Multiple sequence alignment - TraesCS4A01G046700

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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 TraesCS4A01G046700 chr4A 100.000 3013 0 0 1 3013 38328473 38331485 0.000000e+00 5565
1 TraesCS4A01G046700 chr4A 91.453 234 17 3 2781 3012 66340584 66340816 4.850000e-83 318
2 TraesCS4A01G046700 chr4D 88.562 1495 96 41 1 1485 428119851 428118422 0.000000e+00 1744
3 TraesCS4A01G046700 chr4D 95.404 544 5 9 1515 2055 428118356 428117830 0.000000e+00 848
4 TraesCS4A01G046700 chr4D 85.884 588 39 18 2219 2779 428117048 428116478 1.200000e-163 586
5 TraesCS4A01G046700 chr4D 90.558 233 20 2 2781 3012 55304074 55304305 1.050000e-79 307
6 TraesCS4A01G046700 chr4D 89.796 147 10 4 2060 2202 428117253 428117108 1.840000e-42 183
7 TraesCS4A01G046700 chr4B 91.645 1137 39 21 374 1484 524708432 524707326 0.000000e+00 1522
8 TraesCS4A01G046700 chr4B 95.345 580 8 6 1483 2055 524707285 524706718 0.000000e+00 904
9 TraesCS4A01G046700 chr4B 83.421 380 38 12 1 378 524708867 524708511 2.240000e-86 329
10 TraesCS4A01G046700 chr4B 84.528 265 17 9 2511 2758 524705648 524705391 1.080000e-59 241
11 TraesCS4A01G046700 chr4B 90.909 143 10 3 2062 2202 524706118 524705977 3.970000e-44 189
12 TraesCS4A01G046700 chr7D 90.717 237 21 1 2777 3012 10012071 10011835 6.270000e-82 315
13 TraesCS4A01G046700 chr6A 90.987 233 20 1 2781 3012 600699093 600699325 2.260000e-81 313
14 TraesCS4A01G046700 chr5D 90.987 233 19 2 2781 3012 475353950 475353719 2.260000e-81 313
15 TraesCS4A01G046700 chr2A 90.558 233 20 2 2781 3012 648636208 648636439 1.050000e-79 307
16 TraesCS4A01G046700 chr3A 90.558 233 19 3 2781 3012 642706680 642706910 3.770000e-79 305
17 TraesCS4A01G046700 chr7A 90.129 233 22 1 2781 3012 102099661 102099429 4.880000e-78 302
18 TraesCS4A01G046700 chr5A 89.583 240 22 3 2775 3012 300371728 300371490 4.880000e-78 302


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 TraesCS4A01G046700 chr4A 38328473 38331485 3012 False 5565.00 5565 100.0000 1 3013 1 chr4A.!!$F1 3012
1 TraesCS4A01G046700 chr4D 428116478 428119851 3373 True 840.25 1744 89.9115 1 2779 4 chr4D.!!$R1 2778
2 TraesCS4A01G046700 chr4B 524705391 524708867 3476 True 637.00 1522 89.1696 1 2758 5 chr4B.!!$R1 2757

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
143 145 0.036010 ATGGTCAAGGCCTTCTCGTG 60.036 55.0 17.29 4.76 0.0 4.35 F
826 913 0.106719 ACCACACCAAACCAGACCAG 60.107 55.0 0.00 0.00 0.0 4.00 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1495 1676 1.096416 ACGGTGCAAGGAAACGAAAA 58.904 45.0 0.0 0.0 0.0 2.29 R
2786 3715 0.039074 GATAGGATCGCACGGTGGAG 60.039 60.0 10.6 0.0 0.0 3.86 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
19 20 2.974489 GCATTGCTCACAGCGCACT 61.974 57.895 11.47 0.00 46.26 4.40
48 49 6.415573 ACAAGTGTAGAAGGAAGACAAAGTT 58.584 36.000 0.00 0.00 0.00 2.66
61 62 8.375506 AGGAAGACAAAGTTGATATACACAAGA 58.624 33.333 0.00 0.00 0.00 3.02
101 103 5.590259 TCTGCTTTTATAAGGATGGTCTTGC 59.410 40.000 0.00 0.00 30.84 4.01
104 106 6.127647 TGCTTTTATAAGGATGGTCTTGCAAG 60.128 38.462 20.81 20.81 31.76 4.01
112 114 0.178992 TGGTCTTGCAAGGGTTGGAG 60.179 55.000 25.73 0.00 30.85 3.86
121 123 5.208463 TGCAAGGGTTGGAGAATTTTAAC 57.792 39.130 0.00 0.00 0.00 2.01
126 128 7.492344 GCAAGGGTTGGAGAATTTTAACATATG 59.508 37.037 0.00 0.00 0.00 1.78
128 130 7.189087 AGGGTTGGAGAATTTTAACATATGGT 58.811 34.615 7.80 2.31 0.00 3.55
131 133 8.527810 GGTTGGAGAATTTTAACATATGGTCAA 58.472 33.333 7.80 0.00 0.00 3.18
138 140 6.524101 TTTTAACATATGGTCAAGGCCTTC 57.476 37.500 17.29 5.14 0.00 3.46
140 142 3.567478 ACATATGGTCAAGGCCTTCTC 57.433 47.619 17.29 11.44 0.00 2.87
143 145 0.036010 ATGGTCAAGGCCTTCTCGTG 60.036 55.000 17.29 4.76 0.00 4.35
147 149 3.330720 AAGGCCTTCTCGTGGGGG 61.331 66.667 13.78 0.00 0.00 5.40
148 150 4.658786 AGGCCTTCTCGTGGGGGT 62.659 66.667 0.00 0.00 0.00 4.95
149 151 4.410400 GGCCTTCTCGTGGGGGTG 62.410 72.222 0.00 0.00 0.00 4.61
150 152 4.410400 GCCTTCTCGTGGGGGTGG 62.410 72.222 0.00 0.00 0.00 4.61
151 153 3.717294 CCTTCTCGTGGGGGTGGG 61.717 72.222 0.00 0.00 0.00 4.61
152 154 3.717294 CTTCTCGTGGGGGTGGGG 61.717 72.222 0.00 0.00 0.00 4.96
176 178 2.197465 GGGAGGAGGTACCAAGTCATT 58.803 52.381 15.94 0.00 42.04 2.57
248 250 8.589338 ACATACAATTTGGTATTTTTGGCAGTA 58.411 29.630 0.78 0.00 31.75 2.74
258 260 3.591196 TTTTGGCAGTAATCATGGTGC 57.409 42.857 0.00 0.00 35.07 5.01
378 380 3.493334 ACAACCCCTGCTAAAAAGTACC 58.507 45.455 0.00 0.00 0.00 3.34
379 381 3.139584 ACAACCCCTGCTAAAAAGTACCT 59.860 43.478 0.00 0.00 0.00 3.08
380 382 4.149598 CAACCCCTGCTAAAAAGTACCTT 58.850 43.478 0.00 0.00 0.00 3.50
382 384 3.396611 ACCCCTGCTAAAAAGTACCTTCA 59.603 43.478 0.00 0.00 0.00 3.02
383 385 4.044191 ACCCCTGCTAAAAAGTACCTTCAT 59.956 41.667 0.00 0.00 0.00 2.57
422 506 6.241207 TGGAGAAGAAAGAAAATACAAGCG 57.759 37.500 0.00 0.00 0.00 4.68
