Multiple sequence alignment - TraesCS4A01G349300

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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 TraesCS4A01G349300 chr4A 100.000 4723 0 0 1 4723 626115348 626120070 0.000000e+00 8722.0
1 TraesCS4A01G349300 chr4A 100.000 29 0 0 801 829 626116090 626116118 2.000000e-03 54.7
2 TraesCS4A01G349300 chr4A 100.000 29 0 0 743 771 626116148 626116176 2.000000e-03 54.7
3 TraesCS4A01G349300 chr5D 93.982 1994 89 11 2757 4723 543058668 543056679 0.000000e+00 2988.0
4 TraesCS4A01G349300 chr5D 91.293 1160 76 14 1010 2158 543060567 543059422 0.000000e+00 1559.0
5 TraesCS4A01G349300 chr5D 83.975 805 93 25 1 789 543062174 543061390 0.000000e+00 739.0
6 TraesCS4A01G349300 chr5D 87.480 615 58 9 2154 2750 543059384 543058771 0.000000e+00 691.0
7 TraesCS4A01G349300 chr5D 94.828 58 3 0 832 889 543060908 543060851 1.810000e-14 91.6
8 TraesCS4A01G349300 chr5B 93.357 1987 87 11 2757 4723 684495260 684493299 0.000000e+00 2896.0
9 TraesCS4A01G349300 chr5B 91.412 1176 66 17 998 2156 684497194 684496037 0.000000e+00 1580.0
10 TraesCS4A01G349300 chr5B 87.196 617 60 11 2154 2752 684496004 684495389 0.000000e+00 684.0
11 TraesCS4A01G349300 chr5B 81.200 750 104 22 1 732 684501153 684500423 1.910000e-158 569.0
12 TraesCS4A01G349300 chr5B 84.024 338 53 1 1 338 684545524 684545188 1.640000e-84 324.0
13 TraesCS4A01G349300 chr5B 96.104 77 1 1 829 903 684497579 684497503 1.780000e-24 124.0
14 TraesCS4A01G349300 chrUn 86.087 575 43 24 1162 1718 73933202 73933757 6.810000e-163 584.0
15 TraesCS4A01G349300 chr6B 85.490 572 51 18 1165 1718 559066405 559065848 6.860000e-158 568.0
16 TraesCS4A01G349300 chr7D 83.521 267 17 9 4473 4723 529383289 529383034 1.710000e-54 224.0
17 TraesCS4A01G349300 chr7D 83.908 261 15 9 4473 4717 529384226 529384475 1.710000e-54 224.0
18 TraesCS4A01G349300 chr2B 78.341 217 34 10 2443 2653 349512728 349512519 1.380000e-25 128.0
19 TraesCS4A01G349300 chr7B 100.000 28 0 0 1038 1065 702568947 702568920 9.000000e-03 52.8


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 TraesCS4A01G349300 chr4A 626115348 626120070 4722 False 2943.80 8722 100.0000 1 4723 3 chr4A.!!$F1 4722
1 TraesCS4A01G349300 chr5D 543056679 543062174 5495 True 1213.72 2988 90.3116 1 4723 5 chr5D.!!$R1 4722
2 TraesCS4A01G349300 chr5B 684493299 684501153 7854 True 1170.60 2896 89.8538 1 4723 5 chr5B.!!$R2 4722
3 TraesCS4A01G349300 chrUn 73933202 73933757 555 False 584.00 584 86.0870 1162 1718 1 chrUn.!!$F1 556
4 TraesCS4A01G349300 chr6B 559065848 559066405 557 True 568.00 568 85.4900 1165 1718 1 chr6B.!!$R1 553

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
494 502 0.107214 TCTATGCGCCAAGGAAAGGG 60.107 55.0 4.18 0.0 0.00 3.95 F
759 800 0.248843 GGATCGAGGCCATCATCTCC 59.751 60.0 5.01 0.0 0.00 3.71 F
992 3824 0.322975 CCAGCCCTAGATCCCATTCG 59.677 60.0 0.00 0.0 0.00 3.34 F
1800 4886 0.606401 AGATGGTGTTTGTGCGAGGG 60.606 55.0 0.00 0.0 0.00 4.30 F
2223 5391 0.656785 GACCGTACAACGCCAAACAA 59.343 50.0 0.00 0.0 40.91 2.83 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2019 5105 0.317770 AACAAATGTGGCTTCGCACG 60.318 50.000 0.0 0.0 33.32 5.34 R
2425 5596 0.602638 CACACTACCCGCACACACAT 60.603 55.000 0.0 0.0 0.00 3.21 R
2761 6071 0.320374 CCCGTTGTGAGAAGCTACCA 59.680 55.000 0.0 0.0 0.00 3.25 R
3005 6315 1.134580 ACAGATTGGATGAGCTGACCG 60.135 52.381 0.0 0.0 32.86 4.79 R
4157 7508 0.036010 TGCTAGAAGGAAGCTGTGCC 60.036 55.000 0.0 0.0 40.73 5.01 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
81 82 6.889198 TCAAAGGCTATAGTAAAGATGCACT 58.111 36.000 0.84 0.00 0.00 4.40
102 103 5.852738 CTCATTTGAGTCAACACCTACAG 57.147 43.478 4.68 0.00 37.40 2.74
124 125 1.845809 GCAAGCAACCGTCCTCTGTG 61.846 60.000 0.00 0.00 0.00 3.66
126 127 0.532862 AAGCAACCGTCCTCTGTGTG 60.533 55.000 0.00 0.00 0.00 3.82
131 132 0.959553 ACCGTCCTCTGTGTGTAGTG 59.040 55.000 0.00 0.00 0.00 2.74
144 145 8.757164 TCTGTGTGTAGTGTTAATATGACAAG 57.243 34.615 0.00 0.00 0.00 3.16
152 153 6.349300 AGTGTTAATATGACAAGCACCTAGG 58.651 40.000 7.41 7.41 0.00 3.02
162 163 2.031495 AGCACCTAGGAAGACCACTT 57.969 50.000 17.98 0.00 38.94 3.16
165 166 0.608640 ACCTAGGAAGACCACTTGCG 59.391 55.000 17.98 0.00 46.51 4.85
173 174 1.965930 GACCACTTGCGTGCATCCA 60.966 57.895 0.00 0.00 39.86 3.41
203 204 2.156917 CCACTCTTGCAAGCATCAAGA 58.843 47.619 21.99 12.57 45.25 3.02
204 205 2.555325 CCACTCTTGCAAGCATCAAGAA 59.445 45.455 21.99 0.62 46.25 2.52
208 209 3.968649 TCTTGCAAGCATCAAGAAACAC 58.031 40.909 21.99 0.00 44.70 3.32
219 220 7.810658 AGCATCAAGAAACACTGTATAGTTTG 58.189 34.615 0.00 0.00 38.01 2.93
239 240 5.389859 TTGGTAAACTTCATTGCCTCATG 57.610 39.130 0.00 0.00 36.19 3.07
287 294 3.465871 GTTGCTCCTCCTGATCTCATTC 58.534 50.000 0.00 0.00 0.00 2.67
288 295 2.755686 TGCTCCTCCTGATCTCATTCA 58.244 47.619 0.00 0.00 0.00 2.57
393 401 3.634397 TTCATCCTTCCAGGTGTCATC 57.366 47.619 0.00 0.00 36.53 2.92
394 402 2.550175 TCATCCTTCCAGGTGTCATCA 58.450 47.619 0.00 0.00 36.53 3.07
395 403 3.117745 TCATCCTTCCAGGTGTCATCAT 58.882 45.455 0.00 0.00 36.53 2.45
413 421 5.655090 TCATCATGTGCCATTCTTTCTGAAT 59.345 36.000 0.00 0.00 45.52 2.57
418 426 7.339976 TCATGTGCCATTCTTTCTGAATAATCA 59.660 33.333 0.00 0.00 43.00 2.57
455 463 0.824109 TTCATGTCCTAGTCTGCCCG 59.176 55.000 0.00 0.00 0.00 6.13
