Multiple sequence alignment - TraesCS2D01G397900

Loading Multiple Alignment...

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 TraesCS2D01G397900 chr2D 100.000 5129 0 0 1 5129 509940274 509945402 0.000000e+00 9472.0
1 TraesCS2D01G397900 chr2D 99.206 126 1 0 5004 5129 600972488 600972363 1.440000e-55 228.0
2 TraesCS2D01G397900 chr2D 93.617 94 5 1 54 147 509940291 509940383 6.920000e-29 139.0
3 TraesCS2D01G397900 chr2D 93.617 94 5 1 18 110 509940327 509940420 6.920000e-29 139.0
4 TraesCS2D01G397900 chr2A 90.521 2954 151 50 2131 5001 653678705 653681612 0.000000e+00 3784.0
5 TraesCS2D01G397900 chr2A 91.825 1211 49 22 922 2106 653677438 653678624 0.000000e+00 1642.0
6 TraesCS2D01G397900 chr2A 84.078 358 22 10 1 355 653674908 653675233 3.860000e-81 313.0
7 TraesCS2D01G397900 chr2A 86.555 238 18 2 456 693 653676752 653676975 3.070000e-62 250.0
8 TraesCS2D01G397900 chr2A 95.370 108 1 2 725 828 653677304 653677411 8.830000e-38 169.0
9 TraesCS2D01G397900 chr2A 93.617 94 4 2 18 110 653674962 653675054 6.920000e-29 139.0
10 TraesCS2D01G397900 chr2B 92.535 1621 85 13 2101 3695 599596129 599597739 0.000000e+00 2290.0
11 TraesCS2D01G397900 chr2B 90.296 1587 63 30 464 1991 599594476 599596030 0.000000e+00 1993.0
12 TraesCS2D01G397900 chr2B 90.647 866 39 22 4160 5001 599598260 599599107 0.000000e+00 1112.0
13 TraesCS2D01G397900 chr2B 93.231 458 16 5 3733 4175 599597745 599598202 0.000000e+00 660.0
14 TraesCS2D01G397900 chr2B 89.734 263 27 0 181 443 99276834 99276572 2.290000e-88 337.0
15 TraesCS2D01G397900 chr2B 90.038 261 25 1 183 443 368084435 368084694 2.290000e-88 337.0
16 TraesCS2D01G397900 chr2B 97.895 95 2 0 2012 2106 599596013 599596107 1.140000e-36 165.0
17 TraesCS2D01G397900 chr6A 76.854 1106 206 40 2437 3516 475000347 474999266 3.440000e-161 579.0
18 TraesCS2D01G397900 chr6A 90.977 399 35 1 1434 1831 475001584 475001186 2.100000e-148 536.0
19 TraesCS2D01G397900 chr6B 90.977 399 35 1 1434 1831 485291609 485292007 2.100000e-148 536.0
20 TraesCS2D01G397900 chr6B 80.614 619 98 16 2433 3037 485292906 485293516 4.680000e-125 459.0
21 TraesCS2D01G397900 chr6B 93.443 122 7 1 5008 5129 444317756 444317876 4.080000e-41 180.0
22 TraesCS2D01G397900 chr6D 90.727 399 36 1 1434 1831 335377029 335376631 9.780000e-147 531.0
23 TraesCS2D01G397900 chr6D 81.068 618 92 20 2437 3037 335375779 335375170 2.160000e-128 470.0
24 TraesCS2D01G397900 chr7D 90.458 262 22 3 183 443 107948788 107949047 4.920000e-90 342.0
25 TraesCS2D01G397900 chr7D 90.458 262 22 3 183 443 174488869 174489128 4.920000e-90 342.0
26 TraesCS2D01G397900 chr7D 90.076 262 23 3 183 443 219168139 219168398 2.290000e-88 337.0
27 TraesCS2D01G397900 chr7D 99.174 121 1 0 5009 5129 135783281 135783161 8.650000e-53 219.0
28 TraesCS2D01G397900 chr7D 93.023 43 3 0 34 76 189248594 189248636 4.290000e-06 63.9
29 TraesCS2D01G397900 chr4D 90.458 262 22 3 183 443 180102895 180103154 4.920000e-90 342.0
30 TraesCS2D01G397900 chr4D 95.745 141 1 5 4992 5129 344374892 344375030 6.680000e-54 222.0
31 TraesCS2D01G397900 chr4D 80.288 208 37 4 2437 2642 168197115 168197320 2.470000e-33 154.0
32 TraesCS2D01G397900 chr7A 90.076 262 23 3 183 443 321124164 321124423 2.290000e-88 337.0
33 TraesCS2D01G397900 chr7A 100.000 35 0 0 70 104 70832926 70832960 1.190000e-06 65.8
34 TraesCS2D01G397900 chr7A 97.143 35 1 0 70 104 74647324 74647290 5.550000e-05 60.2
35 TraesCS2D01G397900 chr5D 90.076 262 23 3 183 443 309577124 309577383 2.290000e-88 337.0
36 TraesCS2D01G397900 chr5D 74.634 205 48 4 2442 2644 197152199 197151997 2.540000e-13 87.9
37 TraesCS2D01G397900 chr4B 90.076 262 22 3 183 443 165186047 165185789 2.290000e-88 337.0
38 TraesCS2D01G397900 chr4B 85.185 162 22 2 2482 2642 155379321 155379161 1.140000e-36 165.0
39 TraesCS2D01G397900 chr4B 95.000 40 2 0 70 109 184237382 184237421 4.290000e-06 63.9
40 TraesCS2D01G397900 chr5B 95.041 121 6 0 5009 5129 473808736 473808856 1.880000e-44 191.0
41 TraesCS2D01G397900 chr5B 92.562 121 9 0 5009 5129 473808875 473808995 1.900000e-39 174.0
42 TraesCS2D01G397900 chr3A 95.041 121 6 0 5009 5129 20311536 20311656 1.880000e-44 191.0
43 TraesCS2D01G397900 chr4A 94.215 121 6 1 5009 5129 661004640 661004521 3.150000e-42 183.0
44 TraesCS2D01G397900 chr1A 92.623 122 9 0 5008 5129 337449823 337449944 5.280000e-40 176.0
45 TraesCS2D01G397900 chr1A 77.564 156 30 4 1672 1823 357063031 357063185 7.070000e-14 89.8
46 TraesCS2D01G397900 chr1A 95.349 43 2 0 34 76 547409947 547409989 9.220000e-08 69.4
47 TraesCS2D01G397900 chr1A 93.023 43 3 0 70 112 547409947 547409989 4.290000e-06 63.9
48 TraesCS2D01G397900 chr5A 75.243 206 45 6 2442 2644 227923959 227924161 5.470000e-15 93.5
49 TraesCS2D01G397900 chr1D 77.564 156 30 4 1672 1823 285442421 285442575 7.070000e-14 89.8
