Multiple sequence alignment - TraesCS1D01G435800

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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 TraesCS1D01G435800 chr1D 100.000 3641 0 0 1 3641 483971613 483975253 0.000000e+00 6724.0
1 TraesCS1D01G435800 chr1D 85.057 87 11 2 3414 3499 357427544 357427459 1.800000e-13 87.9
2 TraesCS1D01G435800 chr1D 82.353 102 14 4 3414 3512 216407854 216407954 6.480000e-13 86.1
3 TraesCS1D01G435800 chr1D 81.308 107 16 4 3396 3499 420526658 420526553 2.330000e-12 84.2
4 TraesCS1D01G435800 chr1A 94.482 2229 80 20 669 2866 580987931 580990147 0.000000e+00 3395.0
5 TraesCS1D01G435800 chr1A 90.120 749 62 10 2864 3608 580990858 580991598 0.000000e+00 963.0
6 TraesCS1D01G435800 chr1A 82.373 573 64 27 1 538 580986929 580987499 7.120000e-127 464.0
7 TraesCS1D01G435800 chr1B 90.020 2004 97 41 697 2640 674005063 674003103 0.000000e+00 2497.0
8 TraesCS1D01G435800 chr1B 95.136 1542 64 5 1210 2742 673992407 673993946 0.000000e+00 2422.0
9 TraesCS1D01G435800 chr1B 82.635 334 36 11 818 1131 673991987 673992318 3.580000e-70 276.0
10 TraesCS1D01G435800 chr1B 76.000 425 81 18 3110 3526 451641949 451641538 2.220000e-47 200.0
11 TraesCS1D01G435800 chr1B 81.481 108 16 4 3414 3518 675583939 675583833 6.480000e-13 86.1
12 TraesCS1D01G435800 chr2B 86.902 1672 188 20 977 2641 207482048 207483695 0.000000e+00 1845.0
13 TraesCS1D01G435800 chr2B 77.931 145 28 3 1 142 613204161 613204018 1.800000e-13 87.9
14 TraesCS1D01G435800 chr2B 79.787 94 17 2 3474 3566 563689604 563689696 2.350000e-07 67.6
15 TraesCS1D01G435800 chr2A 86.715 1671 188 24 980 2641 154422791 154421146 0.000000e+00 1825.0
16 TraesCS1D01G435800 chr2A 82.240 1357 233 8 1212 2564 155074674 155073322 0.000000e+00 1164.0
17 TraesCS1D01G435800 chr2D 86.603 1672 188 26 980 2641 147953492 147955137 0.000000e+00 1814.0
18 TraesCS1D01G435800 chr2D 82.180 1358 232 10 1212 2564 147426250 147427602 0.000000e+00 1158.0
19 TraesCS1D01G435800 chr2D 75.758 198 43 4 4 200 108743339 108743146 1.080000e-15 95.3
20 TraesCS1D01G435800 chr3B 86.022 1674 193 24 980 2642 64538122 64539765 0.000000e+00 1757.0
21 TraesCS1D01G435800 chr3B 74.171 422 87 18 3114 3526 547275903 547275495 4.870000e-34 156.0
22 TraesCS1D01G435800 chr3B 74.000 200 42 9 5 199 362050253 362050059 5.040000e-09 73.1
23 TraesCS1D01G435800 chr5B 78.846 364 62 11 3099 3454 111973506 111973150 7.860000e-57 231.0
24 TraesCS1D01G435800 chr5B 75.236 424 80 21 3110 3524 42112160 42111753 1.040000e-40 178.0
25 TraesCS1D01G435800 chr5B 76.730 159 31 6 2865 3020 430748618 430748463 2.330000e-12 84.2
26 TraesCS1D01G435800 chr7D 75.644 427 79 21 3110 3526 125398386 125398797 4.800000e-44 189.0
27 TraesCS1D01G435800 chr7D 74.747 198 42 7 4 196 184095584 184095390 8.380000e-12 82.4
28 TraesCS1D01G435800 chr7B 75.476 420 77 22 3110 3518 203189772 203190176 8.030000e-42 182.0
29 TraesCS1D01G435800 chr7B 75.176 427 82 20 3110 3526 203197126 203197538 2.890000e-41 180.0
30 TraesCS1D01G435800 chrUn 74.648 426 86 18 3110 3526 23787738 23788150 6.250000e-38 169.0
31 TraesCS1D01G435800 chr5D 75.980 204 44 4 1 200 495372413 495372615 2.310000e-17 100.0
32 TraesCS1D01G435800 chr5D 78.947 133 24 3 1 130 333989768 333989899 1.800000e-13 87.9
33 TraesCS1D01G435800 chr5D 73.980 196 47 4 5 199 402731632 402731440 3.900000e-10 76.8
34 TraesCS1D01G435800 chr6A 82.407 108 15 4 3414 3518 535448709 535448603 1.390000e-14 91.6
35 TraesCS1D01G435800 chr6B 75.904 166 34 5 4 165 665884470 665884633 3.010000e-11 80.5
36 TraesCS1D01G435800 chr4D 80.556 108 17 4 3414 3518 370652794 370652688 3.010000e-11 80.5
37 TraesCS1D01G435800 chr5A 75.595 168 33 6 5 168 394263225 394263062 3.900000e-10 76.8
38 TraesCS1D01G435800 chr6D 80.392 102 16 4 3414 3512 392292487 392292587 1.400000e-09 75.0
39 TraesCS1D01G435800 chr3D 79.630 108 18 4 3414 3518 215973494 215973388 1.400000e-09 75.0


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 TraesCS1D01G435800 chr1D 483971613 483975253 3640 False 6724.000000 6724 100.000000 1 3641 1 chr1D.!!$F2 3640
1 TraesCS1D01G435800 chr1A 580986929 580991598 4669 False 1607.333333 3395 88.991667 1 3608 3 chr1A.!!$F1 3607
2 TraesCS1D01G435800 chr1B 674003103 674005063 1960 True 2497.000000 2497 90.020000 697 2640 1 chr1B.!!$R2 1943
3 TraesCS1D01G435800 chr1B 673991987 673993946 1959 False 1349.000000 2422 88.885500 818 2742 2 chr1B.!!$F1 1924
4 TraesCS1D01G435800 chr2B 207482048 207483695 1647 False 1845.000000 1845 86.902000 977 2641 1 chr2B.!!$F1 1664
5 TraesCS1D01G435800 chr2A 154421146 154422791 1645 True 1825.000000 1825 86.715000 980 2641 1 chr2A.!!$R1 1661
6 TraesCS1D01G435800 chr2A 155073322 155074674 1352 True 1164.000000 1164 82.240000 1212 2564 1 chr2A.!!$R2 1352
7 TraesCS1D01G435800 chr2D 147953492 147955137 1645 False 1814.000000 1814 86.603000 980 2641 1 chr2D.!!$F2 1661
8 TraesCS1D01G435800 chr2D 147426250 147427602 1352 False 1158.000000 1158 82.180000 1212 2564 1 chr2D.!!$F1 1352
9 TraesCS1D01G435800 chr3B 64538122 64539765 1643 False 1757.000000 1757 86.022000 980 2642 1 chr3B.!!$F1 1662

