Multiple sequence alignment - TraesCS7D01G251600

Loading Multiple Alignment...

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 TraesCS7D01G251600 chr7D 100.000 6237 0 0 2536 8772 224477295 224471059 0.000000e+00 11518.0
1 TraesCS7D01G251600 chr7D 100.000 2226 0 0 1 2226 224479830 224477605 0.000000e+00 4111.0
2 TraesCS7D01G251600 chr7D 97.101 69 2 0 2588 2656 224477173 224477105 5.560000e-22 117.0
3 TraesCS7D01G251600 chr7D 97.101 69 2 0 2658 2726 224477243 224477175 5.560000e-22 117.0
4 TraesCS7D01G251600 chr7D 100.000 41 0 0 5035 5075 588679963 588680003 9.440000e-10 76.8
5 TraesCS7D01G251600 chr7A 94.911 5306 181 37 2658 7903 237954862 237949586 0.000000e+00 8220.0
6 TraesCS7D01G251600 chr7A 93.703 2255 98 25 2 2226 237957241 237955001 0.000000e+00 3338.0
7 TraesCS7D01G251600 chr7A 95.728 515 8 5 7914 8416 237949546 237949034 0.000000e+00 817.0
8 TraesCS7D01G251600 chr7A 89.313 393 29 10 2 388 238008181 238007796 1.710000e-131 481.0
9 TraesCS7D01G251600 chr7A 89.059 393 30 10 2 388 238006315 238005930 7.970000e-130 475.0
10 TraesCS7D01G251600 chr7A 88.175 389 35 8 5 388 238010048 238009666 3.730000e-123 453.0
11 TraesCS7D01G251600 chr7A 87.089 395 34 14 2 388 238004444 238004059 1.750000e-116 431.0
12 TraesCS7D01G251600 chr7A 86.275 408 19 17 8401 8772 237949001 237948595 8.200000e-110 409.0
13 TraesCS7D01G251600 chr7A 88.667 300 24 7 9 303 238002275 238001981 3.010000e-94 357.0
14 TraesCS7D01G251600 chr7A 90.672 268 16 6 125 388 237987822 237987560 1.810000e-91 348.0
15 TraesCS7D01G251600 chr7A 95.868 121 5 0 2536 2656 237954914 237954794 6.950000e-46 196.0
16 TraesCS7D01G251600 chr7B 94.122 3709 98 48 5075 8712 172576554 172580213 0.000000e+00 5531.0
17 TraesCS7D01G251600 chr7B 96.741 2209 60 8 2830 5035 172574159 172576358 0.000000e+00 3670.0
18 TraesCS7D01G251600 chr7B 93.886 1750 74 15 183 1920 172571124 172572852 0.000000e+00 2608.0
19 TraesCS7D01G251600 chr7B 97.682 302 7 0 2537 2838 172573471 172573772 3.630000e-143 520.0
20 TraesCS7D01G251600 chr7B 94.928 276 13 1 1951 2226 172573109 172573383 1.750000e-116 431.0
21 TraesCS7D01G251600 chr7B 81.653 496 68 10 2964 3453 172573109 172573587 2.970000e-104 390.0
22 TraesCS7D01G251600 chr7B 95.327 107 2 1 4929 5035 172576369 172576472 5.450000e-37 167.0
23 TraesCS7D01G251600 chr7B 98.551 69 1 0 2658 2726 172573522 172573590 1.200000e-23 122.0
24 TraesCS7D01G251600 chr7B 95.652 69 3 0 2588 2656 172573592 172573660 2.590000e-20 111.0
25 TraesCS7D01G251600 chr4A 85.714 133 12 4 2 134 640180143 640180018 5.520000e-27 134.0
26 TraesCS7D01G251600 chr2B 85.714 133 10 5 2 134 481752840 481752717 1.990000e-26 132.0
27 TraesCS7D01G251600 chr4B 87.611 113 7 5 32 144 307894191 307894086 3.330000e-24 124.0
28 TraesCS7D01G251600 chr2D 94.340 53 2 1 5033 5085 36748720 36748669 7.300000e-11 80.5
29 TraesCS7D01G251600 chr2D 95.652 46 2 0 5034 5079 395597162 395597207 3.400000e-09 75.0
30 TraesCS7D01G251600 chr6A 94.231 52 2 1 5033 5084 562943131 562943081 2.630000e-10 78.7
31 TraesCS7D01G251600 chr5D 97.727 44 1 0 5035 5078 373214761 373214718 9.440000e-10 76.8
32 TraesCS7D01G251600 chr2A 94.000 50 1 1 5035 5082 727188154 727188105 3.400000e-09 75.0
33 TraesCS7D01G251600 chr6D 95.652 46 1 1 5034 5079 26757905 26757861 1.220000e-08 73.1
34 TraesCS7D01G251600 chr5B 92.308 52 1 3 5034 5083 8543962 8543912 4.390000e-08 71.3


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 TraesCS7D01G251600 chr7D 224471059 224479830 8771 True 3965.750000 11518 98.550500 1 8772 4 chr7D.!!$R1 8771
1 TraesCS7D01G251600 chr7A 237948595 237957241 8646 True 2596.000000 8220 93.297000 2 8772 5 chr7A.!!$R2 8770
2 TraesCS7D01G251600 chr7A 238001981 238010048 8067 True 439.400000 481 88.460600 2 388 5 chr7A.!!$R3 386
3 TraesCS7D01G251600 chr7B 172571124 172580213 9089 False 1505.555556 5531 94.282444 183 8712 9 chr7B.!!$F1 8529

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
851 2741 0.398318 GCTCCTGTCCTGTTCCTGTT 59.602 55.000 0.00 0.00 0.00 3.16 F
853 2743 1.002544 CTCCTGTCCTGTTCCTGTTCC 59.997 57.143 0.00 0.00 0.00 3.62 F
866 2766 1.152419 TGTTCCTGTCCCTGTCGGA 60.152 57.895 0.00 0.00 38.83 4.55 F
1921 3822 2.128771 TTTAGCCCATCCAGAAGTGC 57.871 50.000 0.00 0.00 0.00 4.40 F
2870 5462 2.421424 CTGGCCACATTAGTCTTGAAGC 59.579 50.000 0.00 0.00 0.00 3.86 F
4437 7065 0.108585 ACAGCACACGGAACTTCCAT 59.891 50.000 8.59 0.00 35.91 3.41 F
