Multiple sequence alignment - TraesCS4B01G207400

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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 TraesCS4B01G207400 chr4B 100.000 4572 0 0 1 4572 442585140 442589711 0.000000e+00 8444
1 TraesCS4B01G207400 chr4B 94.340 159 9 0 4414 4572 33199481 33199639 1.270000e-60 244
2 TraesCS4B01G207400 chr4A 91.588 3828 161 64 701 4424 106583658 106579888 0.000000e+00 5136
3 TraesCS4B01G207400 chr4D 93.029 3285 111 43 1188 4418 358715395 358718615 0.000000e+00 4689
4 TraesCS4B01G207400 chr4D 92.950 539 22 6 661 1188 358714832 358715365 0.000000e+00 771
5 TraesCS4B01G207400 chr4D 92.476 412 31 0 250 661 482345509 482345098 1.420000e-164 590
6 TraesCS4B01G207400 chr4D 92.258 155 12 0 1 155 482345662 482345508 2.140000e-53 220
7 TraesCS4B01G207400 chr5D 90.498 663 57 4 1 663 520631049 520631705 0.000000e+00 870
8 TraesCS4B01G207400 chr5D 89.125 377 34 5 1 372 509946141 509945767 3.220000e-126 462
9 TraesCS4B01G207400 chr5D 91.176 272 23 1 370 641 509945685 509945415 7.230000e-98 368
10 TraesCS4B01G207400 chr3A 89.940 666 56 8 1 661 728542444 728541785 0.000000e+00 848
11 TraesCS4B01G207400 chr3A 89.474 665 61 7 1 661 728572892 728572233 0.000000e+00 832
12 TraesCS4B01G207400 chr3A 88.872 665 65 7 1 661 728593320 728592661 0.000000e+00 809
13 TraesCS4B01G207400 chr3A 97.436 156 4 0 4417 4572 684880520 684880675 2.710000e-67 267
14 TraesCS4B01G207400 chr3A 96.795 156 5 0 4417 4572 68865262 68865107 1.260000e-65 261
15 TraesCS4B01G207400 chrUn 88.571 665 67 6 1 661 383290625 383291284 0.000000e+00 798
16 TraesCS4B01G207400 chr2A 88.351 661 72 4 1 660 425865121 425865777 0.000000e+00 789
17 TraesCS4B01G207400 chr6B 87.253 659 69 12 5 660 694658256 694658902 0.000000e+00 737
18 TraesCS4B01G207400 chr6B 94.839 155 8 0 4418 4572 99073844 99073998 4.570000e-60 243
19 TraesCS4B01G207400 chr7B 96.154 156 6 0 4417 4572 379734332 379734487 5.870000e-64 255
20 TraesCS4B01G207400 chr3B 95.062 162 8 0 4411 4572 499187360 499187521 5.870000e-64 255
21 TraesCS4B01G207400 chr3B 93.373 166 10 1 4408 4572 75658999 75659164 1.270000e-60 244
22 TraesCS4B01G207400 chr5A 94.340 159 9 0 4414 4572 402134055 402134213 1.270000e-60 244
23 TraesCS4B01G207400 chr2B 94.872 156 8 0 4417 4572 159851220 159851065 1.270000e-60 244


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 TraesCS4B01G207400 chr4B 442585140 442589711 4571 False 8444 8444 100.0000 1 4572 1 chr4B.!!$F2 4571
1 TraesCS4B01G207400 chr4A 106579888 106583658 3770 True 5136 5136 91.5880 701 4424 1 chr4A.!!$R1 3723
2 TraesCS4B01G207400 chr4D 358714832 358718615 3783 False 2730 4689 92.9895 661 4418 2 chr4D.!!$F1 3757
3 TraesCS4B01G207400 chr4D 482345098 482345662 564 True 405 590 92.3670 1 661 2 chr4D.!!$R1 660
4 TraesCS4B01G207400 chr5D 520631049 520631705 656 False 870 870 90.4980 1 663 1 chr5D.!!$F1 662
5 TraesCS4B01G207400 chr5D 509945415 509946141 726 True 415 462 90.1505 1 641 2 chr5D.!!$R1 640
6 TraesCS4B01G207400 chr3A 728541785 728542444 659 True 848 848 89.9400 1 661 1 chr3A.!!$R2 660
7 TraesCS4B01G207400 chr3A 728572233 728572892 659 True 832 832 89.4740 1 661 1 chr3A.!!$R3 660
8 TraesCS4B01G207400 chr3A 728592661 728593320 659 True 809 809 88.8720 1 661 1 chr3A.!!$R4 660
9 TraesCS4B01G207400 chrUn 383290625 383291284 659 False 798 798 88.5710 1 661 1 chrUn.!!$F1 660
10 TraesCS4B01G207400 chr2A 425865121 425865777 656 False 789 789 88.3510 1 660 1 chr2A.!!$F1 659
11 TraesCS4B01G207400 chr6B 694658256 694658902 646 False 737 737 87.2530 5 660 1 chr6B.!!$F2 655

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
592 690 1.065102 GATCGGACGGTTGAATCTCGA 59.935 52.381 0.0 0.0 0.00 4.04 F
1400 1550 0.033504 AACGCTTGTCCTCACATCGT 59.966 50.000 0.0 0.0 41.20 3.73 F
2532 2716 0.251077 ACCGTCTCCGAGGTACTGTT 60.251 55.000 0.0 0.0 41.55 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1551 1703 1.485480 TGTACACCCAGACGGAAAACA 59.515 47.619 0.0 0.0 34.64 2.83 R
3085 3294 0.103026 CGAGGGAGATGTCGATGCAA 59.897 55.000 0.0 0.0 38.50 4.08 R
4203 4463 0.041535 TACACTCCACCCATACCCGT 59.958 55.000 0.0 0.0 0.00 5.28 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
32 33 4.361748 GGTTTGTTACCACCATACGCAGT 61.362 47.826 0.00 0.00 46.92 4.40
54 55 2.099427 GGCGGGCCGACATTTATTTTTA 59.901 45.455 33.44 0.00 33.63 1.52
86 87 4.121317 CAACCACATCAATTGTTTGCTGT 58.879 39.130 5.13 3.49 41.57 4.40
