Multiple sequence alignment - TraesCS2D01G497000

Loading Multiple Alignment...

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 TraesCS2D01G497000 chr2D 100.000 3914 0 0 1 3914 593208071 593211984 0.000000e+00 7228
1 TraesCS2D01G497000 chr2A 95.465 2646 95 10 797 3433 727948706 727951335 0.000000e+00 4198
2 TraesCS2D01G497000 chr2A 89.127 699 65 8 79 770 727947899 727948593 0.000000e+00 859
3 TraesCS2D01G497000 chr2A 92.194 474 26 1 3431 3904 727952004 727952466 0.000000e+00 660
4 TraesCS2D01G497000 chr2B 95.002 2061 85 5 910 2970 719462812 719464854 0.000000e+00 3219
5 TraesCS2D01G497000 chr2B 87.360 356 33 7 3561 3912 719465255 719465602 7.880000e-107 398
6 TraesCS2D01G497000 chr5D 89.899 99 9 1 1044 1142 370950954 370950857 4.110000e-25 126


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 TraesCS2D01G497000 chr2D 593208071 593211984 3913 False 7228.000000 7228 100.000 1 3914 1 chr2D.!!$F1 3913
1 TraesCS2D01G497000 chr2A 727947899 727952466 4567 False 1905.666667 4198 92.262 79 3904 3 chr2A.!!$F1 3825
2 TraesCS2D01G497000 chr2B 719462812 719465602 2790 False 1808.500000 3219 91.181 910 3912 2 chr2B.!!$F1 3002

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
355 356 0.106819 TTCCCCCGTCGGAACAAAAA 60.107 50.000 14.39 0.0 36.98 1.94 F
778 785 0.250901 CATGGCGAGGGGGAAATAGG 60.251 60.000 0.00 0.0 0.00 2.57 F
781 788 0.765519 GGCGAGGGGGAAATAGGGTA 60.766 60.000 0.00 0.0 0.00 3.69 F
937 1036 1.138671 GCTCTCGCTGTCTGTCTCC 59.861 63.158 0.00 0.0 0.00 3.71 F
1692 1794 1.142748 GCCGGTGAGAGATGAGGTG 59.857 63.158 1.90 0.0 0.00 4.00 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1494 1596 0.098200 CGTTCCGCACGTAGAGATCA 59.902 55.000 0.00 0.00 44.49 2.92 R
1951 2053 0.250727 TCGAAAACTTCCCTGGCCAG 60.251 55.000 26.87 26.87 0.00 4.85 R
1989 2091 0.596083 TGGCGTTCCATGCAAAAACG 60.596 50.000 20.61 20.61 46.28 3.60 R
2188 2290 2.507484 CTCCATTTCTGGCTCAACACA 58.493 47.619 0.00 0.00 42.80 3.72 R
3438 4551 0.316204 CCAAGGCTCTTGTTGCTTGG 59.684 55.000 12.18 0.00 34.80 3.61 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
17 18 2.574399 GGAGTCTGGACTGTCCGC 59.426 66.667 21.15 13.71 42.66 5.54
18 19 2.574399 GAGTCTGGACTGTCCGCC 59.426 66.667 21.15 11.47 42.66 6.13
19 20 2.203640 AGTCTGGACTGTCCGCCA 60.204 61.111 21.15 4.49 40.17 5.69
20 21 2.048127 GTCTGGACTGTCCGCCAC 60.048 66.667 21.15 13.37 40.17 5.01
21 22 3.680786 TCTGGACTGTCCGCCACG 61.681 66.667 21.15 7.74 40.17 4.94
22 23 3.991051 CTGGACTGTCCGCCACGT 61.991 66.667 21.15 0.00 40.17 4.49
23 24 3.916392 CTGGACTGTCCGCCACGTC 62.916 68.421 21.15 0.00 40.17 4.34
34 35 4.420143 CCACGTCGGCCAGATAAG 57.580 61.111 2.24 0.38 0.00 1.73
35 36 1.883084 CCACGTCGGCCAGATAAGC 60.883 63.158 2.24 0.00 0.00 3.09
36 37 1.141881 CACGTCGGCCAGATAAGCT 59.858 57.895 2.24 0.00 0.00 3.74
37 38 1.141881 ACGTCGGCCAGATAAGCTG 59.858 57.895 2.24 0.00 44.49 4.24
52 53 7.430760 AGATAAGCTGACCCTATCCAATATC 57.569 40.000 0.00 0.00 0.00 1.63
53 54 4.917906 AAGCTGACCCTATCCAATATCC 57.082 45.455 0.00 0.00 0.00 2.59
54 55 4.153371 AGCTGACCCTATCCAATATCCT 57.847 45.455 0.00 0.00 0.00 3.24
55 56 5.291100 AGCTGACCCTATCCAATATCCTA 57.709 43.478 0.00 0.00 0.00 2.94
56 57 5.026790 AGCTGACCCTATCCAATATCCTAC 58.973 45.833 0.00 0.00 0.00 3.18
57 58 4.162509 GCTGACCCTATCCAATATCCTACC 59.837 50.000 0.00 0.00 0.00 3.18
58 59 5.342017 CTGACCCTATCCAATATCCTACCA 58.658 45.833 0.00 0.00 0.00 3.25
59 60 5.927465 TGACCCTATCCAATATCCTACCAT 58.073 41.667 0.00 0.00 0.00 3.55
60 61 5.726308 TGACCCTATCCAATATCCTACCATG 59.274 44.000 0.00 0.00 0.00 3.66
61 62 5.927465 ACCCTATCCAATATCCTACCATGA 58.073 41.667 0.00 0.00 0.00 3.07
62 63 5.726793 ACCCTATCCAATATCCTACCATGAC 59.273 44.000 0.00 0.00 0.00 3.06
63 64 5.966935 CCCTATCCAATATCCTACCATGACT 59.033 44.000 0.00 0.00 0.00 3.41
64 65 7.132805 CCCTATCCAATATCCTACCATGACTA 58.867 42.308 0.00 0.00 0.00 2.59
65 66 7.070074 CCCTATCCAATATCCTACCATGACTAC 59.930 44.444 0.00 0.00 0.00 2.73
66 67 7.841729 CCTATCCAATATCCTACCATGACTACT 59.158 40.741 0.00 0.00 0.00 2.57
67 68 7.726033 ATCCAATATCCTACCATGACTACTC 57.274 40.000 0.00 0.00 0.00 2.59
68 69 6.017192 TCCAATATCCTACCATGACTACTCC 58.983 44.000 0.00 0.00 0.00 3.85
69 70 6.019748 CCAATATCCTACCATGACTACTCCT 58.980 44.000 0.00 0.00 0.00 3.69
70 71 6.153680 CCAATATCCTACCATGACTACTCCTC 59.846 46.154 0.00 0.00 0.00 3.71
71 72 3.210232 TCCTACCATGACTACTCCTCG 57.790 52.381 0.00 0.00 0.00 4.63
72 73 2.508716 TCCTACCATGACTACTCCTCGT 59.491 50.000 0.00 0.00 0.00 4.18
