Multiple sequence alignment - TraesCS5D01G347600

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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 TraesCS5D01G347600 chr5D 100.000 4394 0 0 985 5378 433061020 433065413 0.000000e+00 8115.0
1 TraesCS5D01G347600 chr5D 100.000 797 0 0 1 797 433060036 433060832 0.000000e+00 1472.0
2 TraesCS5D01G347600 chr5D 94.059 101 6 0 2945 3045 192552229 192552329 2.590000e-33 154.0
3 TraesCS5D01G347600 chr5D 94.059 101 4 2 2941 3041 504793023 504792925 9.330000e-33 152.0
4 TraesCS5D01G347600 chr5D 85.484 62 7 2 4884 4945 526618391 526618332 4.500000e-06 63.9
5 TraesCS5D01G347600 chr5A 92.734 1335 40 17 985 2272 547719261 547720585 0.000000e+00 1875.0
6 TraesCS5D01G347600 chr5A 89.316 1067 75 14 3656 4686 547722363 547723426 0.000000e+00 1303.0
7 TraesCS5D01G347600 chr5A 93.851 683 35 4 4697 5378 547724569 547725245 0.000000e+00 1022.0
8 TraesCS5D01G347600 chr5A 90.613 522 40 5 281 796 547718721 547719239 0.000000e+00 684.0
9 TraesCS5D01G347600 chr5A 94.521 292 13 1 2669 2960 547721185 547721473 1.060000e-121 448.0
10 TraesCS5D01G347600 chr5A 92.308 312 22 2 3346 3656 547722007 547722317 4.940000e-120 442.0
11 TraesCS5D01G347600 chr5A 92.095 253 17 3 3078 3329 547721769 547722019 2.380000e-93 353.0
12 TraesCS5D01G347600 chr5A 89.161 286 15 6 1 285 547716138 547716408 5.160000e-90 342.0
13 TraesCS5D01G347600 chr5A 80.693 202 27 7 2336 2526 94800340 94800540 4.340000e-31 147.0
14 TraesCS5D01G347600 chr5A 80.829 193 29 5 2339 2526 111608260 111608071 1.560000e-30 145.0
15 TraesCS5D01G347600 chr5B 90.200 1347 66 24 985 2306 526642585 526643890 0.000000e+00 1696.0
16 TraesCS5D01G347600 chr5B 89.942 686 58 9 4693 5375 526647803 526648480 0.000000e+00 874.0
17 TraesCS5D01G347600 chr5B 83.573 627 71 22 3823 4422 526645464 526646085 4.700000e-155 558.0
18 TraesCS5D01G347600 chr5B 92.705 329 16 3 474 794 526642231 526642559 8.160000e-128 468.0
19 TraesCS5D01G347600 chr5B 87.108 287 31 4 2669 2951 526643887 526644171 2.420000e-83 320.0
20 TraesCS5D01G347600 chr5B 93.069 101 6 1 2950 3050 406172763 406172664 4.340000e-31 147.0
21 TraesCS5D01G347600 chr5B 79.894 189 29 6 2341 2526 670797106 670796924 4.370000e-26 130.0
22 TraesCS5D01G347600 chr7B 92.172 511 32 6 1588 2094 732644736 732645242 0.000000e+00 715.0
23 TraesCS5D01G347600 chr7B 80.800 750 104 24 3862 4587 732646345 732647078 7.870000e-153 551.0
24 TraesCS5D01G347600 chr7B 82.599 431 68 6 1668 2096 144077986 144077561 1.830000e-99 374.0
25 TraesCS5D01G347600 chr7B 86.435 317 24 11 1006 1308 732644158 732644469 4.020000e-86 329.0
26 TraesCS5D01G347600 chr7B 86.188 181 8 6 2692 2864 732645311 732645482 4.280000e-41 180.0
27 TraesCS5D01G347600 chr7A 90.944 519 35 6 1588 2094 725912603 725913121 0.000000e+00 688.0
28 TraesCS5D01G347600 chr7A 82.074 569 88 12 3824 4382 725915103 725915667 1.750000e-129 473.0
29 TraesCS5D01G347600 chr7A 87.931 174 17 4 3348 3519 725913730 725913901 9.130000e-48 202.0
30 TraesCS5D01G347600 chr7A 89.873 158 6 2 2708 2864 725913206 725913354 1.530000e-45 195.0
31 TraesCS5D01G347600 chr7A 88.732 142 13 2 569 710 725911873 725912011 2.580000e-38 171.0
32 TraesCS5D01G347600 chr7D 90.366 519 38 6 1588 2094 629824207 629824725 0.000000e+00 671.0
33 TraesCS5D01G347600 chr7D 78.239 795 103 33 3764 4527 629825749 629826504 3.820000e-121 446.0
34 TraesCS5D01G347600 chr7D 82.160 426 69 6 1668 2091 178010042 178009622 5.120000e-95 359.0
35 TraesCS5D01G347600 chr7D 89.873 158 6 2 2708 2864 629824814 629824962 1.530000e-45 195.0
36 TraesCS5D01G347600 chr3D 84.247 292 31 6 992 1274 98970522 98970807 2.470000e-68 270.0
37 TraesCS5D01G347600 chr3D 81.461 178 24 5 2339 2515 591608888 591608719 2.610000e-28 137.0
38 TraesCS5D01G347600 chr1D 81.227 277 43 7 4975 5244 282186968 282187242 1.170000e-51 215.0
39 TraesCS5D01G347600 chr1D 97.778 45 0 1 2521 2565 254399535 254399578 5.780000e-10 76.8
40 TraesCS5D01G347600 chr3A 79.752 242 39 10 4970 5203 77723042 77722803 3.330000e-37 167.0
41 TraesCS5D01G347600 chr3A 100.000 45 0 0 2521 2565 311495173 311495217 3.450000e-12 84.2
42 TraesCS5D01G347600 chr2B 96.809 94 2 1 2941 3034 575874895 575874987 7.210000e-34 156.0
43 TraesCS5D01G347600 chr6A 96.703 91 3 0 2948 3038 27342893 27342983 9.330000e-33 152.0
44 TraesCS5D01G347600 chrUn 93.878 98 5 1 2945 3042 135090713 135090809 4.340000e-31 147.0
45 TraesCS5D01G347600 chrUn 93.878 98 5 1 2945 3042 152687569 152687665 4.340000e-31 147.0
46 TraesCS5D01G347600 chrUn 97.778 45 0 1 2521 2565 239345689 239345732 5.780000e-10 76.8
47 TraesCS5D01G347600 chr1A 91.509 106 6 3 2936 3038 572633161 572633056 5.610000e-30 143.0
48 TraesCS5D01G347600 chr1A 100.000 45 0 0 2521 2565 554510831 554510787 3.450000e-12 84.2
49 TraesCS5D01G347600 chr3B 90.000 110 8 2 2945 3054 43050315 43050421 7.260000e-29 139.0
50 TraesCS5D01G347600 chr3B 75.445 281 57 9 4973 5244 676699923 676700200 5.650000e-25 126.0
51 TraesCS5D01G347600 chr3B 76.582 158 30 6 2336 2492 518998031 518998182 4.470000e-11 80.5
