Multiple sequence alignment - TraesCS7A01G133300

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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 TraesCS7A01G133300 chr7A 100.000 3655 0 0 1 3655 85603299 85599645 0.000000e+00 6750.0
1 TraesCS7A01G133300 chr7D 90.714 1400 90 21 667 2046 84237363 84235984 0.000000e+00 1829.0
2 TraesCS7A01G133300 chr7D 87.648 761 54 23 2877 3610 84234723 84233976 0.000000e+00 848.0
3 TraesCS7A01G133300 chr7D 90.199 653 44 7 1 651 84247207 84246573 0.000000e+00 833.0
4 TraesCS7A01G133300 chr7D 89.279 569 24 16 2302 2862 84235562 84235023 0.000000e+00 678.0
5 TraesCS7A01G133300 chr7D 93.038 158 10 1 2049 2205 84235795 84235638 2.840000e-56 230.0
6 TraesCS7A01G133300 chr7D 86.620 142 14 3 2052 2193 610615195 610615331 6.320000e-33 152.0
7 TraesCS7A01G133300 chr7B 89.671 881 56 17 767 1630 33885785 33884923 0.000000e+00 1090.0
8 TraesCS7A01G133300 chr7B 91.076 706 42 10 2239 2925 33884154 33883451 0.000000e+00 935.0
9 TraesCS7A01G133300 chr7B 85.047 428 37 15 1629 2046 33884862 33884452 9.450000e-111 411.0
10 TraesCS7A01G133300 chr7B 92.763 152 10 1 2049 2199 33884308 33884157 6.150000e-53 219.0
11 TraesCS7A01G133300 chr1B 90.909 66 5 1 42 107 403100475 403100411 1.810000e-13 87.9
12 TraesCS7A01G133300 chr1A 90.000 60 5 1 42 101 372944287 372944229 3.910000e-10 76.8
13 TraesCS7A01G133300 chr1D 91.837 49 3 1 42 90 298950212 298950165 2.360000e-07 67.6


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 TraesCS7A01G133300 chr7A 85599645 85603299 3654 True 6750.00 6750 100.00000 1 3655 1 chr7A.!!$R1 3654
1 TraesCS7A01G133300 chr7D 84233976 84237363 3387 True 896.25 1829 90.16975 667 3610 4 chr7D.!!$R2 2943
2 TraesCS7A01G133300 chr7D 84246573 84247207 634 True 833.00 833 90.19900 1 651 1 chr7D.!!$R1 650
3 TraesCS7A01G133300 chr7B 33883451 33885785 2334 True 663.75 1090 89.63925 767 2925 4 chr7B.!!$R1 2158

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
283 284 0.179081 GAATAGGGAGTCCACGTGCC 60.179 60.0 10.91 5.63 34.83 5.01 F
656 659 0.249699 TCGCCATGAACAACAGTCGT 60.250 50.0 0.00 0.00 0.00 4.34 F
657 660 0.586319 CGCCATGAACAACAGTCGTT 59.414 50.0 0.00 0.00 35.01 3.85 F
1664 1759 0.318441 TAGCTATGCAGGCCGATGTC 59.682 55.0 10.28 0.00 0.00 3.06 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1581 1614 0.548031 TTGGGAGGAGTGATGATGGC 59.452 55.0 0.00 0.00 0.0 4.40 R
1591 1624 0.689623 AGCTGTTGACTTGGGAGGAG 59.310 55.0 0.00 0.00 0.0 3.69 R
2582 2900 0.752009 TCCTCCGGATCGTCCTGAAG 60.752 60.0 3.57 0.00 33.3 3.02 R
3623 4266 0.179189 GTTTGATCTTTGCGCGAGGG 60.179 55.0 12.10 0.12 0.0 4.30 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
68 69 5.388408 TCATGTCTTTTGTATGCATGCAA 57.612 34.783 26.68 24.06 37.44 4.08
112 113 7.545615 ACACATTTTGTTCTCTTTGAGGAAAAC 59.454 33.333 0.00 0.00 33.09 2.43
113 114 7.010460 CACATTTTGTTCTCTTTGAGGAAAACC 59.990 37.037 0.00 0.00 0.00 3.27
129 130 3.550437 AAACCAGTAGCCATGCTCTAG 57.450 47.619 0.00 0.00 40.44 2.43
249 250 9.755804 TCATGTATAGAACTCAGATCAATTGAC 57.244 33.333 11.07 5.15 0.00 3.18
253 254 9.755804 GTATAGAACTCAGATCAATTGACATCA 57.244 33.333 11.07 0.00 0.00 3.07
260 261 8.967918 ACTCAGATCAATTGACATCAATGAATT 58.032 29.630 11.07 0.00 45.06 2.17
264 265 9.726232 AGATCAATTGACATCAATGAATTTACG 57.274 29.630 11.07 0.00 45.06 3.18
283 284 0.179081 GAATAGGGAGTCCACGTGCC 60.179 60.000 10.91 5.63 34.83 5.01
290 291 1.077357 AGTCCACGTGCCCAACAAA 60.077 52.632 10.91 0.00 0.00 2.83
308 309 6.127619 CCAACAAATGAACTATTTCCTCCTCC 60.128 42.308 0.00 0.00 36.87 4.30
309 310 6.139679 ACAAATGAACTATTTCCTCCTCCA 57.860 37.500 0.00 0.00 36.87 3.86
337 338 3.139025 ACCATTGGTCAGATTATGGGAGG 59.861 47.826 1.37 0.00 41.45 4.30
339 340 2.196742 TGGTCAGATTATGGGAGGCT 57.803 50.000 0.00 0.00 0.00 4.58
340 341 2.050144 TGGTCAGATTATGGGAGGCTC 58.950 52.381 5.78 5.78 0.00 4.70
368 369 1.202348 GCTAACCAATGTTGTGAGGGC 59.798 52.381 0.00 0.00 35.87 5.19
373 374 0.374758 CAATGTTGTGAGGGCGATCG 59.625 55.000 11.69 11.69 0.00 3.69
375 376 1.899437 ATGTTGTGAGGGCGATCGGT 61.899 55.000 18.30 0.00 0.00 4.69
398 399 2.229062 GGCTCTAGTTGGCCAAAAGAAC 59.771 50.000 22.47 19.64 46.84 3.01
399 400 2.884639 GCTCTAGTTGGCCAAAAGAACA 59.115 45.455 22.47 4.42 0.00 3.18
400 401 3.507622 GCTCTAGTTGGCCAAAAGAACAT 59.492 43.478 22.47 2.98 0.00 2.71
401 402 4.379918 GCTCTAGTTGGCCAAAAGAACATC 60.380 45.833 22.47 4.89 0.00 3.06
402 403 3.751175 TCTAGTTGGCCAAAAGAACATCG 59.249 43.478 22.47 0.72 0.00 3.84
403 404 1.613437 AGTTGGCCAAAAGAACATCGG 59.387 47.619 22.47 0.00 0.00 4.18
404 405 1.339929 GTTGGCCAAAAGAACATCGGT 59.660 47.619 22.47 0.00 0.00 4.69
405 406 2.554893 GTTGGCCAAAAGAACATCGGTA 59.445 45.455 22.47 0.00 0.00 4.02
406 407 2.865079 TGGCCAAAAGAACATCGGTAA 58.135 42.857 0.61 0.00 0.00 2.85
407 408 3.426615 TGGCCAAAAGAACATCGGTAAT 58.573 40.909 0.61 0.00 0.00 1.89
408 409 3.192422 TGGCCAAAAGAACATCGGTAATG 59.808 43.478 0.61 0.00 41.48 1.90
409 410 3.179048 GCCAAAAGAACATCGGTAATGC 58.821 45.455 0.00 0.00 39.12 3.56
410 411 3.119495 GCCAAAAGAACATCGGTAATGCT 60.119 43.478 0.00 0.00 39.12 3.79
411 412 4.095782 GCCAAAAGAACATCGGTAATGCTA 59.904 41.667 0.00 0.00 39.12 3.49
412 413 5.392595 GCCAAAAGAACATCGGTAATGCTAA 60.393 40.000 0.00 0.00 39.12 3.09
