Multiple sequence alignment - TraesCS7D01G140200

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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 TraesCS7D01G140200 chr7D 100.000 8782 0 0 1 8782 89606808 89598027 0.000000e+00 16218.0
1 TraesCS7D01G140200 chr7D 85.043 702 73 22 8084 8775 89523667 89522988 0.000000e+00 686.0
2 TraesCS7D01G140200 chr7D 85.174 688 75 23 8101 8775 89487795 89487122 0.000000e+00 680.0
3 TraesCS7D01G140200 chr7D 84.810 474 58 13 8312 8775 89730579 89731048 1.730000e-126 464.0
4 TraesCS7D01G140200 chr7D 85.266 414 47 10 8369 8771 89790312 89790722 1.760000e-111 414.0
5 TraesCS7D01G140200 chr7D 82.698 341 27 20 7477 7812 89729944 89730257 3.120000e-69 274.0
6 TraesCS7D01G140200 chr7A 94.324 4933 188 36 3412 8314 90621338 90616468 0.000000e+00 7474.0
7 TraesCS7D01G140200 chr7A 88.981 2169 132 50 710 2831 90624155 90622047 0.000000e+00 2582.0
8 TraesCS7D01G140200 chr7A 93.888 589 34 2 2829 3416 90622004 90621417 0.000000e+00 887.0
9 TraesCS7D01G140200 chr7A 85.675 719 72 16 1 697 90624985 90624276 0.000000e+00 728.0
10 TraesCS7D01G140200 chr7A 84.113 705 82 20 8087 8775 90587882 90587192 0.000000e+00 654.0
11 TraesCS7D01G140200 chr7A 80.591 711 89 33 8086 8764 622950270 622950963 3.660000e-138 503.0
12 TraesCS7D01G140200 chr7A 90.331 362 34 1 8415 8775 90663981 90664342 2.870000e-129 473.0
13 TraesCS7D01G140200 chr7A 82.203 354 37 19 7464 7812 90663222 90663554 1.870000e-71 281.0
14 TraesCS7D01G140200 chr7B 94.983 4166 147 25 2829 6969 40358247 40354119 0.000000e+00 6479.0
15 TraesCS7D01G140200 chr7B 91.180 1848 108 25 6952 8774 40353938 40352121 0.000000e+00 2459.0
16 TraesCS7D01G140200 chr7B 93.577 903 44 8 1937 2835 40359176 40358284 0.000000e+00 1334.0
17 TraesCS7D01G140200 chr7B 84.162 1187 91 39 1 1110 40361395 40360229 0.000000e+00 1061.0
18 TraesCS7D01G140200 chr7B 85.601 632 31 31 1241 1844 40359809 40359210 7.540000e-170 608.0
19 TraesCS7D01G140200 chr7B 88.432 389 40 5 8390 8775 40442663 40443049 1.730000e-126 464.0
20 TraesCS7D01G140200 chr7B 83.754 357 28 18 7464 7812 40441935 40442269 2.380000e-80 311.0
21 TraesCS7D01G140200 chr7B 85.526 228 31 2 7550 7777 40557328 40557553 4.100000e-58 237.0
22 TraesCS7D01G140200 chr1D 100.000 31 0 0 1367 1397 50033873 50033843 3.420000e-04 58.4


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 TraesCS7D01G140200 chr7D 89598027 89606808 8781 True 16218.00 16218 100.0000 1 8782 1 chr7D.!!$R3 8781
1 TraesCS7D01G140200 chr7D 89522988 89523667 679 True 686.00 686 85.0430 8084 8775 1 chr7D.!!$R2 691
2 TraesCS7D01G140200 chr7D 89487122 89487795 673 True 680.00 680 85.1740 8101 8775 1 chr7D.!!$R1 674
3 TraesCS7D01G140200 chr7D 89729944 89731048 1104 False 369.00 464 83.7540 7477 8775 2 chr7D.!!$F2 1298
4 TraesCS7D01G140200 chr7A 90616468 90624985 8517 True 2917.75 7474 90.7170 1 8314 4 chr7A.!!$R2 8313
5 TraesCS7D01G140200 chr7A 90587192 90587882 690 True 654.00 654 84.1130 8087 8775 1 chr7A.!!$R1 688
6 TraesCS7D01G140200 chr7A 622950270 622950963 693 False 503.00 503 80.5910 8086 8764 1 chr7A.!!$F1 678
7 TraesCS7D01G140200 chr7A 90663222 90664342 1120 False 377.00 473 86.2670 7464 8775 2 chr7A.!!$F2 1311
8 TraesCS7D01G140200 chr7B 40352121 40361395 9274 True 2388.20 6479 89.9006 1 8774 5 chr7B.!!$R1 8773
9 TraesCS7D01G140200 chr7B 40441935 40443049 1114 False 387.50 464 86.0930 7464 8775 2 chr7B.!!$F2 1311

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
582 610 0.242825 TGTCCGTGAGTTCGTCCATC 59.757 55.0 0.00 0.00 0.00 3.51 F
1989 2487 0.468226 TGTGGGTGAGTGGTGTCTTC 59.532 55.0 0.00 0.00 0.00 2.87 F
2645 3160 0.475044 TACAAGGTCGGGCCACTTTT 59.525 50.0 4.39 0.33 40.61 2.27 F
3848 4494 1.149148 GTGCCCTTCGAGAAGTTGAC 58.851 55.0 11.38 1.99 36.72 3.18 F
5534 6205 1.649664 CTTCAACCTCATCAGCTCCG 58.350 55.0 0.00 0.00 0.00 4.63 F
6698 7382 0.678395 CTGCTGTGGCCGAGATAGAT 59.322 55.0 5.77 0.00 37.74 1.98 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2355 2868 0.238553 GAACGGTTCCAGCTTTGCTC 59.761 55.000 9.75 0.0 36.40 4.26 R
3420 4065 1.715931 AGGACAAACCATCCATCCCAA 59.284 47.619 0.00 0.0 42.04 4.12 R
4177 4837 1.002274 AGGGGAGACTAGCCTGGTG 59.998 63.158 0.00 0.0 0.00 4.17 R
5714 6388 0.249911 AGAACTTCTCACCACGTGCC 60.250 55.000 10.91 0.0 32.98 5.01 R
6912 7597 1.725931 GCGACGGCAGTTTCATTTGAG 60.726 52.381 0.00 0.0 39.62 3.02 R
8442 9455 0.179073 ATGGGATCGGTTGAGCTTCG 60.179 55.000 0.00 0.0 0.00 3.79 R

All possible primers

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

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
61 72 5.936686 ATGAAATTACCTCGATCTGCATG 57.063 39.130 0.00 0.00 0.00 4.06
110 121 2.265467 TTTAGGCATCCCTCCCGCAC 62.265 60.000 0.00 0.00 41.75 5.34
121 132 1.392589 CTCCCGCACCATTAAGCATT 58.607 50.000 0.00 0.00 0.00 3.56
160 171 5.121768 ACTTGATTTATTGTACACACTCGCC 59.878 40.000 0.00 0.00 0.00 5.54
182 193 5.479027 GCCTAAAATTGGGACCAAACTTAGA 59.521 40.000 23.57 8.87 39.55 2.10
192 205 5.768164 GGGACCAAACTTAGACATCTTCAAA 59.232 40.000 0.00 0.00 0.00 2.69
195 208 7.228706 GGACCAAACTTAGACATCTTCAAAAGA 59.771 37.037 0.00 0.00 42.69 2.52
199 212 7.736447 AACTTAGACATCTTCAAAAGAGTGG 57.264 36.000 0.00 0.00 41.61 4.00
