Multiple sequence alignment - TraesCS7D01G230600

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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 TraesCS7D01G230600 chr7D 100.000 3064 0 0 1 3064 191572046 191568983 0.000000e+00 5659.0
1 TraesCS7D01G230600 chr7D 81.548 168 30 1 2741 2908 517342625 517342791 1.480000e-28 137.0
2 TraesCS7D01G230600 chr7D 84.615 65 8 2 2928 2992 38257668 38257730 2.550000e-06 63.9
3 TraesCS7D01G230600 chr7A 92.462 2348 110 26 669 2991 200231685 200229380 0.000000e+00 3293.0
4 TraesCS7D01G230600 chr7A 96.296 54 0 1 1 54 39198833 39198782 1.510000e-13 87.9
5 TraesCS7D01G230600 chr7A 84.375 64 8 2 2930 2993 37947579 37947640 9.170000e-06 62.1
6 TraesCS7D01G230600 chr7B 87.396 2531 175 70 63 2541 336812654 336810216 0.000000e+00 2774.0
7 TraesCS7D01G230600 chr7B 79.730 222 35 9 2695 2912 82697361 82697146 5.290000e-33 152.0
8 TraesCS7D01G230600 chr7B 94.643 56 1 1 1 56 633044643 633044590 5.440000e-13 86.1
9 TraesCS7D01G230600 chr1A 80.315 254 37 9 2750 2993 202090678 202090928 2.430000e-41 180.0
10 TraesCS7D01G230600 chr5D 76.038 313 57 11 2699 2995 533002799 533003109 2.460000e-31 147.0
11 TraesCS7D01G230600 chr5D 95.000 60 1 1 1 60 164651255 164651312 3.250000e-15 93.5
12 TraesCS7D01G230600 chr5D 96.296 54 0 1 1 54 56999369 56999318 1.510000e-13 87.9
13 TraesCS7D01G230600 chr5A 82.993 147 23 2 2714 2860 482942159 482942015 6.890000e-27 132.0
14 TraesCS7D01G230600 chr6D 82.051 156 25 3 2699 2853 427717342 427717495 2.480000e-26 130.0
15 TraesCS7D01G230600 chr6D 94.737 57 1 1 1 57 36549567 36549621 1.510000e-13 87.9
16 TraesCS7D01G230600 chr3D 79.365 189 36 3 2716 2903 62916585 62916399 2.480000e-26 130.0
17 TraesCS7D01G230600 chr3D 94.828 58 1 1 1 58 540560987 540561042 4.210000e-14 89.8
18 TraesCS7D01G230600 chr1D 81.013 158 28 2 2705 2861 315618553 315618709 1.150000e-24 124.0
19 TraesCS7D01G230600 chr1D 93.333 60 2 1 1 60 365304449 365304392 1.510000e-13 87.9
20 TraesCS7D01G230600 chr1D 83.077 65 6 5 2559 2620 45262607 45262545 2.000000e-03 54.7
21 TraesCS7D01G230600 chr3B 79.762 168 26 7 2745 2908 257036459 257036296 6.940000e-22 115.0
22 TraesCS7D01G230600 chr4D 95.000 60 1 1 1 60 139307570 139307513 3.250000e-15 93.5
23 TraesCS7D01G230600 chr6A 96.296 54 0 1 1 54 539872863 539872812 1.510000e-13 87.9
24 TraesCS7D01G230600 chr6B 83.544 79 12 1 217 294 551910221 551910299 4.240000e-09 73.1


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 TraesCS7D01G230600 chr7D 191568983 191572046 3063 True 5659 5659 100.000 1 3064 1 chr7D.!!$R1 3063
1 TraesCS7D01G230600 chr7A 200229380 200231685 2305 True 3293 3293 92.462 669 2991 1 chr7A.!!$R2 2322
2 TraesCS7D01G230600 chr7B 336810216 336812654 2438 True 2774 2774 87.396 63 2541 1 chr7B.!!$R2 2478

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
943 978 0.031585 ACATACACACGTGTCGCTGT 59.968 50.0 20.49 18.06 43.74 4.4 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2756 2844 0.389948 GCACCGGTGTCAAGACTAGG 60.39 60.0 33.92 6.1 0.0 3.02 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
18 19 3.549997 CCAGGCGGCGATTTTTATG 57.450 52.632 12.98 0.00 0.00 1.90
19 20 0.594796 CCAGGCGGCGATTTTTATGC 60.595 55.000 12.98 0.00 0.00 3.14
20 21 0.594796 CAGGCGGCGATTTTTATGCC 60.595 55.000 12.98 0.00 45.39 4.40
21 22 1.733526 GGCGGCGATTTTTATGCCT 59.266 52.632 12.98 0.00 46.67 4.75
22 23 0.317854 GGCGGCGATTTTTATGCCTC 60.318 55.000 12.98 0.00 46.67 4.70
23 24 0.317854 GCGGCGATTTTTATGCCTCC 60.318 55.000 12.98 0.00 46.67 4.30
24 25 1.308998 CGGCGATTTTTATGCCTCCT 58.691 50.000 0.00 0.00 46.67 3.69
25 26 1.002468 CGGCGATTTTTATGCCTCCTG 60.002 52.381 0.00 0.00 46.67 3.86
26 27 1.338020 GGCGATTTTTATGCCTCCTGG 59.662 52.381 0.00 0.00 45.40 4.45
27 28 1.338020 GCGATTTTTATGCCTCCTGGG 59.662 52.381 0.00 0.00 38.36 4.45
28 29 2.930950 CGATTTTTATGCCTCCTGGGA 58.069 47.619 0.00 0.00 38.31 4.37
29 30 3.287222 CGATTTTTATGCCTCCTGGGAA 58.713 45.455 0.00 0.00 37.19 3.97
30 31 3.316308 CGATTTTTATGCCTCCTGGGAAG 59.684 47.826 0.00 0.00 37.19 3.46
31 32 2.826674 TTTTATGCCTCCTGGGAAGG 57.173 50.000 0.00 0.00 37.19 3.46
32 33 0.926293 TTTATGCCTCCTGGGAAGGG 59.074 55.000 3.81 0.00 37.19 3.95
33 34 0.993509 TTATGCCTCCTGGGAAGGGG 60.994 60.000 3.81 0.00 37.19 4.79
37 38 2.941025 CTCCTGGGAAGGGGCCAA 60.941 66.667 4.39 0.00 0.00 4.52
38 39 3.264845 TCCTGGGAAGGGGCCAAC 61.265 66.667 4.39 0.00 0.00 3.77
39 40 4.740822 CCTGGGAAGGGGCCAACG 62.741 72.222 4.39 0.00 0.00 4.10
40 41 4.740822 CTGGGAAGGGGCCAACGG 62.741 72.222 4.39 0.00 0.00 4.44
52 53 3.805267 CAACGGCTGGAGATGCTC 58.195 61.111 0.00 0.00 0.00 4.26
53 54 1.220206 CAACGGCTGGAGATGCTCT 59.780 57.895 0.00 0.00 0.00 4.09
54 55 0.461548 CAACGGCTGGAGATGCTCTA 59.538 55.000 0.00 0.00 0.00 2.43
55 56 1.134699 CAACGGCTGGAGATGCTCTAA 60.135 52.381 0.00 0.00 0.00 2.10
