Multiple sequence alignment - TraesCS7A01G119800

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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 TraesCS7A01G119800 chr7A 100.000 9220 0 0 1 9220 77156182 77165401 0.000000e+00 17027.0
1 TraesCS7A01G119800 chr7A 96.357 549 17 2 8672 9220 257151034 257150489 0.000000e+00 900.0
2 TraesCS7A01G119800 chr7A 95.479 553 20 4 8669 9220 24448277 24447729 0.000000e+00 878.0
3 TraesCS7A01G119800 chr7A 95.463 551 23 2 8670 9220 645073894 645074442 0.000000e+00 878.0
4 TraesCS7A01G119800 chr7A 83.767 961 107 23 5691 6616 76982539 76981593 0.000000e+00 865.0
5 TraesCS7A01G119800 chr7A 83.838 792 103 13 5802 6569 77024698 77023908 0.000000e+00 730.0
6 TraesCS7A01G119800 chr7B 94.647 5399 235 21 1 5384 14993049 14998408 0.000000e+00 8320.0
7 TraesCS7A01G119800 chr7B 94.751 1810 84 7 6872 8673 14999744 15001550 0.000000e+00 2806.0
8 TraesCS7A01G119800 chr7B 87.467 2290 229 27 3126 5384 14068566 14066304 0.000000e+00 2586.0
9 TraesCS7A01G119800 chr7B 86.673 2116 270 6 955 3063 14071574 14069464 0.000000e+00 2335.0
10 TraesCS7A01G119800 chr7B 96.560 1279 36 7 5583 6857 14998485 14999759 0.000000e+00 2111.0
11 TraesCS7A01G119800 chr7B 89.231 1690 161 16 3065 4737 13117204 13115519 0.000000e+00 2093.0
12 TraesCS7A01G119800 chr7B 87.877 1625 181 14 3077 4690 13879724 13878105 0.000000e+00 1895.0
13 TraesCS7A01G119800 chr7B 86.780 885 93 14 5709 6576 14065964 14065087 0.000000e+00 965.0
14 TraesCS7A01G119800 chr7B 86.798 659 74 8 7635 8288 13873466 13872816 0.000000e+00 723.0
15 TraesCS7A01G119800 chr7B 85.606 660 78 10 7631 8287 14064372 14063727 0.000000e+00 676.0
16 TraesCS7A01G119800 chr7B 88.148 540 53 7 4723 5257 13115472 13114939 4.700000e-177 632.0
17 TraesCS7A01G119800 chr7B 86.454 502 66 1 6159 6660 13818464 13817965 4.870000e-152 549.0
18 TraesCS7A01G119800 chr7B 82.234 197 27 6 8064 8258 13801174 13800984 7.410000e-36 163.0
19 TraesCS7A01G119800 chr7B 95.000 40 1 1 557 595 13881331 13881292 2.780000e-05 62.1
20 TraesCS7A01G119800 chr7D 95.890 3066 115 7 1 3063 72165700 72168757 0.000000e+00 4953.0
21 TraesCS7A01G119800 chr7D 94.300 2263 105 9 3127 5384 72169218 72171461 0.000000e+00 3443.0
22 TraesCS7A01G119800 chr7D 95.080 1809 55 10 6872 8673 72172976 72174757 0.000000e+00 2817.0
23 TraesCS7A01G119800 chr7D 86.907 2299 240 28 3125 5384 71548773 71546497 0.000000e+00 2521.0
24 TraesCS7A01G119800 chr7D 86.842 2090 267 3 977 3063 71551579 71549495 0.000000e+00 2329.0
25 TraesCS7A01G119800 chr7D 86.178 2185 265 24 3073 5234 71319069 71316899 0.000000e+00 2327.0
26 TraesCS7A01G119800 chr7D 86.727 2087 268 4 986 3063 70746505 70748591 0.000000e+00 2311.0
27 TraesCS7A01G119800 chr7D 85.992 2106 278 9 974 3063 70229743 70231847 0.000000e+00 2239.0
28 TraesCS7A01G119800 chr7D 85.473 2072 286 6 1006 3062 70833321 70831250 0.000000e+00 2145.0
29 TraesCS7A01G119800 chr7D 96.546 1274 37 5 5583 6852 72171717 72172987 0.000000e+00 2102.0
30 TraesCS7A01G119800 chr7D 87.877 1625 179 14 3077 4690 71344894 71346511 0.000000e+00 1893.0
31 TraesCS7A01G119800 chr7D 86.089 1639 201 24 3063 4690 71216268 71214646 0.000000e+00 1738.0
32 TraesCS7A01G119800 chr7D 83.684 950 125 14 5723 6646 71316501 71315556 0.000000e+00 869.0
33 TraesCS7A01G119800 chr7D 82.704 1006 129 28 5691 6660 70751601 70752597 0.000000e+00 852.0
34 TraesCS7A01G119800 chr7D 87.858 733 73 7 5841 6557 71546055 71545323 0.000000e+00 846.0
35 TraesCS7A01G119800 chr7D 81.909 1006 137 24 5691 6660 69938874 69937878 0.000000e+00 808.0
36 TraesCS7A01G119800 chr7D 84.086 842 111 10 4432 5256 71361821 71362656 0.000000e+00 791.0
37 TraesCS7A01G119800 chr7D 84.019 851 102 16 5785 6602 71213702 71212853 0.000000e+00 787.0
38 TraesCS7A01G119800 chr7D 82.034 885 112 30 7635 8501 71349014 71349869 0.000000e+00 710.0
39 TraesCS7A01G119800 chr7D 86.424 604 68 9 7631 8231 71544800 71544208 0.000000e+00 649.0
40 TraesCS7A01G119800 chr7D 93.785 177 10 1 5376 5552 149136088 149135913 1.970000e-66 265.0
41 TraesCS7A01G119800 chr7D 95.455 154 4 1 5583 5733 72171538 72171691 9.250000e-60 243.0
42 TraesCS7A01G119800 chr7D 85.354 198 24 4 8065 8258 71313760 71313564 5.650000e-47 200.0
43 TraesCS7A01G119800 chrUn 87.554 2073 253 2 991 3063 82531476 82529409 0.000000e+00 2394.0
44 TraesCS7A01G119800 chrUn 87.004 2116 262 7 955 3063 84401668 84403777 0.000000e+00 2372.0
45 TraesCS7A01G119800 chrUn 86.362 2185 265 23 3073 5234 84435519 84437693 0.000000e+00 2353.0
46 TraesCS7A01G119800 chrUn 84.872 2221 283 35 3063 5256 84238373 84236179 0.000000e+00 2191.0
47 TraesCS7A01G119800 chrUn 85.400 1637 198 28 3064 4690 84286715 84285110 0.000000e+00 1661.0
48 TraesCS7A01G119800 chrUn 85.400 1637 198 28 3064 4690 226940040 226938435 0.000000e+00 1661.0
49 TraesCS7A01G119800 chrUn 85.892 886 101 13 5691 6557 82526399 82525519 0.000000e+00 922.0
50 TraesCS7A01G119800 chrUn 85.843 890 100 13 5691 6557 84246851 84245965 0.000000e+00 922.0
51 TraesCS7A01G119800 chrUn 82.968 1004 133 18 5688 6655 82516097 82515096 0.000000e+00 872.0
52 TraesCS7A01G119800 chrUn 84.713 870 101 12 5765 6602 84284282 84283413 0.000000e+00 841.0
53 TraesCS7A01G119800 chrUn 84.713 870 101 12 5765 6602 226937607 226936738 0.000000e+00 841.0
54 TraesCS7A01G119800 chrUn 84.824 626 68 19 7628 8250 82514516 82513915 1.020000e-168 604.0
