Multiple sequence alignment - TraesCS5A01G513900

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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 TraesCS5A01G513900 chr5A 100.000 2832 0 0 1 2832 677838540 677835709 0.000000e+00 5230.0
1 TraesCS5A01G513900 chr5A 84.948 485 57 10 999 1483 677805297 677804829 7.100000e-131 477.0
2 TraesCS5A01G513900 chr5A 87.733 375 32 5 2111 2483 677804815 677804453 2.610000e-115 425.0
3 TraesCS5A01G513900 chr5A 99.167 120 0 1 2714 2832 677794987 677794868 6.140000e-52 215.0
4 TraesCS5A01G513900 chr5A 72.419 620 85 56 1126 1726 677778278 677777726 4.960000e-23 119.0
5 TraesCS5A01G513900 chr5A 96.078 51 1 1 10 59 312255818 312255768 6.500000e-12 82.4
6 TraesCS5A01G513900 chr4B 84.340 1590 125 61 837 2359 638580381 638578849 0.000000e+00 1443.0
7 TraesCS5A01G513900 chr4B 84.728 478 40 14 2359 2832 638577763 638577315 5.570000e-122 448.0
8 TraesCS5A01G513900 chr4B 85.904 376 49 4 1132 1506 638542589 638542217 5.680000e-107 398.0
9 TraesCS5A01G513900 chr4B 91.353 266 19 2 112 373 638581054 638580789 7.460000e-96 361.0
10 TraesCS5A01G513900 chr4B 87.195 164 15 3 2358 2517 638453495 638453334 6.230000e-42 182.0
11 TraesCS5A01G513900 chr4B 77.703 296 42 18 1437 1720 638422842 638422559 2.920000e-35 159.0
12 TraesCS5A01G513900 chr4B 80.476 210 21 13 2631 2832 638539037 638538840 2.940000e-30 143.0
13 TraesCS5A01G513900 chr4B 89.091 110 8 3 2108 2216 638542205 638542099 1.770000e-27 134.0
14 TraesCS5A01G513900 chr4D 85.843 1328 93 55 836 2142 497628260 497627007 0.000000e+00 1323.0
15 TraesCS5A01G513900 chr4D 84.813 507 60 13 999 1504 497612809 497612319 7.050000e-136 494.0
16 TraesCS5A01G513900 chr4D 84.664 476 31 19 2313 2753 497626740 497626272 1.200000e-118 436.0
17 TraesCS5A01G513900 chr4D 82.639 432 43 11 2111 2517 497612308 497611884 1.250000e-93 353.0
18 TraesCS5A01G513900 chr4D 89.226 297 8 11 199 485 497628768 497628486 1.610000e-92 350.0
19 TraesCS5A01G513900 chr4D 92.742 124 4 2 2714 2832 497611677 497611554 1.040000e-39 174.0
20 TraesCS5A01G513900 chr4D 91.379 116 5 2 618 732 497628482 497628371 1.360000e-33 154.0
21 TraesCS5A01G513900 chr4D 97.959 49 1 0 11 59 338447141 338447189 5.030000e-13 86.1
22 TraesCS5A01G513900 chr4D 100.000 46 0 0 14 59 449453743 449453788 5.030000e-13 86.1
23 TraesCS5A01G513900 chr2D 86.047 258 30 5 1157 1414 645284351 645284602 3.590000e-69 272.0
24 TraesCS5A01G513900 chr2D 100.000 47 0 0 13 59 318335441 318335395 1.400000e-13 87.9
25 TraesCS5A01G513900 chr2B 86.730 211 22 5 1157 1366 627651476 627651681 2.190000e-56 230.0
26 TraesCS5A01G513900 chr3B 100.000 49 0 0 11 59 24694162 24694210 1.080000e-14 91.6
27 TraesCS5A01G513900 chr7A 93.103 58 4 0 2 59 158648161 158648104 5.030000e-13 86.1
28 TraesCS5A01G513900 chr1B 100.000 46 0 0 14 59 198150199 198150154 5.030000e-13 86.1
29 TraesCS5A01G513900 chr6A 96.078 51 1 1 9 59 6917557 6917606 6.500000e-12 82.4
30 TraesCS5A01G513900 chr5D 96.078 51 1 1 9 59 503764635 503764586 6.500000e-12 82.4


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 TraesCS5A01G513900 chr5A 677835709 677838540 2831 True 5230.000000 5230 100.000000 1 2832 1 chr5A.!!$R4 2831
1 TraesCS5A01G513900 chr5A 677804453 677805297 844 True 451.000000 477 86.340500 999 2483 2 chr5A.!!$R5 1484
2 TraesCS5A01G513900 chr4B 638577315 638581054 3739 True 750.666667 1443 86.807000 112 2832 3 chr4B.!!$R4 2720
3 TraesCS5A01G513900 chr4B 638538840 638542589 3749 True 225.000000 398 85.157000 1132 2832 3 chr4B.!!$R3 1700
4 TraesCS5A01G513900 chr4D 497626272 497628768 2496 True 565.750000 1323 87.778000 199 2753 4 chr4D.!!$R2 2554
5 TraesCS5A01G513900 chr4D 497611554 497612809 1255 True 340.333333 494 86.731333 999 2832 3 chr4D.!!$R1 1833

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
553 571 0.03601 ACCCAAGAGAAGACCGCATG 60.036 55.0 0.0 0.0 0.0 4.06 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2173 2313 0.179137 TGCATAACTCGAGCCGACAG 60.179 55.0 13.61 0.0 0.0 3.51 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
42 43 3.520569 TGAAACAAGGCAAAAGACTTGC 58.479 40.909 10.80 0.78 46.03 4.01
52 53 5.678132 GCAAAAGACTTGCCATTTTCATT 57.322 34.783 0.00 0.00 39.38 2.57
53 54 6.063640 GCAAAAGACTTGCCATTTTCATTT 57.936 33.333 0.00 0.00 39.38 2.32
54 55 7.188468 GCAAAAGACTTGCCATTTTCATTTA 57.812 32.000 0.00 0.00 39.38 1.40
55 56 7.638134 GCAAAAGACTTGCCATTTTCATTTAA 58.362 30.769 0.00 0.00 39.38 1.52
