Multiple sequence alignment - TraesCS5B01G541600

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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 TraesCS5B01G541600 chr5B 100.000 8536 0 0 1 8536 696015552 696024087 0.000000e+00 15764.0
1 TraesCS5B01G541600 chr5B 83.830 1175 161 25 5662 6823 696091419 696092577 0.000000e+00 1090.0
2 TraesCS5B01G541600 chr5B 85.437 618 88 2 6933 7549 696092747 696093363 7.220000e-180 641.0
3 TraesCS5B01G541600 chr5B 78.089 1036 190 23 1958 2971 710478131 710479151 9.410000e-174 621.0
4 TraesCS5B01G541600 chr5B 77.829 875 146 32 1877 2736 696127689 696128530 1.650000e-136 497.0
5 TraesCS5B01G541600 chr5B 95.221 272 11 2 845 1115 439487079 439487349 6.120000e-116 429.0
6 TraesCS5B01G541600 chr5B 95.167 269 12 1 851 1119 526525716 526525449 2.850000e-114 424.0
7 TraesCS5B01G541600 chr5B 83.054 478 63 13 7121 7587 696130794 696131264 1.330000e-112 418.0
8 TraesCS5B01G541600 chr5B 91.919 297 23 1 4183 4478 533063370 533063074 1.710000e-111 414.0
9 TraesCS5B01G541600 chr5B 74.754 915 170 39 5766 6641 696129745 696130637 3.790000e-93 353.0
10 TraesCS5B01G541600 chr5B 80.469 384 53 17 4978 5352 696090010 696090380 3.040000e-69 274.0
11 TraesCS5B01G541600 chr5B 87.442 215 16 5 50 262 696086684 696086889 3.980000e-58 237.0
12 TraesCS5B01G541600 chr5B 94.118 119 7 0 1 119 696120273 696120391 1.890000e-41 182.0
13 TraesCS5B01G541600 chr4A 96.603 7448 191 28 1114 8536 613806338 613813748 0.000000e+00 12296.0
14 TraesCS5B01G541600 chr4A 91.680 1911 142 13 6595 8491 613979478 613981385 0.000000e+00 2632.0
15 TraesCS5B01G541600 chr4A 81.454 1224 168 39 5624 6823 613859771 613860959 0.000000e+00 948.0
16 TraesCS5B01G541600 chr4A 77.153 1138 226 25 1846 2967 613700202 613701321 1.560000e-176 630.0
17 TraesCS5B01G541600 chr4A 84.628 605 90 3 6933 7536 613861128 613861730 4.410000e-167 599.0
18 TraesCS5B01G541600 chr4A 91.349 289 20 3 1 285 613804174 613804461 2.890000e-104 390.0
19 TraesCS5B01G541600 chr4A 97.902 143 3 0 711 853 613806198 613806340 1.840000e-61 248.0
20 TraesCS5B01G541600 chr4A 87.442 215 16 5 50 262 613855395 613855600 3.980000e-58 237.0
21 TraesCS5B01G541600 chr4A 95.556 90 4 0 622 711 613804543 613804632 2.480000e-30 145.0
22 TraesCS5B01G541600 chr4A 86.667 120 16 0 4 123 613697343 613697462 5.380000e-27 134.0
23 TraesCS5B01G541600 chr4A 97.143 35 0 1 8494 8528 556629133 556629100 3.330000e-04 58.4
24 TraesCS5B01G541600 chr4A 94.444 36 2 0 8494 8529 146663812 146663777 1.000000e-03 56.5
25 TraesCS5B01G541600 chr4A 90.476 42 2 2 8494 8535 90407021 90406982 4.000000e-03 54.7
26 TraesCS5B01G541600 chr5D 91.099 2966 219 30 5351 8299 555020336 555017399 0.000000e+00 3973.0
27 TraesCS5B01G541600 chr5D 87.244 2438 216 43 2985 5351 555022862 555020449 0.000000e+00 2691.0
28 TraesCS5B01G541600 chr5D 89.912 1923 156 13 1119 3028 555024763 555022866 0.000000e+00 2442.0
29 TraesCS5B01G541600 chr5D 89.340 1060 85 12 5550 6597 554774086 554775129 0.000000e+00 1306.0
30 TraesCS5B01G541600 chr5D 92.244 851 57 6 7648 8491 554817364 554818212 0.000000e+00 1197.0
31 TraesCS5B01G541600 chr5D 83.005 1218 172 28 5624 6823 554926821 554925621 0.000000e+00 1070.0
32 TraesCS5B01G541600 chr5D 91.618 692 45 7 4667 5348 554771448 554772136 0.000000e+00 944.0
33 TraesCS5B01G541600 chr5D 93.509 570 37 0 7020 7589 554816786 554817355 0.000000e+00 848.0
34 TraesCS5B01G541600 chr5D 79.921 1016 179 20 1958 2957 560036544 560037550 0.000000e+00 723.0
35 TraesCS5B01G541600 chr5D 93.439 442 25 4 6595 7033 554815721 554816161 0.000000e+00 652.0
36 TraesCS5B01G541600 chr5D 84.084 622 93 3 6933 7549 554925449 554924829 5.700000e-166 595.0
37 TraesCS5B01G541600 chr5D 91.919 297 17 4 292 585 555026625 555026333 7.980000e-110 409.0
38 TraesCS5B01G541600 chr5D 77.316 626 117 20 5769 6385 554601901 554601292 6.340000e-91 346.0
39 TraesCS5B01G541600 chr5D 77.568 584 121 8 7137 7714 560049430 560050009 2.280000e-90 344.0
40 TraesCS5B01G541600 chr5D 78.767 438 84 9 5741 6172 560039715 560040149 1.400000e-72 285.0
41 TraesCS5B01G541600 chr5D 93.197 147 9 1 140 285 555026820 555026674 1.870000e-51 215.0
42 TraesCS5B01G541600 chr5D 95.122 123 6 0 4 126 554614661 554614539 2.430000e-45 195.0
43 TraesCS5B01G541600 chr5D 85.638 188 22 5 5171 5356 554927670 554927486 8.740000e-45 193.0
44 TraesCS5B01G541600 chr5D 92.079 101 6 1 754 852 555024891 555024791 3.210000e-29 141.0
45 TraesCS5B01G541600 chr5D 98.571 70 1 0 50 119 554929522 554929453 3.240000e-24 124.0
46 TraesCS5B01G541600 chr5D 78.771 179 24 11 50 226 560035733 560035899 3.260000e-19 108.0
47 TraesCS5B01G541600 chr5D 94.828 58 3 0 656 713 458786076 458786019 3.280000e-14 91.6
48 TraesCS5B01G541600 chr3B 95.502 289 9 4 829 1115 558663362 558663648 7.810000e-125 459.0
49 TraesCS5B01G541600 chr3B 92.256 297 22 1 4183 4478 92323095 92322799 3.680000e-113 420.0
50 TraesCS5B01G541600 chr3B 91.919 297 23 1 4183 4478 6037132 6036836 1.710000e-111 414.0
51 TraesCS5B01G541600 chr1B 96.992 266 6 1 850 1115 171126970 171126707 6.080000e-121 446.0
52 TraesCS5B01G541600 chr1B 94.624 279 11 2 851 1129 308795852 308795578 6.120000e-116 429.0
53 TraesCS5B01G541600 chr1B 94.828 58 3 0 656 713 566997610 566997667 3.280000e-14 91.6
54 TraesCS5B01G541600 chr1B 88.000 75 9 0 639 713 480834226 480834300 1.180000e-13 89.8
55 TraesCS5B01G541600 chr1B 92.308 39 1 1 8494 8530 585880190 585880152 4.000000e-03 54.7
