Multiple sequence alignment - TraesCS4A01G039700

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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 TraesCS4A01G039700 chr4A 100.000 3298 0 0 1 3298 32463954 32460657 0.000000e+00 6091.0
1 TraesCS4A01G039700 chr4A 95.745 47 1 1 45 91 714207217 714207262 1.270000e-09 75.0
2 TraesCS4A01G039700 chr4A 100.000 37 0 0 45 81 48517266 48517302 5.910000e-08 69.4
3 TraesCS4A01G039700 chr4B 90.600 2468 120 52 876 3298 529298476 529296076 0.000000e+00 3169.0
4 TraesCS4A01G039700 chr4B 81.703 787 58 28 78 840 529299312 529298588 7.940000e-161 577.0
5 TraesCS4A01G039700 chr4B 97.561 41 0 1 45 85 670967759 670967798 5.910000e-08 69.4
6 TraesCS4A01G039700 chr4D 88.489 2476 136 73 880 3298 430794840 430792457 0.000000e+00 2856.0
7 TraesCS4A01G039700 chr4D 90.000 270 13 5 571 840 430795178 430794923 1.470000e-88 337.0
8 TraesCS4A01G039700 chr7D 90.886 801 55 13 1178 1972 234344749 234345537 0.000000e+00 1059.0
9 TraesCS4A01G039700 chr3D 90.637 801 57 13 1178 1972 456654123 456654911 0.000000e+00 1048.0
10 TraesCS4A01G039700 chr2B 78.850 539 82 20 987 1508 659064343 659064866 5.270000e-88 335.0
11 TraesCS4A01G039700 chr2B 96.226 53 2 0 1000 1052 58689434 58689486 1.630000e-13 87.9
12 TraesCS4A01G039700 chr2D 79.827 347 48 17 1169 1508 553330497 553330828 1.980000e-57 233.0
13 TraesCS4A01G039700 chr2D 90.000 130 8 3 1634 1763 553330915 553331039 2.630000e-36 163.0
14 TraesCS4A01G039700 chr2D 80.292 137 19 7 1000 1132 35639076 35639208 2.710000e-16 97.1
15 TraesCS4A01G039700 chr5B 97.674 43 1 0 45 87 163522369 163522411 1.270000e-09 75.0
16 TraesCS4A01G039700 chr3B 97.674 43 1 0 45 87 85626767 85626809 1.270000e-09 75.0
17 TraesCS4A01G039700 chr3A 100.000 39 0 0 45 83 594498282 594498244 4.570000e-09 73.1
18 TraesCS4A01G039700 chr7B 93.750 48 1 2 45 91 153939384 153939338 1.640000e-08 71.3
19 TraesCS4A01G039700 chr5A 97.561 41 0 1 45 85 38128883 38128844 5.910000e-08 69.4
20 TraesCS4A01G039700 chr5A 93.333 45 3 0 45 89 552885081 552885037 2.120000e-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 TraesCS4A01G039700 chr4A 32460657 32463954 3297 True 6091.0 6091 100.0000 1 3298 1 chr4A.!!$R1 3297
1 TraesCS4A01G039700 chr4B 529296076 529299312 3236 True 1873.0 3169 86.1515 78 3298 2 chr4B.!!$R1 3220
2 TraesCS4A01G039700 chr4D 430792457 430795178 2721 True 1596.5 2856 89.2445 571 3298 2 chr4D.!!$R1 2727
3 TraesCS4A01G039700 chr7D 234344749 234345537 788 False 1059.0 1059 90.8860 1178 1972 1 chr7D.!!$F1 794
4 TraesCS4A01G039700 chr3D 456654123 456654911 788 False 1048.0 1048 90.6370 1178 1972 1 chr3D.!!$F1 794
5 TraesCS4A01G039700 chr2B 659064343 659064866 523 False 335.0 335 78.8500 987 1508 1 chr2B.!!$F2 521

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
536 560 0.028902 GACCACCAAACACGCTCAAC 59.971 55.0 0.0 0.0 0.0 3.18 F
857 881 0.107116 ACCCGCACGTATCTCTCTCT 60.107 55.0 0.0 0.0 0.0 3.10 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2058 2208 0.462581 GACTGGCGCATGATCTGGAA 60.463 55.0 10.83 0.0 0.00 3.53 R
2657 2852 0.250684 TTCAGATGCCCAAACGAGCA 60.251 50.0 0.00 0.0 44.45 4.26 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
27 28 9.893305 AATTCAATAAACTAAAACCTCGACAAG 57.107 29.630 0.00 0.00 0.00 3.16
28 29 8.441312 TTCAATAAACTAAAACCTCGACAAGT 57.559 30.769 0.00 0.00 0.00 3.16
29 30 9.545105 TTCAATAAACTAAAACCTCGACAAGTA 57.455 29.630 0.00 0.00 0.00 2.24
30 31 9.545105 TCAATAAACTAAAACCTCGACAAGTAA 57.455 29.630 0.00 0.00 0.00 2.24
35 36 7.198306 ACTAAAACCTCGACAAGTAATTTGG 57.802 36.000 0.00 0.00 41.25 3.28
36 37 6.993902 ACTAAAACCTCGACAAGTAATTTGGA 59.006 34.615 0.00 0.00 41.25 3.53
37 38 6.702716 AAAACCTCGACAAGTAATTTGGAA 57.297 33.333 0.00 0.00 41.25 3.53
38 39 5.684550 AACCTCGACAAGTAATTTGGAAC 57.315 39.130 0.00 0.00 41.25 3.62
39 40 3.744426 ACCTCGACAAGTAATTTGGAACG 59.256 43.478 0.00 0.00 41.25 3.95
40 41 3.124636 CCTCGACAAGTAATTTGGAACGG 59.875 47.826 0.00 0.00 41.25 4.44
41 42 3.991773 CTCGACAAGTAATTTGGAACGGA 59.008 43.478 0.00 0.00 41.25 4.69
42 43 3.991773 TCGACAAGTAATTTGGAACGGAG 59.008 43.478 0.00 0.00 41.25 4.63
43 44 3.124636 CGACAAGTAATTTGGAACGGAGG 59.875 47.826 0.00 0.00 41.25 4.30
44 45 4.070009 GACAAGTAATTTGGAACGGAGGT 58.930 43.478 0.00 0.00 41.25 3.85