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
586 620 0.035458 AAAGGAGCGGACCAACTGAG 59.965 55.0 0.0 0.0 0.00 3.35 F
624 921 0.166814 GATTGCTCGTTCCAGTGCAC 59.833 55.0 9.4 9.4 39.85 4.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2397 2854 2.190313 GTCATGGAGATGGCGGCA 59.810 61.111 16.34 16.34 0.00 5.69 R
2661 3134 2.811431 TGCATGTTAGAGAAACCAACCG 59.189 45.455 0.00 0.00 37.27 4.44 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
34 37 2.584608 CCGGATTTGGCCTCGAGT 59.415 61.111 12.31 0.00 0.00 4.18
35 38 1.820581 CCGGATTTGGCCTCGAGTA 59.179 57.895 12.31 0.00 0.00 2.59
36 39 0.529992 CCGGATTTGGCCTCGAGTAC 60.530 60.000 12.31 4.10 0.00 2.73
47 50 1.298993 TCGAGTACCGAGCCAGACT 59.701 57.895 2.81 0.00 43.23 3.24
60 63 1.450848 CAGACTGGCACCATGCGAT 60.451 57.895 0.00 0.00 46.21 4.58
74 77 0.251121 TGCGATGTTCACACCCCATT 60.251 50.000 0.00 0.00 0.00 3.16
75 78 1.003696 TGCGATGTTCACACCCCATTA 59.996 47.619 0.00 0.00 0.00 1.90
79 82 3.545703 GATGTTCACACCCCATTAGAGG 58.454 50.000 0.00 0.00 0.00 3.69
86 89 1.831736 CACCCCATTAGAGGAGACGTT 59.168 52.381 0.00 0.00 0.00 3.99
94 97 0.392729 AGAGGAGACGTTCGTCGGAT 60.393 55.000 17.46 8.78 43.72 4.18
96 99 1.297451 GGAGACGTTCGTCGGATCG 60.297 63.158 17.46 0.00 44.69 3.69
111 114 1.456892 ATCGTCGGGTATCCTGGCA 60.457 57.895 0.21 0.00 33.39 4.92
117 120 0.182537 CGGGTATCCTGGCAATTCCA 59.817 55.000 0.00 0.00 44.18 3.53
121 124 1.670811 GTATCCTGGCAATTCCACGTG 59.329 52.381 9.08 9.08 40.72 4.49
122 125 0.327924 ATCCTGGCAATTCCACGTGA 59.672 50.000 19.30 0.00 40.72 4.35
131 134 0.991920 ATTCCACGTGAGACCCCAAT 59.008 50.000 19.30 0.04 0.00 3.16
132 135 0.036164 TTCCACGTGAGACCCCAATG 59.964 55.000 19.30 0.00 0.00 2.82
150 162 1.080705 GTCAGTCGGACTTGGTCGG 60.081 63.158 8.18 0.00 43.46 4.79
172 184 2.519302 GCCCAGGCGCACCATATT 60.519 61.111 10.83 0.00 39.06 1.28
175 187 1.523711 CCAGGCGCACCATATTCGT 60.524 57.895 10.83 0.00 39.06 3.85
177 189 0.304705 CAGGCGCACCATATTCGTTC 59.695 55.000 10.83 0.00 39.06 3.95
178 190 0.814010 AGGCGCACCATATTCGTTCC 60.814 55.000 10.83 0.00 39.06 3.62
186 198 5.277779 CGCACCATATTCGTTCCATATTTGT 60.278 40.000 0.00 0.00 0.00 2.83
196 208 6.764379 TCGTTCCATATTTGTGCTGGATATA 58.236 36.000 0.00 0.00 38.79 0.86
199 211 7.361201 CGTTCCATATTTGTGCTGGATATAAGG 60.361 40.741 0.00 0.00 38.79 2.69
201 213 5.126061 CCATATTTGTGCTGGATATAAGGCC 59.874 44.000 0.00 0.00 31.38 5.19
225 244 1.060465 GAGGCGCGGTCGAATTTTC 59.940 57.895 8.83 0.00 38.10 2.29
243 263 4.353437 GTGACCGAACGACCCGCT 62.353 66.667 0.00 0.00 0.00 5.52
245 265 4.047059 GACCGAACGACCCGCTCA 62.047 66.667 0.00 0.00 0.00 4.26
253 273 2.372690 CGACCCGCTCAGACGTTTG 61.373 63.158 0.00 0.00 0.00 2.93
264 284 0.393820 AGACGTTTGAGGCCGGTTTA 59.606 50.000 1.90 0.00 0.00 2.01
279 299 1.003112 TTTATGGCGCCGGACTGTT 60.003 52.632 23.90 2.59 0.00 3.16
280 300 0.249676 TTTATGGCGCCGGACTGTTA 59.750 50.000 23.90 0.49 0.00 2.41
281 301 0.179094 TTATGGCGCCGGACTGTTAG 60.179 55.000 23.90 0.00 0.00 2.34
282 302 1.038681 TATGGCGCCGGACTGTTAGA 61.039 55.000 23.90 0.00 0.00 2.10
283 303 1.686325 ATGGCGCCGGACTGTTAGAT 61.686 55.000 23.90 1.75 0.00 1.98
346 376 1.972795 GTGTGTTAGGTGGTCCCTGTA 59.027 52.381 0.00 0.00 45.81 2.74
349 379 2.028385 GTGTTAGGTGGTCCCTGTACTG 60.028 54.545 0.00 0.00 45.81 2.74
374 404 1.160137 GTGCTGGTTCTTGCTGTAGG 58.840 55.000 0.00 0.00 0.00 3.18
379 409 1.235724 GGTTCTTGCTGTAGGCGTTT 58.764 50.000 0.00 0.00 45.43 3.60
384 414 0.464735 TTGCTGTAGGCGTTTGGTGT 60.465 50.000 0.00 0.00 45.43 4.16
386 416 0.040425 GCTGTAGGCGTTTGGTGTTG 60.040 55.000 0.00 0.00 0.00 3.33
393 423 2.124693 CGTTTGGTGTTGGTGGGCT 61.125 57.895 0.00 0.00 0.00 5.19
422 452 3.067084 TTGCCACCCCACTGCTGAA 62.067 57.895 0.00 0.00 0.00 3.02
441 471 2.859165 ATGTGGGTGGTTGTAGTCTG 57.141 50.000 0.00 0.00 0.00 3.51
445 475 0.605589 GGGTGGTTGTAGTCTGGTGC 60.606 60.000 0.00 0.00 0.00 5.01
458 492 1.411246 TCTGGTGCACGTACTTGTCTT 59.589 47.619 11.45 0.00 0.00 3.01
459 493 1.526887 CTGGTGCACGTACTTGTCTTG 59.473 52.381 11.45 0.00 0.00 3.02
468 502 5.395642 CACGTACTTGTCTTGGTTGTTTTT 58.604 37.500 0.00 0.00 0.00 1.94
471 505 6.372381 ACGTACTTGTCTTGGTTGTTTTTAGT 59.628 34.615 0.00 0.00 0.00 2.24
473 507 6.203808 ACTTGTCTTGGTTGTTTTTAGTCC 57.796 37.500 0.00 0.00 0.00 3.85
474 508 5.949952 ACTTGTCTTGGTTGTTTTTAGTCCT 59.050 36.000 0.00 0.00 0.00 3.85
505 539 2.281761 GCACAGTGGTGTCCCCAG 60.282 66.667 1.84 0.00 46.45 4.45
521 555 2.086869 CCCAGTATGCTTGACTGTTGG 58.913 52.381 10.84 4.25 42.35 3.77
526 560 3.891366 AGTATGCTTGACTGTTGGCTTTT 59.109 39.130 0.00 0.00 0.00 2.27
527 561 2.582728 TGCTTGACTGTTGGCTTTTG 57.417 45.000 0.00 0.00 0.00 2.44
528 562 1.824230 TGCTTGACTGTTGGCTTTTGT 59.176 42.857 0.00 0.00 0.00 2.83
529 563 3.020274 TGCTTGACTGTTGGCTTTTGTA 58.980 40.909 0.00 0.00 0.00 2.41
530 564 3.636300 TGCTTGACTGTTGGCTTTTGTAT 59.364 39.130 0.00 0.00 0.00 2.29
533 567 6.015519 TGCTTGACTGTTGGCTTTTGTATAAT 60.016 34.615 0.00 0.00 0.00 1.28
538 572 6.245408 ACTGTTGGCTTTTGTATAATCTGGA 58.755 36.000 0.00 0.00 0.00 3.86