56 57 0.749649 ACGGCTGGAGATGCTCTAAG 59.250 55.000 0.00 0.00 0.00 2.18
57 58 0.599728 CGGCTGGAGATGCTCTAAGC 60.600 60.000 11.59 11.59 42.82 3.09
68 69 2.346099 GCTCTAAGCATCCGAGCTAG 57.654 55.000 9.22 0.00 45.89 3.42
89 90 1.678635 TGAAGCTCCGGCCCAAATG 60.679 57.895 0.00 0.00 39.73 2.32
101 105 3.056607 CGGCCCAAATGAAGAAGATGTTT 60.057 43.478 0.00 0.00 0.00 2.83
104 108 5.279657 GGCCCAAATGAAGAAGATGTTTTCT 60.280 40.000 0.00 0.00 39.03 2.52
118 122 8.891671 AAGATGTTTTCTGTGTATGCAAAATT 57.108 26.923 0.00 0.00 33.93 1.82
168 172 4.142271 ACTTGCACTGGAAAATTCGTCAAA 60.142 37.500 0.00 0.00 0.00 2.69
183 187 3.623960 TCGTCAAACCAAACTTCATCGTT 59.376 39.130 0.00 0.00 0.00 3.85
198 202 5.152623 TCATCGTTTGGATCTCAAGTCTT 57.847 39.130 0.00 0.00 36.62 3.01
199 203 5.171476 TCATCGTTTGGATCTCAAGTCTTC 58.829 41.667 0.00 0.00 36.62 2.87
200 204 3.926616 TCGTTTGGATCTCAAGTCTTCC 58.073 45.455 0.00 0.00 36.62 3.46
201 205 3.323691 TCGTTTGGATCTCAAGTCTTCCA 59.676 43.478 0.00 0.00 36.62 3.53
202 206 3.681897 CGTTTGGATCTCAAGTCTTCCAG 59.318 47.826 0.00 0.00 39.33 3.86
203 207 4.646572 GTTTGGATCTCAAGTCTTCCAGT 58.353 43.478 0.00 0.00 39.33 4.00
204 208 4.982241 TTGGATCTCAAGTCTTCCAGTT 57.018 40.909 0.00 0.00 39.33 3.16
205 209 4.982241 TGGATCTCAAGTCTTCCAGTTT 57.018 40.909 0.00 0.00 33.40 2.66
206 210 4.899502 TGGATCTCAAGTCTTCCAGTTTC 58.100 43.478 0.00 0.00 33.40 2.78
207 211 4.594920 TGGATCTCAAGTCTTCCAGTTTCT 59.405 41.667 0.00 0.00 33.40 2.52
208 212 5.072329 TGGATCTCAAGTCTTCCAGTTTCTT 59.928 40.000 0.00 0.00 33.40 2.52
219 223 6.863645 GTCTTCCAGTTTCTTTTCAATAAGGC 59.136 38.462 0.00 0.00 0.00 4.35
222 226 4.528206 CCAGTTTCTTTTCAATAAGGCCCT 59.472 41.667 0.00 0.00 0.00 5.19
231 235 2.378547 TCAATAAGGCCCTGTTTGGAGT 59.621 45.455 0.00 0.00 38.35 3.85
232 236 2.493278 CAATAAGGCCCTGTTTGGAGTG 59.507 50.000 0.00 0.00 38.35 3.51
233 237 0.251165 TAAGGCCCTGTTTGGAGTGC 60.251 55.000 0.00 0.00 38.35 4.40
253 257 2.678769 GCAGGAATTCAAAATGCTGGGG 60.679 50.000 7.93 0.00 35.75 4.96
257 261 4.023291 GGAATTCAAAATGCTGGGGTAGA 58.977 43.478 7.93 0.00 0.00 2.59
259 263 5.046663 GGAATTCAAAATGCTGGGGTAGAAA 60.047 40.000 7.93 0.00 0.00 2.52
261 265 5.878406 TTCAAAATGCTGGGGTAGAAAAA 57.122 34.783 0.00 0.00 0.00 1.94
262 266 5.208463 TCAAAATGCTGGGGTAGAAAAAC 57.792 39.130 0.00 0.00 0.00 2.43
263 267 4.651503 TCAAAATGCTGGGGTAGAAAAACA 59.348 37.500 0.00 0.00 0.00 2.83
264 268 5.129485 TCAAAATGCTGGGGTAGAAAAACAA 59.871 36.000 0.00 0.00 0.00 2.83
296 300 5.545588 AGATGTCATGTATCCTGAATTCCG 58.454 41.667 2.27 0.00 0.00 4.30
312 316 3.410631 TTCCGATTTGAACTAGCCACA 57.589 42.857 0.00 0.00 0.00 4.17
313 317 3.410631 TCCGATTTGAACTAGCCACAA 57.589 42.857 0.00 0.00 0.00 3.33
343 347 4.851558 GCATAACTGTCGTTTGGAAATCAC 59.148 41.667 0.00 0.00 34.59 3.06
347 351 2.734606 CTGTCGTTTGGAAATCACGCTA 59.265 45.455 0.00 0.00 30.63 4.26
371 376 5.398603 AAAACACTGAAAACATGGACACA 57.601 34.783 0.00 0.00 0.00 3.72
423 428 7.965718 TCATGTTTGATTTCCTCCAAAATTCT 58.034 30.769 0.00 0.00 34.52 2.40
424 429 8.431222 TCATGTTTGATTTCCTCCAAAATTCTT 58.569 29.630 0.00 0.00 34.52 2.52
452 458 9.565090 TGAGATACCTTCATAGGAATTTCAATG 57.435 33.333 0.00 2.24 45.05 2.82
454 460 8.727149 AGATACCTTCATAGGAATTTCAATGGA 58.273 33.333 0.00 2.86 45.05 3.41
455 461 9.354673 GATACCTTCATAGGAATTTCAATGGAA 57.645 33.333 0.00 3.30 45.05 3.53
485 491 4.836825 TGGCAATTCCTTTGTTTCAAACA 58.163 34.783 0.00 0.00 37.65 2.83
534 540 3.119352 AGGATTCGCAAGCCAATTCTTTC 60.119 43.478 6.07 0.00 40.13 2.62
536 542 1.614996 TCGCAAGCCAATTCTTTCCA 58.385 45.000 0.00 0.00 37.18 3.53
541 547 4.552572 CGCAAGCCAATTCTTTCCAAAAAC 60.553 41.667 0.00 0.00 0.00 2.43
595 614 0.390472 CCGAAGTCCTGAACCAGCTC 60.390 60.000 0.00 0.00 0.00 4.09
609 628 3.788766 GCTCGCGCGTCCATTTGT 61.789 61.111 30.98 0.00 0.00 2.83
610 629 2.860293 CTCGCGCGTCCATTTGTT 59.140 55.556 30.98 0.00 0.00 2.83
611 630 1.509787 CTCGCGCGTCCATTTGTTG 60.510 57.895 30.98 0.00 0.00 3.33
612 631 2.170260 CTCGCGCGTCCATTTGTTGT 62.170 55.000 30.98 0.00 0.00 3.32
613 632 1.369930 CGCGCGTCCATTTGTTGTT 60.370 52.632 24.19 0.00 0.00 2.83
614 633 1.327292 CGCGCGTCCATTTGTTGTTC 61.327 55.000 24.19 0.00 0.00 3.18
615 634 0.040425 GCGCGTCCATTTGTTGTTCT 60.040 50.000 8.43 0.00 0.00 3.01
617 636 2.726633 CGCGTCCATTTGTTGTTCTTT 58.273 42.857 0.00 0.00 0.00 2.52
618 637 2.467305 CGCGTCCATTTGTTGTTCTTTG 59.533 45.455 0.00 0.00 0.00 2.77
619 638 2.218530 GCGTCCATTTGTTGTTCTTTGC 59.781 45.455 0.00 0.00 0.00 3.68
620 639 3.443037 CGTCCATTTGTTGTTCTTTGCA 58.557 40.909 0.00 0.00 0.00 4.08
621 640 3.486841 CGTCCATTTGTTGTTCTTTGCAG 59.513 43.478 0.00 0.00 0.00 4.41
622 641 4.681744 GTCCATTTGTTGTTCTTTGCAGA 58.318 39.130 0.00 0.00 0.00 4.26
623 642 5.291971 GTCCATTTGTTGTTCTTTGCAGAT 58.708 37.500 0.00 0.00 0.00 2.90
624 643 5.176223 GTCCATTTGTTGTTCTTTGCAGATG 59.824 40.000 0.00 0.00 0.00 2.90
