Multiple sequence alignment - TraesCS5D01G111500

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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 TraesCS5D01G111500 chr5D 100.000 7539 0 0 1 7539 126574670 126567132 0.000000e+00 13923.0
1 TraesCS5D01G111500 chr5D 86.121 281 29 6 4426 4704 139449324 139449596 2.060000e-75 294.0
2 TraesCS5D01G111500 chr5D 78.093 388 43 33 2913 3269 167035839 167036215 2.760000e-49 207.0
3 TraesCS5D01G111500 chr5D 96.491 114 4 0 4591 4704 126569949 126569836 9.990000e-44 189.0
4 TraesCS5D01G111500 chr5D 96.491 114 4 0 4722 4835 126570080 126569967 9.990000e-44 189.0
5 TraesCS5D01G111500 chr5D 81.600 250 26 18 3062 3300 190492000 190492240 9.990000e-44 189.0
6 TraesCS5D01G111500 chr5D 79.195 149 14 11 2957 3097 159301663 159301802 3.750000e-13 87.9
7 TraesCS5D01G111500 chr5D 90.769 65 5 1 2239 2303 255076525 255076462 1.350000e-12 86.1
8 TraesCS5D01G111500 chr5D 87.931 58 5 1 2241 2296 462076908 462076851 4.880000e-07 67.6
9 TraesCS5D01G111500 chr5A 95.391 4752 157 29 1 4704 141883309 141878572 0.000000e+00 7505.0
10 TraesCS5D01G111500 chr5A 96.078 2830 65 15 4722 7539 141878686 141875891 0.000000e+00 4569.0
11 TraesCS5D01G111500 chr5A 82.800 250 26 17 3062 3300 229505363 229505120 2.760000e-49 207.0
12 TraesCS5D01G111500 chr5A 77.692 390 44 30 2913 3269 218605390 218605011 1.660000e-46 198.0
13 TraesCS5D01G111500 chr5A 76.050 238 34 19 2870 3097 78433080 78432856 1.340000e-17 102.0
14 TraesCS5D01G111500 chr5A 89.552 67 5 2 2239 2305 338287874 338287810 4.850000e-12 84.2
15 TraesCS5D01G111500 chr5A 97.436 39 1 0 7309 7347 599815531 599815569 4.880000e-07 67.6
16 TraesCS5D01G111500 chr5B 95.127 2442 74 15 536 2947 139351768 139349342 0.000000e+00 3808.0
17 TraesCS5D01G111500 chr5B 95.914 1762 54 4 2943 4704 139343830 139342087 0.000000e+00 2839.0
18 TraesCS5D01G111500 chr5B 96.927 1074 19 4 5209 6276 139341758 139340693 0.000000e+00 1788.0
19 TraesCS5D01G111500 chr5B 91.922 718 26 10 6339 7050 139340373 139339682 0.000000e+00 976.0
20 TraesCS5D01G111500 chr5B 97.279 441 12 0 4722 5162 139342200 139341760 0.000000e+00 749.0
21 TraesCS5D01G111500 chr5B 89.894 564 41 11 1 556 139352905 139352350 0.000000e+00 712.0
22 TraesCS5D01G111500 chr5B 78.621 145 23 7 2957 3097 153881967 153882107 1.040000e-13 89.8
23 TraesCS5D01G111500 chr5B 89.474 57 6 0 2240 2296 568404291 568404235 1.050000e-08 73.1
24 TraesCS5D01G111500 chr2A 87.342 316 20 2 4409 4704 13020810 13020495 2.010000e-90 344.0
25 TraesCS5D01G111500 chr2A 75.217 230 41 14 2874 3097 339088499 339088280 2.240000e-15 95.3
26 TraesCS5D01G111500 chr4B 87.248 298 36 1 4409 4704 22911199 22911496 9.370000e-89 339.0
27 TraesCS5D01G111500 chr4B 83.036 224 25 11 3025 3243 347374339 347374124 2.780000e-44 191.0
28 TraesCS5D01G111500 chr4B 89.796 49 4 1 7362 7410 593381030 593380983 2.270000e-05 62.1
29 TraesCS5D01G111500 chr3B 85.714 315 25 4 4410 4704 342869957 342869643 1.580000e-81 315.0
30 TraesCS5D01G111500 chr3B 85.926 135 15 4 4711 4843 71405169 71405301 2.840000e-29 141.0
31 TraesCS5D01G111500 chr1A 85.897 312 24 4 4412 4704 208883814 208884124 1.580000e-81 315.0
32 TraesCS5D01G111500 chr1A 95.322 171 7 1 4409 4579 292773762 292773931 3.470000e-68 270.0
33 TraesCS5D01G111500 chr1A 90.323 124 12 0 4722 4845 208884011 208884134 6.050000e-36 163.0
34 TraesCS5D01G111500 chr1A 91.176 68 2 2 2240 2303 398460992 398460925 1.040000e-13 89.8
35 TraesCS5D01G111500 chr6A 85.911 291 21 11 4403 4676 61027789 61027502 7.400000e-75 292.0
36 TraesCS5D01G111500 chr6A 79.167 168 34 1 7373 7539 537465550 537465383 1.720000e-21 115.0
37 TraesCS5D01G111500 chr1B 83.486 327 30 9 4371 4674 424541232 424541557 4.450000e-72 283.0
38 TraesCS5D01G111500 chr1B 90.840 131 11 1 4574 4704 309493678 309493807 2.800000e-39 174.0
39 TraesCS5D01G111500 chr1B 90.625 64 6 0 2240 2303 565664564 565664627 1.350000e-12 86.1
40 TraesCS5D01G111500 chr1B 89.552 67 3 2 2240 2302 429597353 429597287 1.740000e-11 82.4
41 TraesCS5D01G111500 chr1B 87.234 47 5 1 7373 7418 613188791 613188745 1.400000e-02 52.8
42 TraesCS5D01G111500 chr1D 95.238 168 8 0 4408 4575 148657432 148657599 4.480000e-67 267.0
43 TraesCS5D01G111500 chr1D 89.706 68 3 2 2240 2303 317439596 317439529 4.850000e-12 84.2
44 TraesCS5D01G111500 chr7B 84.454 238 14 5 4488 4704 511301835 511302070 5.930000e-51 213.0
45 TraesCS5D01G111500 chr7B 91.597 119 10 0 4722 4840 511301957 511302075 1.680000e-36 165.0
46 TraesCS5D01G111500 chr7B 80.108 186 29 6 3668 3850 261051735 261051915 1.710000e-26 132.0
47 TraesCS5D01G111500 chr7D 83.500 200 25 4 7311 7503 165859959 165859761 6.010000e-41 180.0
48 TraesCS5D01G111500 chr7D 75.000 216 42 11 2886 3097 184173694 184173487 1.040000e-13 89.8
49 TraesCS5D01G111500 chr7D 76.571 175 27 11 2929 3097 184173717 184173883 4.850000e-12 84.2
50 TraesCS5D01G111500 chr7D 92.000 50 2 2 3048 3097 360360599 360360646 1.360000e-07 69.4
51 TraesCS5D01G111500 chr3D 91.597 119 9 1 4722 4840 104810014 104809897 6.050000e-36 163.0
52 TraesCS5D01G111500 chr3D 77.333 150 18 12 2954 3097 604308704 604308565 2.920000e-09 75.0
53 TraesCS5D01G111500 chr4A 90.833 120 10 1 4722 4841 464563341 464563459 7.830000e-35 159.0
54 TraesCS5D01G111500 chr4A 83.117 154 19 6 3025 3173 292092365 292092214 4.750000e-27 134.0
