Multiple sequence alignment - TraesCS5A01G154300

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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 TraesCS5A01G154300 chr5A 100.000 6567 0 0 1 6567 331873464 331880030 0.000000e+00 12128.0
1 TraesCS5A01G154300 chr1A 95.579 5383 179 21 1233 6564 155130735 155136109 0.000000e+00 8567.0
2 TraesCS5A01G154300 chr1A 95.380 1212 37 4 42 1237 155123646 155124854 0.000000e+00 1910.0
3 TraesCS5A01G154300 chr1A 97.826 46 1 0 1 46 155106243 155106288 5.460000e-11 80.5


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS5A01G154300 chr5A 331873464 331880030 6566 False 12128 12128 100.000 1 6567 1 chr5A.!!$F1 6566
1 TraesCS5A01G154300 chr1A 155130735 155136109 5374 False 8567 8567 95.579 1233 6564 1 chr1A.!!$F3 5331
2 TraesCS5A01G154300 chr1A 155123646 155124854 1208 False 1910 1910 95.380 42 1237 1 chr1A.!!$F2 1195

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
23 24 0.178975 ATGAAGGGTTTGGGCGAACA 60.179 50.0 5.02 0.00 0.00 3.18 F
24 25 0.178975 TGAAGGGTTTGGGCGAACAT 60.179 50.0 5.02 0.00 0.00 2.71 F
1883 1900 0.101219 GATCAAGCAATGTTCCGGCC 59.899 55.0 0.00 0.00 0.00 6.13 F
2643 2660 0.179134 ATGCTCGTCGTAGGCTCAAC 60.179 55.0 0.00 0.00 0.00 3.18 F
3593 3611 0.179156 CCAGGCGCACACATTGAATC 60.179 55.0 10.83 0.00 0.00 2.52 F
4013 4049 0.321919 TCCTTGCCAGCTACAAGCAG 60.322 55.0 18.75 9.66 45.56 4.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1745 1762 0.028242 CTAGGACTCTAGCACACGCG 59.972 60.0 3.53 3.53 45.49 6.01 R
1981 1998 0.970937 TCGTGGGGCTAGGAAGACTG 60.971 60.0 0.00 0.00 0.00 3.51 R
2908 2925 0.032678 CGCCATGTTCGCTATCTCCT 59.967 55.0 0.00 0.00 0.00 3.69 R
3933 3969 0.038343 AAATGGCGGCAACATGTGAC 60.038 50.0 18.31 0.00 0.00 3.67 R
4497 4547 0.748367 TCCCGGAGAGATCACTGTCG 60.748 60.0 0.73 1.76 37.31 4.35 R
5601 5652 0.669318 CGAACGTGTACAGGCACCAT 60.669 55.0 15.25 0.00 36.08 3.55 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
20 21 3.485463 CTATATGAAGGGTTTGGGCGA 57.515 47.619 0.00 0.00 0.00 5.54
21 22 2.818751 ATATGAAGGGTTTGGGCGAA 57.181 45.000 0.00 0.00 0.00 4.70
22 23 1.828979 TATGAAGGGTTTGGGCGAAC 58.171 50.000 0.00 0.00 0.00 3.95
23 24 0.178975 ATGAAGGGTTTGGGCGAACA 60.179 50.000 5.02 0.00 0.00 3.18
24 25 0.178975 TGAAGGGTTTGGGCGAACAT 60.179 50.000 5.02 0.00 0.00 2.71
25 26 0.243636 GAAGGGTTTGGGCGAACATG 59.756 55.000 0.00 0.00 0.00 3.21
26 27 1.815817 AAGGGTTTGGGCGAACATGC 61.816 55.000 0.00 0.00 0.00 4.06
27 28 2.126502 GGTTTGGGCGAACATGCG 60.127 61.111 0.00 0.00 35.06 4.73
28 29 2.642700 GTTTGGGCGAACATGCGT 59.357 55.556 0.00 0.00 35.06 5.24
29 30 1.442017 GTTTGGGCGAACATGCGTC 60.442 57.895 0.00 0.00 35.06 5.19
30 31 2.960512 TTTGGGCGAACATGCGTCG 61.961 57.895 13.56 13.56 36.61 5.12
31 32 3.867700 TTGGGCGAACATGCGTCGA 62.868 57.895 20.24 1.03 36.61 4.20
32 33 3.554692 GGGCGAACATGCGTCGAG 61.555 66.667 20.24 0.00 36.61 4.04
33 34 2.809601 GGCGAACATGCGTCGAGT 60.810 61.111 20.24 0.00 35.06 4.18
34 35 2.391821 GCGAACATGCGTCGAGTG 59.608 61.111 20.24 0.00 0.00 3.51
35 36 3.071459 GCGAACATGCGTCGAGTGG 62.071 63.158 20.24 0.00 0.00 4.00
36 37 2.778679 GAACATGCGTCGAGTGGC 59.221 61.111 0.00 0.00 0.00 5.01
37 38 3.071459 GAACATGCGTCGAGTGGCG 62.071 63.158 0.00 0.00 42.69 5.69
38 39 3.858868 AACATGCGTCGAGTGGCGT 62.859 57.895 0.00 0.00 41.80 5.68
39 40 3.842126 CATGCGTCGAGTGGCGTG 61.842 66.667 9.89 9.89 41.80 5.34
54 55 2.747686 GTGGTTCTGGGAGCGGAA 59.252 61.111 0.00 0.00 0.00 4.30
117 118 2.066340 CAACACCACTCTGCCCCTA 58.934 57.895 0.00 0.00 0.00 3.53
154 155 6.019779 TCCGAAAACATTGTTATTCCCTTG 57.980 37.500 1.76 0.00 0.00 3.61
162 163 4.513198 TTGTTATTCCCTTGCCTTTTCG 57.487 40.909 0.00 0.00 0.00 3.46
167 168 1.770294 TCCCTTGCCTTTTCGTTGTT 58.230 45.000 0.00 0.00 0.00 2.83
305 306 4.241681 GAGACTGCTCCTACAGAAAGTTG 58.758 47.826 0.00 0.00 40.25 3.16
558 575 1.523758 ACTCGTTGCCACTTCCAATC 58.476 50.000 0.00 0.00 0.00 2.67
588 605 0.690192 TTCGACCAATCAGCCCTCAA 59.310 50.000 0.00 0.00 0.00 3.02