55 TraesCS7A01G119800 chrUn 83.601 622 62 19 7652 8268 329448586 329449172 1.750000e-151 547.0
56 TraesCS7A01G119800 chrUn 87.943 423 46 3 7631 8051 82524997 82524578 2.310000e-135 494.0
57 TraesCS7A01G119800 chrUn 83.673 196 31 1 8064 8258 84440642 84440837 5.690000e-42 183.0
58 TraesCS7A01G119800 chrUn 90.196 51 3 2 547 595 82520447 82520397 2.150000e-06 65.8
59 TraesCS7A01G119800 chr2B 87.877 1625 181 14 3077 4690 723403652 723402033 0.000000e+00 1895.0
60 TraesCS7A01G119800 chr2B 86.441 649 78 7 7635 8280 723399400 723398759 0.000000e+00 702.0
61 TraesCS7A01G119800 chr3A 97.283 552 14 1 8669 9220 30524580 30525130 0.000000e+00 935.0
62 TraesCS7A01G119800 chr3A 95.307 554 24 2 8668 9220 56722582 56723134 0.000000e+00 878.0
63 TraesCS7A01G119800 chr3A 96.000 175 6 1 5375 5549 40915061 40914888 5.450000e-72 283.0
64 TraesCS7A01G119800 chr5A 95.826 551 23 0 8670 9220 546514435 546514985 0.000000e+00 891.0
65 TraesCS7A01G119800 chr5A 95.644 551 23 1 8670 9220 588408853 588409402 0.000000e+00 883.0
66 TraesCS7A01G119800 chr5A 95.264 549 24 1 8672 9220 645000423 644999877 0.000000e+00 869.0
67 TraesCS7A01G119800 chr2A 96.000 550 19 3 8672 9220 744076631 744077178 0.000000e+00 891.0
68 TraesCS7A01G119800 chr5D 96.970 165 5 0 5383 5547 60139909 60139745 2.540000e-70 278.0
69 TraesCS7A01G119800 chr3D 96.407 167 6 0 5383 5549 592154816 592154650 9.120000e-70 276.0
70 TraesCS7A01G119800 chr3D 96.364 165 6 0 5383 5547 396430331 396430167 1.180000e-68 272.0
71 TraesCS7A01G119800 chr3B 96.364 165 6 0 5383 5547 190901964 190902128 1.180000e-68 272.0
72 TraesCS7A01G119800 chr3B 96.970 33 1 0 6749 6781 20096758 20096790 1.000000e-03 56.5
73 TraesCS7A01G119800 chr6D 95.294 170 8 0 5383 5552 249983546 249983377 4.240000e-68 270.0
74 TraesCS7A01G119800 chr6D 81.553 103 13 5 6699 6797 411402453 411402353 7.670000e-11 80.5
75 TraesCS7A01G119800 chr2D 94.318 176 10 0 5374 5549 26502224 26502399 4.240000e-68 270.0
76 TraesCS7A01G119800 chr2D 95.294 170 8 0 5380 5549 637587907 637588076 4.240000e-68 270.0
77 TraesCS7A01G119800 chr5B 80.000 175 27 4 6670 6842 166540405 166540573 1.260000e-23 122.0


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 TraesCS7A01G119800 chr7A 77156182 77165401 9219 False 17027.000000 17027 100.000000 1 9220 1 chr7A.!!$F1 9219
1 TraesCS7A01G119800 chr7A 257150489 257151034 545 True 900.000000 900 96.357000 8672 9220 1 chr7A.!!$R4 548
2 TraesCS7A01G119800 chr7A 24447729 24448277 548 True 878.000000 878 95.479000 8669 9220 1 chr7A.!!$R1 551
3 TraesCS7A01G119800 chr7A 645073894 645074442 548 False 878.000000 878 95.463000 8670 9220 1 chr7A.!!$F2 550
4 TraesCS7A01G119800 chr7A 76981593 76982539 946 True 865.000000 865 83.767000 5691 6616 1 chr7A.!!$R2 925
5 TraesCS7A01G119800 chr7A 77023908 77024698 790 True 730.000000 730 83.838000 5802 6569 1 chr7A.!!$R3 767
6 TraesCS7A01G119800 chr7B 14993049 15001550 8501 False 4412.333333 8320 95.319333 1 8673 3 chr7B.!!$F1 8672
7 TraesCS7A01G119800 chr7B 14063727 14071574 7847 True 1640.500000 2586 86.631500 955 8287 4 chr7B.!!$R6 7332
8 TraesCS7A01G119800 chr7B 13114939 13117204 2265 True 1362.500000 2093 88.689500 3065 5257 2 chr7B.!!$R4 2192
9 TraesCS7A01G119800 chr7B 13878105 13881331 3226 True 978.550000 1895 91.438500 557 4690 2 chr7B.!!$R5 4133
10 TraesCS7A01G119800 chr7B 13872816 13873466 650 True 723.000000 723 86.798000 7635 8288 1 chr7B.!!$R3 653
11 TraesCS7A01G119800 chr7D 72165700 72174757 9057 False 2711.600000 4953 95.454200 1 8673 5 chr7D.!!$F5 8672
12 TraesCS7A01G119800 chr7D 70229743 70231847 2104 False 2239.000000 2239 85.992000 974 3063 1 chr7D.!!$F1 2089
13 TraesCS7A01G119800 chr7D 70831250 70833321 2071 True 2145.000000 2145 85.473000 1006 3062 1 chr7D.!!$R2 2056
14 TraesCS7A01G119800 chr7D 71544208 71551579 7371 True 1586.250000 2521 87.007750 977 8231 4 chr7D.!!$R6 7254
15 TraesCS7A01G119800 chr7D 70746505 70752597 6092 False 1581.500000 2311 84.715500 986 6660 2 chr7D.!!$F3 5674
16 TraesCS7A01G119800 chr7D 71344894 71349869 4975 False 1301.500000 1893 84.955500 3077 8501 2 chr7D.!!$F4 5424
17 TraesCS7A01G119800 chr7D 71212853 71216268 3415 True 1262.500000 1738 85.054000 3063 6602 2 chr7D.!!$R4 3539
18 TraesCS7A01G119800 chr7D 71313564 71319069 5505 True 1132.000000 2327 85.072000 3073 8258 3 chr7D.!!$R5 5185
19 TraesCS7A01G119800 chr7D 69937878 69938874 996 True 808.000000 808 81.909000 5691 6660 1 chr7D.!!$R1 969
20 TraesCS7A01G119800 chr7D 71361821 71362656 835 False 791.000000 791 84.086000 4432 5256 1 chr7D.!!$F2 824
21 TraesCS7A01G119800 chrUn 84401668 84403777 2109 False 2372.000000 2372 87.004000 955 3063 1 chrUn.!!$F1 2108
22 TraesCS7A01G119800 chrUn 84236179 84238373 2194 True 2191.000000 2191 84.872000 3063 5256 1 chrUn.!!$R2 2193
23 TraesCS7A01G119800 chrUn 82524578 82531476 6898 True 1270.000000 2394 87.129667 991 8051 3 chrUn.!!$R5 7060
24 TraesCS7A01G119800 chrUn 84435519 84440837 5318 False 1268.000000 2353 85.017500 3073 8258 2 chrUn.!!$F3 5185
25 TraesCS7A01G119800 chrUn 84283413 84286715 3302 True 1251.000000 1661 85.056500 3064 6602 2 chrUn.!!$R6 3538
26 TraesCS7A01G119800 chrUn 226936738 226940040 3302 True 1251.000000 1661 85.056500 3064 6602 2 chrUn.!!$R7 3538
27 TraesCS7A01G119800 chrUn 84245965 84246851 886 True 922.000000 922 85.843000 5691 6557 1 chrUn.!!$R3 866