55 TraesCS5D01G111500 chr6D 90.000 120 11 1 4722 4841 271609775 271609893 3.640000e-33 154.0
56 TraesCS5D01G111500 chr6D 75.325 231 39 15 2874 3097 126368434 126368215 2.240000e-15 95.3
57 TraesCS5D01G111500 chr4D 90.000 120 11 1 4722 4841 502760643 502760761 3.640000e-33 154.0
58 TraesCS5D01G111500 chr4D 81.818 176 19 8 7311 7477 170707735 170707906 1.320000e-27 135.0
59 TraesCS5D01G111500 chr4D 84.507 142 15 6 3025 3161 214335722 214335861 4.750000e-27 134.0
60 TraesCS5D01G111500 chr4D 75.238 315 51 19 2870 3173 277407920 277407622 2.860000e-24 124.0
61 TraesCS5D01G111500 chr4D 88.889 63 7 0 2241 2303 486932211 486932149 2.260000e-10 78.7
62 TraesCS5D01G111500 chr4D 86.538 52 7 0 2245 2296 89432377 89432428 2.940000e-04 58.4
63 TraesCS5D01G111500 chr7A 77.093 227 43 7 3628 3850 309411575 309411796 1.030000e-23 122.0
64 TraesCS5D01G111500 chr6B 82.301 113 16 4 3132 3244 691636923 691636815 2.240000e-15 95.3
65 TraesCS5D01G111500 chr2D 90.625 64 6 0 2240 2303 394525197 394525134 1.350000e-12 86.1
66 TraesCS5D01G111500 chr2D 90.244 41 3 1 7373 7412 377054931 377054891 1.400000e-02 52.8
67 TraesCS5D01G111500 chr2B 90.625 64 6 0 2240 2303 466165305 466165242 1.350000e-12 86.1


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 TraesCS5D01G111500 chr5D 126567132 126574670 7538 True 13923 13923 100.0000 1 7539 1 chr5D.!!$R1 7538
1 TraesCS5D01G111500 chr5A 141875891 141883309 7418 True 6037 7505 95.7345 1 7539 2 chr5A.!!$R5 7538
2 TraesCS5D01G111500 chr5B 139349342 139352905 3563 True 2260 3808 92.5105 1 2947 2 chr5B.!!$R3 2946
3 TraesCS5D01G111500 chr5B 139339682 139343830 4148 True 1588 2839 95.5105 2943 7050 4 chr5B.!!$R2 4107

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
601 1214 2.572191 AATGGAACTGCATTGCGATG 57.428 45.000 9.80 9.8 36.32 3.84 F
1657 2308 0.036388 TTTAGTGGAGCTCTTGGGCG 60.036 55.000 14.64 0.0 37.29 6.13 F
1718 2373 3.119352 GGCAGGTTGATGATTTCACTTCC 60.119 47.826 0.00 0.0 32.84 3.46 F
3038 3727 0.725686 CGTCAAGATCCAAGCAGCAG 59.274 55.000 0.00 0.0 0.00 4.24 F
3820 4512 0.331278 TGTGGGGTTGATGATGGGTC 59.669 55.000 0.00 0.0 0.00 4.46 F
4795 5489 0.521735 GCCATCACAACCGAAAGTCC 59.478 55.000 0.00 0.0 0.00 3.85 F
5578 6280 0.317160 ACGGTCTTGATGTGCGAGAA 59.683 50.000 0.00 0.0 38.75 2.87 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2482 3141 0.525761 TAGCAAATTGACGGCTTGCC 59.474 50.000 9.88 0.75 45.23 4.52 R
3018 3707 0.674581 TGCTGCTTGGATCTTGACGG 60.675 55.000 0.00 0.00 0.00 4.79 R
3462 4151 1.134220 TGTCCAACCAACCAGACAGTC 60.134 52.381 0.00 0.00 34.44 3.51 R
4776 5470 0.521735 GGACTTTCGGTTGTGATGGC 59.478 55.000 0.00 0.00 0.00 4.40 R
5352 6048 1.117150 ATAGCCCTGCAAAGCATTGG 58.883 50.000 10.03 0.00 38.13 3.16 R
6125 6836 0.549950 CCATGGAGAGGCTGGAATGT 59.450 55.000 5.56 0.00 31.38 2.71 R
7507 8511 0.571661 GCACAACACAAACATGCACG 59.428 50.000 0.00 0.00 36.30 5.34 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
306 314 7.660208 GGTACATGGTCCTAATCACGAATATTT 59.340 37.037 0.00 0.00 0.00 1.40
419 427 6.374333 TGACATGGGTATCTTTCTAAAAGCAC 59.626 38.462 0.00 0.00 0.00 4.40
492 500 4.124238 CTCACCACCGTTCTTTCTTTGTA 58.876 43.478 0.00 0.00 0.00 2.41
529 537 4.764050 TCAGTTTCCAGTTTCTGTACCA 57.236 40.909 0.00 0.00 0.00 3.25
567 1180 6.378661 TCCTCTATGGTTCCCAATCATATG 57.621 41.667 0.00 0.00 36.95 1.78
601 1214 2.572191 AATGGAACTGCATTGCGATG 57.428 45.000 9.80 9.80 36.32 3.84
634 1247 6.128363 GCAAGACAAAATAGTGTGGTACTACC 60.128 42.308 6.93 0.00 44.30 3.18
789 1409 5.640158 TTTCCAACTGGAGGACTTCTTTA 57.360 39.130 0.00 0.00 46.36 1.85
902 1522 4.823989 CCTCCATTTTCCTAGAAATCGCAT 59.176 41.667 0.00 0.00 0.00 4.73
908 1528 2.972348 TCCTAGAAATCGCATACCCCT 58.028 47.619 0.00 0.00 0.00 4.79
985 1613 2.933878 TTCTTCACGCGCCCAACACT 62.934 55.000 5.73 0.00 0.00 3.55
1192 1820 2.328099 CCAAGCTCAGGACCGCAAC 61.328 63.158 0.00 0.00 0.00 4.17
1207 1857 2.293122 CCGCAACCTTTGAATGAGTGAA 59.707 45.455 0.00 0.00 0.00 3.18
1214 1864 6.773976 ACCTTTGAATGAGTGAACTTTGAA 57.226 33.333 0.00 0.00 0.00 2.69
1219 1869 4.024893 TGAATGAGTGAACTTTGAAGCGAC 60.025 41.667 0.00 0.00 0.00 5.19
1333 1984 1.617947 GGTCCACGCTCCAATCTCCT 61.618 60.000 0.00 0.00 0.00 3.69
1565 2216 7.699391 AGCTCACAAAATCATGTCAATTATTCG 59.301 33.333 0.00 0.00 0.00 3.34
1569 2220 8.914654 CACAAAATCATGTCAATTATTCGTGTT 58.085 29.630 0.00 0.00 0.00 3.32
1657 2308 0.036388 TTTAGTGGAGCTCTTGGGCG 60.036 55.000 14.64 0.00 37.29 6.13
1677 2328 3.444034 GCGGATAGCCTGATACAGTCATA 59.556 47.826 0.00 0.00 40.81 2.15
1718 2373 3.119352 GGCAGGTTGATGATTTCACTTCC 60.119 47.826 0.00 0.00 32.84 3.46
1761 2416 4.400251 GGAAGATGATGGATGCAAACAAGA 59.600 41.667 0.00 0.00 0.00 3.02
1805 2460 8.908903 ACCTCTACTATTCAGTCAACTTCTATG 58.091 37.037 0.00 0.00 36.14 2.23
1887 2542 5.424757 TGTATGGTACTGACAAATGCTACC 58.575 41.667 0.00 0.00 0.00 3.18
2238 2897 6.612049 ACTTAGAGATAAGAATTCCTTCCCGT 59.388 38.462 0.65 0.00 36.34 5.28
2346 3005 7.970102 AGTTTTGTACTTTGTACCTATCAGGA 58.030 34.615 0.00 0.00 33.99 3.86
2482 3141 3.259123 CCAAAAGGGTTCCTGGAAATGAG 59.741 47.826 11.40 0.00 32.13 2.90
2606 3265 6.430000 ACCAATTGAGTATTAACTGACACACC 59.570 38.462 7.12 0.00 35.56 4.16
2794 3453 7.913674 ACTTAAGTTCTTGCTTATCAGAAGG 57.086 36.000 1.12 0.00 31.83 3.46
2848 3507 4.201970 TGTTAAAACGTTCTTCCTGCCAAG 60.202 41.667 0.00 0.00 0.00 3.61
2937 3596 3.768468 GGGTGAAACACGAAGAACAAA 57.232 42.857 0.00 0.00 39.98 2.83
