Multiple sequence alignment - TraesCS1B01G237200

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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 TraesCS1B01G237200 chr1B 100.000 3558 0 0 675 4232 424082537 424086094 0.000000e+00 6571.0
1 TraesCS1B01G237200 chr1B 100.000 301 0 0 1 301 424081863 424082163 1.330000e-154 556.0
2 TraesCS1B01G237200 chr1B 97.500 40 1 0 2379 2418 424083506 424083467 7.590000e-08 69.4
3 TraesCS1B01G237200 chr1B 97.500 40 1 0 1605 1644 424084280 424084241 7.590000e-08 69.4
4 TraesCS1B01G237200 chr1D 93.258 1943 70 26 729 2643 314012353 314014262 0.000000e+00 2806.0
5 TraesCS1B01G237200 chr1D 92.402 895 50 6 2642 3518 314014421 314015315 0.000000e+00 1260.0
6 TraesCS1B01G237200 chr1D 85.309 388 32 17 3597 3974 314015308 314015680 1.110000e-100 377.0
7 TraesCS1B01G237200 chr1D 84.177 316 15 15 1 301 314011862 314012157 1.500000e-69 274.0
8 TraesCS1B01G237200 chr1D 86.782 174 5 7 4070 4232 314016093 314016259 1.210000e-40 178.0
9 TraesCS1B01G237200 chr1D 97.500 40 1 0 1605 1644 314014034 314013995 7.590000e-08 69.4
10 TraesCS1B01G237200 chr1A 93.343 1367 70 8 2137 3489 394320852 394322211 0.000000e+00 2001.0
11 TraesCS1B01G237200 chr1A 90.057 1237 66 21 677 1898 394319592 394320786 0.000000e+00 1550.0
12 TraesCS1B01G237200 chr1A 93.631 157 10 0 145 301 394319362 394319518 7.070000e-58 235.0
13 TraesCS1B01G237200 chr1A 91.026 156 13 1 1900 2054 155857860 155857705 4.290000e-50 209.0
14 TraesCS1B01G237200 chr1A 94.545 110 5 1 1 110 394307002 394307110 7.280000e-38 169.0
15 TraesCS1B01G237200 chr1A 94.828 58 3 0 2052 2109 394320794 394320851 1.620000e-14 91.6
16 TraesCS1B01G237200 chr1A 97.143 35 1 0 110 144 394307125 394307159 4.570000e-05 60.2
17 TraesCS1B01G237200 chr5A 84.863 621 73 13 973 1585 670272455 670271848 1.300000e-169 606.0
18 TraesCS1B01G237200 chr5A 88.043 92 9 2 3513 3603 688704961 688705051 1.610000e-19 108.0
19 TraesCS1B01G237200 chr4B 82.986 623 80 13 973 1585 625225589 625224983 1.340000e-149 540.0
20 TraesCS1B01G237200 chr4B 91.083 157 12 2 1901 2056 106227561 106227406 1.190000e-50 211.0
21 TraesCS1B01G237200 chr4D 81.862 623 79 15 973 1585 488507193 488506595 1.060000e-135 494.0
22 TraesCS1B01G237200 chr4D 77.035 958 127 45 2247 3147 488506156 488505235 8.290000e-127 464.0
23 TraesCS1B01G237200 chr4D 91.139 158 13 1 1901 2057 74079504 74079347 3.310000e-51 213.0
24 TraesCS1B01G237200 chr3D 86.076 316 43 1 989 1304 253662001 253662315 5.240000e-89 339.0
25 TraesCS1B01G237200 chr3D 89.130 92 8 2 3516 3605 180838456 180838547 3.460000e-21 113.0
26 TraesCS1B01G237200 chr2A 91.558 154 11 2 1901 2053 141506318 141506470 1.190000e-50 211.0
27 TraesCS1B01G237200 chr2A 85.246 61 5 4 4041 4099 629644015 629643957 4.570000e-05 60.2
28 TraesCS1B01G237200 chr6D 88.372 172 18 2 1894 2064 256728609 256728439 5.550000e-49 206.0
29 TraesCS1B01G237200 chr6D 88.372 172 18 2 1894 2064 256729406 256729236 5.550000e-49 206.0
30 TraesCS1B01G237200 chr6D 90.062 161 12 4 1894 2053 320698237 320698080 5.550000e-49 206.0
31 TraesCS1B01G237200 chr6D 97.436 39 1 0 4041 4079 225939722 225939760 2.730000e-07 67.6
32 TraesCS1B01G237200 chr6D 100.000 31 0 0 4041 4071 455902743 455902773 1.640000e-04 58.4
33 TraesCS1B01G237200 chr6A 88.372 172 18 2 1894 2064 366029452 366029622 5.550000e-49 206.0
34 TraesCS1B01G237200 chrUn 91.011 89 8 0 3513 3601 42479328 42479240 2.070000e-23 121.0
35 TraesCS1B01G237200 chr5D 91.860 86 7 0 3516 3601 188826620 188826535 2.070000e-23 121.0
36 TraesCS1B01G237200 chr5D 89.888 89 7 1 3515 3601 535136262 535136174 3.460000e-21 113.0
37 TraesCS1B01G237200 chr5D 89.362 47 4 1 4041 4086 44299404 44299358 1.640000e-04 58.4
38 TraesCS1B01G237200 chr7D 89.888 89 9 0 3517 3605 83656213 83656301 9.620000e-22 115.0
39 TraesCS1B01G237200 chr7D 89.362 47 4 1 4041 4086 591506075 591506029 1.640000e-04 58.4
40 TraesCS1B01G237200 chr5B 90.698 86 8 0 3516 3601 217907768 217907683 9.620000e-22 115.0
41 TraesCS1B01G237200 chr7B 90.588 85 8 0 3517 3601 428965845 428965929 3.460000e-21 113.0
42 TraesCS1B01G237200 chr2D 87.097 93 12 0 3509 3601 512165932 512165840 5.790000e-19 106.0
43 TraesCS1B01G237200 chr3B 93.023 43 1 2 4042 4082 793564851 793564809 1.270000e-05 62.1
44 TraesCS1B01G237200 chr6B 91.111 45 2 2 4043 4086 502727195 502727152 4.570000e-05 60.2
45 TraesCS1B01G237200 chr7A 89.362 47 4 1 4041 4086 368952122 368952168 1.640000e-04 58.4
46 TraesCS1B01G237200 chr3A 89.362 47 4 1 4041 4086 170889931 170889885 1.640000e-04 58.4


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 TraesCS1B01G237200 chr1B 424081863 424086094 4231 False 3563.5 6571 100.00000 1 4232 2 chr1B.!!$F1 4231
1 TraesCS1B01G237200 chr1D 314011862 314016259 4397 False 979.0 2806 88.38560 1 4232 5 chr1D.!!$F1 4231
2 TraesCS1B01G237200 chr1A 394319362 394322211 2849 False 969.4 2001 92.96475 145 3489 4 chr1A.!!$F2 3344
3 TraesCS1B01G237200 chr5A 670271848 670272455 607 True 606.0 606 84.86300 973 1585 1 chr5A.!!$R1 612
4 TraesCS1B01G237200 chr4B 625224983 625225589 606 True 540.0 540 82.98600 973 1585 1 chr4B.!!$R2 612
5 TraesCS1B01G237200 chr4D 488505235 488507193 1958 True 479.0 494 79.44850 973 3147 2 chr4D.!!$R2 2174
6 TraesCS1B01G237200 chr6D 256728439 256729406 967 True 206.0 206 88.37200 1894 2064 2 chr6D.!!$R2 170

