Multiple sequence alignment - TraesCS3D01G243200

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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 TraesCS3D01G243200 chr3D 100.000 3307 0 0 1 3307 338488598 338491904 0.000000e+00 6107.0
1 TraesCS3D01G243200 chr3D 91.026 78 4 3 1 76 114346145 114346069 5.840000e-18 102.0
2 TraesCS3D01G243200 chr3A 92.629 2035 96 18 1291 3307 456775967 456777965 0.000000e+00 2878.0
3 TraesCS3D01G243200 chr3A 88.967 707 68 7 67 770 456728122 456728821 0.000000e+00 865.0
4 TraesCS3D01G243200 chr3A 93.145 496 15 4 804 1296 456775461 456775940 0.000000e+00 710.0
5 TraesCS3D01G243200 chr3B 92.100 2038 105 18 1292 3307 436740185 436742188 0.000000e+00 2820.0
6 TraesCS3D01G243200 chr3B 94.553 459 16 4 845 1296 436739701 436740157 0.000000e+00 701.0
7 TraesCS3D01G243200 chr3B 92.105 76 4 2 1 75 662086914 662086840 4.510000e-19 106.0
8 TraesCS3D01G243200 chr3B 96.226 53 2 0 808 860 436734247 436734299 1.630000e-13 87.9
9 TraesCS3D01G243200 chr5D 93.421 76 2 3 1 74 417943169 417943243 3.490000e-20 110.0
10 TraesCS3D01G243200 chr4D 93.243 74 2 3 1 72 504360919 504360847 4.510000e-19 106.0
11 TraesCS3D01G243200 chr1D 93.151 73 4 1 1 72 402158709 402158637 4.510000e-19 106.0
12 TraesCS3D01G243200 chr1D 94.118 68 3 1 1 67 102511443 102511510 5.840000e-18 102.0
13 TraesCS3D01G243200 chr1D 94.030 67 3 1 1 66 362023575 362023641 2.100000e-17 100.0
14 TraesCS3D01G243200 chr7B 94.118 68 2 2 1 67 327670203 327670269 5.840000e-18 102.0
15 TraesCS3D01G243200 chr2D 94.118 68 1 3 1 66 117793052 117793118 2.100000e-17 100.0


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 TraesCS3D01G243200 chr3D 338488598 338491904 3306 False 6107.0 6107 100.0000 1 3307 1 chr3D.!!$F1 3306
1 TraesCS3D01G243200 chr3A 456775461 456777965 2504 False 1794.0 2878 92.8870 804 3307 2 chr3A.!!$F2 2503
2 TraesCS3D01G243200 chr3A 456728122 456728821 699 False 865.0 865 88.9670 67 770 1 chr3A.!!$F1 703
3 TraesCS3D01G243200 chr3B 436739701 436742188 2487 False 1760.5 2820 93.3265 845 3307 2 chr3B.!!$F2 2462

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
502 505 0.042731 TTGATCTCCGGGTCCTCCTT 59.957 55.0 0.0 0.0 0.00 3.36 F
746 750 0.179000 ACCGCTTATTGGAGCCTCAG 59.821 55.0 0.0 0.0 39.51 3.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1441 1487 0.179043 TTAAGTCACAGGGCGTGCAA 60.179 50.0 7.17 0.0 45.92 4.08 R
2466 2531 0.673437 CCGTGGTTGAAATGCACCTT 59.327 50.0 0.00 0.0 0.00 3.50 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
25 26 5.720371 TGCTTCTCCTAGATAGATCTTGC 57.280 43.478 0.00 0.00 38.32 4.01
26 27 4.217334 TGCTTCTCCTAGATAGATCTTGCG 59.783 45.833 0.00 0.00 38.32 4.85
27 28 4.217550 GCTTCTCCTAGATAGATCTTGCGT 59.782 45.833 0.00 0.00 38.32 5.24
28 29 5.697473 TTCTCCTAGATAGATCTTGCGTG 57.303 43.478 0.00 0.00 38.32 5.34
29 30 4.974399 TCTCCTAGATAGATCTTGCGTGA 58.026 43.478 0.00 0.00 38.32 4.35
30 31 5.565509 TCTCCTAGATAGATCTTGCGTGAT 58.434 41.667 0.00 0.00 38.32 3.06
31 32 5.645929 TCTCCTAGATAGATCTTGCGTGATC 59.354 44.000 0.00 9.82 42.18 2.92
41 42 6.610741 GATCTTGCGTGATCTAGGAATTTT 57.389 37.500 10.37 0.00 39.61 1.82
42 43 7.020914 GATCTTGCGTGATCTAGGAATTTTT 57.979 36.000 10.37 0.00 39.61 1.94
70 71 7.388437 AGAATACTACGTTACCCAACAAATGA 58.612 34.615 0.00 0.00 34.05 2.57
100 101 5.436175 TGAATCCGAATGTAATCACCATGT 58.564 37.500 0.00 0.00 0.00 3.21
105 106 5.885352 TCCGAATGTAATCACCATGTGAATT 59.115 36.000 0.46 0.00 45.96 2.17
117 118 6.543465 TCACCATGTGAATTATCTGACAATCC 59.457 38.462 0.00 0.00 39.78 3.01
118 119 6.319405 CACCATGTGAATTATCTGACAATCCA 59.681 38.462 0.00 0.00 35.23 3.41
119 120 6.319658 ACCATGTGAATTATCTGACAATCCAC 59.680 38.462 0.00 0.00 0.00 4.02
120 121 6.544931 CCATGTGAATTATCTGACAATCCACT 59.455 38.462 0.00 0.00 0.00 4.00
122 123 7.615582 TGTGAATTATCTGACAATCCACTTC 57.384 36.000 0.00 0.00 0.00 3.01
134 136 0.110486 TCCACTTCCAGAACCTTGCC 59.890 55.000 0.00 0.00 0.00 4.52
169 171 3.067106 TCGGCTTCTTGACAATGTCTTC 58.933 45.455 14.97 0.00 33.15 2.87
205 207 2.941720 GCTTGTGGATTTGCAACCAAAA 59.058 40.909 10.17 10.32 43.58 2.44
207 209 4.036616 GCTTGTGGATTTGCAACCAAAATT 59.963 37.500 11.13 0.00 43.58 1.82
233 235 2.857592 ACATGAATTGCGCATCTTCC 57.142 45.000 22.90 9.03 0.00 3.46