2951 3610 6.530181 ACGAAGAACAAATGTGGAAAACTTTC 59.470 34.615 0.00 0.00 36.46 2.62
3015 3704 4.701651 TCAAATCTCATGCCAAAACGAGAT 59.298 37.500 0.00 0.00 44.99 2.75
3018 3707 0.810648 TCATGCCAAAACGAGATGCC 59.189 50.000 0.00 0.00 0.00 4.40
3038 3727 0.725686 CGTCAAGATCCAAGCAGCAG 59.274 55.000 0.00 0.00 0.00 4.24
3116 3805 8.214364 GTCTTGAGAGATAGTTATTCCCCAATT 58.786 37.037 0.00 0.00 33.70 2.32
3314 4003 2.664015 GGGAGATACACGGACCTTACT 58.336 52.381 0.00 0.00 0.00 2.24
3380 4069 2.520536 GGGACAGTCTGGTGGTGCT 61.521 63.158 4.53 0.00 0.00 4.40
3461 4150 3.345808 GCGAGCGCCAACAAGACA 61.346 61.111 2.29 0.00 34.56 3.41
3462 4151 2.856032 CGAGCGCCAACAAGACAG 59.144 61.111 2.29 0.00 0.00 3.51
3648 4339 2.030027 TCCTTCCTTGCTTCTCCAGA 57.970 50.000 0.00 0.00 0.00 3.86
3654 4346 4.581309 TCCTTGCTTCTCCAGATTCATT 57.419 40.909 0.00 0.00 0.00 2.57
3664 4356 8.099537 GCTTCTCCAGATTCATTCCTTCATATA 58.900 37.037 0.00 0.00 0.00 0.86
3728 4420 5.911178 TCTCATCCAAATACATAGGGACCTT 59.089 40.000 0.00 0.00 31.04 3.50
3763 4455 0.518636 CACCTCAGTTTGATGGCACG 59.481 55.000 0.00 0.00 0.00 5.34
3820 4512 0.331278 TGTGGGGTTGATGATGGGTC 59.669 55.000 0.00 0.00 0.00 4.46
4353 5045 9.573133 CTGATTGAAAACCAAATTACCATAGAC 57.427 33.333 0.00 0.00 38.43 2.59
4371 5063 8.041323 ACCATAGACGTGTTTTCTTTGAGATAT 58.959 33.333 0.00 0.00 0.00 1.63
4372 5064 9.529325 CCATAGACGTGTTTTCTTTGAGATATA 57.471 33.333 0.00 0.00 0.00 0.86
4376 5068 9.436957 AGACGTGTTTTCTTTGAGATATAATGT 57.563 29.630 0.00 0.00 0.00 2.71
4534 5226 3.678548 GGAAGTCAACACGTGAATAGACC 59.321 47.826 25.01 12.74 38.23 3.85
4628 5322 5.329399 AGACCTTAGGCTCTGATACCATAG 58.671 45.833 0.00 0.00 0.00 2.23
4637 5331 5.157781 GCTCTGATACCATAGTAAGCTTCG 58.842 45.833 0.00 0.00 29.61 3.79
4638 5332 5.122512 TCTGATACCATAGTAAGCTTCGC 57.877 43.478 0.00 0.00 30.59 4.70
4639 5333 4.583073 TCTGATACCATAGTAAGCTTCGCA 59.417 41.667 0.00 0.00 30.59 5.10
4657 5351 1.078709 CACACTAGCCATCACAACCG 58.921 55.000 0.00 0.00 0.00 4.44
4685 5379 4.587684 TCCGAACTAATAGAAAGGGCTAGG 59.412 45.833 0.00 0.00 0.00 3.02
4686 5380 4.308265 CGAACTAATAGAAAGGGCTAGGC 58.692 47.826 8.00 8.00 0.00 3.93
4687 5381 4.202223 CGAACTAATAGAAAGGGCTAGGCA 60.202 45.833 19.14 0.00 0.00 4.75
4688 5382 5.681639 GAACTAATAGAAAGGGCTAGGCAA 58.318 41.667 19.14 0.00 0.00 4.52
4689 5383 5.913946 ACTAATAGAAAGGGCTAGGCAAT 57.086 39.130 19.14 2.76 0.00 3.56
4690 5384 5.870706 ACTAATAGAAAGGGCTAGGCAATC 58.129 41.667 19.14 12.21 0.00 2.67
4691 5385 3.797559 ATAGAAAGGGCTAGGCAATCC 57.202 47.619 19.14 4.38 0.00 3.01
4692 5386 1.298953 AGAAAGGGCTAGGCAATCCA 58.701 50.000 19.14 0.00 33.74 3.41
4693 5387 1.064389 AGAAAGGGCTAGGCAATCCAC 60.064 52.381 19.14 0.00 33.74 4.02
4694 5388 0.704076 AAAGGGCTAGGCAATCCACA 59.296 50.000 19.14 0.00 33.74 4.17
4695 5389 0.929244 AAGGGCTAGGCAATCCACAT 59.071 50.000 19.14 0.00 33.74 3.21
4696 5390 1.819753 AGGGCTAGGCAATCCACATA 58.180 50.000 19.14 0.00 33.74 2.29
4697 5391 2.352371 AGGGCTAGGCAATCCACATAT 58.648 47.619 19.14 0.00 33.74 1.78
4698 5392 3.531059 AGGGCTAGGCAATCCACATATA 58.469 45.455 19.14 0.00 33.74 0.86
4699 5393 3.264450 AGGGCTAGGCAATCCACATATAC 59.736 47.826 19.14 0.00 33.74 1.47
4700 5394 3.009033 GGGCTAGGCAATCCACATATACA 59.991 47.826 19.14 0.00 33.74 2.29
4701 5395 4.003648 GGCTAGGCAATCCACATATACAC 58.996 47.826 12.16 0.00 33.74 2.90
4702 5396 4.263068 GGCTAGGCAATCCACATATACACT 60.263 45.833 12.16 0.00 33.74 3.55
4703 5397 5.308825 GCTAGGCAATCCACATATACACTT 58.691 41.667 0.00 0.00 33.74 3.16
4704 5398 5.180117 GCTAGGCAATCCACATATACACTTG 59.820 44.000 0.00 0.00 33.74 3.16
4705 5399 5.372343 AGGCAATCCACATATACACTTGA 57.628 39.130 0.00 0.00 33.74 3.02
4706 5400 5.126067 AGGCAATCCACATATACACTTGAC 58.874 41.667 0.00 0.00 33.74 3.18
4707 5401 4.275936 GGCAATCCACATATACACTTGACC 59.724 45.833 0.00 0.00 0.00 4.02
4708 5402 5.126067 GCAATCCACATATACACTTGACCT 58.874 41.667 0.00 0.00 0.00 3.85
4709 5403 5.590259 GCAATCCACATATACACTTGACCTT 59.410 40.000 0.00 0.00 0.00 3.50
4710 5404 6.765989 GCAATCCACATATACACTTGACCTTA 59.234 38.462 0.00 0.00 0.00 2.69
4711 5405 7.041780 GCAATCCACATATACACTTGACCTTAG 60.042 40.741 0.00 0.00 0.00 2.18
4712 5406 6.479972 TCCACATATACACTTGACCTTAGG 57.520 41.667 0.00 0.00 0.00 2.69
4713 5407 5.057149 CCACATATACACTTGACCTTAGGC 58.943 45.833 0.00 0.00 0.00 3.93
4714 5408 5.163301 CCACATATACACTTGACCTTAGGCT 60.163 44.000 0.00 0.00 0.00 4.58
4715 5409 5.986135 CACATATACACTTGACCTTAGGCTC 59.014 44.000 0.00 0.00 0.00 4.70
4716 5410 5.900123 ACATATACACTTGACCTTAGGCTCT 59.100 40.000 0.00 0.00 0.00 4.09
4717 5411 4.744795 ATACACTTGACCTTAGGCTCTG 57.255 45.455 0.00 0.00 0.00 3.35
4718 5412 2.609747 ACACTTGACCTTAGGCTCTGA 58.390 47.619 0.00 0.00 0.00 3.27
4719 5413 3.177228 ACACTTGACCTTAGGCTCTGAT 58.823 45.455 0.00 0.00 0.00 2.90
4720 5414 4.353777 ACACTTGACCTTAGGCTCTGATA 58.646 43.478 0.00 0.00 0.00 2.15
4721 5415 4.160626 ACACTTGACCTTAGGCTCTGATAC 59.839 45.833 0.00 0.00 0.00 2.24
4722 5416 4.160439 CACTTGACCTTAGGCTCTGATACA 59.840 45.833 0.00 0.00 0.00 2.29
4723 5417 4.404073 ACTTGACCTTAGGCTCTGATACAG 59.596 45.833 0.00 0.00 0.00 2.74
4724 5418 3.300388 TGACCTTAGGCTCTGATACAGG 58.700 50.000 0.00 0.00 31.51 4.00
4725 5419 3.052869 TGACCTTAGGCTCTGATACAGGA 60.053 47.826 0.00 0.00 31.51 3.86
4726 5420 3.301274 ACCTTAGGCTCTGATACAGGAC 58.699 50.000 0.00 0.00 31.51 3.85
