Multiple sequence alignment - TraesCS6B01G121100

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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 TraesCS6B01G121100 chr6B 100.000 2735 0 0 1 2735 116111959 116114693 0.000000e+00 5051.0
1 TraesCS6B01G121100 chr6B 92.500 160 10 2 2578 2735 116140393 116140552 7.620000e-56 228.0
2 TraesCS6B01G121100 chr6B 90.541 148 7 4 2336 2480 116188579 116188722 3.600000e-44 189.0
3 TraesCS6B01G121100 chr6B 78.673 211 25 9 2496 2706 116281342 116281532 3.700000e-24 122.0
4 TraesCS6B01G121100 chr6D 87.697 951 51 22 876 1798 46873381 46874293 0.000000e+00 1048.0
5 TraesCS6B01G121100 chr6D 82.592 764 94 18 126 873 46872553 46873293 2.970000e-179 638.0
6 TraesCS6B01G121100 chr6D 84.711 641 34 35 2127 2735 46874359 46874967 1.410000e-162 582.0
7 TraesCS6B01G121100 chr6D 80.412 388 41 20 2130 2505 54835685 54835321 2.090000e-66 263.0
8 TraesCS6B01G121100 chr6D 95.775 71 3 0 2586 2656 54896667 54896597 6.190000e-22 115.0
9 TraesCS6B01G121100 chr6D 88.636 88 9 1 2496 2583 54835294 54835208 3.720000e-19 106.0
10 TraesCS6B01G121100 chr6D 96.667 60 2 0 2671 2730 54896602 54896543 1.730000e-17 100.0
11 TraesCS6B01G121100 chr6A 88.045 619 37 14 1367 1952 60505488 60506102 0.000000e+00 699.0
12 TraesCS6B01G121100 chr6A 90.150 467 34 5 876 1335 60505029 60505490 5.040000e-167 597.0
13 TraesCS6B01G121100 chr6A 82.074 675 86 25 1 661 60501129 60501782 6.660000e-151 544.0
14 TraesCS6B01G121100 chr6A 89.189 407 21 8 2190 2583 60529934 60530330 1.140000e-133 486.0
15 TraesCS6B01G121100 chr6A 85.586 333 25 12 1764 2089 60557702 60558018 7.300000e-86 327.0
16 TraesCS6B01G121100 chr6A 88.272 162 11 6 2572 2729 60538671 60538828 1.290000e-43 187.0
17 TraesCS6B01G121100 chr6A 97.368 38 1 0 2698 2735 60530952 60530989 6.320000e-07 65.8
18 TraesCS6B01G121100 chr4D 81.203 532 93 6 69 597 4822226 4821699 3.260000e-114 422.0
19 TraesCS6B01G121100 chr2B 80.113 533 93 12 69 596 75687703 75687179 4.270000e-103 385.0
20 TraesCS6B01G121100 chr5D 81.186 489 81 9 69 553 546925276 546925757 1.540000e-102 383.0
21 TraesCS6B01G121100 chr5D 75.681 551 104 25 73 613 27490772 27490242 5.850000e-62 248.0
22 TraesCS6B01G121100 chr7B 78.464 534 104 8 69 597 117791927 117792454 3.370000e-89 339.0
23 TraesCS6B01G121100 chr5B 76.923 546 103 21 69 604 128332554 128333086 3.450000e-74 289.0
24 TraesCS6B01G121100 chr1D 77.419 465 87 15 69 528 233337997 233338448 7.510000e-66 261.0


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 TraesCS6B01G121100 chr6B 116111959 116114693 2734 False 5051.000000 5051 100.000000 1 2735 1 chr6B.!!$F1 2734
1 TraesCS6B01G121100 chr6D 46872553 46874967 2414 False 756.000000 1048 85.000000 126 2735 3 chr6D.!!$F1 2609
2 TraesCS6B01G121100 chr6A 60501129 60506102 4973 False 613.333333 699 86.756333 1 1952 3 chr6A.!!$F3 1951
3 TraesCS6B01G121100 chr6A 60529934 60530989 1055 False 275.900000 486 93.278500 2190 2735 2 chr6A.!!$F4 545
4 TraesCS6B01G121100 chr4D 4821699 4822226 527 True 422.000000 422 81.203000 69 597 1 chr4D.!!$R1 528
5 TraesCS6B01G121100 chr2B 75687179 75687703 524 True 385.000000 385 80.113000 69 596 1 chr2B.!!$R1 527
6 TraesCS6B01G121100 chr5D 27490242 27490772 530 True 248.000000 248 75.681000 73 613 1 chr5D.!!$R1 540
7 TraesCS6B01G121100 chr7B 117791927 117792454 527 False 339.000000 339 78.464000 69 597 1 chr7B.!!$F1 528
8 TraesCS6B01G121100 chr5B 128332554 128333086 532 False 289.000000 289 76.923000 69 604 1 chr5B.!!$F1 535

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
924 4016 0.02877 CGAGGTGAGCTCGCTTCTAG 59.971 60.0 29.61 16.14 37.52 2.43 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2616 5832 0.179134 CGCAGGAGGAACTTACTCGG 60.179 60.0 0.0 0.0 41.55 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
47 48 9.311916 CTATGAGAGTTGATTTTTCACTAGAGG 57.688 37.037 0.00 0.00 0.00 3.69
48 49 6.467677 TGAGAGTTGATTTTTCACTAGAGGG 58.532 40.000 0.00 0.00 0.00 4.30
49 50 5.249420 AGAGTTGATTTTTCACTAGAGGGC 58.751 41.667 0.00 0.00 0.00 5.19
67 68 1.224722 GCTAGAGGCTAACATGCGGC 61.225 60.000 0.00 0.00 38.06 6.53
83 84 2.296190 TGCGGCTTCATATATCGTGTCT 59.704 45.455 0.00 0.00 0.00 3.41
90 91 3.638484 TCATATATCGTGTCTGGTTGCG 58.362 45.455 0.00 0.00 0.00 4.85
121 122 6.824305 ACCATATTTGTTTTCAGTGGAGAG 57.176 37.500 0.00 0.00 0.00 3.20
123 124 6.777580 ACCATATTTGTTTTCAGTGGAGAGTT 59.222 34.615 0.00 0.00 0.00 3.01
144 173 3.291584 TGAGTTGTTTGGTGCATGGTTA 58.708 40.909 0.00 0.00 0.00 2.85
186 215 1.003355 CTGATGTCAGCCGGTGGTT 60.003 57.895 1.90 0.00 37.15 3.67
197 226 1.362717 CGGTGGTTGTCGTCTGAGT 59.637 57.895 0.00 0.00 0.00 3.41
