57.164 40.909 0.00 0.00 35.56 3.06
4540 4792 6.061441 AGAATATTGCCATCAAATACGGACA 58.939 36.000 0.00 0.00 35.56 4.02
4545 4797 9.415544 GGAAATGAGAATATTGCCATCAAATAC 57.584 33.333 0.00 0.00 36.02 1.89
4597 4849 4.927267 ATCAGTCCCACCAGAAACAATA 57.073 40.909 0.00 0.00 0.00 1.90
4603 4855 2.626785 TGGTTATCAGTCCCACCAGAA 58.373 47.619 0.00 0.00 34.23 3.02
4676 4928 6.206634 AGCAACATTCTGGTCGAAAGAATAAA 59.793 34.615 19.08 0.00 41.39 1.40
4678 4930 5.245531 AGCAACATTCTGGTCGAAAGAATA 58.754 37.500 19.08 0.19 41.39 1.75
4686 4938 4.024556 GGATATCAAGCAACATTCTGGTCG 60.025 45.833 4.83 0.00 0.00 4.79
4691 4943 6.485984 GTCAGATGGATATCAAGCAACATTCT 59.514 38.462 4.83 0.00 35.70 2.40
4829 5082 6.208797 CGTGAACCATCTATTCCCTAGACATA 59.791 42.308 0.00 0.00 39.28 2.29
4998 5252 7.201839 GGAACAGGTAATCAGGTTTTGTTAACA 60.202 37.037 3.59 3.59 0.00 2.41
5439 5695 2.923020 CACACCTTTGCTGTTGAAACAC 59.077 45.455 0.00 0.00 34.70 3.32
5454 5710 3.695830 TTTATTTCTCGGAGCACACCT 57.304 42.857 0.00 0.00 0.00 4.00
5479 5735 6.183361 TGTGTTTCTTAAGGACTGGATGAGAA 60.183 38.462 1.85 0.00 0.00 2.87
5484 5740 6.443849 TCCTATGTGTTTCTTAAGGACTGGAT 59.556 38.462 1.85 0.22 0.00 3.41
5485 5741 5.783360 TCCTATGTGTTTCTTAAGGACTGGA 59.217 40.000 1.85 4.61 0.00 3.86
5521 5778 5.485620 CTTCTCCTGATGACAACTGAATCA 58.514 41.667 0.00 0.00 0.00 2.57
5558 5815 1.009389 GGACTGGAGCAAACGAGACG 61.009 60.000 0.00 0.00 0.00 4.18
5587 5844 3.670625 TGGTCCAAGATCTAAAACGGTG 58.329 45.455 0.00 0.00 0.00 4.94
5588 5845 4.324267 CTTGGTCCAAGATCTAAAACGGT 58.676 43.478 25.15 0.00 43.42 4.83
5590 5847 4.003648 AGCTTGGTCCAAGATCTAAAACG 58.996 43.478 31.94 5.86 43.42 3.60
5604 5861 2.704572 ACTGCAGATGTAAGCTTGGTC 58.295 47.619 23.35 4.37 0.00 4.02
5702 5959 3.369546 AAAACCCAAAGCAGAATGTCG 57.630 42.857 0.00 0.00 39.31 4.35
5942 6203 2.107204 GTTATCCCCAGAGCACATGGAT 59.893 50.000 0.00 4.35 40.51 3.41
6016 6278 7.391148 TTTGGCAGGAACTTCATAAGATAAC 57.609 36.000 0.00 0.00 34.60 1.89
6066 6332 1.299976 GGACGGCAAGGGACAGATT 59.700 57.895 0.00 0.00 0.00 2.40
6067 6333 1.903877 CTGGACGGCAAGGGACAGAT 61.904 60.000 0.00 0.00 0.00 2.90
6068 6334 2.525629 TGGACGGCAAGGGACAGA 60.526 61.111 0.00 0.00 0.00 3.41
6118 6384 9.888878 CAGAATTTTCATATTCATAGCGACATT 57.111 29.630 0.00 0.00 37.06 2.71
6119 6385 9.060347 ACAGAATTTTCATATTCATAGCGACAT 57.940 29.630 0.00 0.00 37.06 3.06
6120 6386 8.337532 CACAGAATTTTCATATTCATAGCGACA 58.662 33.333 0.00 0.00 37.06 4.35
6121 6387 8.338259 ACACAGAATTTTCATATTCATAGCGAC 58.662 33.333 0.00 0.00 37.06 5.19
6130 6396 8.917088 CCCAGGATTACACAGAATTTTCATATT 58.083 33.333 0.00 0.00 0.00 1.28
6168 7591 8.757164 AAATTTCGGATAAGTTGGAAAATGTC 57.243 30.769 0.00 0.00 32.73 3.06
6172 7595 7.439655 CACCAAAATTTCGGATAAGTTGGAAAA 59.560 33.333 1.12 0.00 32.73 2.29