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
801 839 0.710588 TAGCCTCCTCTGTTCTGGGA 59.289 55.000 0.00 0.00 0.00 4.37 F
912 966 1.078848 GGCTAGTGTGCACCTCCTG 60.079 63.158 15.69 2.01 34.04 3.86 F
2155 2641 1.338973 CATTCCCCAGAAATGCATCCG 59.661 52.381 0.00 0.00 35.09 4.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1827 1910 0.831307 ATACTGTTCCGCCTTCCTCC 59.169 55.0 0.0 0.0 0.00 4.30 R
2370 3225 1.171308 TCTCATCAAGCTTTGCTGCC 58.829 50.0 0.0 0.0 39.62 4.85 R
4103 5557 0.106419 TGGGCGGTTCTCCAAAAACT 60.106 50.0 0.0 0.0 0.00 2.66 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
39 40 2.435059 GCAGGTTCGGCCACTCTC 60.435 66.667 2.24 0.00 40.61 3.20
74 75 0.904865 TGAGGTGAGGCCGTTCTCAT 60.905 55.000 14.16 0.00 44.43 2.90
79 80 2.158957 GGTGAGGCCGTTCTCATGATAA 60.159 50.000 0.00 0.00 44.43 1.75
82 83 4.576463 GTGAGGCCGTTCTCATGATAATTT 59.424 41.667 0.00 0.00 44.43 1.82
95 96 9.474920 TCTCATGATAATTTTGAAACACCAAAC 57.525 29.630 0.00 0.00 35.95 2.93
103 104 5.730296 TTTGAAACACCAAACCTCTTTCA 57.270 34.783 0.00 0.00 31.73 2.69
105 106 5.261209 TGAAACACCAAACCTCTTTCATG 57.739 39.130 0.00 0.00 0.00 3.07
110 111 1.666888 CCAAACCTCTTTCATGTGCGC 60.667 52.381 0.00 0.00 0.00 6.09
111 112 1.267806 CAAACCTCTTTCATGTGCGCT 59.732 47.619 9.73 0.00 0.00 5.92
136 152 2.439409 CAAACCAGTGGATGCTCATCA 58.561 47.619 18.40 0.00 39.54 3.07
182 217 1.762708 AGCTCTCACTCTACCTCTGC 58.237 55.000 0.00 0.00 0.00 4.26
183 218 1.284785 AGCTCTCACTCTACCTCTGCT 59.715 52.381 0.00 0.00 0.00 4.24
184 219 2.099405 GCTCTCACTCTACCTCTGCTT 58.901 52.381 0.00 0.00 0.00 3.91
185 220 2.495669 GCTCTCACTCTACCTCTGCTTT 59.504 50.000 0.00 0.00 0.00 3.51
186 221 3.675775 GCTCTCACTCTACCTCTGCTTTG 60.676 52.174 0.00 0.00 0.00 2.77
187 222 2.232452 TCTCACTCTACCTCTGCTTTGC 59.768 50.000 0.00 0.00 0.00 3.68
188 223 2.233431 CTCACTCTACCTCTGCTTTGCT 59.767 50.000 0.00 0.00 0.00 3.91
189 224 3.431415 TCACTCTACCTCTGCTTTGCTA 58.569 45.455 0.00 0.00 0.00 3.49
190 225 4.026744 TCACTCTACCTCTGCTTTGCTAT 58.973 43.478 0.00 0.00 0.00 2.97
191 226 4.098654 TCACTCTACCTCTGCTTTGCTATC 59.901 45.833 0.00 0.00 0.00 2.08
192 227 3.386402 ACTCTACCTCTGCTTTGCTATCC 59.614 47.826 0.00 0.00 0.00 2.59
193 228 2.700897 TCTACCTCTGCTTTGCTATCCC 59.299 50.000 0.00 0.00 0.00 3.85
194 229 1.589414 ACCTCTGCTTTGCTATCCCT 58.411 50.000 0.00 0.00 0.00 4.20
195 230 1.211457 ACCTCTGCTTTGCTATCCCTG 59.789 52.381 0.00 0.00 0.00 4.45
196 231 1.307097 CTCTGCTTTGCTATCCCTGC 58.693 55.000 0.00 0.00 0.00 4.85
197 232 0.914644 TCTGCTTTGCTATCCCTGCT 59.085 50.000 0.00 0.00 0.00 4.24
198 233 1.134280 TCTGCTTTGCTATCCCTGCTC 60.134 52.381 0.00 0.00 0.00 4.26
199 234 0.914644 TGCTTTGCTATCCCTGCTCT 59.085 50.000 0.00 0.00 0.00 4.09
200 235 1.307097 GCTTTGCTATCCCTGCTCTG 58.693 55.000 0.00 0.00 0.00 3.35
241 276 2.221169 TGAACACTTGCAGGTAGCTTG 58.779 47.619 0.00 0.00 45.94 4.01
253 288 3.993081 CAGGTAGCTTGTGAACTCTGAAG 59.007 47.826 0.00 0.00 0.00 3.02
284 319 6.089551 ACACTTTCAGACGTCTTCATATTTCG 59.910 38.462 17.26 0.92 0.00 3.46
295 330 1.202486 TCATATTTCGGGCGTCAGGTC 60.202 52.381 0.00 0.00 0.00 3.85
801 839 0.710588 TAGCCTCCTCTGTTCTGGGA 59.289 55.000 0.00 0.00 0.00 4.37
912 966 1.078848 GGCTAGTGTGCACCTCCTG 60.079 63.158 15.69 2.01 34.04 3.86
920 974 2.272471 GCACCTCCTGCCCTAACC 59.728 66.667 0.00 0.00 40.42 2.85
950 1004 3.095911 CCTCGTAGTCGCACGCTA 58.904 61.111 0.00 0.00 41.67 4.26
964 1018 2.786495 CGCTACCGCATCTGAGGGT 61.786 63.158 4.95 2.31 39.47 4.34
1479 1543 1.881903 CTGGCTCTGCTTCGACTCCA 61.882 60.000 0.00 0.00 0.00 3.86
1534 1603 7.775093 TCAATTCCTATGTTTCTTCATGTAGGG 59.225 37.037 0.00 0.00 29.41 3.53
1646 1718 5.365025 TGCTTAAAGATCTCATCCAGCTAGT 59.635 40.000 0.00 0.00 0.00 2.57
1726 1809 8.472413 TGAGCTTTAGACGTTAGGTGTAAATAT 58.528 33.333 7.62 1.33 41.73 1.28
1752 1835 5.250543 AGCCAAAATAATGCCCCTAAAACTT 59.749 36.000 0.00 0.00 0.00 2.66
1760 1843 1.467342 GCCCCTAAAACTTGCGTACTG 59.533 52.381 0.00 0.00 0.00 2.74
1851 1934 5.470047 AGGAAGGCGGAACAGTATATAAG 57.530 43.478 0.00 0.00 0.00 1.73
1858 1941 4.982916 GCGGAACAGTATATAAGTGACTGG 59.017 45.833 7.35 0.00 43.98 4.00
2115 2601 4.636206 CCTACAAACAGAGTAATCCTTGCC 59.364 45.833 0.00 0.00 0.00 4.52
2124 2610 1.472480 GTAATCCTTGCCGCACACAAT 59.528 47.619 0.00 0.00 0.00 2.71
2153 2639 2.363359 GGTCATTCCCCAGAAATGCATC 59.637 50.000 0.00 0.00 35.09 3.91
2154 2640 2.363359 GTCATTCCCCAGAAATGCATCC 59.637 50.000 0.00 0.00 35.09 3.51
2155 2641 1.338973 CATTCCCCAGAAATGCATCCG 59.661 52.381 0.00 0.00 35.09 4.18
2370 3225 1.472728 GGGGGTGCAGATTACTACACG 60.473 57.143 0.00 0.00 40.27 4.49
2499 3354 0.400594 AGGAGGCGGCAGTAAGTTTT 59.599 50.000 13.08 0.00 0.00 2.43
2500 3355 0.521735 GGAGGCGGCAGTAAGTTTTG 59.478 55.000 13.08 0.00 0.00 2.44
2573 3432 6.862209 AGTCTTGTAGATCTTGAACTAGCAG 58.138 40.000 0.00 0.00 0.00 4.24
2587 3446 9.102757 CTTGAACTAGCAGATAAAATTGAGCTA 57.897 33.333 0.00 0.00 33.83 3.32
2625 3487 4.022849 ACAAGATAGGAGTTTGCAAGCAAC 60.023 41.667 16.04 7.52 35.46 4.17
2629 3507 2.010817 GAGTTTGCAAGCAACCGCG 61.011 57.895 16.04 0.00 45.49 6.46
2682 3720 5.412594 TGCTGTCTCTGTTTATGGTTCAATC 59.587 40.000 0.00 0.00 0.00 2.67
2689 3727 9.246670 TCTCTGTTTATGGTTCAATCATCAATT 57.753 29.630 0.00 0.00 0.00 2.32
2726 3764 8.218423 TGTACCATTTCCATATCATATCACCT 57.782 34.615 0.00 0.00 0.00 4.00
