Multiple sequence alignment - TraesCS2D01G341500

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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 TraesCS2D01G341500 chr2D 100.000 4423 0 0 1 4423 436369858 436365436 0.000000e+00 8168.0
1 TraesCS2D01G341500 chr2D 90.511 137 13 0 4287 4423 29185741 29185877 9.770000e-42 182.0
2 TraesCS2D01G341500 chr2B 92.541 2239 122 30 1642 3856 514866476 514868693 0.000000e+00 3168.0
3 TraesCS2D01G341500 chr2B 93.504 1601 68 21 5 1586 514864762 514866345 0.000000e+00 2348.0
4 TraesCS2D01G341500 chr2B 85.492 386 37 12 1203 1573 30333220 30332839 6.940000e-103 385.0
5 TraesCS2D01G341500 chr2B 87.132 272 29 6 3984 4251 514868768 514869037 2.000000e-78 303.0
6 TraesCS2D01G341500 chr2A 90.379 2245 137 36 1671 3879 550538123 550535922 0.000000e+00 2876.0
7 TraesCS2D01G341500 chr2A 92.454 1683 76 20 5 1677 550539933 550538292 0.000000e+00 2357.0
8 TraesCS2D01G341500 chr2A 89.855 138 14 0 4286 4423 102328527 102328390 1.260000e-40 178.0
9 TraesCS2D01G341500 chr2A 87.500 112 14 0 4285 4396 695287192 695287303 3.590000e-26 130.0
10 TraesCS2D01G341500 chr6D 75.963 857 149 46 2022 2854 271006918 271007741 5.360000e-104 388.0
11 TraesCS2D01G341500 chr6D 88.649 185 19 2 2967 3150 271007831 271008014 1.600000e-54 224.0
12 TraesCS2D01G341500 chr6D 93.478 138 9 0 4286 4423 410135525 410135388 5.800000e-49 206.0
13 TraesCS2D01G341500 chr6D 86.364 176 24 0 3247 3422 271008170 271008345 4.510000e-45 193.0
14 TraesCS2D01G341500 chr6A 77.976 672 105 31 2194 2854 384968085 384967446 8.980000e-102 381.0
15 TraesCS2D01G341500 chr6A 89.011 182 18 2 2970 3150 384967353 384967173 1.600000e-54 224.0
16 TraesCS2D01G341500 chr6A 86.364 176 24 0 3247 3422 384967017 384966842 4.510000e-45 193.0
17 TraesCS2D01G341500 chr5B 83.166 398 35 17 1203 1573 649446537 649446145 7.090000e-88 335.0
18 TraesCS2D01G341500 chr5B 89.781 137 14 0 4287 4423 100551543 100551407 4.550000e-40 176.0
19 TraesCS2D01G341500 chr5B 93.443 61 4 0 4225 4285 360620683 360620623 1.690000e-14 91.6
20 TraesCS2D01G341500 chr3D 93.478 138 8 1 4286 4423 68441162 68441298 2.090000e-48 204.0
21 TraesCS2D01G341500 chr3D 93.443 61 4 0 4225 4285 388689938 388689998 1.690000e-14 91.6
22 TraesCS2D01G341500 chr6B 85.227 176 26 0 3247 3422 431702842 431703017 9.770000e-42 182.0
23 TraesCS2D01G341500 chr6B 92.308 65 4 1 4225 4288 629439669 629439605 1.690000e-14 91.6
24 TraesCS2D01G341500 chr7A 89.855 138 14 0 4286 4423 254846123 254846260 1.260000e-40 178.0
25 TraesCS2D01G341500 chr7A 92.241 116 9 0 4285 4400 679853096 679853211 9.840000e-37 165.0
26 TraesCS2D01G341500 chr7A 82.836 134 21 2 4264 4396 336728580 336728712 7.770000e-23 119.0
27 TraesCS2D01G341500 chr7A 93.443 61 4 0 4225 4285 233866353 233866293 1.690000e-14 91.6
28 TraesCS2D01G341500 chr3B 89.855 138 14 0 4286 4423 782679639 782679776 1.260000e-40 178.0
29 TraesCS2D01G341500 chr3B 85.965 114 15 1 4284 4396 706775287 706775400 2.160000e-23 121.0
30 TraesCS2D01G341500 chr3B 95.000 60 3 0 4225 4284 105305178 105305119 1.310000e-15 95.3
31 TraesCS2D01G341500 chr3A 87.662 154 17 2 4271 4423 457660668 457660516 1.260000e-40 178.0
32 TraesCS2D01G341500 chr3A 87.500 112 14 0 4285 4396 601354818 601354707 3.590000e-26 130.0
33 TraesCS2D01G341500 chr3A 84.921 126 18 1 4271 4396 743686116 743686240 4.640000e-25 126.0
34 TraesCS2D01G341500 chr7B 87.050 139 16 1 4285 4423 9702981 9703117 5.920000e-34 156.0
35 TraesCS2D01G341500 chr7B 93.443 61 4 0 4225 4285 112147540 112147480 1.690000e-14 91.6
36 TraesCS2D01G341500 chr7B 93.333 60 4 0 4225 4284 75992369 75992310 6.090000e-14 89.8
37 TraesCS2D01G341500 chr5A 87.931 116 11 3 4282 4396 596587298 596587411 2.780000e-27 134.0
38 TraesCS2D01G341500 chr1A 95.238 63 3 0 4222 4284 437438403 437438465 2.810000e-17 100.0
39 TraesCS2D01G341500 chr7D 93.443 61 4 0 4225 4285 131527141 131527201 1.690000e-14 91.6


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 TraesCS2D01G341500 chr2D 436365436 436369858 4422 True 8168.000000 8168 100.000000 1 4423 1 chr2D.!!$R1 4422
1 TraesCS2D01G341500 chr2B 514864762 514869037 4275 False 1939.666667 3168 91.059000 5 4251 3 chr2B.!!$F1 4246
2 TraesCS2D01G341500 chr2A 550535922 550539933 4011 True 2616.500000 2876 91.416500 5 3879 2 chr2A.!!$R2 3874
3 TraesCS2D01G341500 chr6D 271006918 271008345 1427 False 268.333333 388 83.658667 2022 3422 3 chr6D.!!$F1 1400
4 TraesCS2D01G341500 chr6A 384966842 384968085 1243 True 266.000000 381 84.450333 2194 3422 3 chr6A.!!$R1 1228

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
821 830 0.108186 CCAGCACAGCCGTTAGATCA 60.108 55.0 0.00 0.00 0.00 2.92 F
1514 1528 0.099082 ACAGCGTTACGAGCTCTAGC 59.901 55.0 9.62 9.57 44.06 3.42 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2619 2909 0.300491 CGCGGTCCAATGTGATAACG 59.700 55.0 0.0 0.0 0.0 3.18 R
3490 3887 1.107114 TCGCAGGAACCAAAGCAAAA 58.893 45.0 0.0 0.0 0.0 2.44 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
61 62 5.992217 AGTGAACAACTAGAGAACATTGGTC 59.008 40.000 0.00 0.00 38.89 4.02
98 106 0.329596 AATGAGACCTTGCCCCTCAC 59.670 55.000 0.00 0.00 39.43 3.51