4727 5421 3.052490 ACCTTAGGCTCTGATACAGGACT 60.052 47.826 0.00 0.00 31.51 3.85
4728 5422 3.964031 CCTTAGGCTCTGATACAGGACTT 59.036 47.826 0.00 0.00 31.51 3.01
4729 5423 4.202202 CCTTAGGCTCTGATACAGGACTTG 60.202 50.000 0.00 0.00 31.51 3.16
4730 5424 3.107402 AGGCTCTGATACAGGACTTGA 57.893 47.619 0.00 0.00 31.51 3.02
4731 5425 3.445008 AGGCTCTGATACAGGACTTGAA 58.555 45.455 0.00 0.00 31.51 2.69
4732 5426 3.196685 AGGCTCTGATACAGGACTTGAAC 59.803 47.826 0.00 0.00 31.51 3.18
4733 5427 3.055819 GGCTCTGATACAGGACTTGAACA 60.056 47.826 0.00 0.00 31.51 3.18
4734 5428 3.929610 GCTCTGATACAGGACTTGAACAC 59.070 47.826 0.00 0.00 31.51 3.32
4735 5429 4.561530 GCTCTGATACAGGACTTGAACACA 60.562 45.833 0.00 0.00 31.51 3.72
4736 5430 5.541845 CTCTGATACAGGACTTGAACACAA 58.458 41.667 0.00 0.00 31.51 3.33
4737 5431 5.541845 TCTGATACAGGACTTGAACACAAG 58.458 41.667 8.18 8.18 38.39 3.16
4738 5432 5.304357 TCTGATACAGGACTTGAACACAAGA 59.696 40.000 15.32 0.00 37.31 3.02
4739 5433 5.297547 TGATACAGGACTTGAACACAAGAC 58.702 41.667 15.32 9.71 42.26 3.01
4745 5439 4.065789 GGACTTGAACACAAGACCTTAGG 58.934 47.826 18.47 0.00 45.56 2.69
4746 5440 3.477530 ACTTGAACACAAGACCTTAGGC 58.522 45.455 15.32 0.00 42.26 3.93
4747 5441 3.136626 ACTTGAACACAAGACCTTAGGCT 59.863 43.478 15.32 0.00 42.26 4.58
4748 5442 3.402628 TGAACACAAGACCTTAGGCTC 57.597 47.619 0.00 0.00 0.00 4.70
4749 5443 2.972713 TGAACACAAGACCTTAGGCTCT 59.027 45.455 0.00 0.00 0.00 4.09
4750 5444 3.244215 TGAACACAAGACCTTAGGCTCTG 60.244 47.826 0.00 0.00 0.00 3.35
4751 5445 2.609747 ACACAAGACCTTAGGCTCTGA 58.390 47.619 0.00 0.00 0.00 3.27
4752 5446 3.177228 ACACAAGACCTTAGGCTCTGAT 58.823 45.455 0.00 0.00 0.00 2.90
4753 5447 4.353777 ACACAAGACCTTAGGCTCTGATA 58.646 43.478 0.00 0.00 0.00 2.15
4754 5448 4.160626 ACACAAGACCTTAGGCTCTGATAC 59.839 45.833 0.00 0.00 0.00 2.24
4755 5449 3.707102 ACAAGACCTTAGGCTCTGATACC 59.293 47.826 0.00 0.00 0.00 2.73
4756 5450 3.689872 AGACCTTAGGCTCTGATACCA 57.310 47.619 0.00 0.00 0.00 3.25
4757 5451 4.206244 AGACCTTAGGCTCTGATACCAT 57.794 45.455 0.00 0.00 0.00 3.55
4758 5452 5.340891 AGACCTTAGGCTCTGATACCATA 57.659 43.478 0.00 0.00 0.00 2.74
4759 5453 5.909760 AGACCTTAGGCTCTGATACCATAT 58.090 41.667 0.00 0.00 0.00 1.78
4760 5454 6.326970 AGACCTTAGGCTCTGATACCATATT 58.673 40.000 0.00 0.00 0.00 1.28
4761 5455 7.479579 AGACCTTAGGCTCTGATACCATATTA 58.520 38.462 0.00 0.00 0.00 0.98
4762 5456 7.956315 AGACCTTAGGCTCTGATACCATATTAA 59.044 37.037 0.00 0.00 0.00 1.40
4763 5457 8.140112 ACCTTAGGCTCTGATACCATATTAAG 57.860 38.462 0.00 0.38 0.00 1.85
4764 5458 7.044798 CCTTAGGCTCTGATACCATATTAAGC 58.955 42.308 0.00 0.00 0.00 3.09
4765 5459 7.093112 CCTTAGGCTCTGATACCATATTAAGCT 60.093 40.741 0.00 0.00 0.00 3.74
4766 5460 6.694445 AGGCTCTGATACCATATTAAGCTT 57.306 37.500 3.48 3.48 0.00 3.74
4767 5461 6.706295 AGGCTCTGATACCATATTAAGCTTC 58.294 40.000 0.00 0.00 0.00 3.86
4768 5462 6.270927 AGGCTCTGATACCATATTAAGCTTCA 59.729 38.462 0.00 0.00 0.00 3.02
4769 5463 6.370166 GGCTCTGATACCATATTAAGCTTCAC 59.630 42.308 0.00 0.00 0.00 3.18
4770 5464 6.931281 GCTCTGATACCATATTAAGCTTCACA 59.069 38.462 0.00 0.00 0.00 3.58
4771 5465 7.095439 GCTCTGATACCATATTAAGCTTCACAC 60.095 40.741 0.00 0.00 0.00 3.82
4772 5466 7.791029 TCTGATACCATATTAAGCTTCACACA 58.209 34.615 0.00 0.00 0.00 3.72
4773 5467 7.710907 TCTGATACCATATTAAGCTTCACACAC 59.289 37.037 0.00 0.00 0.00 3.82
4774 5468 7.564793 TGATACCATATTAAGCTTCACACACT 58.435 34.615 0.00 0.00 0.00 3.55
4775 5469 8.700973 TGATACCATATTAAGCTTCACACACTA 58.299 33.333 0.00 0.00 0.00 2.74
4776 5470 9.197694 GATACCATATTAAGCTTCACACACTAG 57.802 37.037 0.00 0.00 0.00 2.57
4777 5471 5.817816 ACCATATTAAGCTTCACACACTAGC 59.182 40.000 0.00 0.00 35.16 3.42
4778 5472 5.237344 CCATATTAAGCTTCACACACTAGCC 59.763 44.000 0.00 0.00 35.53 3.93
4779 5473 3.762407 TTAAGCTTCACACACTAGCCA 57.238 42.857 0.00 0.00 35.53 4.75
4780 5474 2.867109 AAGCTTCACACACTAGCCAT 57.133 45.000 0.00 0.00 35.53 4.40
4781 5475 2.393271 AGCTTCACACACTAGCCATC 57.607 50.000 0.00 0.00 35.53 3.51
4782 5476 1.625315 AGCTTCACACACTAGCCATCA 59.375 47.619 0.00 0.00 35.53 3.07
4783 5477 1.734465 GCTTCACACACTAGCCATCAC 59.266 52.381 0.00 0.00 0.00 3.06
4784 5478 2.871637 GCTTCACACACTAGCCATCACA 60.872 50.000 0.00 0.00 0.00 3.58
4785 5479 3.402110 CTTCACACACTAGCCATCACAA 58.598 45.455 0.00 0.00 0.00 3.33
4786 5480 2.766313 TCACACACTAGCCATCACAAC 58.234 47.619 0.00 0.00 0.00 3.32
4787 5481 1.806542 CACACACTAGCCATCACAACC 59.193 52.381 0.00 0.00 0.00 3.77
4788 5482 1.078709 CACACTAGCCATCACAACCG 58.921 55.000 0.00 0.00 0.00 4.44
4789 5483 0.973632 ACACTAGCCATCACAACCGA 59.026 50.000 0.00 0.00 0.00 4.69
4790 5484 1.346395 ACACTAGCCATCACAACCGAA 59.654 47.619 0.00 0.00 0.00 4.30
4791 5485 2.224426 ACACTAGCCATCACAACCGAAA 60.224 45.455 0.00 0.00 0.00 3.46
4792 5486 2.416547 CACTAGCCATCACAACCGAAAG 59.583 50.000 0.00 0.00 0.00 2.62
4793 5487 2.038557 ACTAGCCATCACAACCGAAAGT 59.961 45.455 0.00 0.00 0.00 2.66
4794 5488 1.523758 AGCCATCACAACCGAAAGTC 58.476 50.000 0.00 0.00 0.00 3.01
4795 5489 0.521735 GCCATCACAACCGAAAGTCC 59.478 55.000 0.00 0.00 0.00 3.85
4796 5490 1.890876 CCATCACAACCGAAAGTCCA 58.109 50.000 0.00 0.00 0.00 4.02
4797 5491 2.226330 CCATCACAACCGAAAGTCCAA 58.774 47.619 0.00 0.00 0.00 3.53
4798 5492 2.621055 CCATCACAACCGAAAGTCCAAA 59.379 45.455 0.00 0.00 0.00 3.28
4799 5493 3.550030 CCATCACAACCGAAAGTCCAAAC 60.550 47.826 0.00 0.00 0.00 2.93
