Multiple sequence alignment - TraesCS3A01G370600

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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 TraesCS3A01G370600 chr3A 100.000 4383 0 0 1 4383 621221647 621217265 0.000000e+00 8094
1 TraesCS3A01G370600 chr3B 88.070 1601 105 37 535 2086 637066987 637065424 0.000000e+00 1820
2 TraesCS3A01G370600 chr3B 84.419 1688 145 43 2133 3794 637065419 637063824 0.000000e+00 1552
3 TraesCS3A01G370600 chr3B 86.687 323 30 7 97 417 637067449 637067138 3.240000e-91 346
4 TraesCS3A01G370600 chr3D 88.868 1042 65 28 676 1697 477884277 477883267 0.000000e+00 1234
5 TraesCS3A01G370600 chr3D 83.952 1346 118 46 1790 3095 477883218 477881931 0.000000e+00 1199
6 TraesCS3A01G370600 chr3D 84.840 686 49 29 24 678 477884976 477884315 1.330000e-179 640
7 TraesCS3A01G370600 chr3D 87.828 534 39 12 3262 3794 477881767 477881259 1.740000e-168 603
8 TraesCS3A01G370600 chr5A 95.455 594 26 1 3791 4383 640950487 640951080 0.000000e+00 946
9 TraesCS3A01G370600 chr5A 95.110 593 29 0 3791 4383 482130294 482129702 0.000000e+00 935
10 TraesCS3A01G370600 chr5A 94.305 597 34 0 3787 4383 598301621 598301025 0.000000e+00 915
11 TraesCS3A01G370600 chr4A 95.110 593 29 0 3791 4383 628816249 628816841 0.000000e+00 935
12 TraesCS3A01G370600 chr4A 94.444 594 31 2 3791 4383 21854197 21854789 0.000000e+00 913
13 TraesCS3A01G370600 chr6A 94.781 594 31 0 3787 4380 542386805 542387398 0.000000e+00 926
14 TraesCS3A01G370600 chr2A 94.755 591 31 0 3791 4381 148863844 148863254 0.000000e+00 920
15 TraesCS3A01G370600 chr2A 94.463 596 32 1 3788 4383 750326632 750327226 0.000000e+00 917
16 TraesCS3A01G370600 chr2A 93.864 603 36 1 3781 4383 592462750 592463351 0.000000e+00 907
17 TraesCS3A01G370600 chr7A 84.091 308 33 5 841 1141 188918937 188919235 2.580000e-72 283
18 TraesCS3A01G370600 chr2B 87.432 183 16 1 966 1141 273753397 273753579 2.070000e-48 204


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 TraesCS3A01G370600 chr3A 621217265 621221647 4382 True 8094.000000 8094 100.000 1 4383 1 chr3A.!!$R1 4382
1 TraesCS3A01G370600 chr3B 637063824 637067449 3625 True 1239.333333 1820 86.392 97 3794 3 chr3B.!!$R1 3697
2 TraesCS3A01G370600 chr3D 477881259 477884976 3717 True 919.000000 1234 86.372 24 3794 4 chr3D.!!$R1 3770
3 TraesCS3A01G370600 chr5A 640950487 640951080 593 False 946.000000 946 95.455 3791 4383 1 chr5A.!!$F1 592
4 TraesCS3A01G370600 chr5A 482129702 482130294 592 True 935.000000 935 95.110 3791 4383 1 chr5A.!!$R1 592
5 TraesCS3A01G370600 chr5A 598301025 598301621 596 True 915.000000 915 94.305 3787 4383 1 chr5A.!!$R2 596
6 TraesCS3A01G370600 chr4A 628816249 628816841 592 False 935.000000 935 95.110 3791 4383 1 chr4A.!!$F2 592
7 TraesCS3A01G370600 chr4A 21854197 21854789 592 False 913.000000 913 94.444 3791 4383 1 chr4A.!!$F1 592
8 TraesCS3A01G370600 chr6A 542386805 542387398 593 False 926.000000 926 94.781 3787 4380 1 chr6A.!!$F1 593
9 TraesCS3A01G370600 chr2A 148863254 148863844 590 True 920.000000 920 94.755 3791 4381 1 chr2A.!!$R1 590
10 TraesCS3A01G370600 chr2A 750326632 750327226 594 False 917.000000 917 94.463 3788 4383 1 chr2A.!!$F2 595
11 TraesCS3A01G370600 chr2A 592462750 592463351 601 False 907.000000 907 93.864 3781 4383 1 chr2A.!!$F1 602

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
413 425 0.035176 TTTGGATTTTGCAGCCCAGC 59.965 50.0 0.00 0.0 0.00 4.85 F
1151 1284 0.026156 CGCGCGCATTCTTGTCAATA 59.974 50.0 32.61 0.0 0.00 1.90 F
1169 1302 0.108662 TATCAGTGTCGCTGTGGCAG 60.109 55.0 13.00 0.0 45.23 4.85 F
2783 2963 0.097674 CCGTACCGACCTCTACAACG 59.902 60.0 0.00 0.0 0.00 4.10 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2363 2516 0.179040 TTGGGTGGTCTGGAAACGAC 60.179 55.0 0.00 0.0 34.54 4.34 R
2635 2815 0.107703 TCTCCACATCGATGTTGCCC 60.108 55.0 28.04 0.0 39.39 5.36 R
3125 3323 0.321653 GCCACAACCTCAATCGACCT 60.322 55.0 0.00 0.0 0.00 3.85 R
3873 4117 0.033366 CACATCACAGGACACGACCA 59.967 55.0 0.00 0.0 0.00 4.02 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
32 33 6.753744 GTCATCCAGTTTTTATCCATTGCTTC 59.246 38.462 0.00 0.00 0.00 3.86
38 39 7.767198 CCAGTTTTTATCCATTGCTTCATCATT 59.233 33.333 0.00 0.00 0.00 2.57
48 49 7.827729 TCCATTGCTTCATCATTATCATCCTAG 59.172 37.037 0.00 0.00 0.00 3.02
64 65 1.680249 CCTAGGAAGGCCTGAAGTTGC 60.680 57.143 5.69 0.00 46.45 4.17
79 80 3.152261 AGTTGCGCACAGATCTAGTAC 57.848 47.619 11.12 0.44 0.00 2.73
80 81 2.755655 AGTTGCGCACAGATCTAGTACT 59.244 45.455 11.12 3.42 0.00 2.73
81 82 2.851805 TGCGCACAGATCTAGTACTG 57.148 50.000 5.66 14.02 39.65 2.74
82 83 2.092323 TGCGCACAGATCTAGTACTGT 58.908 47.619 5.66 15.00 46.32 3.55
83 84 3.275999 TGCGCACAGATCTAGTACTGTA 58.724 45.455 5.66 0.00 44.07 2.74
84 85 3.883489 TGCGCACAGATCTAGTACTGTAT 59.117 43.478 5.66 0.00 44.07 2.29
85 86 4.222886 GCGCACAGATCTAGTACTGTATG 58.777 47.826 18.40 15.38 44.07 2.39
86 87 4.023963 GCGCACAGATCTAGTACTGTATGA 60.024 45.833 18.40 0.00 44.07 2.15
87 88 5.684850 CGCACAGATCTAGTACTGTATGAG 58.315 45.833 18.40 10.98 44.07 2.90
88 89 5.467063 CGCACAGATCTAGTACTGTATGAGA 59.533 44.000 18.40 0.00 44.07 3.27