200 229 1.068741 GGTGGTTGTCGTCTGAGTCTT 59.931 52.381 0.00 0.00 0.00 3.01
231 261 5.616204 GCTCTTATTTCACGCTAAAACCGTT 60.616 40.000 0.00 0.00 36.69 4.44
239 269 2.033550 ACGCTAAAACCGTTGAATTGCA 59.966 40.909 0.00 0.00 34.96 4.08
249 279 3.308595 CCGTTGAATTGCAGCTATAACGA 59.691 43.478 19.91 4.01 41.09 3.85
289 320 2.007360 ATCTCTCGCTTGCTCAACTG 57.993 50.000 0.00 0.00 0.00 3.16
310 341 1.666209 GCTCTCTGCTCCTCTCGCTT 61.666 60.000 0.00 0.00 38.95 4.68
321 353 4.563580 GCTCCTCTCGCTTACTTAGTTTTC 59.436 45.833 0.00 0.00 0.00 2.29
327 359 7.170998 CCTCTCGCTTACTTAGTTTTCTTTTCA 59.829 37.037 0.00 0.00 0.00 2.69
333 366 7.518529 GCTTACTTAGTTTTCTTTTCACTCGCT 60.519 37.037 0.00 0.00 0.00 4.93
334 368 6.679327 ACTTAGTTTTCTTTTCACTCGCTT 57.321 33.333 0.00 0.00 0.00 4.68
651 693 3.013921 TCCTTTGTTATTCACGATGGCC 58.986 45.455 0.00 0.00 35.01 5.36
676 1777 7.041303 CCACCTTTTACTACTCTGTTTTCTTCC 60.041 40.741 0.00 0.00 0.00 3.46
680 1781 7.781548 TTTACTACTCTGTTTTCTTCCACAC 57.218 36.000 0.00 0.00 0.00 3.82
695 1796 0.532862 CACACCCAGACCACTCACAC 60.533 60.000 0.00 0.00 0.00 3.82
727 1829 1.584495 GCTTAAAAGCCCACCACCG 59.416 57.895 3.22 0.00 46.20 4.94
730 1832 2.642183 TTAAAAGCCCACCACCGCCA 62.642 55.000 0.00 0.00 0.00 5.69
745 3748 0.868602 CGCCAGGTCACCGTAATACG 60.869 60.000 5.74 5.74 42.11 3.06
791 3798 1.545428 GCCACTTCACTCCACATCCAA 60.545 52.381 0.00 0.00 0.00 3.53
798 3805 0.321653 ACTCCACATCCAAAGCGGTC 60.322 55.000 0.00 0.00 35.57 4.79
800 3807 1.375396 CCACATCCAAAGCGGTCGA 60.375 57.895 0.00 0.00 35.57 4.20
812 3819 3.723348 GGTCGAACCAACGGCAGC 61.723 66.667 0.00 0.00 39.76 5.25
842 3849 2.602568 AGCCGGAACCAGGTACGT 60.603 61.111 5.05 0.00 0.00 3.57
843 3850 2.433664 GCCGGAACCAGGTACGTG 60.434 66.667 5.05 8.61 0.00 4.49
865 3872 3.151022 CACTCTCCTCGGCCCCTC 61.151 72.222 0.00 0.00 0.00 4.30
866 3873 3.351885 ACTCTCCTCGGCCCCTCT 61.352 66.667 0.00 0.00 0.00 3.69
880 3900 1.211456 CCCTCTTTCTCTGCCCTGAT 58.789 55.000 0.00 0.00 0.00 2.90
883 3903 3.181456 CCCTCTTTCTCTGCCCTGATTAG 60.181 52.174 0.00 0.00 0.00 1.73
884 3904 3.708631 CCTCTTTCTCTGCCCTGATTAGA 59.291 47.826 0.00 0.00 0.00 2.10
891 3911 1.067582 GCCCTGATTAGACCGACGG 59.932 63.158 13.61 13.61 0.00 4.79
892 3912 1.673808 GCCCTGATTAGACCGACGGT 61.674 60.000 21.93 21.93 39.44 4.83
922 4014 2.881389 CGAGGTGAGCTCGCTTCT 59.119 61.111 29.61 19.00 37.52 2.85
923 4015 2.099143 CGAGGTGAGCTCGCTTCTA 58.901 57.895 29.61 1.46 37.52 2.10
924 4016 0.028770 CGAGGTGAGCTCGCTTCTAG 59.971 60.000 29.61 16.14 37.52 2.43
925 4017 0.248866 GAGGTGAGCTCGCTTCTAGC 60.249 60.000 26.93 10.80 40.40 3.42
948 4044 1.538047 AGCTGCATGGTGTCGATTTT 58.462 45.000 1.02 0.00 0.00 1.82
973 4069 7.479980 TGTTCGAATCTTGATTTGTGTCTTTT 58.520 30.769 0.00 0.00 0.00 2.27
1029 4125 2.159043 CGAAGGGAAGATCTGCAAGCTA 60.159 50.000 2.29 0.00 0.00 3.32
1337 4445 1.516603 GCGACAGCGAGGTACTTCC 60.517 63.158 0.00 0.00 41.55 3.46
1338 4446 1.226323 CGACAGCGAGGTACTTCCG 60.226 63.158 0.00 0.00 41.55 4.30
1339 4447 1.881602 GACAGCGAGGTACTTCCGT 59.118 57.895 0.00 0.00 41.55 4.69
1340 4448 1.089920 GACAGCGAGGTACTTCCGTA 58.910 55.000 0.00 0.00 41.55 4.02
1341 4449 0.807496 ACAGCGAGGTACTTCCGTAC 59.193 55.000 0.00 0.00 41.55 3.67
1342 4450 1.093159 CAGCGAGGTACTTCCGTACT 58.907 55.000 0.00 0.00 44.30 2.73
1343 4451 1.471684 CAGCGAGGTACTTCCGTACTT 59.528 52.381 0.00 0.00 44.30 2.24
1344 4452 1.471684 AGCGAGGTACTTCCGTACTTG 59.528 52.381 0.00 0.00 44.30 3.16
1345 4453 1.200948 GCGAGGTACTTCCGTACTTGT 59.799 52.381 0.00 0.00 44.30 3.16
1346 4454 2.730402 GCGAGGTACTTCCGTACTTGTC 60.730 54.545 0.00 0.00 44.30 3.18
1347 4455 2.475187 CGAGGTACTTCCGTACTTGTCG 60.475 54.545 0.00 5.73 44.30 4.35
1348 4456 2.485814 GAGGTACTTCCGTACTTGTCGT 59.514 50.000 0.00 0.00 44.30 4.34
1349 4457 2.485814 AGGTACTTCCGTACTTGTCGTC 59.514 50.000 0.00 0.00 44.30 4.20
1350 4458 2.499896 GTACTTCCGTACTTGTCGTCG 58.500 52.381 0.00 0.00 42.16 5.12
1351 4459 0.947244 ACTTCCGTACTTGTCGTCGT 59.053 50.000 0.00 0.00 0.00 4.34
1352 4460 1.069636 ACTTCCGTACTTGTCGTCGTC 60.070 52.381 0.00 0.00 0.00 4.20
1353 4461 1.196354 CTTCCGTACTTGTCGTCGTCT 59.804 52.381 0.00 0.00 0.00 4.18
1354 4462 1.229428 TCCGTACTTGTCGTCGTCTT 58.771 50.000 0.00 0.00 0.00 3.01
1355 4463 1.069703 TCCGTACTTGTCGTCGTCTTG 60.070 52.381 0.00 0.00 0.00 3.02
1356 4464 0.701303 CGTACTTGTCGTCGTCTTGC 59.299 55.000 0.00 0.00 0.00 4.01
1357 4465 1.662309 CGTACTTGTCGTCGTCTTGCT 60.662 52.381 0.00 0.00 0.00 3.91
1358 4466 1.977412 GTACTTGTCGTCGTCTTGCTC 59.023 52.381 0.00 0.00 0.00 4.26
1359 4467 0.660595 ACTTGTCGTCGTCTTGCTCG 60.661 55.000 0.00 0.00 0.00 5.03
1360 4468 0.660595 CTTGTCGTCGTCTTGCTCGT 60.661 55.000 0.00 0.00 0.00 4.18
