Multiple sequence alignment - TraesCS6A01G309200

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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 TraesCS6A01G309200 chr6A 100.000 8628 0 0 784 9411 544481170 544472543 0.000000e+00 15934.0
1 TraesCS6A01G309200 chr6A 83.991 1699 249 15 6145 7835 544206262 544204579 0.000000e+00 1609.0
2 TraesCS6A01G309200 chr6A 78.098 2534 454 55 2968 5445 544209338 544206850 0.000000e+00 1511.0
3 TraesCS6A01G309200 chr6A 100.000 357 0 0 1 357 544481953 544481597 0.000000e+00 660.0
4 TraesCS6A01G309200 chr6A 86.885 61 8 0 2642 2702 1139634 1139574 1.700000e-07 69.4
5 TraesCS6A01G309200 chr6D 96.183 6654 165 43 2781 9384 398740970 398734356 0.000000e+00 10798.0
6 TraesCS6A01G309200 chr6D 94.006 1852 50 17 857 2669 398742794 398740965 0.000000e+00 2748.0
7 TraesCS6A01G309200 chr6D 83.863 1698 253 12 6145 7835 398228929 398227246 0.000000e+00 1598.0
8 TraesCS6A01G309200 chr6D 78.326 2533 450 54 2968 5445 398232005 398229517 0.000000e+00 1544.0
9 TraesCS6A01G309200 chr6D 96.369 358 12 1 1 357 398743647 398743290 1.050000e-163 588.0
10 TraesCS6A01G309200 chr6B 94.842 6766 219 59 2701 9403 595956787 595950089 0.000000e+00 10442.0
11 TraesCS6A01G309200 chr6B 91.807 1904 93 31 784 2658 595958651 595956782 0.000000e+00 2593.0
12 TraesCS6A01G309200 chr6B 83.008 1842 269 30 6023 7835 595288799 595286973 0.000000e+00 1628.0
13 TraesCS6A01G309200 chr6B 78.185 2535 447 63 2968 5445 595291729 595289244 0.000000e+00 1520.0
14 TraesCS6A01G309200 chr6B 94.551 312 14 2 1 309 595959330 595959019 6.610000e-131 479.0
15 TraesCS6A01G309200 chr6B 90.756 119 10 1 2666 2784 559352038 559352155 3.520000e-34 158.0
16 TraesCS6A01G309200 chr6B 91.228 57 3 2 2650 2706 89141954 89141900 1.010000e-09 76.8
17 TraesCS6A01G309200 chr7B 88.372 129 13 1 2658 2784 312542051 312542179 4.550000e-33 154.0
18 TraesCS6A01G309200 chr7B 96.154 52 1 1 2655 2706 648164274 648164224 6.060000e-12 84.2
19 TraesCS6A01G309200 chr5A 97.647 85 2 0 2701 2785 362781606 362781690 7.620000e-31 147.0
20 TraesCS6A01G309200 chr3B 94.505 91 4 1 2708 2798 430513709 430513620 1.270000e-28 139.0
21 TraesCS6A01G309200 chr3B 87.097 62 5 3 2647 2706 9936606 9936666 6.100000e-07 67.6
22 TraesCS6A01G309200 chr2D 87.603 121 13 2 2664 2784 620197520 620197638 1.270000e-28 139.0
23 TraesCS6A01G309200 chr5D 96.386 83 3 0 2707 2789 267842755 267842673 4.580000e-28 137.0
24 TraesCS6A01G309200 chr7D 94.318 88 4 1 2707 2793 626199962 626199875 5.930000e-27 134.0
25 TraesCS6A01G309200 chr4A 89.423 104 10 1 2695 2798 743141119 743141221 7.670000e-26 130.0
26 TraesCS6A01G309200 chr4A 86.667 60 4 4 2643 2698 576606412 576606353 7.890000e-06 63.9
27 TraesCS6A01G309200 chr3A 88.235 102 8 2 1517 1617 62269022 62268924 1.660000e-22 119.0
28 TraesCS6A01G309200 chr3A 91.667 60 3 2 2648 2707 12779143 12779200 2.180000e-11 82.4
29 TraesCS6A01G309200 chr2B 92.857 56 3 1 2651 2706 723358732 723358678 7.830000e-11 80.5
30 TraesCS6A01G309200 chr2B 95.122 41 2 0 2666 2706 799161139 799161099 2.190000e-06 65.8
31 TraesCS6A01G309200 chr2B 95.122 41 2 0 2666 2706 799214295 799214255 2.190000e-06 65.8
32 TraesCS6A01G309200 chrUn 91.228 57 4 1 2646 2702 24697985 24697930 1.010000e-09 76.8
33 TraesCS6A01G309200 chrUn 95.122 41 2 0 2666 2706 23900937 23900897 2.190000e-06 65.8
34 TraesCS6A01G309200 chr1A 92.308 52 4 0 2655 2706 477033558 477033507 3.640000e-09 75.0
35 TraesCS6A01G309200 chr4D 86.207 58 6 1 2643 2698 73330302 73330359 2.840000e-05 62.1
36 TraesCS6A01G309200 chr1D 86.207 58 6 1 2643 2698 20943055 20943112 2.840000e-05 62.1


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 TraesCS6A01G309200 chr6A 544472543 544481953 9410 True 8297.000000 15934 100.000000 1 9411 2 chr6A.!!$R3 9410
1 TraesCS6A01G309200 chr6A 544204579 544209338 4759 True 1560.000000 1609 81.044500 2968 7835 2 chr6A.!!$R2 4867
2 TraesCS6A01G309200 chr6D 398734356 398743647 9291 True 4711.333333 10798 95.519333 1 9384 3 chr6D.!!$R2 9383
3 TraesCS6A01G309200 chr6D 398227246 398232005 4759 True 1571.000000 1598 81.094500 2968 7835 2 chr6D.!!$R1 4867
4 TraesCS6A01G309200 chr6B 595950089 595959330 9241 True 4504.666667 10442 93.733333 1 9403 3 chr6B.!!$R3 9402
5 TraesCS6A01G309200 chr6B 595286973 595291729 4756 True 1574.000000 1628 80.596500 2968 7835 2 chr6B.!!$R2 4867

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
159 160 1.691219 GCCCATTTCCACTCCTGGA 59.309 57.895 0.00 0.00 45.68 3.86 F
1020 1312 1.622173 CCCTGCCTCTTTCCTCTCTCT 60.622 57.143 0.00 0.00 0.00 3.10 F
2004 2306 0.972883 GCTTGGTTTGGTAATGGCCA 59.027 50.000 8.56 8.56 36.62 5.36 F
2886 3284 0.103390 TTTGACGTGTTCTCCGAGCA 59.897 50.000 0.00 0.00 0.00 4.26 F
3743 4144 0.178990 ACAAAGGTGGGCTTCCTCAC 60.179 55.000 2.01 0.00 33.76 3.51 F
4413 4835 1.075374 CCAACTCAAAGGATCCACCCA 59.925 52.381 15.82 0.00 40.05 4.51 F
5487 5936 1.218316 CGTAACCAGAGGGCTCACC 59.782 63.158 0.00 0.00 37.90 4.02 F
6017 6484 0.179045 GTGTGTCCACTGGCTCTTGT 60.179 55.000 0.00 0.00 38.61 3.16 F
6792 7280 0.248949 GTAGAAGTCGCGATGGTCCC 60.249 60.000 14.06 0.00 0.00 4.46 F