89 90 6.347321 CGCACAGATCTAGTACTGTATGAGAG 60.347 46.154 18.40 10.25 44.07 3.20
90 91 6.708502 GCACAGATCTAGTACTGTATGAGAGA 59.291 42.308 18.40 0.00 44.07 3.10
121 122 4.277174 CGGGTGTGCATTTATAATGGCTTA 59.723 41.667 9.45 0.00 0.00 3.09
133 134 9.893305 ATTTATAATGGCTTAATAGAAACGTGC 57.107 29.630 0.00 0.00 0.00 5.34
139 140 3.424433 GCTTAATAGAAACGTGCGTGCTT 60.424 43.478 0.00 0.00 0.00 3.91
148 149 4.875544 AACGTGCGTGCTTGATATTATT 57.124 36.364 0.00 0.00 0.00 1.40
149 150 5.977171 AACGTGCGTGCTTGATATTATTA 57.023 34.783 0.00 0.00 0.00 0.98
150 151 6.539649 AACGTGCGTGCTTGATATTATTAT 57.460 33.333 0.00 0.00 0.00 1.28
174 178 2.082366 CGGTGCACTGCAATTTCGC 61.082 57.895 17.98 0.00 41.47 4.70
195 199 1.688197 CATGGCCTCTTTGTTTGGTGT 59.312 47.619 3.32 0.00 0.00 4.16
196 200 1.110442 TGGCCTCTTTGTTTGGTGTG 58.890 50.000 3.32 0.00 0.00 3.82
202 206 1.671845 TCTTTGTTTGGTGTGGTACGC 59.328 47.619 0.00 0.00 40.62 4.42
236 240 6.698766 CCTTGATTTTCTTCTTGTTGTTGGAG 59.301 38.462 0.00 0.00 0.00 3.86
293 298 3.733960 GGAGGTTTTCCGTGCGGC 61.734 66.667 5.64 0.00 46.35 6.53
299 307 1.083242 GTTTTCCGTGCGGCCGTATA 61.083 55.000 28.70 11.11 34.68 1.47
300 308 0.179078 TTTTCCGTGCGGCCGTATAT 60.179 50.000 28.70 0.00 34.68 0.86
301 309 0.672889 TTTCCGTGCGGCCGTATATA 59.327 50.000 28.70 8.70 34.68 0.86
302 310 0.889994 TTCCGTGCGGCCGTATATAT 59.110 50.000 28.70 0.00 34.68 0.86
303 311 0.171679 TCCGTGCGGCCGTATATATG 59.828 55.000 28.70 12.97 34.68 1.78
304 312 0.171679 CCGTGCGGCCGTATATATGA 59.828 55.000 28.70 0.00 0.00 2.15
305 313 1.545759 CGTGCGGCCGTATATATGAG 58.454 55.000 28.70 5.38 0.00 2.90
306 314 1.797713 CGTGCGGCCGTATATATGAGG 60.798 57.143 28.70 1.80 0.00 3.86
357 365 2.892852 TCCAGGCACAAAAAGATTCCAG 59.107 45.455 0.00 0.00 0.00 3.86
371 379 4.738998 CCAGGCGGGGCATGACAA 62.739 66.667 0.00 0.00 43.36 3.18
374 382 3.585990 GGCGGGGCATGACAATCG 61.586 66.667 0.00 1.95 0.00 3.34
410 422 2.743664 GACATTTTGGATTTTGCAGCCC 59.256 45.455 0.00 0.00 0.00 5.19
412 424 2.547299 TTTTGGATTTTGCAGCCCAG 57.453 45.000 0.00 0.00 0.00 4.45
413 425 0.035176 TTTGGATTTTGCAGCCCAGC 59.965 50.000 0.00 0.00 0.00 4.85
415 427 2.285024 GGATTTTGCAGCCCAGCCA 61.285 57.895 0.00 0.00 0.00 4.75
416 428 1.217244 GATTTTGCAGCCCAGCCAG 59.783 57.895 0.00 0.00 0.00 4.85
417 429 1.534717 ATTTTGCAGCCCAGCCAGT 60.535 52.632 0.00 0.00 0.00 4.00
418 430 1.123246 ATTTTGCAGCCCAGCCAGTT 61.123 50.000 0.00 0.00 0.00 3.16
419 431 2.030490 TTTTGCAGCCCAGCCAGTTG 62.030 55.000 0.00 0.00 0.00 3.16
420 432 4.980702 TGCAGCCCAGCCAGTTGG 62.981 66.667 0.00 0.00 38.00 3.77
421 433 4.666253 GCAGCCCAGCCAGTTGGA 62.666 66.667 1.45 0.00 40.87 3.53
422 434 2.674380 CAGCCCAGCCAGTTGGAC 60.674 66.667 1.45 0.00 40.87 4.02
423 435 3.177884 AGCCCAGCCAGTTGGACA 61.178 61.111 1.45 0.00 40.87 4.02
424 436 2.674380 GCCCAGCCAGTTGGACAG 60.674 66.667 1.45 0.00 40.87 3.51
425 437 2.674380 CCCAGCCAGTTGGACAGC 60.674 66.667 1.45 0.00 40.87 4.40
426 438 2.113774 CCAGCCAGTTGGACAGCA 59.886 61.111 1.45 0.00 40.87 4.41
427 439 2.263741 CCAGCCAGTTGGACAGCAC 61.264 63.158 1.45 0.00 40.87 4.40
428 440 1.526686 CAGCCAGTTGGACAGCACA 60.527 57.895 1.45 0.00 37.39 4.57
429 441 1.228063 AGCCAGTTGGACAGCACAG 60.228 57.895 1.45 0.00 37.39 3.66
436 448 0.819259 TTGGACAGCACAGCAGTTCC 60.819 55.000 0.00 0.00 0.00 3.62
455 467 2.506217 CTGTACCGCGCACGACAT 60.506 61.111 8.75 0.00 43.93 3.06
456 468 2.788176 CTGTACCGCGCACGACATG 61.788 63.158 8.75 0.00 43.93 3.21
463 513 0.645355 CGCGCACGACATGATAAACT 59.355 50.000 8.75 0.00 43.93 2.66
473 523 3.109151 ACATGATAAACTACGGACCCCA 58.891 45.455 0.00 0.00 0.00 4.96
489 539 1.076485 CCAATGCAAGGAGGGAGGG 60.076 63.158 2.49 0.00 0.00 4.30
490 540 1.574526 CCAATGCAAGGAGGGAGGGA 61.575 60.000 2.49 0.00 0.00 4.20
491 541 0.106819 CAATGCAAGGAGGGAGGGAG 60.107 60.000 0.00 0.00 0.00 4.30
492 542 1.284841 AATGCAAGGAGGGAGGGAGG 61.285 60.000 0.00 0.00 0.00 4.30
511 561 1.827399 GACCTCCGTCCAGCCAGAAA 61.827 60.000 0.00 0.00 32.40 2.52
520 570 2.293399 GTCCAGCCAGAAAATCGTTTGT 59.707 45.455 0.00 0.00 0.00 2.83
611 675 3.499737 CGTTGCGCTAGCTTGGGG 61.500 66.667 13.93 6.70 45.42 4.96
783 904 1.666888 CCGTGTTGGTGTAGACCGTAC 60.667 57.143 4.34 5.92 46.62 3.67
963 1087 4.039357 GCTGTGCTGGTGCTGCAG 62.039 66.667 10.11 10.11 38.86 4.41
964 1088 4.039357 CTGTGCTGGTGCTGCAGC 62.039 66.667 31.89 31.89 44.13 5.25
965 1089 4.574271 TGTGCTGGTGCTGCAGCT 62.574 61.111 36.61 0.00 44.19 4.24
966 1090 3.292936 GTGCTGGTGCTGCAGCTT 61.293 61.111 36.61 0.00 44.19 3.74
970 1094 3.569049 CTGGTGCTGCAGCTTTGGC 62.569 63.158 36.61 20.95 42.66 4.52
981 1105 2.646719 CTTTGGCGTGTGCATGCT 59.353 55.556 20.33 0.00 45.35 3.79
986 1114 4.471726 GCGTGTGCATGCTGAGGC 62.472 66.667 20.33 17.27 42.15 4.70
1148 1281 4.444024 GCGCGCGCATTCTTGTCA 62.444 61.111 46.11 0.00 41.49 3.58
1151 1284 0.026156 CGCGCGCATTCTTGTCAATA 59.974 50.000 32.61 0.00 0.00 1.90
1155 1288 3.538780 CGCGCATTCTTGTCAATATCAG 58.461 45.455 8.75 0.00 0.00 2.90
1161 1294 5.496387 CATTCTTGTCAATATCAGTGTCGC 58.504 41.667 0.00 0.00 0.00 5.19
1162 1295 4.456280 TCTTGTCAATATCAGTGTCGCT 57.544 40.909 0.00 0.00 0.00 4.93