4800 5494 2.993937 TCACAACCGAAAGTCCAAACT 58.006 42.857 0.00 0.00 37.32 2.66
4801 5495 4.139859 TCACAACCGAAAGTCCAAACTA 57.860 40.909 0.00 0.00 33.48 2.24
4802 5496 4.515361 TCACAACCGAAAGTCCAAACTAA 58.485 39.130 0.00 0.00 33.48 2.24
4803 5497 5.127491 TCACAACCGAAAGTCCAAACTAAT 58.873 37.500 0.00 0.00 33.48 1.73
4804 5498 6.289834 TCACAACCGAAAGTCCAAACTAATA 58.710 36.000 0.00 0.00 33.48 0.98
4805 5499 6.425721 TCACAACCGAAAGTCCAAACTAATAG 59.574 38.462 0.00 0.00 33.48 1.73
4806 5500 6.425721 CACAACCGAAAGTCCAAACTAATAGA 59.574 38.462 0.00 0.00 33.48 1.98
4807 5501 6.993902 ACAACCGAAAGTCCAAACTAATAGAA 59.006 34.615 0.00 0.00 33.48 2.10
4808 5502 7.499895 ACAACCGAAAGTCCAAACTAATAGAAA 59.500 33.333 0.00 0.00 33.48 2.52
4809 5503 7.668525 ACCGAAAGTCCAAACTAATAGAAAG 57.331 36.000 0.00 0.00 33.48 2.62
4810 5504 6.653740 ACCGAAAGTCCAAACTAATAGAAAGG 59.346 38.462 0.00 0.00 33.48 3.11
4811 5505 6.093633 CCGAAAGTCCAAACTAATAGAAAGGG 59.906 42.308 0.00 0.00 33.48 3.95
4812 5506 6.653740 CGAAAGTCCAAACTAATAGAAAGGGT 59.346 38.462 0.00 0.00 33.48 4.34
4813 5507 7.174426 CGAAAGTCCAAACTAATAGAAAGGGTT 59.826 37.037 0.00 0.00 33.48 4.11
4814 5508 9.511272 GAAAGTCCAAACTAATAGAAAGGGTTA 57.489 33.333 0.00 0.00 33.48 2.85
4815 5509 9.516546 AAAGTCCAAACTAATAGAAAGGGTTAG 57.483 33.333 0.00 0.00 33.48 2.34
4816 5510 7.631007 AGTCCAAACTAATAGAAAGGGTTAGG 58.369 38.462 0.00 0.00 32.59 2.69
5093 5789 7.817418 TCAACAAGAACTAGCAAAACCTAAT 57.183 32.000 0.00 0.00 0.00 1.73
5213 5909 6.014647 ACTGAACATAGGGTAGTAAGACACA 58.985 40.000 0.00 0.00 0.00 3.72
5352 6048 1.153765 GGAAATTGCCAAGCTCCGC 60.154 57.895 0.00 0.00 0.00 5.54
5548 6250 2.979814 TATGCTATTCGTGCACAGGT 57.020 45.000 18.64 3.82 43.59 4.00
5578 6280 0.317160 ACGGTCTTGATGTGCGAGAA 59.683 50.000 0.00 0.00 38.75 2.87
5980 6682 1.076332 GACAAGGTGATACACGGTGC 58.924 55.000 8.30 0.00 34.83 5.01
6048 6750 2.694628 TCTGTTTGAAGTGCATTGGCTT 59.305 40.909 0.00 0.00 41.91 4.35
6171 6882 2.036217 TGCAAACAGCCAGGAAAATCTG 59.964 45.455 0.00 0.00 44.83 2.90
6179 6891 4.096081 CAGCCAGGAAAATCTGAATGACTC 59.904 45.833 0.00 0.00 36.93 3.36
6338 7335 7.440856 GCAATGTTACAGATTTTTGGAAAAGGA 59.559 33.333 0.00 0.00 0.00 3.36
6428 7425 1.942657 TGTGCACTGAGTTCTTTCAGC 59.057 47.619 19.41 0.00 46.77 4.26
6449 7449 7.895759 TCAGCTTGGCTTAGAAATGTTATTTT 58.104 30.769 0.00 0.00 36.40 1.82
7010 8013 0.879765 GGATGCTATCATGCACCAGC 59.120 55.000 0.00 0.00 46.33 4.85
7075 8079 7.848223 GCCAAATAAAGAAGGCATGTATTTT 57.152 32.000 0.00 0.00 46.26 1.82
7247 8251 3.754323 CACCACGATCTCTAGGGTAGATC 59.246 52.174 9.04 9.04 43.91 2.75
7255 8259 2.625790 CTCTAGGGTAGATCAGTGCCAC 59.374 54.545 0.00 0.00 33.66 5.01
7263 8267 4.686554 GGTAGATCAGTGCCACGAAATATC 59.313 45.833 0.00 0.00 0.00 1.63
7266 8270 6.352016 AGATCAGTGCCACGAAATATCTAT 57.648 37.500 0.00 0.00 0.00 1.98
7267 8271 6.393990 AGATCAGTGCCACGAAATATCTATC 58.606 40.000 0.00 0.00 0.00 2.08
7271 8275 5.403766 CAGTGCCACGAAATATCTATCTGTC 59.596 44.000 0.00 0.00 0.00 3.51
7272 8276 5.069119 AGTGCCACGAAATATCTATCTGTCA 59.931 40.000 0.00 0.00 0.00 3.58
7315 8319 7.423199 TGGTTATCATAGACTAATGACGTGTC 58.577 38.462 0.00 0.00 38.65 3.67
7351 8355 1.016627 TATTGCCTGCATTGCGTCTC 58.983 50.000 3.84 0.00 0.00 3.36
7361 8365 0.322975 ATTGCGTCTCAACTCAGCCT 59.677 50.000 0.00 0.00 37.53 4.58
7375 8379 1.152694 AGCCTGGCTGAGCACAAAA 60.153 52.632 22.71 0.00 37.57 2.44
7412 8416 0.311790 CTGCATGTTGTTTGGTCGCT 59.688 50.000 0.00 0.00 0.00 4.93
7414 8418 0.310543 GCATGTTGTTTGGTCGCTGA 59.689 50.000 0.00 0.00 0.00 4.26
7424 8428 1.921243 TGGTCGCTGACATTGTATCG 58.079 50.000 10.14 0.00 33.68 2.92
7480 8484 2.128771 TTTATGCTTCAGGGGTCAGC 57.871 50.000 0.00 0.00 0.00 4.26
7493 8497 1.580845 GGTCAGCAGATGCACACCAC 61.581 60.000 16.37 2.89 45.16 4.16
7496 8500 2.669569 GCAGATGCACACCACGGT 60.670 61.111 0.00 0.00 41.59 4.83
7507 8511 2.027460 CCACGGTTGTTTGGCTGC 59.973 61.111 0.00 0.00 0.00 5.25
7528 8532 0.527169 TGCATGTTTGTGTTGTGCCG 60.527 50.000 0.00 0.00 35.03 5.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
16 17 2.793585 GCACATTTGAGCGGTGATCATG 60.794 50.000 0.00 0.00 34.52 3.07
101 107 7.234661 AAGAAAAACTTTCCAGTGGTAACAA 57.765 32.000 9.54 0.00 42.39 2.83
171 177 6.516739 TTAGTGTCTCGATTCACTGAATCT 57.483 37.500 23.42 10.13 44.22 2.40
172 178 7.167302 CAGATTAGTGTCTCGATTCACTGAATC 59.833 40.741 23.63 18.43 43.46 2.52
173 179 6.977502 CAGATTAGTGTCTCGATTCACTGAAT 59.022 38.462 23.63 18.99 43.46 2.57
253 261 8.677148 TTTTTGTTAGACTAGCTTGTCAAGAT 57.323 30.769 26.45 12.83 39.27 2.40
281 289 8.603242 AAATATTCGTGATTAGGACCATGTAC 57.397 34.615 0.00 0.00 0.00 2.90
306 314 6.687604 TGTTGAAAGTTGATCATCTCGACTA 58.312 36.000 6.75 0.00 46.20 2.59
419 427 5.766150 TGGTACACAATGAAACAGGAAAG 57.234 39.130 0.00 0.00 0.00 2.62
503 511 4.998788 ACAGAAACTGGAAACTGAAAAGC 58.001 39.130 0.00 0.00 35.51 3.51
529 537 7.293073 ACCATAGAGGAAATCTTGCATTGTAT 58.707 34.615 0.00 0.00 41.22 2.29
567 1180 6.570571 GCAGTTCCATTAGGTTTTCTTCCTTC 60.571 42.308 0.00 0.00 36.60 3.46
710 1327 5.353123 GCGAATCCAAACCATTCTAGTACAA 59.647 40.000 0.00 0.00 0.00 2.41
902 1522 1.488390 GTTATCGGTGTGGAGGGGTA 58.512 55.000 0.00 0.00 0.00 3.69
908 1528 2.463752 AGCTTAGGTTATCGGTGTGGA 58.536 47.619 0.00 0.00 0.00 4.02
1031 1659 3.112205 GCCATCTCCTCCACCGCAT 62.112 63.158 0.00 0.00 0.00 4.73
1192 1820 5.689068 GCTTCAAAGTTCACTCATTCAAAGG 59.311 40.000 0.00 0.00 0.00 3.11
