Multiple sequence alignment - TraesCS2D01G419000

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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 TraesCS2D01G419000 chr2D 100.000 6222 0 0 1 6222 533132046 533138267 0.000000e+00 11490
1 TraesCS2D01G419000 chr2D 88.732 142 15 1 5712 5852 482892620 482892761 8.290000e-39 172
2 TraesCS2D01G419000 chr2B 96.138 2356 74 10 3371 5718 632918900 632921246 0.000000e+00 3831
3 TraesCS2D01G419000 chr2B 90.439 2782 158 50 3 2746 632915609 632918320 0.000000e+00 3565
4 TraesCS2D01G419000 chr2B 95.146 515 24 1 2866 3380 632918317 632918830 0.000000e+00 811
5 TraesCS2D01G419000 chr2B 89.516 372 27 10 5712 6074 632921283 632921651 1.580000e-125 460
6 TraesCS2D01G419000 chr2B 92.537 134 10 0 6089 6222 632921727 632921860 6.370000e-45 193
7 TraesCS2D01G419000 chr2B 78.616 318 41 12 3388 3692 769596687 769596384 1.070000e-42 185
8 TraesCS2D01G419000 chr2A 91.401 2791 163 44 3 2746 677524822 677527582 0.000000e+00 3753
9 TraesCS2D01G419000 chr2A 95.315 2241 66 8 3371 5606 677528190 677530396 0.000000e+00 3520
10 TraesCS2D01G419000 chr2A 89.299 542 31 19 2866 3380 677527579 677528120 0.000000e+00 654
11 TraesCS2D01G419000 chr2A 87.187 359 31 4 5864 6222 677530401 677530744 1.630000e-105 394
12 TraesCS2D01G419000 chr2A 89.706 136 13 1 5718 5852 65743781 65743916 8.290000e-39 172
13 TraesCS2D01G419000 chr2A 89.706 136 13 1 5718 5852 65769710 65769845 8.290000e-39 172
14 TraesCS2D01G419000 chr2A 90.164 122 9 3 5600 5718 18596683 18596804 8.350000e-34 156
15 TraesCS2D01G419000 chr6B 82.927 328 35 13 4917 5241 376339400 376339709 6.140000e-70 276
16 TraesCS2D01G419000 chr6B 78.095 315 47 13 3388 3692 376339094 376339396 4.960000e-41 180
17 TraesCS2D01G419000 chr5D 82.510 263 22 13 5614 5852 507887742 507888004 6.320000e-50 209
18 TraesCS2D01G419000 chr5B 90.441 136 12 1 5718 5852 416592022 416591887 1.780000e-40 178
19 TraesCS2D01G419000 chr6D 88.112 143 15 2 5712 5852 412938648 412938790 1.070000e-37 169
20 TraesCS2D01G419000 chr6D 92.793 111 6 2 5610 5718 353638201 353638091 6.460000e-35 159
21 TraesCS2D01G419000 chr5A 88.971 136 14 1 5718 5852 248537408 248537273 3.860000e-37 167
22 TraesCS2D01G419000 chr5A 88.971 136 14 1 5718 5852 350901394 350901259 3.860000e-37 167
23 TraesCS2D01G419000 chr5A 91.129 124 7 4 5599 5718 151066924 151067047 1.390000e-36 165
24 TraesCS2D01G419000 chr5A 92.105 114 8 1 5606 5718 631276062 631275949 6.460000e-35 159
25 TraesCS2D01G419000 chr1D 88.028 142 15 2 5712 5852 334450261 334450401 3.860000e-37 167
26 TraesCS2D01G419000 chr1D 92.105 114 7 2 5607 5718 290446046 290446159 6.460000e-35 159
27 TraesCS2D01G419000 chr6A 92.793 111 6 2 5610 5718 65071371 65071261 6.460000e-35 159
28 TraesCS2D01G419000 chr6A 92.793 111 6 2 5610 5718 87253806 87253696 6.460000e-35 159
29 TraesCS2D01G419000 chr4A 90.164 122 9 3 5600 5718 535469087 535468966 8.350000e-34 156


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 TraesCS2D01G419000 chr2D 533132046 533138267 6221 False 11490.00 11490 100.0000 1 6222 1 chr2D.!!$F2 6221
1 TraesCS2D01G419000 chr2B 632915609 632921860 6251 False 1772.00 3831 92.7552 3 6222 5 chr2B.!!$F1 6219
2 TraesCS2D01G419000 chr2A 677524822 677530744 5922 False 2080.25 3753 90.8005 3 6222 4 chr2A.!!$F4 6219
3 TraesCS2D01G419000 chr6B 376339094 376339709 615 False 228.00 276 80.5110 3388 5241 2 chr6B.!!$F1 1853

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
598 638 0.485543 GGGAGGTTTTCTTTGGGGGA 59.514 55.000 0.00 0.0 0.00 4.81 F
732 772 0.811281 CGCTTCCATTTCTGTTCCCC 59.189 55.000 0.00 0.0 0.00 4.81 F
1356 1419 0.883153 TAGTGCGCGAAGTAACCTGA 59.117 50.000 12.10 0.0 0.00 3.86 F
2169 2237 0.179702 TGGTCATGAGATGCCAGAGC 59.820 55.000 0.00 0.0 40.48 4.09 F
3299 3398 0.541392 AGCCCGTATGACATGCAGAA 59.459 50.000 4.34 0.0 0.00 3.02 F
3742 3937 1.759445 AGTCAAGCCACGATATCTGCT 59.241 47.619 0.34 3.5 35.08 4.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1789 1856 0.518636 CCTCGTCGTCGTTTACTCCA 59.481 55.0 1.33 0.00 38.33 3.86 R
1886 1953 0.887247 TGACCATTGTCATTTGCCCG 59.113 50.0 0.00 0.00 46.40 6.13 R
2794 2865 0.721154 TCGTTGCAGTGATTCGATGC 59.279 50.0 0.97 0.97 40.40 3.91 R
4164 4360 0.466007 TGCAGTGCCTGTTCACACAT 60.466 50.0 13.72 0.00 39.30 3.21 R
5044 5244 0.249120 TCCCTAGGATGTGCACAACG 59.751 55.0 25.72 8.53 0.00 4.10 R
5295 5495 0.709992 TTTAAAGCAGCCATCCCCCT 59.290 50.0 0.00 0.00 0.00 4.79 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
25 26 7.661040 CCAATTAAGAAAGAAACATGAGGTGT 58.339 34.615 0.00 0.00 44.84 4.16
47 48 4.729227 AACAACCTGGGTTTGTTTAGTG 57.271 40.909 9.03 0.00 36.00 2.74
134 141 1.064296 GCATTAGCAGCAGCAGCAG 59.936 57.895 12.92 0.00 45.49 4.24
140 147 2.794621 CAGCAGCAGCAGCATCAG 59.205 61.111 12.92 0.00 45.49 2.90
144 151 1.028330 GCAGCAGCAGCATCAGGTAA 61.028 55.000 4.63 0.00 45.49 2.85
191 199 4.351192 CAGTTTTGGTGCTACAGTTCAAC 58.649 43.478 0.00 0.00 0.00 3.18
