Multiple sequence alignment - TraesCS5A01G141700

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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 TraesCS5A01G141700 chr5A 100.000 6201 0 0 1 6201 314662922 314669122 0.000000e+00 11452
1 TraesCS5A01G141700 chr5D 93.572 5383 192 67 663 5959 239282163 239276849 0.000000e+00 7882
2 TraesCS5A01G141700 chr5D 85.824 649 76 10 7 652 239282782 239282147 0.000000e+00 675
3 TraesCS5A01G141700 chr5D 93.902 246 13 2 5957 6201 239276818 239276574 2.730000e-98 370
4 TraesCS5A01G141700 chr5B 92.798 2416 106 38 3249 5621 264284440 264286830 0.000000e+00 3435
5 TraesCS5A01G141700 chr5B 90.940 596 29 10 5620 6201 264287093 264287677 0.000000e+00 778
6 TraesCS5A01G141700 chr5B 84.929 491 59 12 7 496 264283967 264284443 3.360000e-132 483


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 TraesCS5A01G141700 chr5A 314662922 314669122 6200 False 11452.000000 11452 100.000000 1 6201 1 chr5A.!!$F1 6200
1 TraesCS5A01G141700 chr5D 239276574 239282782 6208 True 2975.666667 7882 91.099333 7 6201 3 chr5D.!!$R1 6194
2 TraesCS5A01G141700 chr5B 264283967 264287677 3710 False 1565.333333 3435 89.555667 7 6201 3 chr5B.!!$F1 6194

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
171 172 0.037303 AGTACGAGTCGAAGGGTCCA 59.963 55.0 21.50 0.0 0.00 4.02 F
647 650 0.185175 AAGGGCCAAGGTTTTCGAGT 59.815 50.0 6.18 0.0 0.00 4.18 F
649 652 0.313987 GGGCCAAGGTTTTCGAGTTG 59.686 55.0 4.39 0.0 0.00 3.16 F
2204 2215 0.615331 CACACATCCAGCCTACCTGT 59.385 55.0 0.00 0.0 40.06 4.00 F
2922 2939 0.605589 AGCAGCTCCGTTTGGGTAAC 60.606 55.0 0.00 0.0 37.00 2.50 F
3911 3970 0.251297 TCCTGTGTGCAATCCCAAGG 60.251 55.0 0.00 0.0 0.00 3.61 F
4804 4895 0.106708 ACTCAGGTGAAGCGCAGAAA 59.893 50.0 11.47 0.0 0.00 2.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1080 1084 0.033894 AGTCGGAGGAGGAAGGAGAC 60.034 60.000 0.00 0.00 0.00 3.36 R
2544 2556 0.469892 TCTCTCTGCTGTCACCACCA 60.470 55.000 0.00 0.00 0.00 4.17 R
2625 2638 0.519961 GGCCGTCTTTTTATGCGTGT 59.480 50.000 0.00 0.00 0.00 4.49 R
3911 3970 0.613012 AGGGCAAGTTGAGCAATCCC 60.613 55.000 7.16 6.46 0.00 3.85 R
4639 4730 0.111001 CGAAGTTGGTTACGGCGTTG 60.111 55.000 21.24 0.00 0.00 4.10 R
4990 5087 0.106769 TGTTGCTCTCAAAGGTGGCA 60.107 50.000 0.00 0.00 33.37 4.92 R
6129 6551 1.961277 CGCCGAAGCACTTGTTCCT 60.961 57.895 0.00 0.00 39.83 3.36 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
18 19 3.450115 CGACCCCCTCCTCACGAC 61.450 72.222 0.00 0.00 0.00 4.34
40 41 2.280186 CTGCTCCCGTAATCGCCC 60.280 66.667 0.00 0.00 35.54 6.13
41 42 2.762459 TGCTCCCGTAATCGCCCT 60.762 61.111 0.00 0.00 35.54 5.19
55 56 2.752238 CCCTCGTCGCTCTCCACT 60.752 66.667 0.00 0.00 0.00 4.00
63 64 1.001158 GTCGCTCTCCACTATGGCTAC 60.001 57.143 0.00 0.00 37.47 3.58
76 77 6.703607 CCACTATGGCTACAAACATAGAAGAG 59.296 42.308 16.07 5.47 45.90 2.85
78 79 4.551702 TGGCTACAAACATAGAAGAGCA 57.448 40.909 0.00 0.00 0.00 4.26
90 91 1.996191 AGAAGAGCAAAACGATCGAGC 59.004 47.619 24.34 18.58 34.30 5.03
94 95 0.037326 AGCAAAACGATCGAGCTGGA 60.037 50.000 24.34 0.00 33.67 3.86
102 103 1.469767 CGATCGAGCTGGATCACACAA 60.470 52.381 30.49 0.00 42.35 3.33
108 109 3.141398 GAGCTGGATCACACAAAACTCA 58.859 45.455 0.00 0.00 0.00 3.41
109 110 2.880890 AGCTGGATCACACAAAACTCAC 59.119 45.455 0.00 0.00 0.00 3.51
111 112 3.213506 CTGGATCACACAAAACTCACCA 58.786 45.455 0.00 0.00 0.00 4.17
112 113 3.213506 TGGATCACACAAAACTCACCAG 58.786 45.455 0.00 0.00 0.00 4.00
113 114 2.554032 GGATCACACAAAACTCACCAGG 59.446 50.000 0.00 0.00 0.00 4.45
145 146 2.060383 TCGGGAGAGGTCATGGCTG 61.060 63.158 0.00 0.00 0.00 4.85
151 152 0.690411 AGAGGTCATGGCTGAGGAGG 60.690 60.000 0.00 0.00 30.18 4.30
156 157 1.410882 GTCATGGCTGAGGAGGAGTAC 59.589 57.143 0.00 0.00 30.18 2.73
157 158 0.387202 CATGGCTGAGGAGGAGTACG 59.613 60.000 0.00 0.00 0.00 3.67
158 159 0.259065 ATGGCTGAGGAGGAGTACGA 59.741 55.000 0.00 0.00 0.00 3.43
171 172 0.037303 AGTACGAGTCGAAGGGTCCA 59.963 55.000 21.50 0.00 0.00 4.02
178 179 1.749634 AGTCGAAGGGTCCAACGATAG 59.250 52.381 10.40 0.00 37.14 2.08
234 235 2.725312 GGCAGAGGTGGCGATGAGA 61.725 63.158 0.00 0.00 39.84 3.27
239 240 1.213182 AGAGGTGGCGATGAGACTCTA 59.787 52.381 3.68 0.00 33.87 2.43
256 257 1.615124 TAGCCCTTGCCAGCTGGTA 60.615 57.895 32.81 27.30 40.28 3.25
277 279 2.081161 GGGAGGATCATGCTGGGGT 61.081 63.158 0.00 0.00 36.25 4.95
283 285 2.972892 GATCATGCTGGGGTGGAGGC 62.973 65.000 0.00 0.00 0.00 4.70
301 303 4.828296 GTAGGAGGTCGGCCCGGA 62.828 72.222 0.08 0.00 38.74 5.14
313 315 3.411517 CCCGGATGAGGCCCTGTT 61.412 66.667 0.73 0.00 0.00 3.16
355 357 3.135530 AGACAATGAAGTCATAGCCCCTC 59.864 47.826 0.00 0.00 40.98 4.30
366 368 4.028131 TCATAGCCCCTCTCGTTTTAGAA 58.972 43.478 0.00 0.00 0.00 2.10
