Multiple sequence alignment - TraesCS5A01G202000

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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 TraesCS5A01G202000 chr5A 100.000 6894 0 0 1 6894 408836966 408843859 0.000000e+00 12731
1 TraesCS5A01G202000 chr5A 93.130 131 8 1 4596 4726 680554881 680554752 2.540000e-44 191
2 TraesCS5A01G202000 chr5B 95.462 4407 133 23 228 4603 362809803 362814173 0.000000e+00 6968
3 TraesCS5A01G202000 chr5B 96.253 1548 37 9 4719 6251 362814171 362815712 0.000000e+00 2518
4 TraesCS5A01G202000 chr5B 97.895 285 6 0 6610 6894 362816113 362816397 1.730000e-135 494
5 TraesCS5A01G202000 chr5B 94.239 243 8 3 6244 6483 362815871 362816110 3.930000e-97 366
6 TraesCS5A01G202000 chr5B 96.703 182 2 2 49 228 362809550 362809729 4.040000e-77 300
7 TraesCS5A01G202000 chr5D 97.085 3980 97 8 631 4603 314836480 314840447 0.000000e+00 6689
8 TraesCS5A01G202000 chr5D 96.063 1778 43 11 4719 6486 314840445 314842205 0.000000e+00 2870
9 TraesCS5A01G202000 chr5D 95.498 311 5 4 228 531 314836162 314836470 8.040000e-134 488
10 TraesCS5A01G202000 chr5D 97.527 283 7 0 6610 6892 314842205 314842487 1.040000e-132 484
11 TraesCS5A01G202000 chr5D 91.379 232 10 7 1 228 314835863 314836088 6.720000e-80 309
12 TraesCS5A01G202000 chr5D 96.694 121 4 0 4600 4720 545934158 545934038 1.170000e-47 202
13 TraesCS5A01G202000 chr7B 96.667 120 4 0 4600 4719 510606019 510606138 4.220000e-47 200
14 TraesCS5A01G202000 chr6B 96.667 120 4 0 4600 4719 49371738 49371857 4.220000e-47 200
15 TraesCS5A01G202000 chr6D 95.200 125 6 0 4600 4724 208914938 208915062 1.520000e-46 198
16 TraesCS5A01G202000 chr4A 95.902 122 5 0 4599 4720 3146201 3146322 1.520000e-46 198
17 TraesCS5A01G202000 chr3A 95.902 122 5 0 4599 4720 414863381 414863260 1.520000e-46 198
18 TraesCS5A01G202000 chr2D 95.200 125 6 0 4600 4724 76640624 76640748 1.520000e-46 198
19 TraesCS5A01G202000 chr7A 95.868 121 5 0 4600 4720 460722090 460722210 5.450000e-46 196


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 TraesCS5A01G202000 chr5A 408836966 408843859 6893 False 12731.0 12731 100.0000 1 6894 1 chr5A.!!$F1 6893
1 TraesCS5A01G202000 chr5B 362809550 362816397 6847 False 2129.2 6968 96.1104 49 6894 5 chr5B.!!$F1 6845
2 TraesCS5A01G202000 chr5D 314835863 314842487 6624 False 2168.0 6689 95.5104 1 6892 5 chr5D.!!$F1 6891

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
579 670 0.108520 GGGGCATGTGAACTGCAATG 60.109 55.000 0.00 0.00 41.47 2.82 F
1368 1472 0.034670 ACATCTTTGGGGCTGAGCTC 60.035 55.000 6.82 6.82 0.00 4.09 F
2907 3020 2.042297 TCCATTCCCTTACATTGTGCCA 59.958 45.455 0.00 0.00 0.00 4.92 F
3756 3870 0.972471 TTCGCCCTCTGCAGATGAGA 60.972 55.000 18.63 15.43 41.33 3.27 F
3803 3917 1.270550 GACCCAGAAAACTGGCATGTG 59.729 52.381 10.37 0.37 42.94 3.21 F
4660 4776 0.106918 TGTTGGGTTCGCTCTTTGGT 60.107 50.000 0.00 0.00 0.00 3.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1415 1519 0.179020 TGGAAACCAGCCACTGACAG 60.179 55.000 0.0 0.0 32.44 3.51 R
3020 3133 4.080356 AGCATACAAGATGTTAGGGCTTGA 60.080 41.667 0.0 0.0 41.03 3.02 R
4641 4757 0.106918 ACCAAAGAGCGAACCCAACA 60.107 50.000 0.0 0.0 0.00 3.33 R
4644 4760 0.181587 TGAACCAAAGAGCGAACCCA 59.818 50.000 0.0 0.0 0.00 4.51 R
4697 4813 0.752658 GCCCTGTTTGGTTCAGCTTT 59.247 50.000 0.0 0.0 0.00 3.51 R
6554 6852 0.250124 CCGCGGTATGCCCAAGATAA 60.250 55.000 19.5 0.0 42.08 1.75 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
33 36 3.420893 CAAAACACTTGGCCTCTCCATA 58.579 45.455 3.32 0.00 46.04 2.74
127 130 1.756538 CACCTGCAAGAAAAACCCTGT 59.243 47.619 0.00 0.00 34.07 4.00
128 131 1.756538 ACCTGCAAGAAAAACCCTGTG 59.243 47.619 0.00 0.00 34.07 3.66
241 320 1.239296 CGATGGATGCGGGCAATCAT 61.239 55.000 10.44 10.44 0.00 2.45
249 328 2.124151 GGGCAATCATGGACGCCT 60.124 61.111 16.41 0.00 44.27 5.52
373 458 0.741915 GGACCTGGTCTCGTCTGATC 59.258 60.000 25.01 2.67 32.47 2.92
536 627 1.204941 GGTGCGGTAATGTCTCTGTCT 59.795 52.381 0.00 0.00 0.00 3.41
537 628 2.531206 GTGCGGTAATGTCTCTGTCTC 58.469 52.381 0.00 0.00 0.00 3.36
538 629 2.164624 GTGCGGTAATGTCTCTGTCTCT 59.835 50.000 0.00 0.00 0.00 3.10
542 633 4.732355 GCGGTAATGTCTCTGTCTCTTCTC 60.732 50.000 0.00 0.00 0.00 2.87
546 637 5.404466 AATGTCTCTGTCTCTTCTCCTTG 57.596 43.478 0.00 0.00 0.00 3.61
549 640 4.279671 TGTCTCTGTCTCTTCTCCTTGTTC 59.720 45.833 0.00 0.00 0.00 3.18
558 649 6.201997 GTCTCTTCTCCTTGTTCTTCTTGTTC 59.798 42.308 0.00 0.00 0.00 3.18
579 670 0.108520 GGGGCATGTGAACTGCAATG 60.109 55.000 0.00 0.00 41.47 2.82
586 677 5.461078 GGCATGTGAACTGCAATGATTTATC 59.539 40.000 0.00 0.00 41.47 1.75
594 685 3.016031 TGCAATGATTTATCACAGGCGT 58.984 40.909 0.00 0.00 40.03 5.68
601 692 6.561737 TGATTTATCACAGGCGTGTAAAAA 57.438 33.333 12.40 12.49 44.02 1.94
656 748 5.423015 TCTTACTCCTGATTCTTGTCATGC 58.577 41.667 0.00 0.00 0.00 4.06
658 750 1.329906 CTCCTGATTCTTGTCATGCGC 59.670 52.381 0.00 0.00 0.00 6.09
664 756 0.310543 TTCTTGTCATGCGCAACCAC 59.689 50.000 17.11 12.15 0.00 4.16
677 769 0.600557 CAACCACGCCTTTTATGCCA 59.399 50.000 0.00 0.00 0.00 4.92
715 807 2.295885 GAGCAATCCCATTGTCCTCTG 58.704 52.381 0.00 0.00 42.20 3.35
982 1086 4.720046 TGCACCTTATTGTGGTCTGTTTA 58.280 39.130 0.00 0.00 36.73 2.01
983 1087 5.133941 TGCACCTTATTGTGGTCTGTTTAA 58.866 37.500 0.00 0.00 36.73 1.52