28 TraesCS7A01G119800 chrUn 82513915 82516097 2182 True 738.000000 872 83.896000 5688 8250 2 chrUn.!!$R4 2562
29 TraesCS7A01G119800 chrUn 329448586 329449172 586 False 547.000000 547 83.601000 7652 8268 1 chrUn.!!$F2 616
30 TraesCS7A01G119800 chr2B 723398759 723403652 4893 True 1298.500000 1895 87.159000 3077 8280 2 chr2B.!!$R1 5203
31 TraesCS7A01G119800 chr3A 30524580 30525130 550 False 935.000000 935 97.283000 8669 9220 1 chr3A.!!$F1 551
32 TraesCS7A01G119800 chr3A 56722582 56723134 552 False 878.000000 878 95.307000 8668 9220 1 chr3A.!!$F2 552
33 TraesCS7A01G119800 chr5A 546514435 546514985 550 False 891.000000 891 95.826000 8670 9220 1 chr5A.!!$F1 550
34 TraesCS7A01G119800 chr5A 588408853 588409402 549 False 883.000000 883 95.644000 8670 9220 1 chr5A.!!$F2 550
35 TraesCS7A01G119800 chr5A 644999877 645000423 546 True 869.000000 869 95.264000 8672 9220 1 chr5A.!!$R1 548
36 TraesCS7A01G119800 chr2A 744076631 744077178 547 False 891.000000 891 96.000000 8672 9220 1 chr2A.!!$F1 548

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
50 51 2.231215 ATGCTACCATCTCACTTCGC 57.769 50.000 0.00 0.00 0.00 4.70 F
1128 1143 2.585869 CGTCGCACTGCTCGTGTTT 61.586 57.895 0.00 0.00 45.57 2.83 F
1643 1680 0.037882 CTGCACACGGAGACAGACAT 60.038 55.000 0.00 0.00 30.74 3.06 F
1974 2014 1.992557 TCCACAGGCCCAATACTTCTT 59.007 47.619 0.00 0.00 0.00 2.52 F
2996 3036 0.029300 TCAACGCTTTTGTCTGCTGC 59.971 50.000 0.00 0.00 0.00 5.25 F
3491 4418 0.988063 TGCCCATACAGCCACAAGTA 59.012 50.000 0.00 0.00 0.00 2.24 F
3973 4939 1.860950 CAGACGGTATTCATGGAAGCG 59.139 52.381 11.19 11.19 39.81 4.68 F
5397 6930 1.076677 AGAACTACTCCCTCCGTTCCA 59.923 52.381 0.00 0.00 37.15 3.53 F
5547 7080 0.245539 TTTCGCAACGGAGGGAGTAG 59.754 55.000 0.00 0.00 0.00 2.57 F
5549 7082 0.609957 TCGCAACGGAGGGAGTAGAA 60.610 55.000 0.00 0.00 0.00 2.10 F
5550 7083 0.245539 CGCAACGGAGGGAGTAGAAA 59.754 55.000 0.00 0.00 0.00 2.52 F
5551 7084 1.337447 CGCAACGGAGGGAGTAGAAAA 60.337 52.381 0.00 0.00 0.00 2.29 F
5552 7085 2.774687 GCAACGGAGGGAGTAGAAAAA 58.225 47.619 0.00 0.00 0.00 1.94 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1222 1246 0.251922 AGGCAGCCATTGAACACCAT 60.252 50.000 15.80 0.00 0.00 3.55 R
2515 2555 0.031111 TCCCTCAACCCCTCGATGAT 60.031 55.000 0.00 0.00 0.00 2.45 R
2979 3019 0.248621 GTGCAGCAGACAAAAGCGTT 60.249 50.000 0.00 0.00 35.48 4.84 R
3287 4214 1.095228 CACCTCGCCAGTGTGTTGTT 61.095 55.000 0.00 0.00 0.00 2.83 R
4038 5004 1.685180 GGCTTAACACCTGAATCCCCC 60.685 57.143 0.00 0.00 0.00 5.40 R
5378 6911 1.553706 TGGAACGGAGGGAGTAGTTC 58.446 55.000 0.00 0.00 41.40 3.01 R
5528 7061 0.245539 CTACTCCCTCCGTTGCGAAA 59.754 55.000 0.00 0.00 0.00 3.46 R
7370 10948 1.001378 CGGAGTTTTCTGTTTGCCCAG 60.001 52.381 0.00 0.00 0.00 4.45 R
7637 11272 1.851021 TTCCAAACATCACGCTGGCG 61.851 55.000 13.56 13.56 46.03 5.69 R
7853 11489 8.516234 TGTAATAACGGTGCAATATTTGAACTT 58.484 29.630 0.00 0.00 39.29 2.66 R
8057 11695 9.012161 GTACGGGAAAGATCTACAATATACTCT 57.988 37.037 0.00 0.00 0.00 3.24 R
8098 11738 2.416162 GCTACTCTCCCTGAAGTGTTCG 60.416 54.545 0.00 0.00 0.00 3.95 R
8289 11933 7.221452 GTCGTATCTCTTTTGGAAAGCGTATAA 59.779 37.037 0.00 0.00 0.00 0.98 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
50 51 2.231215 ATGCTACCATCTCACTTCGC 57.769 50.000 0.00 0.00 0.00 4.70
117 118 8.082242 ACTTAGTTCCTATTTTTGCACATCAAC 58.918 33.333 0.00 0.00 33.73 3.18
141 142 5.639506 CAGAACTTCCAGTACGAACATTCAT 59.360 40.000 0.00 0.00 0.00 2.57
211 215 7.144661 TGGTGTATGTGTTCATGTCAATTTTC 58.855 34.615 0.00 0.00 35.70 2.29
218 222 6.530887 TGTGTTCATGTCAATTTTCACACAAG 59.469 34.615 0.00 0.00 40.12 3.16
317 321 7.981789 TCACAATATTCATGTCTTCTCCACTAC 59.018 37.037 0.00 0.00 0.00 2.73
330 334 3.991773 TCTCCACTACGATTTGTTTTCCG 59.008 43.478 0.00 0.00 0.00 4.30
380 384 5.682862 GCATACATCGAGGCACATTAAAAAG 59.317 40.000 0.00 0.00 0.00 2.27
541 548 2.835431 CGAGACCCGATCCAGCCT 60.835 66.667 0.00 0.00 41.76 4.58
822 830 8.844441 TTTAAATTGACTTAAAACACGTCCAG 57.156 30.769 0.00 0.00 29.84 3.86
862 870 8.135529 TGTATTTTGTGATATGGAGAGAGTACG 58.864 37.037 0.00 0.00 0.00 3.67
1128 1143 2.585869 CGTCGCACTGCTCGTGTTT 61.586 57.895 0.00 0.00 45.57 2.83
1222 1246 3.889134 CTGCTGCACTTCTCCGCCA 62.889 63.158 0.00 0.00 0.00 5.69
1255 1279 1.623311 GCTGCCTGGGTTTGGTTTATT 59.377 47.619 0.00 0.00 0.00 1.40
1643 1680 0.037882 CTGCACACGGAGACAGACAT 60.038 55.000 0.00 0.00 30.74 3.06
1743 1783 3.393609 TGAATCCTCTGATGAAGATGGGG 59.606 47.826 0.00 0.00 33.29 4.96
1812 1852 2.629050 ATCGAGCGCGCAACCTGTAT 62.629 55.000 35.10 9.89 37.46 2.29
1974 2014 1.992557 TCCACAGGCCCAATACTTCTT 59.007 47.619 0.00 0.00 0.00 2.52
2005 2045 7.959658 TTCATCAATGTATCACTTGGGAAAT 57.040 32.000 0.00 0.00 0.00 2.17
2007 2047 5.581126 TCAATGTATCACTTGGGAAATGC 57.419 39.130 0.00 0.00 0.00 3.56
2167 2207 7.817418 ATTTACAAGAAACAACAGAGGCTAA 57.183 32.000 0.00 0.00 0.00 3.09
2314 2354 2.493547 GCCCTGGCAATTCTGTACC 58.506 57.895 2.58 0.00 41.49 3.34
2351 2391 2.723124 ATGGTTTCGTCATTGGTTGC 57.277 45.000 0.00 0.00 0.00 4.17
2495 2535 7.994425 TGAAGGTCTTGAAACTTTATGCATA 57.006 32.000 1.16 1.16 0.00 3.14
2586 2626 2.537401 CTTAGTAGGGCGTACAACAGC 58.463 52.381 18.51 0.00 33.55 4.40
2676 2716 3.538591 TCCTCTTGATGCTAGCAATGTG 58.461 45.455 23.54 12.61 0.00 3.21
2864 2904 8.950210 CATTGATTACCCTATAGCGATGAATTT 58.050 33.333 0.00 0.00 0.00 1.82
2877 2917 6.344500 AGCGATGAATTTGTGTATCTTCTCT 58.656 36.000 0.00 0.00 0.00 3.10
