Multiple sequence alignment - TraesCS5D01G459500

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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 TraesCS5D01G459500 chr5D 100.000 4115 0 0 1 4115 503430440 503434554 0.000000e+00 7600.0
1 TraesCS5D01G459500 chr5D 91.200 2409 149 11 537 2908 503650887 503653269 0.000000e+00 3216.0
2 TraesCS5D01G459500 chr5D 89.672 2227 195 20 802 3011 503470437 503472645 0.000000e+00 2806.0
3 TraesCS5D01G459500 chr5D 87.991 2265 225 29 778 3021 503502325 503504563 0.000000e+00 2632.0
4 TraesCS5D01G459500 chr5D 85.773 2207 300 10 864 3060 503642193 503644395 0.000000e+00 2324.0
5 TraesCS5D01G459500 chr5D 86.136 1219 147 10 1814 3025 503637112 503638315 0.000000e+00 1295.0
6 TraesCS5D01G459500 chr5D 88.875 791 77 5 778 1566 503636338 503637119 0.000000e+00 963.0
7 TraesCS5D01G459500 chr5D 83.249 985 147 11 2045 3014 503644445 503645426 0.000000e+00 889.0
8 TraesCS5D01G459500 chr5D 90.561 392 26 4 3733 4115 503199641 503200030 3.670000e-140 508.0
9 TraesCS5D01G459500 chr5D 86.010 386 23 17 3154 3510 503654700 503655083 6.450000e-103 385.0
10 TraesCS5D01G459500 chr5D 88.615 325 23 6 3671 3981 503655103 503655427 2.320000e-102 383.0
11 TraesCS5D01G459500 chr5D 84.197 386 27 18 3154 3510 503472781 503473161 1.100000e-90 344.0
12 TraesCS5D01G459500 chr5D 84.098 327 25 11 3671 3981 503473181 503473496 1.450000e-74 291.0
13 TraesCS5D01G459500 chr5D 88.889 108 8 2 3050 3154 503472642 503472748 3.340000e-26 130.0
14 TraesCS5D01G459500 chr5D 87.952 83 10 0 4014 4096 503656513 503656595 9.410000e-17 99.0
15 TraesCS5D01G459500 chr5D 90.625 64 3 1 3307 3367 503199289 503199352 9.480000e-12 82.4
16 TraesCS5D01G459500 chr5A 91.270 3196 210 20 1 3158 631640731 631643895 0.000000e+00 4292.0
17 TraesCS5D01G459500 chr5A 86.639 1931 219 20 778 2695 631530540 631532444 0.000000e+00 2100.0
18 TraesCS5D01G459500 chr5A 89.579 1046 92 9 1499 2534 631629209 631630247 0.000000e+00 1312.0
19 TraesCS5D01G459500 chr5A 88.540 733 73 6 778 1509 631627411 631628133 0.000000e+00 878.0
20 TraesCS5D01G459500 chr5A 90.385 364 28 3 2 361 631589827 631590187 4.810000e-129 472.0
21 TraesCS5D01G459500 chr5A 91.049 324 19 5 3671 3984 631644531 631644208 2.940000e-116 429.0
22 TraesCS5D01G459500 chr5A 86.453 406 26 19 358 759 631618817 631619197 6.360000e-113 418.0
23 TraesCS5D01G459500 chr5A 85.753 372 40 7 2573 2933 631654920 631654551 8.350000e-102 381.0
24 TraesCS5D01G459500 chr5A 88.073 218 13 6 3154 3363 631631938 631632150 3.180000e-61 246.0
25 TraesCS5D01G459500 chr5A 86.283 226 15 7 3154 3367 631643924 631644145 8.900000e-57 231.0
26 TraesCS5D01G459500 chr5A 88.983 118 13 0 3393 3510 631644668 631644551 3.310000e-31 147.0
27 TraesCS5D01G459500 chr5A 100.000 32 0 0 2975 3006 631630938 631630969 4.440000e-05 60.2
28 TraesCS5D01G459500 chr5B 87.968 2244 235 19 783 3011 632126668 632128891 0.000000e+00 2615.0
29 TraesCS5D01G459500 chr5B 88.624 378 20 14 3154 3510 632129035 632129410 4.880000e-119 438.0
30 TraesCS5D01G459500 chr5B 95.000 60 3 0 3070 3129 632128911 632128970 1.220000e-15 95.3
31 TraesCS5D01G459500 chr2D 74.914 873 205 12 1069 1934 602783148 602782283 1.790000e-103 387.0
32 TraesCS5D01G459500 chr2D 73.539 941 233 14 1047 1979 603129366 603128434 1.100000e-90 344.0
33 TraesCS5D01G459500 chr6D 100.000 42 0 0 3594 3635 102379507 102379548 1.230000e-10 78.7
34 TraesCS5D01G459500 chr6D 100.000 40 0 0 3631 3670 108484474 108484513 1.590000e-09 75.0
35 TraesCS5D01G459500 chr6D 97.500 40 1 0 3631 3670 153944046 153944007 7.380000e-08 69.4
36 TraesCS5D01G459500 chr6D 97.500 40 1 0 3631 3670 172736544 172736505 7.380000e-08 69.4
37 TraesCS5D01G459500 chr6D 97.500 40 1 0 3631 3670 458942086 458942047 7.380000e-08 69.4
38 TraesCS5D01G459500 chr4B 100.000 42 0 0 3594 3635 309284679 309284638 1.230000e-10 78.7
39 TraesCS5D01G459500 chr4B 97.500 40 1 0 3631 3670 495480374 495480335 7.380000e-08 69.4
40 TraesCS5D01G459500 chrUn 100.000 41 0 0 3594 3634 206778682 206778722 4.410000e-10 76.8
41 TraesCS5D01G459500 chr6A 100.000 41 0 0 3594 3634 537591973 537591933 4.410000e-10 76.8
42 TraesCS5D01G459500 chr4D 100.000 41 0 0 3594 3634 123272096 123272136 4.410000e-10 76.8
43 TraesCS5D01G459500 chr3D 100.000 41 0 0 3594 3634 399723398 399723438 4.410000e-10 76.8
44 TraesCS5D01G459500 chr1A 100.000 41 0 0 3594 3634 94558705 94558665 4.410000e-10 76.8
45 TraesCS5D01G459500 chr1A 100.000 41 0 0 3594 3634 94685553 94685593 4.410000e-10 76.8
46 TraesCS5D01G459500 chr1A 100.000 41 0 0 3594 3634 132899821 132899781 4.410000e-10 76.8
47 TraesCS5D01G459500 chr1A 97.619 42 1 0 3631 3672 278520476 278520517 5.710000e-09 73.1