243 245 1.815212 CGCATCTTCCGCATGACTCG 61.815 60.000 0.00 0.00 0.00 4.18
251 253 3.049227 CGCATGACTCGGACAATCA 57.951 52.632 0.00 0.00 0.00 2.57
254 256 2.472861 CGCATGACTCGGACAATCATAC 59.527 50.000 0.00 0.00 31.83 2.39
285 288 4.119136 CAACATTTCCCAAAAGCGAAAGT 58.881 39.130 0.00 0.00 31.85 2.66
288 291 3.446310 TTTCCCAAAAGCGAAAGTTCC 57.554 42.857 0.00 0.00 0.00 3.62
320 323 0.107703 GCATGATCCGTTCCCAGTCA 60.108 55.000 0.00 0.00 0.00 3.41
340 343 1.147817 ACCCAAACAAGAAGCCCTCAT 59.852 47.619 0.00 0.00 0.00 2.90
343 346 2.229784 CCAAACAAGAAGCCCTCATCAC 59.770 50.000 0.00 0.00 0.00 3.06
396 399 1.002403 TCCTATGCGGGGTTCCAGA 59.998 57.895 0.00 0.00 0.00 3.86
410 413 1.916506 TCCAGATAGCCCTCATCTCG 58.083 55.000 0.00 0.00 30.18 4.04
444 447 1.411246 CCCGACCGACATATTTCTCCA 59.589 52.381 0.00 0.00 0.00 3.86
453 456 3.609853 ACATATTTCTCCATGTGCACGT 58.390 40.909 13.13 9.52 34.15 4.49
454 457 3.374988 ACATATTTCTCCATGTGCACGTG 59.625 43.478 28.62 28.62 34.15 4.49
480 483 1.963338 GCAAGCCAACAGACTCGCT 60.963 57.895 0.00 0.00 0.00 4.93
496 499 1.227002 GCTCGTTGATCTCCGGGTC 60.227 63.158 0.00 0.00 0.00 4.46
502 505 0.042731 TTGATCTCCGGGTCCTCCTT 59.957 55.000 0.00 0.00 0.00 3.36
503 506 0.687757 TGATCTCCGGGTCCTCCTTG 60.688 60.000 0.00 0.00 0.00 3.61
526 529 2.311688 ATCACCAGATCGCCGAACCC 62.312 60.000 0.00 0.00 0.00 4.11
543 546 1.211456 CCCCTCTTCAGCAAGATCCT 58.789 55.000 0.00 0.00 38.02 3.24
544 547 2.293184 ACCCCTCTTCAGCAAGATCCTA 60.293 50.000 0.00 0.00 38.02 2.94
545 548 2.978278 CCCCTCTTCAGCAAGATCCTAT 59.022 50.000 0.00 0.00 38.02 2.57
549 552 5.298777 CCCTCTTCAGCAAGATCCTATTTTG 59.701 44.000 0.00 0.00 38.02 2.44
550 553 5.884792 CCTCTTCAGCAAGATCCTATTTTGT 59.115 40.000 0.00 0.00 38.02 2.83
552 555 6.475504 TCTTCAGCAAGATCCTATTTTGTGA 58.524 36.000 0.00 0.00 33.38 3.58
634 637 3.072476 CCGAGGGGGATGCCATAG 58.928 66.667 5.30 0.00 38.47 2.23
664 667 3.219052 GAGGATCTTGTCGTCGAGTTT 57.781 47.619 0.00 0.00 32.65 2.66
667 670 2.917971 GGATCTTGTCGTCGAGTTTCAG 59.082 50.000 0.00 0.00 0.00 3.02
668 671 2.417339 TCTTGTCGTCGAGTTTCAGG 57.583 50.000 0.00 0.00 0.00 3.86
669 672 1.000607 TCTTGTCGTCGAGTTTCAGGG 60.001 52.381 0.00 0.00 0.00 4.45
676 679 1.203994 GTCGAGTTTCAGGGGAATCGA 59.796 52.381 0.00 0.00 40.37 3.59
688 691 2.405172 GGGAATCGATTAAGGACTCGC 58.595 52.381 11.38 1.37 34.94 5.03
693 696 1.143183 GATTAAGGACTCGCCGGCA 59.857 57.895 28.98 12.94 43.43 5.69
696 699 2.515996 TTAAGGACTCGCCGGCAAGG 62.516 60.000 28.98 17.55 43.43 3.61
698 701 4.821589 GGACTCGCCGGCAAGGAG 62.822 72.222 28.98 25.69 45.00 3.69
699 702 4.070552 GACTCGCCGGCAAGGAGT 62.071 66.667 28.58 28.58 45.00 3.85
700 703 3.991536 GACTCGCCGGCAAGGAGTC 62.992 68.421 32.99 32.99 46.72 3.36
701 704 4.069232 CTCGCCGGCAAGGAGTCA 62.069 66.667 28.98 0.00 45.00 3.41
702 705 4.373116 TCGCCGGCAAGGAGTCAC 62.373 66.667 28.98 0.00 45.00 3.67
727 731 3.846588 AGAGGACTTTCAAATCCTAGCCA 59.153 43.478 0.00 0.00 45.74 4.75
746 750 0.179000 ACCGCTTATTGGAGCCTCAG 59.821 55.000 0.00 0.00 39.51 3.35
747 751 0.179000 CCGCTTATTGGAGCCTCAGT 59.821 55.000 0.00 0.00 39.51 3.41
748 752 1.407437 CCGCTTATTGGAGCCTCAGTT 60.407 52.381 0.00 0.00 39.51 3.16
749 753 2.158957 CCGCTTATTGGAGCCTCAGTTA 60.159 50.000 0.00 0.00 39.51 2.24
750 754 3.531538 CGCTTATTGGAGCCTCAGTTAA 58.468 45.455 0.00 0.00 39.51 2.01
751 755 3.309954 CGCTTATTGGAGCCTCAGTTAAC 59.690 47.826 0.00 0.00 39.51 2.01
753 757 4.333926 GCTTATTGGAGCCTCAGTTAACTG 59.666 45.833 26.60 26.60 39.72 3.16
762 766 3.409026 CTCAGTTAACTGTGAGGCCTT 57.591 47.619 29.83 0.00 44.12 4.35
770 774 7.595130 CAGTTAACTGTGAGGCCTTTAAAATTC 59.405 37.037 24.70 0.00 39.09 2.17
771 775 4.766404 ACTGTGAGGCCTTTAAAATTCG 57.234 40.909 6.77 0.00 0.00 3.34
772 776 3.506067 ACTGTGAGGCCTTTAAAATTCGG 59.494 43.478 6.77 0.00 0.00 4.30
773 777 2.823154 TGTGAGGCCTTTAAAATTCGGG 59.177 45.455 6.77 0.00 0.00 5.14
774 778 2.823747 GTGAGGCCTTTAAAATTCGGGT 59.176 45.455 6.77 0.00 0.00 5.28
775 779 2.823154 TGAGGCCTTTAAAATTCGGGTG 59.177 45.455 6.77 0.00 0.00 4.61
776 780 2.165641 GAGGCCTTTAAAATTCGGGTGG 59.834 50.000 6.77 0.00 0.00 4.61
777 781 2.172679 GGCCTTTAAAATTCGGGTGGA 58.827 47.619 0.00 0.00 0.00 4.02
