Multiple sequence alignment - TraesCS4B01G102200

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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 TraesCS4B01G102200 chr4B 100.000 8639 0 0 1 8639 108344849 108353487 0.000000e+00 15954.0
1 TraesCS4B01G102200 chr4B 96.203 79 3 0 5743 5821 108350559 108350637 7.040000e-26 130.0
2 TraesCS4B01G102200 chr4B 96.203 79 3 0 5711 5789 108350591 108350669 7.040000e-26 130.0
3 TraesCS4B01G102200 chr4D 94.494 5122 182 37 4 5089 75776083 75781140 0.000000e+00 7805.0
4 TraesCS4B01G102200 chr4D 92.329 2216 119 25 6291 8495 75783747 75785922 0.000000e+00 3103.0
5 TraesCS4B01G102200 chr4D 94.173 635 33 2 5076 5706 75782351 75782985 0.000000e+00 965.0
6 TraesCS4B01G102200 chr4D 90.484 578 22 12 5745 6292 75783108 75783682 0.000000e+00 732.0
7 TraesCS4B01G102200 chr4D 95.270 148 7 0 8492 8639 75786104 75786251 1.450000e-57 235.0
8 TraesCS4B01G102200 chr4D 88.889 63 5 2 5704 5764 75783098 75783160 9.300000e-10 76.8
9 TraesCS4B01G102200 chr4A 93.155 3287 147 41 884 4119 512012878 512016137 0.000000e+00 4752.0
10 TraesCS4B01G102200 chr4A 93.758 1506 72 8 4116 5608 512018229 512019725 0.000000e+00 2241.0
11 TraesCS4B01G102200 chr4A 94.660 749 26 5 6291 7039 512022281 512023015 0.000000e+00 1149.0
12 TraesCS4B01G102200 chr4A 91.597 833 52 13 7136 7955 512023025 512023852 0.000000e+00 1134.0
13 TraesCS4B01G102200 chr4A 90.312 640 40 10 3 626 512012115 512012748 0.000000e+00 819.0
14 TraesCS4B01G102200 chr4A 91.948 385 21 4 5908 6292 512021837 512022211 1.650000e-146 531.0
15 TraesCS4B01G102200 chr4A 81.222 442 59 17 7939 8377 512024195 512024615 1.390000e-87 335.0
16 TraesCS4B01G102200 chr4A 88.889 207 19 3 8435 8638 512024646 512024851 1.440000e-62 252.0
17 TraesCS4B01G102200 chr4A 89.506 162 12 3 5591 5747 512019738 512019899 5.290000e-47 200.0
18 TraesCS4B01G102200 chr7D 82.121 962 127 27 963 1920 22856413 22857333 0.000000e+00 782.0
19 TraesCS4B01G102200 chr7A 83.495 618 81 18 1305 1920 23350274 23350872 2.720000e-154 556.0
20 TraesCS4B01G102200 chr7A 85.656 244 28 2 1001 1244 23350010 23350246 5.180000e-62 250.0


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 TraesCS4B01G102200 chr4B 108344849 108353487 8638 False 5404.666667 15954 97.468667 1 8639 3 chr4B.!!$F1 8638
1 TraesCS4B01G102200 chr4D 75776083 75786251 10168 False 2152.800000 7805 92.606500 4 8639 6 chr4D.!!$F1 8635
2 TraesCS4B01G102200 chr4A 512012115 512024851 12736 False 1268.111111 4752 90.560778 3 8638 9 chr4A.!!$F1 8635
3 TraesCS4B01G102200 chr7D 22856413 22857333 920 False 782.000000 782 82.121000 963 1920 1 chr7D.!!$F1 957
4 TraesCS4B01G102200 chr7A 23350010 23350872 862 False 403.000000 556 84.575500 1001 1920 2 chr7A.!!$F1 919

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
86 87 0.106149 AGACGCCTGTTCTTTTCGGT 59.894 50.000 0.00 0.0 0.00 4.69 F
1146 1207 0.038166 GCCTGGAGAATGGACACCAA 59.962 55.000 0.00 0.0 36.95 3.67 F
1948 2014 0.324738 CTCACCTGGTAGGCTGAGGA 60.325 60.000 14.07 0.0 39.63 3.71 F
2748 2822 0.657840 GTGCATAACCAAGGCTAGCG 59.342 55.000 9.00 0.0 0.00 4.26 F
4223 6438 0.755686 CCTGGTCATACTGGAGGAGC 59.244 60.000 0.00 0.0 36.89 4.70 F
4244 6463 0.914644 CCTTCTTCTGGGCCATCTCA 59.085 55.000 6.72 0.0 0.00 3.27 F
4645 6874 1.468520 CACAGTTCCATGGTTTAGGCG 59.531 52.381 12.58 0.0 0.00 5.52 F
4662 6891 1.471287 GGCGTTTATGGGAGAACAACC 59.529 52.381 0.00 0.0 0.00 3.77 F
4663 6892 1.471287 GCGTTTATGGGAGAACAACCC 59.529 52.381 0.00 0.0 46.87 4.11 F
5924 11386 1.722034 TCTTCTCTGGTGCTGTTCCT 58.278 50.000 0.00 0.0 0.00 3.36 F
7111 12644 0.820226 CAGACGGAGGATGCAGAGAA 59.180 55.000 0.00 0.0 0.00 2.87 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1928 1994 1.519719 CTCAGCCTACCAGGTGAGC 59.480 63.158 0.76 4.83 37.02 4.26 R
2102 2171 1.815003 GCAATAAGGTGCTTGCAGAGT 59.185 47.619 0.00 0.00 45.50 3.24 R
3413 3498 3.057033 AGACATCAAAAGGCAAGCACATC 60.057 43.478 0.00 0.00 0.00 3.06 R
4225 6440 0.914644 TGAGATGGCCCAGAAGAAGG 59.085 55.000 0.00 0.00 0.00 3.46 R
5534 8989 2.131972 TGCGTGCTACAGTACACAAAG 58.868 47.619 0.00 0.00 36.57 2.77 R
5712 9200 4.105754 TGTTTGTTACCCCATCACATGA 57.894 40.909 0.00 0.00 0.00 3.07 R
6373 11906 1.066573 AGAGGGTGAGCGATCAAACTG 60.067 52.381 4.22 0.00 0.00 3.16 R
6376 11909 1.478510 GAGAGAGGGTGAGCGATCAAA 59.521 52.381 4.22 0.00 0.00 2.69 R
6510 12043 5.573282 GAGAATCAATTGATGCATGCTATGC 59.427 40.000 25.32 12.44 46.32 3.14 R
7451 12985 0.248215 GCGAAGAATGGCGTTGATGG 60.248 55.000 0.00 0.00 0.00 3.51 R
8488 14401 0.677842 ACGGACGCCTTTGTTAGACT 59.322 50.000 0.00 0.00 0.00 3.24 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
86 87 0.106149 AGACGCCTGTTCTTTTCGGT 59.894 50.000 0.00 0.00 0.00 4.69
136 150 3.322466 CAGGCCTCCTTCCACCGT 61.322 66.667 0.00 0.00 0.00 4.83
261 276 4.927267 TGATTTGTTCTCCTGTGGGTAT 57.073 40.909 0.00 0.00 0.00 2.73
361 377 3.305881 GCAGTAGAGTCCAAACGTTACCT 60.306 47.826 0.00 0.00 0.00 3.08
362 378 4.483311 CAGTAGAGTCCAAACGTTACCTC 58.517 47.826 0.00 4.85 0.00 3.85
