Multiple sequence alignment - TraesCS7B01G166500

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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 TraesCS7B01G166500 chr7B 100.000 4431 0 0 1 4431 229826706 229831136 0.000000e+00 8183
1 TraesCS7B01G166500 chr7D 92.087 2161 113 28 762 2894 252545952 252548082 0.000000e+00 2990
2 TraesCS7B01G166500 chr7D 94.821 811 36 4 2887 3693 252548122 252548930 0.000000e+00 1260
3 TraesCS7B01G166500 chr7D 93.933 511 27 3 3726 4236 252548928 252549434 0.000000e+00 769
4 TraesCS7B01G166500 chr7D 88.354 644 51 11 2 630 252545252 252545886 0.000000e+00 752
5 TraesCS7B01G166500 chr7A 92.362 2108 106 23 1854 3952 267567859 267565798 0.000000e+00 2950
6 TraesCS7B01G166500 chr7A 86.477 1930 136 47 1 1868 267569813 267567947 0.000000e+00 2002
7 TraesCS7B01G166500 chr7A 94.479 163 9 0 4080 4242 267564581 267564419 7.360000e-63 252
8 TraesCS7B01G166500 chr3A 86.066 122 16 1 2 123 367859814 367859934 3.600000e-26 130
9 TraesCS7B01G166500 chr1D 86.066 122 16 1 2 123 168799581 168799701 3.600000e-26 130
10 TraesCS7B01G166500 chr6D 85.246 122 17 1 2 123 933769 933649 1.670000e-24 124


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 TraesCS7B01G166500 chr7B 229826706 229831136 4430 False 8183.000000 8183 100.00000 1 4431 1 chr7B.!!$F1 4430
1 TraesCS7B01G166500 chr7D 252545252 252549434 4182 False 1442.750000 2990 92.29875 2 4236 4 chr7D.!!$F1 4234
2 TraesCS7B01G166500 chr7A 267564419 267569813 5394 True 1734.666667 2950 91.10600 1 4242 3 chr7A.!!$R1 4241

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
519 521 0.036022 AAGCTGAACTGAGGCAGTCC 59.964 55.0 0.00 0.0 44.62 3.85 F
658 673 0.322906 GTTCTTCTCCCCTGCCCTTG 60.323 60.0 0.00 0.0 0.00 3.61 F
1286 1351 0.667792 GCCTCTCGTTTTGCTCGTCT 60.668 55.0 0.00 0.0 0.00 4.18 F
2772 2955 0.809636 TAATGCATGGCGTGTCGGAG 60.810 55.0 8.75 0.0 0.00 4.63 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1346 1420 0.743345 GAACCCTATGCGCGGTTTCT 60.743 55.000 16.94 0.0 42.48 2.52 R
1722 1806 1.291272 GGTTACAGACGACCGCCTT 59.709 57.895 0.00 0.0 0.00 4.35 R
3130 3370 1.667236 CAAGTTCAGCCGCATGGATA 58.333 50.000 0.00 0.0 37.49 2.59 R
4359 5747 0.185175 AAACAGCGTTCCTTCCCCTT 59.815 50.000 0.00 0.0 0.00 3.95 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
25 26 1.699634 AGGAAGTACTCAGCAAGGCAA 59.300 47.619 0.00 0.00 0.00 4.52
130 132 8.163408 TCTGGACCAATAATAATGTATTCCAGG 58.837 37.037 12.63 0.00 35.57 4.45
137 139 2.622064 AATGTATTCCAGGCTCGGAC 57.378 50.000 5.34 0.00 33.75 4.79
138 140 1.794714 ATGTATTCCAGGCTCGGACT 58.205 50.000 5.34 3.79 33.75 3.85
154 156 1.880027 GGACTCGCCAAATTTGACACT 59.120 47.619 19.86 0.00 36.34 3.55
155 157 2.350772 GGACTCGCCAAATTTGACACTG 60.351 50.000 19.86 3.48 36.34 3.66
161 163 5.651530 TCGCCAAATTTGACACTGTAAAAA 58.348 33.333 19.86 0.00 0.00 1.94
260 262 9.214957 TCTTTCGTGATGATTTTGTAATGTACT 57.785 29.630 0.00 0.00 0.00 2.73
340 342 0.951558 GTTTGGAAGACGTGGTGCAT 59.048 50.000 0.00 0.00 0.00 3.96
352 354 2.440409 GTGGTGCATGAAATCTCCACT 58.560 47.619 10.67 0.00 41.14 4.00
412 414 1.202806 CCCTTCAAGCTCAAGTGTCCA 60.203 52.381 0.00 0.00 0.00 4.02
519 521 0.036022 AAGCTGAACTGAGGCAGTCC 59.964 55.000 0.00 0.00 44.62 3.85
520 522 0.835543 AGCTGAACTGAGGCAGTCCT 60.836 55.000 0.00 0.00 44.62 3.85
589 604 6.030228 GCATAGCTGAATGTACCTTTGTTTC 58.970 40.000 0.00 0.00 0.00 2.78
646 661 5.992217 ACGAAATAGCAGAAACTGTTCTTCT 59.008 36.000 0.00 0.00 41.55 2.85
652 667 3.406764 CAGAAACTGTTCTTCTCCCCTG 58.593 50.000 0.00 0.00 41.55 4.45
653 668 2.155279 GAAACTGTTCTTCTCCCCTGC 58.845 52.381 0.00 0.00 0.00 4.85
654 669 0.402121 AACTGTTCTTCTCCCCTGCC 59.598 55.000 0.00 0.00 0.00 4.85
655 670 1.301293 CTGTTCTTCTCCCCTGCCC 59.699 63.158 0.00 0.00 0.00 5.36
656 671 1.151810 TGTTCTTCTCCCCTGCCCT 60.152 57.895 0.00 0.00 0.00 5.19
657 672 0.772124 TGTTCTTCTCCCCTGCCCTT 60.772 55.000 0.00 0.00 0.00 3.95
658 673 0.322906 GTTCTTCTCCCCTGCCCTTG 60.323 60.000 0.00 0.00 0.00 3.61
661 676 1.778383 TTCTCCCCTGCCCTTGGTT 60.778 57.895 0.00 0.00 0.00 3.67
668 683 2.043551 TGCCCTTGGTTGTGTGCA 60.044 55.556 0.00 0.00 0.00 4.57
692 707 0.867329 CTGCGCTTCGTGATCGATCA 60.867 55.000 23.99 23.99 45.65 2.92
719 734 3.003689 TGCTTTGCTGAAACTAGCTGTTC 59.996 43.478 0.00 0.00 44.01 3.18
723 738 3.133691 TGCTGAAACTAGCTGTTCACAG 58.866 45.455 19.12 19.12 44.01 3.66
734 749 4.261801 AGCTGTTCACAGTGTTTACTTGT 58.738 39.130 8.72 0.00 45.45 3.16
737 752 5.503520 GCTGTTCACAGTGTTTACTTGTACC 60.504 44.000 8.72 0.00 45.45 3.34
738 753 5.489249 TGTTCACAGTGTTTACTTGTACCA 58.511 37.500 0.00 0.00 34.07 3.25
743 758 4.879545 ACAGTGTTTACTTGTACCAACAGG 59.120 41.667 0.00 0.00 38.60 4.00
746 761 4.337274 GTGTTTACTTGTACCAACAGGCTT 59.663 41.667 0.00 0.00 36.19 4.35
752 767 1.074775 TACCAACAGGCTTGCCTGG 59.925 57.895 35.58 25.30 41.67 4.45
759 774 0.962356 CAGGCTTGCCTGGGTAGTTG 60.962 60.000 28.58 6.34 34.47 3.16
762 777 1.616994 GGCTTGCCTGGGTAGTTGATT 60.617 52.381 4.11 0.00 0.00 2.57
813 831 1.000486 AGGTTCTCTGGGCGCTCTA 60.000 57.895 9.62 0.00 0.00 2.43
847 865 4.572985 TTTGCCAGATTTGAGAACACTG 57.427 40.909 0.00 0.00 0.00 3.66
855 874 6.183360 CCAGATTTGAGAACACTGTCTGTTTT 60.183 38.462 0.00 0.00 43.60 2.43
