Multiple sequence alignment - TraesCS5D01G549200

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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 TraesCS5D01G549200 chr5D 100.000 2735 0 0 1 2735 556422412 556425146 0.000000e+00 5051.0
1 TraesCS5D01G549200 chr5D 84.663 1141 121 23 735 1848 559979230 559978117 0.000000e+00 1088.0
2 TraesCS5D01G549200 chr5D 86.892 679 53 17 1062 1735 556449538 556450185 0.000000e+00 728.0
3 TraesCS5D01G549200 chr5D 83.376 391 39 16 100 467 559979661 559979274 3.370000e-89 339.0
4 TraesCS5D01G549200 chr5B 89.955 2011 130 31 761 2735 694289495 694287521 0.000000e+00 2529.0
5 TraesCS5D01G549200 chr5B 81.427 1093 114 34 891 1946 710326039 710324999 0.000000e+00 811.0
6 TraesCS5D01G549200 chr5B 80.905 995 124 36 959 1920 710314393 710313432 0.000000e+00 725.0
7 TraesCS5D01G549200 chr5B 79.245 1060 137 50 918 1946 694203742 694202735 0.000000e+00 662.0
8 TraesCS5D01G549200 chr5B 86.976 453 50 7 1289 1735 694262161 694261712 4.070000e-138 501.0
9 TraesCS5D01G549200 chr5B 83.816 414 35 17 84 467 710326660 710326249 5.570000e-97 364.0
10 TraesCS5D01G549200 chr5B 77.436 585 88 30 107 660 694290158 694289587 2.650000e-80 309.0
11 TraesCS5D01G549200 chr5B 80.135 297 41 8 896 1189 694262487 694262206 3.570000e-49 206.0
12 TraesCS5D01G549200 chr5B 97.436 39 1 0 842 880 710326072 710326034 1.760000e-07 67.6
13 TraesCS5D01G549200 chr4A 87.202 1008 82 20 761 1735 613544516 613543523 0.000000e+00 1103.0
14 TraesCS5D01G549200 chr4A 83.465 1010 109 15 735 1731 604856577 604857541 0.000000e+00 887.0
15 TraesCS5D01G549200 chr4A 82.113 956 131 30 959 1888 604940696 604941637 0.000000e+00 782.0
16 TraesCS5D01G549200 chr4A 84.156 385 38 15 103 467 604856152 604856533 4.330000e-93 351.0
17 TraesCS5D01G549200 chr4A 97.727 44 1 0 2517 2560 613551652 613551609 2.920000e-10 76.8
18 TraesCS5D01G549200 chr4A 100.000 28 0 0 1820 1847 604857599 604857626 5.000000e-03 52.8
19 TraesCS5D01G549200 chr2D 80.774 827 97 35 950 1736 498532965 498532161 8.440000e-165 590.0
20 TraesCS5D01G549200 chr1A 78.556 928 136 38 846 1740 517519652 517520549 1.110000e-153 553.0
21 TraesCS5D01G549200 chr2B 79.855 829 99 43 950 1735 585757407 585756604 6.660000e-151 544.0
22 TraesCS5D01G549200 chr1D 79.265 844 113 39 935 1741 421226277 421227095 1.440000e-147 532.0
23 TraesCS5D01G549200 chr2A 81.522 184 34 0 1291 1474 709126519 709126336 4.720000e-33 152.0


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 TraesCS5D01G549200 chr5D 556422412 556425146 2734 False 5051.000000 5051 100.000000 1 2735 1 chr5D.!!$F1 2734
1 TraesCS5D01G549200 chr5D 556449538 556450185 647 False 728.000000 728 86.892000 1062 1735 1 chr5D.!!$F2 673
2 TraesCS5D01G549200 chr5D 559978117 559979661 1544 True 713.500000 1088 84.019500 100 1848 2 chr5D.!!$R1 1748
3 TraesCS5D01G549200 chr5B 694287521 694290158 2637 True 1419.000000 2529 83.695500 107 2735 2 chr5B.!!$R4 2628
4 TraesCS5D01G549200 chr5B 710313432 710314393 961 True 725.000000 725 80.905000 959 1920 1 chr5B.!!$R2 961
5 TraesCS5D01G549200 chr5B 694202735 694203742 1007 True 662.000000 662 79.245000 918 1946 1 chr5B.!!$R1 1028
6 TraesCS5D01G549200 chr5B 710324999 710326660 1661 True 414.200000 811 87.559667 84 1946 3 chr5B.!!$R5 1862
7 TraesCS5D01G549200 chr5B 694261712 694262487 775 True 353.500000 501 83.555500 896 1735 2 chr5B.!!$R3 839
8 TraesCS5D01G549200 chr4A 613543523 613544516 993 True 1103.000000 1103 87.202000 761 1735 1 chr4A.!!$R1 974
9 TraesCS5D01G549200 chr4A 604940696 604941637 941 False 782.000000 782 82.113000 959 1888 1 chr4A.!!$F1 929
10 TraesCS5D01G549200 chr4A 604856152 604857626 1474 False 430.266667 887 89.207000 103 1847 3 chr4A.!!$F2 1744
11 TraesCS5D01G549200 chr2D 498532161 498532965 804 True 590.000000 590 80.774000 950 1736 1 chr2D.!!$R1 786
12 TraesCS5D01G549200 chr1A 517519652 517520549 897 False 553.000000 553 78.556000 846 1740 1 chr1A.!!$F1 894
13 TraesCS5D01G549200 chr2B 585756604 585757407 803 True 544.000000 544 79.855000 950 1735 1 chr2B.!!$R1 785
14 TraesCS5D01G549200 chr1D 421226277 421227095 818 False 532.000000 532 79.265000 935 1741 1 chr1D.!!$F1 806

