Multiple sequence alignment - TraesCS5B01G146500

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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 TraesCS5B01G146500 chr5B 100.000 2866 0 0 583 3448 275033101 275035966 0.000000e+00 5293.0
1 TraesCS5B01G146500 chr5B 100.000 402 0 0 1 402 275032519 275032920 0.000000e+00 743.0
2 TraesCS5B01G146500 chr5B 84.914 232 19 8 2930 3159 275056782 275056999 1.610000e-53 220.0
3 TraesCS5B01G146500 chr5B 100.000 75 0 0 583 657 318926706 318926780 4.640000e-29 139.0
4 TraesCS5B01G146500 chr5B 100.000 75 0 0 583 657 613633388 613633462 4.640000e-29 139.0
5 TraesCS5B01G146500 chr5B 92.105 76 6 0 3051 3126 275035495 275035570 1.310000e-19 108.0
6 TraesCS5B01G146500 chr5B 92.105 76 6 0 2977 3052 275035569 275035644 1.310000e-19 108.0
7 TraesCS5B01G146500 chr5B 87.500 80 6 4 3171 3250 275057041 275057116 4.740000e-14 89.8
8 TraesCS5B01G146500 chr5B 92.105 38 3 0 3089 3126 275056854 275056891 2.000000e-03 54.7
9 TraesCS5B01G146500 chr5D 95.090 1955 64 11 659 2586 231352917 231350968 0.000000e+00 3049.0
10 TraesCS5B01G146500 chr5D 91.206 705 18 8 2582 3250 231332637 231331941 0.000000e+00 918.0
11 TraesCS5B01G146500 chr5D 86.667 405 40 12 1 402 231353297 231352904 1.470000e-118 436.0
12 TraesCS5B01G146500 chr5D 93.421 76 5 0 2977 3052 231332132 231332057 2.810000e-21 113.0
13 TraesCS5B01G146500 chr5D 85.526 76 7 4 3175 3250 231331331 231331260 3.690000e-10 76.8
14 TraesCS5B01G146500 chr5A 95.256 1855 54 9 658 2488 325931471 325933315 0.000000e+00 2907.0
15 TraesCS5B01G146500 chr5A 87.455 550 49 14 2690 3233 325950208 325950743 1.760000e-172 616.0
16 TraesCS5B01G146500 chr5A 85.608 403 41 13 1 395 325931076 325931469 1.150000e-109 407.0
17 TraesCS5B01G146500 chr5A 87.500 232 15 3 2930 3159 325951505 325951724 4.420000e-64 255.0
18 TraesCS5B01G146500 chr5A 100.000 75 0 0 583 657 645605657 645605731 4.640000e-29 139.0
19 TraesCS5B01G146500 chr5A 80.405 148 26 2 2774 2921 325951306 325951450 3.640000e-20 110.0
20 TraesCS5B01G146500 chr5A 87.654 81 6 4 3172 3252 325951767 325951843 1.320000e-14 91.6
21 TraesCS5B01G146500 chr5A 92.105 38 3 0 3089 3126 325951579 325951616 2.000000e-03 54.7
22 TraesCS5B01G146500 chr4A 84.621 1320 178 12 1006 2307 476979050 476980362 0.000000e+00 1290.0
23 TraesCS5B01G146500 chr4A 98.571 210 3 0 3236 3445 62543182 62543391 4.200000e-99 372.0
24 TraesCS5B01G146500 chr4B 81.581 1607 246 22 752 2316 141429202 141427604 0.000000e+00 1282.0
25 TraesCS5B01G146500 chr4B 88.136 177 5 8 2436 2597 366392356 366392181 2.710000e-46 196.0
26 TraesCS5B01G146500 chr4D 80.855 1661 260 33 705 2316 99163033 99161382 0.000000e+00 1253.0
27 TraesCS5B01G146500 chr4D 100.000 210 0 0 3236 3445 15918111 15918320 4.170000e-104 388.0
28 TraesCS5B01G146500 chr7D 99.524 210 1 0 3236 3445 511077145 511077354 1.940000e-102 383.0
29 TraesCS5B01G146500 chr2D 99.048 210 2 0 3236 3445 603519358 603519567 9.030000e-101 377.0
30 TraesCS5B01G146500 chr1D 97.653 213 5 0 3236 3448 388969066 388968854 1.960000e-97 366.0
31 TraesCS5B01G146500 chr1D 87.222 180 7 8 2433 2597 91722023 91722201 1.260000e-44 191.0
32 TraesCS5B01G146500 chr7A 97.619 210 5 0 3236 3445 669731699 669731908 9.100000e-96 361.0
33 TraesCS5B01G146500 chr7A 100.000 75 0 0 583 657 218258459 218258385 4.640000e-29 139.0
34 TraesCS5B01G146500 chr3A 97.608 209 5 0 3237 3445 502500737 502500945 3.270000e-95 359.0
35 TraesCS5B01G146500 chr1A 97.143 210 6 0 3236 3445 543647654 543647863 4.230000e-94 355.0
36 TraesCS5B01G146500 chr1B 96.244 213 8 0 3236 3448 348401394 348401182 1.970000e-92 350.0
37 TraesCS5B01G146500 chr1B 100.000 75 0 0 583 657 517502520 517502594 4.640000e-29 139.0
38 TraesCS5B01G146500 chr6D 87.778 180 6 9 2433 2597 27782718 27782896 2.710000e-46 196.0
39 TraesCS5B01G146500 chr6D 87.778 180 6 8 2433 2597 212696284 212696462 2.710000e-46 196.0
40 TraesCS5B01G146500 chr6D 87.222 180 7 9 2433 2597 9648127 9648305 1.260000e-44 191.0
41 TraesCS5B01G146500 chr6B 88.136 177 5 8 2436 2597 10696454 10696279 2.710000e-46 196.0
42 TraesCS5B01G146500 chr3D 87.778 180 6 8 2433 2597 207581657 207581835 2.710000e-46 196.0
43 TraesCS5B01G146500 chr3D 98.667 75 1 0 583 657 606564616 606564542 2.160000e-27 134.0
44 TraesCS5B01G146500 chr2A 87.006 177 7 9 2436 2597 161021937 161021762 5.880000e-43 185.0
45 TraesCS5B01G146500 chr3B 100.000 75 0 0 583 657 553100763 553100689 4.640000e-29 139.0
46 TraesCS5B01G146500 chr2B 100.000 75 0 0 583 657 183513680 183513754 4.640000e-29 139.0
47 TraesCS5B01G146500 chrUn 98.667 75 1 0 583 657 47456184 47456258 2.160000e-27 134.0


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 TraesCS5B01G146500 chr5B 275032519 275035966 3447 False 1563.000000 5293 96.0525 1 3448 4 chr5B.!!$F3 3447