1361 4469 0.659417 TTGTCGTCGTCTTGCTCGTC 60.659 55.000 0.00 0.00 0.00 4.20
1362 4470 1.082300 GTCGTCGTCTTGCTCGTCA 60.082 57.895 0.00 0.00 0.00 4.35
1363 4471 1.082300 TCGTCGTCTTGCTCGTCAC 60.082 57.895 0.00 0.00 0.00 3.67
1364 4472 1.082038 CGTCGTCTTGCTCGTCACT 60.082 57.895 0.00 0.00 0.00 3.41
1365 4473 1.060726 CGTCGTCTTGCTCGTCACTC 61.061 60.000 0.00 0.00 0.00 3.51
1366 4474 0.040336 GTCGTCTTGCTCGTCACTCA 60.040 55.000 0.00 0.00 0.00 3.41
1367 4475 0.040336 TCGTCTTGCTCGTCACTCAC 60.040 55.000 0.00 0.00 0.00 3.51
1368 4476 0.039978 CGTCTTGCTCGTCACTCACT 60.040 55.000 0.00 0.00 0.00 3.41
1369 4477 1.692296 GTCTTGCTCGTCACTCACTC 58.308 55.000 0.00 0.00 0.00 3.51
1370 4478 0.598562 TCTTGCTCGTCACTCACTCC 59.401 55.000 0.00 0.00 0.00 3.85
1371 4479 0.600557 CTTGCTCGTCACTCACTCCT 59.399 55.000 0.00 0.00 0.00 3.69
1372 4480 1.000283 CTTGCTCGTCACTCACTCCTT 60.000 52.381 0.00 0.00 0.00 3.36
1377 4485 2.420722 CTCGTCACTCACTCCTTAGTCC 59.579 54.545 0.00 0.00 31.97 3.85
1426 4538 8.228464 TCAACGTCTCTTATATATGATGTCGAC 58.772 37.037 9.11 9.11 0.00 4.20
1434 4546 8.726988 TCTTATATATGATGTCGACGATTGTCA 58.273 33.333 11.62 9.98 45.80 3.58
1440 4552 1.459209 TGTCGACGATTGTCAATGTGC 59.541 47.619 11.62 0.00 45.80 4.57
1447 4559 2.282555 CGATTGTCAATGTGCTAGGTCG 59.717 50.000 1.88 0.00 0.00 4.79
1499 4623 3.790437 CCTGATCTGGCCGGTGCT 61.790 66.667 12.43 0.00 37.74 4.40
1580 4704 3.118738 GGATTTCGAGAGGCTTCTTACCA 60.119 47.826 0.00 0.00 32.53 3.25
1610 4734 4.030452 GGCTGTGTTGTGCTCGGC 62.030 66.667 0.00 0.00 41.01 5.54
1618 4742 1.609501 TTGTGCTCGGCCCTACTCT 60.610 57.895 0.00 0.00 0.00 3.24
1619 4743 1.605058 TTGTGCTCGGCCCTACTCTC 61.605 60.000 0.00 0.00 0.00 3.20
1647 4771 1.033202 TCTACATCGGTGCTGCGGTA 61.033 55.000 0.00 0.00 0.00 4.02
1713 4837 0.689080 TCAGGATGAGTCTCAGGCCC 60.689 60.000 16.87 13.22 42.56 5.80
1715 4839 0.690411 AGGATGAGTCTCAGGCCCAG 60.690 60.000 16.87 0.00 0.00 4.45
1716 4840 1.145819 GATGAGTCTCAGGCCCAGC 59.854 63.158 8.82 0.00 0.00 4.85
1826 4969 5.365314 TCAGGCCCAAACTAAATTTTCAGTT 59.635 36.000 0.00 0.00 36.56 3.16
1919 5062 1.462616 AAACTGTCAGTTGCTGCACA 58.537 45.000 18.84 0.00 38.66 4.57
1945 5088 8.454106 ACTATTGCAGTGTTTTCATCTGTTATC 58.546 33.333 0.00 0.00 35.62 1.75
1952 5095 8.446273 CAGTGTTTTCATCTGTTATCTGTAAGG 58.554 37.037 0.00 0.00 0.00 2.69
1953 5096 8.375506 AGTGTTTTCATCTGTTATCTGTAAGGA 58.624 33.333 0.00 0.00 0.00 3.36
1954 5097 9.167311 GTGTTTTCATCTGTTATCTGTAAGGAT 57.833 33.333 0.00 0.00 0.00 3.24
1959 5102 9.547753 TTCATCTGTTATCTGTAAGGATAAAGC 57.452 33.333 0.00 0.00 39.10 3.51
1960 5103 8.150945 TCATCTGTTATCTGTAAGGATAAAGCC 58.849 37.037 0.00 0.00 39.10 4.35
1961 5104 7.432148 TCTGTTATCTGTAAGGATAAAGCCA 57.568 36.000 0.00 0.00 39.10 4.75
1962 5105 7.272978 TCTGTTATCTGTAAGGATAAAGCCAC 58.727 38.462 0.00 0.00 39.10 5.01
1963 5106 6.046593 TGTTATCTGTAAGGATAAAGCCACG 58.953 40.000 0.00 0.00 39.10 4.94
1964 5107 4.755266 ATCTGTAAGGATAAAGCCACGT 57.245 40.909 0.00 0.00 0.00 4.49
1965 5108 4.546829 TCTGTAAGGATAAAGCCACGTT 57.453 40.909 0.00 0.00 0.00 3.99
1966 5109 4.901868 TCTGTAAGGATAAAGCCACGTTT 58.098 39.130 0.00 0.00 0.00 3.60
1967 5110 4.933400 TCTGTAAGGATAAAGCCACGTTTC 59.067 41.667 0.00 0.00 0.00 2.78
1968 5111 4.004982 TGTAAGGATAAAGCCACGTTTCC 58.995 43.478 0.00 0.00 0.00 3.13
1969 5112 2.871096 AGGATAAAGCCACGTTTCCA 57.129 45.000 0.00 0.00 0.00 3.53
1970 5113 3.366052 AGGATAAAGCCACGTTTCCAT 57.634 42.857 0.00 0.00 0.00 3.41
1971 5114 3.279434 AGGATAAAGCCACGTTTCCATC 58.721 45.455 0.00 0.00 0.00 3.51
1972 5115 2.357952 GGATAAAGCCACGTTTCCATCC 59.642 50.000 0.00 0.00 0.00 3.51
1973 5116 2.570415 TAAAGCCACGTTTCCATCCA 57.430 45.000 0.00 0.00 0.00 3.41
1974 5117 1.923356 AAAGCCACGTTTCCATCCAT 58.077 45.000 0.00 0.00 0.00 3.41
1975 5118 1.176527 AAGCCACGTTTCCATCCATG 58.823 50.000 0.00 0.00 0.00 3.66
1984 5127 6.698999 ACGTTTCCATCCATGGTAGACGTC 62.699 50.000 20.57 7.70 46.91 4.34
1985 5128 3.569916 CCATCCATGGTAGACGTCG 57.430 57.895 12.58 0.00 43.05 5.12
1986 5129 0.032130 CCATCCATGGTAGACGTCGG 59.968 60.000 12.58 4.13 43.05 4.79
1987 5130 0.744874 CATCCATGGTAGACGTCGGT 59.255 55.000 12.58 0.00 0.00 4.69
1988 5131 1.951602 CATCCATGGTAGACGTCGGTA 59.048 52.381 12.58 0.00 0.00 4.02
1989 5132 1.671979 TCCATGGTAGACGTCGGTAG 58.328 55.000 12.58 0.00 0.00 3.18
1990 5133 1.210234 TCCATGGTAGACGTCGGTAGA 59.790 52.381 12.58 0.00 0.00 2.59
1991 5134 1.332997 CCATGGTAGACGTCGGTAGAC 59.667 57.143 10.46 4.64 43.72 2.59
1992 5135 2.286872 CATGGTAGACGTCGGTAGACT 58.713 52.381 10.46 0.00 44.93 3.24
1993 5136 3.461061 CATGGTAGACGTCGGTAGACTA 58.539 50.000 10.46 3.28 44.93 2.59