105 113 3.316573 CTTGCCCCTCACCCGTCTC 62.317 68.421 0.00 0.00 0.00 3.36
128 136 5.360999 TCACAGTCACATAGGTAGGATTCAG 59.639 44.000 0.00 0.00 0.00 3.02
452 460 2.419198 GCGGCGATCATCTCCACT 59.581 61.111 12.98 0.00 0.00 4.00
821 830 0.108186 CCAGCACAGCCGTTAGATCA 60.108 55.000 0.00 0.00 0.00 2.92
822 831 1.473965 CCAGCACAGCCGTTAGATCAT 60.474 52.381 0.00 0.00 0.00 2.45
823 832 2.224042 CCAGCACAGCCGTTAGATCATA 60.224 50.000 0.00 0.00 0.00 2.15
840 849 0.529119 ATAAACGGACGGTGCGGATC 60.529 55.000 25.31 0.00 34.75 3.36
844 853 2.237751 CGGACGGTGCGGATCAATC 61.238 63.158 14.59 0.00 0.00 2.67
871 880 5.467399 CGTGGAACCAGAATGTAAACAAGTA 59.533 40.000 0.00 0.00 0.00 2.24
900 909 6.319911 GGCCAGTAATTAAATTCTTCTGCTCT 59.680 38.462 0.00 0.00 0.00 4.09
904 913 7.492669 CAGTAATTAAATTCTTCTGCTCTCGGA 59.507 37.037 0.00 0.00 0.00 4.55
1170 1184 2.731374 CGCCTCCTCCTCGAATCC 59.269 66.667 0.00 0.00 0.00 3.01
1339 1353 0.174617 CGAGGAGGAGACCAAGAAGC 59.825 60.000 0.00 0.00 0.00 3.86
1356 1370 2.096220 AGCTCGACGAGAAGTGAGTA 57.904 50.000 28.43 0.00 33.50 2.59
1416 1430 4.828072 AGGCTACTTTCTAGGGTTTCAG 57.172 45.455 0.00 0.00 0.00 3.02
1423 1437 6.210287 ACTTTCTAGGGTTTCAGATACTCG 57.790 41.667 0.00 0.00 0.00 4.18
1430 1444 2.334838 GTTTCAGATACTCGTGCCGTT 58.665 47.619 0.00 0.00 0.00 4.44
1434 1448 1.854743 CAGATACTCGTGCCGTTGATG 59.145 52.381 0.00 0.00 0.00 3.07
1450 1464 6.677920 GCCGTTGATGCATCTAACATAGTTTT 60.678 38.462 26.32 0.00 0.00 2.43
1457 1471 8.807948 ATGCATCTAACATAGTTTTACCACTT 57.192 30.769 0.00 0.00 0.00 3.16
1484 1498 8.867935 CAGATAGATTGTCTGATAATTTAGCCG 58.132 37.037 8.58 0.00 44.57 5.52
1485 1499 5.931441 AGATTGTCTGATAATTTAGCCGC 57.069 39.130 1.06 0.00 0.00 6.53
1487 1501 2.479837 TGTCTGATAATTTAGCCGCGG 58.520 47.619 24.05 24.05 0.00 6.46
1488 1502 2.159014 TGTCTGATAATTTAGCCGCGGT 60.159 45.455 28.70 16.08 0.00 5.68
1514 1528 0.099082 ACAGCGTTACGAGCTCTAGC 59.901 55.000 9.62 9.57 44.06 3.42
1569 1587 3.819368 TGATGCTCCTGTTGTTTCTGAA 58.181 40.909 0.00 0.00 0.00 3.02
1602 1635 5.606348 ACTAGAACTAGCTAGCATTTGCT 57.394 39.130 20.91 10.34 44.41 3.91
1810 2081 4.692625 ACAAACAAATCACTGATCTCGAGG 59.307 41.667 13.56 0.00 0.00 4.63
1821 2092 0.820871 ATCTCGAGGAAGGTCTGCAC 59.179 55.000 13.56 0.00 0.00 4.57
1837 2108 2.305928 TGCACTTTAAGCAGCCAGAAA 58.694 42.857 7.37 0.00 37.02 2.52
1864 2135 3.191162 TCTGCAAAGATTGTTCCATTCCG 59.809 43.478 0.00 0.00 0.00 4.30
1883 2154 2.547642 CCGCCCAAATGAAAATGTGTGT 60.548 45.455 0.00 0.00 0.00 3.72
1886 2157 4.125703 GCCCAAATGAAAATGTGTGTTCA 58.874 39.130 0.00 0.00 38.09 3.18
1910 2182 7.831690 TCATGTATCTAGACTCTGAACTTCTGT 59.168 37.037 0.00 0.00 0.00 3.41
1932 2204 4.766404 AGTGTATTGCTTCTTTTTCCCG 57.234 40.909 0.00 0.00 0.00 5.14
1965 2237 5.868257 TCATCTGATTTCACATTACGTTGC 58.132 37.500 0.00 0.00 0.00 4.17
1971 2243 0.785378 TCACATTACGTTGCGTTCGG 59.215 50.000 0.00 0.00 41.54 4.30
1977 2249 0.248990 TACGTTGCGTTCGGTCTTGT 60.249 50.000 0.00 0.00 41.54 3.16
2018 2294 7.797121 TCACCTATCTATGCATAAAGGATCA 57.203 36.000 25.37 12.37 0.00 2.92
2083 2359 5.493977 AGCCCATCTAGCCAAATCCTTATAT 59.506 40.000 0.00 0.00 0.00 0.86
2108 2384 0.323957 AAGGGTTGGCGAGAAGGTAC 59.676 55.000 0.00 0.00 0.00 3.34
2148 2435 3.755112 TTCACCATGTTAGGTTGTCGA 57.245 42.857 0.00 0.00 40.77 4.20
2353 2641 5.582689 AGGCCAAAATGTAAGTATGAAGC 57.417 39.130 5.01 0.00 0.00 3.86
2428 2718 6.374417 AATACTGAGCAACTTCCTTTCCTA 57.626 37.500 0.00 0.00 0.00 2.94
2619 2909 4.060205 TCTTTTACACGGTCCTTACAAGC 58.940 43.478 0.00 0.00 0.00 4.01
2640 2930 1.062002 GTTATCACATTGGACCGCGTG 59.938 52.381 4.92 0.00 0.00 5.34
2652 2942 1.719780 GACCGCGTGTCTCTAAAACAG 59.280 52.381 17.12 0.00 41.03 3.16
2658 2948 3.184581 GCGTGTCTCTAAAACAGAAGGTG 59.815 47.826 0.00 0.00 31.12 4.00
2676 2966 7.388776 CAGAAGGTGTGTATTCATCTTTTCTCA 59.611 37.037 0.00 0.00 38.65 3.27
2750 3044 1.411246 TGTTGACAGGTTGTAGACGCT 59.589 47.619 0.00 0.00 0.00 5.07
2831 3125 4.575885 TCTACAATTGCCAGTACAAGTCC 58.424 43.478 5.05 0.00 31.96 3.85
2859 3153 2.749621 GTGGCATTCTGTAAGTGAAGGG 59.250 50.000 0.00 0.00 33.76 3.95
2922 3218 3.737266 CAGTAATGCTTGTTTGGCTGTTG 59.263 43.478 0.00 0.00 0.00 3.33
2931 3227 3.747521 TTGGCTGTTGTGGTGGGGG 62.748 63.158 0.00 0.00 0.00 5.40
2935 3231 0.468400 GCTGTTGTGGTGGGGGTTAA 60.468 55.000 0.00 0.00 0.00 2.01
2937 3233 0.106116 TGTTGTGGTGGGGGTTAACC 60.106 55.000 16.85 16.85 36.96 2.85
3064 3360 1.067693 TGCGCACTGTTGTCTATTCG 58.932 50.000 5.66 0.00 0.00 3.34
3173 3540 9.736023 AAGAATTTCTATCGATGTTATTTTGGC 57.264 29.630 8.54 0.00 0.00 4.52
3174 3541 8.902806 AGAATTTCTATCGATGTTATTTTGGCA 58.097 29.630 8.54 0.00 0.00 4.92
3176 3543 9.467258 AATTTCTATCGATGTTATTTTGGCATG 57.533 29.630 8.54 0.00 0.00 4.06
3177 3544 7.566760 TTCTATCGATGTTATTTTGGCATGT 57.433 32.000 8.54 0.00 0.00 3.21
3178 3545 8.669946 TTCTATCGATGTTATTTTGGCATGTA 57.330 30.769 8.54 0.00 0.00 2.29
3179 3546 8.669946 TCTATCGATGTTATTTTGGCATGTAA 57.330 30.769 8.54 0.00 0.00 2.41
3180 3547 8.556194 TCTATCGATGTTATTTTGGCATGTAAC 58.444 33.333 8.54 9.09 0.00 2.50
3181 3548 6.502136 TCGATGTTATTTTGGCATGTAACA 57.498 33.333 16.76 16.76 40.20 2.41