4503 7131 1.065701 TCGCTCCAAGATCTAACGCTC 59.934 52.381 0.00 0.00 0.00 5.03 F
4899 7529 2.030805 GGGCGTGGAAATGAATAGCATC 60.031 50.000 0.00 0.00 35.78 3.91 F
5453 8245 2.361104 GGCATCCCGCTTTGGACA 60.361 61.111 0.00 0.00 42.00 4.02 F
6904 9947 1.341080 TGCATCCTGACTGTCACAGA 58.659 50.000 13.14 7.28 37.54 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2141 4268 3.049912 GCGACAAATTTTTGGAGTGGAC 58.950 45.455 7.85 0.00 42.34 4.02 R
2654 4781 4.082463 TGAAAGTTGAAAGGTGTGGTTCAC 60.082 41.667 0.00 0.00 45.47 3.18 R
2655 4782 4.082845 TGAAAGTTGAAAGGTGTGGTTCA 58.917 39.130 0.00 0.00 31.99 3.18 R
3115 5709 1.270625 CCTACACTCGGCACCAAAAGA 60.271 52.381 0.00 0.00 0.00 2.52 R
4796 7426 0.902048 CAGAGCTCACAGGAGTCCCA 60.902 60.000 17.77 0.00 43.37 4.37 R
5780 8587 2.107031 TGGATATCAACATGGCTCCCAG 59.893 50.000 4.83 0.00 36.75 4.45 R
6438 9245 1.269998 GGCCACCTAGTCATACGCTAG 59.730 57.143 0.00 0.00 36.57 3.42 R
6439 9246 1.325355 GGCCACCTAGTCATACGCTA 58.675 55.000 0.00 0.00 0.00 4.26 R
7451 11458 0.040157 CAACCGCACATGTGTTGAGG 60.040 55.000 26.01 23.35 0.00 3.86 R
7797 11827 0.035739 GAGGGGCCAAACGAACACTA 59.964 55.000 4.39 0.00 0.00 2.74 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
26 27 3.621268 TGGAATTTATCGAAACAGAGGCG 59.379 43.478 0.00 0.00 0.00 5.52
27 28 3.869246 GGAATTTATCGAAACAGAGGCGA 59.131 43.478 0.00 0.00 38.51 5.54
29 30 5.409643 AATTTATCGAAACAGAGGCGATG 57.590 39.130 0.00 0.00 43.69 3.84
61 1934 1.538075 CAAAAACGTAATGGGCCGAGT 59.462 47.619 0.00 0.00 0.00 4.18
62 1935 1.445871 AAAACGTAATGGGCCGAGTC 58.554 50.000 0.00 0.00 0.00 3.36
65 1938 1.227263 CGTAATGGGCCGAGTCCAG 60.227 63.158 0.00 0.00 42.12 3.86
66 1939 1.905512 GTAATGGGCCGAGTCCAGT 59.094 57.895 0.00 3.40 42.12 4.00
98 1971 3.272334 CGCCGGCTTGCAGGATAC 61.272 66.667 26.68 0.00 0.00 2.24
115 1988 0.945265 TACACAGTTGTAACCGGCGC 60.945 55.000 0.00 0.00 35.14 6.53
116 1989 2.667199 ACAGTTGTAACCGGCGCC 60.667 61.111 19.07 19.07 0.00 6.53
119 1992 4.097863 GTTGTAACCGGCGCCTGC 62.098 66.667 26.68 10.34 41.71 4.85
254 2131 0.968901 TTGCCGTAGTCCTCGTCCAT 60.969 55.000 0.00 0.00 0.00 3.41
255 2132 1.359475 GCCGTAGTCCTCGTCCATC 59.641 63.158 0.00 0.00 0.00 3.51
256 2133 2.031360 CCGTAGTCCTCGTCCATCC 58.969 63.158 0.00 0.00 0.00 3.51
413 2290 0.906775 CGCCTAAACCCCTCCTAACA 59.093 55.000 0.00 0.00 0.00 2.41
557 2435 2.126424 GTGACGACGAGGCTCACC 60.126 66.667 15.95 4.18 0.00 4.02
799 2678 4.185286 AGGTATTTCCGGGCGGCC 62.185 66.667 20.04 20.04 41.99 6.13
829 2708 2.495409 GCTAGGGTTCTTCTAGCGAC 57.505 55.000 7.25 0.00 46.54 5.19
845 2735 3.575351 GACGCGCTCCTGTCCTGTT 62.575 63.158 5.73 0.00 0.00 3.16
849 2739 1.079543 CGCTCCTGTCCTGTTCCTG 60.080 63.158 0.00 0.00 0.00 3.86
851 2741 0.398318 GCTCCTGTCCTGTTCCTGTT 59.602 55.000 0.00 0.00 0.00 3.16
852 2742 1.609320 GCTCCTGTCCTGTTCCTGTTC 60.609 57.143 0.00 0.00 0.00 3.18
853 2743 1.002544 CTCCTGTCCTGTTCCTGTTCC 59.997 57.143 0.00 0.00 0.00 3.62
855 2745 1.271054 CCTGTCCTGTTCCTGTTCCTG 60.271 57.143 0.00 0.00 0.00 3.86
857 2747 1.416401 TGTCCTGTTCCTGTTCCTGTC 59.584 52.381 0.00 0.00 0.00 3.51
866 2766 1.152419 TGTTCCTGTCCCTGTCGGA 60.152 57.895 0.00 0.00 38.83 4.55
953 2853 3.562732 AACCGGGGAAAGGCGAAGG 62.563 63.158 6.32 0.00 0.00 3.46
1057 2957 4.704103 AGGGCTCCAGGCGTGAGA 62.704 66.667 8.24 2.81 42.94 3.27
1066 2966 3.844090 GGCGTGAGAGAGAGGCCC 61.844 72.222 0.00 0.00 38.24 5.80
1083 2983 2.487428 CTGGAGTGCGACGAGGAG 59.513 66.667 0.00 0.00 0.00 3.69
1394 3294 2.278013 GATGGAGTCCGACGTCGC 60.278 66.667 31.73 19.21 38.18 5.19
1469 3369 4.526970 AGAATGGTGGCGTTTGATAAGAT 58.473 39.130 0.00 0.00 0.00 2.40
1510 3410 7.588497 AAGGATTCAGGTGAAAAATATAGCC 57.412 36.000 0.00 0.00 37.61 3.93
1521 3421 8.129211 GGTGAAAAATATAGCCACATTGTAGTC 58.871 37.037 0.00 0.00 0.00 2.59
1687 3587 7.716998 CACTATTTTATCCACCTAGAAGTGCAT 59.283 37.037 0.00 0.00 36.38 3.96
1814 3715 2.288334 TGAGTTGAATGCCACACAATGC 60.288 45.455 0.00 0.00 0.00 3.56
1921 3822 2.128771 TTTAGCCCATCCAGAAGTGC 57.871 50.000 0.00 0.00 0.00 4.40
1956 4083 5.450818 TTTGGGGGTATATGATAGATGCC 57.549 43.478 0.00 0.00 0.00 4.40
2047 4174 7.654520 GCTAACTGACGGTTATCATTTGGTATA 59.345 37.037 7.33 0.00 39.36 1.47
2107 4234 9.823647 TTTCATATTTTTCACTTTTTGGTGCTA 57.176 25.926 0.00 0.00 37.16 3.49
2134 4261 5.105146 TGTGTGCCTCCATAAAACTTTTGTT 60.105 36.000 0.00 0.00 45.94 2.83
2141 4268 7.254421 GCCTCCATAAAACTTTTGTTGTCTTTG 60.254 37.037 0.00 0.00 42.67 2.77
2173 4300 6.579292 CCAAAAATTTGTCGCGTACTCATAAA 59.421 34.615 5.77 0.00 36.45 1.40
