Multiple sequence alignment - TraesCS5A01G517900

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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 TraesCS5A01G517900 chr5A 100.000 3488 0 0 460 3947 680505243 680501756 0.000000e+00 6442.0
1 TraesCS5A01G517900 chr5A 100.000 222 0 0 1 222 680505702 680505481 1.020000e-110 411.0
2 TraesCS5A01G517900 chr5A 86.747 249 23 8 999 1239 680512104 680511858 6.500000e-68 268.0
3 TraesCS5A01G517900 chr5A 84.127 252 32 4 996 1240 627014970 627015220 1.830000e-58 237.0
4 TraesCS5A01G517900 chr4B 90.867 2573 175 27 460 2997 642459257 642456710 0.000000e+00 3395.0
5 TraesCS5A01G517900 chr4B 82.148 633 48 25 3246 3829 642455898 642455282 2.130000e-132 483.0
6 TraesCS5A01G517900 chr4B 89.474 209 22 0 13 221 642459517 642459309 8.410000e-67 265.0
7 TraesCS5A01G517900 chr4B 84.000 250 30 8 999 1240 642463193 642462946 8.530000e-57 231.0
8 TraesCS5A01G517900 chr4B 76.286 447 84 18 1870 2312 642774364 642773936 6.640000e-53 219.0
9 TraesCS5A01G517900 chr4D 91.009 1635 134 11 1311 2938 499504305 499502677 0.000000e+00 2193.0
10 TraesCS5A01G517900 chr4D 91.952 584 29 10 705 1271 499504884 499504302 0.000000e+00 802.0
11 TraesCS5A01G517900 chr4D 80.677 709 59 31 3246 3901 499501853 499501170 2.760000e-131 479.0
12 TraesCS5A01G517900 chr4D 83.200 250 32 8 999 1240 499547321 499547074 1.850000e-53 220.0
13 TraesCS5A01G517900 chr1B 79.599 848 144 15 1867 2697 492334749 492335584 7.350000e-162 580.0
14 TraesCS5A01G517900 chr1B 76.580 807 135 31 804 1602 492333489 492334249 1.030000e-105 394.0
15 TraesCS5A01G517900 chr1A 79.478 843 151 9 1867 2697 467256718 467257550 2.640000e-161 579.0
16 TraesCS5A01G517900 chr1A 76.989 704 126 21 911 1595 467255851 467256537 1.730000e-98 370.0
17 TraesCS5A01G517900 chr1D 79.147 844 152 12 1867 2697 368318945 368319777 2.660000e-156 562.0
18 TraesCS5A01G517900 chr1D 78.707 634 108 15 974 1595 368318158 368318776 7.950000e-107 398.0
19 TraesCS5A01G517900 chr7D 88.462 52 6 0 518 569 501507827 501507776 3.290000e-06 63.9


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 TraesCS5A01G517900 chr5A 680501756 680505702 3946 True 3426.5 6442 100.000000 1 3947 2 chr5A.!!$R2 3946
1 TraesCS5A01G517900 chr4B 642455282 642463193 7911 True 1093.5 3395 86.622250 13 3829 4 chr4B.!!$R2 3816
2 TraesCS5A01G517900 chr4D 499501170 499504884 3714 True 1158.0 2193 87.879333 705 3901 3 chr4D.!!$R2 3196
3 TraesCS5A01G517900 chr1B 492333489 492335584 2095 False 487.0 580 78.089500 804 2697 2 chr1B.!!$F1 1893
4 TraesCS5A01G517900 chr1A 467255851 467257550 1699 False 474.5 579 78.233500 911 2697 2 chr1A.!!$F1 1786
5 TraesCS5A01G517900 chr1D 368318158 368319777 1619 False 480.0 562 78.927000 974 2697 2 chr1D.!!$F1 1723

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
186 3851 0.171903 GTCGAAGAATTCCCGGTCGA 59.828 55.0 15.07 14.42 43.81 4.20 F
514 4179 0.747283 CTTGATGAGTGGGCTCCAGC 60.747 60.0 0.00 0.00 40.95 4.85 F
2239 6337 0.039437 ACATCAGCGTCGTCGAACTT 60.039 50.0 6.17 0.00 39.71 2.66 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1185 4891 0.246635 TGAGCAGCTTACCTTCGGTC 59.753 55.0 0.00 0.00 37.09 4.79 R
2319 6417 0.179059 TTGAGAGTGCCGCACTTTGA 60.179 50.0 26.38 13.24 45.44 2.69 R
3130 7830 0.032130 GCGCCATTGATACGAGGAGA 59.968 55.0 0.00 0.00 0.00 3.71 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
29 3694 2.887152 AGGTGTTTGTTGATCTCCTTGC 59.113 45.455 0.00 0.00 0.00 4.01
39 3704 0.610232 ATCTCCTTGCTTGTGTGGGC 60.610 55.000 0.00 0.00 0.00 5.36
68 3733 2.904434 AGTGGTCCTAGTAAGGTTGTGG 59.096 50.000 0.00 0.00 44.09 4.17
69 3734 1.626825 TGGTCCTAGTAAGGTTGTGGC 59.373 52.381 0.00 0.00 44.09 5.01
70 3735 1.405121 GGTCCTAGTAAGGTTGTGGCG 60.405 57.143 0.00 0.00 44.09 5.69
89 3754 2.124983 CGATGTGGGCTCAGTGGG 60.125 66.667 0.00 0.00 0.00 4.61
115 3780 1.699634 TCTTCAACAAGGTCTGAGGGG 59.300 52.381 0.00 0.00 0.00 4.79
130 3795 4.934989 GGGGGTACAGAGCGAAAG 57.065 61.111 0.00 0.00 0.00 2.62
184 3849 1.356938 GTGTCGAAGAATTCCCGGTC 58.643 55.000 15.07 10.49 43.81 4.79
186 3851 0.171903 GTCGAAGAATTCCCGGTCGA 59.828 55.000 15.07 14.42 43.81 4.20
207 3872 4.976925 CGGCTCCCTATGCAGCGG 62.977 72.222 0.00 0.00 36.41 5.52
221 3886 1.202114 GCAGCGGAGAGATAGAGATGG 59.798 57.143 0.00 0.00 0.00 3.51
480 4145 1.739929 CACCGGCTGCGTTGACATA 60.740 57.895 0.00 0.00 0.00 2.29
496 4161 5.999205 TGACATATTTTGCCATTTGGACT 57.001 34.783 0.00 0.00 37.39 3.85
504 4169 3.159213 TGCCATTTGGACTTGATGAGT 57.841 42.857 0.00 0.00 42.70 3.41
509 4174 1.067295 TTGGACTTGATGAGTGGGCT 58.933 50.000 0.00 0.00 39.19 5.19
514 4179 0.747283 CTTGATGAGTGGGCTCCAGC 60.747 60.000 0.00 0.00 40.95 4.85
527 4192 2.012673 GCTCCAGCTGTCATAAACCTG 58.987 52.381 13.81 0.00 38.21 4.00
546 4211 5.630121 ACCTGATCAAATGTTAACCACTCA 58.370 37.500 2.48 0.00 0.00 3.41
557 4222 2.610438 AACCACTCAGCCATTTGGAT 57.390 45.000 0.00 0.00 37.39 3.41
558 4223 2.610438 ACCACTCAGCCATTTGGATT 57.390 45.000 0.00 0.00 37.39 3.01
559 4224 2.893424 ACCACTCAGCCATTTGGATTT 58.107 42.857 0.00 0.00 37.39 2.17
585 4250 4.829064 TTGAAACAGCTAACCACACATC 57.171 40.909 0.00 0.00 0.00 3.06
587 4252 5.222079 TGAAACAGCTAACCACACATCTA 57.778 39.130 0.00 0.00 0.00 1.98