3186 3553 8.876275 ATGTTATTTTGGCATGTAACATCATC 57.124 30.769 18.78 0.00 41.42 2.92
3281 3672 3.674410 GCTTTATTGCTGCTGGGAAACTC 60.674 47.826 0.00 0.00 0.00 3.01
3481 3878 1.321074 AACCCTACTCGAGCTTCCCG 61.321 60.000 13.61 0.00 0.00 5.14
3482 3879 1.453379 CCCTACTCGAGCTTCCCGA 60.453 63.158 13.61 0.00 34.61 5.14
3501 3898 1.604278 GAGCGAGACTTTTGCTTTGGT 59.396 47.619 0.00 0.00 46.85 3.67
3509 3906 1.066908 CTTTTGCTTTGGTTCCTGCGA 59.933 47.619 0.00 0.00 0.00 5.10
3511 3908 1.107114 TTGCTTTGGTTCCTGCGAAA 58.893 45.000 0.00 0.00 0.00 3.46
3550 3947 2.679355 TGCGTTTCAAATCGGTCAAG 57.321 45.000 0.00 0.00 0.00 3.02
3554 3951 1.544246 GTTTCAAATCGGTCAAGGGGG 59.456 52.381 0.00 0.00 0.00 5.40
3567 3964 2.039724 GGGGGAAGAGGGGTAGGG 60.040 72.222 0.00 0.00 0.00 3.53
3568 3965 2.773053 GGGGAAGAGGGGTAGGGC 60.773 72.222 0.00 0.00 0.00 5.19
3628 4025 3.821421 AACTATGTGGATCGAGGGAAC 57.179 47.619 0.00 0.00 0.00 3.62
3649 4046 3.815401 ACTGCAGACCATTGTTTGTAGAC 59.185 43.478 23.35 0.00 40.34 2.59
3655 4052 2.292292 ACCATTGTTTGTAGACGGTTGC 59.708 45.455 0.00 0.00 0.00 4.17
3667 4064 0.036388 ACGGTTGCTTCCACGATGAT 60.036 50.000 0.00 0.00 0.00 2.45
3668 4065 0.374758 CGGTTGCTTCCACGATGATG 59.625 55.000 0.00 0.00 0.00 3.07
3669 4066 1.737838 GGTTGCTTCCACGATGATGA 58.262 50.000 0.00 0.00 0.00 2.92
3670 4067 2.083774 GGTTGCTTCCACGATGATGAA 58.916 47.619 0.00 0.00 0.00 2.57
3671 4068 2.684881 GGTTGCTTCCACGATGATGAAT 59.315 45.455 0.00 0.00 0.00 2.57
3674 4071 3.608796 TGCTTCCACGATGATGAATTCA 58.391 40.909 11.26 11.26 39.12 2.57
3710 4107 1.139256 TCTGTCACCAGCGTTTTACCA 59.861 47.619 0.00 0.00 38.66 3.25
3720 4117 4.698304 CCAGCGTTTTACCATTCTTCCTTA 59.302 41.667 0.00 0.00 0.00 2.69
3819 4218 4.320202 GCAAAAGTGAGGAACGCAAGATTA 60.320 41.667 0.00 0.00 41.67 1.75
3820 4219 5.619981 GCAAAAGTGAGGAACGCAAGATTAT 60.620 40.000 0.00 0.00 41.67 1.28
3859 4258 9.484806 AATTGGTATTCCTCTTTTCATGATTCT 57.515 29.630 0.00 0.00 34.23 2.40
3879 4278 3.077359 CTCTCTCACAACCCATTCCAAC 58.923 50.000 0.00 0.00 0.00 3.77
3880 4279 2.441375 TCTCTCACAACCCATTCCAACA 59.559 45.455 0.00 0.00 0.00 3.33
3885 4284 4.158786 TCACAACCCATTCCAACAATGAT 58.841 39.130 0.00 0.00 0.00 2.45
3893 4292 5.221762 CCCATTCCAACAATGATGCCAATAT 60.222 40.000 0.00 0.00 0.00 1.28
3914 4313 5.730296 ATATATCTGACGTTCCCTGAAGG 57.270 43.478 0.00 0.00 34.20 3.46
3925 4324 3.527507 TCCCTGAAGGAGATATAGCGT 57.472 47.619 0.00 0.00 40.93 5.07
3926 4325 3.845860 TCCCTGAAGGAGATATAGCGTT 58.154 45.455 0.00 0.00 40.93 4.84
3927 4326 4.223953 TCCCTGAAGGAGATATAGCGTTT 58.776 43.478 0.00 0.00 40.93 3.60
3928 4327 4.039245 TCCCTGAAGGAGATATAGCGTTTG 59.961 45.833 0.00 0.00 40.93 2.93
3929 4328 3.743396 CCTGAAGGAGATATAGCGTTTGC 59.257 47.826 0.00 0.00 38.44 3.68
3930 4329 4.502259 CCTGAAGGAGATATAGCGTTTGCT 60.502 45.833 0.00 0.00 46.65 3.91
3931 4330 6.303137 CCTGAAGGAGATATAGCGTTTGCTC 61.303 48.000 0.00 0.00 44.70 4.26
3961 4360 8.463930 AAAAAGACATTCCAGTGAATACTTCA 57.536 30.769 0.00 0.00 39.20 3.02
3962 4361 7.678947 AAAGACATTCCAGTGAATACTTCAG 57.321 36.000 0.00 0.00 39.20 3.02
3963 4362 6.611613 AGACATTCCAGTGAATACTTCAGA 57.388 37.500 0.00 0.00 39.20 3.27
3964 4363 7.009179 AGACATTCCAGTGAATACTTCAGAA 57.991 36.000 0.00 0.00 39.20 3.02
3965 4364 6.876257 AGACATTCCAGTGAATACTTCAGAAC 59.124 38.462 0.00 0.00 39.20 3.01
3966 4365 6.533730 ACATTCCAGTGAATACTTCAGAACA 58.466 36.000 0.00 0.00 39.20 3.18
3967 4366 6.652481 ACATTCCAGTGAATACTTCAGAACAG 59.348 38.462 0.00 0.00 39.20 3.16
3968 4367 4.569943 TCCAGTGAATACTTCAGAACAGC 58.430 43.478 0.00 0.00 41.01 4.40
3969 4368 3.369147 CCAGTGAATACTTCAGAACAGCG 59.631 47.826 0.00 0.00 41.01 5.18
3970 4369 4.237724 CAGTGAATACTTCAGAACAGCGA 58.762 43.478 0.00 0.00 41.01 4.93
3971 4370 4.686091 CAGTGAATACTTCAGAACAGCGAA 59.314 41.667 0.00 0.00 41.01 4.70
3972 4371 5.349817 CAGTGAATACTTCAGAACAGCGAAT 59.650 40.000 0.00 0.00 41.01 3.34
3973 4372 5.934625 AGTGAATACTTCAGAACAGCGAATT 59.065 36.000 0.00 0.00 41.01 2.17
3974 4373 6.428159 AGTGAATACTTCAGAACAGCGAATTT 59.572 34.615 0.00 0.00 41.01 1.82
3975 4374 7.041098 AGTGAATACTTCAGAACAGCGAATTTT 60.041 33.333 0.00 0.00 41.01 1.82
3976 4375 7.591426 GTGAATACTTCAGAACAGCGAATTTTT 59.409 33.333 0.00 0.00 41.01 1.94
4006 4405 5.761234 ACAGTGAACGCTTTAGAATTACCAA 59.239 36.000 0.00 0.00 0.00 3.67
4008 4407 5.086727 GTGAACGCTTTAGAATTACCAAGC 58.913 41.667 5.32 5.32 38.64 4.01
4027 4426 8.050778 ACCAAGCGAAAATAGATGAATTTACA 57.949 30.769 0.00 0.00 0.00 2.41
4031 4430 8.566008 AGCGAAAATAGATGAATTTACAATGC 57.434 30.769 0.00 0.00 0.00 3.56
4040 4439 7.995289 AGATGAATTTACAATGCCGTTGAATA 58.005 30.769 3.13 0.00 40.37 1.75
4084 4483 5.815222 GGTAAAAATTGCCCCATGTTGTATC 59.185 40.000 0.00 0.00 0.00 2.24
4086 4485 4.741321 AAATTGCCCCATGTTGTATCTG 57.259 40.909 0.00 0.00 0.00 2.90
4112 4512 3.225104 TCTCAGAAAATTGCCTTGCTGT 58.775 40.909 0.00 0.00 0.00 4.40
4130 4530 9.276590 CCTTGCTGTATGAGAATAATTGTCATA 57.723 33.333 0.00 0.00 37.72 2.15
4132 4532 8.298030 TGCTGTATGAGAATAATTGTCATACG 57.702 34.615 22.03 18.66 37.72 3.06
4133 4533 7.926018 TGCTGTATGAGAATAATTGTCATACGT 59.074 33.333 22.03 0.00 37.72 3.57
4172 4572 4.247258 TGATGCAAACATGAAGAATTGCC 58.753 39.130 0.00 0.00 45.71 4.52
