Multiple sequence alignment - TraesCS4B01G069900

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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 TraesCS4B01G069900 chr4B 100.000 5791 0 0 1 5791 63999289 63993499 0.000000e+00 10695.0
1 TraesCS4B01G069900 chr4A 89.872 2419 135 58 2 2370 555745102 555747460 0.000000e+00 3009.0
2 TraesCS4B01G069900 chr4A 93.207 1531 42 16 2492 3996 555747888 555749382 0.000000e+00 2194.0
3 TraesCS4B01G069900 chr4A 93.908 1264 58 10 3991 5242 555749462 555750718 0.000000e+00 1890.0
4 TraesCS4B01G069900 chr4A 91.218 854 60 13 1360 2200 673872942 673873793 0.000000e+00 1147.0
5 TraesCS4B01G069900 chr4A 86.311 431 50 7 2 430 555744701 555745124 1.470000e-125 460.0
6 TraesCS4B01G069900 chr4A 100.000 29 0 0 2433 2461 555747862 555747890 3.000000e-03 54.7
7 TraesCS4B01G069900 chr4D 88.333 2417 176 55 1 2370 44206446 44204089 0.000000e+00 2804.0
8 TraesCS4B01G069900 chr4D 90.105 1809 103 34 3991 5791 44201918 44200178 0.000000e+00 2279.0
9 TraesCS4B01G069900 chr4D 87.910 976 69 24 3036 3992 44202946 44202001 0.000000e+00 1103.0
10 TraesCS4B01G069900 chr4D 87.167 639 53 14 2433 3057 44203580 44202957 0.000000e+00 699.0
11 TraesCS4B01G069900 chr3D 92.155 854 52 9 1360 2200 31599429 31598578 0.000000e+00 1192.0
12 TraesCS4B01G069900 chr3D 88.941 425 44 1 3991 4415 426482908 426483329 6.650000e-144 521.0
13 TraesCS4B01G069900 chr3D 92.000 100 6 2 3893 3990 426482720 426482819 7.820000e-29 139.0
14 TraesCS4B01G069900 chr5B 91.569 854 57 9 1360 2200 34429694 34428843 0.000000e+00 1164.0
15 TraesCS4B01G069900 chr5B 88.686 274 23 7 1360 1626 661394324 661394052 1.560000e-85 327.0
16 TraesCS4B01G069900 chr5B 84.211 95 15 0 1235 1329 224624228 224624134 6.180000e-15 93.5
17 TraesCS4B01G069900 chr3A 88.345 429 45 2 3991 4415 562353021 562353448 1.440000e-140 510.0
18 TraesCS4B01G069900 chr3A 89.815 108 8 3 3886 3990 562352825 562352932 1.010000e-27 135.0
19 TraesCS4B01G069900 chr1B 90.884 362 24 3 1360 1712 469592365 469592726 1.460000e-130 477.0
20 TraesCS4B01G069900 chr3B 87.361 269 26 5 3991 4255 556056466 556056202 9.430000e-78 302.0
21 TraesCS4B01G069900 chr3B 88.535 157 15 3 4259 4415 556053000 556052847 2.760000e-43 187.0
22 TraesCS4B01G069900 chr2B 88.163 245 22 2 1360 1597 747410890 747411134 9.500000e-73 285.0
23 TraesCS4B01G069900 chr2D 94.286 140 7 1 1361 1499 5624203 5624342 4.550000e-51 213.0
24 TraesCS4B01G069900 chr5D 83.158 95 16 0 1235 1329 210988644 210988738 2.870000e-13 87.9


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 TraesCS4B01G069900 chr4B 63993499 63999289 5790 True 10695.00 10695 100.00000 1 5791 1 chr4B.!!$R1 5790
1 TraesCS4B01G069900 chr4A 555744701 555750718 6017 False 1521.54 3009 92.65960 2 5242 5 chr4A.!!$F2 5240
2 TraesCS4B01G069900 chr4A 673872942 673873793 851 False 1147.00 1147 91.21800 1360 2200 1 chr4A.!!$F1 840
3 TraesCS4B01G069900 chr4D 44200178 44206446 6268 True 1721.25 2804 88.37875 1 5791 4 chr4D.!!$R1 5790
4 TraesCS4B01G069900 chr3D 31598578 31599429 851 True 1192.00 1192 92.15500 1360 2200 1 chr3D.!!$R1 840
5 TraesCS4B01G069900 chr3D 426482720 426483329 609 False 330.00 521 90.47050 3893 4415 2 chr3D.!!$F1 522
6 TraesCS4B01G069900 chr5B 34428843 34429694 851 True 1164.00 1164 91.56900 1360 2200 1 chr5B.!!$R1 840
7 TraesCS4B01G069900 chr3A 562352825 562353448 623 False 322.50 510 89.08000 3886 4415 2 chr3A.!!$F1 529
8 TraesCS4B01G069900 chr3B 556052847 556056466 3619 True 244.50 302 87.94800 3991 4415 2 chr3B.!!$R1 424

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
594 996 0.249322 GATTGCGCCGACCTAGCTTA 60.249 55.000 4.18 0.00 0.00 3.09 F
607 1009 0.306840 TAGCTTATCACGACTCGCCG 59.693 55.000 0.00 0.00 0.00 6.46 F
1195 1627 0.392461 TAGCCCAAGCCGTGATTCAC 60.392 55.000 6.73 6.73 41.25 3.18 F
1735 2197 0.958091 TCGTGCAGGATTTTTGGGTG 59.042 50.000 4.68 0.00 0.00 4.61 F
1873 2337 1.044611 GCTAGCTAGGACTGGAAGGG 58.955 60.000 22.10 0.00 39.30 3.95 F
2710 3639 1.242076 CCTTTTGGTGCTGTCTGAGG 58.758 55.000 0.00 0.00 34.07 3.86 F
3883 4883 2.230992 TCGAATGGAGGTTTGCAAATGG 59.769 45.455 16.21 0.00 0.00 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1404 1856 0.943835 CACCATGTCGACGCACAAGA 60.944 55.000 11.62 0.00 0.00 3.02 R
1414 1866 1.153489 CTCCTCCTGCACCATGTCG 60.153 63.158 0.00 0.00 0.00 4.35 R
