Multiple sequence alignment - TraesCS1D01G409800

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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 TraesCS1D01G409800 chr1D 100.000 9765 0 0 1 9765 471605600 471595836 0.000000e+00 18033.0
1 TraesCS1D01G409800 chr1D 89.218 371 37 3 3570 3938 471601962 471601593 2.480000e-125 460.0
2 TraesCS1D01G409800 chr1D 89.218 371 37 3 3639 4008 471602031 471601663 2.480000e-125 460.0
3 TraesCS1D01G409800 chr1D 87.375 301 37 1 3708 4008 471602031 471601732 2.610000e-90 344.0
4 TraesCS1D01G409800 chr1D 84.694 98 8 4 9350 9441 249030311 249030407 3.760000e-14 91.6
5 TraesCS1D01G409800 chr1A 94.894 3643 114 34 2279 5858 566003851 566000218 0.000000e+00 5631.0
6 TraesCS1D01G409800 chr1A 94.074 1772 51 19 7108 8871 565998757 565997032 0.000000e+00 2641.0
7 TraesCS1D01G409800 chr1A 87.973 2220 138 57 65 2222 566006301 566004149 0.000000e+00 2501.0
8 TraesCS1D01G409800 chr1A 93.881 1095 47 8 5992 7075 565999837 565998752 0.000000e+00 1633.0
9 TraesCS1D01G409800 chr1A 90.459 828 56 10 8869 9687 565997005 565996192 0.000000e+00 1070.0
10 TraesCS1D01G409800 chr1A 89.488 371 36 3 3639 4008 566002526 566002158 5.340000e-127 466.0
11 TraesCS1D01G409800 chr1A 89.218 371 37 3 3570 3938 566002457 566002088 2.480000e-125 460.0
12 TraesCS1D01G409800 chr1A 94.048 84 5 0 5917 6000 566000219 566000136 2.860000e-25 128.0
13 TraesCS1D01G409800 chr1A 83.962 106 10 4 9350 9448 298603697 298603592 2.900000e-15 95.3
14 TraesCS1D01G409800 chr1B 96.425 2685 65 19 3334 5994 655774285 655771608 0.000000e+00 4397.0
15 TraesCS1D01G409800 chr1B 89.612 3090 157 72 301 3325 655777345 655774355 0.000000e+00 3777.0
16 TraesCS1D01G409800 chr1B 93.452 1741 59 17 7140 8871 655767617 655765923 0.000000e+00 2532.0
17 TraesCS1D01G409800 chr1B 95.063 790 29 4 5981 6760 655769501 655768712 0.000000e+00 1234.0
18 TraesCS1D01G409800 chr1B 88.877 908 62 17 8865 9765 655765900 655765025 0.000000e+00 1081.0
19 TraesCS1D01G409800 chr1B 85.696 776 89 16 5102 5863 17307401 17308168 0.000000e+00 798.0
20 TraesCS1D01G409800 chr1B 89.942 517 22 8 6756 7270 655768105 655767617 2.970000e-179 640.0
21 TraesCS1D01G409800 chr1B 89.197 361 35 4 3648 4008 655774039 655773683 1.930000e-121 448.0
22 TraesCS1D01G409800 chr1B 88.108 370 41 3 3570 3938 655773980 655773613 4.190000e-118 436.0
23 TraesCS1D01G409800 chr1B 85.837 233 30 3 3570 3800 655773844 655773613 2.720000e-60 244.0
24 TraesCS1D01G409800 chr3A 88.767 1816 177 23 4024 5826 621326753 621324952 0.000000e+00 2198.0
25 TraesCS1D01G409800 chr3A 78.397 1148 168 44 7738 8847 621322876 621321771 0.000000e+00 673.0
26 TraesCS1D01G409800 chr3A 90.852 317 25 4 3336 3649 621328077 621327762 1.170000e-113 422.0
27 TraesCS1D01G409800 chr3A 86.765 272 31 5 5977 6247 621324422 621324155 2.060000e-76 298.0
28 TraesCS1D01G409800 chr3D 89.022 1667 157 22 4162 5817 477909094 477907443 0.000000e+00 2041.0
29 TraesCS1D01G409800 chr3D 79.106 828 123 18 8050 8847 477905308 477904501 8.690000e-145 525.0
30 TraesCS1D01G409800 chr3D 90.566 318 24 6 3336 3649 477910486 477910171 5.460000e-112 416.0
31 TraesCS1D01G409800 chr3D 81.568 472 50 11 1489 1959 477912498 477912063 1.210000e-93 355.0
32 TraesCS1D01G409800 chr3D 87.259 259 27 5 5991 6247 477906892 477906638 3.450000e-74 291.0
33 TraesCS1D01G409800 chr3B 88.602 1667 164 22 4162 5817 637091432 637089781 0.000000e+00 2002.0
34 TraesCS1D01G409800 chr3B 77.672 1151 176 39 7740 8850 637087642 637086533 2.320000e-175 627.0
35 TraesCS1D01G409800 chr3B 88.644 317 32 4 3336 3649 637092824 637092509 5.530000e-102 383.0
36 TraesCS1D01G409800 chr3B 87.645 259 26 5 5991 6247 637089231 637088977 7.420000e-76 296.0
37 TraesCS1D01G409800 chr7D 83.636 770 77 23 5111 5868 60375252 60374520 0.000000e+00 678.0
38 TraesCS1D01G409800 chr7D 83.442 767 82 22 5111 5868 60382304 60381574 0.000000e+00 671.0
39 TraesCS1D01G409800 chr7D 83.377 770 79 23 5111 5868 60377913 60377181 0.000000e+00 667.0
40 TraesCS1D01G409800 chr7D 83.312 767 83 22 5111 5868 60379646 60378916 0.000000e+00 665.0
41 TraesCS1D01G409800 chr7D 89.320 309 23 5 5567 5868 60372168 60371863 7.160000e-101 379.0
42 TraesCS1D01G409800 chr5A 83.398 771 79 28 5111 5868 52409636 52408902 0.000000e+00 669.0
43 TraesCS1D01G409800 chr5A 83.721 301 36 11 5094 5388 119059912 119059619 1.250000e-68 272.0
44 TraesCS1D01G409800 chr5A 84.360 211 26 4 7459 7663 5653424 5653633 5.980000e-47 200.0
45 TraesCS1D01G409800 chrUn 88.945 398 38 4 4336 4733 479196020 479195629 4.100000e-133 486.0
46 TraesCS1D01G409800 chr2A 83.721 301 36 11 5094 5388 43442648 43442941 1.250000e-68 272.0
47 TraesCS1D01G409800 chr2A 88.732 71 4 2 9357 9423 694471446 694471516 6.280000e-12 84.2
48 TraesCS1D01G409800 chr5D 85.778 225 19 9 3337 3557 3550002 3549787 9.870000e-55 226.0
49 TraesCS1D01G409800 chr5D 82.938 211 29 4 7459 7663 7631752 7631543 6.020000e-42 183.0
50 TraesCS1D01G409800 chr5D 80.711 197 26 5 2912 3097 3550434 3550239 1.020000e-29 143.0
51 TraesCS1D01G409800 chr5D 85.714 77 7 2 9352 9424 319689943 319690019 2.920000e-10 78.7
52 TraesCS1D01G409800 chr7A 88.571 70 4 2 9358 9423 632520644 632520575 2.260000e-11 82.4
53 TraesCS1D01G409800 chr4D 85.057 87 6 4 9352 9431 34659944 34660030 2.260000e-11 82.4
54 TraesCS1D01G409800 chr5B 81.000 100 11 5 9356 9448 681345094 681344996 1.360000e-08 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 TraesCS1D01G409800 chr1D 471595836 471605600 9764 True 18033.000000 18033 100.000000 1 9765 1 chr1D.!!$R1 9764