1994 5137 3.170791 TGGTAGACGTCGGTAGACTAG 57.829 52.381 10.46 0.00 44.93 2.57
1995 5138 2.497675 TGGTAGACGTCGGTAGACTAGT 59.502 50.000 10.46 0.00 44.93 2.57
1996 5139 3.699538 TGGTAGACGTCGGTAGACTAGTA 59.300 47.826 10.46 0.00 44.93 1.82
1997 5140 4.159693 TGGTAGACGTCGGTAGACTAGTAA 59.840 45.833 10.46 0.00 44.93 2.24
1998 5141 5.163405 TGGTAGACGTCGGTAGACTAGTAAT 60.163 44.000 10.46 0.00 44.93 1.89
1999 5142 6.040504 TGGTAGACGTCGGTAGACTAGTAATA 59.959 42.308 10.46 0.00 44.93 0.98
2000 5143 6.924060 GGTAGACGTCGGTAGACTAGTAATAA 59.076 42.308 10.46 0.00 44.93 1.40
2001 5144 6.836577 AGACGTCGGTAGACTAGTAATAAC 57.163 41.667 10.46 0.00 44.93 1.89
2002 5145 6.578023 AGACGTCGGTAGACTAGTAATAACT 58.422 40.000 10.46 0.00 44.93 2.24
2003 5146 7.044798 AGACGTCGGTAGACTAGTAATAACTT 58.955 38.462 10.46 0.00 44.93 2.66
2004 5147 7.550906 AGACGTCGGTAGACTAGTAATAACTTT 59.449 37.037 10.46 0.00 44.93 2.66
2005 5148 8.045176 ACGTCGGTAGACTAGTAATAACTTTT 57.955 34.615 0.00 0.00 44.93 2.27
2006 5149 8.178313 ACGTCGGTAGACTAGTAATAACTTTTC 58.822 37.037 0.00 0.00 44.93 2.29
2007 5150 8.394121 CGTCGGTAGACTAGTAATAACTTTTCT 58.606 37.037 0.00 0.00 44.93 2.52
2010 5153 9.219497 CGGTAGACTAGTAATAACTTTTCTTCG 57.781 37.037 0.00 0.00 37.15 3.79
2033 5176 9.997482 TTCGTATTAATCCTCTAATTTTTGCAC 57.003 29.630 0.00 0.00 0.00 4.57
2034 5177 9.391006 TCGTATTAATCCTCTAATTTTTGCACT 57.609 29.630 0.00 0.00 0.00 4.40
2073 5216 9.842775 ATATCACTTGAAATGTCATCTACACAT 57.157 29.630 0.00 0.00 42.09 3.21
2074 5217 7.368480 TCACTTGAAATGTCATCTACACATG 57.632 36.000 0.00 0.00 42.09 3.21
2075 5218 7.160726 TCACTTGAAATGTCATCTACACATGA 58.839 34.615 0.00 0.00 42.09 3.07
2076 5219 7.661027 TCACTTGAAATGTCATCTACACATGAA 59.339 33.333 0.00 0.00 42.09 2.57
2077 5220 8.291740 CACTTGAAATGTCATCTACACATGAAA 58.708 33.333 0.00 0.00 42.09 2.69
2078 5221 8.849168 ACTTGAAATGTCATCTACACATGAAAA 58.151 29.630 0.00 0.00 42.09 2.29
2079 5222 9.681692 CTTGAAATGTCATCTACACATGAAAAA 57.318 29.630 0.00 0.00 42.09 1.94
2080 5223 9.681692 TTGAAATGTCATCTACACATGAAAAAG 57.318 29.630 0.00 0.00 42.09 2.27
2081 5224 8.298854 TGAAATGTCATCTACACATGAAAAAGG 58.701 33.333 0.00 0.00 42.09 3.11
2082 5225 8.408043 AAATGTCATCTACACATGAAAAAGGA 57.592 30.769 0.00 0.00 42.09 3.36
2083 5226 8.585471 AATGTCATCTACACATGAAAAAGGAT 57.415 30.769 0.00 0.00 42.09 3.24
2084 5227 8.585471 ATGTCATCTACACATGAAAAAGGATT 57.415 30.769 0.00 0.00 42.09 3.01
2085 5228 8.044060 TGTCATCTACACATGAAAAAGGATTC 57.956 34.615 0.00 0.00 34.50 2.52
2086 5229 7.665145 TGTCATCTACACATGAAAAAGGATTCA 59.335 33.333 0.00 0.00 37.14 2.57
2087 5230 7.965107 GTCATCTACACATGAAAAAGGATTCAC 59.035 37.037 0.00 0.00 41.78 3.18
2088 5231 7.665145 TCATCTACACATGAAAAAGGATTCACA 59.335 33.333 0.00 0.00 41.78 3.58
2089 5232 7.815840 TCTACACATGAAAAAGGATTCACAA 57.184 32.000 0.00 0.00 41.78 3.33
2090 5233 8.231692 TCTACACATGAAAAAGGATTCACAAA 57.768 30.769 0.00 0.00 41.78 2.83
2091 5234 8.859090 TCTACACATGAAAAAGGATTCACAAAT 58.141 29.630 0.00 0.00 41.78 2.32
2092 5235 7.951530 ACACATGAAAAAGGATTCACAAATC 57.048 32.000 0.00 0.00 41.78 2.17
2093 5236 7.499292 ACACATGAAAAAGGATTCACAAATCA 58.501 30.769 0.00 0.00 42.66 2.57
2094 5237 7.439056 ACACATGAAAAAGGATTCACAAATCAC 59.561 33.333 0.00 0.00 42.66 3.06
2095 5238 7.438757 CACATGAAAAAGGATTCACAAATCACA 59.561 33.333 0.00 0.00 42.66 3.58
2096 5239 7.986320 ACATGAAAAAGGATTCACAAATCACAA 59.014 29.630 0.00 0.00 42.66 3.33
2097 5240 7.769272 TGAAAAAGGATTCACAAATCACAAC 57.231 32.000 1.05 0.00 42.66 3.32
2098 5241 6.760770 TGAAAAAGGATTCACAAATCACAACC 59.239 34.615 1.05 0.00 42.66 3.77
2099 5242 5.867903 AAAGGATTCACAAATCACAACCA 57.132 34.783 1.05 0.00 42.66 3.67
2100 5243 4.853924 AGGATTCACAAATCACAACCAC 57.146 40.909 1.05 0.00 42.66 4.16
2101 5244 4.214310 AGGATTCACAAATCACAACCACA 58.786 39.130 1.05 0.00 42.66 4.17
2102 5245 4.648762 AGGATTCACAAATCACAACCACAA 59.351 37.500 1.05 0.00 42.66 3.33
2103 5246 5.128499 AGGATTCACAAATCACAACCACAAA 59.872 36.000 1.05 0.00 42.66 2.83
2145 5311 4.503734 CACTTGTTGTGTGGTTTATTGCTG 59.496 41.667 0.00 0.00 41.53 4.41
2148 5314 1.697284 TGTGTGGTTTATTGCTGCCA 58.303 45.000 0.00 0.00 0.00 4.92
2186 5352 1.133976 ACATGCTGACCATAGGCCTTC 60.134 52.381 12.58 1.95 31.47 3.46
2187 5353 1.134007 CATGCTGACCATAGGCCTTCA 60.134 52.381 12.58 7.80 31.47 3.02
2188 5354 0.253044 TGCTGACCATAGGCCTTCAC 59.747 55.000 12.58 4.30 0.00 3.18
2196 5362 3.523564 ACCATAGGCCTTCACACAGTTAT 59.476 43.478 12.58 0.00 0.00 1.89
2222 5390 0.168788 CATTTACTGGCAGGTGCACG 59.831 55.000 20.34 0.00 44.36 5.34
2256 5431 1.472201 GCAGCAAGATGACGGAGATCA 60.472 52.381 0.00 0.00 0.00 2.92
2257 5432 2.471818 CAGCAAGATGACGGAGATCAG 58.528 52.381 0.00 0.00 30.46 2.90