7072 7560 0.877743 GCCTCAAGTTGCTGGTCTTC 59.122 55.000 13.67 0.00 0.00 2.87 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1055 1353 0.179043 CGGAGAGACGGAGATGAGGA 60.179 60.000 0.00 0.00 0.00 3.71 R
2183 2486 0.180642 TGCACCCGTAAACACCTTCA 59.819 50.000 0.00 0.00 0.00 3.02 R
3146 3544 1.005037 ATCTCGTTTGGTGCAGCGA 60.005 52.632 11.91 6.57 0.00 4.93 R
4064 4465 0.855349 GGCTACGCAGATGATTGACG 59.145 55.000 0.00 0.00 0.00 4.35 R
5509 5958 1.003580 ACAGCCCAGTAGATGTTGTGG 59.996 52.381 0.00 0.00 0.00 4.17 R
5747 6196 0.706433 ACCATCTTCAACTGGCCCAT 59.294 50.000 0.00 0.00 35.88 4.00 R
6616 7104 0.248565 TCAGGTGCAGTCAGAGATGC 59.751 55.000 0.00 1.17 42.86 3.91 R
7072 7560 0.446222 ATTTCGGTGCCGTTCATTCG 59.554 50.000 10.60 0.00 40.74 3.34 R
8231 8726 0.036294 GAAGAGAAGAACCACCGGGG 60.036 60.000 6.32 0.00 44.81 5.73 R
8923 9476 0.187361 CTTTTTCCCCCACCTCACCA 59.813 55.000 0.00 0.00 0.00 4.17 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
159 160 1.691219 GCCCATTTCCACTCCTGGA 59.309 57.895 0.00 0.00 45.68 3.86
191 192 4.736896 GTCCACGTGCCCGAGTCC 62.737 72.222 10.91 0.00 37.88 3.85
805 809 2.343758 CGAGTCCACCCACCACAG 59.656 66.667 0.00 0.00 0.00 3.66
971 1254 4.514577 AGGGGATCTTCGTGCGCG 62.515 66.667 14.79 14.79 39.92 6.86
1020 1312 1.622173 CCCTGCCTCTTTCCTCTCTCT 60.622 57.143 0.00 0.00 0.00 3.10
1052 1350 2.530701 TCCGCTCTCCTCTTTCTCTTT 58.469 47.619 0.00 0.00 0.00 2.52
1053 1351 2.494073 TCCGCTCTCCTCTTTCTCTTTC 59.506 50.000 0.00 0.00 0.00 2.62
1054 1352 2.495669 CCGCTCTCCTCTTTCTCTTTCT 59.504 50.000 0.00 0.00 0.00 2.52
1055 1353 3.056179 CCGCTCTCCTCTTTCTCTTTCTT 60.056 47.826 0.00 0.00 0.00 2.52
1072 1370 2.925724 TCTTCCTCATCTCCGTCTCTC 58.074 52.381 0.00 0.00 0.00 3.20
1112 1410 3.044894 ACCATCTCTCTCCTCCAAATCC 58.955 50.000 0.00 0.00 0.00 3.01
1197 1495 4.271816 CAGATCGAGACCGGCCCG 62.272 72.222 0.00 0.00 36.24 6.13
1607 1909 4.423209 GGACCAGCCTCCCCTCCT 62.423 72.222 0.00 0.00 0.00 3.69
1608 1910 2.766229 GACCAGCCTCCCCTCCTC 60.766 72.222 0.00 0.00 0.00 3.71
1770 2072 5.701290 GTGCCTCATACTTTGGTGGATATAC 59.299 44.000 0.00 0.00 0.00 1.47
1793 2095 3.507233 CACTTTGGGATTTGCTAAGCTCA 59.493 43.478 0.00 0.00 0.00 4.26
1800 2102 2.795231 TTTGCTAAGCTCAGCCAGAT 57.205 45.000 6.35 0.00 41.04 2.90
1838 2140 2.034104 TGCTGCTCAAGTCATCATCC 57.966 50.000 0.00 0.00 0.00 3.51
1924 2226 1.330213 GAGAGGTTACCGTAGTCTCGC 59.670 57.143 3.20 3.04 0.00 5.03
1932 2234 1.442184 CGTAGTCTCGCGTTGCTGT 60.442 57.895 5.77 0.00 0.00 4.40
1942 2244 1.510480 GCGTTGCTGTGAAGCTCCTT 61.510 55.000 0.00 0.00 35.49 3.36
1944 2246 1.597742 GTTGCTGTGAAGCTCCTTGA 58.402 50.000 0.00 0.00 35.49 3.02
2004 2306 0.972883 GCTTGGTTTGGTAATGGCCA 59.027 50.000 8.56 8.56 36.62 5.36
2005 2307 1.066929 GCTTGGTTTGGTAATGGCCAG 60.067 52.381 13.05 0.00 40.01 4.85
2027 2329 5.533903 CAGGCTATCTTCTAAATGGTGCAAT 59.466 40.000 0.00 0.00 0.00 3.56
2032 2335 4.272489 TCTTCTAAATGGTGCAATGAGGG 58.728 43.478 0.00 0.00 0.00 4.30
2035 2338 3.763360 TCTAAATGGTGCAATGAGGGTTG 59.237 43.478 0.00 0.00 0.00 3.77
2094 2397 3.500448 TCTGGCACTCCACATGTAAAA 57.500 42.857 0.00 0.00 37.47 1.52
2119 2422 3.496884 GTGTCAAAGATGTCGCCTTGTTA 59.503 43.478 0.00 0.00 0.00 2.41
2140 2443 9.624697 TTGTTACTTGCATGATAAGAATTGTTC 57.375 29.630 14.69 0.00 0.00 3.18
2145 2448 5.185454 TGCATGATAAGAATTGTTCGGAGT 58.815 37.500 0.00 0.00 34.02 3.85
2148 2451 6.257849 GCATGATAAGAATTGTTCGGAGTGTA 59.742 38.462 0.00 0.00 34.02 2.90
2157 2460 1.990563 GTTCGGAGTGTATCGTTGGTG 59.009 52.381 0.00 0.00 0.00 4.17
2183 2486 9.726438 GTATTGGATAGTGAAGCTATACCATTT 57.274 33.333 0.00 0.00 39.73 2.32
2262 2568 8.181573 ACGTATTTTGCCAACTGTTTCTATATG 58.818 33.333 0.00 0.00 0.00 1.78
2264 2570 6.588719 TTTTGCCAACTGTTTCTATATGCT 57.411 33.333 0.00 0.00 0.00 3.79
2265 2571 5.565592 TTGCCAACTGTTTCTATATGCTG 57.434 39.130 0.00 0.00 0.00 4.41
2267 2573 3.947834 GCCAACTGTTTCTATATGCTGGT 59.052 43.478 0.00 0.00 0.00 4.00
2269 2575 5.677091 GCCAACTGTTTCTATATGCTGGTTG 60.677 44.000 0.00 0.00 33.62 3.77
2270 2576 5.335127 CAACTGTTTCTATATGCTGGTTGC 58.665 41.667 0.00 0.00 43.25 4.17
2271 2577 4.848357 ACTGTTTCTATATGCTGGTTGCT 58.152 39.130 0.00 0.00 43.37 3.91
2417 2727 9.880157 CCTAAAATTCATCATGGAAATTTCAGT 57.120 29.630 19.49 4.75 33.32 3.41
2605 2931 7.341769 TGGCAGCTTAAGGAAATATATGTTGTT 59.658 33.333 4.29 0.00 0.00 2.83
2606 2932 8.846211 GGCAGCTTAAGGAAATATATGTTGTTA 58.154 33.333 4.29 0.00 0.00 2.41
2674 3071 8.530804 TCAACTACTTATTTAGTACTCCCTCC 57.469 38.462 0.00 0.00 38.33 4.30
2675 3072 7.284034 TCAACTACTTATTTAGTACTCCCTCCG 59.716 40.741 0.00 0.00 38.33 4.63
2676 3073 6.667661 ACTACTTATTTAGTACTCCCTCCGT 58.332 40.000 0.00 0.00 38.33 4.69
2677 3074 6.770303 ACTACTTATTTAGTACTCCCTCCGTC 59.230 42.308 0.00 0.00 38.33 4.79
2678 3075 4.892345 ACTTATTTAGTACTCCCTCCGTCC 59.108 45.833 0.00 0.00 34.56 4.79
2679 3076 2.149973 TTTAGTACTCCCTCCGTCCC 57.850 55.000 0.00 0.00 0.00 4.46
2680 3077 1.002069 TTAGTACTCCCTCCGTCCCA 58.998 55.000 0.00 0.00 0.00 4.37
2681 3078 1.229131 TAGTACTCCCTCCGTCCCAT 58.771 55.000 0.00 0.00 0.00 4.00
