Multiple sequence alignment - TraesCS3B01G077900

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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 TraesCS3B01G077900 chr3B 100.000 5138 0 0 1 5138 48890314 48885177 0.000000e+00 9489.0
1 TraesCS3B01G077900 chr3B 92.181 486 37 1 3220 3704 48803256 48802771 0.000000e+00 686.0
2 TraesCS3B01G077900 chr3B 90.210 143 11 3 3723 3865 772411449 772411588 3.160000e-42 183.0
3 TraesCS3B01G077900 chr3B 89.600 125 11 1 3729 3853 696703329 696703207 1.920000e-34 158.0
4 TraesCS3B01G077900 chr2D 95.253 1896 76 8 1850 3740 645011691 645009805 0.000000e+00 2990.0
5 TraesCS3B01G077900 chr2D 91.398 744 49 6 139 880 645013774 645013044 0.000000e+00 1005.0
6 TraesCS3B01G077900 chr2D 87.875 767 89 2 4344 5110 644987933 644988695 0.000000e+00 898.0
7 TraesCS3B01G077900 chr2D 92.952 454 28 3 3842 4293 645009808 645009357 0.000000e+00 658.0
8 TraesCS3B01G077900 chr2D 90.968 465 21 8 894 1350 645012923 645012472 1.580000e-169 606.0
9 TraesCS3B01G077900 chr2D 91.127 417 19 6 1406 1807 645012374 645011961 2.700000e-152 549.0
10 TraesCS3B01G077900 chr2D 95.455 88 2 1 2763 2848 24916184 24916271 6.940000e-29 139.0
11 TraesCS3B01G077900 chr2D 91.071 56 1 4 4280 4332 645009346 645009292 7.140000e-09 73.1
12 TraesCS3B01G077900 chr2D 100.000 28 0 0 4770 4797 528638658 528638685 9.000000e-03 52.8
13 TraesCS3B01G077900 chr2B 94.139 1894 92 10 1847 3736 790584703 790586581 0.000000e+00 2865.0
14 TraesCS3B01G077900 chr2B 90.591 999 33 9 894 1852 790583494 790584471 0.000000e+00 1267.0
15 TraesCS3B01G077900 chr2B 91.899 790 47 10 1 781 790581867 790582648 0.000000e+00 1088.0
16 TraesCS3B01G077900 chr2B 86.862 784 99 2 4352 5134 790588236 790589016 0.000000e+00 874.0
17 TraesCS3B01G077900 chr2B 85.596 361 23 17 3842 4201 790586579 790586911 8.190000e-93 351.0
18 TraesCS3B01G077900 chr2B 94.958 119 4 1 3735 3853 146781183 146781067 8.790000e-43 185.0
19 TraesCS3B01G077900 chr2B 92.553 94 6 1 4200 4293 790587787 790587879 3.230000e-27 134.0
20 TraesCS3B01G077900 chr2A 92.611 1394 69 17 1850 3220 770360568 770359186 0.000000e+00 1973.0
21 TraesCS3B01G077900 chr2A 91.122 811 52 2 4328 5138 770357769 770356979 0.000000e+00 1081.0
22 TraesCS3B01G077900 chr2A 95.349 516 23 1 3226 3740 770359079 770358564 0.000000e+00 819.0
23 TraesCS3B01G077900 chr2A 92.140 458 30 2 3842 4293 770358567 770358110 4.340000e-180 641.0
24 TraesCS3B01G077900 chr2A 89.375 480 19 6 894 1350 770361881 770361411 4.460000e-160 575.0
25 TraesCS3B01G077900 chr2A 89.196 398 30 8 1467 1851 770361227 770360830 7.730000e-133 484.0
26 TraesCS3B01G077900 chr2A 95.798 119 4 1 3736 3853 572097633 572097751 1.890000e-44 191.0
27 TraesCS3B01G077900 chr2A 93.496 123 5 3 3733 3855 507071272 507071153 4.090000e-41 180.0
28 TraesCS3B01G077900 chr2A 94.017 117 7 0 3737 3853 166094908 166094792 1.470000e-40 178.0
29 TraesCS3B01G077900 chr2A 94.444 108 6 0 3737 3844 736449223 736449330 3.180000e-37 167.0
30 TraesCS3B01G077900 chr2A 91.597 119 8 2 3730 3847 672629056 672629173 4.120000e-36 163.0
31 TraesCS3B01G077900 chr2A 89.764 127 11 2 3725 3851 208346812 208346936 1.480000e-35 161.0
32 TraesCS3B01G077900 chr2A 89.394 66 3 3 4280 4343 770358099 770358036 4.260000e-11 80.5
33 TraesCS3B01G077900 chrUn 98.261 115 1 1 3737 3851 218382135 218382248 3.140000e-47 200.0
34 TraesCS3B01G077900 chrUn 98.261 115 1 1 3737 3851 218399683 218399796 3.140000e-47 200.0
35 TraesCS3B01G077900 chr4B 97.436 117 3 0 3729 3845 565865969 565865853 3.140000e-47 200.0
36 TraesCS3B01G077900 chr7B 96.667 120 3 1 3733 3852 174674127 174674009 1.130000e-46 198.0
37 TraesCS3B01G077900 chr7D 96.610 118 4 0 3727 3844 42694737 42694854 4.060000e-46 196.0
38 TraesCS3B01G077900 chr6B 95.833 120 5 0 3724 3843 212571896 212572015 1.460000e-45 195.0
39 TraesCS3B01G077900 chr5B 96.581 117 4 0 3727 3843 666202109 666201993 1.460000e-45 195.0
40 TraesCS3B01G077900 chr5B 95.082 122 4 2 3729 3850 228061834 228061953 1.890000e-44 191.0
41 TraesCS3B01G077900 chr1B 81.915 94 15 2 3891 3983 28764935 28764843 1.530000e-10 78.7
42 TraesCS3B01G077900 chr1B 92.857 42 2 1 3890 3931 13592270 13592310 5.560000e-05 60.2
43 TraesCS3B01G077900 chr1D 97.368 38 0 1 3890 3927 367848832 367848868 4.290000e-06 63.9
44 TraesCS3B01G077900 chr1A 97.368 38 0 1 3890 3927 467185713 467185749 4.290000e-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 TraesCS3B01G077900 chr3B 48885177 48890314 5137 True 9489.000000 9489 100.000000 1 5138 1 chr3B.!!$R2 5137
1 TraesCS3B01G077900 chr2D 645009292 645013774 4482 True 980.183333 2990 92.128167 139 4332 6 chr2D.!!$R1 4193