198 206 1.156736 GCTACAGTTCAACGGCACAT 58.843 50.000 0.00 0.00 0.00 3.21
199 207 2.289133 TGCTACAGTTCAACGGCACATA 60.289 45.455 0.00 0.00 0.00 2.29
200 208 2.348666 GCTACAGTTCAACGGCACATAG 59.651 50.000 0.00 0.00 0.00 2.23
201 209 1.808411 ACAGTTCAACGGCACATAGG 58.192 50.000 0.00 0.00 0.00 2.57
202 210 1.071699 ACAGTTCAACGGCACATAGGT 59.928 47.619 0.00 0.00 0.00 3.08
299 314 6.072175 TCCTCTTCTCTTCTTCTTCTTCTTCG 60.072 42.308 0.00 0.00 0.00 3.79
312 330 2.303022 TCTTCTTCGCCTCCTTGTCATT 59.697 45.455 0.00 0.00 0.00 2.57
318 336 1.941999 GCCTCCTTGTCATTGCTGCC 61.942 60.000 0.00 0.00 0.00 4.85
405 434 4.150454 CTCCTCCTCCGCCCCTCT 62.150 72.222 0.00 0.00 0.00 3.69
406 435 4.144727 TCCTCCTCCGCCCCTCTC 62.145 72.222 0.00 0.00 0.00 3.20
488 518 1.889454 CTTCTCTCGCTCTGCCAGT 59.111 57.895 0.00 0.00 0.00 4.00
495 525 4.792804 GCTCTGCCAGTGCCCTCC 62.793 72.222 7.52 0.00 36.33 4.30
496 526 3.007920 CTCTGCCAGTGCCCTCCT 61.008 66.667 0.00 0.00 36.33 3.69
497 527 3.005539 TCTGCCAGTGCCCTCCTC 61.006 66.667 0.00 0.00 36.33 3.71
520 550 1.691196 CTCCTCGCTGAATCTCTCCT 58.309 55.000 0.00 0.00 0.00 3.69
522 552 0.673437 CCTCGCTGAATCTCTCCTCC 59.327 60.000 0.00 0.00 0.00 4.30
525 555 1.299773 GCTGAATCTCTCCTCCGCG 60.300 63.158 0.00 0.00 0.00 6.46
590 630 2.346365 GTCGCGGGGAGGTTTTCT 59.654 61.111 6.13 0.00 0.00 2.52
598 638 0.485543 GGGAGGTTTTCTTTGGGGGA 59.514 55.000 0.00 0.00 0.00 4.81
644 684 4.377021 GTTGGTTGGGATTTTGGTTCTTC 58.623 43.478 0.00 0.00 0.00 2.87
652 692 4.931601 GGGATTTTGGTTCTTCATTTGAGC 59.068 41.667 0.00 0.00 0.00 4.26
681 721 1.401018 CGGTTGGTTTTCTGCGATTCC 60.401 52.381 0.00 0.00 0.00 3.01
709 749 3.512516 GCTGTGATTCCTGCCGCC 61.513 66.667 0.00 0.00 0.00 6.13
732 772 0.811281 CGCTTCCATTTCTGTTCCCC 59.189 55.000 0.00 0.00 0.00 4.81
810 850 4.340617 GTCCATGTAAGAATTGGGTTGGA 58.659 43.478 0.00 0.00 0.00 3.53
858 898 1.002250 GTCGAACTTTGAGCGAGCGA 61.002 55.000 0.00 0.00 34.41 4.93
1352 1415 1.973138 TCTGTAGTGCGCGAAGTAAC 58.027 50.000 12.10 2.26 0.00 2.50
1356 1419 0.883153 TAGTGCGCGAAGTAACCTGA 59.117 50.000 12.10 0.00 0.00 3.86
1474 1537 2.200170 AAAATGACGCGCTTCCAGGC 62.200 55.000 11.76 0.00 0.00 4.85
1564 1627 7.550551 TCGATGAAACAATTAGCAGAAGAATCT 59.449 33.333 0.00 0.00 35.88 2.40
1633 1700 9.809096 TGAATGCTTGTTTTATTGAAGTTGTTA 57.191 25.926 0.00 0.00 0.00 2.41
1650 1717 9.384764 GAAGTTGTTAGGCTACTAAATCAAGAT 57.615 33.333 0.00 0.00 40.66 2.40
1789 1856 6.662755 TGTGTTCTATAATGCCTTTCCTCAT 58.337 36.000 0.00 0.00 0.00 2.90
1796 1863 4.591321 AATGCCTTTCCTCATGGAGTAA 57.409 40.909 0.00 0.00 44.24 2.24
1807 1874 2.159612 TCATGGAGTAAACGACGACGAG 60.160 50.000 15.32 0.00 42.66 4.18
1829 1896 4.476479 AGGATGTTATTGGAGCTCTTTCCT 59.524 41.667 14.64 10.28 38.12 3.36
1862 1929 3.133721 CACCCTTACTCTCATCCCTCTTG 59.866 52.174 0.00 0.00 0.00 3.02
1886 1953 6.529829 TGTGAAGTATGTTTTTGTTGTCTTGC 59.470 34.615 0.00 0.00 0.00 4.01
1922 1989 7.616935 ACAATGGTCAAGGTGAGATGATTTATT 59.383 33.333 0.00 0.00 0.00 1.40
1924 1991 6.962182 TGGTCAAGGTGAGATGATTTATTCT 58.038 36.000 0.00 0.00 0.00 2.40
1934 2001 7.567458 TGAGATGATTTATTCTCACATGGTCA 58.433 34.615 0.00 0.00 34.70 4.02
1937 2004 8.900781 AGATGATTTATTCTCACATGGTCAAAG 58.099 33.333 0.00 0.00 0.00 2.77
1966 2033 5.153950 ACTGGTTAGACCTTCAATGAGAC 57.846 43.478 0.00 0.00 39.58 3.36
1995 2062 7.123397 TGTCTCTTATGATCTGCTCTGTACTTT 59.877 37.037 0.00 0.00 0.00 2.66
2038 2105 8.791327 TGACTGAAATACATCTCAAATGCTTA 57.209 30.769 0.00 0.00 0.00 3.09
2070 2137 0.684153 AGCCAACACCAAGCACAGTT 60.684 50.000 0.00 0.00 0.00 3.16
2090 2157 7.116233 CACAGTTGAATTTAATAAGTGGCAACC 59.884 37.037 0.00 0.00 36.08 3.77
2132 2200 7.392766 TCCATCAGATTGGTAGGTGAATATT 57.607 36.000 0.00 0.00 38.01 1.28
2137 2205 8.677148 TCAGATTGGTAGGTGAATATTTTAGC 57.323 34.615 0.00 0.00 0.00 3.09
2139 2207 8.562892 CAGATTGGTAGGTGAATATTTTAGCAG 58.437 37.037 0.00 0.00 0.00 4.24
2169 2237 0.179702 TGGTCATGAGATGCCAGAGC 59.820 55.000 0.00 0.00 40.48 4.09
2228 2296 4.973168 AGATCACTTTACTGTTGCCTCAA 58.027 39.130 0.00 0.00 0.00 3.02
2231 2299 4.713553 TCACTTTACTGTTGCCTCAATGA 58.286 39.130 0.00 0.00 0.00 2.57
2232 2300 5.129634 TCACTTTACTGTTGCCTCAATGAA 58.870 37.500 0.00 0.00 0.00 2.57
2233 2301 5.008613 TCACTTTACTGTTGCCTCAATGAAC 59.991 40.000 0.00 0.00 0.00 3.18
2238 2306 3.003689 ACTGTTGCCTCAATGAACGAAAG 59.996 43.478 0.00 0.00 0.00 2.62
2239 2307 3.210227 TGTTGCCTCAATGAACGAAAGA 58.790 40.909 0.00 0.00 0.00 2.52
2262 2330 1.065102 CTCTTCCATGCGCAATTCTGG 59.935 52.381 17.11 18.60 0.00 3.86
2281 2349 7.928307 TTCTGGGACTTCTTGATTTGATAAG 57.072 36.000 0.00 0.00 0.00 1.73
2317 2386 2.640316 ACTGGTGGTGACCTCTTTTC 57.360 50.000 2.11 0.00 43.58 2.29
2354 2424 5.221641 TGGTACACTTGCTCTGTATTCACTT 60.222 40.000 0.00 0.00 0.00 3.16
2412 2482 3.244353 CCAACACAAGACTGATGAGGACT 60.244 47.826 0.00 0.00 0.00 3.85
2414 2484 4.000331 ACACAAGACTGATGAGGACTTG 58.000 45.455 15.41 15.41 40.44 3.16
2459 2529 0.694771 AGGAGAACTCATTGGCAGCA 59.305 50.000 0.00 0.00 0.00 4.41