50 TraesCS2D01G397900 chr1D 97.561 41 1 0 34 74 450464449 450464409 2.560000e-08 71.3
51 TraesCS2D01G397900 chr1D 95.122 41 2 0 70 110 450464449 450464409 1.190000e-06 65.8
52 TraesCS2D01G397900 chr1D 93.023 43 3 0 34 76 231020512 231020470 4.290000e-06 63.9
53 TraesCS2D01G397900 chr1B 77.564 156 30 4 1672 1823 388009185 388009339 7.070000e-14 89.8
54 TraesCS2D01G397900 chrUn 93.023 43 3 0 34 76 60962313 60962355 4.290000e-06 63.9


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 TraesCS2D01G397900 chr2D 509940274 509945402 5128 False 9472.0 9472 100.000000 1 5129 1 chr2D.!!$F1 5128
1 TraesCS2D01G397900 chr2A 653674908 653681612 6704 False 1049.5 3784 90.327667 1 5001 6 chr2A.!!$F1 5000
2 TraesCS2D01G397900 chr2B 599594476 599599107 4631 False 1244.0 2290 92.920800 464 5001 5 chr2B.!!$F2 4537
3 TraesCS2D01G397900 chr6A 474999266 475001584 2318 True 557.5 579 83.915500 1434 3516 2 chr6A.!!$R1 2082
4 TraesCS2D01G397900 chr6B 485291609 485293516 1907 False 497.5 536 85.795500 1434 3037 2 chr6B.!!$F2 1603
5 TraesCS2D01G397900 chr6D 335375170 335377029 1859 True 500.5 531 85.897500 1434 3037 2 chr6D.!!$R1 1603

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
638 2060 0.320771 GCTCTGTTCGCTTTCCCTGA 60.321 55.000 0.00 0.0 0.0 3.86 F
1066 2816 2.046507 CAGCCAGTCCAGTCCAGC 60.047 66.667 0.00 0.0 0.0 4.85 F
2218 4621 0.690192 TTTGCCGGATCAGGTTCTCA 59.310 50.000 13.75 0.0 0.0 3.27 F
3041 5563 0.320421 GACGCTGCCTGGTAAAGTGA 60.320 55.000 11.84 0.0 0.0 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1920 3701 1.639108 ACCTCAATTAACCCCTCACCC 59.361 52.381 0.00 0.0 0.00 4.61 R
2669 5163 1.075212 TGGATGATGGTTTGAGGTGCA 59.925 47.619 0.00 0.0 0.00 4.57 R
3216 5741 0.184451 CTAGCAATCCTGGGTGGCAT 59.816 55.000 9.45 0.0 35.26 4.40 R
5037 7719 0.033405 TGACGTAAGAGGGGAGAGGG 60.033 60.000 0.00 0.0 43.62 4.30 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
42 44 8.434661 CAAACATTTATTTACACAATCACAGGC 58.565 33.333 0.00 0.00 0.00 4.85
61 63 6.311935 CACAGGCAGGATTTGATAAACATTTG 59.688 38.462 0.00 0.00 0.00 2.32
80 82 6.476380 ACATTTGTTTACACAATCACAAGCAG 59.524 34.615 0.00 0.00 42.66 4.24
92 94 7.062605 CACAATCACAAGCAGGATTTGATAAAC 59.937 37.037 0.00 0.00 31.63 2.01
93 95 6.839124 ATCACAAGCAGGATTTGATAAACA 57.161 33.333 0.00 0.00 0.00 2.83
94 96 6.839124 TCACAAGCAGGATTTGATAAACAT 57.161 33.333 0.00 0.00 0.00 2.71
116 119 6.815641 ACATTTGTTTACACAATCACAAGCAA 59.184 30.769 0.00 0.00 42.66 3.91
120 123 6.437928 TGTTTACACAATCACAAGCAAGATC 58.562 36.000 0.00 0.00 0.00 2.75
164 168 9.407380 ACACAATCAAATTAATATGAGCAGGTA 57.593 29.630 0.00 0.00 0.00 3.08
180 184 3.427503 GCAGGTAAATCCCAAATCACGTG 60.428 47.826 9.94 9.94 36.75 4.49
184 188 4.095334 GGTAAATCCCAAATCACGTGGTAC 59.905 45.833 17.00 0.00 34.01 3.34
187 191 2.253610 TCCCAAATCACGTGGTACTCT 58.746 47.619 17.00 0.00 34.01 3.24
192 196 4.169508 CAAATCACGTGGTACTCTCTCTG 58.830 47.826 17.00 0.00 0.00 3.35
227 231 8.659925 ACTCTGCATATTAGATTTGACTGAAG 57.340 34.615 0.00 0.00 0.00 3.02
229 233 8.654230 TCTGCATATTAGATTTGACTGAAGTC 57.346 34.615 3.41 3.41 44.97 3.01
419 1806 5.640732 ACTTTGTTTAAAGCTGATATGCGG 58.359 37.500 0.00 0.00 45.72 5.69
432 1819 8.396272 AGCTGATATGCGGAGTAAATAAAAAT 57.604 30.769 0.00 0.00 38.13 1.82
433 1820 9.502091 AGCTGATATGCGGAGTAAATAAAAATA 57.498 29.630 0.00 0.00 38.13 1.40
492 1914 3.454573 CTGCATGCCGGCAACCAT 61.455 61.111 36.33 15.14 44.40 3.55
544 1966 1.794785 CTGCACGCAATCTGCAACG 60.795 57.895 0.00 0.00 45.36 4.10
610 2032 3.746949 CTCGCTCCACTGCATCCCC 62.747 68.421 0.00 0.00 0.00 4.81
612 2034 4.101448 GCTCCACTGCATCCCCGT 62.101 66.667 0.00 0.00 0.00 5.28
635 2057 0.603975 ACAGCTCTGTTCGCTTTCCC 60.604 55.000 0.00 0.00 41.83 3.97
637 2059 0.321122 AGCTCTGTTCGCTTTCCCTG 60.321 55.000 0.00 0.00 32.98 4.45
638 2060 0.320771 GCTCTGTTCGCTTTCCCTGA 60.321 55.000 0.00 0.00 0.00 3.86
862 2587 2.280186 ATTTCGGAGCGCGATCCC 60.280 61.111 35.38 18.96 35.82 3.85
914 2646 2.747855 CGCTCTCCCCTGCCAAAC 60.748 66.667 0.00 0.00 0.00 2.93
1066 2816 2.046507 CAGCCAGTCCAGTCCAGC 60.047 66.667 0.00 0.00 0.00 4.85
1067 2817 3.699894 AGCCAGTCCAGTCCAGCG 61.700 66.667 0.00 0.00 0.00 5.18
1068 2818 4.767255 GCCAGTCCAGTCCAGCGG 62.767 72.222 0.00 0.00 0.00 5.52
1069 2819 2.997315 CCAGTCCAGTCCAGCGGA 60.997 66.667 0.00 0.00 0.00 5.54
1094 2858 2.104729 CAGAGGAGAGCAGAGCGC 59.895 66.667 0.00 0.00 42.91 5.92
1288 3057 2.725008 CTCCCTCGTCTCCATCGC 59.275 66.667 0.00 0.00 0.00 4.58
2110 4483 4.101448 CCCGGGAAGGAGCACTGG 62.101 72.222 18.48 0.00 45.00 4.00
2212 4615 1.533625 TTGTTCTTTGCCGGATCAGG 58.466 50.000 5.05 7.64 0.00 3.86
2218 4621 0.690192 TTTGCCGGATCAGGTTCTCA 59.310 50.000 13.75 0.00 0.00 3.27
2264 4667 4.082625 TGTGCAGTGATGTTGAATTGGATC 60.083 41.667 0.00 0.00 0.00 3.36