1 TraesCS1D01G409800 chr1A 565996192 566006301 10109 True 1816.250000 5631 91.754375 65 9687 8 chr1A.!!$R2 9622
2 TraesCS1D01G409800 chr1B 655765025 655777345 12320 True 1643.222222 4397 90.723667 301 9765 9 chr1B.!!$R1 9464
3 TraesCS1D01G409800 chr1B 17307401 17308168 767 False 798.000000 798 85.696000 5102 5863 1 chr1B.!!$F1 761
4 TraesCS1D01G409800 chr3A 621321771 621328077 6306 True 897.750000 2198 86.195250 3336 8847 4 chr3A.!!$R1 5511
5 TraesCS1D01G409800 chr3D 477904501 477912498 7997 True 725.600000 2041 85.504200 1489 8847 5 chr3D.!!$R1 7358
6 TraesCS1D01G409800 chr3B 637086533 637092824 6291 True 827.000000 2002 85.640750 3336 8850 4 chr3B.!!$R1 5514
7 TraesCS1D01G409800 chr7D 60371863 60382304 10441 True 612.000000 678 84.617400 5111 5868 5 chr7D.!!$R1 757
8 TraesCS1D01G409800 chr5A 52408902 52409636 734 True 669.000000 669 83.398000 5111 5868 1 chr5A.!!$R1 757

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
344 371 0.325203 AGCCCCTCTCTCTCTGGAAC 60.325 60.0 0.00 0.00 0.00 3.62 F
1274 1346 0.320073 TCGTCGGCCGAATGAACTTT 60.320 50.0 32.93 0.00 44.03 2.66 F
1465 1568 2.621998 GGATTCCATTCTGCCAGACATG 59.378 50.0 0.00 2.13 0.00 3.21 F
2215 2395 2.231215 ACAGCTAGCTGATTAAGGCG 57.769 50.0 43.42 19.72 46.30 5.52 F
2605 3056 0.170561 CATGCAAGGTTCTGCTGCTC 59.829 55.0 0.00 0.00 43.07 4.26 F
3870 4895 2.375509 CCAAGGGGTAGACCAAGAAAGT 59.624 50.0 0.21 0.00 42.91 2.66 F
5288 14317 0.811616 AGGTGATGCGCCGAGAATTC 60.812 55.0 4.18 0.00 39.30 2.17 F
6583 20906 2.876079 GCCCTGCTGTAGCTTGTACTTT 60.876 50.0 5.38 0.00 42.66 2.66 F
7079 22192 0.174845 TGCTGCGTCTATAAAGCGGT 59.825 50.0 0.00 0.00 40.47 5.68 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2172 2352 0.035152 TGCGCTCAAACCTCATCCAT 60.035 50.0 9.73 0.0 0.00 3.41 R
2186 2366 0.678395 AGCTAGCTGTATCATGCGCT 59.322 50.0 18.57 0.0 36.56 5.92 R
2269 2701 1.079503 GGAAAGTGGCGTTAGAGCAG 58.920 55.0 0.00 0.0 39.27 4.24 R
3873 4898 0.675837 TCATCAGCAGTTGCAGGCTC 60.676 55.0 6.90 0.0 45.16 4.70 R
3875 4900 0.815734 AATCATCAGCAGTTGCAGGC 59.184 50.0 6.90 0.0 45.16 4.85 R
5515 17214 5.801380 ACATTAACCAGAACAGACGGTTAT 58.199 37.5 0.00 0.0 43.09 1.89 R
7075 22188 0.248289 TGAAACTACCAGCCTACCGC 59.752 55.0 0.00 0.0 37.98 5.68 R
8448 23959 2.603892 GCCAATGATATGACTTGCAGCG 60.604 50.0 0.00 0.0 0.00 5.18 R
8781 24305 0.179004 CCTGGTTTGCGGCCCATATA 60.179 55.0 0.00 0.0 0.00 0.86 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
20 21 2.012673 ACGGTACTAGCTAGAACACGG 58.987 52.381 27.45 22.74 0.00 4.94
21 22 1.332997 CGGTACTAGCTAGAACACGGG 59.667 57.143 27.45 12.13 0.00 5.28
22 23 1.066757 GGTACTAGCTAGAACACGGGC 59.933 57.143 27.45 7.27 0.00 6.13
23 24 1.747355 GTACTAGCTAGAACACGGGCA 59.253 52.381 27.45 0.00 0.00 5.36
24 25 0.531200 ACTAGCTAGAACACGGGCAC 59.469 55.000 27.45 0.00 0.00 5.01
45 46 4.778143 GCTCCAATGGGGCGACGT 62.778 66.667 9.02 0.00 36.21 4.34
46 47 2.819595 CTCCAATGGGGCGACGTG 60.820 66.667 0.00 0.00 36.21 4.49
47 48 4.402528 TCCAATGGGGCGACGTGG 62.403 66.667 0.00 0.00 36.21 4.94
48 49 4.402528 CCAATGGGGCGACGTGGA 62.403 66.667 0.11 0.00 0.00 4.02
49 50 3.124921 CAATGGGGCGACGTGGAC 61.125 66.667 0.11 0.00 0.00 4.02
50 51 4.404098 AATGGGGCGACGTGGACC 62.404 66.667 15.20 15.20 0.00 4.46
54 55 4.736896 GGGCGACGTGGACCTGTC 62.737 72.222 16.33 7.22 0.00 3.51
58 59 4.240049 GACGTGGACCTGTCGAAC 57.760 61.111 0.00 0.00 0.00 3.95
59 60 1.728426 GACGTGGACCTGTCGAACG 60.728 63.158 17.31 17.31 42.34 3.95
60 61 2.430244 CGTGGACCTGTCGAACGG 60.430 66.667 13.29 0.00 36.98 4.44
67 68 4.003788 CTGTCGAACGGGTGGCCT 62.004 66.667 3.32 0.00 0.00 5.19
68 69 3.530910 CTGTCGAACGGGTGGCCTT 62.531 63.158 3.32 0.00 0.00 4.35
69 70 2.281276 GTCGAACGGGTGGCCTTT 60.281 61.111 3.32 0.00 0.00 3.11
70 71 2.281208 TCGAACGGGTGGCCTTTG 60.281 61.111 3.32 0.00 0.00 2.77
149 150 1.079405 GTCGGATGACCTGCGGAAA 60.079 57.895 0.00 0.00 39.47 3.13
157 158 3.358111 TGACCTGCGGAAAATTATGGA 57.642 42.857 0.00 0.00 0.00 3.41
160 161 1.338020 CCTGCGGAAAATTATGGAGCC 59.662 52.381 0.00 0.00 0.00 4.70
179 180 2.497138 CCGACATGCATCACACCATAT 58.503 47.619 0.00 0.00 0.00 1.78
256 262 1.518367 TGGAGTTTCTTCACCCCTGT 58.482 50.000 0.00 0.00 0.00 4.00
257 263 2.696775 TGGAGTTTCTTCACCCCTGTA 58.303 47.619 0.00 0.00 0.00 2.74
258 264 3.256704 TGGAGTTTCTTCACCCCTGTAT 58.743 45.455 0.00 0.00 0.00 2.29
274 281 9.586435 CACCCCTGTATTTTAAATCTGAAAATC 57.414 33.333 0.00 0.00 37.59 2.17
287 294 8.924511 AAATCTGAAAATCCAACTCAGAGTTA 57.075 30.769 15.73 1.69 46.74 2.24
291 298 8.816894 TCTGAAAATCCAACTCAGAGTTATAGT 58.183 33.333 15.73 3.57 40.44 2.12
317 344 6.266103 TCTGTTTCTCATCCTTTTGAATTGCT 59.734 34.615 0.00 0.00 0.00 3.91
339 366 4.825199 AGTTATTAGCCCCTCTCTCTCT 57.175 45.455 0.00 0.00 0.00 3.10
344 371 0.325203 AGCCCCTCTCTCTCTGGAAC 60.325 60.000 0.00 0.00 0.00 3.62
362 389 1.800805 ACGAAGTGCAGGTTGATGAG 58.199 50.000 0.00 0.00 42.51 2.90
379 406 1.202794 TGAGCTGCAACATTGGACAGA 60.203 47.619 1.02 0.00 31.67 3.41
397 424 3.715097 GAGGGGTGCAGCAGCTCT 61.715 66.667 27.31 27.31 45.98 4.09
398 425 2.284921 AGGGGTGCAGCAGCTCTA 60.285 61.111 25.90 0.00 41.19 2.43
399 426 2.188994 GGGGTGCAGCAGCTCTAG 59.811 66.667 23.44 0.00 42.74 2.43
400 427 2.362369 GGGGTGCAGCAGCTCTAGA 61.362 63.158 23.44 0.00 42.74 2.43
478 508 0.955178 ATCGATCGATCTCAGCCGTT 59.045 50.000 24.60 0.00 0.00 4.44
