Multiple sequence alignment - TraesCS5D01G469700

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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 TraesCS5D01G469700 chr5D 100.000 4643 0 0 1 4643 510654905 510659547 0.000000e+00 8575
1 TraesCS5D01G469700 chr5B 87.162 3256 288 65 795 3992 641713342 641716525 0.000000e+00 3578
2 TraesCS5D01G469700 chr5B 91.923 1139 87 3 2722 3860 641699145 641700278 0.000000e+00 1589
3 TraesCS5D01G469700 chr5B 87.443 1306 135 9 1394 2685 641697855 641699145 0.000000e+00 1476
4 TraesCS5D01G469700 chr5B 88.567 621 44 9 4036 4640 641716608 641717217 0.000000e+00 728
5 TraesCS5D01G469700 chr5B 81.250 816 100 23 503 1272 641670548 641671356 1.100000e-170 610
6 TraesCS5D01G469700 chr5B 91.989 362 26 3 375 734 641712987 641713347 5.360000e-139 505
7 TraesCS5D01G469700 chr5A 92.128 1537 102 7 2321 3850 638817779 638819303 0.000000e+00 2150
8 TraesCS5D01G469700 chr5A 84.649 1622 177 30 574 2163 638816200 638817781 0.000000e+00 1550
9 TraesCS5D01G469700 chr5A 89.006 664 44 15 3995 4643 638820175 638820824 0.000000e+00 795
10 TraesCS5D01G469700 chr5A 82.609 621 65 16 3 583 638814413 638815030 4.140000e-140 508
11 TraesCS5D01G469700 chr2B 79.726 1603 292 24 2061 3651 402557397 402555816 0.000000e+00 1129
12 TraesCS5D01G469700 chr2D 79.775 1513 270 26 2145 3645 334265326 334263838 0.000000e+00 1066
13 TraesCS5D01G469700 chr1D 78.677 1618 295 33 2059 3645 7028146 7029744 0.000000e+00 1031
14 TraesCS5D01G469700 chr1D 77.614 1626 290 59 2055 3645 7082010 7083596 0.000000e+00 918
15 TraesCS5D01G469700 chr6A 78.847 1475 287 17 2067 3536 610269119 610270573 0.000000e+00 972
16 TraesCS5D01G469700 chr6B 78.919 1461 279 21 2065 3521 706973560 706974995 0.000000e+00 965
17 TraesCS5D01G469700 chr6B 78.697 1474 291 15 2067 3536 707008474 707009928 0.000000e+00 961


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 TraesCS5D01G469700 chr5D 510654905 510659547 4642 False 8575.000000 8575 100.000000 1 4643 1 chr5D.!!$F1 4642
1 TraesCS5D01G469700 chr5B 641712987 641717217 4230 False 1603.666667 3578 89.239333 375 4640 3 chr5B.!!$F3 4265
2 TraesCS5D01G469700 chr5B 641697855 641700278 2423 False 1532.500000 1589 89.683000 1394 3860 2 chr5B.!!$F2 2466
3 TraesCS5D01G469700 chr5B 641670548 641671356 808 False 610.000000 610 81.250000 503 1272 1 chr5B.!!$F1 769
4 TraesCS5D01G469700 chr5A 638814413 638820824 6411 False 1250.750000 2150 87.098000 3 4643 4 chr5A.!!$F1 4640
5 TraesCS5D01G469700 chr2B 402555816 402557397 1581 True 1129.000000 1129 79.726000 2061 3651 1 chr2B.!!$R1 1590
6 TraesCS5D01G469700 chr2D 334263838 334265326 1488 True 1066.000000 1066 79.775000 2145 3645 1 chr2D.!!$R1 1500
7 TraesCS5D01G469700 chr1D 7028146 7029744 1598 False 1031.000000 1031 78.677000 2059 3645 1 chr1D.!!$F1 1586
8 TraesCS5D01G469700 chr1D 7082010 7083596 1586 False 918.000000 918 77.614000 2055 3645 1 chr1D.!!$F2 1590
9 TraesCS5D01G469700 chr6A 610269119 610270573 1454 False 972.000000 972 78.847000 2067 3536 1 chr6A.!!$F1 1469
10 TraesCS5D01G469700 chr6B 706973560 706974995 1435 False 965.000000 965 78.919000 2065 3521 1 chr6B.!!$F1 1456
11 TraesCS5D01G469700 chr6B 707008474 707009928 1454 False 961.000000 961 78.697000 2067 3536 1 chr6B.!!$F2 1469

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
223 228 0.389948 AAGTCGCCGACTCAATCACC 60.390 55.0 21.49 0.0 42.59 4.02 F
1333 2598 0.322975 CGGGGCCTATGAGAATGGAG 59.677 60.0 0.84 0.0 0.00 3.86 F
1356 2621 0.388134 CACCACCACTTACCTCGTCG 60.388 60.0 0.00 0.0 0.00 5.12 F
2358 3651 0.394899 GCTCCTGCAGGGCTGTTATT 60.395 55.0 32.23 0.0 39.41 1.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2114 3407 0.035881 AGGAGGACATGTGCACTGTG 59.964 55.000 20.21 19.50 0.00 3.66 R
2720 4074 0.043637 AAATCCACCTCCCCCGAGTA 59.956 55.000 0.00 0.00 33.93 2.59 R
2975 4347 1.511768 GTGGACCAGTCTAGACGGC 59.488 63.158 24.55 18.81 36.20 5.68 R
3809 5193 0.322456 TCCATGGAAAACCTGCCTCG 60.322 55.000 13.46 0.00 0.00 4.63 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
63 64 1.812571 AGCTGGCAGAAAACCAATACG 59.187 47.619 20.86 0.00 36.56 3.06
71 72 5.393027 GGCAGAAAACCAATACGTCATCAAT 60.393 40.000 0.00 0.00 0.00 2.57
72 73 5.512788 GCAGAAAACCAATACGTCATCAATG 59.487 40.000 0.00 0.00 0.00 2.82
79 80 6.112734 ACCAATACGTCATCAATGTACACAT 58.887 36.000 0.00 0.00 38.41 3.21
80 81 6.037062 ACCAATACGTCATCAATGTACACATG 59.963 38.462 0.00 0.27 36.56 3.21
81 82 6.257630 CCAATACGTCATCAATGTACACATGA 59.742 38.462 13.77 13.77 36.56 3.07