200 213 6.234177 ACTTAGACATCTTCAAAAGAGTGGG 58.766 40.000 0.00 0.00 41.61 4.61
273 286 9.651531 GCATATTAAACACGTTTTAAAATGTCG 57.348 29.630 20.41 17.42 36.05 4.35
274 287 9.651531 CATATTAAACACGTTTTAAAATGTCGC 57.348 29.630 20.41 0.00 36.05 5.19
296 309 9.437045 GTCGCAAAATTCAAAAGAAAATTTCAT 57.563 25.926 8.55 0.00 34.78 2.57
336 351 0.528017 TGCGTGGCACAAAGTTTTGA 59.472 45.000 19.09 0.00 44.16 2.69
377 393 4.379174 TGCCTCCGCAAAGAAGAC 57.621 55.556 0.00 0.00 43.74 3.01
379 395 0.884704 TGCCTCCGCAAAGAAGACAC 60.885 55.000 0.00 0.00 43.74 3.67
394 411 4.781071 GAAGACACATTTCAGTGCTTCTG 58.219 43.478 16.53 3.68 42.54 3.02
419 436 3.359654 AGCGTTTCACGACACATTTTTC 58.640 40.909 0.00 0.00 46.05 2.29
427 445 5.806286 TCACGACACATTTTTCTTTGTCTC 58.194 37.500 0.00 0.00 36.93 3.36
443 461 3.700538 TGTCTCTTTTGCATAGGCCAAT 58.299 40.909 5.01 0.00 40.13 3.16
452 470 3.282021 TGCATAGGCCAATGAAAGAGTC 58.718 45.455 5.01 0.00 40.13 3.36
467 485 3.320673 AGAGTCGCTTTTCCTCGAAAT 57.679 42.857 0.00 0.00 36.41 2.17
509 527 4.072839 TGTGACGATGTAAGAGTGAGACT 58.927 43.478 0.00 0.00 0.00 3.24
576 604 2.858344 GGTTCATATGTCCGTGAGTTCG 59.142 50.000 1.90 0.00 0.00 3.95
582 610 0.242825 TGTCCGTGAGTTCGTCCATC 59.757 55.000 0.00 0.00 0.00 3.51
588 616 2.069273 GTGAGTTCGTCCATCCACTTG 58.931 52.381 0.00 0.00 0.00 3.16
590 618 2.104111 TGAGTTCGTCCATCCACTTGTT 59.896 45.455 0.00 0.00 0.00 2.83
591 619 2.480419 GAGTTCGTCCATCCACTTGTTG 59.520 50.000 0.00 0.00 0.00 3.33
593 621 1.877637 TCGTCCATCCACTTGTTGTG 58.122 50.000 0.00 0.00 45.80 3.33
631 659 3.654020 GGCGCCTCCGATGCATTC 61.654 66.667 22.15 0.00 36.29 2.67
641 669 2.896685 TCCGATGCATTCCAACCTTTTT 59.103 40.909 0.00 0.00 0.00 1.94
642 670 3.056891 TCCGATGCATTCCAACCTTTTTC 60.057 43.478 0.00 0.00 0.00 2.29
643 671 3.305950 CCGATGCATTCCAACCTTTTTCA 60.306 43.478 0.00 0.00 0.00 2.69
646 674 5.540911 GATGCATTCCAACCTTTTTCAGAA 58.459 37.500 0.00 0.00 0.00 3.02
707 735 0.474184 CAAAGTCACAGTCACCCCCT 59.526 55.000 0.00 0.00 0.00 4.79
712 848 1.121407 TCACAGTCACCCCCTCACTG 61.121 60.000 0.00 0.00 42.80 3.66
735 871 9.030301 ACTGAAAAATCAAACTAAAATTCCACG 57.970 29.630 0.00 0.00 0.00 4.94
738 874 8.934507 AAAAATCAAACTAAAATTCCACGACA 57.065 26.923 0.00 0.00 0.00 4.35
811 947 2.160813 GGCGACGAATTTAGAAAAGGCA 59.839 45.455 0.00 0.00 0.00 4.75
912 1059 4.120589 GGCTTAATGCGCTCTTAGTAACT 58.879 43.478 9.73 0.00 44.05 2.24
951 1117 2.781681 TTAACTAACCCAGCTGAGCC 57.218 50.000 17.39 0.00 0.00 4.70
999 1171 1.458639 AAAGTTCTGGCTGTGGCTGC 61.459 55.000 0.00 0.00 38.73 5.25
1017 1189 3.106407 GCTGTGTGCGTCGTCTCC 61.106 66.667 0.00 0.00 0.00 3.71
1018 1190 2.430921 CTGTGTGCGTCGTCTCCC 60.431 66.667 0.00 0.00 0.00 4.30
1019 1191 3.916392 CTGTGTGCGTCGTCTCCCC 62.916 68.421 0.00 0.00 0.00 4.81
1020 1192 3.681835 GTGTGCGTCGTCTCCCCT 61.682 66.667 0.00 0.00 0.00 4.79
1021 1193 3.371063 TGTGCGTCGTCTCCCCTC 61.371 66.667 0.00 0.00 0.00 4.30
1121 1297 4.862823 CGACCTCCCCTCCTCCCC 62.863 77.778 0.00 0.00 0.00 4.81
1122 1298 4.500826 GACCTCCCCTCCTCCCCC 62.501 77.778 0.00 0.00 0.00 5.40
1142 1318 1.002274 GCCTCCTCCTCCTCTTCCA 59.998 63.158 0.00 0.00 0.00 3.53
1257 1723 4.463879 CTCCCTGAGGTGCGCCAG 62.464 72.222 20.59 7.95 37.19 4.85
1284 1750 4.413087 CTGCTTAATTTCTCTGCTGCTTG 58.587 43.478 0.00 0.00 0.00 4.01
1287 1753 4.673841 GCTTAATTTCTCTGCTGCTTGGAC 60.674 45.833 0.00 0.00 0.00 4.02
1291 1757 1.930251 TCTCTGCTGCTTGGACTAGT 58.070 50.000 0.00 0.00 0.00 2.57
1436 1903 1.112916 AGCCGTTTGTTTTCCTGGGG 61.113 55.000 0.00 0.00 0.00 4.96
1437 1904 1.365999 CCGTTTGTTTTCCTGGGGC 59.634 57.895 0.00 0.00 0.00 5.80
1438 1905 1.007849 CGTTTGTTTTCCTGGGGCG 60.008 57.895 0.00 0.00 0.00 6.13
1439 1906 1.300620 GTTTGTTTTCCTGGGGCGC 60.301 57.895 0.00 0.00 0.00 6.53
1440 1907 2.503382 TTTGTTTTCCTGGGGCGCC 61.503 57.895 21.18 21.18 0.00 6.53
1466 1933 1.089112 TGCAGCCGAATGATTGTCTG 58.911 50.000 0.00 0.00 0.00 3.51
1468 1935 1.470098 GCAGCCGAATGATTGTCTGTT 59.530 47.619 0.00 0.00 0.00 3.16
1469 1936 2.095059 GCAGCCGAATGATTGTCTGTTT 60.095 45.455 0.00 0.00 0.00 2.83
1470 1937 3.495193 CAGCCGAATGATTGTCTGTTTG 58.505 45.455 0.00 0.00 0.00 2.93
1471 1938 2.095059 AGCCGAATGATTGTCTGTTTGC 60.095 45.455 0.00 0.00 0.00 3.68
1543 2014 2.815647 CTCTCGCTGTTTCCGGCC 60.816 66.667 0.00 0.00 40.02 6.13
1596 2067 4.838152 GCGCGGCTGGATCCAAGA 62.838 66.667 17.00 0.00 0.00 3.02
1627 2098 3.880846 GGATTGCTTGCCGGAGCG 61.881 66.667 5.05 0.00 45.64 5.03
1725 2218 6.661805 TGAATTTATACTTGTCCCCTTGTTCC 59.338 38.462 0.00 0.00 0.00 3.62
1755 2249 1.598130 AGAAGTTTGCGCCGCTTCT 60.598 52.632 23.45 23.45 42.65 2.85
1805 2303 1.741770 CCCGCTCGGTTTGGAGAAG 60.742 63.158 7.59 0.00 36.08 2.85
1822 2320 3.934962 GCCATCCTCTCGGCTCCC 61.935 72.222 0.00 0.00 45.29 4.30
1826 2324 2.705487 ATCCTCTCGGCTCCCCTGA 61.705 63.158 0.00 0.00 0.00 3.86
1841 2339 4.199310 TCCCCTGATTCATTTCGTTCATC 58.801 43.478 0.00 0.00 0.00 2.92
1861 2359 1.260561 CCGCATGGTTATTACGCTGAC 59.739 52.381 0.00 0.00 0.00 3.51
1865 2363 3.531538 CATGGTTATTACGCTGACCAGT 58.468 45.455 0.00 0.00 44.64 4.00
1900 2398 0.804989 GCCTCTGTTCGACCATTTGG 59.195 55.000 0.00 0.00 42.17 3.28
1906 2404 1.202758 TGTTCGACCATTTGGCTCAGT 60.203 47.619 0.00 0.00 39.32 3.41