2258 5433 2.100418 CAGCAAGATGACGGAGATCAGA 59.900 50.000 0.00 0.00 30.46 3.27
2259 5434 2.361757 AGCAAGATGACGGAGATCAGAG 59.638 50.000 0.00 0.00 30.46 3.35
2260 5435 2.741612 CAAGATGACGGAGATCAGAGC 58.258 52.381 0.00 0.00 30.46 4.09
2261 5436 2.361757 CAAGATGACGGAGATCAGAGCT 59.638 50.000 0.00 0.00 30.46 4.09
2289 5467 2.597578 TACTACCAGTGCAGGAGTGA 57.402 50.000 0.00 0.00 0.00 3.41
2315 5505 9.649316 ATTCTGTTTCCTAGCTACTACTATCTT 57.351 33.333 0.00 0.00 0.00 2.40
2453 5647 5.414454 TGTCACTATGGCTGTTTGGTTAATC 59.586 40.000 0.00 0.00 0.00 1.75
2504 5703 5.930569 GGGTTATATTTACCTTACGCTCTGG 59.069 44.000 6.65 0.00 35.92 3.86
2509 5708 4.546829 TTTACCTTACGCTCTGGTGAAT 57.453 40.909 0.00 0.00 35.48 2.57
2515 5714 1.981256 ACGCTCTGGTGAATGGTTTT 58.019 45.000 0.00 0.00 0.00 2.43
2606 5822 2.259281 GCTAGCTAGCTAGGACGGG 58.741 63.158 39.60 22.86 45.62 5.28
2607 5823 1.245376 GCTAGCTAGCTAGGACGGGG 61.245 65.000 39.60 22.25 45.62 5.73
2608 5824 0.609681 CTAGCTAGCTAGGACGGGGG 60.610 65.000 34.95 14.78 41.58 5.40
2629 5845 4.739587 GGAAGAATCCGAGTAAGTTCCT 57.260 45.455 0.00 0.00 35.59 3.36
2630 5846 4.684877 GGAAGAATCCGAGTAAGTTCCTC 58.315 47.826 0.00 0.00 35.59 3.71
2631 5847 4.441773 GGAAGAATCCGAGTAAGTTCCTCC 60.442 50.000 0.00 0.00 35.59 4.30
2632 5848 3.983821 AGAATCCGAGTAAGTTCCTCCT 58.016 45.455 0.00 0.00 0.00 3.69
2633 5849 3.702045 AGAATCCGAGTAAGTTCCTCCTG 59.298 47.826 0.00 0.00 0.00 3.86
2634 5850 1.183549 TCCGAGTAAGTTCCTCCTGC 58.816 55.000 0.00 0.00 0.00 4.85
2635 5851 0.179134 CCGAGTAAGTTCCTCCTGCG 60.179 60.000 0.00 0.00 0.00 5.18
2636 5852 0.179134 CGAGTAAGTTCCTCCTGCGG 60.179 60.000 0.00 0.00 0.00 5.69
2637 5853 0.175989 GAGTAAGTTCCTCCTGCGGG 59.824 60.000 4.71 4.71 0.00 6.13
2638 5854 0.544595 AGTAAGTTCCTCCTGCGGGT 60.545 55.000 12.43 0.00 0.00 5.28
2669 5899 0.668535 GCTTCCCTTGTTGCTTTCGT 59.331 50.000 0.00 0.00 0.00 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
27 28 5.249420 AGCCCTCTAGTGAAAAATCAACTC 58.751 41.667 0.00 0.00 0.00 3.01
38 39 1.227249 AGCCTCTAGCCCTCTAGTGA 58.773 55.000 0.00 0.00 45.47 3.41
39 40 2.888414 GTTAGCCTCTAGCCCTCTAGTG 59.112 54.545 0.00 0.00 45.47 2.74
41 42 3.231207 TGTTAGCCTCTAGCCCTCTAG 57.769 52.381 0.00 0.00 45.47 2.43
42 43 3.501349 CATGTTAGCCTCTAGCCCTCTA 58.499 50.000 0.00 0.00 45.47 2.43
43 44 2.324541 CATGTTAGCCTCTAGCCCTCT 58.675 52.381 0.00 0.00 45.47 3.69
44 45 1.270571 GCATGTTAGCCTCTAGCCCTC 60.271 57.143 0.00 0.00 45.47 4.30
45 46 0.761802 GCATGTTAGCCTCTAGCCCT 59.238 55.000 0.00 0.00 45.47 5.19
46 47 0.601311 CGCATGTTAGCCTCTAGCCC 60.601 60.000 0.00 0.00 45.47 5.19
47 48 0.601311 CCGCATGTTAGCCTCTAGCC 60.601 60.000 0.00 0.00 45.47 3.93
48 49 1.224722 GCCGCATGTTAGCCTCTAGC 61.225 60.000 0.00 0.00 44.25 3.42
49 50 0.390860 AGCCGCATGTTAGCCTCTAG 59.609 55.000 0.00 0.00 0.00 2.43
67 68 4.148871 CGCAACCAGACACGATATATGAAG 59.851 45.833 0.00 0.00 0.00 3.02
83 84 3.527641 GGTTTCCAACCGCAACCA 58.472 55.556 0.00 0.00 42.62 3.67
100 101 7.874940 TCAACTCTCCACTGAAAACAAATATG 58.125 34.615 0.00 0.00 0.00 1.78
115 116 3.278574 CACCAAACAACTCAACTCTCCA 58.721 45.455 0.00 0.00 0.00 3.86
121 122 2.159114 ACCATGCACCAAACAACTCAAC 60.159 45.455 0.00 0.00 0.00 3.18
123 124 1.774110 ACCATGCACCAAACAACTCA 58.226 45.000 0.00 0.00 0.00 3.41
186 215 3.551046 GCTCTCAAAAGACTCAGACGACA 60.551 47.826 0.00 0.00 0.00 4.35
197 226 5.120830 GCGTGAAATAAGAGCTCTCAAAAGA 59.879 40.000 18.55 0.00 0.00 2.52
200 229 4.569943 AGCGTGAAATAAGAGCTCTCAAA 58.430 39.130 18.55 6.26 31.94 2.69
231 261 5.115480 TGTGATCGTTATAGCTGCAATTCA 58.885 37.500 1.02 0.00 0.00 2.57
239 269 3.393800 GGCACATGTGATCGTTATAGCT 58.606 45.455 29.80 0.00 0.00 3.32
249 279 4.045781 TGGGCCGGCACATGTGAT 62.046 61.111 31.83 0.00 0.00 3.06
310 341 7.781548 AAGCGAGTGAAAAGAAAACTAAGTA 57.218 32.000 0.00 0.00 0.00 2.24
327 359 4.015084 TCTAACCTAGCACTAAAGCGAGT 58.985 43.478 0.00 0.00 40.15 4.18
528 564 9.645059 TGATCATTTTTAAAGTTTGTGAACACA 57.355 25.926 3.39 3.39 38.26 3.72
623 665 7.114811 CCATCGTGAATAACAAAGGAAAAAGTG 59.885 37.037 0.00 0.00 0.00 3.16
632 674 3.427503 GGTGGCCATCGTGAATAACAAAG 60.428 47.826 9.72 0.00 0.00 2.77
634 676 2.088423 GGTGGCCATCGTGAATAACAA 58.912 47.619 9.72 0.00 0.00 2.83
651 693 7.497909 TGGAAGAAAACAGAGTAGTAAAAGGTG 59.502 37.037 0.00 0.00 0.00 4.00
676 1777 0.532862 GTGTGAGTGGTCTGGGTGTG 60.533 60.000 0.00 0.00 0.00 3.82
680 1781 1.831652 GAGGGTGTGAGTGGTCTGGG 61.832 65.000 0.00 0.00 0.00 4.45
727 1829 1.149964 GCGTATTACGGTGACCTGGC 61.150 60.000 17.26 0.00 42.82 4.85
730 1832 0.458669 CTGGCGTATTACGGTGACCT 59.541 55.000 17.26 0.00 42.82 3.85
733 1835 1.135315 GTGACTGGCGTATTACGGTGA 60.135 52.381 17.26 0.00 42.82 4.02
