Multiple sequence alignment - TraesCS1D01G081900

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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 TraesCS1D01G081900 chr1D 100.000 4895 0 0 1 4895 63952179 63947285 0.000000e+00 9040
1 TraesCS1D01G081900 chr1B 93.284 4720 237 37 2 4658 104774564 104769862 0.000000e+00 6887
2 TraesCS1D01G081900 chr1A 94.923 4274 157 23 2 4265 63054493 63050270 0.000000e+00 6636
3 TraesCS1D01G081900 chr1A 84.169 379 19 12 4191 4548 63050272 63049914 3.650000e-86 329
4 TraesCS1D01G081900 chr6A 86.722 241 24 4 4561 4794 34187804 34187565 1.350000e-65 261
5 TraesCS1D01G081900 chr3A 87.234 235 23 3 4561 4788 107603148 107602914 1.350000e-65 261
6 TraesCS1D01G081900 chr3A 85.772 246 27 4 4561 4799 107609768 107609524 2.260000e-63 254
7 TraesCS1D01G081900 chr5D 86.383 235 25 3 4561 4788 27262757 27262523 2.930000e-62 250
8 TraesCS1D01G081900 chr5D 84.579 214 21 9 4594 4799 85922090 85921881 8.310000e-48 202
9 TraesCS1D01G081900 chr5B 86.638 232 24 3 4561 4785 36187020 36186789 2.930000e-62 250
10 TraesCS1D01G081900 chr2A 85.957 235 26 3 4561 4788 56103840 56104074 1.360000e-60 244
11 TraesCS1D01G081900 chr3B 83.966 237 29 5 4561 4789 276911162 276910927 8.250000e-53 219
12 TraesCS1D01G081900 chr4A 82.158 241 35 4 4561 4794 201794097 201793858 2.990000e-47 200


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 TraesCS1D01G081900 chr1D 63947285 63952179 4894 True 9040.0 9040 100.000 1 4895 1 chr1D.!!$R1 4894
1 TraesCS1D01G081900 chr1B 104769862 104774564 4702 True 6887.0 6887 93.284 2 4658 1 chr1B.!!$R1 4656
2 TraesCS1D01G081900 chr1A 63049914 63054493 4579 True 3482.5 6636 89.546 2 4548 2 chr1A.!!$R1 4546

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
206 209 0.179129 GAAATGCCTCCGGTTGCATG 60.179 55.000 26.32 0.0 46.97 4.06 F
1152 1186 0.111061 ACAGGCTTGCACTCATTCCA 59.889 50.000 0.00 0.0 0.00 3.53 F
1367 1401 1.213182 TGGTTGTGTGCCTTGTCCTTA 59.787 47.619 0.00 0.0 0.00 2.69 F
2383 2417 2.103094 TGATGATCCCTTGACCGATGTC 59.897 50.000 0.00 0.0 42.12 3.06 F
3747 3796 0.108329 ACGGGTATGAAGGAACTGCG 60.108 55.000 0.00 0.0 36.15 5.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1339 1373 0.179045 GGCACACAACCAGTCACTCT 60.179 55.0 0.0 0.00 0.00 3.24 R
2326 2360 0.321653 ACTGCCATGTCGGGTCTTTC 60.322 55.0 0.0 0.00 34.06 2.62 R
2573 2607 0.599204 GCCTCACCAAGTCGTTTCGA 60.599 55.0 0.0 0.00 0.00 3.71 R
3788 3837 0.238289 AGAAGGTTGCGTGATTTGCG 59.762 50.0 0.0 0.00 34.24 4.85 R
4684 4842 0.032952 TCACGACGGTTCCTGGAAAG 59.967 55.0 11.4 10.85 0.00 2.62 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
163 166 0.465642 AGGCGCCAGGGTAAATTAGC 60.466 55.000 31.54 0.00 0.00 3.09
204 207 1.976474 GGAAATGCCTCCGGTTGCA 60.976 57.895 19.95 19.95 42.52 4.08
206 209 0.179129 GAAATGCCTCCGGTTGCATG 60.179 55.000 26.32 0.00 46.97 4.06
207 210 0.611618 AAATGCCTCCGGTTGCATGA 60.612 50.000 26.32 6.58 46.97 3.07
208 211 0.396139 AATGCCTCCGGTTGCATGAT 60.396 50.000 26.32 14.08 46.97 2.45
273 276 8.792633 CCATGGAGATTTTGTTTAGTTACTCAA 58.207 33.333 5.56 0.00 0.00 3.02
334 340 5.705441 TGGTTGACTTTAGCTTGTATCTTGG 59.295 40.000 0.00 0.00 0.00 3.61
366 373 0.183014 ATCCTGCCTTGCCTCATGAG 59.817 55.000 16.24 16.24 0.00 2.90
382 389 1.742308 TGAGTTTGCCCCTAGGAAGT 58.258 50.000 11.48 0.00 33.47 3.01
384 391 1.351350 GAGTTTGCCCCTAGGAAGTGT 59.649 52.381 11.48 0.00 33.47 3.55
403 410 5.045215 AGTGTCATTTTGTTTACTCGACGA 58.955 37.500 0.00 0.00 0.00 4.20
410 417 2.384382 TGTTTACTCGACGACCGTTTC 58.616 47.619 0.00 0.00 39.75 2.78
430 438 7.172190 CCGTTTCATTCATGCTATGATCTAGTT 59.828 37.037 10.06 0.00 39.39 2.24
462 470 1.375396 CACGCCCCAGTTCGATTCA 60.375 57.895 0.00 0.00 0.00 2.57
474 482 5.004821 CCAGTTCGATTCAGTTTCGATGTAG 59.995 44.000 0.00 0.00 44.32 2.74
476 484 5.800941 AGTTCGATTCAGTTTCGATGTAGTC 59.199 40.000 0.00 0.00 44.32 2.59
504 512 4.397420 TCTATGCCAGTTGTGTGATTTGT 58.603 39.130 0.00 0.00 0.00 2.83
505 513 4.826733 TCTATGCCAGTTGTGTGATTTGTT 59.173 37.500 0.00 0.00 0.00 2.83
506 514 3.162202 TGCCAGTTGTGTGATTTGTTG 57.838 42.857 0.00 0.00 0.00 3.33
508 516 2.738000 GCCAGTTGTGTGATTTGTTGCA 60.738 45.455 0.00 0.00 0.00 4.08
510 518 3.737266 CCAGTTGTGTGATTTGTTGCATC 59.263 43.478 0.00 0.00 0.00 3.91
511 519 3.422876 CAGTTGTGTGATTTGTTGCATCG 59.577 43.478 0.00 0.00 0.00 3.84
512 520 3.066621 AGTTGTGTGATTTGTTGCATCGT 59.933 39.130 0.00 0.00 0.00 3.73
513 521 4.274705 AGTTGTGTGATTTGTTGCATCGTA 59.725 37.500 0.00 0.00 0.00 3.43
595 603 4.876107 TCTCTGCTTTTCTCAACTTTTCGT 59.124 37.500 0.00 0.00 0.00 3.85
596 604 4.908736 TCTGCTTTTCTCAACTTTTCGTG 58.091 39.130 0.00 0.00 0.00 4.35
614 622 2.659428 GTGGATTAGCCCTTGATTGCT 58.341 47.619 0.00 0.00 41.57 3.91
715 723 9.477484 CATGTCTAAGTTGTTACAAACTAGACT 57.523 33.333 28.47 19.45 39.48 3.24
745 753 1.251251 ACTTCTGCATTTCCAGTGCC 58.749 50.000 0.00 0.00 41.83 5.01
747 755 1.471684 CTTCTGCATTTCCAGTGCCTC 59.528 52.381 0.00 0.00 41.83 4.70
774 782 4.035675 GCCATGGCTCACTTGTATTTAGAC 59.964 45.833 29.98 0.00 38.26 2.59
784 792 8.918202 TCACTTGTATTTAGACTTTGGAATGT 57.082 30.769 0.00 0.00 0.00 2.71
833 841 7.749808 TCACAAATTACACTTGAAAACGTGTA 58.250 30.769 0.00 0.00 43.50 2.90
944 978 6.016024 CCATCCATGTCTCAGTGAAAAGAAAA 60.016 38.462 0.00 0.00 0.00 2.29
957 991 9.985318 CAGTGAAAAGAAAATAGATCTGACATC 57.015 33.333 5.18 0.00 0.00 3.06