4173 4573 3.747854 TGCAAACATGAAGAATTGCCA 57.252 38.095 0.00 0.00 45.71 4.92
4175 4575 2.414138 GCAAACATGAAGAATTGCCAGC 59.586 45.455 0.00 0.00 41.67 4.85
4177 4577 2.226962 ACATGAAGAATTGCCAGCCT 57.773 45.000 0.00 0.00 0.00 4.58
4181 4581 4.082026 ACATGAAGAATTGCCAGCCTAAAC 60.082 41.667 0.00 0.00 0.00 2.01
4185 4588 4.525912 AGAATTGCCAGCCTAAACAAAG 57.474 40.909 0.00 0.00 0.00 2.77
4194 4597 4.040339 CCAGCCTAAACAAAGGAAAATGGT 59.960 41.667 0.00 0.00 39.15 3.55
4236 4639 0.032912 TGCCATGTACTCCCTCCGTA 60.033 55.000 0.00 0.00 0.00 4.02
4238 4641 0.666913 CCATGTACTCCCTCCGTACG 59.333 60.000 8.69 8.69 39.98 3.67
4239 4642 0.666913 CATGTACTCCCTCCGTACGG 59.333 60.000 28.66 28.66 39.98 4.02
4251 4654 3.442100 CTCCGTACGGAAATACTTGTCC 58.558 50.000 34.77 0.00 44.66 4.02
4252 4655 3.091545 TCCGTACGGAAATACTTGTCCT 58.908 45.455 33.96 0.00 42.05 3.85
4253 4656 4.269183 TCCGTACGGAAATACTTGTCCTA 58.731 43.478 33.96 6.50 42.05 2.94
4254 4657 4.336433 TCCGTACGGAAATACTTGTCCTAG 59.664 45.833 33.96 2.10 42.05 3.02
4255 4658 4.040376 CGTACGGAAATACTTGTCCTAGC 58.960 47.826 7.57 0.00 0.00 3.42
4256 4659 4.439153 CGTACGGAAATACTTGTCCTAGCA 60.439 45.833 7.57 0.00 0.00 3.49
4257 4660 4.546829 ACGGAAATACTTGTCCTAGCAA 57.453 40.909 0.00 0.00 0.00 3.91
4258 4661 5.099042 ACGGAAATACTTGTCCTAGCAAT 57.901 39.130 0.00 0.00 0.00 3.56
4259 4662 4.876107 ACGGAAATACTTGTCCTAGCAATG 59.124 41.667 0.00 0.00 0.00 2.82
4260 4663 4.273480 CGGAAATACTTGTCCTAGCAATGG 59.727 45.833 0.00 0.00 0.00 3.16
4261 4664 5.193679 GGAAATACTTGTCCTAGCAATGGT 58.806 41.667 0.00 0.00 0.00 3.55
4262 4665 5.652452 GGAAATACTTGTCCTAGCAATGGTT 59.348 40.000 0.00 0.00 0.00 3.67
4263 4666 6.404734 GGAAATACTTGTCCTAGCAATGGTTG 60.405 42.308 0.00 0.00 0.00 3.77
4264 4667 3.508845 ACTTGTCCTAGCAATGGTTGT 57.491 42.857 0.00 0.00 0.00 3.32
4265 4668 4.634012 ACTTGTCCTAGCAATGGTTGTA 57.366 40.909 0.00 0.00 0.00 2.41
4266 4669 5.179452 ACTTGTCCTAGCAATGGTTGTAT 57.821 39.130 0.00 0.00 0.00 2.29
4267 4670 5.186198 ACTTGTCCTAGCAATGGTTGTATC 58.814 41.667 0.00 0.00 0.00 2.24
4268 4671 5.045578 ACTTGTCCTAGCAATGGTTGTATCT 60.046 40.000 0.00 0.00 0.00 1.98
4269 4672 6.156256 ACTTGTCCTAGCAATGGTTGTATCTA 59.844 38.462 0.00 0.00 0.00 1.98
4270 4673 6.161855 TGTCCTAGCAATGGTTGTATCTAG 57.838 41.667 0.00 0.00 0.00 2.43
4271 4674 5.897250 TGTCCTAGCAATGGTTGTATCTAGA 59.103 40.000 0.00 0.00 0.00 2.43
4272 4675 6.183360 TGTCCTAGCAATGGTTGTATCTAGAC 60.183 42.308 0.00 0.00 0.00 2.59
4273 4676 6.041069 GTCCTAGCAATGGTTGTATCTAGACT 59.959 42.308 0.00 0.00 0.00 3.24
4274 4677 6.611642 TCCTAGCAATGGTTGTATCTAGACTT 59.388 38.462 0.00 0.00 0.00 3.01
4275 4678 6.703607 CCTAGCAATGGTTGTATCTAGACTTG 59.296 42.308 0.00 0.00 0.00 3.16
4276 4679 6.054860 AGCAATGGTTGTATCTAGACTTGT 57.945 37.500 0.00 0.00 0.00 3.16
4277 4680 6.476378 AGCAATGGTTGTATCTAGACTTGTT 58.524 36.000 0.00 0.00 0.00 2.83
4278 4681 6.942576 AGCAATGGTTGTATCTAGACTTGTTT 59.057 34.615 0.00 0.00 0.00 2.83
4279 4682 7.119846 AGCAATGGTTGTATCTAGACTTGTTTC 59.880 37.037 0.00 0.00 0.00 2.78
4280 4683 7.094805 GCAATGGTTGTATCTAGACTTGTTTCA 60.095 37.037 0.00 0.00 0.00 2.69
4281 4684 8.446273 CAATGGTTGTATCTAGACTTGTTTCAG 58.554 37.037 0.00 0.00 0.00 3.02
4282 4685 7.062749 TGGTTGTATCTAGACTTGTTTCAGT 57.937 36.000 0.00 0.00 0.00 3.41
4283 4686 7.506114 TGGTTGTATCTAGACTTGTTTCAGTT 58.494 34.615 0.00 0.00 0.00 3.16
4284 4687 8.644216 TGGTTGTATCTAGACTTGTTTCAGTTA 58.356 33.333 0.00 0.00 0.00 2.24
4285 4688 9.485206 GGTTGTATCTAGACTTGTTTCAGTTAA 57.515 33.333 0.00 0.00 0.00 2.01
4292 4695 8.529476 TCTAGACTTGTTTCAGTTAATACTCCC 58.471 37.037 0.00 0.00 30.26 4.30
4293 4696 7.317722 AGACTTGTTTCAGTTAATACTCCCT 57.682 36.000 0.00 0.00 30.26 4.20
4294 4697 7.746703 AGACTTGTTTCAGTTAATACTCCCTT 58.253 34.615 0.00 0.00 30.26 3.95
4295 4698 7.878644 AGACTTGTTTCAGTTAATACTCCCTTC 59.121 37.037 0.00 0.00 30.26 3.46
4296 4699 7.514721 ACTTGTTTCAGTTAATACTCCCTTCA 58.485 34.615 0.00 0.00 30.26 3.02
4297 4700 8.164070 ACTTGTTTCAGTTAATACTCCCTTCAT 58.836 33.333 0.00 0.00 30.26 2.57
4298 4701 8.561738 TTGTTTCAGTTAATACTCCCTTCATC 57.438 34.615 0.00 0.00 30.26 2.92
4299 4702 7.110155 TGTTTCAGTTAATACTCCCTTCATCC 58.890 38.462 0.00 0.00 30.26 3.51
4300 4703 5.531122 TCAGTTAATACTCCCTTCATCCG 57.469 43.478 0.00 0.00 30.26 4.18
4301 4704 4.058817 CAGTTAATACTCCCTTCATCCGC 58.941 47.826 0.00 0.00 30.26 5.54
4302 4705 3.057734 GTTAATACTCCCTTCATCCGCG 58.942 50.000 0.00 0.00 0.00 6.46
4303 4706 1.410004 AATACTCCCTTCATCCGCGA 58.590 50.000 8.23 0.00 0.00 5.87
4304 4707 1.410004 ATACTCCCTTCATCCGCGAA 58.590 50.000 8.23 0.00 0.00 4.70
4305 4708 1.410004 TACTCCCTTCATCCGCGAAT 58.590 50.000 8.23 0.00 0.00 3.34
4306 4709 1.410004 ACTCCCTTCATCCGCGAATA 58.590 50.000 8.23 0.00 0.00 1.75
4307 4710 1.760613 ACTCCCTTCATCCGCGAATAA 59.239 47.619 8.23 0.00 0.00 1.40
4308 4711 2.224066 ACTCCCTTCATCCGCGAATAAG 60.224 50.000 8.23 5.57 0.00 1.73
4309 4712 1.760613 TCCCTTCATCCGCGAATAAGT 59.239 47.619 8.23 0.00 0.00 2.24
4310 4713 1.867233 CCCTTCATCCGCGAATAAGTG 59.133 52.381 8.23 0.00 0.00 3.16
4311 4714 2.550978 CCTTCATCCGCGAATAAGTGT 58.449 47.619 8.23 0.00 0.00 3.55