633 650 2.185867 TTTGTGTTGTGTGATGTGCG 57.814 45.000 0.00 0.00 0.00 5.34
676 693 0.957395 CCTCGTATCCCATGCATGGC 60.957 60.000 36.08 22.66 46.70 4.40
693 710 3.071459 GCTGGTTGATCGACGTGCG 62.071 63.158 7.01 0.00 42.69 5.34
696 713 2.019951 GGTTGATCGACGTGCGTGT 61.020 57.895 7.01 0.00 41.80 4.49
719 736 1.093159 CTGCTCCCTGCTGATGAAAC 58.907 55.000 0.00 0.00 42.27 2.78
764 781 3.937706 CTCTGAGGCCATTCAGTTTGTAG 59.062 47.826 18.71 7.37 43.96 2.74
775 792 3.261580 TCAGTTTGTAGTGCATCCATCG 58.738 45.455 0.00 0.00 0.00 3.84
800 817 4.929479 ACTTTCCTAATTACCATGCACCA 58.071 39.130 0.00 0.00 0.00 4.17
868 885 6.018542 CCGCAAAGAAACAAAACGAAAAATT 58.981 32.000 0.00 0.00 0.00 1.82
884 901 9.731519 AACGAAAAATTAGATTACGTAAACGAG 57.268 29.630 12.81 0.00 43.02 4.18
925 942 1.520342 GAGTGGGCGATCACAGCTC 60.520 63.158 10.41 0.00 39.93 4.09
926 943 2.230994 GAGTGGGCGATCACAGCTCA 62.231 60.000 10.41 0.00 43.70 4.26
1032 1049 2.243774 TACTGCCTCTCTCCCCCTGG 62.244 65.000 0.00 0.00 0.00 4.45
1065 1082 0.914644 CCAGTGGGACCATCATGAGT 59.085 55.000 0.00 0.00 35.59 3.41
1192 1209 1.820906 CCACCACCATCGCATCCAG 60.821 63.158 0.00 0.00 0.00 3.86
1360 1377 2.699954 ACCTTAATGTTGCCGTCTCTG 58.300 47.619 0.00 0.00 0.00 3.35
1371 1388 0.868406 CCGTCTCTGCCTTGTGAAAC 59.132 55.000 0.00 0.00 37.35 2.78
1384 1401 1.475034 TGTGAAACAGAGCCACACTCC 60.475 52.381 0.00 0.00 45.67 3.85
1393 1410 2.456119 GCCACACTCCGATGAAGCG 61.456 63.158 0.00 0.00 0.00 4.68
1626 1643 0.469144 TGGTTTGGGTGGGCTTCTTC 60.469 55.000 0.00 0.00 0.00 2.87
1628 1645 1.408969 GTTTGGGTGGGCTTCTTCAA 58.591 50.000 0.00 0.00 0.00 2.69
1638 1655 3.265737 TGGGCTTCTTCAACTTAGGCATA 59.734 43.478 0.00 0.00 35.12 3.14
1640 1657 5.131977 TGGGCTTCTTCAACTTAGGCATATA 59.868 40.000 0.00 0.00 35.12 0.86
1660 1677 0.947244 GGGAATGTTGATAGGCAGCG 59.053 55.000 0.00 0.00 0.00 5.18
1679 1696 0.250038 GTGCACTCTGGCTCTTGTCA 60.250 55.000 10.32 0.00 34.04 3.58
1745 1762 1.016627 TTGTGCCAATAGATGCTCGC 58.983 50.000 0.00 0.00 0.00 5.03
1755 1772 4.794439 ATGCTCGCGCGTGTGCTA 62.794 61.111 36.45 26.31 39.65 3.49
1778 1795 1.065345 GTCCTAGGTTTGGAGGAAGGC 60.065 57.143 9.08 0.00 43.52 4.35
1848 1865 5.084519 TGACTAGGGTTCTTGCTCTTCTTA 58.915 41.667 0.00 0.00 0.00 2.10
1871 1888 3.839293 CACGGGTATAGCTAGATCAAGC 58.161 50.000 0.29 0.00 43.11 4.01
1883 1900 0.101219 GATCAAGCAATGTTCCGGCC 59.899 55.000 0.00 0.00 0.00 6.13
1958 1975 1.896660 GGAACGGAAGCTGTTGGCA 60.897 57.895 0.00 0.00 44.79 4.92
1997 2014 1.229496 TGCAGTCTTCCTAGCCCCA 60.229 57.895 0.00 0.00 0.00 4.96
1998 2015 1.222113 GCAGTCTTCCTAGCCCCAC 59.778 63.158 0.00 0.00 0.00 4.61
2004 2021 1.536907 TTCCTAGCCCCACGACCAA 60.537 57.895 0.00 0.00 0.00 3.67
2005 2022 1.833787 TTCCTAGCCCCACGACCAAC 61.834 60.000 0.00 0.00 0.00 3.77
2030 2047 1.728971 GCTCGTGTTCCAGATGAGTTG 59.271 52.381 0.00 0.00 0.00 3.16
2042 2059 3.567164 CAGATGAGTTGCTTCCTGTTGTT 59.433 43.478 0.00 0.00 0.00 2.83
2116 2133 4.864334 CCATGAGGGTGCGAGGGC 62.864 72.222 0.00 0.00 40.52 5.19
2130 2147 2.044946 GGGCAATCAGGGAAGCGT 60.045 61.111 0.00 0.00 0.00 5.07
2134 2151 1.508088 CAATCAGGGAAGCGTTGCC 59.492 57.895 0.00 0.00 42.22 4.52
2160 2177 2.159627 CACCCGAGTAATGTTGTGCTTC 59.840 50.000 0.00 0.00 0.00 3.86
2161 2178 2.038557 ACCCGAGTAATGTTGTGCTTCT 59.961 45.455 0.00 0.00 0.00 2.85
2188 2205 4.802051 CATGGTCCCCCTGGTGCG 62.802 72.222 0.00 0.00 0.00 5.34
2272 2289 0.319405 ACTGCTTCTTTTGGCATGGC 59.681 50.000 13.29 13.29 37.83 4.40
2285 2302 1.251251 GCATGGCTGTCCTCTTTTGT 58.749 50.000 0.00 0.00 0.00 2.83
2323 2340 0.883833 CCAAGGAGCATGGTGTTGAC 59.116 55.000 15.11 0.00 33.08 3.18
2363 2380 1.334960 GGCCACGAATCGCCATTTATG 60.335 52.381 1.15 0.00 45.01 1.90
2384 2401 4.984295 TGGATCTTCACTGATGAAAACCA 58.016 39.130 11.34 11.34 44.28 3.67
2387 2404 5.416952 GGATCTTCACTGATGAAAACCATGT 59.583 40.000 0.00 0.00 44.28 3.21
2413 2430 2.554032 CAAGCACTTCCCGACTCATTTT 59.446 45.455 0.00 0.00 0.00 1.82
