Multiple sequence alignment - TraesCS5A01G470700

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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 TraesCS5A01G470700 chr5A 100.000 2893 0 0 1 2893 647375879 647372987 0.000000e+00 5343.0
1 TraesCS5A01G470700 chr5A 87.273 55 6 1 470 524 651571689 651571636 8.660000e-06 62.1
2 TraesCS5A01G470700 chr5D 92.556 2015 84 28 919 2893 520138496 520136508 0.000000e+00 2830.0
3 TraesCS5A01G470700 chr5D 90.159 315 13 8 619 917 520138845 520138533 7.510000e-106 394.0
4 TraesCS5A01G470700 chr5D 100.000 39 0 0 914 952 411166185 411166147 4.000000e-09 73.1
5 TraesCS5A01G470700 chr6D 79.810 1897 213 87 960 2780 473055878 473057680 0.000000e+00 1225.0
6 TraesCS5A01G470700 chr6D 88.655 714 51 14 1137 1838 472997870 472998565 0.000000e+00 843.0
7 TraesCS5A01G470700 chr6D 88.860 386 42 1 91 475 119277429 119277814 9.380000e-130 473.0
8 TraesCS5A01G470700 chr6D 81.169 308 23 16 627 907 473055488 473055787 6.280000e-52 215.0
9 TraesCS5A01G470700 chr6D 100.000 39 0 0 914 952 437774107 437774069 4.000000e-09 73.1
10 TraesCS5A01G470700 chr6D 87.273 55 7 0 914 968 295046664 295046610 2.410000e-06 63.9
11 TraesCS5A01G470700 chr6B 90.550 709 46 10 1137 1836 718361735 718362431 0.000000e+00 918.0
12 TraesCS5A01G470700 chr6B 80.527 986 118 47 1927 2893 718373439 718374369 0.000000e+00 689.0
13 TraesCS5A01G470700 chr6B 86.131 274 23 4 1394 1662 718373131 718373394 6.100000e-72 281.0
14 TraesCS5A01G470700 chr4D 89.930 715 50 13 1137 1837 2804948 2805654 0.000000e+00 902.0
15 TraesCS5A01G470700 chr3D 90.933 386 34 1 91 475 105424987 105425372 4.270000e-143 518.0
16 TraesCS5A01G470700 chr3D 87.273 55 6 1 470 523 105425427 105425481 8.660000e-06 62.1
17 TraesCS5A01G470700 chr2A 90.634 363 33 1 91 452 542664219 542664581 5.610000e-132 481.0
18 TraesCS5A01G470700 chr2A 78.307 189 35 6 1150 1335 101836465 101836650 1.820000e-22 117.0
19 TraesCS5A01G470700 chr2A 100.000 39 0 0 914 952 728785155 728785117 4.000000e-09 73.1
20 TraesCS5A01G470700 chr2A 92.857 42 3 0 472 513 3363446 3363487 8.660000e-06 62.1
21 TraesCS5A01G470700 chr1D 89.863 365 36 1 115 478 477503066 477502702 4.360000e-128 468.0
22 TraesCS5A01G470700 chr1D 100.000 39 0 0 914 952 474818651 474818689 4.000000e-09 73.1
23 TraesCS5A01G470700 chr1D 97.143 35 1 0 470 504 92250886 92250920 3.110000e-05 60.2
24 TraesCS5A01G470700 chr1D 97.143 35 1 0 470 504 401708225 401708259 3.110000e-05 60.2
25 TraesCS5A01G470700 chr7D 88.630 387 35 5 91 475 188365615 188365994 2.030000e-126 462.0
26 TraesCS5A01G470700 chr7D 85.915 71 7 3 470 539 188366049 188366117 4.000000e-09 73.1
27 TraesCS5A01G470700 chr7B 89.373 367 38 1 115 480 44606418 44606784 7.300000e-126 460.0
28 TraesCS5A01G470700 chr7B 87.147 389 49 1 91 478 4212813 4212425 9.520000e-120 440.0
29 TraesCS5A01G470700 chr7B 90.909 44 4 0 470 513 44606834 44606877 3.110000e-05 60.2
30 TraesCS5A01G470700 chr4A 88.830 376 40 2 91 465 627611247 627610873 7.300000e-126 460.0
31 TraesCS5A01G470700 chr4A 97.619 42 1 0 911 952 577983123 577983164 4.000000e-09 73.1
32 TraesCS5A01G470700 chr4B 87.565 386 47 1 91 475 558136926 558137311 2.050000e-121 446.0
33 TraesCS5A01G470700 chr4B 100.000 30 0 0 475 504 558137371 558137400 4.030000e-04 56.5
34 TraesCS5A01G470700 chr2D 79.474 190 31 8 1150 1335 102725407 102725592 8.410000e-26 128.0
35 TraesCS5A01G470700 chr2B 78.421 190 33 8 1150 1335 153903604 153903789 1.820000e-22 117.0
36 TraesCS5A01G470700 chr7A 100.000 39 0 0 914 952 7041079 7041041 4.000000e-09 73.1
37 TraesCS5A01G470700 chr5B 100.000 39 0 0 914 952 655285321 655285283 4.000000e-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 TraesCS5A01G470700 chr5A 647372987 647375879 2892 True 5343.00 5343 100.0000 1 2893 1 chr5A.!!$R1 2892
1 TraesCS5A01G470700 chr5D 520136508 520138845 2337 True 1612.00 2830 91.3575 619 2893 2 chr5D.!!$R2 2274
2 TraesCS5A01G470700 chr6D 472997870 472998565 695 False 843.00 843 88.6550 1137 1838 1 chr6D.!!$F2 701
3 TraesCS5A01G470700 chr6D 473055488 473057680 2192 False 720.00 1225 80.4895 627 2780 2 chr6D.!!$F3 2153
4 TraesCS5A01G470700 chr6B 718361735 718362431 696 False 918.00 918 90.5500 1137 1836 1 chr6B.!!$F1 699
5 TraesCS5A01G470700 chr6B 718373131 718374369 1238 False 485.00 689 83.3290 1394 2893 2 chr6B.!!$F2 1499
6 TraesCS5A01G470700 chr4D 2804948 2805654 706 False 902.00 902 89.9300 1137 1837 1 chr4D.!!$F1 700
7 TraesCS5A01G470700 chr7D 188365615 188366117 502 False 267.55 462 87.2725 91 539 2 chr7D.!!$F1 448

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
78 79 0.099436 GAACTCCGTTGCATGATGGC 59.901 55.0 0.0 0.0 0.00 4.4 F
82 83 0.107066 TCCGTTGCATGATGGCTCAT 60.107 50.0 0.0 0.0 43.02 2.9 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1839 2046 1.219124 CATCGGCCGGATATCCAGG 59.781 63.158 27.83 21.58 32.85 4.45 R
2023 2279 1.455786 AGAAAAACGCACACTCGATCG 59.544 47.619 9.36 9.36 0.00 3.69 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 4.757773 AGGCGTGCACCTCTAGTA 57.242 55.556 12.15 0.00 33.62 1.82
21 22 2.971676 AGGCGTGCACCTCTAGTAA 58.028 52.632 12.15 0.00 33.62 2.24
22 23 1.263356 AGGCGTGCACCTCTAGTAAA 58.737 50.000 12.15 0.00 33.62 2.01
23 24 1.621814 AGGCGTGCACCTCTAGTAAAA 59.378 47.619 12.15 0.00 33.62 1.52