2607 4734 6.783708 ATAAACCACACCTTTCAACTTTCA 57.216 33.333 0.00 0.00 0.00 2.69
2608 4735 5.476091 AAACCACACCTTTCAACTTTCAA 57.524 34.783 0.00 0.00 0.00 2.69
2609 4736 5.476091 AACCACACCTTTCAACTTTCAAA 57.524 34.783 0.00 0.00 0.00 2.69
2610 4737 5.675684 ACCACACCTTTCAACTTTCAAAT 57.324 34.783 0.00 0.00 0.00 2.32
2611 4738 5.418676 ACCACACCTTTCAACTTTCAAATG 58.581 37.500 0.00 0.00 0.00 2.32
2612 4739 4.810491 CCACACCTTTCAACTTTCAAATGG 59.190 41.667 0.00 0.00 0.00 3.16
2613 4740 5.418676 CACACCTTTCAACTTTCAAATGGT 58.581 37.500 0.00 0.00 32.41 3.55
2614 4741 5.874261 CACACCTTTCAACTTTCAAATGGTT 59.126 36.000 0.00 0.00 30.48 3.67
2615 4742 5.874261 ACACCTTTCAACTTTCAAATGGTTG 59.126 36.000 0.00 0.00 40.87 3.77
2616 4743 6.105333 CACCTTTCAACTTTCAAATGGTTGA 58.895 36.000 1.72 1.72 44.69 3.18
2617 4744 6.762661 CACCTTTCAACTTTCAAATGGTTGAT 59.237 34.615 5.94 0.00 45.35 2.57
2618 4745 7.925483 CACCTTTCAACTTTCAAATGGTTGATA 59.075 33.333 5.94 1.97 45.35 2.15
2619 4746 8.482128 ACCTTTCAACTTTCAAATGGTTGATAA 58.518 29.630 5.94 4.04 45.35 1.75
2620 4747 8.764287 CCTTTCAACTTTCAAATGGTTGATAAC 58.236 33.333 5.94 0.00 45.35 1.89
2621 4748 9.311916 CTTTCAACTTTCAAATGGTTGATAACA 57.688 29.630 5.94 0.00 45.35 2.41
2622 4749 9.658799 TTTCAACTTTCAAATGGTTGATAACAA 57.341 25.926 5.94 0.00 45.35 2.83
2623 4750 9.658799 TTCAACTTTCAAATGGTTGATAACAAA 57.341 25.926 5.94 0.00 45.35 2.83
2624 4751 9.092876 TCAACTTTCAAATGGTTGATAACAAAC 57.907 29.630 1.72 0.00 43.29 2.93
2625 4752 9.097257 CAACTTTCAAATGGTTGATAACAAACT 57.903 29.630 2.23 0.00 43.29 2.66
2626 4753 9.665719 AACTTTCAAATGGTTGATAACAAACTT 57.334 25.926 2.23 0.00 43.29 2.66
2627 4754 9.313118 ACTTTCAAATGGTTGATAACAAACTTC 57.687 29.630 2.23 0.00 43.29 3.01
2628 4755 9.533253 CTTTCAAATGGTTGATAACAAACTTCT 57.467 29.630 2.23 0.00 43.29 2.85
2629 4756 9.528018 TTTCAAATGGTTGATAACAAACTTCTC 57.472 29.630 2.23 0.00 43.29 2.87
2630 4757 8.231692 TCAAATGGTTGATAACAAACTTCTCA 57.768 30.769 2.23 0.00 43.37 3.27
2631 4758 8.352201 TCAAATGGTTGATAACAAACTTCTCAG 58.648 33.333 2.23 0.00 43.37 3.35
2632 4759 6.824305 ATGGTTGATAACAAACTTCTCAGG 57.176 37.500 2.23 0.00 43.37 3.86
2633 4760 5.070001 TGGTTGATAACAAACTTCTCAGGG 58.930 41.667 2.23 0.00 43.37 4.45
2634 4761 5.070685 GGTTGATAACAAACTTCTCAGGGT 58.929 41.667 0.00 0.00 40.22 4.34
2635 4762 5.535030 GGTTGATAACAAACTTCTCAGGGTT 59.465 40.000 0.00 0.00 40.22 4.11
2636 4763 6.713450 GGTTGATAACAAACTTCTCAGGGTTA 59.287 38.462 0.00 0.00 40.22 2.85
2637 4764 7.308408 GGTTGATAACAAACTTCTCAGGGTTAC 60.308 40.741 0.00 0.00 40.22 2.50
2638 4765 7.074653 TGATAACAAACTTCTCAGGGTTACT 57.925 36.000 0.00 0.00 0.00 2.24
2639 4766 7.159372 TGATAACAAACTTCTCAGGGTTACTC 58.841 38.462 0.00 0.00 0.00 2.59
2640 4767 5.367945 AACAAACTTCTCAGGGTTACTCA 57.632 39.130 0.00 0.00 0.00 3.41
2641 4768 5.367945 ACAAACTTCTCAGGGTTACTCAA 57.632 39.130 0.00 0.00 0.00 3.02
2642 4769 5.123936 ACAAACTTCTCAGGGTTACTCAAC 58.876 41.667 0.00 0.00 0.00 3.18
2643 4770 5.123227 CAAACTTCTCAGGGTTACTCAACA 58.877 41.667 0.00 0.00 36.29 3.33
2644 4771 5.568620 AACTTCTCAGGGTTACTCAACAT 57.431 39.130 0.00 0.00 36.29 2.71
2645 4772 5.153950 ACTTCTCAGGGTTACTCAACATC 57.846 43.478 0.00 0.00 36.29 3.06
2646 4773 4.841246 ACTTCTCAGGGTTACTCAACATCT 59.159 41.667 0.00 0.00 36.29 2.90
2647 4774 5.046950 ACTTCTCAGGGTTACTCAACATCTC 60.047 44.000 0.00 0.00 36.29 2.75
2648 4775 4.416516 TCTCAGGGTTACTCAACATCTCA 58.583 43.478 0.00 0.00 36.29 3.27
2649 4776 4.838423 TCTCAGGGTTACTCAACATCTCAA 59.162 41.667 0.00 0.00 36.29 3.02
2650 4777 5.306937 TCTCAGGGTTACTCAACATCTCAAA 59.693 40.000 0.00 0.00 36.29 2.69
2651 4778 5.935945 TCAGGGTTACTCAACATCTCAAAA 58.064 37.500 0.00 0.00 36.29 2.44
2652 4779 6.361433 TCAGGGTTACTCAACATCTCAAAAA 58.639 36.000 0.00 0.00 36.29 1.94
2653 4780 6.486657 TCAGGGTTACTCAACATCTCAAAAAG 59.513 38.462 0.00 0.00 36.29 2.27
2654 4781 5.770162 AGGGTTACTCAACATCTCAAAAAGG 59.230 40.000 0.00 0.00 36.29 3.11
2655 4782 5.535030 GGGTTACTCAACATCTCAAAAAGGT 59.465 40.000 0.00 0.00 36.29 3.50
2656 4783 6.438763 GGTTACTCAACATCTCAAAAAGGTG 58.561 40.000 0.00 0.00 42.28 4.00
2657 4784 6.262273 GGTTACTCAACATCTCAAAAAGGTGA 59.738 38.462 0.00 0.00 38.50 4.02
2658 4785 7.201785 GGTTACTCAACATCTCAAAAAGGTGAA 60.202 37.037 0.00 0.00 38.50 3.18
2659 4786 6.136541 ACTCAACATCTCAAAAAGGTGAAC 57.863 37.500 0.00 0.00 38.50 3.18
2660 4787 5.067805 ACTCAACATCTCAAAAAGGTGAACC 59.932 40.000 0.00 0.00 38.50 3.62
