Multiple sequence alignment - TraesCS1A01G039500

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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 TraesCS1A01G039500 chr1A 100.000 6195 0 0 1 6195 21705669 21711863 0.000000e+00 11441.0
1 TraesCS1A01G039500 chr5A 96.253 4057 125 19 1 4041 377332708 377328663 0.000000e+00 6625.0
2 TraesCS1A01G039500 chr5A 95.367 1770 63 18 4078 5839 377328660 377326902 0.000000e+00 2796.0
3 TraesCS1A01G039500 chr7B 79.821 223 34 7 5649 5865 16520939 16521156 1.080000e-32 152.0
4 TraesCS1A01G039500 chr7B 84.713 157 17 3 5709 5865 485612388 485612537 3.870000e-32 150.0
5 TraesCS1A01G039500 chr3B 82.166 157 21 5 5709 5865 805341341 805341192 1.810000e-25 128.0
6 TraesCS1A01G039500 chr4A 83.673 98 10 5 6086 6179 331803628 331803723 3.080000e-13 87.9


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 TraesCS1A01G039500 chr1A 21705669 21711863 6194 False 11441.0 11441 100.00 1 6195 1 chr1A.!!$F1 6194
1 TraesCS1A01G039500 chr5A 377326902 377332708 5806 True 4710.5 6625 95.81 1 5839 2 chr5A.!!$R1 5838

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
728 737 1.361543 AGGGGGCTACTACTGACTCAA 59.638 52.381 0.00 0.0 0.00 3.02 F
992 1001 2.162754 GCGCCTGCAACATTGATGC 61.163 57.895 11.60 11.6 44.08 3.91 F
2350 2362 1.269448 CCCCGAACAACCACATTTCAG 59.731 52.381 0.00 0.0 0.00 3.02 F
3438 3454 0.524862 CAGCCAACAGATTCAGCACC 59.475 55.000 0.00 0.0 0.00 5.01 F
3519 3536 2.158928 AGAGATAAAGCAGCAGCAGAGG 60.159 50.000 3.17 0.0 45.49 3.69 F
4567 4586 1.477195 CCGTTTTGTTCCAGTACCCCA 60.477 52.381 0.00 0.0 0.00 4.96 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2350 2362 1.593196 TGTTCAGCTTGCTGGTGTAC 58.407 50.000 20.62 14.05 43.97 2.90 R
2793 2806 1.432514 TCTCATTCGCTTCTGTGTGC 58.567 50.000 0.00 0.00 0.00 4.57 R
3519 3536 0.674895 AAGTTCTGCATCGGTGGCTC 60.675 55.000 0.00 0.00 0.00 4.70 R
4553 4572 1.132977 TGAGTCTGGGGTACTGGAACA 60.133 52.381 0.00 0.00 0.00 3.18 R
4917 4937 2.557924 CCTGTAGGTCATGCTGCAAAAA 59.442 45.455 6.36 0.00 0.00 1.94 R
6159 6182 0.249405 ATTTTTGCACACACCTGGCG 60.249 50.000 0.00 0.00 0.00 5.69 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
74 75 2.276058 GAGTTGCATTCGCGTCGC 60.276 61.111 7.29 7.29 42.97 5.19
158 159 4.985538 ACCAACTATGAGGTCTAGTTCG 57.014 45.455 0.00 0.00 37.33 3.95
253 262 7.096436 CGAACAAACCTATGAGATATCACTTCG 60.096 40.741 5.32 3.70 0.00 3.79
417 426 9.691362 ATATGTAAAACAGGACAAATGAACAAC 57.309 29.630 0.00 0.00 0.00 3.32
423 432 4.340950 ACAGGACAAATGAACAACGGAAAT 59.659 37.500 0.00 0.00 0.00 2.17
429 438 5.768164 ACAAATGAACAACGGAAATACCTCT 59.232 36.000 0.00 0.00 36.31 3.69
460 469 4.902443 TCCGCACAAAATTAGTGAAACA 57.098 36.364 13.43 0.00 41.43 2.83
569 578 9.574516 ACAACTCCTAATTTGTTCAGTTATTCT 57.425 29.630 0.00 0.00 31.78 2.40
610 619 7.288810 ACTAAATGGAAGAAATGTCAGCAAA 57.711 32.000 0.00 0.00 0.00 3.68
688 697 6.940298 CCCAAAAGAAAGAAGGTACATGTAGA 59.060 38.462 5.62 0.00 0.00 2.59
689 698 7.119846 CCCAAAAGAAAGAAGGTACATGTAGAG 59.880 40.741 5.62 0.00 0.00 2.43
706 715 5.061179 TGTAGAGGCCAGAAAAACAACTAC 58.939 41.667 5.01 0.00 0.00 2.73
728 737 1.361543 AGGGGGCTACTACTGACTCAA 59.638 52.381 0.00 0.00 0.00 3.02
731 740 3.965347 GGGGGCTACTACTGACTCAATTA 59.035 47.826 0.00 0.00 0.00 1.40
743 752 9.376075 CTACTGACTCAATTATTTCACTGACAT 57.624 33.333 0.00 0.00 0.00 3.06
883 892 3.181451 TGTCAGCAATGAAGACAACCTCT 60.181 43.478 5.87 0.00 39.15 3.69
948 957 6.766467 AGAAGAACATAGTTCGAAAACTTGGT 59.234 34.615 0.00 0.00 43.28 3.67
951 960 7.768240 AGAACATAGTTCGAAAACTTGGTTTT 58.232 30.769 0.00 7.92 46.51 2.43
965 974 2.649190 TGGTTTTGCTTCACTGCTACA 58.351 42.857 0.00 0.00 0.00 2.74
972 981 3.743521 TGCTTCACTGCTACAAATCAGT 58.256 40.909 0.00 0.00 43.67 3.41
975 984 4.470462 CTTCACTGCTACAAATCAGTTGC 58.530 43.478 0.00 0.00 41.19 4.17
992 1001 2.162754 GCGCCTGCAACATTGATGC 61.163 57.895 11.60 11.60 44.08 3.91
1193 1202 5.902681 TGTACAATCATCAGCACCTACTAC 58.097 41.667 0.00 0.00 0.00 2.73
1231 1240 4.331443 CGATGATTACGGACAACATTTCCA 59.669 41.667 0.00 0.00 31.94 3.53
1264 1273 8.768501 TTTCTCTACTATATTCTTGCTCCTCA 57.231 34.615 0.00 0.00 0.00 3.86
1265 1274 8.948401 TTCTCTACTATATTCTTGCTCCTCAT 57.052 34.615 0.00 0.00 0.00 2.90
