Multiple sequence alignment - TraesCS4B01G136200

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 TraesCS4B01G136200 chr4B 100.000 2456 0 0 1 2456 179750148 179752603 0.000000e+00 4536.0
1 TraesCS4B01G136200 chr4B 82.940 721 80 21 864 1562 179842716 179842017 5.810000e-171 610.0
2 TraesCS4B01G136200 chr4B 89.655 203 19 2 1 202 543432951 543433152 8.710000e-65 257.0
3 TraesCS4B01G136200 chr4B 90.909 187 17 0 14 200 385385772 385385586 4.050000e-63 252.0
4 TraesCS4B01G136200 chr4A 93.220 1475 72 15 199 1657 456335514 456336976 0.000000e+00 2145.0
5 TraesCS4B01G136200 chr4A 93.778 1318 61 12 199 1507 457567504 457568809 0.000000e+00 1960.0
6 TraesCS4B01G136200 chr4A 84.604 695 76 20 886 1569 456293850 456294524 0.000000e+00 662.0
7 TraesCS4B01G136200 chr4A 92.157 306 23 1 2152 2456 456342452 456342757 4.850000e-117 431.0
8 TraesCS4B01G136200 chr4A 91.503 306 25 1 2152 2456 457575766 457576071 1.050000e-113 420.0
9 TraesCS4B01G136200 chr4A 90.094 212 16 5 1943 2151 457575496 457575705 1.120000e-68 270.0
10 TraesCS4B01G136200 chr4A 88.372 215 16 7 1943 2151 456342180 456342391 1.460000e-62 250.0
11 TraesCS4B01G136200 chr4A 92.073 164 8 2 1499 1657 457570131 457570294 2.460000e-55 226.0
12 TraesCS4B01G136200 chr4A 95.789 95 4 0 1781 1875 456336964 456337058 1.180000e-33 154.0
13 TraesCS4B01G136200 chr4A 94.737 95 5 0 1781 1875 457570282 457570376 5.470000e-32 148.0
14 TraesCS4B01G136200 chr4D 95.173 1326 45 10 296 1613 117663748 117662434 0.000000e+00 2076.0
15 TraesCS4B01G136200 chr4D 84.711 726 72 22 864 1569 117706510 117705804 0.000000e+00 689.0
16 TraesCS4B01G136200 chr4D 90.649 385 22 10 1781 2151 117662093 117661709 1.310000e-137 499.0
17 TraesCS4B01G136200 chr4D 93.464 306 19 1 2152 2456 117661648 117661343 1.040000e-123 453.0
18 TraesCS4B01G136200 chr4D 90.674 193 18 0 1 193 111583930 111584122 8.710000e-65 257.0
19 TraesCS4B01G136200 chr7A 83.232 656 73 16 864 1504 701462731 701462098 3.540000e-158 568.0
20 TraesCS4B01G136200 chr7A 93.532 201 12 1 1 200 36634086 36633886 5.130000e-77 298.0
21 TraesCS4B01G136200 chr7A 89.604 202 21 0 1 202 57736296 57736095 8.710000e-65 257.0
22 TraesCS4B01G136200 chr7A 90.306 196 19 0 5 200 80732971 80733166 8.710000e-65 257.0
23 TraesCS4B01G136200 chr7D 82.317 656 92 12 864 1504 611445273 611444627 4.620000e-152 547.0
24 TraesCS4B01G136200 chr7D 81.055 739 92 16 847 1569 611459241 611458535 1.660000e-151 545.0
25 TraesCS4B01G136200 chr7B 81.711 678 95 14 864 1525 700630511 700629847 2.780000e-149 538.0
26 TraesCS4B01G136200 chr6A 92.718 206 13 2 1 205 25804437 25804233 1.850000e-76 296.0
27 TraesCS4B01G136200 chr5B 92.079 202 16 0 1 202 577847977 577848178 4.000000e-73 285.0
28 TraesCS4B01G136200 chr5B 96.875 32 1 0 2156 2187 362957404 362957373 1.000000e-03 54.7
29 TraesCS4B01G136200 chr1B 89.340 197 21 0 6 202 383634381 383634185 5.240000e-62 248.0
30 TraesCS4B01G136200 chr1B 87.273 110 11 1 1668 1777 264844011 264843905 3.320000e-24 122.0
31 TraesCS4B01G136200 chr2D 85.876 177 19 4 206 378 72605449 72605623 1.500000e-42 183.0
32 TraesCS4B01G136200 chrUn 86.066 122 12 3 1656 1777 2710270 2710154 2.560000e-25 126.0
33 TraesCS4B01G136200 chr6B 85.714 77 8 3 1704 1780 562094245 562094172 7.280000e-11 78.7
34 TraesCS4B01G136200 chr5A 100.000 32 0 0 2156 2187 408932011 408931980 2.640000e-05 60.2
35 TraesCS4B01G136200 chr5D 96.875 32 1 0 2156 2187 314903341 314903310 1.000000e-03 54.7


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 TraesCS4B01G136200 chr4B 179750148 179752603 2455 False 4536.000000 4536 100.000000 1 2456 1 chr4B.!!$F1 2455
1 TraesCS4B01G136200 chr4B 179842017 179842716 699 True 610.000000 610 82.940000 864 1562 1 chr4B.!!$R1 698
2 TraesCS4B01G136200 chr4A 456335514 456337058 1544 False 1149.500000 2145 94.504500 199 1875 2 chr4A.!!$F2 1676
3 TraesCS4B01G136200 chr4A 457567504 457570376 2872 False 778.000000 1960 93.529333 199 1875 3 chr4A.!!$F4 1676
4 TraesCS4B01G136200 chr4A 456293850 456294524 674 False 662.000000 662 84.604000 886 1569 1 chr4A.!!$F1 683
5 TraesCS4B01G136200 chr4A 457575496 457576071 575 False 345.000000 420 90.798500 1943 2456 2 chr4A.!!$F5 513
6 TraesCS4B01G136200 chr4A 456342180 456342757 577 False 340.500000 431 90.264500 1943 2456 2 chr4A.!!$F3 513
7 TraesCS4B01G136200 chr4D 117661343 117663748 2405 True 1009.333333 2076 93.095333 296 2456 3 chr4D.!!$R2 2160
8 TraesCS4B01G136200 chr4D 117705804 117706510 706 True 689.000000 689 84.711000 864 1569 1 chr4D.!!$R1 705
9 TraesCS4B01G136200 chr7A 701462098 701462731 633 True 568.000000 568 83.232000 864 1504 1 chr7A.!!$R3 640
10 TraesCS4B01G136200 chr7D 611444627 611445273 646 True 547.000000 547 82.317000 864 1504 1 chr7D.!!$R1 640