625 644 4.449743 CCATTTGTTGTTCTTTGCAGATGG 59.550 41.667 0.00 0.00 37.30 3.51
626 645 4.998671 TTTGTTGTTCTTTGCAGATGGA 57.001 36.364 0.00 0.00 0.00 3.41
627 646 4.572985 TTGTTGTTCTTTGCAGATGGAG 57.427 40.909 0.00 0.00 0.00 3.86
628 647 3.554934 TGTTGTTCTTTGCAGATGGAGT 58.445 40.909 0.00 0.00 0.00 3.85
629 648 4.713553 TGTTGTTCTTTGCAGATGGAGTA 58.286 39.130 0.00 0.00 0.00 2.59
630 649 4.756642 TGTTGTTCTTTGCAGATGGAGTAG 59.243 41.667 0.00 0.00 0.00 2.57
631 650 4.890158 TGTTCTTTGCAGATGGAGTAGA 57.110 40.909 0.00 0.00 0.00 2.59
632 651 4.569943 TGTTCTTTGCAGATGGAGTAGAC 58.430 43.478 0.00 0.00 0.00 2.59
633 652 4.284490 TGTTCTTTGCAGATGGAGTAGACT 59.716 41.667 0.00 0.00 0.00 3.24
634 653 5.221722 TGTTCTTTGCAGATGGAGTAGACTT 60.222 40.000 0.00 0.00 0.00 3.01
635 654 4.825422 TCTTTGCAGATGGAGTAGACTTG 58.175 43.478 0.00 0.00 0.00 3.16
636 655 4.528206 TCTTTGCAGATGGAGTAGACTTGA 59.472 41.667 0.00 0.00 0.00 3.02
637 656 4.462508 TTGCAGATGGAGTAGACTTGAG 57.537 45.455 0.00 0.00 0.00 3.02
638 657 2.167281 TGCAGATGGAGTAGACTTGAGC 59.833 50.000 0.00 0.00 0.00 4.26
639 658 2.167281 GCAGATGGAGTAGACTTGAGCA 59.833 50.000 0.00 0.00 0.00 4.26
640 659 3.368843 GCAGATGGAGTAGACTTGAGCAA 60.369 47.826 0.00 0.00 0.00 3.91
641 660 4.431809 CAGATGGAGTAGACTTGAGCAAG 58.568 47.826 8.60 8.60 43.79 4.01
642 661 3.450457 AGATGGAGTAGACTTGAGCAAGG 59.550 47.826 14.14 0.00 42.53 3.61
643 662 2.889512 TGGAGTAGACTTGAGCAAGGA 58.110 47.619 14.14 0.00 42.53 3.36
644 663 3.445008 TGGAGTAGACTTGAGCAAGGAT 58.555 45.455 14.14 5.21 42.53 3.24
645 664 3.196469 TGGAGTAGACTTGAGCAAGGATG 59.804 47.826 14.14 0.00 42.53 3.51
667 686 3.493129 GCGCAATTATACGTGAATCTGGA 59.507 43.478 0.30 0.00 0.00 3.86
686 717 1.746220 GATCGATCATACGGAGGGGAG 59.254 57.143 20.52 0.00 0.00 4.30
865 896 1.278127 GCTGTGCCCAAGAGTACCTTA 59.722 52.381 0.00 0.00 32.86 2.69
881 912 3.421844 ACCTTACCAAATCACAGAAGCC 58.578 45.455 0.00 0.00 0.00 4.35
891 922 2.180276 TCACAGAAGCCTAGTTCCTCC 58.820 52.381 0.00 0.00 0.00 4.30
895 926 0.833949 GAAGCCTAGTTCCTCCCCTG 59.166 60.000 0.00 0.00 0.00 4.45
906 937 1.374758 CTCCCCTGTTCTCGTGTGC 60.375 63.158 0.00 0.00 0.00 4.57
907 938 1.821061 CTCCCCTGTTCTCGTGTGCT 61.821 60.000 0.00 0.00 0.00 4.40
908 939 0.541063 TCCCCTGTTCTCGTGTGCTA 60.541 55.000 0.00 0.00 0.00 3.49
909 940 0.108615 CCCCTGTTCTCGTGTGCTAG 60.109 60.000 0.00 0.00 0.00 3.42
943 978 0.031585 ACATACACACGTGTCGCTGT 59.968 50.000 20.49 18.06 43.74 4.40
953 988 1.126113 CGTGTCGCTGTTTGATACACC 59.874 52.381 0.00 0.00 37.70 4.16
1029 1079 2.594592 GGTCAGCCAGCCACGTTT 60.595 61.111 0.00 0.00 34.09 3.60
1225 1278 2.659244 GTGTCAACGCGTTCGGGA 60.659 61.111 23.92 14.20 40.69 5.14
1550 1621 3.201708 AGGAAATCAGCAGTCAAGCCTAT 59.798 43.478 0.00 0.00 34.23 2.57
1581 1652 1.832167 GGCCACCACTTCAGCCAAA 60.832 57.895 0.00 0.00 45.07 3.28
1599 1670 0.326264 AAGACCCTCAAAGCGATGCT 59.674 50.000 0.00 0.00 42.56 3.79
1870 1943 7.915397 ACATTAATCGGTTTAGCAATGTGAATC 59.085 33.333 6.50 0.00 35.79 2.52
1877 1950 1.062525 GCAATGTGAATCCGGCGTC 59.937 57.895 6.01 0.00 0.00 5.19
1917 1990 1.478510 CGGCACTTGTCTGATCCTAGT 59.521 52.381 0.00 0.00 0.00 2.57
1918 1991 2.688446 CGGCACTTGTCTGATCCTAGTA 59.312 50.000 0.00 0.00 0.00 1.82
1919 1992 3.243234 CGGCACTTGTCTGATCCTAGTAG 60.243 52.174 0.00 0.00 0.00 2.57
2082 2155 2.209838 ACAGCGAACCGATACATCAG 57.790 50.000 0.00 0.00 0.00 2.90
2089 2162 3.488553 CGAACCGATACATCAGCACTACA 60.489 47.826 0.00 0.00 0.00 2.74
2099 2172 9.295214 GATACATCAGCACTACACATATACATC 57.705 37.037 0.00 0.00 0.00 3.06
2113 2186 6.652481 CACATATACATCCTCCCAGAATTCAC 59.348 42.308 8.44 0.00 0.00 3.18
2175 2248 5.309282 GTCCCATTCCCTAATCTTCTCATCT 59.691 44.000 0.00 0.00 0.00 2.90
2192 2270 4.682787 TCATCTTTGCTATGTACTCACCG 58.317 43.478 0.00 0.00 0.00 4.94
2245 2323 2.580470 GATGGCGTGCACTCGATCG 61.580 63.158 16.19 9.36 0.00 3.69
2297 2375 6.292919 GCACTTCATCGTCACTAGTTTCTTTT 60.293 38.462 0.00 0.00 0.00 2.27
2512 2592 2.219080 TCAGATGGCTGCATCCAAAA 57.781 45.000 14.28 0.00 42.01 2.44
2547 2627 1.060553 CACGTTGCGATGACCACATAC 59.939 52.381 0.00 0.00 36.82 2.39
2549 2629 1.635844 GTTGCGATGACCACATACGA 58.364 50.000 0.00 0.00 36.82 3.43
2551 2631 2.371910 TGCGATGACCACATACGAAA 57.628 45.000 0.00 0.00 36.82 3.46
2558 2638 6.910433 GCGATGACCACATACGAAATAATTTT 59.090 34.615 0.00 0.00 36.82 1.82
2564 2644 8.276252 ACCACATACGAAATAATTTTGTAGCT 57.724 30.769 0.00 0.00 41.47 3.32
2663 2743 3.776158 TGGCACAAACTCCCATGC 58.224 55.556 0.00 0.00 37.35 4.06
2664 2744 1.152589 TGGCACAAACTCCCATGCA 60.153 52.632 0.00 0.00 39.92 3.96
2665 2745 1.180456 TGGCACAAACTCCCATGCAG 61.180 55.000 0.00 0.00 39.92 4.41
2667 2747 0.961019 GCACAAACTCCCATGCAGAA 59.039 50.000 0.00 0.00 38.00 3.02
2688 2768 7.282585 CAGAATTGACCCTTAGATTATGGTGA 58.717 38.462 0.00 0.00 0.00 4.02