495 580 8.501580 GGTAAAATAAAATATACTCGCCACTCC 58.498 37.037 0.00 0.00 0.00 3.85
510 595 3.324268 GCCACTCCCCTTAATCTAGTACC 59.676 52.174 0.00 0.00 0.00 3.34
552 637 1.883926 ACAAAACTGTACGATTGCCCC 59.116 47.619 0.00 0.00 0.00 5.80
553 638 1.883275 CAAAACTGTACGATTGCCCCA 59.117 47.619 0.00 0.00 0.00 4.96
557 642 3.126001 ACTGTACGATTGCCCCATATG 57.874 47.619 0.00 0.00 0.00 1.78
584 671 9.371136 CAGCTAATAAAGAAGACAGTGATGTTA 57.629 33.333 0.00 0.00 0.00 2.41
585 672 9.593134 AGCTAATAAAGAAGACAGTGATGTTAG 57.407 33.333 0.00 0.00 0.00 2.34
643 730 3.181451 TGACATATTGACATCTCTGGGCC 60.181 47.826 0.00 0.00 0.00 5.80
701 788 6.120220 ACAAAACCTAGCGGCTAGAATTATT 58.880 36.000 32.93 18.58 36.26 1.40
705 792 5.085219 ACCTAGCGGCTAGAATTATTAGGT 58.915 41.667 32.93 21.04 36.26 3.08
790 877 5.179555 CCTCCAAAACGGAAACAAAACAAAA 59.820 36.000 0.00 0.00 45.75 2.44
800 887 5.737757 GGAAACAAAACAAAACTCTCTCGTC 59.262 40.000 0.00 0.00 0.00 4.20
825 912 0.395036 CACCACACCAAACCAGACCA 60.395 55.000 0.00 0.00 0.00 4.02
826 913 0.106719 ACCACACCAAACCAGACCAG 60.107 55.000 0.00 0.00 0.00 4.00
837 924 3.441500 ACCAGACCAGGAAAGAAATCC 57.558 47.619 0.00 0.00 39.96 3.01
841 928 4.260170 CAGACCAGGAAAGAAATCCAGAG 58.740 47.826 0.00 0.00 42.27 3.35
1017 1145 3.785859 ATGCTCCGGTCCACGCAT 61.786 61.111 0.00 6.72 42.52 4.73
1020 1148 4.530857 CTCCGGTCCACGCATCCC 62.531 72.222 0.00 0.00 42.52 3.85
1323 1460 0.602905 GCTACAACAACCTGGACGCT 60.603 55.000 0.00 0.00 0.00 5.07
1495 1676 5.132144 CCTAGGTGGGTGGTCAATTATAGTT 59.868 44.000 0.00 0.00 0.00 2.24
1500 1681 6.319399 GTGGGTGGTCAATTATAGTTTTTCG 58.681 40.000 0.00 0.00 0.00 3.46
1506 1687 8.294577 GTGGTCAATTATAGTTTTTCGTTTCCT 58.705 33.333 0.00 0.00 0.00 3.36
1507 1688 8.852135 TGGTCAATTATAGTTTTTCGTTTCCTT 58.148 29.630 0.00 0.00 0.00 3.36
1508 1689 9.124807 GGTCAATTATAGTTTTTCGTTTCCTTG 57.875 33.333 0.00 0.00 0.00 3.61
1509 1690 8.635983 GTCAATTATAGTTTTTCGTTTCCTTGC 58.364 33.333 0.00 0.00 0.00 4.01
1510 1691 8.353684 TCAATTATAGTTTTTCGTTTCCTTGCA 58.646 29.630 0.00 0.00 0.00 4.08
1511 1692 8.424731 CAATTATAGTTTTTCGTTTCCTTGCAC 58.575 33.333 0.00 0.00 0.00 4.57
1512 1693 3.159353 AGTTTTTCGTTTCCTTGCACC 57.841 42.857 0.00 0.00 0.00 5.01
1513 1694 1.849829 GTTTTTCGTTTCCTTGCACCG 59.150 47.619 0.00 0.00 0.00 4.94
2051 2241 7.680442 AAAAGAGAGAGAAGAAATTACTGCC 57.320 36.000 0.00 0.00 0.00 4.85
2055 2245 3.526534 AGAGAAGAAATTACTGCCGCTC 58.473 45.455 0.00 0.00 0.00 5.03
2056 2246 3.196685 AGAGAAGAAATTACTGCCGCTCT 59.803 43.478 0.00 0.00 0.00 4.09
2057 2247 3.265791 AGAAGAAATTACTGCCGCTCTG 58.734 45.455 0.00 0.00 0.00 3.35
2058 2248 2.029838 AGAAATTACTGCCGCTCTGG 57.970 50.000 0.00 0.00 42.50 3.86
2072 2891 2.487445 CGCTCTGGTCTACTCCTATGGA 60.487 54.545 0.00 0.00 0.00 3.41
2083 2902 7.066043 GGTCTACTCCTATGGATGAGTATAACG 59.934 44.444 0.00 0.00 41.77 3.18
2121 2940 3.211963 GTCGTGCATGGCCCATCC 61.212 66.667 5.98 0.00 0.00 3.51
2179 3000 0.895530 CGAAGTTGACCTAGCTCCCA 59.104 55.000 0.00 0.00 0.00 4.37
2180 3001 1.482593 CGAAGTTGACCTAGCTCCCAT 59.517 52.381 0.00 0.00 0.00 4.00
2181 3002 2.482142 CGAAGTTGACCTAGCTCCCATC 60.482 54.545 0.00 0.00 0.00 3.51
2195 3022 2.647875 CATCTAGGAGCCGAGCCG 59.352 66.667 0.00 0.00 0.00 5.52
2235 3087 4.487412 CCCGGCGGTGACTCGTAC 62.487 72.222 26.32 0.00 0.00 3.67
2255 3120 3.633235 ACTACGCGATCATCTTGTCATC 58.367 45.455 15.93 0.00 0.00 2.92
2257 3122 2.467838 ACGCGATCATCTTGTCATCTG 58.532 47.619 15.93 0.00 0.00 2.90
2261 3126 2.725206 CGATCATCTTGTCATCTGCTCG 59.275 50.000 0.00 0.00 0.00 5.03
2276 3141 1.079819 CTCGGGCGTGACAAGACAT 60.080 57.895 0.00 0.00 0.00 3.06
2317 3182 1.078848 CTGCTCCACTGCACCTACC 60.079 63.158 0.00 0.00 38.12 3.18
2321 3186 0.247736 CTCCACTGCACCTACCAGAC 59.752 60.000 0.00 0.00 34.47 3.51
2356 3221 6.174049 GGTTTATTATCCAGCCACTATCTCC 58.826 44.000 0.00 0.00 0.00 3.71
2420 3285 8.269424 ACGTACGTACTACTCGTATTTGATTAG 58.731 37.037 21.41 3.93 43.73 1.73
2437 3306 7.645058 TTGATTAGGAAAAAGATAGGCTTGG 57.355 36.000 0.00 0.00 36.80 3.61
2450 3319 1.019805 GGCTTGGTCTAACACGAGCC 61.020 60.000 7.15 7.15 43.68 4.70
2511 3412 2.752036 TAGCCGTGGGGTAAGTGGGT 62.752 60.000 0.00 0.00 32.35 4.51
2517 3420 1.074248 GGGGTAAGTGGGTGTGTGG 59.926 63.158 0.00 0.00 0.00 4.17
2574 3477 6.458751 CGTGATGCTTAGCTTTTGATATGGTT 60.459 38.462 5.60 0.00 0.00 3.67
2589 3492 2.412937 GTTGGTGCGCTGTTGCTT 59.587 55.556 9.73 0.00 36.97 3.91
2604 3507 3.369921 CTTGCTCAAGCCCAACCC 58.630 61.111 0.00 0.00 41.18 4.11
2622 3531 2.193517 CAACCACAACCCACCCGA 59.806 61.111 0.00 0.00 0.00 5.14
2623 3532 2.190841 CAACCACAACCCACCCGAC 61.191 63.158 0.00 0.00 0.00 4.79
2642 3554 6.262720 ACCCGACGCTAATATCTATCTAATCC 59.737 42.308 0.00 0.00 0.00 3.01
2654 3566 1.640428 TCTAATCCAACTCGCTTGCG 58.360 50.000 8.87 8.87 0.00 4.85
2659 3571 3.329231 CAACTCGCTTGCGTTGGA 58.671 55.556 14.70 0.00 37.45 3.53
2676 3588 1.174712 GGATGGGTGGGCATCAATCG 61.175 60.000 0.00 0.00 0.00 3.34