1282 1291 6.073112 GCTCCTCATTATCTCAAGCTTGATTC 60.073 42.308 28.57 2.27 36.46 2.52
1343 1352 4.913924 CAGTGCTCTGCAAAACATTAGTTC 59.086 41.667 2.32 0.00 41.47 3.01
1449 1458 2.371658 AGGCATTTTATCCTGGAGGC 57.628 50.000 1.52 0.00 34.44 4.70
1477 1486 7.806487 GCAAACTAATCTTGGTGGTAAGTTTAC 59.194 37.037 0.00 0.00 34.79 2.01
1479 1488 7.974482 ACTAATCTTGGTGGTAAGTTTACAC 57.026 36.000 4.58 2.06 35.37 2.90
1512 1521 8.924511 ATGAACCTAAGATCACTTTTTCTTCA 57.075 30.769 0.00 0.00 37.53 3.02
1541 1550 5.596836 TTTTGACTGCATCCAACTCTTTT 57.403 34.783 0.00 0.00 0.00 2.27
1747 1757 6.371389 GGAAGACTTCCGATAAGTGTTTTTG 58.629 40.000 18.38 0.00 40.59 2.44
1762 1772 7.258022 AGTGTTTTTGCAACAAAAACTCTTT 57.742 28.000 32.07 19.61 44.56 2.52
1988 1999 6.068010 ACAGTACATCAGTTCCAAATTTCCA 58.932 36.000 0.00 0.00 0.00 3.53
2129 2141 6.949578 TGACATGTCACGCACATATATATG 57.050 37.500 24.56 19.21 44.60 1.78
2137 2149 7.602265 TGTCACGCACATATATATGCAAAGTAT 59.398 33.333 20.46 0.00 42.17 2.12
2274 2286 3.861840 TCTCCATTCGACAATCTCCAAC 58.138 45.455 0.00 0.00 0.00 3.77
2280 2292 4.811555 TTCGACAATCTCCAACAGTTTG 57.188 40.909 0.00 0.00 37.69 2.93
2350 2362 1.269448 CCCCGAACAACCACATTTCAG 59.731 52.381 0.00 0.00 0.00 3.02
2490 2502 5.534278 GGAAAAGGAAGATGGAGATTCATCC 59.466 44.000 0.00 0.00 43.25 3.51
2518 2530 5.972107 ATGGTTGGACAAGAAATTCTCAG 57.028 39.130 0.00 0.00 0.00 3.35
2545 2557 6.016276 GTGCCTCCTTTTAGAAAACTCATCAA 60.016 38.462 0.00 0.00 0.00 2.57
2571 2583 4.836125 TGATGACCTGTTTCAGAAAAGC 57.164 40.909 0.00 0.00 32.44 3.51
2572 2584 3.569701 TGATGACCTGTTTCAGAAAAGCC 59.430 43.478 0.00 0.00 32.44 4.35
2646 2658 6.549242 TGACTACCCAGATATCGATTTCCTA 58.451 40.000 1.71 0.00 0.00 2.94
2658 2670 9.930693 GATATCGATTTCCTACAAGGTAATTCT 57.069 33.333 1.71 0.00 35.80 2.40
2793 2806 9.119329 GCAGTACTCAAAGATTACATCTATACG 57.881 37.037 0.00 0.00 39.08 3.06
2866 2879 5.774498 AGAGAAATTCTGTTTGACCCAAC 57.226 39.130 0.00 0.00 33.93 3.77
3062 3077 1.673920 CTGTTTGCAACAAGGTACGGT 59.326 47.619 0.00 0.00 41.61 4.83
3076 3091 2.096762 GGTACGGTTTCAACAACTACGC 60.097 50.000 0.00 0.00 0.00 4.42
3101 3116 4.141482 TGCCCTAGATGTTTCCAGGAATAC 60.141 45.833 1.58 5.25 0.00 1.89
3106 3121 6.821665 CCTAGATGTTTCCAGGAATACGAAAA 59.178 38.462 1.58 0.00 0.00 2.29
3120 3135 1.241744 CGAAAAGCTCGCAATCAACG 58.758 50.000 0.00 0.00 41.49 4.10
3127 3142 1.699656 CTCGCAATCAACGCCTCCTG 61.700 60.000 0.00 0.00 0.00 3.86
3184 3199 2.864343 GGTAGTACATCCAATGCGTGTC 59.136 50.000 2.06 0.00 0.00 3.67
3192 3207 0.597568 CCAATGCGTGTCAACCACAT 59.402 50.000 0.00 0.00 44.78 3.21
3298 3314 4.463891 ACCAAGCAAATTATTCACCTCCTG 59.536 41.667 0.00 0.00 0.00 3.86
3362 3378 5.001232 TGTAAGGAATTCAGGTAGCAACAC 58.999 41.667 7.93 0.00 0.00 3.32
3366 3382 4.018960 AGGAATTCAGGTAGCAACACTCAT 60.019 41.667 7.93 0.00 0.00 2.90
3387 3403 2.174685 TCCTCTATAGCAACAGCCCA 57.825 50.000 0.00 0.00 0.00 5.36
3433 3449 3.638160 AGAAAAAGCAGCCAACAGATTCA 59.362 39.130 0.00 0.00 0.00 2.57
3435 3451 0.886563 AAGCAGCCAACAGATTCAGC 59.113 50.000 0.00 0.00 0.00 4.26
3438 3454 0.524862 CAGCCAACAGATTCAGCACC 59.475 55.000 0.00 0.00 0.00 5.01
3467 3484 4.164221 CCAGACCCTATCATGTACCAAGTT 59.836 45.833 0.00 0.00 0.00 2.66
3470 3487 6.323996 CAGACCCTATCATGTACCAAGTTCTA 59.676 42.308 0.00 0.00 0.00 2.10
3519 3536 2.158928 AGAGATAAAGCAGCAGCAGAGG 60.159 50.000 3.17 0.00 45.49 3.69
3528 3545 3.385384 CAGCAGAGGAGCCACCGA 61.385 66.667 0.00 0.00 44.74 4.69
3552 3569 3.371591 GCAGAACTTCTCTTCAGCATCAG 59.628 47.826 0.00 0.00 33.90 2.90
3562 3579 3.822167 TCTTCAGCATCAGAATTGCACAA 59.178 39.130 0.00 0.00 42.62 3.33
3582 3599 4.335315 ACAAAACAACTCAGCTCAATTCGA 59.665 37.500 0.00 0.00 0.00 3.71
3673 3690 9.685276 TCATATAGACATCAGGTGAAAATGTTT 57.315 29.630 0.00 0.00 33.91 2.83
3685 3702 7.923344 CAGGTGAAAATGTTTTGTACATGGTTA 59.077 33.333 0.00 0.00 46.75 2.85
3738 3755 4.096382 CCACCATGCTTCATTACTACCAAC 59.904 45.833 0.00 0.00 0.00 3.77
3956 3973 2.839486 ATTGTCCATATCGTCGGCAT 57.161 45.000 0.00 0.00 0.00 4.40
3961 3978 3.319689 TGTCCATATCGTCGGCATAGAAA 59.680 43.478 0.00 0.00 0.00 2.52
4266 4283 9.185192 CGAGCAAATCATTCTAAAAAGAAAACT 57.815 29.630 0.00 0.00 0.00 2.66
4387 4406 6.061441 ACAAACAGTGGATTGTAATCACTGA 58.939 36.000 25.92 3.87 41.60 3.41