2302 4766 3.023946 CTGCGAATCATAGTAGCAGCT 57.976 47.619 0.00 0.00 46.69 4.24
2325 4803 4.022329 TCTGCGTACTCTGAAGAACATCAA 60.022 41.667 0.00 0.00 0.00 2.57
2380 4873 4.554134 CGATAAGCTGATTGCACCATTCAG 60.554 45.833 10.96 10.96 45.94 3.02
2402 4895 5.185635 CAGGCATAGGAATTTGGTTTTCAGA 59.814 40.000 0.00 0.00 0.00 3.27
2617 5111 3.204827 GCCTTCGACATGGCGCAT 61.205 61.111 18.42 0.00 39.71 4.73
2662 5156 2.296471 GCAGCTCTACGGTATGTACCAT 59.704 50.000 9.69 0.00 46.80 3.55
2669 5163 6.516860 GCTCTACGGTATGTACCATTCTGATT 60.517 42.308 9.69 0.00 46.80 2.57
2672 5166 4.126437 CGGTATGTACCATTCTGATTGCA 58.874 43.478 9.69 0.00 46.80 4.08
2686 5205 3.433343 TGATTGCACCTCAAACCATCAT 58.567 40.909 0.00 0.00 38.34 2.45
2703 5222 5.466728 ACCATCATCCATCGAATAACTTTCG 59.533 40.000 1.49 1.49 42.74 3.46
2706 5225 5.047847 TCATCCATCGAATAACTTTCGGTC 58.952 41.667 7.77 0.00 41.78 4.79
2769 5291 1.687563 TCGAGGTGGATCGCATTCTA 58.312 50.000 0.00 0.00 42.43 2.10
2898 5420 0.814457 AGTCTGTCGCTAAGAGCCTG 59.186 55.000 0.00 0.00 38.18 4.85
2983 5505 4.722700 GCAAGGCCTCCCGCAGAA 62.723 66.667 5.23 0.00 40.31 3.02
3040 5562 0.320771 AGACGCTGCCTGGTAAAGTG 60.321 55.000 0.00 0.53 0.00 3.16
3041 5563 0.320421 GACGCTGCCTGGTAAAGTGA 60.320 55.000 11.84 0.00 0.00 3.41
3049 5571 4.331968 TGCCTGGTAAAGTGATTACTTGG 58.668 43.478 3.30 1.79 46.14 3.61
3065 5587 3.473625 ACTTGGTTACTTACACTGCCAC 58.526 45.455 0.00 0.00 0.00 5.01
3076 5601 5.590259 ACTTACACTGCCACATTATCCATTC 59.410 40.000 0.00 0.00 0.00 2.67
3086 5611 5.887598 CCACATTATCCATTCTGAAGTCCAA 59.112 40.000 0.00 0.00 0.00 3.53
3283 5808 5.137403 CGAAATGTTTAACGAAGACACCAG 58.863 41.667 0.00 0.00 0.00 4.00
3374 5899 3.181484 GCAACTTGCTGGATATGAATGCA 60.181 43.478 6.50 0.00 40.96 3.96
3458 5983 4.870363 CAACCATTGGAAATTCAACGACT 58.130 39.130 10.37 0.00 0.00 4.18
3473 5998 4.899457 TCAACGACTCTTGGGGTGATATAT 59.101 41.667 0.00 0.00 0.00 0.86
3537 6062 0.403271 ACTGCAAACATGGCTCCTCT 59.597 50.000 0.00 0.00 0.00 3.69
3542 6067 3.282021 GCAAACATGGCTCCTCTTATGA 58.718 45.455 0.00 0.00 0.00 2.15
3578 6103 0.321021 GCATGCATTTGTTGGGGTGA 59.679 50.000 14.21 0.00 0.00 4.02
3583 6108 3.505386 TGCATTTGTTGGGGTGAGTAAT 58.495 40.909 0.00 0.00 0.00 1.89
3590 6115 3.515502 TGTTGGGGTGAGTAATCTCTCTG 59.484 47.826 0.00 0.00 40.98 3.35
3591 6116 3.474798 TGGGGTGAGTAATCTCTCTGT 57.525 47.619 0.00 0.00 40.98 3.41
3696 6221 1.493022 AGGACAGGTAAACACAAGCCA 59.507 47.619 0.00 0.00 0.00 4.75
3740 6265 5.257082 TGGTTTTCTTGTTCTTGGCTAAC 57.743 39.130 0.00 0.00 0.00 2.34
3746 6271 6.377327 TTCTTGTTCTTGGCTAACTCAAAG 57.623 37.500 0.00 0.00 0.00 2.77
3748 6273 5.296780 TCTTGTTCTTGGCTAACTCAAAGTG 59.703 40.000 0.00 0.00 0.00 3.16
4044 6575 1.658994 TAGCAACGCCCCGAAATAAG 58.341 50.000 0.00 0.00 0.00 1.73
4045 6576 1.226575 GCAACGCCCCGAAATAAGC 60.227 57.895 0.00 0.00 0.00 3.09
4046 6577 1.928706 GCAACGCCCCGAAATAAGCA 61.929 55.000 0.00 0.00 0.00 3.91
4047 6578 0.738389 CAACGCCCCGAAATAAGCAT 59.262 50.000 0.00 0.00 0.00 3.79
4048 6579 0.738389 AACGCCCCGAAATAAGCATG 59.262 50.000 0.00 0.00 0.00 4.06
4049 6580 0.107410 ACGCCCCGAAATAAGCATGA 60.107 50.000 0.00 0.00 0.00 3.07
4050 6581 0.588252 CGCCCCGAAATAAGCATGAG 59.412 55.000 0.00 0.00 0.00 2.90
4071 6611 4.922206 AGAAATTGACAGATACTGGGCAA 58.078 39.130 0.00 0.00 35.51 4.52
4074 6614 7.118723 AGAAATTGACAGATACTGGGCAAATA 58.881 34.615 11.11 0.00 35.08 1.40
4080 6620 5.754782 ACAGATACTGGGCAAATATCACAA 58.245 37.500 0.00 0.00 35.51 3.33
4108 6652 1.592400 CTCTCACCGTGTTCGCCCTA 61.592 60.000 0.00 0.00 35.54 3.53
4131 6675 9.626045 CCTATGGTTTTGAAGTTTTATCTTGTC 57.374 33.333 0.00 0.00 0.00 3.18
4138 6682 8.754991 TTTGAAGTTTTATCTTGTCTGGGTAA 57.245 30.769 0.00 0.00 0.00 2.85
4142 6686 9.232473 GAAGTTTTATCTTGTCTGGGTAATTCT 57.768 33.333 0.00 0.00 0.00 2.40
4147 6691 5.705609 TCTTGTCTGGGTAATTCTTTTGC 57.294 39.130 0.00 0.00 0.00 3.68
4166 6783 7.598493 TCTTTTGCTGAAATAGTTAAACATGGC 59.402 33.333 0.00 0.00 0.00 4.40
4182 6799 3.512516 GCGGAGACATGCCCAAGC 61.513 66.667 0.00 0.00 40.48 4.01
4201 6818 0.397941 CCTGTTCACAGAGGGCAAGA 59.602 55.000 8.61 0.00 46.59 3.02
4228 6845 3.105959 AGATTTTGACATGGGGAAGGG 57.894 47.619 0.00 0.00 0.00 3.95
4260 6881 4.408182 AATGGGGTAGACAGAGATTTCG 57.592 45.455 0.00 0.00 0.00 3.46
4290 6911 4.957296 TCTTCCTGTACAAAGAGTTGGTC 58.043 43.478 5.99 0.00 39.22 4.02
4295 6916 5.305902 TCCTGTACAAAGAGTTGGTCATGTA 59.694 40.000 0.00 0.00 39.22 2.29
4412 7039 4.569719 ACGGGAGTAATTTGGTTCAGAT 57.430 40.909 0.00 0.00 44.60 2.90
4414 7041 6.057321 ACGGGAGTAATTTGGTTCAGATTA 57.943 37.500 0.00 0.00 44.60 1.75
4545 7172 1.294659 GACTGCCGCTCTGAACTTGG 61.295 60.000 0.00 0.00 0.00 3.61
4761 7426 3.916392 GACGTCAGGGTCGGTGCTG 62.916 68.421 11.55 0.00 0.00 4.41
4762 7427 3.680786 CGTCAGGGTCGGTGCTGA 61.681 66.667 0.00 0.00 0.00 4.26
4763 7428 2.741092 GTCAGGGTCGGTGCTGAA 59.259 61.111 0.00 0.00 0.00 3.02