413 414 6.680378 GCCAAAAGAACATCGGTAATGCTAAT 60.680 38.462 0.00 0.00 39.12 1.73
473 475 0.307760 CACAGCCGTTTGGTCAAGAC 59.692 55.000 0.00 0.00 37.67 3.01
489 491 4.097892 GTCAAGACCAAACCATGACAGTTT 59.902 41.667 0.00 0.00 40.02 2.66
493 495 4.111916 GACCAAACCATGACAGTTTTGTG 58.888 43.478 7.28 0.00 37.76 3.33
527 529 5.620738 TCTCTAGGAAGGAATTGTCATGG 57.379 43.478 0.00 0.00 0.00 3.66
528 530 4.133078 CTCTAGGAAGGAATTGTCATGGC 58.867 47.826 0.00 0.00 0.00 4.40
533 535 3.350833 GAAGGAATTGTCATGGCAGTCT 58.649 45.455 0.00 0.00 0.00 3.24
564 566 4.003648 GTCACCTCCCATGACAGTTTTAG 58.996 47.826 0.00 0.00 44.87 1.85
619 622 5.220548 CCATGCTAGTCTGAAGAAATTGTCG 60.221 44.000 0.00 0.00 0.00 4.35
625 628 2.303022 TCTGAAGAAATTGTCGCCTCCT 59.697 45.455 0.00 0.00 0.00 3.69
638 641 4.933400 TGTCGCCTCCTTACAACTAAAATC 59.067 41.667 0.00 0.00 0.00 2.17
647 650 6.027749 CCTTACAACTAAAATCGCCATGAAC 58.972 40.000 0.00 0.00 0.00 3.18
651 654 5.218885 CAACTAAAATCGCCATGAACAACA 58.781 37.500 0.00 0.00 0.00 3.33
652 655 5.046910 ACTAAAATCGCCATGAACAACAG 57.953 39.130 0.00 0.00 0.00 3.16
653 656 4.518970 ACTAAAATCGCCATGAACAACAGT 59.481 37.500 0.00 0.00 0.00 3.55
654 657 3.559238 AAATCGCCATGAACAACAGTC 57.441 42.857 0.00 0.00 0.00 3.51
655 658 1.078709 ATCGCCATGAACAACAGTCG 58.921 50.000 0.00 0.00 0.00 4.18
656 659 0.249699 TCGCCATGAACAACAGTCGT 60.250 50.000 0.00 0.00 0.00 4.34
657 660 0.586319 CGCCATGAACAACAGTCGTT 59.414 50.000 0.00 0.00 35.01 3.85
658 661 1.795872 CGCCATGAACAACAGTCGTTA 59.204 47.619 0.00 0.00 32.75 3.18
659 662 2.159841 CGCCATGAACAACAGTCGTTAG 60.160 50.000 0.00 0.00 32.75 2.34
660 663 2.159627 GCCATGAACAACAGTCGTTAGG 59.840 50.000 0.00 0.00 32.75 2.69
661 664 3.399330 CCATGAACAACAGTCGTTAGGT 58.601 45.455 0.00 0.00 32.75 3.08
662 665 4.562082 CCATGAACAACAGTCGTTAGGTA 58.438 43.478 0.00 0.00 32.75 3.08
663 666 4.992319 CCATGAACAACAGTCGTTAGGTAA 59.008 41.667 0.00 0.00 32.75 2.85
664 667 5.120208 CCATGAACAACAGTCGTTAGGTAAG 59.880 44.000 0.00 0.00 32.75 2.34
665 668 5.266733 TGAACAACAGTCGTTAGGTAAGT 57.733 39.130 0.00 0.00 32.75 2.24
666 669 6.389830 TGAACAACAGTCGTTAGGTAAGTA 57.610 37.500 0.00 0.00 32.75 2.24
667 670 6.985117 TGAACAACAGTCGTTAGGTAAGTAT 58.015 36.000 0.00 0.00 32.75 2.12
668 671 7.086376 TGAACAACAGTCGTTAGGTAAGTATC 58.914 38.462 0.00 0.00 32.75 2.24
669 672 6.830873 ACAACAGTCGTTAGGTAAGTATCT 57.169 37.500 0.00 0.00 32.75 1.98
670 673 6.618811 ACAACAGTCGTTAGGTAAGTATCTG 58.381 40.000 0.00 0.00 32.75 2.90
671 674 6.208204 ACAACAGTCGTTAGGTAAGTATCTGT 59.792 38.462 0.00 0.00 35.58 3.41
672 675 7.391554 ACAACAGTCGTTAGGTAAGTATCTGTA 59.608 37.037 0.00 0.00 34.06 2.74
673 676 7.928307 ACAGTCGTTAGGTAAGTATCTGTAA 57.072 36.000 0.00 0.00 32.95 2.41
674 677 7.756558 ACAGTCGTTAGGTAAGTATCTGTAAC 58.243 38.462 0.00 0.00 32.95 2.50
675 678 6.904011 CAGTCGTTAGGTAAGTATCTGTAACG 59.096 42.308 6.18 6.18 42.43 3.18
692 695 4.746115 TGTAACGCTTGTTTCACTTCGTAT 59.254 37.500 0.00 0.00 37.02 3.06
694 697 4.128554 ACGCTTGTTTCACTTCGTATTG 57.871 40.909 0.00 0.00 0.00 1.90
704 707 3.056393 TCACTTCGTATTGTCCCGTCAAT 60.056 43.478 0.00 0.00 40.50 2.57
705 708 3.062099 CACTTCGTATTGTCCCGTCAATG 59.938 47.826 7.61 0.00 38.32 2.82
752 756 8.868522 TCTCAGTCATTTTTCCTGTTCATATT 57.131 30.769 0.00 0.00 0.00 1.28
759 763 5.902613 TTTTCCTGTTCATATTCCTGCTG 57.097 39.130 0.00 0.00 0.00 4.41
760 764 2.923121 TCCTGTTCATATTCCTGCTGC 58.077 47.619 0.00 0.00 0.00 5.25
762 766 1.600957 CTGTTCATATTCCTGCTGCCG 59.399 52.381 0.00 0.00 0.00 5.69
765 769 2.462456 TCATATTCCTGCTGCCGATC 57.538 50.000 0.00 0.00 0.00 3.69
769 773 1.386533 ATTCCTGCTGCCGATCAAAG 58.613 50.000 0.00 0.00 0.00 2.77
789 793 3.628008 AGAAAAACTCCCGTTTCACCTT 58.372 40.909 0.00 0.00 42.28 3.50
790 794 3.630769 AGAAAAACTCCCGTTTCACCTTC 59.369 43.478 0.00 0.00 42.28 3.46
791 795 2.721425 AAACTCCCGTTTCACCTTCA 57.279 45.000 0.00 0.00 39.00 3.02
818 824 8.587608 TCAGAAATGAAACAGGCAAGAAAATAT 58.412 29.630 0.00 0.00 0.00 1.28
819 825 9.859427 CAGAAATGAAACAGGCAAGAAAATATA 57.141 29.630 0.00 0.00 0.00 0.86
821 827 9.305925 GAAATGAAACAGGCAAGAAAATATAGG 57.694 33.333 0.00 0.00 0.00 2.57
822 828 6.207691 TGAAACAGGCAAGAAAATATAGGC 57.792 37.500 0.00 0.00 0.00 3.93
823 829 5.127031 TGAAACAGGCAAGAAAATATAGGCC 59.873 40.000 0.00 0.00 41.65 5.19
826 832 5.022787 ACAGGCAAGAAAATATAGGCCAAA 58.977 37.500 5.01 0.00 43.72 3.28
897 903 4.828925 GTGGCTCTCAGCGCTCCC 62.829 72.222 7.13 3.62 43.62 4.30
951 973 3.636764 ACAACGAGGGCTCAAGAAAAATT 59.363 39.130 0.00 0.00 0.00 1.82
1206 1232 1.079057 GGGAGCGACCAAGGAAGAC 60.079 63.158 5.45 0.00 41.20 3.01
1233 1259 2.444895 GCCGAGGAGTCAGGGGAT 60.445 66.667 0.00 0.00 0.00 3.85
1235 1261 2.136878 CCGAGGAGTCAGGGGATGG 61.137 68.421 0.00 0.00 0.00 3.51
1373 1402 6.070538 ACTCTTTACTAATCACCATGCTCACT 60.071 38.462 0.00 0.00 0.00 3.41
1393 1422 7.623089 GCTCACTACTCAAGTAAATTTCAGCTG 60.623 40.741 7.63 7.63 35.76 4.24
1471 1504 4.058124 TGACATCTTGAAACGGTTCTGAG 58.942 43.478 15.41 12.20 34.60 3.35
1474 1507 3.107642 TCTTGAAACGGTTCTGAGACC 57.892 47.619 15.41 0.00 34.60 3.85
1581 1614 0.803768 CCAGCAGTTCGTCCTCATCG 60.804 60.000 0.00 0.00 0.00 3.84
1591 1624 1.506493 GTCCTCATCGCCATCATCAC 58.494 55.000 0.00 0.00 0.00 3.06
1608 1641 1.694150 TCACTCCTCCCAAGTCAACAG 59.306 52.381 0.00 0.00 0.00 3.16