52 TraesCS5D01G347600 chr6D 79.703 202 28 13 2339 2532 50674374 50674570 3.380000e-27 134.0
53 TraesCS5D01G347600 chr6D 100.000 45 0 0 2521 2565 429814279 429814235 3.450000e-12 84.2
54 TraesCS5D01G347600 chr6D 97.778 45 1 0 2521 2565 45518146 45518102 1.610000e-10 78.7
55 TraesCS5D01G347600 chr4D 86.239 109 13 2 2414 2522 81970992 81971098 3.400000e-22 117.0
56 TraesCS5D01G347600 chr4D 97.778 45 0 1 2521 2565 207372653 207372610 5.780000e-10 76.8
57 TraesCS5D01G347600 chr4B 84.211 114 14 3 2417 2526 545174460 545174347 2.050000e-19 108.0
58 TraesCS5D01G347600 chr4B 97.778 45 1 0 2521 2565 528412753 528412797 1.610000e-10 78.7
59 TraesCS5D01G347600 chr6B 81.739 115 19 2 2417 2530 120801220 120801107 1.590000e-15 95.3
60 TraesCS5D01G347600 chr1B 100.000 45 0 0 2521 2565 158866837 158866793 3.450000e-12 84.2


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 TraesCS5D01G347600 chr5D 433060036 433065413 5377 False 4793.500000 8115 100.000000 1 5378 2 chr5D.!!$F2 5377
1 TraesCS5D01G347600 chr5A 547716138 547725245 9107 False 808.625000 1875 91.824875 1 5378 8 chr5A.!!$F2 5377
2 TraesCS5D01G347600 chr5B 526642231 526648480 6249 False 783.200000 1696 88.705600 474 5375 5 chr5B.!!$F1 4901
3 TraesCS5D01G347600 chr7B 732644158 732647078 2920 False 443.750000 715 86.398750 1006 4587 4 chr7B.!!$F1 3581
4 TraesCS5D01G347600 chr7A 725911873 725915667 3794 False 345.800000 688 87.910800 569 4382 5 chr7A.!!$F1 3813
5 TraesCS5D01G347600 chr7D 629824207 629826504 2297 False 437.333333 671 86.159333 1588 4527 3 chr7D.!!$F1 2939

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
771 3097 0.179129 GAGCAGAGCAGAGCTGAGAC 60.179 60.0 0.85 0.00 42.04 3.36 F
2332 4930 0.243636 GCGGACATTTGTTTCCTGGG 59.756 55.0 0.00 0.00 0.00 4.45 F
2504 5203 0.178301 GGGTTTTGGTTGGCGGAAAA 59.822 50.0 0.00 0.00 0.00 2.29 F
3803 8441 0.108662 GCCCATGGCTTGTGTAAAGC 60.109 55.0 6.09 1.41 46.69 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2485 5184 0.178301 TTTTCCGCCAACCAAAACCC 59.822 50.000 0.00 0.0 0.00 4.11 R
3785 8423 0.171007 CGCTTTACACAAGCCATGGG 59.829 55.000 15.13 0.0 40.02 4.00 R
4139 8807 1.078072 ACAGCCGTGTCCACACAAA 60.078 52.632 10.39 0.0 46.75 2.83 R
4622 9327 0.395724 CCCCAACTATGCCCTTCACC 60.396 60.000 0.00 0.0 0.00 4.02 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
48 49 5.372373 AGAAACAGAAGAAGTGAGGAAAGG 58.628 41.667 0.00 0.00 0.00 3.11
54 55 1.283321 AGAAGTGAGGAAAGGCCATCC 59.717 52.381 17.63 17.63 40.02 3.51
64 65 1.372501 AAGGCCATCCCACAGTACTT 58.627 50.000 5.01 0.00 35.39 2.24
122 124 4.537135 TCTCTACTTTGTTGCCGAAGAT 57.463 40.909 0.00 0.00 35.87 2.40
133 135 4.020928 TGTTGCCGAAGATTTGAGGTACTA 60.021 41.667 0.00 0.00 41.55 1.82
152 154 8.322091 AGGTACTATGCCTTTTTGCTATATAGG 58.678 37.037 11.72 0.00 36.02 2.57
157 159 5.130350 TGCCTTTTTGCTATATAGGGACAC 58.870 41.667 11.72 0.00 0.00 3.67
175 177 4.024556 GGACACATATTCATTTCTGAGCCG 60.025 45.833 0.00 0.00 31.68 5.52
176 178 3.879295 ACACATATTCATTTCTGAGCCGG 59.121 43.478 0.00 0.00 31.68 6.13
192 194 2.815945 CGGGGCTCATCTGCATCCT 61.816 63.158 0.00 0.00 34.04 3.24
195 197 0.761187 GGGCTCATCTGCATCCTGTA 59.239 55.000 0.00 0.00 34.04 2.74
202 204 5.664457 CTCATCTGCATCCTGTAAACAGTA 58.336 41.667 9.17 0.00 42.27 2.74
273 275 0.603707 ATGTTCCACAGTGTGAGGCG 60.604 55.000 24.99 7.86 35.23 5.52
302 2620 2.704725 TTTCAGCTCGTTTGGAATGC 57.295 45.000 0.00 0.00 0.00 3.56
315 2633 1.005340 GGAATGCGAGTTGCTCTCAG 58.995 55.000 3.50 4.54 46.63 3.35
316 2634 1.404717 GGAATGCGAGTTGCTCTCAGA 60.405 52.381 3.50 0.00 46.63 3.27
317 2635 1.925847 GAATGCGAGTTGCTCTCAGAG 59.074 52.381 3.50 0.00 46.63 3.35
318 2636 1.180907 ATGCGAGTTGCTCTCAGAGA 58.819 50.000 5.62 0.00 46.63 3.10
319 2637 0.961753 TGCGAGTTGCTCTCAGAGAA 59.038 50.000 5.62 0.00 46.63 2.87
359 2677 8.540507 ACAGTACATGACTATTTCATAGACCT 57.459 34.615 0.00 0.00 43.68 3.85
360 2678 8.982723 ACAGTACATGACTATTTCATAGACCTT 58.017 33.333 0.00 0.00 43.68 3.50
389 2707 6.764877 TGTCTTTTTGTTAAGAGCTACTCG 57.235 37.500 0.00 0.00 34.95 4.18
395 2713 4.634184 TGTTAAGAGCTACTCGGATGTC 57.366 45.455 0.00 0.00 35.36 3.06
416 2734 3.818210 TCTAAACGAGCTGAAATTTGGCA 59.182 39.130 13.09 0.00 0.00 4.92
418 2736 1.317613 ACGAGCTGAAATTTGGCACA 58.682 45.000 13.09 0.00 0.00 4.57
430 2748 1.528076 TGGCACAAACCTCACGCAT 60.528 52.632 0.00 0.00 31.92 4.73
435 2753 1.336440 CACAAACCTCACGCATGGAAA 59.664 47.619 0.00 0.00 0.00 3.13
462 2780 3.210227 TCCGTGCAAAAAGATCACAAGA 58.790 40.909 0.00 0.00 0.00 3.02
495 2813 1.341531 AGGACCTCACGTTCTCAACTG 59.658 52.381 0.00 0.00 0.00 3.16
554 2877 1.726853 CCGTAGGCACTCTTCAAAGG 58.273 55.000 0.00 0.00 46.14 3.11
562 2885 7.497854 TAGGCACTCTTCAAAGGAACTTCCC 62.498 48.000 4.01 0.00 46.17 3.97
771 3097 0.179129 GAGCAGAGCAGAGCTGAGAC 60.179 60.000 0.85 0.00 42.04 3.36
794 3120 0.468226 GCCGGAGAGAGAGAGAGAGA 59.532 60.000 5.05 0.00 0.00 3.10
1120 3461 1.288350 CGAGGATTCAGAGCAAGCTG 58.712 55.000 0.00 0.00 37.24 4.24