596 4272 3.462483 ACCACACATCTACGACAAACA 57.538 42.857 0.00 0.00 0.00 2.83
604 4280 8.839914 CACACATCTACGACAAACAAAAATATG 58.160 33.333 0.00 0.00 0.00 1.78
633 4309 5.873146 TTTTGAAACCCTAACCCGAAAAT 57.127 34.783 0.00 0.00 0.00 1.82
638 4314 2.521126 ACCCTAACCCGAAAATTGGTG 58.479 47.619 0.00 0.00 34.34 4.17
653 4329 9.511144 CGAAAATTGGTGGTTTTATACTATTCC 57.489 33.333 0.00 0.00 0.00 3.01
662 4338 5.470437 GGTTTTATACTATTCCCTCAGCTGC 59.530 44.000 9.47 0.00 0.00 5.25
686 4362 2.728007 GAGAGGTCTCCCCCAATTTTG 58.272 52.381 0.00 0.00 37.02 2.44
687 4363 2.041755 GAGAGGTCTCCCCCAATTTTGT 59.958 50.000 0.00 0.00 37.02 2.83
690 4366 1.544246 GGTCTCCCCCAATTTTGTTCG 59.456 52.381 0.00 0.00 0.00 3.95
692 4368 3.414269 GTCTCCCCCAATTTTGTTCGTA 58.586 45.455 0.00 0.00 0.00 3.43
771 4447 5.225642 AGAGCAAAAATAGTGAAAAGCAGC 58.774 37.500 0.00 0.00 0.00 5.25
793 4469 6.317391 CAGCAAAGGATAAAGAGTAAAGGAGG 59.683 42.308 0.00 0.00 0.00 4.30
794 4470 5.066634 GCAAAGGATAAAGAGTAAAGGAGGC 59.933 44.000 0.00 0.00 0.00 4.70
795 4471 5.375283 AAGGATAAAGAGTAAAGGAGGCC 57.625 43.478 0.00 0.00 0.00 5.19
796 4472 3.388350 AGGATAAAGAGTAAAGGAGGCCG 59.612 47.826 0.00 0.00 0.00 6.13
797 4473 3.494573 GGATAAAGAGTAAAGGAGGCCGG 60.495 52.174 0.00 0.00 0.00 6.13
858 4556 4.018195 TGGGGACAAAAGCCCTCT 57.982 55.556 0.00 0.00 45.30 3.69
865 4563 3.368427 GGGACAAAAGCCCTCTAAATTGC 60.368 47.826 0.00 0.00 42.56 3.56
1158 4864 1.152652 ATCGCCGGGATGTCTCTCT 60.153 57.895 2.18 0.00 32.92 3.10
1365 5091 9.702494 ATTTTCTTGACCTTGAATTCTTGATTC 57.298 29.630 7.05 0.00 43.67 2.52
1404 5141 2.202987 GTGCCATCCTCAGGAGCG 60.203 66.667 0.00 0.00 34.05 5.03
1445 5188 1.021202 CGTTTGTCAAGAACCAGCCA 58.979 50.000 0.00 0.00 0.00 4.75
1447 5190 2.541588 CGTTTGTCAAGAACCAGCCAAG 60.542 50.000 0.00 0.00 0.00 3.61
1463 5206 2.398588 CCAAGCCTACAGGTAGATGGA 58.601 52.381 8.01 0.00 35.30 3.41
1537 5280 0.537653 GTAAGCTCTGGGTCTGGGAC 59.462 60.000 0.00 0.00 0.00 4.46
1568 5311 8.784043 GTGAGGTGTAAAGAACAGTTTATGATT 58.216 33.333 0.00 0.00 39.29 2.57
1595 5338 4.889856 TGGACGATCATGCCGGCG 62.890 66.667 23.90 8.74 35.53 6.46
1602 5345 4.794439 TCATGCCGGCGTCGACTG 62.794 66.667 20.90 7.47 39.00 3.51
1631 5374 0.179045 AGTCGCTGGCTCACAACTTT 60.179 50.000 0.00 0.00 0.00 2.66
1675 5424 2.972713 ACTTTGAGGAGCTGGAAGTGTA 59.027 45.455 0.00 0.00 35.30 2.90
1699 5448 2.893398 CTGGACGGAGGTAGCACC 59.107 66.667 0.00 0.00 38.99 5.01
1732 5481 3.653344 GCTTCGGGCTCTTTTCAATTTT 58.347 40.909 0.00 0.00 38.06 1.82
1794 5545 0.107459 GATGCAGAGGAGGGGTGAAC 60.107 60.000 0.00 0.00 0.00 3.18
1798 5549 0.615850 CAGAGGAGGGGTGAACCTTC 59.384 60.000 0.00 0.00 44.32 3.46
1804 5555 3.283259 GAGGGGTGAACCTTCCTATTG 57.717 52.381 0.00 0.00 42.10 1.90
1805 5556 2.844348 GAGGGGTGAACCTTCCTATTGA 59.156 50.000 0.00 0.00 42.10 2.57
1806 5557 3.265489 AGGGGTGAACCTTCCTATTGAA 58.735 45.455 0.00 0.00 37.69 2.69
1906 6004 0.820871 AGGCTTCTCTGTCATCGGAC 59.179 55.000 0.00 0.00 44.57 4.79
1924 6022 4.647399 TCGGACACCATATTCACTGATGTA 59.353 41.667 0.00 0.00 0.00 2.29
1966 6064 0.463295 ATCAGGATGCTCTTGCCACG 60.463 55.000 0.00 0.00 38.71 4.94
1994 6092 6.573664 AACCGATCATCAACAAGAAAATCA 57.426 33.333 0.00 0.00 0.00 2.57
2025 6123 0.818296 AGTGAAGATTCCGGACCTCG 59.182 55.000 1.83 0.00 38.88 4.63
2053 6151 4.035324 CCACTAGAATGCAAGATCAAGCTG 59.965 45.833 10.23 0.00 0.00 4.24
2062 6160 5.434408 TGCAAGATCAAGCTGTTCTATGAT 58.566 37.500 10.23 0.00 35.33 2.45
2067 6165 2.507058 TCAAGCTGTTCTATGATGGGCT 59.493 45.455 0.00 0.00 0.00 5.19
2129 6227 3.149196 GTTGATCTGCTCCTTGGTTTCA 58.851 45.455 0.00 0.00 0.00 2.69
2168 6266 5.124457 GGCTGTGTGATCAAGAACATGTATT 59.876 40.000 0.00 0.00 0.00 1.89
2192 6290 1.679305 GGCGTCACCTCTCCTCTGA 60.679 63.158 0.00 0.00 34.51 3.27
2193 6291 1.040339 GGCGTCACCTCTCCTCTGAT 61.040 60.000 0.00 0.00 34.51 2.90
2239 6337 0.039437 ACATCAGCGTCGTCGAACTT 60.039 50.000 6.17 0.00 39.71 2.66
2242 6340 0.240145 TCAGCGTCGTCGAACTTGAT 59.760 50.000 6.17 0.00 39.71 2.57
2261 6359 1.908344 TGCAGCAGGCTTCATAACAA 58.092 45.000 0.00 0.00 45.15 2.83
2262 6360 2.237643 TGCAGCAGGCTTCATAACAAA 58.762 42.857 0.00 0.00 45.15 2.83
2312 6410 1.538135 ACCCCTTAGCCCGTTCAGT 60.538 57.895 0.00 0.00 0.00 3.41
2321 6419 2.661537 CCGTTCAGTGTGCGCTCA 60.662 61.111 9.73 8.97 0.00 4.26
2372 6470 3.056465 TGGAACCGAAAAATTACATGGGC 60.056 43.478 0.00 0.00 0.00 5.36
2456 6554 3.254411 TGGTGAGCGATGATCTACTGATC 59.746 47.826 0.00 0.00 46.89 2.92
2524 6622 1.719780 CAAGGCTAACGTTGTCGAGAC 59.280 52.381 11.99 1.66 40.62 3.36
2667 6780 3.669036 CTCGAGGACACCGCTGACG 62.669 68.421 3.91 0.00 39.67 4.35
2682 6795 1.661617 CTGACGGACGTGTTGAACAAA 59.338 47.619 0.00 0.00 0.00 2.83
2794 6907 1.150536 ACCATTGCCACCGTCAAGT 59.849 52.632 0.00 0.00 0.00 3.16
2853 6966 2.927477 TCGTCATGAATTGTTCTACGGC 59.073 45.455 0.00 0.00 34.31 5.68
2855 6968 3.242091 CGTCATGAATTGTTCTACGGCAG 60.242 47.826 0.00 0.00 31.89 4.85
2871 6984 2.476241 CGGCAGCAAAATTTTGGAAGAC 59.524 45.455 27.60 13.53 38.57 3.01
2920 7033 3.012518 GTCAGCAAATGTAGCATCACCT 58.987 45.455 0.00 0.00 0.00 4.00
2921 7034 3.011818 TCAGCAAATGTAGCATCACCTG 58.988 45.455 0.00 0.00 0.00 4.00
2935 7048 1.798223 TCACCTGCGAATTTCGTCAAG 59.202 47.619 19.10 13.78 42.81 3.02
2978 7091 1.083489 CGTTTGGTATGATGCGTGGT 58.917 50.000 0.00 0.00 0.00 4.16