2496 2513 6.478512 TTGTGGGAGTTTTCTTTTGCTAAT 57.521 33.333 0.00 0.00 0.00 1.73
2501 2518 8.523658 GTGGGAGTTTTCTTTTGCTAATAGAAT 58.476 33.333 0.00 0.00 0.00 2.40
2512 2529 6.564709 TTGCTAATAGAATGATGGATGTGC 57.435 37.500 0.00 0.00 0.00 4.57
2526 2543 3.134127 GTGCAGATTGGGGGCGAC 61.134 66.667 0.00 0.00 0.00 5.19
2552 2569 1.665442 CCCAAAACCCTTTGCCTCG 59.335 57.895 0.00 0.00 40.61 4.63
2643 2660 0.179134 ATGCTCGTCGTAGGCTCAAC 60.179 55.000 0.00 0.00 0.00 3.18
2689 2706 2.742372 CGCCTTGTTCCCCGTCTG 60.742 66.667 0.00 0.00 0.00 3.51
2752 2769 1.801242 TGGTTTCCCTGACTCTCACA 58.199 50.000 0.00 0.00 0.00 3.58
2895 2912 4.075682 CCGCATACTAGATCTCCAGAAGA 58.924 47.826 0.00 0.00 38.72 2.87
2908 2925 4.042062 TCTCCAGAAGAAAGCAAAGATGGA 59.958 41.667 0.00 0.00 34.55 3.41
2917 2934 3.767902 AGCAAAGATGGAGGAGATAGC 57.232 47.619 0.00 0.00 0.00 2.97
2935 2952 3.918220 GAACATGGCGAGCGAGCG 61.918 66.667 0.00 0.00 38.18 5.03
2994 3011 6.528537 TTGTGGCTGAAATATTGCACTTAT 57.471 33.333 0.00 0.00 0.00 1.73
3203 3220 2.269241 GTAGCAGGGTGACAGGGC 59.731 66.667 0.00 0.00 0.00 5.19
3213 3230 1.541670 GGTGACAGGGCGTTTGTAGAA 60.542 52.381 0.00 0.00 0.00 2.10
3223 3240 4.201980 GGGCGTTTGTAGAACTTTTCTTGT 60.202 41.667 0.00 0.00 41.14 3.16
3317 3334 4.537015 GAGCACAACAAATACTGTCAACC 58.463 43.478 0.00 0.00 37.23 3.77
3318 3335 4.207165 AGCACAACAAATACTGTCAACCT 58.793 39.130 0.00 0.00 37.23 3.50
3319 3336 5.373222 AGCACAACAAATACTGTCAACCTA 58.627 37.500 0.00 0.00 37.23 3.08
3321 3338 6.072508 AGCACAACAAATACTGTCAACCTATG 60.073 38.462 0.00 0.00 37.23 2.23
3322 3339 6.072728 GCACAACAAATACTGTCAACCTATGA 60.073 38.462 0.00 0.00 37.23 2.15
3332 3349 2.683968 TCAACCTATGACGAGCACAAC 58.316 47.619 0.00 0.00 31.50 3.32
3346 3364 1.000274 GCACAACAAATCGCCTTCCTT 60.000 47.619 0.00 0.00 0.00 3.36
3362 3380 5.747248 GCCTTCCTTTGCATCCTAGTGATAT 60.747 44.000 0.00 0.00 30.56 1.63
3365 3383 7.040823 CCTTCCTTTGCATCCTAGTGATATTTC 60.041 40.741 0.00 0.00 30.56 2.17
3370 3388 4.692155 TGCATCCTAGTGATATTTCGCATG 59.308 41.667 0.00 0.00 34.70 4.06
3447 3465 2.035961 TGCTATACAGAGGACGGCAATC 59.964 50.000 0.00 0.00 0.00 2.67
3545 3563 1.748329 CGCATAGCTGGGCTGACCTA 61.748 60.000 0.00 0.00 40.10 3.08
3549 3567 1.879575 TAGCTGGGCTGACCTAACAT 58.120 50.000 0.00 0.00 40.10 2.71
3591 3609 1.228094 TCCAGGCGCACACATTGAA 60.228 52.632 10.83 0.00 0.00 2.69
3592 3610 0.608856 TCCAGGCGCACACATTGAAT 60.609 50.000 10.83 0.00 0.00 2.57
3593 3611 0.179156 CCAGGCGCACACATTGAATC 60.179 55.000 10.83 0.00 0.00 2.52
3596 3614 0.179156 GGCGCACACATTGAATCAGG 60.179 55.000 10.83 0.00 0.00 3.86
3661 3694 7.666388 GTGAGGGTACTATCTATGTACATCACT 59.334 40.741 12.68 1.12 44.53 3.41
3826 3862 2.098117 ACTCTGTGTGCTTTTGAACTGC 59.902 45.455 0.00 0.00 0.00 4.40
3865 3901 1.406539 GACATGCTAATGCTGGGGTTG 59.593 52.381 0.00 0.00 40.48 3.77
3867 3903 1.044790 ATGCTAATGCTGGGGTTGGC 61.045 55.000 0.00 0.00 40.48 4.52
3923 3959 4.307432 TCAGTCGAAGGTGAACTTTCATC 58.693 43.478 6.19 0.00 40.21 2.92
3933 3969 5.352569 AGGTGAACTTTCATCTAGATTTGCG 59.647 40.000 1.33 0.00 46.31 4.85
3984 4020 8.684386 TGTTTAGATAGACAAAAATGTGACCA 57.316 30.769 0.00 0.00 0.00 4.02
4013 4049 0.321919 TCCTTGCCAGCTACAAGCAG 60.322 55.000 18.75 9.66 45.56 4.24
4024 4060 2.813754 GCTACAAGCAGATGGTGTCAAA 59.186 45.455 0.00 0.00 41.89 2.69
4112 4162 2.420628 TTTTCGGTTGCATTCTGCTG 57.579 45.000 0.34 0.00 45.31 4.41
4172 4222 4.985538 TTCAGCTTCCCGTTTGTAAAAA 57.014 36.364 0.00 0.00 0.00 1.94
4217 4267 4.776743 CATTAGTATTGGTCGCATTCTGC 58.223 43.478 0.00 0.00 40.69 4.26
4347 4397 1.480954 AGGCGTCCGTCAACTGAATAT 59.519 47.619 0.00 0.00 0.00 1.28
4469 4519 6.615264 AAATGCAGATGATACTACAAGCAG 57.385 37.500 0.00 0.00 32.85 4.24
4497 4547 7.228108 AGTGATGATGATATTGTTGATGTGGAC 59.772 37.037 0.00 0.00 0.00 4.02
4500 4550 5.523552 TGATGATATTGTTGATGTGGACGAC 59.476 40.000 0.00 0.00 0.00 4.34
4531 4581 1.676006 CCGGGAATGCAAACTACCATC 59.324 52.381 0.00 0.00 0.00 3.51
4543 4593 6.489700 TGCAAACTACCATCAGATTTCTTCAA 59.510 34.615 0.00 0.00 0.00 2.69