24 25 2.038033 AGGCGTGCACCTCTAGTAAAAA 59.962 45.455 12.15 0.00 33.62 1.94
25 26 2.415512 GGCGTGCACCTCTAGTAAAAAG 59.584 50.000 12.15 0.00 0.00 2.27
26 27 3.064931 GCGTGCACCTCTAGTAAAAAGT 58.935 45.455 12.15 0.00 0.00 2.66
27 28 3.497262 GCGTGCACCTCTAGTAAAAAGTT 59.503 43.478 12.15 0.00 0.00 2.66
28 29 4.610680 GCGTGCACCTCTAGTAAAAAGTTG 60.611 45.833 12.15 0.00 0.00 3.16
29 30 4.510340 CGTGCACCTCTAGTAAAAAGTTGT 59.490 41.667 12.15 0.00 0.00 3.32
30 31 5.007332 CGTGCACCTCTAGTAAAAAGTTGTT 59.993 40.000 12.15 0.00 0.00 2.83
31 32 6.199393 GTGCACCTCTAGTAAAAAGTTGTTG 58.801 40.000 5.22 0.00 0.00 3.33
32 33 5.212934 GCACCTCTAGTAAAAAGTTGTTGC 58.787 41.667 0.00 0.00 0.00 4.17
33 34 5.008712 GCACCTCTAGTAAAAAGTTGTTGCT 59.991 40.000 1.76 1.76 0.00 3.91
34 35 6.204108 GCACCTCTAGTAAAAAGTTGTTGCTA 59.796 38.462 3.86 3.86 0.00 3.49
35 36 7.573627 CACCTCTAGTAAAAAGTTGTTGCTAC 58.426 38.462 0.00 0.00 0.00 3.58
36 37 7.225931 CACCTCTAGTAAAAAGTTGTTGCTACA 59.774 37.037 0.00 0.00 0.00 2.74
37 38 7.771826 ACCTCTAGTAAAAAGTTGTTGCTACAA 59.228 33.333 9.74 9.74 41.82 2.41
51 52 5.378292 TTGCTACAACAACAACAAGAACA 57.622 34.783 0.00 0.00 0.00 3.18
52 53 5.378292 TGCTACAACAACAACAAGAACAA 57.622 34.783 0.00 0.00 0.00 2.83
53 54 5.157781 TGCTACAACAACAACAAGAACAAC 58.842 37.500 0.00 0.00 0.00 3.32
54 55 5.157781 GCTACAACAACAACAAGAACAACA 58.842 37.500 0.00 0.00 0.00 3.33
55 56 5.060446 GCTACAACAACAACAAGAACAACAC 59.940 40.000 0.00 0.00 0.00 3.32
56 57 4.938080 ACAACAACAACAAGAACAACACA 58.062 34.783 0.00 0.00 0.00 3.72
57 58 4.742659 ACAACAACAACAAGAACAACACAC 59.257 37.500 0.00 0.00 0.00 3.82
58 59 4.576216 ACAACAACAAGAACAACACACA 57.424 36.364 0.00 0.00 0.00 3.72
59 60 4.545610 ACAACAACAAGAACAACACACAG 58.454 39.130 0.00 0.00 0.00 3.66
60 61 4.277174 ACAACAACAAGAACAACACACAGA 59.723 37.500 0.00 0.00 0.00 3.41
61 62 5.218885 CAACAACAAGAACAACACACAGAA 58.781 37.500 0.00 0.00 0.00 3.02
62 63 4.794169 ACAACAAGAACAACACACAGAAC 58.206 39.130 0.00 0.00 0.00 3.01
63 64 4.518970 ACAACAAGAACAACACACAGAACT 59.481 37.500 0.00 0.00 0.00 3.01
64 65 4.946784 ACAAGAACAACACACAGAACTC 57.053 40.909 0.00 0.00 0.00 3.01
65 66 3.689649 ACAAGAACAACACACAGAACTCC 59.310 43.478 0.00 0.00 0.00 3.85
66 67 2.550978 AGAACAACACACAGAACTCCG 58.449 47.619 0.00 0.00 0.00 4.63
67 68 2.093658 AGAACAACACACAGAACTCCGT 60.094 45.455 0.00 0.00 0.00 4.69
68 69 2.396590 ACAACACACAGAACTCCGTT 57.603 45.000 0.00 0.00 0.00 4.44
69 70 2.006888 ACAACACACAGAACTCCGTTG 58.993 47.619 0.00 0.00 39.61 4.10
70 71 1.014352 AACACACAGAACTCCGTTGC 58.986 50.000 0.00 0.00 0.00 4.17
71 72 0.107897 ACACACAGAACTCCGTTGCA 60.108 50.000 0.00 0.00 0.00 4.08
72 73 1.229428 CACACAGAACTCCGTTGCAT 58.771 50.000 0.00 0.00 0.00 3.96
73 74 1.069703 CACACAGAACTCCGTTGCATG 60.070 52.381 0.00 0.00 0.00 4.06
74 75 1.202639 ACACAGAACTCCGTTGCATGA 60.203 47.619 0.00 0.00 0.00 3.07
75 76 2.079158 CACAGAACTCCGTTGCATGAT 58.921 47.619 0.00 0.00 0.00 2.45
76 77 2.079158 ACAGAACTCCGTTGCATGATG 58.921 47.619 0.00 0.00 0.00 3.07
77 78 1.399440 CAGAACTCCGTTGCATGATGG 59.601 52.381 0.00 0.00 0.00 3.51
78 79 0.099436 GAACTCCGTTGCATGATGGC 59.901 55.000 0.00 0.00 0.00 4.40
79 80 0.322816 AACTCCGTTGCATGATGGCT 60.323 50.000 0.00 0.00 34.04 4.75
80 81 0.745845 ACTCCGTTGCATGATGGCTC 60.746 55.000 0.00 0.00 34.04 4.70
81 82 0.745486 CTCCGTTGCATGATGGCTCA 60.745 55.000 0.00 0.00 35.41 4.26
82 83 0.107066 TCCGTTGCATGATGGCTCAT 60.107 50.000 0.00 0.00 43.02 2.90
83 84 0.742505 CCGTTGCATGATGGCTCATT 59.257 50.000 0.00 0.00 40.20 2.57
84 85 1.135527 CCGTTGCATGATGGCTCATTT 59.864 47.619 0.00 0.00 40.20 2.32
85 86 2.417651 CCGTTGCATGATGGCTCATTTT 60.418 45.455 0.00 0.00 40.20 1.82
86 87 2.855963 CGTTGCATGATGGCTCATTTTC 59.144 45.455 0.00 0.00 40.20 2.29
87 88 3.428452 CGTTGCATGATGGCTCATTTTCT 60.428 43.478 0.00 0.00 40.20 2.52
88 89 3.793797 TGCATGATGGCTCATTTTCTG 57.206 42.857 0.00 0.00 40.20 3.02
89 90 3.093814 TGCATGATGGCTCATTTTCTGT 58.906 40.909 0.00 0.00 40.20 3.41
95 96 3.401033 TGGCTCATTTTCTGTTCTCGA 57.599 42.857 0.00 0.00 0.00 4.04
105 106 3.981071 TCTGTTCTCGATGGATGGTTT 57.019 42.857 0.00 0.00 0.00 3.27
106 107 3.861840 TCTGTTCTCGATGGATGGTTTC 58.138 45.455 0.00 0.00 0.00 2.78
111 112 5.181245 TGTTCTCGATGGATGGTTTCTTTTC 59.819 40.000 0.00 0.00 0.00 2.29
113 114 5.560724 TCTCGATGGATGGTTTCTTTTCTT 58.439 37.500 0.00 0.00 0.00 2.52
124 125 6.523840 TGGTTTCTTTTCTTTTCATGATGGG 58.476 36.000 0.00 0.00 0.00 4.00
125 126 5.409520 GGTTTCTTTTCTTTTCATGATGGGC 59.590 40.000 0.00 0.00 0.00 5.36
127 128 3.193267 TCTTTTCTTTTCATGATGGGCCG 59.807 43.478 0.00 0.00 0.00 6.13
128 129 0.817013 TTCTTTTCATGATGGGCCGC 59.183 50.000 0.00 0.00 0.00 6.53
151 153 1.035139 GACGGGTATGGTGGTACGAT 58.965 55.000 0.00 0.00 0.00 3.73
159 161 4.262463 GGTATGGTGGTACGATGTCATGAT 60.262 45.833 0.00 0.00 0.00 2.45
166 168 1.939974 ACGATGTCATGATGGTTCGG 58.060 50.000 17.76 2.14 0.00 4.30
167 169 0.583438 CGATGTCATGATGGTTCGGC 59.417 55.000 0.00 0.00 0.00 5.54
179 181 1.153958 GTTCGGCCATCTTTGCTGC 60.154 57.895 2.24 0.00 35.03 5.25
180 182 1.603171 TTCGGCCATCTTTGCTGCA 60.603 52.632 2.24 0.00 35.03 4.41
181 183 0.966875 TTCGGCCATCTTTGCTGCAT 60.967 50.000 1.84 0.00 35.03 3.96
182 184 0.107263 TCGGCCATCTTTGCTGCATA 60.107 50.000 1.84 0.00 35.03 3.14
183 185 0.956633 CGGCCATCTTTGCTGCATAT 59.043 50.000 1.84 0.00 0.00 1.78