970 1004 1.135139 CTGACATCGTGATCTTCCGGT 59.865 52.381 0.00 0.00 0.00 5.28
986 1020 6.683715 TCTTCCGGTTATTTGGATTTGTTTC 58.316 36.000 0.00 0.00 33.42 2.78
990 1024 6.014156 TCCGGTTATTTGGATTTGTTTCCATT 60.014 34.615 0.00 0.00 45.08 3.16
1062 1096 3.251484 TCTCACCCTTCCAGTTCAGAAT 58.749 45.455 0.00 0.00 0.00 2.40
1065 1099 1.279271 ACCCTTCCAGTTCAGAATCCG 59.721 52.381 0.00 0.00 0.00 4.18
1152 1186 0.111061 ACAGGCTTGCACTCATTCCA 59.889 50.000 0.00 0.00 0.00 3.53
1367 1401 1.213182 TGGTTGTGTGCCTTGTCCTTA 59.787 47.619 0.00 0.00 0.00 2.69
1868 1902 8.824756 ACCTTCTTACTCACAGATATGTTAGA 57.175 34.615 8.60 0.00 0.00 2.10
2326 2360 5.163982 TGCTCTATATGATCGAGTTCGTACG 60.164 44.000 9.53 9.53 40.80 3.67
2383 2417 2.103094 TGATGATCCCTTGACCGATGTC 59.897 50.000 0.00 0.00 42.12 3.06
2573 2607 2.768253 TGAGAGGCGTTCAATGATGT 57.232 45.000 0.00 0.00 0.00 3.06
2575 2609 1.590238 GAGAGGCGTTCAATGATGTCG 59.410 52.381 0.00 0.00 0.00 4.35
2828 2868 3.016971 TCCAGGGGCATGGACAGG 61.017 66.667 6.58 0.00 44.56 4.00
3015 3055 4.904251 TGGTTGGATGAATTTTCTGGGAAA 59.096 37.500 0.00 0.00 0.00 3.13
3150 3190 1.604278 GTCTGCCAGAAACACAAGGAC 59.396 52.381 0.00 0.00 0.00 3.85
3327 3367 0.675633 AGGCACTGGCAAATGTTGTC 59.324 50.000 5.25 0.00 43.71 3.18
3357 3397 3.196469 CACCCAGTGACTCTGTGATATGT 59.804 47.826 5.35 0.00 42.19 2.29
3369 3409 5.195185 TCTGTGATATGTGACCATGCAATT 58.805 37.500 0.00 0.00 32.29 2.32
3372 3412 3.068448 TGATATGTGACCATGCAATTGCC 59.932 43.478 26.94 11.97 41.18 4.52
3424 3464 1.754621 TTGCTTTCCGCCACCAACA 60.755 52.632 0.00 0.00 38.05 3.33
3447 3487 3.181480 GCAGTTCTCCAGATACCTCACTC 60.181 52.174 0.00 0.00 0.00 3.51
3661 3710 3.137533 GAGAGCAGTCAAGCAACTTCTT 58.862 45.455 0.00 0.00 36.85 2.52
3747 3796 0.108329 ACGGGTATGAAGGAACTGCG 60.108 55.000 0.00 0.00 36.15 5.18
3788 3837 1.916697 GAGGAAGAAACTGCAGCGGC 61.917 60.000 15.27 0.31 41.68 6.53
3844 3893 0.463654 AGCGACTTGTGTGCAGGAAA 60.464 50.000 0.00 0.00 0.00 3.13
3920 3969 0.608640 GACGGTGATGGAGGAACTGT 59.391 55.000 0.00 0.00 41.55 3.55
3927 3976 0.907704 ATGGAGGAACTGTGGCGGTA 60.908 55.000 0.00 0.00 41.55 4.02
3936 3985 0.246635 CTGTGGCGGTACAAGCTAGT 59.753 55.000 11.49 0.00 34.52 2.57
3937 3986 0.682852 TGTGGCGGTACAAGCTAGTT 59.317 50.000 11.49 0.00 34.52 2.24
3938 3987 1.337447 TGTGGCGGTACAAGCTAGTTC 60.337 52.381 11.49 0.00 34.52 3.01
3939 3988 0.970640 TGGCGGTACAAGCTAGTTCA 59.029 50.000 11.49 0.00 34.52 3.18
4094 4147 3.341857 TGTTTGTGCGGTTTGTATGTC 57.658 42.857 0.00 0.00 0.00 3.06
4218 4271 2.624316 AAGCGCAACAATCTCATGTG 57.376 45.000 11.47 0.00 32.81 3.21
4219 4272 0.806868 AGCGCAACAATCTCATGTGG 59.193 50.000 11.47 0.00 32.81 4.17
4220 4273 0.804364 GCGCAACAATCTCATGTGGA 59.196 50.000 0.30 0.00 32.81 4.02
4221 4274 1.202110 GCGCAACAATCTCATGTGGAG 60.202 52.381 0.30 0.00 45.49 3.86
4222 4275 2.079158 CGCAACAATCTCATGTGGAGT 58.921 47.619 0.00 0.00 44.40 3.85
4329 4448 7.398829 TGCTGTTGAAGGAGGTTATGTTAATA 58.601 34.615 0.00 0.00 0.00 0.98
4339 4458 8.368668 AGGAGGTTATGTTAATATTCTCTTCCG 58.631 37.037 0.00 0.00 0.00 4.30
4355 4474 3.561213 CGGCAGCGTGCTCTCATG 61.561 66.667 9.31 0.00 44.28 3.07
4356 4475 2.435586 GGCAGCGTGCTCTCATGT 60.436 61.111 9.31 0.00 44.28 3.21
4363 4482 0.742281 CGTGCTCTCATGTTGGGAGG 60.742 60.000 6.53 0.00 45.03 4.30
4384 4503 2.436646 CAAGCTCGTGCCCCGATT 60.437 61.111 5.73 0.00 46.23 3.34
4455 4585 1.400759 GCCGATACGACTCGATAACCC 60.401 57.143 5.20 0.00 41.12 4.11
4483 4640 1.692519 ACTGAACTTTCGTGGCTACCT 59.307 47.619 0.00 0.00 0.00 3.08
4528 4685 5.880054 ACAAAATCAGTACAAATCCCTCG 57.120 39.130 0.00 0.00 0.00 4.63
4559 4716 3.890527 GGAGTACTCCCTCCGTACA 57.109 57.895 28.87 0.00 43.94 2.90
4599 4757 5.597813 ATCGACAGAGACAATGAACAAAC 57.402 39.130 0.00 0.00 0.00 2.93
4613 4771 5.224562 TGAACAAACGATTCGAACAGTTT 57.775 34.783 20.43 20.43 37.29 2.66
4637 4795 8.578308 TTTTTGTTGATGATGAATGAACACTC 57.422 30.769 0.00 0.00 41.36 3.51
4651 4809 6.560003 ATGAACACTCATATACAGTGGGAA 57.440 37.500 15.10 3.92 44.86 3.97
4658 4816 4.274978 TCATATACAGTGGGAACAGTCGA 58.725 43.478 0.00 0.00 43.90 4.20
4659 4817 4.338400 TCATATACAGTGGGAACAGTCGAG 59.662 45.833 0.00 0.00 43.90 4.04
4660 4818 1.254026 TACAGTGGGAACAGTCGAGG 58.746 55.000 0.00 0.00 43.90 4.63
4661 4819 1.293498 CAGTGGGAACAGTCGAGGG 59.707 63.158 0.00 0.00 43.90 4.30
4662 4820 1.155390 AGTGGGAACAGTCGAGGGA 59.845 57.895 0.00 0.00 41.12 4.20
4663 4821 1.186267 AGTGGGAACAGTCGAGGGAC 61.186 60.000 0.00 0.00 41.12 4.46
4664 4822 1.152419 TGGGAACAGTCGAGGGACA 60.152 57.895 0.00 0.00 45.92 4.02
4665 4823 1.292541 GGGAACAGTCGAGGGACAC 59.707 63.158 0.00 0.00 45.92 3.67
4666 4824 1.469335 GGGAACAGTCGAGGGACACA 61.469 60.000 0.00 0.00 45.92 3.72
4667 4825 0.391597 GGAACAGTCGAGGGACACAA 59.608 55.000 0.00 0.00 45.92 3.33
4668 4826 1.002087 GGAACAGTCGAGGGACACAAT 59.998 52.381 0.00 0.00 45.92 2.71
4669 4827 2.069273 GAACAGTCGAGGGACACAATG 58.931 52.381 0.00 0.00 45.92 2.82
4670 4828 0.321671 ACAGTCGAGGGACACAATGG 59.678 55.000 0.00 0.00 45.92 3.16
4671 4829 0.321671 CAGTCGAGGGACACAATGGT 59.678 55.000 0.00 0.00 45.92 3.55
4672 4830 1.056660 AGTCGAGGGACACAATGGTT 58.943 50.000 0.00 0.00 45.92 3.67
4673 4831 1.002087 AGTCGAGGGACACAATGGTTC 59.998 52.381 0.00 0.00 45.92 3.62
4674 4832 1.052617 TCGAGGGACACAATGGTTCA 58.947 50.000 0.00 0.00 0.00 3.18