4406 4425 4.516698 ACTGATAACTTTGACAGTGGCAAG 59.483 41.667 12.09 8.87 41.16 4.01
4424 4443 9.193806 AGTGGCAAGTTCTTTGATATAATGAAT 57.806 29.630 0.00 0.00 39.21 2.57
4455 4474 6.775142 TGGATCTGGAAACAACAAATTCACTA 59.225 34.615 0.00 0.00 42.06 2.74
4567 4586 1.477195 CCGTTTTGTTCCAGTACCCCA 60.477 52.381 0.00 0.00 0.00 4.96
4628 4648 6.449635 TTTTTCTGTGCACTGTACTCAAAT 57.550 33.333 19.41 0.00 0.00 2.32
4630 4650 7.561021 TTTTCTGTGCACTGTACTCAAATTA 57.439 32.000 19.41 0.00 0.00 1.40
4632 4652 7.744087 TTCTGTGCACTGTACTCAAATTAAT 57.256 32.000 19.41 0.00 0.00 1.40
4634 4654 8.840833 TCTGTGCACTGTACTCAAATTAATTA 57.159 30.769 19.41 0.00 0.00 1.40
4635 4655 9.278978 TCTGTGCACTGTACTCAAATTAATTAA 57.721 29.630 19.41 0.00 0.00 1.40
4816 4836 7.280652 GCTGCCCATGTAAATAATTTGTTGATT 59.719 33.333 0.00 0.00 0.00 2.57
4958 4978 6.986250 ACAGGCCTTAAGAGAAATTTTTCTG 58.014 36.000 11.67 1.47 46.84 3.02
5043 5063 3.530265 ATCACGTTAGTTCCGCCATTA 57.470 42.857 0.00 0.00 0.00 1.90
5068 5088 7.253421 AGAAAACCTCCCCCTACATTTTTAAT 58.747 34.615 0.00 0.00 0.00 1.40
5199 5219 2.103094 TCCGGCTATTCAGGTGAATCAG 59.897 50.000 8.49 6.64 43.17 2.90
5202 5222 4.262635 CCGGCTATTCAGGTGAATCAGTAT 60.263 45.833 8.49 0.00 43.17 2.12
5244 5264 7.819644 TCAAGATACAAGATGACCACATTTTG 58.180 34.615 10.43 10.43 46.84 2.44
5248 5268 7.830697 AGATACAAGATGACCACATTTTGATCA 59.169 33.333 16.34 0.00 45.42 2.92
5257 5277 7.894708 TGACCACATTTTGATCACATAAACAT 58.105 30.769 0.00 0.00 0.00 2.71
5317 5337 5.652518 ACTAATTTCCTTCTCGTGCTACTC 58.347 41.667 0.00 0.00 0.00 2.59
5325 5345 3.132629 TCTCGTGCTACTCGAATGAAC 57.867 47.619 0.00 0.00 36.89 3.18
5328 5348 3.845178 TCGTGCTACTCGAATGAACAAT 58.155 40.909 0.00 0.00 34.36 2.71
5346 5366 4.946646 ACAATATGTTGAGGGGGTCATTT 58.053 39.130 9.40 0.00 38.71 2.32
5347 5367 4.711355 ACAATATGTTGAGGGGGTCATTTG 59.289 41.667 9.40 0.00 38.71 2.32
5349 5369 2.765689 TGTTGAGGGGGTCATTTGTT 57.234 45.000 0.00 0.00 34.17 2.83
5350 5370 2.593026 TGTTGAGGGGGTCATTTGTTC 58.407 47.619 0.00 0.00 34.17 3.18
5354 5374 3.647636 TGAGGGGGTCATTTGTTCAAAA 58.352 40.909 2.11 0.00 0.00 2.44
5495 5516 0.883833 AAGGCACGAGCAAAATCTGG 59.116 50.000 7.26 0.00 44.61 3.86
5634 5656 0.530744 TAGGAATGCTCGCTGACGTT 59.469 50.000 0.00 0.00 41.18 3.99
5715 5738 0.465460 ACAGCGAAACAGAAGGGCAA 60.465 50.000 0.00 0.00 0.00 4.52
5740 5763 3.501349 AGCACAGAAACAGTAGAGGAGA 58.499 45.455 0.00 0.00 0.00 3.71
5851 5874 4.463879 CTCAGTGGGCGCCAGGAG 62.464 72.222 30.85 22.87 32.34 3.69
5853 5876 4.767255 CAGTGGGCGCCAGGAGAC 62.767 72.222 30.85 15.60 32.34 3.36
5860 5883 4.796231 CGCCAGGAGACCGAACCG 62.796 72.222 0.00 0.00 0.00 4.44
5871 5894 4.137872 CGAACCGGCGCCTTAGGA 62.138 66.667 26.68 0.00 0.00 2.94
5872 5895 2.202892 GAACCGGCGCCTTAGGAG 60.203 66.667 26.68 7.40 0.00 3.69
5873 5896 2.682494 AACCGGCGCCTTAGGAGA 60.682 61.111 26.68 0.00 0.00 3.71
5874 5897 2.029307 GAACCGGCGCCTTAGGAGAT 62.029 60.000 26.68 10.23 0.00 2.75
5875 5898 2.029666 CCGGCGCCTTAGGAGATG 59.970 66.667 26.68 4.88 0.00 2.90
5876 5899 2.797278 CCGGCGCCTTAGGAGATGT 61.797 63.158 26.68 0.00 0.00 3.06
5877 5900 1.144057 CGGCGCCTTAGGAGATGTT 59.856 57.895 26.68 0.00 0.00 2.71
5878 5901 0.462047 CGGCGCCTTAGGAGATGTTT 60.462 55.000 26.68 0.00 0.00 2.83
5879 5902 1.751437 GGCGCCTTAGGAGATGTTTT 58.249 50.000 22.15 0.00 0.00 2.43
5880 5903 2.092323 GGCGCCTTAGGAGATGTTTTT 58.908 47.619 22.15 0.00 0.00 1.94
5881 5904 2.159379 GGCGCCTTAGGAGATGTTTTTG 60.159 50.000 22.15 0.00 0.00 2.44
5882 5905 2.488153 GCGCCTTAGGAGATGTTTTTGT 59.512 45.455 6.10 0.00 0.00 2.83
5883 5906 3.057526 GCGCCTTAGGAGATGTTTTTGTT 60.058 43.478 6.10 0.00 0.00 2.83
5884 5907 4.475944 CGCCTTAGGAGATGTTTTTGTTG 58.524 43.478 0.69 0.00 0.00 3.33
5885 5908 4.023193 CGCCTTAGGAGATGTTTTTGTTGT 60.023 41.667 0.69 0.00 0.00 3.32
5886 5909 5.507315 CGCCTTAGGAGATGTTTTTGTTGTT 60.507 40.000 0.69 0.00 0.00 2.83
5887 5910 5.691754 GCCTTAGGAGATGTTTTTGTTGTTG 59.308 40.000 0.69 0.00 0.00 3.33
5888 5911 5.691754 CCTTAGGAGATGTTTTTGTTGTTGC 59.308 40.000 0.00 0.00 0.00 4.17
5889 5912 4.058721 AGGAGATGTTTTTGTTGTTGCC 57.941 40.909 0.00 0.00 0.00 4.52
5890 5913 3.130633 GGAGATGTTTTTGTTGTTGCCC 58.869 45.455 0.00 0.00 0.00 5.36
5891 5914 3.431486 GGAGATGTTTTTGTTGTTGCCCA 60.431 43.478 0.00 0.00 0.00 5.36