2708 2788 6.092748 GGTGAATAACATCAAACATGTGGTC 58.907 40.000 0.00 0.00 31.80 4.02
2712 2792 2.857483 ACATCAAACATGTGGTCCGAA 58.143 42.857 0.00 0.00 0.00 4.30
2730 2818 2.822697 GAAGGTTAGGAGGAGAGTGGT 58.177 52.381 0.00 0.00 0.00 4.16
2733 2821 4.187506 AGGTTAGGAGGAGAGTGGTATC 57.812 50.000 0.00 0.00 0.00 2.24
2768 2856 2.818432 GGTTCGAGTCCTAGTCTTGACA 59.182 50.000 3.49 0.00 33.89 3.58
2797 2885 6.311200 GTGCTCGCATTTTTCTGGATTTATTT 59.689 34.615 0.00 0.00 0.00 1.40
2826 2914 3.081133 GCGATGTGCGTTCGATGT 58.919 55.556 6.90 0.00 43.41 3.06
2832 2920 0.319083 TGTGCGTTCGATGTAAGGGT 59.681 50.000 0.00 0.00 0.00 4.34
2849 2937 3.832615 GGGTATGTTCCCGTTGACTAT 57.167 47.619 0.00 0.00 37.93 2.12
2850 2938 3.463944 GGGTATGTTCCCGTTGACTATG 58.536 50.000 0.00 0.00 37.93 2.23
2856 2944 3.006940 GTTCCCGTTGACTATGAATGCA 58.993 45.455 0.00 0.00 0.00 3.96
2858 2946 3.466836 TCCCGTTGACTATGAATGCATC 58.533 45.455 0.00 0.00 35.94 3.91
2863 2951 5.928264 CCGTTGACTATGAATGCATCTATGA 59.072 40.000 0.00 0.00 35.94 2.15
2864 2952 6.128715 CCGTTGACTATGAATGCATCTATGAC 60.129 42.308 0.00 0.00 35.94 3.06
2870 2958 7.212976 ACTATGAATGCATCTATGACGACTTT 58.787 34.615 0.00 0.00 35.94 2.66
2884 2972 6.048073 TGACGACTTTGTCAATCTCAAAAG 57.952 37.500 0.00 0.00 45.40 2.27
2889 2977 6.293626 CGACTTTGTCAATCTCAAAAGGATGT 60.294 38.462 0.00 0.00 34.96 3.06
2898 2986 0.597568 CAAAAGGATGTTGCGGCTCA 59.402 50.000 0.00 0.98 0.00 4.26
2915 3003 2.494870 GCTCAAGTCTTTCGGGGTACTA 59.505 50.000 0.00 0.00 0.00 1.82
2916 3004 3.429135 GCTCAAGTCTTTCGGGGTACTAG 60.429 52.174 0.00 0.00 0.00 2.57
2917 3005 3.094572 TCAAGTCTTTCGGGGTACTAGG 58.905 50.000 0.00 0.00 0.00 3.02
2918 3006 2.156102 AGTCTTTCGGGGTACTAGGG 57.844 55.000 0.00 0.00 0.00 3.53
2938 3036 2.895372 GGTGCGCGTTCATAGGGG 60.895 66.667 8.43 0.00 0.00 4.79
2966 3064 4.048504 GTGTGTGCATATGTATGAGCGTA 58.951 43.478 4.29 0.00 35.75 4.42
2968 3066 4.685628 TGTGTGCATATGTATGAGCGTATG 59.314 41.667 4.29 0.00 39.86 2.39
2991 3089 7.479897 TGCGTGTGTACTATGTTAAGAAAAA 57.520 32.000 0.00 0.00 0.00 1.94
3013 3111 6.594284 AAAACACTTCTACTTCGGTACAAC 57.406 37.500 0.00 0.00 0.00 3.32
3014 3112 4.248691 ACACTTCTACTTCGGTACAACC 57.751 45.455 0.00 0.00 34.05 3.77
3015 3113 3.638160 ACACTTCTACTTCGGTACAACCA 59.362 43.478 0.00 0.00 38.47 3.67
3016 3114 4.235360 CACTTCTACTTCGGTACAACCAG 58.765 47.826 0.00 0.00 38.47 4.00
3017 3115 4.022589 CACTTCTACTTCGGTACAACCAGA 60.023 45.833 0.00 0.00 38.47 3.86
3018 3116 4.771054 ACTTCTACTTCGGTACAACCAGAT 59.229 41.667 0.00 0.00 38.47 2.90
3019 3117 4.978083 TCTACTTCGGTACAACCAGATC 57.022 45.455 0.00 0.00 38.47 2.75
3020 3118 4.597004 TCTACTTCGGTACAACCAGATCT 58.403 43.478 0.00 0.00 38.47 2.75
3021 3119 3.594603 ACTTCGGTACAACCAGATCTG 57.405 47.619 16.24 16.24 38.47 2.90
3022 3120 2.897969 ACTTCGGTACAACCAGATCTGT 59.102 45.455 21.11 6.28 38.47 3.41
3023 3121 3.056749 ACTTCGGTACAACCAGATCTGTC 60.057 47.826 21.11 4.73 38.47 3.51
3024 3122 1.822990 TCGGTACAACCAGATCTGTCC 59.177 52.381 21.11 11.61 38.47 4.02
3025 3123 1.548719 CGGTACAACCAGATCTGTCCA 59.451 52.381 21.11 0.00 38.47 4.02
3026 3124 2.168521 CGGTACAACCAGATCTGTCCAT 59.831 50.000 21.11 6.96 38.47 3.41
3027 3125 3.383505 CGGTACAACCAGATCTGTCCATA 59.616 47.826 21.11 6.02 38.47 2.74
3028 3126 4.694339 GGTACAACCAGATCTGTCCATAC 58.306 47.826 21.11 16.05 38.42 2.39
3029 3127 3.914426 ACAACCAGATCTGTCCATACC 57.086 47.619 21.11 0.00 0.00 2.73
3030 3128 3.454858 ACAACCAGATCTGTCCATACCT 58.545 45.455 21.11 0.00 0.00 3.08
3031 3129 3.846588 ACAACCAGATCTGTCCATACCTT 59.153 43.478 21.11 0.00 0.00 3.50
3032 3130 4.289672 ACAACCAGATCTGTCCATACCTTT 59.710 41.667 21.11 0.00 0.00 3.11
3033 3131 4.762289 ACCAGATCTGTCCATACCTTTC 57.238 45.455 21.11 0.00 0.00 2.62
3034 3132 4.366267 ACCAGATCTGTCCATACCTTTCT 58.634 43.478 21.11 0.00 0.00 2.52
3035 3133 4.163078 ACCAGATCTGTCCATACCTTTCTG 59.837 45.833 21.11 3.42 0.00 3.02
3036 3134 4.406972 CCAGATCTGTCCATACCTTTCTGA 59.593 45.833 21.11 0.00 0.00 3.27
3037 3135 5.453057 CCAGATCTGTCCATACCTTTCTGAG 60.453 48.000 21.11 0.00 0.00 3.35
3038 3136 5.128499 CAGATCTGTCCATACCTTTCTGAGT 59.872 44.000 14.95 0.00 0.00 3.41
3039 3137 5.362430 AGATCTGTCCATACCTTTCTGAGTC 59.638 44.000 0.00 0.00 0.00 3.36
3040 3138 4.678256 TCTGTCCATACCTTTCTGAGTCT 58.322 43.478 0.00 0.00 0.00 3.24
3041 3139 4.464244 TCTGTCCATACCTTTCTGAGTCTG 59.536 45.833 0.00 0.00 0.00 3.51
3042 3140 3.055819 TGTCCATACCTTTCTGAGTCTGC 60.056 47.826 0.00 0.00 0.00 4.26
3043 3141 2.501723 TCCATACCTTTCTGAGTCTGCC 59.498 50.000 0.00 0.00 0.00 4.85
3044 3142 2.503356 CCATACCTTTCTGAGTCTGCCT 59.497 50.000 0.00 0.00 0.00 4.75
3045 3143 3.054802 CCATACCTTTCTGAGTCTGCCTT 60.055 47.826 0.00 0.00 0.00 4.35
3046 3144 2.557920 ACCTTTCTGAGTCTGCCTTG 57.442 50.000 0.00 0.00 0.00 3.61
3047 3145 1.072965 ACCTTTCTGAGTCTGCCTTGG 59.927 52.381 0.00 0.00 0.00 3.61