1163 1296 4.176271 TCTTGTCAATATCAGTGTCGCTG 58.824 43.478 7.09 7.09 46.34 5.18
1164 1297 3.592898 TGTCAATATCAGTGTCGCTGT 57.407 42.857 13.00 3.91 45.23 4.40
1165 1298 3.253230 TGTCAATATCAGTGTCGCTGTG 58.747 45.455 13.00 4.56 45.23 3.66
1166 1299 2.604914 GTCAATATCAGTGTCGCTGTGG 59.395 50.000 13.00 0.88 45.23 4.17
1167 1300 1.328680 CAATATCAGTGTCGCTGTGGC 59.671 52.381 13.00 0.00 45.23 5.01
1168 1301 0.536724 ATATCAGTGTCGCTGTGGCA 59.463 50.000 13.00 0.00 45.23 4.92
1169 1302 0.108662 TATCAGTGTCGCTGTGGCAG 60.109 55.000 13.00 0.00 45.23 4.85
1170 1303 2.104572 ATCAGTGTCGCTGTGGCAGT 62.105 55.000 13.00 0.00 45.23 4.40
1188 1321 0.109781 GTGCCATTGATTCGTGCGTT 60.110 50.000 0.00 0.00 0.00 4.84
1475 1617 1.222113 GGGCGAAAGGAAGGAGGAG 59.778 63.158 0.00 0.00 0.00 3.69
1529 1671 2.359975 GGGCTGTCGTGGAAAGGG 60.360 66.667 0.00 0.00 0.00 3.95
1703 1845 1.002201 TGACTCTCCTTCTCGTCTCGT 59.998 52.381 0.00 0.00 0.00 4.18
1723 1865 6.472486 TCTCGTTCGTAGATGAGCAATTAAAG 59.528 38.462 0.00 0.00 38.67 1.85
1729 1871 8.716646 TCGTAGATGAGCAATTAAAGATTGAA 57.283 30.769 3.12 0.00 0.00 2.69
1734 1876 9.896645 AGATGAGCAATTAAAGATTGAACTCTA 57.103 29.630 3.12 0.00 0.00 2.43
1753 1895 5.769662 ACTCTACAATGCCATTCTTGTCAAA 59.230 36.000 0.00 0.00 36.92 2.69
1754 1896 6.265196 ACTCTACAATGCCATTCTTGTCAAAA 59.735 34.615 0.00 0.00 36.92 2.44
1779 1923 1.137282 TGACACCGTGCACTTCTGTTA 59.863 47.619 16.19 6.99 0.00 2.41
1961 2105 4.796231 AGGCGCGACGATGGTGAC 62.796 66.667 12.10 0.00 0.00 3.67
2012 2156 4.740235 GAGCTGATCGGGCAGTAC 57.260 61.111 3.14 0.00 38.17 2.73
2036 2180 1.671901 CCGAGGAGAAGGCTCAGACC 61.672 65.000 0.00 0.00 43.14 3.85
2086 2230 0.400594 AGCTCACCCAACAAGGTACC 59.599 55.000 2.73 2.73 38.39 3.34
2092 2236 2.370849 CACCCAACAAGGTACCACTACT 59.629 50.000 15.94 0.00 38.39 2.57
2095 2239 3.836562 CCCAACAAGGTACCACTACTACT 59.163 47.826 15.94 0.00 34.66 2.57
2097 2241 4.243270 CAACAAGGTACCACTACTACTGC 58.757 47.826 15.94 0.00 0.00 4.40
2098 2242 3.775910 ACAAGGTACCACTACTACTGCT 58.224 45.455 15.94 0.00 0.00 4.24
2099 2243 4.927049 ACAAGGTACCACTACTACTGCTA 58.073 43.478 15.94 0.00 0.00 3.49
2100 2244 4.704057 ACAAGGTACCACTACTACTGCTAC 59.296 45.833 15.94 0.00 0.00 3.58
2101 2245 4.858965 AGGTACCACTACTACTGCTACT 57.141 45.455 15.94 0.00 0.00 2.57
2102 2246 5.965033 AGGTACCACTACTACTGCTACTA 57.035 43.478 15.94 0.00 0.00 1.82
2103 2247 5.679601 AGGTACCACTACTACTGCTACTAC 58.320 45.833 15.94 0.00 0.00 2.73
2104 2248 4.819088 GGTACCACTACTACTGCTACTACC 59.181 50.000 7.15 0.00 0.00 3.18
2106 2250 3.198635 ACCACTACTACTGCTACTACCGA 59.801 47.826 0.00 0.00 0.00 4.69
2108 2252 4.451774 CCACTACTACTGCTACTACCGATC 59.548 50.000 0.00 0.00 0.00 3.69
2109 2253 4.150274 CACTACTACTGCTACTACCGATCG 59.850 50.000 8.51 8.51 0.00 3.69
2110 2254 3.191078 ACTACTGCTACTACCGATCGT 57.809 47.619 15.09 4.92 0.00 3.73
2111 2255 2.871022 ACTACTGCTACTACCGATCGTG 59.129 50.000 15.09 8.18 0.00 4.35
2112 2256 0.381089 ACTGCTACTACCGATCGTGC 59.619 55.000 15.09 8.61 0.00 5.34
2113 2257 0.380733 CTGCTACTACCGATCGTGCA 59.619 55.000 15.09 12.36 0.00 4.57
2114 2258 1.001268 CTGCTACTACCGATCGTGCAT 60.001 52.381 15.09 0.00 0.00 3.96
2115 2259 1.269051 TGCTACTACCGATCGTGCATG 60.269 52.381 15.09 0.00 0.00 4.06
2116 2260 1.930817 GCTACTACCGATCGTGCATGG 60.931 57.143 15.09 0.00 0.00 3.66
2117 2261 1.607148 CTACTACCGATCGTGCATGGA 59.393 52.381 15.09 0.00 0.00 3.41
2118 2262 0.821517 ACTACCGATCGTGCATGGAA 59.178 50.000 15.09 0.00 0.00 3.53
2119 2263 1.206132 ACTACCGATCGTGCATGGAAA 59.794 47.619 15.09 0.00 0.00 3.13
2120 2264 2.158957 ACTACCGATCGTGCATGGAAAT 60.159 45.455 15.09 0.00 0.00 2.17
2121 2265 1.750193 ACCGATCGTGCATGGAAATT 58.250 45.000 15.09 0.00 0.00 1.82
2122 2266 1.401552 ACCGATCGTGCATGGAAATTG 59.598 47.619 15.09 0.00 0.00 2.32
2123 2267 1.670295 CCGATCGTGCATGGAAATTGA 59.330 47.619 15.09 0.00 0.00 2.57
2124 2268 2.286595 CCGATCGTGCATGGAAATTGAG 60.287 50.000 15.09 0.00 0.00 3.02
2125 2269 2.609002 CGATCGTGCATGGAAATTGAGA 59.391 45.455 7.03 0.00 0.00 3.27
2126 2270 3.063861 CGATCGTGCATGGAAATTGAGAA 59.936 43.478 7.03 0.00 0.00 2.87
2127 2271 4.260907 CGATCGTGCATGGAAATTGAGAAT 60.261 41.667 7.03 0.00 0.00 2.40
2128 2272 4.359971 TCGTGCATGGAAATTGAGAATG 57.640 40.909 5.98 0.00 0.00 2.67
2129 2273 4.009002 TCGTGCATGGAAATTGAGAATGA 58.991 39.130 5.98 0.00 0.00 2.57
2130 2274 4.095334 TCGTGCATGGAAATTGAGAATGAG 59.905 41.667 5.98 0.00 0.00 2.90
2131 2275 4.095334 CGTGCATGGAAATTGAGAATGAGA 59.905 41.667 0.00 0.00 0.00 3.27
2134 2278 7.039882 GTGCATGGAAATTGAGAATGAGATTT 58.960 34.615 0.00 0.00 0.00 2.17
2172 2316 4.864916 TTCTGTCAAAATATCGCAGAGC 57.135 40.909 0.00 0.00 43.63 4.09
2173 2317 4.128925 TCTGTCAAAATATCGCAGAGCT 57.871 40.909 0.00 0.00 43.63 4.09
2174 2318 5.262588 TCTGTCAAAATATCGCAGAGCTA 57.737 39.130 0.00 0.00 43.63 3.32
2192 2336 7.494952 GCAGAGCTATTAGCATCATGAATGATA 59.505 37.037 17.59 0.00 45.23 2.15
2195 2339 8.678593 AGCTATTAGCATCATGAATGATATGG 57.321 34.615 17.59 0.38 45.23 2.74
2196 2340 8.491958 AGCTATTAGCATCATGAATGATATGGA 58.508 33.333 17.59 0.00 45.23 3.41
2197 2341 9.286170 GCTATTAGCATCATGAATGATATGGAT 57.714 33.333 10.83 0.00 45.23 3.41