1276 3634 1.200716 CGGGCATGCATGATTATCCAC 59.799 52.381 30.64 11.24 0.00 4.02
1350 3710 0.542333 GGTAGGAGAGAAACAGGGCC 59.458 60.000 0.00 0.00 0.00 5.80
1364 3724 1.053424 AGGGCCGAGTTCAAACACTA 58.947 50.000 0.00 0.00 0.00 2.74
1415 3775 0.663153 ACAACTTTCGTCTGCAAGGC 59.337 50.000 0.00 0.00 33.03 4.35
1416 3776 0.662619 CAACTTTCGTCTGCAAGGCA 59.337 50.000 0.00 0.00 39.79 4.75
1417 3777 0.663153 AACTTTCGTCTGCAAGGCAC 59.337 50.000 0.00 0.00 39.79 5.01
1435 3809 1.103803 ACTACACGTGATGAGCCGAT 58.896 50.000 25.01 0.00 0.00 4.18
1436 3810 2.032924 CACTACACGTGATGAGCCGATA 59.967 50.000 25.01 0.00 46.81 2.92
1551 4028 4.948847 TGTGCTCAGTCTTCGCATTATAT 58.051 39.130 0.00 0.00 35.93 0.86
1553 4030 5.234972 TGTGCTCAGTCTTCGCATTATATTG 59.765 40.000 0.00 0.00 35.93 1.90
1554 4031 4.212004 TGCTCAGTCTTCGCATTATATTGC 59.788 41.667 9.15 9.15 39.29 3.56
1555 4032 4.212004 GCTCAGTCTTCGCATTATATTGCA 59.788 41.667 17.29 4.62 42.91 4.08
1557 4034 6.567321 GCTCAGTCTTCGCATTATATTGCAAT 60.567 38.462 17.56 17.56 42.91 3.56
1558 4035 7.263100 TCAGTCTTCGCATTATATTGCAATT 57.737 32.000 18.75 8.19 42.91 2.32
1559 4036 7.134163 TCAGTCTTCGCATTATATTGCAATTG 58.866 34.615 18.75 10.81 42.91 2.32
1560 4037 6.361481 CAGTCTTCGCATTATATTGCAATTGG 59.639 38.462 18.75 4.37 42.91 3.16
1561 4038 5.630680 GTCTTCGCATTATATTGCAATTGGG 59.369 40.000 18.75 17.02 42.91 4.12
1665 4177 3.792736 GGACCATGGGCGCAGGTA 61.793 66.667 18.09 0.00 35.36 3.08
2104 4616 2.418334 GCCGTAAGTAAACTGGAGGAGG 60.418 54.545 3.20 0.00 0.00 4.30
2105 4617 3.094572 CCGTAAGTAAACTGGAGGAGGA 58.905 50.000 0.00 0.00 0.00 3.71
2106 4618 3.130693 CCGTAAGTAAACTGGAGGAGGAG 59.869 52.174 0.00 0.00 0.00 3.69
2114 4626 0.820871 CTGGAGGAGGAGTACTGTGC 59.179 60.000 0.00 0.00 0.00 4.57
2184 4730 7.940178 ACTAATTTTTGAAAAATCACCGGTC 57.060 32.000 15.43 0.00 0.00 4.79
2239 4785 2.029828 CACCACACACCTCAGTCTACTC 60.030 54.545 0.00 0.00 0.00 2.59
2245 4791 4.461081 ACACACCTCAGTCTACTCAAGATC 59.539 45.833 0.00 0.00 36.36 2.75
2246 4792 4.704540 CACACCTCAGTCTACTCAAGATCT 59.295 45.833 0.00 0.00 36.36 2.75
2314 4912 1.264557 TCGCTATCTACTCAAGAGCGC 59.735 52.381 9.56 0.00 44.36 5.92
2319 4917 0.958876 TCTACTCAAGAGCGCGGACA 60.959 55.000 8.83 0.00 0.00 4.02
2322 4920 0.320771 ACTCAAGAGCGCGGACATTT 60.321 50.000 8.83 0.00 0.00 2.32
2324 4922 0.602638 TCAAGAGCGCGGACATTTGT 60.603 50.000 8.83 0.00 0.00 2.83
2326 4924 0.951558 AAGAGCGCGGACATTTGTTT 59.048 45.000 8.83 0.00 0.00 2.83
2328 4926 0.454452 GAGCGCGGACATTTGTTTCC 60.454 55.000 8.83 0.00 0.00 3.13
2329 4927 0.889186 AGCGCGGACATTTGTTTCCT 60.889 50.000 8.83 0.00 0.00 3.36
2332 4930 0.243636 GCGGACATTTGTTTCCTGGG 59.756 55.000 0.00 0.00 0.00 4.45
2333 4931 1.616159 CGGACATTTGTTTCCTGGGT 58.384 50.000 0.00 0.00 0.00 4.51
2334 4932 1.269448 CGGACATTTGTTTCCTGGGTG 59.731 52.381 0.00 0.00 0.00 4.61
2337 5033 3.506067 GGACATTTGTTTCCTGGGTGTAG 59.494 47.826 0.00 0.00 0.00 2.74
2344 5040 3.181458 TGTTTCCTGGGTGTAGACTTGAC 60.181 47.826 0.00 0.00 0.00 3.18
2346 5042 2.972348 TCCTGGGTGTAGACTTGACTT 58.028 47.619 0.00 0.00 0.00 3.01
2357 5053 7.279313 GGTGTAGACTTGACTTTCTTTTACACA 59.721 37.037 11.55 0.00 33.37 3.72
2359 5055 9.221933 TGTAGACTTGACTTTCTTTTACACAAA 57.778 29.630 0.00 0.00 0.00 2.83
2389 5086 1.974265 TCATCGACCAAAAACCAGCA 58.026 45.000 0.00 0.00 0.00 4.41
2396 5093 3.490761 CGACCAAAAACCAGCATTGACTT 60.491 43.478 0.00 0.00 0.00 3.01
2442 5141 8.914011 TGCTATATACAAGACACTATTCACACT 58.086 33.333 0.00 0.00 0.00 3.55
2450 5149 9.507329 ACAAGACACTATTCACACTAATTTGAT 57.493 29.630 0.00 0.00 0.00 2.57
2483 5182 1.305201 TTTCACCCTGAAGTCAACGC 58.695 50.000 0.00 0.00 37.70 4.84
2485 5184 0.249868 TCACCCTGAAGTCAACGCTG 60.250 55.000 0.00 0.00 0.00 5.18
2504 5203 0.178301 GGGTTTTGGTTGGCGGAAAA 59.822 50.000 0.00 0.00 0.00 2.29
2512 5211 4.705337 TGGTTGGCGGAAAATTACATAC 57.295 40.909 0.00 0.00 0.00 2.39
2514 5213 5.498393 TGGTTGGCGGAAAATTACATACTA 58.502 37.500 0.00 0.00 0.00 1.82
2516 5215 5.505159 GGTTGGCGGAAAATTACATACTAGC 60.505 44.000 0.00 0.00 0.00 3.42
2521 5220 5.728344 GCGGAAAATTACATACTAGCGCAAA 60.728 40.000 11.47 0.00 0.00 3.68
2522 5221 5.901884 CGGAAAATTACATACTAGCGCAAAG 59.098 40.000 11.47 9.47 0.00 2.77
2523 5222 6.237996 CGGAAAATTACATACTAGCGCAAAGA 60.238 38.462 11.47 0.00 0.00 2.52
2524 5223 7.469260 GGAAAATTACATACTAGCGCAAAGAA 58.531 34.615 11.47 0.00 0.00 2.52
2525 5224 7.966204 GGAAAATTACATACTAGCGCAAAGAAA 59.034 33.333 11.47 1.17 0.00 2.52
2526 5225 9.337091 GAAAATTACATACTAGCGCAAAGAAAA 57.663 29.630 11.47 0.00 0.00 2.29
2527 5226 9.685828 AAAATTACATACTAGCGCAAAGAAAAA 57.314 25.926 11.47 0.00 0.00 1.94
2687 5481 8.553153 TCCCATATACTCAACTAATTGTTTCCA 58.447 33.333 0.00 0.00 36.63 3.53
2722 5516 2.039480 TCTCTTGCAGATTGGTGAGCTT 59.961 45.455 0.00 0.00 0.00 3.74
2846 5644 1.686052 TGGTTGTCAACAAAGCCATCC 59.314 47.619 17.29 0.00 37.63 3.51
2885 5715 4.394729 TGATGGGTTCCTTTCTTACACAC 58.605 43.478 0.00 0.00 0.00 3.82
2887 5717 2.435069 TGGGTTCCTTTCTTACACACGA 59.565 45.455 0.00 0.00 0.00 4.35
2907 5740 6.865205 ACACGACGCTTTTAGACTTAGTTATT 59.135 34.615 0.00 0.00 0.00 1.40