5892 5915 4.379652 GAGATGTTTTTGTTGTTGCCCAT 58.620 39.130 0.00 0.00 0.00 4.00
5893 5916 4.379652 AGATGTTTTTGTTGTTGCCCATC 58.620 39.130 0.00 0.00 0.00 3.51
5894 5917 3.902881 TGTTTTTGTTGTTGCCCATCT 57.097 38.095 0.00 0.00 0.00 2.90
5895 5918 5.304101 AGATGTTTTTGTTGTTGCCCATCTA 59.696 36.000 0.00 0.00 36.83 1.98
5896 5919 4.688021 TGTTTTTGTTGTTGCCCATCTAC 58.312 39.130 0.00 0.00 0.00 2.59
5897 5920 4.404073 TGTTTTTGTTGTTGCCCATCTACT 59.596 37.500 0.00 0.00 0.00 2.57
5898 5921 5.105146 TGTTTTTGTTGTTGCCCATCTACTT 60.105 36.000 0.00 0.00 0.00 2.24
5899 5922 5.606348 TTTTGTTGTTGCCCATCTACTTT 57.394 34.783 0.00 0.00 0.00 2.66
5900 5923 5.606348 TTTGTTGTTGCCCATCTACTTTT 57.394 34.783 0.00 0.00 0.00 2.27
5901 5924 5.606348 TTGTTGTTGCCCATCTACTTTTT 57.394 34.783 0.00 0.00 0.00 1.94
5993 6016 8.859236 TTTTGAATGCATGGATATTTTTGGAA 57.141 26.923 0.00 0.00 0.00 3.53
5994 6017 8.859236 TTTGAATGCATGGATATTTTTGGAAA 57.141 26.923 0.00 0.00 0.00 3.13
5995 6018 8.859236 TTGAATGCATGGATATTTTTGGAAAA 57.141 26.923 0.00 0.00 0.00 2.29
5996 6019 8.859236 TGAATGCATGGATATTTTTGGAAAAA 57.141 26.923 0.00 0.00 41.59 1.94
6092 6115 9.942850 AATTTCTTAATTTTCCCGATGAACAAT 57.057 25.926 0.00 0.00 29.68 2.71
6100 6123 9.717942 AATTTTCCCGATGAACAATAAATCAAA 57.282 25.926 0.00 0.00 31.05 2.69
6101 6124 9.717942 ATTTTCCCGATGAACAATAAATCAAAA 57.282 25.926 0.00 0.00 31.05 2.44
6102 6125 9.717942 TTTTCCCGATGAACAATAAATCAAAAT 57.282 25.926 0.00 0.00 31.05 1.82
6144 6167 5.580911 AAAGTCTGAAATTTTTCGCATGC 57.419 34.783 7.91 7.91 40.01 4.06
6145 6168 4.241590 AGTCTGAAATTTTTCGCATGCA 57.758 36.364 19.57 1.73 40.01 3.96
6146 6169 4.619973 AGTCTGAAATTTTTCGCATGCAA 58.380 34.783 19.57 8.45 40.01 4.08
6147 6170 4.682860 AGTCTGAAATTTTTCGCATGCAAG 59.317 37.500 19.57 1.83 40.01 4.01
6148 6171 4.681025 GTCTGAAATTTTTCGCATGCAAGA 59.319 37.500 19.57 4.66 40.01 3.02
6149 6172 5.346822 GTCTGAAATTTTTCGCATGCAAGAT 59.653 36.000 19.57 3.20 40.01 2.40
6150 6173 5.346551 TCTGAAATTTTTCGCATGCAAGATG 59.653 36.000 19.57 0.14 40.01 2.90
6151 6174 4.143073 TGAAATTTTTCGCATGCAAGATGC 60.143 37.500 19.57 0.49 40.97 3.91
6152 6175 2.728690 TTTTTCGCATGCAAGATGCT 57.271 40.000 19.57 0.00 45.31 3.79
6153 6176 2.728690 TTTTCGCATGCAAGATGCTT 57.271 40.000 19.57 0.00 45.31 3.91
6154 6177 9.611627 TGAAATTTTTCGCATGCAAGATGCTTG 62.612 37.037 19.57 12.34 41.08 4.01
6160 6183 0.450583 ATGCAAGATGCTTGAGTGCG 59.549 50.000 11.08 0.00 45.31 5.34
6161 6184 1.513586 GCAAGATGCTTGAGTGCGC 60.514 57.895 11.08 0.00 40.96 6.09
6162 6185 1.136147 CAAGATGCTTGAGTGCGCC 59.864 57.895 4.18 0.00 35.36 6.53
6163 6186 1.302752 AAGATGCTTGAGTGCGCCA 60.303 52.632 4.18 0.00 35.36 5.69
6164 6187 1.303799 AAGATGCTTGAGTGCGCCAG 61.304 55.000 4.18 0.00 35.36 4.85
6165 6188 2.749044 ATGCTTGAGTGCGCCAGG 60.749 61.111 4.18 0.00 35.36 4.45
6166 6189 3.557903 ATGCTTGAGTGCGCCAGGT 62.558 57.895 4.18 0.00 35.36 4.00
6167 6190 3.730761 GCTTGAGTGCGCCAGGTG 61.731 66.667 4.18 0.00 0.00 4.00
6168 6191 2.281070 CTTGAGTGCGCCAGGTGT 60.281 61.111 4.18 0.00 0.00 4.16
6169 6192 2.591429 TTGAGTGCGCCAGGTGTG 60.591 61.111 4.18 0.00 0.00 3.82
6170 6193 3.399105 TTGAGTGCGCCAGGTGTGT 62.399 57.895 4.18 0.00 0.00 3.72
6171 6194 3.349006 GAGTGCGCCAGGTGTGTG 61.349 66.667 4.18 0.00 0.00 3.82
6175 6198 3.898509 GCGCCAGGTGTGTGCAAA 61.899 61.111 0.00 0.00 39.02 3.68
6176 6199 2.804167 CGCCAGGTGTGTGCAAAA 59.196 55.556 0.00 0.00 0.00 2.44
6177 6200 1.140589 CGCCAGGTGTGTGCAAAAA 59.859 52.632 0.00 0.00 0.00 1.94
6178 6201 0.249405 CGCCAGGTGTGTGCAAAAAT 60.249 50.000 0.00 0.00 0.00 1.82
6179 6202 1.000827 CGCCAGGTGTGTGCAAAAATA 60.001 47.619 0.00 0.00 0.00 1.40
6180 6203 2.352617 CGCCAGGTGTGTGCAAAAATAT 60.353 45.455 0.00 0.00 0.00 1.28
6181 6204 2.995258 GCCAGGTGTGTGCAAAAATATG 59.005 45.455 0.00 0.00 0.00 1.78
6182 6205 3.554752 GCCAGGTGTGTGCAAAAATATGT 60.555 43.478 0.00 0.00 0.00 2.29
6183 6206 3.989167 CCAGGTGTGTGCAAAAATATGTG 59.011 43.478 0.00 0.00 0.00 3.21
6184 6207 3.989167 CAGGTGTGTGCAAAAATATGTGG 59.011 43.478 0.00 0.00 0.00 4.17
6185 6208 3.006752 AGGTGTGTGCAAAAATATGTGGG 59.993 43.478 0.00 0.00 0.00 4.61
6186 6209 2.736192 GTGTGTGCAAAAATATGTGGGC 59.264 45.455 0.00 0.00 0.00 5.36
6187 6210 2.366590 TGTGTGCAAAAATATGTGGGCA 59.633 40.909 0.00 0.00 0.00 5.36
