Multiple sequence alignment - TraesCS2A01G557500

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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 TraesCS2A01G557500 chr2A 100.000 4741 0 0 1 4741 761131634 761136374 0.000000e+00 8756.0
1 TraesCS2A01G557500 chr2A 97.902 143 2 1 4600 4741 58987565 58987707 3.660000e-61 246.0
2 TraesCS2A01G557500 chr2A 97.902 143 2 1 4600 4741 632422812 632422954 3.660000e-61 246.0
3 TraesCS2A01G557500 chr2A 96.970 99 3 0 4482 4580 58992710 58992612 2.930000e-37 167.0
4 TraesCS2A01G557500 chr2A 90.909 44 2 2 4570 4612 58985726 58985684 1.840000e-04 58.4
5 TraesCS2A01G557500 chr2A 100.000 31 0 0 4570 4600 58992986 58993016 1.840000e-04 58.4
6 TraesCS2A01G557500 chr2A 100.000 31 0 0 4570 4600 761129257 761129227 1.840000e-04 58.4
7 TraesCS2A01G557500 chr5B 98.282 4483 72 4 1 4480 663247962 663243482 0.000000e+00 7847.0
8 TraesCS2A01G557500 chr5B 98.592 142 2 0 4600 4741 586799334 586799193 7.880000e-63 252.0
9 TraesCS2A01G557500 chr6B 97.970 4483 82 4 1 4481 522436849 522432374 0.000000e+00 7766.0
10 TraesCS2A01G557500 chr6B 97.656 3583 83 1 1 3583 49682119 49678538 0.000000e+00 6150.0
11 TraesCS2A01G557500 chr6B 95.484 465 21 0 1052 1516 29510578 29511042 0.000000e+00 743.0
12 TraesCS2A01G557500 chr1B 97.926 4485 90 2 1 4482 37922659 37918175 0.000000e+00 7764.0
13 TraesCS2A01G557500 chr1B 93.359 1054 64 5 1 1050 31636341 31635290 0.000000e+00 1554.0
14 TraesCS2A01G557500 chr3B 97.770 4484 96 4 1 4481 545705651 545710133 0.000000e+00 7723.0
15 TraesCS2A01G557500 chr3B 97.657 4481 105 0 1 4481 292883111 292887591 0.000000e+00 7694.0
16 TraesCS2A01G557500 chr5A 96.744 2703 79 6 1786 4481 149693847 149691147 0.000000e+00 4495.0
17 TraesCS2A01G557500 chr5A 96.474 2723 85 9 1786 4500 522675297 522672578 0.000000e+00 4486.0
18 TraesCS2A01G557500 chr5A 98.917 277 3 0 1514 1790 149694662 149694386 3.300000e-136 496.0
19 TraesCS2A01G557500 chr5A 98.195 277 5 0 1514 1790 522676113 522675837 7.130000e-133 484.0
20 TraesCS2A01G557500 chr5A 97.902 143 2 1 4600 4741 438796718 438796576 3.660000e-61 246.0
21 TraesCS2A01G557500 chr5A 97.203 143 3 1 4600 4741 626201216 626201074 1.700000e-59 241.0
22 TraesCS2A01G557500 chr5A 97.917 96 2 0 4482 4577 438791484 438791579 2.930000e-37 167.0
23 TraesCS2A01G557500 chr1A 95.858 2704 101 9 1786 4481 565926223 565928923 0.000000e+00 4362.0
24 TraesCS2A01G557500 chr1A 97.500 280 7 0 1511 1790 565925404 565925683 3.320000e-131 479.0
25 TraesCS2A01G557500 chr1A 97.917 96 2 0 4482 4577 381103702 381103797 2.930000e-37 167.0
26 TraesCS2A01G557500 chr1A 90.909 44 2 2 4570 4612 381103426 381103384 1.840000e-04 58.4
27 TraesCS2A01G557500 chr2B 90.970 1052 56 16 1 1050 6773481 6772467 0.000000e+00 1380.0
28 TraesCS2A01G557500 chr2B 90.684 1052 60 14 1 1050 6908914 6907899 0.000000e+00 1365.0
29 TraesCS2A01G557500 chr2B 97.917 96 2 0 4482 4577 692617689 692617784 2.930000e-37 167.0
30 TraesCS2A01G557500 chr7B 95.054 465 23 0 1052 1516 699808841 699808377 0.000000e+00 732.0
31 TraesCS2A01G557500 chr7B 94.194 465 27 0 1052 1516 646000990 646000526 0.000000e+00 710.0
32 TraesCS2A01G557500 chr7B 97.887 142 2 1 4600 4741 126216235 126216095 1.320000e-60 244.0
33 TraesCS2A01G557500 chr7B 87.234 47 4 2 4573 4618 72770818 72770773 9.000000e-03 52.8
34 TraesCS2A01G557500 chr7B 100.000 28 0 0 4573 4600 72975021 72975048 9.000000e-03 52.8
35 TraesCS2A01G557500 chr6A 97.902 143 2 1 4600 4741 710101 710243 3.660000e-61 246.0
36 TraesCS2A01G557500 chr4A 97.203 143 3 1 4600 4741 49219160 49219018 1.700000e-59 241.0
37 TraesCS2A01G557500 chr4A 97.183 142 4 0 4600 4741 676498853 676498994 1.700000e-59 241.0
38 TraesCS2A01G557500 chr4A 96.970 99 3 0 4482 4580 676503032 676502934 2.930000e-37 167.0
39 TraesCS2A01G557500 chr7A 97.917 96 2 0 4482 4577 172222638 172222733 2.930000e-37 167.0
40 TraesCS2A01G557500 chr7A 89.362 47 3 2 4570 4615 172222360 172222315 1.840000e-04 58.4
41 TraesCS2A01G557500 chr7A 100.000 31 0 0 4570 4600 172225442 172225472 1.840000e-04 58.4
42 TraesCS2A01G557500 chr4B 97.917 96 2 0 4482 4577 639146372 639146467 2.930000e-37 167.0
43 TraesCS2A01G557500 chr4D 96.875 96 3 0 4482 4577 493005235 493005330 1.370000e-35 161.0
44 TraesCS2A01G557500 chr3D 96.875 96 3 0 4482 4577 4836466 4836561 1.370000e-35 161.0
45 TraesCS2A01G557500 chr7D 100.000 31 0 0 4570 4600 617270034 617270064 1.840000e-04 58.4


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 TraesCS2A01G557500 chr2A 761131634 761136374 4740 False 8756.0 8756 100.0000 1 4741 1 chr2A.!!$F4 4740
1 TraesCS2A01G557500 chr5B 663243482 663247962 4480 True 7847.0 7847 98.2820 1 4480 1 chr5B.!!$R2 4479
2 TraesCS2A01G557500 chr6B 522432374 522436849 4475 True 7766.0 7766 97.9700 1 4481 1 chr6B.!!$R2 4480
3 TraesCS2A01G557500 chr6B 49678538 49682119 3581 True 6150.0 6150 97.6560 1 3583 1 chr6B.!!$R1 3582
4 TraesCS2A01G557500 chr1B 37918175 37922659 4484 True 7764.0 7764 97.9260 1 4482 1 chr1B.!!$R2 4481
5 TraesCS2A01G557500 chr1B 31635290 31636341 1051 True 1554.0 1554 93.3590 1 1050 1 chr1B.!!$R1 1049