437 453 2.047274 CGTCCGTTCATGGCACCT 60.047 61.111 0.00 0.00 0.00 4.00
438 454 1.671054 CGTCCGTTCATGGCACCTT 60.671 57.895 0.00 0.00 0.00 3.50
439 455 0.390603 CGTCCGTTCATGGCACCTTA 60.391 55.000 0.00 0.00 0.00 2.69
440 456 1.742411 CGTCCGTTCATGGCACCTTAT 60.742 52.381 0.00 0.00 0.00 1.73
588 604 7.268586 TCTTGCTATGAATCAGTTAGTTCCTC 58.731 38.462 0.00 0.00 0.00 3.71
590 606 6.577103 TGCTATGAATCAGTTAGTTCCTCTG 58.423 40.000 0.00 0.00 0.00 3.35
634 689 2.488153 GGCTGAATTGTTCTGGTGGTAC 59.512 50.000 0.00 0.00 0.00 3.34
655 710 6.935208 GGTACTAGATTGGTTGAAACTCTTGT 59.065 38.462 0.00 0.00 0.00 3.16
656 711 7.117956 GGTACTAGATTGGTTGAAACTCTTGTC 59.882 40.741 0.00 0.00 0.00 3.18
657 712 6.831976 ACTAGATTGGTTGAAACTCTTGTCT 58.168 36.000 0.00 0.00 0.00 3.41
658 713 7.283329 ACTAGATTGGTTGAAACTCTTGTCTT 58.717 34.615 0.00 0.00 0.00 3.01
659 714 6.382869 AGATTGGTTGAAACTCTTGTCTTG 57.617 37.500 0.00 0.00 0.00 3.02
660 715 4.370364 TTGGTTGAAACTCTTGTCTTGC 57.630 40.909 0.00 0.00 0.00 4.01
661 716 2.354510 TGGTTGAAACTCTTGTCTTGCG 59.645 45.455 0.00 0.00 0.00 4.85
662 717 2.612212 GGTTGAAACTCTTGTCTTGCGA 59.388 45.455 0.00 0.00 0.00 5.10
663 718 3.546218 GGTTGAAACTCTTGTCTTGCGAC 60.546 47.826 0.00 0.00 40.64 5.19
710 765 4.384940 GCCTTCCATCTCTACAAATCCTC 58.615 47.826 0.00 0.00 0.00 3.71
711 766 4.745172 GCCTTCCATCTCTACAAATCCTCC 60.745 50.000 0.00 0.00 0.00 4.30
712 767 4.657969 CCTTCCATCTCTACAAATCCTCCT 59.342 45.833 0.00 0.00 0.00 3.69
713 768 5.841237 CCTTCCATCTCTACAAATCCTCCTA 59.159 44.000 0.00 0.00 0.00 2.94
714 769 6.500049 CCTTCCATCTCTACAAATCCTCCTAT 59.500 42.308 0.00 0.00 0.00 2.57
715 770 7.017056 CCTTCCATCTCTACAAATCCTCCTATT 59.983 40.741 0.00 0.00 0.00 1.73
716 771 7.937700 TCCATCTCTACAAATCCTCCTATTT 57.062 36.000 0.00 0.00 0.00 1.40
717 772 9.447279 TTCCATCTCTACAAATCCTCCTATTTA 57.553 33.333 0.00 0.00 0.00 1.40
718 773 9.621239 TCCATCTCTACAAATCCTCCTATTTAT 57.379 33.333 0.00 0.00 0.00 1.40
719 774 9.664332 CCATCTCTACAAATCCTCCTATTTATG 57.336 37.037 0.00 0.00 0.00 1.90
734 789 6.094325 TCCTATTTATGTTTTTCACGGCGATT 59.906 34.615 16.62 0.00 0.00 3.34
736 791 2.629639 ATGTTTTTCACGGCGATTCC 57.370 45.000 16.62 0.00 0.00 3.01
743 798 2.627863 TCACGGCGATTCCATTTTTG 57.372 45.000 16.62 0.00 34.01 2.44
751 806 3.827625 CGATTCCATTTTTGTTGCGGTA 58.172 40.909 0.00 0.00 0.00 4.02
766 826 1.300634 GGTAGCCGGCCTGGTAAAA 59.699 57.895 26.15 0.00 41.21 1.52
783 843 9.025041 CCTGGTAAAATATTGGGGATTTAGATC 57.975 37.037 0.00 0.00 0.00 2.75
807 867 2.545106 CCAGCAACATTTTGGCTTGTTC 59.455 45.455 0.00 0.00 33.93 3.18
820 880 2.726241 GGCTTGTTCGAAGCAAAACATC 59.274 45.455 9.64 0.00 44.71 3.06
858 918 2.084546 GTCCATTGTAGTGTGAAGCCC 58.915 52.381 0.00 0.00 0.00 5.19
863 923 0.618458 TGTAGTGTGAAGCCCCCATC 59.382 55.000 0.00 0.00 0.00 3.51
876 936 0.606401 CCCCATCACATATGACCGCC 60.606 60.000 10.38 0.00 37.79 6.13
877 937 0.397941 CCCATCACATATGACCGCCT 59.602 55.000 10.38 0.00 37.79 5.52
878 938 1.202806 CCCATCACATATGACCGCCTT 60.203 52.381 10.38 0.00 37.79 4.35
879 939 1.875514 CCATCACATATGACCGCCTTG 59.124 52.381 10.38 0.00 37.79 3.61
880 940 2.564771 CATCACATATGACCGCCTTGT 58.435 47.619 10.38 0.00 37.79 3.16
881 941 2.779755 TCACATATGACCGCCTTGTT 57.220 45.000 10.38 0.00 0.00 2.83
882 942 2.355197 TCACATATGACCGCCTTGTTG 58.645 47.619 10.38 0.00 0.00 3.33
928 989 5.237344 GTCTGTTGCTGTTTCTAGTTGTCAT 59.763 40.000 0.00 0.00 0.00 3.06
937 998 5.698089 TGTTTCTAGTTGTCATCTTCTGCAG 59.302 40.000 7.63 7.63 0.00 4.41
1146 1207 0.038166 GCCTGGAGAATGGACACCAA 59.962 55.000 0.00 0.00 36.95 3.67
1200 1261 5.241662 GGTTCTGTTCTCTCTATTTGCTGT 58.758 41.667 0.00 0.00 0.00 4.40
1238 1299 8.758633 AAACTGTAGTTGCTTACATAGTACAG 57.241 34.615 12.41 12.41 41.09 2.74
1257 1318 1.716503 AGCCTTTCTACCCCCAAATGT 59.283 47.619 0.00 0.00 0.00 2.71
1303 1364 3.357079 GGTGTTGCTGGAGGTGCG 61.357 66.667 0.00 0.00 0.00 5.34
1544 1610 6.357367 TCCACTTTCCCTTGCTAGATATTTC 58.643 40.000 0.00 0.00 0.00 2.17
1555 1621 9.281371 CCTTGCTAGATATTTCATTCTCATCAA 57.719 33.333 0.00 0.00 0.00 2.57
1558 1624 9.617523 TGCTAGATATTTCATTCTCATCAAACA 57.382 29.630 0.00 0.00 0.00 2.83
1566 1632 7.470935 TTCATTCTCATCAAACATGAACCAT 57.529 32.000 0.00 0.00 30.60 3.55
1567 1633 7.470935 TCATTCTCATCAAACATGAACCATT 57.529 32.000 0.00 0.00 0.00 3.16
1568 1634 7.898918 TCATTCTCATCAAACATGAACCATTT 58.101 30.769 0.00 0.00 0.00 2.32
1573 1639 7.231115 TCTCATCAAACATGAACCATTTTCTCA 59.769 33.333 0.00 0.00 0.00 3.27
1574 1640 7.898918 TCATCAAACATGAACCATTTTCTCAT 58.101 30.769 0.00 0.00 0.00 2.90
1575 1641 8.030692 TCATCAAACATGAACCATTTTCTCATC 58.969 33.333 0.00 0.00 0.00 2.92
1576 1642 7.287512 TCAAACATGAACCATTTTCTCATCA 57.712 32.000 0.00 0.00 0.00 3.07
1577 1643 7.898918 TCAAACATGAACCATTTTCTCATCAT 58.101 30.769 0.00 0.00 0.00 2.45
1578 1644 9.022884 TCAAACATGAACCATTTTCTCATCATA 57.977 29.630 0.00 0.00 0.00 2.15
1579 1645 9.079833 CAAACATGAACCATTTTCTCATCATAC 57.920 33.333 0.00 0.00 0.00 2.39
1651 1717 3.118992 CGGACTGTCTGATGAGGAAATGA 60.119 47.826 11.20 0.00 0.00 2.57
1653 1719 5.435291 GGACTGTCTGATGAGGAAATGATT 58.565 41.667 7.85 0.00 0.00 2.57