2979 7092 1.062002 CGTTTGGTATGATGCGTGGTC 59.938 52.381 0.00 0.00 0.00 4.02
2980 7093 1.062002 GTTTGGTATGATGCGTGGTCG 59.938 52.381 0.00 0.00 40.37 4.79
2981 7094 0.533032 TTGGTATGATGCGTGGTCGA 59.467 50.000 0.00 0.00 39.71 4.20
2997 7110 2.412325 GGTCGATCGTGCAATCGTTTTT 60.412 45.455 15.94 0.00 46.64 1.94
3021 7721 1.285078 ACCTAAAGAATCACCTGGCCC 59.715 52.381 0.00 0.00 0.00 5.80
3029 7729 1.595311 ATCACCTGGCCCAATACAGA 58.405 50.000 0.00 0.00 36.86 3.41
3030 7730 1.367346 TCACCTGGCCCAATACAGAA 58.633 50.000 0.00 0.00 36.86 3.02
3031 7731 1.281867 TCACCTGGCCCAATACAGAAG 59.718 52.381 0.00 0.00 36.86 2.85
3033 7733 0.753111 CCTGGCCCAATACAGAAGCC 60.753 60.000 0.00 0.00 44.13 4.35
3034 7734 0.753111 CTGGCCCAATACAGAAGCCC 60.753 60.000 0.00 0.00 43.18 5.19
3035 7735 1.214305 TGGCCCAATACAGAAGCCCT 61.214 55.000 0.00 0.00 43.18 5.19
3037 7737 1.387295 GCCCAATACAGAAGCCCTGC 61.387 60.000 3.85 0.00 46.81 4.85
3038 7738 0.257039 CCCAATACAGAAGCCCTGCT 59.743 55.000 3.85 0.00 46.81 4.24
3039 7739 1.490490 CCCAATACAGAAGCCCTGCTA 59.510 52.381 3.85 0.00 46.81 3.49
3040 7740 2.565841 CCAATACAGAAGCCCTGCTAC 58.434 52.381 3.85 0.00 46.81 3.58
3041 7741 2.171448 CCAATACAGAAGCCCTGCTACT 59.829 50.000 3.85 0.00 46.81 2.57
3042 7742 3.388024 CCAATACAGAAGCCCTGCTACTA 59.612 47.826 3.85 0.00 46.81 1.82
3043 7743 4.040952 CCAATACAGAAGCCCTGCTACTAT 59.959 45.833 3.85 0.00 46.81 2.12
3044 7744 5.455326 CCAATACAGAAGCCCTGCTACTATT 60.455 44.000 3.85 0.00 46.81 1.73
3045 7745 5.896073 ATACAGAAGCCCTGCTACTATTT 57.104 39.130 3.85 0.00 46.81 1.40
3046 7746 4.143986 ACAGAAGCCCTGCTACTATTTC 57.856 45.455 3.85 0.00 46.81 2.17
3047 7747 3.777522 ACAGAAGCCCTGCTACTATTTCT 59.222 43.478 3.85 0.00 46.81 2.52
3048 7748 4.226168 ACAGAAGCCCTGCTACTATTTCTT 59.774 41.667 3.85 0.00 46.81 2.52
3049 7749 5.189180 CAGAAGCCCTGCTACTATTTCTTT 58.811 41.667 0.00 0.00 38.25 2.52
3050 7750 5.649831 CAGAAGCCCTGCTACTATTTCTTTT 59.350 40.000 0.00 0.00 38.25 2.27
3051 7751 5.883115 AGAAGCCCTGCTACTATTTCTTTTC 59.117 40.000 0.00 0.00 38.25 2.29
3052 7752 5.443230 AGCCCTGCTACTATTTCTTTTCT 57.557 39.130 0.00 0.00 36.99 2.52
3053 7753 5.821097 AGCCCTGCTACTATTTCTTTTCTT 58.179 37.500 0.00 0.00 36.99 2.52
3054 7754 6.249192 AGCCCTGCTACTATTTCTTTTCTTT 58.751 36.000 0.00 0.00 36.99 2.52
3055 7755 6.151817 AGCCCTGCTACTATTTCTTTTCTTTG 59.848 38.462 0.00 0.00 36.99 2.77
3056 7756 6.151144 GCCCTGCTACTATTTCTTTTCTTTGA 59.849 38.462 0.00 0.00 0.00 2.69
3057 7757 7.530863 CCCTGCTACTATTTCTTTTCTTTGAC 58.469 38.462 0.00 0.00 0.00 3.18
3058 7758 7.237173 CCTGCTACTATTTCTTTTCTTTGACG 58.763 38.462 0.00 0.00 0.00 4.35
3059 7759 7.095187 CCTGCTACTATTTCTTTTCTTTGACGT 60.095 37.037 0.00 0.00 0.00 4.34
3060 7760 7.572759 TGCTACTATTTCTTTTCTTTGACGTG 58.427 34.615 0.00 0.00 0.00 4.49
3061 7761 6.520104 GCTACTATTTCTTTTCTTTGACGTGC 59.480 38.462 0.00 0.00 0.00 5.34
3062 7762 5.758924 ACTATTTCTTTTCTTTGACGTGCC 58.241 37.500 0.00 0.00 0.00 5.01
3063 7763 4.918810 ATTTCTTTTCTTTGACGTGCCT 57.081 36.364 0.00 0.00 0.00 4.75
3064 7764 6.708949 ACTATTTCTTTTCTTTGACGTGCCTA 59.291 34.615 0.00 0.00 0.00 3.93
3065 7765 5.418310 TTTCTTTTCTTTGACGTGCCTAG 57.582 39.130 0.00 0.00 0.00 3.02
3066 7766 4.067972 TCTTTTCTTTGACGTGCCTAGT 57.932 40.909 0.00 0.00 0.00 2.57
3067 7767 5.204409 TCTTTTCTTTGACGTGCCTAGTA 57.796 39.130 0.00 0.00 0.00 1.82
3068 7768 4.986659 TCTTTTCTTTGACGTGCCTAGTAC 59.013 41.667 0.00 0.00 0.00 2.73
3080 7780 7.919091 TGACGTGCCTAGTACTATTTCTTATTG 59.081 37.037 2.33 0.00 0.00 1.90
3089 7789 8.910351 AGTACTATTTCTTATTGGAATCCAGC 57.090 34.615 0.86 0.00 33.81 4.85
3090 7790 7.939588 AGTACTATTTCTTATTGGAATCCAGCC 59.060 37.037 0.86 0.00 33.81 4.85
3092 7792 4.329638 TTTCTTATTGGAATCCAGCCCA 57.670 40.909 0.86 0.00 33.81 5.36
3093 7793 3.297134 TCTTATTGGAATCCAGCCCAC 57.703 47.619 0.86 0.00 33.81 4.61
3094 7794 2.580322 TCTTATTGGAATCCAGCCCACA 59.420 45.455 0.86 0.00 33.81 4.17
3095 7795 2.734755 TATTGGAATCCAGCCCACAG 57.265 50.000 0.86 0.00 33.81 3.66
3096 7796 0.685458 ATTGGAATCCAGCCCACAGC 60.685 55.000 0.86 0.00 44.25 4.40
3107 7807 2.037136 CCCACAGCTGCTTCCTTCG 61.037 63.158 15.27 0.00 0.00 3.79
3108 7808 1.004560 CCACAGCTGCTTCCTTCGA 60.005 57.895 15.27 0.00 0.00 3.71
3109 7809 0.392193 CCACAGCTGCTTCCTTCGAT 60.392 55.000 15.27 0.00 0.00 3.59
3110 7810 1.005340 CACAGCTGCTTCCTTCGATC 58.995 55.000 15.27 0.00 0.00 3.69
3111 7811 0.107945 ACAGCTGCTTCCTTCGATCC 60.108 55.000 15.27 0.00 0.00 3.36
3112 7812 0.177604 CAGCTGCTTCCTTCGATCCT 59.822 55.000 0.00 0.00 0.00 3.24
3115 7815 0.249238 CTGCTTCCTTCGATCCTCGG 60.249 60.000 0.00 0.00 40.88 4.63
3116 7816 1.592939 GCTTCCTTCGATCCTCGGC 60.593 63.158 0.00 0.00 40.88 5.54
3117 7817 1.068250 CTTCCTTCGATCCTCGGCC 59.932 63.158 0.00 0.00 40.88 6.13
3118 7818 2.685387 CTTCCTTCGATCCTCGGCCG 62.685 65.000 22.12 22.12 40.88 6.13
3119 7819 4.951963 CCTTCGATCCTCGGCCGC 62.952 72.222 23.51 4.66 40.88 6.53
3120 7820 3.905678 CTTCGATCCTCGGCCGCT 61.906 66.667 23.51 4.40 40.88 5.52
3121 7821 3.832720 CTTCGATCCTCGGCCGCTC 62.833 68.421 23.51 13.18 40.88 5.03
3122 7822 4.877619 TCGATCCTCGGCCGCTCT 62.878 66.667 23.51 4.40 40.88 4.09
3123 7823 4.637489 CGATCCTCGGCCGCTCTG 62.637 72.222 23.51 10.27 36.00 3.35