878 897 1.066605 AGCAATTCTTCATGCCGCATC 59.933 47.619 1.86 0.00 43.57 3.91
894 913 1.471501 GCATCACTGACTGCATCGGTA 60.472 52.381 9.39 2.14 45.83 4.02
905 924 5.069119 TGACTGCATCGGTATCATAGAAAGT 59.931 40.000 0.00 0.00 0.00 2.66
906 925 6.264518 TGACTGCATCGGTATCATAGAAAGTA 59.735 38.462 0.00 0.00 0.00 2.24
907 926 7.039714 TGACTGCATCGGTATCATAGAAAGTAT 60.040 37.037 0.00 0.00 0.00 2.12
922 941 9.113838 CATAGAAAGTATAGAATGTGGCAAACT 57.886 33.333 0.00 0.00 0.00 2.66
989 1018 1.064208 CGAGATAGCGGCGTATATGCT 59.936 52.381 16.31 6.89 42.58 3.79
990 1019 2.722071 GAGATAGCGGCGTATATGCTC 58.278 52.381 16.31 11.68 40.06 4.26
991 1020 1.064208 AGATAGCGGCGTATATGCTCG 59.936 52.381 16.31 17.29 40.06 5.03
998 1027 2.615116 CGTATATGCTCGCTCGTCG 58.385 57.895 0.00 0.00 40.15 5.12
1002 1031 2.739523 ATATGCTCGCTCGTCGGCTG 62.740 60.000 0.00 0.00 39.05 4.85
1005 1034 3.506096 CTCGCTCGTCGGCTGGTA 61.506 66.667 0.00 0.00 39.05 3.25
1018 1047 1.035932 GCTGGTAGCCTGGTACTCGA 61.036 60.000 6.48 0.00 34.48 4.04
1028 1057 2.280552 GGTACTCGACCCAGCCACA 61.281 63.158 0.00 0.00 43.25 4.17
1089 1135 0.820871 GAGCTCCATCGTCTCCACTT 59.179 55.000 0.87 0.00 0.00 3.16
1119 1178 2.185350 CTCCACCTACCGCAGCAG 59.815 66.667 0.00 0.00 0.00 4.24
1124 1183 2.821366 CCTACCGCAGCAGCAAGG 60.821 66.667 0.82 0.73 42.27 3.61
1163 1222 2.029666 CGGGGAGGATGTCATCGC 59.970 66.667 6.74 3.50 38.61 4.58
1241 1300 2.754664 CTTCAAGGCAAGCTCCCCGT 62.755 60.000 0.00 0.00 0.00 5.28
1259 1324 3.782443 GCCCCCACCCTACTCACG 61.782 72.222 0.00 0.00 0.00 4.35
1283 1348 1.078759 ATCGCCTCTCGTTTTGCTCG 61.079 55.000 0.00 0.00 39.67 5.03
1285 1350 1.782181 GCCTCTCGTTTTGCTCGTC 59.218 57.895 0.00 0.00 0.00 4.20
1286 1351 0.667792 GCCTCTCGTTTTGCTCGTCT 60.668 55.000 0.00 0.00 0.00 4.18
1287 1352 1.784525 CCTCTCGTTTTGCTCGTCTT 58.215 50.000 0.00 0.00 0.00 3.01
1288 1353 1.721926 CCTCTCGTTTTGCTCGTCTTC 59.278 52.381 0.00 0.00 0.00 2.87
1289 1354 1.721926 CTCTCGTTTTGCTCGTCTTCC 59.278 52.381 0.00 0.00 0.00 3.46
1290 1355 1.067974 TCTCGTTTTGCTCGTCTTCCA 59.932 47.619 0.00 0.00 0.00 3.53
1291 1356 1.864711 CTCGTTTTGCTCGTCTTCCAA 59.135 47.619 0.00 0.00 0.00 3.53
1292 1357 1.864711 TCGTTTTGCTCGTCTTCCAAG 59.135 47.619 0.00 0.00 0.00 3.61
1293 1358 1.597663 CGTTTTGCTCGTCTTCCAAGT 59.402 47.619 0.00 0.00 0.00 3.16
1301 1366 3.861131 GCTCGTCTTCCAAGTAGCAGAAA 60.861 47.826 0.00 0.00 32.05 2.52
1302 1367 3.650139 TCGTCTTCCAAGTAGCAGAAAC 58.350 45.455 0.00 0.00 0.00 2.78
1310 1375 3.182967 CAAGTAGCAGAAACGCTAGGAG 58.817 50.000 0.00 0.00 44.92 3.69
1346 1420 2.556257 TGCGCTGCTAATTCGGATAAA 58.444 42.857 9.73 0.00 0.00 1.40
1351 1425 5.198274 CGCTGCTAATTCGGATAAAGAAAC 58.802 41.667 0.00 0.00 0.00 2.78
1353 1427 5.728351 TGCTAATTCGGATAAAGAAACCG 57.272 39.130 0.00 0.00 46.71 4.44
1437 1511 1.942657 CCCATAGCATCTGGTCGTTTG 59.057 52.381 0.00 0.00 31.44 2.93
1448 1522 1.135527 TGGTCGTTTGTATCGCTAGGG 59.864 52.381 0.00 0.00 0.00 3.53
1480 1554 3.243101 CCATTTGCTTCTGCTGCTATGAG 60.243 47.826 0.00 0.00 40.48 2.90
1491 1565 3.070018 GCTGCTATGAGTTGTTCACAGT 58.930 45.455 0.00 0.00 38.99 3.55
1597 1671 3.066291 TGTATGTTGGTCCACACATCC 57.934 47.619 17.63 10.81 0.00 3.51
1608 1682 6.591935 TGGTCCACACATCCTAATTTATCTC 58.408 40.000 0.00 0.00 0.00 2.75
1619 1693 9.838339 CATCCTAATTTATCTCCAGTTTACTGT 57.162 33.333 8.91 0.00 42.27 3.55
1849 1933 6.094048 TGACAAGTAAGCCTTTTATGCTGATC 59.906 38.462 0.00 0.00 39.48 2.92
1871 1955 6.877611 TCTTTCTTCTGTGGTTATTTGGTC 57.122 37.500 0.00 0.00 0.00 4.02
1965 2147 2.938756 GCATCTCTGGGAAGGAAGTGTG 60.939 54.545 0.00 0.00 0.00 3.82
2047 2229 2.851195 TCTCTGGCAGTTGTTTCTTCC 58.149 47.619 15.27 0.00 0.00 3.46
2064 2246 7.833682 TGTTTCTTCCAAGGAATATTAGCATCA 59.166 33.333 1.35 0.00 33.28 3.07
2133 2315 9.646427 GGTCATCTAACATATATGAAGAAGTCC 57.354 37.037 19.63 17.65 31.77 3.85
2148 2330 9.829507 ATGAAGAAGTCCTAATAATGACAAGAG 57.170 33.333 0.00 0.00 33.89 2.85
2186 2368 5.355350 AGCATTGTTACTTATGAGGCACTTC 59.645 40.000 3.06 0.00 41.55 3.01
2197 2379 5.690464 ATGAGGCACTTCTACAAGATTCT 57.310 39.130 0.00 0.00 41.55 2.40
2198 2380 4.825422 TGAGGCACTTCTACAAGATTCTG 58.175 43.478 0.00 0.00 41.55 3.02
2459 2641 1.750778 CATGCCTGGTGGGTTAATGAC 59.249 52.381 0.00 0.00 37.43 3.06
2468 2650 6.607198 CCTGGTGGGTTAATGACTTTCATATT 59.393 38.462 0.00 0.00 35.76 1.28
2655 2838 2.094545 GGCCATCTTTTACAGTGCCAAG 60.095 50.000 0.00 0.00 34.68 3.61
2764 2947 2.485426 CCTGATAAGGTAATGCATGGCG 59.515 50.000 0.00 0.00 0.00 5.69
2769 2952 1.089481 AGGTAATGCATGGCGTGTCG 61.089 55.000 8.75 0.00 0.00 4.35
2770 2953 1.351707 GTAATGCATGGCGTGTCGG 59.648 57.895 8.75 0.00 0.00 4.79
2771 2954 1.087202 GTAATGCATGGCGTGTCGGA 61.087 55.000 8.75 0.00 0.00 4.55
2772 2955 0.809636 TAATGCATGGCGTGTCGGAG 60.810 55.000 8.75 0.00 0.00 4.63
2773 2956 2.803155 AATGCATGGCGTGTCGGAGT 62.803 55.000 8.75 0.00 0.00 3.85
2774 2957 1.955495 ATGCATGGCGTGTCGGAGTA 61.955 55.000 8.75 0.00 0.00 2.59
2785 2968 4.730657 CGTGTCGGAGTATTTGTAGACTT 58.269 43.478 0.00 0.00 0.00 3.01
2823 3016 7.703328 ACAACTTAAACACAATACAGAACTGG 58.297 34.615 6.76 0.00 34.19 4.00
2835 3028 3.705051 ACAGAACTGGAATGGCATTCAT 58.295 40.909 34.04 20.02 41.03 2.57
