Multiple sequence alignment - TraesCS4A01G003900

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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 TraesCS4A01G003900 chr4A 100.000 4283 0 0 1 4283 2941968 2946250 0.000000e+00 7910.0
1 TraesCS4A01G003900 chr4A 97.059 34 0 1 205 237 743700517 743700550 5.980000e-04 56.5
2 TraesCS4A01G003900 chr4A 94.286 35 2 0 205 239 584545444 584545410 2.000000e-03 54.7
3 TraesCS4A01G003900 chr4D 89.582 3561 209 84 783 4283 468601024 468597566 0.000000e+00 4372.0
4 TraesCS4A01G003900 chr4D 86.425 442 28 10 247 656 468602704 468602263 5.050000e-124 455.0
5 TraesCS4A01G003900 chr4D 98.049 205 4 0 1 205 468602995 468602791 1.460000e-94 357.0
6 TraesCS4A01G003900 chr4D 94.286 35 2 0 205 239 16054681 16054647 2.000000e-03 54.7
7 TraesCS4A01G003900 chr4B 94.315 1249 45 15 2331 3570 588199940 588198709 0.000000e+00 1890.0
8 TraesCS4A01G003900 chr4B 85.537 1535 130 42 783 2272 588201522 588200035 0.000000e+00 1520.0
9 TraesCS4A01G003900 chr4B 93.096 478 18 7 3680 4156 588198341 588197878 0.000000e+00 686.0
10 TraesCS4A01G003900 chr4B 84.325 504 30 19 231 686 588203226 588202724 8.450000e-122 448.0
11 TraesCS4A01G003900 chr4B 97.573 206 5 0 1 206 588203516 588203311 1.890000e-93 353.0
12 TraesCS4A01G003900 chr4B 89.630 135 13 1 4150 4283 588197495 588197361 2.050000e-38 171.0
13 TraesCS4A01G003900 chr4B 95.238 63 3 0 3605 3667 588198513 588198451 2.730000e-17 100.0
14 TraesCS4A01G003900 chr4B 97.297 37 1 0 3571 3607 588198662 588198626 3.580000e-06 63.9
15 TraesCS4A01G003900 chr3B 88.353 1099 64 26 937 1998 509971996 509970925 0.000000e+00 1262.0
16 TraesCS4A01G003900 chr3B 100.000 31 0 0 207 237 753123501 753123471 1.660000e-04 58.4
17 TraesCS4A01G003900 chr1B 88.076 1107 69 26 928 1998 186139947 186141026 0.000000e+00 1254.0
18 TraesCS4A01G003900 chr1B 80.392 408 56 16 1750 2153 685041611 685041998 5.420000e-74 289.0
19 TraesCS4A01G003900 chr7B 88.102 1101 65 34 937 1998 707547497 707546424 0.000000e+00 1247.0
20 TraesCS4A01G003900 chr7B 87.568 1102 70 28 937 1998 669096405 669095331 0.000000e+00 1214.0
21 TraesCS4A01G003900 chrUn 87.027 1110 70 25 928 1998 65799388 65800462 0.000000e+00 1184.0
22 TraesCS4A01G003900 chr6B 86.792 1113 76 31 928 1998 54643095 54644178 0.000000e+00 1175.0
23 TraesCS4A01G003900 chr6B 86.306 1110 75 30 928 1998 9465353 9466424 0.000000e+00 1136.0
24 TraesCS4A01G003900 chr6B 79.562 411 64 14 1750 2158 650680797 650681189 4.220000e-70 276.0
25 TraesCS4A01G003900 chr6B 82.203 118 13 4 2327 2438 68103974 68104089 1.270000e-15 95.3
26 TraesCS4A01G003900 chr6B 96.875 32 1 0 206 237 661073222 661073191 2.000000e-03 54.7
27 TraesCS4A01G003900 chr2B 87.276 1061 82 28 966 1998 263969515 263970550 0.000000e+00 1162.0
28 TraesCS4A01G003900 chr2B 80.846 402 51 19 1762 2158 274994135 274994515 4.190000e-75 292.0
29 TraesCS4A01G003900 chr5B 87.112 1063 77 26 967 1998 534717779 534718812 0.000000e+00 1149.0
30 TraesCS4A01G003900 chr5B 100.000 31 0 0 205 235 90985789 90985819 1.660000e-04 58.4
31 TraesCS4A01G003900 chr5D 80.198 404 61 12 1750 2152 28564175 28564560 7.010000e-73 285.0
32 TraesCS4A01G003900 chr3D 79.512 410 66 11 1750 2158 111998528 111998920 4.220000e-70 276.0
33 TraesCS4A01G003900 chr3D 79.950 399 60 14 1762 2158 542663466 542663086 4.220000e-70 276.0
34 TraesCS4A01G003900 chr3D 96.875 32 1 0 206 237 501289652 501289621 2.000000e-03 54.7
35 TraesCS4A01G003900 chr5A 81.923 260 44 2 1900 2158 609691739 609691996 2.590000e-52 217.0
36 TraesCS4A01G003900 chr6A 88.406 69 8 0 2327 2395 17041893 17041961 2.740000e-12 84.2
37 TraesCS4A01G003900 chr6D 100.000 28 0 0 206 233 24231433 24231460 8.000000e-03 52.8
38 TraesCS4A01G003900 chr6D 94.286 35 1 1 200 234 82643044 82643077 8.000000e-03 52.8


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 TraesCS4A01G003900 chr4A 2941968 2946250 4282 False 7910.0000 7910 100.000000 1 4283 1 chr4A.!!$F1 4282
1 TraesCS4A01G003900 chr4D 468597566 468602995 5429 True 1728.0000 4372 91.352000 1 4283 3 chr4D.!!$R2 4282
2 TraesCS4A01G003900 chr4B 588197361 588203516 6155 True 653.9875 1890 92.126375 1 4283 8 chr4B.!!$R1 4282
3 TraesCS4A01G003900 chr3B 509970925 509971996 1071 True 1262.0000 1262 88.353000 937 1998 1 chr3B.!!$R1 1061
4 TraesCS4A01G003900 chr1B 186139947 186141026 1079 False 1254.0000 1254 88.076000 928 1998 1 chr1B.!!$F1 1070
