Multiple sequence alignment - TraesCS2D01G413300

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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 TraesCS2D01G413300 chr2D 100.000 2312 0 0 1 2312 527805545 527803234 0.000000e+00 4270
1 TraesCS2D01G413300 chr2D 88.310 1018 74 24 685 1694 528994421 528995401 0.000000e+00 1179
2 TraesCS2D01G413300 chr2D 84.444 1080 116 34 743 1783 527648433 527647367 0.000000e+00 1016
3 TraesCS2D01G413300 chr2D 84.211 969 91 33 745 1690 527684526 527683597 0.000000e+00 885
4 TraesCS2D01G413300 chr2D 96.479 284 10 0 2029 2312 527783324 527783041 9.670000e-129 470
5 TraesCS2D01G413300 chr2D 93.033 244 16 1 1781 2023 527683255 527683012 2.830000e-94 355
6 TraesCS2D01G413300 chr2B 89.366 1025 69 14 685 1690 627317433 627318436 0.000000e+00 1253
7 TraesCS2D01G413300 chr2B 90.363 965 57 21 742 1690 625239184 625238240 0.000000e+00 1234
8 TraesCS2D01G413300 chr2B 91.281 757 45 11 713 1451 627322844 627323597 0.000000e+00 1013
9 TraesCS2D01G413300 chr2B 83.868 1060 129 29 743 1778 625009297 625008256 0.000000e+00 972
10 TraesCS2D01G413300 chr2B 81.381 478 78 5 84 557 627320792 627321262 1.680000e-101 379
11 TraesCS2D01G413300 chr2B 78.219 629 105 21 1 627 625262020 625261422 7.800000e-100 374
12 TraesCS2D01G413300 chr2B 89.370 254 18 3 1772 2023 625238202 625237956 6.200000e-81 311
13 TraesCS2D01G413300 chr2B 93.130 131 9 0 1765 1895 627318467 627318597 2.340000e-45 193
14 TraesCS2D01G413300 chr2A 88.111 1043 66 25 676 1694 673419652 673420660 0.000000e+00 1186
15 TraesCS2D01G413300 chr2A 87.282 1030 82 14 676 1668 672746582 672745565 0.000000e+00 1131
16 TraesCS2D01G413300 chr2A 88.235 969 70 15 685 1624 673417494 673418447 0.000000e+00 1118
17 TraesCS2D01G413300 chr2A 92.632 285 21 0 2028 2312 775196996 775197280 5.950000e-111 411
18 TraesCS2D01G413300 chr2A 88.115 244 26 2 1617 1860 672745685 672745445 1.050000e-73 287
19 TraesCS2D01G413300 chr2A 91.304 115 8 2 514 627 672750242 672750129 3.080000e-34 156
20 TraesCS2D01G413300 chr2A 86.713 143 10 4 1857 1996 672745420 672745284 1.430000e-32 150
21 TraesCS2D01G413300 chr7D 93.250 637 34 5 684 1312 134467363 134466728 0.000000e+00 929
22 TraesCS2D01G413300 chr7D 93.310 284 19 0 2029 2312 593499900 593500183 9.880000e-114 420
23 TraesCS2D01G413300 chr4D 94.014 284 16 1 2030 2312 488248561 488248278 1.640000e-116 429
24 TraesCS2D01G413300 chr6B 93.640 283 18 0 2030 2312 54208518 54208236 7.640000e-115 424
25 TraesCS2D01G413300 chr6D 93.031 287 17 1 2029 2312 67351839 67351553 1.280000e-112 416
26 TraesCS2D01G413300 chr4A 92.933 283 20 0 2030 2312 31427373 31427091 1.650000e-111 412
27 TraesCS2D01G413300 chr6A 92.606 284 21 0 2029 2312 604611477 604611194 2.140000e-110 409
28 TraesCS2D01G413300 chr5A 92.606 284 21 0 2029 2312 312234985 312234702 2.140000e-110 409


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 TraesCS2D01G413300 chr2D 527803234 527805545 2311 True 4270.0 4270 100.0000 1 2312 1 chr2D.!!$R3 2311
1 TraesCS2D01G413300 chr2D 528994421 528995401 980 False 1179.0 1179 88.3100 685 1694 1 chr2D.!!$F1 1009
2 TraesCS2D01G413300 chr2D 527647367 527648433 1066 True 1016.0 1016 84.4440 743 1783 1 chr2D.!!$R1 1040
3 TraesCS2D01G413300 chr2D 527683012 527684526 1514 True 620.0 885 88.6220 745 2023 2 chr2D.!!$R4 1278
4 TraesCS2D01G413300 chr2B 625008256 625009297 1041 True 972.0 972 83.8680 743 1778 1 chr2B.!!$R1 1035
5 TraesCS2D01G413300 chr2B 625237956 625239184 1228 True 772.5 1234 89.8665 742 2023 2 chr2B.!!$R3 1281
6 TraesCS2D01G413300 chr2B 627317433 627323597 6164 False 709.5 1253 88.7895 84 1895 4 chr2B.!!$F1 1811