3124 7824 4.292178 GATCCTCGGCCGCTCTGG 62.292 72.222 23.51 19.09 42.50 3.86
3125 7825 4.841617 ATCCTCGGCCGCTCTGGA 62.842 66.667 23.51 23.56 42.00 3.86
3128 7828 3.898509 CTCGGCCGCTCTGGAGAG 61.899 72.222 23.51 5.96 44.75 3.20
3129 7829 4.426313 TCGGCCGCTCTGGAGAGA 62.426 66.667 23.51 0.00 44.74 3.10
3130 7830 3.222855 CGGCCGCTCTGGAGAGAT 61.223 66.667 14.67 0.00 44.74 2.75
3131 7831 2.733945 GGCCGCTCTGGAGAGATC 59.266 66.667 7.89 0.00 44.74 2.75
3132 7832 1.832167 GGCCGCTCTGGAGAGATCT 60.832 63.158 7.89 0.00 44.74 2.75
3133 7833 1.659794 GCCGCTCTGGAGAGATCTC 59.340 63.158 15.29 15.29 44.74 2.75
3148 7848 2.230025 AGATCTCCTCGTATCAATGGCG 59.770 50.000 0.00 0.00 0.00 5.69
3152 7852 1.151777 CCTCGTATCAATGGCGCGTT 61.152 55.000 8.43 0.00 0.00 4.84
3157 7857 3.671459 TCGTATCAATGGCGCGTTATTAG 59.329 43.478 8.43 4.64 0.00 1.73
3158 7858 3.181534 CGTATCAATGGCGCGTTATTAGG 60.182 47.826 8.43 0.00 0.00 2.69
3163 7863 0.462937 TGGCGCGTTATTAGGCACAT 60.463 50.000 8.43 0.00 35.49 3.21
3166 7873 1.862201 GCGCGTTATTAGGCACATACA 59.138 47.619 8.43 0.00 34.90 2.29
3168 7875 3.242478 GCGCGTTATTAGGCACATACAAA 60.242 43.478 8.43 0.00 34.90 2.83
3169 7876 4.268522 CGCGTTATTAGGCACATACAAAC 58.731 43.478 0.00 0.00 34.90 2.93
3171 7878 5.632959 GCGTTATTAGGCACATACAAACAA 58.367 37.500 0.00 0.00 35.30 2.83
3173 7880 6.604012 CGTTATTAGGCACATACAAACAACA 58.396 36.000 0.00 0.00 0.00 3.33
3174 7881 7.078851 CGTTATTAGGCACATACAAACAACAA 58.921 34.615 0.00 0.00 0.00 2.83
3175 7882 7.753132 CGTTATTAGGCACATACAAACAACAAT 59.247 33.333 0.00 0.00 0.00 2.71
3177 7884 4.519540 AGGCACATACAAACAACAATCC 57.480 40.909 0.00 0.00 0.00 3.01
3178 7885 4.151883 AGGCACATACAAACAACAATCCT 58.848 39.130 0.00 0.00 0.00 3.24
3179 7886 5.321102 AGGCACATACAAACAACAATCCTA 58.679 37.500 0.00 0.00 0.00 2.94
3180 7887 5.183140 AGGCACATACAAACAACAATCCTAC 59.817 40.000 0.00 0.00 0.00 3.18
3181 7888 5.086058 GCACATACAAACAACAATCCTACG 58.914 41.667 0.00 0.00 0.00 3.51
3184 7891 7.526608 CACATACAAACAACAATCCTACGAAT 58.473 34.615 0.00 0.00 0.00 3.34
3189 7896 8.385898 ACAAACAACAATCCTACGAATAAAGA 57.614 30.769 0.00 0.00 0.00 2.52
3193 7900 7.985476 ACAACAATCCTACGAATAAAGAATGG 58.015 34.615 0.00 0.00 0.00 3.16
3201 7908 4.389374 ACGAATAAAGAATGGGATGCGAT 58.611 39.130 0.00 0.00 0.00 4.58
3202 7909 4.452455 ACGAATAAAGAATGGGATGCGATC 59.548 41.667 0.00 0.00 0.00 3.69
3203 7910 4.434725 CGAATAAAGAATGGGATGCGATCG 60.435 45.833 11.69 11.69 0.00 3.69
3207 7914 1.621301 GAATGGGATGCGATCGCGAG 61.621 60.000 32.64 2.31 44.36 5.03
3215 7922 0.179137 TGCGATCGCGAGACAAGAAT 60.179 50.000 32.64 0.00 46.97 2.40
3219 7926 2.791560 CGATCGCGAGACAAGAATGAAT 59.208 45.455 16.66 0.00 46.97 2.57
3220 7927 3.361435 CGATCGCGAGACAAGAATGAATG 60.361 47.826 16.66 0.00 46.97 2.67
3223 7930 3.993736 TCGCGAGACAAGAATGAATGAAA 59.006 39.130 3.71 0.00 33.31 2.69
3224 7931 4.450757 TCGCGAGACAAGAATGAATGAAAA 59.549 37.500 3.71 0.00 33.31 2.29
3225 7932 4.551126 CGCGAGACAAGAATGAATGAAAAC 59.449 41.667 0.00 0.00 0.00 2.43
3227 7934 5.914635 GCGAGACAAGAATGAATGAAAACAA 59.085 36.000 0.00 0.00 0.00 2.83
3228 7935 6.129352 GCGAGACAAGAATGAATGAAAACAAC 60.129 38.462 0.00 0.00 0.00 3.32
3229 7936 6.085458 CGAGACAAGAATGAATGAAAACAACG 59.915 38.462 0.00 0.00 0.00 4.10
3512 8283 2.111878 CATCATCCCGACCCTGCC 59.888 66.667 0.00 0.00 0.00 4.85
3513 8284 2.040464 ATCATCCCGACCCTGCCT 60.040 61.111 0.00 0.00 0.00 4.75
3514 8285 2.143419 ATCATCCCGACCCTGCCTC 61.143 63.158 0.00 0.00 0.00 4.70
3515 8286 4.227134 CATCCCGACCCTGCCTCG 62.227 72.222 0.00 0.00 0.00 4.63
3560 8331 0.603439 GTTCGCGTTAGGGTTTGGGA 60.603 55.000 5.77 0.00 0.00 4.37
3562 8333 1.004200 CGCGTTAGGGTTTGGGACT 60.004 57.895 0.00 0.00 0.00 3.85
3563 8334 0.604511 CGCGTTAGGGTTTGGGACTT 60.605 55.000 0.00 0.00 0.00 3.01
3564 8335 1.612676 GCGTTAGGGTTTGGGACTTT 58.387 50.000 0.00 0.00 0.00 2.66
3565 8336 1.268625 GCGTTAGGGTTTGGGACTTTG 59.731 52.381 0.00 0.00 0.00 2.77
3582 8353 4.335584 GGATCGCGGCGAGAGAGG 62.336 72.222 29.64 0.00 39.91 3.69
3615 8408 5.984926 TCGTAGCCGTTTTATTTATACAGGG 59.015 40.000 0.00 0.00 35.01 4.45
3755 8587 7.174946 CCGCTCACTAATTCCACCATTATTATT 59.825 37.037 0.00 0.00 0.00 1.40
3756 8588 9.214957 CGCTCACTAATTCCACCATTATTATTA 57.785 33.333 0.00 0.00 0.00 0.98
3800 8632 1.401552 TGATGGCGCAGTGCTATTTTC 59.598 47.619 14.33 4.46 45.89 2.29
3807 8639 2.096496 CGCAGTGCTATTTTCTTCCCTG 59.904 50.000 14.33 0.00 0.00 4.45
3812 8646 4.400567 AGTGCTATTTTCTTCCCTGCATTC 59.599 41.667 0.00 0.00 0.00 2.67
3830 8664 5.878332 CATTCATGCACTGGTAGTACAAA 57.122 39.130 2.06 0.00 0.00 2.83
3831 8665 6.252967 CATTCATGCACTGGTAGTACAAAA 57.747 37.500 2.06 0.00 0.00 2.44
3832 8666 6.676950 CATTCATGCACTGGTAGTACAAAAA 58.323 36.000 2.06 0.00 0.00 1.94
3928 8762 9.743057 TTGTCATTAAGTGTTGATTAAAACTGG 57.257 29.630 0.00 0.00 0.00 4.00
3929 8763 9.126151 TGTCATTAAGTGTTGATTAAAACTGGA 57.874 29.630 0.00 0.00 0.00 3.86
3936 8770 9.533253 AAGTGTTGATTAAAACTGGATTTCTTG 57.467 29.630 0.00 0.00 0.00 3.02
3937 8771 8.695456 AGTGTTGATTAAAACTGGATTTCTTGT 58.305 29.630 0.00 0.00 0.00 3.16
3938 8772 8.755018 GTGTTGATTAAAACTGGATTTCTTGTG 58.245 33.333 0.00 0.00 0.00 3.33
3939 8773 7.925483 TGTTGATTAAAACTGGATTTCTTGTGG 59.075 33.333 0.00 0.00 0.00 4.17
3940 8774 6.454795 TGATTAAAACTGGATTTCTTGTGGC 58.545 36.000 0.00 0.00 0.00 5.01