1696 1762 6.933514 TTGATCATCCAGGTATAGCACATA 57.066 37.500 4.48 0.00 0.00 2.29
1800 1866 5.484173 TTTCAGATGCATTTGATACGGAC 57.516 39.130 19.57 0.00 0.00 4.79
1948 2014 0.324738 CTCACCTGGTAGGCTGAGGA 60.325 60.000 14.07 0.00 39.63 3.71
2174 2243 8.281212 TCTCTCCAAGAAGTTAATTTATTGCC 57.719 34.615 11.38 0.00 0.00 4.52
2179 2248 7.825270 TCCAAGAAGTTAATTTATTGCCGAGTA 59.175 33.333 11.38 0.00 0.00 2.59
2286 2355 6.126863 TGTCAGGTTAATCCTTCAGATGTT 57.873 37.500 0.00 0.00 45.67 2.71
2432 2501 2.094026 CCTCTTTTATGCCTTGCAACCC 60.094 50.000 0.00 0.00 43.62 4.11
2478 2549 8.641541 AGGACATTTAGTTTCACATTCATGTTT 58.358 29.630 0.00 0.00 39.39 2.83
2500 2571 8.946085 TGTTTTTAGATGTGGAGTGTCAATATC 58.054 33.333 0.00 0.00 0.00 1.63
2532 2603 3.511362 TGGCACACATGTGTTCCTT 57.489 47.368 36.49 13.72 45.25 3.36
2592 2665 9.612620 GACCATTAATTTCTTGTCAGTTTACAG 57.387 33.333 0.00 0.00 0.00 2.74
2651 2725 7.878036 ACAACGTACTTAAGGTTTTGCAATAT 58.122 30.769 7.53 0.00 34.00 1.28
2748 2822 0.657840 GTGCATAACCAAGGCTAGCG 59.342 55.000 9.00 0.00 0.00 4.26
2773 2847 7.485913 CGCTCTGTTGCAGTAAATGATAAATTT 59.514 33.333 0.00 0.00 32.61 1.82
2792 2866 7.406031 AAATTTGAGAGACGTCCTACTGATA 57.594 36.000 13.01 0.00 0.00 2.15
2803 2877 5.127194 ACGTCCTACTGATATGTTGTCATGT 59.873 40.000 0.00 0.00 35.70 3.21
2844 2919 7.251321 ACTTTGAATTCTCCATCAGTAGAGT 57.749 36.000 7.05 0.00 0.00 3.24
3155 3240 8.094548 TGTCACAAAAGTGTCTATGCTAACTAT 58.905 33.333 0.00 0.00 35.07 2.12
3170 3255 8.873215 ATGCTAACTATACATGTTCTGTACAC 57.127 34.615 2.30 0.00 43.01 2.90
3343 3428 3.796717 TCGTTCAGCATATTCGCACTAAG 59.203 43.478 0.00 0.00 0.00 2.18
3413 3498 7.589958 ATTCAGACTACTTACCAGGTATCTG 57.410 40.000 16.64 16.64 40.59 2.90
3470 3555 3.557595 GCATGTGTATTGCAGGACTCTAC 59.442 47.826 0.00 0.00 39.90 2.59
3474 3559 5.865085 TGTGTATTGCAGGACTCTACTTTT 58.135 37.500 2.23 0.00 0.00 2.27
3547 3641 2.134201 TAATACGAGATGCTGCCACG 57.866 50.000 0.00 0.30 0.00 4.94
3615 3709 6.106003 TGGTTAGTATGTACAAGCATGTGAG 58.894 40.000 4.51 0.00 40.84 3.51
3628 3722 6.316890 ACAAGCATGTGAGCATTTTTCTTTTT 59.683 30.769 0.00 0.00 38.69 1.94
3863 3975 9.412460 TCTAGAAATGCATCATTGGATAAGTTT 57.588 29.630 0.00 0.00 34.04 2.66
3864 3976 9.674824 CTAGAAATGCATCATTGGATAAGTTTC 57.325 33.333 0.00 0.00 34.04 2.78
3867 3979 5.840243 TGCATCATTGGATAAGTTTCCTG 57.160 39.130 0.00 0.00 36.68 3.86
3908 4024 9.806203 CATCTAATTCAAGTATGCATTTTGGAA 57.194 29.630 18.14 11.31 0.00 3.53
3931 4047 3.838244 TCCTGTACTTGTTTGCAGTCT 57.162 42.857 0.00 0.00 0.00 3.24
3933 4049 3.876914 TCCTGTACTTGTTTGCAGTCTTG 59.123 43.478 0.00 0.00 0.00 3.02
4034 4152 7.946207 TGTTTTCACCATGTAGCTAAAATTCA 58.054 30.769 0.00 0.00 0.00 2.57
4169 6384 9.368674 CTACAGAAATGCTAGGATATCAATCTG 57.631 37.037 4.83 15.66 39.02 2.90
4223 6438 0.755686 CCTGGTCATACTGGAGGAGC 59.244 60.000 0.00 0.00 36.89 4.70
4224 6439 1.690845 CCTGGTCATACTGGAGGAGCT 60.691 57.143 5.28 0.00 37.26 4.09
4225 6440 1.686052 CTGGTCATACTGGAGGAGCTC 59.314 57.143 4.71 4.71 37.26 4.09
4244 6463 0.914644 CCTTCTTCTGGGCCATCTCA 59.085 55.000 6.72 0.00 0.00 3.27
4335 6554 7.441458 AGGAATTTAGTACCACATAAGATTCGC 59.559 37.037 0.00 0.00 0.00 4.70
4490 6718 4.887071 ACTTCAAAGTAACCACATTGCTCA 59.113 37.500 0.00 0.00 37.52 4.26
4645 6874 1.468520 CACAGTTCCATGGTTTAGGCG 59.531 52.381 12.58 0.00 0.00 5.52
4662 6891 1.471287 GGCGTTTATGGGAGAACAACC 59.529 52.381 0.00 0.00 0.00 3.77
4663 6892 1.471287 GCGTTTATGGGAGAACAACCC 59.529 52.381 0.00 0.00 46.87 4.11
4734 6963 5.012148 AGGGACAATAGTTTATCCATCTCCG 59.988 44.000 0.00 0.00 32.45 4.63
4754 6983 8.543862 TCTCCGTAATTCCTTTTTCTTCTAAC 57.456 34.615 0.00 0.00 0.00 2.34
4805 7034 7.204243 TGTGTATCCTCTCCTGTTAGTAGTA 57.796 40.000 0.00 0.00 0.00 1.82
4833 7062 4.100808 TGTTTGCCCTTATGCACTTTCTTT 59.899 37.500 0.00 0.00 41.88 2.52
4913 7142 5.834460 TCAGTGATTAGGAGGTACCAACTA 58.166 41.667 15.94 12.75 42.04 2.24
4947 7176 5.606348 TTTAACCATTGCTTTGTTGAGGT 57.394 34.783 0.00 0.00 0.00 3.85
4949 7178 4.486125 AACCATTGCTTTGTTGAGGTTT 57.514 36.364 0.00 0.00 34.45 3.27
4950 7179 3.795877 ACCATTGCTTTGTTGAGGTTTG 58.204 40.909 0.00 0.00 0.00 2.93
4999 7228 6.882140 TCACACAGAGACAAAAGTTCCTTAAA 59.118 34.615 0.00 0.00 0.00 1.52
5012 7241 9.816787 AAAAGTTCCTTAAAATGTATACCTGGA 57.183 29.630 0.00 0.00 0.00 3.86
5059 7288 8.627403 CAATTGTAGTTTATGAATGCTCCAGAT 58.373 33.333 0.00 0.00 0.00 2.90
5123 8576 3.565902 GCTATATGGGTTTGAGCCTTCAC 59.434 47.826 0.00 0.00 36.53 3.18
5233 8688 8.801715 AAACATGTCATACAACTTTGAATGAC 57.198 30.769 0.00 7.23 38.93 3.06
5261 8716 7.509141 TCATTGTGTTAGTGATTTGTCACAT 57.491 32.000 10.76 0.03 42.68 3.21
5582 9037 5.828299 TCCCGTGAATGAATTATGAAACC 57.172 39.130 0.00 0.00 0.00 3.27
5608 9094 8.571336 CATAAATTTCTCTCTCTCTCTCTCTCC 58.429 40.741 0.00 0.00 0.00 3.71
5609 9095 4.503714 TTTCTCTCTCTCTCTCTCTCCC 57.496 50.000 0.00 0.00 0.00 4.30
5723 9211 8.908786 AATATGTAGTACTTTCATGTGATGGG 57.091 34.615 17.70 0.00 0.00 4.00
5772 9377 7.606456 ACGTGATGGAGTAACAAATAAGATGTT 59.394 33.333 0.00 0.00 43.14 2.71