2474 3403 3.057526 GCTTGGGCGTTACAAGAATTCTT 60.058 43.478 15.11 15.11 46.27 2.52 R
2710 3639 3.951775 AAGACAGAGTGACAGACCATC 57.048 47.619 0.00 0.00 0.00 3.51 R
3132 4108 4.450976 AGTCAACAAGTACTCACAATGCA 58.549 39.130 0.00 0.00 0.00 3.96 R
4415 8722 0.617413 CTCTCCAGCCTCCAATGTGT 59.383 55.000 0.00 0.00 0.00 3.72 R
5706 10048 0.037232 GGGGCGTCATGGCTACTATC 60.037 60.000 0.00 0.00 44.11 2.08 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
27 28 8.103305 AGGCTCTTGAGTAAACTAATTTCATCA 58.897 33.333 0.00 0.00 0.00 3.07
59 61 1.202830 ACTTGCACACCCGTCCAATAA 60.203 47.619 0.00 0.00 0.00 1.40
68 70 1.375551 CCGTCCAATAAACCCTTCCG 58.624 55.000 0.00 0.00 0.00 4.30
80 82 0.331616 CCCTTCCGGAATCACCCTTT 59.668 55.000 19.21 0.00 34.64 3.11
105 107 1.788229 TCATGTCTCGCCCCTCAATA 58.212 50.000 0.00 0.00 0.00 1.90
120 122 5.394553 CCCCTCAATAATTTTGTGCCTTCTC 60.395 44.000 0.00 0.00 0.00 2.87
126 128 2.978156 TTTTGTGCCTTCTCCCATCT 57.022 45.000 0.00 0.00 0.00 2.90
129 131 1.661463 TGTGCCTTCTCCCATCTCTT 58.339 50.000 0.00 0.00 0.00 2.85
159 161 2.499289 TGTGCAACTGTCAAACCCAATT 59.501 40.909 0.00 0.00 38.04 2.32
168 170 5.423931 ACTGTCAAACCCAATTTAAGTTGGT 59.576 36.000 23.61 12.16 45.78 3.67
172 174 7.070074 TGTCAAACCCAATTTAAGTTGGTGTAT 59.930 33.333 23.61 8.33 45.78 2.29
174 176 5.400066 ACCCAATTTAAGTTGGTGTATGC 57.600 39.130 23.61 0.00 45.78 3.14
179 181 2.018542 TAAGTTGGTGTATGCGGCTC 57.981 50.000 0.00 0.00 0.00 4.70
189 191 3.062234 GTGTATGCGGCTCTTGAGTAAAC 59.938 47.826 0.00 0.00 0.00 2.01
196 198 4.475944 CGGCTCTTGAGTAAACCAAATTG 58.524 43.478 0.00 0.00 0.00 2.32
222 225 1.605165 TTTCCCATGGTTCCGTGGC 60.605 57.895 21.12 0.00 40.72 5.01
321 324 4.438145 CGAATCACTCTTCCTTTATCGTCG 59.562 45.833 0.00 0.00 0.00 5.12
323 326 1.846782 CACTCTTCCTTTATCGTCGCG 59.153 52.381 0.00 0.00 0.00 5.87
330 333 4.557605 TTATCGTCGCGCGTCCCC 62.558 66.667 30.98 14.85 42.13 4.81
339 342 2.591715 CGCGTCCCCCAATCATCC 60.592 66.667 0.00 0.00 0.00 3.51
340 343 2.203351 GCGTCCCCCAATCATCCC 60.203 66.667 0.00 0.00 0.00 3.85
341 344 2.111043 CGTCCCCCAATCATCCCG 59.889 66.667 0.00 0.00 0.00 5.14
377 550 3.248602 CGCTAATCTTATCTGTGCCAACC 59.751 47.826 0.00 0.00 0.00 3.77
379 552 2.332063 ATCTTATCTGTGCCAACCGG 57.668 50.000 0.00 0.00 0.00 5.28
397 799 1.384191 GCCAGACCCCCAATCAAGT 59.616 57.895 0.00 0.00 0.00 3.16
400 802 1.075374 CCAGACCCCCAATCAAGTTGA 59.925 52.381 8.27 8.27 40.37 3.18
406 808 2.290071 CCCCCAATCAAGTTGACGTACT 60.290 50.000 7.96 0.00 40.37 2.73
412 814 3.844577 TCAAGTTGACGTACTAGGCTC 57.155 47.619 0.08 0.00 0.00 4.70
429 831 4.254492 AGGCTCTCGAGTAAACCAAATTC 58.746 43.478 13.13 0.00 0.00 2.17
430 832 4.020128 AGGCTCTCGAGTAAACCAAATTCT 60.020 41.667 13.13 0.00 0.00 2.40
431 833 5.187186 AGGCTCTCGAGTAAACCAAATTCTA 59.813 40.000 13.13 0.00 0.00 2.10
432 834 5.291371 GGCTCTCGAGTAAACCAAATTCTAC 59.709 44.000 13.13 0.00 0.00 2.59
433 835 5.291371 GCTCTCGAGTAAACCAAATTCTACC 59.709 44.000 13.13 0.00 0.00 3.18
434 836 6.600882 TCTCGAGTAAACCAAATTCTACCT 57.399 37.500 13.13 0.00 0.00 3.08
435 837 7.001099 TCTCGAGTAAACCAAATTCTACCTT 57.999 36.000 13.13 0.00 0.00 3.50
436 838 6.872020 TCTCGAGTAAACCAAATTCTACCTTG 59.128 38.462 13.13 0.00 0.00 3.61
443 845 4.149598 ACCAAATTCTACCTTGTTCCCAC 58.850 43.478 0.00 0.00 0.00 4.61
453 855 1.098712 TTGTTCCCACGGTTCTGTGC 61.099 55.000 6.28 0.00 38.55 4.57
593 995 1.521681 GATTGCGCCGACCTAGCTT 60.522 57.895 4.18 0.00 0.00 3.74
594 996 0.249322 GATTGCGCCGACCTAGCTTA 60.249 55.000 4.18 0.00 0.00 3.09
607 1009 0.306840 TAGCTTATCACGACTCGCCG 59.693 55.000 0.00 0.00 0.00 6.46
722 1127 0.916086 TTCCAGCCCATACCAATCGT 59.084 50.000 0.00 0.00 0.00 3.73
725 1130 1.140052 CCAGCCCATACCAATCGTACA 59.860 52.381 0.00 0.00 0.00 2.90
774 1185 3.998672 GGCGTCGACAGGAACCCA 61.999 66.667 17.16 0.00 0.00 4.51
925 1336 4.835927 CGATTTGCGGCTAGTCCT 57.164 55.556 0.00 0.00 36.03 3.85
1052 1468 4.379243 CGCGGTGCTCCTCAACCT 62.379 66.667 0.00 0.00 0.00 3.50
1053 1469 2.435059 GCGGTGCTCCTCAACCTC 60.435 66.667 2.85 0.00 0.00 3.85
1054 1470 3.059982 CGGTGCTCCTCAACCTCA 58.940 61.111 2.85 0.00 0.00 3.86
1059 1475 1.131638 TGCTCCTCAACCTCAAGTGT 58.868 50.000 0.00 0.00 0.00 3.55
1135 1551 0.892755 GGAGACCGTGTGTATGTCCA 59.107 55.000 0.00 0.00 0.00 4.02
1145 1561 2.106683 GTATGTCCACGCCACCAGC 61.107 63.158 0.00 0.00 38.52 4.85
1146 1562 2.290287 TATGTCCACGCCACCAGCT 61.290 57.895 0.00 0.00 40.39 4.24