2932 3172 6.090483 TCTCGGATCATCCTTTCTGTATTC 57.910 41.667 1.10 0.00 33.30 1.75
3043 3283 2.430465 CTAGCAGGTGTTGAAGCACAT 58.570 47.619 0.00 0.00 40.89 3.21
3130 3370 1.911357 TCTGCATTCATCACTGGAGGT 59.089 47.619 0.00 0.00 32.31 3.85
3456 3697 3.090210 TGCAATCATGTGTGGAGGAAT 57.910 42.857 0.00 0.00 0.00 3.01
3526 3769 3.554337 CCCAGGCGGTATACAACATACTC 60.554 52.174 5.01 0.00 0.00 2.59
3529 3772 3.958798 AGGCGGTATACAACATACTCTGT 59.041 43.478 5.01 0.00 40.84 3.41
3562 3805 3.623203 GCTTGATGGTTTGATCTGGAGGA 60.623 47.826 0.00 0.00 0.00 3.71
3586 3831 2.544721 AGTCTTGATTCTGGCAGAGGA 58.455 47.619 17.91 4.08 0.00 3.71
3630 3875 4.953269 ACGTTGTAATGATGCTACGTTTG 58.047 39.130 0.00 0.00 46.94 2.93
3662 3907 2.990479 GGCGATCTTCAGGTGGGT 59.010 61.111 0.00 0.00 0.00 4.51
3720 3965 3.826466 GCAACTTGCAAGAACTCCATAC 58.174 45.455 32.50 7.45 44.26 2.39
3721 3966 3.366374 GCAACTTGCAAGAACTCCATACC 60.366 47.826 32.50 5.09 44.26 2.73
3722 3967 3.788227 ACTTGCAAGAACTCCATACCA 57.212 42.857 32.50 0.00 0.00 3.25
3723 3968 4.098914 ACTTGCAAGAACTCCATACCAA 57.901 40.909 32.50 0.00 0.00 3.67
3724 3969 4.666512 ACTTGCAAGAACTCCATACCAAT 58.333 39.130 32.50 1.82 0.00 3.16
3732 3977 6.115448 AGAACTCCATACCAATACCATAGC 57.885 41.667 0.00 0.00 0.00 2.97
3968 4214 6.073385 CCATTACAAGATCATGAGGAATGTCG 60.073 42.308 13.67 0.54 37.56 4.35
3981 4227 2.415893 GGAATGTCGAAGCCAAACATGG 60.416 50.000 0.00 0.00 0.00 3.66
4065 4311 6.885922 AGTCAGTGTTATTATCCCCTTGTAC 58.114 40.000 0.00 0.00 0.00 2.90
4066 4312 6.442564 AGTCAGTGTTATTATCCCCTTGTACA 59.557 38.462 0.00 0.00 0.00 2.90
4132 5520 5.858381 TCAACATATAGCTCATGGAGTTCC 58.142 41.667 11.71 0.00 31.39 3.62
4177 5565 6.824958 TTATAAGCCTCCACATCTAAAGGT 57.175 37.500 0.00 0.00 0.00 3.50
4216 5604 0.685785 CTAGGACCAGCAGCTCCTCA 60.686 60.000 4.95 0.00 38.01 3.86
4258 5646 7.949903 TTTTTCATGATGACCAAACAGATTG 57.050 32.000 0.00 0.00 38.84 2.67
4266 5654 1.883021 CAAACAGATTGGACCCCGC 59.117 57.895 0.00 0.00 35.27 6.13
4267 5655 1.304134 AAACAGATTGGACCCCGCC 60.304 57.895 0.00 0.00 0.00 6.13
4268 5656 2.781431 AAACAGATTGGACCCCGCCC 62.781 60.000 0.00 0.00 0.00 6.13
4269 5657 4.506255 CAGATTGGACCCCGCCCC 62.506 72.222 0.00 0.00 0.00 5.80
4270 5658 4.760220 AGATTGGACCCCGCCCCT 62.760 66.667 0.00 0.00 0.00 4.79
4271 5659 3.739613 GATTGGACCCCGCCCCTT 61.740 66.667 0.00 0.00 0.00 3.95
4272 5660 2.286578 ATTGGACCCCGCCCCTTA 60.287 61.111 0.00 0.00 0.00 2.69
4273 5661 1.928714 GATTGGACCCCGCCCCTTAA 61.929 60.000 0.00 0.00 0.00 1.85
4274 5662 1.511316 ATTGGACCCCGCCCCTTAAA 61.511 55.000 0.00 0.00 0.00 1.52
4275 5663 1.727215 TTGGACCCCGCCCCTTAAAA 61.727 55.000 0.00 0.00 0.00 1.52
4276 5664 1.308666 GGACCCCGCCCCTTAAAAT 59.691 57.895 0.00 0.00 0.00 1.82
4277 5665 0.552363 GGACCCCGCCCCTTAAAATA 59.448 55.000 0.00 0.00 0.00 1.40
4278 5666 1.683943 GACCCCGCCCCTTAAAATAC 58.316 55.000 0.00 0.00 0.00 1.89
4279 5667 1.213678 GACCCCGCCCCTTAAAATACT 59.786 52.381 0.00 0.00 0.00 2.12
4280 5668 1.642238 ACCCCGCCCCTTAAAATACTT 59.358 47.619 0.00 0.00 0.00 2.24
4281 5669 2.304092 CCCCGCCCCTTAAAATACTTC 58.696 52.381 0.00 0.00 0.00 3.01
4282 5670 2.092049 CCCCGCCCCTTAAAATACTTCT 60.092 50.000 0.00 0.00 0.00 2.85
4283 5671 3.626475 CCCCGCCCCTTAAAATACTTCTT 60.626 47.826 0.00 0.00 0.00 2.52
4284 5672 4.385532 CCCCGCCCCTTAAAATACTTCTTA 60.386 45.833 0.00 0.00 0.00 2.10
4285 5673 5.195185 CCCGCCCCTTAAAATACTTCTTAA 58.805 41.667 0.00 0.00 0.00 1.85
4286 5674 5.653330 CCCGCCCCTTAAAATACTTCTTAAA 59.347 40.000 0.00 0.00 0.00 1.52
4287 5675 6.405065 CCCGCCCCTTAAAATACTTCTTAAAC 60.405 42.308 0.00 0.00 0.00 2.01
4288 5676 6.405065 CCGCCCCTTAAAATACTTCTTAAACC 60.405 42.308 0.00 0.00 0.00 3.27
4289 5677 6.376299 CGCCCCTTAAAATACTTCTTAAACCT 59.624 38.462 0.00 0.00 0.00 3.50
4290 5678 7.414873 CGCCCCTTAAAATACTTCTTAAACCTC 60.415 40.741 0.00 0.00 0.00 3.85
4291 5679 7.614583 GCCCCTTAAAATACTTCTTAAACCTCT 59.385 37.037 0.00 0.00 0.00 3.69
4292 5680 9.529823 CCCCTTAAAATACTTCTTAAACCTCTT 57.470 33.333 0.00 0.00 0.00 2.85
4311 5699 8.868522 ACCTCTTGATTTTGATATTCAGAACA 57.131 30.769 0.00 0.00 0.00 3.18
4312 5700 9.471702 ACCTCTTGATTTTGATATTCAGAACAT 57.528 29.630 0.00 0.00 0.00 2.71
4313 5701 9.947669 CCTCTTGATTTTGATATTCAGAACATC 57.052 33.333 0.00 0.00 0.00 3.06
4327 5715 8.850007 ATTCAGAACATCAATAGGATCATCAG 57.150 34.615 0.00 0.00 32.57 2.90
4328 5716 7.607615 TCAGAACATCAATAGGATCATCAGA 57.392 36.000 0.00 0.00 32.57 3.27
4329 5717 8.026396 TCAGAACATCAATAGGATCATCAGAA 57.974 34.615 0.00 0.00 32.57 3.02
4330 5718 8.148999 TCAGAACATCAATAGGATCATCAGAAG 58.851 37.037 0.00 0.00 32.57 2.85
4331 5719 6.935771 AGAACATCAATAGGATCATCAGAAGC 59.064 38.462 0.00 0.00 32.57 3.86
4332 5720 5.558818 ACATCAATAGGATCATCAGAAGCC 58.441 41.667 0.00 0.00 32.57 4.35
4333 5721 5.072736 ACATCAATAGGATCATCAGAAGCCA 59.927 40.000 0.00 0.00 32.57 4.75
4334 5722 4.965814 TCAATAGGATCATCAGAAGCCAC 58.034 43.478 0.00 0.00 0.00 5.01
4335 5723 4.409901 TCAATAGGATCATCAGAAGCCACA 59.590 41.667 0.00 0.00 0.00 4.17
4336 5724 5.072736 TCAATAGGATCATCAGAAGCCACAT 59.927 40.000 0.00 0.00 0.00 3.21
4337 5725 3.947612 AGGATCATCAGAAGCCACATT 57.052 42.857 0.00 0.00 0.00 2.71