4675 4833 1.628340 TCGAGGGACACAATGGTTCAT 59.372 47.619 0.00 0.00 0.00 2.57
4676 4834 2.835156 TCGAGGGACACAATGGTTCATA 59.165 45.455 0.00 0.00 0.00 2.15
4677 4835 3.118775 TCGAGGGACACAATGGTTCATAG 60.119 47.826 0.00 0.00 0.00 2.23
4678 4836 3.118775 CGAGGGACACAATGGTTCATAGA 60.119 47.826 0.00 0.00 0.00 1.98
4679 4837 4.446371 GAGGGACACAATGGTTCATAGAG 58.554 47.826 0.00 0.00 0.00 2.43
4680 4838 4.104086 AGGGACACAATGGTTCATAGAGA 58.896 43.478 0.00 0.00 0.00 3.10
4681 4839 4.723789 AGGGACACAATGGTTCATAGAGAT 59.276 41.667 0.00 0.00 0.00 2.75
4682 4840 4.818546 GGGACACAATGGTTCATAGAGATG 59.181 45.833 0.00 0.00 0.00 2.90
4683 4841 4.274459 GGACACAATGGTTCATAGAGATGC 59.726 45.833 0.00 0.00 32.62 3.91
4684 4842 4.202441 ACACAATGGTTCATAGAGATGCC 58.798 43.478 0.00 0.00 32.62 4.40
4685 4843 4.080129 ACACAATGGTTCATAGAGATGCCT 60.080 41.667 0.00 0.00 32.62 4.75
4686 4844 4.885907 CACAATGGTTCATAGAGATGCCTT 59.114 41.667 0.00 0.00 32.62 4.35
4687 4845 5.359009 CACAATGGTTCATAGAGATGCCTTT 59.641 40.000 0.00 0.00 32.62 3.11
4688 4846 5.591877 ACAATGGTTCATAGAGATGCCTTTC 59.408 40.000 0.00 0.00 32.62 2.62
4689 4847 4.156455 TGGTTCATAGAGATGCCTTTCC 57.844 45.455 0.00 0.00 32.62 3.13
4690 4848 3.523157 TGGTTCATAGAGATGCCTTTCCA 59.477 43.478 0.00 0.00 32.62 3.53
4691 4849 4.133078 GGTTCATAGAGATGCCTTTCCAG 58.867 47.826 0.00 0.00 32.62 3.86
4692 4850 4.133078 GTTCATAGAGATGCCTTTCCAGG 58.867 47.826 0.00 0.00 44.28 4.45
4693 4851 3.657610 TCATAGAGATGCCTTTCCAGGA 58.342 45.455 0.00 0.00 44.19 3.86
4694 4852 4.040047 TCATAGAGATGCCTTTCCAGGAA 58.960 43.478 0.00 0.00 44.19 3.36
4695 4853 2.797177 AGAGATGCCTTTCCAGGAAC 57.203 50.000 0.00 0.00 44.19 3.62
4696 4854 1.283321 AGAGATGCCTTTCCAGGAACC 59.717 52.381 0.00 0.00 44.19 3.62
4697 4855 0.035056 AGATGCCTTTCCAGGAACCG 60.035 55.000 0.00 0.00 44.19 4.44
4698 4856 0.322546 GATGCCTTTCCAGGAACCGT 60.323 55.000 0.00 0.00 44.19 4.83
4699 4857 0.322546 ATGCCTTTCCAGGAACCGTC 60.323 55.000 0.00 0.00 44.19 4.79
4700 4858 2.033194 GCCTTTCCAGGAACCGTCG 61.033 63.158 0.00 0.00 44.19 5.12
4701 4859 1.370064 CCTTTCCAGGAACCGTCGT 59.630 57.895 0.00 0.00 44.19 4.34
4702 4860 0.949105 CCTTTCCAGGAACCGTCGTG 60.949 60.000 0.00 0.00 44.19 4.35
4703 4861 0.032952 CTTTCCAGGAACCGTCGTGA 59.967 55.000 0.00 0.00 41.28 4.35
4704 4862 0.249573 TTTCCAGGAACCGTCGTGAC 60.250 55.000 0.00 0.00 41.28 3.67
4714 4872 2.028484 GTCGTGACGGTTGCTGGA 59.972 61.111 4.70 0.00 0.00 3.86
4715 4873 1.593209 GTCGTGACGGTTGCTGGAA 60.593 57.895 4.70 0.00 0.00 3.53
4716 4874 1.300620 TCGTGACGGTTGCTGGAAG 60.301 57.895 4.70 0.00 0.00 3.46
4717 4875 1.594293 CGTGACGGTTGCTGGAAGT 60.594 57.895 0.00 0.00 35.30 3.01
4718 4876 1.831389 CGTGACGGTTGCTGGAAGTG 61.831 60.000 0.00 0.00 35.30 3.16
4719 4877 0.814010 GTGACGGTTGCTGGAAGTGT 60.814 55.000 0.00 0.00 35.30 3.55
4720 4878 0.813610 TGACGGTTGCTGGAAGTGTG 60.814 55.000 0.00 0.00 35.30 3.82
4721 4879 2.117941 GACGGTTGCTGGAAGTGTGC 62.118 60.000 0.00 0.00 35.30 4.57
4722 4880 2.186160 CGGTTGCTGGAAGTGTGCA 61.186 57.895 0.00 0.00 35.30 4.57
4723 4881 1.723608 CGGTTGCTGGAAGTGTGCAA 61.724 55.000 0.00 0.00 43.25 4.08
4725 4883 2.114638 TTGCTGGAAGTGTGCAACC 58.885 52.632 0.00 0.00 41.06 3.77
4726 4884 1.723608 TTGCTGGAAGTGTGCAACCG 61.724 55.000 0.00 0.00 41.06 4.44
4727 4885 2.639286 CTGGAAGTGTGCAACCGC 59.361 61.111 0.00 0.00 34.36 5.68
4736 4894 3.342909 TGCAACCGCACATGTGAG 58.657 55.556 29.80 25.37 45.36 3.51
4737 4895 1.227793 TGCAACCGCACATGTGAGA 60.228 52.632 29.80 6.93 45.36 3.27
4738 4896 0.817229 TGCAACCGCACATGTGAGAA 60.817 50.000 29.80 7.31 45.36 2.87
4739 4897 0.110056 GCAACCGCACATGTGAGAAG 60.110 55.000 29.80 18.20 38.36 2.85
4740 4898 0.518636 CAACCGCACATGTGAGAAGG 59.481 55.000 29.80 24.38 31.84 3.46
4741 4899 0.396435 AACCGCACATGTGAGAAGGA 59.604 50.000 29.80 0.00 31.84 3.36
4742 4900 0.036952 ACCGCACATGTGAGAAGGAG 60.037 55.000 29.80 14.68 31.84 3.69
4743 4901 1.364626 CCGCACATGTGAGAAGGAGC 61.365 60.000 29.80 10.18 31.84 4.70
4744 4902 1.690283 CGCACATGTGAGAAGGAGCG 61.690 60.000 29.80 18.28 37.91 5.03
4745 4903 1.364626 GCACATGTGAGAAGGAGCGG 61.365 60.000 29.80 0.00 0.00 5.52
4746 4904 0.742281 CACATGTGAGAAGGAGCGGG 60.742 60.000 21.64 0.00 0.00 6.13
4747 4905 1.153289 CATGTGAGAAGGAGCGGGG 60.153 63.158 0.00 0.00 0.00 5.73
4748 4906 2.370445 ATGTGAGAAGGAGCGGGGG 61.370 63.158 0.00 0.00 0.00 5.40
4749 4907 3.003763 GTGAGAAGGAGCGGGGGT 61.004 66.667 0.00 0.00 0.00 4.95
4750 4908 2.203938 TGAGAAGGAGCGGGGGTT 60.204 61.111 0.00 0.00 0.00 4.11
4751 4909 1.079621 TGAGAAGGAGCGGGGGTTA 59.920 57.895 0.00 0.00 0.00 2.85
4752 4910 0.326238 TGAGAAGGAGCGGGGGTTAT 60.326 55.000 0.00 0.00 0.00 1.89
4753 4911 0.393448 GAGAAGGAGCGGGGGTTATC 59.607 60.000 0.00 0.00 0.00 1.75
4754 4912 1.054978 AGAAGGAGCGGGGGTTATCC 61.055 60.000 0.00 0.00 0.00 2.59
4767 4925 3.775261 GGTTATCCCCTAATAACCGCA 57.225 47.619 9.39 0.00 46.74 5.69
4768 4926 4.089408 GGTTATCCCCTAATAACCGCAA 57.911 45.455 9.39 0.00 46.74 4.85
4769 4927 4.070009 GGTTATCCCCTAATAACCGCAAG 58.930 47.826 9.39 0.00 46.74 4.01
4789 4947 7.659159 CGCAAGGGTTATTTATTTTTAACACG 58.341 34.615 0.00 0.00 36.93 4.49
4790 4948 7.326547 CGCAAGGGTTATTTATTTTTAACACGT 59.673 33.333 0.00 0.00 36.93 4.49
4791 4949 8.641155 GCAAGGGTTATTTATTTTTAACACGTC 58.359 33.333 0.00 0.00 36.93 4.34