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
48 49 0.033504 CACTTGGCACTACGTCCACT 59.966 55.0 0.0 0.0 30.97 4.0 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1755 2085 0.458025 GACCCATCCGTCGTCTTCAC 60.458 60.0 0.0 0.0 0.0 3.18 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
35 36 4.388499 CCGGTCGGGTCCACTTGG 62.388 72.222 0.74 0.00 0.00 3.61
37 38 3.948719 GGTCGGGTCCACTTGGCA 61.949 66.667 0.00 0.00 34.44 4.92
38 39 2.668550 GTCGGGTCCACTTGGCAC 60.669 66.667 0.00 0.00 34.44 5.01
39 40 2.847234 TCGGGTCCACTTGGCACT 60.847 61.111 0.00 0.00 34.44 4.40
40 41 1.534476 TCGGGTCCACTTGGCACTA 60.534 57.895 0.00 0.00 34.44 2.74
41 42 1.375523 CGGGTCCACTTGGCACTAC 60.376 63.158 0.00 0.00 34.44 2.73
42 43 1.375523 GGGTCCACTTGGCACTACG 60.376 63.158 0.00 0.00 34.44 3.51
43 44 1.370064 GGTCCACTTGGCACTACGT 59.630 57.895 0.00 0.00 34.44 3.57
44 45 0.669625 GGTCCACTTGGCACTACGTC 60.670 60.000 0.00 0.00 34.44 4.34
45 46 0.669625 GTCCACTTGGCACTACGTCC 60.670 60.000 0.00 0.00 34.44 4.79
46 47 1.116536 TCCACTTGGCACTACGTCCA 61.117 55.000 0.00 0.00 34.44 4.02
47 48 0.949105 CCACTTGGCACTACGTCCAC 60.949 60.000 0.00 0.00 30.97 4.02
48 49 0.033504 CACTTGGCACTACGTCCACT 59.966 55.000 0.00 0.00 30.97 4.00
49 50 0.756903 ACTTGGCACTACGTCCACTT 59.243 50.000 0.00 0.00 30.97 3.16
50 51 1.148310 CTTGGCACTACGTCCACTTG 58.852 55.000 0.00 0.00 30.97 3.16
51 52 0.753867 TTGGCACTACGTCCACTTGA 59.246 50.000 0.00 0.00 30.97 3.02
52 53 0.973632 TGGCACTACGTCCACTTGAT 59.026 50.000 0.00 0.00 0.00 2.57
53 54 1.346395 TGGCACTACGTCCACTTGATT 59.654 47.619 0.00 0.00 0.00 2.57
54 55 1.732259 GGCACTACGTCCACTTGATTG 59.268 52.381 0.00 0.00 0.00 2.67
55 56 2.413837 GCACTACGTCCACTTGATTGT 58.586 47.619 0.00 0.00 0.00 2.71
56 57 2.806244 GCACTACGTCCACTTGATTGTT 59.194 45.455 0.00 0.00 0.00 2.83
57 58 3.363970 GCACTACGTCCACTTGATTGTTG 60.364 47.826 0.00 0.00 0.00 3.33
58 59 2.806244 ACTACGTCCACTTGATTGTTGC 59.194 45.455 0.00 0.00 0.00 4.17
59 60 1.967319 ACGTCCACTTGATTGTTGCT 58.033 45.000 0.00 0.00 0.00 3.91
60 61 3.120321 ACGTCCACTTGATTGTTGCTA 57.880 42.857 0.00 0.00 0.00 3.49
61 62 3.472652 ACGTCCACTTGATTGTTGCTAA 58.527 40.909 0.00 0.00 0.00 3.09
62 63 3.880490 ACGTCCACTTGATTGTTGCTAAA 59.120 39.130 0.00 0.00 0.00 1.85
63 64 4.518970 ACGTCCACTTGATTGTTGCTAAAT 59.481 37.500 0.00 0.00 0.00 1.40
64 65 5.703592 ACGTCCACTTGATTGTTGCTAAATA 59.296 36.000 0.00 0.00 0.00 1.40
65 66 6.205853 ACGTCCACTTGATTGTTGCTAAATAA 59.794 34.615 0.00 0.00 0.00 1.40
66 67 6.742718 CGTCCACTTGATTGTTGCTAAATAAG 59.257 38.462 0.00 0.00 0.00 1.73
138 146 5.104776 CCCCATGATCGTTCACATATCCTAT 60.105 44.000 0.00 0.00 33.85 2.57
162 170 2.289631 TGCTCTTTTGCTTCCGATCTCA 60.290 45.455 0.00 0.00 0.00 3.27
196 205 8.394877 GTGATGAACGGTGAATATGAAAACATA 58.605 33.333 0.00 0.00 0.00 2.29
197 206 8.951243 TGATGAACGGTGAATATGAAAACATAA 58.049 29.630 0.00 0.00 0.00 1.90
198 207 9.781834 GATGAACGGTGAATATGAAAACATAAA 57.218 29.630 0.00 0.00 0.00 1.40
234 248 1.774110 TCCTTTTTCACCTGCAGCAA 58.226 45.000 8.66 0.00 0.00 3.91
241 272 6.532657 CCTTTTTCACCTGCAGCAATATTTAG 59.467 38.462 8.66 0.00 0.00 1.85
249 282 6.833416 ACCTGCAGCAATATTTAGGTTCAATA 59.167 34.615 8.66 0.00 35.09 1.90
345 386 8.603181 AGTTCAAAAATTGCATTTTGTGTAGAC 58.397 29.630 19.74 16.34 45.86 2.59
361 402 3.872771 TGTAGACCACCGACTTTGTTTTC 59.127 43.478 0.00 0.00 0.00 2.29
394 435 2.226437 ACCACGAATGTCATTTCTGCAC 59.774 45.455 0.00 0.00 0.00 4.57
412 454 3.171277 GCACGAAAAATACAGGCATGTC 58.829 45.455 7.56 0.00 41.01 3.06
413 455 3.119849 GCACGAAAAATACAGGCATGTCT 60.120 43.478 7.56 0.00 41.01 3.41
420 462 8.612619 CGAAAAATACAGGCATGTCTAATACTT 58.387 33.333 7.56 0.00 41.01 2.24
438 480 2.620115 ACTTGAACATGTCCACTGCAAG 59.380 45.455 0.00 8.96 42.29 4.01
497 544 8.786826 TTTAATTGTACACTTCATAGAGGTGG 57.213 34.615 12.83 0.00 42.66 4.61
499 546 6.814954 ATTGTACACTTCATAGAGGTGGAT 57.185 37.500 12.83 0.00 42.66 3.41
501 548 7.914427 TTGTACACTTCATAGAGGTGGATAT 57.086 36.000 12.83 0.00 42.66 1.63
512 559 2.439507 GAGGTGGATATGAGCTTGGGAA 59.560 50.000 0.00 0.00 0.00 3.97
533 580 3.314553 ACCAAAACTCTATGTCGTGACG 58.685 45.455 0.00 0.00 0.00 4.35
536 583 4.174009 CAAAACTCTATGTCGTGACGGAT 58.826 43.478 4.70 0.07 0.00 4.18