3048 3146 1.349026 CCTTTCTGAGTCTGCCTTGGA 59.651 52.381 0.00 0.00 0.00 3.53
3049 3147 2.421619 CTTTCTGAGTCTGCCTTGGAC 58.578 52.381 0.00 0.00 0.00 4.02
3050 3148 0.687354 TTCTGAGTCTGCCTTGGACC 59.313 55.000 0.00 0.00 34.56 4.46
3051 3149 1.079543 CTGAGTCTGCCTTGGACCG 60.080 63.158 0.00 0.00 34.56 4.79
3052 3150 2.266055 GAGTCTGCCTTGGACCGG 59.734 66.667 0.00 0.00 34.56 5.28
3058 3156 4.986708 GCCTTGGACCGGCCCAAA 62.987 66.667 23.44 7.53 44.78 3.28
3059 3157 2.203567 CCTTGGACCGGCCCAAAA 60.204 61.111 23.44 1.85 44.78 2.44
3060 3158 1.834822 CCTTGGACCGGCCCAAAAA 60.835 57.895 23.44 1.02 44.78 1.94
3061 3159 1.191489 CCTTGGACCGGCCCAAAAAT 61.191 55.000 23.44 0.00 44.78 1.82
3062 3160 1.551452 CTTGGACCGGCCCAAAAATA 58.449 50.000 23.44 0.19 44.78 1.40
3063 3161 1.896465 CTTGGACCGGCCCAAAAATAA 59.104 47.619 23.44 0.00 44.78 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.594796 GCATAAAAATCGCCGCCTGG 60.595 55.000 0.00 0.00 38.77 4.45
1 2 0.594796 GGCATAAAAATCGCCGCCTG 60.595 55.000 0.00 0.00 35.79 4.85
2 3 1.733526 GGCATAAAAATCGCCGCCT 59.266 52.632 0.00 0.00 35.79 5.52
3 4 4.319249 GGCATAAAAATCGCCGCC 57.681 55.556 0.00 0.00 35.79 6.13
6 7 1.338020 CCAGGAGGCATAAAAATCGCC 59.662 52.381 0.00 0.00 46.62 5.54
7 8 1.338020 CCCAGGAGGCATAAAAATCGC 59.662 52.381 0.00 0.00 0.00 4.58
8 9 2.930950 TCCCAGGAGGCATAAAAATCG 58.069 47.619 0.00 0.00 34.51 3.34
9 10 3.638627 CCTTCCCAGGAGGCATAAAAATC 59.361 47.826 0.00 0.00 44.19 2.17
10 11 3.630828 CCCTTCCCAGGAGGCATAAAAAT 60.631 47.826 0.00 0.00 44.19 1.82
11 12 2.292192 CCCTTCCCAGGAGGCATAAAAA 60.292 50.000 0.00 0.00 44.19 1.94
12 13 1.287739 CCCTTCCCAGGAGGCATAAAA 59.712 52.381 0.00 0.00 44.19 1.52
13 14 0.926293 CCCTTCCCAGGAGGCATAAA 59.074 55.000 0.00 0.00 44.19 1.40
14 15 0.993509 CCCCTTCCCAGGAGGCATAA 60.994 60.000 0.00 0.00 44.19 1.90
15 16 1.385915 CCCCTTCCCAGGAGGCATA 60.386 63.158 0.00 0.00 44.19 3.14
16 17 2.697644 CCCCTTCCCAGGAGGCAT 60.698 66.667 0.00 0.00 44.19 4.40
20 21 2.941025 TTGGCCCCTTCCCAGGAG 60.941 66.667 0.00 0.00 44.19 3.69
21 22 3.264845 GTTGGCCCCTTCCCAGGA 61.265 66.667 0.00 0.00 44.19 3.86
22 23 4.740822 CGTTGGCCCCTTCCCAGG 62.741 72.222 0.00 0.00 40.45 4.45
23 24 4.740822 CCGTTGGCCCCTTCCCAG 62.741 72.222 0.00 0.00 33.13 4.45
35 36 3.805267 GAGCATCTCCAGCCGTTG 58.195 61.111 0.00 0.00 0.00 4.10
50 51 1.400888 CGCTAGCTCGGATGCTTAGAG 60.401 57.143 13.93 0.00 43.74 2.43
51 52 0.593618 CGCTAGCTCGGATGCTTAGA 59.406 55.000 13.93 0.00 43.74 2.10
52 53 0.312416 ACGCTAGCTCGGATGCTTAG 59.688 55.000 13.93 0.00 43.74 2.18
53 54 0.030773 CACGCTAGCTCGGATGCTTA 59.969 55.000 13.93 0.00 43.74 3.09
54 55 1.227089 CACGCTAGCTCGGATGCTT 60.227 57.895 13.93 0.00 43.74 3.91
55 56 1.667154 TTCACGCTAGCTCGGATGCT 61.667 55.000 13.93 7.05 46.11 3.79
56 57 1.211818 CTTCACGCTAGCTCGGATGC 61.212 60.000 13.93 0.00 0.00 3.91
57 58 1.211818 GCTTCACGCTAGCTCGGATG 61.212 60.000 13.93 10.20 35.74 3.51
58 59 1.066587 GCTTCACGCTAGCTCGGAT 59.933 57.895 13.93 0.00 35.74 4.18
59 60 2.490217 GCTTCACGCTAGCTCGGA 59.510 61.111 13.93 4.44 35.74 4.55
81 82 5.636543 CAGAAAACATCTTCTTCATTTGGGC 59.363 40.000 0.00 0.00 35.73 5.36
89 90 6.902341 TGCATACACAGAAAACATCTTCTTC 58.098 36.000 0.00 0.00 35.73 2.87
124 128 8.335356 GCAAGTGATGCGAATTTTCTATACTTA 58.665 33.333 0.00 0.00 46.87 2.24
142 146 3.569701 ACGAATTTTCCAGTGCAAGTGAT 59.430 39.130 0.00 0.00 40.62 3.06
152 156 5.348164 AGTTTGGTTTGACGAATTTTCCAG 58.652 37.500 0.00 0.00 0.00 3.86
153 157 5.331876 AGTTTGGTTTGACGAATTTTCCA 57.668 34.783 0.00 0.00 0.00 3.53
157 161 5.685511 CGATGAAGTTTGGTTTGACGAATTT 59.314 36.000 0.00 0.00 0.00 1.82
183 187 4.982241 AACTGGAAGACTTGAGATCCAA 57.018 40.909 0.00 0.00 41.20 3.53
189 193 6.683974 TGAAAAGAAACTGGAAGACTTGAG 57.316 37.500 0.00 0.00 37.43 3.02
198 202 4.526650 GGGCCTTATTGAAAAGAAACTGGA 59.473 41.667 0.84 0.00 0.00 3.86
199 203 4.528206 AGGGCCTTATTGAAAAGAAACTGG 59.472 41.667 0.00 0.00 0.00 4.00
200 204 5.011023 ACAGGGCCTTATTGAAAAGAAACTG 59.989 40.000 1.32 0.00 0.00 3.16
201 205 5.147767 ACAGGGCCTTATTGAAAAGAAACT 58.852 37.500 1.32 0.00 0.00 2.66
202 206 5.468540 ACAGGGCCTTATTGAAAAGAAAC 57.531 39.130 1.32 0.00 0.00 2.78
203 207 6.287525 CAAACAGGGCCTTATTGAAAAGAAA 58.712 36.000 18.84 0.00 0.00 2.52
204 208 5.221621 CCAAACAGGGCCTTATTGAAAAGAA 60.222 40.000 23.25 0.00 0.00 2.52
205 209 4.283212 CCAAACAGGGCCTTATTGAAAAGA 59.717 41.667 23.25 0.00 0.00 2.52
206 210 4.283212 TCCAAACAGGGCCTTATTGAAAAG 59.717 41.667 23.25 10.92 38.24 2.27
207 211 4.227197 TCCAAACAGGGCCTTATTGAAAA 58.773 39.130 23.25 10.13 38.24 2.29
208 212 3.831911 CTCCAAACAGGGCCTTATTGAAA 59.168 43.478 23.25 13.16 38.24 2.69
219 223 4.085876 CCTGCACTCCAAACAGGG 57.914 61.111 0.19 0.00 45.97 4.45
222 226 2.942804 TGAATTCCTGCACTCCAAACA 58.057 42.857 2.27 0.00 0.00 2.83
231 235 2.027929 CCCAGCATTTTGAATTCCTGCA 60.028 45.455 16.65 0.00 35.32 4.41