4792 4950 9.131416 CAAGGGTTATTTATTTTTAACACGTCC 57.869 33.333 0.00 0.00 36.93 4.79
4793 4951 7.829725 AGGGTTATTTATTTTTAACACGTCCC 58.170 34.615 0.00 0.00 36.93 4.46
4794 4952 7.450944 AGGGTTATTTATTTTTAACACGTCCCA 59.549 33.333 0.00 0.00 36.93 4.37
4795 4953 8.252417 GGGTTATTTATTTTTAACACGTCCCAT 58.748 33.333 0.00 0.00 31.38 4.00
4818 4976 9.944376 CCATAATATTAATATATGGGACGGAGG 57.056 37.037 21.72 8.14 35.31 4.30
4819 4977 9.944376 CATAATATTAATATATGGGACGGAGGG 57.056 37.037 8.39 0.00 0.00 4.30
4820 4978 9.907819 ATAATATTAATATATGGGACGGAGGGA 57.092 33.333 8.39 0.00 0.00 4.20
4821 4979 7.857404 ATATTAATATATGGGACGGAGGGAG 57.143 40.000 6.16 0.00 0.00 4.30
4822 4980 3.562108 AATATATGGGACGGAGGGAGT 57.438 47.619 0.00 0.00 0.00 3.85
4823 4981 4.687262 AATATATGGGACGGAGGGAGTA 57.313 45.455 0.00 0.00 0.00 2.59
4824 4982 2.305858 ATATGGGACGGAGGGAGTAC 57.694 55.000 0.00 0.00 0.00 2.73
4825 4983 1.229131 TATGGGACGGAGGGAGTACT 58.771 55.000 0.00 0.00 0.00 2.73
4826 4984 0.106116 ATGGGACGGAGGGAGTACTC 60.106 60.000 14.87 14.87 36.76 2.59
4827 4985 1.212934 TGGGACGGAGGGAGTACTCT 61.213 60.000 21.88 3.41 37.63 3.24
4828 4986 0.466007 GGGACGGAGGGAGTACTCTC 60.466 65.000 21.88 18.89 42.48 3.20
4829 4987 0.547553 GGACGGAGGGAGTACTCTCT 59.452 60.000 25.60 25.60 44.55 3.10
4830 4988 1.767681 GGACGGAGGGAGTACTCTCTA 59.232 57.143 25.38 0.00 41.29 2.43
4831 4989 2.172293 GGACGGAGGGAGTACTCTCTAA 59.828 54.545 25.38 0.00 41.29 2.10
4832 4990 3.205338 GACGGAGGGAGTACTCTCTAAC 58.795 54.545 25.38 18.94 41.29 2.34
4833 4991 2.211806 CGGAGGGAGTACTCTCTAACG 58.788 57.143 25.38 25.56 41.29 3.18
4834 4992 2.158986 CGGAGGGAGTACTCTCTAACGA 60.159 54.545 30.89 0.00 41.29 3.85
4835 4993 3.469739 GGAGGGAGTACTCTCTAACGAG 58.530 54.545 25.38 0.00 41.29 4.18
4836 4994 3.118298 GGAGGGAGTACTCTCTAACGAGT 60.118 52.174 25.38 1.22 41.29 4.18
4837 4995 3.872771 GAGGGAGTACTCTCTAACGAGTG 59.127 52.174 25.38 0.00 41.29 3.51
4838 4996 2.355444 GGGAGTACTCTCTAACGAGTGC 59.645 54.545 21.88 2.67 43.68 4.40
4839 4997 3.008330 GGAGTACTCTCTAACGAGTGCA 58.992 50.000 21.88 0.00 45.43 4.57
4840 4998 3.064271 GGAGTACTCTCTAACGAGTGCAG 59.936 52.174 21.88 0.00 45.43 4.41
4841 4999 3.933955 GAGTACTCTCTAACGAGTGCAGA 59.066 47.826 15.91 0.00 45.43 4.26
4842 5000 3.936453 AGTACTCTCTAACGAGTGCAGAG 59.064 47.826 10.73 8.15 45.43 3.35
4843 5001 2.785562 ACTCTCTAACGAGTGCAGAGT 58.214 47.619 12.14 9.30 42.39 3.24
4844 5002 3.150767 ACTCTCTAACGAGTGCAGAGTT 58.849 45.455 12.14 6.61 40.79 3.01
4845 5003 3.189702 ACTCTCTAACGAGTGCAGAGTTC 59.810 47.826 12.14 0.00 40.79 3.01
4846 5004 3.413327 TCTCTAACGAGTGCAGAGTTCT 58.587 45.455 12.14 0.00 37.62 3.01
4847 5005 3.437395 TCTCTAACGAGTGCAGAGTTCTC 59.563 47.826 12.14 0.00 37.62 2.87
4848 5006 3.413327 TCTAACGAGTGCAGAGTTCTCT 58.587 45.455 4.87 0.00 0.00 3.10
4849 5007 4.576879 TCTAACGAGTGCAGAGTTCTCTA 58.423 43.478 1.83 0.00 0.00 2.43
4850 5008 3.840890 AACGAGTGCAGAGTTCTCTAG 57.159 47.619 1.83 0.00 0.00 2.43
4851 5009 2.088423 ACGAGTGCAGAGTTCTCTAGG 58.912 52.381 1.83 0.00 0.00 3.02
4852 5010 2.290387 ACGAGTGCAGAGTTCTCTAGGA 60.290 50.000 1.83 0.00 0.00 2.94
4853 5011 2.750166 CGAGTGCAGAGTTCTCTAGGAA 59.250 50.000 1.83 0.00 0.00 3.36
4854 5012 3.380004 CGAGTGCAGAGTTCTCTAGGAAT 59.620 47.826 1.83 0.00 36.24 3.01
4855 5013 4.576873 CGAGTGCAGAGTTCTCTAGGAATA 59.423 45.833 1.83 0.00 36.24 1.75
4856 5014 5.277779 CGAGTGCAGAGTTCTCTAGGAATAG 60.278 48.000 1.83 0.00 36.24 1.73
4857 5015 5.761205 AGTGCAGAGTTCTCTAGGAATAGA 58.239 41.667 1.83 0.00 36.24 1.98
4858 5016 5.592688 AGTGCAGAGTTCTCTAGGAATAGAC 59.407 44.000 1.83 0.00 36.24 2.59
4859 5017 5.358442 GTGCAGAGTTCTCTAGGAATAGACA 59.642 44.000 1.83 0.00 36.24 3.41
4860 5018 6.040391 GTGCAGAGTTCTCTAGGAATAGACAT 59.960 42.308 1.83 0.00 36.24 3.06
4861 5019 6.040278 TGCAGAGTTCTCTAGGAATAGACATG 59.960 42.308 1.83 0.00 36.24 3.21
4862 5020 6.040391 GCAGAGTTCTCTAGGAATAGACATGT 59.960 42.308 0.00 0.00 36.24 3.21
4863 5021 7.417342 GCAGAGTTCTCTAGGAATAGACATGTT 60.417 40.741 0.00 0.00 36.24 2.71
4864 5022 8.474025 CAGAGTTCTCTAGGAATAGACATGTTT 58.526 37.037 0.00 0.00 36.24 2.83
4865 5023 8.474025 AGAGTTCTCTAGGAATAGACATGTTTG 58.526 37.037 0.00 0.00 36.24 2.93
4866 5024 8.140112 AGTTCTCTAGGAATAGACATGTTTGT 57.860 34.615 0.00 0.00 36.05 2.83
4867 5025 8.598041 AGTTCTCTAGGAATAGACATGTTTGTT 58.402 33.333 0.00 0.00 34.55 2.83
4868 5026 8.874816 GTTCTCTAGGAATAGACATGTTTGTTC 58.125 37.037 15.02 15.02 34.55 3.18
4869 5027 7.258441 TCTCTAGGAATAGACATGTTTGTTCG 58.742 38.462 16.28 6.41 35.79 3.95
4870 5028 6.931838 TCTAGGAATAGACATGTTTGTTCGT 58.068 36.000 19.67 19.67 35.79 3.85
4871 5029 7.383687 TCTAGGAATAGACATGTTTGTTCGTT 58.616 34.615 20.54 13.32 35.79 3.85
4872 5030 6.241207 AGGAATAGACATGTTTGTTCGTTG 57.759 37.500 16.28 0.00 35.79 4.10
4873 5031 5.181245 AGGAATAGACATGTTTGTTCGTTGG 59.819 40.000 16.28 0.00 35.79 3.77
4874 5032 5.180492 GGAATAGACATGTTTGTTCGTTGGA 59.820 40.000 16.28 0.00 35.79 3.53
4875 5033 5.862924 ATAGACATGTTTGTTCGTTGGAG 57.137 39.130 0.00 0.00 35.79 3.86
4876 5034 3.541632 AGACATGTTTGTTCGTTGGAGT 58.458 40.909 0.00 0.00 35.79 3.85
4877 5035 3.945285 AGACATGTTTGTTCGTTGGAGTT 59.055 39.130 0.00 0.00 35.79 3.01
4878 5036 4.035208 AGACATGTTTGTTCGTTGGAGTTC 59.965 41.667 0.00 0.00 35.79 3.01
4879 5037 3.692101 ACATGTTTGTTCGTTGGAGTTCA 59.308 39.130 0.00 0.00 29.55 3.18