4312 4715 3.491964 CCCTTCATCCGCGAATAAGTGTA 60.492 47.826 8.23 0.00 0.00 2.90
4313 4716 4.307432 CCTTCATCCGCGAATAAGTGTAT 58.693 43.478 8.23 0.00 0.00 2.29
4314 4717 5.466819 CCTTCATCCGCGAATAAGTGTATA 58.533 41.667 8.23 0.00 0.00 1.47
4315 4718 6.100004 CCTTCATCCGCGAATAAGTGTATAT 58.900 40.000 8.23 0.00 0.00 0.86
4316 4719 6.253727 CCTTCATCCGCGAATAAGTGTATATC 59.746 42.308 8.23 0.00 0.00 1.63
4317 4720 6.510879 TCATCCGCGAATAAGTGTATATCT 57.489 37.500 8.23 0.00 0.00 1.98
4318 4721 7.619964 TCATCCGCGAATAAGTGTATATCTA 57.380 36.000 8.23 0.00 0.00 1.98
4319 4722 8.221965 TCATCCGCGAATAAGTGTATATCTAT 57.778 34.615 8.23 0.00 0.00 1.98
4320 4723 8.343366 TCATCCGCGAATAAGTGTATATCTATC 58.657 37.037 8.23 0.00 0.00 2.08
4321 4724 7.860918 TCCGCGAATAAGTGTATATCTATCT 57.139 36.000 8.23 0.00 0.00 1.98
4322 4725 8.277490 TCCGCGAATAAGTGTATATCTATCTT 57.723 34.615 8.23 0.00 0.00 2.40
4323 4726 8.737175 TCCGCGAATAAGTGTATATCTATCTTT 58.263 33.333 8.23 0.00 0.00 2.52
4324 4727 9.355215 CCGCGAATAAGTGTATATCTATCTTTT 57.645 33.333 8.23 0.00 0.00 2.27
4390 4793 5.520376 AAAGTAGCATCATTTATGGCACC 57.480 39.130 0.00 0.00 35.99 5.01
4391 4794 4.169059 AGTAGCATCATTTATGGCACCA 57.831 40.909 0.00 0.00 35.99 4.17
4392 4795 4.535781 AGTAGCATCATTTATGGCACCAA 58.464 39.130 0.00 0.00 35.99 3.67
4393 4796 4.955450 AGTAGCATCATTTATGGCACCAAA 59.045 37.500 0.00 0.00 35.99 3.28
4394 4797 5.599656 AGTAGCATCATTTATGGCACCAAAT 59.400 36.000 0.00 0.00 35.99 2.32
4395 4798 5.362105 AGCATCATTTATGGCACCAAATT 57.638 34.783 6.24 0.00 35.99 1.82
4396 4799 6.482898 AGCATCATTTATGGCACCAAATTA 57.517 33.333 6.24 0.82 35.99 1.40
4397 4800 6.518493 AGCATCATTTATGGCACCAAATTAG 58.482 36.000 6.24 2.37 35.99 1.73
4398 4801 5.178067 GCATCATTTATGGCACCAAATTAGC 59.822 40.000 6.24 7.18 35.99 3.09
4399 4802 5.929058 TCATTTATGGCACCAAATTAGCA 57.071 34.783 6.24 0.00 0.00 3.49
4400 4803 6.482898 TCATTTATGGCACCAAATTAGCAT 57.517 33.333 6.24 0.00 0.00 3.79
4401 4804 6.514947 TCATTTATGGCACCAAATTAGCATC 58.485 36.000 6.24 0.00 0.00 3.91
4402 4805 4.566545 TTATGGCACCAAATTAGCATCG 57.433 40.909 0.00 0.00 0.00 3.84
4403 4806 1.832883 TGGCACCAAATTAGCATCGT 58.167 45.000 0.00 0.00 0.00 3.73
4404 4807 2.166829 TGGCACCAAATTAGCATCGTT 58.833 42.857 0.00 0.00 0.00 3.85
4405 4808 3.348119 TGGCACCAAATTAGCATCGTTA 58.652 40.909 0.00 0.00 0.00 3.18
4406 4809 3.376859 TGGCACCAAATTAGCATCGTTAG 59.623 43.478 0.00 0.00 0.00 2.34
4407 4810 3.625764 GGCACCAAATTAGCATCGTTAGA 59.374 43.478 0.00 0.00 0.00 2.10
4408 4811 4.275936 GGCACCAAATTAGCATCGTTAGAT 59.724 41.667 0.00 0.00 37.65 1.98
4409 4812 5.221048 GGCACCAAATTAGCATCGTTAGATT 60.221 40.000 0.00 0.00 34.23 2.40
4410 4813 5.909610 GCACCAAATTAGCATCGTTAGATTC 59.090 40.000 0.00 0.00 34.23 2.52
4411 4814 6.458206 GCACCAAATTAGCATCGTTAGATTCA 60.458 38.462 0.00 0.00 34.23 2.57
4412 4815 7.642669 CACCAAATTAGCATCGTTAGATTCAT 58.357 34.615 0.00 0.00 34.23 2.57
4413 4816 8.131100 CACCAAATTAGCATCGTTAGATTCATT 58.869 33.333 0.00 0.00 34.23 2.57
4414 4817 8.686334 ACCAAATTAGCATCGTTAGATTCATTT 58.314 29.630 0.00 0.00 34.23 2.32
4415 4818 9.520204 CCAAATTAGCATCGTTAGATTCATTTT 57.480 29.630 0.00 0.00 34.23 1.82
4421 4824 8.624701 AGCATCGTTAGATTCATTTTGAAATG 57.375 30.769 9.61 9.61 40.12 2.32
4422 4825 8.246180 AGCATCGTTAGATTCATTTTGAAATGT 58.754 29.630 14.22 0.00 40.12 2.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.259356 TCTCTGCACATGAAAATCTGGAG 58.741 43.478 0.00 0.00 0.00 3.86
1 2 4.290711 TCTCTGCACATGAAAATCTGGA 57.709 40.909 0.00 0.00 0.00 3.86
2 3 4.638865 TGATCTCTGCACATGAAAATCTGG 59.361 41.667 0.00 0.00 0.00 3.86
3 4 5.813080 TGATCTCTGCACATGAAAATCTG 57.187 39.130 0.00 0.00 0.00 2.90
55 56 4.634443 GGACTGTTAATTAGTGCGACCAAT 59.366 41.667 0.66 0.00 0.00 3.16
59 60 5.350365 TCATTGGACTGTTAATTAGTGCGAC 59.650 40.000 6.47 0.00 39.08 5.19
61 62 5.580691 TCTCATTGGACTGTTAATTAGTGCG 59.419 40.000 8.88 0.00 39.08 5.34
98 106 1.135139 CCTATGTGACTGTGAGACGGG 59.865 57.143 0.00 0.00 0.00 5.28
102 110 4.586306 TCCTACCTATGTGACTGTGAGA 57.414 45.455 0.00 0.00 0.00 3.27
105 113 5.127845 ACTGAATCCTACCTATGTGACTGTG 59.872 44.000 0.00 0.00 0.00 3.66
142 150 9.270640 TGTTAGAAATACAAAATGCATGCTTTT 57.729 25.926 22.07 22.07 0.00 2.27
143 151 8.830201 TGTTAGAAATACAAAATGCATGCTTT 57.170 26.923 20.33 16.30 0.00 3.51
792 801 3.320879 CTGTGCTGGGCGGAGATGT 62.321 63.158 0.00 0.00 0.00 3.06
794 803 4.479993 GCTGTGCTGGGCGGAGAT 62.480 66.667 0.00 0.00 0.00 2.75
815 824 2.542205 CGCACCGTCCGTTTATGATCTA 60.542 50.000 0.00 0.00 0.00 1.98
821 830 0.529119 GATCCGCACCGTCCGTTTAT 60.529 55.000 0.00 0.00 0.00 1.40
822 831 1.153784 GATCCGCACCGTCCGTTTA 60.154 57.895 0.00 0.00 0.00 2.01
823 832 2.433664 GATCCGCACCGTCCGTTT 60.434 61.111 0.00 0.00 0.00 3.60
840 849 1.890876 TTCTGGTTCCACGTGGATTG 58.109 50.000 36.52 24.38 44.98 2.67
844 853 2.465860 TACATTCTGGTTCCACGTGG 57.534 50.000 29.26 29.26 0.00 4.94
871 880 8.633561 GCAGAAGAATTTAATTACTGGCCTATT 58.366 33.333 3.32 1.25 0.00 1.73
904 913 5.008980 CAGAGCAGAGGAGAAAGGATTTTT 58.991 41.667 0.00 0.00 39.27 1.94
1170 1184 4.760047 CCCACGGGTGAGGAAGCG 62.760 72.222 0.00 0.00 0.00 4.68
1196 1210 1.399744 CGGATCGAATCAGACCCCCA 61.400 60.000 0.00 0.00 0.00 4.96
