Multiple sequence alignment - TraesCS2A01G086600

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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 TraesCS2A01G086600 chr2A 100.000 2390 0 0 1 2390 40317214 40314825 0.000000e+00 4414.0
1 TraesCS2A01G086600 chr2A 88.443 424 49 0 968 1391 40446103 40445680 1.640000e-141 512.0
2 TraesCS2A01G086600 chr2A 94.253 261 14 1 1824 2083 40254933 40254673 4.790000e-107 398.0
3 TraesCS2A01G086600 chr2A 95.930 172 7 0 2087 2258 755482499 755482328 1.810000e-71 279.0
4 TraesCS2A01G086600 chr2A 77.303 445 82 16 911 1339 40374127 40373686 6.600000e-61 244.0
5 TraesCS2A01G086600 chr2A 85.714 196 19 4 759 952 40471513 40471325 5.210000e-47 198.0
6 TraesCS2A01G086600 chr2A 77.072 362 71 7 984 1339 40492238 40491883 5.210000e-47 198.0
7 TraesCS2A01G086600 chr2A 76.471 323 53 17 1041 1347 39686293 39686608 1.140000e-33 154.0
8 TraesCS2A01G086600 chr2A 88.679 53 6 0 577 629 19661053 19661001 5.510000e-07 65.8
9 TraesCS2A01G086600 chr2D 89.872 1797 109 26 1 1762 36426830 36425072 0.000000e+00 2242.0
10 TraesCS2A01G086600 chr2D 87.713 586 59 7 808 1391 36445591 36445017 0.000000e+00 671.0
11 TraesCS2A01G086600 chr2D 88.148 135 14 1 2258 2390 36424827 36424693 2.460000e-35 159.0
12 TraesCS2A01G086600 chr2B 91.211 842 42 13 759 1585 59223958 59224782 0.000000e+00 1116.0
13 TraesCS2A01G086600 chr2B 84.749 518 55 14 1583 2086 59224977 59225484 4.590000e-137 497.0
14 TraesCS2A01G086600 chr2B 79.252 294 54 3 1051 1339 59105205 59105496 5.210000e-47 198.0
15 TraesCS2A01G086600 chr2B 91.743 109 9 0 2278 2386 59225487 59225595 4.110000e-33 152.0
16 TraesCS2A01G086600 chr2B 80.460 174 23 7 1041 1207 59303312 59303481 3.230000e-24 122.0
17 TraesCS2A01G086600 chr5B 86.217 341 27 9 1 341 335490528 335490848 3.780000e-93 351.0
18 TraesCS2A01G086600 chr5B 96.667 90 3 0 667 756 335513935 335514024 1.480000e-32 150.0
19 TraesCS2A01G086600 chr7D 95.930 172 7 0 2087 2258 382090087 382089916 1.810000e-71 279.0
20 TraesCS2A01G086600 chr7A 95.429 175 8 0 2084 2258 638507373 638507547 1.810000e-71 279.0
21 TraesCS2A01G086600 chr7A 95.930 172 7 0 2087 2258 708245913 708245742 1.810000e-71 279.0
22 TraesCS2A01G086600 chr7A 79.699 266 36 10 407 668 709765567 709765818 2.440000e-40 176.0
23 TraesCS2A01G086600 chr6B 95.429 175 8 0 2084 2258 596601567 596601741 1.810000e-71 279.0
24 TraesCS2A01G086600 chr6B 81.765 170 20 8 490 659 707525514 707525356 5.360000e-27 132.0
25 TraesCS2A01G086600 chr4D 95.930 172 7 0 2087 2258 123401807 123401636 1.810000e-71 279.0
26 TraesCS2A01G086600 chr4D 84.091 176 24 3 490 662 507004885 507005059 1.470000e-37 167.0
27 TraesCS2A01G086600 chrUn 95.376 173 7 1 2087 2258 171008575 171008403 8.420000e-70 274.0
28 TraesCS2A01G086600 chr4B 95.349 172 8 0 2087 2258 495568250 495568079 8.420000e-70 274.0
29 TraesCS2A01G086600 chr1D 94.857 175 9 0 2084 2258 212444426 212444600 8.420000e-70 274.0
30 TraesCS2A01G086600 chr1D 81.132 265 45 4 407 668 490054932 490055194 8.660000e-50 207.0
31 TraesCS2A01G086600 chr1B 83.459 266 40 4 406 668 580213802 580213538 6.600000e-61 244.0
32 TraesCS2A01G086600 chr7B 89.881 168 17 0 1 168 715118940 715119107 1.440000e-52 217.0
33 TraesCS2A01G086600 chr7B 89.881 168 17 0 1 168 715151621 715151788 1.440000e-52 217.0
34 TraesCS2A01G086600 chr7B 83.846 130 18 2 539 666 740260022 740260150 1.160000e-23 121.0
35 TraesCS2A01G086600 chr4A 77.711 166 35 2 398 561 584462518 584462353 1.510000e-17 100.0


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 TraesCS2A01G086600 chr2A 40314825 40317214 2389 True 4414.000000 4414 100.000000 1 2390 1 chr2A.!!$R3 2389
1 TraesCS2A01G086600 chr2D 36424693 36426830 2137 True 1200.500000 2242 89.010000 1 2390 2 chr2D.!!$R2 2389
2 TraesCS2A01G086600 chr2D 36445017 36445591 574 True 671.000000 671 87.713000 808 1391 1 chr2D.!!$R1 583
3 TraesCS2A01G086600 chr2B 59223958 59225595 1637 False 588.333333 1116 89.234333 759 2386 3 chr2B.!!$F3 1627

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
72 73 0.028505 CAGCGTCATTGCAGCATACC 59.971 55.0 0.0 0.0 37.31 2.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1737 1987 0.036765 TGGTAGCGATTTCTGGCGTT 60.037 50.0 0.0 0.0 0.0 4.84 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
48 49 4.465512 CGCAACATCGCCAGTGCC 62.466 66.667 0.00 0.00 0.00 5.01
52 53 2.616330 AACATCGCCAGTGCCGTTG 61.616 57.895 3.23 3.23 0.00 4.10
72 73 0.028505 CAGCGTCATTGCAGCATACC 59.971 55.000 0.00 0.00 37.31 2.73
129 130 2.627791 TGGAACACGCCTTGTCATG 58.372 52.632 0.00 0.00 37.51 3.07
146 147 0.459585 ATGGTCGTCGAAACATCCCG 60.460 55.000 0.00 0.00 0.00 5.14
148 149 1.080298 GTCGTCGAAACATCCCGGT 60.080 57.895 0.00 0.00 0.00 5.28
170 171 2.979676 CCCGAGCTTGCAGCACAA 60.980 61.111 0.00 0.00 45.56 3.33
216 217 1.227234 CGCATACCACTCGGCATGA 60.227 57.895 0.00 0.00 38.20 3.07
232 233 1.830587 ATGACAACAGGCGAGCTCCA 61.831 55.000 8.47 0.00 0.00 3.86
233 234 2.029844 GACAACAGGCGAGCTCCAC 61.030 63.158 8.47 0.61 0.00 4.02
234 235 2.031012 CAACAGGCGAGCTCCACA 59.969 61.111 8.47 0.00 0.00 4.17
235 236 2.031516 CAACAGGCGAGCTCCACAG 61.032 63.158 8.47 0.50 0.00 3.66
236 237 2.210013 AACAGGCGAGCTCCACAGA 61.210 57.895 8.47 0.00 0.00 3.41
237 238 2.125753 CAGGCGAGCTCCACAGAC 60.126 66.667 8.47 0.00 0.00 3.51