1918 2416 3.540211 GCTCAGTAGCCTTCTGCAA 57.460 52.632 0.00 0.00 43.40 4.08
1919 2417 2.035530 GCTCAGTAGCCTTCTGCAAT 57.964 50.000 0.00 0.00 43.40 3.56
1920 2418 1.939255 GCTCAGTAGCCTTCTGCAATC 59.061 52.381 0.00 0.00 43.40 2.67
1921 2419 2.679059 GCTCAGTAGCCTTCTGCAATCA 60.679 50.000 0.00 0.00 43.40 2.57
1922 2420 2.935201 CTCAGTAGCCTTCTGCAATCAC 59.065 50.000 0.00 0.00 44.83 3.06
1923 2421 2.302733 TCAGTAGCCTTCTGCAATCACA 59.697 45.455 0.00 0.00 44.83 3.58
1924 2422 3.054875 TCAGTAGCCTTCTGCAATCACAT 60.055 43.478 0.00 0.00 44.83 3.21
1925 2423 3.311871 CAGTAGCCTTCTGCAATCACATC 59.688 47.826 0.00 0.00 44.83 3.06
1926 2424 2.502142 AGCCTTCTGCAATCACATCA 57.498 45.000 0.00 0.00 44.83 3.07
1927 2425 2.366533 AGCCTTCTGCAATCACATCAG 58.633 47.619 0.00 0.00 44.83 2.90
1928 2426 1.202268 GCCTTCTGCAATCACATCAGC 60.202 52.381 0.00 0.00 40.77 4.26
1929 2427 2.366533 CCTTCTGCAATCACATCAGCT 58.633 47.619 0.00 0.00 0.00 4.24
1930 2428 2.355132 CCTTCTGCAATCACATCAGCTC 59.645 50.000 0.00 0.00 0.00 4.09
1931 2429 3.271729 CTTCTGCAATCACATCAGCTCT 58.728 45.455 0.00 0.00 0.00 4.09
1932 2430 2.629051 TCTGCAATCACATCAGCTCTG 58.371 47.619 0.00 0.00 0.00 3.35
1933 2431 1.064208 CTGCAATCACATCAGCTCTGC 59.936 52.381 0.00 0.00 0.00 4.26
1934 2432 1.339727 TGCAATCACATCAGCTCTGCT 60.340 47.619 0.00 0.00 40.77 4.24
1935 2433 2.093341 TGCAATCACATCAGCTCTGCTA 60.093 45.455 0.00 0.00 36.40 3.49
1936 2434 2.287373 GCAATCACATCAGCTCTGCTAC 59.713 50.000 0.00 0.00 36.40 3.58
1937 2435 3.794717 CAATCACATCAGCTCTGCTACT 58.205 45.455 0.00 0.00 36.40 2.57
1938 2436 4.190001 CAATCACATCAGCTCTGCTACTT 58.810 43.478 0.00 0.00 36.40 2.24
1939 2437 3.969287 TCACATCAGCTCTGCTACTTT 57.031 42.857 0.00 0.00 36.40 2.66
1940 2438 3.593096 TCACATCAGCTCTGCTACTTTG 58.407 45.455 0.00 0.00 36.40 2.77
1941 2439 3.259123 TCACATCAGCTCTGCTACTTTGA 59.741 43.478 0.00 0.00 36.40 2.69
1973 2471 1.718396 TCTTGCGATTCTGCTCTGTG 58.282 50.000 0.00 0.00 35.36 3.66
1985 2483 2.044806 GCTCTGTGGGTGAGTGGTGT 62.045 60.000 0.00 0.00 34.30 4.16
1989 2487 0.468226 TGTGGGTGAGTGGTGTCTTC 59.532 55.000 0.00 0.00 0.00 2.87
1991 2489 1.375326 GGGTGAGTGGTGTCTTCCC 59.625 63.158 0.00 0.00 0.00 3.97
1992 2490 1.415672 GGGTGAGTGGTGTCTTCCCA 61.416 60.000 0.00 0.00 34.53 4.37
2137 2649 2.084546 GAATATATCCCTTGGGTGCGC 58.915 52.381 0.00 0.00 0.00 6.09
2221 2733 2.675348 CCGCTTTCTTGGTGATCTTCTC 59.325 50.000 0.00 0.00 0.00 2.87
2233 2746 2.695666 TGATCTTCTCCTGGATCCGTTC 59.304 50.000 7.39 0.00 37.96 3.95
2243 2756 3.458189 CTGGATCCGTTCCTGTATTGAC 58.542 50.000 7.39 0.00 45.68 3.18
2245 2758 4.283337 TGGATCCGTTCCTGTATTGACTA 58.717 43.478 7.39 0.00 45.68 2.59
2265 2778 4.627467 ACTAATCTTGCGTGTTCTTGCTAG 59.373 41.667 0.00 0.00 35.67 3.42
2273 2786 5.175127 TGCGTGTTCTTGCTAGAATTATCA 58.825 37.500 13.68 4.57 42.14 2.15
2352 2865 5.990668 AGTTTGGTGAGAAGTAGTTCTTGT 58.009 37.500 14.03 0.00 43.50 3.16
2355 2868 4.703897 TGGTGAGAAGTAGTTCTTGTTGG 58.296 43.478 14.03 0.00 43.50 3.77
2357 2870 4.991687 GGTGAGAAGTAGTTCTTGTTGGAG 59.008 45.833 14.03 0.00 43.50 3.86
2405 2918 1.136305 GCACCCGTCATCTAGCTGTTA 59.864 52.381 0.00 0.00 0.00 2.41
2423 2936 5.619981 GCTGTTACATTGTCTGGTTCATTCC 60.620 44.000 0.00 0.00 0.00 3.01
2523 3038 1.893137 AGCTAGGACATCACACGTGAA 59.107 47.619 25.01 10.37 43.58 3.18
2598 3113 0.537371 CCCTCAAGGACACCACAACC 60.537 60.000 0.00 0.00 38.24 3.77
2610 3125 4.988598 ACAACCGTGAGCCTGGCG 62.989 66.667 13.96 0.43 0.00 5.69
2645 3160 0.475044 TACAAGGTCGGGCCACTTTT 59.525 50.000 4.39 0.33 40.61 2.27
2658 3173 4.466015 GGGCCACTTTTATGATTCCTTTGA 59.534 41.667 4.39 0.00 0.00 2.69
2739 3254 4.922206 TCACTGCTGGATTACCATTTCTT 58.078 39.130 0.00 0.00 45.87 2.52
2827 3342 6.042208 AGGGAGAAGTACATAAGAGGTAATGC 59.958 42.308 0.00 0.00 0.00 3.56
2917 3477 8.892723 CAACTGAATATATGCCAGAACAAACTA 58.107 33.333 17.43 0.00 0.00 2.24
2999 3559 1.472082 CTGGTATTTGCATTGCGGACA 59.528 47.619 3.84 0.00 0.00 4.02
3020 3580 6.757010 GGACACGCTAATTTTCTCTCTGATTA 59.243 38.462 0.00 0.00 0.00 1.75
3046 3606 6.978659 TGAGTAGATATCTTTTACAACTGCCG 59.021 38.462 11.25 0.00 0.00 5.69
3062 3622 3.002791 CTGCCGTCACTCACATGTTTAT 58.997 45.455 0.00 0.00 0.00 1.40
3090 3650 6.073058 GGTTTGCAGAAATTTTCCTTTCCATC 60.073 38.462 5.52 0.00 36.06 3.51
3096 3656 5.186603 AGAAATTTTCCTTTCCATCTCTGCC 59.813 40.000 5.52 0.00 36.06 4.85
3237 3797 5.371629 CCGTCGTCTTTGTTTTCTTATGAC 58.628 41.667 0.00 0.00 0.00 3.06
3420 4065 9.528489 AAATTTTGTACTGATATGTACTTGGGT 57.472 29.630 6.41 0.00 42.22 4.51
3572 4217 5.130477 TGTTGAACTAACATATCTCCTCCCC 59.870 44.000 0.00 0.00 44.07 4.81
3591 4236 2.954318 CCCCATGGTGCTTAATTCTGAG 59.046 50.000 11.73 0.00 0.00 3.35
3788 4434 9.791801 ATAAACATTCTTTGCCTGGTTATTTTT 57.208 25.926 0.00 0.00 30.54 1.94
3806 4452 8.736244 GTTATTTTTATTCCTCAGGTTGCACTA 58.264 33.333 0.00 0.00 0.00 2.74
3848 4494 1.149148 GTGCCCTTCGAGAAGTTGAC 58.851 55.000 11.38 1.99 36.72 3.18
4177 4837 3.488363 AGTCAGATCCTCCGGTATGTAC 58.512 50.000 0.00 0.00 0.00 2.90
4189 4849 2.034305 CGGTATGTACACCAGGCTAGTC 59.966 54.545 0.00 0.00 38.61 2.59
4221 4881 9.632807 TCAACAGCAAAATAACCATAAATACAC 57.367 29.630 0.00 0.00 0.00 2.90
4359 5019 8.753133 CAATGCATAATAGATAGTACTCCCTGA 58.247 37.037 0.00 0.00 0.00 3.86