82 83 7.201600 CCAATACGTCATCAATGTACACATGAA 60.202 37.037 15.00 3.08 36.56 2.57
83 84 5.784750 ACGTCATCAATGTACACATGAAG 57.215 39.130 15.00 16.69 36.56 3.02
84 85 5.478407 ACGTCATCAATGTACACATGAAGA 58.522 37.500 22.73 17.89 36.56 2.87
85 86 5.931724 ACGTCATCAATGTACACATGAAGAA 59.068 36.000 22.73 9.69 36.56 2.52
86 87 6.091305 ACGTCATCAATGTACACATGAAGAAG 59.909 38.462 22.73 21.34 36.56 2.85
89 90 8.506437 GTCATCAATGTACACATGAAGAAGAAA 58.494 33.333 15.81 0.00 36.56 2.52
94 96 5.122519 TGTACACATGAAGAAGAAACTGCA 58.877 37.500 0.00 0.00 0.00 4.41
132 137 0.457851 CACCACCCGAGCAAACAAAA 59.542 50.000 0.00 0.00 0.00 2.44
134 139 0.593773 CCACCCGAGCAAACAAAACG 60.594 55.000 0.00 0.00 0.00 3.60
144 149 3.311596 AGCAAACAAAACGGACACTCTAC 59.688 43.478 0.00 0.00 0.00 2.59
154 159 2.755655 CGGACACTCTACAACCAGATCT 59.244 50.000 0.00 0.00 0.00 2.75
164 169 3.834610 ACAACCAGATCTAAAGTCGTCG 58.165 45.455 0.00 0.00 0.00 5.12
169 174 1.331138 AGATCTAAAGTCGTCGCTCCG 59.669 52.381 0.00 0.00 0.00 4.63
210 215 2.022129 CGTGGACCAGACAAGTCGC 61.022 63.158 0.00 0.00 34.97 5.19
223 228 0.389948 AAGTCGCCGACTCAATCACC 60.390 55.000 21.49 0.00 42.59 4.02
236 241 1.542915 CAATCACCCAAGCAACCAGAG 59.457 52.381 0.00 0.00 0.00 3.35
249 254 3.557054 GCAACCAGAGATGACAACCTACA 60.557 47.826 0.00 0.00 0.00 2.74
257 262 1.942677 TGACAACCTACAACACCACG 58.057 50.000 0.00 0.00 0.00 4.94
268 273 1.151777 AACACCACGACAGTTGCTCG 61.152 55.000 0.00 0.00 37.17 5.03
269 274 2.029073 ACCACGACAGTTGCTCGG 59.971 61.111 0.00 0.00 35.37 4.63
356 361 8.621532 TGAAGAAAAAGTAGATAGCATTGTGT 57.378 30.769 0.00 0.00 0.00 3.72
358 363 9.334693 GAAGAAAAAGTAGATAGCATTGTGTTG 57.665 33.333 0.00 0.00 0.00 3.33
416 449 3.741344 GCAGATTCAGTACACAAACTCGT 59.259 43.478 0.00 0.00 0.00 4.18
432 465 5.418310 AACTCGTGAAATCGACAAACAAT 57.582 34.783 0.00 0.00 35.91 2.71
440 473 5.116831 TGAAATCGACAAACAATTCGCAATG 59.883 36.000 0.00 0.00 35.15 2.82
452 488 9.507280 AAACAATTCGCAATGTAAATATCTGAG 57.493 29.630 0.00 0.00 0.00 3.35
458 494 4.276678 GCAATGTAAATATCTGAGCAGCCA 59.723 41.667 0.00 0.00 0.00 4.75
465 501 6.630444 AAATATCTGAGCAGCCAACATAAG 57.370 37.500 0.00 0.00 0.00 1.73
512 551 1.134788 CGACGGTTAGCAAGGAGGATT 60.135 52.381 0.00 0.00 0.00 3.01
529 568 4.723309 AGGATTCCATGGCAGACTTAATC 58.277 43.478 6.96 9.08 0.00 1.75
542 581 5.669848 GCAGACTTAATCACGAAGCTTCTTG 60.670 44.000 23.27 23.27 0.00 3.02
659 1878 0.684479 TGACAGGCTAGGACGAGCAT 60.684 55.000 6.75 0.00 44.76 3.79
704 1924 1.362355 CAACCCGTGACCTTTTGGC 59.638 57.895 0.00 0.00 45.59 4.52
741 1965 2.400399 CACGTACGGAGAGCTGAAAAA 58.600 47.619 21.06 0.00 0.00 1.94
745 1969 3.366070 CGTACGGAGAGCTGAAAAAGAGA 60.366 47.826 7.57 0.00 0.00 3.10
808 2038 2.559231 AGACGAAGGAAGACCAAGACTC 59.441 50.000 0.00 0.00 38.94 3.36
859 2100 2.668212 CACCTTTCCGGCGAGCAA 60.668 61.111 9.30 0.00 35.61 3.91
862 2103 1.305930 ACCTTTCCGGCGAGCAAATC 61.306 55.000 9.30 0.00 35.61 2.17
883 2124 0.465097 ATCTGCTCATTTGGCTCCGG 60.465 55.000 0.00 0.00 0.00 5.14
905 2146 5.106157 CGGTCTGCAGGTTTGATAATTTCTT 60.106 40.000 15.13 0.00 0.00 2.52
910 2151 8.950210 TCTGCAGGTTTGATAATTTCTTCTTAG 58.050 33.333 15.13 0.00 0.00 2.18
916 2157 8.951243 GGTTTGATAATTTCTTCTTAGTCTGCT 58.049 33.333 0.00 0.00 0.00 4.24
917 2158 9.980780 GTTTGATAATTTCTTCTTAGTCTGCTC 57.019 33.333 0.00 0.00 0.00 4.26
919 2160 6.980978 TGATAATTTCTTCTTAGTCTGCTCCG 59.019 38.462 0.00 0.00 0.00 4.63
920 2161 5.407407 AATTTCTTCTTAGTCTGCTCCGA 57.593 39.130 0.00 0.00 0.00 4.55
921 2162 5.606348 ATTTCTTCTTAGTCTGCTCCGAT 57.394 39.130 0.00 0.00 0.00 4.18
922 2163 4.640789 TTCTTCTTAGTCTGCTCCGATC 57.359 45.455 0.00 0.00 0.00 3.69
924 2165 3.629855 TCTTCTTAGTCTGCTCCGATCTG 59.370 47.826 0.00 0.00 0.00 2.90
925 2166 1.678627 TCTTAGTCTGCTCCGATCTGC 59.321 52.381 0.00 0.00 0.00 4.26
926 2167 1.406898 CTTAGTCTGCTCCGATCTGCA 59.593 52.381 5.14 5.14 37.63 4.41
948 2206 0.766131 TCCCGTTTCTTGCCACCTAA 59.234 50.000 0.00 0.00 0.00 2.69
949 2207 1.353022 TCCCGTTTCTTGCCACCTAAT 59.647 47.619 0.00 0.00 0.00 1.73
951 2209 2.163613 CCCGTTTCTTGCCACCTAATTC 59.836 50.000 0.00 0.00 0.00 2.17
963 2221 4.804108 CCACCTAATTCGTCAAAAATGCA 58.196 39.130 0.00 0.00 0.00 3.96
964 2222 4.858692 CCACCTAATTCGTCAAAAATGCAG 59.141 41.667 0.00 0.00 0.00 4.41
965 2223 5.460646 CACCTAATTCGTCAAAAATGCAGT 58.539 37.500 0.00 0.00 0.00 4.40
966 2224 5.343058 CACCTAATTCGTCAAAAATGCAGTG 59.657 40.000 0.00 0.00 0.00 3.66
989 2248 8.723942 GTGTCTTCTTACACCATTCATATTCT 57.276 34.615 0.00 0.00 43.23 2.40