238 239 3.753434 AGGCGAGCTCCACAGACG 61.753 66.667 8.47 0.00 0.00 4.18
239 240 3.749064 GGCGAGCTCCACAGACGA 61.749 66.667 8.47 0.00 0.00 4.20
240 241 2.505118 GCGAGCTCCACAGACGAC 60.505 66.667 8.47 0.00 0.00 4.34
241 242 2.954611 CGAGCTCCACAGACGACA 59.045 61.111 8.47 0.00 0.00 4.35
242 243 1.154131 CGAGCTCCACAGACGACAG 60.154 63.158 8.47 0.00 0.00 3.51
243 244 1.214062 GAGCTCCACAGACGACAGG 59.786 63.158 0.87 0.00 0.00 4.00
244 245 2.433318 GCTCCACAGACGACAGGC 60.433 66.667 0.00 0.00 0.00 4.85
246 247 2.596338 TCCACAGACGACAGGCGA 60.596 61.111 0.22 0.00 44.57 5.54
247 248 2.126307 CCACAGACGACAGGCGAG 60.126 66.667 0.22 0.00 44.57 5.03
248 249 2.807045 CACAGACGACAGGCGAGC 60.807 66.667 0.22 0.00 44.57 5.03
249 250 2.986413 ACAGACGACAGGCGAGCT 60.986 61.111 0.22 0.00 44.57 4.09
250 251 2.202544 CAGACGACAGGCGAGCTC 60.203 66.667 0.22 2.73 44.57 4.09
251 252 3.444805 AGACGACAGGCGAGCTCC 61.445 66.667 0.22 0.47 44.57 4.70
312 313 2.476051 CATGGCTCACGTCGTTGC 59.524 61.111 10.61 10.61 0.00 4.17
314 315 1.375908 ATGGCTCACGTCGTTGCAT 60.376 52.632 18.08 9.47 0.00 3.96
320 321 0.249699 TCACGTCGTTGCATGAGGTT 60.250 50.000 10.91 0.00 30.64 3.50
324 325 1.262950 CGTCGTTGCATGAGGTTGAAA 59.737 47.619 0.00 0.00 0.00 2.69
366 371 2.712709 TGGTCGTAGAGAACCAGAGAG 58.287 52.381 0.00 0.00 36.95 3.20
373 378 2.603021 AGAGAACCAGAGAGCTTGTGA 58.397 47.619 0.00 0.00 0.00 3.58
405 410 0.387878 GGATCAGAGGATGCTACGCG 60.388 60.000 3.53 3.53 38.69 6.01
457 462 7.881775 AATTTGGACCTCACTGAAATATACC 57.118 36.000 0.00 0.00 0.00 2.73
458 463 5.367945 TTGGACCTCACTGAAATATACCC 57.632 43.478 0.00 0.00 0.00 3.69
475 480 9.744468 AAATATACCCAATTTCAGAAATTACGC 57.256 29.630 18.84 0.00 38.97 4.42
476 481 6.767524 ATACCCAATTTCAGAAATTACGCA 57.232 33.333 18.84 7.46 38.97 5.24
477 482 5.659440 ACCCAATTTCAGAAATTACGCAT 57.341 34.783 18.84 3.34 38.97 4.73
478 483 6.767524 ACCCAATTTCAGAAATTACGCATA 57.232 33.333 18.84 0.00 38.97 3.14
479 484 7.346751 ACCCAATTTCAGAAATTACGCATAT 57.653 32.000 18.84 1.25 38.97 1.78
480 485 7.781056 ACCCAATTTCAGAAATTACGCATATT 58.219 30.769 18.84 0.00 38.97 1.28
481 486 8.257306 ACCCAATTTCAGAAATTACGCATATTT 58.743 29.630 18.84 0.00 38.97 1.40
482 487 8.755018 CCCAATTTCAGAAATTACGCATATTTC 58.245 33.333 18.84 8.58 38.97 2.17
483 488 9.299963 CCAATTTCAGAAATTACGCATATTTCA 57.700 29.630 18.84 1.33 41.99 2.69
612 619 4.038282 GGTAAAAATGTTTCGAACCCCACT 59.962 41.667 0.00 0.00 0.00 4.00
630 637 6.496565 ACCCCACTGAAATATGTGAAATTTCA 59.503 34.615 16.91 16.91 46.08 2.69
631 638 7.016072 ACCCCACTGAAATATGTGAAATTTCAA 59.984 33.333 22.07 12.81 46.93 2.69
695 702 4.760047 GGAGGCCACATGACGCGT 62.760 66.667 13.85 13.85 0.00 6.01
773 780 5.220605 GGAGTTTCCAATCTTATTCGGAACG 60.221 44.000 0.00 0.00 46.03 3.95
823 834 1.336148 TGGACGTACGCAATCTTTCGT 60.336 47.619 16.72 0.00 42.09 3.85
824 835 1.058695 GGACGTACGCAATCTTTCGTG 59.941 52.381 16.72 0.00 39.46 4.35
851 862 0.798771 GTCTTGCAGTAGACGCGAGG 60.799 60.000 15.93 0.00 40.68 4.63
868 879 2.741433 GGGGTCCAAACTCCAAACC 58.259 57.895 0.00 0.00 46.37 3.27
963 997 4.641645 CCCACCTTCGCCACAGCA 62.642 66.667 0.00 0.00 39.83 4.41
964 998 3.357079 CCACCTTCGCCACAGCAC 61.357 66.667 0.00 0.00 39.83 4.40
965 999 3.357079 CACCTTCGCCACAGCACC 61.357 66.667 0.00 0.00 39.83 5.01
966 1000 4.643387 ACCTTCGCCACAGCACCC 62.643 66.667 0.00 0.00 39.83 4.61
1408 1442 4.874396 ACTGATCATAGTGATGCTGTTGTG 59.126 41.667 0.00 0.00 37.20 3.33
1409 1443 5.088680 TGATCATAGTGATGCTGTTGTGA 57.911 39.130 0.00 0.00 37.20 3.58
1410 1444 5.677567 TGATCATAGTGATGCTGTTGTGAT 58.322 37.500 0.00 0.00 37.20 3.06
1411 1445 5.526111 TGATCATAGTGATGCTGTTGTGATG 59.474 40.000 0.00 0.00 37.20 3.07
1412 1446 4.835678 TCATAGTGATGCTGTTGTGATGT 58.164 39.130 0.00 0.00 32.62 3.06
1518 1557 5.450818 ACTGTATAATTCTTTCCCTGCCA 57.549 39.130 0.00 0.00 0.00 4.92
1612 1853 8.608185 AATTACATCCATGGAGGTTATTTTGT 57.392 30.769 34.68 24.21 35.57 2.83
1632 1873 5.427036 TGTTATTCGGGTTGTTCAGTTTC 57.573 39.130 0.00 0.00 0.00 2.78
1636 1877 5.592104 ATTCGGGTTGTTCAGTTTCTTTT 57.408 34.783 0.00 0.00 0.00 2.27
1637 1878 5.394224 TTCGGGTTGTTCAGTTTCTTTTT 57.606 34.783 0.00 0.00 0.00 1.94
1684 1934 3.644823 TGTCAAGCTGTGAATGCAATTG 58.355 40.909 0.00 0.00 36.07 2.32
1712 1962 6.310711 GTGTAAAATACTGTGCTCTGTAGTCC 59.689 42.308 10.60 2.73 32.98 3.85
1713 1963 4.473477 AAATACTGTGCTCTGTAGTCCC 57.527 45.455 10.60 0.00 32.98 4.46
1737 1987 2.957060 CCCGTATGATAGAGGGCGA 58.043 57.895 0.68 0.00 37.07 5.54
1739 1989 1.067776 CCCGTATGATAGAGGGCGAAC 60.068 57.143 0.68 0.00 37.07 3.95
1763 2013 4.504858 CCAGAAATCGCTACCAAACTAGT 58.495 43.478 0.00 0.00 0.00 2.57
1764 2014 5.657474 CCAGAAATCGCTACCAAACTAGTA 58.343 41.667 0.00 0.00 0.00 1.82
1765 2015 5.519206 CCAGAAATCGCTACCAAACTAGTAC 59.481 44.000 0.00 0.00 0.00 2.73
1766 2016 6.331061 CAGAAATCGCTACCAAACTAGTACT 58.669 40.000 0.00 0.00 0.00 2.73
1767 2017 6.472808 CAGAAATCGCTACCAAACTAGTACTC 59.527 42.308 0.00 0.00 0.00 2.59
1768 2018 6.377712 AGAAATCGCTACCAAACTAGTACTCT 59.622 38.462 0.00 0.00 0.00 3.24
1769 2019 7.555554 AGAAATCGCTACCAAACTAGTACTCTA 59.444 37.037 0.00 0.00 0.00 2.43
1770 2020 6.864360 ATCGCTACCAAACTAGTACTCTAG 57.136 41.667 0.00 0.00 46.43 2.43
1878 2128 3.659786 ACAAGCTGCGAGTACAATGTTA 58.340 40.909 0.00 0.00 0.00 2.41
1888 2138 8.090250 TGCGAGTACAATGTTAACACTTTTAT 57.910 30.769 11.22 0.00 0.00 1.40