3941 8775 6.267471 TGATTAAAACTGGATTTCTTGTGGCT 59.733 34.615 0.00 0.00 0.00 4.75
3942 8776 7.450014 TGATTAAAACTGGATTTCTTGTGGCTA 59.550 33.333 0.00 0.00 0.00 3.93
3943 8777 7.775053 TTAAAACTGGATTTCTTGTGGCTAT 57.225 32.000 0.00 0.00 0.00 2.97
3944 8778 8.871629 TTAAAACTGGATTTCTTGTGGCTATA 57.128 30.769 0.00 0.00 0.00 1.31
3945 8779 7.775053 AAAACTGGATTTCTTGTGGCTATAA 57.225 32.000 0.00 0.00 0.00 0.98
3946 8780 7.775053 AAACTGGATTTCTTGTGGCTATAAA 57.225 32.000 0.00 0.00 0.00 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 0.521735 GATCAACAAACACCTCCGCC 59.478 55.000 0.00 0.00 0.00 6.13
5 6 2.076863 GGAGATCAACAAACACCTCCG 58.923 52.381 0.00 0.00 32.06 4.63
6 7 3.425162 AGGAGATCAACAAACACCTCC 57.575 47.619 0.00 0.00 40.21 4.30
7 8 3.057946 GCAAGGAGATCAACAAACACCTC 60.058 47.826 0.00 0.00 0.00 3.85
8 9 2.887152 GCAAGGAGATCAACAAACACCT 59.113 45.455 0.00 0.00 0.00 4.00
9 10 2.887152 AGCAAGGAGATCAACAAACACC 59.113 45.455 0.00 0.00 0.00 4.16
10 11 4.202050 ACAAGCAAGGAGATCAACAAACAC 60.202 41.667 0.00 0.00 0.00 3.32
11 12 3.953612 ACAAGCAAGGAGATCAACAAACA 59.046 39.130 0.00 0.00 0.00 2.83
12 13 4.202050 ACACAAGCAAGGAGATCAACAAAC 60.202 41.667 0.00 0.00 0.00 2.93
13 14 3.953612 ACACAAGCAAGGAGATCAACAAA 59.046 39.130 0.00 0.00 0.00 2.83
14 15 3.316029 CACACAAGCAAGGAGATCAACAA 59.684 43.478 0.00 0.00 0.00 2.83
15 16 2.880268 CACACAAGCAAGGAGATCAACA 59.120 45.455 0.00 0.00 0.00 3.33
16 17 2.227388 CCACACAAGCAAGGAGATCAAC 59.773 50.000 0.00 0.00 0.00 3.18
29 3694 1.171308 CTCTCCATTGCCCACACAAG 58.829 55.000 0.00 0.00 31.96 3.16
39 3704 4.100189 CCTTACTAGGACCACTCTCCATTG 59.900 50.000 0.00 0.00 45.05 2.82
69 3734 4.457496 ACTGAGCCCACATCGCCG 62.457 66.667 0.00 0.00 0.00 6.46
70 3735 2.821366 CACTGAGCCCACATCGCC 60.821 66.667 0.00 0.00 0.00 5.54
89 3754 0.591659 GACCTTGTTGAAGAACCCGC 59.408 55.000 0.00 0.00 0.00 6.13
96 3761 1.271597 CCCCCTCAGACCTTGTTGAAG 60.272 57.143 0.00 0.00 0.00 3.02
115 3780 1.202428 CCTAGCTTTCGCTCTGTACCC 60.202 57.143 0.00 0.00 45.15 3.69
121 3786 2.202810 GCGCCTAGCTTTCGCTCT 60.203 61.111 16.25 0.00 45.15 4.09
133 3798 4.732106 GCGAACACTATAGCGCCT 57.268 55.556 2.29 0.00 43.33 5.52
141 3806 0.956633 AGGAACTCGTGCGAACACTA 59.043 50.000 0.00 0.00 45.10 2.74
151 3816 3.222354 GACACCGCCAGGAACTCGT 62.222 63.158 0.00 0.00 41.02 4.18
153 3818 2.430382 TTCGACACCGCCAGGAACTC 62.430 60.000 0.00 0.00 41.02 3.01
184 3849 4.647615 CATAGGGAGCCGCCGTCG 62.648 72.222 0.00 0.00 37.63 5.12
199 3864 2.284754 TCTCTATCTCTCCGCTGCAT 57.715 50.000 0.00 0.00 0.00 3.96
463 4128 0.392461 AATATGTCAACGCAGCCGGT 60.392 50.000 1.90 0.00 39.22 5.28
464 4129 0.732571 AAATATGTCAACGCAGCCGG 59.267 50.000 0.00 0.00 39.22 6.13
465 4130 2.176369 CAAAATATGTCAACGCAGCCG 58.824 47.619 0.00 0.00 41.14 5.52
466 4131 1.919918 GCAAAATATGTCAACGCAGCC 59.080 47.619 0.00 0.00 0.00 4.85
467 4132 1.919918 GGCAAAATATGTCAACGCAGC 59.080 47.619 0.00 0.00 32.41 5.25
468 4133 3.214697 TGGCAAAATATGTCAACGCAG 57.785 42.857 0.00 0.00 41.69 5.18
480 4145 5.012354 ACTCATCAAGTCCAAATGGCAAAAT 59.988 36.000 0.00 0.00 30.02 1.82
496 4161 1.203441 AGCTGGAGCCCACTCATCAA 61.203 55.000 0.00 0.00 45.42 2.57
504 4169 0.991146 TTTATGACAGCTGGAGCCCA 59.009 50.000 19.93 7.97 43.38 5.36
509 4174 3.519107 TGATCAGGTTTATGACAGCTGGA 59.481 43.478 19.93 4.16 39.73 3.86
514 4179 9.559958 GTTAACATTTGATCAGGTTTATGACAG 57.440 33.333 12.70 0.00 30.46 3.51
527 4192 4.458989 TGGCTGAGTGGTTAACATTTGATC 59.541 41.667 8.10 0.00 0.00 2.92
572 4237 3.226346 TGTCGTAGATGTGTGGTTAGC 57.774 47.619 0.00 0.00 40.67 3.09
613 4289 4.039366 CCAATTTTCGGGTTAGGGTTTCAA 59.961 41.667 0.00 0.00 0.00 2.69
627 4303 9.511144 GGAATAGTATAAAACCACCAATTTTCG 57.489 33.333 0.00 0.00 31.79 3.46
633 4309 7.273457 TGAGGGAATAGTATAAAACCACCAA 57.727 36.000 0.00 0.00 0.00 3.67
638 4314 5.470437 GCAGCTGAGGGAATAGTATAAAACC 59.530 44.000 20.43 0.00 0.00 3.27
653 4329 2.733669 CCTCTCCCAGCAGCTGAGG 61.734 68.421 24.90 21.48 38.38 3.86
678 4354 6.324819 AGATTGATGCTACGAACAAAATTGG 58.675 36.000 0.00 0.00 0.00 3.16
686 4362 7.436673 ACTTATTCAGAGATTGATGCTACGAAC 59.563 37.037 0.00 0.00 35.27 3.95
687 4363 7.436376 CACTTATTCAGAGATTGATGCTACGAA 59.564 37.037 0.00 0.00 35.27 3.85
690 4366 8.654230 TTCACTTATTCAGAGATTGATGCTAC 57.346 34.615 0.00 0.00 35.27 3.58
692 4368 7.563020 TCTTCACTTATTCAGAGATTGATGCT 58.437 34.615 0.00 0.00 35.27 3.79
744 4420 7.584987 TGCTTTTCACTATTTTTGCTCTACTC 58.415 34.615 0.00 0.00 0.00 2.59
771 4447 5.590663 GGCCTCCTTTACTCTTTATCCTTTG 59.409 44.000 0.00 0.00 0.00 2.77
793 4469 2.526120 GCGATTACACTGAGCCGGC 61.526 63.158 21.89 21.89 0.00 6.13
794 4470 1.153647 TGCGATTACACTGAGCCGG 60.154 57.895 0.00 0.00 0.00 6.13
795 4471 1.999051 GTGCGATTACACTGAGCCG 59.001 57.895 0.00 0.00 37.58 5.52
855 4553 1.213926 AGCAGAGGGGGCAATTTAGAG 59.786 52.381 0.00 0.00 0.00 2.43
858 4556 2.621556 AAAGCAGAGGGGGCAATTTA 57.378 45.000 0.00 0.00 0.00 1.40
865 4563 0.253327 GTGGAGTAAAGCAGAGGGGG 59.747 60.000 0.00 0.00 0.00 5.40
1041 4747 4.719616 GCGAACAGCACGCGGTTC 62.720 66.667 20.60 20.60 46.05 3.62
1078 4784 0.681564 AAGCTGAGGAGGACGTCGAT 60.682 55.000 9.92 0.00 34.17 3.59
1152 4858 2.360844 CTGTCGCAGAGGTTAGAGAGA 58.639 52.381 1.18 0.00 36.95 3.10