1165 1581 7.384660 CACCAGCTCTCTCTTTGCTATTAATAG 59.615 40.741 16.79 16.79 35.05 1.73
1188 1620 2.116238 TCTAAGAATAGCCCAAGCCGT 58.884 47.619 0.00 0.00 41.25 5.68
1195 1627 0.392461 TAGCCCAAGCCGTGATTCAC 60.392 55.000 6.73 6.73 41.25 3.18
1200 1632 1.229428 CAAGCCGTGATTCACTGTGT 58.771 50.000 14.54 0.00 31.34 3.72
1211 1643 6.603095 GTGATTCACTGTGTTCTGTTTATCC 58.397 40.000 9.59 0.00 0.00 2.59
1213 1645 6.650807 TGATTCACTGTGTTCTGTTTATCCTC 59.349 38.462 7.79 0.00 0.00 3.71
1241 1674 2.798976 AATGTGATTTGCGTGCAGTT 57.201 40.000 0.00 0.00 0.00 3.16
1350 1783 1.396996 GATCAACACCCATTTCGTCGG 59.603 52.381 0.00 0.00 0.00 4.79
1404 1856 6.603201 AGTGATGAATAACCCGAATTGTGATT 59.397 34.615 0.00 0.00 0.00 2.57
1414 1866 3.155998 CGAATTGTGATTCTTGTGCGTC 58.844 45.455 0.00 0.00 39.61 5.19
1527 1979 3.332761 TGTGAACACGAATTTGCTGTC 57.667 42.857 0.00 0.00 0.00 3.51
1573 2031 8.241367 TCTGTTGTTTTCTCTTCTTTTTGGTAC 58.759 33.333 0.00 0.00 0.00 3.34
1685 2147 8.530311 ACATTCTGTAGGAATCATGAGCTATAG 58.470 37.037 0.09 0.00 42.20 1.31
1698 2160 1.160137 GCTATAGATGGCAAAGGGCG 58.840 55.000 3.21 0.00 46.16 6.13
1735 2197 0.958091 TCGTGCAGGATTTTTGGGTG 59.042 50.000 4.68 0.00 0.00 4.61
1754 2216 4.261801 GGTGCTCAAGTACATGTATGGTT 58.738 43.478 9.18 0.75 32.02 3.67
1756 2218 5.878116 GGTGCTCAAGTACATGTATGGTTAA 59.122 40.000 9.18 0.00 32.02 2.01
1873 2337 1.044611 GCTAGCTAGGACTGGAAGGG 58.955 60.000 22.10 0.00 39.30 3.95
1874 2338 1.689892 GCTAGCTAGGACTGGAAGGGT 60.690 57.143 22.10 0.00 39.30 4.34
2027 2492 4.285260 CGCTACCCCTTATATACACCCTTT 59.715 45.833 0.00 0.00 0.00 3.11
2044 2509 3.196254 CCCTTTAGTCAGGCATTGCAATT 59.804 43.478 9.83 0.00 31.69 2.32
2370 2843 7.435068 TGGCAGTAGATTAGTGAAAAGTTTC 57.565 36.000 0.00 0.00 37.69 2.78
2372 2845 7.173218 TGGCAGTAGATTAGTGAAAAGTTTCTG 59.827 37.037 5.45 0.00 38.02 3.02
2375 2848 8.778358 CAGTAGATTAGTGAAAAGTTTCTGCTT 58.222 33.333 5.45 0.00 38.02 3.91
2376 2849 8.778358 AGTAGATTAGTGAAAAGTTTCTGCTTG 58.222 33.333 5.45 0.00 38.02 4.01
2377 2850 7.573968 AGATTAGTGAAAAGTTTCTGCTTGT 57.426 32.000 5.45 0.00 38.02 3.16
2378 2851 8.000780 AGATTAGTGAAAAGTTTCTGCTTGTT 57.999 30.769 5.45 0.00 38.02 2.83
2379 2852 7.917505 AGATTAGTGAAAAGTTTCTGCTTGTTG 59.082 33.333 5.45 0.00 38.02 3.33
2380 2853 4.747810 AGTGAAAAGTTTCTGCTTGTTGG 58.252 39.130 5.45 0.00 38.02 3.77
2383 3043 3.825143 AAAGTTTCTGCTTGTTGGCAT 57.175 38.095 0.00 0.00 41.63 4.40
2388 3048 5.070001 AGTTTCTGCTTGTTGGCATAGTTA 58.930 37.500 0.00 0.00 41.63 2.24
2389 3049 5.182001 AGTTTCTGCTTGTTGGCATAGTTAG 59.818 40.000 0.00 0.00 41.63 2.34
2390 3050 3.609853 TCTGCTTGTTGGCATAGTTAGG 58.390 45.455 0.00 0.00 41.63 2.69
2391 3051 3.009033 TCTGCTTGTTGGCATAGTTAGGT 59.991 43.478 0.00 0.00 41.63 3.08
2394 3054 5.317808 TGCTTGTTGGCATAGTTAGGTTAA 58.682 37.500 0.00 0.00 37.29 2.01
2399 3059 7.826918 TGTTGGCATAGTTAGGTTAACTTTT 57.173 32.000 5.42 0.00 46.27 2.27
2592 3521 3.090790 TGTGTGGATGTGAATGGATTGG 58.909 45.455 0.00 0.00 0.00 3.16
2710 3639 1.242076 CCTTTTGGTGCTGTCTGAGG 58.758 55.000 0.00 0.00 34.07 3.86
2737 3666 5.992217 GGTCTGTCACTCTGTCTTAAACAAT 59.008 40.000 0.00 0.00 37.45 2.71
2791 3728 9.447040 CTTTCTGCTTGTTTGATGTGATATATG 57.553 33.333 0.00 0.00 0.00 1.78
2989 3932 8.218338 AGAGGTATTTTGCTAATCAGAATGTG 57.782 34.615 0.00 0.00 37.40 3.21
3040 3983 7.018349 AGGATCAAGGATACCATTCATCTCATT 59.982 37.037 0.00 0.00 37.17 2.57
3092 4068 9.542462 TTTATGTTCAGTTATCTCCCTTAATCG 57.458 33.333 0.00 0.00 0.00 3.34
3132 4108 2.309755 TCAATGAATCCAACTCCAGCCT 59.690 45.455 0.00 0.00 0.00 4.58
3177 4154 3.750371 TGATAAGTTTGACAGGTGGTGG 58.250 45.455 0.00 0.00 0.00 4.61
3320 4301 9.502091 CTGATCTGTATATCTCCTATAGGTAGC 57.498 40.741 18.51 4.45 36.34 3.58
3443 4424 9.141400 AGAATATACGTTCTGAAGTCAAAGAAC 57.859 33.333 0.00 5.65 45.74 3.01
3456 4437 6.054860 AGTCAAAGAACTGTGGCATATAGT 57.945 37.500 0.00 0.00 31.33 2.12
3580 4566 7.621428 TGAATCAGGAATGAATCTTTCAGAC 57.379 36.000 10.41 0.00 43.98 3.51
3772 4770 5.393352 GCCATCATTTGTTAGCATGTCTTCA 60.393 40.000 0.00 0.00 0.00 3.02
3785 4783 4.447054 GCATGTCTTCACCTTGATAGATCG 59.553 45.833 0.00 0.00 0.00 3.69
3796 4794 6.419413 CACCTTGATAGATCGAACTAGAAAGC 59.581 42.308 15.89 0.00 0.00 3.51
3883 4883 2.230992 TCGAATGGAGGTTTGCAAATGG 59.769 45.455 16.21 0.00 0.00 3.16
3953 4962 5.932303 TGCTGTTGAGTAGGTAATGAACTTC 59.068 40.000 0.00 0.00 0.00 3.01