2205 2349 4.458256 TGAATGATATGGATGTGGCCTT 57.542 40.909 3.32 0.00 0.00 4.35
2206 2350 4.146564 TGAATGATATGGATGTGGCCTTG 58.853 43.478 3.32 0.00 0.00 3.61
2247 2397 6.420903 GCATTGGAGATTTGACATGATGAATG 59.579 38.462 0.00 0.00 42.48 2.67
2280 2430 3.122948 CGACAGTTCTTACACCGATTTGG 59.877 47.826 0.00 0.00 46.41 3.28
2314 2464 2.242043 CTTTCCAAACTGCAGGGTGAT 58.758 47.619 19.93 0.00 0.00 3.06
2317 2467 0.883833 CCAAACTGCAGGGTGATGTC 59.116 55.000 19.93 0.00 0.00 3.06
2363 2516 4.537015 GAAATCAGGTGGTGAAAAACTCG 58.463 43.478 0.00 0.00 39.19 4.18
2386 2539 2.814097 CGTTTCCAGACCACCCAAGAAT 60.814 50.000 0.00 0.00 0.00 2.40
2387 2540 3.230976 GTTTCCAGACCACCCAAGAATT 58.769 45.455 0.00 0.00 0.00 2.17
2406 2559 1.382522 TCATCAGAAGAAATGGCGCC 58.617 50.000 22.73 22.73 0.00 6.53
2411 2564 2.750237 AAGAAATGGCGCCGACCC 60.750 61.111 23.90 11.31 0.00 4.46
2485 2638 2.771763 AAGACCAGCAAGGAGACGCG 62.772 60.000 3.53 3.53 41.22 6.01
2515 2668 1.655654 CTGCTCGAGCCGATACACG 60.656 63.158 33.23 8.52 41.18 4.49
2517 2670 1.654743 GCTCGAGCCGATACACGAC 60.655 63.158 27.22 0.00 45.77 4.34
2526 2682 1.298190 GATACACGACCTCCGCGTC 60.298 63.158 4.92 0.00 40.44 5.19
2527 2683 1.985447 GATACACGACCTCCGCGTCA 61.985 60.000 4.92 0.00 40.44 4.35
2528 2684 1.381928 ATACACGACCTCCGCGTCAT 61.382 55.000 4.92 0.00 40.44 3.06
2629 2791 4.771356 CACGACCACGCCGACGAT 62.771 66.667 0.00 0.00 43.93 3.73
2630 2792 4.471726 ACGACCACGCCGACGATC 62.472 66.667 0.00 0.00 43.93 3.69
2632 2794 2.579787 GACCACGCCGACGATCAG 60.580 66.667 0.00 0.00 43.93 2.90
2635 2815 3.250323 CACGCCGACGATCAGCAG 61.250 66.667 0.00 0.00 43.93 4.24
2647 2827 0.182061 ATCAGCAGGGCAACATCGAT 59.818 50.000 0.00 0.00 39.74 3.59
2768 2948 1.386525 GCCGGGTGATGAGTACCGTA 61.387 60.000 2.18 0.00 44.57 4.02
2770 2950 0.383231 CGGGTGATGAGTACCGTACC 59.617 60.000 5.02 0.00 41.34 3.34
2778 2958 1.831106 TGAGTACCGTACCGACCTCTA 59.169 52.381 5.02 0.00 0.00 2.43
2779 2959 2.205911 GAGTACCGTACCGACCTCTAC 58.794 57.143 5.02 0.00 0.00 2.59
2780 2960 1.555075 AGTACCGTACCGACCTCTACA 59.445 52.381 5.02 0.00 0.00 2.74
2781 2961 2.027192 AGTACCGTACCGACCTCTACAA 60.027 50.000 5.02 0.00 0.00 2.41
2782 2962 1.168714 ACCGTACCGACCTCTACAAC 58.831 55.000 0.00 0.00 0.00 3.32
2783 2963 0.097674 CCGTACCGACCTCTACAACG 59.902 60.000 0.00 0.00 0.00 4.10
2806 2986 3.112709 GACGACGGCAGCAGTTCC 61.113 66.667 0.00 0.00 0.00 3.62
2817 2997 1.134280 CAGCAGTTCCTACAGGGATGG 60.134 57.143 0.00 0.00 44.66 3.51
2913 3093 0.455633 CATGGAAGCGCAAACTGCTC 60.456 55.000 11.47 0.00 43.14 4.26
2939 3122 2.105128 GCGCCGATACTGCACTCT 59.895 61.111 0.00 0.00 0.00 3.24
2947 3130 2.539953 CGATACTGCACTCTCGGAGAAC 60.540 54.545 9.32 2.59 34.09 3.01
3015 3213 3.209812 CGATGGCGACGGAGAGGA 61.210 66.667 0.00 0.00 40.82 3.71
3019 3217 3.878519 GGCGACGGAGAGGACGAG 61.879 72.222 0.00 0.00 34.93 4.18
3026 3224 1.658686 CGGAGAGGACGAGGTGAAGG 61.659 65.000 0.00 0.00 0.00 3.46
3031 3229 2.657066 GGACGAGGTGAAGGTCCCC 61.657 68.421 0.00 0.00 43.51 4.81
3128 3326 1.217511 CACGATGCAGAGCTCAGGT 59.782 57.895 17.77 0.00 0.00 4.00
3129 3327 0.805322 CACGATGCAGAGCTCAGGTC 60.805 60.000 17.77 7.36 0.00 3.85
3141 3339 1.338200 GCTCAGGTCGATTGAGGTTGT 60.338 52.381 23.20 0.00 41.82 3.32
3189 3387 1.106285 GATGATGGTGCTGGGGTTTC 58.894 55.000 0.00 0.00 0.00 2.78
3190 3388 0.409092 ATGATGGTGCTGGGGTTTCA 59.591 50.000 0.00 0.00 0.00 2.69
3191 3389 0.251297 TGATGGTGCTGGGGTTTCAG 60.251 55.000 0.00 0.00 37.79 3.02
3265 3496 2.185608 GGCTCAGGCTTCGTCTCC 59.814 66.667 0.00 0.00 38.73 3.71
3280 3511 2.041922 TCCGGGATCCCAGGACTG 60.042 66.667 29.60 15.15 35.18 3.51
3327 3558 3.358076 CTCTTGGAGACGCGGACCC 62.358 68.421 12.47 8.61 0.00 4.46
3355 3586 2.633657 CCGCGGCTGCATGATTAC 59.366 61.111 14.67 0.00 42.97 1.89
3356 3587 2.179547 CCGCGGCTGCATGATTACA 61.180 57.895 14.67 0.00 42.97 2.41
3357 3588 1.010797 CGCGGCTGCATGATTACAC 60.011 57.895 19.50 0.00 42.97 2.90
3435 3666 1.404035 GTGTGTTGGTCGGCTTTTTCT 59.596 47.619 0.00 0.00 0.00 2.52
3463 3694 1.630244 GATGACAGACAGTGGCGTGC 61.630 60.000 0.00 0.00 36.69 5.34
3488 3719 3.352222 GCTCTGCAGCAGCGTTGT 61.352 61.111 18.43 0.00 46.06 3.32
3489 3720 2.858868 CTCTGCAGCAGCGTTGTC 59.141 61.111 18.43 0.00 46.23 3.18
3490 3721 1.957695 CTCTGCAGCAGCGTTGTCA 60.958 57.895 18.43 0.00 46.23 3.58
3491 3722 1.501337 CTCTGCAGCAGCGTTGTCAA 61.501 55.000 18.43 0.00 46.23 3.18
3492 3723 1.082300 CTGCAGCAGCGTTGTCAAG 60.082 57.895 10.14 0.00 46.23 3.02
3546 3777 2.368439 GCAGTGGATGTAAAGATGCCA 58.632 47.619 0.00 0.00 0.00 4.92
3550 3781 3.382546 AGTGGATGTAAAGATGCCATTGC 59.617 43.478 0.00 0.00 38.26 3.56
3559 3790 1.203994 AGATGCCATTGCTTGCTTGAC 59.796 47.619 0.00 0.00 38.71 3.18
3610 3847 1.516864 GGAAAAGTTGCGTCGCTTTTG 59.483 47.619 19.50 0.00 42.71 2.44
3631 3869 1.295357 CCGGTTGCATGCGTTAGTGA 61.295 55.000 14.09 0.00 0.00 3.41
3642 3880 0.108615 CGTTAGTGAGACCCTGCAGG 60.109 60.000 26.87 26.87 43.78 4.85
3643 3881 0.391793 GTTAGTGAGACCCTGCAGGC 60.392 60.000 28.39 14.93 40.58 4.85
3644 3882 0.835971 TTAGTGAGACCCTGCAGGCA 60.836 55.000 28.39 16.87 40.58 4.75
