Multiple sequence alignment - TraesCS1B01G351600

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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 TraesCS1B01G351600 chr1B 100.000 8251 0 0 1 8251 582100119 582091869 0.000000e+00 15237
1 TraesCS1B01G351600 chr1B 86.174 622 57 13 4602 5207 604837523 604838131 0.000000e+00 645
2 TraesCS1B01G351600 chr1D 91.566 8027 317 114 368 8246 430983885 430976071 0.000000e+00 10741
3 TraesCS1B01G351600 chr1D 91.850 319 23 3 22 337 430984199 430983881 7.600000e-120 442
4 TraesCS1B01G351600 chr1A 91.912 7505 311 104 881 8246 529250784 529243437 0.000000e+00 10224
5 TraesCS1B01G351600 chr1A 89.906 852 65 17 1 842 529251897 529251057 0.000000e+00 1077
6 TraesCS1B01G351600 chr2D 90.409 1418 85 26 3806 5204 432763027 432764412 0.000000e+00 1818
7 TraesCS1B01G351600 chr2D 81.759 773 62 17 3058 3793 432761959 432762689 2.580000e-159 573
8 TraesCS1B01G351600 chr2A 88.686 1423 97 28 3806 5204 554134910 554133528 0.000000e+00 1677
9 TraesCS1B01G351600 chr2A 92.248 258 20 0 3542 3799 554135527 554135270 4.710000e-97 366
10 TraesCS1B01G351600 chr2A 82.772 267 24 10 3046 3312 554136303 554136059 1.390000e-52 219
11 TraesCS1B01G351600 chr2B 88.262 1099 74 20 3806 4894 511122750 511123803 0.000000e+00 1264
12 TraesCS1B01G351600 chr2B 86.373 499 48 5 3046 3531 511121606 511122097 2.040000e-145 527
13 TraesCS1B01G351600 chr4B 88.439 173 20 0 1 173 617700179 617700351 8.390000e-50 209
14 TraesCS1B01G351600 chr5B 88.652 141 13 3 2121 2260 710871824 710871686 1.420000e-37 169
15 TraesCS1B01G351600 chr7A 88.073 109 10 3 4370 4478 14507539 14507434 8.690000e-25 126


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 TraesCS1B01G351600 chr1B 582091869 582100119 8250 True 15237.0 15237 100.0000 1 8251 1 chr1B.!!$R1 8250
1 TraesCS1B01G351600 chr1B 604837523 604838131 608 False 645.0 645 86.1740 4602 5207 1 chr1B.!!$F1 605
2 TraesCS1B01G351600 chr1D 430976071 430984199 8128 True 5591.5 10741 91.7080 22 8246 2 chr1D.!!$R1 8224
3 TraesCS1B01G351600 chr1A 529243437 529251897 8460 True 5650.5 10224 90.9090 1 8246 2 chr1A.!!$R1 8245
4 TraesCS1B01G351600 chr2D 432761959 432764412 2453 False 1195.5 1818 86.0840 3058 5204 2 chr2D.!!$F1 2146
5 TraesCS1B01G351600 chr2A 554133528 554136303 2775 True 754.0 1677 87.9020 3046 5204 3 chr2A.!!$R1 2158
6 TraesCS1B01G351600 chr2B 511121606 511123803 2197 False 895.5 1264 87.3175 3046 4894 2 chr2B.!!$F1 1848

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
776 788 0.252103 AACACCTCTAGGCCCGAAGA 60.252 55.000 0.00 0.00 39.32 2.87 F
1152 1427 0.379669 GATCCCATTGCAGCAACGAG 59.620 55.000 10.85 3.47 0.00 4.18 F
2665 3030 0.108804 ATGTCGACGCGAAGTGGATT 60.109 50.000 15.93 0.00 45.78 3.01 F
2963 3328 1.153549 GCCGCTCTTCCACTACCTG 60.154 63.158 0.00 0.00 0.00 4.00 F
3086 3451 1.486726 CACTACCAGGAAGGGGATGTC 59.513 57.143 0.00 0.00 43.89 3.06 F
3386 3769 2.167219 CGTGAGCGCATGTACCAGG 61.167 63.158 11.47 0.00 0.00 4.45 F
3895 5095 4.220602 ACTCATAAATGCCACCTTGAAACC 59.779 41.667 0.00 0.00 0.00 3.27 F
5534 6780 0.542702 CTGGCCATCACTGGGGTTTT 60.543 55.000 5.51 0.00 43.36 2.43 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2578 2940 0.040336 GCAGGATTCTGATGCATGCG 60.040 55.000 14.09 0.00 43.49 4.73 R
2996 3361 0.241481 ACTGCGACTCGAAGTTCCTC 59.759 55.000 6.22 0.00 44.06 3.71 R
4318 5525 1.506493 AAAGAGACAGCAAGCTGACG 58.494 50.000 27.17 2.67 46.30 4.35 R
4949 6180 3.497262 GGAGACTGTGTAAAAGAAACGGG 59.503 47.826 0.00 0.00 0.00 5.28 R
5113 6345 6.380560 TCTCTCTCTCATCAGATGTCATTGTT 59.619 38.462 10.34 0.00 0.00 2.83 R
5409 6654 2.203070 GCTGGATGGCCGTTCGAT 60.203 61.111 0.00 0.00 36.79 3.59 R
5833 7080 4.246458 CTCTCAAAGGACCCTTTAAGTCG 58.754 47.826 13.18 2.26 43.56 4.18 R
7479 8751 0.331616 TCTCCTCGGGATCACTCACA 59.668 55.000 0.00 0.00 0.00 3.58 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
123 124 1.745087 CATCCGGAATCCCAACTTGTG 59.255 52.381 9.01 0.00 0.00 3.33
138 139 6.279882 CCAACTTGTGTTTGTATGTTTCCAT 58.720 36.000 0.00 0.00 33.52 3.41
143 144 2.809119 TGTTTGTATGTTTCCATCGCGT 59.191 40.909 5.77 0.00 32.29 6.01
209 210 4.920112 CCCACGTCGTTGCCCACA 62.920 66.667 0.00 0.00 0.00 4.17
210 211 2.668212 CCACGTCGTTGCCCACAT 60.668 61.111 0.00 0.00 0.00 3.21
233 236 0.627451 TTCTCCAAGGCCTCATGCAT 59.373 50.000 5.23 0.00 43.89 3.96
236 239 0.918258 TCCAAGGCCTCATGCATACA 59.082 50.000 5.23 0.00 43.89 2.29