6 TraesCS2A01G557500 chr3B 545705651 545710133 4482 False 7723.0 7723 97.7700 1 4481 1 chr3B.!!$F2 4480
7 TraesCS2A01G557500 chr3B 292883111 292887591 4480 False 7694.0 7694 97.6570 1 4481 1 chr3B.!!$F1 4480
8 TraesCS2A01G557500 chr5A 149691147 149694662 3515 True 2495.5 4495 97.8305 1514 4481 2 chr5A.!!$R3 2967
9 TraesCS2A01G557500 chr5A 522672578 522676113 3535 True 2485.0 4486 97.3345 1514 4500 2 chr5A.!!$R4 2986
10 TraesCS2A01G557500 chr1A 565925404 565928923 3519 False 2420.5 4362 96.6790 1511 4481 2 chr1A.!!$F2 2970
11 TraesCS2A01G557500 chr2B 6772467 6773481 1014 True 1380.0 1380 90.9700 1 1050 1 chr2B.!!$R1 1049
12 TraesCS2A01G557500 chr2B 6907899 6908914 1015 True 1365.0 1365 90.6840 1 1050 1 chr2B.!!$R2 1049

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
24 25 2.025981 TGACCGTTCCTAGCTAGTGGTA 60.026 50.000 19.31 7.89 0.00 3.25 F
872 881 4.147449 CGGAGATGGACGCTGCCA 62.147 66.667 0.00 0.00 43.23 4.92 F
2345 2902 3.391296 GTGGCCTAATTGATGAGGTCCTA 59.609 47.826 3.32 0.00 36.56 2.94 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1174 1183 0.681243 GGGACCTTGTTCCAGATGCC 60.681 60.000 0.00 0.0 37.40 4.40 R
2348 2905 1.270625 TGAACTAAGACCAAGGCCACG 60.271 52.381 5.01 0.0 0.00 4.94 R
4080 4645 2.918571 GCCTTTGGCCTTTTTGCTC 58.081 52.632 3.32 0.0 44.06 4.26 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
24 25 2.025981 TGACCGTTCCTAGCTAGTGGTA 60.026 50.000 19.31 7.89 0.00 3.25
480 485 9.939802 AACACCCATAGTTTTAGTACTTAGAAG 57.060 33.333 0.00 0.00 0.00 2.85
872 881 4.147449 CGGAGATGGACGCTGCCA 62.147 66.667 0.00 0.00 43.23 4.92
1723 1733 7.373493 AGAACAGAGCAATGTTTCCTTTATTG 58.627 34.615 7.84 0.00 43.32 1.90
1791 2347 8.527810 TGGGTTTGATTTAATCTCATGGTTTAC 58.472 33.333 6.50 0.00 0.00 2.01
1808 2364 6.177610 TGGTTTACTAATCTAGCACTTTGGG 58.822 40.000 0.00 0.00 0.00 4.12
1863 2420 3.896888 TGGTTTGAGTGCCATGAAGAATT 59.103 39.130 0.00 0.00 0.00 2.17
2149 2706 7.659799 TGTAAAAATTGTTGCTAGCTCTGTCTA 59.340 33.333 17.23 0.00 0.00 2.59
2345 2902 3.391296 GTGGCCTAATTGATGAGGTCCTA 59.609 47.826 3.32 0.00 36.56 2.94
2348 2905 5.248477 TGGCCTAATTGATGAGGTCCTATAC 59.752 44.000 3.32 0.00 36.56 1.47
2461 3018 5.702865 TGTTTTGCTACTGAATGAATGCTC 58.297 37.500 0.00 0.00 0.00 4.26
2487 3044 7.661536 TTCAGTTTGTACCTCATCTAGCTAT 57.338 36.000 0.00 0.00 0.00 2.97
2908 3465 4.702131 CAGGAGAAGAATCCCAACGAAAAT 59.298 41.667 0.00 0.00 40.53 1.82
3625 4186 8.745837 GCATTTTCAAGTATGCACAATGTATAC 58.254 33.333 8.50 8.50 44.99 1.47
4080 4645 3.287222 TGAGGCCCAAATAAGAAATCGG 58.713 45.455 0.00 0.00 0.00 4.18
4194 4761 3.386932 AAGGCTGAATTAATGGGCTCA 57.613 42.857 10.99 0.00 33.51 4.26
4437 5004 9.270640 CATAAATGGAAATTTGTGACCTTTCAA 57.729 29.630 0.00 0.00 35.51 2.69
4484 5051 8.918202 AGTTGACATATTTCTTGTAGTGGAAA 57.082 30.769 0.00 0.00 36.17 3.13
4486 5053 8.784043 GTTGACATATTTCTTGTAGTGGAAACT 58.216 33.333 0.00 0.00 34.83 2.66
4490 5057 8.893727 ACATATTTCTTGTAGTGGAAACTATGC 58.106 33.333 0.57 0.00 34.83 3.14
4491 5058 5.856126 TTTCTTGTAGTGGAAACTATGCG 57.144 39.130 0.00 0.00 0.00 4.73
4492 5059 4.794278 TCTTGTAGTGGAAACTATGCGA 57.206 40.909 0.00 0.00 0.00 5.10
4493 5060 5.339008 TCTTGTAGTGGAAACTATGCGAT 57.661 39.130 0.00 0.00 0.00 4.58
4495 5062 3.792401 TGTAGTGGAAACTATGCGATGG 58.208 45.455 0.00 0.00 0.00 3.51
4496 5063 1.668419 AGTGGAAACTATGCGATGGC 58.332 50.000 0.00 0.00 40.52 4.40
4498 5065 0.813610 TGGAAACTATGCGATGGCGG 60.814 55.000 0.00 0.00 44.10 6.13
4499 5066 1.279840 GAAACTATGCGATGGCGGC 59.720 57.895 0.00 0.00 44.10 6.53
4500 5067 2.117941 GAAACTATGCGATGGCGGCC 62.118 60.000 13.32 13.32 44.10 6.13
4501 5068 2.884997 AAACTATGCGATGGCGGCCA 62.885 55.000 26.11 26.11 44.10 5.36
4503 5070 1.968017 CTATGCGATGGCGGCCATT 60.968 57.895 33.35 20.74 45.26 3.16
4504 5071 1.915614 CTATGCGATGGCGGCCATTC 61.916 60.000 33.35 26.33 45.26 2.67
4505 5072 2.672966 TATGCGATGGCGGCCATTCA 62.673 55.000 33.35 30.21 45.26 2.57
4506 5073 3.517140 GCGATGGCGGCCATTCAA 61.517 61.111 33.35 7.26 45.26 2.69
4507 5074 2.408835 CGATGGCGGCCATTCAAC 59.591 61.111 33.35 20.09 45.26 3.18
4508 5075 2.408835 GATGGCGGCCATTCAACG 59.591 61.111 33.35 0.00 45.26 4.10
4509 5076 2.045438 ATGGCGGCCATTCAACGA 60.045 55.556 28.37 0.59 42.23 3.85
4510 5077 2.051804 GATGGCGGCCATTCAACGAG 62.052 60.000 33.35 0.00 45.26 4.18
4511 5078 2.746277 GGCGGCCATTCAACGAGT 60.746 61.111 15.62 0.00 0.00 4.18
4512 5079 2.480555 GCGGCCATTCAACGAGTG 59.519 61.111 2.24 0.00 0.00 3.51
4513 5080 3.039202 GCGGCCATTCAACGAGTGG 62.039 63.158 2.24 1.39 41.50 4.00
4514 5081 1.375396 CGGCCATTCAACGAGTGGA 60.375 57.895 2.24 0.00 41.15 4.02
4515 5082 1.361668 CGGCCATTCAACGAGTGGAG 61.362 60.000 2.24 0.00 41.15 3.86
4516 5083 1.026718 GGCCATTCAACGAGTGGAGG 61.027 60.000 9.49 0.00 41.15 4.30
4517 5084 0.321653 GCCATTCAACGAGTGGAGGT 60.322 55.000 9.49 0.00 41.15 3.85
4518 5085 1.442769 CCATTCAACGAGTGGAGGTG 58.557 55.000 0.00 0.00 41.15 4.00
4519 5086 1.442769 CATTCAACGAGTGGAGGTGG 58.557 55.000 0.00 0.00 0.00 4.61
4520 5087 1.001974 CATTCAACGAGTGGAGGTGGA 59.998 52.381 0.00 0.00 0.00 4.02