1032 2291 2.154007 CAGTTTCTTCTTCGTCGTGCTC 59.846 50.000 0.00 0.00 0.00 4.26
1047 2306 2.818274 CTCGCAGCTGCAGCATCA 60.818 61.111 38.24 18.81 45.16 3.07
1049 2308 2.107151 CTCGCAGCTGCAGCATCATC 62.107 60.000 38.24 20.48 45.16 2.92
1050 2309 2.180862 CGCAGCTGCAGCATCATCT 61.181 57.895 38.24 15.93 45.16 2.90
1078 2337 2.442272 AGGGCCGCGACTATGACT 60.442 61.111 8.23 0.00 0.00 3.41
1081 2340 1.731433 GGGCCGCGACTATGACTACA 61.731 60.000 8.23 0.00 0.00 2.74
1084 2343 1.836383 CCGCGACTATGACTACAACC 58.164 55.000 8.23 0.00 0.00 3.77
1094 2353 1.338674 TGACTACAACCCGGATGCAAG 60.339 52.381 0.73 5.86 0.00 4.01
1123 2382 1.006832 CAATAACAACGCCTCCCTCG 58.993 55.000 0.00 0.00 0.00 4.63
1129 2388 4.681978 ACGCCTCCCTCGCAACAC 62.682 66.667 0.00 0.00 0.00 3.32
1140 2399 1.206578 CGCAACACGGTGGATCAAC 59.793 57.895 13.48 0.00 38.44 3.18
1155 2414 3.306502 GGATCAACAACAACGTCTCCCTA 60.307 47.826 0.00 0.00 0.00 3.53
1162 2421 2.803956 ACAACGTCTCCCTATCAGACA 58.196 47.619 0.00 0.00 40.42 3.41
1163 2422 3.162666 ACAACGTCTCCCTATCAGACAA 58.837 45.455 0.00 0.00 40.42 3.18
1166 2428 3.162666 ACGTCTCCCTATCAGACAACAA 58.837 45.455 1.08 0.00 40.42 2.83
1172 2437 3.119245 TCCCTATCAGACAACAAGTACGC 60.119 47.826 0.00 0.00 0.00 4.42
1173 2438 3.187700 CCTATCAGACAACAAGTACGCC 58.812 50.000 0.00 0.00 0.00 5.68
1179 2444 2.735857 AACAAGTACGCCGACGGC 60.736 61.111 29.10 29.10 46.75 5.68
1248 2513 0.930726 TTCAGGGGTGGTCTTTTGGT 59.069 50.000 0.00 0.00 0.00 3.67
1272 2537 2.607750 TTCTTCTGCGCCTCCCCT 60.608 61.111 4.18 0.00 0.00 4.79
1304 2569 1.656095 CGTCTTCTCCGTCTTCATTGC 59.344 52.381 0.00 0.00 0.00 3.56
1331 2596 1.302832 GCGGGGCCTATGAGAATGG 60.303 63.158 0.84 0.00 0.00 3.16
1332 2597 1.768684 GCGGGGCCTATGAGAATGGA 61.769 60.000 0.84 0.00 0.00 3.41
1333 2598 0.322975 CGGGGCCTATGAGAATGGAG 59.677 60.000 0.84 0.00 0.00 3.86
1334 2599 1.734655 GGGGCCTATGAGAATGGAGA 58.265 55.000 0.84 0.00 0.00 3.71
1335 2600 2.057922 GGGGCCTATGAGAATGGAGAA 58.942 52.381 0.84 0.00 0.00 2.87
1336 2601 2.646798 GGGGCCTATGAGAATGGAGAAT 59.353 50.000 0.84 0.00 0.00 2.40
1337 2602 3.308046 GGGGCCTATGAGAATGGAGAATC 60.308 52.174 0.84 0.00 0.00 2.52
1339 2604 4.322567 GGCCTATGAGAATGGAGAATCAC 58.677 47.826 0.00 0.00 36.25 3.06
1340 2605 4.322567 GCCTATGAGAATGGAGAATCACC 58.677 47.826 0.00 0.00 36.25 4.02
1341 2606 4.202398 GCCTATGAGAATGGAGAATCACCA 60.202 45.833 1.11 1.11 41.83 4.17
1343 2608 3.634397 TGAGAATGGAGAATCACCACC 57.366 47.619 0.52 0.00 40.36 4.61
1344 2609 2.912295 TGAGAATGGAGAATCACCACCA 59.088 45.455 0.52 0.00 40.36 4.17
1345 2610 3.274288 GAGAATGGAGAATCACCACCAC 58.726 50.000 0.52 0.00 40.36 4.16
1349 2614 3.695830 TGGAGAATCACCACCACTTAC 57.304 47.619 0.00 0.00 36.25 2.34
1351 2616 2.572104 GGAGAATCACCACCACTTACCT 59.428 50.000 0.00 0.00 36.25 3.08
1356 2621 0.388134 CACCACCACTTACCTCGTCG 60.388 60.000 0.00 0.00 0.00 5.12
1455 2720 2.362369 CCTGGTCCTCCGTGATGCT 61.362 63.158 0.00 0.00 36.30 3.79
1560 2825 5.571784 TGTTTGATCAGAAGAATGCCATC 57.428 39.130 0.00 0.00 0.00 3.51
1599 2864 3.454447 ACCATCCGACTGATTCATTGGTA 59.546 43.478 0.00 0.00 0.00 3.25
1616 2881 1.660167 GTACCCGGGCAATCACTTAC 58.340 55.000 24.08 9.32 0.00 2.34
1640 2917 2.752030 AGGTATGAGGCTCACAGCTAA 58.248 47.619 24.70 0.00 41.99 3.09
1641 2918 3.312890 AGGTATGAGGCTCACAGCTAAT 58.687 45.455 24.70 7.71 41.99 1.73
1642 2919 4.483950 AGGTATGAGGCTCACAGCTAATA 58.516 43.478 24.70 6.67 41.99 0.98
1643 2920 4.282195 AGGTATGAGGCTCACAGCTAATAC 59.718 45.833 24.70 17.45 41.99 1.89
1644 2921 4.039245 GGTATGAGGCTCACAGCTAATACA 59.961 45.833 21.37 0.00 41.99 2.29
1645 2922 4.970860 ATGAGGCTCACAGCTAATACAT 57.029 40.909 21.37 0.00 41.99 2.29
1646 2923 4.327982 TGAGGCTCACAGCTAATACATC 57.672 45.455 14.43 0.00 41.99 3.06
1647 2924 3.963374 TGAGGCTCACAGCTAATACATCT 59.037 43.478 14.43 0.00 41.99 2.90
1648 2925 4.202192 TGAGGCTCACAGCTAATACATCTG 60.202 45.833 14.43 0.00 41.99 2.90
1649 2926 2.805099 GGCTCACAGCTAATACATCTGC 59.195 50.000 0.00 0.00 41.99 4.26
1650 2927 3.461061 GCTCACAGCTAATACATCTGCA 58.539 45.455 0.00 0.00 38.45 4.41
1651 2928 3.873361 GCTCACAGCTAATACATCTGCAA 59.127 43.478 0.00 0.00 38.45 4.08
1663 2940 4.151258 ACATCTGCAACAAATTCGACTG 57.849 40.909 0.00 0.00 0.00 3.51
1775 3052 7.386025 ACCGGTGAAAAGTAATAAGACTGTAAC 59.614 37.037 6.12 0.00 0.00 2.50
1788 3065 8.918202 ATAAGACTGTAACTGATCCAACAAAA 57.082 30.769 0.00 0.00 0.00 2.44
1827 3104 9.474313 AATGGCAACCTTAGTATCATTTTAGAA 57.526 29.630 0.00 0.00 0.00 2.10
1833 3111 6.761714 ACCTTAGTATCATTTTAGAAGCACCG 59.238 38.462 0.00 0.00 0.00 4.94