2886 2926 6.373005 TTGTGTATCTTCTCTTGGGATGAA 57.627 37.500 0.00 0.00 0.00 2.57
2904 2944 6.156519 GGATGAAAGTACATCAAAACCAACC 58.843 40.000 0.00 0.00 45.68 3.77
2979 3019 3.833070 GAGAGGTAGGTTCAGGAAAGTCA 59.167 47.826 0.00 0.00 0.00 3.41
2996 3036 0.029300 TCAACGCTTTTGTCTGCTGC 59.971 50.000 0.00 0.00 0.00 5.25
3182 4109 8.741841 TGATCTTTGCATAAACATTTCAGATCA 58.258 29.630 0.00 0.00 36.13 2.92
3273 4200 2.100197 TCTCTTTGGATCGTCGATGGT 58.900 47.619 13.54 0.00 0.00 3.55
3287 4214 3.132289 GTCGATGGTCAGGGAAAGATACA 59.868 47.826 0.00 0.00 0.00 2.29
3343 4270 3.451902 ACCTTGAAATGTTGCCATATGGG 59.548 43.478 23.30 5.41 40.85 4.00
3491 4418 0.988063 TGCCCATACAGCCACAAGTA 59.012 50.000 0.00 0.00 0.00 2.24
3671 4599 6.442541 TTTGACTCCATTTTGGTACCTCTA 57.557 37.500 14.36 0.00 39.03 2.43
3690 4618 5.578727 CCTCTATCCACTTCGAAAAAGTCAG 59.421 44.000 0.00 0.00 0.00 3.51
3759 4717 9.520204 AATGAGCTTTATTTATTTGTGGATTCG 57.480 29.630 0.00 0.00 0.00 3.34
3870 4836 8.307483 TGTGAAGAATTTAAAAACCTTGTCACA 58.693 29.630 12.94 12.94 0.00 3.58
3898 4864 4.737855 AAAGATACTACTGGTGCATCGT 57.262 40.909 0.00 0.00 0.00 3.73
3957 4923 7.787028 AGGAAGTATCAATAAAGGAGACAGAC 58.213 38.462 0.00 0.00 0.00 3.51
3973 4939 1.860950 CAGACGGTATTCATGGAAGCG 59.139 52.381 11.19 11.19 39.81 4.68
4038 5004 8.388484 TGATCAAGAAAGAGGAAAGAGAAAAG 57.612 34.615 0.00 0.00 0.00 2.27
4245 5211 8.531622 TTATAATTGGAGTTTGCACAATGTTG 57.468 30.769 0.72 0.00 35.22 3.33
4309 5275 8.321650 GATCCAGACATCAAGATCCTTATTTC 57.678 38.462 0.00 0.00 30.97 2.17
4422 5388 9.649024 CTTAAACAAATGGCAAATACAACAAAG 57.351 29.630 0.00 0.00 0.00 2.77
4510 5478 4.356405 TGCAGGTCTCTTCAGATTTGAA 57.644 40.909 0.00 0.00 40.92 2.69
4991 6396 5.759059 TGGATCTTATTGACAAGAATGCCT 58.241 37.500 0.00 0.00 38.03 4.75
5123 6528 3.914435 AGGAACTTTTAGCCCTGGTAAGA 59.086 43.478 0.00 0.00 27.25 2.10
5215 6632 6.687105 GGTGCTTACAACTAATTTGCGATAAG 59.313 38.462 0.00 0.00 39.01 1.73
5270 6718 9.994432 CTACCTTTTCATATCTTTTGTCATGAC 57.006 33.333 19.27 19.27 0.00 3.06
5378 6911 7.862372 ACTTTTGTTATGTGCATGTTTGTAGAG 59.138 33.333 0.00 0.00 0.00 2.43
5384 6917 6.727824 ATGTGCATGTTTGTAGAGAACTAC 57.272 37.500 0.00 0.00 46.36 2.73
5385 6918 5.853936 TGTGCATGTTTGTAGAGAACTACT 58.146 37.500 0.00 0.00 46.33 2.57
5386 6919 5.926542 TGTGCATGTTTGTAGAGAACTACTC 59.073 40.000 0.00 0.00 46.33 2.59
5387 6920 5.348997 GTGCATGTTTGTAGAGAACTACTCC 59.651 44.000 0.00 0.00 46.33 3.85
5388 6921 4.870991 GCATGTTTGTAGAGAACTACTCCC 59.129 45.833 0.00 0.00 46.33 4.30
5389 6922 5.337652 GCATGTTTGTAGAGAACTACTCCCT 60.338 44.000 0.00 0.00 46.33 4.20
5390 6923 5.979288 TGTTTGTAGAGAACTACTCCCTC 57.021 43.478 0.00 0.00 46.33 4.30
5391 6924 4.771054 TGTTTGTAGAGAACTACTCCCTCC 59.229 45.833 0.00 0.00 46.33 4.30
5392 6925 3.278668 TGTAGAGAACTACTCCCTCCG 57.721 52.381 0.00 0.00 46.33 4.63
5394 6927 2.903375 AGAGAACTACTCCCTCCGTT 57.097 50.000 0.00 0.00 45.96 4.44
5395 6928 2.725637 AGAGAACTACTCCCTCCGTTC 58.274 52.381 0.00 0.00 45.96 3.95
5396 6929 1.750206 GAGAACTACTCCCTCCGTTCC 59.250 57.143 0.00 0.00 39.53 3.62
5397 6930 1.076677 AGAACTACTCCCTCCGTTCCA 59.923 52.381 0.00 0.00 37.15 3.53
5398 6931 1.897802 GAACTACTCCCTCCGTTCCAA 59.102 52.381 0.00 0.00 31.89 3.53
5399 6932 2.019807 ACTACTCCCTCCGTTCCAAA 57.980 50.000 0.00 0.00 0.00 3.28
5400 6933 2.332117 ACTACTCCCTCCGTTCCAAAA 58.668 47.619 0.00 0.00 0.00 2.44
5401 6934 2.910977 ACTACTCCCTCCGTTCCAAAAT 59.089 45.455 0.00 0.00 0.00 1.82
5402 6935 4.098894 ACTACTCCCTCCGTTCCAAAATA 58.901 43.478 0.00 0.00 0.00 1.40
5403 6936 4.720273 ACTACTCCCTCCGTTCCAAAATAT 59.280 41.667 0.00 0.00 0.00 1.28
5404 6937 4.586306 ACTCCCTCCGTTCCAAAATATT 57.414 40.909 0.00 0.00 0.00 1.28
5405 6938 5.703730 ACTCCCTCCGTTCCAAAATATTA 57.296 39.130 0.00 0.00 0.00 0.98
5406 6939 5.681639 ACTCCCTCCGTTCCAAAATATTAG 58.318 41.667 0.00 0.00 0.00 1.73
5407 6940 5.191124 ACTCCCTCCGTTCCAAAATATTAGT 59.809 40.000 0.00 0.00 0.00 2.24
5408 6941 5.677567 TCCCTCCGTTCCAAAATATTAGTC 58.322 41.667 0.00 0.00 0.00 2.59
5409 6942 5.427481 TCCCTCCGTTCCAAAATATTAGTCT 59.573 40.000 0.00 0.00 0.00 3.24
5410 6943 6.069847 TCCCTCCGTTCCAAAATATTAGTCTT 60.070 38.462 0.00 0.00 0.00 3.01
5411 6944 6.602009 CCCTCCGTTCCAAAATATTAGTCTTT 59.398 38.462 0.00 0.00 0.00 2.52
5412 6945 7.201705 CCCTCCGTTCCAAAATATTAGTCTTTC 60.202 40.741 0.00 0.00 0.00 2.62
5413 6946 7.553044 CCTCCGTTCCAAAATATTAGTCTTTCT 59.447 37.037 0.00 0.00 0.00 2.52
5414 6947 9.595823 CTCCGTTCCAAAATATTAGTCTTTCTA 57.404 33.333 0.00 0.00 0.00 2.10
5415 6948 9.595823 TCCGTTCCAAAATATTAGTCTTTCTAG 57.404 33.333 0.00 0.00 0.00 2.43
5416 6949 9.595823 CCGTTCCAAAATATTAGTCTTTCTAGA 57.404 33.333 0.00 0.00 0.00 2.43
5429 6962 9.716556 TTAGTCTTTCTAGAGATTCCAATAGGT 57.283 33.333 0.00 0.00 35.89 3.08
5430 6963 8.017418 AGTCTTTCTAGAGATTCCAATAGGTG 57.983 38.462 0.00 0.00 35.89 4.00
5431 6964 7.841729 AGTCTTTCTAGAGATTCCAATAGGTGA 59.158 37.037 0.00 0.00 35.89 4.02
5432 6965 7.923878 GTCTTTCTAGAGATTCCAATAGGTGAC 59.076 40.741 0.00 0.00 35.89 3.67
5445 6978 2.139323 AGGTGACTACATACGGAGCA 57.861 50.000 0.00 0.00 40.61 4.26
5446 6979 2.453521 AGGTGACTACATACGGAGCAA 58.546 47.619 0.00 0.00 40.61 3.91
5447 6980 2.829720 AGGTGACTACATACGGAGCAAA 59.170 45.455 0.00 0.00 40.61 3.68
5448 6981 3.259876 AGGTGACTACATACGGAGCAAAA 59.740 43.478 0.00 0.00 40.61 2.44
5449 6982 4.081087 AGGTGACTACATACGGAGCAAAAT 60.081 41.667 0.00 0.00 40.61 1.82