184 186 2.153645 CGGCCATCTTTGCTGCATATA 58.846 47.619 1.84 0.00 0.00 0.86
185 187 2.751259 CGGCCATCTTTGCTGCATATAT 59.249 45.455 1.84 0.00 0.00 0.86
209 211 6.575267 TGGTTTTATTCAGATGCAATGATGG 58.425 36.000 5.88 0.00 0.00 3.51
213 215 7.649533 TTTATTCAGATGCAATGATGGTCTT 57.350 32.000 5.88 0.00 0.00 3.01
231 233 0.252761 TTGAAGCGGAGATCCATGCA 59.747 50.000 0.00 0.00 35.14 3.96
259 261 0.914644 AGGCATGGCTTTAGCTCTCA 59.085 50.000 17.44 0.00 41.70 3.27
296 298 4.320494 GCAAGTCATCGTCCAGTCAAATTT 60.320 41.667 0.00 0.00 0.00 1.82
307 309 6.093495 CGTCCAGTCAAATTTAATTGAGGCTA 59.907 38.462 0.00 0.00 39.84 3.93
345 347 0.820871 AGAATCTCTCACCGTCAGCC 59.179 55.000 0.00 0.00 0.00 4.85
382 384 1.767088 CTGAGATCAAGGCCCTGATGA 59.233 52.381 21.80 10.88 36.15 2.92
402 404 6.900186 TGATGAAGGAGAGAGAGTTTATTCCT 59.100 38.462 0.00 0.00 36.65 3.36
408 410 6.957020 AGGAGAGAGAGTTTATTCCTCAGAAA 59.043 38.462 0.00 0.00 35.09 2.52
430 432 9.768215 AGAAAATTTGTAGGGATCAAAATAGGA 57.232 29.630 0.00 0.00 38.11 2.94
431 433 9.803315 GAAAATTTGTAGGGATCAAAATAGGAC 57.197 33.333 0.00 0.00 38.11 3.85
453 455 4.878397 ACAGCAGATTGTCTGGCTAATTAC 59.122 41.667 8.85 0.00 44.43 1.89
468 470 6.158175 GCTAATTACAGCCATACAGAATCG 57.842 41.667 0.00 0.00 35.40 3.34
473 535 3.782046 ACAGCCATACAGAATCGTGTAC 58.218 45.455 0.00 0.00 35.74 2.90
507 569 7.443259 TTTGGAATAAAACTCCTCTTTACCG 57.557 36.000 0.00 0.00 33.77 4.02
513 575 5.762825 AAAACTCCTCTTTACCGGAAAAC 57.237 39.130 9.46 0.00 0.00 2.43
516 578 4.132336 ACTCCTCTTTACCGGAAAACAAC 58.868 43.478 9.46 0.00 0.00 3.32
522 584 5.400703 TCTTTACCGGAAAACAACAACAAC 58.599 37.500 9.46 0.00 0.00 3.32
523 585 4.778534 TTACCGGAAAACAACAACAACA 57.221 36.364 9.46 0.00 0.00 3.33
524 586 3.662247 ACCGGAAAACAACAACAACAA 57.338 38.095 9.46 0.00 0.00 2.83
525 587 3.318886 ACCGGAAAACAACAACAACAAC 58.681 40.909 9.46 0.00 0.00 3.32
526 588 3.243771 ACCGGAAAACAACAACAACAACA 60.244 39.130 9.46 0.00 0.00 3.33
528 590 4.376514 CCGGAAAACAACAACAACAACAAC 60.377 41.667 0.00 0.00 0.00 3.32
534 596 5.396750 ACAACAACAACAACAACAACAAC 57.603 34.783 0.00 0.00 0.00 3.32
539 601 5.351465 ACAACAACAACAACAACAACAACAA 59.649 32.000 0.00 0.00 0.00 2.83
540 602 5.396750 ACAACAACAACAACAACAACAAC 57.603 34.783 0.00 0.00 0.00 3.32
541 603 4.870426 ACAACAACAACAACAACAACAACA 59.130 33.333 0.00 0.00 0.00 3.33
542 604 5.351465 ACAACAACAACAACAACAACAACAA 59.649 32.000 0.00 0.00 0.00 2.83
543 605 5.396750 ACAACAACAACAACAACAACAAC 57.603 34.783 0.00 0.00 0.00 3.32
544 606 4.870426 ACAACAACAACAACAACAACAACA 59.130 33.333 0.00 0.00 0.00 3.33
545 607 5.351465 ACAACAACAACAACAACAACAACAA 59.649 32.000 0.00 0.00 0.00 2.83
546 608 5.396750 ACAACAACAACAACAACAACAAC 57.603 34.783 0.00 0.00 0.00 3.32
547 609 4.870426 ACAACAACAACAACAACAACAACA 59.130 33.333 0.00 0.00 0.00 3.33
548 610 5.351465 ACAACAACAACAACAACAACAACAA 59.649 32.000 0.00 0.00 0.00 2.83
549 611 5.396750 ACAACAACAACAACAACAACAAC 57.603 34.783 0.00 0.00 0.00 3.32
550 612 4.870426 ACAACAACAACAACAACAACAACA 59.130 33.333 0.00 0.00 0.00 3.33
551 613 5.351465 ACAACAACAACAACAACAACAACAA 59.649 32.000 0.00 0.00 0.00 2.83
552 614 5.396750 ACAACAACAACAACAACAACAAC 57.603 34.783 0.00 0.00 0.00 3.32
553 615 4.870426 ACAACAACAACAACAACAACAACA 59.130 33.333 0.00 0.00 0.00 3.33
554 616 5.351465 ACAACAACAACAACAACAACAACAA 59.649 32.000 0.00 0.00 0.00 2.83
555 617 5.396750 ACAACAACAACAACAACAACAAC 57.603 34.783 0.00 0.00 0.00 3.32
556 618 4.870426 ACAACAACAACAACAACAACAACA 59.130 33.333 0.00 0.00 0.00 3.33
557 619 5.351465 ACAACAACAACAACAACAACAACAA 59.649 32.000 0.00 0.00 0.00 2.83
558 620 5.396750 ACAACAACAACAACAACAACAAC 57.603 34.783 0.00 0.00 0.00 3.32
559 621 4.870426 ACAACAACAACAACAACAACAACA 59.130 33.333 0.00 0.00 0.00 3.33
560 622 5.351465 ACAACAACAACAACAACAACAACAA 59.649 32.000 0.00 0.00 0.00 2.83
561 623 5.396750 ACAACAACAACAACAACAACAAC 57.603 34.783 0.00 0.00 0.00 3.32
562 624 4.870426 ACAACAACAACAACAACAACAACA 59.130 33.333 0.00 0.00 0.00 3.33
563 625 5.351465 ACAACAACAACAACAACAACAACAA 59.649 32.000 0.00 0.00 0.00 2.83
564 626 5.396750 ACAACAACAACAACAACAACAAC 57.603 34.783 0.00 0.00 0.00 3.32
565 627 4.870426 ACAACAACAACAACAACAACAACA 59.130 33.333 0.00 0.00 0.00 3.33
566 628 5.351465 ACAACAACAACAACAACAACAACAA 59.649 32.000 0.00 0.00 0.00 2.83
567 629 5.396750 ACAACAACAACAACAACAACAAC 57.603 34.783 0.00 0.00 0.00 3.32
568 630 4.870426 ACAACAACAACAACAACAACAACA 59.130 33.333 0.00 0.00 0.00 3.33
569 631 5.351465 ACAACAACAACAACAACAACAACAA 59.649 32.000 0.00 0.00 0.00 2.83
570 632 5.396750 ACAACAACAACAACAACAACAAC 57.603 34.783 0.00 0.00 0.00 3.32
571 633 4.870426 ACAACAACAACAACAACAACAACA 59.130 33.333 0.00 0.00 0.00 3.33
572 634 5.351465 ACAACAACAACAACAACAACAACAA 59.649 32.000 0.00 0.00 0.00 2.83
573 635 5.649602 ACAACAACAACAACAACAACAAG 57.350 34.783 0.00 0.00 0.00 3.16
574 636 5.112686 ACAACAACAACAACAACAACAAGT 58.887 33.333 0.00 0.00 0.00 3.16
575 637 6.273825 ACAACAACAACAACAACAACAAGTA 58.726 32.000 0.00 0.00 0.00 2.24
576 638 6.199342 ACAACAACAACAACAACAACAAGTAC 59.801 34.615 0.00 0.00 0.00 2.73
577 639 6.079424 ACAACAACAACAACAACAAGTACT 57.921 33.333 0.00 0.00 0.00 2.73
578 640 5.918011 ACAACAACAACAACAACAAGTACTG 59.082 36.000 0.00 0.00 0.00 2.74
579 641 5.950758 ACAACAACAACAACAAGTACTGA 57.049 34.783 0.00 0.00 0.00 3.41