56 TraesCS5B01G541600 chr2B 95.572 271 8 3 850 1118 576921558 576921290 1.700000e-116 431.0
57 TraesCS5B01G541600 chr2B 100.000 37 0 0 622 658 11174808 11174772 1.540000e-07 69.4
58 TraesCS5B01G541600 chr4B 94.872 273 10 3 846 1117 475693393 475693662 2.850000e-114 424.0
59 TraesCS5B01G541600 chr4B 100.000 29 0 0 8494 8522 167934354 167934382 4.000000e-03 54.7
60 TraesCS5B01G541600 chr6B 95.131 267 11 1 849 1115 188397728 188397992 3.680000e-113 420.0
61 TraesCS5B01G541600 chr6B 91.919 297 23 1 4183 4478 596625583 596625287 1.710000e-111 414.0
62 TraesCS5B01G541600 chr6B 90.909 66 5 1 656 721 716541537 716541473 4.240000e-13 87.9
63 TraesCS5B01G541600 chr6B 94.737 38 0 2 8494 8531 93917815 93917850 3.330000e-04 58.4
64 TraesCS5B01G541600 chr6B 90.909 44 1 2 8494 8536 460499178 460499219 1.000000e-03 56.5
65 TraesCS5B01G541600 chrUn 91.919 297 23 1 4183 4478 260198488 260198784 1.710000e-111 414.0
66 TraesCS5B01G541600 chrUn 91.919 297 23 1 4183 4478 393426432 393426728 1.710000e-111 414.0
67 TraesCS5B01G541600 chrUn 94.737 38 0 2 8494 8531 18916944 18916909 3.330000e-04 58.4
68 TraesCS5B01G541600 chrUn 100.000 31 0 0 8494 8524 156678539 156678569 3.330000e-04 58.4
69 TraesCS5B01G541600 chrUn 94.286 35 2 0 8488 8522 36303806 36303840 4.000000e-03 54.7
70 TraesCS5B01G541600 chrUn 94.286 35 2 0 8487 8521 76775359 76775393 4.000000e-03 54.7
71 TraesCS5B01G541600 chrUn 94.286 35 2 0 8488 8522 325223426 325223460 4.000000e-03 54.7
72 TraesCS5B01G541600 chrUn 94.286 35 2 0 8487 8521 347687550 347687584 4.000000e-03 54.7
73 TraesCS5B01G541600 chrUn 94.286 35 0 2 8489 8521 12829417 12829451 1.500000e-02 52.8
74 TraesCS5B01G541600 chrUn 100.000 28 0 0 8494 8521 13405869 13405896 1.500000e-02 52.8
75 TraesCS5B01G541600 chrUn 100.000 28 0 0 8495 8522 35513270 35513243 1.500000e-02 52.8
76 TraesCS5B01G541600 chr7A 91.919 297 23 1 4183 4478 563588431 563588135 1.710000e-111 414.0
77 TraesCS5B01G541600 chr7A 97.222 36 1 0 8494 8529 506273510 506273475 2.570000e-05 62.1
78 TraesCS5B01G541600 chr7A 100.000 28 0 0 630 657 309899800 309899827 1.500000e-02 52.8
79 TraesCS5B01G541600 chr3A 94.139 273 14 1 850 1122 482524030 482523760 1.710000e-111 414.0
80 TraesCS5B01G541600 chr3A 94.872 39 0 2 8494 8531 550144920 550144883 9.250000e-05 60.2
81 TraesCS5B01G541600 chr3A 94.872 39 1 1 8494 8531 708069384 708069346 9.250000e-05 60.2
82 TraesCS5B01G541600 chr3A 100.000 28 0 0 630 657 148706317 148706290 1.500000e-02 52.8
83 TraesCS5B01G541600 chr1A 91.582 297 24 1 4183 4478 238114197 238113901 7.980000e-110 409.0
84 TraesCS5B01G541600 chr1A 100.000 36 0 0 622 657 435510065 435510030 5.530000e-07 67.6
85 TraesCS5B01G541600 chr1A 93.182 44 0 3 8494 8536 500630287 500630328 2.570000e-05 62.1
86 TraesCS5B01G541600 chr1A 94.595 37 2 0 8494 8530 533688379 533688415 3.330000e-04 58.4
87 TraesCS5B01G541600 chr1A 94.444 36 2 0 8494 8529 529167125 529167090 1.000000e-03 56.5
88 TraesCS5B01G541600 chr1D 89.333 75 8 0 639 713 77665590 77665664 2.540000e-15 95.3
89 TraesCS5B01G541600 chr1D 94.444 36 1 1 8494 8529 442820277 442820311 4.000000e-03 54.7
90 TraesCS5B01G541600 chr7D 94.828 58 3 0 656 713 548054406 548054463 3.280000e-14 91.6
91 TraesCS5B01G541600 chr5A 94.828 58 3 0 656 713 417306519 417306462 3.280000e-14 91.6
92 TraesCS5B01G541600 chr5A 94.828 58 3 0 656 713 705285274 705285331 3.280000e-14 91.6
93 TraesCS5B01G541600 chr5A 94.872 39 0 2 8494 8531 410795818 410795781 9.250000e-05 60.2
94 TraesCS5B01G541600 chr4D 100.000 30 0 0 8494 8523 9068031 9068060 1.000000e-03 56.5
95 TraesCS5B01G541600 chr4D 100.000 30 0 0 8494 8523 43647782 43647753 1.000000e-03 56.5
96 TraesCS5B01G541600 chr4D 100.000 30 0 0 8494 8523 115516173 115516202 1.000000e-03 56.5
97 TraesCS5B01G541600 chr4D 94.286 35 2 0 8494 8528 108861152 108861118 4.000000e-03 54.7
98 TraesCS5B01G541600 chr4D 94.286 35 0 2 8494 8528 439873616 439873584 1.500000e-02 52.8
99 TraesCS5B01G541600 chr4D 94.286 35 1 1 8494 8528 506933890 506933857 1.500000e-02 52.8
100 TraesCS5B01G541600 chr7B 100.000 28 0 0 630 657 187190602 187190629 1.500000e-02 52.8


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 TraesCS5B01G541600 chr5B 696015552 696024087 8535 False 15764.000000 15764 100.000000 1 8536 1 chr5B.!!$F2 8535
1 TraesCS5B01G541600 chr5B 710478131 710479151 1020 False 621.000000 621 78.089000 1958 2971 1 chr5B.!!$F4 1013
2 TraesCS5B01G541600 chr5B 696086684 696093363 6679 False 560.500000 1090 84.294500 50 7549 4 chr5B.!!$F5 7499
3 TraesCS5B01G541600 chr5B 696127689 696131264 3575 False 422.666667 497 78.545667 1877 7587 3 chr5B.!!$F6 5710
4 TraesCS5B01G541600 chr4A 613804174 613813748 9574 False 3269.750000 12296 95.352500 1 8536 4 chr4A.!!$F4 8535
5 TraesCS5B01G541600 chr4A 613979478 613981385 1907 False 2632.000000 2632 91.680000 6595 8491 1 chr4A.!!$F2 1896
6 TraesCS5B01G541600 chr4A 613859771 613861730 1959 False 773.500000 948 83.041000 5624 7536 2 chr4A.!!$F5 1912
7 TraesCS5B01G541600 chr4A 613697343 613701321 3978 False 382.000000 630 81.910000 4 2967 2 chr4A.!!$F3 2963
8 TraesCS5B01G541600 chr5D 555017399 555026820 9421 True 1645.166667 3973 90.908333 140 8299 6 chr5D.!!$R5 8159
9 TraesCS5B01G541600 chr5D 554771448 554775129 3681 False 1125.000000 1306 90.479000 4667 6597 2 chr5D.!!$F2 1930
10 TraesCS5B01G541600 chr5D 554815721 554818212 2491 False 899.000000 1197 93.064000 6595 8491 3 chr5D.!!$F3 1896