778 782 2.094390 GGCCTTTAAAATTCGGGTGGAC 60.094 50.000 0.00 0.00 0.00 4.02
779 783 2.559231 GCCTTTAAAATTCGGGTGGACA 59.441 45.455 0.00 0.00 0.00 4.02
780 784 3.366985 GCCTTTAAAATTCGGGTGGACAG 60.367 47.826 0.00 0.00 0.00 3.51
781 785 3.824443 CCTTTAAAATTCGGGTGGACAGT 59.176 43.478 0.00 0.00 0.00 3.55
782 786 4.320935 CCTTTAAAATTCGGGTGGACAGTG 60.321 45.833 0.00 0.00 0.00 3.66
783 787 2.649531 AAAATTCGGGTGGACAGTGA 57.350 45.000 0.00 0.00 0.00 3.41
784 788 2.185004 AAATTCGGGTGGACAGTGAG 57.815 50.000 0.00 0.00 0.00 3.51
785 789 1.056660 AATTCGGGTGGACAGTGAGT 58.943 50.000 0.00 0.00 0.00 3.41
786 790 1.056660 ATTCGGGTGGACAGTGAGTT 58.943 50.000 0.00 0.00 0.00 3.01
787 791 1.707106 TTCGGGTGGACAGTGAGTTA 58.293 50.000 0.00 0.00 0.00 2.24
788 792 1.254026 TCGGGTGGACAGTGAGTTAG 58.746 55.000 0.00 0.00 0.00 2.34
789 793 1.202964 TCGGGTGGACAGTGAGTTAGA 60.203 52.381 0.00 0.00 0.00 2.10
790 794 1.616865 CGGGTGGACAGTGAGTTAGAA 59.383 52.381 0.00 0.00 0.00 2.10
791 795 2.036733 CGGGTGGACAGTGAGTTAGAAA 59.963 50.000 0.00 0.00 0.00 2.52
792 796 3.493699 CGGGTGGACAGTGAGTTAGAAAA 60.494 47.826 0.00 0.00 0.00 2.29
793 797 3.813724 GGGTGGACAGTGAGTTAGAAAAC 59.186 47.826 0.00 0.00 35.72 2.43
795 799 5.221581 GGGTGGACAGTGAGTTAGAAAACTA 60.222 44.000 0.00 0.00 46.09 2.24
796 800 5.927115 GGTGGACAGTGAGTTAGAAAACTAG 59.073 44.000 0.00 0.00 46.09 2.57
797 801 5.927115 GTGGACAGTGAGTTAGAAAACTAGG 59.073 44.000 0.00 0.00 46.09 3.02
798 802 4.930405 GGACAGTGAGTTAGAAAACTAGGC 59.070 45.833 0.00 0.00 46.09 3.93
799 803 5.510861 GGACAGTGAGTTAGAAAACTAGGCA 60.511 44.000 0.00 0.00 46.09 4.75
800 804 5.298347 ACAGTGAGTTAGAAAACTAGGCAC 58.702 41.667 0.00 0.00 46.09 5.01
801 805 4.386049 CAGTGAGTTAGAAAACTAGGCACG 59.614 45.833 0.00 0.00 46.09 5.34
802 806 3.123116 GTGAGTTAGAAAACTAGGCACGC 59.877 47.826 0.00 0.00 46.09 5.34
960 966 1.039856 AAATTCACACCACAGCCCAC 58.960 50.000 0.00 0.00 0.00 4.61
968 975 2.125310 CACAGCCCACGCCGAATA 60.125 61.111 0.00 0.00 34.57 1.75
971 978 2.510691 AGCCCACGCCGAATAACG 60.511 61.111 0.00 0.00 42.18 3.18
992 1006 0.321387 GACGAACCCTTCTTCCACCC 60.321 60.000 0.00 0.00 0.00 4.61
997 1011 0.547954 ACCCTTCTTCCACCCCTCTC 60.548 60.000 0.00 0.00 0.00 3.20
998 1012 0.252927 CCCTTCTTCCACCCCTCTCT 60.253 60.000 0.00 0.00 0.00 3.10
999 1013 1.199615 CCTTCTTCCACCCCTCTCTC 58.800 60.000 0.00 0.00 0.00 3.20
1128 1142 2.317230 CGTGAAGAACGCAAGGGTT 58.683 52.632 1.90 1.90 46.99 4.11
1143 1157 2.046217 GTTCCCCTCAAGGCGTCC 60.046 66.667 0.00 0.00 0.00 4.79
1233 1247 1.751924 GATCCAAGCGTCTCAGGTACT 59.248 52.381 0.00 0.00 43.88 2.73
1252 1266 0.545309 TGCCTGTCAGCTCCCTAACT 60.545 55.000 0.00 0.00 0.00 2.24
1300 1346 3.442625 TGACTCGATTTCTGTACCATCGT 59.557 43.478 11.38 0.00 40.57 3.73
1341 1387 1.272781 GTGAGGAAATCAGAGTCGCG 58.727 55.000 0.00 0.00 39.07 5.87
1366 1412 1.664321 ATACGGTCACTCTGCCCGAC 61.664 60.000 4.10 0.00 44.41 4.79
1405 1451 6.672218 TGGGTAGGATTGAAATGAAGAGAGTA 59.328 38.462 0.00 0.00 0.00 2.59
1444 1490 8.915871 ACTATATGTTCATGTTCAAATGTTGC 57.084 30.769 0.00 0.00 0.00 4.17
1445 1491 8.522003 ACTATATGTTCATGTTCAAATGTTGCA 58.478 29.630 0.00 0.00 0.00 4.08
1446 1492 5.910637 ATGTTCATGTTCAAATGTTGCAC 57.089 34.783 0.00 0.00 0.00 4.57
1447 1493 3.795639 TGTTCATGTTCAAATGTTGCACG 59.204 39.130 0.00 0.00 28.99 5.34
1448 1494 2.392821 TCATGTTCAAATGTTGCACGC 58.607 42.857 0.00 0.00 28.99 5.34
1449 1495 1.456544 CATGTTCAAATGTTGCACGCC 59.543 47.619 0.00 0.00 28.99 5.68
1450 1496 0.249238 TGTTCAAATGTTGCACGCCC 60.249 50.000 0.00 0.00 28.99 6.13
1465 1511 2.490991 ACGCCCTGTGACTTAAGAAAC 58.509 47.619 10.09 7.37 0.00 2.78
1478 1524 7.712205 GTGACTTAAGAAACCCAGTAGTTTGTA 59.288 37.037 10.09 0.00 40.01 2.41
1554 1600 4.439289 GCTCGATTGCAGAGGCTTTAAATT 60.439 41.667 3.87 0.00 41.91 1.82
1560 1606 6.594788 TTGCAGAGGCTTTAAATTCATCTT 57.405 33.333 0.00 0.00 41.91 2.40
1561 1607 7.701539 TTGCAGAGGCTTTAAATTCATCTTA 57.298 32.000 0.00 0.00 41.91 2.10
1562 1608 7.325660 TGCAGAGGCTTTAAATTCATCTTAG 57.674 36.000 0.00 0.00 41.91 2.18
1563 1609 6.183360 TGCAGAGGCTTTAAATTCATCTTAGC 60.183 38.462 0.00 5.43 41.91 3.09
1565 1611 7.629222 GCAGAGGCTTTAAATTCATCTTAGCAA 60.629 37.037 0.00 0.00 36.96 3.91
1566 1612 8.411683 CAGAGGCTTTAAATTCATCTTAGCAAT 58.588 33.333 0.00 0.00 0.00 3.56