456 464 1.227380 CATGTCCTAGTCTGCCCGC 60.227 63.158 0.00 0.00 0.00 6.13
457 465 1.381872 ATGTCCTAGTCTGCCCGCT 60.382 57.895 0.00 0.00 0.00 5.52
458 466 1.395826 ATGTCCTAGTCTGCCCGCTC 61.396 60.000 0.00 0.00 0.00 5.03
459 467 1.755008 GTCCTAGTCTGCCCGCTCT 60.755 63.158 0.00 0.00 0.00 4.09
460 468 1.454111 TCCTAGTCTGCCCGCTCTC 60.454 63.158 0.00 0.00 0.00 3.20
469 477 1.299773 GCCCGCTCTCAATCTCTCG 60.300 63.158 0.00 0.00 0.00 4.04
472 480 1.135139 CCCGCTCTCAATCTCTCGAAA 59.865 52.381 0.00 0.00 0.00 3.46
481 489 7.220683 GCTCTCAATCTCTCGAAATATCTATGC 59.779 40.741 0.00 0.00 0.00 3.14
483 491 5.802451 TCAATCTCTCGAAATATCTATGCGC 59.198 40.000 0.00 0.00 0.00 6.09
494 502 0.107214 TCTATGCGCCAAGGAAAGGG 60.107 55.000 4.18 0.00 0.00 3.95
505 513 3.387699 CCAAGGAAAGGGTTTGTGAATGT 59.612 43.478 0.00 0.00 0.00 2.71
511 519 6.040504 AGGAAAGGGTTTGTGAATGTCTTAAC 59.959 38.462 0.00 0.00 0.00 2.01
512 520 5.784578 AAGGGTTTGTGAATGTCTTAACC 57.215 39.130 0.00 0.00 35.45 2.85
513 521 5.061721 AGGGTTTGTGAATGTCTTAACCT 57.938 39.130 0.00 0.00 36.24 3.50
554 564 1.006813 TGCCCATCCACATACCCTTT 58.993 50.000 0.00 0.00 0.00 3.11
572 582 5.125356 CCCTTTTGATTGTGAAAGCCTTTT 58.875 37.500 0.00 0.00 32.78 2.27
595 606 9.528489 TTTTTACTATTATTGAAGAAGCCCACT 57.472 29.630 0.00 0.00 0.00 4.00
627 645 4.695396 TGCATCACACTTTGCTTTCAATT 58.305 34.783 0.00 0.00 39.60 2.32
631 649 7.042590 TGCATCACACTTTGCTTTCAATTTTAG 60.043 33.333 0.00 0.00 39.60 1.85
658 676 8.976471 CCGCATTATATTCATCTACATGATCTC 58.024 37.037 0.00 0.00 38.89 2.75
668 686 5.682234 TCTACATGATCTCTTTCCAAGCA 57.318 39.130 0.00 0.00 0.00 3.91
670 690 6.053650 TCTACATGATCTCTTTCCAAGCATG 58.946 40.000 0.00 0.00 38.03 4.06
697 717 4.439305 TCAGGTTTATGCTCATTTGCAC 57.561 40.909 0.00 0.00 46.33 4.57
714 734 1.203287 GCACCATCTTTTCCTCAAGCC 59.797 52.381 0.00 0.00 0.00 4.35
721 741 4.937201 TCTTTTCCTCAAGCCTTTTTCC 57.063 40.909 0.00 0.00 0.00 3.13
722 742 3.317993 TCTTTTCCTCAAGCCTTTTTCCG 59.682 43.478 0.00 0.00 0.00 4.30
723 743 2.358322 TTCCTCAAGCCTTTTTCCGT 57.642 45.000 0.00 0.00 0.00 4.69
724 744 1.604604 TCCTCAAGCCTTTTTCCGTG 58.395 50.000 0.00 0.00 0.00 4.94
725 745 1.142060 TCCTCAAGCCTTTTTCCGTGA 59.858 47.619 0.00 0.00 0.00 4.35
742 783 4.649088 CGTGAGGTCTACATTATGTGGA 57.351 45.455 7.31 7.31 35.44 4.02
743 784 5.201713 CGTGAGGTCTACATTATGTGGAT 57.798 43.478 14.17 0.00 39.99 3.41
744 785 5.223382 CGTGAGGTCTACATTATGTGGATC 58.777 45.833 14.17 13.62 39.99 3.36
745 786 5.223382 GTGAGGTCTACATTATGTGGATCG 58.777 45.833 14.17 0.00 42.83 3.69
746 787 5.009710 GTGAGGTCTACATTATGTGGATCGA 59.990 44.000 14.17 4.04 42.83 3.59
747 788 5.241728 TGAGGTCTACATTATGTGGATCGAG 59.758 44.000 14.17 0.00 42.83 4.04
748 789 4.524714 AGGTCTACATTATGTGGATCGAGG 59.475 45.833 14.17 0.00 42.83 4.63
750 791 2.550830 ACATTATGTGGATCGAGGCC 57.449 50.000 0.00 0.00 0.00 5.19
751 792 1.768275 ACATTATGTGGATCGAGGCCA 59.232 47.619 5.01 5.74 0.00 5.36
752 793 2.373169 ACATTATGTGGATCGAGGCCAT 59.627 45.455 5.01 4.38 37.81 4.40
754 795 1.715785 TATGTGGATCGAGGCCATCA 58.284 50.000 5.01 11.97 37.81 3.07
755 796 1.062364 ATGTGGATCGAGGCCATCAT 58.938 50.000 5.01 13.33 37.81 2.45
756 797 0.394192 TGTGGATCGAGGCCATCATC 59.606 55.000 5.01 2.01 37.81 2.92
757 798 0.683973 GTGGATCGAGGCCATCATCT 59.316 55.000 5.01 0.00 37.81 2.90
758 799 0.972134 TGGATCGAGGCCATCATCTC 59.028 55.000 5.01 0.00 0.00 2.75
759 800 0.248843 GGATCGAGGCCATCATCTCC 59.751 60.000 5.01 0.00 0.00 3.71
760 801 0.972134 GATCGAGGCCATCATCTCCA 59.028 55.000 5.01 0.00 0.00 3.86
761 802 1.554160 GATCGAGGCCATCATCTCCAT 59.446 52.381 5.01 0.00 0.00 3.41
762 803 2.309136 TCGAGGCCATCATCTCCATA 57.691 50.000 5.01 0.00 0.00 2.74
778 819 8.210946 TCATCTCCATAAACCTATTTCATCGTT 58.789 33.333 0.00 0.00 0.00 3.85
783 824 8.564574 TCCATAAACCTATTTCATCGTTAATGC 58.435 33.333 0.00 0.00 35.17 3.56
790 831 7.094634 ACCTATTTCATCGTTAATGCCATCATC 60.095 37.037 0.00 0.00 35.17 2.92
791 832 6.889301 ATTTCATCGTTAATGCCATCATCT 57.111 33.333 0.00 0.00 35.17 2.90
795 836 4.356405 TCGTTAATGCCATCATCTCCAT 57.644 40.909 0.00 0.00 31.27 3.41
796 837 4.318332 TCGTTAATGCCATCATCTCCATC 58.682 43.478 0.00 0.00 31.27 3.51
797 838 4.040829 TCGTTAATGCCATCATCTCCATCT 59.959 41.667 0.00 0.00 31.27 2.90
798 839 5.245977 TCGTTAATGCCATCATCTCCATCTA 59.754 40.000 0.00 0.00 31.27 1.98
801 842 5.516059 AATGCCATCATCTCCATCTACAT 57.484 39.130 0.00 0.00 31.27 2.29
803 844 3.056322 TGCCATCATCTCCATCTACATCG 60.056 47.826 0.00 0.00 0.00 3.84
804 845 3.194329 GCCATCATCTCCATCTACATCGA 59.806 47.826 0.00 0.00 0.00 3.59
805 846 4.677514 GCCATCATCTCCATCTACATCGAG 60.678 50.000 0.00 0.00 0.00 4.04
808 849 1.621992 TCTCCATCTACATCGAGGCC 58.378 55.000 0.00 0.00 0.00 5.19
809 850 1.133482 TCTCCATCTACATCGAGGCCA 60.133 52.381 5.01 0.00 0.00 5.36
810 851 1.898472 CTCCATCTACATCGAGGCCAT 59.102 52.381 5.01 0.00 0.00 4.40
813 854 2.235650 CCATCTACATCGAGGCCATCAT 59.764 50.000 5.01 0.00 0.00 2.45
818 859 0.683412 CATCGAGGCCATCATCTCCA 59.317 55.000 5.01 0.00 0.00 3.86
820 861 2.309136 TCGAGGCCATCATCTCCATA 57.691 50.000 5.01 0.00 0.00 2.74
821 862 2.608623 TCGAGGCCATCATCTCCATAA 58.391 47.619 5.01 0.00 0.00 1.90
822 863 2.972021 TCGAGGCCATCATCTCCATAAA 59.028 45.455 5.01 0.00 0.00 1.40
823 864 3.070018 CGAGGCCATCATCTCCATAAAC 58.930 50.000 5.01 0.00 0.00 2.01
824 865 3.416156 GAGGCCATCATCTCCATAAACC 58.584 50.000 5.01 0.00 0.00 3.27