538 585 3.694535 ACTCTATGTCGTGACGGATTC 57.305 47.619 4.70 0.00 0.00 2.52
544 591 3.870723 TGTCGTGACGGATTCTTTTTG 57.129 42.857 4.70 0.00 0.00 2.44
545 592 3.199677 TGTCGTGACGGATTCTTTTTGT 58.800 40.909 4.70 0.00 0.00 2.83
547 594 3.493503 GTCGTGACGGATTCTTTTTGTCT 59.506 43.478 4.70 0.00 0.00 3.41
549 596 4.025229 TCGTGACGGATTCTTTTTGTCTTG 60.025 41.667 4.70 0.00 0.00 3.02
550 597 4.025229 CGTGACGGATTCTTTTTGTCTTGA 60.025 41.667 0.00 0.00 0.00 3.02
553 600 5.007626 TGACGGATTCTTTTTGTCTTGACAG 59.992 40.000 3.61 0.00 0.00 3.51
554 601 4.881850 ACGGATTCTTTTTGTCTTGACAGT 59.118 37.500 3.61 0.00 0.00 3.55
555 602 5.007724 ACGGATTCTTTTTGTCTTGACAGTC 59.992 40.000 3.61 0.00 0.00 3.51
556 603 5.007626 CGGATTCTTTTTGTCTTGACAGTCA 59.992 40.000 0.00 0.00 0.00 3.41
558 605 5.560966 TTCTTTTTGTCTTGACAGTCACC 57.439 39.130 1.52 0.00 0.00 4.02
559 606 4.584874 TCTTTTTGTCTTGACAGTCACCA 58.415 39.130 1.52 0.00 0.00 4.17
560 607 4.394920 TCTTTTTGTCTTGACAGTCACCAC 59.605 41.667 1.52 3.44 0.00 4.16
561 608 3.627395 TTTGTCTTGACAGTCACCACT 57.373 42.857 1.52 0.00 0.00 4.00
568 619 0.679505 GACAGTCACCACTAGTGCCA 59.320 55.000 17.86 0.00 46.81 4.92
570 621 0.036952 CAGTCACCACTAGTGCCAGG 60.037 60.000 17.86 6.39 46.81 4.45
608 659 6.866010 TGGATCTTAACATTCATGAATCCG 57.134 37.500 18.16 10.72 0.00 4.18
610 661 6.260714 TGGATCTTAACATTCATGAATCCGTG 59.739 38.462 18.16 11.24 0.00 4.94
612 663 6.662414 TCTTAACATTCATGAATCCGTGTC 57.338 37.500 18.16 0.00 0.00 3.67
613 664 6.406370 TCTTAACATTCATGAATCCGTGTCT 58.594 36.000 18.16 8.36 0.00 3.41
615 666 5.964958 AACATTCATGAATCCGTGTCTTT 57.035 34.783 18.16 0.00 0.00 2.52
618 669 7.447374 ACATTCATGAATCCGTGTCTTTTTA 57.553 32.000 18.16 0.00 0.00 1.52
619 670 8.055279 ACATTCATGAATCCGTGTCTTTTTAT 57.945 30.769 18.16 0.00 0.00 1.40
620 671 7.970061 ACATTCATGAATCCGTGTCTTTTTATG 59.030 33.333 18.16 5.58 0.00 1.90
621 672 6.435430 TCATGAATCCGTGTCTTTTTATGG 57.565 37.500 0.00 0.00 0.00 2.74
645 700 4.924305 TCCATAATTTGCTGGAATCTGC 57.076 40.909 2.54 0.00 38.59 4.26
646 701 4.279982 TCCATAATTTGCTGGAATCTGCA 58.720 39.130 2.54 0.00 44.27 4.41
652 707 0.913924 TGCTGGAATCTGCATCTCCA 59.086 50.000 10.25 10.25 41.77 3.86
660 715 4.455190 GGAATCTGCATCTCCATTTCTAGC 59.545 45.833 4.42 0.00 0.00 3.42
662 717 3.801698 TCTGCATCTCCATTTCTAGCAC 58.198 45.455 0.00 0.00 0.00 4.40
663 718 3.453717 TCTGCATCTCCATTTCTAGCACT 59.546 43.478 0.00 0.00 0.00 4.40
664 719 4.651045 TCTGCATCTCCATTTCTAGCACTA 59.349 41.667 0.00 0.00 0.00 2.74
668 723 5.868801 GCATCTCCATTTCTAGCACTATCTC 59.131 44.000 0.00 0.00 0.00 2.75
669 724 6.518032 GCATCTCCATTTCTAGCACTATCTCA 60.518 42.308 0.00 0.00 0.00 3.27
672 727 5.918608 TCCATTTCTAGCACTATCTCAACC 58.081 41.667 0.00 0.00 0.00 3.77
673 728 5.425217 TCCATTTCTAGCACTATCTCAACCA 59.575 40.000 0.00 0.00 0.00 3.67
674 729 6.070251 TCCATTTCTAGCACTATCTCAACCAA 60.070 38.462 0.00 0.00 0.00 3.67
675 730 6.037610 CCATTTCTAGCACTATCTCAACCAAC 59.962 42.308 0.00 0.00 0.00 3.77
676 731 5.738619 TTCTAGCACTATCTCAACCAACA 57.261 39.130 0.00 0.00 0.00 3.33
677 732 5.738619 TCTAGCACTATCTCAACCAACAA 57.261 39.130 0.00 0.00 0.00 2.83
678 733 6.109156 TCTAGCACTATCTCAACCAACAAA 57.891 37.500 0.00 0.00 0.00 2.83
680 735 7.168219 TCTAGCACTATCTCAACCAACAAAAT 58.832 34.615 0.00 0.00 0.00 1.82
682 737 7.759489 AGCACTATCTCAACCAACAAAATAA 57.241 32.000 0.00 0.00 0.00 1.40
683 738 8.353423 AGCACTATCTCAACCAACAAAATAAT 57.647 30.769 0.00 0.00 0.00 1.28
723 802 1.966451 CCCCAGCAAACTCCACGTC 60.966 63.158 0.00 0.00 0.00 4.34
726 805 2.665185 AGCAAACTCCACGTCGCC 60.665 61.111 0.00 0.00 0.00 5.54
727 806 2.970324 GCAAACTCCACGTCGCCA 60.970 61.111 0.00 0.00 0.00 5.69
728 807 2.325082 GCAAACTCCACGTCGCCAT 61.325 57.895 0.00 0.00 0.00 4.40
729 808 1.787847 CAAACTCCACGTCGCCATC 59.212 57.895 0.00 0.00 0.00 3.51
730 809 0.948623 CAAACTCCACGTCGCCATCA 60.949 55.000 0.00 0.00 0.00 3.07
731 810 0.949105 AAACTCCACGTCGCCATCAC 60.949 55.000 0.00 0.00 0.00 3.06
732 811 1.816863 AACTCCACGTCGCCATCACT 61.817 55.000 0.00 0.00 0.00 3.41
733 812 1.079819 CTCCACGTCGCCATCACTT 60.080 57.895 0.00 0.00 0.00 3.16
734 813 1.354337 CTCCACGTCGCCATCACTTG 61.354 60.000 0.00 0.00 0.00 3.16
735 814 2.476051 CACGTCGCCATCACTTGC 59.524 61.111 0.00 0.00 0.00 4.01