4546 4596 9.918630 CAAACTACCATCAGATTTCTTCAAATT 57.081 29.630 0.00 0.00 31.94 1.82
4568 4618 1.205655 TGAAACTCCTCGCCAGATCAG 59.794 52.381 0.00 0.00 0.00 2.90
4570 4620 0.820871 AACTCCTCGCCAGATCAGAC 59.179 55.000 0.00 0.00 0.00 3.51
4585 4635 4.988065 GACGGCTGTCAGCTAACA 57.012 55.556 23.68 0.00 44.82 2.41
4594 4644 3.618507 GCTGTCAGCTAACAGTCCAAGAT 60.619 47.826 18.40 0.00 46.77 2.40
4825 4875 3.005554 CCTGCTCAACCAGACAATGTAG 58.994 50.000 0.00 0.00 34.77 2.74
4905 4955 4.941263 CGTTGGGTCAATTTCTATCAGGAA 59.059 41.667 0.00 0.00 0.00 3.36
4930 4980 1.660560 GGCTTGCCGCAATGATGAGT 61.661 55.000 6.19 0.00 41.67 3.41
4948 4998 6.366061 TGATGAGTTGTTCATGTAAGTTCTCG 59.634 38.462 0.00 0.00 46.51 4.04
4969 5019 4.872124 TCGCTGCACATATCATAATGATCC 59.128 41.667 0.00 0.00 38.26 3.36
5160 5210 5.147330 TGGAACCATGACTTACTACACAG 57.853 43.478 0.00 0.00 0.00 3.66
5172 5222 0.526211 CTACACAGTAGACGCTGGCA 59.474 55.000 0.00 0.00 40.59 4.92
5183 5233 1.599542 GACGCTGGCATTAGGATGTTC 59.400 52.381 0.00 0.00 35.63 3.18
5244 5294 1.100463 TGTGTGGCGCTGTTTGACAT 61.100 50.000 7.64 0.00 0.00 3.06
5288 5338 9.651913 AGTTTCATCAAACAATAAACTTGTTGT 57.348 25.926 4.27 0.00 43.98 3.32
5324 5374 9.490083 ACTAGGCTACTCCTAAAAGAATTTCTA 57.510 33.333 0.00 0.00 46.38 2.10
5403 5454 4.251268 GGAAACTGCCGTTAGTATGTTCT 58.749 43.478 0.00 0.00 31.86 3.01
5477 5528 5.702865 TGCAATCTACTTTCTCATGTTTGC 58.297 37.500 0.00 0.00 37.90 3.68
5562 5613 5.330271 TGGTTTCGTTGTTTGTTGTTTTG 57.670 34.783 0.00 0.00 0.00 2.44
5601 5652 0.405198 TGCTGGAAGATTCAAGGGCA 59.595 50.000 0.00 0.00 34.07 5.36
5627 5678 1.404391 CCTGTACACGTTCGATAGGCT 59.596 52.381 0.00 0.00 0.00 4.58
5628 5679 2.615447 CCTGTACACGTTCGATAGGCTA 59.385 50.000 0.00 0.00 0.00 3.93
5629 5680 3.303857 CCTGTACACGTTCGATAGGCTAG 60.304 52.174 0.00 0.00 0.00 3.42
5784 5835 3.264193 TCACTATCAACAGGGCTGAATGT 59.736 43.478 0.00 0.00 0.00 2.71
5855 5906 6.595716 GTGCATACTCCTCTGTTCTATTGTTT 59.404 38.462 0.00 0.00 0.00 2.83
5905 5956 6.382859 ACAACCCTTCTTTCCTGTAATTTTGT 59.617 34.615 0.00 0.00 0.00 2.83
5929 5980 0.533032 GTTTCAGAGAGGAGTCCGGG 59.467 60.000 0.00 0.00 0.00 5.73
5975 6026 3.475566 TCTTCACTGGAGAACACCTTG 57.524 47.619 0.00 0.00 0.00 3.61
6024 6075 5.517054 TCCGTTTGCAGATTGTTTGTTTTAC 59.483 36.000 0.00 0.00 0.00 2.01
6053 6104 7.986320 TCCATCTTGATTTCACAACAACATTTT 59.014 29.630 0.00 0.00 0.00 1.82
6059 6110 6.325028 TGATTTCACAACAACATTTTCCCCTA 59.675 34.615 0.00 0.00 0.00 3.53
6093 6144 1.195900 TGTTTCGATGCGGCAACTAAC 59.804 47.619 6.82 11.69 0.00 2.34
6131 6182 3.896122 TCTGCGCAAAAGGATGTTTTAC 58.104 40.909 13.05 0.00 0.00 2.01
6135 6186 2.900046 CGCAAAAGGATGTTTTACGACG 59.100 45.455 0.00 0.00 0.00 5.12
6141 6192 3.921677 AGGATGTTTTACGACGTGATGT 58.078 40.909 11.56 0.00 0.00 3.06
6142 6193 4.312443 AGGATGTTTTACGACGTGATGTT 58.688 39.130 11.56 0.00 0.00 2.71
6152 6203 0.889186 ACGTGATGTTGACAAGGGGC 60.889 55.000 0.00 0.00 0.00 5.80
6187 6238 2.017113 GCCTGGCTTTATGCTAACCGT 61.017 52.381 12.43 0.00 42.39 4.83
6280 6345 3.428532 TCCTAACTAAGGTTGCTCGACT 58.571 45.455 0.00 0.00 46.62 4.18
6302 6367 3.554934 AGTGTGGCTGATTTGTCTTCAA 58.445 40.909 0.00 0.00 0.00 2.69
6309 6374 4.553323 GCTGATTTGTCTTCAATGCAACT 58.447 39.130 0.00 0.00 33.32 3.16
6388 6453 4.286297 AGTAGTAATTGTGCCTGCTGAA 57.714 40.909 0.00 0.00 0.00 3.02
6484 6549 5.989168 TGAACTACTGGTGTGTAATGTCTTG 59.011 40.000 0.00 0.00 0.00 3.02
6554 6619 0.614697 AGGGTTATGCCAAAGGGTGC 60.615 55.000 0.00 0.00 39.65 5.01
6564 6629 3.685435 AAGGGTGCCTTTCATGCG 58.315 55.556 0.00 0.00 41.69 4.73
6565 6630 1.074775 AAGGGTGCCTTTCATGCGA 59.925 52.632 0.00 0.00 41.69 5.10
6566 6631 0.539438 AAGGGTGCCTTTCATGCGAA 60.539 50.000 0.00 0.00 41.69 4.70
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.485463 TCGCCCAAACCCTTCATATAG 57.515 47.619 0.00 0.00 0.00 1.31
1 2 3.054287 TGTTCGCCCAAACCCTTCATATA 60.054 43.478 0.00 0.00 0.00 0.86
2 3 2.291282 TGTTCGCCCAAACCCTTCATAT 60.291 45.455 0.00 0.00 0.00 1.78