540 574 6.245408 TGTTGGCTTTTGTATAATCTGGACT 58.755 36.000 0.00 0.00 0.00 3.85
541 575 6.719370 TGTTGGCTTTTGTATAATCTGGACTT 59.281 34.615 0.00 0.00 0.00 3.01
546 580 8.778358 GGCTTTTGTATAATCTGGACTTAGATG 58.222 37.037 0.00 0.00 37.48 2.90
547 581 8.286097 GCTTTTGTATAATCTGGACTTAGATGC 58.714 37.037 0.00 0.00 37.48 3.91
548 582 8.677148 TTTTGTATAATCTGGACTTAGATGCC 57.323 34.615 0.00 0.00 37.48 4.40
550 584 7.618019 TGTATAATCTGGACTTAGATGCCTT 57.382 36.000 0.00 0.00 37.48 4.35
551 585 8.034313 TGTATAATCTGGACTTAGATGCCTTT 57.966 34.615 0.00 0.00 37.48 3.11
552 586 8.150945 TGTATAATCTGGACTTAGATGCCTTTC 58.849 37.037 0.00 0.00 37.48 2.62
553 587 3.914426 TCTGGACTTAGATGCCTTTCC 57.086 47.619 0.00 0.00 0.00 3.13
554 588 3.454858 TCTGGACTTAGATGCCTTTCCT 58.545 45.455 0.00 0.00 0.00 3.36
555 589 3.198635 TCTGGACTTAGATGCCTTTCCTG 59.801 47.826 0.00 0.00 0.00 3.86
556 590 2.912956 TGGACTTAGATGCCTTTCCTGT 59.087 45.455 0.00 0.00 0.00 4.00
557 591 3.330701 TGGACTTAGATGCCTTTCCTGTT 59.669 43.478 0.00 0.00 0.00 3.16
558 592 3.691609 GGACTTAGATGCCTTTCCTGTTG 59.308 47.826 0.00 0.00 0.00 3.33
559 593 3.084786 ACTTAGATGCCTTTCCTGTTGC 58.915 45.455 0.00 0.00 0.00 4.17
560 594 1.737838 TAGATGCCTTTCCTGTTGCG 58.262 50.000 0.00 0.00 0.00 4.85
562 596 0.169009 GATGCCTTTCCTGTTGCGTC 59.831 55.000 0.00 0.00 33.15 5.19
563 597 0.250901 ATGCCTTTCCTGTTGCGTCT 60.251 50.000 0.00 0.00 0.00 4.18
564 598 0.394938 TGCCTTTCCTGTTGCGTCTA 59.605 50.000 0.00 0.00 0.00 2.59
565 599 1.202710 TGCCTTTCCTGTTGCGTCTAA 60.203 47.619 0.00 0.00 0.00 2.10
566 600 1.877443 GCCTTTCCTGTTGCGTCTAAA 59.123 47.619 0.00 0.00 0.00 1.85
567 601 2.292292 GCCTTTCCTGTTGCGTCTAAAA 59.708 45.455 0.00 0.00 0.00 1.52
583 617 3.821306 AAAAAGGAGCGGACCAACT 57.179 47.368 0.00 0.00 0.00 3.16
584 618 1.318576 AAAAAGGAGCGGACCAACTG 58.681 50.000 0.00 0.00 0.00 3.16
585 619 0.472471 AAAAGGAGCGGACCAACTGA 59.528 50.000 0.00 0.00 0.00 3.41
586 620 0.035458 AAAGGAGCGGACCAACTGAG 59.965 55.000 0.00 0.00 0.00 3.35
587 621 0.832135 AAGGAGCGGACCAACTGAGA 60.832 55.000 0.00 0.00 0.00 3.27
588 622 0.616111 AGGAGCGGACCAACTGAGAT 60.616 55.000 0.00 0.00 0.00 2.75
589 623 0.250513 GGAGCGGACCAACTGAGATT 59.749 55.000 0.00 0.00 0.00 2.40
590 624 1.363744 GAGCGGACCAACTGAGATTG 58.636 55.000 0.00 0.00 0.00 2.67
591 625 0.976641 AGCGGACCAACTGAGATTGA 59.023 50.000 0.00 0.00 0.00 2.57
592 626 1.066573 AGCGGACCAACTGAGATTGAG 60.067 52.381 0.00 0.00 0.00 3.02
593 627 1.066858 GCGGACCAACTGAGATTGAGA 60.067 52.381 0.00 0.00 0.00 3.27
594 628 2.419297 GCGGACCAACTGAGATTGAGAT 60.419 50.000 0.00 0.00 0.00 2.75
603 900 8.986991 ACCAACTGAGATTGAGATAAAGAGTAT 58.013 33.333 0.00 0.00 0.00 2.12
605 902 9.179552 CAACTGAGATTGAGATAAAGAGTATCG 57.820 37.037 0.00 0.00 42.67 2.92
609 906 9.905171 TGAGATTGAGATAAAGAGTATCGATTG 57.095 33.333 1.71 0.00 42.67 2.67
611 908 8.584157 AGATTGAGATAAAGAGTATCGATTGCT 58.416 33.333 1.71 2.13 42.67 3.91
614 911 6.017026 TGAGATAAAGAGTATCGATTGCTCGT 60.017 38.462 17.99 14.40 45.25 4.18
615 912 6.740110 AGATAAAGAGTATCGATTGCTCGTT 58.260 36.000 22.99 22.99 45.25 3.85
616 913 6.858993 AGATAAAGAGTATCGATTGCTCGTTC 59.141 38.462 23.05 15.42 45.25 3.95
617 914 3.357166 AGAGTATCGATTGCTCGTTCC 57.643 47.619 17.99 2.36 45.25 3.62
618 915 2.688446 AGAGTATCGATTGCTCGTTCCA 59.312 45.455 17.99 0.00 45.25 3.53
619 916 3.046390 GAGTATCGATTGCTCGTTCCAG 58.954 50.000 1.71 0.00 45.25 3.86
620 917 2.427453 AGTATCGATTGCTCGTTCCAGT 59.573 45.455 1.71 0.00 45.25 4.00
621 918 1.645034 ATCGATTGCTCGTTCCAGTG 58.355 50.000 0.00 0.00 45.25 3.66
622 919 1.014044 TCGATTGCTCGTTCCAGTGC 61.014 55.000 0.00 0.00 45.25 4.40
624 921 0.166814 GATTGCTCGTTCCAGTGCAC 59.833 55.000 9.40 9.40 39.85 4.57
625 922 0.250467 ATTGCTCGTTCCAGTGCACT 60.250 50.000 15.25 15.25 39.85 4.40
626 923 1.159713 TTGCTCGTTCCAGTGCACTG 61.160 55.000 35.15 35.15 39.85 3.66
627 924 2.959357 GCTCGTTCCAGTGCACTGC 61.959 63.158 36.38 23.58 42.47 4.40
628 925 1.301244 CTCGTTCCAGTGCACTGCT 60.301 57.895 36.38 6.26 42.47 4.24
629 926 1.563435 CTCGTTCCAGTGCACTGCTG 61.563 60.000 36.38 25.30 42.47 4.41
630 927 1.889105 CGTTCCAGTGCACTGCTGT 60.889 57.895 36.38 5.42 42.47 4.40
631 928 0.599991 CGTTCCAGTGCACTGCTGTA 60.600 55.000 36.38 20.26 42.47 2.74
632 929 1.593196 GTTCCAGTGCACTGCTGTAA 58.407 50.000 36.38 24.08 42.47 2.41
633 930 1.264288 GTTCCAGTGCACTGCTGTAAC 59.736 52.381 36.38 29.04 42.47 2.50
634 931 0.758734 TCCAGTGCACTGCTGTAACT 59.241 50.000 36.38 2.13 42.47 2.24
635 932 0.870393 CCAGTGCACTGCTGTAACTG 59.130 55.000 36.38 19.10 42.47 3.16
636 933 1.586422 CAGTGCACTGCTGTAACTGT 58.414 50.000 32.39 0.00 36.30 3.55
637 934 2.547855 CCAGTGCACTGCTGTAACTGTA 60.548 50.000 36.38 2.92 42.47 2.74
638 935 3.130633 CAGTGCACTGCTGTAACTGTAA 58.869 45.455 32.39 0.00 36.30 2.41
639 936 3.185188 CAGTGCACTGCTGTAACTGTAAG 59.815 47.826 32.39 5.29 36.30 2.34
640 937 2.096218 GTGCACTGCTGTAACTGTAAGC 60.096 50.000 10.32 3.79 37.60 3.09
641 938 1.464997 GCACTGCTGTAACTGTAAGCC 59.535 52.381 0.00 0.00 37.60 4.35
642 939 2.766313 CACTGCTGTAACTGTAAGCCA 58.234 47.619 0.00 0.00 37.60 4.75