4361 5021 8.721133 TGCATAATAGATAGTACTCCCTGAAA 57.279 34.615 0.00 0.00 0.00 2.69
4380 5040 7.041576 CCCTGAAACCAAACTTACACTAGTTAC 60.042 40.741 0.00 0.00 37.37 2.50
4573 5233 2.205074 CTTGCCAGGTAACGAGCTATG 58.795 52.381 0.00 0.00 46.39 2.23
4808 5470 4.895668 AAGTGGTTTGGCATTCAATGAT 57.104 36.364 0.00 0.00 34.98 2.45
5075 5738 6.387041 AAAGAGCAACTAACCAGGTAAAAC 57.613 37.500 0.00 0.00 0.00 2.43
5122 5785 7.833682 TGATCCACTATTACATTGTTCATTGGT 59.166 33.333 0.00 0.00 0.00 3.67
5203 5866 6.128007 ACTCAAAATCCTTGCACGTATAAAGG 60.128 38.462 14.08 14.08 41.60 3.11
5258 5921 6.160459 ACAATAGGAAGACAATGGGATAACCT 59.840 38.462 0.00 0.00 41.11 3.50
5276 5939 9.841295 GGATAACCTACTAATTATTGTGGACAA 57.159 33.333 0.00 0.00 40.51 3.18
5454 6120 9.313118 GGATTCAACAACTTCTGTTTAATTTGT 57.687 29.630 0.15 0.00 46.49 2.83
5534 6205 1.649664 CTTCAACCTCATCAGCTCCG 58.350 55.000 0.00 0.00 0.00 4.63
5585 6257 8.421249 AAATTCTGAACCACTGATTTAATCCA 57.579 30.769 2.22 0.00 0.00 3.41
5681 6355 5.465051 TCTTTTCAGTCTGAGAGATTGTCG 58.535 41.667 11.81 0.00 34.11 4.35
5754 6428 6.928979 TCTTGAAAATTGAACAGGTTCGTA 57.071 33.333 7.58 0.00 42.28 3.43
5971 6645 9.971922 TGTGTAGATATCAAGTAAGACATCATG 57.028 33.333 5.32 0.00 0.00 3.07
6017 6691 7.443575 CACTATCAGGAGGACAATGAATTTAGG 59.556 40.741 0.00 0.00 0.00 2.69
6030 6704 9.220767 ACAATGAATTTAGGTCAGAACTAGTTC 57.779 33.333 25.24 25.24 39.78 3.01
6033 6707 7.386851 TGAATTTAGGTCAGAACTAGTTCCTG 58.613 38.462 28.05 23.55 40.33 3.86
6051 6725 6.998673 AGTTCCTGACAAACTAACTAGCATTT 59.001 34.615 0.00 0.00 35.25 2.32
6056 6730 6.734137 TGACAAACTAACTAGCATTTGTTGG 58.266 36.000 12.69 5.09 43.46 3.77
6063 6737 5.959618 AACTAGCATTTGTTGGGTACTTC 57.040 39.130 0.00 0.00 0.00 3.01
6094 6768 4.160439 TGGGTTGCTAGTCAGTTCTCTATG 59.840 45.833 0.00 0.00 0.00 2.23
6121 6795 7.864307 TCGTTTCAGTTAGCTTTCTAGTAAC 57.136 36.000 0.00 0.00 0.00 2.50
6172 6846 7.928307 ATTAGAGAAGTGCAGCTAAATTCAA 57.072 32.000 10.33 0.00 0.00 2.69
6189 6863 5.633830 ATTCAAGTTCTGTATGCTGGTTG 57.366 39.130 0.00 0.00 0.00 3.77
6193 6867 1.135575 GTTCTGTATGCTGGTTGCTGC 60.136 52.381 0.00 0.00 43.37 5.25
6308 6984 7.039853 TGGAACTTCTCATGTAATGCAAATTGA 60.040 33.333 0.00 0.00 46.21 2.57
6364 7042 9.662947 GATCATTTCCTTTTCATGATTTTCCTT 57.337 29.630 0.00 0.00 37.70 3.36
6369 7047 9.709495 TTTCCTTTTCATGATTTTCCTTATGTG 57.291 29.630 0.00 0.00 0.00 3.21
6404 7082 3.966979 TGCTCTGAGCCCATTTGATTTA 58.033 40.909 25.61 0.49 41.51 1.40
6414 7092 5.045724 AGCCCATTTGATTTATTTTCAGGCA 60.046 36.000 0.00 0.00 34.72 4.75
6474 7152 2.597510 AAGCCAACTTCACCGCCC 60.598 61.111 0.00 0.00 0.00 6.13
6698 7382 0.678395 CTGCTGTGGCCGAGATAGAT 59.322 55.000 5.77 0.00 37.74 1.98
6776 7460 4.278678 CTGTGAACTGAAACAGGTGTTC 57.721 45.455 0.00 0.00 40.12 3.18
6781 7465 6.156519 GTGAACTGAAACAGGTGTTCTTTTT 58.843 36.000 0.00 0.00 39.38 1.94
6816 7500 1.892474 GGTCAATGCACAGCCCTTAAA 59.108 47.619 0.00 0.00 0.00 1.52
6888 7573 1.270414 ATGGAGTCACAGGCTGGGAG 61.270 60.000 22.07 8.67 25.25 4.30
6912 7597 2.263741 CCTTGTCACTGCACCCAGC 61.264 63.158 0.00 0.00 43.02 4.85
7023 7911 6.884295 TCATCCTTTGGTCATACTAAACTTGG 59.116 38.462 0.00 0.00 0.00 3.61
7984 8894 0.683179 GGGCATCAACTTGTACCCCC 60.683 60.000 0.00 0.00 0.00 5.40
7992 8902 6.601332 CATCAACTTGTACCCCCATACTAAT 58.399 40.000 0.00 0.00 0.00 1.73
8099 9024 7.098477 TGATTCTAATTGCAAGATTGGTTTGG 58.902 34.615 4.94 0.00 0.00 3.28
8121 9046 5.077424 GGCTCGTTTTTGTGAGTATTAACG 58.923 41.667 0.00 0.00 39.55 3.18
8124 9049 5.976586 TCGTTTTTGTGAGTATTAACGTGG 58.023 37.500 0.00 0.00 39.31 4.94
8146 9076 7.040617 CGTGGACTCCTATGCTAACTATCTTTA 60.041 40.741 0.00 0.00 0.00 1.85
8196 9146 7.892778 TTCTGTCTTTGTAACGCATACATAA 57.107 32.000 2.86 1.40 43.84 1.90
8197 9147 8.487313 TTCTGTCTTTGTAACGCATACATAAT 57.513 30.769 2.86 0.00 43.84 1.28
8198 9148 9.589111 TTCTGTCTTTGTAACGCATACATAATA 57.411 29.630 2.86 0.00 43.84 0.98
8199 9149 9.027129 TCTGTCTTTGTAACGCATACATAATAC 57.973 33.333 2.86 4.89 43.84 1.89
8200 9150 8.705048 TGTCTTTGTAACGCATACATAATACA 57.295 30.769 2.86 6.70 43.84 2.29
8201 9151 9.320352 TGTCTTTGTAACGCATACATAATACAT 57.680 29.630 2.86 0.00 43.84 2.29
8388 9384 4.336713 GCACATGTCCTAGGAAAATCCTTC 59.663 45.833 14.65 0.00 46.91 3.46
8389 9385 5.500234 CACATGTCCTAGGAAAATCCTTCA 58.500 41.667 14.65 4.87 46.91 3.02
8390 9386 5.945784 CACATGTCCTAGGAAAATCCTTCAA 59.054 40.000 14.65 0.00 46.91 2.69
8391 9387 6.604795 CACATGTCCTAGGAAAATCCTTCAAT 59.395 38.462 14.65 0.00 46.91 2.57
8392 9388 7.123247 CACATGTCCTAGGAAAATCCTTCAATT 59.877 37.037 14.65 0.00 46.91 2.32
8393 9389 8.336235 ACATGTCCTAGGAAAATCCTTCAATTA 58.664 33.333 14.65 0.00 46.91 1.40
8394 9390 8.624776 CATGTCCTAGGAAAATCCTTCAATTAC 58.375 37.037 14.65 0.00 46.91 1.89
8395 9391 7.695055 TGTCCTAGGAAAATCCTTCAATTACA 58.305 34.615 14.65 0.00 46.91 2.41
8442 9455 1.260206 CGTGACGACAGACACATAGC 58.740 55.000 0.00 0.00 41.81 2.97
8495 9508 1.352083 CTTTCCTCTCCACCACCTCA 58.648 55.000 0.00 0.00 0.00 3.86
8530 9543 3.470888 CGGTCCCCGCATCTCCTT 61.471 66.667 0.00 0.00 41.17 3.36
8542 9555 5.300286 CCCGCATCTCCTTGATTATTTTTCT 59.700 40.000 0.00 0.00 32.05 2.52
8546 9559 7.414429 CGCATCTCCTTGATTATTTTTCTGTCA 60.414 37.037 0.00 0.00 32.05 3.58
8548 9561 8.954350 CATCTCCTTGATTATTTTTCTGTCAGT 58.046 33.333 0.00 0.00 32.05 3.41