56 57 8.291740 GCAAAAGACTTGCCATTTTCATTTAAT 58.708 29.630 0.00 0.00 39.38 1.40
82 83 8.561738 AACTTTTCTTTTCTTTTCTTTTCCCC 57.438 30.769 0.00 0.00 0.00 4.81
83 84 6.816640 ACTTTTCTTTTCTTTTCTTTTCCCCG 59.183 34.615 0.00 0.00 0.00 5.73
84 85 4.929819 TCTTTTCTTTTCTTTTCCCCGG 57.070 40.909 0.00 0.00 0.00 5.73
85 86 4.283337 TCTTTTCTTTTCTTTTCCCCGGT 58.717 39.130 0.00 0.00 0.00 5.28
86 87 4.098807 TCTTTTCTTTTCTTTTCCCCGGTG 59.901 41.667 0.00 0.00 0.00 4.94
87 88 1.989706 TCTTTTCTTTTCCCCGGTGG 58.010 50.000 0.00 0.82 0.00 4.61
88 89 1.495574 TCTTTTCTTTTCCCCGGTGGA 59.504 47.619 7.51 7.51 43.18 4.02
95 96 3.305314 TCCCCGGTGGAATCGAAG 58.695 61.111 9.03 0.00 41.40 3.79
96 97 1.305465 TCCCCGGTGGAATCGAAGA 60.305 57.895 9.03 0.00 41.40 2.87
97 98 0.689745 TCCCCGGTGGAATCGAAGAT 60.690 55.000 9.03 0.00 41.40 2.40
98 99 0.180406 CCCCGGTGGAATCGAAGATT 59.820 55.000 0.00 0.00 37.66 2.40
99 100 1.299541 CCCGGTGGAATCGAAGATTG 58.700 55.000 0.00 0.00 45.12 2.67
100 101 1.299541 CCGGTGGAATCGAAGATTGG 58.700 55.000 0.00 0.00 45.12 3.16
101 102 1.406887 CCGGTGGAATCGAAGATTGGT 60.407 52.381 0.00 0.00 45.12 3.67
102 103 2.356135 CGGTGGAATCGAAGATTGGTT 58.644 47.619 0.00 0.00 45.12 3.67
103 104 2.747446 CGGTGGAATCGAAGATTGGTTT 59.253 45.455 0.00 0.00 45.12 3.27
104 105 3.190535 CGGTGGAATCGAAGATTGGTTTT 59.809 43.478 0.00 0.00 45.12 2.43
105 106 4.320935 CGGTGGAATCGAAGATTGGTTTTT 60.321 41.667 0.00 0.00 45.12 1.94
106 107 4.923281 GGTGGAATCGAAGATTGGTTTTTG 59.077 41.667 0.00 0.00 45.12 2.44
107 108 4.923281 GTGGAATCGAAGATTGGTTTTTGG 59.077 41.667 0.00 0.00 45.12 3.28
108 109 4.586841 TGGAATCGAAGATTGGTTTTTGGT 59.413 37.500 0.00 0.00 45.12 3.67
109 110 5.161358 GGAATCGAAGATTGGTTTTTGGTC 58.839 41.667 0.00 0.00 45.12 4.02
110 111 4.783764 ATCGAAGATTGGTTTTTGGTCC 57.216 40.909 0.00 0.00 45.12 4.46
131 132 0.109913 TGGATGGATGGATGCTGCTC 59.890 55.000 0.00 0.00 0.00 4.26
142 143 3.695606 GCTGCTCTCCCGTGTCCA 61.696 66.667 0.00 0.00 0.00 4.02
170 171 1.660575 ACGTTTGTGGAGTCGCGAG 60.661 57.895 10.24 0.00 0.00 5.03
175 176 1.934220 TTGTGGAGTCGCGAGCTAGG 61.934 60.000 10.24 0.00 0.00 3.02
184 185 1.063811 GCGAGCTAGGGTACGTGAC 59.936 63.158 0.00 0.00 0.00 3.67
188 189 2.603953 GAGCTAGGGTACGTGACAAAC 58.396 52.381 0.00 0.00 0.00 2.93
191 192 2.029649 GCTAGGGTACGTGACAAACTCA 60.030 50.000 0.00 0.00 0.00 3.41
195 196 1.525619 GGTACGTGACAAACTCACTGC 59.474 52.381 0.00 0.00 46.50 4.40
298 308 1.234615 ATCGCTGGGTTTTGTCACGG 61.235 55.000 0.00 0.00 0.00 4.94
331 341 0.740737 CCGACTAACCCGTCCGTATT 59.259 55.000 0.00 0.00 0.00 1.89
348 358 4.143597 CCGTATTATAAGCGCTTCGTCTTG 60.144 45.833 28.82 12.11 0.00 3.02
413 423 1.569653 TTTGGTTTCGGGGGTTTGTT 58.430 45.000 0.00 0.00 0.00 2.83
414 424 1.112950 TTGGTTTCGGGGGTTTGTTC 58.887 50.000 0.00 0.00 0.00 3.18
415 425 0.756070 TGGTTTCGGGGGTTTGTTCC 60.756 55.000 0.00 0.00 0.00 3.62
416 426 0.756070 GGTTTCGGGGGTTTGTTCCA 60.756 55.000 0.00 0.00 0.00 3.53
421 431 1.680989 GGGGGTTTGTTCCATCGGG 60.681 63.158 0.00 0.00 0.00 5.14
436 446 1.243902 TCGGGTGCTTGTCATTTTCC 58.756 50.000 0.00 0.00 0.00 3.13
438 448 0.958822 GGGTGCTTGTCATTTTCCGT 59.041 50.000 0.00 0.00 0.00 4.69
439 449 1.339929 GGGTGCTTGTCATTTTCCGTT 59.660 47.619 0.00 0.00 0.00 4.44
440 450 2.393764 GGTGCTTGTCATTTTCCGTTG 58.606 47.619 0.00 0.00 0.00 4.10
441 451 2.393764 GTGCTTGTCATTTTCCGTTGG 58.606 47.619 0.00 0.00 0.00 3.77
442 452 2.034053 GTGCTTGTCATTTTCCGTTGGA 59.966 45.455 0.00 0.00 0.00 3.53
443 453 2.890311 TGCTTGTCATTTTCCGTTGGAT 59.110 40.909 0.00 0.00 0.00 3.41
444 454 3.244976 GCTTGTCATTTTCCGTTGGATG 58.755 45.455 0.00 0.00 0.00 3.51
445 455 3.244976 CTTGTCATTTTCCGTTGGATGC 58.755 45.455 0.00 0.00 0.00 3.91
446 456 2.513753 TGTCATTTTCCGTTGGATGCT 58.486 42.857 0.00 0.00 0.00 3.79
447 457 2.890311 TGTCATTTTCCGTTGGATGCTT 59.110 40.909 0.00 0.00 0.00 3.91
485 501 4.021925 GACCAGCCACCCTTCGCT 62.022 66.667 0.00 0.00 35.10 4.93
490 506 4.475135 GCCACCCTTCGCTCCCTC 62.475 72.222 0.00 0.00 0.00 4.30
491 507 4.148825 CCACCCTTCGCTCCCTCG 62.149 72.222 0.00 0.00 0.00 4.63
492 508 4.821589 CACCCTTCGCTCCCTCGC 62.822 72.222 0.00 0.00 0.00 5.03
496 512 3.515286 CTTCGCTCCCTCGCCGTA 61.515 66.667 0.00 0.00 0.00 4.02
497 513 3.753070 CTTCGCTCCCTCGCCGTAC 62.753 68.421 0.00 0.00 0.00 3.67
500 516 3.204827 GCTCCCTCGCCGTACGTA 61.205 66.667 15.21 0.00 44.19 3.57
517 533 2.116533 TAGTACGCGGCTGCTGCTA 61.117 57.895 28.80 17.62 39.65 3.49
519 535 3.449227 TACGCGGCTGCTGCTACT 61.449 61.111 28.80 14.63 39.65 2.57
