Multiple sequence alignment - TraesCS6D01G115200

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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 TraesCS6D01G115200 chr6D 100.000 5156 0 0 1 5156 81774852 81769697 0.000000e+00 9522.0
1 TraesCS6D01G115200 chr6D 82.942 3318 534 30 1047 4346 81926109 81922806 0.000000e+00 2963.0
2 TraesCS6D01G115200 chr6D 83.693 3109 483 18 1031 4130 81759654 81756561 0.000000e+00 2911.0
3 TraesCS6D01G115200 chr6D 83.128 3171 491 30 982 4124 82139150 82135996 0.000000e+00 2852.0
4 TraesCS6D01G115200 chr6D 82.117 3411 533 55 982 4349 82203991 82200615 0.000000e+00 2848.0
5 TraesCS6D01G115200 chr6D 81.831 3418 539 53 982 4351 81935398 81932015 0.000000e+00 2796.0
6 TraesCS6D01G115200 chr6D 82.482 3191 519 30 967 4131 81763967 81760791 0.000000e+00 2760.0
7 TraesCS6D01G115200 chr6D 80.622 3215 563 44 982 4162 82220502 82217314 0.000000e+00 2431.0
8 TraesCS6D01G115200 chr6D 86.916 107 11 2 4391 4496 338411416 338411520 3.260000e-22 117.0
9 TraesCS6D01G115200 chr6B 94.384 4291 191 20 136 4387 156551802 156547523 0.000000e+00 6543.0
10 TraesCS6D01G115200 chr6B 83.400 3235 508 28 1047 4265 156654764 156651543 0.000000e+00 2972.0
11 TraesCS6D01G115200 chr6B 83.349 3177 503 20 967 4130 156528938 156525775 0.000000e+00 2913.0
12 TraesCS6D01G115200 chr6B 82.138 3415 528 62 982 4349 157109395 157106016 0.000000e+00 2852.0
13 TraesCS6D01G115200 chr6B 82.410 3178 515 31 982 4131 156533208 156530047 0.000000e+00 2732.0
14 TraesCS6D01G115200 chr6B 91.451 386 23 3 4766 5151 156546974 156546599 5.920000e-144 521.0
15 TraesCS6D01G115200 chr6B 87.363 182 11 4 4595 4766 156547450 156547271 1.130000e-46 198.0
16 TraesCS6D01G115200 chr6B 80.165 121 21 2 5025 5144 157484857 157484739 2.560000e-13 87.9
17 TraesCS6D01G115200 chr6A 93.662 3471 167 16 851 4292 98310113 98306667 0.000000e+00 5142.0
18 TraesCS6D01G115200 chr6A 84.333 3319 485 28 1047 4346 98315894 98312592 0.000000e+00 3216.0
19 TraesCS6D01G115200 chr6A 83.333 3180 488 31 982 4131 98250013 98246846 0.000000e+00 2898.0
20 TraesCS6D01G115200 chr6A 82.484 3317 524 44 1031 4315 98888050 98884759 0.000000e+00 2854.0
21 TraesCS6D01G115200 chr6A 82.065 3245 524 44 982 4189 98323868 98320645 0.000000e+00 2715.0
22 TraesCS6D01G115200 chr6A 79.941 3410 583 75 982 4349 99016188 99012838 0.000000e+00 2414.0
23 TraesCS6D01G115200 chr6A 82.435 2579 418 27 1783 4335 98916425 98913856 0.000000e+00 2220.0
24 TraesCS6D01G115200 chr6A 89.886 791 47 11 2 783 98310880 98310114 0.000000e+00 987.0
25 TraesCS6D01G115200 chr6A 93.769 321 20 0 4836 5156 98305945 98305625 2.790000e-132 483.0
26 TraesCS6D01G115200 chr6A 87.978 183 9 5 4595 4766 98306439 98306259 2.430000e-48 204.0
27 TraesCS6D01G115200 chr6A 87.879 99 9 3 4253 4349 98979129 98979032 4.220000e-21 113.0
28 TraesCS6D01G115200 chr6A 84.810 79 10 2 5067 5144 98913307 98913230 1.540000e-10 78.7
29 TraesCS6D01G115200 chrUn 93.252 163 8 2 4435 4596 128516438 128516278 2.400000e-58 237.0
30 TraesCS6D01G115200 chr3D 99.219 128 1 0 4470 4597 443434365 443434238 1.120000e-56 231.0
31 TraesCS6D01G115200 chr3D 94.444 144 8 0 4467 4610 496172753 496172896 6.720000e-54 222.0
32 TraesCS6D01G115200 chr3D 90.110 91 7 2 4375 4464 290868923 290869012 3.260000e-22 117.0
33 TraesCS6D01G115200 chr3D 87.879 99 9 3 4368 4464 606951461 606951364 4.220000e-21 113.0
34 TraesCS6D01G115200 chr4B 97.080 137 3 1 4462 4598 450453465 450453600 4.020000e-56 230.0
35 TraesCS6D01G115200 chr2D 97.744 133 3 0 4468 4600 340252740 340252872 4.020000e-56 230.0
36 TraesCS6D01G115200 chr7D 95.172 145 4 2 4459 4601 6484608 6484465 5.190000e-55 226.0
37 TraesCS6D01G115200 chr7D 92.771 83 5 1 4382 4464 266214391 266214310 9.070000e-23 119.0
38 TraesCS6D01G115200 chr5D 95.745 141 4 2 4469 4607 29496051 29496191 5.190000e-55 226.0
39 TraesCS6D01G115200 chr7A 93.793 145 9 0 4462 4606 442265889 442265745 8.690000e-53 219.0
40 TraesCS6D01G115200 chr7B 94.286 140 7 1 4462 4601 295083160 295083298 4.040000e-51 213.0
41 TraesCS6D01G115200 chr1B 80.184 217 27 12 4393 4596 518802259 518802046 1.160000e-31 148.0
42 TraesCS6D01G115200 chr2B 84.672 137 11 7 4392 4525 457679949 457680078 1.510000e-25 128.0
43 TraesCS6D01G115200 chr5B 93.902 82 4 1 4384 4464 308553715 308553796 7.010000e-24 122.0
44 TraesCS6D01G115200 chr3A 91.954 87 5 2 4379 4464 529615256 529615341 2.520000e-23 121.0
45 TraesCS6D01G115200 chr3B 90.110 91 7 2 4375 4464 383716472 383716561 3.260000e-22 117.0
46 TraesCS6D01G115200 chr4D 77.037 135 29 2 1446 1579 16387463 16387330 5.540000e-10 76.8


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 TraesCS6D01G115200 chr6D 81769697 81774852 5155 True 9522.000000 9522 100.0000 1 5156 1 chr6D.!!$R1 5155
1 TraesCS6D01G115200 chr6D 81922806 81926109 3303 True 2963.000000 2963 82.9420 1047 4346 1 chr6D.!!$R2 3299
2 TraesCS6D01G115200 chr6D 82135996 82139150 3154 True 2852.000000 2852 83.1280 982 4124 1 chr6D.!!$R4 3142
3 TraesCS6D01G115200 chr6D 82200615 82203991 3376 True 2848.000000 2848 82.1170 982 4349 1 chr6D.!!$R5 3367