4521 5088 1.124780 TTCAACGAGTGGAGGTGGAA 58.875 50.000 0.00 0.00 0.00 3.53
4522 5089 0.679505 TCAACGAGTGGAGGTGGAAG 59.320 55.000 0.00 0.00 0.00 3.46
4523 5090 0.320771 CAACGAGTGGAGGTGGAAGG 60.321 60.000 0.00 0.00 0.00 3.46
4524 5091 1.481056 AACGAGTGGAGGTGGAAGGG 61.481 60.000 0.00 0.00 0.00 3.95
4525 5092 2.660064 CGAGTGGAGGTGGAAGGGG 61.660 68.421 0.00 0.00 0.00 4.79
4526 5093 2.204151 AGTGGAGGTGGAAGGGGG 60.204 66.667 0.00 0.00 0.00 5.40
4543 5110 4.162690 GGATGGAGGCGGCGAGTT 62.163 66.667 12.98 0.00 0.00 3.01
4544 5111 2.586357 GATGGAGGCGGCGAGTTC 60.586 66.667 12.98 3.90 0.00 3.01
4545 5112 3.077556 ATGGAGGCGGCGAGTTCT 61.078 61.111 12.98 0.96 0.00 3.01
4546 5113 2.962697 GATGGAGGCGGCGAGTTCTC 62.963 65.000 12.98 11.06 0.00 2.87
4547 5114 3.760035 GGAGGCGGCGAGTTCTCA 61.760 66.667 12.98 0.00 0.00 3.27
4548 5115 2.202676 GAGGCGGCGAGTTCTCAG 60.203 66.667 12.98 0.00 0.00 3.35
4549 5116 2.676822 AGGCGGCGAGTTCTCAGA 60.677 61.111 12.98 0.00 0.00 3.27
4550 5117 2.202676 GGCGGCGAGTTCTCAGAG 60.203 66.667 12.98 0.00 0.00 3.35
4551 5118 2.202676 GCGGCGAGTTCTCAGAGG 60.203 66.667 12.98 0.00 0.00 3.69
4552 5119 2.995872 GCGGCGAGTTCTCAGAGGT 61.996 63.158 12.98 0.00 0.00 3.85
4553 5120 1.587054 CGGCGAGTTCTCAGAGGTT 59.413 57.895 0.00 0.00 0.00 3.50
4554 5121 0.734253 CGGCGAGTTCTCAGAGGTTG 60.734 60.000 0.00 0.00 0.00 3.77
4555 5122 0.603569 GGCGAGTTCTCAGAGGTTGA 59.396 55.000 0.00 0.00 0.00 3.18
4556 5123 1.205893 GGCGAGTTCTCAGAGGTTGAT 59.794 52.381 0.00 0.00 34.68 2.57
4557 5124 2.427453 GGCGAGTTCTCAGAGGTTGATA 59.573 50.000 0.00 0.00 34.68 2.15
4558 5125 3.119101 GGCGAGTTCTCAGAGGTTGATAA 60.119 47.826 0.00 0.00 34.68 1.75
4559 5126 3.860536 GCGAGTTCTCAGAGGTTGATAAC 59.139 47.826 0.00 0.00 41.02 1.89
4561 5128 5.098893 CGAGTTCTCAGAGGTTGATAACTG 58.901 45.833 11.19 0.00 46.92 3.16
4562 5129 5.413309 AGTTCTCAGAGGTTGATAACTGG 57.587 43.478 7.01 0.00 45.89 4.00
4563 5130 3.895232 TCTCAGAGGTTGATAACTGGC 57.105 47.619 0.00 0.00 34.68 4.85
4564 5131 3.445008 TCTCAGAGGTTGATAACTGGCT 58.555 45.455 0.00 0.00 34.68 4.75
4565 5132 3.196469 TCTCAGAGGTTGATAACTGGCTG 59.804 47.826 0.00 0.00 34.68 4.85
4566 5133 2.237143 TCAGAGGTTGATAACTGGCTGG 59.763 50.000 0.00 0.00 0.00 4.85
4567 5134 1.561542 AGAGGTTGATAACTGGCTGGG 59.438 52.381 0.00 0.00 0.00 4.45
4568 5135 0.625849 AGGTTGATAACTGGCTGGGG 59.374 55.000 0.00 0.00 0.00 4.96
4569 5136 0.623723 GGTTGATAACTGGCTGGGGA 59.376 55.000 0.00 0.00 0.00 4.81
4570 5137 1.408822 GGTTGATAACTGGCTGGGGAG 60.409 57.143 0.00 0.00 0.00 4.30
4571 5138 0.255890 TTGATAACTGGCTGGGGAGC 59.744 55.000 0.00 0.00 0.00 4.70
4572 5139 1.227674 GATAACTGGCTGGGGAGCG 60.228 63.158 0.00 0.00 35.24 5.03
4573 5140 2.666596 GATAACTGGCTGGGGAGCGG 62.667 65.000 0.00 0.00 35.24 5.52
4575 5142 2.808761 TAACTGGCTGGGGAGCGGTA 62.809 60.000 0.00 0.00 35.24 4.02
4576 5143 3.854669 CTGGCTGGGGAGCGGTAG 61.855 72.222 0.00 0.00 35.24 3.18
4577 5144 4.715130 TGGCTGGGGAGCGGTAGT 62.715 66.667 0.00 0.00 35.24 2.73
4578 5145 3.400054 GGCTGGGGAGCGGTAGTT 61.400 66.667 0.00 0.00 35.24 2.24
4579 5146 2.669240 GCTGGGGAGCGGTAGTTT 59.331 61.111 0.00 0.00 0.00 2.66
4580 5147 1.002502 GCTGGGGAGCGGTAGTTTT 60.003 57.895 0.00 0.00 0.00 2.43
4581 5148 1.025113 GCTGGGGAGCGGTAGTTTTC 61.025 60.000 0.00 0.00 0.00 2.29
4582 5149 0.392595 CTGGGGAGCGGTAGTTTTCC 60.393 60.000 0.00 0.00 0.00 3.13
4584 5151 1.449070 GGGAGCGGTAGTTTTCCGG 60.449 63.158 0.00 0.00 46.90 5.14
4585 5152 1.593265 GGAGCGGTAGTTTTCCGGA 59.407 57.895 0.00 0.00 46.90 5.14
4586 5153 0.037046 GGAGCGGTAGTTTTCCGGAA 60.037 55.000 14.35 14.35 46.90 4.30
4587 5154 1.073964 GAGCGGTAGTTTTCCGGAAC 58.926 55.000 18.64 7.39 46.90 3.62
4602 5169 1.849097 GGAACGATAGCCCGTAACTG 58.151 55.000 0.00 0.00 42.54 3.16
4603 5170 1.537562 GGAACGATAGCCCGTAACTGG 60.538 57.143 0.00 0.00 42.54 4.00
4610 5177 4.813346 CCCGTAACTGGGCTGTTT 57.187 55.556 2.30 0.00 43.70 2.83
4611 5178 3.030415 CCCGTAACTGGGCTGTTTT 57.970 52.632 2.30 0.00 43.70 2.43
4612 5179 2.188062 CCCGTAACTGGGCTGTTTTA 57.812 50.000 2.30 0.00 43.70 1.52
4613 5180 2.718563 CCCGTAACTGGGCTGTTTTAT 58.281 47.619 2.30 0.00 43.70 1.40
4614 5181 3.086282 CCCGTAACTGGGCTGTTTTATT 58.914 45.455 2.30 0.00 43.70 1.40
4615 5182 4.263435 CCCGTAACTGGGCTGTTTTATTA 58.737 43.478 2.30 0.00 43.70 0.98
4616 5183 4.095334 CCCGTAACTGGGCTGTTTTATTAC 59.905 45.833 2.30 0.00 43.70 1.89
4617 5184 4.939439 CCGTAACTGGGCTGTTTTATTACT 59.061 41.667 2.30 0.00 0.00 2.24
4618 5185 5.064325 CCGTAACTGGGCTGTTTTATTACTC 59.936 44.000 2.30 0.00 0.00 2.59
4619 5186 5.064325 CGTAACTGGGCTGTTTTATTACTCC 59.936 44.000 2.30 0.00 0.00 3.85
4620 5187 4.650972 ACTGGGCTGTTTTATTACTCCA 57.349 40.909 0.00 0.00 0.00 3.86
4621 5188 4.332828 ACTGGGCTGTTTTATTACTCCAC 58.667 43.478 0.00 0.00 0.00 4.02
4622 5189 3.692690 TGGGCTGTTTTATTACTCCACC 58.307 45.455 0.00 0.00 0.00 4.61
4623 5190 3.332485 TGGGCTGTTTTATTACTCCACCT 59.668 43.478 0.00 0.00 0.00 4.00
4624 5191 4.536888 TGGGCTGTTTTATTACTCCACCTA 59.463 41.667 0.00 0.00 0.00 3.08
4625 5192 4.880120 GGGCTGTTTTATTACTCCACCTAC 59.120 45.833 0.00 0.00 0.00 3.18