520 536 3.699955 TACGCGGCTGCTGCTACTG 62.700 63.158 28.80 16.75 39.65 2.74
525 543 0.740868 CGGCTGCTGCTACTGCTTAA 60.741 55.000 15.64 0.00 40.48 1.85
530 548 3.273434 CTGCTGCTACTGCTTAATTCCA 58.727 45.455 0.00 0.00 40.48 3.53
536 554 6.693315 TGCTACTGCTTAATTCCAATAACC 57.307 37.500 0.00 0.00 40.48 2.85
537 555 5.592688 TGCTACTGCTTAATTCCAATAACCC 59.407 40.000 0.00 0.00 40.48 4.11
552 570 0.693049 AACCCAAGAGAAGACCGCAT 59.307 50.000 0.00 0.00 0.00 4.73
553 571 0.036010 ACCCAAGAGAAGACCGCATG 60.036 55.000 0.00 0.00 0.00 4.06
555 573 0.674581 CCAAGAGAAGACCGCATGCA 60.675 55.000 19.57 0.00 0.00 3.96
556 574 0.725686 CAAGAGAAGACCGCATGCAG 59.274 55.000 19.57 9.32 0.00 4.41
557 575 1.023513 AAGAGAAGACCGCATGCAGC 61.024 55.000 19.57 5.89 40.87 5.25
558 576 2.437359 AGAAGACCGCATGCAGCC 60.437 61.111 19.57 0.00 41.38 4.85
559 577 3.869272 GAAGACCGCATGCAGCCG 61.869 66.667 19.57 3.97 41.38 5.52
567 585 3.499737 CATGCAGCCGGTCGGTTC 61.500 66.667 11.25 1.67 37.65 3.62
568 586 4.015406 ATGCAGCCGGTCGGTTCA 62.015 61.111 11.25 6.99 37.65 3.18
569 587 3.958147 ATGCAGCCGGTCGGTTCAG 62.958 63.158 11.25 0.00 37.65 3.02
571 589 4.680237 CAGCCGGTCGGTTCAGCA 62.680 66.667 11.25 0.00 37.65 4.41
572 590 4.681978 AGCCGGTCGGTTCAGCAC 62.682 66.667 11.25 0.00 37.65 4.40
575 593 4.003788 CGGTCGGTTCAGCACCCT 62.004 66.667 0.00 0.00 43.83 4.34
576 594 2.358737 GGTCGGTTCAGCACCCTG 60.359 66.667 0.00 0.00 43.83 4.45
577 595 2.741092 GTCGGTTCAGCACCCTGA 59.259 61.111 0.00 0.00 46.03 3.86
583 601 2.431683 TCAGCACCCTGACCTTGC 59.568 61.111 0.00 0.00 42.98 4.01
584 602 2.113774 CAGCACCCTGACCTTGCA 59.886 61.111 0.00 0.00 41.77 4.08
585 603 1.970114 CAGCACCCTGACCTTGCAG 60.970 63.158 0.00 0.00 41.77 4.41
586 604 3.368571 GCACCCTGACCTTGCAGC 61.369 66.667 0.00 0.00 36.22 5.25
590 608 2.435586 CCTGACCTTGCAGCTCGG 60.436 66.667 0.00 0.00 34.56 4.63
604 622 4.357947 TCGGCGTGGAGCTCACAC 62.358 66.667 17.19 18.66 46.36 3.82
605 623 4.662961 CGGCGTGGAGCTCACACA 62.663 66.667 25.32 10.65 46.36 3.72
606 624 2.740055 GGCGTGGAGCTCACACAG 60.740 66.667 25.32 20.14 46.36 3.66
609 633 1.160329 GCGTGGAGCTCACACAGTTT 61.160 55.000 25.32 0.00 46.36 2.66
612 636 2.801699 CGTGGAGCTCACACAGTTTACA 60.802 50.000 25.32 6.93 46.36 2.41
648 672 0.834612 AGTTCAACTTGGTCCGGTCA 59.165 50.000 0.00 0.00 0.00 4.02
712 737 2.373540 TTTCCGGTCCACGTTATCAG 57.626 50.000 0.00 0.00 42.24 2.90
713 738 0.108520 TTCCGGTCCACGTTATCAGC 60.109 55.000 0.00 0.00 42.24 4.26
714 739 1.216977 CCGGTCCACGTTATCAGCA 59.783 57.895 0.00 0.00 42.24 4.41
715 740 0.806102 CCGGTCCACGTTATCAGCAG 60.806 60.000 0.00 0.00 42.24 4.24
716 741 1.421410 CGGTCCACGTTATCAGCAGC 61.421 60.000 0.00 0.00 37.93 5.25
717 742 1.090052 GGTCCACGTTATCAGCAGCC 61.090 60.000 0.00 0.00 0.00 4.85
718 743 1.090052 GTCCACGTTATCAGCAGCCC 61.090 60.000 0.00 0.00 0.00 5.19
719 744 1.078497 CCACGTTATCAGCAGCCCA 60.078 57.895 0.00 0.00 0.00 5.36
720 745 0.676466 CCACGTTATCAGCAGCCCAA 60.676 55.000 0.00 0.00 0.00 4.12
721 746 1.164411 CACGTTATCAGCAGCCCAAA 58.836 50.000 0.00 0.00 0.00 3.28
722 747 1.131126 CACGTTATCAGCAGCCCAAAG 59.869 52.381 0.00 0.00 0.00 2.77
723 748 0.099436 CGTTATCAGCAGCCCAAAGC 59.901 55.000 0.00 0.00 44.25 3.51
733 758 3.957383 GCCCAAAGCACGAAAAAGA 57.043 47.368 0.00 0.00 42.97 2.52
734 759 2.217429 GCCCAAAGCACGAAAAAGAA 57.783 45.000 0.00 0.00 42.97 2.52
735 760 2.545731 GCCCAAAGCACGAAAAAGAAA 58.454 42.857 0.00 0.00 42.97 2.52
736 761 3.130633 GCCCAAAGCACGAAAAAGAAAT 58.869 40.909 0.00 0.00 42.97 2.17
737 762 4.303282 GCCCAAAGCACGAAAAAGAAATA 58.697 39.130 0.00 0.00 42.97 1.40
738 763 4.149922 GCCCAAAGCACGAAAAAGAAATAC 59.850 41.667 0.00 0.00 42.97 1.89
739 764 5.528870 CCCAAAGCACGAAAAAGAAATACT 58.471 37.500 0.00 0.00 0.00 2.12
740 765 5.629435 CCCAAAGCACGAAAAAGAAATACTC 59.371 40.000 0.00 0.00 0.00 2.59
744 769 4.024387 AGCACGAAAAAGAAATACTCGCAA 60.024 37.500 0.00 0.00 0.00 4.85
746 771 5.172411 GCACGAAAAAGAAATACTCGCAAAA 59.828 36.000 0.00 0.00 0.00 2.44
790 815 4.536090 AGAGAGAGAGAGAGAGAGGACAAA 59.464 45.833 0.00 0.00 0.00 2.83
794 819 1.134175 GAGAGAGAGAGGACAAAGGCG 59.866 57.143 0.00 0.00 0.00 5.52
795 820 0.892063 GAGAGAGAGGACAAAGGCGT 59.108 55.000 0.00 0.00 0.00 5.68
824 849 1.003597 GGCAACATGGGCATTTGCA 60.004 52.632 16.85 0.00 46.12 4.08
871 932 0.390340 CTATATCTGCGCCATGCCGT 60.390 55.000 4.18 0.00 45.60 5.68
887 948 2.281484 GTCCCGTGCCAAGCTTCA 60.281 61.111 0.00 0.00 0.00 3.02