48 TraesCS5D01G459500 chr6B 100.000 40 0 0 3631 3670 320192448 320192487 1.590000e-09 75.0
49 TraesCS5D01G459500 chr7A 97.619 42 1 0 3631 3672 563522832 563522791 5.710000e-09 73.1
50 TraesCS5D01G459500 chr4A 97.619 42 1 0 3631 3672 67518764 67518805 5.710000e-09 73.1


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS5D01G459500 chr5D 503430440 503434554 4114 False 7600.000000 7600 100.000000 1 4115 1 chr5D.!!$F1 4114
1 TraesCS5D01G459500 chr5D 503502325 503504563 2238 False 2632.000000 2632 87.991000 778 3021 1 chr5D.!!$F2 2243
2 TraesCS5D01G459500 chr5D 503636338 503645426 9088 False 1367.750000 2324 86.008250 778 3060 4 chr5D.!!$F5 2282
3 TraesCS5D01G459500 chr5D 503650887 503656595 5708 False 1020.750000 3216 88.444250 537 4096 4 chr5D.!!$F6 3559
4 TraesCS5D01G459500 chr5D 503470437 503473496 3059 False 892.750000 2806 86.714000 802 3981 4 chr5D.!!$F4 3179
5 TraesCS5D01G459500 chr5D 503199289 503200030 741 False 295.200000 508 90.593000 3307 4115 2 chr5D.!!$F3 808
6 TraesCS5D01G459500 chr5A 631640731 631644145 3414 False 2261.500000 4292 88.776500 1 3367 2 chr5A.!!$F5 3366
7 TraesCS5D01G459500 chr5A 631530540 631532444 1904 False 2100.000000 2100 86.639000 778 2695 1 chr5A.!!$F1 1917
8 TraesCS5D01G459500 chr5A 631627411 631632150 4739 False 624.050000 1312 91.548000 778 3363 4 chr5A.!!$F4 2585
9 TraesCS5D01G459500 chr5B 632126668 632129410 2742 False 1049.433333 2615 90.530667 783 3510 3 chr5B.!!$F1 2727
10 TraesCS5D01G459500 chr2D 602782283 602783148 865 True 387.000000 387 74.914000 1069 1934 1 chr2D.!!$R1 865
11 TraesCS5D01G459500 chr2D 603128434 603129366 932 True 344.000000 344 73.539000 1047 1979 1 chr2D.!!$R2 932

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
48 49 0.179076 CTCCATGGCGATGTGTGCTA 60.179 55.0 6.96 0.00 0.00 3.49 F
468 470 0.250209 CCTCCATCGATCAAGCCCAG 60.250 60.0 0.00 0.00 0.00 4.45 F
1906 8809 0.460811 TGAGATGCGAGATGTGGCAC 60.461 55.0 11.55 11.55 40.59 5.01 F
2071 8986 0.169009 GTGCCGCCATTTCTCACTTC 59.831 55.0 0.00 0.00 0.00 3.01 F
2686 10684 0.764369 TCGGGCTGCTTATGATCCCT 60.764 55.0 0.00 0.00 34.84 4.20 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1996 8911 0.244721 GCAGATTGCCAGTTGTTCCC 59.755 55.0 0.0 0.0 37.42 3.97 R
1997 8912 1.251251 AGCAGATTGCCAGTTGTTCC 58.749 50.0 0.0 0.0 46.52 3.62 R
2898 10896 0.040067 GGCTTCCGCTTTGTTCTGTG 60.040 55.0 0.0 0.0 36.09 3.66 R
2899 10897 0.179018 AGGCTTCCGCTTTGTTCTGT 60.179 50.0 0.0 0.0 36.09 3.41 R
4092 15467 1.061799 CGTCAATTGCAGCAGCGTTC 61.062 55.0 0.0 0.0 46.23 3.95 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
46 47 1.746615 ACTCCATGGCGATGTGTGC 60.747 57.895 9.17 0.00 0.00 4.57
47 48 1.450848 CTCCATGGCGATGTGTGCT 60.451 57.895 6.96 0.00 0.00 4.40
48 49 0.179076 CTCCATGGCGATGTGTGCTA 60.179 55.000 6.96 0.00 0.00 3.49
49 50 0.179076 TCCATGGCGATGTGTGCTAG 60.179 55.000 6.96 0.00 0.00 3.42
66 67 8.935844 TGTGTGCTAGTACAAAATATGAGAAAG 58.064 33.333 15.68 0.00 31.36 2.62
74 75 8.897752 AGTACAAAATATGAGAAAGATGCTTCC 58.102 33.333 0.00 0.00 0.00 3.46
75 76 7.951347 ACAAAATATGAGAAAGATGCTTCCT 57.049 32.000 0.00 0.00 0.00 3.36
84 85 7.993101 TGAGAAAGATGCTTCCTCATAAATTG 58.007 34.615 0.00 0.00 0.00 2.32
107 108 1.448985 TGCCGCATCAGTTCCTAAAC 58.551 50.000 0.00 0.00 35.50 2.01
114 115 5.452776 CCGCATCAGTTCCTAAACAGGTATA 60.453 44.000 0.00 0.00 37.88 1.47
143 144 4.960938 TCAGCAGCGACCATCTTTATAAT 58.039 39.130 0.00 0.00 0.00 1.28
152 153 8.421784 AGCGACCATCTTTATAATCTTACTGAA 58.578 33.333 0.00 0.00 0.00 3.02
201 202 5.752955 GCTTTCTACAGGTTTGCATTTTTCA 59.247 36.000 0.00 0.00 0.00 2.69
229 230 6.920569 TTAAATCTTCGGTTCTATGCTTCC 57.079 37.500 0.00 0.00 0.00 3.46
230 231 4.487714 AATCTTCGGTTCTATGCTTCCA 57.512 40.909 0.00 0.00 0.00 3.53
231 232 4.696479 ATCTTCGGTTCTATGCTTCCAT 57.304 40.909 0.00 0.00 35.44 3.41
232 233 4.060038 TCTTCGGTTCTATGCTTCCATC 57.940 45.455 0.00 0.00 32.85 3.51
233 234 3.450817 TCTTCGGTTCTATGCTTCCATCA 59.549 43.478 0.00 0.00 32.85 3.07
234 235 3.459232 TCGGTTCTATGCTTCCATCAG 57.541 47.619 0.00 0.00 32.85 2.90
235 236 2.766263 TCGGTTCTATGCTTCCATCAGT 59.234 45.455 0.00 0.00 32.85 3.41
236 237 3.197766 TCGGTTCTATGCTTCCATCAGTT 59.802 43.478 0.00 0.00 32.85 3.16
237 238 4.404394 TCGGTTCTATGCTTCCATCAGTTA 59.596 41.667 0.00 0.00 32.85 2.24
238 239 4.747108 CGGTTCTATGCTTCCATCAGTTAG 59.253 45.833 0.00 0.00 32.85 2.34
239 240 5.675538 GGTTCTATGCTTCCATCAGTTAGT 58.324 41.667 0.00 0.00 32.85 2.24
240 241 6.116126 GGTTCTATGCTTCCATCAGTTAGTT 58.884 40.000 0.00 0.00 32.85 2.24
241 242 6.599638 GGTTCTATGCTTCCATCAGTTAGTTT 59.400 38.462 0.00 0.00 32.85 2.66
242 243 7.201652 GGTTCTATGCTTCCATCAGTTAGTTTC 60.202 40.741 0.00 0.00 32.85 2.78
243 244 7.187824 TCTATGCTTCCATCAGTTAGTTTCT 57.812 36.000 0.00 0.00 32.85 2.52