657 954 5.299148 TGTAAGCCAGTTTTACGCTTTCTA 58.701 37.500 0.00 0.00 42.60 2.10
661 958 7.443259 AAGCCAGTTTTACGCTTTCTATAAA 57.557 32.000 0.00 0.00 39.80 1.40
694 1045 2.349755 GAGGTGGCCGGTTAAGCA 59.650 61.111 1.90 0.00 0.00 3.91
747 1107 6.266131 ACTATTCCCTGCCTTGATTGATTA 57.734 37.500 0.00 0.00 0.00 1.75
756 1116 4.141892 TGCCTTGATTGATTAATTGGCTGG 60.142 41.667 17.18 5.13 37.83 4.85
949 1352 3.286751 CACCACCGGGCAACACAG 61.287 66.667 6.32 0.00 37.90 3.66
964 1367 3.411351 CAGCACGTACGGCGCTTT 61.411 61.111 25.96 9.23 46.11 3.51
993 1396 2.432510 ACAAGCTAGGAAGAAGGATCGG 59.567 50.000 0.00 0.00 0.00 4.18
1083 1498 0.796312 ATTTCAAGTACGCCTGCACG 59.204 50.000 0.00 0.00 39.50 5.34
1131 1546 0.820891 TCGTCCTCGGCTATGGTACC 60.821 60.000 4.43 4.43 37.69 3.34
1148 1564 4.264941 TGGTACCTACCTCCTACATTTCCA 60.265 45.833 14.36 0.00 46.58 3.53
1156 1572 5.548406 ACCTCCTACATTTCCAATATACGC 58.452 41.667 0.00 0.00 0.00 4.42
1164 1580 4.364415 TTTCCAATATACGCACCAAAGC 57.636 40.909 0.00 0.00 0.00 3.51
1168 1584 3.434637 CAATATACGCACCAAAGCCAAC 58.565 45.455 0.00 0.00 0.00 3.77
1169 1585 1.080298 TATACGCACCAAAGCCAACG 58.920 50.000 0.00 0.00 0.00 4.10
1170 1586 2.195123 ATACGCACCAAAGCCAACGC 62.195 55.000 0.00 0.00 0.00 4.84
1185 1603 1.740025 CAACGCCCATCTTCTTCCTTC 59.260 52.381 0.00 0.00 0.00 3.46
1200 1634 0.664761 CCTTCCGCCATGCATAACTG 59.335 55.000 0.00 0.00 0.00 3.16
1203 1637 1.882912 TCCGCCATGCATAACTGATC 58.117 50.000 0.00 0.00 0.00 2.92
1204 1638 0.514255 CCGCCATGCATAACTGATCG 59.486 55.000 0.00 0.00 0.00 3.69
1205 1639 0.514255 CGCCATGCATAACTGATCGG 59.486 55.000 0.00 0.00 0.00 4.18
1206 1640 1.873486 CGCCATGCATAACTGATCGGA 60.873 52.381 9.00 0.00 0.00 4.55
1914 2371 2.626840 GTGTGGAAGGAGCTCATCTTC 58.373 52.381 17.19 18.34 38.79 2.87
2037 2494 2.359850 TTCAAGAGCGCCGGCATT 60.360 55.556 28.98 14.11 43.41 3.56
2397 2854 4.539083 TGCAACCGCGTCACCAGT 62.539 61.111 4.92 0.00 42.97 4.00
2645 3117 4.653341 AGCTGTGGAGATGAACTAGCTAAT 59.347 41.667 0.00 0.00 38.17 1.73
2672 3145 2.434774 GGGGAGCGGTTGGTTTCT 59.565 61.111 0.00 0.00 0.00 2.52
2700 3178 2.337361 ATGCATGCATGGACGGATG 58.663 52.632 31.74 1.74 37.74 3.51
2728 3206 3.006859 CCATTGGGGGTTCTTTTGAGTTC 59.993 47.826 0.00 0.00 0.00 3.01
2757 3235 7.504238 TGCTACTTCTTTCTTGGGTTTTTGATA 59.496 33.333 0.00 0.00 0.00 2.15
2827 3305 6.549364 TCCACCAAAGTGTATCAGAATGTTTT 59.451 34.615 0.00 0.00 42.88 2.43
2855 3333 5.701290 GCCTACTGACAAATAAGAGTGTGTT 59.299 40.000 0.00 0.00 0.00 3.32
2857 3335 7.576236 CCTACTGACAAATAAGAGTGTGTTTG 58.424 38.462 0.00 0.00 37.52 2.93
2858 3336 7.226720 CCTACTGACAAATAAGAGTGTGTTTGT 59.773 37.037 2.36 2.36 44.71 2.83
2875 4067 9.419297 GTGTGTTTGTCTTACATAATGAGAGTA 57.581 33.333 0.00 0.00 0.00 2.59
2877 4069 8.584600 GTGTTTGTCTTACATAATGAGAGTACG 58.415 37.037 0.00 0.00 0.00 3.67
2905 4097 7.012894 TGTTAGTAGGACAATGTTGTTGGAAAG 59.987 37.037 0.00 0.00 42.43 2.62
2907 4099 4.918810 AGGACAATGTTGTTGGAAAGAC 57.081 40.909 0.00 0.00 42.43 3.01
2937 4129 4.357018 TGACACACTACGAGATCACATC 57.643 45.455 0.00 0.00 0.00 3.06
3006 4198 4.033358 CACGTCTTTAGACCATGAGAATGC 59.967 45.833 4.40 0.00 41.86 3.56
3010 4202 2.890808 TAGACCATGAGAATGCCGTC 57.109 50.000 0.00 0.00 0.00 4.79
3023 4215 1.262417 TGCCGTCTACCTTCATGTCA 58.738 50.000 0.00 0.00 0.00 3.58
3028 4220 2.736719 CGTCTACCTTCATGTCAGCCAG 60.737 54.545 0.00 0.00 0.00 4.85
3034 4226 3.265791 CCTTCATGTCAGCCAGTTACTC 58.734 50.000 0.00 0.00 0.00 2.59
3048 4241 3.247648 CAGTTACTCTGGGTTGTCAAACG 59.752 47.826 0.00 0.00 40.23 3.60
3098 4291 8.081517 TGGAACTTCTAGGTATATCGGAAAAA 57.918 34.615 0.00 0.00 0.00 1.94
3101 4294 9.374838 GAACTTCTAGGTATATCGGAAAAACAA 57.625 33.333 0.00 0.00 0.00 2.83
3127 4321 6.018507 GTCTAGGACTCGATAGTTCAAGACTC 60.019 46.154 0.00 0.00 39.86 3.36
3135 4329 6.925211 TCGATAGTTCAAGACTCAGATTTGT 58.075 36.000 0.00 0.00 39.86 2.83
3140 4334 6.360618 AGTTCAAGACTCAGATTTGTTCCTT 58.639 36.000 0.00 0.00 31.20 3.36
3145 4339 5.174395 AGACTCAGATTTGTTCCTTCGATG 58.826 41.667 0.00 0.00 0.00 3.84
3158 4352 6.268617 TGTTCCTTCGATGATGGAGAGATATT 59.731 38.462 0.00 0.00 37.23 1.28
3189 4383 7.376615 GGCCATATCTATATTACGGTATCCAC 58.623 42.308 0.00 0.00 0.00 4.02
3196 4390 8.603898 TCTATATTACGGTATCCACCATCATT 57.396 34.615 0.00 0.00 46.14 2.57
3198 4392 7.921786 ATATTACGGTATCCACCATCATTTG 57.078 36.000 0.00 0.00 46.14 2.32
3215 4409 0.323302 TTGGCCAGATACAGCGTGAA 59.677 50.000 5.11 0.00 0.00 3.18
3263 4458 7.224167 ACGATAACGAGAAAAGAGAACAAAACT 59.776 33.333 0.00 0.00 42.66 2.66
3264 4459 8.697067 CGATAACGAGAAAAGAGAACAAAACTA 58.303 33.333 0.00 0.00 42.66 2.24
3270 4465 8.814235 CGAGAAAAGAGAACAAAACTAGTAACA 58.186 33.333 0.00 0.00 0.00 2.41
3354 4549 4.938832 CCTCGGGTTTTGTTATGTATCACA 59.061 41.667 0.00 0.00 0.00 3.58
3466 4661 6.039270 CCCGCTATTGATTATTGACCAAAAGA 59.961 38.462 0.00 0.00 0.00 2.52
3473 4668 7.773489 TGATTATTGACCAAAAGATGTTCCA 57.227 32.000 0.00 0.00 0.00 3.53
3492 4687 4.960938 TCCAGGTCATGTCTGCATATTAC 58.039 43.478 11.50 0.00 33.30 1.89
3502 4697 1.526887 CTGCATATTACCGAACCTGCG 59.473 52.381 0.00 0.00 31.13 5.18