5785 9390 9.773328 ACAAATAAGATGTTATTTCACGTGATG 57.227 29.630 20.80 10.83 43.90 3.07
5788 9393 6.668541 AAGATGTTATTTCACGTGATGGAG 57.331 37.500 20.80 0.00 0.00 3.86
5789 9394 5.734720 AGATGTTATTTCACGTGATGGAGT 58.265 37.500 20.80 3.91 0.00 3.85
5792 9397 6.715344 TGTTATTTCACGTGATGGAGTAAC 57.285 37.500 20.80 19.85 0.00 2.50
5795 9400 7.226918 TGTTATTTCACGTGATGGAGTAACAAA 59.773 33.333 23.44 12.30 31.60 2.83
5796 9401 6.817765 ATTTCACGTGATGGAGTAACAAAT 57.182 33.333 20.80 8.93 0.00 2.32
5797 9402 7.915293 ATTTCACGTGATGGAGTAACAAATA 57.085 32.000 20.80 0.00 0.00 1.40
5799 9404 6.961359 TCACGTGATGGAGTAACAAATAAG 57.039 37.500 15.76 0.00 0.00 1.73
5923 11385 2.777832 ATCTTCTCTGGTGCTGTTCC 57.222 50.000 0.00 0.00 0.00 3.62
5924 11386 1.722034 TCTTCTCTGGTGCTGTTCCT 58.278 50.000 0.00 0.00 0.00 3.36
5982 11444 4.223953 TGTCTACCCTGTCTTGAGAGTTT 58.776 43.478 0.00 0.00 0.00 2.66
6208 11670 7.515841 GCTCATTCAAGTGTGATATAACTGTCG 60.516 40.741 0.00 0.00 32.48 4.35
6274 11736 3.259314 AGCCACCCATCAGTGCCA 61.259 61.111 0.00 0.00 36.38 4.92
6292 11754 2.633488 CCAGCAACTAGGGAACTTAGC 58.367 52.381 0.00 0.00 43.67 3.09
6294 11756 3.003480 CAGCAACTAGGGAACTTAGCAC 58.997 50.000 0.00 0.00 43.67 4.40
6295 11757 2.000447 GCAACTAGGGAACTTAGCACG 59.000 52.381 0.00 0.00 43.67 5.34
6296 11758 2.612221 GCAACTAGGGAACTTAGCACGT 60.612 50.000 0.00 0.00 43.67 4.49
6297 11759 3.367703 GCAACTAGGGAACTTAGCACGTA 60.368 47.826 0.00 0.00 43.67 3.57
6511 12044 7.153315 AGTTCCTTGTGTTTCTAGTAAGTAGC 58.847 38.462 0.00 0.00 0.00 3.58
6512 12045 6.659745 TCCTTGTGTTTCTAGTAAGTAGCA 57.340 37.500 0.00 0.00 0.00 3.49
6535 12068 6.914259 CATAGCATGCATCAATTGATTCTCT 58.086 36.000 21.98 13.54 31.21 3.10
6544 12077 6.541641 GCATCAATTGATTCTCTGTAACTCCT 59.458 38.462 18.41 0.00 31.21 3.69
6596 12129 5.032846 TCACTGAGGGAAGGATATTTGTCT 58.967 41.667 0.00 0.00 0.00 3.41
6859 12392 5.109903 CAATTAGGTCACTACAGGTGCTAC 58.890 45.833 0.00 0.00 44.98 3.58
6868 12401 5.105473 TCACTACAGGTGCTACTTAATGACC 60.105 44.000 0.00 0.00 44.98 4.02
6911 12444 3.882888 CCTTTTATATTGGCTCTGCGGAA 59.117 43.478 0.00 0.00 0.00 4.30
6927 12460 2.666619 GCGGAATGTTGAGCAGAACAAG 60.667 50.000 4.83 0.21 39.25 3.16
7043 12576 4.501071 TCAATGTACTAAAGCCGAGGTTC 58.499 43.478 0.00 0.00 0.00 3.62
7083 12616 2.714250 ACTACAAATGTGGTTCTGGGGA 59.286 45.455 0.00 0.00 36.27 4.81
7084 12617 2.999185 ACAAATGTGGTTCTGGGGAT 57.001 45.000 0.00 0.00 0.00 3.85
7085 12618 2.528564 ACAAATGTGGTTCTGGGGATG 58.471 47.619 0.00 0.00 0.00 3.51
7086 12619 2.109834 ACAAATGTGGTTCTGGGGATGA 59.890 45.455 0.00 0.00 0.00 2.92
7111 12644 0.820226 CAGACGGAGGATGCAGAGAA 59.180 55.000 0.00 0.00 0.00 2.87
7160 12693 8.867112 AGAAATATGTTATTTTCAGCAGCATG 57.133 30.769 0.00 0.00 34.91 4.06
7161 12694 7.437267 AGAAATATGTTATTTTCAGCAGCATGC 59.563 33.333 10.51 10.51 44.59 4.06
7180 12714 2.290197 TGCCATGTATCAAGTGCAGTCA 60.290 45.455 0.00 0.00 0.00 3.41
7183 12717 2.768253 TGTATCAAGTGCAGTCAGGG 57.232 50.000 0.00 0.00 0.00 4.45
7190 12724 3.820467 TCAAGTGCAGTCAGGGTAAATTG 59.180 43.478 0.00 0.00 0.00 2.32
7199 12733 5.047802 CAGTCAGGGTAAATTGCTCATTGTT 60.048 40.000 0.00 0.00 0.00 2.83
7247 12781 7.028962 ACGCATTACATTTACAGTTAGTACGA 58.971 34.615 0.00 0.00 30.91 3.43
7429 12963 2.509964 GGGTGAGTTTGGGGACAGATAT 59.490 50.000 0.00 0.00 44.54 1.63
7451 12985 9.837525 GATATTTTGGAACAGATGATTATCAGC 57.162 33.333 1.78 1.78 42.39 4.26
7471 13005 0.248215 CATCAACGCCATTCTTCGCC 60.248 55.000 0.00 0.00 0.00 5.54
7609 13147 5.479306 TGTCATGCTAAGAGTTAACCAGTC 58.521 41.667 0.88 0.00 0.00 3.51
7643 13181 2.294233 TGTGCAGGCTTTTGTGAGAATC 59.706 45.455 0.00 0.00 0.00 2.52
7644 13182 2.555757 GTGCAGGCTTTTGTGAGAATCT 59.444 45.455 0.00 0.00 34.92 2.40
7666 13204 2.821366 GACATGCCACCTCCTGCG 60.821 66.667 0.00 0.00 0.00 5.18
7735 13273 5.132648 TCCCAAACTATCAGATGCCAATACT 59.867 40.000 0.00 0.00 0.00 2.12
7808 13346 4.957954 ACATCCACTTGACATAAATGGCAT 59.042 37.500 0.00 0.00 46.90 4.40
7810 13348 6.039717 ACATCCACTTGACATAAATGGCATAC 59.960 38.462 0.00 0.00 46.90 2.39
7913 13456 4.503714 TTTCACCTCTACCCCATGATTC 57.496 45.455 0.00 0.00 0.00 2.52
7914 13457 3.421394 TCACCTCTACCCCATGATTCT 57.579 47.619 0.00 0.00 0.00 2.40
7915 13458 3.736094 TCACCTCTACCCCATGATTCTT 58.264 45.455 0.00 0.00 0.00 2.52
7918 13461 5.015178 TCACCTCTACCCCATGATTCTTTTT 59.985 40.000 0.00 0.00 0.00 1.94
7950 13854 4.916870 ACGGTGACTTAACTTTTGCTTTC 58.083 39.130 0.00 0.00 0.00 2.62
7983 13887 2.611518 GCTGAACTCAGACGTGCTTAT 58.388 47.619 10.95 0.00 46.59 1.73
8001 13905 8.551205 CGTGCTTATGATCTTGAAAGCTATTTA 58.449 33.333 14.01 0.00 43.69 1.40
8038 13942 2.771089 TGAGGCACATGAAGTTGAGTC 58.229 47.619 0.00 0.00 0.00 3.36
8039 13943 2.104622 TGAGGCACATGAAGTTGAGTCA 59.895 45.455 0.00 0.00 0.00 3.41
8040 13944 3.244665 TGAGGCACATGAAGTTGAGTCAT 60.245 43.478 0.00 0.00 36.11 3.06
8049 13953 5.534207 TGAAGTTGAGTCATTGGCAAAAT 57.466 34.783 3.01 0.00 0.00 1.82
8061 13965 6.587608 GTCATTGGCAAAATGGTCTCTTTAAG 59.412 38.462 3.01 0.00 0.00 1.85
8089 13993 9.423061 GAGTAGCAAATTTGGTGATAATTTGTT 57.577 29.630 28.47 15.00 46.84 2.83