745 3748 4.314440 TGGCTCGGTGTGACTGGC 62.314 66.667 0.00 0.00 0.00 4.85
791 3798 2.663852 CCGTTGGTTCGACCGCTT 60.664 61.111 0.00 0.00 42.58 4.68
825 3832 2.602568 ACGTACCTGGTTCCGGCT 60.603 61.111 18.69 1.17 0.00 5.52
849 3856 2.463497 AAAGAGGGGCCGAGGAGAGT 62.463 60.000 0.00 0.00 0.00 3.24
858 3865 2.273776 GGCAGAGAAAGAGGGGCC 59.726 66.667 0.00 0.00 0.00 5.80
859 3866 2.273776 GGGCAGAGAAAGAGGGGC 59.726 66.667 0.00 0.00 0.00 5.80
864 3871 3.452627 GGTCTAATCAGGGCAGAGAAAGA 59.547 47.826 0.00 0.00 0.00 2.52
865 3872 3.739519 CGGTCTAATCAGGGCAGAGAAAG 60.740 52.174 0.00 0.00 0.00 2.62
866 3873 2.168521 CGGTCTAATCAGGGCAGAGAAA 59.831 50.000 0.00 0.00 0.00 2.52
880 3900 2.283388 AGGCCACCGTCGGTCTAA 60.283 61.111 15.67 0.00 39.96 2.10
883 3903 4.436998 CTCAGGCCACCGTCGGTC 62.437 72.222 15.67 3.97 31.02 4.79
891 3911 4.767255 CTCGCACCCTCAGGCCAC 62.767 72.222 5.01 0.00 36.11 5.01
924 4016 1.150567 CGACACCATGCAGCTAGAGC 61.151 60.000 0.00 0.00 42.49 4.09
925 4017 0.457443 TCGACACCATGCAGCTAGAG 59.543 55.000 0.00 0.00 0.00 2.43
926 4018 1.114627 ATCGACACCATGCAGCTAGA 58.885 50.000 0.00 0.00 0.00 2.43
927 4019 1.945387 AATCGACACCATGCAGCTAG 58.055 50.000 0.00 0.00 0.00 3.42
948 4044 6.618287 AAGACACAAATCAAGATTCGAACA 57.382 33.333 0.00 0.00 0.00 3.18
973 4069 2.099141 CCTGAAACAGATCGAGGCAA 57.901 50.000 0.00 0.00 32.44 4.52
1008 4104 1.012841 GCTTGCAGATCTTCCCTTCG 58.987 55.000 0.00 0.00 0.00 3.79
1203 4307 2.665185 GAGGCGACGGTGCAGTTT 60.665 61.111 0.00 0.00 36.28 2.66
1316 4420 2.202623 GTACCTCGCTGTCGCTGG 60.203 66.667 0.00 0.00 35.97 4.85
1335 4443 1.069703 CAAGACGACGACAAGTACGGA 60.070 52.381 0.00 0.00 34.93 4.69
1337 4445 0.701303 GCAAGACGACGACAAGTACG 59.299 55.000 0.00 0.00 0.00 3.67
1338 4446 1.977412 GAGCAAGACGACGACAAGTAC 59.023 52.381 0.00 0.00 0.00 2.73
1339 4447 1.399343 CGAGCAAGACGACGACAAGTA 60.399 52.381 0.00 0.00 0.00 2.24
1340 4448 0.660595 CGAGCAAGACGACGACAAGT 60.661 55.000 0.00 0.00 0.00 3.16
1341 4449 0.660595 ACGAGCAAGACGACGACAAG 60.661 55.000 0.00 0.00 34.70 3.16
1342 4450 0.659417 GACGAGCAAGACGACGACAA 60.659 55.000 0.00 0.00 34.70 3.18
1343 4451 1.082300 GACGAGCAAGACGACGACA 60.082 57.895 0.00 0.00 34.70 4.35
1344 4452 1.082300 TGACGAGCAAGACGACGAC 60.082 57.895 0.00 0.00 34.70 4.34
1345 4453 1.082300 GTGACGAGCAAGACGACGA 60.082 57.895 0.00 0.00 34.70 4.20
1346 4454 1.060726 GAGTGACGAGCAAGACGACG 61.061 60.000 0.00 0.00 34.70 5.12
1347 4455 0.040336 TGAGTGACGAGCAAGACGAC 60.040 55.000 0.00 0.00 34.70 4.34
1348 4456 0.040336 GTGAGTGACGAGCAAGACGA 60.040 55.000 0.00 0.00 34.70 4.20
1349 4457 0.039978 AGTGAGTGACGAGCAAGACG 60.040 55.000 0.00 0.00 0.00 4.18
1350 4458 1.667467 GGAGTGAGTGACGAGCAAGAC 60.667 57.143 0.00 0.00 0.00 3.01
1351 4459 0.598562 GGAGTGAGTGACGAGCAAGA 59.401 55.000 0.00 0.00 0.00 3.02
1352 4460 0.600557 AGGAGTGAGTGACGAGCAAG 59.399 55.000 0.00 0.00 0.00 4.01
1353 4461 1.040646 AAGGAGTGAGTGACGAGCAA 58.959 50.000 0.00 0.00 0.00 3.91
1354 4462 1.813178 CTAAGGAGTGAGTGACGAGCA 59.187 52.381 0.00 0.00 0.00 4.26
1355 4463 1.813786 ACTAAGGAGTGAGTGACGAGC 59.186 52.381 0.00 0.00 33.41 5.03
1356 4464 2.420722 GGACTAAGGAGTGAGTGACGAG 59.579 54.545 0.00 0.00 35.45 4.18
1357 4465 2.434428 GGACTAAGGAGTGAGTGACGA 58.566 52.381 0.00 0.00 35.45 4.20
1358 4466 1.473278 GGGACTAAGGAGTGAGTGACG 59.527 57.143 0.00 0.00 35.45 4.35
1359 4467 1.826096 GGGGACTAAGGAGTGAGTGAC 59.174 57.143 0.00 0.00 35.45 3.67
1360 4468 1.616187 CGGGGACTAAGGAGTGAGTGA 60.616 57.143 0.00 0.00 35.45 3.41
1361 4469 0.818296 CGGGGACTAAGGAGTGAGTG 59.182 60.000 0.00 0.00 35.45 3.51
1362 4470 0.971447 GCGGGGACTAAGGAGTGAGT 60.971 60.000 0.00 0.00 35.45 3.41
1363 4471 1.677637 GGCGGGGACTAAGGAGTGAG 61.678 65.000 0.00 0.00 35.45 3.51
1364 4472 1.684734 GGCGGGGACTAAGGAGTGA 60.685 63.158 0.00 0.00 35.45 3.41
1365 4473 2.732619 GGGCGGGGACTAAGGAGTG 61.733 68.421 0.00 0.00 35.45 3.51
1366 4474 2.365237 GGGCGGGGACTAAGGAGT 60.365 66.667 0.00 0.00 39.20 3.85
1367 4475 3.162154 GGGGCGGGGACTAAGGAG 61.162 72.222 0.00 0.00 0.00 3.69
1368 4476 3.691297 GAGGGGCGGGGACTAAGGA 62.691 68.421 0.00 0.00 0.00 3.36
1369 4477 3.162154 GAGGGGCGGGGACTAAGG 61.162 72.222 0.00 0.00 0.00 2.69
1370 4478 3.162154 GGAGGGGCGGGGACTAAG 61.162 72.222 0.00 0.00 0.00 2.18
1371 4479 4.810184 GGGAGGGGCGGGGACTAA 62.810 72.222 0.00 0.00 0.00 2.24
1426 4538 2.282555 CGACCTAGCACATTGACAATCG 59.717 50.000 0.00 0.00 0.00 3.34
1434 4546 0.456221 CGTCCTCGACCTAGCACATT 59.544 55.000 0.00 0.00 39.71 2.71
1440 4552 1.515081 GATCCTCGTCCTCGACCTAG 58.485 60.000 0.00 0.00 41.35 3.02
1447 4559 0.816018 TCAGAGCGATCCTCGTCCTC 60.816 60.000 0.00 0.00 45.54 3.71