2 TraesCS3B01G077900 chr2D 644987933 644988695 762 False 898.000000 898 87.875000 4344 5110 1 chr2D.!!$F3 766
3 TraesCS3B01G077900 chr2B 790581867 790589016 7149 False 1096.500000 2865 90.273333 1 5134 6 chr2B.!!$F1 5133
4 TraesCS3B01G077900 chr2A 770356979 770361881 4902 True 807.642857 1973 91.312429 894 5138 7 chr2A.!!$R3 4244

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
989 1732 0.179129 CCATTTTAAGCGCCTGCCAG 60.179 55.0 2.29 0.0 44.31 4.85 F
1570 2428 0.179043 TCTCGAGATCGGTGAGGAGG 60.179 60.0 12.08 0.0 40.29 4.30 F
2975 4150 0.109153 ATGCACCTCTGTTGCTGTGA 59.891 50.0 0.00 0.0 0.00 3.58 F
3753 5034 0.038744 ACTACTCCCTCCGTTCCGAA 59.961 55.0 0.00 0.0 0.00 4.30 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1941 3090 2.256306 TCAGACATAGCCCAAGTCACA 58.744 47.619 0.0 0.0 34.80 3.58 R
3192 4367 1.441738 TGGAGTGCATGAACATCGTG 58.558 50.000 6.6 0.0 36.50 4.35 R
3827 5108 0.113776 ACAGTACTCCCTCCGTTCCA 59.886 55.000 0.0 0.0 0.00 3.53 R
4793 7357 0.326264 AGCGGAAGGAGCTTCACAAT 59.674 50.000 0.0 0.0 43.24 2.71 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
33 34 6.183360 ACAGAGCTAAAATCATCACATCTTGC 60.183 38.462 0.00 0.00 0.00 4.01
71 72 2.299297 AGTGGACACTTAGTCTTTCGGG 59.701 50.000 0.00 0.00 46.72 5.14
80 81 5.179555 CACTTAGTCTTTCGGGGAAAAGAAG 59.820 44.000 0.95 0.00 44.54 2.85
81 82 5.071384 ACTTAGTCTTTCGGGGAAAAGAAGA 59.929 40.000 0.95 0.00 44.54 2.87
102 103 5.574188 AGAAAATGGATAGACAAAGGTGCT 58.426 37.500 0.00 0.00 0.00 4.40
106 107 5.649782 ATGGATAGACAAAGGTGCTTTTG 57.350 39.130 5.42 5.42 42.38 2.44
115 116 5.356426 ACAAAGGTGCTTTTGTTATGTTCC 58.644 37.500 6.60 0.00 46.18 3.62
120 121 5.010012 AGGTGCTTTTGTTATGTTCCTTGAG 59.990 40.000 0.00 0.00 0.00 3.02
123 124 6.017109 GTGCTTTTGTTATGTTCCTTGAGAGA 60.017 38.462 0.00 0.00 0.00 3.10
124 125 6.205464 TGCTTTTGTTATGTTCCTTGAGAGAG 59.795 38.462 0.00 0.00 0.00 3.20
125 126 6.205658 GCTTTTGTTATGTTCCTTGAGAGAGT 59.794 38.462 0.00 0.00 0.00 3.24
126 127 7.255277 GCTTTTGTTATGTTCCTTGAGAGAGTT 60.255 37.037 0.00 0.00 0.00 3.01
133 134 4.522405 TGTTCCTTGAGAGAGTTGAGAGAG 59.478 45.833 0.00 0.00 0.00 3.20
157 158 5.762179 TGATCATTTTGTACCCTCTCTGT 57.238 39.130 0.00 0.00 0.00 3.41
161 162 4.020218 TCATTTTGTACCCTCTCTGTCCAG 60.020 45.833 0.00 0.00 0.00 3.86
162 163 1.267121 TTGTACCCTCTCTGTCCAGC 58.733 55.000 0.00 0.00 0.00 4.85
181 182 5.368230 TCCAGCCTTTTCCTTTTAACCAAAT 59.632 36.000 0.00 0.00 0.00 2.32
186 187 6.934083 GCCTTTTCCTTTTAACCAAATCATGA 59.066 34.615 0.00 0.00 0.00 3.07
254 256 2.970640 CTCCCCCACTTACTACATACCC 59.029 54.545 0.00 0.00 0.00 3.69
343 350 6.183360 CCACTCATTTCTATTTCAAGCGCTTA 60.183 38.462 24.55 8.15 0.00 3.09
369 376 1.205055 TCTCTCTCGCCTCTACCTCA 58.795 55.000 0.00 0.00 0.00 3.86
423 430 2.500910 CAAGGCAGATGACTCTTCCTCT 59.499 50.000 0.00 0.00 43.43 3.69
517 524 2.009774 GGAGCATGCGTAGTCATGTTT 58.990 47.619 13.01 0.00 41.57 2.83
519 526 3.419915 GAGCATGCGTAGTCATGTTTTG 58.580 45.455 13.01 0.00 41.57 2.44
528 535 4.437390 CGTAGTCATGTTTTGGGATGAAGC 60.437 45.833 0.00 0.00 30.45 3.86
563 570 4.760204 AGCTCGCTAACAAATTTAGGTGTT 59.240 37.500 0.00 0.00 40.88 3.32
599 606 1.153823 CCTCGACGAATCAACGGCT 60.154 57.895 0.00 0.00 39.34 5.52
704 711 3.753272 CACCTGCAACACTAGCACTAAAT 59.247 43.478 0.00 0.00 37.02 1.40
823 1459 7.010160 TGTCCCTTTTCTTTATGTTCCTTGAT 58.990 34.615 0.00 0.00 0.00 2.57
880 1516 7.908082 GCCATCTTTTGTTTTTAACCAAACTTC 59.092 33.333 4.79 0.00 37.51 3.01
881 1517 8.940952 CCATCTTTTGTTTTTAACCAAACTTCA 58.059 29.630 4.79 0.00 37.51 3.02
884 1520 9.936759 TCTTTTGTTTTTAACCAAACTTCATCT 57.063 25.926 4.79 0.00 37.51 2.90
987 1730 0.530288 TTCCATTTTAAGCGCCTGCC 59.470 50.000 2.29 0.00 44.31 4.85
988 1731 0.610509 TCCATTTTAAGCGCCTGCCA 60.611 50.000 2.29 0.00 44.31 4.92
989 1732 0.179129 CCATTTTAAGCGCCTGCCAG 60.179 55.000 2.29 0.00 44.31 4.85
990 1733 0.803380 CATTTTAAGCGCCTGCCAGC 60.803 55.000 2.29 0.00 44.31 4.85
1001 1744 1.217511 CTGCCAGCGACAGAGTGAT 59.782 57.895 0.00 0.00 37.32 3.06
1006 1753 0.389556 CAGCGACAGAGTGATGCAGT 60.390 55.000 0.00 0.00 0.00 4.40
1154 1932 0.391263 GTTAGCTAGGCGCCAGTGTT 60.391 55.000 31.54 17.69 40.39 3.32
1161 1939 1.734117 GGCGCCAGTGTTGATTTGC 60.734 57.895 24.80 0.00 0.00 3.68
1162 1940 1.286880 GCGCCAGTGTTGATTTGCT 59.713 52.632 0.00 0.00 0.00 3.91
1163 1941 0.730494 GCGCCAGTGTTGATTTGCTC 60.730 55.000 0.00 0.00 0.00 4.26
1164 1942 0.877071 CGCCAGTGTTGATTTGCTCT 59.123 50.000 0.00 0.00 0.00 4.09
1165 1943 1.400629 CGCCAGTGTTGATTTGCTCTG 60.401 52.381 0.00 0.00 0.00 3.35