7 TraesCS2D01G413300 chr2B 625261422 625262020 598 True 374.0 374 78.2190 1 627 1 chr2B.!!$R2 626
8 TraesCS2D01G413300 chr2A 673417494 673420660 3166 False 1152.0 1186 88.1730 676 1694 2 chr2A.!!$F2 1018
9 TraesCS2D01G413300 chr2A 672745284 672750242 4958 True 431.0 1131 88.3535 514 1996 4 chr2A.!!$R1 1482
10 TraesCS2D01G413300 chr7D 134466728 134467363 635 True 929.0 929 93.2500 684 1312 1 chr7D.!!$R1 628

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
652 655 0.029834 CAAGCAGCCCACATTATCGC 59.97 55.0 0.0 0.0 0.0 4.58 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2182 6868 0.03563 ACCTCTGCTTCCACTGCATC 60.036 55.0 0.0 0.0 39.86 3.91 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
29 30 2.675423 CCTCCGAGACCACCGTCA 60.675 66.667 0.00 0.00 41.87 4.35
43 44 1.440476 CGTCATTACCCCCTCCGTC 59.560 63.158 0.00 0.00 0.00 4.79
47 48 0.179092 CATTACCCCCTCCGTCGTTC 60.179 60.000 0.00 0.00 0.00 3.95
53 54 4.430765 CCTCCGTCGTTCCCACCG 62.431 72.222 0.00 0.00 0.00 4.94
69 70 3.195002 CGCCGCCATCATTGTCGT 61.195 61.111 0.00 0.00 0.00 4.34
70 71 2.404789 GCCGCCATCATTGTCGTG 59.595 61.111 0.00 0.00 0.00 4.35
72 73 1.449423 CCGCCATCATTGTCGTGGA 60.449 57.895 8.84 0.00 34.94 4.02
75 76 0.107703 GCCATCATTGTCGTGGAGGA 60.108 55.000 8.84 0.00 34.94 3.71
78 79 1.482182 CATCATTGTCGTGGAGGAGGA 59.518 52.381 0.00 0.00 0.00 3.71
86 87 1.831652 CGTGGAGGAGGAAAGCCACT 61.832 60.000 0.00 0.00 46.57 4.00
92 93 0.256177 GGAGGAAAGCCACTAAGGGG 59.744 60.000 0.00 0.00 38.09 4.79
93 94 0.992695 GAGGAAAGCCACTAAGGGGT 59.007 55.000 0.00 0.00 41.27 4.95
96 97 1.002502 AAAGCCACTAAGGGGTCGC 60.003 57.895 0.00 0.00 37.78 5.19
98 99 1.562672 AAGCCACTAAGGGGTCGCAT 61.563 55.000 0.00 0.00 37.78 4.73
101 102 0.251916 CCACTAAGGGGTCGCATCAA 59.748 55.000 0.00 0.00 0.00 2.57
104 105 0.251916 CTAAGGGGTCGCATCAACCA 59.748 55.000 0.00 0.00 38.62 3.67
111 112 1.269448 GGTCGCATCAACCATGTTTGT 59.731 47.619 2.68 0.00 36.75 2.83
120 121 4.000325 TCAACCATGTTTGTCCGTCTATG 59.000 43.478 2.68 0.00 0.00 2.23
122 123 1.327460 CCATGTTTGTCCGTCTATGCG 59.673 52.381 0.00 0.00 0.00 4.73
154 155 4.189188 CCGCTTGGCTGCTGCATC 62.189 66.667 17.89 0.00 41.91 3.91
156 157 4.189188 GCTTGGCTGCTGCATCCG 62.189 66.667 16.84 5.65 41.91 4.18
172 173 3.545481 CGCCTGACACATCGCGTC 61.545 66.667 5.77 0.00 39.78 5.19
174 175 2.573869 CCTGACACATCGCGTCCT 59.426 61.111 5.77 0.00 32.15 3.85
178 179 0.388520 TGACACATCGCGTCCTTCTG 60.389 55.000 5.77 0.00 32.15 3.02
184 185 4.124351 CGCGTCCTTCTGGCGGTA 62.124 66.667 0.00 0.00 45.69 4.02
186 187 2.098831 GCGTCCTTCTGGCGGTAAC 61.099 63.158 0.00 0.00 34.86 2.50
187 188 1.590147 CGTCCTTCTGGCGGTAACT 59.410 57.895 0.00 0.00 32.18 2.24
191 192 0.320374 CCTTCTGGCGGTAACTGTCA 59.680 55.000 0.00 0.00 0.00 3.58
245 247 3.812019 CGAGGGCACTAGCGACGT 61.812 66.667 0.00 0.00 43.41 4.34
246 248 2.202623 GAGGGCACTAGCGACGTG 60.203 66.667 0.00 0.00 43.41 4.49
258 260 0.109226 GCGACGTGCTTAGACTCCTT 60.109 55.000 0.00 0.00 41.73 3.36
260 262 1.199327 CGACGTGCTTAGACTCCTTCA 59.801 52.381 0.00 0.00 0.00 3.02
263 265 2.628657 ACGTGCTTAGACTCCTTCAACT 59.371 45.455 0.00 0.00 0.00 3.16
264 266 3.069729 ACGTGCTTAGACTCCTTCAACTT 59.930 43.478 0.00 0.00 0.00 2.66
266 268 3.675698 GTGCTTAGACTCCTTCAACTTCG 59.324 47.826 0.00 0.00 0.00 3.79
270 272 3.033368 AGACTCCTTCAACTTCGCTTC 57.967 47.619 0.00 0.00 0.00 3.86
271 273 2.070028 GACTCCTTCAACTTCGCTTCC 58.930 52.381 0.00 0.00 0.00 3.46
273 275 2.158813 ACTCCTTCAACTTCGCTTCCAA 60.159 45.455 0.00 0.00 0.00 3.53
277 279 2.169832 TCAACTTCGCTTCCAAGAGG 57.830 50.000 0.00 0.00 0.00 3.69
289 291 1.519455 CAAGAGGTGGTCGCCGATC 60.519 63.158 0.00 0.00 0.00 3.69