2683 3595 2.221169 GTGGGCATCAATCGAGCATTA 58.779 47.619 0.00 0.00 0.00 1.90
2684 3596 2.618241 GTGGGCATCAATCGAGCATTAA 59.382 45.455 0.00 0.00 0.00 1.40
2685 3597 3.254166 GTGGGCATCAATCGAGCATTAAT 59.746 43.478 0.00 0.00 0.00 1.40
2686 3598 3.890756 TGGGCATCAATCGAGCATTAATT 59.109 39.130 0.00 0.00 0.00 1.40
2687 3599 5.048782 GTGGGCATCAATCGAGCATTAATTA 60.049 40.000 0.00 0.00 0.00 1.40
2688 3600 5.534278 TGGGCATCAATCGAGCATTAATTAA 59.466 36.000 0.00 0.00 0.00 1.40
2689 3601 5.858581 GGGCATCAATCGAGCATTAATTAAC 59.141 40.000 0.00 0.00 0.00 2.01
2739 3661 1.081242 CGCCCGCATTGCATATTCC 60.081 57.895 9.69 0.00 0.00 3.01
2779 3708 2.360165 CCCGCCAACTAGTACGAACTAT 59.640 50.000 12.83 0.00 37.57 2.12
2780 3709 3.369385 CCGCCAACTAGTACGAACTATG 58.631 50.000 12.83 0.00 37.57 2.23
2781 3710 3.369385 CGCCAACTAGTACGAACTATGG 58.631 50.000 0.00 0.00 39.72 2.74
2783 3712 3.714391 CCAACTAGTACGAACTATGGCC 58.286 50.000 0.00 0.00 37.57 5.36
2784 3713 3.131577 CCAACTAGTACGAACTATGGCCA 59.868 47.826 8.56 8.56 37.57 5.36
2785 3714 4.382254 CCAACTAGTACGAACTATGGCCAA 60.382 45.833 10.96 0.00 37.57 4.52
2786 3715 4.382345 ACTAGTACGAACTATGGCCAAC 57.618 45.455 10.96 0.00 37.57 3.77
2787 3716 4.021916 ACTAGTACGAACTATGGCCAACT 58.978 43.478 10.96 8.81 37.57 3.16
2788 3717 3.521947 AGTACGAACTATGGCCAACTC 57.478 47.619 10.96 2.84 32.84 3.01
2789 3718 2.167900 AGTACGAACTATGGCCAACTCC 59.832 50.000 10.96 0.00 32.84 3.85
2790 3719 0.981183 ACGAACTATGGCCAACTCCA 59.019 50.000 10.96 0.00 40.97 3.86
2791 3720 1.338769 ACGAACTATGGCCAACTCCAC 60.339 52.381 10.96 0.00 39.25 4.02
2792 3721 1.751437 GAACTATGGCCAACTCCACC 58.249 55.000 10.96 0.00 39.25 4.61
2793 3722 0.035439 AACTATGGCCAACTCCACCG 60.035 55.000 10.96 0.00 39.25 4.94
2794 3723 1.198759 ACTATGGCCAACTCCACCGT 61.199 55.000 10.96 0.00 39.25 4.83
2795 3724 0.744414 CTATGGCCAACTCCACCGTG 60.744 60.000 10.96 0.00 39.25 4.94
2796 3725 2.813226 TATGGCCAACTCCACCGTGC 62.813 60.000 10.96 0.00 39.25 5.34
2798 3727 4.980805 GCCAACTCCACCGTGCGA 62.981 66.667 0.00 0.00 0.00 5.10
2799 3728 2.047274 CCAACTCCACCGTGCGAT 60.047 61.111 0.00 0.00 0.00 4.58
2800 3729 2.100631 CCAACTCCACCGTGCGATC 61.101 63.158 0.00 0.00 0.00 3.69
2801 3730 2.100631 CAACTCCACCGTGCGATCC 61.101 63.158 0.00 0.00 0.00 3.36
2802 3731 2.283529 AACTCCACCGTGCGATCCT 61.284 57.895 0.00 0.00 0.00 3.24
2803 3732 0.968901 AACTCCACCGTGCGATCCTA 60.969 55.000 0.00 0.00 0.00 2.94
2804 3733 0.755698 ACTCCACCGTGCGATCCTAT 60.756 55.000 0.00 0.00 0.00 2.57
2805 3734 0.039074 CTCCACCGTGCGATCCTATC 60.039 60.000 0.00 0.00 0.00 2.08
2806 3735 0.753848 TCCACCGTGCGATCCTATCA 60.754 55.000 0.00 0.00 0.00 2.15
2807 3736 0.318441 CCACCGTGCGATCCTATCAT 59.682 55.000 0.00 0.00 0.00 2.45
2808 3737 1.422388 CACCGTGCGATCCTATCATG 58.578 55.000 0.00 0.00 0.00 3.07
2809 3738 1.040646 ACCGTGCGATCCTATCATGT 58.959 50.000 0.00 0.00 0.00 3.21
2810 3739 1.000163 ACCGTGCGATCCTATCATGTC 60.000 52.381 0.00 0.00 0.00 3.06
2811 3740 1.670087 CCGTGCGATCCTATCATGTCC 60.670 57.143 0.00 0.00 0.00 4.02
2812 3741 1.702886 GTGCGATCCTATCATGTCCG 58.297 55.000 0.00 0.00 0.00 4.79
2813 3742 0.603065 TGCGATCCTATCATGTCCGG 59.397 55.000 0.00 0.00 0.00 5.14
2814 3743 0.737715 GCGATCCTATCATGTCCGGC 60.738 60.000 0.00 0.00 0.00 6.13
2815 3744 0.108615 CGATCCTATCATGTCCGGCC 60.109 60.000 0.00 0.00 0.00 6.13
2816 3745 0.250513 GATCCTATCATGTCCGGCCC 59.749 60.000 0.00 0.00 0.00 5.80
2817 3746 1.201429 ATCCTATCATGTCCGGCCCC 61.201 60.000 0.00 0.00 0.00 5.80
2818 3747 2.343758 CTATCATGTCCGGCCCCG 59.656 66.667 0.00 0.00 39.44 5.73
2819 3748 2.445085 TATCATGTCCGGCCCCGT 60.445 61.111 5.93 0.00 37.81 5.28
2820 3749 2.436087 CTATCATGTCCGGCCCCGTC 62.436 65.000 5.93 0.00 37.81 4.79
2844 3773 6.019779 CGTTTGGATAAAATGGACAAAGGA 57.980 37.500 0.00 0.00 38.47 3.36
2845 3774 6.092748 CGTTTGGATAAAATGGACAAAGGAG 58.907 40.000 0.00 0.00 38.47 3.69
2846 3775 6.072175 CGTTTGGATAAAATGGACAAAGGAGA 60.072 38.462 0.00 0.00 38.47 3.71
2847 3776 6.834168 TTGGATAAAATGGACAAAGGAGAC 57.166 37.500 0.00 0.00 0.00 3.36
2848 3777 4.941263 TGGATAAAATGGACAAAGGAGACG 59.059 41.667 0.00 0.00 0.00 4.18
2849 3778 4.335594 GGATAAAATGGACAAAGGAGACGG 59.664 45.833 0.00 0.00 0.00 4.79
2850 3779 1.534729 AAATGGACAAAGGAGACGGC 58.465 50.000 0.00 0.00 0.00 5.68
2851 3780 0.693049 AATGGACAAAGGAGACGGCT 59.307 50.000 0.00 0.00 0.00 5.52
2852 3781 0.250513 ATGGACAAAGGAGACGGCTC 59.749 55.000 10.76 10.76 40.54 4.70
2853 3782 1.118965 TGGACAAAGGAGACGGCTCA 61.119 55.000 22.31 0.00 43.14 4.26
2854 3783 0.390472 GGACAAAGGAGACGGCTCAG 60.390 60.000 22.31 9.15 43.14 3.35
2855 3784 1.004440 ACAAAGGAGACGGCTCAGC 60.004 57.895 22.31 3.02 43.14 4.26
2856 3785 2.097038 CAAAGGAGACGGCTCAGCG 61.097 63.158 22.31 0.70 43.14 5.18
2857 3786 3.941657 AAAGGAGACGGCTCAGCGC 62.942 63.158 22.31 0.00 43.14 5.92
2876 3805 4.570663 CGACGGCCCGGACTCATC 62.571 72.222 8.57 0.00 0.00 2.92
2877 3806 3.148279 GACGGCCCGGACTCATCT 61.148 66.667 8.57 0.00 0.00 2.90