2599 2669 9.315363 AGGTATTCTACATAATCTCTTCCGAAT 57.685 33.333 0.00 0.00 0.00 3.34
2648 2718 8.421249 TGAGTAAATTGAACATTTCCAGGAAT 57.579 30.769 1.58 0.00 0.00 3.01
2693 2764 2.373169 AGTTCTTTCTGCATCAGGTGGA 59.627 45.455 0.00 0.00 31.51 4.02
2742 2813 9.214957 TGAGTACTGGTAATATTGTGTTTTCAG 57.785 33.333 0.00 0.00 0.00 3.02
2743 2814 9.216117 GAGTACTGGTAATATTGTGTTTTCAGT 57.784 33.333 0.00 0.00 36.92 3.41
2744 2815 9.216117 AGTACTGGTAATATTGTGTTTTCAGTC 57.784 33.333 0.00 0.00 35.10 3.51
2745 2816 9.216117 GTACTGGTAATATTGTGTTTTCAGTCT 57.784 33.333 0.00 0.00 35.10 3.24
2746 2817 8.691661 ACTGGTAATATTGTGTTTTCAGTCTT 57.308 30.769 0.00 0.00 0.00 3.01
2747 2818 9.131791 ACTGGTAATATTGTGTTTTCAGTCTTT 57.868 29.630 0.00 0.00 0.00 2.52
2748 2819 9.612620 CTGGTAATATTGTGTTTTCAGTCTTTC 57.387 33.333 0.00 0.00 0.00 2.62
2749 2820 9.126151 TGGTAATATTGTGTTTTCAGTCTTTCA 57.874 29.630 0.00 0.00 0.00 2.69
2752 2823 8.524870 AATATTGTGTTTTCAGTCTTTCATGC 57.475 30.769 0.00 0.00 0.00 4.06
2753 2824 5.581126 TTGTGTTTTCAGTCTTTCATGCT 57.419 34.783 0.00 0.00 0.00 3.79
2754 2825 4.923893 TGTGTTTTCAGTCTTTCATGCTG 58.076 39.130 0.00 0.00 0.00 4.41
2755 2826 4.398988 TGTGTTTTCAGTCTTTCATGCTGT 59.601 37.500 0.00 0.00 0.00 4.40
2756 2827 5.588246 TGTGTTTTCAGTCTTTCATGCTGTA 59.412 36.000 0.00 0.00 0.00 2.74
2757 2828 6.094742 TGTGTTTTCAGTCTTTCATGCTGTAA 59.905 34.615 0.00 0.00 0.00 2.41
2758 2829 6.414987 GTGTTTTCAGTCTTTCATGCTGTAAC 59.585 38.462 0.00 0.61 32.38 2.50
2759 2830 6.318648 TGTTTTCAGTCTTTCATGCTGTAACT 59.681 34.615 13.33 2.70 32.66 2.24
2760 2831 6.942532 TTTCAGTCTTTCATGCTGTAACTT 57.057 33.333 0.00 0.00 0.00 2.66
2761 2832 6.545504 TTCAGTCTTTCATGCTGTAACTTC 57.454 37.500 0.00 0.00 0.00 3.01
2762 2833 5.610398 TCAGTCTTTCATGCTGTAACTTCA 58.390 37.500 0.00 0.00 0.00 3.02
2763 2834 5.698089 TCAGTCTTTCATGCTGTAACTTCAG 59.302 40.000 0.00 0.00 38.35 3.02
2764 2835 5.468072 CAGTCTTTCATGCTGTAACTTCAGT 59.532 40.000 0.00 0.00 37.70 3.41
2765 2836 6.646653 CAGTCTTTCATGCTGTAACTTCAGTA 59.353 38.462 0.00 0.00 37.70 2.74
2766 2837 7.171508 CAGTCTTTCATGCTGTAACTTCAGTAA 59.828 37.037 0.00 0.00 37.70 2.24
2767 2838 7.715249 AGTCTTTCATGCTGTAACTTCAGTAAA 59.285 33.333 0.00 0.00 37.70 2.01
2768 2839 8.507249 GTCTTTCATGCTGTAACTTCAGTAAAT 58.493 33.333 0.00 0.00 37.70 1.40
2769 2840 9.066892 TCTTTCATGCTGTAACTTCAGTAAATT 57.933 29.630 0.00 0.00 37.70 1.82
2770 2841 9.334693 CTTTCATGCTGTAACTTCAGTAAATTC 57.665 33.333 0.00 0.00 37.70 2.17
2771 2842 8.621532 TTCATGCTGTAACTTCAGTAAATTCT 57.378 30.769 0.00 0.00 37.70 2.40
2772 2843 8.621532 TCATGCTGTAACTTCAGTAAATTCTT 57.378 30.769 0.00 0.00 37.70 2.52
2773 2844 8.721478 TCATGCTGTAACTTCAGTAAATTCTTC 58.279 33.333 0.00 0.00 37.70 2.87
2774 2845 8.506437 CATGCTGTAACTTCAGTAAATTCTTCA 58.494 33.333 0.00 0.00 37.70 3.02
2775 2846 8.445275 TGCTGTAACTTCAGTAAATTCTTCAA 57.555 30.769 0.00 0.00 37.70 2.69
2776 2847 8.559536 TGCTGTAACTTCAGTAAATTCTTCAAG 58.440 33.333 0.00 0.00 37.70 3.02
2777 2848 8.560374 GCTGTAACTTCAGTAAATTCTTCAAGT 58.440 33.333 0.00 0.00 37.70 3.16
2796 2867 9.803315 CTTCAAGTATGTTAGTACATAGAAGCA 57.197 33.333 0.00 0.00 45.42 3.91
2798 2869 9.967346 TCAAGTATGTTAGTACATAGAAGCATC 57.033 33.333 0.00 0.00 45.42 3.91
2799 2870 8.906693 CAAGTATGTTAGTACATAGAAGCATCG 58.093 37.037 0.00 0.00 45.42 3.84
2800 2871 8.392372 AGTATGTTAGTACATAGAAGCATCGA 57.608 34.615 0.00 0.00 45.42 3.59
2801 2872 8.847196 AGTATGTTAGTACATAGAAGCATCGAA 58.153 33.333 0.00 0.00 45.42 3.71
2802 2873 9.627395 GTATGTTAGTACATAGAAGCATCGAAT 57.373 33.333 0.00 0.00 45.42 3.34
2803 2874 8.749841 ATGTTAGTACATAGAAGCATCGAATC 57.250 34.615 0.00 0.00 43.12 2.52
2804 2875 7.712797 TGTTAGTACATAGAAGCATCGAATCA 58.287 34.615 0.00 0.00 0.00 2.57
2805 2876 7.648112 TGTTAGTACATAGAAGCATCGAATCAC 59.352 37.037 0.00 0.00 0.00 3.06
2806 2877 6.398234 AGTACATAGAAGCATCGAATCACT 57.602 37.500 0.00 0.00 0.00 3.41
2807 2878 6.212235 AGTACATAGAAGCATCGAATCACTG 58.788 40.000 0.00 0.00 0.00 3.66
2808 2879 3.806521 ACATAGAAGCATCGAATCACTGC 59.193 43.478 0.00 0.00 36.15 4.40
2809 2880 2.391616 AGAAGCATCGAATCACTGCA 57.608 45.000 10.33 0.00 38.37 4.41
2810 2881 2.703416 AGAAGCATCGAATCACTGCAA 58.297 42.857 10.33 0.00 38.37 4.08
2811 2882 2.417933 AGAAGCATCGAATCACTGCAAC 59.582 45.455 10.33 4.07 38.37 4.17
2812 2883 0.723414 AGCATCGAATCACTGCAACG 59.277 50.000 10.33 0.00 38.37 4.10
2813 2884 0.721154 GCATCGAATCACTGCAACGA 59.279 50.000 3.13 0.00 35.96 3.85
2814 2885 1.328680 GCATCGAATCACTGCAACGAT 59.671 47.619 3.13 0.00 42.89 3.73
2816 2887 2.362169 TCGAATCACTGCAACGATGA 57.638 45.000 0.00 0.00 0.00 2.92
2817 2888 2.682836 TCGAATCACTGCAACGATGAA 58.317 42.857 0.00 0.00 0.00 2.57
2818 2889 3.063485 TCGAATCACTGCAACGATGAAA 58.937 40.909 0.00 0.00 0.00 2.69
2819 2890 3.496507 TCGAATCACTGCAACGATGAAAA 59.503 39.130 0.00 0.00 0.00 2.29
2820 2891 3.842428 CGAATCACTGCAACGATGAAAAG 59.158 43.478 0.00 0.00 0.00 2.27
2821 2892 4.611355 CGAATCACTGCAACGATGAAAAGT 60.611 41.667 0.00 0.00 0.00 2.66
