Multiple sequence alignment - TraesCS3B01G509100

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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 TraesCS3B01G509100 chr3B 100.000 3421 0 0 1 3421 753175317 753171897 0.000000e+00 6318
1 TraesCS3B01G509100 chr3B 88.746 311 34 1 1 311 173337187 173336878 2.490000e-101 379
2 TraesCS3B01G509100 chr3B 86.709 158 10 6 294 450 173336509 173336362 7.590000e-37 165
3 TraesCS3B01G509100 chr3A 84.619 2035 167 58 506 2459 699520802 699522771 0.000000e+00 1890
4 TraesCS3B01G509100 chr3A 85.408 980 114 19 2456 3419 699523033 699523999 0.000000e+00 990
5 TraesCS3B01G509100 chr3A 82.828 297 37 8 2130 2414 114570739 114571033 1.580000e-63 254
6 TraesCS3B01G509100 chr3A 82.119 302 41 8 2130 2420 576419631 576419930 2.640000e-61 246
7 TraesCS3B01G509100 chr3A 80.087 231 30 14 3202 3421 144268330 144268555 1.270000e-34 158
8 TraesCS3B01G509100 chr3D 88.088 1276 67 24 713 1974 565037370 565038574 0.000000e+00 1435
9 TraesCS3B01G509100 chr3D 86.104 806 80 19 2456 3254 565051936 565052716 0.000000e+00 839
10 TraesCS3B01G509100 chr1B 92.157 306 23 1 1 306 41359340 41359036 6.780000e-117 431
11 TraesCS3B01G509100 chr1B 91.176 306 27 0 1 306 660777822 660778127 1.900000e-112 416
12 TraesCS3B01G509100 chr1B 93.151 146 10 0 306 451 660778511 660778656 7.440000e-52 215
13 TraesCS3B01G509100 chr1B 91.096 146 10 2 306 451 41358652 41358510 9.690000e-46 195
14 TraesCS3B01G509100 chr5D 82.508 303 38 9 2130 2420 201312265 201311966 5.670000e-63 252
15 TraesCS3B01G509100 chr5D 80.795 302 45 8 2130 2420 99307148 99307447 1.240000e-54 224
16 TraesCS3B01G509100 chr7A 82.492 297 39 8 2130 2415 649425091 649424797 7.330000e-62 248
17 TraesCS3B01G509100 chr7A 86.700 203 22 5 2218 2416 230301187 230300986 1.600000e-53 220
18 TraesCS3B01G509100 chr4A 82.237 304 38 10 2130 2420 166730254 166729954 7.330000e-62 248
19 TraesCS3B01G509100 chr4A 83.511 188 21 7 124 311 737221387 737221210 2.110000e-37 167
20 TraesCS3B01G509100 chr4A 85.443 158 22 1 294 450 737220472 737220315 2.730000e-36 163
21 TraesCS3B01G509100 chr4A 79.825 228 32 13 3203 3419 2397124 2396900 1.640000e-33 154
22 TraesCS3B01G509100 chr4A 86.555 119 16 0 6 124 737239411 737239293 7.700000e-27 132
23 TraesCS3B01G509100 chr2A 82.178 303 40 8 2130 2420 769575748 769576048 7.330000e-62 248
24 TraesCS3B01G509100 chr5A 81.879 298 42 10 2130 2416 210535684 210535388 1.230000e-59 241
25 TraesCS3B01G509100 chr5A 89.000 100 10 1 294 392 506338019 506337920 4.640000e-24 122
26 TraesCS3B01G509100 chr2D 82.857 175 21 7 3202 3370 58733828 58733999 7.650000e-32 148
27 TraesCS3B01G509100 chr4D 78.947 190 29 8 1199 1381 112197199 112197014 6.000000e-23 119
28 TraesCS3B01G509100 chr4B 88.506 87 10 0 1295 1381 658966977 658967063 4.670000e-19 106


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 TraesCS3B01G509100 chr3B 753171897 753175317 3420 True 6318.0 6318 100.0000 1 3421 1 chr3B.!!$R1 3420
1 TraesCS3B01G509100 chr3B 173336362 173337187 825 True 272.0 379 87.7275 1 450 2 chr3B.!!$R2 449
2 TraesCS3B01G509100 chr3A 699520802 699523999 3197 False 1440.0 1890 85.0135 506 3419 2 chr3A.!!$F4 2913
3 TraesCS3B01G509100 chr3D 565037370 565038574 1204 False 1435.0 1435 88.0880 713 1974 1 chr3D.!!$F1 1261
4 TraesCS3B01G509100 chr3D 565051936 565052716 780 False 839.0 839 86.1040 2456 3254 1 chr3D.!!$F2 798
5 TraesCS3B01G509100 chr1B 660777822 660778656 834 False 315.5 416 92.1635 1 451 2 chr1B.!!$F1 450
6 TraesCS3B01G509100 chr1B 41358510 41359340 830 True 313.0 431 91.6265 1 451 2 chr1B.!!$R1 450

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
511 903 0.035152 TCAGCCAGCGTGGAATTCAT 60.035 50.0 7.93 0.0 40.96 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2426 2899 0.038343 CGTCATGGGCCCAAAAACAG 60.038 55.0 32.58 17.71 0.0 3.16 R

All possible primers

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

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
61 62 1.274476 GTTTGAAGTTGCGTCGCGA 59.726 52.632 13.38 3.71 0.00 5.87
64 65 0.042535 TTGAAGTTGCGTCGCGAAAG 60.043 50.000 12.06 9.75 0.00 2.62
65 66 1.154654 GAAGTTGCGTCGCGAAAGG 60.155 57.895 12.06 4.27 0.00 3.11
157 159 1.207791 CAGCAGACCAGGGGAGTTAT 58.792 55.000 0.00 0.00 0.00 1.89
158 160 1.139853 CAGCAGACCAGGGGAGTTATC 59.860 57.143 0.00 0.00 0.00 1.75
162 164 1.380785 ACCAGGGGAGTTATCGCGA 60.381 57.895 13.09 13.09 39.23 5.87
171 173 0.244450 AGTTATCGCGAACGGGAACA 59.756 50.000 15.24 6.48 40.40 3.18
246 248 1.959226 TCGCTTTCTCACCAACCGC 60.959 57.895 0.00 0.00 0.00 5.68