5 TraesCS4A01G003900 chr7B 707546424 707547497 1073 True 1247.0000 1247 88.102000 937 1998 1 chr7B.!!$R2 1061
6 TraesCS4A01G003900 chr7B 669095331 669096405 1074 True 1214.0000 1214 87.568000 937 1998 1 chr7B.!!$R1 1061
7 TraesCS4A01G003900 chrUn 65799388 65800462 1074 False 1184.0000 1184 87.027000 928 1998 1 chrUn.!!$F1 1070
8 TraesCS4A01G003900 chr6B 54643095 54644178 1083 False 1175.0000 1175 86.792000 928 1998 1 chr6B.!!$F2 1070
9 TraesCS4A01G003900 chr6B 9465353 9466424 1071 False 1136.0000 1136 86.306000 928 1998 1 chr6B.!!$F1 1070
10 TraesCS4A01G003900 chr2B 263969515 263970550 1035 False 1162.0000 1162 87.276000 966 1998 1 chr2B.!!$F1 1032
11 TraesCS4A01G003900 chr5B 534717779 534718812 1033 False 1149.0000 1149 87.112000 967 1998 1 chr5B.!!$F2 1031

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
872 2159 0.243636 CCCCGAGGCACATTGAAAAC 59.756 55.0 0.00 0.0 0.00 2.43 F
2235 3608 0.036010 CCTGTTGCAGAACCGGAGAT 60.036 55.0 9.46 0.0 38.43 2.75 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2651 4074 0.460987 AGTAGATGCTGCCACTTCGC 60.461 55.0 0.0 0.0 0.0 4.70 R
4148 6234 0.891373 CGCTCAGTTTCTCCTCCTCA 59.109 55.0 0.0 0.0 0.0 3.86 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
107 108 1.273986 TGCCCTTCTCCATAGCTGCA 61.274 55.000 1.02 0.00 0.00 4.41
191 192 1.819632 GCCAGGTAGACGGCCATTG 60.820 63.158 2.24 0.00 42.82 2.82
231 232 8.915036 GTCTTATATTTTGAGACAGAGGGAGTA 58.085 37.037 0.00 0.00 39.59 2.59
238 239 9.607333 ATTTTGAGACAGAGGGAGTATATATGA 57.393 33.333 0.00 0.00 0.00 2.15
239 240 8.410673 TTTGAGACAGAGGGAGTATATATGAC 57.589 38.462 0.00 0.00 0.00 3.06
241 242 7.760607 TGAGACAGAGGGAGTATATATGACTT 58.239 38.462 0.00 0.00 0.00 3.01
242 243 8.891501 TGAGACAGAGGGAGTATATATGACTTA 58.108 37.037 0.00 0.00 0.00 2.24
243 244 9.914834 GAGACAGAGGGAGTATATATGACTTAT 57.085 37.037 0.00 0.00 0.00 1.73
260 321 4.273318 ACTTATTCATGGGCAAGAAGGTC 58.727 43.478 5.36 0.00 0.00 3.85
261 322 1.755179 ATTCATGGGCAAGAAGGTCG 58.245 50.000 0.00 0.00 0.00 4.79
421 482 5.837437 TCATACTCCGTGCAAAATGTTTTT 58.163 33.333 0.00 0.00 0.00 1.94
491 553 2.036556 CGTTTGCGCAAAATCTCTGT 57.963 45.000 35.09 0.00 31.33 3.41
492 554 1.710249 CGTTTGCGCAAAATCTCTGTG 59.290 47.619 35.09 14.34 31.33 3.66
498 560 4.475028 TGCGCAAAATCTCTGTGTAAATG 58.525 39.130 8.16 0.00 0.00 2.32
545 638 2.214376 AGCAGAGTAGCAGTCTGACT 57.786 50.000 19.12 4.06 46.12 3.41
571 664 6.015180 AGCAGAATTGTTCTTGGAAATAGCAA 60.015 34.615 0.00 0.00 38.11 3.91
575 668 4.503741 TGTTCTTGGAAATAGCAACAGC 57.496 40.909 0.00 0.00 0.00 4.40
581 674 1.810151 GGAAATAGCAACAGCGACCAA 59.190 47.619 0.00 0.00 0.00 3.67
583 676 3.492313 GAAATAGCAACAGCGACCAAAG 58.508 45.455 0.00 0.00 0.00 2.77
596 689 2.875933 CGACCAAAGCAGTTAGGTTTCA 59.124 45.455 0.00 0.00 45.55 2.69
599 692 3.636764 ACCAAAGCAGTTAGGTTTCAAGG 59.363 43.478 0.00 0.00 45.55 3.61
605 698 6.071051 AAAGCAGTTAGGTTTCAAGGTTTGAA 60.071 34.615 0.36 0.36 44.10 2.69
636 729 9.593134 GTAGAATATCTATCTACCCTTGCAATG 57.407 37.037 0.00 0.00 42.14 2.82
687 803 2.536761 TGTAAACCAACGTGCTAGCT 57.463 45.000 17.23 0.00 0.00 3.32
688 804 3.663995 TGTAAACCAACGTGCTAGCTA 57.336 42.857 17.23 0.00 0.00 3.32
689 805 3.992643 TGTAAACCAACGTGCTAGCTAA 58.007 40.909 17.23 0.00 0.00 3.09
690 806 3.742369 TGTAAACCAACGTGCTAGCTAAC 59.258 43.478 17.23 5.65 0.00 2.34
691 807 2.536761 AACCAACGTGCTAGCTAACA 57.463 45.000 17.23 0.00 0.00 2.41
692 808 2.536761 ACCAACGTGCTAGCTAACAA 57.463 45.000 17.23 0.00 0.00 2.83
693 809 2.841215 ACCAACGTGCTAGCTAACAAA 58.159 42.857 17.23 0.00 0.00 2.83
694 810 2.546789 ACCAACGTGCTAGCTAACAAAC 59.453 45.455 17.23 3.27 0.00 2.93
695 811 2.546368 CCAACGTGCTAGCTAACAAACA 59.454 45.455 17.23 0.00 0.00 2.83
696 812 3.363970 CCAACGTGCTAGCTAACAAACAG 60.364 47.826 17.23 4.00 0.00 3.16
697 813 1.798813 ACGTGCTAGCTAACAAACAGC 59.201 47.619 17.23 0.00 39.41 4.40
698 814 1.798223 CGTGCTAGCTAACAAACAGCA 59.202 47.619 17.23 0.00 41.66 4.41
699 815 2.416547 CGTGCTAGCTAACAAACAGCAT 59.583 45.455 17.23 0.00 43.53 3.79
700 816 3.120199 CGTGCTAGCTAACAAACAGCATT 60.120 43.478 17.23 0.00 43.53 3.56
701 817 4.161333 GTGCTAGCTAACAAACAGCATTG 58.839 43.478 17.23 0.00 43.53 2.82
702 818 4.071423 TGCTAGCTAACAAACAGCATTGA 58.929 39.130 17.23 0.00 41.66 2.57