2732 3770 3.769300 TCCATATCATATCACCTCGTGGG 59.231 47.826 8.63 2.00 41.89 4.61
2753 3791 6.092259 GTGGGTCTTTAACAAGCTGTACTATG 59.908 42.308 0.00 0.00 0.00 2.23
2800 3838 0.237498 GTGCGGCTAACCAACACTTC 59.763 55.000 0.00 0.00 38.85 3.01
3084 4151 5.334414 CGCAGCTAGTGAACAAAGAAAATCT 60.334 40.000 0.00 0.00 0.00 2.40
3129 4196 9.394477 GTTTCTTTTACAAGGTAGTTTAGCATG 57.606 33.333 0.00 0.00 0.00 4.06
3132 4199 5.873179 TTACAAGGTAGTTTAGCATGTGC 57.127 39.130 6.46 0.00 38.38 4.57
3150 4224 1.393196 TGCGTTGCGTGATAAGACATG 59.607 47.619 0.00 0.00 0.00 3.21
3162 4236 4.935205 TGATAAGACATGTACTTGTGTGCC 59.065 41.667 18.24 4.91 0.00 5.01
3328 4402 4.336713 GGGCAATCCAGAACAATCTTCTAC 59.663 45.833 0.00 0.00 32.03 2.59
3332 4406 7.500559 GGCAATCCAGAACAATCTTCTACTATT 59.499 37.037 0.00 0.00 32.03 1.73
3368 4442 7.098477 TCTTTTGATGGGTATTTTGCATCTTG 58.902 34.615 0.00 0.00 0.00 3.02
3417 4491 2.418669 AGGAGAGGTGAAAGGGAAACA 58.581 47.619 0.00 0.00 0.00 2.83
3435 4520 2.430465 ACAGAGCCATTACTTGTGCTG 58.570 47.619 0.00 0.00 33.63 4.41
3441 4526 2.420022 GCCATTACTTGTGCTGTCGATT 59.580 45.455 0.00 0.00 0.00 3.34
3492 4577 2.715046 TCATAGCCCACTGAAAGCAAG 58.285 47.619 0.00 0.00 37.60 4.01
3503 4588 5.182001 CCACTGAAAGCAAGCAATTACTACT 59.818 40.000 0.00 0.00 37.60 2.57
3529 4614 8.709272 ATACTAAATTACTACTCCCTCAGTCC 57.291 38.462 0.00 0.00 36.43 3.85
3530 4615 5.898397 ACTAAATTACTACTCCCTCAGTCCC 59.102 44.000 0.00 0.00 36.43 4.46
3531 4616 4.348020 AATTACTACTCCCTCAGTCCCA 57.652 45.455 0.00 0.00 36.43 4.37
3532 4617 2.822707 TACTACTCCCTCAGTCCCAC 57.177 55.000 0.00 0.00 36.43 4.61
3533 4618 0.784495 ACTACTCCCTCAGTCCCACA 59.216 55.000 0.00 0.00 36.43 4.17
3534 4619 1.149288 ACTACTCCCTCAGTCCCACAA 59.851 52.381 0.00 0.00 36.43 3.33
3535 4620 2.225650 ACTACTCCCTCAGTCCCACAAT 60.226 50.000 0.00 0.00 36.43 2.71
3536 4621 2.642171 ACTCCCTCAGTCCCACAATA 57.358 50.000 0.00 0.00 0.00 1.90
3537 4622 3.136641 ACTCCCTCAGTCCCACAATAT 57.863 47.619 0.00 0.00 0.00 1.28
3538 4623 4.280789 ACTCCCTCAGTCCCACAATATA 57.719 45.455 0.00 0.00 0.00 0.86
3539 4624 4.631234 ACTCCCTCAGTCCCACAATATAA 58.369 43.478 0.00 0.00 0.00 0.98
3540 4625 4.656112 ACTCCCTCAGTCCCACAATATAAG 59.344 45.833 0.00 0.00 0.00 1.73
3541 4626 4.890988 TCCCTCAGTCCCACAATATAAGA 58.109 43.478 0.00 0.00 0.00 2.10
3542 4627 4.654262 TCCCTCAGTCCCACAATATAAGAC 59.346 45.833 0.00 0.00 0.00 3.01
3543 4628 4.501571 CCCTCAGTCCCACAATATAAGACG 60.502 50.000 0.00 0.00 32.70 4.18
3544 4629 4.099573 CCTCAGTCCCACAATATAAGACGT 59.900 45.833 0.00 0.00 32.70 4.34
3545 4630 5.395324 CCTCAGTCCCACAATATAAGACGTT 60.395 44.000 0.00 0.00 32.70 3.99
3546 4631 6.045072 TCAGTCCCACAATATAAGACGTTT 57.955 37.500 0.00 0.00 32.70 3.60
3547 4632 6.469410 TCAGTCCCACAATATAAGACGTTTT 58.531 36.000 0.00 0.00 32.70 2.43
3548 4633 6.938030 TCAGTCCCACAATATAAGACGTTTTT 59.062 34.615 0.00 0.00 32.70 1.94
3549 4634 7.021196 CAGTCCCACAATATAAGACGTTTTTG 58.979 38.462 0.00 0.00 32.70 2.44
3550 4635 5.798434 GTCCCACAATATAAGACGTTTTTGC 59.202 40.000 0.00 0.00 0.00 3.68
3551 4636 5.473846 TCCCACAATATAAGACGTTTTTGCA 59.526 36.000 0.00 0.00 0.00 4.08
3552 4637 6.016192 TCCCACAATATAAGACGTTTTTGCAA 60.016 34.615 0.00 0.00 0.00 4.08
3553 4638 6.307800 CCCACAATATAAGACGTTTTTGCAAG 59.692 38.462 0.00 0.00 0.00 4.01
3554 4639 6.183359 CCACAATATAAGACGTTTTTGCAAGC 60.183 38.462 0.00 0.00 0.00 4.01
3555 4640 6.582295 CACAATATAAGACGTTTTTGCAAGCT 59.418 34.615 0.00 0.00 0.00 3.74
3556 4641 7.748683 CACAATATAAGACGTTTTTGCAAGCTA 59.251 33.333 0.00 0.00 0.00 3.32
3557 4642 8.293867 ACAATATAAGACGTTTTTGCAAGCTAA 58.706 29.630 0.00 0.00 0.00 3.09
3558 4643 8.575454 CAATATAAGACGTTTTTGCAAGCTAAC 58.425 33.333 0.00 5.28 0.00 2.34
3559 4644 4.364415 AAGACGTTTTTGCAAGCTAACA 57.636 36.364 16.37 0.00 0.00 2.41
3560 4645 4.568152 AGACGTTTTTGCAAGCTAACAT 57.432 36.364 16.37 5.95 0.00 2.71
3561 4646 4.290155 AGACGTTTTTGCAAGCTAACATG 58.710 39.130 16.37 0.00 0.00 3.21
3562 4647 4.036262 AGACGTTTTTGCAAGCTAACATGA 59.964 37.500 16.37 0.00 0.00 3.07
3563 4648 4.041723 ACGTTTTTGCAAGCTAACATGAC 58.958 39.130 16.37 0.00 0.00 3.06
3564 4649 4.202010 ACGTTTTTGCAAGCTAACATGACT 60.202 37.500 16.37 0.00 0.00 3.41
3565 4650 4.739716 CGTTTTTGCAAGCTAACATGACTT 59.260 37.500 16.37 0.00 0.00 3.01
3566 4651 5.912396 CGTTTTTGCAAGCTAACATGACTTA 59.088 36.000 16.37 0.00 0.00 2.24
3567 4652 6.129457 CGTTTTTGCAAGCTAACATGACTTAC 60.129 38.462 16.37 0.00 0.00 2.34
3568 4653 6.384258 TTTTGCAAGCTAACATGACTTACA 57.616 33.333 0.00 0.00 0.00 2.41
3569 4654 6.384258 TTTGCAAGCTAACATGACTTACAA 57.616 33.333 0.00 2.29 0.00 2.41
3570 4655 6.384258 TTGCAAGCTAACATGACTTACAAA 57.616 33.333 0.00 0.00 0.00 2.83
3571 4656 6.384258 TGCAAGCTAACATGACTTACAAAA 57.616 33.333 0.00 0.00 0.00 2.44
3572 4657 6.800543 TGCAAGCTAACATGACTTACAAAAA 58.199 32.000 0.00 0.00 0.00 1.94
3573 4658 6.695278 TGCAAGCTAACATGACTTACAAAAAC 59.305 34.615 0.00 0.00 0.00 2.43
3574 4659 6.129457 GCAAGCTAACATGACTTACAAAAACG 60.129 38.462 0.00 0.00 0.00 3.60
3575 4660 6.613755 AGCTAACATGACTTACAAAAACGT 57.386 33.333 0.00 0.00 0.00 3.99
3576 4661 6.656003 AGCTAACATGACTTACAAAAACGTC 58.344 36.000 0.00 0.00 0.00 4.34
3577 4662 6.482308 AGCTAACATGACTTACAAAAACGTCT 59.518 34.615 0.00 0.00 0.00 4.18
3578 4663 7.012044 AGCTAACATGACTTACAAAAACGTCTT 59.988 33.333 0.00 0.00 0.00 3.01
3579 4664 8.277713 GCTAACATGACTTACAAAAACGTCTTA 58.722 33.333 0.00 0.00 0.00 2.10