286 288 2.732016 CAGCAGCTGCAGCCAAAA 59.268 55.556 38.24 0.00 45.16 2.44
288 290 2.732094 GCAGCTGCAGCCAAAACG 60.732 61.111 34.39 16.78 43.38 3.60
294 296 2.909965 GCAGCCAAAACGTCCCCA 60.910 61.111 0.00 0.00 0.00 4.96
380 772 2.160171 TGGAGGTGGTGGAAAGGGG 61.160 63.158 0.00 0.00 0.00 4.79
463 855 3.410960 CTCATCTAGCTTTGGGCCC 57.589 57.895 17.59 17.59 43.05 5.80
464 856 0.842635 CTCATCTAGCTTTGGGCCCT 59.157 55.000 25.70 4.09 43.05 5.19
465 857 1.213926 CTCATCTAGCTTTGGGCCCTT 59.786 52.381 25.70 5.94 43.05 3.95
466 858 1.640670 TCATCTAGCTTTGGGCCCTTT 59.359 47.619 25.70 6.32 43.05 3.11
467 859 2.042979 TCATCTAGCTTTGGGCCCTTTT 59.957 45.455 25.70 6.71 43.05 2.27
468 860 2.215942 TCTAGCTTTGGGCCCTTTTC 57.784 50.000 25.70 9.97 43.05 2.29
469 861 1.186200 CTAGCTTTGGGCCCTTTTCC 58.814 55.000 25.70 7.64 43.05 3.13
470 862 0.485099 TAGCTTTGGGCCCTTTTCCA 59.515 50.000 25.70 0.00 43.05 3.53
471 863 0.399806 AGCTTTGGGCCCTTTTCCAA 60.400 50.000 25.70 4.23 43.05 3.53
472 864 0.035317 GCTTTGGGCCCTTTTCCAAG 59.965 55.000 25.70 15.26 43.05 3.61
473 865 1.715785 CTTTGGGCCCTTTTCCAAGA 58.284 50.000 25.70 0.00 43.05 3.02
474 866 1.344438 CTTTGGGCCCTTTTCCAAGAC 59.656 52.381 25.70 0.00 43.05 3.01
475 867 0.263172 TTGGGCCCTTTTCCAAGACA 59.737 50.000 25.70 0.00 38.04 3.41
476 868 0.469144 TGGGCCCTTTTCCAAGACAC 60.469 55.000 25.70 0.00 30.57 3.67
477 869 1.185618 GGGCCCTTTTCCAAGACACC 61.186 60.000 17.04 0.00 30.57 4.16
478 870 0.469144 GGCCCTTTTCCAAGACACCA 60.469 55.000 0.00 0.00 30.57 4.17
479 871 1.408969 GCCCTTTTCCAAGACACCAA 58.591 50.000 0.00 0.00 30.57 3.67
480 872 1.970640 GCCCTTTTCCAAGACACCAAT 59.029 47.619 0.00 0.00 30.57 3.16
481 873 2.368548 GCCCTTTTCCAAGACACCAATT 59.631 45.455 0.00 0.00 30.57 2.32
482 874 3.181455 GCCCTTTTCCAAGACACCAATTT 60.181 43.478 0.00 0.00 30.57 1.82
483 875 4.379652 CCCTTTTCCAAGACACCAATTTG 58.620 43.478 0.00 0.00 30.57 2.32
484 876 4.379652 CCTTTTCCAAGACACCAATTTGG 58.620 43.478 14.02 14.02 42.12 3.28
485 877 4.141733 CCTTTTCCAAGACACCAATTTGGT 60.142 41.667 15.48 15.48 41.38 3.67
486 878 5.427378 CTTTTCCAAGACACCAATTTGGTT 58.573 37.500 18.52 10.16 39.67 3.67
487 879 5.523552 CTTTTCCAAGACACCAATTTGGTTC 59.476 40.000 18.52 17.29 39.67 3.62
488 880 6.630188 CTTTTCCAAGACACCAATTTGGTTCT 60.630 38.462 18.52 18.95 39.67 3.01
489 881 8.062512 CTTTTCCAAGACACCAATTTGGTTCTT 61.063 37.037 24.77 24.77 42.74 2.52
496 888 3.030668 CCAATTTGGTTCTTGGTCAGC 57.969 47.619 7.31 0.00 37.67 4.26
497 889 2.289010 CCAATTTGGTTCTTGGTCAGCC 60.289 50.000 7.31 0.00 37.67 4.85
498 890 2.364970 CAATTTGGTTCTTGGTCAGCCA 59.635 45.455 0.00 0.00 44.38 4.75
499 891 1.691196 TTTGGTTCTTGGTCAGCCAG 58.309 50.000 0.00 0.00 46.91 4.85
500 892 0.823356 TTGGTTCTTGGTCAGCCAGC 60.823 55.000 0.00 0.00 46.91 4.85
501 893 2.328099 GGTTCTTGGTCAGCCAGCG 61.328 63.158 0.00 0.00 46.91 5.18
502 894 1.598130 GTTCTTGGTCAGCCAGCGT 60.598 57.895 0.00 0.00 46.91 5.07
503 895 1.597854 TTCTTGGTCAGCCAGCGTG 60.598 57.895 0.00 0.00 46.91 5.34
504 896 3.052082 CTTGGTCAGCCAGCGTGG 61.052 66.667 0.25 0.25 46.91 4.94
511 903 0.035152 TCAGCCAGCGTGGAATTCAT 60.035 50.000 7.93 0.00 40.96 2.57
523 915 1.690352 GGAATTCATCCCATTGGGCTG 59.310 52.381 17.87 17.87 43.94 4.85
527 919 2.323999 TCATCCCATTGGGCTGTTTT 57.676 45.000 21.91 0.00 43.94 2.43
528 920 1.901159 TCATCCCATTGGGCTGTTTTG 59.099 47.619 21.91 10.53 43.94 2.44
532 924 1.415659 CCCATTGGGCTGTTTTGAACA 59.584 47.619 9.28 0.00 35.35 3.18
537 929 6.275335 CCATTGGGCTGTTTTGAACATATAG 58.725 40.000 0.00 0.00 41.26 1.31
541 933 7.624360 TGGGCTGTTTTGAACATATAGTAAG 57.376 36.000 0.00 0.00 41.26 2.34
546 938 9.057089 GCTGTTTTGAACATATAGTAAGCCTAT 57.943 33.333 0.00 0.00 41.26 2.57
632 1028 3.560251 ACTCGTGCCCAGCCTTGT 61.560 61.111 0.00 0.00 0.00 3.16
633 1029 3.052082 CTCGTGCCCAGCCTTGTG 61.052 66.667 0.00 0.00 0.00 3.33
643 1039 4.533566 GCCTTGTGCGCAAAGTAC 57.466 55.556 14.00 8.91 33.73 2.73
644 1040 1.652012 GCCTTGTGCGCAAAGTACA 59.348 52.632 14.00 1.50 43.67 2.90
645 1041 0.385974 GCCTTGTGCGCAAAGTACAG 60.386 55.000 14.00 0.00 45.82 2.74
646 1042 0.385974 CCTTGTGCGCAAAGTACAGC 60.386 55.000 14.00 0.00 45.82 4.40
698 1094 0.913205 TATAAACTTGCCGGGCCAGA 59.087 50.000 25.32 4.82 0.00 3.86
743 1151 0.105408 ACGCTAATACCGGCCGATTT 59.895 50.000 30.73 18.79 0.00 2.17
767 1175 1.078637 GGTTTGCTACGGGTCCCTC 60.079 63.158 6.29 0.00 0.00 4.30
780 1188 1.409661 GGTCCCTCTCTCTGTCTCTCC 60.410 61.905 0.00 0.00 0.00 3.71
810 1229 0.251077 CATCCCCTTCCTATGCAGGC 60.251 60.000 0.00 0.00 42.30 4.85
811 1230 0.698886 ATCCCCTTCCTATGCAGGCA 60.699 55.000 0.00 0.00 42.30 4.75
812 1231 1.150081 CCCCTTCCTATGCAGGCAG 59.850 63.158 0.00 0.00 42.30 4.85