90 91 5.068987 ACCACATCAATTGTTTGCTGTAACT 59.931 36.000 5.13 0.00 39.51 2.24
91 92 5.984926 CCACATCAATTGTTTGCTGTAACTT 59.015 36.000 5.13 0.00 39.51 2.66
259 271 2.270352 TTTTTCTGTGAGGGCATCGT 57.730 45.000 0.00 0.00 0.00 3.73
300 312 1.213013 CGTCGCCACTAGAAGCTGT 59.787 57.895 0.00 0.00 0.00 4.40
450 548 2.046023 CAGCACGGGATGGCAGAA 60.046 61.111 0.00 0.00 0.00 3.02
458 556 2.761465 GGATGGCAGAAGGGGAGGG 61.761 68.421 0.00 0.00 0.00 4.30
554 652 2.501723 CGGGGAGGAAGAAGAAGATGAA 59.498 50.000 0.00 0.00 0.00 2.57
568 666 4.576463 AGAAGATGAAAAAGTCAACGCACT 59.424 37.500 0.00 0.00 40.50 4.40
592 690 1.065102 GATCGGACGGTTGAATCTCGA 59.935 52.381 0.00 0.00 0.00 4.04
656 755 2.494445 CACCGGCGCAGATCACTA 59.506 61.111 10.83 0.00 0.00 2.74
668 767 5.394663 GCGCAGATCACTACCCTATATCATT 60.395 44.000 0.30 0.00 0.00 2.57
671 770 6.820656 GCAGATCACTACCCTATATCATTTGG 59.179 42.308 0.00 0.00 0.00 3.28
674 773 8.949421 AGATCACTACCCTATATCATTTGGTTT 58.051 33.333 0.00 0.00 0.00 3.27
732 831 3.394606 TCCCTATAGATCAAACAAGGCCC 59.605 47.826 0.00 0.00 0.00 5.80
739 838 3.782523 AGATCAAACAAGGCCCTATCTGA 59.217 43.478 0.00 0.00 0.00 3.27
743 842 1.207791 ACAAGGCCCTATCTGAGTGG 58.792 55.000 0.00 0.00 0.00 4.00
883 999 1.518929 CGCACGCACTATTAAGCTCTC 59.481 52.381 0.00 0.00 0.00 3.20
886 1002 3.786635 CACGCACTATTAAGCTCTCCTT 58.213 45.455 0.00 0.00 37.57 3.36
1202 1351 1.302993 TACGGTTCCCTTTGCTGCC 60.303 57.895 0.00 0.00 0.00 4.85
1219 1368 4.003788 CGTGTGCTCCTCCCCGTT 62.004 66.667 0.00 0.00 0.00 4.44
1228 1377 0.836400 TCCTCCCCGTTCAGCTTCTT 60.836 55.000 0.00 0.00 0.00 2.52
1280 1429 3.637769 TCCTTTGTTTGCTTAGGTGGTT 58.362 40.909 0.00 0.00 0.00 3.67
1301 1450 3.104519 TCCATGGCATTGGATCTTTGT 57.895 42.857 6.96 0.00 40.90 2.83
1375 1525 3.787001 CTTCCCTGTCGCCCCCTC 61.787 72.222 0.00 0.00 0.00 4.30
1376 1526 4.649705 TTCCCTGTCGCCCCCTCA 62.650 66.667 0.00 0.00 0.00 3.86
1383 1533 3.319198 TCGCCCCCTCAGTGGAAC 61.319 66.667 0.00 0.00 38.35 3.62
1400 1550 0.033504 AACGCTTGTCCTCACATCGT 59.966 50.000 0.00 0.00 41.20 3.73
1451 1601 4.451150 GCGATGCACGGGAGGACA 62.451 66.667 10.02 0.00 42.83 4.02
1723 1877 0.615331 TCTTCTCAGAGCCGCCATTT 59.385 50.000 0.00 0.00 0.00 2.32
1817 1972 3.317795 GGATACGCGCGGTTCGTC 61.318 66.667 35.22 21.59 40.89 4.20
2153 2322 2.280592 GACTCCGTTGGGTGCGTT 60.281 61.111 0.00 0.00 33.83 4.84
2154 2323 2.590575 ACTCCGTTGGGTGCGTTG 60.591 61.111 0.00 0.00 33.83 4.10
2155 2324 2.590575 CTCCGTTGGGTGCGTTGT 60.591 61.111 0.00 0.00 33.83 3.32
2175 2346 6.400940 CGTTGTCATTTTCTTGCAAAAACACT 60.401 34.615 0.00 0.00 31.35 3.55
2294 2470 1.537202 GAATTCCATATGAGGTGGCGC 59.463 52.381 3.65 0.00 36.66 6.53
2310 2486 3.885521 GCTGAAGCGAGGGCATGC 61.886 66.667 9.90 9.90 43.41 4.06
2531 2715 0.959372 CACCGTCTCCGAGGTACTGT 60.959 60.000 0.00 0.00 41.55 3.55
2532 2716 0.251077 ACCGTCTCCGAGGTACTGTT 60.251 55.000 0.00 0.00 41.55 3.16
2533 2717 0.450983 CCGTCTCCGAGGTACTGTTC 59.549 60.000 0.00 0.00 41.55 3.18
2534 2718 1.451067 CGTCTCCGAGGTACTGTTCT 58.549 55.000 0.00 0.00 41.55 3.01
2535 2719 2.625737 CGTCTCCGAGGTACTGTTCTA 58.374 52.381 0.00 0.00 41.55 2.10
2536 2720 2.351111 CGTCTCCGAGGTACTGTTCTAC 59.649 54.545 0.00 0.00 41.55 2.59
2537 2721 2.682352 GTCTCCGAGGTACTGTTCTACC 59.318 54.545 0.00 0.00 41.55 3.18
2538 2722 1.669779 CTCCGAGGTACTGTTCTACCG 59.330 57.143 0.00 0.00 41.55 4.02
2539 2723 1.003580 TCCGAGGTACTGTTCTACCGT 59.996 52.381 0.00 0.00 41.55 4.83
2540 2724 2.236146 TCCGAGGTACTGTTCTACCGTA 59.764 50.000 0.00 0.00 41.55 4.02
2541 2725 2.352960 CCGAGGTACTGTTCTACCGTAC 59.647 54.545 0.00 3.78 41.55 3.67
2542 2726 3.265791 CGAGGTACTGTTCTACCGTACT 58.734 50.000 10.09 0.08 41.55 2.73
2543 2727 3.063180 CGAGGTACTGTTCTACCGTACTG 59.937 52.174 10.09 0.00 41.55 2.74
2544 2728 2.751806 AGGTACTGTTCTACCGTACTGC 59.248 50.000 10.09 0.00 41.18 4.40
2611 2799 3.743911 TCACACGCACGAAATAGTTCAAT 59.256 39.130 3.55 0.00 32.89 2.57
2612 2800 4.924462 TCACACGCACGAAATAGTTCAATA 59.076 37.500 3.55 0.00 32.89 1.90
2666 2858 1.028905 TGTTTCTTTCCTTGGCACGG 58.971 50.000 3.10 3.10 0.00 4.94
2673 2865 2.799126 TTCCTTGGCACGGACAATAT 57.201 45.000 12.90 0.00 26.61 1.28
2674 2866 3.916359 TTCCTTGGCACGGACAATATA 57.084 42.857 12.90 0.00 26.61 0.86
2676 2868 3.537580 TCCTTGGCACGGACAATATAAC 58.462 45.455 8.90 0.00 26.61 1.89
2677 2869 3.055021 TCCTTGGCACGGACAATATAACA 60.055 43.478 8.90 0.00 26.61 2.41
2678 2870 3.312421 CCTTGGCACGGACAATATAACAG 59.688 47.826 3.47 0.00 26.61 3.16
2680 2872 3.266636 TGGCACGGACAATATAACAGTG 58.733 45.455 0.00 0.00 34.12 3.66