1 TraesCS5B01G146500 chr5D 231350968 231353297 2329 True 1742.500000 3049 90.8785 1 2586 2 chr5D.!!$R2 2585
2 TraesCS5B01G146500 chr5D 231331260 231332637 1377 True 369.266667 918 90.0510 2582 3250 3 chr5D.!!$R1 668
3 TraesCS5B01G146500 chr5A 325931076 325933315 2239 False 1657.000000 2907 90.4320 1 2488 2 chr5A.!!$F2 2487
4 TraesCS5B01G146500 chr5A 325950208 325951843 1635 False 225.460000 616 87.0238 2690 3252 5 chr5A.!!$F3 562
5 TraesCS5B01G146500 chr4A 476979050 476980362 1312 False 1290.000000 1290 84.6210 1006 2307 1 chr4A.!!$F2 1301
6 TraesCS5B01G146500 chr4B 141427604 141429202 1598 True 1282.000000 1282 81.5810 752 2316 1 chr4B.!!$R1 1564
7 TraesCS5B01G146500 chr4D 99161382 99163033 1651 True 1253.000000 1253 80.8550 705 2316 1 chr4D.!!$R1 1611

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
49 53 0.710588 TCTGGAAGGGTCCTGCTAGA 59.289 55.0 6.94 6.94 45.22 2.43 F
1109 1152 0.602638 TGCACTACGCCAAGAACCTG 60.603 55.0 0.00 0.00 41.33 4.00 F
2060 2118 0.035725 CTGCCTCAGCCATTGTCTCA 60.036 55.0 0.00 0.00 38.69 3.27 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1805 1848 0.109913 GACCTTTCCGGAACCAGGTT 59.890 55.0 31.85 20.15 39.90 3.50 R
2253 2311 0.764890 CGGATGCCCTCCTCCAATAA 59.235 55.0 1.38 0.00 42.47 1.40 R
3275 3374 0.107703 TTACAGCGAAGGCATCCAGG 60.108 55.0 0.00 0.00 43.41 4.45 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
20 21 2.694043 CGGTCAGATTTCGAAATTCGC 58.306 47.619 23.49 11.75 40.21 4.70
22 23 2.678336 GGTCAGATTTCGAAATTCGCCT 59.322 45.455 23.49 13.41 40.21 5.52
26 27 2.352960 AGATTTCGAAATTCGCCTCAGC 59.647 45.455 23.49 8.34 40.21 4.26
29 30 1.808411 TCGAAATTCGCCTCAGCTTT 58.192 45.000 10.93 0.00 40.21 3.51
38 39 1.172175 GCCTCAGCTTTTCTGGAAGG 58.828 55.000 0.00 0.00 43.06 3.46
49 53 0.710588 TCTGGAAGGGTCCTGCTAGA 59.289 55.000 6.94 6.94 45.22 2.43
65 69 6.265422 TCCTGCTAGATGTCGAATCATTAGAA 59.735 38.462 0.00 0.82 0.00 2.10
81 85 1.512926 AGAAGCACAAAGGTAGCACG 58.487 50.000 0.00 0.00 0.00 5.34
94 99 2.876550 GGTAGCACGGTTTTCTCTGTTT 59.123 45.455 0.00 0.00 0.00 2.83
95 100 3.314357 GGTAGCACGGTTTTCTCTGTTTT 59.686 43.478 0.00 0.00 0.00 2.43
96 101 3.692791 AGCACGGTTTTCTCTGTTTTC 57.307 42.857 0.00 0.00 0.00 2.29
99 104 3.791353 GCACGGTTTTCTCTGTTTTCTTG 59.209 43.478 0.00 0.00 0.00 3.02
100 105 4.674362 GCACGGTTTTCTCTGTTTTCTTGT 60.674 41.667 0.00 0.00 0.00 3.16
101 106 4.793216 CACGGTTTTCTCTGTTTTCTTGTG 59.207 41.667 0.00 0.00 0.00 3.33
103 108 4.682787 GGTTTTCTCTGTTTTCTTGTGGG 58.317 43.478 0.00 0.00 0.00 4.61
104 109 4.401202 GGTTTTCTCTGTTTTCTTGTGGGA 59.599 41.667 0.00 0.00 0.00 4.37
105 110 5.069119 GGTTTTCTCTGTTTTCTTGTGGGAT 59.931 40.000 0.00 0.00 0.00 3.85
106 111 6.264518 GGTTTTCTCTGTTTTCTTGTGGGATA 59.735 38.462 0.00 0.00 0.00 2.59
107 112 6.877611 TTTCTCTGTTTTCTTGTGGGATAC 57.122 37.500 0.00 0.00 0.00 2.24
133 138 6.273965 TGGGATCCTAATCTCATCATGTGATT 59.726 38.462 17.00 17.00 37.47 2.57
146 151 2.957402 TGTGATTTGTCCCTCTTGCT 57.043 45.000 0.00 0.00 0.00 3.91
151 156 2.978156 TTTGTCCCTCTTGCTGGATT 57.022 45.000 0.00 0.00 32.20 3.01
160 165 3.307691 CCTCTTGCTGGATTGTTGGTAGA 60.308 47.826 0.00 0.00 0.00 2.59
186 191 4.384056 CGTCTTCTCCCGATACCTAGTTA 58.616 47.826 0.00 0.00 0.00 2.24
196 201 5.472820 CCCGATACCTAGTTAGTTAGAGGTG 59.527 48.000 2.66 0.00 42.36 4.00
201 206 8.694581 ATACCTAGTTAGTTAGAGGTGATCAC 57.305 38.462 17.91 17.91 42.36 3.06
209 214 2.457366 AGAGGTGATCACGGTTTCAC 57.543 50.000 19.33 10.92 41.19 3.18
220 225 2.066262 ACGGTTTCACAAGTCATAGCG 58.934 47.619 0.00 0.00 0.00 4.26
227 232 4.718940 TCACAAGTCATAGCGATTCAGA 57.281 40.909 0.00 0.00 0.00 3.27
228 233 4.424626 TCACAAGTCATAGCGATTCAGAC 58.575 43.478 0.00 0.00 0.00 3.51
232 237 3.291584 AGTCATAGCGATTCAGACCTGA 58.708 45.455 0.00 0.00 37.91 3.86
243 248 4.750021 TTCAGACCTGATGATGAAGGAG 57.250 45.455 0.01 0.00 39.64 3.69
250 255 5.026121 ACCTGATGATGAAGGAGTCACTTA 58.974 41.667 0.00 0.00 39.72 2.24
289 295 3.641434 ACTCTGAATTACATGCAGGCT 57.359 42.857 0.00 0.00 0.00 4.58
300 306 8.980481 AATTACATGCAGGCTTAGTAGTAATT 57.020 30.769 0.00 12.37 36.59 1.40
301 307 7.786178 TTACATGCAGGCTTAGTAGTAATTG 57.214 36.000 0.00 0.00 0.00 2.32
357 367 6.441093 TTCGATTTTCTTTCCATCCATCTG 57.559 37.500 0.00 0.00 0.00 2.90
360 370 6.763135 TCGATTTTCTTTCCATCCATCTGTAG 59.237 38.462 0.00 0.00 0.00 2.74
361 371 6.763135 CGATTTTCTTTCCATCCATCTGTAGA 59.237 38.462 0.00 0.00 0.00 2.59
362 372 7.254590 CGATTTTCTTTCCATCCATCTGTAGAC 60.255 40.741 0.00 0.00 0.00 2.59
364 374 5.604758 TCTTTCCATCCATCTGTAGACTG 57.395 43.478 0.00 0.00 0.00 3.51
365 375 5.026121 TCTTTCCATCCATCTGTAGACTGT 58.974 41.667 0.00 0.00 0.00 3.55
366 376 6.194967 TCTTTCCATCCATCTGTAGACTGTA 58.805 40.000 0.00 0.00 0.00 2.74
367 377 6.322456 TCTTTCCATCCATCTGTAGACTGTAG 59.678 42.308 0.00 0.00 0.00 2.74