1158 4864 1.211969 GACGCTGTCGCAGAGGTTA 59.788 57.895 10.46 0.00 36.95 2.85
1185 4891 0.246635 TGAGCAGCTTACCTTCGGTC 59.753 55.000 0.00 0.00 37.09 4.79
1190 4896 2.106511 TCAACCTTGAGCAGCTTACCTT 59.893 45.455 0.00 0.00 32.50 3.50
1365 5091 7.483691 GGCACGGTAAGATGTAAATTTTAACAG 59.516 37.037 0.00 0.00 0.00 3.16
1404 5141 5.065218 ACGTATCATGAGAATTGCAGAAACC 59.935 40.000 0.09 0.00 0.00 3.27
1445 5188 3.689872 TCTCCATCTACCTGTAGGCTT 57.310 47.619 0.00 0.00 39.32 4.35
1447 5190 4.591072 AGAAATCTCCATCTACCTGTAGGC 59.409 45.833 4.58 0.00 39.32 3.93
1463 5206 1.251251 GCCAACACCTGCAGAAATCT 58.749 50.000 17.39 0.00 0.00 2.40
1499 5242 2.677199 ACTCTGTTGTAGACATGCACG 58.323 47.619 0.00 0.00 37.69 5.34
1537 5280 3.117794 TGTTCTTTACACCTCACGAACG 58.882 45.455 0.00 0.00 34.93 3.95
1568 5311 1.675552 TGATCGTCCAGTCATCGCTA 58.324 50.000 0.00 0.00 0.00 4.26
1595 5338 2.358615 TGCATGGTGCCAGTCGAC 60.359 61.111 7.70 7.70 44.23 4.20
1598 5341 2.393768 CGACTGCATGGTGCCAGTC 61.394 63.158 16.77 16.77 44.23 3.51
1602 5345 3.807538 CAGCGACTGCATGGTGCC 61.808 66.667 0.00 0.00 44.23 5.01
1604 5347 3.807538 GCCAGCGACTGCATGGTG 61.808 66.667 5.23 5.70 46.23 4.17
1675 5424 2.849096 TACCTCCGTCCAGCCGATGT 62.849 60.000 0.00 0.00 0.00 3.06
1741 5490 7.913297 GCACACAACTAAAGTTCAAAGTATGAA 59.087 33.333 0.00 0.00 45.71 2.57
1742 5491 7.066404 TGCACACAACTAAAGTTCAAAGTATGA 59.934 33.333 0.00 0.00 35.83 2.15
1743 5492 7.192913 TGCACACAACTAAAGTTCAAAGTATG 58.807 34.615 0.00 0.00 35.83 2.39
1744 5493 7.328277 TGCACACAACTAAAGTTCAAAGTAT 57.672 32.000 0.00 0.00 35.83 2.12
1745 5494 6.745159 TGCACACAACTAAAGTTCAAAGTA 57.255 33.333 0.00 0.00 35.83 2.24
1746 5495 5.637006 TGCACACAACTAAAGTTCAAAGT 57.363 34.783 0.00 0.00 35.83 2.66
1785 5534 2.929301 TCAATAGGAAGGTTCACCCCT 58.071 47.619 0.00 0.00 36.42 4.79
1821 5572 7.766278 GGAGAAAATGATTCACTTCTAGCACTA 59.234 37.037 11.10 0.00 0.00 2.74
1822 5573 6.597280 GGAGAAAATGATTCACTTCTAGCACT 59.403 38.462 11.10 0.00 0.00 4.40
1823 5574 6.372659 TGGAGAAAATGATTCACTTCTAGCAC 59.627 38.462 11.10 5.50 0.00 4.40
1825 5576 6.597280 AGTGGAGAAAATGATTCACTTCTAGC 59.403 38.462 11.10 6.53 32.34 3.42
1826 5577 9.658799 TTAGTGGAGAAAATGATTCACTTCTAG 57.341 33.333 11.10 0.00 36.87 2.43
1827 5578 9.436957 GTTAGTGGAGAAAATGATTCACTTCTA 57.563 33.333 11.10 0.00 36.87 2.10
1828 5579 8.160106 AGTTAGTGGAGAAAATGATTCACTTCT 58.840 33.333 10.99 10.99 36.87 2.85
1829 5580 8.329203 AGTTAGTGGAGAAAATGATTCACTTC 57.671 34.615 2.44 0.00 36.87 3.01
1831 5582 7.175641 CCAAGTTAGTGGAGAAAATGATTCACT 59.824 37.037 0.00 0.00 41.65 3.41
1832 5583 7.174946 TCCAAGTTAGTGGAGAAAATGATTCAC 59.825 37.037 0.00 0.00 42.97 3.18
1906 6004 8.993121 GGTAGAAATACATCAGTGAATATGGTG 58.007 37.037 0.00 0.00 34.84 4.17
1924 6022 1.920351 ACGGTTCCCATGGGTAGAAAT 59.080 47.619 30.28 10.28 36.47 2.17
1944 6042 1.282738 TGGCAAGAGCATCCTGATCAA 59.717 47.619 0.00 0.00 44.61 2.57
1966 6064 3.751175 TCTTGTTGATGATCGGTTTCACC 59.249 43.478 0.00 0.00 34.05 4.02
1977 6075 9.102757 GAGCTACTATGATTTTCTTGTTGATGA 57.897 33.333 0.00 0.00 0.00 2.92
1994 6092 4.591072 GGAATCTTCACTGGGAGCTACTAT 59.409 45.833 0.00 0.00 0.00 2.12
2025 6123 2.977914 TCTTGCATTCTAGTGGAGCAC 58.022 47.619 0.00 0.00 34.56 4.40
2053 6151 3.845781 TTCTCCAGCCCATCATAGAAC 57.154 47.619 0.00 0.00 0.00 3.01
2062 6160 0.850100 TCACCTTTTTCTCCAGCCCA 59.150 50.000 0.00 0.00 0.00 5.36
2067 6165 4.701651 CAGCATACATCACCTTTTTCTCCA 59.298 41.667 0.00 0.00 0.00 3.86
2129 6227 1.930656 AGCCCAGTGGGTAAGCCAT 60.931 57.895 29.23 4.47 46.51 4.40
2168 6266 2.891580 GAGGAGAGGTGACGCCATTATA 59.108 50.000 7.99 0.00 40.61 0.98
2192 6290 0.327924 TCGAAGCCACCACCATTGAT 59.672 50.000 0.00 0.00 0.00 2.57
2193 6291 0.605319 GTCGAAGCCACCACCATTGA 60.605 55.000 0.00 0.00 0.00 2.57
2242 6340 1.908344 TTGTTATGAAGCCTGCTGCA 58.092 45.000 1.50 1.50 44.83 4.41
2275 6373 1.461127 GTGGATTCAGCAACGTCTCAC 59.539 52.381 0.00 0.00 0.00 3.51
2319 6417 0.179059 TTGAGAGTGCCGCACTTTGA 60.179 50.000 26.38 13.24 45.44 2.69
2321 6419 0.947244 CTTTGAGAGTGCCGCACTTT 59.053 50.000 26.38 21.26 45.44 2.66
2329 6427 2.866762 ACTTCGTGTTCTTTGAGAGTGC 59.133 45.455 0.00 0.00 0.00 4.40
2363 6461 5.104527 GCTATATGATACCAGGCCCATGTAA 60.105 44.000 0.00 0.00 0.00 2.41
2372 6470 4.825422 CACACCAGCTATATGATACCAGG 58.175 47.826 0.00 0.00 0.00 4.45
2524 6622 0.464036 TTTCCCGATGGTGATCTCCG 59.536 55.000 9.20 0.00 0.00 4.63
2667 6780 1.404035 AGCCTTTTGTTCAACACGTCC 59.596 47.619 0.00 0.00 0.00 4.79
2676 6789 2.034685 GTGTTCCTCCAGCCTTTTGTTC 59.965 50.000 0.00 0.00 0.00 3.18
2727 6840 0.895530 TCTTACCTGCAGGGAACTCG 59.104 55.000 35.42 21.82 40.21 4.18
2794 6907 1.211212 CACCTGATCCTTGATCCTGCA 59.789 52.381 1.88 0.00 38.20 4.41
2853 6966 4.442073 CACGAGTCTTCCAAAATTTTGCTG 59.558 41.667 22.90 14.87 36.86 4.41
2855 6968 3.182372 GCACGAGTCTTCCAAAATTTTGC 59.818 43.478 22.90 10.62 36.86 3.68
2920 7033 3.490155 TCGTTTACTTGACGAAATTCGCA 59.510 39.130 15.90 11.41 45.45 5.10
2921 7034 4.043761 TCGTTTACTTGACGAAATTCGC 57.956 40.909 15.90 8.90 45.45 4.70
2935 7048 5.446607 GGTCGTAGTCTTCCTAGTCGTTTAC 60.447 48.000 0.00 0.00 0.00 2.01
2997 7110 4.079253 GCCAGGTGATTCTTTAGGTGAAA 58.921 43.478 0.00 0.00 0.00 2.69
2998 7111 3.561313 GGCCAGGTGATTCTTTAGGTGAA 60.561 47.826 0.00 0.00 0.00 3.18