2681 2873 2.612212 GGCACGGACAATATAACAGTGG 59.388 50.000 0.00 0.00 32.32 4.00
2682 2874 2.612212 GCACGGACAATATAACAGTGGG 59.388 50.000 0.00 0.00 32.32 4.61
2683 2875 3.680475 GCACGGACAATATAACAGTGGGA 60.680 47.826 0.00 0.00 32.32 4.37
2808 3008 2.023414 AACGTGCCGTCAGGTCTCAA 62.023 55.000 0.00 0.00 39.99 3.02
2843 3043 1.448985 CCCAGAAATGTACCACACCG 58.551 55.000 0.00 0.00 0.00 4.94
2858 3061 6.999705 ACCACACCGGGAGTATAATATTTA 57.000 37.500 6.32 0.00 40.22 1.40
2903 3106 0.616371 ACTAATTGGGTGCAGGCGTA 59.384 50.000 0.00 0.00 0.00 4.42
2904 3107 1.014352 CTAATTGGGTGCAGGCGTAC 58.986 55.000 0.00 0.00 0.00 3.67
2905 3108 0.616371 TAATTGGGTGCAGGCGTACT 59.384 50.000 0.00 0.00 0.00 2.73
3019 3228 3.881952 ATTGCCGCACGTCTGAGCA 62.882 57.895 0.00 0.00 0.00 4.26
3053 3262 5.282778 CACGAAACATTATTCAAACGCGATT 59.717 36.000 15.93 3.59 0.00 3.34
3085 3294 2.514592 CATGCACGATCCCGCCTT 60.515 61.111 0.00 0.00 39.95 4.35
3201 3421 1.219124 GCATCTGCTTCGACCAGGA 59.781 57.895 11.22 0.00 38.21 3.86
3206 3426 2.343758 GCTTCGACCAGGAGTGCA 59.656 61.111 0.00 0.00 0.00 4.57
3452 3681 4.452733 GCCGGTCCCTGAACCTCG 62.453 72.222 1.90 0.00 37.15 4.63
3455 3684 3.319198 GGTCCCTGAACCTCGGCA 61.319 66.667 0.00 0.00 36.32 5.69
3626 3864 5.580691 TCATTCATTCACTCACCGTGTTATC 59.419 40.000 0.00 0.00 44.16 1.75
3751 3989 3.958147 TGTGTAGATTCGATCCCAAGCTA 59.042 43.478 0.00 0.00 0.00 3.32
3781 4019 5.738909 AGATCCAGTCAGTCCAAATAAGTG 58.261 41.667 0.00 0.00 0.00 3.16
3799 4037 1.664965 GAAGAGTGCGGTCGTTGCT 60.665 57.895 0.00 0.00 0.00 3.91
3800 4038 1.222115 GAAGAGTGCGGTCGTTGCTT 61.222 55.000 0.00 0.00 0.00 3.91
3815 4059 2.689691 GCTTGGTAGCCCCCATCCA 61.690 63.158 0.00 0.00 41.74 3.41
3817 4061 1.542628 TTGGTAGCCCCCATCCACA 60.543 57.895 0.00 0.00 33.60 4.17
3818 4062 1.858739 TTGGTAGCCCCCATCCACAC 61.859 60.000 0.00 0.00 33.60 3.82
3819 4063 2.595655 GTAGCCCCCATCCACACC 59.404 66.667 0.00 0.00 0.00 4.16
3820 4064 2.694616 TAGCCCCCATCCACACCC 60.695 66.667 0.00 0.00 0.00 4.61
3823 4067 3.420482 CCCCCATCCACACCCCTC 61.420 72.222 0.00 0.00 0.00 4.30
3824 4068 3.420482 CCCCATCCACACCCCTCC 61.420 72.222 0.00 0.00 0.00 4.30
3833 4077 2.352805 CACCCCTCCTGGAGTTGC 59.647 66.667 21.70 0.00 35.39 4.17
3858 4102 2.985896 AGGTTGTACATGTCCGGATTG 58.014 47.619 7.81 11.81 0.00 2.67
3869 4113 0.546747 TCCGGATTGAGAGGGGTTGT 60.547 55.000 0.00 0.00 0.00 3.32
3870 4114 0.328258 CCGGATTGAGAGGGGTTGTT 59.672 55.000 0.00 0.00 0.00 2.83
3871 4115 1.453155 CGGATTGAGAGGGGTTGTTG 58.547 55.000 0.00 0.00 0.00 3.33
3872 4116 1.839424 GGATTGAGAGGGGTTGTTGG 58.161 55.000 0.00 0.00 0.00 3.77
3873 4117 1.177401 GATTGAGAGGGGTTGTTGGC 58.823 55.000 0.00 0.00 0.00 4.52
3911 4155 4.015872 TGAGAACCCAGTACAAATCCAC 57.984 45.455 0.00 0.00 0.00 4.02
3928 4172 1.081833 ACCCATGTGCTCTCCCTCT 59.918 57.895 0.00 0.00 0.00 3.69
3957 4203 1.303317 CTTTGGCTGGGGCTACGTT 60.303 57.895 0.00 0.00 38.73 3.99
4011 4266 3.572255 TCTGCAAGTGTTATTTTGGGGTC 59.428 43.478 0.00 0.00 33.76 4.46
4018 4273 4.018233 AGTGTTATTTTGGGGTCCCGATTA 60.018 41.667 0.48 0.00 39.42 1.75
4063 4322 1.456196 CGCTTAGGATCCCTCGAGCA 61.456 60.000 19.83 0.00 40.59 4.26
4094 4354 0.324738 TGGGGACAGTGTTTTTGGCA 60.325 50.000 0.00 0.00 35.01 4.92
4176 4436 0.764369 TGTCTTGTCCCCAGTCAGCT 60.764 55.000 0.00 0.00 0.00 4.24
4185 4445 2.027192 TCCCCAGTCAGCTTGTGTTATC 60.027 50.000 0.00 0.00 0.00 1.75
4187 4447 3.560025 CCCCAGTCAGCTTGTGTTATCTT 60.560 47.826 0.00 0.00 0.00 2.40
4208 4468 1.808411 CACTTATGCTCAACACGGGT 58.192 50.000 0.00 0.00 0.00 5.28
4227 4487 0.335705 TATGGGTGGAGTGTACCGGA 59.664 55.000 9.46 0.00 39.14 5.14
4242 4502 2.659016 GGAAGCAGCAAAAGGCCC 59.341 61.111 0.00 0.00 46.50 5.80
4266 4526 2.842485 CGAAAATGAAATGAGCAGCGAC 59.158 45.455 0.00 0.00 0.00 5.19
4392 4656 0.323302 TCGACTGGGCAAAGCATGTA 59.677 50.000 0.00 0.00 0.00 2.29
4393 4657 0.729116 CGACTGGGCAAAGCATGTAG 59.271 55.000 0.00 0.00 0.00 2.74
4394 4658 1.826385 GACTGGGCAAAGCATGTAGT 58.174 50.000 0.00 0.00 0.00 2.73
4395 4659 1.470098 GACTGGGCAAAGCATGTAGTG 59.530 52.381 0.00 0.00 0.00 2.74
4396 4660 1.202927 ACTGGGCAAAGCATGTAGTGT 60.203 47.619 0.00 0.00 0.00 3.55
4397 4661 2.039746 ACTGGGCAAAGCATGTAGTGTA 59.960 45.455 0.00 0.00 0.00 2.90
4410 4674 0.752009 TAGTGTAGAGAGCAGCGGGG 60.752 60.000 0.00 0.00 0.00 5.73
4430 4694 4.850193 CAGTGGCCCTGTTTGGAT 57.150 55.556 0.00 0.00 38.35 3.41
4431 4695 2.571548 CAGTGGCCCTGTTTGGATC 58.428 57.895 0.00 0.00 38.35 3.36