4338 5726 4.246712 AGGATCATCAGAAGCCACATTT 57.753 40.909 0.00 0.00 0.00 2.32
4339 5727 3.952323 AGGATCATCAGAAGCCACATTTG 59.048 43.478 0.00 0.00 0.00 2.32
4340 5728 3.490419 GGATCATCAGAAGCCACATTTGC 60.490 47.826 0.00 0.00 0.00 3.68
4341 5729 2.516906 TCATCAGAAGCCACATTTGCA 58.483 42.857 0.00 0.00 0.00 4.08
4342 5730 2.229543 TCATCAGAAGCCACATTTGCAC 59.770 45.455 0.00 0.00 0.00 4.57
4343 5731 1.689984 TCAGAAGCCACATTTGCACA 58.310 45.000 0.00 0.00 0.00 4.57
4344 5732 1.337703 TCAGAAGCCACATTTGCACAC 59.662 47.619 0.00 0.00 0.00 3.82
4345 5733 0.675633 AGAAGCCACATTTGCACACC 59.324 50.000 0.00 0.00 0.00 4.16
4346 5734 0.388659 GAAGCCACATTTGCACACCA 59.611 50.000 0.00 0.00 0.00 4.17
4347 5735 0.829333 AAGCCACATTTGCACACCAA 59.171 45.000 0.00 0.00 0.00 3.67
4348 5736 0.829333 AGCCACATTTGCACACCAAA 59.171 45.000 0.00 0.00 46.64 3.28
4357 5745 4.991153 TTTGCACACCAAATGTCTGTAA 57.009 36.364 0.00 0.00 40.64 2.41
4358 5746 3.980646 TGCACACCAAATGTCTGTAAC 57.019 42.857 0.00 0.00 40.64 2.50
4359 5747 3.282885 TGCACACCAAATGTCTGTAACA 58.717 40.909 0.00 0.00 40.64 2.41
4360 5748 3.696548 TGCACACCAAATGTCTGTAACAA 59.303 39.130 0.00 0.00 40.64 2.83
4361 5749 4.202000 TGCACACCAAATGTCTGTAACAAG 60.202 41.667 0.00 0.00 40.64 3.16
4362 5750 4.792704 GCACACCAAATGTCTGTAACAAGG 60.793 45.833 0.00 0.00 40.64 3.61
4363 5751 3.888930 ACACCAAATGTCTGTAACAAGGG 59.111 43.478 0.00 0.00 42.37 3.95
4364 5752 3.255642 CACCAAATGTCTGTAACAAGGGG 59.744 47.826 0.00 0.00 42.37 4.79
4365 5753 3.139397 ACCAAATGTCTGTAACAAGGGGA 59.861 43.478 0.00 0.00 42.37 4.81
4366 5754 4.148838 CCAAATGTCTGTAACAAGGGGAA 58.851 43.478 0.00 0.00 42.37 3.97
4367 5755 4.218417 CCAAATGTCTGTAACAAGGGGAAG 59.782 45.833 0.00 0.00 42.37 3.46
4368 5756 3.721087 ATGTCTGTAACAAGGGGAAGG 57.279 47.619 0.00 0.00 42.37 3.46
4369 5757 2.696775 TGTCTGTAACAAGGGGAAGGA 58.303 47.619 0.00 0.00 34.03 3.36
4370 5758 3.050089 TGTCTGTAACAAGGGGAAGGAA 58.950 45.455 0.00 0.00 34.03 3.36
4371 5759 3.181448 TGTCTGTAACAAGGGGAAGGAAC 60.181 47.826 0.00 0.00 34.03 3.62
4372 5760 2.038033 TCTGTAACAAGGGGAAGGAACG 59.962 50.000 0.00 0.00 0.00 3.95
4373 5761 1.162698 GTAACAAGGGGAAGGAACGC 58.837 55.000 0.00 0.00 0.00 4.84
4374 5762 1.061546 TAACAAGGGGAAGGAACGCT 58.938 50.000 0.00 0.00 0.00 5.07
4375 5763 0.537371 AACAAGGGGAAGGAACGCTG 60.537 55.000 0.00 0.00 0.00 5.18
4376 5764 1.073199 CAAGGGGAAGGAACGCTGT 59.927 57.895 0.00 0.00 0.00 4.40
4377 5765 0.537371 CAAGGGGAAGGAACGCTGTT 60.537 55.000 0.00 0.00 0.00 3.16
4378 5766 0.185175 AAGGGGAAGGAACGCTGTTT 59.815 50.000 0.00 0.00 0.00 2.83
4379 5767 1.061546 AGGGGAAGGAACGCTGTTTA 58.938 50.000 0.00 0.00 0.00 2.01
4380 5768 1.633945 AGGGGAAGGAACGCTGTTTAT 59.366 47.619 0.00 0.00 0.00 1.40
4381 5769 2.841881 AGGGGAAGGAACGCTGTTTATA 59.158 45.455 0.00 0.00 0.00 0.98
4382 5770 3.264964 AGGGGAAGGAACGCTGTTTATAA 59.735 43.478 0.00 0.00 0.00 0.98
4383 5771 4.011698 GGGGAAGGAACGCTGTTTATAAA 58.988 43.478 0.00 0.00 0.00 1.40
4384 5772 4.142534 GGGGAAGGAACGCTGTTTATAAAC 60.143 45.833 19.44 19.44 39.33 2.01
4385 5773 4.142534 GGGAAGGAACGCTGTTTATAAACC 60.143 45.833 22.47 9.57 38.11 3.27
4386 5774 4.456566 GGAAGGAACGCTGTTTATAAACCA 59.543 41.667 22.47 11.58 38.11 3.67
4387 5775 5.048573 GGAAGGAACGCTGTTTATAAACCAA 60.049 40.000 22.47 6.98 38.11 3.67
4388 5776 5.622770 AGGAACGCTGTTTATAAACCAAG 57.377 39.130 22.47 15.91 38.11 3.61
4389 5777 4.082949 AGGAACGCTGTTTATAAACCAAGC 60.083 41.667 22.47 22.21 38.11 4.01
4390 5778 3.842732 ACGCTGTTTATAAACCAAGCC 57.157 42.857 24.17 13.27 35.62 4.35
4391 5779 3.150767 ACGCTGTTTATAAACCAAGCCA 58.849 40.909 24.17 8.66 35.62 4.75
4392 5780 3.190535 ACGCTGTTTATAAACCAAGCCAG 59.809 43.478 24.17 17.46 35.62 4.85
4393 5781 3.438781 CGCTGTTTATAAACCAAGCCAGA 59.561 43.478 24.17 7.49 35.62 3.86
4394 5782 4.096382 CGCTGTTTATAAACCAAGCCAGAT 59.904 41.667 24.17 0.00 35.62 2.90
4395 5783 5.582550 GCTGTTTATAAACCAAGCCAGATC 58.417 41.667 22.47 1.07 38.11 2.75
4396 5784 5.125417 GCTGTTTATAAACCAAGCCAGATCA 59.875 40.000 22.47 2.07 38.11 2.92
4397 5785 6.350110 GCTGTTTATAAACCAAGCCAGATCAA 60.350 38.462 22.47 1.83 38.11 2.57
4398 5786 7.531857 TGTTTATAAACCAAGCCAGATCAAA 57.468 32.000 22.47 0.00 38.11 2.69
4399 5787 7.375053 TGTTTATAAACCAAGCCAGATCAAAC 58.625 34.615 22.47 0.00 38.11 2.93
4400 5788 4.701956 ATAAACCAAGCCAGATCAAACG 57.298 40.909 0.00 0.00 0.00 3.60
4401 5789 2.270352 AACCAAGCCAGATCAAACGA 57.730 45.000 0.00 0.00 0.00 3.85
4402 5790 2.270352 ACCAAGCCAGATCAAACGAA 57.730 45.000 0.00 0.00 0.00 3.85
4403 5791 2.582052 ACCAAGCCAGATCAAACGAAA 58.418 42.857 0.00 0.00 0.00 3.46
4404 5792 2.554032 ACCAAGCCAGATCAAACGAAAG 59.446 45.455 0.00 0.00 0.00 2.62
4405 5793 2.589014 CAAGCCAGATCAAACGAAAGC 58.411 47.619 0.00 0.00 0.00 3.51
4406 5794 1.168714 AGCCAGATCAAACGAAAGCC 58.831 50.000 0.00 0.00 0.00 4.35
4407 5795 1.168714 GCCAGATCAAACGAAAGCCT 58.831 50.000 0.00 0.00 0.00 4.58
4408 5796 1.131315 GCCAGATCAAACGAAAGCCTC 59.869 52.381 0.00 0.00 0.00 4.70
4409 5797 2.704572 CCAGATCAAACGAAAGCCTCT 58.295 47.619 0.00 0.00 0.00 3.69
4410 5798 2.417933 CCAGATCAAACGAAAGCCTCTG 59.582 50.000 0.00 0.00 0.00 3.35
4411 5799 2.417933 CAGATCAAACGAAAGCCTCTGG 59.582 50.000 0.00 0.00 0.00 3.86