374 376 2.742589 CTCTCGTTTTAGAACTTGGGGC 59.257 50.000 0.00 0.00 33.51 5.80
376 378 3.081804 CTCGTTTTAGAACTTGGGGCAT 58.918 45.455 0.00 0.00 33.51 4.40
388 390 2.040544 GGGGCATGACACCTTGACG 61.041 63.158 0.00 0.00 0.00 4.35
407 409 1.138859 CGCCATTGGTGTAGATCCTGA 59.861 52.381 8.14 0.00 0.00 3.86
424 426 3.946907 ACGCAGTAGACGCCAAAC 58.053 55.556 0.00 0.00 41.94 2.93
426 428 2.410638 ACGCAGTAGACGCCAAACGA 62.411 55.000 0.00 0.00 43.11 3.85
475 477 2.045926 CCGACAGAGGCAAAGGGG 60.046 66.667 0.00 0.00 0.00 4.79
478 480 1.676967 GACAGAGGCAAAGGGGCAG 60.677 63.158 0.00 0.00 46.44 4.85
480 482 2.532715 AGAGGCAAAGGGGCAGGA 60.533 61.111 0.00 0.00 46.44 3.86
489 491 2.441001 CAAAGGGGCAGGATGTATCTCT 59.559 50.000 0.00 0.00 39.31 3.10
491 493 1.061812 AGGGGCAGGATGTATCTCTGT 60.062 52.381 10.15 0.00 39.31 3.41
523 525 1.895020 CGGGGATGTCGGTTTGGAGA 61.895 60.000 0.00 0.00 0.00 3.71
524 526 0.326927 GGGGATGTCGGTTTGGAGAA 59.673 55.000 0.00 0.00 0.00 2.87
530 532 5.183228 GGATGTCGGTTTGGAGAATAAAGA 58.817 41.667 0.00 0.00 0.00 2.52
538 540 6.246163 GGTTTGGAGAATAAAGAAGAGGGAA 58.754 40.000 0.00 0.00 0.00 3.97
593 595 2.904434 GTGGGAGTTAACTGAGGGAAGA 59.096 50.000 14.14 0.00 0.00 2.87
595 597 3.174779 GGGAGTTAACTGAGGGAAGAGT 58.825 50.000 14.14 0.00 0.00 3.24
606 608 3.582647 TGAGGGAAGAGTAAGATGCAACA 59.417 43.478 0.00 0.00 0.00 3.33
608 610 4.985538 AGGGAAGAGTAAGATGCAACAAA 58.014 39.130 0.00 0.00 0.00 2.83
617 620 9.066892 AGAGTAAGATGCAACAAAATTAACTCA 57.933 29.630 0.00 0.00 0.00 3.41
634 637 5.921962 AACTCATCAAAATCTAAAGGGCC 57.078 39.130 0.00 0.00 0.00 5.80
643 646 5.483685 AAATCTAAAGGGCCAAGGTTTTC 57.516 39.130 6.18 0.00 0.00 2.29
644 647 2.510613 TCTAAAGGGCCAAGGTTTTCG 58.489 47.619 6.18 0.00 0.00 3.46
645 648 2.106857 TCTAAAGGGCCAAGGTTTTCGA 59.893 45.455 6.18 0.00 0.00 3.71
646 649 1.328279 AAAGGGCCAAGGTTTTCGAG 58.672 50.000 6.18 0.00 0.00 4.04
647 650 0.185175 AAGGGCCAAGGTTTTCGAGT 59.815 50.000 6.18 0.00 0.00 4.18
648 651 0.185175 AGGGCCAAGGTTTTCGAGTT 59.815 50.000 6.18 0.00 0.00 3.01
649 652 0.313987 GGGCCAAGGTTTTCGAGTTG 59.686 55.000 4.39 0.00 0.00 3.16
650 653 1.029681 GGCCAAGGTTTTCGAGTTGT 58.970 50.000 0.00 0.00 0.00 3.32
651 654 1.407618 GGCCAAGGTTTTCGAGTTGTT 59.592 47.619 0.00 0.00 0.00 2.83
652 655 2.543031 GGCCAAGGTTTTCGAGTTGTTC 60.543 50.000 0.00 0.00 0.00 3.18
653 656 2.543031 GCCAAGGTTTTCGAGTTGTTCC 60.543 50.000 0.00 0.00 0.00 3.62
654 657 2.034179 CCAAGGTTTTCGAGTTGTTCCC 59.966 50.000 0.00 0.00 0.00 3.97
655 658 2.949644 CAAGGTTTTCGAGTTGTTCCCT 59.050 45.455 0.00 0.00 0.00 4.20
656 659 4.131596 CAAGGTTTTCGAGTTGTTCCCTA 58.868 43.478 0.00 0.00 0.00 3.53
657 660 4.426736 AGGTTTTCGAGTTGTTCCCTAA 57.573 40.909 0.00 0.00 0.00 2.69
658 661 4.784177 AGGTTTTCGAGTTGTTCCCTAAA 58.216 39.130 0.00 0.00 0.00 1.85
659 662 5.195185 AGGTTTTCGAGTTGTTCCCTAAAA 58.805 37.500 0.00 0.00 0.00 1.52
660 663 5.653330 AGGTTTTCGAGTTGTTCCCTAAAAA 59.347 36.000 0.00 0.00 0.00 1.94
742 746 1.560505 CCTGCCTTTTAACCATGGCT 58.439 50.000 13.04 0.95 45.11 4.75
751 755 3.931907 TTAACCATGGCTAGCTGTCAT 57.068 42.857 13.04 6.91 42.53 3.06
1012 1016 4.800249 GCACAGAGATCATGAAGAGATCCC 60.800 50.000 0.00 0.00 42.19 3.85
1013 1017 3.903090 ACAGAGATCATGAAGAGATCCCC 59.097 47.826 0.00 0.00 42.19 4.81
1014 1018 4.161876 CAGAGATCATGAAGAGATCCCCT 58.838 47.826 0.00 0.00 42.19 4.79
1029 1033 2.018086 CCCTCCTCCTCCTCCTCCT 61.018 68.421 0.00 0.00 0.00 3.69
1213 1217 2.182732 GAGCAGGAGCAGCAAGGAGT 62.183 60.000 0.00 0.00 45.49 3.85
1215 1219 1.981636 CAGGAGCAGCAAGGAGTCT 59.018 57.895 0.00 0.00 0.00 3.24
1263 1267 0.758123 CAGGGAAGAGGAGCTCCATC 59.242 60.000 33.90 25.73 38.89 3.51
1314 1318 3.632145 GCCTGTATTCCGTGGATTGATTT 59.368 43.478 0.00 0.00 0.00 2.17
1332 1336 0.740868 TTCGATCTCTGCCCGCAAAG 60.741 55.000 0.00 0.00 0.00 2.77
1340 1344 0.889186 CTGCCCGCAAAGTAACCAGT 60.889 55.000 0.00 0.00 0.00 4.00
1366 1370 2.124011 CGCATTGCCGCTGATTAATT 57.876 45.000 2.41 0.00 0.00 1.40
1367 1371 3.266541 CGCATTGCCGCTGATTAATTA 57.733 42.857 2.41 0.00 0.00 1.40
1368 1372 3.228749 CGCATTGCCGCTGATTAATTAG 58.771 45.455 2.41 2.91 0.00 1.73
1369 1373 3.568538 GCATTGCCGCTGATTAATTAGG 58.431 45.455 9.11 2.95 0.00 2.69
1370 1374 3.253188 GCATTGCCGCTGATTAATTAGGA 59.747 43.478 9.11 0.00 0.00 2.94
1371 1375 4.614535 GCATTGCCGCTGATTAATTAGGAG 60.615 45.833 9.11 0.00 0.00 3.69
1372 1376 3.838244 TGCCGCTGATTAATTAGGAGT 57.162 42.857 9.11 0.00 0.00 3.85
1373 1377 3.728845 TGCCGCTGATTAATTAGGAGTC 58.271 45.455 9.11 0.00 0.00 3.36
1374 1378 2.731976 GCCGCTGATTAATTAGGAGTCG 59.268 50.000 9.11 4.21 0.00 4.18
1375 1379 2.731976 CCGCTGATTAATTAGGAGTCGC 59.268 50.000 9.11 0.00 0.00 5.19
1376 1380 3.381045 CGCTGATTAATTAGGAGTCGCA 58.619 45.455 9.11 0.00 0.00 5.10