4432 4696 0.967380 CAGTGGCCCTGTTTGGATCC 60.967 60.000 4.20 4.20 38.35 3.36
4433 4697 1.682344 GTGGCCCTGTTTGGATCCC 60.682 63.158 9.90 0.00 38.35 3.85
4434 4698 2.166346 TGGCCCTGTTTGGATCCCA 61.166 57.895 9.90 0.00 38.35 4.37
4435 4699 1.380380 GGCCCTGTTTGGATCCCAG 60.380 63.158 9.90 9.37 38.35 4.45
4436 4700 1.380380 GCCCTGTTTGGATCCCAGG 60.380 63.158 22.43 22.43 44.39 4.45
4438 4702 1.380380 CCTGTTTGGATCCCAGGGC 60.380 63.158 21.90 5.15 41.69 5.19
4439 4703 1.693640 CTGTTTGGATCCCAGGGCT 59.306 57.895 9.90 0.00 33.81 5.19
4440 4704 0.918983 CTGTTTGGATCCCAGGGCTA 59.081 55.000 9.90 0.00 33.81 3.93
4441 4705 0.918983 TGTTTGGATCCCAGGGCTAG 59.081 55.000 9.90 0.00 33.81 3.42
4442 4706 1.213296 GTTTGGATCCCAGGGCTAGA 58.787 55.000 9.90 0.00 33.81 2.43
4443 4707 1.141858 GTTTGGATCCCAGGGCTAGAG 59.858 57.143 9.90 0.00 33.81 2.43
4444 4708 1.056700 TTGGATCCCAGGGCTAGAGC 61.057 60.000 9.90 0.00 33.81 4.09
4445 4709 1.152139 GGATCCCAGGGCTAGAGCT 60.152 63.158 0.00 0.00 41.70 4.09
4446 4710 0.115349 GGATCCCAGGGCTAGAGCTA 59.885 60.000 0.00 0.00 41.70 3.32
4447 4711 1.262417 GATCCCAGGGCTAGAGCTAC 58.738 60.000 0.00 0.00 41.70 3.58
4448 4712 0.863956 ATCCCAGGGCTAGAGCTACT 59.136 55.000 0.00 0.00 41.70 2.57
4449 4713 0.637195 TCCCAGGGCTAGAGCTACTT 59.363 55.000 0.00 0.00 41.70 2.24
4450 4714 1.008449 TCCCAGGGCTAGAGCTACTTT 59.992 52.381 0.00 0.00 41.70 2.66
4451 4715 1.139853 CCCAGGGCTAGAGCTACTTTG 59.860 57.143 0.00 0.00 41.70 2.77
4452 4716 2.111384 CCAGGGCTAGAGCTACTTTGA 58.889 52.381 0.81 0.00 41.70 2.69
4453 4717 2.102252 CCAGGGCTAGAGCTACTTTGAG 59.898 54.545 0.81 0.00 41.70 3.02
4454 4718 1.760029 AGGGCTAGAGCTACTTTGAGC 59.240 52.381 0.81 0.00 43.19 4.26
4463 4727 2.633488 GCTACTTTGAGCTACTTGGGG 58.367 52.381 0.00 0.00 39.50 4.96
4464 4728 2.633488 CTACTTTGAGCTACTTGGGGC 58.367 52.381 0.00 0.00 0.00 5.80
4465 4729 1.068121 ACTTTGAGCTACTTGGGGCT 58.932 50.000 0.00 0.00 41.88 5.19
4466 4730 1.271597 ACTTTGAGCTACTTGGGGCTG 60.272 52.381 0.00 0.00 39.05 4.85
4467 4731 1.003580 CTTTGAGCTACTTGGGGCTGA 59.996 52.381 0.00 0.00 39.05 4.26
4468 4732 1.064003 TTGAGCTACTTGGGGCTGAA 58.936 50.000 0.00 0.00 39.05 3.02
4469 4733 0.324943 TGAGCTACTTGGGGCTGAAC 59.675 55.000 0.00 0.00 39.05 3.18
4470 4734 0.615850 GAGCTACTTGGGGCTGAACT 59.384 55.000 0.00 0.00 39.05 3.01
4471 4735 1.831736 GAGCTACTTGGGGCTGAACTA 59.168 52.381 0.00 0.00 39.05 2.24
4472 4736 2.236395 GAGCTACTTGGGGCTGAACTAA 59.764 50.000 0.00 0.00 39.05 2.24
4473 4737 2.027100 AGCTACTTGGGGCTGAACTAAC 60.027 50.000 0.00 0.00 37.41 2.34
4474 4738 2.027100 GCTACTTGGGGCTGAACTAACT 60.027 50.000 0.00 0.00 0.00 2.24
4475 4739 2.861147 ACTTGGGGCTGAACTAACTC 57.139 50.000 0.00 0.00 0.00 3.01
4476 4740 2.339769 ACTTGGGGCTGAACTAACTCT 58.660 47.619 0.00 0.00 0.00 3.24
4477 4741 2.711547 ACTTGGGGCTGAACTAACTCTT 59.288 45.455 0.00 0.00 0.00 2.85
4478 4742 3.908103 ACTTGGGGCTGAACTAACTCTTA 59.092 43.478 0.00 0.00 0.00 2.10
4479 4743 4.349930 ACTTGGGGCTGAACTAACTCTTAA 59.650 41.667 0.00 0.00 0.00 1.85
4480 4744 4.986054 TGGGGCTGAACTAACTCTTAAA 57.014 40.909 0.00 0.00 0.00 1.52
4481 4745 5.313280 TGGGGCTGAACTAACTCTTAAAA 57.687 39.130 0.00 0.00 0.00 1.52
4482 4746 5.887754 TGGGGCTGAACTAACTCTTAAAAT 58.112 37.500 0.00 0.00 0.00 1.82
4483 4747 7.023171 TGGGGCTGAACTAACTCTTAAAATA 57.977 36.000 0.00 0.00 0.00 1.40
4484 4748 7.639378 TGGGGCTGAACTAACTCTTAAAATAT 58.361 34.615 0.00 0.00 0.00 1.28
4485 4749 7.773690 TGGGGCTGAACTAACTCTTAAAATATC 59.226 37.037 0.00 0.00 0.00 1.63
4486 4750 7.228906 GGGGCTGAACTAACTCTTAAAATATCC 59.771 40.741 0.00 0.00 0.00 2.59
4487 4751 7.773690 GGGCTGAACTAACTCTTAAAATATCCA 59.226 37.037 0.00 0.00 0.00 3.41
4488 4752 9.174166 GGCTGAACTAACTCTTAAAATATCCAA 57.826 33.333 0.00 0.00 0.00 3.53
4497 4761 8.066612 ACTCTTAAAATATCCAAACACATGGG 57.933 34.615 0.00 0.00 41.05 4.00
4498 4762 6.872920 TCTTAAAATATCCAAACACATGGGC 58.127 36.000 0.00 0.00 41.05 5.36
4499 4763 6.667414 TCTTAAAATATCCAAACACATGGGCT 59.333 34.615 0.00 0.00 41.05 5.19
4500 4764 7.836685 TCTTAAAATATCCAAACACATGGGCTA 59.163 33.333 0.00 0.00 41.05 3.93
4501 4765 6.469782 AAAATATCCAAACACATGGGCTAG 57.530 37.500 0.00 0.00 41.05 3.42
4502 4766 4.796110 ATATCCAAACACATGGGCTAGT 57.204 40.909 0.00 0.00 41.05 2.57
4503 4767 2.969821 TCCAAACACATGGGCTAGTT 57.030 45.000 0.00 0.00 41.05 2.24
4504 4768 3.237268 TCCAAACACATGGGCTAGTTT 57.763 42.857 0.00 0.00 41.05 2.66
4505 4769 2.890311 TCCAAACACATGGGCTAGTTTG 59.110 45.455 16.26 16.26 46.23 2.93