2822 2893 3.878086 TCACTGCAACGATGAAAAGTC 57.122 42.857 0.00 0.00 0.00 3.01
2823 2894 3.202097 TCACTGCAACGATGAAAAGTCA 58.798 40.909 0.00 0.00 38.41 3.41
2824 2895 3.248363 TCACTGCAACGATGAAAAGTCAG 59.752 43.478 0.00 0.00 37.14 3.51
2825 2896 3.002656 CACTGCAACGATGAAAAGTCAGT 59.997 43.478 0.00 0.00 37.14 3.41
2826 2897 3.002656 ACTGCAACGATGAAAAGTCAGTG 59.997 43.478 0.00 0.00 37.14 3.66
2827 2898 2.286950 TGCAACGATGAAAAGTCAGTGC 60.287 45.455 0.00 0.00 37.14 4.40
2828 2899 2.286950 GCAACGATGAAAAGTCAGTGCA 60.287 45.455 0.00 0.00 37.14 4.57
2829 2900 3.791789 GCAACGATGAAAAGTCAGTGCAA 60.792 43.478 0.00 0.00 37.14 4.08
2830 2901 4.539870 CAACGATGAAAAGTCAGTGCAAT 58.460 39.130 0.00 0.00 37.14 3.56
2831 2902 4.836125 ACGATGAAAAGTCAGTGCAATT 57.164 36.364 0.00 0.00 37.14 2.32
2832 2903 4.787598 ACGATGAAAAGTCAGTGCAATTC 58.212 39.130 0.00 0.00 37.14 2.17
2833 2904 4.275689 ACGATGAAAAGTCAGTGCAATTCA 59.724 37.500 0.00 0.00 37.14 2.57
2834 2905 4.614284 CGATGAAAAGTCAGTGCAATTCAC 59.386 41.667 0.00 0.00 45.98 3.18
2835 2906 4.305989 TGAAAAGTCAGTGCAATTCACC 57.694 40.909 0.00 0.00 46.81 4.02
2836 2907 3.953612 TGAAAAGTCAGTGCAATTCACCT 59.046 39.130 0.00 0.00 46.81 4.00
2837 2908 4.036734 TGAAAAGTCAGTGCAATTCACCTC 59.963 41.667 0.00 0.00 46.81 3.85
2838 2909 3.498774 AAGTCAGTGCAATTCACCTCT 57.501 42.857 0.00 0.00 46.81 3.69
2839 2910 2.775890 AGTCAGTGCAATTCACCTCTG 58.224 47.619 0.00 0.00 46.81 3.35
2840 2911 2.105477 AGTCAGTGCAATTCACCTCTGT 59.895 45.455 0.00 0.00 46.81 3.41
2841 2912 2.880890 GTCAGTGCAATTCACCTCTGTT 59.119 45.455 0.00 0.00 46.81 3.16
2842 2913 3.316308 GTCAGTGCAATTCACCTCTGTTT 59.684 43.478 0.00 0.00 46.81 2.83
2843 2914 3.953612 TCAGTGCAATTCACCTCTGTTTT 59.046 39.130 0.00 0.00 46.81 2.43
2844 2915 5.008613 GTCAGTGCAATTCACCTCTGTTTTA 59.991 40.000 0.00 0.00 46.81 1.52
2845 2916 5.769662 TCAGTGCAATTCACCTCTGTTTTAT 59.230 36.000 0.00 0.00 46.81 1.40
2846 2917 5.860182 CAGTGCAATTCACCTCTGTTTTATG 59.140 40.000 0.00 0.00 46.81 1.90
2847 2918 5.536161 AGTGCAATTCACCTCTGTTTTATGT 59.464 36.000 0.00 0.00 46.81 2.29
2848 2919 6.714810 AGTGCAATTCACCTCTGTTTTATGTA 59.285 34.615 0.00 0.00 46.81 2.29
2849 2920 6.801862 GTGCAATTCACCTCTGTTTTATGTAC 59.198 38.462 0.00 0.00 39.79 2.90
2850 2921 6.714810 TGCAATTCACCTCTGTTTTATGTACT 59.285 34.615 0.00 0.00 0.00 2.73
2851 2922 7.880713 TGCAATTCACCTCTGTTTTATGTACTA 59.119 33.333 0.00 0.00 0.00 1.82
2852 2923 8.175716 GCAATTCACCTCTGTTTTATGTACTAC 58.824 37.037 0.00 0.00 0.00 2.73
2853 2924 8.380644 CAATTCACCTCTGTTTTATGTACTACG 58.619 37.037 0.00 0.00 0.00 3.51
2854 2925 6.579666 TCACCTCTGTTTTATGTACTACGT 57.420 37.500 0.00 0.00 0.00 3.57
2855 2926 7.686438 TCACCTCTGTTTTATGTACTACGTA 57.314 36.000 0.00 0.00 0.00 3.57
2856 2927 8.284945 TCACCTCTGTTTTATGTACTACGTAT 57.715 34.615 0.00 0.00 0.00 3.06
2857 2928 8.742777 TCACCTCTGTTTTATGTACTACGTATT 58.257 33.333 0.00 0.00 0.00 1.89
2922 2993 9.770097 TCTTTTGCATAAATCCATGTTGTAAAA 57.230 25.926 0.00 0.00 0.00 1.52
3042 3114 5.079643 ACAGACAAAGTTGGATGGCTATTT 58.920 37.500 0.00 0.00 31.64 1.40
3087 3159 6.443792 GTTCATTTTAATTGGAAGTGTCGGT 58.556 36.000 0.00 0.00 0.00 4.69
3106 3178 2.350772 GGTGCACTGAACATACACAAGC 60.351 50.000 17.98 0.00 32.89 4.01
3271 3370 8.170730 AGGTTTAGAAATTACCTTCCATCAACT 58.829 33.333 0.00 0.00 39.19 3.16
3299 3398 0.541392 AGCCCGTATGACATGCAGAA 59.459 50.000 4.34 0.00 0.00 3.02
3315 3414 6.703165 ACATGCAGAAATTTGTTTCTTTCTCC 59.297 34.615 0.00 0.00 39.15 3.71
3339 3438 2.159627 AGGAACTGAAGCGTTATTTGCG 59.840 45.455 0.00 0.00 37.18 4.85
3360 3459 4.576463 GCGGATCTATGTCATTTTCCTGTT 59.424 41.667 0.00 0.00 0.00 3.16
3527 3715 9.368416 ACTATAGCTTGTCCTATTGACTAATCA 57.632 33.333 0.00 0.00 44.75 2.57
3564 3752 1.805254 GTGCCAGCACATCACATCC 59.195 57.895 17.61 0.00 45.53 3.51
3566 3754 3.104766 CCAGCACATCACATCCGC 58.895 61.111 0.00 0.00 0.00 5.54
3619 3814 2.672961 TGACAGTGCATACTAGTGCC 57.327 50.000 5.39 0.00 44.43 5.01
3646 3841 8.338259 GTTGCTTTATGTACTATGGTTCTCATG 58.662 37.037 0.00 0.00 37.30 3.07
3733 3928 2.987413 TAATTGCAAGTCAAGCCACG 57.013 45.000 1.02 0.00 38.22 4.94
3742 3937 1.759445 AGTCAAGCCACGATATCTGCT 59.241 47.619 0.34 3.50 35.08 4.24
3751 3946 4.072839 CCACGATATCTGCTACCTACTCA 58.927 47.826 0.34 0.00 0.00 3.41
3971 4166 4.365514 TCTGGTGAGCATTCCTTGTTTA 57.634 40.909 0.00 0.00 0.00 2.01
4036 4231 6.930722 ACATGCAGACAATTTAAAAGGAAAGG 59.069 34.615 0.00 0.00 0.00 3.11
4060 4255 8.548877 AGGTTGCCTTATAATAGAAAGAGTGAA 58.451 33.333 0.00 0.00 0.00 3.18
4104 4299 4.246458 GTCCTGAAATAAGAACTGTCGCT 58.754 43.478 0.00 0.00 0.00 4.93
4117 4312 5.413833 AGAACTGTCGCTGAATTTTCATGAT 59.586 36.000 0.00 0.00 36.46 2.45
4121 4316 8.437360 ACTGTCGCTGAATTTTCATGATATAA 57.563 30.769 0.00 0.00 36.46 0.98
4125 4320 9.752274 GTCGCTGAATTTTCATGATATAATCTC 57.248 33.333 0.00 0.32 36.46 2.75
4140 4336 7.777440 TGATATAATCTCCGCTCATATCTCAGT 59.223 37.037 0.00 0.00 32.32 3.41
4549 4746 2.959275 CGTACCGCACATCTTCTCC 58.041 57.895 0.00 0.00 0.00 3.71