6188 6211 3.181462 TGTGTGCAAAAATATGTGGGCAA 60.181 39.130 0.00 0.00 32.50 4.52
6189 6212 3.812053 GTGTGCAAAAATATGTGGGCAAA 59.188 39.130 0.00 0.00 32.50 3.68
6190 6213 3.812053 TGTGCAAAAATATGTGGGCAAAC 59.188 39.130 0.00 0.00 32.50 2.93
6191 6214 3.812053 GTGCAAAAATATGTGGGCAAACA 59.188 39.130 0.00 0.00 32.50 2.83
6192 6215 4.274459 GTGCAAAAATATGTGGGCAAACAA 59.726 37.500 0.00 0.00 32.81 2.83
6193 6216 4.274459 TGCAAAAATATGTGGGCAAACAAC 59.726 37.500 0.00 0.00 32.81 3.32
6194 6217 4.274459 GCAAAAATATGTGGGCAAACAACA 59.726 37.500 0.00 0.00 32.81 3.33
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 4.210537 ACGATGAGTAAACAGTCCAAAACG 59.789 41.667 0.00 0.00 0.00 3.60
6 7 5.361427 TCACGATGAGTAAACAGTCCAAAA 58.639 37.500 0.00 0.00 0.00 2.44
49 50 0.522626 CGAATGCAACTCACATGCCA 59.477 50.000 0.00 0.00 43.16 4.92
74 75 1.579698 TAGTCGCAGTAGTAGAGCCG 58.420 55.000 0.00 0.00 0.00 5.52
158 159 6.657836 AATGTTTGTGGCTCGTACTATAAC 57.342 37.500 0.00 0.00 0.00 1.89
298 307 6.867519 TGTTCCCAACTCATATCTACAGAA 57.132 37.500 0.00 0.00 0.00 3.02
339 348 3.664107 GTTGGACTGCAGTACATTCTCA 58.336 45.455 31.90 14.53 38.92 3.27
417 426 6.322491 GGATTGTCAAAAAGAGGTATTTCCG 58.678 40.000 0.00 0.00 41.99 4.30
423 432 3.500680 GTGCGGATTGTCAAAAAGAGGTA 59.499 43.478 0.00 0.00 0.00 3.08
429 438 6.758886 ACTAATTTTGTGCGGATTGTCAAAAA 59.241 30.769 7.13 0.00 41.07 1.94
569 578 9.540538 TCCATTTAGTTGAATTCCTGGAAAATA 57.459 29.630 14.03 0.00 0.00 1.40
576 585 9.362539 CATTTCTTCCATTTAGTTGAATTCCTG 57.637 33.333 2.27 0.00 0.00 3.86
610 619 4.392940 CAGATGTTGGTTGTTCCTCTTCT 58.607 43.478 0.00 0.00 37.07 2.85
653 662 7.179160 ACCTTCTTTCTTTTGGGAGGATTATTG 59.821 37.037 0.00 0.00 0.00 1.90
688 697 3.222603 CTGGTAGTTGTTTTTCTGGCCT 58.777 45.455 3.32 0.00 0.00 5.19
689 698 2.296190 CCTGGTAGTTGTTTTTCTGGCC 59.704 50.000 0.00 0.00 0.00 5.36
706 715 0.032017 AGTCAGTAGTAGCCCCCTGG 60.032 60.000 0.00 0.00 0.00 4.45
728 737 7.447374 TTGAAACGGATGTCAGTGAAATAAT 57.553 32.000 0.00 0.00 0.00 1.28
731 740 5.964958 ATTGAAACGGATGTCAGTGAAAT 57.035 34.783 0.00 0.00 0.00 2.17
948 957 5.512753 TGATTTGTAGCAGTGAAGCAAAA 57.487 34.783 0.00 0.00 36.85 2.44
975 984 0.734309 TAGCATCAATGTTGCAGGCG 59.266 50.000 17.28 0.00 42.62 5.52
992 1001 6.331845 TGTAATGCAAGCCACATGAAAATAG 58.668 36.000 0.00 0.00 0.00 1.73
1044 1053 7.543359 TTCAAAATTGAATCCATTCCTCAGT 57.457 32.000 4.52 0.00 41.88 3.41
1193 1202 5.608676 AATCATCGCAATAAGATGCTCTG 57.391 39.130 1.67 0.00 44.21 3.35
1264 1273 6.512514 AGGAGGAATCAAGCTTGAGATAAT 57.487 37.500 31.14 17.23 41.08 1.28
1265 1274 5.965033 AGGAGGAATCAAGCTTGAGATAA 57.035 39.130 31.14 11.11 41.08 1.75
1282 1291 2.289565 GGAACCTTTCGCATTAGGAGG 58.710 52.381 0.00 0.00 35.45 4.30
1343 1352 1.888512 ACCAGTTGTATTTGCCAGCAG 59.111 47.619 0.00 0.00 0.00 4.24
1449 1458 5.473504 ACTTACCACCAAGATTAGTTTGCAG 59.526 40.000 0.00 0.00 0.00 4.41
1512 1521 8.370182 AGAGTTGGATGCAGTCAAAAATTAAAT 58.630 29.630 6.14 0.00 0.00 1.40
1523 1532 5.444663 AAAGAAAAGAGTTGGATGCAGTC 57.555 39.130 0.00 0.00 0.00 3.51
1568 1578 4.095782 GCGCAACCTGATATTAGGAACAAA 59.904 41.667 19.88 0.00 40.42 2.83
1735 1745 8.546597 AGAGTTTTTGTTGCAAAAACACTTAT 57.453 26.923 32.81 21.24 46.78 1.73
1747 1757 7.258441 AGAGAAGGTAAAAGAGTTTTTGTTGC 58.742 34.615 0.00 0.00 37.12 4.17
1818 1829 9.170734 GACCTACGTAGAATACATATATGTGGA 57.829 37.037 25.48 9.47 43.24 4.02
1866 1877 5.863397 ACTGTTTTGCATCATAAATGAACCG 59.137 36.000 0.00 0.00 40.69 4.44
1988 1999 7.016153 TCCAACCTGTAAGTTGTAGATTGAT 57.984 36.000 3.95 0.00 44.60 2.57
2027 2038 9.745880 CATGATAAGAAGAAAATGGAAGAATGG 57.254 33.333 0.00 0.00 0.00 3.16
2102 2114 9.822185 ATATATATGTGCGTGACATGTCAATAT 57.178 29.630 29.42 25.80 45.43 1.28
2158 2170 2.125773 AGCATTGCCTTCTCCTGAAG 57.874 50.000 4.70 0.00 46.82 3.02
2173 2185 7.893124 ATTTCTTGGTCATATCTTCAAGCAT 57.107 32.000 0.00 0.00 37.21 3.79
2274 2286 4.037803 TCATTGTTGATGTGGGTCAAACTG 59.962 41.667 0.00 0.00 39.61 3.16
2280 2292 5.163513 GTCATTTCATTGTTGATGTGGGTC 58.836 41.667 0.00 0.00 37.06 4.46
2350 2362 1.593196 TGTTCAGCTTGCTGGTGTAC 58.407 50.000 20.62 14.05 43.97 2.90
2490 2502 7.156673 AGAATTTCTTGTCCAACCATTGAATG 58.843 34.615 0.00 0.00 0.00 2.67
2545 2557 4.025040 TCTGAAACAGGTCATCAATGCT 57.975 40.909 0.00 0.00 31.51 3.79