1076 1180 5.053145 GGACATACAGATAGTGGAAGCAAG 58.947 45.833 0.00 0.00 0.00 4.01
1311 1415 3.010584 ACTTCTATGTTCAGGTTGCCCAT 59.989 43.478 0.00 0.00 0.00 4.00
1368 1472 0.034670 ACATCTTTGGGGCTGAGCTC 60.035 55.000 6.82 6.82 0.00 4.09
1415 1519 4.162320 TGAACAGATCACAGAAGGGGATAC 59.838 45.833 0.00 0.00 31.50 2.24
1482 1586 9.618890 CCAAAGATATCTCCTGAACTCAATTTA 57.381 33.333 5.51 0.00 0.00 1.40
1563 1667 4.876107 GGTGGTACTGAGAATATTGGTGTG 59.124 45.833 0.00 0.00 0.00 3.82
2079 2183 5.826208 AGTTTTTCCTCCAAAACGTAGACAT 59.174 36.000 0.00 0.00 46.84 3.06
2199 2305 4.567747 GGGGTAGACAGTTTTGTGATGGAT 60.568 45.833 0.00 0.00 37.76 3.41
2728 2835 5.613358 GCTGTGGCCATATTAGACAATAC 57.387 43.478 9.72 0.00 29.44 1.89
2733 2840 5.864474 GTGGCCATATTAGACAATACTCGAG 59.136 44.000 9.72 11.84 29.44 4.04
2877 2990 3.431905 CCTCTCTCATTCATCACCACCTG 60.432 52.174 0.00 0.00 0.00 4.00
2907 3020 2.042297 TCCATTCCCTTACATTGTGCCA 59.958 45.455 0.00 0.00 0.00 4.92
2939 3052 3.495100 CCTGATGGTGGTAGTTATCCTGC 60.495 52.174 0.00 0.00 0.00 4.85
3018 3131 8.831715 ATGTTTTCACTTTTCACTTTTCACTT 57.168 26.923 0.00 0.00 0.00 3.16
3019 3132 8.655651 TGTTTTCACTTTTCACTTTTCACTTT 57.344 26.923 0.00 0.00 0.00 2.66
3020 3133 9.103861 TGTTTTCACTTTTCACTTTTCACTTTT 57.896 25.926 0.00 0.00 0.00 2.27
3021 3134 9.580916 GTTTTCACTTTTCACTTTTCACTTTTC 57.419 29.630 0.00 0.00 0.00 2.29
3022 3135 8.879342 TTTCACTTTTCACTTTTCACTTTTCA 57.121 26.923 0.00 0.00 0.00 2.69
3038 3151 5.010012 CACTTTTCAAGCCCTAACATCTTGT 59.990 40.000 0.00 0.00 38.56 3.16
3050 3164 6.828785 CCCTAACATCTTGTATGCTACCTTTT 59.171 38.462 0.00 0.00 0.00 2.27
3053 3167 7.944729 AACATCTTGTATGCTACCTTTTGAT 57.055 32.000 0.00 0.00 0.00 2.57
3066 3180 8.904834 TGCTACCTTTTGATAAGTTAAACAACA 58.095 29.630 5.70 0.87 0.00 3.33
3710 3824 4.400251 AGTTGGCATCATGATACTTTGGTG 59.600 41.667 8.15 0.00 0.00 4.17
3756 3870 0.972471 TTCGCCCTCTGCAGATGAGA 60.972 55.000 18.63 15.43 41.33 3.27
3803 3917 1.270550 GACCCAGAAAACTGGCATGTG 59.729 52.381 10.37 0.37 42.94 3.21
3823 3937 7.218773 GCATGTGCAGGTATTATATTTTATGCG 59.781 37.037 0.00 0.00 41.59 4.73
3975 4090 5.505181 TCCCTAAAGATGTTCAAGAAGCT 57.495 39.130 0.00 0.00 0.00 3.74
4300 4416 9.003658 CAGGTAATGAAGTTGTTTCTCAGTTAT 57.996 33.333 0.00 0.00 36.71 1.89
4315 4431 6.810911 TCTCAGTTATGGTAATCTCTTCTGC 58.189 40.000 0.00 0.00 0.00 4.26
4317 4433 6.810911 TCAGTTATGGTAATCTCTTCTGCTC 58.189 40.000 0.00 0.00 0.00 4.26
4426 4542 4.759693 TCGTATTCCATGCTTCACACTTTT 59.240 37.500 0.00 0.00 0.00 2.27
4552 4668 6.096141 TGGACTTTTCACAGCTTTTTATGACA 59.904 34.615 0.00 0.00 0.00 3.58
4554 4670 7.168135 GGACTTTTCACAGCTTTTTATGACAAG 59.832 37.037 0.00 0.00 35.79 3.16
4603 4719 9.068008 TCTTTTTACGAAAACTAGCACTTTTTG 57.932 29.630 0.00 0.00 31.72 2.44
4604 4720 7.743520 TTTTACGAAAACTAGCACTTTTTGG 57.256 32.000 8.41 4.00 0.00 3.28
4605 4721 4.976224 ACGAAAACTAGCACTTTTTGGT 57.024 36.364 8.41 4.49 39.92 3.67
4607 4723 5.337554 ACGAAAACTAGCACTTTTTGGTTC 58.662 37.500 8.41 0.00 37.13 3.62
4608 4724 5.106078 ACGAAAACTAGCACTTTTTGGTTCA 60.106 36.000 8.41 0.00 37.13 3.18
4609 4725 5.455525 CGAAAACTAGCACTTTTTGGTTCAG 59.544 40.000 0.00 0.00 37.13 3.02
4611 4727 6.715347 AAACTAGCACTTTTTGGTTCAGAT 57.285 33.333 0.00 0.00 37.13 2.90
4612 4728 6.715347 AACTAGCACTTTTTGGTTCAGATT 57.285 33.333 0.00 0.00 37.13 2.40
4613 4729 6.715347 ACTAGCACTTTTTGGTTCAGATTT 57.285 33.333 0.00 0.00 37.13 2.17
4614 4730 7.112452 ACTAGCACTTTTTGGTTCAGATTTT 57.888 32.000 0.00 0.00 37.13 1.82
4615 4731 6.980397 ACTAGCACTTTTTGGTTCAGATTTTG 59.020 34.615 0.00 0.00 37.13 2.44
4616 4732 5.118286 AGCACTTTTTGGTTCAGATTTTGG 58.882 37.500 0.00 0.00 28.85 3.28
4617 4733 4.260743 GCACTTTTTGGTTCAGATTTTGGC 60.261 41.667 0.00 0.00 0.00 4.52
4618 4734 4.874966 CACTTTTTGGTTCAGATTTTGGCA 59.125 37.500 0.00 0.00 0.00 4.92
4619 4735 5.006941 CACTTTTTGGTTCAGATTTTGGCAG 59.993 40.000 0.00 0.00 0.00 4.85
4620 4736 4.751767 TTTTGGTTCAGATTTTGGCAGT 57.248 36.364 0.00 0.00 0.00 4.40
4621 4737 3.731652 TTGGTTCAGATTTTGGCAGTG 57.268 42.857 0.00 0.00 0.00 3.66
4622 4738 1.962807 TGGTTCAGATTTTGGCAGTGG 59.037 47.619 0.00 0.00 0.00 4.00
4623 4739 2.238521 GGTTCAGATTTTGGCAGTGGA 58.761 47.619 0.00 0.00 0.00 4.02
4624 4740 2.827921 GGTTCAGATTTTGGCAGTGGAT 59.172 45.455 0.00 0.00 0.00 3.41
4625 4741 3.259123 GGTTCAGATTTTGGCAGTGGATT 59.741 43.478 0.00 0.00 0.00 3.01
4626 4742 4.262592 GGTTCAGATTTTGGCAGTGGATTT 60.263 41.667 0.00 0.00 0.00 2.17
4627 4743 4.789012 TCAGATTTTGGCAGTGGATTTC 57.211 40.909 0.00 0.00 0.00 2.17
4628 4744 4.410099 TCAGATTTTGGCAGTGGATTTCT 58.590 39.130 0.00 0.00 0.00 2.52
4629 4745 4.219070 TCAGATTTTGGCAGTGGATTTCTG 59.781 41.667 0.00 0.00 36.18 3.02
4630 4746 3.512724 AGATTTTGGCAGTGGATTTCTGG 59.487 43.478 0.00 0.00 33.98 3.86
4631 4747 2.673775 TTTGGCAGTGGATTTCTGGA 57.326 45.000 0.00 0.00 33.98 3.86
4632 4748 2.673775 TTGGCAGTGGATTTCTGGAA 57.326 45.000 0.00 0.00 33.98 3.53
4633 4749 2.905415 TGGCAGTGGATTTCTGGAAT 57.095 45.000 0.00 0.00 33.98 3.01
4634 4750 2.726821 TGGCAGTGGATTTCTGGAATC 58.273 47.619 0.00 0.00 42.84 2.52
4635 4751 1.672881 GGCAGTGGATTTCTGGAATCG 59.327 52.381 2.68 0.00 44.21 3.34
4636 4752 1.672881 GCAGTGGATTTCTGGAATCGG 59.327 52.381 2.68 0.00 44.21 4.18