4 TraesCS6D01G115200 chr6D 81756561 81763967 7406 True 2835.500000 2911 83.0875 967 4131 2 chr6D.!!$R7 3164
5 TraesCS6D01G115200 chr6D 81932015 81935398 3383 True 2796.000000 2796 81.8310 982 4351 1 chr6D.!!$R3 3369
6 TraesCS6D01G115200 chr6D 82217314 82220502 3188 True 2431.000000 2431 80.6220 982 4162 1 chr6D.!!$R6 3180
7 TraesCS6D01G115200 chr6B 156651543 156654764 3221 True 2972.000000 2972 83.4000 1047 4265 1 chr6B.!!$R1 3218
8 TraesCS6D01G115200 chr6B 157106016 157109395 3379 True 2852.000000 2852 82.1380 982 4349 1 chr6B.!!$R2 3367
9 TraesCS6D01G115200 chr6B 156525775 156533208 7433 True 2822.500000 2913 82.8795 967 4131 2 chr6B.!!$R4 3164
10 TraesCS6D01G115200 chr6B 156546599 156551802 5203 True 2420.666667 6543 91.0660 136 5151 3 chr6B.!!$R5 5015
11 TraesCS6D01G115200 chr6A 98246846 98250013 3167 True 2898.000000 2898 83.3330 982 4131 1 chr6A.!!$R1 3149
12 TraesCS6D01G115200 chr6A 98884759 98888050 3291 True 2854.000000 2854 82.4840 1031 4315 1 chr6A.!!$R3 3284
13 TraesCS6D01G115200 chr6A 98320645 98323868 3223 True 2715.000000 2715 82.0650 982 4189 1 chr6A.!!$R2 3207
14 TraesCS6D01G115200 chr6A 99012838 99016188 3350 True 2414.000000 2414 79.9410 982 4349 1 chr6A.!!$R5 3367
15 TraesCS6D01G115200 chr6A 98305625 98315894 10269 True 2006.400000 5142 89.9256 2 5156 5 chr6A.!!$R6 5154
16 TraesCS6D01G115200 chr6A 98913230 98916425 3195 True 1149.350000 2220 83.6225 1783 5144 2 chr6A.!!$R7 3361

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
611 5646 0.035458 CCCCATGAACTATCTCGCCC 59.965 60.0 0.00 0.00 0.00 6.13 F
1616 10960 0.679002 CCATCCCTCACTGTGCTTGG 60.679 60.0 2.12 5.26 0.00 3.61 F
2095 15670 0.954452 CGGCAAAGTTCCAGAAAGCT 59.046 50.0 0.00 0.00 0.00 3.74 F
2925 16506 1.152649 AAGGGCCTATTCCATCTGGG 58.847 55.0 6.41 0.00 35.41 4.45 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2431 16006 2.621338 TCCATTGAGTCGATTGTCAGC 58.379 47.619 0.00 0.0 0.00 4.26 R
3365 16952 1.538687 AATTGCCAGCTTGGAGCCAC 61.539 55.000 6.40 0.0 43.77 5.01 R
3612 17199 1.589716 GGCTTGCTCCTTGTGCGATT 61.590 55.000 0.00 0.0 0.00 3.34 R
4721 18476 0.321653 GGTGATTCACCGCCAACTCT 60.322 55.000 19.65 0.0 44.95 3.24 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
53 5067 0.810031 AATCGCGGGAGAAATGTCGG 60.810 55.000 6.13 0.00 0.00 4.79
60 5074 2.289072 CGGGAGAAATGTCGGATATGCT 60.289 50.000 0.00 0.00 0.00 3.79
61 5075 3.056821 CGGGAGAAATGTCGGATATGCTA 60.057 47.826 0.00 0.00 0.00 3.49
62 5076 4.246458 GGGAGAAATGTCGGATATGCTAC 58.754 47.826 0.00 0.00 0.00 3.58
63 5077 4.262463 GGGAGAAATGTCGGATATGCTACA 60.262 45.833 4.06 4.06 0.00 2.74
65 5079 5.578727 GGAGAAATGTCGGATATGCTACATC 59.421 44.000 13.57 4.97 31.53 3.06
66 5080 5.164233 AGAAATGTCGGATATGCTACATCG 58.836 41.667 13.57 0.00 31.53 3.84
67 5081 4.521130 AATGTCGGATATGCTACATCGT 57.479 40.909 13.57 0.00 31.53 3.73
68 5082 3.282831 TGTCGGATATGCTACATCGTG 57.717 47.619 0.00 0.00 0.00 4.35
77 5092 1.621317 TGCTACATCGTGGTGGAAAGA 59.379 47.619 0.00 0.00 0.00 2.52
108 5123 0.616111 CTGCTCCTGTCTACCCCAGT 60.616 60.000 0.00 0.00 0.00 4.00
116 5131 2.101582 CTGTCTACCCCAGTATCTGCAC 59.898 54.545 0.00 0.00 0.00 4.57
134 5149 4.953667 TGCACAATAAAACAATCCAAGCA 58.046 34.783 0.00 0.00 0.00 3.91
376 5391 2.872245 TCAAGTTTGAACGGCTTCAGAG 59.128 45.455 0.00 0.00 37.70 3.35
389 5404 4.201950 CGGCTTCAGAGTTCAATTAATGGG 60.202 45.833 0.00 0.00 0.00 4.00
563 5585 1.601663 CGAGACGCAGATGATTCCTCC 60.602 57.143 0.00 0.00 0.00 4.30
608 5643 3.829026 TGATCTCCCCATGAACTATCTCG 59.171 47.826 0.00 0.00 0.00 4.04
609 5644 1.964223 TCTCCCCATGAACTATCTCGC 59.036 52.381 0.00 0.00 0.00 5.03
610 5645 1.001406 CTCCCCATGAACTATCTCGCC 59.999 57.143 0.00 0.00 0.00 5.54
611 5646 0.035458 CCCCATGAACTATCTCGCCC 59.965 60.000 0.00 0.00 0.00 6.13
612 5647 1.051812 CCCATGAACTATCTCGCCCT 58.948 55.000 0.00 0.00 0.00 5.19
613 5648 1.417890 CCCATGAACTATCTCGCCCTT 59.582 52.381 0.00 0.00 0.00 3.95
614 5649 2.548920 CCCATGAACTATCTCGCCCTTC 60.549 54.545 0.00 0.00 0.00 3.46
615 5650 2.398498 CATGAACTATCTCGCCCTTCG 58.602 52.381 0.00 0.00 40.15 3.79
616 5651 0.744874 TGAACTATCTCGCCCTTCGG 59.255 55.000 0.00 0.00 39.05 4.30
617 5652 1.030457 GAACTATCTCGCCCTTCGGA 58.970 55.000 0.00 0.00 39.05 4.55
618 5653 1.614413 GAACTATCTCGCCCTTCGGAT 59.386 52.381 0.00 0.00 39.05 4.18
619 5654 2.581216 ACTATCTCGCCCTTCGGATA 57.419 50.000 0.00 0.00 39.05 2.59
620 5655 3.088789 ACTATCTCGCCCTTCGGATAT 57.911 47.619 0.00 0.00 39.05 1.63
621 5656 3.018149 ACTATCTCGCCCTTCGGATATC 58.982 50.000 0.00 0.00 39.05 1.63
645 5680 3.319122 GCAAATCTCCACCAACTGTTTCT 59.681 43.478 0.00 0.00 0.00 2.52
670 5705 2.527547 GAATGCGTGGCGTTTCCTGG 62.528 60.000 0.00 0.00 37.94 4.45
832 5870 5.790593 AGACGGCTACAAAAGTCAGAAATA 58.209 37.500 0.00 0.00 36.18 1.40
833 5871 5.638234 AGACGGCTACAAAAGTCAGAAATAC 59.362 40.000 0.00 0.00 36.18 1.89
834 5872 5.548406 ACGGCTACAAAAGTCAGAAATACT 58.452 37.500 0.00 0.00 0.00 2.12
916 5954 2.137523 GCAAGGAGCACAACAAAATGG 58.862 47.619 0.00 0.00 44.79 3.16