4880 5038 4.201910 ACATGTTTGTTCGTTGGAGTTCAG 60.202 41.667 0.00 0.00 29.55 3.02
4881 5039 2.096819 TGTTTGTTCGTTGGAGTTCAGC 59.903 45.455 0.00 0.00 0.00 4.26
4882 5040 1.305201 TTGTTCGTTGGAGTTCAGCC 58.695 50.000 0.00 0.00 0.00 4.85
4883 5041 0.534203 TGTTCGTTGGAGTTCAGCCC 60.534 55.000 0.00 0.00 0.00 5.19
4884 5042 1.301401 TTCGTTGGAGTTCAGCCCG 60.301 57.895 0.00 0.00 0.00 6.13
4885 5043 3.423154 CGTTGGAGTTCAGCCCGC 61.423 66.667 0.00 0.00 0.00 6.13
4886 5044 3.056328 GTTGGAGTTCAGCCCGCC 61.056 66.667 0.00 0.00 0.00 6.13
4887 5045 3.249189 TTGGAGTTCAGCCCGCCT 61.249 61.111 0.00 0.00 0.00 5.52
4888 5046 3.551496 TTGGAGTTCAGCCCGCCTG 62.551 63.158 0.00 0.00 43.17 4.85
4889 5047 4.785453 GGAGTTCAGCCCGCCTGG 62.785 72.222 0.00 0.00 42.05 4.45
4890 5048 3.706373 GAGTTCAGCCCGCCTGGA 61.706 66.667 0.00 0.00 42.05 3.86
4891 5049 3.011517 AGTTCAGCCCGCCTGGAT 61.012 61.111 0.00 0.00 42.05 3.41
4892 5050 2.044946 GTTCAGCCCGCCTGGATT 60.045 61.111 0.00 0.00 42.05 3.01
4893 5051 2.115291 GTTCAGCCCGCCTGGATTC 61.115 63.158 0.00 0.00 42.05 2.52
4894 5052 3.344137 TTCAGCCCGCCTGGATTCC 62.344 63.158 0.00 0.00 42.05 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
117 120 3.319198 TGGGAGGTCTGCCGGAAC 61.319 66.667 5.05 0.00 44.85 3.62
163 166 1.469940 CCTCAGACGTCGGATTGGAAG 60.470 57.143 18.73 6.17 0.00 3.46
204 207 2.956333 GCCGCCCCTAACTAAAAATCAT 59.044 45.455 0.00 0.00 0.00 2.45
205 208 2.371306 GCCGCCCCTAACTAAAAATCA 58.629 47.619 0.00 0.00 0.00 2.57
206 209 1.332686 CGCCGCCCCTAACTAAAAATC 59.667 52.381 0.00 0.00 0.00 2.17
207 210 1.065272 TCGCCGCCCCTAACTAAAAAT 60.065 47.619 0.00 0.00 0.00 1.82
208 211 0.324285 TCGCCGCCCCTAACTAAAAA 59.676 50.000 0.00 0.00 0.00 1.94
240 243 3.782992 ACAAAATCTCCATGGAAGCCTT 58.217 40.909 17.00 4.51 0.00 4.35
273 276 2.589494 CTGCTCAGCACCTCTACCT 58.411 57.895 0.00 0.00 33.79 3.08
294 297 3.843619 TCAACCAGATAACACCTCATCCA 59.156 43.478 0.00 0.00 0.00 3.41
295 298 4.080863 AGTCAACCAGATAACACCTCATCC 60.081 45.833 0.00 0.00 0.00 3.51
296 299 5.091261 AGTCAACCAGATAACACCTCATC 57.909 43.478 0.00 0.00 0.00 2.92
297 300 5.505181 AAGTCAACCAGATAACACCTCAT 57.495 39.130 0.00 0.00 0.00 2.90
334 340 1.718757 GCAGGATGACACGGGATTGC 61.719 60.000 0.00 0.00 39.69 3.56
366 373 1.073284 TGACACTTCCTAGGGGCAAAC 59.927 52.381 9.46 0.00 40.85 2.93
382 389 4.209703 GGTCGTCGAGTAAACAAAATGACA 59.790 41.667 0.00 0.00 0.00 3.58
384 391 3.426191 CGGTCGTCGAGTAAACAAAATGA 59.574 43.478 0.00 0.00 42.43 2.57
403 410 5.371526 AGATCATAGCATGAATGAAACGGT 58.628 37.500 13.27 0.00 43.50 4.83
430 438 2.156098 GGGCGTGACATCCTAAACAAA 58.844 47.619 0.00 0.00 0.00 2.83
462 470 5.422214 AGAATTGGGACTACATCGAAACT 57.578 39.130 0.00 0.00 0.00 2.66
474 482 3.129287 CACAACTGGCATAGAATTGGGAC 59.871 47.826 0.00 0.00 0.00 4.46
476 484 3.091545 ACACAACTGGCATAGAATTGGG 58.908 45.455 0.00 0.00 0.00 4.12
504 512 1.459209 CTCGCAAACAGTACGATGCAA 59.541 47.619 13.08 0.00 38.69 4.08
505 513 1.067693 CTCGCAAACAGTACGATGCA 58.932 50.000 13.08 0.00 38.69 3.96
506 514 1.346365 TCTCGCAAACAGTACGATGC 58.654 50.000 0.00 5.50 34.94 3.91
508 516 2.348666 GCATTCTCGCAAACAGTACGAT 59.651 45.455 0.00 0.00 34.94 3.73
510 518 1.201921 GGCATTCTCGCAAACAGTACG 60.202 52.381 0.00 0.00 0.00 3.67
511 519 1.804151 TGGCATTCTCGCAAACAGTAC 59.196 47.619 0.00 0.00 0.00 2.73
512 520 2.177394 TGGCATTCTCGCAAACAGTA 57.823 45.000 0.00 0.00 0.00 2.74
513 521 1.200716 CATGGCATTCTCGCAAACAGT 59.799 47.619 0.00 0.00 0.00 3.55
565 573 6.471146 AGTTGAGAAAAGCAGAGATATGTGT 58.529 36.000 0.00 0.00 0.00 3.72
595 603 2.025037 ACAGCAATCAAGGGCTAATCCA 60.025 45.455 0.00 0.00 38.56 3.41
596 604 2.360165 CACAGCAATCAAGGGCTAATCC 59.640 50.000 0.00 0.00 38.56 3.01
641 649 7.544650 TGTCCCTTTTCCTCCATCTATCTATA 58.455 38.462 0.00 0.00 0.00 1.31
642 650 6.393897 TGTCCCTTTTCCTCCATCTATCTAT 58.606 40.000 0.00 0.00 0.00 1.98
643 651 5.788430 TGTCCCTTTTCCTCCATCTATCTA 58.212 41.667 0.00 0.00 0.00 1.98
644 652 4.635473 TGTCCCTTTTCCTCCATCTATCT 58.365 43.478 0.00 0.00 0.00 1.98
645 653 5.373812 TTGTCCCTTTTCCTCCATCTATC 57.626 43.478 0.00 0.00 0.00 2.08
745 753 0.323178 AAGTGAGCCATGGCCTTGAG 60.323 55.000 33.14 10.81 43.17 3.02
747 755 0.896940 ACAAGTGAGCCATGGCCTTG 60.897 55.000 34.32 34.32 43.17 3.61
774 782 5.299279 ACAAGACCACAGTTACATTCCAAAG 59.701 40.000 0.00 0.00 0.00 2.77
833 841 5.858381 ACAGTCAGATGTGTCTTGTTGTAT 58.142 37.500 0.00 0.00 30.42 2.29
944 978 5.106357 CGGAAGATCACGATGTCAGATCTAT 60.106 44.000 12.51 0.00 45.62 1.98
957 991 3.527533 TCCAAATAACCGGAAGATCACG 58.472 45.455 9.46 0.00 0.00 4.35
986 1020 7.555554 ACAGAGTCATCATCCTTAAAAGAATGG 59.444 37.037 0.00 0.00 0.00 3.16
990 1024 5.877012 GCACAGAGTCATCATCCTTAAAAGA 59.123 40.000 0.00 0.00 0.00 2.52
1062 1096 5.105106 TGCTGAAAACTCTAATATGGTCGGA 60.105 40.000 0.00 0.00 0.00 4.55
1065 1099 5.586243 TGCTGCTGAAAACTCTAATATGGTC 59.414 40.000 0.00 0.00 0.00 4.02
1152 1186 5.402630 ACAAAATCACCCACCCTAGAAAAT 58.597 37.500 0.00 0.00 0.00 1.82
1339 1373 0.179045 GGCACACAACCAGTCACTCT 60.179 55.000 0.00 0.00 0.00 3.24
1345 1379 0.751643 GGACAAGGCACACAACCAGT 60.752 55.000 0.00 0.00 0.00 4.00
1431 1465 1.303155 TGCATGGAATGGTGTCGCA 60.303 52.632 0.00 0.00 46.86 5.10
1844 1878 9.743057 CTTCTAACATATCTGTGAGTAAGAAGG 57.257 37.037 0.00 0.00 35.57 3.46
1868 1902 2.289010 CCGCATTTTTCTTTCCAGCCTT 60.289 45.455 0.00 0.00 0.00 4.35