1166 1944 1.668047 GCCAGTGTTGATTTGCTCTGC 60.668 52.381 0.00 0.00 0.00 4.26
1167 1945 1.400629 CCAGTGTTGATTTGCTCTGCG 60.401 52.381 0.00 0.00 0.00 5.18
1168 1946 0.239347 AGTGTTGATTTGCTCTGCGC 59.761 50.000 0.00 0.00 39.77 6.09
1226 2004 2.094649 GGTTCGATCTCTCCGTGTTCTT 60.095 50.000 0.00 0.00 0.00 2.52
1285 2063 2.525284 TAGGCGTGGCTAGGAACCCT 62.525 60.000 0.00 0.00 37.71 4.34
1455 2286 2.026542 TCATCTTTGCAGCAGGATGAGT 60.027 45.455 26.09 3.42 39.37 3.41
1506 2364 1.859302 AGCTCAACGAGAGGATCCTT 58.141 50.000 17.42 5.91 44.86 3.36
1568 2426 1.885560 GATCTCGAGATCGGTGAGGA 58.114 55.000 33.30 2.89 41.15 3.71
1569 2427 1.804151 GATCTCGAGATCGGTGAGGAG 59.196 57.143 33.30 0.00 41.15 3.69
1570 2428 0.179043 TCTCGAGATCGGTGAGGAGG 60.179 60.000 12.08 0.00 40.29 4.30
1580 2438 2.124693 GTGAGGAGGAGGAGGAGCG 61.125 68.421 0.00 0.00 0.00 5.03
1639 2516 2.496070 AGCATGCTGAATTGCTGATTGT 59.504 40.909 21.98 0.00 46.96 2.71
1648 2525 2.222007 TTGCTGATTGTGTGTTTGGC 57.778 45.000 0.00 0.00 0.00 4.52
1696 2573 6.349033 GGTGTTCAATGTTGTAAGTACCATCC 60.349 42.308 0.00 0.00 0.00 3.51
1762 2639 5.238432 TGATGTTCTGTTGTCGCAAAGTAAT 59.762 36.000 0.00 0.00 0.00 1.89
1808 2685 2.203209 GGCAGGGGACTATTGGCG 60.203 66.667 0.00 0.00 40.21 5.69
1848 2997 4.278170 TCATTGTTGACCTCATTGTTGTCC 59.722 41.667 6.07 0.00 0.00 4.02
1909 3058 2.368221 AGAATATGCCAGACAGCCTCTC 59.632 50.000 0.00 0.00 0.00 3.20
1946 3095 3.181575 GGTTGCGCTTGTTAAAATGTGAC 59.818 43.478 9.73 0.00 0.00 3.67
2020 3170 1.912043 AGAGCCTGTGGTAGCATTTCT 59.088 47.619 0.00 0.00 0.00 2.52
2070 3220 7.013369 TCAGTAGTGTATAGACATGCCAGTTAG 59.987 40.741 2.50 0.00 38.04 2.34
2074 3224 8.478775 AGTGTATAGACATGCCAGTTAGAATA 57.521 34.615 2.50 0.00 38.04 1.75
2123 3274 5.031066 TGGCACATAAATCTACCCAGTAC 57.969 43.478 0.00 0.00 0.00 2.73
2124 3275 4.141574 TGGCACATAAATCTACCCAGTACC 60.142 45.833 0.00 0.00 0.00 3.34
2125 3276 4.056050 GCACATAAATCTACCCAGTACCG 58.944 47.826 0.00 0.00 0.00 4.02
2126 3277 4.202182 GCACATAAATCTACCCAGTACCGA 60.202 45.833 0.00 0.00 0.00 4.69
2130 3281 1.772836 ATCTACCCAGTACCGACCAC 58.227 55.000 0.00 0.00 0.00 4.16
2448 3614 9.893305 CGGAATTTTGTCCCTTGATATTATTAC 57.107 33.333 0.00 0.00 33.74 1.89
2534 3700 4.839668 TCTAACCATTTTTCCCAACGTG 57.160 40.909 0.00 0.00 0.00 4.49
2546 3712 4.065321 TCCCAACGTGCAATTTTTCAAT 57.935 36.364 0.00 0.00 0.00 2.57
2682 3853 5.445964 AGTGGTCTTGGTTGTTCTGTTAAT 58.554 37.500 0.00 0.00 0.00 1.40
2728 3901 1.024271 GTCCAGCAGTGCTTTGAACA 58.976 50.000 16.89 0.00 36.40 3.18
2795 3968 3.571401 AGATCACAAAGGGAAGCAAAGTG 59.429 43.478 0.00 0.00 0.00 3.16
2975 4150 0.109153 ATGCACCTCTGTTGCTGTGA 59.891 50.000 0.00 0.00 0.00 3.58
2994 4169 8.955388 TGCTGTGATTGCTAAATTGATTTAGTA 58.045 29.630 19.29 14.60 46.78 1.82
2995 4170 9.443283 GCTGTGATTGCTAAATTGATTTAGTAG 57.557 33.333 19.29 7.95 46.78 2.57
3334 4614 4.274214 TGACTTGAGACAAATTGTGCAGAG 59.726 41.667 2.20 5.17 0.00 3.35
3366 4646 1.486211 AACAGAGGGGGTAGTGATCG 58.514 55.000 0.00 0.00 0.00 3.69
3515 4796 5.123936 AGATGAACGAAAATAGCCTTACCC 58.876 41.667 0.00 0.00 0.00 3.69
3746 5027 8.891671 GAGTATCTTATATACTACTCCCTCCG 57.108 42.308 11.74 0.00 35.93 4.63
3747 5028 8.391305 AGTATCTTATATACTACTCCCTCCGT 57.609 38.462 0.00 0.00 33.45 4.69
3748 5029 8.834733 AGTATCTTATATACTACTCCCTCCGTT 58.165 37.037 0.00 0.00 33.45 4.44
3749 5030 9.108284 GTATCTTATATACTACTCCCTCCGTTC 57.892 40.741 0.00 0.00 0.00 3.95
3750 5031 6.479884 TCTTATATACTACTCCCTCCGTTCC 58.520 44.000 0.00 0.00 0.00 3.62
3751 5032 1.978454 ATACTACTCCCTCCGTTCCG 58.022 55.000 0.00 0.00 0.00 4.30
3752 5033 0.911769 TACTACTCCCTCCGTTCCGA 59.088 55.000 0.00 0.00 0.00 4.55
3753 5034 0.038744 ACTACTCCCTCCGTTCCGAA 59.961 55.000 0.00 0.00 0.00 4.30
3754 5035 1.341778 ACTACTCCCTCCGTTCCGAAT 60.342 52.381 0.00 0.00 0.00 3.34
3755 5036 1.755380 CTACTCCCTCCGTTCCGAATT 59.245 52.381 0.00 0.00 0.00 2.17
3756 5037 1.856629 ACTCCCTCCGTTCCGAATTA 58.143 50.000 0.00 0.00 0.00 1.40
3757 5038 1.479730 ACTCCCTCCGTTCCGAATTAC 59.520 52.381 0.00 0.00 0.00 1.89
3758 5039 1.755380 CTCCCTCCGTTCCGAATTACT 59.245 52.381 0.00 0.00 0.00 2.24
3759 5040 2.167900 CTCCCTCCGTTCCGAATTACTT 59.832 50.000 0.00 0.00 0.00 2.24
3760 5041 2.093869 TCCCTCCGTTCCGAATTACTTG 60.094 50.000 0.00 0.00 0.00 3.16
3761 5042 2.354403 CCCTCCGTTCCGAATTACTTGT 60.354 50.000 0.00 0.00 0.00 3.16
3762 5043 2.928116 CCTCCGTTCCGAATTACTTGTC 59.072 50.000 0.00 0.00 0.00 3.18
3763 5044 2.597305 CTCCGTTCCGAATTACTTGTCG 59.403 50.000 0.00 0.00 37.01 4.35
3764 5045 1.060122 CCGTTCCGAATTACTTGTCGC 59.940 52.381 0.00 0.00 35.93 5.19
3765 5046 1.722464 CGTTCCGAATTACTTGTCGCA 59.278 47.619 0.00 0.00 35.93 5.10