481 511 1.335415 CGATCGATCTCAGCCGTTGAT 60.335 52.381 22.43 0.00 34.68 2.57
488 518 1.667154 CTCAGCCGTTGATCGAGGGA 61.667 60.000 23.33 3.94 42.86 4.20
501 531 1.229853 GAGGGACCCAAGGGAAGGA 60.230 63.158 14.60 0.00 38.96 3.36
535 565 1.894466 TCCGTTAACTGAACCCGATCA 59.106 47.619 3.71 0.00 34.21 2.92
795 843 1.454847 CGCCTCACCTAGCTCCTCT 60.455 63.158 0.00 0.00 0.00 3.69
803 851 2.123683 TAGCTCCTCTCCTGCCCG 60.124 66.667 0.00 0.00 0.00 6.13
892 951 2.935849 GTTGGTTTTTCCTTTGGCAGTG 59.064 45.455 0.00 0.00 37.07 3.66
905 964 1.518903 GGCAGTGGACAGTTCTTGGC 61.519 60.000 0.00 0.00 0.00 4.52
906 965 0.536006 GCAGTGGACAGTTCTTGGCT 60.536 55.000 0.00 0.00 34.18 4.75
907 966 1.972872 CAGTGGACAGTTCTTGGCTT 58.027 50.000 0.00 0.00 34.18 4.35
908 967 1.876156 CAGTGGACAGTTCTTGGCTTC 59.124 52.381 0.00 0.00 34.18 3.86
909 968 1.771255 AGTGGACAGTTCTTGGCTTCT 59.229 47.619 0.00 0.00 34.18 2.85
910 969 2.173569 AGTGGACAGTTCTTGGCTTCTT 59.826 45.455 0.00 0.00 34.18 2.52
911 970 2.550180 GTGGACAGTTCTTGGCTTCTTC 59.450 50.000 0.00 0.00 34.18 2.87
919 978 2.508526 TCTTGGCTTCTTCCTTCTTGC 58.491 47.619 0.00 0.00 0.00 4.01
921 980 2.592102 TGGCTTCTTCCTTCTTGCAT 57.408 45.000 0.00 0.00 0.00 3.96
1193 1253 3.087031 CCTCAGTAACGTTCCTCAGGTA 58.913 50.000 2.82 0.00 0.00 3.08
1200 1260 3.564053 ACGTTCCTCAGGTAAAAACCA 57.436 42.857 0.00 0.00 0.00 3.67
1269 1341 4.508128 GGCTCGTCGGCCGAATGA 62.508 66.667 32.93 28.00 46.75 2.57
1274 1346 0.320073 TCGTCGGCCGAATGAACTTT 60.320 50.000 32.93 0.00 44.03 2.66
1286 1358 6.404734 GCCGAATGAACTTTTGAGTAATCCAT 60.405 38.462 0.00 0.00 0.00 3.41
1288 1360 6.968904 CGAATGAACTTTTGAGTAATCCATGG 59.031 38.462 4.97 4.97 0.00 3.66
1388 1463 3.111853 TCTCCAATTAGGTATGCTGCG 57.888 47.619 0.00 0.00 39.02 5.18
1428 1520 8.100791 TGTGCTAAGATTATGGTTAAACAGAGT 58.899 33.333 0.00 0.00 0.00 3.24
1439 1531 7.581213 TGGTTAAACAGAGTCATCAAATGTT 57.419 32.000 0.00 0.00 35.70 2.71
1465 1568 2.621998 GGATTCCATTCTGCCAGACATG 59.378 50.000 0.00 2.13 0.00 3.21
1472 1575 2.685850 TCTGCCAGACATGTGATCTG 57.314 50.000 1.15 4.37 42.79 2.90
1480 1583 5.530171 GCCAGACATGTGATCTGTTGATAAT 59.470 40.000 1.15 0.00 41.78 1.28
1539 1642 4.985538 TCTCTTATGAGCCAAAAGGTGTT 58.014 39.130 0.72 0.00 40.03 3.32
1643 1746 9.945904 ATCTTTTCCTCAGGTTAGTAAAACTAG 57.054 33.333 0.00 0.00 31.47 2.57
1653 1756 8.443937 CAGGTTAGTAAAACTAGAACTGATTGC 58.556 37.037 0.00 0.00 32.90 3.56
1654 1757 7.606839 AGGTTAGTAAAACTAGAACTGATTGCC 59.393 37.037 0.00 0.00 31.47 4.52
1679 1783 5.965918 GGCGCTAATTTGTGAGTCTAAATTC 59.034 40.000 7.64 7.71 37.57 2.17
1687 1791 7.739498 TTTGTGAGTCTAAATTCCCTGTTAC 57.261 36.000 0.00 0.00 0.00 2.50
1693 1797 7.606456 TGAGTCTAAATTCCCTGTTACAACATC 59.394 37.037 0.00 0.00 38.41 3.06
1694 1798 7.458397 AGTCTAAATTCCCTGTTACAACATCA 58.542 34.615 0.00 0.00 38.41 3.07
1697 1801 8.160765 TCTAAATTCCCTGTTACAACATCAGAA 58.839 33.333 0.00 0.68 38.41 3.02
1700 1804 2.749621 CCCTGTTACAACATCAGAAGGC 59.250 50.000 0.00 0.00 38.41 4.35
1737 1841 8.216423 AGCTGATTTCTTGGATCATATAAGTGT 58.784 33.333 0.00 0.00 33.39 3.55
1797 1901 9.315363 AGGGATAAGAATACAGACAGGTATTAG 57.685 37.037 0.00 0.00 42.43 1.73
1869 1978 9.575868 TGTTGTTACATGATTTTCCCTAACTAA 57.424 29.630 0.00 0.00 0.00 2.24
1926 2035 9.178758 ACATTATGATTTAAGTTCCTCTGGTTC 57.821 33.333 0.00 0.00 0.00 3.62
1995 2175 5.525378 CCAGTACCTATTCTCATCTTGTTGC 59.475 44.000 0.00 0.00 0.00 4.17
2080 2260 4.839668 TTTCAAATACACCTTTGACCCG 57.160 40.909 0.00 0.00 43.03 5.28
2215 2395 2.231215 ACAGCTAGCTGATTAAGGCG 57.769 50.000 43.42 19.72 46.30 5.52
2269 2701 4.529716 TTTATCCAATTCCCCCACCTAC 57.470 45.455 0.00 0.00 0.00 3.18
2362 2794 3.319031 AATTAGCATCTCCCCCTTTGG 57.681 47.619 0.00 0.00 0.00 3.28
2605 3056 0.170561 CATGCAAGGTTCTGCTGCTC 59.829 55.000 0.00 0.00 43.07 4.26
2734 3567 6.202379 GGATACGCTACTAAATTTGACCTTCC 59.798 42.308 0.00 0.00 0.00 3.46
2735 3568 4.901868 ACGCTACTAAATTTGACCTTCCA 58.098 39.130 0.00 0.00 0.00 3.53
3196 4045 8.606830 AGAAATATGTCTAAGAAAACCTCAGGT 58.393 33.333 0.00 0.00 37.65 4.00
3619 4641 5.695851 AAACTGACAACCACTGATGATTC 57.304 39.130 0.00 0.00 0.00 2.52
3682 4707 6.211584 AGAAAGATAGAACCAGCAACTACTGA 59.788 38.462 0.00 0.00 40.25 3.41
3689 4714 3.866651 ACCAGCAACTACTGATGATCAC 58.133 45.455 0.00 0.00 44.60 3.06
3870 4895 2.375509 CCAAGGGGTAGACCAAGAAAGT 59.624 50.000 0.21 0.00 42.91 2.66
3873 4898 5.246307 CAAGGGGTAGACCAAGAAAGTTAG 58.754 45.833 0.21 0.00 42.91 2.34
3875 4900 4.778427 AGGGGTAGACCAAGAAAGTTAGAG 59.222 45.833 0.21 0.00 42.91 2.43
4254 6224 2.181021 GGCGTGTACGACCTCCTG 59.819 66.667 8.82 0.00 42.67 3.86
4525 6495 2.939103 CTCCTTTTGAAGATAGTGCCCG 59.061 50.000 0.00 0.00 0.00 6.13
4532 6502 3.506398 TGAAGATAGTGCCCGGATGATA 58.494 45.455 0.73 0.00 0.00 2.15
4654 6624 1.322442 GGCATTCATCTACCAAGGGC 58.678 55.000 0.00 0.00 0.00 5.19
5288 14317 0.811616 AGGTGATGCGCCGAGAATTC 60.812 55.000 4.18 0.00 39.30 2.17
5899 17699 8.384607 AGTCAGTACAATTTCTTTTCTTCTCC 57.615 34.615 0.00 0.00 0.00 3.71
5954 17756 3.482786 CACAAGCGAATTAACTGCACTC 58.517 45.455 0.00 0.00 0.00 3.51
6220 20449 3.963383 AGTAAACAAAACCTGCAGACG 57.037 42.857 17.39 1.02 0.00 4.18
6244 20473 5.643777 GCTAATGTTACTCAGCTTCCTTCAA 59.356 40.000 0.00 0.00 0.00 2.69
6247 20476 9.553064 CTAATGTTACTCAGCTTCCTTCAATAT 57.447 33.333 0.00 0.00 0.00 1.28
6523 20843 8.649973 ACGTAAATGATTCTCCATTAACTCTC 57.350 34.615 0.00 0.00 35.86 3.20
6583 20906 2.876079 GCCCTGCTGTAGCTTGTACTTT 60.876 50.000 5.38 0.00 42.66 2.66