3 4 1.074084 TGTTCGCCCAAACCCTTCATA 59.926 47.619 0.00 0.00 0.00 2.15
4 5 0.178975 TGTTCGCCCAAACCCTTCAT 60.179 50.000 0.00 0.00 0.00 2.57
5 6 0.178975 ATGTTCGCCCAAACCCTTCA 60.179 50.000 0.00 0.00 0.00 3.02
6 7 0.243636 CATGTTCGCCCAAACCCTTC 59.756 55.000 0.00 0.00 0.00 3.46
7 8 1.815817 GCATGTTCGCCCAAACCCTT 61.816 55.000 0.00 0.00 0.00 3.95
8 9 2.275380 GCATGTTCGCCCAAACCCT 61.275 57.895 0.00 0.00 0.00 4.34
9 10 2.261361 GCATGTTCGCCCAAACCC 59.739 61.111 0.00 0.00 0.00 4.11
10 11 2.126502 CGCATGTTCGCCCAAACC 60.127 61.111 0.00 0.00 0.00 3.27
11 12 1.442017 GACGCATGTTCGCCCAAAC 60.442 57.895 0.00 0.00 0.00 2.93
12 13 2.950673 GACGCATGTTCGCCCAAA 59.049 55.556 0.00 0.00 0.00 3.28
13 14 3.418913 CGACGCATGTTCGCCCAA 61.419 61.111 6.01 0.00 0.00 4.12
14 15 4.365505 TCGACGCATGTTCGCCCA 62.366 61.111 12.46 0.00 0.00 5.36
15 16 3.554692 CTCGACGCATGTTCGCCC 61.555 66.667 12.46 0.00 0.00 6.13
16 17 2.809601 ACTCGACGCATGTTCGCC 60.810 61.111 12.46 0.00 0.00 5.54
17 18 2.391821 CACTCGACGCATGTTCGC 59.608 61.111 12.46 0.00 0.00 4.70
18 19 3.071459 GCCACTCGACGCATGTTCG 62.071 63.158 11.38 11.38 0.00 3.95
19 20 2.778679 GCCACTCGACGCATGTTC 59.221 61.111 0.00 0.00 0.00 3.18
20 21 3.112075 CGCCACTCGACGCATGTT 61.112 61.111 0.00 0.00 41.67 2.71
21 22 4.357947 ACGCCACTCGACGCATGT 62.358 61.111 0.00 0.00 41.67 3.21
22 23 3.842126 CACGCCACTCGACGCATG 61.842 66.667 0.00 0.00 41.67 4.06
26 27 3.103911 GAACCACGCCACTCGACG 61.104 66.667 0.00 0.00 41.67 5.12
27 28 2.022129 CAGAACCACGCCACTCGAC 61.022 63.158 0.00 0.00 41.67 4.20
28 29 2.338620 CAGAACCACGCCACTCGA 59.661 61.111 0.00 0.00 41.67 4.04
29 30 2.738521 CCAGAACCACGCCACTCG 60.739 66.667 0.00 0.00 45.38 4.18
30 31 2.358737 CCCAGAACCACGCCACTC 60.359 66.667 0.00 0.00 0.00 3.51
31 32 2.847234 TCCCAGAACCACGCCACT 60.847 61.111 0.00 0.00 0.00 4.00
32 33 2.358737 CTCCCAGAACCACGCCAC 60.359 66.667 0.00 0.00 0.00 5.01
33 34 4.329545 GCTCCCAGAACCACGCCA 62.330 66.667 0.00 0.00 0.00 5.69
36 37 2.725203 TTTCCGCTCCCAGAACCACG 62.725 60.000 0.00 0.00 0.00 4.94
37 38 0.536460 TTTTCCGCTCCCAGAACCAC 60.536 55.000 0.00 0.00 0.00 4.16
38 39 0.536460 GTTTTCCGCTCCCAGAACCA 60.536 55.000 0.00 0.00 0.00 3.67
39 40 0.536460 TGTTTTCCGCTCCCAGAACC 60.536 55.000 0.00 0.00 0.00 3.62
40 41 0.875059 CTGTTTTCCGCTCCCAGAAC 59.125 55.000 0.00 0.00 0.00 3.01
54 55 0.878523 TTGTAGCTGACGCGCTGTTT 60.879 50.000 5.73 0.00 41.12 2.83
70 71 2.421073 CGATGCCATTGATGTCTGTTGT 59.579 45.455 0.00 0.00 0.00 3.32
167 168 5.471797 TCAATCCTTATCACTCACGCAAAAA 59.528 36.000 0.00 0.00 0.00 1.94
179 180 9.656040 CAAATGGAAAAACATCAATCCTTATCA 57.344 29.630 0.00 0.00 33.02 2.15
223 224 4.194640 TCAACAGGATTAGCATCTTCAGC 58.805 43.478 0.00 0.00 0.00 4.26
251 252 0.250727 CATGGGGTTGAAGTCACCGT 60.251 55.000 0.00 0.00 0.00 4.83
253 254 2.961424 CCATGGGGTTGAAGTCACC 58.039 57.895 2.85 0.00 0.00 4.02
403 404 5.011329 ACCTAGACGACTAATGTCAAACCAA 59.989 40.000 0.00 0.00 43.06 3.67
549 566 5.588648 TCGAACAGTTCTTTTGATTGGAAGT 59.411 36.000 11.60 0.00 0.00 3.01
558 575 5.168526 TGATTGGTCGAACAGTTCTTTTG 57.831 39.130 2.09 0.00 0.00 2.44
588 605 7.508687 AGAAAAACATCCAAAAATAGCAAGGT 58.491 30.769 0.00 0.00 0.00 3.50
633 650 1.405463 GATCACCGATTTTTGGAGGCC 59.595 52.381 0.00 0.00 0.00 5.19
676 693 1.733041 ACGCACGTCGATCAACCAG 60.733 57.895 13.06 0.00 41.67 4.00
693 710 3.660621 GCAGGGAGCAGTGAACAC 58.339 61.111 0.00 0.00 44.79 3.32
719 736 4.806247 GCAGCTAGGTCATTACACTAACAG 59.194 45.833 0.00 0.00 0.00 3.16
764 781 3.270877 AGGAAAGTAACGATGGATGCAC 58.729 45.455 0.00 0.00 0.00 4.57
775 792 6.376018 TGGTGCATGGTAATTAGGAAAGTAAC 59.624 38.462 0.00 0.00 0.00 2.50
823 840 1.628447 CCAAAACACATGCGGCATGC 61.628 55.000 35.80 9.90 44.80 4.06
837 854 0.537188 TGTTTCTTTGCGGCCCAAAA 59.463 45.000 16.87 8.60 42.51 2.44
868 885 7.751732 TCTTGCTTACTCGTTTACGTAATCTA 58.248 34.615 9.18 0.00 40.80 1.98
920 937 0.928922 GCACATCGATCAGTGAGCTG 59.071 55.000 17.46 1.37 43.87 4.24