4637 4753 2.680805 GCAGTGGATTTCTGGAATCGGA 60.681 50.000 2.68 0.00 44.21 4.55
4638 4754 3.813443 CAGTGGATTTCTGGAATCGGAT 58.187 45.455 2.68 0.00 44.21 4.18
4639 4755 4.202441 CAGTGGATTTCTGGAATCGGATT 58.798 43.478 2.19 2.19 44.21 3.01
4640 4756 4.274459 CAGTGGATTTCTGGAATCGGATTC 59.726 45.833 20.01 20.01 44.21 2.52
4641 4757 4.164988 AGTGGATTTCTGGAATCGGATTCT 59.835 41.667 25.29 8.76 44.21 2.40
4642 4758 4.274459 GTGGATTTCTGGAATCGGATTCTG 59.726 45.833 25.29 19.01 44.21 3.02
4643 4759 4.080356 TGGATTTCTGGAATCGGATTCTGT 60.080 41.667 25.29 9.27 44.21 3.41
4644 4760 4.884164 GGATTTCTGGAATCGGATTCTGTT 59.116 41.667 25.29 8.96 44.21 3.16
4645 4761 5.220931 GGATTTCTGGAATCGGATTCTGTTG 60.221 44.000 25.29 14.88 44.21 3.33
4646 4762 3.266510 TCTGGAATCGGATTCTGTTGG 57.733 47.619 25.29 13.47 39.24 3.77
4647 4763 2.092968 TCTGGAATCGGATTCTGTTGGG 60.093 50.000 25.29 12.15 39.24 4.12
4648 4764 1.633432 TGGAATCGGATTCTGTTGGGT 59.367 47.619 25.29 0.00 39.24 4.51
4649 4765 2.041081 TGGAATCGGATTCTGTTGGGTT 59.959 45.455 25.29 0.00 39.24 4.11
4650 4766 2.683362 GGAATCGGATTCTGTTGGGTTC 59.317 50.000 25.29 6.43 39.24 3.62
4651 4767 2.024176 ATCGGATTCTGTTGGGTTCG 57.976 50.000 0.00 0.00 0.00 3.95
4652 4768 0.672401 TCGGATTCTGTTGGGTTCGC 60.672 55.000 0.00 0.00 0.00 4.70
4653 4769 0.673644 CGGATTCTGTTGGGTTCGCT 60.674 55.000 0.00 0.00 0.00 4.93
4654 4770 1.087501 GGATTCTGTTGGGTTCGCTC 58.912 55.000 0.00 0.00 0.00 5.03
4655 4771 1.339151 GGATTCTGTTGGGTTCGCTCT 60.339 52.381 0.00 0.00 0.00 4.09
4656 4772 2.427506 GATTCTGTTGGGTTCGCTCTT 58.572 47.619 0.00 0.00 0.00 2.85
4657 4773 2.341846 TTCTGTTGGGTTCGCTCTTT 57.658 45.000 0.00 0.00 0.00 2.52
4658 4774 1.593196 TCTGTTGGGTTCGCTCTTTG 58.407 50.000 0.00 0.00 0.00 2.77
4659 4775 0.593128 CTGTTGGGTTCGCTCTTTGG 59.407 55.000 0.00 0.00 0.00 3.28
4660 4776 0.106918 TGTTGGGTTCGCTCTTTGGT 60.107 50.000 0.00 0.00 0.00 3.67
4661 4777 1.029681 GTTGGGTTCGCTCTTTGGTT 58.970 50.000 0.00 0.00 0.00 3.67
4662 4778 1.001706 GTTGGGTTCGCTCTTTGGTTC 60.002 52.381 0.00 0.00 0.00 3.62
4663 4779 0.181587 TGGGTTCGCTCTTTGGTTCA 59.818 50.000 0.00 0.00 0.00 3.18
4664 4780 0.875059 GGGTTCGCTCTTTGGTTCAG 59.125 55.000 0.00 0.00 0.00 3.02
4665 4781 1.542547 GGGTTCGCTCTTTGGTTCAGA 60.543 52.381 0.00 0.00 0.00 3.27
4666 4782 2.427506 GGTTCGCTCTTTGGTTCAGAT 58.572 47.619 0.00 0.00 0.00 2.90
4667 4783 2.814336 GGTTCGCTCTTTGGTTCAGATT 59.186 45.455 0.00 0.00 0.00 2.40
4668 4784 3.120165 GGTTCGCTCTTTGGTTCAGATTC 60.120 47.826 0.00 0.00 0.00 2.52
4669 4785 3.685139 TCGCTCTTTGGTTCAGATTCT 57.315 42.857 0.00 0.00 0.00 2.40
4670 4786 3.329386 TCGCTCTTTGGTTCAGATTCTG 58.671 45.455 7.38 7.38 0.00 3.02
4671 4787 2.159599 CGCTCTTTGGTTCAGATTCTGC 60.160 50.000 8.89 0.00 0.00 4.26
4672 4788 3.080319 GCTCTTTGGTTCAGATTCTGCT 58.920 45.455 8.89 0.00 0.00 4.24
4673 4789 3.119919 GCTCTTTGGTTCAGATTCTGCTG 60.120 47.826 8.89 0.00 37.24 4.41
4674 4790 2.816087 TCTTTGGTTCAGATTCTGCTGC 59.184 45.455 8.89 0.00 35.86 5.25
4675 4791 1.159285 TTGGTTCAGATTCTGCTGCG 58.841 50.000 8.89 0.00 35.86 5.18
4676 4792 1.300971 TGGTTCAGATTCTGCTGCGC 61.301 55.000 8.89 0.00 35.86 6.09
4677 4793 1.059994 GTTCAGATTCTGCTGCGCG 59.940 57.895 8.89 0.00 35.86 6.86
4678 4794 2.102438 TTCAGATTCTGCTGCGCGG 61.102 57.895 13.18 13.18 35.86 6.46
4679 4795 4.233635 CAGATTCTGCTGCGCGGC 62.234 66.667 34.00 34.00 34.49 6.53
4680 4796 4.765449 AGATTCTGCTGCGCGGCA 62.765 61.111 39.10 39.10 40.15 5.69
4692 4808 3.134127 GCGGCAGCGGAATCCTTT 61.134 61.111 3.69 0.00 0.00 3.11
4693 4809 2.793946 CGGCAGCGGAATCCTTTG 59.206 61.111 0.00 0.00 0.00 2.77
4694 4810 1.745115 CGGCAGCGGAATCCTTTGA 60.745 57.895 0.00 0.00 0.00 2.69
4695 4811 1.097547 CGGCAGCGGAATCCTTTGAT 61.098 55.000 0.00 0.00 0.00 2.57
4696 4812 1.810031 CGGCAGCGGAATCCTTTGATA 60.810 52.381 0.00 0.00 0.00 2.15
4697 4813 2.297701 GGCAGCGGAATCCTTTGATAA 58.702 47.619 0.00 0.00 0.00 1.75
4698 4814 2.687935 GGCAGCGGAATCCTTTGATAAA 59.312 45.455 0.00 0.00 0.00 1.40
4699 4815 3.130340 GGCAGCGGAATCCTTTGATAAAA 59.870 43.478 0.00 0.00 0.00 1.52
4700 4816 4.354587 GCAGCGGAATCCTTTGATAAAAG 58.645 43.478 0.00 0.00 0.00 2.27
4701 4817 4.354587 CAGCGGAATCCTTTGATAAAAGC 58.645 43.478 0.00 0.00 0.00 3.51
4702 4818 4.096984 CAGCGGAATCCTTTGATAAAAGCT 59.903 41.667 0.00 0.00 31.93 3.74
4703 4819 4.096984 AGCGGAATCCTTTGATAAAAGCTG 59.903 41.667 0.00 0.00 31.19 4.24
4704 4820 4.096382 GCGGAATCCTTTGATAAAAGCTGA 59.904 41.667 0.00 0.00 0.00 4.26
4705 4821 5.393027 GCGGAATCCTTTGATAAAAGCTGAA 60.393 40.000 0.00 0.00 0.00 3.02
4706 4822 6.030228 CGGAATCCTTTGATAAAAGCTGAAC 58.970 40.000 0.00 0.00 0.00 3.18
4707 4823 6.333416 GGAATCCTTTGATAAAAGCTGAACC 58.667 40.000 0.00 0.00 0.00 3.62
4708 4824 6.071391 GGAATCCTTTGATAAAAGCTGAACCA 60.071 38.462 0.00 0.00 0.00 3.67
4709 4825 6.916360 ATCCTTTGATAAAAGCTGAACCAA 57.084 33.333 0.00 0.00 0.00 3.67
4710 4826 6.723298 TCCTTTGATAAAAGCTGAACCAAA 57.277 33.333 0.00 0.00 0.00 3.28
4711 4827 6.512297 TCCTTTGATAAAAGCTGAACCAAAC 58.488 36.000 0.00 0.00 0.00 2.93
4712 4828 6.097554 TCCTTTGATAAAAGCTGAACCAAACA 59.902 34.615 0.00 0.00 0.00 2.83
4713 4829 6.421801 CCTTTGATAAAAGCTGAACCAAACAG 59.578 38.462 0.00 0.00 38.27 3.16
4714 4830 5.452078 TGATAAAAGCTGAACCAAACAGG 57.548 39.130 0.00 0.00 45.67 4.00
4715 4831 4.280677 TGATAAAAGCTGAACCAAACAGGG 59.719 41.667 0.00 0.00 43.89 4.45