3766 5047 2.471749 CGTTCCGAATTACTTGTCGCAC 60.472 50.000 0.00 0.00 35.93 5.34
3767 5048 1.342555 TCCGAATTACTTGTCGCACG 58.657 50.000 0.00 0.00 35.93 5.34
3768 5049 1.065358 CCGAATTACTTGTCGCACGT 58.935 50.000 0.00 0.00 35.93 4.49
3769 5050 2.095314 TCCGAATTACTTGTCGCACGTA 60.095 45.455 0.00 0.00 35.93 3.57
3770 5051 2.855963 CCGAATTACTTGTCGCACGTAT 59.144 45.455 0.00 0.00 35.93 3.06
3771 5052 3.301579 CCGAATTACTTGTCGCACGTATG 60.302 47.826 0.00 0.00 35.93 2.39
3772 5053 3.301579 CGAATTACTTGTCGCACGTATGG 60.302 47.826 0.00 0.00 0.00 2.74
3773 5054 3.513680 ATTACTTGTCGCACGTATGGA 57.486 42.857 0.00 0.00 0.00 3.41
3774 5055 3.513680 TTACTTGTCGCACGTATGGAT 57.486 42.857 0.00 0.00 0.00 3.41
3775 5056 1.640428 ACTTGTCGCACGTATGGATG 58.360 50.000 0.00 0.00 0.00 3.51
3776 5057 1.067142 ACTTGTCGCACGTATGGATGT 60.067 47.619 0.00 0.00 0.00 3.06
3777 5058 2.164827 ACTTGTCGCACGTATGGATGTA 59.835 45.455 0.00 0.00 0.00 2.29
3778 5059 3.181479 ACTTGTCGCACGTATGGATGTAT 60.181 43.478 0.00 0.00 0.00 2.29
3779 5060 3.007979 TGTCGCACGTATGGATGTATC 57.992 47.619 0.00 0.00 0.00 2.24
3780 5061 2.621526 TGTCGCACGTATGGATGTATCT 59.378 45.455 0.00 0.00 0.00 1.98
3781 5062 3.816523 TGTCGCACGTATGGATGTATCTA 59.183 43.478 0.00 0.00 0.00 1.98
3782 5063 4.083484 TGTCGCACGTATGGATGTATCTAG 60.083 45.833 0.00 0.00 0.00 2.43
3783 5064 4.153655 GTCGCACGTATGGATGTATCTAGA 59.846 45.833 0.00 0.00 0.00 2.43
3784 5065 4.941873 TCGCACGTATGGATGTATCTAGAT 59.058 41.667 10.73 10.73 0.00 1.98
3785 5066 5.030936 CGCACGTATGGATGTATCTAGATG 58.969 45.833 15.79 0.00 0.00 2.90
3786 5067 5.392057 CGCACGTATGGATGTATCTAGATGT 60.392 44.000 15.79 1.25 30.36 3.06
3787 5068 6.183360 CGCACGTATGGATGTATCTAGATGTA 60.183 42.308 15.79 4.44 29.44 2.29
3788 5069 7.467403 CGCACGTATGGATGTATCTAGATGTAT 60.467 40.741 15.79 9.11 29.44 2.29
3789 5070 8.191446 GCACGTATGGATGTATCTAGATGTATT 58.809 37.037 15.79 0.00 29.44 1.89
3814 5095 9.582431 TTTTAGTTCTAGATACATCCGTTTCAG 57.418 33.333 0.00 0.00 0.00 3.02
3815 5096 5.593010 AGTTCTAGATACATCCGTTTCAGC 58.407 41.667 0.00 0.00 0.00 4.26
3816 5097 4.224715 TCTAGATACATCCGTTTCAGCG 57.775 45.455 0.00 0.00 0.00 5.18
3817 5098 3.881089 TCTAGATACATCCGTTTCAGCGA 59.119 43.478 0.00 0.00 0.00 4.93
3818 5099 2.810650 AGATACATCCGTTTCAGCGAC 58.189 47.619 0.00 0.00 0.00 5.19
3819 5100 1.517276 GATACATCCGTTTCAGCGACG 59.483 52.381 0.00 0.00 40.05 5.12
3820 5101 0.522626 TACATCCGTTTCAGCGACGA 59.477 50.000 0.00 0.00 42.82 4.20
3821 5102 0.732880 ACATCCGTTTCAGCGACGAG 60.733 55.000 0.00 0.00 42.82 4.18
3822 5103 0.732880 CATCCGTTTCAGCGACGAGT 60.733 55.000 0.00 0.00 42.82 4.18
3823 5104 0.806868 ATCCGTTTCAGCGACGAGTA 59.193 50.000 0.00 0.00 42.82 2.59
3824 5105 0.592637 TCCGTTTCAGCGACGAGTAA 59.407 50.000 0.00 0.00 42.82 2.24
3825 5106 1.200716 TCCGTTTCAGCGACGAGTAAT 59.799 47.619 0.00 0.00 42.82 1.89
3826 5107 1.990563 CCGTTTCAGCGACGAGTAATT 59.009 47.619 0.00 0.00 42.82 1.40
3827 5108 2.410730 CCGTTTCAGCGACGAGTAATTT 59.589 45.455 0.00 0.00 42.82 1.82
3828 5109 3.395671 CGTTTCAGCGACGAGTAATTTG 58.604 45.455 0.00 0.00 42.82 2.32
3829 5110 3.720920 CGTTTCAGCGACGAGTAATTTGG 60.721 47.826 0.00 0.00 42.82 3.28
3830 5111 3.306917 TTCAGCGACGAGTAATTTGGA 57.693 42.857 0.00 0.00 0.00 3.53
3831 5112 3.306917 TCAGCGACGAGTAATTTGGAA 57.693 42.857 0.00 0.00 0.00 3.53
3832 5113 2.991190 TCAGCGACGAGTAATTTGGAAC 59.009 45.455 0.00 0.00 0.00 3.62
3833 5114 1.990563 AGCGACGAGTAATTTGGAACG 59.009 47.619 0.00 0.00 0.00 3.95
3834 5115 1.060122 GCGACGAGTAATTTGGAACGG 59.940 52.381 0.00 0.00 0.00 4.44
3835 5116 2.598589 CGACGAGTAATTTGGAACGGA 58.401 47.619 0.00 0.00 0.00 4.69
3836 5117 2.597305 CGACGAGTAATTTGGAACGGAG 59.403 50.000 0.00 0.00 0.00 4.63
3837 5118 2.928116 GACGAGTAATTTGGAACGGAGG 59.072 50.000 0.00 0.00 0.00 4.30
3838 5119 2.277084 CGAGTAATTTGGAACGGAGGG 58.723 52.381 0.00 0.00 0.00 4.30
3839 5120 2.093869 CGAGTAATTTGGAACGGAGGGA 60.094 50.000 0.00 0.00 0.00 4.20
3840 5121 3.532542 GAGTAATTTGGAACGGAGGGAG 58.467 50.000 0.00 0.00 0.00 4.30
3920 5201 4.904241 AGAAGAATGAGAACAAGGAGGTG 58.096 43.478 0.00 0.00 0.00 4.00
3974 5255 0.861837 GCGAGGCCATTCAGTATTCG 59.138 55.000 5.01 2.71 0.00 3.34
4025 5306 5.897377 ACCAAGATGTATTTTTCCCTTCG 57.103 39.130 0.00 0.00 0.00 3.79
4026 5307 4.157840 ACCAAGATGTATTTTTCCCTTCGC 59.842 41.667 0.00 0.00 0.00 4.70
4057 5339 4.000325 TGATGACGGTGAAGGTGTATTTG 59.000 43.478 0.00 0.00 0.00 2.32
4059 5341 2.105134 TGACGGTGAAGGTGTATTTGGT 59.895 45.455 0.00 0.00 0.00 3.67
4066 5348 6.459848 CGGTGAAGGTGTATTTGGTTTTACAA 60.460 38.462 0.00 0.00 30.59 2.41
4138 5425 2.167281 CTGCAGAGCTTAAGGCAGTAGA 59.833 50.000 8.42 0.00 46.47 2.59