925 942 0.741927 TGCAGGCACATCGATCAGTG 60.742 55.000 10.67 10.67 38.74 3.66
926 943 0.036105 TTGCAGGCACATCGATCAGT 60.036 50.000 0.00 0.00 0.00 3.41
964 981 6.036844 GGTTCGATACCTTCTCATTAAACCAC 59.963 42.308 8.87 0.00 44.10 4.16
1192 1209 3.186613 GGTTTTGAATCACTCCGTGTCTC 59.813 47.826 0.00 0.00 34.79 3.36
1263 1280 2.613026 TTGCAAAGTTCGTGAGGAGA 57.387 45.000 0.00 0.00 0.00 3.71
1264 1281 2.160417 GGATTGCAAAGTTCGTGAGGAG 59.840 50.000 1.71 0.00 0.00 3.69
1265 1282 2.151202 GGATTGCAAAGTTCGTGAGGA 58.849 47.619 1.71 0.00 0.00 3.71
1306 1323 5.596772 AGAAAAGAGGGAGTACAGATCTAGC 59.403 44.000 0.00 0.00 0.00 3.42
1360 1377 0.312102 GTGGCTCTGTTTCACAAGGC 59.688 55.000 0.00 0.00 34.73 4.35
1400 1417 2.956194 TGCTGCCGCAATGAACTG 59.044 55.556 0.00 0.00 44.62 3.16
1626 1643 6.998074 TCAACATTCCCTATATGCCTAAGTTG 59.002 38.462 0.00 0.00 34.44 3.16
1628 1645 6.763715 TCAACATTCCCTATATGCCTAAGT 57.236 37.500 0.00 0.00 0.00 2.24
1638 1655 3.557898 CGCTGCCTATCAACATTCCCTAT 60.558 47.826 0.00 0.00 0.00 2.57
1640 1657 1.475751 CGCTGCCTATCAACATTCCCT 60.476 52.381 0.00 0.00 0.00 4.20
1660 1677 0.250038 TGACAAGAGCCAGAGTGCAC 60.250 55.000 9.40 9.40 0.00 4.57
1666 1683 0.894835 TATGCGTGACAAGAGCCAGA 59.105 50.000 0.00 0.00 0.00 3.86
1679 1696 0.394762 TAGTGTCGGGGTCTATGCGT 60.395 55.000 0.00 0.00 0.00 5.24
1745 1762 0.028242 CTAGGACTCTAGCACACGCG 59.972 60.000 3.53 3.53 45.49 6.01
1755 1772 3.445987 CTTCCTCCAAACCTAGGACTCT 58.554 50.000 17.98 0.00 41.63 3.24
1778 1795 1.575922 CAATGGGATGCGTATGCCG 59.424 57.895 18.52 1.44 46.98 5.69
1822 1839 2.569404 AGAGCAAGAACCCTAGTCAAGG 59.431 50.000 0.00 0.00 46.09 3.61
1827 1844 4.081365 GCTAAGAAGAGCAAGAACCCTAGT 60.081 45.833 0.00 0.00 42.36 2.57
1848 1865 3.156288 TGATCTAGCTATACCCGTGCT 57.844 47.619 0.00 0.00 40.43 4.40
1871 1888 1.750399 CCTCTGGGCCGGAACATTG 60.750 63.158 17.43 3.93 0.00 2.82
1883 1900 2.683768 AGGATAGCTAACACCCTCTGG 58.316 52.381 0.00 0.00 37.80 3.86
1981 1998 0.970937 TCGTGGGGCTAGGAAGACTG 60.971 60.000 0.00 0.00 0.00 3.51
1997 2014 4.052229 CGAGCCGAGGTTGGTCGT 62.052 66.667 3.92 0.00 45.70 4.34
2004 2021 2.915659 TGGAACACGAGCCGAGGT 60.916 61.111 1.50 0.00 0.00 3.85
2005 2022 1.949847 ATCTGGAACACGAGCCGAGG 61.950 60.000 1.50 0.00 0.00 4.63
2030 2047 2.167487 TGGGTTTTCAACAACAGGAAGC 59.833 45.455 0.00 0.00 0.00 3.86
2042 2059 2.093341 GGCTATACGGTCTGGGTTTTCA 60.093 50.000 0.00 0.00 0.00 2.69
2116 2133 1.508088 GGCAACGCTTCCCTGATTG 59.492 57.895 0.00 0.00 0.00 2.67
2134 2151 0.672401 AACATTACTCGGGTGGTGCG 60.672 55.000 0.00 0.00 0.00 5.34
2160 2177 1.150081 GGACCATGAGGCATCCCAG 59.850 63.158 0.00 0.00 39.06 4.45
2161 2178 2.386100 GGGACCATGAGGCATCCCA 61.386 63.158 3.20 0.00 45.50 4.37
2188 2205 9.404348 GTAGTACAGGAGAAGTAAAACTTGTAC 57.596 37.037 0.00 0.00 38.80 2.90
2238 2255 6.482898 AGAAGCAGTATCACTCATGAGAAT 57.517 37.500 29.27 21.44 38.57 2.40
2247 2264 3.754965 TGCCAAAAGAAGCAGTATCACT 58.245 40.909 0.00 0.00 33.08 3.41
2272 2289 4.636249 AGAGCAACTACAAAAGAGGACAG 58.364 43.478 0.00 0.00 0.00 3.51
2285 2302 1.337823 GGCGTCCAAGAAGAGCAACTA 60.338 52.381 0.00 0.00 0.00 2.24
2323 2340 2.124942 GGAAGGCTCTCAAGGGCG 60.125 66.667 0.00 0.00 0.00 6.13
2345 2362 2.686558 CCATAAATGGCGATTCGTGG 57.313 50.000 8.03 9.56 41.75 4.94
2363 2380 5.416952 ACATGGTTTTCATCAGTGAAGATCC 59.583 40.000 0.00 2.73 44.62 3.36
2371 2388 2.299867 GGCCAACATGGTTTTCATCAGT 59.700 45.455 0.00 0.00 40.46 3.41
2384 2401 1.187567 GGGAAGTGCTTGGCCAACAT 61.188 55.000 16.05 0.00 0.00 2.71
2387 2404 2.597217 CGGGAAGTGCTTGGCCAA 60.597 61.111 19.25 19.25 0.00 4.52
2413 2430 1.907807 AAGCATGCCGCCAAGGAAA 60.908 52.632 15.66 0.00 45.00 3.13
2496 2513 5.067954 CCAATCTGCACATCCATCATTCTA 58.932 41.667 0.00 0.00 0.00 2.10
2501 2518 1.410507 CCCCAATCTGCACATCCATCA 60.411 52.381 0.00 0.00 0.00 3.07
2512 2529 1.815421 CTTCGTCGCCCCCAATCTG 60.815 63.158 0.00 0.00 0.00 2.90
2526 2543 1.463553 AAGGGTTTTGGGCTGCTTCG 61.464 55.000 0.00 0.00 0.00 3.79