1610 4734 1.075896 AAGAGGGCGGAGAGTAGGG 60.076 63.158 0.00 0.00 0.00 3.53
1618 4742 1.107538 CCGATGTAGAAGAGGGCGGA 61.108 60.000 0.00 0.00 39.62 5.54
1619 4743 1.364171 CCGATGTAGAAGAGGGCGG 59.636 63.158 0.00 0.00 0.00 6.13
1647 4771 0.179062 GATTCATCCTCCACAGCGCT 60.179 55.000 2.64 2.64 0.00 5.92
1713 4837 2.594303 TCCGCCACCTTGTTGCTG 60.594 61.111 0.00 0.00 0.00 4.41
1715 4839 1.298859 CTACTCCGCCACCTTGTTGC 61.299 60.000 0.00 0.00 0.00 4.17
1716 4840 1.298859 GCTACTCCGCCACCTTGTTG 61.299 60.000 0.00 0.00 0.00 3.33
1826 4969 5.476599 AGTTCATAGCAAACAAGCATAACCA 59.523 36.000 0.00 0.00 36.85 3.67
1869 5012 9.705290 AAAGAATAACATTTGATGGTTGGTAAC 57.295 29.630 0.00 0.00 33.60 2.50
1919 5062 6.639632 AACAGATGAAAACACTGCAATAGT 57.360 33.333 0.00 0.00 41.36 2.12
1945 5088 4.094442 GGAAACGTGGCTTTATCCTTACAG 59.906 45.833 0.00 0.00 0.00 2.74
1952 5095 3.013921 TGGATGGAAACGTGGCTTTATC 58.986 45.455 0.00 0.00 0.00 1.75
1953 5096 3.080300 TGGATGGAAACGTGGCTTTAT 57.920 42.857 0.00 0.00 0.00 1.40
1954 5097 2.570415 TGGATGGAAACGTGGCTTTA 57.430 45.000 0.00 0.00 0.00 1.85
1955 5098 1.545582 CATGGATGGAAACGTGGCTTT 59.454 47.619 0.00 0.00 0.00 3.51
1956 5099 1.176527 CATGGATGGAAACGTGGCTT 58.823 50.000 0.00 0.00 0.00 4.35
1957 5100 2.872408 CATGGATGGAAACGTGGCT 58.128 52.632 0.00 0.00 0.00 4.75
1968 5111 0.744874 ACCGACGTCTACCATGGATG 59.255 55.000 21.47 10.61 0.00 3.51
1969 5112 2.158711 TCTACCGACGTCTACCATGGAT 60.159 50.000 21.47 5.32 0.00 3.41
1970 5113 1.210234 TCTACCGACGTCTACCATGGA 59.790 52.381 21.47 0.67 0.00 3.41
1971 5114 1.332997 GTCTACCGACGTCTACCATGG 59.667 57.143 11.19 11.19 0.00 3.66
1972 5115 2.286872 AGTCTACCGACGTCTACCATG 58.713 52.381 14.70 0.00 44.93 3.66
1973 5116 2.706339 AGTCTACCGACGTCTACCAT 57.294 50.000 14.70 0.00 44.93 3.55
1974 5117 2.497675 ACTAGTCTACCGACGTCTACCA 59.502 50.000 14.70 0.00 44.93 3.25
1975 5118 3.172229 ACTAGTCTACCGACGTCTACC 57.828 52.381 14.70 0.00 44.93 3.18
1976 5119 7.650104 AGTTATTACTAGTCTACCGACGTCTAC 59.350 40.741 14.70 4.10 44.93 2.59
1977 5120 7.717568 AGTTATTACTAGTCTACCGACGTCTA 58.282 38.462 14.70 0.00 44.93 2.59
1978 5121 6.578023 AGTTATTACTAGTCTACCGACGTCT 58.422 40.000 14.70 0.00 44.93 4.18
1979 5122 6.836577 AGTTATTACTAGTCTACCGACGTC 57.163 41.667 5.18 5.18 44.93 4.34
1980 5123 7.617041 AAAGTTATTACTAGTCTACCGACGT 57.383 36.000 0.00 0.00 38.26 4.34
1981 5124 8.394121 AGAAAAGTTATTACTAGTCTACCGACG 58.606 37.037 0.00 0.00 38.26 5.12
1984 5127 9.219497 CGAAGAAAAGTTATTACTAGTCTACCG 57.781 37.037 0.00 3.10 33.17 4.02
2007 5150 9.997482 GTGCAAAAATTAGAGGATTAATACGAA 57.003 29.630 0.00 0.00 0.00 3.85
2008 5151 9.391006 AGTGCAAAAATTAGAGGATTAATACGA 57.609 29.630 0.00 0.00 0.00 3.43
2047 5190 9.842775 ATGTGTAGATGACATTTCAAGTGATAT 57.157 29.630 0.00 0.00 41.14 1.63
2048 5191 9.101655 CATGTGTAGATGACATTTCAAGTGATA 57.898 33.333 0.00 0.00 41.14 2.15
2049 5192 7.825761 TCATGTGTAGATGACATTTCAAGTGAT 59.174 33.333 0.00 0.00 41.14 3.06
2050 5193 7.160726 TCATGTGTAGATGACATTTCAAGTGA 58.839 34.615 0.00 0.00 41.14 3.41
2051 5194 7.368480 TCATGTGTAGATGACATTTCAAGTG 57.632 36.000 0.00 0.00 41.14 3.16
2052 5195 7.984422 TTCATGTGTAGATGACATTTCAAGT 57.016 32.000 0.00 0.00 41.14 3.16
2053 5196 9.681692 TTTTTCATGTGTAGATGACATTTCAAG 57.318 29.630 0.00 0.00 41.14 3.02
2054 5197 9.681692 CTTTTTCATGTGTAGATGACATTTCAA 57.318 29.630 0.00 0.00 41.14 2.69
2055 5198 8.298854 CCTTTTTCATGTGTAGATGACATTTCA 58.701 33.333 0.00 0.00 41.14 2.69
2056 5199 8.514594 TCCTTTTTCATGTGTAGATGACATTTC 58.485 33.333 0.00 0.00 41.14 2.17
2057 5200 8.408043 TCCTTTTTCATGTGTAGATGACATTT 57.592 30.769 0.00 0.00 41.14 2.32
2058 5201 8.585471 ATCCTTTTTCATGTGTAGATGACATT 57.415 30.769 0.00 0.00 41.14 2.71
2059 5202 8.585471 AATCCTTTTTCATGTGTAGATGACAT 57.415 30.769 0.00 0.00 41.14 3.06
2060 5203 7.665145 TGAATCCTTTTTCATGTGTAGATGACA 59.335 33.333 0.00 0.00 31.92 3.58
2061 5204 7.965107 GTGAATCCTTTTTCATGTGTAGATGAC 59.035 37.037 0.00 0.00 37.88 3.06
2062 5205 7.665145 TGTGAATCCTTTTTCATGTGTAGATGA 59.335 33.333 0.00 0.00 37.88 2.92
2063 5206 7.819644 TGTGAATCCTTTTTCATGTGTAGATG 58.180 34.615 0.00 0.00 37.88 2.90
2064 5207 8.408043 TTGTGAATCCTTTTTCATGTGTAGAT 57.592 30.769 0.00 0.00 37.88 1.98
2065 5208 7.815840 TTGTGAATCCTTTTTCATGTGTAGA 57.184 32.000 0.00 0.00 37.88 2.59
2066 5209 9.132521 GATTTGTGAATCCTTTTTCATGTGTAG 57.867 33.333 0.00 0.00 37.88 2.74
2067 5210 8.637099 TGATTTGTGAATCCTTTTTCATGTGTA 58.363 29.630 0.00 0.00 40.79 2.90
2068 5211 7.439056 GTGATTTGTGAATCCTTTTTCATGTGT 59.561 33.333 0.00 0.00 40.79 3.72
2069 5212 7.438757 TGTGATTTGTGAATCCTTTTTCATGTG 59.561 33.333 0.00 0.00 40.79 3.21
2070 5213 7.499292 TGTGATTTGTGAATCCTTTTTCATGT 58.501 30.769 0.00 0.00 40.79 3.21