2661 4788 4.952957 TCAACATCTCAAAAAGGTGAACCA 59.047 37.500 1.62 0.00 38.50 3.67
2662 4789 4.918810 ACATCTCAAAAAGGTGAACCAC 57.081 40.909 1.62 0.00 38.50 4.16
2663 4790 4.277476 ACATCTCAAAAAGGTGAACCACA 58.723 39.130 1.62 0.00 38.50 4.17
2675 4802 4.450082 GTGAACCACACCTTTCAACTTT 57.550 40.909 0.00 0.00 43.05 2.66
2676 4803 4.421058 GTGAACCACACCTTTCAACTTTC 58.579 43.478 0.00 0.00 43.05 2.62
2870 5462 2.421424 CTGGCCACATTAGTCTTGAAGC 59.579 50.000 0.00 0.00 0.00 3.86
3079 5673 3.850122 TGACTGTAGTTGTCATCTCCG 57.150 47.619 0.00 0.00 39.23 4.63
3115 5709 8.610248 TGTTTGAGCAATTTCATGATTTTCAT 57.390 26.923 0.00 0.00 37.65 2.57
3153 5747 5.007682 TGTAGGTTGCCTCCATAAAACTTC 58.992 41.667 0.00 0.00 34.61 3.01
3265 5860 2.095110 TGTGTTGCTGCTATGTGATTGC 60.095 45.455 0.00 0.00 0.00 3.56
3323 5928 9.317936 TCTTGTGTAATATGCTTCTCTTATGTG 57.682 33.333 0.00 0.00 0.00 3.21
4006 6634 1.593933 GCCACATTGCAACTTGTTGTG 59.406 47.619 18.83 18.83 37.90 3.33
4040 6668 3.648339 TTTGCTTGGTCAAGAATCAGC 57.352 42.857 14.20 0.00 40.79 4.26
4084 6712 2.080693 TCACACAGTGACAACCAACAC 58.919 47.619 7.81 0.00 37.67 3.32
4120 6748 6.811170 GCCTTCTGAGTTCTGATATATGTAGC 59.189 42.308 0.00 0.00 0.00 3.58
4145 6773 2.297315 CAGTGACAGGCTCTAACAGTCA 59.703 50.000 0.00 0.00 36.92 3.41
4198 6826 7.254522 GCATTACATAATTGTTTGCCATTGGAG 60.255 37.037 6.95 0.00 37.60 3.86
4248 6876 7.142680 GCAGATTTAGAAGTACTACTGCCTAG 58.857 42.308 0.00 0.00 40.09 3.02
4249 6877 7.201839 GCAGATTTAGAAGTACTACTGCCTAGT 60.202 40.741 0.00 0.00 40.09 2.57
4420 7048 7.114095 GGATTTGGACTTATAGGGTTTGTACA 58.886 38.462 0.00 0.00 0.00 2.90
4437 7065 0.108585 ACAGCACACGGAACTTCCAT 59.891 50.000 8.59 0.00 35.91 3.41
4485 7113 1.071605 CTTCCTTTTCTCAGCCGTCG 58.928 55.000 0.00 0.00 0.00 5.12
4503 7131 1.065701 TCGCTCCAAGATCTAACGCTC 59.934 52.381 0.00 0.00 0.00 5.03
4585 7213 2.237143 TCTCTGCCCACAATCTCGATTT 59.763 45.455 0.00 0.00 0.00 2.17
4796 7426 4.040829 TGTGAATCTCATAAGGCCATCGAT 59.959 41.667 5.01 0.00 0.00 3.59
4899 7529 2.030805 GGGCGTGGAAATGAATAGCATC 60.031 50.000 0.00 0.00 35.78 3.91
4993 7737 7.239763 TGTCATGTACCTGAAAGATGAACTA 57.760 36.000 2.11 0.00 34.07 2.24
5151 7939 7.553334 ACATGAACGTGGTACTAAGATGTAAT 58.447 34.615 0.00 0.00 0.00 1.89
5178 7966 9.020731 AGAAAGATGTATTTTGAAAATACCGGT 57.979 29.630 28.19 13.98 33.37 5.28
5383 8175 3.838244 AGCATGCCTAATAGTTTCGGA 57.162 42.857 15.66 0.00 0.00 4.55
5453 8245 2.361104 GGCATCCCGCTTTGGACA 60.361 61.111 0.00 0.00 42.00 4.02
5858 8665 4.314961 TCATGCTTGTACGAGACAATGTT 58.685 39.130 14.70 0.00 46.95 2.71
6014 8821 5.740290 TTCTTACTTCCCCTACAGTCTTG 57.260 43.478 0.00 0.00 0.00 3.02
6017 8824 6.023603 TCTTACTTCCCCTACAGTCTTGATT 58.976 40.000 0.00 0.00 0.00 2.57
6087 8894 8.200120 TGGTAGATCTCAGACATCTTGTTTATG 58.800 37.037 0.00 0.00 32.61 1.90
6106 8913 9.620259 TGTTTATGCTTATACACACATGGATTA 57.380 29.630 0.00 0.00 29.54 1.75
6315 9122 3.039252 TGGTTGGTGAATCTGGGTTTT 57.961 42.857 0.00 0.00 0.00 2.43
6438 9245 9.167311 CCTACTTTTAAGATCCATACATATGCC 57.833 37.037 1.58 0.00 32.40 4.40
6439 9246 9.950496 CTACTTTTAAGATCCATACATATGCCT 57.050 33.333 1.58 0.00 32.40 4.75
6461 9491 1.935933 CGTATGACTAGGTGGCCAAC 58.064 55.000 14.82 14.82 0.00 3.77
6702 9734 4.582869 ACTGATGTGATGTGCTTATGTGT 58.417 39.130 0.00 0.00 0.00 3.72
6705 9737 6.092670 ACTGATGTGATGTGCTTATGTGTAAC 59.907 38.462 0.00 0.00 37.35 2.50
6708 9740 5.471257 TGTGATGTGCTTATGTGTAACGTA 58.529 37.500 0.00 0.00 42.39 3.57
6709 9741 5.927115 TGTGATGTGCTTATGTGTAACGTAA 59.073 36.000 0.00 0.00 45.44 3.18
6811 9852 4.560136 TTTTTGCTGCATCGTAGTTTCA 57.440 36.364 1.84 0.00 0.00 2.69
6903 9946 2.174363 TTGCATCCTGACTGTCACAG 57.826 50.000 6.36 2.22 37.52 3.66
6904 9947 1.341080 TGCATCCTGACTGTCACAGA 58.659 50.000 13.14 7.28 37.54 3.41
6927 9970 1.348036 ACCCTTCTACCACTGCTTGTC 59.652 52.381 0.00 0.00 0.00 3.18
6969 10012 9.613428 ATCTTTTTGTATACTTGCTGCTATACA 57.387 29.630 13.21 13.21 35.13 2.29
7228 10273 9.984190 CTGGATAAGGTTAGACTTAATAACTCC 57.016 37.037 0.00 0.00 36.60 3.85
7250 10299 4.739716 CCCGTCAAAAATCAGTTCTGTTTG 59.260 41.667 0.00 4.42 0.00 2.93
7266 10315 4.276431 TCTGTTTGTCACCGGGTATTTTTC 59.724 41.667 6.32 0.00 0.00 2.29
7278 10327 4.279922 CGGGTATTTTTCCAGTTCCTTGTT 59.720 41.667 0.00 0.00 0.00 2.83
7298 10347 1.477700 TGCTACCTTCCATTGCATTGC 59.522 47.619 0.46 0.46 0.00 3.56
7299 10348 1.477700 GCTACCTTCCATTGCATTGCA 59.522 47.619 7.38 7.38 36.47 4.08
7301 10350 3.431207 GCTACCTTCCATTGCATTGCATT 60.431 43.478 12.95 6.17 38.76 3.56