580 642 6.509418 ACAACAACAACAACAAGTACTGAT 57.491 33.333 0.00 0.00 0.00 2.90
581 643 6.321717 ACAACAACAACAACAAGTACTGATG 58.678 36.000 0.00 0.00 34.11 3.07
582 644 6.072175 ACAACAACAACAACAAGTACTGATGT 60.072 34.615 0.00 0.00 42.44 3.06
583 645 5.879237 ACAACAACAACAAGTACTGATGTG 58.121 37.500 0.00 0.00 39.94 3.21
584 646 5.414454 ACAACAACAACAAGTACTGATGTGT 59.586 36.000 0.00 0.00 39.94 3.72
585 647 5.734855 ACAACAACAAGTACTGATGTGTC 57.265 39.130 0.00 0.00 39.94 3.67
586 648 4.574828 ACAACAACAAGTACTGATGTGTCC 59.425 41.667 0.00 0.00 39.94 4.02
587 649 3.740115 ACAACAAGTACTGATGTGTCCC 58.260 45.455 0.00 0.00 39.41 4.46
588 650 2.736721 CAACAAGTACTGATGTGTCCCG 59.263 50.000 0.00 0.00 0.00 5.14
589 651 1.275291 ACAAGTACTGATGTGTCCCGG 59.725 52.381 0.00 0.00 0.00 5.73
590 652 0.249398 AAGTACTGATGTGTCCCGGC 59.751 55.000 0.00 0.00 0.00 6.13
591 653 1.153429 GTACTGATGTGTCCCGGCC 60.153 63.158 0.00 0.00 0.00 6.13
592 654 2.717044 TACTGATGTGTCCCGGCCG 61.717 63.158 21.04 21.04 0.00 6.13
607 669 3.716195 CCGCCTGGGTGATGGTGA 61.716 66.667 1.28 0.00 36.02 4.02
608 670 2.436646 CGCCTGGGTGATGGTGAC 60.437 66.667 0.00 0.00 36.02 3.67
609 671 2.436646 GCCTGGGTGATGGTGACG 60.437 66.667 0.00 0.00 0.00 4.35
610 672 2.954684 GCCTGGGTGATGGTGACGA 61.955 63.158 0.00 0.00 0.00 4.20
611 673 1.079127 CCTGGGTGATGGTGACGAC 60.079 63.158 0.00 0.00 0.00 4.34
612 674 1.446099 CTGGGTGATGGTGACGACG 60.446 63.158 0.00 0.00 0.00 5.12
613 675 2.125673 GGGTGATGGTGACGACGG 60.126 66.667 0.00 0.00 0.00 4.79
614 676 2.642254 GGGTGATGGTGACGACGGA 61.642 63.158 0.00 0.00 0.00 4.69
615 677 1.290955 GGTGATGGTGACGACGGAA 59.709 57.895 0.00 0.00 0.00 4.30
616 678 0.736325 GGTGATGGTGACGACGGAAG 60.736 60.000 0.00 0.00 0.00 3.46
617 679 0.242825 GTGATGGTGACGACGGAAGA 59.757 55.000 0.00 0.00 0.00 2.87
618 680 0.963225 TGATGGTGACGACGGAAGAA 59.037 50.000 0.00 0.00 0.00 2.52
619 681 1.548719 TGATGGTGACGACGGAAGAAT 59.451 47.619 0.00 0.00 0.00 2.40
620 682 2.028476 TGATGGTGACGACGGAAGAATT 60.028 45.455 0.00 0.00 0.00 2.17
621 683 3.193903 TGATGGTGACGACGGAAGAATTA 59.806 43.478 0.00 0.00 0.00 1.40
622 684 3.663995 TGGTGACGACGGAAGAATTAA 57.336 42.857 0.00 0.00 0.00 1.40
640 702 0.178068 AACTGTCACTCGTGCTGGTT 59.822 50.000 0.00 0.00 0.00 3.67
742 815 2.382882 TGAGAGAGTGGAAGCATCGAT 58.617 47.619 0.00 0.00 0.00 3.59
743 816 2.360483 TGAGAGAGTGGAAGCATCGATC 59.640 50.000 0.00 0.00 0.00 3.69
744 817 1.336440 AGAGAGTGGAAGCATCGATCG 59.664 52.381 9.36 9.36 0.00 3.69
745 818 1.335182 GAGAGTGGAAGCATCGATCGA 59.665 52.381 21.86 21.86 0.00 3.59
746 819 1.336440 AGAGTGGAAGCATCGATCGAG 59.664 52.381 23.84 15.68 0.00 4.04
753 829 2.713895 AGCATCGATCGAGTGTATGG 57.286 50.000 23.84 7.57 0.00 2.74
820 902 1.732259 GTACTATACATGCATGCCGGC 59.268 52.381 26.53 22.73 0.00 6.13
890 989 6.376978 CATCTGGTGCTTATTTATTGCTAGC 58.623 40.000 8.10 8.10 0.00 3.42
907 1008 3.181487 GCTAGCCTCTTTCTGTCTCTCTG 60.181 52.174 2.29 0.00 0.00 3.35
914 1015 5.064198 CCTCTTTCTGTCTCTCTGTAGTACG 59.936 48.000 0.00 0.00 0.00 3.67
917 1018 6.485984 TCTTTCTGTCTCTCTGTAGTACGTTT 59.514 38.462 0.00 0.00 0.00 3.60
1005 1143 0.535335 GCCAGACGTAGGTCATTCCA 59.465 55.000 17.27 0.00 45.92 3.53
1006 1144 1.739371 GCCAGACGTAGGTCATTCCAC 60.739 57.143 17.27 0.00 45.92 4.02
1007 1145 1.469251 CCAGACGTAGGTCATTCCACG 60.469 57.143 17.27 0.00 45.92 4.94
1008 1146 1.471287 CAGACGTAGGTCATTCCACGA 59.529 52.381 17.27 0.00 45.92 4.35
1009 1147 2.099263 CAGACGTAGGTCATTCCACGAT 59.901 50.000 17.27 0.00 45.92 3.73
1042 1195 4.947645 TCTCAATTTGGTTTCAAGCAAGG 58.052 39.130 4.49 0.48 45.75 3.61
1045 1198 6.097554 TCTCAATTTGGTTTCAAGCAAGGTAA 59.902 34.615 4.49 0.00 45.75 2.85
1113 1276 3.273788 AAAGAGGAGCCGCCCAAGG 62.274 63.158 1.37 0.00 37.37 3.61
1405 1571 2.725203 TTCACGCCCTTCAACTCCGG 62.725 60.000 0.00 0.00 0.00 5.14
1411 1580 2.045926 CTTCAACTCCGGCCCTGG 60.046 66.667 0.00 0.00 0.00 4.45
1718 1904 2.358247 ACCGACACCAATGCCGAC 60.358 61.111 0.00 0.00 0.00 4.79
1740 1938 1.215647 GCCGTCAAGAGTGATCCGT 59.784 57.895 0.00 0.00 35.80 4.69
1742 1940 0.526211 CCGTCAAGAGTGATCCGTCA 59.474 55.000 0.00 0.00 35.80 4.35
1756 1954 2.210116 TCCGTCAAAGAACAGCAAGAC 58.790 47.619 0.00 0.00 0.00 3.01
1790 1988 4.717313 GACACCCGAGTTGCCCCC 62.717 72.222 0.00 0.00 0.00 5.40
1807 2005 0.467384 CCCTCCACCAGCTATGACTG 59.533 60.000 0.00 0.00 37.42 3.51
1838 2045 1.268352 CATGCCGTCTAGCTCCTCTAC 59.732 57.143 0.00 0.00 0.00 2.59
1839 2046 0.465824 TGCCGTCTAGCTCCTCTACC 60.466 60.000 0.00 0.00 0.00 3.18
1846 2053 3.331294 GTCTAGCTCCTCTACCCTGGATA 59.669 52.174 0.00 0.00 0.00 2.59
1847 2054 4.017867 GTCTAGCTCCTCTACCCTGGATAT 60.018 50.000 0.00 0.00 0.00 1.63
1848 2055 3.466395 AGCTCCTCTACCCTGGATATC 57.534 52.381 0.00 0.00 0.00 1.63
1892 2113 9.274206 AGTGAGTGTTCCTCTTCTTTAAATAAC 57.726 33.333 0.00 0.00 41.11 1.89
1893 2114 8.221766 GTGAGTGTTCCTCTTCTTTAAATAACG 58.778 37.037 0.00 0.00 41.11 3.18
1894 2115 8.145767 TGAGTGTTCCTCTTCTTTAAATAACGA 58.854 33.333 0.00 0.00 41.11 3.85
1895 2116 9.152595 GAGTGTTCCTCTTCTTTAAATAACGAT 57.847 33.333 0.00 0.00 37.22 3.73
1896 2117 8.936864 AGTGTTCCTCTTCTTTAAATAACGATG 58.063 33.333 0.00 0.00 0.00 3.84
1897 2118 8.718734 GTGTTCCTCTTCTTTAAATAACGATGT 58.281 33.333 0.00 0.00 0.00 3.06
1898 2119 8.717821 TGTTCCTCTTCTTTAAATAACGATGTG 58.282 33.333 0.00 0.00 0.00 3.21