1896 2146 8.856103 ACAATGTTAACACTTTTATTACCTGCT 58.144 29.630 11.22 0.00 0.00 4.24
1908 2158 6.677781 TTATTACCTGCTGTAAACTCATGC 57.322 37.500 3.99 0.00 42.51 4.06
1949 2199 9.906660 TTATGTAGATGATCAAAACAAACAACC 57.093 29.630 0.00 0.00 0.00 3.77
1950 2200 6.434596 TGTAGATGATCAAAACAAACAACCG 58.565 36.000 0.00 0.00 0.00 4.44
1961 2211 3.028130 ACAAACAACCGAAATTCCCACT 58.972 40.909 0.00 0.00 0.00 4.00
1992 2243 2.572290 ACTAACTTGTGTGGGCAACTC 58.428 47.619 0.00 0.00 0.00 3.01
2004 2255 3.005684 GTGGGCAACTCATGTGAAAATCA 59.994 43.478 0.94 0.00 0.00 2.57
2013 2264 9.297586 CAACTCATGTGAAAATCATATTTGGAG 57.702 33.333 0.94 0.00 28.76 3.86
2019 2270 6.374053 TGTGAAAATCATATTTGGAGCGAAGA 59.626 34.615 0.00 0.00 0.00 2.87
2070 2321 5.648960 TGGATAAAGTAAAACCCTAAAGGCG 59.351 40.000 0.00 0.00 40.58 5.52
2083 2334 4.461198 CCTAAAGGCGATTGGATAAACCT 58.539 43.478 0.00 0.00 39.86 3.50
2084 2335 5.455612 CCCTAAAGGCGATTGGATAAACCTA 60.456 44.000 0.00 0.00 39.86 3.08
2086 2337 6.715264 CCTAAAGGCGATTGGATAAACCTAAT 59.285 38.462 0.00 0.00 39.86 1.73
2087 2338 7.230712 CCTAAAGGCGATTGGATAAACCTAATT 59.769 37.037 0.00 0.00 39.86 1.40
2088 2339 6.635030 AAGGCGATTGGATAAACCTAATTC 57.365 37.500 0.00 0.00 39.86 2.17
2090 2341 6.365520 AGGCGATTGGATAAACCTAATTCTT 58.634 36.000 0.00 0.00 39.86 2.52
2092 2343 6.363473 GCGATTGGATAAACCTAATTCTTCG 58.637 40.000 0.00 0.00 39.86 3.79
2093 2344 6.018180 GCGATTGGATAAACCTAATTCTTCGT 60.018 38.462 0.00 0.00 39.86 3.85
2094 2345 7.345192 CGATTGGATAAACCTAATTCTTCGTG 58.655 38.462 0.00 0.00 39.86 4.35
2095 2346 7.223971 CGATTGGATAAACCTAATTCTTCGTGA 59.776 37.037 0.00 0.00 39.86 4.35
2096 2347 8.801882 ATTGGATAAACCTAATTCTTCGTGAA 57.198 30.769 0.00 0.00 39.86 3.18
2097 2348 8.801882 TTGGATAAACCTAATTCTTCGTGAAT 57.198 30.769 0.00 1.70 42.11 2.57
2098 2349 8.433421 TGGATAAACCTAATTCTTCGTGAATC 57.567 34.615 6.82 0.00 40.77 2.52
2099 2350 8.265055 TGGATAAACCTAATTCTTCGTGAATCT 58.735 33.333 6.82 2.42 40.77 2.40
2100 2351 8.766151 GGATAAACCTAATTCTTCGTGAATCTC 58.234 37.037 6.82 0.00 38.81 2.75
2101 2352 9.535878 GATAAACCTAATTCTTCGTGAATCTCT 57.464 33.333 6.82 0.00 43.99 3.10
2102 2353 7.602517 AAACCTAATTCTTCGTGAATCTCTG 57.397 36.000 6.82 1.51 43.99 3.35
2103 2354 5.112686 ACCTAATTCTTCGTGAATCTCTGC 58.887 41.667 6.82 0.00 43.99 4.26
2104 2355 5.105146 ACCTAATTCTTCGTGAATCTCTGCT 60.105 40.000 6.82 0.00 43.99 4.24
2105 2356 6.096987 ACCTAATTCTTCGTGAATCTCTGCTA 59.903 38.462 6.82 0.00 43.99 3.49
2106 2357 7.151308 CCTAATTCTTCGTGAATCTCTGCTAT 58.849 38.462 6.82 0.00 43.99 2.97
2107 2358 7.655328 CCTAATTCTTCGTGAATCTCTGCTATT 59.345 37.037 6.82 0.00 43.99 1.73
2108 2359 7.856145 AATTCTTCGTGAATCTCTGCTATTT 57.144 32.000 6.82 0.00 43.99 1.40
2109 2360 6.653273 TTCTTCGTGAATCTCTGCTATTTG 57.347 37.500 0.00 0.00 0.00 2.32
2110 2361 5.965922 TCTTCGTGAATCTCTGCTATTTGA 58.034 37.500 0.00 0.00 0.00 2.69
2111 2362 6.398095 TCTTCGTGAATCTCTGCTATTTGAA 58.602 36.000 0.00 0.00 0.00 2.69
2112 2363 7.044181 TCTTCGTGAATCTCTGCTATTTGAAT 58.956 34.615 0.00 0.00 0.00 2.57
2113 2364 8.197439 TCTTCGTGAATCTCTGCTATTTGAATA 58.803 33.333 0.00 0.00 0.00 1.75
2114 2365 8.893219 TTCGTGAATCTCTGCTATTTGAATAT 57.107 30.769 0.00 0.00 0.00 1.28
2115 2366 8.893219 TCGTGAATCTCTGCTATTTGAATATT 57.107 30.769 0.00 0.00 0.00 1.28
2116 2367 8.768019 TCGTGAATCTCTGCTATTTGAATATTG 58.232 33.333 0.00 0.00 0.00 1.90
2117 2368 8.768019 CGTGAATCTCTGCTATTTGAATATTGA 58.232 33.333 0.00 0.00 0.00 2.57
2123 2374 9.617523 TCTCTGCTATTTGAATATTGAACATCA 57.382 29.630 0.00 0.00 0.00 3.07
2131 2382 9.734620 ATTTGAATATTGAACATCATAACCACG 57.265 29.630 0.00 0.00 0.00 4.94
2132 2383 8.499403 TTGAATATTGAACATCATAACCACGA 57.501 30.769 0.00 0.00 0.00 4.35
2133 2384 8.499403 TGAATATTGAACATCATAACCACGAA 57.501 30.769 0.00 0.00 0.00 3.85
2134 2385 9.119418 TGAATATTGAACATCATAACCACGAAT 57.881 29.630 0.00 0.00 0.00 3.34
2137 2388 6.918892 TTGAACATCATAACCACGAATAGG 57.081 37.500 0.00 0.00 0.00 2.57
2138 2389 6.228616 TGAACATCATAACCACGAATAGGA 57.771 37.500 0.00 0.00 0.00 2.94
2139 2390 6.645306 TGAACATCATAACCACGAATAGGAA 58.355 36.000 0.00 0.00 0.00 3.36
2140 2391 7.279615 TGAACATCATAACCACGAATAGGAAT 58.720 34.615 0.00 0.00 0.00 3.01
2141 2392 7.226523 TGAACATCATAACCACGAATAGGAATG 59.773 37.037 0.00 0.00 0.00 2.67
2142 2393 6.826668 ACATCATAACCACGAATAGGAATGA 58.173 36.000 0.00 0.00 36.90 2.57
2143 2394 7.279615 ACATCATAACCACGAATAGGAATGAA 58.720 34.615 0.00 0.00 36.45 2.57
2144 2395 7.773224 ACATCATAACCACGAATAGGAATGAAA 59.227 33.333 0.00 0.00 36.45 2.69
2145 2396 7.548196 TCATAACCACGAATAGGAATGAAAC 57.452 36.000 0.00 0.00 32.88 2.78
2146 2397 4.939509 AACCACGAATAGGAATGAAACG 57.060 40.909 0.00 0.00 0.00 3.60
2147 2398 3.934068 ACCACGAATAGGAATGAAACGT 58.066 40.909 0.00 0.00 0.00 3.99
2148 2399 3.930848 ACCACGAATAGGAATGAAACGTC 59.069 43.478 0.00 0.00 0.00 4.34
2149 2400 3.930229 CCACGAATAGGAATGAAACGTCA 59.070 43.478 0.00 0.00 38.41 4.35
2150 2401 4.390603 CCACGAATAGGAATGAAACGTCAA 59.609 41.667 0.00 0.00 37.30 3.18
2151 2402 5.064707 CCACGAATAGGAATGAAACGTCAAT 59.935 40.000 0.00 0.00 37.30 2.57
2152 2403 6.256975 CCACGAATAGGAATGAAACGTCAATA 59.743 38.462 0.00 0.00 37.30 1.90
2153 2404 7.337718 CACGAATAGGAATGAAACGTCAATAG 58.662 38.462 0.00 0.00 37.30 1.73