4508 4772 3.508845 AACACATGGGCTAGTTTGAGT 57.491 42.857 0.00 0.00 0.00 3.41
4509 4773 3.508845 ACACATGGGCTAGTTTGAGTT 57.491 42.857 0.00 0.00 0.00 3.01
4510 4774 4.634012 ACACATGGGCTAGTTTGAGTTA 57.366 40.909 0.00 0.00 0.00 2.24
4511 4775 4.579869 ACACATGGGCTAGTTTGAGTTAG 58.420 43.478 0.00 0.00 0.00 2.34
4512 4776 4.286032 ACACATGGGCTAGTTTGAGTTAGA 59.714 41.667 0.00 0.00 0.00 2.10
4513 4777 5.045578 ACACATGGGCTAGTTTGAGTTAGAT 60.046 40.000 0.00 0.00 0.00 1.98
4514 4778 5.882557 CACATGGGCTAGTTTGAGTTAGATT 59.117 40.000 0.00 0.00 0.00 2.40
4515 4779 5.882557 ACATGGGCTAGTTTGAGTTAGATTG 59.117 40.000 0.00 0.00 0.00 2.67
4516 4780 5.755409 TGGGCTAGTTTGAGTTAGATTGA 57.245 39.130 0.00 0.00 0.00 2.57
4517 4781 6.121776 TGGGCTAGTTTGAGTTAGATTGAA 57.878 37.500 0.00 0.00 0.00 2.69
4518 4782 6.539173 TGGGCTAGTTTGAGTTAGATTGAAA 58.461 36.000 0.00 0.00 0.00 2.69
4519 4783 6.430000 TGGGCTAGTTTGAGTTAGATTGAAAC 59.570 38.462 0.00 0.00 0.00 2.78
4520 4784 6.655425 GGGCTAGTTTGAGTTAGATTGAAACT 59.345 38.462 0.00 0.00 39.84 2.66
4521 4785 7.822822 GGGCTAGTTTGAGTTAGATTGAAACTA 59.177 37.037 0.00 0.00 37.31 2.24
4522 4786 9.216117 GGCTAGTTTGAGTTAGATTGAAACTAA 57.784 33.333 0.00 0.00 38.18 2.24
4526 4790 9.793259 AGTTTGAGTTAGATTGAAACTAATCCA 57.207 29.630 0.00 0.00 37.31 3.41
4527 4791 9.827411 GTTTGAGTTAGATTGAAACTAATCCAC 57.173 33.333 0.00 0.00 37.31 4.02
4528 4792 9.567776 TTTGAGTTAGATTGAAACTAATCCACA 57.432 29.630 0.00 0.00 37.31 4.17
4529 4793 9.567776 TTGAGTTAGATTGAAACTAATCCACAA 57.432 29.630 0.00 0.00 37.31 3.33
4530 4794 9.567776 TGAGTTAGATTGAAACTAATCCACAAA 57.432 29.630 0.00 0.00 37.31 2.83
4555 4819 4.489306 AACTATCCCTGTAAAGAGGTGC 57.511 45.455 0.00 0.00 0.00 5.01
4556 4820 3.725634 ACTATCCCTGTAAAGAGGTGCT 58.274 45.455 0.00 0.00 0.00 4.40
4557 4821 4.880164 ACTATCCCTGTAAAGAGGTGCTA 58.120 43.478 0.00 0.00 0.00 3.49
4558 4822 5.278061 ACTATCCCTGTAAAGAGGTGCTAA 58.722 41.667 0.00 0.00 0.00 3.09
4559 4823 5.905913 ACTATCCCTGTAAAGAGGTGCTAAT 59.094 40.000 0.00 0.00 0.00 1.73
4560 4824 5.717119 ATCCCTGTAAAGAGGTGCTAATT 57.283 39.130 0.00 0.00 0.00 1.40
4561 4825 4.843728 TCCCTGTAAAGAGGTGCTAATTG 58.156 43.478 0.00 0.00 0.00 2.32
4562 4826 3.947834 CCCTGTAAAGAGGTGCTAATTGG 59.052 47.826 0.00 0.00 0.00 3.16
4563 4827 4.324254 CCCTGTAAAGAGGTGCTAATTGGA 60.324 45.833 0.00 0.00 0.00 3.53
4564 4828 4.878397 CCTGTAAAGAGGTGCTAATTGGAG 59.122 45.833 0.00 0.00 0.00 3.86
4565 4829 4.261801 TGTAAAGAGGTGCTAATTGGAGC 58.738 43.478 0.00 0.00 43.16 4.70
4567 4831 4.844349 AAAGAGGTGCTAATTGGAGCTA 57.156 40.909 2.08 0.00 44.72 3.32
4568 4832 4.414337 AAGAGGTGCTAATTGGAGCTAG 57.586 45.455 2.08 0.00 44.72 3.42
4569 4833 3.379452 AGAGGTGCTAATTGGAGCTAGT 58.621 45.455 2.08 0.00 44.72 2.57
4570 4834 3.777522 AGAGGTGCTAATTGGAGCTAGTT 59.222 43.478 2.08 0.00 44.72 2.24
4571 4835 3.873952 GAGGTGCTAATTGGAGCTAGTTG 59.126 47.826 2.08 0.00 44.72 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
32 33 0.681564 AAATAAATGTCGGCCCGCCA 60.682 50.000 6.52 0.00 35.37 5.69
36 37 6.964370 GCAAAAATAAAAATAAATGTCGGCCC 59.036 34.615 0.00 0.00 0.00 5.80
48 49 9.553064 TGATGTGGTTGTAGCAAAAATAAAAAT 57.447 25.926 0.00 0.00 0.00 1.82
54 55 6.991531 ACAATTGATGTGGTTGTAGCAAAAAT 59.008 30.769 13.59 0.00 41.93 1.82
86 87 2.944129 AGCTTCCTTGGTTGCAAGTTA 58.056 42.857 0.00 0.00 0.00 2.24
90 91 2.356665 TGTAGCTTCCTTGGTTGCAA 57.643 45.000 0.00 0.00 0.00 4.08
91 92 2.436417 GATGTAGCTTCCTTGGTTGCA 58.564 47.619 0.00 0.00 0.00 4.08
216 224 4.154347 CTCCCTCGAGGTGCTGGC 62.154 72.222 29.25 0.00 36.75 4.85
217 225 2.363018 TCTCCCTCGAGGTGCTGG 60.363 66.667 29.25 14.15 36.70 4.85
219 227 0.394625 GTACTCTCCCTCGAGGTGCT 60.395 60.000 29.25 9.77 36.70 4.40
245 257 2.202797 CCGACGATGCCCTCACAG 60.203 66.667 0.00 0.00 0.00 3.66
415 513 2.573869 CTGGATGTCGTGGTCGCT 59.426 61.111 0.00 0.00 36.96 4.93
450 548 2.713741 ATCTAGGCCCCCTCCCCT 60.714 66.667 0.00 0.00 34.61 4.79
458 556 1.204113 CCATCCCCTCATCTAGGCCC 61.204 65.000 0.00 0.00 45.03 5.80
554 652 2.325583 TCCTGAGTGCGTTGACTTTT 57.674 45.000 0.00 0.00 0.00 2.27
568 666 1.136305 GATTCAACCGTCCGATCCTGA 59.864 52.381 0.00 0.00 0.00 3.86
687 786 9.374838 GGGATTTTGTAAGAACGAAAGATAGTA 57.625 33.333 0.00 0.00 41.28 1.82
688 787 8.101419 AGGGATTTTGTAAGAACGAAAGATAGT 58.899 33.333 0.00 0.00 41.28 2.12
689 788 8.494016 AGGGATTTTGTAAGAACGAAAGATAG 57.506 34.615 0.00 0.00 41.28 2.08
693 792 9.595823 TCTATAGGGATTTTGTAAGAACGAAAG 57.404 33.333 0.00 0.00 41.28 2.62