4626 5193 4.880120 GGCTGTTTTATTACTCCACCTACC 59.120 45.833 0.00 0.00 0.00 3.18
4627 5194 5.338953 GGCTGTTTTATTACTCCACCTACCT 60.339 44.000 0.00 0.00 0.00 3.08
4628 5195 6.126968 GGCTGTTTTATTACTCCACCTACCTA 60.127 42.308 0.00 0.00 0.00 3.08
4629 5196 6.760298 GCTGTTTTATTACTCCACCTACCTAC 59.240 42.308 0.00 0.00 0.00 3.18
4630 5197 7.186570 TGTTTTATTACTCCACCTACCTACC 57.813 40.000 0.00 0.00 0.00 3.18
4631 5198 6.730038 TGTTTTATTACTCCACCTACCTACCA 59.270 38.462 0.00 0.00 0.00 3.25
4632 5199 6.796785 TTTATTACTCCACCTACCTACCAC 57.203 41.667 0.00 0.00 0.00 4.16
4633 5200 2.834638 TACTCCACCTACCTACCACC 57.165 55.000 0.00 0.00 0.00 4.61
4634 5201 0.788383 ACTCCACCTACCTACCACCA 59.212 55.000 0.00 0.00 0.00 4.17
4635 5202 1.150560 ACTCCACCTACCTACCACCAA 59.849 52.381 0.00 0.00 0.00 3.67
4636 5203 1.553704 CTCCACCTACCTACCACCAAC 59.446 57.143 0.00 0.00 0.00 3.77
4637 5204 0.616891 CCACCTACCTACCACCAACC 59.383 60.000 0.00 0.00 0.00 3.77
4638 5205 1.354101 CACCTACCTACCACCAACCA 58.646 55.000 0.00 0.00 0.00 3.67
4639 5206 1.913419 CACCTACCTACCACCAACCAT 59.087 52.381 0.00 0.00 0.00 3.55
4640 5207 2.307686 CACCTACCTACCACCAACCATT 59.692 50.000 0.00 0.00 0.00 3.16
4641 5208 3.520317 CACCTACCTACCACCAACCATTA 59.480 47.826 0.00 0.00 0.00 1.90
4642 5209 3.778629 ACCTACCTACCACCAACCATTAG 59.221 47.826 0.00 0.00 0.00 1.73
4643 5210 3.778629 CCTACCTACCACCAACCATTAGT 59.221 47.826 0.00 0.00 0.00 2.24
4644 5211 4.964262 CCTACCTACCACCAACCATTAGTA 59.036 45.833 0.00 0.00 0.00 1.82
4645 5212 5.070047 CCTACCTACCACCAACCATTAGTAG 59.930 48.000 0.00 0.00 0.00 2.57
4646 5213 4.432316 ACCTACCACCAACCATTAGTAGT 58.568 43.478 0.00 0.00 0.00 2.73
4647 5214 4.468868 ACCTACCACCAACCATTAGTAGTC 59.531 45.833 0.00 0.00 0.00 2.59
4648 5215 4.715297 CCTACCACCAACCATTAGTAGTCT 59.285 45.833 0.00 0.00 0.00 3.24
4649 5216 5.895534 CCTACCACCAACCATTAGTAGTCTA 59.104 44.000 0.00 0.00 0.00 2.59
4650 5217 6.553852 CCTACCACCAACCATTAGTAGTCTAT 59.446 42.308 0.00 0.00 0.00 1.98
4651 5218 7.727186 CCTACCACCAACCATTAGTAGTCTATA 59.273 40.741 0.00 0.00 0.00 1.31
4652 5219 7.983166 ACCACCAACCATTAGTAGTCTATAA 57.017 36.000 0.00 0.00 0.00 0.98
4653 5220 8.383374 ACCACCAACCATTAGTAGTCTATAAA 57.617 34.615 0.00 0.00 0.00 1.40
4654 5221 8.483758 ACCACCAACCATTAGTAGTCTATAAAG 58.516 37.037 0.00 0.00 0.00 1.85
4655 5222 7.441458 CCACCAACCATTAGTAGTCTATAAAGC 59.559 40.741 0.00 0.00 0.00 3.51
4656 5223 7.441458 CACCAACCATTAGTAGTCTATAAAGCC 59.559 40.741 0.00 0.00 0.00 4.35
4657 5224 6.935208 CCAACCATTAGTAGTCTATAAAGCCC 59.065 42.308 0.00 0.00 0.00 5.19
4658 5225 7.419750 CCAACCATTAGTAGTCTATAAAGCCCA 60.420 40.741 0.00 0.00 0.00 5.36
4659 5226 7.063934 ACCATTAGTAGTCTATAAAGCCCAC 57.936 40.000 0.00 0.00 0.00 4.61
4660 5227 6.042897 ACCATTAGTAGTCTATAAAGCCCACC 59.957 42.308 0.00 0.00 0.00 4.61
4661 5228 6.465084 CATTAGTAGTCTATAAAGCCCACCC 58.535 44.000 0.00 0.00 0.00 4.61
4662 5229 3.315596 AGTAGTCTATAAAGCCCACCCC 58.684 50.000 0.00 0.00 0.00 4.95
4663 5230 2.588925 AGTCTATAAAGCCCACCCCT 57.411 50.000 0.00 0.00 0.00 4.79
4664 5231 3.719368 AGTCTATAAAGCCCACCCCTA 57.281 47.619 0.00 0.00 0.00 3.53
4665 5232 3.588569 AGTCTATAAAGCCCACCCCTAG 58.411 50.000 0.00 0.00 0.00 3.02
4666 5233 3.209152 AGTCTATAAAGCCCACCCCTAGA 59.791 47.826 0.00 0.00 0.00 2.43
4667 5234 3.579151 GTCTATAAAGCCCACCCCTAGAG 59.421 52.174 0.00 0.00 0.00 2.43
4668 5235 2.588925 ATAAAGCCCACCCCTAGAGT 57.411 50.000 0.00 0.00 0.00 3.24
4669 5236 1.580059 TAAAGCCCACCCCTAGAGTG 58.420 55.000 6.03 6.03 34.91 3.51
4670 5237 0.178873 AAAGCCCACCCCTAGAGTGA 60.179 55.000 12.85 0.00 37.42 3.41
4671 5238 0.178873 AAGCCCACCCCTAGAGTGAA 60.179 55.000 12.85 0.00 37.42 3.18
4672 5239 0.178873 AGCCCACCCCTAGAGTGAAA 60.179 55.000 12.85 0.00 37.42 2.69
4673 5240 0.035343 GCCCACCCCTAGAGTGAAAC 60.035 60.000 12.85 1.08 37.42 2.78
4674 5241 0.618981 CCCACCCCTAGAGTGAAACC 59.381 60.000 12.85 0.00 37.80 3.27
4675 5242 0.249398 CCACCCCTAGAGTGAAACCG 59.751 60.000 12.85 0.00 37.80 4.44
4676 5243 0.391263 CACCCCTAGAGTGAAACCGC 60.391 60.000 6.97 0.00 37.80 5.68
4677 5244 0.834687 ACCCCTAGAGTGAAACCGCA 60.835 55.000 0.00 0.00 37.80 5.69
4678 5245 0.108138 CCCCTAGAGTGAAACCGCAG 60.108 60.000 0.00 0.00 37.80 5.18
4679 5246 0.608640 CCCTAGAGTGAAACCGCAGT 59.391 55.000 0.00 0.00 37.80 4.40
4680 5247 1.404315 CCCTAGAGTGAAACCGCAGTC 60.404 57.143 0.00 0.00 37.80 3.51
4681 5248 1.272490 CCTAGAGTGAAACCGCAGTCA 59.728 52.381 0.00 0.00 40.01 3.41
4682 5249 2.288825 CCTAGAGTGAAACCGCAGTCAA 60.289 50.000 0.00 0.00 40.01 3.18
4683 5250 2.550830 AGAGTGAAACCGCAGTCAAT 57.449 45.000 0.00 0.00 40.01 2.57
4684 5251 2.417719 AGAGTGAAACCGCAGTCAATC 58.582 47.619 0.00 0.00 40.01 2.67
4685 5252 1.464997 GAGTGAAACCGCAGTCAATCC 59.535 52.381 0.00 0.00 37.80 3.01
4686 5253 0.521735 GTGAAACCGCAGTCAATCCC 59.478 55.000 0.00 0.00 0.00 3.85
4687 5254 0.608035 TGAAACCGCAGTCAATCCCC 60.608 55.000 0.00 0.00 0.00 4.81
4688 5255 1.304134 AAACCGCAGTCAATCCCCC 60.304 57.895 0.00 0.00 0.00 5.40
4689 5256 2.075355 AAACCGCAGTCAATCCCCCA 62.075 55.000 0.00 0.00 0.00 4.96
4690 5257 1.863155 AACCGCAGTCAATCCCCCAT 61.863 55.000 0.00 0.00 0.00 4.00