11 TraesCS5B01G541600 chr5D 554924829 554929522 4693 True 495.500000 1070 87.824500 50 7549 4 chr5D.!!$R4 7499
12 TraesCS5B01G541600 chr5D 560035733 560040149 4416 False 372.000000 723 79.153000 50 6172 3 chr5D.!!$F4 6122
13 TraesCS5B01G541600 chr5D 554601292 554601901 609 True 346.000000 346 77.316000 5769 6385 1 chr5D.!!$R2 616
14 TraesCS5B01G541600 chr5D 560049430 560050009 579 False 344.000000 344 77.568000 7137 7714 1 chr5D.!!$F1 577

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
341 473 0.030638 ACGTGCATGCAAAAGTGGTC 59.969 50.000 24.58 6.26 0.00 4.02 F
934 4267 0.311790 CTTGCGTTGCACCACTCATT 59.688 50.000 0.00 0.00 38.71 2.57 F
938 4271 0.950836 CGTTGCACCACTCATTTGGA 59.049 50.000 0.00 0.00 39.24 3.53 F
2223 5704 1.003355 ACTCCAACATCACAGCCCG 60.003 57.895 0.00 0.00 0.00 6.13 F
2233 5714 1.968017 CACAGCCCGTGCAATCACT 60.968 57.895 0.00 0.00 40.99 3.41 F
3069 6654 2.661176 ATCCTGAGGAAACCTACCCA 57.339 50.000 4.76 0.00 34.34 4.51 F
3923 7542 1.960689 GTGCCAAACTACCCATGTGTT 59.039 47.619 0.00 0.00 0.00 3.32 F
4253 7907 2.492025 AGGTCCATCTCATTAAGGCCA 58.508 47.619 5.01 0.00 0.00 5.36 F
5670 12213 0.450983 TGTGTGTGCATGTGTGTGTG 59.549 50.000 0.00 0.00 0.00 3.82 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2001 5475 0.813184 CGAATGCAGGCTGTTTGGAT 59.187 50.000 17.16 0.00 0.00 3.41 R
2649 6135 2.513753 CTGTTGCCATTGTAGGAACCA 58.486 47.619 0.00 0.00 0.00 3.67 R
2880 6382 5.699097 TTAAGTTGTCAACATGCCCTTAC 57.301 39.130 17.78 0.00 0.00 2.34 R
3111 6696 3.011818 TGGCATGTGTTAAGAGATGCAG 58.988 45.455 28.41 0.11 42.50 4.41 R
3367 6954 3.273434 TGTGAGGAATAATGCACTGAGC 58.727 45.455 0.00 0.00 45.96 4.26 R
4683 8646 4.424626 ACGTCATGCAAGTATACAGAGTG 58.575 43.478 5.50 0.00 0.00 3.51 R
5508 10386 5.353956 GGTCATGCAAATATAGTGTGACACA 59.646 40.000 18.95 3.56 36.97 3.72 R
6005 12970 4.883585 TCCTGTTGTTTGATATGCATCTCC 59.116 41.667 0.19 0.00 31.93 3.71 R
7651 15387 0.810648 AATGCGGCCATACACACAAG 59.189 50.000 2.24 0.00 0.00 3.16 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
169 208 4.391405 TCAGTCTGATTGTACGATGCAT 57.609 40.909 0.00 0.00 0.00 3.96
240 280 3.562973 CCATGCATCTGTAACTAGCTTGG 59.437 47.826 0.00 0.00 41.85 3.61
290 419 7.811236 GCATGTTTATCATTAGCTTGCACATAT 59.189 33.333 0.00 0.00 34.09 1.78
341 473 0.030638 ACGTGCATGCAAAAGTGGTC 59.969 50.000 24.58 6.26 0.00 4.02
352 484 2.200373 AAAGTGGTCCATGCAGGTAC 57.800 50.000 0.00 0.00 39.02 3.34
377 511 3.501911 AGTTGCCCACCCTGCACT 61.502 61.111 0.00 0.00 38.72 4.40
389 523 0.678048 CCTGCACTCTAAAGGTGGCC 60.678 60.000 0.00 0.00 35.47 5.36
469 665 1.674221 GCTGAACACTCTCGCTTCCAT 60.674 52.381 0.00 0.00 0.00 3.41
470 666 1.998315 CTGAACACTCTCGCTTCCATG 59.002 52.381 0.00 0.00 0.00 3.66
524 720 1.546029 GGCCACTCCCAATCAAGTTTC 59.454 52.381 0.00 0.00 0.00 2.78
525 721 1.546029 GCCACTCCCAATCAAGTTTCC 59.454 52.381 0.00 0.00 0.00 3.13
576 772 4.895668 TCATACGGTTTTACAGGTCCTT 57.104 40.909 0.00 0.00 0.00 3.36
606 802 6.582437 TTTTTGCGAGAAAAACTTCCAATC 57.418 33.333 0.00 0.00 0.00 2.67
607 803 5.514274 TTTGCGAGAAAAACTTCCAATCT 57.486 34.783 0.00 0.00 0.00 2.40
608 804 6.627395 TTTGCGAGAAAAACTTCCAATCTA 57.373 33.333 0.00 0.00 0.00 1.98
609 805 5.607119 TGCGAGAAAAACTTCCAATCTAC 57.393 39.130 0.00 0.00 0.00 2.59
610 806 5.305585 TGCGAGAAAAACTTCCAATCTACT 58.694 37.500 0.00 0.00 0.00 2.57
611 807 5.408604 TGCGAGAAAAACTTCCAATCTACTC 59.591 40.000 0.00 0.00 0.00 2.59
612 808 5.163844 GCGAGAAAAACTTCCAATCTACTCC 60.164 44.000 0.00 0.00 0.00 3.85
613 809 5.351740 CGAGAAAAACTTCCAATCTACTCCC 59.648 44.000 0.00 0.00 0.00 4.30
614 810 6.455690 AGAAAAACTTCCAATCTACTCCCT 57.544 37.500 0.00 0.00 0.00 4.20
615 811 6.477253 AGAAAAACTTCCAATCTACTCCCTC 58.523 40.000 0.00 0.00 0.00 4.30
616 812 4.846168 AAACTTCCAATCTACTCCCTCC 57.154 45.455 0.00 0.00 0.00 4.30
617 813 3.491766 ACTTCCAATCTACTCCCTCCA 57.508 47.619 0.00 0.00 0.00 3.86
618 814 4.014273 ACTTCCAATCTACTCCCTCCAT 57.986 45.455 0.00 0.00 0.00 3.41
619 815 4.375313 ACTTCCAATCTACTCCCTCCATT 58.625 43.478 0.00 0.00 0.00 3.16
620 816 4.410555 ACTTCCAATCTACTCCCTCCATTC 59.589 45.833 0.00 0.00 0.00 2.67
647 843 3.304911 TGGGTCATCTGTTTTGGAACA 57.695 42.857 0.00 0.00 43.23 3.18
695 891 6.208644 TGGTAGTACAACGAACACTAGAAAC 58.791 40.000 2.06 0.00 0.00 2.78
823 4154 6.992063 AGAAATCAACTTACTGCGATGAAT 57.008 33.333 0.00 0.00 0.00 2.57
856 4189 9.281371 GTAGGTTCATGGTTAAAATATACTCCC 57.719 37.037 0.00 0.00 0.00 4.30
857 4190 8.114301 AGGTTCATGGTTAAAATATACTCCCT 57.886 34.615 0.00 0.00 0.00 4.20
860 4193 9.057089 GTTCATGGTTAAAATATACTCCCTCAG 57.943 37.037 0.00 0.00 0.00 3.35
861 4194 8.331931 TCATGGTTAAAATATACTCCCTCAGT 57.668 34.615 0.00 0.00 39.41 3.41
862 4195 8.778059 TCATGGTTAAAATATACTCCCTCAGTT 58.222 33.333 0.00 0.00 36.43 3.16
863 4196 9.057089 CATGGTTAAAATATACTCCCTCAGTTC 57.943 37.037 0.00 0.00 36.43 3.01
864 4197 7.571025 TGGTTAAAATATACTCCCTCAGTTCC 58.429 38.462 0.00 0.00 36.43 3.62
865 4198 7.404980 TGGTTAAAATATACTCCCTCAGTTCCT 59.595 37.037 0.00 0.00 36.43 3.36
866 4199 8.272889 GGTTAAAATATACTCCCTCAGTTCCTT 58.727 37.037 0.00 0.00 36.43 3.36
867 4200 9.110502 GTTAAAATATACTCCCTCAGTTCCTTG 57.889 37.037 0.00 0.00 36.43 3.61
868 4201 7.510675 AAAATATACTCCCTCAGTTCCTTGA 57.489 36.000 0.00 0.00 36.43 3.02
869 4202 7.698163 AAATATACTCCCTCAGTTCCTTGAT 57.302 36.000 0.00 0.00 36.43 2.57
870 4203 8.798975 AAATATACTCCCTCAGTTCCTTGATA 57.201 34.615 0.00 0.00 36.43 2.15