2878 3807 2.683933 ACGGCCCGGACTCATCTT 60.684 61.111 8.57 0.00 0.00 2.40
2879 3808 2.202932 CGGCCCGGACTCATCTTG 60.203 66.667 0.73 0.00 0.00 3.02
2880 3809 2.990479 GGCCCGGACTCATCTTGT 59.010 61.111 0.73 0.00 0.00 3.16
2881 3810 1.299976 GGCCCGGACTCATCTTGTT 59.700 57.895 0.73 0.00 0.00 2.83
2882 3811 0.322546 GGCCCGGACTCATCTTGTTT 60.323 55.000 0.73 0.00 0.00 2.83
2883 3812 0.804989 GCCCGGACTCATCTTGTTTG 59.195 55.000 0.73 0.00 0.00 2.93
2884 3813 1.882352 GCCCGGACTCATCTTGTTTGT 60.882 52.381 0.73 0.00 0.00 2.83
2885 3814 2.504367 CCCGGACTCATCTTGTTTGTT 58.496 47.619 0.73 0.00 0.00 2.83
2886 3815 2.884639 CCCGGACTCATCTTGTTTGTTT 59.115 45.455 0.73 0.00 0.00 2.83
2887 3816 3.317993 CCCGGACTCATCTTGTTTGTTTT 59.682 43.478 0.73 0.00 0.00 2.43
2888 3817 4.290155 CCGGACTCATCTTGTTTGTTTTG 58.710 43.478 0.00 0.00 0.00 2.44
2889 3818 4.202010 CCGGACTCATCTTGTTTGTTTTGT 60.202 41.667 0.00 0.00 0.00 2.83
2890 3819 4.734854 CGGACTCATCTTGTTTGTTTTGTG 59.265 41.667 0.00 0.00 0.00 3.33
2891 3820 5.650543 GGACTCATCTTGTTTGTTTTGTGT 58.349 37.500 0.00 0.00 0.00 3.72
2892 3821 5.743872 GGACTCATCTTGTTTGTTTTGTGTC 59.256 40.000 0.00 0.00 0.00 3.67
2893 3822 5.650543 ACTCATCTTGTTTGTTTTGTGTCC 58.349 37.500 0.00 0.00 0.00 4.02
2894 3823 4.667262 TCATCTTGTTTGTTTTGTGTCCG 58.333 39.130 0.00 0.00 0.00 4.79
2895 3824 3.495670 TCTTGTTTGTTTTGTGTCCGG 57.504 42.857 0.00 0.00 0.00 5.14
2896 3825 2.164624 TCTTGTTTGTTTTGTGTCCGGG 59.835 45.455 0.00 0.00 0.00 5.73
2897 3826 0.173708 TGTTTGTTTTGTGTCCGGGC 59.826 50.000 0.00 0.00 0.00 6.13
2898 3827 0.528901 GTTTGTTTTGTGTCCGGGCC 60.529 55.000 2.12 0.00 0.00 5.80
2899 3828 2.005960 TTTGTTTTGTGTCCGGGCCG 62.006 55.000 21.46 21.46 0.00 6.13
2900 3829 2.592287 GTTTTGTGTCCGGGCCGA 60.592 61.111 30.79 11.12 0.00 5.54
2901 3830 2.592287 TTTTGTGTCCGGGCCGAC 60.592 61.111 30.79 22.88 0.00 4.79
2902 3831 4.629523 TTTGTGTCCGGGCCGACC 62.630 66.667 30.79 17.72 31.35 4.79
2912 3841 3.202706 GGCCGACCCATTTCGAGC 61.203 66.667 0.00 0.00 41.78 5.03
2913 3842 3.564027 GCCGACCCATTTCGAGCG 61.564 66.667 0.00 0.00 41.78 5.03
2914 3843 3.564027 CCGACCCATTTCGAGCGC 61.564 66.667 0.00 0.00 41.78 5.92
2915 3844 2.813474 CGACCCATTTCGAGCGCA 60.813 61.111 11.47 0.00 41.78 6.09
2916 3845 2.387445 CGACCCATTTCGAGCGCAA 61.387 57.895 11.47 0.00 41.78 4.85
2917 3846 1.873165 GACCCATTTCGAGCGCAAA 59.127 52.632 11.47 1.09 0.00 3.68
2918 3847 0.454452 GACCCATTTCGAGCGCAAAC 60.454 55.000 11.47 0.00 0.00 2.93
2919 3848 0.889186 ACCCATTTCGAGCGCAAACT 60.889 50.000 11.47 0.00 0.00 2.66
2920 3849 0.240945 CCCATTTCGAGCGCAAACTT 59.759 50.000 11.47 0.00 0.00 2.66
2921 3850 1.466950 CCCATTTCGAGCGCAAACTTA 59.533 47.619 11.47 0.00 0.00 2.24
2922 3851 2.505866 CCATTTCGAGCGCAAACTTAC 58.494 47.619 11.47 0.00 0.00 2.34
2923 3852 2.158143 CATTTCGAGCGCAAACTTACG 58.842 47.619 11.47 3.63 0.00 3.18
2924 3853 1.210870 TTTCGAGCGCAAACTTACGT 58.789 45.000 11.47 0.00 0.00 3.57
2925 3854 0.780002 TTCGAGCGCAAACTTACGTC 59.220 50.000 11.47 0.00 0.00 4.34
2926 3855 0.318022 TCGAGCGCAAACTTACGTCA 60.318 50.000 11.47 0.00 0.00 4.35
2927 3856 0.091344 CGAGCGCAAACTTACGTCAG 59.909 55.000 11.47 0.00 0.00 3.51
2928 3857 1.415374 GAGCGCAAACTTACGTCAGA 58.585 50.000 11.47 0.00 0.00 3.27
2929 3858 1.993370 GAGCGCAAACTTACGTCAGAT 59.007 47.619 11.47 0.00 0.00 2.90
2930 3859 2.412089 GAGCGCAAACTTACGTCAGATT 59.588 45.455 11.47 0.00 0.00 2.40
2931 3860 2.806244 AGCGCAAACTTACGTCAGATTT 59.194 40.909 11.47 0.00 0.00 2.17
2932 3861 2.902484 GCGCAAACTTACGTCAGATTTG 59.098 45.455 0.30 10.96 34.17 2.32
2933 3862 3.479006 CGCAAACTTACGTCAGATTTGG 58.521 45.455 18.08 10.10 32.17 3.28
2934 3863 3.666902 CGCAAACTTACGTCAGATTTGGG 60.667 47.826 18.02 18.02 37.03 4.12
2935 3864 3.252458 GCAAACTTACGTCAGATTTGGGT 59.748 43.478 18.08 0.00 32.17 4.51
2936 3865 4.612939 GCAAACTTACGTCAGATTTGGGTC 60.613 45.833 18.08 6.28 32.17 4.46
2937 3866 2.955614 ACTTACGTCAGATTTGGGTCG 58.044 47.619 3.23 0.00 0.00 4.79
2938 3867 1.659098 CTTACGTCAGATTTGGGTCGC 59.341 52.381 0.00 0.00 0.00 5.19
2939 3868 0.457166 TACGTCAGATTTGGGTCGCG 60.457 55.000 0.00 0.00 0.00 5.87
2940 3869 1.445410 CGTCAGATTTGGGTCGCGA 60.445 57.895 3.71 3.71 0.00 5.87
2941 3870 1.683790 CGTCAGATTTGGGTCGCGAC 61.684 60.000 30.67 30.67 0.00 5.19
2942 3871 1.445410 TCAGATTTGGGTCGCGACG 60.445 57.895 30.99 15.74 0.00 5.12
2943 3872 2.125673 AGATTTGGGTCGCGACGG 60.126 61.111 30.99 0.00 0.00 4.79
2944 3873 2.125832 GATTTGGGTCGCGACGGA 60.126 61.111 30.99 18.10 0.00 4.69
2945 3874 2.433664 ATTTGGGTCGCGACGGAC 60.434 61.111 30.99 23.28 36.18 4.79
2946 3875 3.229156 ATTTGGGTCGCGACGGACA 62.229 57.895 30.99 25.40 38.70 4.02
2947 3876 2.515996 ATTTGGGTCGCGACGGACAT 62.516 55.000 30.99 18.01 38.70 3.06
2948 3877 3.636313 TTGGGTCGCGACGGACATC 62.636 63.158 30.99 16.80 38.70 3.06
2949 3878 4.124351 GGGTCGCGACGGACATCA 62.124 66.667 30.99 0.00 38.70 3.07