232 236 2.624636 CCCAGCATTTTGAATTCCTGC 58.375 47.619 2.27 7.08 0.00 4.85
233 237 2.568509 ACCCCAGCATTTTGAATTCCTG 59.431 45.455 2.27 1.76 0.00 3.86
257 261 9.550406 ACATGACATCTCAATTCATTTGTTTTT 57.450 25.926 0.00 0.00 36.65 1.94
261 265 8.627403 GGATACATGACATCTCAATTCATTTGT 58.373 33.333 0.00 0.00 36.65 2.83
262 266 8.847196 AGGATACATGACATCTCAATTCATTTG 58.153 33.333 0.00 0.00 41.41 2.32
263 267 8.847196 CAGGATACATGACATCTCAATTCATTT 58.153 33.333 0.00 0.00 41.41 2.32
264 268 8.215736 TCAGGATACATGACATCTCAATTCATT 58.784 33.333 0.00 0.00 41.41 2.57
313 317 5.040635 CCAAACGACAGTTATGCAGTTTTT 58.959 37.500 0.00 0.00 40.18 1.94
356 361 5.827267 TCTTCTCATTGTGTCCATGTTTTCA 59.173 36.000 0.00 0.00 0.00 2.69
363 368 6.906157 ATGTTTTCTTCTCATTGTGTCCAT 57.094 33.333 0.00 0.00 0.00 3.41
451 457 5.865977 AGGAATTGCCATCCTATATTCCA 57.134 39.130 13.00 0.00 45.51 3.53
452 458 6.494835 ACAAAGGAATTGCCATCCTATATTCC 59.505 38.462 0.00 0.00 46.65 3.01
454 460 7.919385 AACAAAGGAATTGCCATCCTATATT 57.081 32.000 2.80 0.00 46.65 1.28
455 461 7.564660 TGAAACAAAGGAATTGCCATCCTATAT 59.435 33.333 2.80 0.00 46.65 0.86
464 470 4.273235 CCTGTTTGAAACAAAGGAATTGCC 59.727 41.667 12.26 0.00 43.13 4.52
497 503 5.299279 TGCGAATCCTTGTTTTCTTCTTCTT 59.701 36.000 0.00 0.00 0.00 2.52
498 504 4.821805 TGCGAATCCTTGTTTTCTTCTTCT 59.178 37.500 0.00 0.00 0.00 2.85
505 511 2.288152 TGGCTTGCGAATCCTTGTTTTC 60.288 45.455 0.00 0.00 0.00 2.29
508 514 1.327303 TTGGCTTGCGAATCCTTGTT 58.673 45.000 0.00 0.00 0.00 2.83
509 515 1.549203 ATTGGCTTGCGAATCCTTGT 58.451 45.000 0.00 0.00 0.00 3.16
511 517 2.450476 AGAATTGGCTTGCGAATCCTT 58.550 42.857 3.51 0.00 0.00 3.36
553 559 1.622607 AAAGATCGGCGGGATGGTGA 61.623 55.000 7.21 0.00 34.82 4.02
554 560 1.153168 AAAGATCGGCGGGATGGTG 60.153 57.895 7.21 0.00 34.82 4.17
555 561 1.153168 CAAAGATCGGCGGGATGGT 60.153 57.895 7.21 0.00 34.82 3.55
557 563 1.502163 GAGCAAAGATCGGCGGGATG 61.502 60.000 7.21 0.76 34.82 3.51
558 564 1.227674 GAGCAAAGATCGGCGGGAT 60.228 57.895 7.21 0.00 38.35 3.85
559 565 2.186903 GAGCAAAGATCGGCGGGA 59.813 61.111 7.21 0.00 34.54 5.14
560 566 2.897350 GGAGCAAAGATCGGCGGG 60.897 66.667 7.21 0.00 34.54 6.13
595 614 1.327292 GAACAACAAATGGACGCGCG 61.327 55.000 30.96 30.96 0.00 6.86
602 621 4.449743 CCATCTGCAAAGAACAACAAATGG 59.550 41.667 0.00 0.00 0.00 3.16
606 625 3.953612 ACTCCATCTGCAAAGAACAACAA 59.046 39.130 0.00 0.00 0.00 2.83
609 628 4.997395 GTCTACTCCATCTGCAAAGAACAA 59.003 41.667 0.00 0.00 0.00 2.83
610 629 4.284490 AGTCTACTCCATCTGCAAAGAACA 59.716 41.667 0.00 0.00 0.00 3.18
611 630 4.826556 AGTCTACTCCATCTGCAAAGAAC 58.173 43.478 0.00 0.00 0.00 3.01
612 631 5.012046 TCAAGTCTACTCCATCTGCAAAGAA 59.988 40.000 0.00 0.00 0.00 2.52
613 632 4.528206 TCAAGTCTACTCCATCTGCAAAGA 59.472 41.667 0.00 0.00 0.00 2.52
614 633 4.825422 TCAAGTCTACTCCATCTGCAAAG 58.175 43.478 0.00 0.00 0.00 2.77
615 634 4.825422 CTCAAGTCTACTCCATCTGCAAA 58.175 43.478 0.00 0.00 0.00 3.68
617 636 2.167281 GCTCAAGTCTACTCCATCTGCA 59.833 50.000 0.00 0.00 0.00 4.41
618 637 2.167281 TGCTCAAGTCTACTCCATCTGC 59.833 50.000 0.00 0.00 0.00 4.26
619 638 4.431809 CTTGCTCAAGTCTACTCCATCTG 58.568 47.826 1.61 0.00 33.87 2.90
620 639 3.450457 CCTTGCTCAAGTCTACTCCATCT 59.550 47.826 8.60 0.00 36.72 2.90
621 640 3.449018 TCCTTGCTCAAGTCTACTCCATC 59.551 47.826 8.60 0.00 36.72 3.51
622 641 3.445008 TCCTTGCTCAAGTCTACTCCAT 58.555 45.455 8.60 0.00 36.72 3.41
623 642 2.889512 TCCTTGCTCAAGTCTACTCCA 58.110 47.619 8.60 0.00 36.72 3.86
624 643 3.791245 CATCCTTGCTCAAGTCTACTCC 58.209 50.000 8.60 0.00 36.72 3.85
625 644 3.194062 GCATCCTTGCTCAAGTCTACTC 58.806 50.000 8.60 0.00 45.77 2.59
626 645 3.258971 GCATCCTTGCTCAAGTCTACT 57.741 47.619 8.60 0.00 45.77 2.57
628 647 5.735981 TTGCGCATCCTTGCTCAAGTCTA 62.736 47.826 12.75 0.00 45.81 2.59
630 649 2.807840 TTGCGCATCCTTGCTCAAGTC 61.808 52.381 12.75 0.00 45.81 3.01
631 650 0.890542 TTGCGCATCCTTGCTCAAGT 60.891 50.000 12.75 0.00 45.81 3.16
632 651 1.878070 TTGCGCATCCTTGCTCAAG 59.122 52.632 12.75 2.74 45.81 3.02
637 656 2.032030 ACGTATAATTGCGCATCCTTGC 60.032 45.455 12.75 0.00 45.78 4.01
638 657 3.247411 TCACGTATAATTGCGCATCCTTG 59.753 43.478 12.75 0.51 33.92 3.61
639 658 3.462982 TCACGTATAATTGCGCATCCTT 58.537 40.909 12.75 8.32 33.92 3.36
640 659 3.106242 TCACGTATAATTGCGCATCCT 57.894 42.857 12.75 0.45 33.92 3.24
641 660 3.870723 TTCACGTATAATTGCGCATCC 57.129 42.857 12.75 0.00 33.92 3.51
642 661 5.075448 CAGATTCACGTATAATTGCGCATC 58.925 41.667 12.75 0.00 33.92 3.91
643 662 4.083855 CCAGATTCACGTATAATTGCGCAT 60.084 41.667 12.75 0.00 33.92 4.73
644 663 3.247411 CCAGATTCACGTATAATTGCGCA 59.753 43.478 5.66 5.66 33.92 6.09
645 664 3.493129 TCCAGATTCACGTATAATTGCGC 59.507 43.478 0.00 0.00 33.92 6.09
646 665 5.443301 CGATCCAGATTCACGTATAATTGCG 60.443 44.000 0.00 0.00 36.97 4.85