244 245 8.306313 TCTATGCTTCCATCAGTTAGTTTCTA 57.694 34.615 0.00 0.00 32.85 2.10
245 246 8.198109 TCTATGCTTCCATCAGTTAGTTTCTAC 58.802 37.037 0.00 0.00 32.85 2.59
246 247 5.488341 TGCTTCCATCAGTTAGTTTCTACC 58.512 41.667 0.00 0.00 0.00 3.18
307 308 2.576191 AGTTATGGGGCTTTAGCTGTCA 59.424 45.455 0.00 0.00 41.70 3.58
364 366 1.066143 ACGCCTACCATGAAACTCCAG 60.066 52.381 0.00 0.00 0.00 3.86
374 376 6.180472 ACCATGAAACTCCAGTTAATACCAG 58.820 40.000 0.00 0.00 37.25 4.00
392 394 5.304686 ACCAGGACAGAACTGAACAATAA 57.695 39.130 8.87 0.00 38.20 1.40
393 395 5.063880 ACCAGGACAGAACTGAACAATAAC 58.936 41.667 8.87 0.00 38.20 1.89
394 396 4.152402 CCAGGACAGAACTGAACAATAACG 59.848 45.833 8.87 0.00 38.20 3.18
401 403 9.690434 GACAGAACTGAACAATAACGATTAATC 57.310 33.333 8.87 5.30 0.00 1.75
409 411 8.946085 TGAACAATAACGATTAATCTTGCTCTT 58.054 29.630 13.45 2.57 0.00 2.85
426 428 4.120589 GCTCTTCCCTACCTACAATTTCG 58.879 47.826 0.00 0.00 0.00 3.46
427 429 4.142004 GCTCTTCCCTACCTACAATTTCGA 60.142 45.833 0.00 0.00 0.00 3.71
428 430 5.626116 GCTCTTCCCTACCTACAATTTCGAA 60.626 44.000 0.00 0.00 0.00 3.71
429 431 6.363167 TCTTCCCTACCTACAATTTCGAAA 57.637 37.500 13.91 13.91 0.00 3.46
430 432 6.954232 TCTTCCCTACCTACAATTTCGAAAT 58.046 36.000 17.60 17.60 0.00 2.17
431 433 7.399634 TCTTCCCTACCTACAATTTCGAAATT 58.600 34.615 26.51 26.51 39.07 1.82
432 434 7.886446 TCTTCCCTACCTACAATTTCGAAATTT 59.114 33.333 28.91 21.87 36.52 1.82
451 453 2.097110 TCCTTATGGACGTATGCCCT 57.903 50.000 0.00 0.00 37.46 5.19
452 454 1.968493 TCCTTATGGACGTATGCCCTC 59.032 52.381 0.00 0.00 37.46 4.30
460 462 0.603569 ACGTATGCCCTCCATCGATC 59.396 55.000 0.00 0.00 35.34 3.69
464 466 0.250640 ATGCCCTCCATCGATCAAGC 60.251 55.000 0.00 0.00 0.00 4.01
468 470 0.250209 CCTCCATCGATCAAGCCCAG 60.250 60.000 0.00 0.00 0.00 4.45
471 473 0.749091 CCATCGATCAAGCCCAGCAA 60.749 55.000 0.00 0.00 0.00 3.91
510 514 9.816354 ATTTTCTACAGTTTTGTGCAAATTACT 57.184 25.926 0.00 0.00 38.23 2.24
719 748 3.544684 TGGATGCTGGATATGTGTTGTC 58.455 45.455 0.00 0.00 0.00 3.18
720 749 3.200605 TGGATGCTGGATATGTGTTGTCT 59.799 43.478 0.00 0.00 0.00 3.41
983 1022 4.508662 AGCTTGTATACTCAGTCTTTGCC 58.491 43.478 4.17 0.00 0.00 4.52
1025 1066 2.963782 ACCTTCGAGAAAGTACAGTGGT 59.036 45.455 0.00 0.00 32.69 4.16
1140 1181 5.109903 ACCAGCAACTACGAAACTATCATC 58.890 41.667 0.00 0.00 0.00 2.92
1254 1295 6.990341 AATTTTGCAAAAGAGCTGAAAGTT 57.010 29.167 27.08 11.55 35.30 2.66
1725 8628 2.103941 GGCAACAACAAGAAATGGGGAA 59.896 45.455 0.00 0.00 0.00 3.97
1827 8730 3.788227 AGCCAGAACAACATGAAGGTA 57.212 42.857 0.00 0.00 0.00 3.08
1873 8776 2.686915 GGACAATGCTTGAGAATGGAGG 59.313 50.000 3.37 0.00 0.00 4.30
1894 8797 0.965439 AGATAGACGCCCTGAGATGC 59.035 55.000 0.00 0.00 0.00 3.91
1906 8809 0.460811 TGAGATGCGAGATGTGGCAC 60.461 55.000 11.55 11.55 40.59 5.01
1995 8910 2.282745 AGGAACAAGCCAGCAGCC 60.283 61.111 0.00 0.00 45.47 4.85
1996 8911 3.741476 GGAACAAGCCAGCAGCCG 61.741 66.667 0.00 0.00 45.47 5.52
1997 8912 3.741476 GAACAAGCCAGCAGCCGG 61.741 66.667 0.00 0.00 45.47 6.13
2014 8929 0.523072 CGGGAACAACTGGCAATCTG 59.477 55.000 0.00 0.00 0.00 2.90
2038 8953 1.354040 CTCAGTCACGCCACAATCTC 58.646 55.000 0.00 0.00 0.00 2.75
2040 8955 1.067565 TCAGTCACGCCACAATCTCTC 60.068 52.381 0.00 0.00 0.00 3.20
2071 8986 0.169009 GTGCCGCCATTTCTCACTTC 59.831 55.000 0.00 0.00 0.00 3.01
2189 9104 2.215942 ACCAAGGTGGCTATCAAACC 57.784 50.000 0.00 0.00 42.67 3.27
2190 9105 1.427368 ACCAAGGTGGCTATCAAACCA 59.573 47.619 0.00 0.00 42.67 3.67
2191 9106 2.042979 ACCAAGGTGGCTATCAAACCAT 59.957 45.455 0.00 0.00 42.67 3.55
2602 10600 5.810587 GTCGATCCTGAATTTTACTGCACTA 59.189 40.000 0.00 0.00 0.00 2.74
2686 10684 0.764369 TCGGGCTGCTTATGATCCCT 60.764 55.000 0.00 0.00 34.84 4.20
2706 10704 3.868077 CCTATCTTCCAGAAAGACAAGCG 59.132 47.826 0.00 0.00 46.61 4.68
2732 10730 4.650972 TGGTAGAATGTGCCCTTAGTTT 57.349 40.909 0.00 0.00 0.00 2.66
2898 10896 0.540923 AGAAGCTGGAGATGTGCCTC 59.459 55.000 0.00 0.00 0.00 4.70
2899 10897 0.251354 GAAGCTGGAGATGTGCCTCA 59.749 55.000 0.00 0.00 34.94 3.86
2930 11362 2.208431 CGGAAGCCTTGATGATGAGAC 58.792 52.381 0.00 0.00 0.00 3.36
3025 12035 2.019249 ACGATGATTCCAGCCATTGTG 58.981 47.619 0.00 0.00 36.38 3.33
3136 12442 1.302832 GGCAGGAAGTGGTCACCAG 60.303 63.158 0.00 0.00 32.34 4.00
3137 12443 1.451936 GCAGGAAGTGGTCACCAGT 59.548 57.895 0.00 0.00 39.10 4.00
3163 13286 6.387041 TTCCTACTGTCAATACTCCATACG 57.613 41.667 0.00 0.00 0.00 3.06
3210 13343 7.862873 CCTTTCTTTTCTGAAGCGAGTATTTTT 59.137 33.333 0.00 0.00 0.00 1.94
3247 13380 2.028876 TCATGCTTCCTCGTTATCCGA 58.971 47.619 0.00 0.00 45.00 4.55
3304 13444 7.265673 TGCACTATTATGTCCTGTTAGTCTTC 58.734 38.462 0.00 0.00 0.00 2.87
3363 13513 5.465390 GCATAAAACTGGTTCCTTTGTTTCC 59.535 40.000 0.00 0.00 32.35 3.13