3587 4672 9.882856 GACTTACAAAAACGTCTTATATTCTCG 57.117 33.333 0.00 0.00 0.00 4.04
3588 4673 8.866956 ACTTACAAAAACGTCTTATATTCTCGG 58.133 33.333 0.00 0.00 0.00 4.63
3589 4674 8.984891 TTACAAAAACGTCTTATATTCTCGGA 57.015 30.769 0.00 0.00 0.00 4.55
3590 4675 7.287050 ACAAAAACGTCTTATATTCTCGGAC 57.713 36.000 0.00 0.00 0.00 4.79
3594 4679 4.067999 CGTCTTATATTCTCGGACGGAG 57.932 50.000 3.68 3.68 43.69 4.63
3595 4680 3.120269 CGTCTTATATTCTCGGACGGAGG 60.120 52.174 9.88 0.00 43.69 4.30
3596 4681 4.070716 GTCTTATATTCTCGGACGGAGGA 58.929 47.826 9.88 1.75 43.34 3.71
3597 4682 4.518211 GTCTTATATTCTCGGACGGAGGAA 59.482 45.833 9.88 4.34 43.34 3.36
3598 4683 4.760715 TCTTATATTCTCGGACGGAGGAAG 59.239 45.833 9.88 6.67 43.34 3.46
3599 4684 2.431954 TATTCTCGGACGGAGGAAGT 57.568 50.000 9.88 0.00 43.34 3.01
3600 4685 2.431954 ATTCTCGGACGGAGGAAGTA 57.568 50.000 9.88 0.00 43.34 2.24
3601 4686 1.747709 TTCTCGGACGGAGGAAGTAG 58.252 55.000 9.88 0.00 43.34 2.57
3602 4687 0.617413 TCTCGGACGGAGGAAGTAGT 59.383 55.000 9.88 0.00 43.34 2.73
3603 4688 1.833630 TCTCGGACGGAGGAAGTAGTA 59.166 52.381 9.88 0.00 43.34 1.82
3629 4714 5.278071 CGATCTTCGGGTAGATAGATATGCC 60.278 48.000 0.00 0.00 35.06 4.40
3645 4730 4.225497 CCGATGGAAGGCAAGTCC 57.775 61.111 0.00 0.00 35.55 3.85
3653 4738 4.380843 TGGAAGGCAAGTCCAGAATAAA 57.619 40.909 0.89 0.00 40.33 1.40
3660 4745 6.458210 AGGCAAGTCCAGAATAAATTGTTTG 58.542 36.000 0.00 0.00 37.29 2.93
3664 4749 7.095102 GCAAGTCCAGAATAAATTGTTTGCATT 60.095 33.333 0.00 0.00 37.65 3.56
3724 4809 2.094854 ACGAACGGGAAGAGACACATAC 60.095 50.000 0.00 0.00 0.00 2.39
3725 4810 2.527100 GAACGGGAAGAGACACATACG 58.473 52.381 0.00 0.00 0.00 3.06
3726 4811 1.542492 ACGGGAAGAGACACATACGT 58.458 50.000 0.00 0.00 0.00 3.57
3727 4812 2.715046 ACGGGAAGAGACACATACGTA 58.285 47.619 0.00 0.00 0.00 3.57
3741 4826 2.218953 TACGTACATAGCTGCTTGCC 57.781 50.000 7.79 0.57 44.23 4.52
3744 4829 0.811616 GTACATAGCTGCTTGCCGCT 60.812 55.000 7.79 15.16 44.23 5.52
3747 4832 2.768492 ATAGCTGCTTGCCGCTTGC 61.768 57.895 15.92 0.00 44.23 4.01
3771 4856 0.179015 TGCCGGGCAAAGTAAAGTGA 60.179 50.000 21.55 0.00 34.76 3.41
3804 4905 3.127721 GGAGAACTGAGCTATTTGCAACC 59.872 47.826 0.00 0.00 45.94 3.77
3806 4907 4.144297 AGAACTGAGCTATTTGCAACCAA 58.856 39.130 0.00 0.00 45.94 3.67
3807 4908 3.923017 ACTGAGCTATTTGCAACCAAC 57.077 42.857 0.00 0.00 45.94 3.77
3808 4909 3.490348 ACTGAGCTATTTGCAACCAACT 58.510 40.909 0.00 0.00 45.94 3.16
3809 4910 3.503748 ACTGAGCTATTTGCAACCAACTC 59.496 43.478 0.00 5.22 45.94 3.01
3810 4911 3.485394 TGAGCTATTTGCAACCAACTCA 58.515 40.909 14.24 14.24 45.94 3.41
3811 4912 3.888323 TGAGCTATTTGCAACCAACTCAA 59.112 39.130 15.34 4.04 45.94 3.02
3812 4913 4.022935 TGAGCTATTTGCAACCAACTCAAG 60.023 41.667 15.34 0.90 45.94 3.02
3813 4914 3.891366 AGCTATTTGCAACCAACTCAAGT 59.109 39.130 0.00 0.00 45.94 3.16
3814 4915 3.983344 GCTATTTGCAACCAACTCAAGTG 59.017 43.478 0.00 0.00 42.31 3.16
3815 4916 2.957491 TTTGCAACCAACTCAAGTGG 57.043 45.000 0.00 0.00 0.00 4.00
3816 4917 2.136298 TTGCAACCAACTCAAGTGGA 57.864 45.000 0.00 0.00 0.00 4.02
3817 4918 2.136298 TGCAACCAACTCAAGTGGAA 57.864 45.000 0.00 0.00 0.00 3.53
3818 4919 2.023673 TGCAACCAACTCAAGTGGAAG 58.976 47.619 0.00 0.00 0.00 3.46
3822 4923 1.771255 ACCAACTCAAGTGGAAGAGCT 59.229 47.619 0.00 0.00 35.28 4.09
3876 4977 2.599645 CTAGCTGGATTGGCGGCACT 62.600 60.000 12.92 6.26 34.52 4.40
3890 4991 1.464608 CGGCACTATGTTGGTGTTGAG 59.535 52.381 0.00 0.00 37.07 3.02
3926 5027 3.628942 GGTCATCATGCATAGTGCTGAAA 59.371 43.478 0.00 0.00 45.31 2.69
3927 5028 4.497006 GGTCATCATGCATAGTGCTGAAAC 60.497 45.833 0.00 0.00 45.31 2.78
3928 5029 3.310501 TCATCATGCATAGTGCTGAAACG 59.689 43.478 0.00 0.00 45.31 3.60
3929 5030 2.009051 TCATGCATAGTGCTGAAACGG 58.991 47.619 0.00 0.00 45.31 4.44
3930 5031 2.009051 CATGCATAGTGCTGAAACGGA 58.991 47.619 0.00 0.00 45.31 4.69
3931 5032 2.401583 TGCATAGTGCTGAAACGGAT 57.598 45.000 3.41 0.00 45.31 4.18
3932 5033 3.535280 TGCATAGTGCTGAAACGGATA 57.465 42.857 3.41 0.00 45.31 2.59
3933 5034 3.194861 TGCATAGTGCTGAAACGGATAC 58.805 45.455 3.41 0.00 45.31 2.24
3935 5036 4.881886 GCATAGTGCTGAAACGGATACCG 61.882 52.174 8.67 8.67 46.30 4.02
3977 5078 0.676736 GAGCTCCTCCAGGTAATCCG 59.323 60.000 0.87 0.00 39.05 4.18
3978 5079 0.032017 AGCTCCTCCAGGTAATCCGT 60.032 55.000 0.00 0.00 39.05 4.69
4026 5480 2.256461 CCCGACAAGCAAGCAAGC 59.744 61.111 0.00 0.00 0.00 4.01
4028 5482 1.359833 CCGACAAGCAAGCAAGCAA 59.640 52.632 3.19 0.00 36.85 3.91
4029 5483 0.662374 CCGACAAGCAAGCAAGCAAG 60.662 55.000 3.19 0.00 36.85 4.01
4030 5484 0.662374 CGACAAGCAAGCAAGCAAGG 60.662 55.000 3.19 0.00 36.85 3.61
4031 5485 0.670162 GACAAGCAAGCAAGCAAGGA 59.330 50.000 3.19 0.00 36.85 3.36
4032 5486 0.672342 ACAAGCAAGCAAGCAAGGAG 59.328 50.000 3.19 0.00 36.85 3.69
4033 5487 0.956633 CAAGCAAGCAAGCAAGGAGA 59.043 50.000 3.19 0.00 36.85 3.71
4037 5491 1.068679 GCAAGCAAGCAAGGAGAAGTC 60.069 52.381 0.00 0.00 0.00 3.01
4038 5492 1.196354 CAAGCAAGCAAGGAGAAGTCG 59.804 52.381 0.00 0.00 0.00 4.18
4039 5493 0.952984 AGCAAGCAAGGAGAAGTCGC 60.953 55.000 0.00 0.00 0.00 5.19
4040 5494 1.916697 GCAAGCAAGGAGAAGTCGCC 61.917 60.000 0.00 0.00 35.95 5.54
4041 5495 1.374758 AAGCAAGGAGAAGTCGCCG 60.375 57.895 0.00 0.00 40.98 6.46
4042 5496 1.816863 AAGCAAGGAGAAGTCGCCGA 61.817 55.000 0.00 0.00 40.98 5.54