2326 2360 0.321653 ACTGCCATGTCGGGTCTTTC 60.322 55.000 0.00 0.00 34.06 2.62
2383 2417 5.539048 AGCATTAGTTACCTTATAGTGCGG 58.461 41.667 0.00 0.00 35.39 5.69
2573 2607 0.599204 GCCTCACCAAGTCGTTTCGA 60.599 55.000 0.00 0.00 0.00 3.71
2575 2609 1.305201 TTGCCTCACCAAGTCGTTTC 58.695 50.000 0.00 0.00 0.00 2.78
2584 2618 0.918258 TGCTGGATATTGCCTCACCA 59.082 50.000 0.00 0.00 0.00 4.17
2587 2621 2.812983 GCAGATGCTGGATATTGCCTCA 60.813 50.000 6.80 0.00 38.21 3.86
2828 2868 1.671379 GGGTTGGTCTTCAGGACGC 60.671 63.158 0.00 0.00 45.35 5.19
3015 3055 4.142790 TCCAGTAACGAGAGAAACTGTCT 58.857 43.478 0.00 0.00 42.00 3.41
3090 3130 8.985315 TGCCTTCAATTACAATATCAGAATCT 57.015 30.769 0.00 0.00 0.00 2.40
3150 3190 2.684881 GTTCAGTATGGCATGGGACTTG 59.315 50.000 10.98 1.78 36.16 3.16
3327 3367 1.978617 GTCACTGGGTGGGCAATGG 60.979 63.158 0.00 0.00 33.87 3.16
3357 3397 1.585517 CACGGCAATTGCATGGTCA 59.414 52.632 30.32 0.00 44.36 4.02
3372 3412 1.261619 GTTCTCACAGAAACTGCCACG 59.738 52.381 0.00 0.00 35.75 4.94
3424 3464 2.763448 GTGAGGTATCTGGAGAACTGCT 59.237 50.000 0.00 0.00 0.00 4.24
3447 3487 2.558359 GGTTGATTGTGGACCCTTGAAG 59.442 50.000 0.00 0.00 0.00 3.02
3500 3540 4.276058 CCATTTTCAATGTTGGCTTCCT 57.724 40.909 0.00 0.00 0.00 3.36
3661 3710 3.193903 TGACATCGATCAAGTTCCCGTAA 59.806 43.478 0.00 0.00 0.00 3.18
3747 3796 4.635765 TCGTCATCAGAAATTTCCATCACC 59.364 41.667 14.61 0.00 0.00 4.02
3788 3837 0.238289 AGAAGGTTGCGTGATTTGCG 59.762 50.000 0.00 0.00 34.24 4.85
3844 3893 4.573900 GGACTATCCTGATTGCGATCAAT 58.426 43.478 17.39 11.44 41.55 2.57
3920 3969 0.970640 TGAACTAGCTTGTACCGCCA 59.029 50.000 0.00 0.00 0.00 5.69
3927 3976 0.679505 TGTCGCCTGAACTAGCTTGT 59.320 50.000 0.00 0.00 0.00 3.16
3936 3985 1.593196 CAGTTTCCTTGTCGCCTGAA 58.407 50.000 0.00 0.00 0.00 3.02
3937 3986 0.884704 GCAGTTTCCTTGTCGCCTGA 60.885 55.000 0.00 0.00 0.00 3.86
3938 3987 1.165907 TGCAGTTTCCTTGTCGCCTG 61.166 55.000 0.00 0.00 0.00 4.85
3939 3988 0.886490 CTGCAGTTTCCTTGTCGCCT 60.886 55.000 5.25 0.00 0.00 5.52
4094 4147 4.217118 AGCATGAAGTTTTGGTAGCTGAAG 59.783 41.667 0.00 0.00 0.00 3.02
4197 4250 3.311106 CACATGAGATTGTTGCGCTTTT 58.689 40.909 9.73 0.00 0.00 2.27
4218 4271 4.309099 TGTGATTGTAAACCACGTACTCC 58.691 43.478 0.00 0.00 45.87 3.85
4219 4272 5.636121 TCATGTGATTGTAAACCACGTACTC 59.364 40.000 0.00 0.00 45.87 2.59
4220 4273 5.543714 TCATGTGATTGTAAACCACGTACT 58.456 37.500 0.00 0.00 45.87 2.73
4221 4274 5.670341 GCTCATGTGATTGTAAACCACGTAC 60.670 44.000 0.00 0.00 45.87 3.67
4222 4275 4.390603 GCTCATGTGATTGTAAACCACGTA 59.609 41.667 0.00 0.00 45.87 3.57
4313 4432 8.368668 CGGAAGAGAATATTAACATAACCTCCT 58.631 37.037 0.00 0.00 0.00 3.69
4329 4448 1.448540 CACGCTGCCGGAAGAGAAT 60.449 57.895 21.55 0.00 39.22 2.40
4339 4458 2.037136 AACATGAGAGCACGCTGCC 61.037 57.895 0.00 0.00 46.52 4.85
4355 4474 1.377856 GAGCTTGCTCCCTCCCAAC 60.378 63.158 11.24 0.00 0.00 3.77
4356 4475 2.959484 CGAGCTTGCTCCCTCCCAA 61.959 63.158 15.87 0.00 0.00 4.12
4384 4503 4.142315 GCCATGAAGCAGCTTCTTATTTCA 60.142 41.667 30.82 14.03 40.73 2.69
4424 4543 3.802685 AGTCGTATCGGCTGAAATTTAGC 59.197 43.478 0.00 0.69 41.45 3.09
4455 4585 3.741344 CCACGAAAGTTCAGTTAGGTGAG 59.259 47.826 0.00 0.00 46.40 3.51
4483 4640 1.152830 GTTTGGGTTGGGGAGCTCA 59.847 57.895 17.19 0.00 0.00 4.26
4552 4709 6.873997 ACAATTCTATTCATCACTGTACGGA 58.126 36.000 9.17 0.00 0.00 4.69
4554 4711 8.630840 CGATACAATTCTATTCATCACTGTACG 58.369 37.037 0.00 0.00 0.00 3.67
4559 4716 8.633561 TCTGTCGATACAATTCTATTCATCACT 58.366 33.333 0.00 0.00 34.49 3.41
4613 4771 7.714703 TGAGTGTTCATTCATCATCAACAAAA 58.285 30.769 0.00 0.00 25.81 2.44
4637 4795 4.499865 CCTCGACTGTTCCCACTGTATATG 60.500 50.000 0.00 0.00 35.34 1.78
4651 4809 0.321671 CCATTGTGTCCCTCGACTGT 59.678 55.000 0.00 0.00 39.94 3.55
4658 4816 4.104086 TCTCTATGAACCATTGTGTCCCT 58.896 43.478 0.00 0.00 0.00 4.20
4659 4817 4.487714 TCTCTATGAACCATTGTGTCCC 57.512 45.455 0.00 0.00 0.00 4.46
4660 4818 4.274459 GCATCTCTATGAACCATTGTGTCC 59.726 45.833 0.00 0.00 34.84 4.02
4661 4819 4.274459 GGCATCTCTATGAACCATTGTGTC 59.726 45.833 0.00 0.00 34.84 3.67
4662 4820 4.080129 AGGCATCTCTATGAACCATTGTGT 60.080 41.667 0.00 0.00 34.84 3.72
4663 4821 4.458397 AGGCATCTCTATGAACCATTGTG 58.542 43.478 0.00 0.00 34.84 3.33
4664 4822 4.785346 AGGCATCTCTATGAACCATTGT 57.215 40.909 0.00 0.00 34.84 2.71
4665 4823 5.009410 GGAAAGGCATCTCTATGAACCATTG 59.991 44.000 0.00 0.00 34.84 2.82
4666 4824 5.136105 GGAAAGGCATCTCTATGAACCATT 58.864 41.667 0.00 0.00 34.84 3.16
4667 4825 4.166725 TGGAAAGGCATCTCTATGAACCAT 59.833 41.667 0.00 0.00 34.84 3.55
4668 4826 3.523157 TGGAAAGGCATCTCTATGAACCA 59.477 43.478 0.00 0.00 34.84 3.67
4669 4827 4.133078 CTGGAAAGGCATCTCTATGAACC 58.867 47.826 0.00 0.00 34.84 3.62
4670 4828 4.133078 CCTGGAAAGGCATCTCTATGAAC 58.867 47.826 0.00 0.00 34.84 3.18
4671 4829 4.040047 TCCTGGAAAGGCATCTCTATGAA 58.960 43.478 0.00 0.00 34.84 2.57
4672 4830 3.657610 TCCTGGAAAGGCATCTCTATGA 58.342 45.455 0.00 0.00 34.84 2.15
4673 4831 4.133078 GTTCCTGGAAAGGCATCTCTATG 58.867 47.826 11.40 0.00 36.09 2.23
4674 4832 3.137360 GGTTCCTGGAAAGGCATCTCTAT 59.863 47.826 11.40 0.00 0.00 1.98
4675 4833 2.505819 GGTTCCTGGAAAGGCATCTCTA 59.494 50.000 11.40 0.00 0.00 2.43
4676 4834 1.283321 GGTTCCTGGAAAGGCATCTCT 59.717 52.381 11.40 0.00 0.00 3.10