4412 5800 2.039084 AGATCAAACGAAAGCCTCTGGT 59.961 45.455 0.00 0.00 0.00 4.00
4413 5801 2.341846 TCAAACGAAAGCCTCTGGTT 57.658 45.000 0.00 0.00 0.00 3.67
4414 5802 2.650322 TCAAACGAAAGCCTCTGGTTT 58.350 42.857 0.00 0.00 44.45 3.27
4415 5803 3.020984 TCAAACGAAAGCCTCTGGTTTT 58.979 40.909 0.00 0.00 41.99 2.43
4416 5804 3.115554 CAAACGAAAGCCTCTGGTTTTG 58.884 45.455 3.27 2.43 45.05 2.44
4417 5805 2.052782 ACGAAAGCCTCTGGTTTTGT 57.947 45.000 3.27 4.69 46.64 2.83
4420 5808 4.766404 CGAAAGCCTCTGGTTTTGTTAT 57.234 40.909 3.27 0.00 41.99 1.89
4421 5809 4.723248 CGAAAGCCTCTGGTTTTGTTATC 58.277 43.478 3.27 0.00 41.99 1.75
4422 5810 4.379499 CGAAAGCCTCTGGTTTTGTTATCC 60.379 45.833 3.27 0.00 41.99 2.59
4423 5811 3.087370 AGCCTCTGGTTTTGTTATCCC 57.913 47.619 0.00 0.00 0.00 3.85
4424 5812 2.100197 GCCTCTGGTTTTGTTATCCCC 58.900 52.381 0.00 0.00 0.00 4.81
4425 5813 2.291605 GCCTCTGGTTTTGTTATCCCCT 60.292 50.000 0.00 0.00 0.00 4.79
4426 5814 3.356290 CCTCTGGTTTTGTTATCCCCTG 58.644 50.000 0.00 0.00 0.00 4.45
4427 5815 3.010138 CCTCTGGTTTTGTTATCCCCTGA 59.990 47.826 0.00 0.00 0.00 3.86
4428 5816 4.508405 CCTCTGGTTTTGTTATCCCCTGAA 60.508 45.833 0.00 0.00 0.00 3.02
4429 5817 5.068215 TCTGGTTTTGTTATCCCCTGAAA 57.932 39.130 0.00 0.00 0.00 2.69
4430 5818 5.076873 TCTGGTTTTGTTATCCCCTGAAAG 58.923 41.667 0.00 0.00 0.00 2.62
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
130 132 0.179189 CAAATTTGGCGAGTCCGAGC 60.179 55.000 10.49 0.00 38.22 5.03
137 139 4.481930 TTACAGTGTCAAATTTGGCGAG 57.518 40.909 17.44 11.83 35.00 5.03
138 140 4.902443 TTTACAGTGTCAAATTTGGCGA 57.098 36.364 17.44 4.75 35.00 5.54
237 239 8.771920 AGAGTACATTACAAAATCATCACGAA 57.228 30.769 0.00 0.00 0.00 3.85
260 262 7.490079 ACAAAGCACGTACGATGATTATAAAGA 59.510 33.333 24.41 0.00 0.00 2.52
340 342 0.036388 GCCCGACAGTGGAGATTTCA 60.036 55.000 0.00 0.00 0.00 2.69
352 354 4.680237 CTGAAGTGCGGCCCGACA 62.680 66.667 7.68 0.69 0.00 4.35
412 414 0.032316 TCATCTGCAGCCTCCTCTCT 60.032 55.000 9.47 0.00 0.00 3.10
519 521 1.863267 GGATCCATCGCTTGTCTGAG 58.137 55.000 6.95 0.00 0.00 3.35
520 522 0.103026 CGGATCCATCGCTTGTCTGA 59.897 55.000 13.41 0.00 0.00 3.27
523 525 2.218953 TAACGGATCCATCGCTTGTC 57.781 50.000 13.41 0.00 0.00 3.18
589 604 4.016706 ACTCGGGCAGGGTTTCCG 62.017 66.667 0.00 0.00 44.59 4.30
618 633 5.786401 ACAGTTTCTGCTATTTCGTGATC 57.214 39.130 0.00 0.00 34.37 2.92
646 661 2.780924 ACAACCAAGGGCAGGGGA 60.781 61.111 0.00 0.00 0.00 4.81
652 667 2.417097 GTGCACACAACCAAGGGC 59.583 61.111 13.17 0.00 0.00 5.19
653 668 2.721231 CGTGCACACAACCAAGGG 59.279 61.111 18.64 0.00 0.00 3.95
654 669 2.026014 GCGTGCACACAACCAAGG 59.974 61.111 18.64 0.00 0.00 3.61
655 670 1.009675 GAGCGTGCACACAACCAAG 60.010 57.895 18.64 0.00 0.00 3.61
656 671 1.451207 AGAGCGTGCACACAACCAA 60.451 52.632 18.64 0.00 0.00 3.67
657 672 2.179547 CAGAGCGTGCACACAACCA 61.180 57.895 18.64 0.00 0.00 3.67
658 673 2.633657 CAGAGCGTGCACACAACC 59.366 61.111 18.64 0.77 0.00 3.77
692 707 1.103398 AGTTTCAGCAAAGCACGGCT 61.103 50.000 0.00 0.00 42.56 5.52
743 758 1.745653 GAATCAACTACCCAGGCAAGC 59.254 52.381 0.00 0.00 0.00 4.01
746 761 0.981183 ACGAATCAACTACCCAGGCA 59.019 50.000 0.00 0.00 0.00 4.75
752 767 3.000727 CCAACCTCACGAATCAACTACC 58.999 50.000 0.00 0.00 0.00 3.18
759 774 5.334414 GCAATATCATCCAACCTCACGAATC 60.334 44.000 0.00 0.00 0.00 2.52
762 777 3.118445 TGCAATATCATCCAACCTCACGA 60.118 43.478 0.00 0.00 0.00 4.35
813 831 9.189156 TCAAATCTGGCAAAATAGCTAAAGTAT 57.811 29.630 0.00 0.00 34.17 2.12
855 874 1.401552 GCGGCATGAAGAATTGCTGTA 59.598 47.619 0.00 0.00 45.12 2.74
878 897 2.584492 TGATACCGATGCAGTCAGTG 57.416 50.000 0.00 0.00 0.00 3.66
894 913 9.851686 TTTGCCACATTCTATACTTTCTATGAT 57.148 29.630 0.00 0.00 0.00 2.45
905 924 3.947196 CCTGCAGTTTGCCACATTCTATA 59.053 43.478 13.81 0.00 44.23 1.31
906 925 2.756760 CCTGCAGTTTGCCACATTCTAT 59.243 45.455 13.81 0.00 44.23 1.98
907 926 2.161855 CCTGCAGTTTGCCACATTCTA 58.838 47.619 13.81 0.00 44.23 2.10
925 944 4.101448 GGACACGGATGCAGGCCT 62.101 66.667 0.00 0.00 0.00 5.19
926 945 4.408821 TGGACACGGATGCAGGCC 62.409 66.667 0.00 0.00 0.00 5.19
989 1018 3.506096 CTACCAGCCGACGAGCGA 61.506 66.667 0.00 0.00 44.57 4.93
1089 1135 2.449518 TGGAGGTGGGCTGTGGAA 60.450 61.111 0.00 0.00 0.00 3.53
1149 1208 2.663188 GCGGCGATGACATCCTCC 60.663 66.667 12.98 9.97 0.00 4.30
1171 1230 1.392710 CCAGCCTCTCGAATACCGGT 61.393 60.000 13.98 13.98 39.14 5.28
1177 1236 3.854669 CCGGCCAGCCTCTCGAAT 61.855 66.667 2.24 0.00 0.00 3.34
1241 1300 2.609610 GTGAGTAGGGTGGGGGCA 60.610 66.667 0.00 0.00 0.00 5.36
1253 1318 1.153745 GAGGCGATTCTGCGTGAGT 60.154 57.895 0.00 0.00 35.06 3.41
1259 1324 1.079503 AAAACGAGAGGCGATTCTGC 58.920 50.000 0.00 0.00 44.57 4.26
1283 1348 2.157863 GCGTTTCTGCTACTTGGAAGAC 59.842 50.000 0.00 0.00 0.00 3.01
1285 1350 2.417719 AGCGTTTCTGCTACTTGGAAG 58.582 47.619 0.00 0.00 45.14 3.46
1286 1351 2.543777 AGCGTTTCTGCTACTTGGAA 57.456 45.000 0.00 0.00 45.14 3.53
1287 1352 2.094182 CCTAGCGTTTCTGCTACTTGGA 60.094 50.000 0.00 0.00 45.14 3.53
1288 1353 2.094182 TCCTAGCGTTTCTGCTACTTGG 60.094 50.000 0.00 0.00 45.14 3.61
1289 1354 3.182967 CTCCTAGCGTTTCTGCTACTTG 58.817 50.000 0.00 0.00 45.14 3.16