11 TraesCS4B01G136200 chr7D 611458535 611459241 706 True 545.000000 545 81.055000 847 1569 1 chr7D.!!$R2 722
12 TraesCS4B01G136200 chr7B 700629847 700630511 664 True 538.000000 538 81.711000 864 1525 1 chr7B.!!$R1 661

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
383 388 0.243636 AGGTGTAGCATTTTTGCGCC 59.756 50.0 4.18 0.0 40.27 6.53 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1766 3520 0.040058 AATGATGTGGGCTGCCTGAA 59.96 50.0 19.68 4.37 0.0 3.02 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
62 63 9.903682 ATGACTTTATTTATTAGCATGCATGAC 57.096 29.630 30.64 20.09 0.00 3.06
63 64 8.901793 TGACTTTATTTATTAGCATGCATGACA 58.098 29.630 30.64 13.52 0.00 3.58
64 65 9.173939 GACTTTATTTATTAGCATGCATGACAC 57.826 33.333 30.64 12.65 0.00 3.67
65 66 8.685427 ACTTTATTTATTAGCATGCATGACACA 58.315 29.630 30.64 10.58 0.00 3.72
66 67 9.687210 CTTTATTTATTAGCATGCATGACACAT 57.313 29.630 30.64 16.60 0.00 3.21
69 70 7.806409 TTTATTAGCATGCATGACACATAGT 57.194 32.000 30.64 12.21 0.00 2.12
70 71 8.900983 TTTATTAGCATGCATGACACATAGTA 57.099 30.769 30.64 11.35 0.00 1.82
71 72 8.900983 TTATTAGCATGCATGACACATAGTAA 57.099 30.769 30.64 15.65 0.00 2.24
72 73 7.991084 ATTAGCATGCATGACACATAGTAAT 57.009 32.000 30.64 14.98 0.00 1.89
74 75 9.676861 ATTAGCATGCATGACACATAGTAATAT 57.323 29.630 30.64 4.07 0.00 1.28
77 78 8.939929 AGCATGCATGACACATAGTAATATAAC 58.060 33.333 30.64 5.56 0.00 1.89
78 79 8.720562 GCATGCATGACACATAGTAATATAACA 58.279 33.333 30.64 0.00 0.00 2.41
125 126 9.639563 TGATATGATAGTCAACTCTCTCTTTCT 57.360 33.333 0.00 0.00 0.00 2.52
128 129 7.767250 TGATAGTCAACTCTCTCTTTCTTCA 57.233 36.000 0.00 0.00 0.00 3.02
129 130 8.359875 TGATAGTCAACTCTCTCTTTCTTCAT 57.640 34.615 0.00 0.00 0.00 2.57
130 131 8.811017 TGATAGTCAACTCTCTCTTTCTTCATT 58.189 33.333 0.00 0.00 0.00 2.57
131 132 9.651913 GATAGTCAACTCTCTCTTTCTTCATTT 57.348 33.333 0.00 0.00 0.00 2.32
160 161 9.803507 TTCTATATCATCTCATCAAATTTGCCT 57.196 29.630 13.54 0.38 0.00 4.75
164 165 7.893124 ATCATCTCATCAAATTTGCCTAGTT 57.107 32.000 13.54 3.00 0.00 2.24
165 166 7.092137 TCATCTCATCAAATTTGCCTAGTTG 57.908 36.000 13.54 13.25 0.00 3.16
166 167 6.885918 TCATCTCATCAAATTTGCCTAGTTGA 59.114 34.615 13.54 14.92 34.68 3.18
167 168 6.500684 TCTCATCAAATTTGCCTAGTTGAC 57.499 37.500 13.54 0.00 33.09 3.18
168 169 6.003326 TCTCATCAAATTTGCCTAGTTGACA 58.997 36.000 13.54 0.00 33.09 3.58
169 170 6.660521 TCTCATCAAATTTGCCTAGTTGACAT 59.339 34.615 13.54 0.00 33.09 3.06
170 171 6.623486 TCATCAAATTTGCCTAGTTGACATG 58.377 36.000 13.54 7.85 33.09 3.21
171 172 4.808558 TCAAATTTGCCTAGTTGACATGC 58.191 39.130 13.54 0.00 0.00 4.06
172 173 4.280425 TCAAATTTGCCTAGTTGACATGCA 59.720 37.500 13.54 0.00 0.00 3.96
173 174 5.047164 TCAAATTTGCCTAGTTGACATGCAT 60.047 36.000 13.54 0.00 0.00 3.96
174 175 3.853831 TTTGCCTAGTTGACATGCATG 57.146 42.857 25.09 25.09 0.00 4.06
175 176 2.785540 TGCCTAGTTGACATGCATGA 57.214 45.000 32.75 9.00 0.00 3.07
176 177 3.286329 TGCCTAGTTGACATGCATGAT 57.714 42.857 32.75 16.80 0.00 2.45
177 178 4.420522 TGCCTAGTTGACATGCATGATA 57.579 40.909 32.75 17.43 0.00 2.15
178 179 4.129380 TGCCTAGTTGACATGCATGATAC 58.871 43.478 32.75 23.37 0.00 2.24
179 180 4.141642 TGCCTAGTTGACATGCATGATACT 60.142 41.667 32.75 27.82 0.00 2.12
180 181 5.070313 TGCCTAGTTGACATGCATGATACTA 59.930 40.000 32.75 27.51 0.00 1.82
181 182 5.406780 GCCTAGTTGACATGCATGATACTAC 59.593 44.000 32.75 24.38 0.00 2.73
182 183 5.928839 CCTAGTTGACATGCATGATACTACC 59.071 44.000 32.75 12.77 0.00 3.18
183 184 5.620738 AGTTGACATGCATGATACTACCT 57.379 39.130 32.75 14.63 0.00 3.08
184 185 6.731292 AGTTGACATGCATGATACTACCTA 57.269 37.500 32.75 6.88 0.00 3.08
185 186 7.308450 AGTTGACATGCATGATACTACCTAT 57.692 36.000 32.75 6.24 0.00 2.57
186 187 7.157347 AGTTGACATGCATGATACTACCTATG 58.843 38.462 32.75 3.42 0.00 2.23
187 188 6.916360 TGACATGCATGATACTACCTATGA 57.084 37.500 32.75 0.00 0.00 2.15
188 189 7.486407 TGACATGCATGATACTACCTATGAT 57.514 36.000 32.75 4.97 0.00 2.45
189 190 8.593945 TGACATGCATGATACTACCTATGATA 57.406 34.615 32.75 2.03 0.00 2.15
190 191 8.470002 TGACATGCATGATACTACCTATGATAC 58.530 37.037 32.75 1.74 0.00 2.24
191 192 8.601047 ACATGCATGATACTACCTATGATACT 57.399 34.615 32.75 0.57 0.00 2.12
192 193 8.690884 ACATGCATGATACTACCTATGATACTC 58.309 37.037 32.75 0.00 0.00 2.59
193 194 8.911965 CATGCATGATACTACCTATGATACTCT 58.088 37.037 22.59 0.00 0.00 3.24
195 196 9.975218 TGCATGATACTACCTATGATACTCTAA 57.025 33.333 0.00 0.00 0.00 2.10
203 204 9.165035 ACTACCTATGATACTCTAATTACGAGC 57.835 37.037 10.19 0.00 31.71 5.03
204 205 7.393841 ACCTATGATACTCTAATTACGAGCC 57.606 40.000 10.19 3.87 31.71 4.70
224 225 5.024785 GCCTAATGCTAGACCAACTTAGT 57.975 43.478 0.00 0.00 36.87 2.24
225 226 6.158023 GCCTAATGCTAGACCAACTTAGTA 57.842 41.667 0.00 0.00 36.87 1.82
226 227 6.579865 GCCTAATGCTAGACCAACTTAGTAA 58.420 40.000 0.00 0.00 36.87 2.24