2950 3879 2.126228 GGTCGCGACGGACATCAA 60.126 61.111 30.99 0.00 38.70 2.57
2951 3880 1.735198 GGTCGCGACGGACATCAAA 60.735 57.895 30.99 0.00 38.70 2.69
2952 3881 1.414897 GTCGCGACGGACATCAAAC 59.585 57.895 25.19 0.00 36.91 2.93
2953 3882 2.084101 TCGCGACGGACATCAAACG 61.084 57.895 3.71 0.00 0.00 3.60
2954 3883 2.776072 GCGACGGACATCAAACGG 59.224 61.111 0.00 0.00 0.00 4.44
2955 3884 1.735198 GCGACGGACATCAAACGGA 60.735 57.895 0.00 0.00 0.00 4.69
2956 3885 1.952266 GCGACGGACATCAAACGGAC 61.952 60.000 0.00 0.00 0.00 4.79
2957 3886 1.670971 CGACGGACATCAAACGGACG 61.671 60.000 0.00 0.00 0.00 4.79
2958 3887 1.952266 GACGGACATCAAACGGACGC 61.952 60.000 0.00 0.00 0.00 5.19
2959 3888 2.776072 GGACATCAAACGGACGCG 59.224 61.111 3.53 3.53 0.00 6.01
2960 3889 2.095843 GACATCAAACGGACGCGC 59.904 61.111 5.73 0.00 0.00 6.86
2961 3890 3.362851 GACATCAAACGGACGCGCC 62.363 63.158 5.73 7.90 0.00 6.53
2962 3891 4.160635 CATCAAACGGACGCGCCC 62.161 66.667 5.73 2.39 0.00 6.13
3000 3929 3.702048 GTGACAGGCGGCCACCTA 61.702 66.667 23.09 0.00 38.26 3.08
3001 3930 3.702048 TGACAGGCGGCCACCTAC 61.702 66.667 23.09 10.43 38.26 3.18
3002 3931 4.468689 GACAGGCGGCCACCTACC 62.469 72.222 23.09 3.27 38.26 3.18
3004 3933 4.162690 CAGGCGGCCACCTACCTC 62.163 72.222 23.09 0.00 38.26 3.85
3008 3937 3.782443 CGGCCACCTACCTCCCAC 61.782 72.222 2.24 0.00 0.00 4.61
3009 3938 3.408853 GGCCACCTACCTCCCACC 61.409 72.222 0.00 0.00 0.00 4.61
3010 3939 3.408853 GCCACCTACCTCCCACCC 61.409 72.222 0.00 0.00 0.00 4.61
3011 3940 3.081409 CCACCTACCTCCCACCCG 61.081 72.222 0.00 0.00 0.00 5.28
3012 3941 2.284405 CACCTACCTCCCACCCGT 60.284 66.667 0.00 0.00 0.00 5.28
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
19 20 1.334160 TCCTTCTACACTTGTCGCCA 58.666 50.000 0.00 0.00 0.00 5.69
26 27 6.650120 TCAACTTTGTCTTCCTTCTACACTT 58.350 36.000 0.00 0.00 0.00 3.16
31 32 9.871238 GTGTATATCAACTTTGTCTTCCTTCTA 57.129 33.333 0.00 0.00 0.00 2.10
101 103 7.981225 CCATATGTTAAAATTCTCCAACCCTTG 59.019 37.037 1.24 0.00 0.00 3.61
104 106 7.123547 TGACCATATGTTAAAATTCTCCAACCC 59.876 37.037 1.24 0.00 0.00 4.11
112 114 7.112452 AGGCCTTGACCATATGTTAAAATTC 57.888 36.000 0.00 0.00 0.00 2.17
121 123 2.158900 ACGAGAAGGCCTTGACCATATG 60.159 50.000 26.25 6.14 0.00 1.78
126 128 1.376037 CCACGAGAAGGCCTTGACC 60.376 63.158 26.25 8.91 0.00 4.02
128 130 2.592993 CCCCACGAGAAGGCCTTGA 61.593 63.158 26.25 0.00 0.00 3.02
131 133 4.658786 ACCCCCACGAGAAGGCCT 62.659 66.667 0.00 0.00 0.00 5.19
154 156 0.981801 GACTTGGTACCTCCTCCCCC 60.982 65.000 14.36 0.00 37.07 5.40
155 157 0.252558 TGACTTGGTACCTCCTCCCC 60.253 60.000 14.36 0.00 37.07 4.81
157 159 3.263425 TCAAATGACTTGGTACCTCCTCC 59.737 47.826 14.36 0.00 35.56 4.30
158 160 4.553330 TCAAATGACTTGGTACCTCCTC 57.447 45.455 14.36 4.98 35.56 3.71
159 161 4.993705 TTCAAATGACTTGGTACCTCCT 57.006 40.909 14.36 0.00 35.56 3.69
160 162 6.389906 CATTTTCAAATGACTTGGTACCTCC 58.610 40.000 14.36 0.10 46.72 4.30
161 163 5.863935 GCATTTTCAAATGACTTGGTACCTC 59.136 40.000 14.36 2.82 46.72 3.85
162 164 5.304101 TGCATTTTCAAATGACTTGGTACCT 59.696 36.000 14.36 0.00 46.72 3.08
163 165 5.405269 GTGCATTTTCAAATGACTTGGTACC 59.595 40.000 15.13 4.43 46.72 3.34
164 166 6.215845 AGTGCATTTTCAAATGACTTGGTAC 58.784 36.000 15.13 0.00 46.72 3.34
165 167 6.403866 AGTGCATTTTCAAATGACTTGGTA 57.596 33.333 15.13 0.00 46.72 3.25
166 168 5.280654 AGTGCATTTTCAAATGACTTGGT 57.719 34.783 15.13 0.00 46.72 3.67
167 169 9.590451 AATATAGTGCATTTTCAAATGACTTGG 57.410 29.630 15.13 0.00 46.72 3.61
248 250 5.425196 AAATTAGGCTTTGCACCATGATT 57.575 34.783 0.00 0.00 0.00 2.57
476 560 4.228824 AGGGGAGTGGCGAGTATATTTTA 58.771 43.478 0.00 0.00 0.00 1.52
483 568 2.037144 GATTAAGGGGAGTGGCGAGTA 58.963 52.381 0.00 0.00 0.00 2.59
484 569 0.831307 GATTAAGGGGAGTGGCGAGT 59.169 55.000 0.00 0.00 0.00 4.18
495 580 6.469782 TTTGGTACGGTACTAGATTAAGGG 57.530 41.667 17.14 0.00 0.00 3.95
535 620 2.507407 ATGGGGCAATCGTACAGTTT 57.493 45.000 0.00 0.00 0.00 2.66
552 637 8.281194 CACTGTCTTCTTTATTAGCTGCATATG 58.719 37.037 1.02 0.00 0.00 1.78
553 638 8.206867 TCACTGTCTTCTTTATTAGCTGCATAT 58.793 33.333 1.02 0.00 0.00 1.78
557 642 6.314896 ACATCACTGTCTTCTTTATTAGCTGC 59.685 38.462 0.00 0.00 0.00 5.25
643 730 4.680349 TTTTTGTGCGCGTGACAG 57.320 50.000 8.43 0.00 0.00 3.51
701 788 3.134081 CGGATAAAAAGGAGAGGCACCTA 59.866 47.826 0.00 0.00 36.67 3.08
705 792 1.913419 ACCGGATAAAAAGGAGAGGCA 59.087 47.619 9.46 0.00 0.00 4.75
731 818 3.890756 TGATGATGTGCCCAATTATCCAC 59.109 43.478 0.00 0.00 0.00 4.02
790 877 2.282251 TGTGGGCGACGAGAGAGT 60.282 61.111 0.00 0.00 0.00 3.24
800 887 2.830827 TTTGGTGTGGTGTGGGCG 60.831 61.111 0.00 0.00 0.00 6.13
825 912 2.849318 CTCCCCTCTGGATTTCTTTCCT 59.151 50.000 0.00 0.00 44.07 3.36
826 913 2.685224 GCTCCCCTCTGGATTTCTTTCC 60.685 54.545 0.00 0.00 44.07 3.13
837 924 1.221293 CTTGCTCTGCTCCCCTCTG 59.779 63.158 0.00 0.00 0.00 3.35
841 928 4.087892 TCGCTTGCTCTGCTCCCC 62.088 66.667 0.00 0.00 0.00 4.81