7452 11459 6.969993 TTTTTATGGATATGGTAGTTGCCC 57.030 37.500 0.00 0.00 0.00 5.36
7456 11463 3.119319 TGGATATGGTAGTTGCCCTCAA 58.881 45.455 0.00 0.00 0.00 3.02
7481 11488 2.202878 GCGGTTGCAGCGATCCTA 60.203 61.111 11.05 0.00 42.41 2.94
7561 11576 5.277731 GGTGAAAGAGCTGTTCAAGAAGAAG 60.278 44.000 10.29 0.00 36.77 2.85
7788 11818 1.741706 CTGACGCATTCTCTTTGGCAT 59.258 47.619 0.00 0.00 0.00 4.40
7789 11819 2.938451 CTGACGCATTCTCTTTGGCATA 59.062 45.455 0.00 0.00 0.00 3.14
7790 11820 3.544684 TGACGCATTCTCTTTGGCATAT 58.455 40.909 0.00 0.00 0.00 1.78
7791 11821 3.313249 TGACGCATTCTCTTTGGCATATG 59.687 43.478 0.00 0.00 0.00 1.78
7792 11822 2.033801 ACGCATTCTCTTTGGCATATGC 59.966 45.455 19.79 19.79 41.14 3.14
7793 11823 2.292569 CGCATTCTCTTTGGCATATGCT 59.707 45.455 26.12 0.89 41.70 3.79
7794 11824 3.499537 CGCATTCTCTTTGGCATATGCTA 59.500 43.478 26.12 18.86 41.70 3.49
7795 11825 4.378149 CGCATTCTCTTTGGCATATGCTAG 60.378 45.833 26.12 19.50 41.70 3.42
7796 11826 4.518211 GCATTCTCTTTGGCATATGCTAGT 59.482 41.667 26.12 4.36 41.70 2.57
7797 11827 5.009410 GCATTCTCTTTGGCATATGCTAGTT 59.991 40.000 26.12 7.11 41.70 2.24
7798 11828 6.205464 GCATTCTCTTTGGCATATGCTAGTTA 59.795 38.462 26.12 9.53 41.70 2.24
7799 11829 7.572724 GCATTCTCTTTGGCATATGCTAGTTAG 60.573 40.741 26.12 17.50 41.70 2.34
7800 11830 6.485830 TCTCTTTGGCATATGCTAGTTAGT 57.514 37.500 26.12 0.00 41.70 2.24
7890 11920 6.944234 AGGCTGGAATGTTTATACTAAAGC 57.056 37.500 0.00 0.00 0.00 3.51
7903 11933 9.866798 GTTTATACTAAAGCCAAGTGTAGTACT 57.133 33.333 0.00 0.00 42.89 2.73
7905 11935 5.402997 ACTAAAGCCAAGTGTAGTACTCC 57.597 43.478 0.00 0.00 39.18 3.85
7909 11939 1.134560 GCCAAGTGTAGTACTCCCGAG 59.865 57.143 0.00 0.00 39.18 4.63
7911 11941 1.816835 CAAGTGTAGTACTCCCGAGCA 59.183 52.381 0.00 0.00 39.18 4.26
8441 14695 4.141597 TGGACCACTTTGACATTGACACTA 60.142 41.667 0.00 0.00 0.00 2.74
8473 14727 4.740934 GCATTACTCTTTACCTGCCGATCT 60.741 45.833 0.00 0.00 0.00 2.75
8477 14731 4.215908 ACTCTTTACCTGCCGATCTCATA 58.784 43.478 0.00 0.00 0.00 2.15
8502 14756 5.714806 TGGAAACTTTGTTGAGACTTTCCTT 59.285 36.000 8.12 0.00 37.32 3.36
8589 14861 2.353610 GGGCTTGCCAACTGGATGG 61.354 63.158 14.04 0.00 43.70 3.51
8591 14863 1.318158 GGCTTGCCAACTGGATGGAG 61.318 60.000 6.79 0.00 43.54 3.86
8600 14872 0.835941 ACTGGATGGAGCAGGTCATC 59.164 55.000 1.20 3.17 39.08 2.92
8721 15008 2.862512 ACAGTTTTCACAGCAAACACG 58.137 42.857 0.19 0.00 36.71 4.49
8731 15018 4.336993 TCACAGCAAACACGGTTTCTATTT 59.663 37.500 0.00 0.00 0.00 1.40
8733 15020 5.518487 CACAGCAAACACGGTTTCTATTTTT 59.482 36.000 0.00 0.00 0.00 1.94
8756 15046 3.837146 TCTCAGAGAGAAGAAATGCAGGT 59.163 43.478 0.00 0.00 35.59 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 6.528072 GCCTCTGTTTCGATAAATTCCAAAAG 59.472 38.462 0.00 0.00 0.00 2.27
3 4 4.094294 CGCCTCTGTTTCGATAAATTCCAA 59.906 41.667 0.00 0.00 0.00 3.53
29 30 2.804647 ACGTTTTTGTTAGCAACCTGC 58.195 42.857 0.00 0.00 45.46 4.85
61 1934 2.027073 CTGCAGCGCGTTAACTGGA 61.027 57.895 8.43 6.74 34.38 3.86
62 1935 2.476051 CTGCAGCGCGTTAACTGG 59.524 61.111 8.43 0.00 34.38 4.00
87 1960 4.154195 GGTTACAACTGTGTATCCTGCAAG 59.846 45.833 6.70 0.00 42.96 4.01
96 1969 0.945265 GCGCCGGTTACAACTGTGTA 60.945 55.000 1.90 0.00 39.30 2.90
97 1970 2.248835 GCGCCGGTTACAACTGTGT 61.249 57.895 1.90 0.00 42.09 3.72
98 1971 2.554272 GCGCCGGTTACAACTGTG 59.446 61.111 1.90 0.00 33.38 3.66
115 1988 1.442526 CTCCTATTTGGCGCTGCAGG 61.443 60.000 17.12 6.85 35.26 4.85
116 1989 1.442526 CCTCCTATTTGGCGCTGCAG 61.443 60.000 10.11 10.11 35.26 4.41
119 1992 3.425422 GCCTCCTATTTGGCGCTG 58.575 61.111 7.64 0.00 39.71 5.18
254 2131 3.427098 CGCGCGATTATAATAGTGGAGGA 60.427 47.826 28.94 0.00 0.00 3.71
255 2132 2.852413 CGCGCGATTATAATAGTGGAGG 59.148 50.000 28.94 0.00 0.00 4.30
256 2133 2.852413 CCGCGCGATTATAATAGTGGAG 59.148 50.000 34.63 3.95 0.00 3.86
676 2554 3.488090 CGCGGAGAGAAAACGGCC 61.488 66.667 0.00 0.00 0.00 6.13
799 2678 3.996124 CCCTAGCGGATCAGCGGG 61.996 72.222 19.64 19.64 43.00 6.13
829 2708 2.811317 GAACAGGACAGGAGCGCG 60.811 66.667 0.00 0.00 0.00 6.86
845 2735 1.185618 CGACAGGGACAGGAACAGGA 61.186 60.000 0.00 0.00 0.00 3.86
849 2739 3.787394 TCCGACAGGGACAGGAAC 58.213 61.111 0.00 0.00 40.94 3.62
857 2747 0.031721 GCGTATAAGGTCCGACAGGG 59.968 60.000 0.00 0.00 38.33 4.45
866 2766 2.502577 GCCCGGTGCGTATAAGGT 59.497 61.111 0.00 0.00 0.00 3.50
923 2823 3.361977 CCGGTTGGTCCAAAGGCG 61.362 66.667 5.69 0.00 35.57 5.52