695 794 9.760077 GATCTATAGGGATTTTGTAAGAACGAA 57.240 33.333 0.00 0.00 0.00 3.85
696 795 8.920174 TGATCTATAGGGATTTTGTAAGAACGA 58.080 33.333 0.00 0.00 0.00 3.85
697 796 9.542462 TTGATCTATAGGGATTTTGTAAGAACG 57.458 33.333 0.00 0.00 0.00 3.95
732 831 0.817654 TGTCACCGCCACTCAGATAG 59.182 55.000 0.00 0.00 0.00 2.08
739 838 2.108976 CACACTGTCACCGCCACT 59.891 61.111 0.00 0.00 0.00 4.00
743 842 1.292061 TACAAACACACTGTCACCGC 58.708 50.000 0.00 0.00 0.00 5.68
991 1110 4.476752 GTGCCCCATCGCCCGTTA 62.477 66.667 0.00 0.00 0.00 3.18
1202 1351 3.934391 GAACGGGGAGGAGCACACG 62.934 68.421 0.00 0.00 0.00 4.49
1219 1368 2.156098 AGGGGTGGCAAGAAGCTGA 61.156 57.895 0.00 0.00 44.79 4.26
1375 1525 0.249868 TGAGGACAAGCGTTCCACTG 60.250 55.000 4.38 0.00 0.00 3.66
1376 1526 0.249911 GTGAGGACAAGCGTTCCACT 60.250 55.000 4.38 0.00 0.00 4.00
1383 1533 1.354337 CCACGATGTGAGGACAAGCG 61.354 60.000 0.00 0.00 38.90 4.68
1400 1550 2.281484 GTCTGCGGCAAAGTCCCA 60.281 61.111 3.44 0.00 0.00 4.37
1451 1601 4.280494 AACCGTCGCACGCACTCT 62.280 61.111 3.56 0.00 40.91 3.24
1551 1703 1.485480 TGTACACCCAGACGGAAAACA 59.515 47.619 0.00 0.00 34.64 2.83
1817 1972 1.802636 GGTGTCATCCCGCACATTG 59.197 57.895 0.00 0.00 37.35 2.82
2022 2191 2.786539 AATCTGCAGGAACGCGAGCA 62.787 55.000 15.93 13.53 35.43 4.26
2153 2322 7.275341 CAGTAGTGTTTTTGCAAGAAAATGACA 59.725 33.333 3.66 0.00 31.80 3.58
2154 2323 7.487829 TCAGTAGTGTTTTTGCAAGAAAATGAC 59.512 33.333 3.66 2.11 31.80 3.06
2155 2324 7.542890 TCAGTAGTGTTTTTGCAAGAAAATGA 58.457 30.769 3.66 1.48 31.80 2.57
2175 2346 5.708230 GGTATTGTGGTGTTGGAATTCAGTA 59.292 40.000 7.93 0.00 0.00 2.74
2294 2470 3.570638 CGCATGCCCTCGCTTCAG 61.571 66.667 13.15 0.00 35.36 3.02
2531 2715 3.607163 CCGGGCAGTACGGTAGAA 58.393 61.111 0.00 0.00 46.03 2.10
2537 2721 2.813908 GCAAGACCGGGCAGTACG 60.814 66.667 11.69 0.00 0.00 3.67
2538 2722 2.436115 GGCAAGACCGGGCAGTAC 60.436 66.667 11.69 0.00 0.00 2.73
2539 2723 2.221299 AAGGCAAGACCGGGCAGTA 61.221 57.895 11.69 0.00 46.52 2.74
2540 2724 3.570212 AAGGCAAGACCGGGCAGT 61.570 61.111 11.69 0.00 46.52 4.40
2541 2725 3.058160 CAAGGCAAGACCGGGCAG 61.058 66.667 11.69 1.58 46.52 4.85
2544 2728 2.597217 TTGCAAGGCAAGACCGGG 60.597 61.111 6.32 0.00 43.99 5.73
2562 2746 6.018669 GTCAGCAATGGAATAGCAGTAGTAAC 60.019 42.308 0.00 0.00 0.00 2.50
2666 2858 8.788325 AAGTAAGTTCCCACTGTTATATTGTC 57.212 34.615 0.00 0.00 31.60 3.18
2673 2865 5.511888 GCTGGTAAGTAAGTTCCCACTGTTA 60.512 44.000 0.00 0.00 31.60 2.41
2674 2866 4.745783 GCTGGTAAGTAAGTTCCCACTGTT 60.746 45.833 0.00 0.00 31.60 3.16
2676 2868 3.244422 TGCTGGTAAGTAAGTTCCCACTG 60.244 47.826 0.00 0.00 31.60 3.66
2677 2869 2.976882 TGCTGGTAAGTAAGTTCCCACT 59.023 45.455 0.00 0.00 33.11 4.00
2678 2870 3.412237 TGCTGGTAAGTAAGTTCCCAC 57.588 47.619 0.00 0.00 0.00 4.61
2808 3008 2.036256 GGGCAAGTGGCTCCATGT 59.964 61.111 4.74 0.00 44.01 3.21
2858 3061 1.191535 TTCGTCCCTCGGATCAACAT 58.808 50.000 0.00 0.00 40.32 2.71
2904 3107 8.443953 AGGATTAAACTAGTACTGGTACGTAG 57.556 38.462 12.76 0.00 40.80 3.51
2905 3108 8.807948 AAGGATTAAACTAGTACTGGTACGTA 57.192 34.615 12.76 3.13 40.80 3.57
2934 3137 6.539173 TGACACCTAACTTGTCATTACCAAT 58.461 36.000 1.05 0.00 46.64 3.16
3019 3228 7.939782 TGAATAATGTTTCGTGCATATGGATT 58.060 30.769 4.56 0.00 0.00 3.01
3085 3294 0.103026 CGAGGGAGATGTCGATGCAA 59.897 55.000 0.00 0.00 38.50 4.08
3201 3421 2.885861 GGACCTCGATCGTGCACT 59.114 61.111 16.19 0.00 0.00 4.40
3206 3426 2.516460 CTCCCGGACCTCGATCGT 60.516 66.667 15.94 0.00 42.43 3.73
3388 3614 1.519719 CCTGCCTTCTCCTTCCTCG 59.480 63.158 0.00 0.00 0.00 4.63
3430 3659 2.363795 TTCAGGGACCGGCGAGAT 60.364 61.111 9.30 0.00 0.00 2.75
3626 3864 5.442001 CGATGACGTATTATGATGCTTCGTG 60.442 44.000 4.63 0.00 34.56 4.35
3634 3872 5.478407 TCATTGGCGATGACGTATTATGAT 58.522 37.500 13.49 0.00 39.83 2.45
3751 3989 3.141083 TGGACTGACTGGATCTAGCCTAT 59.859 47.826 5.91 0.00 0.00 2.57
3781 4019 1.222115 AAGCAACGACCGCACTCTTC 61.222 55.000 0.00 0.00 0.00 2.87
3799 4037 1.542628 TGTGGATGGGGGCTACCAA 60.543 57.895 5.61 0.00 45.13 3.67
3800 4038 2.126142 TGTGGATGGGGGCTACCA 59.874 61.111 4.05 4.05 46.24 3.25
3818 4062 1.492133 TTCAGCAACTCCAGGAGGGG 61.492 60.000 21.31 12.80 43.03 4.79
3819 4063 0.401738 TTTCAGCAACTCCAGGAGGG 59.598 55.000 21.31 13.16 33.35 4.30
3820 4064 1.612726 CCTTTCAGCAACTCCAGGAGG 60.613 57.143 21.31 4.87 33.35 4.30
3821 4065 1.072965 ACCTTTCAGCAACTCCAGGAG 59.927 52.381 15.72 15.72 35.52 3.69
3822 4066 1.140312 ACCTTTCAGCAACTCCAGGA 58.860 50.000 0.00 0.00 0.00 3.86