1290 1355 2.826725 ACTCCTAGCGTTTCTGCTACTT 59.173 45.455 0.00 0.00 45.14 2.24
1291 1356 2.448453 ACTCCTAGCGTTTCTGCTACT 58.552 47.619 0.00 0.00 45.14 2.57
1292 1357 2.943449 ACTCCTAGCGTTTCTGCTAC 57.057 50.000 0.00 0.00 45.14 3.58
1293 1358 3.349927 TGTACTCCTAGCGTTTCTGCTA 58.650 45.455 0.00 0.00 45.14 3.49
1301 1366 3.451178 ACCAATTCATGTACTCCTAGCGT 59.549 43.478 0.00 0.00 0.00 5.07
1302 1367 4.051922 GACCAATTCATGTACTCCTAGCG 58.948 47.826 0.00 0.00 0.00 4.26
1310 1375 2.420022 AGCGCAAGACCAATTCATGTAC 59.580 45.455 11.47 0.00 43.02 2.90
1346 1420 0.743345 GAACCCTATGCGCGGTTTCT 60.743 55.000 16.94 0.00 42.48 2.52
1351 1425 2.896801 GCATGAACCCTATGCGCGG 61.897 63.158 8.83 0.00 41.16 6.46
1480 1554 3.617263 AGACAAACTCGACTGTGAACAAC 59.383 43.478 0.00 0.00 0.00 3.32
1491 1565 1.301716 GCCTGCCAGACAAACTCGA 60.302 57.895 0.00 0.00 0.00 4.04
1608 1682 6.519586 GCACAAAGATGCAACAGTAAACTGG 61.520 44.000 14.30 0.00 45.34 4.00
1722 1806 1.291272 GGTTACAGACGACCGCCTT 59.709 57.895 0.00 0.00 0.00 4.35
1849 1933 6.884280 AGACCAAATAACCACAGAAGAAAG 57.116 37.500 0.00 0.00 0.00 2.62
1910 2092 3.855689 TCCCTCCTACGTTTACGAAAG 57.144 47.619 9.53 5.95 43.02 2.62
2047 2229 9.037737 CACCAAATTTGATGCTAATATTCCTTG 57.962 33.333 19.86 0.00 0.00 3.61
2064 2246 8.710749 ATATATGAGTATGCCACACCAAATTT 57.289 30.769 0.00 0.00 0.00 1.82
2132 2314 9.987272 TGATATCACACTCTTGTCATTATTAGG 57.013 33.333 0.00 0.00 31.66 2.69
2148 2330 8.970691 AGTAACAATGCTTTTTGATATCACAC 57.029 30.769 4.48 0.00 0.00 3.82
2186 2368 9.552114 GAAATCATTTGACACAGAATCTTGTAG 57.448 33.333 0.00 0.00 0.00 2.74
2197 2379 7.706179 GGAGAAAACAAGAAATCATTTGACACA 59.294 33.333 0.00 0.00 0.00 3.72
2198 2380 7.922811 AGGAGAAAACAAGAAATCATTTGACAC 59.077 33.333 0.00 0.00 0.00 3.67
2459 2641 5.838529 TCAGCATGGCATCAAATATGAAAG 58.161 37.500 0.00 0.00 36.29 2.62
2468 2650 3.965379 AAACAATCAGCATGGCATCAA 57.035 38.095 0.00 0.00 36.16 2.57
2615 2798 7.677745 AGATGGCCATACTTCTAACATATCTCT 59.322 37.037 20.84 2.60 0.00 3.10
2655 2838 9.561069 AGAGAAACATTATATTACCACCATCAC 57.439 33.333 0.00 0.00 0.00 3.06
2691 2874 1.667724 CTCTCGTATTTTGCTGCCAGG 59.332 52.381 0.00 0.00 0.00 4.45
2764 2947 5.736358 CGTAAGTCTACAAATACTCCGACAC 59.264 44.000 0.00 0.00 0.00 3.67
2769 2952 7.081526 TCAGTCGTAAGTCTACAAATACTCC 57.918 40.000 0.00 0.00 33.42 3.85
2770 2953 9.224058 GAATCAGTCGTAAGTCTACAAATACTC 57.776 37.037 0.00 0.00 33.42 2.59
2771 2954 8.737175 TGAATCAGTCGTAAGTCTACAAATACT 58.263 33.333 0.00 0.00 33.42 2.12
2772 2955 8.906636 TGAATCAGTCGTAAGTCTACAAATAC 57.093 34.615 0.00 0.00 33.42 1.89
2773 2956 9.350357 GTTGAATCAGTCGTAAGTCTACAAATA 57.650 33.333 0.00 0.00 33.42 1.40
2774 2957 7.870954 TGTTGAATCAGTCGTAAGTCTACAAAT 59.129 33.333 0.00 0.00 33.42 2.32
2785 2968 7.278203 TGTGTTTAAGTTGTTGAATCAGTCGTA 59.722 33.333 0.00 0.00 0.00 3.43
2835 3028 3.786656 GCTGTGGGTCATCATAGCA 57.213 52.632 8.35 0.00 46.56 3.49
2857 3050 4.924305 ACAGTTGCAATCACAAGTTCAT 57.076 36.364 0.59 0.00 30.73 2.57
2932 3172 4.565022 ACAGTTTCCCACACAAAAACTTG 58.435 39.130 0.00 0.00 40.32 3.16
3130 3370 1.667236 CAAGTTCAGCCGCATGGATA 58.333 50.000 0.00 0.00 37.49 2.59
3487 3728 3.056607 CCTGGGTTTTGGAGCATAGTTTG 60.057 47.826 0.00 0.00 0.00 2.93
3491 3732 1.106285 GCCTGGGTTTTGGAGCATAG 58.894 55.000 0.00 0.00 0.00 2.23
3526 3769 0.538057 TCAAGCCAGCTTCCCAACAG 60.538 55.000 0.90 0.00 33.42 3.16
3529 3772 0.612732 CCATCAAGCCAGCTTCCCAA 60.613 55.000 0.90 0.00 33.42 4.12
3562 3805 5.190528 TCCTCTGCCAGAATCAAGACTTTAT 59.809 40.000 0.00 0.00 0.00 1.40
3647 3892 0.824109 TAGCACCCACCTGAAGATCG 59.176 55.000 0.00 0.00 0.00 3.69
3649 3894 1.207791 CCTAGCACCCACCTGAAGAT 58.792 55.000 0.00 0.00 0.00 2.40
3662 3907 1.748403 GATGCCCACGATCCTAGCA 59.252 57.895 0.00 0.00 37.94 3.49
3708 3953 6.465894 GGCTATGGTATTGGTATGGAGTTCTT 60.466 42.308 0.00 0.00 0.00 2.52
3711 3956 4.913968 AGGCTATGGTATTGGTATGGAGTT 59.086 41.667 0.00 0.00 0.00 3.01
3716 3961 5.013079 TCCTCAAGGCTATGGTATTGGTATG 59.987 44.000 0.00 0.00 34.44 2.39
3717 3962 5.162637 TCCTCAAGGCTATGGTATTGGTAT 58.837 41.667 0.00 0.00 34.44 2.73
3718 3963 4.562767 TCCTCAAGGCTATGGTATTGGTA 58.437 43.478 0.00 0.00 34.44 3.25
3719 3964 3.392616 CTCCTCAAGGCTATGGTATTGGT 59.607 47.826 0.00 0.00 34.44 3.67
3720 3965 3.808618 GCTCCTCAAGGCTATGGTATTGG 60.809 52.174 0.00 0.00 34.44 3.16
3721 3966 3.181451 TGCTCCTCAAGGCTATGGTATTG 60.181 47.826 0.00 0.00 34.44 1.90
3722 3967 3.048600 TGCTCCTCAAGGCTATGGTATT 58.951 45.455 0.00 0.00 34.44 1.89
3723 3968 2.694397 TGCTCCTCAAGGCTATGGTAT 58.306 47.619 0.00 0.00 34.44 2.73
3724 3969 2.174685 TGCTCCTCAAGGCTATGGTA 57.825 50.000 0.00 0.00 34.44 3.25
3732 3977 1.242076 CAGTGGTTTGCTCCTCAAGG 58.758 55.000 0.00 0.00 35.84 3.61
3766 4011 5.241285 TCATGCTTCAGTGCAAAAGAATGTA 59.759 36.000 18.43 8.49 46.61 2.29
3767 4012 4.038282 TCATGCTTCAGTGCAAAAGAATGT 59.962 37.500 18.43 0.63 46.61 2.71
3907 4153 6.078202 TGGTTGTTGAATAAAATTGAGCGA 57.922 33.333 0.00 0.00 0.00 4.93
3981 4227 6.364976 AGCAAAAACAATTATTTGTAGGTCGC 59.635 34.615 3.55 4.30 45.30 5.19
4007 4253 9.985730 TCGAGTTACTAATGGTAAAGAAAAGAA 57.014 29.630 0.00 0.00 41.41 2.52
4010 4256 9.932207 TCATCGAGTTACTAATGGTAAAGAAAA 57.068 29.630 7.18 0.00 41.41 2.29