930 5968 6.323739 ACAACAAAATGGGAGCTTCTTCTTTA 59.676 34.615 0.00 0.00 0.00 1.85
976 6014 5.479375 AGACAACCATTGATGCTCAGATTTT 59.521 36.000 0.00 0.00 0.00 1.82
1019 6057 2.624838 CCATGCAGACACTCCAGTTTTT 59.375 45.455 0.00 0.00 0.00 1.94
1051 6119 1.980036 ACATGCCTTCATTTGCCCTTT 59.020 42.857 0.00 0.00 0.00 3.11
1075 6143 0.689055 TGTGCTGCTGATCTCCTTGT 59.311 50.000 0.00 0.00 0.00 3.16
1114 6182 4.247380 CGGAGCATGAGAGGGGCC 62.247 72.222 0.00 0.00 0.00 5.80
1443 6514 2.356667 CTGCCCTCTTCAACCCCC 59.643 66.667 0.00 0.00 0.00 5.40
1616 10960 0.679002 CCATCCCTCACTGTGCTTGG 60.679 60.000 2.12 5.26 0.00 3.61
1641 10985 3.692101 TGTGTTTCAACGAATTCAGTGGT 59.308 39.130 6.22 0.00 0.00 4.16
2030 15605 5.953571 ACTTACAAAGGTCAATTTCTCCCT 58.046 37.500 0.00 0.00 0.00 4.20
2095 15670 0.954452 CGGCAAAGTTCCAGAAAGCT 59.046 50.000 0.00 0.00 0.00 3.74
2925 16506 1.152649 AAGGGCCTATTCCATCTGGG 58.847 55.000 6.41 0.00 35.41 4.45
3055 16636 6.054941 CCAAAACAACAAAATAAGAAGGCCT 58.945 36.000 0.00 0.00 0.00 5.19
3365 16952 2.832129 TCTACAAGGCAGAACTACCTGG 59.168 50.000 0.00 0.00 36.07 4.45
3828 17415 0.030501 ACATTCCCCCGGAGTATGGA 60.031 55.000 0.73 0.00 31.21 3.41
3909 17496 1.748879 GCTTACTGGAATGCGGCCA 60.749 57.895 2.24 0.00 0.00 5.36
3998 17585 1.566231 GGTTGAGGTCCTGGATCCAAT 59.434 52.381 17.00 0.00 0.00 3.16
3999 17586 2.024941 GGTTGAGGTCCTGGATCCAATT 60.025 50.000 17.00 0.00 0.00 2.32
4089 17676 3.833650 ACAATCAATTCATGAGGCCAACA 59.166 39.130 5.01 5.11 42.53 3.33
4140 17732 2.654749 TAGACGCTGAACACAGATGG 57.345 50.000 0.00 0.00 33.94 3.51
4172 17772 7.361894 CAGTCATGATACAATGAACAACACAA 58.638 34.615 0.00 0.00 38.28 3.33
4209 17829 9.864034 CTTGTAAACATCTTGTGTACTTGTAAG 57.136 33.333 8.90 2.09 40.77 2.34
4285 18028 5.482908 ACTTTGTACAGAGCCTAACAGATG 58.517 41.667 13.09 0.00 0.00 2.90
4286 18029 5.246203 ACTTTGTACAGAGCCTAACAGATGA 59.754 40.000 13.09 0.00 0.00 2.92
4313 18057 5.591643 TTGAGCTTTACGTGCTTCTTTAG 57.408 39.130 0.00 0.00 41.30 1.85
4317 18061 3.124806 GCTTTACGTGCTTCTTTAGGGAC 59.875 47.826 0.00 0.00 0.00 4.46
4319 18063 2.922740 ACGTGCTTCTTTAGGGACAA 57.077 45.000 0.00 0.00 0.00 3.18
4380 18125 8.337532 CCTTTTTCTTTTGCAAGAACATTTAGG 58.662 33.333 0.00 0.00 46.71 2.69
4389 18134 5.827797 TGCAAGAACATTTAGGTGTTTCTCT 59.172 36.000 0.00 0.00 42.08 3.10
4390 18135 6.321181 TGCAAGAACATTTAGGTGTTTCTCTT 59.679 34.615 0.00 0.00 42.08 2.85
4395 18140 9.708092 AGAACATTTAGGTGTTTCTCTTAGTAC 57.292 33.333 0.00 0.00 42.08 2.73
4396 18141 9.485206 GAACATTTAGGTGTTTCTCTTAGTACA 57.515 33.333 0.00 0.00 42.08 2.90
4397 18142 8.828688 ACATTTAGGTGTTTCTCTTAGTACAC 57.171 34.615 0.00 0.00 40.01 2.90
4398 18143 8.648693 ACATTTAGGTGTTTCTCTTAGTACACT 58.351 33.333 0.00 0.00 40.45 3.55
4399 18144 9.141400 CATTTAGGTGTTTCTCTTAGTACACTC 57.859 37.037 0.00 0.00 40.45 3.51
4400 18145 8.474710 TTTAGGTGTTTCTCTTAGTACACTCT 57.525 34.615 0.00 0.00 40.45 3.24
4402 18147 5.477637 AGGTGTTTCTCTTAGTACACTCTCC 59.522 44.000 0.00 0.00 40.45 3.71
4403 18148 5.243283 GGTGTTTCTCTTAGTACACTCTCCA 59.757 44.000 0.00 0.00 40.45 3.86
4404 18149 6.071278 GGTGTTTCTCTTAGTACACTCTCCAT 60.071 42.308 0.00 0.00 40.45 3.41
4405 18150 7.030768 GTGTTTCTCTTAGTACACTCTCCATC 58.969 42.308 0.00 0.00 38.23 3.51
4406 18151 6.153000 TGTTTCTCTTAGTACACTCTCCATCC 59.847 42.308 0.00 0.00 0.00 3.51
4407 18152 4.794334 TCTCTTAGTACACTCTCCATCCC 58.206 47.826 0.00 0.00 0.00 3.85
4408 18153 4.229812 TCTCTTAGTACACTCTCCATCCCA 59.770 45.833 0.00 0.00 0.00 4.37
4410 18155 5.338632 TCTTAGTACACTCTCCATCCCAAA 58.661 41.667 0.00 0.00 0.00 3.28
4411 18156 5.783360 TCTTAGTACACTCTCCATCCCAAAA 59.217 40.000 0.00 0.00 0.00 2.44
4413 18158 5.520748 AGTACACTCTCCATCCCAAAATT 57.479 39.130 0.00 0.00 0.00 1.82
4414 18159 5.501156 AGTACACTCTCCATCCCAAAATTC 58.499 41.667 0.00 0.00 0.00 2.17
4415 18160 4.664688 ACACTCTCCATCCCAAAATTCT 57.335 40.909 0.00 0.00 0.00 2.40
4417 18162 4.768968 ACACTCTCCATCCCAAAATTCTTG 59.231 41.667 0.00 0.00 0.00 3.02
4419 18164 5.012893 ACTCTCCATCCCAAAATTCTTGTC 58.987 41.667 0.00 0.00 0.00 3.18
4420 18165 5.222213 ACTCTCCATCCCAAAATTCTTGTCT 60.222 40.000 0.00 0.00 0.00 3.41
4421 18166 5.644188 TCTCCATCCCAAAATTCTTGTCTT 58.356 37.500 0.00 0.00 0.00 3.01
4422 18167 6.789268 TCTCCATCCCAAAATTCTTGTCTTA 58.211 36.000 0.00 0.00 0.00 2.10
4423 18168 6.886459 TCTCCATCCCAAAATTCTTGTCTTAG 59.114 38.462 0.00 0.00 0.00 2.18
4425 18170 7.413446 TCCATCCCAAAATTCTTGTCTTAGAT 58.587 34.615 0.00 0.00 0.00 1.98
4426 18171 7.895429 TCCATCCCAAAATTCTTGTCTTAGATT 59.105 33.333 0.00 0.00 0.00 2.40
4427 18172 8.534496 CCATCCCAAAATTCTTGTCTTAGATTT 58.466 33.333 0.00 0.00 0.00 2.17
4429 18174 8.477419 TCCCAAAATTCTTGTCTTAGATTTGT 57.523 30.769 0.00 0.00 28.79 2.83
4439 18184 9.582431 TCTTGTCTTAGATTTGTCTAAATACGG 57.418 33.333 0.26 0.99 36.66 4.02
4440 18185 9.582431 CTTGTCTTAGATTTGTCTAAATACGGA 57.418 33.333 0.26 0.00 36.66 4.69
4442 18187 9.529325 TGTCTTAGATTTGTCTAAATACGGATG 57.471 33.333 0.26 0.00 36.66 3.51
4451 18196 8.867112 TTGTCTAAATACGGATGTATCAAGTC 57.133 34.615 0.00 0.00 40.42 3.01
4453 18198 7.919091 TGTCTAAATACGGATGTATCAAGTCAC 59.081 37.037 0.00 0.00 40.42 3.67