73 74 2.879646 CCTACCATGACTACTCCTCGTC 59.120 54.545 0.00 0.00 0.00 4.20
74 75 1.765230 ACCATGACTACTCCTCGTCC 58.235 55.000 0.00 0.00 0.00 4.79
75 76 1.033574 CCATGACTACTCCTCGTCCC 58.966 60.000 0.00 0.00 0.00 4.46
76 77 1.685180 CCATGACTACTCCTCGTCCCA 60.685 57.143 0.00 0.00 0.00 4.37
77 78 1.405821 CATGACTACTCCTCGTCCCAC 59.594 57.143 0.00 0.00 0.00 4.61
78 79 0.402887 TGACTACTCCTCGTCCCACA 59.597 55.000 0.00 0.00 0.00 4.17
79 80 0.810016 GACTACTCCTCGTCCCACAC 59.190 60.000 0.00 0.00 0.00 3.82
80 81 0.404812 ACTACTCCTCGTCCCACACT 59.595 55.000 0.00 0.00 0.00 3.55
81 82 0.811915 CTACTCCTCGTCCCACACTG 59.188 60.000 0.00 0.00 0.00 3.66
82 83 1.248785 TACTCCTCGTCCCACACTGC 61.249 60.000 0.00 0.00 0.00 4.40
83 84 2.523168 TCCTCGTCCCACACTGCA 60.523 61.111 0.00 0.00 0.00 4.41
84 85 2.357517 CCTCGTCCCACACTGCAC 60.358 66.667 0.00 0.00 0.00 4.57
85 86 2.737180 CTCGTCCCACACTGCACT 59.263 61.111 0.00 0.00 0.00 4.40
127 128 0.396435 TGAAAGTCGCCATCACACCT 59.604 50.000 0.00 0.00 0.00 4.00
142 143 3.006728 CCTACCTTGTCGCCCCCA 61.007 66.667 0.00 0.00 0.00 4.96
150 151 4.280019 GTCGCCCCCAACCCTTGT 62.280 66.667 0.00 0.00 0.00 3.16
160 161 2.899303 CAACCCTTGTTGGATACCCT 57.101 50.000 0.00 0.00 46.56 4.34
168 169 1.760613 TGTTGGATACCCTGTCGGATC 59.239 52.381 0.00 0.00 34.64 3.36
193 194 0.507358 CATCATGCAGTCGCTCATCG 59.493 55.000 0.00 0.00 39.64 3.84
238 239 2.871182 TCTCGATCGACCCATCTTTG 57.129 50.000 15.15 0.94 0.00 2.77
241 242 3.697542 TCTCGATCGACCCATCTTTGTTA 59.302 43.478 15.15 0.00 0.00 2.41
259 260 6.639671 TTGTTATTGAGTTTGTTGTGTTGC 57.360 33.333 0.00 0.00 0.00 4.17
295 296 0.798776 GGCATCAGTCCGTGACTTTG 59.201 55.000 4.08 6.60 41.37 2.77
297 298 1.728971 GCATCAGTCCGTGACTTTGAG 59.271 52.381 13.40 2.36 41.37 3.02
306 307 2.030540 CCGTGACTTTGAGAGGTCGTTA 60.031 50.000 0.00 0.00 35.45 3.18
345 346 4.461431 ACATTTAGTTTTGATTCCCCCGTC 59.539 41.667 0.00 0.00 0.00 4.79
355 356 0.106819 TTCCCCCGTCGGAACAAAAA 60.107 50.000 14.39 0.00 36.98 1.94
386 387 7.509141 TGAAGACTTCACATAGATGCAAAAA 57.491 32.000 13.99 0.00 34.08 1.94
397 398 7.058354 CACATAGATGCAAAAATATAACGCGAC 59.942 37.037 15.93 0.00 0.00 5.19
426 427 7.273381 TCGCTTATAGTACGGTTCTTAACAAAC 59.727 37.037 0.00 0.00 0.00 2.93
429 430 9.415544 CTTATAGTACGGTTCTTAACAAACTGT 57.584 33.333 12.67 12.67 45.64 3.55
464 465 9.788960 GTAAGAATAAAGGATACAAAAGGCAAG 57.211 33.333 0.00 0.00 41.41 4.01
470 471 9.875691 ATAAAGGATACAAAAGGCAAGAATTTC 57.124 29.630 0.00 0.00 41.41 2.17
471 472 6.916360 AGGATACAAAAGGCAAGAATTTCA 57.084 33.333 0.00 0.00 41.41 2.69
472 473 6.691508 AGGATACAAAAGGCAAGAATTTCAC 58.308 36.000 0.00 0.00 41.41 3.18
473 474 5.572896 GGATACAAAAGGCAAGAATTTCACG 59.427 40.000 0.00 0.00 0.00 4.35
474 475 4.385358 ACAAAAGGCAAGAATTTCACGT 57.615 36.364 0.00 0.00 0.00 4.49
475 476 4.111916 ACAAAAGGCAAGAATTTCACGTG 58.888 39.130 9.94 9.94 0.00 4.49
476 477 2.422276 AAGGCAAGAATTTCACGTGC 57.578 45.000 11.67 9.86 40.73 5.34
480 481 2.863137 GGCAAGAATTTCACGTGCAAAA 59.137 40.909 11.67 7.83 42.53 2.44
481 482 3.302415 GGCAAGAATTTCACGTGCAAAAC 60.302 43.478 11.67 5.21 42.53 2.43
491 492 3.369147 TCACGTGCAAAACAAAATGGTTG 59.631 39.130 11.67 0.00 0.00 3.77
517 518 4.886579 AGAAATGTCATCAAAGGGTTTGC 58.113 39.130 0.00 0.00 40.43 3.68
529 531 1.139163 GGGTTTGCGTGATTTTGCAG 58.861 50.000 0.00 0.00 42.89 4.41
564 568 3.651803 TTTGTAAGCGGGACAAAATGG 57.348 42.857 10.25 0.00 42.33 3.16
567 571 3.223435 TGTAAGCGGGACAAAATGGAAA 58.777 40.909 0.00 0.00 0.00 3.13
594 598 6.661304 AAATCATCTTTCCTTTGCTTCACT 57.339 33.333 0.00 0.00 0.00 3.41
667 674 7.979115 TTTTTAGTGAAGGACATGTTTTTCG 57.021 32.000 0.00 0.00 0.00 3.46
698 705 4.219725 TGATTGAGTTGACGTAGGACATGA 59.780 41.667 0.00 0.00 0.00 3.07
701 708 5.147330 TGAGTTGACGTAGGACATGATTT 57.853 39.130 0.00 0.00 0.00 2.17
702 709 5.168569 TGAGTTGACGTAGGACATGATTTC 58.831 41.667 0.00 0.00 0.00 2.17
703 710 4.504858 AGTTGACGTAGGACATGATTTCC 58.495 43.478 0.00 0.00 0.00 3.13
704 711 4.020573 AGTTGACGTAGGACATGATTTCCA 60.021 41.667 0.00 0.00 35.33 3.53
705 712 4.545208 TGACGTAGGACATGATTTCCAA 57.455 40.909 0.00 0.00 35.33 3.53
706 713 5.097742 TGACGTAGGACATGATTTCCAAT 57.902 39.130 0.00 0.00 35.33 3.16
707 714 6.228616 TGACGTAGGACATGATTTCCAATA 57.771 37.500 0.00 0.00 35.33 1.90
708 715 6.280643 TGACGTAGGACATGATTTCCAATAG 58.719 40.000 0.00 0.00 35.33 1.73
709 716 5.057149 ACGTAGGACATGATTTCCAATAGC 58.943 41.667 0.00 0.00 35.33 2.97
710 717 5.056480 CGTAGGACATGATTTCCAATAGCA 58.944 41.667 0.00 0.00 35.33 3.49