1207 1857 0.032130 TCTGCTCGTCGCTTCAAAGT 59.968 50.000 0.00 0.00 40.11 2.66
1333 1984 4.415332 GAGACGCGACGGGAGCAA 62.415 66.667 15.93 0.00 34.19 3.91
1642 2293 1.686325 TATCCGCCCAAGAGCTCCAC 61.686 60.000 10.93 0.00 0.00 4.02
1657 2308 6.015010 ACAAGTATGACTGTATCAGGCTATCC 60.015 42.308 4.24 0.00 40.76 2.59
1718 2373 5.798125 TCCTGTGAATATCTAAGAGCCTG 57.202 43.478 0.00 0.00 0.00 4.85
1805 2460 8.317679 ACTAGATGGATCTATTAATGTTCAGGC 58.682 37.037 0.00 0.00 38.60 4.85
1887 2542 7.011482 CCCCAGTCGAATATTCTAGTGAAAAAG 59.989 40.741 20.81 8.08 35.63 2.27
2088 2743 7.974504 ACCTAACCAGATTTCTCAAGTAAAGA 58.025 34.615 0.00 0.00 0.00 2.52
2145 2800 9.601217 AGCATCGTTTAGAAGTGTAGAAATAAT 57.399 29.630 0.00 0.00 0.00 1.28
2238 2897 9.077885 AGCTAGAACTTCAAATAATTTGGAACA 57.922 29.630 0.00 0.00 40.98 3.18
2482 3141 0.525761 TAGCAAATTGACGGCTTGCC 59.474 50.000 9.88 0.75 45.23 4.52
2606 3265 5.981315 ACAGCACTGAACATTTCATGAAAAG 59.019 36.000 23.91 21.36 39.30 2.27
2773 3432 5.643777 GCACCTTCTGATAAGCAAGAACTTA 59.356 40.000 0.00 0.00 36.60 2.24
2787 3446 1.277273 CTGAGTCATGGCACCTTCTGA 59.723 52.381 0.00 0.00 0.00 3.27
2790 3449 1.808945 CAACTGAGTCATGGCACCTTC 59.191 52.381 0.00 0.00 0.00 3.46
2794 3453 1.242076 AAGCAACTGAGTCATGGCAC 58.758 50.000 0.00 0.00 0.00 5.01
2883 3542 3.409026 AATAGTGAAGATCGGGCCATC 57.591 47.619 4.39 6.09 0.00 3.51
2928 3587 6.750039 TCGAAAGTTTTCCACATTTGTTCTTC 59.250 34.615 0.00 0.00 33.68 2.87
2937 3596 4.642885 TGTTTCCTCGAAAGTTTTCCACAT 59.357 37.500 0.00 0.00 31.87 3.21
2951 3610 4.174411 TGTCTATGTGAGTGTTTCCTCG 57.826 45.455 0.00 0.00 34.04 4.63
3015 3704 1.377202 GCTTGGATCTTGACGGGCA 60.377 57.895 0.00 0.00 0.00 5.36
3018 3707 0.674581 TGCTGCTTGGATCTTGACGG 60.675 55.000 0.00 0.00 0.00 4.79
3038 3727 6.835819 ACCCTAGTTATCTTTTCCTTTTGC 57.164 37.500 0.00 0.00 0.00 3.68
3116 3805 9.730705 GATTATCAAGACATCCATATCCTTTGA 57.269 33.333 0.00 0.00 0.00 2.69
3220 3909 9.030452 CAGATCTAGGGTTAGCAAAGTATAGAT 57.970 37.037 0.00 0.00 32.80 1.98
3380 4069 2.739932 GCGCTGAAGCCTCTGAAGAATA 60.740 50.000 0.00 0.00 37.91 1.75
3461 4150 1.141053 GTCCAACCAACCAGACAGTCT 59.859 52.381 0.00 0.00 0.00 3.24
3462 4151 1.134220 TGTCCAACCAACCAGACAGTC 60.134 52.381 0.00 0.00 34.44 3.51
3507 4198 1.920835 GGCCTCAACCCTCTGGAGT 60.921 63.158 0.00 0.00 34.81 3.85
3534 4225 2.486042 GACAGTCGGGAGAGCGTC 59.514 66.667 0.00 0.00 41.26 5.19
3535 4226 3.063084 GGACAGTCGGGAGAGCGT 61.063 66.667 0.00 0.00 41.26 5.07
3664 4356 7.928307 AATCCGAAATGCTATGTATGCTTAT 57.072 32.000 0.00 0.00 0.00 1.73
3682 4374 3.388024 ACATGGCTTCTAGCTTAATCCGA 59.612 43.478 0.00 0.00 41.99 4.55
3763 4455 4.742201 TGACAAGAGCTCGCCCGC 62.742 66.667 8.37 0.00 0.00 6.13
3820 4512 0.620030 TCCCATGGACATCACTGTGG 59.380 55.000 15.22 0.00 35.14 4.17
4218 4910 4.579869 CCAGCTCTAAAATACACCACAGT 58.420 43.478 0.00 0.00 0.00 3.55
4534 5226 1.415659 CCTCTTGAGCCATACCTCTGG 59.584 57.143 0.00 0.00 39.45 3.86
4562 5254 3.879295 CGCAATTTATCCTCTGTGTCCAT 59.121 43.478 0.00 0.00 0.00 3.41
4637 5331 0.804989 GGTTGTGATGGCTAGTGTGC 59.195 55.000 0.00 0.00 0.00 4.57
4638 5332 1.078709 CGGTTGTGATGGCTAGTGTG 58.921 55.000 0.00 0.00 0.00 3.82
4639 5333 0.973632 TCGGTTGTGATGGCTAGTGT 59.026 50.000 0.00 0.00 0.00 3.55
4657 5351 5.293814 GCCCTTTCTATTAGTTCGGACTTTC 59.706 44.000 0.00 0.00 37.33 2.62
4685 5379 5.126067 AGGTCAAGTGTATATGTGGATTGC 58.874 41.667 0.00 0.00 0.00 3.56
4686 5380 7.442364 CCTAAGGTCAAGTGTATATGTGGATTG 59.558 40.741 0.00 0.00 0.00 2.67
4687 5381 7.509546 CCTAAGGTCAAGTGTATATGTGGATT 58.490 38.462 0.00 0.00 0.00 3.01
4688 5382 6.464465 GCCTAAGGTCAAGTGTATATGTGGAT 60.464 42.308 0.00 0.00 0.00 3.41
4689 5383 5.163343 GCCTAAGGTCAAGTGTATATGTGGA 60.163 44.000 0.00 0.00 0.00 4.02
4690 5384 5.057149 GCCTAAGGTCAAGTGTATATGTGG 58.943 45.833 0.00 0.00 0.00 4.17
4691 5385 5.918608 AGCCTAAGGTCAAGTGTATATGTG 58.081 41.667 0.00 0.00 0.00 3.21
4692 5386 5.900123 AGAGCCTAAGGTCAAGTGTATATGT 59.100 40.000 0.00 0.00 43.21 2.29
4693 5387 6.040955 TCAGAGCCTAAGGTCAAGTGTATATG 59.959 42.308 0.00 0.00 43.21 1.78
4694 5388 6.136857 TCAGAGCCTAAGGTCAAGTGTATAT 58.863 40.000 0.00 0.00 43.21 0.86
4695 5389 5.516044 TCAGAGCCTAAGGTCAAGTGTATA 58.484 41.667 0.00 0.00 43.21 1.47
4696 5390 4.353777 TCAGAGCCTAAGGTCAAGTGTAT 58.646 43.478 0.00 0.00 43.21 2.29
4697 5391 3.774734 TCAGAGCCTAAGGTCAAGTGTA 58.225 45.455 0.00 0.00 43.21 2.90
4698 5392 2.609747 TCAGAGCCTAAGGTCAAGTGT 58.390 47.619 0.00 0.00 43.21 3.55
4699 5393 3.902881 ATCAGAGCCTAAGGTCAAGTG 57.097 47.619 0.00 0.00 43.21 3.16
4700 5394 4.353777 TGTATCAGAGCCTAAGGTCAAGT 58.646 43.478 0.00 0.00 43.21 3.16
4701 5395 4.202202 CCTGTATCAGAGCCTAAGGTCAAG 60.202 50.000 0.00 0.00 43.21 3.02
4702 5396 3.706594 CCTGTATCAGAGCCTAAGGTCAA 59.293 47.826 0.00 0.00 43.21 3.18
4703 5397 3.052869 TCCTGTATCAGAGCCTAAGGTCA 60.053 47.826 0.00 0.00 43.21 4.02
4704 5398 3.319689 GTCCTGTATCAGAGCCTAAGGTC 59.680 52.174 0.00 0.00 40.98 3.85
4705 5399 3.052490 AGTCCTGTATCAGAGCCTAAGGT 60.052 47.826 0.00 0.00 32.44 3.50
4706 5400 3.571590 AGTCCTGTATCAGAGCCTAAGG 58.428 50.000 0.00 0.00 32.44 2.69
4707 5401 4.646945 TCAAGTCCTGTATCAGAGCCTAAG 59.353 45.833 0.00 0.00 32.44 2.18
4708 5402 4.610333 TCAAGTCCTGTATCAGAGCCTAA 58.390 43.478 0.00 0.00 32.44 2.69
4709 5403 4.251103 TCAAGTCCTGTATCAGAGCCTA 57.749 45.455 0.00 0.00 32.44 3.93