1867 3151 5.147330 TCATGACTCACAGATTACCGTTT 57.853 39.130 0.00 0.00 0.00 3.60
1874 3158 7.175467 TGACTCACAGATTACCGTTTTCTACTA 59.825 37.037 0.00 0.00 0.00 1.82
1875 3159 8.064336 ACTCACAGATTACCGTTTTCTACTAT 57.936 34.615 0.00 0.00 0.00 2.12
1903 3187 3.628942 TGTTGATTATCTCATGCTGCCAC 59.371 43.478 0.00 0.00 32.72 5.01
1904 3188 3.851458 TGATTATCTCATGCTGCCACT 57.149 42.857 0.00 0.00 0.00 4.00
2017 3301 6.428465 GTCTGATGTAATGGAGATCTCTCGTA 59.572 42.308 21.81 8.81 43.76 3.43
2026 3310 6.471233 TGGAGATCTCTCGTAATTGTGATT 57.529 37.500 21.81 0.00 43.76 2.57
2027 3311 6.878317 TGGAGATCTCTCGTAATTGTGATTT 58.122 36.000 21.81 0.00 43.76 2.17
2028 3312 6.980978 TGGAGATCTCTCGTAATTGTGATTTC 59.019 38.462 21.81 0.19 43.76 2.17
2030 3314 7.118496 AGATCTCTCGTAATTGTGATTTCCT 57.882 36.000 0.00 0.00 0.00 3.36
2032 3316 8.696374 AGATCTCTCGTAATTGTGATTTCCTAA 58.304 33.333 0.00 0.00 0.00 2.69
2033 3317 8.649973 ATCTCTCGTAATTGTGATTTCCTAAC 57.350 34.615 0.00 0.00 0.00 2.34
2035 3319 7.544566 TCTCTCGTAATTGTGATTTCCTAACAC 59.455 37.037 0.00 0.00 35.45 3.32
2036 3320 6.592607 TCTCGTAATTGTGATTTCCTAACACC 59.407 38.462 0.00 0.00 34.18 4.16
2037 3321 5.349270 TCGTAATTGTGATTTCCTAACACCG 59.651 40.000 0.00 0.00 34.18 4.94
2039 3323 5.371115 AATTGTGATTTCCTAACACCGTG 57.629 39.130 0.00 0.00 34.18 4.94
2040 3324 2.147958 TGTGATTTCCTAACACCGTGC 58.852 47.619 0.00 0.00 34.18 5.34
2041 3325 1.127951 GTGATTTCCTAACACCGTGCG 59.872 52.381 0.00 0.00 0.00 5.34
2053 3346 4.189188 CGTGCGGGAGGGAGTACG 62.189 72.222 0.00 0.00 39.71 3.67
2054 3347 2.753043 GTGCGGGAGGGAGTACGA 60.753 66.667 0.00 0.00 0.00 3.43
2132 3425 1.580845 GCACAGTGCACATGTCCTCC 61.581 60.000 21.22 0.09 44.26 4.30
2207 3500 1.148310 CTTGGTTGTACGCCACTGAG 58.852 55.000 8.29 1.37 35.46 3.35
2211 3504 1.007336 GTTGTACGCCACTGAGTCCG 61.007 60.000 1.23 1.23 0.00 4.79
2328 3621 4.768968 AGAAATGATTGTAAGCAAGCCTGT 59.231 37.500 0.00 0.00 40.02 4.00
2358 3651 0.394899 GCTCCTGCAGGGCTGTTATT 60.395 55.000 32.23 0.00 39.41 1.40
2374 3673 4.277476 TGTTATTTTCAGGTATGGCCAGG 58.723 43.478 13.05 0.00 40.61 4.45
2376 3675 3.756082 ATTTTCAGGTATGGCCAGGAA 57.244 42.857 13.05 7.02 40.61 3.36
2774 4128 3.878160 AGGGAAACTCGATGAAGAGAC 57.122 47.619 0.62 0.00 40.57 3.36
2799 4153 1.673920 GCAGTGAAACGTTTGGAAGGA 59.326 47.619 20.10 0.00 45.86 3.36
2975 4347 5.751990 GGATCTATAACCGCCGTAATAATGG 59.248 44.000 0.00 0.00 34.56 3.16
2985 4357 3.572584 CCGTAATAATGGCCGTCTAGAC 58.427 50.000 13.18 13.18 0.00 2.59
2996 4368 0.611062 CGTCTAGACTGGTCCACCCA 60.611 60.000 20.34 0.00 42.51 4.51
3085 4457 3.256383 TGCTCATTTGGACATCAAACCAG 59.744 43.478 0.00 0.00 46.72 4.00
3339 4713 9.442047 CCTGAGGAGGATGTTCATATTATTTAC 57.558 37.037 0.00 0.00 42.93 2.01
3364 4738 8.237267 ACTTATTACGAGAAAAGGCTCAAAATG 58.763 33.333 0.00 0.00 34.56 2.32
3415 4789 9.755804 ATAATAATAGTGATGATATGGTCGCAG 57.244 33.333 0.00 0.00 0.00 5.18
3676 5053 1.614903 TGCAGCCAAGAAATTCCACAG 59.385 47.619 0.00 0.00 0.00 3.66
3701 5078 6.421801 GTGCAGAGTTTGATTTTTGCAACTAT 59.578 34.615 0.00 0.00 42.41 2.12
3705 5082 8.909671 CAGAGTTTGATTTTTGCAACTATTCTC 58.090 33.333 0.00 0.69 0.00 2.87
3754 5131 4.314121 TGGAAGCATGTTTTAAATGGCAC 58.686 39.130 0.00 0.00 0.00 5.01
3760 5137 5.769162 AGCATGTTTTAAATGGCACCAAATT 59.231 32.000 0.00 0.00 0.00 1.82
3797 5178 6.509677 GCCAGTATGTTAAGCGAAGTTGTATC 60.510 42.308 0.00 0.00 0.00 2.24
3809 5193 5.688176 GCGAAGTTGTATCTCTCCTCATAAC 59.312 44.000 0.00 0.00 0.00 1.89
3832 5216 1.337118 GCAGGTTTTCCATGGAACCA 58.663 50.000 29.39 17.30 46.11 3.67
3860 5894 7.614583 AGGTGAGTAGTATAAGCAAAGTCTGTA 59.385 37.037 0.00 0.00 0.00 2.74
3861 5895 8.414778 GGTGAGTAGTATAAGCAAAGTCTGTAT 58.585 37.037 0.00 0.00 0.00 2.29
3862 5896 9.453325 GTGAGTAGTATAAGCAAAGTCTGTATC 57.547 37.037 0.00 0.00 0.00 2.24
3863 5897 9.409918 TGAGTAGTATAAGCAAAGTCTGTATCT 57.590 33.333 0.00 0.00 0.00 1.98
3876 5924 5.756918 AGTCTGTATCTGCTCTGTTAGGTA 58.243 41.667 0.00 0.00 0.00 3.08
4015 6129 3.956199 CAACCATCTATCAGCACCCAAAT 59.044 43.478 0.00 0.00 0.00 2.32
4019 6133 6.376248 ACCATCTATCAGCACCCAAATAAAT 58.624 36.000 0.00 0.00 0.00 1.40
4020 6134 7.526041 ACCATCTATCAGCACCCAAATAAATA 58.474 34.615 0.00 0.00 0.00 1.40
4021 6135 7.667219 ACCATCTATCAGCACCCAAATAAATAG 59.333 37.037 0.00 0.00 0.00 1.73
4022 6136 7.667219 CCATCTATCAGCACCCAAATAAATAGT 59.333 37.037 0.00 0.00 0.00 2.12
4024 6138 8.677148 TCTATCAGCACCCAAATAAATAGTTC 57.323 34.615 0.00 0.00 0.00 3.01
4025 6139 8.494433 TCTATCAGCACCCAAATAAATAGTTCT 58.506 33.333 0.00 0.00 0.00 3.01