711 718 5.050091 CGTAGGACATGATTTCCAATAGCAC 60.050 44.000 0.00 0.00 35.33 4.40
712 719 4.858850 AGGACATGATTTCCAATAGCACA 58.141 39.130 0.00 0.00 35.33 4.57
713 720 5.263599 AGGACATGATTTCCAATAGCACAA 58.736 37.500 0.00 0.00 35.33 3.33
714 721 5.359009 AGGACATGATTTCCAATAGCACAAG 59.641 40.000 0.00 0.00 35.33 3.16
715 722 5.450965 GGACATGATTTCCAATAGCACAAGG 60.451 44.000 0.00 0.00 32.82 3.61
731 738 6.643388 AGCACAAGGAAAGAAAAGTGATTTT 58.357 32.000 0.00 0.00 0.00 1.82
774 781 4.440829 GGCATGGCGAGGGGGAAA 62.441 66.667 2.41 0.00 0.00 3.13
775 782 2.123726 GCATGGCGAGGGGGAAAT 60.124 61.111 0.00 0.00 0.00 2.17
776 783 1.150536 GCATGGCGAGGGGGAAATA 59.849 57.895 0.00 0.00 0.00 1.40
777 784 0.890996 GCATGGCGAGGGGGAAATAG 60.891 60.000 0.00 0.00 0.00 1.73
778 785 0.250901 CATGGCGAGGGGGAAATAGG 60.251 60.000 0.00 0.00 0.00 2.57
779 786 1.427072 ATGGCGAGGGGGAAATAGGG 61.427 60.000 0.00 0.00 0.00 3.53
780 787 2.076803 GGCGAGGGGGAAATAGGGT 61.077 63.158 0.00 0.00 0.00 4.34
781 788 0.765519 GGCGAGGGGGAAATAGGGTA 60.766 60.000 0.00 0.00 0.00 3.69
782 789 1.359168 GCGAGGGGGAAATAGGGTAT 58.641 55.000 0.00 0.00 0.00 2.73
785 792 2.714808 GAGGGGGAAATAGGGTATGGT 58.285 52.381 0.00 0.00 0.00 3.55
786 793 3.759452 CGAGGGGGAAATAGGGTATGGTA 60.759 52.174 0.00 0.00 0.00 3.25
787 794 4.445564 GAGGGGGAAATAGGGTATGGTAT 58.554 47.826 0.00 0.00 0.00 2.73
788 795 4.183916 AGGGGGAAATAGGGTATGGTATG 58.816 47.826 0.00 0.00 0.00 2.39
791 798 4.324331 GGGGAAATAGGGTATGGTATGAGC 60.324 50.000 0.00 0.00 0.00 4.26
792 799 4.288626 GGGAAATAGGGTATGGTATGAGCA 59.711 45.833 0.00 0.00 0.00 4.26
793 800 5.044846 GGGAAATAGGGTATGGTATGAGCAT 60.045 44.000 0.00 0.00 39.88 3.79
794 801 6.485171 GGAAATAGGGTATGGTATGAGCATT 58.515 40.000 0.00 0.00 37.51 3.56
795 802 6.375455 GGAAATAGGGTATGGTATGAGCATTG 59.625 42.308 0.00 0.00 37.51 2.82
796 803 6.454223 AATAGGGTATGGTATGAGCATTGT 57.546 37.500 0.00 0.00 37.51 2.71
797 804 4.357918 AGGGTATGGTATGAGCATTGTC 57.642 45.455 0.00 0.00 37.51 3.18
798 805 3.976654 AGGGTATGGTATGAGCATTGTCT 59.023 43.478 0.00 0.00 37.51 3.41
799 806 4.413520 AGGGTATGGTATGAGCATTGTCTT 59.586 41.667 0.00 0.00 37.51 3.01
801 808 6.273260 AGGGTATGGTATGAGCATTGTCTTAT 59.727 38.462 0.00 0.00 37.51 1.73
802 809 6.942576 GGGTATGGTATGAGCATTGTCTTATT 59.057 38.462 0.00 0.00 37.51 1.40
803 810 7.119846 GGGTATGGTATGAGCATTGTCTTATTC 59.880 40.741 0.00 0.00 37.51 1.75
804 811 7.119846 GGTATGGTATGAGCATTGTCTTATTCC 59.880 40.741 0.00 0.00 37.51 3.01
805 812 6.000246 TGGTATGAGCATTGTCTTATTCCA 58.000 37.500 6.92 6.92 30.77 3.53
809 816 4.272489 TGAGCATTGTCTTATTCCAAGGG 58.728 43.478 0.00 0.00 0.00 3.95
810 817 4.018506 TGAGCATTGTCTTATTCCAAGGGA 60.019 41.667 0.00 0.00 0.00 4.20
891 990 4.173256 CAAATTTGCAATACTCCCGTTCC 58.827 43.478 5.01 0.00 0.00 3.62
899 998 4.184629 CAATACTCCCGTTCCTTCAAGAG 58.815 47.826 0.00 0.00 0.00 2.85
903 1002 3.135895 ACTCCCGTTCCTTCAAGAGAAAA 59.864 43.478 0.00 0.00 32.35 2.29
906 1005 3.251004 CCCGTTCCTTCAAGAGAAAACTG 59.749 47.826 0.00 0.00 32.35 3.16
935 1034 4.413928 AGCTCTCGCTGTCTGTCT 57.586 55.556 0.00 0.00 46.86 3.41
936 1035 2.179764 AGCTCTCGCTGTCTGTCTC 58.820 57.895 0.00 0.00 46.86 3.36
937 1036 1.138671 GCTCTCGCTGTCTGTCTCC 59.861 63.158 0.00 0.00 0.00 3.71
938 1037 1.806568 CTCTCGCTGTCTGTCTCCC 59.193 63.158 0.00 0.00 0.00 4.30
939 1038 1.987704 CTCTCGCTGTCTGTCTCCCG 61.988 65.000 0.00 0.00 0.00 5.14
940 1039 2.282251 TCGCTGTCTGTCTCCCGT 60.282 61.111 0.00 0.00 0.00 5.28
941 1040 2.179517 CGCTGTCTGTCTCCCGTC 59.820 66.667 0.00 0.00 0.00 4.79
942 1041 2.336478 CGCTGTCTGTCTCCCGTCT 61.336 63.158 0.00 0.00 0.00 4.18
953 1052 2.296471 GTCTCCCGTCTTTCTGAAGTCA 59.704 50.000 0.00 0.00 34.41 3.41
957 1056 4.714632 TCCCGTCTTTCTGAAGTCAAAAT 58.285 39.130 0.00 0.00 34.41 1.82
969 1068 2.519013 AGTCAAAATCTTGGAGGCACC 58.481 47.619 0.00 0.00 39.54 5.01
1268 1367 4.070552 GCTCTCCCTGTTCCGCGT 62.071 66.667 4.92 0.00 0.00 6.01
1449 1551 2.042435 CCGGCCTCCTCCTCTCTT 60.042 66.667 0.00 0.00 0.00 2.85
1620 1722 4.243008 TGGAACGCGGTCCTTGCA 62.243 61.111 40.37 20.86 38.62 4.08
1692 1794 1.142748 GCCGGTGAGAGATGAGGTG 59.857 63.158 1.90 0.00 0.00 4.00
1695 1797 1.468985 CGGTGAGAGATGAGGTGTCT 58.531 55.000 0.00 0.00 32.20 3.41
1803 1905 1.675641 GGTGAATGAGGCTGCGGTT 60.676 57.895 0.00 0.00 0.00 4.44
1989 2091 3.551407 GGGATGCCGAGGAGGGAC 61.551 72.222 0.00 0.00 45.60 4.46
2181 2283 4.974275 CGCTATTTTGAATTGATGGCTGAG 59.026 41.667 0.00 0.00 0.00 3.35
2585 2687 2.304470 TGGATCACAAGGATTCCGTTCA 59.696 45.455 0.00 0.00 36.00 3.18