2960 5796 4.776308 ACAAAAGAATACTACTCCCTCCGT 59.224 41.667 0.00 0.00 0.00 4.69
2961 5797 5.105432 ACAAAAGAATACTACTCCCTCCGTC 60.105 44.000 0.00 0.00 0.00 4.79
2962 5798 3.226682 AGAATACTACTCCCTCCGTCC 57.773 52.381 0.00 0.00 0.00 4.79
2963 5799 2.158490 AGAATACTACTCCCTCCGTCCC 60.158 54.545 0.00 0.00 0.00 4.46
2964 5800 1.229131 ATACTACTCCCTCCGTCCCA 58.771 55.000 0.00 0.00 0.00 4.37
2965 5801 1.229131 TACTACTCCCTCCGTCCCAT 58.771 55.000 0.00 0.00 0.00 4.00
2966 5802 1.229131 ACTACTCCCTCCGTCCCATA 58.771 55.000 0.00 0.00 0.00 2.74
2967 5803 1.572415 ACTACTCCCTCCGTCCCATAA 59.428 52.381 0.00 0.00 0.00 1.90
2968 5804 2.179424 ACTACTCCCTCCGTCCCATAAT 59.821 50.000 0.00 0.00 0.00 1.28
2969 5805 3.400322 ACTACTCCCTCCGTCCCATAATA 59.600 47.826 0.00 0.00 0.00 0.98
2970 5806 3.562108 ACTCCCTCCGTCCCATAATAT 57.438 47.619 0.00 0.00 0.00 1.28
2971 5807 3.173965 ACTCCCTCCGTCCCATAATATG 58.826 50.000 0.00 0.00 0.00 1.78
2972 5808 3.181410 ACTCCCTCCGTCCCATAATATGA 60.181 47.826 1.10 0.00 0.00 2.15
2973 5809 3.441101 TCCCTCCGTCCCATAATATGAG 58.559 50.000 1.10 0.00 0.00 2.90
2974 5810 3.076937 TCCCTCCGTCCCATAATATGAGA 59.923 47.826 1.10 0.00 0.00 3.27
2975 5811 3.195825 CCCTCCGTCCCATAATATGAGAC 59.804 52.174 5.01 5.01 35.00 3.36
3008 5844 4.690122 ACTACACTAGTGTCAAAAAGCGT 58.310 39.130 31.11 13.23 43.74 5.07
3009 5845 4.743644 ACTACACTAGTGTCAAAAAGCGTC 59.256 41.667 31.11 0.00 43.74 5.19
3010 5846 3.793559 ACACTAGTGTCAAAAAGCGTCT 58.206 40.909 22.95 0.00 40.24 4.18
3011 5847 4.189231 ACACTAGTGTCAAAAAGCGTCTT 58.811 39.130 22.95 0.00 40.24 3.01
3012 5848 5.353938 ACACTAGTGTCAAAAAGCGTCTTA 58.646 37.500 22.95 0.00 40.24 2.10
3013 5849 5.233689 ACACTAGTGTCAAAAAGCGTCTTAC 59.766 40.000 22.95 0.00 40.24 2.34
3014 5850 5.233476 CACTAGTGTCAAAAAGCGTCTTACA 59.767 40.000 15.06 0.00 0.00 2.41
3015 5851 5.989777 ACTAGTGTCAAAAAGCGTCTTACAT 59.010 36.000 0.00 0.00 0.00 2.29
3016 5852 5.751243 AGTGTCAAAAAGCGTCTTACATT 57.249 34.783 0.00 0.00 0.00 2.71
3017 5853 6.854496 AGTGTCAAAAAGCGTCTTACATTA 57.146 33.333 0.00 0.00 0.00 1.90
3018 5854 7.435068 AGTGTCAAAAAGCGTCTTACATTAT 57.565 32.000 0.00 0.00 0.00 1.28
3019 5855 7.298122 AGTGTCAAAAAGCGTCTTACATTATG 58.702 34.615 0.00 0.00 0.00 1.90
3020 5856 6.523201 GTGTCAAAAAGCGTCTTACATTATGG 59.477 38.462 0.00 0.00 0.00 2.74
3021 5857 6.027749 GTCAAAAAGCGTCTTACATTATGGG 58.972 40.000 0.00 0.00 0.00 4.00
3022 5858 5.941058 TCAAAAAGCGTCTTACATTATGGGA 59.059 36.000 0.00 0.00 0.00 4.37
3023 5859 5.813080 AAAAGCGTCTTACATTATGGGAC 57.187 39.130 0.00 1.75 0.00 4.46
3025 5861 2.132762 GCGTCTTACATTATGGGACGG 58.867 52.381 25.20 14.78 46.26 4.79
3026 5862 2.223876 GCGTCTTACATTATGGGACGGA 60.224 50.000 25.20 5.94 46.26 4.69
3027 5863 3.639538 CGTCTTACATTATGGGACGGAG 58.360 50.000 20.50 2.74 43.69 4.63
3028 5864 3.552273 CGTCTTACATTATGGGACGGAGG 60.552 52.174 20.50 5.87 43.69 4.30
3029 5865 2.969950 TCTTACATTATGGGACGGAGGG 59.030 50.000 0.00 0.00 0.00 4.30
3030 5866 2.779429 TACATTATGGGACGGAGGGA 57.221 50.000 0.00 0.00 0.00 4.20
3031 5867 1.424638 ACATTATGGGACGGAGGGAG 58.575 55.000 0.00 0.00 0.00 4.30
3032 5868 1.344087 ACATTATGGGACGGAGGGAGT 60.344 52.381 0.00 0.00 0.00 3.85
3033 5869 2.090943 ACATTATGGGACGGAGGGAGTA 60.091 50.000 0.00 0.00 0.00 2.59
3034 5870 2.077687 TTATGGGACGGAGGGAGTAC 57.922 55.000 0.00 0.00 0.00 2.73
3035 5871 1.229131 TATGGGACGGAGGGAGTACT 58.771 55.000 0.00 0.00 0.00 2.73
3044 5880 3.454812 ACGGAGGGAGTACTTATTTGCAT 59.545 43.478 0.00 0.00 0.00 3.96
3176 6299 3.790820 CCATGTCAAACAACACTGAAACG 59.209 43.478 0.00 0.00 30.55 3.60
3178 6301 4.335082 TGTCAAACAACACTGAAACGAG 57.665 40.909 0.00 0.00 0.00 4.18
3184 6307 2.676342 ACAACACTGAAACGAGTTGGAC 59.324 45.455 8.72 0.00 44.10 4.02
3197 6320 3.182967 GAGTTGGACTCGCAATGTAGAG 58.817 50.000 6.38 6.38 35.28 2.43
3262 6394 7.372714 ACTGTACGTCTGTCATTTGTACATTA 58.627 34.615 0.00 0.00 42.95 1.90
3271 6403 7.817478 TCTGTCATTTGTACATTAGTGTGGTAG 59.183 37.037 0.34 0.00 39.39 3.18
3274 6406 8.995220 GTCATTTGTACATTAGTGTGGTAGAAA 58.005 33.333 0.34 0.00 39.39 2.52
3288 6420 8.837389 AGTGTGGTAGAAATTTAGTGAGTTTTC 58.163 33.333 0.00 0.00 0.00 2.29
3301 6434 6.811253 AGTGAGTTTTCTACACAAACAACA 57.189 33.333 0.00 0.00 36.71 3.33
3316 6449 8.081633 ACACAAACAACATGATTTACATACCAG 58.918 33.333 0.00 0.00 37.46 4.00
3317 6450 7.062138 CACAAACAACATGATTTACATACCAGC 59.938 37.037 0.00 0.00 37.46 4.85
3326 6459 7.843490 TGATTTACATACCAGCTTACTGTTC 57.157 36.000 0.00 0.00 42.81 3.18
3328 6461 8.046708 TGATTTACATACCAGCTTACTGTTCAT 58.953 33.333 0.00 0.00 42.81 2.57
3329 6462 7.609760 TTTACATACCAGCTTACTGTTCATG 57.390 36.000 0.00 0.00 42.81 3.07
3330 6463 5.165961 ACATACCAGCTTACTGTTCATGT 57.834 39.130 0.00 0.00 42.81 3.21
3331 6464 6.294361 ACATACCAGCTTACTGTTCATGTA 57.706 37.500 0.00 0.00 42.81 2.29
3332 6465 6.106673 ACATACCAGCTTACTGTTCATGTAC 58.893 40.000 0.00 0.00 42.81 2.90
3333 6466 3.939066 ACCAGCTTACTGTTCATGTACC 58.061 45.455 0.00 0.00 42.81 3.34
3334 6467 3.270877 CCAGCTTACTGTTCATGTACCC 58.729 50.000 0.00 0.00 42.81 3.69