3958 4967 5.967088 TGAGTAGGTAATGAACTTCAGAGC 58.033 41.667 0.00 0.00 0.00 4.09
3999 5097 4.309099 CTTGTTATTGCAGTGCATTGGTT 58.691 39.130 20.50 4.56 38.76 3.67
4003 5101 5.221322 TGTTATTGCAGTGCATTGGTTGTAA 60.221 36.000 20.50 0.00 38.76 2.41
4103 5201 3.462021 AGAAGAATGGCGCAATCTAGTC 58.538 45.455 10.83 4.94 0.00 2.59
4139 5237 7.323420 CCTCATTACTGAAGAACATGACACTA 58.677 38.462 0.00 0.00 0.00 2.74
4214 5323 9.844790 TTTTCATCAGTTTATTATGCTCAAGTG 57.155 29.630 0.00 0.00 0.00 3.16
4268 8575 9.965902 ATAAGAGTATCAACTGTCCTTGAATTT 57.034 29.630 0.00 0.00 37.82 1.82
4390 8697 6.017400 ACCAGCAAACAGAATATGAAACAG 57.983 37.500 0.00 0.00 0.00 3.16
4449 8756 2.027192 TGGAGAGTATGCTGAACCAACC 60.027 50.000 0.00 0.00 0.00 3.77
4465 8772 5.784578 ACCAACCCATTGTTTTCTTCTAC 57.215 39.130 0.00 0.00 34.00 2.59
4525 8833 3.745975 TGTCGTATTGTTTCTCAAGGCAG 59.254 43.478 0.00 0.00 39.55 4.85
4581 8889 1.338020 CAAGTTCAACCAAGGGAGTGC 59.662 52.381 0.00 0.00 0.00 4.40
4630 8942 7.281774 GGATATACTGGAGGCATGTGAATATTG 59.718 40.741 0.00 0.00 0.00 1.90
4720 9032 8.350722 TCTATATTCACTAATCAGGTCAACGTC 58.649 37.037 0.00 0.00 0.00 4.34
4877 9207 4.598257 CGATGGTTCAGCGGAAGT 57.402 55.556 0.00 0.00 39.68 3.01
4878 9208 2.373938 CGATGGTTCAGCGGAAGTC 58.626 57.895 0.00 0.00 39.68 3.01
4879 9209 0.389817 CGATGGTTCAGCGGAAGTCA 60.390 55.000 0.00 2.35 39.68 3.41
4880 9210 1.740380 CGATGGTTCAGCGGAAGTCAT 60.740 52.381 12.68 12.68 39.68 3.06
4881 9211 1.936547 GATGGTTCAGCGGAAGTCATC 59.063 52.381 19.16 19.16 37.54 2.92
4882 9212 0.389817 TGGTTCAGCGGAAGTCATCG 60.390 55.000 0.00 0.00 32.62 3.84
4883 9213 0.389948 GGTTCAGCGGAAGTCATCGT 60.390 55.000 0.00 0.00 32.62 3.73
4884 9214 1.135199 GGTTCAGCGGAAGTCATCGTA 60.135 52.381 0.00 0.00 32.62 3.43
4885 9215 2.186076 GTTCAGCGGAAGTCATCGTAG 58.814 52.381 0.00 0.00 32.62 3.51
4886 9216 1.460504 TCAGCGGAAGTCATCGTAGT 58.539 50.000 0.00 0.00 0.00 2.73
4887 9217 1.132453 TCAGCGGAAGTCATCGTAGTG 59.868 52.381 0.00 0.00 0.00 2.74
4973 9306 3.732048 TTTCTTTAGCTTAGGGTGGGG 57.268 47.619 0.00 0.00 0.00 4.96
5123 9463 0.457337 CGGAGCAGAAATGCCTTTGC 60.457 55.000 0.00 0.00 36.83 3.68
5138 9478 4.340666 TGCCTTTGCTGATAAAGTTTGTCA 59.659 37.500 13.60 13.60 36.22 3.58
5208 9548 3.535561 CTTGATGTTCAGGGACGCTTAT 58.464 45.455 0.00 0.00 0.00 1.73
5209 9549 4.693283 CTTGATGTTCAGGGACGCTTATA 58.307 43.478 0.00 0.00 0.00 0.98
5247 9587 2.904434 ACTCCGGTTTCAGGTCTAACAT 59.096 45.455 0.00 0.00 0.00 2.71
5248 9588 3.056035 ACTCCGGTTTCAGGTCTAACATC 60.056 47.826 0.00 0.00 0.00 3.06
5249 9589 2.094390 TCCGGTTTCAGGTCTAACATCG 60.094 50.000 0.00 0.00 0.00 3.84
5250 9590 2.094390 CCGGTTTCAGGTCTAACATCGA 60.094 50.000 0.00 0.00 0.00 3.59
5251 9591 3.430374 CCGGTTTCAGGTCTAACATCGAT 60.430 47.826 0.00 0.00 0.00 3.59
5252 9592 3.551890 CGGTTTCAGGTCTAACATCGATG 59.448 47.826 23.68 23.68 0.00 3.84
5278 9619 9.482627 GGAATAACTCAGAGTTACATGGAATAG 57.517 37.037 22.86 0.00 42.78 1.73
5357 9698 2.003937 TTTTGTAGGGGAAAGCCACC 57.996 50.000 0.00 0.00 38.89 4.61
5424 9765 3.440522 GTCCTGAAGCAAAATACTGGGAC 59.559 47.826 0.00 0.00 34.84 4.46
5429 9770 3.914426 AGCAAAATACTGGGACGATCT 57.086 42.857 0.00 0.00 0.00 2.75
5432 9773 3.309954 GCAAAATACTGGGACGATCTCAC 59.690 47.826 0.00 0.00 0.00 3.51
5433 9774 3.821421 AAATACTGGGACGATCTCACC 57.179 47.619 0.00 0.00 0.00 4.02
5442 9783 2.280628 GACGATCTCACCATCCCAAAC 58.719 52.381 0.00 0.00 0.00 2.93
5450 9791 4.714308 TCTCACCATCCCAAACAAAAAGTT 59.286 37.500 0.00 0.00 43.89 2.66
5454 9795 5.645497 CACCATCCCAAACAAAAAGTTGAAA 59.355 36.000 0.00 0.00 41.19 2.69
5456 9797 6.542005 ACCATCCCAAACAAAAAGTTGAAATC 59.458 34.615 0.00 0.00 41.19 2.17
5461 9802 8.672815 TCCCAAACAAAAAGTTGAAATCAAATC 58.327 29.630 0.00 0.00 41.19 2.17
5496 9838 7.442364 GTCTAGCTATAATTTGGACAATGAGCA 59.558 37.037 0.00 0.00 0.00 4.26
5510 9852 6.294176 GGACAATGAGCAAAAGATACAACACT 60.294 38.462 0.00 0.00 0.00 3.55
5532 9874 7.661040 CACTTATGTGGAAGACCTTTTGAAAT 58.339 34.615 0.80 0.00 40.33 2.17
5538 9880 6.323482 TGTGGAAGACCTTTTGAAATCAATCA 59.677 34.615 0.00 0.00 34.87 2.57
5555 9897 4.988540 TCAATCAGCCAATATAGCGTGTAC 59.011 41.667 0.00 0.00 34.64 2.90
5558 9900 1.000506 AGCCAATATAGCGTGTACGGG 59.999 52.381 6.55 0.00 40.23 5.28
5559 9901 1.425412 CCAATATAGCGTGTACGGGC 58.575 55.000 6.55 0.00 40.23 6.13
5592 9934 0.320073 CACACCATTGCAAGCTTGGG 60.320 55.000 27.10 20.82 34.72 4.12