4455 18200 4.913335 ATACGGATGTATCAAGTCACGT 57.087 40.909 0.00 0.00 36.56 4.49
4456 18201 3.587797 ACGGATGTATCAAGTCACGTT 57.412 42.857 0.00 0.00 0.00 3.99
4457 18202 3.921677 ACGGATGTATCAAGTCACGTTT 58.078 40.909 0.00 0.00 0.00 3.60
4458 18203 4.312443 ACGGATGTATCAAGTCACGTTTT 58.688 39.130 0.00 0.00 0.00 2.43
4459 18204 5.472148 ACGGATGTATCAAGTCACGTTTTA 58.528 37.500 0.00 0.00 0.00 1.52
4460 18205 5.575606 ACGGATGTATCAAGTCACGTTTTAG 59.424 40.000 0.00 0.00 0.00 1.85
4461 18206 5.575606 CGGATGTATCAAGTCACGTTTTAGT 59.424 40.000 0.00 0.00 0.00 2.24
4462 18207 6.748658 CGGATGTATCAAGTCACGTTTTAGTA 59.251 38.462 0.00 0.00 0.00 1.82
4463 18208 7.434307 CGGATGTATCAAGTCACGTTTTAGTAT 59.566 37.037 0.00 0.00 0.00 2.12
4464 18209 9.740239 GGATGTATCAAGTCACGTTTTAGTATA 57.260 33.333 0.00 0.00 0.00 1.47
4475 18220 9.670719 GTCACGTTTTAGTATAGTAATACTCCC 57.329 37.037 14.92 0.00 44.05 4.30
4476 18221 9.632638 TCACGTTTTAGTATAGTAATACTCCCT 57.367 33.333 14.92 0.00 44.05 4.20
4477 18222 9.890352 CACGTTTTAGTATAGTAATACTCCCTC 57.110 37.037 14.92 0.00 44.05 4.30
4478 18223 9.072375 ACGTTTTAGTATAGTAATACTCCCTCC 57.928 37.037 14.92 0.00 44.05 4.30
4479 18224 8.233190 CGTTTTAGTATAGTAATACTCCCTCCG 58.767 40.741 14.92 1.97 44.05 4.63
4480 18225 9.072375 GTTTTAGTATAGTAATACTCCCTCCGT 57.928 37.037 11.54 0.00 44.05 4.69
4481 18226 8.854614 TTTAGTATAGTAATACTCCCTCCGTC 57.145 38.462 0.00 0.00 44.05 4.79
4482 18227 5.814481 AGTATAGTAATACTCCCTCCGTCC 58.186 45.833 0.00 0.00 44.05 4.79
4483 18228 2.378378 AGTAATACTCCCTCCGTCCC 57.622 55.000 0.00 0.00 0.00 4.46
4484 18229 1.572415 AGTAATACTCCCTCCGTCCCA 59.428 52.381 0.00 0.00 0.00 4.37
4485 18230 2.023695 AGTAATACTCCCTCCGTCCCAA 60.024 50.000 0.00 0.00 0.00 4.12
4486 18231 1.961133 AATACTCCCTCCGTCCCAAA 58.039 50.000 0.00 0.00 0.00 3.28
4487 18232 1.961133 ATACTCCCTCCGTCCCAAAA 58.039 50.000 0.00 0.00 0.00 2.44
4488 18233 1.961133 TACTCCCTCCGTCCCAAAAT 58.039 50.000 0.00 0.00 0.00 1.82
4489 18234 1.073098 ACTCCCTCCGTCCCAAAATT 58.927 50.000 0.00 0.00 0.00 1.82
4490 18235 1.004394 ACTCCCTCCGTCCCAAAATTC 59.996 52.381 0.00 0.00 0.00 2.17
4491 18236 1.282157 CTCCCTCCGTCCCAAAATTCT 59.718 52.381 0.00 0.00 0.00 2.40
4492 18237 1.708551 TCCCTCCGTCCCAAAATTCTT 59.291 47.619 0.00 0.00 0.00 2.52
4493 18238 1.818674 CCCTCCGTCCCAAAATTCTTG 59.181 52.381 0.00 0.00 0.00 3.02
4494 18239 2.514803 CCTCCGTCCCAAAATTCTTGT 58.485 47.619 0.00 0.00 0.00 3.16
4495 18240 2.488153 CCTCCGTCCCAAAATTCTTGTC 59.512 50.000 0.00 0.00 0.00 3.18
4496 18241 3.412386 CTCCGTCCCAAAATTCTTGTCT 58.588 45.455 0.00 0.00 0.00 3.41
4497 18242 3.821033 CTCCGTCCCAAAATTCTTGTCTT 59.179 43.478 0.00 0.00 0.00 3.01
4498 18243 4.975631 TCCGTCCCAAAATTCTTGTCTTA 58.024 39.130 0.00 0.00 0.00 2.10
4499 18244 5.001232 TCCGTCCCAAAATTCTTGTCTTAG 58.999 41.667 0.00 0.00 0.00 2.18
4500 18245 5.001232 CCGTCCCAAAATTCTTGTCTTAGA 58.999 41.667 0.00 0.00 0.00 2.10
4501 18246 5.648092 CCGTCCCAAAATTCTTGTCTTAGAT 59.352 40.000 0.00 0.00 0.00 1.98
4502 18247 6.151144 CCGTCCCAAAATTCTTGTCTTAGATT 59.849 38.462 0.00 0.00 0.00 2.40
4503 18248 7.309194 CCGTCCCAAAATTCTTGTCTTAGATTT 60.309 37.037 0.00 0.00 0.00 2.17
4504 18249 7.538678 CGTCCCAAAATTCTTGTCTTAGATTTG 59.461 37.037 0.00 0.00 29.84 2.32
4505 18250 8.360390 GTCCCAAAATTCTTGTCTTAGATTTGT 58.640 33.333 0.00 0.00 28.79 2.83
4506 18251 8.576442 TCCCAAAATTCTTGTCTTAGATTTGTC 58.424 33.333 0.00 0.00 28.79 3.18
4507 18252 8.579863 CCCAAAATTCTTGTCTTAGATTTGTCT 58.420 33.333 0.00 0.00 28.79 3.41
4515 18260 8.622157 TCTTGTCTTAGATTTGTCTAGATACGG 58.378 37.037 0.00 0.00 0.00 4.02
4516 18261 8.515695 TTGTCTTAGATTTGTCTAGATACGGA 57.484 34.615 0.00 0.00 0.00 4.69
4517 18262 8.693120 TGTCTTAGATTTGTCTAGATACGGAT 57.307 34.615 0.00 0.00 0.00 4.18
4518 18263 8.568794 TGTCTTAGATTTGTCTAGATACGGATG 58.431 37.037 0.00 0.00 0.00 3.51
4519 18264 8.569641 GTCTTAGATTTGTCTAGATACGGATGT 58.430 37.037 0.00 0.00 0.00 3.06
4520 18265 9.788889 TCTTAGATTTGTCTAGATACGGATGTA 57.211 33.333 0.00 0.00 34.45 2.29
4536 18281 7.976135 ACGGATGTATCTAATACTAAGACGT 57.024 36.000 0.00 0.00 36.70 4.34
4537 18282 7.804712 ACGGATGTATCTAATACTAAGACGTG 58.195 38.462 0.00 0.00 36.70 4.49
4538 18283 7.658982 ACGGATGTATCTAATACTAAGACGTGA 59.341 37.037 0.00 0.00 36.70 4.35
4539 18284 7.956403 CGGATGTATCTAATACTAAGACGTGAC 59.044 40.741 0.00 0.00 36.70 3.67
4540 18285 9.001542 GGATGTATCTAATACTAAGACGTGACT 57.998 37.037 0.00 0.00 36.70 3.41
4543 18288 9.387257 TGTATCTAATACTAAGACGTGACTTGA 57.613 33.333 0.00 0.00 36.70 3.02
4547 18292 9.387257 TCTAATACTAAGACGTGACTTGATACA 57.613 33.333 0.00 0.00 0.00 2.29
4550 18295 6.761099 ACTAAGACGTGACTTGATACATCT 57.239 37.500 0.00 0.00 0.00 2.90
4551 18296 6.556212 ACTAAGACGTGACTTGATACATCTG 58.444 40.000 0.00 0.00 0.00 2.90
4552 18297 5.392767 AAGACGTGACTTGATACATCTGT 57.607 39.130 0.00 0.00 0.00 3.41
4553 18298 6.510879 AAGACGTGACTTGATACATCTGTA 57.489 37.500 0.00 0.00 34.67 2.74
4554 18299 6.701145 AGACGTGACTTGATACATCTGTAT 57.299 37.500 0.00 2.53 43.38 2.29
4555 18300 7.101652 AGACGTGACTTGATACATCTGTATT 57.898 36.000 0.00 0.00 40.99 1.89