826 867 4.242811 AGGCCATCATCTCCATAAACCTA 58.757 43.478 5.01 0.00 0.00 3.08
827 868 4.854436 AGGCCATCATCTCCATAAACCTAT 59.146 41.667 5.01 0.00 0.00 2.57
828 869 5.314306 AGGCCATCATCTCCATAAACCTATT 59.686 40.000 5.01 0.00 0.00 1.73
830 871 5.649831 GCCATCATCTCCATAAACCTATTCC 59.350 44.000 0.00 0.00 0.00 3.01
903 3735 3.415983 TGGCCACCACACCACACT 61.416 61.111 0.00 0.00 0.00 3.55
904 3736 2.123897 GGCCACCACACCACACTT 60.124 61.111 0.00 0.00 0.00 3.16
905 3737 2.489275 GGCCACCACACCACACTTG 61.489 63.158 0.00 0.00 0.00 3.16
906 3738 3.119193 CCACCACACCACACTTGC 58.881 61.111 0.00 0.00 0.00 4.01
908 3740 1.453745 CACCACACCACACTTGCCT 60.454 57.895 0.00 0.00 0.00 4.75
909 3741 1.037030 CACCACACCACACTTGCCTT 61.037 55.000 0.00 0.00 0.00 4.35
910 3742 1.037030 ACCACACCACACTTGCCTTG 61.037 55.000 0.00 0.00 0.00 3.61
911 3743 1.066257 CACACCACACTTGCCTTGC 59.934 57.895 0.00 0.00 0.00 4.01
915 3747 1.364901 CCACACTTGCCTTGCCTTG 59.635 57.895 0.00 0.00 0.00 3.61
917 3749 1.456331 ACACTTGCCTTGCCTTGCT 60.456 52.632 0.00 0.00 0.00 3.91
918 3750 1.288127 CACTTGCCTTGCCTTGCTC 59.712 57.895 0.00 0.00 0.00 4.26
919 3751 1.905354 ACTTGCCTTGCCTTGCTCC 60.905 57.895 0.00 0.00 0.00 4.70
920 3752 2.601367 TTGCCTTGCCTTGCTCCC 60.601 61.111 0.00 0.00 0.00 4.30
923 3755 3.983420 CCTTGCCTTGCTCCCCCA 61.983 66.667 0.00 0.00 0.00 4.96
924 3756 2.677875 CTTGCCTTGCTCCCCCAC 60.678 66.667 0.00 0.00 0.00 4.61
925 3757 4.299796 TTGCCTTGCTCCCCCACC 62.300 66.667 0.00 0.00 0.00 4.61
927 3759 4.432741 GCCTTGCTCCCCCACCTC 62.433 72.222 0.00 0.00 0.00 3.85
928 3760 3.732849 CCTTGCTCCCCCACCTCC 61.733 72.222 0.00 0.00 0.00 4.30
929 3761 2.935481 CTTGCTCCCCCACCTCCA 60.935 66.667 0.00 0.00 0.00 3.86
930 3762 2.204291 TTGCTCCCCCACCTCCAT 60.204 61.111 0.00 0.00 0.00 3.41
931 3763 0.988145 CTTGCTCCCCCACCTCCATA 60.988 60.000 0.00 0.00 0.00 2.74
932 3764 1.279025 TTGCTCCCCCACCTCCATAC 61.279 60.000 0.00 0.00 0.00 2.39
933 3765 2.452937 GCTCCCCCACCTCCATACC 61.453 68.421 0.00 0.00 0.00 2.73
934 3766 2.041301 TCCCCCACCTCCATACCG 60.041 66.667 0.00 0.00 0.00 4.02
935 3767 2.041301 CCCCCACCTCCATACCGA 60.041 66.667 0.00 0.00 0.00 4.69
936 3768 1.461461 CCCCCACCTCCATACCGAT 60.461 63.158 0.00 0.00 0.00 4.18
937 3769 1.481056 CCCCCACCTCCATACCGATC 61.481 65.000 0.00 0.00 0.00 3.69
938 3770 0.471971 CCCCACCTCCATACCGATCT 60.472 60.000 0.00 0.00 0.00 2.75
939 3771 0.969894 CCCACCTCCATACCGATCTC 59.030 60.000 0.00 0.00 0.00 2.75
940 3772 1.704641 CCACCTCCATACCGATCTCA 58.295 55.000 0.00 0.00 0.00 3.27
941 3773 1.341531 CCACCTCCATACCGATCTCAC 59.658 57.143 0.00 0.00 0.00 3.51
942 3774 1.341531 CACCTCCATACCGATCTCACC 59.658 57.143 0.00 0.00 0.00 4.02
943 3775 0.969894 CCTCCATACCGATCTCACCC 59.030 60.000 0.00 0.00 0.00 4.61
944 3776 0.969894 CTCCATACCGATCTCACCCC 59.030 60.000 0.00 0.00 0.00 4.95
945 3777 0.471211 TCCATACCGATCTCACCCCC 60.471 60.000 0.00 0.00 0.00 5.40
946 3778 0.762842 CCATACCGATCTCACCCCCA 60.763 60.000 0.00 0.00 0.00 4.96
947 3779 1.128200 CATACCGATCTCACCCCCAA 58.872 55.000 0.00 0.00 0.00 4.12
948 3780 1.699634 CATACCGATCTCACCCCCAAT 59.300 52.381 0.00 0.00 0.00 3.16
949 3781 1.128200 TACCGATCTCACCCCCAATG 58.872 55.000 0.00 0.00 0.00 2.82
950 3782 1.149174 CCGATCTCACCCCCAATGG 59.851 63.158 0.00 0.00 0.00 3.16
951 3783 1.635817 CCGATCTCACCCCCAATGGT 61.636 60.000 0.00 0.00 39.96 3.55
957 3789 4.315264 ACCCCCAATGGTGGCCAC 62.315 66.667 28.57 28.57 44.46 5.01
971 3803 4.394712 CCACGCCCACACTCTCCC 62.395 72.222 0.00 0.00 0.00 4.30
972 3804 4.394712 CACGCCCACACTCTCCCC 62.395 72.222 0.00 0.00 0.00 4.81
987 3819 2.530406 CCCCCAGCCCTAGATCCC 60.530 72.222 0.00 0.00 0.00 3.85
988 3820 2.290393 CCCCAGCCCTAGATCCCA 59.710 66.667 0.00 0.00 0.00 4.37
989 3821 1.151721 CCCCAGCCCTAGATCCCAT 60.152 63.158 0.00 0.00 0.00 4.00
990 3822 0.773700 CCCCAGCCCTAGATCCCATT 60.774 60.000 0.00 0.00 0.00 3.16
991 3823 0.695347 CCCAGCCCTAGATCCCATTC 59.305 60.000 0.00 0.00 0.00 2.67
992 3824 0.322975 CCAGCCCTAGATCCCATTCG 59.677 60.000 0.00 0.00 0.00 3.34
993 3825 1.051812 CAGCCCTAGATCCCATTCGT 58.948 55.000 0.00 0.00 0.00 3.85
994 3826 1.417890 CAGCCCTAGATCCCATTCGTT 59.582 52.381 0.00 0.00 0.00 3.85
995 3827 2.127708 AGCCCTAGATCCCATTCGTTT 58.872 47.619 0.00 0.00 0.00 3.60
996 3828 2.158755 AGCCCTAGATCCCATTCGTTTG 60.159 50.000 0.00 0.00 0.00 2.93
1357 4421 4.497984 ACCAGCCGCAACCACACA 62.498 61.111 0.00 0.00 0.00 3.72
1358 4422 3.215568 CCAGCCGCAACCACACAA 61.216 61.111 0.00 0.00 0.00 3.33
1359 4423 2.026014 CAGCCGCAACCACACAAC 59.974 61.111 0.00 0.00 0.00 3.32
1360 4424 3.216292 AGCCGCAACCACACAACC 61.216 61.111 0.00 0.00 0.00 3.77
1361 4425 4.279043 GCCGCAACCACACAACCC 62.279 66.667 0.00 0.00 0.00 4.11
1419 4489 2.123033 GAGGAGGAGGAGGAGGGC 60.123 72.222 0.00 0.00 0.00 5.19
1711 4795 1.066152 TCGAGGTGAGAATGAGATGCG 59.934 52.381 0.00 0.00 0.00 4.73
1756 4842 7.416890 GCTGTACAGTTCAGTTCTGATAGGTAT 60.417 40.741 23.44 0.00 36.81 2.73
1760 4846 6.895756 ACAGTTCAGTTCTGATAGGTATACCA 59.104 38.462 23.87 10.26 36.29 3.25
1766 4852 6.042093 CAGTTCTGATAGGTATACCATGGTGT 59.958 42.308 28.17 23.41 38.89 4.16
1800 4886 0.606401 AGATGGTGTTTGTGCGAGGG 60.606 55.000 0.00 0.00 0.00 4.30
1844 4930 1.972795 ACAGTGCAAATTGATTGGCCT 59.027 42.857 3.32 0.00 39.54 5.19
1846 4932 1.551883 AGTGCAAATTGATTGGCCTCC 59.448 47.619 3.32 0.00 39.54 4.30