290 292 2.722201 AAGAGGTGGTCGCCGATCC 61.722 63.158 0.00 0.00 0.00 3.36
317 319 1.686355 ACGAATGGTGGACTTTTGCA 58.314 45.000 0.00 0.00 0.00 4.08
318 320 1.336755 ACGAATGGTGGACTTTTGCAC 59.663 47.619 0.00 0.00 43.17 4.57
319 321 1.662876 CGAATGGTGGACTTTTGCACG 60.663 52.381 0.00 0.00 44.79 5.34
323 325 1.299089 GTGGACTTTTGCACGGTGC 60.299 57.895 25.55 25.55 45.29 5.01
325 327 0.179043 TGGACTTTTGCACGGTGCTA 60.179 50.000 30.81 22.57 45.31 3.49
329 331 0.238289 CTTTTGCACGGTGCTACTGG 59.762 55.000 30.81 14.82 45.31 4.00
366 368 2.572104 AGGTGGAGTACATGGGAAGAAC 59.428 50.000 0.00 0.00 0.00 3.01
367 369 2.618053 GTGGAGTACATGGGAAGAACG 58.382 52.381 0.00 0.00 0.00 3.95
368 370 2.232941 GTGGAGTACATGGGAAGAACGA 59.767 50.000 0.00 0.00 0.00 3.85
378 380 2.986306 GAAGAACGACGGAGGCGGA 61.986 63.158 0.00 0.00 0.00 5.54
399 401 0.536687 AGGGTCTCAACGTCGAGTCA 60.537 55.000 2.94 0.00 34.46 3.41
418 420 2.548057 TCACCTCGACATGAGCAAAAAC 59.452 45.455 0.00 0.00 43.82 2.43
419 421 1.880027 ACCTCGACATGAGCAAAAACC 59.120 47.619 0.00 0.00 43.82 3.27
470 472 7.363793 GGCACAAGTATATTTTTGTCCTTCCAT 60.364 37.037 2.54 0.00 35.46 3.41
471 473 7.702348 GCACAAGTATATTTTTGTCCTTCCATC 59.298 37.037 2.54 0.00 35.46 3.51
480 482 3.034721 TGTCCTTCCATCGTGTGTAAC 57.965 47.619 0.00 0.00 37.35 2.50
627 630 8.728088 AAAATACGACTTAGCACAAATCTTTG 57.272 30.769 1.19 1.19 43.62 2.77
640 643 3.565905 AATCTTTGTAGCACAAGCAGC 57.434 42.857 2.73 0.00 45.49 5.25
641 644 1.238439 TCTTTGTAGCACAAGCAGCC 58.762 50.000 0.00 0.00 45.49 4.85
642 645 0.242017 CTTTGTAGCACAAGCAGCCC 59.758 55.000 0.00 0.00 45.49 5.19
644 647 1.172180 TTGTAGCACAAGCAGCCCAC 61.172 55.000 0.00 0.00 45.49 4.61
646 649 0.962356 GTAGCACAAGCAGCCCACAT 60.962 55.000 0.00 0.00 45.49 3.21
647 650 0.251297 TAGCACAAGCAGCCCACATT 60.251 50.000 0.00 0.00 45.49 2.71
648 651 0.251297 AGCACAAGCAGCCCACATTA 60.251 50.000 0.00 0.00 45.49 1.90
649 652 0.819582 GCACAAGCAGCCCACATTAT 59.180 50.000 0.00 0.00 41.58 1.28
650 653 1.202336 GCACAAGCAGCCCACATTATC 60.202 52.381 0.00 0.00 41.58 1.75
652 655 0.029834 CAAGCAGCCCACATTATCGC 59.970 55.000 0.00 0.00 0.00 4.58
653 656 0.107017 AAGCAGCCCACATTATCGCT 60.107 50.000 0.00 0.00 0.00 4.93
657 660 2.418368 AGCCCACATTATCGCTGAAA 57.582 45.000 0.00 0.00 0.00 2.69
659 662 3.088532 AGCCCACATTATCGCTGAAAAA 58.911 40.909 0.00 0.00 0.00 1.94
660 663 3.701040 AGCCCACATTATCGCTGAAAAAT 59.299 39.130 0.00 0.00 0.00 1.82
661 664 3.798337 GCCCACATTATCGCTGAAAAATG 59.202 43.478 11.63 11.63 35.83 2.32
662 665 4.362279 CCCACATTATCGCTGAAAAATGG 58.638 43.478 14.88 0.00 34.38 3.16
664 667 3.798337 CACATTATCGCTGAAAAATGGGC 59.202 43.478 14.88 0.00 34.38 5.36
665 668 3.701040 ACATTATCGCTGAAAAATGGGCT 59.299 39.130 14.88 0.00 34.38 5.19
668 671 1.459450 TCGCTGAAAAATGGGCTACC 58.541 50.000 0.00 0.00 37.24 3.18
679 682 0.177141 TGGGCTACCAACACTATCGC 59.823 55.000 0.00 0.00 45.87 4.58
680 683 0.464452 GGGCTACCAACACTATCGCT 59.536 55.000 0.00 0.00 36.50 4.93
681 684 1.538419 GGGCTACCAACACTATCGCTC 60.538 57.143 0.00 0.00 36.50 5.03
724 4439 1.342174 CACAAGCAGCCCACATTTCTT 59.658 47.619 0.00 0.00 0.00 2.52
730 4445 3.760684 AGCAGCCCACATTTCTTTCTAAG 59.239 43.478 0.00 0.00 0.00 2.18
798 4519 2.286121 TCCCACCTCATCCCACCC 60.286 66.667 0.00 0.00 0.00 4.61
799 4520 3.797353 CCCACCTCATCCCACCCG 61.797 72.222 0.00 0.00 0.00 5.28
855 4576 1.459455 CGGATCGACCCAGCAGAGAT 61.459 60.000 0.00 0.00 34.64 2.75
1221 4994 1.579932 CGACGCTGTCACCTACACT 59.420 57.895 8.91 0.00 33.45 3.55
1423 5222 2.116238 GTCATGGGGTTCAGTAGGCTA 58.884 52.381 0.00 0.00 0.00 3.93
1436 5241 7.418712 GGTTCAGTAGGCTATGTAATACCTTGT 60.419 40.741 0.00 0.00 33.99 3.16