4556 18301 7.548097 AGACGTGACTTGATACATCTGTATTT 58.452 34.615 0.00 0.00 40.99 1.40
4557 18302 8.683615 AGACGTGACTTGATACATCTGTATTTA 58.316 33.333 0.00 0.00 40.99 1.40
4558 18303 8.858003 ACGTGACTTGATACATCTGTATTTAG 57.142 34.615 4.44 7.42 40.99 1.85
4559 18304 8.683615 ACGTGACTTGATACATCTGTATTTAGA 58.316 33.333 14.44 0.00 40.99 2.10
4560 18305 8.959058 CGTGACTTGATACATCTGTATTTAGAC 58.041 37.037 14.44 10.85 40.99 2.59
4561 18306 9.803315 GTGACTTGATACATCTGTATTTAGACA 57.197 33.333 14.44 12.43 40.99 3.41
4583 18328 8.143835 AGACAAATGTAAGACAAGAATTTTGGG 58.856 33.333 7.26 0.00 31.16 4.12
4584 18329 8.017418 ACAAATGTAAGACAAGAATTTTGGGA 57.983 30.769 7.26 0.00 31.16 4.37
4585 18330 7.926018 ACAAATGTAAGACAAGAATTTTGGGAC 59.074 33.333 7.26 0.00 31.16 4.46
4586 18331 5.682943 TGTAAGACAAGAATTTTGGGACG 57.317 39.130 5.68 0.00 0.00 4.79
4587 18332 4.517453 TGTAAGACAAGAATTTTGGGACGG 59.483 41.667 0.00 0.00 0.00 4.79
4588 18333 3.502123 AGACAAGAATTTTGGGACGGA 57.498 42.857 0.00 0.00 0.00 4.69
4589 18334 3.412386 AGACAAGAATTTTGGGACGGAG 58.588 45.455 0.00 0.00 0.00 4.63
4590 18335 2.488153 GACAAGAATTTTGGGACGGAGG 59.512 50.000 0.00 0.00 0.00 4.30
4591 18336 1.818674 CAAGAATTTTGGGACGGAGGG 59.181 52.381 0.00 0.00 0.00 4.30
4592 18337 1.368374 AGAATTTTGGGACGGAGGGA 58.632 50.000 0.00 0.00 0.00 4.20
4593 18338 1.282157 AGAATTTTGGGACGGAGGGAG 59.718 52.381 0.00 0.00 0.00 4.30
4638 18383 4.239304 TGGACAACGTATACACATGTGAC 58.761 43.478 31.94 18.18 0.00 3.67
4646 18396 5.977725 ACGTATACACATGTGACTATCTTGC 59.022 40.000 31.94 10.16 0.00 4.01
4690 18445 3.286353 TGGTTTCAAGTGCAGATGTCAA 58.714 40.909 0.00 0.00 0.00 3.18
4691 18446 3.890756 TGGTTTCAAGTGCAGATGTCAAT 59.109 39.130 0.00 0.00 0.00 2.57
4693 18448 5.534278 TGGTTTCAAGTGCAGATGTCAATTA 59.466 36.000 0.00 0.00 0.00 1.40
4721 18476 4.517453 GTCAGCTGTTTTTACATACCACCA 59.483 41.667 14.67 0.00 0.00 4.17
4738 18493 0.321564 CCAGAGTTGGCGGTGAATCA 60.322 55.000 0.00 0.00 37.73 2.57
4766 18521 9.599322 CAAATTACTAGCTACAGAAACTGTTTG 57.401 33.333 11.03 0.26 42.59 2.93
4769 18825 5.542779 ACTAGCTACAGAAACTGTTTGGAG 58.457 41.667 11.03 5.31 42.59 3.86
4775 18831 4.589908 ACAGAAACTGTTTGGAGTTGACT 58.410 39.130 11.03 0.00 42.59 3.41
4776 18832 4.396166 ACAGAAACTGTTTGGAGTTGACTG 59.604 41.667 11.03 10.88 42.59 3.51
4784 18840 7.054124 ACTGTTTGGAGTTGACTGAGAAATTA 58.946 34.615 0.00 0.00 0.00 1.40
4789 18845 6.837312 TGGAGTTGACTGAGAAATTAAGGAA 58.163 36.000 0.00 0.00 0.00 3.36
4833 18889 3.389925 AAATGTGCACAAGTCCAATGG 57.610 42.857 25.72 0.00 0.00 3.16
4834 18890 2.291209 ATGTGCACAAGTCCAATGGA 57.709 45.000 25.72 0.00 0.00 3.41
4905 18961 6.935167 TCTGAAACACATATAACTCAGCAGA 58.065 36.000 0.00 0.00 32.22 4.26
4937 19000 3.728076 TTTCGACACTAGCAGAACACT 57.272 42.857 0.00 0.00 0.00 3.55
4938 19001 3.728076 TTCGACACTAGCAGAACACTT 57.272 42.857 0.00 0.00 0.00 3.16
4948 19011 2.107204 AGCAGAACACTTGAGGAATGGT 59.893 45.455 0.00 0.00 0.00 3.55
5020 19118 0.664761 CCACCAGCACACACAAAGAG 59.335 55.000 0.00 0.00 0.00 2.85
5045 19143 1.959226 GAACGCGTCCCAAGCTTGA 60.959 57.895 28.05 5.82 0.00 3.02
5065 19163 1.817099 CTGTGAGCCCGAATCAGCC 60.817 63.158 0.00 0.00 0.00 4.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
53 5067 3.660501 TCCACCACGATGTAGCATATC 57.339 47.619 0.00 0.00 0.00 1.63
60 5074 5.670792 AATAGTCTTTCCACCACGATGTA 57.329 39.130 0.00 0.00 0.00 2.29
61 5075 4.553330 AATAGTCTTTCCACCACGATGT 57.447 40.909 0.00 0.00 0.00 3.06
62 5076 5.178797 AGAAATAGTCTTTCCACCACGATG 58.821 41.667 0.00 0.00 29.66 3.84
63 5077 5.046591 TGAGAAATAGTCTTTCCACCACGAT 60.047 40.000 0.00 0.00 36.41 3.73
65 5079 4.389077 GTGAGAAATAGTCTTTCCACCACG 59.611 45.833 9.51 0.00 36.41 4.94
66 5080 4.695928 GGTGAGAAATAGTCTTTCCACCAC 59.304 45.833 22.61 16.12 42.57 4.16
67 5081 4.597507 AGGTGAGAAATAGTCTTTCCACCA 59.402 41.667 25.80 11.30 43.83 4.17
68 5082 4.938226 CAGGTGAGAAATAGTCTTTCCACC 59.062 45.833 21.32 21.32 42.91 4.61
77 5092 3.177228 ACAGGAGCAGGTGAGAAATAGT 58.823 45.455 0.00 0.00 0.00 2.12
108 5123 7.035004 GCTTGGATTGTTTTATTGTGCAGATA 58.965 34.615 0.00 0.00 0.00 1.98
116 5131 3.613737 CCGCTGCTTGGATTGTTTTATTG 59.386 43.478 0.00 0.00 0.00 1.90
376 5391 1.748493 TCTGCGGCCCATTAATTGAAC 59.252 47.619 0.00 0.00 0.00 3.18
381 5396 4.164258 GCTCTGCGGCCCATTAAT 57.836 55.556 0.00 0.00 0.00 1.40
563 5585 2.046314 AAAGGTGGGCGTGATCGG 60.046 61.111 0.00 0.00 37.56 4.18
611 5646 4.450419 GTGGAGATTTGCAGATATCCGAAG 59.550 45.833 21.90 0.00 39.69 3.79
612 5647 4.380531 GTGGAGATTTGCAGATATCCGAA 58.619 43.478 21.90 6.62 39.69 4.30
613 5648 3.244215 GGTGGAGATTTGCAGATATCCGA 60.244 47.826 21.90 11.21 39.69 4.55
614 5649 3.070018 GGTGGAGATTTGCAGATATCCG 58.930 50.000 21.90 0.00 39.69 4.18
615 5650 4.090761 TGGTGGAGATTTGCAGATATCC 57.909 45.455 20.97 20.97 37.81 2.59
616 5651 5.008415 CAGTTGGTGGAGATTTGCAGATATC 59.992 44.000 3.34 3.34 0.00 1.63
617 5652 4.885907 CAGTTGGTGGAGATTTGCAGATAT 59.114 41.667 0.00 0.00 0.00 1.63
618 5653 4.263462 ACAGTTGGTGGAGATTTGCAGATA 60.263 41.667 0.00 0.00 0.00 1.98