8121 14025 6.949463 TGATGATGTGATATGTTTGCCCATAT 59.051 34.615 0.00 0.00 40.00 1.78
8174 14078 9.273016 GAAATGCTACAGATTTAGCCTACATTA 57.727 33.333 0.00 0.00 43.43 1.90
8175 14079 8.608844 AATGCTACAGATTTAGCCTACATTAC 57.391 34.615 0.00 0.00 43.43 1.89
8185 14089 3.359033 AGCCTACATTACACGTCTGGTA 58.641 45.455 0.00 0.00 0.00 3.25
8189 14093 5.163923 GCCTACATTACACGTCTGGTAAAAC 60.164 44.000 1.62 0.00 34.67 2.43
8266 14170 6.796705 AACCCATAACGTTTCTTAACTCAG 57.203 37.500 5.91 0.00 31.89 3.35
8276 14180 4.640771 TTCTTAACTCAGATGGCAGGTT 57.359 40.909 0.00 0.00 0.00 3.50
8378 14282 2.628657 GGGTCCACGCACTAGATAATCT 59.371 50.000 0.00 0.00 0.00 2.40
8387 14291 9.938670 CCACGCACTAGATAATCTATTAGTATC 57.061 37.037 0.00 0.00 35.77 2.24
8428 14332 9.956640 AATCTGTTGAACTAATCTCTCATTTCT 57.043 29.630 0.00 0.00 0.00 2.52
8465 14376 2.359531 ACTAATCTCCTCTTTCCGCTCG 59.640 50.000 0.00 0.00 0.00 5.03
8466 14377 0.461961 AATCTCCTCTTTCCGCTCGG 59.538 55.000 1.14 1.14 0.00 4.63
8488 14401 5.634439 CGGCTTCATTTGAACAAATCATCAA 59.366 36.000 9.42 0.00 38.84 2.57
8489 14402 6.183360 CGGCTTCATTTGAACAAATCATCAAG 60.183 38.462 9.42 9.97 38.84 3.02
8490 14403 6.647895 GGCTTCATTTGAACAAATCATCAAGT 59.352 34.615 9.42 0.00 38.84 3.16
8592 14689 1.260544 GTCAAGAAAGGCAAGCCCAT 58.739 50.000 7.62 0.00 36.58 4.00
8621 14718 5.507482 GGAGAAGAAAACTAAACAACTGCCC 60.507 44.000 0.00 0.00 0.00 5.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 2.891941 TATTTGGCTGGCGCAGGGAG 62.892 60.000 10.83 0.00 38.10 4.30
86 87 3.845259 CGGCGGGAATCGGGAAGA 61.845 66.667 0.00 0.00 39.69 2.87
136 150 1.744368 CGACGAGGGAAGACTCCGA 60.744 63.158 0.00 0.00 43.51 4.55
361 377 1.803334 CAACGAAATGAACGAGGGGA 58.197 50.000 0.00 0.00 34.70 4.81
362 378 0.168128 GCAACGAAATGAACGAGGGG 59.832 55.000 0.00 0.00 34.70 4.79
437 453 9.990360 TGCCAACGATTAATTAGATCACTATAA 57.010 29.630 0.00 0.00 0.00 0.98
438 454 9.639601 CTGCCAACGATTAATTAGATCACTATA 57.360 33.333 0.00 0.00 0.00 1.31
439 455 8.367911 TCTGCCAACGATTAATTAGATCACTAT 58.632 33.333 0.00 0.00 0.00 2.12
440 456 7.722363 TCTGCCAACGATTAATTAGATCACTA 58.278 34.615 0.00 0.00 0.00 2.74
634 689 7.579726 CAAGACAAGAGTTTCAACCAATCTAG 58.420 38.462 0.00 0.00 0.00 2.43
656 711 6.509317 TTAATCAAAAGCAAAAGTCGCAAG 57.491 33.333 0.00 0.00 0.00 4.01
657 712 6.893958 TTTAATCAAAAGCAAAAGTCGCAA 57.106 29.167 0.00 0.00 0.00 4.85
658 713 6.699204 TGATTTAATCAAAAGCAAAAGTCGCA 59.301 30.769 5.03 0.00 40.38 5.10
659 714 7.096065 ACTGATTTAATCAAAAGCAAAAGTCGC 60.096 33.333 9.05 0.00 42.57 5.19
660 715 8.285776 ACTGATTTAATCAAAAGCAAAAGTCG 57.714 30.769 9.05 0.00 42.57 4.18
662 717 9.180678 CGTACTGATTTAATCAAAAGCAAAAGT 57.819 29.630 9.05 3.10 42.57 2.66
663 718 8.155923 GCGTACTGATTTAATCAAAAGCAAAAG 58.844 33.333 16.64 4.20 42.57 2.27
710 765 5.224562 TCGCCGTGAAAAACATAAATAGG 57.775 39.130 0.00 0.00 0.00 2.57
711 766 6.413818 GGAATCGCCGTGAAAAACATAAATAG 59.586 38.462 0.00 0.00 0.00 1.73
712 767 6.127980 TGGAATCGCCGTGAAAAACATAAATA 60.128 34.615 0.00 0.00 40.66 1.40
713 768 5.099575 GGAATCGCCGTGAAAAACATAAAT 58.900 37.500 0.00 0.00 0.00 1.40
714 769 4.023107 TGGAATCGCCGTGAAAAACATAAA 60.023 37.500 0.00 0.00 40.66 1.40
715 770 3.502595 TGGAATCGCCGTGAAAAACATAA 59.497 39.130 0.00 0.00 40.66 1.90
716 771 3.075148 TGGAATCGCCGTGAAAAACATA 58.925 40.909 0.00 0.00 40.66 2.29
717 772 1.883275 TGGAATCGCCGTGAAAAACAT 59.117 42.857 0.00 0.00 40.66 2.71
718 773 1.309950 TGGAATCGCCGTGAAAAACA 58.690 45.000 0.00 0.00 40.66 2.83
719 774 2.629639 ATGGAATCGCCGTGAAAAAC 57.370 45.000 0.00 0.00 40.66 2.43
720 775 3.651803 AAATGGAATCGCCGTGAAAAA 57.348 38.095 0.00 0.00 40.66 1.94
721 776 3.651803 AAAATGGAATCGCCGTGAAAA 57.348 38.095 0.00 0.00 40.66 2.29
722 777 3.243569 ACAAAAATGGAATCGCCGTGAAA 60.244 39.130 0.00 0.00 40.66 2.69
723 778 2.294791 ACAAAAATGGAATCGCCGTGAA 59.705 40.909 0.00 0.00 40.66 3.18
724 779 1.883275 ACAAAAATGGAATCGCCGTGA 59.117 42.857 0.00 0.00 40.66 4.35
725 780 2.346099 ACAAAAATGGAATCGCCGTG 57.654 45.000 0.00 0.00 40.66 4.94
726 781 2.671596 CAACAAAAATGGAATCGCCGT 58.328 42.857 0.00 0.00 40.66 5.68
727 782 1.389784 GCAACAAAAATGGAATCGCCG 59.610 47.619 0.00 0.00 40.66 6.46
734 789 1.271102 GGCTACCGCAACAAAAATGGA 59.729 47.619 0.00 0.00 38.10 3.41
736 791 1.335935 CGGCTACCGCAACAAAAATG 58.664 50.000 0.00 0.00 41.17 2.32
751 806 2.306847 CAATATTTTACCAGGCCGGCT 58.693 47.619 28.56 9.11 39.03 5.52
758 813 9.813826 AGATCTAAATCCCCAATATTTTACCAG 57.186 33.333 0.00 0.00 31.78 4.00
766 826 6.045931 TGCTGGAAGATCTAAATCCCCAATAT 59.954 38.462 9.07 0.00 35.77 1.28
783 843 2.803956 CAAGCCAAAATGTTGCTGGAAG 59.196 45.455 0.00 0.00 33.01 3.46
785 845 1.761784 ACAAGCCAAAATGTTGCTGGA 59.238 42.857 0.00 0.00 33.01 3.86
807 867 0.168128 GGGACGGATGTTTTGCTTCG 59.832 55.000 0.00 0.00 0.00 3.79
820 880 2.148768 GACTTGTTTAACCAGGGACGG 58.851 52.381 1.36 0.00 0.00 4.79
858 918 0.397941 AGGCGGTCATATGTGATGGG 59.602 55.000 1.90 0.00 36.60 4.00
863 923 2.083774 ACAACAAGGCGGTCATATGTG 58.916 47.619 1.90 0.00 0.00 3.21
876 936 7.914871 TGTGTTCACAAATCATAAGACAACAAG 59.085 33.333 2.99 0.00 0.00 3.16