3028 3470 7.214381 CAGCATATCCCAATTCATTTGACATT 58.786 34.615 0.00 0.00 37.53 2.71
3065 3507 6.508563 GCTGCTTAAGTTTTCAGCTGTTTTTC 60.509 38.462 19.57 2.35 46.00 2.29
3090 3532 1.507140 CCAATACTGTAGGGGAGGCA 58.493 55.000 2.30 0.00 0.00 4.75
3093 3535 0.341961 ATACTGTAGGGGAGGCACCA 59.658 55.000 2.69 0.00 41.20 4.17
3112 3554 6.598064 GGCACCAACAGTAAATTCTATACAGT 59.402 38.462 0.00 0.00 0.00 3.55
3145 3587 0.235926 GAGTCAAGCCAGACGCAAAC 59.764 55.000 5.25 0.00 43.24 2.93
3168 3610 4.322567 GGGATCAGCAATATCAGACTTCC 58.677 47.826 0.00 0.00 0.00 3.46
3190 3632 9.810545 CTTCCTTCTAAAGTAGATGAGGTAAAG 57.189 37.037 3.91 0.00 35.33 1.85
3191 3633 7.783042 TCCTTCTAAAGTAGATGAGGTAAAGC 58.217 38.462 3.91 0.00 35.33 3.51
3196 3638 4.273300 AGTAGATGAGGTAAAGCTCCCT 57.727 45.455 6.71 6.58 0.00 4.20
3209 3651 8.268605 AGGTAAAGCTCCCTCTTAGAAATAAAG 58.731 37.037 0.00 0.00 0.00 1.85
3236 3678 5.779771 CCAAGATCCTAAGCTAGAGGAGATT 59.220 44.000 19.26 14.06 46.27 2.40
3241 3683 6.472686 TCCTAAGCTAGAGGAGATTTTGTC 57.527 41.667 12.31 0.00 38.22 3.18
3246 3688 4.707448 AGCTAGAGGAGATTTTGTCGAAGA 59.293 41.667 0.00 0.00 0.00 2.87
3268 3710 8.652810 AAGATTTTCACATTCCTTTGTTTCTG 57.347 30.769 0.00 0.00 0.00 3.02
3280 3722 4.156739 CCTTTGTTTCTGAATGGACTAGGC 59.843 45.833 0.00 0.00 0.00 3.93
3301 3743 4.168760 GCAACAATGATGTAAGCTTCCAC 58.831 43.478 0.00 0.00 39.40 4.02
3345 3787 2.219080 TTTGGCAGAGGCAATCATGA 57.781 45.000 6.83 0.00 46.84 3.07
3353 3795 4.213694 GCAGAGGCAATCATGATGTAGAAG 59.786 45.833 9.46 0.00 40.72 2.85
3377 3819 1.672881 CGAGATGAATTCTGGGGCAAC 59.327 52.381 7.05 0.00 33.74 4.17
3401 3843 6.185511 CCTTATATGATCCAGCATTCCATGT 58.814 40.000 0.00 0.00 0.00 3.21
3407 3849 5.067954 TGATCCAGCATTCCATGTTATGAG 58.932 41.667 8.11 1.25 0.00 2.90
3408 3850 3.824133 TCCAGCATTCCATGTTATGAGG 58.176 45.455 8.11 8.39 0.00 3.86
3409 3851 3.459227 TCCAGCATTCCATGTTATGAGGA 59.541 43.478 8.11 10.05 0.00 3.71
3411 3853 5.310331 TCCAGCATTCCATGTTATGAGGATA 59.690 40.000 8.11 0.00 0.00 2.59
3412 3854 5.646793 CCAGCATTCCATGTTATGAGGATAG 59.353 44.000 8.11 0.00 0.00 2.08
3413 3855 5.123502 CAGCATTCCATGTTATGAGGATAGC 59.876 44.000 8.11 0.00 34.03 2.97
3438 4551 5.358922 CCAGAAGAGATGATCACTTTCTCC 58.641 45.833 17.41 6.95 27.56 3.71
3457 4570 0.316204 CCAAGCAACAAGAGCCTTGG 59.684 55.000 16.21 9.14 35.53 3.61
3458 4571 0.319297 CAAGCAACAAGAGCCTTGGC 60.319 55.000 16.21 2.97 0.00 4.52
3461 4574 1.174712 GCAACAAGAGCCTTGGCTCA 61.175 55.000 34.40 0.00 39.13 4.26
3512 4625 0.767375 ATATGCCGGGCTCTGTCAAT 59.233 50.000 21.46 5.77 0.00 2.57
3550 4663 6.556974 ATGATCTCTTGATGGAAGAACTCA 57.443 37.500 0.00 0.00 40.33 3.41
3556 4669 4.758674 TCTTGATGGAAGAACTCAAAGCTG 59.241 41.667 0.00 0.00 37.78 4.24
3617 4730 6.260936 CAGCGGGTAAGAGATATGTTTTCATT 59.739 38.462 0.00 0.00 41.25 2.57
3674 4787 5.123979 AGCGGAACCATAATTCTTGAAGAAC 59.876 40.000 10.18 0.00 37.00 3.01
3699 4812 9.167311 ACTATTCACAAATCACAATTACTCCTC 57.833 33.333 0.00 0.00 0.00 3.71
3718 4831 5.694995 TCCTCTTTTGTCATTTTCTCAGGT 58.305 37.500 0.00 0.00 0.00 4.00
3751 4864 1.339438 ACTGATGGATATCCCGCATGC 60.339 52.381 19.34 7.91 37.93 4.06
3772 4885 5.592054 TGCTGATACCTTAACGATCTCTTG 58.408 41.667 0.00 0.00 0.00 3.02
3805 4918 3.265791 CCTTCAGCTCAAGGTATCACAC 58.734 50.000 8.49 0.00 38.58 3.82
3829 4953 2.950309 GGCTGCATTCTCTTCATGATGT 59.050 45.455 0.50 0.00 0.00 3.06
3830 4954 3.243101 GGCTGCATTCTCTTCATGATGTG 60.243 47.826 0.50 6.43 0.00 3.21
3831 4955 3.626217 GCTGCATTCTCTTCATGATGTGA 59.374 43.478 8.33 8.56 34.25 3.58
3832 4956 4.276183 GCTGCATTCTCTTCATGATGTGAT 59.724 41.667 12.49 2.61 36.54 3.06
3833 4957 5.221067 GCTGCATTCTCTTCATGATGTGATT 60.221 40.000 12.49 7.79 36.54 2.57
3834 4958 6.373186 TGCATTCTCTTCATGATGTGATTC 57.627 37.500 12.49 7.06 36.54 2.52
3835 4959 6.120220 TGCATTCTCTTCATGATGTGATTCT 58.880 36.000 12.49 1.55 36.54 2.40
3836 4960 7.277396 TGCATTCTCTTCATGATGTGATTCTA 58.723 34.615 12.49 1.23 36.54 2.10
3837 4961 7.771826 TGCATTCTCTTCATGATGTGATTCTAA 59.228 33.333 12.49 0.94 36.54 2.10
3838 4962 8.784994 GCATTCTCTTCATGATGTGATTCTAAT 58.215 33.333 12.49 2.86 36.54 1.73
3876 5004 5.527582 TCTTGATCTCTTCACATCATGCATG 59.472 40.000 21.07 21.07 38.64 4.06
3908 5036 6.325919 TGCAATACCCTTTTTCAGTTGTAG 57.674 37.500 0.00 0.00 0.00 2.74
3912 5040 7.040271 GCAATACCCTTTTTCAGTTGTAGGTTA 60.040 37.037 0.00 0.00 0.00 2.85
3913 5041 9.020731 CAATACCCTTTTTCAGTTGTAGGTTAT 57.979 33.333 0.00 0.00 0.00 1.89
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.574399 GCGGACAGTCCAGACTCC 59.426 66.667 20.13 0.00 40.20 3.85