4691 5258 1.526917 CCGCAGTCAATCCCCCATC 60.527 63.158 0.00 0.00 0.00 3.51
4692 5259 1.526917 CGCAGTCAATCCCCCATCC 60.527 63.158 0.00 0.00 0.00 3.51
4693 5260 1.152673 GCAGTCAATCCCCCATCCC 60.153 63.158 0.00 0.00 0.00 3.85
4694 5261 1.538666 CAGTCAATCCCCCATCCCC 59.461 63.158 0.00 0.00 0.00 4.81
4695 5262 1.086565 AGTCAATCCCCCATCCCCA 59.913 57.895 0.00 0.00 0.00 4.96
4696 5263 1.230212 GTCAATCCCCCATCCCCAC 59.770 63.158 0.00 0.00 0.00 4.61
4697 5264 2.012210 TCAATCCCCCATCCCCACC 61.012 63.158 0.00 0.00 0.00 4.61
4698 5265 2.703808 AATCCCCCATCCCCACCC 60.704 66.667 0.00 0.00 0.00 4.61
4699 5266 3.318364 AATCCCCCATCCCCACCCT 62.318 63.158 0.00 0.00 0.00 4.34
4700 5267 2.841743 AATCCCCCATCCCCACCCTT 62.842 60.000 0.00 0.00 0.00 3.95
4701 5268 3.429580 CCCCCATCCCCACCCTTC 61.430 72.222 0.00 0.00 0.00 3.46
4702 5269 2.287194 CCCCATCCCCACCCTTCT 60.287 66.667 0.00 0.00 0.00 2.85
4703 5270 2.386935 CCCCATCCCCACCCTTCTC 61.387 68.421 0.00 0.00 0.00 2.87
4704 5271 1.619363 CCCATCCCCACCCTTCTCA 60.619 63.158 0.00 0.00 0.00 3.27
4705 5272 1.214305 CCCATCCCCACCCTTCTCAA 61.214 60.000 0.00 0.00 0.00 3.02
4706 5273 0.034089 CCATCCCCACCCTTCTCAAC 60.034 60.000 0.00 0.00 0.00 3.18
4707 5274 0.034089 CATCCCCACCCTTCTCAACC 60.034 60.000 0.00 0.00 0.00 3.77
4708 5275 1.214992 ATCCCCACCCTTCTCAACCC 61.215 60.000 0.00 0.00 0.00 4.11
4709 5276 2.763902 CCCACCCTTCTCAACCCC 59.236 66.667 0.00 0.00 0.00 4.95
4710 5277 1.852626 CCCACCCTTCTCAACCCCT 60.853 63.158 0.00 0.00 0.00 4.79
4711 5278 1.685820 CCACCCTTCTCAACCCCTC 59.314 63.158 0.00 0.00 0.00 4.30
4712 5279 1.133809 CCACCCTTCTCAACCCCTCA 61.134 60.000 0.00 0.00 0.00 3.86
4713 5280 0.326264 CACCCTTCTCAACCCCTCAG 59.674 60.000 0.00 0.00 0.00 3.35
4714 5281 1.301293 CCCTTCTCAACCCCTCAGC 59.699 63.158 0.00 0.00 0.00 4.26
4715 5282 1.301293 CCTTCTCAACCCCTCAGCC 59.699 63.158 0.00 0.00 0.00 4.85
4716 5283 1.078848 CTTCTCAACCCCTCAGCCG 60.079 63.158 0.00 0.00 0.00 5.52
4717 5284 3.254024 TTCTCAACCCCTCAGCCGC 62.254 63.158 0.00 0.00 0.00 6.53
4718 5285 4.785453 CTCAACCCCTCAGCCGCC 62.785 72.222 0.00 0.00 0.00 6.13
4720 5287 4.659172 CAACCCCTCAGCCGCCAA 62.659 66.667 0.00 0.00 0.00 4.52
4721 5288 3.897122 AACCCCTCAGCCGCCAAA 61.897 61.111 0.00 0.00 0.00 3.28
4722 5289 3.868200 AACCCCTCAGCCGCCAAAG 62.868 63.158 0.00 0.00 0.00 2.77
4723 5290 4.033776 CCCCTCAGCCGCCAAAGA 62.034 66.667 0.00 0.00 0.00 2.52
4724 5291 2.034066 CCCTCAGCCGCCAAAGAA 59.966 61.111 0.00 0.00 0.00 2.52
4725 5292 1.603455 CCCTCAGCCGCCAAAGAAA 60.603 57.895 0.00 0.00 0.00 2.52
4726 5293 1.581447 CCTCAGCCGCCAAAGAAAC 59.419 57.895 0.00 0.00 0.00 2.78
4727 5294 1.581447 CTCAGCCGCCAAAGAAACC 59.419 57.895 0.00 0.00 0.00 3.27
4728 5295 1.866853 CTCAGCCGCCAAAGAAACCC 61.867 60.000 0.00 0.00 0.00 4.11
4729 5296 1.903404 CAGCCGCCAAAGAAACCCT 60.903 57.895 0.00 0.00 0.00 4.34
4730 5297 0.608035 CAGCCGCCAAAGAAACCCTA 60.608 55.000 0.00 0.00 0.00 3.53
4731 5298 0.322546 AGCCGCCAAAGAAACCCTAG 60.323 55.000 0.00 0.00 0.00 3.02
4732 5299 0.322187 GCCGCCAAAGAAACCCTAGA 60.322 55.000 0.00 0.00 0.00 2.43
4733 5300 1.884928 GCCGCCAAAGAAACCCTAGAA 60.885 52.381 0.00 0.00 0.00 2.10
4734 5301 2.723273 CCGCCAAAGAAACCCTAGAAT 58.277 47.619 0.00 0.00 0.00 2.40
4735 5302 2.683362 CCGCCAAAGAAACCCTAGAATC 59.317 50.000 0.00 0.00 0.00 2.52
4736 5303 2.683362 CGCCAAAGAAACCCTAGAATCC 59.317 50.000 0.00 0.00 0.00 3.01
4737 5304 3.697166 GCCAAAGAAACCCTAGAATCCA 58.303 45.455 0.00 0.00 0.00 3.41
4738 5305 4.086457 GCCAAAGAAACCCTAGAATCCAA 58.914 43.478 0.00 0.00 0.00 3.53
4739 5306 4.158579 GCCAAAGAAACCCTAGAATCCAAG 59.841 45.833 0.00 0.00 0.00 3.61
4740 5307 4.706962 CCAAAGAAACCCTAGAATCCAAGG 59.293 45.833 0.00 0.00 0.00 3.61
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
348 353 4.731000 CGCCAATTTGCATGCATTTTTATG 59.269 37.500 23.37 14.07 0.00 1.90
413 418 5.938438 AAATATTTTGCAAAACGGCACAT 57.062 30.435 26.05 11.48 44.86 3.21
987 996 0.040058 TCACCATGGCTGCCAAATCT 59.960 50.000 27.24 5.99 36.95 2.40
1174 1183 0.681243 GGGACCTTGTTCCAGATGCC 60.681 60.000 0.00 0.00 37.40 4.40
1723 1733 5.824904 ACAATGCATTGATACAAGACTCC 57.175 39.130 38.99 0.00 40.14 3.85
1786 1796 5.066117 GCCCCAAAGTGCTAGATTAGTAAAC 59.934 44.000 0.00 0.00 0.00 2.01
1791 2347 3.209410 CAGCCCCAAAGTGCTAGATTAG 58.791 50.000 0.00 0.00 35.69 1.73
1808 2364 3.769536 ACAATTTATTTACGCTGCAGCC 58.230 40.909 32.07 15.05 37.91 4.85
1863 2420 8.959548 AGTCAATTCATACAAGCATGATAAACA 58.040 29.630 0.00 0.00 34.95 2.83
2149 2706 8.914011 GGAAGAAACAAGTAAATATGGGCTTAT 58.086 33.333 0.00 0.00 0.00 1.73
2190 2747 2.060980 GTCGTCCATGGAGGGCTCT 61.061 63.158 27.65 0.00 40.99 4.09
2345 2902 2.185387 ACTAAGACCAAGGCCACGTAT 58.815 47.619 5.01 0.00 0.00 3.06
2348 2905 1.270625 TGAACTAAGACCAAGGCCACG 60.271 52.381 5.01 0.00 0.00 4.94
2461 3018 6.402222 AGCTAGATGAGGTACAAACTGAAAG 58.598 40.000 0.00 0.00 34.80 2.62
2487 3044 6.865205 GCCGTCTAGTTTAGAGAACTAAAACA 59.135 38.462 0.00 0.00 45.97 2.83
3647 4208 5.664294 TGATCTGCAGCACCATAAAAATT 57.336 34.783 9.47 0.00 0.00 1.82
4080 4645 2.918571 GCCTTTGGCCTTTTTGCTC 58.081 52.632 3.32 0.00 44.06 4.26