2154 2405 6.018994 ACGAATAGGAATGAAACGTCAATAGC 60.019 38.462 0.00 0.00 37.30 2.97
2155 2406 6.201044 CGAATAGGAATGAAACGTCAATAGCT 59.799 38.462 0.00 0.00 37.30 3.32
2156 2407 7.484035 AATAGGAATGAAACGTCAATAGCTC 57.516 36.000 0.00 0.00 37.30 4.09
2157 2408 4.192317 AGGAATGAAACGTCAATAGCTCC 58.808 43.478 0.00 0.00 37.30 4.70
2158 2409 4.080863 AGGAATGAAACGTCAATAGCTCCT 60.081 41.667 0.00 0.00 37.30 3.69
2159 2410 5.128827 AGGAATGAAACGTCAATAGCTCCTA 59.871 40.000 0.00 0.00 37.30 2.94
2160 2411 5.992217 GGAATGAAACGTCAATAGCTCCTAT 59.008 40.000 0.00 0.00 37.30 2.57
2161 2412 7.015292 AGGAATGAAACGTCAATAGCTCCTATA 59.985 37.037 0.00 0.00 37.30 1.31
2162 2413 7.819900 GGAATGAAACGTCAATAGCTCCTATAT 59.180 37.037 0.00 0.00 37.30 0.86
2163 2414 8.539770 AATGAAACGTCAATAGCTCCTATATG 57.460 34.615 0.00 0.00 37.30 1.78
2164 2415 7.284919 TGAAACGTCAATAGCTCCTATATGA 57.715 36.000 0.00 0.00 0.00 2.15
2165 2416 7.722363 TGAAACGTCAATAGCTCCTATATGAA 58.278 34.615 0.00 0.00 0.00 2.57
2166 2417 7.652105 TGAAACGTCAATAGCTCCTATATGAAC 59.348 37.037 0.00 0.00 0.00 3.18
2167 2418 6.902771 ACGTCAATAGCTCCTATATGAACT 57.097 37.500 0.00 0.00 0.00 3.01
2168 2419 7.997773 ACGTCAATAGCTCCTATATGAACTA 57.002 36.000 0.00 0.00 0.00 2.24
2169 2420 7.818642 ACGTCAATAGCTCCTATATGAACTAC 58.181 38.462 0.00 0.00 0.00 2.73
2170 2421 7.666388 ACGTCAATAGCTCCTATATGAACTACT 59.334 37.037 0.00 0.00 0.00 2.57
2171 2422 7.965655 CGTCAATAGCTCCTATATGAACTACTG 59.034 40.741 0.00 0.00 0.00 2.74
2172 2423 8.247562 GTCAATAGCTCCTATATGAACTACTGG 58.752 40.741 0.00 0.00 0.00 4.00
2173 2424 8.170730 TCAATAGCTCCTATATGAACTACTGGA 58.829 37.037 0.00 0.00 0.00 3.86
2174 2425 8.465999 CAATAGCTCCTATATGAACTACTGGAG 58.534 40.741 0.00 0.00 41.61 3.86
2175 2426 6.207509 AGCTCCTATATGAACTACTGGAGA 57.792 41.667 9.93 0.00 41.31 3.71
2176 2427 6.245408 AGCTCCTATATGAACTACTGGAGAG 58.755 44.000 9.93 0.00 41.31 3.20
2177 2428 6.044989 AGCTCCTATATGAACTACTGGAGAGA 59.955 42.308 9.93 0.00 41.31 3.10
2178 2429 6.889722 GCTCCTATATGAACTACTGGAGAGAT 59.110 42.308 9.93 0.00 41.31 2.75
2179 2430 7.067008 GCTCCTATATGAACTACTGGAGAGATC 59.933 44.444 9.93 0.00 41.31 2.75
2180 2431 7.990055 TCCTATATGAACTACTGGAGAGATCA 58.010 38.462 0.00 0.00 0.00 2.92
2181 2432 8.619281 TCCTATATGAACTACTGGAGAGATCAT 58.381 37.037 0.00 3.62 33.85 2.45
2182 2433 9.913310 CCTATATGAACTACTGGAGAGATCATA 57.087 37.037 13.23 13.23 35.39 2.15
2184 2435 6.588719 ATGAACTACTGGAGAGATCATAGC 57.411 41.667 0.00 0.00 30.28 2.97
2185 2436 4.517075 TGAACTACTGGAGAGATCATAGCG 59.483 45.833 0.00 0.00 0.00 4.26
2186 2437 3.417101 ACTACTGGAGAGATCATAGCGG 58.583 50.000 0.00 0.00 0.00 5.52
2187 2438 2.666272 ACTGGAGAGATCATAGCGGA 57.334 50.000 0.00 0.00 0.00 5.54
2188 2439 2.513753 ACTGGAGAGATCATAGCGGAG 58.486 52.381 0.00 0.00 0.00 4.63
2189 2440 2.107378 ACTGGAGAGATCATAGCGGAGA 59.893 50.000 0.00 0.00 0.00 3.71
2190 2441 3.153130 CTGGAGAGATCATAGCGGAGAA 58.847 50.000 0.00 0.00 0.00 2.87
2191 2442 3.153130 TGGAGAGATCATAGCGGAGAAG 58.847 50.000 0.00 0.00 0.00 2.85
2192 2443 3.153919 GGAGAGATCATAGCGGAGAAGT 58.846 50.000 0.00 0.00 0.00 3.01
2193 2444 3.190535 GGAGAGATCATAGCGGAGAAGTC 59.809 52.174 0.00 0.00 0.00 3.01
2194 2445 2.811431 AGAGATCATAGCGGAGAAGTCG 59.189 50.000 0.00 0.00 0.00 4.18
2195 2446 2.809119 GAGATCATAGCGGAGAAGTCGA 59.191 50.000 0.00 0.00 0.00 4.20
2196 2447 2.811431 AGATCATAGCGGAGAAGTCGAG 59.189 50.000 0.00 0.00 0.00 4.04
2197 2448 2.327200 TCATAGCGGAGAAGTCGAGA 57.673 50.000 0.00 0.00 0.00 4.04
2198 2449 1.941294 TCATAGCGGAGAAGTCGAGAC 59.059 52.381 0.00 0.00 0.00 3.36
2199 2450 1.002251 CATAGCGGAGAAGTCGAGACC 60.002 57.143 0.00 0.00 0.00 3.85
2200 2451 0.252479 TAGCGGAGAAGTCGAGACCT 59.748 55.000 0.00 0.00 0.00 3.85
2201 2452 0.252479 AGCGGAGAAGTCGAGACCTA 59.748 55.000 0.00 0.00 0.00 3.08
2202 2453 1.093159 GCGGAGAAGTCGAGACCTAA 58.907 55.000 0.00 0.00 0.00 2.69
2203 2454 1.202166 GCGGAGAAGTCGAGACCTAAC 60.202 57.143 0.00 0.00 0.00 2.34
2204 2455 2.082231 CGGAGAAGTCGAGACCTAACA 58.918 52.381 0.00 0.00 0.00 2.41
2205 2456 2.486982 CGGAGAAGTCGAGACCTAACAA 59.513 50.000 0.00 0.00 0.00 2.83
2206 2457 3.057736 CGGAGAAGTCGAGACCTAACAAA 60.058 47.826 0.00 0.00 0.00 2.83
2207 2458 4.558095 CGGAGAAGTCGAGACCTAACAAAA 60.558 45.833 0.00 0.00 0.00 2.44
2208 2459 5.480205 GGAGAAGTCGAGACCTAACAAAAT 58.520 41.667 0.00 0.00 0.00 1.82
2209 2460 6.624423 CGGAGAAGTCGAGACCTAACAAAATA 60.624 42.308 0.00 0.00 0.00 1.40
2210 2461 7.095270 GGAGAAGTCGAGACCTAACAAAATAA 58.905 38.462 0.00 0.00 0.00 1.40
2211 2462 7.601508 GGAGAAGTCGAGACCTAACAAAATAAA 59.398 37.037 0.00 0.00 0.00 1.40
2212 2463 9.152595 GAGAAGTCGAGACCTAACAAAATAAAT 57.847 33.333 0.00 0.00 0.00 1.40
2219 2470 9.769093 CGAGACCTAACAAAATAAATAAACAGG 57.231 33.333 0.00 0.00 0.00 4.00
2226 2477 8.601845 AACAAAATAAATAAACAGGAAGTGCC 57.398 30.769 0.00 0.00 0.00 5.01
2227 2478 6.866248 ACAAAATAAATAAACAGGAAGTGCCG 59.134 34.615 0.00 0.00 43.43 5.69
2228 2479 4.632538 ATAAATAAACAGGAAGTGCCGC 57.367 40.909 0.00 0.00 43.43 6.53
2229 2480 1.904287 AATAAACAGGAAGTGCCGCA 58.096 45.000 0.00 0.00 43.43 5.69
2230 2481 1.904287 ATAAACAGGAAGTGCCGCAA 58.096 45.000 0.00 0.00 43.43 4.85
2231 2482 1.681538 TAAACAGGAAGTGCCGCAAA 58.318 45.000 0.00 0.00 43.43 3.68
2232 2483 0.820871 AAACAGGAAGTGCCGCAAAA 59.179 45.000 0.00 0.00 43.43 2.44
2233 2484 0.385390 AACAGGAAGTGCCGCAAAAG 59.615 50.000 0.00 0.00 43.43 2.27