703 819 4.701651 TGCTAGCTAACAAACAGCATTGAT 59.298 37.500 17.23 0.00 41.66 2.57
704 820 5.879777 TGCTAGCTAACAAACAGCATTGATA 59.120 36.000 17.23 0.00 41.66 2.15
705 821 6.374053 TGCTAGCTAACAAACAGCATTGATAA 59.626 34.615 17.23 0.00 41.66 1.75
706 822 7.067372 TGCTAGCTAACAAACAGCATTGATAAT 59.933 33.333 17.23 0.00 41.66 1.28
707 823 7.377928 GCTAGCTAACAAACAGCATTGATAATG 59.622 37.037 7.70 0.00 41.66 1.90
716 832 2.642139 CATTGATAATGCATCCGCCC 57.358 50.000 0.00 0.00 37.32 6.13
724 840 2.825836 GCATCCGCCCAGAACAGG 60.826 66.667 0.00 0.00 0.00 4.00
736 852 2.550208 CCAGAACAGGACTACCAACCAC 60.550 54.545 0.00 0.00 38.94 4.16
737 853 2.104111 CAGAACAGGACTACCAACCACA 59.896 50.000 0.00 0.00 38.94 4.17
738 854 2.775384 AGAACAGGACTACCAACCACAA 59.225 45.455 0.00 0.00 38.94 3.33
739 855 2.632987 ACAGGACTACCAACCACAAC 57.367 50.000 0.00 0.00 38.94 3.32
741 857 1.069513 CAGGACTACCAACCACAACGA 59.930 52.381 0.00 0.00 38.94 3.85
742 858 1.764134 AGGACTACCAACCACAACGAA 59.236 47.619 0.00 0.00 38.94 3.85
743 859 1.869132 GGACTACCAACCACAACGAAC 59.131 52.381 0.00 0.00 35.97 3.95
754 1877 0.808453 ACAACGAACTCACCACCACG 60.808 55.000 0.00 0.00 0.00 4.94
755 1878 0.528901 CAACGAACTCACCACCACGA 60.529 55.000 0.00 0.00 0.00 4.35
756 1879 0.249322 AACGAACTCACCACCACGAG 60.249 55.000 0.00 0.00 35.30 4.18
757 1880 1.105167 ACGAACTCACCACCACGAGA 61.105 55.000 0.00 0.00 33.33 4.04
758 1881 0.663568 CGAACTCACCACCACGAGAC 60.664 60.000 0.00 0.00 33.33 3.36
759 1882 0.663568 GAACTCACCACCACGAGACG 60.664 60.000 0.00 0.00 33.33 4.18
761 1884 3.916392 CTCACCACCACGAGACGGC 62.916 68.421 0.00 0.00 0.00 5.68
768 1891 4.293648 CACGAGACGGCCCACACA 62.294 66.667 0.00 0.00 0.00 3.72
769 1892 3.542676 ACGAGACGGCCCACACAA 61.543 61.111 0.00 0.00 0.00 3.33
770 1893 2.738521 CGAGACGGCCCACACAAG 60.739 66.667 0.00 0.00 0.00 3.16
772 1895 2.847234 AGACGGCCCACACAAGGA 60.847 61.111 0.00 0.00 0.00 3.36
773 1896 2.358737 GACGGCCCACACAAGGAG 60.359 66.667 0.00 0.00 0.00 3.69
774 1897 2.847234 ACGGCCCACACAAGGAGA 60.847 61.111 0.00 0.00 0.00 3.71
775 1898 2.358737 CGGCCCACACAAGGAGAC 60.359 66.667 0.00 0.00 0.00 3.36
776 1899 2.358737 GGCCCACACAAGGAGACG 60.359 66.667 0.00 0.00 0.00 4.18
777 1900 2.426023 GCCCACACAAGGAGACGT 59.574 61.111 0.00 0.00 0.00 4.34
778 1901 1.227853 GCCCACACAAGGAGACGTT 60.228 57.895 0.00 0.00 0.00 3.99
779 1902 0.818040 GCCCACACAAGGAGACGTTT 60.818 55.000 0.00 0.00 0.00 3.60
780 1903 0.944386 CCCACACAAGGAGACGTTTG 59.056 55.000 0.00 0.00 0.00 2.93
816 2100 3.047877 CGGCCCACACGTTCTTCC 61.048 66.667 0.00 0.00 0.00 3.46
872 2159 0.243636 CCCCGAGGCACATTGAAAAC 59.756 55.000 0.00 0.00 0.00 2.43
918 2205 0.324923 AAATCCCCGGCTTAAACCCC 60.325 55.000 0.00 0.00 0.00 4.95
919 2206 1.511316 AATCCCCGGCTTAAACCCCA 61.511 55.000 0.00 0.00 0.00 4.96
920 2207 1.511316 ATCCCCGGCTTAAACCCCAA 61.511 55.000 0.00 0.00 0.00 4.12
922 2209 1.228613 CCCGGCTTAAACCCCAACA 60.229 57.895 0.00 0.00 0.00 3.33
929 2216 2.184533 CTTAAACCCCAACATTCCCCC 58.815 52.381 0.00 0.00 0.00 5.40
988 2297 2.835431 CTGCTCCGGGATCGAGGT 60.835 66.667 0.00 0.00 39.00 3.85
1149 2460 4.779486 ACCCCCTCCCCCATGGTC 62.779 72.222 11.73 0.00 34.77 4.02
1155 2466 2.938798 TCCCCCATGGTCACCACC 60.939 66.667 11.73 0.00 44.10 4.61
1156 2467 4.060667 CCCCCATGGTCACCACCC 62.061 72.222 11.73 0.00 42.99 4.61
1157 2468 4.060667 CCCCATGGTCACCACCCC 62.061 72.222 11.73 0.00 42.99 4.95
1158 2469 2.941025 CCCATGGTCACCACCCCT 60.941 66.667 11.73 0.00 42.99 4.79
1159 2470 2.677228 CCATGGTCACCACCCCTC 59.323 66.667 0.00 0.00 42.99 4.30
1160 2471 1.925455 CCATGGTCACCACCCCTCT 60.925 63.158 0.00 0.00 42.99 3.69
1161 2472 1.604378 CATGGTCACCACCCCTCTC 59.396 63.158 0.00 0.00 42.99 3.20
1162 2473 1.616628 ATGGTCACCACCCCTCTCC 60.617 63.158 0.00 0.00 42.99 3.71
1163 2474 3.009714 GGTCACCACCCCTCTCCC 61.010 72.222 0.00 0.00 36.54 4.30
1164 2475 2.122954 GTCACCACCCCTCTCCCT 59.877 66.667 0.00 0.00 0.00 4.20
1165 2476 1.990614 GTCACCACCCCTCTCCCTC 60.991 68.421 0.00 0.00 0.00 4.30
1166 2477 2.122729 CACCACCCCTCTCCCTCA 59.877 66.667 0.00 0.00 0.00 3.86
1167 2478 1.307343 CACCACCCCTCTCCCTCAT 60.307 63.158 0.00 0.00 0.00 2.90
1198 2512 3.188786 CCGCCTTCTCTTTCCGCG 61.189 66.667 0.00 0.00 42.37 6.46
1204 2533 3.524648 TTCTCTTTCCGCGGCCGTT 62.525 57.895 28.70 0.00 0.00 4.44
1224 2553 0.673644 CCCTTTGCTGAATCGGTCGT 60.674 55.000 0.00 0.00 0.00 4.34