1 2 2.276116 TGGCGGACAGTCCAGACTC 61.276 63.158 20.13 4.34 40.20 3.36
2 3 2.203640 TGGCGGACAGTCCAGACT 60.204 61.111 20.13 0.00 43.61 3.24
3 4 2.048127 GTGGCGGACAGTCCAGAC 60.048 66.667 20.13 14.40 35.91 3.51
4 5 3.680786 CGTGGCGGACAGTCCAGA 61.681 66.667 20.13 0.00 35.91 3.86
5 6 3.916392 GACGTGGCGGACAGTCCAG 62.916 68.421 20.13 12.91 35.91 3.86
6 7 3.986006 GACGTGGCGGACAGTCCA 61.986 66.667 20.13 0.00 35.91 4.02
17 18 1.883084 GCTTATCTGGCCGACGTGG 60.883 63.158 0.00 0.00 42.50 4.94
18 19 1.141881 AGCTTATCTGGCCGACGTG 59.858 57.895 0.00 0.00 0.00 4.49
19 20 1.141881 CAGCTTATCTGGCCGACGT 59.858 57.895 0.00 0.00 39.15 4.34
20 21 0.872021 GTCAGCTTATCTGGCCGACG 60.872 60.000 0.00 0.00 41.49 5.12
21 22 2.979130 GTCAGCTTATCTGGCCGAC 58.021 57.895 0.00 0.00 41.49 4.79
25 26 2.027653 GGATAGGGTCAGCTTATCTGGC 60.028 54.545 6.01 0.00 46.47 4.85
26 27 3.242867 TGGATAGGGTCAGCTTATCTGG 58.757 50.000 6.01 0.00 43.06 3.86
27 28 4.963318 TTGGATAGGGTCAGCTTATCTG 57.037 45.455 6.01 0.00 44.21 2.90
28 29 6.385467 GGATATTGGATAGGGTCAGCTTATCT 59.615 42.308 6.01 0.00 0.00 1.98
29 30 6.385467 AGGATATTGGATAGGGTCAGCTTATC 59.615 42.308 0.00 0.00 0.00 1.75
30 31 6.275461 AGGATATTGGATAGGGTCAGCTTAT 58.725 40.000 0.00 0.00 0.00 1.73
31 32 5.665701 AGGATATTGGATAGGGTCAGCTTA 58.334 41.667 0.00 0.00 0.00 3.09
32 33 4.507342 AGGATATTGGATAGGGTCAGCTT 58.493 43.478 0.00 0.00 0.00 3.74
33 34 4.153371 AGGATATTGGATAGGGTCAGCT 57.847 45.455 0.00 0.00 0.00 4.24
34 35 4.162509 GGTAGGATATTGGATAGGGTCAGC 59.837 50.000 0.00 0.00 0.00 4.26
35 36 5.342017 TGGTAGGATATTGGATAGGGTCAG 58.658 45.833 0.00 0.00 0.00 3.51
36 37 5.363124 TGGTAGGATATTGGATAGGGTCA 57.637 43.478 0.00 0.00 0.00 4.02
37 38 5.964477 TCATGGTAGGATATTGGATAGGGTC 59.036 44.000 0.00 0.00 0.00 4.46
38 39 5.726793 GTCATGGTAGGATATTGGATAGGGT 59.273 44.000 0.00 0.00 0.00 4.34
39 40 5.966935 AGTCATGGTAGGATATTGGATAGGG 59.033 44.000 0.00 0.00 0.00 3.53
40 41 7.841729 AGTAGTCATGGTAGGATATTGGATAGG 59.158 40.741 0.00 0.00 0.00 2.57
41 42 8.830915 AGTAGTCATGGTAGGATATTGGATAG 57.169 38.462 0.00 0.00 0.00 2.08
42 43 7.839705 GGAGTAGTCATGGTAGGATATTGGATA 59.160 40.741 0.00 0.00 0.00 2.59
43 44 6.670027 GGAGTAGTCATGGTAGGATATTGGAT 59.330 42.308 0.00 0.00 0.00 3.41
44 45 6.017192 GGAGTAGTCATGGTAGGATATTGGA 58.983 44.000 0.00 0.00 0.00 3.53
45 46 6.019748 AGGAGTAGTCATGGTAGGATATTGG 58.980 44.000 0.00 0.00 0.00 3.16
46 47 6.127869 CGAGGAGTAGTCATGGTAGGATATTG 60.128 46.154 0.00 0.00 0.00 1.90
47 48 5.946972 CGAGGAGTAGTCATGGTAGGATATT 59.053 44.000 0.00 0.00 0.00 1.28
48 49 5.014333 ACGAGGAGTAGTCATGGTAGGATAT 59.986 44.000 0.00 0.00 0.00 1.63
49 50 4.350225 ACGAGGAGTAGTCATGGTAGGATA 59.650 45.833 0.00 0.00 0.00 2.59
50 51 3.138653 ACGAGGAGTAGTCATGGTAGGAT 59.861 47.826 0.00 0.00 0.00 3.24
51 52 2.508716 ACGAGGAGTAGTCATGGTAGGA 59.491 50.000 0.00 0.00 0.00 2.94
52 53 2.879646 GACGAGGAGTAGTCATGGTAGG 59.120 54.545 0.00 0.00 37.34 3.18
53 54 2.879646 GGACGAGGAGTAGTCATGGTAG 59.120 54.545 0.00 0.00 39.01 3.18
54 55 2.422519 GGGACGAGGAGTAGTCATGGTA 60.423 54.545 0.00 0.00 39.01 3.25
55 56 1.685491 GGGACGAGGAGTAGTCATGGT 60.685 57.143 0.00 0.00 39.01 3.55
56 57 1.033574 GGGACGAGGAGTAGTCATGG 58.966 60.000 0.00 0.00 39.01 3.66
57 58 1.405821 GTGGGACGAGGAGTAGTCATG 59.594 57.143 0.00 0.00 39.01 3.07
58 59 1.005569 TGTGGGACGAGGAGTAGTCAT 59.994 52.381 0.00 0.00 39.01 3.06
59 60 0.402887 TGTGGGACGAGGAGTAGTCA 59.597 55.000 0.00 0.00 39.01 3.41
60 61 0.810016 GTGTGGGACGAGGAGTAGTC 59.190 60.000 0.00 0.00 36.70 2.59
61 62 0.404812 AGTGTGGGACGAGGAGTAGT 59.595 55.000 0.00 0.00 0.00 2.73
62 63 0.811915 CAGTGTGGGACGAGGAGTAG 59.188 60.000 0.00 0.00 0.00 2.57
63 64 1.248785 GCAGTGTGGGACGAGGAGTA 61.249 60.000 0.00 0.00 0.00 2.59
64 65 2.574955 GCAGTGTGGGACGAGGAGT 61.575 63.158 0.00 0.00 0.00 3.85
65 66 2.262915 GCAGTGTGGGACGAGGAG 59.737 66.667 0.00 0.00 0.00 3.69
66 67 2.523168 TGCAGTGTGGGACGAGGA 60.523 61.111 0.00 0.00 0.00 3.71
67 68 2.357517 GTGCAGTGTGGGACGAGG 60.358 66.667 0.00 0.00 0.00 4.63
68 69 1.373497 GAGTGCAGTGTGGGACGAG 60.373 63.158 0.00 0.00 33.93 4.18
69 70 2.734591 GAGTGCAGTGTGGGACGA 59.265 61.111 0.00 0.00 33.93 4.20
70 71 2.357517 GGAGTGCAGTGTGGGACG 60.358 66.667 0.00 0.00 33.93 4.79
71 72 2.032681 GGGAGTGCAGTGTGGGAC 59.967 66.667 0.00 0.00 0.00 4.46
72 73 2.122413 AGGGAGTGCAGTGTGGGA 60.122 61.111 0.00 0.00 0.00 4.37
73 74 2.177594 GAGAGGGAGTGCAGTGTGGG 62.178 65.000 0.00 0.00 0.00 4.61
74 75 1.294780 GAGAGGGAGTGCAGTGTGG 59.705 63.158 0.00 0.00 0.00 4.17