368 378 5.130705 TCCATCCATCTGTAGACTGTAGT 57.869 43.478 0.00 0.00 0.00 2.73
369 379 5.519808 TCCATCCATCTGTAGACTGTAGTT 58.480 41.667 0.00 0.00 0.00 2.24
605 615 6.949352 CCACCTGAATATATTGCTCAAAGT 57.051 37.500 1.78 0.00 0.00 2.66
606 616 6.732154 CCACCTGAATATATTGCTCAAAGTG 58.268 40.000 1.78 5.90 0.00 3.16
607 617 6.238842 CCACCTGAATATATTGCTCAAAGTGG 60.239 42.308 1.78 10.45 37.30 4.00
608 618 5.300286 ACCTGAATATATTGCTCAAAGTGGC 59.700 40.000 1.78 0.00 0.00 5.01
609 619 5.278660 CCTGAATATATTGCTCAAAGTGGCC 60.279 44.000 1.78 0.00 0.00 5.36
610 620 5.199723 TGAATATATTGCTCAAAGTGGCCA 58.800 37.500 0.00 0.00 0.00 5.36
611 621 5.655974 TGAATATATTGCTCAAAGTGGCCAA 59.344 36.000 7.24 0.00 0.00 4.52
612 622 6.154192 TGAATATATTGCTCAAAGTGGCCAAA 59.846 34.615 7.24 0.00 0.00 3.28
613 623 4.888326 ATATTGCTCAAAGTGGCCAAAA 57.112 36.364 7.24 0.00 0.00 2.44
614 624 3.775261 ATTGCTCAAAGTGGCCAAAAT 57.225 38.095 7.24 0.00 0.00 1.82
615 625 2.529780 TGCTCAAAGTGGCCAAAATG 57.470 45.000 7.24 6.81 0.00 2.32
616 626 1.150827 GCTCAAAGTGGCCAAAATGC 58.849 50.000 7.24 3.75 0.00 3.56
627 637 2.559440 GCCAAAATGCCAAGTGTTTGA 58.441 42.857 0.00 0.00 36.36 2.69
628 638 3.140623 GCCAAAATGCCAAGTGTTTGAT 58.859 40.909 0.00 0.00 36.36 2.57
629 639 3.187022 GCCAAAATGCCAAGTGTTTGATC 59.813 43.478 0.00 0.00 36.36 2.92
630 640 3.747529 CCAAAATGCCAAGTGTTTGATCC 59.252 43.478 0.00 0.00 36.36 3.36
631 641 4.378774 CAAAATGCCAAGTGTTTGATCCA 58.621 39.130 0.00 0.00 36.36 3.41
632 642 3.947910 AATGCCAAGTGTTTGATCCAG 57.052 42.857 0.00 0.00 36.36 3.86
633 643 2.363306 TGCCAAGTGTTTGATCCAGT 57.637 45.000 0.00 0.00 36.36 4.00
634 644 2.665165 TGCCAAGTGTTTGATCCAGTT 58.335 42.857 0.00 0.00 36.36 3.16
635 645 3.030291 TGCCAAGTGTTTGATCCAGTTT 58.970 40.909 0.00 0.00 36.36 2.66
636 646 4.211125 TGCCAAGTGTTTGATCCAGTTTA 58.789 39.130 0.00 0.00 36.36 2.01
637 647 4.832266 TGCCAAGTGTTTGATCCAGTTTAT 59.168 37.500 0.00 0.00 36.36 1.40
638 648 6.007076 TGCCAAGTGTTTGATCCAGTTTATA 58.993 36.000 0.00 0.00 36.36 0.98
639 649 6.491745 TGCCAAGTGTTTGATCCAGTTTATAA 59.508 34.615 0.00 0.00 36.36 0.98
640 650 7.029563 GCCAAGTGTTTGATCCAGTTTATAAG 58.970 38.462 0.00 0.00 36.36 1.73
641 651 7.538575 CCAAGTGTTTGATCCAGTTTATAAGG 58.461 38.462 0.00 0.00 36.36 2.69
642 652 7.393234 CCAAGTGTTTGATCCAGTTTATAAGGA 59.607 37.037 0.00 0.00 36.36 3.36
643 653 8.792633 CAAGTGTTTGATCCAGTTTATAAGGAA 58.207 33.333 0.00 0.00 36.36 3.36
644 654 8.934023 AGTGTTTGATCCAGTTTATAAGGAAA 57.066 30.769 0.00 0.00 34.62 3.13
645 655 9.362151 AGTGTTTGATCCAGTTTATAAGGAAAA 57.638 29.630 0.00 0.00 34.62 2.29
646 656 9.406828 GTGTTTGATCCAGTTTATAAGGAAAAC 57.593 33.333 10.10 10.10 34.80 2.43
647 657 8.581578 TGTTTGATCCAGTTTATAAGGAAAACC 58.418 33.333 12.50 0.00 37.51 3.27
648 658 6.995511 TGATCCAGTTTATAAGGAAAACCG 57.004 37.500 0.00 0.00 37.51 4.44
649 659 5.883673 TGATCCAGTTTATAAGGAAAACCGG 59.116 40.000 0.00 0.00 37.51 5.28
650 660 5.502089 TCCAGTTTATAAGGAAAACCGGA 57.498 39.130 9.46 0.63 39.79 5.14
651 661 6.069705 TCCAGTTTATAAGGAAAACCGGAT 57.930 37.500 9.46 0.00 38.09 4.18
652 662 6.117488 TCCAGTTTATAAGGAAAACCGGATC 58.883 40.000 9.46 2.88 38.09 3.36
653 663 5.007332 CCAGTTTATAAGGAAAACCGGATCG 59.993 44.000 9.46 0.00 36.79 3.69
654 664 5.813672 CAGTTTATAAGGAAAACCGGATCGA 59.186 40.000 9.46 0.00 37.51 3.59
655 665 6.314400 CAGTTTATAAGGAAAACCGGATCGAA 59.686 38.462 9.46 0.00 37.51 3.71
656 666 6.880529 AGTTTATAAGGAAAACCGGATCGAAA 59.119 34.615 9.46 0.00 37.51 3.46
668 678 6.311055 ACCGGATCGAAAGTAGTACTTATC 57.689 41.667 15.84 14.09 37.47 1.75
672 682 7.173907 CCGGATCGAAAGTAGTACTTATCCTTA 59.826 40.741 26.50 10.34 38.11 2.69
720 730 4.761739 TCTGCCAAATCTGAAGGTTACTTG 59.238 41.667 0.00 0.00 36.97 3.16
733 743 6.609616 TGAAGGTTACTTGTTTTTCAGGGAAT 59.390 34.615 0.00 0.00 36.97 3.01
790 806 3.488721 GCTGAAAGATGTGCTTGCATAGG 60.489 47.826 0.00 0.00 41.37 2.57
864 883 2.344950 GTCACCTCTTGATGTGAGCAG 58.655 52.381 8.58 0.00 41.82 4.24
1109 1152 0.602638 TGCACTACGCCAAGAACCTG 60.603 55.000 0.00 0.00 41.33 4.00
1447 1490 3.133721 CCTGAGAACCTACTCCTTGATGG 59.866 52.174 0.00 0.00 36.22 3.51
1715 1758 2.355115 GATTTCAGGTGCCCCGGT 59.645 61.111 0.00 0.00 35.12 5.28
1784 1827 4.480541 CTGATCCGAACAAGAGGATATCG 58.519 47.826 0.00 0.00 46.42 2.92
1805 1848 5.201243 TCGATCCAGAAGATAAAGGAGTCA 58.799 41.667 0.00 0.00 34.42 3.41
1888 1946 1.340502 TGCTCCAACACTTGGTGTGAA 60.341 47.619 4.02 0.00 46.79 3.18
2028 2086 2.127251 GCAAAAAGGAAGCAAGGTTCG 58.873 47.619 5.99 0.00 0.00 3.95
2060 2118 0.035725 CTGCCTCAGCCATTGTCTCA 60.036 55.000 0.00 0.00 38.69 3.27
2084 2142 2.677979 GGAAGCCGTCGCAAAGACC 61.678 63.158 0.00 0.00 46.92 3.85
2120 2178 5.119694 GTGAGGAAGAAGGATAATGGTGTC 58.880 45.833 0.00 0.00 0.00 3.67
2265 2323 4.717280 AGTACCAGAAGTTATTGGAGGAGG 59.283 45.833 11.76 0.00 37.89 4.30