318 322 0.450184 ACAACGGTGACTTTGCACAC 59.550 50.000 7.88 0.00 42.92 3.82
334 338 2.223157 GCACACGTGAAAGCACAGTAAA 60.223 45.455 25.01 0.00 45.41 2.01
524 529 7.072177 ACACGAATTATGGTTGAGTACATTG 57.928 36.000 0.00 0.00 0.00 2.82
534 539 7.341445 TGGTTGAGTACATTGCTTACTTTTT 57.659 32.000 0.00 0.00 29.58 1.94
535 541 8.453238 TGGTTGAGTACATTGCTTACTTTTTA 57.547 30.769 0.00 0.00 29.58 1.52
682 688 8.734386 ACATTGTCATGTATTTCCTTTCTCTTC 58.266 33.333 0.00 0.00 42.24 2.87
683 689 8.954350 CATTGTCATGTATTTCCTTTCTCTTCT 58.046 33.333 0.00 0.00 0.00 2.85
697 703 9.491406 TCCTTTCTCTTCTACTAGTCTACTAGA 57.509 37.037 21.12 1.03 46.80 2.43
698 704 9.760077 CCTTTCTCTTCTACTAGTCTACTAGAG 57.240 40.741 21.12 14.13 46.80 2.43
719 731 7.150783 AGAGAATTCCATTACAAGAGCAAAC 57.849 36.000 0.65 0.00 0.00 2.93
774 786 1.829222 CTAAACACCTCTAGGCCCGAA 59.171 52.381 0.00 0.00 39.32 4.30
776 788 0.252103 AACACCTCTAGGCCCGAAGA 60.252 55.000 0.00 0.00 39.32 2.87
789 801 1.004560 CGAAGAGTTGCAGCCCTGA 60.005 57.895 0.00 0.00 0.00 3.86
815 827 1.970640 AGGAGGGGCAATTTCACAAAC 59.029 47.619 0.00 0.00 0.00 2.93
818 831 3.328505 GAGGGGCAATTTCACAAACATG 58.671 45.455 0.00 0.00 0.00 3.21
823 836 1.124658 CAATTTCACAAACATGCGCGG 59.875 47.619 8.83 0.00 0.00 6.46
824 837 1.008361 ATTTCACAAACATGCGCGGC 61.008 50.000 8.83 0.00 0.00 6.53
825 838 2.069465 TTTCACAAACATGCGCGGCT 62.069 50.000 8.83 0.00 0.00 5.52
827 840 4.088762 ACAAACATGCGCGGCTCG 62.089 61.111 8.83 0.00 42.12 5.03
828 841 4.088762 CAAACATGCGCGGCTCGT 62.089 61.111 8.83 0.00 41.07 4.18
829 842 3.353836 AAACATGCGCGGCTCGTT 61.354 55.556 8.83 5.41 41.07 3.85
830 843 3.308878 AAACATGCGCGGCTCGTTC 62.309 57.895 8.83 0.00 41.07 3.95
833 846 4.760047 ATGCGCGGCTCGTTCCTT 62.760 61.111 8.83 0.00 41.07 3.36
834 847 4.980805 TGCGCGGCTCGTTCCTTT 62.981 61.111 8.83 0.00 41.07 3.11
862 1116 8.761575 TCTTTCTTTATAAATACGGTTCGTGT 57.238 30.769 0.00 0.00 41.39 4.49
867 1121 9.033481 TCTTTATAAATACGGTTCGTGTATTGG 57.967 33.333 0.00 0.00 40.62 3.16
868 1122 5.662211 ATAAATACGGTTCGTGTATTGGC 57.338 39.130 3.03 0.00 40.62 4.52
869 1123 1.944032 ATACGGTTCGTGTATTGGCC 58.056 50.000 0.00 0.00 41.39 5.36
870 1124 0.458197 TACGGTTCGTGTATTGGCCG 60.458 55.000 0.00 0.00 41.39 6.13
874 1128 1.087771 GTTCGTGTATTGGCCGAGGG 61.088 60.000 0.00 0.00 31.54 4.30
979 1242 1.858458 TCAAACAAGAGTGCGAGTTCG 59.142 47.619 0.00 0.00 43.27 3.95
984 1247 1.806461 AAGAGTGCGAGTTCGAGGCA 61.806 55.000 5.60 0.00 43.02 4.75
987 1250 1.446099 GTGCGAGTTCGAGGCATGA 60.446 57.895 5.60 0.00 43.02 3.07
1050 1314 1.410932 CCTCTCTCCCTCCCTAGTGTG 60.411 61.905 0.00 0.00 0.00 3.82
1055 1319 1.827969 CTCCCTCCCTAGTGTGTTCTG 59.172 57.143 0.00 0.00 0.00 3.02
1102 1377 1.152226 ATCCCCCGGACTCATCTCC 60.152 63.158 0.73 0.00 32.98 3.71
1103 1378 1.669927 ATCCCCCGGACTCATCTCCT 61.670 60.000 0.73 0.00 32.98 3.69
1114 1389 5.278266 CGGACTCATCTCCTCTCTTGTTATC 60.278 48.000 0.00 0.00 0.00 1.75
1142 1417 4.758692 CGGAGTCGGATCCCATTG 57.241 61.111 6.06 0.00 35.82 2.82
1144 1419 1.526887 GGAGTCGGATCCCATTGCA 59.473 57.895 6.06 0.00 32.79 4.08
1145 1420 0.533755 GGAGTCGGATCCCATTGCAG 60.534 60.000 6.06 0.00 32.79 4.41
1146 1421 1.153086 AGTCGGATCCCATTGCAGC 60.153 57.895 6.06 0.00 0.00 5.25
1147 1422 1.451927 GTCGGATCCCATTGCAGCA 60.452 57.895 6.06 0.00 0.00 4.41
1148 1423 1.031571 GTCGGATCCCATTGCAGCAA 61.032 55.000 11.07 11.07 0.00 3.91
1149 1424 1.031571 TCGGATCCCATTGCAGCAAC 61.032 55.000 10.85 0.00 0.00 4.17
1150 1425 1.434696 GGATCCCATTGCAGCAACG 59.565 57.895 10.85 0.87 0.00 4.10
1151 1426 1.031571 GGATCCCATTGCAGCAACGA 61.032 55.000 10.85 6.92 0.00 3.85
1152 1427 0.379669 GATCCCATTGCAGCAACGAG 59.620 55.000 10.85 3.47 0.00 4.18
1153 1428 1.660560 ATCCCATTGCAGCAACGAGC 61.661 55.000 10.85 0.00 46.19 5.03
1195 1507 1.002087 ACCGATCTGGGTGAGTTGTTC 59.998 52.381 8.20 0.00 44.64 3.18
1209 1521 2.137523 GTTGTTCATCCGTACCACGTT 58.862 47.619 0.00 0.00 40.58 3.99
1210 1522 2.068837 TGTTCATCCGTACCACGTTC 57.931 50.000 0.00 0.00 40.58 3.95
1211 1523 1.337074 TGTTCATCCGTACCACGTTCC 60.337 52.381 0.00 0.00 40.58 3.62
1212 1524 1.067354 GTTCATCCGTACCACGTTCCT 60.067 52.381 0.00 0.00 40.58 3.36
1213 1525 1.259609 TCATCCGTACCACGTTCCTT 58.740 50.000 0.00 0.00 40.58 3.36
1214 1526 1.619827 TCATCCGTACCACGTTCCTTT 59.380 47.619 0.00 0.00 40.58 3.11
1324 1641 5.322754 TCGGGGACTAGTAGATTAGATTGG 58.677 45.833 3.59 0.00 0.00 3.16
1325 1642 4.082136 CGGGGACTAGTAGATTAGATTGGC 60.082 50.000 3.59 0.00 0.00 4.52