1225 2554 1.156736 CCTTTGCTGAATCGGTCGTT 58.843 50.000 0.00 0.00 0.00 3.85
1229 2558 0.319211 TGCTGAATCGGTCGTTTCGT 60.319 50.000 8.87 0.00 0.00 3.85
1230 2559 0.365859 GCTGAATCGGTCGTTTCGTC 59.634 55.000 8.87 1.70 0.00 4.20
1294 2626 4.711949 AGCACAAGAGGCGCAGGG 62.712 66.667 10.83 0.00 36.08 4.45
1302 2634 3.371097 GAGGCGCAGGGTCATCGAA 62.371 63.158 10.83 0.00 0.00 3.71
1408 2740 0.324943 GGTATCCATCCATCCACCCG 59.675 60.000 0.00 0.00 0.00 5.28
1424 2760 1.144936 CCGTCCATCTCTTCCTGCC 59.855 63.158 0.00 0.00 0.00 4.85
1451 2787 2.680339 GCCTGATCTGTACCAAGCTTTC 59.320 50.000 0.00 0.00 0.00 2.62
1471 2807 3.761897 TCGGGGGAAATGCTTATAATGG 58.238 45.455 0.00 0.00 0.00 3.16
1504 2840 4.026640 CCTGTTTCTTGTGATTTTTGCGTG 60.027 41.667 0.00 0.00 0.00 5.34
1600 2936 1.896220 TTGGTGTGAGATGGCAACTC 58.104 50.000 16.99 16.99 37.61 3.01
1732 3078 3.685139 TGACTTGTCTTGTCCCAGATC 57.315 47.619 2.35 0.00 33.83 2.75
1742 3088 5.065731 GTCTTGTCCCAGATCATGTCAATTC 59.934 44.000 0.00 0.00 0.00 2.17
1850 3220 5.065090 TGAAGATGATATTTGCTCCACGTTG 59.935 40.000 0.00 0.00 0.00 4.10
1853 3225 4.418013 TGATATTTGCTCCACGTTGTTG 57.582 40.909 0.00 0.00 0.00 3.33
1863 3235 2.675844 TCCACGTTGTTGTCTGTTGAAG 59.324 45.455 0.00 0.00 0.00 3.02
1998 3370 3.758554 GAGGCATCTGAACAAAAGGCTTA 59.241 43.478 0.00 0.00 31.68 3.09
2004 3377 7.293018 GCATCTGAACAAAAGGCTTAAAAATG 58.707 34.615 0.00 0.00 0.00 2.32
2062 3435 9.241317 GAGCCATTGTATTGTGATCTTTAAATG 57.759 33.333 0.00 0.00 0.00 2.32
2064 3437 7.492020 GCCATTGTATTGTGATCTTTAAATGCA 59.508 33.333 0.00 0.00 0.00 3.96
2113 3486 3.648339 TTTGCCTTTTGCTGTGAGATC 57.352 42.857 0.00 0.00 42.00 2.75
2123 3496 2.166254 TGCTGTGAGATCGCAACTGATA 59.834 45.455 0.00 0.00 35.77 2.15
2126 3499 4.620609 GCTGTGAGATCGCAACTGATATAG 59.379 45.833 0.00 0.00 35.77 1.31
2176 3549 5.888412 ATTTGCTTTTTACTCGCTGTTTG 57.112 34.783 0.00 0.00 0.00 2.93
2202 3575 2.819115 CCTAGTGCTGCTCATACTGTG 58.181 52.381 0.00 0.00 0.00 3.66
2229 3602 2.647297 GCAGCCTGTTGCAGAACC 59.353 61.111 0.81 0.00 44.83 3.62
2235 3608 0.036010 CCTGTTGCAGAACCGGAGAT 60.036 55.000 9.46 0.00 38.43 2.75
2274 3647 4.974645 TTATCTGTTGAACTGTCCCTGT 57.025 40.909 0.00 0.00 0.00 4.00
2289 3668 8.511604 ACTGTCCCTGTCAATTTATTATGAAG 57.488 34.615 0.00 0.00 0.00 3.02
2290 3669 7.067494 ACTGTCCCTGTCAATTTATTATGAAGC 59.933 37.037 0.00 0.00 0.00 3.86
2386 3808 3.760684 AGGCAGCTTGTATTCTTTTCTGG 59.239 43.478 0.00 0.00 0.00 3.86
2402 3824 7.394816 TCTTTTCTGGAAAATCTCGTATCCTT 58.605 34.615 8.64 0.00 39.29 3.36
2404 3826 9.162764 CTTTTCTGGAAAATCTCGTATCCTTAA 57.837 33.333 8.64 0.00 39.29 1.85
2405 3827 8.718102 TTTCTGGAAAATCTCGTATCCTTAAG 57.282 34.615 0.00 0.00 33.02 1.85
2406 3828 7.655521 TCTGGAAAATCTCGTATCCTTAAGA 57.344 36.000 3.36 0.00 33.02 2.10
2407 3829 7.717568 TCTGGAAAATCTCGTATCCTTAAGAG 58.282 38.462 3.36 0.00 35.86 2.85
2410 3832 7.980099 TGGAAAATCTCGTATCCTTAAGAGAAC 59.020 37.037 3.36 0.00 43.25 3.01
2411 3833 8.198778 GGAAAATCTCGTATCCTTAAGAGAACT 58.801 37.037 3.36 0.00 43.25 3.01
2455 3878 8.598202 TGTAGTATTGTCCCTACTGTAATCAA 57.402 34.615 0.00 0.00 35.62 2.57
2556 3979 6.238759 GGGAAGGTTTGTGAATATGTGCTATC 60.239 42.308 0.00 0.00 0.00 2.08
2573 3996 6.438425 TGTGCTATCATTATCATAGGAGCTCA 59.562 38.462 17.19 0.00 31.82 4.26
2608 4031 5.643777 CCTCTTCCATCGTGTGAAATAACTT 59.356 40.000 0.00 0.00 0.00 2.66
2609 4032 6.183360 CCTCTTCCATCGTGTGAAATAACTTC 60.183 42.308 0.00 0.00 34.31 3.01
2651 4074 0.827368 GCAGGTGGTCTCCTAGAAGG 59.173 60.000 0.00 0.00 35.87 3.46
2760 4183 5.552178 AGTTAGAATCACAACTTGACCCTC 58.448 41.667 0.00 0.00 36.92 4.30
2839 4262 5.523916 GGTTGGTGAGTATTGCACTACTATG 59.476 44.000 15.93 0.00 37.72 2.23
2847 4270 6.574350 AGTATTGCACTACTATGACTTGTCC 58.426 40.000 14.54 0.00 34.98 4.02
2908 4332 3.749088 TGCGTCCTAACTTTGTTGTATGG 59.251 43.478 0.00 0.00 0.00 2.74
2998 4422 5.123502 CACTTTGGTGGATGAGAAAGATGAG 59.876 44.000 0.00 0.00 39.59 2.90
3173 4597 8.144478 ACTAATATCTGAATGATACGCAGTTGT 58.856 33.333 0.00 0.00 45.11 3.32
3188 4613 3.304257 GCAGTTGTGAACTCAAGATGGTG 60.304 47.826 0.00 0.00 40.46 4.17
3189 4614 3.879295 CAGTTGTGAACTCAAGATGGTGT 59.121 43.478 0.00 0.00 40.46 4.16
3193 4618 6.038271 AGTTGTGAACTCAAGATGGTGTTTAC 59.962 38.462 0.00 0.00 37.02 2.01
3195 4620 6.119536 TGTGAACTCAAGATGGTGTTTACTT 58.880 36.000 0.00 0.00 32.53 2.24
3197 4622 7.122055 TGTGAACTCAAGATGGTGTTTACTTTT 59.878 33.333 0.00 0.00 32.53 2.27