227 228 7.217906 GCCTAATGCTAGACCAACTTAGTAAT 58.782 38.462 0.00 0.00 36.87 1.89
263 267 5.872635 CGTGATAGTAAACGTGGAGACTTA 58.127 41.667 0.00 0.00 35.13 2.24
269 273 6.356186 AGTAAACGTGGAGACTTAGGATTT 57.644 37.500 0.00 0.00 0.00 2.17
309 314 1.822371 GCCCACACCCGTAAAAATCAT 59.178 47.619 0.00 0.00 0.00 2.45
315 320 1.006639 ACCCGTAAAAATCATGGGCCT 59.993 47.619 4.53 0.00 44.95 5.19
339 344 9.367444 CCTATAGAATTAATTAGGCAGGTTACG 57.633 37.037 0.00 0.00 0.00 3.18
381 386 9.329913 GAATTATATAGGTGTAGCATTTTTGCG 57.670 33.333 0.00 0.00 40.27 4.85
382 387 2.911819 TAGGTGTAGCATTTTTGCGC 57.088 45.000 0.00 0.00 40.27 6.09
383 388 0.243636 AGGTGTAGCATTTTTGCGCC 59.756 50.000 4.18 0.00 40.27 6.53
384 389 1.070471 GGTGTAGCATTTTTGCGCCG 61.070 55.000 4.18 0.00 40.27 6.46
385 390 0.386731 GTGTAGCATTTTTGCGCCGT 60.387 50.000 4.18 0.00 40.27 5.68
386 391 0.386605 TGTAGCATTTTTGCGCCGTG 60.387 50.000 4.18 0.00 40.27 4.94
387 392 1.443533 TAGCATTTTTGCGCCGTGC 60.444 52.632 4.18 8.21 46.70 5.34
407 412 0.973632 ACACCTCACCTGCGTCAATA 59.026 50.000 0.00 0.00 0.00 1.90
412 417 2.353704 CCTCACCTGCGTCAATAGTGAA 60.354 50.000 0.00 0.00 37.04 3.18
481 487 7.256655 CCTCATTACCAATACCACCTCATATCA 60.257 40.741 0.00 0.00 0.00 2.15
497 503 7.230108 ACCTCATATCAATCAATCCACATGTTC 59.770 37.037 0.00 0.00 0.00 3.18
670 679 2.160219 TGTACGCGTGAACTACTACCAG 59.840 50.000 24.59 0.00 0.00 4.00
1065 1112 4.980805 GGCGACGGCAAGGTGTCA 62.981 66.667 17.49 0.00 42.47 3.58
1118 1165 3.974757 GGGCGAGGACGTATCGGG 61.975 72.222 20.32 2.22 40.50 5.14
1354 1443 4.025858 GCAGGCTGGGCTCTCACA 62.026 66.667 17.64 0.00 0.00 3.58
1637 3391 1.891919 TGCAAACTCGGCAGTGTCC 60.892 57.895 0.00 0.00 36.11 4.02
1680 3434 5.956068 TTTTATTTTGGAAAATGCTGCCC 57.044 34.783 7.47 0.00 38.90 5.36
1681 3435 4.906747 TTATTTTGGAAAATGCTGCCCT 57.093 36.364 7.47 0.00 38.90 5.19
1682 3436 3.793819 ATTTTGGAAAATGCTGCCCTT 57.206 38.095 0.00 0.00 37.24 3.95
1683 3437 3.574354 TTTTGGAAAATGCTGCCCTTT 57.426 38.095 0.00 0.00 0.00 3.11
1684 3438 4.696479 TTTTGGAAAATGCTGCCCTTTA 57.304 36.364 0.00 0.00 0.00 1.85
1685 3439 4.906747 TTTGGAAAATGCTGCCCTTTAT 57.093 36.364 0.00 0.00 0.00 1.40
1686 3440 4.906747 TTGGAAAATGCTGCCCTTTATT 57.093 36.364 0.00 0.00 0.00 1.40
1687 3441 6.365970 TTTGGAAAATGCTGCCCTTTATTA 57.634 33.333 0.00 0.00 0.00 0.98
1688 3442 6.365970 TTGGAAAATGCTGCCCTTTATTAA 57.634 33.333 0.00 0.00 0.00 1.40
1689 3443 6.365970 TGGAAAATGCTGCCCTTTATTAAA 57.634 33.333 0.00 0.00 0.00 1.52
1690 3444 6.169800 TGGAAAATGCTGCCCTTTATTAAAC 58.830 36.000 0.00 0.00 0.00 2.01
1691 3445 6.013812 TGGAAAATGCTGCCCTTTATTAAACT 60.014 34.615 0.00 0.00 0.00 2.66
1692 3446 7.179338 TGGAAAATGCTGCCCTTTATTAAACTA 59.821 33.333 0.00 0.00 0.00 2.24
1693 3447 8.038351 GGAAAATGCTGCCCTTTATTAAACTAA 58.962 33.333 0.00 0.00 0.00 2.24
1694 3448 9.087424 GAAAATGCTGCCCTTTATTAAACTAAG 57.913 33.333 0.00 0.00 0.00 2.18
1695 3449 5.576447 TGCTGCCCTTTATTAAACTAAGC 57.424 39.130 0.00 0.00 0.00 3.09
1696 3450 5.013547 TGCTGCCCTTTATTAAACTAAGCA 58.986 37.500 0.00 0.00 34.77 3.91
1697 3451 5.125417 TGCTGCCCTTTATTAAACTAAGCAG 59.875 40.000 14.58 14.58 46.06 4.24
1698 3452 5.576447 TGCCCTTTATTAAACTAAGCAGC 57.424 39.130 0.00 0.00 0.00 5.25
1699 3453 4.401202 TGCCCTTTATTAAACTAAGCAGCC 59.599 41.667 0.00 0.00 0.00 4.85
1700 3454 4.202121 GCCCTTTATTAAACTAAGCAGCCC 60.202 45.833 0.00 0.00 0.00 5.19
1701 3455 4.341235 CCCTTTATTAAACTAAGCAGCCCC 59.659 45.833 0.00 0.00 0.00 5.80
1702 3456 4.036380 CCTTTATTAAACTAAGCAGCCCCG 59.964 45.833 0.00 0.00 0.00 5.73
1703 3457 2.052782 ATTAAACTAAGCAGCCCCGG 57.947 50.000 0.00 0.00 0.00 5.73
1704 3458 0.678684 TTAAACTAAGCAGCCCCGGC 60.679 55.000 0.00 0.00 42.33 6.13
1705 3459 2.546114 TAAACTAAGCAGCCCCGGCC 62.546 60.000 1.02 0.00 43.17 6.13
1715 3469 4.619227 CCCCGGCCGCGATAATGT 62.619 66.667 22.85 0.00 0.00 2.71
1716 3470 3.041940 CCCGGCCGCGATAATGTC 61.042 66.667 22.85 0.00 0.00 3.06
1717 3471 2.279851 CCGGCCGCGATAATGTCA 60.280 61.111 22.85 0.00 0.00 3.58
1718 3472 2.594962 CCGGCCGCGATAATGTCAC 61.595 63.158 22.85 0.00 0.00 3.67
1719 3473 2.927618 CGGCCGCGATAATGTCACG 61.928 63.158 14.67 0.00 32.34 4.35
1720 3474 1.590525 GGCCGCGATAATGTCACGA 60.591 57.895 8.23 0.00 34.39 4.35
1721 3475 1.149361 GGCCGCGATAATGTCACGAA 61.149 55.000 8.23 0.00 34.39 3.85
1722 3476 0.859232 GCCGCGATAATGTCACGAAT 59.141 50.000 8.23 0.00 34.39 3.34
1723 3477 2.055838 GCCGCGATAATGTCACGAATA 58.944 47.619 8.23 0.00 34.39 1.75
1724 3478 2.160013 GCCGCGATAATGTCACGAATAC 60.160 50.000 8.23 0.00 34.39 1.89
1725 3479 3.047093 CCGCGATAATGTCACGAATACA 58.953 45.455 8.23 0.00 34.39 2.29
1726 3480 3.487942 CCGCGATAATGTCACGAATACAA 59.512 43.478 8.23 0.00 34.39 2.41
1727 3481 4.026393 CCGCGATAATGTCACGAATACAAA 60.026 41.667 8.23 0.00 34.39 2.83