3518 4713 0.250381 TGCGGGGTCACACGTTTAAT 60.250 50.000 0.00 0.00 0.00 1.40
3521 4716 0.524414 GGGGTCACACGTTTAATGGC 59.476 55.000 0.00 0.00 0.00 4.40
3527 4722 2.746904 TCACACGTTTAATGGCCATCAG 59.253 45.455 21.08 11.14 0.00 2.90
3531 4726 4.038642 ACACGTTTAATGGCCATCAGTTTT 59.961 37.500 21.08 5.33 0.00 2.43
3569 4764 5.288952 GGTGTTAAGAGTACGAGAGAAATGC 59.711 44.000 0.00 0.00 0.00 3.56
3573 4768 2.493675 AGAGTACGAGAGAAATGCAGCA 59.506 45.455 0.00 0.00 0.00 4.41
3574 4769 3.056536 AGAGTACGAGAGAAATGCAGCAA 60.057 43.478 0.00 0.00 0.00 3.91
3583 4778 3.332034 AGAAATGCAGCAAAAATGCTCC 58.668 40.909 0.00 0.00 44.30 4.70
3594 4789 6.814644 CAGCAAAAATGCTCCAGAAATATCAA 59.185 34.615 0.00 0.00 44.30 2.57
3596 4791 7.548075 AGCAAAAATGCTCCAGAAATATCAAAG 59.452 33.333 0.00 0.00 42.12 2.77
3604 4799 6.494893 TCCAGAAATATCAAAGGTGTTTCG 57.505 37.500 0.00 0.00 34.79 3.46
3605 4800 6.234920 TCCAGAAATATCAAAGGTGTTTCGA 58.765 36.000 0.00 0.00 34.79 3.71
3607 4802 7.023575 CCAGAAATATCAAAGGTGTTTCGAAG 58.976 38.462 0.00 0.00 34.79 3.79
3608 4803 7.094805 CCAGAAATATCAAAGGTGTTTCGAAGA 60.095 37.037 0.00 0.00 34.79 2.87
3609 4804 7.959651 CAGAAATATCAAAGGTGTTTCGAAGAG 59.040 37.037 0.00 0.00 38.43 2.85
3610 4805 6.743575 AATATCAAAGGTGTTTCGAAGAGG 57.256 37.500 0.00 0.00 38.43 3.69
3611 4806 3.553828 TCAAAGGTGTTTCGAAGAGGT 57.446 42.857 0.00 0.00 38.43 3.85
3612 4807 3.881220 TCAAAGGTGTTTCGAAGAGGTT 58.119 40.909 0.00 0.00 38.43 3.50
3613 4808 4.266714 TCAAAGGTGTTTCGAAGAGGTTT 58.733 39.130 0.00 0.00 38.43 3.27
3614 4809 4.334481 TCAAAGGTGTTTCGAAGAGGTTTC 59.666 41.667 0.00 0.00 38.43 2.78
3615 4810 3.553828 AGGTGTTTCGAAGAGGTTTCA 57.446 42.857 0.00 0.00 38.43 2.69
3616 4811 3.467803 AGGTGTTTCGAAGAGGTTTCAG 58.532 45.455 0.00 0.00 38.43 3.02
3617 4812 3.134081 AGGTGTTTCGAAGAGGTTTCAGA 59.866 43.478 0.00 0.00 38.43 3.27
3618 4813 3.875134 GGTGTTTCGAAGAGGTTTCAGAA 59.125 43.478 0.00 0.00 38.43 3.02
3619 4814 4.024809 GGTGTTTCGAAGAGGTTTCAGAAG 60.025 45.833 0.00 0.00 38.43 2.85
3620 4815 4.571176 GTGTTTCGAAGAGGTTTCAGAAGT 59.429 41.667 0.00 0.00 38.43 3.01
3621 4816 4.570772 TGTTTCGAAGAGGTTTCAGAAGTG 59.429 41.667 0.00 0.00 38.43 3.16
3622 4817 4.402056 TTCGAAGAGGTTTCAGAAGTGT 57.598 40.909 0.00 0.00 38.43 3.55
3623 4818 4.402056 TCGAAGAGGTTTCAGAAGTGTT 57.598 40.909 0.00 0.00 0.00 3.32
3624 4819 4.766375 TCGAAGAGGTTTCAGAAGTGTTT 58.234 39.130 0.00 0.00 0.00 2.83
3625 4820 5.183228 TCGAAGAGGTTTCAGAAGTGTTTT 58.817 37.500 0.00 0.00 0.00 2.43
3626 4821 5.064707 TCGAAGAGGTTTCAGAAGTGTTTTG 59.935 40.000 0.00 0.00 0.00 2.44
3627 4822 5.582550 GAAGAGGTTTCAGAAGTGTTTTGG 58.417 41.667 0.00 0.00 0.00 3.28
3628 4823 4.855340 AGAGGTTTCAGAAGTGTTTTGGA 58.145 39.130 0.00 0.00 0.00 3.53
3629 4824 4.884164 AGAGGTTTCAGAAGTGTTTTGGAG 59.116 41.667 0.00 0.00 0.00 3.86
3630 4825 4.600062 AGGTTTCAGAAGTGTTTTGGAGT 58.400 39.130 0.00 0.00 0.00 3.85
3631 4826 5.751586 AGGTTTCAGAAGTGTTTTGGAGTA 58.248 37.500 0.00 0.00 0.00 2.59
3632 4827 6.184789 AGGTTTCAGAAGTGTTTTGGAGTAA 58.815 36.000 0.00 0.00 0.00 2.24
3633 4828 6.661805 AGGTTTCAGAAGTGTTTTGGAGTAAA 59.338 34.615 0.00 0.00 0.00 2.01
3634 4829 6.750501 GGTTTCAGAAGTGTTTTGGAGTAAAC 59.249 38.462 0.00 0.00 38.26 2.01
3635 4830 6.445357 TTCAGAAGTGTTTTGGAGTAAACC 57.555 37.500 0.00 0.00 37.24 3.27
3636 4831 4.573201 TCAGAAGTGTTTTGGAGTAAACCG 59.427 41.667 0.00 0.00 37.24 4.44
3637 4832 4.573201 CAGAAGTGTTTTGGAGTAAACCGA 59.427 41.667 0.00 0.00 37.24 4.69
3638 4833 5.065474 CAGAAGTGTTTTGGAGTAAACCGAA 59.935 40.000 0.00 0.00 37.24 4.30
3639 4834 5.648960 AGAAGTGTTTTGGAGTAAACCGAAA 59.351 36.000 0.00 0.00 39.95 3.46
3640 4835 5.494632 AGTGTTTTGGAGTAAACCGAAAG 57.505 39.130 0.00 0.00 41.99 2.62
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
32 35 4.019983 CCAGTCTGGCTCGGTACT 57.980 61.111 5.79 0.00 0.00 2.73
47 50 1.303155 TGAACATCGCATGGTGCCA 60.303 52.632 0.00 0.00 41.12 4.92
51 54 0.960364 GGGTGTGAACATCGCATGGT 60.960 55.000 0.00 0.00 39.28 3.55
55 58 2.832498 TGGGGTGTGAACATCGCA 59.168 55.556 9.18 9.18 45.81 5.10
60 63 2.571653 CTCCTCTAATGGGGTGTGAACA 59.428 50.000 0.00 0.00 0.00 3.18
74 77 0.247460 TCCGACGAACGTCTCCTCTA 59.753 55.000 21.67 2.19 42.54 2.43
75 78 0.392729 ATCCGACGAACGTCTCCTCT 60.393 55.000 21.67 3.29 42.54 3.69
79 82 1.423056 ACGATCCGACGAACGTCTC 59.577 57.895 21.67 13.26 43.15 3.36
86 89 1.224069 GATACCCGACGATCCGACGA 61.224 60.000 12.03 0.00 46.01 4.20
94 97 1.046472 ATTGCCAGGATACCCGACGA 61.046 55.000 0.00 0.00 37.58 4.20
96 99 1.594331 GAATTGCCAGGATACCCGAC 58.406 55.000 0.00 0.00 37.58 4.79
111 114 0.768622 TTGGGGTCTCACGTGGAATT 59.231 50.000 17.00 0.00 0.00 2.17
117 120 0.321671 CTGACATTGGGGTCTCACGT 59.678 55.000 0.00 0.00 38.61 4.49
121 124 0.108138 CCGACTGACATTGGGGTCTC 60.108 60.000 0.00 0.00 38.61 3.36
122 125 0.544357 TCCGACTGACATTGGGGTCT 60.544 55.000 0.00 0.00 38.61 3.85
132 135 1.080705 CCGACCAAGTCCGACTGAC 60.081 63.158 0.65 0.00 44.82 3.51
154 166 3.357444 AATATGGTGCGCCTGGGCA 62.357 57.895 18.96 4.63 42.06 5.36
155 167 2.519302 AATATGGTGCGCCTGGGC 60.519 61.111 18.96 0.82 35.27 5.36