953 2853 0.466124 CGAAGAATCTCCACTCCCCC 59.534 60.000 0.00 0.00 0.00 5.40
960 2860 1.066430 CCGAAACCCGAAGAATCTCCA 60.066 52.381 0.00 0.00 41.76 3.86
966 2866 2.419667 CTAAAGCCGAAACCCGAAGAA 58.580 47.619 0.00 0.00 41.76 2.52
1057 2957 2.686835 GCACTCCAGGGCCTCTCT 60.687 66.667 0.95 0.00 0.00 3.10
1066 2966 2.487428 CTCCTCGTCGCACTCCAG 59.513 66.667 0.00 0.00 0.00 3.86
1083 2983 2.046285 CACATTCCCTCCGTTGGCC 61.046 63.158 0.00 0.00 0.00 5.36
1117 3017 1.474879 CTCAGGGTTCTCCTCGAAGAC 59.525 57.143 0.00 0.00 46.12 3.01
1191 3091 1.690985 CTCCCCAACCTCCTCTCCC 60.691 68.421 0.00 0.00 0.00 4.30
1469 3369 9.605275 CTGAATCCTTAAAGATCTGTGTAATCA 57.395 33.333 0.00 0.00 0.00 2.57
1510 3410 5.582269 CACCCATACAAGAGACTACAATGTG 59.418 44.000 0.00 0.00 0.00 3.21
1521 3421 4.744795 ACTCTAAGCACCCATACAAGAG 57.255 45.455 0.00 0.00 36.06 2.85
1732 3633 8.188531 ACAATGTGCTATATTTTTCACAATGC 57.811 30.769 8.61 0.00 41.49 3.56
1736 3637 9.448438 AGACTACAATGTGCTATATTTTTCACA 57.552 29.630 0.00 0.00 42.66 3.58
1814 3715 4.154195 ACCAGATAGCAGCAAAGTAAAACG 59.846 41.667 0.00 0.00 0.00 3.60
1956 4083 6.051074 TGCTCAGTCACCATGTAGATTTATG 58.949 40.000 0.00 0.00 0.00 1.90
1994 4121 7.341256 ACAAGAATCTATTTGTGGCTGATCATT 59.659 33.333 0.00 0.00 36.26 2.57
2107 4234 3.832527 AGTTTTATGGAGGCACACACTT 58.167 40.909 0.00 0.00 0.00 3.16
2134 4261 5.930837 AATTTTTGGAGTGGACAAAGACA 57.069 34.783 0.00 0.00 38.84 3.41
2141 4268 3.049912 GCGACAAATTTTTGGAGTGGAC 58.950 45.455 7.85 0.00 42.34 4.02
2173 4300 6.617953 GCTTTAGCGACGTTTGAAAGAGTTAT 60.618 38.462 10.11 0.00 30.29 1.89
2607 4734 7.255942 CCCTGAGAAGTTTGTTATCAACCATTT 60.256 37.037 0.00 0.00 32.93 2.32
2608 4735 6.209391 CCCTGAGAAGTTTGTTATCAACCATT 59.791 38.462 0.00 0.00 32.93 3.16
2609 4736 5.711976 CCCTGAGAAGTTTGTTATCAACCAT 59.288 40.000 0.00 0.00 32.93 3.55
2610 4737 5.070001 CCCTGAGAAGTTTGTTATCAACCA 58.930 41.667 0.00 0.00 32.93 3.67
2611 4738 5.070685 ACCCTGAGAAGTTTGTTATCAACC 58.929 41.667 0.00 0.00 32.93 3.77
2612 4739 6.635030 AACCCTGAGAAGTTTGTTATCAAC 57.365 37.500 0.00 0.00 32.93 3.18
2613 4740 7.514721 AGTAACCCTGAGAAGTTTGTTATCAA 58.485 34.615 0.00 0.00 0.00 2.57
2614 4741 7.074653 AGTAACCCTGAGAAGTTTGTTATCA 57.925 36.000 0.00 0.00 0.00 2.15
2615 4742 7.159372 TGAGTAACCCTGAGAAGTTTGTTATC 58.841 38.462 0.00 0.00 0.00 1.75
2616 4743 7.074653 TGAGTAACCCTGAGAAGTTTGTTAT 57.925 36.000 0.00 0.00 0.00 1.89
2617 4744 6.488769 TGAGTAACCCTGAGAAGTTTGTTA 57.511 37.500 0.00 0.00 0.00 2.41
2618 4745 5.367945 TGAGTAACCCTGAGAAGTTTGTT 57.632 39.130 0.00 0.00 0.00 2.83
2619 4746 5.123936 GTTGAGTAACCCTGAGAAGTTTGT 58.876 41.667 0.00 0.00 0.00 2.83
2620 4747 5.123227 TGTTGAGTAACCCTGAGAAGTTTG 58.877 41.667 0.00 0.00 35.92 2.93
2621 4748 5.367945 TGTTGAGTAACCCTGAGAAGTTT 57.632 39.130 0.00 0.00 35.92 2.66
2622 4749 5.308237 AGATGTTGAGTAACCCTGAGAAGTT 59.692 40.000 0.00 0.00 35.92 2.66
2623 4750 4.841246 AGATGTTGAGTAACCCTGAGAAGT 59.159 41.667 0.00 0.00 35.92 3.01
2624 4751 5.047021 TGAGATGTTGAGTAACCCTGAGAAG 60.047 44.000 0.00 0.00 35.92 2.85
2625 4752 4.838423 TGAGATGTTGAGTAACCCTGAGAA 59.162 41.667 0.00 0.00 35.92 2.87
2626 4753 4.416516 TGAGATGTTGAGTAACCCTGAGA 58.583 43.478 0.00 0.00 35.92 3.27
2627 4754 4.808414 TGAGATGTTGAGTAACCCTGAG 57.192 45.455 0.00 0.00 35.92 3.35
2628 4755 5.560722 TTTGAGATGTTGAGTAACCCTGA 57.439 39.130 0.00 0.00 35.92 3.86
2629 4756 6.294176 CCTTTTTGAGATGTTGAGTAACCCTG 60.294 42.308 0.00 0.00 35.92 4.45
2630 4757 5.770162 CCTTTTTGAGATGTTGAGTAACCCT 59.230 40.000 0.00 0.00 35.92 4.34
2631 4758 5.535030 ACCTTTTTGAGATGTTGAGTAACCC 59.465 40.000 0.00 0.00 35.92 4.11
2632 4759 6.262273 TCACCTTTTTGAGATGTTGAGTAACC 59.738 38.462 0.00 0.00 35.92 2.85
2633 4760 7.259290 TCACCTTTTTGAGATGTTGAGTAAC 57.741 36.000 0.00 0.00 37.32 2.50
2634 4761 7.201785 GGTTCACCTTTTTGAGATGTTGAGTAA 60.202 37.037 0.00 0.00 0.00 2.24
2635 4762 6.262273 GGTTCACCTTTTTGAGATGTTGAGTA 59.738 38.462 0.00 0.00 0.00 2.59
2636 4763 5.067805 GGTTCACCTTTTTGAGATGTTGAGT 59.932 40.000 0.00 0.00 0.00 3.41
2637 4764 5.067674 TGGTTCACCTTTTTGAGATGTTGAG 59.932 40.000 0.00 0.00 36.82 3.02
2638 4765 4.952957 TGGTTCACCTTTTTGAGATGTTGA 59.047 37.500 0.00 0.00 36.82 3.18
2639 4766 5.043248 GTGGTTCACCTTTTTGAGATGTTG 58.957 41.667 0.00 0.00 36.82 3.33
2640 4767 4.709397 TGTGGTTCACCTTTTTGAGATGTT 59.291 37.500 0.00 0.00 36.82 2.71
2641 4768 4.097892 GTGTGGTTCACCTTTTTGAGATGT 59.902 41.667 0.00 0.00 40.84 3.06