2234 2485 0.465460 ACAGGAAGTGCCGCAAAAGA 60.465 50.000 0.00 0.00 43.43 2.52
2235 2486 0.040067 CAGGAAGTGCCGCAAAAGAC 60.040 55.000 0.00 0.00 43.43 3.01
2236 2487 0.179018 AGGAAGTGCCGCAAAAGACT 60.179 50.000 0.00 0.00 43.43 3.24
2237 2488 1.071699 AGGAAGTGCCGCAAAAGACTA 59.928 47.619 0.00 0.00 43.43 2.59
2238 2489 1.464997 GGAAGTGCCGCAAAAGACTAG 59.535 52.381 0.00 0.00 0.00 2.57
2239 2490 1.464997 GAAGTGCCGCAAAAGACTAGG 59.535 52.381 0.00 0.00 0.00 3.02
2240 2491 0.685097 AGTGCCGCAAAAGACTAGGA 59.315 50.000 0.00 0.00 0.00 2.94
2241 2492 1.279271 AGTGCCGCAAAAGACTAGGAT 59.721 47.619 0.00 0.00 0.00 3.24
2242 2493 1.398390 GTGCCGCAAAAGACTAGGATG 59.602 52.381 0.00 0.00 0.00 3.51
2243 2494 1.017387 GCCGCAAAAGACTAGGATGG 58.983 55.000 0.00 0.00 0.00 3.51
2244 2495 1.668419 CCGCAAAAGACTAGGATGGG 58.332 55.000 0.00 0.00 0.00 4.00
2245 2496 1.209504 CCGCAAAAGACTAGGATGGGA 59.790 52.381 0.00 0.00 0.00 4.37
2246 2497 2.355716 CCGCAAAAGACTAGGATGGGAA 60.356 50.000 0.00 0.00 0.00 3.97
2247 2498 3.343617 CGCAAAAGACTAGGATGGGAAA 58.656 45.455 0.00 0.00 0.00 3.13
2248 2499 3.127030 CGCAAAAGACTAGGATGGGAAAC 59.873 47.826 0.00 0.00 0.00 2.78
2249 2500 4.079253 GCAAAAGACTAGGATGGGAAACA 58.921 43.478 0.00 0.00 0.00 2.83
2250 2501 4.522789 GCAAAAGACTAGGATGGGAAACAA 59.477 41.667 0.00 0.00 0.00 2.83
2251 2502 5.010617 GCAAAAGACTAGGATGGGAAACAAA 59.989 40.000 0.00 0.00 0.00 2.83
2252 2503 6.462347 GCAAAAGACTAGGATGGGAAACAAAA 60.462 38.462 0.00 0.00 0.00 2.44
2253 2504 6.650427 AAAGACTAGGATGGGAAACAAAAC 57.350 37.500 0.00 0.00 0.00 2.43
2254 2505 4.324267 AGACTAGGATGGGAAACAAAACG 58.676 43.478 0.00 0.00 0.00 3.60
2255 2506 3.418047 ACTAGGATGGGAAACAAAACGG 58.582 45.455 0.00 0.00 0.00 4.44
2256 2507 2.668144 AGGATGGGAAACAAAACGGA 57.332 45.000 0.00 0.00 0.00 4.69
2257 2508 2.952116 AGGATGGGAAACAAAACGGAA 58.048 42.857 0.00 0.00 0.00 4.30
2258 2509 2.890945 AGGATGGGAAACAAAACGGAAG 59.109 45.455 0.00 0.00 0.00 3.46
2259 2510 2.888414 GGATGGGAAACAAAACGGAAGA 59.112 45.455 0.00 0.00 0.00 2.87
2260 2511 3.057526 GGATGGGAAACAAAACGGAAGAG 60.058 47.826 0.00 0.00 0.00 2.85
2261 2512 3.007473 TGGGAAACAAAACGGAAGAGT 57.993 42.857 0.00 0.00 0.00 3.24
2262 2513 2.685897 TGGGAAACAAAACGGAAGAGTG 59.314 45.455 0.00 0.00 0.00 3.51
2263 2514 2.543031 GGGAAACAAAACGGAAGAGTGC 60.543 50.000 0.00 0.00 0.00 4.40
2264 2515 2.357952 GGAAACAAAACGGAAGAGTGCT 59.642 45.455 0.00 0.00 0.00 4.40
2319 2572 5.043762 TCTCCCCTACCCTAAACAATGAAT 58.956 41.667 0.00 0.00 0.00 2.57
2321 2574 6.855061 TCTCCCCTACCCTAAACAATGAATAT 59.145 38.462 0.00 0.00 0.00 1.28
2322 2575 6.848069 TCCCCTACCCTAAACAATGAATATG 58.152 40.000 0.00 0.00 0.00 1.78
2354 2607 5.179742 AGAGAGTGTACTTCAACTACGACTG 59.820 44.000 0.00 0.00 0.00 3.51
2358 2611 4.023365 GTGTACTTCAACTACGACTGACCT 60.023 45.833 0.00 0.00 0.00 3.85
2360 2613 5.410746 TGTACTTCAACTACGACTGACCTAG 59.589 44.000 0.00 0.00 0.00 3.02
2386 2639 3.985925 AGGTTTGACGAACTTCGATACAC 59.014 43.478 17.97 8.64 43.74 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
48 49 2.251963 TGCAATGACGCTGCAACG 59.748 55.556 8.18 8.18 46.47 4.10
55 56 0.451383 TTGGTATGCTGCAATGACGC 59.549 50.000 6.36 1.12 0.00 5.19
57 58 3.489738 GGATGTTGGTATGCTGCAATGAC 60.490 47.826 6.36 5.27 0.00 3.06
100 101 1.868997 GTGTTCCATGGCTGTGACG 59.131 57.895 6.96 0.00 0.00 4.35
129 130 1.808390 CCGGGATGTTTCGACGACC 60.808 63.158 0.00 0.00 0.00 4.79
146 147 3.512516 GCAAGCTCGGGCATCACC 61.513 66.667 11.40 0.00 41.70 4.02
148 149 2.437180 CTGCAAGCTCGGGCATCA 60.437 61.111 11.40 2.58 39.65 3.07
170 171 1.400494 GAACTGCCACAAACGAACACT 59.600 47.619 0.00 0.00 0.00 3.55
174 175 1.757682 AAGGAACTGCCACAAACGAA 58.242 45.000 0.00 0.00 40.86 3.85
216 217 2.031163 GTGGAGCTCGCCTGTTGT 59.969 61.111 7.83 0.00 0.00 3.32
232 233 2.983930 GAGCTCGCCTGTCGTCTGT 61.984 63.158 0.00 0.00 39.67 3.41
233 234 2.202544 GAGCTCGCCTGTCGTCTG 60.203 66.667 0.00 0.00 39.67 3.51
234 235 3.444805 GGAGCTCGCCTGTCGTCT 61.445 66.667 7.83 0.00 39.67 4.18
235 236 4.838486 CGGAGCTCGCCTGTCGTC 62.838 72.222 7.83 0.00 39.67 4.20
305 306 3.347958 TTTTCAACCTCATGCAACGAC 57.652 42.857 0.00 0.00 0.00 4.34
324 325 2.036733 TCGGTCCATCTCACGAAGTTTT 59.963 45.455 0.00 0.00 41.61 2.43
329 330 0.459899 CCATCGGTCCATCTCACGAA 59.540 55.000 0.00 0.00 38.94 3.85
366 371 4.439057 TCCTTATACCGAACATCACAAGC 58.561 43.478 0.00 0.00 0.00 4.01
373 378 5.394738 TCCTCTGATCCTTATACCGAACAT 58.605 41.667 0.00 0.00 0.00 2.71
405 410 6.591313 TGTTTCCGAAATTTAAAACCTTGC 57.409 33.333 15.31 0.00 32.04 4.01
437 442 4.367166 TGGGTATATTTCAGTGAGGTCCA 58.633 43.478 0.00 0.00 0.00 4.02
438 443 5.367945 TTGGGTATATTTCAGTGAGGTCC 57.632 43.478 0.00 0.00 0.00 4.46
457 462 9.299963 TGAAATATGCGTAATTTCTGAAATTGG 57.700 29.630 29.33 22.85 41.72 3.16
578 585 9.372369 TCGAAACATTTTTACCACTGAAATTTT 57.628 25.926 0.00 0.00 0.00 1.82
586 593 4.038282 GGGGTTCGAAACATTTTTACCACT 59.962 41.667 16.38 0.00 0.00 4.00
590 597 4.979815 CAGTGGGGTTCGAAACATTTTTAC 59.020 41.667 16.38 4.32 0.00 2.01
594 601 2.938838 TCAGTGGGGTTCGAAACATTT 58.061 42.857 16.38 0.00 0.00 2.32
602 609 3.605634 TCACATATTTCAGTGGGGTTCG 58.394 45.455 0.00 0.00 36.43 3.95
682 689 4.134187 CGACACGCGTCATGTGGC 62.134 66.667 9.86 0.00 42.74 5.01
706 713 3.917760 CCCGAGTCATCCGCCTCC 61.918 72.222 0.00 0.00 0.00 4.30