1442 5247 6.958767 AGGCTATGTAATACCTTGTTCTGTT 58.041 36.000 0.00 0.00 29.72 3.16
1444 5249 6.821665 GGCTATGTAATACCTTGTTCTGTTCA 59.178 38.462 0.00 0.00 0.00 3.18
1445 5250 7.335924 GGCTATGTAATACCTTGTTCTGTTCAA 59.664 37.037 0.00 0.00 0.00 2.69
1486 5295 3.525537 TCTGAATCCTGACGAAATGCTC 58.474 45.455 0.00 0.00 0.00 4.26
1539 5369 6.528321 AGACTGACTGATTTGATCTGTTTGA 58.472 36.000 0.00 0.00 40.84 2.69
1540 5370 7.166851 AGACTGACTGATTTGATCTGTTTGAT 58.833 34.615 0.00 0.00 40.84 2.57
1541 5371 7.664731 AGACTGACTGATTTGATCTGTTTGATT 59.335 33.333 0.00 0.00 40.84 2.57
1542 5372 8.174733 ACTGACTGATTTGATCTGTTTGATTT 57.825 30.769 0.00 0.00 40.84 2.17
1543 5373 8.295288 ACTGACTGATTTGATCTGTTTGATTTC 58.705 33.333 0.00 0.00 40.84 2.17
1544 5374 8.400184 TGACTGATTTGATCTGTTTGATTTCT 57.600 30.769 0.00 0.00 40.84 2.52
1545 5375 8.509690 TGACTGATTTGATCTGTTTGATTTCTC 58.490 33.333 0.00 0.00 40.84 2.87
1546 5376 8.632906 ACTGATTTGATCTGTTTGATTTCTCT 57.367 30.769 0.00 0.00 38.11 3.10
1547 5377 8.512956 ACTGATTTGATCTGTTTGATTTCTCTG 58.487 33.333 0.00 0.00 38.11 3.35
1548 5378 8.400184 TGATTTGATCTGTTTGATTTCTCTGT 57.600 30.769 0.00 0.00 35.14 3.41
1549 5379 8.853126 TGATTTGATCTGTTTGATTTCTCTGTT 58.147 29.630 0.00 0.00 35.14 3.16
1550 5380 9.688592 GATTTGATCTGTTTGATTTCTCTGTTT 57.311 29.630 0.00 0.00 35.14 2.83
1560 5390 7.962964 TTGATTTCTCTGTTTAGATCGTGTT 57.037 32.000 0.00 0.00 31.21 3.32
1567 5397 3.073678 TGTTTAGATCGTGTTGCTGCAT 58.926 40.909 1.84 0.00 0.00 3.96
1627 5526 4.378459 CGTTGCTTCCCAGTTTAGATTGTC 60.378 45.833 0.00 0.00 0.00 3.18
1700 5604 9.250624 GTTGCTTCTCATTTTAGATCGTATAGT 57.749 33.333 0.00 0.00 0.00 2.12
1705 5609 8.575565 TCTCATTTTAGATCGTATAGTTGTGC 57.424 34.615 0.00 0.00 0.00 4.57
1713 5617 1.067974 CGTATAGTTGTGCGGGGATCA 59.932 52.381 0.00 0.00 0.00 2.92
1714 5618 2.482316 CGTATAGTTGTGCGGGGATCAA 60.482 50.000 0.00 0.00 0.00 2.57
1769 5673 3.181512 GCAAGCTGTAGAAGAGATGCAAC 60.182 47.826 0.00 0.00 33.17 4.17
1805 6004 2.229792 AGCACATCGTCCATGTTTTGT 58.770 42.857 0.00 0.00 43.89 2.83
1852 6051 5.777802 TGTGAGCTTTTCTGTTGTTTTCAA 58.222 33.333 0.00 0.00 37.48 2.69
1871 6098 1.523758 ATGGTCTGTTTCTGAACGCC 58.476 50.000 0.00 0.00 38.65 5.68
1872 6099 0.878523 TGGTCTGTTTCTGAACGCCG 60.879 55.000 0.00 0.00 38.65 6.46
1934 6161 6.128849 GCACATACAAAATTAACAAGTGCCTG 60.129 38.462 0.00 0.00 42.74 4.85
1974 6290 3.603532 TCTGAGGCTCTGCATTAAACAG 58.396 45.455 16.72 1.04 36.44 3.16
2027 6438 9.548208 GCTTTGAGAATTGTACAGTAGATTTTC 57.452 33.333 0.00 0.00 0.00 2.29
2034 6445 9.612620 GAATTGTACAGTAGATTTTCTTGTTGG 57.387 33.333 0.00 0.00 0.00 3.77
2036 6447 8.918202 TTGTACAGTAGATTTTCTTGTTGGAT 57.082 30.769 0.00 0.00 0.00 3.41
2053 6464 9.850628 CTTGTTGGATTAATTATGCATCTATGG 57.149 33.333 0.19 0.00 34.29 2.74
2054 6465 8.352137 TGTTGGATTAATTATGCATCTATGGG 57.648 34.615 0.19 0.00 34.29 4.00
2056 6467 9.193806 GTTGGATTAATTATGCATCTATGGGAT 57.806 33.333 0.19 0.00 34.29 3.85
2080 6491 4.502604 GCCATTAGCAGGATCAAATTGCAT 60.503 41.667 11.57 2.63 42.97 3.96
2081 6492 5.227908 CCATTAGCAGGATCAAATTGCATC 58.772 41.667 11.57 0.00 40.22 3.91
2083 6494 6.208007 CCATTAGCAGGATCAAATTGCATCTA 59.792 38.462 11.57 0.00 40.22 1.98
2084 6495 6.872628 TTAGCAGGATCAAATTGCATCTAG 57.127 37.500 11.57 0.00 40.22 2.43
2085 6496 5.045012 AGCAGGATCAAATTGCATCTAGA 57.955 39.130 0.00 0.00 40.22 2.43
2086 6497 5.632118 AGCAGGATCAAATTGCATCTAGAT 58.368 37.500 0.00 0.00 40.22 1.98
2087 6498 5.706369 AGCAGGATCAAATTGCATCTAGATC 59.294 40.000 1.03 9.82 40.22 2.75
2088 6499 5.472478 GCAGGATCAAATTGCATCTAGATCA 59.528 40.000 1.03 1.64 37.75 2.92