1611 1644 0.687354 TCCTCCCAAGTCAACAGCTC 59.313 55.000 0.00 0.00 0.00 4.09
1643 1738 7.188834 TGATCAAATTTAATGCAGTGATCGTC 58.811 34.615 0.00 0.00 42.69 4.20
1649 1744 3.533606 AATGCAGTGATCGTCTTAGCT 57.466 42.857 0.00 0.00 0.00 3.32
1664 1759 0.318441 TAGCTATGCAGGCCGATGTC 59.682 55.000 10.28 0.00 0.00 3.06
1743 1838 0.620410 TCTCAGGGTATGTGGGGTGG 60.620 60.000 0.00 0.00 0.00 4.61
1744 1839 0.914417 CTCAGGGTATGTGGGGTGGT 60.914 60.000 0.00 0.00 0.00 4.16
1745 1840 1.204786 TCAGGGTATGTGGGGTGGTG 61.205 60.000 0.00 0.00 0.00 4.17
1761 1856 2.285220 GTGGTGATCCATCGATTTGTCG 59.715 50.000 0.00 0.00 46.20 4.35
1763 1858 1.261619 GTGATCCATCGATTTGTCGGC 59.738 52.381 0.00 0.00 0.00 5.54
1788 1883 1.301479 GACCCTGTTTTCCGACGCT 60.301 57.895 0.00 0.00 0.00 5.07
1802 1897 2.518949 CGACGCTGGAAATTGAATTGG 58.481 47.619 0.00 0.00 0.00 3.16
1809 1904 5.870978 CGCTGGAAATTGAATTGGAATTTCT 59.129 36.000 20.99 0.50 44.21 2.52
1812 1907 7.557875 TGGAAATTGAATTGGAATTTCTCCT 57.442 32.000 20.99 0.00 44.21 3.69
1947 2051 4.624913 AGAACATACTCTTCAGGGATGGA 58.375 43.478 0.00 0.00 0.00 3.41
2000 2104 5.407407 TTCTTGTAGGGAAGTAGAAGCAG 57.593 43.478 0.00 0.00 0.00 4.24
2020 2124 3.187227 CAGTGTACTGTTGCTAAAGCCAG 59.813 47.826 3.88 3.34 38.53 4.85
2028 2132 2.200373 TGCTAAAGCCAGAACTTCCC 57.800 50.000 0.00 0.00 41.18 3.97
2046 2150 9.921637 GAACTTCCCTTCATATAACTAGATCTG 57.078 37.037 5.18 0.00 0.00 2.90
2047 2151 9.440761 AACTTCCCTTCATATAACTAGATCTGT 57.559 33.333 5.18 0.00 0.00 3.41
2074 2364 5.701290 GGATAATCAGGAGTTAATTGGTCGG 59.299 44.000 0.00 0.00 0.00 4.79
2075 2365 3.560636 ATCAGGAGTTAATTGGTCGGG 57.439 47.619 0.00 0.00 0.00 5.14
2084 2374 3.958147 ATTGGTCGGGCTGTCTGCG 62.958 63.158 0.00 0.00 44.05 5.18
2125 2416 5.728471 TCTTCTGAAGATGACCTCACAATC 58.272 41.667 15.82 0.00 31.20 2.67
2189 2480 5.414454 TGGGAAAACTTGGTATGAATTCTCG 59.586 40.000 7.05 0.00 0.00 4.04
2199 2490 7.526142 TGGTATGAATTCTCGCTACTTCTAT 57.474 36.000 7.05 0.00 0.00 1.98
2200 2491 7.952671 TGGTATGAATTCTCGCTACTTCTATT 58.047 34.615 7.05 0.00 0.00 1.73
2201 2492 9.074576 TGGTATGAATTCTCGCTACTTCTATTA 57.925 33.333 7.05 0.00 0.00 0.98
2202 2493 9.344309 GGTATGAATTCTCGCTACTTCTATTAC 57.656 37.037 7.05 0.00 0.00 1.89
2203 2494 9.344309 GTATGAATTCTCGCTACTTCTATTACC 57.656 37.037 7.05 0.00 0.00 2.85
2204 2495 7.584122 TGAATTCTCGCTACTTCTATTACCT 57.416 36.000 7.05 0.00 0.00 3.08
2205 2496 7.649973 TGAATTCTCGCTACTTCTATTACCTC 58.350 38.462 7.05 0.00 0.00 3.85
2206 2497 6.578163 ATTCTCGCTACTTCTATTACCTCC 57.422 41.667 0.00 0.00 0.00 4.30
2207 2498 4.063689 TCTCGCTACTTCTATTACCTCCG 58.936 47.826 0.00 0.00 0.00 4.63
2208 2499 3.813443 TCGCTACTTCTATTACCTCCGT 58.187 45.455 0.00 0.00 0.00 4.69
2209 2500 4.202441 TCGCTACTTCTATTACCTCCGTT 58.798 43.478 0.00 0.00 0.00 4.44
2210 2501 4.274459 TCGCTACTTCTATTACCTCCGTTC 59.726 45.833 0.00 0.00 0.00 3.95
2211 2502 4.036027 CGCTACTTCTATTACCTCCGTTCA 59.964 45.833 0.00 0.00 0.00 3.18
2212 2503 5.521544 GCTACTTCTATTACCTCCGTTCAG 58.478 45.833 0.00 0.00 0.00 3.02
2213 2504 5.298777 GCTACTTCTATTACCTCCGTTCAGA 59.701 44.000 0.00 0.00 0.00 3.27
2214 2505 6.183360 GCTACTTCTATTACCTCCGTTCAGAA 60.183 42.308 0.00 0.00 0.00 3.02
2215 2506 6.793505 ACTTCTATTACCTCCGTTCAGAAT 57.206 37.500 0.00 0.00 0.00 2.40
2216 2507 7.184067 ACTTCTATTACCTCCGTTCAGAATT 57.816 36.000 0.00 0.00 0.00 2.17
2217 2508 8.302515 ACTTCTATTACCTCCGTTCAGAATTA 57.697 34.615 0.00 0.00 0.00 1.40
2218 2509 8.755977 ACTTCTATTACCTCCGTTCAGAATTAA 58.244 33.333 0.00 0.00 0.00 1.40
2219 2510 8.937634 TTCTATTACCTCCGTTCAGAATTAAC 57.062 34.615 0.00 0.00 0.00 2.01
2220 2511 8.302515 TCTATTACCTCCGTTCAGAATTAACT 57.697 34.615 0.00 0.00 0.00 2.24
2221 2512 8.195436 TCTATTACCTCCGTTCAGAATTAACTG 58.805 37.037 0.00 0.00 39.02 3.16
2222 2513 4.618920 ACCTCCGTTCAGAATTAACTGT 57.381 40.909 0.00 0.00 38.79 3.55
2223 2514 4.566987 ACCTCCGTTCAGAATTAACTGTC 58.433 43.478 0.00 0.00 38.79 3.51
2224 2515 3.612860 CCTCCGTTCAGAATTAACTGTCG 59.387 47.826 0.00 0.00 38.79 4.35
2225 2516 2.991190 TCCGTTCAGAATTAACTGTCGC 59.009 45.455 0.00 0.00 38.79 5.19
2226 2517 2.993899 CCGTTCAGAATTAACTGTCGCT 59.006 45.455 0.00 0.00 38.79 4.93
2227 2518 3.181530 CCGTTCAGAATTAACTGTCGCTG 60.182 47.826 0.00 0.00 38.79 5.18
2228 2519 3.673338 CGTTCAGAATTAACTGTCGCTGA 59.327 43.478 0.00 0.00 38.79 4.26
2229 2520 4.149922 CGTTCAGAATTAACTGTCGCTGAA 59.850 41.667 0.00 0.00 39.30 3.02
2230 2521 5.333035 CGTTCAGAATTAACTGTCGCTGAAA 60.333 40.000 0.00 0.00 42.05 2.69
2231 2522 6.603095 GTTCAGAATTAACTGTCGCTGAAAT 58.397 36.000 0.00 0.00 42.05 2.17
2232 2523 6.169419 TCAGAATTAACTGTCGCTGAAATG 57.831 37.500 0.00 0.00 38.79 2.32
2233 2524 5.931724 TCAGAATTAACTGTCGCTGAAATGA 59.068 36.000 0.00 0.00 38.79 2.57
2234 2525 6.091305 TCAGAATTAACTGTCGCTGAAATGAG 59.909 38.462 0.00 0.00 38.79 2.90
2235 2526 4.606457 ATTAACTGTCGCTGAAATGAGC 57.394 40.909 0.00 0.00 35.46 4.26
2236 2527 2.175878 AACTGTCGCTGAAATGAGCT 57.824 45.000 0.00 0.00 36.77 4.09
2269 2560 3.416156 CCTCCCTGAAACCAAGAAGAAG 58.584 50.000 0.00 0.00 0.00 2.85
2296 2587 0.872388 GGCGAAAACCACGACTTGAT 59.128 50.000 0.00 0.00 35.75 2.57
2307 2609 5.794894 ACCACGACTTGATTGAGAAGTTAT 58.205 37.500 0.00 0.00 33.71 1.89