3200 4625 7.027778 ACTCAAGATGGTGTTTACTTTTGAC 57.972 36.000 0.00 0.00 0.00 3.18
3286 4711 1.556911 ACGAGGAAATGGAGTGAGCAT 59.443 47.619 0.00 0.00 0.00 3.79
3327 4752 7.002879 TGCTAAGAACTAACCTATCGGTAGAT 58.997 38.462 3.68 0.00 44.73 1.98
3344 4771 5.700373 CGGTAGATGGTACTAGTTAGGAGTC 59.300 48.000 0.00 0.00 0.00 3.36
3345 4772 6.464180 CGGTAGATGGTACTAGTTAGGAGTCT 60.464 46.154 0.00 0.91 0.00 3.24
3353 4780 4.216708 ACTAGTTAGGAGTCTGGTATGGC 58.783 47.826 0.00 0.00 0.00 4.40
3384 4811 0.678395 CTATCTGGATCGCCTGTGCT 59.322 55.000 0.00 0.00 34.91 4.40
3385 4812 0.390492 TATCTGGATCGCCTGTGCTG 59.610 55.000 0.00 0.00 34.91 4.41
3386 4813 2.937379 ATCTGGATCGCCTGTGCTGC 62.937 60.000 0.00 0.00 34.91 5.25
3511 4942 6.073765 GCTATGTAATATGTTTCCGTGTCCAG 60.074 42.308 0.00 0.00 0.00 3.86
3688 5385 8.849543 TGTATGTACCTAAAGTCCTAATTCCT 57.150 34.615 0.00 0.00 0.00 3.36
3689 5386 9.940974 TGTATGTACCTAAAGTCCTAATTCCTA 57.059 33.333 0.00 0.00 0.00 2.94
3734 5431 5.221581 GGCTCAAAAGGATGCCAAATATCAT 60.222 40.000 0.00 0.00 44.34 2.45
3803 5500 3.055094 TCATCCTACACTTTCTGAAGCCC 60.055 47.826 0.00 0.00 36.29 5.19
3858 5555 7.210174 TCTCTTGTATACATAAGTGCACCATC 58.790 38.462 14.63 0.00 0.00 3.51
3864 5561 7.657354 TGTATACATAAGTGCACCATCAGATTC 59.343 37.037 14.63 0.03 0.00 2.52
3916 5613 3.493176 GCCAGCCTCATTGAAGTTTGTTT 60.493 43.478 0.00 0.00 0.00 2.83
3961 5658 9.350357 GTTATTCATGCAAACCATATCATCATC 57.650 33.333 0.00 0.00 31.47 2.92
3964 5661 6.919721 TCATGCAAACCATATCATCATCATG 58.080 36.000 0.00 0.00 31.47 3.07
3965 5662 6.717540 TCATGCAAACCATATCATCATCATGA 59.282 34.615 0.00 0.00 36.30 3.07
3966 5663 6.569179 TGCAAACCATATCATCATCATGAG 57.431 37.500 0.09 0.00 42.53 2.90
3967 5664 5.475564 TGCAAACCATATCATCATCATGAGG 59.524 40.000 0.00 0.00 42.53 3.86
3968 5665 5.708697 GCAAACCATATCATCATCATGAGGA 59.291 40.000 13.16 13.16 42.53 3.71
3973 5670 8.405418 ACCATATCATCATCATGAGGAAAAAG 57.595 34.615 14.88 5.28 40.75 2.27
3983 5680 7.505585 TCATCATGAGGAAAAAGGTAAACAACT 59.494 33.333 7.78 0.00 0.00 3.16
4009 5706 1.202110 GGAGCGATTCGTTACTCGTCA 60.202 52.381 8.03 0.00 40.80 4.35
4010 5707 2.541178 GGAGCGATTCGTTACTCGTCAT 60.541 50.000 8.03 0.00 40.80 3.06
4011 5708 2.714985 GAGCGATTCGTTACTCGTCATC 59.285 50.000 8.03 0.00 40.80 2.92
4145 6231 2.621526 GGAAGAAAGCCGGTGAAAGAAA 59.378 45.455 1.90 0.00 0.00 2.52
4148 6234 3.288092 AGAAAGCCGGTGAAAGAAACTT 58.712 40.909 1.90 0.00 0.00 2.66
4152 6238 1.266989 GCCGGTGAAAGAAACTTGAGG 59.733 52.381 1.90 0.00 0.00 3.86
4229 6315 1.139734 GATCGCTCCGCTGAACTGA 59.860 57.895 0.00 0.00 0.00 3.41
4273 6360 8.755696 TTTTGAAATGTGGAATGTTAGTATGC 57.244 30.769 0.00 0.00 0.00 3.14
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
41 42 3.126171 CCGGCGAAAACTTGTCATTCATA 59.874 43.478 9.30 0.00 0.00 2.15
107 108 2.487762 CGATGTTGTTAGTGGGCACATT 59.512 45.455 0.00 0.00 0.00 2.71
206 207 7.979786 ACTCCCTCTGTCTCAAAATATAAGA 57.020 36.000 0.00 0.00 0.00 2.10
213 214 8.861086 GTCATATATACTCCCTCTGTCTCAAAA 58.139 37.037 0.00 0.00 0.00 2.44
214 215 8.228206 AGTCATATATACTCCCTCTGTCTCAAA 58.772 37.037 0.00 0.00 0.00 2.69
215 216 7.760607 AGTCATATATACTCCCTCTGTCTCAA 58.239 38.462 0.00 0.00 0.00 3.02
217 218 9.914834 ATAAGTCATATATACTCCCTCTGTCTC 57.085 37.037 0.00 0.00 0.00 3.36
224 225 9.218525 CCCATGAATAAGTCATATATACTCCCT 57.781 37.037 0.00 0.00 45.69 4.20
225 226 7.934120 GCCCATGAATAAGTCATATATACTCCC 59.066 40.741 0.00 0.00 45.69 4.30
226 227 8.486210 TGCCCATGAATAAGTCATATATACTCC 58.514 37.037 0.00 0.00 45.69 3.85
227 228 9.890629 TTGCCCATGAATAAGTCATATATACTC 57.109 33.333 0.00 0.00 45.69 2.59
231 232 9.458727 CTTCTTGCCCATGAATAAGTCATATAT 57.541 33.333 0.00 0.00 45.69 0.86
233 234 6.718454 CCTTCTTGCCCATGAATAAGTCATAT 59.282 38.462 0.00 0.00 45.69 1.78
236 237 4.263905 ACCTTCTTGCCCATGAATAAGTCA 60.264 41.667 0.00 0.00 41.67 3.41
237 238 4.273318 ACCTTCTTGCCCATGAATAAGTC 58.727 43.478 0.00 0.00 0.00 3.01
238 239 4.273318 GACCTTCTTGCCCATGAATAAGT 58.727 43.478 0.00 0.00 0.00 2.24
239 240 3.313526 CGACCTTCTTGCCCATGAATAAG 59.686 47.826 0.00 0.00 0.00 1.73
241 242 2.238646 ACGACCTTCTTGCCCATGAATA 59.761 45.455 0.00 0.00 0.00 1.75
242 243 1.004745 ACGACCTTCTTGCCCATGAAT 59.995 47.619 0.00 0.00 0.00 2.57
243 244 0.400213 ACGACCTTCTTGCCCATGAA 59.600 50.000 0.00 0.00 0.00 2.57
244 245 0.036388 GACGACCTTCTTGCCCATGA 60.036 55.000 0.00 0.00 0.00 3.07