1377 1381 3.182572 CGCTGATTAATTAGGAGTCGCAC 59.817 47.826 9.11 0.00 0.00 5.34
1419 1423 3.485394 TGGCTTGCATGTCAAAAGTCTA 58.515 40.909 4.13 0.00 33.65 2.59
1493 1497 2.290896 TGGAGTTCTTGAATTCGGCCAT 60.291 45.455 2.24 0.00 0.00 4.40
1528 1532 4.282068 CCGTGCTCCATTTGAATAATTCG 58.718 43.478 0.00 0.00 0.00 3.34
1536 1540 6.851609 TCCATTTGAATAATTCGGTCAACTG 58.148 36.000 8.11 8.11 33.86 3.16
1692 1701 4.083110 GCTGCATCCATGTCAATATGTACC 60.083 45.833 0.00 0.00 0.00 3.34
1708 1717 4.704833 CCCAGGCACAGGTGGACG 62.705 72.222 1.10 0.00 35.67 4.79
1962 1973 1.907936 GGCTGCTCTGGATCCTGATAT 59.092 52.381 20.45 0.00 0.00 1.63
1964 1975 3.598299 GCTGCTCTGGATCCTGATATTC 58.402 50.000 20.45 11.17 0.00 1.75
1966 1977 2.909006 TGCTCTGGATCCTGATATTCCC 59.091 50.000 20.45 7.06 0.00 3.97
1967 1978 2.909006 GCTCTGGATCCTGATATTCCCA 59.091 50.000 20.45 0.00 0.00 4.37
1968 1979 3.522750 GCTCTGGATCCTGATATTCCCAT 59.477 47.826 20.45 0.00 0.00 4.00
1969 1980 4.383989 GCTCTGGATCCTGATATTCCCATC 60.384 50.000 20.45 0.70 0.00 3.51
1970 1981 5.031495 CTCTGGATCCTGATATTCCCATCT 58.969 45.833 20.45 0.00 0.00 2.90
1972 1983 5.031495 CTGGATCCTGATATTCCCATCTCT 58.969 45.833 14.23 0.00 0.00 3.10
1973 1984 4.781621 TGGATCCTGATATTCCCATCTCTG 59.218 45.833 14.23 0.00 0.00 3.35
1974 1985 5.028802 GGATCCTGATATTCCCATCTCTGA 58.971 45.833 3.84 0.00 0.00 3.27
1980 1991 9.431690 TCCTGATATTCCCATCTCTGATATTAG 57.568 37.037 0.00 0.00 0.00 1.73
2118 2129 1.750778 TCTGCATGTGACTGCGATCTA 59.249 47.619 0.00 0.00 45.30 1.98
2124 2135 3.766676 TGTGACTGCGATCTACTTCTC 57.233 47.619 0.00 0.00 0.00 2.87
2157 2168 5.664457 TGTGTTGGCTCAATAGTCTATCTG 58.336 41.667 0.00 0.00 0.00 2.90
2193 2204 6.094048 ACAAGCATATTTGTAGACACACATCC 59.906 38.462 0.00 0.00 39.40 3.51
2204 2215 0.615331 CACACATCCAGCCTACCTGT 59.385 55.000 0.00 0.00 40.06 4.00
2336 2347 0.690411 ATACAGAGGAGGCAGCTGCT 60.690 55.000 35.82 22.72 41.70 4.24
2342 2353 4.756458 GAGGCAGCTGCTCGTGCT 62.756 66.667 35.82 24.52 42.06 4.40
2345 2356 2.744768 GGCAGCTGCTCGTGCTTAC 61.745 63.158 35.82 14.01 38.92 2.34
2351 2362 1.914634 CTGCTCGTGCTTACGATCTT 58.085 50.000 11.19 0.00 41.56 2.40
2354 2365 1.629013 CTCGTGCTTACGATCTTGCA 58.371 50.000 2.81 0.00 41.56 4.08
2396 2407 4.339247 CCTGAAACCACACTGAATTTCACT 59.661 41.667 0.00 0.00 36.42 3.41
2400 2411 6.545666 TGAAACCACACTGAATTTCACTGTAT 59.454 34.615 10.21 2.09 36.42 2.29
2429 2440 7.998964 TGTTCTCCTCTTGGAAATAGAAAAAGT 59.001 33.333 0.00 0.00 42.66 2.66
2544 2556 3.769844 ACCACCATTGACTCGAGAGTTAT 59.230 43.478 21.68 3.92 42.66 1.89
2547 2559 4.392921 CCATTGACTCGAGAGTTATGGT 57.607 45.455 21.68 0.00 42.58 3.55
2573 2585 3.677190 ACAGCAGAGAGAGTAGTAACGT 58.323 45.455 0.00 0.00 0.00 3.99
2601 2614 1.268352 GCCCATGTCGCTTGTGTTTTA 59.732 47.619 0.00 0.00 0.00 1.52
2606 2619 4.394795 CATGTCGCTTGTGTTTTAGTAGC 58.605 43.478 0.00 0.00 0.00 3.58
2611 2624 4.682860 TCGCTTGTGTTTTAGTAGCACTAC 59.317 41.667 0.00 0.00 34.52 2.73
2625 2638 6.621316 GTAGCACTACTACTAGATGAGCAA 57.379 41.667 0.00 0.00 46.65 3.91
2629 2642 5.267009 CACTACTACTAGATGAGCAACACG 58.733 45.833 0.00 0.00 0.00 4.49
2747 2764 1.439353 ATTCATGGACGGACGCATGC 61.439 55.000 7.91 7.91 31.80 4.06
2748 2765 2.512286 CATGGACGGACGCATGCT 60.512 61.111 17.13 2.38 0.00 3.79
2749 2766 2.512286 ATGGACGGACGCATGCTG 60.512 61.111 17.13 11.87 0.00 4.41
2797 2814 1.306997 GGAGATGGAGGGGGTGTCA 60.307 63.158 0.00 0.00 0.00 3.58
2899 2916 7.470981 GCCAGGTACTACACTATTACTGCATTA 60.471 40.741 0.00 0.00 36.02 1.90
2916 2933 4.037690 GCATTAATTAGCAGCTCCGTTTG 58.962 43.478 0.00 0.00 0.00 2.93
2920 2937 0.978151 TTAGCAGCTCCGTTTGGGTA 59.022 50.000 0.00 0.00 37.00 3.69
2922 2939 0.605589 AGCAGCTCCGTTTGGGTAAC 60.606 55.000 0.00 0.00 37.00 2.50
2929 2963 3.126343 GCTCCGTTTGGGTAACACTATTG 59.874 47.826 0.00 0.00 36.50 1.90
2931 2965 2.159626 CCGTTTGGGTAACACTATTGCG 60.160 50.000 0.00 0.00 36.50 4.85
2934 2968 2.684001 TGGGTAACACTATTGCGAGG 57.316 50.000 0.00 0.00 39.74 4.63
2951 2985 3.513662 CGAGGCATGCAAAATTCATGAA 58.486 40.909 21.36 11.26 42.84 2.57
2995 3037 3.069016 CCAAGTGTATGCTACGTGGGATA 59.931 47.826 9.05 9.05 41.88 2.59
2999 3041 2.626266 TGTATGCTACGTGGGATACAGG 59.374 50.000 32.24 0.85 42.55 4.00
3080 3122 1.003349 GCAGCTAGGATCCATCTGCAT 59.997 52.381 31.02 9.60 46.64 3.96
3278 3322 1.880027 ACTGGAATTCACAGAAACGGC 59.120 47.619 22.86 0.00 39.24 5.68
3329 3373 5.960683 TCGTGACTAATTTTGACAAAACACG 59.039 36.000 29.25 29.25 45.11 4.49
3375 3424 6.122277 TCAGAGAGAAACAGTTGGATTTGTT 58.878 36.000 0.00 0.00 39.08 2.83
3376 3425 6.038603 TCAGAGAGAAACAGTTGGATTTGTTG 59.961 38.462 0.00 0.00 37.57 3.33
3377 3426 5.888161 AGAGAGAAACAGTTGGATTTGTTGT 59.112 36.000 0.00 0.00 37.57 3.32
3555 3607 8.311109 AGTTTTAATTAATCGGCATTGAAAGGT 58.689 29.630 0.00 0.00 0.00 3.50