1567 1613 8.628280 AGAGGCTTTAAATTCATCTTAGCAATC 58.372 33.333 0.00 0.00 0.00 2.67
1568 1614 7.720442 AGGCTTTAAATTCATCTTAGCAATCC 58.280 34.615 0.00 0.00 0.00 3.01
1569 1615 6.638468 GGCTTTAAATTCATCTTAGCAATCCG 59.362 38.462 0.00 0.00 0.00 4.18
1571 1617 7.166473 GCTTTAAATTCATCTTAGCAATCCGTG 59.834 37.037 0.00 0.00 0.00 4.94
1578 1628 3.088532 TCTTAGCAATCCGTGGCAAAAT 58.911 40.909 0.00 0.00 0.00 1.82
1592 1642 5.569059 CGTGGCAAAATTCAGAAGTAATCAC 59.431 40.000 0.00 0.00 0.00 3.06
1593 1643 5.863935 GTGGCAAAATTCAGAAGTAATCACC 59.136 40.000 0.00 0.00 0.00 4.02
1596 1646 5.863935 GCAAAATTCAGAAGTAATCACCACC 59.136 40.000 0.00 0.00 0.00 4.61
1607 1657 1.979809 ATCACCACCTTCCCCATGTA 58.020 50.000 0.00 0.00 0.00 2.29
1608 1658 1.979809 TCACCACCTTCCCCATGTAT 58.020 50.000 0.00 0.00 0.00 2.29
1609 1659 3.138123 TCACCACCTTCCCCATGTATA 57.862 47.619 0.00 0.00 0.00 1.47
1610 1660 3.045634 TCACCACCTTCCCCATGTATAG 58.954 50.000 0.00 0.00 0.00 1.31
1611 1661 1.774856 ACCACCTTCCCCATGTATAGC 59.225 52.381 0.00 0.00 0.00 2.97
1612 1662 1.774254 CCACCTTCCCCATGTATAGCA 59.226 52.381 0.00 0.00 0.00 3.49
1613 1663 2.224621 CCACCTTCCCCATGTATAGCAG 60.225 54.545 0.00 0.00 0.00 4.24
1614 1664 2.439507 CACCTTCCCCATGTATAGCAGT 59.560 50.000 0.00 0.00 0.00 4.40
1615 1665 3.646162 CACCTTCCCCATGTATAGCAGTA 59.354 47.826 0.00 0.00 0.00 2.74
1616 1666 4.287067 CACCTTCCCCATGTATAGCAGTAT 59.713 45.833 0.00 0.00 0.00 2.12
1617 1667 5.483937 CACCTTCCCCATGTATAGCAGTATA 59.516 44.000 0.00 0.00 0.00 1.47
1618 1668 5.721960 ACCTTCCCCATGTATAGCAGTATAG 59.278 44.000 0.00 0.00 0.00 1.31
1619 1669 5.129485 CCTTCCCCATGTATAGCAGTATAGG 59.871 48.000 0.00 0.00 0.00 2.57
1620 1670 4.030913 TCCCCATGTATAGCAGTATAGGC 58.969 47.826 0.00 0.00 0.00 3.93
1877 1927 3.389329 TCCCCTTATGCTCAGAGAATGAC 59.611 47.826 0.00 0.00 33.22 3.06
1927 1977 0.684479 ATCCGTGAGCAGCTGGTAGA 60.684 55.000 20.22 13.51 0.00 2.59
2078 2128 0.392595 CCAAGGTTAGCGGGAGGAAC 60.393 60.000 0.00 0.00 0.00 3.62
2141 2191 0.517316 CGCCTATCGCCATTTTAGCC 59.483 55.000 0.00 0.00 0.00 3.93
2144 2194 3.343617 GCCTATCGCCATTTTAGCCATA 58.656 45.455 0.00 0.00 0.00 2.74
2349 2399 9.295825 TGGCATAAGTATGTTTTATCCATTAGG 57.704 33.333 0.54 0.00 36.11 2.69
2403 2454 7.010160 TCAACAAGGAGGGTCAAAAATAAGAT 58.990 34.615 0.00 0.00 0.00 2.40
2405 2456 8.802267 CAACAAGGAGGGTCAAAAATAAGATTA 58.198 33.333 0.00 0.00 0.00 1.75
2406 2457 8.581253 ACAAGGAGGGTCAAAAATAAGATTAG 57.419 34.615 0.00 0.00 0.00 1.73
2407 2458 7.122799 ACAAGGAGGGTCAAAAATAAGATTAGC 59.877 37.037 0.00 0.00 0.00 3.09
2408 2459 6.731467 AGGAGGGTCAAAAATAAGATTAGCA 58.269 36.000 0.00 0.00 0.00 3.49
2409 2460 6.603599 AGGAGGGTCAAAAATAAGATTAGCAC 59.396 38.462 0.00 0.00 0.00 4.40
2412 2476 5.124936 GGGTCAAAAATAAGATTAGCACCGT 59.875 40.000 0.00 0.00 0.00 4.83
2431 2495 4.873827 ACCGTACGCTTTGATATTGACAAT 59.126 37.500 10.49 5.87 0.00 2.71
2466 2531 6.094742 TGTTGCACAAAGAACATGAAGACTAA 59.905 34.615 0.00 0.00 0.00 2.24
2484 2549 2.507339 AAAGGTGCATTTCAACCACG 57.493 45.000 0.00 0.00 30.95 4.94
2622 2687 2.037251 TCAAGCTACAACACCAGAGGTC 59.963 50.000 0.00 0.00 31.02 3.85
2653 2718 6.036517 CCTCTGCAATCTCAACACAAGTATAC 59.963 42.308 0.00 0.00 0.00 1.47
2779 2844 4.060900 TCAATCTTCACACTGACTTCTGC 58.939 43.478 0.00 0.00 0.00 4.26
2791 2856 5.580297 CACTGACTTCTGCCTTCTCTTATTC 59.420 44.000 0.00 0.00 0.00 1.75
2989 3054 2.035442 GTCCAAAGGCTCACGCTCC 61.035 63.158 0.00 0.00 36.09 4.70
3034 3099 2.097825 GGAGGCCAGAGTAGACGTTTA 58.902 52.381 5.01 0.00 0.00 2.01
3093 3158 1.494721 TGGAAGAAGAACCACAGGCTT 59.505 47.619 0.00 0.00 0.00 4.35
3182 3263 3.700538 TGAAAAGGATGCAAGGTGCTAT 58.299 40.909 0.00 0.00 45.31 2.97
3250 3331 0.379669 GCTGAAGCCACATGAATCCG 59.620 55.000 0.00 0.00 34.31 4.18
3298 3379 4.023107 TGACTGTTACTGAAGGAGTTCTCG 60.023 45.833 0.00 0.00 35.96 4.04
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 7.483307 GCAAGATCTATCTAGGAGAAGCATAG 58.517 42.308 0.00 0.00 35.76 2.23
1 2 6.094742 CGCAAGATCTATCTAGGAGAAGCATA 59.905 42.308 0.00 0.00 43.02 3.14
2 3 5.105797 CGCAAGATCTATCTAGGAGAAGCAT 60.106 44.000 0.00 0.00 43.02 3.79
3 4 4.217334 CGCAAGATCTATCTAGGAGAAGCA 59.783 45.833 0.00 0.00 43.02 3.91