245 246 0.321564 TGACGACCTTCTTGCCCATG 60.322 55.000 0.00 0.00 0.00 3.66
260 321 1.735018 TGTTTCCCGCATTGTATGACG 59.265 47.619 0.00 0.00 0.00 4.35
261 322 3.427503 CCTTGTTTCCCGCATTGTATGAC 60.428 47.826 0.00 0.00 0.00 3.06
472 533 1.710249 CACAGAGATTTTGCGCAAACG 59.290 47.619 33.73 19.24 44.07 3.60
478 539 7.060600 TCTACATTTACACAGAGATTTTGCG 57.939 36.000 0.00 0.00 0.00 4.85
485 546 9.244292 ACTGAGTTATCTACATTTACACAGAGA 57.756 33.333 0.00 0.00 33.53 3.10
491 553 7.620491 TGGGGTACTGAGTTATCTACATTTACA 59.380 37.037 0.00 0.00 0.00 2.41
492 554 8.015185 TGGGGTACTGAGTTATCTACATTTAC 57.985 38.462 0.00 0.00 0.00 2.01
498 560 9.895138 TTAAAATTGGGGTACTGAGTTATCTAC 57.105 33.333 0.00 0.00 0.00 2.59
510 572 7.041303 GCTACTCTGCTATTAAAATTGGGGTAC 60.041 40.741 0.00 0.00 0.00 3.34
545 638 6.658816 TGCTATTTCCAAGAACAATTCTGCTA 59.341 34.615 0.00 0.00 40.59 3.49
571 664 1.512926 CTAACTGCTTTGGTCGCTGT 58.487 50.000 0.00 0.00 40.57 4.40
575 668 2.875933 TGAAACCTAACTGCTTTGGTCG 59.124 45.455 0.00 0.00 34.75 4.79
581 674 4.953579 TCAAACCTTGAAACCTAACTGCTT 59.046 37.500 0.00 0.00 36.59 3.91
583 676 4.911514 TCAAACCTTGAAACCTAACTGC 57.088 40.909 0.00 0.00 36.59 4.40
609 702 8.721133 TTGCAAGGGTAGATAGATATTCTACA 57.279 34.615 12.82 0.00 38.36 2.74
636 729 7.545362 ACAGATATTTACTTGACTGCATCAC 57.455 36.000 0.00 0.00 36.92 3.06
644 737 9.319143 ACAAGAGCATACAGATATTTACTTGAC 57.681 33.333 0.00 0.00 36.14 3.18
697 813 1.887854 TGGGCGGATGCATTATCAATG 59.112 47.619 0.00 0.00 45.35 2.82
698 814 2.165167 CTGGGCGGATGCATTATCAAT 58.835 47.619 0.00 0.00 45.35 2.57
699 815 1.142667 TCTGGGCGGATGCATTATCAA 59.857 47.619 0.00 0.00 45.35 2.57
700 816 0.764271 TCTGGGCGGATGCATTATCA 59.236 50.000 0.00 0.00 45.35 2.15
701 817 1.537202 GTTCTGGGCGGATGCATTATC 59.463 52.381 0.00 0.00 45.35 1.75
702 818 1.133823 TGTTCTGGGCGGATGCATTAT 60.134 47.619 0.00 0.00 45.35 1.28
703 819 0.254462 TGTTCTGGGCGGATGCATTA 59.746 50.000 0.00 0.00 45.35 1.90
704 820 1.001020 TGTTCTGGGCGGATGCATT 60.001 52.632 0.00 0.00 45.35 3.56
705 821 1.452651 CTGTTCTGGGCGGATGCAT 60.453 57.895 0.00 0.00 45.35 3.96
706 822 2.046023 CTGTTCTGGGCGGATGCA 60.046 61.111 0.00 0.00 45.35 3.96
707 823 2.825836 CCTGTTCTGGGCGGATGC 60.826 66.667 0.00 0.00 41.71 3.91
708 824 1.450312 GTCCTGTTCTGGGCGGATG 60.450 63.158 0.00 0.00 0.00 3.51
709 825 0.325296 TAGTCCTGTTCTGGGCGGAT 60.325 55.000 0.00 0.00 36.69 4.18
710 826 1.077805 TAGTCCTGTTCTGGGCGGA 59.922 57.895 0.00 0.00 36.69 5.54
711 827 1.218316 GTAGTCCTGTTCTGGGCGG 59.782 63.158 0.00 0.00 36.69 6.13
712 828 1.218316 GGTAGTCCTGTTCTGGGCG 59.782 63.158 0.00 0.00 36.69 6.13
713 829 0.690762 TTGGTAGTCCTGTTCTGGGC 59.309 55.000 0.00 0.00 34.23 5.36
714 830 1.003233 GGTTGGTAGTCCTGTTCTGGG 59.997 57.143 0.00 0.00 34.23 4.45
715 831 1.697432 TGGTTGGTAGTCCTGTTCTGG 59.303 52.381 0.00 0.00 34.23 3.86
716 832 2.104111 TGTGGTTGGTAGTCCTGTTCTG 59.896 50.000 0.00 0.00 34.23 3.02
724 840 2.798847 GAGTTCGTTGTGGTTGGTAGTC 59.201 50.000 0.00 0.00 0.00 2.59
736 852 0.528901 TCGTGGTGGTGAGTTCGTTG 60.529 55.000 0.00 0.00 0.00 4.10
737 853 0.249322 CTCGTGGTGGTGAGTTCGTT 60.249 55.000 0.00 0.00 0.00 3.85
738 854 1.105167 TCTCGTGGTGGTGAGTTCGT 61.105 55.000 0.00 0.00 33.88 3.85
739 855 0.663568 GTCTCGTGGTGGTGAGTTCG 60.664 60.000 0.00 0.00 33.88 3.95
741 857 1.362717 CGTCTCGTGGTGGTGAGTT 59.637 57.895 0.00 0.00 33.88 3.01
742 858 2.561956 CCGTCTCGTGGTGGTGAGT 61.562 63.158 0.00 0.00 33.88 3.41
743 859 2.258591 CCGTCTCGTGGTGGTGAG 59.741 66.667 0.00 0.00 0.00 3.51
754 1877 2.358737 CCTTGTGTGGGCCGTCTC 60.359 66.667 0.00 0.00 0.00 3.36
755 1878 2.847234 TCCTTGTGTGGGCCGTCT 60.847 61.111 0.00 0.00 0.00 4.18
756 1879 2.358737 CTCCTTGTGTGGGCCGTC 60.359 66.667 0.00 0.00 0.00 4.79
757 1880 2.847234 TCTCCTTGTGTGGGCCGT 60.847 61.111 0.00 0.00 0.00 5.68
758 1881 2.358737 GTCTCCTTGTGTGGGCCG 60.359 66.667 0.00 0.00 0.00 6.13
759 1882 2.358737 CGTCTCCTTGTGTGGGCC 60.359 66.667 0.00 0.00 0.00 5.80
761 1884 0.944386 CAAACGTCTCCTTGTGTGGG 59.056 55.000 0.00 0.00 0.00 4.61
763 1886 0.944386 CCCAAACGTCTCCTTGTGTG 59.056 55.000 0.00 0.00 0.00 3.82
764 1887 0.818040 GCCCAAACGTCTCCTTGTGT 60.818 55.000 0.00 0.00 0.00 3.72
766 1889 1.228154 GGCCCAAACGTCTCCTTGT 60.228 57.895 0.00 0.00 0.00 3.16
767 1890 1.228124 TGGCCCAAACGTCTCCTTG 60.228 57.895 0.00 0.00 0.00 3.61
768 1891 1.073199 CTGGCCCAAACGTCTCCTT 59.927 57.895 0.00 0.00 0.00 3.36