647 666 5.633601 TCGATCCAGATTCACGTATAATTGC 59.366 40.000 0.00 0.00 0.00 3.56
648 667 7.542130 TGATCGATCCAGATTCACGTATAATTG 59.458 37.037 22.31 0.00 0.00 2.32
649 668 7.602753 TGATCGATCCAGATTCACGTATAATT 58.397 34.615 22.31 0.00 0.00 1.40
650 669 7.158099 TGATCGATCCAGATTCACGTATAAT 57.842 36.000 22.31 0.00 0.00 1.28
651 670 6.569179 TGATCGATCCAGATTCACGTATAA 57.431 37.500 22.31 0.00 0.00 0.98
656 675 3.848582 CGTATGATCGATCCAGATTCACG 59.151 47.826 22.31 15.28 0.00 4.35
667 686 1.075698 ACTCCCCTCCGTATGATCGAT 59.924 52.381 0.00 0.00 0.00 3.59
686 717 0.315568 CGCTAGGGAGATACTGGCAC 59.684 60.000 0.00 0.00 41.85 5.01
736 767 3.826524 TGGCCGGATTATAGAAATGCAA 58.173 40.909 5.05 0.00 0.00 4.08
858 889 4.395231 GGCTTCTGTGATTTGGTAAGGTAC 59.605 45.833 0.00 0.00 0.00 3.34
865 896 4.327680 GAACTAGGCTTCTGTGATTTGGT 58.672 43.478 0.00 0.00 0.00 3.67
881 912 1.751924 CGAGAACAGGGGAGGAACTAG 59.248 57.143 0.00 0.00 41.55 2.57
891 922 0.737715 GCTAGCACACGAGAACAGGG 60.738 60.000 10.63 0.00 0.00 4.45
895 926 2.854777 CTGTATGCTAGCACACGAGAAC 59.145 50.000 22.07 9.99 0.00 3.01
906 937 8.352942 TGTGTATGTAATGTCTCTGTATGCTAG 58.647 37.037 0.00 0.00 0.00 3.42
907 938 8.135529 GTGTGTATGTAATGTCTCTGTATGCTA 58.864 37.037 0.00 0.00 0.00 3.49
908 939 6.980978 GTGTGTATGTAATGTCTCTGTATGCT 59.019 38.462 0.00 0.00 0.00 3.79
909 940 6.074835 CGTGTGTATGTAATGTCTCTGTATGC 60.075 42.308 0.00 0.00 0.00 3.14
1085 1135 3.136123 CGTAGCCGAACCCGAGGA 61.136 66.667 0.00 0.00 38.22 3.71
1086 1136 4.203076 CCGTAGCCGAACCCGAGG 62.203 72.222 0.00 0.00 38.22 4.63
1087 1137 4.203076 CCCGTAGCCGAACCCGAG 62.203 72.222 0.00 0.00 38.22 4.63
1209 1262 2.355363 CTCCCGAACGCGTTGACA 60.355 61.111 31.89 9.24 35.23 3.58
1302 1364 3.782244 GCAGCGCACTTGTCCTCG 61.782 66.667 11.47 0.00 0.00 4.63
1479 1550 2.143925 GTAGTGCTTTCTTGCTCCGTT 58.856 47.619 0.00 0.00 0.00 4.44
1550 1621 4.912485 TGGCCGCGGACGTTTTGA 62.912 61.111 33.48 5.59 37.70 2.69
1571 1642 2.276732 TTGAGGGTCTTTGGCTGAAG 57.723 50.000 0.00 0.00 0.00 3.02
1575 1646 0.890996 CGCTTTGAGGGTCTTTGGCT 60.891 55.000 0.00 0.00 0.00 4.75
1581 1652 0.392193 CAGCATCGCTTTGAGGGTCT 60.392 55.000 0.00 0.00 36.91 3.85
1599 1670 1.078497 CCATGAGCGTACCTTGGCA 60.078 57.895 0.00 0.00 0.00 4.92
1843 1916 7.851387 TCACATTGCTAAACCGATTAATGTA 57.149 32.000 0.00 0.00 36.83 2.29
1877 1950 1.000145 GCTAAGAAACGAGGCCGAAG 59.000 55.000 0.00 0.00 39.50 3.79
2082 2155 4.283467 TGGGAGGATGTATATGTGTAGTGC 59.717 45.833 0.00 0.00 0.00 4.40
2089 2162 6.329986 TGTGAATTCTGGGAGGATGTATATGT 59.670 38.462 7.05 0.00 0.00 2.29
2099 2172 3.710209 AACTCTGTGAATTCTGGGAGG 57.290 47.619 18.66 5.66 0.00 4.30
2175 2248 5.449588 GCTACTACGGTGAGTACATAGCAAA 60.450 44.000 0.00 0.00 40.85 3.68
2192 2270 6.756299 AGTAGAGTTTACTGTGGCTACTAC 57.244 41.667 0.64 0.00 37.40 2.73
2229 2307 3.743636 TCGATCGAGTGCACGCCA 61.744 61.111 15.15 1.99 0.00 5.69
2245 2323 8.547894 TGAGCACAATGTTTATATTACATCGTC 58.452 33.333 4.26 0.50 35.26 4.20
2512 2592 3.390135 CAACGTGTGGACACTTATGACT 58.610 45.455 8.24 0.00 44.34 3.41
2531 2611 2.371910 TTCGTATGTGGTCATCGCAA 57.628 45.000 0.00 0.00 39.55 4.85
2558 2638 3.702548 TGCGGGTTATCTTTAGAGCTACA 59.297 43.478 0.00 0.00 0.00 2.74
2621 2701 2.655090 TGGGCAGTTTGAGATTGTCA 57.345 45.000 0.00 0.00 0.00 3.58
2663 2743 7.282585 TCACCATAATCTAAGGGTCAATTCTG 58.717 38.462 0.00 0.00 0.00 3.02
2664 2744 7.451731 TCACCATAATCTAAGGGTCAATTCT 57.548 36.000 0.00 0.00 0.00 2.40
2665 2745 8.697507 ATTCACCATAATCTAAGGGTCAATTC 57.302 34.615 0.00 0.00 0.00 2.17
2667 2747 9.574516 GTTATTCACCATAATCTAAGGGTCAAT 57.425 33.333 0.00 0.00 29.70 2.57
2688 2768 5.007034 TCGGACCACATGTTTGATGTTATT 58.993 37.500 0.00 0.00 0.00 1.40
2708 2788 1.751924 CACTCTCCTCCTAACCTTCGG 59.248 57.143 0.00 0.00 0.00 4.30
2712 2792 3.117054 GGATACCACTCTCCTCCTAACCT 60.117 52.174 0.00 0.00 0.00 3.50
2730 2818 4.639726 CCTCGTGGGATGGGGATA 57.360 61.111 0.00 0.00 37.23 2.59
2741 2829 0.733729 CTAGGACTCGAACCCTCGTG 59.266 60.000 8.38 0.00 45.62 4.35
2752 2840 1.473278 CCGGTGTCAAGACTAGGACTC 59.527 57.143 0.00 5.21 35.11 3.36
2756 2844 0.389948 GCACCGGTGTCAAGACTAGG 60.390 60.000 33.92 6.10 0.00 3.02
2768 2856 0.889186 AGAAAAATGCGAGCACCGGT 60.889 50.000 0.00 0.00 39.04 5.28
2797 2885 2.749839 CATCGCCAAAAGGCCCGA 60.750 61.111 0.00 0.00 0.00 5.14
2832 2920 4.814234 GCATTCATAGTCAACGGGAACATA 59.186 41.667 0.00 0.00 0.00 2.29
2842 2930 6.642540 GTCGTCATAGATGCATTCATAGTCAA 59.357 38.462 0.00 0.00 31.96 3.18
2849 2937 5.178061 ACAAAGTCGTCATAGATGCATTCA 58.822 37.500 0.00 0.00 0.00 2.57
2850 2938 5.291858 TGACAAAGTCGTCATAGATGCATTC 59.708 40.000 0.00 0.00 40.94 2.67
2856 2944 6.867550 TGAGATTGACAAAGTCGTCATAGAT 58.132 36.000 0.00 0.00 45.03 1.98
2858 2946 6.951256 TTGAGATTGACAAAGTCGTCATAG 57.049 37.500 0.00 0.00 45.03 2.23
2863 2951 5.123227 TCCTTTTGAGATTGACAAAGTCGT 58.877 37.500 0.00 0.00 38.25 4.34