4 5 4.217550 ACGCAAGATCTATCTAGGAGAAGC 59.782 45.833 0.00 2.65 43.62 3.86
5 6 5.471797 TCACGCAAGATCTATCTAGGAGAAG 59.528 44.000 0.00 0.00 43.62 2.85
6 7 5.377478 TCACGCAAGATCTATCTAGGAGAA 58.623 41.667 0.00 0.00 43.62 2.87
7 8 4.974399 TCACGCAAGATCTATCTAGGAGA 58.026 43.478 0.00 0.00 43.62 3.71
8 9 5.879237 GATCACGCAAGATCTATCTAGGAG 58.121 45.833 0.00 0.00 40.93 3.69
9 10 5.888691 GATCACGCAAGATCTATCTAGGA 57.111 43.478 0.00 0.00 40.93 2.94
18 19 6.610741 AAAATTCCTAGATCACGCAAGATC 57.389 37.500 7.17 7.17 43.73 2.75
40 41 9.553064 TTGTTGGGTAACGTAGTATTCTAAAAA 57.447 29.630 0.00 0.00 45.00 1.94
41 42 9.553064 TTTGTTGGGTAACGTAGTATTCTAAAA 57.447 29.630 0.00 0.00 45.00 1.52
42 43 9.723601 ATTTGTTGGGTAACGTAGTATTCTAAA 57.276 29.630 0.00 0.00 45.00 1.85
43 44 9.153721 CATTTGTTGGGTAACGTAGTATTCTAA 57.846 33.333 0.00 0.00 45.00 2.10
44 45 8.530311 TCATTTGTTGGGTAACGTAGTATTCTA 58.470 33.333 0.00 0.00 45.00 2.10
45 46 7.388437 TCATTTGTTGGGTAACGTAGTATTCT 58.612 34.615 0.00 0.00 45.00 2.40
46 47 7.599630 TCATTTGTTGGGTAACGTAGTATTC 57.400 36.000 0.00 0.00 45.00 1.75
47 48 7.414762 GCATCATTTGTTGGGTAACGTAGTATT 60.415 37.037 0.00 0.00 45.00 1.89
48 49 6.037830 GCATCATTTGTTGGGTAACGTAGTAT 59.962 38.462 0.00 0.00 45.00 2.12
49 50 5.352016 GCATCATTTGTTGGGTAACGTAGTA 59.648 40.000 0.00 0.00 45.00 1.82
51 52 4.155099 TGCATCATTTGTTGGGTAACGTAG 59.845 41.667 0.00 0.00 39.71 3.51
52 53 4.072839 TGCATCATTTGTTGGGTAACGTA 58.927 39.130 0.00 0.00 39.71 3.57
53 54 2.887783 TGCATCATTTGTTGGGTAACGT 59.112 40.909 0.00 0.00 39.71 3.99
54 55 3.241701 GTGCATCATTTGTTGGGTAACG 58.758 45.455 0.00 0.00 39.71 3.18
55 56 3.258123 AGGTGCATCATTTGTTGGGTAAC 59.742 43.478 0.00 0.00 37.32 2.50
56 57 3.257873 CAGGTGCATCATTTGTTGGGTAA 59.742 43.478 0.00 0.00 0.00 2.85
57 58 2.824936 CAGGTGCATCATTTGTTGGGTA 59.175 45.455 0.00 0.00 0.00 3.69
58 59 1.619827 CAGGTGCATCATTTGTTGGGT 59.380 47.619 0.00 0.00 0.00 4.51
59 60 1.894466 TCAGGTGCATCATTTGTTGGG 59.106 47.619 0.00 0.00 0.00 4.12
60 61 3.663995 TTCAGGTGCATCATTTGTTGG 57.336 42.857 0.00 0.00 0.00 3.77
61 62 4.178540 GGATTCAGGTGCATCATTTGTTG 58.821 43.478 0.00 0.00 0.00 3.33
62 63 3.119388 CGGATTCAGGTGCATCATTTGTT 60.119 43.478 0.00 0.00 0.00 2.83
63 64 2.424601 CGGATTCAGGTGCATCATTTGT 59.575 45.455 0.00 0.00 0.00 2.83
64 65 2.684374 TCGGATTCAGGTGCATCATTTG 59.316 45.455 0.00 0.00 0.00 2.32
65 66 3.003394 TCGGATTCAGGTGCATCATTT 57.997 42.857 0.00 0.00 0.00 2.32
70 71 2.425143 ACATTCGGATTCAGGTGCAT 57.575 45.000 0.00 0.00 0.00 3.96
100 101 6.720309 TGGAAGTGGATTGTCAGATAATTCA 58.280 36.000 0.00 0.00 0.00 2.57
105 106 5.338381 GGTTCTGGAAGTGGATTGTCAGATA 60.338 44.000 0.00 0.00 31.70 1.98
117 118 1.237285 CGGGCAAGGTTCTGGAAGTG 61.237 60.000 0.00 0.00 33.76 3.16
118 119 1.073199 CGGGCAAGGTTCTGGAAGT 59.927 57.895 0.00 0.00 33.76 3.01
119 120 2.335712 GCGGGCAAGGTTCTGGAAG 61.336 63.158 0.00 0.00 0.00 3.46
120 121 2.282180 GCGGGCAAGGTTCTGGAA 60.282 61.111 0.00 0.00 0.00 3.53
122 123 3.868200 AAGGCGGGCAAGGTTCTGG 62.868 63.158 3.78 0.00 0.00 3.86
134 136 2.606275 GCCGATAAAGAGAAGGCGG 58.394 57.895 0.00 0.00 41.51 6.13
169 171 1.070758 ACAAGCTCCCATATGGCTACG 59.929 52.381 16.97 2.69 35.06 3.51
224 226 1.815212 CGAGTCATGCGGAAGATGCG 61.815 60.000 0.00 0.00 34.24 4.73
233 235 1.575244 ATGATTGTCCGAGTCATGCG 58.425 50.000 0.00 0.00 31.75 4.73
243 245 2.158957 TGCTCCTTCCGTATGATTGTCC 60.159 50.000 0.00 0.00 0.00 4.02
244 246 3.179443 TGCTCCTTCCGTATGATTGTC 57.821 47.619 0.00 0.00 0.00 3.18
251 253 3.279434 GGAAATGTTGCTCCTTCCGTAT 58.721 45.455 0.00 0.00 0.00 3.06
254 256 0.811281 GGGAAATGTTGCTCCTTCCG 59.189 55.000 0.00 0.00 38.60 4.30
285 288 2.091775 TCATGCATCATGGTCCATGGAA 60.092 45.455 28.01 13.14 41.66 3.53
288 291 3.850122 GATCATGCATCATGGTCCATG 57.150 47.619 23.92 23.92 43.79 3.66
320 323 0.555769 TGAGGGCTTCTTGTTTGGGT 59.444 50.000 0.00 0.00 0.00 4.51
340 343 2.357034 GCGCCAACCTCTTCGTGA 60.357 61.111 0.00 0.00 0.00 4.35
343 346 4.735132 TCGGCGCCAACCTCTTCG 62.735 66.667 28.98 9.06 0.00 3.79
365 368 1.618837 GCATAGGAGGTGCGATTCCTA 59.381 52.381 11.04 11.04 46.94 2.94
366 369 0.394565 GCATAGGAGGTGCGATTCCT 59.605 55.000 7.70 7.70 45.56 3.36
367 370 2.919971 GCATAGGAGGTGCGATTCC 58.080 57.895 0.00 0.00 32.29 3.01