1728 3482 5.123706 CGCGATAATGTCACGAATACAAAG 58.876 41.667 0.00 0.00 34.39 2.77
1729 3483 5.276207 CGCGATAATGTCACGAATACAAAGT 60.276 40.000 0.00 0.00 34.39 2.66
1730 3484 6.075257 CGCGATAATGTCACGAATACAAAGTA 60.075 38.462 0.00 0.00 34.39 2.24
1731 3485 7.274367 GCGATAATGTCACGAATACAAAGTAG 58.726 38.462 0.00 0.00 0.00 2.57
1732 3486 7.043590 GCGATAATGTCACGAATACAAAGTAGT 60.044 37.037 0.00 0.00 0.00 2.73
1733 3487 8.259872 CGATAATGTCACGAATACAAAGTAGTG 58.740 37.037 0.00 0.00 0.00 2.74
1734 3488 6.721571 AATGTCACGAATACAAAGTAGTGG 57.278 37.500 0.00 0.00 0.00 4.00
1735 3489 4.562082 TGTCACGAATACAAAGTAGTGGG 58.438 43.478 0.00 0.00 0.00 4.61
1736 3490 3.930848 GTCACGAATACAAAGTAGTGGGG 59.069 47.826 0.00 0.00 0.00 4.96
1737 3491 3.833650 TCACGAATACAAAGTAGTGGGGA 59.166 43.478 0.00 0.00 0.00 4.81
1738 3492 4.283978 TCACGAATACAAAGTAGTGGGGAA 59.716 41.667 0.00 0.00 0.00 3.97
1739 3493 4.998672 CACGAATACAAAGTAGTGGGGAAA 59.001 41.667 0.00 0.00 0.00 3.13
1740 3494 5.646360 CACGAATACAAAGTAGTGGGGAAAT 59.354 40.000 0.00 0.00 0.00 2.17
1741 3495 6.819649 CACGAATACAAAGTAGTGGGGAAATA 59.180 38.462 0.00 0.00 0.00 1.40
1742 3496 7.011109 CACGAATACAAAGTAGTGGGGAAATAG 59.989 40.741 0.00 0.00 0.00 1.73
1743 3497 7.093201 ACGAATACAAAGTAGTGGGGAAATAGA 60.093 37.037 0.00 0.00 0.00 1.98
1744 3498 7.767198 CGAATACAAAGTAGTGGGGAAATAGAA 59.233 37.037 0.00 0.00 0.00 2.10
1745 3499 9.457436 GAATACAAAGTAGTGGGGAAATAGAAA 57.543 33.333 0.00 0.00 0.00 2.52
1746 3500 9.816787 AATACAAAGTAGTGGGGAAATAGAAAA 57.183 29.630 0.00 0.00 0.00 2.29
1747 3501 7.520451 ACAAAGTAGTGGGGAAATAGAAAAC 57.480 36.000 0.00 0.00 0.00 2.43
1748 3502 6.492429 ACAAAGTAGTGGGGAAATAGAAAACC 59.508 38.462 0.00 0.00 0.00 3.27
1749 3503 5.853572 AGTAGTGGGGAAATAGAAAACCA 57.146 39.130 0.00 0.00 0.00 3.67
1750 3504 6.208840 AGTAGTGGGGAAATAGAAAACCAA 57.791 37.500 0.00 0.00 0.00 3.67
1751 3505 6.246163 AGTAGTGGGGAAATAGAAAACCAAG 58.754 40.000 0.00 0.00 0.00 3.61
1752 3506 5.074746 AGTGGGGAAATAGAAAACCAAGT 57.925 39.130 0.00 0.00 0.00 3.16
1753 3507 5.077564 AGTGGGGAAATAGAAAACCAAGTC 58.922 41.667 0.00 0.00 0.00 3.01
1754 3508 5.077564 GTGGGGAAATAGAAAACCAAGTCT 58.922 41.667 0.00 0.00 0.00 3.24
1755 3509 5.538813 GTGGGGAAATAGAAAACCAAGTCTT 59.461 40.000 0.00 0.00 0.00 3.01
1756 3510 6.717997 GTGGGGAAATAGAAAACCAAGTCTTA 59.282 38.462 0.00 0.00 0.00 2.10
1757 3511 6.717997 TGGGGAAATAGAAAACCAAGTCTTAC 59.282 38.462 0.00 0.00 0.00 2.34
1758 3512 6.717997 GGGGAAATAGAAAACCAAGTCTTACA 59.282 38.462 0.00 0.00 0.00 2.41
1759 3513 7.309012 GGGGAAATAGAAAACCAAGTCTTACAC 60.309 40.741 0.00 0.00 0.00 2.90
1760 3514 7.229907 GGGAAATAGAAAACCAAGTCTTACACA 59.770 37.037 0.00 0.00 0.00 3.72
1761 3515 8.626526 GGAAATAGAAAACCAAGTCTTACACAA 58.373 33.333 0.00 0.00 0.00 3.33
1762 3516 9.447040 GAAATAGAAAACCAAGTCTTACACAAC 57.553 33.333 0.00 0.00 0.00 3.32
1763 3517 8.747538 AATAGAAAACCAAGTCTTACACAACT 57.252 30.769 0.00 0.00 0.00 3.16
1764 3518 8.747538 ATAGAAAACCAAGTCTTACACAACTT 57.252 30.769 0.00 0.00 36.16 2.66
1765 3519 9.841295 ATAGAAAACCAAGTCTTACACAACTTA 57.159 29.630 0.00 0.00 34.05 2.24
1766 3520 8.747538 AGAAAACCAAGTCTTACACAACTTAT 57.252 30.769 0.00 0.00 34.05 1.73
1767 3521 9.185680 AGAAAACCAAGTCTTACACAACTTATT 57.814 29.630 0.00 0.00 34.05 1.40
1768 3522 9.447040 GAAAACCAAGTCTTACACAACTTATTC 57.553 33.333 0.00 0.00 34.05 1.75
1769 3523 8.514330 AAACCAAGTCTTACACAACTTATTCA 57.486 30.769 0.00 0.00 34.05 2.57
1770 3524 7.730364 ACCAAGTCTTACACAACTTATTCAG 57.270 36.000 0.00 0.00 34.05 3.02
1771 3525 6.710744 ACCAAGTCTTACACAACTTATTCAGG 59.289 38.462 0.00 0.00 34.05 3.86
1772 3526 6.348540 CCAAGTCTTACACAACTTATTCAGGC 60.349 42.308 0.00 0.00 34.05 4.85
1773 3527 5.865085 AGTCTTACACAACTTATTCAGGCA 58.135 37.500 0.00 0.00 0.00 4.75
1774 3528 5.934625 AGTCTTACACAACTTATTCAGGCAG 59.065 40.000 0.00 0.00 0.00 4.85
1775 3529 4.695455 TCTTACACAACTTATTCAGGCAGC 59.305 41.667 0.00 0.00 0.00 5.25
1776 3530 2.162681 ACACAACTTATTCAGGCAGCC 58.837 47.619 1.84 1.84 0.00 4.85
1777 3531 1.474077 CACAACTTATTCAGGCAGCCC 59.526 52.381 8.22 0.00 0.00 5.19
1778 3532 1.075374 ACAACTTATTCAGGCAGCCCA 59.925 47.619 8.22 0.00 0.00 5.36
1779 3533 1.474077 CAACTTATTCAGGCAGCCCAC 59.526 52.381 8.22 0.00 0.00 4.61
1780 3534 0.698238 ACTTATTCAGGCAGCCCACA 59.302 50.000 8.22 0.00 0.00 4.17
1781 3535 1.285962 ACTTATTCAGGCAGCCCACAT 59.714 47.619 8.22 0.00 0.00 3.21
1782 3536 1.952296 CTTATTCAGGCAGCCCACATC 59.048 52.381 8.22 0.00 0.00 3.06
1783 3537 0.918258 TATTCAGGCAGCCCACATCA 59.082 50.000 8.22 0.00 0.00 3.07
1784 3538 0.260816 ATTCAGGCAGCCCACATCAT 59.739 50.000 8.22 0.00 0.00 2.45
1785 3539 0.040058 TTCAGGCAGCCCACATCATT 59.960 50.000 8.22 0.00 0.00 2.57
1786 3540 0.040058 TCAGGCAGCCCACATCATTT 59.960 50.000 8.22 0.00 0.00 2.32
1787 3541 0.174845 CAGGCAGCCCACATCATTTG 59.825 55.000 8.22 0.00 0.00 2.32