773 780 0.031585 GGTGGGTTCCAAGTTTTCGC 59.968 55.000 0.00 0.00 34.18 4.70
804 811 1.058695 CACGAAAGATTGCGTACGTCC 59.941 52.381 17.90 1.08 38.92 4.79
823 834 4.495844 CGTCTACTGCAAGACATCGATACA 60.496 45.833 16.70 0.00 45.13 2.29
824 835 3.969352 CGTCTACTGCAAGACATCGATAC 59.031 47.826 16.70 0.00 45.13 2.24
851 862 1.176619 CGGGTTTGGAGTTTGGACCC 61.177 60.000 0.00 0.00 45.19 4.46
962 996 2.304901 TATCACGGTCGGCATGGGTG 62.305 60.000 0.00 0.00 0.00 4.61
963 997 2.028125 CTATCACGGTCGGCATGGGT 62.028 60.000 0.00 0.00 0.00 4.51
964 998 1.300931 CTATCACGGTCGGCATGGG 60.301 63.158 0.00 0.00 0.00 4.00
965 999 1.300931 CCTATCACGGTCGGCATGG 60.301 63.158 0.00 0.00 0.00 3.66
966 1000 1.956170 GCCTATCACGGTCGGCATG 60.956 63.158 0.00 0.00 42.06 4.06
1122 1156 2.607750 GTGAGGACTCCCTGGGCA 60.608 66.667 8.22 0.00 44.53 5.36
1131 1165 4.719369 GGCGCGTTCGTGAGGACT 62.719 66.667 8.43 0.00 37.50 3.85
1341 1375 0.980754 TGTACATGGCGATCCCCACT 60.981 55.000 0.00 0.00 37.79 4.00
1453 1492 7.927048 AGACAAGTTGATGTGGTTTAACTAAC 58.073 34.615 10.54 0.00 33.37 2.34
1457 1496 6.019881 GCAAAGACAAGTTGATGTGGTTTAAC 60.020 38.462 10.54 0.00 32.57 2.01
1511 1550 5.594317 AGTAAAGCTGTAATAATTGGCAGGG 59.406 40.000 0.00 0.00 0.00 4.45
1518 1557 9.449719 AGTACAAGCAGTAAAGCTGTAATAATT 57.550 29.630 0.00 0.00 45.89 1.40
1612 1853 6.702716 AAAGAAACTGAACAACCCGAATAA 57.297 33.333 0.00 0.00 0.00 1.40
1640 1881 7.987649 ACAAGTGTTAACTGGAATAACGAAAA 58.012 30.769 7.22 0.00 36.51 2.29
1684 1934 6.300354 ACAGAGCACAGTATTTTACACAAC 57.700 37.500 0.00 0.00 0.00 3.32
1712 1962 2.755655 CCTCTATCATACGGGCAGTAGG 59.244 54.545 3.01 3.01 38.94 3.18
1713 1963 2.755655 CCCTCTATCATACGGGCAGTAG 59.244 54.545 3.49 0.00 38.94 2.57
1737 1987 0.036765 TGGTAGCGATTTCTGGCGTT 60.037 50.000 0.00 0.00 0.00 4.84
1739 1989 1.083489 TTTGGTAGCGATTTCTGGCG 58.917 50.000 0.00 0.00 0.00 5.69
1742 1992 6.331061 AGTACTAGTTTGGTAGCGATTTCTG 58.669 40.000 0.00 0.00 0.00 3.02
1801 2051 8.749354 CCCTAATGGCAACTTTATTTTTCTAGT 58.251 33.333 0.00 0.00 35.84 2.57
1802 2052 8.966868 TCCCTAATGGCAACTTTATTTTTCTAG 58.033 33.333 0.00 0.00 35.84 2.43
1803 2053 8.887264 TCCCTAATGGCAACTTTATTTTTCTA 57.113 30.769 0.00 0.00 35.84 2.10
1810 2060 9.267071 AGTAATTTTCCCTAATGGCAACTTTAT 57.733 29.630 0.00 0.00 35.84 1.40
1813 2063 6.723977 TCAGTAATTTTCCCTAATGGCAACTT 59.276 34.615 0.00 0.00 37.61 2.66
1814 2064 6.252995 TCAGTAATTTTCCCTAATGGCAACT 58.747 36.000 0.00 0.00 37.61 3.16
1854 2104 4.062293 ACATTGTACTCGCAGCTTGTAAA 58.938 39.130 0.00 0.00 0.00 2.01
1856 2106 3.313012 ACATTGTACTCGCAGCTTGTA 57.687 42.857 0.00 0.00 0.00 2.41
1878 2128 8.459911 AGTTTACAGCAGGTAATAAAAGTGTT 57.540 30.769 2.37 0.00 41.43 3.32
1888 2138 4.014569 TGCATGAGTTTACAGCAGGTAA 57.985 40.909 0.00 0.00 40.15 2.85
1925 2175 7.040755 TCGGTTGTTTGTTTTGATCATCTACAT 60.041 33.333 0.00 0.00 0.00 2.29
1928 2178 6.869315 TCGGTTGTTTGTTTTGATCATCTA 57.131 33.333 0.00 0.00 0.00 1.98
1941 2191 3.067461 TCAGTGGGAATTTCGGTTGTTTG 59.933 43.478 0.00 0.00 0.00 2.93
1944 2194 2.649531 TCAGTGGGAATTTCGGTTGT 57.350 45.000 0.00 0.00 0.00 3.32
1949 2199 1.402968 CTGCCATCAGTGGGAATTTCG 59.597 52.381 0.00 0.00 45.98 3.46
1961 2211 4.754618 CACACAAGTTAGTTACTGCCATCA 59.245 41.667 0.00 0.00 37.12 3.07
1973 2223 2.571212 TGAGTTGCCCACACAAGTTAG 58.429 47.619 0.00 0.00 33.35 2.34
1992 2243 6.497437 TCGCTCCAAATATGATTTTCACATG 58.503 36.000 0.00 0.00 0.00 3.21
2013 2264 1.940613 ACTTGTGTGGAGTTTCTTCGC 59.059 47.619 0.00 0.00 0.00 4.70
2019 2270 6.068010 TCAATCCAATACTTGTGTGGAGTTT 58.932 36.000 11.71 2.96 44.45 2.66
2026 2277 5.630121 TCCAGTTCAATCCAATACTTGTGT 58.370 37.500 0.00 0.00 0.00 3.72
2027 2278 6.764308 ATCCAGTTCAATCCAATACTTGTG 57.236 37.500 0.00 0.00 0.00 3.33
2029 2280 8.960591 ACTTTATCCAGTTCAATCCAATACTTG 58.039 33.333 0.00 0.00 0.00 3.16
2045 2296 6.183360 CGCCTTTAGGGTTTTACTTTATCCAG 60.183 42.308 0.00 0.00 37.43 3.86
2051 2302 5.047590 CCAATCGCCTTTAGGGTTTTACTTT 60.048 40.000 0.00 0.00 37.43 2.66
2052 2303 4.461431 CCAATCGCCTTTAGGGTTTTACTT 59.539 41.667 0.00 0.00 37.43 2.24
2070 2321 8.433421 TCACGAAGAATTAGGTTTATCCAATC 57.567 34.615 0.00 0.00 39.02 2.67
2083 2334 8.820933 CAAATAGCAGAGATTCACGAAGAATTA 58.179 33.333 8.74 0.00 46.76 1.40
2084 2335 7.550551 TCAAATAGCAGAGATTCACGAAGAATT 59.449 33.333 8.74 0.00 46.76 2.17
2086 2337 6.398095 TCAAATAGCAGAGATTCACGAAGAA 58.602 36.000 0.00 0.00 41.28 2.52
2087 2338 5.965922 TCAAATAGCAGAGATTCACGAAGA 58.034 37.500 0.00 0.00 0.00 2.87
2088 2339 6.653273 TTCAAATAGCAGAGATTCACGAAG 57.347 37.500 0.00 0.00 0.00 3.79
2090 2341 8.768019 CAATATTCAAATAGCAGAGATTCACGA 58.232 33.333 0.00 0.00 0.00 4.35
2097 2348 9.617523 TGATGTTCAATATTCAAATAGCAGAGA 57.382 29.630 0.00 0.00 0.00 3.10
2105 2356 9.734620 CGTGGTTATGATGTTCAATATTCAAAT 57.265 29.630 0.00 0.00 0.00 2.32
2106 2357 8.951243 TCGTGGTTATGATGTTCAATATTCAAA 58.049 29.630 0.00 0.00 0.00 2.69
2107 2358 8.499403 TCGTGGTTATGATGTTCAATATTCAA 57.501 30.769 0.00 0.00 0.00 2.69
2108 2359 8.499403 TTCGTGGTTATGATGTTCAATATTCA 57.501 30.769 0.00 0.00 0.00 2.57
2111 2362 9.219603 CCTATTCGTGGTTATGATGTTCAATAT 57.780 33.333 0.00 0.00 0.00 1.28
2112 2363 8.425703 TCCTATTCGTGGTTATGATGTTCAATA 58.574 33.333 0.00 0.00 0.00 1.90
2113 2364 7.279615 TCCTATTCGTGGTTATGATGTTCAAT 58.720 34.615 0.00 0.00 0.00 2.57
2114 2365 6.645306 TCCTATTCGTGGTTATGATGTTCAA 58.355 36.000 0.00 0.00 0.00 2.69