165 177 5.827797 AGCACAAATATGGAACGAATATGGT 59.172 36.000 0.00 0.00 0.00 3.55
172 184 3.342377 TCCAGCACAAATATGGAACGA 57.658 42.857 0.00 0.00 40.13 3.85
175 187 6.434028 GCCTTATATCCAGCACAAATATGGAA 59.566 38.462 0.00 0.00 45.82 3.53
177 189 5.126061 GGCCTTATATCCAGCACAAATATGG 59.874 44.000 0.00 0.00 35.30 2.74
178 190 5.126061 GGGCCTTATATCCAGCACAAATATG 59.874 44.000 0.84 0.00 0.00 1.78
186 198 1.136828 AACGGGCCTTATATCCAGCA 58.863 50.000 0.84 0.00 0.00 4.41
226 245 4.353437 AGCGGGTCGTTCGGTCAC 62.353 66.667 0.00 0.00 32.68 3.67
233 252 2.359570 AAACGTCTGAGCGGGTCGTT 62.360 55.000 2.41 0.81 44.51 3.85
243 263 2.035237 AACCGGCCTCAAACGTCTGA 62.035 55.000 0.00 0.00 0.00 3.27
245 265 0.393820 TAAACCGGCCTCAAACGTCT 59.606 50.000 0.00 0.00 0.00 4.18
264 284 1.686325 ATCTAACAGTCCGGCGCCAT 61.686 55.000 28.98 5.86 0.00 4.40
270 290 4.833390 AGGAAAGAAATCTAACAGTCCGG 58.167 43.478 0.00 0.00 0.00 5.14
272 292 7.573283 CGGAAAAGGAAAGAAATCTAACAGTCC 60.573 40.741 0.00 0.00 0.00 3.85
274 294 6.206829 CCGGAAAAGGAAAGAAATCTAACAGT 59.793 38.462 0.00 0.00 0.00 3.55
279 299 3.687698 CGCCGGAAAAGGAAAGAAATCTA 59.312 43.478 5.05 0.00 0.00 1.98
280 300 2.488153 CGCCGGAAAAGGAAAGAAATCT 59.512 45.455 5.05 0.00 0.00 2.40
281 301 2.228103 ACGCCGGAAAAGGAAAGAAATC 59.772 45.455 5.05 0.00 0.00 2.17
282 302 2.235891 ACGCCGGAAAAGGAAAGAAAT 58.764 42.857 5.05 0.00 0.00 2.17
283 303 1.682740 ACGCCGGAAAAGGAAAGAAA 58.317 45.000 5.05 0.00 0.00 2.52
310 339 4.173036 ACACACACAACACAAAAGGAAG 57.827 40.909 0.00 0.00 0.00 3.46
346 376 0.258774 AGAACCAGCACCAAACCAGT 59.741 50.000 0.00 0.00 0.00 4.00
349 379 0.249447 GCAAGAACCAGCACCAAACC 60.249 55.000 0.00 0.00 0.00 3.27
374 404 2.415426 CCCACCAACACCAAACGC 59.585 61.111 0.00 0.00 0.00 4.84
379 409 3.099841 TCCAGCCCACCAACACCA 61.100 61.111 0.00 0.00 0.00 4.17
384 414 1.770110 ACTGACTCCAGCCCACCAA 60.770 57.895 0.00 0.00 44.16 3.67
386 416 2.056906 AACACTGACTCCAGCCCACC 62.057 60.000 0.00 0.00 44.16 4.61
422 452 1.351017 CCAGACTACAACCACCCACAT 59.649 52.381 0.00 0.00 0.00 3.21
441 471 0.865769 CCAAGACAAGTACGTGCACC 59.134 55.000 12.15 0.00 0.00 5.01
445 475 4.609691 AAACAACCAAGACAAGTACGTG 57.390 40.909 7.29 7.29 0.00 4.49
458 492 5.986501 ACAACAAGGACTAAAAACAACCA 57.013 34.783 0.00 0.00 0.00 3.67
459 493 7.094631 AGAAACAACAAGGACTAAAAACAACC 58.905 34.615 0.00 0.00 0.00 3.77
468 502 4.515191 GTGCATGAGAAACAACAAGGACTA 59.485 41.667 0.00 0.00 0.00 2.59
471 505 3.286353 TGTGCATGAGAAACAACAAGGA 58.714 40.909 0.00 0.00 0.00 3.36
473 507 4.039703 CACTGTGCATGAGAAACAACAAG 58.960 43.478 0.00 0.00 0.00 3.16
474 508 3.181488 CCACTGTGCATGAGAAACAACAA 60.181 43.478 1.29 0.00 0.00 2.83
505 539 3.923017 AAAGCCAACAGTCAAGCATAC 57.077 42.857 0.00 0.00 0.00 2.39
521 555 8.286097 GCATCTAAGTCCAGATTATACAAAAGC 58.714 37.037 0.00 0.00 32.83 3.51
526 560 7.618019 AAGGCATCTAAGTCCAGATTATACA 57.382 36.000 0.00 0.00 32.83 2.29
527 561 7.604545 GGAAAGGCATCTAAGTCCAGATTATAC 59.395 40.741 0.00 0.00 32.83 1.47
528 562 7.514127 AGGAAAGGCATCTAAGTCCAGATTATA 59.486 37.037 0.00 0.00 32.83 0.98
529 563 6.331307 AGGAAAGGCATCTAAGTCCAGATTAT 59.669 38.462 0.00 0.00 32.83 1.28
530 564 5.667626 AGGAAAGGCATCTAAGTCCAGATTA 59.332 40.000 0.00 0.00 32.83 1.75
533 567 3.198635 CAGGAAAGGCATCTAAGTCCAGA 59.801 47.826 0.00 0.00 0.00 3.86
538 572 3.084786 GCAACAGGAAAGGCATCTAAGT 58.915 45.455 0.00 0.00 0.00 2.24
540 574 2.083774 CGCAACAGGAAAGGCATCTAA 58.916 47.619 0.00 0.00 0.00 2.10
541 575 1.003118 ACGCAACAGGAAAGGCATCTA 59.997 47.619 0.00 0.00 0.00 1.98
546 580 1.519408 TTAGACGCAACAGGAAAGGC 58.481 50.000 0.00 0.00 0.00 4.35
547 581 4.561735 TTTTTAGACGCAACAGGAAAGG 57.438 40.909 0.00 0.00 0.00 3.11
565 599 1.133915 TCAGTTGGTCCGCTCCTTTTT 60.134 47.619 0.00 0.00 0.00 1.94
566 600 0.472471 TCAGTTGGTCCGCTCCTTTT 59.528 50.000 0.00 0.00 0.00 2.27
567 601 0.035458 CTCAGTTGGTCCGCTCCTTT 59.965 55.000 0.00 0.00 0.00 3.11
569 603 0.616111 ATCTCAGTTGGTCCGCTCCT 60.616 55.000 0.00 0.00 0.00 3.69
570 604 0.250513 AATCTCAGTTGGTCCGCTCC 59.749 55.000 0.00 0.00 0.00 4.70
571 605 1.066858 TCAATCTCAGTTGGTCCGCTC 60.067 52.381 0.00 0.00 0.00 5.03
572 606 0.976641 TCAATCTCAGTTGGTCCGCT 59.023 50.000 0.00 0.00 0.00 5.52
573 607 1.066858 TCTCAATCTCAGTTGGTCCGC 60.067 52.381 0.00 0.00 0.00 5.54
574 608 3.533606 ATCTCAATCTCAGTTGGTCCG 57.466 47.619 0.00 0.00 0.00 4.79
575 609 6.644347 TCTTTATCTCAATCTCAGTTGGTCC 58.356 40.000 0.00 0.00 0.00 4.46
576 610 7.327214 ACTCTTTATCTCAATCTCAGTTGGTC 58.673 38.462 0.00 0.00 0.00 4.02
577 611 7.251321 ACTCTTTATCTCAATCTCAGTTGGT 57.749 36.000 0.00 0.00 0.00 3.67
578 612 9.474920 GATACTCTTTATCTCAATCTCAGTTGG 57.525 37.037 0.00 0.00 0.00 3.77
580 614 9.126151 TCGATACTCTTTATCTCAATCTCAGTT 57.874 33.333 0.00 0.00 0.00 3.16
581 615 8.684386 TCGATACTCTTTATCTCAATCTCAGT 57.316 34.615 0.00 0.00 0.00 3.41
583 617 9.905171 CAATCGATACTCTTTATCTCAATCTCA 57.095 33.333 0.00 0.00 0.00 3.27
584 618 8.859156 GCAATCGATACTCTTTATCTCAATCTC 58.141 37.037 0.00 0.00 0.00 2.75
585 619 8.584157 AGCAATCGATACTCTTTATCTCAATCT 58.416 33.333 0.00 0.00 0.00 2.40
586 620 8.755696 AGCAATCGATACTCTTTATCTCAATC 57.244 34.615 0.00 0.00 0.00 2.67