4026 6140 6.757897 TCAGCACCCAAATAAATAGTTCTG 57.242 37.500 0.00 0.00 0.00 3.02
4027 6141 5.125417 TCAGCACCCAAATAAATAGTTCTGC 59.875 40.000 0.00 0.00 0.00 4.26
4029 6143 6.318648 CAGCACCCAAATAAATAGTTCTGCTA 59.681 38.462 0.00 0.00 30.28 3.49
4031 6145 7.561356 AGCACCCAAATAAATAGTTCTGCTAAT 59.439 33.333 0.00 0.00 32.72 1.73
4054 6168 6.515272 TTTGTATTTCTCTTCTTGGATGGC 57.485 37.500 0.00 0.00 0.00 4.40
4067 6181 1.611491 TGGATGGCGAAACAGGAAAAC 59.389 47.619 0.00 0.00 0.00 2.43
4073 6187 2.483106 GGCGAAACAGGAAAACTAGACC 59.517 50.000 0.00 0.00 0.00 3.85
4074 6188 3.135994 GCGAAACAGGAAAACTAGACCA 58.864 45.455 0.00 0.00 0.00 4.02
4075 6189 3.562557 GCGAAACAGGAAAACTAGACCAA 59.437 43.478 0.00 0.00 0.00 3.67
4096 6210 1.993370 GTCTTTTGACCGGATCACGAG 59.007 52.381 9.46 8.68 43.37 4.18
4166 6280 9.367444 AGTTTCACGATAAACGATCTTCTAAAT 57.633 29.630 10.27 0.00 45.77 1.40
4209 6337 6.312399 CTAGACAATTGTGTAGTTTTGCCA 57.688 37.500 26.74 2.47 38.41 4.92
4210 6338 5.789643 AGACAATTGTGTAGTTTTGCCAT 57.210 34.783 17.58 0.00 38.41 4.40
4211 6339 6.892658 AGACAATTGTGTAGTTTTGCCATA 57.107 33.333 17.58 0.00 38.41 2.74
4212 6340 6.677913 AGACAATTGTGTAGTTTTGCCATAC 58.322 36.000 17.58 0.00 38.41 2.39
4213 6341 6.264292 AGACAATTGTGTAGTTTTGCCATACA 59.736 34.615 17.58 0.00 38.41 2.29
4214 6342 6.810911 ACAATTGTGTAGTTTTGCCATACAA 58.189 32.000 11.07 0.00 35.72 2.41
4260 6391 8.701908 TGTAAGAGACAGTACTAAAAGGAAGA 57.298 34.615 0.00 0.00 32.86 2.87
4278 6409 6.657875 AGGAAGATAATTGAAGTTGAGAGGG 58.342 40.000 0.00 0.00 0.00 4.30
4300 6431 9.131791 GAGGGAGATAATAAATTTGGCAGTTAA 57.868 33.333 0.00 0.00 0.00 2.01
4316 6447 4.728595 GCAGTTAACAAACCTCGAAAACGT 60.729 41.667 8.61 0.00 0.00 3.99
4317 6448 5.326292 CAGTTAACAAACCTCGAAAACGTT 58.674 37.500 8.61 0.00 0.00 3.99
4318 6449 5.796437 CAGTTAACAAACCTCGAAAACGTTT 59.204 36.000 7.96 7.96 0.00 3.60
4391 6522 3.334691 TGCACCTTCTTCACCTTTATCG 58.665 45.455 0.00 0.00 0.00 2.92
4550 6681 9.840427 ATTTTGAATCATTAAAACTGTAGGACG 57.160 29.630 0.00 0.00 0.00 4.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
28 29 5.245301 TCTGCCAGCTTTACTTACTAACTGA 59.755 40.000 0.00 0.00 0.00 3.41
63 64 7.601073 TCTTCTTCATGTGTACATTGATGAC 57.399 36.000 18.72 0.24 33.61 3.06
71 72 5.122519 TGCAGTTTCTTCTTCATGTGTACA 58.877 37.500 0.00 0.00 0.00 2.90
72 73 5.466728 TCTGCAGTTTCTTCTTCATGTGTAC 59.533 40.000 14.67 0.00 0.00 2.90
79 80 3.206150 GTGGTCTGCAGTTTCTTCTTCA 58.794 45.455 14.67 0.00 0.00 3.02
80 81 2.221981 CGTGGTCTGCAGTTTCTTCTTC 59.778 50.000 14.67 0.00 0.00 2.87
81 82 2.213499 CGTGGTCTGCAGTTTCTTCTT 58.787 47.619 14.67 0.00 0.00 2.52
82 83 1.871080 CGTGGTCTGCAGTTTCTTCT 58.129 50.000 14.67 0.00 0.00 2.85
83 84 0.235926 GCGTGGTCTGCAGTTTCTTC 59.764 55.000 14.67 0.42 0.00 2.87
84 85 1.498865 CGCGTGGTCTGCAGTTTCTT 61.499 55.000 14.67 0.00 0.00 2.52
85 86 1.956170 CGCGTGGTCTGCAGTTTCT 60.956 57.895 14.67 0.00 0.00 2.52
86 87 1.891060 CTCGCGTGGTCTGCAGTTTC 61.891 60.000 14.67 5.73 0.00 2.78
111 113 2.112297 GTTTGCTCGGGTGGTGGA 59.888 61.111 0.00 0.00 0.00 4.02
112 114 1.388065 TTTGTTTGCTCGGGTGGTGG 61.388 55.000 0.00 0.00 0.00 4.61
123 128 2.844122 AGAGTGTCCGTTTTGTTTGC 57.156 45.000 0.00 0.00 0.00 3.68
124 129 4.868450 TGTAGAGTGTCCGTTTTGTTTG 57.132 40.909 0.00 0.00 0.00 2.93
132 137 1.991121 TCTGGTTGTAGAGTGTCCGT 58.009 50.000 0.00 0.00 0.00 4.69
134 139 5.916661 TTAGATCTGGTTGTAGAGTGTCC 57.083 43.478 5.18 0.00 0.00 4.02
144 149 2.599082 GCGACGACTTTAGATCTGGTTG 59.401 50.000 5.18 8.04 0.00 3.77
184 189 1.458777 TCTGGTCCACGGTCTTGGT 60.459 57.895 0.00 0.00 37.93 3.67
185 190 1.004918 GTCTGGTCCACGGTCTTGG 60.005 63.158 0.00 0.00 38.10 3.61
194 199 2.741092 GGCGACTTGTCTGGTCCA 59.259 61.111 0.00 0.00 0.00 4.02
195 200 2.432628 CGGCGACTTGTCTGGTCC 60.433 66.667 0.00 0.00 0.00 4.46
196 201 1.733399 GTCGGCGACTTGTCTGGTC 60.733 63.158 31.15 1.61 0.00 4.02
210 215 0.321564 TGCTTGGGTGATTGAGTCGG 60.322 55.000 0.00 0.00 0.00 4.79
223 228 2.189594 TGTCATCTCTGGTTGCTTGG 57.810 50.000 0.00 0.00 0.00 3.61
236 241 2.478894 CGTGGTGTTGTAGGTTGTCATC 59.521 50.000 0.00 0.00 0.00 2.92
249 254 1.151777 CGAGCAACTGTCGTGGTGTT 61.152 55.000 0.00 0.00 32.62 3.32
303 308 9.915629 CTTATAAGGCTATGATTCTTCGTAACT 57.084 33.333 4.42 0.00 0.00 2.24
368 373 2.098934 TGATGTGCAGCGTTTGTTCTTT 59.901 40.909 0.00 0.00 0.00 2.52
369 374 1.675483 TGATGTGCAGCGTTTGTTCTT 59.325 42.857 0.00 0.00 0.00 2.52
371 376 1.780860 GTTGATGTGCAGCGTTTGTTC 59.219 47.619 0.00 0.00 0.00 3.18
374 379 1.782569 CAAGTTGATGTGCAGCGTTTG 59.217 47.619 0.00 0.00 32.34 2.93