2682 3079 1.229131 AGTACTCCCTCCGTCCCATA 58.771 55.000 0.00 0.00 0.00 2.74
2683 3080 1.572415 AGTACTCCCTCCGTCCCATAA 59.428 52.381 0.00 0.00 0.00 1.90
2684 3081 2.179424 AGTACTCCCTCCGTCCCATAAT 59.821 50.000 0.00 0.00 0.00 1.28
2685 3082 1.424638 ACTCCCTCCGTCCCATAATG 58.575 55.000 0.00 0.00 0.00 1.90
2686 3083 1.344087 ACTCCCTCCGTCCCATAATGT 60.344 52.381 0.00 0.00 0.00 2.71
2687 3084 2.090943 ACTCCCTCCGTCCCATAATGTA 60.091 50.000 0.00 0.00 0.00 2.29
2688 3085 2.969950 CTCCCTCCGTCCCATAATGTAA 59.030 50.000 0.00 0.00 0.00 2.41
2689 3086 2.969950 TCCCTCCGTCCCATAATGTAAG 59.030 50.000 0.00 0.00 0.00 2.34
2690 3087 2.969950 CCCTCCGTCCCATAATGTAAGA 59.030 50.000 0.00 0.00 0.00 2.10
2691 3088 3.244112 CCCTCCGTCCCATAATGTAAGAC 60.244 52.174 0.00 0.00 0.00 3.01
2693 3090 3.025978 TCCGTCCCATAATGTAAGACGT 58.974 45.455 9.63 0.00 46.62 4.34
2694 3091 3.448301 TCCGTCCCATAATGTAAGACGTT 59.552 43.478 9.63 0.00 46.62 3.99
2695 3092 4.081531 TCCGTCCCATAATGTAAGACGTTT 60.082 41.667 9.63 0.00 46.62 3.60
2696 3093 4.632688 CCGTCCCATAATGTAAGACGTTTT 59.367 41.667 9.63 0.00 46.62 2.43
2697 3094 5.122711 CCGTCCCATAATGTAAGACGTTTTT 59.877 40.000 9.63 0.00 46.62 1.94
2698 3095 6.245724 CGTCCCATAATGTAAGACGTTTTTC 58.754 40.000 0.00 0.00 43.89 2.29
2699 3096 6.245724 GTCCCATAATGTAAGACGTTTTTCG 58.754 40.000 0.00 0.00 46.00 3.46
2700 3097 6.091169 GTCCCATAATGTAAGACGTTTTTCGA 59.909 38.462 0.00 0.00 42.86 3.71
2701 3098 6.091169 TCCCATAATGTAAGACGTTTTTCGAC 59.909 38.462 0.00 0.00 42.86 4.20
2702 3099 6.091713 CCCATAATGTAAGACGTTTTTCGACT 59.908 38.462 0.00 0.00 45.03 4.18
2703 3100 7.171434 CCATAATGTAAGACGTTTTTCGACTC 58.829 38.462 0.00 0.00 42.74 3.36
2704 3101 7.063074 CCATAATGTAAGACGTTTTTCGACTCT 59.937 37.037 0.00 0.00 42.74 3.24
2705 3102 9.069078 CATAATGTAAGACGTTTTTCGACTCTA 57.931 33.333 0.00 0.00 42.74 2.43
2706 3103 9.798994 ATAATGTAAGACGTTTTTCGACTCTAT 57.201 29.630 0.00 0.00 42.74 1.98
2707 3104 7.737525 ATGTAAGACGTTTTTCGACTCTATC 57.262 36.000 0.00 0.00 42.74 2.08
2708 3105 6.088824 TGTAAGACGTTTTTCGACTCTATCC 58.911 40.000 0.00 0.00 42.74 2.59
2709 3106 3.756069 AGACGTTTTTCGACTCTATCCG 58.244 45.455 0.00 0.00 39.99 4.18
2710 3107 3.190118 AGACGTTTTTCGACTCTATCCGT 59.810 43.478 0.00 0.00 39.99 4.69
2711 3108 3.496155 ACGTTTTTCGACTCTATCCGTC 58.504 45.455 0.00 0.00 42.86 4.79
2712 3109 2.850647 CGTTTTTCGACTCTATCCGTCC 59.149 50.000 0.00 0.00 42.86 4.79
2713 3110 3.185330 GTTTTTCGACTCTATCCGTCCC 58.815 50.000 0.00 0.00 0.00 4.46
2714 3111 2.133281 TTTCGACTCTATCCGTCCCA 57.867 50.000 0.00 0.00 0.00 4.37
2715 3112 2.359981 TTCGACTCTATCCGTCCCAT 57.640 50.000 0.00 0.00 0.00 4.00
2716 3113 3.497103 TTCGACTCTATCCGTCCCATA 57.503 47.619 0.00 0.00 0.00 2.74
2717 3114 3.497103 TCGACTCTATCCGTCCCATAA 57.503 47.619 0.00 0.00 0.00 1.90
2718 3115 4.030314 TCGACTCTATCCGTCCCATAAT 57.970 45.455 0.00 0.00 0.00 1.28
2719 3116 3.756963 TCGACTCTATCCGTCCCATAATG 59.243 47.826 0.00 0.00 0.00 1.90
2720 3117 3.506455 CGACTCTATCCGTCCCATAATGT 59.494 47.826 0.00 0.00 0.00 2.71
2721 3118 4.698780 CGACTCTATCCGTCCCATAATGTA 59.301 45.833 0.00 0.00 0.00 2.29
2722 3119 5.182570 CGACTCTATCCGTCCCATAATGTAA 59.817 44.000 0.00 0.00 0.00 2.41
2723 3120 6.591750 ACTCTATCCGTCCCATAATGTAAG 57.408 41.667 0.00 0.00 0.00 2.34
2724 3121 6.312529 ACTCTATCCGTCCCATAATGTAAGA 58.687 40.000 0.00 0.00 0.00 2.10
2725 3122 6.208994 ACTCTATCCGTCCCATAATGTAAGAC 59.791 42.308 0.00 0.00 0.00 3.01
2727 3124 3.025978 TCCGTCCCATAATGTAAGACGT 58.974 45.455 9.63 0.00 46.62 4.34
2728 3125 3.448301 TCCGTCCCATAATGTAAGACGTT 59.552 43.478 9.63 0.00 46.62 3.99
2729 3126 4.081531 TCCGTCCCATAATGTAAGACGTTT 60.082 41.667 9.63 0.00 46.62 3.60
2730 3127 4.632688 CCGTCCCATAATGTAAGACGTTTT 59.367 41.667 9.63 0.00 46.62 2.43
2731 3128 5.122711 CCGTCCCATAATGTAAGACGTTTTT 59.877 40.000 9.63 0.00 46.62 1.94
2754 3151 8.651391 TTTTGACACTACATTAGAGTCGAAAA 57.349 30.769 17.14 14.27 46.83 2.29
2755 3152 8.651391 TTTGACACTACATTAGAGTCGAAAAA 57.349 30.769 9.67 2.67 45.53 1.94
2756 3153 7.633361 TGACACTACATTAGAGTCGAAAAAC 57.367 36.000 6.38 0.00 45.53 2.43
2757 3154 6.361481 TGACACTACATTAGAGTCGAAAAACG 59.639 38.462 6.38 0.00 45.53 3.60
2758 3155 6.211515 ACACTACATTAGAGTCGAAAAACGT 58.788 36.000 0.00 0.00 43.13 3.99
2759 3156 6.361748 ACACTACATTAGAGTCGAAAAACGTC 59.638 38.462 0.00 0.00 43.13 4.34
2760 3157 6.581542 CACTACATTAGAGTCGAAAAACGTCT 59.418 38.462 0.00 0.00 42.23 4.18
2761 3158 7.114529 CACTACATTAGAGTCGAAAAACGTCTT 59.885 37.037 0.00 0.00 40.02 3.01
2762 3159 8.292448 ACTACATTAGAGTCGAAAAACGTCTTA 58.708 33.333 0.00 0.00 40.02 2.10
2763 3160 7.330720 ACATTAGAGTCGAAAAACGTCTTAC 57.669 36.000 0.00 0.00 40.02 2.34
2764 3161 6.919662 ACATTAGAGTCGAAAAACGTCTTACA 59.080 34.615 0.00 0.00 40.02 2.41
2765 3162 7.597743 ACATTAGAGTCGAAAAACGTCTTACAT 59.402 33.333 0.00 0.00 40.02 2.29
2766 3163 7.935338 TTAGAGTCGAAAAACGTCTTACATT 57.065 32.000 0.00 0.00 40.02 2.71
2767 3164 9.630098 ATTAGAGTCGAAAAACGTCTTACATTA 57.370 29.630 0.00 0.00 40.02 1.90
2768 3165 9.630098 TTAGAGTCGAAAAACGTCTTACATTAT 57.370 29.630 0.00 0.00 40.02 1.28
2769 3166 7.950236 AGAGTCGAAAAACGTCTTACATTATG 58.050 34.615 0.00 0.00 40.02 1.90