45 46 5.231702 ACAAGTAATTTGGAACGGAGGTA 57.768 39.130 0.00 0.00 41.25 3.08
46 47 5.623169 ACAAGTAATTTGGAACGGAGGTAA 58.377 37.500 0.00 0.00 41.25 2.85
47 48 6.063404 ACAAGTAATTTGGAACGGAGGTAAA 58.937 36.000 0.00 0.00 41.25 2.01
48 49 6.546772 ACAAGTAATTTGGAACGGAGGTAAAA 59.453 34.615 0.00 0.00 41.25 1.52
49 50 6.564709 AGTAATTTGGAACGGAGGTAAAAC 57.435 37.500 0.00 0.00 0.00 2.43
50 51 4.859304 AATTTGGAACGGAGGTAAAACC 57.141 40.909 0.00 0.00 38.99 3.27
51 52 3.294038 TTTGGAACGGAGGTAAAACCA 57.706 42.857 0.00 0.00 41.95 3.67
52 53 2.259266 TGGAACGGAGGTAAAACCAC 57.741 50.000 0.00 0.00 41.95 4.16
53 54 1.150827 GGAACGGAGGTAAAACCACG 58.849 55.000 10.40 10.40 41.95 4.94
54 55 1.270252 GGAACGGAGGTAAAACCACGA 60.270 52.381 16.56 0.00 41.95 4.35
55 56 1.794701 GAACGGAGGTAAAACCACGAC 59.205 52.381 16.56 8.71 41.95 4.34
56 57 0.752054 ACGGAGGTAAAACCACGACA 59.248 50.000 16.56 0.00 41.95 4.35
57 58 1.138661 ACGGAGGTAAAACCACGACAA 59.861 47.619 16.56 0.00 41.95 3.18
58 59 1.796459 CGGAGGTAAAACCACGACAAG 59.204 52.381 7.22 0.00 41.95 3.16
59 60 2.804212 CGGAGGTAAAACCACGACAAGT 60.804 50.000 7.22 0.00 41.95 3.16
60 61 3.552684 CGGAGGTAAAACCACGACAAGTA 60.553 47.826 7.22 0.00 41.95 2.24
61 62 4.379652 GGAGGTAAAACCACGACAAGTAA 58.620 43.478 0.00 0.00 41.95 2.24
62 63 4.999311 GGAGGTAAAACCACGACAAGTAAT 59.001 41.667 0.00 0.00 41.95 1.89
63 64 5.471116 GGAGGTAAAACCACGACAAGTAATT 59.529 40.000 0.00 0.00 41.95 1.40
64 65 6.016860 GGAGGTAAAACCACGACAAGTAATTT 60.017 38.462 0.00 0.00 41.95 1.82
65 66 6.731164 AGGTAAAACCACGACAAGTAATTTG 58.269 36.000 0.00 0.00 41.95 2.32
66 67 5.916320 GGTAAAACCACGACAAGTAATTTGG 59.084 40.000 0.00 0.00 38.50 3.28
67 68 5.838531 AAAACCACGACAAGTAATTTGGA 57.161 34.783 0.00 0.00 41.25 3.53
68 69 5.838531 AAACCACGACAAGTAATTTGGAA 57.161 34.783 0.00 0.00 41.25 3.53
69 70 4.823790 ACCACGACAAGTAATTTGGAAC 57.176 40.909 0.00 0.00 41.25 3.62
70 71 3.249080 ACCACGACAAGTAATTTGGAACG 59.751 43.478 0.00 0.00 41.25 3.95
71 72 3.364565 CCACGACAAGTAATTTGGAACGG 60.365 47.826 0.00 0.00 41.25 4.44
72 73 3.495377 CACGACAAGTAATTTGGAACGGA 59.505 43.478 0.00 0.00 41.25 4.69
73 74 3.744426 ACGACAAGTAATTTGGAACGGAG 59.256 43.478 0.00 0.00 41.25 4.63
74 75 3.124636 CGACAAGTAATTTGGAACGGAGG 59.875 47.826 0.00 0.00 41.25 4.30
75 76 3.418047 ACAAGTAATTTGGAACGGAGGG 58.582 45.455 0.00 0.00 41.25 4.30
76 77 3.073356 ACAAGTAATTTGGAACGGAGGGA 59.927 43.478 0.00 0.00 41.25 4.20
83 84 2.905415 TGGAACGGAGGGAGTAACTA 57.095 50.000 0.00 0.00 0.00 2.24
86 87 4.870636 TGGAACGGAGGGAGTAACTATTA 58.129 43.478 0.00 0.00 0.00 0.98
131 132 6.954232 AGAAAAGTATAATTTCGGTCCCTCA 58.046 36.000 0.00 0.00 40.78 3.86
192 209 3.132925 CCGTTAAGTCTCAAAACCGGAA 58.867 45.455 9.46 0.00 0.00 4.30
194 211 4.035441 CCGTTAAGTCTCAAAACCGGAAAA 59.965 41.667 9.46 0.00 0.00 2.29
200 217 4.033019 GTCTCAAAACCGGAAAAGTTTCG 58.967 43.478 9.46 0.00 36.44 3.46
284 307 1.308998 CCAGACGTGCTCCAAGTTTT 58.691 50.000 0.00 0.00 0.00 2.43
285 308 1.264288 CCAGACGTGCTCCAAGTTTTC 59.736 52.381 0.00 0.00 0.00 2.29
288 311 0.182775 ACGTGCTCCAAGTTTTCCCT 59.817 50.000 0.00 0.00 0.00 4.20
299 322 4.156008 CCAAGTTTTCCCTCTTAATCCACG 59.844 45.833 0.00 0.00 0.00 4.94
332 356 4.410400 GGGGGCCTCGTGTCCTTG 62.410 72.222 0.84 0.00 0.00 3.61
337 361 2.358737 CCTCGTGTCCTTGGTGGC 60.359 66.667 0.00 0.00 35.26 5.01
338 362 2.425592 CTCGTGTCCTTGGTGGCA 59.574 61.111 0.00 0.00 35.26 4.92
339 363 1.961277 CTCGTGTCCTTGGTGGCAC 60.961 63.158 9.70 9.70 38.55 5.01
341 365 1.116536 TCGTGTCCTTGGTGGCACTA 61.117 55.000 18.45 8.99 39.24 2.74
342 366 0.949105 CGTGTCCTTGGTGGCACTAC 60.949 60.000 18.45 8.78 39.24 2.73
343 367 0.949105 GTGTCCTTGGTGGCACTACG 60.949 60.000 18.45 9.20 38.73 3.51
344 368 1.370064 GTCCTTGGTGGCACTACGT 59.630 57.895 18.45 0.00 35.26 3.57
345 369 0.604578 GTCCTTGGTGGCACTACGTA 59.395 55.000 18.45 0.00 35.26 3.57
346 370 0.604578 TCCTTGGTGGCACTACGTAC 59.395 55.000 18.45 0.00 35.26 3.67
347 371 0.734942 CCTTGGTGGCACTACGTACG 60.735 60.000 18.45 15.01 0.00 3.67
348 372 0.038892 CTTGGTGGCACTACGTACGT 60.039 55.000 25.98 25.98 0.00 3.57
349 373 0.039256 TTGGTGGCACTACGTACGTC 60.039 55.000 26.53 10.41 0.00 4.34
357 381 1.351012 CTACGTACGTCCTCTGCCG 59.649 63.158 26.53 0.69 0.00 5.69
382 406 3.308688 CCATCCTCATTCCACACTTTCCT 60.309 47.826 0.00 0.00 0.00 3.36