6609 20937 7.827236 TGAACTCTTCTACCTTTTCAGTGAAAA 59.173 33.333 25.48 25.48 38.90 2.29
6677 21005 7.831193 AGAACCATGCCTAATCATATATTGACC 59.169 37.037 0.00 0.00 37.11 4.02
6692 21020 8.618677 CATATATTGACCATGATTAGGCATGAC 58.381 37.037 0.00 0.00 46.64 3.06
6693 21021 4.508551 TTGACCATGATTAGGCATGACT 57.491 40.909 6.20 6.20 46.64 3.41
6696 21024 6.191657 TGACCATGATTAGGCATGACTAAT 57.808 37.500 30.04 30.04 46.64 1.73
6698 21026 5.319453 ACCATGATTAGGCATGACTAATGG 58.681 41.667 33.70 30.16 46.64 3.16
6789 21861 9.783256 GTGTTACATTCTTTATTATTGACCCAC 57.217 33.333 0.00 0.00 0.00 4.61
6796 21868 9.762381 ATTCTTTATTATTGACCCACCTAACAA 57.238 29.630 0.00 0.00 0.00 2.83
6936 22011 5.959583 AATTTTACCTTGGTGTTTTCCCA 57.040 34.783 2.03 0.00 0.00 4.37
7075 22188 5.107104 TGTCAAAACTGCTGCGTCTATAAAG 60.107 40.000 0.00 0.00 0.00 1.85
7076 22189 4.091424 CAAAACTGCTGCGTCTATAAAGC 58.909 43.478 0.00 0.00 36.18 3.51
7077 22190 1.560923 ACTGCTGCGTCTATAAAGCG 58.439 50.000 0.00 0.00 38.53 4.68
7078 22191 0.855349 CTGCTGCGTCTATAAAGCGG 59.145 55.000 0.00 0.00 41.20 5.52
7079 22192 0.174845 TGCTGCGTCTATAAAGCGGT 59.825 50.000 0.00 0.00 40.47 5.68
7080 22193 1.406180 TGCTGCGTCTATAAAGCGGTA 59.594 47.619 0.00 0.00 40.47 4.02
7081 22194 2.052157 GCTGCGTCTATAAAGCGGTAG 58.948 52.381 0.00 0.00 40.47 3.18
7082 22195 2.662700 CTGCGTCTATAAAGCGGTAGG 58.337 52.381 0.00 0.00 34.42 3.18
7083 22196 1.269413 TGCGTCTATAAAGCGGTAGGC 60.269 52.381 0.00 0.00 44.05 3.93
7093 22206 3.061093 GCGGTAGGCTGGTAGTTTC 57.939 57.895 0.00 0.00 39.11 2.78
7094 22207 0.248289 GCGGTAGGCTGGTAGTTTCA 59.752 55.000 0.00 0.00 39.11 2.69
7095 22208 1.338389 GCGGTAGGCTGGTAGTTTCAA 60.338 52.381 0.00 0.00 39.11 2.69
7096 22209 2.344025 CGGTAGGCTGGTAGTTTCAAC 58.656 52.381 0.00 0.00 0.00 3.18
7097 22210 2.028385 CGGTAGGCTGGTAGTTTCAACT 60.028 50.000 0.00 0.00 42.91 3.16
7098 22211 3.556423 CGGTAGGCTGGTAGTTTCAACTT 60.556 47.826 0.00 0.00 40.37 2.66
7099 22212 4.395625 GGTAGGCTGGTAGTTTCAACTTT 58.604 43.478 0.00 0.00 40.37 2.66
7100 22213 4.825634 GGTAGGCTGGTAGTTTCAACTTTT 59.174 41.667 0.00 0.00 40.37 2.27
7101 22214 5.048921 GGTAGGCTGGTAGTTTCAACTTTTC 60.049 44.000 0.00 0.00 40.37 2.29
7102 22215 4.532834 AGGCTGGTAGTTTCAACTTTTCA 58.467 39.130 0.00 0.00 40.37 2.69
7103 22216 4.580580 AGGCTGGTAGTTTCAACTTTTCAG 59.419 41.667 0.00 5.22 40.37 3.02
7104 22217 4.261614 GGCTGGTAGTTTCAACTTTTCAGG 60.262 45.833 0.00 0.00 40.37 3.86
7105 22218 4.338400 GCTGGTAGTTTCAACTTTTCAGGT 59.662 41.667 0.00 0.00 40.37 4.00
7106 22219 5.529800 GCTGGTAGTTTCAACTTTTCAGGTA 59.470 40.000 0.00 0.00 40.37 3.08
7107 22220 6.206829 GCTGGTAGTTTCAACTTTTCAGGTAT 59.793 38.462 0.00 0.00 40.37 2.73
7108 22221 7.389607 GCTGGTAGTTTCAACTTTTCAGGTATA 59.610 37.037 0.00 0.00 40.37 1.47
7109 22222 9.449719 CTGGTAGTTTCAACTTTTCAGGTATAT 57.550 33.333 0.00 0.00 40.37 0.86
7131 22244 2.795231 ACCCTGAGGAACATGACATG 57.205 50.000 14.02 14.02 36.73 3.21
7195 22437 0.543749 ATAGGACTCAGGTGGCTTGC 59.456 55.000 0.00 0.00 0.00 4.01
7227 22469 9.618890 TTGGTTGGAATTTAATTGACATTGAAA 57.381 25.926 0.00 0.00 0.00 2.69
7293 22542 4.591321 TTTGTCCATGATTAGGCTTCCT 57.409 40.909 0.00 0.00 37.71 3.36
7442 22704 8.248945 GTCTACTAGGTTAACAATGCTAACTGA 58.751 37.037 8.10 0.00 31.26 3.41
7722 22984 2.588720 TCCTAGTAAGAAGCCCTGGGTA 59.411 50.000 15.56 0.00 0.00 3.69
7735 22997 3.520721 GCCCTGGGTAGTACCTTTTCTTA 59.479 47.826 18.85 0.00 38.64 2.10
8008 23501 0.973632 ACTGAAGCACATACGGGTGA 59.026 50.000 8.11 0.00 41.32 4.02
8021 23514 5.820947 ACATACGGGTGAAATGTTATCTTCC 59.179 40.000 0.00 0.00 29.68 3.46
8381 23892 4.030134 AGATGTAGATCAAACGGACGAC 57.970 45.455 2.30 0.00 0.00 4.34
8385 23896 2.743636 AGATCAAACGGACGACATGT 57.256 45.000 0.00 0.00 0.00 3.21
8448 23959 7.997773 AGTAAAGTAAAACCCTCTCCATTTC 57.002 36.000 0.00 0.00 0.00 2.17
8486 23997 2.858622 GCTTACTGCCTGACATGCA 58.141 52.632 5.26 5.26 37.17 3.96
8629 24153 1.923356 ACGGCCCAGTTGATGAAAAT 58.077 45.000 0.00 0.00 0.00 1.82
8636 24160 5.422145 GCCCAGTTGATGAAAATGCTAAAT 58.578 37.500 0.00 0.00 32.44 1.40
8781 24305 7.609375 AGGATCTAAGGGACAGGCATATATAT 58.391 38.462 0.00 0.00 0.00 0.86
8867 24394 4.613622 GCAGCAATATATGGTAGGTTTGCG 60.614 45.833 0.00 0.00 43.07 4.85
8871 24427 5.334105 GCAATATATGGTAGGTTTGCGTGAG 60.334 44.000 0.00 0.00 31.37 3.51
8966 24522 3.317406 TGGAGCTTCATATCTTGGGCTA 58.683 45.455 0.00 0.00 35.85 3.93
9010 24566 2.827921 TGAGAAGTATCAGCTCAGCACA 59.172 45.455 0.00 0.00 34.02 4.57
9011 24567 3.259123 TGAGAAGTATCAGCTCAGCACAA 59.741 43.478 0.00 0.00 34.02 3.33
9012 24568 4.081254 TGAGAAGTATCAGCTCAGCACAAT 60.081 41.667 0.00 0.00 34.02 2.71
9052 24608 8.512138 GTTTTTCTTAGGCTGTAACATGTGTAT 58.488 33.333 0.00 0.00 0.00 2.29
9065 24621 9.930693 TGTAACATGTGTATATGTACTGTTGAA 57.069 29.630 0.00 2.78 40.24 2.69
9082 24638 5.904941 TGTTGAAGCAATCAGACAAATTGT 58.095 33.333 0.00 0.00 39.77 2.71
9085 24641 4.038282 TGAAGCAATCAGACAAATTGTGCT 59.962 37.500 2.20 1.72 42.39 4.40
9210 24772 5.934402 TTCTTAAAGGGCTGGACTAGTAG 57.066 43.478 0.00 0.00 0.00 2.57
9228 24790 7.560368 ACTAGTAGTCCCATCTTCTCAAAATG 58.440 38.462 0.00 0.00 0.00 2.32
9241 24803 8.908786 TCTTCTCAAAATGTGACTTGTATTCT 57.091 30.769 0.00 0.00 31.13 2.40
9245 24807 8.724229 TCTCAAAATGTGACTTGTATTCTCATG 58.276 33.333 0.00 0.00 29.76 3.07
9375 24937 5.632034 AAAGTACTCCCTCCATTCCATAC 57.368 43.478 0.00 0.00 0.00 2.39
9383 24945 4.164221 TCCCTCCATTCCATACTTCTTGTC 59.836 45.833 0.00 0.00 0.00 3.18