6257 7680 8.819974 GCACGTTGCTTTATTAGTAGGTATAAA 58.180 33.333 0.00 0.00 40.96 1.40
6258 7681 7.167968 CGCACGTTGCTTTATTAGTAGGTATAA 59.832 37.037 8.07 0.00 42.25 0.98
6259 7682 6.638063 CGCACGTTGCTTTATTAGTAGGTATA 59.362 38.462 8.07 0.00 42.25 1.47
6260 7683 5.461078 CGCACGTTGCTTTATTAGTAGGTAT 59.539 40.000 8.07 0.00 42.25 2.73
6261 7684 4.799949 CGCACGTTGCTTTATTAGTAGGTA 59.200 41.667 8.07 0.00 42.25 3.08
6262 7685 3.615496 CGCACGTTGCTTTATTAGTAGGT 59.385 43.478 8.07 0.00 42.25 3.08
6263 7686 3.615496 ACGCACGTTGCTTTATTAGTAGG 59.385 43.478 8.07 0.00 42.25 3.18
6264 7687 4.835199 ACGCACGTTGCTTTATTAGTAG 57.165 40.909 8.07 0.00 42.25 2.57
6265 7688 5.406175 AGAAACGCACGTTGCTTTATTAGTA 59.594 36.000 10.63 0.00 40.92 1.82
6266 7689 4.212636 AGAAACGCACGTTGCTTTATTAGT 59.787 37.500 10.63 0.00 40.92 2.24
6267 7690 4.708601 AGAAACGCACGTTGCTTTATTAG 58.291 39.130 10.63 0.00 40.92 1.73
6268 7691 4.735662 AGAAACGCACGTTGCTTTATTA 57.264 36.364 10.63 0.00 40.92 0.98
6269 7692 3.619233 AGAAACGCACGTTGCTTTATT 57.381 38.095 10.63 0.00 40.92 1.40
6274 7697 0.730265 TTGAAGAAACGCACGTTGCT 59.270 45.000 10.63 10.63 45.34 3.91
6275 7698 1.753956 ATTGAAGAAACGCACGTTGC 58.246 45.000 9.46 7.56 38.47 4.17
6276 7699 4.753516 AAAATTGAAGAAACGCACGTTG 57.246 36.364 9.46 0.00 38.47 4.10
6295 7718 3.123157 TCGGTGGTGAACGGATAAAAA 57.877 42.857 0.00 0.00 33.52 1.94
6296 7719 2.835580 TCGGTGGTGAACGGATAAAA 57.164 45.000 0.00 0.00 33.52 1.52
6297 7720 2.835580 TTCGGTGGTGAACGGATAAA 57.164 45.000 0.00 0.00 37.89 1.40
6298 7721 2.835580 TTTCGGTGGTGAACGGATAA 57.164 45.000 0.00 0.00 37.89 1.75
6299 7722 2.835580 TTTTCGGTGGTGAACGGATA 57.164 45.000 0.00 0.00 37.89 2.59
6300 7723 2.194201 ATTTTCGGTGGTGAACGGAT 57.806 45.000 0.00 0.00 37.89 4.18
6301 7724 2.835580 TATTTTCGGTGGTGAACGGA 57.164 45.000 0.00 0.00 36.42 4.69
6302 7725 4.428615 AAATATTTTCGGTGGTGAACGG 57.571 40.909 0.00 0.00 0.00 4.44
6328 7751 9.416284 ACAAAATTTTAATACCACCTCGGATAT 57.584 29.630 2.44 0.00 38.63 1.63
6329 7752 8.679100 CACAAAATTTTAATACCACCTCGGATA 58.321 33.333 2.44 0.00 38.63 2.59
6330 7753 7.394923 TCACAAAATTTTAATACCACCTCGGAT 59.605 33.333 2.44 0.00 38.63 4.18
6331 7754 6.715718 TCACAAAATTTTAATACCACCTCGGA 59.284 34.615 2.44 0.00 38.63 4.55
6332 7755 6.915349 TCACAAAATTTTAATACCACCTCGG 58.085 36.000 2.44 0.00 42.50 4.63
6333 7756 7.700656 GGATCACAAAATTTTAATACCACCTCG 59.299 37.037 2.44 0.00 0.00 4.63
6334 7757 8.527810 TGGATCACAAAATTTTAATACCACCTC 58.472 33.333 2.44 0.00 0.00 3.85
6335 7758 8.429237 TGGATCACAAAATTTTAATACCACCT 57.571 30.769 2.44 0.00 0.00 4.00
6336 7759 9.313118 GATGGATCACAAAATTTTAATACCACC 57.687 33.333 2.44 3.12 0.00 4.61
6339 7762 9.034544 GCAGATGGATCACAAAATTTTAATACC 57.965 33.333 2.44 5.04 0.00 2.73