1849 4935 2.234414 TGCAAATTGATTGGCCTCCTTC 59.766 45.455 3.32 0.00 39.54 3.46
1852 4938 4.501071 CAAATTGATTGGCCTCCTTCAAG 58.499 43.478 3.32 0.00 35.27 3.02
1943 5029 6.974622 CACATGTTATTGGATTTTAGCCTGTC 59.025 38.462 0.00 0.00 0.00 3.51
1957 5043 1.142474 CCTGTCGTAACGGTGGAAAC 58.858 55.000 0.00 0.00 0.00 2.78
1963 5049 1.528161 CGTAACGGTGGAAACTGAACC 59.472 52.381 0.00 0.00 0.00 3.62
1986 5072 1.464189 GCTTTCTGCGTCGAAATCACC 60.464 52.381 0.00 0.00 32.90 4.02
2087 5175 1.885887 TGGTGCAAGCCATACAACTTC 59.114 47.619 0.00 0.00 32.81 3.01
2113 5201 4.105537 TGGGATTATAGTGCCCATAAAGCA 59.894 41.667 3.27 0.00 46.57 3.91
2114 5202 5.222316 TGGGATTATAGTGCCCATAAAGCAT 60.222 40.000 3.27 0.00 46.57 3.79
2178 5343 1.002134 ATGGGCGCAAGTTAGCTGT 60.002 52.632 10.83 0.00 41.68 4.40
2189 5354 2.034879 TTAGCTGTGCAGGCGCTTC 61.035 57.895 7.64 0.00 39.64 3.86
2196 5361 1.823470 TGCAGGCGCTTCAGTTGTT 60.823 52.632 7.64 0.00 39.64 2.83
2206 5374 0.730265 TTCAGTTGTTGCGTGGTGAC 59.270 50.000 0.00 0.00 0.00 3.67
2223 5391 0.656785 GACCGTACAACGCCAAACAA 59.343 50.000 0.00 0.00 40.91 2.83
2245 5413 7.806180 ACAAATGTATCCAGATAAGCTAGGTT 58.194 34.615 12.54 12.54 0.00 3.50
2275 5443 1.407618 GGGAGTGTGAAACCAACCAAC 59.592 52.381 0.00 0.00 34.36 3.77
2284 5452 6.254804 GTGTGAAACCAACCAACAAGTAATTC 59.745 38.462 0.00 0.00 34.36 2.17
2328 5496 7.121168 TCACTTCTTGGCTAGTGAATTAAATGG 59.879 37.037 0.00 0.00 45.60 3.16
2373 5544 5.428253 GAACATTGTCTACCTAATCAGCCA 58.572 41.667 0.00 0.00 0.00 4.75
2374 5545 5.636903 ACATTGTCTACCTAATCAGCCAT 57.363 39.130 0.00 0.00 0.00 4.40
2379 5550 6.025749 TGTCTACCTAATCAGCCATTATCG 57.974 41.667 0.00 0.00 0.00 2.92
2391 5562 4.462834 CAGCCATTATCGTGGTCCTATCTA 59.537 45.833 0.00 0.00 41.47 1.98
2394 5565 6.043411 GCCATTATCGTGGTCCTATCTATTC 58.957 44.000 0.00 0.00 41.47 1.75
2435 5606 6.414694 GGACAAATCAATAATATGTGTGTGCG 59.585 38.462 0.00 0.00 0.00 5.34
2437 5608 5.437289 AATCAATAATATGTGTGTGCGGG 57.563 39.130 0.00 0.00 0.00 6.13
2441 5612 4.682778 ATAATATGTGTGTGCGGGTAGT 57.317 40.909 0.00 0.00 0.00 2.73
2445 5616 1.959226 GTGTGTGCGGGTAGTGTGG 60.959 63.158 0.00 0.00 0.00 4.17
2446 5617 2.424302 GTGTGCGGGTAGTGTGGT 59.576 61.111 0.00 0.00 0.00 4.16
2448 5619 2.134933 TGTGCGGGTAGTGTGGTCA 61.135 57.895 0.00 0.00 0.00 4.02
2474 5645 4.412796 TCTGAAGTCAGCCCATTGATAG 57.587 45.455 3.30 0.00 43.46 2.08
2487 5659 5.511373 GCCCATTGATAGTAGTATGACAGCA 60.511 44.000 0.00 0.00 0.00 4.41
2500 5672 4.668576 ATGACAGCACGACAACATAAAG 57.331 40.909 0.00 0.00 0.00 1.85
2509 5681 4.033358 CACGACAACATAAAGGCTCTGATC 59.967 45.833 0.00 0.00 0.00 2.92
2539 5715 7.147312 TGGAAACATCAGCAGAGTTAATTTTG 58.853 34.615 0.00 0.00 33.40 2.44
2547 5723 5.473504 CAGCAGAGTTAATTTTGGTGGTACT 59.526 40.000 11.42 0.00 35.90 2.73
2548 5724 5.473504 AGCAGAGTTAATTTTGGTGGTACTG 59.526 40.000 0.00 0.00 0.00 2.74
2565 5741 5.943416 TGGTACTGAAATTGGTACAGAATGG 59.057 40.000 14.34 0.00 43.62 3.16
2571 5747 4.789012 AATTGGTACAGAATGGTTGCAG 57.211 40.909 0.00 0.00 43.62 4.41
2572 5748 2.949177 TGGTACAGAATGGTTGCAGT 57.051 45.000 0.00 0.00 43.62 4.40
2576 5752 6.247229 TGGTACAGAATGGTTGCAGTATAT 57.753 37.500 0.00 0.00 43.62 0.86
2615 5791 7.954788 TTATGTTAACTTTGGACAAATTGCC 57.045 32.000 7.22 0.00 0.00 4.52
2619 5795 7.556844 TGTTAACTTTGGACAAATTGCCTTTA 58.443 30.769 7.22 0.23 0.00 1.85
2620 5796 8.207545 TGTTAACTTTGGACAAATTGCCTTTAT 58.792 29.630 7.22 0.00 0.00 1.40
2642 5818 2.108075 TCCATGACACATTGGTTGGTCT 59.892 45.455 0.00 0.00 34.48 3.85
2651 5837 8.865090 TGACACATTGGTTGGTCTTTTAATTAT 58.135 29.630 0.00 0.00 0.00 1.28
2658 5844 8.133024 TGGTTGGTCTTTTAATTATTCTGCAT 57.867 30.769 0.00 0.00 0.00 3.96
2688 5874 9.821662 GTTTATATTGAACCTCTTGTAACACAC 57.178 33.333 0.00 0.00 0.00 3.82
2696 5882 3.270877 CTCTTGTAACACACTATGGCCC 58.729 50.000 0.00 0.00 0.00 5.80
2697 5883 2.640332 TCTTGTAACACACTATGGCCCA 59.360 45.455 0.00 0.00 0.00 5.36
2705 5891 2.029838 CACTATGGCCCAGTGTTCTC 57.970 55.000 21.13 0.00 38.86 2.87
2716 5902 4.220602 GCCCAGTGTTCTCCATTTTTACAT 59.779 41.667 0.00 0.00 0.00 2.29
2737 5923 7.962964 ACATAGTGATACCAATTACGGATTG 57.037 36.000 6.76 6.76 43.89 2.67
2752 5938 2.359900 GGATTGGGTCTGCAGTTGTAG 58.640 52.381 14.67 0.00 0.00 2.74
2753 5939 1.740025 GATTGGGTCTGCAGTTGTAGC 59.260 52.381 14.67 3.51 0.00 3.58
2761 6071 1.002468 CTGCAGTTGTAGCGCAGTTTT 60.002 47.619 11.47 0.00 46.36 2.43
2768 6078 1.270625 TGTAGCGCAGTTTTGGTAGCT 60.271 47.619 11.47 0.00 38.57 3.32
2777 6087 4.789802 GCAGTTTTGGTAGCTTCTCACAAC 60.790 45.833 0.00 0.00 0.00 3.32
2788 6098 3.616560 GCTTCTCACAACGGGTCTGATAA 60.617 47.826 0.00 0.00 0.00 1.75
2794 6104 5.067273 TCACAACGGGTCTGATAAATGTTT 58.933 37.500 0.00 0.00 0.00 2.83
2825 6135 2.642311 TGAATTACAGGTGGCTTCCTCA 59.358 45.455 0.00 0.00 35.37 3.86
2879 6189 2.673368 GGAGTACATTGAAGCAGTTCCG 59.327 50.000 0.00 0.00 0.00 4.30
2958 6268 6.461698 CGTTGAAGCGTTATCAAAAGATGTAC 59.538 38.462 2.08 0.00 38.44 2.90
3005 6315 1.216710 CAGCTCGGAAGACCTGACC 59.783 63.158 0.00 0.00 44.66 4.02
3116 6426 8.635765 AAAGCTCAGTGTATCAAAAGGATTTA 57.364 30.769 0.00 0.00 37.28 1.40
3155 6465 1.912043 AGCCTCTACCAGATTTGCTGT 59.088 47.619 0.00 0.00 43.33 4.40
3389 6702 3.767230 CACGAGCAAGCGTCACCG 61.767 66.667 0.00 0.00 43.59 4.94
3659 6972 2.678934 TGCTTCGCGTCTAGGGGT 60.679 61.111 5.77 0.00 0.00 4.95