3645 3883 1.260538 TAGTGAGACCCTGCAGGCAG 61.261 60.000 28.39 17.26 43.26 4.85
3672 3910 4.222124 AGGTGACTGAAACTCAAACAGT 57.778 40.909 0.00 0.00 45.62 3.55
3676 3914 3.621268 TGACTGAAACTCAAACAGTTCCG 59.379 43.478 0.00 0.00 45.32 4.30
3857 4101 3.327757 AGATTCTGTCTGTTTGGGTAGCA 59.672 43.478 0.00 0.00 35.31 3.49
3873 4117 0.110486 AGCAATTTGGGGTCGTGTCT 59.890 50.000 0.00 0.00 0.00 3.41
3876 4120 0.476771 AATTTGGGGTCGTGTCTGGT 59.523 50.000 0.00 0.00 0.00 4.00
3886 4130 1.740285 GTGTCTGGTCGTGTCCTGT 59.260 57.895 0.00 0.00 0.00 4.00
4149 4393 0.304705 CACGTGCTCAACCAAGTCAC 59.695 55.000 0.82 0.00 0.00 3.67
4153 4397 2.869801 CGTGCTCAACCAAGTCACTTTA 59.130 45.455 0.00 0.00 0.00 1.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 5.357032 GGATAAAAACTGGATGACCGATTGT 59.643 40.000 0.00 0.00 39.42 2.71
1 2 5.356751 TGGATAAAAACTGGATGACCGATTG 59.643 40.000 0.00 0.00 39.42 2.67
2 3 5.505780 TGGATAAAAACTGGATGACCGATT 58.494 37.500 0.00 0.00 39.42 3.34
3 4 5.110814 TGGATAAAAACTGGATGACCGAT 57.889 39.130 0.00 0.00 39.42 4.18
5 6 5.581605 CAATGGATAAAAACTGGATGACCG 58.418 41.667 0.00 0.00 39.42 4.79
6 7 5.127682 AGCAATGGATAAAAACTGGATGACC 59.872 40.000 0.00 0.00 0.00 4.02
7 8 6.212888 AGCAATGGATAAAAACTGGATGAC 57.787 37.500 0.00 0.00 0.00 3.06
8 9 6.436847 TGAAGCAATGGATAAAAACTGGATGA 59.563 34.615 0.00 0.00 0.00 2.92
9 10 6.632909 TGAAGCAATGGATAAAAACTGGATG 58.367 36.000 0.00 0.00 0.00 3.51
10 11 6.855763 TGAAGCAATGGATAAAAACTGGAT 57.144 33.333 0.00 0.00 0.00 3.41
11 12 6.436847 TGATGAAGCAATGGATAAAAACTGGA 59.563 34.615 0.00 0.00 0.00 3.86
12 13 6.632909 TGATGAAGCAATGGATAAAAACTGG 58.367 36.000 0.00 0.00 0.00 4.00
13 14 8.712285 AATGATGAAGCAATGGATAAAAACTG 57.288 30.769 0.00 0.00 0.00 3.16
19 20 8.963725 GGATGATAATGATGAAGCAATGGATAA 58.036 33.333 0.00 0.00 0.00 1.75
20 21 8.333984 AGGATGATAATGATGAAGCAATGGATA 58.666 33.333 0.00 0.00 0.00 2.59
21 22 7.182760 AGGATGATAATGATGAAGCAATGGAT 58.817 34.615 0.00 0.00 0.00 3.41
22 23 6.549242 AGGATGATAATGATGAAGCAATGGA 58.451 36.000 0.00 0.00 0.00 3.41
32 33 5.191323 AGGCCTTCCTAGGATGATAATGATG 59.809 44.000 23.06 7.39 45.05 3.07
38 39 3.923273 TCAGGCCTTCCTAGGATGATA 57.077 47.619 23.06 3.54 45.05 2.15
48 49 2.982744 GCGCAACTTCAGGCCTTCC 61.983 63.158 0.00 0.00 0.00 3.46
64 65 5.467063 TCTCATACAGTACTAGATCTGTGCG 59.533 44.000 23.75 17.46 43.46 5.34
79 80 3.443037 CCGCACTTCTTCTCTCATACAG 58.557 50.000 0.00 0.00 0.00 2.74
80 81 2.166459 CCCGCACTTCTTCTCTCATACA 59.834 50.000 0.00 0.00 0.00 2.29
81 82 2.166664 ACCCGCACTTCTTCTCTCATAC 59.833 50.000 0.00 0.00 0.00 2.39
82 83 2.166459 CACCCGCACTTCTTCTCTCATA 59.834 50.000 0.00 0.00 0.00 2.15
83 84 1.066573 CACCCGCACTTCTTCTCTCAT 60.067 52.381 0.00 0.00 0.00 2.90
84 85 0.318441 CACCCGCACTTCTTCTCTCA 59.682 55.000 0.00 0.00 0.00 3.27
85 86 0.318762 ACACCCGCACTTCTTCTCTC 59.681 55.000 0.00 0.00 0.00 3.20
86 87 0.034059 CACACCCGCACTTCTTCTCT 59.966 55.000 0.00 0.00 0.00 3.10
87 88 1.569479 GCACACCCGCACTTCTTCTC 61.569 60.000 0.00 0.00 0.00 2.87
88 89 1.598130 GCACACCCGCACTTCTTCT 60.598 57.895 0.00 0.00 0.00 2.85
89 90 1.237285 ATGCACACCCGCACTTCTTC 61.237 55.000 0.00 0.00 46.56 2.87
90 91 0.823356 AATGCACACCCGCACTTCTT 60.823 50.000 0.00 0.00 46.56 2.52
110 111 6.702723 ACGCACGTTTCTATTAAGCCATTATA 59.297 34.615 0.00 0.00 0.00 0.98
111 112 5.526111 ACGCACGTTTCTATTAAGCCATTAT 59.474 36.000 0.00 0.00 0.00 1.28
112 113 4.871557 ACGCACGTTTCTATTAAGCCATTA 59.128 37.500 0.00 0.00 0.00 1.90
121 122 2.139917 TCAAGCACGCACGTTTCTATT 58.860 42.857 0.00 0.00 0.00 1.73
133 134 8.922676 ACCGAGTAAATAATAATATCAAGCACG 58.077 33.333 0.00 0.00 0.00 5.34
139 140 9.203421 CAGTGCACCGAGTAAATAATAATATCA 57.797 33.333 14.63 0.00 0.00 2.15
148 149 2.753055 TGCAGTGCACCGAGTAAATA 57.247 45.000 15.37 0.00 31.71 1.40
149 150 1.890876 TTGCAGTGCACCGAGTAAAT 58.109 45.000 19.58 0.00 38.71 1.40
150 151 1.890876 ATTGCAGTGCACCGAGTAAA 58.109 45.000 19.58 0.00 38.71 2.01
174 178 1.001181 CACCAAACAAAGAGGCCATGG 59.999 52.381 7.63 7.63 0.00 3.66
195 199 3.755628 GGTCAGCTCCGCGTACCA 61.756 66.667 4.92 0.00 37.86 3.25
196 200 3.003113 AAGGTCAGCTCCGCGTACC 62.003 63.158 4.92 2.63 38.09 3.34
202 206 2.704572 AGAAAATCAAGGTCAGCTCCG 58.295 47.619 0.00 0.00 0.00 4.63
236 240 5.447818 CCTCATTTAAATCAAGCTCACCGTC 60.448 44.000 0.00 0.00 0.00 4.79
293 298 2.695666 CCAGCCTCCCTCATATATACGG 59.304 54.545 0.00 0.00 0.00 4.02
299 307 1.143813 CCAACCAGCCTCCCTCATAT 58.856 55.000 0.00 0.00 0.00 1.78
300 308 0.253160 ACCAACCAGCCTCCCTCATA 60.253 55.000 0.00 0.00 0.00 2.15
301 309 1.542375 ACCAACCAGCCTCCCTCAT 60.542 57.895 0.00 0.00 0.00 2.90
302 310 2.121963 ACCAACCAGCCTCCCTCA 60.122 61.111 0.00 0.00 0.00 3.86
303 311 2.190488 CTCACCAACCAGCCTCCCTC 62.190 65.000 0.00 0.00 0.00 4.30
304 312 2.121963 TCACCAACCAGCCTCCCT 60.122 61.111 0.00 0.00 0.00 4.20
305 313 2.352805 CTCACCAACCAGCCTCCC 59.647 66.667 0.00 0.00 0.00 4.30
306 314 2.352805 CCTCACCAACCAGCCTCC 59.647 66.667 0.00 0.00 0.00 4.30
357 365 3.585990 CGATTGTCATGCCCCGCC 61.586 66.667 0.00 0.00 0.00 6.13
371 379 2.202932 GCTGGGATCACGCACGAT 60.203 61.111 6.87 0.00 35.23 3.73
374 382 3.188786 GTCGCTGGGATCACGCAC 61.189 66.667 11.38 5.89 35.23 5.34