871 4204 8.980832 AATATACTCCCTCAGTTCCTTGATAT 57.019 34.615 0.00 0.00 36.43 1.63
875 4208 5.604650 ACTCCCTCAGTTCCTTGATATAAGG 59.395 44.000 0.00 0.00 38.78 2.69
876 4209 5.538877 TCCCTCAGTTCCTTGATATAAGGT 58.461 41.667 5.67 0.00 38.55 3.50
879 4212 6.326583 CCCTCAGTTCCTTGATATAAGGTGTA 59.673 42.308 5.67 0.00 38.55 2.90
881 4214 9.090103 CCTCAGTTCCTTGATATAAGGTGTATA 57.910 37.037 5.67 0.00 38.55 1.47
917 4250 7.494922 AAACATCCAAAATATAAGGTGCCTT 57.505 32.000 8.65 8.65 39.83 4.35
918 4251 6.469782 ACATCCAAAATATAAGGTGCCTTG 57.530 37.500 13.34 0.00 37.47 3.61
920 4253 3.380004 TCCAAAATATAAGGTGCCTTGCG 59.620 43.478 13.34 0.00 37.47 4.85
921 4254 3.130340 CCAAAATATAAGGTGCCTTGCGT 59.870 43.478 13.34 2.86 37.47 5.24
922 4255 4.381505 CCAAAATATAAGGTGCCTTGCGTT 60.382 41.667 13.34 2.97 37.47 4.84
925 4258 0.893270 ATAAGGTGCCTTGCGTTGCA 60.893 50.000 13.34 0.00 37.47 4.08
929 4262 3.898509 TGCCTTGCGTTGCACCAC 61.899 61.111 0.00 0.00 38.71 4.16
930 4263 3.595758 GCCTTGCGTTGCACCACT 61.596 61.111 0.00 0.00 38.71 4.00
933 4266 1.518056 CCTTGCGTTGCACCACTCAT 61.518 55.000 0.00 0.00 38.71 2.90
934 4267 0.311790 CTTGCGTTGCACCACTCATT 59.688 50.000 0.00 0.00 38.71 2.57
938 4271 0.950836 CGTTGCACCACTCATTTGGA 59.049 50.000 0.00 0.00 39.24 3.53
939 4272 1.541147 CGTTGCACCACTCATTTGGAT 59.459 47.619 0.00 0.00 39.24 3.41
940 4273 2.746904 CGTTGCACCACTCATTTGGATA 59.253 45.455 0.00 0.00 39.24 2.59
942 4275 4.142403 CGTTGCACCACTCATTTGGATAAT 60.142 41.667 0.00 0.00 39.24 1.28
943 4276 5.622007 CGTTGCACCACTCATTTGGATAATT 60.622 40.000 0.00 0.00 39.24 1.40
944 4277 5.999205 TGCACCACTCATTTGGATAATTT 57.001 34.783 0.00 0.00 39.24 1.82
946 4279 6.767456 TGCACCACTCATTTGGATAATTTTT 58.233 32.000 0.00 0.00 39.24 1.94
989 4322 8.440771 ACATTTACTTATATTAGGCAAGCTCCT 58.559 33.333 0.00 0.00 40.21 3.69
990 4323 8.940952 CATTTACTTATATTAGGCAAGCTCCTC 58.059 37.037 0.00 0.00 37.66 3.71
991 4324 7.857404 TTACTTATATTAGGCAAGCTCCTCT 57.143 36.000 0.00 0.00 37.66 3.69
994 4327 8.442660 ACTTATATTAGGCAAGCTCCTCTATT 57.557 34.615 0.00 0.00 37.66 1.73
996 4329 9.732130 CTTATATTAGGCAAGCTCCTCTATTTT 57.268 33.333 0.00 0.00 37.66 1.82
997 4330 9.726438 TTATATTAGGCAAGCTCCTCTATTTTC 57.274 33.333 0.00 0.00 37.66 2.29
998 4331 5.700402 TTAGGCAAGCTCCTCTATTTTCT 57.300 39.130 0.00 0.00 37.66 2.52
999 4332 4.149511 AGGCAAGCTCCTCTATTTTCTC 57.850 45.455 0.00 0.00 0.00 2.87
1000 4333 3.521126 AGGCAAGCTCCTCTATTTTCTCA 59.479 43.478 0.00 0.00 0.00 3.27
1002 4335 4.275443 GGCAAGCTCCTCTATTTTCTCATG 59.725 45.833 0.00 0.00 0.00 3.07
1003 4336 4.880696 GCAAGCTCCTCTATTTTCTCATGT 59.119 41.667 0.00 0.00 0.00 3.21
1004 4337 5.007528 GCAAGCTCCTCTATTTTCTCATGTC 59.992 44.000 0.00 0.00 0.00 3.06
1006 4339 6.305272 AGCTCCTCTATTTTCTCATGTCAA 57.695 37.500 0.00 0.00 0.00 3.18
1007 4340 6.897986 AGCTCCTCTATTTTCTCATGTCAAT 58.102 36.000 0.00 0.00 0.00 2.57
1009 4342 8.489489 AGCTCCTCTATTTTCTCATGTCAATTA 58.511 33.333 0.00 0.00 0.00 1.40
1011 4344 9.829507 CTCCTCTATTTTCTCATGTCAATTAGT 57.170 33.333 0.00 0.00 0.00 2.24
1013 4346 9.605275 CCTCTATTTTCTCATGTCAATTAGTCA 57.395 33.333 0.00 0.00 0.00 3.41
1015 4348 9.087424 TCTATTTTCTCATGTCAATTAGTCACG 57.913 33.333 0.00 0.00 0.00 4.35
1026 4479 6.586463 TGTCAATTAGTCACGTGAAATCTCTC 59.414 38.462 21.95 5.85 0.00 3.20
1027 4480 6.035112 GTCAATTAGTCACGTGAAATCTCTCC 59.965 42.308 21.95 5.03 0.00 3.71
1028 4481 4.451629 TTAGTCACGTGAAATCTCTCCC 57.548 45.455 21.95 4.23 0.00 4.30
1031 4484 3.071023 AGTCACGTGAAATCTCTCCCAAA 59.929 43.478 21.95 0.00 0.00 3.28
1037 4490 4.275936 CGTGAAATCTCTCCCAAAACTTGT 59.724 41.667 0.00 0.00 0.00 3.16
1038 4491 5.523369 GTGAAATCTCTCCCAAAACTTGTG 58.477 41.667 0.00 0.00 0.00 3.33
1039 4492 5.299279 GTGAAATCTCTCCCAAAACTTGTGA 59.701 40.000 0.00 0.00 0.00 3.58
1040 4493 5.890985 TGAAATCTCTCCCAAAACTTGTGAA 59.109 36.000 0.00 0.00 0.00 3.18
1041 4494 6.379703 TGAAATCTCTCCCAAAACTTGTGAAA 59.620 34.615 0.00 0.00 0.00 2.69
1042 4495 6.983906 AATCTCTCCCAAAACTTGTGAAAT 57.016 33.333 0.00 0.00 0.00 2.17
1043 4496 6.983906 ATCTCTCCCAAAACTTGTGAAATT 57.016 33.333 0.00 0.00 0.00 1.82
1044 4497 6.790232 TCTCTCCCAAAACTTGTGAAATTT 57.210 33.333 0.00 0.00 0.00 1.82
1045 4498 7.181569 TCTCTCCCAAAACTTGTGAAATTTT 57.818 32.000 0.00 0.00 0.00 1.82
1046 4499 7.264947 TCTCTCCCAAAACTTGTGAAATTTTC 58.735 34.615 2.05 2.05 0.00 2.29
1047 4500 6.940739 TCTCCCAAAACTTGTGAAATTTTCA 58.059 32.000 7.74 7.74 37.33 2.69
1048 4501 7.041107 TCTCCCAAAACTTGTGAAATTTTCAG 58.959 34.615 12.02 4.01 41.01 3.02
1049 4502 6.706295 TCCCAAAACTTGTGAAATTTTCAGT 58.294 32.000 12.02 4.61 41.01 3.41
1050 4503 6.816140 TCCCAAAACTTGTGAAATTTTCAGTC 59.184 34.615 12.02 2.82 41.01 3.51
1051 4504 6.037062 CCCAAAACTTGTGAAATTTTCAGTCC 59.963 38.462 12.02 2.15 41.01 3.85
1052 4505 6.593382 CCAAAACTTGTGAAATTTTCAGTCCA 59.407 34.615 12.02 4.68 41.01 4.02
1053 4506 7.412891 CCAAAACTTGTGAAATTTTCAGTCCAC 60.413 37.037 12.02 2.02 41.01 4.02
1054 4507 5.913137 ACTTGTGAAATTTTCAGTCCACA 57.087 34.783 12.02 4.54 41.01 4.17
1055 4508 6.469782 ACTTGTGAAATTTTCAGTCCACAT 57.530 33.333 12.02 0.00 41.01 3.21
1056 4509 6.275335 ACTTGTGAAATTTTCAGTCCACATG 58.725 36.000 12.02 14.52 41.01 3.21
1057 4510 4.619973 TGTGAAATTTTCAGTCCACATGC 58.380 39.130 12.02 0.00 41.01 4.06
1058 4511 4.099113 TGTGAAATTTTCAGTCCACATGCA 59.901 37.500 12.02 0.00 41.01 3.96
1059 4512 5.221481 TGTGAAATTTTCAGTCCACATGCAT 60.221 36.000 12.02 0.00 41.01 3.96
1060 4513 5.697633 GTGAAATTTTCAGTCCACATGCATT 59.302 36.000 12.02 0.00 41.01 3.56