3713 7026 2.365582 GTATGGTGGCGAAGGTCATTT 58.634 47.619 0.00 0.00 0.00 2.32
3725 7039 5.347364 GCGAAGGTCATTTGCTAGATAGATC 59.653 44.000 2.11 0.00 43.93 2.75
3778 7092 0.861837 GAGATATTGCTTGGTCCGCG 59.138 55.000 0.00 0.00 0.00 6.46
3793 7107 1.002142 TCCGCGTGAGTTATATCGGTG 60.002 52.381 4.92 0.00 38.18 4.94
3806 7124 7.156673 AGTTATATCGGTGTTTGTAGTGTGTT 58.843 34.615 0.00 0.00 0.00 3.32
3875 7193 8.587608 TGAATTTTTGTTTATGATCTTGCCTCT 58.412 29.630 0.00 0.00 0.00 3.69
3894 7212 2.002586 CTGTTCTTCCCAGTGTATGCG 58.997 52.381 0.00 0.00 0.00 4.73
3927 7256 4.874966 AGTCAGAGTCAGCAATAGAATTGC 59.125 41.667 15.14 15.14 45.22 3.56
3984 7313 6.892658 ACAAATTAACAAGTGGACATAGCA 57.107 33.333 0.00 0.00 0.00 3.49
4050 7381 2.242043 CCTGAACATGGCCTCACTTTT 58.758 47.619 3.32 0.00 0.00 2.27
4067 7398 4.706476 CACTTTTCATGGCCTTATTCCTGA 59.294 41.667 3.32 0.00 0.00 3.86
4068 7399 4.706962 ACTTTTCATGGCCTTATTCCTGAC 59.293 41.667 3.32 0.00 0.00 3.51
4069 7400 3.297134 TTCATGGCCTTATTCCTGACC 57.703 47.619 3.32 0.00 0.00 4.02
4088 7419 4.202419 TGACCAAATACAGGCACAGTAGTT 60.202 41.667 0.00 0.00 39.04 2.24
4118 7464 0.324552 ATGCAGGCAGGGCAAACATA 60.325 50.000 0.00 0.00 45.60 2.29
4133 7479 6.878923 GGGCAAACATATATATACAGCACAGA 59.121 38.462 0.00 0.00 0.00 3.41
4147 7498 1.735386 CACAGACATGCTCTCCTTGG 58.265 55.000 0.00 0.00 0.00 3.61
4156 7507 4.202336 ACATGCTCTCCTTGGTATCATCAG 60.202 45.833 0.00 0.00 0.00 2.90
4157 7508 2.702478 TGCTCTCCTTGGTATCATCAGG 59.298 50.000 0.00 0.00 0.00 3.86
4158 7509 2.038295 GCTCTCCTTGGTATCATCAGGG 59.962 54.545 0.00 0.00 33.29 4.45
4159 7510 2.038295 CTCTCCTTGGTATCATCAGGGC 59.962 54.545 0.00 0.00 32.23 5.19
4160 7511 1.770658 CTCCTTGGTATCATCAGGGCA 59.229 52.381 0.00 0.00 32.23 5.36
4161 7512 1.490490 TCCTTGGTATCATCAGGGCAC 59.510 52.381 0.00 0.00 32.23 5.01
4162 7513 1.212688 CCTTGGTATCATCAGGGCACA 59.787 52.381 0.00 0.00 0.00 4.57
4163 7514 2.569059 CTTGGTATCATCAGGGCACAG 58.431 52.381 0.00 0.00 0.00 3.66
4165 7516 0.471617 GGTATCATCAGGGCACAGCT 59.528 55.000 0.00 0.00 0.00 4.24
4166 7517 1.133976 GGTATCATCAGGGCACAGCTT 60.134 52.381 0.00 0.00 0.00 3.74
4167 7518 2.216898 GTATCATCAGGGCACAGCTTC 58.783 52.381 0.00 0.00 0.00 3.86
4190 7541 0.654683 CTAGCAGCCGATCTTGTTGC 59.345 55.000 11.33 11.33 35.09 4.17
4192 7543 0.250234 AGCAGCCGATCTTGTTGCTA 59.750 50.000 17.65 0.00 42.81 3.49
4450 7804 2.112815 CGGGTTCGAAATGGGCTCC 61.113 63.158 0.00 0.00 39.00 4.70
4672 8026 2.718094 CCAGTTGCACATGGTGTCA 58.282 52.632 8.02 0.00 35.75 3.58
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 4.003648 GGAACTGGTTTCTGGATACACTG 58.996 47.826 0.00 0.00 46.17 3.66
36 37 3.576078 TGTTGTTGAAGTGGAGGACAT 57.424 42.857 0.00 0.00 0.00 3.06
81 82 4.065088 GCTGTAGGTGTTGACTCAAATGA 58.935 43.478 0.00 0.00 0.00 2.57
102 103 2.970974 GAGGACGGTTGCTTGCAGC 61.971 63.158 0.77 0.77 42.82 5.25
113 114 0.959553 ACACTACACACAGAGGACGG 59.040 55.000 0.00 0.00 0.00 4.79
124 125 6.594159 AGGTGCTTGTCATATTAACACTACAC 59.406 38.462 0.00 0.00 0.00 2.90
126 127 7.438459 CCTAGGTGCTTGTCATATTAACACTAC 59.562 40.741 0.00 0.00 0.00 2.73
131 132 7.224949 GTCTTCCTAGGTGCTTGTCATATTAAC 59.775 40.741 9.08 0.00 0.00 2.01
144 145 1.946283 GCAAGTGGTCTTCCTAGGTGC 60.946 57.143 9.08 3.97 34.23 5.01
162 163 1.469703 CTTTCTTCATGGATGCACGCA 59.530 47.619 0.00 0.00 0.00 5.24
165 166 1.820519 TGGCTTTCTTCATGGATGCAC 59.179 47.619 0.00 0.00 0.00 4.57
173 174 2.867624 TGCAAGAGTGGCTTTCTTCAT 58.132 42.857 1.85 0.00 33.60 2.57
219 220 5.643379 TTCATGAGGCAATGAAGTTTACC 57.357 39.130 10.51 0.00 40.72 2.85
235 236 3.990092 ACTTCTACGTGTTGCTTCATGA 58.010 40.909 0.00 0.00 0.00 3.07
239 240 4.686554 AGATCAACTTCTACGTGTTGCTTC 59.313 41.667 10.69 9.91 42.11 3.86
244 245 4.771054 ACCCTAGATCAACTTCTACGTGTT 59.229 41.667 0.00 0.00 0.00 3.32
287 294 2.682856 CAACCACCTCCGGAATTATGTG 59.317 50.000 5.23 8.07 0.00 3.21
288 295 2.307686 ACAACCACCTCCGGAATTATGT 59.692 45.455 5.23 3.50 0.00 2.29
302 309 3.153919 TGAAGAAGGGCAATACAACCAC 58.846 45.455 0.00 0.00 0.00 4.16
351 359 6.103205 TGAAATTATAGAGGGAGGGCAAGATT 59.897 38.462 0.00 0.00 0.00 2.40
352 360 5.612688 TGAAATTATAGAGGGAGGGCAAGAT 59.387 40.000 0.00 0.00 0.00 2.40
358 366 6.296720 GGAAGGATGAAATTATAGAGGGAGGG 60.297 46.154 0.00 0.00 0.00 4.30
359 367 6.273260 TGGAAGGATGAAATTATAGAGGGAGG 59.727 42.308 0.00 0.00 0.00 4.30
360 368 7.321717 TGGAAGGATGAAATTATAGAGGGAG 57.678 40.000 0.00 0.00 0.00 4.30
361 369 7.321717 CTGGAAGGATGAAATTATAGAGGGA 57.678 40.000 0.00 0.00 0.00 4.20
393 401 8.141909 ATGATTATTCAGAAAGAATGGCACATG 58.858 33.333 0.00 0.00 46.24 3.21
394 402 8.246430 ATGATTATTCAGAAAGAATGGCACAT 57.754 30.769 0.00 0.00 46.24 3.21
395 403 7.649533 ATGATTATTCAGAAAGAATGGCACA 57.350 32.000 0.00 0.00 46.24 4.57
413 421 9.076781 TGAACCTCATGAACTTTTCAATGATTA 57.923 29.630 0.00 0.00 43.95 1.75
446 454 0.975040 AGATTGAGAGCGGGCAGACT 60.975 55.000 0.00 0.00 0.00 3.24
455 463 7.220683 GCATAGATATTTCGAGAGATTGAGAGC 59.779 40.741 0.00 0.00 41.60 4.09
456 464 7.429051 CGCATAGATATTTCGAGAGATTGAGAG 59.571 40.741 0.00 0.00 41.60 3.20
457 465 7.247019 CGCATAGATATTTCGAGAGATTGAGA 58.753 38.462 0.00 0.00 41.60 3.27
458 466 6.020758 GCGCATAGATATTTCGAGAGATTGAG 60.021 42.308 0.30 0.00 41.60 3.02
459 467 5.802451 GCGCATAGATATTTCGAGAGATTGA 59.198 40.000 0.30 0.00 41.60 2.57
460 468 5.005203 GGCGCATAGATATTTCGAGAGATTG 59.995 44.000 10.83 0.00 41.60 2.67