877 937 7.766283 TGTGTTCACAAATCATAAGACAACAA 58.234 30.769 2.99 0.00 0.00 2.83
878 938 7.326968 TGTGTTCACAAATCATAAGACAACA 57.673 32.000 2.99 0.00 0.00 3.33
879 939 7.862372 ACATGTGTTCACAAATCATAAGACAAC 59.138 33.333 9.68 0.00 30.24 3.32
880 940 7.939782 ACATGTGTTCACAAATCATAAGACAA 58.060 30.769 9.68 0.00 30.24 3.18
881 941 7.445096 AGACATGTGTTCACAAATCATAAGACA 59.555 33.333 1.15 0.00 30.89 3.41
882 942 7.747799 CAGACATGTGTTCACAAATCATAAGAC 59.252 37.037 1.15 0.00 0.00 3.01
928 989 3.265221 AGGTCATCCAAATCTGCAGAAGA 59.735 43.478 22.50 15.22 36.22 2.87
994 1055 7.067129 GCTTGTCGAGTATGATCCCATATAGTA 59.933 40.741 0.00 0.00 37.56 1.82
1200 1261 6.073440 GCAACTACAGTTTACTGAATTTCCGA 60.073 38.462 16.31 0.00 46.59 4.55
1238 1299 1.824852 CACATTTGGGGGTAGAAAGGC 59.175 52.381 0.00 0.00 0.00 4.35
1257 1318 4.314121 GCAAACAAAATTATGGTGAGGCA 58.686 39.130 0.00 0.00 0.00 4.75
1303 1364 6.037830 TGCAAACAGTACTTTTACCTGAAGAC 59.962 38.462 0.00 0.00 0.00 3.01
1544 1610 8.542497 AAAATGGTTCATGTTTGATGAGAATG 57.458 30.769 0.00 0.00 0.00 2.67
1555 1621 7.475015 CGTATGATGAGAAAATGGTTCATGTT 58.525 34.615 0.00 0.00 32.03 2.71
1558 1624 5.589855 TGCGTATGATGAGAAAATGGTTCAT 59.410 36.000 0.00 0.00 34.43 2.57
1559 1625 4.940654 TGCGTATGATGAGAAAATGGTTCA 59.059 37.500 0.00 0.00 0.00 3.18
1560 1626 5.484173 TGCGTATGATGAGAAAATGGTTC 57.516 39.130 0.00 0.00 0.00 3.62
1561 1627 5.677091 GCTTGCGTATGATGAGAAAATGGTT 60.677 40.000 0.00 0.00 0.00 3.67
1562 1628 4.201950 GCTTGCGTATGATGAGAAAATGGT 60.202 41.667 0.00 0.00 0.00 3.55
1563 1629 4.201940 TGCTTGCGTATGATGAGAAAATGG 60.202 41.667 0.00 0.00 0.00 3.16
1564 1630 4.912214 TGCTTGCGTATGATGAGAAAATG 58.088 39.130 0.00 0.00 0.00 2.32
1566 1632 5.565592 ATTGCTTGCGTATGATGAGAAAA 57.434 34.783 0.00 0.00 0.00 2.29
1567 1633 6.538381 TCTTATTGCTTGCGTATGATGAGAAA 59.462 34.615 0.00 0.00 0.00 2.52
1568 1634 6.048509 TCTTATTGCTTGCGTATGATGAGAA 58.951 36.000 0.00 0.00 0.00 2.87
1573 1639 6.624352 ACATTCTTATTGCTTGCGTATGAT 57.376 33.333 0.00 0.00 0.00 2.45
1574 1640 6.093357 TCAACATTCTTATTGCTTGCGTATGA 59.907 34.615 0.00 0.00 0.00 2.15
1575 1641 6.257423 TCAACATTCTTATTGCTTGCGTATG 58.743 36.000 0.00 0.00 0.00 2.39
1576 1642 6.435430 TCAACATTCTTATTGCTTGCGTAT 57.565 33.333 0.00 0.00 0.00 3.06
1577 1643 5.871465 TCAACATTCTTATTGCTTGCGTA 57.129 34.783 0.00 0.00 0.00 4.42
1578 1644 4.764679 TCAACATTCTTATTGCTTGCGT 57.235 36.364 0.00 0.00 0.00 5.24
1579 1645 5.575957 AGATCAACATTCTTATTGCTTGCG 58.424 37.500 0.00 0.00 0.00 4.85
1696 1762 9.398170 CAAAAAGACATTACGTTCTCATGAAAT 57.602 29.630 0.00 0.00 33.52 2.17
1737 1803 6.093219 CAGCAGTAATAAAGTCAGAGCACATT 59.907 38.462 0.00 0.00 0.00 2.71
1928 1994 1.519719 CTCAGCCTACCAGGTGAGC 59.480 63.158 0.76 4.83 37.02 4.26
1948 2014 5.211973 TCATAAAGCACAGGACTAGGAGAT 58.788 41.667 0.00 0.00 0.00 2.75
2102 2171 1.815003 GCAATAAGGTGCTTGCAGAGT 59.185 47.619 0.00 0.00 45.50 3.24
2174 2243 7.215194 GTGGCGTACGATATTTATAAGTACTCG 59.785 40.741 21.65 13.23 36.48 4.18
2179 2248 9.918630 AATAAGTGGCGTACGATATTTATAAGT 57.081 29.630 21.65 2.64 0.00 2.24
2411 2480 2.094026 GGGTTGCAAGGCATAAAAGAGG 60.094 50.000 0.00 0.00 38.76 3.69
2432 2501 2.192605 GCCATAAGCCACAGTTGGG 58.807 57.895 0.00 0.00 44.15 4.12
2478 2549 8.078060 TGAGATATTGACACTCCACATCTAAA 57.922 34.615 0.00 0.00 0.00 1.85
2500 2571 9.401873 CACATGTGTGCCATTAAATATTATGAG 57.598 33.333 18.03 0.00 39.39 2.90
2581 2654 8.989980 AGCTACTCAAATTTACTGTAAACTGAC 58.010 33.333 14.68 8.87 0.00 3.51
2651 2725 8.018520 CGACTGCTTTGTATTAAATACACCAAA 58.981 33.333 0.00 0.00 44.79 3.28
2668 2742 7.675962 TTATGGTGTTAATAACGACTGCTTT 57.324 32.000 0.00 0.00 0.00 3.51
2748 2822 8.589629 CAAATTTATCATTTACTGCAACAGAGC 58.410 33.333 0.78 0.00 35.18 4.09
2773 2847 5.037383 ACATATCAGTAGGACGTCTCTCA 57.963 43.478 16.46 0.00 0.00 3.27
2780 2854 5.460091 CACATGACAACATATCAGTAGGACG 59.540 44.000 0.00 0.00 35.09 4.79
2792 2866 6.017109 GGACTGAACTAAACACATGACAACAT 60.017 38.462 0.00 0.00 37.19 2.71
2803 2877 6.488769 TCAAAGTAGGGACTGAACTAAACA 57.511 37.500 0.00 0.00 41.52 2.83
2844 2919 7.876896 AAGAAACTGTTTGCGTAAAGAAAAA 57.123 28.000 11.03 0.00 0.00 1.94
3170 3255 9.373603 TGCATGAAATTCCAAAAATGAGATAAG 57.626 29.630 0.00 0.00 0.00 1.73
3217 3302 8.303876 TCTTCAAAAGCTGTCTTTACAAACTTT 58.696 29.630 0.00 0.00 41.40 2.66
3343 3428 9.807649 ATTTTACATAGATCATTTTGACCAAGC 57.192 29.630 0.00 0.00 0.00 4.01
3413 3498 3.057033 AGACATCAAAAGGCAAGCACATC 60.057 43.478 0.00 0.00 0.00 3.06
3547 3641 8.895845 GCATAAAATATGAAATCATGTGTCGTC 58.104 33.333 6.17 0.00 37.15 4.20
3628 3722 6.998074 AGTGAAATTCAAGACACCACTCATAA 59.002 34.615 0.00 0.00 34.33 1.90
3846 3958 5.504665 CGACAGGAAACTTATCCAATGATGC 60.505 44.000 0.00 0.00 42.27 3.91
3863 3975 6.540438 AGATGGAAAACTATTACGACAGGA 57.460 37.500 0.00 0.00 0.00 3.86
3864 3976 8.888579 ATTAGATGGAAAACTATTACGACAGG 57.111 34.615 0.00 0.00 0.00 4.00
3897 4011 6.663093 ACAAGTACAGGATATTCCAAAATGCA 59.337 34.615 0.00 0.00 39.61 3.96
3908 4024 6.054860 AGACTGCAAACAAGTACAGGATAT 57.945 37.500 0.00 0.00 34.40 1.63