2089 6500 6.568081 GCAGGATCAAATTGCATCTAGATCAC 60.568 42.308 1.03 0.00 37.75 3.06
2095 6781 5.363562 AATTGCATCTAGATCACCTCACA 57.636 39.130 1.03 0.00 0.00 3.58
2105 6791 4.321718 AGATCACCTCACAACATGAACAG 58.678 43.478 0.00 0.00 36.69 3.16
2107 6793 3.732212 TCACCTCACAACATGAACAGAG 58.268 45.455 0.00 1.39 36.69 3.35
2108 6794 3.387699 TCACCTCACAACATGAACAGAGA 59.612 43.478 0.00 0.00 36.69 3.10
2109 6795 4.129380 CACCTCACAACATGAACAGAGAA 58.871 43.478 0.00 0.00 36.69 2.87
2110 6796 4.212847 CACCTCACAACATGAACAGAGAAG 59.787 45.833 0.00 0.00 36.69 2.85
2111 6797 3.750130 CCTCACAACATGAACAGAGAAGG 59.250 47.826 0.00 0.00 36.69 3.46
2113 6799 5.233083 TCACAACATGAACAGAGAAGGAT 57.767 39.130 0.00 0.00 33.02 3.24
2115 6801 6.064060 TCACAACATGAACAGAGAAGGATTT 58.936 36.000 0.00 0.00 33.02 2.17
2116 6802 7.223584 TCACAACATGAACAGAGAAGGATTTA 58.776 34.615 0.00 0.00 33.02 1.40
2117 6803 7.388776 TCACAACATGAACAGAGAAGGATTTAG 59.611 37.037 0.00 0.00 33.02 1.85
2118 6804 6.656693 ACAACATGAACAGAGAAGGATTTAGG 59.343 38.462 0.00 0.00 0.00 2.69
2122 6808 6.240549 TGAACAGAGAAGGATTTAGGGATC 57.759 41.667 0.00 0.00 0.00 3.36
2123 6809 5.131142 TGAACAGAGAAGGATTTAGGGATCC 59.869 44.000 1.92 1.92 44.91 3.36
2134 6820 6.601332 GGATTTAGGGATCCTTTACATGTCA 58.399 40.000 12.58 0.00 41.96 3.58
2135 6821 6.486993 GGATTTAGGGATCCTTTACATGTCAC 59.513 42.308 12.58 0.00 41.96 3.67
2136 6822 3.543680 AGGGATCCTTTACATGTCACG 57.456 47.619 12.58 0.00 0.00 4.35
2137 6823 2.170607 AGGGATCCTTTACATGTCACGG 59.829 50.000 12.58 0.00 0.00 4.94
2138 6824 2.561569 GGATCCTTTACATGTCACGGG 58.438 52.381 0.00 0.96 0.00 5.28
2139 6825 2.169769 GGATCCTTTACATGTCACGGGA 59.830 50.000 0.00 6.92 0.00 5.14
2140 6826 3.458189 GATCCTTTACATGTCACGGGAG 58.542 50.000 0.00 0.00 0.00 4.30
2152 6838 1.816537 ACGGGAGTGGACATGATCG 59.183 57.895 0.00 0.00 44.82 3.69
2153 6839 1.592669 CGGGAGTGGACATGATCGC 60.593 63.158 0.00 0.00 0.00 4.58
2154 6840 1.227674 GGGAGTGGACATGATCGCC 60.228 63.158 0.00 0.00 0.00 5.54
2155 6841 1.690219 GGGAGTGGACATGATCGCCT 61.690 60.000 0.00 0.00 0.00 5.52
2156 6842 0.531532 GGAGTGGACATGATCGCCTG 60.532 60.000 0.00 0.00 0.00 4.85
2157 6843 1.153289 AGTGGACATGATCGCCTGC 60.153 57.895 0.00 0.00 0.00 4.85
2158 6844 1.153289 GTGGACATGATCGCCTGCT 60.153 57.895 0.00 0.00 0.00 4.24
2159 6845 1.144716 TGGACATGATCGCCTGCTC 59.855 57.895 0.00 0.00 0.00 4.26
2160 6846 1.953138 GGACATGATCGCCTGCTCG 60.953 63.158 0.00 0.00 0.00 5.03
2163 6849 2.107750 ATGATCGCCTGCTCGGTG 59.892 61.111 0.41 0.41 44.95 4.94
2174 6860 3.190849 CTCGGTGCAGGCGTGATG 61.191 66.667 11.29 0.00 0.00 3.07
2184 6870 2.124570 GCGTGATGCAGGGGTGAT 60.125 61.111 0.00 0.00 45.45 3.06
2185 6871 2.475466 GCGTGATGCAGGGGTGATG 61.475 63.158 0.00 0.00 45.45 3.07
2186 6872 2.475466 CGTGATGCAGGGGTGATGC 61.475 63.158 0.00 0.00 44.11 3.91
2191 6877 2.753043 GCAGGGGTGATGCAGTGG 60.753 66.667 0.00 0.00 43.31 4.00
2192 6878 3.080641 CAGGGGTGATGCAGTGGA 58.919 61.111 0.00 0.00 0.00 4.02
2193 6879 1.379916 CAGGGGTGATGCAGTGGAA 59.620 57.895 0.00 0.00 0.00 3.53
2197 6883 1.310933 GGGTGATGCAGTGGAAGCAG 61.311 60.000 0.00 0.00 46.36 4.24
2198 6884 0.321919 GGTGATGCAGTGGAAGCAGA 60.322 55.000 0.00 0.00 46.36 4.26
2199 6885 1.085091 GTGATGCAGTGGAAGCAGAG 58.915 55.000 0.00 0.00 46.36 3.35
2200 6886 0.035725 TGATGCAGTGGAAGCAGAGG 60.036 55.000 0.00 0.00 46.36 3.69
2201 6887 0.035630 GATGCAGTGGAAGCAGAGGT 60.036 55.000 0.00 0.00 46.36 3.85
2203 6889 0.250467 TGCAGTGGAAGCAGAGGTTC 60.250 55.000 0.58 0.58 39.04 3.62
2204 6890 0.036022 GCAGTGGAAGCAGAGGTTCT 59.964 55.000 8.59 0.00 39.61 3.01
2205 6891 1.943507 GCAGTGGAAGCAGAGGTTCTC 60.944 57.143 8.59 3.65 39.61 2.87