1061 4514 5.927689 TGAAATTTTCAGTCCACATGCATTC 59.072 36.000 7.74 0.00 34.08 2.67
1062 4515 5.733620 AATTTTCAGTCCACATGCATTCT 57.266 34.783 0.00 0.00 0.00 2.40
1063 4516 5.733620 ATTTTCAGTCCACATGCATTCTT 57.266 34.783 0.00 0.00 0.00 2.52
1064 4517 5.534207 TTTTCAGTCCACATGCATTCTTT 57.466 34.783 0.00 0.00 0.00 2.52
1065 4518 6.647334 TTTTCAGTCCACATGCATTCTTTA 57.353 33.333 0.00 0.00 0.00 1.85
1066 4519 6.647334 TTTCAGTCCACATGCATTCTTTAA 57.353 33.333 0.00 0.00 0.00 1.52
1067 4520 6.839124 TTCAGTCCACATGCATTCTTTAAT 57.161 33.333 0.00 0.00 0.00 1.40
1068 4521 6.839124 TCAGTCCACATGCATTCTTTAATT 57.161 33.333 0.00 0.00 0.00 1.40
1069 4522 7.230849 TCAGTCCACATGCATTCTTTAATTT 57.769 32.000 0.00 0.00 0.00 1.82
1070 4523 7.315142 TCAGTCCACATGCATTCTTTAATTTC 58.685 34.615 0.00 0.00 0.00 2.17
1071 4524 6.532657 CAGTCCACATGCATTCTTTAATTTCC 59.467 38.462 0.00 0.00 0.00 3.13
1072 4525 5.516339 GTCCACATGCATTCTTTAATTTCCG 59.484 40.000 0.00 0.00 0.00 4.30
1073 4526 5.184864 TCCACATGCATTCTTTAATTTCCGT 59.815 36.000 0.00 0.00 0.00 4.69
1074 4527 5.289193 CCACATGCATTCTTTAATTTCCGTG 59.711 40.000 0.00 0.00 0.00 4.94
1075 4528 4.864247 ACATGCATTCTTTAATTTCCGTGC 59.136 37.500 0.00 0.00 0.00 5.34
1076 4529 3.843999 TGCATTCTTTAATTTCCGTGCC 58.156 40.909 0.00 0.00 0.00 5.01
1077 4530 3.256879 TGCATTCTTTAATTTCCGTGCCA 59.743 39.130 0.00 0.00 0.00 4.92
1078 4531 4.241681 GCATTCTTTAATTTCCGTGCCAA 58.758 39.130 0.00 0.00 0.00 4.52
1079 4532 4.688413 GCATTCTTTAATTTCCGTGCCAAA 59.312 37.500 0.00 0.00 0.00 3.28
1080 4533 5.178438 GCATTCTTTAATTTCCGTGCCAAAA 59.822 36.000 0.00 0.00 0.00 2.44
1081 4534 6.293135 GCATTCTTTAATTTCCGTGCCAAAAA 60.293 34.615 0.00 0.00 0.00 1.94
1082 4535 6.591313 TTCTTTAATTTCCGTGCCAAAAAC 57.409 33.333 0.00 0.00 0.00 2.43
1083 4536 5.908341 TCTTTAATTTCCGTGCCAAAAACT 58.092 33.333 0.00 0.00 0.00 2.66
1084 4537 7.040473 TCTTTAATTTCCGTGCCAAAAACTA 57.960 32.000 0.00 0.00 0.00 2.24
1085 4538 7.662897 TCTTTAATTTCCGTGCCAAAAACTAT 58.337 30.769 0.00 0.00 0.00 2.12
1086 4539 8.794553 TCTTTAATTTCCGTGCCAAAAACTATA 58.205 29.630 0.00 0.00 0.00 1.31
1087 4540 8.745464 TTTAATTTCCGTGCCAAAAACTATAC 57.255 30.769 0.00 0.00 0.00 1.47
1088 4541 5.968528 ATTTCCGTGCCAAAAACTATACA 57.031 34.783 0.00 0.00 0.00 2.29
1089 4542 4.752661 TTCCGTGCCAAAAACTATACAC 57.247 40.909 0.00 0.00 0.00 2.90
1090 4543 3.075884 TCCGTGCCAAAAACTATACACC 58.924 45.455 0.00 0.00 0.00 4.16
1091 4544 2.162809 CCGTGCCAAAAACTATACACCC 59.837 50.000 0.00 0.00 0.00 4.61
1291 4746 8.860128 GTCCCTTTAAAGAAATTTTTCTATGCG 58.140 33.333 16.98 0.00 46.22 4.73
1387 4843 7.490725 TGCCGAATAATGTTAACAAATGATTGG 59.509 33.333 13.23 11.85 41.01 3.16
1394 4850 8.633075 AATGTTAACAAATGATTGGCTTATCG 57.367 30.769 13.23 0.00 41.01 2.92
1452 4908 5.604010 TTTGCACCACAAAGTTTCTTTTG 57.396 34.783 0.00 0.00 43.35 2.44
1501 4957 1.206878 TGTCAGAGTATGCCCATGCT 58.793 50.000 0.00 0.00 38.71 3.79
1522 4978 4.943705 GCTGGGTGAGTTTGAAATATCTCA 59.056 41.667 0.00 0.00 35.06 3.27
2001 5475 4.799564 TGTCATAGACTGTGTGCACATA 57.200 40.909 24.69 20.05 41.01 2.29
2079 5554 5.815581 ACACTTAGCACATCATTTCCCTTA 58.184 37.500 0.00 0.00 0.00 2.69
2223 5704 1.003355 ACTCCAACATCACAGCCCG 60.003 57.895 0.00 0.00 0.00 6.13
2233 5714 1.968017 CACAGCCCGTGCAATCACT 60.968 57.895 0.00 0.00 40.99 3.41
2721 6208 5.509670 GGTGAGACCTCAAAGGGAAAAATTG 60.510 44.000 0.70 0.00 40.58 2.32
2880 6382 8.841444 ATTCTAGCAGCATTATTTTTAACACG 57.159 30.769 0.00 0.00 0.00 4.49
3069 6654 2.661176 ATCCTGAGGAAACCTACCCA 57.339 50.000 4.76 0.00 34.34 4.51
3111 6696 9.581099 TTCAAACTTCTTCATGTCCTTAAAAAC 57.419 29.630 0.00 0.00 0.00 2.43
3163 6748 7.346751 TGTGGCTCACTAAAGAGAAATTTTT 57.653 32.000 6.83 0.00 37.87 1.94
3304 6891 5.121811 CAACTCATAGGAGATGAACCTTGG 58.878 45.833 12.12 0.00 44.27 3.61
3352 6939 6.688637 TGCCAAACTAGATCATTTCTCATG 57.311 37.500 0.00 0.00 35.79 3.07
3577 7165 8.437742 CAAAGTAAATAAGCCTTGCAATTTCAG 58.562 33.333 0.00 0.00 31.98 3.02
3603 7191 6.542821 AGAGGTGGTATGAAACATGAAAGAA 58.457 36.000 0.00 0.00 0.00 2.52
3825 7419 6.007076 TGCTTTGAGTCCACCATGTTAATTA 58.993 36.000 0.00 0.00 0.00 1.40
3923 7542 1.960689 GTGCCAAACTACCCATGTGTT 59.039 47.619 0.00 0.00 0.00 3.32
4108 7762 8.106247 TCACTACCTTTGCCTTTATTACAAAG 57.894 34.615 7.55 7.55 46.25 2.77
4253 7907 2.492025 AGGTCCATCTCATTAAGGCCA 58.508 47.619 5.01 0.00 0.00 5.36
4267 7921 6.945435 TCATTAAGGCCAAACATTTAGTCTCA 59.055 34.615 5.01 0.00 0.00 3.27
4339 7994 5.787380 AGGATTTTGTCTTTCTGCAATTCC 58.213 37.500 0.00 0.00 32.24 3.01
4487 8160 8.001881 ACTCGATGTTATCACTAGATTTGTCT 57.998 34.615 0.00 0.00 35.67 3.41
4506 8179 5.423015 TGTCTTTCCTCATCTGCATCTAAC 58.577 41.667 0.00 0.00 0.00 2.34
4959 8965 5.432645 TCCTTAATGAGTCACACAACAACA 58.567 37.500 0.00 0.00 0.00 3.33
5150 9171 4.701765 TGCAATGTGTGTTGGCTAAAATT 58.298 34.783 0.00 0.00 0.00 1.82
5508 10386 3.652057 ATTGGTGCACCTACTAGCAAT 57.348 42.857 34.75 21.23 43.20 3.56
5533 10411 5.353956 GTGTCACACTATATTTGCATGACCA 59.646 40.000 0.00 0.00 35.26 4.02
5670 12213 0.450983 TGTGTGTGCATGTGTGTGTG 59.549 50.000 0.00 0.00 0.00 3.82
5680 12591 1.598882 TGTGTGTGTGTGTGTGTGTT 58.401 45.000 0.00 0.00 0.00 3.32
5702 12649 6.098409 TGTTTGTCTATCTATCTCTTCCACCC 59.902 42.308 0.00 0.00 0.00 4.61
6181 13147 5.725110 ACACAATAAGCTTCGACATCATC 57.275 39.130 0.00 0.00 0.00 2.92
6312 13281 7.201670 CCTTATACCCAAACGTTCAAATAGGAC 60.202 40.741 0.00 0.00 0.00 3.85