818 1237 2.203308 CTATGCAGGCAGGGGCAG 60.203 66.667 0.00 0.00 44.24 4.85
894 1313 6.935208 AGGAGCGGATAATAAATCTGGTAAAC 59.065 38.462 0.00 0.00 35.52 2.01
914 1333 5.373812 AACATCGTCTCCCCTTTATCATT 57.626 39.130 0.00 0.00 0.00 2.57
921 1340 6.489361 TCGTCTCCCCTTTATCATTACTCTAC 59.511 42.308 0.00 0.00 0.00 2.59
928 1347 6.383415 CCTTTATCATTACTCTACCTCTCGC 58.617 44.000 0.00 0.00 0.00 5.03
1008 1427 0.673985 TCGATCCAGTAATGGAGGCG 59.326 55.000 23.32 23.32 41.88 5.52
1197 1622 1.299648 CAAGAACTCCATGGCGGGA 59.700 57.895 6.96 0.00 34.36 5.14
1462 1887 0.588252 TGCTGCTGACGAAGAAAAGC 59.412 50.000 0.00 0.00 36.18 3.51
1485 1910 0.934496 CGGCAACTGAAGAACGTTCA 59.066 50.000 28.78 9.64 0.00 3.18
1519 1944 7.225538 AGTGAGTGAACTGAACTAATGTTTCAG 59.774 37.037 9.94 9.94 36.39 3.02
1533 1958 3.860641 TGTTTCAGCAGATTAGCGATGA 58.139 40.909 0.00 0.00 40.15 2.92
1534 1959 4.445453 TGTTTCAGCAGATTAGCGATGAT 58.555 39.130 0.00 0.00 40.15 2.45
1535 1960 4.877823 TGTTTCAGCAGATTAGCGATGATT 59.122 37.500 0.00 0.00 40.15 2.57
1536 1961 5.007039 TGTTTCAGCAGATTAGCGATGATTC 59.993 40.000 0.00 0.00 40.15 2.52
1537 1962 4.326504 TCAGCAGATTAGCGATGATTCA 57.673 40.909 0.00 0.00 40.15 2.57
1538 1963 4.696455 TCAGCAGATTAGCGATGATTCAA 58.304 39.130 0.00 0.00 40.15 2.69
1539 1964 4.509230 TCAGCAGATTAGCGATGATTCAAC 59.491 41.667 0.00 0.00 40.15 3.18
1540 1965 4.271776 CAGCAGATTAGCGATGATTCAACA 59.728 41.667 0.00 0.00 40.15 3.33
1541 1966 5.049612 CAGCAGATTAGCGATGATTCAACAT 60.050 40.000 0.00 0.00 40.15 2.71
1542 1967 5.530171 AGCAGATTAGCGATGATTCAACATT 59.470 36.000 0.00 0.00 40.15 2.71
1543 1968 5.850128 GCAGATTAGCGATGATTCAACATTC 59.150 40.000 0.00 0.00 0.00 2.67
1544 1969 6.069563 CAGATTAGCGATGATTCAACATTCG 58.930 40.000 3.59 3.59 0.00 3.34
1545 1970 5.985530 AGATTAGCGATGATTCAACATTCGA 59.014 36.000 10.68 0.00 0.00 3.71
1546 1971 6.479990 AGATTAGCGATGATTCAACATTCGAA 59.520 34.615 10.68 0.00 0.00 3.71
1547 1972 4.944962 AGCGATGATTCAACATTCGAAA 57.055 36.364 0.00 0.00 0.00 3.46
1548 1973 5.295431 AGCGATGATTCAACATTCGAAAA 57.705 34.783 0.00 0.00 0.00 2.29
1549 1974 5.698832 AGCGATGATTCAACATTCGAAAAA 58.301 33.333 0.00 0.00 0.00 1.94
1550 1975 5.796935 AGCGATGATTCAACATTCGAAAAAG 59.203 36.000 0.00 0.00 0.00 2.27
1551 1976 5.794945 GCGATGATTCAACATTCGAAAAAGA 59.205 36.000 0.00 0.00 0.00 2.52
1552 1977 6.470235 GCGATGATTCAACATTCGAAAAAGAT 59.530 34.615 0.00 0.00 0.00 2.40
1553 1978 7.008628 GCGATGATTCAACATTCGAAAAAGATT 59.991 33.333 0.00 0.00 0.00 2.40
1554 1979 9.489393 CGATGATTCAACATTCGAAAAAGATTA 57.511 29.630 0.00 0.00 0.00 1.75
1556 1981 8.673626 TGATTCAACATTCGAAAAAGATTAGC 57.326 30.769 0.00 0.00 0.00 3.09
1557 1982 7.481483 TGATTCAACATTCGAAAAAGATTAGCG 59.519 33.333 0.00 0.00 0.00 4.26
1601 2026 5.707298 TCTGATTCGAAATGGCTCTTCTTTT 59.293 36.000 0.00 0.00 0.00 2.27
1666 2091 3.783191 GGTAGTGTACCTCTAGCAAAGC 58.217 50.000 14.96 0.00 45.52 3.51
1684 2109 7.075674 GCAAAGCTGCCATTTTTATTTGTAT 57.924 32.000 0.00 0.00 43.26 2.29
1688 2113 6.340522 AGCTGCCATTTTTATTTGTATGTCC 58.659 36.000 0.00 0.00 0.00 4.02
1719 2144 8.547967 TTATGTCTGTCAGACCTTTTTATCAC 57.452 34.615 26.51 2.21 44.44 3.06
1726 2151 4.225267 TCAGACCTTTTTATCACCCTCTCC 59.775 45.833 0.00 0.00 0.00 3.71
1727 2152 4.019321 CAGACCTTTTTATCACCCTCTCCA 60.019 45.833 0.00 0.00 0.00 3.86
1728 2153 4.226168 AGACCTTTTTATCACCCTCTCCAG 59.774 45.833 0.00 0.00 0.00 3.86
1729 2154 3.916989 ACCTTTTTATCACCCTCTCCAGT 59.083 43.478 0.00 0.00 0.00 4.00
1730 2155 4.263506 ACCTTTTTATCACCCTCTCCAGTG 60.264 45.833 0.00 0.00 35.24 3.66
1731 2156 4.265073 CTTTTTATCACCCTCTCCAGTGG 58.735 47.826 1.40 1.40 34.67 4.00
1732 2157 1.204146 TTATCACCCTCTCCAGTGGC 58.796 55.000 3.51 0.00 34.67 5.01
1745 2170 4.697756 GTGGCCAGTGCTACCGCA 62.698 66.667 5.11 0.00 42.66 5.69
1755 2180 1.812507 GCTACCGCACTTTACCCCG 60.813 63.158 0.00 0.00 35.78 5.73
1769 2194 0.755686 ACCCCGGTTACACGTTTGTA 59.244 50.000 0.00 0.00 37.15 2.41
1773 2198 2.412770 CCCGGTTACACGTTTGTATGTC 59.587 50.000 0.00 0.00 38.05 3.06
1783 2208 9.911138 TTACACGTTTGTATGTCTAAAGATACA 57.089 29.630 0.00 0.00 39.23 2.29
1784 2209 8.462143 ACACGTTTGTATGTCTAAAGATACAG 57.538 34.615 0.00 0.00 41.21 2.74
1785 2210 8.086522 ACACGTTTGTATGTCTAAAGATACAGT 58.913 33.333 0.00 0.00 41.21 3.55
1786 2211 9.563898 CACGTTTGTATGTCTAAAGATACAGTA 57.436 33.333 0.00 0.00 41.21 2.74
1787 2212 9.784680 ACGTTTGTATGTCTAAAGATACAGTAG 57.215 33.333 0.00 0.00 41.21 2.57
1815 2243 9.913310 TGTATATTGTAAAATCCATCCTGACAA 57.087 29.630 0.00 0.00 0.00 3.18
1899 2337 9.561069 AAACAGTCTATTCAAATCACAACTACT 57.439 29.630 0.00 0.00 0.00 2.57