9423 24985 8.211116 TGAACTAAAACCACGACAAGAATTAA 57.789 30.769 0.00 0.00 0.00 1.40
9424 24986 8.675504 TGAACTAAAACCACGACAAGAATTAAA 58.324 29.630 0.00 0.00 0.00 1.52
9425 24987 8.845942 AACTAAAACCACGACAAGAATTAAAC 57.154 30.769 0.00 0.00 0.00 2.01
9427 24989 8.126700 ACTAAAACCACGACAAGAATTAAACAG 58.873 33.333 0.00 0.00 0.00 3.16
9428 24990 6.687081 AAACCACGACAAGAATTAAACAGA 57.313 33.333 0.00 0.00 0.00 3.41
9429 24991 5.924475 ACCACGACAAGAATTAAACAGAG 57.076 39.130 0.00 0.00 0.00 3.35
9432 24994 5.238650 CCACGACAAGAATTAAACAGAGGTT 59.761 40.000 0.00 0.00 39.43 3.50
9434 24996 5.820947 ACGACAAGAATTAAACAGAGGTTGT 59.179 36.000 0.00 0.00 43.45 3.32
9435 24997 6.987992 ACGACAAGAATTAAACAGAGGTTGTA 59.012 34.615 0.00 0.00 39.73 2.41
9436 24998 7.170998 ACGACAAGAATTAAACAGAGGTTGTAG 59.829 37.037 0.00 0.00 39.73 2.74
9453 25018 5.009210 GGTTGTAGGTATGCAAGAAAACACA 59.991 40.000 0.00 0.00 31.17 3.72
9459 25027 6.392354 AGGTATGCAAGAAAACACATTGATG 58.608 36.000 0.00 0.00 0.00 3.07
9461 25029 6.646240 GGTATGCAAGAAAACACATTGATGTT 59.354 34.615 0.00 0.00 44.76 2.71
9527 25095 8.340443 GTGGTTGAAGTTTTAAGACGTTATTCT 58.660 33.333 0.00 0.00 0.00 2.40
9581 25149 8.623310 TGACCGCATGTATGTATAATAATACG 57.377 34.615 0.00 0.00 40.84 3.06
9612 25180 8.248945 ACATTTTGAGAAAGATGGAATGCTTAG 58.751 33.333 0.00 0.00 0.00 2.18
9625 25193 7.373617 TGGAATGCTTAGTAGATATTGGACA 57.626 36.000 0.00 0.00 0.00 4.02
9657 25225 5.153950 GACTCCAGTCAAATCCAGTAGTT 57.846 43.478 1.61 0.00 44.18 2.24
9727 25295 3.649073 TCGAAGCAATTCGAGAACAAGA 58.351 40.909 8.86 0.00 46.98 3.02
9728 25296 3.675225 TCGAAGCAATTCGAGAACAAGAG 59.325 43.478 8.86 0.00 46.98 2.85
9729 25297 3.675225 CGAAGCAATTCGAGAACAAGAGA 59.325 43.478 4.44 0.00 46.52 3.10
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.012673 CCGTGTTCTAGCTAGTACCGT 58.987 52.381 23.09 0.00 0.00 4.83
2 3 1.066757 GCCCGTGTTCTAGCTAGTACC 59.933 57.143 23.09 15.07 0.00 3.34
3 4 1.747355 TGCCCGTGTTCTAGCTAGTAC 59.253 52.381 20.30 20.30 0.00 2.73
5 6 0.531200 GTGCCCGTGTTCTAGCTAGT 59.469 55.000 20.10 0.00 0.00 2.57
6 7 0.179108 GGTGCCCGTGTTCTAGCTAG 60.179 60.000 15.01 15.01 0.00 3.42
7 8 1.610554 GGGTGCCCGTGTTCTAGCTA 61.611 60.000 0.00 0.00 0.00 3.32
8 9 2.663196 GGTGCCCGTGTTCTAGCT 59.337 61.111 0.00 0.00 0.00 3.32
9 10 2.436115 GGGTGCCCGTGTTCTAGC 60.436 66.667 0.00 0.00 0.00 3.42
10 11 2.267961 GGGGTGCCCGTGTTCTAG 59.732 66.667 0.54 0.00 36.85 2.43
28 29 4.778143 ACGTCGCCCCATTGGAGC 62.778 66.667 3.62 0.59 35.39 4.70
29 30 2.819595 CACGTCGCCCCATTGGAG 60.820 66.667 3.62 0.00 35.39 3.86
30 31 4.402528 CCACGTCGCCCCATTGGA 62.403 66.667 3.62 0.00 35.39 3.53
31 32 4.402528 TCCACGTCGCCCCATTGG 62.403 66.667 0.00 0.00 37.09 3.16
32 33 3.124921 GTCCACGTCGCCCCATTG 61.125 66.667 0.00 0.00 0.00 2.82
33 34 4.404098 GGTCCACGTCGCCCCATT 62.404 66.667 0.00 0.00 0.00 3.16
37 38 4.736896 GACAGGTCCACGTCGCCC 62.737 72.222 0.00 0.00 0.00 6.13
41 42 1.728426 CGTTCGACAGGTCCACGTC 60.728 63.158 9.50 0.00 31.71 4.34
42 43 2.333938 CGTTCGACAGGTCCACGT 59.666 61.111 9.50 0.00 31.71 4.49
43 44 2.430244 CCGTTCGACAGGTCCACG 60.430 66.667 10.36 10.36 34.42 4.94
44 45 2.048503 CCCGTTCGACAGGTCCAC 60.049 66.667 4.83 0.00 0.00 4.02
45 46 2.522436 ACCCGTTCGACAGGTCCA 60.522 61.111 4.83 0.00 0.00 4.02
46 47 2.048503 CACCCGTTCGACAGGTCC 60.049 66.667 4.83 0.00 0.00 4.46
47 48 2.048503 CCACCCGTTCGACAGGTC 60.049 66.667 4.83 0.00 0.00 3.85
48 49 4.309950 GCCACCCGTTCGACAGGT 62.310 66.667 4.83 0.00 0.00 4.00
50 51 3.530910 AAGGCCACCCGTTCGACAG 62.531 63.158 5.01 0.00 35.76 3.51
51 52 3.109592 AAAGGCCACCCGTTCGACA 62.110 57.895 5.01 0.00 35.76 4.35
52 53 2.281276 AAAGGCCACCCGTTCGAC 60.281 61.111 5.01 0.00 35.76 4.20
53 54 2.281208 CAAAGGCCACCCGTTCGA 60.281 61.111 5.01 0.00 35.76 3.71
54 55 3.361977 CCAAAGGCCACCCGTTCG 61.362 66.667 5.01 0.00 35.76 3.95
55 56 2.989253 CCCAAAGGCCACCCGTTC 60.989 66.667 5.01 0.00 35.76 3.95
56 57 3.503839 TCCCAAAGGCCACCCGTT 61.504 61.111 5.01 0.00 35.76 4.44
57 58 3.966543 CTCCCAAAGGCCACCCGT 61.967 66.667 5.01 0.00 35.76 5.28
58 59 2.893682 GATCTCCCAAAGGCCACCCG 62.894 65.000 5.01 0.00 35.76 5.28
59 60 1.076705 GATCTCCCAAAGGCCACCC 60.077 63.158 5.01 0.00 0.00 4.61
60 61 0.039618 TTGATCTCCCAAAGGCCACC 59.960 55.000 5.01 0.00 0.00 4.61
61 62 1.177401 GTTGATCTCCCAAAGGCCAC 58.823 55.000 5.01 0.00 0.00 5.01
62 63 0.322456 CGTTGATCTCCCAAAGGCCA 60.322 55.000 5.01 0.00 0.00 5.36
63 64 0.322546 ACGTTGATCTCCCAAAGGCC 60.323 55.000 0.00 0.00 31.37 5.19
64 65 1.534729 AACGTTGATCTCCCAAAGGC 58.465 50.000 0.00 0.00 31.37 4.35
65 66 4.584327 AAAAACGTTGATCTCCCAAAGG 57.416 40.909 0.00 0.00 31.37 3.11
117 118 3.641436 TCATCCGACCATAGTGCATAAGT 59.359 43.478 0.00 0.00 0.00 2.24
119 120 3.990092 GTCATCCGACCATAGTGCATAA 58.010 45.455 0.00 0.00 36.02 1.90
149 150 2.346766 TGCATGTCGGCTCCATAATT 57.653 45.000 0.00 0.00 34.04 1.40
157 158 1.746615 GGTGTGATGCATGTCGGCT 60.747 57.895 2.46 0.00 34.04 5.52
160 161 3.132925 TGATATGGTGTGATGCATGTCG 58.867 45.455 2.46 0.00 0.00 4.35
274 281 8.091449 AGAAACAGAACTATAACTCTGAGTTGG 58.909 37.037 28.46 20.30 41.38 3.77
287 294 8.924511 TTCAAAAGGATGAGAAACAGAACTAT 57.075 30.769 0.00 0.00 0.00 2.12
291 298 6.925165 GCAATTCAAAAGGATGAGAAACAGAA 59.075 34.615 0.00 0.00 0.00 3.02
317 344 5.458362 CCAGAGAGAGAGGGGCTAATAACTA 60.458 48.000 0.00 0.00 0.00 2.24
329 356 2.163412 CACTTCGTTCCAGAGAGAGAGG 59.837 54.545 0.00 0.00 0.00 3.69
338 365 0.588252 CAACCTGCACTTCGTTCCAG 59.412 55.000 0.00 0.00 0.00 3.86