4172 4739 3.701040 TGAGCCCATTAATTCAGCCTTTC 59.299 43.478 0.00 0.00 0.00 2.62
4194 4761 3.966665 CCAATTGGGTGTTTATATGGGCT 59.033 43.478 17.36 0.00 0.00 5.19
4482 5049 2.186826 GGCCGCCATCGCATAGTTT 61.187 57.895 3.91 0.00 34.03 2.66
4484 5051 2.680974 AATGGCCGCCATCGCATAGT 62.681 55.000 25.27 4.97 44.40 2.12
4486 5053 1.965930 GAATGGCCGCCATCGCATA 60.966 57.895 25.27 0.00 44.40 3.14
4487 5054 3.289834 GAATGGCCGCCATCGCAT 61.290 61.111 25.27 9.78 44.40 4.73
4488 5055 4.792804 TGAATGGCCGCCATCGCA 62.793 61.111 25.27 21.57 44.40 5.10
4489 5056 3.517140 TTGAATGGCCGCCATCGC 61.517 61.111 25.27 19.38 44.40 4.58
4490 5057 2.408835 GTTGAATGGCCGCCATCG 59.591 61.111 25.27 0.00 44.40 3.84
4491 5058 2.051804 CTCGTTGAATGGCCGCCATC 62.052 60.000 25.27 17.74 44.40 3.51
4493 5060 2.745884 CTCGTTGAATGGCCGCCA 60.746 61.111 16.17 16.17 38.19 5.69
4495 5062 2.480555 CACTCGTTGAATGGCCGC 59.519 61.111 0.00 0.00 0.00 6.53
4496 5063 1.361668 CTCCACTCGTTGAATGGCCG 61.362 60.000 0.00 0.00 33.20 6.13
4498 5065 0.321653 ACCTCCACTCGTTGAATGGC 60.322 55.000 0.00 0.00 33.20 4.40
4499 5066 1.442769 CACCTCCACTCGTTGAATGG 58.557 55.000 0.00 0.00 34.58 3.16
4500 5067 1.001974 TCCACCTCCACTCGTTGAATG 59.998 52.381 0.00 0.00 0.00 2.67
4501 5068 1.348064 TCCACCTCCACTCGTTGAAT 58.652 50.000 0.00 0.00 0.00 2.57
4502 5069 1.070134 CTTCCACCTCCACTCGTTGAA 59.930 52.381 0.00 0.00 0.00 2.69
4503 5070 0.679505 CTTCCACCTCCACTCGTTGA 59.320 55.000 0.00 0.00 0.00 3.18
4504 5071 0.320771 CCTTCCACCTCCACTCGTTG 60.321 60.000 0.00 0.00 0.00 4.10
4505 5072 1.481056 CCCTTCCACCTCCACTCGTT 61.481 60.000 0.00 0.00 0.00 3.85
4506 5073 1.913762 CCCTTCCACCTCCACTCGT 60.914 63.158 0.00 0.00 0.00 4.18
4507 5074 2.660064 CCCCTTCCACCTCCACTCG 61.660 68.421 0.00 0.00 0.00 4.18
4508 5075 2.301738 CCCCCTTCCACCTCCACTC 61.302 68.421 0.00 0.00 0.00 3.51
4509 5076 2.204151 CCCCCTTCCACCTCCACT 60.204 66.667 0.00 0.00 0.00 4.00
4526 5093 4.162690 AACTCGCCGCCTCCATCC 62.163 66.667 0.00 0.00 0.00 3.51
4527 5094 2.586357 GAACTCGCCGCCTCCATC 60.586 66.667 0.00 0.00 0.00 3.51
4528 5095 3.077556 AGAACTCGCCGCCTCCAT 61.078 61.111 0.00 0.00 0.00 3.41
4529 5096 3.760035 GAGAACTCGCCGCCTCCA 61.760 66.667 0.00 0.00 0.00 3.86
4530 5097 3.708220 CTGAGAACTCGCCGCCTCC 62.708 68.421 0.00 0.00 0.00 4.30
4531 5098 2.202676 CTGAGAACTCGCCGCCTC 60.203 66.667 0.00 0.00 0.00 4.70
4532 5099 2.676822 TCTGAGAACTCGCCGCCT 60.677 61.111 0.00 0.00 0.00 5.52
4533 5100 2.202676 CTCTGAGAACTCGCCGCC 60.203 66.667 0.00 0.00 0.00 6.13
4534 5101 2.202676 CCTCTGAGAACTCGCCGC 60.203 66.667 6.17 0.00 0.00 6.53
4535 5102 0.734253 CAACCTCTGAGAACTCGCCG 60.734 60.000 6.17 0.00 0.00 6.46
4536 5103 0.603569 TCAACCTCTGAGAACTCGCC 59.396 55.000 6.17 0.00 0.00 5.54
4537 5104 2.663826 ATCAACCTCTGAGAACTCGC 57.336 50.000 6.17 0.00 37.52 5.03
4542 5109 3.840666 AGCCAGTTATCAACCTCTGAGAA 59.159 43.478 6.17 0.00 37.52 2.87
4543 5110 3.196469 CAGCCAGTTATCAACCTCTGAGA 59.804 47.826 6.17 0.00 37.52 3.27
4544 5111 3.529533 CAGCCAGTTATCAACCTCTGAG 58.470 50.000 0.00 0.00 37.52 3.35
4545 5112 2.237143 CCAGCCAGTTATCAACCTCTGA 59.763 50.000 0.00 0.00 38.81 3.27
4546 5113 2.636830 CCAGCCAGTTATCAACCTCTG 58.363 52.381 0.00 0.00 0.00 3.35
4547 5114 1.561542 CCCAGCCAGTTATCAACCTCT 59.438 52.381 0.00 0.00 0.00 3.69
4548 5115 1.408822 CCCCAGCCAGTTATCAACCTC 60.409 57.143 0.00 0.00 0.00 3.85
4549 5116 0.625849 CCCCAGCCAGTTATCAACCT 59.374 55.000 0.00 0.00 0.00 3.50
4550 5117 0.623723 TCCCCAGCCAGTTATCAACC 59.376 55.000 0.00 0.00 0.00 3.77
4551 5118 2.019156 GCTCCCCAGCCAGTTATCAAC 61.019 57.143 0.00 0.00 40.14 3.18
4552 5119 0.255890 GCTCCCCAGCCAGTTATCAA 59.744 55.000 0.00 0.00 40.14 2.57
4553 5120 1.915228 GCTCCCCAGCCAGTTATCA 59.085 57.895 0.00 0.00 40.14 2.15
4554 5121 1.227674 CGCTCCCCAGCCAGTTATC 60.228 63.158 0.00 0.00 43.56 1.75
4555 5122 2.746375 CCGCTCCCCAGCCAGTTAT 61.746 63.158 0.00 0.00 43.56 1.89
4556 5123 2.808761 TACCGCTCCCCAGCCAGTTA 62.809 60.000 0.00 0.00 43.56 2.24
4558 5125 4.715130 TACCGCTCCCCAGCCAGT 62.715 66.667 0.00 0.00 43.56 4.00
4559 5126 3.854669 CTACCGCTCCCCAGCCAG 61.855 72.222 0.00 0.00 43.56 4.85
4560 5127 4.715130 ACTACCGCTCCCCAGCCA 62.715 66.667 0.00 0.00 43.56 4.75
4561 5128 2.479820 AAAACTACCGCTCCCCAGCC 62.480 60.000 0.00 0.00 43.56 4.85
4562 5129 1.002502 AAAACTACCGCTCCCCAGC 60.003 57.895 0.00 0.00 42.96 4.85
4563 5130 0.392595 GGAAAACTACCGCTCCCCAG 60.393 60.000 0.00 0.00 0.00 4.45
4564 5131 1.681076 GGAAAACTACCGCTCCCCA 59.319 57.895 0.00 0.00 0.00 4.96
4565 5132 1.449070 CGGAAAACTACCGCTCCCC 60.449 63.158 0.00 0.00 43.74 4.81
4566 5133 4.196965 CGGAAAACTACCGCTCCC 57.803 61.111 0.00 0.00 43.74 4.30
4572 5139 2.862536 GCTATCGTTCCGGAAAACTACC 59.137 50.000 20.79 4.11 0.00 3.18
4573 5140 2.862536 GGCTATCGTTCCGGAAAACTAC 59.137 50.000 20.79 5.71 0.00 2.73
4574 5141 2.159057 GGGCTATCGTTCCGGAAAACTA 60.159 50.000 20.79 9.37 0.00 2.24
4575 5142 1.406477 GGGCTATCGTTCCGGAAAACT 60.406 52.381 20.79 8.65 0.00 2.66
4576 5143 1.012086 GGGCTATCGTTCCGGAAAAC 58.988 55.000 20.79 7.43 0.00 2.43
4577 5144 0.460635 CGGGCTATCGTTCCGGAAAA 60.461 55.000 20.79 10.95 40.07 2.29