2310 2368 2.836360 GTCTGGGCATGGCATGGG 60.836 66.667 27.48 4.98 0.00 4.00
2376 2434 7.985184 TCTCACTTATTATGTTTAGTTCCGCAT 59.015 33.333 0.00 0.00 0.00 4.73
2377 2435 8.500753 TCACTTATTATGTTTAGTTCCGCATT 57.499 30.769 0.00 0.00 0.00 3.56
2378 2436 8.952278 TCACTTATTATGTTTAGTTCCGCATTT 58.048 29.630 0.00 0.00 0.00 2.32
2379 2437 9.567848 CACTTATTATGTTTAGTTCCGCATTTT 57.432 29.630 0.00 0.00 0.00 1.82
2491 2551 7.129109 TGACAAGTAATAACTGTTGCTAAGC 57.871 36.000 2.69 0.00 35.62 3.09
2497 2557 1.528129 AACTGTTGCTAAGCTGAGGC 58.472 50.000 0.00 0.00 39.06 4.70
2520 2580 4.866486 CCATGGATTAAGCTGTTTCTTTGC 59.134 41.667 5.56 0.00 0.00 3.68
2624 2684 3.621268 GTCAAATACTGTGCCGAGCATAA 59.379 43.478 1.90 0.00 41.91 1.90
2928 3019 8.641499 TGGAAGTAAATTGACAAACAAATCAC 57.359 30.769 0.00 0.00 42.03 3.06
3239 3338 2.222227 AAAACTTCCTCCTGATGGGC 57.778 50.000 0.00 0.00 34.39 5.36
3240 3339 1.075601 AAACTTCCTCCTGATGGGCA 58.924 50.000 0.00 0.00 34.39 5.36
3244 3343 1.424302 CTTCCTCCTGATGGGCATCAT 59.576 52.381 0.00 0.00 45.74 2.45
3253 3352 1.683943 ATGGGCATCATCAAGAACGG 58.316 50.000 0.00 0.00 0.00 4.44
3254 3353 0.394216 TGGGCATCATCAAGAACGGG 60.394 55.000 0.00 0.00 0.00 5.28
3255 3354 1.728490 GGGCATCATCAAGAACGGGC 61.728 60.000 0.00 0.00 0.00 6.13
3256 3355 1.031571 GGCATCATCAAGAACGGGCA 61.032 55.000 0.00 0.00 0.00 5.36
3257 3356 0.379669 GCATCATCAAGAACGGGCAG 59.620 55.000 0.00 0.00 0.00 4.85
3258 3357 1.019673 CATCATCAAGAACGGGCAGG 58.980 55.000 0.00 0.00 0.00 4.85
3260 3359 0.036388 TCATCAAGAACGGGCAGGAC 60.036 55.000 0.00 0.00 0.00 3.85
3261 3360 1.079127 ATCAAGAACGGGCAGGACG 60.079 57.895 0.00 0.00 37.36 4.79
3264 3363 2.504274 AAGAACGGGCAGGACGTCA 61.504 57.895 18.91 0.00 44.83 4.35
3269 3368 3.626924 GGGCAGGACGTCACCACT 61.627 66.667 18.91 1.61 0.00 4.00
3270 3369 2.357517 GGCAGGACGTCACCACTG 60.358 66.667 18.91 15.66 0.00 3.66
3272 3371 2.357517 CAGGACGTCACCACTGCC 60.358 66.667 18.91 0.00 0.00 4.85
3274 3373 2.665185 GGACGTCACCACTGCCAC 60.665 66.667 18.91 0.00 0.00 5.01
3275 3374 2.665185 GACGTCACCACTGCCACC 60.665 66.667 11.55 0.00 0.00 4.61
3276 3375 4.250305 ACGTCACCACTGCCACCC 62.250 66.667 0.00 0.00 0.00 4.61
3277 3376 3.941188 CGTCACCACTGCCACCCT 61.941 66.667 0.00 0.00 0.00 4.34
3279 3378 3.569210 TCACCACTGCCACCCTGG 61.569 66.667 0.00 0.00 41.55 4.45
3281 3380 2.532715 ACCACTGCCACCCTGGAT 60.533 61.111 0.00 0.00 40.96 3.41
3282 3381 2.044650 CCACTGCCACCCTGGATG 60.045 66.667 0.00 0.00 40.96 3.51
3283 3382 2.753043 CACTGCCACCCTGGATGC 60.753 66.667 0.00 0.00 40.96 3.91
3284 3383 4.052518 ACTGCCACCCTGGATGCC 62.053 66.667 0.00 0.00 40.96 4.40
3285 3384 3.736224 CTGCCACCCTGGATGCCT 61.736 66.667 0.00 0.00 40.96 4.75
3286 3385 3.267233 TGCCACCCTGGATGCCTT 61.267 61.111 0.00 0.00 40.96 4.35
3287 3386 2.440980 GCCACCCTGGATGCCTTC 60.441 66.667 0.00 0.00 40.96 3.46
3288 3387 2.124570 CCACCCTGGATGCCTTCG 60.125 66.667 0.00 0.00 40.96 3.79
3289 3388 2.825836 CACCCTGGATGCCTTCGC 60.826 66.667 0.00 0.00 0.00 4.70
3290 3389 3.011517 ACCCTGGATGCCTTCGCT 61.012 61.111 0.00 0.00 35.36 4.93
3291 3390 2.515523 CCCTGGATGCCTTCGCTG 60.516 66.667 0.00 0.00 35.36 5.18
3292 3391 2.270205 CCTGGATGCCTTCGCTGT 59.730 61.111 0.00 0.00 35.36 4.40
3293 3392 1.522092 CCTGGATGCCTTCGCTGTA 59.478 57.895 0.00 0.00 35.36 2.74
3294 3393 0.107703 CCTGGATGCCTTCGCTGTAA 60.108 55.000 0.00 0.00 35.36 2.41
3295 3394 1.678728 CCTGGATGCCTTCGCTGTAAA 60.679 52.381 0.00 0.00 35.36 2.01
3296 3395 1.667724 CTGGATGCCTTCGCTGTAAAG 59.332 52.381 0.00 0.00 35.36 1.85
3297 3396 1.003118 TGGATGCCTTCGCTGTAAAGT 59.997 47.619 0.00 0.00 35.36 2.66
3298 3397 2.084546 GGATGCCTTCGCTGTAAAGTT 58.915 47.619 0.00 0.00 35.36 2.66
3299 3398 2.096013 GGATGCCTTCGCTGTAAAGTTC 59.904 50.000 0.00 0.00 35.36 3.01
3303 3402 3.003275 TGCCTTCGCTGTAAAGTTCAAAG 59.997 43.478 0.00 0.00 35.36 2.77
3305 3404 4.611581 GCCTTCGCTGTAAAGTTCAAAGAG 60.612 45.833 0.00 0.00 0.00 2.85
3307 3406 3.462982 TCGCTGTAAAGTTCAAAGAGCA 58.537 40.909 0.00 0.00 0.00 4.26
3308 3407 3.494626 TCGCTGTAAAGTTCAAAGAGCAG 59.505 43.478 0.00 0.00 0.00 4.24
3309 3408 3.559504 GCTGTAAAGTTCAAAGAGCAGC 58.440 45.455 0.00 0.00 40.66 5.25
3310 3409 3.251972 GCTGTAAAGTTCAAAGAGCAGCT 59.748 43.478 0.00 0.00 43.08 4.24
3314 3413 2.947127 AGTTCAAAGAGCAGCTTCCT 57.053 45.000 0.00 0.00 35.24 3.36
3316 3415 1.809547 GTTCAAAGAGCAGCTTCCTCC 59.190 52.381 0.00 0.00 35.24 4.30
3318 3417 1.002888 TCAAAGAGCAGCTTCCTCCTG 59.997 52.381 0.00 6.17 35.24 3.86
3319 3418 1.002888 CAAAGAGCAGCTTCCTCCTGA 59.997 52.381 0.00 0.00 35.24 3.86
3320 3419 1.582389 AAGAGCAGCTTCCTCCTGAT 58.418 50.000 0.00 0.00 32.03 2.90
3321 3420 0.831966 AGAGCAGCTTCCTCCTGATG 59.168 55.000 0.00 0.00 32.03 3.07
3322 3421 0.540923 GAGCAGCTTCCTCCTGATGT 59.459 55.000 0.00 0.00 32.03 3.06