2326 2643 7.472334 AGTTATTTTGCCATCTCTGAATTGT 57.528 32.000 0.00 0.00 0.00 2.71
2424 2741 0.693049 ATCCCCAAGGTCTGTGACAC 59.307 55.000 0.00 0.00 33.68 3.67
2440 2757 1.534595 GACACTGCTTGCTCTTCTTGG 59.465 52.381 0.00 0.00 0.00 3.61
2448 2765 3.755378 GCTTGCTCTTCTTGGATCTTGAA 59.245 43.478 0.00 0.00 0.00 2.69
2479 2797 6.743110 TGCAATAATTGTGAAGTGCAGTTAA 58.257 32.000 6.80 0.00 37.09 2.01
2484 2802 9.855021 AATAATTGTGAAGTGCAGTTAATTACC 57.145 29.630 17.15 3.10 0.00 2.85
2582 2900 2.761195 GCCCTTGACGAAATCCGCC 61.761 63.158 0.00 0.00 43.32 6.13
2595 2913 1.749334 ATCCGCCTTCAGGACGATCC 61.749 60.000 10.20 0.00 41.10 3.36
2668 2992 0.995024 CCATGACCAAGGGAGGACTT 59.005 55.000 0.00 0.00 0.00 3.01
2753 3084 3.614092 TCTCCAGCCAAAGATTCATGTC 58.386 45.455 0.00 0.00 0.00 3.06
2781 3113 0.987294 ACCAGCTCTGTACATGCCTT 59.013 50.000 14.76 0.00 0.00 4.35
2868 3201 4.116961 CAAGAAACCGACTTGAGTGTACA 58.883 43.478 0.00 0.00 44.92 2.90
2875 3208 1.726791 GACTTGAGTGTACATGCCACG 59.273 52.381 0.00 0.00 37.88 4.94
2876 3209 1.070134 ACTTGAGTGTACATGCCACGT 59.930 47.619 0.00 0.00 37.88 4.49
2935 3554 1.348366 TGGAACGCTAAGGCCTTGTAA 59.652 47.619 28.77 7.32 34.44 2.41
2955 3574 2.990740 AATGCAAGGTGTTTAGGGGA 57.009 45.000 0.00 0.00 0.00 4.81
2956 3575 2.990740 ATGCAAGGTGTTTAGGGGAA 57.009 45.000 0.00 0.00 0.00 3.97
2965 3584 3.244805 GGTGTTTAGGGGAAGTGCTTAGT 60.245 47.826 0.00 0.00 0.00 2.24
2975 3594 6.662234 AGGGGAAGTGCTTAGTAAAATAAACC 59.338 38.462 0.00 0.00 0.00 3.27
2992 3611 4.322080 AAACCAAGCTTTTCCTAAGCAC 57.678 40.909 11.59 0.00 45.30 4.40
2993 3612 2.944129 ACCAAGCTTTTCCTAAGCACA 58.056 42.857 11.59 0.00 45.30 4.57
2995 3614 3.319122 ACCAAGCTTTTCCTAAGCACAAG 59.681 43.478 11.59 1.09 45.30 3.16
3015 3634 7.665690 CACAAGTGCTTATCTCTATATGAGGT 58.334 38.462 0.00 0.00 42.86 3.85
3019 3638 5.866633 GTGCTTATCTCTATATGAGGTGTGC 59.133 44.000 0.00 0.00 42.86 4.57
3041 3670 7.807433 TGTGCTTAATTAATATGCAAATAGGCG 59.193 33.333 11.03 0.00 43.74 5.52
3048 3677 3.583086 GCAAATAGGCGCCGGTCC 61.583 66.667 23.20 4.86 0.00 4.46
3061 3690 1.130561 GCCGGTCCTTCTGAAAAATCG 59.869 52.381 1.90 0.00 0.00 3.34
3092 3721 3.574749 TCTGAGCATCTCTCCTAAGCAT 58.425 45.455 0.00 0.00 41.18 3.79
3096 3725 4.408270 TGAGCATCTCTCCTAAGCATCTTT 59.592 41.667 0.00 0.00 41.18 2.52
3125 3754 9.439500 TTGTACAACGCCTAAGAATTTACTAAT 57.561 29.630 3.59 0.00 0.00 1.73
3195 3828 6.948309 ACATAGAGGGCTACTTGTTCATTTTT 59.052 34.615 0.00 0.00 0.00 1.94
3228 3861 7.799081 TCATTTGATCACATAGAGACCTTGAT 58.201 34.615 0.00 0.00 0.00 2.57
3256 3889 7.090173 CGACTTGAATATTGGTTGTTTGGAAT 58.910 34.615 0.00 0.00 0.00 3.01
3263 3896 3.584406 TGGTTGTTTGGAATTATGCGG 57.416 42.857 0.00 0.00 0.00 5.69
3275 3908 0.747852 TTATGCGGACGTGATGGCTA 59.252 50.000 0.00 0.00 0.00 3.93
3281 3914 1.593006 CGGACGTGATGGCTACATTTC 59.407 52.381 0.00 0.00 37.47 2.17
3282 3915 2.627945 GGACGTGATGGCTACATTTCA 58.372 47.619 0.00 0.00 37.47 2.69
3283 3916 3.206150 GGACGTGATGGCTACATTTCAT 58.794 45.455 0.00 0.00 37.47 2.57
3324 3959 0.535335 TGGTTAGCCATCACTCCGTC 59.465 55.000 0.00 0.00 40.46 4.79
3325 3960 0.824759 GGTTAGCCATCACTCCGTCT 59.175 55.000 0.00 0.00 34.09 4.18
3326 3961 1.202428 GGTTAGCCATCACTCCGTCTC 60.202 57.143 0.00 0.00 34.09 3.36
3327 3962 1.112113 TTAGCCATCACTCCGTCTCC 58.888 55.000 0.00 0.00 0.00 3.71
3328 3963 0.033503 TAGCCATCACTCCGTCTCCA 60.034 55.000 0.00 0.00 0.00 3.86
3329 3964 0.689080 AGCCATCACTCCGTCTCCAT 60.689 55.000 0.00 0.00 0.00 3.41
3356 3991 7.269316 TCCGTTTGCATATCTAGTGATGTTTA 58.731 34.615 0.00 0.00 34.32 2.01
3358 3993 7.850982 CCGTTTGCATATCTAGTGATGTTTAAC 59.149 37.037 0.00 0.00 34.32 2.01
3360 3995 7.477144 TTGCATATCTAGTGATGTTTAACCG 57.523 36.000 0.00 0.00 34.32 4.44
3374 4014 5.131784 TGTTTAACCGTGTATTTTGGTCCT 58.868 37.500 0.00 0.00 34.11 3.85
3381 4021 6.184789 ACCGTGTATTTTGGTCCTGATTAAT 58.815 36.000 0.00 0.00 0.00 1.40
3383 4023 7.177744 ACCGTGTATTTTGGTCCTGATTAATTT 59.822 33.333 0.00 0.00 0.00 1.82
3384 4024 7.487829 CCGTGTATTTTGGTCCTGATTAATTTG 59.512 37.037 0.00 0.00 0.00 2.32
3385 4025 8.026607 CGTGTATTTTGGTCCTGATTAATTTGT 58.973 33.333 0.00 0.00 0.00 2.83
3386 4026 9.139174 GTGTATTTTGGTCCTGATTAATTTGTG 57.861 33.333 0.00 0.00 0.00 3.33
3387 4027 9.083422 TGTATTTTGGTCCTGATTAATTTGTGA 57.917 29.630 0.00 0.00 0.00 3.58
3400 4040 6.667981 TTAATTTGTGATATTTATGCGCGC 57.332 33.333 27.26 27.26 0.00 6.86
3406 4046 4.271291 TGTGATATTTATGCGCGCTTGTTA 59.729 37.500 33.29 17.97 0.00 2.41
3410 4050 7.162546 GTGATATTTATGCGCGCTTGTTATATG 59.837 37.037 33.29 0.00 0.00 1.78
3413 4053 2.450365 TGCGCGCTTGTTATATGTTG 57.550 45.000 33.29 0.00 0.00 3.33
3415 4055 1.375496 CGCGCTTGTTATATGTTGCG 58.625 50.000 5.56 0.00 45.12 4.85
3421 4061 4.670621 CGCTTGTTATATGTTGCGGAATTC 59.329 41.667 0.00 0.00 39.76 2.17
3443 4083 8.964476 ATTCCGTTGATGATCTACATAGTTTT 57.036 30.769 7.71 0.00 39.56 2.43
3495 4135 8.975663 TTAGGGATCATATATGAGGTACTACG 57.024 38.462 19.73 0.00 41.55 3.51
3496 4136 6.971340 AGGGATCATATATGAGGTACTACGT 58.029 40.000 19.73 3.62 41.55 3.57
3497 4137 8.098963 AGGGATCATATATGAGGTACTACGTA 57.901 38.462 19.73 0.00 41.55 3.57
3498 4138 7.992033 AGGGATCATATATGAGGTACTACGTAC 59.008 40.741 19.73 1.76 41.55 3.67
3499 4139 7.772292 GGGATCATATATGAGGTACTACGTACA 59.228 40.741 19.73 0.00 41.55 2.90