6455 13453 8.945481 TTAAGCATACAATCCAAAATTCATGG 57.055 30.769 4.25 4.25 39.41 3.66
6654 13668 5.477637 CCCGGTTAGAGTTGGGAAAAATAAA 59.522 40.000 0.00 0.00 44.88 1.40
6839 13886 0.933097 GCACGCATCGTCAAGATCAT 59.067 50.000 0.00 0.00 38.32 2.45
6952 14029 8.007405 AGTAAGGAACATATTTTTACCATGCC 57.993 34.615 0.00 0.00 0.00 4.40
7062 14778 3.515104 CTCAACCTGGCCCATTAATGTTT 59.485 43.478 14.25 0.00 0.00 2.83
7397 15123 5.407407 ACATTCAAGTGGTAGATTCGTCT 57.593 39.130 0.00 0.00 0.00 4.18
7651 15387 9.624697 TTTCAATTATGTTGTAATGCTCACTTC 57.375 29.630 0.00 0.00 0.00 3.01
7988 15731 7.176340 ACCAAGAAAATTTCTCTCTCTCAATGG 59.824 37.037 8.86 11.33 39.61 3.16
8244 15990 8.699283 AGTTCGTTACTATAAACTTCCATGTC 57.301 34.615 0.00 0.00 34.56 3.06
8395 16141 6.585702 CCAACTTCGCAATGTTTGAATGATTA 59.414 34.615 0.00 0.00 0.00 1.75
8398 16144 8.039603 ACTTCGCAATGTTTGAATGATTAGTA 57.960 30.769 0.00 0.00 0.00 1.82
8452 16198 5.513788 GGGTATGCAATGGTCACATAGAGAT 60.514 44.000 0.00 0.00 35.94 2.75
8491 16237 4.228210 TGATGCCCTCTAAGATCTGGTTTT 59.772 41.667 0.00 0.00 0.00 2.43
8492 16238 3.955471 TGCCCTCTAAGATCTGGTTTTG 58.045 45.455 0.00 0.00 0.00 2.44
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
35 36 2.103143 CTGCGCTGTACTCTCCGG 59.897 66.667 9.73 0.00 0.00 5.14
37 38 2.580867 CGCTGCGCTGTACTCTCC 60.581 66.667 9.88 0.00 0.00 3.71
39 40 4.803426 GCCGCTGCGCTGTACTCT 62.803 66.667 18.00 0.00 0.00 3.24
169 208 2.092968 ACAACACCAGAGAAGCAAGACA 60.093 45.455 0.00 0.00 0.00 3.41
228 268 9.343539 AGGATCAAATAAATCCAAGCTAGTTAC 57.656 33.333 5.05 0.00 44.39 2.50
290 419 5.221342 ACAATGTTCCCGTTTCTTTTGCATA 60.221 36.000 0.00 0.00 0.00 3.14
329 461 0.675083 CTGCATGGACCACTTTTGCA 59.325 50.000 17.39 17.39 40.73 4.08
341 473 3.606886 GGTATCCGTACCTGCATGG 57.393 57.895 0.00 0.00 45.78 3.66
352 484 1.451387 GGTGGGCAACTGGTATCCG 60.451 63.158 0.00 0.00 0.00 4.18
364 496 0.678048 CTTTAGAGTGCAGGGTGGGC 60.678 60.000 0.00 0.00 0.00 5.36
377 511 7.622479 AGAATTACTAACTAGGCCACCTTTAGA 59.378 37.037 5.01 0.00 34.61 2.10
469 665 3.018856 CCACAAAGGAATCTATGCTGCA 58.981 45.455 4.13 4.13 41.22 4.41
470 666 3.019564 ACCACAAAGGAATCTATGCTGC 58.980 45.455 0.00 0.00 41.22 5.25
524 720 3.415457 AGACTGGCAGAGAGAAAAAGG 57.585 47.619 23.66 0.00 0.00 3.11
525 721 5.764487 AAAAGACTGGCAGAGAGAAAAAG 57.236 39.130 23.66 0.00 0.00 2.27
558 754 4.420522 ACAAAGGACCTGTAAAACCGTA 57.579 40.909 0.00 0.00 0.00 4.02
559 755 3.286329 ACAAAGGACCTGTAAAACCGT 57.714 42.857 0.00 0.00 0.00 4.83
585 781 5.514274 AGATTGGAAGTTTTTCTCGCAAA 57.486 34.783 0.00 0.00 33.68 3.68
586 782 5.763204 AGTAGATTGGAAGTTTTTCTCGCAA 59.237 36.000 0.00 0.00 33.68 4.85
588 784 5.163844 GGAGTAGATTGGAAGTTTTTCTCGC 60.164 44.000 0.00 0.00 33.68 5.03
589 785 5.351740 GGGAGTAGATTGGAAGTTTTTCTCG 59.648 44.000 0.00 0.00 33.68 4.04
590 786 6.477253 AGGGAGTAGATTGGAAGTTTTTCTC 58.523 40.000 0.00 0.00 33.68 2.87
591 787 6.455690 AGGGAGTAGATTGGAAGTTTTTCT 57.544 37.500 0.00 0.00 33.68 2.52
592 788 5.648526 GGAGGGAGTAGATTGGAAGTTTTTC 59.351 44.000 0.00 0.00 0.00 2.29
593 789 5.074515 TGGAGGGAGTAGATTGGAAGTTTTT 59.925 40.000 0.00 0.00 0.00 1.94
594 790 4.601857 TGGAGGGAGTAGATTGGAAGTTTT 59.398 41.667 0.00 0.00 0.00 2.43
595 791 4.175962 TGGAGGGAGTAGATTGGAAGTTT 58.824 43.478 0.00 0.00 0.00 2.66
596 792 3.803340 TGGAGGGAGTAGATTGGAAGTT 58.197 45.455 0.00 0.00 0.00 2.66
597 793 3.491766 TGGAGGGAGTAGATTGGAAGT 57.508 47.619 0.00 0.00 0.00 3.01
598 794 4.202409 GGAATGGAGGGAGTAGATTGGAAG 60.202 50.000 0.00 0.00 0.00 3.46
599 795 3.716872 GGAATGGAGGGAGTAGATTGGAA 59.283 47.826 0.00 0.00 0.00 3.53
600 796 3.311327 TGGAATGGAGGGAGTAGATTGGA 60.311 47.826 0.00 0.00 0.00 3.53
601 797 3.048600 TGGAATGGAGGGAGTAGATTGG 58.951 50.000 0.00 0.00 0.00 3.16
602 798 4.778213 TTGGAATGGAGGGAGTAGATTG 57.222 45.455 0.00 0.00 0.00 2.67
603 799 4.790790 ACTTTGGAATGGAGGGAGTAGATT 59.209 41.667 0.00 0.00 0.00 2.40
604 800 4.375313 ACTTTGGAATGGAGGGAGTAGAT 58.625 43.478 0.00 0.00 0.00 1.98
605 801 3.803340 ACTTTGGAATGGAGGGAGTAGA 58.197 45.455 0.00 0.00 0.00 2.59
606 802 4.265073 CAACTTTGGAATGGAGGGAGTAG 58.735 47.826 0.00 0.00 0.00 2.57
607 803 4.301072 CAACTTTGGAATGGAGGGAGTA 57.699 45.455 0.00 0.00 0.00 2.59
608 804 3.160679 CAACTTTGGAATGGAGGGAGT 57.839 47.619 0.00 0.00 0.00 3.85
637 833 5.561679 AGAATACTCCCTCTGTTCCAAAAC 58.438 41.667 0.00 0.00 35.85 2.43
647 843 7.419981 CCATGATTGAAGAAGAATACTCCCTCT 60.420 40.741 0.00 0.00 0.00 3.69
706 902 2.793278 AGGAAACAAAACGTGGATGC 57.207 45.000 0.00 0.00 0.00 3.91
857 4190 9.877222 TCTATACACCTTATATCAAGGAACTGA 57.123 33.333 9.96 0.00 40.86 3.41
890 4223 7.400052 AGGCACCTTATATTTTGGATGTTTTCT 59.600 33.333 0.00 0.00 0.00 2.52
894 4227 6.630188 GCAAGGCACCTTATATTTTGGATGTT 60.630 38.462 0.61 0.00 34.50 2.71
897 4230 4.037923 CGCAAGGCACCTTATATTTTGGAT 59.962 41.667 0.61 0.00 34.50 3.41
903 4236 2.099098 GCAACGCAAGGCACCTTATATT 59.901 45.455 0.61 0.00 46.39 1.28
905 4238 1.091537 GCAACGCAAGGCACCTTATA 58.908 50.000 0.61 0.00 46.39 0.98
907 4240 1.527148 TGCAACGCAAGGCACCTTA 60.527 52.632 0.61 0.00 46.39 2.69
908 4241 2.832661 TGCAACGCAAGGCACCTT 60.833 55.556 0.00 0.00 46.39 3.50
917 4250 0.030504 CAAATGAGTGGTGCAACGCA 59.969 50.000 19.16 7.82 38.12 5.24
918 4251 0.664166 CCAAATGAGTGGTGCAACGC 60.664 55.000 7.36 7.36 38.12 4.84
920 4253 4.782019 TTATCCAAATGAGTGGTGCAAC 57.218 40.909 0.00 0.00 39.88 4.17
921 4254 5.999205 AATTATCCAAATGAGTGGTGCAA 57.001 34.783 0.00 0.00 39.88 4.08
922 4255 5.999205 AAATTATCCAAATGAGTGGTGCA 57.001 34.783 0.00 0.00 39.88 4.57