469 477 5.335191 CCTTTCCTTGGCGCATAGATATTTC 60.335 44.000 10.83 0.00 0.00 2.17
472 480 3.560025 CCCTTTCCTTGGCGCATAGATAT 60.560 47.826 10.83 0.00 0.00 1.63
481 489 0.031994 CACAAACCCTTTCCTTGGCG 59.968 55.000 0.00 0.00 0.00 5.69
483 491 3.387699 ACATTCACAAACCCTTTCCTTGG 59.612 43.478 0.00 0.00 0.00 3.61
494 502 6.019881 GTGCAAAGGTTAAGACATTCACAAAC 60.020 38.462 0.00 0.00 0.00 2.93
530 540 1.668419 GTATGTGGATGGGCACACTC 58.332 55.000 0.00 0.00 38.39 3.51
572 582 8.989131 ACTAGTGGGCTTCTTCAATAATAGTAA 58.011 33.333 0.00 0.00 0.00 2.24
580 590 2.040278 TGCACTAGTGGGCTTCTTCAAT 59.960 45.455 23.95 0.00 0.00 2.57
627 645 8.882736 CATGTAGATGAATATAATGCGGCTAAA 58.117 33.333 0.00 0.00 0.00 1.85
631 649 6.908870 TCATGTAGATGAATATAATGCGGC 57.091 37.500 0.00 0.00 35.55 6.53
668 686 7.414222 AATGAGCATAAACCTGATCAAACAT 57.586 32.000 0.00 0.00 43.98 2.71
670 690 6.035327 GCAAATGAGCATAAACCTGATCAAAC 59.965 38.462 0.00 0.00 43.98 2.93
697 717 4.879197 AAAAGGCTTGAGGAAAAGATGG 57.121 40.909 0.00 0.00 0.00 3.51
714 734 6.594159 ACATAATGTAGACCTCACGGAAAAAG 59.406 38.462 0.00 0.00 0.00 2.27
721 741 4.649088 TCCACATAATGTAGACCTCACG 57.351 45.455 0.00 0.00 0.00 4.35
722 742 5.009710 TCGATCCACATAATGTAGACCTCAC 59.990 44.000 0.00 0.00 0.00 3.51
723 743 5.137551 TCGATCCACATAATGTAGACCTCA 58.862 41.667 0.00 0.00 0.00 3.86
724 744 5.336055 CCTCGATCCACATAATGTAGACCTC 60.336 48.000 0.00 0.00 0.00 3.85
725 745 4.524714 CCTCGATCCACATAATGTAGACCT 59.475 45.833 0.00 0.00 0.00 3.85
727 747 4.238514 GCCTCGATCCACATAATGTAGAC 58.761 47.826 0.00 0.00 0.00 2.59
739 780 0.972134 GAGATGATGGCCTCGATCCA 59.028 55.000 3.32 8.72 38.09 3.41
742 783 1.654159 ATGGAGATGATGGCCTCGAT 58.346 50.000 3.32 0.00 0.00 3.59
743 784 2.309136 TATGGAGATGATGGCCTCGA 57.691 50.000 3.32 0.00 0.00 4.04
744 785 3.070018 GTTTATGGAGATGATGGCCTCG 58.930 50.000 3.32 0.00 0.00 4.63
745 786 3.073650 AGGTTTATGGAGATGATGGCCTC 59.926 47.826 3.32 0.00 0.00 4.70
746 787 3.059097 AGGTTTATGGAGATGATGGCCT 58.941 45.455 3.32 0.00 0.00 5.19
747 788 3.515602 AGGTTTATGGAGATGATGGCC 57.484 47.619 0.00 0.00 0.00 5.36
748 789 6.716628 TGAAATAGGTTTATGGAGATGATGGC 59.283 38.462 0.00 0.00 0.00 4.40
750 791 8.663025 CGATGAAATAGGTTTATGGAGATGATG 58.337 37.037 0.00 0.00 0.00 3.07
751 792 8.378565 ACGATGAAATAGGTTTATGGAGATGAT 58.621 33.333 0.00 0.00 0.00 2.45
752 793 7.735917 ACGATGAAATAGGTTTATGGAGATGA 58.264 34.615 0.00 0.00 0.00 2.92
757 798 8.564574 GCATTAACGATGAAATAGGTTTATGGA 58.435 33.333 0.00 0.00 38.03 3.41
758 799 7.807907 GGCATTAACGATGAAATAGGTTTATGG 59.192 37.037 0.00 0.00 38.03 2.74
759 800 8.349245 TGGCATTAACGATGAAATAGGTTTATG 58.651 33.333 0.00 0.00 38.03 1.90
760 801 8.458573 TGGCATTAACGATGAAATAGGTTTAT 57.541 30.769 0.00 0.00 38.03 1.40
761 802 7.867305 TGGCATTAACGATGAAATAGGTTTA 57.133 32.000 0.00 0.00 38.03 2.01
762 803 6.767524 TGGCATTAACGATGAAATAGGTTT 57.232 33.333 0.00 0.00 38.03 3.27
778 819 6.628844 CGATGTAGATGGAGATGATGGCATTA 60.629 42.308 0.00 0.00 34.11 1.90
783 824 4.142204 CCTCGATGTAGATGGAGATGATGG 60.142 50.000 12.69 0.00 36.73 3.51
790 831 1.332195 TGGCCTCGATGTAGATGGAG 58.668 55.000 3.32 5.05 34.91 3.86
791 832 1.895798 GATGGCCTCGATGTAGATGGA 59.104 52.381 3.32 0.00 0.00 3.41
795 836 2.822561 GAGATGATGGCCTCGATGTAGA 59.177 50.000 3.32 0.00 0.00 2.59
796 837 2.094286 GGAGATGATGGCCTCGATGTAG 60.094 54.545 3.32 0.00 0.00 2.74
797 838 1.895798 GGAGATGATGGCCTCGATGTA 59.104 52.381 3.32 0.00 0.00 2.29
798 839 0.683973 GGAGATGATGGCCTCGATGT 59.316 55.000 3.32 0.00 0.00 3.06
801 842 2.309136 TATGGAGATGATGGCCTCGA 57.691 50.000 3.32 0.00 0.00 4.04
803 844 3.073650 AGGTTTATGGAGATGATGGCCTC 59.926 47.826 3.32 0.00 0.00 4.70
804 845 3.059097 AGGTTTATGGAGATGATGGCCT 58.941 45.455 3.32 0.00 0.00 5.19
805 846 3.515602 AGGTTTATGGAGATGATGGCC 57.484 47.619 0.00 0.00 0.00 5.36
808 849 6.782986 TGGGAATAGGTTTATGGAGATGATG 58.217 40.000 0.00 0.00 0.00 3.07
809 850 7.312183 GGATGGGAATAGGTTTATGGAGATGAT 60.312 40.741 0.00 0.00 0.00 2.45
810 851 6.012508 GGATGGGAATAGGTTTATGGAGATGA 60.013 42.308 0.00 0.00 0.00 2.92
813 854 4.601857 GGGATGGGAATAGGTTTATGGAGA 59.398 45.833 0.00 0.00 0.00 3.71
818 859 4.018415 CCGATGGGATGGGAATAGGTTTAT 60.018 45.833 0.00 0.00 34.06 1.40
820 861 2.108250 CCGATGGGATGGGAATAGGTTT 59.892 50.000 0.00 0.00 34.06 3.27
821 862 1.705186 CCGATGGGATGGGAATAGGTT 59.295 52.381 0.00 0.00 34.06 3.50
822 863 1.362224 CCGATGGGATGGGAATAGGT 58.638 55.000 0.00 0.00 34.06 3.08
823 864 0.035056 GCCGATGGGATGGGAATAGG 60.035 60.000 0.00 0.00 34.06 2.57
824 865 0.035056 GGCCGATGGGATGGGAATAG 60.035 60.000 0.00 0.00 34.06 1.73
826 867 2.845345 GGGCCGATGGGATGGGAAT 61.845 63.158 0.00 0.00 34.06 3.01
827 868 3.498071 GGGCCGATGGGATGGGAA 61.498 66.667 0.00 0.00 34.06 3.97
892 3724 1.735360 CAAGGCAAGTGTGGTGTGG 59.265 57.895 0.00 0.00 0.00 4.17
903 3735 2.601367 GGGAGCAAGGCAAGGCAA 60.601 61.111 0.00 0.00 0.00 4.52
904 3736 4.684134 GGGGAGCAAGGCAAGGCA 62.684 66.667 0.00 0.00 0.00 4.75
906 3738 3.983420 TGGGGGAGCAAGGCAAGG 61.983 66.667 0.00 0.00 0.00 3.61
908 3740 4.299796 GGTGGGGGAGCAAGGCAA 62.300 66.667 0.00 0.00 0.00 4.52
910 3742 4.432741 GAGGTGGGGGAGCAAGGC 62.433 72.222 0.00 0.00 0.00 4.35
911 3743 3.732849 GGAGGTGGGGGAGCAAGG 61.733 72.222 0.00 0.00 0.00 3.61
915 3747 2.452937 GGTATGGAGGTGGGGGAGC 61.453 68.421 0.00 0.00 0.00 4.70