5593 9935 1.375013 CACCATTGCAAGCTTGGGC 60.375 57.895 27.10 14.84 34.72 5.36
5599 9941 0.104671 TTGCAAGCTTGGGCAACTTC 59.895 50.000 27.10 8.86 44.41 3.01
5600 9942 1.005748 GCAAGCTTGGGCAACTTCC 60.006 57.895 27.10 3.94 41.70 3.46
5602 9944 0.316204 CAAGCTTGGGCAACTTCCAG 59.684 55.000 19.14 0.00 41.70 3.86
5603 9945 0.106015 AAGCTTGGGCAACTTCCAGT 60.106 50.000 0.00 0.00 41.70 4.00
5604 9946 0.825010 AGCTTGGGCAACTTCCAGTG 60.825 55.000 0.00 0.00 41.70 3.66
5605 9947 0.823356 GCTTGGGCAACTTCCAGTGA 60.823 55.000 0.00 0.00 38.54 3.41
5606 9948 1.691196 CTTGGGCAACTTCCAGTGAA 58.309 50.000 0.00 0.00 35.48 3.18
5607 9949 2.242043 CTTGGGCAACTTCCAGTGAAT 58.758 47.619 0.00 0.00 35.48 2.57
5608 9950 1.909700 TGGGCAACTTCCAGTGAATC 58.090 50.000 0.00 0.00 0.00 2.52
5609 9951 1.425066 TGGGCAACTTCCAGTGAATCT 59.575 47.619 0.00 0.00 0.00 2.40
5610 9952 1.815003 GGGCAACTTCCAGTGAATCTG 59.185 52.381 0.00 0.00 43.27 2.90
5611 9953 2.553028 GGGCAACTTCCAGTGAATCTGA 60.553 50.000 0.00 0.00 46.27 3.27
5612 9954 3.350833 GGCAACTTCCAGTGAATCTGAT 58.649 45.455 0.00 0.00 46.27 2.90
5613 9955 3.760684 GGCAACTTCCAGTGAATCTGATT 59.239 43.478 1.81 1.81 46.27 2.57
5614 9956 4.142513 GGCAACTTCCAGTGAATCTGATTC 60.143 45.833 20.74 20.74 46.27 2.52
5615 9957 4.456911 GCAACTTCCAGTGAATCTGATTCA 59.543 41.667 25.05 25.05 46.27 2.57
5629 9971 2.073056 TGATTCAACGATCACCGGTTG 58.927 47.619 2.97 0.00 43.93 3.77
5630 9972 2.289133 TGATTCAACGATCACCGGTTGA 60.289 45.455 2.97 6.80 43.93 3.18
5633 9975 0.790207 CAACGATCACCGGTTGACAG 59.210 55.000 2.97 6.69 43.93 3.51
5660 10002 1.133482 CCTTCCACCAGTTCCAAACCT 60.133 52.381 0.00 0.00 0.00 3.50
5661 10003 2.666317 CTTCCACCAGTTCCAAACCTT 58.334 47.619 0.00 0.00 0.00 3.50
5701 10043 1.497278 CGGTTGTTGCGTCATGGAG 59.503 57.895 0.00 0.00 0.00 3.86
5702 10044 0.948623 CGGTTGTTGCGTCATGGAGA 60.949 55.000 0.00 0.00 0.00 3.71
5703 10045 1.453155 GGTTGTTGCGTCATGGAGAT 58.547 50.000 0.00 0.00 0.00 2.75
5706 10048 0.392863 TGTTGCGTCATGGAGATGGG 60.393 55.000 0.00 0.00 33.68 4.00
5717 10059 3.567375 TGGAGATGGGATAGTAGCCAT 57.433 47.619 6.80 0.00 0.00 4.40
5751 10093 0.388659 AGCTTCGCTCCTGCTATCTG 59.611 55.000 0.00 0.00 30.62 2.90
5752 10094 0.387202 GCTTCGCTCCTGCTATCTGA 59.613 55.000 0.00 0.00 36.97 3.27
5753 10095 1.602668 GCTTCGCTCCTGCTATCTGAG 60.603 57.143 0.00 0.00 36.97 3.35
5779 10124 4.172512 CTGCTGAGCCCGAGCCAT 62.173 66.667 0.23 0.00 41.25 4.40
5784 10129 0.394192 CTGAGCCCGAGCCATTATCA 59.606 55.000 0.00 0.00 41.25 2.15
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
47 49 1.005097 GGAAGGGTTTATTGGACGGGT 59.995 52.381 0.00 0.00 0.00 5.28
80 82 3.054728 TGAGGGGCGAGACATGATAAAAA 60.055 43.478 0.00 0.00 0.00 1.94
99 101 5.185635 TGGGAGAAGGCACAAAATTATTGAG 59.814 40.000 7.18 2.06 0.00 3.02
105 107 3.766051 GAGATGGGAGAAGGCACAAAATT 59.234 43.478 0.00 0.00 0.00 1.82
120 122 4.040095 TGCACAGATGAGATAAGAGATGGG 59.960 45.833 0.00 0.00 0.00 4.00
126 128 5.047092 TGACAGTTGCACAGATGAGATAAGA 60.047 40.000 0.00 0.00 0.00 2.10
129 131 4.806640 TGACAGTTGCACAGATGAGATA 57.193 40.909 0.00 0.00 0.00 1.98
159 161 2.027561 AGAGCCGCATACACCAACTTAA 60.028 45.455 0.00 0.00 0.00 1.85
168 170 3.259064 GTTTACTCAAGAGCCGCATACA 58.741 45.455 0.00 0.00 0.00 2.29
172 174 0.394938 TGGTTTACTCAAGAGCCGCA 59.605 50.000 0.00 0.00 0.00 5.69
174 176 4.023193 ACAATTTGGTTTACTCAAGAGCCG 60.023 41.667 0.78 0.00 0.00 5.52
179 181 7.712797 ACAAGGTACAATTTGGTTTACTCAAG 58.287 34.615 0.78 0.00 0.00 3.02
189 191 4.946478 TGGGAAACAAGGTACAATTTGG 57.054 40.909 0.78 0.00 0.00 3.28
222 225 1.502231 AGCAAGTTGACAGTGCTACG 58.498 50.000 7.16 0.00 46.52 3.51
323 326 2.203351 GGGATGATTGGGGGACGC 60.203 66.667 0.00 0.00 43.69 5.19
330 333 2.093500 TGAGAAGACACGGGATGATTGG 60.093 50.000 0.00 0.00 0.00 3.16
339 342 0.109086 AGCGATGTGAGAAGACACGG 60.109 55.000 0.00 0.00 42.86 4.94
340 343 2.544480 TAGCGATGTGAGAAGACACG 57.456 50.000 0.00 0.00 42.86 4.49
341 344 4.677584 AGATTAGCGATGTGAGAAGACAC 58.322 43.478 0.00 0.00 40.68 3.67
377 550 3.280938 TTGATTGGGGGTCTGGCCG 62.281 63.158 0.00 0.00 38.44 6.13
379 552 0.251787 AACTTGATTGGGGGTCTGGC 60.252 55.000 0.00 0.00 0.00 4.85
381 554 2.162681 GTCAACTTGATTGGGGGTCTG 58.837 52.381 0.00 0.00 38.98 3.51
383 556 1.165270 CGTCAACTTGATTGGGGGTC 58.835 55.000 0.00 0.00 38.98 4.46
384 557 0.476771 ACGTCAACTTGATTGGGGGT 59.523 50.000 0.00 0.00 38.98 4.95