8634 9647 1.140312 TGCCACCCAATATCCTCCTC 58.860 55.000 0.00 0.00 0.00 3.71
8642 9655 3.969976 CCCAATATCCTCCTCTCTTGTCA 59.030 47.826 0.00 0.00 0.00 3.58
8660 9673 0.679002 CAGGCCTCACATTGTCTGGG 60.679 60.000 0.00 2.06 0.00 4.45
8676 9689 2.043248 GGTAGCCAGGGAGGTCGA 60.043 66.667 0.00 0.00 40.61 4.20
8691 9704 1.337071 GGTCGACGAATAGCTCCATCA 59.663 52.381 9.92 0.00 0.00 3.07
8698 9711 0.767375 AATAGCTCCATCATGCCCGT 59.233 50.000 0.00 0.00 0.00 5.28
8733 9746 4.767409 TGATCCAGTATCGTAGCAGCTTAT 59.233 41.667 0.00 0.00 37.42 1.73
8746 9760 1.659644 GCTTATACGGCCGGTCGAC 60.660 63.158 38.47 12.85 0.00 4.20
8747 9761 1.729276 CTTATACGGCCGGTCGACA 59.271 57.895 38.47 22.87 0.00 4.35
8775 9789 2.015736 AGATGTGTCTGATCAACGCC 57.984 50.000 14.71 5.19 32.13 5.68
8776 9790 1.009829 GATGTGTCTGATCAACGCCC 58.990 55.000 14.71 6.99 0.00 6.13
8777 9791 0.392998 ATGTGTCTGATCAACGCCCC 60.393 55.000 14.71 0.00 0.00 5.80
8778 9792 1.745489 GTGTCTGATCAACGCCCCC 60.745 63.158 0.00 0.00 0.00 5.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
32 33 9.567848 GCAGATCGAGGTAATTTCATTTTAAAA 57.432 29.630 2.51 2.51 0.00 1.52
36 37 6.757897 TGCAGATCGAGGTAATTTCATTTT 57.242 33.333 0.00 0.00 0.00 1.82
37 38 6.238842 CCATGCAGATCGAGGTAATTTCATTT 60.239 38.462 0.00 0.00 0.00 2.32
38 39 5.240183 CCATGCAGATCGAGGTAATTTCATT 59.760 40.000 0.00 0.00 0.00 2.57
39 40 4.758674 CCATGCAGATCGAGGTAATTTCAT 59.241 41.667 0.00 0.00 0.00 2.57
40 41 4.129380 CCATGCAGATCGAGGTAATTTCA 58.871 43.478 0.00 0.00 0.00 2.69
41 42 3.499918 CCCATGCAGATCGAGGTAATTTC 59.500 47.826 0.00 0.00 0.00 2.17
42 43 3.117888 ACCCATGCAGATCGAGGTAATTT 60.118 43.478 0.00 0.00 0.00 1.82
61 72 9.397280 ACTTCTATTCTCTAAAAATAAGCACCC 57.603 33.333 0.00 0.00 0.00 4.61
91 102 1.998438 TGCGGGAGGGATGCCTAAA 60.998 57.895 5.42 0.00 0.00 1.85
121 132 9.995003 AATAAATCAAGTTTTTGGTAAGCATCA 57.005 25.926 0.00 0.00 34.97 3.07
160 171 7.519032 TGTCTAAGTTTGGTCCCAATTTTAG 57.481 36.000 16.41 16.41 35.68 1.85
182 193 4.202326 ACGTACCCACTCTTTTGAAGATGT 60.202 41.667 0.00 0.00 36.82 3.06
192 205 1.270147 GCTCAACACGTACCCACTCTT 60.270 52.381 0.00 0.00 0.00 2.85
195 208 1.370064 GGCTCAACACGTACCCACT 59.630 57.895 0.00 0.00 0.00 4.00
199 212 1.024579 CCATGGGCTCAACACGTACC 61.025 60.000 2.85 0.00 0.00 3.34
200 213 1.024579 CCCATGGGCTCAACACGTAC 61.025 60.000 20.41 0.00 0.00 3.67
247 260 9.651531 CGACATTTTAAAACGTGTTTAATATGC 57.348 29.630 24.71 20.30 37.09 3.14
248 261 9.651531 GCGACATTTTAAAACGTGTTTAATATG 57.348 29.630 24.05 24.05 38.30 1.78
249 262 9.395707 TGCGACATTTTAAAACGTGTTTAATAT 57.604 25.926 4.09 5.05 31.63 1.28
250 263 8.778141 TGCGACATTTTAAAACGTGTTTAATA 57.222 26.923 4.09 3.05 31.63 0.98
251 264 7.681125 TGCGACATTTTAAAACGTGTTTAAT 57.319 28.000 4.09 0.00 31.63 1.40
252 265 7.502177 TTGCGACATTTTAAAACGTGTTTAA 57.498 28.000 4.09 4.14 31.63 1.52
253 266 7.502177 TTTGCGACATTTTAAAACGTGTTTA 57.498 28.000 4.09 0.00 31.63 2.01
273 286 9.021863 TGCATGAAATTTTCTTTTGAATTTTGC 57.978 25.926 10.33 9.53 38.36 3.68
296 309 3.009026 ACACATGTTGCGAAGATATGCA 58.991 40.909 0.00 0.00 39.81 3.96
404 421 5.584649 AGAGACAAAGAAAAATGTGTCGTGA 59.415 36.000 0.00 0.00 42.72 4.35
419 436 3.507233 TGGCCTATGCAAAAGAGACAAAG 59.493 43.478 3.32 0.00 40.13 2.77
427 445 5.075858 TCTTTCATTGGCCTATGCAAAAG 57.924 39.130 23.56 23.56 40.13 2.27
443 461 2.035449 TCGAGGAAAAGCGACTCTTTCA 59.965 45.455 0.00 0.00 43.84 2.69
452 470 2.908626 CGGAAAATTTCGAGGAAAAGCG 59.091 45.455 0.00 0.00 35.11 4.68
548 575 5.013547 TCACGGACATATGAACCCATTTTT 58.986 37.500 10.38 0.00 34.31 1.94
552 579 2.771943 ACTCACGGACATATGAACCCAT 59.228 45.455 10.38 0.29 36.81 4.00
590 618 8.704234 GCCGTTATTATTTTGATTTTGAACACA 58.296 29.630 0.00 0.00 0.00 3.72
591 619 7.890717 CGCCGTTATTATTTTGATTTTGAACAC 59.109 33.333 0.00 0.00 0.00 3.32
593 621 6.892430 GCGCCGTTATTATTTTGATTTTGAAC 59.108 34.615 0.00 0.00 0.00 3.18
631 659 3.823304 CCTCTCCTTCTGAAAAAGGTTGG 59.177 47.826 2.81 1.24 45.16 3.77
641 669 5.646215 AGTACTTTTCTCCTCTCCTTCTGA 58.354 41.667 0.00 0.00 0.00 3.27
642 670 5.993748 AGTACTTTTCTCCTCTCCTTCTG 57.006 43.478 0.00 0.00 0.00 3.02
643 671 6.192044 CCTAGTACTTTTCTCCTCTCCTTCT 58.808 44.000 0.00 0.00 0.00 2.85
646 674 4.544968 TCCCTAGTACTTTTCTCCTCTCCT 59.455 45.833 0.00 0.00 0.00 3.69
648 676 4.646040 GGTCCCTAGTACTTTTCTCCTCTC 59.354 50.000 0.00 0.00 0.00 3.20
649 677 4.045590 TGGTCCCTAGTACTTTTCTCCTCT 59.954 45.833 0.00 0.00 0.00 3.69
689 717 0.765510 GAGGGGGTGACTGTGACTTT 59.234 55.000 0.00 0.00 0.00 2.66
712 848 9.026074 TGTCGTGGAATTTTAGTTTGATTTTTC 57.974 29.630 0.00 0.00 0.00 2.29
744 880 0.942252 GGGAATACGGGATGCGTTTC 59.058 55.000 0.00 0.00 0.00 2.78
745 881 0.253610 TGGGAATACGGGATGCGTTT 59.746 50.000 0.00 0.00 0.00 3.60
746 882 0.472471 ATGGGAATACGGGATGCGTT 59.528 50.000 0.00 0.00 0.00 4.84
747 883 0.034896 GATGGGAATACGGGATGCGT 59.965 55.000 0.00 0.00 0.00 5.24
748 884 0.673644 GGATGGGAATACGGGATGCG 60.674 60.000 0.00 0.00 0.00 4.73
749 885 0.322546 GGGATGGGAATACGGGATGC 60.323 60.000 0.00 0.00 0.00 3.91
751 887 2.059756 ATGGGATGGGAATACGGGAT 57.940 50.000 0.00 0.00 0.00 3.85
752 888 1.702957 GAATGGGATGGGAATACGGGA 59.297 52.381 0.00 0.00 0.00 5.14