4764 7429 1.374758 GTCAGGGTCGGTGCTGAAG 60.375 63.158 0.00 0.00 0.00 3.02
4765 7430 2.743928 CAGGGTCGGTGCTGAAGC 60.744 66.667 0.00 0.00 42.50 3.86
4939 7617 6.400515 CGTTTTGTTTTGCTGCAAGTTTTCTA 60.401 34.615 15.39 0.00 35.30 2.10
4940 7618 6.645700 TTTGTTTTGCTGCAAGTTTTCTAG 57.354 33.333 15.39 0.00 35.30 2.43
4941 7619 4.111916 TGTTTTGCTGCAAGTTTTCTAGC 58.888 39.130 15.39 1.77 35.30 3.42
4942 7620 2.686558 TTGCTGCAAGTTTTCTAGCG 57.313 45.000 11.69 0.00 37.20 4.26
4943 7621 1.877637 TGCTGCAAGTTTTCTAGCGA 58.122 45.000 0.00 0.00 37.20 4.93
4944 7622 2.217750 TGCTGCAAGTTTTCTAGCGAA 58.782 42.857 0.00 0.00 37.20 4.70
4949 7631 5.283953 GCTGCAAGTTTTCTAGCGAAATAAC 59.716 40.000 0.00 0.00 38.81 1.89
4977 7659 4.766404 ATTAGTGGCACCTTTTTCTTCG 57.234 40.909 15.27 0.00 0.00 3.79
4982 7664 3.562557 GTGGCACCTTTTTCTTCGTCTTA 59.437 43.478 6.29 0.00 0.00 2.10
5012 7694 9.930158 AAAGGAACATACTACTATCTCTTCTCT 57.070 33.333 0.00 0.00 0.00 3.10
5044 7726 4.383931 AAAAACCTAAGGTTCCCTCTCC 57.616 45.455 0.00 0.00 46.20 3.71
5045 7727 1.968278 AACCTAAGGTTCCCTCTCCC 58.032 55.000 0.00 0.00 43.05 4.30
5046 7728 0.044397 ACCTAAGGTTCCCTCTCCCC 59.956 60.000 0.00 0.00 30.89 4.81
5047 7729 0.343726 CCTAAGGTTCCCTCTCCCCT 59.656 60.000 0.00 0.00 30.89 4.79
5048 7730 1.693083 CCTAAGGTTCCCTCTCCCCTC 60.693 61.905 0.00 0.00 30.89 4.30
5049 7731 1.292546 CTAAGGTTCCCTCTCCCCTCT 59.707 57.143 0.00 0.00 30.89 3.69
5050 7732 0.498685 AAGGTTCCCTCTCCCCTCTT 59.501 55.000 0.00 0.00 30.89 2.85
5051 7733 1.405243 AGGTTCCCTCTCCCCTCTTA 58.595 55.000 0.00 0.00 0.00 2.10
5052 7734 1.008571 AGGTTCCCTCTCCCCTCTTAC 59.991 57.143 0.00 0.00 0.00 2.34
5053 7735 1.112950 GTTCCCTCTCCCCTCTTACG 58.887 60.000 0.00 0.00 0.00 3.18
5054 7736 0.708802 TTCCCTCTCCCCTCTTACGT 59.291 55.000 0.00 0.00 0.00 3.57
5055 7737 0.258194 TCCCTCTCCCCTCTTACGTC 59.742 60.000 0.00 0.00 0.00 4.34
5056 7738 0.033405 CCCTCTCCCCTCTTACGTCA 60.033 60.000 0.00 0.00 0.00 4.35
5057 7739 1.618888 CCCTCTCCCCTCTTACGTCAA 60.619 57.143 0.00 0.00 0.00 3.18
5058 7740 2.176889 CCTCTCCCCTCTTACGTCAAA 58.823 52.381 0.00 0.00 0.00 2.69
5059 7741 2.766828 CCTCTCCCCTCTTACGTCAAAT 59.233 50.000 0.00 0.00 0.00 2.32
5060 7742 3.181474 CCTCTCCCCTCTTACGTCAAATC 60.181 52.174 0.00 0.00 0.00 2.17
5061 7743 3.702045 CTCTCCCCTCTTACGTCAAATCT 59.298 47.826 0.00 0.00 0.00 2.40
5062 7744 4.094476 TCTCCCCTCTTACGTCAAATCTT 58.906 43.478 0.00 0.00 0.00 2.40
5063 7745 4.530946 TCTCCCCTCTTACGTCAAATCTTT 59.469 41.667 0.00 0.00 0.00 2.52
5064 7746 4.828829 TCCCCTCTTACGTCAAATCTTTC 58.171 43.478 0.00 0.00 0.00 2.62
5065 7747 3.617263 CCCCTCTTACGTCAAATCTTTCG 59.383 47.826 0.00 0.00 0.00 3.46
5066 7748 4.243270 CCCTCTTACGTCAAATCTTTCGT 58.757 43.478 0.00 0.00 39.74 3.85
5067 7749 4.326548 CCCTCTTACGTCAAATCTTTCGTC 59.673 45.833 0.00 0.00 37.66 4.20
5068 7750 4.326548 CCTCTTACGTCAAATCTTTCGTCC 59.673 45.833 0.00 0.00 37.66 4.79
5069 7751 4.873817 TCTTACGTCAAATCTTTCGTCCA 58.126 39.130 0.00 0.00 37.66 4.02
5070 7752 5.291178 TCTTACGTCAAATCTTTCGTCCAA 58.709 37.500 0.00 0.00 37.66 3.53
5071 7753 3.872560 ACGTCAAATCTTTCGTCCAAC 57.127 42.857 0.00 0.00 30.71 3.77
5072 7754 2.546789 ACGTCAAATCTTTCGTCCAACC 59.453 45.455 0.00 0.00 30.71 3.77
5073 7755 2.806244 CGTCAAATCTTTCGTCCAACCT 59.194 45.455 0.00 0.00 0.00 3.50
5074 7756 3.250040 CGTCAAATCTTTCGTCCAACCTT 59.750 43.478 0.00 0.00 0.00 3.50
5075 7757 4.261031 CGTCAAATCTTTCGTCCAACCTTT 60.261 41.667 0.00 0.00 0.00 3.11
5076 7758 5.588240 GTCAAATCTTTCGTCCAACCTTTT 58.412 37.500 0.00 0.00 0.00 2.27
5077 7759 5.685954 GTCAAATCTTTCGTCCAACCTTTTC 59.314 40.000 0.00 0.00 0.00 2.29
5078 7760 5.592688 TCAAATCTTTCGTCCAACCTTTTCT 59.407 36.000 0.00 0.00 0.00 2.52
5079 7761 6.096282 TCAAATCTTTCGTCCAACCTTTTCTT 59.904 34.615 0.00 0.00 0.00 2.52
5080 7762 5.690997 ATCTTTCGTCCAACCTTTTCTTC 57.309 39.130 0.00 0.00 0.00 2.87
5081 7763 3.881089 TCTTTCGTCCAACCTTTTCTTCC 59.119 43.478 0.00 0.00 0.00 3.46
5082 7764 3.284793 TTCGTCCAACCTTTTCTTCCA 57.715 42.857 0.00 0.00 0.00 3.53
5083 7765 2.567985 TCGTCCAACCTTTTCTTCCAC 58.432 47.619 0.00 0.00 0.00 4.02
5084 7766 1.607148 CGTCCAACCTTTTCTTCCACC 59.393 52.381 0.00 0.00 0.00 4.61
5085 7767 1.961394 GTCCAACCTTTTCTTCCACCC 59.039 52.381 0.00 0.00 0.00 4.61
5086 7768 1.133294 TCCAACCTTTTCTTCCACCCC 60.133 52.381 0.00 0.00 0.00 4.95
5087 7769 1.133167 CCAACCTTTTCTTCCACCCCT 60.133 52.381 0.00 0.00 0.00 4.79
5088 7770 2.239400 CAACCTTTTCTTCCACCCCTC 58.761 52.381 0.00 0.00 0.00 4.30
5089 7771 0.778083 ACCTTTTCTTCCACCCCTCC 59.222 55.000 0.00 0.00 0.00 4.30
5090 7772 1.076438 CCTTTTCTTCCACCCCTCCT 58.924 55.000 0.00 0.00 0.00 3.69
5091 7773 1.429299 CCTTTTCTTCCACCCCTCCTT 59.571 52.381 0.00 0.00 0.00 3.36
5092 7774 2.647802 CCTTTTCTTCCACCCCTCCTTA 59.352 50.000 0.00 0.00 0.00 2.69