1339 1353 4.116961 AGATCTACTCACTTCTCGTCGAG 58.883 47.826 16.33 16.33 0.00 4.04
1356 1370 1.525175 AGGGTAGACCGGAGAGATCT 58.475 55.000 9.46 1.74 46.96 2.75
1383 1397 4.876679 AGAAAGTAGCCTAAAATTCGAGCC 59.123 41.667 0.00 0.00 0.00 4.70
1394 1408 5.586877 TCTGAAACCCTAGAAAGTAGCCTA 58.413 41.667 0.00 0.00 0.00 3.93
1423 1437 1.737236 TGTTAGATGCATCAACGGCAC 59.263 47.619 27.81 14.26 45.23 5.01
1430 1444 8.046708 AGTGGTAAAACTATGTTAGATGCATCA 58.953 33.333 27.81 11.65 0.00 3.07
1434 1448 8.263940 TGAAGTGGTAAAACTATGTTAGATGC 57.736 34.615 0.00 0.00 0.00 3.91
1468 1482 2.480845 ACCGCGGCTAAATTATCAGAC 58.519 47.619 28.58 0.00 0.00 3.51
1485 1499 0.792031 GTAACGCTGTGGGTTTACCG 59.208 55.000 5.40 0.00 44.64 4.02
1487 1501 1.723003 CTCGTAACGCTGTGGGTTTAC 59.277 52.381 5.40 2.58 39.36 2.01
1488 1502 1.936203 GCTCGTAACGCTGTGGGTTTA 60.936 52.381 5.40 0.00 39.36 2.01
1514 1528 7.258441 TGAAGAATTCCACGATTACAGTCTAG 58.742 38.462 0.65 0.00 46.93 2.43
1515 1529 7.165460 TGAAGAATTCCACGATTACAGTCTA 57.835 36.000 0.65 0.00 46.93 2.59
1516 1530 6.037786 TGAAGAATTCCACGATTACAGTCT 57.962 37.500 0.65 0.00 46.93 3.24
1517 1531 6.910536 ATGAAGAATTCCACGATTACAGTC 57.089 37.500 0.65 0.00 46.93 3.51
1526 1540 6.437928 TCAAGAACAAATGAAGAATTCCACG 58.562 36.000 0.65 0.00 46.93 4.94
1599 1632 9.407380 TCCAAATTTAGCAATATTAGAAGAGCA 57.593 29.630 0.00 0.00 0.00 4.26
1677 1773 9.565090 CATTTCAGTATTCCCTTCATCTCATAA 57.435 33.333 0.00 0.00 0.00 1.90
1679 1775 7.501559 CACATTTCAGTATTCCCTTCATCTCAT 59.498 37.037 0.00 0.00 0.00 2.90
1683 1954 5.591877 AGCACATTTCAGTATTCCCTTCATC 59.408 40.000 0.00 0.00 0.00 2.92
1698 1969 7.422399 TCAGTAACCTTAAACAAGCACATTTC 58.578 34.615 0.00 0.00 0.00 2.17
1781 2052 4.652421 TCAGTGATTTGTTTGTGCACAT 57.348 36.364 22.39 3.78 32.16 3.21
1864 2135 4.125703 TGAACACACATTTTCATTTGGGC 58.874 39.130 0.00 0.00 0.00 5.36
1883 2154 8.681806 CAGAAGTTCAGAGTCTAGATACATGAA 58.318 37.037 5.50 2.37 0.00 2.57
1886 2157 9.337396 CTACAGAAGTTCAGAGTCTAGATACAT 57.663 37.037 5.50 0.00 0.00 2.29
1910 2182 4.155280 GCGGGAAAAAGAAGCAATACACTA 59.845 41.667 0.00 0.00 0.00 2.74
1932 2204 5.048504 TGTGAAATCAGATGAAACAGAAGGC 60.049 40.000 0.00 0.00 0.00 4.35
1965 2237 3.058432 TCAGTAGAAGACAAGACCGAACG 60.058 47.826 0.00 0.00 0.00 3.95
2018 2294 3.012518 CCAAATTCTCTTCAGCATCCGT 58.987 45.455 0.00 0.00 0.00 4.69
2083 2359 3.343617 CTTCTCGCCAACCCTTATGAAA 58.656 45.455 0.00 0.00 0.00 2.69
2108 2384 6.480320 GGTGAAAGCCAGTAGATATGTGTAAG 59.520 42.308 0.00 0.00 0.00 2.34
2109 2385 6.070481 TGGTGAAAGCCAGTAGATATGTGTAA 60.070 38.462 0.00 0.00 33.97 2.41
2122 2409 2.795329 ACCTAACATGGTGAAAGCCAG 58.205 47.619 0.00 0.00 42.47 4.85
2125 2412 3.364964 CGACAACCTAACATGGTGAAAGC 60.365 47.826 0.00 0.00 40.73 3.51
2428 2718 3.503748 CCCTCTTCAAACAAGCTTCGATT 59.496 43.478 0.00 0.00 0.00 3.34
2619 2909 0.300491 CGCGGTCCAATGTGATAACG 59.700 55.000 0.00 0.00 0.00 3.18
2640 2930 7.656137 TGAATACACACCTTCTGTTTTAGAGAC 59.344 37.037 0.00 0.00 36.61 3.36
2652 2942 7.672983 TGAGAAAAGATGAATACACACCTTC 57.327 36.000 0.00 0.00 0.00 3.46
2658 2948 9.766277 GACTTGAATGAGAAAAGATGAATACAC 57.234 33.333 0.00 0.00 0.00 2.90
2750 3044 2.550277 TTACAGCCAGGATCTCAGGA 57.450 50.000 0.00 0.00 0.00 3.86
2883 3179 6.073058 GCATTACTGCTCATCGGAATAAATGA 60.073 38.462 0.00 0.00 45.32 2.57
2931 3227 8.753497 AGATATGAGAAATCCAAAGGGTTAAC 57.247 34.615 0.00 0.00 34.93 2.01
2935 3231 7.202139 GGACTAGATATGAGAAATCCAAAGGGT 60.202 40.741 0.00 0.00 34.93 4.34
2937 3233 7.739825 TGGACTAGATATGAGAAATCCAAAGG 58.260 38.462 0.00 0.00 32.13 3.11
3064 3360 4.569943 TCTTGTATGACTCAAGGAACTGC 58.430 43.478 5.95 0.00 40.86 4.40
3155 3522 8.341903 TGTTACATGCCAAAATAACATCGATAG 58.658 33.333 0.00 0.00 33.67 2.08
3159 3526 7.380438 GATGTTACATGCCAAAATAACATCG 57.620 36.000 20.08 0.00 46.70 3.84
3170 3537 4.201657 CAGGAAGATGATGTTACATGCCA 58.798 43.478 1.24 0.00 0.00 4.92
3171 3538 3.567164 CCAGGAAGATGATGTTACATGCC 59.433 47.826 1.24 0.00 0.00 4.40
3172 3539 4.036027 CACCAGGAAGATGATGTTACATGC 59.964 45.833 1.24 0.00 0.00 4.06
3173 3540 4.036027 GCACCAGGAAGATGATGTTACATG 59.964 45.833 1.24 0.00 0.00 3.21
3174 3541 4.080129 AGCACCAGGAAGATGATGTTACAT 60.080 41.667 0.00 0.00 0.00 2.29
3176 3543 3.624861 CAGCACCAGGAAGATGATGTTAC 59.375 47.826 0.00 0.00 0.00 2.50
3177 3544 3.519107 TCAGCACCAGGAAGATGATGTTA 59.481 43.478 0.00 0.00 31.74 2.41
3178 3545 2.306805 TCAGCACCAGGAAGATGATGTT 59.693 45.455 0.00 0.00 31.74 2.71
3179 3546 1.911357 TCAGCACCAGGAAGATGATGT 59.089 47.619 0.00 0.00 31.74 3.06
3180 3547 2.704464 TCAGCACCAGGAAGATGATG 57.296 50.000 0.00 0.00 0.00 3.07
3181 3548 3.972638 AGTATCAGCACCAGGAAGATGAT 59.027 43.478 17.39 17.39 0.00 2.45
3183 3550 3.118482 ACAGTATCAGCACCAGGAAGATG 60.118 47.826 0.00 0.00 0.00 2.90
3184 3551 3.110705 ACAGTATCAGCACCAGGAAGAT 58.889 45.455 0.00 0.00 0.00 2.40
3186 3553 2.027745 ACACAGTATCAGCACCAGGAAG 60.028 50.000 0.00 0.00 0.00 3.46
3281 3672 4.676196 GCAACCTTATCAATCTTGCAGTGG 60.676 45.833 0.00 0.00 37.70 4.00
3481 3878 1.604278 ACCAAAGCAAAAGTCTCGCTC 59.396 47.619 0.00 0.00 34.11 5.03
3482 3879 1.680338 ACCAAAGCAAAAGTCTCGCT 58.320 45.000 0.00 0.00 37.68 4.93