4146 5433 2.596904 TAAGGCAGTAGAATGTCGGC 57.403 50.000 0.00 0.00 0.00 5.54
4147 5434 0.613260 AAGGCAGTAGAATGTCGGCA 59.387 50.000 0.00 0.00 0.00 5.69
4162 5450 1.355210 GGCATTGTTGTATCGCGGG 59.645 57.895 6.13 0.00 0.00 6.13
4180 5468 5.860182 TCGCGGGAATCTTCTATTAATAACG 59.140 40.000 6.13 0.00 0.00 3.18
4364 6927 0.458543 ATATCGATCCATGGCGTCGC 60.459 55.000 25.47 9.22 35.48 5.19
4505 7069 3.272581 GAAGACCTGCTAGACTACGTCT 58.727 50.000 0.00 1.82 45.54 4.18
4552 7116 2.523168 TCCAGCACCGTCTGTCCA 60.523 61.111 0.00 0.00 32.32 4.02
4642 7206 0.249120 TTCACCCTCGCATCGACAAT 59.751 50.000 0.00 0.00 0.00 2.71
4643 7207 0.460109 TCACCCTCGCATCGACAATG 60.460 55.000 0.00 0.00 38.50 2.82
4663 7227 2.066262 GGACGTTTTCTGAATCTCGCA 58.934 47.619 0.00 0.00 0.00 5.10
4666 7230 3.131396 ACGTTTTCTGAATCTCGCAACT 58.869 40.909 0.00 0.00 0.00 3.16
4708 7272 0.251354 TGCCTCTCTTGATGGACTGC 59.749 55.000 0.00 0.00 0.00 4.40
4727 7291 0.037697 CCGTGTCCTTGATTCGGTCA 60.038 55.000 0.00 0.00 36.99 4.02
4757 7321 3.569194 TTGTCCTCTACAAAGCCAACA 57.431 42.857 0.00 0.00 45.11 3.33
4761 7325 2.375174 TCCTCTACAAAGCCAACACCAT 59.625 45.455 0.00 0.00 0.00 3.55
4769 7333 1.181098 AGCCAACACCATGACCTTGC 61.181 55.000 0.00 0.00 0.00 4.01
4806 7370 0.674895 GGCGACATTGTGAAGCTCCT 60.675 55.000 0.00 0.00 0.00 3.69
4807 7371 1.160137 GCGACATTGTGAAGCTCCTT 58.840 50.000 0.00 0.00 0.00 3.36
4820 7384 0.729690 GCTCCTTCCGCTCATGAAAC 59.270 55.000 0.00 0.00 0.00 2.78
4859 7423 1.153628 GAGGGACGGTGTGATTCGG 60.154 63.158 0.00 0.00 0.00 4.30
4860 7424 1.885163 GAGGGACGGTGTGATTCGGT 61.885 60.000 0.00 0.00 0.00 4.69
4861 7425 1.740296 GGGACGGTGTGATTCGGTG 60.740 63.158 0.00 0.00 0.00 4.94
4862 7426 1.005394 GGACGGTGTGATTCGGTGT 60.005 57.895 0.00 0.00 0.00 4.16
4863 7427 0.601841 GGACGGTGTGATTCGGTGTT 60.602 55.000 0.00 0.00 0.00 3.32
4864 7428 0.511221 GACGGTGTGATTCGGTGTTG 59.489 55.000 0.00 0.00 0.00 3.33
4865 7429 1.206578 CGGTGTGATTCGGTGTTGC 59.793 57.895 0.00 0.00 0.00 4.17
4866 7430 1.227999 CGGTGTGATTCGGTGTTGCT 61.228 55.000 0.00 0.00 0.00 3.91
4867 7431 0.517316 GGTGTGATTCGGTGTTGCTC 59.483 55.000 0.00 0.00 0.00 4.26
4868 7432 1.225855 GTGTGATTCGGTGTTGCTCA 58.774 50.000 0.00 0.00 0.00 4.26
4869 7433 1.601903 GTGTGATTCGGTGTTGCTCAA 59.398 47.619 0.00 0.00 0.00 3.02
4942 7517 2.285026 CGTGCATCAATATATACGCCGC 60.285 50.000 0.00 0.00 0.00 6.53
4962 7537 1.595794 CGTATTTTTCGCTACCGCCAT 59.404 47.619 0.00 0.00 0.00 4.40
5021 7596 3.394606 ACCCTTGTCCATACCCATATCAC 59.605 47.826 0.00 0.00 0.00 3.06
5027 7602 4.913355 TGTCCATACCCATATCACTCCAAT 59.087 41.667 0.00 0.00 0.00 3.16
5072 7647 2.359981 TACTACAGGTAGCAGCGGAT 57.640 50.000 6.38 0.00 36.66 4.18
5074 7649 0.747255 CTACAGGTAGCAGCGGATGT 59.253 55.000 0.00 0.00 0.00 3.06
5098 7673 0.609662 TACTACAACTTGACCCGCCC 59.390 55.000 0.00 0.00 0.00 6.13
5120 7695 3.254166 CAGTTATGAGTATGGGGCAATGC 59.746 47.826 0.00 0.00 0.00 3.56
5134 7709 1.067915 GCAATGCCGCCTTCTTTGTTA 60.068 47.619 0.00 0.00 0.00 2.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 7.934855 AGATGTGATGATTTTAGCTCTGTTT 57.065 32.000 0.00 0.00 0.00 2.83
7 8 7.627939 GCAAGATGTGATGATTTTAGCTCTGTT 60.628 37.037 0.00 0.00 0.00 3.16
33 34 1.542915 CACTTGCTTGGATGAACAGGG 59.457 52.381 0.00 0.00 0.00 4.45
56 57 4.638304 TCTTTTCCCCGAAAGACTAAGTG 58.362 43.478 0.00 0.00 39.90 3.16
60 61 5.556006 TTCTTCTTTTCCCCGAAAGACTA 57.444 39.130 0.00 0.00 43.32 2.59
71 72 9.631452 CTTTGTCTATCCATTTTCTTCTTTTCC 57.369 33.333 0.00 0.00 0.00 3.13
80 81 5.904362 AGCACCTTTGTCTATCCATTTTC 57.096 39.130 0.00 0.00 0.00 2.29
81 82 6.670695 AAAGCACCTTTGTCTATCCATTTT 57.329 33.333 0.00 0.00 31.98 1.82
102 103 7.773224 TCAACTCTCTCAAGGAACATAACAAAA 59.227 33.333 0.00 0.00 0.00 2.44
106 107 6.692486 TCTCAACTCTCTCAAGGAACATAAC 58.308 40.000 0.00 0.00 0.00 1.89
109 110 5.083122 TCTCTCAACTCTCTCAAGGAACAT 58.917 41.667 0.00 0.00 0.00 2.71
110 111 4.474394 TCTCTCAACTCTCTCAAGGAACA 58.526 43.478 0.00 0.00 0.00 3.18
115 116 6.319405 TGATCATCTCTCTCAACTCTCTCAAG 59.681 42.308 0.00 0.00 0.00 3.02
120 121 7.765360 ACAAAATGATCATCTCTCTCAACTCTC 59.235 37.037 9.06 0.00 0.00 3.20
123 124 7.768120 GGTACAAAATGATCATCTCTCTCAACT 59.232 37.037 9.06 0.00 0.00 3.16
124 125 7.011857 GGGTACAAAATGATCATCTCTCTCAAC 59.988 40.741 9.06 0.94 0.00 3.18
125 126 7.050377 GGGTACAAAATGATCATCTCTCTCAA 58.950 38.462 9.06 0.00 0.00 3.02
126 127 6.385176 AGGGTACAAAATGATCATCTCTCTCA 59.615 38.462 9.06 0.00 0.00 3.27
133 134 6.352516 ACAGAGAGGGTACAAAATGATCATC 58.647 40.000 9.06 0.00 0.00 2.92
157 158 3.917300 TGGTTAAAAGGAAAAGGCTGGA 58.083 40.909 0.00 0.00 0.00 3.86