917 3749 1.968541 ATCGGTATGGAGGTGGGGGA 61.969 60.000 0.00 0.00 0.00 4.81
918 3750 1.461461 ATCGGTATGGAGGTGGGGG 60.461 63.158 0.00 0.00 0.00 5.40
919 3751 0.471971 AGATCGGTATGGAGGTGGGG 60.472 60.000 0.00 0.00 0.00 4.96
920 3752 0.969894 GAGATCGGTATGGAGGTGGG 59.030 60.000 0.00 0.00 0.00 4.61
923 3755 1.705873 GGTGAGATCGGTATGGAGGT 58.294 55.000 0.00 0.00 0.00 3.85
924 3756 0.969894 GGGTGAGATCGGTATGGAGG 59.030 60.000 0.00 0.00 0.00 4.30
925 3757 0.969894 GGGGTGAGATCGGTATGGAG 59.030 60.000 0.00 0.00 0.00 3.86
926 3758 0.471211 GGGGGTGAGATCGGTATGGA 60.471 60.000 0.00 0.00 0.00 3.41
927 3759 0.762842 TGGGGGTGAGATCGGTATGG 60.763 60.000 0.00 0.00 0.00 2.74
928 3760 1.128200 TTGGGGGTGAGATCGGTATG 58.872 55.000 0.00 0.00 0.00 2.39
929 3761 1.699634 CATTGGGGGTGAGATCGGTAT 59.300 52.381 0.00 0.00 0.00 2.73
930 3762 1.128200 CATTGGGGGTGAGATCGGTA 58.872 55.000 0.00 0.00 0.00 4.02
931 3763 1.635817 CCATTGGGGGTGAGATCGGT 61.636 60.000 0.00 0.00 0.00 4.69
932 3764 1.149174 CCATTGGGGGTGAGATCGG 59.851 63.158 0.00 0.00 0.00 4.18
933 3765 1.915228 ACCATTGGGGGTGAGATCG 59.085 57.895 7.78 0.00 40.44 3.69
954 3786 4.394712 GGGAGAGTGTGGGCGTGG 62.395 72.222 0.00 0.00 0.00 4.94
955 3787 4.394712 GGGGAGAGTGTGGGCGTG 62.395 72.222 0.00 0.00 0.00 5.34
970 3802 2.530406 GGGATCTAGGGCTGGGGG 60.530 72.222 0.00 0.00 0.00 5.40
971 3803 0.773700 AATGGGATCTAGGGCTGGGG 60.774 60.000 0.00 0.00 0.00 4.96
972 3804 0.695347 GAATGGGATCTAGGGCTGGG 59.305 60.000 0.00 0.00 0.00 4.45
973 3805 0.322975 CGAATGGGATCTAGGGCTGG 59.677 60.000 0.00 0.00 0.00 4.85
974 3806 1.051812 ACGAATGGGATCTAGGGCTG 58.948 55.000 0.00 0.00 0.00 4.85
975 3807 1.807814 AACGAATGGGATCTAGGGCT 58.192 50.000 0.00 0.00 0.00 5.19
976 3808 2.222027 CAAACGAATGGGATCTAGGGC 58.778 52.381 0.00 0.00 0.00 5.19
977 3809 2.222027 GCAAACGAATGGGATCTAGGG 58.778 52.381 0.00 0.00 0.00 3.53
978 3810 1.867233 CGCAAACGAATGGGATCTAGG 59.133 52.381 0.00 0.00 43.93 3.02
979 3811 1.261619 GCGCAAACGAATGGGATCTAG 59.738 52.381 0.30 0.00 43.93 2.43
980 3812 1.295792 GCGCAAACGAATGGGATCTA 58.704 50.000 0.30 0.00 43.93 1.98
981 3813 0.676466 TGCGCAAACGAATGGGATCT 60.676 50.000 8.16 0.00 43.93 2.75
982 3814 0.381801 ATGCGCAAACGAATGGGATC 59.618 50.000 17.11 0.00 43.93 3.36
983 3815 2.492418 ATGCGCAAACGAATGGGAT 58.508 47.368 17.11 0.00 43.93 3.85
984 3816 3.995074 ATGCGCAAACGAATGGGA 58.005 50.000 17.11 0.00 43.93 4.37
1133 4182 0.913451 AGATCCTGCTGCTGGTCCTT 60.913 55.000 22.62 8.63 0.00 3.36
1135 4184 1.153208 CAGATCCTGCTGCTGGTCC 60.153 63.158 22.62 15.74 0.00 4.46
1136 4185 0.743701 CACAGATCCTGCTGCTGGTC 60.744 60.000 22.62 18.41 39.51 4.02
1137 4186 1.298993 CACAGATCCTGCTGCTGGT 59.701 57.895 22.62 11.83 39.51 4.00
1138 4187 1.025113 CACACAGATCCTGCTGCTGG 61.025 60.000 18.44 18.44 39.51 4.85
1139 4188 1.645704 GCACACAGATCCTGCTGCTG 61.646 60.000 0.00 0.00 39.51 4.41
1140 4189 1.376942 GCACACAGATCCTGCTGCT 60.377 57.895 0.00 0.00 39.51 4.24
1350 4414 4.265056 GGCTCCGGGTTGTGTGGT 62.265 66.667 0.00 0.00 0.00 4.16
1711 4795 4.884164 ACAGCAAATAGTAGGAAAGGATGC 59.116 41.667 0.00 0.00 0.00 3.91
1756 4842 1.122632 ACCACACGGACACCATGGTA 61.123 55.000 19.28 0.00 41.90 3.25
1760 4846 1.896660 GCAACCACACGGACACCAT 60.897 57.895 0.00 0.00 35.59 3.55
1800 4886 1.714899 AACCTGCAACGTGCTGTCAC 61.715 55.000 10.54 0.00 45.31 3.67
1849 4935 9.020813 CATCAATCATCAAGCTCATAAAACTTG 57.979 33.333 0.00 0.00 41.70 3.16
1852 4938 7.486647 ACCATCAATCATCAAGCTCATAAAAC 58.513 34.615 0.00 0.00 0.00 2.43
1926 5012 4.331717 CGTTACGACAGGCTAAAATCCAAT 59.668 41.667 0.00 0.00 0.00 3.16
1943 5029 1.528161 GGTTCAGTTTCCACCGTTACG 59.472 52.381 0.00 0.00 0.00 3.18
1986 5072 4.384547 TGACGTAATATCGATGCAATTCCG 59.615 41.667 8.54 5.54 34.70 4.30
2019 5105 0.317770 AACAAATGTGGCTTCGCACG 60.318 50.000 0.00 0.00 33.32 5.34
2042 5128 6.027749 GCAAAATTGTCGGTATAACTCCAAG 58.972 40.000 0.00 0.00 0.00 3.61
2178 5343 1.823470 AACAACTGAAGCGCCTGCA 60.823 52.632 2.29 0.00 46.23 4.41
2189 5354 1.355210 GGTCACCACGCAACAACTG 59.645 57.895 0.00 0.00 0.00 3.16
2196 5361 1.592131 GTTGTACGGTCACCACGCA 60.592 57.895 0.00 0.00 34.00 5.24
2206 5374 2.047769 CATTTGTTTGGCGTTGTACGG 58.952 47.619 1.14 0.00 42.82 4.02
2245 5413 1.728323 TCACACTCCCATCTGTCCAA 58.272 50.000 0.00 0.00 0.00 3.53
2311 5479 8.686334 TCAATTCTTCCATTTAATTCACTAGCC 58.314 33.333 0.00 0.00 0.00 3.93
2344 5512 6.823182 TGATTAGGTAGACAATGTTCCATGTG 59.177 38.462 0.00 0.00 0.00 3.21
2373 5544 7.451877 ACACTGAATAGATAGGACCACGATAAT 59.548 37.037 0.00 0.00 0.00 1.28
2374 5545 6.776116 ACACTGAATAGATAGGACCACGATAA 59.224 38.462 0.00 0.00 0.00 1.75
2391 5562 6.575244 TGTCCTCCCATAATTACACTGAAT 57.425 37.500 0.00 0.00 0.00 2.57
2394 5565 6.828273 TGATTTGTCCTCCCATAATTACACTG 59.172 38.462 0.00 0.00 0.00 3.66
2425 5596 0.602638 CACACTACCCGCACACACAT 60.603 55.000 0.00 0.00 0.00 3.21
2435 5606 2.119495 AGATCCATGACCACACTACCC 58.881 52.381 0.00 0.00 0.00 3.69
2437 5608 4.081420 ACTTCAGATCCATGACCACACTAC 60.081 45.833 0.00 0.00 0.00 2.73
2441 5612 2.905736 TGACTTCAGATCCATGACCACA 59.094 45.455 0.00 0.00 0.00 4.17
2445 5616 2.559440 GGCTGACTTCAGATCCATGAC 58.441 52.381 10.54 0.00 46.59 3.06
2446 5617 1.487976 GGGCTGACTTCAGATCCATGA 59.512 52.381 10.54 0.00 46.59 3.07
2448 5619 1.588239 TGGGCTGACTTCAGATCCAT 58.412 50.000 10.54 0.00 46.59 3.41
2474 5645 3.571571 TGTTGTCGTGCTGTCATACTAC 58.428 45.455 0.00 0.00 0.00 2.73