376 381 0.318107 GCAAGTTGATGTGCAGCGTT 60.318 50.000 7.16 0.00 40.58 4.84
383 416 4.761235 ACTGAATCTGCAAGTTGATGTG 57.239 40.909 7.16 0.00 33.76 3.21
384 417 5.180117 GTGTACTGAATCTGCAAGTTGATGT 59.820 40.000 7.16 0.00 33.76 3.06
416 449 4.216366 TGCGAATTGTTTGTCGATTTCA 57.784 36.364 0.00 0.00 39.64 2.69
432 465 5.277490 GCTGCTCAGATATTTACATTGCGAA 60.277 40.000 0.29 0.00 0.00 4.70
440 473 7.496529 TTATGTTGGCTGCTCAGATATTTAC 57.503 36.000 0.00 0.00 0.00 2.01
452 488 0.602562 TGGTTGCTTATGTTGGCTGC 59.397 50.000 0.00 0.00 0.00 5.25
458 494 4.309099 CATGTTGCTTGGTTGCTTATGTT 58.691 39.130 0.00 0.00 0.00 2.71
465 501 1.223417 GGTGCATGTTGCTTGGTTGC 61.223 55.000 0.00 0.00 45.31 4.17
512 551 2.499693 TCGTGATTAAGTCTGCCATGGA 59.500 45.455 18.40 0.00 0.00 3.41
529 568 4.963953 CACAGTTAAACAAGAAGCTTCGTG 59.036 41.667 32.26 32.26 41.49 4.35
542 581 8.743099 GCATTTTCAGAGTAAACACAGTTAAAC 58.257 33.333 0.00 0.00 0.00 2.01
659 1878 6.571605 TGTTCAAAGTCATTGCATGAGAAAA 58.428 32.000 0.00 0.00 40.53 2.29
704 1924 1.885388 TGGACTGTCCAAACGCGTG 60.885 57.895 26.54 0.00 45.00 5.34
741 1965 0.605589 CCTCTCAGCGTGGTTTCTCT 59.394 55.000 0.00 0.00 0.00 3.10
745 1969 1.004440 GAGCCTCTCAGCGTGGTTT 60.004 57.895 0.00 0.00 38.01 3.27
808 2038 2.156098 GAGAGGTGCCTATAGACTCGG 58.844 57.143 0.00 0.00 33.58 4.63
859 2100 2.957006 GAGCCAAATGAGCAGATGGATT 59.043 45.455 8.11 0.00 34.82 3.01
862 2103 1.030457 GGAGCCAAATGAGCAGATGG 58.970 55.000 0.00 0.00 36.00 3.51
872 2113 1.377725 CTGCAGACCGGAGCCAAAT 60.378 57.895 9.46 0.00 0.00 2.32
883 2124 7.150783 AGAAGAAATTATCAAACCTGCAGAC 57.849 36.000 17.39 0.00 0.00 3.51
905 2146 1.678627 GCAGATCGGAGCAGACTAAGA 59.321 52.381 0.00 0.00 0.00 2.10
910 2151 1.520342 GGTGCAGATCGGAGCAGAC 60.520 63.158 10.17 4.41 42.14 3.51
916 2157 3.147595 CGGGAGGTGCAGATCGGA 61.148 66.667 0.00 0.00 0.00 4.55
917 2158 2.521958 AAACGGGAGGTGCAGATCGG 62.522 60.000 0.00 0.00 0.00 4.18
919 2160 0.250513 AGAAACGGGAGGTGCAGATC 59.749 55.000 0.00 0.00 0.00 2.75
920 2161 0.693049 AAGAAACGGGAGGTGCAGAT 59.307 50.000 0.00 0.00 0.00 2.90
921 2162 0.250295 CAAGAAACGGGAGGTGCAGA 60.250 55.000 0.00 0.00 0.00 4.26
922 2163 1.856265 GCAAGAAACGGGAGGTGCAG 61.856 60.000 0.00 0.00 32.29 4.41
924 2165 2.626780 GGCAAGAAACGGGAGGTGC 61.627 63.158 0.00 0.00 0.00 5.01
925 2166 1.228124 TGGCAAGAAACGGGAGGTG 60.228 57.895 0.00 0.00 0.00 4.00
926 2167 1.228154 GTGGCAAGAAACGGGAGGT 60.228 57.895 0.00 0.00 0.00 3.85
948 2206 4.836125 AGACACTGCATTTTTGACGAAT 57.164 36.364 0.00 0.00 0.00 3.34
949 2207 4.335315 AGAAGACACTGCATTTTTGACGAA 59.665 37.500 0.00 0.00 0.00 3.85
951 2209 4.214980 AGAAGACACTGCATTTTTGACG 57.785 40.909 0.00 0.00 0.00 4.35
965 2223 9.166173 CAAGAATATGAATGGTGTAAGAAGACA 57.834 33.333 0.00 0.00 0.00 3.41
966 2224 8.125448 GCAAGAATATGAATGGTGTAAGAAGAC 58.875 37.037 0.00 0.00 0.00 3.01
977 2236 3.243636 GGTGCCTGCAAGAATATGAATGG 60.244 47.826 0.00 0.00 34.07 3.16
983 2242 2.313317 CCATGGTGCCTGCAAGAATAT 58.687 47.619 2.57 0.00 34.07 1.28
989 2248 1.907807 GAACCCATGGTGCCTGCAA 60.908 57.895 11.73 0.00 35.34 4.08
1032 2291 2.107151 GAGATGATGCTGCAGCTGCG 62.107 60.000 36.61 26.07 45.83 5.18
1047 2306 3.790437 CCCTGCACGGCCAGAGAT 61.790 66.667 2.24 0.00 34.77 2.75
1067 2326 1.535437 CCGGGTTGTAGTCATAGTCGC 60.535 57.143 0.00 0.00 0.00 5.19
1073 2332 0.908910 TGCATCCGGGTTGTAGTCAT 59.091 50.000 0.00 0.00 0.00 3.06
1078 2337 0.981183 AGTCTTGCATCCGGGTTGTA 59.019 50.000 0.00 0.00 0.00 2.41
1081 2340 1.002134 CCAGTCTTGCATCCGGGTT 60.002 57.895 0.00 0.00 0.00 4.11
1084 2343 1.987807 ATCCCCAGTCTTGCATCCGG 61.988 60.000 0.00 0.00 0.00 5.14
1094 2353 2.354821 GCGTTGTTATTGATCCCCAGTC 59.645 50.000 0.00 0.00 0.00 3.51
1123 2382 0.665835 TTGTTGATCCACCGTGTTGC 59.334 50.000 0.00 0.00 0.00 4.17
1129 2388 0.941542 ACGTTGTTGTTGATCCACCG 59.058 50.000 0.00 0.00 0.00 4.94
1140 2399 3.056821 TGTCTGATAGGGAGACGTTGTTG 60.057 47.826 0.00 0.00 42.46 3.33
1155 2414 1.271379 TCGGCGTACTTGTTGTCTGAT 59.729 47.619 6.85 0.00 0.00 2.90
1162 2421 2.735857 GCCGTCGGCGTACTTGTT 60.736 61.111 22.50 0.00 39.62 2.83
1279 2544 2.882761 TGAAGACGGAGAAGACGAAGAA 59.117 45.455 0.00 0.00 34.93 2.52
1318 2583 4.202398 TGGTGATTCTCCATTCTCATAGGC 60.202 45.833 3.33 0.00 0.00 3.93
1319 2584 5.303971 GTGGTGATTCTCCATTCTCATAGG 58.696 45.833 10.47 0.00 37.30 2.57
1325 2590 2.915604 AGTGGTGGTGATTCTCCATTCT 59.084 45.455 10.47 6.99 37.30 2.40
1326 2591 3.356529 AGTGGTGGTGATTCTCCATTC 57.643 47.619 10.47 7.25 37.30 2.67
1331 2596 3.676324 CGAGGTAAGTGGTGGTGATTCTC 60.676 52.174 0.00 0.00 0.00 2.87