753 889 1.271926 GGAATGGGATGGGAATACGGG 60.272 57.143 0.00 0.00 0.00 5.28
754 890 1.271926 GGGAATGGGATGGGAATACGG 60.272 57.143 0.00 0.00 0.00 4.02
755 891 1.271926 GGGGAATGGGATGGGAATACG 60.272 57.143 0.00 0.00 0.00 3.06
756 892 2.041755 GAGGGGAATGGGATGGGAATAC 59.958 54.545 0.00 0.00 0.00 1.89
757 893 2.358258 GAGGGGAATGGGATGGGAATA 58.642 52.381 0.00 0.00 0.00 1.75
758 894 1.161603 GAGGGGAATGGGATGGGAAT 58.838 55.000 0.00 0.00 0.00 3.01
759 895 0.998945 GGAGGGGAATGGGATGGGAA 60.999 60.000 0.00 0.00 0.00 3.97
886 1025 3.953887 GAGCGCATTAAGCCCCGC 61.954 66.667 11.47 0.00 46.14 6.13
887 1026 0.531974 TAAGAGCGCATTAAGCCCCG 60.532 55.000 11.47 0.00 41.38 5.73
888 1027 1.230324 CTAAGAGCGCATTAAGCCCC 58.770 55.000 11.47 0.00 41.38 5.80
951 1117 1.600663 CCAGATTAGCGTACCAGCTCG 60.601 57.143 0.00 0.00 45.67 5.03
957 1128 7.678947 TTACTATACTCCAGATTAGCGTACC 57.321 40.000 0.00 0.00 0.00 3.34
1010 1182 0.687757 CAATGGGAGAGGGGAGACGA 60.688 60.000 0.00 0.00 0.00 4.20
1013 1185 2.059756 AAACAATGGGAGAGGGGAGA 57.940 50.000 0.00 0.00 0.00 3.71
1015 1187 4.119155 AGATTAAACAATGGGAGAGGGGA 58.881 43.478 0.00 0.00 0.00 4.81
1016 1188 4.464947 GAGATTAAACAATGGGAGAGGGG 58.535 47.826 0.00 0.00 0.00 4.79
1017 1189 4.464947 GGAGATTAAACAATGGGAGAGGG 58.535 47.826 0.00 0.00 0.00 4.30
1018 1190 4.130118 CGGAGATTAAACAATGGGAGAGG 58.870 47.826 0.00 0.00 0.00 3.69
1019 1191 4.130118 CCGGAGATTAAACAATGGGAGAG 58.870 47.826 0.00 0.00 0.00 3.20
1020 1192 3.521937 ACCGGAGATTAAACAATGGGAGA 59.478 43.478 9.46 0.00 0.00 3.71
1021 1193 3.627577 CACCGGAGATTAAACAATGGGAG 59.372 47.826 9.46 0.00 0.00 4.30
1121 1297 3.687828 AAGAGGAGGAGGAGGCGGG 62.688 68.421 0.00 0.00 0.00 6.13
1122 1298 2.042435 AAGAGGAGGAGGAGGCGG 60.042 66.667 0.00 0.00 0.00 6.13
1123 1299 2.131067 GGAAGAGGAGGAGGAGGCG 61.131 68.421 0.00 0.00 0.00 5.52
1124 1300 1.002274 TGGAAGAGGAGGAGGAGGC 59.998 63.158 0.00 0.00 0.00 4.70
1125 1301 0.689412 GGTGGAAGAGGAGGAGGAGG 60.689 65.000 0.00 0.00 0.00 4.30
1126 1302 0.689412 GGGTGGAAGAGGAGGAGGAG 60.689 65.000 0.00 0.00 0.00 3.69
1127 1303 1.392534 GGGTGGAAGAGGAGGAGGA 59.607 63.158 0.00 0.00 0.00 3.71
1128 1304 1.690985 GGGGTGGAAGAGGAGGAGG 60.691 68.421 0.00 0.00 0.00 4.30
1129 1305 1.690985 GGGGGTGGAAGAGGAGGAG 60.691 68.421 0.00 0.00 0.00 3.69
1130 1306 2.454941 GGGGGTGGAAGAGGAGGA 59.545 66.667 0.00 0.00 0.00 3.71
1257 1723 3.119566 AGCAGAGAAATTAAGCAGCTTGC 60.120 43.478 18.54 9.78 45.46 4.01
1284 1750 5.959618 ATTAGCCACACAAAAACTAGTCC 57.040 39.130 0.00 0.00 0.00 3.85
1287 1753 4.923281 GCCAATTAGCCACACAAAAACTAG 59.077 41.667 0.00 0.00 0.00 2.57
1347 1814 2.598619 GAATCGCCCGAAAAGCTGGC 62.599 60.000 1.91 1.91 42.86 4.85
1466 1933 2.034591 GCGAACAAGAAAGCAAGCAAAC 60.035 45.455 0.00 0.00 0.00 2.93
1468 1935 1.405105 AGCGAACAAGAAAGCAAGCAA 59.595 42.857 0.00 0.00 0.00 3.91
1469 1936 1.024271 AGCGAACAAGAAAGCAAGCA 58.976 45.000 0.00 0.00 0.00 3.91
1470 1937 1.783140 CAAGCGAACAAGAAAGCAAGC 59.217 47.619 0.00 0.00 0.00 4.01
1471 1938 1.783140 GCAAGCGAACAAGAAAGCAAG 59.217 47.619 0.00 0.00 0.00 4.01
1543 2014 2.271800 GATCCAGTTGAGCAACGGTAG 58.728 52.381 17.33 7.30 45.50 3.18
1627 2098 1.376553 GCAAGAGTCCACCTGCTCC 60.377 63.158 0.00 0.00 32.47 4.70
1629 2100 1.422161 AAGGCAAGAGTCCACCTGCT 61.422 55.000 0.00 0.00 31.32 4.24
1630 2101 0.957888 GAAGGCAAGAGTCCACCTGC 60.958 60.000 0.00 0.00 31.32 4.85
1725 2218 2.159517 GCAAACTTCTATGCCCGACAAG 60.160 50.000 0.00 0.00 36.56 3.16
1811 2309 1.045350 TGAATCAGGGGAGCCGAGAG 61.045 60.000 0.00 0.00 0.00 3.20
1812 2310 0.399091 ATGAATCAGGGGAGCCGAGA 60.399 55.000 0.00 0.00 0.00 4.04
1822 2320 3.546815 GCGGATGAACGAAATGAATCAGG 60.547 47.826 0.00 0.00 35.47 3.86
1826 2324 3.243168 CCATGCGGATGAACGAAATGAAT 60.243 43.478 19.50 0.00 33.82 2.57
1841 2339 1.260561 GTCAGCGTAATAACCATGCGG 59.739 52.381 0.00 0.00 38.77 5.69
1861 2359 2.864097 GCTGCACCGATGATACTACTGG 60.864 54.545 0.00 0.00 0.00 4.00
1865 2363 1.613925 GAGGCTGCACCGATGATACTA 59.386 52.381 0.50 0.00 46.52 1.82
1906 2404 3.538591 CTGATGTGATTGCAGAAGGCTA 58.461 45.455 0.00 0.00 45.15 3.93
1917 2415 4.484537 AAGTAGCAGAGCTGATGTGATT 57.515 40.909 0.85 0.00 40.10 2.57
1918 2416 4.081254 TCAAAGTAGCAGAGCTGATGTGAT 60.081 41.667 0.85 0.00 40.10 3.06
1919 2417 3.259123 TCAAAGTAGCAGAGCTGATGTGA 59.741 43.478 0.85 0.00 40.10 3.58
1920 2418 3.593096 TCAAAGTAGCAGAGCTGATGTG 58.407 45.455 0.85 0.00 40.10 3.21
1921 2419 3.969287 TCAAAGTAGCAGAGCTGATGT 57.031 42.857 0.85 0.00 40.10 3.06
1922 2420 5.006844 CAGAATCAAAGTAGCAGAGCTGATG 59.993 44.000 0.85 0.00 40.10 3.07
1923 2421 5.117584 CAGAATCAAAGTAGCAGAGCTGAT 58.882 41.667 0.85 0.00 40.10 2.90
1924 2422 4.020751 ACAGAATCAAAGTAGCAGAGCTGA 60.021 41.667 0.85 0.00 40.10 4.26
1925 2423 4.252073 ACAGAATCAAAGTAGCAGAGCTG 58.748 43.478 0.00 0.00 40.10 4.24
1926 2424 4.502962 GACAGAATCAAAGTAGCAGAGCT 58.497 43.478 0.00 0.00 43.41 4.09
1927 2425 3.305629 CGACAGAATCAAAGTAGCAGAGC 59.694 47.826 0.00 0.00 0.00 4.09
1928 2426 3.862267 CCGACAGAATCAAAGTAGCAGAG 59.138 47.826 0.00 0.00 0.00 3.35
1929 2427 3.258372 ACCGACAGAATCAAAGTAGCAGA 59.742 43.478 0.00 0.00 0.00 4.26
1930 2428 3.369147 CACCGACAGAATCAAAGTAGCAG 59.631 47.826 0.00 0.00 0.00 4.24
1931 2429 3.244078 ACACCGACAGAATCAAAGTAGCA 60.244 43.478 0.00 0.00 0.00 3.49