3323 3422 1.759445 GAGCAGCTTCCTCCTGATGTA 59.241 52.381 0.00 0.00 32.03 2.29
3324 3423 2.169352 GAGCAGCTTCCTCCTGATGTAA 59.831 50.000 0.00 0.00 32.03 2.41
3325 3424 2.776536 AGCAGCTTCCTCCTGATGTAAT 59.223 45.455 0.00 0.00 32.03 1.89
3327 3426 3.314635 GCAGCTTCCTCCTGATGTAATTG 59.685 47.826 0.00 0.00 32.03 2.32
3330 3429 3.629398 GCTTCCTCCTGATGTAATTGTGG 59.371 47.826 0.00 0.00 0.00 4.17
3331 3430 3.281727 TCCTCCTGATGTAATTGTGGC 57.718 47.619 0.00 0.00 0.00 5.01
3338 3530 4.201657 CTGATGTAATTGTGGCCATGAGA 58.798 43.478 9.72 0.00 0.00 3.27
3340 3532 3.998913 TGTAATTGTGGCCATGAGAGA 57.001 42.857 9.72 0.00 0.00 3.10
3342 3534 3.264193 TGTAATTGTGGCCATGAGAGAGT 59.736 43.478 9.72 0.00 0.00 3.24
3349 3541 2.639347 TGGCCATGAGAGAGTTCTTTGA 59.361 45.455 0.00 0.00 32.53 2.69
3350 3542 3.269178 GGCCATGAGAGAGTTCTTTGAG 58.731 50.000 0.00 0.00 32.53 3.02
3351 3543 2.677337 GCCATGAGAGAGTTCTTTGAGC 59.323 50.000 0.00 0.00 32.53 4.26
3352 3544 3.619487 GCCATGAGAGAGTTCTTTGAGCT 60.619 47.826 0.00 0.00 32.53 4.09
3354 3546 5.350633 CCATGAGAGAGTTCTTTGAGCTAG 58.649 45.833 0.00 0.00 32.53 3.42
3356 3548 5.637006 TGAGAGAGTTCTTTGAGCTAGAC 57.363 43.478 0.00 0.00 32.53 2.59
3359 3551 6.210385 TGAGAGAGTTCTTTGAGCTAGACAAT 59.790 38.462 0.00 0.00 32.53 2.71
3360 3552 6.397272 AGAGAGTTCTTTGAGCTAGACAATG 58.603 40.000 0.00 2.15 0.00 2.82
3362 3554 4.583871 AGTTCTTTGAGCTAGACAATGGG 58.416 43.478 0.00 0.00 0.00 4.00
3363 3555 3.634397 TCTTTGAGCTAGACAATGGGG 57.366 47.619 0.00 0.00 0.00 4.96
3364 3556 2.019984 CTTTGAGCTAGACAATGGGGC 58.980 52.381 0.00 0.00 0.00 5.80
3366 3558 0.543277 TGAGCTAGACAATGGGGCTG 59.457 55.000 0.00 0.00 33.13 4.85
3369 3561 2.170607 GAGCTAGACAATGGGGCTGTTA 59.829 50.000 0.00 0.00 33.13 2.41
3370 3562 2.092914 AGCTAGACAATGGGGCTGTTAC 60.093 50.000 0.00 0.00 31.68 2.50
3371 3563 2.355716 GCTAGACAATGGGGCTGTTACA 60.356 50.000 0.00 0.00 0.00 2.41
3372 3564 2.496899 AGACAATGGGGCTGTTACAG 57.503 50.000 8.18 8.18 34.12 2.74
3391 4406 0.179062 GCGGTGGAAGATGCTCTGAT 60.179 55.000 0.00 0.00 0.00 2.90
3392 4407 1.863267 CGGTGGAAGATGCTCTGATC 58.137 55.000 0.00 0.00 0.00 2.92
3393 4408 1.863267 GGTGGAAGATGCTCTGATCG 58.137 55.000 0.00 0.00 0.00 3.69
3394 4409 1.410517 GGTGGAAGATGCTCTGATCGA 59.589 52.381 0.00 0.00 0.00 3.59
3395 4410 2.545532 GGTGGAAGATGCTCTGATCGAG 60.546 54.545 9.37 9.37 42.88 4.04
3405 4420 0.749049 TCTGATCGAGCATGGTGGAG 59.251 55.000 14.93 2.46 0.00 3.86
3406 4421 0.879400 CTGATCGAGCATGGTGGAGC 60.879 60.000 16.85 16.85 0.00 4.70
3407 4422 1.953138 GATCGAGCATGGTGGAGCG 60.953 63.158 14.93 6.58 35.48 5.03
3408 4423 3.451556 ATCGAGCATGGTGGAGCGG 62.452 63.158 14.93 0.00 35.48 5.52
3410 4425 4.864334 GAGCATGGTGGAGCGGGG 62.864 72.222 0.00 0.00 35.48 5.73
3425 4440 4.436998 GGGGTCCTCGACGCTGTG 62.437 72.222 8.50 0.00 43.54 3.66
3426 4441 4.436998 GGGTCCTCGACGCTGTGG 62.437 72.222 1.92 0.00 41.34 4.17
3427 4442 4.436998 GGTCCTCGACGCTGTGGG 62.437 72.222 0.00 0.00 32.65 4.61
3428 4443 3.371063 GTCCTCGACGCTGTGGGA 61.371 66.667 0.00 0.00 0.00 4.37
3429 4444 3.062466 TCCTCGACGCTGTGGGAG 61.062 66.667 0.00 5.02 0.00 4.30
3430 4445 4.803426 CCTCGACGCTGTGGGAGC 62.803 72.222 6.16 0.00 45.20 4.70
3447 4462 2.434884 CAGATGTTGCCGCGGACT 60.435 61.111 33.48 14.00 0.00 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
26 27 1.074566 AGCAGGACCCTTCCAGAAAAG 59.925 52.381 0.00 0.00 45.72 2.27
29 30 1.078823 TCTAGCAGGACCCTTCCAGAA 59.921 52.381 0.00 0.00 45.72 3.02
38 39 2.362397 TGATTCGACATCTAGCAGGACC 59.638 50.000 8.41 0.00 0.00 4.46
49 53 6.183360 CCTTTGTGCTTCTAATGATTCGACAT 60.183 38.462 0.00 0.00 0.00 3.06
65 69 0.179029 AACCGTGCTACCTTTGTGCT 60.179 50.000 0.00 0.00 0.00 4.40
81 85 4.401202 TCCCACAAGAAAACAGAGAAAACC 59.599 41.667 0.00 0.00 0.00 3.27
94 99 2.777692 GGATCCCAGTATCCCACAAGAA 59.222 50.000 0.00 0.00 39.74 2.52
95 100 2.022035 AGGATCCCAGTATCCCACAAGA 60.022 50.000 8.55 0.00 45.74 3.02
96 101 2.412591 AGGATCCCAGTATCCCACAAG 58.587 52.381 8.55 0.00 45.74 3.16
99 104 4.430441 AGATTAGGATCCCAGTATCCCAC 58.570 47.826 8.55 0.00 45.74 4.61
100 105 4.109600 TGAGATTAGGATCCCAGTATCCCA 59.890 45.833 8.55 0.87 45.74 4.37
101 106 4.689062 TGAGATTAGGATCCCAGTATCCC 58.311 47.826 8.55 0.00 45.74 3.85
103 108 7.125507 ACATGATGAGATTAGGATCCCAGTATC 59.874 40.741 8.55 6.52 32.44 2.24
104 109 6.964679 ACATGATGAGATTAGGATCCCAGTAT 59.035 38.462 8.55 0.00 32.44 2.12
105 110 6.212187 CACATGATGAGATTAGGATCCCAGTA 59.788 42.308 8.55 0.00 32.44 2.74
106 111 5.012871 CACATGATGAGATTAGGATCCCAGT 59.987 44.000 8.55 0.00 32.44 4.00
107 112 5.247792 TCACATGATGAGATTAGGATCCCAG 59.752 44.000 8.55 0.00 32.44 4.45
133 138 1.425066 ACAATCCAGCAAGAGGGACAA 59.575 47.619 0.00 0.00 35.67 3.18
146 151 0.390603 CGGCGTCTACCAACAATCCA 60.391 55.000 0.00 0.00 0.00 3.41