4016 4132 7.629222 GCTTGACATGAATTTTAGCTACATGGT 60.629 37.037 19.65 9.61 41.41 3.55
4034 4152 7.880195 ACTCTCAACTAACTAAATGCTTGACAT 59.120 33.333 0.00 0.00 42.30 3.06
4097 4217 4.497473 TTAGGTGTTTTTCCATTGCTCG 57.503 40.909 0.00 0.00 0.00 5.03
4169 6384 3.501445 GCTTCTTCAGCCATGGTCATATC 59.499 47.826 14.67 0.00 43.65 1.63
4223 6438 1.140652 GAGATGGCCCAGAAGAAGGAG 59.859 57.143 0.00 0.00 0.00 3.69
4224 6439 1.207791 GAGATGGCCCAGAAGAAGGA 58.792 55.000 0.00 0.00 0.00 3.36
4225 6440 0.914644 TGAGATGGCCCAGAAGAAGG 59.085 55.000 0.00 0.00 0.00 3.46
4228 6443 1.883678 TCATGAGATGGCCCAGAAGA 58.116 50.000 0.00 0.00 0.00 2.87
4244 6463 4.989279 ACAAGGCGCAAGATTAATTCAT 57.011 36.364 10.83 0.00 43.02 2.57
4273 6492 2.262423 AAAGGCAGCTTCGAAGAAGT 57.738 45.000 28.95 9.25 45.90 3.01
4335 6554 1.473677 TGCGCAGAGAATGGAAAATGG 59.526 47.619 5.66 0.00 0.00 3.16
4490 6718 3.067461 GGATTACATGAGCTGAGAGACGT 59.933 47.826 0.00 0.00 0.00 4.34
4645 6874 2.089201 CCGGGTTGTTCTCCCATAAAC 58.911 52.381 0.00 0.00 44.81 2.01
4662 6891 2.396590 ACAACTAGCAACCATACCGG 57.603 50.000 0.00 0.00 42.50 5.28
4663 6892 4.247258 TGTAACAACTAGCAACCATACCG 58.753 43.478 0.00 0.00 0.00 4.02
4754 6983 5.078411 AGTAACTCCAGCAGACAGTATTG 57.922 43.478 0.00 0.00 0.00 1.90
4805 7034 4.280819 AGTGCATAAGGGCAAACATATGT 58.719 39.130 1.41 1.41 46.93 2.29
4833 7062 3.191162 GTGTAAACAGATCCTGCATGCAA 59.809 43.478 22.88 8.38 34.37 4.08
4947 7176 5.580297 GCCAAAGTTGTTCAGTCATTTCAAA 59.420 36.000 0.00 0.00 0.00 2.69
4949 7178 4.159321 TGCCAAAGTTGTTCAGTCATTTCA 59.841 37.500 0.00 0.00 0.00 2.69
4950 7179 4.504097 GTGCCAAAGTTGTTCAGTCATTTC 59.496 41.667 0.00 0.00 0.00 2.17
4999 7228 3.523564 ACAGGCTGTTCCAGGTATACATT 59.476 43.478 15.88 0.00 37.29 2.71
5012 7241 2.553086 CATTGTTTTGCACAGGCTGTT 58.447 42.857 19.43 0.00 41.91 3.16
5059 7288 5.957771 AACTGAGTTCCCAGCATATCTAA 57.042 39.130 0.00 0.00 37.68 2.10
5423 8878 5.181748 AGATGAGCTGTGAGGACATTTAAC 58.818 41.667 0.00 0.00 0.00 2.01
5424 8879 5.426689 AGATGAGCTGTGAGGACATTTAA 57.573 39.130 0.00 0.00 0.00 1.52
5534 8989 2.131972 TGCGTGCTACAGTACACAAAG 58.868 47.619 0.00 0.00 36.57 2.77
5562 9017 9.748708 ATTTATGGTTTCATAATTCATTCACGG 57.251 29.630 0.00 0.00 43.11 4.94
5582 9037 8.571336 GGAGAGAGAGAGAGAGAGAAATTTATG 58.429 40.741 0.00 0.00 0.00 1.90
5659 9147 9.059260 GGAGTAACAAACACAAGTTTCCTATTA 57.941 33.333 0.00 0.00 45.80 0.98
5702 9190 4.534500 ACCCCATCACATGAAAGTACTACA 59.466 41.667 0.00 0.00 0.00 2.74
5712 9200 4.105754 TGTTTGTTACCCCATCACATGA 57.894 40.909 0.00 0.00 0.00 3.07
5714 9202 4.735369 TCTTGTTTGTTACCCCATCACAT 58.265 39.130 0.00 0.00 0.00 3.21
5716 9204 4.522789 ACATCTTGTTTGTTACCCCATCAC 59.477 41.667 0.00 0.00 0.00 3.06
5717 9205 4.735369 ACATCTTGTTTGTTACCCCATCA 58.265 39.130 0.00 0.00 0.00 3.07
5719 9207 7.790782 AATAACATCTTGTTTGTTACCCCAT 57.209 32.000 0.00 0.00 41.08 4.00
5720 9208 7.287927 TGAAATAACATCTTGTTTGTTACCCCA 59.712 33.333 0.00 0.00 41.08 4.96
5721 9209 7.597369 GTGAAATAACATCTTGTTTGTTACCCC 59.403 37.037 0.00 0.00 41.08 4.95
5722 9210 7.325097 CGTGAAATAACATCTTGTTTGTTACCC 59.675 37.037 0.00 0.00 41.08 3.69
5723 9211 7.858879 ACGTGAAATAACATCTTGTTTGTTACC 59.141 33.333 0.00 0.00 41.08 2.85
5772 9377 7.915293 ATTTGTTACTCCATCACGTGAAATA 57.085 32.000 24.13 9.51 0.00 1.40
5792 9397 9.225201 CCATCACGTGAAATAACATCTTATTTG 57.775 33.333 24.13 9.83 40.97 2.32
5795 9400 7.442364 CCTCCATCACGTGAAATAACATCTTAT 59.558 37.037 24.13 0.00 0.00 1.73
5796 9401 6.761242 CCTCCATCACGTGAAATAACATCTTA 59.239 38.462 24.13 0.00 0.00 2.10
5797 9402 5.586243 CCTCCATCACGTGAAATAACATCTT 59.414 40.000 24.13 0.00 0.00 2.40
5799 9404 4.876107 ACCTCCATCACGTGAAATAACATC 59.124 41.667 24.13 0.00 0.00 3.06
5923 11385 5.241949 ACTCTCAAGACAAGGTACACACTAG 59.758 44.000 0.00 0.00 0.00 2.57
5924 11386 5.138276 ACTCTCAAGACAAGGTACACACTA 58.862 41.667 0.00 0.00 0.00 2.74
6274 11736 2.353803 CGTGCTAAGTTCCCTAGTTGCT 60.354 50.000 0.00 0.00 0.00 3.91
6292 11754 4.732285 ATGCTTTCACTTCAAGTACGTG 57.268 40.909 0.00 1.96 0.00 4.49
6294 11756 8.728088 AAAATTATGCTTTCACTTCAAGTACG 57.272 30.769 0.00 0.00 0.00 3.67
6373 11906 1.066573 AGAGGGTGAGCGATCAAACTG 60.067 52.381 4.22 0.00 0.00 3.16
6376 11909 1.478510 GAGAGAGGGTGAGCGATCAAA 59.521 52.381 4.22 0.00 0.00 2.69
6490 12023 7.222999 GCTATGCTACTTACTAGAAACACAAGG 59.777 40.741 0.00 0.00 0.00 3.61
6491 12024 7.759886 TGCTATGCTACTTACTAGAAACACAAG 59.240 37.037 0.00 0.00 0.00 3.16
6508 12041 7.361799 GAGAATCAATTGATGCATGCTATGCTA 60.362 37.037 25.32 0.00 46.29 3.49
6509 12042 6.570571 GAGAATCAATTGATGCATGCTATGCT 60.571 38.462 25.32 4.78 46.29 3.79
6510 12043 5.573282 GAGAATCAATTGATGCATGCTATGC 59.427 40.000 25.32 12.44 46.32 3.14
6511 12044 6.803807 CAGAGAATCAATTGATGCATGCTATG 59.196 38.462 25.32 17.40 37.82 2.23
6512 12045 6.490381 ACAGAGAATCAATTGATGCATGCTAT 59.510 34.615 25.32 10.71 37.82 2.97
6535 12068 8.750298 CAAAAGATAGGAGAACTAGGAGTTACA 58.250 37.037 0.00 0.00 38.80 2.41
6544 12077 9.273016 CAACTGAAACAAAAGATAGGAGAACTA 57.727 33.333 0.00 0.00 35.80 2.24
6859 12392 7.637229 CAATTGCACTAGAGATGGTCATTAAG 58.363 38.462 0.00 0.00 0.00 1.85