736 815 2.030412 ACGTCGCCATCACTTGCA 59.970 55.556 0.00 0.00 0.00 4.08
737 816 2.029288 ACGTCGCCATCACTTGCAG 61.029 57.895 0.00 0.00 0.00 4.41
738 817 2.029288 CGTCGCCATCACTTGCAGT 61.029 57.895 0.00 0.00 0.00 4.40
739 818 1.568612 CGTCGCCATCACTTGCAGTT 61.569 55.000 0.00 0.00 0.00 3.16
740 819 1.438651 GTCGCCATCACTTGCAGTTA 58.561 50.000 0.00 0.00 0.00 2.24
741 820 1.804151 GTCGCCATCACTTGCAGTTAA 59.196 47.619 0.00 0.00 0.00 2.01
742 821 2.225491 GTCGCCATCACTTGCAGTTAAA 59.775 45.455 0.00 0.00 0.00 1.52
743 822 2.225491 TCGCCATCACTTGCAGTTAAAC 59.775 45.455 0.00 0.00 0.00 2.01
744 823 2.031245 CGCCATCACTTGCAGTTAAACA 60.031 45.455 0.00 0.00 0.00 2.83
745 824 3.549827 CGCCATCACTTGCAGTTAAACAA 60.550 43.478 0.00 0.00 0.00 2.83
746 825 4.559153 GCCATCACTTGCAGTTAAACAAT 58.441 39.130 0.00 0.00 0.00 2.71
747 826 4.622740 GCCATCACTTGCAGTTAAACAATC 59.377 41.667 0.00 0.00 0.00 2.67
814 900 0.625683 ACCCTCCCCTGCATCATTCT 60.626 55.000 0.00 0.00 0.00 2.40
815 901 0.110104 CCCTCCCCTGCATCATTCTC 59.890 60.000 0.00 0.00 0.00 2.87
816 902 0.841961 CCTCCCCTGCATCATTCTCA 59.158 55.000 0.00 0.00 0.00 3.27
817 903 1.202782 CCTCCCCTGCATCATTCTCAG 60.203 57.143 0.00 0.00 0.00 3.35
818 904 0.841961 TCCCCTGCATCATTCTCAGG 59.158 55.000 0.00 0.00 45.24 3.86
819 905 0.549950 CCCCTGCATCATTCTCAGGT 59.450 55.000 6.74 0.00 44.41 4.00
820 906 1.476471 CCCCTGCATCATTCTCAGGTC 60.476 57.143 6.74 0.00 44.41 3.85
821 907 1.489649 CCCTGCATCATTCTCAGGTCT 59.510 52.381 6.74 0.00 44.41 3.85
822 908 2.485124 CCCTGCATCATTCTCAGGTCTC 60.485 54.545 6.74 0.00 44.41 3.36
823 909 2.169978 CCTGCATCATTCTCAGGTCTCA 59.830 50.000 0.00 0.00 41.76 3.27
824 910 3.459145 CTGCATCATTCTCAGGTCTCAG 58.541 50.000 0.00 0.00 0.00 3.35
825 911 2.211806 GCATCATTCTCAGGTCTCAGC 58.788 52.381 0.00 0.00 0.00 4.26
826 912 2.419713 GCATCATTCTCAGGTCTCAGCA 60.420 50.000 0.00 0.00 0.00 4.41
827 913 3.196463 CATCATTCTCAGGTCTCAGCAC 58.804 50.000 0.00 0.00 0.00 4.40
828 914 2.533916 TCATTCTCAGGTCTCAGCACT 58.466 47.619 0.00 0.00 0.00 4.40
829 915 2.233186 TCATTCTCAGGTCTCAGCACTG 59.767 50.000 0.00 0.00 0.00 3.66
830 916 0.319728 TTCTCAGGTCTCAGCACTGC 59.680 55.000 0.00 0.00 32.42 4.40
831 917 0.541530 TCTCAGGTCTCAGCACTGCT 60.542 55.000 0.00 0.00 40.77 4.24
832 918 0.108709 CTCAGGTCTCAGCACTGCTC 60.109 60.000 0.00 0.00 36.40 4.26
833 919 0.829182 TCAGGTCTCAGCACTGCTCA 60.829 55.000 0.00 0.00 36.40 4.26
834 920 0.034476 CAGGTCTCAGCACTGCTCAA 59.966 55.000 0.00 0.00 36.40 3.02
835 921 0.761187 AGGTCTCAGCACTGCTCAAA 59.239 50.000 0.00 0.00 36.40 2.69
836 922 1.155042 GGTCTCAGCACTGCTCAAAG 58.845 55.000 0.00 0.00 36.40 2.77
837 923 1.270518 GGTCTCAGCACTGCTCAAAGA 60.271 52.381 0.00 2.07 36.40 2.52
838 924 2.487934 GTCTCAGCACTGCTCAAAGAA 58.512 47.619 0.00 0.00 36.40 2.52
839 925 2.222911 GTCTCAGCACTGCTCAAAGAAC 59.777 50.000 0.00 0.00 36.40 3.01
840 926 2.103771 TCTCAGCACTGCTCAAAGAACT 59.896 45.455 0.00 0.00 36.40 3.01
889 999 2.267642 CGCCTCCATCCGTTCCAA 59.732 61.111 0.00 0.00 0.00 3.53
891 1001 1.749258 GCCTCCATCCGTTCCAACC 60.749 63.158 0.00 0.00 0.00 3.77
907 1039 3.107601 CCAACCTCCAACTCCATCTCTA 58.892 50.000 0.00 0.00 0.00 2.43
982 1127 3.708734 CAACCGGCGTCGACAACC 61.709 66.667 12.93 15.05 39.00 3.77
1013 1166 2.669229 TGCCATGACCACACAGCG 60.669 61.111 0.00 0.00 32.30 5.18
1248 1488 0.179073 CGGTGAATCAAGAGGCCGAT 60.179 55.000 3.51 0.00 41.45 4.18
1277 1572 0.766674 AAGGTGGCACTAGGTGTGGA 60.767 55.000 18.45 0.00 46.27 4.02
1539 1834 4.865761 GTATCGCCCGTGCTCGCA 62.866 66.667 1.89 0.00 35.54 5.10
1598 1907 1.871772 CGGTGAGCAAGAAGGCAAG 59.128 57.895 0.00 0.00 35.83 4.01
1753 2083 1.467734 GATGCAAGTCAAGCACTCAGG 59.532 52.381 0.00 0.00 45.95 3.86
1755 2085 1.864862 CAAGTCAAGCACTCAGGCG 59.135 57.895 0.00 0.00 39.27 5.52
1792 2123 2.299170 GTCGCTCGCTGTTTTTCTTTC 58.701 47.619 0.00 0.00 0.00 2.62
1795 2126 3.805422 TCGCTCGCTGTTTTTCTTTCTTA 59.195 39.130 0.00 0.00 0.00 2.10
1797 2128 5.636121 TCGCTCGCTGTTTTTCTTTCTTATA 59.364 36.000 0.00 0.00 0.00 0.98
1799 2130 6.625310 CGCTCGCTGTTTTTCTTTCTTATATC 59.375 38.462 0.00 0.00 0.00 1.63
1800 2131 7.464710 CGCTCGCTGTTTTTCTTTCTTATATCT 60.465 37.037 0.00 0.00 0.00 1.98
1801 2132 8.178313 GCTCGCTGTTTTTCTTTCTTATATCTT 58.822 33.333 0.00 0.00 0.00 2.40