3367 13517 2.239400 CTGGTTCCTTTGTTTCCTCCC 58.761 52.381 0.00 0.00 0.00 4.30
3368 13518 1.856920 TGGTTCCTTTGTTTCCTCCCT 59.143 47.619 0.00 0.00 0.00 4.20
3369 13519 2.246327 TGGTTCCTTTGTTTCCTCCCTT 59.754 45.455 0.00 0.00 0.00 3.95
3373 13523 4.469469 TCCTTTGTTTCCTCCCTTTGAT 57.531 40.909 0.00 0.00 0.00 2.57
3374 13524 4.407365 TCCTTTGTTTCCTCCCTTTGATC 58.593 43.478 0.00 0.00 0.00 2.92
3376 13526 4.774200 CCTTTGTTTCCTCCCTTTGATCAT 59.226 41.667 0.00 0.00 0.00 2.45
3377 13527 5.951747 CCTTTGTTTCCTCCCTTTGATCATA 59.048 40.000 0.00 0.00 0.00 2.15
3378 13528 6.127619 CCTTTGTTTCCTCCCTTTGATCATAC 60.128 42.308 0.00 0.00 0.00 2.39
3379 13529 5.779241 TGTTTCCTCCCTTTGATCATACT 57.221 39.130 0.00 0.00 0.00 2.12
3406 13569 5.023533 TGTACTAGCATCTTGTTCCATCC 57.976 43.478 0.00 0.00 0.00 3.51
3467 13630 1.807573 GCTCAGAAGCGAGAACCCG 60.808 63.158 0.00 0.00 39.10 5.28
3508 13671 2.760092 GGCTATGGAAAACCTGCAATCA 59.240 45.455 0.00 0.00 0.00 2.57
3509 13672 3.181483 GGCTATGGAAAACCTGCAATCAG 60.181 47.826 0.00 0.00 40.02 2.90
3510 13673 3.736126 GCTATGGAAAACCTGCAATCAGC 60.736 47.826 0.00 0.00 45.96 4.26
3511 13674 1.999648 TGGAAAACCTGCAATCAGCT 58.000 45.000 0.00 0.00 45.94 4.24
3512 13675 1.888512 TGGAAAACCTGCAATCAGCTC 59.111 47.619 0.00 0.00 45.94 4.09
3513 13676 1.888512 GGAAAACCTGCAATCAGCTCA 59.111 47.619 0.00 0.00 45.94 4.26
3514 13677 2.297033 GGAAAACCTGCAATCAGCTCAA 59.703 45.455 0.00 0.00 45.94 3.02
3515 13678 3.572584 GAAAACCTGCAATCAGCTCAAG 58.427 45.455 0.00 0.00 45.94 3.02
3516 13679 0.886563 AACCTGCAATCAGCTCAAGC 59.113 50.000 0.00 0.00 45.94 4.01
3517 13680 0.251033 ACCTGCAATCAGCTCAAGCA 60.251 50.000 4.59 0.00 45.94 3.91
3518 13681 1.103803 CCTGCAATCAGCTCAAGCAT 58.896 50.000 4.59 0.00 45.94 3.79
3519 13682 2.294979 CCTGCAATCAGCTCAAGCATA 58.705 47.619 4.59 0.00 45.94 3.14
3520 13683 2.686405 CCTGCAATCAGCTCAAGCATAA 59.314 45.455 4.59 0.00 45.94 1.90
3521 13684 3.243101 CCTGCAATCAGCTCAAGCATAAG 60.243 47.826 4.59 0.00 45.94 1.73
3522 13685 3.613030 TGCAATCAGCTCAAGCATAAGA 58.387 40.909 4.59 0.00 45.94 2.10
3523 13686 4.204799 TGCAATCAGCTCAAGCATAAGAT 58.795 39.130 4.59 0.00 45.94 2.40
3524 13687 4.643334 TGCAATCAGCTCAAGCATAAGATT 59.357 37.500 4.59 5.67 45.94 2.40
3525 13688 5.126545 TGCAATCAGCTCAAGCATAAGATTT 59.873 36.000 4.59 0.00 45.94 2.17
3526 13689 6.040878 GCAATCAGCTCAAGCATAAGATTTT 58.959 36.000 4.59 0.00 45.16 1.82
3527 13690 6.198591 GCAATCAGCTCAAGCATAAGATTTTC 59.801 38.462 4.59 0.81 45.16 2.29
3528 13691 7.481642 CAATCAGCTCAAGCATAAGATTTTCT 58.518 34.615 4.59 0.00 45.16 2.52
3529 13692 7.642082 ATCAGCTCAAGCATAAGATTTTCTT 57.358 32.000 4.59 0.00 45.16 2.52
3530 13693 7.081526 TCAGCTCAAGCATAAGATTTTCTTC 57.918 36.000 4.59 0.00 45.16 2.87
3531 13694 6.883217 TCAGCTCAAGCATAAGATTTTCTTCT 59.117 34.615 4.59 0.00 45.16 2.85
3532 13695 6.967767 CAGCTCAAGCATAAGATTTTCTTCTG 59.032 38.462 4.59 0.00 45.16 3.02
3533 13696 6.095160 AGCTCAAGCATAAGATTTTCTTCTGG 59.905 38.462 4.59 0.00 45.16 3.86
3534 13697 6.199937 TCAAGCATAAGATTTTCTTCTGGC 57.800 37.500 5.23 3.39 37.89 4.85
3535 13698 5.948162 TCAAGCATAAGATTTTCTTCTGGCT 59.052 36.000 5.23 5.16 38.21 4.75
3536 13699 5.831702 AGCATAAGATTTTCTTCTGGCTG 57.168 39.130 8.50 0.00 37.89 4.85
3537 13700 4.097589 AGCATAAGATTTTCTTCTGGCTGC 59.902 41.667 8.50 0.00 37.89 5.25
3538 13701 4.097589 GCATAAGATTTTCTTCTGGCTGCT 59.902 41.667 0.00 0.00 37.89 4.24
3539 13702 5.393896 GCATAAGATTTTCTTCTGGCTGCTT 60.394 40.000 0.00 0.00 37.89 3.91
3540 13703 6.183360 GCATAAGATTTTCTTCTGGCTGCTTA 60.183 38.462 0.00 0.00 37.89 3.09
3541 13704 7.469732 GCATAAGATTTTCTTCTGGCTGCTTAT 60.470 37.037 0.00 0.00 37.89 1.73
3542 13705 6.448207 AAGATTTTCTTCTGGCTGCTTATC 57.552 37.500 0.00 0.00 28.99 1.75
3543 13706 5.503927 AGATTTTCTTCTGGCTGCTTATCA 58.496 37.500 0.00 0.00 0.00 2.15
3544 13707 5.948162 AGATTTTCTTCTGGCTGCTTATCAA 59.052 36.000 0.00 0.00 0.00 2.57
3545 13708 6.606395 AGATTTTCTTCTGGCTGCTTATCAAT 59.394 34.615 0.00 0.00 0.00 2.57
3546 13709 7.776969 AGATTTTCTTCTGGCTGCTTATCAATA 59.223 33.333 0.00 0.00 0.00 1.90
3547 13710 7.701539 TTTTCTTCTGGCTGCTTATCAATAA 57.298 32.000 0.00 0.00 0.00 1.40
3548 13711 6.683974 TTCTTCTGGCTGCTTATCAATAAC 57.316 37.500 0.00 0.00 0.00 1.89
3549 13712 5.744171 TCTTCTGGCTGCTTATCAATAACA 58.256 37.500 0.00 0.00 0.00 2.41
3550 13713 5.819379 TCTTCTGGCTGCTTATCAATAACAG 59.181 40.000 0.00 0.00 0.00 3.16
3551 13714 4.454678 TCTGGCTGCTTATCAATAACAGG 58.545 43.478 0.00 0.00 0.00 4.00
3552 13715 2.951642 TGGCTGCTTATCAATAACAGGC 59.048 45.455 19.78 19.78 41.49 4.85
3553 13716 3.217626 GGCTGCTTATCAATAACAGGCT 58.782 45.455 19.56 0.00 40.04 4.58
3554 13717 3.004106 GGCTGCTTATCAATAACAGGCTG 59.996 47.826 14.16 14.16 40.04 4.85