2864 2952 5.673337 TCCTTTTGAGATTGACAAAGTCG 57.327 39.130 0.00 0.00 38.25 4.18
2870 2958 4.320421 CGCAACATCCTTTTGAGATTGACA 60.320 41.667 0.00 0.00 0.00 3.58
2884 2972 0.674895 AGACTTGAGCCGCAACATCC 60.675 55.000 0.00 0.00 31.96 3.51
2889 2977 1.227999 CCGAAAGACTTGAGCCGCAA 61.228 55.000 0.00 0.00 34.73 4.85
2898 2986 2.464782 CCCTAGTACCCCGAAAGACTT 58.535 52.381 0.00 0.00 0.00 3.01
2918 3006 2.895372 CTATGAACGCGCACCCCC 60.895 66.667 5.73 0.00 0.00 5.40
2922 3010 2.125269 ACCCCTATGAACGCGCAC 60.125 61.111 5.73 0.00 0.00 5.34
2923 3011 2.125310 CACCCCTATGAACGCGCA 60.125 61.111 5.73 0.00 0.00 6.09
2925 3013 0.806102 CACTCACCCCTATGAACGCG 60.806 60.000 3.53 3.53 0.00 6.01
2938 3036 4.869861 TCATACATATGCACACACACTCAC 59.130 41.667 1.58 0.00 33.76 3.51
2966 3064 7.661127 TTTTCTTAACATAGTACACACGCAT 57.339 32.000 0.00 0.00 0.00 4.73
2991 3089 5.052481 GGTTGTACCGAAGTAGAAGTGTTT 58.948 41.667 0.00 0.00 32.80 2.83
2992 3090 4.099881 TGGTTGTACCGAAGTAGAAGTGTT 59.900 41.667 0.00 0.00 42.58 3.32
2993 3091 3.638160 TGGTTGTACCGAAGTAGAAGTGT 59.362 43.478 0.00 0.00 42.58 3.55
2994 3092 4.022589 TCTGGTTGTACCGAAGTAGAAGTG 60.023 45.833 0.00 0.00 42.58 3.16
2995 3093 4.147321 TCTGGTTGTACCGAAGTAGAAGT 58.853 43.478 0.00 0.00 42.58 3.01
2996 3094 4.778534 TCTGGTTGTACCGAAGTAGAAG 57.221 45.455 0.00 0.00 42.58 2.85
2997 3095 5.014858 AGATCTGGTTGTACCGAAGTAGAA 58.985 41.667 0.00 0.00 42.58 2.10
2998 3096 4.398358 CAGATCTGGTTGTACCGAAGTAGA 59.602 45.833 15.38 0.00 42.58 2.59
2999 3097 4.158025 ACAGATCTGGTTGTACCGAAGTAG 59.842 45.833 26.08 0.00 42.58 2.57
3000 3098 4.084287 ACAGATCTGGTTGTACCGAAGTA 58.916 43.478 26.08 0.00 42.58 2.24
3001 3099 2.897969 ACAGATCTGGTTGTACCGAAGT 59.102 45.455 26.08 0.00 42.58 3.01
3002 3100 3.512680 GACAGATCTGGTTGTACCGAAG 58.487 50.000 26.08 0.00 42.58 3.79
3003 3101 2.232941 GGACAGATCTGGTTGTACCGAA 59.767 50.000 26.08 0.00 42.58 4.30
3004 3102 1.822990 GGACAGATCTGGTTGTACCGA 59.177 52.381 26.08 0.00 42.58 4.69
3005 3103 1.548719 TGGACAGATCTGGTTGTACCG 59.451 52.381 26.08 0.00 42.58 4.02
3006 3104 3.914426 ATGGACAGATCTGGTTGTACC 57.086 47.619 26.08 17.39 39.22 3.34
3007 3105 4.406003 AGGTATGGACAGATCTGGTTGTAC 59.594 45.833 26.08 20.08 34.19 2.90
3008 3106 4.620723 AGGTATGGACAGATCTGGTTGTA 58.379 43.478 26.08 11.06 34.19 2.41
3009 3107 3.454858 AGGTATGGACAGATCTGGTTGT 58.545 45.455 26.08 11.99 34.19 3.32
3010 3108 4.494091 AAGGTATGGACAGATCTGGTTG 57.506 45.455 26.08 2.75 34.19 3.77
3011 3109 4.785376 AGAAAGGTATGGACAGATCTGGTT 59.215 41.667 26.08 6.61 34.19 3.67
3012 3110 4.163078 CAGAAAGGTATGGACAGATCTGGT 59.837 45.833 26.08 12.09 31.39 4.00
3013 3111 4.406972 TCAGAAAGGTATGGACAGATCTGG 59.593 45.833 26.08 8.94 33.77 3.86
3014 3112 5.128499 ACTCAGAAAGGTATGGACAGATCTG 59.872 44.000 21.37 21.37 34.03 2.90
3015 3113 5.276440 ACTCAGAAAGGTATGGACAGATCT 58.724 41.667 0.00 0.00 0.00 2.75
3016 3114 5.362430 AGACTCAGAAAGGTATGGACAGATC 59.638 44.000 0.00 0.00 0.00 2.75
3017 3115 5.128499 CAGACTCAGAAAGGTATGGACAGAT 59.872 44.000 0.00 0.00 0.00 2.90
3018 3116 4.464244 CAGACTCAGAAAGGTATGGACAGA 59.536 45.833 0.00 0.00 0.00 3.41
3019 3117 4.753233 CAGACTCAGAAAGGTATGGACAG 58.247 47.826 0.00 0.00 0.00 3.51
3020 3118 3.055819 GCAGACTCAGAAAGGTATGGACA 60.056 47.826 0.00 0.00 0.00 4.02
3021 3119 3.526534 GCAGACTCAGAAAGGTATGGAC 58.473 50.000 0.00 0.00 0.00 4.02
3022 3120 2.501723 GGCAGACTCAGAAAGGTATGGA 59.498 50.000 0.00 0.00 0.00 3.41
3023 3121 2.503356 AGGCAGACTCAGAAAGGTATGG 59.497 50.000 0.00 0.00 0.00 2.74
3024 3122 3.902881 AGGCAGACTCAGAAAGGTATG 57.097 47.619 0.00 0.00 0.00 2.39
3025 3123 3.054802 CCAAGGCAGACTCAGAAAGGTAT 60.055 47.826 0.00 0.00 0.00 2.73
3026 3124 2.303022 CCAAGGCAGACTCAGAAAGGTA 59.697 50.000 0.00 0.00 0.00 3.08
3027 3125 1.072965 CCAAGGCAGACTCAGAAAGGT 59.927 52.381 0.00 0.00 0.00 3.50
3028 3126 1.349026 TCCAAGGCAGACTCAGAAAGG 59.651 52.381 0.00 0.00 0.00 3.11
3029 3127 2.421619 GTCCAAGGCAGACTCAGAAAG 58.578 52.381 0.00 0.00 0.00 2.62
3030 3128 1.072331 GGTCCAAGGCAGACTCAGAAA 59.928 52.381 2.97 0.00 34.56 2.52
3031 3129 0.687354 GGTCCAAGGCAGACTCAGAA 59.313 55.000 2.97 0.00 34.56 3.02
3032 3130 1.536073 CGGTCCAAGGCAGACTCAGA 61.536 60.000 2.97 0.00 34.56 3.27
3033 3131 1.079543 CGGTCCAAGGCAGACTCAG 60.080 63.158 2.97 0.00 34.56 3.35
3034 3132 2.583441 CCGGTCCAAGGCAGACTCA 61.583 63.158 0.00 0.00 34.56 3.41
3035 3133 2.266055 CCGGTCCAAGGCAGACTC 59.734 66.667 0.00 0.00 34.56 3.36
3042 3140 1.191489 ATTTTTGGGCCGGTCCAAGG 61.191 55.000 37.13 0.00 46.19 3.61
3043 3141 1.551452 TATTTTTGGGCCGGTCCAAG 58.449 50.000 37.13 0.00 46.19 3.61
3044 3142 2.011122 TTATTTTTGGGCCGGTCCAA 57.989 45.000 36.45 36.45 44.29 3.53
3045 3143 3.768008 TTATTTTTGGGCCGGTCCA 57.232 47.368 27.82 27.82 36.21 4.02


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

AutoCloner maintained by Alex Coulton.