3598 3650 1.810151 GTCCTGCTTAACATTCCGCAA 59.190 47.619 0.00 0.00 31.24 4.85
3599 3651 2.083774 TCCTGCTTAACATTCCGCAAG 58.916 47.619 0.00 0.00 31.24 4.01
3600 3652 2.083774 CCTGCTTAACATTCCGCAAGA 58.916 47.619 0.00 0.00 43.02 3.02
3601 3653 2.096496 CCTGCTTAACATTCCGCAAGAG 59.904 50.000 0.00 0.00 43.02 2.85
3602 3654 1.468520 TGCTTAACATTCCGCAAGAGC 59.531 47.619 0.00 0.00 43.02 4.09
3714 3767 3.372730 CAATGCACCACACCCGGG 61.373 66.667 22.25 22.25 0.00 5.73
3752 3805 7.542824 GCTGCTACCATAATCTTTACTACTAGC 59.457 40.741 0.00 0.00 0.00 3.42
3911 3970 0.251297 TCCTGTGTGCAATCCCAAGG 60.251 55.000 0.00 0.00 0.00 3.61
3956 4020 7.369803 AGAATAACATTAAGCACACAGACAG 57.630 36.000 0.00 0.00 0.00 3.51
4231 4301 8.442632 AATGATATGATTCACCACACTAACAG 57.557 34.615 0.00 0.00 0.00 3.16
4342 4412 2.584791 CAGTAGCAAAACACCGCAATC 58.415 47.619 0.00 0.00 0.00 2.67
4450 4520 9.979897 ATTCAGCATCTTCTACTCTAGATATCT 57.020 33.333 10.73 10.73 34.22 1.98
4451 4521 8.791327 TCAGCATCTTCTACTCTAGATATCTG 57.209 38.462 15.79 5.75 34.91 2.90
4452 4522 8.601546 TCAGCATCTTCTACTCTAGATATCTGA 58.398 37.037 15.79 9.58 37.35 3.27
4453 4523 9.399797 CAGCATCTTCTACTCTAGATATCTGAT 57.600 37.037 15.79 3.31 35.22 2.90
4454 4524 9.399797 AGCATCTTCTACTCTAGATATCTGATG 57.600 37.037 15.79 15.19 34.22 3.07
4455 4525 8.131100 GCATCTTCTACTCTAGATATCTGATGC 58.869 40.741 22.51 22.51 37.90 3.91
4456 4526 9.399797 CATCTTCTACTCTAGATATCTGATGCT 57.600 37.037 15.79 0.54 34.22 3.79
4457 4527 9.979897 ATCTTCTACTCTAGATATCTGATGCTT 57.020 33.333 15.79 0.00 34.22 3.91
4458 4528 9.230122 TCTTCTACTCTAGATATCTGATGCTTG 57.770 37.037 15.79 1.03 34.22 4.01
4459 4529 7.389803 TCTACTCTAGATATCTGATGCTTGC 57.610 40.000 15.79 0.00 0.00 4.01
4460 4530 5.058149 ACTCTAGATATCTGATGCTTGCG 57.942 43.478 15.79 1.01 0.00 4.85
4461 4531 3.842820 TCTAGATATCTGATGCTTGCGC 58.157 45.455 15.79 0.00 0.00 6.09
4462 4532 2.835580 AGATATCTGATGCTTGCGCT 57.164 45.000 9.73 0.00 36.97 5.92
4467 4537 1.012086 TCTGATGCTTGCGCTCATTC 58.988 50.000 9.73 0.00 36.97 2.67
4475 4545 2.286067 GCTTGCGCTCATTCACTGATAC 60.286 50.000 9.73 0.00 32.10 2.24
4479 4549 2.205074 CGCTCATTCACTGATACCACC 58.795 52.381 0.00 0.00 32.10 4.61
4490 4560 4.821805 CACTGATACCACCAAACAACTCTT 59.178 41.667 0.00 0.00 0.00 2.85
4496 4587 3.023832 CCACCAAACAACTCTTGTCCTT 58.976 45.455 0.00 0.00 44.59 3.36
4499 4590 3.447229 ACCAAACAACTCTTGTCCTTTGG 59.553 43.478 12.48 12.48 44.59 3.28
4554 4645 6.374333 TGGTAAATTCTGTGATTTAGCTCACC 59.626 38.462 18.97 11.61 44.38 4.02
4684 4775 3.390521 CGCTACCTGGACCAGCCA 61.391 66.667 16.72 4.57 46.96 4.75
4694 4785 0.685097 GGACCAGCCACAGTTACTGA 59.315 55.000 20.07 0.00 35.18 3.41
4756 4847 3.871485 AGAGGAGCTTCAACATGATCAC 58.129 45.455 0.00 0.00 0.00 3.06
4804 4895 0.106708 ACTCAGGTGAAGCGCAGAAA 59.893 50.000 11.47 0.00 0.00 2.52
4807 4898 1.148273 AGGTGAAGCGCAGAAACCA 59.852 52.632 11.47 0.00 33.13 3.67
4825 4916 2.508663 GGTAGCGTCAACGAGCCC 60.509 66.667 6.75 0.00 43.02 5.19
4861 4952 1.270305 ACAGACAACACCGGAGACATG 60.270 52.381 9.46 5.48 0.00 3.21
4928 5025 2.936202 GCCCTTGCTATGAATTGGAGA 58.064 47.619 0.00 0.00 33.53 3.71
4929 5026 3.290710 GCCCTTGCTATGAATTGGAGAA 58.709 45.455 0.00 0.00 33.53 2.87
4931 5028 4.530875 CCCTTGCTATGAATTGGAGAACT 58.469 43.478 0.00 0.00 0.00 3.01
4939 5036 5.990120 ATGAATTGGAGAACTTCTTTGGG 57.010 39.130 0.00 0.00 0.00 4.12
4941 5038 1.995376 TTGGAGAACTTCTTTGGGCC 58.005 50.000 0.00 0.00 0.00 5.80
4943 5040 0.112412 GGAGAACTTCTTTGGGCCCA 59.888 55.000 24.45 24.45 0.00 5.36
4947 5044 1.760029 GAACTTCTTTGGGCCCAACAA 59.240 47.619 37.33 28.25 35.46 2.83
4974 5071 3.887339 CTCGATGAATCTGAGCGAGTA 57.113 47.619 0.00 0.00 42.35 2.59
4983 5080 1.878088 TCTGAGCGAGTACTTCAACGT 59.122 47.619 0.00 0.00 0.00 3.99
4984 5081 3.069289 TCTGAGCGAGTACTTCAACGTA 58.931 45.455 0.00 0.00 0.00 3.57
4985 5082 3.499537 TCTGAGCGAGTACTTCAACGTAA 59.500 43.478 0.00 0.00 0.00 3.18
4986 5083 4.023792 TCTGAGCGAGTACTTCAACGTAAA 60.024 41.667 0.00 0.00 0.00 2.01
4987 5084 3.976942 TGAGCGAGTACTTCAACGTAAAC 59.023 43.478 0.00 0.00 0.00 2.01
4988 5085 2.975851 AGCGAGTACTTCAACGTAAACG 59.024 45.455 0.00 0.04 46.33 3.60
4989 5086 2.973224 GCGAGTACTTCAACGTAAACGA 59.027 45.455 9.86 0.00 43.02 3.85
4990 5087 3.605486 GCGAGTACTTCAACGTAAACGAT 59.395 43.478 9.86 0.00 43.02 3.73
4991 5088 4.488258 GCGAGTACTTCAACGTAAACGATG 60.488 45.833 9.86 7.99 42.39 3.84
4999 5096 1.886886 ACGTAAACGATGCCACCTTT 58.113 45.000 9.86 0.00 43.02 3.11
5269 5366 6.040616 TGTTGGGTATACTTCTTAGCTAGCTC 59.959 42.308 23.26 1.99 0.00 4.09
5340 5440 2.567169 CCCCATCCTTTGAGAAAAACCC 59.433 50.000 0.00 0.00 0.00 4.11
5395 5495 6.015434 GCCAATGTTCCTTTTTCTTCTCCTTA 60.015 38.462 0.00 0.00 0.00 2.69
5405 5505 8.358148 CCTTTTTCTTCTCCTTAAAAGTTACCC 58.642 37.037 0.00 0.00 36.39 3.69