769 1892 2.750350 CTGGCCCAAACGTCTCCT 59.250 61.111 0.00 0.00 0.00 3.69
770 1893 3.056328 GCTGGCCCAAACGTCTCC 61.056 66.667 0.00 0.00 0.00 3.71
805 2089 1.301479 GGCTTCCGGAAGAACGTGT 60.301 57.895 41.64 0.00 40.79 4.49
888 2175 2.306384 GGGGATTTCGGGGAGTGGT 61.306 63.158 0.00 0.00 0.00 4.16
935 2235 1.000896 ATTGGGTTTCCTGGAGGCG 60.001 57.895 0.00 0.00 34.44 5.52
943 2243 0.902984 GGTGGTGGGATTGGGTTTCC 60.903 60.000 0.00 0.00 0.00 3.13
1125 2436 4.695791 GGGGAGGGGGTCTTGGGT 62.696 72.222 0.00 0.00 0.00 4.51
1149 2460 1.307343 ATGAGGGAGAGGGGTGGTG 60.307 63.158 0.00 0.00 0.00 4.17
1155 2466 1.152139 GGAGGGATGAGGGAGAGGG 60.152 68.421 0.00 0.00 0.00 4.30
1156 2467 1.152139 GGGAGGGATGAGGGAGAGG 60.152 68.421 0.00 0.00 0.00 3.69
1157 2468 0.178935 GAGGGAGGGATGAGGGAGAG 60.179 65.000 0.00 0.00 0.00 3.20
1158 2469 1.669927 GGAGGGAGGGATGAGGGAGA 61.670 65.000 0.00 0.00 0.00 3.71
1159 2470 1.152139 GGAGGGAGGGATGAGGGAG 60.152 68.421 0.00 0.00 0.00 4.30
1160 2471 1.630333 AGGAGGGAGGGATGAGGGA 60.630 63.158 0.00 0.00 0.00 4.20
1161 2472 1.152139 GAGGAGGGAGGGATGAGGG 60.152 68.421 0.00 0.00 0.00 4.30
1162 2473 1.532794 CGAGGAGGGAGGGATGAGG 60.533 68.421 0.00 0.00 0.00 3.86
1163 2474 2.206536 GCGAGGAGGGAGGGATGAG 61.207 68.421 0.00 0.00 0.00 2.90
1164 2475 2.123251 GCGAGGAGGGAGGGATGA 60.123 66.667 0.00 0.00 0.00 2.92
1165 2476 3.237741 GGCGAGGAGGGAGGGATG 61.238 72.222 0.00 0.00 0.00 3.51
1166 2477 4.924187 CGGCGAGGAGGGAGGGAT 62.924 72.222 0.00 0.00 0.00 3.85
1198 2512 1.250840 ATTCAGCAAAGGGAACGGCC 61.251 55.000 0.00 0.00 0.00 6.13
1204 2533 0.391130 CGACCGATTCAGCAAAGGGA 60.391 55.000 0.00 0.00 0.00 4.20
1207 2536 2.721797 CGAAACGACCGATTCAGCAAAG 60.722 50.000 11.76 0.00 0.00 2.77
1224 2553 1.061421 GCACGATTAATGGCGACGAAA 59.939 47.619 0.00 0.00 0.00 3.46
1225 2554 0.648441 GCACGATTAATGGCGACGAA 59.352 50.000 0.00 0.00 0.00 3.85
1229 2558 2.032799 GGAAATGCACGATTAATGGCGA 59.967 45.455 3.79 0.00 0.00 5.54
1230 2559 2.384382 GGAAATGCACGATTAATGGCG 58.616 47.619 0.00 0.00 0.00 5.69
1294 2626 3.255379 GGTCGCGGCTTCGATGAC 61.255 66.667 11.94 0.00 40.84 3.06
1408 2740 1.529309 GGGGCAGGAAGAGATGGAC 59.471 63.158 0.00 0.00 0.00 4.02
1424 2760 0.181350 GGTACAGATCAGGCAAGGGG 59.819 60.000 0.00 0.00 0.00 4.79
1451 2787 3.761897 TCCATTATAAGCATTTCCCCCG 58.238 45.455 0.00 0.00 0.00 5.73
1471 2807 6.012658 TCACAAGAAACAGGTGCATTTATC 57.987 37.500 0.00 0.00 32.69 1.75
1504 2840 2.159747 GGACGAAATAGAAACCGTGTGC 60.160 50.000 0.00 0.00 35.22 4.57
1549 2885 0.463295 ATCAGTTGCCATCTCGCAGG 60.463 55.000 0.00 0.00 40.53 4.85
1715 3058 3.937706 GACATGATCTGGGACAAGACAAG 59.062 47.826 0.00 0.00 38.70 3.16
1742 3088 6.199719 AGGAAAAGTCAAACTAGTTCGTAACG 59.800 38.462 8.95 0.00 36.23 3.18
1850 3220 2.614057 CTGGGTCACTTCAACAGACAAC 59.386 50.000 0.00 0.00 34.04 3.32
1853 3225 2.910688 TCTGGGTCACTTCAACAGAC 57.089 50.000 0.00 0.00 33.62 3.51
1927 3299 1.531423 CTATGCTAATGCTGCCCCTG 58.469 55.000 0.00 0.00 40.48 4.45
1990 3362 9.541884 TTTAGGATAGGACATTTTTAAGCCTTT 57.458 29.630 0.00 0.00 0.00 3.11
1998 3370 9.996554 CCTTTTGTTTTAGGATAGGACATTTTT 57.003 29.630 0.00 0.00 33.13 1.94
2004 3377 5.262009 AGGCCTTTTGTTTTAGGATAGGAC 58.738 41.667 0.00 0.00 33.13 3.85
2062 3435 4.176271 GCAAGGGACAACATAGAAAATGC 58.824 43.478 0.00 0.00 0.00 3.56
2064 3437 6.183360 GCTATGCAAGGGACAACATAGAAAAT 60.183 38.462 11.90 0.00 42.94 1.82
2073 3446 5.343249 CAAATTAGCTATGCAAGGGACAAC 58.657 41.667 0.00 0.00 0.00 3.32
2113 3486 2.533266 AGGTGGCTATATCAGTTGCG 57.467 50.000 0.00 0.00 0.00 4.85
2123 3496 2.040278 TCTCACAGCAAAAGGTGGCTAT 59.960 45.455 0.00 0.00 38.56 2.97
2126 3499 1.251251 ATCTCACAGCAAAAGGTGGC 58.749 50.000 0.00 0.00 35.74 5.01
2176 3549 7.949035 CAGTATGAGCAGCACTAGGCAGTAC 62.949 52.000 0.00 0.00 42.76 2.73
2222 3595 4.192317 AGTAAAATCATCTCCGGTTCTGC 58.808 43.478 0.00 0.00 0.00 4.26
2289 3668 9.893305 ACATACACTTGTTTTTATTCTTACTGC 57.107 29.630 0.00 0.00 0.00 4.40
2323 3745 8.137745 TGGCAGGAAATTTTAGAATCAGAATT 57.862 30.769 0.00 0.00 0.00 2.17
2324 3746 7.722949 TGGCAGGAAATTTTAGAATCAGAAT 57.277 32.000 0.00 0.00 0.00 2.40
2325 3747 7.233348 AGTTGGCAGGAAATTTTAGAATCAGAA 59.767 33.333 0.00 0.00 0.00 3.02
2326 3748 6.721208 AGTTGGCAGGAAATTTTAGAATCAGA 59.279 34.615 0.00 0.00 0.00 3.27
2327 3749 6.810182 CAGTTGGCAGGAAATTTTAGAATCAG 59.190 38.462 0.00 0.00 0.00 2.90