397 799 2.277969 CTCGAGAGCCTAGTACGTCAA 58.722 52.381 6.58 0.00 0.00 3.18
400 802 3.533606 TTACTCGAGAGCCTAGTACGT 57.466 47.619 21.68 0.00 0.00 3.57
406 808 5.187186 AGAATTTGGTTTACTCGAGAGCCTA 59.813 40.000 21.68 9.08 0.00 3.93
412 814 6.649557 ACAAGGTAGAATTTGGTTTACTCGAG 59.350 38.462 11.84 11.84 0.00 4.04
433 835 0.944386 CACAGAACCGTGGGAACAAG 59.056 55.000 0.00 0.00 46.06 3.16
434 836 1.098712 GCACAGAACCGTGGGAACAA 61.099 55.000 0.00 0.00 46.06 2.83
435 837 1.525077 GCACAGAACCGTGGGAACA 60.525 57.895 0.00 0.00 37.37 3.18
436 838 2.258726 GGCACAGAACCGTGGGAAC 61.259 63.158 0.00 0.00 37.37 3.62
464 866 2.286418 GCGATATACACCAGCAAGTTGC 60.286 50.000 20.44 20.44 45.46 4.17
551 953 3.397482 CTCCCTTGCTATTCGATCCAAG 58.603 50.000 0.00 0.00 35.61 3.61
593 995 0.099968 CCTTTCGGCGAGTCGTGATA 59.900 55.000 15.08 7.08 0.00 2.15
594 996 1.153823 CCTTTCGGCGAGTCGTGAT 60.154 57.895 15.08 0.00 0.00 3.06
607 1009 6.362686 GTTTGCGATTTTGAATTTCCCTTTC 58.637 36.000 0.00 0.00 0.00 2.62
678 1083 5.279006 CGGATTGGATCGAGGATTTCTCTTA 60.279 44.000 0.00 0.00 40.30 2.10
679 1084 4.502259 CGGATTGGATCGAGGATTTCTCTT 60.502 45.833 0.00 0.00 40.30 2.85
722 1127 1.287815 CAGTCGTCGGCTGGTTGTA 59.712 57.895 19.13 0.00 0.00 2.41
761 1166 3.691342 CCGCTGGGTTCCTGTCGA 61.691 66.667 0.00 0.00 0.00 4.20
861 1272 4.796231 CCGAACGAGCCGAGTGGG 62.796 72.222 1.50 0.00 39.58 4.61
943 1354 0.323908 CCGTCTCTCTCTCCAGGGTT 60.324 60.000 0.00 0.00 0.00 4.11
1008 1424 3.406200 CTCACCCCCTCCAGGCAG 61.406 72.222 0.00 0.00 0.00 4.85
1037 1453 0.671781 CTTGAGGTTGAGGAGCACCG 60.672 60.000 0.00 0.00 41.83 4.94
1038 1454 0.398318 ACTTGAGGTTGAGGAGCACC 59.602 55.000 0.00 0.00 0.00 5.01
1049 1465 1.512926 GATGTCGCAACACTTGAGGT 58.487 50.000 0.00 0.00 38.48 3.85
1050 1466 0.439985 CGATGTCGCAACACTTGAGG 59.560 55.000 0.00 0.00 38.48 3.86
1051 1467 1.125021 GTCGATGTCGCAACACTTGAG 59.875 52.381 0.00 0.00 38.48 3.02
1052 1468 1.136690 GTCGATGTCGCAACACTTGA 58.863 50.000 0.00 0.00 38.48 3.02
1053 1469 0.163788 GGTCGATGTCGCAACACTTG 59.836 55.000 0.00 0.00 38.48 3.16
1054 1470 0.033504 AGGTCGATGTCGCAACACTT 59.966 50.000 0.00 0.00 38.48 3.16
1059 1475 1.014044 GCTTGAGGTCGATGTCGCAA 61.014 55.000 0.00 0.00 39.60 4.85
1165 1581 1.867865 GCTTGGGCTATTCTTAGACGC 59.132 52.381 0.00 0.00 33.87 5.19
1172 1588 0.839946 ATCACGGCTTGGGCTATTCT 59.160 50.000 0.00 0.00 38.73 2.40
1173 1589 1.604278 GAATCACGGCTTGGGCTATTC 59.396 52.381 0.00 0.00 38.73 1.75
1174 1590 1.064758 TGAATCACGGCTTGGGCTATT 60.065 47.619 0.00 0.00 38.73 1.73
1188 1620 6.533730 AGGATAAACAGAACACAGTGAATCA 58.466 36.000 7.81 0.00 0.00 2.57
1195 1627 6.091849 CACATCAGAGGATAAACAGAACACAG 59.908 42.308 0.00 0.00 30.87 3.66
1200 1632 8.321353 ACATTACACATCAGAGGATAAACAGAA 58.679 33.333 0.00 0.00 30.87 3.02
1211 1643 5.163824 ACGCAAATCACATTACACATCAGAG 60.164 40.000 0.00 0.00 0.00 3.35
1213 1645 4.789629 CACGCAAATCACATTACACATCAG 59.210 41.667 0.00 0.00 0.00 2.90
1241 1674 0.803117 CTTCGACCTCACTGACGCTA 59.197 55.000 0.00 0.00 0.00 4.26
1304 1737 0.321564 CCTTGTTGATCAGCCCGTCA 60.322 55.000 7.13 0.00 0.00 4.35
1393 1845 3.155998 GACGCACAAGAATCACAATTCG 58.844 45.455 0.00 0.00 45.01 3.34
1404 1856 0.943835 CACCATGTCGACGCACAAGA 60.944 55.000 11.62 0.00 0.00 3.02
1414 1866 1.153489 CTCCTCCTGCACCATGTCG 60.153 63.158 0.00 0.00 0.00 4.35
1527 1979 4.391216 CAGAGAGGCATTTTCACTGTACAG 59.609 45.833 21.44 21.44 31.34 2.74
1573 2031 8.498054 ACTCCACAGTAATGACATTAGAATTG 57.502 34.615 8.17 7.50 0.00 2.32
1610 2068 5.454613 GGTCCAAATAATATGCCCAAAAGGG 60.455 44.000 0.00 0.00 35.41 3.95
1685 2147 3.056313 GCAGACGCCCTTTGCCATC 62.056 63.158 0.00 0.00 36.24 3.51
1698 2160 4.025647 GCACGATTCTACAATTAGGCAGAC 60.026 45.833 0.00 0.00 0.00 3.51
1735 2197 9.273016 ACATATTAACCATACATGTACTTGAGC 57.727 33.333 15.13 0.00 0.00 4.26
1789 2253 3.568007 GTGGTGAGTACATTTGCTTCCAA 59.432 43.478 0.00 0.00 0.00 3.53
2027 2492 7.880160 AAGTTATAATTGCAATGCCTGACTA 57.120 32.000 13.82 0.00 0.00 2.59
2176 2648 9.971922 CAAACAAATCAAAGACCTAGAAGAAAT 57.028 29.630 0.00 0.00 0.00 2.17
2177 2649 9.184523 TCAAACAAATCAAAGACCTAGAAGAAA 57.815 29.630 0.00 0.00 0.00 2.52
2370 2843 6.622896 GTTAACCTAACTATGCCAACAAGCAG 60.623 42.308 0.00 0.00 39.76 4.24
2372 2845 5.414765 AGTTAACCTAACTATGCCAACAAGC 59.585 40.000 0.88 0.00 46.53 4.01