1332 2597 2.233922 CGAGGTAAGTGGTGGTGATTCT 59.766 50.000 0.00 0.00 0.00 2.40
1333 2598 2.028385 ACGAGGTAAGTGGTGGTGATTC 60.028 50.000 0.00 0.00 0.00 2.52
1334 2599 1.975680 ACGAGGTAAGTGGTGGTGATT 59.024 47.619 0.00 0.00 0.00 2.57
1335 2600 1.549170 GACGAGGTAAGTGGTGGTGAT 59.451 52.381 0.00 0.00 0.00 3.06
1336 2601 0.963962 GACGAGGTAAGTGGTGGTGA 59.036 55.000 0.00 0.00 0.00 4.02
1337 2602 0.388134 CGACGAGGTAAGTGGTGGTG 60.388 60.000 0.00 0.00 0.00 4.17
1339 2604 1.214589 CCGACGAGGTAAGTGGTGG 59.785 63.158 0.00 0.00 34.51 4.61
1340 2605 1.214589 CCCGACGAGGTAAGTGGTG 59.785 63.158 0.00 0.00 38.74 4.17
1341 2606 1.075482 TCCCGACGAGGTAAGTGGT 59.925 57.895 0.00 0.00 38.74 4.16
1343 2608 1.246056 TGGTCCCGACGAGGTAAGTG 61.246 60.000 0.00 0.00 38.74 3.16
1344 2609 1.075482 TGGTCCCGACGAGGTAAGT 59.925 57.895 0.00 0.00 38.74 2.24
1345 2610 1.246056 TGTGGTCCCGACGAGGTAAG 61.246 60.000 0.00 0.00 38.74 2.34
1349 2614 3.760035 CCTGTGGTCCCGACGAGG 61.760 72.222 0.00 0.00 40.63 4.63
1351 2616 2.522436 AACCTGTGGTCCCGACGA 60.522 61.111 0.00 0.00 33.12 4.20
1356 2621 1.073199 CCAGACAACCTGTGGTCCC 59.927 63.158 1.15 0.00 41.33 4.46
1455 2720 1.685765 CCAGACCGTCCTCCCATCA 60.686 63.158 0.00 0.00 0.00 3.07
1560 2825 0.238289 GGTCAAATGACTGCCACACG 59.762 55.000 12.87 0.00 44.20 4.49
1599 2864 1.078708 CGTAAGTGATTGCCCGGGT 60.079 57.895 24.63 0.58 0.00 5.28
1616 2881 0.824109 TGTGAGCCTCATACCTTCCG 59.176 55.000 0.00 0.00 0.00 4.30
1640 2917 5.643348 TCAGTCGAATTTGTTGCAGATGTAT 59.357 36.000 0.00 0.00 0.00 2.29
1641 2918 4.994217 TCAGTCGAATTTGTTGCAGATGTA 59.006 37.500 0.00 0.00 0.00 2.29
1642 2919 3.814842 TCAGTCGAATTTGTTGCAGATGT 59.185 39.130 0.00 0.00 0.00 3.06
1643 2920 4.152938 TCTCAGTCGAATTTGTTGCAGATG 59.847 41.667 0.00 0.00 0.00 2.90
1644 2921 4.318332 TCTCAGTCGAATTTGTTGCAGAT 58.682 39.130 0.00 0.00 0.00 2.90
1645 2922 3.727726 TCTCAGTCGAATTTGTTGCAGA 58.272 40.909 0.00 0.00 0.00 4.26
1646 2923 4.472691 TTCTCAGTCGAATTTGTTGCAG 57.527 40.909 0.00 0.00 0.00 4.41
1647 2924 4.514816 TGATTCTCAGTCGAATTTGTTGCA 59.485 37.500 0.00 0.00 33.96 4.08
1648 2925 5.034554 TGATTCTCAGTCGAATTTGTTGC 57.965 39.130 0.00 0.00 33.96 4.17
1663 2940 8.764524 AGTACAGTCACATAAAACTGATTCTC 57.235 34.615 9.32 0.00 44.54 2.87
1775 3052 6.980593 TGGAATGTAACTTTTGTTGGATCAG 58.019 36.000 0.00 0.00 43.41 2.90
1788 3065 3.763897 GGTTGCCATTCTGGAATGTAACT 59.236 43.478 23.49 0.00 44.97 2.24
1859 3143 9.153721 CAACAATACCATAGTAGAAAACGGTAA 57.846 33.333 0.00 0.00 33.01 2.85
1874 3158 7.309012 GCAGCATGAGATAATCAACAATACCAT 60.309 37.037 0.00 0.00 42.53 3.55
1875 3159 6.016860 GCAGCATGAGATAATCAACAATACCA 60.017 38.462 0.00 0.00 42.53 3.25
1895 3179 0.253044 GAACTGGGATAGTGGCAGCA 59.747 55.000 0.00 0.00 40.26 4.41
1903 3187 7.667635 TCTCATATACTGACTGAACTGGGATAG 59.332 40.741 0.00 0.00 0.00 2.08
1904 3188 7.526918 TCTCATATACTGACTGAACTGGGATA 58.473 38.462 0.00 0.00 0.00 2.59
2017 3301 4.320935 GCACGGTGTTAGGAAATCACAATT 60.321 41.667 10.24 0.00 34.27 2.32
2026 3310 2.162338 CTCCCGCACGGTGTTAGGAA 62.162 60.000 16.85 0.85 0.00 3.36
2027 3311 2.601067 TCCCGCACGGTGTTAGGA 60.601 61.111 16.85 13.80 0.00 2.94
2028 3312 2.125673 CTCCCGCACGGTGTTAGG 60.126 66.667 10.24 10.61 0.00 2.69
2030 3314 3.697747 CCCTCCCGCACGGTGTTA 61.698 66.667 10.24 0.00 0.00 2.41
2035 3319 3.834799 GTACTCCCTCCCGCACGG 61.835 72.222 1.02 1.02 0.00 4.94
2036 3320 4.189188 CGTACTCCCTCCCGCACG 62.189 72.222 0.00 0.00 0.00 5.34
2037 3321 2.753043 TCGTACTCCCTCCCGCAC 60.753 66.667 0.00 0.00 0.00 5.34
2039 3323 1.517210 GATCTCGTACTCCCTCCCGC 61.517 65.000 0.00 0.00 0.00 6.13
2040 3324 0.108963 AGATCTCGTACTCCCTCCCG 59.891 60.000 0.00 0.00 0.00 5.14
2041 3325 1.422402 AGAGATCTCGTACTCCCTCCC 59.578 57.143 16.97 0.00 34.13 4.30
2053 3346 3.540314 AGCACAATCACCAGAGATCTC 57.460 47.619 15.29 15.29 0.00 2.75
2054 3347 3.996921 AAGCACAATCACCAGAGATCT 57.003 42.857 0.00 0.00 0.00 2.75
2093 3386 2.349438 GCATTTGTGCATATCCCGTACG 60.349 50.000 8.69 8.69 34.41 3.67
2114 3407 0.035881 AGGAGGACATGTGCACTGTG 59.964 55.000 20.21 19.50 0.00 3.66
2132 3425 5.184711 AGTTCGAACTAGTAGTACCCTCAG 58.815 45.833 28.80 0.00 37.52 3.35
2207 3500 1.819288 TGTCCTGACAAGAGATCGGAC 59.181 52.381 0.00 5.49 38.56 4.79
2211 3504 3.257469 TGCATGTCCTGACAAGAGATC 57.743 47.619 3.79 0.00 45.41 2.75
2277 3570 0.527565 AATTCACAATGGCGTGGCTC 59.472 50.000 0.00 0.00 37.50 4.70
2358 3651 2.274542 TCTTCCTGGCCATACCTGAAA 58.725 47.619 5.51 0.00 39.72 2.69
2374 3673 7.705325 CCAGAAACATTCATCATTGGAATCTTC 59.295 37.037 0.00 0.00 32.86 2.87