5450 6983 4.034048 GGTGACTACATACGGAGCAAAATG 59.966 45.833 0.00 0.00 0.00 2.32
5451 6984 4.868171 GTGACTACATACGGAGCAAAATGA 59.132 41.667 0.00 0.00 0.00 2.57
5452 6985 5.005779 GTGACTACATACGGAGCAAAATGAG 59.994 44.000 0.00 0.00 0.00 2.90
5453 6986 5.086104 ACTACATACGGAGCAAAATGAGT 57.914 39.130 0.00 0.00 0.00 3.41
5454 6987 4.870426 ACTACATACGGAGCAAAATGAGTG 59.130 41.667 0.00 0.00 0.00 3.51
5455 6988 3.937814 ACATACGGAGCAAAATGAGTGA 58.062 40.909 0.00 0.00 0.00 3.41
5456 6989 4.323417 ACATACGGAGCAAAATGAGTGAA 58.677 39.130 0.00 0.00 0.00 3.18
5457 6990 4.943705 ACATACGGAGCAAAATGAGTGAAT 59.056 37.500 0.00 0.00 0.00 2.57
5458 6991 5.065218 ACATACGGAGCAAAATGAGTGAATC 59.935 40.000 0.00 0.00 0.00 2.52
5459 6992 3.679389 ACGGAGCAAAATGAGTGAATCT 58.321 40.909 0.00 0.00 0.00 2.40
5460 6993 4.832248 ACGGAGCAAAATGAGTGAATCTA 58.168 39.130 0.00 0.00 0.00 1.98
5461 6994 4.631813 ACGGAGCAAAATGAGTGAATCTAC 59.368 41.667 0.00 0.00 0.00 2.59
5462 6995 4.631377 CGGAGCAAAATGAGTGAATCTACA 59.369 41.667 0.00 0.00 0.00 2.74
5463 6996 5.446473 CGGAGCAAAATGAGTGAATCTACAC 60.446 44.000 0.00 0.00 40.60 2.90
5499 7032 9.511272 TGTCTACATACATCCGTATATTGTAGT 57.489 33.333 0.00 0.00 38.60 2.73
5500 7033 9.985318 GTCTACATACATCCGTATATTGTAGTC 57.015 37.037 0.00 0.00 38.60 2.59
5501 7034 9.170734 TCTACATACATCCGTATATTGTAGTCC 57.829 37.037 0.00 0.00 38.60 3.85
5502 7035 9.175312 CTACATACATCCGTATATTGTAGTCCT 57.825 37.037 0.00 0.00 35.67 3.85
5503 7036 8.418597 ACATACATCCGTATATTGTAGTCCTT 57.581 34.615 0.00 0.00 36.11 3.36
5504 7037 8.867097 ACATACATCCGTATATTGTAGTCCTTT 58.133 33.333 0.00 0.00 36.11 3.11
5505 7038 9.706691 CATACATCCGTATATTGTAGTCCTTTT 57.293 33.333 0.00 0.00 36.11 2.27
5506 7039 9.706691 ATACATCCGTATATTGTAGTCCTTTTG 57.293 33.333 0.00 0.00 36.53 2.44
5507 7040 7.788026 ACATCCGTATATTGTAGTCCTTTTGA 58.212 34.615 0.00 0.00 0.00 2.69
5508 7041 8.262227 ACATCCGTATATTGTAGTCCTTTTGAA 58.738 33.333 0.00 0.00 0.00 2.69
5509 7042 9.104965 CATCCGTATATTGTAGTCCTTTTGAAA 57.895 33.333 0.00 0.00 0.00 2.69
5510 7043 9.847224 ATCCGTATATTGTAGTCCTTTTGAAAT 57.153 29.630 0.00 0.00 0.00 2.17
5511 7044 9.104965 TCCGTATATTGTAGTCCTTTTGAAATG 57.895 33.333 0.00 0.00 0.00 2.32
5512 7045 8.889717 CCGTATATTGTAGTCCTTTTGAAATGT 58.110 33.333 0.00 0.00 0.00 2.71
5513 7046 9.916397 CGTATATTGTAGTCCTTTTGAAATGTC 57.084 33.333 0.00 0.00 0.00 3.06
5523 7056 9.190317 AGTCCTTTTGAAATGTCTAAAAAGACT 57.810 29.630 14.26 14.26 40.46 3.24
5524 7057 9.803315 GTCCTTTTGAAATGTCTAAAAAGACTT 57.197 29.630 9.12 0.00 40.46 3.01
5537 7070 9.195831 GTCTAAAAAGACTTATATTTCGCAACG 57.804 33.333 0.00 0.00 36.01 4.10
5538 7071 8.385111 TCTAAAAAGACTTATATTTCGCAACGG 58.615 33.333 0.00 0.00 0.00 4.44
5539 7072 6.730960 AAAAGACTTATATTTCGCAACGGA 57.269 33.333 0.00 0.00 0.00 4.69
5540 7073 5.968387 AAGACTTATATTTCGCAACGGAG 57.032 39.130 0.00 0.00 0.00 4.63
5541 7074 4.369182 AGACTTATATTTCGCAACGGAGG 58.631 43.478 0.00 0.00 0.00 4.30
5542 7075 3.463944 ACTTATATTTCGCAACGGAGGG 58.536 45.455 0.00 0.00 0.00 4.30
5543 7076 3.133362 ACTTATATTTCGCAACGGAGGGA 59.867 43.478 0.00 0.00 0.00 4.20
5544 7077 2.240493 ATATTTCGCAACGGAGGGAG 57.760 50.000 0.00 0.00 0.00 4.30
5545 7078 0.899720 TATTTCGCAACGGAGGGAGT 59.100 50.000 0.00 0.00 0.00 3.85
5546 7079 0.899720 ATTTCGCAACGGAGGGAGTA 59.100 50.000 0.00 0.00 0.00 2.59
5547 7080 0.245539 TTTCGCAACGGAGGGAGTAG 59.754 55.000 0.00 0.00 0.00 2.57
5548 7081 0.609957 TTCGCAACGGAGGGAGTAGA 60.610 55.000 0.00 0.00 0.00 2.59
5549 7082 0.609957 TCGCAACGGAGGGAGTAGAA 60.610 55.000 0.00 0.00 0.00 2.10
5550 7083 0.245539 CGCAACGGAGGGAGTAGAAA 59.754 55.000 0.00 0.00 0.00 2.52
5551 7084 1.337447 CGCAACGGAGGGAGTAGAAAA 60.337 52.381 0.00 0.00 0.00 2.29
5552 7085 2.774687 GCAACGGAGGGAGTAGAAAAA 58.225 47.619 0.00 0.00 0.00 1.94
6047 8607 3.496884 GGACATACAAAGTGAAGCAACGA 59.503 43.478 0.00 0.00 0.00 3.85
6310 8901 4.023878 GTGGCAAGACAACGTTAATTGGTA 60.024 41.667 16.41 0.00 33.63 3.25
6325 8916 8.222433 CGTTAATTGGTACATTGTTTCGTCTTA 58.778 33.333 0.00 0.00 39.30 2.10
6630 9239 6.631016 TCATGTGACAGTCATCTTTAGTACC 58.369 40.000 6.51 0.00 0.00 3.34
6689 9303 6.481976 TCCGAAAATATAGTGCACATTCGAAT 59.518 34.615 25.19 4.39 40.22 3.34
6730 9344 9.908152 ATTTGTAAGCTTTGACCAAGTTTATAC 57.092 29.630 3.20 0.00 39.54 1.47
6782 9396 4.024670 TCAATGCCATTGGATTCATCACA 58.975 39.130 16.96 0.00 40.61 3.58
6783 9397 4.651962 TCAATGCCATTGGATTCATCACAT 59.348 37.500 16.96 0.00 40.61 3.21
6848 9462 5.841957 AGTTTGTGAAGCTTGACTTTCAT 57.158 34.783 17.14 0.00 39.29 2.57
6853 9467 6.395426 TGTGAAGCTTGACTTTCATGAATT 57.605 33.333 17.14 0.00 39.29 2.17
6854 9468 7.509141 TGTGAAGCTTGACTTTCATGAATTA 57.491 32.000 17.14 0.00 39.29 1.40
6855 9469 7.362662 TGTGAAGCTTGACTTTCATGAATTAC 58.637 34.615 17.14 4.36 39.29 1.89
6856 9470 6.803807 GTGAAGCTTGACTTTCATGAATTACC 59.196 38.462 9.40 0.25 39.29 2.85
6857 9471 5.904362 AGCTTGACTTTCATGAATTACCC 57.096 39.130 9.40 0.00 0.00 3.69
6858 9472 4.396166 AGCTTGACTTTCATGAATTACCCG 59.604 41.667 9.40 0.00 0.00 5.28
6859 9473 4.662145 CTTGACTTTCATGAATTACCCGC 58.338 43.478 9.40 0.00 0.00 6.13
6860 9474 3.680490 TGACTTTCATGAATTACCCGCA 58.320 40.909 9.40 0.00 0.00 5.69
6861 9475 4.075682 TGACTTTCATGAATTACCCGCAA 58.924 39.130 9.40 0.00 0.00 4.85
6862 9476 4.520874 TGACTTTCATGAATTACCCGCAAA 59.479 37.500 9.40 0.00 0.00 3.68
6863 9477 5.010112 TGACTTTCATGAATTACCCGCAAAA 59.990 36.000 9.40 0.00 0.00 2.44