930 1052 0.032515 TACTACTGGCTGGCTGGCTA 60.033 55.000 18.27 4.40 42.34 3.93
931 1053 0.692419 ATACTACTGGCTGGCTGGCT 60.692 55.000 18.27 2.43 42.34 4.75
932 1054 1.048601 TATACTACTGGCTGGCTGGC 58.951 55.000 11.09 11.09 42.18 4.85
933 1055 4.081420 CCTTATATACTACTGGCTGGCTGG 60.081 50.000 12.46 3.50 0.00 4.85
934 1056 4.772624 TCCTTATATACTACTGGCTGGCTG 59.227 45.833 6.56 6.56 0.00 4.85
935 1057 5.011982 TCCTTATATACTACTGGCTGGCT 57.988 43.478 2.00 0.00 0.00 4.75
936 1058 4.382147 GCTCCTTATATACTACTGGCTGGC 60.382 50.000 0.00 0.00 0.00 4.85
937 1059 4.142359 CGCTCCTTATATACTACTGGCTGG 60.142 50.000 0.00 0.00 0.00 4.85
989 1117 1.875813 CGGAGCATGAGACGACTGC 60.876 63.158 0.00 0.00 36.15 4.40
1038 1166 4.880537 CTGCTACCTCCGCTGCCG 62.881 72.222 0.00 0.00 0.00 5.69
1041 1169 4.537433 GGGCTGCTACCTCCGCTG 62.537 72.222 0.00 0.00 0.00 5.18
1323 1460 1.582968 GAGCAGGTCGTCCACGTAA 59.417 57.895 0.51 0.00 40.80 3.18
1495 1676 1.096416 ACGGTGCAAGGAAACGAAAA 58.904 45.000 0.00 0.00 0.00 2.29
2051 2241 1.883275 CCATAGGAGTAGACCAGAGCG 59.117 57.143 0.00 0.00 0.00 5.03
2055 2245 4.735369 ACTCATCCATAGGAGTAGACCAG 58.265 47.826 0.00 0.00 44.60 4.00
2056 2246 4.816048 ACTCATCCATAGGAGTAGACCA 57.184 45.455 0.00 0.00 44.60 4.02
2090 2909 2.732094 CGACGTGGACAACCGACC 60.732 66.667 0.00 0.00 39.42 4.79
2093 2912 3.698463 GCACGACGTGGACAACCG 61.698 66.667 27.86 1.66 39.42 4.44
2176 2997 2.578714 GGCTCGGCTCCTAGATGGG 61.579 68.421 0.00 0.00 36.20 4.00
2177 2998 2.925262 CGGCTCGGCTCCTAGATGG 61.925 68.421 0.00 0.00 37.10 3.51
2179 3000 1.602323 CTCGGCTCGGCTCCTAGAT 60.602 63.158 0.00 0.00 0.00 1.98
2180 3001 2.203224 CTCGGCTCGGCTCCTAGA 60.203 66.667 0.00 0.00 0.00 2.43
2181 3002 3.972276 GCTCGGCTCGGCTCCTAG 61.972 72.222 0.00 0.00 0.00 3.02
2223 3075 1.296432 CGCGTAGTACGAGTCACCG 60.296 63.158 26.29 14.36 46.05 4.94
2225 3077 1.325640 TGATCGCGTAGTACGAGTCAC 59.674 52.381 26.29 16.81 46.05 3.67
2226 3078 1.643880 TGATCGCGTAGTACGAGTCA 58.356 50.000 26.29 22.05 46.05 3.41
2228 3080 2.481854 AGATGATCGCGTAGTACGAGT 58.518 47.619 26.29 13.10 46.05 4.18
2229 3081 3.219189 CAAGATGATCGCGTAGTACGAG 58.781 50.000 26.29 22.48 46.05 4.18
2230 3082 2.610833 ACAAGATGATCGCGTAGTACGA 59.389 45.455 26.29 6.72 46.05 3.43
2231 3083 2.965414 GACAAGATGATCGCGTAGTACG 59.035 50.000 18.37 18.37 45.88 3.67
2232 3084 3.948851 TGACAAGATGATCGCGTAGTAC 58.051 45.455 5.77 0.00 0.00 2.73
2233 3085 4.515567 AGATGACAAGATGATCGCGTAGTA 59.484 41.667 5.77 0.00 0.00 1.82
2234 3086 3.316588 AGATGACAAGATGATCGCGTAGT 59.683 43.478 5.77 0.00 0.00 2.73
2235 3087 3.667726 CAGATGACAAGATGATCGCGTAG 59.332 47.826 5.77 0.00 0.00 3.51
2255 3120 3.114616 CTTGTCACGCCCGAGCAG 61.115 66.667 0.00 0.00 39.83 4.24
2257 3122 3.112709 GTCTTGTCACGCCCGAGC 61.113 66.667 0.00 0.00 0.00 5.03
2261 3126 1.787847 CGAATGTCTTGTCACGCCC 59.212 57.895 0.00 0.00 0.00 6.13
2317 3182 9.543783 GGATAATAAACCCAGTAAAGTAGTCTG 57.456 37.037 0.00 0.00 0.00 3.51
2321 3186 7.444487 GGCTGGATAATAAACCCAGTAAAGTAG 59.556 40.741 0.00 0.00 46.86 2.57
2356 3221 9.270576 CTTGATGTTACAAAATGAGATTTCTCG 57.729 33.333 3.29 0.00 45.72 4.04
2407 3272 9.052759 GCCTATCTTTTTCCTAATCAAATACGA 57.947 33.333 0.00 0.00 0.00 3.43
2408 3273 9.057089 AGCCTATCTTTTTCCTAATCAAATACG 57.943 33.333 0.00 0.00 0.00 3.06
2411 3276 8.699130 CCAAGCCTATCTTTTTCCTAATCAAAT 58.301 33.333 0.00 0.00 31.27 2.32
2420 3285 5.944007 TGTTAGACCAAGCCTATCTTTTTCC 59.056 40.000 0.00 0.00 31.27 3.13
2432 3301 1.352156 CGGCTCGTGTTAGACCAAGC 61.352 60.000 0.00 0.00 0.00 4.01
2437 3306 4.916099 ATAAAAACGGCTCGTGTTAGAC 57.084 40.909 3.97 0.00 36.19 2.59
2450 3319 5.564048 TCCCGTCCCAAATAATAAAAACG 57.436 39.130 0.00 0.00 0.00 3.60
2535 3438 0.595053 ATCACGCCGATCATCACGTC 60.595 55.000 0.00 0.00 36.45 4.34
2574 3477 4.268939 GCAAGCAACAGCGCACCA 62.269 61.111 11.47 0.00 0.00 4.17
2589 3492 3.080158 TTGGGGTTGGGCTTGAGCA 62.080 57.895 5.24 0.00 44.36 4.26
2597 3500 2.137528 GGTTGTGGTTGGGGTTGGG 61.138 63.158 0.00 0.00 0.00 4.12
2604 3507 2.909965 CGGGTGGGTTGTGGTTGG 60.910 66.667 0.00 0.00 0.00 3.77
2622 3531 8.399425 CGAGTTGGATTAGATAGATATTAGCGT 58.601 37.037 0.00 0.00 0.00 5.07
2623 3532 7.377397 GCGAGTTGGATTAGATAGATATTAGCG 59.623 40.741 0.00 0.00 0.00 4.26
2654 3566 0.614415 TTGATGCCCACCCATCCAAC 60.614 55.000 0.00 0.00 40.66 3.77
2659 3571 0.179009 CTCGATTGATGCCCACCCAT 60.179 55.000 0.00 0.00 0.00 4.00
2683 3595 7.832769 ACGGCTAATTACCATTGTTGTTAATT 58.167 30.769 0.00 0.00 0.00 1.40
2684 3596 7.399245 ACGGCTAATTACCATTGTTGTTAAT 57.601 32.000 0.00 0.00 0.00 1.40
2685 3597 6.402334 CGACGGCTAATTACCATTGTTGTTAA 60.402 38.462 0.00 0.00 0.00 2.01
2686 3598 5.063691 CGACGGCTAATTACCATTGTTGTTA 59.936 40.000 0.00 0.00 0.00 2.41
2687 3599 4.142773 CGACGGCTAATTACCATTGTTGTT 60.143 41.667 0.00 0.00 0.00 2.83
2688 3600 3.372822 CGACGGCTAATTACCATTGTTGT 59.627 43.478 0.00 0.00 0.00 3.32
2689 3601 3.372822 ACGACGGCTAATTACCATTGTTG 59.627 43.478 0.00 2.70 0.00 3.33