1326 1643 4.838986 GGGGACTAGTAGATTAGATTGGCA 59.161 45.833 3.59 0.00 0.00 4.92
1327 1644 5.046950 GGGGACTAGTAGATTAGATTGGCAG 60.047 48.000 3.59 0.00 0.00 4.85
1328 1645 5.474825 GGACTAGTAGATTAGATTGGCAGC 58.525 45.833 3.59 0.00 0.00 5.25
1329 1646 5.011125 GGACTAGTAGATTAGATTGGCAGCA 59.989 44.000 3.59 0.00 0.00 4.41
1392 1709 3.199891 GTATGGGCCGTGAACGCC 61.200 66.667 8.97 2.77 38.18 5.68
1480 1807 5.643379 TGGCTAAGCTTATTTTCCTGTTG 57.357 39.130 6.64 0.00 0.00 3.33
1496 1823 9.895138 TTTTCCTGTTGTTAGTAGTAGAGTTTT 57.105 29.630 0.00 0.00 0.00 2.43
1497 1824 9.895138 TTTCCTGTTGTTAGTAGTAGAGTTTTT 57.105 29.630 0.00 0.00 0.00 1.94
1568 1900 4.999751 TTTTGCGCTTGAAACTTTTTGT 57.000 31.818 9.73 0.00 0.00 2.83
1569 1901 3.987807 TTGCGCTTGAAACTTTTTGTG 57.012 38.095 9.73 0.00 0.00 3.33
1572 1904 3.990469 TGCGCTTGAAACTTTTTGTGAAA 59.010 34.783 9.73 0.00 0.00 2.69
1574 1906 4.781026 GCGCTTGAAACTTTTTGTGAAAAC 59.219 37.500 0.00 0.00 31.72 2.43
1592 1924 5.192722 TGAAAACAAAAAGGGGGAGGAATTT 59.807 36.000 0.00 0.00 0.00 1.82
1593 1925 4.705110 AACAAAAAGGGGGAGGAATTTG 57.295 40.909 0.00 0.00 34.75 2.32
1595 1927 2.305635 CAAAAAGGGGGAGGAATTTGGG 59.694 50.000 0.00 0.00 0.00 4.12
1597 1929 1.527434 AAGGGGGAGGAATTTGGGGG 61.527 60.000 0.00 0.00 0.00 5.40
1703 2051 1.220749 GGCTATCCCACTGACGCAA 59.779 57.895 0.00 0.00 0.00 4.85
1727 2075 3.355455 CACCCCGCGCCGTTTTAA 61.355 61.111 0.00 0.00 0.00 1.52
1934 2290 2.182842 GCCGCCCATGAGTGATGAC 61.183 63.158 0.00 0.00 33.31 3.06
1956 2312 2.874780 CGTCTCGTTTCTCCGCCG 60.875 66.667 0.00 0.00 0.00 6.46
2603 2965 2.502947 TGCATCAGAATCCTGCACTAGT 59.497 45.455 0.00 0.00 40.75 2.57
2620 2985 5.595885 CACTAGTAGCTGCATGTACTGAAT 58.404 41.667 15.24 2.07 31.79 2.57
2629 2994 6.016024 AGCTGCATGTACTGAATTTTTCTGAA 60.016 34.615 1.02 0.00 33.42 3.02
2665 3030 0.108804 ATGTCGACGCGAAGTGGATT 60.109 50.000 15.93 0.00 45.78 3.01
2760 3125 4.081697 TCGTTGCAATCCACAGAATCTAGA 60.082 41.667 0.59 0.00 0.00 2.43
2770 3135 8.915057 ATCCACAGAATCTAGAACATATTTGG 57.085 34.615 0.00 0.00 0.00 3.28
2804 3169 4.516698 ACCAATAGAACAGTGCTTTCTGTG 59.483 41.667 6.31 4.84 46.25 3.66
2942 3307 2.348666 CGGCTACTGCAACAACATACTC 59.651 50.000 0.00 0.00 41.91 2.59
2963 3328 1.153549 GCCGCTCTTCCACTACCTG 60.154 63.158 0.00 0.00 0.00 4.00
2996 3361 3.357079 GACAGGCTGGCAACCACG 61.357 66.667 17.39 2.22 0.00 4.94
2997 3362 3.825160 GACAGGCTGGCAACCACGA 62.825 63.158 17.39 0.00 0.00 4.35
3086 3451 1.486726 CACTACCAGGAAGGGGATGTC 59.513 57.143 0.00 0.00 43.89 3.06
3386 3769 2.167219 CGTGAGCGCATGTACCAGG 61.167 63.158 11.47 0.00 0.00 4.45
3894 5094 5.391312 ACTCATAAATGCCACCTTGAAAC 57.609 39.130 0.00 0.00 0.00 2.78
3895 5095 4.220602 ACTCATAAATGCCACCTTGAAACC 59.779 41.667 0.00 0.00 0.00 3.27
4064 5271 8.092687 GTCTTACAGAGTATTTGTTCCTGGTTA 58.907 37.037 0.00 0.00 0.00 2.85
4184 5391 7.395190 TGAATGGATTGATAAAGTGGTTCTG 57.605 36.000 0.00 0.00 0.00 3.02
4259 5466 5.129634 TCTGTATTTTGTTCTTGCCACTCA 58.870 37.500 0.00 0.00 0.00 3.41
4901 6132 4.926238 GGTAAGTGATCAGCTATCGATTGG 59.074 45.833 1.71 0.00 37.42 3.16
4978 6210 6.920569 TCTTTTACACAGTCTCCTGAAAAC 57.079 37.500 0.00 0.00 41.50 2.43
5113 6345 7.213216 TGCAGACTCAATAAAACATGCTTTA 57.787 32.000 3.88 3.88 33.68 1.85
5282 6525 9.405587 TGGATTAAATGTTTCTTTTTCATCGTC 57.594 29.630 0.00 0.00 0.00 4.20
5304 6547 8.335356 TCGTCAATATAAATTTGTTAGCTGCTC 58.665 33.333 4.91 0.00 0.00 4.26
5327 6570 4.451900 CCAGACTTTCTTGTAACCACACT 58.548 43.478 0.00 0.00 33.30 3.55
5328 6571 4.273480 CCAGACTTTCTTGTAACCACACTG 59.727 45.833 0.00 0.00 33.30 3.66
5409 6654 3.562108 AGTTCCTCCTGACCTTCCTAA 57.438 47.619 0.00 0.00 0.00 2.69
5467 6712 9.651913 AAAAATCGTTTGCTCATATTGGTAAAT 57.348 25.926 0.00 0.00 0.00 1.40
5534 6780 0.542702 CTGGCCATCACTGGGGTTTT 60.543 55.000 5.51 0.00 43.36 2.43
5580 6827 8.308207 GTTTACTCTTCTCAGTAACTTCTCCAT 58.692 37.037 0.00 0.00 38.36 3.41
5698 6945 6.449635 ACAATGAACTTAGCACTCAAACAA 57.550 33.333 0.00 0.00 0.00 2.83
6138 7385 2.297033 TGGGTCGACAGTGTAAAGGTAC 59.703 50.000 18.91 0.00 0.00 3.34
6201 7448 7.490657 TGTATACCTTCTCACACCATTTACT 57.509 36.000 0.00 0.00 0.00 2.24
6207 7454 6.833933 ACCTTCTCACACCATTTACTCTTTTT 59.166 34.615 0.00 0.00 0.00 1.94
6264 7511 5.032863 CCAAGATCTCATTTTGAACATCGC 58.967 41.667 0.00 0.00 0.00 4.58
6322 7569 2.983229 AGTGATCAGGTCTTCATGCAC 58.017 47.619 0.00 0.00 0.00 4.57