619 5654 3.087031 CAGTTGGTGGAGATTTGCAGAT 58.913 45.455 0.00 0.00 0.00 2.90
620 5655 2.158623 ACAGTTGGTGGAGATTTGCAGA 60.159 45.455 0.00 0.00 0.00 4.26
621 5656 2.233271 ACAGTTGGTGGAGATTTGCAG 58.767 47.619 0.00 0.00 0.00 4.41
670 5705 2.622942 TCTTGATGCACCCTTTTGTGAC 59.377 45.455 0.00 0.00 38.55 3.67
832 5870 8.496088 ACTCTGACCACTATACTGAATACTAGT 58.504 37.037 0.00 0.00 0.00 2.57
833 5871 8.911918 ACTCTGACCACTATACTGAATACTAG 57.088 38.462 0.00 0.00 0.00 2.57
834 5872 8.715842 AGACTCTGACCACTATACTGAATACTA 58.284 37.037 0.00 0.00 0.00 1.82
916 5954 3.314541 TGACGGTAAAGAAGAAGCTCC 57.685 47.619 0.00 0.00 0.00 4.70
930 5968 2.839486 TCATTGAAGAGCTTGACGGT 57.161 45.000 0.00 0.00 0.00 4.83
976 6014 5.104693 TGGTTTTCTGGTGAAACTAGTCTGA 60.105 40.000 0.00 0.00 46.64 3.27
1051 6119 0.251354 GAGATCAGCAGCACAAGGGA 59.749 55.000 0.00 0.00 0.00 4.20
1075 6143 0.324183 CAGGAGCTGGTGAGAGAGGA 60.324 60.000 0.00 0.00 0.00 3.71
1114 6182 1.901085 CGAGGAACTGGAGAAGGGG 59.099 63.158 0.00 0.00 41.55 4.79
1572 10916 3.258622 AGGTACTACAGAGTTGAGTTGGC 59.741 47.826 0.00 0.00 36.02 4.52
1616 10960 5.399301 CCACTGAATTCGTTGAAACACAATC 59.601 40.000 7.51 0.00 40.76 2.67
1709 11053 6.332976 AGAGTTCATTTGGGATTACTCCAT 57.667 37.500 1.05 0.00 44.08 3.41
1801 11145 8.738645 ACAAGATTTCTGAGGTTGGTTATATC 57.261 34.615 0.00 0.00 0.00 1.63
2030 15605 7.749377 TCTAATGTTCTTAGATTGGGAAGGA 57.251 36.000 0.00 0.00 0.00 3.36
2095 15670 5.733676 TGTCAGATTGCTGCAAGAGTATAA 58.266 37.500 20.72 1.15 42.01 0.98
2431 16006 2.621338 TCCATTGAGTCGATTGTCAGC 58.379 47.619 0.00 0.00 0.00 4.26
2925 16506 6.524101 TTCTGAAATGTATTAAACTGCCCC 57.476 37.500 0.00 0.00 0.00 5.80
3069 16650 2.167487 GCCTCCAAAGAACACACCAAAA 59.833 45.455 0.00 0.00 0.00 2.44
3169 16753 4.993584 AGATGCATCAACGTCTCCATTATC 59.006 41.667 27.81 0.00 29.75 1.75
3324 16911 3.069729 AGACTAATCCATAACCTCCGCAC 59.930 47.826 0.00 0.00 0.00 5.34
3365 16952 1.538687 AATTGCCAGCTTGGAGCCAC 61.539 55.000 6.40 0.00 43.77 5.01
3612 17199 1.589716 GGCTTGCTCCTTGTGCGATT 61.590 55.000 0.00 0.00 0.00 3.34
3998 17585 3.031013 TCATATCCTGTGCCTCGAAGAA 58.969 45.455 0.00 0.00 34.09 2.52
3999 17586 2.666317 TCATATCCTGTGCCTCGAAGA 58.334 47.619 0.00 0.00 0.00 2.87
4089 17676 4.411540 AGGCAAGAGACTACATCCATGATT 59.588 41.667 0.00 0.00 0.00 2.57
4140 17732 7.119699 TGTTCATTGTATCATGACTGGTCTTTC 59.880 37.037 0.00 0.00 0.00 2.62
4202 17802 8.718734 GTCCCACTGAAACTATAAACTTACAAG 58.281 37.037 0.00 0.00 0.00 3.16
4209 17829 8.747471 AGTAGTAGTCCCACTGAAACTATAAAC 58.253 37.037 0.00 0.00 30.57 2.01
4285 18028 4.147219 AGCACGTAAAGCTCAAAATGTC 57.853 40.909 0.00 0.00 38.01 3.06
4286 18029 4.275936 AGAAGCACGTAAAGCTCAAAATGT 59.724 37.500 0.00 0.00 42.53 2.71
4355 18100 8.882736 ACCTAAATGTTCTTGCAAAAGAAAAAG 58.117 29.630 0.00 0.00 40.15 2.27
4356 18101 8.663911 CACCTAAATGTTCTTGCAAAAGAAAAA 58.336 29.630 0.00 0.00 40.15 1.94
4364 18109 6.321181 AGAGAAACACCTAAATGTTCTTGCAA 59.679 34.615 0.00 0.00 42.01 4.08
4380 18125 6.328641 TGGAGAGTGTACTAAGAGAAACAC 57.671 41.667 0.00 0.00 41.97 3.32
4389 18134 6.636454 ATTTTGGGATGGAGAGTGTACTAA 57.364 37.500 0.00 0.00 0.00 2.24
4390 18135 6.443849 AGAATTTTGGGATGGAGAGTGTACTA 59.556 38.462 0.00 0.00 0.00 1.82
4394 18139 4.664688 AGAATTTTGGGATGGAGAGTGT 57.335 40.909 0.00 0.00 0.00 3.55
4395 18140 4.768968 ACAAGAATTTTGGGATGGAGAGTG 59.231 41.667 5.68 0.00 0.00 3.51
4396 18141 5.003096 ACAAGAATTTTGGGATGGAGAGT 57.997 39.130 5.68 0.00 0.00 3.24
4397 18142 5.259632 AGACAAGAATTTTGGGATGGAGAG 58.740 41.667 5.68 0.00 0.00 3.20
4398 18143 5.261040 AGACAAGAATTTTGGGATGGAGA 57.739 39.130 5.68 0.00 0.00 3.71
4399 18144 5.990120 AAGACAAGAATTTTGGGATGGAG 57.010 39.130 5.68 0.00 0.00 3.86
4400 18145 6.789268 TCTAAGACAAGAATTTTGGGATGGA 58.211 36.000 5.68 0.00 0.00 3.41
4402 18147 9.362539 CAAATCTAAGACAAGAATTTTGGGATG 57.637 33.333 5.68 0.00 28.49 3.51
4403 18148 9.093458 ACAAATCTAAGACAAGAATTTTGGGAT 57.907 29.630 0.00 0.00 33.04 3.85
4404 18149 8.477419 ACAAATCTAAGACAAGAATTTTGGGA 57.523 30.769 0.00 0.00 33.04 4.37
4405 18150 8.579863 AGACAAATCTAAGACAAGAATTTTGGG 58.420 33.333 0.00 0.00 33.04 4.12
4413 18158 9.582431 CCGTATTTAGACAAATCTAAGACAAGA 57.418 33.333 9.81 0.00 45.93 3.02
4414 18159 9.582431 TCCGTATTTAGACAAATCTAAGACAAG 57.418 33.333 9.81 3.88 45.93 3.16
4417 18162 9.530633 ACATCCGTATTTAGACAAATCTAAGAC 57.469 33.333 0.00 0.83 45.93 3.01
4425 18170 9.309516 GACTTGATACATCCGTATTTAGACAAA 57.690 33.333 0.00 0.00 38.48 2.83
4426 18171 8.471609 TGACTTGATACATCCGTATTTAGACAA 58.528 33.333 0.00 0.00 38.48 3.18
4427 18172 7.919091 GTGACTTGATACATCCGTATTTAGACA 59.081 37.037 0.00 0.00 38.48 3.41
4429 18174 7.136772 CGTGACTTGATACATCCGTATTTAGA 58.863 38.462 0.00 0.00 38.48 2.10
4432 18177 5.657474 ACGTGACTTGATACATCCGTATTT 58.343 37.500 0.00 0.00 38.48 1.40
4433 18178 5.258456 ACGTGACTTGATACATCCGTATT 57.742 39.130 0.00 0.00 38.48 1.89
4434 18179 4.913335 ACGTGACTTGATACATCCGTAT 57.087 40.909 0.00 0.00 41.16 3.06
4435 18180 4.707030 AACGTGACTTGATACATCCGTA 57.293 40.909 0.00 0.00 0.00 4.02
4436 18181 3.587797 AACGTGACTTGATACATCCGT 57.412 42.857 0.00 0.00 0.00 4.69