2758 3680 0.529378 AGTTCGTACTAGTTGGCGGG 59.471 55.000 0.00 0.00 31.21 6.13
2779 3708 4.947147 GCACGGTGGAGTTGGCCA 62.947 66.667 0.00 0.00 35.02 5.36
2781 3710 4.980805 TCGCACGGTGGAGTTGGC 62.981 66.667 10.60 0.00 0.00 4.52
2782 3711 2.047274 ATCGCACGGTGGAGTTGG 60.047 61.111 10.60 0.00 0.00 3.77
2783 3712 2.100631 GGATCGCACGGTGGAGTTG 61.101 63.158 10.60 0.00 0.00 3.16
2784 3713 0.968901 TAGGATCGCACGGTGGAGTT 60.969 55.000 10.60 0.00 0.00 3.01
2785 3714 0.755698 ATAGGATCGCACGGTGGAGT 60.756 55.000 10.60 0.00 0.00 3.85
2786 3715 0.039074 GATAGGATCGCACGGTGGAG 60.039 60.000 10.60 0.00 0.00 3.86
2787 3716 0.753848 TGATAGGATCGCACGGTGGA 60.754 55.000 10.60 6.05 0.00 4.02
2788 3717 0.318441 ATGATAGGATCGCACGGTGG 59.682 55.000 10.60 0.26 0.00 4.61
2789 3718 1.269778 ACATGATAGGATCGCACGGTG 60.270 52.381 3.15 3.15 0.00 4.94
2790 3719 1.000163 GACATGATAGGATCGCACGGT 60.000 52.381 0.00 0.00 0.00 4.83
2791 3720 1.670087 GGACATGATAGGATCGCACGG 60.670 57.143 0.00 0.00 0.00 4.94
2792 3721 1.702886 GGACATGATAGGATCGCACG 58.297 55.000 0.00 0.00 0.00 5.34
2793 3722 1.670087 CCGGACATGATAGGATCGCAC 60.670 57.143 0.00 0.00 0.00 5.34
2794 3723 0.603065 CCGGACATGATAGGATCGCA 59.397 55.000 0.00 0.00 0.00 5.10
2795 3724 0.737715 GCCGGACATGATAGGATCGC 60.738 60.000 5.05 0.00 0.00 4.58
2796 3725 0.108615 GGCCGGACATGATAGGATCG 60.109 60.000 5.05 0.00 0.00 3.69
2797 3726 0.250513 GGGCCGGACATGATAGGATC 59.749 60.000 11.00 0.00 0.00 3.36
2798 3727 1.201429 GGGGCCGGACATGATAGGAT 61.201 60.000 11.00 0.00 0.00 3.24
2799 3728 1.841556 GGGGCCGGACATGATAGGA 60.842 63.158 11.00 0.00 0.00 2.94
2800 3729 2.750350 GGGGCCGGACATGATAGG 59.250 66.667 11.00 0.00 0.00 2.57
2801 3730 2.343758 CGGGGCCGGACATGATAG 59.656 66.667 11.00 0.00 35.56 2.08
2802 3731 2.445085 ACGGGGCCGGACATGATA 60.445 61.111 18.95 0.00 44.69 2.15
2803 3732 3.861797 GACGGGGCCGGACATGAT 61.862 66.667 18.95 0.00 44.69 2.45
2812 3741 2.540028 TTATCCAAACGGACGGGGCC 62.540 60.000 0.00 0.00 34.62 5.80
2813 3742 0.677414 TTTATCCAAACGGACGGGGC 60.677 55.000 0.00 0.00 34.62 5.80
2814 3743 1.823797 TTTTATCCAAACGGACGGGG 58.176 50.000 0.00 0.00 34.62 5.73
2815 3744 2.098443 CCATTTTATCCAAACGGACGGG 59.902 50.000 0.00 0.00 34.62 5.28
2816 3745 3.011119 TCCATTTTATCCAAACGGACGG 58.989 45.455 0.00 0.00 34.62 4.79
2817 3746 3.437395 TGTCCATTTTATCCAAACGGACG 59.563 43.478 7.77 0.00 43.40 4.79
2818 3747 5.379732 TTGTCCATTTTATCCAAACGGAC 57.620 39.130 5.76 5.76 42.12 4.79
2819 3748 5.047660 CCTTTGTCCATTTTATCCAAACGGA 60.048 40.000 0.00 0.00 36.85 4.69
2820 3749 5.047660 TCCTTTGTCCATTTTATCCAAACGG 60.048 40.000 0.00 0.00 0.00 4.44
2821 3750 6.019779 TCCTTTGTCCATTTTATCCAAACG 57.980 37.500 0.00 0.00 0.00 3.60
2822 3751 7.090808 GTCTCCTTTGTCCATTTTATCCAAAC 58.909 38.462 0.00 0.00 0.00 2.93
2823 3752 6.072175 CGTCTCCTTTGTCCATTTTATCCAAA 60.072 38.462 0.00 0.00 0.00 3.28
2824 3753 5.414454 CGTCTCCTTTGTCCATTTTATCCAA 59.586 40.000 0.00 0.00 0.00 3.53
2825 3754 4.941263 CGTCTCCTTTGTCCATTTTATCCA 59.059 41.667 0.00 0.00 0.00 3.41
2826 3755 4.335594 CCGTCTCCTTTGTCCATTTTATCC 59.664 45.833 0.00 0.00 0.00 2.59
2827 3756 4.201920 GCCGTCTCCTTTGTCCATTTTATC 60.202 45.833 0.00 0.00 0.00 1.75
2828 3757 3.694566 GCCGTCTCCTTTGTCCATTTTAT 59.305 43.478 0.00 0.00 0.00 1.40
2829 3758 3.078837 GCCGTCTCCTTTGTCCATTTTA 58.921 45.455 0.00 0.00 0.00 1.52
2830 3759 1.886542 GCCGTCTCCTTTGTCCATTTT 59.113 47.619 0.00 0.00 0.00 1.82
2831 3760 1.073923 AGCCGTCTCCTTTGTCCATTT 59.926 47.619 0.00 0.00 0.00 2.32
2832 3761 0.693049 AGCCGTCTCCTTTGTCCATT 59.307 50.000 0.00 0.00 0.00 3.16
2833 3762 0.250513 GAGCCGTCTCCTTTGTCCAT 59.749 55.000 0.00 0.00 33.19 3.41
2834 3763 1.118965 TGAGCCGTCTCCTTTGTCCA 61.119 55.000 0.00 0.00 38.58 4.02
2835 3764 0.390472 CTGAGCCGTCTCCTTTGTCC 60.390 60.000 0.00 0.00 38.58 4.02
2836 3765 1.016653 GCTGAGCCGTCTCCTTTGTC 61.017 60.000 0.00 0.00 38.58 3.18
2837 3766 1.004440 GCTGAGCCGTCTCCTTTGT 60.004 57.895 0.00 0.00 38.58 2.83
2838 3767 2.097038 CGCTGAGCCGTCTCCTTTG 61.097 63.158 0.00 0.00 38.58 2.77
2839 3768 2.262915 CGCTGAGCCGTCTCCTTT 59.737 61.111 0.00 0.00 38.58 3.11
2840 3769 4.443266 GCGCTGAGCCGTCTCCTT 62.443 66.667 0.00 0.00 40.81 3.36
2859 3788 4.570663 GATGAGTCCGGGCCGTCG 62.571 72.222 26.32 10.85 0.00 5.12
2860 3789 2.722201 AAGATGAGTCCGGGCCGTC 61.722 63.158 26.32 16.59 0.00 4.79
2861 3790 2.683933 AAGATGAGTCCGGGCCGT 60.684 61.111 26.32 6.13 0.00 5.68
2862 3791 2.202932 CAAGATGAGTCCGGGCCG 60.203 66.667 21.46 21.46 0.00 6.13
2863 3792 0.322546 AAACAAGATGAGTCCGGGCC 60.323 55.000 0.08 0.00 0.00 5.80
2864 3793 0.804989 CAAACAAGATGAGTCCGGGC 59.195 55.000 0.00 0.00 0.00 6.13
2865 3794 2.185004 ACAAACAAGATGAGTCCGGG 57.815 50.000 0.00 0.00 0.00 5.73
2866 3795 4.202010 ACAAAACAAACAAGATGAGTCCGG 60.202 41.667 0.00 0.00 0.00 5.14
2867 3796 4.734854 CACAAAACAAACAAGATGAGTCCG 59.265 41.667 0.00 0.00 0.00 4.79
2868 3797 5.650543 ACACAAAACAAACAAGATGAGTCC 58.349 37.500 0.00 0.00 0.00 3.85