1899 2120 8.718734 GTTCCTCTTCTTTAAATAACGATGTGT 58.281 33.333 0.00 0.00 0.00 3.72
1900 2121 8.251750 TCCTCTTCTTTAAATAACGATGTGTG 57.748 34.615 0.00 0.00 0.00 3.82
1901 2122 6.961554 CCTCTTCTTTAAATAACGATGTGTGC 59.038 38.462 0.00 0.00 0.00 4.57
1902 2123 6.837992 TCTTCTTTAAATAACGATGTGTGCC 58.162 36.000 0.00 0.00 0.00 5.01
1904 2125 4.396790 TCTTTAAATAACGATGTGTGCCCC 59.603 41.667 0.00 0.00 0.00 5.80
1905 2126 2.208132 AAATAACGATGTGTGCCCCA 57.792 45.000 0.00 0.00 0.00 4.96
2023 2279 4.740205 CGTACTATGTGTGATGTGGATGTC 59.260 45.833 0.00 0.00 0.00 3.06
2024 2280 3.785486 ACTATGTGTGATGTGGATGTCG 58.215 45.455 0.00 0.00 0.00 4.35
2025 2281 3.447229 ACTATGTGTGATGTGGATGTCGA 59.553 43.478 0.00 0.00 0.00 4.20
2026 2282 3.548745 ATGTGTGATGTGGATGTCGAT 57.451 42.857 0.00 0.00 0.00 3.59
2027 2283 2.892374 TGTGTGATGTGGATGTCGATC 58.108 47.619 0.00 0.00 0.00 3.69
2094 2353 5.992829 CCCATTTTACTTTAACCAACCAACC 59.007 40.000 0.00 0.00 0.00 3.77
2095 2354 6.408206 CCCATTTTACTTTAACCAACCAACCA 60.408 38.462 0.00 0.00 0.00 3.67
2142 2401 7.377398 TGTTGATCCAATTGTAACATCCAAAG 58.623 34.615 4.43 0.00 0.00 2.77
2181 2443 5.011943 AGCCAAATCCACACACAAAATATGT 59.988 36.000 0.00 0.00 45.34 2.29
2182 2444 5.700373 GCCAAATCCACACACAAAATATGTT 59.300 36.000 0.00 0.00 41.46 2.71
2221 2483 8.814733 TTTATGTATGTAGTTTTCGCATTTCG 57.185 30.769 0.00 0.00 40.15 3.46
2322 2584 6.761242 TGAAATGGATCGAAACTATGTGGTAG 59.239 38.462 0.00 0.00 36.44 3.18
2327 2589 5.010719 GGATCGAAACTATGTGGTAGGATCA 59.989 44.000 0.00 0.00 34.56 2.92
2339 2601 6.820335 TGTGGTAGGATCACAATAGAATCAG 58.180 40.000 0.00 0.00 41.50 2.90
2340 2602 6.611236 TGTGGTAGGATCACAATAGAATCAGA 59.389 38.462 0.00 0.00 41.50 3.27
2341 2603 7.290948 TGTGGTAGGATCACAATAGAATCAGAT 59.709 37.037 0.00 0.00 41.50 2.90
2342 2604 7.816995 GTGGTAGGATCACAATAGAATCAGATC 59.183 40.741 0.00 0.00 35.39 2.75
2376 2638 7.044706 GCATTATAGCGATTTTTCACAGAACAC 60.045 37.037 0.00 0.00 0.00 3.32
2427 2698 3.366883 CCATACCACACAAAACAATCCGG 60.367 47.826 0.00 0.00 0.00 5.14
2433 2704 3.549873 CACACAAAACAATCCGGAAACAC 59.450 43.478 9.01 0.00 0.00 3.32
2434 2705 3.120041 CACAAAACAATCCGGAAACACC 58.880 45.455 9.01 0.00 0.00 4.16
2435 2706 2.761208 ACAAAACAATCCGGAAACACCA 59.239 40.909 9.01 0.00 38.90 4.17
2436 2707 3.195825 ACAAAACAATCCGGAAACACCAA 59.804 39.130 9.01 0.00 38.90 3.67
2437 2708 4.184629 CAAAACAATCCGGAAACACCAAA 58.815 39.130 9.01 0.00 38.90 3.28
2438 2709 4.473477 AAACAATCCGGAAACACCAAAA 57.527 36.364 9.01 0.00 38.90 2.44
2439 2710 4.473477 AACAATCCGGAAACACCAAAAA 57.527 36.364 9.01 0.00 38.90 1.94
2440 2711 4.681074 ACAATCCGGAAACACCAAAAAT 57.319 36.364 9.01 0.00 38.90 1.82
2441 2712 5.793030 ACAATCCGGAAACACCAAAAATA 57.207 34.783 9.01 0.00 38.90 1.40
2497 2776 2.959707 GGGGTTCACAAACATGTAACCA 59.040 45.455 22.78 0.00 41.12 3.67
2532 2811 7.584987 ACATTGAGCTATAACTCACAAACAAC 58.415 34.615 5.32 0.00 46.13 3.32
2596 2878 2.042297 TGCACCTGGGGATTATGAAACA 59.958 45.455 0.00 0.00 0.00 2.83
2602 2884 5.658190 ACCTGGGGATTATGAAACATGAAAG 59.342 40.000 0.00 0.00 0.00 2.62
2702 2993 2.028020 GGAAGGAGACAGGAACACGAAT 60.028 50.000 0.00 0.00 0.00 3.34
2742 3033 5.474189 ACGAGGAGAATAGGATAACTAGCAC 59.526 44.000 0.00 0.00 34.56 4.40
2780 3071 1.273886 ACCCAACCAACAACACACAAC 59.726 47.619 0.00 0.00 0.00 3.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 2.088950 TTTTACTAGAGGTGCACGCC 57.911 50.000 11.45 4.80 0.00 5.68
5 6 3.064931 ACTTTTTACTAGAGGTGCACGC 58.935 45.455 11.45 5.43 0.00 5.34
6 7 4.510340 ACAACTTTTTACTAGAGGTGCACG 59.490 41.667 11.45 0.00 31.32 5.34
7 8 6.199393 CAACAACTTTTTACTAGAGGTGCAC 58.801 40.000 8.80 8.80 31.32 4.57
8 9 5.220970 GCAACAACTTTTTACTAGAGGTGCA 60.221 40.000 0.00 0.00 36.05 4.57
9 10 5.008712 AGCAACAACTTTTTACTAGAGGTGC 59.991 40.000 0.00 0.00 36.16 5.01
10 11 6.619801 AGCAACAACTTTTTACTAGAGGTG 57.380 37.500 0.00 0.00 34.34 4.00
11 12 7.277396 TGTAGCAACAACTTTTTACTAGAGGT 58.723 34.615 0.00 0.00 30.91 3.85
12 13 7.724305 TGTAGCAACAACTTTTTACTAGAGG 57.276 36.000 0.00 0.00 30.91 3.69
28 29 5.157781 TGTTCTTGTTGTTGTTGTAGCAAC 58.842 37.500 4.87 4.87 46.82 4.17
29 30 5.378292 TGTTCTTGTTGTTGTTGTAGCAA 57.622 34.783 0.00 0.00 0.00 3.91
30 31 5.157781 GTTGTTCTTGTTGTTGTTGTAGCA 58.842 37.500 0.00 0.00 0.00 3.49
31 32 5.060446 GTGTTGTTCTTGTTGTTGTTGTAGC 59.940 40.000 0.00 0.00 0.00 3.58
32 33 6.087555 GTGTGTTGTTCTTGTTGTTGTTGTAG 59.912 38.462 0.00 0.00 0.00 2.74
33 34 5.915758 GTGTGTTGTTCTTGTTGTTGTTGTA 59.084 36.000 0.00 0.00 0.00 2.41
34 35 4.742659 GTGTGTTGTTCTTGTTGTTGTTGT 59.257 37.500 0.00 0.00 0.00 3.32
35 36 4.742167 TGTGTGTTGTTCTTGTTGTTGTTG 59.258 37.500 0.00 0.00 0.00 3.33
36 37 4.938080 TGTGTGTTGTTCTTGTTGTTGTT 58.062 34.783 0.00 0.00 0.00 2.83
37 38 4.277174 TCTGTGTGTTGTTCTTGTTGTTGT 59.723 37.500 0.00 0.00 0.00 3.32
38 39 4.793071 TCTGTGTGTTGTTCTTGTTGTTG 58.207 39.130 0.00 0.00 0.00 3.33
39 40 5.009610 AGTTCTGTGTGTTGTTCTTGTTGTT 59.990 36.000 0.00 0.00 0.00 2.83
40 41 4.518970 AGTTCTGTGTGTTGTTCTTGTTGT 59.481 37.500 0.00 0.00 0.00 3.32
41 42 5.046910 AGTTCTGTGTGTTGTTCTTGTTG 57.953 39.130 0.00 0.00 0.00 3.33
42 43 4.156008 GGAGTTCTGTGTGTTGTTCTTGTT 59.844 41.667 0.00 0.00 0.00 2.83
43 44 3.689649 GGAGTTCTGTGTGTTGTTCTTGT 59.310 43.478 0.00 0.00 0.00 3.16
44 45 3.242413 CGGAGTTCTGTGTGTTGTTCTTG 60.242 47.826 0.00 0.00 0.00 3.02