339 366 0.179234 TCAACCTGCACTTCGTTCCA 59.821 50.000 0.00 0.00 0.00 3.53
344 371 0.445436 GCTCATCAACCTGCACTTCG 59.555 55.000 0.00 0.00 0.00 3.79
362 389 1.467734 CTCTCTGTCCAATGTTGCAGC 59.532 52.381 0.00 0.00 0.00 5.25
379 406 2.812218 TAGAGCTGCTGCACCCCTCT 62.812 60.000 18.42 19.87 42.74 3.69
397 424 1.073548 GTTGTTGGCCCGGGTTCTA 59.926 57.895 24.63 9.21 0.00 2.10
398 425 2.203437 GTTGTTGGCCCGGGTTCT 60.203 61.111 24.63 0.00 0.00 3.01
399 426 2.519780 TGTTGTTGGCCCGGGTTC 60.520 61.111 24.63 15.66 0.00 3.62
400 427 2.520741 CTGTTGTTGGCCCGGGTT 60.521 61.111 24.63 0.00 0.00 4.11
478 508 1.689233 CCCTTGGGTCCCTCGATCA 60.689 63.158 10.00 0.00 0.00 2.92
481 511 1.612442 CTTCCCTTGGGTCCCTCGA 60.612 63.158 10.00 0.00 0.00 4.04
488 518 2.203938 TCGCTCCTTCCCTTGGGT 60.204 61.111 5.51 0.00 0.00 4.51
535 565 5.734720 TCTTCAGATAAAAAGCCGAGACAT 58.265 37.500 0.00 0.00 0.00 3.06
543 573 7.522374 AGTGTCGAATTCTTCAGATAAAAAGC 58.478 34.615 3.52 0.00 0.00 3.51
783 821 1.075600 GGCAGGAGAGGAGCTAGGT 60.076 63.158 0.00 0.00 0.00 3.08
784 822 1.836604 GGGCAGGAGAGGAGCTAGG 60.837 68.421 0.00 0.00 0.00 3.02
785 823 2.199652 CGGGCAGGAGAGGAGCTAG 61.200 68.421 0.00 0.00 0.00 3.42
786 824 2.123683 CGGGCAGGAGAGGAGCTA 60.124 66.667 0.00 0.00 0.00 3.32
892 951 2.155279 GGAAGAAGCCAAGAACTGTCC 58.845 52.381 0.00 0.00 0.00 4.02
905 964 7.330900 ACATTCATATGCAAGAAGGAAGAAG 57.669 36.000 15.35 4.95 35.03 2.85
906 965 7.394077 TCAACATTCATATGCAAGAAGGAAGAA 59.606 33.333 15.35 2.54 35.03 2.52
907 966 6.885918 TCAACATTCATATGCAAGAAGGAAGA 59.114 34.615 15.35 10.49 35.03 2.87
908 967 7.092137 TCAACATTCATATGCAAGAAGGAAG 57.908 36.000 15.35 8.92 35.03 3.46
909 968 7.649533 ATCAACATTCATATGCAAGAAGGAA 57.350 32.000 15.35 7.39 35.03 3.36
910 969 7.485810 CAATCAACATTCATATGCAAGAAGGA 58.514 34.615 15.35 7.00 35.03 3.36
911 970 6.200286 GCAATCAACATTCATATGCAAGAAGG 59.800 38.462 0.00 9.16 35.03 3.46
919 978 7.591426 CACAGATCAGCAATCAACATTCATATG 59.409 37.037 0.00 0.00 36.79 1.78
921 980 6.824704 TCACAGATCAGCAATCAACATTCATA 59.175 34.615 0.00 0.00 36.79 2.15
1193 1253 2.959030 GGAGCAAAGGAGAGTGGTTTTT 59.041 45.455 0.00 0.00 0.00 1.94
1227 1299 7.186128 CCAAAACTGAAACTTGCCAATTTTAC 58.814 34.615 0.00 0.00 0.00 2.01
1263 1335 6.968904 CCATGGATTACTCAAAAGTTCATTCG 59.031 38.462 5.56 0.00 36.92 3.34
1269 1341 7.781324 ATGTTCCATGGATTACTCAAAAGTT 57.219 32.000 17.06 0.00 36.92 2.66
1305 1377 9.927081 ACTCCATACTTTCCTATTTTCATTCAT 57.073 29.630 0.00 0.00 0.00 2.57
1361 1436 5.882557 AGCATACCTAATTGGAGAACACAAG 59.117 40.000 0.00 0.00 39.71 3.16
1439 1531 4.021192 GTCTGGCAGAATGGAATCCAAAAA 60.021 41.667 20.62 0.00 36.95 1.94
1444 1536 2.425143 TGTCTGGCAGAATGGAATCC 57.575 50.000 20.62 4.58 35.86 3.01
1445 1537 3.066342 CACATGTCTGGCAGAATGGAATC 59.934 47.826 27.63 14.81 35.86 2.52
1446 1538 3.021695 CACATGTCTGGCAGAATGGAAT 58.978 45.455 27.63 14.27 35.86 3.01
1447 1539 2.040145 TCACATGTCTGGCAGAATGGAA 59.960 45.455 27.63 18.78 35.86 3.53
1448 1540 1.629861 TCACATGTCTGGCAGAATGGA 59.370 47.619 27.63 21.93 35.86 3.41
1449 1541 2.118313 TCACATGTCTGGCAGAATGG 57.882 50.000 27.63 19.70 35.86 3.16
1450 1542 3.312697 CAGATCACATGTCTGGCAGAATG 59.687 47.826 20.62 23.53 39.48 2.67
1451 1543 3.054582 ACAGATCACATGTCTGGCAGAAT 60.055 43.478 20.62 12.07 45.72 2.40
1452 1544 2.303890 ACAGATCACATGTCTGGCAGAA 59.696 45.455 20.62 10.19 45.72 3.02
1453 1545 1.904537 ACAGATCACATGTCTGGCAGA 59.095 47.619 14.43 14.43 45.72 4.26
1455 1547 2.038820 TCAACAGATCACATGTCTGGCA 59.961 45.455 15.27 0.00 45.72 4.92
1456 1548 2.703416 TCAACAGATCACATGTCTGGC 58.297 47.619 15.27 0.00 45.72 4.85
1457 1549 6.764560 TCATTATCAACAGATCACATGTCTGG 59.235 38.462 15.27 0.00 45.72 3.86
1480 1583 9.973661 TTCTCTGGGAAGATAACAAATTTATCA 57.026 29.630 6.75 0.00 34.66 2.15
1485 1588 7.413446 TCCATTCTCTGGGAAGATAACAAATT 58.587 34.615 0.00 0.00 45.98 1.82
1486 1589 6.973642 TCCATTCTCTGGGAAGATAACAAAT 58.026 36.000 0.00 0.00 45.98 2.32
1539 1642 1.532007 CCAGCGCCGTAAACAAAACTA 59.468 47.619 2.29 0.00 0.00 2.24
1643 1746 1.366111 TTAGCGCCGGCAATCAGTTC 61.366 55.000 28.98 4.10 43.41 3.01
1653 1756 0.373716 GACTCACAAATTAGCGCCGG 59.626 55.000 2.29 0.00 0.00 6.13
1654 1757 1.359848 AGACTCACAAATTAGCGCCG 58.640 50.000 2.29 0.00 0.00 6.46
1679 1783 2.749621 GCCTTCTGATGTTGTAACAGGG 59.250 50.000 3.66 0.00 43.04 4.45
1687 1791 2.996631 AGCCTAAGCCTTCTGATGTTG 58.003 47.619 0.00 0.00 41.25 3.33
1693 1797 3.376546 CAGCTAAAAGCCTAAGCCTTCTG 59.623 47.826 0.00 0.00 43.77 3.02
1694 1798 3.264450 TCAGCTAAAAGCCTAAGCCTTCT 59.736 43.478 0.00 0.00 43.77 2.85
1697 1801 3.941704 ATCAGCTAAAAGCCTAAGCCT 57.058 42.857 0.00 0.00 43.77 4.58
1700 1804 6.375455 TCCAAGAAATCAGCTAAAAGCCTAAG 59.625 38.462 0.00 0.00 43.77 2.18
1713 1817 9.551734 TCACACTTATATGATCCAAGAAATCAG 57.448 33.333 0.00 0.00 36.63 2.90
1737 1841 2.553602 GTGTGTGACCTGCATTGATTCA 59.446 45.455 0.00 0.00 0.00 2.57
1869 1978 7.913789 TCCACAACAATACTACCTTGAGTAAT 58.086 34.615 0.00 0.00 35.58 1.89
1995 2175 5.799213 ACTTCTGTAGAAATCCTTCACCAG 58.201 41.667 0.00 0.00 34.92 4.00
2112 2292 0.458669 TAGTTTCGGATGGGTCGCTC 59.541 55.000 0.00 0.00 0.00 5.03
2172 2352 0.035152 TGCGCTCAAACCTCATCCAT 60.035 50.000 9.73 0.00 0.00 3.41
2186 2366 0.678395 AGCTAGCTGTATCATGCGCT 59.322 50.000 18.57 0.00 36.56 5.92
2215 2395 3.766691 CCCCCTGCAGCAATGCAC 61.767 66.667 8.66 0.00 40.23 4.57
2240 2672 4.772624 GGGGGAATTGGATAAATAAGAGCC 59.227 45.833 0.00 0.00 0.00 4.70