2999 7112 2.026262 GGCCAGGTGATTCTTTAGGTGA 60.026 50.000 0.00 0.00 0.00 4.02
3000 7113 2.369394 GGCCAGGTGATTCTTTAGGTG 58.631 52.381 0.00 0.00 0.00 4.00
3001 7114 1.285078 GGGCCAGGTGATTCTTTAGGT 59.715 52.381 4.39 0.00 0.00 3.08
3002 7115 1.284785 TGGGCCAGGTGATTCTTTAGG 59.715 52.381 0.00 0.00 0.00 2.69
3003 7116 2.806945 TGGGCCAGGTGATTCTTTAG 57.193 50.000 0.00 0.00 0.00 1.85
3007 7707 1.922447 TGTATTGGGCCAGGTGATTCT 59.078 47.619 6.23 0.00 0.00 2.40
3008 7708 2.092429 TCTGTATTGGGCCAGGTGATTC 60.092 50.000 6.23 0.00 0.00 2.52
3014 7714 0.753111 GGCTTCTGTATTGGGCCAGG 60.753 60.000 6.23 0.00 42.08 4.45
3021 7721 3.550437 AGTAGCAGGGCTTCTGTATTG 57.450 47.619 0.00 0.00 45.08 1.90
3029 7729 5.821097 AGAAAAGAAATAGTAGCAGGGCTT 58.179 37.500 0.00 0.00 40.44 4.35
3030 7730 5.443230 AGAAAAGAAATAGTAGCAGGGCT 57.557 39.130 0.00 0.00 43.41 5.19
3031 7731 6.151144 TCAAAGAAAAGAAATAGTAGCAGGGC 59.849 38.462 0.00 0.00 0.00 5.19
3033 7733 7.095187 ACGTCAAAGAAAAGAAATAGTAGCAGG 60.095 37.037 0.00 0.00 0.00 4.85
3034 7734 7.742089 CACGTCAAAGAAAAGAAATAGTAGCAG 59.258 37.037 0.00 0.00 0.00 4.24
3035 7735 7.572759 CACGTCAAAGAAAAGAAATAGTAGCA 58.427 34.615 0.00 0.00 0.00 3.49
3036 7736 6.520104 GCACGTCAAAGAAAAGAAATAGTAGC 59.480 38.462 0.00 0.00 0.00 3.58
3037 7737 7.015877 GGCACGTCAAAGAAAAGAAATAGTAG 58.984 38.462 0.00 0.00 0.00 2.57
3038 7738 6.708949 AGGCACGTCAAAGAAAAGAAATAGTA 59.291 34.615 0.00 0.00 0.00 1.82
3039 7739 5.531287 AGGCACGTCAAAGAAAAGAAATAGT 59.469 36.000 0.00 0.00 0.00 2.12
3040 7740 6.002062 AGGCACGTCAAAGAAAAGAAATAG 57.998 37.500 0.00 0.00 0.00 1.73
3041 7741 6.708949 ACTAGGCACGTCAAAGAAAAGAAATA 59.291 34.615 0.00 0.00 0.00 1.40
3042 7742 4.918810 AGGCACGTCAAAGAAAAGAAAT 57.081 36.364 0.00 0.00 0.00 2.17
3043 7743 4.879545 ACTAGGCACGTCAAAGAAAAGAAA 59.120 37.500 0.00 0.00 0.00 2.52
3044 7744 4.448210 ACTAGGCACGTCAAAGAAAAGAA 58.552 39.130 0.00 0.00 0.00 2.52
3045 7745 4.067972 ACTAGGCACGTCAAAGAAAAGA 57.932 40.909 0.00 0.00 0.00 2.52
3046 7746 4.989168 AGTACTAGGCACGTCAAAGAAAAG 59.011 41.667 0.00 0.00 0.00 2.27
3047 7747 4.952460 AGTACTAGGCACGTCAAAGAAAA 58.048 39.130 0.00 0.00 0.00 2.29
3048 7748 4.595762 AGTACTAGGCACGTCAAAGAAA 57.404 40.909 0.00 0.00 0.00 2.52
3049 7749 5.909621 ATAGTACTAGGCACGTCAAAGAA 57.090 39.130 8.85 0.00 0.00 2.52
3050 7750 5.909621 AATAGTACTAGGCACGTCAAAGA 57.090 39.130 8.85 0.00 0.00 2.52
3051 7751 6.331061 AGAAATAGTACTAGGCACGTCAAAG 58.669 40.000 8.85 0.00 0.00 2.77
3052 7752 6.276832 AGAAATAGTACTAGGCACGTCAAA 57.723 37.500 8.85 0.00 0.00 2.69
3053 7753 5.909621 AGAAATAGTACTAGGCACGTCAA 57.090 39.130 8.85 0.00 0.00 3.18
3054 7754 5.909621 AAGAAATAGTACTAGGCACGTCA 57.090 39.130 8.85 0.00 0.00 4.35
3055 7755 7.381678 CCAATAAGAAATAGTACTAGGCACGTC 59.618 40.741 8.85 0.02 0.00 4.34
3056 7756 7.069085 TCCAATAAGAAATAGTACTAGGCACGT 59.931 37.037 8.85 1.79 0.00 4.49
3057 7757 7.431249 TCCAATAAGAAATAGTACTAGGCACG 58.569 38.462 8.85 0.00 0.00 5.34
3058 7758 9.780186 ATTCCAATAAGAAATAGTACTAGGCAC 57.220 33.333 8.85 0.65 0.00 5.01
3059 7759 9.998106 GATTCCAATAAGAAATAGTACTAGGCA 57.002 33.333 8.85 0.00 0.00 4.75
3060 7760 9.438228 GGATTCCAATAAGAAATAGTACTAGGC 57.562 37.037 8.85 0.46 0.00 3.93
3063 7763 9.998106 GCTGGATTCCAATAAGAAATAGTACTA 57.002 33.333 6.88 4.77 30.80 1.82
3064 7764 7.939588 GGCTGGATTCCAATAAGAAATAGTACT 59.060 37.037 6.88 0.00 30.80 2.73
3065 7765 7.175119 GGGCTGGATTCCAATAAGAAATAGTAC 59.825 40.741 6.88 0.00 30.80 2.73
3066 7766 7.147213 TGGGCTGGATTCCAATAAGAAATAGTA 60.147 37.037 6.88 0.00 30.80 1.82
3067 7767 6.071320 GGGCTGGATTCCAATAAGAAATAGT 58.929 40.000 6.88 0.00 30.80 2.12
3068 7768 6.015940 GTGGGCTGGATTCCAATAAGAAATAG 60.016 42.308 6.88 0.00 34.47 1.73
3088 7788 2.282745 AAGGAAGCAGCTGTGGGC 60.283 61.111 16.64 0.00 42.19 5.36
3089 7789 2.037136 CGAAGGAAGCAGCTGTGGG 61.037 63.158 16.64 0.00 0.00 4.61
3090 7790 0.392193 ATCGAAGGAAGCAGCTGTGG 60.392 55.000 16.64 0.00 0.00 4.17
3092 7792 0.107945 GGATCGAAGGAAGCAGCTGT 60.108 55.000 16.64 0.00 0.00 4.40
3093 7793 0.177604 AGGATCGAAGGAAGCAGCTG 59.822 55.000 10.11 10.11 0.00 4.24
3094 7794 0.463620 GAGGATCGAAGGAAGCAGCT 59.536 55.000 0.00 0.00 0.00 4.24
3095 7795 2.984871 GAGGATCGAAGGAAGCAGC 58.015 57.895 0.00 0.00 0.00 5.25
3107 7807 4.292178 CCAGAGCGGCCGAGGATC 62.292 72.222 33.48 19.98 0.00 3.36
3108 7808 4.841617 TCCAGAGCGGCCGAGGAT 62.842 66.667 33.48 11.34 33.14 3.24
3111 7811 3.898509 CTCTCCAGAGCGGCCGAG 61.899 72.222 33.48 16.86 35.13 4.63
3112 7812 3.723097 ATCTCTCCAGAGCGGCCGA 62.723 63.158 33.48 5.32 41.80 5.54
3115 7815 1.659794 GAGATCTCTCCAGAGCGGC 59.340 63.158 15.80 0.00 40.26 6.53
3124 7824 4.380444 GCCATTGATACGAGGAGATCTCTC 60.380 50.000 21.81 15.30 40.30 3.20
3125 7825 3.509575 GCCATTGATACGAGGAGATCTCT 59.490 47.826 21.81 8.41 40.30 3.10
3126 7826 3.671971 CGCCATTGATACGAGGAGATCTC 60.672 52.174 14.75 14.75 39.10 2.75
3127 7827 2.230025 CGCCATTGATACGAGGAGATCT 59.770 50.000 0.00 0.00 0.00 2.75
3128 7828 2.600731 CGCCATTGATACGAGGAGATC 58.399 52.381 0.00 0.00 0.00 2.75
3129 7829 1.337260 GCGCCATTGATACGAGGAGAT 60.337 52.381 0.00 0.00 0.00 2.75
3130 7830 0.032130 GCGCCATTGATACGAGGAGA 59.968 55.000 0.00 0.00 0.00 3.71
3131 7831 1.278172 CGCGCCATTGATACGAGGAG 61.278 60.000 0.00 0.00 0.00 3.69