2770 3167 7.057149 AGTCGAAAAACGTCTTACATTATGG 57.943 36.000 0.00 0.00 43.13 2.74
2771 3168 6.091713 AGTCGAAAAACGTCTTACATTATGGG 59.908 38.462 0.00 0.00 43.13 4.00
2772 3169 6.091169 GTCGAAAAACGTCTTACATTATGGGA 59.909 38.462 0.00 0.00 43.13 4.37
2773 3170 6.091169 TCGAAAAACGTCTTACATTATGGGAC 59.909 38.462 0.00 1.75 43.13 4.46
2774 3171 6.128499 CGAAAAACGTCTTACATTATGGGACA 60.128 38.462 12.60 0.00 39.32 4.02
2775 3172 7.882517 CGAAAAACGTCTTACATTATGGGACAG 60.883 40.741 12.60 9.07 38.61 3.51
2803 3200 3.097877 ACTTTTTAGCTGTTTGGCTGC 57.902 42.857 0.00 0.00 43.01 5.25
2886 3284 0.103390 TTTGACGTGTTCTCCGAGCA 59.897 50.000 0.00 0.00 0.00 4.26
3146 3544 5.256474 ACTTAACAAGGCAATACAGCTCAT 58.744 37.500 0.00 0.00 34.17 2.90
3198 3596 1.142748 CCAGGACGAGACATCTGCC 59.857 63.158 0.00 0.00 0.00 4.85
3743 4144 0.178990 ACAAAGGTGGGCTTCCTCAC 60.179 55.000 2.01 0.00 33.76 3.51
4064 4465 2.872858 GAGTTGCAGTATCGGGAAATCC 59.127 50.000 0.00 0.00 0.00 3.01
4298 4699 2.667473 AAAACCCAGTATCTCGGACG 57.333 50.000 0.00 0.00 0.00 4.79
4339 4761 3.570926 TGCTGTTACGAAGTCGAATCT 57.429 42.857 7.87 0.00 43.93 2.40
4413 4835 1.075374 CCAACTCAAAGGATCCACCCA 59.925 52.381 15.82 0.00 40.05 4.51
4589 5020 4.082787 GCTTCTGGCAATGCTAGTAAAACA 60.083 41.667 17.92 0.00 38.31 2.83
4667 5098 4.700213 GGGATACAAAAAGAAGCTACTGCA 59.300 41.667 0.00 0.00 39.57 4.41
4961 5398 2.568956 ACCTGAGTTAGCTTCTGATGCA 59.431 45.455 16.56 0.00 0.00 3.96
5255 5701 1.967319 TGAACCTTCTTGCCAGTGTC 58.033 50.000 0.00 0.00 0.00 3.67
5487 5936 1.218316 CGTAACCAGAGGGCTCACC 59.782 63.158 0.00 0.00 37.90 4.02
5509 5958 4.616802 CCTATCATTGCACGACAACAAAAC 59.383 41.667 0.00 0.00 42.27 2.43
5747 6196 1.093972 CGTAATGCATGTTCCAGCCA 58.906 50.000 0.00 0.00 0.00 4.75
5850 6299 1.442769 ATCGCACGTCAGAATTGCTT 58.557 45.000 0.00 0.00 33.90 3.91
5891 6340 1.065126 GTCTGCCCCTGATAAACAGCT 60.065 52.381 0.00 0.00 44.52 4.24
5939 6388 3.428282 GCCGCTTGGGGTTGTACG 61.428 66.667 5.63 0.00 35.78 3.67
6017 6484 0.179045 GTGTGTCCACTGGCTCTTGT 60.179 55.000 0.00 0.00 38.61 3.16
6125 6598 1.133790 CAAGCTAGTTGCATTCCCAGC 59.866 52.381 0.00 0.00 45.94 4.85
6143 6631 1.031571 GCTGATGTGCCGAATGGGAA 61.032 55.000 0.00 0.00 37.33 3.97
6174 6662 5.745227 TCAAAGGATAGTTCCAGTGAATCC 58.255 41.667 0.00 0.00 45.30 3.01
6183 6671 4.221703 AGTTCCAGTGAATCCAGTAGTCAG 59.778 45.833 0.00 0.00 31.70 3.51
6335 6823 2.632512 AGGCCAAACCAAATGTTACTGG 59.367 45.455 5.01 0.00 43.14 4.00
6603 7091 3.414700 CGTCCTGCAGAACCACGC 61.415 66.667 17.39 0.00 0.00 5.34
6616 7104 3.294493 CACGCAAGGTTGTGGGGG 61.294 66.667 8.09 0.00 42.72 5.40
6646 7134 4.469586 TGACTGCACCTGATATTGTAGGAA 59.530 41.667 8.18 0.00 37.52 3.36
6717 7205 5.627182 ATGTAGCAGATGACCAGATTCTT 57.373 39.130 0.00 0.00 0.00 2.52
6723 7211 4.444591 GCAGATGACCAGATTCTTGAGGAT 60.445 45.833 0.00 0.00 0.00 3.24
6792 7280 0.248949 GTAGAAGTCGCGATGGTCCC 60.249 60.000 14.06 0.00 0.00 4.46
7072 7560 0.877743 GCCTCAAGTTGCTGGTCTTC 59.122 55.000 13.67 0.00 0.00 2.87
7410 7898 1.610554 ATGCCAATTCTGCACCTGCC 61.611 55.000 1.45 0.00 42.38 4.85
7530 8018 3.027412 AGGTAGCAGTAGTGATGGTCTG 58.973 50.000 0.42 0.00 0.00 3.51
7534 8022 1.469940 GCAGTAGTGATGGTCTGGACG 60.470 57.143 0.42 0.00 0.00 4.79
7586 8074 3.194005 TGATCTTAATTCTGGTCCCGC 57.806 47.619 0.00 0.00 0.00 6.13
7653 8141 5.457140 GTTAGACAAAATTTGATGACGCCA 58.543 37.500 13.19 0.00 0.00 5.69
8231 8726 1.599542 CCTCAAGCCGCTGTAATTAGC 59.400 52.381 0.00 0.00 40.29 3.09
8250 8745 0.036294 CCCCGGTGGTTCTTCTCTTC 60.036 60.000 0.00 0.00 0.00 2.87
8256 8751 3.498777 CGGTGGTTCTTCTCTTCCTTTTC 59.501 47.826 0.00 0.00 0.00 2.29
8257 8752 4.720046 GGTGGTTCTTCTCTTCCTTTTCT 58.280 43.478 0.00 0.00 0.00 2.52
8262 8757 7.702772 GTGGTTCTTCTCTTCCTTTTCTTTTTC 59.297 37.037 0.00 0.00 0.00 2.29
8263 8758 7.615757 TGGTTCTTCTCTTCCTTTTCTTTTTCT 59.384 33.333 0.00 0.00 0.00 2.52
8412 8908 2.359230 GCTGTGGCTGACCCTGTC 60.359 66.667 0.00 0.00 35.22 3.51
8418 8914 0.321564 TGGCTGACCCTGTCATTTCG 60.322 55.000 0.00 0.00 41.94 3.46
8419 8915 1.026718 GGCTGACCCTGTCATTTCGG 61.027 60.000 0.00 0.00 41.94 4.30
8420 8916 0.321653 GCTGACCCTGTCATTTCGGT 60.322 55.000 0.00 0.00 41.94 4.69
8423 8919 1.972075 TGACCCTGTCATTTCGGTGTA 59.028 47.619 0.00 0.00 37.67 2.90
8433 8929 5.533154 TGTCATTTCGGTGTATTGGTTTCTT 59.467 36.000 0.00 0.00 0.00 2.52
8451 8951 2.881513 TCTTTTCTGTGTGGCGCAAATA 59.118 40.909 10.83 0.00 0.00 1.40
8463 8963 3.181491 TGGCGCAAATACTCTATTTTGCC 60.181 43.478 10.83 15.02 46.77 4.52
8465 8965 3.486875 GCGCAAATACTCTATTTTGCCGT 60.487 43.478 0.30 0.00 36.29 5.68
8483 8983 2.350772 CCGTGACTTGTTTCTCCATTGC 60.351 50.000 0.00 0.00 0.00 3.56
8497 8997 1.331214 CATTGCAGGTGGAGGTTGTT 58.669 50.000 0.00 0.00 0.00 2.83
8501 9001 2.594592 AGGTGGAGGTTGTTGCGC 60.595 61.111 0.00 0.00 0.00 6.09
8502 9002 2.594592 GGTGGAGGTTGTTGCGCT 60.595 61.111 9.73 0.00 0.00 5.92
8503 9003 2.639286 GTGGAGGTTGTTGCGCTG 59.361 61.111 9.73 0.00 0.00 5.18
8504 9004 2.186826 GTGGAGGTTGTTGCGCTGT 61.187 57.895 9.73 0.00 0.00 4.40
8505 9005 2.186160 TGGAGGTTGTTGCGCTGTG 61.186 57.895 9.73 0.00 0.00 3.66