75 76 1.294780 GGAGAGGGAGTGCAGTGTG 59.705 63.158 0.00 0.00 0.00 3.82
76 77 1.915769 GGGAGAGGGAGTGCAGTGT 60.916 63.158 0.00 0.00 0.00 3.55
77 78 2.664081 GGGGAGAGGGAGTGCAGTG 61.664 68.421 0.00 0.00 0.00 3.66
78 79 2.284995 GGGGAGAGGGAGTGCAGT 60.285 66.667 0.00 0.00 0.00 4.40
79 80 3.465403 CGGGGAGAGGGAGTGCAG 61.465 72.222 0.00 0.00 0.00 4.41
82 83 2.765807 ATGCGGGGAGAGGGAGTG 60.766 66.667 0.00 0.00 0.00 3.51
83 84 2.444895 GATGCGGGGAGAGGGAGT 60.445 66.667 0.00 0.00 0.00 3.85
84 85 3.610669 CGATGCGGGGAGAGGGAG 61.611 72.222 0.00 0.00 0.00 4.30
127 128 2.751688 GTTGGGGGCGACAAGGTA 59.248 61.111 0.00 0.00 0.00 3.08
142 143 2.041216 GACAGGGTATCCAACAAGGGTT 59.959 50.000 0.00 0.00 38.24 4.11
150 151 2.039418 CTGATCCGACAGGGTATCCAA 58.961 52.381 0.00 0.00 38.33 3.53
168 169 1.434622 GCGACTGCATGATGGACCTG 61.435 60.000 0.00 0.00 42.15 4.00
172 173 0.466963 ATGAGCGACTGCATGATGGA 59.533 50.000 0.00 0.00 46.23 3.41
193 194 2.748605 CTTGACATAGATGCCCTCGTC 58.251 52.381 0.00 0.00 0.00 4.20
195 196 1.069823 AGCTTGACATAGATGCCCTCG 59.930 52.381 0.00 0.00 0.00 4.63
238 239 4.796312 ACGCAACACAACAAACTCAATAAC 59.204 37.500 0.00 0.00 0.00 1.89
241 242 3.502191 ACGCAACACAACAAACTCAAT 57.498 38.095 0.00 0.00 0.00 2.57
259 260 5.339177 TGATGCCATTACATTGCTAAAACG 58.661 37.500 0.00 0.00 0.00 3.60
269 270 2.170397 TCACGGACTGATGCCATTACAT 59.830 45.455 0.00 0.00 0.00 2.29
270 271 1.552792 TCACGGACTGATGCCATTACA 59.447 47.619 0.00 0.00 0.00 2.41
273 274 0.615331 AGTCACGGACTGATGCCATT 59.385 50.000 5.85 0.00 41.76 3.16
274 275 0.615331 AAGTCACGGACTGATGCCAT 59.385 50.000 7.23 0.00 42.59 4.40
295 296 9.828852 CATACTTGTATATTCTAACGACCTCTC 57.171 37.037 0.00 0.00 0.00 3.20
297 298 9.609950 GTCATACTTGTATATTCTAACGACCTC 57.390 37.037 0.00 0.00 0.00 3.85
326 327 2.616001 CCGACGGGGGAATCAAAACTAA 60.616 50.000 5.81 0.00 0.00 2.24
330 331 0.400975 TTCCGACGGGGGAATCAAAA 59.599 50.000 15.25 0.00 41.08 2.44
345 346 5.804979 AGTCTTCACAATTGTTTTTGTTCCG 59.195 36.000 8.77 0.00 37.73 4.30
378 379 3.064271 ACCGTCGCGTTATATTTTTGCAT 59.936 39.130 5.77 0.00 0.00 3.96
381 382 3.266067 CGACCGTCGCGTTATATTTTTG 58.734 45.455 8.21 0.00 31.14 2.44
397 398 2.289002 AGAACCGTACTATAAGCGACCG 59.711 50.000 0.00 0.00 0.00 4.79
404 405 9.762933 AACAGTTTGTTAAGAACCGTACTATAA 57.237 29.630 0.00 0.00 39.09 0.98
411 412 5.883503 TTGAACAGTTTGTTAAGAACCGT 57.116 34.783 0.00 0.00 41.28 4.83
412 413 6.548171 TCTTTGAACAGTTTGTTAAGAACCG 58.452 36.000 5.23 0.00 41.28 4.44
464 465 5.676310 CCATTTTGTTTTGCACGTGAAATTC 59.324 36.000 22.23 11.67 0.00 2.17
469 470 3.238108 ACCATTTTGTTTTGCACGTGA 57.762 38.095 22.23 1.04 0.00 4.35
470 471 3.369147 TCAACCATTTTGTTTTGCACGTG 59.631 39.130 12.28 12.28 0.00 4.49
471 472 3.589988 TCAACCATTTTGTTTTGCACGT 58.410 36.364 0.00 0.00 0.00 4.49
472 473 4.590400 TTCAACCATTTTGTTTTGCACG 57.410 36.364 0.00 0.00 0.00 5.34
473 474 6.606768 TCTTTTCAACCATTTTGTTTTGCAC 58.393 32.000 0.00 0.00 0.00 4.57
474 475 6.808008 TCTTTTCAACCATTTTGTTTTGCA 57.192 29.167 0.00 0.00 0.00 4.08
475 476 8.585436 CATTTCTTTTCAACCATTTTGTTTTGC 58.415 29.630 0.00 0.00 0.00 3.68
476 477 9.623350 ACATTTCTTTTCAACCATTTTGTTTTG 57.377 25.926 0.00 0.00 0.00 2.44
480 481 8.735692 ATGACATTTCTTTTCAACCATTTTGT 57.264 26.923 0.00 0.00 0.00 2.83
481 482 8.828644 TGATGACATTTCTTTTCAACCATTTTG 58.171 29.630 0.00 0.00 0.00 2.44
491 492 7.518848 GCAAACCCTTTGATGACATTTCTTTTC 60.519 37.037 0.00 0.00 43.26 2.29
517 518 3.000872 CACACAACAACTGCAAAATCACG 60.001 43.478 0.00 0.00 0.00 4.35
576 580 7.823745 TTTAGAAGTGAAGCAAAGGAAAGAT 57.176 32.000 0.00 0.00 0.00 2.40
645 649 6.687081 ACGAAAAACATGTCCTTCACTAAA 57.313 33.333 16.08 0.00 0.00 1.85
649 656 6.295039 TCTTACGAAAAACATGTCCTTCAC 57.705 37.500 16.08 4.99 0.00 3.18
660 667 9.445786 TCAACTCAATCAAATCTTACGAAAAAC 57.554 29.630 0.00 0.00 0.00 2.43
663 670 7.042321 ACGTCAACTCAATCAAATCTTACGAAA 60.042 33.333 0.00 0.00 0.00 3.46
667 674 7.544566 TCCTACGTCAACTCAATCAAATCTTAC 59.455 37.037 0.00 0.00 0.00 2.34
679 686 4.801330 AATCATGTCCTACGTCAACTCA 57.199 40.909 0.00 0.00 0.00 3.41
685 692 5.177696 GCTATTGGAAATCATGTCCTACGTC 59.822 44.000 0.00 0.00 36.03 4.34
686 693 5.057149 GCTATTGGAAATCATGTCCTACGT 58.943 41.667 0.00 0.00 36.03 3.57
698 705 6.916360 TTCTTTCCTTGTGCTATTGGAAAT 57.084 33.333 12.38 0.00 44.41 2.17
701 708 5.833131 ACTTTTCTTTCCTTGTGCTATTGGA 59.167 36.000 0.00 0.00 0.00 3.53
702 709 5.922544 CACTTTTCTTTCCTTGTGCTATTGG 59.077 40.000 0.00 0.00 0.00 3.16
703 710 6.738114 TCACTTTTCTTTCCTTGTGCTATTG 58.262 36.000 0.00 0.00 0.00 1.90