2376 3675 6.097839 CCCAGAAACATTCATCATTGGAATCT 59.902 38.462 0.00 0.00 32.86 2.40
2387 3686 5.838521 ACCTTTGTTACCCAGAAACATTCAT 59.161 36.000 0.00 0.00 36.75 2.57
2720 4074 0.043637 AAATCCACCTCCCCCGAGTA 59.956 55.000 0.00 0.00 33.93 2.59
2774 4128 2.159448 TCCAAACGTTTCACTGCAACTG 60.159 45.455 11.37 0.00 0.00 3.16
2799 4153 4.373156 TTCTTTCTTTCCTTGCCTAGCT 57.627 40.909 0.00 0.00 0.00 3.32
2867 4221 7.946207 TGCACAGAAACCAATAAACTTTATGA 58.054 30.769 0.00 0.00 0.00 2.15
2868 4222 8.081633 TCTGCACAGAAACCAATAAACTTTATG 58.918 33.333 0.00 0.00 33.91 1.90
2869 4223 8.177119 TCTGCACAGAAACCAATAAACTTTAT 57.823 30.769 0.00 0.00 33.91 1.40
2870 4224 7.500892 TCTCTGCACAGAAACCAATAAACTTTA 59.499 33.333 1.42 0.00 36.94 1.85
2871 4225 6.321181 TCTCTGCACAGAAACCAATAAACTTT 59.679 34.615 1.42 0.00 36.94 2.66
2872 4226 5.827797 TCTCTGCACAGAAACCAATAAACTT 59.172 36.000 1.42 0.00 36.94 2.66
2873 4227 5.376625 TCTCTGCACAGAAACCAATAAACT 58.623 37.500 1.42 0.00 36.94 2.66
2874 4228 5.689383 TCTCTGCACAGAAACCAATAAAC 57.311 39.130 1.42 0.00 36.94 2.01
2875 4229 6.707440 TTTCTCTGCACAGAAACCAATAAA 57.293 33.333 12.51 0.00 37.45 1.40
2883 4255 5.219343 TCTGAGATTTCTCTGCACAGAAA 57.781 39.130 17.86 17.86 44.59 2.52
2975 4347 1.511768 GTGGACCAGTCTAGACGGC 59.488 63.158 24.55 18.81 36.20 5.68
2996 4368 9.565090 TTGCAATATCTAGAATAATCTTGCACT 57.435 29.630 18.33 0.00 41.64 4.40
3228 4601 7.149307 TGTACACATCGACTTTTTCAGTGATA 58.851 34.615 0.00 0.00 35.01 2.15
3339 4713 8.450964 TCATTTTGAGCCTTTTCTCGTAATAAG 58.549 33.333 0.00 0.00 35.90 1.73
3412 4786 1.919600 ATCACTTCCTCCTGGCCTGC 61.920 60.000 3.32 0.00 0.00 4.85
3415 4789 1.274703 TGGATCACTTCCTCCTGGCC 61.275 60.000 0.00 0.00 45.68 5.36
3603 4977 2.561733 TAGATGCTTCACGAACCGAG 57.438 50.000 2.07 0.00 0.00 4.63
3676 5053 4.567959 AGTTGCAAAAATCAAACTCTGCAC 59.432 37.500 0.00 0.00 39.36 4.57
3754 5131 9.044150 CATACTGGCCAACAATTATTAATTTGG 57.956 33.333 7.01 12.61 33.71 3.28
3760 5137 8.410141 GCTTAACATACTGGCCAACAATTATTA 58.590 33.333 7.01 0.00 0.00 0.98
3769 5146 2.772077 TCGCTTAACATACTGGCCAA 57.228 45.000 7.01 0.00 0.00 4.52
3809 5193 0.322456 TCCATGGAAAACCTGCCTCG 60.322 55.000 13.46 0.00 0.00 4.63
3832 5216 8.634444 CAGACTTTGCTTATACTACTCACCTAT 58.366 37.037 0.00 0.00 0.00 2.57
3860 5894 6.721318 TGGAAAATTACCTAACAGAGCAGAT 58.279 36.000 3.79 0.00 0.00 2.90
3861 5895 6.121776 TGGAAAATTACCTAACAGAGCAGA 57.878 37.500 3.79 0.00 0.00 4.26
3862 5896 5.355350 CCTGGAAAATTACCTAACAGAGCAG 59.645 44.000 0.00 0.00 0.00 4.24
3863 5897 5.253330 CCTGGAAAATTACCTAACAGAGCA 58.747 41.667 0.00 0.00 0.00 4.26
3916 5964 9.435688 AACATCAAAATTACCCTTATGAAAAGC 57.564 29.630 0.00 0.00 0.00 3.51
3977 6027 4.032960 TGGTTGAACCTGCTTACATCAT 57.967 40.909 16.33 0.00 39.58 2.45
3981 6031 3.788227 AGATGGTTGAACCTGCTTACA 57.212 42.857 16.33 0.00 39.58 2.41
3992 6042 2.195727 TGGGTGCTGATAGATGGTTGA 58.804 47.619 0.00 0.00 0.00 3.18
3993 6043 2.715749 TGGGTGCTGATAGATGGTTG 57.284 50.000 0.00 0.00 0.00 3.77
4020 6134 9.732130 AGAAGAGAAATACAAATTAGCAGAACT 57.268 29.630 0.00 0.00 0.00 3.01
4024 6138 8.950210 TCCAAGAAGAGAAATACAAATTAGCAG 58.050 33.333 0.00 0.00 0.00 4.24
4025 6139 8.862325 TCCAAGAAGAGAAATACAAATTAGCA 57.138 30.769 0.00 0.00 0.00 3.49
4026 6140 9.727627 CATCCAAGAAGAGAAATACAAATTAGC 57.272 33.333 0.00 0.00 0.00 3.09
4029 6143 7.550712 GCCATCCAAGAAGAGAAATACAAATT 58.449 34.615 0.00 0.00 0.00 1.82
4031 6145 5.123820 CGCCATCCAAGAAGAGAAATACAAA 59.876 40.000 0.00 0.00 0.00 2.83
4033 6147 4.081142 TCGCCATCCAAGAAGAGAAATACA 60.081 41.667 0.00 0.00 0.00 2.29
4034 6148 4.442706 TCGCCATCCAAGAAGAGAAATAC 58.557 43.478 0.00 0.00 0.00 1.89
4054 6168 4.814771 ACTTGGTCTAGTTTTCCTGTTTCG 59.185 41.667 0.00 0.00 0.00 3.46
4067 6181 3.006537 TCCGGTCAAAAGACTTGGTCTAG 59.993 47.826 0.00 0.00 42.59 2.43
4073 6187 2.157668 CGTGATCCGGTCAAAAGACTTG 59.842 50.000 0.00 0.00 38.90 3.16
4074 6188 2.036733 TCGTGATCCGGTCAAAAGACTT 59.963 45.455 0.00 0.00 38.90 3.01
4075 6189 1.616865 TCGTGATCCGGTCAAAAGACT 59.383 47.619 0.00 0.00 38.90 3.24
4100 6214 5.047847 AGGAATATTAACCATCACGTGACG 58.952 41.667 22.71 13.58 0.00 4.35
4103 6217 8.601845 TCAATAGGAATATTAACCATCACGTG 57.398 34.615 9.94 9.94 0.00 4.49
4182 6296 7.308589 GGCAAAACTACACAATTGTCTAGTCAT 60.309 37.037 22.00 13.79 37.15 3.06
4289 6420 3.280295 TCGAGGTTTGTTAACTGCCAAA 58.720 40.909 7.22 0.00 34.59 3.28
4550 6681 7.435068 TCAGATTGTTGTTTAGCCTTTCTAC 57.565 36.000 0.00 0.00 0.00 2.59


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

AutoCloner maintained by Alex Coulton.