394 418 4.649674 CCACACTTTCCTAGCAGTCCTATA 59.350 45.833 0.00 0.00 0.00 1.31
399 423 7.730784 ACACTTTCCTAGCAGTCCTATACATAT 59.269 37.037 0.00 0.00 0.00 1.78
400 424 9.244292 CACTTTCCTAGCAGTCCTATACATATA 57.756 37.037 0.00 0.00 0.00 0.86
401 425 9.245481 ACTTTCCTAGCAGTCCTATACATATAC 57.755 37.037 0.00 0.00 0.00 1.47
402 426 7.860918 TTCCTAGCAGTCCTATACATATACG 57.139 40.000 0.00 0.00 0.00 3.06
405 429 8.712103 TCCTAGCAGTCCTATACATATACGTAT 58.288 37.037 13.54 13.54 36.13 3.06
453 477 5.530519 TGTTACAGATTCATTGTTCTCGC 57.469 39.130 0.00 0.00 0.00 5.03
456 480 4.675190 ACAGATTCATTGTTCTCGCAAG 57.325 40.909 0.00 0.00 0.00 4.01
465 489 1.800586 TGTTCTCGCAAGCTTGACATC 59.199 47.619 30.39 11.04 37.18 3.06
482 506 7.327032 GCTTGACATCAACTTTAGGACAATTTC 59.673 37.037 0.00 0.00 0.00 2.17
484 508 9.567776 TTGACATCAACTTTAGGACAATTTCTA 57.432 29.630 0.00 0.00 0.00 2.10
510 534 2.186532 TTTTGTACGCCTGCCACATA 57.813 45.000 0.00 0.00 0.00 2.29
536 560 0.028902 GACCACCAAACACGCTCAAC 59.971 55.000 0.00 0.00 0.00 3.18
548 572 0.523072 CGCTCAACATTTCCCCACTG 59.477 55.000 0.00 0.00 0.00 3.66
549 573 1.881925 CGCTCAACATTTCCCCACTGA 60.882 52.381 0.00 0.00 0.00 3.41
550 574 1.815003 GCTCAACATTTCCCCACTGAG 59.185 52.381 0.00 0.00 34.69 3.35
551 575 2.815589 GCTCAACATTTCCCCACTGAGT 60.816 50.000 0.00 0.00 34.20 3.41
552 576 3.559171 GCTCAACATTTCCCCACTGAGTA 60.559 47.826 0.00 0.00 34.20 2.59
553 577 4.256920 CTCAACATTTCCCCACTGAGTAG 58.743 47.826 0.00 0.00 0.00 2.57
554 578 3.650942 TCAACATTTCCCCACTGAGTAGT 59.349 43.478 0.00 0.00 37.75 2.73
555 579 4.104102 TCAACATTTCCCCACTGAGTAGTT 59.896 41.667 0.00 0.00 34.07 2.24
556 580 4.287766 ACATTTCCCCACTGAGTAGTTC 57.712 45.455 0.00 0.00 34.07 3.01
557 581 3.009143 ACATTTCCCCACTGAGTAGTTCC 59.991 47.826 0.00 0.00 34.07 3.62
558 582 2.715763 TTCCCCACTGAGTAGTTCCT 57.284 50.000 0.00 0.00 34.07 3.36
559 583 3.839323 TTCCCCACTGAGTAGTTCCTA 57.161 47.619 0.00 0.00 34.07 2.94
560 584 3.383698 TCCCCACTGAGTAGTTCCTAG 57.616 52.381 0.00 0.00 34.07 3.02
561 585 2.653366 TCCCCACTGAGTAGTTCCTAGT 59.347 50.000 0.00 0.00 34.07 2.57
724 748 1.885871 ACGGCCTAGTAACGTGGAC 59.114 57.895 0.00 0.00 39.64 4.02
793 817 1.276140 CGGGTGGGAGGGAAATACCA 61.276 60.000 0.00 0.00 41.20 3.25
824 848 6.370442 TCCAATAATTAACTTCGGTCACACAG 59.630 38.462 0.00 0.00 0.00 3.66
827 851 4.602340 ATTAACTTCGGTCACACAGAGT 57.398 40.909 0.00 0.00 0.00 3.24
828 852 5.717078 ATTAACTTCGGTCACACAGAGTA 57.283 39.130 0.00 0.00 0.00 2.59
830 854 1.269998 ACTTCGGTCACACAGAGTAGC 59.730 52.381 0.00 0.00 0.00 3.58
831 855 0.601558 TTCGGTCACACAGAGTAGCC 59.398 55.000 0.00 0.00 0.00 3.93
832 856 1.154016 CGGTCACACAGAGTAGCCG 60.154 63.158 0.00 0.00 39.26 5.52
833 857 1.215647 GGTCACACAGAGTAGCCGG 59.784 63.158 0.00 0.00 0.00 6.13
834 858 1.446272 GTCACACAGAGTAGCCGGC 60.446 63.158 21.89 21.89 0.00 6.13
835 859 2.125512 CACACAGAGTAGCCGGCC 60.126 66.667 26.15 9.10 0.00 6.13
836 860 3.760035 ACACAGAGTAGCCGGCCG 61.760 66.667 26.15 21.04 0.00 6.13
857 881 0.107116 ACCCGCACGTATCTCTCTCT 60.107 55.000 0.00 0.00 0.00 3.10
859 883 1.588674 CCGCACGTATCTCTCTCTCT 58.411 55.000 0.00 0.00 0.00 3.10
870 960 0.533978 TCTCTCTCTCTCCATCGGCG 60.534 60.000 0.00 0.00 0.00 6.46
970 1077 4.753877 TCGCCTCTCGAACGCACG 62.754 66.667 0.00 0.00 45.36 5.34
979 1086 2.372690 CGAACGCACGAGGGAACAG 61.373 63.158 3.50 0.00 35.09 3.16
1291 1414 4.400961 GTCTGCCGCCTCCAAGCT 62.401 66.667 0.00 0.00 0.00 3.74
1292 1415 4.087892 TCTGCCGCCTCCAAGCTC 62.088 66.667 0.00 0.00 0.00 4.09
1325 1455 2.802667 CTCCGATCGCTTGCGTTGG 61.803 63.158 10.32 14.09 0.00 3.77
1388 1527 2.630137 GTACGTGCGTACCTTCGAC 58.370 57.895 20.31 0.40 43.60 4.20
1413 1552 1.755384 GGGCGAGGGAGGGATTAAG 59.245 63.158 0.00 0.00 0.00 1.85
1509 1648 3.639672 ACCCGTAATAACTTTCTGGGG 57.360 47.619 0.00 0.00 39.54 4.96
1536 1675 1.007336 GCGTTCTAGGTGTCACCGTG 61.007 60.000 16.44 12.79 44.90 4.94
1550 1689 1.102978 ACCGTGCTCCATTATTTGCC 58.897 50.000 0.00 0.00 0.00 4.52
1562 1701 7.521261 GCTCCATTATTTGCCAGTATCTTCTTC 60.521 40.741 0.00 0.00 0.00 2.87
1577 1716 6.613153 ATCTTCTTCCCTATTCTATTCCCG 57.387 41.667 0.00 0.00 0.00 5.14
1632 1775 4.512961 TGCTGTGCGGCGATCGAT 62.513 61.111 21.57 0.00 42.43 3.59
1633 1776 3.696426 GCTGTGCGGCGATCGATC 61.696 66.667 21.57 15.68 42.43 3.69