1974 2412 9.256477 CAATAGCAAAATCACCGTCTATAAGTA 57.744 33.333 0.00 0.00 0.00 2.24
1975 2413 9.998106 AATAGCAAAATCACCGTCTATAAGTAT 57.002 29.630 0.00 0.00 0.00 2.12
1983 2447 9.962783 AATCACCGTCTATAAGTATTCTTGTAC 57.037 33.333 0.00 0.00 35.36 2.90
2001 2465 7.486647 TCTTGTACGTTTACATATTCCCTCTC 58.513 38.462 0.00 0.00 38.05 3.20
2006 2470 9.807649 GTACGTTTACATATTCCCTCTCTAAAA 57.192 33.333 0.00 0.00 0.00 1.52
2034 2498 4.982999 TCAGAGCGTTTAGATCACTACAC 58.017 43.478 0.00 0.00 37.82 2.90
2075 2539 9.587772 TTTTATCTTCTCTCGATTCCTTTGTAG 57.412 33.333 0.00 0.00 0.00 2.74
2079 2543 5.344743 TCTCTCGATTCCTTTGTAGCAAT 57.655 39.130 0.00 0.00 0.00 3.56
2081 2545 5.127845 TCTCTCGATTCCTTTGTAGCAATCT 59.872 40.000 0.00 0.00 0.00 2.40
2086 2550 6.035650 TCGATTCCTTTGTAGCAATCTTTACG 59.964 38.462 0.00 0.00 0.00 3.18
2103 2567 5.708697 TCTTTACGGATGACTGACTAGACAA 59.291 40.000 0.00 0.00 32.61 3.18
2139 2604 3.726004 GGGGGCCCCTTTGATTTG 58.274 61.111 39.92 0.00 41.34 2.32
2143 2608 1.552254 GGGGCCCCTTTGATTTGAAGA 60.552 52.381 35.49 0.00 0.00 2.87
2209 2674 6.718454 TTTTCTGTTGGTTGTTTGTGATTG 57.282 33.333 0.00 0.00 0.00 2.67
2211 2676 5.651387 TCTGTTGGTTGTTTGTGATTGAA 57.349 34.783 0.00 0.00 0.00 2.69
2212 2677 6.219417 TCTGTTGGTTGTTTGTGATTGAAT 57.781 33.333 0.00 0.00 0.00 2.57
2213 2678 6.272318 TCTGTTGGTTGTTTGTGATTGAATC 58.728 36.000 0.00 0.00 0.00 2.52
2214 2679 5.970592 TGTTGGTTGTTTGTGATTGAATCA 58.029 33.333 3.29 3.29 36.84 2.57
2215 2680 6.580788 TGTTGGTTGTTTGTGATTGAATCAT 58.419 32.000 11.46 0.00 42.04 2.45
2216 2681 7.720442 TGTTGGTTGTTTGTGATTGAATCATA 58.280 30.769 11.46 5.78 42.04 2.15
2218 2683 9.853555 GTTGGTTGTTTGTGATTGAATCATATA 57.146 29.630 11.46 1.03 42.04 0.86
2259 2730 9.838339 GGATTTCTTTGTTCTATTCTCCATAGA 57.162 33.333 0.00 0.00 42.00 1.98
2284 2755 9.178758 GAATTTCTAGTATCCATTTGAACCTGT 57.821 33.333 0.00 0.00 0.00 4.00
2287 2758 7.921786 TCTAGTATCCATTTGAACCTGTTTG 57.078 36.000 0.00 0.00 0.00 2.93
2292 2763 6.729690 ATCCATTTGAACCTGTTTGAAAGA 57.270 33.333 0.00 0.00 0.00 2.52
2310 2781 9.594478 TTTGAAAGAATCCTTTGTTTTTCCTAC 57.406 29.630 0.00 0.00 42.30 3.18
2334 2806 5.389725 CGATGCAATCAAACAACCAAAATCC 60.390 40.000 0.00 0.00 45.97 3.01
2338 2810 5.277442 GCAATCAAACAACCAAAATCCTGTG 60.277 40.000 0.00 0.00 0.00 3.66
2356 2828 1.952296 GTGGGATTGAGATGACCATGC 59.048 52.381 0.00 0.00 33.19 4.06
2361 2833 3.640029 GGATTGAGATGACCATGCCATTT 59.360 43.478 1.21 0.00 0.00 2.32
2362 2834 4.261909 GGATTGAGATGACCATGCCATTTC 60.262 45.833 8.80 8.80 0.00 2.17
2377 2849 7.011669 CCATGCCATTTCAATCCTATGTTTTTC 59.988 37.037 0.00 0.00 0.00 2.29
2379 2851 6.213195 TGCCATTTCAATCCTATGTTTTTCCT 59.787 34.615 0.00 0.00 0.00 3.36
2398 2870 7.916077 TTTCCTATTCCAGGGTTTTTACAAA 57.084 32.000 0.00 0.00 45.58 2.83
2401 2874 6.492087 TCCTATTCCAGGGTTTTTACAAACTG 59.508 38.462 4.59 0.00 45.58 3.16
2414 2887 7.769272 TTTTACAAACTGCAAATCAAAGAGG 57.231 32.000 0.00 0.00 0.00 3.69
2420 2893 3.755378 ACTGCAAATCAAAGAGGCACTAG 59.245 43.478 0.00 0.00 41.55 2.57
2426 2899 3.963428 TCAAAGAGGCACTAGTCTTCC 57.037 47.619 0.00 0.00 41.55 3.46
2429 2902 2.614134 AGAGGCACTAGTCTTCCTGT 57.386 50.000 11.44 6.03 41.55 4.00
2441 2914 1.132881 TCTTCCTGTTTTTGGGCCCAT 60.133 47.619 29.23 0.00 0.00 4.00
2445 2918 0.038343 CTGTTTTTGGGCCCATGACG 60.038 55.000 29.23 15.65 0.00 4.35
2448 2921 1.814772 TTTTTGGGCCCATGACGCAG 61.815 55.000 29.23 0.00 0.00 5.18
2459 2932 2.031682 CCATGACGCAGCCTTTATTAGC 60.032 50.000 0.00 0.00 0.00 3.09
2461 2934 3.812156 TGACGCAGCCTTTATTAGCTA 57.188 42.857 0.00 0.00 37.18 3.32
2464 2937 2.100252 ACGCAGCCTTTATTAGCTACGA 59.900 45.455 11.23 0.00 46.39 3.43
2465 2938 3.120792 CGCAGCCTTTATTAGCTACGAA 58.879 45.455 0.00 0.00 46.39 3.85
2469 3208 5.007724 GCAGCCTTTATTAGCTACGAAATGT 59.992 40.000 0.00 0.00 37.18 2.71
2564 3304 1.207089 CTGTACCGAAGAATGGAGGCA 59.793 52.381 0.00 0.00 0.00 4.75
2626 3368 2.968574 TCATAGTTCTCCTCATGAGCCC 59.031 50.000 17.76 2.58 41.18 5.19
2631 3373 0.615331 TCTCCTCATGAGCCCAACAC 59.385 55.000 17.76 0.00 41.18 3.32
2641 3383 3.645975 CCCAACACACCGCACGAC 61.646 66.667 0.00 0.00 0.00 4.34
2642 3384 2.892914 CCAACACACCGCACGACA 60.893 61.111 0.00 0.00 0.00 4.35
2643 3385 2.323105 CAACACACCGCACGACAC 59.677 61.111 0.00 0.00 0.00 3.67
2644 3386 2.125472 AACACACCGCACGACACA 60.125 55.556 0.00 0.00 0.00 3.72
2645 3387 2.171079 AACACACCGCACGACACAG 61.171 57.895 0.00 0.00 0.00 3.66
2646 3388 4.000557 CACACCGCACGACACAGC 62.001 66.667 0.00 0.00 0.00 4.40
2660 3402 2.508887 CAGCCACGCAGAGCTCTC 60.509 66.667 14.96 8.15 38.45 3.20
2668 3410 3.898509 CAGAGCTCTCGCCTCCGG 61.899 72.222 14.96 0.00 36.60 5.14