587 621 7.540400 CGAGCAATCGATACTCTTTATCTCAAT 59.460 37.037 20.18 0.00 34.64 2.57
588 622 6.858478 CGAGCAATCGATACTCTTTATCTCAA 59.142 38.462 20.18 0.00 34.64 3.02
589 623 6.017026 ACGAGCAATCGATACTCTTTATCTCA 60.017 38.462 20.18 0.00 36.85 3.27
590 624 6.375377 ACGAGCAATCGATACTCTTTATCTC 58.625 40.000 20.18 6.31 36.85 2.75
591 625 6.320494 ACGAGCAATCGATACTCTTTATCT 57.680 37.500 20.18 0.00 36.85 1.98
592 626 6.088350 GGAACGAGCAATCGATACTCTTTATC 59.912 42.308 20.18 13.99 36.85 1.75
593 627 5.921408 GGAACGAGCAATCGATACTCTTTAT 59.079 40.000 20.18 8.39 36.85 1.40
594 628 5.163591 TGGAACGAGCAATCGATACTCTTTA 60.164 40.000 20.18 6.45 36.85 1.85
603 900 1.014044 GCACTGGAACGAGCAATCGA 61.014 55.000 4.44 0.00 36.85 3.59
605 902 0.166814 GTGCACTGGAACGAGCAATC 59.833 55.000 10.32 0.00 38.91 2.67
609 906 2.959357 GCAGTGCACTGGAACGAGC 61.959 63.158 39.92 24.61 43.94 5.03
611 908 1.595109 CAGCAGTGCACTGGAACGA 60.595 57.895 39.92 0.00 43.94 3.85
614 911 1.140852 AGTTACAGCAGTGCACTGGAA 59.859 47.619 39.92 21.43 43.94 3.53
615 912 0.758734 AGTTACAGCAGTGCACTGGA 59.241 50.000 39.92 16.72 43.94 3.86
616 913 0.870393 CAGTTACAGCAGTGCACTGG 59.130 55.000 39.92 29.00 43.94 4.00
617 914 1.586422 ACAGTTACAGCAGTGCACTG 58.414 50.000 37.09 37.09 46.40 3.66
618 915 3.393800 CTTACAGTTACAGCAGTGCACT 58.606 45.455 15.25 15.25 0.00 4.40
619 916 2.096218 GCTTACAGTTACAGCAGTGCAC 60.096 50.000 19.20 9.40 33.45 4.57
620 917 2.143122 GCTTACAGTTACAGCAGTGCA 58.857 47.619 19.20 0.00 33.45 4.57
621 918 1.464997 GGCTTACAGTTACAGCAGTGC 59.535 52.381 7.13 7.13 35.05 4.40
622 919 2.738846 CTGGCTTACAGTTACAGCAGTG 59.261 50.000 0.00 0.00 42.42 3.66
634 931 4.131596 AGAAAGCGTAAAACTGGCTTACA 58.868 39.130 0.00 0.00 45.58 2.41
635 932 4.744136 AGAAAGCGTAAAACTGGCTTAC 57.256 40.909 0.00 0.00 45.58 2.34
636 933 8.550710 TTTATAGAAAGCGTAAAACTGGCTTA 57.449 30.769 0.00 0.00 45.58 3.09
638 935 7.443259 TTTTATAGAAAGCGTAAAACTGGCT 57.557 32.000 0.00 0.00 39.01 4.75
639 936 8.158306 CTTTTTATAGAAAGCGTAAAACTGGC 57.842 34.615 3.06 0.00 30.66 4.85
657 954 3.146066 TCGACACTGCCAAGCTTTTTAT 58.854 40.909 0.00 0.00 0.00 1.40
661 958 0.886490 CCTCGACACTGCCAAGCTTT 60.886 55.000 0.00 0.00 0.00 3.51
666 963 2.425592 CCACCTCGACACTGCCAA 59.574 61.111 0.00 0.00 0.00 4.52
667 964 4.314440 GCCACCTCGACACTGCCA 62.314 66.667 0.00 0.00 0.00 4.92
694 1045 2.419851 GGCTTGAGCTAGACAGATGCTT 60.420 50.000 2.66 0.00 41.70 3.91
747 1107 1.305549 CCCCTTCTGCCAGCCAATT 60.306 57.895 0.00 0.00 0.00 2.32
756 1116 0.035439 TTTGTCCGATCCCCTTCTGC 60.035 55.000 0.00 0.00 0.00 4.26
901 1295 4.143115 CGTTGCTTCCATTATATACGCAGG 60.143 45.833 0.00 0.00 0.00 4.85
964 1367 5.186021 CCTTCTTCCTAGCTTGTTCTCAGTA 59.814 44.000 0.00 0.00 0.00 2.74
1038 1450 3.951769 CTTCTTGGGCTGGGGCTGG 62.952 68.421 0.00 0.00 38.73 4.85
1039 1451 2.362120 CTTCTTGGGCTGGGGCTG 60.362 66.667 0.00 0.00 38.73 4.85
1040 1452 2.147433 CTTCTTCTTGGGCTGGGGCT 62.147 60.000 0.00 0.00 38.73 5.19
1131 1546 6.812160 GCGTATATTGGAAATGTAGGAGGTAG 59.188 42.308 2.03 0.00 0.00 3.18
1148 1564 2.096819 CGTTGGCTTTGGTGCGTATATT 59.903 45.455 0.00 0.00 0.00 1.28
1156 1572 2.490993 GATGGGCGTTGGCTTTGGTG 62.491 60.000 0.00 0.00 39.81 4.17
1164 1580 0.035056 AGGAAGAAGATGGGCGTTGG 60.035 55.000 0.00 0.00 0.00 3.77
1168 1584 0.811616 CGGAAGGAAGAAGATGGGCG 60.812 60.000 0.00 0.00 0.00 6.13
1169 1585 1.098129 GCGGAAGGAAGAAGATGGGC 61.098 60.000 0.00 0.00 0.00 5.36
1170 1586 0.464554 GGCGGAAGGAAGAAGATGGG 60.465 60.000 0.00 0.00 0.00 4.00
1185 1603 0.514255 CGATCAGTTATGCATGGCGG 59.486 55.000 10.16 2.83 0.00 6.13
1200 1634 0.317103 CGACGTCTGGACATCCGATC 60.317 60.000 14.70 0.00 39.43 3.69
1203 1637 2.102357 CCGACGTCTGGACATCCG 59.898 66.667 17.91 0.93 39.43 4.18
1204 1638 2.494918 CCCGACGTCTGGACATCC 59.505 66.667 20.35 0.00 0.00 3.51
1205 1639 2.348888 ACCCCGACGTCTGGACATC 61.349 63.158 25.78 0.00 0.00 3.06
1206 1640 2.283676 ACCCCGACGTCTGGACAT 60.284 61.111 25.78 9.24 0.00 3.06
1625 2082 3.925630 ATGCGCCAGTTGAGGTGGG 62.926 63.158 4.18 0.00 39.57 4.61
1663 2120 4.168291 GAGCAAGGCGGAGGGGAG 62.168 72.222 0.00 0.00 0.00 4.30
2397 2854 2.190313 GTCATGGAGATGGCGGCA 59.810 61.111 16.34 16.34 0.00 5.69
2661 3134 2.811431 TGCATGTTAGAGAAACCAACCG 59.189 45.455 0.00 0.00 37.27 4.44
2666 3139 4.357142 CATGCATGCATGTTAGAGAAACC 58.643 43.478 40.30 7.53 46.20 3.27
2728 3206 2.040412 ACCCAAGAAAGAAGTAGCAGGG 59.960 50.000 0.00 0.00 39.66 4.45
2757 3235 5.163353 ACATCCCGAAAACAGGACAAATTTT 60.163 36.000 0.00 0.00 34.20 1.82
2763 3241 2.649531 AACATCCCGAAAACAGGACA 57.350 45.000 0.00 0.00 34.20 4.02
2827 3305 4.219944 ACTCTTATTTGTCAGTAGGCGACA 59.780 41.667 0.00 0.00 41.53 4.35
2855 3333 8.301720 ACAACGTACTCTCATTATGTAAGACAA 58.698 33.333 0.00 0.00 0.00 3.18
2857 3335 8.684973 AACAACGTACTCTCATTATGTAAGAC 57.315 34.615 0.00 0.00 0.00 3.01
2858 3336 9.999009 CTAACAACGTACTCTCATTATGTAAGA 57.001 33.333 0.00 0.00 0.00 2.10
2859 3337 9.784680 ACTAACAACGTACTCTCATTATGTAAG 57.215 33.333 0.00 0.00 0.00 2.34
2862 3340 8.404000 CCTACTAACAACGTACTCTCATTATGT 58.596 37.037 0.00 0.00 0.00 2.29