1717 1863 4.760047 CCAAGGACGAGGTGGCGG 62.760 72.222 0.00 0.00 35.12 6.13
1836 1982 2.260869 AAAGGTGCGTTCGCATGCT 61.261 52.632 21.98 7.47 43.37 3.79
1842 1988 2.103042 GCGTTCGCATGCTTCTCCT 61.103 57.895 17.13 0.00 31.45 3.69
1845 1991 0.933796 GTTCGCATGCTTCTCCTAGC 59.066 55.000 17.13 0.00 41.59 3.42
1861 2007 2.932614 CCTAGCTTCCGAATGTTCACTG 59.067 50.000 0.00 0.00 0.00 3.66
1900 2048 1.512694 GGCTCGGCCCAAATCTTTG 59.487 57.895 0.00 0.00 44.06 2.77
1936 2084 1.004560 CATCGACGGGGATCATGGG 60.005 63.158 0.00 0.00 0.00 4.00
1966 2114 1.419374 GCGGCTCGTACCAATATCTG 58.581 55.000 0.00 0.00 0.00 2.90
2003 2152 2.278206 CCTCGTCATCGCTGTCCG 60.278 66.667 0.00 0.00 36.96 4.79
2045 2194 3.345808 CGTGTCACCAACCCTGCG 61.346 66.667 0.00 0.00 0.00 5.18
2051 2201 1.040339 TCACCAACCCTGCGCTTTTT 61.040 50.000 9.73 0.00 0.00 1.94
2052 2202 0.597377 CACCAACCCTGCGCTTTTTC 60.597 55.000 9.73 0.00 0.00 2.29
2054 2204 1.006220 CAACCCTGCGCTTTTTCCC 60.006 57.895 9.73 0.00 0.00 3.97
2055 2205 1.152546 AACCCTGCGCTTTTTCCCT 60.153 52.632 9.73 0.00 0.00 4.20
2058 2208 1.272480 ACCCTGCGCTTTTTCCCTTAT 60.272 47.619 9.73 0.00 0.00 1.73
2090 2241 4.113617 CAGTCGGTGGAGGAGGAA 57.886 61.111 0.00 0.00 0.00 3.36
2374 2563 7.007009 GTGTATGTATGTGTAAAATGTTGCGTG 59.993 37.037 0.00 0.00 0.00 5.34
2392 2581 4.166888 GCTGCGGCTCCAGATGGA 62.167 66.667 11.21 0.79 43.08 3.41
2394 2583 1.597302 CTGCGGCTCCAGATGGATG 60.597 63.158 1.15 0.00 44.46 3.51
2395 2584 2.976903 GCGGCTCCAGATGGATGC 60.977 66.667 1.15 8.17 44.46 3.91
2396 2585 2.281345 CGGCTCCAGATGGATGCC 60.281 66.667 22.40 22.40 46.14 4.40
2401 2592 1.270732 GCTCCAGATGGATGCCTAGTG 60.271 57.143 1.15 0.00 44.46 2.74
2404 2595 2.090775 TCCAGATGGATGCCTAGTGGTA 60.091 50.000 0.00 0.00 39.78 3.25
2408 2599 4.219507 CAGATGGATGCCTAGTGGTAGTAG 59.780 50.000 0.00 0.00 35.27 2.57
2412 2603 3.506844 GGATGCCTAGTGGTAGTAGTAGC 59.493 52.174 0.00 0.00 35.27 3.58
2459 2650 4.498916 GTGTAAAAGTGTGTAACGTGACG 58.501 43.478 2.24 2.24 42.39 4.35
2473 2667 3.483421 ACGTGACGGATGATATGGACTA 58.517 45.455 10.66 0.00 0.00 2.59
2597 2792 3.539604 AGGCTCAATCTCTTTTGATCGG 58.460 45.455 0.00 0.00 35.20 4.18
2627 2822 1.869774 TCGGGATGCTCAATTGATCG 58.130 50.000 8.96 6.82 0.00 3.69
2628 2823 1.412343 TCGGGATGCTCAATTGATCGA 59.588 47.619 8.96 8.84 0.00 3.59
2629 2824 2.037641 TCGGGATGCTCAATTGATCGAT 59.962 45.455 8.96 0.00 0.00 3.59
2630 2825 2.414481 CGGGATGCTCAATTGATCGATC 59.586 50.000 18.72 18.72 0.00 3.69
2631 2826 2.414481 GGGATGCTCAATTGATCGATCG 59.586 50.000 20.03 9.36 0.00 3.69
2632 2827 3.320626 GGATGCTCAATTGATCGATCGA 58.679 45.455 21.86 21.86 0.00 3.59
2633 2828 3.931468 GGATGCTCAATTGATCGATCGAT 59.069 43.478 29.76 29.76 37.59 3.59
2656 2851 0.753479 TCGATCTCCAGTCAGAGGCC 60.753 60.000 0.00 0.00 34.46 5.19
2657 2852 0.754957 CGATCTCCAGTCAGAGGCCT 60.755 60.000 3.86 3.86 34.46 5.19
2665 2860 1.004440 GTCAGAGGCCTGCTCGTTT 60.004 57.895 12.00 0.00 40.20 3.60
2734 2930 3.566322 ACGTGTAGCAGAGACTATCATCC 59.434 47.826 0.00 0.00 0.00 3.51
2748 2944 3.353836 ATCCAACACGTGCACGGC 61.354 61.111 39.21 3.05 44.95 5.68
2779 2975 0.467290 GTCTGATCTCCCTCGCTCCT 60.467 60.000 0.00 0.00 0.00 3.69
2780 2976 0.179004 TCTGATCTCCCTCGCTCCTC 60.179 60.000 0.00 0.00 0.00 3.71
2781 2977 1.152652 TGATCTCCCTCGCTCCTCC 60.153 63.158 0.00 0.00 0.00 4.30
2831 3036 0.690411 CCTGGTCTCTGGGCTGATCT 60.690 60.000 0.00 0.00 0.00 2.75
2833 3038 0.041684 TGGTCTCTGGGCTGATCTGA 59.958 55.000 3.42 0.00 0.00 3.27
2836 3041 2.037901 GTCTCTGGGCTGATCTGATCA 58.962 52.381 18.61 18.61 37.76 2.92
2868 3074 4.241555 CCAGGGAGGGATTCGGCG 62.242 72.222 0.00 0.00 0.00 6.46
2894 3100 1.069668 TCAGACGATGCATGGATGGAG 59.930 52.381 16.26 4.51 0.00 3.86
2895 3101 0.395686 AGACGATGCATGGATGGAGG 59.604 55.000 16.26 0.00 0.00 4.30
2898 3104 0.604780 CGATGCATGGATGGAGGGAC 60.605 60.000 2.46 0.00 0.00 4.46
2899 3105 0.475475 GATGCATGGATGGAGGGACA 59.525 55.000 2.46 0.00 0.00 4.02
2903 3109 1.544982 GCATGGATGGAGGGACAGATG 60.545 57.143 0.00 0.00 0.00 2.90
2921 3127 2.125106 GCGTGTGGGAGATGGGTC 60.125 66.667 0.00 0.00 0.00 4.46
2944 3159 1.878656 GACTGACCCGACCTGACCTG 61.879 65.000 0.00 0.00 0.00 4.00
2945 3160 1.606601 CTGACCCGACCTGACCTGA 60.607 63.158 0.00 0.00 0.00 3.86
2946 3161 1.878656 CTGACCCGACCTGACCTGAC 61.879 65.000 0.00 0.00 0.00 3.51