2473 3402 4.155280 GCTTGGGCGTTACAAGAATTCTTA 59.845 41.667 20.07 3.42 46.27 2.10
2474 3403 3.057526 GCTTGGGCGTTACAAGAATTCTT 60.058 43.478 15.11 15.11 46.27 2.52
2592 3521 8.789762 TGTTTTCTTACAGTTTAGGCCTAAATC 58.210 33.333 34.61 26.93 37.37 2.17
2710 3639 3.951775 AAGACAGAGTGACAGACCATC 57.048 47.619 0.00 0.00 0.00 3.51
2831 3768 9.227777 GACTAAAAGAGCTTAAGGGAATTAACA 57.772 33.333 4.29 0.00 30.16 2.41
2899 3842 4.479786 AAGAGACTGCAAGGATTAGACC 57.520 45.455 0.00 0.00 39.30 3.85
2902 3845 4.836825 TGGAAAGAGACTGCAAGGATTAG 58.163 43.478 0.00 0.00 39.30 1.73
3068 4044 7.015292 AGCGATTAAGGGAGATAACTGAACATA 59.985 37.037 0.00 0.00 0.00 2.29
3102 4078 7.835682 TGGAGTTGGATTCATTGATGATACTTT 59.164 33.333 0.00 0.00 36.56 2.66
3132 4108 4.450976 AGTCAACAAGTACTCACAATGCA 58.549 39.130 0.00 0.00 0.00 3.96
3443 4424 4.813161 CACAAAGGAGACTATATGCCACAG 59.187 45.833 0.00 0.00 42.68 3.66
3494 4480 8.782144 GCCAAACAAGAAAAATCATTGGAATAA 58.218 29.630 5.86 0.00 38.44 1.40
3580 4566 5.527033 TCAATGATGCTCTCTATGACTTCG 58.473 41.667 0.00 0.00 0.00 3.79
3772 4770 6.322712 AGCTTTCTAGTTCGATCTATCAAGGT 59.677 38.462 14.74 14.74 0.00 3.50
3908 4915 7.012704 ACAGCATTAATGAAATAGGCAGTACTG 59.987 37.037 19.73 18.93 0.00 2.74
3953 4962 0.666913 GGCACAATGGCATAGCTCTG 59.333 55.000 15.86 6.94 43.14 3.35
4103 5201 3.963374 TCAGTAATGAGGGATGTCTGAGG 59.037 47.826 0.00 0.00 0.00 3.86
4198 5307 8.579850 AGTTCAATCCACTTGAGCATAATAAA 57.420 30.769 4.94 0.00 44.86 1.40
4214 5323 0.966179 AACCCCGCAAAGTTCAATCC 59.034 50.000 0.00 0.00 0.00 3.01
4222 5331 1.533625 TCATTCTGAACCCCGCAAAG 58.466 50.000 0.00 0.00 0.00 2.77
4224 5333 2.214376 ATTCATTCTGAACCCCGCAA 57.786 45.000 0.00 0.00 39.45 4.85
4268 8575 9.311916 GATAATGCACAAGTATTTTGGCAATAA 57.688 29.630 0.00 0.00 34.64 1.40
4285 8592 4.172505 CTCGGCTCTATGAGATAATGCAC 58.827 47.826 0.00 0.00 34.04 4.57
4390 8697 9.361712 GTACAAAACTGTCGTTTAACTAATCAC 57.638 33.333 0.00 0.00 42.28 3.06
4415 8722 0.617413 CTCTCCAGCCTCCAATGTGT 59.383 55.000 0.00 0.00 0.00 3.72
4416 8723 0.617413 ACTCTCCAGCCTCCAATGTG 59.383 55.000 0.00 0.00 0.00 3.21
4489 8796 9.734620 AAACAATACGACATACGCTAATAGTTA 57.265 29.630 0.00 0.00 46.94 2.24
4525 8833 4.614946 ACTTAACACTTCGTAGTCACACC 58.385 43.478 0.00 0.00 30.26 4.16
4581 8889 2.642139 TTGAAGCCGGAACTACTACG 57.358 50.000 5.05 0.00 0.00 3.51
4630 8942 5.210715 CAGACTGAACTGAAGCAATGAAAC 58.789 41.667 0.00 0.00 39.94 2.78
4679 8991 8.589338 AGTGAATATAGAGTAGGGCAATAACAG 58.411 37.037 0.00 0.00 0.00 3.16
4720 9032 2.436646 GGTGGTGATGTCCCTGCG 60.437 66.667 0.00 0.00 0.00 5.18
4871 9201 2.527100 GGAACACTACGATGACTTCCG 58.473 52.381 0.00 0.00 0.00 4.30
4872 9202 2.163010 TCGGAACACTACGATGACTTCC 59.837 50.000 0.00 0.00 33.69 3.46
4873 9203 3.482722 TCGGAACACTACGATGACTTC 57.517 47.619 0.00 0.00 33.69 3.01
4874 9204 3.834610 CTTCGGAACACTACGATGACTT 58.165 45.455 0.00 0.00 39.06 3.01
4875 9205 2.415625 GCTTCGGAACACTACGATGACT 60.416 50.000 0.00 0.00 39.06 3.41
4876 9206 1.918609 GCTTCGGAACACTACGATGAC 59.081 52.381 0.00 0.00 39.06 3.06
4877 9207 1.542472 TGCTTCGGAACACTACGATGA 59.458 47.619 0.00 0.00 39.06 2.92
4878 9208 1.990799 TGCTTCGGAACACTACGATG 58.009 50.000 0.00 0.00 39.06 3.84
4879 9209 2.961526 ATGCTTCGGAACACTACGAT 57.038 45.000 0.00 0.00 39.06 3.73
4880 9210 2.751259 AGTATGCTTCGGAACACTACGA 59.249 45.455 0.00 0.00 37.33 3.43
4881 9211 2.852413 CAGTATGCTTCGGAACACTACG 59.148 50.000 0.00 0.00 0.00 3.51
4911 9241 5.668558 ATAAACCAGCGGAATAATCGAAC 57.331 39.130 0.00 0.00 0.00 3.95
4973 9306 7.819900 ACTTTGAACATTCTGATCTACTACCAC 59.180 37.037 0.00 0.00 0.00 4.16
5208 9548 5.481105 CGGAGTACCCTTTTGTGTATGTTA 58.519 41.667 0.00 0.00 0.00 2.41
5209 9549 4.320870 CGGAGTACCCTTTTGTGTATGTT 58.679 43.478 0.00 0.00 0.00 2.71
5247 9587 6.769134 TGTAACTCTGAGTTATTCCATCGA 57.231 37.500 27.52 6.65 42.06 3.59
5248 9588 6.422100 CCATGTAACTCTGAGTTATTCCATCG 59.578 42.308 27.52 17.06 42.06 3.84
5249 9589 7.500992 TCCATGTAACTCTGAGTTATTCCATC 58.499 38.462 27.52 16.55 42.06 3.51
5250 9590 7.437713 TCCATGTAACTCTGAGTTATTCCAT 57.562 36.000 27.52 22.67 42.06 3.41
5251 9591 6.867519 TCCATGTAACTCTGAGTTATTCCA 57.132 37.500 27.52 21.71 42.06 3.53
5252 9592 9.482627 CTATTCCATGTAACTCTGAGTTATTCC 57.517 37.037 27.52 17.72 42.06 3.01
5334 9675 3.323691 GTGGCTTTCCCCTACAAAAATGT 59.676 43.478 0.00 0.00 0.00 2.71
5336 9677 2.903784 GGTGGCTTTCCCCTACAAAAAT 59.096 45.455 0.00 0.00 0.00 1.82