3485 3882 3.796844 GCAGGAACCAAAGCAAAAGTCTC 60.797 47.826 0.00 0.00 0.00 3.36
3490 3887 1.107114 TCGCAGGAACCAAAGCAAAA 58.893 45.000 0.00 0.00 0.00 2.44
3501 3898 1.737838 CTGCCAGTATTTCGCAGGAA 58.262 50.000 0.33 0.00 45.00 3.36
3509 3906 5.581874 GCAAAATGCAATACTGCCAGTATTT 59.418 36.000 24.03 11.21 46.48 1.40
3550 3947 2.039724 CCCTACCCCTCTTCCCCC 60.040 72.222 0.00 0.00 0.00 5.40
3554 3951 2.901338 AAAAAGCCCTACCCCTCTTC 57.099 50.000 0.00 0.00 0.00 2.87
3580 3977 9.612620 GGTTACAAGTCAAATACTCAGATTTTG 57.387 33.333 0.00 0.00 37.50 2.44
3581 3978 9.574516 AGGTTACAAGTCAAATACTCAGATTTT 57.425 29.630 0.00 0.00 37.50 1.82
3591 3988 9.661563 CCACATAGTTAGGTTACAAGTCAAATA 57.338 33.333 0.00 0.00 0.00 1.40
3614 4011 0.460987 CTGCAGTTCCCTCGATCCAC 60.461 60.000 5.25 0.00 0.00 4.02
3628 4025 3.120546 CGTCTACAAACAATGGTCTGCAG 60.121 47.826 7.63 7.63 0.00 4.41
3649 4046 0.374758 CATCATCGTGGAAGCAACCG 59.625 55.000 0.00 0.00 0.00 4.44
3670 4067 9.685276 TGACAGACTTGTAATAAATGGATGAAT 57.315 29.630 0.00 0.00 37.76 2.57
3671 4068 8.946085 GTGACAGACTTGTAATAAATGGATGAA 58.054 33.333 0.00 0.00 37.76 2.57
3674 4071 7.402054 TGGTGACAGACTTGTAATAAATGGAT 58.598 34.615 0.00 0.00 37.76 3.41
3675 4072 6.774673 TGGTGACAGACTTGTAATAAATGGA 58.225 36.000 0.00 0.00 37.76 3.41
3695 4092 3.365969 GGAAGAATGGTAAAACGCTGGTG 60.366 47.826 0.00 0.00 0.00 4.17
3720 4117 5.132897 TGCCAATTATGCTCGTTTTCTTT 57.867 34.783 1.40 0.00 0.00 2.52
3819 4218 7.072076 AGGAATACCAATTAGAAACCCTCGTAT 59.928 37.037 0.00 0.00 38.94 3.06
3820 4219 6.384886 AGGAATACCAATTAGAAACCCTCGTA 59.615 38.462 0.00 0.00 38.94 3.43
3859 4258 2.441375 TGTTGGAATGGGTTGTGAGAGA 59.559 45.455 0.00 0.00 0.00 3.10
3879 4278 8.429493 ACGTCAGATATATATTGGCATCATTG 57.571 34.615 0.00 0.00 0.00 2.82
3880 4279 9.102757 GAACGTCAGATATATATTGGCATCATT 57.897 33.333 0.00 0.00 0.00 2.57
3885 4284 5.483937 AGGGAACGTCAGATATATATTGGCA 59.516 40.000 0.00 0.00 0.00 4.92
3893 4292 4.800023 TCCTTCAGGGAACGTCAGATATA 58.200 43.478 0.00 0.00 41.91 0.86
3914 4313 3.386768 TGGGAGCAAACGCTATATCTC 57.613 47.619 0.00 0.00 40.78 2.75
3977 4376 9.654417 GTAATTCTAAAGCGTTCACTGTAAAAA 57.346 29.630 0.00 0.00 0.00 1.94
3978 4377 8.284693 GGTAATTCTAAAGCGTTCACTGTAAAA 58.715 33.333 0.00 0.00 0.00 1.52
3979 4378 7.441760 TGGTAATTCTAAAGCGTTCACTGTAAA 59.558 33.333 0.00 0.00 0.00 2.01
3980 4379 6.930164 TGGTAATTCTAAAGCGTTCACTGTAA 59.070 34.615 0.00 0.00 0.00 2.41
3981 4380 6.457355 TGGTAATTCTAAAGCGTTCACTGTA 58.543 36.000 0.00 0.00 0.00 2.74
3982 4381 5.302360 TGGTAATTCTAAAGCGTTCACTGT 58.698 37.500 0.00 0.00 0.00 3.55
3995 4394 9.607988 TTCATCTATTTTCGCTTGGTAATTCTA 57.392 29.630 0.00 0.00 0.00 2.10
4002 4401 8.050778 TGTAAATTCATCTATTTTCGCTTGGT 57.949 30.769 0.00 0.00 0.00 3.67
4006 4405 7.649306 GGCATTGTAAATTCATCTATTTTCGCT 59.351 33.333 0.00 0.00 0.00 4.93
4008 4407 7.643764 ACGGCATTGTAAATTCATCTATTTTCG 59.356 33.333 0.00 0.00 0.00 3.46
4009 4408 8.856490 ACGGCATTGTAAATTCATCTATTTTC 57.144 30.769 0.00 0.00 0.00 2.29
4010 4409 9.086336 CAACGGCATTGTAAATTCATCTATTTT 57.914 29.630 0.00 0.00 33.20 1.82
4014 4413 6.993786 TCAACGGCATTGTAAATTCATCTA 57.006 33.333 0.00 0.00 39.54 1.98
4027 4426 7.721286 TGACAAATTTTTATTCAACGGCATT 57.279 28.000 0.00 0.00 0.00 3.56
4031 4430 8.977505 AGAACATGACAAATTTTTATTCAACGG 58.022 29.630 0.00 0.00 0.00 4.44
4086 4485 5.930569 AGCAAGGCAATTTTCTGAGATTTTC 59.069 36.000 0.00 0.00 0.00 2.29
4130 4530 6.586082 GCATCATGACAAATCCTTAAAAACGT 59.414 34.615 0.00 0.00 0.00 3.99
4132 4532 7.887996 TGCATCATGACAAATCCTTAAAAAC 57.112 32.000 0.00 0.00 0.00 2.43
4133 4533 8.772705 GTTTGCATCATGACAAATCCTTAAAAA 58.227 29.630 12.92 0.00 38.01 1.94
4138 4538 5.471556 TGTTTGCATCATGACAAATCCTT 57.528 34.783 12.92 0.00 38.01 3.36
4140 4540 5.412640 TCATGTTTGCATCATGACAAATCC 58.587 37.500 22.57 4.39 44.14 3.01
4162 4562 4.519540 TTGTTTAGGCTGGCAATTCTTC 57.480 40.909 3.38 0.00 0.00 2.87
4163 4563 4.262592 CCTTTGTTTAGGCTGGCAATTCTT 60.263 41.667 3.38 0.00 0.00 2.52
4172 4572 5.213891 ACCATTTTCCTTTGTTTAGGCTG 57.786 39.130 0.00 0.00 35.15 4.85
4173 4573 6.780522 TCTTACCATTTTCCTTTGTTTAGGCT 59.219 34.615 0.00 0.00 35.15 4.58
4175 4575 9.996554 AATTCTTACCATTTTCCTTTGTTTAGG 57.003 29.630 0.00 0.00 36.59 2.69
4194 4597 6.017934 GCAAATCTCGAGCATGGTAATTCTTA 60.018 38.462 7.81 0.00 0.00 2.10
4211 4614 3.471680 GAGGGAGTACATGGCAAATCTC 58.528 50.000 0.00 0.00 0.00 2.75
4212 4615 2.173569 GGAGGGAGTACATGGCAAATCT 59.826 50.000 0.00 0.00 0.00 2.40
4236 4639 4.546829 TTGCTAGGACAAGTATTTCCGT 57.453 40.909 0.00 0.00 36.95 4.69
4238 4641 5.193679 ACCATTGCTAGGACAAGTATTTCC 58.806 41.667 0.00 0.00 31.96 3.13
4239 4642 6.151144 ACAACCATTGCTAGGACAAGTATTTC 59.849 38.462 0.00 0.00 31.96 2.17
4251 4654 7.268586 ACAAGTCTAGATACAACCATTGCTAG 58.731 38.462 0.00 0.00 0.00 3.42
4252 4655 7.182817 ACAAGTCTAGATACAACCATTGCTA 57.817 36.000 0.00 0.00 0.00 3.49
4253 4656 6.054860 ACAAGTCTAGATACAACCATTGCT 57.945 37.500 0.00 0.00 0.00 3.91
4254 4657 6.743575 AACAAGTCTAGATACAACCATTGC 57.256 37.500 0.00 0.00 0.00 3.56
4255 4658 8.322906 TGAAACAAGTCTAGATACAACCATTG 57.677 34.615 0.00 0.00 0.00 2.82
4256 4659 8.157476 ACTGAAACAAGTCTAGATACAACCATT 58.843 33.333 0.00 0.00 0.00 3.16