4677 4835 1.756430 GGTTCCTGGAAAGGCATCTC 58.244 55.000 11.40 0.00 0.00 2.75
4678 4836 0.035056 CGGTTCCTGGAAAGGCATCT 60.035 55.000 11.40 0.00 0.00 2.90
4679 4837 0.322546 ACGGTTCCTGGAAAGGCATC 60.323 55.000 11.40 0.00 0.00 3.91
4680 4838 0.322546 GACGGTTCCTGGAAAGGCAT 60.323 55.000 11.40 0.00 0.00 4.40
4681 4839 1.072505 GACGGTTCCTGGAAAGGCA 59.927 57.895 11.40 0.00 0.00 4.75
4682 4840 2.033194 CGACGGTTCCTGGAAAGGC 61.033 63.158 11.40 9.69 0.00 4.35
4683 4841 0.949105 CACGACGGTTCCTGGAAAGG 60.949 60.000 11.40 8.48 0.00 3.11
4684 4842 0.032952 TCACGACGGTTCCTGGAAAG 59.967 55.000 11.40 10.85 0.00 2.62
4685 4843 0.249573 GTCACGACGGTTCCTGGAAA 60.250 55.000 11.40 0.00 0.00 3.13
4686 4844 1.364901 GTCACGACGGTTCCTGGAA 59.635 57.895 4.68 4.68 0.00 3.53
4687 4845 3.045142 GTCACGACGGTTCCTGGA 58.955 61.111 0.00 0.00 0.00 3.86
4697 4855 1.557443 CTTCCAGCAACCGTCACGAC 61.557 60.000 0.00 0.00 0.00 4.34
4698 4856 1.300620 CTTCCAGCAACCGTCACGA 60.301 57.895 0.00 0.00 0.00 4.35
4699 4857 1.594293 ACTTCCAGCAACCGTCACG 60.594 57.895 0.00 0.00 0.00 4.35
4700 4858 0.814010 ACACTTCCAGCAACCGTCAC 60.814 55.000 0.00 0.00 0.00 3.67
4701 4859 0.813610 CACACTTCCAGCAACCGTCA 60.814 55.000 0.00 0.00 0.00 4.35
4702 4860 1.941812 CACACTTCCAGCAACCGTC 59.058 57.895 0.00 0.00 0.00 4.79
4703 4861 2.186826 GCACACTTCCAGCAACCGT 61.187 57.895 0.00 0.00 0.00 4.83
4704 4862 1.723608 TTGCACACTTCCAGCAACCG 61.724 55.000 0.00 0.00 42.71 4.44
4705 4863 2.114638 TTGCACACTTCCAGCAACC 58.885 52.632 0.00 0.00 42.71 3.77
4707 4865 1.723608 CGGTTGCACACTTCCAGCAA 61.724 55.000 0.00 0.00 45.07 3.91
4708 4866 2.186160 CGGTTGCACACTTCCAGCA 61.186 57.895 0.00 0.00 36.32 4.41
4709 4867 2.639286 CGGTTGCACACTTCCAGC 59.361 61.111 0.00 0.00 0.00 4.85
4710 4868 2.639286 GCGGTTGCACACTTCCAG 59.361 61.111 0.00 0.00 42.15 3.86
4720 4878 0.110056 CTTCTCACATGTGCGGTTGC 60.110 55.000 21.38 0.00 43.20 4.17
4721 4879 0.518636 CCTTCTCACATGTGCGGTTG 59.481 55.000 21.38 9.37 0.00 3.77
4722 4880 0.396435 TCCTTCTCACATGTGCGGTT 59.604 50.000 21.38 0.00 0.00 4.44
4723 4881 0.036952 CTCCTTCTCACATGTGCGGT 60.037 55.000 21.38 0.00 0.00 5.68
4724 4882 1.364626 GCTCCTTCTCACATGTGCGG 61.365 60.000 21.38 16.74 0.00 5.69
4725 4883 1.690283 CGCTCCTTCTCACATGTGCG 61.690 60.000 21.38 15.52 36.41 5.34
4726 4884 1.364626 CCGCTCCTTCTCACATGTGC 61.365 60.000 21.38 5.71 0.00 4.57
4727 4885 0.742281 CCCGCTCCTTCTCACATGTG 60.742 60.000 20.18 20.18 0.00 3.21
4728 4886 1.599047 CCCGCTCCTTCTCACATGT 59.401 57.895 0.00 0.00 0.00 3.21
4729 4887 1.153289 CCCCGCTCCTTCTCACATG 60.153 63.158 0.00 0.00 0.00 3.21
4730 4888 2.370445 CCCCCGCTCCTTCTCACAT 61.370 63.158 0.00 0.00 0.00 3.21
4731 4889 3.003173 CCCCCGCTCCTTCTCACA 61.003 66.667 0.00 0.00 0.00 3.58
4732 4890 1.262640 TAACCCCCGCTCCTTCTCAC 61.263 60.000 0.00 0.00 0.00 3.51
4733 4891 0.326238 ATAACCCCCGCTCCTTCTCA 60.326 55.000 0.00 0.00 0.00 3.27
4734 4892 0.393448 GATAACCCCCGCTCCTTCTC 59.607 60.000 0.00 0.00 0.00 2.87
4735 4893 1.054978 GGATAACCCCCGCTCCTTCT 61.055 60.000 0.00 0.00 0.00 2.85
4736 4894 1.450642 GGATAACCCCCGCTCCTTC 59.549 63.158 0.00 0.00 0.00 3.46
4737 4895 3.656697 GGATAACCCCCGCTCCTT 58.343 61.111 0.00 0.00 0.00 3.36
4748 4906 4.070009 CCTTGCGGTTATTAGGGGATAAC 58.930 47.826 0.00 0.00 40.26 1.89
4749 4907 3.073356 CCCTTGCGGTTATTAGGGGATAA 59.927 47.826 0.00 0.00 43.04 1.75
4750 4908 2.640826 CCCTTGCGGTTATTAGGGGATA 59.359 50.000 0.00 0.00 43.04 2.59
4751 4909 1.423921 CCCTTGCGGTTATTAGGGGAT 59.576 52.381 0.00 0.00 43.04 3.85
4752 4910 0.841289 CCCTTGCGGTTATTAGGGGA 59.159 55.000 0.00 0.00 43.04 4.81
4753 4911 3.414486 CCCTTGCGGTTATTAGGGG 57.586 57.895 0.00 0.00 43.04 4.79
4763 4921 7.201367 CGTGTTAAAAATAAATAACCCTTGCGG 60.201 37.037 0.00 0.00 32.31 5.69
4764 4922 7.326547 ACGTGTTAAAAATAAATAACCCTTGCG 59.673 33.333 0.00 0.00 32.31 4.85
4765 4923 8.523523 ACGTGTTAAAAATAAATAACCCTTGC 57.476 30.769 0.00 0.00 32.31 4.01
4766 4924 9.131416 GGACGTGTTAAAAATAAATAACCCTTG 57.869 33.333 0.00 0.00 32.31 3.61
4767 4925 8.306038 GGGACGTGTTAAAAATAAATAACCCTT 58.694 33.333 0.00 0.00 32.31 3.95
4768 4926 7.450944 TGGGACGTGTTAAAAATAAATAACCCT 59.549 33.333 0.00 0.00 32.31 4.34
4769 4927 7.600960 TGGGACGTGTTAAAAATAAATAACCC 58.399 34.615 0.00 0.00 32.31 4.11
4792 4950 9.944376 CCTCCGTCCCATATATTAATATTATGG 57.056 37.037 22.10 22.10 37.88 2.74
4793 4951 9.944376 CCCTCCGTCCCATATATTAATATTATG 57.056 37.037 13.09 13.00 0.00 1.90
4794 4952 9.907819 TCCCTCCGTCCCATATATTAATATTAT 57.092 33.333 13.09 3.21 0.00 1.28
4795 4953 9.375974 CTCCCTCCGTCCCATATATTAATATTA 57.624 37.037 13.09 0.00 0.00 0.98
4796 4954 7.849904 ACTCCCTCCGTCCCATATATTAATATT 59.150 37.037 13.09 0.00 0.00 1.28
4797 4955 7.371043 ACTCCCTCCGTCCCATATATTAATAT 58.629 38.462 12.51 12.51 0.00 1.28
4798 4956 6.748969 ACTCCCTCCGTCCCATATATTAATA 58.251 40.000 0.00 0.00 0.00 0.98
4799 4957 5.600749 ACTCCCTCCGTCCCATATATTAAT 58.399 41.667 0.00 0.00 0.00 1.40
4800 4958 5.019657 ACTCCCTCCGTCCCATATATTAA 57.980 43.478 0.00 0.00 0.00 1.40
4801 4959 4.687262 ACTCCCTCCGTCCCATATATTA 57.313 45.455 0.00 0.00 0.00 0.98
4802 4960 3.562108 ACTCCCTCCGTCCCATATATT 57.438 47.619 0.00 0.00 0.00 1.28
4803 4961 3.596956 AGTACTCCCTCCGTCCCATATAT 59.403 47.826 0.00 0.00 0.00 0.86
4804 4962 2.991713 AGTACTCCCTCCGTCCCATATA 59.008 50.000 0.00 0.00 0.00 0.86