1932 2430 3.326747 ACACCGACAGAATCAAAGTAGC 58.673 45.455 0.00 0.00 0.00 3.58
1933 2431 5.230942 AGAACACCGACAGAATCAAAGTAG 58.769 41.667 0.00 0.00 0.00 2.57
1934 2432 5.209818 AGAACACCGACAGAATCAAAGTA 57.790 39.130 0.00 0.00 0.00 2.24
1935 2433 4.073293 AGAACACCGACAGAATCAAAGT 57.927 40.909 0.00 0.00 0.00 2.66
1936 2434 4.776743 CAAGAACACCGACAGAATCAAAG 58.223 43.478 0.00 0.00 0.00 2.77
1937 2435 3.003275 GCAAGAACACCGACAGAATCAAA 59.997 43.478 0.00 0.00 0.00 2.69
1938 2436 2.548057 GCAAGAACACCGACAGAATCAA 59.452 45.455 0.00 0.00 0.00 2.57
1939 2437 2.143122 GCAAGAACACCGACAGAATCA 58.857 47.619 0.00 0.00 0.00 2.57
1940 2438 1.126846 CGCAAGAACACCGACAGAATC 59.873 52.381 0.00 0.00 43.02 2.52
1941 2439 1.148310 CGCAAGAACACCGACAGAAT 58.852 50.000 0.00 0.00 43.02 2.40
1973 2471 1.375326 GGGAAGACACCACTCACCC 59.625 63.158 0.00 0.00 32.68 4.61
1991 2489 3.244700 CCTATCTACCAAGGCCCATCTTG 60.245 52.174 0.00 0.00 42.63 3.02
1992 2490 2.982488 CCTATCTACCAAGGCCCATCTT 59.018 50.000 0.00 0.00 0.00 2.40
2005 2517 4.023021 GTCAGGACCACGAATCCTATCTAC 60.023 50.000 6.57 1.61 45.25 2.59
2137 2649 1.247567 AACGCCACCAAAATCTCTGG 58.752 50.000 0.00 0.00 40.05 3.86
2233 2746 4.870426 ACACGCAAGATTAGTCAATACAGG 59.130 41.667 0.00 0.00 43.62 4.00
2243 2756 4.864806 TCTAGCAAGAACACGCAAGATTAG 59.135 41.667 0.00 0.00 43.62 1.73
2245 2758 3.664107 TCTAGCAAGAACACGCAAGATT 58.336 40.909 0.00 0.00 43.62 2.40
2352 2865 1.172180 CGGTTCCAGCTTTGCTCCAA 61.172 55.000 0.00 0.00 36.40 3.53
2355 2868 0.238553 GAACGGTTCCAGCTTTGCTC 59.761 55.000 9.75 0.00 36.40 4.26
2357 2870 4.944249 GAACGGTTCCAGCTTTGC 57.056 55.556 9.75 0.00 0.00 3.68
2405 2918 3.007940 TCTCGGAATGAACCAGACAATGT 59.992 43.478 0.00 0.00 0.00 2.71
2423 2936 3.859386 GCCAAATAAATGCTGGTTTCTCG 59.141 43.478 0.00 0.00 32.46 4.04
2523 3038 1.696314 ACCCGCCATTATCCCCAGT 60.696 57.895 0.00 0.00 0.00 4.00
2598 3113 2.357517 ACTTTCGCCAGGCTCACG 60.358 61.111 10.54 0.00 0.00 4.35
2610 3125 4.213482 ACCTTGTAATCGCTGTTCACTTTC 59.787 41.667 0.00 0.00 0.00 2.62
2645 3160 9.642327 CACAATTCAACATTCAAAGGAATCATA 57.358 29.630 0.00 0.00 41.78 2.15
2658 3173 7.201635 GGAAAGCTTCAAACACAATTCAACATT 60.202 33.333 0.00 0.00 0.00 2.71
2739 3254 0.761323 TCCAGTTCCTGTTGTCCCGA 60.761 55.000 0.00 0.00 0.00 5.14
2917 3477 5.288472 GCAGAACAGTGTTTTTCGTTGAAAT 59.712 36.000 10.45 0.00 31.34 2.17
2963 3523 8.413229 GCAAATACCAGGACAAATGTATGTAAT 58.587 33.333 0.00 0.00 32.57 1.89
2999 3559 8.200792 ACTCATAATCAGAGAGAAAATTAGCGT 58.799 33.333 0.00 0.00 36.91 5.07
3020 3580 7.653713 CGGCAGTTGTAAAAGATATCTACTCAT 59.346 37.037 5.46 0.00 0.00 2.90
3046 3606 6.074356 GCAAACCAAATAAACATGTGAGTGAC 60.074 38.462 0.00 0.00 0.00 3.67
3062 3622 6.094742 GGAAAGGAAAATTTCTGCAAACCAAA 59.905 34.615 5.65 0.00 38.86 3.28
3162 3722 2.052782 AAATCCATACCGCCCAGTTC 57.947 50.000 0.00 0.00 0.00 3.01
3237 3797 7.316640 ACTAGTACATTCTAACAGAACAGCAG 58.683 38.462 0.00 0.00 37.00 4.24
3420 4065 1.715931 AGGACAAACCATCCATCCCAA 59.284 47.619 0.00 0.00 42.04 4.12
3572 4217 4.095483 GTCACTCAGAATTAAGCACCATGG 59.905 45.833 11.19 11.19 0.00 3.66
3733 4379 7.002250 TCTTTATTGCATCACCCATGAAAAA 57.998 32.000 0.00 0.00 38.69 1.94
3777 4423 7.035612 GCAACCTGAGGAATAAAAATAACCAG 58.964 38.462 4.99 0.00 0.00 4.00
3787 4433 5.938125 GTCTTTAGTGCAACCTGAGGAATAA 59.062 40.000 4.99 0.00 37.80 1.40
3788 4434 5.012664 TGTCTTTAGTGCAACCTGAGGAATA 59.987 40.000 4.99 0.00 37.80 1.75
4015 4675 9.835389 TCATGAAAAGTTCTCAAAATTGGAATT 57.165 25.926 0.00 0.00 0.00 2.17
4017 4677 9.835389 AATCATGAAAAGTTCTCAAAATTGGAA 57.165 25.926 0.00 0.00 0.00 3.53
4018 4678 9.263538 CAATCATGAAAAGTTCTCAAAATTGGA 57.736 29.630 0.00 0.00 31.57 3.53
4019 4679 9.048446 ACAATCATGAAAAGTTCTCAAAATTGG 57.952 29.630 15.68 4.66 35.34 3.16
4177 4837 1.002274 AGGGGAGACTAGCCTGGTG 59.998 63.158 0.00 0.00 0.00 4.17
4189 4849 3.193479 GGTTATTTTGCTGTTGAGGGGAG 59.807 47.826 0.00 0.00 0.00 4.30
4221 4881 6.969993 AAGAGGAATAAGTAGGACTAGCAG 57.030 41.667 0.00 0.00 0.00 4.24
4353 5013 4.513406 AGTGTAAGTTTGGTTTCAGGGA 57.487 40.909 0.00 0.00 0.00 4.20
4361 5021 9.716531 GGATAAAGTAACTAGTGTAAGTTTGGT 57.283 33.333 0.00 0.00 40.20 3.67
4428 5088 5.597813 AACTTAGATGCGAAACTGAACTG 57.402 39.130 0.00 0.00 0.00 3.16
4573 5233 2.793278 AAAGAAATTGTGGTCGGCAC 57.207 45.000 0.00 0.00 0.00 5.01
4787 5449 4.895668 ATCATTGAATGCCAAACCACTT 57.104 36.364 0.00 0.00 38.43 3.16
4808 5470 7.271511 ACCTTTCAGTAATGCATGAAACAAAA 58.728 30.769 8.73 7.76 39.76 2.44
4966 5629 2.831526 AGGTGTAAATTGGATGGGCAAC 59.168 45.455 0.00 0.00 0.00 4.17
5075 5738 4.100653 TCAGCAACAGAGAAGGGATATGAG 59.899 45.833 0.00 0.00 0.00 2.90
5122 5785 4.938575 TGCTATAAACAGGGGAGGAAAA 57.061 40.909 0.00 0.00 0.00 2.29
5203 5866 7.617041 AAGTGCTAACAGATAATCAAGTTCC 57.383 36.000 0.00 0.00 0.00 3.62
5211 5874 7.661536 TGTCTCCTAAGTGCTAACAGATAAT 57.338 36.000 0.00 0.00 0.00 1.28
5276 5939 5.474532 TCAATCAAGCACTGAAGCAATAGTT 59.525 36.000 0.00 0.00 37.67 2.24
5534 6205 7.543172 TCAGTTTTAAAATCAATCAGCATCAGC 59.457 33.333 3.52 0.00 42.56 4.26
5663 6336 3.073274 TCCGACAATCTCTCAGACTGA 57.927 47.619 4.78 4.78 0.00 3.41
5714 6388 0.249911 AGAACTTCTCACCACGTGCC 60.250 55.000 10.91 0.00 32.98 5.01
5822 6496 3.099267 CCGGAGGCTGTAGAAGTTATG 57.901 52.381 0.00 0.00 46.14 1.90