1891 2242 1.246737 GGCTGAGCAGGTTTGGAAGG 61.247 60.000 6.82 0.00 0.00 3.46
1955 2311 3.519107 TGAATAGTTCACCAGATGCCTCA 59.481 43.478 0.00 0.00 34.08 3.86
1987 2343 9.371136 CTCACATCTTACATTCTTAACAAGCTA 57.629 33.333 0.00 0.00 0.00 3.32
1996 2352 2.504175 TCTTAACAAGCTAATCCCCGCT 59.496 45.455 0.00 0.00 38.30 5.52
2001 2357 2.364647 ACAAGCTAATCCCCGCTACTAC 59.635 50.000 0.00 0.00 34.96 2.73
2013 2369 3.243569 CCCGCTACTACCAATTCTCTCAG 60.244 52.174 0.00 0.00 0.00 3.35
2027 2383 2.627221 TCTCTCAGCATGCATACTCTCC 59.373 50.000 21.98 0.00 34.76 3.71
2071 2427 0.310854 CGGCAAGTTTGGGTCACTTC 59.689 55.000 0.00 0.00 31.83 3.01
2076 2432 2.281208 TTTGGGTCACTTCGGCCG 60.281 61.111 22.12 22.12 0.00 6.13
2081 2437 2.322830 GGTCACTTCGGCCGTTTCC 61.323 63.158 27.15 15.62 0.00 3.13
2093 2449 2.543031 GGCCGTTTCCTTTCAGACAAAC 60.543 50.000 0.00 0.00 0.00 2.93
2096 2452 4.351192 CCGTTTCCTTTCAGACAAACAAG 58.649 43.478 0.00 0.00 0.00 3.16
2097 2453 4.095782 CCGTTTCCTTTCAGACAAACAAGA 59.904 41.667 0.00 0.00 0.00 3.02
2098 2454 5.028375 CGTTTCCTTTCAGACAAACAAGAC 58.972 41.667 0.00 0.00 0.00 3.01
2099 2455 5.391523 CGTTTCCTTTCAGACAAACAAGACA 60.392 40.000 0.00 0.00 0.00 3.41
2100 2456 6.386654 GTTTCCTTTCAGACAAACAAGACAA 58.613 36.000 0.00 0.00 0.00 3.18
2103 2459 6.987386 TCCTTTCAGACAAACAAGACAAAAA 58.013 32.000 0.00 0.00 0.00 1.94
2147 2503 1.065928 GTGTGGATAGCGGACGGAG 59.934 63.158 0.00 0.00 0.00 4.63
2188 2544 4.371855 TGTTTTGCAAAATGTACGGTCA 57.628 36.364 26.24 14.37 0.00 4.02
2200 2556 4.088421 CGGTCACGTATCAGGTGC 57.912 61.111 0.00 0.00 34.28 5.01
2206 2564 4.321008 CGGTCACGTATCAGGTGCTATATT 60.321 45.833 0.00 0.00 34.28 1.28
2231 2589 6.489700 TCTTACTCAAGTTGATTGGCATTGAA 59.510 34.615 5.91 0.00 39.54 2.69
2270 2628 6.813152 GCAATGGTTACTGCACTCAAATTAAT 59.187 34.615 0.00 0.00 38.48 1.40
2271 2629 7.331687 GCAATGGTTACTGCACTCAAATTAATT 59.668 33.333 0.00 0.00 38.48 1.40
2272 2630 8.649841 CAATGGTTACTGCACTCAAATTAATTG 58.350 33.333 0.39 0.00 40.58 2.32
2328 2686 8.686334 GGCCAAAAGATCAAGATAAAATCACTA 58.314 33.333 0.00 0.00 0.00 2.74
2352 2710 2.528564 AGCTAGCTTTTCCATTGCCAA 58.471 42.857 12.68 0.00 0.00 4.52
2360 2718 4.335037 GCTTTTCCATTGCCAAGAAAAACA 59.665 37.500 6.20 0.00 38.60 2.83
2395 2753 4.699637 AGACAGTCACCACGTTTGAATTA 58.300 39.130 2.66 0.00 0.00 1.40
2463 2821 1.132643 GGAGTTAGACGTGTGAGCGAT 59.867 52.381 0.00 0.00 35.59 4.58
2480 2838 2.347939 GCGATAATGCTGACGTGTCATG 60.348 50.000 2.72 0.00 39.13 3.07
2498 2856 6.873076 GTGTCATGTCAAAGAAGAAGAGATCT 59.127 38.462 0.00 0.00 41.32 2.75
2516 2874 3.388552 TCTCAGCTGAAGGTAGATGGA 57.611 47.619 18.85 5.13 34.94 3.41
2583 2941 5.435686 TTGTTGAGCTAGTGATACCCAAT 57.564 39.130 0.00 0.00 0.00 3.16
2588 2946 4.038042 TGAGCTAGTGATACCCAATCGAAG 59.962 45.833 0.00 0.00 37.42 3.79
2589 2947 4.215908 AGCTAGTGATACCCAATCGAAGA 58.784 43.478 0.00 0.00 45.75 2.87
2590 2948 4.279671 AGCTAGTGATACCCAATCGAAGAG 59.720 45.833 0.00 0.00 43.63 2.85
2591 2949 4.038162 GCTAGTGATACCCAATCGAAGAGT 59.962 45.833 0.00 0.00 43.63 3.24
2633 2992 4.000325 CCGAGTGTTACATTGATGGTGAA 59.000 43.478 0.00 0.00 0.00 3.18
2634 2993 4.635765 CCGAGTGTTACATTGATGGTGAAT 59.364 41.667 0.00 0.00 0.00 2.57
2682 3041 1.829222 CTGGCATCCCAAAGCTTGAAT 59.171 47.619 0.00 0.00 41.58 2.57
2697 3056 6.319048 AGCTTGAATAAGGAATGGAGAGAA 57.681 37.500 0.00 0.00 34.40 2.87
2707 3066 0.833287 ATGGAGAGAACCATCGTGGG 59.167 55.000 8.57 1.74 46.24 4.61
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.504032 CCACCACCACGTGTGTCT 59.496 61.111 15.65 0.00 43.85 3.41
1 2 3.276846 GCCACCACCACGTGTGTC 61.277 66.667 15.65 0.00 43.85 3.67
18 19 4.388499 CCAAGTGGACCCGACCGG 62.388 72.222 0.00 0.00 37.39 5.28
20 21 3.948719 TGCCAAGTGGACCCGACC 61.949 66.667 0.18 0.00 37.39 4.79
21 22 1.823169 TAGTGCCAAGTGGACCCGAC 61.823 60.000 0.18 0.00 37.39 4.79
22 23 1.534476 TAGTGCCAAGTGGACCCGA 60.534 57.895 0.18 0.00 37.39 5.14
23 24 1.375523 GTAGTGCCAAGTGGACCCG 60.376 63.158 0.18 0.00 37.39 5.28
24 25 1.375523 CGTAGTGCCAAGTGGACCC 60.376 63.158 0.18 0.00 37.39 4.46
25 26 1.370064 ACGTAGTGCCAAGTGGACC 59.630 57.895 0.18 0.00 42.51 4.46
38 39 3.067106 AGCAACAATCAAGTGGACGTAG 58.933 45.455 0.00 0.00 0.00 3.51