4043 5497 2.095252 GCAAGGAGAAGTCGCCGAC 61.095 63.158 9.71 9.71 40.98 4.79
4044 5498 1.801913 CAAGGAGAAGTCGCCGACG 60.802 63.158 12.13 0.00 40.98 5.12
4054 5508 3.038946 TCGCCGACGAGTAATTTGG 57.961 52.632 0.00 0.00 45.12 3.28
4055 5509 0.527113 TCGCCGACGAGTAATTTGGA 59.473 50.000 0.00 0.00 45.12 3.53
4056 5510 1.067706 TCGCCGACGAGTAATTTGGAA 60.068 47.619 0.00 0.00 45.12 3.53
4057 5511 1.060122 CGCCGACGAGTAATTTGGAAC 59.940 52.381 0.00 0.00 43.93 3.62
4058 5512 1.060122 GCCGACGAGTAATTTGGAACG 59.940 52.381 0.00 0.00 0.00 3.95
4059 5513 1.657094 CCGACGAGTAATTTGGAACGG 59.343 52.381 0.00 0.00 0.00 4.44
4060 5514 2.598589 CGACGAGTAATTTGGAACGGA 58.401 47.619 0.00 0.00 0.00 4.69
4061 5515 2.597305 CGACGAGTAATTTGGAACGGAG 59.403 50.000 0.00 0.00 0.00 4.63
4062 5516 2.928116 GACGAGTAATTTGGAACGGAGG 59.072 50.000 0.00 0.00 0.00 4.30
4063 5517 2.277084 CGAGTAATTTGGAACGGAGGG 58.723 52.381 0.00 0.00 0.00 4.30
4064 5518 2.093869 CGAGTAATTTGGAACGGAGGGA 60.094 50.000 0.00 0.00 0.00 4.20
4065 5519 3.532542 GAGTAATTTGGAACGGAGGGAG 58.467 50.000 0.00 0.00 0.00 4.30
4066 5520 2.910977 AGTAATTTGGAACGGAGGGAGT 59.089 45.455 0.00 0.00 0.00 3.85
4067 5521 4.098894 AGTAATTTGGAACGGAGGGAGTA 58.901 43.478 0.00 0.00 0.00 2.59
4068 5522 3.345508 AATTTGGAACGGAGGGAGTAC 57.654 47.619 0.00 0.00 0.00 2.73
4069 5523 2.019807 TTTGGAACGGAGGGAGTACT 57.980 50.000 0.00 0.00 0.00 2.73
4070 5524 2.905415 TTGGAACGGAGGGAGTACTA 57.095 50.000 0.00 0.00 0.00 1.82
4071 5525 2.431954 TGGAACGGAGGGAGTACTAG 57.568 55.000 0.00 0.00 0.00 2.57
4072 5526 1.637553 TGGAACGGAGGGAGTACTAGT 59.362 52.381 0.00 0.00 0.00 2.57
4073 5527 2.846206 TGGAACGGAGGGAGTACTAGTA 59.154 50.000 0.00 0.00 0.00 1.82
4194 5658 7.206981 CGGAGCATATTTGATTGAATAGGTT 57.793 36.000 0.00 0.00 0.00 3.50
4195 5659 7.301054 CGGAGCATATTTGATTGAATAGGTTC 58.699 38.462 0.00 0.00 34.72 3.62
4196 5660 7.041167 CGGAGCATATTTGATTGAATAGGTTCA 60.041 37.037 7.88 0.00 42.41 3.18
4197 5661 8.295288 GGAGCATATTTGATTGAATAGGTTCAG 58.705 37.037 7.88 0.00 44.62 3.02
4209 5673 8.690203 TTGAATAGGTTCAGTCAGAAAATCAA 57.310 30.769 0.00 0.00 44.62 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 3.828451 ACCTGCAATTCTGTATTGTGCTT 59.172 39.130 8.49 0.00 44.52 3.91
30 31 1.127343 AGCCTATCTTGAGAGTGGCC 58.873 55.000 17.67 0.00 43.04 5.36
39 40 3.066342 CACCTCATGCAAAGCCTATCTTG 59.934 47.826 0.00 0.00 34.67 3.02
74 75 8.017418 AGAGGTTTGGTGTTTCAAAATTATCA 57.983 30.769 0.00 0.00 38.21 2.15
79 80 6.706295 TGAAAGAGGTTTGGTGTTTCAAAAT 58.294 32.000 0.00 0.00 38.21 1.82
82 83 5.186797 ACATGAAAGAGGTTTGGTGTTTCAA 59.813 36.000 0.00 0.00 39.77 2.69
95 96 0.169672 CCAAGCGCACATGAAAGAGG 59.830 55.000 11.47 0.00 0.00 3.69
103 104 2.339712 GTTTGGCCAAGCGCACAT 59.660 55.556 19.48 0.00 40.31 3.21
105 106 3.910490 TGGTTTGGCCAAGCGCAC 61.910 61.111 23.95 16.63 45.94 5.34
136 152 5.426689 AGATGTGATATTGAGTGTGGTGT 57.573 39.130 0.00 0.00 0.00 4.16
182 217 2.706339 ACAGAGCAGGGATAGCAAAG 57.294 50.000 0.00 0.00 0.00 2.77
183 218 2.677902 CGAACAGAGCAGGGATAGCAAA 60.678 50.000 0.00 0.00 0.00 3.68
184 219 1.134699 CGAACAGAGCAGGGATAGCAA 60.135 52.381 0.00 0.00 0.00 3.91
185 220 0.461548 CGAACAGAGCAGGGATAGCA 59.538 55.000 0.00 0.00 0.00 3.49
186 221 0.249657 CCGAACAGAGCAGGGATAGC 60.250 60.000 0.00 0.00 0.00 2.97
187 222 1.403814 TCCGAACAGAGCAGGGATAG 58.596 55.000 0.00 0.00 0.00 2.08
188 223 1.480954 GTTCCGAACAGAGCAGGGATA 59.519 52.381 6.38 0.00 0.00 2.59
189 224 0.250513 GTTCCGAACAGAGCAGGGAT 59.749 55.000 6.38 0.00 0.00 3.85
190 225 1.671742 GTTCCGAACAGAGCAGGGA 59.328 57.895 6.38 0.00 0.00 4.20
191 226 1.738099 CGTTCCGAACAGAGCAGGG 60.738 63.158 11.74 0.00 0.00 4.45
192 227 0.600255 AACGTTCCGAACAGAGCAGG 60.600 55.000 11.74 0.00 0.00 4.85
193 228 0.784778 GAACGTTCCGAACAGAGCAG 59.215 55.000 17.68 0.00 0.00 4.24
194 229 0.387929 AGAACGTTCCGAACAGAGCA 59.612 50.000 24.22 0.00 0.00 4.26
195 230 0.784778 CAGAACGTTCCGAACAGAGC 59.215 55.000 24.22 0.00 0.00 4.09
196 231 2.417339 TCAGAACGTTCCGAACAGAG 57.583 50.000 24.22 5.20 0.00 3.35
197 232 2.875087 TTCAGAACGTTCCGAACAGA 57.125 45.000 24.22 10.23 0.00 3.41
198 233 5.779806 AATATTCAGAACGTTCCGAACAG 57.220 39.130 25.06 9.81 0.00 3.16
199 234 5.697178 TCAAATATTCAGAACGTTCCGAACA 59.303 36.000 25.06 16.93 0.00 3.18
200 235 6.160664 TCAAATATTCAGAACGTTCCGAAC 57.839 37.500 25.06 2.51 0.00 3.95
218 253 3.490348 AGCTACCTGCAAGTGTTCAAAT 58.510 40.909 0.00 0.00 45.94 2.32
241 276 4.688021 AGTGTTCAGACTTCAGAGTTCAC 58.312 43.478 0.00 0.00 35.88 3.18
716 753 0.395311 ACCGCGAAGTATCTCCAGGA 60.395 55.000 8.23 0.00 0.00 3.86
719 756 1.822990 AGAAACCGCGAAGTATCTCCA 59.177 47.619 8.23 0.00 0.00 3.86
722 759 3.251571 GTGAAGAAACCGCGAAGTATCT 58.748 45.455 8.23 0.34 0.00 1.98
725 762 1.606224 GGGTGAAGAAACCGCGAAGTA 60.606 52.381 8.23 0.00 41.52 2.24
888 942 3.370231 TGCACACTAGCCGAGCGA 61.370 61.111 0.00 0.00 0.00 4.93
889 943 3.181967 GTGCACACTAGCCGAGCG 61.182 66.667 13.17 0.00 0.00 5.03
890 944 2.815647 GGTGCACACTAGCCGAGC 60.816 66.667 20.43 0.00 0.00 5.03
891 945 1.153745 GAGGTGCACACTAGCCGAG 60.154 63.158 20.43 0.00 0.00 4.63
892 946 2.646175 GGAGGTGCACACTAGCCGA 61.646 63.158 20.43 0.00 0.00 5.54
893 947 2.125512 GGAGGTGCACACTAGCCG 60.126 66.667 20.43 0.00 0.00 5.52
894 948 1.078848 CAGGAGGTGCACACTAGCC 60.079 63.158 20.43 11.45 0.00 3.93