151 156 0.038892 GAAGACGGCGTCTACCAACA 60.039 55.000 39.15 0.00 42.59 3.33
160 165 1.452651 TATCGGGAGAAGACGGCGT 60.453 57.895 14.65 14.65 45.37 5.68
186 191 3.576982 TGAAACCGTGATCACCTCTAACT 59.423 43.478 20.03 0.00 0.00 2.24
196 201 4.201724 GCTATGACTTGTGAAACCGTGATC 60.202 45.833 0.00 0.00 34.36 2.92
201 206 2.333926 TCGCTATGACTTGTGAAACCG 58.666 47.619 0.00 0.00 34.36 4.44
209 214 3.801050 CAGGTCTGAATCGCTATGACTTG 59.199 47.826 0.00 0.00 0.00 3.16
220 225 5.163322 ACTCCTTCATCATCAGGTCTGAATC 60.163 44.000 4.67 0.00 43.58 2.52
227 232 3.448934 AGTGACTCCTTCATCATCAGGT 58.551 45.455 0.00 0.00 36.32 4.00
228 233 4.484537 AAGTGACTCCTTCATCATCAGG 57.515 45.455 0.00 0.00 36.32 3.86
259 265 9.230122 TGCATGTAATTCAGAGTTCAAAGATAA 57.770 29.630 0.00 0.00 0.00 1.75
260 266 8.791327 TGCATGTAATTCAGAGTTCAAAGATA 57.209 30.769 0.00 0.00 0.00 1.98
277 283 7.335627 ACAATTACTACTAAGCCTGCATGTAA 58.664 34.615 0.00 0.00 0.00 2.41
279 285 5.745227 ACAATTACTACTAAGCCTGCATGT 58.255 37.500 0.00 0.00 0.00 3.21
289 295 9.127277 AGGAGCAAACAAAACAATTACTACTAA 57.873 29.630 0.00 0.00 0.00 2.24
357 367 9.424319 TGAATGATTGAAGAAACTACAGTCTAC 57.576 33.333 0.00 0.00 0.00 2.59
361 371 9.950496 AGTATGAATGATTGAAGAAACTACAGT 57.050 29.630 0.00 0.00 0.00 3.55
582 592 6.238842 CCACTTTGAGCAATATATTCAGGTGG 60.239 42.308 16.68 16.68 38.66 4.61
583 593 6.732154 CCACTTTGAGCAATATATTCAGGTG 58.268 40.000 0.00 5.03 0.00 4.00
584 594 5.300286 GCCACTTTGAGCAATATATTCAGGT 59.700 40.000 0.00 0.00 0.00 4.00
585 595 5.278660 GGCCACTTTGAGCAATATATTCAGG 60.279 44.000 0.00 0.00 0.00 3.86
586 596 5.300034 TGGCCACTTTGAGCAATATATTCAG 59.700 40.000 0.00 0.00 0.00 3.02
587 597 5.199723 TGGCCACTTTGAGCAATATATTCA 58.800 37.500 0.00 0.00 0.00 2.57
588 598 5.772825 TGGCCACTTTGAGCAATATATTC 57.227 39.130 0.00 0.00 0.00 1.75
589 599 6.543430 TTTGGCCACTTTGAGCAATATATT 57.457 33.333 3.88 0.00 0.00 1.28
590 600 6.543430 TTTTGGCCACTTTGAGCAATATAT 57.457 33.333 3.88 0.00 0.00 0.86
591 601 5.991933 TTTTGGCCACTTTGAGCAATATA 57.008 34.783 3.88 0.00 0.00 0.86
592 602 4.888326 TTTTGGCCACTTTGAGCAATAT 57.112 36.364 3.88 0.00 0.00 1.28
593 603 4.567971 CATTTTGGCCACTTTGAGCAATA 58.432 39.130 3.88 0.00 0.00 1.90
594 604 3.404899 CATTTTGGCCACTTTGAGCAAT 58.595 40.909 3.88 0.00 0.00 3.56
595 605 2.836262 CATTTTGGCCACTTTGAGCAA 58.164 42.857 3.88 0.00 0.00 3.91
596 606 1.540797 GCATTTTGGCCACTTTGAGCA 60.541 47.619 3.88 0.00 0.00 4.26
597 607 1.150827 GCATTTTGGCCACTTTGAGC 58.849 50.000 3.88 0.89 0.00 4.26
607 617 2.559440 TCAAACACTTGGCATTTTGGC 58.441 42.857 9.92 0.00 44.03 4.52
608 618 3.747529 GGATCAAACACTTGGCATTTTGG 59.252 43.478 0.00 0.00 33.01 3.28
609 619 4.378774 TGGATCAAACACTTGGCATTTTG 58.621 39.130 0.00 0.00 33.01 2.44
610 620 4.101430 ACTGGATCAAACACTTGGCATTTT 59.899 37.500 0.00 0.00 33.01 1.82
611 621 3.642848 ACTGGATCAAACACTTGGCATTT 59.357 39.130 0.00 0.00 33.01 2.32
612 622 3.233507 ACTGGATCAAACACTTGGCATT 58.766 40.909 0.00 0.00 33.01 3.56
613 623 2.880443 ACTGGATCAAACACTTGGCAT 58.120 42.857 0.00 0.00 33.01 4.40
614 624 2.363306 ACTGGATCAAACACTTGGCA 57.637 45.000 0.00 0.00 33.01 4.92
615 625 3.733443 AAACTGGATCAAACACTTGGC 57.267 42.857 0.00 0.00 33.01 4.52
616 626 7.393234 TCCTTATAAACTGGATCAAACACTTGG 59.607 37.037 0.00 0.00 33.01 3.61
617 627 8.335532 TCCTTATAAACTGGATCAAACACTTG 57.664 34.615 0.00 0.00 0.00 3.16
618 628 8.934023 TTCCTTATAAACTGGATCAAACACTT 57.066 30.769 0.00 0.00 0.00 3.16
619 629 8.934023 TTTCCTTATAAACTGGATCAAACACT 57.066 30.769 0.00 0.00 0.00 3.55
620 630 9.406828 GTTTTCCTTATAAACTGGATCAAACAC 57.593 33.333 11.25 0.00 33.87 3.32
621 631 8.581578 GGTTTTCCTTATAAACTGGATCAAACA 58.418 33.333 14.95 0.00 34.66 2.83
622 632 7.753580 CGGTTTTCCTTATAAACTGGATCAAAC 59.246 37.037 0.00 9.20 37.92 2.93
623 633 7.822658 CGGTTTTCCTTATAAACTGGATCAAA 58.177 34.615 0.00 0.00 37.92 2.69
624 634 7.385778 CGGTTTTCCTTATAAACTGGATCAA 57.614 36.000 0.00 0.00 37.92 2.57
625 635 6.995511 CGGTTTTCCTTATAAACTGGATCA 57.004 37.500 0.00 0.00 37.92 2.92
630 640 5.813672 TCGATCCGGTTTTCCTTATAAACTG 59.186 40.000 0.00 0.00 40.12 3.16
631 641 5.981174 TCGATCCGGTTTTCCTTATAAACT 58.019 37.500 0.00 0.00 36.12 2.66
632 642 6.667007 TTCGATCCGGTTTTCCTTATAAAC 57.333 37.500 0.00 0.00 37.95 2.01
633 643 6.880529 ACTTTCGATCCGGTTTTCCTTATAAA 59.119 34.615 0.00 0.00 37.95 1.40
634 644 6.408869 ACTTTCGATCCGGTTTTCCTTATAA 58.591 36.000 0.00 0.00 37.95 0.98
635 645 5.981174 ACTTTCGATCCGGTTTTCCTTATA 58.019 37.500 0.00 0.00 37.95 0.98
636 646 4.840271 ACTTTCGATCCGGTTTTCCTTAT 58.160 39.130 0.00 0.00 37.95 1.73
637 647 4.276058 ACTTTCGATCCGGTTTTCCTTA 57.724 40.909 0.00 0.00 37.95 2.69
638 648 3.136009 ACTTTCGATCCGGTTTTCCTT 57.864 42.857 0.00 0.00 37.95 3.36
639 649 2.853235 ACTTTCGATCCGGTTTTCCT 57.147 45.000 0.00 0.00 37.95 3.36
640 650 3.593096 ACTACTTTCGATCCGGTTTTCC 58.407 45.455 0.00 0.00 0.00 3.13