4065 4311 5.293814 CAGAGTGCTAATGAGAGATGGTTTG 59.706 44.000 0.00 0.00 0.00 2.93
4066 4312 5.188555 TCAGAGTGCTAATGAGAGATGGTTT 59.811 40.000 0.00 0.00 0.00 3.27
4140 5528 7.556275 TGGAGGCTTATAATTGTAAAGTGGAAG 59.444 37.037 0.00 0.00 0.00 3.46
4177 5565 7.873505 GTCCTAGAAAGTTTAGAAGAGCTTTCA 59.126 37.037 15.29 4.30 45.29 2.69
4248 5636 1.595093 GGCGGGGTCCAATCTGTTTG 61.595 60.000 0.00 0.00 34.93 2.93
4249 5637 1.304134 GGCGGGGTCCAATCTGTTT 60.304 57.895 0.00 0.00 0.00 2.83
4250 5638 2.355115 GGCGGGGTCCAATCTGTT 59.645 61.111 0.00 0.00 0.00 3.16
4251 5639 3.728373 GGGCGGGGTCCAATCTGT 61.728 66.667 0.00 0.00 0.00 3.41
4252 5640 4.506255 GGGGCGGGGTCCAATCTG 62.506 72.222 0.00 0.00 0.00 2.90
4253 5641 2.850851 TAAGGGGCGGGGTCCAATCT 62.851 60.000 0.00 0.00 0.00 2.40
4254 5642 1.928714 TTAAGGGGCGGGGTCCAATC 61.929 60.000 0.00 0.00 0.00 2.67
4255 5643 1.511316 TTTAAGGGGCGGGGTCCAAT 61.511 55.000 0.00 0.00 0.00 3.16
4256 5644 1.727215 TTTTAAGGGGCGGGGTCCAA 61.727 55.000 0.00 0.00 0.00 3.53
4257 5645 1.511316 ATTTTAAGGGGCGGGGTCCA 61.511 55.000 0.00 0.00 0.00 4.02
4258 5646 0.552363 TATTTTAAGGGGCGGGGTCC 59.448 55.000 0.00 0.00 0.00 4.46
4259 5647 1.213678 AGTATTTTAAGGGGCGGGGTC 59.786 52.381 0.00 0.00 0.00 4.46
4260 5648 1.301916 AGTATTTTAAGGGGCGGGGT 58.698 50.000 0.00 0.00 0.00 4.95
4261 5649 2.092049 AGAAGTATTTTAAGGGGCGGGG 60.092 50.000 0.00 0.00 0.00 5.73
4262 5650 3.292492 AGAAGTATTTTAAGGGGCGGG 57.708 47.619 0.00 0.00 0.00 6.13
4263 5651 6.405065 GGTTTAAGAAGTATTTTAAGGGGCGG 60.405 42.308 0.00 0.00 0.00 6.13
4264 5652 6.376299 AGGTTTAAGAAGTATTTTAAGGGGCG 59.624 38.462 0.00 0.00 0.00 6.13
4265 5653 7.614583 AGAGGTTTAAGAAGTATTTTAAGGGGC 59.385 37.037 0.00 0.00 0.00 5.80
4266 5654 9.529823 AAGAGGTTTAAGAAGTATTTTAAGGGG 57.470 33.333 0.00 0.00 0.00 4.79
4285 5673 9.300681 TGTTCTGAATATCAAAATCAAGAGGTT 57.699 29.630 0.00 0.00 0.00 3.50
4286 5674 8.868522 TGTTCTGAATATCAAAATCAAGAGGT 57.131 30.769 0.00 0.00 0.00 3.85
4287 5675 9.947669 GATGTTCTGAATATCAAAATCAAGAGG 57.052 33.333 18.61 0.00 0.00 3.69
4301 5689 9.939802 CTGATGATCCTATTGATGTTCTGAATA 57.060 33.333 0.00 0.00 32.41 1.75
4302 5690 8.657712 TCTGATGATCCTATTGATGTTCTGAAT 58.342 33.333 0.00 0.00 32.41 2.57
4303 5691 8.026396 TCTGATGATCCTATTGATGTTCTGAA 57.974 34.615 0.00 0.00 32.41 3.02
4304 5692 7.607615 TCTGATGATCCTATTGATGTTCTGA 57.392 36.000 0.00 0.00 32.41 3.27
4305 5693 7.095144 GCTTCTGATGATCCTATTGATGTTCTG 60.095 40.741 0.00 0.00 32.41 3.02
4306 5694 6.935771 GCTTCTGATGATCCTATTGATGTTCT 59.064 38.462 0.00 0.00 32.41 3.01
4307 5695 6.149142 GGCTTCTGATGATCCTATTGATGTTC 59.851 42.308 0.00 0.00 32.41 3.18
4308 5696 6.002704 GGCTTCTGATGATCCTATTGATGTT 58.997 40.000 0.00 0.00 32.41 2.71
4309 5697 5.072736 TGGCTTCTGATGATCCTATTGATGT 59.927 40.000 0.00 0.00 32.41 3.06
4310 5698 5.411977 GTGGCTTCTGATGATCCTATTGATG 59.588 44.000 0.00 0.00 32.41 3.07
4311 5699 5.072736 TGTGGCTTCTGATGATCCTATTGAT 59.927 40.000 0.00 0.00 36.01 2.57
4312 5700 4.409901 TGTGGCTTCTGATGATCCTATTGA 59.590 41.667 0.00 0.00 0.00 2.57
4313 5701 4.711399 TGTGGCTTCTGATGATCCTATTG 58.289 43.478 0.00 0.00 0.00 1.90
4314 5702 5.579753 ATGTGGCTTCTGATGATCCTATT 57.420 39.130 0.00 0.00 0.00 1.73
4315 5703 5.579753 AATGTGGCTTCTGATGATCCTAT 57.420 39.130 0.00 0.00 0.00 2.57
4316 5704 5.128205 CAAATGTGGCTTCTGATGATCCTA 58.872 41.667 0.00 0.00 0.00 2.94
4317 5705 3.947612 AATGTGGCTTCTGATGATCCT 57.052 42.857 0.00 0.00 0.00 3.24
4318 5706 3.490419 GCAAATGTGGCTTCTGATGATCC 60.490 47.826 0.00 0.00 0.00 3.36
4319 5707 3.129813 TGCAAATGTGGCTTCTGATGATC 59.870 43.478 0.00 0.00 0.00 2.92
4320 5708 3.093814 TGCAAATGTGGCTTCTGATGAT 58.906 40.909 0.00 0.00 0.00 2.45
4321 5709 2.229543 GTGCAAATGTGGCTTCTGATGA 59.770 45.455 0.00 0.00 0.00 2.92
4322 5710 2.029739 TGTGCAAATGTGGCTTCTGATG 60.030 45.455 0.00 0.00 0.00 3.07
4323 5711 2.029649 GTGTGCAAATGTGGCTTCTGAT 60.030 45.455 0.00 0.00 0.00 2.90
4324 5712 1.337703 GTGTGCAAATGTGGCTTCTGA 59.662 47.619 0.00 0.00 0.00 3.27
4325 5713 1.603678 GGTGTGCAAATGTGGCTTCTG 60.604 52.381 0.00 0.00 0.00 3.02
4326 5714 0.675633 GGTGTGCAAATGTGGCTTCT 59.324 50.000 0.00 0.00 0.00 2.85
4327 5715 0.388659 TGGTGTGCAAATGTGGCTTC 59.611 50.000 0.00 0.00 0.00 3.86
4328 5716 0.829333 TTGGTGTGCAAATGTGGCTT 59.171 45.000 0.00 0.00 0.00 4.35
4329 5717 0.829333 TTTGGTGTGCAAATGTGGCT 59.171 45.000 0.00 0.00 0.00 4.75
4330 5718 1.532007 CATTTGGTGTGCAAATGTGGC 59.468 47.619 1.52 0.00 42.12 5.01
4335 5723 5.163468 TGTTACAGACATTTGGTGTGCAAAT 60.163 36.000 0.00 0.00 44.26 2.32
4336 5724 4.158579 TGTTACAGACATTTGGTGTGCAAA 59.841 37.500 0.00 0.00 44.26 3.68
4337 5725 3.696548 TGTTACAGACATTTGGTGTGCAA 59.303 39.130 0.00 0.00 44.26 4.08
4338 5726 3.282885 TGTTACAGACATTTGGTGTGCA 58.717 40.909 0.00 0.00 44.26 4.57
4339 5727 3.980646 TGTTACAGACATTTGGTGTGC 57.019 42.857 0.00 0.00 44.26 4.57
4340 5728 4.261572 CCCTTGTTACAGACATTTGGTGTG 60.262 45.833 0.00 0.00 45.79 3.82
4341 5729 3.888930 CCCTTGTTACAGACATTTGGTGT 59.111 43.478 0.00 0.00 45.83 4.16
4342 5730 3.255642 CCCCTTGTTACAGACATTTGGTG 59.744 47.826 0.00 0.00 38.26 4.17
4343 5731 3.139397 TCCCCTTGTTACAGACATTTGGT 59.861 43.478 0.00 0.00 38.26 3.67