2241 2673 5.243954 GTGGGGGAATTGGATAAATAAGAGC 59.756 44.000 0.00 0.00 0.00 4.09
2269 2701 1.079503 GGAAAGTGGCGTTAGAGCAG 58.920 55.000 0.00 0.00 39.27 4.24
2605 3056 8.796475 TCTCTTTTTATCAACAAATCTCCCAAG 58.204 33.333 0.00 0.00 0.00 3.61
2734 3567 8.807667 AAAAAGTGAAAGAGTGCAGAAATATG 57.192 30.769 0.00 0.00 0.00 1.78
2825 3659 8.339714 CAAAATGAAATCAGAACTGCAACAATT 58.660 29.630 0.00 0.00 0.00 2.32
2826 3660 7.496591 ACAAAATGAAATCAGAACTGCAACAAT 59.503 29.630 0.00 0.00 0.00 2.71
2827 3661 6.817641 ACAAAATGAAATCAGAACTGCAACAA 59.182 30.769 0.00 0.00 0.00 2.83
3027 3861 6.546428 TTTCTCCAGATAGTCTTACAAGGG 57.454 41.667 0.00 0.00 0.00 3.95
3196 4045 8.690203 TTTGAGAAAAGTACTTTGATGGATGA 57.310 30.769 21.22 2.22 32.36 2.92
3325 4286 5.241285 TGCAACAGATAGAAAATTGTGAGCA 59.759 36.000 0.00 0.00 34.88 4.26
3327 4288 6.906659 ACTGCAACAGATAGAAAATTGTGAG 58.093 36.000 0.78 0.00 35.18 3.51
3328 4289 6.882610 ACTGCAACAGATAGAAAATTGTGA 57.117 33.333 0.78 0.00 35.18 3.58
3331 4292 9.499585 CAAGATACTGCAACAGATAGAAAATTG 57.500 33.333 0.78 0.00 35.18 2.32
3332 4293 8.186821 GCAAGATACTGCAACAGATAGAAAATT 58.813 33.333 0.78 0.00 42.17 1.82
3619 4641 4.916983 TTTTTCAGACATGGTTCTGTGG 57.083 40.909 11.82 0.00 43.19 4.17
3682 4707 5.977635 TCATACTTGGTTCTTCGTGATCAT 58.022 37.500 0.00 0.00 0.00 2.45
3857 4882 4.322801 GCAGGCTCTAACTTTCTTGGTCTA 60.323 45.833 0.00 0.00 0.00 2.59
3870 4895 0.686789 TCAGCAGTTGCAGGCTCTAA 59.313 50.000 6.90 0.00 45.16 2.10
3873 4898 0.675837 TCATCAGCAGTTGCAGGCTC 60.676 55.000 6.90 0.00 45.16 4.70
3875 4900 0.815734 AATCATCAGCAGTTGCAGGC 59.184 50.000 6.90 0.00 45.16 4.85
4050 6020 3.992643 TGTAATTTGCATTGCACAAGCT 58.007 36.364 11.66 4.13 38.71 3.74
4121 6091 4.852138 CACTGAATGTGGTTGAAGAACTG 58.148 43.478 0.00 0.00 42.68 3.16
4254 6224 3.127548 TCATTCGGAGCAGATTTCTTTGC 59.872 43.478 0.00 0.00 40.57 3.68
4525 6495 8.506168 TGTATTTTCCACTTCAACTATCATCC 57.494 34.615 0.00 0.00 0.00 3.51
4532 6502 8.211629 ACTACTTCTGTATTTTCCACTTCAACT 58.788 33.333 0.00 0.00 0.00 3.16
4654 6624 4.201589 CGTTATGAGCTAAACACAAGACGG 60.202 45.833 0.00 0.00 32.06 4.79
5288 14317 6.457355 TGGAACATCAAAATCCAACAATGAG 58.543 36.000 0.00 0.00 40.19 2.90
5508 17207 5.930569 ACCAGAACAGACGGTTATTTAAGAC 59.069 40.000 0.00 0.00 40.63 3.01
5509 17208 6.105397 ACCAGAACAGACGGTTATTTAAGA 57.895 37.500 0.00 0.00 40.63 2.10
5510 17209 6.796705 AACCAGAACAGACGGTTATTTAAG 57.203 37.500 0.00 0.00 41.22 1.85
5511 17210 8.723311 CATTAACCAGAACAGACGGTTATTTAA 58.277 33.333 0.00 0.00 43.09 1.52
5513 17212 6.713450 ACATTAACCAGAACAGACGGTTATTT 59.287 34.615 0.00 0.00 43.09 1.40
5515 17214 5.801380 ACATTAACCAGAACAGACGGTTAT 58.199 37.500 0.00 0.00 43.09 1.89
5899 17699 7.475137 TCCTGGGTGAAATATTAACCAAAAG 57.525 36.000 17.63 12.60 35.56 2.27
5954 17756 6.618811 AGATGCATCTTTCTAAAAACTGCAG 58.381 36.000 23.75 13.48 39.45 4.41
6220 20449 5.178797 TGAAGGAAGCTGAGTAACATTAGC 58.821 41.667 0.00 0.00 36.45 3.09
6244 20473 7.097623 ACCTAGTCACTATCTCACTGGATAT 57.902 40.000 0.00 0.00 0.00 1.63
6247 20476 4.864483 ACCTAGTCACTATCTCACTGGA 57.136 45.455 0.00 0.00 0.00 3.86
6265 20524 7.994425 AAAAATGGAAAACAAGACAAAACCT 57.006 28.000 0.00 0.00 0.00 3.50
6295 20555 7.175119 GCATCTGAAGTTCCCTAGTTTTAACTT 59.825 37.037 0.00 0.00 43.06 2.66
6297 20557 6.430000 TGCATCTGAAGTTCCCTAGTTTTAAC 59.570 38.462 0.00 0.00 0.00 2.01
6298 20558 6.539173 TGCATCTGAAGTTCCCTAGTTTTAA 58.461 36.000 0.00 0.00 0.00 1.52
6519 20839 3.755378 ACCAATAGCAAAGCAACAGAGAG 59.245 43.478 0.00 0.00 0.00 3.20
6523 20843 2.029649 AGCACCAATAGCAAAGCAACAG 60.030 45.455 0.00 0.00 0.00 3.16
6583 20906 6.479972 TCACTGAAAAGGTAGAAGAGTTCA 57.520 37.500 0.00 0.00 0.00 3.18
6609 20937 4.462483 TCAAGAAGACACAAAACCTTTGCT 59.538 37.500 0.00 0.00 0.00 3.91
6677 21005 7.514784 TTTCCATTAGTCATGCCTAATCATG 57.485 36.000 6.04 0.00 43.84 3.07
6692 21020 7.004086 TGGGTAGATAAAGCCATTTCCATTAG 58.996 38.462 0.00 0.00 41.99 1.73
6693 21021 6.916909 TGGGTAGATAAAGCCATTTCCATTA 58.083 36.000 0.00 0.00 41.99 1.90
6696 21024 4.871871 TGGGTAGATAAAGCCATTTCCA 57.128 40.909 0.00 0.00 41.99 3.53
6796 21868 8.289939 AGACTTTATTCATCAGCAACAATCAT 57.710 30.769 0.00 0.00 0.00 2.45
6964 22039 7.933577 CGATGTTGATATAGGGCATAATGGTAT 59.066 37.037 0.00 0.00 0.00 2.73
7015 22090 1.431243 AGTCCCCAATTTACTTGCCCA 59.569 47.619 0.00 0.00 33.20 5.36
7075 22188 0.248289 TGAAACTACCAGCCTACCGC 59.752 55.000 0.00 0.00 37.98 5.68
7076 22189 2.028385 AGTTGAAACTACCAGCCTACCG 60.028 50.000 0.00 0.00 37.52 4.02
7077 22190 3.697619 AGTTGAAACTACCAGCCTACC 57.302 47.619 0.00 0.00 37.52 3.18
7078 22191 5.529800 TGAAAAGTTGAAACTACCAGCCTAC 59.470 40.000 0.00 0.00 38.57 3.18
7079 22192 5.686753 TGAAAAGTTGAAACTACCAGCCTA 58.313 37.500 0.00 0.00 38.57 3.93
7080 22193 4.532834 TGAAAAGTTGAAACTACCAGCCT 58.467 39.130 0.00 0.00 38.57 4.58
7081 22194 4.261614 CCTGAAAAGTTGAAACTACCAGCC 60.262 45.833 0.00 0.00 38.57 4.85
7082 22195 4.338400 ACCTGAAAAGTTGAAACTACCAGC 59.662 41.667 0.00 0.00 38.57 4.85
7083 22196 7.745620 ATACCTGAAAAGTTGAAACTACCAG 57.254 36.000 0.00 4.73 38.57 4.00
7089 22202 9.850628 GGGTTTATATACCTGAAAAGTTGAAAC 57.149 33.333 11.56 0.00 38.30 2.78
7090 22203 9.816787 AGGGTTTATATACCTGAAAAGTTGAAA 57.183 29.630 11.56 0.00 38.30 2.69
7102 22215 6.849697 TCATGTTCCTCAGGGTTTATATACCT 59.150 38.462 11.56 0.00 38.30 3.08
7103 22216 6.935208 GTCATGTTCCTCAGGGTTTATATACC 59.065 42.308 3.88 3.88 37.47 2.73
7104 22217 7.506114 TGTCATGTTCCTCAGGGTTTATATAC 58.494 38.462 0.00 0.00 0.00 1.47