1788 3542 0.974010 AGGCAGCCCACATCATTTGG 60.974 55.000 8.22 0.00 0.00 3.28
1789 3543 0.971959 GGCAGCCCACATCATTTGGA 60.972 55.000 0.00 0.00 36.02 3.53
1840 3594 3.801698 CAGCTACCAGTGCATCTACAAT 58.198 45.455 0.00 0.00 0.00 2.71
1887 3641 3.936566 AGGGGGAAGGTCCGGTCA 61.937 66.667 0.00 0.00 37.43 4.02
1897 3651 0.387929 GGTCCGGTCAATGCTCGATA 59.612 55.000 0.00 0.00 0.00 2.92
1898 3652 1.202486 GGTCCGGTCAATGCTCGATAA 60.202 52.381 0.00 0.00 0.00 1.75
1899 3653 2.128035 GTCCGGTCAATGCTCGATAAG 58.872 52.381 0.00 0.00 0.00 1.73
1936 3698 1.597027 CCGGACGCCTTCACTTTGT 60.597 57.895 0.00 0.00 0.00 2.83
1968 3730 7.767250 TGTCTAGGTTATCCACATATCTCTG 57.233 40.000 0.00 0.00 35.89 3.35
1990 3753 5.765510 TGTATCCAGCCCAATATGAAAAGT 58.234 37.500 0.00 0.00 0.00 2.66
1991 3754 5.593909 TGTATCCAGCCCAATATGAAAAGTG 59.406 40.000 0.00 0.00 0.00 3.16
2016 3779 0.108329 GGATGTCCGGTCATGTTCGT 60.108 55.000 19.17 0.00 0.00 3.85
2054 3817 2.400269 TTTGGCCCACTACGGACCAC 62.400 60.000 0.00 0.00 36.56 4.16
2094 3857 7.797121 ATTCTTTCTTCCTTCTCTCTCTCTT 57.203 36.000 0.00 0.00 0.00 2.85
2196 4026 2.493091 AGATGCCCTTAAACCCTAGCT 58.507 47.619 0.00 0.00 0.00 3.32
2226 4056 4.447138 TGGATCTAGAGAGAGGGAGAAC 57.553 50.000 0.00 0.00 34.35 3.01
2349 4180 8.919145 CATCAAGTAGTCTAGGGATTCTTAGTT 58.081 37.037 0.00 0.00 0.00 2.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
36 37 9.903682 GTCATGCATGCTAATAAATAAAGTCAT 57.096 29.630 22.25 0.00 0.00 3.06
37 38 8.901793 TGTCATGCATGCTAATAAATAAAGTCA 58.098 29.630 22.25 0.00 0.00 3.41
38 39 9.173939 GTGTCATGCATGCTAATAAATAAAGTC 57.826 33.333 22.25 0.00 0.00 3.01
39 40 8.685427 TGTGTCATGCATGCTAATAAATAAAGT 58.315 29.630 22.25 0.00 0.00 2.66
40 41 9.687210 ATGTGTCATGCATGCTAATAAATAAAG 57.313 29.630 22.25 0.00 0.00 1.85
43 44 9.506018 ACTATGTGTCATGCATGCTAATAAATA 57.494 29.630 22.25 7.43 0.00 1.40
44 45 8.400184 ACTATGTGTCATGCATGCTAATAAAT 57.600 30.769 22.25 6.66 0.00 1.40
45 46 7.806409 ACTATGTGTCATGCATGCTAATAAA 57.194 32.000 22.25 0.00 0.00 1.40
46 47 8.900983 TTACTATGTGTCATGCATGCTAATAA 57.099 30.769 22.25 8.86 0.00 1.40
48 49 7.991084 ATTACTATGTGTCATGCATGCTAAT 57.009 32.000 22.25 13.96 0.00 1.73
51 52 8.939929 GTTATATTACTATGTGTCATGCATGCT 58.060 33.333 22.25 1.07 0.00 3.79
52 53 8.720562 TGTTATATTACTATGTGTCATGCATGC 58.279 33.333 22.25 11.82 0.00 4.06
99 100 9.639563 AGAAAGAGAGAGTTGACTATCATATCA 57.360 33.333 8.33 0.00 36.71 2.15
102 103 9.467796 TGAAGAAAGAGAGAGTTGACTATCATA 57.532 33.333 8.33 0.00 36.71 2.15
103 104 8.359875 TGAAGAAAGAGAGAGTTGACTATCAT 57.640 34.615 8.33 0.00 36.71 2.45
104 105 7.767250 TGAAGAAAGAGAGAGTTGACTATCA 57.233 36.000 8.33 0.00 36.71 2.15
105 106 9.651913 AAATGAAGAAAGAGAGAGTTGACTATC 57.348 33.333 0.00 0.00 34.59 2.08
134 135 9.803507 AGGCAAATTTGATGAGATGATATAGAA 57.196 29.630 22.31 0.00 0.00 2.10
138 139 9.584008 AACTAGGCAAATTTGATGAGATGATAT 57.416 29.630 22.31 0.00 0.00 1.63
139 140 8.843262 CAACTAGGCAAATTTGATGAGATGATA 58.157 33.333 22.31 0.32 0.00 2.15
140 141 7.558807 TCAACTAGGCAAATTTGATGAGATGAT 59.441 33.333 22.31 0.00 0.00 2.45
141 142 6.885918 TCAACTAGGCAAATTTGATGAGATGA 59.114 34.615 22.31 18.31 0.00 2.92
142 143 6.971184 GTCAACTAGGCAAATTTGATGAGATG 59.029 38.462 22.31 16.64 30.96 2.90
143 144 6.660521 TGTCAACTAGGCAAATTTGATGAGAT 59.339 34.615 22.31 6.50 30.96 2.75
144 145 6.003326 TGTCAACTAGGCAAATTTGATGAGA 58.997 36.000 22.31 10.26 30.96 3.27
145 146 6.258230 TGTCAACTAGGCAAATTTGATGAG 57.742 37.500 22.31 15.31 30.96 2.90
146 147 6.623486 CATGTCAACTAGGCAAATTTGATGA 58.377 36.000 22.31 11.47 34.09 2.92
147 148 5.290158 GCATGTCAACTAGGCAAATTTGATG 59.710 40.000 22.31 12.39 34.09 3.07
148 149 5.047164 TGCATGTCAACTAGGCAAATTTGAT 60.047 36.000 22.31 11.45 34.09 2.57
149 150 4.280425 TGCATGTCAACTAGGCAAATTTGA 59.720 37.500 22.31 0.00 34.09 2.69
150 151 4.558178 TGCATGTCAACTAGGCAAATTTG 58.442 39.130 14.03 14.03 34.09 2.32
151 152 4.870123 TGCATGTCAACTAGGCAAATTT 57.130 36.364 0.00 0.00 34.09 1.82
152 153 4.463539 TCATGCATGTCAACTAGGCAAATT 59.536 37.500 25.43 0.00 38.08 1.82
153 154 4.018490 TCATGCATGTCAACTAGGCAAAT 58.982 39.130 25.43 0.00 38.08 2.32
154 155 3.419943 TCATGCATGTCAACTAGGCAAA 58.580 40.909 25.43 0.00 38.08 3.68
155 156 3.070476 TCATGCATGTCAACTAGGCAA 57.930 42.857 25.43 0.00 38.08 4.52
156 157 2.785540 TCATGCATGTCAACTAGGCA 57.214 45.000 25.43 0.00 39.03 4.75
157 158 4.384056 AGTATCATGCATGTCAACTAGGC 58.616 43.478 25.43 7.61 0.00 3.93
158 159 5.928839 GGTAGTATCATGCATGTCAACTAGG 59.071 44.000 25.43 0.00 0.00 3.02
159 160 6.753180 AGGTAGTATCATGCATGTCAACTAG 58.247 40.000 25.43 0.00 0.00 2.57
160 161 6.731292 AGGTAGTATCATGCATGTCAACTA 57.269 37.500 25.43 23.80 0.00 2.24
161 162 5.620738 AGGTAGTATCATGCATGTCAACT 57.379 39.130 25.43 24.67 0.00 3.16