902 963 3.439154 AGCTTCATCTCCTCAGACTCAA 58.561 45.455 0.00 0.00 0.00 3.02
940 1006 3.411351 CTGCGCACCACACGTACC 61.411 66.667 5.66 0.00 0.00 3.34
945 1011 1.666872 GCACCACACGTACCACTCC 60.667 63.158 0.00 0.00 0.00 3.85
948 1014 1.183676 ACCACACGTACCACTCCTCC 61.184 60.000 0.00 0.00 0.00 4.30
950 1016 0.038526 CACACGTACCACTCCTCCAC 60.039 60.000 0.00 0.00 0.00 4.02
953 1019 0.700564 ACGTACCACTCCTCCACCTA 59.299 55.000 0.00 0.00 0.00 3.08
954 1020 1.101331 CGTACCACTCCTCCACCTAC 58.899 60.000 0.00 0.00 0.00 3.18
955 1021 1.615116 CGTACCACTCCTCCACCTACA 60.615 57.143 0.00 0.00 0.00 2.74
956 1022 2.532843 GTACCACTCCTCCACCTACAA 58.467 52.381 0.00 0.00 0.00 2.41
957 1023 2.112279 ACCACTCCTCCACCTACAAA 57.888 50.000 0.00 0.00 0.00 2.83
961 1027 1.903183 ACTCCTCCACCTACAAAGCTC 59.097 52.381 0.00 0.00 0.00 4.09
962 1028 0.895530 TCCTCCACCTACAAAGCTCG 59.104 55.000 0.00 0.00 0.00 5.03
963 1029 0.608640 CCTCCACCTACAAAGCTCGT 59.391 55.000 0.00 0.00 0.00 4.18
964 1030 1.822990 CCTCCACCTACAAAGCTCGTA 59.177 52.381 0.00 0.00 0.00 3.43
965 1031 2.416972 CCTCCACCTACAAAGCTCGTAC 60.417 54.545 0.00 0.00 0.00 3.67
966 1032 1.200716 TCCACCTACAAAGCTCGTACG 59.799 52.381 9.53 9.53 0.00 3.67
967 1033 1.068055 CCACCTACAAAGCTCGTACGT 60.068 52.381 16.05 0.00 0.00 3.57
968 1034 2.162208 CCACCTACAAAGCTCGTACGTA 59.838 50.000 16.05 0.00 0.00 3.57
1112 1178 0.248949 GACGCCGGTCAGTATTCCTC 60.249 60.000 1.90 0.00 42.91 3.71
1563 1630 3.264897 CTGATGCCGCTGTACCGC 61.265 66.667 0.00 0.00 0.00 5.68
1732 1803 3.406764 AGTGCACCTTCTCAGATCAAAC 58.593 45.455 14.63 0.00 0.00 2.93
1733 1804 3.072184 AGTGCACCTTCTCAGATCAAACT 59.928 43.478 14.63 0.00 0.00 2.66
1736 1807 5.293079 GTGCACCTTCTCAGATCAAACTATC 59.707 44.000 5.22 0.00 0.00 2.08
1737 1808 4.505922 GCACCTTCTCAGATCAAACTATCG 59.494 45.833 0.00 0.00 0.00 2.92
1741 1812 6.097554 ACCTTCTCAGATCAAACTATCGTCAT 59.902 38.462 0.00 0.00 0.00 3.06
1751 1822 5.063817 TCAAACTATCGTCATGTGCTGATTG 59.936 40.000 0.00 0.00 35.97 2.67
1752 1823 4.128925 ACTATCGTCATGTGCTGATTGT 57.871 40.909 0.00 0.00 35.97 2.71
1756 1827 4.661993 TCGTCATGTGCTGATTGTTTAC 57.338 40.909 0.00 0.00 35.97 2.01
1782 1875 9.698309 CTATCGACATGTTCTCCTAATTAACAT 57.302 33.333 0.00 0.00 42.91 2.71
1786 1879 8.883731 CGACATGTTCTCCTAATTAACATCTTT 58.116 33.333 0.00 0.00 40.83 2.52
1787 1880 9.994432 GACATGTTCTCCTAATTAACATCTTTG 57.006 33.333 0.00 0.00 40.83 2.77
1804 1897 9.865321 AACATCTTTGATTAATTTGATGTCTGG 57.135 29.630 18.10 2.86 42.13 3.86
1854 1960 4.129737 ACCAGTCGCCGATCACCG 62.130 66.667 0.00 0.00 38.18 4.94
1867 1973 0.391661 ATCACCGAGCGCATGAGTTT 60.392 50.000 11.47 0.00 0.00 2.66
1909 2026 1.317613 TGACCTTGTGTTGTGCCATC 58.682 50.000 0.00 0.00 0.00 3.51
1925 2042 1.543614 CATCTCAGCTCGAGTTCGTG 58.456 55.000 15.13 7.05 42.88 4.35
1935 2052 3.495193 CTCGAGTTCGTGTCCGATTTTA 58.505 45.455 3.62 0.00 43.80 1.52
1936 2053 4.100707 TCGAGTTCGTGTCCGATTTTAT 57.899 40.909 1.07 0.00 43.80 1.40
1954 2077 5.858159 TTTATTTTTGTGCGTGTTCTTCG 57.142 34.783 0.00 0.00 0.00 3.79
1970 2093 2.037902 TCTTCGAATGCCTTGGTGTGTA 59.962 45.455 0.00 0.00 0.00 2.90
1972 2095 3.897141 TCGAATGCCTTGGTGTGTATA 57.103 42.857 0.00 0.00 0.00 1.47
2063 2200 6.219302 TCCGTTTTCATTCGTCTTTCTTAC 57.781 37.500 0.00 0.00 0.00 2.34
2064 2201 5.754406 TCCGTTTTCATTCGTCTTTCTTACA 59.246 36.000 0.00 0.00 0.00 2.41
2066 2203 7.041644 TCCGTTTTCATTCGTCTTTCTTACATT 60.042 33.333 0.00 0.00 0.00 2.71
2067 2204 7.059488 CCGTTTTCATTCGTCTTTCTTACATTG 59.941 37.037 0.00 0.00 0.00 2.82
2069 2206 6.494893 TTCATTCGTCTTTCTTACATTGGG 57.505 37.500 0.00 0.00 0.00 4.12
2072 2209 4.610605 TCGTCTTTCTTACATTGGGACA 57.389 40.909 0.00 0.00 0.00 4.02
2073 2210 4.312443 TCGTCTTTCTTACATTGGGACAC 58.688 43.478 0.00 0.00 39.29 3.67
2074 2211 4.039973 TCGTCTTTCTTACATTGGGACACT 59.960 41.667 0.00 0.00 39.29 3.55
2075 2212 4.755123 CGTCTTTCTTACATTGGGACACTT 59.245 41.667 0.00 0.00 39.29 3.16
2076 2213 5.929992 CGTCTTTCTTACATTGGGACACTTA 59.070 40.000 0.00 0.00 39.29 2.24
2077 2214 6.594159 CGTCTTTCTTACATTGGGACACTTAT 59.406 38.462 0.00 0.00 39.29 1.73
2078 2215 7.119262 CGTCTTTCTTACATTGGGACACTTATT 59.881 37.037 0.00 0.00 39.29 1.40
2079 2216 8.793592 GTCTTTCTTACATTGGGACACTTATTT 58.206 33.333 0.00 0.00 39.29 1.40
2080 2217 9.362151 TCTTTCTTACATTGGGACACTTATTTT 57.638 29.630 0.00 0.00 39.29 1.82
2081 2218 9.410556 CTTTCTTACATTGGGACACTTATTTTG 57.589 33.333 0.00 0.00 39.29 2.44
2082 2219 8.698973 TTCTTACATTGGGACACTTATTTTGA 57.301 30.769 0.00 0.00 39.29 2.69