4438 18183 6.963049 ACTAAAACGTGACTTGATACATCC 57.037 37.500 0.00 0.00 0.00 3.51
4449 18194 9.670719 GGGAGTATTACTATACTAAAACGTGAC 57.329 37.037 0.00 0.00 45.43 3.67
4451 18196 9.890352 GAGGGAGTATTACTATACTAAAACGTG 57.110 37.037 0.00 0.00 45.43 4.49
4453 18198 8.233190 CGGAGGGAGTATTACTATACTAAAACG 58.767 40.741 0.00 0.00 45.43 3.60
4455 18200 9.289782 GACGGAGGGAGTATTACTATACTAAAA 57.710 37.037 0.00 0.00 45.43 1.52
4456 18201 7.885399 GGACGGAGGGAGTATTACTATACTAAA 59.115 40.741 0.00 0.00 45.43 1.85
4457 18202 7.398024 GGACGGAGGGAGTATTACTATACTAA 58.602 42.308 0.00 0.00 45.43 2.24
4458 18203 6.069963 GGGACGGAGGGAGTATTACTATACTA 60.070 46.154 0.00 0.00 45.43 1.82
4460 18205 4.946772 GGGACGGAGGGAGTATTACTATAC 59.053 50.000 0.00 0.00 37.48 1.47
4461 18206 4.603171 TGGGACGGAGGGAGTATTACTATA 59.397 45.833 0.00 0.00 0.00 1.31
4462 18207 3.400322 TGGGACGGAGGGAGTATTACTAT 59.600 47.826 0.00 0.00 0.00 2.12
4463 18208 2.785269 TGGGACGGAGGGAGTATTACTA 59.215 50.000 0.00 0.00 0.00 1.82
4464 18209 1.572415 TGGGACGGAGGGAGTATTACT 59.428 52.381 0.00 0.00 0.00 2.24
4465 18210 2.077687 TGGGACGGAGGGAGTATTAC 57.922 55.000 0.00 0.00 0.00 1.89
4466 18211 2.852714 TTGGGACGGAGGGAGTATTA 57.147 50.000 0.00 0.00 0.00 0.98
4467 18212 1.961133 TTTGGGACGGAGGGAGTATT 58.039 50.000 0.00 0.00 0.00 1.89
4468 18213 1.961133 TTTTGGGACGGAGGGAGTAT 58.039 50.000 0.00 0.00 0.00 2.12
4469 18214 1.961133 ATTTTGGGACGGAGGGAGTA 58.039 50.000 0.00 0.00 0.00 2.59
4470 18215 1.004394 GAATTTTGGGACGGAGGGAGT 59.996 52.381 0.00 0.00 0.00 3.85
4471 18216 1.282157 AGAATTTTGGGACGGAGGGAG 59.718 52.381 0.00 0.00 0.00 4.30
4472 18217 1.368374 AGAATTTTGGGACGGAGGGA 58.632 50.000 0.00 0.00 0.00 4.20
4473 18218 1.818674 CAAGAATTTTGGGACGGAGGG 59.181 52.381 0.00 0.00 0.00 4.30
4474 18219 2.488153 GACAAGAATTTTGGGACGGAGG 59.512 50.000 0.00 0.00 0.00 4.30
4475 18220 3.412386 AGACAAGAATTTTGGGACGGAG 58.588 45.455 0.00 0.00 0.00 4.63
4476 18221 3.502123 AGACAAGAATTTTGGGACGGA 57.498 42.857 0.00 0.00 0.00 4.69
4477 18222 5.001232 TCTAAGACAAGAATTTTGGGACGG 58.999 41.667 0.00 0.00 0.00 4.79
4478 18223 6.743575 ATCTAAGACAAGAATTTTGGGACG 57.256 37.500 5.68 0.00 0.00 4.79
4479 18224 8.360390 ACAAATCTAAGACAAGAATTTTGGGAC 58.640 33.333 0.00 0.00 33.04 4.46
4480 18225 8.477419 ACAAATCTAAGACAAGAATTTTGGGA 57.523 30.769 0.00 0.00 33.04 4.37
4481 18226 8.579863 AGACAAATCTAAGACAAGAATTTTGGG 58.420 33.333 0.00 0.00 33.04 4.12
4489 18234 8.622157 CCGTATCTAGACAAATCTAAGACAAGA 58.378 37.037 0.00 0.00 36.98 3.02
4490 18235 8.622157 TCCGTATCTAGACAAATCTAAGACAAG 58.378 37.037 0.00 0.00 36.98 3.16
4491 18236 8.515695 TCCGTATCTAGACAAATCTAAGACAA 57.484 34.615 0.00 0.00 36.98 3.18
4492 18237 8.568794 CATCCGTATCTAGACAAATCTAAGACA 58.431 37.037 0.00 0.00 36.98 3.41
4493 18238 8.569641 ACATCCGTATCTAGACAAATCTAAGAC 58.430 37.037 0.00 0.00 36.98 3.01
4494 18239 8.693120 ACATCCGTATCTAGACAAATCTAAGA 57.307 34.615 0.00 0.00 36.98 2.10
4510 18255 9.664332 ACGTCTTAGTATTAGATACATCCGTAT 57.336 33.333 1.42 0.00 41.16 3.06
4511 18256 8.929746 CACGTCTTAGTATTAGATACATCCGTA 58.070 37.037 0.00 0.00 38.21 4.02
4512 18257 7.658982 TCACGTCTTAGTATTAGATACATCCGT 59.341 37.037 0.00 0.00 38.21 4.69
4513 18258 7.956403 GTCACGTCTTAGTATTAGATACATCCG 59.044 40.741 0.00 0.00 38.21 4.18
4514 18259 9.001542 AGTCACGTCTTAGTATTAGATACATCC 57.998 37.037 0.00 0.00 38.21 3.51
4517 18262 9.387257 TCAAGTCACGTCTTAGTATTAGATACA 57.613 33.333 0.00 0.00 38.21 2.29
4521 18266 9.387257 TGTATCAAGTCACGTCTTAGTATTAGA 57.613 33.333 0.00 0.00 0.00 2.10
4524 18269 8.904834 AGATGTATCAAGTCACGTCTTAGTATT 58.095 33.333 0.00 0.00 37.69 1.89
4525 18270 8.346300 CAGATGTATCAAGTCACGTCTTAGTAT 58.654 37.037 0.00 0.00 38.64 2.12
4526 18271 7.336176 ACAGATGTATCAAGTCACGTCTTAGTA 59.664 37.037 0.00 0.00 38.64 1.82
4527 18272 6.151312 ACAGATGTATCAAGTCACGTCTTAGT 59.849 38.462 0.00 0.00 38.64 2.24
4528 18273 6.556212 ACAGATGTATCAAGTCACGTCTTAG 58.444 40.000 0.00 0.00 38.64 2.18
4529 18274 6.510879 ACAGATGTATCAAGTCACGTCTTA 57.489 37.500 0.00 0.00 38.64 2.10
4530 18275 5.392767 ACAGATGTATCAAGTCACGTCTT 57.607 39.130 0.00 0.00 38.64 3.01
4531 18276 6.701145 ATACAGATGTATCAAGTCACGTCT 57.299 37.500 0.00 0.00 40.77 4.18
4532 18277 7.757097 AAATACAGATGTATCAAGTCACGTC 57.243 36.000 5.97 0.00 40.10 4.34
4533 18278 8.683615 TCTAAATACAGATGTATCAAGTCACGT 58.316 33.333 5.97 0.00 40.10 4.49
4534 18279 8.959058 GTCTAAATACAGATGTATCAAGTCACG 58.041 37.037 5.97 0.00 40.10 4.35
4535 18280 9.803315 TGTCTAAATACAGATGTATCAAGTCAC 57.197 33.333 5.97 3.82 40.10 3.67
4557 18302 8.143835 CCCAAAATTCTTGTCTTACATTTGTCT 58.856 33.333 0.00 0.00 27.14 3.41
4558 18303 8.141268 TCCCAAAATTCTTGTCTTACATTTGTC 58.859 33.333 0.00 0.00 27.14 3.18
4559 18304 7.926018 GTCCCAAAATTCTTGTCTTACATTTGT 59.074 33.333 0.00 0.00 27.14 2.83
4560 18305 7.114811 CGTCCCAAAATTCTTGTCTTACATTTG 59.885 37.037 0.00 0.00 0.00 2.32
4561 18306 7.145323 CGTCCCAAAATTCTTGTCTTACATTT 58.855 34.615 0.00 0.00 0.00 2.32
4562 18307 6.294508 CCGTCCCAAAATTCTTGTCTTACATT 60.295 38.462 0.00 0.00 0.00 2.71