39 40 3.120321 AGCAACAATCAAGTGGACGTA 57.880 42.857 0.00 0.00 0.00 3.57
40 41 1.967319 AGCAACAATCAAGTGGACGT 58.033 45.000 0.00 0.00 0.00 4.34
41 42 4.481930 TTTAGCAACAATCAAGTGGACG 57.518 40.909 0.00 0.00 0.00 4.79
53 54 8.850033 GCTGATGAGCTAGCTTATTTAGCAACA 61.850 40.741 31.95 22.18 46.38 3.33
54 55 6.565623 GCTGATGAGCTAGCTTATTTAGCAAC 60.566 42.308 31.95 19.85 46.38 4.17
55 56 5.468072 GCTGATGAGCTAGCTTATTTAGCAA 59.532 40.000 31.95 14.77 46.38 3.91
56 57 4.993584 GCTGATGAGCTAGCTTATTTAGCA 59.006 41.667 31.95 21.86 46.38 3.49
57 58 5.529014 GCTGATGAGCTAGCTTATTTAGC 57.471 43.478 27.79 27.79 45.31 3.09
70 71 3.329386 TGAACTTGTGTAGCTGATGAGC 58.671 45.455 0.00 0.00 46.64 4.26
71 72 6.492007 AATTGAACTTGTGTAGCTGATGAG 57.508 37.500 0.00 0.00 0.00 2.90
72 73 7.977789 TTAATTGAACTTGTGTAGCTGATGA 57.022 32.000 0.00 0.00 0.00 2.92
138 146 4.517285 AGATCGGAAGCAAAAGAGCATAA 58.483 39.130 0.00 0.00 36.85 1.90
217 231 6.532657 CCTAAATATTGCTGCAGGTGAAAAAG 59.467 38.462 17.12 0.00 0.00 2.27
249 282 9.985730 TCAAATGCAGTAATTTCTTCAGAAAAT 57.014 25.926 6.09 0.91 45.81 1.82
345 386 2.021457 ACTGGAAAACAAAGTCGGTGG 58.979 47.619 0.00 0.00 0.00 4.61
361 402 0.249120 TTCGTGGTGCTATGGACTGG 59.751 55.000 0.00 0.00 0.00 4.00
394 435 8.142994 AGTATTAGACATGCCTGTATTTTTCG 57.857 34.615 0.00 0.00 35.14 3.46
412 454 5.643348 TGCAGTGGACATGTTCAAGTATTAG 59.357 40.000 8.85 0.00 0.00 1.73
413 455 5.555966 TGCAGTGGACATGTTCAAGTATTA 58.444 37.500 8.85 0.00 0.00 0.98
420 462 0.953727 GCTTGCAGTGGACATGTTCA 59.046 50.000 1.52 1.52 0.00 3.18
474 521 7.727578 TCCACCTCTATGAAGTGTACAATTA 57.272 36.000 8.79 0.00 0.00 1.40
475 522 6.620877 TCCACCTCTATGAAGTGTACAATT 57.379 37.500 8.54 8.54 0.00 2.32
479 526 7.526142 TCATATCCACCTCTATGAAGTGTAC 57.474 40.000 0.00 0.00 32.77 2.90
482 529 5.245751 AGCTCATATCCACCTCTATGAAGTG 59.754 44.000 0.00 0.00 34.77 3.16
491 538 2.050144 TCCCAAGCTCATATCCACCTC 58.950 52.381 0.00 0.00 0.00 3.85
492 539 2.173569 GTTCCCAAGCTCATATCCACCT 59.826 50.000 0.00 0.00 0.00 4.00
496 543 3.297134 TTGGTTCCCAAGCTCATATCC 57.703 47.619 0.00 0.00 38.75 2.59
497 544 4.706962 AGTTTTGGTTCCCAAGCTCATATC 59.293 41.667 0.00 0.00 44.84 1.63
499 546 4.079253 GAGTTTTGGTTCCCAAGCTCATA 58.921 43.478 17.30 0.00 44.84 2.15
501 548 2.091885 AGAGTTTTGGTTCCCAAGCTCA 60.092 45.455 21.07 0.00 44.84 4.26
512 559 3.314553 CGTCACGACATAGAGTTTTGGT 58.685 45.455 0.00 0.00 0.00 3.67
518 565 3.280295 AGAATCCGTCACGACATAGAGT 58.720 45.455 0.00 0.00 0.00 3.24
522 569 4.992319 ACAAAAAGAATCCGTCACGACATA 59.008 37.500 0.00 0.00 0.00 2.29
524 571 3.199677 ACAAAAAGAATCCGTCACGACA 58.800 40.909 0.00 0.00 0.00 4.35
533 580 6.202226 GTGACTGTCAAGACAAAAAGAATCC 58.798 40.000 12.81 0.00 41.33 3.01
536 583 5.007034 TGGTGACTGTCAAGACAAAAAGAA 58.993 37.500 12.81 0.00 41.33 2.52
538 585 4.396166 AGTGGTGACTGTCAAGACAAAAAG 59.604 41.667 12.81 0.00 41.33 2.27
556 603 3.181434 TGAAATTTCCTGGCACTAGTGGT 60.181 43.478 23.95 0.00 0.00 4.16
558 605 5.452078 TTTGAAATTTCCTGGCACTAGTG 57.548 39.130 18.93 18.93 0.00 2.74
559 606 6.670695 AATTTGAAATTTCCTGGCACTAGT 57.329 33.333 15.48 0.00 0.00 2.57
560 607 7.967890 AAAATTTGAAATTTCCTGGCACTAG 57.032 32.000 15.43 0.00 0.00 2.57
561 608 7.228308 CCAAAAATTTGAAATTTCCTGGCACTA 59.772 33.333 21.52 0.00 40.55 2.74
602 653 6.090783 GGAAACCATAAAAAGACACGGATTC 58.909 40.000 0.00 0.00 0.00 2.52
606 657 4.839668 TGGAAACCATAAAAAGACACGG 57.160 40.909 0.00 0.00 0.00 4.94
630 685 2.957006 GGAGATGCAGATTCCAGCAAAT 59.043 45.455 8.58 0.00 44.88 2.32
637 692 4.455190 GCTAGAAATGGAGATGCAGATTCC 59.545 45.833 0.00 6.91 0.00 3.01
642 697 3.806380 AGTGCTAGAAATGGAGATGCAG 58.194 45.455 0.00 0.00 0.00 4.41
645 700 6.990798 TGAGATAGTGCTAGAAATGGAGATG 58.009 40.000 0.00 0.00 0.00 2.90
646 701 7.441017 GTTGAGATAGTGCTAGAAATGGAGAT 58.559 38.462 0.00 0.00 0.00 2.75
652 707 6.711277 TGTTGGTTGAGATAGTGCTAGAAAT 58.289 36.000 0.00 0.00 0.00 2.17
680 735 9.149225 GGCACATTTGTTTTGACATGAATATTA 57.851 29.630 0.00 0.00 0.00 0.98
682 737 6.594937 GGGCACATTTGTTTTGACATGAATAT 59.405 34.615 0.00 0.00 0.00 1.28
683 738 5.931146 GGGCACATTTGTTTTGACATGAATA 59.069 36.000 0.00 0.00 0.00 1.75
685 740 4.125703 GGGCACATTTGTTTTGACATGAA 58.874 39.130 0.00 0.00 0.00 2.57