7105 22218 7.684317 TGTCATGTTCCTCAGGGTTTATATA 57.316 36.000 0.00 0.00 0.00 0.86
7106 22219 6.575244 TGTCATGTTCCTCAGGGTTTATAT 57.425 37.500 0.00 0.00 0.00 0.86
7107 22220 6.356556 CATGTCATGTTCCTCAGGGTTTATA 58.643 40.000 4.53 0.00 0.00 0.98
7108 22221 4.927267 TGTCATGTTCCTCAGGGTTTAT 57.073 40.909 0.00 0.00 0.00 1.40
7109 22222 4.567537 CCATGTCATGTTCCTCAGGGTTTA 60.568 45.833 11.84 0.00 0.00 2.01
7110 22223 3.424703 CATGTCATGTTCCTCAGGGTTT 58.575 45.455 4.53 0.00 0.00 3.27
7111 22224 2.291153 CCATGTCATGTTCCTCAGGGTT 60.291 50.000 11.84 0.00 0.00 4.11
7112 22225 1.283029 CCATGTCATGTTCCTCAGGGT 59.717 52.381 11.84 0.00 0.00 4.34
7171 22413 1.834263 GCCACCTGAGTCCTATGTCTT 59.166 52.381 0.00 0.00 0.00 3.01
7195 22437 8.834465 TGTCAATTAAATTCCAACCAAACATTG 58.166 29.630 0.00 0.00 0.00 2.82
7227 22469 7.865706 ATACGAAAGTTTTGATTAGCCATCT 57.134 32.000 9.93 0.00 46.40 2.90
7293 22542 9.707957 AATCCAGACCATACCATTATAAACAAA 57.292 29.630 0.00 0.00 0.00 2.83
7329 22586 7.113658 TCAACCCATAGAGATTCTACAACTC 57.886 40.000 0.00 0.00 30.79 3.01
7337 22594 8.261522 AGTAGAACTTTCAACCCATAGAGATTC 58.738 37.037 0.00 0.00 0.00 2.52
7430 22692 7.255491 TGAAAGATAGCATCAGTTAGCATTG 57.745 36.000 0.00 0.00 0.00 2.82
7442 22704 4.411540 ACCTCTGGACATGAAAGATAGCAT 59.588 41.667 0.00 0.00 0.00 3.79
7722 22984 6.985059 GACACAACAGTCTAAGAAAAGGTACT 59.015 38.462 0.00 0.00 36.27 2.73
7735 22997 6.757897 TTCATTTCTTTGACACAACAGTCT 57.242 33.333 0.00 0.00 39.27 3.24
7873 23356 9.461312 AGGAGAGCATTGTTAAAATTATACACA 57.539 29.630 0.00 0.00 0.00 3.72
8021 23514 9.991906 AATTATTGCCAATTCAAGAATCATAGG 57.008 29.630 0.00 0.00 37.02 2.57
8381 23892 3.056107 TCCGTAGTTCCTCTTTCCACATG 60.056 47.826 0.00 0.00 0.00 3.21
8385 23896 2.824341 GAGTCCGTAGTTCCTCTTTCCA 59.176 50.000 0.00 0.00 0.00 3.53
8448 23959 2.603892 GCCAATGATATGACTTGCAGCG 60.604 50.000 0.00 0.00 0.00 5.18
8486 23997 2.934364 GCTCTGCAGTGTAGTTCAGCAT 60.934 50.000 14.67 0.00 34.35 3.79
8629 24153 3.693085 AGACCTCGAAGTCGTATTTAGCA 59.307 43.478 8.48 0.00 41.83 3.49
8636 24160 1.457346 GGGAAGACCTCGAAGTCGTA 58.543 55.000 8.48 0.00 41.83 3.43
8771 24295 5.097742 TGCGGCCCATATATATATATGCC 57.902 43.478 27.24 24.88 42.53 4.40
8781 24305 0.179004 CCTGGTTTGCGGCCCATATA 60.179 55.000 0.00 0.00 0.00 0.86
8784 24311 3.944250 CTCCTGGTTTGCGGCCCAT 62.944 63.158 0.00 0.00 0.00 4.00
8867 24394 3.882888 AGATACACAGCTAGCTCTCTCAC 59.117 47.826 16.15 5.84 0.00 3.51
8871 24427 4.277174 TGCTAAGATACACAGCTAGCTCTC 59.723 45.833 16.15 6.94 36.26 3.20
8966 24522 7.224297 TCACAAGTAGCTCCTATTGTTTTCTT 58.776 34.615 0.00 0.00 33.76 2.52
9010 24566 6.152932 AGAAAAACATCAGTCAGTTGCATT 57.847 33.333 0.00 0.00 0.00 3.56
9011 24567 5.779529 AGAAAAACATCAGTCAGTTGCAT 57.220 34.783 0.00 0.00 0.00 3.96
9012 24568 5.581126 AAGAAAAACATCAGTCAGTTGCA 57.419 34.783 0.00 0.00 0.00 4.08
9052 24608 6.463360 TGTCTGATTGCTTCAACAGTACATA 58.537 36.000 0.00 0.00 32.78 2.29
9065 24621 3.570975 TCAGCACAATTTGTCTGATTGCT 59.429 39.130 19.11 12.94 37.89 3.91
9150 24712 5.503662 TCGACCAATCATGATTTCCATTG 57.496 39.130 18.41 7.78 31.94 2.82
9210 24772 5.302357 GTCACATTTTGAGAAGATGGGAC 57.698 43.478 6.50 6.50 44.18 4.46
9228 24790 9.683069 AAATTTTGACATGAGAATACAAGTCAC 57.317 29.630 0.00 0.00 44.26 3.67
9241 24803 9.645059 TCAAACACAACTTAAATTTTGACATGA 57.355 25.926 0.00 0.00 30.11 3.07
9323 24885 9.817809 GTCATGTCTTTTTACTCTGGACATATA 57.182 33.333 6.57 0.00 43.09 0.86
9407 24969 4.755123 CCTCTGTTTAATTCTTGTCGTGGT 59.245 41.667 0.00 0.00 0.00 4.16
9423 24985 4.286032 TCTTGCATACCTACAACCTCTGTT 59.714 41.667 0.00 0.00 39.64 3.16
9424 24986 3.838317 TCTTGCATACCTACAACCTCTGT 59.162 43.478 0.00 0.00 42.47 3.41
9425 24987 4.471904 TCTTGCATACCTACAACCTCTG 57.528 45.455 0.00 0.00 0.00 3.35
9427 24989 5.472137 TGTTTTCTTGCATACCTACAACCTC 59.528 40.000 0.00 0.00 0.00 3.85
9428 24990 5.240844 GTGTTTTCTTGCATACCTACAACCT 59.759 40.000 0.00 0.00 0.00 3.50
9429 24991 5.009210 TGTGTTTTCTTGCATACCTACAACC 59.991 40.000 0.00 0.00 0.00 3.77
9432 24994 6.488344 TCAATGTGTTTTCTTGCATACCTACA 59.512 34.615 0.00 0.00 0.00 2.74
9434 24996 7.176515 ACATCAATGTGTTTTCTTGCATACCTA 59.823 33.333 0.00 0.00 40.03 3.08
9435 24997 6.015180 ACATCAATGTGTTTTCTTGCATACCT 60.015 34.615 0.00 0.00 40.03 3.08
9436 24998 6.158598 ACATCAATGTGTTTTCTTGCATACC 58.841 36.000 0.00 0.00 40.03 2.73
9489 25057 7.730364 AAACTTCAACCACTAATACTCACAG 57.270 36.000 0.00 0.00 0.00 3.66
9581 25149 9.947669 CATTCCATCTTTCTCAAAATGTAGATC 57.052 33.333 0.00 0.00 0.00 2.75
9612 25180 7.288158 AGTCTAGAAACCCTGTCCAATATCTAC 59.712 40.741 0.00 0.00 0.00 2.59
9625 25193 3.544698 TGACTGGAGTCTAGAAACCCT 57.455 47.619 10.93 0.00 44.99 4.34
9657 25225 4.588951 TGTTTGGCCATATTGTTTGGTACA 59.411 37.500 6.09 0.00 36.57 2.90
9697 25265 2.019984 GAATTGCTTCGAATGGCCTCT 58.980 47.619 3.32 0.00 0.00 3.69
9709 25277 4.887748 TCTCTCTTGTTCTCGAATTGCTT 58.112 39.130 0.00 0.00 0.00 3.91
9720 25288 3.644884 TCGAACACCTCTCTCTTGTTC 57.355 47.619 4.02 4.02 43.75 3.18
9725 25293 2.564947 AGCAAATCGAACACCTCTCTCT 59.435 45.455 0.00 0.00 0.00 3.10
9726 25294 2.926838 GAGCAAATCGAACACCTCTCTC 59.073 50.000 0.00 0.00 0.00 3.20
9727 25295 2.354203 GGAGCAAATCGAACACCTCTCT 60.354 50.000 0.00 0.00 0.00 3.10
9728 25296 2.003301 GGAGCAAATCGAACACCTCTC 58.997 52.381 0.00 0.00 0.00 3.20
9729 25297 1.625818 AGGAGCAAATCGAACACCTCT 59.374 47.619 0.00 0.00 0.00 3.69


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

AutoCloner maintained by Alex Coulton.