4716 4832 0.752658 AAAGCTGAACCAAACAGGGC 59.247 50.000 0.00 0.00 43.89 5.19
4717 4833 1.115326 AAGCTGAACCAAACAGGGCC 61.115 55.000 0.00 0.00 43.89 5.80
4819 4935 1.202818 GGAACAGGTGCAGAGAACCTT 60.203 52.381 0.00 0.00 46.14 3.50
4832 4948 6.599244 TGCAGAGAACCTTATACCAATTGAAG 59.401 38.462 7.12 2.27 0.00 3.02
5128 5250 3.717842 CGAAAGGAAGGGTTGGACA 57.282 52.632 0.00 0.00 0.00 4.02
5259 5381 9.528018 GTAACTCTATTTCATTCTCTTCTCCTG 57.472 37.037 0.00 0.00 0.00 3.86
5362 5484 3.632604 TCAGGAGGTTCATGATCTACGTC 59.367 47.826 9.29 9.29 31.68 4.34
5499 5621 2.674380 CCACAGCTGGGCAGGAAC 60.674 66.667 19.93 0.00 33.23 3.62
5608 5730 0.250234 TCTGTCTGCAGGTGTATGGC 59.750 55.000 15.13 0.00 42.78 4.40
5722 5844 2.742116 GGCGGAGGATAACTGGGCA 61.742 63.158 0.00 0.00 0.00 5.36
5837 5959 1.900351 CATGAGAGCTTCCCGGACA 59.100 57.895 0.73 0.00 0.00 4.02
6009 6131 4.124851 TCCTCGGAAACTCAGAATTAGC 57.875 45.455 0.00 0.00 0.00 3.09
6044 6167 7.648112 TGCATATACGTCTGACTTTTAGCTTAG 59.352 37.037 6.21 0.00 0.00 2.18
6090 6215 4.344359 AAAAGAGAGACCAGACAGAACC 57.656 45.455 0.00 0.00 0.00 3.62
6161 6287 5.102953 TGGAGTCTATTGCTATGCACTTT 57.897 39.130 0.00 0.00 38.71 2.66
6171 6297 9.390795 CTATTGCTATGCACTTTTGATGTAATC 57.609 33.333 0.00 0.00 40.68 1.75
6303 6598 1.438651 CGAGAATTGTTCTTGCCCGA 58.561 50.000 0.00 0.00 40.87 5.14
6405 6702 0.938637 TGCAAATTCGCGCAAACCTG 60.939 50.000 8.75 0.00 34.59 4.00
6455 6753 1.363744 GAATGCCCAACTCAGTCGAG 58.636 55.000 0.00 0.00 45.49 4.04
6486 6784 3.804036 TCCGGCTACATAATTGGACTTG 58.196 45.455 0.00 0.00 0.00 3.16
6487 6785 2.290641 CCGGCTACATAATTGGACTTGC 59.709 50.000 0.00 0.00 0.00 4.01
6488 6786 2.942376 CGGCTACATAATTGGACTTGCA 59.058 45.455 0.00 0.00 0.00 4.08
6489 6787 3.565482 CGGCTACATAATTGGACTTGCAT 59.435 43.478 0.00 0.00 0.00 3.96
6490 6788 4.036734 CGGCTACATAATTGGACTTGCATT 59.963 41.667 0.00 0.00 0.00 3.56
6491 6789 5.523369 GGCTACATAATTGGACTTGCATTC 58.477 41.667 0.00 0.00 0.00 2.67
6492 6790 5.067674 GGCTACATAATTGGACTTGCATTCA 59.932 40.000 0.00 0.00 0.00 2.57
6493 6791 5.973565 GCTACATAATTGGACTTGCATTCAC 59.026 40.000 0.00 0.00 0.00 3.18
6494 6792 6.183360 GCTACATAATTGGACTTGCATTCACT 60.183 38.462 0.00 0.00 0.00 3.41
6495 6793 6.594788 ACATAATTGGACTTGCATTCACTT 57.405 33.333 0.00 0.00 0.00 3.16
6496 6794 6.996509 ACATAATTGGACTTGCATTCACTTT 58.003 32.000 0.00 0.00 0.00 2.66
6497 6795 6.869913 ACATAATTGGACTTGCATTCACTTTG 59.130 34.615 0.00 0.00 0.00 2.77
6498 6796 4.942761 ATTGGACTTGCATTCACTTTGT 57.057 36.364 0.00 0.00 0.00 2.83
6499 6797 6.403866 AATTGGACTTGCATTCACTTTGTA 57.596 33.333 0.00 0.00 0.00 2.41
6500 6798 5.437289 TTGGACTTGCATTCACTTTGTAG 57.563 39.130 0.00 0.00 0.00 2.74
6501 6799 3.820467 TGGACTTGCATTCACTTTGTAGG 59.180 43.478 0.00 0.00 0.00 3.18
6502 6800 3.821033 GGACTTGCATTCACTTTGTAGGT 59.179 43.478 0.00 0.00 0.00 3.08
6503 6801 4.278419 GGACTTGCATTCACTTTGTAGGTT 59.722 41.667 0.00 0.00 0.00 3.50
6504 6802 5.221244 GGACTTGCATTCACTTTGTAGGTTT 60.221 40.000 0.00 0.00 0.00 3.27
6505 6803 6.220726 ACTTGCATTCACTTTGTAGGTTTT 57.779 33.333 0.00 0.00 0.00 2.43
6506 6804 6.639563 ACTTGCATTCACTTTGTAGGTTTTT 58.360 32.000 0.00 0.00 0.00 1.94
6528 6826 5.957910 TTTTTGCGGTTGACACTTTATTG 57.042 34.783 0.00 0.00 0.00 1.90
6529 6827 4.640789 TTTGCGGTTGACACTTTATTGT 57.359 36.364 0.00 0.00 0.00 2.71
6530 6828 4.640789 TTGCGGTTGACACTTTATTGTT 57.359 36.364 0.00 0.00 0.00 2.83
6531 6829 4.640789 TGCGGTTGACACTTTATTGTTT 57.359 36.364 0.00 0.00 0.00 2.83
6532 6830 4.355437 TGCGGTTGACACTTTATTGTTTG 58.645 39.130 0.00 0.00 0.00 2.93
6533 6831 4.096532 TGCGGTTGACACTTTATTGTTTGA 59.903 37.500 0.00 0.00 0.00 2.69
6534 6832 5.219633 GCGGTTGACACTTTATTGTTTGAT 58.780 37.500 0.00 0.00 0.00 2.57
6535 6833 6.017026 TGCGGTTGACACTTTATTGTTTGATA 60.017 34.615 0.00 0.00 0.00 2.15
6536 6834 6.304683 GCGGTTGACACTTTATTGTTTGATAC 59.695 38.462 0.00 0.00 0.00 2.24
6537 6835 6.799925 CGGTTGACACTTTATTGTTTGATACC 59.200 38.462 0.00 0.00 0.00 2.73
6538 6836 7.520776 CGGTTGACACTTTATTGTTTGATACCA 60.521 37.037 0.00 0.00 0.00 3.25
6539 6837 8.303876 GGTTGACACTTTATTGTTTGATACCAT 58.696 33.333 0.00 0.00 0.00 3.55
6552 6850 9.887629 TTGTTTGATACCATAATTGAATGCATT 57.112 25.926 12.83 12.83 0.00 3.56
6553 6851 9.315525 TGTTTGATACCATAATTGAATGCATTG 57.684 29.630 18.59 0.34 0.00 2.82
6554 6852 9.316730 GTTTGATACCATAATTGAATGCATTGT 57.683 29.630 18.59 8.29 0.00 2.71
6555 6853 9.887629 TTTGATACCATAATTGAATGCATTGTT 57.112 25.926 18.59 11.11 0.00 2.83
6561 6859 9.537192 ACCATAATTGAATGCATTGTTATCTTG 57.463 29.630 18.59 8.31 0.00 3.02
6562 6860 8.984764 CCATAATTGAATGCATTGTTATCTTGG 58.015 33.333 18.59 12.66 0.00 3.61
6563 6861 8.984764 CATAATTGAATGCATTGTTATCTTGGG 58.015 33.333 18.59 3.48 0.00 4.12
6564 6862 4.389890 TGAATGCATTGTTATCTTGGGC 57.610 40.909 18.59 0.00 0.00 5.36
6565 6863 3.768215 TGAATGCATTGTTATCTTGGGCA 59.232 39.130 18.59 0.50 0.00 5.36
6566 6864 4.406326 TGAATGCATTGTTATCTTGGGCAT 59.594 37.500 18.59 0.00 41.79 4.40
6567 6865 5.597594 TGAATGCATTGTTATCTTGGGCATA 59.402 36.000 18.59 0.00 39.36 3.14
6568 6866 4.916983 TGCATTGTTATCTTGGGCATAC 57.083 40.909 0.00 0.00 0.00 2.39
6569 6867 3.636300 TGCATTGTTATCTTGGGCATACC 59.364 43.478 0.00 0.00 40.81 2.73