6378 7625 3.255725 CAATACCATTTGCACTTGCCTG 58.744 45.455 0.00 0.00 41.18 4.85
6415 7662 2.044551 GGGAGGCTCCAAGCAAGG 60.045 66.667 33.27 0.00 44.75 3.61
6487 7734 2.434359 GTTCAAGGGAGCCGGTCG 60.434 66.667 1.90 0.00 0.00 4.79
6533 7780 1.537202 CAAAGGTCAGTTAGGCAGTGC 59.463 52.381 6.55 6.55 0.00 4.40
6558 7806 7.282916 CGATTTTTAAACATGGTGAAAGCTTG 58.717 34.615 0.00 0.00 44.06 4.01
6582 7830 9.448438 TTGTCATGTTATTTAGCTAACTGATGT 57.552 29.630 5.45 0.00 33.62 3.06
6583 7831 9.448438 TGTCATGTTATTTAGCTAACTGATGTT 57.552 29.630 5.45 0.00 39.98 2.71
6666 7914 2.035066 AGTTCACAGCAAAAGCATGGTC 59.965 45.455 0.00 0.00 0.00 4.02
6696 7944 9.392259 CCGATTGACTATGTACTATGTATAGGA 57.608 37.037 4.12 0.00 34.69 2.94
6730 7978 5.106515 GGAAAGGTAATTCTGCACTGACTTC 60.107 44.000 0.00 0.00 0.00 3.01
6738 7986 4.077300 TCTGCACTGACTTCATGTTCTT 57.923 40.909 0.00 0.00 0.00 2.52
6740 7988 3.544684 TGCACTGACTTCATGTTCTTGT 58.455 40.909 0.00 0.00 0.00 3.16
6757 8005 8.603242 TGTTCTTGTATTCCTTTCTAGTTCAC 57.397 34.615 0.00 0.00 0.00 3.18
6785 8035 8.684386 TTCAATGTGTGTGATAGTAGGAAAAA 57.316 30.769 0.00 0.00 0.00 1.94
6972 8222 3.764466 AGAAGCCTCAGGTCGCGG 61.764 66.667 6.13 0.00 0.00 6.46
7037 8287 1.473080 GCAAACAACAACAGCCACCAT 60.473 47.619 0.00 0.00 0.00 3.55
7256 8517 5.648330 TCTTGGATAGGCAGTAGACTCTA 57.352 43.478 0.00 0.00 32.95 2.43
7261 8522 6.297582 TGGATAGGCAGTAGACTCTACTAAC 58.702 44.000 16.86 12.81 32.95 2.34
7264 8525 4.931914 AGGCAGTAGACTCTACTAACCAA 58.068 43.478 25.60 0.00 0.00 3.67
7346 8618 2.746277 ATTGGTGTTCGCCGGAGC 60.746 61.111 5.05 0.00 0.00 4.70
7407 8679 4.081642 TCCTGTACAAAGTATGACTGAGCC 60.082 45.833 0.00 0.00 0.00 4.70
7414 8686 1.291033 AGTATGACTGAGCCCCTGGTA 59.709 52.381 0.00 0.00 0.00 3.25
7434 8706 4.097589 GGTATTACTGTTACTGCGAGAGGT 59.902 45.833 0.00 0.00 0.00 3.85
7435 8707 3.844577 TTACTGTTACTGCGAGAGGTC 57.155 47.619 0.00 0.00 0.00 3.85
7436 8708 1.912417 ACTGTTACTGCGAGAGGTCT 58.088 50.000 0.00 0.00 0.00 3.85
7445 8717 4.996976 GAGAGGTCTCGCAGCAAA 57.003 55.556 0.00 0.00 32.78 3.68
7446 8718 2.450619 GAGAGGTCTCGCAGCAAAC 58.549 57.895 0.00 0.00 32.78 2.93
7447 8719 1.347817 GAGAGGTCTCGCAGCAAACG 61.348 60.000 0.00 0.00 32.78 3.60
7448 8720 2.357517 AGGTCTCGCAGCAAACGG 60.358 61.111 0.00 0.00 0.00 4.44
7449 8721 2.357034 GGTCTCGCAGCAAACGGA 60.357 61.111 0.00 0.00 0.00 4.69
7450 8722 1.959226 GGTCTCGCAGCAAACGGAA 60.959 57.895 0.00 0.00 0.00 4.30
7451 8723 1.204312 GTCTCGCAGCAAACGGAAC 59.796 57.895 0.00 0.00 0.00 3.62
7469 8741 0.629596 ACGGGGAGGAGACTATGACA 59.370 55.000 0.00 0.00 44.43 3.58
7479 8751 4.013728 GGAGACTATGACACTCTGTGACT 58.986 47.826 4.61 0.00 36.96 3.41
7492 8764 0.603065 TGTGACTGTGAGTGATCCCG 59.397 55.000 0.00 0.00 0.00 5.14
7493 8765 0.888619 GTGACTGTGAGTGATCCCGA 59.111 55.000 0.00 0.00 0.00 5.14
7494 8766 1.135257 GTGACTGTGAGTGATCCCGAG 60.135 57.143 0.00 0.00 0.00 4.63
7516 8788 3.135994 GAGAGTTTGTGTTAGGCGGAAA 58.864 45.455 0.00 0.00 0.00 3.13
7630 8902 2.287103 ACTTTTTCGTTCGACTGGCTTC 59.713 45.455 0.00 0.00 0.00 3.86
7653 8931 4.615223 CGGATTCTGTCGTTTCTCACACTA 60.615 45.833 0.00 0.00 0.00 2.74
7654 8932 5.227908 GGATTCTGTCGTTTCTCACACTAA 58.772 41.667 0.00 0.00 0.00 2.24
7658 8936 6.764877 TCTGTCGTTTCTCACACTAAAATC 57.235 37.500 0.00 0.00 0.00 2.17
7741 9020 6.238648 GCATTTGCGTAGTTATTTGACCCTAT 60.239 38.462 0.00 0.00 0.00 2.57
7795 9075 4.122337 TGTGAGACTGAAGGGTTAGGTA 57.878 45.455 0.00 0.00 0.00 3.08
7820 9100 3.551250 GCTAGCTCCTGACGGAATCTAAC 60.551 52.174 7.70 0.00 39.29 2.34
7830 9110 6.587990 CCTGACGGAATCTAACTGCATATAAG 59.412 42.308 0.00 0.00 0.00 1.73
7831 9111 5.926542 TGACGGAATCTAACTGCATATAAGC 59.073 40.000 0.00 0.00 0.00 3.09
7877 9166 4.100084 TGAGCCGTGGCCATCCTG 62.100 66.667 9.72 0.00 43.17 3.86
7878 9167 4.864334 GAGCCGTGGCCATCCTGG 62.864 72.222 9.72 10.47 43.17 4.45
7918 9207 4.484872 GGGGCTCCCTAACCGCAC 62.485 72.222 4.74 0.00 41.34 5.34
7927 9216 1.677552 CTAACCGCACCCCTTGTCT 59.322 57.895 0.00 0.00 0.00 3.41
7950 9239 1.670811 GTTACCCGGTCAAGCATCATG 59.329 52.381 0.00 0.00 0.00 3.07
8033 9323 2.184533 ACCGTCACTCCATCACCAATA 58.815 47.619 0.00 0.00 0.00 1.90
8133 9426 3.818961 AAAATCGCTGTCACTGACATG 57.181 42.857 12.34 8.47 41.94 3.21
8142 9435 4.800993 GCTGTCACTGACATGTAGTATGAC 59.199 45.833 12.34 18.32 41.94 3.06
8143 9436 5.622233 GCTGTCACTGACATGTAGTATGACA 60.622 44.000 22.95 22.95 41.94 3.58
8231 9524 2.143122 CAACACAGACCAGCACGTATT 58.857 47.619 0.00 0.00 0.00 1.89