2206 6892 0.980423 AGTGGAAGCAGAGGTTCTCC 59.020 55.000 8.59 0.00 39.61 3.71
2208 6894 1.349357 GTGGAAGCAGAGGTTCTCCTT 59.651 52.381 8.59 0.00 45.24 3.36
2209 6895 1.349026 TGGAAGCAGAGGTTCTCCTTG 59.651 52.381 8.59 0.00 45.24 3.61
2211 6897 2.614229 GGAAGCAGAGGTTCTCCTTGAC 60.614 54.545 8.59 0.00 45.24 3.18
2212 6898 0.605589 AGCAGAGGTTCTCCTTGACG 59.394 55.000 0.00 0.00 45.24 4.35
2214 6900 1.670380 GCAGAGGTTCTCCTTGACGTC 60.670 57.143 9.11 9.11 45.24 4.34
2215 6901 1.889829 CAGAGGTTCTCCTTGACGTCT 59.110 52.381 17.92 0.00 45.24 4.18
2216 6902 2.297597 CAGAGGTTCTCCTTGACGTCTT 59.702 50.000 17.92 0.00 45.24 3.01
2217 6903 2.297597 AGAGGTTCTCCTTGACGTCTTG 59.702 50.000 17.92 9.12 45.24 3.02
2225 9632 3.926616 TCCTTGACGTCTTGATTCCTTC 58.073 45.455 17.92 0.00 0.00 3.46
2236 9643 0.744771 GATTCCTTCAGGACGCCACC 60.745 60.000 0.00 0.00 45.39 4.61
2237 9644 2.521958 ATTCCTTCAGGACGCCACCG 62.522 60.000 0.00 0.00 45.39 4.94
2238 9645 4.760047 CCTTCAGGACGCCACCGG 62.760 72.222 0.00 0.00 39.22 5.28
2275 10694 4.208686 CGGCGGCTGGAGTAGGTC 62.209 72.222 7.61 0.00 0.00 3.85
2276 10695 2.760385 GGCGGCTGGAGTAGGTCT 60.760 66.667 0.00 0.00 0.00 3.85
2277 10696 2.359967 GGCGGCTGGAGTAGGTCTT 61.360 63.158 0.00 0.00 0.00 3.01
2278 10697 1.142097 GCGGCTGGAGTAGGTCTTC 59.858 63.158 0.00 0.00 0.00 2.87
2279 10698 1.817209 CGGCTGGAGTAGGTCTTCC 59.183 63.158 0.00 0.00 0.00 3.46
2280 10699 1.677637 CGGCTGGAGTAGGTCTTCCC 61.678 65.000 0.00 0.00 0.00 3.97
2281 10700 1.677637 GGCTGGAGTAGGTCTTCCCG 61.678 65.000 0.00 0.00 38.74 5.14
2282 10701 0.971447 GCTGGAGTAGGTCTTCCCGT 60.971 60.000 0.00 0.00 38.74 5.28
2283 10702 1.104630 CTGGAGTAGGTCTTCCCGTC 58.895 60.000 0.00 0.00 38.74 4.79
2286 10705 1.001145 AGTAGGTCTTCCCGTCGCT 60.001 57.895 0.00 0.00 38.74 4.93
2287 10706 1.139095 GTAGGTCTTCCCGTCGCTG 59.861 63.158 0.00 0.00 38.74 5.18
2290 10709 2.811317 GTCTTCCCGTCGCTGCAG 60.811 66.667 10.11 10.11 0.00 4.41
2291 10710 4.742201 TCTTCCCGTCGCTGCAGC 62.742 66.667 29.12 29.12 37.78 5.25
2304 10723 4.925861 GCAGCGCTCCCCCTGATC 62.926 72.222 7.13 0.00 0.00 2.92
2305 10724 4.598894 CAGCGCTCCCCCTGATCG 62.599 72.222 7.13 0.00 35.74 3.69
2309 10728 2.746359 GCTCCCCCTGATCGGATG 59.254 66.667 2.08 0.00 33.16 3.51
2310 10729 2.888447 GCTCCCCCTGATCGGATGG 61.888 68.421 2.08 2.97 33.16 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
29 30 1.332889 GGAACGACGGAGGGGGTAAT 61.333 60.000 0.00 0.00 0.00 1.89
50 51 2.824041 GACAATGATGGCGGCGGT 60.824 61.111 9.78 0.00 0.00 5.68
59 60 1.866015 TCCTCCTCCACGACAATGAT 58.134 50.000 0.00 0.00 0.00 2.45
69 70 1.909302 CTTAGTGGCTTTCCTCCTCCA 59.091 52.381 0.00 0.00 0.00 3.86
70 71 1.210722 CCTTAGTGGCTTTCCTCCTCC 59.789 57.143 0.00 0.00 0.00 4.30
72 73 1.290134 CCCTTAGTGGCTTTCCTCCT 58.710 55.000 0.00 0.00 0.00 3.69
75 76 0.992695 GACCCCTTAGTGGCTTTCCT 59.007 55.000 0.00 0.00 0.00 3.36
78 79 1.002502 GCGACCCCTTAGTGGCTTT 60.003 57.895 0.00 0.00 38.33 3.51
86 87 0.916086 ATGGTTGATGCGACCCCTTA 59.084 50.000 1.55 0.00 37.11 2.69
92 93 2.584791 GACAAACATGGTTGATGCGAC 58.415 47.619 29.74 9.50 35.15 5.19
93 94 1.539388 GGACAAACATGGTTGATGCGA 59.461 47.619 29.74 0.00 35.15 5.10
96 97 2.813754 AGACGGACAAACATGGTTGATG 59.186 45.455 29.74 19.04 38.15 3.07
98 99 2.631160 AGACGGACAAACATGGTTGA 57.369 45.000 29.74 0.00 32.59 3.18
101 102 2.356135 GCATAGACGGACAAACATGGT 58.644 47.619 0.00 0.00 0.00 3.55
156 157 3.188786 GGACGCGATGTGTCAGGC 61.189 66.667 15.93 0.00 43.87 4.85
172 173 0.320374 TGACAGTTACCGCCAGAAGG 59.680 55.000 0.00 0.00 38.23 3.46
174 175 0.320421 GCTGACAGTTACCGCCAGAA 60.320 55.000 3.99 0.00 0.00 3.02
178 179 2.391389 GCAGCTGACAGTTACCGCC 61.391 63.158 20.43 0.00 0.00 6.13