2083 2220 8.335532 TCTTACATTGGGACACTTATTTTGAG 57.664 34.615 0.00 0.00 39.29 3.02
2084 2221 8.160765 TCTTACATTGGGACACTTATTTTGAGA 58.839 33.333 0.00 0.00 39.29 3.27
2085 2222 6.575162 ACATTGGGACACTTATTTTGAGAC 57.425 37.500 0.00 0.00 39.29 3.36
2086 2223 5.181245 ACATTGGGACACTTATTTTGAGACG 59.819 40.000 0.00 0.00 39.29 4.18
2087 2224 3.670625 TGGGACACTTATTTTGAGACGG 58.329 45.455 0.00 0.00 0.00 4.79
2088 2225 3.325425 TGGGACACTTATTTTGAGACGGA 59.675 43.478 0.00 0.00 0.00 4.69
2092 2229 4.822026 ACACTTATTTTGAGACGGAGGAG 58.178 43.478 0.00 0.00 0.00 3.69
2094 2231 5.187967 ACACTTATTTTGAGACGGAGGAGAT 59.812 40.000 0.00 0.00 0.00 2.75
2109 2246 5.059833 GGAGGAGATCATTTCTTGCGTTAT 58.940 41.667 0.00 0.00 33.74 1.89
2192 2332 0.179137 CTGTCGGCTCGAGTTATGCA 60.179 55.000 15.13 6.49 36.23 3.96
2195 2335 0.815095 TCGGCTCGAGTTATGCAAGA 59.185 50.000 15.13 0.86 0.00 3.02
2305 4864 3.945285 TGGGCTCGAATTATGTCCTTTTC 59.055 43.478 0.00 0.00 0.00 2.29
2308 4867 4.496507 GGCTCGAATTATGTCCTTTTCAGC 60.497 45.833 0.00 0.00 0.00 4.26
2349 5011 3.685139 ACATATTCGAGGGATTGCGAT 57.315 42.857 0.00 0.00 36.31 4.58
2387 6146 0.918799 TATCCCAAGCCCCTGCAAGA 60.919 55.000 0.00 0.00 41.13 3.02
2489 6288 2.008242 TTGTGTTGATTTGGGAGGGG 57.992 50.000 0.00 0.00 0.00 4.79
2490 6289 0.856982 TGTGTTGATTTGGGAGGGGT 59.143 50.000 0.00 0.00 0.00 4.95
2491 6290 1.203001 TGTGTTGATTTGGGAGGGGTC 60.203 52.381 0.00 0.00 0.00 4.46
2492 6291 1.153539 TGTTGATTTGGGAGGGGTCA 58.846 50.000 0.00 0.00 0.00 4.02
2493 6292 1.075374 TGTTGATTTGGGAGGGGTCAG 59.925 52.381 0.00 0.00 0.00 3.51
2494 6293 1.354368 GTTGATTTGGGAGGGGTCAGA 59.646 52.381 0.00 0.00 0.00 3.27
2588 6417 0.393808 TTATTGGGCGCCCTTCTCAC 60.394 55.000 43.34 18.31 36.94 3.51
2619 6781 6.567602 ATCCTAAGCAGAAGAAATACCAGT 57.432 37.500 0.00 0.00 0.00 4.00
2620 6782 7.676683 ATCCTAAGCAGAAGAAATACCAGTA 57.323 36.000 0.00 0.00 0.00 2.74
2621 6783 7.113658 TCCTAAGCAGAAGAAATACCAGTAG 57.886 40.000 0.00 0.00 0.00 2.57
2637 6803 6.328641 ACCAGTAGAGTTGTACTACTTGTG 57.671 41.667 11.32 6.81 45.24 3.33
2705 6875 6.139679 TCAATTAGAAAACTCCACCCATCT 57.860 37.500 0.00 0.00 0.00 2.90
2706 6876 7.037586 ACTCAATTAGAAAACTCCACCCATCTA 60.038 37.037 0.00 0.00 0.00 1.98
2707 6877 7.110155 TCAATTAGAAAACTCCACCCATCTAC 58.890 38.462 0.00 0.00 0.00 2.59
2708 6878 3.611766 AGAAAACTCCACCCATCTACG 57.388 47.619 0.00 0.00 0.00 3.51
2801 6981 2.274542 TCCCACCAGCCAAGAGAAATA 58.725 47.619 0.00 0.00 0.00 1.40
2808 6990 4.195416 CCAGCCAAGAGAAATAAGAGGAC 58.805 47.826 0.00 0.00 0.00 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 6.567511 GCAAGTCTTTTGCCTTGTTTCAAAAA 60.568 34.615 0.54 0.00 40.36 1.94
18 19 5.106752 GCAAGTCTTTTGCCTTGTTTCAAAA 60.107 36.000 0.54 0.00 40.13 2.44
19 20 4.391523 GCAAGTCTTTTGCCTTGTTTCAAA 59.608 37.500 0.54 0.00 40.13 2.69
20 21 3.932089 GCAAGTCTTTTGCCTTGTTTCAA 59.068 39.130 0.54 0.00 40.13 2.69
21 22 3.520569 GCAAGTCTTTTGCCTTGTTTCA 58.479 40.909 0.54 0.00 40.13 2.69
30 31 5.678132 AATGAAAATGGCAAGTCTTTTGC 57.322 34.783 1.54 3.39 44.22 3.68
56 57 9.661563 GGGGAAAAGAAAAGAAAAGAAAAGTTA 57.338 29.630 0.00 0.00 0.00 2.24
57 58 7.333423 CGGGGAAAAGAAAAGAAAAGAAAAGTT 59.667 33.333 0.00 0.00 0.00 2.66
58 59 6.816640 CGGGGAAAAGAAAAGAAAAGAAAAGT 59.183 34.615 0.00 0.00 0.00 2.66
59 60 6.257849 CCGGGGAAAAGAAAAGAAAAGAAAAG 59.742 38.462 0.00 0.00 0.00 2.27
60 61 6.110033 CCGGGGAAAAGAAAAGAAAAGAAAA 58.890 36.000 0.00 0.00 0.00 2.29
61 62 5.188163 ACCGGGGAAAAGAAAAGAAAAGAAA 59.812 36.000 6.32 0.00 0.00 2.52
62 63 4.712829 ACCGGGGAAAAGAAAAGAAAAGAA 59.287 37.500 6.32 0.00 0.00 2.52
63 64 4.098807 CACCGGGGAAAAGAAAAGAAAAGA 59.901 41.667 6.32 0.00 0.00 2.52
64 65 4.368315 CACCGGGGAAAAGAAAAGAAAAG 58.632 43.478 6.32 0.00 0.00 2.27
65 66 3.133183 CCACCGGGGAAAAGAAAAGAAAA 59.867 43.478 4.41 0.00 40.01 2.29
66 67 2.696187 CCACCGGGGAAAAGAAAAGAAA 59.304 45.455 4.41 0.00 40.01 2.52
67 68 2.091775 TCCACCGGGGAAAAGAAAAGAA 60.092 45.455 4.41 0.00 44.80 2.52
68 69 1.495574 TCCACCGGGGAAAAGAAAAGA 59.504 47.619 4.41 0.00 44.80 2.52
69 70 1.989706 TCCACCGGGGAAAAGAAAAG 58.010 50.000 4.41 0.00 44.80 2.27
78 79 0.689745 ATCTTCGATTCCACCGGGGA 60.690 55.000 4.41 6.39 46.61 4.81
79 80 0.180406 AATCTTCGATTCCACCGGGG 59.820 55.000 6.32 0.00 38.37 5.73
80 81 1.299541 CAATCTTCGATTCCACCGGG 58.700 55.000 6.32 0.00 0.00 5.73
81 82 1.299541 CCAATCTTCGATTCCACCGG 58.700 55.000 0.00 0.00 0.00 5.28
82 83 2.024176 ACCAATCTTCGATTCCACCG 57.976 50.000 0.00 0.00 0.00 4.94