3555 13718 3.879295 GCTGCTTATCAATAACAGGCTGA 59.121 43.478 23.66 0.00 0.00 4.26
3556 13719 4.336433 GCTGCTTATCAATAACAGGCTGAA 59.664 41.667 23.66 9.24 0.00 3.02
3557 13720 5.009410 GCTGCTTATCAATAACAGGCTGAAT 59.991 40.000 23.66 11.32 0.00 2.57
3558 13721 6.205464 GCTGCTTATCAATAACAGGCTGAATA 59.795 38.462 23.66 13.94 0.00 1.75
3559 13722 7.496529 TGCTTATCAATAACAGGCTGAATAC 57.503 36.000 23.66 0.00 0.00 1.89
3560 13723 7.282585 TGCTTATCAATAACAGGCTGAATACT 58.717 34.615 23.66 0.55 0.00 2.12
3561 13724 8.428852 TGCTTATCAATAACAGGCTGAATACTA 58.571 33.333 23.66 4.64 0.00 1.82
3562 13725 8.930760 GCTTATCAATAACAGGCTGAATACTAG 58.069 37.037 23.66 7.95 0.00 2.57
3565 13728 7.898014 TCAATAACAGGCTGAATACTAGAGA 57.102 36.000 23.66 4.26 0.00 3.10
3566 13729 8.306313 TCAATAACAGGCTGAATACTAGAGAA 57.694 34.615 23.66 0.00 0.00 2.87
3567 13730 8.198109 TCAATAACAGGCTGAATACTAGAGAAC 58.802 37.037 23.66 0.00 0.00 3.01
3568 13731 7.906199 ATAACAGGCTGAATACTAGAGAACT 57.094 36.000 23.66 0.00 0.00 3.01
3569 13732 5.845391 ACAGGCTGAATACTAGAGAACTC 57.155 43.478 23.66 0.00 0.00 3.01
3570 13733 4.647399 ACAGGCTGAATACTAGAGAACTCC 59.353 45.833 23.66 0.00 0.00 3.85
3571 13734 4.892934 CAGGCTGAATACTAGAGAACTCCT 59.107 45.833 9.42 0.00 0.00 3.69
3572 13735 5.009610 CAGGCTGAATACTAGAGAACTCCTC 59.990 48.000 9.42 0.00 42.28 3.71
3594 13757 7.920160 CTCTAGAGGAAGAGCTTTTTCATTT 57.080 36.000 12.27 5.05 36.84 2.32
3595 13758 8.334263 CTCTAGAGGAAGAGCTTTTTCATTTT 57.666 34.615 12.27 3.40 36.84 1.82
3596 13759 8.329203 TCTAGAGGAAGAGCTTTTTCATTTTC 57.671 34.615 12.29 5.91 0.00 2.29
3597 13760 8.160106 TCTAGAGGAAGAGCTTTTTCATTTTCT 58.840 33.333 12.29 10.85 0.00 2.52
3598 13761 7.594351 AGAGGAAGAGCTTTTTCATTTTCTT 57.406 32.000 12.29 0.00 0.00 2.52
3599 13762 8.697507 AGAGGAAGAGCTTTTTCATTTTCTTA 57.302 30.769 12.29 0.00 0.00 2.10
3600 13763 9.306777 AGAGGAAGAGCTTTTTCATTTTCTTAT 57.693 29.630 12.29 0.00 0.00 1.73
3601 13764 9.920133 GAGGAAGAGCTTTTTCATTTTCTTATT 57.080 29.630 12.29 0.00 0.00 1.40
3632 13795 9.436957 ACGACATAAATGTTGATTTTCTACTCT 57.563 29.630 15.68 0.00 43.40 3.24
3633 13796 9.907576 CGACATAAATGTTGATTTTCTACTCTC 57.092 33.333 4.57 0.00 43.40 3.20
3660 13823 8.478775 AAAAAGAAAGGCAGAGGTAAATACTT 57.521 30.769 0.00 0.00 0.00 2.24
3661 13824 7.689446 AAAGAAAGGCAGAGGTAAATACTTC 57.311 36.000 0.00 0.00 33.03 3.01
3662 13825 6.374417 AGAAAGGCAGAGGTAAATACTTCA 57.626 37.500 5.63 0.00 35.05 3.02
3663 13826 6.779860 AGAAAGGCAGAGGTAAATACTTCAA 58.220 36.000 5.63 0.00 35.05 2.69
3664 13827 7.231467 AGAAAGGCAGAGGTAAATACTTCAAA 58.769 34.615 5.63 0.00 35.05 2.69
3665 13828 7.391833 AGAAAGGCAGAGGTAAATACTTCAAAG 59.608 37.037 5.63 0.00 35.05 2.77
3666 13829 6.374417 AGGCAGAGGTAAATACTTCAAAGA 57.626 37.500 5.63 0.00 35.05 2.52
3667 13830 6.410540 AGGCAGAGGTAAATACTTCAAAGAG 58.589 40.000 5.63 0.00 35.05 2.85
3668 13831 5.586643 GGCAGAGGTAAATACTTCAAAGAGG 59.413 44.000 5.63 0.00 35.05 3.69
3669 13832 5.065346 GCAGAGGTAAATACTTCAAAGAGGC 59.935 44.000 5.63 0.00 35.05 4.70
3701 13864 3.062122 TGTGTCATGTGTGATCAGCAT 57.938 42.857 0.00 0.83 36.60 3.79
3707 13870 5.472820 TGTCATGTGTGATCAGCATGTTTTA 59.527 36.000 26.40 13.60 40.40 1.52
3709 13872 5.706833 TCATGTGTGATCAGCATGTTTTAGT 59.293 36.000 26.40 1.76 40.40 2.24
3741 14028 1.202758 ACTTGTTCGTTCATCTGCCCA 60.203 47.619 0.00 0.00 0.00 5.36
3787 14078 5.877012 GGTATTCAAAATCAGCTCAGTCAGA 59.123 40.000 0.00 0.00 0.00 3.27
3793 14084 7.164122 TCAAAATCAGCTCAGTCAGATAGTTT 58.836 34.615 0.00 0.00 0.00 2.66
3828 14125 4.394439 TCCATTTGCAATGGATGTCATG 57.606 40.909 20.14 10.34 42.81 3.07
3837 14134 6.771573 TGCAATGGATGTCATGATACTGATA 58.228 36.000 0.00 0.00 35.99 2.15
3872 14169 3.833706 GCACGAGGAATGCTTATGC 57.166 52.632 0.00 0.00 40.08 3.14
3927 14243 1.076677 AGACGTAGGTTCAGGGAGGAA 59.923 52.381 0.00 0.00 0.00 3.36
3928 14244 2.108970 GACGTAGGTTCAGGGAGGAAT 58.891 52.381 0.00 0.00 0.00 3.01
3946 14266 7.339482 GGAGGAATTTCAGTGGTTACTTCTAT 58.661 38.462 0.00 0.00 34.07 1.98
3947 14267 8.483758 GGAGGAATTTCAGTGGTTACTTCTATA 58.516 37.037 0.00 0.00 34.07 1.31
4054 15429 1.731720 GGAGATCAGCACTGTGGAAC 58.268 55.000 10.21 0.00 37.35 3.62
4101 15476 0.792640 CAAAGATGACGAACGCTGCT 59.207 50.000 0.00 0.00 0.00 4.24
4102 15477 0.792640 AAAGATGACGAACGCTGCTG 59.207 50.000 0.00 0.00 0.00 4.41
4106 15481 1.300971 ATGACGAACGCTGCTGCAAT 61.301 50.000 16.29 3.02 39.64 3.56
4111 15486 1.061799 GAACGCTGCTGCAATTGACG 61.062 55.000 16.29 5.54 39.64 4.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
36 37 4.600012 ATTTTGTACTAGCACACATCGC 57.400 40.909 0.00 0.00 0.00 4.58
48 49 8.897752 GGAAGCATCTTTCTCATATTTTGTACT 58.102 33.333 0.00 0.00 0.00 2.73
49 50 8.897752 AGGAAGCATCTTTCTCATATTTTGTAC 58.102 33.333 0.00 0.00 0.00 2.90