4578 5145 1.142314 CGGGCTATCGTTCCGGAAA 59.858 57.895 20.79 4.38 40.07 3.13
4579 5146 2.809706 CGGGCTATCGTTCCGGAA 59.190 61.111 14.35 14.35 40.07 4.30
4583 5150 1.537562 CCAGTTACGGGCTATCGTTCC 60.538 57.143 5.74 0.00 43.59 3.62
4584 5151 1.537562 CCCAGTTACGGGCTATCGTTC 60.538 57.143 0.00 1.81 43.59 3.95
4585 5152 0.462789 CCCAGTTACGGGCTATCGTT 59.537 55.000 0.00 0.00 43.59 3.85
4586 5153 2.121645 CCCAGTTACGGGCTATCGT 58.878 57.895 0.00 5.74 45.88 3.73
4594 5161 4.939439 AGTAATAAAACAGCCCAGTTACGG 59.061 41.667 0.00 0.00 0.00 4.02
4595 5162 5.064325 GGAGTAATAAAACAGCCCAGTTACG 59.936 44.000 0.00 0.00 0.00 3.18
4596 5163 5.941647 TGGAGTAATAAAACAGCCCAGTTAC 59.058 40.000 0.00 0.00 0.00 2.50
4597 5164 5.941647 GTGGAGTAATAAAACAGCCCAGTTA 59.058 40.000 0.00 0.00 0.00 2.24
4598 5165 4.765339 GTGGAGTAATAAAACAGCCCAGTT 59.235 41.667 0.00 0.00 0.00 3.16
4599 5166 4.332828 GTGGAGTAATAAAACAGCCCAGT 58.667 43.478 0.00 0.00 0.00 4.00
4600 5167 3.694566 GGTGGAGTAATAAAACAGCCCAG 59.305 47.826 0.00 0.00 0.00 4.45
4601 5168 3.332485 AGGTGGAGTAATAAAACAGCCCA 59.668 43.478 0.00 0.00 0.00 5.36
4602 5169 3.964411 AGGTGGAGTAATAAAACAGCCC 58.036 45.455 0.00 0.00 0.00 5.19
4603 5170 4.880120 GGTAGGTGGAGTAATAAAACAGCC 59.120 45.833 0.00 0.00 0.00 4.85
4604 5171 5.742063 AGGTAGGTGGAGTAATAAAACAGC 58.258 41.667 0.00 0.00 0.00 4.40
4605 5172 7.093201 TGGTAGGTAGGTGGAGTAATAAAACAG 60.093 40.741 0.00 0.00 0.00 3.16
4606 5173 6.730038 TGGTAGGTAGGTGGAGTAATAAAACA 59.270 38.462 0.00 0.00 0.00 2.83
4607 5174 7.044181 GTGGTAGGTAGGTGGAGTAATAAAAC 58.956 42.308 0.00 0.00 0.00 2.43
4608 5175 6.156775 GGTGGTAGGTAGGTGGAGTAATAAAA 59.843 42.308 0.00 0.00 0.00 1.52
4609 5176 5.662657 GGTGGTAGGTAGGTGGAGTAATAAA 59.337 44.000 0.00 0.00 0.00 1.40
4610 5177 5.211201 GGTGGTAGGTAGGTGGAGTAATAA 58.789 45.833 0.00 0.00 0.00 1.40
4611 5178 4.232587 TGGTGGTAGGTAGGTGGAGTAATA 59.767 45.833 0.00 0.00 0.00 0.98
4612 5179 3.013188 TGGTGGTAGGTAGGTGGAGTAAT 59.987 47.826 0.00 0.00 0.00 1.89
4613 5180 2.382993 TGGTGGTAGGTAGGTGGAGTAA 59.617 50.000 0.00 0.00 0.00 2.24
4614 5181 2.002315 TGGTGGTAGGTAGGTGGAGTA 58.998 52.381 0.00 0.00 0.00 2.59
4615 5182 0.788383 TGGTGGTAGGTAGGTGGAGT 59.212 55.000 0.00 0.00 0.00 3.85
4616 5183 1.553704 GTTGGTGGTAGGTAGGTGGAG 59.446 57.143 0.00 0.00 0.00 3.86
4617 5184 1.648116 GTTGGTGGTAGGTAGGTGGA 58.352 55.000 0.00 0.00 0.00 4.02
4618 5185 0.616891 GGTTGGTGGTAGGTAGGTGG 59.383 60.000 0.00 0.00 0.00 4.61
4619 5186 1.354101 TGGTTGGTGGTAGGTAGGTG 58.646 55.000 0.00 0.00 0.00 4.00
4620 5187 2.354261 ATGGTTGGTGGTAGGTAGGT 57.646 50.000 0.00 0.00 0.00 3.08
4621 5188 3.778629 ACTAATGGTTGGTGGTAGGTAGG 59.221 47.826 0.00 0.00 0.00 3.18
4622 5189 5.659971 ACTACTAATGGTTGGTGGTAGGTAG 59.340 44.000 0.00 0.00 34.26 3.18
4623 5190 5.592795 ACTACTAATGGTTGGTGGTAGGTA 58.407 41.667 0.00 0.00 34.26 3.08
4624 5191 4.432316 ACTACTAATGGTTGGTGGTAGGT 58.568 43.478 0.00 0.00 34.26 3.08
4625 5192 4.715297 AGACTACTAATGGTTGGTGGTAGG 59.285 45.833 0.00 0.00 36.06 3.18
4626 5193 5.934402 AGACTACTAATGGTTGGTGGTAG 57.066 43.478 0.00 0.00 36.06 3.18
4627 5194 9.491406 TTTATAGACTACTAATGGTTGGTGGTA 57.509 33.333 0.00 0.00 36.06 3.25
4628 5195 7.983166 TTATAGACTACTAATGGTTGGTGGT 57.017 36.000 0.00 0.00 38.48 4.16
4629 5196 7.441458 GCTTTATAGACTACTAATGGTTGGTGG 59.559 40.741 0.00 0.00 32.04 4.61
4630 5197 7.441458 GGCTTTATAGACTACTAATGGTTGGTG 59.559 40.741 0.00 0.00 32.04 4.17
4631 5198 7.419865 GGGCTTTATAGACTACTAATGGTTGGT 60.420 40.741 0.00 0.00 32.04 3.67
4632 5199 6.935208 GGGCTTTATAGACTACTAATGGTTGG 59.065 42.308 0.00 0.00 32.04 3.77
4633 5200 7.441458 GTGGGCTTTATAGACTACTAATGGTTG 59.559 40.741 0.00 0.00 37.86 3.77
4634 5201 7.419865 GGTGGGCTTTATAGACTACTAATGGTT 60.420 40.741 2.70 0.00 40.56 3.67
4635 5202 6.042897 GGTGGGCTTTATAGACTACTAATGGT 59.957 42.308 2.70 0.00 40.56 3.55
4636 5203 6.465084 GGTGGGCTTTATAGACTACTAATGG 58.535 44.000 2.70 0.00 40.56 3.16
4637 5204 6.465084 GGGTGGGCTTTATAGACTACTAATG 58.535 44.000 2.70 0.00 40.56 1.90
4638 5205 5.546887 GGGGTGGGCTTTATAGACTACTAAT 59.453 44.000 2.70 0.00 40.56 1.73
4639 5206 4.903649 GGGGTGGGCTTTATAGACTACTAA 59.096 45.833 2.70 0.00 40.56 2.24
4640 5207 4.171442 AGGGGTGGGCTTTATAGACTACTA 59.829 45.833 2.70 0.00 40.56 1.82
4641 5208 3.051264 AGGGGTGGGCTTTATAGACTACT 60.051 47.826 2.70 0.00 40.56 2.57
4642 5209 3.315596 AGGGGTGGGCTTTATAGACTAC 58.684 50.000 0.00 0.00 40.03 2.73
4643 5210 3.719368 AGGGGTGGGCTTTATAGACTA 57.281 47.619 0.00 0.00 0.00 2.59
4644 5211 2.588925 AGGGGTGGGCTTTATAGACT 57.411 50.000 0.00 0.00 0.00 3.24
4645 5212 3.579151 CTCTAGGGGTGGGCTTTATAGAC 59.421 52.174 0.00 0.00 0.00 2.59
4646 5213 3.209152 ACTCTAGGGGTGGGCTTTATAGA 59.791 47.826 0.00 0.00 0.00 1.98
4647 5214 3.325135 CACTCTAGGGGTGGGCTTTATAG 59.675 52.174 0.00 0.00 0.00 1.31
4648 5215 3.051650 TCACTCTAGGGGTGGGCTTTATA 60.052 47.826 13.83 0.00 35.61 0.98
4649 5216 2.127708 CACTCTAGGGGTGGGCTTTAT 58.872 52.381 0.00 0.00 0.00 1.40
4650 5217 1.079825 TCACTCTAGGGGTGGGCTTTA 59.920 52.381 13.83 0.00 35.61 1.85
4651 5218 0.178873 TCACTCTAGGGGTGGGCTTT 60.179 55.000 13.83 0.00 35.61 3.51