83 84 4.783764 AAAACCAATCTTCGATTCCACC 57.216 40.909 0.00 0.00 0.00 4.61
84 85 4.923281 CCAAAAACCAATCTTCGATTCCAC 59.077 41.667 0.00 0.00 0.00 4.02
85 86 4.586841 ACCAAAAACCAATCTTCGATTCCA 59.413 37.500 0.00 0.00 0.00 3.53
86 87 5.134202 ACCAAAAACCAATCTTCGATTCC 57.866 39.130 0.00 0.00 0.00 3.01
87 88 5.161358 GGACCAAAAACCAATCTTCGATTC 58.839 41.667 0.00 0.00 0.00 2.52
88 89 4.586841 TGGACCAAAAACCAATCTTCGATT 59.413 37.500 0.00 0.00 32.93 3.34
89 90 4.148838 TGGACCAAAAACCAATCTTCGAT 58.851 39.130 0.00 0.00 32.93 3.59
90 91 3.556999 TGGACCAAAAACCAATCTTCGA 58.443 40.909 0.00 0.00 32.93 3.71
91 92 4.236935 CATGGACCAAAAACCAATCTTCG 58.763 43.478 0.00 0.00 39.69 3.79
92 93 4.283212 TCCATGGACCAAAAACCAATCTTC 59.717 41.667 11.44 0.00 39.69 2.87
93 94 4.230455 TCCATGGACCAAAAACCAATCTT 58.770 39.130 11.44 0.00 39.69 2.40
94 95 3.855668 TCCATGGACCAAAAACCAATCT 58.144 40.909 11.44 0.00 39.69 2.40
95 96 4.506758 CATCCATGGACCAAAAACCAATC 58.493 43.478 18.99 0.00 39.69 2.67
96 97 4.556592 CATCCATGGACCAAAAACCAAT 57.443 40.909 18.99 0.00 39.69 3.16
110 111 0.888619 GCAGCATCCATCCATCCATG 59.111 55.000 0.00 0.00 0.00 3.66
131 132 0.608130 TCATCAACTGGACACGGGAG 59.392 55.000 0.00 0.00 0.00 4.30
142 143 2.872245 CTCCACAAACGTGTCATCAACT 59.128 45.455 0.00 0.00 35.07 3.16
165 166 2.024305 CACGTACCCTAGCTCGCG 59.976 66.667 0.00 0.00 0.00 5.87
170 171 2.029649 TGAGTTTGTCACGTACCCTAGC 60.030 50.000 0.00 0.00 0.00 3.42
184 185 2.301346 AGGACTTTGGCAGTGAGTTTG 58.699 47.619 0.00 0.00 35.01 2.93
188 189 2.564947 AGAGTAGGACTTTGGCAGTGAG 59.435 50.000 0.00 0.00 35.01 3.51
191 192 5.026790 AGATTAGAGTAGGACTTTGGCAGT 58.973 41.667 0.00 0.00 39.07 4.40
195 196 6.775629 AGAGCTAGATTAGAGTAGGACTTTGG 59.224 42.308 0.00 0.00 0.00 3.28
274 280 1.062587 GACAAAACCCAGCGATCGATG 59.937 52.381 25.72 25.72 0.00 3.84
298 308 0.616891 AGTCGGGTGGTTGGGATAAC 59.383 55.000 0.00 0.00 0.00 1.89
331 341 2.793585 CGACCAAGACGAAGCGCTTATA 60.794 50.000 25.11 0.00 0.00 0.98
348 358 1.296056 ACTTATGTTGCCACGCGACC 61.296 55.000 15.93 0.00 41.86 4.79
413 423 0.327924 AATGACAAGCACCCGATGGA 59.672 50.000 0.00 0.00 34.81 3.41
414 424 1.176527 AAATGACAAGCACCCGATGG 58.823 50.000 0.00 0.00 37.80 3.51
415 425 2.415893 GGAAAATGACAAGCACCCGATG 60.416 50.000 0.00 0.00 0.00 3.84
416 426 1.818674 GGAAAATGACAAGCACCCGAT 59.181 47.619 0.00 0.00 0.00 4.18
421 431 2.034053 TCCAACGGAAAATGACAAGCAC 59.966 45.455 0.00 0.00 0.00 4.40
436 446 1.269726 ACCAAAGCAAAGCATCCAACG 60.270 47.619 0.00 0.00 0.00 4.10
438 448 3.940209 CTACCAAAGCAAAGCATCCAA 57.060 42.857 0.00 0.00 0.00 3.53
485 501 0.810031 GTACTACGTACGGCGAGGGA 60.810 60.000 21.06 0.00 44.77 4.20
494 510 1.936398 GCAGCCGCGTACTACGTAC 60.936 63.158 4.92 0.00 44.73 3.67
495 511 2.108514 AGCAGCCGCGTACTACGTA 61.109 57.895 4.92 0.00 44.73 3.57
496 512 3.437795 AGCAGCCGCGTACTACGT 61.438 61.111 4.92 0.00 44.73 3.57
497 513 2.949678 CAGCAGCCGCGTACTACG 60.950 66.667 4.92 4.12 45.49 3.51
498 514 2.332362 TAGCAGCAGCCGCGTACTAC 62.332 60.000 4.92 0.00 45.49 2.73
499 515 2.116533 TAGCAGCAGCCGCGTACTA 61.117 57.895 4.92 0.00 45.49 1.82
500 516 3.449227 TAGCAGCAGCCGCGTACT 61.449 61.111 4.92 0.00 45.49 2.73
508 524 2.032675 GGAATTAAGCAGTAGCAGCAGC 59.967 50.000 0.00 0.00 45.49 5.25
517 533 6.252995 TCTTGGGTTATTGGAATTAAGCAGT 58.747 36.000 0.00 0.00 0.00 4.40
519 535 6.489603 TCTCTTGGGTTATTGGAATTAAGCA 58.510 36.000 0.00 0.00 0.00 3.91
520 536 7.339466 TCTTCTCTTGGGTTATTGGAATTAAGC 59.661 37.037 0.00 0.00 0.00 3.09
521 537 8.678199 GTCTTCTCTTGGGTTATTGGAATTAAG 58.322 37.037 0.00 0.00 0.00 1.85
522 538 7.614192 GGTCTTCTCTTGGGTTATTGGAATTAA 59.386 37.037 0.00 0.00 0.00 1.40
525 543 5.510430 GGTCTTCTCTTGGGTTATTGGAAT 58.490 41.667 0.00 0.00 0.00 3.01
530 548 2.304761 TGCGGTCTTCTCTTGGGTTATT 59.695 45.455 0.00 0.00 0.00 1.40
536 554 0.674581 TGCATGCGGTCTTCTCTTGG 60.675 55.000 14.09 0.00 0.00 3.61
537 555 0.725686 CTGCATGCGGTCTTCTCTTG 59.274 55.000 18.84 0.00 0.00 3.02
552 570 4.680237 CTGAACCGACCGGCTGCA 62.680 66.667 8.55 3.62 39.32 4.41
555 573 4.681978 GTGCTGAACCGACCGGCT 62.682 66.667 8.55 0.00 39.32 5.52
564 582 1.518903 GCAAGGTCAGGGTGCTGAAC 61.519 60.000 0.00 0.00 41.12 3.18
565 583 1.228245 GCAAGGTCAGGGTGCTGAA 60.228 57.895 0.00 0.00 34.88 3.02
566 584 2.401699 CTGCAAGGTCAGGGTGCTGA 62.402 60.000 0.00 0.00 38.94 4.26
567 585 1.970114 CTGCAAGGTCAGGGTGCTG 60.970 63.158 0.00 0.00 39.09 4.41
568 586 2.433446 CTGCAAGGTCAGGGTGCT 59.567 61.111 0.00 0.00 39.09 4.40