6864 9478 5.848406 ACTTTCATGAATTACCCGCAAAAA 58.152 33.333 9.40 0.00 0.00 1.94
6907 9521 5.207354 ACCAATGTGCACATTATTATGGGA 58.793 37.500 37.40 6.15 44.10 4.37
6944 9558 6.860023 CCTAACAAATTCAGAAAGTTCAGCAG 59.140 38.462 3.15 0.00 0.00 4.24
6949 9563 8.078596 ACAAATTCAGAAAGTTCAGCAGATTAC 58.921 33.333 0.00 0.00 0.00 1.89
7025 9642 8.088365 ACAAGTTGCCTTTCTCATATAAAAACC 58.912 33.333 1.81 0.00 0.00 3.27
7188 9922 4.201950 CCTCCTTTCTCATTTTATGGCACG 60.202 45.833 0.00 0.00 0.00 5.34
7240 10243 4.938832 TGGTCACTCCATTTGTTATTACGG 59.061 41.667 0.00 0.00 41.93 4.02
7322 10325 4.702131 GGATTCACTTGGTATGAAACTGCT 59.298 41.667 0.00 0.00 39.43 4.24
7370 10948 7.279090 GGAGTTCCTCTTTTGAAGCTAATAGAC 59.721 40.741 0.00 0.00 0.00 2.59
7853 11489 3.496884 CCTTCAGAAAACGATCCGAACAA 59.503 43.478 0.00 0.00 0.00 2.83
7890 11526 2.809119 CCGTTATTACAGTTGCACACCA 59.191 45.455 0.00 0.00 0.00 4.17
8093 11733 6.516718 AGATCTTTCCCGTACTAATGATGTG 58.483 40.000 0.00 0.00 0.00 3.21
8098 11738 5.252969 TCCCGTACTAATGATGTGTGTAC 57.747 43.478 0.00 0.00 0.00 2.90
8314 11959 3.921677 ACGCTTTCCAAAAGAGATACGA 58.078 40.909 9.64 0.00 0.00 3.43
8315 11960 3.678548 ACGCTTTCCAAAAGAGATACGAC 59.321 43.478 9.64 0.00 0.00 4.34
8316 11961 3.241678 CGCTTTCCAAAAGAGATACGACG 60.242 47.826 3.68 0.00 0.00 5.12
8501 12157 1.340017 CCGGAGATTTCCTTGCTCCAA 60.340 52.381 0.00 0.00 46.74 3.53
8598 12254 9.011095 AGAGCTCATAATATGTTCATTGATTGG 57.989 33.333 17.77 0.00 0.00 3.16
8665 12321 9.840427 AGAAAATAAAATAAACATGTCAGTCGG 57.160 29.630 0.00 0.00 0.00 4.79
8684 12340 1.453669 GGCTAAGGGCATCTCCAGG 59.546 63.158 0.00 0.00 44.01 4.45
8796 12452 4.947147 TGGGCCGAAAACAGCGCT 62.947 61.111 2.64 2.64 42.05 5.92
9121 12779 1.274167 CCTATATAAGACGCGCCCCAA 59.726 52.381 5.73 0.00 0.00 4.12
9155 12813 1.792941 GTACTCTCTCGCCGTCGTT 59.207 57.895 0.00 0.00 36.96 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
163 164 6.091713 CCAACATGATGCTGGATTTTCTTTTC 59.908 38.462 9.20 0.00 35.69 2.29
166 167 4.529377 ACCAACATGATGCTGGATTTTCTT 59.471 37.500 20.80 0.00 35.69 2.52
168 169 4.178540 CACCAACATGATGCTGGATTTTC 58.821 43.478 20.80 0.00 35.69 2.29
340 344 9.487790 TCGATGTATGCACTGAAATATAATTGA 57.512 29.630 0.00 0.00 0.00 2.57
341 345 9.750882 CTCGATGTATGCACTGAAATATAATTG 57.249 33.333 0.00 0.00 0.00 2.32
458 465 3.066621 AGACAAAGCAGCGAAAATGTTGA 59.933 39.130 0.00 0.00 0.00 3.18
541 548 4.460263 GAACCCATATGTATTGCACTCCA 58.540 43.478 1.24 0.00 0.00 3.86
822 830 8.942669 TCACAAAATACAAATACATGTCGTTC 57.057 30.769 0.00 0.00 34.75 3.95
839 847 7.113658 ACGTACTCTCTCCATATCACAAAAT 57.886 36.000 0.00 0.00 0.00 1.82
1128 1143 1.239296 GCAACTGGAGCATGAGCACA 61.239 55.000 0.00 0.00 45.49 4.57
1222 1246 0.251922 AGGCAGCCATTGAACACCAT 60.252 50.000 15.80 0.00 0.00 3.55
1255 1279 0.325296 ATCCACAGTCCTAGCCCGAA 60.325 55.000 0.00 0.00 0.00 4.30
1643 1680 3.898123 ACTTTCAGAGTCAGCTACCTCAA 59.102 43.478 12.80 0.00 31.20 3.02
1743 1783 3.017442 GTCCTCAAGGGGCTTTTCATAC 58.983 50.000 0.00 0.00 36.61 2.39
1812 1852 3.008266 TGAGCTTCTCCATGAACATCACA 59.992 43.478 0.00 0.00 0.00 3.58
1974 2014 7.720957 CCAAGTGATACATTGATGAATTCCCTA 59.279 37.037 2.27 0.00 0.00 3.53
2005 2045 8.995027 ACATATCCTTCATATTTAAAGGTGCA 57.005 30.769 7.74 0.00 42.28 4.57
2100 2140 2.114616 ACCTGCAGTCCTAATCTCCTG 58.885 52.381 13.81 0.00 0.00 3.86
2167 2207 3.878103 TGCTTCATTTTTGCTGCATTTGT 59.122 34.783 1.84 0.00 0.00 2.83
2351 2391 3.990469 GCAGAGTACGGTGATAATGATGG 59.010 47.826 2.00 0.00 0.00 3.51
2515 2555 0.031111 TCCCTCAACCCCTCGATGAT 60.031 55.000 0.00 0.00 0.00 2.45
2586 2626 1.457346 GTGATGCCCAGAACAGGAAG 58.543 55.000 0.00 0.00 0.00 3.46
2689 2729 2.882927 TGCACAAGACGTAGAGTTGT 57.117 45.000 0.00 0.00 37.42 3.32
2731 2771 6.808212 GCTTGTATCACAACTGCAATTACATT 59.192 34.615 0.00 0.00 33.96 2.71
2864 2904 6.013379 ACTTTCATCCCAAGAGAAGATACACA 60.013 38.462 0.00 0.00 0.00 3.72
2877 2917 5.835819 TGGTTTTGATGTACTTTCATCCCAA 59.164 36.000 0.00 0.00 42.24 4.12
2886 2926 7.064229 TCTTTAGGGTTGGTTTTGATGTACTT 58.936 34.615 0.00 0.00 0.00 2.24
2979 3019 0.248621 GTGCAGCAGACAAAAGCGTT 60.249 50.000 0.00 0.00 35.48 4.84
3056 3105 8.351495 TCATAACAACTTTGCAAACTTTCATC 57.649 30.769 8.05 0.00 0.00 2.92
3273 4200 4.819630 GTGTGTTGTTGTATCTTTCCCTGA 59.180 41.667 0.00 0.00 0.00 3.86
3287 4214 1.095228 CACCTCGCCAGTGTGTTGTT 61.095 55.000 0.00 0.00 0.00 2.83
3516 4443 9.060347 CCAAATAGTAATACAATCTGCATCTGT 57.940 33.333 0.00 0.00 0.00 3.41
3638 4566 5.391312 AAATGGAGTCAAATGCAGGTAAC 57.609 39.130 0.00 0.00 0.00 2.50
3671 4599 3.476552 TGCTGACTTTTTCGAAGTGGAT 58.523 40.909 0.00 0.00 0.00 3.41
3690 4618 5.353938 ACAGGCACAAATATCATCAAATGC 58.646 37.500 0.00 0.00 0.00 3.56
3815 4781 5.979517 GCCAATAAATCTTGATAAGGTGCAC 59.020 40.000 8.80 8.80 0.00 4.57
3870 4836 4.202367 GCACCAGTAGTATCTTTATGGGCT 60.202 45.833 0.00 0.00 31.95 5.19
3957 4923 2.169832 ATCCGCTTCCATGAATACCG 57.830 50.000 0.00 0.00 0.00 4.02
3973 4939 6.842437 TGGCTTCATAGACTCTGTATATCC 57.158 41.667 0.00 0.00 0.00 2.59
4038 5004 1.685180 GGCTTAACACCTGAATCCCCC 60.685 57.143 0.00 0.00 0.00 5.40
4245 5211 9.757227 ACTACTAAAGATCTTGATAGCATGAAC 57.243 33.333 9.17 0.00 32.71 3.18
4309 5275 4.210724 ACAATGAATTGAGCAATTGGGG 57.789 40.909 12.73 3.43 40.77 4.96
4422 5388 6.228258 TCTCTGGGTGTAAAACAGATTGTAC 58.772 40.000 0.00 0.00 40.16 2.90
4510 5478 6.617782 ATGGAAGATCGAGGTCAATGATAT 57.382 37.500 0.00 0.00 0.00 1.63