641 651 5.405797 AGTACTACTTTCGATCCGGTTTTC 58.594 41.667 0.00 0.00 0.00 2.29
642 652 5.397142 AGTACTACTTTCGATCCGGTTTT 57.603 39.130 0.00 0.00 0.00 2.43
643 653 5.397142 AAGTACTACTTTCGATCCGGTTT 57.603 39.130 0.00 0.00 34.11 3.27
644 654 6.238869 GGATAAGTACTACTTTCGATCCGGTT 60.239 42.308 6.77 0.00 39.51 4.44
645 655 5.240403 GGATAAGTACTACTTTCGATCCGGT 59.760 44.000 6.77 0.00 39.51 5.28
646 656 5.472820 AGGATAAGTACTACTTTCGATCCGG 59.527 44.000 16.78 0.00 41.98 5.14
647 657 6.557291 AGGATAAGTACTACTTTCGATCCG 57.443 41.667 16.78 0.00 41.98 4.18
676 686 8.700644 GGCAGACACAGATTTAATAATACGTAG 58.299 37.037 0.08 0.00 0.00 3.51
697 707 4.640771 AGTAACCTTCAGATTTGGCAGA 57.359 40.909 0.00 0.00 0.00 4.26
790 806 3.119316 TGGTCTCGCAGAAGAAATCTCTC 60.119 47.826 0.00 0.00 35.73 3.20
864 883 2.277591 TTGATGCAGGCAAGGTGGC 61.278 57.895 0.00 0.00 44.10 5.01
993 1027 6.994496 TCCATGCCTTCAAGAGTATAAATCAG 59.006 38.462 0.00 0.00 0.00 2.90
995 1029 7.220030 TCTCCATGCCTTCAAGAGTATAAATC 58.780 38.462 0.00 0.00 31.96 2.17
996 1030 7.141758 TCTCCATGCCTTCAAGAGTATAAAT 57.858 36.000 0.00 0.00 31.96 1.40
1109 1152 0.666577 CGACACCTCGGTTTGACTCC 60.667 60.000 0.00 0.00 36.16 3.85
1215 1258 2.462889 CTGAACAATGCTTTTGTGCGT 58.537 42.857 6.40 0.00 35.36 5.24
1784 1827 6.052360 GGTTGACTCCTTTATCTTCTGGATC 58.948 44.000 0.00 0.00 35.98 3.36
1805 1848 0.109913 GACCTTTCCGGAACCAGGTT 59.890 55.000 31.85 20.15 39.90 3.50
1888 1946 2.359230 GGCTGTTCTTCCTGCGCT 60.359 61.111 9.73 0.00 0.00 5.92
1923 1981 3.743396 GCATTTAAATTTGTCACCGCCAA 59.257 39.130 0.00 0.00 0.00 4.52
2028 2086 1.303155 AGGCAGGCTGTTCTGAAGC 60.303 57.895 17.16 0.00 40.06 3.86
2060 2118 3.050275 GCGACGGCTTCCAGCTTT 61.050 61.111 0.00 0.00 41.99 3.51
2120 2178 2.084610 TCCTCACTTGCATCTTGACG 57.915 50.000 0.00 0.00 0.00 4.35
2253 2311 0.764890 CGGATGCCCTCCTCCAATAA 59.235 55.000 1.38 0.00 42.47 1.40
2328 2386 5.426833 AGACATCTAAAGCTACCCTTGATGT 59.573 40.000 13.58 13.58 43.91 3.06
2330 2388 5.663106 TGAGACATCTAAAGCTACCCTTGAT 59.337 40.000 0.00 0.00 33.01 2.57
2385 2443 5.523369 ACACAATTACTTGAGCTGAAAAGC 58.477 37.500 0.00 0.00 36.20 3.51
2491 2551 2.228059 CAGCTTAATCCATGGCCTCAG 58.772 52.381 6.96 1.56 0.00 3.35
2497 2557 4.866486 GCAAAGAAACAGCTTAATCCATGG 59.134 41.667 4.97 4.97 0.00 3.66
2600 2660 1.943968 GCTCGGCACAGTATTTGACCA 60.944 52.381 0.00 0.00 0.00 4.02
2647 2707 7.896811 TCAGTATCCAGTGATATAATGACACC 58.103 38.462 9.93 0.00 35.94 4.16
2949 3046 5.233050 CGTGAAGTACATTGATCCTGCTTAG 59.767 44.000 0.00 0.00 0.00 2.18
2950 3047 5.109210 CGTGAAGTACATTGATCCTGCTTA 58.891 41.667 0.00 0.00 0.00 3.09
3006 3104 2.154462 TCTTTAACTTGCAGCTGGAGC 58.846 47.619 17.12 0.87 42.49 4.70
3012 3110 3.304726 GGACAACCTCTTTAACTTGCAGC 60.305 47.826 0.00 0.00 0.00 5.25
3225 3324 3.025986 TGATGCCCATCAGGAGGAA 57.974 52.632 6.85 0.00 42.42 3.36
3234 3333 1.683943 CCGTTCTTGATGATGCCCAT 58.316 50.000 0.00 0.00 38.43 4.00
3235 3334 0.394216 CCCGTTCTTGATGATGCCCA 60.394 55.000 0.00 0.00 0.00 5.36
3236 3335 1.728490 GCCCGTTCTTGATGATGCCC 61.728 60.000 0.00 0.00 0.00 5.36
3237 3336 1.031571 TGCCCGTTCTTGATGATGCC 61.032 55.000 0.00 0.00 0.00 4.40
3238 3337 0.379669 CTGCCCGTTCTTGATGATGC 59.620 55.000 0.00 0.00 0.00 3.91
3239 3338 1.019673 CCTGCCCGTTCTTGATGATG 58.980 55.000 0.00 0.00 0.00 3.07
3240 3339 0.911769 TCCTGCCCGTTCTTGATGAT 59.088 50.000 0.00 0.00 0.00 2.45
3244 3343 2.342279 CGTCCTGCCCGTTCTTGA 59.658 61.111 0.00 0.00 0.00 3.02
3245 3344 2.027625 GACGTCCTGCCCGTTCTTG 61.028 63.158 3.51 0.00 38.92 3.02
3247 3346 2.915659 TGACGTCCTGCCCGTTCT 60.916 61.111 14.12 0.00 38.92 3.01
3248 3347 2.737376 GTGACGTCCTGCCCGTTC 60.737 66.667 14.12 0.00 38.92 3.95
3253 3352 2.357517 CAGTGGTGACGTCCTGCC 60.358 66.667 14.12 13.00 0.00 4.85
3254 3353 3.044305 GCAGTGGTGACGTCCTGC 61.044 66.667 22.77 22.77 40.39 4.85
3255 3354 2.357517 GGCAGTGGTGACGTCCTG 60.358 66.667 14.12 13.64 0.00 3.86
3256 3355 2.842462 TGGCAGTGGTGACGTCCT 60.842 61.111 14.12 0.00 32.20 3.85
3257 3356 2.665185 GTGGCAGTGGTGACGTCC 60.665 66.667 14.12 4.20 32.20 4.79
3258 3357 2.665185 GGTGGCAGTGGTGACGTC 60.665 66.667 9.11 9.11 32.20 4.34
3260 3359 3.941188 AGGGTGGCAGTGGTGACG 61.941 66.667 0.00 0.00 32.20 4.35
3261 3360 2.281761 CAGGGTGGCAGTGGTGAC 60.282 66.667 0.00 0.00 0.00 3.67
3264 3363 2.532715 ATCCAGGGTGGCAGTGGT 60.533 61.111 9.62 0.00 37.47 4.16
3267 3366 4.052518 GGCATCCAGGGTGGCAGT 62.053 66.667 21.56 0.00 41.35 4.40
3268 3367 3.292481 AAGGCATCCAGGGTGGCAG 62.292 63.158 27.50 0.00 43.86 4.85
3269 3368 3.267233 AAGGCATCCAGGGTGGCA 61.267 61.111 27.50 0.00 43.86 4.92
3270 3369 2.440980 GAAGGCATCCAGGGTGGC 60.441 66.667 18.98 18.98 41.96 5.01
3272 3371 2.825836 GCGAAGGCATCCAGGGTG 60.826 66.667 0.00 0.00 39.62 4.61
3274 3373 1.971505 TACAGCGAAGGCATCCAGGG 61.972 60.000 0.00 0.00 43.41 4.45