8506 9006 2.639286 GAGGTTGTTGCGCTGTGG 59.361 61.111 9.73 0.00 0.00 4.17
8507 9007 3.542629 GAGGTTGTTGCGCTGTGGC 62.543 63.158 9.73 0.00 0.00 5.01
8535 9045 2.157738 GATGCACCTTCTTGCTCAGTT 58.842 47.619 0.00 0.00 43.41 3.16
8552 9062 5.344743 TCAGTTTGTTGTAAATTTGGGCA 57.655 34.783 0.00 0.00 0.00 5.36
8597 9107 6.265196 TCTGTTGCATCAGTAATTTTTGACCT 59.735 34.615 21.24 0.00 36.85 3.85
8602 9112 5.327091 CATCAGTAATTTTTGACCTCTGCG 58.673 41.667 0.00 0.00 0.00 5.18
8645 9168 1.205655 CTGATGGACGATGGTGACTGT 59.794 52.381 0.00 0.00 0.00 3.55
8676 9202 3.126831 GCTGATCTCCATGAGTAAACCG 58.873 50.000 0.00 0.00 0.00 4.44
8706 9232 9.881529 GTATTCTGCTACTACTACTTGTCATAC 57.118 37.037 0.00 0.00 0.00 2.39
8707 9233 6.939132 TCTGCTACTACTACTTGTCATACC 57.061 41.667 0.00 0.00 0.00 2.73
8723 9250 3.815962 TCATACCTCGACATCTCTACAGC 59.184 47.826 0.00 0.00 0.00 4.40
8776 9312 3.309138 CGATGGAAGCAAGTGAAGATGAG 59.691 47.826 0.00 0.00 0.00 2.90
8779 9315 2.430465 GAAGCAAGTGAAGATGAGGCA 58.570 47.619 0.00 0.00 0.00 4.75
9073 9626 1.168714 CGCTTTCTTTCCCTTCCCTG 58.831 55.000 0.00 0.00 0.00 4.45
9096 9649 0.998928 TGCCATGCCTTCCTTCCTTA 59.001 50.000 0.00 0.00 0.00 2.69
9098 9651 1.064389 GCCATGCCTTCCTTCCTTACT 60.064 52.381 0.00 0.00 0.00 2.24
9099 9652 2.621668 GCCATGCCTTCCTTCCTTACTT 60.622 50.000 0.00 0.00 0.00 2.24
9100 9653 3.019564 CCATGCCTTCCTTCCTTACTTG 58.980 50.000 0.00 0.00 0.00 3.16
9101 9654 2.200373 TGCCTTCCTTCCTTACTTGC 57.800 50.000 0.00 0.00 0.00 4.01
9103 9656 1.955683 GCCTTCCTTCCTTACTTGCCC 60.956 57.143 0.00 0.00 0.00 5.36
9104 9657 1.354368 CCTTCCTTCCTTACTTGCCCA 59.646 52.381 0.00 0.00 0.00 5.36
9107 9660 1.026718 CCTTCCTTACTTGCCCAGCG 61.027 60.000 0.00 0.00 0.00 5.18
9108 9661 1.648467 CTTCCTTACTTGCCCAGCGC 61.648 60.000 0.00 0.00 38.31 5.92
9109 9662 3.499737 CCTTACTTGCCCAGCGCG 61.500 66.667 0.00 0.00 42.08 6.86
9234 9801 1.340795 GGCTCCATCCATCCATCCATC 60.341 57.143 0.00 0.00 0.00 3.51
9235 9802 1.340795 GCTCCATCCATCCATCCATCC 60.341 57.143 0.00 0.00 0.00 3.51
9236 9803 1.990327 CTCCATCCATCCATCCATCCA 59.010 52.381 0.00 0.00 0.00 3.41
9237 9804 2.581246 CTCCATCCATCCATCCATCCAT 59.419 50.000 0.00 0.00 0.00 3.41
9243 9810 2.640184 CATCCATCCATCCATCCATCG 58.360 52.381 0.00 0.00 0.00 3.84
9255 9822 2.284515 ATCCATCGCCCCTTTCACCC 62.285 60.000 0.00 0.00 0.00 4.61
9277 9844 1.612442 CTCCTCGGTCCTTTCCCCA 60.612 63.158 0.00 0.00 0.00 4.96
9278 9845 1.151987 TCCTCGGTCCTTTCCCCAA 60.152 57.895 0.00 0.00 0.00 4.12
9384 9951 0.742990 TTCCCGTCAACATCATCCGC 60.743 55.000 0.00 0.00 0.00 5.54
9386 9953 2.180204 CCGTCAACATCATCCGCCC 61.180 63.158 0.00 0.00 0.00 6.13
9389 9956 0.815615 GTCAACATCATCCGCCCTCC 60.816 60.000 0.00 0.00 0.00 4.30
9397 9964 1.109323 CATCCGCCCTCCCCATTTTC 61.109 60.000 0.00 0.00 0.00 2.29
9403 9970 1.379843 CCTCCCCATTTTCCCCGTG 60.380 63.158 0.00 0.00 0.00 4.94
9404 9971 1.379843 CTCCCCATTTTCCCCGTGG 60.380 63.158 0.00 0.00 0.00 4.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 0.331954 TAGTGAGCCTTCTCCCTCGT 59.668 55.000 0.00 0.00 38.58 4.18
18 19 3.428862 GCTGTCTTCTAGTGAGCCTTCTC 60.429 52.174 0.00 0.00 39.78 2.87
159 160 0.176219 TGGACGTCCGTGTTGTTTCT 59.824 50.000 28.70 0.00 39.43 2.52
786 790 4.016706 GTGGTGGGTGGACTCGGG 62.017 72.222 0.00 0.00 0.00 5.14
992 1282 0.967380 AAAGAGGCAGGGGCATTTCG 60.967 55.000 0.00 0.00 43.71 3.46
1052 1350 2.422235 GGAGAGACGGAGATGAGGAAGA 60.422 54.545 0.00 0.00 0.00 2.87
1053 1351 1.953686 GGAGAGACGGAGATGAGGAAG 59.046 57.143 0.00 0.00 0.00 3.46
1054 1352 1.747552 CGGAGAGACGGAGATGAGGAA 60.748 57.143 0.00 0.00 0.00 3.36
1055 1353 0.179043 CGGAGAGACGGAGATGAGGA 60.179 60.000 0.00 0.00 0.00 3.71
1112 1410 2.627510 GAAATGGCGATTTGGGGGCG 62.628 60.000 11.72 0.00 31.58 6.13
1606 1908 4.150454 AGCGGGGAGGAGGAGGAG 62.150 72.222 0.00 0.00 0.00 3.69
1607 1909 4.144727 GAGCGGGGAGGAGGAGGA 62.145 72.222 0.00 0.00 0.00 3.71
1770 2072 2.827921 AGCTTAGCAAATCCCAAAGTGG 59.172 45.455 7.07 0.00 37.25 4.00
1793 2095 6.012745 ACTGAATTTGGTCTAAAATCTGGCT 58.987 36.000 8.00 0.00 33.73 4.75
1838 2140 1.315690 AGCAGAAATGATGGCCATCG 58.684 50.000 34.70 22.62 40.63 3.84
1932 2234 5.227569 TGTAAACTCATCAAGGAGCTTCA 57.772 39.130 0.00 0.00 38.50 3.02
1944 2246 9.212641 GCACAGATGATGTATATGTAAACTCAT 57.787 33.333 0.00 0.00 39.11 2.90
2004 2306 4.778213 TGCACCATTTAGAAGATAGCCT 57.222 40.909 0.00 0.00 0.00 4.58
2005 2307 5.532406 TCATTGCACCATTTAGAAGATAGCC 59.468 40.000 0.00 0.00 0.00 3.93
2027 2329 3.639094 CCAACCATACAAAACAACCCTCA 59.361 43.478 0.00 0.00 0.00 3.86
2032 2335 6.540551 ACCAAAATCCAACCATACAAAACAAC 59.459 34.615 0.00 0.00 0.00 3.32
2035 2338 6.647481 GGTACCAAAATCCAACCATACAAAAC 59.353 38.462 7.15 0.00 0.00 2.43
2094 2397 1.291877 GGCGACATCTTTGACACGCT 61.292 55.000 0.00 0.00 40.26 5.07
2119 2422 5.647658 TCCGAACAATTCTTATCATGCAAGT 59.352 36.000 0.00 0.00 0.00 3.16
2140 2443 2.925578 TACACCAACGATACACTCCG 57.074 50.000 0.00 0.00 0.00 4.63
2145 2448 6.097129 TCACTATCCAATACACCAACGATACA 59.903 38.462 0.00 0.00 0.00 2.29
2148 2451 5.607939 TCACTATCCAATACACCAACGAT 57.392 39.130 0.00 0.00 0.00 3.73