3335 6468 3.270877 CAGCTTACTGTTCATGTACCCC 58.729 50.000 0.00 0.00 39.22 4.95
3338 6471 3.119029 GCTTACTGTTCATGTACCCCGTA 60.119 47.826 0.00 0.00 0.00 4.02
3339 6472 4.621274 GCTTACTGTTCATGTACCCCGTAA 60.621 45.833 0.00 4.96 0.00 3.18
3342 6475 4.716794 ACTGTTCATGTACCCCGTAAAAA 58.283 39.130 0.00 0.00 0.00 1.94
3365 6498 7.624360 AAAAACTTACTGTTCATGTGAGTGA 57.376 32.000 0.00 0.00 38.03 3.41
3366 6499 6.851222 AAACTTACTGTTCATGTGAGTGAG 57.149 37.500 9.91 9.91 38.03 3.51
3367 6500 5.537300 ACTTACTGTTCATGTGAGTGAGT 57.463 39.130 10.80 10.80 33.86 3.41
3368 6501 6.650427 ACTTACTGTTCATGTGAGTGAGTA 57.350 37.500 13.37 0.00 35.46 2.59
3369 6502 6.448006 ACTTACTGTTCATGTGAGTGAGTAC 58.552 40.000 13.37 0.00 35.46 2.73
3370 6503 4.937201 ACTGTTCATGTGAGTGAGTACA 57.063 40.909 0.00 0.00 0.00 2.90
3398 6532 9.471084 AAAAACTGGATTTTATTAGGTGAAACG 57.529 29.630 0.00 0.00 39.70 3.60
3406 6540 7.416154 TTTTATTAGGTGAAACGACACTGAG 57.584 36.000 0.00 0.00 40.22 3.35
3568 7041 6.832520 AATTAATTTGAAAACAATGGGGGC 57.167 33.333 0.00 0.00 0.00 5.80
3571 7044 3.415457 TTTGAAAACAATGGGGGCATC 57.585 42.857 0.00 0.00 0.00 3.91
3590 7063 9.301897 GGGGCATCTGTCTTTTATTTAAGATAT 57.698 33.333 0.00 0.00 36.60 1.63
3699 7997 3.565902 GGTTGCATAGCCAGGAATTACTC 59.434 47.826 0.00 0.00 0.00 2.59
3706 8146 1.597742 CCAGGAATTACTCATGCCCG 58.402 55.000 0.00 0.00 34.39 6.13
3729 8169 4.290942 AGGCCAACTTAGAGCTACAGTAT 58.709 43.478 5.01 0.00 0.00 2.12
3761 8201 0.747255 ATGGTAGCTACGGTCAGCAG 59.253 55.000 17.48 0.00 44.35 4.24
3777 8415 1.527034 GCAGATGGAGTTGCTGTCAA 58.473 50.000 0.00 0.00 37.35 3.18
3803 8441 0.108662 GCCCATGGCTTGTGTAAAGC 60.109 55.000 6.09 1.41 46.69 3.51
3804 8442 0.171007 CCCATGGCTTGTGTAAAGCG 59.829 55.000 6.09 0.00 43.89 4.68
3888 8542 9.842775 TCTTTCTGAAATCATATAAGCACTGAT 57.157 29.630 2.88 0.00 0.00 2.90
3903 8557 5.459505 AGCACTGATACTGGATAGTAGGTT 58.540 41.667 0.00 0.00 42.36 3.50
3953 8611 8.856153 TTTTAAACAGTGATATGGAAGCAGTA 57.144 30.769 0.00 0.00 0.00 2.74
4024 8686 6.211587 AGCATTAATTTGTGCATAGAAGCA 57.788 33.333 14.66 0.00 43.63 3.91
4032 8694 5.512753 TTGTGCATAGAAGCAGTTGAAAA 57.487 34.783 0.00 0.00 46.69 2.29
4268 8938 4.439289 GGTGTATATCGTCGGCCCTATTAC 60.439 50.000 0.00 0.00 0.00 1.89
4308 8978 0.539986 GGGCTTACAACCTCATCCGA 59.460 55.000 0.00 0.00 0.00 4.55
4432 9126 2.156098 TGTTGTAATTCTCCAACCGCC 58.844 47.619 11.03 0.00 40.12 6.13
4434 9128 0.034863 TGTAATTCTCCAACCGCCCC 60.035 55.000 0.00 0.00 0.00 5.80
4534 9228 7.967908 TGATTTTCTCTCTGAAGAAAGTAGGT 58.032 34.615 11.83 3.12 43.95 3.08
4573 9269 2.613223 GGCTCTGTTCTACCACAACCTC 60.613 54.545 0.00 0.00 0.00 3.85
4593 9295 8.353684 CAACCTCGACTTATGTCTCTAATGTAT 58.646 37.037 7.13 0.00 40.86 2.29
4622 9327 2.520979 GACCGATGAGTGAAGTCTTCG 58.479 52.381 13.61 13.61 41.44 3.79
4624 9329 2.638556 CGATGAGTGAAGTCTTCGGT 57.361 50.000 8.06 0.00 39.32 4.69
4625 9330 2.254459 CGATGAGTGAAGTCTTCGGTG 58.746 52.381 8.06 0.00 39.32 4.94
4642 9347 0.395724 GTGAAGGGCATAGTTGGGGG 60.396 60.000 0.00 0.00 0.00 5.40
4647 9352 1.150764 GGCATAGTTGGGGGCCTAC 59.849 63.158 0.84 0.00 43.09 3.18
4669 9374 3.462021 GTCAAGAGGATATGTGTGCCTC 58.538 50.000 0.00 0.00 46.75 4.70
4680 9385 0.388649 GTGTGCCTCCTAGTGACGTG 60.389 60.000 0.00 0.00 0.00 4.49
4686 9391 2.893637 CCTCCTAGTGACGTGATTTGG 58.106 52.381 0.00 0.00 0.00 3.28
4688 9393 1.553248 TCCTAGTGACGTGATTTGGGG 59.447 52.381 0.00 0.00 0.00 4.96
4689 9394 1.369625 CTAGTGACGTGATTTGGGGC 58.630 55.000 0.00 0.00 0.00 5.80
4690 9395 0.981183 TAGTGACGTGATTTGGGGCT 59.019 50.000 0.00 0.00 0.00 5.19
4691 9396 0.321653 AGTGACGTGATTTGGGGCTC 60.322 55.000 0.00 0.00 0.00 4.70
4807 11843 0.972883 GCTGAGTGTGAGAGAGGGTT 59.027 55.000 0.00 0.00 0.00 4.11
4856 11892 4.141482 CCTATGGTGTAGGCTGGTTGTATT 60.141 45.833 0.00 0.00 0.00 1.89
4857 11893 3.066291 TGGTGTAGGCTGGTTGTATTG 57.934 47.619 0.00 0.00 0.00 1.90
4858 11894 2.373836 TGGTGTAGGCTGGTTGTATTGT 59.626 45.455 0.00 0.00 0.00 2.71
4859 11895 3.007635 GGTGTAGGCTGGTTGTATTGTC 58.992 50.000 0.00 0.00 0.00 3.18
4860 11896 3.007635 GTGTAGGCTGGTTGTATTGTCC 58.992 50.000 0.00 0.00 0.00 4.02
4876 11913 1.286248 GTCCTGGGGTGTATGGAAGT 58.714 55.000 0.00 0.00 0.00 3.01
4901 11938 9.333724 GTAGATGCTTCTTACTAGTAGAAGACT 57.666 37.037 28.04 24.30 40.89 3.24
4902 11939 8.446599 AGATGCTTCTTACTAGTAGAAGACTC 57.553 38.462 28.04 23.59 40.89 3.36
4968 12006 0.606096 AAAAACTAACCATGCCCCGC 59.394 50.000 0.00 0.00 0.00 6.13
4982 12020 1.345715 CCCCGCCTTCCTGATAACCT 61.346 60.000 0.00 0.00 0.00 3.50
4992 12030 7.309867 CGCCTTCCTGATAACCTACAAGTATAT 60.310 40.741 0.00 0.00 0.00 0.86
5004 12042 8.596781 ACCTACAAGTATATGGGATCTATCAC 57.403 38.462 0.00 0.00 0.00 3.06
5129 12167 5.746721 GGTTTGTTTGAAAGCAAGTAATCGT 59.253 36.000 0.00 0.00 35.04 3.73
5225 12263 4.412796 ACGGTTTTACTTATAGGGCTCC 57.587 45.455 0.00 0.00 0.00 4.70
5347 12386 5.506708 GAGGGGGTTATCGGCAATATAATT 58.493 41.667 0.00 0.00 0.00 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
48 49 2.200373 ACAAAGTACTGTGGGATGGC 57.800 50.000 17.46 0.00 0.00 4.40