3823 4067 1.610522 CAACCTTTCAGCAACTCCAGG 59.389 52.381 0.00 0.00 0.00 4.45
3824 4068 2.301346 ACAACCTTTCAGCAACTCCAG 58.699 47.619 0.00 0.00 0.00 3.86
3833 4077 2.742053 CCGGACATGTACAACCTTTCAG 59.258 50.000 9.21 0.00 0.00 3.02
3858 4102 2.035783 GGGCCAACAACCCCTCTC 59.964 66.667 4.39 0.00 42.01 3.20
3869 4113 1.135960 TATCATCATGTCGGGGCCAA 58.864 50.000 4.39 0.00 0.00 4.52
3870 4114 1.135960 TTATCATCATGTCGGGGCCA 58.864 50.000 4.39 0.00 0.00 5.36
3871 4115 2.086869 CATTATCATCATGTCGGGGCC 58.913 52.381 0.00 0.00 0.00 5.80
3872 4116 3.005554 CTCATTATCATCATGTCGGGGC 58.994 50.000 0.00 0.00 0.00 5.80
3873 4117 4.541973 TCTCATTATCATCATGTCGGGG 57.458 45.455 0.00 0.00 0.00 5.73
3879 4123 7.219322 TGTACTGGGTTCTCATTATCATCATG 58.781 38.462 0.00 0.00 0.00 3.07
3911 4155 1.347050 CATAGAGGGAGAGCACATGGG 59.653 57.143 0.00 0.00 0.00 4.00
3928 4172 3.030291 CCCAGCCAAAGCCAATTACATA 58.970 45.455 0.00 0.00 41.25 2.29
4011 4266 5.059161 TCAGATTCAGAAAGCATAATCGGG 58.941 41.667 0.00 0.00 34.31 5.14
4018 4273 2.957006 GCCCATCAGATTCAGAAAGCAT 59.043 45.455 0.00 0.00 0.00 3.79
4113 4373 1.662608 CACCTCAGCACAGTCGAGT 59.337 57.895 0.00 0.00 0.00 4.18
4203 4463 0.041535 TACACTCCACCCATACCCGT 59.958 55.000 0.00 0.00 0.00 5.28
4204 4464 0.462789 GTACACTCCACCCATACCCG 59.537 60.000 0.00 0.00 0.00 5.28
4208 4468 0.335705 TCCGGTACACTCCACCCATA 59.664 55.000 0.00 0.00 31.96 2.74
4227 4487 2.875804 GCTGGGCCTTTTGCTGCTT 61.876 57.895 4.53 0.00 40.92 3.91
4242 4502 2.597305 GCTGCTCATTTCATTTTCGCTG 59.403 45.455 0.00 0.00 0.00 5.18
4266 4526 1.066358 TCTCCTGCTGCTCAGTCAATG 60.066 52.381 0.00 0.00 41.25 2.82
4307 4571 2.520020 TGCCAAGCTGCTTGTGCT 60.520 55.556 34.19 10.31 39.58 4.40
4392 4656 2.055042 CCCCGCTGCTCTCTACACT 61.055 63.158 0.00 0.00 0.00 3.55
4393 4657 2.496817 CCCCGCTGCTCTCTACAC 59.503 66.667 0.00 0.00 0.00 2.90
4394 4658 2.759973 CCCCCGCTGCTCTCTACA 60.760 66.667 0.00 0.00 0.00 2.74
4395 4659 2.442272 TCCCCCGCTGCTCTCTAC 60.442 66.667 0.00 0.00 0.00 2.59
4396 4660 2.442272 GTCCCCCGCTGCTCTCTA 60.442 66.667 0.00 0.00 0.00 2.43
4397 4661 4.704103 TGTCCCCCGCTGCTCTCT 62.704 66.667 0.00 0.00 0.00 3.10
4418 4682 1.380380 CCTGGGATCCAAACAGGGC 60.380 63.158 21.90 1.18 46.24 5.19
4424 4688 1.511613 CTCTAGCCCTGGGATCCAAA 58.488 55.000 19.27 0.00 30.80 3.28
4425 4689 1.056700 GCTCTAGCCCTGGGATCCAA 61.057 60.000 19.27 0.00 30.87 3.53
4426 4690 1.460305 GCTCTAGCCCTGGGATCCA 60.460 63.158 19.27 0.00 34.31 3.41
4427 4691 0.115349 TAGCTCTAGCCCTGGGATCC 59.885 60.000 19.27 1.92 43.38 3.36
4428 4692 1.203125 AGTAGCTCTAGCCCTGGGATC 60.203 57.143 19.27 0.00 43.38 3.36
4429 4693 0.863956 AGTAGCTCTAGCCCTGGGAT 59.136 55.000 19.27 14.27 43.38 3.85
4430 4694 0.637195 AAGTAGCTCTAGCCCTGGGA 59.363 55.000 19.27 0.00 43.38 4.37
4431 4695 1.139853 CAAAGTAGCTCTAGCCCTGGG 59.860 57.143 8.86 8.86 43.38 4.45
4432 4696 2.102252 CTCAAAGTAGCTCTAGCCCTGG 59.898 54.545 0.00 0.00 43.38 4.45
4433 4697 2.482839 GCTCAAAGTAGCTCTAGCCCTG 60.483 54.545 0.00 0.00 43.38 4.45
4434 4698 1.760029 GCTCAAAGTAGCTCTAGCCCT 59.240 52.381 0.00 0.00 43.38 5.19
4435 4699 2.232756 GCTCAAAGTAGCTCTAGCCC 57.767 55.000 0.00 0.00 43.38 5.19
4443 4707 2.633488 CCCCAAGTAGCTCAAAGTAGC 58.367 52.381 0.00 0.00 43.11 3.58
4444 4708 2.237392 AGCCCCAAGTAGCTCAAAGTAG 59.763 50.000 0.00 0.00 32.71 2.57
4445 4709 2.027192 CAGCCCCAAGTAGCTCAAAGTA 60.027 50.000 0.00 0.00 37.18 2.24
4446 4710 1.068121 AGCCCCAAGTAGCTCAAAGT 58.932 50.000 0.00 0.00 32.71 2.66
4447 4711 1.003580 TCAGCCCCAAGTAGCTCAAAG 59.996 52.381 0.00 0.00 37.18 2.77
4448 4712 1.064003 TCAGCCCCAAGTAGCTCAAA 58.936 50.000 0.00 0.00 37.18 2.69
4449 4713 1.064003 TTCAGCCCCAAGTAGCTCAA 58.936 50.000 0.00 0.00 37.18 3.02
4450 4714 0.324943 GTTCAGCCCCAAGTAGCTCA 59.675 55.000 0.00 0.00 37.18 4.26
4451 4715 0.615850 AGTTCAGCCCCAAGTAGCTC 59.384 55.000 0.00 0.00 37.18 4.09
4452 4716 1.952621 TAGTTCAGCCCCAAGTAGCT 58.047 50.000 0.00 0.00 40.89 3.32
4453 4717 2.027100 AGTTAGTTCAGCCCCAAGTAGC 60.027 50.000 0.00 0.00 0.00 3.58
4454 4718 3.515901 AGAGTTAGTTCAGCCCCAAGTAG 59.484 47.826 0.00 0.00 0.00 2.57
4455 4719 3.517612 AGAGTTAGTTCAGCCCCAAGTA 58.482 45.455 0.00 0.00 0.00 2.24
4456 4720 2.339769 AGAGTTAGTTCAGCCCCAAGT 58.660 47.619 0.00 0.00 0.00 3.16
4457 4721 3.425162 AAGAGTTAGTTCAGCCCCAAG 57.575 47.619 0.00 0.00 0.00 3.61
4458 4722 4.986054 TTAAGAGTTAGTTCAGCCCCAA 57.014 40.909 0.00 0.00 0.00 4.12
4459 4723 4.986054 TTTAAGAGTTAGTTCAGCCCCA 57.014 40.909 0.00 0.00 0.00 4.96