161 162 6.934083 TCATGATTTGGTTAAAAGGAAAAGGC 59.066 34.615 0.00 0.00 0.00 4.35
162 163 7.387673 GGTCATGATTTGGTTAAAAGGAAAAGG 59.612 37.037 0.00 0.00 0.00 3.11
181 182 9.695526 CTTTTGTATTTTGAAATGAGGTCATGA 57.304 29.630 0.00 0.00 36.56 3.07
186 187 7.610580 TCCCTTTTGTATTTTGAAATGAGGT 57.389 32.000 0.00 0.00 0.00 3.85
324 330 9.807649 ATCAAATTAAGCGCTTGAAATAGAAAT 57.192 25.926 32.23 17.59 33.08 2.17
343 350 4.038642 GGTAGAGGCGAGAGAGATCAAATT 59.961 45.833 0.00 0.00 0.00 1.82
423 430 4.274978 AGGAAAAGAAAGTTTCGGAACCA 58.725 39.130 19.03 0.00 38.21 3.67
517 524 0.685131 CTGGCATGGCTTCATCCCAA 60.685 55.000 21.08 0.00 38.18 4.12
519 526 0.685458 AACTGGCATGGCTTCATCCC 60.685 55.000 21.08 0.00 0.00 3.85
563 570 3.684305 CGAGGACAAGCAATCACAATACA 59.316 43.478 0.00 0.00 0.00 2.29
704 711 1.881591 GTAACCACGGGTTGCACTAA 58.118 50.000 15.93 0.00 46.35 2.24
781 789 3.821033 GGGACACCTTATTGTATCCATGC 59.179 47.826 0.00 0.00 0.00 4.06
801 1433 8.807948 TCTATCAAGGAACATAAAGAAAAGGG 57.192 34.615 0.00 0.00 0.00 3.95
880 1516 7.995488 AGATCAGTCCCTGGTAAAATTAAGATG 59.005 37.037 0.00 0.00 31.51 2.90
881 1517 7.995488 CAGATCAGTCCCTGGTAAAATTAAGAT 59.005 37.037 0.00 0.00 31.51 2.40
884 1520 7.027874 ACAGATCAGTCCCTGGTAAAATTAA 57.972 36.000 0.00 0.00 34.85 1.40
886 1522 5.014123 TGACAGATCAGTCCCTGGTAAAATT 59.986 40.000 14.91 0.00 37.73 1.82
891 1527 2.043115 AGTGACAGATCAGTCCCTGGTA 59.957 50.000 14.91 0.00 32.71 3.25
987 1730 0.389556 ACTGCATCACTCTGTCGCTG 60.390 55.000 0.00 0.00 0.00 5.18
988 1731 0.389556 CACTGCATCACTCTGTCGCT 60.390 55.000 0.00 0.00 0.00 4.93
989 1732 1.964290 GCACTGCATCACTCTGTCGC 61.964 60.000 0.00 0.00 0.00 5.19
990 1733 0.668401 TGCACTGCATCACTCTGTCG 60.668 55.000 0.00 0.00 31.71 4.35
1001 1744 0.689055 ATTGACTCCTCTGCACTGCA 59.311 50.000 3.11 3.11 36.92 4.41
1006 1753 3.974719 AGAGTAGATTGACTCCTCTGCA 58.025 45.455 0.02 0.00 45.97 4.41
1161 1939 2.818714 CAAGGCAGAGGCGCAGAG 60.819 66.667 10.83 0.00 42.47 3.35
1162 1940 3.596066 GACAAGGCAGAGGCGCAGA 62.596 63.158 10.83 0.00 42.47 4.26
1163 1941 3.123620 GACAAGGCAGAGGCGCAG 61.124 66.667 10.83 0.00 42.47 5.18
1164 1942 4.704833 GGACAAGGCAGAGGCGCA 62.705 66.667 10.83 0.00 42.47 6.09
1167 1945 2.543067 AATCGGGACAAGGCAGAGGC 62.543 60.000 0.00 0.00 40.13 4.70
1168 1946 0.035056 AAATCGGGACAAGGCAGAGG 60.035 55.000 0.00 0.00 0.00 3.69
1226 2004 1.089112 CATGAACAGATCAGCCGCAA 58.911 50.000 0.00 0.00 42.53 4.85
1358 2141 5.239525 GCGAAAATCCATGCTAAATAGGACT 59.760 40.000 0.00 0.00 32.04 3.85
1455 2286 1.306642 GGCTCGTCGAGTCCTCTTCA 61.307 60.000 22.61 0.00 31.39 3.02
1506 2364 2.687805 CCTCCTCGACAGCGACGAA 61.688 63.158 0.00 0.00 42.51 3.85
1568 2426 0.545548 AAAAGACCGCTCCTCCTCCT 60.546 55.000 0.00 0.00 0.00 3.69
1569 2427 0.108089 GAAAAGACCGCTCCTCCTCC 60.108 60.000 0.00 0.00 0.00 4.30
1570 2428 0.899019 AGAAAAGACCGCTCCTCCTC 59.101 55.000 0.00 0.00 0.00 3.71
1580 2438 5.163612 GGCATTCAGTAATGGAGAAAAGACC 60.164 44.000 0.00 0.00 42.39 3.85
1639 2516 3.898509 GCCTGTGCGCCAAACACA 61.899 61.111 4.18 0.09 45.42 3.72
1696 2573 0.390124 TTCAGCTGGCAAGGCAAAAG 59.610 50.000 15.13 0.00 0.00 2.27
1762 2639 3.075283 TGCCCAAGATCCAACTTCCTAAA 59.925 43.478 0.00 0.00 0.00 1.85
1848 2997 7.744715 AGTTTAAGAAATATTTCAGCAACGACG 59.255 33.333 26.02 0.00 39.61 5.12
1909 3058 8.395633 ACAAGCGCAACCTTATATAAACTAAAG 58.604 33.333 11.47 0.00 0.00 1.85
1941 3090 2.256306 TCAGACATAGCCCAAGTCACA 58.744 47.619 0.00 0.00 34.80 3.58
1946 3095 5.902613 TTTTGATTCAGACATAGCCCAAG 57.097 39.130 0.00 0.00 0.00 3.61
2120 3271 4.988708 TTTATTTTCGTGTGGTCGGTAC 57.011 40.909 0.00 0.00 0.00 3.34
2121 3272 5.998454 TTTTTATTTTCGTGTGGTCGGTA 57.002 34.783 0.00 0.00 0.00 4.02
2122 3273 4.897025 TTTTTATTTTCGTGTGGTCGGT 57.103 36.364 0.00 0.00 0.00 4.69
2123 3274 5.510323 GCTATTTTTATTTTCGTGTGGTCGG 59.490 40.000 0.00 0.00 0.00 4.79
2124 3275 6.081049 TGCTATTTTTATTTTCGTGTGGTCG 58.919 36.000 0.00 0.00 0.00 4.79
2125 3276 7.753132 TCATGCTATTTTTATTTTCGTGTGGTC 59.247 33.333 0.00 0.00 0.00 4.02
2126 3277 7.598278 TCATGCTATTTTTATTTTCGTGTGGT 58.402 30.769 0.00 0.00 0.00 4.16
2390 3556 7.680730 ACTACAGGTCTAAAATCACAGTGAAT 58.319 34.615 7.50 0.00 0.00 2.57
2391 3557 7.062749 ACTACAGGTCTAAAATCACAGTGAA 57.937 36.000 7.50 0.00 0.00 3.18
2448 3614 6.580041 GTGCTACAATTCATCAGTCACAAAAG 59.420 38.462 0.00 0.00 0.00 2.27
2459 3625 7.042389 GCCTAGAAACTAGTGCTACAATTCATC 60.042 40.741 0.00 0.00 0.00 2.92
2461 3627 6.070767 AGCCTAGAAACTAGTGCTACAATTCA 60.071 38.462 14.91 0.00 0.00 2.57
2682 3853 9.371136 CAACTTTACATAAAGAGTCTAGCATCA 57.629 33.333 16.46 0.00 44.07 3.07