4565 4762 4.597507 TCTTCTCCCACTTTATCACCAACT 59.402 41.667 0.00 0.00 0.00 3.16
4687 4884 4.929808 CCGAAGAACTTCCATATATTCCGG 59.070 45.833 0.00 0.00 36.27 5.14
4852 5049 2.102252 GCAGAGGACTGAAGGATCGATT 59.898 50.000 0.00 0.00 46.03 3.34
5113 5313 5.363101 TCAGGGATCATCAAGAAGATTTCG 58.637 41.667 0.00 0.00 33.72 3.46
5161 5361 0.463474 GGATCTGCAGGGAGAACAGC 60.463 60.000 15.13 0.00 0.00 4.40
5236 5436 4.737054 ACATCTGAAACATCATTTTCCGC 58.263 39.130 0.00 0.00 35.01 5.54
5278 5478 3.494045 GCAAAAAGCTCTGATGTACCC 57.506 47.619 0.00 0.00 41.15 3.69
5301 5502 1.082954 CTGGAAGGGAGAAGGGGGA 59.917 63.158 0.00 0.00 0.00 4.81
5383 5584 0.732538 CAGATTTTGTTTCGCGCCCC 60.733 55.000 0.00 0.00 0.00 5.80
5428 5629 4.037446 TGCTAGAAATGTTCGCCTTTTGTT 59.963 37.500 0.00 0.00 34.02 2.83
5437 5638 6.969828 TGTTCGCCTTTTGTTTTGTAATTT 57.030 29.167 0.00 0.00 0.00 1.82
5559 5760 5.296780 CAGCTTTCTAAGTTGTCACCTTTGA 59.703 40.000 0.00 0.00 35.32 2.69
5564 5765 7.873719 TTCTAAGTTGTCACCTTTGATTTCA 57.126 32.000 0.00 0.00 33.11 2.69
5573 5774 8.422973 TGTCACCTTTGATTTCATTGAAAAAG 57.577 30.769 15.34 13.51 35.11 2.27
5634 5835 5.245977 TCCTTTGGTTTGGAGGAATTTCATC 59.754 40.000 2.47 2.47 36.67 2.92
5639 5840 4.402474 GGTTTGGAGGAATTTCATCGGAAT 59.598 41.667 5.09 0.00 31.93 3.01
5722 5968 6.098552 GGATTCCTATTCCTACATAGGCCTAC 59.901 46.154 16.61 0.00 44.08 3.18
5728 5974 3.833732 TCCTACATAGGCCTACACTCAG 58.166 50.000 16.61 8.06 43.31 3.35
5730 5976 4.414514 TCCTACATAGGCCTACACTCAGTA 59.585 45.833 16.61 10.11 43.31 2.74
5768 6015 8.245491 TGATGTGAACCAAATGACATATCTTTG 58.755 33.333 0.00 0.00 33.98 2.77
5820 6067 5.587844 GCATGTCATCTCATTTCCTACAAGT 59.412 40.000 0.00 0.00 0.00 3.16
5861 6108 6.992664 ATCCTATCCTATGAGATACATGCC 57.007 41.667 0.00 0.00 39.77 4.40
5870 6125 6.938596 CCTATGAGATACATGCCATTTTCAGA 59.061 38.462 0.00 0.00 39.77 3.27
5874 6129 6.604396 TGAGATACATGCCATTTTCAGAATGT 59.396 34.615 0.00 0.00 37.40 2.71
5908 6163 7.761249 TGATGTGACAGTCAGATAAATGTACAG 59.239 37.037 13.06 0.00 29.83 2.74
6025 6280 7.250032 TCAGGGTAATCATATTCTCATCTGG 57.750 40.000 0.00 0.00 0.00 3.86
6049 6304 2.023673 CAGCAACAAAGGAGTTCCACA 58.976 47.619 0.28 0.00 38.89 4.17
6073 6328 9.144298 ACAATAGCTAGCAGATAAAACTACCTA 57.856 33.333 18.83 0.00 0.00 3.08
6190 6507 1.745890 CTGGACCACGAACCACTCA 59.254 57.895 0.00 0.00 32.44 3.41
6197 6514 2.205074 CCACGAACCACTCAGCATATC 58.795 52.381 0.00 0.00 0.00 1.63
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 7.661040 ACACCTCATGTTTCTTTCTTAATTGG 58.339 34.615 0.00 0.00 38.98 3.16
23 24 5.125739 CACTAAACAAACCCAGGTTGTTACA 59.874 40.000 10.90 2.53 38.47 2.41
24 25 5.357596 TCACTAAACAAACCCAGGTTGTTAC 59.642 40.000 10.90 0.00 38.47 2.50
25 26 5.357596 GTCACTAAACAAACCCAGGTTGTTA 59.642 40.000 10.90 5.09 38.47 2.41
47 48 0.535553 TTGGCCGGTTAACCAGTGTC 60.536 55.000 24.14 13.48 37.24 3.67
134 141 5.334105 CGTGGCATATTACTTTACCTGATGC 60.334 44.000 0.00 0.00 37.95 3.91
137 144 5.347620 ACGTGGCATATTACTTTACCTGA 57.652 39.130 0.00 0.00 0.00 3.86
138 145 4.208460 CGACGTGGCATATTACTTTACCTG 59.792 45.833 0.00 0.00 0.00 4.00
139 146 4.365723 CGACGTGGCATATTACTTTACCT 58.634 43.478 0.00 0.00 0.00 3.08
140 147 3.492011 CCGACGTGGCATATTACTTTACC 59.508 47.826 0.00 0.00 0.00 2.85
144 151 2.093869 ACACCGACGTGGCATATTACTT 60.094 45.455 0.00 0.00 44.86 2.24
191 199 2.159014 TGCTAACCTAACCTATGTGCCG 60.159 50.000 0.00 0.00 0.00 5.69
198 206 1.485066 GCTGGCTGCTAACCTAACCTA 59.515 52.381 9.31 0.00 38.95 3.08
199 207 0.253327 GCTGGCTGCTAACCTAACCT 59.747 55.000 9.31 0.00 38.95 3.50
200 208 0.748367 GGCTGGCTGCTAACCTAACC 60.748 60.000 16.14 0.00 42.39 2.85
201 209 0.035439 TGGCTGGCTGCTAACCTAAC 60.035 55.000 16.14 0.00 42.39 2.34
202 210 0.695924 TTGGCTGGCTGCTAACCTAA 59.304 50.000 16.14 0.00 42.39 2.69
229 237 2.286121 TGACCCATCACCCCCTCC 60.286 66.667 0.00 0.00 0.00 4.30
230 238 3.049080 GCTGACCCATCACCCCCTC 62.049 68.421 0.00 0.00 0.00 4.30
299 314 1.509923 GCAGCAATGACAAGGAGGC 59.490 57.895 0.00 0.00 0.00 4.70
488 518 2.955246 AGGAGGAGGAGGAGGGCA 60.955 66.667 0.00 0.00 0.00 5.36
495 525 0.673437 GATTCAGCGAGGAGGAGGAG 59.327 60.000 0.00 0.00 0.00 3.69
496 526 0.260230 AGATTCAGCGAGGAGGAGGA 59.740 55.000 0.00 0.00 0.00 3.71
497 527 0.673437 GAGATTCAGCGAGGAGGAGG 59.327 60.000 0.00 0.00 0.00 4.30
574 614 0.887387 CAAAGAAAACCTCCCCGCGA 60.887 55.000 8.23 0.00 0.00 5.87
576 616 1.532604 CCCAAAGAAAACCTCCCCGC 61.533 60.000 0.00 0.00 0.00 6.13
590 630 0.111639 CCGACCTTTCTTCCCCCAAA 59.888 55.000 0.00 0.00 0.00 3.28
598 638 1.601166 CGAAAACCCCGACCTTTCTT 58.399 50.000 0.00 0.00 0.00 2.52
644 684 0.589729 CCGAAATCGCCGCTCAAATG 60.590 55.000 0.00 0.00 38.18 2.32
652 692 0.039888 AAAACCAACCGAAATCGCCG 60.040 50.000 0.00 0.00 38.18 6.46
681 721 0.036952 AATCACAGCACAGGGACTCG 60.037 55.000 0.00 0.00 34.60 4.18
709 749 1.586154 AACAGAAATGGAAGCGCGGG 61.586 55.000 8.83 0.00 0.00 6.13
712 752 0.171231 GGGAACAGAAATGGAAGCGC 59.829 55.000 0.00 0.00 0.00 5.92