5558 5665 5.126707 ACTTGTTCCTATAGAAGTACGGTGG 59.873 44.000 0.00 0.00 34.29 4.61
5658 6030 0.179111 TTCCCGCTACGAATGCAGAG 60.179 55.000 0.00 0.00 0.00 3.35
5659 6031 1.035385 TCCCGCTACGAATGCAGAGA 61.035 55.000 0.00 0.00 0.00 3.10
5660 6032 0.179111 CCCGCTACGAATGCAGAGAA 60.179 55.000 0.00 0.00 0.00 2.87
5662 6034 1.524355 CCGCTACGAATGCAGAGAATG 59.476 52.381 0.00 0.00 0.00 2.67
5664 6036 2.217393 CGCTACGAATGCAGAGAATGTC 59.783 50.000 0.00 0.00 0.00 3.06
5665 6037 2.541762 GCTACGAATGCAGAGAATGTCC 59.458 50.000 0.00 0.00 0.00 4.02
5666 6038 3.739519 GCTACGAATGCAGAGAATGTCCT 60.740 47.826 0.00 0.00 0.00 3.85
5667 6039 4.499865 GCTACGAATGCAGAGAATGTCCTA 60.500 45.833 0.00 0.00 0.00 2.94
5668 6040 4.052159 ACGAATGCAGAGAATGTCCTAG 57.948 45.455 0.00 0.00 0.00 3.02
5669 6041 3.181471 ACGAATGCAGAGAATGTCCTAGG 60.181 47.826 0.82 0.82 0.00 3.02
5670 6042 3.181471 CGAATGCAGAGAATGTCCTAGGT 60.181 47.826 9.08 0.00 0.00 3.08
5672 6044 2.111384 TGCAGAGAATGTCCTAGGTCC 58.889 52.381 9.08 1.26 0.00 4.46
5673 6045 1.414550 GCAGAGAATGTCCTAGGTCCC 59.585 57.143 9.08 0.00 0.00 4.46
5724 6097 6.922957 TCTTAACTTCCATTCAACACAAATGC 59.077 34.615 0.00 0.00 33.65 3.56
5754 6129 5.734963 GTGGTAAAAACAAAAACAAATGCCG 59.265 36.000 0.00 0.00 0.00 5.69
5818 6193 9.983804 CGTAGAAATAGTTCAATAAAAGTTCCC 57.016 33.333 5.62 0.00 36.09 3.97
5826 6201 4.658063 TCAATAAAAGTTCCCGTCATGGT 58.342 39.130 0.00 0.00 35.15 3.55
5844 6219 7.865385 CGTCATGGTTATTCTTTTTCCTTTTCA 59.135 33.333 0.00 0.00 0.00 2.69
5884 6270 5.486526 GGCAGAACCTCAGGATATATTCTG 58.513 45.833 14.17 14.17 43.74 3.02
5892 6278 6.553852 ACCTCAGGATATATTCTGGTAAACGT 59.446 38.462 19.14 5.73 0.00 3.99
5992 6413 8.866093 ACTTAACAAAGGGCTACATAACATTTT 58.134 29.630 0.00 0.00 0.00 1.82
5998 6419 9.271828 CAAAGGGCTACATAACATTTTCTTTTT 57.728 29.630 0.00 0.00 0.00 1.94
6077 6499 1.228124 CGGCAAGGTGGGAGACAAA 60.228 57.895 0.00 0.00 0.00 2.83
6182 6604 2.527123 TTCACCCTACCACGGCCA 60.527 61.111 2.24 0.00 0.00 5.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.654143 TCGTGAGGAGGGGGTCGA 61.654 66.667 0.00 0.00 0.00 4.20
1 2 3.450115 GTCGTGAGGAGGGGGTCG 61.450 72.222 0.00 0.00 0.00 4.79
2 3 3.075641 GGTCGTGAGGAGGGGGTC 61.076 72.222 0.00 0.00 0.00 4.46
18 19 3.809374 GATTACGGGAGCAGGGCGG 62.809 68.421 0.00 0.00 0.00 6.13
23 24 2.280186 GGGCGATTACGGGAGCAG 60.280 66.667 0.00 0.00 40.15 4.24
32 33 1.783031 GAGAGCGACGAGGGCGATTA 61.783 60.000 0.00 0.00 41.64 1.75
40 41 0.309302 CCATAGTGGAGAGCGACGAG 59.691 60.000 0.00 0.00 40.96 4.18
41 42 1.725557 GCCATAGTGGAGAGCGACGA 61.726 60.000 0.00 0.00 40.96 4.20
55 56 6.233905 TGCTCTTCTATGTTTGTAGCCATA 57.766 37.500 0.00 0.00 0.00 2.74
63 64 5.729883 CGATCGTTTTGCTCTTCTATGTTTG 59.270 40.000 7.03 0.00 0.00 2.93
76 77 1.004504 GATCCAGCTCGATCGTTTTGC 60.005 52.381 15.94 14.61 29.96 3.68
78 79 2.271800 GTGATCCAGCTCGATCGTTTT 58.728 47.619 15.94 0.00 41.39 2.43
90 91 3.213506 TGGTGAGTTTTGTGTGATCCAG 58.786 45.455 0.00 0.00 0.00 3.86
94 95 3.480470 CTCCTGGTGAGTTTTGTGTGAT 58.520 45.455 0.00 0.00 36.27 3.06
111 112 2.889200 CGAGAGGCCAGTAACTCCT 58.111 57.895 5.01 0.00 34.27 3.69
145 146 1.935199 CTTCGACTCGTACTCCTCCTC 59.065 57.143 0.00 0.00 0.00 3.71
151 152 0.731994 GGACCCTTCGACTCGTACTC 59.268 60.000 0.00 0.00 0.00 2.59
156 157 1.443872 CGTTGGACCCTTCGACTCG 60.444 63.158 0.00 0.00 0.00 4.18
157 158 0.531200 ATCGTTGGACCCTTCGACTC 59.469 55.000 5.20 0.00 35.24 3.36
158 159 1.749634 CTATCGTTGGACCCTTCGACT 59.250 52.381 5.20 0.26 35.24 4.18
171 172 2.871022 AGCACGACTATCGACTATCGTT 59.129 45.455 14.83 2.26 44.98 3.85
178 179 1.400846 TGAAGGAGCACGACTATCGAC 59.599 52.381 5.04 0.00 43.74 4.20
207 208 2.527624 ACCTCTGCCACCAGCTCA 60.528 61.111 0.00 0.00 44.23 4.26
239 240 2.311854 ATACCAGCTGGCAAGGGCT 61.312 57.895 33.06 13.90 40.87 5.19
256 257 1.432852 CCCAGCATGATCCTCCCCAT 61.433 60.000 0.00 0.00 39.69 4.00
277 279 2.439701 CGACCTCCTACGCCTCCA 60.440 66.667 0.00 0.00 0.00 3.86
297 299 2.124570 CAACAGGGCCTCATCCGG 60.125 66.667 0.95 0.00 0.00 5.14
301 303 1.693640 CTTCCCAACAGGGCCTCAT 59.306 57.895 0.95 0.00 42.73 2.90
313 315 1.220749 GTCTATGTGCGGCTTCCCA 59.779 57.895 0.00 0.00 0.00 4.37
320 322 3.261580 TCATTGTCTTGTCTATGTGCGG 58.738 45.455 0.00 0.00 0.00 5.69
355 357 2.500229 TGCCCCAAGTTCTAAAACGAG 58.500 47.619 0.00 0.00 40.48 4.18
366 368 0.540365 CAAGGTGTCATGCCCCAAGT 60.540 55.000 0.00 0.00 0.00 3.16
374 376 1.135603 CAATGGCGTCAAGGTGTCATG 60.136 52.381 0.00 0.00 0.00 3.07
376 378 0.888736 CCAATGGCGTCAAGGTGTCA 60.889 55.000 0.00 0.00 0.00 3.58
388 390 2.565841 GTCAGGATCTACACCAATGGC 58.434 52.381 0.00 0.00 0.00 4.40
407 409 2.019951 CGTTTGGCGTCTACTGCGT 61.020 57.895 0.00 0.00 35.54 5.24