2689 3431 4.293662 GGAATTCAGGTTCCAACTCTCT 57.706 45.455 7.93 0.00 45.63 3.10
2700 3442 1.000171 CCAACTCTCTTTGCAAAGGCC 60.000 52.381 33.01 0.00 40.13 5.19
2708 3450 0.177604 TTTGCAAAGGCCCACAACAG 59.822 50.000 8.05 0.00 40.13 3.16
2710 3452 1.832167 GCAAAGGCCCACAACAGGA 60.832 57.895 0.00 0.00 0.00 3.86
2715 3457 0.032615 AGGCCCACAACAGGAAACAA 60.033 50.000 0.00 0.00 0.00 2.83
2748 3490 0.114954 ATGGTCCAGGCCAACAACAT 59.885 50.000 5.01 0.00 42.48 2.71
2791 3533 4.238761 CAGGAAATATTGCTGCATCAGG 57.761 45.455 1.84 0.00 42.18 3.86
2809 3551 6.626623 GCATCAGGCATGAAAAGAATTGTACT 60.627 38.462 4.62 0.00 43.97 2.73
2813 3555 6.805271 CAGGCATGAAAAGAATTGTACTTGAG 59.195 38.462 0.00 0.00 0.00 3.02
2836 3578 0.389948 GGCGGAAAGACAGACGTGAT 60.390 55.000 0.00 0.00 0.00 3.06
2847 3589 4.627467 AGACAGACGTGATTGAAATAGTGC 59.373 41.667 0.00 0.00 0.00 4.40
2858 3600 4.707030 TGAAATAGTGCTTTCATGCCTG 57.293 40.909 0.00 0.00 39.55 4.85
2878 3620 1.808945 GGTCTCAGGTGCAGATTTGTG 59.191 52.381 0.00 0.00 0.00 3.33
2915 3657 7.964604 ATTGAGGTCGGTATAAGCTTTAATC 57.035 36.000 3.20 0.00 0.00 1.75
2924 3666 6.603095 GGTATAAGCTTTAATCTTCATGGCG 58.397 40.000 3.20 0.00 0.00 5.69
2961 3703 5.816955 AGGAGCCTCACTATTATTTCTCC 57.183 43.478 0.00 0.00 39.20 3.71
2966 3708 5.848921 AGCCTCACTATTATTTCTCCCAGAT 59.151 40.000 0.00 0.00 0.00 2.90
2981 3723 1.328680 CCAGATTTTCGTGCATCCGAG 59.671 52.381 0.00 0.00 38.23 4.63
2993 3735 1.422388 CATCCGAGATATGCCACACG 58.578 55.000 0.00 0.00 0.00 4.49
3009 3751 2.293122 CACACGGTGACAACCATGATTT 59.707 45.455 16.29 0.00 42.45 2.17
3053 3795 3.125316 GCGAGAGAAAATCGAACAACCAT 59.875 43.478 0.00 0.00 42.76 3.55
3075 3817 1.377366 TTGGGTTGCGAAAACTGCGA 61.377 50.000 0.00 0.00 34.24 5.10
3132 3874 0.687920 TGGCAAACCACCGACTCATA 59.312 50.000 0.00 0.00 42.67 2.15
3170 3914 8.175925 TGACAAAACTCCATGAAATTACATCA 57.824 30.769 0.00 0.00 0.00 3.07
3171 3915 8.805175 TGACAAAACTCCATGAAATTACATCAT 58.195 29.630 0.00 0.00 38.02 2.45
3194 3938 0.534877 AGTGTTCCTGCATCGCACAA 60.535 50.000 11.51 0.00 33.79 3.33
3198 3942 2.035704 TGTTCCTGCATCGCACAAAAAT 59.964 40.909 0.00 0.00 33.79 1.82
3199 3943 2.634982 TCCTGCATCGCACAAAAATC 57.365 45.000 0.00 0.00 33.79 2.17
3232 3977 5.041951 TGTCACTCAATTACGATTTTGGC 57.958 39.130 0.00 0.00 0.00 4.52
3285 4037 3.985279 TGTCGGTTGTCAAGTTTATCTCG 59.015 43.478 0.00 0.00 0.00 4.04
3297 4049 5.019785 AGTTTATCTCGGGACATTGGTAC 57.980 43.478 0.00 0.00 0.00 3.34
3303 4055 1.006758 TCGGGACATTGGTACCTCTCT 59.993 52.381 14.36 0.00 46.84 3.10
3324 4076 1.246056 TGGTCTACGGACTTCGGTGG 61.246 60.000 0.00 0.00 44.45 4.61
3348 4101 3.560105 CCCCATTCAAAAAGGGCAAAAA 58.440 40.909 0.00 0.00 41.42 1.94
3349 4102 3.569277 CCCCATTCAAAAAGGGCAAAAAG 59.431 43.478 0.00 0.00 41.42 2.27
3350 4103 3.004629 CCCATTCAAAAAGGGCAAAAAGC 59.995 43.478 0.00 0.00 44.65 3.51
3375 4128 2.920912 TTCGGTGGCTCGGAAGGT 60.921 61.111 5.58 0.00 32.84 3.50
3403 4159 5.007332 TCGGTTGTTTTTGAGCTAGAGAAAC 59.993 40.000 0.00 0.00 0.00 2.78
3404 4160 5.520632 GGTTGTTTTTGAGCTAGAGAAACC 58.479 41.667 0.00 4.09 31.11 3.27
3415 4171 6.376299 TGAGCTAGAGAAACCGTACTATCAAA 59.624 38.462 0.00 0.00 0.00 2.69
3419 4175 5.731591 AGAGAAACCGTACTATCAAAAGGG 58.268 41.667 0.00 0.00 0.00 3.95
3420 4176 4.840271 AGAAACCGTACTATCAAAAGGGG 58.160 43.478 0.00 0.00 0.00 4.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
36 37 0.099791 CGCAACTTCAAACCCACGTT 59.900 50.000 0.00 0.00 0.00 3.99
37 38 1.027792 ACGCAACTTCAAACCCACGT 61.028 50.000 0.00 0.00 0.00 4.49
43 44 0.315544 TTCGCGACGCAACTTCAAAC 60.316 50.000 21.35 0.00 0.00 2.93
204 206 2.009042 GCTGCATTGACTAAGGCTCGT 61.009 52.381 0.00 0.00 43.58 4.18
246 248 2.124983 CAGCCCGTCATCACTGGG 60.125 66.667 0.00 0.00 46.22 4.45
286 288 0.978146 CATCTCTCCCTTGGGGACGT 60.978 60.000 5.78 0.00 46.17 4.34
288 290 1.529309 GCATCTCTCCCTTGGGGAC 59.471 63.158 5.78 0.00 46.17 4.46
294 296 0.820871 GTGAGTCGCATCTCTCCCTT 59.179 55.000 0.00 0.00 35.68 3.95
357 749 4.954118 TCCACCACCTCCACCGCT 62.954 66.667 0.00 0.00 0.00 5.52
362 754 2.160171 CCCCTTTCCACCACCTCCA 61.160 63.158 0.00 0.00 0.00 3.86
418 810 3.114616 CTCAACTGGCGACGCTGG 61.115 66.667 20.77 14.59 0.00 4.85
419 811 2.356313 ACTCAACTGGCGACGCTG 60.356 61.111 20.77 15.01 0.00 5.18
420 812 2.049063 GACTCAACTGGCGACGCT 60.049 61.111 20.77 0.00 0.00 5.07
421 813 3.470567 CGACTCAACTGGCGACGC 61.471 66.667 12.43 12.43 0.00 5.19
422 814 3.470567 GCGACTCAACTGGCGACG 61.471 66.667 0.00 0.00 0.00 5.12
431 823 0.099613 GATGAGCTCTCGCGACTCAA 59.900 55.000 25.62 13.32 43.23 3.02
450 842 1.186200 GGAAAAGGGCCCAAAGCTAG 58.814 55.000 27.56 0.00 43.05 3.42
451 843 0.485099 TGGAAAAGGGCCCAAAGCTA 59.515 50.000 27.56 5.53 43.05 3.32