2571 2583 3.387699 ACAAATCTTCAAAGGTTGGTGGG 59.612 43.478 0.00 0.00 32.11 4.61
2572 2584 4.670896 ACAAATCTTCAAAGGTTGGTGG 57.329 40.909 0.00 0.00 32.11 4.61
2617 2629 9.522804 GAAATCGATATCTGGGTAGTCATATTC 57.477 37.037 0.00 0.00 0.00 1.75
2677 2689 6.042437 AGGAGAAACATGCTGGAAAAGAAAAT 59.958 34.615 0.00 0.00 0.00 1.82
2681 2693 4.104383 AGGAGAAACATGCTGGAAAAGA 57.896 40.909 0.00 0.00 0.00 2.52
2793 2806 1.432514 TCTCATTCGCTTCTGTGTGC 58.567 50.000 0.00 0.00 0.00 4.57
2810 2823 6.808829 TCAATTTTGTCTGTTTCTTGCATCT 58.191 32.000 0.00 0.00 0.00 2.90
3062 3077 1.335496 GGGCAAGCGTAGTTGTTGAAA 59.665 47.619 0.00 0.00 0.00 2.69
3076 3091 2.239654 TCCTGGAAACATCTAGGGCAAG 59.760 50.000 8.18 0.00 41.51 4.01
3106 3121 2.046892 AGGCGTTGATTGCGAGCT 60.047 55.556 0.00 0.00 0.00 4.09
3118 3133 2.056906 AAACTTCTGGCAGGAGGCGT 62.057 55.000 26.16 8.79 46.16 5.68
3120 3135 0.884514 GAAAACTTCTGGCAGGAGGC 59.115 55.000 26.16 9.28 43.74 4.70
3127 3142 2.031870 AGTGGTTGGAAAACTTCTGGC 58.968 47.619 0.00 0.00 32.01 4.85
3184 3199 9.888878 GATGTCAATATCTGAATTATGTGGTTG 57.111 33.333 0.00 0.00 35.22 3.77
3298 3314 3.430453 TGGGAAGGATTGATGAACAACC 58.570 45.455 0.00 0.00 41.52 3.77
3362 3378 4.754114 GGCTGTTGCTATAGAGGAAATGAG 59.246 45.833 3.21 0.00 34.43 2.90
3366 3382 2.843730 TGGGCTGTTGCTATAGAGGAAA 59.156 45.455 3.21 0.00 34.43 3.13
3387 3403 5.191722 TGAAGAATTGTGATAGGCCCTAAGT 59.808 40.000 0.00 0.00 0.00 2.24
3394 3410 6.529477 GCTTTTTCTGAAGAATTGTGATAGGC 59.471 38.462 0.00 0.00 33.54 3.93
3395 3411 7.596494 TGCTTTTTCTGAAGAATTGTGATAGG 58.404 34.615 0.00 0.00 33.54 2.57
3433 3449 2.001269 GGGTCTGGTATGGGGTGCT 61.001 63.158 0.00 0.00 0.00 4.40
3435 3451 1.978580 GATAGGGTCTGGTATGGGGTG 59.021 57.143 0.00 0.00 0.00 4.61
3438 3454 3.251484 ACATGATAGGGTCTGGTATGGG 58.749 50.000 0.00 0.00 0.00 4.00
3467 3484 9.896645 AAACATTCAGCTTCATAATCTTCTAGA 57.103 29.630 0.00 0.00 0.00 2.43
3470 3487 7.122353 AGCAAACATTCAGCTTCATAATCTTCT 59.878 33.333 0.00 0.00 34.37 2.85
3519 3536 0.674895 AAGTTCTGCATCGGTGGCTC 60.675 55.000 0.00 0.00 0.00 4.70
3552 3569 4.114794 AGCTGAGTTGTTTTGTGCAATTC 58.885 39.130 0.00 0.00 34.51 2.17
3562 3579 5.163663 TGTTTCGAATTGAGCTGAGTTGTTT 60.164 36.000 0.00 0.00 0.00 2.83
3582 3599 6.476706 GCTGCTGTTGAGAAAATAACTTGTTT 59.523 34.615 0.00 0.00 0.00 2.83
3703 3720 6.007076 TGAAGCATGGTGGTGAAAATTAGTA 58.993 36.000 0.00 0.00 0.00 1.82
3930 3947 3.912563 CGACGATATGGACAATAGGTTCG 59.087 47.826 0.00 0.00 30.51 3.95
3987 4004 8.859090 TCTTTGTGTGATGAAAAACCAAGATAT 58.141 29.630 0.00 0.00 0.00 1.63
3997 4014 7.067372 ACTCATGTCTTCTTTGTGTGATGAAAA 59.933 33.333 0.00 0.00 0.00 2.29
4056 4073 9.967451 TGTAGACAAAATAGGAATAATCACCAA 57.033 29.630 0.00 0.00 0.00 3.67
4057 4074 9.391006 GTGTAGACAAAATAGGAATAATCACCA 57.609 33.333 0.00 0.00 0.00 4.17
4058 4075 9.391006 TGTGTAGACAAAATAGGAATAATCACC 57.609 33.333 0.00 0.00 0.00 4.02
4066 4083 9.952030 TGTATGAATGTGTAGACAAAATAGGAA 57.048 29.630 0.00 0.00 35.11 3.36
4067 4084 9.952030 TTGTATGAATGTGTAGACAAAATAGGA 57.048 29.630 0.00 0.00 35.11 2.94
4074 4091 9.772973 AGTAAGTTTGTATGAATGTGTAGACAA 57.227 29.630 0.00 0.00 35.11 3.18
4075 4092 9.419297 GAGTAAGTTTGTATGAATGTGTAGACA 57.581 33.333 0.00 0.00 36.22 3.41
4076 4093 9.640963 AGAGTAAGTTTGTATGAATGTGTAGAC 57.359 33.333 0.00 0.00 0.00 2.59
4110 4127 9.519191 TCATTAGAAGTTCCTGATGAAAAATGA 57.481 29.630 0.00 0.00 36.59 2.57
4266 4283 7.560368 AGTGGAACATAAAAATTTGGTGTTCA 58.440 30.769 27.10 18.11 44.52 3.18
4387 4406 5.133221 AGAACTTGCCACTGTCAAAGTTAT 58.867 37.500 10.35 6.47 36.83 1.89
4455 4474 7.686438 TGAATGTAACAGTGCTGATAATTGT 57.314 32.000 6.17 0.00 0.00 2.71
4553 4572 1.132977 TGAGTCTGGGGTACTGGAACA 60.133 52.381 0.00 0.00 0.00 3.18
4567 4586 8.432805 TCTTTCTTTTCTACCTGAAATGAGTCT 58.567 33.333 0.00 0.00 44.27 3.24
4635 4655 9.592720 GCGCAAAAATATTACAAAGTGAAAAAT 57.407 25.926 0.30 0.00 0.00 1.82
4638 4658 7.436673 AGTGCGCAAAAATATTACAAAGTGAAA 59.563 29.630 14.00 0.00 0.00 2.69
4647 4667 6.782150 AGTTAGGAGTGCGCAAAAATATTAC 58.218 36.000 14.00 4.11 0.00 1.89
4786 4806 6.070881 ACAAATTATTTACATGGGCAGCTTGA 60.071 34.615 0.00 0.00 0.00 3.02
4917 4937 2.557924 CCTGTAGGTCATGCTGCAAAAA 59.442 45.455 6.36 0.00 0.00 1.94