54 55 5.927115 GGTCTAAGAGAACAAAGTACTGTGG 59.073 44.000 17.46 2.76 30.64 4.17
90 92 6.478588 CAACAAAGTAGAGAAAGTGTGACAC 58.521 40.000 7.83 7.83 34.10 3.67
122 124 5.076873 AGCAAAAAGGCATAGTACCTCAAA 58.923 37.500 0.00 0.00 36.14 2.69
133 135 5.770162 GTGTCCCTATATAGCAAAAAGGCAT 59.230 40.000 4.04 0.00 35.83 4.40
152 154 4.024556 CGGCTCAGAAATGAATATGTGTCC 60.025 45.833 0.00 0.00 0.00 4.02
157 159 2.816087 CCCCGGCTCAGAAATGAATATG 59.184 50.000 0.00 0.00 0.00 1.78
175 177 1.228184 CAGGATGCAGATGAGCCCC 60.228 63.158 0.00 0.00 0.00 5.80
176 178 0.761187 TACAGGATGCAGATGAGCCC 59.239 55.000 0.00 0.00 42.53 5.19
259 261 2.359107 ATGCGCCTCACACTGTGG 60.359 61.111 13.09 1.42 33.87 4.17
273 275 1.274596 CGAGCTGAAATTTGGCATGC 58.725 50.000 9.90 9.90 0.00 4.06
279 281 4.143263 GCATTCCAAACGAGCTGAAATTTG 60.143 41.667 0.00 0.00 32.89 2.32
325 2643 3.096852 AGTCATGTACTGTTGGGATCGA 58.903 45.455 0.00 0.00 36.93 3.59
326 2644 3.526931 AGTCATGTACTGTTGGGATCG 57.473 47.619 0.00 0.00 36.93 3.69
328 2646 6.957631 TGAAATAGTCATGTACTGTTGGGAT 58.042 36.000 7.74 0.00 38.47 3.85
332 2650 9.035607 GGTCTATGAAATAGTCATGTACTGTTG 57.964 37.037 7.74 0.00 46.85 3.33
367 2685 5.924825 TCCGAGTAGCTCTTAACAAAAAGAC 59.075 40.000 0.00 0.00 32.18 3.01
377 2695 5.007430 CGTTTAGACATCCGAGTAGCTCTTA 59.993 44.000 0.00 0.00 0.00 2.10
383 2701 3.312973 AGCTCGTTTAGACATCCGAGTAG 59.687 47.826 9.31 0.00 46.30 2.57
389 2707 5.803020 AATTTCAGCTCGTTTAGACATCC 57.197 39.130 0.00 0.00 0.00 3.51
395 2713 3.914364 GTGCCAAATTTCAGCTCGTTTAG 59.086 43.478 10.28 0.00 0.00 1.85
416 2734 1.336755 GTTTCCATGCGTGAGGTTTGT 59.663 47.619 7.72 0.00 0.00 2.83
418 2736 1.686355 TGTTTCCATGCGTGAGGTTT 58.314 45.000 7.72 0.00 0.00 3.27
430 2748 1.974265 TTGCACGGAAGATGTTTCCA 58.026 45.000 6.73 0.00 38.49 3.53
435 2753 3.820467 TGATCTTTTTGCACGGAAGATGT 59.180 39.130 18.10 2.29 39.52 3.06
442 2760 3.624326 TCTTGTGATCTTTTTGCACGG 57.376 42.857 0.00 0.00 35.37 4.94
444 2762 8.524870 AATGTTATCTTGTGATCTTTTTGCAC 57.475 30.769 0.00 0.00 34.32 4.57
462 2780 7.598759 ACGTGAGGTCCTATTAGAATGTTAT 57.401 36.000 0.00 0.00 0.00 1.89
495 2813 3.684305 CCAAAATCCGCAAAAATTCCTCC 59.316 43.478 0.00 0.00 0.00 4.30
537 2860 4.009370 AGTTCCTTTGAAGAGTGCCTAC 57.991 45.455 0.00 0.00 0.00 3.18
544 2867 5.560724 TGTATGGGAAGTTCCTTTGAAGAG 58.439 41.667 21.25 0.00 36.57 2.85
554 2877 4.038883 ACGGTAGCTATGTATGGGAAGTTC 59.961 45.833 0.00 0.00 0.00 3.01
713 3039 2.470983 TGGATCTGCGTGTTGATCAA 57.529 45.000 3.38 3.38 40.41 2.57
720 3046 1.873591 GTCTTGTTTGGATCTGCGTGT 59.126 47.619 0.00 0.00 0.00 4.49
771 3097 0.393673 TCTCTCTCTCTCCGGCTGTG 60.394 60.000 0.00 0.00 0.00 3.66
1120 3461 3.044059 GATTGGCCGTGCTGCTCAC 62.044 63.158 0.00 0.45 42.23 3.51
1276 3634 1.001378 GTGCAACTACTTTGTGCTGGG 60.001 52.381 0.00 0.00 37.54 4.45
1318 3676 0.685458 TCCTACCTGAACTACGGCCC 60.685 60.000 0.00 0.00 0.00 5.80
1350 3710 7.531716 ACTCTTCTATCTAGTGTTTGAACTCG 58.468 38.462 0.00 0.00 0.00 4.18
1364 3724 6.042093 TGTCCACTTGTTTGACTCTTCTATCT 59.958 38.462 0.00 0.00 0.00 1.98
1416 3776 1.103803 ATCGGCTCATCACGTGTAGT 58.896 50.000 16.51 0.00 0.00 2.73
1417 3777 3.560902 ATATCGGCTCATCACGTGTAG 57.439 47.619 16.51 12.50 0.00 2.74
1435 3809 5.574891 ATTGTTGCGTTTGGATTGCTATA 57.425 34.783 0.00 0.00 0.00 1.31
1436 3810 3.932545 TTGTTGCGTTTGGATTGCTAT 57.067 38.095 0.00 0.00 0.00 2.97
1502 3969 1.270550 AGGCGACATTTTCAAAGGCAG 59.729 47.619 0.00 0.00 0.00 4.85
1551 4028 2.161855 CTACTGCTGACCCAATTGCAA 58.838 47.619 0.00 0.00 34.90 4.08
1553 4030 0.453390 GCTACTGCTGACCCAATTGC 59.547 55.000 0.00 0.00 36.03 3.56
1665 4177 2.835431 CCCAGGATCTCGGCGAGT 60.835 66.667 33.31 21.83 0.00 4.18
2176 4722 1.447140 GCTGCGTTATGACCGGTGA 60.447 57.895 14.63 2.52 0.00 4.02
2177 4723 2.461110 GGCTGCGTTATGACCGGTG 61.461 63.158 14.63 0.00 0.00 4.94
2239 4785 7.769220 AGCTCCATAATTTTGACAAGATCTTG 58.231 34.615 29.74 29.74 45.58 3.02
2258 4804 4.894784 ACTTCGTCAATCTTTAAGCTCCA 58.105 39.130 0.00 0.00 0.00 3.86
2314 4912 1.269448 CACCCAGGAAACAAATGTCCG 59.731 52.381 0.00 0.00 39.06 4.79
2319 4917 4.724279 AGTCTACACCCAGGAAACAAAT 57.276 40.909 0.00 0.00 0.00 2.32
2322 4920 3.042682 TCAAGTCTACACCCAGGAAACA 58.957 45.455 0.00 0.00 0.00 2.83
2324 4922 3.314693 AGTCAAGTCTACACCCAGGAAA 58.685 45.455 0.00 0.00 0.00 3.13
2326 4924 2.696526 AGTCAAGTCTACACCCAGGA 57.303 50.000 0.00 0.00 0.00 3.86
2328 4926 4.608948 AGAAAGTCAAGTCTACACCCAG 57.391 45.455 0.00 0.00 0.00 4.45
2329 4927 5.367945 AAAGAAAGTCAAGTCTACACCCA 57.632 39.130 0.00 0.00 0.00 4.51
2332 4930 8.193250 TGTGTAAAAGAAAGTCAAGTCTACAC 57.807 34.615 0.00 0.00 33.99 2.90
2333 4931 8.780846 TTGTGTAAAAGAAAGTCAAGTCTACA 57.219 30.769 0.00 0.00 0.00 2.74
2359 5055 9.581099 GGTTTTTGGTCGATGAAAATTACATAT 57.419 29.630 5.64 0.00 0.00 1.78
2375 5072 3.733443 AGTCAATGCTGGTTTTTGGTC 57.267 42.857 0.00 0.00 0.00 4.02
2383 5080 0.610232 GCCCAGAAGTCAATGCTGGT 60.610 55.000 0.00 0.00 46.05 4.00
2450 5149 9.323985 CTTCAGGGTGAAAAACAAAATAATTGA 57.676 29.630 0.00 0.00 35.73 2.57