3275 3374 0.107703 TTACAGCGAAGGCATCCAGG 60.108 55.000 0.00 0.00 43.41 4.45
3276 3375 1.667724 CTTTACAGCGAAGGCATCCAG 59.332 52.381 0.00 0.00 43.41 3.86
3277 3376 1.003118 ACTTTACAGCGAAGGCATCCA 59.997 47.619 0.00 0.00 43.41 3.41
3279 3378 2.742053 TGAACTTTACAGCGAAGGCATC 59.258 45.455 0.00 0.00 43.41 3.91
3281 3380 2.248280 TGAACTTTACAGCGAAGGCA 57.752 45.000 0.00 0.00 43.41 4.75
3282 3381 3.250040 TCTTTGAACTTTACAGCGAAGGC 59.750 43.478 0.00 0.00 40.37 4.35
3283 3382 4.611581 GCTCTTTGAACTTTACAGCGAAGG 60.612 45.833 0.00 0.00 0.00 3.46
3284 3383 4.024893 TGCTCTTTGAACTTTACAGCGAAG 60.025 41.667 0.00 0.00 0.00 3.79
3285 3384 3.874543 TGCTCTTTGAACTTTACAGCGAA 59.125 39.130 0.00 0.00 0.00 4.70
3286 3385 3.462982 TGCTCTTTGAACTTTACAGCGA 58.537 40.909 0.00 0.00 0.00 4.93
3287 3386 3.803555 CTGCTCTTTGAACTTTACAGCG 58.196 45.455 0.00 0.00 0.00 5.18
3288 3387 3.559504 GCTGCTCTTTGAACTTTACAGC 58.440 45.455 0.00 0.00 42.00 4.40
3289 3388 5.429957 AAGCTGCTCTTTGAACTTTACAG 57.570 39.130 1.00 0.00 0.00 2.74
3290 3389 4.275936 GGAAGCTGCTCTTTGAACTTTACA 59.724 41.667 1.00 0.00 34.56 2.41
3291 3390 4.517075 AGGAAGCTGCTCTTTGAACTTTAC 59.483 41.667 1.00 0.00 34.56 2.01
3292 3391 4.718961 AGGAAGCTGCTCTTTGAACTTTA 58.281 39.130 1.00 0.00 34.56 1.85
3293 3392 3.560105 AGGAAGCTGCTCTTTGAACTTT 58.440 40.909 1.00 0.00 34.56 2.66
3294 3393 3.145286 GAGGAAGCTGCTCTTTGAACTT 58.855 45.455 1.00 0.00 34.56 2.66
3295 3394 2.551938 GGAGGAAGCTGCTCTTTGAACT 60.552 50.000 1.00 0.00 35.01 3.01
3296 3395 1.809547 GGAGGAAGCTGCTCTTTGAAC 59.190 52.381 1.00 0.00 35.01 3.18
3297 3396 1.701847 AGGAGGAAGCTGCTCTTTGAA 59.298 47.619 1.00 0.00 35.01 2.69
3298 3397 1.002888 CAGGAGGAAGCTGCTCTTTGA 59.997 52.381 1.00 0.00 35.01 2.69
3299 3398 1.002888 TCAGGAGGAAGCTGCTCTTTG 59.997 52.381 1.00 0.59 35.01 2.77
3303 3402 0.540923 ACATCAGGAGGAAGCTGCTC 59.459 55.000 1.00 0.00 33.75 4.26
3305 3404 2.698855 TTACATCAGGAGGAAGCTGC 57.301 50.000 0.00 0.00 0.00 5.25
3307 3406 4.521146 CACAATTACATCAGGAGGAAGCT 58.479 43.478 0.00 0.00 0.00 3.74
3308 3407 3.629398 CCACAATTACATCAGGAGGAAGC 59.371 47.826 0.00 0.00 0.00 3.86
3309 3408 3.629398 GCCACAATTACATCAGGAGGAAG 59.371 47.826 0.00 0.00 0.00 3.46
3310 3409 3.620488 GCCACAATTACATCAGGAGGAA 58.380 45.455 0.00 0.00 0.00 3.36
3314 3413 3.053768 TCATGGCCACAATTACATCAGGA 60.054 43.478 8.16 0.00 0.00 3.86
3316 3415 4.201657 TCTCATGGCCACAATTACATCAG 58.798 43.478 8.16 0.00 0.00 2.90
3318 3417 4.454678 TCTCTCATGGCCACAATTACATC 58.545 43.478 8.16 0.00 0.00 3.06
3319 3418 4.080129 ACTCTCTCATGGCCACAATTACAT 60.080 41.667 8.16 0.00 0.00 2.29
3320 3419 3.264193 ACTCTCTCATGGCCACAATTACA 59.736 43.478 8.16 0.00 0.00 2.41
3321 3420 3.878778 ACTCTCTCATGGCCACAATTAC 58.121 45.455 8.16 0.00 0.00 1.89
3322 3421 4.225942 AGAACTCTCTCATGGCCACAATTA 59.774 41.667 8.16 0.00 0.00 1.40
3323 3422 3.009916 AGAACTCTCTCATGGCCACAATT 59.990 43.478 8.16 0.00 0.00 2.32
3324 3423 2.575279 AGAACTCTCTCATGGCCACAAT 59.425 45.455 8.16 0.00 0.00 2.71
3325 3424 1.980765 AGAACTCTCTCATGGCCACAA 59.019 47.619 8.16 0.00 0.00 3.33
3327 3426 2.746362 CAAAGAACTCTCTCATGGCCAC 59.254 50.000 8.16 0.00 0.00 5.01
3330 3429 2.677337 GCTCAAAGAACTCTCTCATGGC 59.323 50.000 0.00 0.00 0.00 4.40
3331 3430 4.205065 AGCTCAAAGAACTCTCTCATGG 57.795 45.455 0.00 0.00 0.00 3.66
3338 3530 5.486526 CCATTGTCTAGCTCAAAGAACTCT 58.513 41.667 0.00 0.00 0.00 3.24
3340 3532 4.566488 CCCCATTGTCTAGCTCAAAGAACT 60.566 45.833 0.00 0.00 0.00 3.01
3342 3534 3.873801 GCCCCATTGTCTAGCTCAAAGAA 60.874 47.826 0.00 0.00 0.00 2.52
3349 3541 0.995024 AACAGCCCCATTGTCTAGCT 59.005 50.000 0.00 0.00 0.00 3.32
3350 3542 2.289565 GTAACAGCCCCATTGTCTAGC 58.710 52.381 0.00 0.00 0.00 3.42
3351 3543 3.535561 CTGTAACAGCCCCATTGTCTAG 58.464 50.000 0.00 0.00 0.00 2.43
3352 3544 3.627395 CTGTAACAGCCCCATTGTCTA 57.373 47.619 0.00 0.00 0.00 2.59
3364 3556 2.002586 CATCTTCCACCGCTGTAACAG 58.997 52.381 0.00 0.00 34.12 3.16
3366 3558 0.727398 GCATCTTCCACCGCTGTAAC 59.273 55.000 0.00 0.00 0.00 2.50
3369 3561 1.078848 GAGCATCTTCCACCGCTGT 60.079 57.895 0.00 0.00 34.12 4.40
3370 3562 3.805267 GAGCATCTTCCACCGCTG 58.195 61.111 0.00 0.00 34.12 5.18
3391 4406 4.147449 CCGCTCCACCATGCTCGA 62.147 66.667 0.00 0.00 0.00 4.04
3393 4408 4.864334 CCCCGCTCCACCATGCTC 62.864 72.222 0.00 0.00 0.00 4.26
3408 4423 4.436998 CACAGCGTCGAGGACCCC 62.437 72.222 9.75 0.00 0.00 4.95
3409 4424 4.436998 CCACAGCGTCGAGGACCC 62.437 72.222 9.75 0.00 0.00 4.46
3410 4425 4.436998 CCCACAGCGTCGAGGACC 62.437 72.222 9.75 0.00 0.00 4.46
3411 4426 3.343788 CTCCCACAGCGTCGAGGAC 62.344 68.421 9.75 0.27 0.00 3.85
3430 4445 2.434884 AGTCCGCGGCAACATCTG 60.435 61.111 23.51 0.00 0.00 2.90


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

AutoCloner maintained by Alex Coulton.