66 67 6.865205 GGCAATACAATTTATGAGGAAGCATC 59.135 38.462 0.00 0.00 0.00 3.91
74 75 5.761003 TGATGCGGCAATACAATTTATGAG 58.239 37.500 6.82 0.00 0.00 2.90
75 76 5.299028 ACTGATGCGGCAATACAATTTATGA 59.701 36.000 6.82 0.00 0.00 2.15
84 85 1.668419 AGGAACTGATGCGGCAATAC 58.332 50.000 6.82 2.39 37.18 1.89
107 108 2.775890 CTGCTGAGCCCAATATACCTG 58.224 52.381 0.23 0.00 0.00 4.00
114 115 2.437359 GTCGCTGCTGAGCCCAAT 60.437 61.111 0.23 0.00 42.91 3.16
178 179 6.756074 TGTGAAAAATGCAAACCTGTAGAAAG 59.244 34.615 0.00 0.00 0.00 2.62
201 202 8.281212 AGCATAGAACCGAAGATTTAAAATGT 57.719 30.769 0.00 0.00 0.00 2.71
223 224 5.248477 AGGTAGAAACTAACTGATGGAAGCA 59.752 40.000 0.00 0.00 0.00 3.91
224 225 5.735766 AGGTAGAAACTAACTGATGGAAGC 58.264 41.667 0.00 0.00 0.00 3.86
254 255 5.885912 GGAAAAGGCATTAACACTATGAGGA 59.114 40.000 0.00 0.00 0.00 3.71
266 267 4.985538 ACTCTGACAAGGAAAAGGCATTA 58.014 39.130 0.00 0.00 0.00 1.90
267 268 3.837355 ACTCTGACAAGGAAAAGGCATT 58.163 40.909 0.00 0.00 0.00 3.56
321 323 3.244875 TGTGTAATTCTGCATCCAGGTGT 60.245 43.478 0.00 0.00 39.61 4.16
364 366 6.228258 TGTTCAGTTCTGTCCTGGTATTAAC 58.772 40.000 0.00 0.00 0.00 2.01
374 376 6.481954 AATCGTTATTGTTCAGTTCTGTCC 57.518 37.500 0.00 0.00 0.00 4.02
392 394 4.762289 AGGGAAGAGCAAGATTAATCGT 57.238 40.909 9.78 3.84 0.00 3.73
393 395 4.991687 GGTAGGGAAGAGCAAGATTAATCG 59.008 45.833 9.78 0.00 0.00 3.34
394 396 6.181206 AGGTAGGGAAGAGCAAGATTAATC 57.819 41.667 7.41 7.41 0.00 1.75
401 403 4.762289 ATTGTAGGTAGGGAAGAGCAAG 57.238 45.455 0.00 0.00 0.00 4.01
409 411 6.600427 GGAAATTTCGAAATTGTAGGTAGGGA 59.400 38.462 31.04 0.00 38.53 4.20
432 434 1.968493 GAGGGCATACGTCCATAAGGA 59.032 52.381 0.00 0.00 40.51 3.36
451 453 1.146930 GCTGGGCTTGATCGATGGA 59.853 57.895 0.54 0.00 0.00 3.41
452 454 0.749091 TTGCTGGGCTTGATCGATGG 60.749 55.000 0.54 0.00 0.00 3.51
460 462 1.737838 TAATCTCGTTGCTGGGCTTG 58.262 50.000 0.00 0.00 0.00 4.01
464 466 8.190784 AGAAAATTATTTAATCTCGTTGCTGGG 58.809 33.333 0.00 0.00 0.00 4.45
494 498 7.755582 ACTTCTTCAGTAATTTGCACAAAAC 57.244 32.000 0.00 0.00 31.97 2.43
581 585 2.569134 GAGTGCTCGACTTCGCCT 59.431 61.111 0.00 0.00 39.60 5.52
719 748 6.425114 CGGGTTCCACTATCATCAGATAAAAG 59.575 42.308 0.00 0.00 36.35 2.27
720 749 6.288294 CGGGTTCCACTATCATCAGATAAAA 58.712 40.000 0.00 0.00 36.35 1.52
770 800 4.818546 ACTGACTGAAACACTGAATTGAGG 59.181 41.667 0.00 0.00 0.00 3.86
772 802 5.462068 CGTACTGACTGAAACACTGAATTGA 59.538 40.000 0.00 0.00 0.00 2.57
786 817 0.532573 AGATGGCCACGTACTGACTG 59.467 55.000 8.16 0.00 0.00 3.51
787 818 0.532573 CAGATGGCCACGTACTGACT 59.467 55.000 8.16 0.00 0.00 3.41
962 1001 3.307242 CGGCAAAGACTGAGTATACAAGC 59.693 47.826 5.50 0.00 0.00 4.01
983 1022 4.034510 GGTCCATCTTATGAAAGTGAAGCG 59.965 45.833 0.00 0.00 34.13 4.68
1140 1181 2.200170 CTCCAAAGCCGCCTTTTCCG 62.200 60.000 0.00 0.00 39.20 4.30
1254 1295 4.522114 TCTTGTGGTTGATTTCACAGTGA 58.478 39.130 0.00 0.00 43.55 3.41
1418 7235 1.081892 CAATGCCTCTGAACACTCCG 58.918 55.000 0.00 0.00 0.00 4.63
1645 8548 6.238211 CCGAAGCTATAAACATCACTCTTTGG 60.238 42.308 0.00 0.00 0.00 3.28
1725 8628 4.864704 AAAACATTCAACTATGCCGGTT 57.135 36.364 1.90 0.00 0.00 4.44
1827 8730 0.752658 GCTTTGCAACCCCTTCAAGT 59.247 50.000 0.00 0.00 0.00 3.16
1873 8776 2.094957 GCATCTCAGGGCGTCTATCTAC 60.095 54.545 0.00 0.00 0.00 2.59
1894 8797 0.667487 AGACGTTGTGCCACATCTCG 60.667 55.000 0.00 7.17 0.00 4.04
1906 8809 0.878523 TGAAGTGCCCGAAGACGTTG 60.879 55.000 0.00 0.00 37.88 4.10
1995 8910 0.523072 CAGATTGCCAGTTGTTCCCG 59.477 55.000 0.00 0.00 0.00 5.14
1996 8911 0.244721 GCAGATTGCCAGTTGTTCCC 59.755 55.000 0.00 0.00 37.42 3.97
1997 8912 1.251251 AGCAGATTGCCAGTTGTTCC 58.749 50.000 0.00 0.00 46.52 3.62
2014 8929 1.807573 GTGGCGTGACTGAGCTAGC 60.808 63.158 6.62 6.62 0.00 3.42
2038 8953 1.308069 CGGCACAAGTTGGATGGGAG 61.308 60.000 7.96 0.00 0.00 4.30
2040 8955 2.993471 GCGGCACAAGTTGGATGGG 61.993 63.158 7.96 0.00 0.00 4.00
2071 8986 3.251479 TGTCACAGATTTCATCTCCCG 57.749 47.619 0.00 0.00 37.58 5.14
2189 9104 3.325293 ACTTACTCACACCTCTGCATG 57.675 47.619 0.00 0.00 0.00 4.06
2190 9105 3.307059 GGAACTTACTCACACCTCTGCAT 60.307 47.826 0.00 0.00 0.00 3.96
2191 9106 2.037251 GGAACTTACTCACACCTCTGCA 59.963 50.000 0.00 0.00 0.00 4.41
2247 9171 4.321230 CCGACCAATGATACGAGATGATGA 60.321 45.833 0.00 0.00 0.00 2.92
2327 9251 1.302993 TAAAGGTTCCCACGCAGGC 60.303 57.895 0.00 0.00 35.39 4.85
2440 9364 2.299867 ACACAACAAAAGGGATGATGGC 59.700 45.455 0.00 0.00 0.00 4.40
2558 10556 1.209504 CACAACCCAGACGTCCCATAT 59.790 52.381 13.01 0.00 0.00 1.78
2602 10600 3.626930 TGGTTTTCTGTGTTAGTTGCCT 58.373 40.909 0.00 0.00 0.00 4.75
2686 10684 3.262420 GCGCTTGTCTTTCTGGAAGATA 58.738 45.455 0.00 0.00 46.36 1.98
2732 10730 3.424640 AGGATGCCCTTCTTCTGGA 57.575 52.632 0.00 0.00 40.78 3.86