4257 4660 7.680730 ACTGAAACAAGTCTAGATACAACCAT 58.319 34.615 0.00 0.00 0.00 3.55
4258 4661 7.062749 ACTGAAACAAGTCTAGATACAACCA 57.937 36.000 0.00 0.00 0.00 3.67
4259 4662 7.964604 AACTGAAACAAGTCTAGATACAACC 57.035 36.000 0.00 0.00 0.00 3.77
4266 4669 8.529476 GGGAGTATTAACTGAAACAAGTCTAGA 58.471 37.037 0.00 0.00 35.56 2.43
4267 4670 8.532819 AGGGAGTATTAACTGAAACAAGTCTAG 58.467 37.037 0.00 0.00 35.56 2.43
4268 4671 8.431910 AGGGAGTATTAACTGAAACAAGTCTA 57.568 34.615 0.00 0.00 35.56 2.59
4269 4672 7.317722 AGGGAGTATTAACTGAAACAAGTCT 57.682 36.000 0.00 0.00 35.56 3.24
4270 4673 7.660208 TGAAGGGAGTATTAACTGAAACAAGTC 59.340 37.037 0.00 0.00 35.56 3.01
4271 4674 7.514721 TGAAGGGAGTATTAACTGAAACAAGT 58.485 34.615 0.00 0.00 35.56 3.16
4272 4675 7.979444 TGAAGGGAGTATTAACTGAAACAAG 57.021 36.000 0.00 0.00 35.56 3.16
4273 4676 7.610305 GGATGAAGGGAGTATTAACTGAAACAA 59.390 37.037 0.00 0.00 35.56 2.83
4274 4677 7.110155 GGATGAAGGGAGTATTAACTGAAACA 58.890 38.462 0.00 0.00 35.56 2.83
4275 4678 6.258068 CGGATGAAGGGAGTATTAACTGAAAC 59.742 42.308 0.00 0.00 35.56 2.78
4276 4679 6.346096 CGGATGAAGGGAGTATTAACTGAAA 58.654 40.000 0.00 0.00 35.56 2.69
4277 4680 5.684030 GCGGATGAAGGGAGTATTAACTGAA 60.684 44.000 0.00 0.00 35.56 3.02
4278 4681 4.202223 GCGGATGAAGGGAGTATTAACTGA 60.202 45.833 0.00 0.00 35.56 3.41
4279 4682 4.058817 GCGGATGAAGGGAGTATTAACTG 58.941 47.826 0.00 0.00 35.56 3.16
4280 4683 3.243771 CGCGGATGAAGGGAGTATTAACT 60.244 47.826 0.00 0.00 39.21 2.24
4281 4684 3.057734 CGCGGATGAAGGGAGTATTAAC 58.942 50.000 0.00 0.00 0.00 2.01
4282 4685 2.960384 TCGCGGATGAAGGGAGTATTAA 59.040 45.455 6.13 0.00 0.00 1.40
4283 4686 2.589720 TCGCGGATGAAGGGAGTATTA 58.410 47.619 6.13 0.00 0.00 0.98
4284 4687 1.410004 TCGCGGATGAAGGGAGTATT 58.590 50.000 6.13 0.00 0.00 1.89
4285 4688 1.410004 TTCGCGGATGAAGGGAGTAT 58.590 50.000 6.13 0.00 32.22 2.12
4286 4689 1.410004 ATTCGCGGATGAAGGGAGTA 58.590 50.000 6.13 0.00 32.22 2.59
4287 4690 1.410004 TATTCGCGGATGAAGGGAGT 58.590 50.000 11.02 0.00 32.22 3.85
4288 4691 2.224066 ACTTATTCGCGGATGAAGGGAG 60.224 50.000 11.02 1.04 32.22 4.30
4289 4692 1.760613 ACTTATTCGCGGATGAAGGGA 59.239 47.619 11.02 0.00 0.00 4.20
4290 4693 1.867233 CACTTATTCGCGGATGAAGGG 59.133 52.381 11.02 7.26 0.00 3.95
4291 4694 2.550978 ACACTTATTCGCGGATGAAGG 58.449 47.619 11.02 0.00 0.00 3.46
4292 4695 7.030165 AGATATACACTTATTCGCGGATGAAG 58.970 38.462 11.02 11.86 0.00 3.02
4293 4696 6.920817 AGATATACACTTATTCGCGGATGAA 58.079 36.000 11.02 0.00 0.00 2.57
4294 4697 6.510879 AGATATACACTTATTCGCGGATGA 57.489 37.500 11.02 0.00 0.00 2.92
4295 4698 8.346300 AGATAGATATACACTTATTCGCGGATG 58.654 37.037 11.02 0.00 0.00 3.51
4296 4699 8.453238 AGATAGATATACACTTATTCGCGGAT 57.547 34.615 4.69 4.69 0.00 4.18
4297 4700 7.860918 AGATAGATATACACTTATTCGCGGA 57.139 36.000 6.13 0.00 0.00 5.54
4298 4701 8.912787 AAAGATAGATATACACTTATTCGCGG 57.087 34.615 6.13 0.00 0.00 6.46
4366 4769 6.070881 TGGTGCCATAAATGATGCTACTTTTT 60.071 34.615 0.00 0.00 33.79 1.94
4367 4770 5.421693 TGGTGCCATAAATGATGCTACTTTT 59.578 36.000 0.00 0.00 33.79 2.27
4368 4771 4.955450 TGGTGCCATAAATGATGCTACTTT 59.045 37.500 0.00 0.00 33.79 2.66
4369 4772 4.535781 TGGTGCCATAAATGATGCTACTT 58.464 39.130 0.00 0.00 33.79 2.24
4370 4773 4.169059 TGGTGCCATAAATGATGCTACT 57.831 40.909 0.00 0.00 33.79 2.57
4371 4774 4.916983 TTGGTGCCATAAATGATGCTAC 57.083 40.909 0.00 0.00 33.79 3.58
4372 4775 6.482898 AATTTGGTGCCATAAATGATGCTA 57.517 33.333 0.00 0.00 33.79 3.49
4373 4776 5.362105 AATTTGGTGCCATAAATGATGCT 57.638 34.783 0.00 0.00 33.79 3.79
4374 4777 5.178067 GCTAATTTGGTGCCATAAATGATGC 59.822 40.000 0.00 0.00 33.79 3.91
4375 4778 6.282167 TGCTAATTTGGTGCCATAAATGATG 58.718 36.000 0.00 0.00 35.05 3.07
4376 4779 6.482898 TGCTAATTTGGTGCCATAAATGAT 57.517 33.333 0.00 0.00 0.00 2.45
4377 4780 5.929058 TGCTAATTTGGTGCCATAAATGA 57.071 34.783 0.00 0.00 0.00 2.57
4378 4781 5.403166 CGATGCTAATTTGGTGCCATAAATG 59.597 40.000 0.00 0.00 0.00 2.32
4379 4782 5.068987 ACGATGCTAATTTGGTGCCATAAAT 59.931 36.000 0.00 0.00 0.00 1.40
4380 4783 4.400884 ACGATGCTAATTTGGTGCCATAAA 59.599 37.500 0.00 0.00 0.00 1.40
4381 4784 3.951037 ACGATGCTAATTTGGTGCCATAA 59.049 39.130 0.00 0.00 0.00 1.90
4382 4785 3.550820 ACGATGCTAATTTGGTGCCATA 58.449 40.909 0.00 0.00 0.00 2.74
4383 4786 2.378038 ACGATGCTAATTTGGTGCCAT 58.622 42.857 0.00 0.00 0.00 4.40
4384 4787 1.832883 ACGATGCTAATTTGGTGCCA 58.167 45.000 0.00 0.00 0.00 4.92
4385 4788 2.939460 AACGATGCTAATTTGGTGCC 57.061 45.000 0.00 0.00 0.00 5.01
4386 4789 4.875544 TCTAACGATGCTAATTTGGTGC 57.124 40.909 0.00 0.00 0.00 5.01
4387 4790 7.015226 TGAATCTAACGATGCTAATTTGGTG 57.985 36.000 0.00 0.00 0.00 4.17
4388 4791 7.807977 ATGAATCTAACGATGCTAATTTGGT 57.192 32.000 0.00 0.00 0.00 3.67
4389 4792 9.520204 AAAATGAATCTAACGATGCTAATTTGG 57.480 29.630 0.00 0.00 0.00 3.28
4395 4798 9.720667 CATTTCAAAATGAATCTAACGATGCTA 57.279 29.630 9.38 0.00 46.72 3.49
4396 4799 8.246180 ACATTTCAAAATGAATCTAACGATGCT 58.754 29.630 19.50 0.00 46.72 3.79
4397 4800 8.398491 ACATTTCAAAATGAATCTAACGATGC 57.602 30.769 19.50 0.00 46.72 3.91


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

AutoCloner maintained by Alex Coulton.