4563 18308 5.183140 CCGTCCCAAAATTCTTGTCTTACAT 59.817 40.000 0.00 0.00 0.00 2.29
4564 18309 4.517453 CCGTCCCAAAATTCTTGTCTTACA 59.483 41.667 0.00 0.00 0.00 2.41
4565 18310 4.758165 TCCGTCCCAAAATTCTTGTCTTAC 59.242 41.667 0.00 0.00 0.00 2.34
4566 18311 4.975631 TCCGTCCCAAAATTCTTGTCTTA 58.024 39.130 0.00 0.00 0.00 2.10
4567 18312 3.821033 CTCCGTCCCAAAATTCTTGTCTT 59.179 43.478 0.00 0.00 0.00 3.01
4568 18313 3.412386 CTCCGTCCCAAAATTCTTGTCT 58.588 45.455 0.00 0.00 0.00 3.41
4569 18314 2.488153 CCTCCGTCCCAAAATTCTTGTC 59.512 50.000 0.00 0.00 0.00 3.18
4570 18315 2.514803 CCTCCGTCCCAAAATTCTTGT 58.485 47.619 0.00 0.00 0.00 3.16
4571 18316 1.818674 CCCTCCGTCCCAAAATTCTTG 59.181 52.381 0.00 0.00 0.00 3.02
4572 18317 1.708551 TCCCTCCGTCCCAAAATTCTT 59.291 47.619 0.00 0.00 0.00 2.52
4573 18318 1.282157 CTCCCTCCGTCCCAAAATTCT 59.718 52.381 0.00 0.00 0.00 2.40
4574 18319 1.004394 ACTCCCTCCGTCCCAAAATTC 59.996 52.381 0.00 0.00 0.00 2.17
4575 18320 1.073098 ACTCCCTCCGTCCCAAAATT 58.927 50.000 0.00 0.00 0.00 1.82
4576 18321 1.961133 TACTCCCTCCGTCCCAAAAT 58.039 50.000 0.00 0.00 0.00 1.82
4577 18322 1.557832 CATACTCCCTCCGTCCCAAAA 59.442 52.381 0.00 0.00 0.00 2.44
4578 18323 1.200519 CATACTCCCTCCGTCCCAAA 58.799 55.000 0.00 0.00 0.00 3.28
4579 18324 0.337082 TCATACTCCCTCCGTCCCAA 59.663 55.000 0.00 0.00 0.00 4.12
4580 18325 0.561184 ATCATACTCCCTCCGTCCCA 59.439 55.000 0.00 0.00 0.00 4.37
4581 18326 1.718280 AATCATACTCCCTCCGTCCC 58.282 55.000 0.00 0.00 0.00 4.46
4582 18327 4.344390 ACTTAAATCATACTCCCTCCGTCC 59.656 45.833 0.00 0.00 0.00 4.79
4583 18328 5.532664 ACTTAAATCATACTCCCTCCGTC 57.467 43.478 0.00 0.00 0.00 4.79
4584 18329 5.952347 AACTTAAATCATACTCCCTCCGT 57.048 39.130 0.00 0.00 0.00 4.69
4585 18330 6.258068 GTGAAACTTAAATCATACTCCCTCCG 59.742 42.308 0.00 0.00 0.00 4.63
4586 18331 7.110155 TGTGAAACTTAAATCATACTCCCTCC 58.890 38.462 0.00 0.00 38.04 4.30
4587 18332 8.561738 TTGTGAAACTTAAATCATACTCCCTC 57.438 34.615 0.00 0.00 38.04 4.30
4588 18333 7.121315 GCTTGTGAAACTTAAATCATACTCCCT 59.879 37.037 0.00 0.00 38.04 4.20
4589 18334 7.094377 TGCTTGTGAAACTTAAATCATACTCCC 60.094 37.037 0.00 0.00 38.04 4.30
4590 18335 7.816640 TGCTTGTGAAACTTAAATCATACTCC 58.183 34.615 0.00 0.00 38.04 3.85
4591 18336 9.282247 CATGCTTGTGAAACTTAAATCATACTC 57.718 33.333 0.00 0.00 38.04 2.59
4592 18337 8.246180 CCATGCTTGTGAAACTTAAATCATACT 58.754 33.333 0.00 0.00 38.04 2.12
4593 18338 8.243426 TCCATGCTTGTGAAACTTAAATCATAC 58.757 33.333 0.00 0.00 38.04 2.39
4638 18383 6.974932 TCTTTCACAGCTAAAGCAAGATAG 57.025 37.500 4.54 4.16 45.16 2.08
4646 18396 7.869429 ACCATTTTCAATCTTTCACAGCTAAAG 59.131 33.333 1.64 1.64 35.66 1.85
4693 18448 8.458843 GTGGTATGTAAAAACAGCTGACATTAT 58.541 33.333 23.35 8.12 33.05 1.28
4721 18476 0.321653 GGTGATTCACCGCCAACTCT 60.322 55.000 19.65 0.00 44.95 3.24
4738 18493 7.450903 ACAGTTTCTGTAGCTAGTAATTTGGT 58.549 34.615 0.00 0.00 43.46 3.67
4741 18496 8.784043 CCAAACAGTTTCTGTAGCTAGTAATTT 58.216 33.333 0.00 0.00 44.62 1.82
4766 18521 6.937465 AGTTCCTTAATTTCTCAGTCAACTCC 59.063 38.462 0.00 0.00 0.00 3.85
4784 18840 9.213777 TGGAGATGACAGTAATATTAGTTCCTT 57.786 33.333 13.78 3.81 0.00 3.36
4814 18870 2.559668 CTCCATTGGACTTGTGCACATT 59.440 45.455 22.39 11.06 0.00 2.71
4815 18871 2.165167 CTCCATTGGACTTGTGCACAT 58.835 47.619 22.39 6.49 0.00 3.21
4817 18873 1.896220 TCTCCATTGGACTTGTGCAC 58.104 50.000 10.75 10.75 0.00 4.57
4819 18875 2.165030 CCATTCTCCATTGGACTTGTGC 59.835 50.000 0.00 0.00 34.81 4.57
4822 18878 3.693085 CACTCCATTCTCCATTGGACTTG 59.307 47.826 0.00 0.00 37.10 3.16
4823 18879 3.308688 CCACTCCATTCTCCATTGGACTT 60.309 47.826 0.00 0.00 37.10 3.01
4824 18880 2.240667 CCACTCCATTCTCCATTGGACT 59.759 50.000 0.00 0.00 37.10 3.85
4825 18881 2.239654 TCCACTCCATTCTCCATTGGAC 59.760 50.000 0.00 0.00 37.10 4.02
4826 18882 2.561187 TCCACTCCATTCTCCATTGGA 58.439 47.619 5.05 5.05 39.70 3.53
4827 18883 3.370840 TTCCACTCCATTCTCCATTGG 57.629 47.619 0.00 0.00 0.00 3.16
4828 18884 4.529897 TCATTCCACTCCATTCTCCATTG 58.470 43.478 0.00 0.00 0.00 2.82
4829 18885 4.476113 TCTCATTCCACTCCATTCTCCATT 59.524 41.667 0.00 0.00 0.00 3.16
4830 18886 4.042884 TCTCATTCCACTCCATTCTCCAT 58.957 43.478 0.00 0.00 0.00 3.41
4831 18887 3.453868 TCTCATTCCACTCCATTCTCCA 58.546 45.455 0.00 0.00 0.00 3.86
4832 18888 4.494091 TTCTCATTCCACTCCATTCTCC 57.506 45.455 0.00 0.00 0.00 3.71
4833 18889 6.600822 TCAATTTCTCATTCCACTCCATTCTC 59.399 38.462 0.00 0.00 0.00 2.87
4834 18890 6.487828 TCAATTTCTCATTCCACTCCATTCT 58.512 36.000 0.00 0.00 0.00 2.40
4905 18961 1.796459 GTGTCGAAATACCGCTTGTGT 59.204 47.619 0.00 0.00 0.00 3.72
4937 19000 2.553028 GCTTCTGACCACCATTCCTCAA 60.553 50.000 0.00 0.00 0.00 3.02
4938 19001 1.003580 GCTTCTGACCACCATTCCTCA 59.996 52.381 0.00 0.00 0.00 3.86
4948 19011 1.388547 GTTGTTGGTGCTTCTGACCA 58.611 50.000 0.00 0.00 41.93 4.02
5045 19143 0.179062 GCTGATTCGGGCTCACAGAT 60.179 55.000 0.00 0.00 0.00 2.90
5065 19163 0.527817 GTTACGGTGGCCATCGAGAG 60.528 60.000 43.29 16.54 38.51 3.20


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

AutoCloner maintained by Alex Coulton.