2869 3798 5.743872 GGACACAAAACAAACAAGATGAGTC 59.256 40.000 0.00 0.00 0.00 3.36
2870 3799 5.650543 GGACACAAAACAAACAAGATGAGT 58.349 37.500 0.00 0.00 0.00 3.41
2871 3800 4.734854 CGGACACAAAACAAACAAGATGAG 59.265 41.667 0.00 0.00 0.00 2.90
2872 3801 4.439426 CCGGACACAAAACAAACAAGATGA 60.439 41.667 0.00 0.00 0.00 2.92
2873 3802 3.796178 CCGGACACAAAACAAACAAGATG 59.204 43.478 0.00 0.00 0.00 2.90
2874 3803 3.181480 CCCGGACACAAAACAAACAAGAT 60.181 43.478 0.73 0.00 0.00 2.40
2875 3804 2.164624 CCCGGACACAAAACAAACAAGA 59.835 45.455 0.73 0.00 0.00 3.02
2876 3805 2.535331 CCCGGACACAAAACAAACAAG 58.465 47.619 0.73 0.00 0.00 3.16
2877 3806 1.404315 GCCCGGACACAAAACAAACAA 60.404 47.619 0.73 0.00 0.00 2.83
2878 3807 0.173708 GCCCGGACACAAAACAAACA 59.826 50.000 0.73 0.00 0.00 2.83
2879 3808 0.528901 GGCCCGGACACAAAACAAAC 60.529 55.000 0.73 0.00 0.00 2.93
2880 3809 1.817209 GGCCCGGACACAAAACAAA 59.183 52.632 0.73 0.00 0.00 2.83
2881 3810 2.482333 CGGCCCGGACACAAAACAA 61.482 57.895 0.73 0.00 0.00 2.83
2882 3811 2.902846 CGGCCCGGACACAAAACA 60.903 61.111 0.73 0.00 0.00 2.83
2883 3812 2.592287 TCGGCCCGGACACAAAAC 60.592 61.111 0.73 0.00 0.00 2.43
2884 3813 2.592287 GTCGGCCCGGACACAAAA 60.592 61.111 0.73 0.00 36.91 2.44
2885 3814 4.629523 GGTCGGCCCGGACACAAA 62.630 66.667 0.73 0.00 38.70 2.83
2895 3824 3.202706 GCTCGAAATGGGTCGGCC 61.203 66.667 0.00 0.00 41.43 6.13
2896 3825 3.564027 CGCTCGAAATGGGTCGGC 61.564 66.667 0.00 0.00 41.43 5.54
2897 3826 3.564027 GCGCTCGAAATGGGTCGG 61.564 66.667 0.00 0.00 41.43 4.79
2898 3827 1.906994 TTTGCGCTCGAAATGGGTCG 61.907 55.000 9.73 0.00 42.48 4.79
2899 3828 0.454452 GTTTGCGCTCGAAATGGGTC 60.454 55.000 9.73 0.00 0.00 4.46
2900 3829 0.889186 AGTTTGCGCTCGAAATGGGT 60.889 50.000 9.73 0.00 0.00 4.51
2901 3830 0.240945 AAGTTTGCGCTCGAAATGGG 59.759 50.000 9.73 0.00 0.00 4.00
2902 3831 2.505866 GTAAGTTTGCGCTCGAAATGG 58.494 47.619 9.73 0.00 0.00 3.16
2903 3832 2.158143 CGTAAGTTTGCGCTCGAAATG 58.842 47.619 9.73 0.00 0.00 2.32
2904 3833 2.503943 CGTAAGTTTGCGCTCGAAAT 57.496 45.000 9.73 0.00 0.00 2.17
2919 3848 1.717194 GCGACCCAAATCTGACGTAA 58.283 50.000 0.00 0.00 0.00 3.18
2920 3849 0.457166 CGCGACCCAAATCTGACGTA 60.457 55.000 0.00 0.00 0.00 3.57
2921 3850 1.736645 CGCGACCCAAATCTGACGT 60.737 57.895 0.00 0.00 0.00 4.34
2922 3851 1.445410 TCGCGACCCAAATCTGACG 60.445 57.895 3.71 0.00 0.00 4.35
2923 3852 1.683790 CGTCGCGACCCAAATCTGAC 61.684 60.000 31.84 4.84 0.00 3.51
2924 3853 1.445410 CGTCGCGACCCAAATCTGA 60.445 57.895 31.84 0.00 0.00 3.27
2925 3854 2.452813 CCGTCGCGACCCAAATCTG 61.453 63.158 31.84 15.69 0.00 2.90
2926 3855 2.125673 CCGTCGCGACCCAAATCT 60.126 61.111 31.84 0.00 0.00 2.40
2927 3856 2.125832 TCCGTCGCGACCCAAATC 60.126 61.111 31.84 7.13 0.00 2.17
2928 3857 2.433664 GTCCGTCGCGACCCAAAT 60.434 61.111 31.84 0.00 0.00 2.32
2929 3858 3.229156 ATGTCCGTCGCGACCCAAA 62.229 57.895 31.84 15.09 31.35 3.28
2930 3859 3.636313 GATGTCCGTCGCGACCCAA 62.636 63.158 31.84 16.29 31.35 4.12
2931 3860 4.124351 GATGTCCGTCGCGACCCA 62.124 66.667 31.84 24.76 31.35 4.51
2932 3861 3.636313 TTGATGTCCGTCGCGACCC 62.636 63.158 31.84 20.24 31.35 4.46
2933 3862 1.735198 TTTGATGTCCGTCGCGACC 60.735 57.895 31.84 19.17 31.35 4.79
2934 3863 1.414897 GTTTGATGTCCGTCGCGAC 59.585 57.895 28.96 28.96 0.00 5.19
2935 3864 2.084101 CGTTTGATGTCCGTCGCGA 61.084 57.895 3.71 3.71 0.00 5.87
2936 3865 2.390288 CGTTTGATGTCCGTCGCG 59.610 61.111 0.00 0.00 0.00 5.87
2937 3866 1.735198 TCCGTTTGATGTCCGTCGC 60.735 57.895 0.00 0.00 0.00 5.19
2938 3867 1.670971 CGTCCGTTTGATGTCCGTCG 61.671 60.000 0.00 0.00 0.00 5.12
2939 3868 1.952266 GCGTCCGTTTGATGTCCGTC 61.952 60.000 0.00 0.00 32.20 4.79
2940 3869 2.025418 GCGTCCGTTTGATGTCCGT 61.025 57.895 0.00 0.00 32.20 4.69
2941 3870 2.776072 GCGTCCGTTTGATGTCCG 59.224 61.111 0.00 0.00 32.20 4.79
2942 3871 2.776072 CGCGTCCGTTTGATGTCC 59.224 61.111 0.00 0.00 32.20 4.02
2943 3872 2.095843 GCGCGTCCGTTTGATGTC 59.904 61.111 8.43 0.00 36.67 3.06
2944 3873 3.419759 GGCGCGTCCGTTTGATGT 61.420 61.111 8.43 0.00 36.67 3.06
2945 3874 4.160635 GGGCGCGTCCGTTTGATG 62.161 66.667 16.93 0.00 36.67 3.07
2983 3912 3.702048 TAGGTGGCCGCCTGTCAC 61.702 66.667 42.20 13.48 39.60 3.67
2984 3913 3.702048 GTAGGTGGCCGCCTGTCA 61.702 66.667 42.20 24.22 39.60 3.58
2985 3914 4.468689 GGTAGGTGGCCGCCTGTC 62.469 72.222 42.20 32.51 39.60 3.51
2987 3916 4.162690 GAGGTAGGTGGCCGCCTG 62.163 72.222 42.20 0.00 39.60 4.85
2991 3920 3.782443 GTGGGAGGTAGGTGGCCG 61.782 72.222 0.00 0.00 0.00 6.13
2992 3921 3.408853 GGTGGGAGGTAGGTGGCC 61.409 72.222 0.00 0.00 0.00 5.36
2993 3922 3.408853 GGGTGGGAGGTAGGTGGC 61.409 72.222 0.00 0.00 0.00 5.01
2994 3923 3.081409 CGGGTGGGAGGTAGGTGG 61.081 72.222 0.00 0.00 0.00 4.61
2995 3924 2.284405 ACGGGTGGGAGGTAGGTG 60.284 66.667 0.00 0.00 0.00 4.00


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

AutoCloner maintained by Alex Coulton.