2795 3968 7.540055 CCAGTTTTCTTGTCAAGCTCATATTTC 59.460 37.037 7.78 0.00 0.00 2.17
2995 4170 9.543018 GCAAAATAAGTTAACTCATGAGTACAC 57.457 33.333 28.10 24.41 41.58 2.90
3060 4235 7.124901 ACTCTATCAACCTGTCATGTTGTAGAT 59.875 37.037 17.29 8.96 42.82 1.98
3062 4237 6.634805 ACTCTATCAACCTGTCATGTTGTAG 58.365 40.000 17.29 16.48 42.82 2.74
3192 4367 1.441738 TGGAGTGCATGAACATCGTG 58.558 50.000 6.60 0.00 36.50 4.35
3252 4531 8.621532 TTATGAGTGCTCAACTTAAGACAAAT 57.378 30.769 10.09 0.00 43.58 2.32
3301 4580 6.633500 TTTGTCTCAAGTCAAACCCATAAG 57.367 37.500 0.00 0.00 30.47 1.73
3334 4614 4.640647 CCCCCTCTGTTTCAGTTTATAAGC 59.359 45.833 0.00 0.00 32.61 3.09
3366 4646 8.589335 TGTGAGAGATAAAAGAGTAACACAAC 57.411 34.615 0.00 0.00 32.90 3.32
3515 4796 4.021102 ACCACCATCCTCAGTAAAACAG 57.979 45.455 0.00 0.00 0.00 3.16
3746 5027 2.471749 CGTGCGACAAGTAATTCGGAAC 60.472 50.000 0.00 0.00 37.32 3.62
3747 5028 1.722464 CGTGCGACAAGTAATTCGGAA 59.278 47.619 0.00 0.00 37.32 4.30
3748 5029 1.336148 ACGTGCGACAAGTAATTCGGA 60.336 47.619 0.00 0.00 35.73 4.55
3749 5030 1.065358 ACGTGCGACAAGTAATTCGG 58.935 50.000 0.00 0.00 35.73 4.30
3750 5031 3.301579 CCATACGTGCGACAAGTAATTCG 60.302 47.826 0.00 0.00 32.82 3.34
3751 5032 3.861113 TCCATACGTGCGACAAGTAATTC 59.139 43.478 0.00 0.00 32.82 2.17
3752 5033 3.852286 TCCATACGTGCGACAAGTAATT 58.148 40.909 0.00 0.00 32.82 1.40
3753 5034 3.513680 TCCATACGTGCGACAAGTAAT 57.486 42.857 0.00 0.00 32.82 1.89
3754 5035 3.183754 CATCCATACGTGCGACAAGTAA 58.816 45.455 0.00 0.00 32.82 2.24
3755 5036 2.164827 ACATCCATACGTGCGACAAGTA 59.835 45.455 0.00 7.72 33.49 2.24
3756 5037 1.067142 ACATCCATACGTGCGACAAGT 60.067 47.619 0.00 0.00 0.00 3.16
3757 5038 1.640428 ACATCCATACGTGCGACAAG 58.360 50.000 0.00 0.00 0.00 3.16
3758 5039 2.943449 TACATCCATACGTGCGACAA 57.057 45.000 0.00 0.00 0.00 3.18
3759 5040 2.621526 AGATACATCCATACGTGCGACA 59.378 45.455 0.00 0.00 0.00 4.35
3760 5041 3.284323 AGATACATCCATACGTGCGAC 57.716 47.619 0.00 0.00 0.00 5.19
3761 5042 4.320870 TCTAGATACATCCATACGTGCGA 58.679 43.478 0.00 0.00 0.00 5.10
3762 5043 4.680171 TCTAGATACATCCATACGTGCG 57.320 45.455 0.00 0.00 0.00 5.34
3763 5044 5.955488 ACATCTAGATACATCCATACGTGC 58.045 41.667 4.54 0.00 0.00 5.34
3788 5069 9.582431 CTGAAACGGATGTATCTAGAACTAAAA 57.418 33.333 0.00 0.00 0.00 1.52
3789 5070 7.705325 GCTGAAACGGATGTATCTAGAACTAAA 59.295 37.037 0.00 0.00 0.00 1.85
3790 5071 7.201145 GCTGAAACGGATGTATCTAGAACTAA 58.799 38.462 0.00 0.00 0.00 2.24
3791 5072 6.512903 CGCTGAAACGGATGTATCTAGAACTA 60.513 42.308 0.00 0.00 0.00 2.24
3792 5073 5.593010 GCTGAAACGGATGTATCTAGAACT 58.407 41.667 0.00 0.00 0.00 3.01
3793 5074 4.441415 CGCTGAAACGGATGTATCTAGAAC 59.559 45.833 0.00 0.00 0.00 3.01
3794 5075 4.337274 TCGCTGAAACGGATGTATCTAGAA 59.663 41.667 0.00 0.00 0.00 2.10
3795 5076 3.881089 TCGCTGAAACGGATGTATCTAGA 59.119 43.478 0.00 0.00 0.00 2.43
3796 5077 3.975670 GTCGCTGAAACGGATGTATCTAG 59.024 47.826 0.00 0.00 0.00 2.43
3797 5078 3.547413 CGTCGCTGAAACGGATGTATCTA 60.547 47.826 0.00 0.00 36.51 1.98
3798 5079 2.794981 CGTCGCTGAAACGGATGTATCT 60.795 50.000 0.00 0.00 36.51 1.98
3799 5080 1.517276 CGTCGCTGAAACGGATGTATC 59.483 52.381 0.00 0.00 36.51 2.24
3800 5081 1.133598 TCGTCGCTGAAACGGATGTAT 59.866 47.619 0.00 0.00 40.45 2.29
3801 5082 0.522626 TCGTCGCTGAAACGGATGTA 59.477 50.000 0.00 0.00 40.45 2.29
3802 5083 0.732880 CTCGTCGCTGAAACGGATGT 60.733 55.000 0.00 0.00 40.45 3.06
3803 5084 0.732880 ACTCGTCGCTGAAACGGATG 60.733 55.000 0.00 0.00 40.45 3.51
3804 5085 0.806868 TACTCGTCGCTGAAACGGAT 59.193 50.000 0.00 0.00 40.45 4.18
3805 5086 0.592637 TTACTCGTCGCTGAAACGGA 59.407 50.000 0.00 0.00 40.45 4.69
3806 5087 1.625616 ATTACTCGTCGCTGAAACGG 58.374 50.000 0.00 0.00 40.45 4.44
3807 5088 3.395671 CAAATTACTCGTCGCTGAAACG 58.604 45.455 0.00 0.00 41.39 3.60
3808 5089 3.430895 TCCAAATTACTCGTCGCTGAAAC 59.569 43.478 0.00 0.00 0.00 2.78
3809 5090 3.655486 TCCAAATTACTCGTCGCTGAAA 58.345 40.909 0.00 0.00 0.00 2.69
3810 5091 3.306917 TCCAAATTACTCGTCGCTGAA 57.693 42.857 0.00 0.00 0.00 3.02
3811 5092 2.991190 GTTCCAAATTACTCGTCGCTGA 59.009 45.455 0.00 0.00 0.00 4.26
3812 5093 2.222508 CGTTCCAAATTACTCGTCGCTG 60.223 50.000 0.00 0.00 0.00 5.18
3813 5094 1.990563 CGTTCCAAATTACTCGTCGCT 59.009 47.619 0.00 0.00 0.00 4.93
3814 5095 1.060122 CCGTTCCAAATTACTCGTCGC 59.940 52.381 0.00 0.00 0.00 5.19
3815 5096 2.597305 CTCCGTTCCAAATTACTCGTCG 59.403 50.000 0.00 0.00 0.00 5.12
3816 5097 2.928116 CCTCCGTTCCAAATTACTCGTC 59.072 50.000 0.00 0.00 0.00 4.20
3817 5098 2.354403 CCCTCCGTTCCAAATTACTCGT 60.354 50.000 0.00 0.00 0.00 4.18
3818 5099 2.093869 TCCCTCCGTTCCAAATTACTCG 60.094 50.000 0.00 0.00 0.00 4.18