3500 4140 8.610896 GGATCATATATGAGGTACTACGTACAC 58.389 40.741 19.73 0.00 41.55 2.90
3501 4141 9.381033 GATCATATATGAGGTACTACGTACACT 57.619 37.037 19.73 0.00 41.55 3.55
3511 4151 5.988462 GTACTACGTACACTGCTATGGGCA 61.988 50.000 0.00 0.00 42.30 5.36
3520 4160 3.536917 CTATGGGCACGGGCGAGA 61.537 66.667 2.17 0.00 42.47 4.04
3523 4163 2.377628 TATGGGCACGGGCGAGAATC 62.378 60.000 2.17 0.00 42.47 2.52
3544 4184 3.681835 GGTCACTGTCCGCGGACT 61.682 66.667 46.72 32.19 44.80 3.85
3565 4208 6.042208 GGACTTACAAGGAGGATTAGCTATGT 59.958 42.308 0.00 0.00 0.00 2.29
3571 4214 3.326297 AGGAGGATTAGCTATGTCTTGCC 59.674 47.826 0.00 0.66 0.00 4.52
3578 4221 5.474578 TTAGCTATGTCTTGCCCTAGATG 57.525 43.478 0.00 0.00 0.00 2.90
3583 4226 1.127343 GTCTTGCCCTAGATGAGCCT 58.873 55.000 0.00 0.00 0.00 4.58
3591 4234 1.686052 CCTAGATGAGCCTGGTCACTC 59.314 57.143 0.47 1.79 0.00 3.51
3592 4235 1.336440 CTAGATGAGCCTGGTCACTCG 59.664 57.143 0.47 0.00 35.61 4.18
3637 4280 2.821366 CTGCCCTCGCGCAAAGAT 60.821 61.111 8.75 0.00 38.56 2.40
3638 4281 2.817423 CTGCCCTCGCGCAAAGATC 61.817 63.158 8.75 0.09 38.56 2.75
3639 4282 2.819595 GCCCTCGCGCAAAGATCA 60.820 61.111 8.75 0.00 0.00 2.92
3640 4283 2.398554 GCCCTCGCGCAAAGATCAA 61.399 57.895 8.75 0.00 0.00 2.57
3641 4284 1.922135 GCCCTCGCGCAAAGATCAAA 61.922 55.000 8.75 0.00 0.00 2.69
3642 4285 0.179189 CCCTCGCGCAAAGATCAAAC 60.179 55.000 8.75 0.00 0.00 2.93
3643 4286 0.798776 CCTCGCGCAAAGATCAAACT 59.201 50.000 8.75 0.00 0.00 2.66
3644 4287 1.464687 CCTCGCGCAAAGATCAAACTG 60.465 52.381 8.75 0.00 0.00 3.16
3645 4288 1.460743 CTCGCGCAAAGATCAAACTGA 59.539 47.619 8.75 0.00 0.00 3.41
3646 4289 2.076100 TCGCGCAAAGATCAAACTGAT 58.924 42.857 8.75 0.00 40.34 2.90
3647 4290 3.258228 TCGCGCAAAGATCAAACTGATA 58.742 40.909 8.75 0.00 37.20 2.15
3648 4291 3.871006 TCGCGCAAAGATCAAACTGATAT 59.129 39.130 8.75 0.00 37.20 1.63
3649 4292 4.332543 TCGCGCAAAGATCAAACTGATATT 59.667 37.500 8.75 0.00 39.70 1.28
3650 4293 4.435554 CGCGCAAAGATCAAACTGATATTG 59.564 41.667 8.75 4.44 37.32 1.90
3651 4294 4.205792 GCGCAAAGATCAAACTGATATTGC 59.794 41.667 19.68 19.68 45.91 3.56
3652 4295 4.736793 CGCAAAGATCAAACTGATATTGCC 59.263 41.667 21.69 11.99 46.24 4.52
3653 4296 5.449588 CGCAAAGATCAAACTGATATTGCCT 60.450 40.000 21.69 3.00 46.24 4.75
3654 4297 5.747197 GCAAAGATCAAACTGATATTGCCTG 59.253 40.000 19.27 8.23 44.90 4.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
40 41 5.162794 TGCATACAAAAGACATGAACATGC 58.837 37.500 13.71 7.63 42.39 4.06
51 52 7.725818 TGAAAATTTGCATGCATACAAAAGA 57.274 28.000 24.94 7.03 39.09 2.52
112 113 3.827008 TTTCTAGAGCATGGCTACTGG 57.173 47.619 0.00 0.00 39.88 4.00
113 114 6.695429 TCATATTTCTAGAGCATGGCTACTG 58.305 40.000 0.00 0.00 39.88 2.74
156 157 0.622136 AGTGCTCAAGATCCATGCCA 59.378 50.000 0.00 0.00 0.00 4.92
249 250 8.383318 ACTCCCTATTCGTAAATTCATTGATG 57.617 34.615 0.00 0.00 0.00 3.07
253 254 6.766467 GTGGACTCCCTATTCGTAAATTCATT 59.234 38.462 0.00 0.00 0.00 2.57
254 255 6.289064 GTGGACTCCCTATTCGTAAATTCAT 58.711 40.000 0.00 0.00 0.00 2.57
260 261 2.424601 CACGTGGACTCCCTATTCGTAA 59.575 50.000 7.95 0.00 0.00 3.18
264 265 0.179081 GGCACGTGGACTCCCTATTC 60.179 60.000 18.88 0.00 0.00 1.75
283 284 6.127619 GGAGGAGGAAATAGTTCATTTGTTGG 60.128 42.308 5.15 0.00 36.96 3.77
290 291 5.728741 AGAAGTGGAGGAGGAAATAGTTCAT 59.271 40.000 5.15 0.00 35.25 2.57
308 309 6.484643 CCATAATCTGACCAATGGTAGAAGTG 59.515 42.308 4.23 8.93 35.25 3.16
309 310 6.409695 CCCATAATCTGACCAATGGTAGAAGT 60.410 42.308 4.23 4.71 37.73 3.01
337 338 6.127897 ACAACATTGGTTAGCTTTATCTGAGC 60.128 38.462 0.00 0.00 36.33 4.26
339 340 6.939730 TCACAACATTGGTTAGCTTTATCTGA 59.060 34.615 0.00 0.00 34.87 3.27
340 341 7.144722 TCACAACATTGGTTAGCTTTATCTG 57.855 36.000 0.00 0.00 34.87 2.90
373 374 2.187163 GGCCAACTAGAGCCGACC 59.813 66.667 0.00 0.00 39.87 4.79
398 399 4.566545 TTGCCAATTAGCATTACCGATG 57.433 40.909 0.00 0.00 43.64 3.84
399 400 4.497340 CGTTTGCCAATTAGCATTACCGAT 60.497 41.667 0.00 0.00 43.64 4.18
400 401 3.181505 CGTTTGCCAATTAGCATTACCGA 60.182 43.478 0.00 0.00 43.64 4.69
401 402 3.105203 CGTTTGCCAATTAGCATTACCG 58.895 45.455 0.00 0.00 43.64 4.02
402 403 4.104696 ACGTTTGCCAATTAGCATTACC 57.895 40.909 0.00 0.00 43.64 2.85
403 404 5.842377 CAAACGTTTGCCAATTAGCATTAC 58.158 37.500 26.55 0.91 43.64 1.89
405 406 4.988708 CAAACGTTTGCCAATTAGCATT 57.011 36.364 26.55 0.00 43.64 3.56
432 433 2.032071 CGTTCGCAGGGGTTCCTT 59.968 61.111 0.00 0.00 42.67 3.36
473 475 4.383850 TCACAAAACTGTCATGGTTTGG 57.616 40.909 13.73 0.00 37.05 3.28
513 515 3.087031 CAGACTGCCATGACAATTCCTT 58.913 45.455 0.00 0.00 0.00 3.36
517 519 4.025040 TCTTCAGACTGCCATGACAATT 57.975 40.909 0.00 0.00 0.00 2.32
527 529 3.406764 AGGTGACATTTCTTCAGACTGC 58.593 45.455 0.00 0.00 0.00 4.40
528 530 3.999663 GGAGGTGACATTTCTTCAGACTG 59.000 47.826 0.00 0.00 0.00 3.51
533 535 3.330405 TCATGGGAGGTGACATTTCTTCA 59.670 43.478 0.00 0.00 0.00 3.02
573 575 5.487488 TGGCAATTTCCTCTAAGAGAAGGTA 59.513 40.000 0.00 0.00 0.00 3.08
619 622 3.064958 GGCGATTTTAGTTGTAAGGAGGC 59.935 47.826 0.00 0.00 0.00 4.70
625 628 6.561737 TGTTCATGGCGATTTTAGTTGTAA 57.438 33.333 0.00 0.00 0.00 2.41
638 641 0.586319 AACGACTGTTGTTCATGGCG 59.414 50.000 7.61 0.00 36.81 5.69
647 650 6.618811 ACAGATACTTACCTAACGACTGTTG 58.381 40.000 0.00 0.00 39.12 3.33