895 949 4.606071 CAGGAGGTGCACACTAGC 57.394 61.111 20.43 0.00 0.00 3.42
912 966 3.682292 CTGCTCGGGTGGTTAGGGC 62.682 68.421 0.00 0.00 0.00 5.19
950 1004 4.148825 GCGACCCTCAGATGCGGT 62.149 66.667 0.00 0.00 0.00 5.68
964 1018 2.501223 ATTCGGCGAAACAGGAGCGA 62.501 55.000 27.40 0.00 0.00 4.93
1479 1543 8.153550 AGATTCAAACAACAGAGAGACATTACT 58.846 33.333 0.00 0.00 0.00 2.24
1527 1596 1.762957 ACAGCGCTATCAACCCTACAT 59.237 47.619 10.99 0.00 0.00 2.29
1726 1809 6.442244 AGTTTTAGGGGCATTATTTTGGCTTA 59.558 34.615 0.00 0.00 41.61 3.09
1752 1835 6.695713 CAGTAATACTAATTCAGCAGTACGCA 59.304 38.462 11.30 0.00 46.13 5.24
1760 1843 9.757227 ATCACTCTTCAGTAATACTAATTCAGC 57.243 33.333 0.00 0.00 0.00 4.26
1827 1910 0.831307 ATACTGTTCCGCCTTCCTCC 59.169 55.000 0.00 0.00 0.00 4.30
1851 1934 3.118629 TCCTCAATGCTACATCCAGTCAC 60.119 47.826 0.00 0.00 0.00 3.67
1858 1941 9.372369 GTAGGTTATTATCCTCAATGCTACATC 57.628 37.037 0.00 0.00 36.60 3.06
2124 2610 1.770658 CTGGGGAATGACCTATCAGCA 59.229 52.381 0.00 0.00 38.57 4.41
2370 3225 1.171308 TCTCATCAAGCTTTGCTGCC 58.829 50.000 0.00 0.00 39.62 4.85
2587 3446 8.324191 TCCTATCTTGTAGTGGATCTGAAATT 57.676 34.615 0.00 0.00 0.00 1.82
2625 3487 1.937223 TGATAAAACATAGGCACGCGG 59.063 47.619 12.47 0.00 0.00 6.46
2629 3507 5.221303 ACCATGCATGATAAAACATAGGCAC 60.221 40.000 28.31 0.00 34.02 5.01
2704 3742 6.013379 ACGAGGTGATATGATATGGAAATGGT 60.013 38.462 0.00 0.00 0.00 3.55
2726 3764 2.158871 ACAGCTTGTTAAAGACCCACGA 60.159 45.455 0.00 0.00 35.19 4.35
2732 3770 7.410513 CGACACATAGTACAGCTTGTTAAAGAC 60.411 40.741 0.00 0.00 35.19 3.01
2738 3776 3.257375 TCCGACACATAGTACAGCTTGTT 59.743 43.478 0.00 0.00 0.00 2.83
2739 3777 2.823747 TCCGACACATAGTACAGCTTGT 59.176 45.455 0.00 0.00 0.00 3.16
2753 3791 9.567848 ACAAAAACATATAATCAATTCCGACAC 57.432 29.630 0.00 0.00 0.00 3.67
2913 3952 0.107831 TCCTCGGTTCAGGTGTTTGG 59.892 55.000 0.00 0.00 34.76 3.28
3005 4069 5.714806 AGTGGAAACTGAAGAAGAACCAAAA 59.285 36.000 0.00 0.00 31.75 2.44
3063 4130 9.732130 AAGATAGATTTTCTTTGTTCACTAGCT 57.268 29.630 0.00 0.00 29.12 3.32
3129 4196 0.787787 TGTCTTATCACGCAACGCAC 59.212 50.000 0.00 0.00 0.00 5.34
3132 4199 3.857665 AGTACATGTCTTATCACGCAACG 59.142 43.478 0.00 0.00 0.00 4.10
3150 4224 4.886247 TTTGTACAAGGCACACAAGTAC 57.114 40.909 8.56 0.00 33.96 2.73
3193 4267 0.112995 TTCTGGGCCTGCAAAGTCAT 59.887 50.000 4.53 0.00 0.00 3.06
3332 4406 9.747898 AATACCCATCAAAAGATAACAGTAACA 57.252 29.630 0.00 0.00 0.00 2.41
3344 4418 6.314400 CCAAGATGCAAAATACCCATCAAAAG 59.686 38.462 0.00 0.00 38.21 2.27
3417 4491 2.704572 GACAGCACAAGTAATGGCTCT 58.295 47.619 0.00 0.00 34.56 4.09
3435 4520 1.195448 CAGGACAAGTGTGCAATCGAC 59.805 52.381 5.72 0.00 38.96 4.20
3441 4526 4.557554 CACCAGGACAAGTGTGCA 57.442 55.556 5.72 0.00 38.96 4.57
3503 4588 9.804977 GGACTGAGGGAGTAGTAATTTAGTATA 57.195 37.037 0.00 0.00 33.83 1.47
3518 4603 4.901849 TCTTATATTGTGGGACTGAGGGAG 59.098 45.833 0.00 0.00 0.00 4.30
3519 4604 4.654262 GTCTTATATTGTGGGACTGAGGGA 59.346 45.833 0.00 0.00 0.00 4.20
3520 4605 4.501571 CGTCTTATATTGTGGGACTGAGGG 60.502 50.000 0.00 0.00 0.00 4.30
3521 4606 4.099573 ACGTCTTATATTGTGGGACTGAGG 59.900 45.833 0.00 0.00 0.00 3.86
3522 4607 5.263968 ACGTCTTATATTGTGGGACTGAG 57.736 43.478 0.00 0.00 0.00 3.35
3523 4608 5.670792 AACGTCTTATATTGTGGGACTGA 57.329 39.130 0.00 0.00 0.00 3.41
3524 4609 6.737254 AAAACGTCTTATATTGTGGGACTG 57.263 37.500 0.00 0.00 0.00 3.51
3525 4610 6.349033 GCAAAAACGTCTTATATTGTGGGACT 60.349 38.462 0.00 0.00 0.00 3.85
3526 4611 5.798434 GCAAAAACGTCTTATATTGTGGGAC 59.202 40.000 0.00 0.00 0.00 4.46
3527 4612 5.473846 TGCAAAAACGTCTTATATTGTGGGA 59.526 36.000 0.00 0.00 0.00 4.37
3528 4613 5.704888 TGCAAAAACGTCTTATATTGTGGG 58.295 37.500 0.00 0.00 0.00 4.61
3529 4614 6.183359 GCTTGCAAAAACGTCTTATATTGTGG 60.183 38.462 0.00 0.00 0.00 4.17
3530 4615 6.582295 AGCTTGCAAAAACGTCTTATATTGTG 59.418 34.615 0.00 0.00 0.00 3.33
3531 4616 6.677913 AGCTTGCAAAAACGTCTTATATTGT 58.322 32.000 0.00 0.00 0.00 2.71
3532 4617 8.575454 GTTAGCTTGCAAAAACGTCTTATATTG 58.425 33.333 0.00 0.00 0.00 1.90
3533 4618 8.293867 TGTTAGCTTGCAAAAACGTCTTATATT 58.706 29.630 0.00 0.00 0.00 1.28
3534 4619 7.812648 TGTTAGCTTGCAAAAACGTCTTATAT 58.187 30.769 0.00 0.00 0.00 0.86
3535 4620 7.192148 TGTTAGCTTGCAAAAACGTCTTATA 57.808 32.000 0.00 0.00 0.00 0.98
3536 4621 6.067263 TGTTAGCTTGCAAAAACGTCTTAT 57.933 33.333 0.00 0.00 0.00 1.73
3537 4622 5.487153 TGTTAGCTTGCAAAAACGTCTTA 57.513 34.783 0.00 0.00 0.00 2.10
3538 4623 4.364415 TGTTAGCTTGCAAAAACGTCTT 57.636 36.364 0.00 0.00 0.00 3.01
3539 4624 4.036262 TCATGTTAGCTTGCAAAAACGTCT 59.964 37.500 0.00 0.00 0.00 4.18
3540 4625 4.146443 GTCATGTTAGCTTGCAAAAACGTC 59.854 41.667 0.00 0.00 0.00 4.34
3541 4626 4.041723 GTCATGTTAGCTTGCAAAAACGT 58.958 39.130 0.00 4.38 0.00 3.99
3542 4627 4.290155 AGTCATGTTAGCTTGCAAAAACG 58.710 39.130 0.00 0.00 0.00 3.60
3543 4628 6.695278 TGTAAGTCATGTTAGCTTGCAAAAAC 59.305 34.615 0.00 6.33 33.29 2.43
3544 4629 6.800543 TGTAAGTCATGTTAGCTTGCAAAAA 58.199 32.000 0.00 0.00 33.29 1.94
3545 4630 6.384258 TGTAAGTCATGTTAGCTTGCAAAA 57.616 33.333 0.00 0.00 33.29 2.44
3546 4631 6.384258 TTGTAAGTCATGTTAGCTTGCAAA 57.616 33.333 15.97 0.00 40.15 3.68
3547 4632 6.384258 TTTGTAAGTCATGTTAGCTTGCAA 57.616 33.333 15.10 15.10 40.89 4.08
3548 4633 6.384258 TTTTGTAAGTCATGTTAGCTTGCA 57.616 33.333 0.00 0.00 34.12 4.08