426 428 2.762459 TATTCACCGAGCGGGGCT 60.762 61.111 14.07 2.76 43.88 5.19
475 477 3.827008 TCCAACAGAGATACATCCTGC 57.173 47.619 0.00 0.00 32.10 4.85
478 480 4.202264 ACCGAATCCAACAGAGATACATCC 60.202 45.833 0.00 0.00 0.00 3.51
480 482 4.405680 TGACCGAATCCAACAGAGATACAT 59.594 41.667 0.00 0.00 0.00 2.29
489 491 1.004320 CCCGTGACCGAATCCAACA 60.004 57.895 0.00 0.00 35.63 3.33
491 493 1.268992 ATCCCCGTGACCGAATCCAA 61.269 55.000 0.00 0.00 35.63 3.53
523 525 6.601217 GCATGTCTCTTTCCCTCTTCTTTATT 59.399 38.462 0.00 0.00 0.00 1.40
524 526 6.069731 AGCATGTCTCTTTCCCTCTTCTTTAT 60.070 38.462 0.00 0.00 0.00 1.40
530 532 3.308046 GGAAGCATGTCTCTTTCCCTCTT 60.308 47.826 0.00 0.00 0.00 2.85
538 540 1.376543 CGCATGGAAGCATGTCTCTT 58.623 50.000 0.00 0.00 35.16 2.85
565 567 4.565028 CCTCAGTTAACTCCCACTAAACCC 60.565 50.000 4.77 0.00 0.00 4.11
567 569 4.285260 TCCCTCAGTTAACTCCCACTAAAC 59.715 45.833 4.77 0.00 0.00 2.01
568 570 4.495565 TCCCTCAGTTAACTCCCACTAAA 58.504 43.478 4.77 0.00 0.00 1.85
569 571 4.136341 TCCCTCAGTTAACTCCCACTAA 57.864 45.455 4.77 0.00 0.00 2.24
570 572 3.839323 TCCCTCAGTTAACTCCCACTA 57.161 47.619 4.77 0.00 0.00 2.74
593 595 9.846248 GATGAGTTAATTTTGTTGCATCTTACT 57.154 29.630 0.00 0.00 0.00 2.24
608 610 8.478066 GGCCCTTTAGATTTTGATGAGTTAATT 58.522 33.333 0.00 0.00 0.00 1.40
617 620 4.687976 ACCTTGGCCCTTTAGATTTTGAT 58.312 39.130 0.00 0.00 0.00 2.57
625 628 2.488153 CTCGAAAACCTTGGCCCTTTAG 59.512 50.000 0.00 0.00 0.00 1.85
631 634 1.029681 ACAACTCGAAAACCTTGGCC 58.970 50.000 0.00 0.00 0.00 5.36
634 637 2.949644 AGGGAACAACTCGAAAACCTTG 59.050 45.455 0.00 0.00 0.00 3.61
659 662 8.669946 TTCTCAAACAACTTCAAAACCTTTTT 57.330 26.923 0.00 0.00 0.00 1.94
660 663 8.669946 TTTCTCAAACAACTTCAAAACCTTTT 57.330 26.923 0.00 0.00 0.00 2.27
661 664 8.720562 CATTTCTCAAACAACTTCAAAACCTTT 58.279 29.630 0.00 0.00 0.00 3.11
662 665 8.093927 TCATTTCTCAAACAACTTCAAAACCTT 58.906 29.630 0.00 0.00 0.00 3.50
663 666 7.610865 TCATTTCTCAAACAACTTCAAAACCT 58.389 30.769 0.00 0.00 0.00 3.50
664 667 7.826260 TCATTTCTCAAACAACTTCAAAACC 57.174 32.000 0.00 0.00 0.00 3.27
670 673 9.706846 CCAATTTTTCATTTCTCAAACAACTTC 57.293 29.630 0.00 0.00 0.00 3.01
671 674 9.447157 TCCAATTTTTCATTTCTCAAACAACTT 57.553 25.926 0.00 0.00 0.00 2.66
692 695 2.160721 TCTCTAGCCGTTCCTCCAAT 57.839 50.000 0.00 0.00 0.00 3.16
695 698 0.032815 GCATCTCTAGCCGTTCCTCC 59.967 60.000 0.00 0.00 0.00 4.30
742 746 0.536724 ACATGCACCGATGACAGCTA 59.463 50.000 0.00 0.00 0.00 3.32
879 883 1.435515 GCCTGGTACTCTGCTCGAG 59.564 63.158 8.45 8.45 45.56 4.04
1012 1016 1.292941 TGAGGAGGAGGAGGAGGAGG 61.293 65.000 0.00 0.00 0.00 4.30
1013 1017 0.185901 CTGAGGAGGAGGAGGAGGAG 59.814 65.000 0.00 0.00 0.00 3.69
1014 1018 1.943730 GCTGAGGAGGAGGAGGAGGA 61.944 65.000 0.00 0.00 0.00 3.71
1029 1033 2.167281 CGAAGAAGAAGGAGATGGCTGA 59.833 50.000 0.00 0.00 0.00 4.26
1080 1084 0.033894 AGTCGGAGGAGGAAGGAGAC 60.034 60.000 0.00 0.00 0.00 3.36
1243 1247 1.344191 ATGGAGCTCCTCTTCCCTGC 61.344 60.000 32.28 3.29 36.82 4.85
1245 1249 0.641601 AGATGGAGCTCCTCTTCCCT 59.358 55.000 32.28 16.49 36.82 4.20
1263 1267 1.645710 ACCTTGTGACCCCTCTGTAG 58.354 55.000 0.00 0.00 0.00 2.74
1314 1318 1.153568 CTTTGCGGGCAGAGATCGA 60.154 57.895 5.33 0.00 30.72 3.59
1332 1336 2.919666 ATGCGCAATTGACTGGTTAC 57.080 45.000 17.11 0.00 0.00 2.50
1366 1370 2.422597 CAACCAATTGTGCGACTCCTA 58.577 47.619 4.43 0.00 0.00 2.94
1367 1371 1.238439 CAACCAATTGTGCGACTCCT 58.762 50.000 4.43 0.00 0.00 3.69
1368 1372 0.240945 CCAACCAATTGTGCGACTCC 59.759 55.000 4.43 0.00 33.60 3.85
1369 1373 0.951558 ACCAACCAATTGTGCGACTC 59.048 50.000 4.43 0.00 33.60 3.36
1370 1374 0.951558 GACCAACCAATTGTGCGACT 59.048 50.000 4.43 0.00 33.60 4.18
1371 1375 0.039527 GGACCAACCAATTGTGCGAC 60.040 55.000 4.43 0.00 38.79 5.19
1372 1376 1.175983 GGGACCAACCAATTGTGCGA 61.176 55.000 4.43 0.00 41.20 5.10
1373 1377 1.288752 GGGACCAACCAATTGTGCG 59.711 57.895 4.43 0.00 41.20 5.34
1402 1406 3.568007 GGGTGTAGACTTTTGACATGCAA 59.432 43.478 0.00 0.00 33.88 4.08
1493 1497 0.605319 AGCACGGCAAGAAAATCCGA 60.605 50.000 6.91 0.00 45.53 4.55
1536 1540 6.034161 TCCTACTTCCTAACAACTAACAGC 57.966 41.667 0.00 0.00 0.00 4.40
1692 1701 4.704833 CCGTCCACCTGTGCCTGG 62.705 72.222 0.00 0.00 0.00 4.45
1708 1717 2.109126 GTGTGCCTCGAATCTGCCC 61.109 63.158 0.00 0.00 0.00 5.36
1868 1877 8.506168 TCGTATTGCATCTCTATTTTTCCTTT 57.494 30.769 0.00 0.00 0.00 3.11
1870 1879 6.708054 CCTCGTATTGCATCTCTATTTTTCCT 59.292 38.462 0.00 0.00 0.00 3.36
1877 1887 4.774726 ACCATCCTCGTATTGCATCTCTAT 59.225 41.667 0.00 0.00 0.00 1.98
1962 1973 6.499106 TTGTGCTAATATCAGAGATGGGAA 57.501 37.500 0.00 0.00 0.00 3.97
1964 1975 5.180868 GCTTTGTGCTAATATCAGAGATGGG 59.819 44.000 0.00 0.00 38.95 4.00
1966 1977 6.856135 TGCTTTGTGCTAATATCAGAGATG 57.144 37.500 0.00 0.00 43.37 2.90