713 753 0.811281 GGGGAACAGAAATGGAAGCG 59.189 55.000 0.00 0.00 0.00 4.68
810 850 2.125512 GCATCGACGCCTCCAACT 60.126 61.111 0.00 0.00 0.00 3.16
1235 1289 1.741706 GATGAACTGGTCACATGCAGG 59.258 52.381 0.00 0.00 39.72 4.85
1277 1331 4.437682 TCAAACTGTTCCAGATGTCCTT 57.562 40.909 0.00 0.00 35.18 3.36
1280 1334 6.115446 TCCATATCAAACTGTTCCAGATGTC 58.885 40.000 11.14 0.00 35.18 3.06
1307 1370 5.224888 ACAAACAATATGTTCAAGCAGCAG 58.775 37.500 0.00 0.00 40.14 4.24
1352 1415 4.347876 TCCCATCATACCAACTACATCAGG 59.652 45.833 0.00 0.00 0.00 3.86
1356 1419 6.331572 TGGTAATCCCATCATACCAACTACAT 59.668 38.462 1.57 0.00 44.50 2.29
1386 1449 8.694540 CAGTAATCCCACCATCATTGAAAATAA 58.305 33.333 0.00 0.00 0.00 1.40
1388 1451 6.896860 TCAGTAATCCCACCATCATTGAAAAT 59.103 34.615 0.00 0.00 0.00 1.82
1439 1502 5.073478 GTCATTTTCACTACGAAGAAAGCG 58.927 41.667 0.00 0.00 35.41 4.68
1535 1598 7.521529 TCTTCTGCTAATTGTTTCATCGAAAG 58.478 34.615 0.00 0.00 31.87 2.62
1594 1657 7.529880 AACAAGCATTCAGTTTCTTTTCAAG 57.470 32.000 0.00 0.00 0.00 3.02
1624 1691 8.773404 TCTTGATTTAGTAGCCTAACAACTTC 57.227 34.615 0.00 0.00 32.91 3.01
1789 1856 0.518636 CCTCGTCGTCGTTTACTCCA 59.481 55.000 1.33 0.00 38.33 3.86
1796 1863 3.176708 CAATAACATCCTCGTCGTCGTT 58.823 45.455 1.33 0.00 38.33 3.85
1807 1874 4.786425 AGGAAAGAGCTCCAATAACATCC 58.214 43.478 10.93 6.82 38.02 3.51
1829 1896 7.252612 TGAGAGTAAGGGTGTAAATGATCAA 57.747 36.000 0.00 0.00 0.00 2.57
1862 1929 6.291060 CGCAAGACAACAAAAACATACTTCAC 60.291 38.462 0.00 0.00 43.02 3.18
1886 1953 0.887247 TGACCATTGTCATTTGCCCG 59.113 50.000 0.00 0.00 46.40 6.13
1910 1977 8.442632 TTGACCATGTGAGAATAAATCATCTC 57.557 34.615 0.00 0.00 41.95 2.75
1922 1989 7.267857 CAGTATGATACTTTGACCATGTGAGA 58.732 38.462 1.60 0.00 39.69 3.27
1924 1991 6.070251 ACCAGTATGATACTTTGACCATGTGA 60.070 38.462 1.60 0.00 39.69 3.58
1929 1996 7.364408 GGTCTAACCAGTATGATACTTTGACCA 60.364 40.741 21.08 0.09 39.69 4.02
1934 2001 8.375493 TGAAGGTCTAACCAGTATGATACTTT 57.625 34.615 1.60 0.00 41.95 2.66
1937 2004 8.421784 TCATTGAAGGTCTAACCAGTATGATAC 58.578 37.037 0.00 0.00 41.95 2.24
1966 2033 3.317711 AGAGCAGATCATAAGAGACACCG 59.682 47.826 0.00 0.00 0.00 4.94
2038 2105 5.321102 TGGTGTTGGCTAATGTGTAGAAAT 58.679 37.500 0.00 0.00 0.00 2.17
2070 2137 8.807118 TGTTATGGTTGCCACTTATTAAATTCA 58.193 29.630 0.00 0.00 35.80 2.57
2139 2207 3.614092 TCTCATGACCAGAAAGGCATTC 58.386 45.455 0.00 0.00 43.14 2.67
2169 2237 9.906660 TTTCCATATAAAATAATTTAGCTGCCG 57.093 29.630 0.00 0.00 34.62 5.69
2187 2255 8.986991 AGTGATCTCAGACTAAACTTTCCATAT 58.013 33.333 0.00 0.00 0.00 1.78
2228 2296 5.335191 GCATGGAAGAGTTTCTTTCGTTCAT 60.335 40.000 0.00 0.00 36.73 2.57
2231 2299 3.058914 CGCATGGAAGAGTTTCTTTCGTT 60.059 43.478 0.00 0.00 36.73 3.85
2232 2300 2.480419 CGCATGGAAGAGTTTCTTTCGT 59.520 45.455 0.00 0.00 36.73 3.85
2233 2301 2.726066 GCGCATGGAAGAGTTTCTTTCG 60.726 50.000 0.30 0.00 36.73 3.46
2238 2306 2.927553 ATTGCGCATGGAAGAGTTTC 57.072 45.000 12.75 0.00 0.00 2.78
2239 2307 2.821969 AGAATTGCGCATGGAAGAGTTT 59.178 40.909 12.75 0.00 0.00 2.66
2262 2330 7.150783 AGCAACTTATCAAATCAAGAAGTCC 57.849 36.000 0.00 0.00 30.20 3.85
2317 2386 1.873591 GTGTACCACCTGCAAGACAAG 59.126 52.381 0.00 0.00 34.07 3.16
2345 2415 3.232213 TGACGGCAGAGAAGTGAATAC 57.768 47.619 0.00 0.00 0.00 1.89
2354 2424 2.845019 CTTTGCATGACGGCAGAGA 58.155 52.632 0.00 0.00 45.90 3.10
2459 2529 8.237267 CGTGTTTCTAGCCATCTCTTTATTTTT 58.763 33.333 0.00 0.00 0.00 1.94
2582 2652 7.770433 TGAACATGAATTCGGAAGAGATTATGT 59.230 33.333 0.00 0.00 43.69 2.29
2589 2659 3.686241 TGCTGAACATGAATTCGGAAGAG 59.314 43.478 0.00 0.00 43.69 2.85
2595 2665 8.570096 AAAATATGATGCTGAACATGAATTCG 57.430 30.769 0.00 0.00 39.84 3.34
2599 2669 8.741841 TCAGAAAAATATGATGCTGAACATGAA 58.258 29.630 0.00 0.00 39.84 2.57
2622 2692 7.452880 TCCTGGAAATGTTCAATTTACTCAG 57.547 36.000 0.00 0.00 0.00 3.35
2637 2707 7.729124 AATCACAAATCAGATTCCTGGAAAT 57.271 32.000 14.03 2.30 40.76 2.17
2742 2813 5.931441 ACTGAAGTTACAGCATGAAAGAC 57.069 39.130 0.00 0.00 39.69 3.01
2743 2814 8.621532 ATTTACTGAAGTTACAGCATGAAAGA 57.378 30.769 0.00 0.00 39.69 2.52
2744 2815 9.334693 GAATTTACTGAAGTTACAGCATGAAAG 57.665 33.333 0.00 0.00 39.69 2.62
2745 2816 9.066892 AGAATTTACTGAAGTTACAGCATGAAA 57.933 29.630 0.00 0.00 39.69 2.69
2746 2817 8.621532 AGAATTTACTGAAGTTACAGCATGAA 57.378 30.769 0.00 0.00 39.69 2.57
2747 2818 8.621532 AAGAATTTACTGAAGTTACAGCATGA 57.378 30.769 0.00 0.00 39.69 3.07
2748 2819 8.506437 TGAAGAATTTACTGAAGTTACAGCATG 58.494 33.333 0.00 0.00 46.00 4.06
2749 2820 8.621532 TGAAGAATTTACTGAAGTTACAGCAT 57.378 30.769 0.00 0.00 41.06 3.79
2750 2821 8.445275 TTGAAGAATTTACTGAAGTTACAGCA 57.555 30.769 0.00 0.00 41.06 4.41
2751 2822 8.560374 ACTTGAAGAATTTACTGAAGTTACAGC 58.440 33.333 0.00 0.00 41.06 4.40
2770 2841 9.803315 TGCTTCTATGTACTAACATACTTGAAG 57.197 33.333 15.06 15.06 44.66 3.02
2772 2843 9.967346 GATGCTTCTATGTACTAACATACTTGA 57.033 33.333 0.00 0.00 44.66 3.02