3549 4634 6.129457 CGTTTTTGTAAGTCATGTTAGCTTGC 60.129 38.462 0.00 0.00 0.00 4.01
3550 4635 6.910433 ACGTTTTTGTAAGTCATGTTAGCTTG 59.090 34.615 0.00 0.00 0.00 4.01
3551 4636 7.012044 AGACGTTTTTGTAAGTCATGTTAGCTT 59.988 33.333 0.00 0.00 36.18 3.74
3552 4637 6.482308 AGACGTTTTTGTAAGTCATGTTAGCT 59.518 34.615 0.00 0.00 36.18 3.32
3553 4638 6.656003 AGACGTTTTTGTAAGTCATGTTAGC 58.344 36.000 0.00 0.00 36.18 3.09
3561 4646 9.882856 CGAGAATATAAGACGTTTTTGTAAGTC 57.117 33.333 0.00 0.00 0.00 3.01
3562 4647 8.866956 CCGAGAATATAAGACGTTTTTGTAAGT 58.133 33.333 0.00 0.00 0.00 2.24
3563 4648 9.079833 TCCGAGAATATAAGACGTTTTTGTAAG 57.920 33.333 0.00 0.00 0.00 2.34
3564 4649 8.863049 GTCCGAGAATATAAGACGTTTTTGTAA 58.137 33.333 0.00 0.00 0.00 2.41
3565 4650 7.218773 CGTCCGAGAATATAAGACGTTTTTGTA 59.781 37.037 0.00 0.00 43.89 2.41
3566 4651 6.034256 CGTCCGAGAATATAAGACGTTTTTGT 59.966 38.462 0.00 0.00 43.89 2.83
3567 4652 6.400422 CGTCCGAGAATATAAGACGTTTTTG 58.600 40.000 0.00 0.00 43.89 2.44
3568 4653 5.517770 CCGTCCGAGAATATAAGACGTTTTT 59.482 40.000 9.63 0.00 46.62 1.94
3569 4654 5.039333 CCGTCCGAGAATATAAGACGTTTT 58.961 41.667 9.63 0.00 46.62 2.43
3570 4655 4.336433 TCCGTCCGAGAATATAAGACGTTT 59.664 41.667 9.63 0.00 46.62 3.60
3571 4656 3.879295 TCCGTCCGAGAATATAAGACGTT 59.121 43.478 9.63 0.00 46.62 3.99
3572 4657 3.470709 TCCGTCCGAGAATATAAGACGT 58.529 45.455 9.63 0.00 46.62 4.34
3574 4659 4.070716 TCCTCCGTCCGAGAATATAAGAC 58.929 47.826 0.00 0.00 41.63 3.01
3575 4660 4.362470 TCCTCCGTCCGAGAATATAAGA 57.638 45.455 0.00 0.00 41.63 2.10
3576 4661 4.519730 ACTTCCTCCGTCCGAGAATATAAG 59.480 45.833 0.00 0.00 41.63 1.73
3577 4662 4.467769 ACTTCCTCCGTCCGAGAATATAA 58.532 43.478 0.00 0.00 41.63 0.98
3578 4663 4.096190 ACTTCCTCCGTCCGAGAATATA 57.904 45.455 0.00 0.00 41.63 0.86
3579 4664 2.946785 ACTTCCTCCGTCCGAGAATAT 58.053 47.619 0.00 0.00 41.63 1.28
3580 4665 2.431954 ACTTCCTCCGTCCGAGAATA 57.568 50.000 0.00 0.00 41.63 1.75
3581 4666 2.299521 CTACTTCCTCCGTCCGAGAAT 58.700 52.381 0.00 0.00 41.63 2.40
3582 4667 1.004044 ACTACTTCCTCCGTCCGAGAA 59.996 52.381 0.00 0.00 41.63 2.87
3583 4668 0.617413 ACTACTTCCTCCGTCCGAGA 59.383 55.000 0.00 0.00 41.63 4.04
3584 4669 2.322355 TACTACTTCCTCCGTCCGAG 57.678 55.000 0.00 0.00 38.46 4.63
3585 4670 2.804572 CGATACTACTTCCTCCGTCCGA 60.805 54.545 0.00 0.00 0.00 4.55
3586 4671 1.530293 CGATACTACTTCCTCCGTCCG 59.470 57.143 0.00 0.00 0.00 4.79
3587 4672 2.843701 TCGATACTACTTCCTCCGTCC 58.156 52.381 0.00 0.00 0.00 4.79
3588 4673 4.317488 AGATCGATACTACTTCCTCCGTC 58.683 47.826 0.00 0.00 0.00 4.79
3589 4674 4.354893 AGATCGATACTACTTCCTCCGT 57.645 45.455 0.00 0.00 0.00 4.69
3590 4675 4.143073 CGAAGATCGATACTACTTCCTCCG 60.143 50.000 15.23 4.74 43.74 4.63
3591 4676 4.154556 CCGAAGATCGATACTACTTCCTCC 59.845 50.000 15.23 0.00 43.74 4.30
3592 4677 4.154556 CCCGAAGATCGATACTACTTCCTC 59.845 50.000 15.23 0.00 43.74 3.71
3593 4678 4.073549 CCCGAAGATCGATACTACTTCCT 58.926 47.826 15.23 0.00 43.74 3.36
3594 4679 3.819902 ACCCGAAGATCGATACTACTTCC 59.180 47.826 15.23 3.09 43.74 3.46
3595 4680 5.931146 TCTACCCGAAGATCGATACTACTTC 59.069 44.000 12.36 12.36 43.74 3.01
3596 4681 5.862845 TCTACCCGAAGATCGATACTACTT 58.137 41.667 0.00 0.00 43.74 2.24
3597 4682 5.480642 TCTACCCGAAGATCGATACTACT 57.519 43.478 0.00 0.00 43.74 2.57
3598 4683 7.264221 TCTATCTACCCGAAGATCGATACTAC 58.736 42.308 0.00 0.00 43.74 2.73
3599 4684 7.415592 TCTATCTACCCGAAGATCGATACTA 57.584 40.000 0.00 0.00 43.74 1.82
3600 4685 6.297080 TCTATCTACCCGAAGATCGATACT 57.703 41.667 0.00 0.00 43.74 2.12
3601 4686 8.714179 CATATCTATCTACCCGAAGATCGATAC 58.286 40.741 0.00 0.00 43.74 2.24
3602 4687 7.388224 GCATATCTATCTACCCGAAGATCGATA 59.612 40.741 0.00 13.70 43.74 2.92
3603 4688 6.205853 GCATATCTATCTACCCGAAGATCGAT 59.794 42.308 0.00 0.00 43.74 3.59
3629 4714 0.250234 TCTGGACTTGCCTTCCATCG 59.750 55.000 0.00 0.00 42.43 3.84
3677 4762 7.748847 ACTGCATACGTGGTTAAGAAAAATAG 58.251 34.615 0.00 0.00 0.00 1.73
3679 4764 6.569179 ACTGCATACGTGGTTAAGAAAAAT 57.431 33.333 0.00 0.00 0.00 1.82
3680 4765 6.890558 GTACTGCATACGTGGTTAAGAAAAA 58.109 36.000 0.00 0.00 0.00 1.94
3681 4766 6.470557 GTACTGCATACGTGGTTAAGAAAA 57.529 37.500 0.00 0.00 0.00 2.29
3724 4809 1.927210 CGGCAAGCAGCTATGTACG 59.073 57.895 0.00 2.92 44.79 3.67
3753 4838 0.240145 GTCACTTTACTTTGCCCGGC 59.760 55.000 1.04 1.04 0.00 6.13
3771 4856 0.886490 CAGTTCTCCGGCTTGCTTGT 60.886 55.000 0.00 0.00 0.00 3.16
3804 4905 2.805099 GTCAGCTCTTCCACTTGAGTTG 59.195 50.000 0.00 0.00 41.01 3.16
3806 4907 2.042464 TGTCAGCTCTTCCACTTGAGT 58.958 47.619 0.00 0.00 33.22 3.41
3807 4908 2.827800 TGTCAGCTCTTCCACTTGAG 57.172 50.000 0.00 0.00 0.00 3.02
3808 4909 3.777106 ATTGTCAGCTCTTCCACTTGA 57.223 42.857 0.00 0.00 0.00 3.02
3809 4910 3.817084 TCAATTGTCAGCTCTTCCACTTG 59.183 43.478 5.13 0.00 0.00 3.16
3810 4911 4.070716 CTCAATTGTCAGCTCTTCCACTT 58.929 43.478 5.13 0.00 0.00 3.16
3811 4912 3.672808 CTCAATTGTCAGCTCTTCCACT 58.327 45.455 5.13 0.00 0.00 4.00
3812 4913 2.161211 GCTCAATTGTCAGCTCTTCCAC 59.839 50.000 10.98 0.00 32.48 4.02
3813 4914 2.430465 GCTCAATTGTCAGCTCTTCCA 58.570 47.619 10.98 0.00 32.48 3.53
3814 4915 1.742268 GGCTCAATTGTCAGCTCTTCC 59.258 52.381 16.21 0.00 35.82 3.46
3815 4916 2.419324 CTGGCTCAATTGTCAGCTCTTC 59.581 50.000 16.21 3.54 35.82 2.87
3816 4917 2.434428 CTGGCTCAATTGTCAGCTCTT 58.566 47.619 16.21 0.00 35.82 2.85