183 184 3.521995 GCTCTGCAGCTGACAGTTA 57.478 52.632 26.61 14.63 43.09 2.24
184 185 4.375569 GCTCTGCAGCTGACAGTT 57.624 55.556 26.61 0.00 43.09 3.16
226 228 4.874977 GTCGCTAGTGCCCTCGCC 62.875 72.222 0.00 0.00 35.36 5.54
228 230 3.812019 ACGTCGCTAGTGCCCTCG 61.812 66.667 0.00 3.80 35.36 4.63
229 231 2.202623 CACGTCGCTAGTGCCCTC 60.203 66.667 0.00 0.00 35.36 4.30
244 246 3.675698 CGAAGTTGAAGGAGTCTAAGCAC 59.324 47.826 0.00 0.00 0.00 4.40
245 247 3.861131 GCGAAGTTGAAGGAGTCTAAGCA 60.861 47.826 0.00 0.00 0.00 3.91
246 248 2.668945 GCGAAGTTGAAGGAGTCTAAGC 59.331 50.000 0.00 0.00 0.00 3.09
258 260 1.416401 ACCTCTTGGAAGCGAAGTTGA 59.584 47.619 0.00 0.00 37.04 3.18
260 262 1.884235 CACCTCTTGGAAGCGAAGTT 58.116 50.000 0.00 0.00 37.04 2.66
271 273 1.519455 GATCGGCGACCACCTCTTG 60.519 63.158 13.76 0.00 0.00 3.02
273 275 3.148279 GGATCGGCGACCACCTCT 61.148 66.667 13.76 0.00 0.00 3.69
296 298 2.223688 TGCAAAAGTCCACCATTCGTTG 60.224 45.455 0.00 0.00 0.00 4.10
299 301 1.662876 CGTGCAAAAGTCCACCATTCG 60.663 52.381 0.00 0.00 0.00 3.34
306 308 3.115556 GCACCGTGCAAAAGTCCA 58.884 55.556 18.79 0.00 44.26 4.02
319 321 2.577593 GACCGGTCCAGTAGCACC 59.422 66.667 24.75 0.00 0.00 5.01
339 341 0.175760 CATGTACTCCACCTGGGTCG 59.824 60.000 0.00 0.00 38.11 4.79
361 363 2.987547 TCCGCCTCCGTCGTTCTT 60.988 61.111 0.00 0.00 0.00 2.52
378 380 0.822532 ACTCGACGTTGAGACCCTGT 60.823 55.000 34.38 12.89 39.35 4.00
399 401 1.880027 GGTTTTTGCTCATGTCGAGGT 59.120 47.619 0.00 0.00 42.55 3.85
408 410 2.875933 CTCGTGTTAGGGTTTTTGCTCA 59.124 45.455 0.00 0.00 0.00 4.26
411 413 2.699251 CCTCGTGTTAGGGTTTTTGC 57.301 50.000 0.00 0.00 32.55 3.68
419 421 3.690475 AAAACCTACCCTCGTGTTAGG 57.310 47.619 7.52 7.52 36.30 2.69
441 443 7.296628 AGGACAAAAATATACTTGTGCCAAA 57.703 32.000 14.10 0.00 42.82 3.28
443 445 6.071616 GGAAGGACAAAAATATACTTGTGCCA 60.072 38.462 14.10 0.00 42.82 4.92
444 446 6.071616 TGGAAGGACAAAAATATACTTGTGCC 60.072 38.462 14.10 11.11 42.82 5.01
445 447 6.919721 TGGAAGGACAAAAATATACTTGTGC 58.080 36.000 11.27 11.27 42.33 4.57
453 455 5.710099 ACACACGATGGAAGGACAAAAATAT 59.290 36.000 0.00 0.00 0.00 1.28
456 458 3.283751 ACACACGATGGAAGGACAAAAA 58.716 40.909 0.00 0.00 0.00 1.94
601 604 8.840867 CAAAGATTTGTGCTAAGTCGTATTTTC 58.159 33.333 0.00 0.00 33.59 2.29
616 619 4.609947 TGCTTGTGCTACAAAGATTTGTG 58.390 39.130 18.76 10.89 43.70 3.33
627 630 0.962356 ATGTGGGCTGCTTGTGCTAC 60.962 55.000 0.00 0.00 40.48 3.58
628 631 0.251297 AATGTGGGCTGCTTGTGCTA 60.251 50.000 0.00 0.00 40.48 3.49
629 632 0.251297 TAATGTGGGCTGCTTGTGCT 60.251 50.000 0.00 0.00 40.48 4.40
631 634 1.064505 CGATAATGTGGGCTGCTTGTG 59.935 52.381 0.00 0.00 0.00 3.33
632 635 1.382522 CGATAATGTGGGCTGCTTGT 58.617 50.000 0.00 0.00 0.00 3.16
633 636 0.029834 GCGATAATGTGGGCTGCTTG 59.970 55.000 0.00 0.00 0.00 4.01
634 637 0.107017 AGCGATAATGTGGGCTGCTT 60.107 50.000 0.00 0.00 33.81 3.91
635 638 0.816825 CAGCGATAATGTGGGCTGCT 60.817 55.000 0.00 0.00 45.28 4.24
636 639 1.650912 CAGCGATAATGTGGGCTGC 59.349 57.895 0.00 0.00 45.28 5.25
640 643 4.362279 CCATTTTTCAGCGATAATGTGGG 58.638 43.478 0.00 0.00 0.00 4.61
641 644 4.362279 CCCATTTTTCAGCGATAATGTGG 58.638 43.478 0.00 0.00 0.00 4.17
642 645 3.798337 GCCCATTTTTCAGCGATAATGTG 59.202 43.478 0.00 0.00 0.00 3.21
644 647 4.311816 AGCCCATTTTTCAGCGATAATG 57.688 40.909 0.00 0.00 0.00 1.90
646 649 3.630312 GGTAGCCCATTTTTCAGCGATAA 59.370 43.478 0.00 0.00 0.00 1.75
647 650 3.211045 GGTAGCCCATTTTTCAGCGATA 58.789 45.455 0.00 0.00 0.00 2.92
648 651 2.024414 GGTAGCCCATTTTTCAGCGAT 58.976 47.619 0.00 0.00 0.00 4.58
649 652 1.271652 TGGTAGCCCATTTTTCAGCGA 60.272 47.619 0.00 0.00 35.17 4.93