2773 2844 8.906693 CGATGCTTCTATGTACTAACATACTTG 58.093 37.037 0.00 0.00 44.66 3.16
2774 2845 8.847196 TCGATGCTTCTATGTACTAACATACTT 58.153 33.333 0.00 0.00 44.66 2.24
2775 2846 8.392372 TCGATGCTTCTATGTACTAACATACT 57.608 34.615 0.00 0.00 44.66 2.12
2776 2847 9.627395 ATTCGATGCTTCTATGTACTAACATAC 57.373 33.333 0.00 0.00 44.66 2.39
2777 2848 9.841880 GATTCGATGCTTCTATGTACTAACATA 57.158 33.333 0.00 0.00 44.66 2.29
2779 2850 7.648112 GTGATTCGATGCTTCTATGTACTAACA 59.352 37.037 0.00 0.00 40.69 2.41
2780 2851 7.863375 AGTGATTCGATGCTTCTATGTACTAAC 59.137 37.037 0.00 0.00 0.00 2.34
2781 2852 7.862873 CAGTGATTCGATGCTTCTATGTACTAA 59.137 37.037 0.00 0.00 0.00 2.24
2782 2853 7.363431 CAGTGATTCGATGCTTCTATGTACTA 58.637 38.462 0.00 0.00 0.00 1.82
2783 2854 6.212235 CAGTGATTCGATGCTTCTATGTACT 58.788 40.000 0.00 0.00 0.00 2.73
2784 2855 5.107683 GCAGTGATTCGATGCTTCTATGTAC 60.108 44.000 0.00 0.00 37.00 2.90
2785 2856 4.984785 GCAGTGATTCGATGCTTCTATGTA 59.015 41.667 0.00 0.00 37.00 2.29
2786 2857 3.806521 GCAGTGATTCGATGCTTCTATGT 59.193 43.478 0.00 0.00 37.00 2.29
2787 2858 3.805971 TGCAGTGATTCGATGCTTCTATG 59.194 43.478 9.19 0.00 40.62 2.23
2788 2859 4.063998 TGCAGTGATTCGATGCTTCTAT 57.936 40.909 9.19 0.00 40.62 1.98
2789 2860 3.525268 TGCAGTGATTCGATGCTTCTA 57.475 42.857 9.19 0.00 40.62 2.10
2790 2861 2.391616 TGCAGTGATTCGATGCTTCT 57.608 45.000 9.19 0.00 40.62 2.85
2791 2862 2.778659 GTTGCAGTGATTCGATGCTTC 58.221 47.619 9.19 0.00 40.62 3.86
2792 2863 1.129251 CGTTGCAGTGATTCGATGCTT 59.871 47.619 9.19 0.00 40.62 3.91
2793 2864 0.723414 CGTTGCAGTGATTCGATGCT 59.277 50.000 9.19 0.00 40.62 3.79
2794 2865 0.721154 TCGTTGCAGTGATTCGATGC 59.279 50.000 0.97 0.97 40.40 3.91
2795 2866 2.965239 CATCGTTGCAGTGATTCGATG 58.035 47.619 20.58 20.58 46.73 3.84
2796 2867 2.892374 TCATCGTTGCAGTGATTCGAT 58.108 42.857 0.00 2.67 40.95 3.59
2797 2868 2.362169 TCATCGTTGCAGTGATTCGA 57.638 45.000 0.00 0.06 35.14 3.71
2798 2869 3.454042 TTTCATCGTTGCAGTGATTCG 57.546 42.857 0.00 0.00 0.00 3.34
2799 2870 4.787598 ACTTTTCATCGTTGCAGTGATTC 58.212 39.130 0.00 0.00 0.00 2.52
2800 2871 4.275689 TGACTTTTCATCGTTGCAGTGATT 59.724 37.500 0.00 0.00 0.00 2.57
2801 2872 3.814842 TGACTTTTCATCGTTGCAGTGAT 59.185 39.130 0.00 0.00 0.00 3.06
2802 2873 3.202097 TGACTTTTCATCGTTGCAGTGA 58.798 40.909 0.00 0.00 0.00 3.41
2803 2874 3.002656 ACTGACTTTTCATCGTTGCAGTG 59.997 43.478 0.00 0.00 34.42 3.66
2804 2875 3.002656 CACTGACTTTTCATCGTTGCAGT 59.997 43.478 0.00 0.00 35.92 4.40
2805 2876 3.548587 CACTGACTTTTCATCGTTGCAG 58.451 45.455 0.00 0.00 0.00 4.41
2806 2877 2.286950 GCACTGACTTTTCATCGTTGCA 60.287 45.455 0.00 0.00 0.00 4.08
2807 2878 2.286950 TGCACTGACTTTTCATCGTTGC 60.287 45.455 0.00 0.00 0.00 4.17
2808 2879 3.607422 TGCACTGACTTTTCATCGTTG 57.393 42.857 0.00 0.00 0.00 4.10
2809 2880 4.836125 ATTGCACTGACTTTTCATCGTT 57.164 36.364 0.00 0.00 0.00 3.85
2810 2881 4.275689 TGAATTGCACTGACTTTTCATCGT 59.724 37.500 0.00 0.00 0.00 3.73
2811 2882 4.614284 GTGAATTGCACTGACTTTTCATCG 59.386 41.667 0.00 0.00 44.27 3.84
2812 2883 4.919754 GGTGAATTGCACTGACTTTTCATC 59.080 41.667 0.00 0.00 46.86 2.92
2813 2884 4.586001 AGGTGAATTGCACTGACTTTTCAT 59.414 37.500 0.00 0.00 46.86 2.57
2814 2885 3.953612 AGGTGAATTGCACTGACTTTTCA 59.046 39.130 0.00 0.00 46.86 2.69
2815 2886 4.276926 AGAGGTGAATTGCACTGACTTTTC 59.723 41.667 0.00 0.00 46.86 2.29
2816 2887 4.037208 CAGAGGTGAATTGCACTGACTTTT 59.963 41.667 0.00 0.00 46.86 2.27
2817 2888 3.567164 CAGAGGTGAATTGCACTGACTTT 59.433 43.478 0.00 0.00 46.86 2.66
2818 2889 3.144506 CAGAGGTGAATTGCACTGACTT 58.855 45.455 0.00 0.00 46.86 3.01
2819 2890 2.105477 ACAGAGGTGAATTGCACTGACT 59.895 45.455 0.00 0.00 46.86 3.41
2820 2891 2.498167 ACAGAGGTGAATTGCACTGAC 58.502 47.619 0.00 0.00 46.86 3.51
2821 2892 2.936919 ACAGAGGTGAATTGCACTGA 57.063 45.000 0.00 0.00 46.86 3.41
2822 2893 3.996150 AAACAGAGGTGAATTGCACTG 57.004 42.857 0.00 0.00 46.86 3.66
2823 2894 5.536161 ACATAAAACAGAGGTGAATTGCACT 59.464 36.000 0.00 0.00 46.86 4.40
2824 2895 5.772521 ACATAAAACAGAGGTGAATTGCAC 58.227 37.500 0.00 0.00 46.98 4.57
2825 2896 6.714810 AGTACATAAAACAGAGGTGAATTGCA 59.285 34.615 0.00 0.00 0.00 4.08
2826 2897 7.145932 AGTACATAAAACAGAGGTGAATTGC 57.854 36.000 0.00 0.00 0.00 3.56
2827 2898 8.380644 CGTAGTACATAAAACAGAGGTGAATTG 58.619 37.037 0.38 0.00 0.00 2.32
2828 2899 8.092687 ACGTAGTACATAAAACAGAGGTGAATT 58.907 33.333 0.38 0.00 41.94 2.17
2829 2900 7.609056 ACGTAGTACATAAAACAGAGGTGAAT 58.391 34.615 0.38 0.00 41.94 2.57
2830 2901 6.985117 ACGTAGTACATAAAACAGAGGTGAA 58.015 36.000 0.38 0.00 41.94 3.18
2831 2902 6.579666 ACGTAGTACATAAAACAGAGGTGA 57.420 37.500 0.38 0.00 41.94 4.02
2878 2949 8.764558 TGCAAAAGATAGAGTATAAGGGTAACA 58.235 33.333 0.00 0.00 39.74 2.41
2922 2993 6.812160 GCAAAGAGAATCAAAGATGAAGCAAT 59.188 34.615 0.00 0.00 39.49 3.56
3087 3159 2.570135 TGCTTGTGTATGTTCAGTGCA 58.430 42.857 0.00 0.00 0.00 4.57
3106 3178 6.925610 TGCTTTTAATACAGAGCTACCATG 57.074 37.500 0.00 0.00 36.16 3.66