2947 3162 2.603776 ACCCGACCTGACCTGACC 60.604 66.667 0.00 0.00 0.00 4.02
2948 3163 2.283966 CCCGACCTGACCTGACCT 60.284 66.667 0.00 0.00 0.00 3.85
3014 3232 2.632028 AGCTGGTATCTGTATCTGCCTG 59.368 50.000 0.00 0.00 36.77 4.85
3023 3241 0.103208 GTATCTGCCTGTCCGTCTGG 59.897 60.000 0.00 0.00 38.06 3.86
3024 3242 0.033503 TATCTGCCTGTCCGTCTGGA 60.034 55.000 5.28 0.00 43.88 3.86
3099 3317 2.470821 AGACAAGAAAAGTCGACACGG 58.529 47.619 19.50 2.26 40.84 4.94
3226 3444 1.407936 ACCTGATGGACTGATCGGAG 58.592 55.000 9.00 0.00 37.04 4.63
3286 3504 2.630158 TCGTTTCGTTTTGTTCTCCCA 58.370 42.857 0.00 0.00 0.00 4.37
3293 3511 1.000843 GTTTTGTTCTCCCATGGGCAC 59.999 52.381 27.41 21.11 34.68 5.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 9.893305 CTTGTCGAGGTTTTAGTTTATTGAATT 57.107 29.630 0.00 0.00 0.00 2.17
2 3 9.063615 ACTTGTCGAGGTTTTAGTTTATTGAAT 57.936 29.630 0.00 0.00 0.00 2.57
3 4 8.441312 ACTTGTCGAGGTTTTAGTTTATTGAA 57.559 30.769 0.00 0.00 0.00 2.69
4 5 9.545105 TTACTTGTCGAGGTTTTAGTTTATTGA 57.455 29.630 0.00 0.00 0.00 2.57
9 10 8.132995 CCAAATTACTTGTCGAGGTTTTAGTTT 58.867 33.333 0.00 0.00 32.65 2.66
10 11 7.499895 TCCAAATTACTTGTCGAGGTTTTAGTT 59.500 33.333 0.00 0.00 32.65 2.24
11 12 6.993902 TCCAAATTACTTGTCGAGGTTTTAGT 59.006 34.615 0.00 0.00 32.65 2.24
12 13 7.429636 TCCAAATTACTTGTCGAGGTTTTAG 57.570 36.000 0.00 0.00 32.65 1.85
13 14 7.518689 CGTTCCAAATTACTTGTCGAGGTTTTA 60.519 37.037 0.00 0.00 32.65 1.52
14 15 6.500910 GTTCCAAATTACTTGTCGAGGTTTT 58.499 36.000 0.00 0.00 32.65 2.43
15 16 5.277634 CGTTCCAAATTACTTGTCGAGGTTT 60.278 40.000 0.00 0.00 32.65 3.27
16 17 4.212636 CGTTCCAAATTACTTGTCGAGGTT 59.787 41.667 0.00 0.00 32.65 3.50
17 18 3.744426 CGTTCCAAATTACTTGTCGAGGT 59.256 43.478 0.00 0.00 32.65 3.85
18 19 3.124636 CCGTTCCAAATTACTTGTCGAGG 59.875 47.826 0.00 0.00 32.65 4.63
19 20 3.991773 TCCGTTCCAAATTACTTGTCGAG 59.008 43.478 0.00 0.00 32.65 4.04
20 21 3.991773 CTCCGTTCCAAATTACTTGTCGA 59.008 43.478 0.00 0.00 32.65 4.20
21 22 3.124636 CCTCCGTTCCAAATTACTTGTCG 59.875 47.826 0.00 0.00 32.65 4.35
22 23 4.070009 ACCTCCGTTCCAAATTACTTGTC 58.930 43.478 0.00 0.00 32.65 3.18
23 24 4.094830 ACCTCCGTTCCAAATTACTTGT 57.905 40.909 0.00 0.00 32.65 3.16
24 25 6.563222 TTTACCTCCGTTCCAAATTACTTG 57.437 37.500 0.00 0.00 34.52 3.16
25 26 6.016024 GGTTTTACCTCCGTTCCAAATTACTT 60.016 38.462 0.00 0.00 34.73 2.24
26 27 5.474532 GGTTTTACCTCCGTTCCAAATTACT 59.525 40.000 0.00 0.00 34.73 2.24
27 28 5.241285 TGGTTTTACCTCCGTTCCAAATTAC 59.759 40.000 0.00 0.00 39.58 1.89
28 29 5.241285 GTGGTTTTACCTCCGTTCCAAATTA 59.759 40.000 0.00 0.00 39.58 1.40
29 30 4.038282 GTGGTTTTACCTCCGTTCCAAATT 59.962 41.667 0.00 0.00 39.58 1.82
30 31 3.570975 GTGGTTTTACCTCCGTTCCAAAT 59.429 43.478 0.00 0.00 39.58 2.32
31 32 2.950975 GTGGTTTTACCTCCGTTCCAAA 59.049 45.455 0.00 0.00 39.58 3.28
32 33 2.574450 GTGGTTTTACCTCCGTTCCAA 58.426 47.619 0.00 0.00 39.58 3.53
33 34 1.540797 CGTGGTTTTACCTCCGTTCCA 60.541 52.381 0.00 0.00 39.58 3.53
34 35 1.150827 CGTGGTTTTACCTCCGTTCC 58.849 55.000 0.00 0.00 39.58 3.62
35 36 1.794701 GTCGTGGTTTTACCTCCGTTC 59.205 52.381 0.00 0.00 39.58 3.95
36 37 1.138661 TGTCGTGGTTTTACCTCCGTT 59.861 47.619 0.00 0.00 39.58 4.44
37 38 0.752054 TGTCGTGGTTTTACCTCCGT 59.248 50.000 0.00 0.00 39.58 4.69
38 39 1.796459 CTTGTCGTGGTTTTACCTCCG 59.204 52.381 0.00 0.00 39.58 4.63
39 40 2.842457 ACTTGTCGTGGTTTTACCTCC 58.158 47.619 0.00 0.00 39.58 4.30
40 41 6.549912 AATTACTTGTCGTGGTTTTACCTC 57.450 37.500 0.00 0.00 39.58 3.85
41 42 6.238814 CCAAATTACTTGTCGTGGTTTTACCT 60.239 38.462 0.00 0.00 34.49 3.08
42 43 5.916320 CCAAATTACTTGTCGTGGTTTTACC 59.084 40.000 0.00 0.00 34.17 2.85
43 44 6.727215 TCCAAATTACTTGTCGTGGTTTTAC 58.273 36.000 0.00 0.00 32.65 2.01
44 45 6.939132 TCCAAATTACTTGTCGTGGTTTTA 57.061 33.333 0.00 0.00 32.65 1.52
45 46 5.838531 TCCAAATTACTTGTCGTGGTTTT 57.161 34.783 0.00 0.00 32.65 2.43
46 47 5.584442 GTTCCAAATTACTTGTCGTGGTTT 58.416 37.500 0.00 0.00 32.65 3.27
47 48 4.260866 CGTTCCAAATTACTTGTCGTGGTT 60.261 41.667 0.00 0.00 32.65 3.67
48 49 3.249080 CGTTCCAAATTACTTGTCGTGGT 59.751 43.478 0.00 0.00 32.65 4.16
49 50 3.364565 CCGTTCCAAATTACTTGTCGTGG 60.365 47.826 0.00 0.00 32.65 4.94
50 51 3.495377 TCCGTTCCAAATTACTTGTCGTG 59.505 43.478 0.00 0.00 32.65 4.35