6017 6691 5.602628 AGTTTGTCAGGAACTAGTTCTGAC 58.397 41.667 33.48 33.48 41.95 3.51
6030 6704 6.560253 ACAAATGCTAGTTAGTTTGTCAGG 57.440 37.500 9.53 0.00 39.77 3.86
6033 6707 6.149633 CCCAACAAATGCTAGTTAGTTTGTC 58.850 40.000 13.37 0.00 42.17 3.18
6051 6725 4.019681 CCCAGATAACAGAAGTACCCAACA 60.020 45.833 0.00 0.00 0.00 3.33
6056 6730 3.939592 GCAACCCAGATAACAGAAGTACC 59.060 47.826 0.00 0.00 0.00 3.34
6063 6737 4.081420 ACTGACTAGCAACCCAGATAACAG 60.081 45.833 0.00 0.00 0.00 3.16
6094 6768 4.733972 AGAAAGCTAACTGAAACGAAGC 57.266 40.909 0.00 0.00 0.00 3.86
6121 6795 1.542030 ACTCGGCTCTAACAGACACTG 59.458 52.381 0.00 0.00 37.52 3.66
6170 6844 3.207474 GCAACCAGCATACAGAACTTG 57.793 47.619 0.00 0.00 44.79 3.16
6308 6984 1.490910 GCAGGGCCAAGTAACTCCTAT 59.509 52.381 6.18 0.00 0.00 2.57
6364 7042 5.822519 AGAGCAAACTCAACAAGAACACATA 59.177 36.000 0.00 0.00 46.09 2.29
6365 7043 4.641989 AGAGCAAACTCAACAAGAACACAT 59.358 37.500 0.00 0.00 46.09 3.21
6366 7044 4.009675 AGAGCAAACTCAACAAGAACACA 58.990 39.130 0.00 0.00 46.09 3.72
6367 7045 4.094887 TCAGAGCAAACTCAACAAGAACAC 59.905 41.667 0.00 0.00 46.09 3.32
6369 7047 4.787882 GCTCAGAGCAAACTCAACAAGAAC 60.788 45.833 18.17 0.00 46.09 3.01
6404 7082 6.841601 TCTATAGCCAGTATTGCCTGAAAAT 58.158 36.000 0.00 0.00 34.23 1.82
6581 7259 2.029828 GTGAGTAGCAGTGTAGCACAGT 60.030 50.000 2.01 0.00 36.74 3.55
6618 7302 5.048991 TGTTAGCAGAATCTATGCATGCATG 60.049 40.000 37.43 27.00 46.31 4.06
6619 7303 5.048921 GTGTTAGCAGAATCTATGCATGCAT 60.049 40.000 33.92 33.92 46.31 3.96
6620 7304 4.274214 GTGTTAGCAGAATCTATGCATGCA 59.726 41.667 25.04 25.04 46.31 3.96
6621 7305 4.514441 AGTGTTAGCAGAATCTATGCATGC 59.486 41.667 11.82 11.82 46.31 4.06
6776 7460 5.123820 TGACCAGATTCCAAGCGATAAAAAG 59.876 40.000 0.00 0.00 0.00 2.27
6781 7465 3.904800 TTGACCAGATTCCAAGCGATA 57.095 42.857 0.00 0.00 0.00 2.92
6888 7573 3.368571 GCAGTGACAAGGGCCAGC 61.369 66.667 6.18 0.00 0.00 4.85
6912 7597 1.725931 GCGACGGCAGTTTCATTTGAG 60.726 52.381 0.00 0.00 39.62 3.02
7433 8321 3.659089 ATCAGCCCGGTGTACGCAC 62.659 63.158 8.97 0.00 44.53 5.34
7788 8681 0.964358 GCAGAGCAACAGGAGGCAAT 60.964 55.000 0.00 0.00 0.00 3.56
7796 8689 0.882042 AGTGGTTCGCAGAGCAACAG 60.882 55.000 3.62 0.00 44.55 3.16
7984 8894 7.905126 TGTGCACATCGAAAACTATTAGTATG 58.095 34.615 17.42 0.00 0.00 2.39
7992 8902 5.211454 CAATGTTGTGCACATCGAAAACTA 58.789 37.500 22.39 6.09 46.23 2.24
8081 8993 3.667360 GAGCCAAACCAATCTTGCAATT 58.333 40.909 0.00 0.00 0.00 2.32
8082 8994 2.353011 CGAGCCAAACCAATCTTGCAAT 60.353 45.455 0.00 0.00 0.00 3.56
8099 9024 5.558888 CACGTTAATACTCACAAAAACGAGC 59.441 40.000 11.79 0.00 41.48 5.03
8121 9046 6.658188 AAGATAGTTAGCATAGGAGTCCAC 57.342 41.667 12.86 0.00 0.00 4.02
8146 9076 5.068987 AGGCACTAACATTGTTGTGAACATT 59.931 36.000 23.96 9.86 38.06 2.71
8162 9100 6.238266 CGTTACAAAGACAGAAAAGGCACTAA 60.238 38.462 0.00 0.00 38.49 2.24
8258 9208 4.361420 TCTGTTTGACGACGTTCATGTAA 58.639 39.130 0.13 0.00 0.00 2.41
8388 9384 9.586435 GGAAAATCAGTTAGGGATTTGTAATTG 57.414 33.333 0.00 0.00 42.48 2.32
8389 9385 9.547279 AGGAAAATCAGTTAGGGATTTGTAATT 57.453 29.630 0.00 0.00 42.48 1.40
8393 9389 9.547279 AAATAGGAAAATCAGTTAGGGATTTGT 57.453 29.630 0.00 0.00 42.48 2.83
8394 9390 9.807649 CAAATAGGAAAATCAGTTAGGGATTTG 57.192 33.333 0.00 0.00 42.48 2.32
8395 9391 8.478066 GCAAATAGGAAAATCAGTTAGGGATTT 58.522 33.333 0.00 0.00 44.52 2.17
8399 9397 5.733373 GCGCAAATAGGAAAATCAGTTAGGG 60.733 44.000 0.30 0.00 0.00 3.53
8405 9418 3.100817 CACGCGCAAATAGGAAAATCAG 58.899 45.455 5.73 0.00 0.00 2.90
8412 9425 1.074319 GTCGTCACGCGCAAATAGGA 61.074 55.000 5.73 0.00 41.07 2.94
8413 9426 1.343821 GTCGTCACGCGCAAATAGG 59.656 57.895 5.73 0.00 41.07 2.57
8432 9445 2.611518 GTTGAGCTTCGCTATGTGTCT 58.388 47.619 0.00 0.00 39.88 3.41
8442 9455 0.179073 ATGGGATCGGTTGAGCTTCG 60.179 55.000 0.00 0.00 0.00 3.79
8450 9463 3.282021 CAGATTGTTCATGGGATCGGTT 58.718 45.455 0.00 0.00 0.00 4.44
8453 9466 1.605710 GGCAGATTGTTCATGGGATCG 59.394 52.381 0.00 0.00 0.00 3.69
8495 9508 2.526873 AAGGGTGTGAGGCCGACT 60.527 61.111 9.12 0.00 0.00 4.18
8530 9543 7.064609 GGATCGACACTGACAGAAAAATAATCA 59.935 37.037 10.08 0.00 0.00 2.57
8542 9555 2.675032 GCATTGAGGATCGACACTGACA 60.675 50.000 10.56 0.00 38.61 3.58
8546 9559 2.223923 GCTAGCATTGAGGATCGACACT 60.224 50.000 10.63 0.00 38.61 3.55
8548 9561 1.756538 TGCTAGCATTGAGGATCGACA 59.243 47.619 14.93 0.00 38.61 4.35
8579 9592 2.436824 GAGCTCCCCTTTGGCGTC 60.437 66.667 0.87 0.00 0.00 5.19
8634 9647 2.082231 CAATGTGAGGCCTGACAAGAG 58.918 52.381 29.26 17.07 29.00 2.85
8642 9655 1.136329 ACCCAGACAATGTGAGGCCT 61.136 55.000 3.86 3.86 0.00 5.19
8660 9673 2.772691 CGTCGACCTCCCTGGCTAC 61.773 68.421 10.58 0.00 40.22 3.58
8676 9689 1.271054 GGGCATGATGGAGCTATTCGT 60.271 52.381 0.00 0.00 0.00 3.85
8691 9704 4.115199 GGGCTCCAAGACGGGCAT 62.115 66.667 0.00 0.00 33.81 4.40
8698 9711 0.914644 CTGGATCAAGGGCTCCAAGA 59.085 55.000 0.00 0.00 40.92 3.02
8733 9746 0.747644 TATCTTGTCGACCGGCCGTA 60.748 55.000 26.12 2.09 0.00 4.02
8747 9761 9.254133 CGTTGATCAGACACATCTAATTATCTT 57.746 33.333 0.00 0.00 32.25 2.40


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

AutoCloner maintained by Alex Coulton.