5093 7775 3.561528 CCTTTTCTTCCACCCCTCCTTAC 60.562 52.174 0.00 0.00 0.00 2.34
5094 7776 1.272807 TTCTTCCACCCCTCCTTACG 58.727 55.000 0.00 0.00 0.00 3.18
5095 7777 0.115745 TCTTCCACCCCTCCTTACGT 59.884 55.000 0.00 0.00 0.00 3.57
5096 7778 1.358787 TCTTCCACCCCTCCTTACGTA 59.641 52.381 0.00 0.00 0.00 3.57
5097 7779 1.479730 CTTCCACCCCTCCTTACGTAC 59.520 57.143 0.00 0.00 0.00 3.67
5098 7780 0.680921 TCCACCCCTCCTTACGTACG 60.681 60.000 15.01 15.01 0.00 3.67
5099 7781 1.140375 CACCCCTCCTTACGTACGC 59.860 63.158 16.72 0.00 0.00 4.42
5100 7782 1.000396 ACCCCTCCTTACGTACGCT 60.000 57.895 16.72 5.36 0.00 5.07
5101 7783 1.034292 ACCCCTCCTTACGTACGCTC 61.034 60.000 16.72 0.00 0.00 5.03
5102 7784 1.732308 CCCTCCTTACGTACGCTCC 59.268 63.158 16.72 0.00 0.00 4.70
5103 7785 1.033746 CCCTCCTTACGTACGCTCCA 61.034 60.000 16.72 0.00 0.00 3.86
5104 7786 0.100146 CCTCCTTACGTACGCTCCAC 59.900 60.000 16.72 0.00 0.00 4.02
5105 7787 0.100146 CTCCTTACGTACGCTCCACC 59.900 60.000 16.72 0.00 0.00 4.61
5106 7788 1.140375 CCTTACGTACGCTCCACCC 59.860 63.158 16.72 0.00 0.00 4.61
5107 7789 1.318158 CCTTACGTACGCTCCACCCT 61.318 60.000 16.72 0.00 0.00 4.34
5108 7790 0.100146 CTTACGTACGCTCCACCCTC 59.900 60.000 16.72 0.00 0.00 4.30
5109 7791 1.315257 TTACGTACGCTCCACCCTCC 61.315 60.000 16.72 0.00 0.00 4.30
5110 7792 3.834799 CGTACGCTCCACCCTCCC 61.835 72.222 0.52 0.00 0.00 4.30
5111 7793 3.834799 GTACGCTCCACCCTCCCG 61.835 72.222 0.00 0.00 0.00 5.14
5112 7794 4.051167 TACGCTCCACCCTCCCGA 62.051 66.667 0.00 0.00 0.00 5.14
5113 7795 3.369410 TACGCTCCACCCTCCCGAT 62.369 63.158 0.00 0.00 0.00 4.18
5114 7796 2.866523 TACGCTCCACCCTCCCGATT 62.867 60.000 0.00 0.00 0.00 3.34
5115 7797 2.998949 GCTCCACCCTCCCGATTT 59.001 61.111 0.00 0.00 0.00 2.17
5116 7798 1.303282 GCTCCACCCTCCCGATTTT 59.697 57.895 0.00 0.00 0.00 1.82
5117 7799 0.748367 GCTCCACCCTCCCGATTTTC 60.748 60.000 0.00 0.00 0.00 2.29
5118 7800 0.912486 CTCCACCCTCCCGATTTTCT 59.088 55.000 0.00 0.00 0.00 2.52
5119 7801 2.116238 CTCCACCCTCCCGATTTTCTA 58.884 52.381 0.00 0.00 0.00 2.10
5120 7802 2.706190 CTCCACCCTCCCGATTTTCTAT 59.294 50.000 0.00 0.00 0.00 1.98
5121 7803 3.120108 TCCACCCTCCCGATTTTCTATT 58.880 45.455 0.00 0.00 0.00 1.73
5122 7804 3.526019 TCCACCCTCCCGATTTTCTATTT 59.474 43.478 0.00 0.00 0.00 1.40
5123 7805 3.883489 CCACCCTCCCGATTTTCTATTTC 59.117 47.826 0.00 0.00 0.00 2.17
5124 7806 4.523083 CACCCTCCCGATTTTCTATTTCA 58.477 43.478 0.00 0.00 0.00 2.69
5125 7807 4.335594 CACCCTCCCGATTTTCTATTTCAC 59.664 45.833 0.00 0.00 0.00 3.18
5126 7808 4.018779 ACCCTCCCGATTTTCTATTTCACA 60.019 41.667 0.00 0.00 0.00 3.58
5127 7809 5.133221 CCCTCCCGATTTTCTATTTCACAT 58.867 41.667 0.00 0.00 0.00 3.21
5128 7810 5.009010 CCCTCCCGATTTTCTATTTCACATG 59.991 44.000 0.00 0.00 0.00 3.21
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
40 42 7.671495 AAACAAATGTTTATCAAATCCTGCC 57.329 32.000 9.67 0.00 45.47 4.85
61 63 4.829064 TCCTGCTTGTGATTGTGTAAAC 57.171 40.909 0.00 0.00 0.00 2.01
92 94 6.825284 TGCTTGTGATTGTGTAAACAAATG 57.175 33.333 1.76 0.00 32.50 2.32
93 95 7.264221 TCTTGCTTGTGATTGTGTAAACAAAT 58.736 30.769 1.76 0.00 32.50 2.32
94 96 6.625362 TCTTGCTTGTGATTGTGTAAACAAA 58.375 32.000 1.76 0.00 32.50 2.83
147 150 9.432982 TTTGGGATTTACCTGCTCATATTAATT 57.567 29.630 0.00 0.00 38.98 1.40
155 159 4.016444 GTGATTTGGGATTTACCTGCTCA 58.984 43.478 0.00 0.00 38.98 4.26
157 161 3.016736 CGTGATTTGGGATTTACCTGCT 58.983 45.455 0.00 0.00 38.98 4.24
159 163 3.128589 CCACGTGATTTGGGATTTACCTG 59.871 47.826 19.30 0.00 38.98 4.00
164 168 4.007659 GAGTACCACGTGATTTGGGATTT 58.992 43.478 19.30 0.00 38.59 2.17
184 188 8.539770 TGCAGAGTAAATAAAAACAGAGAGAG 57.460 34.615 0.00 0.00 0.00 3.20
402 1789 7.801716 ATTTACTCCGCATATCAGCTTTAAA 57.198 32.000 0.00 0.00 0.00 1.52
403 1790 8.896320 TTATTTACTCCGCATATCAGCTTTAA 57.104 30.769 0.00 0.00 0.00 1.52
404 1791 8.896320 TTTATTTACTCCGCATATCAGCTTTA 57.104 30.769 0.00 0.00 0.00 1.85
405 1792 7.801716 TTTATTTACTCCGCATATCAGCTTT 57.198 32.000 0.00 0.00 0.00 3.51
459 1881 1.905894 TGCAGCCCATACAGAGTACAA 59.094 47.619 0.00 0.00 0.00 2.41
462 1884 1.202687 GCATGCAGCCCATACAGAGTA 60.203 52.381 14.21 0.00 37.23 2.59
464 1886 2.328235 GCATGCAGCCCATACAGAG 58.672 57.895 14.21 0.00 37.23 3.35
492 1914 1.277579 TTGGGTAACATGGGCGTCTA 58.722 50.000 0.00 0.00 39.74 2.59
610 2032 3.150895 GAACAGAGCTGTGCGACG 58.849 61.111 11.42 0.00 44.13 5.12
620 2042 1.270305 TGTCAGGGAAAGCGAACAGAG 60.270 52.381 0.00 0.00 0.00 3.35
635 2057 0.671781 CTCCGGTCCTTGCTTGTCAG 60.672 60.000 0.00 0.00 0.00 3.51
637 2059 2.035442 GCTCCGGTCCTTGCTTGTC 61.035 63.158 0.00 0.00 0.00 3.18
638 2060 2.032681 GCTCCGGTCCTTGCTTGT 59.967 61.111 0.00 0.00 0.00 3.16
662 2084 6.489022 AGTTAAACCACTGGAGTAAATGTTCC 59.511 38.462 0.71 0.00 0.00 3.62
663 2085 7.308408 GGAGTTAAACCACTGGAGTAAATGTTC 60.308 40.741 0.71 0.00 0.00 3.18