410 422 1.512996 CTGTGCTGTCCAACTGGCTG 61.513 60.000 0.00 0.00 34.44 4.85
412 424 2.912624 GCTGTGCTGTCCAACTGGC 61.913 63.158 0.00 0.00 34.44 4.85
413 425 1.512996 CTGCTGTGCTGTCCAACTGG 61.513 60.000 0.00 0.00 0.00 4.00
415 427 0.107017 AACTGCTGTGCTGTCCAACT 60.107 50.000 0.00 0.00 39.66 3.16
416 428 0.308993 GAACTGCTGTGCTGTCCAAC 59.691 55.000 0.00 0.00 39.66 3.77
417 429 0.819259 GGAACTGCTGTGCTGTCCAA 60.819 55.000 1.26 0.00 39.66 3.53
418 430 1.227943 GGAACTGCTGTGCTGTCCA 60.228 57.895 1.26 0.00 39.66 4.02
419 431 2.320587 CGGAACTGCTGTGCTGTCC 61.321 63.158 2.32 2.61 39.66 4.02
420 432 2.959357 GCGGAACTGCTGTGCTGTC 61.959 63.158 11.85 1.57 39.66 3.51
421 433 2.974698 GCGGAACTGCTGTGCTGT 60.975 61.111 11.85 0.00 42.21 4.40
422 434 2.667536 AGCGGAACTGCTGTGCTG 60.668 61.111 7.37 6.17 45.28 4.41
449 461 3.181483 GGGTCCGTAGTTTATCATGTCGT 60.181 47.826 0.00 0.00 0.00 4.34
455 467 3.683281 GCATTGGGGTCCGTAGTTTATCA 60.683 47.826 0.00 0.00 0.00 2.15
456 468 2.876550 GCATTGGGGTCCGTAGTTTATC 59.123 50.000 0.00 0.00 0.00 1.75
463 513 1.202099 TCCTTGCATTGGGGTCCGTA 61.202 55.000 6.44 0.00 0.00 4.02
473 523 1.284841 CCTCCCTCCCTCCTTGCATT 61.285 60.000 0.00 0.00 0.00 3.56
492 542 1.827399 TTTCTGGCTGGACGGAGGTC 61.827 60.000 0.00 0.00 42.66 3.85
511 561 0.586319 CGTGCTGTGGACAAACGATT 59.414 50.000 8.32 0.00 37.88 3.34
611 675 3.543536 GAGGGCCATGGGATCGAGC 62.544 68.421 15.13 0.00 0.00 5.03
613 677 3.233980 CGAGGGCCATGGGATCGA 61.234 66.667 15.13 0.00 35.47 3.59
614 678 3.550431 ACGAGGGCCATGGGATCG 61.550 66.667 15.13 7.79 39.22 3.69
718 833 2.027625 GTTTGGTCCTCTCGTGCCG 61.028 63.158 0.00 0.00 0.00 5.69
719 834 1.671379 GGTTTGGTCCTCTCGTGCC 60.671 63.158 0.00 0.00 0.00 5.01
720 835 2.027625 CGGTTTGGTCCTCTCGTGC 61.028 63.158 0.00 0.00 0.00 5.34
721 836 0.944311 CACGGTTTGGTCCTCTCGTG 60.944 60.000 11.10 11.10 41.09 4.35
722 837 1.366366 CACGGTTTGGTCCTCTCGT 59.634 57.895 0.00 0.00 0.00 4.18
723 838 1.374252 CCACGGTTTGGTCCTCTCG 60.374 63.158 0.00 0.00 41.10 4.04
764 879 1.001487 TGTACGGTCTACACCAACACG 60.001 52.381 0.00 0.00 44.02 4.49
946 1070 4.039357 CTGCAGCACCAGCACAGC 62.039 66.667 0.00 0.00 45.49 4.40
953 1077 3.608662 GCCAAAGCTGCAGCACCA 61.609 61.111 38.24 0.00 45.16 4.17
955 1079 3.969802 ACGCCAAAGCTGCAGCAC 61.970 61.111 38.24 20.78 45.16 4.40
956 1080 3.968568 CACGCCAAAGCTGCAGCA 61.969 61.111 38.24 0.00 45.16 4.41
958 1082 2.050714 CACACGCCAAAGCTGCAG 60.051 61.111 10.11 10.11 36.60 4.41
959 1083 4.268939 GCACACGCCAAAGCTGCA 62.269 61.111 1.02 0.00 37.57 4.41
961 1085 1.731613 CATGCACACGCCAAAGCTG 60.732 57.895 0.00 0.00 37.32 4.24
963 1087 3.107661 GCATGCACACGCCAAAGC 61.108 61.111 14.21 0.00 37.32 3.51
964 1088 1.731613 CAGCATGCACACGCCAAAG 60.732 57.895 21.98 0.00 37.32 2.77
965 1089 2.132517 CTCAGCATGCACACGCCAAA 62.133 55.000 21.98 0.00 37.32 3.28
966 1090 2.594013 TCAGCATGCACACGCCAA 60.594 55.556 21.98 0.00 37.32 4.52
970 1094 1.859427 AAAGCCTCAGCATGCACACG 61.859 55.000 21.98 5.25 43.56 4.49
981 1105 3.043713 CGCACGCTCAAAGCCTCA 61.044 61.111 0.00 0.00 38.18 3.86
986 1114 2.787249 CCATCCGCACGCTCAAAG 59.213 61.111 0.00 0.00 0.00 2.77
1155 1288 4.017877 GCACTGCCACAGCGACAC 62.018 66.667 0.00 0.00 44.31 3.67
1166 1299 0.799534 GCACGAATCAATGGCACTGC 60.800 55.000 0.00 0.00 0.00 4.40
1167 1300 0.521867 CGCACGAATCAATGGCACTG 60.522 55.000 0.00 0.00 0.00 3.66
1168 1301 0.955428 ACGCACGAATCAATGGCACT 60.955 50.000 0.00 0.00 0.00 4.40
1169 1302 0.109781 AACGCACGAATCAATGGCAC 60.110 50.000 0.00 0.00 0.00 5.01
1170 1303 0.595588 AAACGCACGAATCAATGGCA 59.404 45.000 0.00 0.00 0.00 4.92
1183 1316 2.591311 GCGACCTGAACGAAACGCA 61.591 57.895 0.00 0.00 44.29 5.24
1188 1321 2.257371 CTCCGCGACCTGAACGAA 59.743 61.111 8.23 0.00 0.00 3.85
1277 1410 4.400251 CCCCGGGACTCCAGGACT 62.400 72.222 26.32 0.00 32.11 3.85
1343 1476 4.507916 TCCCGCTCCTCCTCCTCG 62.508 72.222 0.00 0.00 0.00 4.63
1346 1485 4.816984 TCGTCCCGCTCCTCCTCC 62.817 72.222 0.00 0.00 0.00 4.30
1426 1565 4.527583 GCTCCTGCTCCTGCTCCG 62.528 72.222 0.00 0.00 40.48 4.63
1427 1566 3.388703 CTGCTCCTGCTCCTGCTCC 62.389 68.421 0.00 0.00 40.48 4.70
1428 1567 2.187424 CTGCTCCTGCTCCTGCTC 59.813 66.667 0.00 0.00 40.48 4.26
1429 1568 4.098722 GCTGCTCCTGCTCCTGCT 62.099 66.667 0.00 0.00 40.48 4.24
1431 1570 4.834453 CGGCTGCTCCTGCTCCTG 62.834 72.222 0.00 0.00 40.48 3.86
1451 1590 1.376037 CTTCCTTTCGCCCTTCGCT 60.376 57.895 0.00 0.00 38.27 4.93
1465 1604 2.428085 GCGTCCTCCTCCTCCTTCC 61.428 68.421 0.00 0.00 0.00 3.46
1475 1617 4.493747 CCGGAAGTCGCGTCCTCC 62.494 72.222 10.51 10.51 37.59 4.30
1703 1845 8.716646 TCAATCTTTAATTGCTCATCTACGAA 57.283 30.769 0.00 0.00 0.00 3.85
1723 1865 6.690194 AGAATGGCATTGTAGAGTTCAATC 57.310 37.500 19.07 0.00 33.92 2.67
1729 1871 4.910195 TGACAAGAATGGCATTGTAGAGT 58.090 39.130 19.07 12.89 40.56 3.24
1734 1876 7.571080 AAATTTTTGACAAGAATGGCATTGT 57.429 28.000 19.07 11.34 46.21 2.71
1753 1895 3.130340 AGAAGTGCACGGTGTCAAAATTT 59.870 39.130 12.01 0.00 0.00 1.82
1754 1896 2.687935 AGAAGTGCACGGTGTCAAAATT 59.312 40.909 12.01 0.00 0.00 1.82
1765 1909 2.068519 TGAGCATAACAGAAGTGCACG 58.931 47.619 12.01 0.00 41.19 5.34