2487 5659 3.678056 TCAGAGCCTTTATGTTGTCGT 57.322 42.857 0.00 0.00 0.00 4.34
2500 5672 3.614092 TGTTTCCATCTTGATCAGAGCC 58.386 45.455 0.00 0.00 33.87 4.70
2509 5681 4.008330 ACTCTGCTGATGTTTCCATCTTG 58.992 43.478 4.51 0.00 46.38 3.02
2523 5695 4.853924 ACCACCAAAATTAACTCTGCTG 57.146 40.909 0.00 0.00 0.00 4.41
2525 5697 5.472137 TCAGTACCACCAAAATTAACTCTGC 59.528 40.000 0.00 0.00 0.00 4.26
2539 5715 4.901868 TCTGTACCAATTTCAGTACCACC 58.098 43.478 7.41 0.00 38.45 4.61
2547 5723 4.586421 TGCAACCATTCTGTACCAATTTCA 59.414 37.500 0.00 0.00 0.00 2.69
2548 5724 5.132897 TGCAACCATTCTGTACCAATTTC 57.867 39.130 0.00 0.00 0.00 2.17
2582 5758 9.906660 TGTCCAAAGTTAACATAATTTGTCATC 57.093 29.630 8.61 1.82 37.68 2.92
2595 5771 6.918892 AAAGGCAATTTGTCCAAAGTTAAC 57.081 33.333 0.00 0.00 33.32 2.01
2615 5791 6.101332 CCAACCAATGTGTCATGGAATAAAG 58.899 40.000 0.00 0.00 39.12 1.85
2619 5795 3.509442 ACCAACCAATGTGTCATGGAAT 58.491 40.909 0.00 0.00 39.12 3.01
2620 5796 2.890311 GACCAACCAATGTGTCATGGAA 59.110 45.455 0.00 0.00 39.12 3.53
2651 5837 6.377996 AGGTTCAATATAAACAGCATGCAGAA 59.622 34.615 21.98 3.77 42.53 3.02
2658 5844 8.726988 GTTACAAGAGGTTCAATATAAACAGCA 58.273 33.333 3.98 0.00 0.00 4.41
2688 5874 0.911769 TGGAGAACACTGGGCCATAG 59.088 55.000 6.72 5.06 0.00 2.23
2696 5882 8.322906 TCACTATGTAAAAATGGAGAACACTG 57.677 34.615 0.00 0.00 0.00 3.66
2701 5887 9.967451 TTGGTATCACTATGTAAAAATGGAGAA 57.033 29.630 0.00 0.00 0.00 2.87
2732 5918 2.359900 CTACAACTGCAGACCCAATCC 58.640 52.381 23.35 0.00 0.00 3.01
2737 5923 2.391389 GCGCTACAACTGCAGACCC 61.391 63.158 23.35 1.25 0.00 4.46
2752 5938 0.875059 AGAAGCTACCAAAACTGCGC 59.125 50.000 0.00 0.00 0.00 6.09
2753 5939 2.096218 GTGAGAAGCTACCAAAACTGCG 60.096 50.000 0.00 0.00 0.00 5.18
2761 6071 0.320374 CCCGTTGTGAGAAGCTACCA 59.680 55.000 0.00 0.00 0.00 3.25
2768 6078 4.610605 TTTATCAGACCCGTTGTGAGAA 57.389 40.909 0.00 0.00 0.00 2.87
2794 6104 9.620259 AAGCCACCTGTAATTCAAATTTAAAAA 57.380 25.926 0.00 0.00 0.00 1.94
2801 6111 4.677182 AGGAAGCCACCTGTAATTCAAAT 58.323 39.130 0.00 0.00 39.01 2.32
2810 6120 3.010584 ACATAATTGAGGAAGCCACCTGT 59.989 43.478 3.95 0.00 40.73 4.00
2879 6189 5.350504 TCTCTTCCTCATTCTCATTCCAC 57.649 43.478 0.00 0.00 0.00 4.02
2935 6245 7.360861 CCAGTACATCTTTTGATAACGCTTCAA 60.361 37.037 0.00 0.00 37.40 2.69
3005 6315 1.134580 ACAGATTGGATGAGCTGACCG 60.135 52.381 0.00 0.00 32.86 4.79
3116 6426 3.699538 GGCTCCTTTTGTTTAATCCGGAT 59.300 43.478 12.38 12.38 0.00 4.18
3217 6527 1.134995 GCCTAATTTTCAGTGCCTGGC 60.135 52.381 12.87 12.87 31.51 4.85
3383 6696 1.200716 TCGTACCTGAACATCGGTGAC 59.799 52.381 0.65 0.00 34.76 3.67
3389 6702 2.803451 CTCAGCTCGTACCTGAACATC 58.197 52.381 2.55 0.00 38.73 3.06
3713 7026 4.496360 CTCTACCGACGATCTATCTAGCA 58.504 47.826 0.00 0.00 0.00 3.49
3725 7039 3.528370 CCAGGGGCTCTACCGACG 61.528 72.222 0.00 0.00 40.62 5.12
3778 7092 6.810182 ACACTACAAACACCGATATAACTCAC 59.190 38.462 0.00 0.00 0.00 3.51
3832 7150 7.817418 AAAATTCAACTCTACAGGCTAACAA 57.183 32.000 0.00 0.00 0.00 2.83
3875 7193 1.943968 GCGCATACACTGGGAAGAACA 60.944 52.381 0.30 0.00 40.13 3.18
3894 7212 3.832276 CTGACTCTGACTGTCAAGTAGC 58.168 50.000 18.76 11.86 42.85 3.58
3927 7256 5.009010 ACTGTGGTTTGAAGCAATTCTACAG 59.991 40.000 17.94 17.94 39.79 2.74
4050 7381 2.204463 TGGTCAGGAATAAGGCCATGA 58.796 47.619 5.01 0.00 0.00 3.07
4067 7398 4.367039 AACTACTGTGCCTGTATTTGGT 57.633 40.909 0.00 0.00 0.00 3.67
4068 7399 8.500753 TTAATAACTACTGTGCCTGTATTTGG 57.499 34.615 0.00 0.00 0.00 3.28
4069 7400 8.122952 GCTTAATAACTACTGTGCCTGTATTTG 58.877 37.037 0.00 0.00 0.00 2.32
4079 7410 7.307493 TGCATTCTGCTTAATAACTACTGTG 57.693 36.000 0.34 0.00 45.31 3.66
4088 7419 3.216800 CCTGCCTGCATTCTGCTTAATA 58.783 45.455 0.34 0.00 45.31 0.98
4133 7479 3.713248 TGATGATACCAAGGAGAGCATGT 59.287 43.478 0.00 0.00 0.00 3.21
4147 7498 2.216898 GAAGCTGTGCCCTGATGATAC 58.783 52.381 0.00 0.00 0.00 2.24
4156 7507 0.746204 GCTAGAAGGAAGCTGTGCCC 60.746 60.000 0.00 0.00 37.01 5.36
4157 7508 0.036010 TGCTAGAAGGAAGCTGTGCC 60.036 55.000 0.00 0.00 40.73 5.01
4158 7509 1.367659 CTGCTAGAAGGAAGCTGTGC 58.632 55.000 0.00 0.00 40.73 4.57
4159 7510 1.367659 GCTGCTAGAAGGAAGCTGTG 58.632 55.000 0.00 0.00 40.73 3.66
4160 7511 0.251634 GGCTGCTAGAAGGAAGCTGT 59.748 55.000 0.00 0.00 40.73 4.40
4161 7512 0.809241 CGGCTGCTAGAAGGAAGCTG 60.809 60.000 0.00 0.00 40.73 4.24
4162 7513 0.972983 TCGGCTGCTAGAAGGAAGCT 60.973 55.000 0.00 0.00 40.73 3.74
4163 7514 0.105778 ATCGGCTGCTAGAAGGAAGC 59.894 55.000 0.00 0.00 40.50 3.86
4165 7516 1.781786 AGATCGGCTGCTAGAAGGAA 58.218 50.000 0.00 0.00 0.00 3.36
4166 7517 1.410517 CAAGATCGGCTGCTAGAAGGA 59.589 52.381 0.00 0.00 0.00 3.36
4167 7518 1.137872 ACAAGATCGGCTGCTAGAAGG 59.862 52.381 0.00 0.00 0.00 3.46
4190 7541 1.609061 CCTTCGCTATGCCCATGGTAG 60.609 57.143 11.73 7.25 0.00 3.18
4192 7543 1.149174 CCTTCGCTATGCCCATGGT 59.851 57.895 11.73 0.00 0.00 3.55
4214 7565 3.518552 ATGCCCAGCCTGCAAGTGT 62.519 57.895 0.00 0.00 42.92 3.55
4351 7705 1.641677 GCTCACGCACAACTCGTTT 59.358 52.632 0.00 0.00 38.19 3.60
4471 7825 1.059098 AGAGCATGGTGTTCACCTCA 58.941 50.000 20.48 4.27 32.60 3.86
4488 7842 1.535444 TTCAGCCCGGACTCCAAGA 60.535 57.895 0.73 0.00 0.00 3.02


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

AutoCloner maintained by Alex Coulton.