2157 2460 9.726438 AAATGGTATAGCTTCACTATCCAATAC 57.274 33.333 3.20 0.00 40.89 1.89
2183 2486 0.180642 TGCACCCGTAAACACCTTCA 59.819 50.000 0.00 0.00 0.00 3.02
2417 2727 4.075963 ACCTAACCGTAGAGCACAAAAA 57.924 40.909 0.00 0.00 0.00 1.94
2605 2931 5.765677 TGCAAAGGTAGCAAACATTAGTGTA 59.234 36.000 0.00 0.00 39.39 2.90
2606 2932 4.582656 TGCAAAGGTAGCAAACATTAGTGT 59.417 37.500 0.00 0.00 39.39 3.55
2669 3066 2.969950 TCTTACATTATGGGACGGAGGG 59.030 50.000 0.00 0.00 0.00 4.30
2670 3067 3.552273 CGTCTTACATTATGGGACGGAGG 60.552 52.174 20.50 5.87 43.69 4.30
2671 3068 3.639538 CGTCTTACATTATGGGACGGAG 58.360 50.000 20.50 2.74 43.69 4.63
2672 3069 3.720949 CGTCTTACATTATGGGACGGA 57.279 47.619 20.50 2.30 43.69 4.69
2675 3072 6.091169 TCGAAAAACGTCTTACATTATGGGAC 59.909 38.462 0.00 1.75 43.13 4.46
2676 3073 6.091169 GTCGAAAAACGTCTTACATTATGGGA 59.909 38.462 0.00 0.00 43.13 4.37
2677 3074 6.091713 AGTCGAAAAACGTCTTACATTATGGG 59.908 38.462 0.00 0.00 43.13 4.00
2678 3075 7.057149 AGTCGAAAAACGTCTTACATTATGG 57.943 36.000 0.00 0.00 43.13 2.74
2679 3076 7.950236 AGAGTCGAAAAACGTCTTACATTATG 58.050 34.615 0.00 0.00 40.02 1.90
2680 3077 9.798994 ATAGAGTCGAAAAACGTCTTACATTAT 57.201 29.630 0.00 0.00 40.02 1.28
2681 3078 9.282247 GATAGAGTCGAAAAACGTCTTACATTA 57.718 33.333 0.00 0.00 40.02 1.90
2682 3079 7.275123 GGATAGAGTCGAAAAACGTCTTACATT 59.725 37.037 0.00 0.00 40.02 2.71
2683 3080 6.750963 GGATAGAGTCGAAAAACGTCTTACAT 59.249 38.462 0.00 0.00 40.02 2.29
2684 3081 6.088824 GGATAGAGTCGAAAAACGTCTTACA 58.911 40.000 0.00 0.00 40.02 2.41
2685 3082 5.226772 CGGATAGAGTCGAAAAACGTCTTAC 59.773 44.000 0.00 0.00 40.02 2.34
2686 3083 5.106555 ACGGATAGAGTCGAAAAACGTCTTA 60.107 40.000 0.00 0.00 40.02 2.10
2687 3084 4.164294 CGGATAGAGTCGAAAAACGTCTT 58.836 43.478 0.00 0.00 40.02 3.01
2688 3085 3.190118 ACGGATAGAGTCGAAAAACGTCT 59.810 43.478 0.00 0.00 42.23 4.18
2689 3086 3.496155 ACGGATAGAGTCGAAAAACGTC 58.504 45.455 0.00 0.00 43.13 4.34
2690 3087 3.496155 GACGGATAGAGTCGAAAAACGT 58.504 45.455 0.00 0.00 43.13 3.99
2691 3088 2.850647 GGACGGATAGAGTCGAAAAACG 59.149 50.000 0.00 0.00 39.38 3.60
2692 3089 3.185330 GGGACGGATAGAGTCGAAAAAC 58.815 50.000 0.00 0.00 39.38 2.43
2693 3090 2.827322 TGGGACGGATAGAGTCGAAAAA 59.173 45.455 0.00 0.00 39.38 1.94
2694 3091 2.449464 TGGGACGGATAGAGTCGAAAA 58.551 47.619 0.00 0.00 39.38 2.29
2695 3092 2.133281 TGGGACGGATAGAGTCGAAA 57.867 50.000 0.00 0.00 39.38 3.46
2696 3093 2.359981 ATGGGACGGATAGAGTCGAA 57.640 50.000 0.00 0.00 39.38 3.71
2697 3094 3.497103 TTATGGGACGGATAGAGTCGA 57.503 47.619 0.00 0.00 39.38 4.20
2698 3095 3.506455 ACATTATGGGACGGATAGAGTCG 59.494 47.826 0.00 0.00 39.38 4.18
2699 3096 6.433404 TCTTACATTATGGGACGGATAGAGTC 59.567 42.308 0.00 0.00 37.86 3.36
2700 3097 6.208994 GTCTTACATTATGGGACGGATAGAGT 59.791 42.308 0.00 0.00 0.00 3.24
2701 3098 6.622549 GTCTTACATTATGGGACGGATAGAG 58.377 44.000 0.00 0.00 0.00 2.43
2702 3099 5.182570 CGTCTTACATTATGGGACGGATAGA 59.817 44.000 20.50 2.24 43.69 1.98
2703 3100 5.399858 CGTCTTACATTATGGGACGGATAG 58.600 45.833 20.50 3.12 43.69 2.08
2704 3101 5.381174 CGTCTTACATTATGGGACGGATA 57.619 43.478 20.50 0.00 43.69 2.59
2705 3102 4.252971 CGTCTTACATTATGGGACGGAT 57.747 45.455 20.50 0.00 43.69 4.18
2706 3103 3.720949 CGTCTTACATTATGGGACGGA 57.279 47.619 20.50 2.30 43.69 4.69
2728 3125 8.651391 TTTCGACTCTAATGTAGTGTCAAAAA 57.349 30.769 14.46 11.50 45.03 1.94
2729 3126 8.651391 TTTTCGACTCTAATGTAGTGTCAAAA 57.349 30.769 14.46 14.69 45.03 2.44
2730 3127 8.545420 GTTTTTCGACTCTAATGTAGTGTCAAA 58.455 33.333 14.46 11.38 45.03 2.69
2731 3128 7.096353 CGTTTTTCGACTCTAATGTAGTGTCAA 60.096 37.037 14.46 7.66 45.03 3.18
2732 3129 6.361481 CGTTTTTCGACTCTAATGTAGTGTCA 59.639 38.462 14.46 3.46 45.03 3.58
2733 3130 6.361748 ACGTTTTTCGACTCTAATGTAGTGTC 59.638 38.462 7.21 7.21 42.71 3.67
2734 3131 6.211515 ACGTTTTTCGACTCTAATGTAGTGT 58.788 36.000 0.00 0.00 42.86 3.55
2735 3132 6.581542 AGACGTTTTTCGACTCTAATGTAGTG 59.418 38.462 0.00 0.00 39.99 2.74
2736 3133 6.675987 AGACGTTTTTCGACTCTAATGTAGT 58.324 36.000 0.00 0.00 39.99 2.73
2737 3134 7.564044 AAGACGTTTTTCGACTCTAATGTAG 57.436 36.000 0.00 0.00 42.74 2.74
2738 3135 8.075574 TGTAAGACGTTTTTCGACTCTAATGTA 58.924 33.333 0.00 0.00 42.74 2.29
2739 3136 6.919662 TGTAAGACGTTTTTCGACTCTAATGT 59.080 34.615 0.00 0.00 42.74 2.71
2740 3137 7.329438 TGTAAGACGTTTTTCGACTCTAATG 57.671 36.000 0.00 0.00 42.74 1.90
2741 3138 8.530269 AATGTAAGACGTTTTTCGACTCTAAT 57.470 30.769 0.00 0.00 42.74 1.73
2742 3139 7.935338 AATGTAAGACGTTTTTCGACTCTAA 57.065 32.000 0.00 0.00 42.74 2.10
2743 3140 9.069078 CATAATGTAAGACGTTTTTCGACTCTA 57.931 33.333 0.00 0.00 42.74 2.43
2744 3141 7.063074 CCATAATGTAAGACGTTTTTCGACTCT 59.937 37.037 0.00 0.00 42.74 3.24
2745 3142 7.171434 CCATAATGTAAGACGTTTTTCGACTC 58.829 38.462 0.00 0.00 42.74 3.36
2746 3143 6.091713 CCCATAATGTAAGACGTTTTTCGACT 59.908 38.462 0.00 0.00 45.03 4.18
2747 3144 6.091169 TCCCATAATGTAAGACGTTTTTCGAC 59.909 38.462 0.00 0.00 42.86 4.20
2748 3145 6.091169 GTCCCATAATGTAAGACGTTTTTCGA 59.909 38.462 0.00 0.00 42.86 3.71
2749 3146 6.128499 TGTCCCATAATGTAAGACGTTTTTCG 60.128 38.462 0.00 0.00 46.00 3.46