45 46 2.936498 CGGAGTTCTGTGTGTTGTTCTT 59.064 45.455 0.00 0.00 0.00 2.52
46 47 2.093658 ACGGAGTTCTGTGTGTTGTTCT 60.094 45.455 0.00 0.00 37.78 3.01
47 48 2.277084 ACGGAGTTCTGTGTGTTGTTC 58.723 47.619 0.00 0.00 37.78 3.18
48 49 2.396590 ACGGAGTTCTGTGTGTTGTT 57.603 45.000 0.00 0.00 37.78 2.83
61 62 4.652102 ATGAGCCATCATGCAACGGAGT 62.652 50.000 0.00 0.00 44.75 3.85
62 63 0.745486 TGAGCCATCATGCAACGGAG 60.745 55.000 0.00 0.00 0.00 4.63
63 64 0.107066 ATGAGCCATCATGCAACGGA 60.107 50.000 0.00 0.00 44.67 4.69
64 65 0.742505 AATGAGCCATCATGCAACGG 59.257 50.000 0.00 0.00 45.67 4.44
65 66 2.572191 AAATGAGCCATCATGCAACG 57.428 45.000 0.00 0.00 45.67 4.10
66 67 3.863424 CAGAAAATGAGCCATCATGCAAC 59.137 43.478 0.00 0.00 45.67 4.17
67 68 3.512329 ACAGAAAATGAGCCATCATGCAA 59.488 39.130 0.00 0.00 45.67 4.08
68 69 3.093814 ACAGAAAATGAGCCATCATGCA 58.906 40.909 0.00 0.00 45.67 3.96
69 70 3.795623 ACAGAAAATGAGCCATCATGC 57.204 42.857 0.00 0.00 45.67 4.06
70 71 5.578005 AGAACAGAAAATGAGCCATCATG 57.422 39.130 0.00 0.00 45.67 3.07
72 73 3.686241 CGAGAACAGAAAATGAGCCATCA 59.314 43.478 0.00 0.00 40.50 3.07
73 74 3.935203 TCGAGAACAGAAAATGAGCCATC 59.065 43.478 0.00 0.00 0.00 3.51
74 75 3.942829 TCGAGAACAGAAAATGAGCCAT 58.057 40.909 0.00 0.00 0.00 4.40
75 76 3.401033 TCGAGAACAGAAAATGAGCCA 57.599 42.857 0.00 0.00 0.00 4.75
76 77 3.064545 CCATCGAGAACAGAAAATGAGCC 59.935 47.826 0.00 0.00 0.00 4.70
77 78 3.935203 TCCATCGAGAACAGAAAATGAGC 59.065 43.478 0.00 0.00 0.00 4.26
78 79 5.007430 CCATCCATCGAGAACAGAAAATGAG 59.993 44.000 0.00 0.00 0.00 2.90
79 80 4.877823 CCATCCATCGAGAACAGAAAATGA 59.122 41.667 0.00 0.00 0.00 2.57
80 81 4.637534 ACCATCCATCGAGAACAGAAAATG 59.362 41.667 0.00 0.00 0.00 2.32
81 82 4.848357 ACCATCCATCGAGAACAGAAAAT 58.152 39.130 0.00 0.00 0.00 1.82
82 83 4.286297 ACCATCCATCGAGAACAGAAAA 57.714 40.909 0.00 0.00 0.00 2.29
83 84 3.981071 ACCATCCATCGAGAACAGAAA 57.019 42.857 0.00 0.00 0.00 2.52
84 85 3.981071 AACCATCCATCGAGAACAGAA 57.019 42.857 0.00 0.00 0.00 3.02
85 86 3.515502 AGAAACCATCCATCGAGAACAGA 59.484 43.478 0.00 0.00 0.00 3.41
86 87 3.866651 AGAAACCATCCATCGAGAACAG 58.133 45.455 0.00 0.00 0.00 3.16
87 88 3.981071 AGAAACCATCCATCGAGAACA 57.019 42.857 0.00 0.00 0.00 3.18
88 89 5.412904 AGAAAAGAAACCATCCATCGAGAAC 59.587 40.000 0.00 0.00 0.00 3.01
89 90 5.560724 AGAAAAGAAACCATCCATCGAGAA 58.439 37.500 0.00 0.00 0.00 2.87
95 96 7.965718 TCATGAAAAGAAAAGAAACCATCCAT 58.034 30.769 0.00 0.00 0.00 3.41
105 106 3.193267 CGGCCCATCATGAAAAGAAAAGA 59.807 43.478 0.00 0.00 0.00 2.52
106 107 3.514645 CGGCCCATCATGAAAAGAAAAG 58.485 45.455 0.00 0.00 0.00 2.27
111 112 0.101759 CAGCGGCCCATCATGAAAAG 59.898 55.000 0.00 0.00 0.00 2.27
113 114 2.417257 GCAGCGGCCCATCATGAAA 61.417 57.895 0.00 0.00 0.00 2.69
127 128 2.890474 CACCATACCCGTCGCAGC 60.890 66.667 0.00 0.00 0.00 5.25
128 129 1.669049 TACCACCATACCCGTCGCAG 61.669 60.000 0.00 0.00 0.00 5.18
135 137 1.758280 TGACATCGTACCACCATACCC 59.242 52.381 0.00 0.00 0.00 3.69
151 153 1.682257 TGGCCGAACCATCATGACA 59.318 52.632 0.00 0.00 46.36 3.58
166 168 3.508793 ACCATATATGCAGCAAAGATGGC 59.491 43.478 23.41 0.00 36.61 4.40
167 169 5.717078 AACCATATATGCAGCAAAGATGG 57.283 39.130 22.48 22.48 38.65 3.51
182 184 9.923143 CATCATTGCATCTGAATAAAACCATAT 57.077 29.630 3.85 0.00 0.00 1.78
183 185 8.361889 CCATCATTGCATCTGAATAAAACCATA 58.638 33.333 3.85 0.00 0.00 2.74
184 186 7.147620 ACCATCATTGCATCTGAATAAAACCAT 60.148 33.333 3.85 0.00 0.00 3.55
185 187 6.154877 ACCATCATTGCATCTGAATAAAACCA 59.845 34.615 3.85 0.00 0.00 3.67
209 211 2.208431 CATGGATCTCCGCTTCAAGAC 58.792 52.381 0.00 0.00 39.43 3.01
213 215 0.462581 GTGCATGGATCTCCGCTTCA 60.463 55.000 0.00 0.00 39.43 3.02
246 248 2.878406 TGTGTGTTTGAGAGCTAAAGCC 59.122 45.455 0.00 0.00 43.38 4.35
259 261 3.081061 TGACTTGCAGTTCTGTGTGTTT 58.919 40.909 1.78 0.00 0.00 2.83
279 281 6.968904 CCTCAATTAAATTTGACTGGACGATG 59.031 38.462 0.00 0.00 32.39 3.84
296 298 8.206126 TGATAAGATGGACATAGCCTCAATTA 57.794 34.615 0.00 0.00 0.00 1.40
307 309 9.504708 GAGATTCTCATTTGATAAGATGGACAT 57.495 33.333 8.84 0.00 0.00 3.06
345 347 3.323115 TCTCAGCTATCAACTGCCCATAG 59.677 47.826 0.00 0.00 35.04 2.23
354 356 3.137533 GGCCTTGATCTCAGCTATCAAC 58.862 50.000 6.34 0.00 38.19 3.18
382 384 6.498538 TCTGAGGAATAAACTCTCTCTCCTT 58.501 40.000 0.00 0.00 33.42 3.36
408 410 7.068716 GCTGTCCTATTTTGATCCCTACAAATT 59.931 37.037 0.00 0.00 37.15 1.82
413 415 5.036117 TGCTGTCCTATTTTGATCCCTAC 57.964 43.478 0.00 0.00 0.00 3.18
430 432 3.641434 ATTAGCCAGACAATCTGCTGT 57.359 42.857 0.02 0.00 42.98 4.40
431 433 4.877823 TGTAATTAGCCAGACAATCTGCTG 59.122 41.667 0.02 0.00 42.98 4.41
453 455 4.045104 GAGTACACGATTCTGTATGGCTG 58.955 47.826 0.00 0.00 0.00 4.85
463 465 8.882415 TCCAAAATTATAGGAGTACACGATTC 57.118 34.615 0.00 0.00 0.00 2.52
504 566 3.243771 TGTTGTTGTTGTTGTTTTCCGGT 60.244 39.130 0.00 0.00 0.00 5.28
505 567 3.318017 TGTTGTTGTTGTTGTTTTCCGG 58.682 40.909 0.00 0.00 0.00 5.14
507 569 5.659048 TGTTGTTGTTGTTGTTGTTTTCC 57.341 34.783 0.00 0.00 0.00 3.13
513 575 5.395325 TGTTGTTGTTGTTGTTGTTGTTG 57.605 34.783 0.00 0.00 0.00 3.33
516 578 5.395325 TGTTGTTGTTGTTGTTGTTGTTG 57.605 34.783 0.00 0.00 0.00 3.33
522 584 5.395325 TGTTGTTGTTGTTGTTGTTGTTG 57.605 34.783 0.00 0.00 0.00 3.33