452 844 0.399806 TTGGAAAAGGGCCCAAAGCT 60.400 50.000 27.56 0.00 43.05 3.74
453 845 0.035317 CTTGGAAAAGGGCCCAAAGC 59.965 55.000 27.56 10.56 41.41 3.51
454 846 1.344438 GTCTTGGAAAAGGGCCCAAAG 59.656 52.381 27.56 16.45 41.41 2.77
455 847 1.343478 TGTCTTGGAAAAGGGCCCAAA 60.343 47.619 27.56 7.20 41.41 3.28
456 848 0.263172 TGTCTTGGAAAAGGGCCCAA 59.737 50.000 27.56 7.25 39.88 4.12
457 849 0.469144 GTGTCTTGGAAAAGGGCCCA 60.469 55.000 27.56 0.00 0.00 5.36
458 850 1.185618 GGTGTCTTGGAAAAGGGCCC 61.186 60.000 16.46 16.46 0.00 5.80
459 851 0.469144 TGGTGTCTTGGAAAAGGGCC 60.469 55.000 0.00 0.00 0.00 5.80
460 852 1.408969 TTGGTGTCTTGGAAAAGGGC 58.591 50.000 0.00 0.00 0.00 5.19
461 853 4.379652 CAAATTGGTGTCTTGGAAAAGGG 58.620 43.478 0.00 0.00 0.00 3.95
462 854 4.379652 CCAAATTGGTGTCTTGGAAAAGG 58.620 43.478 3.34 0.00 41.88 3.11
477 869 2.364970 TGGCTGACCAAGAACCAAATTG 59.635 45.455 0.00 0.00 45.37 2.32
478 870 2.676748 TGGCTGACCAAGAACCAAATT 58.323 42.857 0.00 0.00 45.37 1.82
479 871 2.380064 TGGCTGACCAAGAACCAAAT 57.620 45.000 0.00 0.00 45.37 2.32
480 872 3.913855 TGGCTGACCAAGAACCAAA 57.086 47.368 0.00 0.00 45.37 3.28
489 881 2.410322 AATTCCACGCTGGCTGACCA 62.410 55.000 0.00 0.00 46.51 4.02
490 882 1.648467 GAATTCCACGCTGGCTGACC 61.648 60.000 0.00 0.00 37.47 4.02
491 883 0.955428 TGAATTCCACGCTGGCTGAC 60.955 55.000 2.27 0.00 37.47 3.51
492 884 0.035152 ATGAATTCCACGCTGGCTGA 60.035 50.000 2.27 0.00 37.47 4.26
493 885 0.379669 GATGAATTCCACGCTGGCTG 59.620 55.000 2.27 0.00 37.47 4.85
494 886 0.749454 GGATGAATTCCACGCTGGCT 60.749 55.000 2.27 0.00 44.74 4.75
495 887 1.729881 GGATGAATTCCACGCTGGC 59.270 57.895 2.27 0.00 44.74 4.85
511 903 2.956848 TGTTCAAAACAGCCCAATGGGA 60.957 45.455 25.00 0.00 40.16 4.37
630 1026 2.258013 GGGCTGTACTTTGCGCACA 61.258 57.895 11.12 1.28 41.00 4.57
632 1028 0.391130 CTAGGGCTGTACTTTGCGCA 60.391 55.000 5.66 5.66 43.26 6.09
633 1029 1.090052 CCTAGGGCTGTACTTTGCGC 61.090 60.000 0.00 0.00 41.52 6.09
634 1030 1.090052 GCCTAGGGCTGTACTTTGCG 61.090 60.000 11.72 0.00 46.69 4.85
635 1031 2.781911 GCCTAGGGCTGTACTTTGC 58.218 57.895 11.72 0.00 46.69 3.68
666 1062 4.096984 GCAAGTTTATAATCAGGCTGTGCT 59.903 41.667 15.27 2.77 0.00 4.40
675 1071 2.303175 GGCCCGGCAAGTTTATAATCA 58.697 47.619 12.58 0.00 0.00 2.57
703 1099 4.557385 GGCCCGATAACCCCGTGG 62.557 72.222 0.00 0.00 37.80 4.94
743 1151 2.033448 CCGTAGCAAACCTGGCCA 59.967 61.111 4.71 4.71 0.00 5.36
767 1175 0.934496 CTACGCGGAGAGACAGAGAG 59.066 60.000 14.92 0.00 0.00 3.20
780 1188 0.460311 AAGGGGATGAACTCTACGCG 59.540 55.000 3.53 3.53 0.00 6.01
818 1237 0.966920 TCGACTTCTGAACAGGGGAC 59.033 55.000 1.93 0.00 0.00 4.46
853 1272 0.465705 TCCTGGTCGGATTCATGCTC 59.534 55.000 0.00 0.00 36.69 4.26
894 1313 6.015010 AGAGTAATGATAAAGGGGAGACGATG 60.015 42.308 0.00 0.00 0.00 3.84
1152 1577 2.025441 GGCTCTCTGCTACGCTCG 59.975 66.667 0.00 0.00 42.39 5.03
1440 1865 1.442769 TTTCTTCGTCAGCAGCATCC 58.557 50.000 0.00 0.00 0.00 3.51
1443 1868 0.588252 GCTTTTCTTCGTCAGCAGCA 59.412 50.000 0.00 0.00 32.17 4.41
1485 1910 3.234353 TCAGTTCACTCACTCACTGGAT 58.766 45.455 0.00 0.00 37.77 3.41
1519 1944 4.801147 TGTTGAATCATCGCTAATCTGC 57.199 40.909 0.00 0.00 0.00 4.26
1533 1958 7.526608 TCGCTAATCTTTTTCGAATGTTGAAT 58.473 30.769 0.00 0.00 0.00 2.57
1534 1959 6.893759 TCGCTAATCTTTTTCGAATGTTGAA 58.106 32.000 0.00 0.00 0.00 2.69
1535 1960 6.474819 TCGCTAATCTTTTTCGAATGTTGA 57.525 33.333 0.00 0.00 0.00 3.18
1536 1961 6.960992 TCATCGCTAATCTTTTTCGAATGTTG 59.039 34.615 0.00 0.00 32.74 3.33
1537 1962 7.072177 TCATCGCTAATCTTTTTCGAATGTT 57.928 32.000 0.00 0.00 32.74 2.71
1538 1963 6.662414 TCATCGCTAATCTTTTTCGAATGT 57.338 33.333 0.00 0.00 32.74 2.71
1539 1964 6.576313 CCATCATCGCTAATCTTTTTCGAATG 59.424 38.462 0.00 0.00 32.74 2.67
1540 1965 6.260936 ACCATCATCGCTAATCTTTTTCGAAT 59.739 34.615 0.00 0.00 32.74 3.34
1541 1966 5.584649 ACCATCATCGCTAATCTTTTTCGAA 59.415 36.000 0.00 0.00 32.74 3.71
1542 1967 5.116180 ACCATCATCGCTAATCTTTTTCGA 58.884 37.500 0.00 0.00 0.00 3.71
1543 1968 5.409643 ACCATCATCGCTAATCTTTTTCG 57.590 39.130 0.00 0.00 0.00 3.46
1544 1969 8.559536 TCATTACCATCATCGCTAATCTTTTTC 58.440 33.333 0.00 0.00 0.00 2.29
1545 1970 8.450578 TCATTACCATCATCGCTAATCTTTTT 57.549 30.769 0.00 0.00 0.00 1.94
1546 1971 8.627208 ATCATTACCATCATCGCTAATCTTTT 57.373 30.769 0.00 0.00 0.00 2.27
1547 1972 8.627208 AATCATTACCATCATCGCTAATCTTT 57.373 30.769 0.00 0.00 0.00 2.52
1548 1973 8.627208 AAATCATTACCATCATCGCTAATCTT 57.373 30.769 0.00 0.00 0.00 2.40
1549 1974 8.627208 AAAATCATTACCATCATCGCTAATCT 57.373 30.769 0.00 0.00 0.00 2.40