396 399 1.040646 TTTCGCGAGATGAGGGCTAT 58.959 50.000 9.59 0.00 41.60 2.97
426 429 3.490896 CACATGGAGAAATATGTCGGTCG 59.509 47.826 0.00 0.00 0.00 4.79
430 433 3.302675 CGTGCACATGGAGAAATATGTCG 60.303 47.826 18.64 0.00 0.00 4.35
435 438 1.737236 GCACGTGCACATGGAGAAATA 59.263 47.619 34.52 0.00 41.59 1.40
467 470 0.318699 TCAACGAGCGAGTCTGTTGG 60.319 55.000 15.65 0.00 38.81 3.77
480 483 1.000019 AGGACCCGGAGATCAACGA 60.000 57.895 0.73 0.00 0.00 3.85
496 499 1.186200 TCTGGTGATCGACAAGGAGG 58.814 55.000 0.00 0.00 0.00 4.30
520 523 0.321671 TCTTGCTGAAGAGGGGTTCG 59.678 55.000 0.00 0.00 32.98 3.95
521 524 2.637947 GATCTTGCTGAAGAGGGGTTC 58.362 52.381 0.00 0.00 41.62 3.62
522 525 1.283321 GGATCTTGCTGAAGAGGGGTT 59.717 52.381 0.00 0.00 41.62 4.11
523 526 0.915364 GGATCTTGCTGAAGAGGGGT 59.085 55.000 0.00 0.00 41.62 4.95
526 529 5.884792 ACAAAATAGGATCTTGCTGAAGAGG 59.115 40.000 0.00 0.00 41.62 3.69
616 619 3.249189 TATGGCATCCCCCTCGGC 61.249 66.667 1.65 0.00 0.00 5.54
617 620 3.072476 CTATGGCATCCCCCTCGG 58.928 66.667 1.65 0.00 0.00 4.63
618 621 2.348998 GCTATGGCATCCCCCTCG 59.651 66.667 1.65 0.00 38.54 4.63
634 637 1.216122 CAAGATCCTCTTGCTAGCGC 58.784 55.000 10.77 0.00 46.03 5.92
650 653 1.419374 CCCTGAAACTCGACGACAAG 58.581 55.000 0.00 0.00 0.00 3.16
652 655 0.824595 TCCCCTGAAACTCGACGACA 60.825 55.000 0.00 0.00 0.00 4.35
653 656 0.316204 TTCCCCTGAAACTCGACGAC 59.684 55.000 0.00 0.00 0.00 4.34
664 667 3.641906 GAGTCCTTAATCGATTCCCCTGA 59.358 47.826 15.25 3.01 0.00 3.86
667 670 2.866855 GCGAGTCCTTAATCGATTCCCC 60.867 54.545 15.25 0.00 41.40 4.81
668 671 2.405172 GCGAGTCCTTAATCGATTCCC 58.595 52.381 15.25 0.00 41.40 3.97
669 672 2.405172 GGCGAGTCCTTAATCGATTCC 58.595 52.381 15.25 2.32 41.40 3.01
676 679 0.462047 CTTGCCGGCGAGTCCTTAAT 60.462 55.000 32.28 0.00 0.00 1.40
688 691 3.649277 CTCGGTGACTCCTTGCCGG 62.649 68.421 0.00 0.00 43.87 6.13
693 696 0.406361 AGTCCTCTCGGTGACTCCTT 59.594 55.000 0.00 0.00 37.24 3.36
696 699 1.887198 TGAAAGTCCTCTCGGTGACTC 59.113 52.381 0.00 0.00 40.84 3.36
697 700 1.996798 TGAAAGTCCTCTCGGTGACT 58.003 50.000 0.00 0.00 43.47 3.41
698 701 2.814280 TTGAAAGTCCTCTCGGTGAC 57.186 50.000 0.00 0.00 0.00 3.67
699 702 3.306780 GGATTTGAAAGTCCTCTCGGTGA 60.307 47.826 0.00 0.00 0.00 4.02
700 703 3.003480 GGATTTGAAAGTCCTCTCGGTG 58.997 50.000 0.00 0.00 0.00 4.94
701 704 2.907042 AGGATTTGAAAGTCCTCTCGGT 59.093 45.455 1.46 0.00 40.87 4.69
702 705 3.618690 AGGATTTGAAAGTCCTCTCGG 57.381 47.619 1.46 0.00 40.87 4.63
704 707 4.080863 TGGCTAGGATTTGAAAGTCCTCTC 60.081 45.833 10.11 4.49 43.63 3.20
727 731 0.179000 CTGAGGCTCCAATAAGCGGT 59.821 55.000 12.86 0.00 43.45 5.68
732 736 5.012664 TCACAGTTAACTGAGGCTCCAATAA 59.987 40.000 36.14 11.05 46.59 1.40
746 750 6.581166 CGAATTTTAAAGGCCTCACAGTTAAC 59.419 38.462 5.23 0.00 0.00 2.01
747 751 6.294286 CCGAATTTTAAAGGCCTCACAGTTAA 60.294 38.462 5.23 3.79 0.00 2.01
748 752 5.182380 CCGAATTTTAAAGGCCTCACAGTTA 59.818 40.000 5.23 0.00 0.00 2.24
749 753 4.022329 CCGAATTTTAAAGGCCTCACAGTT 60.022 41.667 5.23 0.00 0.00 3.16
750 754 3.506067 CCGAATTTTAAAGGCCTCACAGT 59.494 43.478 5.23 0.00 0.00 3.55
751 755 3.119495 CCCGAATTTTAAAGGCCTCACAG 60.119 47.826 5.23 0.00 0.00 3.66
753 757 2.823747 ACCCGAATTTTAAAGGCCTCAC 59.176 45.455 5.23 0.00 0.00 3.51
762 766 4.069304 CTCACTGTCCACCCGAATTTTAA 58.931 43.478 0.00 0.00 0.00 1.52
770 774 1.254026 TCTAACTCACTGTCCACCCG 58.746 55.000 0.00 0.00 0.00 5.28
771 775 3.764237 TTTCTAACTCACTGTCCACCC 57.236 47.619 0.00 0.00 0.00 4.61
772 776 4.704965 AGTTTTCTAACTCACTGTCCACC 58.295 43.478 0.00 0.00 40.60 4.61
773 777 5.927115 CCTAGTTTTCTAACTCACTGTCCAC 59.073 44.000 0.00 0.00 43.45 4.02
774 778 5.510861 GCCTAGTTTTCTAACTCACTGTCCA 60.511 44.000 0.00 0.00 43.45 4.02
775 779 4.930405 GCCTAGTTTTCTAACTCACTGTCC 59.070 45.833 0.00 0.00 43.45 4.02
776 780 5.405873 GTGCCTAGTTTTCTAACTCACTGTC 59.594 44.000 0.00 0.00 43.45 3.51
777 781 5.298347 GTGCCTAGTTTTCTAACTCACTGT 58.702 41.667 0.00 0.00 43.45 3.55
778 782 4.386049 CGTGCCTAGTTTTCTAACTCACTG 59.614 45.833 0.00 0.00 43.45 3.66
779 783 4.557205 CGTGCCTAGTTTTCTAACTCACT 58.443 43.478 0.00 0.00 43.45 3.41
780 784 3.123116 GCGTGCCTAGTTTTCTAACTCAC 59.877 47.826 0.00 0.00 43.45 3.51
781 785 3.323243 GCGTGCCTAGTTTTCTAACTCA 58.677 45.455 0.00 0.00 43.45 3.41