51 52 3.731089 TCCGTTCCAAATTACTTGTCGT 58.269 40.909 0.00 0.00 32.65 4.34
52 53 3.124636 CCTCCGTTCCAAATTACTTGTCG 59.875 47.826 0.00 0.00 32.65 4.35
53 54 3.439129 CCCTCCGTTCCAAATTACTTGTC 59.561 47.826 0.00 0.00 32.65 3.18
54 55 3.073356 TCCCTCCGTTCCAAATTACTTGT 59.927 43.478 0.00 0.00 32.65 3.16
55 56 3.681593 TCCCTCCGTTCCAAATTACTTG 58.318 45.455 0.00 0.00 34.52 3.16
56 57 3.329814 ACTCCCTCCGTTCCAAATTACTT 59.670 43.478 0.00 0.00 0.00 2.24
57 58 2.910977 ACTCCCTCCGTTCCAAATTACT 59.089 45.455 0.00 0.00 0.00 2.24
58 59 3.345508 ACTCCCTCCGTTCCAAATTAC 57.654 47.619 0.00 0.00 0.00 1.89
59 60 4.533311 AGTTACTCCCTCCGTTCCAAATTA 59.467 41.667 0.00 0.00 0.00 1.40
60 61 3.329814 AGTTACTCCCTCCGTTCCAAATT 59.670 43.478 0.00 0.00 0.00 1.82
61 62 2.910977 AGTTACTCCCTCCGTTCCAAAT 59.089 45.455 0.00 0.00 0.00 2.32
62 63 2.332117 AGTTACTCCCTCCGTTCCAAA 58.668 47.619 0.00 0.00 0.00 3.28
63 64 2.019807 AGTTACTCCCTCCGTTCCAA 57.980 50.000 0.00 0.00 0.00 3.53
64 65 2.905415 TAGTTACTCCCTCCGTTCCA 57.095 50.000 0.00 0.00 0.00 3.53
65 66 5.859205 TTAATAGTTACTCCCTCCGTTCC 57.141 43.478 0.00 0.00 0.00 3.62
66 67 6.814043 ACATTAATAGTTACTCCCTCCGTTC 58.186 40.000 0.00 0.00 0.00 3.95
67 68 6.183360 GGACATTAATAGTTACTCCCTCCGTT 60.183 42.308 0.00 0.00 0.00 4.44
68 69 5.303845 GGACATTAATAGTTACTCCCTCCGT 59.696 44.000 0.00 0.00 0.00 4.69
69 70 5.303589 TGGACATTAATAGTTACTCCCTCCG 59.696 44.000 0.00 0.00 0.00 4.63
70 71 6.742559 TGGACATTAATAGTTACTCCCTCC 57.257 41.667 0.00 0.00 0.00 4.30
104 105 7.631007 AGGGACCGAAATTATACTTTTCTCTT 58.369 34.615 6.03 0.00 32.18 2.85
108 109 6.260271 CCTGAGGGACCGAAATTATACTTTTC 59.740 42.308 0.00 0.00 33.58 2.29
143 144 3.221771 TGTCACCCAAAGACAATTGAGG 58.778 45.455 13.59 5.66 42.57 3.86
173 190 6.127810 ACTTTTCCGGTTTTGAGACTTAAC 57.872 37.500 0.00 0.00 0.00 2.01
176 193 5.647589 GAAACTTTTCCGGTTTTGAGACTT 58.352 37.500 0.00 0.00 37.07 3.01
182 199 3.110358 GGACGAAACTTTTCCGGTTTTG 58.890 45.455 0.00 0.33 41.35 2.44
192 209 5.935206 ACAATTTGGTTTTGGACGAAACTTT 59.065 32.000 13.27 2.81 38.52 2.66
194 211 5.079689 ACAATTTGGTTTTGGACGAAACT 57.920 34.783 13.27 0.00 38.52 2.66
200 217 8.831715 AATATGAAGACAATTTGGTTTTGGAC 57.168 30.769 0.78 0.00 0.00 4.02
268 291 0.591659 GGGAAAACTTGGAGCACGTC 59.408 55.000 0.00 0.00 0.00 4.34
323 347 0.949105 GTAGTGCCACCAAGGACACG 60.949 60.000 0.00 0.00 44.21 4.49
332 356 1.153958 GGACGTACGTAGTGCCACC 60.154 63.158 22.87 12.60 45.73 4.61
337 361 0.098376 GGCAGAGGACGTACGTAGTG 59.902 60.000 22.87 16.24 45.73 2.74
338 362 1.364626 CGGCAGAGGACGTACGTAGT 61.365 60.000 22.87 11.56 41.88 2.73
339 363 1.351012 CGGCAGAGGACGTACGTAG 59.649 63.158 22.87 10.09 41.88 3.51
341 365 3.437795 CCGGCAGAGGACGTACGT 61.438 66.667 23.04 23.04 46.78 3.57
342 366 4.849329 GCCGGCAGAGGACGTACG 62.849 72.222 24.80 15.01 46.78 3.67
343 367 4.509737 GGCCGGCAGAGGACGTAC 62.510 72.222 30.85 1.84 46.78 3.67
347 371 4.554036 GATGGGCCGGCAGAGGAC 62.554 72.222 30.85 9.47 39.05 3.85
357 381 0.753111 GTGTGGAATGAGGATGGGCC 60.753 60.000 0.00 0.00 0.00 5.80
426 450 8.655970 CGAGAACAATGAATCTGTAACATGTTA 58.344 33.333 14.35 14.35 0.00 2.41
427 451 7.521529 CGAGAACAATGAATCTGTAACATGTT 58.478 34.615 16.68 16.68 0.00 2.71
428 452 6.402550 GCGAGAACAATGAATCTGTAACATGT 60.403 38.462 0.00 0.00 0.00 3.21
429 453 5.961843 GCGAGAACAATGAATCTGTAACATG 59.038 40.000 0.00 0.00 0.00 3.21
430 454 5.643348 TGCGAGAACAATGAATCTGTAACAT 59.357 36.000 0.00 0.00 0.00 2.71
431 455 4.994217 TGCGAGAACAATGAATCTGTAACA 59.006 37.500 0.00 0.00 0.00 2.41
432 456 5.530519 TGCGAGAACAATGAATCTGTAAC 57.469 39.130 0.00 0.00 0.00 2.50
433 457 5.390885 GCTTGCGAGAACAATGAATCTGTAA 60.391 40.000 4.70 0.00 0.00 2.41
434 458 4.093408 GCTTGCGAGAACAATGAATCTGTA 59.907 41.667 4.70 0.00 0.00 2.74
435 459 3.120060 GCTTGCGAGAACAATGAATCTGT 60.120 43.478 4.70 0.00 0.00 3.41
436 460 3.126514 AGCTTGCGAGAACAATGAATCTG 59.873 43.478 4.70 0.00 0.00 2.90
437 461 3.341823 AGCTTGCGAGAACAATGAATCT 58.658 40.909 4.70 0.00 0.00 2.40
438 462 3.754188 AGCTTGCGAGAACAATGAATC 57.246 42.857 4.70 0.00 0.00 2.52
439 463 3.503363 TCAAGCTTGCGAGAACAATGAAT 59.497 39.130 21.99 0.00 0.00 2.57
440 464 2.877786 TCAAGCTTGCGAGAACAATGAA 59.122 40.909 21.99 0.00 0.00 2.57
441 465 2.224079 GTCAAGCTTGCGAGAACAATGA 59.776 45.455 21.99 0.00 0.00 2.57