2115 2366 6.228616 TCCTATTCGTGGTTATGATGTTCA 57.771 37.500 0.00 0.00 0.00 3.18
2116 2367 7.441157 TCATTCCTATTCGTGGTTATGATGTTC 59.559 37.037 0.00 0.00 0.00 3.18
2117 2368 7.279615 TCATTCCTATTCGTGGTTATGATGTT 58.720 34.615 0.00 0.00 0.00 2.71
2118 2369 6.826668 TCATTCCTATTCGTGGTTATGATGT 58.173 36.000 0.00 0.00 0.00 3.06
2119 2370 7.728847 TTCATTCCTATTCGTGGTTATGATG 57.271 36.000 0.00 0.00 31.95 3.07
2120 2371 7.042051 CGTTTCATTCCTATTCGTGGTTATGAT 60.042 37.037 0.00 0.00 31.95 2.45
2121 2372 6.256975 CGTTTCATTCCTATTCGTGGTTATGA 59.743 38.462 0.00 0.00 0.00 2.15
2122 2373 6.036735 ACGTTTCATTCCTATTCGTGGTTATG 59.963 38.462 0.00 0.00 0.00 1.90
2123 2374 6.110707 ACGTTTCATTCCTATTCGTGGTTAT 58.889 36.000 0.00 0.00 0.00 1.89
2124 2375 5.481105 ACGTTTCATTCCTATTCGTGGTTA 58.519 37.500 0.00 0.00 0.00 2.85
2125 2376 4.320870 ACGTTTCATTCCTATTCGTGGTT 58.679 39.130 0.00 0.00 0.00 3.67
2126 2377 3.930848 GACGTTTCATTCCTATTCGTGGT 59.069 43.478 0.00 0.00 0.00 4.16
2127 2378 3.930229 TGACGTTTCATTCCTATTCGTGG 59.070 43.478 0.00 0.00 0.00 4.94
2128 2379 5.524511 TTGACGTTTCATTCCTATTCGTG 57.475 39.130 0.00 0.00 0.00 4.35
2129 2380 6.018994 GCTATTGACGTTTCATTCCTATTCGT 60.019 38.462 0.00 0.00 0.00 3.85
2130 2381 6.201044 AGCTATTGACGTTTCATTCCTATTCG 59.799 38.462 0.00 0.00 0.00 3.34
2131 2382 7.307455 GGAGCTATTGACGTTTCATTCCTATTC 60.307 40.741 0.00 0.00 0.00 1.75
2132 2383 6.483640 GGAGCTATTGACGTTTCATTCCTATT 59.516 38.462 0.00 0.00 0.00 1.73
2133 2384 5.992217 GGAGCTATTGACGTTTCATTCCTAT 59.008 40.000 0.00 0.00 0.00 2.57
2134 2385 5.128827 AGGAGCTATTGACGTTTCATTCCTA 59.871 40.000 0.00 0.00 0.00 2.94
2135 2386 4.080863 AGGAGCTATTGACGTTTCATTCCT 60.081 41.667 0.00 0.00 0.00 3.36
2136 2387 4.192317 AGGAGCTATTGACGTTTCATTCC 58.808 43.478 0.00 0.00 0.00 3.01
2137 2388 8.651588 CATATAGGAGCTATTGACGTTTCATTC 58.348 37.037 0.00 0.00 0.00 2.67
2138 2389 8.367911 TCATATAGGAGCTATTGACGTTTCATT 58.632 33.333 0.00 0.00 0.00 2.57
2139 2390 7.896811 TCATATAGGAGCTATTGACGTTTCAT 58.103 34.615 0.00 0.00 0.00 2.57
2140 2391 7.284919 TCATATAGGAGCTATTGACGTTTCA 57.715 36.000 0.00 0.00 0.00 2.69
2141 2392 7.868415 AGTTCATATAGGAGCTATTGACGTTTC 59.132 37.037 1.59 0.00 0.00 2.78
2142 2393 7.727181 AGTTCATATAGGAGCTATTGACGTTT 58.273 34.615 1.59 0.00 0.00 3.60
2143 2394 7.291411 AGTTCATATAGGAGCTATTGACGTT 57.709 36.000 1.59 0.00 0.00 3.99
2144 2395 6.902771 AGTTCATATAGGAGCTATTGACGT 57.097 37.500 1.59 0.00 0.00 4.34
2145 2396 7.965655 CAGTAGTTCATATAGGAGCTATTGACG 59.034 40.741 21.19 2.91 39.20 4.35
2146 2397 8.247562 CCAGTAGTTCATATAGGAGCTATTGAC 58.752 40.741 24.92 12.29 39.20 3.18
2147 2398 8.170730 TCCAGTAGTTCATATAGGAGCTATTGA 58.829 37.037 24.92 14.70 39.20 2.57
2148 2399 8.354711 TCCAGTAGTTCATATAGGAGCTATTG 57.645 38.462 19.75 19.75 37.75 1.90
2149 2400 8.394822 TCTCCAGTAGTTCATATAGGAGCTATT 58.605 37.037 13.06 7.24 37.28 1.73
2150 2401 7.934313 TCTCCAGTAGTTCATATAGGAGCTAT 58.066 38.462 13.06 2.11 37.28 2.97
2151 2402 7.237887 TCTCTCCAGTAGTTCATATAGGAGCTA 59.762 40.741 6.85 6.85 37.28 3.32
2152 2403 6.044989 TCTCTCCAGTAGTTCATATAGGAGCT 59.955 42.308 8.80 8.80 37.28 4.09
2153 2404 6.242396 TCTCTCCAGTAGTTCATATAGGAGC 58.758 44.000 0.00 0.00 37.28 4.70
2154 2405 8.106462 TGATCTCTCCAGTAGTTCATATAGGAG 58.894 40.741 0.00 0.00 38.06 3.69
2155 2406 7.990055 TGATCTCTCCAGTAGTTCATATAGGA 58.010 38.462 0.00 0.00 0.00 2.94
2156 2407 8.821686 ATGATCTCTCCAGTAGTTCATATAGG 57.178 38.462 0.00 0.00 0.00 2.57
2158 2409 9.402320 GCTATGATCTCTCCAGTAGTTCATATA 57.598 37.037 0.00 0.00 30.10 0.86
2159 2410 7.066887 CGCTATGATCTCTCCAGTAGTTCATAT 59.933 40.741 0.00 0.00 30.10 1.78
2160 2411 6.372937 CGCTATGATCTCTCCAGTAGTTCATA 59.627 42.308 0.00 0.00 0.00 2.15
2161 2412 5.182950 CGCTATGATCTCTCCAGTAGTTCAT 59.817 44.000 0.00 0.00 0.00 2.57
2162 2413 4.517075 CGCTATGATCTCTCCAGTAGTTCA 59.483 45.833 0.00 0.00 0.00 3.18
2163 2414 4.083003 CCGCTATGATCTCTCCAGTAGTTC 60.083 50.000 0.00 0.00 0.00 3.01
2164 2415 3.823873 CCGCTATGATCTCTCCAGTAGTT 59.176 47.826 0.00 0.00 0.00 2.24
2165 2416 3.073209 TCCGCTATGATCTCTCCAGTAGT 59.927 47.826 0.00 0.00 0.00 2.73
2166 2417 3.680490 TCCGCTATGATCTCTCCAGTAG 58.320 50.000 0.00 0.00 0.00 2.57
2167 2418 3.328050 TCTCCGCTATGATCTCTCCAGTA 59.672 47.826 0.00 0.00 0.00 2.74
2168 2419 2.107378 TCTCCGCTATGATCTCTCCAGT 59.893 50.000 0.00 0.00 0.00 4.00
2169 2420 2.789213 TCTCCGCTATGATCTCTCCAG 58.211 52.381 0.00 0.00 0.00 3.86
2170 2421 2.959465 TCTCCGCTATGATCTCTCCA 57.041 50.000 0.00 0.00 0.00 3.86
2171 2422 3.153919 ACTTCTCCGCTATGATCTCTCC 58.846 50.000 0.00 0.00 0.00 3.71
2172 2423 3.120338 CGACTTCTCCGCTATGATCTCTC 60.120 52.174 0.00 0.00 0.00 3.20
2173 2424 2.811431 CGACTTCTCCGCTATGATCTCT 59.189 50.000 0.00 0.00 0.00 3.10
2174 2425 2.809119 TCGACTTCTCCGCTATGATCTC 59.191 50.000 0.00 0.00 0.00 2.75
2175 2426 2.811431 CTCGACTTCTCCGCTATGATCT 59.189 50.000 0.00 0.00 0.00 2.75
2176 2427 2.809119 TCTCGACTTCTCCGCTATGATC 59.191 50.000 0.00 0.00 0.00 2.92
2177 2428 2.550606 GTCTCGACTTCTCCGCTATGAT 59.449 50.000 0.00 0.00 0.00 2.45
2178 2429 1.941294 GTCTCGACTTCTCCGCTATGA 59.059 52.381 0.00 0.00 0.00 2.15
2179 2430 1.002251 GGTCTCGACTTCTCCGCTATG 60.002 57.143 0.00 0.00 0.00 2.23
2180 2431 1.134037 AGGTCTCGACTTCTCCGCTAT 60.134 52.381 0.00 0.00 0.00 2.97