2454 5153 7.841956 TGACTTCAGGGTGAAAAACAAAATAA 58.158 30.769 0.00 0.00 35.73 1.40
2455 5154 7.411486 TGACTTCAGGGTGAAAAACAAAATA 57.589 32.000 0.00 0.00 35.73 1.40
2457 5156 5.730296 TGACTTCAGGGTGAAAAACAAAA 57.270 34.783 0.00 0.00 35.73 2.44
2458 5157 5.474825 GTTGACTTCAGGGTGAAAAACAAA 58.525 37.500 0.00 0.00 35.73 2.83
2466 5165 0.249868 CAGCGTTGACTTCAGGGTGA 60.250 55.000 0.00 0.00 34.04 4.02
2468 5167 1.071471 CCAGCGTTGACTTCAGGGT 59.929 57.895 0.00 0.00 0.00 4.34
2471 5170 1.308998 AAACCCAGCGTTGACTTCAG 58.691 50.000 0.00 0.00 33.93 3.02
2483 5182 1.395826 TTCCGCCAACCAAAACCCAG 61.396 55.000 0.00 0.00 0.00 4.45
2485 5184 0.178301 TTTTCCGCCAACCAAAACCC 59.822 50.000 0.00 0.00 0.00 4.11
2553 5252 9.588096 AAACTTGACTTTCTTAAGATATTGGGT 57.412 29.630 5.89 0.00 35.30 4.51
2639 5350 4.440145 CCCCTTGGTTCATGGGTG 57.560 61.111 15.01 5.85 44.42 4.61
2687 5481 3.181429 TGCAAGAGAGGGAGAAAATGGTT 60.181 43.478 0.00 0.00 0.00 3.67
2846 5644 5.184479 ACCCATCAACATGTCTCAATCAAAG 59.816 40.000 0.00 0.00 0.00 2.77
2885 5715 6.290956 CGGAATAACTAAGTCTAAAAGCGTCG 60.291 42.308 0.00 0.00 0.00 5.12
2887 5717 6.393171 ACGGAATAACTAAGTCTAAAAGCGT 58.607 36.000 0.00 0.00 0.00 5.07
2907 5740 5.845103 TCAGTTAATTGTTCACACTACGGA 58.155 37.500 0.00 0.00 0.00 4.69
2986 5822 4.690122 ACGCTTTTTGACACTAGTGTAGT 58.310 39.130 27.98 14.12 45.05 2.73
2987 5823 4.982916 AGACGCTTTTTGACACTAGTGTAG 59.017 41.667 27.98 20.94 45.05 2.74
2988 5824 4.940463 AGACGCTTTTTGACACTAGTGTA 58.060 39.130 27.98 11.50 45.05 2.90
2990 5826 4.795970 AAGACGCTTTTTGACACTAGTG 57.204 40.909 21.44 21.44 0.00 2.74
2991 5827 5.353938 TGTAAGACGCTTTTTGACACTAGT 58.646 37.500 0.00 0.00 0.00 2.57
2992 5828 5.900339 TGTAAGACGCTTTTTGACACTAG 57.100 39.130 0.00 0.00 0.00 2.57
2993 5829 6.854496 AATGTAAGACGCTTTTTGACACTA 57.146 33.333 0.00 0.00 0.00 2.74
2994 5830 5.751243 AATGTAAGACGCTTTTTGACACT 57.249 34.783 0.00 0.00 0.00 3.55
2995 5831 6.523201 CCATAATGTAAGACGCTTTTTGACAC 59.477 38.462 0.00 0.00 0.00 3.67
2996 5832 6.348950 CCCATAATGTAAGACGCTTTTTGACA 60.349 38.462 0.00 0.00 0.00 3.58
2997 5833 6.027749 CCCATAATGTAAGACGCTTTTTGAC 58.972 40.000 0.00 0.00 0.00 3.18
2998 5834 5.941058 TCCCATAATGTAAGACGCTTTTTGA 59.059 36.000 0.00 0.00 0.00 2.69
2999 5835 6.027749 GTCCCATAATGTAAGACGCTTTTTG 58.972 40.000 0.00 0.00 0.00 2.44
3000 5836 5.163794 CGTCCCATAATGTAAGACGCTTTTT 60.164 40.000 0.00 0.00 43.07 1.94
3001 5837 4.331717 CGTCCCATAATGTAAGACGCTTTT 59.668 41.667 0.00 0.00 43.07 2.27
3002 5838 3.869246 CGTCCCATAATGTAAGACGCTTT 59.131 43.478 0.00 0.00 43.07 3.51
3003 5839 3.454375 CGTCCCATAATGTAAGACGCTT 58.546 45.455 0.00 0.00 43.07 4.68
3004 5840 2.223971 CCGTCCCATAATGTAAGACGCT 60.224 50.000 5.39 0.00 46.66 5.07
3005 5841 2.132762 CCGTCCCATAATGTAAGACGC 58.867 52.381 5.39 0.00 46.66 5.19
3007 5843 3.244112 CCCTCCGTCCCATAATGTAAGAC 60.244 52.174 0.00 0.00 0.00 3.01
3008 5844 2.969950 CCCTCCGTCCCATAATGTAAGA 59.030 50.000 0.00 0.00 0.00 2.10
3009 5845 2.969950 TCCCTCCGTCCCATAATGTAAG 59.030 50.000 0.00 0.00 0.00 2.34
3010 5846 2.969950 CTCCCTCCGTCCCATAATGTAA 59.030 50.000 0.00 0.00 0.00 2.41
3011 5847 2.090943 ACTCCCTCCGTCCCATAATGTA 60.091 50.000 0.00 0.00 0.00 2.29
3012 5848 1.344087 ACTCCCTCCGTCCCATAATGT 60.344 52.381 0.00 0.00 0.00 2.71
3013 5849 1.424638 ACTCCCTCCGTCCCATAATG 58.575 55.000 0.00 0.00 0.00 1.90
3014 5850 2.179424 AGTACTCCCTCCGTCCCATAAT 59.821 50.000 0.00 0.00 0.00 1.28
3015 5851 1.572415 AGTACTCCCTCCGTCCCATAA 59.428 52.381 0.00 0.00 0.00 1.90
3016 5852 1.229131 AGTACTCCCTCCGTCCCATA 58.771 55.000 0.00 0.00 0.00 2.74
3017 5853 0.338814 AAGTACTCCCTCCGTCCCAT 59.661 55.000 0.00 0.00 0.00 4.00
3018 5854 1.002069 TAAGTACTCCCTCCGTCCCA 58.998 55.000 0.00 0.00 0.00 4.37
3019 5855 2.378378 ATAAGTACTCCCTCCGTCCC 57.622 55.000 0.00 0.00 0.00 4.46
3020 5856 3.740452 GCAAATAAGTACTCCCTCCGTCC 60.740 52.174 0.00 0.00 0.00 4.79
3021 5857 3.118884 TGCAAATAAGTACTCCCTCCGTC 60.119 47.826 0.00 0.00 0.00 4.79
3022 5858 2.835764 TGCAAATAAGTACTCCCTCCGT 59.164 45.455 0.00 0.00 0.00 4.69
3023 5859 3.536956 TGCAAATAAGTACTCCCTCCG 57.463 47.619 0.00 0.00 0.00 4.63
3024 5860 6.354130 TGTTATGCAAATAAGTACTCCCTCC 58.646 40.000 0.00 0.00 0.00 4.30
3025 5861 7.859325 TTGTTATGCAAATAAGTACTCCCTC 57.141 36.000 0.00 0.00 33.53 4.30
3055 5915 2.898612 ACCATGACCATGCAACAAATCA 59.101 40.909 4.53 0.00 37.49 2.57
3176 6299 3.182967 CTCTACATTGCGAGTCCAACTC 58.817 50.000 0.00 0.00 41.71 3.01
3178 6301 2.271800 CCTCTACATTGCGAGTCCAAC 58.728 52.381 0.00 0.00 0.00 3.77
3184 6307 6.561614 TCTAGTTTTACCTCTACATTGCGAG 58.438 40.000 0.00 0.00 0.00 5.03
3197 6320 5.526111 TCTGCGGCAATTATCTAGTTTTACC 59.474 40.000 3.44 0.00 0.00 2.85
3238 6370 6.706055 AATGTACAAATGACAGACGTACAG 57.294 37.500 0.00 0.00 43.90 2.74
3262 6394 8.747538 AAAACTCACTAAATTTCTACCACACT 57.252 30.769 0.00 0.00 0.00 3.55
3274 6406 9.783256 GTTGTTTGTGTAGAAAACTCACTAAAT 57.217 29.630 0.00 0.00 38.17 1.40
3288 6420 9.554724 GGTATGTAAATCATGTTGTTTGTGTAG 57.445 33.333 0.00 0.00 37.91 2.74
3296 6429 7.829211 AGTAAGCTGGTATGTAAATCATGTTGT 59.171 33.333 0.00 0.00 37.91 3.32