651 654 6.457528 GCGTTACAGATACTTACCTAACGACT 60.458 42.308 10.94 0.00 39.02 4.18
652 655 5.678919 GCGTTACAGATACTTACCTAACGAC 59.321 44.000 10.94 0.97 39.02 4.34
653 656 5.586243 AGCGTTACAGATACTTACCTAACGA 59.414 40.000 10.94 0.00 39.02 3.85
654 657 5.814783 AGCGTTACAGATACTTACCTAACG 58.185 41.667 0.00 0.00 39.46 3.18
655 658 7.031975 ACAAGCGTTACAGATACTTACCTAAC 58.968 38.462 0.00 0.00 0.00 2.34
656 659 7.161773 ACAAGCGTTACAGATACTTACCTAA 57.838 36.000 0.00 0.00 0.00 2.69
657 660 6.764308 ACAAGCGTTACAGATACTTACCTA 57.236 37.500 0.00 0.00 0.00 3.08
658 661 5.656213 ACAAGCGTTACAGATACTTACCT 57.344 39.130 0.00 0.00 0.00 3.08
659 662 6.366877 TGAAACAAGCGTTACAGATACTTACC 59.633 38.462 0.00 0.00 33.99 2.85
660 663 7.115947 AGTGAAACAAGCGTTACAGATACTTAC 59.884 37.037 0.00 0.00 41.43 2.34
661 664 7.149973 AGTGAAACAAGCGTTACAGATACTTA 58.850 34.615 0.00 0.00 41.43 2.24
662 665 5.989777 AGTGAAACAAGCGTTACAGATACTT 59.010 36.000 0.00 0.00 41.43 2.24
663 666 5.539048 AGTGAAACAAGCGTTACAGATACT 58.461 37.500 0.00 0.00 41.43 2.12
664 667 5.840940 AGTGAAACAAGCGTTACAGATAC 57.159 39.130 0.00 0.00 41.43 2.24
665 668 5.118050 CGAAGTGAAACAAGCGTTACAGATA 59.882 40.000 0.00 0.00 41.43 1.98
666 669 4.084537 CGAAGTGAAACAAGCGTTACAGAT 60.085 41.667 0.00 0.00 41.43 2.90
667 670 3.244345 CGAAGTGAAACAAGCGTTACAGA 59.756 43.478 0.00 0.00 41.43 3.41
668 671 3.000925 ACGAAGTGAAACAAGCGTTACAG 59.999 43.478 0.00 0.00 42.51 2.74
669 672 2.931325 ACGAAGTGAAACAAGCGTTACA 59.069 40.909 0.00 0.00 42.51 2.41
670 673 3.580794 ACGAAGTGAAACAAGCGTTAC 57.419 42.857 0.00 0.00 42.51 2.50
671 674 5.234757 ACAATACGAAGTGAAACAAGCGTTA 59.765 36.000 0.00 0.00 45.73 3.18
672 675 4.034742 ACAATACGAAGTGAAACAAGCGTT 59.965 37.500 0.00 0.00 45.73 4.84
673 676 3.558418 ACAATACGAAGTGAAACAAGCGT 59.442 39.130 0.00 0.00 45.73 5.07
674 677 4.128554 ACAATACGAAGTGAAACAAGCG 57.871 40.909 0.00 0.00 45.73 4.68
675 678 4.464112 GGACAATACGAAGTGAAACAAGC 58.536 43.478 0.00 0.00 45.73 4.01
692 695 2.235016 CCTTTTCCATTGACGGGACAA 58.765 47.619 0.00 0.00 33.18 3.18
694 697 1.810755 GACCTTTTCCATTGACGGGAC 59.189 52.381 0.00 0.00 33.18 4.46
704 707 4.712122 GTCAACTTGTTGACCTTTTCCA 57.288 40.909 26.98 0.00 44.06 3.53
727 730 8.868522 AATATGAACAGGAAAAATGACTGAGA 57.131 30.769 0.00 0.00 36.17 3.27
728 731 8.186821 GGAATATGAACAGGAAAAATGACTGAG 58.813 37.037 0.00 0.00 36.17 3.35
729 732 7.890127 AGGAATATGAACAGGAAAAATGACTGA 59.110 33.333 0.00 0.00 36.17 3.41
736 739 5.336690 GCAGCAGGAATATGAACAGGAAAAA 60.337 40.000 0.00 0.00 0.00 1.94
741 744 1.952296 GGCAGCAGGAATATGAACAGG 59.048 52.381 0.00 0.00 0.00 4.00
743 746 1.209261 TCGGCAGCAGGAATATGAACA 59.791 47.619 0.00 0.00 0.00 3.18
744 747 1.953559 TCGGCAGCAGGAATATGAAC 58.046 50.000 0.00 0.00 0.00 3.18
745 748 2.104622 TGATCGGCAGCAGGAATATGAA 59.895 45.455 0.00 0.00 0.00 2.57
752 756 0.324614 TTCTTTGATCGGCAGCAGGA 59.675 50.000 0.00 0.00 0.00 3.86
759 763 2.414161 CGGGAGTTTTTCTTTGATCGGC 60.414 50.000 0.00 0.00 0.00 5.54
760 764 2.812011 ACGGGAGTTTTTCTTTGATCGG 59.188 45.455 0.00 0.00 43.33 4.18
789 793 5.072055 TCTTGCCTGTTTCATTTCTGATGA 58.928 37.500 0.00 0.00 0.00 2.92
790 794 5.381174 TCTTGCCTGTTTCATTTCTGATG 57.619 39.130 0.00 0.00 0.00 3.07
791 795 6.409524 TTTCTTGCCTGTTTCATTTCTGAT 57.590 33.333 0.00 0.00 0.00 2.90
804 808 5.596836 TTTGGCCTATATTTTCTTGCCTG 57.403 39.130 3.32 0.00 39.60 4.85
839 845 5.543507 AGCATGGACGAAATATCTCTCTT 57.456 39.130 0.00 0.00 0.00 2.85
842 848 5.923204 AGAAAGCATGGACGAAATATCTCT 58.077 37.500 0.00 0.00 0.00 3.10
919 941 1.997669 CCCTCGTTGTCTTGTAGCTC 58.002 55.000 0.00 0.00 0.00 4.09
1188 1214 1.079057 GTCTTCCTTGGTCGCTCCC 60.079 63.158 0.00 0.00 34.77 4.30
1191 1217 1.289380 GTCGTCTTCCTTGGTCGCT 59.711 57.895 0.00 0.00 0.00 4.93
1235 1261 3.112205 ATGATCAGCACGGCCTCCC 62.112 63.158 0.00 0.00 0.00 4.30
1361 1390 3.325293 ACTTGAGTAGTGAGCATGGTG 57.675 47.619 0.00 0.00 35.19 4.17
1373 1402 9.897744 CATTTTCAGCTGAAATTTACTTGAGTA 57.102 29.630 35.66 20.08 42.83 2.59
1393 1422 3.126858 TGCTCACGCTAATCACCATTTTC 59.873 43.478 0.00 0.00 36.97 2.29
1442 1475 5.762045 ACCGTTTCAAGATGTCAATCAAAG 58.238 37.500 0.00 0.00 35.03 2.77
1451 1484 4.058817 GTCTCAGAACCGTTTCAAGATGT 58.941 43.478 0.00 0.00 33.72 3.06
1489 1522 0.723981 GCTTCCAGCAGACGACATTC 59.276 55.000 0.00 0.00 41.89 2.67
1572 1605 1.069823 AGTGATGATGGCGATGAGGAC 59.930 52.381 0.00 0.00 0.00 3.85
1573 1606 1.342496 GAGTGATGATGGCGATGAGGA 59.658 52.381 0.00 0.00 0.00 3.71
1574 1607 1.607509 GGAGTGATGATGGCGATGAGG 60.608 57.143 0.00 0.00 0.00 3.86
1581 1614 0.548031 TTGGGAGGAGTGATGATGGC 59.452 55.000 0.00 0.00 0.00 4.40
1591 1624 0.689623 AGCTGTTGACTTGGGAGGAG 59.310 55.000 0.00 0.00 0.00 3.69
1608 1641 6.237755 GCATTAAATTTGATCAGCAGTTGAGC 60.238 38.462 0.00 0.00 42.56 4.26
1611 1644 6.954616 TGCATTAAATTTGATCAGCAGTTG 57.045 33.333 0.00 0.00 0.00 3.16
1626 1659 5.419542 AGCTAAGACGATCACTGCATTAAA 58.580 37.500 0.00 0.00 0.00 1.52
1643 1738 1.270518 ACATCGGCCTGCATAGCTAAG 60.271 52.381 0.00 0.00 0.00 2.18
1649 1744 1.447217 CAGGACATCGGCCTGCATA 59.553 57.895 2.21 0.00 45.66 3.14
1664 1759 2.544686 CGTCTGATCGTAGTACTCCAGG 59.455 54.545 0.00 0.00 0.00 4.45
1761 1856 2.160205 GAAAACAGGGTCTAAGTGGCC 58.840 52.381 0.00 0.00 40.45 5.36