1550 1975 9.979270 CTAAAATCATTACCATCATCGCTAATC 57.021 33.333 0.00 0.00 0.00 1.75
1551 1976 9.507329 ACTAAAATCATTACCATCATCGCTAAT 57.493 29.630 0.00 0.00 0.00 1.73
1552 1977 8.902540 ACTAAAATCATTACCATCATCGCTAA 57.097 30.769 0.00 0.00 0.00 3.09
1553 1978 8.367911 AGACTAAAATCATTACCATCATCGCTA 58.632 33.333 0.00 0.00 0.00 4.26
1554 1979 7.172190 CAGACTAAAATCATTACCATCATCGCT 59.828 37.037 0.00 0.00 0.00 4.93
1555 1980 7.171508 TCAGACTAAAATCATTACCATCATCGC 59.828 37.037 0.00 0.00 0.00 4.58
1556 1981 8.593492 TCAGACTAAAATCATTACCATCATCG 57.407 34.615 0.00 0.00 0.00 3.84
1613 2038 6.202188 AGAGCGGGTAAACAAATATTCATACG 59.798 38.462 0.00 0.00 0.00 3.06
1666 2091 5.231991 GCGGACATACAAATAAAAATGGCAG 59.768 40.000 0.00 0.00 0.00 4.85
1677 2102 5.885912 AGACATAAAAGGCGGACATACAAAT 59.114 36.000 0.00 0.00 0.00 2.32
1681 2106 4.189231 ACAGACATAAAAGGCGGACATAC 58.811 43.478 0.00 0.00 0.00 2.39
1684 2109 2.037902 TGACAGACATAAAAGGCGGACA 59.962 45.455 0.00 0.00 0.00 4.02
1688 2113 2.673368 GGTCTGACAGACATAAAAGGCG 59.327 50.000 31.35 0.00 46.79 5.52
1719 2144 2.608988 ACTGGCCACTGGAGAGGG 60.609 66.667 0.00 0.00 0.00 4.30
1726 2151 2.434884 CGGTAGCACTGGCCACTG 60.435 66.667 0.00 4.27 42.56 3.66
1727 2152 4.394712 GCGGTAGCACTGGCCACT 62.395 66.667 0.00 0.00 44.35 4.00
1745 2170 1.047801 ACGTGTAACCGGGGTAAAGT 58.952 50.000 6.32 0.00 0.00 2.66
1755 2180 7.642071 TCTTTAGACATACAAACGTGTAACC 57.358 36.000 0.00 0.00 43.41 2.85
1974 2412 8.483758 AGAGGGAATATGTAAACGTACAAGAAT 58.516 33.333 0.00 0.00 43.41 2.40
1975 2413 7.844009 AGAGGGAATATGTAAACGTACAAGAA 58.156 34.615 0.00 0.00 43.41 2.52
2006 2470 9.250624 GTAGTGATCTAAACGCTCTGATATTTT 57.749 33.333 0.00 0.00 0.00 1.82
2013 2477 4.987832 AGTGTAGTGATCTAAACGCTCTG 58.012 43.478 0.00 0.00 38.89 3.35
2075 2539 4.184629 AGTCAGTCATCCGTAAAGATTGC 58.815 43.478 0.00 0.00 0.00 3.56
2079 2543 5.250982 TGTCTAGTCAGTCATCCGTAAAGA 58.749 41.667 0.00 0.00 0.00 2.52
2081 2545 5.970317 TTGTCTAGTCAGTCATCCGTAAA 57.030 39.130 0.00 0.00 0.00 2.01
2086 2550 5.482908 ACAACATTGTCTAGTCAGTCATCC 58.517 41.667 0.00 0.00 36.50 3.51
2123 2587 0.904649 CTTCAAATCAAAGGGGCCCC 59.095 55.000 35.90 35.90 0.00 5.80
2127 2591 9.374838 CTATGAAAATTCTTCAAATCAAAGGGG 57.625 33.333 7.01 0.00 31.55 4.79
2192 2657 8.761575 ATATGATTCAATCACAAACAACCAAC 57.238 30.769 0.98 0.00 43.01 3.77
2228 2699 9.892130 GGAGAATAGAACAAAGAAATCCTTAGA 57.108 33.333 0.00 0.00 34.00 2.10
2229 2700 9.672673 TGGAGAATAGAACAAAGAAATCCTTAG 57.327 33.333 0.00 0.00 34.00 2.18
2259 2730 9.533831 AACAGGTTCAAATGGATACTAGAAATT 57.466 29.630 0.00 0.00 37.61 1.82
2268 2739 7.831691 TCTTTCAAACAGGTTCAAATGGATA 57.168 32.000 0.00 0.00 0.00 2.59
2274 2745 6.790232 AGGATTCTTTCAAACAGGTTCAAA 57.210 33.333 0.00 0.00 0.00 2.69
2276 2747 6.154363 ACAAAGGATTCTTTCAAACAGGTTCA 59.846 34.615 0.00 0.00 40.92 3.18
2277 2748 6.573434 ACAAAGGATTCTTTCAAACAGGTTC 58.427 36.000 0.00 0.00 40.92 3.62
2279 2750 6.544928 AACAAAGGATTCTTTCAAACAGGT 57.455 33.333 0.00 0.00 40.92 4.00
2284 2755 9.594478 GTAGGAAAAACAAAGGATTCTTTCAAA 57.406 29.630 0.00 0.00 40.92 2.69
2287 2758 7.645402 TCGTAGGAAAAACAAAGGATTCTTTC 58.355 34.615 0.00 0.00 40.92 2.62
2292 2763 5.242838 TGCATCGTAGGAAAAACAAAGGATT 59.757 36.000 0.00 0.00 0.00 3.01
2310 2781 5.389725 GGATTTTGGTTGTTTGATTGCATCG 60.390 40.000 0.00 0.00 0.00 3.84
2334 2806 3.211865 CATGGTCATCTCAATCCCACAG 58.788 50.000 0.00 0.00 0.00 3.66
2338 2810 1.133699 TGGCATGGTCATCTCAATCCC 60.134 52.381 0.00 0.00 0.00 3.85
2351 2823 5.540400 AACATAGGATTGAAATGGCATGG 57.460 39.130 0.00 0.00 0.00 3.66
2361 2833 8.752005 CTGGAATAGGAAAAACATAGGATTGA 57.248 34.615 0.00 0.00 0.00 2.57
2377 2849 6.687604 CAGTTTGTAAAAACCCTGGAATAGG 58.312 40.000 4.83 0.00 46.88 2.57
2379 2851 5.598830 TGCAGTTTGTAAAAACCCTGGAATA 59.401 36.000 4.83 0.00 33.28 1.75
2398 2870 2.590821 AGTGCCTCTTTGATTTGCAGT 58.409 42.857 0.00 0.00 31.69 4.40
2401 2874 4.006319 AGACTAGTGCCTCTTTGATTTGC 58.994 43.478 0.00 0.00 0.00 3.68
2414 2887 3.253432 CCCAAAAACAGGAAGACTAGTGC 59.747 47.826 0.00 0.00 0.00 4.40
2418 2891 2.490168 GGGCCCAAAAACAGGAAGACTA 60.490 50.000 19.95 0.00 0.00 2.59
2420 2893 0.679505 GGGCCCAAAAACAGGAAGAC 59.320 55.000 19.95 0.00 0.00 3.01
2426 2899 0.038343 CGTCATGGGCCCAAAAACAG 60.038 55.000 32.58 17.71 0.00 3.16
2429 2902 1.814772 CTGCGTCATGGGCCCAAAAA 61.815 55.000 32.58 14.84 0.00 1.94
2441 2914 2.691409 AGCTAATAAAGGCTGCGTCA 57.309 45.000 0.00 0.00 37.41 4.35
2445 2918 5.007724 ACATTTCGTAGCTAATAAAGGCTGC 59.992 40.000 11.53 0.00 39.31 5.25
2448 2921 7.469260 TCAAACATTTCGTAGCTAATAAAGGC 58.531 34.615 11.53 0.00 0.00 4.35
2449 2922 9.490663 CTTCAAACATTTCGTAGCTAATAAAGG 57.509 33.333 10.51 10.51 0.00 3.11