6570 6868 3.304659 GCATTGTTATCTTGGGCATACCG 60.305 47.826 0.00 0.00 44.64 4.02
6571 6869 1.961793 TGTTATCTTGGGCATACCGC 58.038 50.000 0.00 0.00 44.64 5.68
6572 6870 0.865769 GTTATCTTGGGCATACCGCG 59.134 55.000 0.00 0.00 44.64 6.46
6573 6871 0.250124 TTATCTTGGGCATACCGCGG 60.250 55.000 26.86 26.86 44.64 6.46
6574 6872 1.404479 TATCTTGGGCATACCGCGGT 61.404 55.000 36.01 36.01 44.64 5.68
6575 6873 2.660258 ATCTTGGGCATACCGCGGTC 62.660 60.000 38.01 21.31 44.64 4.79
6576 6874 3.385749 CTTGGGCATACCGCGGTCT 62.386 63.158 38.01 24.36 44.64 3.85
6577 6875 2.869503 CTTGGGCATACCGCGGTCTT 62.870 60.000 38.01 21.59 44.64 3.01
6578 6876 2.895372 GGGCATACCGCGGTCTTG 60.895 66.667 38.01 31.78 43.84 3.02
6579 6877 3.573491 GGCATACCGCGGTCTTGC 61.573 66.667 38.43 38.43 43.84 4.01
6580 6878 3.573491 GCATACCGCGGTCTTGCC 61.573 66.667 37.30 25.87 33.81 4.52
6597 6895 2.018542 GCCGAGGCACTTACATTACA 57.981 50.000 9.58 0.00 41.55 2.41
6598 6896 1.933853 GCCGAGGCACTTACATTACAG 59.066 52.381 9.58 0.00 41.55 2.74
6599 6897 2.550978 CCGAGGCACTTACATTACAGG 58.449 52.381 0.00 0.00 41.55 4.00
6600 6898 2.167693 CCGAGGCACTTACATTACAGGA 59.832 50.000 0.00 0.00 41.55 3.86
6601 6899 3.369052 CCGAGGCACTTACATTACAGGAA 60.369 47.826 0.00 0.00 41.55 3.36
6602 6900 3.865745 CGAGGCACTTACATTACAGGAAG 59.134 47.826 0.00 0.00 41.55 3.46
6603 6901 4.381612 CGAGGCACTTACATTACAGGAAGA 60.382 45.833 0.00 0.00 41.55 2.87
6604 6902 4.833390 AGGCACTTACATTACAGGAAGAC 58.167 43.478 0.00 0.00 27.25 3.01
6605 6903 3.939592 GGCACTTACATTACAGGAAGACC 59.060 47.826 0.00 0.00 0.00 3.85
6606 6904 6.520662 AGGCACTTACATTACAGGAAGACCT 61.521 44.000 0.00 0.00 42.35 3.85
6607 6905 5.246307 GCACTTACATTACAGGAAGACCTT 58.754 41.667 0.00 0.00 45.36 3.50
6608 6906 5.122396 GCACTTACATTACAGGAAGACCTTG 59.878 44.000 0.00 0.00 45.36 3.61
6609 6907 6.231211 CACTTACATTACAGGAAGACCTTGT 58.769 40.000 0.00 0.00 45.36 3.16
6839 7137 5.869753 AGCAACAACAGTAGCAAAGATAG 57.130 39.130 0.00 0.00 0.00 2.08
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 2.547642 GCCAAGTGTTTTGCTGGCATAA 60.548 45.455 7.05 0.00 41.63 1.90
33 36 1.022903 AAGGAGAGAGGTGGGAGGAT 58.977 55.000 0.00 0.00 0.00 3.24
347 432 1.539124 GAGACCAGGTCCAACCCCT 60.539 63.158 16.72 0.00 39.75 4.79
373 458 1.089920 CATTTTGCGTGGGAGAGAGG 58.910 55.000 0.00 0.00 0.00 3.69
536 627 5.989477 TGAACAAGAAGAACAAGGAGAAGA 58.011 37.500 0.00 0.00 0.00 2.87
537 628 5.238214 CCTGAACAAGAAGAACAAGGAGAAG 59.762 44.000 0.00 0.00 0.00 2.85
538 629 5.126067 CCTGAACAAGAAGAACAAGGAGAA 58.874 41.667 0.00 0.00 0.00 2.87
542 633 2.887152 CCCCTGAACAAGAAGAACAAGG 59.113 50.000 0.00 0.00 0.00 3.61
546 637 1.981256 TGCCCCTGAACAAGAAGAAC 58.019 50.000 0.00 0.00 0.00 3.01
549 640 1.542915 CACATGCCCCTGAACAAGAAG 59.457 52.381 0.00 0.00 0.00 2.85
558 649 1.180456 TTGCAGTTCACATGCCCCTG 61.180 55.000 0.00 0.00 43.18 4.45
572 663 3.065786 ACGCCTGTGATAAATCATTGCAG 59.934 43.478 0.00 0.00 39.30 4.41
656 748 1.070471 GCATAAAAGGCGTGGTTGCG 61.070 55.000 0.00 0.00 35.06 4.85
658 750 0.600557 TGGCATAAAAGGCGTGGTTG 59.399 50.000 0.00 0.00 36.77 3.77
664 756 6.091986 ACAAAATTTACATGGCATAAAAGGCG 59.908 34.615 0.00 0.00 36.77 5.52
677 769 9.382275 GGATTGCTCCAATTACAAAATTTACAT 57.618 29.630 0.00 0.00 41.64 2.29
715 807 0.741927 GCCTTGCATTGAATGTGGCC 60.742 55.000 20.06 0.00 37.33 5.36
830 933 6.149474 AGCACTTAACTTCATACGAAAGCATT 59.851 34.615 0.00 0.00 0.00 3.56
930 1034 7.230309 GCTAAGCTTTCATTTATCCTGGAGAAT 59.770 37.037 3.20 3.61 0.00 2.40
982 1086 4.043812 CCCCATTGTATGAGGGATGAGATT 59.956 45.833 0.00 0.00 45.80 2.40
983 1087 3.590630 CCCCATTGTATGAGGGATGAGAT 59.409 47.826 0.00 0.00 45.80 2.75
1076 1180 8.756927 TCATGAGATCCATATTAGGAAGACATC 58.243 37.037 0.00 0.00 41.92 3.06
1086 1190 6.496911 TCCTTTCGGTCATGAGATCCATATTA 59.503 38.462 0.00 0.00 33.31 0.98
1215 1319 0.183492 TTGCACCTGAGAGGCAAACT 59.817 50.000 8.00 0.00 43.82 2.66
1311 1415 4.037565 TGAAACTCGAGTCTGCTAACTGAA 59.962 41.667 20.33 0.00 0.00 3.02
1368 1472 3.935203 CTGGTACTGAAGCAACACCTATG 59.065 47.826 0.00 0.00 34.56 2.23
1415 1519 0.179020 TGGAAACCAGCCACTGACAG 60.179 55.000 0.00 0.00 32.44 3.51
1482 1586 8.829746 TGATCAAATGGCTTATACTGGATAGAT 58.170 33.333 0.00 0.00 0.00 1.98
1563 1667 4.800471 CGAAGAGGAAAATAAGCATTTGGC 59.200 41.667 0.00 0.00 45.30 4.52
1716 1820 4.721776 AGGTAAATAAGGTGATGAGCCTCA 59.278 41.667 0.00 0.00 34.81 3.86
2009 2113 9.985730 AATAATGTCATGACAAACAGTTCAAAT 57.014 25.926 31.00 8.43 45.41 2.32
2027 2131 8.648097 CACGGTAGCATCATAACTAATAATGTC 58.352 37.037 0.00 0.00 0.00 3.06
2199 2305 6.627087 ACATTGAACAAGAAGGGAGATAGA 57.373 37.500 0.00 0.00 0.00 1.98
2446 2552 8.530311 CAGCCTACATCATTTCTATCAGACTAT 58.470 37.037 0.00 0.00 0.00 2.12
2639 2746 8.798402 AGAATATGCAGAAGTATAGGTACACTC 58.202 37.037 0.00 0.00 33.09 3.51
2877 2990 5.416271 TGTAAGGGAATGGAGTAGAACAC 57.584 43.478 0.00 0.00 0.00 3.32
2939 3052 5.032863 GCAAGATGTTAAGCTTAGTGCATG 58.967 41.667 18.55 11.50 45.94 4.06
3017 3130 6.350110 GCATACAAGATGTTAGGGCTTGAAAA 60.350 38.462 0.00 0.00 41.03 2.29
3018 3131 5.125417 GCATACAAGATGTTAGGGCTTGAAA 59.875 40.000 0.00 0.00 41.03 2.69
3019 3132 4.640201 GCATACAAGATGTTAGGGCTTGAA 59.360 41.667 0.00 0.00 41.03 2.69
3020 3133 4.080356 AGCATACAAGATGTTAGGGCTTGA 60.080 41.667 0.00 0.00 41.03 3.02
3021 3134 4.202441 AGCATACAAGATGTTAGGGCTTG 58.798 43.478 0.00 0.00 43.41 4.01