451 475 2.693797 AAGTTGATGTCAAGCTTGCG 57.306 45.000 21.99 0.00 36.39 4.85
453 477 5.239306 TGTCCTAAAGTTGATGTCAAGCTTG 59.761 40.000 20.81 20.81 36.39 4.01
456 480 5.689383 TTGTCCTAAAGTTGATGTCAAGC 57.311 39.130 0.00 0.00 36.39 4.01
536 560 3.264450 AGGAACTACTCAGTGGGGAAATG 59.736 47.826 0.00 0.00 36.02 2.32
548 572 6.990798 AGTACCAAAACACTAGGAACTACTC 58.009 40.000 0.00 0.00 41.75 2.59
549 573 6.781507 AGAGTACCAAAACACTAGGAACTACT 59.218 38.462 0.00 0.00 41.75 2.57
550 574 6.990798 AGAGTACCAAAACACTAGGAACTAC 58.009 40.000 0.00 0.00 41.75 2.73
551 575 6.210185 GGAGAGTACCAAAACACTAGGAACTA 59.790 42.308 0.00 0.00 41.75 2.24
552 576 5.011840 GGAGAGTACCAAAACACTAGGAACT 59.988 44.000 0.00 0.00 46.37 3.01
553 577 5.236282 GGAGAGTACCAAAACACTAGGAAC 58.764 45.833 0.00 0.00 0.00 3.62
554 578 4.285260 GGGAGAGTACCAAAACACTAGGAA 59.715 45.833 0.00 0.00 0.00 3.36
555 579 3.836562 GGGAGAGTACCAAAACACTAGGA 59.163 47.826 0.00 0.00 0.00 2.94
556 580 3.055312 GGGGAGAGTACCAAAACACTAGG 60.055 52.174 0.00 0.00 0.00 3.02
557 581 3.368116 CGGGGAGAGTACCAAAACACTAG 60.368 52.174 0.00 0.00 0.00 2.57
558 582 2.564062 CGGGGAGAGTACCAAAACACTA 59.436 50.000 0.00 0.00 0.00 2.74
559 583 1.346722 CGGGGAGAGTACCAAAACACT 59.653 52.381 0.00 0.00 0.00 3.55
560 584 1.609841 CCGGGGAGAGTACCAAAACAC 60.610 57.143 0.00 0.00 0.00 3.32
561 585 0.688487 CCGGGGAGAGTACCAAAACA 59.312 55.000 0.00 0.00 0.00 2.83
640 664 2.950172 TTTTTCGGCTCTCGCGTGC 61.950 57.895 5.77 9.49 39.05 5.34
697 721 2.622903 TACTAGGCCGTGCACGCATC 62.623 60.000 33.17 22.29 38.18 3.91
710 734 3.015327 AGCTACAGTCCACGTTACTAGG 58.985 50.000 0.17 0.00 0.00 3.02
712 736 6.764308 ATTTAGCTACAGTCCACGTTACTA 57.236 37.500 0.00 0.00 0.00 1.82
724 748 2.351726 GGTGTGCCGAATTTAGCTACAG 59.648 50.000 0.00 0.00 0.00 2.74
774 798 1.276140 TGGTATTTCCCTCCCACCCG 61.276 60.000 0.00 0.00 34.77 5.28
784 808 7.418337 AATTATTGGAAGTGGTGGTATTTCC 57.582 36.000 0.00 0.00 39.59 3.13
793 817 6.243148 ACCGAAGTTAATTATTGGAAGTGGT 58.757 36.000 0.00 0.00 0.00 4.16
795 819 7.094975 TGTGACCGAAGTTAATTATTGGAAGTG 60.095 37.037 0.00 0.00 0.00 3.16
836 860 1.589196 GAGAGATACGTGCGGGTGC 60.589 63.158 0.00 0.00 43.20 5.01
837 861 0.029567 GAGAGAGATACGTGCGGGTG 59.970 60.000 0.00 0.00 0.00 4.61
838 862 0.107116 AGAGAGAGATACGTGCGGGT 60.107 55.000 0.00 0.00 0.00 5.28
839 863 0.589223 GAGAGAGAGATACGTGCGGG 59.411 60.000 0.00 0.00 0.00 6.13
857 881 2.124860 TCGACGCCGATGGAGAGA 60.125 61.111 0.00 0.00 40.30 3.10
946 1051 4.816984 TCGAGAGGCGAGGGGGTC 62.817 72.222 0.00 0.00 45.59 4.46
962 1068 1.006571 TCTGTTCCCTCGTGCGTTC 60.007 57.895 0.00 0.00 0.00 3.95
994 1102 1.207488 TGGCAGTTACCCATGGCTCT 61.207 55.000 6.09 0.00 42.16 4.09
995 1103 0.749454 CTGGCAGTTACCCATGGCTC 60.749 60.000 6.09 0.00 42.16 4.70
998 1106 1.754234 GCCTGGCAGTTACCCATGG 60.754 63.158 15.17 4.14 0.00 3.66
1095 1203 4.776322 TTGGCGGCCATGACCTCG 62.776 66.667 24.49 0.00 31.53 4.63
1338 1468 1.033574 TTGACGCCGGGAAACATTTT 58.966 45.000 2.18 0.00 0.00 1.82
1509 1648 2.583593 CCTAGAACGCCAGCTCGC 60.584 66.667 0.00 0.00 0.00 5.03
1536 1675 5.767168 AGAAGATACTGGCAAATAATGGAGC 59.233 40.000 0.00 0.00 0.00 4.70
1550 1689 8.536175 GGGAATAGAATAGGGAAGAAGATACTG 58.464 40.741 0.00 0.00 0.00 2.74
1562 1701 1.204941 CTCGGCGGGAATAGAATAGGG 59.795 57.143 0.00 0.00 0.00 3.53
1577 1716 2.012673 TCTCGTTAGTTACTCCTCGGC 58.987 52.381 0.00 0.00 0.00 5.54
1836 1982 3.513912 TGAACATTCGGAAGCTAGGAGAA 59.486 43.478 0.00 0.00 0.00 2.87
1842 1988 2.935238 GCCAGTGAACATTCGGAAGCTA 60.935 50.000 0.00 0.00 0.00 3.32
1845 1991 1.197721 GTGCCAGTGAACATTCGGAAG 59.802 52.381 0.00 0.00 0.00 3.46
1861 2007 1.004799 TGGTTGCAATGCATGTGCC 60.005 52.632 22.57 9.94 41.49 5.01
1900 2048 2.884207 GCGACCGAACGGATCACC 60.884 66.667 20.14 4.58 38.96 4.02
1949 2097 1.419374 CGCAGATATTGGTACGAGCC 58.581 55.000 0.00 0.00 0.00 4.70
1966 2114 3.386867 CTGGCAGTCAATTCGGCGC 62.387 63.158 6.28 0.00 0.00 6.53
2003 2152 3.063045 CGTTTCGGGGCATTAACTAGTTC 59.937 47.826 12.39 0.00 0.00 3.01
2045 2194 6.510536 CATGATCTGGAATAAGGGAAAAAGC 58.489 40.000 0.00 0.00 0.00 3.51
2051 2201 2.550855 GCGCATGATCTGGAATAAGGGA 60.551 50.000 0.30 0.00 0.00 4.20
2052 2202 1.808945 GCGCATGATCTGGAATAAGGG 59.191 52.381 0.30 0.00 0.00 3.95
2054 2204 2.483106 CTGGCGCATGATCTGGAATAAG 59.517 50.000 10.83 0.00 0.00 1.73