4991 6396 6.559810 CGGCAAAATTACAGAAATATGGACA 58.440 36.000 0.00 0.00 0.00 4.02
5123 6528 3.057315 GCAGCATGGTGTTCATACAGTTT 60.057 43.478 24.73 0.00 32.93 2.66
5215 6632 3.788333 ACATGGCAATGCATCTAACAC 57.212 42.857 7.79 0.00 37.29 3.32
5270 6718 4.321304 CGTGGAGGGAGTATAAGTATGCTG 60.321 50.000 0.00 0.00 0.00 4.41
5378 6911 1.553706 TGGAACGGAGGGAGTAGTTC 58.446 55.000 0.00 0.00 41.40 3.01
5384 6917 5.681639 ACTAATATTTTGGAACGGAGGGAG 58.318 41.667 0.00 0.00 0.00 4.30
5385 6918 5.427481 AGACTAATATTTTGGAACGGAGGGA 59.573 40.000 0.00 0.00 0.00 4.20
5386 6919 5.681639 AGACTAATATTTTGGAACGGAGGG 58.318 41.667 0.00 0.00 0.00 4.30
5387 6920 7.553044 AGAAAGACTAATATTTTGGAACGGAGG 59.447 37.037 0.00 0.00 0.00 4.30
5388 6921 8.494016 AGAAAGACTAATATTTTGGAACGGAG 57.506 34.615 0.00 0.00 0.00 4.63
5389 6922 9.595823 CTAGAAAGACTAATATTTTGGAACGGA 57.404 33.333 0.00 0.00 0.00 4.69
5390 6923 9.595823 TCTAGAAAGACTAATATTTTGGAACGG 57.404 33.333 0.00 0.00 0.00 4.44
5403 6936 9.716556 ACCTATTGGAATCTCTAGAAAGACTAA 57.283 33.333 0.00 0.00 37.04 2.24
5404 6937 9.137459 CACCTATTGGAATCTCTAGAAAGACTA 57.863 37.037 0.00 0.00 37.04 2.59
5405 6938 7.841729 TCACCTATTGGAATCTCTAGAAAGACT 59.158 37.037 0.00 0.00 37.04 3.24
5406 6939 7.923878 GTCACCTATTGGAATCTCTAGAAAGAC 59.076 40.741 0.00 0.00 37.04 3.01
5407 6940 7.841729 AGTCACCTATTGGAATCTCTAGAAAGA 59.158 37.037 0.00 0.00 37.04 2.52
5408 6941 8.017418 AGTCACCTATTGGAATCTCTAGAAAG 57.983 38.462 0.00 0.00 37.04 2.62
5409 6942 7.979786 AGTCACCTATTGGAATCTCTAGAAA 57.020 36.000 0.00 0.00 37.04 2.52
5410 6943 8.059461 TGTAGTCACCTATTGGAATCTCTAGAA 58.941 37.037 0.00 0.00 37.04 2.10
5411 6944 7.583625 TGTAGTCACCTATTGGAATCTCTAGA 58.416 38.462 0.00 0.00 37.04 2.43
5412 6945 7.825331 TGTAGTCACCTATTGGAATCTCTAG 57.175 40.000 0.00 0.00 37.04 2.43
5413 6946 9.298250 GTATGTAGTCACCTATTGGAATCTCTA 57.702 37.037 0.00 0.00 37.04 2.43
5414 6947 7.040340 CGTATGTAGTCACCTATTGGAATCTCT 60.040 40.741 0.00 0.00 37.04 3.10
5415 6948 7.085116 CGTATGTAGTCACCTATTGGAATCTC 58.915 42.308 0.00 0.00 37.04 2.75
5416 6949 6.015350 CCGTATGTAGTCACCTATTGGAATCT 60.015 42.308 0.00 0.00 37.04 2.40
5417 6950 6.015688 TCCGTATGTAGTCACCTATTGGAATC 60.016 42.308 0.00 0.00 37.04 2.52
5418 6951 5.836898 TCCGTATGTAGTCACCTATTGGAAT 59.163 40.000 0.00 0.00 37.04 3.01
5419 6952 5.202765 TCCGTATGTAGTCACCTATTGGAA 58.797 41.667 0.00 0.00 37.04 3.53
5420 6953 4.795469 TCCGTATGTAGTCACCTATTGGA 58.205 43.478 0.00 0.00 37.04 3.53
5421 6954 4.558898 GCTCCGTATGTAGTCACCTATTGG 60.559 50.000 0.00 0.00 39.83 3.16
5422 6955 4.037565 TGCTCCGTATGTAGTCACCTATTG 59.962 45.833 0.00 0.00 0.00 1.90
5423 6956 4.212716 TGCTCCGTATGTAGTCACCTATT 58.787 43.478 0.00 0.00 0.00 1.73
5424 6957 3.828921 TGCTCCGTATGTAGTCACCTAT 58.171 45.455 0.00 0.00 0.00 2.57
5425 6958 3.286329 TGCTCCGTATGTAGTCACCTA 57.714 47.619 0.00 0.00 0.00 3.08
5426 6959 2.139323 TGCTCCGTATGTAGTCACCT 57.861 50.000 0.00 0.00 0.00 4.00
5427 6960 2.953466 TTGCTCCGTATGTAGTCACC 57.047 50.000 0.00 0.00 0.00 4.02
5428 6961 4.868171 TCATTTTGCTCCGTATGTAGTCAC 59.132 41.667 0.00 0.00 0.00 3.67
5429 6962 5.079689 TCATTTTGCTCCGTATGTAGTCA 57.920 39.130 0.00 0.00 0.00 3.41
5430 6963 5.005779 CACTCATTTTGCTCCGTATGTAGTC 59.994 44.000 0.00 0.00 0.00 2.59
5431 6964 4.870426 CACTCATTTTGCTCCGTATGTAGT 59.130 41.667 0.00 0.00 0.00 2.73
5432 6965 5.109210 TCACTCATTTTGCTCCGTATGTAG 58.891 41.667 0.00 0.00 0.00 2.74
5433 6966 5.079689 TCACTCATTTTGCTCCGTATGTA 57.920 39.130 0.00 0.00 0.00 2.29
5434 6967 3.937814 TCACTCATTTTGCTCCGTATGT 58.062 40.909 0.00 0.00 0.00 2.29
5435 6968 4.944962 TTCACTCATTTTGCTCCGTATG 57.055 40.909 0.00 0.00 0.00 2.39
5436 6969 5.431765 AGATTCACTCATTTTGCTCCGTAT 58.568 37.500 0.00 0.00 0.00 3.06
5437 6970 4.832248 AGATTCACTCATTTTGCTCCGTA 58.168 39.130 0.00 0.00 0.00 4.02
5438 6971 3.679389 AGATTCACTCATTTTGCTCCGT 58.321 40.909 0.00 0.00 0.00 4.69
5439 6972 4.631377 TGTAGATTCACTCATTTTGCTCCG 59.369 41.667 0.00 0.00 0.00 4.63
5440 6973 5.645497 AGTGTAGATTCACTCATTTTGCTCC 59.355 40.000 0.00 0.00 44.07 4.70
5441 6974 6.734104 AGTGTAGATTCACTCATTTTGCTC 57.266 37.500 0.00 0.00 44.07 4.26
5473 7006 9.511272 ACTACAATATACGGATGTATGTAGACA 57.489 33.333 24.44 0.00 40.69 3.41
5474 7007 9.985318 GACTACAATATACGGATGTATGTAGAC 57.015 37.037 24.44 18.37 40.69 2.59
5475 7008 9.170734 GGACTACAATATACGGATGTATGTAGA 57.829 37.037 24.44 2.20 40.69 2.59
5476 7009 9.175312 AGGACTACAATATACGGATGTATGTAG 57.825 37.037 19.56 19.56 42.27 2.74
5477 7010 9.524496 AAGGACTACAATATACGGATGTATGTA 57.476 33.333 0.00 0.00 41.37 2.29
5478 7011 8.418597 AAGGACTACAATATACGGATGTATGT 57.581 34.615 0.00 0.00 41.37 2.29
5479 7012 9.706691 AAAAGGACTACAATATACGGATGTATG 57.293 33.333 0.00 0.00 41.37 2.39
5480 7013 9.706691 CAAAAGGACTACAATATACGGATGTAT 57.293 33.333 0.00 0.00 43.62 2.29
5481 7014 8.916062 TCAAAAGGACTACAATATACGGATGTA 58.084 33.333 0.00 0.00 34.45 2.29
5482 7015 7.788026 TCAAAAGGACTACAATATACGGATGT 58.212 34.615 0.00 0.00 0.00 3.06
5483 7016 8.657074 TTCAAAAGGACTACAATATACGGATG 57.343 34.615 0.00 0.00 0.00 3.51
5484 7017 9.847224 ATTTCAAAAGGACTACAATATACGGAT 57.153 29.630 0.00 0.00 0.00 4.18
5485 7018 9.104965 CATTTCAAAAGGACTACAATATACGGA 57.895 33.333 0.00 0.00 0.00 4.69
5486 7019 8.889717 ACATTTCAAAAGGACTACAATATACGG 58.110 33.333 0.00 0.00 0.00 4.02
5487 7020 9.916397 GACATTTCAAAAGGACTACAATATACG 57.084 33.333 0.00 0.00 0.00 3.06