8239 9532 4.024302 CAGACCAGCACGTATTAGTCGATA 60.024 45.833 0.00 0.00 0.00 2.92
8240 9533 4.577693 AGACCAGCACGTATTAGTCGATAA 59.422 41.667 0.00 0.00 0.00 1.75
8246 9539 8.757789 CCAGCACGTATTAGTCGATAATTAAAA 58.242 33.333 0.00 0.00 35.63 1.52
8247 9540 9.779237 CAGCACGTATTAGTCGATAATTAAAAG 57.221 33.333 0.00 0.00 35.63 2.27
8248 9541 8.975439 AGCACGTATTAGTCGATAATTAAAAGG 58.025 33.333 0.00 0.00 35.63 3.11
8249 9542 7.739043 GCACGTATTAGTCGATAATTAAAAGGC 59.261 37.037 0.00 0.00 35.63 4.35
8250 9543 7.943065 CACGTATTAGTCGATAATTAAAAGGCG 59.057 37.037 0.00 0.00 35.63 5.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
26 27 2.925724 ACGTTGTTCATGGGAAGACAA 58.074 42.857 0.00 0.00 32.62 3.18
99 100 1.846439 AGTTGGGATTCCGGATGTCAT 59.154 47.619 4.15 0.00 35.24 3.06
106 107 1.616159 AACACAAGTTGGGATTCCGG 58.384 50.000 13.26 0.00 36.39 5.14
138 139 1.870402 CATGGTATTATGGCAACGCGA 59.130 47.619 15.93 0.00 42.51 5.87
143 144 5.122707 TGGAGTTCATGGTATTATGGCAA 57.877 39.130 0.00 0.00 0.00 4.52
204 205 2.025863 GCCTTGGAGAATGGATGTGGG 61.026 57.143 0.00 0.00 0.00 4.61
207 208 1.213926 GAGGCCTTGGAGAATGGATGT 59.786 52.381 6.77 0.00 0.00 3.06
208 209 1.213678 TGAGGCCTTGGAGAATGGATG 59.786 52.381 6.77 0.00 0.00 3.51
209 210 1.600058 TGAGGCCTTGGAGAATGGAT 58.400 50.000 6.77 0.00 0.00 3.41
210 211 1.213678 CATGAGGCCTTGGAGAATGGA 59.786 52.381 6.77 0.00 0.00 3.41
309 313 1.191096 GTGCTTTCACGTGTGCAAAG 58.809 50.000 25.41 22.25 37.17 2.77
334 338 9.612066 TTTGCTATTCTTCCAGAAAACATTTTT 57.388 25.926 0.00 0.00 37.82 1.94
380 384 7.754069 TCTTGTTTTCATGTTTTGCAGTAAG 57.246 32.000 0.00 0.00 0.00 2.34
386 390 9.801714 CTTCATATTCTTGTTTTCATGTTTTGC 57.198 29.630 0.00 0.00 0.00 3.68
474 479 5.237344 CGTTCATGAACATTCCTAGGAATCC 59.763 44.000 30.52 22.11 42.30 3.01
488 493 5.732647 CCATAATTCGTGTTCGTTCATGAAC 59.267 40.000 25.68 25.68 46.63 3.18
503 508 6.363577 AGCAATGTACTCAACCATAATTCG 57.636 37.500 0.00 0.00 0.00 3.34
641 647 7.673926 ACATGACAATGTACCTTTTTAAGGGAT 59.326 33.333 10.05 0.00 45.27 3.85
697 703 8.635765 TTAGTTTGCTCTTGTAATGGAATTCT 57.364 30.769 5.23 0.00 37.87 2.40
698 704 9.691362 TTTTAGTTTGCTCTTGTAATGGAATTC 57.309 29.630 0.00 0.00 37.87 2.17
699 705 9.696917 CTTTTAGTTTGCTCTTGTAATGGAATT 57.303 29.630 0.00 0.00 41.28 2.17
719 731 2.149973 ATTCCTGGCCCTGCTTTTAG 57.850 50.000 0.00 0.00 0.00 1.85
774 786 2.600729 CCCTCAGGGCTGCAACTCT 61.601 63.158 0.00 0.00 35.35 3.24
802 814 1.460590 CGCGCATGTTTGTGAAATTGC 60.461 47.619 8.75 0.00 35.26 3.56
818 831 3.249973 AAAAAGGAACGAGCCGCGC 62.250 57.895 0.00 0.00 46.04 6.86
842 855 7.795272 GCCAATACACGAACCGTATTTATAAAG 59.205 37.037 3.94 0.00 38.32 1.85
844 857 6.202570 GGCCAATACACGAACCGTATTTATAA 59.797 38.462 0.00 0.00 38.32 0.98
862 1116 2.447765 CCTCCCCCTCGGCCAATA 60.448 66.667 2.24 0.00 0.00 1.90
874 1128 4.537433 CAGCTAGCGGCACCTCCC 62.537 72.222 9.55 0.00 44.79 4.30
984 1247 4.119363 ATGCAGCAGGGCCGTCAT 62.119 61.111 0.00 0.00 0.00 3.06
987 1250 4.666253 AACATGCAGCAGGGCCGT 62.666 61.111 12.54 0.00 0.00 5.68
1027 1291 1.705450 TAGGGAGGGAGAGAGGGGG 60.705 68.421 0.00 0.00 0.00 5.40
1028 1292 1.002242 ACTAGGGAGGGAGAGAGGGG 61.002 65.000 0.00 0.00 0.00 4.79
1032 1296 1.383963 ACACACTAGGGAGGGAGAGA 58.616 55.000 0.00 0.00 0.00 3.10
1050 1314 3.185391 GCAACAGACTAGCAGAACAGAAC 59.815 47.826 0.00 0.00 0.00 3.01
1102 1377 2.544685 CGGCTGGTGATAACAAGAGAG 58.455 52.381 0.00 0.00 0.00 3.20
1103 1378 1.207089 CCGGCTGGTGATAACAAGAGA 59.793 52.381 2.29 0.00 0.00 3.10
1135 1410 2.334946 GCTCGTTGCTGCAATGGGA 61.335 57.895 32.65 21.19 33.04 4.37
1136 1411 2.180017 GCTCGTTGCTGCAATGGG 59.820 61.111 28.58 27.45 38.95 4.00
1138 1413 2.180017 GGGCTCGTTGCTGCAATG 59.820 61.111 24.86 24.86 42.39 2.82
1139 1414 2.282391 TGGGCTCGTTGCTGCAAT 60.282 55.556 19.11 0.00 42.39 3.56
1140 1415 2.979676 CTGGGCTCGTTGCTGCAA 60.980 61.111 11.69 11.69 42.39 4.08
1142 1417 3.123620 CTCTGGGCTCGTTGCTGC 61.124 66.667 0.00 0.00 42.39 5.25
1144 1419 3.602513 CTGCTCTGGGCTCGTTGCT 62.603 63.158 0.00 0.00 42.39 3.91
1145 1420 3.123620 CTGCTCTGGGCTCGTTGC 61.124 66.667 0.00 0.00 42.39 4.17
1146 1421 3.123620 GCTGCTCTGGGCTCGTTG 61.124 66.667 0.00 0.00 42.39 4.10
1147 1422 4.749310 CGCTGCTCTGGGCTCGTT 62.749 66.667 0.00 0.00 42.39 3.85
1176 1451 1.001974 TGAACAACTCACCCAGATCGG 59.998 52.381 0.00 0.00 0.00 4.18
1177 1452 2.455674 TGAACAACTCACCCAGATCG 57.544 50.000 0.00 0.00 0.00 3.69
1179 1454 2.355108 CGGATGAACAACTCACCCAGAT 60.355 50.000 0.00 0.00 37.65 2.90