5342 9683 1.303282 CCAGGTGGCTTTCCCCTAC 59.697 63.158 0.00 0.00 33.43 3.18
5357 9698 4.678509 TTGAGTTATTAAAGTGCGCCAG 57.321 40.909 4.18 0.00 0.00 4.85
5424 9765 2.401583 TGTTTGGGATGGTGAGATCG 57.598 50.000 0.00 0.00 0.00 3.69
5429 9770 4.467795 TCAACTTTTTGTTTGGGATGGTGA 59.532 37.500 0.00 0.00 36.63 4.02
5432 9773 6.541641 TGATTTCAACTTTTTGTTTGGGATGG 59.458 34.615 0.00 0.00 36.63 3.51
5433 9774 7.551035 TGATTTCAACTTTTTGTTTGGGATG 57.449 32.000 0.00 0.00 36.63 3.51
5479 9820 8.801299 TGTATCTTTTGCTCATTGTCCAAATTA 58.199 29.630 5.70 0.47 0.00 1.40
5483 9825 6.040278 TGTTGTATCTTTTGCTCATTGTCCAA 59.960 34.615 0.00 0.00 0.00 3.53
5496 9838 8.784043 GTCTTCCACATAAGTGTTGTATCTTTT 58.216 33.333 0.00 0.00 44.39 2.27
5502 9844 5.818678 AGGTCTTCCACATAAGTGTTGTA 57.181 39.130 0.00 0.00 44.39 2.41
5510 9852 7.831691 TGATTTCAAAAGGTCTTCCACATAA 57.168 32.000 0.00 0.00 35.89 1.90
5532 9874 4.071961 ACACGCTATATTGGCTGATTGA 57.928 40.909 0.00 0.00 0.00 2.57
5538 9880 1.000506 CCCGTACACGCTATATTGGCT 59.999 52.381 0.00 0.00 38.18 4.75
5558 9900 2.487762 TGGTGTGATTGAAATTCGGAGC 59.512 45.455 0.00 0.00 0.00 4.70
5559 9901 4.970662 ATGGTGTGATTGAAATTCGGAG 57.029 40.909 0.00 0.00 0.00 4.63
5563 9905 5.390145 GCTTGCAATGGTGTGATTGAAATTC 60.390 40.000 0.00 0.00 35.65 2.17
5569 9911 2.734606 CAAGCTTGCAATGGTGTGATTG 59.265 45.455 14.65 0.00 36.55 2.67
5574 9916 2.051941 CCCAAGCTTGCAATGGTGT 58.948 52.632 21.43 0.00 32.13 4.16
5602 9944 7.191274 CCGGTGATCGTTGAATCAGATTCAC 62.191 48.000 23.19 16.86 41.34 3.18
5603 9945 3.865164 CGGTGATCGTTGAATCAGATTCA 59.135 43.478 20.18 20.18 46.77 2.57
5604 9946 3.246226 CCGGTGATCGTTGAATCAGATTC 59.754 47.826 15.39 15.39 36.36 2.52
5605 9947 3.198068 CCGGTGATCGTTGAATCAGATT 58.802 45.455 0.00 0.00 36.36 2.40
5606 9948 2.168521 ACCGGTGATCGTTGAATCAGAT 59.831 45.455 6.12 0.00 36.36 2.90
5607 9949 1.548719 ACCGGTGATCGTTGAATCAGA 59.451 47.619 6.12 0.00 36.36 3.27
5608 9950 2.010145 ACCGGTGATCGTTGAATCAG 57.990 50.000 6.12 0.00 36.36 2.90
5609 9951 2.073056 CAACCGGTGATCGTTGAATCA 58.927 47.619 8.52 0.00 37.11 2.57
5610 9952 2.093783 GTCAACCGGTGATCGTTGAATC 59.906 50.000 8.52 0.00 39.03 2.52
5611 9953 2.073816 GTCAACCGGTGATCGTTGAAT 58.926 47.619 8.52 0.00 39.03 2.57
5612 9954 1.202545 TGTCAACCGGTGATCGTTGAA 60.203 47.619 8.52 0.00 39.03 2.69
5613 9955 0.389757 TGTCAACCGGTGATCGTTGA 59.610 50.000 8.52 3.53 38.90 3.18
5614 9956 0.790207 CTGTCAACCGGTGATCGTTG 59.210 55.000 8.52 0.35 38.90 4.10
5615 9957 0.949105 GCTGTCAACCGGTGATCGTT 60.949 55.000 8.52 0.00 38.90 3.85
5616 9958 1.374252 GCTGTCAACCGGTGATCGT 60.374 57.895 8.52 0.00 38.90 3.73
5617 9959 2.100631 GGCTGTCAACCGGTGATCG 61.101 63.158 8.52 4.72 38.90 3.69
5623 9965 3.365265 GCCTTGGCTGTCAACCGG 61.365 66.667 0.00 0.00 0.00 5.28
5629 9971 1.973812 GTGGAAGGCCTTGGCTGTC 60.974 63.158 26.25 7.09 38.81 3.51
5630 9972 2.116125 GTGGAAGGCCTTGGCTGT 59.884 61.111 26.25 0.00 38.81 4.40
5633 9975 2.677875 CTGGTGGAAGGCCTTGGC 60.678 66.667 26.25 9.51 34.31 4.52
5684 10026 1.131126 CATCTCCATGACGCAACAACC 59.869 52.381 0.00 0.00 30.57 3.77
5690 10032 1.620323 CTATCCCATCTCCATGACGCA 59.380 52.381 0.00 0.00 30.57 5.24
5701 10043 2.675317 GCGTCATGGCTACTATCCCATC 60.675 54.545 0.00 0.00 39.76 3.51
5702 10044 1.276421 GCGTCATGGCTACTATCCCAT 59.724 52.381 0.00 0.00 42.41 4.00
5703 10045 0.679505 GCGTCATGGCTACTATCCCA 59.320 55.000 0.00 0.00 35.21 4.37
5706 10048 0.037232 GGGGCGTCATGGCTACTATC 60.037 60.000 0.00 0.00 44.11 2.08
5717 10059 4.704833 GCTCTTGCTGGGGCGTCA 62.705 66.667 0.00 0.00 42.25 4.35
5744 10086 4.509122 GCAGCTGCAATGCTCAGATAGC 62.509 54.545 33.36 5.80 45.80 2.97
5745 10087 1.264557 GCAGCTGCAATGCTCAGATAG 59.735 52.381 33.36 0.00 41.98 2.08
5746 10088 1.306148 GCAGCTGCAATGCTCAGATA 58.694 50.000 33.36 0.00 41.98 1.98
5747 10089 2.107705 GCAGCTGCAATGCTCAGAT 58.892 52.632 33.36 0.00 41.98 2.90
5748 10090 3.587095 GCAGCTGCAATGCTCAGA 58.413 55.556 33.36 0.00 41.98 3.27
5753 10095 2.202623 GCTCAGCAGCTGCAATGC 60.203 61.111 38.24 31.03 43.09 3.56
5754 10096 2.490217 GGCTCAGCAGCTGCAATG 59.510 61.111 38.24 28.32 46.03 2.82
5763 10108 1.699054 ATAATGGCTCGGGCTCAGCA 61.699 55.000 7.48 0.00 38.77 4.41
5766 10111 0.836606 TTGATAATGGCTCGGGCTCA 59.163 50.000 7.48 3.61 38.73 4.26


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

AutoCloner maintained by Alex Coulton.