2883 10881 0.743701 CTGTGAGGCACATCTCCAGC 60.744 60.000 0.20 0.00 43.71 4.85
2898 10896 0.040067 GGCTTCCGCTTTGTTCTGTG 60.040 55.000 0.00 0.00 36.09 3.66
2899 10897 0.179018 AGGCTTCCGCTTTGTTCTGT 60.179 50.000 0.00 0.00 36.09 3.41
2921 11220 1.035923 ATCGTCTGGCGTCTCATCAT 58.964 50.000 0.09 0.00 42.13 2.45
2930 11362 0.179127 AGTGTCATCATCGTCTGGCG 60.179 55.000 0.00 0.00 43.01 5.69
2973 11983 1.153289 CATCTCCAGGTTCAGCCGG 60.153 63.158 0.00 0.00 43.70 6.13
3136 12442 7.923414 ATGGAGTATTGACAGTAGGAAAAAC 57.077 36.000 0.00 0.00 0.00 2.43
3137 12443 7.762615 CGTATGGAGTATTGACAGTAGGAAAAA 59.237 37.037 0.00 0.00 0.00 1.94
3163 13286 5.186198 AGGGACAGAAATTGCAGTATACAC 58.814 41.667 5.50 0.00 0.00 2.90
3212 13345 9.113838 GAGGAAGCATGAGAAAGACATAATAAA 57.886 33.333 0.00 0.00 0.00 1.40
3217 13350 4.160439 ACGAGGAAGCATGAGAAAGACATA 59.840 41.667 0.00 0.00 0.00 2.29
3218 13351 3.055530 ACGAGGAAGCATGAGAAAGACAT 60.056 43.478 0.00 0.00 0.00 3.06
3219 13352 2.300152 ACGAGGAAGCATGAGAAAGACA 59.700 45.455 0.00 0.00 0.00 3.41
3220 13353 2.966050 ACGAGGAAGCATGAGAAAGAC 58.034 47.619 0.00 0.00 0.00 3.01
3222 13355 4.509600 GGATAACGAGGAAGCATGAGAAAG 59.490 45.833 0.00 0.00 0.00 2.62
3223 13356 4.442706 GGATAACGAGGAAGCATGAGAAA 58.557 43.478 0.00 0.00 0.00 2.52
3247 13380 4.218417 GCCTGACAAATCCATTACAACACT 59.782 41.667 0.00 0.00 0.00 3.55
3317 13457 5.125900 TGCATAATGATGACCCAACTGAAAG 59.874 40.000 0.00 0.00 35.81 2.62
3363 13513 6.227298 ACAGTACAGTATGATCAAAGGGAG 57.773 41.667 0.00 0.00 39.69 4.30
3367 13517 8.406297 TGCTAGTACAGTACAGTATGATCAAAG 58.594 37.037 13.37 0.00 39.69 2.77
3368 13518 8.288689 TGCTAGTACAGTACAGTATGATCAAA 57.711 34.615 13.37 0.00 39.69 2.69
3369 13519 7.875327 TGCTAGTACAGTACAGTATGATCAA 57.125 36.000 13.37 0.00 39.69 2.57
3373 13523 7.556635 ACAAGATGCTAGTACAGTACAGTATGA 59.443 37.037 13.37 0.00 39.69 2.15
3374 13524 7.708051 ACAAGATGCTAGTACAGTACAGTATG 58.292 38.462 13.37 6.27 46.00 2.39
3376 13526 7.148120 GGAACAAGATGCTAGTACAGTACAGTA 60.148 40.741 13.37 8.12 0.00 2.74
3377 13527 6.350277 GGAACAAGATGCTAGTACAGTACAGT 60.350 42.308 13.37 0.00 0.00 3.55
3378 13528 6.037098 GGAACAAGATGCTAGTACAGTACAG 58.963 44.000 13.37 9.12 0.00 2.74
3379 13529 5.479027 TGGAACAAGATGCTAGTACAGTACA 59.521 40.000 13.37 0.00 31.92 2.90
3406 13569 1.078759 CTTCTGCACCCTAACGCTCG 61.079 60.000 0.00 0.00 0.00 5.03
3508 13671 6.095160 CCAGAAGAAAATCTTATGCTTGAGCT 59.905 38.462 8.77 0.00 42.57 4.09
3509 13672 6.264088 CCAGAAGAAAATCTTATGCTTGAGC 58.736 40.000 8.77 0.00 42.57 4.26
3510 13673 6.095160 AGCCAGAAGAAAATCTTATGCTTGAG 59.905 38.462 8.77 0.00 42.57 3.02
3511 13674 5.948162 AGCCAGAAGAAAATCTTATGCTTGA 59.052 36.000 8.77 0.00 42.57 3.02
3512 13675 6.034591 CAGCCAGAAGAAAATCTTATGCTTG 58.965 40.000 8.77 5.99 42.57 4.01
3513 13676 5.393896 GCAGCCAGAAGAAAATCTTATGCTT 60.394 40.000 8.77 0.00 42.57 3.91
3514 13677 4.097589 GCAGCCAGAAGAAAATCTTATGCT 59.902 41.667 8.77 7.28 42.57 3.79
3515 13678 4.097589 AGCAGCCAGAAGAAAATCTTATGC 59.902 41.667 8.77 7.18 42.57 3.14
3516 13679 5.831702 AGCAGCCAGAAGAAAATCTTATG 57.168 39.130 7.56 7.56 43.29 1.90
3517 13680 7.776969 TGATAAGCAGCCAGAAGAAAATCTTAT 59.223 33.333 0.00 0.00 36.73 1.73
3518 13681 7.112122 TGATAAGCAGCCAGAAGAAAATCTTA 58.888 34.615 0.00 0.00 36.73 2.10
3519 13682 5.948162 TGATAAGCAGCCAGAAGAAAATCTT 59.052 36.000 0.00 0.00 39.87 2.40
3520 13683 5.503927 TGATAAGCAGCCAGAAGAAAATCT 58.496 37.500 0.00 0.00 0.00 2.40
3521 13684 5.824904 TGATAAGCAGCCAGAAGAAAATC 57.175 39.130 0.00 0.00 0.00 2.17
3522 13685 6.786967 ATTGATAAGCAGCCAGAAGAAAAT 57.213 33.333 0.00 0.00 0.00 1.82
3523 13686 7.176515 TGTTATTGATAAGCAGCCAGAAGAAAA 59.823 33.333 0.00 0.00 0.00 2.29
3524 13687 6.658816 TGTTATTGATAAGCAGCCAGAAGAAA 59.341 34.615 0.00 0.00 0.00 2.52
3525 13688 6.179756 TGTTATTGATAAGCAGCCAGAAGAA 58.820 36.000 0.00 0.00 0.00 2.52
3526 13689 5.744171 TGTTATTGATAAGCAGCCAGAAGA 58.256 37.500 0.00 0.00 0.00 2.87
3527 13690 5.008415 CCTGTTATTGATAAGCAGCCAGAAG 59.992 44.000 0.00 0.00 0.00 2.85
3528 13691 4.883585 CCTGTTATTGATAAGCAGCCAGAA 59.116 41.667 0.00 0.00 0.00 3.02
3529 13692 4.454678 CCTGTTATTGATAAGCAGCCAGA 58.545 43.478 0.00 0.00 0.00 3.86
3530 13693 3.004106 GCCTGTTATTGATAAGCAGCCAG 59.996 47.826 0.00 0.00 0.00 4.85
3531 13694 2.951642 GCCTGTTATTGATAAGCAGCCA 59.048 45.455 0.00 0.00 0.00 4.75
3532 13695 3.004106 CAGCCTGTTATTGATAAGCAGCC 59.996 47.826 0.00 0.00 0.00 4.85
3533 13696 3.879295 TCAGCCTGTTATTGATAAGCAGC 59.121 43.478 0.00 0.00 0.00 5.25
3534 13697 6.630444 ATTCAGCCTGTTATTGATAAGCAG 57.370 37.500 0.00 0.00 0.00 4.24
3535 13698 7.282585 AGTATTCAGCCTGTTATTGATAAGCA 58.717 34.615 0.00 0.00 0.00 3.91
3536 13699 7.736447 AGTATTCAGCCTGTTATTGATAAGC 57.264 36.000 0.00 0.00 0.00 3.09