569 587 3.368571 GCTGCAAGGTCAGGGTGC 61.369 66.667 0.00 0.00 38.78 5.01
595 613 4.222114 GCATTTGTAAACTGTGTGAGCTC 58.778 43.478 6.82 6.82 0.00 4.09
612 636 3.874543 TGAACTAGTGACACAACGCATTT 59.125 39.130 8.59 0.00 0.00 2.32
691 716 2.607635 CTGATAACGTGGACCGGAAATG 59.392 50.000 9.46 0.33 42.24 2.32
712 737 0.529555 TTTTTCGTGCTTTGGGCTGC 60.530 50.000 0.00 0.00 42.39 5.25
713 738 1.066908 TCTTTTTCGTGCTTTGGGCTG 59.933 47.619 0.00 0.00 42.39 4.85
714 739 1.398692 TCTTTTTCGTGCTTTGGGCT 58.601 45.000 0.00 0.00 42.39 5.19
715 740 2.217429 TTCTTTTTCGTGCTTTGGGC 57.783 45.000 0.00 0.00 42.22 5.36
716 741 5.528870 AGTATTTCTTTTTCGTGCTTTGGG 58.471 37.500 0.00 0.00 0.00 4.12
717 742 5.339611 CGAGTATTTCTTTTTCGTGCTTTGG 59.660 40.000 0.00 0.00 0.00 3.28
718 743 5.164282 GCGAGTATTTCTTTTTCGTGCTTTG 60.164 40.000 0.00 0.00 34.05 2.77
719 744 4.909880 GCGAGTATTTCTTTTTCGTGCTTT 59.090 37.500 0.00 0.00 34.05 3.51
720 745 4.024387 TGCGAGTATTTCTTTTTCGTGCTT 60.024 37.500 0.00 0.00 34.05 3.91
721 746 3.496884 TGCGAGTATTTCTTTTTCGTGCT 59.503 39.130 0.00 0.00 34.05 4.40
722 747 3.805823 TGCGAGTATTTCTTTTTCGTGC 58.194 40.909 0.00 0.00 34.05 5.34
723 748 6.726035 TTTTGCGAGTATTTCTTTTTCGTG 57.274 33.333 0.00 0.00 34.05 4.35
762 787 4.592351 CCTCTCTCTCTCTCTCTCTCTCAT 59.408 50.000 0.00 0.00 0.00 2.90
767 792 3.724478 TGTCCTCTCTCTCTCTCTCTCT 58.276 50.000 0.00 0.00 0.00 3.10
771 796 3.877735 GCCTTTGTCCTCTCTCTCTCTCT 60.878 52.174 0.00 0.00 0.00 3.10
824 849 2.035626 CAGGCCAATTCGGTGGGT 59.964 61.111 5.01 0.00 39.26 4.51
871 932 1.377202 GATGAAGCTTGGCACGGGA 60.377 57.895 2.10 0.00 0.00 5.14
887 948 2.760092 GCTGTCTTGAGTCTGAGGAGAT 59.240 50.000 0.00 0.00 0.00 2.75
927 993 1.666872 GGAGTGGTACGTGTGGTGC 60.667 63.158 0.00 0.00 0.00 5.01
940 1006 1.625818 AGCTTTGTAGGTGGAGGAGTG 59.374 52.381 0.00 0.00 0.00 3.51
945 1011 2.731341 CGTACGAGCTTTGTAGGTGGAG 60.731 54.545 10.44 0.00 32.66 3.86
948 1014 2.342910 ACGTACGAGCTTTGTAGGTG 57.657 50.000 24.41 7.87 38.90 4.00
987 1053 2.661537 TCCATGATAAGCCGCGCG 60.662 61.111 25.67 25.67 0.00 6.86
988 1054 2.320587 CCTCCATGATAAGCCGCGC 61.321 63.158 0.00 0.00 0.00 6.86
989 1055 1.069765 ACCTCCATGATAAGCCGCG 59.930 57.895 0.00 0.00 0.00 6.46
990 1056 0.106708 TCACCTCCATGATAAGCCGC 59.893 55.000 0.00 0.00 0.00 6.53
991 1057 1.875576 GCTCACCTCCATGATAAGCCG 60.876 57.143 0.00 0.00 0.00 5.52
992 1058 1.875576 CGCTCACCTCCATGATAAGCC 60.876 57.143 0.00 0.00 0.00 4.35
993 1059 1.506493 CGCTCACCTCCATGATAAGC 58.494 55.000 0.00 0.00 0.00 3.09
994 1060 1.875576 GCCGCTCACCTCCATGATAAG 60.876 57.143 0.00 0.00 0.00 1.73
995 1061 0.106708 GCCGCTCACCTCCATGATAA 59.893 55.000 0.00 0.00 0.00 1.75
996 1062 0.760567 AGCCGCTCACCTCCATGATA 60.761 55.000 0.00 0.00 0.00 2.15
997 1063 2.037620 GAGCCGCTCACCTCCATGAT 62.038 60.000 15.78 0.00 0.00 2.45
1023 1089 4.421479 AAGCTGTCGCCGAGGTCG 62.421 66.667 0.00 0.00 36.60 4.79
1732 1803 5.475273 AAACAATCAGCACATGACGATAG 57.525 39.130 0.00 0.00 41.91 2.08
1733 1804 6.106003 AGTAAACAATCAGCACATGACGATA 58.894 36.000 0.00 0.00 41.91 2.92
1736 1807 4.668576 AGTAAACAATCAGCACATGACG 57.331 40.909 0.00 0.00 41.91 4.35
1737 1808 6.255670 TCGATAGTAAACAATCAGCACATGAC 59.744 38.462 0.00 0.00 37.97 3.06
1741 1812 5.474825 TGTCGATAGTAAACAATCAGCACA 58.525 37.500 0.00 0.00 37.40 4.57
1751 1822 9.530633 AATTAGGAGAACATGTCGATAGTAAAC 57.469 33.333 0.00 0.00 37.40 2.01
1756 1827 9.698309 ATGTTAATTAGGAGAACATGTCGATAG 57.302 33.333 0.00 0.00 41.17 2.08
1782 1875 9.912634 GAAACCAGACATCAAATTAATCAAAGA 57.087 29.630 0.00 0.00 0.00 2.52
1786 1879 7.093814 CCCTGAAACCAGACATCAAATTAATCA 60.094 37.037 0.00 0.00 33.56 2.57
1787 1880 7.122650 TCCCTGAAACCAGACATCAAATTAATC 59.877 37.037 0.00 0.00 33.56 1.75
1791 1884 4.739793 TCCCTGAAACCAGACATCAAATT 58.260 39.130 0.00 0.00 33.56 1.82
1792 1885 4.387026 TCCCTGAAACCAGACATCAAAT 57.613 40.909 0.00 0.00 33.56 2.32
1793 1886 3.874383 TCCCTGAAACCAGACATCAAA 57.126 42.857 0.00 0.00 33.56 2.69
1795 1888 3.874383 TTTCCCTGAAACCAGACATCA 57.126 42.857 0.00 0.00 33.56 3.07
1796 1889 4.398319 TCTTTTCCCTGAAACCAGACATC 58.602 43.478 0.00 0.00 30.83 3.06
1797 1890 4.453480 TCTTTTCCCTGAAACCAGACAT 57.547 40.909 0.00 0.00 30.83 3.06
1798 1891 3.943671 TCTTTTCCCTGAAACCAGACA 57.056 42.857 0.00 0.00 30.83 3.41
1799 1892 3.057245 GCATCTTTTCCCTGAAACCAGAC 60.057 47.826 0.00 0.00 30.83 3.51
1804 1897 3.858503 GCAGTGCATCTTTTCCCTGAAAC 60.859 47.826 11.09 0.00 30.83 2.78
1846 1943 2.278792 TCATGCGCTCGGTGATCG 60.279 61.111 9.73 0.00 40.90 3.69