2569 2586 2.045926 ACCCAAGTCTGGCGATGC 60.046 61.111 0.00 0.00 41.99 3.91
2643 2660 1.792949 GGAATATGAACTACCTGCGCG 59.207 52.381 0.00 0.00 0.00 6.86
2689 2706 1.542915 ACAAGCACATCAATCACTGGC 59.457 47.619 0.00 0.00 0.00 4.85
2752 2769 3.303351 AGGAAATCCAATCAAGGCGAT 57.697 42.857 1.67 0.00 38.89 4.58
2895 2912 4.459330 GCTATCTCCTCCATCTTTGCTTT 58.541 43.478 0.00 0.00 0.00 3.51
2908 2925 0.032678 CGCCATGTTCGCTATCTCCT 59.967 55.000 0.00 0.00 0.00 3.69
2917 2934 3.918220 GCTCGCTCGCCATGTTCG 61.918 66.667 0.00 0.00 0.00 3.95
2935 2952 2.616842 TCTTCCAGTTCTTTTTGGCGTC 59.383 45.455 0.00 0.00 34.38 5.19
2937 2954 2.878406 TCTCTTCCAGTTCTTTTTGGCG 59.122 45.455 0.00 0.00 34.38 5.69
2942 2959 5.240403 GTCAAGCATCTCTTCCAGTTCTTTT 59.760 40.000 0.00 0.00 31.27 2.27
2994 3011 0.538118 GTACCAGGGCCGTATGACAA 59.462 55.000 0.00 0.00 0.00 3.18
3203 3220 5.328691 TGCACAAGAAAAGTTCTACAAACG 58.671 37.500 0.00 0.00 39.61 3.60
3213 3230 6.980397 CCTGTTTTAGATTGCACAAGAAAAGT 59.020 34.615 0.00 0.00 0.00 2.66
3223 3240 5.221621 CCCTTTTTCCCTGTTTTAGATTGCA 60.222 40.000 0.00 0.00 0.00 4.08
3317 3334 3.782250 GCGATTTGTTGTGCTCGTCATAG 60.782 47.826 0.00 0.00 33.80 2.23
3318 3335 2.093625 GCGATTTGTTGTGCTCGTCATA 59.906 45.455 0.00 0.00 33.80 2.15
3319 3336 1.135972 GCGATTTGTTGTGCTCGTCAT 60.136 47.619 0.00 0.00 33.80 3.06
3321 3338 0.452784 GGCGATTTGTTGTGCTCGTC 60.453 55.000 0.00 0.00 33.80 4.20
3322 3339 0.884704 AGGCGATTTGTTGTGCTCGT 60.885 50.000 0.00 0.00 33.80 4.18
3323 3340 0.238289 AAGGCGATTTGTTGTGCTCG 59.762 50.000 0.00 0.00 0.00 5.03
3324 3341 1.401539 GGAAGGCGATTTGTTGTGCTC 60.402 52.381 0.00 0.00 0.00 4.26
3325 3342 0.598065 GGAAGGCGATTTGTTGTGCT 59.402 50.000 0.00 0.00 0.00 4.40
3327 3344 3.052036 CAAAGGAAGGCGATTTGTTGTG 58.948 45.455 0.00 0.00 0.00 3.33
3328 3345 2.545742 GCAAAGGAAGGCGATTTGTTGT 60.546 45.455 0.00 0.00 36.52 3.32
3332 3349 2.533266 GATGCAAAGGAAGGCGATTTG 58.467 47.619 0.00 0.00 37.07 2.32
3346 3364 4.702831 TGCGAAATATCACTAGGATGCAA 58.297 39.130 0.00 0.00 36.72 4.08
3362 3380 3.257393 ACAAAACAACAAGCATGCGAAA 58.743 36.364 13.01 0.00 0.00 3.46
3365 3383 2.725723 CCTACAAAACAACAAGCATGCG 59.274 45.455 13.01 0.84 0.00 4.73
3370 3388 4.134563 TCTCTCCCTACAAAACAACAAGC 58.865 43.478 0.00 0.00 0.00 4.01
3440 3458 3.281341 TGTTTAAGTTGCTGATTGCCG 57.719 42.857 0.00 0.00 42.00 5.69
3442 3460 4.808558 TGGATGTTTAAGTTGCTGATTGC 58.191 39.130 0.00 0.00 43.25 3.56
3447 3465 4.083110 CCTGTCTGGATGTTTAAGTTGCTG 60.083 45.833 0.00 0.00 38.35 4.41
3545 3563 2.299867 GGAAGAACACCAATGGCATGTT 59.700 45.455 7.84 7.84 39.23 2.71
3549 3567 3.737559 ATAGGAAGAACACCAATGGCA 57.262 42.857 0.00 0.00 0.00 4.92
3591 3609 0.040058 TGTTGCCTTCCATGCCTGAT 59.960 50.000 0.00 0.00 0.00 2.90
3592 3610 0.178967 TTGTTGCCTTCCATGCCTGA 60.179 50.000 0.00 0.00 0.00 3.86
3593 3611 0.899720 ATTGTTGCCTTCCATGCCTG 59.100 50.000 0.00 0.00 0.00 4.85
3596 3614 0.741927 GCCATTGTTGCCTTCCATGC 60.742 55.000 0.00 0.00 0.00 4.06
3661 3694 6.057321 AGTTTATATCGAAAACTGGGACCA 57.943 37.500 11.86 0.00 43.66 4.02
3670 3703 7.040062 CCCCATGCCAATAGTTTATATCGAAAA 60.040 37.037 0.00 0.00 0.00 2.29
3746 3782 7.645402 TGTCTCATGCATGATCATTTTCATAC 58.355 34.615 28.81 13.76 34.59 2.39
3826 3862 3.945434 GTCATGCGCCGCTGGATG 61.945 66.667 11.67 6.06 38.86 3.51
3867 3903 3.814268 CCATTGCCGGCTTCCACG 61.814 66.667 29.70 9.82 0.00 4.94
3923 3959 3.419915 GCAACATGTGACGCAAATCTAG 58.580 45.455 0.00 0.00 0.00 2.43
3933 3969 0.038343 AAATGGCGGCAACATGTGAC 60.038 50.000 18.31 0.00 0.00 3.67
3978 4014 3.119708 GCAAGGAATCAATGTCTGGTCAC 60.120 47.826 0.00 0.00 0.00 3.67
3979 4015 3.084039 GCAAGGAATCAATGTCTGGTCA 58.916 45.455 0.00 0.00 0.00 4.02
3984 4020 2.097825 GCTGGCAAGGAATCAATGTCT 58.902 47.619 0.00 0.00 0.00 3.41
4013 4049 5.895636 TTGGACATACATTTGACACCATC 57.104 39.130 0.00 0.00 0.00 3.51
4024 4060 7.520798 ACATGATACCATCTTTGGACATACAT 58.479 34.615 0.00 0.00 46.92 2.29
4112 4162 2.042686 TCATCACTGGCCATAGTTGC 57.957 50.000 5.51 0.00 0.00 4.17