2055 2205 2.158769 ACTGGCGCATGATCTGGAATAA 60.159 45.455 10.83 0.00 0.00 1.40
2058 2208 0.462581 GACTGGCGCATGATCTGGAA 60.463 55.000 10.83 0.00 0.00 3.53
2123 2280 1.164041 CGTTTGTTCCTGCCTTCGGT 61.164 55.000 0.00 0.00 0.00 4.69
2130 2287 2.553079 TTGTTGTCGTTTGTTCCTGC 57.447 45.000 0.00 0.00 0.00 4.85
2136 2293 0.736053 ACGCCATTGTTGTCGTTTGT 59.264 45.000 0.00 0.00 0.00 2.83
2391 2580 4.142790 TGCTACTACTACCACTAGGCATC 58.857 47.826 0.00 0.00 39.06 3.91
2392 2581 4.180377 TGCTACTACTACCACTAGGCAT 57.820 45.455 0.00 0.00 39.06 4.40
2394 2583 3.952967 AGTTGCTACTACTACCACTAGGC 59.047 47.826 0.00 0.00 32.93 3.93
2395 2584 4.948621 ACAGTTGCTACTACTACCACTAGG 59.051 45.833 0.00 0.00 35.21 3.02
2396 2585 5.676584 GCACAGTTGCTACTACTACCACTAG 60.677 48.000 0.00 0.00 46.17 2.57
2412 2603 2.226437 GTGACCCATACTTGCACAGTTG 59.774 50.000 6.82 5.89 36.88 3.16
2459 2650 6.365970 ACCAGTCAATAGTCCATATCATCC 57.634 41.667 0.00 0.00 0.00 3.51
2473 2667 1.550976 GGTTCTCGAGGACCAGTCAAT 59.449 52.381 34.05 0.00 0.00 2.57
2553 2748 4.219070 TCCCGATACGTAATAATGTGGGAG 59.781 45.833 0.00 0.00 38.19 4.30
2597 2792 1.691434 AGCATCCCGATCTTTCTCTCC 59.309 52.381 0.00 0.00 0.00 3.71
2632 2827 3.073678 CTCTGACTGGAGATCGATCGAT 58.926 50.000 29.76 29.76 35.52 3.59
2633 2828 2.488952 CTCTGACTGGAGATCGATCGA 58.511 52.381 21.86 21.86 35.52 3.59
2634 2829 1.535028 CCTCTGACTGGAGATCGATCG 59.465 57.143 19.33 9.36 35.52 3.69
2635 2830 1.269448 GCCTCTGACTGGAGATCGATC 59.731 57.143 17.91 17.91 35.52 3.69
2636 2831 1.327303 GCCTCTGACTGGAGATCGAT 58.673 55.000 0.00 0.00 35.52 3.59
2637 2832 0.753479 GGCCTCTGACTGGAGATCGA 60.753 60.000 0.00 0.00 35.52 3.59
2638 2833 0.754957 AGGCCTCTGACTGGAGATCG 60.755 60.000 0.00 0.00 35.52 3.69
2639 2834 0.752054 CAGGCCTCTGACTGGAGATC 59.248 60.000 0.00 0.00 43.49 2.75
2640 2835 1.336632 GCAGGCCTCTGACTGGAGAT 61.337 60.000 0.00 0.00 43.49 2.75
2641 2836 1.986757 GCAGGCCTCTGACTGGAGA 60.987 63.158 0.00 0.00 43.49 3.71
2642 2837 1.958902 GAGCAGGCCTCTGACTGGAG 61.959 65.000 0.00 0.00 43.49 3.86
2656 2851 0.674581 TCAGATGCCCAAACGAGCAG 60.675 55.000 0.00 0.00 43.38 4.24
2657 2852 0.250684 TTCAGATGCCCAAACGAGCA 60.251 50.000 0.00 0.00 44.45 4.26
2665 2860 2.046023 CCGCTGTTCAGATGCCCA 60.046 61.111 3.84 0.00 0.00 5.36
2701 2896 1.091771 GCTACACGTGCATGATGGCT 61.092 55.000 17.22 0.00 34.04 4.75
2734 2930 3.629491 GATCGCCGTGCACGTGTTG 62.629 63.158 34.81 21.74 37.74 3.33
2748 2944 4.635765 GGGAGATCAGACTATCAGAGATCG 59.364 50.000 0.00 0.00 39.91 3.69
2788 2984 1.152546 AGAGCAAACCGGGGCTTTT 60.153 52.632 17.02 7.76 41.22 2.27
2802 2998 3.678951 GAGACCAGGCAGGCAGAGC 62.679 68.421 0.00 0.00 43.14 4.09
2831 3036 1.941209 GCTTTGTCACGGAGCTGATCA 60.941 52.381 0.00 0.00 33.72 2.92
2833 3038 0.674895 GGCTTTGTCACGGAGCTGAT 60.675 55.000 0.00 0.00 36.66 2.90
2836 3041 1.302033 CTGGCTTTGTCACGGAGCT 60.302 57.895 2.63 0.00 36.66 4.09
2868 3074 4.284123 TGCATCGTCTGAAGCACC 57.716 55.556 0.00 0.00 43.33 5.01
2872 3078 1.871676 CCATCCATGCATCGTCTGAAG 59.128 52.381 0.00 0.00 0.00 3.02
2894 3100 2.436646 CCACACGCCATCTGTCCC 60.437 66.667 0.00 0.00 0.00 4.46
2895 3101 2.436646 CCCACACGCCATCTGTCC 60.437 66.667 0.00 0.00 0.00 4.02
2898 3104 0.812811 CATCTCCCACACGCCATCTG 60.813 60.000 0.00 0.00 0.00 2.90
2899 3105 1.524002 CATCTCCCACACGCCATCT 59.476 57.895 0.00 0.00 0.00 2.90
2903 3109 3.682292 GACCCATCTCCCACACGCC 62.682 68.421 0.00 0.00 0.00 5.68
2944 3159 1.630148 CGGTCAAGTTCGATCAGGTC 58.370 55.000 0.00 0.00 0.00 3.85
2945 3160 0.246635 CCGGTCAAGTTCGATCAGGT 59.753 55.000 0.00 0.00 0.00 4.00
2946 3161 1.084370 GCCGGTCAAGTTCGATCAGG 61.084 60.000 1.90 0.00 0.00 3.86
2947 3162 1.413767 CGCCGGTCAAGTTCGATCAG 61.414 60.000 1.90 0.00 0.00 2.90
2948 3163 1.445410 CGCCGGTCAAGTTCGATCA 60.445 57.895 1.90 0.00 0.00 2.92
3055 3273 1.958323 GCTAGGCTACCGAGCTACC 59.042 63.158 11.00 0.00 46.31 3.18
3099 3317 3.737850 AGCTATCTATGCAGGCACTTTC 58.262 45.455 0.00 0.00 34.60 2.62
3153 3371 1.432251 CCCCTGCACGTACGTAGAG 59.568 63.158 22.34 18.25 0.00 2.43
3155 3373 2.202703 GCCCCTGCACGTACGTAG 60.203 66.667 22.34 15.70 37.47 3.51
3156 3374 2.990395 TGCCCCTGCACGTACGTA 60.990 61.111 22.34 5.54 44.23 3.57


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

AutoCloner maintained by Alex Coulton.