715 794 1.079819 AAGTGATGGCGACGTGGAG 60.080 57.895 0.11 0.00 0.00 3.86
717 796 3.027170 GCAAGTGATGGCGACGTGG 62.027 63.158 0.00 0.00 0.00 4.94
731 810 6.145535 GTCTCCTTGATTGTTTAACTGCAAG 58.854 40.000 13.73 13.73 42.29 4.01
732 811 5.592282 TGTCTCCTTGATTGTTTAACTGCAA 59.408 36.000 0.00 0.00 0.00 4.08
733 812 5.129634 TGTCTCCTTGATTGTTTAACTGCA 58.870 37.500 0.00 0.00 0.00 4.41
734 813 5.470098 TCTGTCTCCTTGATTGTTTAACTGC 59.530 40.000 0.00 0.00 0.00 4.40
735 814 6.931281 TCTCTGTCTCCTTGATTGTTTAACTG 59.069 38.462 0.00 0.00 0.00 3.16
736 815 7.067496 TCTCTGTCTCCTTGATTGTTTAACT 57.933 36.000 0.00 0.00 0.00 2.24
737 816 7.572168 GCTTCTCTGTCTCCTTGATTGTTTAAC 60.572 40.741 0.00 0.00 0.00 2.01
738 817 6.428159 GCTTCTCTGTCTCCTTGATTGTTTAA 59.572 38.462 0.00 0.00 0.00 1.52
739 818 5.934625 GCTTCTCTGTCTCCTTGATTGTTTA 59.065 40.000 0.00 0.00 0.00 2.01
740 819 4.759183 GCTTCTCTGTCTCCTTGATTGTTT 59.241 41.667 0.00 0.00 0.00 2.83
741 820 4.202398 TGCTTCTCTGTCTCCTTGATTGTT 60.202 41.667 0.00 0.00 0.00 2.83
742 821 3.326006 TGCTTCTCTGTCTCCTTGATTGT 59.674 43.478 0.00 0.00 0.00 2.71
743 822 3.933955 CTGCTTCTCTGTCTCCTTGATTG 59.066 47.826 0.00 0.00 0.00 2.67
744 823 3.837146 TCTGCTTCTCTGTCTCCTTGATT 59.163 43.478 0.00 0.00 0.00 2.57
745 824 3.439154 TCTGCTTCTCTGTCTCCTTGAT 58.561 45.455 0.00 0.00 0.00 2.57
746 825 2.824936 CTCTGCTTCTCTGTCTCCTTGA 59.175 50.000 0.00 0.00 0.00 3.02
747 826 2.674747 GCTCTGCTTCTCTGTCTCCTTG 60.675 54.545 0.00 0.00 0.00 3.61
775 861 7.039722 AGGGTAGAGTTGGAATTATTGGAAA 57.960 36.000 0.00 0.00 0.00 3.13
776 862 6.353602 GGAGGGTAGAGTTGGAATTATTGGAA 60.354 42.308 0.00 0.00 0.00 3.53
777 863 5.132144 GGAGGGTAGAGTTGGAATTATTGGA 59.868 44.000 0.00 0.00 0.00 3.53
814 900 0.829182 TGAGCAGTGCTGAGACCTGA 60.829 55.000 25.35 0.00 39.88 3.86
815 901 0.034476 TTGAGCAGTGCTGAGACCTG 59.966 55.000 25.35 0.00 39.88 4.00
816 902 0.761187 TTTGAGCAGTGCTGAGACCT 59.239 50.000 25.35 0.00 39.88 3.85
817 903 1.155042 CTTTGAGCAGTGCTGAGACC 58.845 55.000 25.35 8.21 39.88 3.85
818 904 2.160822 TCTTTGAGCAGTGCTGAGAC 57.839 50.000 25.35 8.63 39.88 3.36
819 905 2.103771 AGTTCTTTGAGCAGTGCTGAGA 59.896 45.455 25.35 18.88 39.88 3.27
820 906 2.492012 AGTTCTTTGAGCAGTGCTGAG 58.508 47.619 25.35 16.88 39.88 3.35
821 907 2.627515 AGTTCTTTGAGCAGTGCTGA 57.372 45.000 25.35 12.51 39.88 4.26
822 908 2.349249 CGAAGTTCTTTGAGCAGTGCTG 60.349 50.000 25.35 8.25 39.88 4.41
823 909 1.869767 CGAAGTTCTTTGAGCAGTGCT 59.130 47.619 19.86 19.86 43.88 4.40
824 910 1.661460 GCGAAGTTCTTTGAGCAGTGC 60.661 52.381 7.13 7.13 0.00 4.40
825 911 1.397693 CGCGAAGTTCTTTGAGCAGTG 60.398 52.381 0.00 0.00 0.00 3.66
826 912 0.861837 CGCGAAGTTCTTTGAGCAGT 59.138 50.000 0.00 0.00 0.00 4.40
827 913 0.451792 GCGCGAAGTTCTTTGAGCAG 60.452 55.000 12.10 8.64 0.00 4.24
828 914 1.569493 GCGCGAAGTTCTTTGAGCA 59.431 52.632 12.10 0.00 0.00 4.26
829 915 1.154395 GGCGCGAAGTTCTTTGAGC 60.154 57.895 12.10 16.39 0.00 4.26
830 916 0.110644 GTGGCGCGAAGTTCTTTGAG 60.111 55.000 12.10 2.17 0.00 3.02
831 917 1.503818 GGTGGCGCGAAGTTCTTTGA 61.504 55.000 12.10 0.00 0.00 2.69
832 918 1.082104 GGTGGCGCGAAGTTCTTTG 60.082 57.895 12.10 0.00 0.00 2.77
833 919 2.604174 CGGTGGCGCGAAGTTCTTT 61.604 57.895 12.10 0.00 0.00 2.52
834 920 3.041940 CGGTGGCGCGAAGTTCTT 61.042 61.111 12.10 0.00 0.00 2.52
836 922 3.797145 TATACCGGTGGCGCGAAGTTC 62.797 57.143 19.93 0.00 0.00 3.01
837 923 1.947597 TATACCGGTGGCGCGAAGTT 61.948 55.000 19.93 0.00 0.00 2.66
838 924 1.947597 TTATACCGGTGGCGCGAAGT 61.948 55.000 19.93 0.00 0.00 3.01
839 925 0.806884 TTTATACCGGTGGCGCGAAG 60.807 55.000 19.93 0.00 0.00 3.79
840 926 0.179078 ATTTATACCGGTGGCGCGAA 60.179 50.000 19.93 3.74 0.00 4.70
889 999 3.970640 GGATTAGAGATGGAGTTGGAGGT 59.029 47.826 0.00 0.00 0.00 3.85
891 1001 3.969976 TGGGATTAGAGATGGAGTTGGAG 59.030 47.826 0.00 0.00 0.00 3.86
907 1039 1.972660 GAGGCCGTGCTACTGGGATT 61.973 60.000 0.00 0.00 0.00 3.01
966 1111 3.853597 GAGGTTGTCGACGCCGGTT 62.854 63.158 19.03 6.22 36.24 4.44
1013 1166 2.617274 GCTGCTCGGTGGTGGTTTC 61.617 63.158 0.00 0.00 0.00 2.78
1236 1476 1.045350 CCTCCTCATCGGCCTCTTGA 61.045 60.000 0.00 0.00 0.00 3.02
1248 1488 1.461268 TGCCACCTTGTCCTCCTCA 60.461 57.895 0.00 0.00 0.00 3.86