2071 5214 7.949903 TGTGATTTGTGAATCCTTTTTCATG 57.050 32.000 0.00 0.00 40.79 3.07
2072 5215 7.442062 GGTTGTGATTTGTGAATCCTTTTTCAT 59.558 33.333 0.00 0.00 40.79 2.57
2073 5216 6.760770 GGTTGTGATTTGTGAATCCTTTTTCA 59.239 34.615 0.00 0.00 40.79 2.69
2074 5217 6.760770 TGGTTGTGATTTGTGAATCCTTTTTC 59.239 34.615 0.00 0.00 40.79 2.29
2075 5218 6.538381 GTGGTTGTGATTTGTGAATCCTTTTT 59.462 34.615 0.00 0.00 40.79 1.94
2076 5219 6.048509 GTGGTTGTGATTTGTGAATCCTTTT 58.951 36.000 0.00 0.00 40.79 2.27
2077 5220 5.128499 TGTGGTTGTGATTTGTGAATCCTTT 59.872 36.000 0.00 0.00 40.79 3.11
2078 5221 4.648762 TGTGGTTGTGATTTGTGAATCCTT 59.351 37.500 0.00 0.00 40.79 3.36
2079 5222 4.214310 TGTGGTTGTGATTTGTGAATCCT 58.786 39.130 0.00 0.00 40.79 3.24
2080 5223 4.582701 TGTGGTTGTGATTTGTGAATCC 57.417 40.909 0.00 0.00 40.79 3.01
2081 5224 6.900568 TTTTGTGGTTGTGATTTGTGAATC 57.099 33.333 0.00 0.00 41.67 2.52
2107 5250 7.915508 CACAACAAGTGTAGATGACAACTAAA 58.084 34.615 0.00 0.00 43.40 1.85
2108 5251 7.477144 CACAACAAGTGTAGATGACAACTAA 57.523 36.000 0.00 0.00 43.40 2.24
2123 5266 4.681744 CAGCAATAAACCACACAACAAGT 58.318 39.130 0.00 0.00 0.00 3.16
2124 5267 3.490526 GCAGCAATAAACCACACAACAAG 59.509 43.478 0.00 0.00 0.00 3.16
2125 5268 3.452474 GCAGCAATAAACCACACAACAA 58.548 40.909 0.00 0.00 0.00 2.83
2133 5299 5.011533 ACAACTAAATGGCAGCAATAAACCA 59.988 36.000 0.00 0.00 36.43 3.67
2168 5334 1.133976 GTGAAGGCCTATGGTCAGCAT 60.134 52.381 5.16 0.00 0.00 3.79
2186 5352 9.345517 CCAGTAAATGATGAAAATAACTGTGTG 57.654 33.333 0.00 0.00 33.02 3.82
2187 5353 8.028938 GCCAGTAAATGATGAAAATAACTGTGT 58.971 33.333 0.00 0.00 33.02 3.72
2188 5354 8.028354 TGCCAGTAAATGATGAAAATAACTGTG 58.972 33.333 0.00 0.00 33.02 3.66
2196 5362 4.321899 GCACCTGCCAGTAAATGATGAAAA 60.322 41.667 0.00 0.00 34.31 2.29
2222 5390 3.430779 GCTGCTGCAAATTCTTCCC 57.569 52.632 11.11 0.00 39.41 3.97
2248 5423 7.101054 AGTATAGTAGTAAGCTCTGATCTCCG 58.899 42.308 0.00 0.00 0.00 4.63
2256 5431 6.711645 GCACTGGTAGTATAGTAGTAAGCTCT 59.288 42.308 0.00 0.00 0.00 4.09
2257 5432 6.485984 TGCACTGGTAGTATAGTAGTAAGCTC 59.514 42.308 0.00 0.00 0.00 4.09
2258 5433 6.363065 TGCACTGGTAGTATAGTAGTAAGCT 58.637 40.000 0.00 0.00 0.00 3.74
2259 5434 6.294065 CCTGCACTGGTAGTATAGTAGTAAGC 60.294 46.154 0.00 0.00 0.00 3.09
2260 5435 6.996879 TCCTGCACTGGTAGTATAGTAGTAAG 59.003 42.308 0.00 0.00 0.00 2.34
2261 5436 6.903516 TCCTGCACTGGTAGTATAGTAGTAA 58.096 40.000 0.00 0.00 0.00 2.24
2289 5467 9.649316 AAGATAGTAGTAGCTAGGAAACAGAAT 57.351 33.333 0.00 0.00 0.00 2.40
2315 5505 7.066887 TCTCTTAATTGTTCACAAGAGCAACAA 59.933 33.333 8.07 0.00 45.71 2.83
2406 5600 1.066152 TCTGACCTCGCATCGAATCAG 59.934 52.381 17.24 17.24 43.95 2.90
2453 5647 0.969894 AGGTCCGGTTCAGACTTCAG 59.030 55.000 0.00 0.00 34.56 3.02
2509 5708 9.996554 ATATATGATCACGTAGAATGAAAACCA 57.003 29.630 0.00 0.00 0.00 3.67
2523 5722 7.330208 TCAGCAGTGAAATGATATATGATCACG 59.670 37.037 0.00 0.00 41.43 4.35
2605 5821 2.117051 ACTTACTCGGATTCTTCCCCC 58.883 52.381 0.00 0.00 39.01 5.40
2606 5822 3.431905 GGAACTTACTCGGATTCTTCCCC 60.432 52.174 0.00 0.00 39.01 4.81
2607 5823 3.451540 AGGAACTTACTCGGATTCTTCCC 59.548 47.826 0.00 0.00 34.27 3.97
2608 5824 4.441773 GGAGGAACTTACTCGGATTCTTCC 60.442 50.000 4.37 4.37 41.55 3.46
2609 5825 4.403113 AGGAGGAACTTACTCGGATTCTTC 59.597 45.833 0.00 0.00 41.55 2.87
2610 5826 4.160626 CAGGAGGAACTTACTCGGATTCTT 59.839 45.833 0.00 0.00 41.55 2.52
2611 5827 3.702045 CAGGAGGAACTTACTCGGATTCT 59.298 47.826 0.00 0.00 41.55 2.40
2612 5828 3.738590 GCAGGAGGAACTTACTCGGATTC 60.739 52.174 0.00 0.00 41.55 2.52
2613 5829 2.168728 GCAGGAGGAACTTACTCGGATT 59.831 50.000 0.00 0.00 41.55 3.01
2614 5830 1.757699 GCAGGAGGAACTTACTCGGAT 59.242 52.381 0.00 0.00 41.55 4.18
2615 5831 1.183549 GCAGGAGGAACTTACTCGGA 58.816 55.000 0.00 0.00 41.55 4.55
2616 5832 0.179134 CGCAGGAGGAACTTACTCGG 60.179 60.000 0.00 0.00 41.55 4.63
2617 5833 3.330766 CGCAGGAGGAACTTACTCG 57.669 57.895 0.00 0.00 41.55 4.18
2631 5847 3.941188 ACACCACTCCACCCGCAG 61.941 66.667 0.00 0.00 0.00 5.18
2632 5848 4.248842 CACACCACTCCACCCGCA 62.249 66.667 0.00 0.00 0.00 5.69
2635 5851 3.133365 AAGCCACACCACTCCACCC 62.133 63.158 0.00 0.00 0.00 4.61
2636 5852 1.600916 GAAGCCACACCACTCCACC 60.601 63.158 0.00 0.00 0.00 4.61
2637 5853 1.600916 GGAAGCCACACCACTCCAC 60.601 63.158 0.00 0.00 0.00 4.02
2638 5854 2.829384 GGGAAGCCACACCACTCCA 61.829 63.158 0.00 0.00 0.00 3.86
2669 5899 2.362375 GGCCCATTTCCGGAAGCA 60.362 61.111 22.98 9.52 0.00 3.91
2695 6412 0.938713 GCACATGCATCTCTCTCTGC 59.061 55.000 0.00 0.00 41.59 4.26


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

AutoCloner maintained by Alex Coulton.