523 585 5.351465 TGTTGTTGTTGTTGTTGTTGTTGTT 59.649 32.000 0.00 0.00 0.00 2.83
524 586 4.870426 TGTTGTTGTTGTTGTTGTTGTTGT 59.130 33.333 0.00 0.00 0.00 3.32
525 587 5.395325 TGTTGTTGTTGTTGTTGTTGTTG 57.605 34.783 0.00 0.00 0.00 3.33
526 588 5.351465 TGTTGTTGTTGTTGTTGTTGTTGTT 59.649 32.000 0.00 0.00 0.00 2.83
528 590 5.395325 TGTTGTTGTTGTTGTTGTTGTTG 57.605 34.783 0.00 0.00 0.00 3.33
534 596 5.395325 TGTTGTTGTTGTTGTTGTTGTTG 57.605 34.783 0.00 0.00 0.00 3.33
539 601 4.870426 TGTTGTTGTTGTTGTTGTTGTTGT 59.130 33.333 0.00 0.00 0.00 3.32
540 602 5.395325 TGTTGTTGTTGTTGTTGTTGTTG 57.605 34.783 0.00 0.00 0.00 3.33
541 603 5.351465 TGTTGTTGTTGTTGTTGTTGTTGTT 59.649 32.000 0.00 0.00 0.00 2.83
542 604 4.870426 TGTTGTTGTTGTTGTTGTTGTTGT 59.130 33.333 0.00 0.00 0.00 3.32
543 605 5.395325 TGTTGTTGTTGTTGTTGTTGTTG 57.605 34.783 0.00 0.00 0.00 3.33
544 606 5.351465 TGTTGTTGTTGTTGTTGTTGTTGTT 59.649 32.000 0.00 0.00 0.00 2.83
545 607 4.870426 TGTTGTTGTTGTTGTTGTTGTTGT 59.130 33.333 0.00 0.00 0.00 3.32
546 608 5.395325 TGTTGTTGTTGTTGTTGTTGTTG 57.605 34.783 0.00 0.00 0.00 3.33
547 609 5.351465 TGTTGTTGTTGTTGTTGTTGTTGTT 59.649 32.000 0.00 0.00 0.00 2.83
548 610 4.870426 TGTTGTTGTTGTTGTTGTTGTTGT 59.130 33.333 0.00 0.00 0.00 3.32
549 611 5.395325 TGTTGTTGTTGTTGTTGTTGTTG 57.605 34.783 0.00 0.00 0.00 3.33
550 612 5.582665 ACTTGTTGTTGTTGTTGTTGTTGTT 59.417 32.000 0.00 0.00 0.00 2.83
551 613 5.112686 ACTTGTTGTTGTTGTTGTTGTTGT 58.887 33.333 0.00 0.00 0.00 3.32
552 614 5.649602 ACTTGTTGTTGTTGTTGTTGTTG 57.350 34.783 0.00 0.00 0.00 3.33
553 615 6.419413 CAGTACTTGTTGTTGTTGTTGTTGTT 59.581 34.615 0.00 0.00 0.00 2.83
554 616 5.918011 CAGTACTTGTTGTTGTTGTTGTTGT 59.082 36.000 0.00 0.00 0.00 3.32
555 617 6.146216 TCAGTACTTGTTGTTGTTGTTGTTG 58.854 36.000 0.00 0.00 0.00 3.33
556 618 6.320494 TCAGTACTTGTTGTTGTTGTTGTT 57.680 33.333 0.00 0.00 0.00 2.83
557 619 5.950758 TCAGTACTTGTTGTTGTTGTTGT 57.049 34.783 0.00 0.00 0.00 3.32
558 620 6.251163 CACATCAGTACTTGTTGTTGTTGTTG 59.749 38.462 0.00 0.00 37.57 3.33
559 621 6.072175 ACACATCAGTACTTGTTGTTGTTGTT 60.072 34.615 0.00 0.00 37.57 2.83
560 622 5.414454 ACACATCAGTACTTGTTGTTGTTGT 59.586 36.000 0.00 0.00 37.57 3.32
561 623 5.879237 ACACATCAGTACTTGTTGTTGTTG 58.121 37.500 0.00 0.00 37.57 3.33
562 624 5.065988 GGACACATCAGTACTTGTTGTTGTT 59.934 40.000 0.00 0.00 37.57 2.83
563 625 4.574828 GGACACATCAGTACTTGTTGTTGT 59.425 41.667 0.00 0.00 37.57 3.32
564 626 4.024048 GGGACACATCAGTACTTGTTGTTG 60.024 45.833 0.00 0.00 37.57 3.33
565 627 4.134563 GGGACACATCAGTACTTGTTGTT 58.865 43.478 0.00 0.00 37.57 2.83
566 628 3.740115 GGGACACATCAGTACTTGTTGT 58.260 45.455 0.00 0.00 39.68 3.32
567 629 2.736721 CGGGACACATCAGTACTTGTTG 59.263 50.000 0.00 0.00 33.58 3.33
568 630 2.289444 CCGGGACACATCAGTACTTGTT 60.289 50.000 0.00 0.00 0.00 2.83
569 631 1.275291 CCGGGACACATCAGTACTTGT 59.725 52.381 0.00 0.00 0.00 3.16
570 632 2.007049 GCCGGGACACATCAGTACTTG 61.007 57.143 2.18 0.00 0.00 3.16
571 633 0.249398 GCCGGGACACATCAGTACTT 59.751 55.000 2.18 0.00 0.00 2.24
572 634 1.614241 GGCCGGGACACATCAGTACT 61.614 60.000 2.18 0.00 0.00 2.73
573 635 1.153429 GGCCGGGACACATCAGTAC 60.153 63.158 2.18 0.00 0.00 2.73
574 636 2.717044 CGGCCGGGACACATCAGTA 61.717 63.158 20.10 0.00 0.00 2.74
575 637 4.082523 CGGCCGGGACACATCAGT 62.083 66.667 20.10 0.00 0.00 3.41
590 652 3.716195 TCACCATCACCCAGGCGG 61.716 66.667 0.00 0.00 37.81 6.13
591 653 2.436646 GTCACCATCACCCAGGCG 60.437 66.667 0.00 0.00 0.00 5.52
592 654 2.436646 CGTCACCATCACCCAGGC 60.437 66.667 0.00 0.00 0.00 4.85
593 655 1.079127 GTCGTCACCATCACCCAGG 60.079 63.158 0.00 0.00 0.00 4.45
594 656 1.446099 CGTCGTCACCATCACCCAG 60.446 63.158 0.00 0.00 0.00 4.45
595 657 2.654289 CGTCGTCACCATCACCCA 59.346 61.111 0.00 0.00 0.00 4.51
596 658 2.125673 CCGTCGTCACCATCACCC 60.126 66.667 0.00 0.00 0.00 4.61
597 659 0.736325 CTTCCGTCGTCACCATCACC 60.736 60.000 0.00 0.00 0.00 4.02
598 660 0.242825 TCTTCCGTCGTCACCATCAC 59.757 55.000 0.00 0.00 0.00 3.06
599 661 0.963225 TTCTTCCGTCGTCACCATCA 59.037 50.000 0.00 0.00 0.00 3.07
600 662 2.295253 ATTCTTCCGTCGTCACCATC 57.705 50.000 0.00 0.00 0.00 3.51
601 663 2.762535 AATTCTTCCGTCGTCACCAT 57.237 45.000 0.00 0.00 0.00 3.55
602 664 3.006110 AGTTAATTCTTCCGTCGTCACCA 59.994 43.478 0.00 0.00 0.00 4.17
603 665 3.367025 CAGTTAATTCTTCCGTCGTCACC 59.633 47.826 0.00 0.00 0.00 4.02
604 666 3.985925 ACAGTTAATTCTTCCGTCGTCAC 59.014 43.478 0.00 0.00 0.00 3.67
605 667 4.232221 GACAGTTAATTCTTCCGTCGTCA 58.768 43.478 0.00 0.00 0.00 4.35
606 668 4.089636 GTGACAGTTAATTCTTCCGTCGTC 59.910 45.833 0.00 0.00 0.00 4.20
607 669 3.985925 GTGACAGTTAATTCTTCCGTCGT 59.014 43.478 0.00 0.00 0.00 4.34
608 670 4.235360 AGTGACAGTTAATTCTTCCGTCG 58.765 43.478 0.00 0.00 0.00 5.12
609 671 4.323868 CGAGTGACAGTTAATTCTTCCGTC 59.676 45.833 0.00 0.00 0.00 4.79
610 672 4.235360 CGAGTGACAGTTAATTCTTCCGT 58.765 43.478 0.00 0.00 0.00 4.69
611 673 4.090066 CACGAGTGACAGTTAATTCTTCCG 59.910 45.833 0.00 0.00 0.00 4.30
612 674 4.143094 GCACGAGTGACAGTTAATTCTTCC 60.143 45.833 7.50 0.00 0.00 3.46
613 675 4.686554 AGCACGAGTGACAGTTAATTCTTC 59.313 41.667 7.50 0.00 0.00 2.87
614 676 4.449068 CAGCACGAGTGACAGTTAATTCTT 59.551 41.667 7.50 0.00 0.00 2.52
615 677 3.990469 CAGCACGAGTGACAGTTAATTCT 59.010 43.478 7.50 0.00 0.00 2.40
616 678 3.123621 CCAGCACGAGTGACAGTTAATTC 59.876 47.826 7.50 0.00 0.00 2.17