1180 1455 1.001974 CGGATGAACAACTCACCCAGA 59.998 52.381 0.00 0.00 37.65 3.86
1181 1456 1.270839 ACGGATGAACAACTCACCCAG 60.271 52.381 0.00 0.00 37.65 4.45
1182 1457 0.762418 ACGGATGAACAACTCACCCA 59.238 50.000 0.00 0.00 37.65 4.51
1219 1531 0.944311 GCACAGGCGAAACGAGAGAA 60.944 55.000 0.00 0.00 0.00 2.87
1221 1533 3.159984 GCACAGGCGAAACGAGAG 58.840 61.111 0.00 0.00 0.00 3.20
1324 1641 1.432270 GGCATCGGAACTACTGCTGC 61.432 60.000 0.00 0.00 43.65 5.25
1325 1642 1.148157 CGGCATCGGAACTACTGCTG 61.148 60.000 1.10 0.00 35.03 4.41
1326 1643 1.141881 CGGCATCGGAACTACTGCT 59.858 57.895 1.10 0.00 35.03 4.24
1327 1644 3.706140 CGGCATCGGAACTACTGC 58.294 61.111 0.00 0.00 0.00 4.40
1361 1678 4.791069 ATACGGACCGGCCACCCT 62.791 66.667 20.00 0.00 35.94 4.34
1362 1679 4.540735 CATACGGACCGGCCACCC 62.541 72.222 20.00 0.00 35.94 4.61
1363 1680 4.540735 CCATACGGACCGGCCACC 62.541 72.222 20.00 1.41 35.94 4.61
1364 1681 4.540735 CCCATACGGACCGGCCAC 62.541 72.222 20.00 0.00 35.94 5.01
1370 1687 3.021473 TTCACGGCCCATACGGACC 62.021 63.158 0.00 0.00 35.34 4.46
1371 1688 1.812507 GTTCACGGCCCATACGGAC 60.813 63.158 0.00 0.00 35.51 4.79
1372 1689 2.580276 GTTCACGGCCCATACGGA 59.420 61.111 0.00 0.00 35.23 4.69
1373 1690 2.888534 CGTTCACGGCCCATACGG 60.889 66.667 0.00 0.00 35.37 4.02
1392 1709 0.598680 GAGAAGGCCGGATCGTGATG 60.599 60.000 5.05 0.00 0.00 3.07
1457 1780 5.538433 ACAACAGGAAAATAAGCTTAGCCAA 59.462 36.000 12.54 0.00 0.00 4.52
1459 1782 5.644977 ACAACAGGAAAATAAGCTTAGCC 57.355 39.130 12.54 10.20 0.00 3.93
1463 1786 8.919777 ACTACTAACAACAGGAAAATAAGCTT 57.080 30.769 3.48 3.48 0.00 3.74
1464 1787 9.654663 CTACTACTAACAACAGGAAAATAAGCT 57.345 33.333 0.00 0.00 0.00 3.74
1465 1788 9.649167 TCTACTACTAACAACAGGAAAATAAGC 57.351 33.333 0.00 0.00 0.00 3.09
1530 1857 3.557508 CAAAAACCGTAATCACGTTCCC 58.442 45.455 0.00 0.00 46.96 3.97
1547 1879 4.449068 TCACAAAAAGTTTCAAGCGCAAAA 59.551 33.333 11.47 4.15 0.00 2.44
1568 1900 3.406512 TCCTCCCCCTTTTTGTTTTCA 57.593 42.857 0.00 0.00 0.00 2.69
1569 1901 4.974645 ATTCCTCCCCCTTTTTGTTTTC 57.025 40.909 0.00 0.00 0.00 2.29
1572 1904 3.394274 CCAAATTCCTCCCCCTTTTTGTT 59.606 43.478 0.00 0.00 0.00 2.83
1574 1906 2.305635 CCCAAATTCCTCCCCCTTTTTG 59.694 50.000 0.00 0.00 0.00 2.44
1595 1927 2.098233 CGTCATACACACACGCCCC 61.098 63.158 0.00 0.00 0.00 5.80
1597 1929 0.437295 GTTCGTCATACACACACGCC 59.563 55.000 0.00 0.00 33.46 5.68
1599 1931 0.706184 CCGTTCGTCATACACACACG 59.294 55.000 0.00 0.00 34.78 4.49
1683 2031 3.077519 GCGTCAGTGGGATAGCCGT 62.078 63.158 0.00 0.00 33.83 5.68
1785 2137 2.744768 GCTTTTCCTCTCGCGCTGG 61.745 63.158 5.56 3.02 0.00 4.85
1786 2138 1.964290 CTGCTTTTCCTCTCGCGCTG 61.964 60.000 5.56 0.00 0.00 5.18
1787 2139 1.739562 CTGCTTTTCCTCTCGCGCT 60.740 57.895 5.56 0.00 0.00 5.92
1788 2140 2.781300 CTGCTTTTCCTCTCGCGC 59.219 61.111 0.00 0.00 0.00 6.86
1789 2141 2.781300 GCTGCTTTTCCTCTCGCG 59.219 61.111 0.00 0.00 0.00 5.87
1790 2142 2.781300 CGCTGCTTTTCCTCTCGC 59.219 61.111 0.00 0.00 0.00 5.03
1791 2143 1.568612 TTGCGCTGCTTTTCCTCTCG 61.569 55.000 9.73 0.00 0.00 4.04
1792 2144 0.807496 ATTGCGCTGCTTTTCCTCTC 59.193 50.000 9.73 0.00 0.00 3.20
1793 2145 1.251251 AATTGCGCTGCTTTTCCTCT 58.749 45.000 9.73 0.00 0.00 3.69
1794 2146 2.919666 TAATTGCGCTGCTTTTCCTC 57.080 45.000 9.73 0.00 0.00 3.71
1795 2147 2.094545 CCTTAATTGCGCTGCTTTTCCT 60.095 45.455 9.73 0.00 0.00 3.36
1796 2148 2.262211 CCTTAATTGCGCTGCTTTTCC 58.738 47.619 9.73 0.00 0.00 3.13
1797 2149 1.655597 GCCTTAATTGCGCTGCTTTTC 59.344 47.619 9.73 0.00 0.00 2.29
1798 2150 1.672737 GGCCTTAATTGCGCTGCTTTT 60.673 47.619 9.73 0.00 0.00 2.27
1934 2290 2.506438 GAGAAACGAGACGGCCCG 60.506 66.667 0.00 0.00 0.00 6.13
2062 2418 4.259356 TCTTCTTCTGCTGATGATGTTGG 58.741 43.478 16.34 5.57 0.00 3.77
2578 2940 0.040336 GCAGGATTCTGATGCATGCG 60.040 55.000 14.09 0.00 43.49 4.73
2603 2965 6.654582 TCAGAAAAATTCAGTACATGCAGCTA 59.345 34.615 0.00 0.00 0.00 3.32
2620 2985 3.629855 TCACACCTGCGAATTCAGAAAAA 59.370 39.130 6.22 0.00 36.19 1.94
2629 2994 1.003580 ACATCCTTCACACCTGCGAAT 59.996 47.619 0.00 0.00 0.00 3.34
2760 3125 5.596361 TGGTTCAGTTGACACCAAATATGTT 59.404 36.000 11.29 0.00 34.60 2.71
2770 3135 5.527582 ACTGTTCTATTGGTTCAGTTGACAC 59.472 40.000 0.00 0.00 36.17 3.67
2804 3169 4.683320 AGAACGAACTAGAGCGGTAAAAAC 59.317 41.667 0.00 0.00 0.00 2.43
2942 3307 1.153549 GTAGTGGAAGAGCGGCCAG 60.154 63.158 2.24 0.00 34.22 4.85