1763 1858 2.038033 TCGGAAAACAGGGTCTAAGTGG 59.962 50.000 0.00 0.00 0.00 4.00
1802 1897 5.688807 TCCATCAGGAATCAGGAGAAATTC 58.311 41.667 0.00 0.00 42.23 2.17
1947 2051 3.445096 GGAATGCTTACTGGCAACTGAAT 59.555 43.478 0.00 0.00 45.68 2.57
1980 2084 4.021016 ACACTGCTTCTACTTCCCTACAAG 60.021 45.833 0.00 0.00 0.00 3.16
1981 2085 3.901844 ACACTGCTTCTACTTCCCTACAA 59.098 43.478 0.00 0.00 0.00 2.41
1995 2099 3.251004 GCTTTAGCAACAGTACACTGCTT 59.749 43.478 17.93 1.14 43.83 3.91
2000 2104 3.399330 TCTGGCTTTAGCAACAGTACAC 58.601 45.455 3.88 0.00 44.36 2.90
2020 2124 9.921637 CAGATCTAGTTATATGAAGGGAAGTTC 57.078 37.037 0.00 0.00 0.00 3.01
2046 2150 9.220767 GACCAATTAACTCCTGATTATCCATAC 57.779 37.037 0.00 0.00 0.00 2.39
2047 2151 8.094548 CGACCAATTAACTCCTGATTATCCATA 58.905 37.037 0.00 0.00 0.00 2.74
2074 2364 3.117171 CAGTCAGCGCAGACAGCC 61.117 66.667 30.89 7.81 40.98 4.85
2075 2365 3.786586 GCAGTCAGCGCAGACAGC 61.787 66.667 28.75 28.75 42.42 4.40
2125 2416 1.669115 GGCCGGGATGACATGATCG 60.669 63.158 2.18 0.00 0.00 3.69
2189 2480 5.298777 TCTGAACGGAGGTAATAGAAGTAGC 59.701 44.000 0.00 0.00 0.00 3.58
2199 2490 6.105397 ACAGTTAATTCTGAACGGAGGTAA 57.895 37.500 1.40 0.00 38.63 2.85
2200 2491 5.620654 CGACAGTTAATTCTGAACGGAGGTA 60.621 44.000 1.40 0.00 38.63 3.08
2201 2492 4.566987 GACAGTTAATTCTGAACGGAGGT 58.433 43.478 1.40 0.00 38.63 3.85
2202 2493 3.612860 CGACAGTTAATTCTGAACGGAGG 59.387 47.826 1.40 0.00 38.63 4.30
2203 2494 3.060895 GCGACAGTTAATTCTGAACGGAG 59.939 47.826 14.40 4.49 38.63 4.63
2204 2495 2.991190 GCGACAGTTAATTCTGAACGGA 59.009 45.455 14.40 0.00 38.63 4.69
2205 2496 2.993899 AGCGACAGTTAATTCTGAACGG 59.006 45.455 14.40 5.09 38.63 4.44
2206 2497 3.673338 TCAGCGACAGTTAATTCTGAACG 59.327 43.478 1.40 7.36 38.63 3.95
2207 2498 5.591643 TTCAGCGACAGTTAATTCTGAAC 57.408 39.130 1.40 0.00 36.15 3.18
2208 2499 6.426633 TCATTTCAGCGACAGTTAATTCTGAA 59.573 34.615 1.40 0.00 38.37 3.02
2209 2500 5.931724 TCATTTCAGCGACAGTTAATTCTGA 59.068 36.000 1.40 0.00 38.63 3.27
2210 2501 6.169419 TCATTTCAGCGACAGTTAATTCTG 57.831 37.500 0.00 0.00 40.80 3.02
2211 2502 5.163814 GCTCATTTCAGCGACAGTTAATTCT 60.164 40.000 0.00 0.00 0.00 2.40
2212 2503 5.024555 GCTCATTTCAGCGACAGTTAATTC 58.975 41.667 0.00 0.00 0.00 2.17
2213 2504 4.697352 AGCTCATTTCAGCGACAGTTAATT 59.303 37.500 0.00 0.00 44.82 1.40
2214 2505 4.256920 AGCTCATTTCAGCGACAGTTAAT 58.743 39.130 0.00 0.00 44.82 1.40
2215 2506 3.664107 AGCTCATTTCAGCGACAGTTAA 58.336 40.909 0.00 0.00 44.82 2.01
2216 2507 3.319137 AGCTCATTTCAGCGACAGTTA 57.681 42.857 0.00 0.00 44.82 2.24
2217 2508 2.175878 AGCTCATTTCAGCGACAGTT 57.824 45.000 0.00 0.00 44.82 3.16
2218 2509 2.175878 AAGCTCATTTCAGCGACAGT 57.824 45.000 0.00 0.00 44.82 3.55
2219 2510 4.118410 AGATAAGCTCATTTCAGCGACAG 58.882 43.478 0.00 0.00 44.82 3.51
2220 2511 4.128925 AGATAAGCTCATTTCAGCGACA 57.871 40.909 0.00 0.00 44.82 4.35
2221 2512 6.777526 ATAAGATAAGCTCATTTCAGCGAC 57.222 37.500 0.00 0.00 44.82 5.19
2222 2513 7.385205 GGTAATAAGATAAGCTCATTTCAGCGA 59.615 37.037 0.00 0.00 44.82 4.93
2223 2514 7.360438 GGGTAATAAGATAAGCTCATTTCAGCG 60.360 40.741 0.00 0.00 44.82 5.18
2224 2515 7.663493 AGGGTAATAAGATAAGCTCATTTCAGC 59.337 37.037 0.00 0.00 39.99 4.26
2225 2516 9.213799 GAGGGTAATAAGATAAGCTCATTTCAG 57.786 37.037 0.00 0.00 0.00 3.02
2226 2517 8.157476 GGAGGGTAATAAGATAAGCTCATTTCA 58.843 37.037 0.00 0.00 0.00 2.69
2227 2518 7.608376 GGGAGGGTAATAAGATAAGCTCATTTC 59.392 40.741 0.00 0.00 0.00 2.17
2228 2519 7.295911 AGGGAGGGTAATAAGATAAGCTCATTT 59.704 37.037 0.00 0.00 0.00 2.32
2229 2520 6.795000 AGGGAGGGTAATAAGATAAGCTCATT 59.205 38.462 0.00 0.00 0.00 2.57
2230 2521 6.214412 CAGGGAGGGTAATAAGATAAGCTCAT 59.786 42.308 0.00 0.00 0.00 2.90
2231 2522 5.544176 CAGGGAGGGTAATAAGATAAGCTCA 59.456 44.000 0.00 0.00 0.00 4.26
2232 2523 5.780793 TCAGGGAGGGTAATAAGATAAGCTC 59.219 44.000 0.00 0.00 0.00 4.09
2233 2524 5.727630 TCAGGGAGGGTAATAAGATAAGCT 58.272 41.667 0.00 0.00 0.00 3.74
2234 2525 6.435292 TTCAGGGAGGGTAATAAGATAAGC 57.565 41.667 0.00 0.00 0.00 3.09
2235 2526 7.147373 TGGTTTCAGGGAGGGTAATAAGATAAG 60.147 40.741 0.00 0.00 0.00 1.73
2236 2527 6.679303 TGGTTTCAGGGAGGGTAATAAGATAA 59.321 38.462 0.00 0.00 0.00 1.75
2269 2560 1.595929 TGGTTTTCGCCACCGACTC 60.596 57.895 0.00 0.00 44.30 3.36
2288 2579 6.524586 GGCAAAATAACTTCTCAATCAAGTCG 59.475 38.462 0.00 0.00 32.71 4.18
2296 2587 6.942005 TCAGAGATGGCAAAATAACTTCTCAA 59.058 34.615 11.71 0.00 37.68 3.02
2307 2609 5.774690 ACCTAACAATTCAGAGATGGCAAAA 59.225 36.000 0.00 0.00 0.00 2.44
2326 2643 3.349927 TCTAGAGCACGCAGTTACCTAA 58.650 45.455 0.00 0.00 41.61 2.69
2338 2655 2.548875 CTGGAGTTGCATCTAGAGCAC 58.451 52.381 14.08 10.48 42.54 4.40
2424 2741 2.988570 AGATCCAAGAAGAGCAAGCAG 58.011 47.619 0.00 0.00 0.00 4.24
2448 2765 8.685427 TGCACTTCACAATTATTGCAGTATTAT 58.315 29.630 4.68 0.00 35.13 1.28
2462 2780 5.703592 TCGGTAATTAACTGCACTTCACAAT 59.296 36.000 0.00 0.00 34.14 2.71
2582 2900 0.752009 TCCTCCGGATCGTCCTGAAG 60.752 60.000 3.57 0.00 33.30 3.02
2668 2992 3.451178 GCTACTGGTTATGGTCTGAAGGA 59.549 47.826 0.00 0.00 0.00 3.36
2753 3084 3.638627 TGTACAGAGCTGGTGATGGATAG 59.361 47.826 0.00 0.00 34.19 2.08
2781 3113 8.862325 TTATTTTCAGAAATCAGAAGGTAGCA 57.138 30.769 0.00 0.00 36.82 3.49
2851 3184 2.413837 GCATGTACACTCAAGTCGGTT 58.586 47.619 0.00 0.00 0.00 4.44