617 679 3.067106 CCAGCACGAGTGACAGTTAATT 58.933 45.455 7.50 0.00 0.00 1.40
618 680 2.037251 ACCAGCACGAGTGACAGTTAAT 59.963 45.455 7.50 0.00 0.00 1.40
619 681 1.411246 ACCAGCACGAGTGACAGTTAA 59.589 47.619 7.50 0.00 0.00 2.01
620 682 1.037493 ACCAGCACGAGTGACAGTTA 58.963 50.000 7.50 0.00 0.00 2.24
621 683 0.178068 AACCAGCACGAGTGACAGTT 59.822 50.000 7.50 3.77 0.00 3.16
622 684 0.178068 AAACCAGCACGAGTGACAGT 59.822 50.000 7.50 0.00 0.00 3.55
640 702 2.942376 CTGCGTGCAGGGAATATAACAA 59.058 45.455 14.00 0.00 40.17 2.83
742 815 5.301045 CCTAACCTAATCACCATACACTCGA 59.699 44.000 0.00 0.00 0.00 4.04
743 816 5.509163 CCCTAACCTAATCACCATACACTCG 60.509 48.000 0.00 0.00 0.00 4.18
744 817 5.365895 ACCCTAACCTAATCACCATACACTC 59.634 44.000 0.00 0.00 0.00 3.51
745 818 5.286221 ACCCTAACCTAATCACCATACACT 58.714 41.667 0.00 0.00 0.00 3.55
746 819 5.625568 ACCCTAACCTAATCACCATACAC 57.374 43.478 0.00 0.00 0.00 2.90
753 829 4.398358 GGCAAAGAACCCTAACCTAATCAC 59.602 45.833 0.00 0.00 0.00 3.06
820 902 0.027979 CCAAAGCAGACACACACACG 59.972 55.000 0.00 0.00 0.00 4.49
890 989 5.064198 CGTACTACAGAGAGACAGAAAGAGG 59.936 48.000 0.00 0.00 0.00 3.69
950 1086 8.771521 TGGCCTTTTATACACTACTACATCTA 57.228 34.615 3.32 0.00 0.00 1.98
1005 1143 6.015010 CCAAATTGAGAGGTAGAGGATATCGT 60.015 42.308 0.00 0.00 0.00 3.73
1006 1144 6.015010 ACCAAATTGAGAGGTAGAGGATATCG 60.015 42.308 0.00 0.00 32.92 2.92
1007 1145 7.309770 ACCAAATTGAGAGGTAGAGGATATC 57.690 40.000 0.00 0.00 32.92 1.63
1008 1146 7.698163 AACCAAATTGAGAGGTAGAGGATAT 57.302 36.000 0.00 0.00 34.63 1.63
1009 1147 7.182026 TGAAACCAAATTGAGAGGTAGAGGATA 59.818 37.037 0.00 0.00 34.63 2.59
1113 1276 2.203070 CCGACCTATGGCTGTGGC 60.203 66.667 0.00 0.00 37.82 5.01
1424 1593 2.052690 CCTGTCGTCGATGGGGACT 61.053 63.158 4.48 0.00 34.75 3.85
1688 1868 3.429141 TCGGTGAGGTCGTCGAGC 61.429 66.667 16.47 16.47 0.00 5.03
1718 1904 3.989698 ATCACTCTTGACGGCGGCG 62.990 63.158 31.06 31.06 33.38 6.46
1790 1988 1.827344 TCACAGTCATAGCTGGTGGAG 59.173 52.381 0.00 0.00 40.59 3.86
1807 2005 2.821366 CGGCATGGTGGAGCTCAC 60.821 66.667 17.19 11.54 45.34 3.51
1838 2045 1.990060 ATCGGCCGGATATCCAGGG 60.990 63.158 27.83 18.58 32.17 4.45
1839 2046 1.219124 CATCGGCCGGATATCCAGG 59.781 63.158 27.83 21.58 32.85 4.45
1846 2053 3.855503 ATGCATGCATCGGCCGGAT 62.856 57.895 27.46 14.79 40.13 4.18
1847 2054 4.567488 ATGCATGCATCGGCCGGA 62.567 61.111 27.46 12.89 40.13 5.14
1848 2055 4.337060 CATGCATGCATCGGCCGG 62.337 66.667 30.07 14.24 40.13 6.13
1902 2123 4.781616 TGCATGCATGGGGGTGGG 62.782 66.667 27.34 0.11 0.00 4.61
1972 2228 2.115266 AACCAAAGCCCAGGACCG 59.885 61.111 0.00 0.00 0.00 4.79
2023 2279 1.455786 AGAAAAACGCACACTCGATCG 59.544 47.619 9.36 9.36 0.00 3.69
2024 2280 3.521524 AAGAAAAACGCACACTCGATC 57.478 42.857 0.00 0.00 0.00 3.69
2025 2281 3.963383 AAAGAAAAACGCACACTCGAT 57.037 38.095 0.00 0.00 0.00 3.59
2026 2282 3.750639 AAAAGAAAAACGCACACTCGA 57.249 38.095 0.00 0.00 0.00 4.04
2027 2283 3.001168 CCAAAAAGAAAAACGCACACTCG 60.001 43.478 0.00 0.00 0.00 4.18
2094 2353 0.591994 CCACACACGCACACACATTG 60.592 55.000 0.00 0.00 0.00 2.82
2095 2354 0.746204 TCCACACACGCACACACATT 60.746 50.000 0.00 0.00 0.00 2.71
2151 2410 7.946381 TTTGTGTGTGGATTTGGCTATATAA 57.054 32.000 0.00 0.00 0.00 0.98
2322 2584 6.471841 CGATCGATCTGATTCTATTGTGATCC 59.528 42.308 22.43 0.00 37.47 3.36
2327 2589 5.465051 CCACGATCGATCTGATTCTATTGT 58.535 41.667 24.34 6.64 37.47 2.71
2339 2601 2.531912 CGCTATAATGCCACGATCGATC 59.468 50.000 24.34 15.68 0.00 3.69
2340 2602 2.163613 TCGCTATAATGCCACGATCGAT 59.836 45.455 24.34 0.00 0.00 3.59
2341 2603 1.538075 TCGCTATAATGCCACGATCGA 59.462 47.619 24.34 0.00 0.00 3.59
2342 2604 1.977188 TCGCTATAATGCCACGATCG 58.023 50.000 14.88 14.88 0.00 3.69
2376 2638 2.161609 GTGGCCACCTGTAAGATTTTCG 59.838 50.000 26.31 0.00 34.07 3.46
2416 2678 4.473477 TTTGGTGTTTCCGGATTGTTTT 57.527 36.364 4.15 0.00 39.52 2.43
2427 2698 8.925700 GTGAAGAATCCATATTTTTGGTGTTTC 58.074 33.333 0.00 0.00 38.01 2.78
2433 2704 9.090692 GATGTTGTGAAGAATCCATATTTTTGG 57.909 33.333 0.00 0.00 38.18 3.28
2434 2705 9.865321 AGATGTTGTGAAGAATCCATATTTTTG 57.135 29.630 0.00 0.00 0.00 2.44
2436 2707 9.471702 AGAGATGTTGTGAAGAATCCATATTTT 57.528 29.630 0.00 0.00 0.00 1.82
2437 2708 8.900781 CAGAGATGTTGTGAAGAATCCATATTT 58.099 33.333 0.00 0.00 0.00 1.40
2438 2709 8.051535 ACAGAGATGTTGTGAAGAATCCATATT 58.948 33.333 0.00 0.00 0.00 1.28
2439 2710 7.571919 ACAGAGATGTTGTGAAGAATCCATAT 58.428 34.615 0.00 0.00 0.00 1.78
2440 2711 6.950842 ACAGAGATGTTGTGAAGAATCCATA 58.049 36.000 0.00 0.00 0.00 2.74
2441 2712 5.813383 ACAGAGATGTTGTGAAGAATCCAT 58.187 37.500 0.00 0.00 0.00 3.41
2497 2776 9.289782 GAGTTATAGCTCAATGTTTTGGGATAT 57.710 33.333 11.38 2.38 44.82 1.63
2532 2811 0.676466 TTGCTTACACCGCTCCATGG 60.676 55.000 4.97 4.97 0.00 3.66
2596 2878 1.272147 GGGTCCCTTGAGCACTTTCAT 60.272 52.381 0.00 0.00 40.83 2.57
2602 2884 0.329596 ATCTTGGGTCCCTTGAGCAC 59.670 55.000 10.00 0.00 40.83 4.40
2670 2961 2.634940 TGTCTCCTTCCTTCTCCAACTG 59.365 50.000 0.00 0.00 0.00 3.16
2742 3033 1.024579 GTGTTATGACGGGGGTGCTG 61.025 60.000 0.00 0.00 0.00 4.41
2780 3071 0.322975 CCCTTCCGATCCCTGCATAG 59.677 60.000 0.00 0.00 0.00 2.23


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

AutoCloner maintained by Alex Coulton.