2750 3147 7.118680 TCTGTCCCATAATGTAAGACGTTTTTC 59.881 37.037 0.00 0.00 0.00 2.29
2751 3148 6.938030 TCTGTCCCATAATGTAAGACGTTTTT 59.062 34.615 0.00 0.00 0.00 1.94
2752 3149 6.469410 TCTGTCCCATAATGTAAGACGTTTT 58.531 36.000 0.00 0.00 0.00 2.43
2753 3150 6.045072 TCTGTCCCATAATGTAAGACGTTT 57.955 37.500 0.00 0.00 0.00 3.60
2754 3151 5.395324 CCTCTGTCCCATAATGTAAGACGTT 60.395 44.000 0.00 0.00 0.00 3.99
2755 3152 4.099573 CCTCTGTCCCATAATGTAAGACGT 59.900 45.833 0.00 0.00 0.00 4.34
2756 3153 4.501571 CCCTCTGTCCCATAATGTAAGACG 60.502 50.000 0.00 0.00 0.00 4.18
2757 3154 4.654262 TCCCTCTGTCCCATAATGTAAGAC 59.346 45.833 0.00 0.00 0.00 3.01
2758 3155 4.890988 TCCCTCTGTCCCATAATGTAAGA 58.109 43.478 0.00 0.00 0.00 2.10
2759 3156 4.656112 ACTCCCTCTGTCCCATAATGTAAG 59.344 45.833 0.00 0.00 0.00 2.34
2760 3157 4.631234 ACTCCCTCTGTCCCATAATGTAA 58.369 43.478 0.00 0.00 0.00 2.41
2761 3158 4.280789 ACTCCCTCTGTCCCATAATGTA 57.719 45.455 0.00 0.00 0.00 2.29
2762 3159 3.136641 ACTCCCTCTGTCCCATAATGT 57.863 47.619 0.00 0.00 0.00 2.71
2763 3160 4.227197 AGTACTCCCTCTGTCCCATAATG 58.773 47.826 0.00 0.00 0.00 1.90
2764 3161 4.561254 AGTACTCCCTCTGTCCCATAAT 57.439 45.455 0.00 0.00 0.00 1.28
2765 3162 4.348020 AAGTACTCCCTCTGTCCCATAA 57.652 45.455 0.00 0.00 0.00 1.90
2766 3163 4.348020 AAAGTACTCCCTCTGTCCCATA 57.652 45.455 0.00 0.00 0.00 2.74
2767 3164 2.950990 AAGTACTCCCTCTGTCCCAT 57.049 50.000 0.00 0.00 0.00 4.00
2768 3165 2.715763 AAAGTACTCCCTCTGTCCCA 57.284 50.000 0.00 0.00 0.00 4.37
2769 3166 4.623409 GCTAAAAAGTACTCCCTCTGTCCC 60.623 50.000 0.00 0.00 0.00 4.46
2770 3167 4.223255 AGCTAAAAAGTACTCCCTCTGTCC 59.777 45.833 0.00 0.00 0.00 4.02
2771 3168 5.172205 CAGCTAAAAAGTACTCCCTCTGTC 58.828 45.833 0.00 0.00 0.00 3.51
2772 3169 4.593634 ACAGCTAAAAAGTACTCCCTCTGT 59.406 41.667 0.00 3.01 0.00 3.41
2773 3170 5.153950 ACAGCTAAAAAGTACTCCCTCTG 57.846 43.478 0.00 2.39 0.00 3.35
2774 3171 5.827326 AACAGCTAAAAAGTACTCCCTCT 57.173 39.130 0.00 0.00 0.00 3.69
2775 3172 5.181433 CCAAACAGCTAAAAAGTACTCCCTC 59.819 44.000 0.00 0.00 0.00 4.30
2776 3173 5.070685 CCAAACAGCTAAAAAGTACTCCCT 58.929 41.667 0.00 0.00 0.00 4.20
2777 3174 4.321008 GCCAAACAGCTAAAAAGTACTCCC 60.321 45.833 0.00 0.00 0.00 4.30
2778 3175 4.519350 AGCCAAACAGCTAAAAAGTACTCC 59.481 41.667 0.00 0.00 42.70 3.85
2779 3176 5.452777 CAGCCAAACAGCTAAAAAGTACTC 58.547 41.667 0.00 0.00 42.61 2.59
2780 3177 4.261614 GCAGCCAAACAGCTAAAAAGTACT 60.262 41.667 0.00 0.00 42.61 2.73
2781 3178 3.981416 GCAGCCAAACAGCTAAAAAGTAC 59.019 43.478 0.00 0.00 42.61 2.73
2782 3179 3.888930 AGCAGCCAAACAGCTAAAAAGTA 59.111 39.130 0.00 0.00 42.61 2.24
2783 3180 2.695147 AGCAGCCAAACAGCTAAAAAGT 59.305 40.909 0.00 0.00 42.61 2.66
2784 3181 3.054878 CAGCAGCCAAACAGCTAAAAAG 58.945 45.455 0.00 0.00 42.61 2.27
2886 3284 4.273148 ACGCTGAAGGAGAAAGTGTAAT 57.727 40.909 0.00 0.00 33.08 1.89
3146 3544 1.005037 ATCTCGTTTGGTGCAGCGA 60.005 52.632 11.91 6.57 0.00 4.93
3198 3596 3.628032 TGCAAGGATGTAGTAGAGAGACG 59.372 47.826 0.00 0.00 0.00 4.18
3380 3778 5.333339 CGCACACATAAGCCACAGAATATAC 60.333 44.000 0.00 0.00 0.00 1.47
3704 4105 4.242475 TGTCTGTGAACTTCGCGATAAAT 58.758 39.130 10.88 0.00 0.00 1.40
3743 4144 1.681945 GCTTCTCGACTGCTTCAGCG 61.682 60.000 0.00 0.00 45.83 5.18
4064 4465 0.855349 GGCTACGCAGATGATTGACG 59.145 55.000 0.00 0.00 0.00 4.35
4298 4699 1.098050 CAGATGCACCAGGTTTAGCC 58.902 55.000 0.00 0.00 37.58 3.93
4339 4761 1.051008 TGAAGAGCCAGAAGTGAGCA 58.949 50.000 0.00 0.00 0.00 4.26
4413 4835 1.228552 AACCACCAGCCGATTTGCT 60.229 52.632 0.00 0.00 44.00 3.91
4589 5020 3.082579 GCGTGAAGAGCTCCCGGAT 62.083 63.158 10.93 0.00 0.00 4.18
4667 5098 3.935818 TCGAGTGAGGTAGATCTTCCT 57.064 47.619 19.99 19.99 36.70 3.36
5255 5701 3.684788 CGGATTTAGATATTTCCCCAGCG 59.315 47.826 0.00 0.00 0.00 5.18
5487 5936 4.616802 GGTTTTGTTGTCGTGCAATGATAG 59.383 41.667 0.00 0.00 39.55 2.08
5509 5958 1.003580 ACAGCCCAGTAGATGTTGTGG 59.996 52.381 0.00 0.00 0.00 4.17
5747 6196 0.706433 ACCATCTTCAACTGGCCCAT 59.294 50.000 0.00 0.00 35.88 4.00
5891 6340 3.640967 AGTTTGCTTTAACAAGGCATGGA 59.359 39.130 0.00 0.00 35.84 3.41
5939 6388 2.092753 TCCATGGCTTCCAACTGATCTC 60.093 50.000 6.96 0.00 36.95 2.75
5965 6414 5.883115 TCAAATCCAATTTACTACCATCGCA 59.117 36.000 0.00 0.00 0.00 5.10
5967 6416 7.985476 ACTTCAAATCCAATTTACTACCATCG 58.015 34.615 0.00 0.00 0.00 3.84
6017 6484 3.312736 AGACTTCAGCCTTTTTGGGAA 57.687 42.857 0.00 0.00 36.00 3.97
6125 6598 1.683943 ATTCCCATTCGGCACATCAG 58.316 50.000 0.00 0.00 0.00 2.90
6143 6631 9.401058 CACTGGAACTATCCTTTGATTCTTTAT 57.599 33.333 0.00 0.00 46.70 1.40
6183 6671 8.150945 TGAGATATGATAGCTTGAGGTTTTACC 58.849 37.037 0.00 0.00 38.99 2.85
6603 7091 0.967380 GAGATGCCCCCACAACCTTG 60.967 60.000 0.00 0.00 0.00 3.61
6616 7104 0.248565 TCAGGTGCAGTCAGAGATGC 59.751 55.000 0.00 1.17 42.86 3.91
6646 7134 1.378250 GCTTCCCAGCAGCATCAGT 60.378 57.895 0.00 0.00 46.49 3.41
6717 7205 6.716173 CAGAACTCTGAGAGATATCATCCTCA 59.284 42.308 17.71 16.44 46.59 3.86
6723 7211 5.444176 TGAGCAGAACTCTGAGAGATATCA 58.556 41.667 17.71 8.20 46.59 2.15
7047 7535 0.595095 CAGCAACTTGAGGCAGGAAC 59.405 55.000 0.00 0.00 0.00 3.62