962 4295 9.720769 GGAGCTTGCCTAATATAAGTAAATGTA 57.279 33.333 0.00 0.00 0.00 2.29
964 4297 8.854614 AGGAGCTTGCCTAATATAAGTAAATG 57.145 34.615 0.00 0.00 36.22 2.32
966 4299 8.263854 AGAGGAGCTTGCCTAATATAAGTAAA 57.736 34.615 0.00 0.00 38.73 2.01
968 4301 9.548631 AATAGAGGAGCTTGCCTAATATAAGTA 57.451 33.333 0.00 0.00 38.73 2.24
969 4302 8.442660 AATAGAGGAGCTTGCCTAATATAAGT 57.557 34.615 0.00 0.00 38.73 2.24
972 4305 9.105844 AGAAAATAGAGGAGCTTGCCTAATATA 57.894 33.333 0.00 0.00 38.73 0.86
973 4306 7.983363 AGAAAATAGAGGAGCTTGCCTAATAT 58.017 34.615 0.00 0.00 38.73 1.28
974 4307 7.071196 TGAGAAAATAGAGGAGCTTGCCTAATA 59.929 37.037 0.00 0.00 38.73 0.98
975 4308 6.126652 TGAGAAAATAGAGGAGCTTGCCTAAT 60.127 38.462 0.00 0.00 38.73 1.73
977 4310 4.716784 TGAGAAAATAGAGGAGCTTGCCTA 59.283 41.667 0.00 0.00 38.73 3.93
978 4311 3.521126 TGAGAAAATAGAGGAGCTTGCCT 59.479 43.478 0.00 0.00 42.17 4.75
979 4312 3.878778 TGAGAAAATAGAGGAGCTTGCC 58.121 45.455 0.00 0.00 0.00 4.52
980 4313 4.880696 ACATGAGAAAATAGAGGAGCTTGC 59.119 41.667 0.00 0.00 0.00 4.01
981 4314 6.111382 TGACATGAGAAAATAGAGGAGCTTG 58.889 40.000 0.00 0.00 0.00 4.01
982 4315 6.305272 TGACATGAGAAAATAGAGGAGCTT 57.695 37.500 0.00 0.00 0.00 3.74
983 4316 5.946942 TGACATGAGAAAATAGAGGAGCT 57.053 39.130 0.00 0.00 0.00 4.09
984 4317 7.565323 AATTGACATGAGAAAATAGAGGAGC 57.435 36.000 0.00 0.00 0.00 4.70
985 4318 9.829507 ACTAATTGACATGAGAAAATAGAGGAG 57.170 33.333 0.00 0.00 0.00 3.69
986 4319 9.823647 GACTAATTGACATGAGAAAATAGAGGA 57.176 33.333 0.00 0.00 0.00 3.71
989 4322 9.087424 CGTGACTAATTGACATGAGAAAATAGA 57.913 33.333 0.00 0.00 30.81 1.98
990 4323 8.873830 ACGTGACTAATTGACATGAGAAAATAG 58.126 33.333 0.00 0.49 32.96 1.73
991 4324 8.655970 CACGTGACTAATTGACATGAGAAAATA 58.344 33.333 10.90 0.00 32.96 1.40
994 4327 6.220201 TCACGTGACTAATTGACATGAGAAA 58.780 36.000 15.76 0.00 32.96 2.52
996 4329 5.385509 TCACGTGACTAATTGACATGAGA 57.614 39.130 15.76 0.00 32.96 3.27
997 4330 6.466308 TTTCACGTGACTAATTGACATGAG 57.534 37.500 19.90 0.00 32.96 2.90
998 4331 6.873605 AGATTTCACGTGACTAATTGACATGA 59.126 34.615 19.90 0.00 32.96 3.07
999 4332 7.063898 AGAGATTTCACGTGACTAATTGACATG 59.936 37.037 19.90 0.00 34.41 3.21
1000 4333 7.099764 AGAGATTTCACGTGACTAATTGACAT 58.900 34.615 19.90 2.20 0.00 3.06
1002 4335 6.035112 GGAGAGATTTCACGTGACTAATTGAC 59.965 42.308 19.90 11.10 0.00 3.18
1003 4336 6.100004 GGAGAGATTTCACGTGACTAATTGA 58.900 40.000 19.90 0.00 0.00 2.57
1004 4337 5.292101 GGGAGAGATTTCACGTGACTAATTG 59.708 44.000 19.90 0.00 0.00 2.32
1006 4339 4.466370 TGGGAGAGATTTCACGTGACTAAT 59.534 41.667 19.90 16.38 0.00 1.73
1007 4340 3.830178 TGGGAGAGATTTCACGTGACTAA 59.170 43.478 19.90 11.73 0.00 2.24
1009 4342 2.248248 TGGGAGAGATTTCACGTGACT 58.752 47.619 19.90 12.64 0.00 3.41
1011 4344 3.762407 TTTGGGAGAGATTTCACGTGA 57.238 42.857 15.76 15.76 0.00 4.35
1013 4346 4.086706 AGTTTTGGGAGAGATTTCACGT 57.913 40.909 0.00 0.00 0.00 4.49
1014 4347 4.275936 ACAAGTTTTGGGAGAGATTTCACG 59.724 41.667 0.00 0.00 34.12 4.35
1015 4348 5.299279 TCACAAGTTTTGGGAGAGATTTCAC 59.701 40.000 0.00 0.00 38.38 3.18
1026 4479 6.037062 GGACTGAAAATTTCACAAGTTTTGGG 59.963 38.462 4.03 0.00 35.46 4.12
1027 4480 6.593382 TGGACTGAAAATTTCACAAGTTTTGG 59.407 34.615 4.03 0.00 35.46 3.28
1028 4481 7.117523 TGTGGACTGAAAATTTCACAAGTTTTG 59.882 33.333 4.03 0.00 35.46 2.44
1031 4484 6.279513 TGTGGACTGAAAATTTCACAAGTT 57.720 33.333 4.03 0.00 35.46 2.66
1037 4490 4.933505 TGCATGTGGACTGAAAATTTCA 57.066 36.364 8.25 8.25 38.17 2.69
1038 4491 6.161381 AGAATGCATGTGGACTGAAAATTTC 58.839 36.000 0.00 0.00 0.00 2.17
1039 4492 6.105397 AGAATGCATGTGGACTGAAAATTT 57.895 33.333 0.00 0.00 0.00 1.82
1040 4493 5.733620 AGAATGCATGTGGACTGAAAATT 57.266 34.783 0.00 0.00 0.00 1.82
1041 4494 5.733620 AAGAATGCATGTGGACTGAAAAT 57.266 34.783 0.00 0.00 0.00 1.82
1042 4495 5.534207 AAAGAATGCATGTGGACTGAAAA 57.466 34.783 0.00 0.00 0.00 2.29
1043 4496 6.647334 TTAAAGAATGCATGTGGACTGAAA 57.353 33.333 0.00 0.00 0.00 2.69
1044 4497 6.839124 ATTAAAGAATGCATGTGGACTGAA 57.161 33.333 0.00 0.00 0.00 3.02
1045 4498 6.839124 AATTAAAGAATGCATGTGGACTGA 57.161 33.333 0.00 0.00 0.00 3.41
1046 4499 6.532657 GGAAATTAAAGAATGCATGTGGACTG 59.467 38.462 0.00 0.00 0.00 3.51
1047 4500 6.625740 CGGAAATTAAAGAATGCATGTGGACT 60.626 38.462 0.00 0.00 0.00 3.85
1048 4501 5.516339 CGGAAATTAAAGAATGCATGTGGAC 59.484 40.000 0.00 0.00 0.00 4.02
1049 4502 5.184864 ACGGAAATTAAAGAATGCATGTGGA 59.815 36.000 0.00 0.00 0.00 4.02
1050 4503 5.289193 CACGGAAATTAAAGAATGCATGTGG 59.711 40.000 0.00 0.00 0.00 4.17
1051 4504 5.220265 GCACGGAAATTAAAGAATGCATGTG 60.220 40.000 0.00 0.00 0.00 3.21
1052 4505 4.864247 GCACGGAAATTAAAGAATGCATGT 59.136 37.500 0.00 0.00 0.00 3.21
1053 4506 4.268405 GGCACGGAAATTAAAGAATGCATG 59.732 41.667 0.00 0.00 33.48 4.06
1054 4507 4.081752 TGGCACGGAAATTAAAGAATGCAT 60.082 37.500 0.00 0.00 33.48 3.96
1055 4508 3.256879 TGGCACGGAAATTAAAGAATGCA 59.743 39.130 0.00 0.00 33.48 3.96
1056 4509 3.843999 TGGCACGGAAATTAAAGAATGC 58.156 40.909 0.00 0.00 0.00 3.56
1057 4510 6.777526 TTTTGGCACGGAAATTAAAGAATG 57.222 33.333 0.00 0.00 0.00 2.67
1058 4511 6.989759 AGTTTTTGGCACGGAAATTAAAGAAT 59.010 30.769 0.00 0.00 0.00 2.40
1059 4512 6.342111 AGTTTTTGGCACGGAAATTAAAGAA 58.658 32.000 0.00 0.00 0.00 2.52
1060 4513 5.908341 AGTTTTTGGCACGGAAATTAAAGA 58.092 33.333 0.00 0.00 0.00 2.52
1061 4514 7.883229 ATAGTTTTTGGCACGGAAATTAAAG 57.117 32.000 0.00 0.00 0.00 1.85