6868 12401 3.181493 GGTTGGCAATTGCACTAGAGATG 60.181 47.826 30.32 0.00 44.36 2.90
6911 12444 1.882912 TCGCTTGTTCTGCTCAACAT 58.117 45.000 2.40 0.00 36.16 2.71
6927 12460 1.869767 CCAGTTTCTAGCCATCATCGC 59.130 52.381 0.00 0.00 0.00 4.58
7054 12587 7.333174 CCAGAACCACATTTGTAGTTTGTTTTT 59.667 33.333 0.00 0.00 30.37 1.94
7083 12616 3.801698 CATCCTCCGTCTGTTCATTCAT 58.198 45.455 0.00 0.00 0.00 2.57
7084 12617 2.677902 GCATCCTCCGTCTGTTCATTCA 60.678 50.000 0.00 0.00 0.00 2.57
7085 12618 1.936547 GCATCCTCCGTCTGTTCATTC 59.063 52.381 0.00 0.00 0.00 2.67
7086 12619 1.278985 TGCATCCTCCGTCTGTTCATT 59.721 47.619 0.00 0.00 0.00 2.57
7111 12644 8.900781 TCTCTACAACTAATAATAAGCTGTCGT 58.099 33.333 0.00 0.00 0.00 4.34
7154 12687 2.543031 GCACTTGATACATGGCATGCTG 60.543 50.000 26.70 11.66 0.00 4.41
7155 12688 1.679680 GCACTTGATACATGGCATGCT 59.320 47.619 26.70 14.75 0.00 3.79
7156 12689 1.406180 TGCACTTGATACATGGCATGC 59.594 47.619 26.70 9.90 0.00 4.06
7160 12693 2.353889 CTGACTGCACTTGATACATGGC 59.646 50.000 0.00 0.00 0.00 4.40
7161 12694 2.941064 CCTGACTGCACTTGATACATGG 59.059 50.000 0.00 0.00 0.00 3.66
7180 12714 4.832266 TGTCAACAATGAGCAATTTACCCT 59.168 37.500 0.00 0.00 35.88 4.34
7183 12717 9.229784 CTATCATGTCAACAATGAGCAATTTAC 57.770 33.333 0.00 0.00 35.88 2.01
7190 12724 4.454678 TCCCTATCATGTCAACAATGAGC 58.545 43.478 0.00 0.00 35.88 4.26
7199 12733 5.698741 AAGTCAACATCCCTATCATGTCA 57.301 39.130 0.00 0.00 33.12 3.58
7247 12781 6.611642 TGAGTTATCTGCCCTTCAACTACTAT 59.388 38.462 0.00 0.00 29.89 2.12
7260 12794 3.334583 TTCAGTGGTGAGTTATCTGCC 57.665 47.619 0.00 0.00 32.98 4.85
7429 12963 5.951148 TGGCTGATAATCATCTGTTCCAAAA 59.049 36.000 0.00 0.00 33.76 2.44
7451 12985 0.248215 GCGAAGAATGGCGTTGATGG 60.248 55.000 0.00 0.00 0.00 3.51
7609 13147 2.162681 CCTGCACAGTTTTAAGAGGGG 58.837 52.381 0.00 0.00 0.00 4.79
7643 13181 1.222936 GAGGTGGCATGTCTGGGAG 59.777 63.158 0.00 0.00 0.00 4.30
7644 13182 2.300967 GGAGGTGGCATGTCTGGGA 61.301 63.158 0.00 0.00 0.00 4.37
7666 13204 6.407475 AAAAGAATTTGAATAATGCCGCAC 57.593 33.333 0.00 0.00 39.02 5.34
7705 13243 6.547141 TGGCATCTGATAGTTTGGGAATAAAG 59.453 38.462 0.00 0.00 0.00 1.85
7707 13245 6.012337 TGGCATCTGATAGTTTGGGAATAA 57.988 37.500 0.00 0.00 0.00 1.40
7735 13273 5.178623 CAGTTTCCGCTAGTGAACATAACAA 59.821 40.000 4.44 0.00 0.00 2.83
7921 13464 7.658575 AGCAAAAGTTAAGTCACCGTATCTAAA 59.341 33.333 0.00 0.00 0.00 1.85
7923 13466 6.694447 AGCAAAAGTTAAGTCACCGTATCTA 58.306 36.000 0.00 0.00 0.00 1.98
7925 13468 5.857822 AGCAAAAGTTAAGTCACCGTATC 57.142 39.130 0.00 0.00 0.00 2.24
7950 13854 3.374988 TGAGTTCAGCCATGATAAAAGCG 59.625 43.478 0.00 0.00 34.73 4.68
8019 13923 2.771089 TGACTCAACTTCATGTGCCTC 58.229 47.619 0.00 0.00 0.00 4.70
8038 13942 6.690530 TCTTAAAGAGACCATTTTGCCAATG 58.309 36.000 0.00 0.00 0.00 2.82
8039 13943 6.721208 TCTCTTAAAGAGACCATTTTGCCAAT 59.279 34.615 0.00 0.00 45.77 3.16
8040 13944 6.068010 TCTCTTAAAGAGACCATTTTGCCAA 58.932 36.000 0.00 0.00 45.77 4.52
8061 13965 9.294030 CAAATTATCACCAAATTTGCTACTCTC 57.706 33.333 12.92 0.00 43.47 3.20
8089 13993 9.955208 GCAAACATATCACATCATCAATCTTTA 57.045 29.630 0.00 0.00 0.00 1.85
8110 14014 4.083003 TCAAGAAACGTGATATGGGCAAAC 60.083 41.667 0.00 0.00 0.00 2.93
8111 14015 4.075682 TCAAGAAACGTGATATGGGCAAA 58.924 39.130 0.00 0.00 0.00 3.68
8121 14025 5.471797 TGGCAAATATCTTCAAGAAACGTGA 59.528 36.000 0.00 0.00 0.00 4.35
8124 14028 7.028962 TCATTGGCAAATATCTTCAAGAAACG 58.971 34.615 3.01 0.00 0.00 3.60
8174 14078 4.011698 ACCAAAAGTTTTACCAGACGTGT 58.988 39.130 0.00 0.00 0.00 4.49
8175 14079 4.625972 ACCAAAAGTTTTACCAGACGTG 57.374 40.909 0.00 0.00 0.00 4.49
8185 14089 4.973663 CGAGCGTCATAAACCAAAAGTTTT 59.026 37.500 0.00 0.00 46.79 2.43
8189 14093 3.059188 ACACGAGCGTCATAAACCAAAAG 60.059 43.478 0.00 0.00 0.00 2.27
8198 14102 2.198406 GGCAAATACACGAGCGTCATA 58.802 47.619 0.00 0.00 0.00 2.15
8266 14170 2.109425 ACTTCCGTTAACCTGCCATC 57.891 50.000 0.00 0.00 0.00 3.51
8317 14221 7.878127 CCGTTTAGGATTGTAATCATACCTCAT 59.122 37.037 6.90 0.00 45.00 2.90
8322 14226 8.086522 TCTAGCCGTTTAGGATTGTAATCATAC 58.913 37.037 6.90 0.00 45.00 2.39
8393 14297 2.954318 AGTTCAACAGATTGTGCTGCTT 59.046 40.909 0.00 0.00 39.51 3.91
8394 14298 2.579873 AGTTCAACAGATTGTGCTGCT 58.420 42.857 0.00 0.00 39.51 4.24
8402 14306 9.956640 AGAAATGAGAGATTAGTTCAACAGATT 57.043 29.630 0.00 0.00 0.00 2.40
8439 14350 6.708285 AGCGGAAAGAGGAGATTAGTTTTTA 58.292 36.000 0.00 0.00 0.00 1.52
8465 14376 6.647895 ACTTGATGATTTGTTCAAATGAAGCC 59.352 34.615 14.29 2.28 38.03 4.35
8466 14377 7.597743 AGACTTGATGATTTGTTCAAATGAAGC 59.402 33.333 14.29 7.04 38.03 3.86
8488 14401 0.677842 ACGGACGCCTTTGTTAGACT 59.322 50.000 0.00 0.00 0.00 3.24
8489 14402 2.352503 TACGGACGCCTTTGTTAGAC 57.647 50.000 0.00 0.00 0.00 2.59
8490 14403 3.598019 AATACGGACGCCTTTGTTAGA 57.402 42.857 0.00 0.00 0.00 2.10
8592 14689 8.458843 CAGTTGTTTAGTTTTCTTCTCCTTTCA 58.541 33.333 0.00 0.00 0.00 2.69


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

AutoCloner maintained by Alex Coulton.