4162 4212 9.858247 GCAAAGTAAGCCTTAATTTTTACAAAC 57.142 29.630 7.14 0.00 31.79 2.93
4217 4267 2.079158 CACCACTGACCATAGTTGCAG 58.921 52.381 0.00 0.00 34.65 4.41
4261 4311 2.514592 GCTGCCGCCAGATGCTAA 60.515 61.111 0.00 0.00 41.77 3.09
4262 4312 3.328093 TTGCTGCCGCCAGATGCTA 62.328 57.895 0.00 0.00 41.77 3.49
4266 4316 3.650298 ATGGTTGCTGCCGCCAGAT 62.650 57.895 15.53 0.49 41.77 2.90
4347 4397 4.261783 CCTGAAGAACTATCATCGCTGCTA 60.262 45.833 0.00 0.00 0.00 3.49
4469 4519 6.856426 CACATCAACAATATCATCATCACTGC 59.144 38.462 0.00 0.00 0.00 4.40
4497 4547 0.748367 TCCCGGAGAGATCACTGTCG 60.748 60.000 0.73 1.76 37.31 4.35
4500 4550 1.539929 GCATTCCCGGAGAGATCACTG 60.540 57.143 0.73 0.00 0.00 3.66
4543 4593 4.487714 TCTGGCGAGGAGTTTCATAATT 57.512 40.909 0.00 0.00 0.00 1.40
4546 4596 3.031013 TGATCTGGCGAGGAGTTTCATA 58.969 45.455 0.00 0.00 0.00 2.15
4568 4618 2.743195 CTGTTAGCTGACAGCCGTC 58.257 57.895 23.81 13.89 43.77 4.79
4585 4635 1.630369 TGCTAGGTTGCATCTTGGACT 59.370 47.619 0.00 0.00 38.12 3.85
4586 4636 2.113860 TGCTAGGTTGCATCTTGGAC 57.886 50.000 0.00 0.00 38.12 4.02
4594 4644 1.255882 CCACCAATTGCTAGGTTGCA 58.744 50.000 0.00 0.00 41.65 4.08
4704 4754 8.999431 CGCATACCAGTAAATAAATCTATGGTT 58.001 33.333 0.00 0.00 40.03 3.67
4723 4773 1.059942 GCTGCAAACAAACGCATACC 58.940 50.000 0.00 0.00 37.54 2.73
4930 4980 3.186409 GCAGCGAGAACTTACATGAACAA 59.814 43.478 0.00 0.00 0.00 2.83
4948 4998 5.448768 GCTGGATCATTATGATATGTGCAGC 60.449 44.000 18.86 18.86 40.17 5.25
4969 5019 2.493278 CCAATCCTTGGTTGTAAGGCTG 59.507 50.000 0.00 0.00 45.52 4.85
5025 5075 8.458573 AATATGGGCGTCAATAACAAGAATTA 57.541 30.769 0.00 0.00 0.00 1.40
5042 5092 1.406539 CTGCCAGACACAAATATGGGC 59.593 52.381 0.00 0.00 40.29 5.36
5086 5136 7.634718 TGTACCATCAATAAATAGTTCCCACA 58.365 34.615 0.00 0.00 0.00 4.17
5160 5210 2.224066 ACATCCTAATGCCAGCGTCTAC 60.224 50.000 0.00 0.00 36.26 2.59
5172 5222 5.677319 TCCTTCTCGTTGAACATCCTAAT 57.323 39.130 0.00 0.00 0.00 1.73
5183 5233 6.510799 GCATCATATCAACTTCCTTCTCGTTG 60.511 42.308 0.00 0.00 39.38 4.10
5427 5478 1.452651 CCAGGCGGCACATCTTGAT 60.453 57.895 13.08 0.00 0.00 2.57
5562 5613 3.065371 GCAACACAGGTGCCATTATCTAC 59.935 47.826 0.00 0.00 0.00 2.59
5601 5652 0.669318 CGAACGTGTACAGGCACCAT 60.669 55.000 15.25 0.00 36.08 3.55
5784 5835 2.039746 CCCCTGGTTGTACTCAATGTCA 59.960 50.000 0.00 0.00 35.92 3.58
5869 5920 6.374613 GGAAAGAAGGGTTGTTAATCTACCAG 59.625 42.308 9.49 0.00 42.27 4.00
5878 5929 8.417884 CAAAATTACAGGAAAGAAGGGTTGTTA 58.582 33.333 0.00 0.00 0.00 2.41
5905 5956 2.834549 GGACTCCTCTCTGAAACCATGA 59.165 50.000 0.00 0.00 0.00 3.07
5929 5980 6.543831 ACTTGGCATAGTGGAAGATGTAAATC 59.456 38.462 0.00 0.00 0.00 2.17
5975 6026 4.613448 GCATACGTCATCGATGTCTTCTAC 59.387 45.833 24.09 13.06 40.62 2.59
6024 6075 5.710513 TGTTGTGAAATCAAGATGGAAGG 57.289 39.130 0.00 0.00 0.00 3.46
6053 6104 5.319043 ACAAGACAAGACAAATTAGGGGA 57.681 39.130 0.00 0.00 0.00 4.81
6059 6110 5.687285 GCATCGAAACAAGACAAGACAAATT 59.313 36.000 0.00 0.00 0.00 1.82
6131 6182 0.790207 CCCTTGTCAACATCACGTCG 59.210 55.000 0.00 0.00 0.00 5.12
6135 6186 1.000274 GTTGCCCCTTGTCAACATCAC 60.000 52.381 0.00 0.00 41.46 3.06
6141 6192 1.388065 CCAACGTTGCCCCTTGTCAA 61.388 55.000 22.93 0.00 0.00 3.18
6142 6193 1.826054 CCAACGTTGCCCCTTGTCA 60.826 57.895 22.93 0.00 0.00 3.58
6182 6233 3.771577 AGTCCAGATTTCAAGACGGTT 57.228 42.857 0.00 0.00 34.41 4.44
6263 6328 3.573110 ACACTAGTCGAGCAACCTTAGTT 59.427 43.478 0.00 0.00 36.33 2.24
6280 6345 4.350368 TGAAGACAAATCAGCCACACTA 57.650 40.909 0.00 0.00 0.00 2.74
6302 6367 3.762293 TGCTTCCGCAAGTTGCAT 58.238 50.000 26.56 0.00 45.36 3.96
6379 6444 4.315803 TCTTAAACTAGTGTTCAGCAGGC 58.684 43.478 0.00 0.00 34.96 4.85
6388 6453 3.899980 ACGGGGAGTTCTTAAACTAGTGT 59.100 43.478 0.00 0.00 45.80 3.55
6524 6589 2.887152 GGCATAACCCTAGGCAATTCAG 59.113 50.000 2.05 0.00 36.53 3.02


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

AutoCloner maintained by Alex Coulton.