2642 4769 4.610945 GTGTGGTTCACCTTTTTGAGATG 58.389 43.478 0.00 0.00 40.84 2.90
2643 4770 4.918810 GTGTGGTTCACCTTTTTGAGAT 57.081 40.909 0.00 0.00 40.84 2.75
2654 4781 4.082463 TGAAAGTTGAAAGGTGTGGTTCAC 60.082 41.667 0.00 0.00 45.47 3.18
2655 4782 4.082845 TGAAAGTTGAAAGGTGTGGTTCA 58.917 39.130 0.00 0.00 31.99 3.18
2656 4783 4.712122 TGAAAGTTGAAAGGTGTGGTTC 57.288 40.909 0.00 0.00 0.00 3.62
2657 4784 5.476091 TTTGAAAGTTGAAAGGTGTGGTT 57.524 34.783 0.00 0.00 0.00 3.67
2658 4785 5.418676 CATTTGAAAGTTGAAAGGTGTGGT 58.581 37.500 0.00 0.00 0.00 4.16
2659 4786 4.810491 CCATTTGAAAGTTGAAAGGTGTGG 59.190 41.667 0.00 0.00 0.00 4.17
2660 4787 5.418676 ACCATTTGAAAGTTGAAAGGTGTG 58.581 37.500 0.00 0.00 0.00 3.82
2661 4788 5.675684 ACCATTTGAAAGTTGAAAGGTGT 57.324 34.783 0.00 0.00 0.00 4.16
2662 4789 6.105333 TCAACCATTTGAAAGTTGAAAGGTG 58.895 36.000 9.44 0.00 45.02 4.00
2663 4790 6.293004 TCAACCATTTGAAAGTTGAAAGGT 57.707 33.333 9.44 0.00 45.02 3.50
2669 4796 9.097257 AGTTTGTTATCAACCATTTGAAAGTTG 57.903 29.630 4.27 4.27 45.01 3.16
2670 4797 9.665719 AAGTTTGTTATCAACCATTTGAAAGTT 57.334 25.926 0.00 0.00 45.01 2.66
2671 4798 9.313118 GAAGTTTGTTATCAACCATTTGAAAGT 57.687 29.630 0.00 0.00 45.01 2.66
2672 4799 9.533253 AGAAGTTTGTTATCAACCATTTGAAAG 57.467 29.630 0.00 0.00 45.01 2.62
2673 4800 9.528018 GAGAAGTTTGTTATCAACCATTTGAAA 57.472 29.630 0.00 0.00 45.01 2.69
2674 4801 8.690884 TGAGAAGTTTGTTATCAACCATTTGAA 58.309 29.630 0.00 0.00 45.01 2.69
2675 4802 8.231692 TGAGAAGTTTGTTATCAACCATTTGA 57.768 30.769 0.00 0.00 45.93 2.69
2676 4803 7.596248 CCTGAGAAGTTTGTTATCAACCATTTG 59.404 37.037 0.00 0.00 32.93 2.32
2870 5462 3.170791 AGAGCGATAACTGACATGGTG 57.829 47.619 0.00 0.00 0.00 4.17
2960 5552 9.551734 TCACCATGTAGATTTTCAGAATCTATG 57.448 33.333 10.61 7.71 40.25 2.23
3079 5673 7.862372 TGAAATTGCTCAAACAATAGAACTGTC 59.138 33.333 0.00 0.00 39.32 3.51
3115 5709 1.270625 CCTACACTCGGCACCAAAAGA 60.271 52.381 0.00 0.00 0.00 2.52
3153 5747 8.433421 TTTAAGTACAAGGAGAAAGACAACAG 57.567 34.615 0.00 0.00 0.00 3.16
3265 5860 2.755103 GCAACCCTCAAGTCCCAAATAG 59.245 50.000 0.00 0.00 0.00 1.73
4040 6668 5.895928 TCCATCAGAACTCAGAATAAGACG 58.104 41.667 0.00 0.00 0.00 4.18
4084 6712 2.037772 ACTCAGAAGGCTAAGTGTGGTG 59.962 50.000 0.00 0.00 0.00 4.17
4120 6748 1.888436 TTAGAGCCTGTCACTGCCCG 61.888 60.000 0.00 0.00 0.00 6.13
4145 6773 8.302965 CACAGTCGATCATGATGTGTATTTAT 57.697 34.615 14.30 0.00 37.17 1.40
4198 6826 8.116753 GCAATGTACTTATGTCTTGTGATGTAC 58.883 37.037 0.00 0.00 0.00 2.90
4248 6876 5.761165 TTAGGCCTTGTGTCAAGTAAAAC 57.239 39.130 12.58 0.00 0.00 2.43
4249 6877 5.068067 GGTTTAGGCCTTGTGTCAAGTAAAA 59.932 40.000 12.58 0.00 0.00 1.52
4420 7048 2.851263 TAATGGAAGTTCCGTGTGCT 57.149 45.000 17.52 4.41 40.17 4.40
4437 7065 7.070198 TCGAAGGATATTAGTGTTGTCCCATAA 59.930 37.037 0.00 0.00 0.00 1.90
4485 7113 1.137086 TGGAGCGTTAGATCTTGGAGC 59.863 52.381 0.00 2.20 32.47 4.70
4503 7131 1.668419 CTAGTTTTGATCGCCCCTGG 58.332 55.000 0.00 0.00 0.00 4.45
4585 7213 4.521075 GCGCAACTAGAGCCATCA 57.479 55.556 0.30 0.00 37.02 3.07
4765 7393 4.443457 CCTTATGAGATTCACATGGACCGT 60.443 45.833 6.82 0.00 0.00 4.83
4766 7394 4.060900 CCTTATGAGATTCACATGGACCG 58.939 47.826 6.82 0.00 0.00 4.79
4796 7426 0.902048 CAGAGCTCACAGGAGTCCCA 60.902 60.000 17.77 0.00 43.37 4.37
5116 7904 1.730064 CACGTTCATGTACGAAAGGGG 59.270 52.381 28.32 1.93 43.99 4.79
5216 8008 6.681777 TGTTCTCCGTCTTAGTTTACTTACC 58.318 40.000 0.00 0.00 0.00 2.85
5764 8558 4.081087 GCTCCCAGAGTGACCAGTAAATTA 60.081 45.833 0.00 0.00 31.39 1.40
5780 8587 2.107031 TGGATATCAACATGGCTCCCAG 59.893 50.000 4.83 0.00 36.75 4.45
5957 8764 8.638565 GTTGTTGCAAATTAGCTTGTACTTATG 58.361 33.333 0.00 0.00 34.99 1.90
6017 8824 8.644374 AGTAAAGCTTAACAATTTCCACCATA 57.356 30.769 0.00 0.00 0.00 2.74
6087 8894 9.801873 ACAAAAATAATCCATGTGTGTATAAGC 57.198 29.630 0.00 0.00 0.00 3.09
6295 9102 2.765689 AAACCCAGATTCACCAACCA 57.234 45.000 0.00 0.00 0.00 3.67
6315 9122 5.686841 CACAGATGAATGCGAAACAGAAAAA 59.313 36.000 0.00 0.00 0.00 1.94
6438 9245 1.269998 GGCCACCTAGTCATACGCTAG 59.730 57.143 0.00 0.00 36.57 3.42
6439 9246 1.325355 GGCCACCTAGTCATACGCTA 58.675 55.000 0.00 0.00 0.00 4.26
6452 9482 1.886542 CTCCTAAACTTGTTGGCCACC 59.113 52.381 3.88 0.00 0.00 4.61
6461 9491 3.003480 GCAGGTACAGCTCCTAAACTTG 58.997 50.000 0.00 0.00 38.05 3.16
6569 9601 3.564225 AGAACTTTTAACCAAGTCCTGCG 59.436 43.478 0.00 0.00 35.87 5.18
6702 9734 8.325421 TCAAAGGATTTTGCTATGTTACGTTA 57.675 30.769 0.00 0.00 42.71 3.18