832 2557 0.815615 CCGAAATCCCCAGCTACAGC 60.816 60.000 0.00 0.00 42.49 4.40
833 2558 0.830648 TCCGAAATCCCCAGCTACAG 59.169 55.000 0.00 0.00 0.00 2.74
834 2559 0.830648 CTCCGAAATCCCCAGCTACA 59.169 55.000 0.00 0.00 0.00 2.74
835 2560 0.533085 GCTCCGAAATCCCCAGCTAC 60.533 60.000 0.00 0.00 0.00 3.58
836 2561 1.830145 GCTCCGAAATCCCCAGCTA 59.170 57.895 0.00 0.00 0.00 3.32
862 2587 2.223180 GGGTTAAATTTAGCACGCGGAG 60.223 50.000 12.47 3.23 0.00 4.63
906 2638 2.051345 GTGCGTTCGGTTTGGCAG 60.051 61.111 0.00 0.00 35.85 4.85
968 2700 3.814268 GGCGTACGCGTAGGTGGA 61.814 66.667 32.02 6.94 43.06 4.02
1067 2817 3.478274 CTCCTCTGCCCTGCCTCC 61.478 72.222 0.00 0.00 0.00 4.30
1068 2818 2.364842 TCTCCTCTGCCCTGCCTC 60.365 66.667 0.00 0.00 0.00 4.70
1069 2819 2.365370 CTCTCCTCTGCCCTGCCT 60.365 66.667 0.00 0.00 0.00 4.75
1077 2841 2.104729 GCGCTCTGCTCTCCTCTG 59.895 66.667 0.00 0.00 41.73 3.35
1265 3034 2.442458 GAGACGAGGGAGGGGGAC 60.442 72.222 0.00 0.00 0.00 4.46
1276 3045 2.678580 TGGTGGCGATGGAGACGA 60.679 61.111 0.00 0.00 0.00 4.20
1849 3630 3.140814 GGGCAGGCGATTGGGAAC 61.141 66.667 0.00 0.00 0.00 3.62
1920 3701 1.639108 ACCTCAATTAACCCCTCACCC 59.361 52.381 0.00 0.00 0.00 4.61
1993 3951 9.066892 CCCATTCCGAATTCTCATAATTCTAAA 57.933 33.333 3.52 3.94 35.17 1.85
1997 3955 7.693969 ATCCCATTCCGAATTCTCATAATTC 57.306 36.000 3.52 0.00 34.26 2.17
2212 4615 3.512033 ACGCTACTGGATTCTGAGAAC 57.488 47.619 0.00 0.00 0.00 3.01
2218 4621 3.005261 CAGCAGATACGCTACTGGATTCT 59.995 47.826 0.00 0.00 41.38 2.40
2264 4667 1.961277 GTGGAACTGTGACAGGGCG 60.961 63.158 17.92 0.00 35.51 6.13
2302 4766 3.506067 TGATGTTCTTCAGAGTACGCAGA 59.494 43.478 0.00 0.00 0.00 4.26
2325 4803 5.070313 ACCAGGTCAAAATAGCAACAATTGT 59.930 36.000 4.92 4.92 0.00 2.71
2380 4873 5.659440 TCTGAAAACCAAATTCCTATGCC 57.341 39.130 0.00 0.00 0.00 4.40
2402 4895 2.097954 CGCAATGCACCACATTCAGTAT 59.902 45.455 5.91 0.00 46.28 2.12
2662 5156 2.942804 TGGTTTGAGGTGCAATCAGAA 58.057 42.857 3.36 0.29 36.15 3.02
2669 5163 1.075212 TGGATGATGGTTTGAGGTGCA 59.925 47.619 0.00 0.00 0.00 4.57
2672 5166 2.505407 TCGATGGATGATGGTTTGAGGT 59.495 45.455 0.00 0.00 0.00 3.85
2686 5205 3.441163 CGACCGAAAGTTATTCGATGGA 58.559 45.455 11.76 0.00 43.97 3.41
2703 5222 3.840890 TGTGCACAATTTAATCCGACC 57.159 42.857 19.28 0.00 0.00 4.79
2706 5225 4.104776 GTCCATGTGCACAATTTAATCCG 58.895 43.478 25.72 3.61 0.00 4.18
2870 5392 1.587613 GCGACAGACTCGATGGCTC 60.588 63.158 0.00 0.00 46.14 4.70
2883 5405 1.079819 GCACAGGCTCTTAGCGACA 60.080 57.895 0.00 0.00 43.62 4.35
2898 5420 3.269178 CTCCTTGATCTTCTTCCAGCAC 58.731 50.000 0.00 0.00 0.00 4.40
2983 5505 1.910580 AACGGCGGGGACTTGATGAT 61.911 55.000 13.24 0.00 0.00 2.45
3040 5562 5.935789 TGGCAGTGTAAGTAACCAAGTAATC 59.064 40.000 0.00 0.00 0.00 1.75
3041 5563 5.704053 GTGGCAGTGTAAGTAACCAAGTAAT 59.296 40.000 0.00 0.00 0.00 1.89
3047 5569 3.780804 ATGTGGCAGTGTAAGTAACCA 57.219 42.857 0.00 0.00 0.00 3.67
3049 5571 5.878116 TGGATAATGTGGCAGTGTAAGTAAC 59.122 40.000 0.00 0.00 0.00 2.50
3059 5581 4.885907 ACTTCAGAATGGATAATGTGGCAG 59.114 41.667 0.00 0.00 36.16 4.85
3065 5587 6.825213 TGAGTTGGACTTCAGAATGGATAATG 59.175 38.462 0.00 0.00 36.16 1.90
3076 5601 0.951040 GGCCGTGAGTTGGACTTCAG 60.951 60.000 0.00 0.00 0.00 3.02
3086 5611 1.210234 TCATGAATCATGGCCGTGAGT 59.790 47.619 30.43 28.86 41.66 3.41
3216 5741 0.184451 CTAGCAATCCTGGGTGGCAT 59.816 55.000 9.45 0.00 35.26 4.40
3283 5808 4.518249 CCCAACTCTCTTCTTCCATAACC 58.482 47.826 0.00 0.00 0.00 2.85
3441 5966 4.218417 CCCAAGAGTCGTTGAATTTCCAAT 59.782 41.667 4.49 0.00 0.00 3.16
3458 5983 3.006859 CACGCTCATATATCACCCCAAGA 59.993 47.826 0.00 0.00 0.00 3.02
3473 5998 2.046023 CCAATGAGGCCACGCTCA 60.046 61.111 5.01 0.00 0.00 4.26
3537 6062 4.800582 GCATGATCCTCATCACCGTCATAA 60.801 45.833 0.00 0.00 42.05 1.90
3542 6067 0.832626 TGCATGATCCTCATCACCGT 59.167 50.000 0.00 0.00 42.05 4.83
3563 6088 3.763897 AGATTACTCACCCCAACAAATGC 59.236 43.478 0.00 0.00 0.00 3.56
3564 6089 5.256474 AGAGATTACTCACCCCAACAAATG 58.744 41.667 0.00 0.00 44.79 2.32
3565 6090 5.251700 AGAGAGATTACTCACCCCAACAAAT 59.748 40.000 0.00 0.00 44.79 2.32
3566 6091 4.597507 AGAGAGATTACTCACCCCAACAAA 59.402 41.667 0.00 0.00 44.79 2.83
3578 6103 6.153510 TGCAGTGATACAACAGAGAGATTACT 59.846 38.462 0.00 0.00 0.00 2.24
3583 6108 3.194329 CCTGCAGTGATACAACAGAGAGA 59.806 47.826 13.81 0.00 0.00 3.10
3620 6145 0.892814 CGTAGGTCCGGGGATAGGTC 60.893 65.000 0.00 0.00 0.00 3.85
3696 6221 8.135382 ACCAATCACTGTCTAAATAGTACTGT 57.865 34.615 5.39 0.00 0.00 3.55
3740 6265 7.041098 AGGTGAAAACAGCTTATACACTTTGAG 60.041 37.037 0.00 0.00 0.00 3.02
3746 6271 4.760204 ACCAGGTGAAAACAGCTTATACAC 59.240 41.667 0.00 0.00 0.00 2.90
3748 6273 5.959618 AACCAGGTGAAAACAGCTTATAC 57.040 39.130 0.00 0.00 0.00 1.47