4958 4978 3.922240 TGGAACAAGTCGCTATTTCGTAC 59.078 43.478 0.00 0.00 31.92 3.67
5043 5063 4.759793 AAAATGTAGGGGGAGGTTTTCT 57.240 40.909 0.00 0.00 0.00 2.52
5199 5219 7.816640 TCTTGAACATGGTTTAAGCTGAATAC 58.183 34.615 8.30 0.00 0.00 1.89
5202 5222 6.899393 ATCTTGAACATGGTTTAAGCTGAA 57.101 33.333 8.30 0.00 0.00 3.02
5212 5232 5.882557 GGTCATCTTGTATCTTGAACATGGT 59.117 40.000 0.00 0.00 0.00 3.55
5216 5236 5.863965 TGTGGTCATCTTGTATCTTGAACA 58.136 37.500 0.00 0.00 33.61 3.18
5278 5298 8.826765 AGGAAATTAGTTCTCATTTGGTAGAGA 58.173 33.333 0.00 0.00 39.01 3.10
5289 5309 4.929808 GCACGAGAAGGAAATTAGTTCTCA 59.070 41.667 17.79 0.00 44.33 3.27
5297 5317 3.192844 TCGAGTAGCACGAGAAGGAAATT 59.807 43.478 0.00 0.00 34.85 1.82
5317 5337 4.036734 CCCCCTCAACATATTGTTCATTCG 59.963 45.833 0.00 0.00 38.77 3.34
5325 5345 4.711355 ACAAATGACCCCCTCAACATATTG 59.289 41.667 0.00 0.00 37.14 1.90
5328 5348 4.202620 TGAACAAATGACCCCCTCAACATA 60.203 41.667 0.00 0.00 30.60 2.29
5383 5403 7.759489 AGGAAGCATTGAATGTTTAGTACAA 57.241 32.000 7.24 0.00 40.89 2.41
5451 5471 9.834628 TTGTTTTGGAGAAGTAATTATTAAGCG 57.165 29.630 0.00 0.00 0.00 4.68
5601 5623 7.540745 GCGAGCATTCCTATTTTTCTTTGTAAA 59.459 33.333 0.00 0.00 0.00 2.01
5602 5624 7.027161 GCGAGCATTCCTATTTTTCTTTGTAA 58.973 34.615 0.00 0.00 0.00 2.41
5603 5625 6.374333 AGCGAGCATTCCTATTTTTCTTTGTA 59.626 34.615 0.00 0.00 0.00 2.41
5608 5630 4.333926 GTCAGCGAGCATTCCTATTTTTCT 59.666 41.667 0.00 0.00 0.00 2.52
5609 5631 4.592179 GTCAGCGAGCATTCCTATTTTTC 58.408 43.478 0.00 0.00 0.00 2.29
5620 5642 2.363788 TTTCTAACGTCAGCGAGCAT 57.636 45.000 0.00 0.00 42.00 3.79
5656 5678 9.685828 CCGTTTGTTTATTAGAAATTCCTTTCA 57.314 29.630 1.40 0.00 42.71 2.69
5691 5714 2.618709 CCCTTCTGTTTCGCTGTTTCTT 59.381 45.455 0.00 0.00 0.00 2.52
5692 5715 2.222027 CCCTTCTGTTTCGCTGTTTCT 58.778 47.619 0.00 0.00 0.00 2.52
5715 5738 3.553096 CCTCTACTGTTTCTGTGCTTCGT 60.553 47.826 0.00 0.00 0.00 3.85
5740 5763 0.663153 GTGCTTCGCTGTCCTGTTTT 59.337 50.000 0.00 0.00 0.00 2.43
5782 5805 5.350633 CCCATTTTACTCGTTATGTCGGTA 58.649 41.667 0.00 0.00 0.00 4.02
5843 5866 4.796231 CGGTTCGGTCTCCTGGCG 62.796 72.222 0.00 0.00 0.00 5.69
5844 5867 4.452733 CCGGTTCGGTCTCCTGGC 62.453 72.222 0.00 0.00 42.73 4.85
5854 5877 4.137872 TCCTAAGGCGCCGGTTCG 62.138 66.667 23.20 6.89 0.00 3.95
5855 5878 2.029307 ATCTCCTAAGGCGCCGGTTC 62.029 60.000 23.20 0.00 0.00 3.62
5856 5879 2.064581 ATCTCCTAAGGCGCCGGTT 61.065 57.895 23.20 13.96 0.00 4.44
5857 5880 2.444140 ATCTCCTAAGGCGCCGGT 60.444 61.111 23.20 16.25 0.00 5.28
5858 5881 2.029666 CATCTCCTAAGGCGCCGG 59.970 66.667 23.20 17.22 0.00 6.13
5859 5882 0.462047 AAACATCTCCTAAGGCGCCG 60.462 55.000 23.20 6.78 0.00 6.46
5860 5883 1.751437 AAAACATCTCCTAAGGCGCC 58.249 50.000 21.89 21.89 0.00 6.53
5861 5884 2.488153 ACAAAAACATCTCCTAAGGCGC 59.512 45.455 0.00 0.00 0.00 6.53
5862 5885 4.023193 ACAACAAAAACATCTCCTAAGGCG 60.023 41.667 0.00 0.00 0.00 5.52
5863 5886 5.453567 ACAACAAAAACATCTCCTAAGGC 57.546 39.130 0.00 0.00 0.00 4.35
5864 5887 5.691754 GCAACAACAAAAACATCTCCTAAGG 59.308 40.000 0.00 0.00 0.00 2.69
5865 5888 5.691754 GGCAACAACAAAAACATCTCCTAAG 59.308 40.000 0.00 0.00 0.00 2.18
5866 5889 5.452636 GGGCAACAACAAAAACATCTCCTAA 60.453 40.000 0.00 0.00 39.74 2.69
5867 5890 4.038642 GGGCAACAACAAAAACATCTCCTA 59.961 41.667 0.00 0.00 39.74 2.94
5868 5891 3.181466 GGGCAACAACAAAAACATCTCCT 60.181 43.478 0.00 0.00 39.74 3.69
5869 5892 3.130633 GGGCAACAACAAAAACATCTCC 58.869 45.455 0.00 0.00 39.74 3.71
5870 5893 3.791245 TGGGCAACAACAAAAACATCTC 58.209 40.909 0.00 0.00 39.74 2.75
5871 5894 3.902881 TGGGCAACAACAAAAACATCT 57.097 38.095 0.00 0.00 39.74 2.90
5872 5895 4.379652 AGATGGGCAACAACAAAAACATC 58.620 39.130 0.00 0.00 39.74 3.06
5873 5896 4.420522 AGATGGGCAACAACAAAAACAT 57.579 36.364 0.00 0.00 39.74 2.71
5874 5897 3.902881 AGATGGGCAACAACAAAAACA 57.097 38.095 0.00 0.00 39.74 2.83
5875 5898 4.944048 AGTAGATGGGCAACAACAAAAAC 58.056 39.130 0.00 0.00 39.74 2.43
5876 5899 5.606348 AAGTAGATGGGCAACAACAAAAA 57.394 34.783 0.00 0.00 39.74 1.94
5877 5900 5.606348 AAAGTAGATGGGCAACAACAAAA 57.394 34.783 0.00 0.00 39.74 2.44
5878 5901 5.606348 AAAAGTAGATGGGCAACAACAAA 57.394 34.783 0.00 0.00 39.74 2.83
5879 5902 5.606348 AAAAAGTAGATGGGCAACAACAA 57.394 34.783 0.00 0.00 39.74 2.83