3301 6434 8.046708 TGAACAGTAAGCTGGTATGTAAATCAT 58.953 33.333 0.00 0.00 43.85 2.45
3316 6449 2.277084 CGGGGTACATGAACAGTAAGC 58.723 52.381 0.00 0.00 0.00 3.09
3317 6450 3.604875 ACGGGGTACATGAACAGTAAG 57.395 47.619 0.00 0.00 0.00 2.34
3342 6475 6.823689 ACTCACTCACATGAACAGTAAGTTTT 59.176 34.615 0.00 0.00 41.51 2.43
3343 6476 6.349300 ACTCACTCACATGAACAGTAAGTTT 58.651 36.000 0.00 0.00 41.51 2.66
3344 6477 5.918608 ACTCACTCACATGAACAGTAAGTT 58.081 37.500 0.00 0.00 44.93 2.66
3345 6478 5.537300 ACTCACTCACATGAACAGTAAGT 57.463 39.130 0.00 0.00 0.00 2.24
3346 6479 6.447162 TGTACTCACTCACATGAACAGTAAG 58.553 40.000 0.00 0.00 0.00 2.34
3347 6480 6.399639 TGTACTCACTCACATGAACAGTAA 57.600 37.500 0.00 0.00 0.00 2.24
3348 6481 6.399639 TTGTACTCACTCACATGAACAGTA 57.600 37.500 0.00 0.00 0.00 2.74
3349 6482 4.937201 TGTACTCACTCACATGAACAGT 57.063 40.909 0.00 0.00 0.00 3.55
3350 6483 6.603237 TTTTGTACTCACTCACATGAACAG 57.397 37.500 0.00 0.00 0.00 3.16
3351 6484 6.993786 TTTTTGTACTCACTCACATGAACA 57.006 33.333 0.00 0.00 0.00 3.18
3398 6532 4.268884 GCAATTCCGAATAGTCTCAGTGTC 59.731 45.833 0.00 0.00 0.00 3.67
3406 6540 4.335315 TCCACATTGCAATTCCGAATAGTC 59.665 41.667 9.83 0.00 0.00 2.59
3683 7981 3.245052 GGGCATGAGTAATTCCTGGCTAT 60.245 47.826 0.00 0.00 43.50 2.97
3706 8146 2.498078 ACTGTAGCTCTAAGTTGGCCTC 59.502 50.000 3.32 0.00 0.00 4.70
3717 8157 6.210784 TGGTTACTGTTCAATACTGTAGCTCT 59.789 38.462 0.00 0.00 40.73 4.09
3729 8169 4.634012 AGCTACCATGGTTACTGTTCAA 57.366 40.909 25.38 0.00 0.00 2.69
3761 8201 1.541588 GGGTTTGACAGCAACTCCATC 59.458 52.381 0.00 0.00 32.79 3.51
3785 8423 0.171007 CGCTTTACACAAGCCATGGG 59.829 55.000 15.13 0.00 40.02 4.00
3804 8442 4.509737 GACGTAGCCAGGCCCGAC 62.510 72.222 24.03 15.83 0.00 4.79
3847 8491 6.829229 TCAGAAAGAACTCTTATCACCGTA 57.171 37.500 0.00 0.00 34.61 4.02
3849 8493 7.331934 TGATTTCAGAAAGAACTCTTATCACCG 59.668 37.037 1.28 0.00 36.97 4.94
3876 8530 8.391699 ACCTACTATCCAGTATCAGTGCTTATA 58.608 37.037 0.00 0.00 36.66 0.98
3927 8585 8.353423 ACTGCTTCCATATCACTGTTTAAAAT 57.647 30.769 0.00 0.00 0.00 1.82
3931 8589 8.264347 TGAATACTGCTTCCATATCACTGTTTA 58.736 33.333 0.00 0.00 0.00 2.01
4032 8694 9.423061 GGTAGAGTGCAACAAAATATTGAAAAT 57.577 29.630 0.00 0.00 41.43 1.82
4139 8807 1.078072 ACAGCCGTGTCCACACAAA 60.078 52.632 10.39 0.00 46.75 2.83
4142 8810 1.301716 ATCACAGCCGTGTCCACAC 60.302 57.895 0.00 0.00 44.02 3.82
4145 8813 1.301637 CACATCACAGCCGTGTCCA 60.302 57.895 0.00 0.00 44.02 4.02
4308 8978 4.000988 CTCGTAGTGGCTTGTTGGTAAAT 58.999 43.478 0.00 0.00 0.00 1.40
4481 9175 7.339212 CACAATTAGAATTAGGTGACCCAATCA 59.661 37.037 0.00 0.00 33.79 2.57
4534 9228 1.675310 CCTCAATTGCAGGGCACGA 60.675 57.895 13.28 0.00 38.71 4.35
4593 9295 2.821378 TCACTCATCGGTCGAGGTTTTA 59.179 45.455 4.99 0.00 34.66 1.52
4597 9299 0.811915 CTTCACTCATCGGTCGAGGT 59.188 55.000 4.99 0.00 34.66 3.85
4598 9300 0.811915 ACTTCACTCATCGGTCGAGG 59.188 55.000 0.00 0.00 34.66 4.63
4599 9301 1.740585 AGACTTCACTCATCGGTCGAG 59.259 52.381 0.00 0.00 36.53 4.04
4600 9302 1.822506 AGACTTCACTCATCGGTCGA 58.177 50.000 0.00 0.00 32.86 4.20
4602 9304 2.520979 CGAAGACTTCACTCATCGGTC 58.479 52.381 15.36 0.00 0.00 4.79
4603 9305 1.202582 CCGAAGACTTCACTCATCGGT 59.797 52.381 15.36 0.00 43.51 4.69
4622 9327 0.395724 CCCCAACTATGCCCTTCACC 60.396 60.000 0.00 0.00 0.00 4.02
4624 9329 2.006748 CCCCCAACTATGCCCTTCA 58.993 57.895 0.00 0.00 0.00 3.02
4625 9330 1.455773 GCCCCCAACTATGCCCTTC 60.456 63.158 0.00 0.00 0.00 3.46
4642 9347 3.068307 ACACATATCCTCTTGACGTAGGC 59.932 47.826 0.00 0.00 32.55 3.93
4647 9352 2.159043 AGGCACACATATCCTCTTGACG 60.159 50.000 0.00 0.00 0.00 4.35
4669 9374 2.012051 GCCCCAAATCACGTCACTAGG 61.012 57.143 0.00 0.00 0.00 3.02
4680 9385 9.077885 TGAAATAATGTAATAGAGCCCCAAATC 57.922 33.333 0.00 0.00 0.00 2.17
4686 9391 8.451908 AACTGTGAAATAATGTAATAGAGCCC 57.548 34.615 0.00 0.00 0.00 5.19
4757 11793 3.583086 ACCTACAGAAGCATAACCACACT 59.417 43.478 0.00 0.00 0.00 3.55
4807 11843 6.842280 TGCTAACATAACTAGGGGAGATACAA 59.158 38.462 0.00 0.00 0.00 2.41
4856 11892 1.285280 CTTCCATACACCCCAGGACA 58.715 55.000 0.00 0.00 0.00 4.02
4857 11893 1.286248 ACTTCCATACACCCCAGGAC 58.714 55.000 0.00 0.00 0.00 3.85
4858 11894 2.316677 TCTACTTCCATACACCCCAGGA 59.683 50.000 0.00 0.00 0.00 3.86
4859 11895 2.759355 TCTACTTCCATACACCCCAGG 58.241 52.381 0.00 0.00 0.00 4.45
4860 11896 3.495100 GCATCTACTTCCATACACCCCAG 60.495 52.174 0.00 0.00 0.00 4.45
4876 11913 9.550406 GAGTCTTCTACTAGTAAGAAGCATCTA 57.450 37.037 23.49 12.44 39.07 1.98
4939 11976 9.830975 GGGCATGGTTAGTTTTTATTTATCAAT 57.169 29.630 0.00 0.00 0.00 2.57
4968 12006 8.314751 CCATATACTTGTAGGTTATCAGGAAGG 58.685 40.741 0.00 0.00 0.00 3.46
4982 12020 7.895962 AGCAGTGATAGATCCCATATACTTGTA 59.104 37.037 0.00 0.00 0.00 2.41
5031 12069 3.389329 CCAATTCCTTCTGCTCCTAGCTA 59.611 47.826 0.03 0.00 42.97 3.32
5225 12263 0.803768 CGTGTCCTCGAGAATGCCTG 60.804 60.000 15.71 0.00 0.00 4.85


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

AutoCloner maintained by Alex Coulton.