2181 2432 0.252479 AGGTCTCGACTTCTCCGCTA 59.748 55.000 0.00 0.00 0.00 4.26
2182 2433 0.252479 TAGGTCTCGACTTCTCCGCT 59.748 55.000 0.00 0.00 0.00 5.52
2183 2434 1.093159 TTAGGTCTCGACTTCTCCGC 58.907 55.000 0.00 0.00 0.00 5.54
2184 2435 2.082231 TGTTAGGTCTCGACTTCTCCG 58.918 52.381 0.00 0.00 0.00 4.63
2185 2436 4.516365 TTTGTTAGGTCTCGACTTCTCC 57.484 45.455 0.00 0.00 0.00 3.71
2186 2437 8.530269 TTTATTTTGTTAGGTCTCGACTTCTC 57.470 34.615 0.00 0.00 0.00 2.87
2193 2444 9.769093 CCTGTTTATTTATTTTGTTAGGTCTCG 57.231 33.333 0.00 0.00 0.00 4.04
2200 2451 9.699703 GGCACTTCCTGTTTATTTATTTTGTTA 57.300 29.630 0.00 0.00 0.00 2.41
2201 2452 7.383843 CGGCACTTCCTGTTTATTTATTTTGTT 59.616 33.333 0.00 0.00 0.00 2.83
2202 2453 6.866248 CGGCACTTCCTGTTTATTTATTTTGT 59.134 34.615 0.00 0.00 0.00 2.83
2203 2454 6.183360 GCGGCACTTCCTGTTTATTTATTTTG 60.183 38.462 0.00 0.00 0.00 2.44
2204 2455 5.867174 GCGGCACTTCCTGTTTATTTATTTT 59.133 36.000 0.00 0.00 0.00 1.82
2205 2456 5.047660 TGCGGCACTTCCTGTTTATTTATTT 60.048 36.000 0.00 0.00 0.00 1.40
2206 2457 4.461081 TGCGGCACTTCCTGTTTATTTATT 59.539 37.500 0.00 0.00 0.00 1.40
2207 2458 4.013728 TGCGGCACTTCCTGTTTATTTAT 58.986 39.130 0.00 0.00 0.00 1.40
2208 2459 3.413327 TGCGGCACTTCCTGTTTATTTA 58.587 40.909 0.00 0.00 0.00 1.40
2209 2460 2.235016 TGCGGCACTTCCTGTTTATTT 58.765 42.857 0.00 0.00 0.00 1.40
2210 2461 1.904287 TGCGGCACTTCCTGTTTATT 58.096 45.000 0.00 0.00 0.00 1.40
2211 2462 1.904287 TTGCGGCACTTCCTGTTTAT 58.096 45.000 0.05 0.00 0.00 1.40
2212 2463 1.681538 TTTGCGGCACTTCCTGTTTA 58.318 45.000 0.05 0.00 0.00 2.01
2213 2464 0.820871 TTTTGCGGCACTTCCTGTTT 59.179 45.000 0.05 0.00 0.00 2.83
2214 2465 0.385390 CTTTTGCGGCACTTCCTGTT 59.615 50.000 0.05 0.00 0.00 3.16
2215 2466 0.465460 TCTTTTGCGGCACTTCCTGT 60.465 50.000 0.05 0.00 0.00 4.00
2216 2467 0.040067 GTCTTTTGCGGCACTTCCTG 60.040 55.000 0.05 0.00 0.00 3.86
2217 2468 0.179018 AGTCTTTTGCGGCACTTCCT 60.179 50.000 0.05 0.00 0.00 3.36
2218 2469 1.464997 CTAGTCTTTTGCGGCACTTCC 59.535 52.381 0.05 0.00 0.00 3.46
2219 2470 1.464997 CCTAGTCTTTTGCGGCACTTC 59.535 52.381 0.05 0.00 0.00 3.01
2220 2471 1.071699 TCCTAGTCTTTTGCGGCACTT 59.928 47.619 0.05 0.00 0.00 3.16
2221 2472 0.685097 TCCTAGTCTTTTGCGGCACT 59.315 50.000 0.05 0.00 0.00 4.40
2222 2473 1.398390 CATCCTAGTCTTTTGCGGCAC 59.602 52.381 0.05 0.00 0.00 5.01
2223 2474 1.678728 CCATCCTAGTCTTTTGCGGCA 60.679 52.381 0.00 0.00 0.00 5.69
2224 2475 1.017387 CCATCCTAGTCTTTTGCGGC 58.983 55.000 0.00 0.00 0.00 6.53
2225 2476 1.209504 TCCCATCCTAGTCTTTTGCGG 59.790 52.381 0.00 0.00 0.00 5.69
2226 2477 2.691409 TCCCATCCTAGTCTTTTGCG 57.309 50.000 0.00 0.00 0.00 4.85
2227 2478 4.079253 TGTTTCCCATCCTAGTCTTTTGC 58.921 43.478 0.00 0.00 0.00 3.68
2228 2479 6.648879 TTTGTTTCCCATCCTAGTCTTTTG 57.351 37.500 0.00 0.00 0.00 2.44
2229 2480 6.238925 CGTTTTGTTTCCCATCCTAGTCTTTT 60.239 38.462 0.00 0.00 0.00 2.27
2230 2481 5.240844 CGTTTTGTTTCCCATCCTAGTCTTT 59.759 40.000 0.00 0.00 0.00 2.52
2231 2482 4.760204 CGTTTTGTTTCCCATCCTAGTCTT 59.240 41.667 0.00 0.00 0.00 3.01
2232 2483 4.324267 CGTTTTGTTTCCCATCCTAGTCT 58.676 43.478 0.00 0.00 0.00 3.24
2233 2484 3.439129 CCGTTTTGTTTCCCATCCTAGTC 59.561 47.826 0.00 0.00 0.00 2.59
2234 2485 3.073356 TCCGTTTTGTTTCCCATCCTAGT 59.927 43.478 0.00 0.00 0.00 2.57
2235 2486 3.681593 TCCGTTTTGTTTCCCATCCTAG 58.318 45.455 0.00 0.00 0.00 3.02
2236 2487 3.791953 TCCGTTTTGTTTCCCATCCTA 57.208 42.857 0.00 0.00 0.00 2.94
2237 2488 2.668144 TCCGTTTTGTTTCCCATCCT 57.332 45.000 0.00 0.00 0.00 3.24
2238 2489 2.888414 TCTTCCGTTTTGTTTCCCATCC 59.112 45.455 0.00 0.00 0.00 3.51
2239 2490 3.568430 ACTCTTCCGTTTTGTTTCCCATC 59.432 43.478 0.00 0.00 0.00 3.51
2240 2491 3.317993 CACTCTTCCGTTTTGTTTCCCAT 59.682 43.478 0.00 0.00 0.00 4.00
2241 2492 2.685897 CACTCTTCCGTTTTGTTTCCCA 59.314 45.455 0.00 0.00 0.00 4.37
2242 2493 2.543031 GCACTCTTCCGTTTTGTTTCCC 60.543 50.000 0.00 0.00 0.00 3.97
2243 2494 2.357952 AGCACTCTTCCGTTTTGTTTCC 59.642 45.455 0.00 0.00 0.00 3.13
2244 2495 3.548214 GGAGCACTCTTCCGTTTTGTTTC 60.548 47.826 0.00 0.00 0.00 2.78
2245 2496 2.357952 GGAGCACTCTTCCGTTTTGTTT 59.642 45.455 0.00 0.00 0.00 2.83
2246 2497 1.947456 GGAGCACTCTTCCGTTTTGTT 59.053 47.619 0.00 0.00 0.00 2.83
2247 2498 1.134220 TGGAGCACTCTTCCGTTTTGT 60.134 47.619 0.00 0.00 0.00 2.83
2248 2499 1.593196 TGGAGCACTCTTCCGTTTTG 58.407 50.000 0.00 0.00 0.00 2.44
2249 2500 2.341846 TTGGAGCACTCTTCCGTTTT 57.658 45.000 0.00 0.00 0.00 2.43
2250 2501 2.341846 TTTGGAGCACTCTTCCGTTT 57.658 45.000 0.00 0.00 0.00 3.60
2251 2502 2.222027 CTTTTGGAGCACTCTTCCGTT 58.778 47.619 0.00 0.00 0.00 4.44
2252 2503 1.884235 CTTTTGGAGCACTCTTCCGT 58.116 50.000 0.00 0.00 0.00 4.69
2263 2514 5.581126 TGGCAAATATAGTGCTTTTGGAG 57.419 39.130 10.27 0.00 41.88 3.86
2264 2515 5.655974 TCATGGCAAATATAGTGCTTTTGGA 59.344 36.000 10.27 1.57 41.88 3.53
2319 2572 5.984695 AGTACACTCTCTTCTGCAACATA 57.015 39.130 0.00 0.00 0.00 2.29
2321 2574 4.099419 TGAAGTACACTCTCTTCTGCAACA 59.901 41.667 0.00 0.00 40.20 3.33
2322 2575 4.621991 TGAAGTACACTCTCTTCTGCAAC 58.378 43.478 0.00 0.00 40.20 4.17
2358 2611 4.276678 TCGAAGTTCGTCAAACCTCTTCTA 59.723 41.667 23.67 0.00 41.35 2.10
2360 2613 3.378339 TCGAAGTTCGTCAAACCTCTTC 58.622 45.455 23.67 0.00 41.35 2.87


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

AutoCloner maintained by Alex Coulton.