1766 1910 3.665323 CGTTGAGCATAACAGAAGTGCAC 60.665 47.826 9.40 9.40 41.19 4.57
1779 1923 1.945387 CTACTGCCATCGTTGAGCAT 58.055 50.000 9.19 4.67 35.64 3.79
1808 1952 4.813526 CGACTCTCCGCGACCACG 62.814 72.222 8.23 1.53 42.93 4.94
1961 2105 2.136878 CACCCTCTCCATCTCCCCG 61.137 68.421 0.00 0.00 0.00 5.73
2012 2156 4.214327 GCCTTCTCCTCGGCCTCG 62.214 72.222 0.00 0.00 40.43 4.63
2036 2180 3.123621 CGTTGAATTTCTTCTCCCAGTCG 59.876 47.826 0.00 0.00 32.29 4.18
2086 2230 4.150274 CGATCGGTAGTAGCAGTAGTAGTG 59.850 50.000 7.38 0.17 0.00 2.74
2092 2236 1.600957 GCACGATCGGTAGTAGCAGTA 59.399 52.381 20.98 0.00 0.00 2.74
2095 2239 1.029681 ATGCACGATCGGTAGTAGCA 58.970 50.000 20.98 17.79 34.78 3.49
2097 2241 1.607148 TCCATGCACGATCGGTAGTAG 59.393 52.381 20.98 4.10 0.00 2.57
2098 2242 1.682740 TCCATGCACGATCGGTAGTA 58.317 50.000 20.98 8.82 0.00 1.82
2099 2243 0.821517 TTCCATGCACGATCGGTAGT 59.178 50.000 20.98 0.00 0.00 2.73
2100 2244 1.934589 TTTCCATGCACGATCGGTAG 58.065 50.000 20.98 9.99 0.00 3.18
2101 2245 2.611751 CAATTTCCATGCACGATCGGTA 59.388 45.455 20.98 8.41 0.00 4.02
2102 2246 1.401552 CAATTTCCATGCACGATCGGT 59.598 47.619 20.98 1.94 0.00 4.69
2103 2247 1.670295 TCAATTTCCATGCACGATCGG 59.330 47.619 20.98 9.59 0.00 4.18
2104 2248 2.609002 TCTCAATTTCCATGCACGATCG 59.391 45.455 14.88 14.88 0.00 3.69
2106 2250 4.641541 TCATTCTCAATTTCCATGCACGAT 59.358 37.500 0.00 0.00 0.00 3.73
2108 2252 4.095334 TCTCATTCTCAATTTCCATGCACG 59.905 41.667 0.00 0.00 0.00 5.34
2109 2253 5.571784 TCTCATTCTCAATTTCCATGCAC 57.428 39.130 0.00 0.00 0.00 4.57
2110 2254 6.785337 AATCTCATTCTCAATTTCCATGCA 57.215 33.333 0.00 0.00 0.00 3.96
2111 2255 6.018994 GCAAATCTCATTCTCAATTTCCATGC 60.019 38.462 0.00 0.00 0.00 4.06
2112 2256 7.039270 TGCAAATCTCATTCTCAATTTCCATG 58.961 34.615 0.00 0.00 0.00 3.66
2113 2257 7.177832 TGCAAATCTCATTCTCAATTTCCAT 57.822 32.000 0.00 0.00 0.00 3.41
2114 2258 6.593268 TGCAAATCTCATTCTCAATTTCCA 57.407 33.333 0.00 0.00 0.00 3.53
2115 2259 6.869913 TGTTGCAAATCTCATTCTCAATTTCC 59.130 34.615 0.00 0.00 0.00 3.13
2116 2260 7.878477 TGTTGCAAATCTCATTCTCAATTTC 57.122 32.000 0.00 0.00 0.00 2.17
2117 2261 8.665643 TTTGTTGCAAATCTCATTCTCAATTT 57.334 26.923 0.00 0.00 0.00 1.82
2118 2262 8.842358 ATTTGTTGCAAATCTCATTCTCAATT 57.158 26.923 0.00 0.00 0.00 2.32
2119 2263 8.842358 AATTTGTTGCAAATCTCATTCTCAAT 57.158 26.923 0.00 0.00 0.00 2.57
2120 2264 7.927092 TGAATTTGTTGCAAATCTCATTCTCAA 59.073 29.630 0.00 0.00 0.00 3.02
2121 2265 7.435305 TGAATTTGTTGCAAATCTCATTCTCA 58.565 30.769 0.00 3.97 0.00 3.27
2122 2266 7.878477 TGAATTTGTTGCAAATCTCATTCTC 57.122 32.000 0.00 1.80 0.00 2.87
2123 2267 8.842358 AATGAATTTGTTGCAAATCTCATTCT 57.158 26.923 21.76 12.52 30.69 2.40
2134 2278 8.883954 TTGACAGAATAAATGAATTTGTTGCA 57.116 26.923 2.91 0.00 32.39 4.08
2150 2294 5.121811 AGCTCTGCGATATTTTGACAGAAT 58.878 37.500 0.00 0.00 36.96 2.40
2164 2308 3.256631 TCATGATGCTAATAGCTCTGCGA 59.743 43.478 13.88 2.43 42.97 5.10
2165 2309 3.582780 TCATGATGCTAATAGCTCTGCG 58.417 45.455 13.88 0.06 42.97 5.18
2174 2318 8.903820 CACATCCATATCATTCATGATGCTAAT 58.096 33.333 11.86 0.00 46.34 1.73
2192 2336 2.537633 AACATCAAGGCCACATCCAT 57.462 45.000 5.01 0.00 0.00 3.41
2216 2360 2.029728 GTCAAATCTCCAATGCTCGACG 59.970 50.000 0.00 0.00 0.00 5.12
2217 2361 3.002791 TGTCAAATCTCCAATGCTCGAC 58.997 45.455 0.00 0.00 0.00 4.20
2220 2364 5.298527 TCATCATGTCAAATCTCCAATGCTC 59.701 40.000 0.00 0.00 0.00 4.26
2223 2373 7.489160 ACATTCATCATGTCAAATCTCCAATG 58.511 34.615 0.00 0.00 43.17 2.82
2227 2377 5.747197 GCAACATTCATCATGTCAAATCTCC 59.253 40.000 0.00 0.00 46.23 3.71
2254 2404 1.200716 CGGTGTAAGAACTGTCGCCTA 59.799 52.381 0.00 0.00 0.00 3.93
2280 2430 3.676291 TGGAAAGCAAAAAGTATGGGC 57.324 42.857 0.00 0.00 0.00 5.36
2332 2482 4.062293 CACCACCTGATTTCGTCTGTAAA 58.938 43.478 0.00 0.00 0.00 2.01
2363 2516 0.179040 TTGGGTGGTCTGGAAACGAC 60.179 55.000 0.00 0.00 34.54 4.34
2386 2539 1.745087 GGCGCCATTTCTTCTGATGAA 59.255 47.619 24.80 2.19 0.00 2.57
2387 2540 1.382522 GGCGCCATTTCTTCTGATGA 58.617 50.000 24.80 0.00 0.00 2.92
2406 2559 1.302033 GCTGATATGGCAGGGGTCG 60.302 63.158 0.00 0.00 36.41 4.79
2411 2564 1.134007 TCCTTGTGCTGATATGGCAGG 60.134 52.381 0.00 0.58 40.54 4.85
2417 2570 2.507058 TGGAGCTTCCTTGTGCTGATAT 59.493 45.455 0.00 0.00 39.91 1.63
2419 2572 0.694771 TGGAGCTTCCTTGTGCTGAT 59.305 50.000 0.00 0.00 39.91 2.90
2443 2596 2.048597 CGTCTTGTGGCCGTGCTA 60.049 61.111 0.00 0.00 0.00 3.49
2485 2638 1.803519 CGAGCAGCCGTCTGAGTTC 60.804 63.158 0.00 0.00 42.95 3.01
2515 2668 2.278013 GACGATGACGCGGAGGTC 60.278 66.667 12.47 6.68 43.96 3.85
2517 2670 4.907034 CGGACGATGACGCGGAGG 62.907 72.222 12.47 0.00 43.96 4.30
2629 2791 0.745486 CATCGATGTTGCCCTGCTGA 60.745 55.000 17.50 0.00 0.00 4.26
2630 2792 1.028330 ACATCGATGTTGCCCTGCTG 61.028 55.000 25.18 0.00 37.90 4.41
2632 2794 1.430632 CACATCGATGTTGCCCTGC 59.569 57.895 28.04 0.00 39.39 4.85
2635 2815 0.107703 TCTCCACATCGATGTTGCCC 60.108 55.000 28.04 0.00 39.39 5.36
2768 2948 0.603707 TCGTCGTTGTAGAGGTCGGT 60.604 55.000 0.00 0.00 0.00 4.69
2770 2950 0.517946 CGTCGTCGTTGTAGAGGTCG 60.518 60.000 0.00 0.00 33.31 4.79