3271 3370 6.071051 TGCATGTCATACGGGCTCTATTATAA 60.071 38.462 0.00 0.00 0.00 0.98
3281 3380 1.378531 TTTCTGCATGTCATACGGGC 58.621 50.000 0.00 0.00 0.00 6.13
3299 3398 6.836007 AGTTCCTGAGGAGAAAGAAACAAATT 59.164 34.615 0.00 0.00 31.21 1.82
3315 3414 4.670221 GCAAATAACGCTTCAGTTCCTGAG 60.670 45.833 0.00 0.00 41.75 3.35
3339 3438 7.260603 CCAAAACAGGAAAATGACATAGATCC 58.739 38.462 6.13 6.13 0.00 3.36
3360 3459 3.261137 TGAATGCAATCTGAATGGCCAAA 59.739 39.130 10.96 0.00 29.89 3.28
3527 3715 5.012046 TGGCACATCGACCAATCTATCTTAT 59.988 40.000 0.00 0.00 31.46 1.73
3578 3773 1.852942 AATGGCTACGCACTATGACG 58.147 50.000 0.00 0.00 0.00 4.35
3619 3814 6.533723 TGAGAACCATAGTACATAAAGCAACG 59.466 38.462 0.00 0.00 0.00 4.10
3646 3841 7.380602 GCATCTGCAATTATTAAACATCTCACC 59.619 37.037 0.00 0.00 41.59 4.02
3742 3937 7.290248 AGAGCCTGCTTTATTATTGAGTAGGTA 59.710 37.037 8.21 0.00 42.92 3.08
3751 3946 6.475596 AATGCAAGAGCCTGCTTTATTATT 57.524 33.333 0.00 0.00 43.07 1.40
4060 4255 9.638176 AGGACAATTTCATTCTTCTATTAGCAT 57.362 29.630 0.00 0.00 0.00 3.79
4073 4268 9.918630 CAGTTCTTATTTCAGGACAATTTCATT 57.081 29.630 0.00 0.00 0.00 2.57
4074 4269 9.082313 ACAGTTCTTATTTCAGGACAATTTCAT 57.918 29.630 0.00 0.00 0.00 2.57
4104 4299 8.853077 AGCGGAGATTATATCATGAAAATTCA 57.147 30.769 0.00 0.00 42.14 2.57
4117 4312 7.112779 TGACTGAGATATGAGCGGAGATTATA 58.887 38.462 0.00 0.00 0.00 0.98
4121 4316 3.760738 TGACTGAGATATGAGCGGAGAT 58.239 45.455 0.00 0.00 0.00 2.75
4125 4320 3.317711 AGAGTTGACTGAGATATGAGCGG 59.682 47.826 0.00 0.00 0.00 5.52
4160 4356 1.141657 AGTGCCTGTTCACACATCAGT 59.858 47.619 0.00 0.00 39.30 3.41
4164 4360 0.466007 TGCAGTGCCTGTTCACACAT 60.466 50.000 13.72 0.00 39.30 3.21
4549 4746 4.156008 GCAGGTAAGTTGGTGATAAAGTGG 59.844 45.833 0.00 0.00 0.00 4.00
4565 4762 2.154567 ACCGAGTGGATAGCAGGTAA 57.845 50.000 0.00 0.00 39.21 2.85
4687 4884 1.094785 ATCCGTACCTTGCAATGCAC 58.905 50.000 7.72 0.00 38.71 4.57
5044 5244 0.249120 TCCCTAGGATGTGCACAACG 59.751 55.000 25.72 8.53 0.00 4.10
5113 5313 7.217200 TCATGAAGGCATACAAGTAATCTACC 58.783 38.462 0.00 0.00 32.27 3.18
5161 5361 6.703165 TCTCATGAGGAATATTGAACATCACG 59.297 38.462 22.42 0.00 0.00 4.35
5236 5436 4.154918 GCTCAGAATCCAGTACAAACCAAG 59.845 45.833 0.00 0.00 0.00 3.61
5295 5495 0.709992 TTTAAAGCAGCCATCCCCCT 59.290 50.000 0.00 0.00 0.00 4.79
5296 5496 0.824109 GTTTAAAGCAGCCATCCCCC 59.176 55.000 0.00 0.00 0.00 5.40
5301 5502 6.096846 CCCTATTTACAGTTTAAAGCAGCCAT 59.903 38.462 0.00 0.00 0.00 4.40
5383 5584 1.577328 AACACCGCCTGAAAGATGCG 61.577 55.000 0.00 0.00 42.92 4.73
5437 5638 5.882557 GGAAAGGAAGCATCTGAATCTTACA 59.117 40.000 7.09 0.00 0.00 2.41
5488 5689 6.814954 TGCCAGTTAGAGATTTTCCTAGAT 57.185 37.500 0.00 0.00 0.00 1.98
5559 5760 9.667107 AAGATGATGATGCTTTTTCAATGAAAT 57.333 25.926 9.41 0.00 31.34 2.17
5564 5765 7.876068 ACACAAAGATGATGATGCTTTTTCAAT 59.124 29.630 0.00 0.00 30.00 2.57
5573 5774 3.488721 GCCAGACACAAAGATGATGATGC 60.489 47.826 0.00 0.00 0.00 3.91
5736 5982 5.303845 TGTCATTTGGTTCACATCATTGGAA 59.696 36.000 0.00 0.00 0.00 3.53
5738 5984 5.136816 TGTCATTTGGTTCACATCATTGG 57.863 39.130 0.00 0.00 0.00 3.16
5740 5986 8.529424 AGATATGTCATTTGGTTCACATCATT 57.471 30.769 0.00 0.00 31.83 2.57
5741 5987 8.529424 AAGATATGTCATTTGGTTCACATCAT 57.471 30.769 0.00 0.00 31.83 2.45
5742 5988 7.943079 AAGATATGTCATTTGGTTCACATCA 57.057 32.000 0.00 0.00 31.83 3.07
5743 5989 7.221452 GCAAAGATATGTCATTTGGTTCACATC 59.779 37.037 12.64 0.00 35.07 3.06
5768 6015 8.589338 TCTCAAATCCTATGAGTAAGAATAGGC 58.411 37.037 4.19 0.00 43.51 3.93
5796 6043 5.587844 ACTTGTAGGAAATGAGATGACATGC 59.412 40.000 0.00 0.00 0.00 4.06
5844 6091 6.840527 TGAAAATGGCATGTATCTCATAGGA 58.159 36.000 0.00 0.00 34.67 2.94
5845 6092 6.938596 TCTGAAAATGGCATGTATCTCATAGG 59.061 38.462 0.00 0.00 34.67 2.57
5846 6093 7.974482 TCTGAAAATGGCATGTATCTCATAG 57.026 36.000 0.00 0.00 34.67 2.23
5847 6094 8.789762 CATTCTGAAAATGGCATGTATCTCATA 58.210 33.333 0.00 0.00 34.67 2.15
5848 6095 7.287005 ACATTCTGAAAATGGCATGTATCTCAT 59.713 33.333 0.00 0.00 33.01 2.90
5850 6097 7.013083 AGACATTCTGAAAATGGCATGTATCTC 59.987 37.037 0.00 0.00 38.12 2.75
5851 6098 6.832384 AGACATTCTGAAAATGGCATGTATCT 59.168 34.615 0.00 0.00 38.12 1.98
5870 6125 6.487668 TGACTGTCACATCAAATTCAGACATT 59.512 34.615 6.36 0.00 35.70 2.71
5874 6129 5.857268 TCTGACTGTCACATCAAATTCAGA 58.143 37.500 6.36 0.00 0.00 3.27
5954 6209 8.458843 GCATTGCTTAATTAGTTTGACTAAGGA 58.541 33.333 0.16 0.00 43.17 3.36
5974 6229 7.202526 ACTATGGTTTATGTAACATGCATTGC 58.797 34.615 0.00 0.46 38.55 3.56
5977 6232 8.965819 TGAAACTATGGTTTATGTAACATGCAT 58.034 29.630 7.22 0.00 44.58 3.96
6025 6280 3.569701 TGGAACTCCTTTGTTGCTGAATC 59.430 43.478 0.00 0.00 38.74 2.52
6073 6328 4.652881 TGTGATCAGTGATCTAGCCATCTT 59.347 41.667 28.73 0.00 39.56 2.40
6190 6507 2.616510 GCCAATTAGCCCTCGATATGCT 60.617 50.000 8.30 8.30 39.10 3.79


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

AutoCloner maintained by Alex Coulton.