1062 4515 8.358148 TGTATAGTTTTTGGCACGGAAATTAAA 58.642 29.630 0.00 0.00 0.00 1.52
1063 4516 7.808856 GTGTATAGTTTTTGGCACGGAAATTAA 59.191 33.333 0.00 0.00 0.00 1.40
1064 4517 7.306953 GTGTATAGTTTTTGGCACGGAAATTA 58.693 34.615 0.00 0.00 0.00 1.40
1065 4518 6.153756 GTGTATAGTTTTTGGCACGGAAATT 58.846 36.000 0.00 0.00 0.00 1.82
1066 4519 5.336134 GGTGTATAGTTTTTGGCACGGAAAT 60.336 40.000 0.00 0.00 0.00 2.17
1067 4520 4.023021 GGTGTATAGTTTTTGGCACGGAAA 60.023 41.667 0.00 0.00 0.00 3.13
1068 4521 3.502979 GGTGTATAGTTTTTGGCACGGAA 59.497 43.478 0.00 0.00 0.00 4.30
1069 4522 3.075884 GGTGTATAGTTTTTGGCACGGA 58.924 45.455 0.00 0.00 0.00 4.69
1070 4523 2.162809 GGGTGTATAGTTTTTGGCACGG 59.837 50.000 0.00 0.00 0.00 4.94
1071 4524 3.078837 AGGGTGTATAGTTTTTGGCACG 58.921 45.455 0.00 0.00 0.00 5.34
1072 4525 8.459911 AATATAGGGTGTATAGTTTTTGGCAC 57.540 34.615 0.00 0.00 0.00 5.01
1091 4544 8.666129 TGTACTCCCTCCATTCCTAAATATAG 57.334 38.462 0.00 0.00 0.00 1.31
1100 4553 7.060421 TCATAAAAATGTACTCCCTCCATTCC 58.940 38.462 0.00 0.00 0.00 3.01
1112 4565 6.307800 AGCACACGCAATTCATAAAAATGTAC 59.692 34.615 0.00 0.00 42.27 2.90
1113 4566 6.385843 AGCACACGCAATTCATAAAAATGTA 58.614 32.000 0.00 0.00 42.27 2.29
1115 4568 5.766702 AGCACACGCAATTCATAAAAATG 57.233 34.783 0.00 0.00 42.27 2.32
1291 4746 6.127980 GGTTGGTTTTTCTGTAGATTCCTAGC 60.128 42.308 0.00 0.00 0.00 3.42
1387 4843 7.527457 ACCAATTTTCTACTTGAACGATAAGC 58.473 34.615 0.00 0.00 33.88 3.09
1394 4850 8.045176 AGCTCATACCAATTTTCTACTTGAAC 57.955 34.615 0.00 0.00 33.88 3.18
1452 4908 4.836125 TGAAAAGCAACTCTCATTCACC 57.164 40.909 0.00 0.00 30.39 4.02
1501 4957 6.947733 ACAATGAGATATTTCAAACTCACCCA 59.052 34.615 0.00 0.00 41.16 4.51
1613 5069 7.307989 CCAACCAACAAGTAGATCACTTTAGTG 60.308 40.741 3.47 3.47 45.54 2.74
1712 5172 4.955811 ACAACTCTGGACAATACTCACA 57.044 40.909 0.00 0.00 0.00 3.58
1753 5213 6.677781 TCCATTTCTTAGAATAAAGCCACG 57.322 37.500 0.00 0.00 0.00 4.94
1954 5428 4.020128 ACCATCCGAGCTCTATAAATTCCC 60.020 45.833 12.85 0.00 0.00 3.97
2001 5475 0.813184 CGAATGCAGGCTGTTTGGAT 59.187 50.000 17.16 0.00 0.00 3.41
2223 5704 4.374843 TGCCATATTTGAGTGATTGCAC 57.625 40.909 0.00 0.00 45.49 4.57
2233 5714 5.117584 GTGCCATTTTGATGCCATATTTGA 58.882 37.500 0.00 0.00 0.00 2.69
2649 6135 2.513753 CTGTTGCCATTGTAGGAACCA 58.486 47.619 0.00 0.00 0.00 3.67
2880 6382 5.699097 TTAAGTTGTCAACATGCCCTTAC 57.301 39.130 17.78 0.00 0.00 2.34
3000 6585 7.435305 TCAAGATTCAAATTGATTCAGTTGCA 58.565 30.769 16.95 0.00 31.24 4.08
3111 6696 3.011818 TGGCATGTGTTAAGAGATGCAG 58.988 45.455 28.41 0.11 42.50 4.41
3304 6891 4.056050 TCAAGTTGTCGTCTCCTAAAAGC 58.944 43.478 2.11 0.00 0.00 3.51
3352 6939 6.617289 GCACTGAGCATTATTGTTTGTTAC 57.383 37.500 0.00 0.00 44.79 2.50
3367 6954 3.273434 TGTGAGGAATAATGCACTGAGC 58.727 45.455 0.00 0.00 45.96 4.26
3577 7165 7.103641 TCTTTCATGTTTCATACCACCTCTAC 58.896 38.462 0.00 0.00 0.00 2.59
3825 7419 8.492673 TCTATTTTTCTAGTGCATTTCGTGAT 57.507 30.769 0.00 0.00 0.00 3.06
4063 7682 7.118496 AGTGAACTGAGATGACTATTTAGGG 57.882 40.000 0.00 0.00 0.00 3.53
4125 7779 8.514330 TGTGGGTAATGTAGATGTAAATTTCC 57.486 34.615 0.00 1.01 0.00 3.13
4253 7907 7.827236 TGTTATCGGGAATGAGACTAAATGTTT 59.173 33.333 0.00 0.00 0.00 2.83
4339 7994 5.860182 AGAAATGATGCATTCAAAGTTCACG 59.140 36.000 0.00 0.00 38.03 4.35
4410 8065 5.574188 AGCTTGATTTACCAGAAATCCTGT 58.426 37.500 7.39 0.00 41.33 4.00
4487 8160 5.163301 GGGTAGTTAGATGCAGATGAGGAAA 60.163 44.000 0.00 0.00 0.00 3.13
4683 8646 4.424626 ACGTCATGCAAGTATACAGAGTG 58.575 43.478 5.50 0.00 0.00 3.51
5364 10239 6.459298 GGCTGATAGAATGTGATGTTTCTTGG 60.459 42.308 0.00 0.00 34.22 3.61
5508 10386 5.353956 GGTCATGCAAATATAGTGTGACACA 59.646 40.000 18.95 3.56 36.97 3.72
5533 10411 6.295292 GCTTGTTTATCCCTTCCTTCATTTGT 60.295 38.462 0.00 0.00 0.00 2.83
5607 12120 7.015682 AGAGAGAGAGATTTTGTTGTTGTCCTA 59.984 37.037 0.00 0.00 0.00 2.94
5670 12213 7.316640 AGAGATAGATAGACAAACACACACAC 58.683 38.462 0.00 0.00 0.00 3.82
5680 12591 5.777449 TGGGTGGAAGAGATAGATAGACAA 58.223 41.667 0.00 0.00 0.00 3.18
6005 12970 4.883585 TCCTGTTGTTTGATATGCATCTCC 59.116 41.667 0.19 0.00 31.93 3.71
6007 12972 5.889853 ACATCCTGTTGTTTGATATGCATCT 59.110 36.000 0.19 0.00 31.93 2.90
6343 13312 9.939802 GAAAGGTCTTGAGTTTAAATCCTAGTA 57.060 33.333 0.00 0.00 0.00 1.82
6455 13453 3.471680 GCATGGATTCTCTAAGTCCACC 58.528 50.000 0.00 0.00 44.21 4.61
6839 13886 3.005367 TGCACATCTACAAGAACGAGACA 59.995 43.478 0.00 0.00 0.00 3.41
6952 14029 4.383774 TCGTTTGCGATGTAAAAGACTG 57.616 40.909 0.00 0.00 42.81 3.51
7012 14090 4.827284 CAGGGATGAGTGTTTTTGGTACTT 59.173 41.667 0.00 0.00 0.00 2.24
7397 15123 3.256704 ACTTGGGGGATTGAGACAGTTA 58.743 45.455 0.00 0.00 0.00 2.24
7651 15387 0.810648 AATGCGGCCATACACACAAG 59.189 50.000 2.24 0.00 0.00 3.16
7786 15522 7.720957 TCAATATAGAATATTTGGCTGCAGTGT 59.279 33.333 16.64 0.00 0.00 3.55
7988 15731 5.010314 AGTCCCCGTTTGGAAAAATTAGTTC 59.990 40.000 0.00 0.00 35.80 3.01
8102 15845 1.325943 GAAAGCTTCCTCAAGATCGCG 59.674 52.381 0.00 0.00 0.00 5.87
8244 15990 8.604890 GTCCAAATTAGAAATCTAGAAGTTCCG 58.395 37.037 13.32 0.00 0.00 4.30
8395 16141 5.106157 CCTTTTTCCTTGCATCGACAATACT 60.106 40.000 0.00 0.00 0.00 2.12
8398 16144 3.056607 CCCTTTTTCCTTGCATCGACAAT 60.057 43.478 0.00 0.00 0.00 2.71
8452 16198 4.644685 GGGCATCAATAAGCAAGGTTCTTA 59.355 41.667 0.00 0.00 0.00 2.10


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

AutoCloner maintained by Alex Coulton.