4805 4963 1.787676 AGTACTCCCTCCGTCCCATAT 59.212 52.381 0.00 0.00 0.00 1.78
4806 4964 1.144503 GAGTACTCCCTCCGTCCCATA 59.855 57.143 12.13 0.00 0.00 2.74
4807 4965 0.106116 GAGTACTCCCTCCGTCCCAT 60.106 60.000 12.13 0.00 0.00 4.00
4808 4966 1.212934 AGAGTACTCCCTCCGTCCCA 61.213 60.000 19.38 0.00 31.53 4.37
4809 4967 0.466007 GAGAGTACTCCCTCCGTCCC 60.466 65.000 19.38 0.00 37.19 4.46
4810 4968 0.547553 AGAGAGTACTCCCTCCGTCC 59.452 60.000 19.38 0.00 43.53 4.79
4811 4969 3.205338 GTTAGAGAGTACTCCCTCCGTC 58.795 54.545 19.38 9.16 43.53 4.79
4812 4970 2.419851 CGTTAGAGAGTACTCCCTCCGT 60.420 54.545 19.38 0.00 43.53 4.69
4813 4971 2.158986 TCGTTAGAGAGTACTCCCTCCG 60.159 54.545 19.38 17.23 43.53 4.63
4814 4972 3.557228 TCGTTAGAGAGTACTCCCTCC 57.443 52.381 19.38 6.60 43.53 4.30
4822 4980 9.620920 AGAGAACTCTGCACTCGTTAGAGAGTA 62.621 44.444 3.39 0.00 42.85 2.59
4823 4981 8.914230 AGAGAACTCTGCACTCGTTAGAGAGT 62.914 46.154 3.39 0.00 44.21 3.24
4824 4982 6.595696 AGAGAACTCTGCACTCGTTAGAGAG 61.596 48.000 3.39 0.00 41.75 3.20
4825 4983 4.804597 AGAGAACTCTGCACTCGTTAGAGA 60.805 45.833 3.39 0.00 41.75 3.10
4826 4984 3.438781 AGAGAACTCTGCACTCGTTAGAG 59.561 47.826 3.39 0.00 43.36 2.43
4827 4985 3.413327 AGAGAACTCTGCACTCGTTAGA 58.587 45.455 3.39 0.00 38.75 2.10
4828 4986 3.840890 AGAGAACTCTGCACTCGTTAG 57.159 47.619 3.39 0.00 38.75 2.34
4829 4987 3.690139 CCTAGAGAACTCTGCACTCGTTA 59.310 47.826 13.73 0.00 40.71 3.18
4830 4988 2.490115 CCTAGAGAACTCTGCACTCGTT 59.510 50.000 13.73 0.00 40.71 3.85
4831 4989 2.088423 CCTAGAGAACTCTGCACTCGT 58.912 52.381 13.73 0.00 40.71 4.18
4832 4990 2.360844 TCCTAGAGAACTCTGCACTCG 58.639 52.381 13.73 0.00 40.71 4.18
4833 4991 5.825679 TCTATTCCTAGAGAACTCTGCACTC 59.174 44.000 13.73 0.00 40.71 3.51
4834 4992 5.592688 GTCTATTCCTAGAGAACTCTGCACT 59.407 44.000 13.73 0.00 40.71 4.40
4835 4993 5.358442 TGTCTATTCCTAGAGAACTCTGCAC 59.642 44.000 13.73 1.33 40.71 4.57
4836 4994 5.510430 TGTCTATTCCTAGAGAACTCTGCA 58.490 41.667 13.73 0.00 40.71 4.41
4837 4995 6.040391 ACATGTCTATTCCTAGAGAACTCTGC 59.960 42.308 13.73 0.00 40.71 4.26
4838 4996 7.581213 ACATGTCTATTCCTAGAGAACTCTG 57.419 40.000 13.73 4.89 40.71 3.35
4839 4997 8.474025 CAAACATGTCTATTCCTAGAGAACTCT 58.526 37.037 0.00 9.33 43.40 3.24
4840 4998 8.254508 ACAAACATGTCTATTCCTAGAGAACTC 58.745 37.037 0.00 0.00 37.29 3.01
4841 4999 8.140112 ACAAACATGTCTATTCCTAGAGAACT 57.860 34.615 0.00 0.00 37.29 3.01
4842 5000 8.779354 AACAAACATGTCTATTCCTAGAGAAC 57.221 34.615 0.00 0.00 37.29 3.01
4843 5001 7.759886 CGAACAAACATGTCTATTCCTAGAGAA 59.240 37.037 0.00 0.00 39.32 2.87
4844 5002 7.093902 ACGAACAAACATGTCTATTCCTAGAGA 60.094 37.037 0.00 0.00 34.63 3.10
4845 5003 7.036220 ACGAACAAACATGTCTATTCCTAGAG 58.964 38.462 0.00 0.00 34.63 2.43
4846 5004 6.931838 ACGAACAAACATGTCTATTCCTAGA 58.068 36.000 0.00 0.00 0.00 2.43
4847 5005 7.413000 CCAACGAACAAACATGTCTATTCCTAG 60.413 40.741 0.00 0.00 0.00 3.02
4848 5006 6.370442 CCAACGAACAAACATGTCTATTCCTA 59.630 38.462 0.00 0.00 0.00 2.94
4849 5007 5.181245 CCAACGAACAAACATGTCTATTCCT 59.819 40.000 0.00 0.00 0.00 3.36
4850 5008 5.180492 TCCAACGAACAAACATGTCTATTCC 59.820 40.000 0.00 0.00 0.00 3.01
4851 5009 6.073222 ACTCCAACGAACAAACATGTCTATTC 60.073 38.462 0.00 2.39 0.00 1.75
4852 5010 5.763204 ACTCCAACGAACAAACATGTCTATT 59.237 36.000 0.00 0.00 0.00 1.73
4853 5011 5.305585 ACTCCAACGAACAAACATGTCTAT 58.694 37.500 0.00 0.00 0.00 1.98
4854 5012 4.699637 ACTCCAACGAACAAACATGTCTA 58.300 39.130 0.00 0.00 0.00 2.59
4855 5013 3.541632 ACTCCAACGAACAAACATGTCT 58.458 40.909 0.00 0.00 0.00 3.41
4856 5014 3.963383 ACTCCAACGAACAAACATGTC 57.037 42.857 0.00 0.00 0.00 3.06
4857 5015 3.692101 TGAACTCCAACGAACAAACATGT 59.308 39.130 0.00 0.00 0.00 3.21
4858 5016 4.282068 CTGAACTCCAACGAACAAACATG 58.718 43.478 0.00 0.00 0.00 3.21
4859 5017 3.243068 GCTGAACTCCAACGAACAAACAT 60.243 43.478 0.00 0.00 0.00 2.71
4860 5018 2.096819 GCTGAACTCCAACGAACAAACA 59.903 45.455 0.00 0.00 0.00 2.83
4861 5019 2.540973 GGCTGAACTCCAACGAACAAAC 60.541 50.000 0.00 0.00 0.00 2.93
4862 5020 1.673920 GGCTGAACTCCAACGAACAAA 59.326 47.619 0.00 0.00 0.00 2.83
4863 5021 1.305201 GGCTGAACTCCAACGAACAA 58.695 50.000 0.00 0.00 0.00 2.83
4864 5022 0.534203 GGGCTGAACTCCAACGAACA 60.534 55.000 0.00 0.00 0.00 3.18
4865 5023 1.566018 CGGGCTGAACTCCAACGAAC 61.566 60.000 0.00 0.00 0.00 3.95
4866 5024 1.301401 CGGGCTGAACTCCAACGAA 60.301 57.895 0.00 0.00 0.00 3.85
4867 5025 2.342279 CGGGCTGAACTCCAACGA 59.658 61.111 0.00 0.00 0.00 3.85
4868 5026 3.423154 GCGGGCTGAACTCCAACG 61.423 66.667 0.00 0.00 0.00 4.10
4869 5027 3.056328 GGCGGGCTGAACTCCAAC 61.056 66.667 0.00 0.00 0.00 3.77
4870 5028 3.249189 AGGCGGGCTGAACTCCAA 61.249 61.111 2.09 0.00 0.00 3.53
4871 5029 4.020617 CAGGCGGGCTGAACTCCA 62.021 66.667 25.76 0.00 0.00 3.86
4872 5030 4.785453 CCAGGCGGGCTGAACTCC 62.785 72.222 30.62 0.00 0.00 3.85
4873 5031 2.543067 AATCCAGGCGGGCTGAACTC 62.543 60.000 30.62 0.00 36.21 3.01
4874 5032 2.543067 GAATCCAGGCGGGCTGAACT 62.543 60.000 30.62 14.81 36.21 3.01
4875 5033 2.044946 AATCCAGGCGGGCTGAAC 60.045 61.111 30.62 0.00 36.21 3.18
4876 5034 2.272146 GAATCCAGGCGGGCTGAA 59.728 61.111 30.62 13.80 36.21 3.02
4877 5035 3.797353 GGAATCCAGGCGGGCTGA 61.797 66.667 30.62 17.58 36.21 4.26


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

AutoCloner maintained by Alex Coulton.