6340 7763 9.807649 AGCAGATGGATCACAAAATTTTAATAC 57.192 29.630 2.44 0.00 0.00 1.89
6343 7766 9.241919 TCTAGCAGATGGATCACAAAATTTTAA 57.758 29.630 2.44 0.00 0.00 1.52
6344 7767 8.806429 TCTAGCAGATGGATCACAAAATTTTA 57.194 30.769 2.44 0.00 0.00 1.52
6345 7768 7.707624 TCTAGCAGATGGATCACAAAATTTT 57.292 32.000 0.00 0.00 0.00 1.82
6346 7769 7.707624 TTCTAGCAGATGGATCACAAAATTT 57.292 32.000 0.00 0.00 0.00 1.82
6347 7770 7.707624 TTTCTAGCAGATGGATCACAAAATT 57.292 32.000 0.00 0.00 0.00 1.82
6348 7771 7.707624 TTTTCTAGCAGATGGATCACAAAAT 57.292 32.000 0.00 0.00 0.00 1.82
6349 7772 7.523293 TTTTTCTAGCAGATGGATCACAAAA 57.477 32.000 0.00 0.00 0.00 2.44
6372 7795 5.372343 AATTCTGGGCAAAACTCCTTTTT 57.628 34.783 0.00 0.00 37.96 1.94
6373 7796 5.368145 GAAATTCTGGGCAAAACTCCTTTT 58.632 37.500 0.00 0.00 0.00 2.27
6374 7797 4.501400 CGAAATTCTGGGCAAAACTCCTTT 60.501 41.667 0.00 0.00 0.00 3.11
6375 7798 3.005791 CGAAATTCTGGGCAAAACTCCTT 59.994 43.478 0.00 0.00 0.00 3.36
6376 7799 2.558359 CGAAATTCTGGGCAAAACTCCT 59.442 45.455 0.00 0.00 0.00 3.69
6377 7800 2.296190 ACGAAATTCTGGGCAAAACTCC 59.704 45.455 0.00 0.00 0.00 3.85
6378 7801 3.643159 ACGAAATTCTGGGCAAAACTC 57.357 42.857 0.00 0.00 0.00 3.01
6379 7802 3.058501 CGTACGAAATTCTGGGCAAAACT 60.059 43.478 10.44 0.00 0.00 2.66
6380 7803 3.231160 CGTACGAAATTCTGGGCAAAAC 58.769 45.455 10.44 0.00 0.00 2.43
6381 7804 2.879646 ACGTACGAAATTCTGGGCAAAA 59.120 40.909 24.41 0.00 0.00 2.44
6382 7805 2.224549 CACGTACGAAATTCTGGGCAAA 59.775 45.455 24.41 0.00 0.00 3.68
6383 7806 1.801771 CACGTACGAAATTCTGGGCAA 59.198 47.619 24.41 0.00 0.00 4.52
6384 7807 1.434555 CACGTACGAAATTCTGGGCA 58.565 50.000 24.41 0.00 0.00 5.36
6385 7808 0.725117 CCACGTACGAAATTCTGGGC 59.275 55.000 24.41 0.00 0.00 5.36
6386 7809 1.365699 CCCACGTACGAAATTCTGGG 58.634 55.000 24.41 22.28 32.62 4.45
6387 7810 0.725117 GCCCACGTACGAAATTCTGG 59.275 55.000 24.41 17.26 0.00 3.86
6388 7811 0.725117 GGCCCACGTACGAAATTCTG 59.275 55.000 24.41 8.36 0.00 3.02
6389 7812 0.738412 CGGCCCACGTACGAAATTCT 60.738 55.000 24.41 0.00 37.93 2.40
6390 7813 1.711500 CGGCCCACGTACGAAATTC 59.289 57.895 24.41 7.38 37.93 2.17
6391 7814 2.392974 GCGGCCCACGTACGAAATT 61.393 57.895 24.41 0.00 46.52 1.82
6392 7815 2.816520 GCGGCCCACGTACGAAAT 60.817 61.111 24.41 0.00 46.52 2.17
6393 7816 4.296593 TGCGGCCCACGTACGAAA 62.297 61.111 24.41 0.00 46.52 3.46
6409 7832 3.599285 TTCTGGGCCTTACCGCGTG 62.599 63.158 4.92 0.00 40.62 5.34
6410 7833 2.400269 TTTTCTGGGCCTTACCGCGT 62.400 55.000 4.92 0.00 40.62 6.01
6411 7834 1.644786 CTTTTCTGGGCCTTACCGCG 61.645 60.000 4.53 0.00 40.62 6.46
6412 7835 2.180674 CTTTTCTGGGCCTTACCGC 58.819 57.895 4.53 0.00 40.62 5.68


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

AutoCloner maintained by Alex Coulton.