3022 3135 4.510167 AGCATACAAGATGTTAGGGCTT 57.490 40.909 0.00 0.00 0.00 4.35
3066 3180 8.696043 ACAACATGCATATTCTTGGTATGTAT 57.304 30.769 0.00 0.00 36.96 2.29
3182 3296 4.218312 AGGGATTTTGCTTCAGAAACACT 58.782 39.130 0.00 0.00 0.00 3.55
3400 3514 9.498176 GTTAACTGTTAGAGAATTACAGGGAAA 57.502 33.333 9.51 0.00 42.70 3.13
3710 3824 5.828299 TCCATGACATCCGGTTTATTTTC 57.172 39.130 0.00 0.00 0.00 2.29
3756 3870 8.659925 TTTTCTTCACAAACATGTGCATTTAT 57.340 26.923 0.00 0.00 39.49 1.40
3823 3937 8.446273 GGTGATGCATCTATGATTTGTATGTAC 58.554 37.037 26.32 10.56 0.00 2.90
4300 4416 2.457598 ACGGAGCAGAAGAGATTACCA 58.542 47.619 0.00 0.00 0.00 3.25
4404 4520 4.685169 AAAGTGTGAAGCATGGAATACG 57.315 40.909 0.00 0.00 0.00 3.06
4552 4668 8.697507 AAACCAATGATGTACTTCTCTTTCTT 57.302 30.769 9.87 0.00 0.00 2.52
4554 4670 8.329203 AGAAACCAATGATGTACTTCTCTTTC 57.671 34.615 9.87 8.67 0.00 2.62
4603 4719 2.238521 TCCACTGCCAAAATCTGAACC 58.761 47.619 0.00 0.00 0.00 3.62
4604 4720 4.525912 AATCCACTGCCAAAATCTGAAC 57.474 40.909 0.00 0.00 0.00 3.18
4605 4721 4.834496 AGAAATCCACTGCCAAAATCTGAA 59.166 37.500 0.00 0.00 0.00 3.02
4607 4723 4.491676 CAGAAATCCACTGCCAAAATCTG 58.508 43.478 0.00 0.00 0.00 2.90
4608 4724 3.512724 CCAGAAATCCACTGCCAAAATCT 59.487 43.478 0.00 0.00 34.47 2.40
4609 4725 3.511146 TCCAGAAATCCACTGCCAAAATC 59.489 43.478 0.00 0.00 34.47 2.17
4611 4727 2.956132 TCCAGAAATCCACTGCCAAAA 58.044 42.857 0.00 0.00 34.47 2.44
4612 4728 2.673775 TCCAGAAATCCACTGCCAAA 57.326 45.000 0.00 0.00 34.47 3.28
4613 4729 2.673775 TTCCAGAAATCCACTGCCAA 57.326 45.000 0.00 0.00 34.47 4.52
4614 4730 2.726821 GATTCCAGAAATCCACTGCCA 58.273 47.619 0.00 0.00 38.27 4.92
4615 4731 1.672881 CGATTCCAGAAATCCACTGCC 59.327 52.381 0.00 0.00 40.69 4.85
4616 4732 1.672881 CCGATTCCAGAAATCCACTGC 59.327 52.381 0.00 0.00 40.69 4.40
4617 4733 3.266510 TCCGATTCCAGAAATCCACTG 57.733 47.619 0.00 0.00 40.69 3.66
4618 4734 4.164988 AGAATCCGATTCCAGAAATCCACT 59.835 41.667 16.09 0.00 40.69 4.00
4619 4735 4.274459 CAGAATCCGATTCCAGAAATCCAC 59.726 45.833 16.09 0.00 40.69 4.02
4620 4736 4.080356 ACAGAATCCGATTCCAGAAATCCA 60.080 41.667 16.09 0.00 40.69 3.41
4621 4737 4.455606 ACAGAATCCGATTCCAGAAATCC 58.544 43.478 16.09 0.00 40.69 3.01
4622 4738 5.220931 CCAACAGAATCCGATTCCAGAAATC 60.221 44.000 16.09 0.00 40.13 2.17
4623 4739 4.641989 CCAACAGAATCCGATTCCAGAAAT 59.358 41.667 16.09 0.00 40.13 2.17
4624 4740 4.009675 CCAACAGAATCCGATTCCAGAAA 58.990 43.478 16.09 0.00 40.13 2.52
4625 4741 3.609853 CCAACAGAATCCGATTCCAGAA 58.390 45.455 16.09 0.00 40.13 3.02
4626 4742 2.092968 CCCAACAGAATCCGATTCCAGA 60.093 50.000 16.09 0.00 40.13 3.86
4627 4743 2.292267 CCCAACAGAATCCGATTCCAG 58.708 52.381 16.09 12.09 40.13 3.86
4628 4744 1.633432 ACCCAACAGAATCCGATTCCA 59.367 47.619 16.09 0.00 40.13 3.53
4629 4745 2.420058 ACCCAACAGAATCCGATTCC 57.580 50.000 16.09 0.95 40.13 3.01
4630 4746 2.351726 CGAACCCAACAGAATCCGATTC 59.648 50.000 12.51 12.51 39.56 2.52
4631 4747 2.356135 CGAACCCAACAGAATCCGATT 58.644 47.619 0.00 0.00 0.00 3.34
4632 4748 2.012051 GCGAACCCAACAGAATCCGAT 61.012 52.381 0.00 0.00 0.00 4.18
4633 4749 0.672401 GCGAACCCAACAGAATCCGA 60.672 55.000 0.00 0.00 0.00 4.55
4634 4750 0.673644 AGCGAACCCAACAGAATCCG 60.674 55.000 0.00 0.00 0.00 4.18
4635 4751 1.087501 GAGCGAACCCAACAGAATCC 58.912 55.000 0.00 0.00 0.00 3.01
4636 4752 2.100605 AGAGCGAACCCAACAGAATC 57.899 50.000 0.00 0.00 0.00 2.52
4637 4753 2.554032 CAAAGAGCGAACCCAACAGAAT 59.446 45.455 0.00 0.00 0.00 2.40
4638 4754 1.946768 CAAAGAGCGAACCCAACAGAA 59.053 47.619 0.00 0.00 0.00 3.02
4639 4755 1.593196 CAAAGAGCGAACCCAACAGA 58.407 50.000 0.00 0.00 0.00 3.41
4640 4756 0.593128 CCAAAGAGCGAACCCAACAG 59.407 55.000 0.00 0.00 0.00 3.16
4641 4757 0.106918 ACCAAAGAGCGAACCCAACA 60.107 50.000 0.00 0.00 0.00 3.33
4642 4758 1.001706 GAACCAAAGAGCGAACCCAAC 60.002 52.381 0.00 0.00 0.00 3.77
4643 4759 1.314730 GAACCAAAGAGCGAACCCAA 58.685 50.000 0.00 0.00 0.00 4.12
4644 4760 0.181587 TGAACCAAAGAGCGAACCCA 59.818 50.000 0.00 0.00 0.00 4.51
4645 4761 0.875059 CTGAACCAAAGAGCGAACCC 59.125 55.000 0.00 0.00 0.00 4.11
4646 4762 1.878953 TCTGAACCAAAGAGCGAACC 58.121 50.000 0.00 0.00 0.00 3.62
4647 4763 3.748568 AGAATCTGAACCAAAGAGCGAAC 59.251 43.478 0.00 0.00 0.00 3.95
4648 4764 3.748048 CAGAATCTGAACCAAAGAGCGAA 59.252 43.478 3.77 0.00 32.44 4.70
4649 4765 3.329386 CAGAATCTGAACCAAAGAGCGA 58.671 45.455 3.77 0.00 32.44 4.93
4650 4766 2.159599 GCAGAATCTGAACCAAAGAGCG 60.160 50.000 15.38 0.00 32.44 5.03
4651 4767 3.080319 AGCAGAATCTGAACCAAAGAGC 58.920 45.455 15.38 0.00 32.44 4.09
4652 4768 3.119919 GCAGCAGAATCTGAACCAAAGAG 60.120 47.826 15.38 0.00 36.19 2.85
4653 4769 2.816087 GCAGCAGAATCTGAACCAAAGA 59.184 45.455 15.38 0.00 36.19 2.52
4654 4770 2.413765 CGCAGCAGAATCTGAACCAAAG 60.414 50.000 15.38 0.00 36.19 2.77
4655 4771 1.536766 CGCAGCAGAATCTGAACCAAA 59.463 47.619 15.38 0.00 36.19 3.28
4656 4772 1.159285 CGCAGCAGAATCTGAACCAA 58.841 50.000 15.38 0.00 36.19 3.67
4657 4773 2.845019 CGCAGCAGAATCTGAACCA 58.155 52.632 15.38 0.00 36.19 3.67
4675 4791 3.134127 AAAGGATTCCGCTGCCGC 61.134 61.111 0.00 0.00 0.00 6.53
4676 4792 1.097547 ATCAAAGGATTCCGCTGCCG 61.098 55.000 0.00 0.00 0.00 5.69
4677 4793 1.967319 TATCAAAGGATTCCGCTGCC 58.033 50.000 0.00 0.00 34.89 4.85