4710 5404 3.107402 TCAAGTCCTGTATCAGAGCCT 57.893 47.619 0.00 0.00 32.44 4.58
4711 5405 3.055819 TGTTCAAGTCCTGTATCAGAGCC 60.056 47.826 0.00 0.00 32.44 4.70
4712 5406 3.929610 GTGTTCAAGTCCTGTATCAGAGC 59.070 47.826 0.00 0.00 32.44 4.09
4713 5407 5.139435 TGTGTTCAAGTCCTGTATCAGAG 57.861 43.478 0.00 0.00 32.44 3.35
4714 5408 5.541845 CTTGTGTTCAAGTCCTGTATCAGA 58.458 41.667 0.00 0.00 44.09 3.27
4715 5409 5.852738 CTTGTGTTCAAGTCCTGTATCAG 57.147 43.478 0.00 0.00 44.09 2.90
4727 5421 3.740115 GAGCCTAAGGTCTTGTGTTCAA 58.260 45.455 0.00 0.00 37.53 2.69
4728 5422 3.402628 GAGCCTAAGGTCTTGTGTTCA 57.597 47.619 0.00 0.00 37.53 3.18
4737 5431 6.613153 AATATGGTATCAGAGCCTAAGGTC 57.387 41.667 0.00 0.00 40.98 3.85
4738 5432 7.310734 GCTTAATATGGTATCAGAGCCTAAGGT 60.311 40.741 0.00 0.00 0.00 3.50
4739 5433 7.044798 GCTTAATATGGTATCAGAGCCTAAGG 58.955 42.308 0.00 0.00 0.00 2.69
4740 5434 7.846066 AGCTTAATATGGTATCAGAGCCTAAG 58.154 38.462 0.00 0.00 0.00 2.18
4741 5435 7.798710 AGCTTAATATGGTATCAGAGCCTAA 57.201 36.000 0.00 0.00 0.00 2.69
4742 5436 7.454694 TGAAGCTTAATATGGTATCAGAGCCTA 59.545 37.037 0.00 0.00 0.00 3.93
4743 5437 6.270927 TGAAGCTTAATATGGTATCAGAGCCT 59.729 38.462 0.00 0.00 0.00 4.58
4744 5438 6.370166 GTGAAGCTTAATATGGTATCAGAGCC 59.630 42.308 0.00 0.00 0.00 4.70
4745 5439 6.931281 TGTGAAGCTTAATATGGTATCAGAGC 59.069 38.462 0.00 0.00 0.00 4.09
4746 5440 7.928167 TGTGTGAAGCTTAATATGGTATCAGAG 59.072 37.037 0.00 0.00 0.00 3.35
4747 5441 7.710907 GTGTGTGAAGCTTAATATGGTATCAGA 59.289 37.037 0.00 0.00 0.00 3.27
4748 5442 7.712639 AGTGTGTGAAGCTTAATATGGTATCAG 59.287 37.037 0.00 0.00 0.00 2.90
4749 5443 7.564793 AGTGTGTGAAGCTTAATATGGTATCA 58.435 34.615 0.00 0.00 0.00 2.15
4750 5444 9.197694 CTAGTGTGTGAAGCTTAATATGGTATC 57.802 37.037 0.00 0.00 0.00 2.24
4751 5445 7.657761 GCTAGTGTGTGAAGCTTAATATGGTAT 59.342 37.037 0.00 0.00 33.40 2.73
4752 5446 6.984474 GCTAGTGTGTGAAGCTTAATATGGTA 59.016 38.462 0.00 0.00 33.40 3.25
4753 5447 5.817816 GCTAGTGTGTGAAGCTTAATATGGT 59.182 40.000 0.00 0.00 33.40 3.55
4754 5448 5.237344 GGCTAGTGTGTGAAGCTTAATATGG 59.763 44.000 0.00 0.00 36.48 2.74
4755 5449 5.817296 TGGCTAGTGTGTGAAGCTTAATATG 59.183 40.000 0.00 0.00 36.48 1.78
4756 5450 5.989477 TGGCTAGTGTGTGAAGCTTAATAT 58.011 37.500 0.00 0.00 36.48 1.28
4757 5451 5.414789 TGGCTAGTGTGTGAAGCTTAATA 57.585 39.130 0.00 0.00 36.48 0.98
4758 5452 4.286297 TGGCTAGTGTGTGAAGCTTAAT 57.714 40.909 0.00 0.00 36.48 1.40
4759 5453 3.762407 TGGCTAGTGTGTGAAGCTTAA 57.238 42.857 0.00 0.00 36.48 1.85
4760 5454 3.260632 TGATGGCTAGTGTGTGAAGCTTA 59.739 43.478 0.00 0.00 36.48 3.09
4761 5455 2.038952 TGATGGCTAGTGTGTGAAGCTT 59.961 45.455 0.00 0.00 36.48 3.74
4762 5456 1.625315 TGATGGCTAGTGTGTGAAGCT 59.375 47.619 0.00 0.00 36.48 3.74
4763 5457 1.734465 GTGATGGCTAGTGTGTGAAGC 59.266 52.381 0.00 0.00 35.47 3.86
4764 5458 3.044235 TGTGATGGCTAGTGTGTGAAG 57.956 47.619 0.00 0.00 0.00 3.02
4765 5459 3.138304 GTTGTGATGGCTAGTGTGTGAA 58.862 45.455 0.00 0.00 0.00 3.18
4766 5460 2.549992 GGTTGTGATGGCTAGTGTGTGA 60.550 50.000 0.00 0.00 0.00 3.58
4767 5461 1.806542 GGTTGTGATGGCTAGTGTGTG 59.193 52.381 0.00 0.00 0.00 3.82
4768 5462 1.608025 CGGTTGTGATGGCTAGTGTGT 60.608 52.381 0.00 0.00 0.00 3.72
4769 5463 1.078709 CGGTTGTGATGGCTAGTGTG 58.921 55.000 0.00 0.00 0.00 3.82
4770 5464 0.973632 TCGGTTGTGATGGCTAGTGT 59.026 50.000 0.00 0.00 0.00 3.55
4771 5465 2.093306 TTCGGTTGTGATGGCTAGTG 57.907 50.000 0.00 0.00 0.00 2.74
4772 5466 2.038557 ACTTTCGGTTGTGATGGCTAGT 59.961 45.455 0.00 0.00 0.00 2.57
4773 5467 2.673368 GACTTTCGGTTGTGATGGCTAG 59.327 50.000 0.00 0.00 0.00 3.42
4774 5468 2.614481 GGACTTTCGGTTGTGATGGCTA 60.614 50.000 0.00 0.00 0.00 3.93
4775 5469 1.523758 GACTTTCGGTTGTGATGGCT 58.476 50.000 0.00 0.00 0.00 4.75
4776 5470 0.521735 GGACTTTCGGTTGTGATGGC 59.478 55.000 0.00 0.00 0.00 4.40
4777 5471 1.890876 TGGACTTTCGGTTGTGATGG 58.109 50.000 0.00 0.00 0.00 3.51
4778 5472 3.315191 AGTTTGGACTTTCGGTTGTGATG 59.685 43.478 0.00 0.00 29.87 3.07
4779 5473 3.551846 AGTTTGGACTTTCGGTTGTGAT 58.448 40.909 0.00 0.00 29.87 3.06
4780 5474 2.993937 AGTTTGGACTTTCGGTTGTGA 58.006 42.857 0.00 0.00 29.87 3.58
4781 5475 4.886247 TTAGTTTGGACTTTCGGTTGTG 57.114 40.909 0.00 0.00 37.33 3.33
4782 5476 6.527423 TCTATTAGTTTGGACTTTCGGTTGT 58.473 36.000 0.00 0.00 37.33 3.32
4783 5477 7.429636 TTCTATTAGTTTGGACTTTCGGTTG 57.570 36.000 0.00 0.00 37.33 3.77
4784 5478 7.174426 CCTTTCTATTAGTTTGGACTTTCGGTT 59.826 37.037 0.00 0.00 37.33 4.44
4785 5479 6.653740 CCTTTCTATTAGTTTGGACTTTCGGT 59.346 38.462 0.00 0.00 37.33 4.69
4786 5480 6.093633 CCCTTTCTATTAGTTTGGACTTTCGG 59.906 42.308 0.00 0.00 37.33 4.30
4787 5481 6.653740 ACCCTTTCTATTAGTTTGGACTTTCG 59.346 38.462 0.00 0.00 37.33 3.46
4788 5482 7.997773 ACCCTTTCTATTAGTTTGGACTTTC 57.002 36.000 0.00 0.00 37.33 2.62
4789 5483 9.516546 CTAACCCTTTCTATTAGTTTGGACTTT 57.483 33.333 0.00 0.00 37.33 2.66
4790 5484 8.107729 CCTAACCCTTTCTATTAGTTTGGACTT 58.892 37.037 0.00 0.00 36.01 3.01
4791 5485 7.631007 CCTAACCCTTTCTATTAGTTTGGACT 58.369 38.462 0.00 0.00 36.01 3.85
4792 5486 6.318144 GCCTAACCCTTTCTATTAGTTTGGAC 59.682 42.308 5.97 0.00 36.01 4.02
4793 5487 6.012333 TGCCTAACCCTTTCTATTAGTTTGGA 60.012 38.462 5.97 0.00 36.01 3.53
4794 5488 6.184789 TGCCTAACCCTTTCTATTAGTTTGG 58.815 40.000 0.00 0.00 36.71 3.28
4795 5489 7.696992 TTGCCTAACCCTTTCTATTAGTTTG 57.303 36.000 0.00 0.00 0.00 2.93