704 711 6.959639 TCACTTTTCTTTCCTTGTGCTATT 57.040 33.333 0.00 0.00 0.00 1.73
705 712 7.530426 AATCACTTTTCTTTCCTTGTGCTAT 57.470 32.000 0.00 0.00 0.00 2.97
706 713 6.959639 AATCACTTTTCTTTCCTTGTGCTA 57.040 33.333 0.00 0.00 0.00 3.49
707 714 5.859205 AATCACTTTTCTTTCCTTGTGCT 57.141 34.783 0.00 0.00 0.00 4.40
708 715 6.313658 ACAAAATCACTTTTCTTTCCTTGTGC 59.686 34.615 0.00 0.00 32.21 4.57
709 716 7.832503 ACAAAATCACTTTTCTTTCCTTGTG 57.167 32.000 0.00 0.00 32.21 3.33
710 717 8.846943 AAACAAAATCACTTTTCTTTCCTTGT 57.153 26.923 0.00 0.00 32.21 3.16
731 738 7.147811 CCCCCTTGATTCGGAATAATTTAAACA 60.148 37.037 2.65 0.00 0.00 2.83
760 767 1.427072 CCCTATTTCCCCCTCGCCAT 61.427 60.000 0.00 0.00 0.00 4.40
763 770 1.003233 CATACCCTATTTCCCCCTCGC 59.997 57.143 0.00 0.00 0.00 5.03
764 771 1.628846 CCATACCCTATTTCCCCCTCG 59.371 57.143 0.00 0.00 0.00 4.63
770 777 5.499004 TGCTCATACCATACCCTATTTCC 57.501 43.478 0.00 0.00 0.00 3.13
771 778 6.942576 ACAATGCTCATACCATACCCTATTTC 59.057 38.462 0.00 0.00 0.00 2.17
774 781 5.787494 AGACAATGCTCATACCATACCCTAT 59.213 40.000 0.00 0.00 0.00 2.57
775 782 5.155161 AGACAATGCTCATACCATACCCTA 58.845 41.667 0.00 0.00 0.00 3.53
776 783 3.976654 AGACAATGCTCATACCATACCCT 59.023 43.478 0.00 0.00 0.00 4.34
777 784 4.357918 AGACAATGCTCATACCATACCC 57.642 45.455 0.00 0.00 0.00 3.69
778 785 7.119846 GGAATAAGACAATGCTCATACCATACC 59.880 40.741 0.00 0.00 0.00 2.73
779 786 7.661437 TGGAATAAGACAATGCTCATACCATAC 59.339 37.037 0.00 0.00 0.00 2.39
780 787 7.744733 TGGAATAAGACAATGCTCATACCATA 58.255 34.615 0.00 0.00 0.00 2.74
781 788 6.604171 TGGAATAAGACAATGCTCATACCAT 58.396 36.000 0.00 0.00 0.00 3.55
782 789 6.000246 TGGAATAAGACAATGCTCATACCA 58.000 37.500 0.00 0.00 0.00 3.25
785 792 6.064060 CCCTTGGAATAAGACAATGCTCATA 58.936 40.000 0.00 0.00 0.00 2.15
786 793 4.891756 CCCTTGGAATAAGACAATGCTCAT 59.108 41.667 0.00 0.00 0.00 2.90
787 794 4.018506 TCCCTTGGAATAAGACAATGCTCA 60.019 41.667 0.00 0.00 0.00 4.26
788 795 4.526970 TCCCTTGGAATAAGACAATGCTC 58.473 43.478 0.00 0.00 0.00 4.26
791 798 6.209391 ACAACTTCCCTTGGAATAAGACAATG 59.791 38.462 0.00 0.00 41.23 2.82
792 799 6.209391 CACAACTTCCCTTGGAATAAGACAAT 59.791 38.462 0.00 0.00 41.23 2.71
793 800 5.534654 CACAACTTCCCTTGGAATAAGACAA 59.465 40.000 0.00 0.00 41.23 3.18
794 801 5.070001 CACAACTTCCCTTGGAATAAGACA 58.930 41.667 0.00 0.00 41.23 3.41
795 802 5.048713 CACACAACTTCCCTTGGAATAAGAC 60.049 44.000 0.00 0.00 41.23 3.01
796 803 5.070001 CACACAACTTCCCTTGGAATAAGA 58.930 41.667 0.00 0.00 41.23 2.10
797 804 5.070001 TCACACAACTTCCCTTGGAATAAG 58.930 41.667 0.00 0.00 41.23 1.73
798 805 5.055265 TCACACAACTTCCCTTGGAATAA 57.945 39.130 0.00 0.00 41.23 1.40
799 806 4.715534 TCACACAACTTCCCTTGGAATA 57.284 40.909 0.00 0.00 41.23 1.75
801 808 3.374042 TTCACACAACTTCCCTTGGAA 57.626 42.857 0.00 0.00 39.66 3.53
802 809 3.374042 TTTCACACAACTTCCCTTGGA 57.626 42.857 0.00 0.00 0.00 3.53
803 810 4.670896 AATTTCACACAACTTCCCTTGG 57.329 40.909 0.00 0.00 0.00 3.61
804 811 7.432869 TCAATAATTTCACACAACTTCCCTTG 58.567 34.615 0.00 0.00 0.00 3.61
805 812 7.595819 TCAATAATTTCACACAACTTCCCTT 57.404 32.000 0.00 0.00 0.00 3.95
886 985 5.266242 CAACAGTTTTCTCTTGAAGGAACG 58.734 41.667 0.00 0.00 33.28 3.95
889 988 5.110814 TCCAACAGTTTTCTCTTGAAGGA 57.889 39.130 0.00 0.00 33.28 3.36
891 990 6.624352 TGATCCAACAGTTTTCTCTTGAAG 57.376 37.500 0.00 0.00 33.28 3.02
899 998 5.182760 AGAGCTCATTGATCCAACAGTTTTC 59.817 40.000 17.77 0.00 0.00 2.29
903 1002 3.678252 CGAGAGCTCATTGATCCAACAGT 60.678 47.826 17.77 0.00 0.00 3.55
927 1026 1.613925 CAGAAAGACGGGAGACAGACA 59.386 52.381 0.00 0.00 0.00 3.41
935 1034 3.830744 TTTGACTTCAGAAAGACGGGA 57.169 42.857 0.00 0.00 36.30 5.14
936 1035 4.757149 AGATTTTGACTTCAGAAAGACGGG 59.243 41.667 0.00 0.00 36.30 5.28
937 1036 5.931441 AGATTTTGACTTCAGAAAGACGG 57.069 39.130 0.00 0.00 36.30 4.79
938 1037 6.017934 TCCAAGATTTTGACTTCAGAAAGACG 60.018 38.462 0.00 0.00 36.36 4.18
939 1038 7.264373 TCCAAGATTTTGACTTCAGAAAGAC 57.736 36.000 0.00 0.00 36.36 3.01
940 1039 6.488006 CCTCCAAGATTTTGACTTCAGAAAGA 59.512 38.462 0.00 0.00 36.36 2.52
941 1040 6.675987 CCTCCAAGATTTTGACTTCAGAAAG 58.324 40.000 0.00 0.00 36.36 2.62
942 1041 5.010012 GCCTCCAAGATTTTGACTTCAGAAA 59.990 40.000 0.00 0.00 36.36 2.52
953 1052 1.250840 GCGGGTGCCTCCAAGATTTT 61.251 55.000 0.00 0.00 38.11 1.82
1226 1325 1.541672 GAGGAGGAGGAGGAGGAGG 59.458 68.421 0.00 0.00 0.00 4.30
1227 1326 0.998945 AGGAGGAGGAGGAGGAGGAG 60.999 65.000 0.00 0.00 0.00 3.69