4678 4794 4.354587 CTTTTATCAAAGGATTCCGCTGC 58.645 43.478 0.00 0.00 36.48 5.25
4679 4795 4.096984 AGCTTTTATCAAAGGATTCCGCTG 59.903 41.667 1.73 0.00 40.03 5.18
4680 4796 4.096984 CAGCTTTTATCAAAGGATTCCGCT 59.903 41.667 1.73 0.00 40.03 5.52
4681 4797 4.096382 TCAGCTTTTATCAAAGGATTCCGC 59.904 41.667 1.73 0.00 40.03 5.54
4682 4798 5.818136 TCAGCTTTTATCAAAGGATTCCG 57.182 39.130 1.73 0.00 40.03 4.30
4683 4799 6.071391 TGGTTCAGCTTTTATCAAAGGATTCC 60.071 38.462 1.73 0.00 40.03 3.01
4684 4800 6.924111 TGGTTCAGCTTTTATCAAAGGATTC 58.076 36.000 1.73 0.00 40.03 2.52
4685 4801 6.916360 TGGTTCAGCTTTTATCAAAGGATT 57.084 33.333 1.73 0.00 40.03 3.01
4686 4802 6.916360 TTGGTTCAGCTTTTATCAAAGGAT 57.084 33.333 1.73 0.00 40.03 3.24
4687 4803 6.097554 TGTTTGGTTCAGCTTTTATCAAAGGA 59.902 34.615 1.73 0.00 40.03 3.36
4688 4804 6.279882 TGTTTGGTTCAGCTTTTATCAAAGG 58.720 36.000 1.73 0.00 40.03 3.11
4689 4805 6.421801 CCTGTTTGGTTCAGCTTTTATCAAAG 59.578 38.462 0.00 0.00 42.26 2.77
4690 4806 6.279882 CCTGTTTGGTTCAGCTTTTATCAAA 58.720 36.000 0.00 0.00 0.00 2.69
4691 4807 5.221422 CCCTGTTTGGTTCAGCTTTTATCAA 60.221 40.000 0.00 0.00 0.00 2.57
4692 4808 4.280677 CCCTGTTTGGTTCAGCTTTTATCA 59.719 41.667 0.00 0.00 0.00 2.15
4693 4809 4.809673 CCCTGTTTGGTTCAGCTTTTATC 58.190 43.478 0.00 0.00 0.00 1.75
4694 4810 3.006859 GCCCTGTTTGGTTCAGCTTTTAT 59.993 43.478 0.00 0.00 0.00 1.40
4695 4811 2.364002 GCCCTGTTTGGTTCAGCTTTTA 59.636 45.455 0.00 0.00 0.00 1.52
4696 4812 1.138859 GCCCTGTTTGGTTCAGCTTTT 59.861 47.619 0.00 0.00 0.00 2.27
4697 4813 0.752658 GCCCTGTTTGGTTCAGCTTT 59.247 50.000 0.00 0.00 0.00 3.51
4698 4814 1.115326 GGCCCTGTTTGGTTCAGCTT 61.115 55.000 0.00 0.00 0.00 3.74
4699 4815 1.531602 GGCCCTGTTTGGTTCAGCT 60.532 57.895 0.00 0.00 0.00 4.24
4700 4816 1.115326 AAGGCCCTGTTTGGTTCAGC 61.115 55.000 0.00 0.00 0.00 4.26
4701 4817 1.413118 AAAGGCCCTGTTTGGTTCAG 58.587 50.000 0.00 0.00 0.00 3.02
4702 4818 2.757894 TAAAGGCCCTGTTTGGTTCA 57.242 45.000 0.00 0.00 0.00 3.18
4703 4819 2.897326 ACATAAAGGCCCTGTTTGGTTC 59.103 45.455 0.00 0.00 0.00 3.62
4704 4820 2.632512 CACATAAAGGCCCTGTTTGGTT 59.367 45.455 0.00 0.00 0.00 3.67
4705 4821 2.247358 CACATAAAGGCCCTGTTTGGT 58.753 47.619 0.00 0.00 0.00 3.67
4706 4822 1.066929 GCACATAAAGGCCCTGTTTGG 60.067 52.381 0.00 0.00 0.00 3.28
4707 4823 1.895131 AGCACATAAAGGCCCTGTTTG 59.105 47.619 0.00 0.00 0.00 2.93
4708 4824 2.309136 AGCACATAAAGGCCCTGTTT 57.691 45.000 0.00 0.00 0.00 2.83
4709 4825 3.203040 AGATAGCACATAAAGGCCCTGTT 59.797 43.478 0.00 0.00 0.00 3.16
4710 4826 2.780010 AGATAGCACATAAAGGCCCTGT 59.220 45.455 0.00 0.00 0.00 4.00
4711 4827 3.144506 CAGATAGCACATAAAGGCCCTG 58.855 50.000 0.00 0.00 0.00 4.45
4712 4828 3.048600 TCAGATAGCACATAAAGGCCCT 58.951 45.455 0.00 0.00 0.00 5.19
4713 4829 3.492102 TCAGATAGCACATAAAGGCCC 57.508 47.619 0.00 0.00 0.00 5.80
4714 4830 4.392940 ACATCAGATAGCACATAAAGGCC 58.607 43.478 0.00 0.00 0.00 5.19
4715 4831 8.253810 TCTATACATCAGATAGCACATAAAGGC 58.746 37.037 0.00 0.00 0.00 4.35
4819 4935 7.350382 TCTTTATGGCCACTTCAATTGGTATA 58.650 34.615 8.16 0.00 36.40 1.47
4832 4948 4.454728 TTCTTGCAATCTTTATGGCCAC 57.545 40.909 8.16 0.00 30.07 5.01
4964 5080 8.671028 CATGACAAAACTGTAATCTGATCATGA 58.329 33.333 0.00 0.00 32.93 3.07
5128 5250 2.424812 GGTAATCCTGTGGATGGGCATT 60.425 50.000 0.00 0.00 42.27 3.56
5362 5484 2.988010 TGATCATCCCTTTCGAGTGG 57.012 50.000 0.00 0.00 0.00 4.00
5499 5621 4.148825 CTCGCGGAGGACCTTGGG 62.149 72.222 6.13 0.07 0.00 4.12
5689 5811 0.893270 CCGCCATCTGGTTCACCAAA 60.893 55.000 0.00 0.00 46.97 3.28
5722 5844 1.884464 CTGCGGCGACACATAGCAT 60.884 57.895 12.98 0.00 37.20 3.79
5769 5891 1.006758 TCTCGACCTTGATGGGGTACT 59.993 52.381 0.00 0.00 41.11 2.73
5837 5959 2.045926 GAGCACCTTGCCACCGAT 60.046 61.111 0.00 0.00 46.52 4.18
6009 6131 5.400782 GTCAGACGTATATGCAACAGATCAG 59.599 44.000 0.00 0.00 0.00 2.90
6044 6167 9.577110 TTATATACACATATACAGCTTAACGGC 57.423 33.333 0.00 0.00 30.80 5.68
6090 6215 5.982890 AAATTTGGTCCAACTGGTATGAG 57.017 39.130 2.98 0.00 36.34 2.90
6161 6287 2.922955 TGGACAAGGGGGATTACATCAA 59.077 45.455 0.00 0.00 0.00 2.57
6171 6297 4.722700 CTGCGGTGGACAAGGGGG 62.723 72.222 0.00 0.00 0.00 5.40
6333 6630 4.804139 TCAACTTGACTGAAGAACTCGTTC 59.196 41.667 1.62 1.62 39.78 3.95
6379 6676 1.732474 GCGCGAATTTGCATCAACGG 61.732 55.000 12.10 0.63 34.15 4.44
6405 6702 4.634184 TCTACGAGCTCATTACCAACTC 57.366 45.455 15.40 0.00 0.00 3.01
6455 6753 8.237267 CCAATTATGTAGCCGGATTATTTCTTC 58.763 37.037 5.05 0.00 0.00 2.87
6506 6804 5.411781 ACAATAAAGTGTCAACCGCAAAAA 58.588 33.333 0.00 0.00 0.00 1.94
6507 6805 5.000012 ACAATAAAGTGTCAACCGCAAAA 58.000 34.783 0.00 0.00 0.00 2.44
6508 6806 4.640789 ACAATAAAGTGTCAACCGCAAA 57.359 36.364 0.00 0.00 0.00 3.68
6509 6807 4.640789 AACAATAAAGTGTCAACCGCAA 57.359 36.364 0.00 0.00 0.00 4.85
6510 6808 4.096532 TCAAACAATAAAGTGTCAACCGCA 59.903 37.500 0.00 0.00 0.00 5.69
6511 6809 4.602995 TCAAACAATAAAGTGTCAACCGC 58.397 39.130 0.00 0.00 0.00 5.68
6512 6810 6.799925 GGTATCAAACAATAAAGTGTCAACCG 59.200 38.462 0.00 0.00 0.00 4.44
6513 6811 7.653647 TGGTATCAAACAATAAAGTGTCAACC 58.346 34.615 0.00 0.00 0.00 3.77
6526 6824 9.887629 AATGCATTCAATTATGGTATCAAACAA 57.112 25.926 5.99 0.00 0.00 2.83