7072 7560 0.446222 ATTTCGGTGCCGTTCATTCG 59.554 50.000 10.60 0.00 40.74 3.34
7410 7898 4.069304 TGGTTGGAAAGTATGAAACTCCG 58.931 43.478 0.00 0.00 37.50 4.63
7530 8018 5.184287 TCTTTTCCATTTCCAATTACCGTCC 59.816 40.000 0.00 0.00 0.00 4.79
7534 8022 6.353404 TGGTCTTTTCCATTTCCAATTACC 57.647 37.500 0.00 0.00 31.96 2.85
7586 8074 7.762588 TCCTTCCCTTCTAAATCTATACTCG 57.237 40.000 0.00 0.00 0.00 4.18
7615 8103 8.842358 TTTTGTCTAACCGATGAAAGTATTCT 57.158 30.769 0.00 0.00 36.48 2.40
7653 8141 1.228367 CTCCACAAAGGCCTGCTGT 60.228 57.895 5.69 10.92 37.29 4.40
7886 8380 3.739519 GCAAACATAAAAGCACACACCCA 60.740 43.478 0.00 0.00 0.00 4.51
7887 8381 2.799978 GCAAACATAAAAGCACACACCC 59.200 45.455 0.00 0.00 0.00 4.61
7892 8386 3.552684 GCCTCTGCAAACATAAAAGCACA 60.553 43.478 0.00 0.00 37.47 4.57
8231 8726 0.036294 GAAGAGAAGAACCACCGGGG 60.036 60.000 6.32 0.00 44.81 5.73
8275 8770 7.113965 CAGCAATGTCAAAGACAGTTGTTTATC 59.886 37.037 6.01 0.05 46.04 1.75
8276 8771 6.919662 CAGCAATGTCAAAGACAGTTGTTTAT 59.080 34.615 6.01 0.00 46.04 1.40
8279 8774 4.440525 CCAGCAATGTCAAAGACAGTTGTT 60.441 41.667 6.01 6.09 46.04 2.83
8280 8775 3.067180 CCAGCAATGTCAAAGACAGTTGT 59.933 43.478 6.01 0.00 46.04 3.32
8281 8776 3.551454 CCCAGCAATGTCAAAGACAGTTG 60.551 47.826 6.01 10.51 46.04 3.16
8282 8777 2.624838 CCCAGCAATGTCAAAGACAGTT 59.375 45.455 6.01 0.00 46.04 3.16
8284 8779 1.068055 GCCCAGCAATGTCAAAGACAG 60.068 52.381 6.01 0.00 46.04 3.51
8285 8780 0.961019 GCCCAGCAATGTCAAAGACA 59.039 50.000 1.95 1.95 46.90 3.41
8286 8781 0.961019 TGCCCAGCAATGTCAAAGAC 59.039 50.000 0.00 0.00 34.76 3.01
8412 8908 7.114811 CAGAAAAGAAACCAATACACCGAAATG 59.885 37.037 0.00 0.00 0.00 2.32
8418 8914 5.977129 CACACAGAAAAGAAACCAATACACC 59.023 40.000 0.00 0.00 0.00 4.16
8419 8915 5.977129 CCACACAGAAAAGAAACCAATACAC 59.023 40.000 0.00 0.00 0.00 2.90
8420 8916 5.451242 GCCACACAGAAAAGAAACCAATACA 60.451 40.000 0.00 0.00 0.00 2.29
8423 8919 3.490761 CGCCACACAGAAAAGAAACCAAT 60.491 43.478 0.00 0.00 0.00 3.16
8433 8929 2.225491 GAGTATTTGCGCCACACAGAAA 59.775 45.455 4.18 0.00 0.00 2.52
8451 8951 3.740115 ACAAGTCACGGCAAAATAGAGT 58.260 40.909 0.00 0.00 0.00 3.24
8463 8963 2.290367 TGCAATGGAGAAACAAGTCACG 59.710 45.455 0.00 0.00 0.00 4.35
8465 8965 2.886523 CCTGCAATGGAGAAACAAGTCA 59.113 45.455 2.50 0.00 0.00 3.41
8483 8983 2.908073 GCGCAACAACCTCCACCTG 61.908 63.158 0.30 0.00 0.00 4.00
8501 9001 1.443194 GCATCTGCAAACGCCACAG 60.443 57.895 0.00 0.00 41.59 3.66
8502 9002 2.644418 GCATCTGCAAACGCCACA 59.356 55.556 0.00 0.00 41.59 4.17
8526 9026 5.814705 CCCAAATTTACAACAAACTGAGCAA 59.185 36.000 0.00 0.00 0.00 3.91
8535 9045 7.296628 AGTAGATTGCCCAAATTTACAACAA 57.703 32.000 0.00 0.00 37.99 2.83
8552 9062 5.221925 ACAGATGACACCAACCAAGTAGATT 60.222 40.000 0.00 0.00 0.00 2.40
8597 9107 3.807538 GCCTACGACCGACGCAGA 61.808 66.667 0.00 0.00 46.94 4.26
8602 9112 1.153628 AGCAATGCCTACGACCGAC 60.154 57.895 0.00 0.00 0.00 4.79
8645 9168 3.076079 TGGAGATCAGCATCAGCAAAA 57.924 42.857 0.00 0.00 45.49 2.44
8676 9202 8.983307 ACAAGTAGTAGTAGCAGAATACAAAC 57.017 34.615 0.00 0.00 0.00 2.93
8706 9232 1.336440 CAGGCTGTAGAGATGTCGAGG 59.664 57.143 6.28 0.00 0.00 4.63
8707 9233 2.032799 GTCAGGCTGTAGAGATGTCGAG 59.967 54.545 15.27 0.00 0.00 4.04
8723 9250 1.300963 CTGGGGGTGTCATGTCAGG 59.699 63.158 0.00 0.00 0.00 3.86
8776 9312 2.352805 CAGACCCCCTGTTCTGCC 59.647 66.667 0.00 0.00 38.10 4.85
8817 9370 1.668294 CTCTCTTGCGTGGGTGTCT 59.332 57.895 0.00 0.00 0.00 3.41
8923 9476 0.187361 CTTTTTCCCCCACCTCACCA 59.813 55.000 0.00 0.00 0.00 4.17
8924 9477 1.185618 GCTTTTTCCCCCACCTCACC 61.186 60.000 0.00 0.00 0.00 4.02
8925 9478 0.469144 TGCTTTTTCCCCCACCTCAC 60.469 55.000 0.00 0.00 0.00 3.51
8958 9511 1.373570 CTGTCGCCTTCCATCCTTTC 58.626 55.000 0.00 0.00 0.00 2.62
9073 9626 3.970746 AAGGAAGGCATGGCAGGGC 62.971 63.158 22.64 18.62 0.00 5.19
9101 9654 4.767255 AAAGAGAGGCGCGCTGGG 62.767 66.667 32.29 0.00 0.00 4.45
9103 9656 3.191539 GGAAAGAGAGGCGCGCTG 61.192 66.667 32.29 0.00 0.00 5.18
9104 9657 4.803426 CGGAAAGAGAGGCGCGCT 62.803 66.667 32.29 17.27 0.00 5.92
9109 9662 2.509561 GGACGCGGAAAGAGAGGC 60.510 66.667 12.47 0.00 0.00 4.70
9212 9779 1.002868 GATGGATGGATGGAGCCCG 60.003 63.158 0.00 0.00 0.00 6.13
9234 9801 1.103398 GTGAAAGGGGCGATGGATGG 61.103 60.000 0.00 0.00 0.00 3.51
9235 9802 1.103398 GGTGAAAGGGGCGATGGATG 61.103 60.000 0.00 0.00 0.00 3.51
9236 9803 1.227383 GGTGAAAGGGGCGATGGAT 59.773 57.895 0.00 0.00 0.00 3.41
9237 9804 2.674754 GGTGAAAGGGGCGATGGA 59.325 61.111 0.00 0.00 0.00 3.41
9243 9810 2.941583 AGAGGGGGTGAAAGGGGC 60.942 66.667 0.00 0.00 0.00 5.80
9255 9822 1.331399 GGAAAGGACCGAGGAGAGGG 61.331 65.000 0.00 0.00 0.00 4.30
9277 9844 4.456911 TCGAGAGGGACGCGTATTAATATT 59.543 41.667 13.97 0.00 42.08 1.28
9278 9845 4.005650 TCGAGAGGGACGCGTATTAATAT 58.994 43.478 13.97 0.00 42.08 1.28
9384 9951 2.278738 CGGGGAAAATGGGGAGGG 59.721 66.667 0.00 0.00 0.00 4.30
9386 9953 1.379843 CCACGGGGAAAATGGGGAG 60.380 63.158 0.00 0.00 35.59 4.30


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

AutoCloner maintained by Alex Coulton.