1967 1978 9.736414 AATATGCTTTGTGCTAATATCAGAGAT 57.264 29.630 0.00 0.00 43.37 2.75
1968 1979 9.565090 AAATATGCTTTGTGCTAATATCAGAGA 57.435 29.630 0.00 0.00 43.37 3.10
2001 2012 7.163032 CCTTAATAAATTCGTTTCGCTTTACGG 59.837 37.037 0.00 0.00 43.89 4.02
2013 2024 7.552687 TCAGAATGTCAGCCTTAATAAATTCGT 59.447 33.333 0.00 0.00 37.40 3.85
2118 2129 3.498774 ACACAGCATCAAAGGAGAAGT 57.501 42.857 0.00 0.00 0.00 3.01
2124 2135 0.963962 AGCCAACACAGCATCAAAGG 59.036 50.000 0.00 0.00 0.00 3.11
2193 2204 1.270550 CTGCCAAAAACAGGTAGGCTG 59.729 52.381 0.00 0.00 45.42 4.85
2204 2215 5.163426 ACAAGTGACATGAATCTGCCAAAAA 60.163 36.000 0.00 0.00 0.00 1.94
2266 2277 7.641411 CCAAATCGTCAACAAGCAGATTATAAG 59.359 37.037 0.00 0.00 32.05 1.73
2351 2362 2.658285 CCCCAATATTTGAGAGCTGCA 58.342 47.619 1.02 0.00 0.00 4.41
2354 2365 1.133356 GGGCCCCAATATTTGAGAGCT 60.133 52.381 12.23 0.00 0.00 4.09
2396 2407 5.560722 TTCCAAGAGGAGAACAACATACA 57.439 39.130 0.00 0.00 46.74 2.29
2400 2411 6.433847 TCTATTTCCAAGAGGAGAACAACA 57.566 37.500 0.00 0.00 46.74 3.33
2443 2455 8.070171 GCAACTTGGATGTATATGTACACATTC 58.930 37.037 4.25 0.00 43.21 2.67
2455 2467 2.009774 GACGCAGCAACTTGGATGTAT 58.990 47.619 0.00 0.00 0.00 2.29
2544 2556 0.469892 TCTCTCTGCTGTCACCACCA 60.470 55.000 0.00 0.00 0.00 4.17
2547 2559 2.224892 ACTACTCTCTCTGCTGTCACCA 60.225 50.000 0.00 0.00 0.00 4.17
2606 2619 5.267009 CGTGTTGCTCATCTAGTAGTAGTG 58.733 45.833 4.51 3.34 0.00 2.74
2611 2624 3.150848 TGCGTGTTGCTCATCTAGTAG 57.849 47.619 0.00 0.00 46.63 2.57
2612 2625 3.801114 ATGCGTGTTGCTCATCTAGTA 57.199 42.857 0.00 0.00 46.63 1.82
2625 2638 0.519961 GGCCGTCTTTTTATGCGTGT 59.480 50.000 0.00 0.00 0.00 4.49
2629 2642 3.569250 TTCAAGGCCGTCTTTTTATGC 57.431 42.857 0.00 0.00 32.41 3.14
2747 2764 0.807667 GCGTACTCATCCACCTGCAG 60.808 60.000 6.78 6.78 0.00 4.41
2748 2765 1.218047 GCGTACTCATCCACCTGCA 59.782 57.895 0.00 0.00 0.00 4.41
2749 2766 1.878522 CGCGTACTCATCCACCTGC 60.879 63.158 0.00 0.00 0.00 4.85
2899 2916 1.271926 ACCCAAACGGAGCTGCTAATT 60.272 47.619 0.15 0.00 34.64 1.40
2916 2933 1.296727 GCCTCGCAATAGTGTTACCC 58.703 55.000 0.00 0.00 0.00 3.69
2920 2937 0.734889 GCATGCCTCGCAATAGTGTT 59.265 50.000 6.36 0.00 43.62 3.32
2922 2939 0.734309 TTGCATGCCTCGCAATAGTG 59.266 50.000 16.68 0.00 44.13 2.74
2929 2963 1.591158 CATGAATTTTGCATGCCTCGC 59.409 47.619 16.68 0.23 37.00 5.03
2931 2965 4.751060 TCTTCATGAATTTTGCATGCCTC 58.249 39.130 16.68 4.66 42.13 4.70
2934 2968 5.061808 GTGTCTCTTCATGAATTTTGCATGC 59.938 40.000 11.82 11.82 42.13 4.06
2951 2985 0.952497 CTTGCATGCCACGTGTCTCT 60.952 55.000 16.68 0.00 0.00 3.10
2995 3037 1.892819 CGAGTCAGCACCATCCCTGT 61.893 60.000 0.00 0.00 0.00 4.00
2999 3041 2.187946 CCCGAGTCAGCACCATCC 59.812 66.667 0.00 0.00 0.00 3.51
3080 3122 1.293179 CATGCCACTGACTCCACGA 59.707 57.895 0.00 0.00 0.00 4.35
3278 3322 7.894376 AAAAAGTTGGATGCATATTGTTGAG 57.106 32.000 0.00 0.00 0.00 3.02
3303 3347 7.184106 GTGTTTTGTCAAAATTAGTCACGAGA 58.816 34.615 13.65 0.00 32.22 4.04
3304 3348 6.138546 CGTGTTTTGTCAAAATTAGTCACGAG 59.861 38.462 28.96 13.11 44.51 4.18
3306 3350 5.170625 CCGTGTTTTGTCAAAATTAGTCACG 59.829 40.000 27.42 27.42 42.48 4.35
3307 3351 5.457473 CCCGTGTTTTGTCAAAATTAGTCAC 59.543 40.000 13.65 14.06 32.22 3.67
3308 3352 5.357314 TCCCGTGTTTTGTCAAAATTAGTCA 59.643 36.000 13.65 4.39 32.22 3.41
3329 3373 7.961325 TGAAATTTCAGCAAAATTAGTTCCC 57.039 32.000 16.91 0.00 44.88 3.97
3499 3548 2.624557 GCTCAAAGGAGTAGGAGGAGGA 60.625 54.545 0.00 0.00 43.37 3.71
3555 3607 5.927689 ACGATTCTACAACGAACAATGGTAA 59.072 36.000 0.00 0.00 0.00 2.85
3602 3654 2.189191 TTAGGTGGGCAGCTGCTCTG 62.189 60.000 36.89 2.28 43.37 3.35
3714 3767 1.587547 GTAGCAGCATCAGGGTAAGC 58.412 55.000 0.00 0.00 0.00 3.09
3721 3774 6.933521 AGTAAAGATTATGGTAGCAGCATCAG 59.066 38.462 15.08 0.00 37.51 2.90
3723 3776 8.091449 AGTAGTAAAGATTATGGTAGCAGCATC 58.909 37.037 0.00 4.51 37.51 3.91
3911 3970 0.613012 AGGGCAAGTTGAGCAATCCC 60.613 55.000 7.16 6.46 0.00 3.85
3956 4020 2.983136 CGTATGATCTGATCCAACGCTC 59.017 50.000 21.13 5.15 32.38 5.03
4013 4083 3.807538 CGTGCTGCTCACATGCCC 61.808 66.667 0.00 0.00 45.92 5.36
4167 4237 4.099633 TCCTGAATCTTGATCTGGTCTGT 58.900 43.478 0.00 0.00 37.24 3.41
4337 4407 2.675348 GCTGGTCACTAGAGTTGATTGC 59.325 50.000 0.00 0.00 0.00 3.56
4342 4412 2.820059 TGTGCTGGTCACTAGAGTTG 57.180 50.000 0.00 0.00 45.81 3.16
4417 4487 6.593382 AGAGTAGAAGATGCTGAATTTCACAC 59.407 38.462 0.00 0.00 0.00 3.82
4455 4525 2.286294 GGTATCAGTGAATGAGCGCAAG 59.714 50.000 11.47 0.00 42.53 4.01
4456 4526 2.279741 GGTATCAGTGAATGAGCGCAA 58.720 47.619 11.47 0.00 42.53 4.85
4457 4527 1.206849 TGGTATCAGTGAATGAGCGCA 59.793 47.619 11.47 0.00 42.53 6.09
4458 4528 1.594862 GTGGTATCAGTGAATGAGCGC 59.405 52.381 0.00 0.00 42.53 5.92