2875 4067 5.362263 ACAACATTGTCCTACTAACAACGT 58.638 37.500 0.00 0.00 39.29 3.99
2877 4069 6.261381 TCCAACAACATTGTCCTACTAACAAC 59.739 38.462 0.00 0.00 41.31 3.32
2905 4097 3.924686 CGTAGTGTGTCATTAGTTGGGTC 59.075 47.826 0.00 0.00 0.00 4.46
2907 4099 4.082408 TCTCGTAGTGTGTCATTAGTTGGG 60.082 45.833 0.00 0.00 0.00 4.12
2919 4111 3.406728 ACGATGTGATCTCGTAGTGTG 57.593 47.619 6.70 0.00 46.71 3.82
3006 4198 1.471676 GGCTGACATGAAGGTAGACGG 60.472 57.143 0.00 0.00 0.00 4.79
3010 4202 3.340814 AACTGGCTGACATGAAGGTAG 57.659 47.619 0.00 0.00 0.00 3.18
3028 4220 3.200483 ACGTTTGACAACCCAGAGTAAC 58.800 45.455 0.00 0.00 0.00 2.50
3075 4268 8.937634 TGTTTTTCCGATATACCTAGAAGTTC 57.062 34.615 0.00 0.00 0.00 3.01
3081 4274 9.680315 CTAGACTTGTTTTTCCGATATACCTAG 57.320 37.037 0.00 0.00 0.00 3.02
3082 4275 8.636213 CCTAGACTTGTTTTTCCGATATACCTA 58.364 37.037 0.00 0.00 0.00 3.08
3090 4283 4.558095 CGAGTCCTAGACTTGTTTTTCCGA 60.558 45.833 0.00 0.00 43.53 4.55
3098 4291 5.498393 TGAACTATCGAGTCCTAGACTTGT 58.502 41.667 10.94 3.20 43.53 3.16
3101 4294 5.818857 GTCTTGAACTATCGAGTCCTAGACT 59.181 44.000 0.00 0.00 46.42 3.24
3127 4321 4.877823 TCCATCATCGAAGGAACAAATCTG 59.122 41.667 0.00 0.00 0.00 2.90
3135 4329 6.723515 AGAATATCTCTCCATCATCGAAGGAA 59.276 38.462 0.00 0.00 28.74 3.36
3158 4352 5.833667 CCGTAATATAGATATGGCCCAGAGA 59.166 44.000 0.00 0.00 0.00 3.10
3165 4359 7.376615 GGTGGATACCGTAATATAGATATGGC 58.623 42.308 6.53 0.00 37.19 4.40
3196 4390 0.323302 TTCACGCTGTATCTGGCCAA 59.677 50.000 7.01 0.00 0.00 4.52
3198 4392 1.668419 ATTTCACGCTGTATCTGGCC 58.332 50.000 0.00 0.00 0.00 5.36
3236 4431 7.473027 TTTGTTCTCTTTTCTCGTTATCGTT 57.527 32.000 0.00 0.00 38.33 3.85
3241 4436 8.937634 ACTAGTTTTGTTCTCTTTTCTCGTTA 57.062 30.769 0.00 0.00 0.00 3.18
3270 4465 9.975218 ACTAAATCACAATACCAAGTTATCCTT 57.025 29.630 0.00 0.00 0.00 3.36
3287 4482 7.816640 TCCTTGTGAAGCAATAACTAAATCAC 58.183 34.615 0.00 0.00 36.36 3.06
3293 4488 6.953101 TGGTATCCTTGTGAAGCAATAACTA 58.047 36.000 0.00 0.00 36.36 2.24
3323 4518 1.318576 CAAAACCCGAGGCAAAGACT 58.681 50.000 0.00 0.00 0.00 3.24
3324 4519 1.029681 ACAAAACCCGAGGCAAAGAC 58.970 50.000 0.00 0.00 0.00 3.01
3325 4520 1.770294 AACAAAACCCGAGGCAAAGA 58.230 45.000 0.00 0.00 0.00 2.52
3326 4521 3.005367 ACATAACAAAACCCGAGGCAAAG 59.995 43.478 0.00 0.00 0.00 2.77
3327 4522 2.959707 ACATAACAAAACCCGAGGCAAA 59.040 40.909 0.00 0.00 0.00 3.68
3385 4580 9.882996 CACACGAATATATTTATTGAGCACAAT 57.117 29.630 13.95 13.95 46.64 2.71
3387 4582 8.432110 ACACACGAATATATTTATTGAGCACA 57.568 30.769 0.00 0.00 0.00 4.57
3442 4637 7.026631 TCTTTTGGTCAATAATCAATAGCGG 57.973 36.000 0.00 0.00 0.00 5.52
3443 4638 8.131100 ACATCTTTTGGTCAATAATCAATAGCG 58.869 33.333 0.00 0.00 0.00 4.26
3466 4661 1.352017 TGCAGACATGACCTGGAACAT 59.648 47.619 17.09 2.93 38.20 2.71
3473 4668 3.641436 TCGGTAATATGCAGACATGACCT 59.359 43.478 0.00 0.00 37.04 3.85
3502 4697 0.524414 GCCATTAAACGTGTGACCCC 59.476 55.000 0.00 0.00 0.00 4.95
3531 4726 8.946797 ACTCTTAACACCTCCTAGTACTTAAA 57.053 34.615 0.00 0.00 0.00 1.52
3534 4729 6.597280 CGTACTCTTAACACCTCCTAGTACTT 59.403 42.308 0.00 0.00 37.01 2.24
3541 4736 4.019501 TCTCTCGTACTCTTAACACCTCCT 60.020 45.833 0.00 0.00 0.00 3.69
3542 4737 4.260170 TCTCTCGTACTCTTAACACCTCC 58.740 47.826 0.00 0.00 0.00 4.30
3543 4738 5.876612 TTCTCTCGTACTCTTAACACCTC 57.123 43.478 0.00 0.00 0.00 3.85
3569 4764 6.334989 TGATATTTCTGGAGCATTTTTGCTG 58.665 36.000 5.01 0.00 46.36 4.41
3573 4768 7.820872 CACCTTTGATATTTCTGGAGCATTTTT 59.179 33.333 0.00 0.00 0.00 1.94
3574 4769 7.038799 ACACCTTTGATATTTCTGGAGCATTTT 60.039 33.333 0.00 0.00 0.00 1.82
3583 4778 7.806690 TCTTCGAAACACCTTTGATATTTCTG 58.193 34.615 0.00 0.00 0.00 3.02
3594 4789 3.877508 CTGAAACCTCTTCGAAACACCTT 59.122 43.478 0.00 0.00 0.00 3.50
3596 4791 3.463944 TCTGAAACCTCTTCGAAACACC 58.536 45.455 0.00 0.00 0.00 4.16
3604 4799 5.357032 TCCAAAACACTTCTGAAACCTCTTC 59.643 40.000 0.00 0.00 0.00 2.87
3605 4800 5.261216 TCCAAAACACTTCTGAAACCTCTT 58.739 37.500 0.00 0.00 0.00 2.85
3607 4802 4.640647 ACTCCAAAACACTTCTGAAACCTC 59.359 41.667 0.00 0.00 0.00 3.85
3608 4803 4.600062 ACTCCAAAACACTTCTGAAACCT 58.400 39.130 0.00 0.00 0.00 3.50
3609 4804 4.983671 ACTCCAAAACACTTCTGAAACC 57.016 40.909 0.00 0.00 0.00 3.27
3610 4805 6.750501 GGTTTACTCCAAAACACTTCTGAAAC 59.249 38.462 2.31 0.00 40.42 2.78
3611 4806 6.403855 CGGTTTACTCCAAAACACTTCTGAAA 60.404 38.462 2.31 0.00 40.42 2.69
3612 4807 5.065474 CGGTTTACTCCAAAACACTTCTGAA 59.935 40.000 2.31 0.00 40.42 3.02
3613 4808 4.573201 CGGTTTACTCCAAAACACTTCTGA 59.427 41.667 2.31 0.00 40.42 3.27
3614 4809 4.573201 TCGGTTTACTCCAAAACACTTCTG 59.427 41.667 2.31 0.00 40.42 3.02
3615 4810 4.773013 TCGGTTTACTCCAAAACACTTCT 58.227 39.130 2.31 0.00 40.42 2.85
3616 4811 5.488645 TTCGGTTTACTCCAAAACACTTC 57.511 39.130 2.31 0.00 40.42 3.01
3617 4812 5.886992 CTTTCGGTTTACTCCAAAACACTT 58.113 37.500 2.31 0.00 40.42 3.16
3618 4813 5.494632 CTTTCGGTTTACTCCAAAACACT 57.505 39.130 2.31 0.00 40.42 3.55


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

AutoCloner maintained by Alex Coulton.