4344 5732 3.761897 TCCCCTTGTTACAGACATTTGG 58.238 45.455 0.00 0.00 38.26 3.28
4345 5733 4.218417 CCTTCCCCTTGTTACAGACATTTG 59.782 45.833 0.00 0.00 38.26 2.32
4346 5734 4.105697 TCCTTCCCCTTGTTACAGACATTT 59.894 41.667 0.00 0.00 38.26 2.32
4347 5735 3.655777 TCCTTCCCCTTGTTACAGACATT 59.344 43.478 0.00 0.00 38.26 2.71
4348 5736 3.256704 TCCTTCCCCTTGTTACAGACAT 58.743 45.455 0.00 0.00 38.26 3.06
4349 5737 2.696775 TCCTTCCCCTTGTTACAGACA 58.303 47.619 0.00 0.00 36.19 3.41
4350 5738 3.409570 GTTCCTTCCCCTTGTTACAGAC 58.590 50.000 0.00 0.00 0.00 3.51
4351 5739 2.038033 CGTTCCTTCCCCTTGTTACAGA 59.962 50.000 0.00 0.00 0.00 3.41
4352 5740 2.423577 CGTTCCTTCCCCTTGTTACAG 58.576 52.381 0.00 0.00 0.00 2.74
4353 5741 1.543871 GCGTTCCTTCCCCTTGTTACA 60.544 52.381 0.00 0.00 0.00 2.41
4354 5742 1.162698 GCGTTCCTTCCCCTTGTTAC 58.837 55.000 0.00 0.00 0.00 2.50
4355 5743 1.061546 AGCGTTCCTTCCCCTTGTTA 58.938 50.000 0.00 0.00 0.00 2.41
4356 5744 0.537371 CAGCGTTCCTTCCCCTTGTT 60.537 55.000 0.00 0.00 0.00 2.83
4357 5745 1.073199 CAGCGTTCCTTCCCCTTGT 59.927 57.895 0.00 0.00 0.00 3.16
4358 5746 0.537371 AACAGCGTTCCTTCCCCTTG 60.537 55.000 0.00 0.00 0.00 3.61
4359 5747 0.185175 AAACAGCGTTCCTTCCCCTT 59.815 50.000 0.00 0.00 0.00 3.95
4360 5748 1.061546 TAAACAGCGTTCCTTCCCCT 58.938 50.000 0.00 0.00 0.00 4.79
4361 5749 2.124277 ATAAACAGCGTTCCTTCCCC 57.876 50.000 0.00 0.00 0.00 4.81
4362 5750 4.142534 GGTTTATAAACAGCGTTCCTTCCC 60.143 45.833 25.59 4.21 40.63 3.97
4363 5751 4.456566 TGGTTTATAAACAGCGTTCCTTCC 59.543 41.667 25.59 8.06 40.63 3.46
4364 5752 5.616488 TGGTTTATAAACAGCGTTCCTTC 57.384 39.130 25.59 8.35 40.63 3.46
4365 5753 5.564063 GCTTGGTTTATAAACAGCGTTCCTT 60.564 40.000 25.59 0.00 40.63 3.36
4366 5754 4.082949 GCTTGGTTTATAAACAGCGTTCCT 60.083 41.667 25.59 0.00 40.63 3.36
4367 5755 4.163552 GCTTGGTTTATAAACAGCGTTCC 58.836 43.478 25.59 10.40 40.63 3.62
4368 5756 4.163552 GGCTTGGTTTATAAACAGCGTTC 58.836 43.478 25.59 12.69 38.25 3.95
4369 5757 3.570550 TGGCTTGGTTTATAAACAGCGTT 59.429 39.130 25.59 0.00 38.25 4.84
4370 5758 3.150767 TGGCTTGGTTTATAAACAGCGT 58.849 40.909 25.59 0.00 38.25 5.07
4371 5759 3.438781 TCTGGCTTGGTTTATAAACAGCG 59.561 43.478 25.59 15.80 38.25 5.18
4372 5760 5.125417 TGATCTGGCTTGGTTTATAAACAGC 59.875 40.000 25.59 24.20 40.63 4.40
4373 5761 6.757897 TGATCTGGCTTGGTTTATAAACAG 57.242 37.500 25.59 17.55 40.63 3.16
4374 5762 7.375053 GTTTGATCTGGCTTGGTTTATAAACA 58.625 34.615 25.59 12.03 40.63 2.83
4375 5763 6.526674 CGTTTGATCTGGCTTGGTTTATAAAC 59.473 38.462 18.30 18.30 38.17 2.01
4376 5764 6.431543 TCGTTTGATCTGGCTTGGTTTATAAA 59.568 34.615 0.00 0.00 0.00 1.40
4377 5765 5.941058 TCGTTTGATCTGGCTTGGTTTATAA 59.059 36.000 0.00 0.00 0.00 0.98
4378 5766 5.492895 TCGTTTGATCTGGCTTGGTTTATA 58.507 37.500 0.00 0.00 0.00 0.98
4379 5767 4.331968 TCGTTTGATCTGGCTTGGTTTAT 58.668 39.130 0.00 0.00 0.00 1.40
4380 5768 3.745799 TCGTTTGATCTGGCTTGGTTTA 58.254 40.909 0.00 0.00 0.00 2.01
4381 5769 2.582052 TCGTTTGATCTGGCTTGGTTT 58.418 42.857 0.00 0.00 0.00 3.27
4382 5770 2.270352 TCGTTTGATCTGGCTTGGTT 57.730 45.000 0.00 0.00 0.00 3.67
4383 5771 2.270352 TTCGTTTGATCTGGCTTGGT 57.730 45.000 0.00 0.00 0.00 3.67
4384 5772 2.669391 GCTTTCGTTTGATCTGGCTTGG 60.669 50.000 0.00 0.00 0.00 3.61
4385 5773 2.589014 GCTTTCGTTTGATCTGGCTTG 58.411 47.619 0.00 0.00 0.00 4.01
4386 5774 1.541588 GGCTTTCGTTTGATCTGGCTT 59.458 47.619 0.00 0.00 0.00 4.35
4387 5775 1.168714 GGCTTTCGTTTGATCTGGCT 58.831 50.000 0.00 0.00 0.00 4.75
4388 5776 1.131315 GAGGCTTTCGTTTGATCTGGC 59.869 52.381 0.00 0.00 0.00 4.85
4389 5777 2.417933 CAGAGGCTTTCGTTTGATCTGG 59.582 50.000 0.00 0.00 31.29 3.86
4390 5778 2.417933 CCAGAGGCTTTCGTTTGATCTG 59.582 50.000 0.00 0.00 34.00 2.90
4391 5779 2.039084 ACCAGAGGCTTTCGTTTGATCT 59.961 45.455 0.00 0.00 0.00 2.75
4392 5780 2.427506 ACCAGAGGCTTTCGTTTGATC 58.572 47.619 0.00 0.00 0.00 2.92
4393 5781 2.568623 ACCAGAGGCTTTCGTTTGAT 57.431 45.000 0.00 0.00 0.00 2.57
4394 5782 2.341846 AACCAGAGGCTTTCGTTTGA 57.658 45.000 0.00 0.00 0.00 2.69
4395 5783 3.115554 CAAAACCAGAGGCTTTCGTTTG 58.884 45.455 1.74 0.57 0.00 2.93
4396 5784 2.758423 ACAAAACCAGAGGCTTTCGTTT 59.242 40.909 0.00 0.00 0.00 3.60
4397 5785 2.375146 ACAAAACCAGAGGCTTTCGTT 58.625 42.857 0.00 0.00 0.00 3.85
4398 5786 2.052782 ACAAAACCAGAGGCTTTCGT 57.947 45.000 0.00 0.00 0.00 3.85
4399 5787 4.379499 GGATAACAAAACCAGAGGCTTTCG 60.379 45.833 0.00 0.00 0.00 3.46
4400 5788 4.082190 GGGATAACAAAACCAGAGGCTTTC 60.082 45.833 0.00 0.00 0.00 2.62
4401 5789 3.832490 GGGATAACAAAACCAGAGGCTTT 59.168 43.478 0.00 0.00 0.00 3.51
4402 5790 3.431415 GGGATAACAAAACCAGAGGCTT 58.569 45.455 0.00 0.00 0.00 4.35
4403 5791 2.291605 GGGGATAACAAAACCAGAGGCT 60.292 50.000 0.00 0.00 0.00 4.58
4404 5792 2.100197 GGGGATAACAAAACCAGAGGC 58.900 52.381 0.00 0.00 0.00 4.70
4405 5793 3.010138 TCAGGGGATAACAAAACCAGAGG 59.990 47.826 0.00 0.00 0.00 3.69
4406 5794 4.301072 TCAGGGGATAACAAAACCAGAG 57.699 45.455 0.00 0.00 0.00 3.35
4407 5795 4.733077 TTCAGGGGATAACAAAACCAGA 57.267 40.909 0.00 0.00 0.00 3.86
4408 5796 5.391312 CTTTCAGGGGATAACAAAACCAG 57.609 43.478 0.00 0.00 0.00 4.00


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

AutoCloner maintained by Alex Coulton.