2875 3208 1.724582 AAGGTCCACGCAAACTGCAC 61.725 55.000 0.00 0.00 45.36 4.57
2876 3209 1.453015 AAGGTCCACGCAAACTGCA 60.453 52.632 0.00 0.00 45.36 4.41
2935 3554 3.252554 TCCCCTAAACACCTTGCATTT 57.747 42.857 0.00 0.00 0.00 2.32
2965 3584 8.643324 TGCTTAGGAAAAGCTTGGTTTATTTTA 58.357 29.630 0.00 0.00 43.38 1.52
2975 3594 4.293415 CACTTGTGCTTAGGAAAAGCTTG 58.707 43.478 0.00 0.00 43.38 4.01
3015 3634 7.807433 CGCCTATTTGCATATTAATTAAGCACA 59.193 33.333 9.44 5.07 34.44 4.57
3019 3638 6.468956 CGGCGCCTATTTGCATATTAATTAAG 59.531 38.462 26.68 0.00 0.00 1.85
3041 3670 1.130561 CGATTTTTCAGAAGGACCGGC 59.869 52.381 0.00 0.00 0.00 6.13
3048 3677 9.334693 CAGAGAAATAAACCGATTTTTCAGAAG 57.665 33.333 0.00 0.00 34.12 2.85
3061 3690 5.757808 GGAGAGATGCTCAGAGAAATAAACC 59.242 44.000 0.00 0.00 45.81 3.27
3092 3721 5.543714 TCTTAGGCGTTGTACAATGAAAGA 58.456 37.500 28.05 25.08 0.00 2.52
3096 3725 6.811253 AAATTCTTAGGCGTTGTACAATGA 57.189 33.333 28.05 7.69 0.00 2.57
3155 3786 4.798433 TGTGAATGCCTCGCACTT 57.202 50.000 0.00 0.00 43.04 3.16
3195 3828 9.506018 TCTCTATGTGATCAAATGAGAAAACAA 57.494 29.630 18.24 3.50 30.68 2.83
3202 3835 7.270779 TCAAGGTCTCTATGTGATCAAATGAG 58.729 38.462 8.76 12.33 0.00 2.90
3205 3838 8.153550 GGTATCAAGGTCTCTATGTGATCAAAT 58.846 37.037 3.32 3.32 31.58 2.32
3215 3848 5.446860 TCAAGTCGGTATCAAGGTCTCTAT 58.553 41.667 0.00 0.00 0.00 1.98
3219 3852 6.732896 ATATTCAAGTCGGTATCAAGGTCT 57.267 37.500 0.00 0.00 0.00 3.85
3228 3861 6.072397 CCAAACAACCAATATTCAAGTCGGTA 60.072 38.462 0.00 0.00 0.00 4.02
3256 3889 0.747852 TAGCCATCACGTCCGCATAA 59.252 50.000 0.00 0.00 0.00 1.90
3263 3896 4.572389 AGAATGAAATGTAGCCATCACGTC 59.428 41.667 0.00 0.00 0.00 4.34
3275 3908 8.408043 TTCCAAACATCACTAGAATGAAATGT 57.592 30.769 14.16 1.65 30.82 2.71
3281 3914 9.740239 CCAATATTTCCAAACATCACTAGAATG 57.260 33.333 0.00 2.45 0.00 2.67
3282 3915 9.479549 ACCAATATTTCCAAACATCACTAGAAT 57.520 29.630 0.00 0.00 0.00 2.40
3283 3916 8.877864 ACCAATATTTCCAAACATCACTAGAA 57.122 30.769 0.00 0.00 0.00 2.10
3324 3959 4.000331 AGATATGCAAACGGAGATGGAG 58.000 45.455 0.00 0.00 0.00 3.86
3325 3960 4.588951 ACTAGATATGCAAACGGAGATGGA 59.411 41.667 0.00 0.00 0.00 3.41
3326 3961 4.687948 CACTAGATATGCAAACGGAGATGG 59.312 45.833 0.00 0.00 0.00 3.51
3327 3962 5.532557 TCACTAGATATGCAAACGGAGATG 58.467 41.667 0.00 0.00 0.00 2.90
3328 3963 5.791336 TCACTAGATATGCAAACGGAGAT 57.209 39.130 0.00 0.00 0.00 2.75
3329 3964 5.069119 ACATCACTAGATATGCAAACGGAGA 59.931 40.000 0.00 0.00 31.88 3.71
3356 3991 3.495434 TCAGGACCAAAATACACGGTT 57.505 42.857 0.00 0.00 31.63 4.44
3358 3993 6.693315 ATTAATCAGGACCAAAATACACGG 57.307 37.500 0.00 0.00 0.00 4.94
3360 3995 9.139174 CACAAATTAATCAGGACCAAAATACAC 57.861 33.333 0.00 0.00 0.00 2.90
3374 4014 7.060518 GCGCGCATAAATATCACAAATTAATCA 59.939 33.333 29.10 0.00 0.00 2.57
3381 4021 3.961477 AGCGCGCATAAATATCACAAA 57.039 38.095 35.10 0.00 0.00 2.83
3383 4023 2.611751 ACAAGCGCGCATAAATATCACA 59.388 40.909 35.10 0.00 0.00 3.58
3384 4024 3.253371 ACAAGCGCGCATAAATATCAC 57.747 42.857 35.10 0.00 0.00 3.06
3385 4025 3.961477 AACAAGCGCGCATAAATATCA 57.039 38.095 35.10 0.00 0.00 2.15
3386 4026 7.180079 ACATATAACAAGCGCGCATAAATATC 58.820 34.615 35.10 0.00 0.00 1.63
3387 4027 7.072177 ACATATAACAAGCGCGCATAAATAT 57.928 32.000 35.10 23.16 0.00 1.28
3388 4028 6.474819 ACATATAACAAGCGCGCATAAATA 57.525 33.333 35.10 22.04 0.00 1.40
3389 4029 5.356882 ACATATAACAAGCGCGCATAAAT 57.643 34.783 35.10 20.64 0.00 1.40
3415 4055 7.155328 ACTATGTAGATCATCAACGGAATTCC 58.845 38.462 15.01 15.01 37.91 3.01
3443 4083 9.825109 ATTCATATGATTCATGCAACATGAAAA 57.175 25.926 22.64 15.80 40.84 2.29
3450 4090 8.579006 TCCCTAAATTCATATGATTCATGCAAC 58.421 33.333 6.17 0.00 0.00 4.17
3517 4157 0.802607 GACAGTGACCGGCGATTCTC 60.803 60.000 9.30 5.43 0.00 2.87
3520 4160 2.264794 GGACAGTGACCGGCGATT 59.735 61.111 9.30 0.00 0.00 3.34
3542 4182 6.841755 AGACATAGCTAATCCTCCTTGTAAGT 59.158 38.462 0.00 0.00 0.00 2.24
3544 4184 7.500992 CAAGACATAGCTAATCCTCCTTGTAA 58.499 38.462 0.00 0.00 0.00 2.41
3565 4208 1.126488 CAGGCTCATCTAGGGCAAGA 58.874 55.000 0.00 0.00 0.00 3.02
3571 4214 1.686052 GAGTGACCAGGCTCATCTAGG 59.314 57.143 0.00 0.00 0.00 3.02
3578 4221 4.803426 CGGCGAGTGACCAGGCTC 62.803 72.222 0.00 0.00 0.00 4.70
3620 4263 2.817423 GATCTTTGCGCGAGGGCAG 61.817 63.158 12.10 5.17 44.94 4.85
3621 4264 2.819595 GATCTTTGCGCGAGGGCA 60.820 61.111 12.10 10.81 42.12 5.36
3622 4265 1.922135 TTTGATCTTTGCGCGAGGGC 61.922 55.000 12.10 5.13 0.00 5.19
3623 4266 0.179189 GTTTGATCTTTGCGCGAGGG 60.179 55.000 12.10 0.12 0.00 4.30
3624 4267 0.798776 AGTTTGATCTTTGCGCGAGG 59.201 50.000 12.10 0.15 0.00 4.63
3625 4268 1.460743 TCAGTTTGATCTTTGCGCGAG 59.539 47.619 12.10 3.17 0.00 5.03
3626 4269 1.507562 TCAGTTTGATCTTTGCGCGA 58.492 45.000 12.10 0.00 0.00 5.87
3627 4270 2.532531 ATCAGTTTGATCTTTGCGCG 57.467 45.000 0.00 0.00 29.59 6.86
3628 4271 4.205792 GCAATATCAGTTTGATCTTTGCGC 59.794 41.667 16.78 0.00 41.67 6.09
3629 4272 4.736793 GGCAATATCAGTTTGATCTTTGCG 59.263 41.667 20.95 0.00 46.23 4.85
3630 4273 5.747197 CAGGCAATATCAGTTTGATCTTTGC 59.253 40.000 20.28 20.28 45.48 3.68


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

AutoCloner maintained by Alex Coulton.