162 163 7.154656 TCATAGGTAGTATCATGCATGTCAAC 58.845 38.462 25.43 19.94 0.00 3.18
163 164 7.301868 TCATAGGTAGTATCATGCATGTCAA 57.698 36.000 25.43 7.83 0.00 3.18
164 165 6.916360 TCATAGGTAGTATCATGCATGTCA 57.084 37.500 25.43 12.19 0.00 3.58
165 166 8.690884 AGTATCATAGGTAGTATCATGCATGTC 58.309 37.037 25.43 16.49 0.00 3.06
166 167 8.601047 AGTATCATAGGTAGTATCATGCATGT 57.399 34.615 25.43 15.34 0.00 3.21
167 168 8.911965 AGAGTATCATAGGTAGTATCATGCATG 58.088 37.037 21.07 21.07 37.82 4.06
169 170 9.975218 TTAGAGTATCATAGGTAGTATCATGCA 57.025 33.333 0.00 0.00 37.82 3.96
177 178 9.165035 GCTCGTAATTAGAGTATCATAGGTAGT 57.835 37.037 11.26 0.00 37.82 2.73
178 179 8.614346 GGCTCGTAATTAGAGTATCATAGGTAG 58.386 40.741 11.26 0.00 37.82 3.18
179 180 8.327271 AGGCTCGTAATTAGAGTATCATAGGTA 58.673 37.037 11.26 0.00 37.82 3.08
180 181 7.176490 AGGCTCGTAATTAGAGTATCATAGGT 58.824 38.462 11.26 0.00 37.82 3.08
181 182 7.633193 AGGCTCGTAATTAGAGTATCATAGG 57.367 40.000 11.26 0.00 37.82 2.57
184 185 7.976734 GCATTAGGCTCGTAATTAGAGTATCAT 59.023 37.037 0.00 0.50 40.25 2.45
185 186 7.313646 GCATTAGGCTCGTAATTAGAGTATCA 58.686 38.462 0.00 0.00 40.25 2.15
186 187 7.743520 GCATTAGGCTCGTAATTAGAGTATC 57.256 40.000 0.00 4.98 40.25 2.24
202 203 5.024785 ACTAAGTTGGTCTAGCATTAGGC 57.975 43.478 7.21 0.00 45.30 3.93
203 204 8.204836 ACATTACTAAGTTGGTCTAGCATTAGG 58.795 37.037 0.00 0.00 0.00 2.69
248 252 6.349243 TCAAATCCTAAGTCTCCACGTTTA 57.651 37.500 0.00 0.00 0.00 2.01
253 257 6.317391 CCTTCAATCAAATCCTAAGTCTCCAC 59.683 42.308 0.00 0.00 0.00 4.02
256 260 5.825151 CCCCTTCAATCAAATCCTAAGTCTC 59.175 44.000 0.00 0.00 0.00 3.36
263 267 2.292455 CCCACCCCTTCAATCAAATCCT 60.292 50.000 0.00 0.00 0.00 3.24
269 273 1.214305 CCCTCCCACCCCTTCAATCA 61.214 60.000 0.00 0.00 0.00 2.57
361 366 3.314080 GGCGCAAAAATGCTACACCTATA 59.686 43.478 10.83 0.00 0.00 1.31
381 386 4.626081 AGGTGAGGTGTGCACGGC 62.626 66.667 13.13 7.53 37.13 5.68
382 387 2.666190 CAGGTGAGGTGTGCACGG 60.666 66.667 13.13 0.00 37.13 4.94
383 388 3.349006 GCAGGTGAGGTGTGCACG 61.349 66.667 13.13 0.00 37.13 5.34
384 389 3.349006 CGCAGGTGAGGTGTGCAC 61.349 66.667 10.75 10.75 37.01 4.57
385 390 3.807631 GACGCAGGTGAGGTGTGCA 62.808 63.158 0.00 0.00 37.01 4.57
386 391 3.044305 GACGCAGGTGAGGTGTGC 61.044 66.667 0.00 0.00 0.00 4.57
387 392 0.603707 ATTGACGCAGGTGAGGTGTG 60.604 55.000 0.00 0.00 0.00 3.82
388 393 0.973632 TATTGACGCAGGTGAGGTGT 59.026 50.000 0.00 0.00 0.00 4.16
389 394 1.066858 ACTATTGACGCAGGTGAGGTG 60.067 52.381 0.00 0.00 0.00 4.00
390 395 1.066858 CACTATTGACGCAGGTGAGGT 60.067 52.381 0.00 0.00 0.00 3.85
391 396 1.204704 TCACTATTGACGCAGGTGAGG 59.795 52.381 0.00 0.00 33.74 3.86
392 397 2.654749 TCACTATTGACGCAGGTGAG 57.345 50.000 0.00 0.00 33.74 3.51
393 398 3.325870 CTTTCACTATTGACGCAGGTGA 58.674 45.455 0.00 0.00 35.51 4.02
394 399 2.159653 GCTTTCACTATTGACGCAGGTG 60.160 50.000 0.00 0.00 31.60 4.00
395 400 2.076863 GCTTTCACTATTGACGCAGGT 58.923 47.619 0.00 0.00 31.60 4.00
481 487 4.588106 TGGTGTTGAACATGTGGATTGATT 59.412 37.500 0.00 0.00 0.00 2.57
670 679 8.753497 AGGACACCTTAATTTCCTTATCATTC 57.247 34.615 0.00 0.00 34.65 2.67
1207 1260 2.623915 CGTCGTCCTCTTCGTGGGT 61.624 63.158 0.00 0.00 0.00 4.51
1242 1304 1.671742 GAACGCCTCCCTCAGACAA 59.328 57.895 0.00 0.00 0.00 3.18
1354 1443 4.681978 GTCGTCCACGCCCAGCTT 62.682 66.667 0.00 0.00 39.60 3.74
1657 3411 6.067350 AGGGCAGCATTTTCCAAAATAAAAA 58.933 32.000 0.00 0.00 36.52 1.94
1658 3412 5.629125 AGGGCAGCATTTTCCAAAATAAAA 58.371 33.333 0.00 0.00 36.52 1.52
1659 3413 5.240013 AGGGCAGCATTTTCCAAAATAAA 57.760 34.783 0.00 0.00 36.52 1.40
1660 3414 4.906747 AGGGCAGCATTTTCCAAAATAA 57.093 36.364 0.00 0.00 36.52 1.40
1661 3415 4.906747 AAGGGCAGCATTTTCCAAAATA 57.093 36.364 0.00 0.00 36.52 1.40
1662 3416 3.793819 AAGGGCAGCATTTTCCAAAAT 57.206 38.095 0.00 0.00 39.07 1.82
1663 3417 3.574354 AAAGGGCAGCATTTTCCAAAA 57.426 38.095 0.00 0.00 0.00 2.44
1664 3418 4.906747 ATAAAGGGCAGCATTTTCCAAA 57.093 36.364 0.00 0.00 0.00 3.28
1665 3419 4.906747 AATAAAGGGCAGCATTTTCCAA 57.093 36.364 0.00 0.00 0.00 3.53
1666 3420 6.013812 AGTTTAATAAAGGGCAGCATTTTCCA 60.014 34.615 0.00 0.00 0.00 3.53
1667 3421 6.406370 AGTTTAATAAAGGGCAGCATTTTCC 58.594 36.000 0.00 0.00 0.00 3.13
1668 3422 8.996024 TTAGTTTAATAAAGGGCAGCATTTTC 57.004 30.769 0.00 0.00 0.00 2.29
1669 3423 7.549134 GCTTAGTTTAATAAAGGGCAGCATTTT 59.451 33.333 0.00 0.00 0.00 1.82
1670 3424 7.041721 GCTTAGTTTAATAAAGGGCAGCATTT 58.958 34.615 0.00 0.00 0.00 2.32
1671 3425 6.154363 TGCTTAGTTTAATAAAGGGCAGCATT 59.846 34.615 0.00 0.00 0.00 3.56
1672 3426 5.656416 TGCTTAGTTTAATAAAGGGCAGCAT 59.344 36.000 0.00 0.00 0.00 3.79
1673 3427 5.013547 TGCTTAGTTTAATAAAGGGCAGCA 58.986 37.500 0.00 5.31 0.00 4.41
1674 3428 5.576447 TGCTTAGTTTAATAAAGGGCAGC 57.424 39.130 0.00 0.00 0.00 5.25