1228 1327 0.350904 TAGGAGGAGGAGGAGGAGGA 59.649 60.000 0.00 0.00 0.00 3.71
1229 1328 0.481128 GTAGGAGGAGGAGGAGGAGG 59.519 65.000 0.00 0.00 0.00 4.30
1230 1329 0.481128 GGTAGGAGGAGGAGGAGGAG 59.519 65.000 0.00 0.00 0.00 3.69
1231 1330 1.000041 GGGTAGGAGGAGGAGGAGGA 61.000 65.000 0.00 0.00 0.00 3.71
1267 1366 1.950973 GCGGAGGAGGAGTTGGAGAC 61.951 65.000 0.00 0.00 0.00 3.36
1268 1367 1.682684 GCGGAGGAGGAGTTGGAGA 60.683 63.158 0.00 0.00 0.00 3.71
1494 1596 0.098200 CGTTCCGCACGTAGAGATCA 59.902 55.000 0.00 0.00 44.49 2.92
1585 1687 4.430765 GGTCACGACGTCCCGCAT 62.431 66.667 10.58 0.00 0.00 4.73
1658 1760 1.984990 CCGGCATTTCATCAAACAACG 59.015 47.619 0.00 0.00 0.00 4.10
1660 1762 2.625314 TCACCGGCATTTCATCAAACAA 59.375 40.909 0.00 0.00 0.00 2.83
1692 1794 1.961277 CACCACGGTGCTCCAAGAC 60.961 63.158 2.68 0.00 39.39 3.01
1695 1797 4.263572 CCCACCACGGTGCTCCAA 62.264 66.667 10.89 0.00 44.16 3.53
1746 1848 0.834612 TATCCCTAAACACCGCCAGG 59.165 55.000 0.00 0.00 45.13 4.45
1951 2053 0.250727 TCGAAAACTTCCCTGGCCAG 60.251 55.000 26.87 26.87 0.00 4.85
1989 2091 0.596083 TGGCGTTCCATGCAAAAACG 60.596 50.000 20.61 20.61 46.28 3.60
2181 2283 6.532657 CCATTTCTGGCTCAACACAATATTTC 59.467 38.462 0.00 0.00 35.23 2.17
2188 2290 2.507484 CTCCATTTCTGGCTCAACACA 58.493 47.619 0.00 0.00 42.80 3.72
2407 2509 5.700402 ATACTTGCAAGGAGGACATAGTT 57.300 39.130 29.18 7.17 0.00 2.24
2935 3037 6.901357 GCAAAATGACTGAATTCAACAACAAC 59.099 34.615 9.88 1.27 0.00 3.32
3065 3507 4.102681 CCTCCCCTACAGTATTGGGTTAAG 59.897 50.000 12.88 5.75 41.59 1.85
3112 3554 3.809832 GCTTGACTCAACTGCTCAAACTA 59.190 43.478 0.00 0.00 0.00 2.24
3145 3587 3.674528 AGTCTGATATTGCTGATCCCG 57.325 47.619 0.00 0.00 0.00 5.14
3168 3610 7.923878 GGAGCTTTACCTCATCTACTTTAGAAG 59.076 40.741 0.00 0.00 38.50 2.85
3190 3632 5.104485 TGGTCCTTTATTTCTAAGAGGGAGC 60.104 44.000 0.00 0.00 39.59 4.70
3191 3633 6.561519 TGGTCCTTTATTTCTAAGAGGGAG 57.438 41.667 0.00 0.00 0.00 4.30
3196 3638 8.393959 AGGATCTTGGTCCTTTATTTCTAAGA 57.606 34.615 0.00 0.00 46.45 2.10
3209 3651 3.576550 CCTCTAGCTTAGGATCTTGGTCC 59.423 52.174 8.77 0.00 36.08 4.46
3236 3678 6.633500 AGGAATGTGAAAATCTTCGACAAA 57.367 33.333 0.00 0.00 33.94 2.83
3241 3683 7.649306 AGAAACAAAGGAATGTGAAAATCTTCG 59.351 33.333 0.00 0.00 33.94 3.79
3246 3688 9.048446 CATTCAGAAACAAAGGAATGTGAAAAT 57.952 29.630 0.00 0.00 40.89 1.82
3268 3710 4.641989 ACATCATTGTTGCCTAGTCCATTC 59.358 41.667 0.00 0.00 29.55 2.67
3280 3722 4.154015 TCGTGGAAGCTTACATCATTGTTG 59.846 41.667 16.04 0.00 37.28 3.33
3301 3743 3.059352 ACTTCCACAATCCCTTCTTCG 57.941 47.619 0.00 0.00 0.00 3.79
3345 3787 6.983307 CAGAATTCATCTCGGAACTTCTACAT 59.017 38.462 8.44 0.00 35.73 2.29
3353 3795 2.565841 CCCCAGAATTCATCTCGGAAC 58.434 52.381 8.44 0.00 38.63 3.62
3377 3819 6.694877 CATGGAATGCTGGATCATATAAGG 57.305 41.667 0.00 0.00 37.62 2.69
3401 3843 3.230976 TCTTCTGGCGCTATCCTCATAA 58.769 45.455 7.64 0.00 0.00 1.90
3407 3849 1.615883 TCATCTCTTCTGGCGCTATCC 59.384 52.381 7.64 0.00 0.00 2.59
3408 3850 3.056962 TGATCATCTCTTCTGGCGCTATC 60.057 47.826 7.64 0.00 0.00 2.08
3409 3851 2.896044 TGATCATCTCTTCTGGCGCTAT 59.104 45.455 7.64 0.00 0.00 2.97
3411 3853 1.117994 TGATCATCTCTTCTGGCGCT 58.882 50.000 7.64 0.00 0.00 5.92
3412 3854 1.202510 AGTGATCATCTCTTCTGGCGC 60.203 52.381 0.00 0.00 0.00 6.53
3413 3855 2.886862 AGTGATCATCTCTTCTGGCG 57.113 50.000 0.00 0.00 0.00 5.69
3438 4551 0.316204 CCAAGGCTCTTGTTGCTTGG 59.684 55.000 12.18 0.00 34.80 3.61
3457 4570 5.463061 GCAAATCTGATCTCTCTAACTGAGC 59.537 44.000 0.00 0.00 42.38 4.26
3458 4571 5.984926 GGCAAATCTGATCTCTCTAACTGAG 59.015 44.000 0.00 0.00 43.96 3.35
3461 4574 4.102367 GGGGCAAATCTGATCTCTCTAACT 59.898 45.833 0.00 0.00 0.00 2.24
3496 4609 2.046023 CATTGACAGAGCCCGGCA 60.046 61.111 13.15 0.00 0.00 5.69
3550 4663 4.106029 CATTGCTAATGCTCACAGCTTT 57.894 40.909 0.00 0.00 42.97 3.51
3674 4787 9.388506 AGAGGAGTAATTGTGATTTGTGAATAG 57.611 33.333 0.00 0.00 0.00 1.73
3699 4812 4.038402 AGCCACCTGAGAAAATGACAAAAG 59.962 41.667 0.00 0.00 0.00 2.27
3718 4831 0.824109 CATCAGTAGGACGGAAGCCA 59.176 55.000 0.00 0.00 0.00 4.75
3751 4864 5.918011 GCTCAAGAGATCGTTAAGGTATCAG 59.082 44.000 0.32 0.00 0.00 2.90
3805 4918 3.014623 TCATGAAGAGAATGCAGCCTTG 58.985 45.455 0.00 0.00 0.00 3.61
3839 4963 7.255695 TGAAGAGATCAAGACAATGCATTTGTT 60.256 33.333 9.83 3.90 41.05 2.83
3876 5004 1.396653 AGGGTATTGCAAGCTGATGC 58.603 50.000 4.94 3.32 46.58 3.91


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

AutoCloner maintained by Alex Coulton.