2996 3361 0.241481 ACTGCGACTCGAAGTTCCTC 59.759 55.000 6.22 0.00 44.06 3.71
2997 3362 2.342478 ACTGCGACTCGAAGTTCCT 58.658 52.632 6.22 0.00 44.06 3.36
3086 3451 1.210234 TGGTAGTCATGGCACCAGATG 59.790 52.381 14.98 0.00 37.42 2.90
3206 3573 4.147449 TCCGAGCGTGATGGCAGG 62.147 66.667 0.00 0.00 35.27 4.85
3492 3878 1.739466 CCACTGATCCCAAACATGTCG 59.261 52.381 0.00 0.00 0.00 4.35
3577 4420 7.215719 TCGTAATGAGATGTAGGAATAGGTG 57.784 40.000 0.00 0.00 0.00 4.00
3627 4470 9.283768 GTAAAAAGAATCACCCATTTTCCAAAT 57.716 29.630 0.00 0.00 0.00 2.32
3894 5094 2.162681 GGACAGAAATGGAAGTGTGGG 58.837 52.381 0.00 0.00 0.00 4.61
3895 5095 2.816087 CAGGACAGAAATGGAAGTGTGG 59.184 50.000 0.00 0.00 0.00 4.17
3938 5140 9.444600 TGGTTTATAAGTTTGTAGGTCAAGATC 57.555 33.333 0.00 0.00 37.35 2.75
4064 5271 5.509498 ACACCAAGCATTACCTATGACAAT 58.491 37.500 0.00 0.00 36.26 2.71
4184 5391 1.528161 GTTGGCACAGCAATTTGAAGC 59.472 47.619 0.00 0.00 42.39 3.86
4307 5514 3.316308 AGCAAGCTGACGAATTGAAAACT 59.684 39.130 0.00 0.00 0.00 2.66
4318 5525 1.506493 AAAGAGACAGCAAGCTGACG 58.494 50.000 27.17 2.67 46.30 4.35
4949 6180 3.497262 GGAGACTGTGTAAAAGAAACGGG 59.503 47.826 0.00 0.00 0.00 5.28
5113 6345 6.380560 TCTCTCTCTCATCAGATGTCATTGTT 59.619 38.462 10.34 0.00 0.00 2.83
5257 6500 9.405587 TGACGATGAAAAAGAAACATTTAATCC 57.594 29.630 0.00 0.00 0.00 3.01
5279 6522 7.587757 GGAGCAGCTAACAAATTTATATTGACG 59.412 37.037 0.00 0.00 0.00 4.35
5282 6525 7.715657 TGGGAGCAGCTAACAAATTTATATTG 58.284 34.615 0.00 0.00 0.00 1.90
5304 6547 3.564225 GTGTGGTTACAAGAAAGTCTGGG 59.436 47.826 0.00 0.00 38.82 4.45
5327 6570 4.960938 AGCTCACTACATGAAAAGACACA 58.039 39.130 0.00 0.00 36.69 3.72
5328 6571 7.291567 GTTTAGCTCACTACATGAAAAGACAC 58.708 38.462 0.00 0.00 36.69 3.67
5409 6654 2.203070 GCTGGATGGCCGTTCGAT 60.203 61.111 0.00 0.00 36.79 3.59
5501 6746 4.634004 TGATGGCCAGTATAAACAACTTCG 59.366 41.667 13.05 0.00 0.00 3.79
5614 6861 8.667463 CCATTCATTTAGTTTAAAATGCAAGGG 58.333 33.333 0.00 7.29 43.49 3.95
5670 6917 8.770828 GTTTGAGTGCTAAGTTCATTGTACTAA 58.229 33.333 0.00 0.00 0.00 2.24
5698 6945 7.346751 ACAAACAGAAATTGTAAGGTCATGT 57.653 32.000 0.00 0.00 39.73 3.21
5833 7080 4.246458 CTCTCAAAGGACCCTTTAAGTCG 58.754 47.826 13.18 2.26 43.56 4.18
5938 7185 5.458041 ACAAATCACAAAATGACAGGAGG 57.542 39.130 0.00 0.00 41.24 4.30
6104 7351 1.065491 TCGACCCAATCCATGTTCAGG 60.065 52.381 0.00 0.00 0.00 3.86
6138 7385 3.425359 GGACATTGCTCATCAAACAGACG 60.425 47.826 0.00 0.00 38.34 4.18
6201 7448 7.771183 AGTACTCAAAAACATGCTGAAAAAGA 58.229 30.769 0.00 0.00 0.00 2.52
6207 7454 5.588246 TGTGAAGTACTCAAAAACATGCTGA 59.412 36.000 0.00 0.00 35.22 4.26
6264 7511 4.858935 AGTTCCACACAAATGATGTTTCG 58.141 39.130 0.00 0.00 41.46 3.46
6363 7610 1.862201 CACAACAGGCAAGTGCAAATG 59.138 47.619 5.52 3.51 44.36 2.32
6378 7625 4.338118 TCCCAAACTCAACATCTTCACAAC 59.662 41.667 0.00 0.00 0.00 3.32
6487 7734 1.264288 CCAACAGAGCGAACTTCAACC 59.736 52.381 0.00 0.00 0.00 3.77
6533 7780 7.042791 ACAAGCTTTCACCATGTTTAAAAATCG 60.043 33.333 0.00 0.00 0.00 3.34
6583 7831 9.632807 CAGAACGGAAATGAATAATTGGTAAAA 57.367 29.630 0.00 0.00 0.00 1.52
6666 7914 6.971602 ACATAGTACATAGTCAATCGGAGTG 58.028 40.000 0.00 0.00 0.00 3.51
6730 7978 9.219603 TGAACTAGAAAGGAATACAAGAACATG 57.780 33.333 0.00 0.00 0.00 3.21
6738 7986 8.190326 TGAAGAGTGAACTAGAAAGGAATACA 57.810 34.615 0.00 0.00 0.00 2.29
6740 7988 9.658799 CATTGAAGAGTGAACTAGAAAGGAATA 57.341 33.333 0.00 0.00 0.00 1.75
6757 8005 6.867550 TCCTACTATCACACACATTGAAGAG 58.132 40.000 0.00 0.00 0.00 2.85
6785 8035 8.792633 TCGTCCTGAAAAGATAAAATTTCACAT 58.207 29.630 0.00 0.00 39.81 3.21
6887 8137 2.266055 CCGTTCTGCCTCCTGTCC 59.734 66.667 0.00 0.00 0.00 4.02
7037 8287 4.373116 GACCCTTCGCGCCAGTCA 62.373 66.667 0.00 0.00 0.00 3.41
7256 8517 1.884928 GCCGGGTGATTGTTGGTTAGT 60.885 52.381 2.18 0.00 0.00 2.24
7261 8522 3.439540 CGGCCGGGTGATTGTTGG 61.440 66.667 20.10 0.00 0.00 3.77
7407 8679 3.131577 TCGCAGTAACAGTAATACCAGGG 59.868 47.826 0.00 0.00 0.00 4.45
7414 8686 4.017808 AGACCTCTCGCAGTAACAGTAAT 58.982 43.478 0.00 0.00 0.00 1.89
7434 8706 2.307309 CGTTCCGTTTGCTGCGAGA 61.307 57.895 0.00 0.00 0.00 4.04
7435 8707 2.170985 CGTTCCGTTTGCTGCGAG 59.829 61.111 0.00 0.00 0.00 5.03
7436 8708 3.342627 CCGTTCCGTTTGCTGCGA 61.343 61.111 0.00 0.00 0.00 5.10
7438 8710 4.038080 CCCCGTTCCGTTTGCTGC 62.038 66.667 0.00 0.00 0.00 5.25
7439 8711 2.281208 TCCCCGTTCCGTTTGCTG 60.281 61.111 0.00 0.00 0.00 4.41