782 786 2.671888 GGCGTGCCTAGTTTTCTAACTC 59.328 50.000 2.98 0.00 43.45 3.01
783 787 2.614734 GGGCGTGCCTAGTTTTCTAACT 60.615 50.000 11.25 0.00 46.18 2.24
784 788 1.736126 GGGCGTGCCTAGTTTTCTAAC 59.264 52.381 11.25 0.00 36.10 2.34
785 789 1.348366 TGGGCGTGCCTAGTTTTCTAA 59.652 47.619 11.25 0.00 36.10 2.10
786 790 0.978151 TGGGCGTGCCTAGTTTTCTA 59.022 50.000 11.25 0.00 36.10 2.10
787 791 0.109723 TTGGGCGTGCCTAGTTTTCT 59.890 50.000 11.25 0.00 36.10 2.52
788 792 0.240145 GTTGGGCGTGCCTAGTTTTC 59.760 55.000 11.25 0.00 36.10 2.29
789 793 1.176619 GGTTGGGCGTGCCTAGTTTT 61.177 55.000 11.25 0.00 36.10 2.43
790 794 1.602605 GGTTGGGCGTGCCTAGTTT 60.603 57.895 11.25 0.00 36.10 2.66
791 795 2.033602 GGTTGGGCGTGCCTAGTT 59.966 61.111 11.25 0.00 36.10 2.24
792 796 4.388499 CGGTTGGGCGTGCCTAGT 62.388 66.667 11.25 0.00 36.10 2.57
793 797 3.385749 ATCGGTTGGGCGTGCCTAG 62.386 63.158 11.25 0.00 36.10 3.02
794 798 3.379865 GATCGGTTGGGCGTGCCTA 62.380 63.158 11.25 0.77 36.10 3.93
795 799 4.778143 GATCGGTTGGGCGTGCCT 62.778 66.667 11.25 0.00 36.10 4.75
798 802 4.096003 AGGGATCGGTTGGGCGTG 62.096 66.667 0.00 0.00 0.00 5.34
799 803 3.782443 GAGGGATCGGTTGGGCGT 61.782 66.667 0.00 0.00 0.00 5.68
800 804 3.447025 GAGAGGGATCGGTTGGGCG 62.447 68.421 0.00 0.00 0.00 6.13
801 805 2.506472 GAGAGGGATCGGTTGGGC 59.494 66.667 0.00 0.00 0.00 5.36
802 806 1.271840 TTGGAGAGGGATCGGTTGGG 61.272 60.000 0.00 0.00 0.00 4.12
960 966 0.564767 GTTCGTCTCGTTATTCGGCG 59.435 55.000 0.00 0.00 40.32 6.46
968 975 1.000618 GGAAGAAGGGTTCGTCTCGTT 59.999 52.381 3.22 0.00 38.11 3.85
971 978 1.337917 GGTGGAAGAAGGGTTCGTCTC 60.338 57.143 3.22 0.00 38.11 3.36
992 1006 1.663695 GACGAGTGGAGAGAGAGAGG 58.336 60.000 0.00 0.00 0.00 3.69
997 1011 1.201181 CAGTTGGACGAGTGGAGAGAG 59.799 57.143 0.00 0.00 0.00 3.20
998 1012 1.248486 CAGTTGGACGAGTGGAGAGA 58.752 55.000 0.00 0.00 0.00 3.10
999 1013 0.244994 CCAGTTGGACGAGTGGAGAG 59.755 60.000 7.53 0.00 41.75 3.20
1233 1247 0.545309 AGTTAGGGAGCTGACAGGCA 60.545 55.000 4.26 0.00 34.17 4.75
1252 1266 2.026636 CGAAACCTTGATGGGAGGGTTA 60.027 50.000 0.00 0.00 44.09 2.85
1318 1364 2.611518 GACTCTGATTTCCTCACACGG 58.388 52.381 0.00 0.00 0.00 4.94
1341 1387 1.269166 CAGAGTGACCGTATCGTTGC 58.731 55.000 0.00 0.00 0.00 4.17
1366 1412 1.971505 TACCCAGCTTCCTGCCATCG 61.972 60.000 0.00 0.00 44.23 3.84
1373 1419 2.270434 TCAATCCTACCCAGCTTCCT 57.730 50.000 0.00 0.00 0.00 3.36
1419 1465 8.522003 TGCAACATTTGAACATGAACATATAGT 58.478 29.630 0.00 0.00 0.00 2.12
1430 1476 1.605202 GGGCGTGCAACATTTGAACAT 60.605 47.619 0.00 0.00 39.28 2.71
1435 1481 0.940519 CACAGGGCGTGCAACATTTG 60.941 55.000 7.17 0.00 39.19 2.32
1436 1482 1.106351 TCACAGGGCGTGCAACATTT 61.106 50.000 7.17 0.00 45.92 2.32
1437 1483 1.528076 TCACAGGGCGTGCAACATT 60.528 52.632 7.17 0.00 45.92 2.71
1438 1484 2.112928 TCACAGGGCGTGCAACAT 59.887 55.556 7.17 0.00 45.92 2.71
1439 1485 2.884997 AAGTCACAGGGCGTGCAACA 62.885 55.000 7.17 0.00 45.92 3.33
1440 1486 0.882927 TAAGTCACAGGGCGTGCAAC 60.883 55.000 7.17 5.81 45.92 4.17
1441 1487 0.179043 TTAAGTCACAGGGCGTGCAA 60.179 50.000 7.17 0.00 45.92 4.08
1442 1488 0.602638 CTTAAGTCACAGGGCGTGCA 60.603 55.000 7.17 0.00 45.92 4.57
1443 1489 0.320421 TCTTAAGTCACAGGGCGTGC 60.320 55.000 7.17 0.00 45.92 5.34
1445 1491 2.490991 GTTTCTTAAGTCACAGGGCGT 58.509 47.619 1.63 0.00 0.00 5.68
1446 1492 1.804748 GGTTTCTTAAGTCACAGGGCG 59.195 52.381 1.63 0.00 0.00 6.13
1447 1493 2.160205 GGGTTTCTTAAGTCACAGGGC 58.840 52.381 1.63 0.00 0.00 5.19
1448 1494 3.181443 ACTGGGTTTCTTAAGTCACAGGG 60.181 47.826 21.31 7.87 0.00 4.45
1449 1495 4.086706 ACTGGGTTTCTTAAGTCACAGG 57.913 45.455 21.31 10.68 0.00 4.00
1450 1496 5.855045 ACTACTGGGTTTCTTAAGTCACAG 58.145 41.667 18.22 18.22 0.00 3.66
1478 1524 7.014615 GCCCACCTGTTTCAATTAGATATCATT 59.985 37.037 5.32 0.00 0.00 2.57
1490 1536 1.411977 CATTGTGCCCACCTGTTTCAA 59.588 47.619 0.00 0.00 0.00 2.69
1494 1540 1.152483 AGCATTGTGCCCACCTGTT 60.152 52.632 0.00 0.00 46.52 3.16
1496 1542 1.303888 AGAGCATTGTGCCCACCTG 60.304 57.895 0.00 0.00 46.52 4.00
1498 1544 0.682209 ATCAGAGCATTGTGCCCACC 60.682 55.000 0.00 0.00 46.52 4.61
1554 1600 1.209261 TGCCACGGATTGCTAAGATGA 59.791 47.619 0.00 0.00 0.00 2.92