4044 6575 5.008415 CCCAGTATCTGTCAATTTCTCATGC 59.992 44.000 0.00 0.00 0.00 4.06
4045 6576 5.008415 GCCCAGTATCTGTCAATTTCTCATG 59.992 44.000 0.00 0.00 0.00 3.07
4046 6577 5.128919 GCCCAGTATCTGTCAATTTCTCAT 58.871 41.667 0.00 0.00 0.00 2.90
4047 6578 4.019411 TGCCCAGTATCTGTCAATTTCTCA 60.019 41.667 0.00 0.00 0.00 3.27
4048 6579 4.517285 TGCCCAGTATCTGTCAATTTCTC 58.483 43.478 0.00 0.00 0.00 2.87
4049 6580 4.574674 TGCCCAGTATCTGTCAATTTCT 57.425 40.909 0.00 0.00 0.00 2.52
4050 6581 5.643379 TTTGCCCAGTATCTGTCAATTTC 57.357 39.130 0.00 0.00 0.00 2.17
4071 6611 4.225942 TGAGAGGAAGCCAGTTGTGATATT 59.774 41.667 0.00 0.00 0.00 1.28
4074 6614 1.980765 TGAGAGGAAGCCAGTTGTGAT 59.019 47.619 0.00 0.00 0.00 3.06
4080 6620 1.534235 ACGGTGAGAGGAAGCCAGT 60.534 57.895 0.00 0.00 0.00 4.00
4108 6652 8.143835 CCAGACAAGATAAAACTTCAAAACCAT 58.856 33.333 0.00 0.00 0.00 3.55
4131 6675 7.830739 ACTATTTCAGCAAAAGAATTACCCAG 58.169 34.615 0.00 0.00 0.00 4.45
4142 6686 6.364706 CGCCATGTTTAACTATTTCAGCAAAA 59.635 34.615 0.00 0.00 0.00 2.44
4147 6691 5.584649 TCTCCGCCATGTTTAACTATTTCAG 59.415 40.000 0.00 0.00 0.00 3.02
4166 6783 2.825836 GGCTTGGGCATGTCTCCG 60.826 66.667 0.00 0.00 40.87 4.63
4182 6799 0.397941 TCTTGCCCTCTGTGAACAGG 59.602 55.000 10.45 1.96 43.91 4.00
4228 6845 3.777910 CCCCATTTGGCTGGCTGC 61.778 66.667 7.96 7.96 41.94 5.25
4260 6881 6.093633 ACTCTTTGTACAGGAAGAAACACAAC 59.906 38.462 10.44 0.00 31.99 3.32
4290 6911 2.368875 AGCCGAGGGGAACTTATACATG 59.631 50.000 0.00 0.00 34.06 3.21
4295 6916 1.209747 GAACAGCCGAGGGGAACTTAT 59.790 52.381 0.00 0.00 34.06 1.73
4545 7172 0.899717 TGGAAGGTCAAAGGCATGGC 60.900 55.000 12.14 12.14 0.00 4.40
4641 7291 3.881089 CCCTCTGAAAAACAGGTTTACGT 59.119 43.478 0.00 0.00 45.76 3.57
4643 7293 6.459670 TTTCCCTCTGAAAAACAGGTTTAC 57.540 37.500 0.00 0.00 45.76 2.01
4670 7334 6.072893 TCCTTATTTCACTTACAAGTTTCGGC 60.073 38.462 0.00 0.00 37.08 5.54
4739 7404 4.778415 CCGACCCTGACGTCTGCG 62.778 72.222 17.92 14.31 44.93 5.18
4761 7426 3.118482 TGTCTTCCTCATCCTCATGCTTC 60.118 47.826 0.00 0.00 0.00 3.86
4762 7427 2.842496 TGTCTTCCTCATCCTCATGCTT 59.158 45.455 0.00 0.00 0.00 3.91
4763 7428 2.435069 CTGTCTTCCTCATCCTCATGCT 59.565 50.000 0.00 0.00 0.00 3.79
4764 7429 2.433604 TCTGTCTTCCTCATCCTCATGC 59.566 50.000 0.00 0.00 0.00 4.06
4765 7430 3.181467 GGTCTGTCTTCCTCATCCTCATG 60.181 52.174 0.00 0.00 0.00 3.07
4766 7431 3.037549 GGTCTGTCTTCCTCATCCTCAT 58.962 50.000 0.00 0.00 0.00 2.90
4767 7432 2.225369 TGGTCTGTCTTCCTCATCCTCA 60.225 50.000 0.00 0.00 0.00 3.86
4768 7433 2.430332 CTGGTCTGTCTTCCTCATCCTC 59.570 54.545 0.00 0.00 0.00 3.71
4769 7434 2.465813 CTGGTCTGTCTTCCTCATCCT 58.534 52.381 0.00 0.00 0.00 3.24
4770 7435 1.484240 CCTGGTCTGTCTTCCTCATCC 59.516 57.143 0.00 0.00 0.00 3.51
4771 7436 1.134551 GCCTGGTCTGTCTTCCTCATC 60.135 57.143 0.00 0.00 0.00 2.92
4772 7437 0.908198 GCCTGGTCTGTCTTCCTCAT 59.092 55.000 0.00 0.00 0.00 2.90
4773 7438 0.471780 TGCCTGGTCTGTCTTCCTCA 60.472 55.000 0.00 0.00 0.00 3.86
4774 7439 0.687354 TTGCCTGGTCTGTCTTCCTC 59.313 55.000 0.00 0.00 0.00 3.71
4775 7440 1.140312 TTTGCCTGGTCTGTCTTCCT 58.860 50.000 0.00 0.00 0.00 3.36
4776 7441 1.981256 TTTTGCCTGGTCTGTCTTCC 58.019 50.000 0.00 0.00 0.00 3.46
4904 7582 3.542310 GCAAAACAAAACGTGTCTCTGAC 59.458 43.478 0.00 0.00 40.60 3.51
4906 7584 3.543494 CAGCAAAACAAAACGTGTCTCTG 59.457 43.478 0.00 0.00 40.60 3.35
4907 7585 3.758300 CAGCAAAACAAAACGTGTCTCT 58.242 40.909 0.00 0.00 40.60 3.10
4939 7617 7.094549 TGCCACTAATTAAGTTGTTATTTCGCT 60.095 33.333 0.00 0.00 35.76 4.93
4940 7618 7.007995 GTGCCACTAATTAAGTTGTTATTTCGC 59.992 37.037 0.00 0.00 35.76 4.70
4941 7619 7.483691 GGTGCCACTAATTAAGTTGTTATTTCG 59.516 37.037 0.00 0.00 35.76 3.46
4942 7620 8.520351 AGGTGCCACTAATTAAGTTGTTATTTC 58.480 33.333 0.00 0.00 35.76 2.17
4943 7621 8.417273 AGGTGCCACTAATTAAGTTGTTATTT 57.583 30.769 0.00 0.00 35.76 1.40
4944 7622 8.417273 AAGGTGCCACTAATTAAGTTGTTATT 57.583 30.769 0.00 0.00 35.76 1.40
4949 7631 7.433680 AGAAAAAGGTGCCACTAATTAAGTTG 58.566 34.615 0.00 0.00 35.76 3.16
5034 7716 1.112950 CGTAAGAGGGGAGAGGGAAC 58.887 60.000 0.00 0.00 43.02 3.62
5035 7717 0.708802 ACGTAAGAGGGGAGAGGGAA 59.291 55.000 0.00 0.00 43.62 3.97
5036 7718 0.258194 GACGTAAGAGGGGAGAGGGA 59.742 60.000 0.00 0.00 43.62 4.20
5037 7719 0.033405 TGACGTAAGAGGGGAGAGGG 60.033 60.000 0.00 0.00 43.62 4.30
5038 7720 1.848652 TTGACGTAAGAGGGGAGAGG 58.151 55.000 0.00 0.00 43.62 3.69
5039 7721 3.702045 AGATTTGACGTAAGAGGGGAGAG 59.298 47.826 0.00 0.00 43.62 3.20
5040 7722 3.709587 AGATTTGACGTAAGAGGGGAGA 58.290 45.455 0.00 0.00 43.62 3.71
5041 7723 4.473477 AAGATTTGACGTAAGAGGGGAG 57.527 45.455 0.00 0.00 43.62 4.30
5042 7724 4.619863 CGAAAGATTTGACGTAAGAGGGGA 60.620 45.833 0.00 0.00 43.62 4.81
5043 7725 3.617263 CGAAAGATTTGACGTAAGAGGGG 59.383 47.826 0.00 0.00 43.62 4.79