6527 6825 9.315525 CAATGCATTCAATTATGGTATCAAACA 57.684 29.630 9.53 0.00 0.00 2.83
6528 6826 9.316730 ACAATGCATTCAATTATGGTATCAAAC 57.683 29.630 9.53 0.00 0.00 2.93
6529 6827 9.887629 AACAATGCATTCAATTATGGTATCAAA 57.112 25.926 9.53 0.00 0.00 2.69
6535 6833 9.537192 CAAGATAACAATGCATTCAATTATGGT 57.463 29.630 9.53 0.00 0.00 3.55
6536 6834 8.984764 CCAAGATAACAATGCATTCAATTATGG 58.015 33.333 9.53 9.22 0.00 2.74
6537 6835 8.984764 CCCAAGATAACAATGCATTCAATTATG 58.015 33.333 9.53 0.00 0.00 1.90
6538 6836 7.658575 GCCCAAGATAACAATGCATTCAATTAT 59.341 33.333 9.53 13.27 0.00 1.28
6539 6837 6.985645 GCCCAAGATAACAATGCATTCAATTA 59.014 34.615 9.53 9.11 0.00 1.40
6540 6838 5.818857 GCCCAAGATAACAATGCATTCAATT 59.181 36.000 9.53 7.12 0.00 2.32
6541 6839 5.104859 TGCCCAAGATAACAATGCATTCAAT 60.105 36.000 9.53 3.14 0.00 2.57
6542 6840 4.222366 TGCCCAAGATAACAATGCATTCAA 59.778 37.500 9.53 0.00 0.00 2.69
6543 6841 3.768215 TGCCCAAGATAACAATGCATTCA 59.232 39.130 9.53 0.00 0.00 2.57
6544 6842 4.389890 TGCCCAAGATAACAATGCATTC 57.610 40.909 9.53 0.00 0.00 2.67
6545 6843 5.221501 GGTATGCCCAAGATAACAATGCATT 60.222 40.000 5.99 5.99 38.72 3.56
6546 6844 4.281688 GGTATGCCCAAGATAACAATGCAT 59.718 41.667 0.00 0.00 40.67 3.96
6547 6845 3.636300 GGTATGCCCAAGATAACAATGCA 59.364 43.478 0.00 0.00 0.00 3.96
6548 6846 3.304659 CGGTATGCCCAAGATAACAATGC 60.305 47.826 0.00 0.00 0.00 3.56
6549 6847 3.304659 GCGGTATGCCCAAGATAACAATG 60.305 47.826 0.00 0.00 37.76 2.82
6550 6848 2.884639 GCGGTATGCCCAAGATAACAAT 59.115 45.455 0.00 0.00 37.76 2.71
6551 6849 2.294074 GCGGTATGCCCAAGATAACAA 58.706 47.619 0.00 0.00 37.76 2.83
6552 6850 1.808512 CGCGGTATGCCCAAGATAACA 60.809 52.381 0.00 0.00 42.08 2.41
6553 6851 0.865769 CGCGGTATGCCCAAGATAAC 59.134 55.000 0.00 0.00 42.08 1.89
6554 6852 0.250124 CCGCGGTATGCCCAAGATAA 60.250 55.000 19.50 0.00 42.08 1.75
6555 6853 1.369692 CCGCGGTATGCCCAAGATA 59.630 57.895 19.50 0.00 42.08 1.98
6556 6854 2.111043 CCGCGGTATGCCCAAGAT 59.889 61.111 19.50 0.00 42.08 2.40
6557 6855 3.379865 GACCGCGGTATGCCCAAGA 62.380 63.158 34.36 0.00 42.08 3.02
6558 6856 2.869503 AAGACCGCGGTATGCCCAAG 62.870 60.000 34.36 0.00 42.08 3.61
6559 6857 2.961893 AAGACCGCGGTATGCCCAA 61.962 57.895 34.36 0.00 42.08 4.12
6560 6858 3.395702 AAGACCGCGGTATGCCCA 61.396 61.111 34.36 0.00 42.08 5.36
6561 6859 2.895372 CAAGACCGCGGTATGCCC 60.895 66.667 34.36 19.02 42.08 5.36
6562 6860 3.573491 GCAAGACCGCGGTATGCC 61.573 66.667 38.89 27.41 42.08 4.40
6563 6861 3.573491 GGCAAGACCGCGGTATGC 61.573 66.667 39.99 39.99 39.09 3.14
6578 6876 1.933853 CTGTAATGTAAGTGCCTCGGC 59.066 52.381 0.00 0.00 42.35 5.54
6579 6877 2.167693 TCCTGTAATGTAAGTGCCTCGG 59.832 50.000 0.00 0.00 0.00 4.63
6580 6878 3.520290 TCCTGTAATGTAAGTGCCTCG 57.480 47.619 0.00 0.00 0.00 4.63
6581 6879 4.870991 GTCTTCCTGTAATGTAAGTGCCTC 59.129 45.833 0.00 0.00 0.00 4.70
6582 6880 4.323562 GGTCTTCCTGTAATGTAAGTGCCT 60.324 45.833 0.00 0.00 0.00 4.75
6583 6881 3.939592 GGTCTTCCTGTAATGTAAGTGCC 59.060 47.826 0.00 0.00 0.00 5.01
6584 6882 4.833390 AGGTCTTCCTGTAATGTAAGTGC 58.167 43.478 0.00 0.00 43.33 4.40
6585 6883 6.231211 ACAAGGTCTTCCTGTAATGTAAGTG 58.769 40.000 0.00 0.00 44.35 3.16
6586 6884 6.435292 ACAAGGTCTTCCTGTAATGTAAGT 57.565 37.500 0.00 0.00 44.35 2.24
6587 6885 8.718734 GTTAACAAGGTCTTCCTGTAATGTAAG 58.281 37.037 0.00 0.00 44.35 2.34
6588 6886 7.662669 GGTTAACAAGGTCTTCCTGTAATGTAA 59.337 37.037 8.10 0.00 44.35 2.41
6589 6887 7.016858 AGGTTAACAAGGTCTTCCTGTAATGTA 59.983 37.037 8.10 0.00 44.35 2.29
6590 6888 6.002082 GGTTAACAAGGTCTTCCTGTAATGT 58.998 40.000 8.10 0.00 44.35 2.71
6591 6889 6.238648 AGGTTAACAAGGTCTTCCTGTAATG 58.761 40.000 8.10 0.00 44.35 1.90
6592 6890 6.449830 AGGTTAACAAGGTCTTCCTGTAAT 57.550 37.500 8.10 0.00 44.35 1.89
6593 6891 5.899631 AGGTTAACAAGGTCTTCCTGTAA 57.100 39.130 8.10 0.00 44.35 2.41
6594 6892 5.367352 TCAAGGTTAACAAGGTCTTCCTGTA 59.633 40.000 8.10 0.00 44.35 2.74
6595 6893 4.165372 TCAAGGTTAACAAGGTCTTCCTGT 59.835 41.667 8.10 0.00 44.35 4.00
6596 6894 4.714632 TCAAGGTTAACAAGGTCTTCCTG 58.285 43.478 8.10 0.00 44.35 3.86
6597 6895 6.408034 TCCTCAAGGTTAACAAGGTCTTCCT 61.408 44.000 8.10 0.00 40.24 3.36
6598 6896 4.072839 CCTCAAGGTTAACAAGGTCTTCC 58.927 47.826 8.10 0.00 0.00 3.46
6599 6897 4.969484 TCCTCAAGGTTAACAAGGTCTTC 58.031 43.478 8.10 0.00 36.34 2.87
6600 6898 5.132144 TCTTCCTCAAGGTTAACAAGGTCTT 59.868 40.000 8.10 0.00 36.34 3.01
6601 6899 4.658901 TCTTCCTCAAGGTTAACAAGGTCT 59.341 41.667 8.10 0.00 36.34 3.85
6602 6900 4.969484 TCTTCCTCAAGGTTAACAAGGTC 58.031 43.478 8.10 0.00 36.34 3.85
6603 6901 4.202472 CCTCTTCCTCAAGGTTAACAAGGT 60.202 45.833 8.10 0.00 36.34 3.50
6604 6902 4.327680 CCTCTTCCTCAAGGTTAACAAGG 58.672 47.826 8.10 8.34 36.34 3.61
6605 6903 3.753797 GCCTCTTCCTCAAGGTTAACAAG 59.246 47.826 8.10 0.80 34.96 3.16
6606 6904 3.137544 TGCCTCTTCCTCAAGGTTAACAA 59.862 43.478 8.10 0.00 34.96 2.83
6607 6905 2.708861 TGCCTCTTCCTCAAGGTTAACA 59.291 45.455 8.10 0.00 34.96 2.41
6608 6906 3.418684 TGCCTCTTCCTCAAGGTTAAC 57.581 47.619 0.00 0.00 34.96 2.01
6609 6907 3.587061 TGATGCCTCTTCCTCAAGGTTAA 59.413 43.478 0.00 0.00 34.96 2.01
6839 7137 7.664082 ATTTGTGTAGTGCTCTATATCATGC 57.336 36.000 0.00 0.00 0.00 4.06


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

AutoCloner maintained by Alex Coulton.