3539 13702 9.588096 TCTCTAGTATTCAGCCTGTTATTGATA 57.412 33.333 0.00 0.00 0.00 2.15
3540 13703 8.484214 TCTCTAGTATTCAGCCTGTTATTGAT 57.516 34.615 0.00 0.00 0.00 2.57
3541 13704 7.898014 TCTCTAGTATTCAGCCTGTTATTGA 57.102 36.000 0.00 0.00 0.00 2.57
3542 13705 8.200792 AGTTCTCTAGTATTCAGCCTGTTATTG 58.799 37.037 0.00 0.00 0.00 1.90
3543 13706 8.312669 AGTTCTCTAGTATTCAGCCTGTTATT 57.687 34.615 0.00 0.00 0.00 1.40
3544 13707 7.014808 GGAGTTCTCTAGTATTCAGCCTGTTAT 59.985 40.741 0.00 0.00 0.00 1.89
3545 13708 6.321690 GGAGTTCTCTAGTATTCAGCCTGTTA 59.678 42.308 0.00 0.00 0.00 2.41
3546 13709 5.128008 GGAGTTCTCTAGTATTCAGCCTGTT 59.872 44.000 0.00 0.00 0.00 3.16
3547 13710 4.647399 GGAGTTCTCTAGTATTCAGCCTGT 59.353 45.833 0.00 0.00 0.00 4.00
3548 13711 4.892934 AGGAGTTCTCTAGTATTCAGCCTG 59.107 45.833 0.00 0.00 0.00 4.85
3549 13712 5.137412 AGGAGTTCTCTAGTATTCAGCCT 57.863 43.478 0.00 0.00 0.00 4.58
3550 13713 5.447624 GAGGAGTTCTCTAGTATTCAGCC 57.552 47.826 0.00 0.00 39.38 4.85
3570 13733 7.920160 AAATGAAAAAGCTCTTCCTCTAGAG 57.080 36.000 13.18 13.18 43.66 2.43
3571 13734 8.160106 AGAAAATGAAAAAGCTCTTCCTCTAGA 58.840 33.333 6.15 0.00 0.00 2.43
3572 13735 8.334263 AGAAAATGAAAAAGCTCTTCCTCTAG 57.666 34.615 6.15 0.00 0.00 2.43
3573 13736 8.697507 AAGAAAATGAAAAAGCTCTTCCTCTA 57.302 30.769 6.15 0.00 0.00 2.43
3606 13769 9.436957 AGAGTAGAAAATCAACATTTATGTCGT 57.563 29.630 0.00 0.00 40.80 4.34
3607 13770 9.907576 GAGAGTAGAAAATCAACATTTATGTCG 57.092 33.333 0.00 0.00 40.80 4.35
3635 13798 8.478775 AAGTATTTACCTCTGCCTTTCTTTTT 57.521 30.769 0.00 0.00 0.00 1.94
3636 13799 7.724061 TGAAGTATTTACCTCTGCCTTTCTTTT 59.276 33.333 0.00 0.00 0.00 2.27
3637 13800 7.231467 TGAAGTATTTACCTCTGCCTTTCTTT 58.769 34.615 0.00 0.00 0.00 2.52
3638 13801 6.779860 TGAAGTATTTACCTCTGCCTTTCTT 58.220 36.000 0.00 0.00 0.00 2.52
3639 13802 6.374417 TGAAGTATTTACCTCTGCCTTTCT 57.626 37.500 0.00 0.00 0.00 2.52
3640 13803 7.390718 TCTTTGAAGTATTTACCTCTGCCTTTC 59.609 37.037 0.00 0.00 0.00 2.62
3641 13804 7.231467 TCTTTGAAGTATTTACCTCTGCCTTT 58.769 34.615 0.00 0.00 0.00 3.11
3642 13805 6.779860 TCTTTGAAGTATTTACCTCTGCCTT 58.220 36.000 0.00 0.00 0.00 4.35
3643 13806 6.374417 TCTTTGAAGTATTTACCTCTGCCT 57.626 37.500 0.00 0.00 0.00 4.75
3644 13807 5.586643 CCTCTTTGAAGTATTTACCTCTGCC 59.413 44.000 0.00 0.00 0.00 4.85
3645 13808 5.065346 GCCTCTTTGAAGTATTTACCTCTGC 59.935 44.000 0.00 0.00 0.00 4.26
3646 13809 6.173339 TGCCTCTTTGAAGTATTTACCTCTG 58.827 40.000 0.00 0.00 0.00 3.35
3647 13810 6.374417 TGCCTCTTTGAAGTATTTACCTCT 57.626 37.500 0.00 0.00 0.00 3.69
3648 13811 5.586643 CCTGCCTCTTTGAAGTATTTACCTC 59.413 44.000 0.00 0.00 0.00 3.85
3649 13812 5.250774 TCCTGCCTCTTTGAAGTATTTACCT 59.749 40.000 0.00 0.00 0.00 3.08
3650 13813 5.354513 GTCCTGCCTCTTTGAAGTATTTACC 59.645 44.000 0.00 0.00 0.00 2.85
3651 13814 6.092807 CAGTCCTGCCTCTTTGAAGTATTTAC 59.907 42.308 0.00 0.00 0.00 2.01
3652 13815 6.173339 CAGTCCTGCCTCTTTGAAGTATTTA 58.827 40.000 0.00 0.00 0.00 1.40
3653 13816 5.006386 CAGTCCTGCCTCTTTGAAGTATTT 58.994 41.667 0.00 0.00 0.00 1.40
3654 13817 4.583871 CAGTCCTGCCTCTTTGAAGTATT 58.416 43.478 0.00 0.00 0.00 1.89
3655 13818 4.213564 CAGTCCTGCCTCTTTGAAGTAT 57.786 45.455 0.00 0.00 0.00 2.12
3656 13819 3.685139 CAGTCCTGCCTCTTTGAAGTA 57.315 47.619 0.00 0.00 0.00 2.24
3657 13820 2.557920 CAGTCCTGCCTCTTTGAAGT 57.442 50.000 0.00 0.00 0.00 3.01
3669 13832 1.467342 CATGACACATGTGCAGTCCTG 59.533 52.381 25.68 14.32 0.00 3.86
3729 13892 1.620822 ACCAACTTGGGCAGATGAAC 58.379 50.000 12.62 0.00 43.37 3.18
3772 14063 4.874966 GCAAACTATCTGACTGAGCTGATT 59.125 41.667 0.00 0.00 0.00 2.57
3787 14078 3.950395 GGAAGATTGAGCAGGCAAACTAT 59.050 43.478 0.00 0.00 31.69 2.12
3793 14084 2.494471 CAAATGGAAGATTGAGCAGGCA 59.506 45.455 0.00 0.00 0.00 4.75
3828 14125 3.710209 ATGGCCCAAGCTATCAGTATC 57.290 47.619 0.00 0.00 34.68 2.24
3837 14134 1.986210 GCTCCAAATGGCCCAAGCT 60.986 57.895 0.00 0.00 39.73 3.74
3927 14243 8.540388 TGCTCTTATAGAAGTAACCACTGAAAT 58.460 33.333 0.00 0.00 34.36 2.17
3928 14244 7.903145 TGCTCTTATAGAAGTAACCACTGAAA 58.097 34.615 0.00 0.00 34.36 2.69
3946 14266 6.655078 AGCAGGATTTTCTTTTTGCTCTTA 57.345 33.333 0.00 0.00 37.31 2.10
3947 14267 5.541953 AGCAGGATTTTCTTTTTGCTCTT 57.458 34.783 0.00 0.00 37.31 2.85
4017 15392 1.680735 TCCGCCATATGGAATTTGTGC 59.319 47.619 26.47 6.10 37.39 4.57
4022 15397 3.871463 GCTGATCTCCGCCATATGGAATT 60.871 47.826 26.47 2.96 37.39 2.17
4054 15429 3.910767 GCTCTCATCTTTGCAAAAGTTCG 59.089 43.478 13.84 0.98 0.00 3.95
4092 15467 1.061799 CGTCAATTGCAGCAGCGTTC 61.062 55.000 0.00 0.00 46.23 3.95
4096 15471 3.708195 AATCGTCAATTGCAGCAGC 57.292 47.368 0.00 0.00 42.57 5.25


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

AutoCloner maintained by Alex Coulton.