5933 5956 9.995003 TGAACCTTTATTTAGTTTCATGCAAAT 57.005 25.926 0.00 0.00 0.00 2.32
5934 5957 9.995003 ATGAACCTTTATTTAGTTTCATGCAAA 57.005 25.926 0.00 0.00 0.00 3.68
5935 5958 9.638239 GATGAACCTTTATTTAGTTTCATGCAA 57.362 29.630 0.00 0.00 0.00 4.08
5936 5959 8.801299 TGATGAACCTTTATTTAGTTTCATGCA 58.199 29.630 1.85 0.00 0.00 3.96
5937 5960 9.638239 TTGATGAACCTTTATTTAGTTTCATGC 57.362 29.630 1.85 0.00 0.00 4.06
5967 5990 9.463902 TTCCAAAAATATCCATGCATTCAAAAT 57.536 25.926 0.00 0.00 0.00 1.82
5968 5991 8.859236 TTCCAAAAATATCCATGCATTCAAAA 57.141 26.923 0.00 0.00 0.00 2.44
5969 5992 8.859236 TTTCCAAAAATATCCATGCATTCAAA 57.141 26.923 0.00 0.00 0.00 2.69
5970 5993 8.859236 TTTTCCAAAAATATCCATGCATTCAA 57.141 26.923 0.00 0.00 0.00 2.69
5971 5994 8.859236 TTTTTCCAAAAATATCCATGCATTCA 57.141 26.923 0.00 0.00 33.29 2.57
6066 6089 9.942850 ATTGTTCATCGGGAAAATTAAGAAATT 57.057 25.926 0.00 0.00 37.23 1.82
6074 6097 9.717942 TTTGATTTATTGTTCATCGGGAAAATT 57.282 25.926 0.00 0.00 37.23 1.82
6075 6098 9.717942 TTTTGATTTATTGTTCATCGGGAAAAT 57.282 25.926 0.00 0.00 37.23 1.82
6076 6099 9.717942 ATTTTGATTTATTGTTCATCGGGAAAA 57.282 25.926 0.00 0.00 37.23 2.29
6120 6143 6.036953 TGCATGCGAAAAATTTCAGACTTTTT 59.963 30.769 14.09 3.34 37.29 1.94
6121 6144 5.523188 TGCATGCGAAAAATTTCAGACTTTT 59.477 32.000 14.09 0.00 37.01 2.27
6122 6145 5.049167 TGCATGCGAAAAATTTCAGACTTT 58.951 33.333 14.09 0.00 37.01 2.66
6123 6146 4.619973 TGCATGCGAAAAATTTCAGACTT 58.380 34.783 14.09 0.00 37.01 3.01
6124 6147 4.241590 TGCATGCGAAAAATTTCAGACT 57.758 36.364 14.09 0.00 37.01 3.24
6125 6148 4.681025 TCTTGCATGCGAAAAATTTCAGAC 59.319 37.500 14.09 0.00 37.01 3.51
6126 6149 4.869215 TCTTGCATGCGAAAAATTTCAGA 58.131 34.783 14.09 0.00 37.01 3.27
6127 6150 5.547341 CATCTTGCATGCGAAAAATTTCAG 58.453 37.500 14.09 0.00 37.01 3.02
6128 6151 4.143073 GCATCTTGCATGCGAAAAATTTCA 60.143 37.500 14.09 0.00 44.26 2.69
6129 6152 4.328667 GCATCTTGCATGCGAAAAATTTC 58.671 39.130 14.09 0.00 44.26 2.17
6130 6153 4.330740 GCATCTTGCATGCGAAAAATTT 57.669 36.364 14.09 0.00 44.26 1.82
6143 6166 1.513586 GCGCACTCAAGCATCTTGC 60.514 57.895 0.30 0.00 45.46 4.01
6144 6167 1.136147 GGCGCACTCAAGCATCTTG 59.864 57.895 10.83 0.37 34.54 3.02
6145 6168 1.302752 TGGCGCACTCAAGCATCTT 60.303 52.632 10.83 0.00 34.54 2.40
6146 6169 1.744368 CTGGCGCACTCAAGCATCT 60.744 57.895 10.83 0.00 34.54 2.90
6147 6170 2.758089 CCTGGCGCACTCAAGCATC 61.758 63.158 10.83 0.00 34.54 3.91
6148 6171 2.749044 CCTGGCGCACTCAAGCAT 60.749 61.111 10.83 0.00 34.54 3.79
6149 6172 4.254709 ACCTGGCGCACTCAAGCA 62.255 61.111 10.83 0.00 34.54 3.91
6150 6173 3.730761 CACCTGGCGCACTCAAGC 61.731 66.667 10.83 0.00 0.00 4.01
6151 6174 2.281070 ACACCTGGCGCACTCAAG 60.281 61.111 10.83 0.00 0.00 3.02
6152 6175 2.591429 CACACCTGGCGCACTCAA 60.591 61.111 10.83 0.00 0.00 3.02
6153 6176 3.860605 ACACACCTGGCGCACTCA 61.861 61.111 10.83 0.00 0.00 3.41
6154 6177 3.349006 CACACACCTGGCGCACTC 61.349 66.667 10.83 0.00 0.00 3.51
6158 6181 2.897641 TTTTTGCACACACCTGGCGC 62.898 55.000 0.00 0.00 0.00 6.53
6159 6182 0.249405 ATTTTTGCACACACCTGGCG 60.249 50.000 0.00 0.00 0.00 5.69
6160 6183 2.810439 TATTTTTGCACACACCTGGC 57.190 45.000 0.00 0.00 0.00 4.85
6161 6184 3.989167 CACATATTTTTGCACACACCTGG 59.011 43.478 0.00 0.00 0.00 4.45
6162 6185 3.989167 CCACATATTTTTGCACACACCTG 59.011 43.478 0.00 0.00 0.00 4.00
6163 6186 3.006752 CCCACATATTTTTGCACACACCT 59.993 43.478 0.00 0.00 0.00 4.00
6164 6187 3.324993 CCCACATATTTTTGCACACACC 58.675 45.455 0.00 0.00 0.00 4.16
6165 6188 2.736192 GCCCACATATTTTTGCACACAC 59.264 45.455 0.00 0.00 0.00 3.82
6166 6189 2.366590 TGCCCACATATTTTTGCACACA 59.633 40.909 0.00 0.00 0.00 3.72
6167 6190 3.037431 TGCCCACATATTTTTGCACAC 57.963 42.857 0.00 0.00 0.00 3.82
6168 6191 3.758755 TTGCCCACATATTTTTGCACA 57.241 38.095 0.00 0.00 0.00 4.57
6169 6192 3.812053 TGTTTGCCCACATATTTTTGCAC 59.188 39.130 0.00 0.00 0.00 4.57
6170 6193 4.077300 TGTTTGCCCACATATTTTTGCA 57.923 36.364 0.00 0.00 0.00 4.08
6171 6194 4.274459 TGTTGTTTGCCCACATATTTTTGC 59.726 37.500 0.00 0.00 0.00 3.68
6172 6195 5.998454 TGTTGTTTGCCCACATATTTTTG 57.002 34.783 0.00 0.00 0.00 2.44


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

AutoCloner maintained by Alex Coulton.