2778 2958 2.424157 CGTCGTCGTCGTCGTTGT 60.424 61.111 12.51 0.00 41.73 3.32
2779 2959 3.154952 CCGTCGTCGTCGTCGTTG 61.155 66.667 17.80 5.65 44.09 4.10
2806 2986 1.405526 CCAACGTGTCCATCCCTGTAG 60.406 57.143 0.00 0.00 0.00 2.74
2817 2997 2.737376 GGCTCGACCCAACGTGTC 60.737 66.667 0.00 0.00 34.70 3.67
2913 3093 4.337060 TATCGGCGCCATCGGTCG 62.337 66.667 28.98 10.71 35.95 4.79
2998 3190 3.209812 TCCTCTCCGTCGCCATCG 61.210 66.667 0.00 0.00 0.00 3.84
3000 3192 3.518998 CGTCCTCTCCGTCGCCAT 61.519 66.667 0.00 0.00 0.00 4.40
3001 3193 4.710167 TCGTCCTCTCCGTCGCCA 62.710 66.667 0.00 0.00 0.00 5.69
3003 3195 3.878519 CCTCGTCCTCTCCGTCGC 61.879 72.222 0.00 0.00 0.00 5.19
3005 3197 0.959372 TTCACCTCGTCCTCTCCGTC 60.959 60.000 0.00 0.00 0.00 4.79
3006 3198 0.961358 CTTCACCTCGTCCTCTCCGT 60.961 60.000 0.00 0.00 0.00 4.69
3009 3201 0.812549 GACCTTCACCTCGTCCTCTC 59.187 60.000 0.00 0.00 0.00 3.20
3010 3202 0.612453 GGACCTTCACCTCGTCCTCT 60.612 60.000 0.00 0.00 42.39 3.69
3125 3323 0.321653 GCCACAACCTCAATCGACCT 60.322 55.000 0.00 0.00 0.00 3.85
3128 3326 0.955428 GCAGCCACAACCTCAATCGA 60.955 55.000 0.00 0.00 0.00 3.59
3129 3327 0.957395 AGCAGCCACAACCTCAATCG 60.957 55.000 0.00 0.00 0.00 3.34
3141 3339 3.601685 TGTCGTGTCGAGCAGCCA 61.602 61.111 0.00 0.00 36.23 4.75
3192 3390 2.995939 TCATACAACTGCTTCGCTGAAG 59.004 45.455 12.17 12.17 42.03 3.02
3193 3391 3.038788 TCATACAACTGCTTCGCTGAA 57.961 42.857 0.00 0.00 0.00 3.02
3194 3392 2.741759 TCATACAACTGCTTCGCTGA 57.258 45.000 0.00 0.00 0.00 4.26
3237 3447 2.671070 CTGAGCCCGGTGGAACAT 59.329 61.111 0.00 0.00 44.52 2.71
3238 3448 3.636231 CCTGAGCCCGGTGGAACA 61.636 66.667 0.00 0.00 39.98 3.18
3260 3470 2.134933 GTCCTGGGATCCCGGAGAC 61.135 68.421 37.45 33.07 45.10 3.36
3265 3496 3.866582 GGCAGTCCTGGGATCCCG 61.867 72.222 26.03 19.24 39.42 5.14
3280 3511 1.219393 CTTCCTCAGGTCTTCCGGC 59.781 63.158 0.00 0.00 39.05 6.13
3348 3579 9.295825 TCAACTTGTTAGAAATGGTGTAATCAT 57.704 29.630 0.00 0.00 0.00 2.45
3349 3580 8.684386 TCAACTTGTTAGAAATGGTGTAATCA 57.316 30.769 0.00 0.00 0.00 2.57
3351 3582 8.028938 GCATCAACTTGTTAGAAATGGTGTAAT 58.971 33.333 0.00 0.00 0.00 1.89
3352 3583 7.230510 AGCATCAACTTGTTAGAAATGGTGTAA 59.769 33.333 0.00 0.00 0.00 2.41
3353 3584 6.714810 AGCATCAACTTGTTAGAAATGGTGTA 59.285 34.615 0.00 0.00 0.00 2.90
3355 3586 5.860182 CAGCATCAACTTGTTAGAAATGGTG 59.140 40.000 0.00 0.00 34.17 4.17
3356 3587 5.536161 ACAGCATCAACTTGTTAGAAATGGT 59.464 36.000 0.00 0.00 0.00 3.55
3357 3588 6.017400 ACAGCATCAACTTGTTAGAAATGG 57.983 37.500 0.00 0.00 0.00 3.16
3435 3666 1.000843 CTGTCTGTCATCGGACCACAA 59.999 52.381 5.00 0.00 46.21 3.33
3478 3709 1.650912 CTTGCTTGACAACGCTGCT 59.349 52.632 0.00 0.00 33.68 4.24
3481 3712 1.356624 GTGCTTGCTTGACAACGCT 59.643 52.632 9.86 0.00 35.05 5.07
3482 3713 0.931662 CTGTGCTTGCTTGACAACGC 60.932 55.000 3.53 3.53 33.68 4.84
3483 3714 0.931662 GCTGTGCTTGCTTGACAACG 60.932 55.000 0.00 0.00 33.68 4.10
3486 3717 1.449726 CTGGCTGTGCTTGCTTGACA 61.450 55.000 0.00 0.00 0.00 3.58
3487 3718 1.285023 CTGGCTGTGCTTGCTTGAC 59.715 57.895 0.00 0.00 0.00 3.18
3488 3719 0.752743 AACTGGCTGTGCTTGCTTGA 60.753 50.000 0.00 0.00 0.00 3.02
3489 3720 0.103572 AAACTGGCTGTGCTTGCTTG 59.896 50.000 0.00 0.00 0.00 4.01
3490 3721 0.103572 CAAACTGGCTGTGCTTGCTT 59.896 50.000 0.00 0.00 0.00 3.91
3491 3722 1.039233 ACAAACTGGCTGTGCTTGCT 61.039 50.000 8.35 0.00 0.00 3.91
3492 3723 0.179103 AACAAACTGGCTGTGCTTGC 60.179 50.000 8.35 0.00 0.00 4.01
3534 3765 2.827322 AGCAAGCAATGGCATCTTTACA 59.173 40.909 0.00 0.00 44.61 2.41
3535 3766 3.515330 AGCAAGCAATGGCATCTTTAC 57.485 42.857 0.00 0.00 44.61 2.01
3537 3768 2.300723 TCAAGCAAGCAATGGCATCTTT 59.699 40.909 0.00 0.00 44.61 2.52
3546 3777 1.200716 CACGGATGTCAAGCAAGCAAT 59.799 47.619 0.00 0.00 0.00 3.56
3550 3781 1.725641 TAGCACGGATGTCAAGCAAG 58.274 50.000 0.00 0.00 0.00 4.01
3559 3790 1.883084 GGCGAGGTTAGCACGGATG 60.883 63.158 3.34 0.00 36.08 3.51
3610 3847 3.395470 CTAACGCATGCAACCGGCC 62.395 63.158 19.57 0.00 43.89 6.13
3642 3880 3.054503 CAGTCACCTGCAGGCTGC 61.055 66.667 33.06 31.91 45.29 5.25
3643 3881 0.535780 TTTCAGTCACCTGCAGGCTG 60.536 55.000 33.06 28.37 38.66 4.85
3644 3882 0.536006 GTTTCAGTCACCTGCAGGCT 60.536 55.000 33.06 18.86 38.66 4.58
3645 3883 0.536006 AGTTTCAGTCACCTGCAGGC 60.536 55.000 33.06 16.71 38.66 4.85
3672 3910 1.300620 CGACAGCACTCAACCGGAA 60.301 57.895 9.46 0.00 0.00 4.30
3676 3914 0.946221 CCAGACGACAGCACTCAACC 60.946 60.000 0.00 0.00 0.00 3.77
3835 4078 3.327757 TGCTACCCAAACAGACAGAATCT 59.672 43.478 0.00 0.00 38.66 2.40
3857 4101 0.476771 ACCAGACACGACCCCAAATT 59.523 50.000 0.00 0.00 0.00 1.82
3873 4117 0.033366 CACATCACAGGACACGACCA 59.967 55.000 0.00 0.00 0.00 4.02
3876 4120 0.033366 CACCACATCACAGGACACGA 59.967 55.000 0.00 0.00 0.00 4.35
3922 4166 1.209504 CGGACAGGATAGGGCAAAAGA 59.790 52.381 0.00 0.00 0.00 2.52
4149 4393 7.596494 TGGCACTCTCATTTGAATCTTTAAAG 58.404 34.615 9.04 9.04 0.00 1.85
4153 4397 6.209986 TGATTGGCACTCTCATTTGAATCTTT 59.790 34.615 6.40 0.00 0.00 2.52


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

AutoCloner maintained by Alex Coulton.