3817 4918 1.949547 GCTGGCTCAATTGTCAGCTCT 60.950 52.381 27.19 0.00 46.29 4.09
3818 4919 0.450983 GCTGGCTCAATTGTCAGCTC 59.549 55.000 27.19 16.13 46.29 4.09
3822 4923 0.537828 TGCTGCTGGCTCAATTGTCA 60.538 50.000 5.13 2.45 42.39 3.58
3890 4991 3.990092 TGATGACCAGTATAATCGGTGC 58.010 45.455 0.00 0.00 31.63 5.01
3926 5027 2.561956 CCGATGAGCCGGTATCCGT 61.562 63.158 1.90 0.00 46.80 4.69
3935 5036 2.503382 GGGTCTCCTCCGATGAGCC 61.503 68.421 0.00 0.00 40.44 4.70
3942 5043 4.124943 TCCTCCGGGTCTCCTCCG 62.125 72.222 0.00 0.00 46.43 4.63
3997 5451 1.555477 TTGTCGGGGCGGATTACCTT 61.555 55.000 0.00 0.00 0.00 3.50
4000 5454 2.178235 GCTTGTCGGGGCGGATTAC 61.178 63.158 0.00 0.00 0.00 1.89
4007 5461 3.273080 CTTGCTTGCTTGTCGGGGC 62.273 63.158 0.00 0.00 0.00 5.80
4009 5463 2.074230 TTGCTTGCTTGCTTGTCGGG 62.074 55.000 3.47 0.00 0.00 5.14
4026 5480 1.801913 CGTCGGCGACTTCTCCTTG 60.802 63.158 33.90 14.79 41.33 3.61
4028 5482 2.359602 TCGTCGGCGACTTCTCCT 60.360 61.111 33.90 0.00 42.81 3.69
4029 5483 1.364626 TACTCGTCGGCGACTTCTCC 61.365 60.000 33.90 10.56 42.81 3.71
4030 5484 0.445436 TTACTCGTCGGCGACTTCTC 59.555 55.000 33.90 11.31 42.81 2.87
4031 5485 1.093159 ATTACTCGTCGGCGACTTCT 58.907 50.000 33.90 19.20 42.81 2.85
4032 5486 1.905449 AATTACTCGTCGGCGACTTC 58.095 50.000 33.90 12.08 42.81 3.01
4033 5487 1.990563 CAAATTACTCGTCGGCGACTT 59.009 47.619 33.90 21.41 42.81 3.01
4037 5491 1.060122 GTTCCAAATTACTCGTCGGCG 59.940 52.381 1.15 1.15 39.92 6.46
4038 5492 1.060122 CGTTCCAAATTACTCGTCGGC 59.940 52.381 0.00 0.00 0.00 5.54
4039 5493 1.657094 CCGTTCCAAATTACTCGTCGG 59.343 52.381 0.00 0.00 0.00 4.79
4040 5494 2.597305 CTCCGTTCCAAATTACTCGTCG 59.403 50.000 0.00 0.00 0.00 5.12
4041 5495 2.928116 CCTCCGTTCCAAATTACTCGTC 59.072 50.000 0.00 0.00 0.00 4.20
4042 5496 2.354403 CCCTCCGTTCCAAATTACTCGT 60.354 50.000 0.00 0.00 0.00 4.18
4043 5497 2.093869 TCCCTCCGTTCCAAATTACTCG 60.094 50.000 0.00 0.00 0.00 4.18
4044 5498 3.055312 ACTCCCTCCGTTCCAAATTACTC 60.055 47.826 0.00 0.00 0.00 2.59
4045 5499 2.910977 ACTCCCTCCGTTCCAAATTACT 59.089 45.455 0.00 0.00 0.00 2.24
4046 5500 3.345508 ACTCCCTCCGTTCCAAATTAC 57.654 47.619 0.00 0.00 0.00 1.89
4047 5501 4.098894 AGTACTCCCTCCGTTCCAAATTA 58.901 43.478 0.00 0.00 0.00 1.40
4048 5502 2.910977 AGTACTCCCTCCGTTCCAAATT 59.089 45.455 0.00 0.00 0.00 1.82
4049 5503 2.547990 AGTACTCCCTCCGTTCCAAAT 58.452 47.619 0.00 0.00 0.00 2.32
4050 5504 2.019807 AGTACTCCCTCCGTTCCAAA 57.980 50.000 0.00 0.00 0.00 3.28
4051 5505 2.042162 ACTAGTACTCCCTCCGTTCCAA 59.958 50.000 0.00 0.00 0.00 3.53
4052 5506 1.637553 ACTAGTACTCCCTCCGTTCCA 59.362 52.381 0.00 0.00 0.00 3.53
4053 5507 2.433662 ACTAGTACTCCCTCCGTTCC 57.566 55.000 0.00 0.00 0.00 3.62
4054 5508 4.337836 CCTTTACTAGTACTCCCTCCGTTC 59.662 50.000 0.91 0.00 0.00 3.95
4055 5509 4.264128 ACCTTTACTAGTACTCCCTCCGTT 60.264 45.833 0.91 0.00 0.00 4.44
4056 5510 3.268072 ACCTTTACTAGTACTCCCTCCGT 59.732 47.826 0.91 0.00 0.00 4.69
4057 5511 3.631227 CACCTTTACTAGTACTCCCTCCG 59.369 52.174 0.91 0.00 0.00 4.63
4058 5512 3.959449 CCACCTTTACTAGTACTCCCTCC 59.041 52.174 0.91 0.00 0.00 4.30
4059 5513 4.608269 ACCACCTTTACTAGTACTCCCTC 58.392 47.826 0.91 0.00 0.00 4.30
4060 5514 4.689014 ACCACCTTTACTAGTACTCCCT 57.311 45.455 0.91 0.00 0.00 4.20
4061 5515 4.529769 ACAACCACCTTTACTAGTACTCCC 59.470 45.833 0.91 0.00 0.00 4.30
4062 5516 5.476614 CACAACCACCTTTACTAGTACTCC 58.523 45.833 0.91 0.00 0.00 3.85
4063 5517 5.476614 CCACAACCACCTTTACTAGTACTC 58.523 45.833 0.91 0.00 0.00 2.59
4064 5518 4.262765 GCCACAACCACCTTTACTAGTACT 60.263 45.833 0.91 0.00 0.00 2.73
4065 5519 3.999001 GCCACAACCACCTTTACTAGTAC 59.001 47.826 0.91 0.00 0.00 2.73
4066 5520 3.008266 GGCCACAACCACCTTTACTAGTA 59.992 47.826 0.00 0.00 0.00 1.82
4067 5521 2.224695 GGCCACAACCACCTTTACTAGT 60.225 50.000 0.00 0.00 0.00 2.57
4068 5522 2.039879 AGGCCACAACCACCTTTACTAG 59.960 50.000 5.01 0.00 0.00 2.57
4069 5523 2.059490 AGGCCACAACCACCTTTACTA 58.941 47.619 5.01 0.00 0.00 1.82
4070 5524 0.850784 AGGCCACAACCACCTTTACT 59.149 50.000 5.01 0.00 0.00 2.24
4071 5525 0.958822 CAGGCCACAACCACCTTTAC 59.041 55.000 5.01 0.00 0.00 2.01
4072 5526 0.178975 CCAGGCCACAACCACCTTTA 60.179 55.000 5.01 0.00 0.00 1.85
4073 5527 1.457455 CCAGGCCACAACCACCTTT 60.457 57.895 5.01 0.00 0.00 3.11
4102 5556 0.313987 GGGCGGTTCTCCAAAAACTG 59.686 55.000 0.00 0.00 36.32 3.16
4103 5557 0.106419 TGGGCGGTTCTCCAAAAACT 60.106 50.000 0.00 0.00 0.00 2.66
4104 5558 0.747852 TTGGGCGGTTCTCCAAAAAC 59.252 50.000 0.00 0.00 39.77 2.43
4105 5559 0.747852 GTTGGGCGGTTCTCCAAAAA 59.252 50.000 0.00 0.00 43.68 1.94
4110 5564 1.002624 TCATGTTGGGCGGTTCTCC 60.003 57.895 0.00 0.00 0.00 3.71
4111 5565 0.321653 AGTCATGTTGGGCGGTTCTC 60.322 55.000 0.00 0.00 0.00 2.87
4182 5646 8.950210 TGATTTTCTGACTGAACCTATTCAATC 58.050 33.333 0.00 1.56 44.28 2.67
4194 5658 5.072055 TGCAATCCTTGATTTTCTGACTGA 58.928 37.500 0.00 0.00 28.87 3.41
4195 5659 5.381174 TGCAATCCTTGATTTTCTGACTG 57.619 39.130 0.00 0.00 28.87 3.51
4196 5660 5.713389 TGATGCAATCCTTGATTTTCTGACT 59.287 36.000 0.00 0.00 44.73 3.41
4197 5661 5.957798 TGATGCAATCCTTGATTTTCTGAC 58.042 37.500 0.00 0.00 44.73 3.51
4209 5673 1.941377 TGCCCTTTTGATGCAATCCT 58.059 45.000 0.00 0.00 44.73 3.24


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

AutoCloner maintained by Alex Coulton.