4796 5490 7.560262 GGATTGCCTAACCCTTTCTATTAGTTT 59.440 37.037 0.00 0.00 0.00 2.66
4797 5491 7.061054 GGATTGCCTAACCCTTTCTATTAGTT 58.939 38.462 0.00 0.00 0.00 2.24
4798 5492 6.159751 TGGATTGCCTAACCCTTTCTATTAGT 59.840 38.462 0.00 0.00 34.31 2.24
4799 5493 6.486993 GTGGATTGCCTAACCCTTTCTATTAG 59.513 42.308 0.00 0.00 34.31 1.73
4800 5494 6.069323 TGTGGATTGCCTAACCCTTTCTATTA 60.069 38.462 0.00 0.00 34.31 0.98
4801 5495 5.201243 GTGGATTGCCTAACCCTTTCTATT 58.799 41.667 0.00 0.00 34.31 1.73
4802 5496 4.229582 TGTGGATTGCCTAACCCTTTCTAT 59.770 41.667 0.00 0.00 34.31 1.98
4803 5497 3.589735 TGTGGATTGCCTAACCCTTTCTA 59.410 43.478 0.00 0.00 34.31 2.10
4804 5498 2.378547 TGTGGATTGCCTAACCCTTTCT 59.621 45.455 0.00 0.00 34.31 2.52
4805 5499 2.802719 TGTGGATTGCCTAACCCTTTC 58.197 47.619 0.00 0.00 34.31 2.62
4806 5500 2.990740 TGTGGATTGCCTAACCCTTT 57.009 45.000 0.00 0.00 34.31 3.11
4807 5501 4.814224 ATATGTGGATTGCCTAACCCTT 57.186 40.909 0.00 0.00 34.31 3.95
4808 5502 4.663120 TGTATATGTGGATTGCCTAACCCT 59.337 41.667 0.00 0.00 34.31 4.34
4809 5503 4.760204 GTGTATATGTGGATTGCCTAACCC 59.240 45.833 0.00 0.00 34.31 4.11
4810 5504 5.621193 AGTGTATATGTGGATTGCCTAACC 58.379 41.667 0.00 0.00 34.31 2.85
4811 5505 6.765989 TGAAGTGTATATGTGGATTGCCTAAC 59.234 38.462 0.00 0.00 34.31 2.34
4812 5506 6.894682 TGAAGTGTATATGTGGATTGCCTAA 58.105 36.000 0.00 0.00 34.31 2.69
4813 5507 6.493189 TGAAGTGTATATGTGGATTGCCTA 57.507 37.500 0.00 0.00 34.31 3.93
4814 5508 5.372343 TGAAGTGTATATGTGGATTGCCT 57.628 39.130 0.00 0.00 34.31 4.75
4815 5509 5.356751 TGTTGAAGTGTATATGTGGATTGCC 59.643 40.000 0.00 0.00 0.00 4.52
4816 5510 6.435430 TGTTGAAGTGTATATGTGGATTGC 57.565 37.500 0.00 0.00 0.00 3.56
4888 5582 4.734398 AATTTTGCTTCAGTGTTGACCA 57.266 36.364 0.00 0.00 31.71 4.02
5093 5789 5.534207 AATTGAATCACCTTTCAAGCACA 57.466 34.783 5.91 0.00 45.83 4.57
5166 5862 6.324254 AGTCATGAACTTAGGTAGACCCATAC 59.676 42.308 0.00 0.00 33.03 2.39
5213 5909 6.752351 CAGAAGTACAGCGACAATACTACAAT 59.248 38.462 0.00 0.00 0.00 2.71
5352 6048 1.117150 ATAGCCCTGCAAAGCATTGG 58.883 50.000 10.03 0.00 38.13 3.16
5548 6250 6.256975 GCACATCAAGACCGTATATGTTGTTA 59.743 38.462 0.00 0.00 0.00 2.41
5578 6280 3.448301 CCTTCTTGAGTCTGATCAGAGCT 59.552 47.826 25.76 22.77 38.27 4.09
6121 6832 2.265367 TGGAGAGGCTGGAATGTAACA 58.735 47.619 0.00 0.00 0.00 2.41
6122 6833 3.209410 CATGGAGAGGCTGGAATGTAAC 58.791 50.000 0.00 0.00 0.00 2.50
6123 6834 2.173356 CCATGGAGAGGCTGGAATGTAA 59.827 50.000 5.56 0.00 31.38 2.41
6124 6835 1.770658 CCATGGAGAGGCTGGAATGTA 59.229 52.381 5.56 0.00 31.38 2.29
6125 6836 0.549950 CCATGGAGAGGCTGGAATGT 59.450 55.000 5.56 0.00 31.38 2.71
6126 6837 0.841961 TCCATGGAGAGGCTGGAATG 59.158 55.000 11.44 0.00 36.15 2.67
6127 6838 1.830486 ATCCATGGAGAGGCTGGAAT 58.170 50.000 21.33 0.00 42.12 3.01
6128 6839 1.213678 CAATCCATGGAGAGGCTGGAA 59.786 52.381 21.33 0.00 42.12 3.53
6129 6840 0.841961 CAATCCATGGAGAGGCTGGA 59.158 55.000 21.33 0.00 42.95 3.86
6171 6882 6.563010 CGCTTCCGAAATTATCAGAGTCATTC 60.563 42.308 0.00 0.00 36.29 2.67
6179 6891 6.420903 TGATAAGTCGCTTCCGAAATTATCAG 59.579 38.462 19.78 0.00 46.22 2.90
6315 7312 7.670364 CCTCCTTTTCCAAAAATCTGTAACAT 58.330 34.615 0.00 0.00 0.00 2.71
6338 7335 3.019564 GGATGCATCTTTAACACTGCCT 58.980 45.455 25.28 0.00 33.70 4.75
6453 7453 6.292865 GCCAAACATTTCTAAGCCAAACTTTC 60.293 38.462 0.00 0.00 39.97 2.62
6495 7495 3.383505 CCATCAACGACTACCCATGTAGA 59.616 47.826 6.73 0.00 46.18 2.59
6750 7752 7.359595 TCCACGAAACAAGAATTTGTAATCTG 58.640 34.615 0.00 0.00 46.54 2.90
6751 7753 7.504924 TCCACGAAACAAGAATTTGTAATCT 57.495 32.000 0.00 0.00 46.54 2.40
6825 7828 1.269517 TGGCAACGCTGAAAATTCACC 60.270 47.619 0.00 0.00 42.51 4.02
6934 7937 1.943340 GAGCGGAGGATTTTCCATGAC 59.057 52.381 0.00 0.00 39.61 3.06
7010 8013 4.161333 GCTTGATTTCGACAACATCTTGG 58.839 43.478 0.00 0.00 0.00 3.61
7075 8079 9.058174 TGACAGACGGAAATAACAGAAAATTTA 57.942 29.630 0.00 0.00 0.00 1.40
7079 8083 6.567701 GCATGACAGACGGAAATAACAGAAAA 60.568 38.462 0.00 0.00 0.00 2.29
7247 8251 5.292765 ACAGATAGATATTTCGTGGCACTG 58.707 41.667 16.72 9.49 0.00 3.66
7263 8267 8.783833 TTTCCTTCTTGAATTCTGACAGATAG 57.216 34.615 5.87 0.13 0.00 2.08
7266 8270 7.040201 CCAATTTCCTTCTTGAATTCTGACAGA 60.040 37.037 7.05 0.00 0.00 3.41
7267 8271 7.088905 CCAATTTCCTTCTTGAATTCTGACAG 58.911 38.462 7.05 0.00 0.00 3.51
7271 8275 9.578439 GATAACCAATTTCCTTCTTGAATTCTG 57.422 33.333 7.05 0.00 0.00 3.02
7272 8276 9.312904 TGATAACCAATTTCCTTCTTGAATTCT 57.687 29.630 7.05 0.00 0.00 2.40
7315 8319 6.259608 CAGGCAATATTAGAGAAGACAACCAG 59.740 42.308 0.00 0.00 0.00 4.00
7361 8365 1.741525 GCCTTTTTGTGCTCAGCCA 59.258 52.632 0.00 0.00 0.00 4.75
7371 8375 4.570369 AGATGTTGGTTTTTCGCCTTTTTG 59.430 37.500 0.00 0.00 0.00 2.44
7375 8379 2.545742 GCAGATGTTGGTTTTTCGCCTT 60.546 45.455 0.00 0.00 0.00 4.35
7412 8416 0.615850 TGGCCACCGATACAATGTCA 59.384 50.000 0.00 0.00 0.00 3.58
7414 8418 2.435372 AATGGCCACCGATACAATGT 57.565 45.000 8.16 0.00 0.00 2.71
7480 8484 1.165907 ACAACCGTGGTGTGCATCTG 61.166 55.000 0.00 0.00 0.00 2.90
7493 8497 2.353376 CACGCAGCCAAACAACCG 60.353 61.111 0.00 0.00 0.00 4.44
7496 8500 1.300003 CATGCACGCAGCCAAACAA 60.300 52.632 0.00 0.00 44.83 2.83
7507 8511 0.571661 GCACAACACAAACATGCACG 59.428 50.000 0.00 0.00 36.30 5.34


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

AutoCloner maintained by Alex Coulton.