1702 2029 1.300963 GGCTCCAGCACCATGAAGA 59.699 57.895 0.03 0.00 44.36 2.87
1703 2030 1.001764 TGGCTCCAGCACCATGAAG 60.002 57.895 0.03 0.00 44.36 3.02
1753 2083 2.158959 CCATCCGTCGTCTTCACGC 61.159 63.158 0.00 0.00 46.28 5.34
1755 2085 0.458025 GACCCATCCGTCGTCTTCAC 60.458 60.000 0.00 0.00 0.00 3.18
1809 2140 8.666573 GCTATCTGAATTCTATCACCATGAATG 58.333 37.037 7.05 0.00 31.70 2.67
1810 2141 8.604184 AGCTATCTGAATTCTATCACCATGAAT 58.396 33.333 7.05 0.00 32.52 2.57
1811 2142 7.971201 AGCTATCTGAATTCTATCACCATGAA 58.029 34.615 7.05 0.00 0.00 2.57
1891 2242 8.513774 ACATGATTCAAACCAAAATATTTTGCC 58.486 29.630 28.17 13.11 44.62 4.52
1947 2303 2.871182 TGTGAGATACGTGAGGCATC 57.129 50.000 0.00 0.00 0.00 3.91
1955 2311 9.517609 GTTAAGAATGTAAGATGTGAGATACGT 57.482 33.333 0.00 0.00 0.00 3.57
1987 2343 3.046374 AGAATTGGTAGTAGCGGGGATT 58.954 45.455 0.00 0.00 0.00 3.01
1996 2352 4.162131 TGCATGCTGAGAGAATTGGTAGTA 59.838 41.667 20.33 0.00 0.00 1.82
2001 2357 4.135306 AGTATGCATGCTGAGAGAATTGG 58.865 43.478 17.13 0.00 0.00 3.16
2013 2369 2.842457 TGATGTGGAGAGTATGCATGC 58.158 47.619 11.82 11.82 0.00 4.06
2027 2383 5.278315 CCTGACATGGCATAAAGATGATGTG 60.278 44.000 0.00 0.00 33.08 3.21
2071 2427 0.882927 TGTCTGAAAGGAAACGGCCG 60.883 55.000 26.86 26.86 0.00 6.13
2076 2432 5.949735 TGTCTTGTTTGTCTGAAAGGAAAC 58.050 37.500 0.00 0.00 37.27 2.78
2100 2456 3.071457 CCTGGTCCCTTGAAGCAATTTTT 59.929 43.478 0.00 0.00 0.00 1.94
2103 2459 1.428912 TCCTGGTCCCTTGAAGCAATT 59.571 47.619 0.00 0.00 0.00 2.32
2104 2460 1.075601 TCCTGGTCCCTTGAAGCAAT 58.924 50.000 0.00 0.00 0.00 3.56
2105 2461 1.075601 ATCCTGGTCCCTTGAAGCAA 58.924 50.000 0.00 0.00 0.00 3.91
2106 2462 1.965414 TATCCTGGTCCCTTGAAGCA 58.035 50.000 0.00 0.00 0.00 3.91
2107 2463 3.282885 CTTTATCCTGGTCCCTTGAAGC 58.717 50.000 0.00 0.00 0.00 3.86
2108 2464 3.267031 ACCTTTATCCTGGTCCCTTGAAG 59.733 47.826 0.00 0.00 29.18 3.02
2109 2465 3.010138 CACCTTTATCCTGGTCCCTTGAA 59.990 47.826 0.00 0.00 33.75 2.69
2110 2466 2.576191 CACCTTTATCCTGGTCCCTTGA 59.424 50.000 0.00 0.00 33.75 3.02
2111 2467 2.308866 ACACCTTTATCCTGGTCCCTTG 59.691 50.000 0.00 0.00 33.75 3.61
2112 2468 2.308866 CACACCTTTATCCTGGTCCCTT 59.691 50.000 0.00 0.00 33.75 3.95
2113 2469 1.916181 CACACCTTTATCCTGGTCCCT 59.084 52.381 0.00 0.00 33.75 4.20
2114 2470 1.064685 CCACACCTTTATCCTGGTCCC 60.065 57.143 0.00 0.00 33.75 4.46
2115 2471 1.913419 TCCACACCTTTATCCTGGTCC 59.087 52.381 0.00 0.00 33.75 4.46
2116 2472 3.933861 ATCCACACCTTTATCCTGGTC 57.066 47.619 0.00 0.00 33.75 4.02
2117 2473 3.136626 GCTATCCACACCTTTATCCTGGT 59.863 47.826 0.00 0.00 36.96 4.00
2118 2474 3.744660 GCTATCCACACCTTTATCCTGG 58.255 50.000 0.00 0.00 0.00 4.45
2147 2503 0.883153 AAACCCGCCGTTTTACATCC 59.117 50.000 0.00 0.00 42.15 3.51
2188 2544 7.447545 TGAGTAAGAATATAGCACCTGATACGT 59.552 37.037 0.00 0.00 0.00 3.57
2200 2556 9.330063 TGCCAATCAACTTGAGTAAGAATATAG 57.670 33.333 0.00 0.00 36.97 1.31
2206 2564 6.003326 TCAATGCCAATCAACTTGAGTAAGA 58.997 36.000 0.00 0.00 36.97 2.10
2231 2589 6.823689 AGTAACCATTGCTTCAATCGAACTAT 59.176 34.615 0.00 0.00 31.05 2.12
2328 2686 4.140536 GGCAATGGAAAAGCTAGCTATCT 58.859 43.478 19.70 5.15 0.00 1.98
2330 2688 3.902218 TGGCAATGGAAAAGCTAGCTAT 58.098 40.909 19.70 10.41 0.00 2.97
2352 2710 7.514721 TGTCTTTATCCACTACCTGTTTTTCT 58.485 34.615 0.00 0.00 0.00 2.52
2360 2718 4.466726 GGTGACTGTCTTTATCCACTACCT 59.533 45.833 9.51 0.00 0.00 3.08
2395 2753 2.457366 GGAACAATCCACGTCAGAGT 57.543 50.000 0.00 0.00 45.79 3.24
2463 2821 3.311486 TGACATGACACGTCAGCATTA 57.689 42.857 0.00 0.00 43.61 1.90
2480 2838 5.577945 CAGCTGAGATCTCTTCTTCTTTGAC 59.422 44.000 22.95 0.00 33.74 3.18
2498 2856 4.155709 CCTATCCATCTACCTTCAGCTGA 58.844 47.826 13.74 13.74 0.00 4.26
2612 2971 5.801350 ATTCACCATCAATGTAACACTCG 57.199 39.130 0.00 0.00 0.00 4.18
2633 2992 5.728637 TGACGTATTCAGGCATGAGATAT 57.271 39.130 0.00 0.00 36.61 1.63
2634 2993 5.163457 TGTTGACGTATTCAGGCATGAGATA 60.163 40.000 0.00 0.48 36.61 1.98
2682 3041 4.030913 ACGATGGTTCTCTCCATTCCTTA 58.969 43.478 0.00 0.00 46.72 2.69
2697 3056 1.684869 CCTAATTTGGCCCACGATGGT 60.685 52.381 0.00 0.00 35.17 3.55


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

AutoCloner maintained by Alex Coulton.