1675 3429 5.450550 GGCTGCTTAGTTTAATAAAGGGCAG 60.451 44.000 16.89 16.89 44.76 4.85
1676 3430 4.401202 GGCTGCTTAGTTTAATAAAGGGCA 59.599 41.667 0.00 0.00 0.00 5.36
1677 3431 4.202121 GGGCTGCTTAGTTTAATAAAGGGC 60.202 45.833 0.00 0.00 0.00 5.19
1678 3432 4.341235 GGGGCTGCTTAGTTTAATAAAGGG 59.659 45.833 0.00 0.00 0.00 3.95
1679 3433 4.036380 CGGGGCTGCTTAGTTTAATAAAGG 59.964 45.833 0.00 0.00 0.00 3.11
1680 3434 4.036380 CCGGGGCTGCTTAGTTTAATAAAG 59.964 45.833 0.00 0.00 0.00 1.85
1681 3435 3.949113 CCGGGGCTGCTTAGTTTAATAAA 59.051 43.478 0.00 0.00 0.00 1.40
1682 3436 3.547746 CCGGGGCTGCTTAGTTTAATAA 58.452 45.455 0.00 0.00 0.00 1.40
1683 3437 2.747135 GCCGGGGCTGCTTAGTTTAATA 60.747 50.000 2.18 0.00 38.26 0.98
1684 3438 2.022238 GCCGGGGCTGCTTAGTTTAAT 61.022 52.381 2.18 0.00 38.26 1.40
1685 3439 0.678684 GCCGGGGCTGCTTAGTTTAA 60.679 55.000 2.18 0.00 38.26 1.52
1686 3440 1.078001 GCCGGGGCTGCTTAGTTTA 60.078 57.895 2.18 0.00 38.26 2.01
1687 3441 2.361230 GCCGGGGCTGCTTAGTTT 60.361 61.111 2.18 0.00 38.26 2.66
1688 3442 4.426313 GGCCGGGGCTGCTTAGTT 62.426 66.667 14.22 0.00 41.60 2.24
1698 3452 4.619227 ACATTATCGCGGCCGGGG 62.619 66.667 37.69 24.88 34.56 5.73
1699 3453 3.041940 GACATTATCGCGGCCGGG 61.042 66.667 34.33 34.33 34.56 5.73
1700 3454 2.279851 TGACATTATCGCGGCCGG 60.280 61.111 29.38 17.41 34.56 6.13
1701 3455 2.928361 GTGACATTATCGCGGCCG 59.072 61.111 24.05 24.05 0.00 6.13
1706 3460 6.032722 ACTTTGTATTCGTGACATTATCGC 57.967 37.500 0.00 0.00 34.20 4.58
1707 3461 8.259872 CACTACTTTGTATTCGTGACATTATCG 58.740 37.037 0.00 0.00 0.00 2.92
1708 3462 8.540492 CCACTACTTTGTATTCGTGACATTATC 58.460 37.037 0.00 0.00 0.00 1.75
1709 3463 7.494625 CCCACTACTTTGTATTCGTGACATTAT 59.505 37.037 0.00 0.00 0.00 1.28
1710 3464 6.814644 CCCACTACTTTGTATTCGTGACATTA 59.185 38.462 0.00 0.00 0.00 1.90
1711 3465 5.642063 CCCACTACTTTGTATTCGTGACATT 59.358 40.000 0.00 0.00 0.00 2.71
1712 3466 5.175859 CCCACTACTTTGTATTCGTGACAT 58.824 41.667 0.00 0.00 0.00 3.06
1713 3467 4.561938 CCCCACTACTTTGTATTCGTGACA 60.562 45.833 0.00 0.00 0.00 3.58
1714 3468 3.930848 CCCCACTACTTTGTATTCGTGAC 59.069 47.826 0.00 0.00 0.00 3.67
1715 3469 3.833650 TCCCCACTACTTTGTATTCGTGA 59.166 43.478 0.00 0.00 0.00 4.35
1716 3470 4.196626 TCCCCACTACTTTGTATTCGTG 57.803 45.455 0.00 0.00 0.00 4.35
1717 3471 4.895668 TTCCCCACTACTTTGTATTCGT 57.104 40.909 0.00 0.00 0.00 3.85
1718 3472 7.270047 TCTATTTCCCCACTACTTTGTATTCG 58.730 38.462 0.00 0.00 0.00 3.34
1719 3473 9.457436 TTTCTATTTCCCCACTACTTTGTATTC 57.543 33.333 0.00 0.00 0.00 1.75
1720 3474 9.816787 TTTTCTATTTCCCCACTACTTTGTATT 57.183 29.630 0.00 0.00 0.00 1.89
1721 3475 9.239551 GTTTTCTATTTCCCCACTACTTTGTAT 57.760 33.333 0.00 0.00 0.00 2.29
1722 3476 7.666804 GGTTTTCTATTTCCCCACTACTTTGTA 59.333 37.037 0.00 0.00 0.00 2.41
1723 3477 6.492429 GGTTTTCTATTTCCCCACTACTTTGT 59.508 38.462 0.00 0.00 0.00 2.83
1724 3478 6.492087 TGGTTTTCTATTTCCCCACTACTTTG 59.508 38.462 0.00 0.00 0.00 2.77
1725 3479 6.616577 TGGTTTTCTATTTCCCCACTACTTT 58.383 36.000 0.00 0.00 0.00 2.66
1726 3480 6.208840 TGGTTTTCTATTTCCCCACTACTT 57.791 37.500 0.00 0.00 0.00 2.24
1727 3481 5.853572 TGGTTTTCTATTTCCCCACTACT 57.146 39.130 0.00 0.00 0.00 2.57
1728 3482 6.008331 ACTTGGTTTTCTATTTCCCCACTAC 58.992 40.000 0.00 0.00 0.00 2.73
1729 3483 6.045106 AGACTTGGTTTTCTATTTCCCCACTA 59.955 38.462 0.00 0.00 0.00 2.74
1730 3484 5.074746 ACTTGGTTTTCTATTTCCCCACT 57.925 39.130 0.00 0.00 0.00 4.00
1731 3485 5.077564 AGACTTGGTTTTCTATTTCCCCAC 58.922 41.667 0.00 0.00 0.00 4.61
1732 3486 5.333566 AGACTTGGTTTTCTATTTCCCCA 57.666 39.130 0.00 0.00 0.00 4.96
1733 3487 6.717997 TGTAAGACTTGGTTTTCTATTTCCCC 59.282 38.462 0.00 0.00 0.00 4.81
1734 3488 7.229907 TGTGTAAGACTTGGTTTTCTATTTCCC 59.770 37.037 0.00 0.00 0.00 3.97
1735 3489 8.161699 TGTGTAAGACTTGGTTTTCTATTTCC 57.838 34.615 0.00 0.00 0.00 3.13
1736 3490 9.447040 GTTGTGTAAGACTTGGTTTTCTATTTC 57.553 33.333 0.00 0.00 0.00 2.17
1737 3491 9.185680 AGTTGTGTAAGACTTGGTTTTCTATTT 57.814 29.630 0.00 0.00 0.00 1.40
1738 3492 8.747538 AGTTGTGTAAGACTTGGTTTTCTATT 57.252 30.769 0.00 0.00 0.00 1.73
1739 3493 8.747538 AAGTTGTGTAAGACTTGGTTTTCTAT 57.252 30.769 0.00 0.00 34.96 1.98
1740 3494 9.841295 ATAAGTTGTGTAAGACTTGGTTTTCTA 57.159 29.630 0.00 0.00 36.79 2.10
1741 3495 8.747538 ATAAGTTGTGTAAGACTTGGTTTTCT 57.252 30.769 0.00 0.00 36.79 2.52
1742 3496 9.447040 GAATAAGTTGTGTAAGACTTGGTTTTC 57.553 33.333 0.00 0.00 36.79 2.29
1743 3497 8.962679 TGAATAAGTTGTGTAAGACTTGGTTTT 58.037 29.630 0.00 0.00 36.79 2.43
1744 3498 8.514330 TGAATAAGTTGTGTAAGACTTGGTTT 57.486 30.769 0.00 0.00 36.79 3.27
1745 3499 7.228706 CCTGAATAAGTTGTGTAAGACTTGGTT 59.771 37.037 0.00 0.00 36.79 3.67
1746 3500 6.710744 CCTGAATAAGTTGTGTAAGACTTGGT 59.289 38.462 0.00 0.00 36.79 3.67
1747 3501 6.348540 GCCTGAATAAGTTGTGTAAGACTTGG 60.349 42.308 0.00 0.00 36.79 3.61