4652 5219 0.178873 TTCACTCTAGGGGTGGGCTT 60.179 55.000 13.83 0.00 35.61 4.35
4653 5220 0.178873 TTTCACTCTAGGGGTGGGCT 60.179 55.000 13.83 0.00 35.61 5.19
4654 5221 0.035343 GTTTCACTCTAGGGGTGGGC 60.035 60.000 13.83 4.68 35.61 5.36
4655 5222 0.618981 GGTTTCACTCTAGGGGTGGG 59.381 60.000 13.83 0.00 35.61 4.61
4656 5223 0.249398 CGGTTTCACTCTAGGGGTGG 59.751 60.000 13.83 0.00 35.61 4.61
4657 5224 0.391263 GCGGTTTCACTCTAGGGGTG 60.391 60.000 0.00 2.52 36.17 4.61
4658 5225 0.834687 TGCGGTTTCACTCTAGGGGT 60.835 55.000 0.00 0.00 0.00 4.95
4659 5226 0.108138 CTGCGGTTTCACTCTAGGGG 60.108 60.000 0.00 0.00 0.00 4.79
4660 5227 0.608640 ACTGCGGTTTCACTCTAGGG 59.391 55.000 0.00 0.00 0.00 3.53
4661 5228 1.272490 TGACTGCGGTTTCACTCTAGG 59.728 52.381 0.00 0.00 0.00 3.02
4662 5229 2.724977 TGACTGCGGTTTCACTCTAG 57.275 50.000 0.00 0.00 0.00 2.43
4663 5230 3.585862 GATTGACTGCGGTTTCACTCTA 58.414 45.455 0.00 0.00 0.00 2.43
4664 5231 2.417719 GATTGACTGCGGTTTCACTCT 58.582 47.619 0.00 0.00 0.00 3.24
4665 5232 1.464997 GGATTGACTGCGGTTTCACTC 59.535 52.381 0.00 0.00 0.00 3.51
4666 5233 1.523758 GGATTGACTGCGGTTTCACT 58.476 50.000 0.00 0.00 0.00 3.41
4667 5234 0.521735 GGGATTGACTGCGGTTTCAC 59.478 55.000 0.00 0.00 0.00 3.18
4668 5235 0.608035 GGGGATTGACTGCGGTTTCA 60.608 55.000 0.00 0.00 0.00 2.69
4669 5236 1.313091 GGGGGATTGACTGCGGTTTC 61.313 60.000 0.00 0.00 0.00 2.78
4670 5237 1.304134 GGGGGATTGACTGCGGTTT 60.304 57.895 0.00 0.00 0.00 3.27
4671 5238 1.863155 ATGGGGGATTGACTGCGGTT 61.863 55.000 0.00 0.00 0.00 4.44
4672 5239 2.270874 GATGGGGGATTGACTGCGGT 62.271 60.000 0.00 0.00 0.00 5.68
4673 5240 1.526917 GATGGGGGATTGACTGCGG 60.527 63.158 0.00 0.00 0.00 5.69
4674 5241 1.526917 GGATGGGGGATTGACTGCG 60.527 63.158 0.00 0.00 0.00 5.18
4675 5242 1.152673 GGGATGGGGGATTGACTGC 60.153 63.158 0.00 0.00 0.00 4.40
4676 5243 1.288508 TGGGGATGGGGGATTGACTG 61.289 60.000 0.00 0.00 0.00 3.51
4677 5244 1.086565 TGGGGATGGGGGATTGACT 59.913 57.895 0.00 0.00 0.00 3.41
4678 5245 1.230212 GTGGGGATGGGGGATTGAC 59.770 63.158 0.00 0.00 0.00 3.18
4679 5246 2.012210 GGTGGGGATGGGGGATTGA 61.012 63.158 0.00 0.00 0.00 2.57
4680 5247 2.608759 GGTGGGGATGGGGGATTG 59.391 66.667 0.00 0.00 0.00 2.67
4681 5248 2.703808 GGGTGGGGATGGGGGATT 60.704 66.667 0.00 0.00 0.00 3.01
4682 5249 3.318364 AAGGGTGGGGATGGGGGAT 62.318 63.158 0.00 0.00 0.00 3.85
4683 5250 3.980600 AAGGGTGGGGATGGGGGA 61.981 66.667 0.00 0.00 0.00 4.81
4684 5251 3.429580 GAAGGGTGGGGATGGGGG 61.430 72.222 0.00 0.00 0.00 5.40
4685 5252 2.287194 AGAAGGGTGGGGATGGGG 60.287 66.667 0.00 0.00 0.00 4.96
4686 5253 1.214305 TTGAGAAGGGTGGGGATGGG 61.214 60.000 0.00 0.00 0.00 4.00
4687 5254 0.034089 GTTGAGAAGGGTGGGGATGG 60.034 60.000 0.00 0.00 0.00 3.51
4688 5255 0.034089 GGTTGAGAAGGGTGGGGATG 60.034 60.000 0.00 0.00 0.00 3.51
4689 5256 1.214992 GGGTTGAGAAGGGTGGGGAT 61.215 60.000 0.00 0.00 0.00 3.85
4690 5257 1.850755 GGGTTGAGAAGGGTGGGGA 60.851 63.158 0.00 0.00 0.00 4.81
4691 5258 2.763902 GGGTTGAGAAGGGTGGGG 59.236 66.667 0.00 0.00 0.00 4.96
4692 5259 1.852626 AGGGGTTGAGAAGGGTGGG 60.853 63.158 0.00 0.00 0.00 4.61
4693 5260 1.133809 TGAGGGGTTGAGAAGGGTGG 61.134 60.000 0.00 0.00 0.00 4.61
4694 5261 0.326264 CTGAGGGGTTGAGAAGGGTG 59.674 60.000 0.00 0.00 0.00 4.61
4695 5262 1.492993 GCTGAGGGGTTGAGAAGGGT 61.493 60.000 0.00 0.00 0.00 4.34
4696 5263 1.301293 GCTGAGGGGTTGAGAAGGG 59.699 63.158 0.00 0.00 0.00 3.95
4697 5264 1.301293 GGCTGAGGGGTTGAGAAGG 59.699 63.158 0.00 0.00 0.00 3.46
4698 5265 1.078848 CGGCTGAGGGGTTGAGAAG 60.079 63.158 0.00 0.00 0.00 2.85
4699 5266 3.068881 CGGCTGAGGGGTTGAGAA 58.931 61.111 0.00 0.00 0.00 2.87
4700 5267 3.706373 GCGGCTGAGGGGTTGAGA 61.706 66.667 0.00 0.00 0.00 3.27
4701 5268 4.785453 GGCGGCTGAGGGGTTGAG 62.785 72.222 0.00 0.00 0.00 3.02
4703 5270 4.659172 TTGGCGGCTGAGGGGTTG 62.659 66.667 11.43 0.00 0.00 3.77
4704 5271 3.868200 CTTTGGCGGCTGAGGGGTT 62.868 63.158 11.43 0.00 0.00 4.11
4705 5272 4.351054 CTTTGGCGGCTGAGGGGT 62.351 66.667 11.43 0.00 0.00 4.95
4706 5273 3.567579 TTCTTTGGCGGCTGAGGGG 62.568 63.158 11.43 0.00 0.00 4.79
4707 5274 1.603455 TTTCTTTGGCGGCTGAGGG 60.603 57.895 11.43 0.00 0.00 4.30
4708 5275 1.581447 GTTTCTTTGGCGGCTGAGG 59.419 57.895 11.43 0.00 0.00 3.86
4709 5276 1.581447 GGTTTCTTTGGCGGCTGAG 59.419 57.895 11.43 8.19 0.00 3.35
4710 5277 1.901464 GGGTTTCTTTGGCGGCTGA 60.901 57.895 11.43 3.03 0.00 4.26
4711 5278 0.608035 TAGGGTTTCTTTGGCGGCTG 60.608 55.000 11.43 0.32 0.00 4.85
4712 5279 0.322546 CTAGGGTTTCTTTGGCGGCT 60.323 55.000 11.43 0.00 0.00 5.52
4713 5280 0.322187 TCTAGGGTTTCTTTGGCGGC 60.322 55.000 0.00 0.00 0.00 6.53
4714 5281 2.194201 TTCTAGGGTTTCTTTGGCGG 57.806 50.000 0.00 0.00 0.00 6.13
4715 5282 2.683362 GGATTCTAGGGTTTCTTTGGCG 59.317 50.000 0.00 0.00 0.00 5.69
4716 5283 3.697166 TGGATTCTAGGGTTTCTTTGGC 58.303 45.455 0.00 0.00 0.00 4.52
4717 5284 4.706962 CCTTGGATTCTAGGGTTTCTTTGG 59.293 45.833 0.00 0.00 33.21 3.28
4718 5285 5.904362 CCTTGGATTCTAGGGTTTCTTTG 57.096 43.478 0.00 0.00 33.21 2.77


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

AutoCloner maintained by Alex Coulton.