6705 9737 7.641411 CAGATCAAAGGATTTTGCTATGTTACG 59.359 37.037 0.00 0.00 42.71 3.18
6708 9740 7.707624 TCAGATCAAAGGATTTTGCTATGTT 57.292 32.000 0.00 0.00 42.71 2.71
6709 9741 7.893124 ATCAGATCAAAGGATTTTGCTATGT 57.107 32.000 0.00 0.00 42.71 2.29
6742 9783 3.209410 GGACTTGCCTTACTGGATGATG 58.791 50.000 0.00 0.00 38.35 3.07
6811 9852 7.810260 AGCTTACTTCTCCATATCAAGGAAAT 58.190 34.615 0.00 0.00 34.08 2.17
6903 9946 2.458620 AGCAGTGGTAGAAGGGTACTC 58.541 52.381 0.00 0.00 0.00 2.59
6904 9947 2.567615 CAAGCAGTGGTAGAAGGGTACT 59.432 50.000 0.00 0.00 0.00 2.73
6927 9970 8.816640 ACAAAAAGATGCCAAAAGTATGTTAG 57.183 30.769 0.00 0.00 0.00 2.34
7228 10273 5.339990 ACAAACAGAACTGATTTTTGACGG 58.660 37.500 17.12 0.00 32.12 4.79
7250 10299 2.786777 ACTGGAAAAATACCCGGTGAC 58.213 47.619 0.00 0.00 40.35 3.67
7266 10315 2.568623 AGGTAGCAACAAGGAACTGG 57.431 50.000 0.00 0.00 40.86 4.00
7278 10327 1.477700 GCAATGCAATGGAAGGTAGCA 59.522 47.619 3.49 0.00 39.79 3.49
7451 11458 0.040157 CAACCGCACATGTGTTGAGG 60.040 55.000 26.01 23.35 0.00 3.86
7452 11459 0.661187 GCAACCGCACATGTGTTGAG 60.661 55.000 26.01 14.66 38.36 3.02
7456 11463 3.033184 CTGCAACCGCACATGTGT 58.967 55.556 26.01 4.58 45.36 3.72
7459 11466 2.908088 GATCGCTGCAACCGCACATG 62.908 60.000 0.00 0.00 45.36 3.21
7476 11483 9.964354 TTAGCAATGCAAATAGTATCATAGGAT 57.036 29.630 8.35 0.00 37.55 3.24
7561 11576 2.637947 GTCTTGCTCTTCCATCCCTTC 58.362 52.381 0.00 0.00 0.00 3.46
7788 11818 4.628333 GCCAAACGAACACTAACTAGCATA 59.372 41.667 0.00 0.00 0.00 3.14
7789 11819 3.435671 GCCAAACGAACACTAACTAGCAT 59.564 43.478 0.00 0.00 0.00 3.79
7790 11820 2.803956 GCCAAACGAACACTAACTAGCA 59.196 45.455 0.00 0.00 0.00 3.49
7791 11821 2.159037 GGCCAAACGAACACTAACTAGC 59.841 50.000 0.00 0.00 0.00 3.42
7792 11822 2.740447 GGGCCAAACGAACACTAACTAG 59.260 50.000 4.39 0.00 0.00 2.57
7793 11823 2.550639 GGGGCCAAACGAACACTAACTA 60.551 50.000 4.39 0.00 0.00 2.24
7794 11824 1.601166 GGGCCAAACGAACACTAACT 58.399 50.000 4.39 0.00 0.00 2.24
7795 11825 0.594602 GGGGCCAAACGAACACTAAC 59.405 55.000 4.39 0.00 0.00 2.34
7796 11826 0.475044 AGGGGCCAAACGAACACTAA 59.525 50.000 4.39 0.00 0.00 2.24
7797 11827 0.035739 GAGGGGCCAAACGAACACTA 59.964 55.000 4.39 0.00 0.00 2.74
7798 11828 1.228154 GAGGGGCCAAACGAACACT 60.228 57.895 4.39 0.00 0.00 3.55
7799 11829 1.228154 AGAGGGGCCAAACGAACAC 60.228 57.895 4.39 0.00 0.00 3.32
7800 11830 1.228124 CAGAGGGGCCAAACGAACA 60.228 57.895 4.39 0.00 0.00 3.18
7890 11920 1.134560 GCTCGGGAGTACTACACTTGG 59.865 57.143 7.57 0.00 37.72 3.61
7903 11933 1.943968 GCAACACAACTATGCTCGGGA 60.944 52.381 0.00 0.00 37.12 5.14
7905 11935 1.442769 AGCAACACAACTATGCTCGG 58.557 50.000 0.00 0.00 46.98 4.63
7909 11939 2.253392 GCAGAGCAACACAACTATGC 57.747 50.000 0.00 0.00 43.07 3.14
7911 11941 5.248640 ACTAATGCAGAGCAACACAACTAT 58.751 37.500 0.00 0.00 43.62 2.12
8056 14250 2.025898 TCATGTGCCAATACCTGCATG 58.974 47.619 0.00 0.00 40.07 4.06
8441 14695 7.268586 CAGGTAAAGAGTAATGCTAGTGTGAT 58.731 38.462 0.00 0.00 0.00 3.06
8473 14727 8.463930 AAAGTCTCAACAAAGTTTCCATATGA 57.536 30.769 3.65 0.00 0.00 2.15
8477 14731 6.149129 GGAAAGTCTCAACAAAGTTTCCAT 57.851 37.500 14.03 0.00 46.99 3.41
8502 14756 2.491621 CGTCAGATGCGGCTCTCA 59.508 61.111 0.00 0.00 0.00 3.27
8589 14861 2.836262 CCTTCATCAGATGACCTGCTC 58.164 52.381 13.01 0.00 42.62 4.26
8591 14863 1.307097 GCCTTCATCAGATGACCTGC 58.693 55.000 13.01 11.59 42.62 4.85
8600 14872 1.761784 AGCTACTCCTGCCTTCATCAG 59.238 52.381 0.00 0.00 0.00 2.90
8731 15018 5.704515 CCTGCATTTCTTCTCTCTGAGAAAA 59.295 40.000 8.95 6.76 46.18 2.29
8733 15020 4.285517 ACCTGCATTTCTTCTCTCTGAGAA 59.714 41.667 8.95 9.30 45.01 2.87
8734 15021 3.837146 ACCTGCATTTCTTCTCTCTGAGA 59.163 43.478 7.24 7.24 36.86 3.27
8735 15022 3.933955 CACCTGCATTTCTTCTCTCTGAG 59.066 47.826 0.00 0.00 0.00 3.35
8736 15023 3.307269 CCACCTGCATTTCTTCTCTCTGA 60.307 47.826 0.00 0.00 0.00 3.27
8737 15024 3.008330 CCACCTGCATTTCTTCTCTCTG 58.992 50.000 0.00 0.00 0.00 3.35
8738 15025 2.641815 ACCACCTGCATTTCTTCTCTCT 59.358 45.455 0.00 0.00 0.00 3.10
8739 15026 3.064900 ACCACCTGCATTTCTTCTCTC 57.935 47.619 0.00 0.00 0.00 3.20
8740 15027 3.515602 AACCACCTGCATTTCTTCTCT 57.484 42.857 0.00 0.00 0.00 3.10
8742 15029 3.565307 TCAAACCACCTGCATTTCTTCT 58.435 40.909 0.00 0.00 0.00 2.85
8747 15037 4.686191 TGAAATCAAACCACCTGCATTT 57.314 36.364 0.00 0.00 0.00 2.32


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

AutoCloner maintained by Alex Coulton.