4460 4724 7.228906 GGATATTTTAAGAGTTAGTTCAGCCCC 59.771 40.741 0.00 0.00 0.00 5.80
4461 4725 7.773690 TGGATATTTTAAGAGTTAGTTCAGCCC 59.226 37.037 0.00 0.00 0.00 5.19
4462 4726 8.732746 TGGATATTTTAAGAGTTAGTTCAGCC 57.267 34.615 0.00 0.00 0.00 4.85
4471 4735 8.531146 CCCATGTGTTTGGATATTTTAAGAGTT 58.469 33.333 0.00 0.00 39.25 3.01
4472 4736 7.363793 GCCCATGTGTTTGGATATTTTAAGAGT 60.364 37.037 0.00 0.00 39.25 3.24
4473 4737 6.980397 GCCCATGTGTTTGGATATTTTAAGAG 59.020 38.462 0.00 0.00 39.25 2.85
4474 4738 6.667414 AGCCCATGTGTTTGGATATTTTAAGA 59.333 34.615 0.00 0.00 39.25 2.10
4475 4739 6.877236 AGCCCATGTGTTTGGATATTTTAAG 58.123 36.000 0.00 0.00 39.25 1.85
4476 4740 6.865834 AGCCCATGTGTTTGGATATTTTAA 57.134 33.333 0.00 0.00 39.25 1.52
4477 4741 7.122715 ACTAGCCCATGTGTTTGGATATTTTA 58.877 34.615 0.00 0.00 39.25 1.52
4478 4742 5.957774 ACTAGCCCATGTGTTTGGATATTTT 59.042 36.000 0.00 0.00 39.25 1.82
4479 4743 5.518865 ACTAGCCCATGTGTTTGGATATTT 58.481 37.500 0.00 0.00 39.25 1.40
4480 4744 5.129368 ACTAGCCCATGTGTTTGGATATT 57.871 39.130 0.00 0.00 39.25 1.28
4481 4745 4.796110 ACTAGCCCATGTGTTTGGATAT 57.204 40.909 0.00 0.00 39.25 1.63
4482 4746 4.584638 AACTAGCCCATGTGTTTGGATA 57.415 40.909 0.00 0.00 39.25 2.59
4483 4747 3.456380 AACTAGCCCATGTGTTTGGAT 57.544 42.857 0.00 0.00 39.25 3.41
4484 4748 2.890311 CAAACTAGCCCATGTGTTTGGA 59.110 45.455 8.90 0.00 42.93 3.53
4485 4749 2.890311 TCAAACTAGCCCATGTGTTTGG 59.110 45.455 14.62 3.98 45.18 3.28
4486 4750 3.569701 ACTCAAACTAGCCCATGTGTTTG 59.430 43.478 10.13 10.13 45.95 2.93
4487 4751 3.832527 ACTCAAACTAGCCCATGTGTTT 58.167 40.909 0.00 0.00 33.56 2.83
4488 4752 3.508845 ACTCAAACTAGCCCATGTGTT 57.491 42.857 0.00 0.00 0.00 3.32
4489 4753 3.508845 AACTCAAACTAGCCCATGTGT 57.491 42.857 0.00 0.00 0.00 3.72
4490 4754 4.832248 TCTAACTCAAACTAGCCCATGTG 58.168 43.478 0.00 0.00 0.00 3.21
4491 4755 5.700402 ATCTAACTCAAACTAGCCCATGT 57.300 39.130 0.00 0.00 0.00 3.21
4492 4756 6.115446 TCAATCTAACTCAAACTAGCCCATG 58.885 40.000 0.00 0.00 0.00 3.66
4493 4757 6.313519 TCAATCTAACTCAAACTAGCCCAT 57.686 37.500 0.00 0.00 0.00 4.00
4494 4758 5.755409 TCAATCTAACTCAAACTAGCCCA 57.245 39.130 0.00 0.00 0.00 5.36
4495 4759 6.655425 AGTTTCAATCTAACTCAAACTAGCCC 59.345 38.462 0.00 0.00 35.91 5.19
4496 4760 7.674471 AGTTTCAATCTAACTCAAACTAGCC 57.326 36.000 0.00 0.00 35.91 3.93
4500 4764 9.793259 TGGATTAGTTTCAATCTAACTCAAACT 57.207 29.630 0.00 0.00 39.85 2.66
4501 4765 9.827411 GTGGATTAGTTTCAATCTAACTCAAAC 57.173 33.333 0.00 0.00 37.12 2.93
4502 4766 9.567776 TGTGGATTAGTTTCAATCTAACTCAAA 57.432 29.630 0.00 0.00 37.12 2.69
4503 4767 9.567776 TTGTGGATTAGTTTCAATCTAACTCAA 57.432 29.630 0.00 0.00 37.12 3.02
4504 4768 9.567776 TTTGTGGATTAGTTTCAATCTAACTCA 57.432 29.630 0.00 0.00 37.12 3.41
4531 4795 5.710567 GCACCTCTTTACAGGGATAGTTTTT 59.289 40.000 0.00 0.00 37.96 1.94
4532 4796 5.014228 AGCACCTCTTTACAGGGATAGTTTT 59.986 40.000 0.00 0.00 37.96 2.43
4533 4797 4.536489 AGCACCTCTTTACAGGGATAGTTT 59.464 41.667 0.00 0.00 37.96 2.66
4534 4798 4.104831 AGCACCTCTTTACAGGGATAGTT 58.895 43.478 0.00 0.00 37.96 2.24
4535 4799 3.725634 AGCACCTCTTTACAGGGATAGT 58.274 45.455 0.00 0.00 37.96 2.12
4536 4800 5.871396 TTAGCACCTCTTTACAGGGATAG 57.129 43.478 0.00 0.00 37.96 2.08
4537 4801 6.409234 CCAATTAGCACCTCTTTACAGGGATA 60.409 42.308 0.00 0.00 37.96 2.59
4538 4802 5.440610 CAATTAGCACCTCTTTACAGGGAT 58.559 41.667 0.00 0.00 37.96 3.85
4539 4803 4.324254 CCAATTAGCACCTCTTTACAGGGA 60.324 45.833 0.00 0.00 37.96 4.20
4540 4804 3.947834 CCAATTAGCACCTCTTTACAGGG 59.052 47.826 0.00 0.00 37.96 4.45
4541 4805 4.843728 TCCAATTAGCACCTCTTTACAGG 58.156 43.478 0.00 0.00 39.80 4.00
4542 4806 4.333926 GCTCCAATTAGCACCTCTTTACAG 59.666 45.833 0.00 0.00 42.30 2.74
4543 4807 4.019321 AGCTCCAATTAGCACCTCTTTACA 60.019 41.667 3.15 0.00 45.30 2.41
4544 4808 4.518249 AGCTCCAATTAGCACCTCTTTAC 58.482 43.478 3.15 0.00 45.30 2.01
4545 4809 4.844349 AGCTCCAATTAGCACCTCTTTA 57.156 40.909 3.15 0.00 45.30 1.85
4546 4810 3.728385 AGCTCCAATTAGCACCTCTTT 57.272 42.857 3.15 0.00 45.30 2.52
4547 4811 3.777522 ACTAGCTCCAATTAGCACCTCTT 59.222 43.478 3.15 0.00 45.30 2.85
4548 4812 3.379452 ACTAGCTCCAATTAGCACCTCT 58.621 45.455 3.15 0.00 45.30 3.69
4549 4813 3.828875 ACTAGCTCCAATTAGCACCTC 57.171 47.619 3.15 0.00 45.30 3.85
4550 4814 3.878778 CAACTAGCTCCAATTAGCACCT 58.121 45.455 3.15 0.00 45.30 4.00


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

AutoCloner maintained by Alex Coulton.