3819 5100 3.055312 ACTCCCTCCGTTCCAAATTACTC 60.055 47.826 0.00 0.00 0.00 2.59
3820 5101 2.910977 ACTCCCTCCGTTCCAAATTACT 59.089 45.455 0.00 0.00 0.00 2.24
3821 5102 3.345508 ACTCCCTCCGTTCCAAATTAC 57.654 47.619 0.00 0.00 0.00 1.89
3822 5103 4.081309 CAGTACTCCCTCCGTTCCAAATTA 60.081 45.833 0.00 0.00 0.00 1.40
3823 5104 2.910977 AGTACTCCCTCCGTTCCAAATT 59.089 45.455 0.00 0.00 0.00 1.82
3824 5105 2.236395 CAGTACTCCCTCCGTTCCAAAT 59.764 50.000 0.00 0.00 0.00 2.32
3825 5106 1.621814 CAGTACTCCCTCCGTTCCAAA 59.378 52.381 0.00 0.00 0.00 3.28
3826 5107 1.263356 CAGTACTCCCTCCGTTCCAA 58.737 55.000 0.00 0.00 0.00 3.53
3827 5108 0.113776 ACAGTACTCCCTCCGTTCCA 59.886 55.000 0.00 0.00 0.00 3.53
3828 5109 2.134789 TACAGTACTCCCTCCGTTCC 57.865 55.000 0.00 0.00 0.00 3.62
3829 5110 7.700022 ATTATATACAGTACTCCCTCCGTTC 57.300 40.000 0.00 0.00 0.00 3.95
3830 5111 8.488308 AAATTATATACAGTACTCCCTCCGTT 57.512 34.615 0.00 0.00 0.00 4.44
3831 5112 9.240734 CTAAATTATATACAGTACTCCCTCCGT 57.759 37.037 0.00 0.00 0.00 4.69
3832 5113 9.458727 TCTAAATTATATACAGTACTCCCTCCG 57.541 37.037 0.00 0.00 0.00 4.63
3920 5201 0.645868 GTAAGAACGCATCGACAGCC 59.354 55.000 6.14 0.00 0.00 4.85
3974 5255 6.758593 TCAACACGAAACTGTACTTACATC 57.241 37.500 0.00 0.00 35.36 3.06
4025 5306 1.328680 CACCGTCATCACTTATGCAGC 59.671 52.381 0.00 0.00 35.38 5.25
4026 5307 2.892374 TCACCGTCATCACTTATGCAG 58.108 47.619 0.00 0.00 35.38 4.41
4057 5339 6.206498 AGAAAAGAAGCGTCATTGTAAAACC 58.794 36.000 1.61 0.00 0.00 3.27
4059 5341 8.696410 AAAAGAAAAGAAGCGTCATTGTAAAA 57.304 26.923 1.61 0.00 0.00 1.52
4146 5433 2.872245 AGATTCCCGCGATACAACAATG 59.128 45.455 8.23 0.00 0.00 2.82
4147 5434 3.194005 AGATTCCCGCGATACAACAAT 57.806 42.857 8.23 0.00 0.00 2.71
4162 5450 8.365647 TCCCCACTCGTTATTAATAGAAGATTC 58.634 37.037 0.00 0.00 0.00 2.52
4180 5468 0.534873 GTCTCAGCTCTTCCCCACTC 59.465 60.000 0.00 0.00 0.00 3.51
4364 6927 2.256461 GCGCTCTGCAGTTTTGGG 59.744 61.111 14.67 11.59 45.45 4.12
4424 6987 0.610687 GGGAGAGAAGACCACTGTGG 59.389 60.000 24.80 24.80 45.02 4.17
4473 7037 4.021925 GGTCTTCGGCCAGCACCT 62.022 66.667 2.24 0.00 0.00 4.00
4552 7116 3.353836 GCAATGCCACGTCCGTGT 61.354 61.111 17.52 0.00 44.02 4.49
4567 7131 2.032634 GTGAAAGCGTGGATCGGCA 61.033 57.895 5.08 0.00 40.26 5.69
4602 7166 1.750399 CCATGACCCTCGGGCAAAG 60.750 63.158 0.82 0.00 39.32 2.77
4642 7206 2.066262 GCGAGATTCAGAAAACGTCCA 58.934 47.619 0.00 0.00 0.00 4.02
4643 7207 2.066262 TGCGAGATTCAGAAAACGTCC 58.934 47.619 0.00 0.00 0.00 4.79
4663 7227 2.354821 GACACAAGCGAAAACTCCAGTT 59.645 45.455 0.00 0.00 40.50 3.16
4666 7230 2.210116 GAGACACAAGCGAAAACTCCA 58.790 47.619 0.00 0.00 0.00 3.86
4708 7272 1.606994 TTGACCGAATCAAGGACACGG 60.607 52.381 0.00 0.00 42.62 4.94
4757 7321 1.067295 TGAAGGAGCAAGGTCATGGT 58.933 50.000 1.42 0.00 0.00 3.55
4761 7325 1.761174 GGGTGAAGGAGCAAGGTCA 59.239 57.895 1.42 0.00 0.00 4.02
4769 7333 1.296715 CGGTGAAGGGGTGAAGGAG 59.703 63.158 0.00 0.00 0.00 3.69
4793 7357 0.326264 AGCGGAAGGAGCTTCACAAT 59.674 50.000 0.00 0.00 43.24 2.71
4806 7370 0.608035 GTGGGGTTTCATGAGCGGAA 60.608 55.000 0.00 0.00 0.00 4.30
4807 7371 1.002624 GTGGGGTTTCATGAGCGGA 60.003 57.895 0.00 0.00 0.00 5.54
4820 7384 0.840722 ACACCTAGGTTCCAGTGGGG 60.841 60.000 13.15 3.65 34.50 4.96
4859 7423 1.082756 CGGCGAACTTGAGCAACAC 60.083 57.895 0.00 0.00 34.54 3.32
4860 7424 2.892334 GCGGCGAACTTGAGCAACA 61.892 57.895 12.98 0.00 34.54 3.33
4861 7425 2.127232 GCGGCGAACTTGAGCAAC 60.127 61.111 12.98 0.00 34.54 4.17
4862 7426 1.911293 GATGCGGCGAACTTGAGCAA 61.911 55.000 12.98 0.00 41.37 3.91
4863 7427 2.358615 ATGCGGCGAACTTGAGCA 60.359 55.556 12.98 0.00 42.28 4.26
4864 7428 2.401195 GATGCGGCGAACTTGAGC 59.599 61.111 12.98 0.00 0.00 4.26
4865 7429 1.021390 AAGGATGCGGCGAACTTGAG 61.021 55.000 12.98 0.00 0.00 3.02
4866 7430 1.003839 AAGGATGCGGCGAACTTGA 60.004 52.632 12.98 0.00 0.00 3.02
4867 7431 1.135315 CAAGGATGCGGCGAACTTG 59.865 57.895 12.98 14.37 33.49 3.16
4868 7432 1.003839 TCAAGGATGCGGCGAACTT 60.004 52.632 12.98 5.48 0.00 2.66
4869 7433 1.448540 CTCAAGGATGCGGCGAACT 60.449 57.895 12.98 0.00 0.00 3.01
4942 7517 1.000884 TGGCGGTAGCGAAAAATACG 58.999 50.000 20.16 0.00 46.35 3.06
5027 7602 7.857456 TGAGGCTCCAGTATATAAAACTTTCA 58.143 34.615 12.86 0.00 0.00 2.69
5072 7647 3.194116 GGGTCAAGTTGTAGTATCGGACA 59.806 47.826 2.11 0.00 0.00 4.02
5074 7649 2.424601 CGGGTCAAGTTGTAGTATCGGA 59.575 50.000 2.11 0.00 0.00 4.55
5098 7673 3.254166 GCATTGCCCCATACTCATAACTG 59.746 47.826 0.00 0.00 0.00 3.16


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

AutoCloner maintained by Alex Coulton.