4459 4529 2.205074 GGTGGTATCAGTGAATGAGCG 58.795 52.381 0.00 0.00 42.53 5.03
4460 4530 3.266510 TGGTGGTATCAGTGAATGAGC 57.733 47.619 0.00 0.00 42.53 4.26
4461 4531 5.003160 TGTTTGGTGGTATCAGTGAATGAG 58.997 41.667 0.00 0.00 42.53 2.90
4462 4532 4.979335 TGTTTGGTGGTATCAGTGAATGA 58.021 39.130 0.00 0.00 43.70 2.57
4467 4537 4.389374 AGAGTTGTTTGGTGGTATCAGTG 58.611 43.478 0.00 0.00 0.00 3.66
4475 4545 2.654863 AGGACAAGAGTTGTTTGGTGG 58.345 47.619 0.00 0.00 45.52 4.61
4479 4549 3.699038 TCCCAAAGGACAAGAGTTGTTTG 59.301 43.478 0.00 0.00 45.52 2.93
4490 4560 2.445145 TCCATTGTTCTCCCAAAGGACA 59.555 45.455 0.00 0.00 42.06 4.02
4496 4587 0.776810 TGGCTCCATTGTTCTCCCAA 59.223 50.000 0.00 0.00 0.00 4.12
4499 4590 3.511146 TCAAATTGGCTCCATTGTTCTCC 59.489 43.478 0.00 0.00 0.00 3.71
4554 4645 5.236047 GCAGGAAGAAAGTAGATGCACTATG 59.764 44.000 0.00 0.00 33.39 2.23
4639 4730 0.111001 CGAAGTTGGTTACGGCGTTG 60.111 55.000 21.24 0.00 0.00 4.10
4694 4785 2.839098 CCCCTGCTCCAGTTGTGT 59.161 61.111 0.00 0.00 0.00 3.72
4756 4847 1.955778 TGGACTGCATTGTCACTTTGG 59.044 47.619 8.22 0.00 38.61 3.28
4768 4859 0.761187 AGTTGAGCTCTTGGACTGCA 59.239 50.000 16.19 0.00 0.00 4.41
4804 4895 1.585006 CTCGTTGACGCTACCTGGT 59.415 57.895 4.05 4.05 39.60 4.00
4807 4898 2.572284 GGCTCGTTGACGCTACCT 59.428 61.111 0.00 0.00 39.60 3.08
4825 4916 2.161012 GTCTGTGTCATCCACTGCAATG 59.839 50.000 0.00 0.00 44.81 2.82
4848 4939 3.068881 CACCCATGTCTCCGGTGT 58.931 61.111 0.00 0.00 41.80 4.16
4850 4941 3.717294 GGCACCCATGTCTCCGGT 61.717 66.667 0.00 0.00 0.00 5.28
4921 5018 2.529632 GGCCCAAAGAAGTTCTCCAAT 58.470 47.619 5.70 0.00 0.00 3.16
4927 5024 1.408969 TGTTGGGCCCAAAGAAGTTC 58.591 50.000 38.70 23.79 37.70 3.01
4928 5025 1.484653 GTTGTTGGGCCCAAAGAAGTT 59.515 47.619 38.70 0.00 37.70 2.66
4929 5026 1.119684 GTTGTTGGGCCCAAAGAAGT 58.880 50.000 38.70 0.00 37.70 3.01
4931 5028 1.118838 CTGTTGTTGGGCCCAAAGAA 58.881 50.000 38.70 28.86 37.70 2.52
4939 5036 1.008538 CGAGTTGCTGTTGTTGGGC 60.009 57.895 0.00 0.00 0.00 5.36
4941 5038 1.872952 TCATCGAGTTGCTGTTGTTGG 59.127 47.619 0.00 0.00 0.00 3.77
4943 5040 4.067896 AGATTCATCGAGTTGCTGTTGTT 58.932 39.130 0.00 0.00 0.00 2.83
4947 5044 3.519579 CTCAGATTCATCGAGTTGCTGT 58.480 45.455 0.00 0.00 0.00 4.40
4974 5071 2.222445 GTGGCATCGTTTACGTTGAAGT 59.778 45.455 15.31 0.00 40.40 3.01
4983 5080 3.334691 CTCTCAAAGGTGGCATCGTTTA 58.665 45.455 0.00 0.00 0.00 2.01
4984 5081 2.154462 CTCTCAAAGGTGGCATCGTTT 58.846 47.619 0.00 0.00 0.00 3.60
4985 5082 1.813513 CTCTCAAAGGTGGCATCGTT 58.186 50.000 0.00 0.00 0.00 3.85
4986 5083 0.674895 GCTCTCAAAGGTGGCATCGT 60.675 55.000 0.00 0.00 0.00 3.73
4987 5084 0.674581 TGCTCTCAAAGGTGGCATCG 60.675 55.000 0.00 0.00 0.00 3.84
4988 5085 1.200948 GTTGCTCTCAAAGGTGGCATC 59.799 52.381 0.00 0.00 33.37 3.91
4989 5086 1.251251 GTTGCTCTCAAAGGTGGCAT 58.749 50.000 0.00 0.00 33.37 4.40
4990 5087 0.106769 TGTTGCTCTCAAAGGTGGCA 60.107 50.000 0.00 0.00 33.37 4.92
4991 5088 1.200948 GATGTTGCTCTCAAAGGTGGC 59.799 52.381 0.00 0.00 33.37 5.01
4999 5096 0.535335 GGTACCCGATGTTGCTCTCA 59.465 55.000 0.00 0.00 0.00 3.27
5044 5141 4.994471 TGCCTGGTGCTGCAGTCG 62.994 66.667 16.64 0.00 42.00 4.18
5141 5238 4.385825 ACATCGTTTGCTTGAGGAGTTAA 58.614 39.130 0.00 0.00 0.00 2.01
5269 5366 1.620819 ACAGACAGACAGCCTACAAGG 59.379 52.381 0.00 0.00 38.80 3.61
5340 5440 4.949856 ACCATACCAAGTAGAATGCCTTTG 59.050 41.667 0.00 0.00 0.00 2.77
5405 5505 7.595502 CGTTGAGGTTAGTATATTAGCCTTCTG 59.404 40.741 11.23 1.02 34.78 3.02
5552 5654 5.320277 GGAGTAGTATATTAGGACCACCGT 58.680 45.833 0.00 0.00 41.83 4.83
5553 5655 4.704057 GGGAGTAGTATATTAGGACCACCG 59.296 50.000 0.00 0.00 41.83 4.94
5554 5656 5.901598 AGGGAGTAGTATATTAGGACCACC 58.098 45.833 0.00 0.00 0.00 4.61
5558 5665 9.804977 TTTACAGAGGGAGTAGTATATTAGGAC 57.195 37.037 0.00 0.00 0.00 3.85
5601 5708 6.033619 GCAAGCTATATTGTAATACGTCCTCG 59.966 42.308 0.00 0.00 36.50 4.63
5635 6007 2.088423 TGCATTCGTAGCGGGAATTTT 58.912 42.857 0.00 0.00 31.98 1.82
5708 6080 3.930229 CAGATGGCATTTGTGTTGAATGG 59.070 43.478 9.72 0.00 35.54 3.16
5754 6129 5.388578 GCAAGAACGTTGCTTCTAAGTACTC 60.389 44.000 5.00 0.00 41.87 2.59
5818 6193 7.865385 TGAAAAGGAAAAAGAATAACCATGACG 59.135 33.333 0.00 0.00 0.00 4.35
5892 6278 8.031864 ACATGACAATTCGCCAAATAAACATTA 58.968 29.630 0.00 0.00 0.00 1.90
5998 6419 6.875726 ACATTTCATGTCATCTCGAGAAGAAA 59.124 34.615 20.99 16.84 39.92 2.52
6077 6499 5.622180 CTTGATGACTGATGATCCATTCCT 58.378 41.667 0.00 0.00 0.00 3.36
6129 6551 1.961277 CGCCGAAGCACTTGTTCCT 60.961 57.895 0.00 0.00 39.83 3.36
6182 6604 2.348998 CCTCAGCCGGCAGAAACT 59.651 61.111 31.54 2.66 0.00 2.66


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

AutoCloner maintained by Alex Coulton.