1847 1944 0.807667 AACTCATGCGCTCGGTGATC 60.808 55.000 9.73 0.00 0.00 2.92
1848 1945 0.391661 AAACTCATGCGCTCGGTGAT 60.392 50.000 9.73 0.00 0.00 3.06
1854 1960 3.302740 CGGATTAAGAAACTCATGCGCTC 60.303 47.826 9.73 0.00 0.00 5.03
1867 1973 2.540515 CAAAGCTCTCGCGGATTAAGA 58.459 47.619 6.13 0.00 42.32 2.10
1886 1998 0.385029 GCACAACACAAGGTCATGCA 59.615 50.000 0.00 0.00 39.11 3.96
1925 2042 4.677832 ACACGCACAAAAATAAAATCGGAC 59.322 37.500 0.00 0.00 0.00 4.79
1935 2052 3.684103 TCGAAGAACACGCACAAAAAT 57.316 38.095 0.00 0.00 0.00 1.82
1936 2053 3.473093 TTCGAAGAACACGCACAAAAA 57.527 38.095 0.00 0.00 45.90 1.94
1954 2077 8.883731 GTCATATATATACACACCAAGGCATTC 58.116 37.037 0.00 0.00 0.00 2.67
1988 2119 7.502696 ACACGGGTTAATTAAGCATACATCTA 58.497 34.615 24.50 0.00 35.51 1.98
2043 2174 7.326063 CCCAATGTAAGAAAGACGAATGAAAAC 59.674 37.037 0.00 0.00 0.00 2.43
2047 2178 5.642063 GTCCCAATGTAAGAAAGACGAATGA 59.358 40.000 0.00 0.00 0.00 2.57
2063 2200 5.391950 CCGTCTCAAAATAAGTGTCCCAATG 60.392 44.000 0.00 0.00 0.00 2.82
2064 2201 4.700213 CCGTCTCAAAATAAGTGTCCCAAT 59.300 41.667 0.00 0.00 0.00 3.16
2066 2203 3.325425 TCCGTCTCAAAATAAGTGTCCCA 59.675 43.478 0.00 0.00 0.00 4.37
2067 2204 3.933332 CTCCGTCTCAAAATAAGTGTCCC 59.067 47.826 0.00 0.00 0.00 4.46
2069 2206 4.817517 TCCTCCGTCTCAAAATAAGTGTC 58.182 43.478 0.00 0.00 0.00 3.67
2072 2209 5.422331 TGATCTCCTCCGTCTCAAAATAAGT 59.578 40.000 0.00 0.00 0.00 2.24
2073 2210 5.907207 TGATCTCCTCCGTCTCAAAATAAG 58.093 41.667 0.00 0.00 0.00 1.73
2074 2211 5.932619 TGATCTCCTCCGTCTCAAAATAA 57.067 39.130 0.00 0.00 0.00 1.40
2075 2212 6.485830 AATGATCTCCTCCGTCTCAAAATA 57.514 37.500 0.00 0.00 0.00 1.40
2076 2213 5.365021 AATGATCTCCTCCGTCTCAAAAT 57.635 39.130 0.00 0.00 0.00 1.82
2077 2214 4.826274 AATGATCTCCTCCGTCTCAAAA 57.174 40.909 0.00 0.00 0.00 2.44
2078 2215 4.467795 AGAAATGATCTCCTCCGTCTCAAA 59.532 41.667 0.00 0.00 30.46 2.69
2079 2216 4.026744 AGAAATGATCTCCTCCGTCTCAA 58.973 43.478 0.00 0.00 30.46 3.02
2080 2217 3.636679 AGAAATGATCTCCTCCGTCTCA 58.363 45.455 0.00 0.00 30.46 3.27
2081 2218 4.367450 CAAGAAATGATCTCCTCCGTCTC 58.633 47.826 0.00 0.00 37.42 3.36
2082 2219 3.431486 GCAAGAAATGATCTCCTCCGTCT 60.431 47.826 0.00 0.00 37.42 4.18
2083 2220 2.869192 GCAAGAAATGATCTCCTCCGTC 59.131 50.000 0.00 0.00 37.42 4.79
2084 2221 2.739932 CGCAAGAAATGATCTCCTCCGT 60.740 50.000 0.00 0.00 37.42 4.69
2085 2222 1.863454 CGCAAGAAATGATCTCCTCCG 59.137 52.381 0.00 0.00 37.42 4.63
2086 2223 2.911484 ACGCAAGAAATGATCTCCTCC 58.089 47.619 0.00 0.00 37.42 4.30
2087 2224 6.610741 AATAACGCAAGAAATGATCTCCTC 57.389 37.500 0.00 0.00 37.42 3.71
2088 2225 7.770897 ACTAAATAACGCAAGAAATGATCTCCT 59.229 33.333 0.00 0.00 37.42 3.69
2092 2229 9.162793 CATGACTAAATAACGCAAGAAATGATC 57.837 33.333 0.00 0.00 43.62 2.92
2094 2231 7.120579 ACCATGACTAAATAACGCAAGAAATGA 59.879 33.333 0.00 0.00 43.62 2.57
2109 2246 8.902540 ATATTCGCTTAATCACCATGACTAAA 57.097 30.769 0.00 0.00 0.00 1.85
2173 2313 0.179137 TGCATAACTCGAGCCGACAG 60.179 55.000 13.61 0.00 0.00 3.51
2221 4748 7.406799 AATCCAAACATTTTGAACGTGATTC 57.593 32.000 0.00 0.00 37.88 2.52
2240 4767 5.708697 TCGAGCCGTAGATTAGATTAATCCA 59.291 40.000 11.92 0.00 44.35 3.41
2281 4840 1.202533 AGGACATAATTCGAGCCCACG 60.203 52.381 0.00 0.00 0.00 4.94
2349 5011 6.556874 TGGGATATAGTACACCATGTTGATGA 59.443 38.462 0.00 0.00 0.00 2.92
2489 6288 6.706270 TCCATTTTTGTTAGTCTGACTCTGAC 59.294 38.462 14.62 11.90 33.50 3.51
2490 6289 6.826668 TCCATTTTTGTTAGTCTGACTCTGA 58.173 36.000 14.62 0.00 0.00 3.27
2491 6290 6.348050 GCTCCATTTTTGTTAGTCTGACTCTG 60.348 42.308 14.62 1.09 0.00 3.35
2492 6291 5.703130 GCTCCATTTTTGTTAGTCTGACTCT 59.297 40.000 14.62 0.00 0.00 3.24
2493 6292 5.470098 TGCTCCATTTTTGTTAGTCTGACTC 59.530 40.000 14.62 1.31 0.00 3.36
2494 6293 5.376625 TGCTCCATTTTTGTTAGTCTGACT 58.623 37.500 15.57 15.57 0.00 3.41
2615 6777 6.570672 TCACAAGTAGTACAACTCTACTGG 57.429 41.667 2.52 6.24 44.67 4.00
2619 6781 7.834681 AGATGGATCACAAGTAGTACAACTCTA 59.165 37.037 2.52 0.00 0.00 2.43
2620 6782 6.665680 AGATGGATCACAAGTAGTACAACTCT 59.334 38.462 2.52 0.00 0.00 3.24
2621 6783 6.868622 AGATGGATCACAAGTAGTACAACTC 58.131 40.000 2.52 0.00 0.00 3.01
2637 6803 7.982761 ATGCTTTTATTGAGAGAGATGGATC 57.017 36.000 0.00 0.00 0.00 3.36
2770 6950 0.810031 CTGGTGGGAAATACGAGCCG 60.810 60.000 0.00 0.00 0.00 5.52


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

AutoCloner maintained by Alex Coulton.