1748 3502 6.204688 TGCCTGAATAAGTTGTGTAAGACTTG 59.795 38.462 0.00 0.00 36.79 3.16
1749 3503 6.296026 TGCCTGAATAAGTTGTGTAAGACTT 58.704 36.000 0.00 0.00 39.32 3.01
1750 3504 5.865085 TGCCTGAATAAGTTGTGTAAGACT 58.135 37.500 0.00 0.00 0.00 3.24
1751 3505 5.390991 GCTGCCTGAATAAGTTGTGTAAGAC 60.391 44.000 0.00 0.00 0.00 3.01
1752 3506 4.695455 GCTGCCTGAATAAGTTGTGTAAGA 59.305 41.667 0.00 0.00 0.00 2.10
1753 3507 4.142600 GGCTGCCTGAATAAGTTGTGTAAG 60.143 45.833 12.43 0.00 0.00 2.34
1754 3508 3.756434 GGCTGCCTGAATAAGTTGTGTAA 59.244 43.478 12.43 0.00 0.00 2.41
1755 3509 3.343617 GGCTGCCTGAATAAGTTGTGTA 58.656 45.455 12.43 0.00 0.00 2.90
1756 3510 2.162681 GGCTGCCTGAATAAGTTGTGT 58.837 47.619 12.43 0.00 0.00 3.72
1757 3511 1.474077 GGGCTGCCTGAATAAGTTGTG 59.526 52.381 19.68 0.00 0.00 3.33
1758 3512 1.075374 TGGGCTGCCTGAATAAGTTGT 59.925 47.619 19.68 0.00 0.00 3.32
1759 3513 1.474077 GTGGGCTGCCTGAATAAGTTG 59.526 52.381 19.68 0.00 0.00 3.16
1760 3514 1.075374 TGTGGGCTGCCTGAATAAGTT 59.925 47.619 19.68 0.00 0.00 2.66
1761 3515 0.698238 TGTGGGCTGCCTGAATAAGT 59.302 50.000 19.68 0.00 0.00 2.24
1762 3516 1.952296 GATGTGGGCTGCCTGAATAAG 59.048 52.381 19.68 0.00 0.00 1.73
1763 3517 1.284491 TGATGTGGGCTGCCTGAATAA 59.716 47.619 19.68 0.00 0.00 1.40
1764 3518 0.918258 TGATGTGGGCTGCCTGAATA 59.082 50.000 19.68 3.62 0.00 1.75
1765 3519 0.260816 ATGATGTGGGCTGCCTGAAT 59.739 50.000 19.68 9.32 0.00 2.57
1766 3520 0.040058 AATGATGTGGGCTGCCTGAA 59.960 50.000 19.68 4.37 0.00 3.02
1767 3521 0.040058 AAATGATGTGGGCTGCCTGA 59.960 50.000 19.68 2.42 0.00 3.86
1768 3522 0.174845 CAAATGATGTGGGCTGCCTG 59.825 55.000 19.68 1.18 0.00 4.85
1769 3523 0.974010 CCAAATGATGTGGGCTGCCT 60.974 55.000 19.68 0.00 32.03 4.75
1770 3524 0.971959 TCCAAATGATGTGGGCTGCC 60.972 55.000 11.05 11.05 36.73 4.85
1771 3525 0.458669 CTCCAAATGATGTGGGCTGC 59.541 55.000 0.95 0.00 36.73 5.25
1772 3526 1.843368 ACTCCAAATGATGTGGGCTG 58.157 50.000 0.95 0.00 36.73 4.85
1773 3527 2.610438 AACTCCAAATGATGTGGGCT 57.390 45.000 0.95 0.00 36.73 5.19
1774 3528 4.160252 ACATTAACTCCAAATGATGTGGGC 59.840 41.667 0.95 0.00 37.68 5.36
1775 3529 5.920193 ACATTAACTCCAAATGATGTGGG 57.080 39.130 0.95 0.00 37.68 4.61
1776 3530 7.031372 CAGAACATTAACTCCAAATGATGTGG 58.969 38.462 0.00 0.00 37.68 4.17
1777 3531 6.529125 GCAGAACATTAACTCCAAATGATGTG 59.471 38.462 3.01 1.75 37.68 3.21
1778 3532 6.209192 TGCAGAACATTAACTCCAAATGATGT 59.791 34.615 3.01 0.00 37.68 3.06
1779 3533 6.623486 TGCAGAACATTAACTCCAAATGATG 58.377 36.000 3.01 1.11 37.68 3.07
1780 3534 6.839124 TGCAGAACATTAACTCCAAATGAT 57.161 33.333 3.01 0.00 37.68 2.45
1781 3535 6.647334 TTGCAGAACATTAACTCCAAATGA 57.353 33.333 3.01 0.00 37.68 2.57
1782 3536 6.925165 ACTTTGCAGAACATTAACTCCAAATG 59.075 34.615 0.00 0.00 39.68 2.32
1783 3537 7.054491 ACTTTGCAGAACATTAACTCCAAAT 57.946 32.000 0.00 0.00 0.00 2.32
1784 3538 6.463995 ACTTTGCAGAACATTAACTCCAAA 57.536 33.333 0.00 0.00 0.00 3.28
1785 3539 5.277779 CGACTTTGCAGAACATTAACTCCAA 60.278 40.000 0.00 0.00 0.00 3.53
1786 3540 4.213270 CGACTTTGCAGAACATTAACTCCA 59.787 41.667 0.00 0.00 0.00 3.86
1787 3541 4.451096 TCGACTTTGCAGAACATTAACTCC 59.549 41.667 0.00 0.00 0.00 3.85
1788 3542 5.050363 TGTCGACTTTGCAGAACATTAACTC 60.050 40.000 17.92 0.00 0.00 3.01
1789 3543 4.814234 TGTCGACTTTGCAGAACATTAACT 59.186 37.500 17.92 0.00 0.00 2.24
1840 3594 1.530013 GGACCGTTTGAGAGGACCGA 61.530 60.000 0.00 0.00 33.16 4.69
1876 3630 1.079127 CGAGCATTGACCGGACCTT 60.079 57.895 9.46 0.00 0.00 3.50
1877 3631 1.330655 ATCGAGCATTGACCGGACCT 61.331 55.000 9.46 0.00 0.00 3.85
1878 3632 0.387929 TATCGAGCATTGACCGGACC 59.612 55.000 9.46 0.00 0.00 4.46
1916 3678 1.147600 AAAGTGAAGGCGTCCGGTT 59.852 52.632 0.00 0.00 0.00 4.44
1936 3698 6.199376 TGTGGATAACCTAGACATACAAGGA 58.801 40.000 0.00 0.00 37.04 3.36
1968 3730 5.594317 ACACTTTTCATATTGGGCTGGATAC 59.406 40.000 0.00 0.00 0.00 2.24
1990 3753 0.325765 TGACCGGACATCCCCATACA 60.326 55.000 9.46 0.00 0.00 2.29
1991 3754 1.056660 ATGACCGGACATCCCCATAC 58.943 55.000 13.89 0.00 0.00 2.39
2016 3779 4.694982 CCAAATACTATGTGACACACTGCA 59.305 41.667 11.22 0.00 35.11 4.41
2084 3847 9.381033 ACACAAATAATTGATGAAGAGAGAGAG 57.619 33.333 0.00 0.00 38.94 3.20
2094 3857 5.772169 TGGGTCACACACAAATAATTGATGA 59.228 36.000 0.00 0.00 38.94 2.92
2196 4026 6.310941 CCTCTCTCTAGATCCATTCTTGGTA 58.689 44.000 0.00 0.00 44.06 3.25
2235 4065 2.386661 ACCTGAATGATGTCGGTGAC 57.613 50.000 0.00 0.00 0.00 3.67
2311 4142 1.154413 CTTGATGCACGCGGAACAC 60.154 57.895 12.47 0.00 0.00 3.32
2349 4180 8.199449 CCGAAACTATACATAGTCAAAACCCTA 58.801 37.037 2.45 0.00 42.47 3.53
2400 4231 5.458362 GGGAGATCTAGAGGACACCTATTCA 60.458 48.000 0.00 0.00 31.76 2.57


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

AutoCloner maintained by Alex Coulton.