3132 7832 1.299850 CGCGCCATTGATACGAGGA 60.300 57.895 0.00 0.00 0.00 3.71
3133 7833 1.151777 AACGCGCCATTGATACGAGG 61.152 55.000 5.73 0.00 0.00 4.63
3137 7837 3.424433 GCCTAATAACGCGCCATTGATAC 60.424 47.826 5.73 0.00 0.00 2.24
3138 7838 2.739913 GCCTAATAACGCGCCATTGATA 59.260 45.455 5.73 0.00 0.00 2.15
3140 7840 0.941542 GCCTAATAACGCGCCATTGA 59.058 50.000 5.73 0.00 0.00 2.57
3144 7844 0.462937 ATGTGCCTAATAACGCGCCA 60.463 50.000 5.73 0.00 34.58 5.69
3148 7848 5.224562 TGTTTGTATGTGCCTAATAACGC 57.775 39.130 0.00 0.00 0.00 4.84
3152 7852 7.613801 AGGATTGTTGTTTGTATGTGCCTAATA 59.386 33.333 0.00 0.00 0.00 0.98
3157 7857 4.519540 AGGATTGTTGTTTGTATGTGCC 57.480 40.909 0.00 0.00 0.00 5.01
3158 7858 5.086058 CGTAGGATTGTTGTTTGTATGTGC 58.914 41.667 0.00 0.00 0.00 4.57
3163 7863 9.491675 TCTTTATTCGTAGGATTGTTGTTTGTA 57.508 29.630 0.00 0.00 0.00 2.41
3166 7873 9.840427 CATTCTTTATTCGTAGGATTGTTGTTT 57.160 29.630 0.00 0.00 0.00 2.83
3168 7875 7.067008 CCCATTCTTTATTCGTAGGATTGTTGT 59.933 37.037 0.00 0.00 0.00 3.32
3169 7876 7.282224 TCCCATTCTTTATTCGTAGGATTGTTG 59.718 37.037 0.00 0.00 0.00 3.33
3171 7878 6.895782 TCCCATTCTTTATTCGTAGGATTGT 58.104 36.000 0.00 0.00 0.00 2.71
3173 7880 6.431234 GCATCCCATTCTTTATTCGTAGGATT 59.569 38.462 0.00 0.00 29.18 3.01
3174 7881 5.940470 GCATCCCATTCTTTATTCGTAGGAT 59.060 40.000 0.00 0.00 31.82 3.24
3175 7882 5.305585 GCATCCCATTCTTTATTCGTAGGA 58.694 41.667 0.00 0.00 0.00 2.94
3177 7884 4.988540 TCGCATCCCATTCTTTATTCGTAG 59.011 41.667 0.00 0.00 0.00 3.51
3178 7885 4.951254 TCGCATCCCATTCTTTATTCGTA 58.049 39.130 0.00 0.00 0.00 3.43
3179 7886 3.804036 TCGCATCCCATTCTTTATTCGT 58.196 40.909 0.00 0.00 0.00 3.85
3180 7887 4.434725 CGATCGCATCCCATTCTTTATTCG 60.435 45.833 0.26 0.00 0.00 3.34
3181 7888 4.670221 GCGATCGCATCCCATTCTTTATTC 60.670 45.833 33.89 0.00 41.49 1.75
3184 7891 2.143122 GCGATCGCATCCCATTCTTTA 58.857 47.619 33.89 0.00 41.49 1.85
3188 7895 1.621301 CTCGCGATCGCATCCCATTC 61.621 60.000 36.45 7.19 42.06 2.67
3189 7896 1.665916 CTCGCGATCGCATCCCATT 60.666 57.895 36.45 0.00 42.06 3.16
3193 7900 1.543941 CTTGTCTCGCGATCGCATCC 61.544 60.000 36.45 21.74 42.06 3.51
3201 7908 3.230743 TCATTCATTCTTGTCTCGCGA 57.769 42.857 9.26 9.26 0.00 5.87
3202 7909 3.997319 TTCATTCATTCTTGTCTCGCG 57.003 42.857 0.00 0.00 0.00 5.87
3203 7910 5.451908 TGTTTTCATTCATTCTTGTCTCGC 58.548 37.500 0.00 0.00 0.00 5.03
3207 7914 7.643764 TCTTCGTTGTTTTCATTCATTCTTGTC 59.356 33.333 0.00 0.00 0.00 3.18
3215 7922 5.180367 TGCATCTTCGTTGTTTTCATTCA 57.820 34.783 0.00 0.00 0.00 2.57
3219 7926 3.243334 TGCATGCATCTTCGTTGTTTTCA 60.243 39.130 18.46 0.00 0.00 2.69
3220 7927 3.307674 TGCATGCATCTTCGTTGTTTTC 58.692 40.909 18.46 0.00 0.00 2.29
3223 7930 2.871133 CATGCATGCATCTTCGTTGTT 58.129 42.857 30.07 3.48 33.90 2.83
3224 7931 2.554806 CATGCATGCATCTTCGTTGT 57.445 45.000 30.07 4.31 33.90 3.32
3512 8283 4.674904 CCGATCGAGCGAGGCGAG 62.675 72.222 26.68 1.94 41.49 5.03
3514 8285 4.965858 GACCGATCGAGCGAGGCG 62.966 72.222 26.68 10.27 0.00 5.52
3560 8331 2.509336 CTCGCCGCGATCCAAAGT 60.509 61.111 17.22 0.00 34.61 2.66
3562 8333 2.202743 CTCTCGCCGCGATCCAAA 60.203 61.111 17.22 0.00 34.61 3.28
3563 8334 3.126074 CTCTCTCGCCGCGATCCAA 62.126 63.158 17.22 1.69 34.61 3.53
3564 8335 3.586961 CTCTCTCGCCGCGATCCA 61.587 66.667 17.22 2.48 34.61 3.41
3565 8336 4.335584 CCTCTCTCGCCGCGATCC 62.336 72.222 17.22 0.00 34.61 3.36
3582 8353 1.641577 AACGGCTACGAGAAATCTGC 58.358 50.000 0.00 0.00 44.60 4.26
3633 8438 2.474410 AACATTCCCGTTCTGTCCTC 57.526 50.000 0.00 0.00 0.00 3.71
3673 8486 2.029020 GGGAATCACTCCTTGCCAAAAC 60.029 50.000 0.00 0.00 44.68 2.43
3775 8607 1.584483 GCACTGCGCCATCAATTCG 60.584 57.895 4.18 0.00 32.94 3.34
3776 8608 1.016627 TAGCACTGCGCCATCAATTC 58.983 50.000 4.18 0.00 44.04 2.17
3781 8613 1.672881 AGAAAATAGCACTGCGCCATC 59.327 47.619 4.18 0.00 44.04 3.51
3789 8621 3.439857 TGCAGGGAAGAAAATAGCACT 57.560 42.857 0.00 0.00 0.00 4.40
3902 8736 9.743057 CCAGTTTTAATCAACACTTAATGACAA 57.257 29.630 0.00 0.00 0.00 3.18
3903 8737 9.126151 TCCAGTTTTAATCAACACTTAATGACA 57.874 29.630 0.00 0.00 0.00 3.58
3910 8744 9.533253 CAAGAAATCCAGTTTTAATCAACACTT 57.467 29.630 0.00 0.00 0.00 3.16
3911 8745 8.695456 ACAAGAAATCCAGTTTTAATCAACACT 58.305 29.630 0.00 0.00 0.00 3.55
3912 8746 8.755018 CACAAGAAATCCAGTTTTAATCAACAC 58.245 33.333 0.00 0.00 0.00 3.32
3913 8747 7.925483 CCACAAGAAATCCAGTTTTAATCAACA 59.075 33.333 0.00 0.00 0.00 3.33
3914 8748 7.095649 GCCACAAGAAATCCAGTTTTAATCAAC 60.096 37.037 0.00 0.00 0.00 3.18
3915 8749 6.928492 GCCACAAGAAATCCAGTTTTAATCAA 59.072 34.615 0.00 0.00 0.00 2.57
3916 8750 6.267471 AGCCACAAGAAATCCAGTTTTAATCA 59.733 34.615 0.00 0.00 0.00 2.57
3917 8751 6.691508 AGCCACAAGAAATCCAGTTTTAATC 58.308 36.000 0.00 0.00 0.00 1.75
3918 8752 6.670695 AGCCACAAGAAATCCAGTTTTAAT 57.329 33.333 0.00 0.00 0.00 1.40
3919 8753 7.775053 ATAGCCACAAGAAATCCAGTTTTAA 57.225 32.000 0.00 0.00 0.00 1.52
3920 8754 8.871629 TTATAGCCACAAGAAATCCAGTTTTA 57.128 30.769 0.00 0.00 0.00 1.52
3921 8755 7.775053 TTATAGCCACAAGAAATCCAGTTTT 57.225 32.000 0.00 0.00 0.00 2.43
3922 8756 7.775053 TTTATAGCCACAAGAAATCCAGTTT 57.225 32.000 0.00 0.00 0.00 2.66


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

AutoCloner maintained by Alex Coulton.