7440 8712 2.032071 CTCCCCGTTCCGTTTGCT 59.968 61.111 0.00 0.00 0.00 3.91
7441 8713 3.053896 CCTCCCCGTTCCGTTTGC 61.054 66.667 0.00 0.00 0.00 3.68
7442 8714 1.375523 CTCCTCCCCGTTCCGTTTG 60.376 63.158 0.00 0.00 0.00 2.93
7443 8715 1.534717 TCTCCTCCCCGTTCCGTTT 60.535 57.895 0.00 0.00 0.00 3.60
7444 8716 2.118951 TCTCCTCCCCGTTCCGTT 59.881 61.111 0.00 0.00 0.00 4.44
7445 8717 1.856539 TAGTCTCCTCCCCGTTCCGT 61.857 60.000 0.00 0.00 0.00 4.69
7446 8718 0.467659 ATAGTCTCCTCCCCGTTCCG 60.468 60.000 0.00 0.00 0.00 4.30
7447 8719 1.041437 CATAGTCTCCTCCCCGTTCC 58.959 60.000 0.00 0.00 0.00 3.62
7448 8720 1.682323 GTCATAGTCTCCTCCCCGTTC 59.318 57.143 0.00 0.00 0.00 3.95
7449 8721 1.006758 TGTCATAGTCTCCTCCCCGTT 59.993 52.381 0.00 0.00 0.00 4.44
7450 8722 0.629596 TGTCATAGTCTCCTCCCCGT 59.370 55.000 0.00 0.00 0.00 5.28
7451 8723 1.033574 GTGTCATAGTCTCCTCCCCG 58.966 60.000 0.00 0.00 0.00 5.73
7452 8724 2.091555 AGAGTGTCATAGTCTCCTCCCC 60.092 54.545 0.00 0.00 33.76 4.81
7453 8725 2.955660 CAGAGTGTCATAGTCTCCTCCC 59.044 54.545 0.00 0.00 36.95 4.30
7454 8726 3.380004 CACAGAGTGTCATAGTCTCCTCC 59.620 52.174 0.00 0.00 36.95 4.30
7455 8727 4.095782 GTCACAGAGTGTCATAGTCTCCTC 59.904 50.000 0.00 0.00 36.95 3.71
7456 8728 4.013728 GTCACAGAGTGTCATAGTCTCCT 58.986 47.826 0.00 0.00 36.95 3.69
7457 8729 4.013728 AGTCACAGAGTGTCATAGTCTCC 58.986 47.826 0.00 0.00 36.95 3.71
7458 8730 4.457603 ACAGTCACAGAGTGTCATAGTCTC 59.542 45.833 1.79 0.00 41.73 3.36
7459 8731 4.217334 CACAGTCACAGAGTGTCATAGTCT 59.783 45.833 4.59 0.00 43.37 3.24
7460 8732 4.216472 TCACAGTCACAGAGTGTCATAGTC 59.784 45.833 4.59 0.00 43.37 2.59
7461 8733 4.145052 TCACAGTCACAGAGTGTCATAGT 58.855 43.478 4.59 0.00 43.37 2.12
7462 8734 4.217334 ACTCACAGTCACAGAGTGTCATAG 59.783 45.833 4.59 5.95 43.37 2.23
7463 8735 4.145052 ACTCACAGTCACAGAGTGTCATA 58.855 43.478 4.59 0.00 43.37 2.15
7464 8736 2.961741 ACTCACAGTCACAGAGTGTCAT 59.038 45.455 4.59 0.00 43.37 3.06
7469 8741 2.560542 GGATCACTCACAGTCACAGAGT 59.439 50.000 0.00 0.00 42.97 3.24
7479 8751 0.331616 TCTCCTCGGGATCACTCACA 59.668 55.000 0.00 0.00 0.00 3.58
7492 8764 2.338500 CGCCTAACACAAACTCTCCTC 58.662 52.381 0.00 0.00 0.00 3.71
7493 8765 1.002087 CCGCCTAACACAAACTCTCCT 59.998 52.381 0.00 0.00 0.00 3.69
7494 8766 1.001633 TCCGCCTAACACAAACTCTCC 59.998 52.381 0.00 0.00 0.00 3.71
7608 8880 1.865340 AGCCAGTCGAACGAAAAAGTC 59.135 47.619 0.00 0.00 0.00 3.01
7609 8881 1.949465 AGCCAGTCGAACGAAAAAGT 58.051 45.000 0.00 0.00 0.00 2.66
7610 8882 2.659291 CGAAGCCAGTCGAACGAAAAAG 60.659 50.000 0.00 0.00 43.86 2.27
7611 8883 1.259507 CGAAGCCAGTCGAACGAAAAA 59.740 47.619 0.00 0.00 43.86 1.94
7630 8902 2.408704 GTGTGAGAAACGACAGAATCCG 59.591 50.000 0.00 0.00 0.00 4.18
7653 8931 8.814931 TGTAATTGGATCATGAACCAAGATTTT 58.185 29.630 32.73 25.61 46.95 1.82
7654 8932 8.253113 GTGTAATTGGATCATGAACCAAGATTT 58.747 33.333 32.73 25.88 46.95 2.17
7658 8936 6.151648 ACAGTGTAATTGGATCATGAACCAAG 59.848 38.462 32.73 22.68 46.95 3.61
7677 8955 4.935495 CCTGCGTGGCCACAGTGT 62.935 66.667 34.16 0.00 31.76 3.55
7771 9051 3.515502 CCTAACCCTTCAGTCTCACATCA 59.484 47.826 0.00 0.00 0.00 3.07
7795 9075 1.000771 TCCGTCAGGAGCTAGCTGT 60.001 57.895 24.99 6.11 42.75 4.40
7830 9110 9.937175 CTTACTATAGAAGTTTTATTTGCCTGC 57.063 33.333 6.78 0.00 39.80 4.85
7877 9166 0.985490 AGCAAGTCATCCTCCCTCCC 60.985 60.000 0.00 0.00 0.00 4.30
7878 9167 0.179936 CAGCAAGTCATCCTCCCTCC 59.820 60.000 0.00 0.00 0.00 4.30
7879 9168 0.908198 ACAGCAAGTCATCCTCCCTC 59.092 55.000 0.00 0.00 0.00 4.30
7880 9169 0.617413 CACAGCAAGTCATCCTCCCT 59.383 55.000 0.00 0.00 0.00 4.20
7918 9207 1.376812 GGGTAACGCAGACAAGGGG 60.377 63.158 0.00 0.00 37.60 4.79
7927 9216 2.357760 GCTTGACCGGGTAACGCA 60.358 61.111 6.32 0.00 42.52 5.24
7950 9239 1.062587 CAACCAATCATTCGCGACCTC 59.937 52.381 9.15 0.00 0.00 3.85
8047 9340 2.199208 TGATTGCAAGAGAGGGATGGA 58.801 47.619 4.94 0.00 0.00 3.41
8077 9370 4.902443 TCGTTATCTGCTTCTAGGACAG 57.098 45.455 0.00 0.00 0.00 3.51
8133 9426 8.774586 AGAAACAAAACTGACATGTCATACTAC 58.225 33.333 28.00 13.17 39.13 2.73
8142 9435 7.329226 ACTTGTGAAAGAAACAAAACTGACATG 59.671 33.333 0.00 0.00 37.10 3.21
8143 9436 7.378181 ACTTGTGAAAGAAACAAAACTGACAT 58.622 30.769 0.00 0.00 37.10 3.06
8145 9438 8.911247 ATACTTGTGAAAGAAACAAAACTGAC 57.089 30.769 0.00 0.00 37.10 3.51


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

AutoCloner maintained by Alex Coulton.