5044 7726 4.243270 ACGAAAGATTTGACGTAAGAGGG 58.757 43.478 0.00 0.00 43.62 4.30
5045 7727 4.326548 GGACGAAAGATTTGACGTAAGAGG 59.673 45.833 0.00 0.00 39.04 3.69
5046 7728 4.921515 TGGACGAAAGATTTGACGTAAGAG 59.078 41.667 0.00 0.00 39.04 2.85
5047 7729 4.873817 TGGACGAAAGATTTGACGTAAGA 58.126 39.130 0.00 0.00 39.04 2.10
5048 7730 5.371629 GTTGGACGAAAGATTTGACGTAAG 58.628 41.667 0.00 0.00 39.04 2.34
5049 7731 4.211794 GGTTGGACGAAAGATTTGACGTAA 59.788 41.667 0.00 0.00 39.04 3.18
5050 7732 3.742369 GGTTGGACGAAAGATTTGACGTA 59.258 43.478 0.00 0.00 39.04 3.57
5051 7733 2.546789 GGTTGGACGAAAGATTTGACGT 59.453 45.455 0.00 0.00 41.57 4.34
5052 7734 2.806244 AGGTTGGACGAAAGATTTGACG 59.194 45.455 0.00 0.00 0.00 4.35
5053 7735 4.830826 AAGGTTGGACGAAAGATTTGAC 57.169 40.909 0.00 0.00 0.00 3.18
5054 7736 5.592688 AGAAAAGGTTGGACGAAAGATTTGA 59.407 36.000 0.00 0.00 0.00 2.69
5055 7737 5.831997 AGAAAAGGTTGGACGAAAGATTTG 58.168 37.500 0.00 0.00 0.00 2.32
5056 7738 6.461092 GGAAGAAAAGGTTGGACGAAAGATTT 60.461 38.462 0.00 0.00 0.00 2.17
5057 7739 5.009710 GGAAGAAAAGGTTGGACGAAAGATT 59.990 40.000 0.00 0.00 0.00 2.40
5058 7740 4.519350 GGAAGAAAAGGTTGGACGAAAGAT 59.481 41.667 0.00 0.00 0.00 2.40
5059 7741 3.881089 GGAAGAAAAGGTTGGACGAAAGA 59.119 43.478 0.00 0.00 0.00 2.52
5060 7742 3.630312 TGGAAGAAAAGGTTGGACGAAAG 59.370 43.478 0.00 0.00 0.00 2.62
5061 7743 3.379057 GTGGAAGAAAAGGTTGGACGAAA 59.621 43.478 0.00 0.00 0.00 3.46
5062 7744 2.946990 GTGGAAGAAAAGGTTGGACGAA 59.053 45.455 0.00 0.00 0.00 3.85
5063 7745 2.567985 GTGGAAGAAAAGGTTGGACGA 58.432 47.619 0.00 0.00 0.00 4.20
5064 7746 1.607148 GGTGGAAGAAAAGGTTGGACG 59.393 52.381 0.00 0.00 0.00 4.79
5065 7747 1.961394 GGGTGGAAGAAAAGGTTGGAC 59.039 52.381 0.00 0.00 0.00 4.02
5066 7748 1.133294 GGGGTGGAAGAAAAGGTTGGA 60.133 52.381 0.00 0.00 0.00 3.53
5067 7749 1.133167 AGGGGTGGAAGAAAAGGTTGG 60.133 52.381 0.00 0.00 0.00 3.77
5068 7750 2.239400 GAGGGGTGGAAGAAAAGGTTG 58.761 52.381 0.00 0.00 0.00 3.77
5069 7751 1.147191 GGAGGGGTGGAAGAAAAGGTT 59.853 52.381 0.00 0.00 0.00 3.50
5070 7752 0.778083 GGAGGGGTGGAAGAAAAGGT 59.222 55.000 0.00 0.00 0.00 3.50
5071 7753 1.076438 AGGAGGGGTGGAAGAAAAGG 58.924 55.000 0.00 0.00 0.00 3.11
5072 7754 2.980246 AAGGAGGGGTGGAAGAAAAG 57.020 50.000 0.00 0.00 0.00 2.27
5073 7755 2.039348 CGTAAGGAGGGGTGGAAGAAAA 59.961 50.000 0.00 0.00 0.00 2.29
5074 7756 1.626825 CGTAAGGAGGGGTGGAAGAAA 59.373 52.381 0.00 0.00 0.00 2.52
5075 7757 1.272807 CGTAAGGAGGGGTGGAAGAA 58.727 55.000 0.00 0.00 0.00 2.52
5076 7758 0.115745 ACGTAAGGAGGGGTGGAAGA 59.884 55.000 0.00 0.00 46.39 2.87
5077 7759 1.479730 GTACGTAAGGAGGGGTGGAAG 59.520 57.143 0.00 0.00 46.39 3.46
5078 7760 1.560505 GTACGTAAGGAGGGGTGGAA 58.439 55.000 0.00 0.00 46.39 3.53
5079 7761 0.680921 CGTACGTAAGGAGGGGTGGA 60.681 60.000 7.22 0.00 46.39 4.02
5080 7762 1.811860 CGTACGTAAGGAGGGGTGG 59.188 63.158 7.22 0.00 46.39 4.61
5081 7763 1.140375 GCGTACGTAAGGAGGGGTG 59.860 63.158 17.90 0.00 46.39 4.61
5082 7764 1.000396 AGCGTACGTAAGGAGGGGT 60.000 57.895 17.90 0.00 46.39 4.95
5083 7765 1.732308 GAGCGTACGTAAGGAGGGG 59.268 63.158 17.90 0.00 46.39 4.79
5084 7766 1.033746 TGGAGCGTACGTAAGGAGGG 61.034 60.000 17.90 0.00 46.39 4.30
5085 7767 0.100146 GTGGAGCGTACGTAAGGAGG 59.900 60.000 17.90 0.00 46.39 4.30
5086 7768 0.100146 GGTGGAGCGTACGTAAGGAG 59.900 60.000 17.90 0.00 46.39 3.69
5087 7769 1.315257 GGGTGGAGCGTACGTAAGGA 61.315 60.000 17.90 0.00 46.39 3.36
5088 7770 1.140375 GGGTGGAGCGTACGTAAGG 59.860 63.158 17.90 0.71 46.39 2.69
5090 7772 1.315257 GGAGGGTGGAGCGTACGTAA 61.315 60.000 17.90 0.00 0.00 3.18
5091 7773 1.750399 GGAGGGTGGAGCGTACGTA 60.750 63.158 17.90 0.00 0.00 3.57
5092 7774 3.066814 GGAGGGTGGAGCGTACGT 61.067 66.667 17.90 3.43 0.00 3.57
5093 7775 3.834799 GGGAGGGTGGAGCGTACG 61.835 72.222 11.84 11.84 0.00 3.67
5094 7776 3.834799 CGGGAGGGTGGAGCGTAC 61.835 72.222 0.00 0.00 0.00 3.67
5095 7777 2.866523 AATCGGGAGGGTGGAGCGTA 62.867 60.000 0.00 0.00 0.00 4.42
5096 7778 4.779733 ATCGGGAGGGTGGAGCGT 62.780 66.667 0.00 0.00 0.00 5.07
5097 7779 2.536997 AAAATCGGGAGGGTGGAGCG 62.537 60.000 0.00 0.00 0.00 5.03
5098 7780 0.748367 GAAAATCGGGAGGGTGGAGC 60.748 60.000 0.00 0.00 0.00 4.70
5099 7781 0.912486 AGAAAATCGGGAGGGTGGAG 59.088 55.000 0.00 0.00 0.00 3.86
5100 7782 2.257391 TAGAAAATCGGGAGGGTGGA 57.743 50.000 0.00 0.00 0.00 4.02
5101 7783 3.577805 AATAGAAAATCGGGAGGGTGG 57.422 47.619 0.00 0.00 0.00 4.61
5102 7784 4.335594 GTGAAATAGAAAATCGGGAGGGTG 59.664 45.833 0.00 0.00 0.00 4.61
5103 7785 4.018779 TGTGAAATAGAAAATCGGGAGGGT 60.019 41.667 0.00 0.00 0.00 4.34
5104 7786 4.523083 TGTGAAATAGAAAATCGGGAGGG 58.477 43.478 0.00 0.00 0.00 4.30
5105 7787 6.064846 CATGTGAAATAGAAAATCGGGAGG 57.935 41.667 0.00 0.00 0.00 4.30


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

AutoCloner maintained by Alex Coulton.