2459 2932 3.365969 GGTGGCCTTCAAACATTTCGTAG 60.366 47.826 3.32 0.00 0.00 3.51
2461 2934 1.339929 GGTGGCCTTCAAACATTTCGT 59.660 47.619 3.32 0.00 0.00 3.85
2463 2936 1.611491 TCGGTGGCCTTCAAACATTTC 59.389 47.619 3.32 0.00 0.00 2.17
2464 2937 1.613437 CTCGGTGGCCTTCAAACATTT 59.387 47.619 3.32 0.00 0.00 2.32
2465 2938 1.247567 CTCGGTGGCCTTCAAACATT 58.752 50.000 3.32 0.00 0.00 2.71
2469 3208 1.228124 CACCTCGGTGGCCTTCAAA 60.228 57.895 3.32 0.00 42.00 2.69
2511 3251 2.329379 GTCGGTTCAGTTGTAGCTGAG 58.671 52.381 0.00 0.00 45.03 3.35
2537 3277 0.606604 TTCTTCGGTACAGGACAGGC 59.393 55.000 0.00 0.00 0.00 4.85
2541 3281 2.159085 CCTCCATTCTTCGGTACAGGAC 60.159 54.545 0.00 0.00 0.00 3.85
2545 3285 1.271856 TGCCTCCATTCTTCGGTACA 58.728 50.000 0.00 0.00 0.00 2.90
2564 3304 2.254546 TTGTCTGTCGCTGGTTGAAT 57.745 45.000 0.00 0.00 0.00 2.57
2626 3368 2.323105 GTGTCGTGCGGTGTGTTG 59.677 61.111 0.00 0.00 0.00 3.33
2641 3383 3.117171 GAGCTCTGCGTGGCTGTG 61.117 66.667 6.43 0.00 39.05 3.66
2642 3384 3.293901 GAGAGCTCTGCGTGGCTGT 62.294 63.158 23.91 0.00 39.05 4.40
2643 3385 2.508887 GAGAGCTCTGCGTGGCTG 60.509 66.667 23.91 0.00 39.05 4.85
2644 3386 4.127040 CGAGAGCTCTGCGTGGCT 62.127 66.667 23.91 0.00 41.88 4.75
2687 3429 0.463620 GTTGTGGGCCTTTGCAAAGA 59.536 50.000 35.25 16.40 38.28 2.52
2689 3431 0.177604 CTGTTGTGGGCCTTTGCAAA 59.822 50.000 12.14 12.14 40.13 3.68
2700 3442 2.746269 CTGCATTGTTTCCTGTTGTGG 58.254 47.619 0.00 0.00 0.00 4.17
2708 3450 2.125952 GGGCGCTGCATTGTTTCC 60.126 61.111 7.64 0.00 0.00 3.13
2710 3452 1.290009 GAAGGGCGCTGCATTGTTT 59.710 52.632 7.64 0.00 0.00 2.83
2715 3457 2.831742 CCATGAAGGGCGCTGCAT 60.832 61.111 18.36 18.36 0.00 3.96
2748 3490 3.452627 GAGAAAGACATCTCTGGGGCTAA 59.547 47.826 0.00 0.00 42.12 3.09
2791 3533 6.095377 CCCTCAAGTACAATTCTTTTCATGC 58.905 40.000 0.00 0.00 0.00 4.06
2809 3551 3.632080 TCTTTCCGCCGCCCTCAA 61.632 61.111 0.00 0.00 0.00 3.02
2813 3555 4.388499 TCTGTCTTTCCGCCGCCC 62.388 66.667 0.00 0.00 0.00 6.13
2858 3600 1.808945 CACAAATCTGCACCTGAGACC 59.191 52.381 0.00 0.00 0.00 3.85
2878 3620 4.437930 CCGACCTCAATTTTCTGCATCTTC 60.438 45.833 0.00 0.00 0.00 2.87
2915 3657 2.326897 CGCTGCATCGCCATGAAG 59.673 61.111 0.00 0.00 38.64 3.02
2924 3666 1.462670 GCTCCTTAATAGCGCTGCATC 59.537 52.381 22.90 0.00 0.00 3.91
2935 3677 8.379331 GGAGAAATAATAGTGAGGCTCCTTAAT 58.621 37.037 12.86 0.37 38.08 1.40
2938 3680 5.072464 GGGAGAAATAATAGTGAGGCTCCTT 59.928 44.000 12.86 2.40 40.31 3.36
2961 3703 1.328680 CTCGGATGCACGAAAATCTGG 59.671 52.381 0.87 0.00 42.98 3.86
2981 3723 3.451793 TGTCACCGTGTGGCATATC 57.548 52.632 7.16 0.00 43.49 1.63
2993 3735 5.048083 TGAAGCTAAAATCATGGTTGTCACC 60.048 40.000 0.00 0.00 44.56 4.02
3009 3751 2.424601 GTGCCAGCAATCATGAAGCTAA 59.575 45.455 21.26 10.61 36.73 3.09
3053 3795 2.605823 CGCAGTTTTCGCAACCCAATAA 60.606 45.455 0.00 0.00 0.00 1.40
3067 3809 1.202698 AGTGCCTTCTTCTCGCAGTTT 60.203 47.619 0.00 0.00 32.26 2.66
3075 3817 0.695347 CCAGGGAAGTGCCTTCTTCT 59.305 55.000 12.71 9.00 42.19 2.85
3132 3874 7.054124 TGGAGTTTTGTCAGTTTCTAGTGAAT 58.946 34.615 0.00 0.00 35.55 2.57
3170 3914 2.093500 TGCGATGCAGGAACACTCTAAT 60.093 45.455 0.00 0.00 33.32 1.73
3171 3915 1.275010 TGCGATGCAGGAACACTCTAA 59.725 47.619 0.00 0.00 33.32 2.10
3232 3977 9.529325 TTCTCACTAATCCTATTGTAATCAACG 57.471 33.333 0.00 0.00 36.33 4.10
3265 4017 3.581755 CCGAGATAAACTTGACAACCGA 58.418 45.455 0.00 0.00 31.94 4.69
3285 4037 3.325135 CCATAGAGAGGTACCAATGTCCC 59.675 52.174 15.94 0.00 0.00 4.46
3297 4049 3.495434 AGTCCGTAGACCATAGAGAGG 57.505 52.381 0.00 0.00 44.72 3.69
3303 4055 2.019249 CACCGAAGTCCGTAGACCATA 58.981 52.381 0.00 0.00 44.72 2.74
3328 4080 3.004629 GCTTTTTGCCCTTTTTGAATGGG 59.995 43.478 7.15 7.15 46.11 4.00
3348 4101 2.436646 CCACCGAAGAATGCCGCT 60.437 61.111 0.00 0.00 0.00 5.52
3349 4102 4.179579 GCCACCGAAGAATGCCGC 62.180 66.667 0.00 0.00 0.00 6.53
3350 4103 2.436646 AGCCACCGAAGAATGCCG 60.437 61.111 0.00 0.00 0.00 5.69
3353 4106 0.391130 TTCCGAGCCACCGAAGAATG 60.391 55.000 0.00 0.00 0.00 2.67
3354 4107 0.108138 CTTCCGAGCCACCGAAGAAT 60.108 55.000 0.00 0.00 0.00 2.40
3355 4108 1.292223 CTTCCGAGCCACCGAAGAA 59.708 57.895 0.00 0.00 0.00 2.52
3357 4110 2.125512 CCTTCCGAGCCACCGAAG 60.126 66.667 0.00 0.00 0.00 3.79
3359 4112 2.047213 AAAACCTTCCGAGCCACCGA 62.047 55.000 0.00 0.00 0.00 4.69
3373 4126 3.930229 AGCTCAAAAACAACCGAAAAACC 59.070 39.130 0.00 0.00 0.00 3.27
3375 4128 6.094325 TCTCTAGCTCAAAAACAACCGAAAAA 59.906 34.615 0.00 0.00 0.00 1.94


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

AutoCloner maintained by Alex Coulton.