1560 1606 2.822561 TGAATTTTGCCACGGATTGCTA 59.177 40.909 0.00 0.00 0.00 3.49
1561 1607 1.617850 TGAATTTTGCCACGGATTGCT 59.382 42.857 0.00 0.00 0.00 3.91
1562 1608 1.994779 CTGAATTTTGCCACGGATTGC 59.005 47.619 0.00 0.00 0.00 3.56
1563 1609 3.574284 TCTGAATTTTGCCACGGATTG 57.426 42.857 0.00 0.00 0.00 2.67
1565 1611 3.157087 ACTTCTGAATTTTGCCACGGAT 58.843 40.909 0.00 0.00 0.00 4.18
1566 1612 2.582052 ACTTCTGAATTTTGCCACGGA 58.418 42.857 0.00 0.00 0.00 4.69
1567 1613 4.497473 TTACTTCTGAATTTTGCCACGG 57.503 40.909 0.00 0.00 0.00 4.94
1568 1614 5.569059 GTGATTACTTCTGAATTTTGCCACG 59.431 40.000 0.00 0.00 0.00 4.94
1569 1615 5.863935 GGTGATTACTTCTGAATTTTGCCAC 59.136 40.000 0.00 0.00 0.00 5.01
1571 1617 5.863935 GTGGTGATTACTTCTGAATTTTGCC 59.136 40.000 0.00 0.00 0.00 4.52
1578 1628 4.263331 GGGAAGGTGGTGATTACTTCTGAA 60.263 45.833 0.00 0.00 39.33 3.02
1592 1642 1.774254 TGCTATACATGGGGAAGGTGG 59.226 52.381 0.00 0.00 0.00 4.61
1593 1643 2.439507 ACTGCTATACATGGGGAAGGTG 59.560 50.000 0.00 0.00 0.00 4.00
1596 1646 5.395768 GCCTATACTGCTATACATGGGGAAG 60.396 48.000 0.00 0.00 0.00 3.46
1607 1657 6.019656 TCCTAGCTATGCCTATACTGCTAT 57.980 41.667 0.00 0.00 33.43 2.97
1608 1658 5.452341 TCCTAGCTATGCCTATACTGCTA 57.548 43.478 0.00 0.00 32.72 3.49
1609 1659 4.323569 TCCTAGCTATGCCTATACTGCT 57.676 45.455 0.00 0.00 34.92 4.24
1610 1660 4.038642 GGATCCTAGCTATGCCTATACTGC 59.961 50.000 3.84 0.00 0.00 4.40
1611 1661 5.454062 AGGATCCTAGCTATGCCTATACTG 58.546 45.833 14.27 0.00 0.00 2.74
1612 1662 5.742562 AGGATCCTAGCTATGCCTATACT 57.257 43.478 14.27 0.00 0.00 2.12
1613 1663 5.659079 ACAAGGATCCTAGCTATGCCTATAC 59.341 44.000 16.55 0.00 0.00 1.47
1614 1664 5.843469 ACAAGGATCCTAGCTATGCCTATA 58.157 41.667 16.55 0.00 0.00 1.31
1615 1665 4.693420 ACAAGGATCCTAGCTATGCCTAT 58.307 43.478 16.55 0.00 0.00 2.57
1616 1666 4.133526 ACAAGGATCCTAGCTATGCCTA 57.866 45.455 16.55 0.00 0.00 3.93
1617 1667 2.983296 ACAAGGATCCTAGCTATGCCT 58.017 47.619 16.55 0.00 0.00 4.75
1618 1668 3.326297 AGAACAAGGATCCTAGCTATGCC 59.674 47.826 16.55 5.11 0.00 4.40
1619 1669 4.039730 TCAGAACAAGGATCCTAGCTATGC 59.960 45.833 16.55 1.30 0.00 3.14
1620 1670 5.798125 TCAGAACAAGGATCCTAGCTATG 57.202 43.478 16.55 11.89 0.00 2.23
1927 1977 2.283529 CCCCTGTCACCGTACAGCT 61.284 63.158 4.70 0.00 44.56 4.24
2078 2128 1.863880 CGCGAAGAAGACCGAGTCG 60.864 63.158 0.00 5.29 37.67 4.18
2141 2191 6.480320 GGACATAACCAGTTAAGACAGCTATG 59.520 42.308 0.17 0.00 0.00 2.23
2144 2194 4.286032 TGGACATAACCAGTTAAGACAGCT 59.714 41.667 0.17 0.00 34.77 4.24
2242 2292 3.525537 ACAGACATACAATTCTCTGGCG 58.474 45.455 0.00 0.00 35.43 5.69
2403 2454 2.373540 ATCAAAGCGTACGGTGCTAA 57.626 45.000 22.08 7.60 43.14 3.09
2405 2456 2.596904 ATATCAAAGCGTACGGTGCT 57.403 45.000 22.08 8.66 46.68 4.40
2406 2457 2.605818 TCAATATCAAAGCGTACGGTGC 59.394 45.455 22.08 1.31 0.00 5.01
2407 2458 3.615056 TGTCAATATCAAAGCGTACGGTG 59.385 43.478 22.08 9.67 0.00 4.94
2408 2459 3.852286 TGTCAATATCAAAGCGTACGGT 58.148 40.909 15.34 15.34 0.00 4.83
2409 2460 4.850859 TTGTCAATATCAAAGCGTACGG 57.149 40.909 18.39 0.00 0.00 4.02
2412 2476 7.763985 TCTTCAGATTGTCAATATCAAAGCGTA 59.236 33.333 0.00 0.00 0.00 4.42
2466 2531 0.673437 CCGTGGTTGAAATGCACCTT 59.327 50.000 0.00 0.00 0.00 3.50
2484 2549 9.833182 GAAGAAATTATCAGAAGTTTCAGAACC 57.167 33.333 0.00 0.00 36.39 3.62
2597 2662 4.380531 CTCTGGTGTTGTAGCTTGAGAAA 58.619 43.478 0.00 0.00 33.33 2.52
2622 2687 2.686915 GTTGAGATTGCAGAGGATTGGG 59.313 50.000 0.00 0.00 0.00 4.12
2653 2718 5.396362 CGTTTGAACAAGATTGTACAGCTTG 59.604 40.000 26.21 26.21 41.31 4.01
2779 2844 6.626302 AGTGAAGTCTTCGAATAAGAGAAGG 58.374 40.000 8.06 0.00 42.85 3.46
2791 2856 1.795286 GGTGCAAGAGTGAAGTCTTCG 59.205 52.381 8.06 0.00 34.38 3.79
2886 2951 1.089920 ACATGATCAAGCAAGGACGC 58.910 50.000 0.00 0.00 0.00 5.19
2989 3054 1.592400 TACCACGAGAGAACCGCCAG 61.592 60.000 0.00 0.00 0.00 4.85
3093 3158 2.103153 ACAGAGGTGTCAAGGGAAGA 57.897 50.000 0.00 0.00 26.76 2.87
3182 3263 9.847224 AGAAAGGTGAGAAAAACTACTTTCATA 57.153 29.630 14.31 0.00 41.25 2.15
3250 3331 5.053145 CAGAGAGTAGGATTGGCATTGTAC 58.947 45.833 0.00 0.00 0.00 2.90


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

AutoCloner maintained by Alex Coulton.