5497 7030 9.190317 AGTCTTTTTAGACATTTCAAAAGGACT 57.810 29.630 17.95 17.95 45.74 3.85
5498 7031 9.803315 AAGTCTTTTTAGACATTTCAAAAGGAC 57.197 29.630 15.65 15.65 43.24 3.85
5511 7044 9.195831 CGTTGCGAAATATAAGTCTTTTTAGAC 57.804 33.333 0.00 0.00 39.00 2.59
5512 7045 8.385111 CCGTTGCGAAATATAAGTCTTTTTAGA 58.615 33.333 0.00 0.00 0.00 2.10
5513 7046 8.385111 TCCGTTGCGAAATATAAGTCTTTTTAG 58.615 33.333 0.00 0.00 0.00 1.85
5514 7047 8.254178 TCCGTTGCGAAATATAAGTCTTTTTA 57.746 30.769 0.00 0.00 0.00 1.52
5515 7048 7.136289 TCCGTTGCGAAATATAAGTCTTTTT 57.864 32.000 0.00 0.00 0.00 1.94
5516 7049 6.183360 CCTCCGTTGCGAAATATAAGTCTTTT 60.183 38.462 0.00 0.00 0.00 2.27
5517 7050 5.293569 CCTCCGTTGCGAAATATAAGTCTTT 59.706 40.000 0.00 0.00 0.00 2.52
5518 7051 4.809426 CCTCCGTTGCGAAATATAAGTCTT 59.191 41.667 0.00 0.00 0.00 3.01
5519 7052 4.369182 CCTCCGTTGCGAAATATAAGTCT 58.631 43.478 0.00 0.00 0.00 3.24
5520 7053 3.493503 CCCTCCGTTGCGAAATATAAGTC 59.506 47.826 0.00 0.00 0.00 3.01
5521 7054 3.133362 TCCCTCCGTTGCGAAATATAAGT 59.867 43.478 0.00 0.00 0.00 2.24
5522 7055 3.724374 TCCCTCCGTTGCGAAATATAAG 58.276 45.455 0.00 0.00 0.00 1.73
5523 7056 3.133362 ACTCCCTCCGTTGCGAAATATAA 59.867 43.478 0.00 0.00 0.00 0.98
5524 7057 2.696707 ACTCCCTCCGTTGCGAAATATA 59.303 45.455 0.00 0.00 0.00 0.86
5525 7058 1.485066 ACTCCCTCCGTTGCGAAATAT 59.515 47.619 0.00 0.00 0.00 1.28
5526 7059 0.899720 ACTCCCTCCGTTGCGAAATA 59.100 50.000 0.00 0.00 0.00 1.40
5527 7060 0.899720 TACTCCCTCCGTTGCGAAAT 59.100 50.000 0.00 0.00 0.00 2.17
5528 7061 0.245539 CTACTCCCTCCGTTGCGAAA 59.754 55.000 0.00 0.00 0.00 3.46
5529 7062 0.609957 TCTACTCCCTCCGTTGCGAA 60.610 55.000 0.00 0.00 0.00 4.70
5530 7063 0.609957 TTCTACTCCCTCCGTTGCGA 60.610 55.000 0.00 0.00 0.00 5.10
5531 7064 0.245539 TTTCTACTCCCTCCGTTGCG 59.754 55.000 0.00 0.00 0.00 4.85
5532 7065 2.467566 TTTTCTACTCCCTCCGTTGC 57.532 50.000 0.00 0.00 0.00 4.17
6047 8607 6.339587 TGGCCGATTTTCTTCAATAACTTT 57.660 33.333 0.00 0.00 0.00 2.66
6310 8901 6.485313 TCAGGTTCAATAAGACGAAACAATGT 59.515 34.615 0.00 0.00 30.97 2.71
6325 8916 8.613922 ATTATTTTCCCTTCATCAGGTTCAAT 57.386 30.769 0.00 0.00 42.02 2.57
6630 9239 8.332464 TCAAAGTAACTAAGTTGAATTGACACG 58.668 33.333 0.00 0.00 0.00 4.49
6661 9275 5.991328 ATGTGCACTATATTTTCGGACAG 57.009 39.130 19.41 0.00 31.30 3.51
6866 9480 8.667463 CACATTGGTTTTCATGAAAGTCTTTTT 58.333 29.630 19.64 3.08 0.00 1.94
6867 9481 7.201635 GCACATTGGTTTTCATGAAAGTCTTTT 60.202 33.333 19.64 3.89 0.00 2.27
6868 9482 6.258507 GCACATTGGTTTTCATGAAAGTCTTT 59.741 34.615 19.64 0.00 0.00 2.52
6869 9483 5.754890 GCACATTGGTTTTCATGAAAGTCTT 59.245 36.000 19.64 4.35 0.00 3.01
6870 9484 5.163426 TGCACATTGGTTTTCATGAAAGTCT 60.163 36.000 19.64 3.55 0.00 3.24
6871 9485 5.049167 TGCACATTGGTTTTCATGAAAGTC 58.951 37.500 19.64 16.11 0.00 3.01
6872 9486 4.810491 GTGCACATTGGTTTTCATGAAAGT 59.190 37.500 19.64 11.09 0.00 2.66
6873 9487 4.809958 TGTGCACATTGGTTTTCATGAAAG 59.190 37.500 17.42 10.49 0.00 2.62
6874 9488 4.763073 TGTGCACATTGGTTTTCATGAAA 58.237 34.783 17.42 16.91 0.00 2.69
6875 9489 4.397481 TGTGCACATTGGTTTTCATGAA 57.603 36.364 17.42 3.38 0.00 2.57
6876 9490 4.603989 ATGTGCACATTGGTTTTCATGA 57.396 36.364 26.61 0.00 31.37 3.07
6877 9491 6.971527 ATAATGTGCACATTGGTTTTCATG 57.028 33.333 41.69 0.00 45.34 3.07
6878 9492 9.100554 CATAATAATGTGCACATTGGTTTTCAT 57.899 29.630 41.69 27.74 45.34 2.57
6879 9493 7.548427 CCATAATAATGTGCACATTGGTTTTCA 59.452 33.333 41.69 26.94 45.34 2.69
6880 9494 7.011295 CCCATAATAATGTGCACATTGGTTTTC 59.989 37.037 41.69 6.02 45.34 2.29
6881 9495 6.822676 CCCATAATAATGTGCACATTGGTTTT 59.177 34.615 41.69 31.18 45.34 2.43
6882 9496 6.155910 TCCCATAATAATGTGCACATTGGTTT 59.844 34.615 41.69 33.00 45.34 3.27
6907 9521 5.011329 TGAATTTGTTAGGTACTCACTCCGT 59.989 40.000 0.00 0.00 41.75 4.69
6944 9558 6.238566 GGTTTATTCGCCCTACTTTGGTAATC 60.239 42.308 0.00 0.00 0.00 1.75
6949 9563 3.349022 TGGTTTATTCGCCCTACTTTGG 58.651 45.455 0.00 0.00 0.00 3.28
7025 9642 6.115446 TGTCAAGTAATTCCTAGGCAATCTG 58.885 40.000 2.96 0.00 0.00 2.90
7188 9922 5.008316 AGTGGTTCCTTTTGAAACGTACATC 59.992 40.000 0.00 0.00 44.06 3.06
7238 10241 1.733402 TTTGCCAAGAACCTGCACCG 61.733 55.000 0.00 0.00 34.16 4.94
7240 10243 1.069049 ACATTTGCCAAGAACCTGCAC 59.931 47.619 0.00 0.00 34.16 4.57
7322 10325 8.701895 ACTCCGTAAACCAATTATAGATGAAGA 58.298 33.333 0.00 0.00 0.00 2.87
7370 10948 1.001378 CGGAGTTTTCTGTTTGCCCAG 60.001 52.381 0.00 0.00 0.00 4.45
7637 11272 1.851021 TTCCAAACATCACGCTGGCG 61.851 55.000 13.56 13.56 46.03 5.69
7853 11489 8.516234 TGTAATAACGGTGCAATATTTGAACTT 58.484 29.630 0.00 0.00 39.29 2.66
8057 11695 9.012161 GTACGGGAAAGATCTACAATATACTCT 57.988 37.037 0.00 0.00 0.00 3.24
8098 11738 2.416162 GCTACTCTCCCTGAAGTGTTCG 60.416 54.545 0.00 0.00 0.00 3.95
8289 11933 7.221452 GTCGTATCTCTTTTGGAAAGCGTATAA 59.779 37.037 0.00 0.00 0.00 0.98
8314 11959 3.220110 TCCGAGGAATATAGCTTCACGT 58.780 45.455 0.00 0.00 0.00 4.49
8315 11960 3.366476 CCTCCGAGGAATATAGCTTCACG 60.366 52.174 9.01 0.00 37.67 4.35
8316 11961 3.827302 TCCTCCGAGGAATATAGCTTCAC 59.173 47.826 15.21 0.00 42.51 3.18
8598 12254 2.697431 TAAAAGATGGTTGCGTGCAC 57.303 45.000 6.82 6.82 0.00 4.57
8665 12321 1.453669 CTGGAGATGCCCTTAGCCC 59.546 63.158 0.00 0.00 42.71 5.19
9155 12813 1.286553 GAGAGAGGAGAGGGAGGAACA 59.713 57.143 0.00 0.00 0.00 3.18


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

AutoCloner maintained by Alex Coulton.