2328 3750 6.690530 CAGTTGGCAGGAAATTTTAGAATCA 58.309 36.000 0.00 0.00 0.00 2.57
2329 3751 5.578336 GCAGTTGGCAGGAAATTTTAGAATC 59.422 40.000 0.00 0.00 43.97 2.52
2330 3752 5.482006 GCAGTTGGCAGGAAATTTTAGAAT 58.518 37.500 0.00 0.00 43.97 2.40
2331 3753 4.881920 GCAGTTGGCAGGAAATTTTAGAA 58.118 39.130 0.00 0.00 43.97 2.10
2332 3754 4.519540 GCAGTTGGCAGGAAATTTTAGA 57.480 40.909 0.00 0.00 43.97 2.10
2402 3824 6.516718 GCTCAATGCCTGTATAGTTCTCTTA 58.483 40.000 0.00 0.00 35.15 2.10
2404 3826 4.954875 GCTCAATGCCTGTATAGTTCTCT 58.045 43.478 0.00 0.00 35.15 3.10
2455 3878 7.066766 GTCAGAGAAGCAAATATGGAATTCAGT 59.933 37.037 7.93 0.00 0.00 3.41
2556 3979 6.164876 CAGGTCTTGAGCTCCTATGATAATG 58.835 44.000 12.15 0.00 0.00 1.90
2573 3996 3.195825 CGATGGAAGAGGTTACAGGTCTT 59.804 47.826 0.00 0.00 33.14 3.01
2608 4031 7.093354 GCAGAAGAAATGGATAGATACGATGA 58.907 38.462 0.00 0.00 0.00 2.92
2609 4032 6.870439 TGCAGAAGAAATGGATAGATACGATG 59.130 38.462 0.00 0.00 0.00 3.84
2651 4074 0.460987 AGTAGATGCTGCCACTTCGC 60.461 55.000 0.00 0.00 0.00 4.70
2760 4183 4.357142 CGCTTCATGAAGGATGGAAATTG 58.643 43.478 31.41 7.89 38.80 2.32
2839 4262 7.654116 GCTATGAATTTACTAGGAGGACAAGTC 59.346 40.741 0.00 0.00 0.00 3.01
2847 4270 7.821652 TCGATGAGCTATGAATTTACTAGGAG 58.178 38.462 0.00 0.00 0.00 3.69
2998 4422 3.889520 AGGTATTTGGACTCGAACTCC 57.110 47.619 2.34 2.34 0.00 3.85
3165 4589 2.096069 CCATCTTGAGTTCACAACTGCG 60.096 50.000 0.00 0.00 43.03 5.18
3170 4594 6.119536 AGTAAACACCATCTTGAGTTCACAA 58.880 36.000 0.00 0.00 0.00 3.33
3173 4597 7.338196 TCAAAAGTAAACACCATCTTGAGTTCA 59.662 33.333 0.00 0.00 0.00 3.18
3218 4643 5.066375 CGGATGATATGCACCTGAAAAGAAA 59.934 40.000 0.00 0.00 0.00 2.52
3327 4752 4.942363 ACCAGACTCCTAACTAGTACCA 57.058 45.455 0.00 0.00 0.00 3.25
3344 4771 8.317679 AGATAGATAAAGCTTAAGCCATACCAG 58.682 37.037 23.71 0.00 43.38 4.00
3345 4772 8.097038 CAGATAGATAAAGCTTAAGCCATACCA 58.903 37.037 23.71 4.84 43.38 3.25
3353 4780 6.533367 GGCGATCCAGATAGATAAAGCTTAAG 59.467 42.308 0.00 0.00 0.00 1.85
3385 4812 2.682836 ACCAACAAAATGCATAACCGC 58.317 42.857 0.00 0.00 0.00 5.68
3386 4813 5.406649 ACATACCAACAAAATGCATAACCG 58.593 37.500 0.00 0.00 0.00 4.44
3413 4840 1.073763 TGCCATCTTGTAAGCCACTGT 59.926 47.619 0.00 0.00 0.00 3.55
3629 5221 6.772716 GCCAAAGAATCATTTCCTGGTCTATA 59.227 38.462 0.00 0.00 37.53 1.31
3687 5384 6.109359 CCATTGTGTCCTTCTCCTAGTTTAG 58.891 44.000 0.00 0.00 0.00 1.85
3688 5385 5.570844 GCCATTGTGTCCTTCTCCTAGTTTA 60.571 44.000 0.00 0.00 0.00 2.01
3689 5386 4.807643 GCCATTGTGTCCTTCTCCTAGTTT 60.808 45.833 0.00 0.00 0.00 2.66
3690 5387 3.307762 GCCATTGTGTCCTTCTCCTAGTT 60.308 47.826 0.00 0.00 0.00 2.24
3803 5500 5.220710 TGAAGAAGGGAGAAGAGTGAAAG 57.779 43.478 0.00 0.00 0.00 2.62
3852 5549 6.198650 TGCTAATTTGTGAATCTGATGGTG 57.801 37.500 0.00 0.00 0.00 4.17
3858 5555 6.110543 TCGTGATGCTAATTTGTGAATCTG 57.889 37.500 0.00 0.00 0.00 2.90
3864 5561 7.642669 AGGAAATATCGTGATGCTAATTTGTG 58.357 34.615 0.00 0.00 0.00 3.33
3916 5613 4.338795 AACTTCTGATAGGACTGAGGGA 57.661 45.455 0.00 0.00 0.00 4.20
3961 5658 9.463443 CTTAAGTTGTTTACCTTTTTCCTCATG 57.537 33.333 0.00 0.00 0.00 3.07
3964 5661 6.635641 CGCTTAAGTTGTTTACCTTTTTCCTC 59.364 38.462 4.02 0.00 0.00 3.71
3965 5662 6.460537 CCGCTTAAGTTGTTTACCTTTTTCCT 60.461 38.462 4.02 0.00 0.00 3.36
3966 5663 5.688621 CCGCTTAAGTTGTTTACCTTTTTCC 59.311 40.000 4.02 0.00 0.00 3.13
3967 5664 6.497437 TCCGCTTAAGTTGTTTACCTTTTTC 58.503 36.000 4.02 0.00 0.00 2.29
3968 5665 6.453926 TCCGCTTAAGTTGTTTACCTTTTT 57.546 33.333 4.02 0.00 0.00 1.94
3973 5670 2.159747 CGCTCCGCTTAAGTTGTTTACC 60.160 50.000 4.02 0.00 0.00 2.85
3983 5680 2.159338 AGTAACGAATCGCTCCGCTTAA 60.159 45.455 1.15 0.00 0.00 1.85
4009 5706 3.071457 TGTCATGAGGTATGCCGATTGAT 59.929 43.478 0.00 0.00 40.50 2.57
4010 5707 2.433970 TGTCATGAGGTATGCCGATTGA 59.566 45.455 0.00 0.00 40.50 2.57
4011 5708 2.837498 TGTCATGAGGTATGCCGATTG 58.163 47.619 0.00 0.00 40.50 2.67
4098 5795 4.460034 TGATACATTTGCTCTGCACAATGT 59.540 37.500 22.68 22.68 44.10 2.71
4145 6231 2.301583 GCTCAGTTTCTCCTCCTCAAGT 59.698 50.000 0.00 0.00 0.00 3.16
4148 6234 0.891373 CGCTCAGTTTCTCCTCCTCA 59.109 55.000 0.00 0.00 0.00 3.86
4152 6238 2.263945 GTAAGCGCTCAGTTTCTCCTC 58.736 52.381 12.06 0.00 0.00 3.71


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

AutoCloner maintained by Alex Coulton.