650 653 1.173043 TGGTAGCCCATTTTTCAGCG 58.827 50.000 0.00 0.00 35.17 5.18
652 655 3.573967 AGTGTTGGTAGCCCATTTTTCAG 59.426 43.478 0.00 0.00 41.49 3.02
653 656 3.571590 AGTGTTGGTAGCCCATTTTTCA 58.428 40.909 0.00 0.00 41.49 2.69
656 659 3.945285 CGATAGTGTTGGTAGCCCATTTT 59.055 43.478 0.00 0.00 41.49 1.82
657 660 3.541632 CGATAGTGTTGGTAGCCCATTT 58.458 45.455 0.00 0.00 41.49 2.32
659 662 1.202651 GCGATAGTGTTGGTAGCCCAT 60.203 52.381 0.00 0.00 38.65 4.00
660 663 0.177141 GCGATAGTGTTGGTAGCCCA 59.823 55.000 0.00 0.00 37.43 5.36
661 664 0.464452 AGCGATAGTGTTGGTAGCCC 59.536 55.000 0.00 0.00 39.35 5.19
662 665 1.854227 GAGCGATAGTGTTGGTAGCC 58.146 55.000 0.00 0.00 39.35 3.93
664 667 1.864435 GCCGAGCGATAGTGTTGGTAG 60.864 57.143 0.00 0.00 39.35 3.18
665 668 0.101759 GCCGAGCGATAGTGTTGGTA 59.898 55.000 0.00 0.00 39.35 3.25
668 671 1.141881 AGGCCGAGCGATAGTGTTG 59.858 57.895 0.00 0.00 39.35 3.33
670 673 2.786495 CCAGGCCGAGCGATAGTGT 61.786 63.158 0.00 0.00 39.35 3.55
671 674 2.028190 CCAGGCCGAGCGATAGTG 59.972 66.667 0.00 0.00 39.35 2.74
672 675 3.917760 GCCAGGCCGAGCGATAGT 61.918 66.667 0.00 0.00 39.35 2.12
673 676 4.671569 GGCCAGGCCGAGCGATAG 62.672 72.222 17.05 0.00 39.62 2.08
724 4439 5.124645 TGTGGGCGTAAGTTTTTCTTAGAA 58.875 37.500 0.00 0.00 39.03 2.10
730 4445 3.119955 GGAGATGTGGGCGTAAGTTTTTC 60.120 47.826 0.00 0.00 41.68 2.29
777 4497 3.866582 GGGATGAGGTGGGAGGCG 61.867 72.222 0.00 0.00 0.00 5.52
855 4576 2.747686 GAGGCGGGAGGTGTTTGA 59.252 61.111 0.00 0.00 0.00 2.69
1209 4982 0.313987 CGTGCTCAGTGTAGGTGACA 59.686 55.000 0.00 0.00 34.94 3.58
1423 5222 8.862325 TGATTGAACAGAACAAGGTATTACAT 57.138 30.769 0.00 0.00 0.00 2.29
1436 5241 6.335471 AGTGATTGCATTGATTGAACAGAA 57.665 33.333 0.00 0.00 0.00 3.02
1442 5247 5.823209 ATCGAAGTGATTGCATTGATTGA 57.177 34.783 0.00 0.00 31.57 2.57
1486 5295 4.183101 AGCAAAACACAATTCAACAGTGG 58.817 39.130 0.00 0.00 37.58 4.00
1539 5369 5.934625 AGCAACACGATCTAAACAGAGAAAT 59.065 36.000 0.00 0.00 0.00 2.17
1540 5370 5.177511 CAGCAACACGATCTAAACAGAGAAA 59.822 40.000 0.00 0.00 0.00 2.52
1541 5371 4.686091 CAGCAACACGATCTAAACAGAGAA 59.314 41.667 0.00 0.00 0.00 2.87
1542 5372 4.237724 CAGCAACACGATCTAAACAGAGA 58.762 43.478 0.00 0.00 0.00 3.10
1543 5373 3.181526 GCAGCAACACGATCTAAACAGAG 60.182 47.826 0.00 0.00 0.00 3.35
1544 5374 2.736721 GCAGCAACACGATCTAAACAGA 59.263 45.455 0.00 0.00 0.00 3.41
1545 5375 2.480037 TGCAGCAACACGATCTAAACAG 59.520 45.455 0.00 0.00 0.00 3.16
1546 5376 2.488952 TGCAGCAACACGATCTAAACA 58.511 42.857 0.00 0.00 0.00 2.83
1547 5377 3.747099 ATGCAGCAACACGATCTAAAC 57.253 42.857 0.00 0.00 0.00 2.01
1548 5378 3.750652 TCAATGCAGCAACACGATCTAAA 59.249 39.130 0.00 0.00 0.00 1.85
1549 5379 3.333804 TCAATGCAGCAACACGATCTAA 58.666 40.909 0.00 0.00 0.00 2.10
1550 5380 2.971307 TCAATGCAGCAACACGATCTA 58.029 42.857 0.00 0.00 0.00 1.98
1560 5390 7.870509 AATAGAAGACTTATTCAATGCAGCA 57.129 32.000 0.00 0.00 0.00 4.41
1596 5495 0.249868 TGGGAAGCAACGAGTGTCAG 60.250 55.000 0.00 0.00 0.00 3.51
1627 5526 6.625362 TGAAAGACTGATTCAGTACAGCTAG 58.375 40.000 19.00 0.00 45.44 3.42
1698 5602 1.303317 GGTTGATCCCCGCACAACT 60.303 57.895 0.00 0.00 42.06 3.16
1700 5604 0.178975 AAAGGTTGATCCCCGCACAA 60.179 50.000 0.00 0.00 36.75 3.33
1704 5608 1.474330 AATGAAAGGTTGATCCCCGC 58.526 50.000 0.00 0.00 36.75 6.13
1705 5609 2.417243 GCAAATGAAAGGTTGATCCCCG 60.417 50.000 0.00 0.00 36.75 5.73
1713 5617 7.521910 GCCAAATACATTTGCAAATGAAAGGTT 60.522 33.333 43.53 29.04 46.72 3.50
1714 5618 6.072563 GCCAAATACATTTGCAAATGAAAGGT 60.073 34.615 43.53 29.11 46.72 3.50
1751 5655 2.093235 AGGGTTGCATCTCTTCTACAGC 60.093 50.000 0.00 0.00 0.00 4.40
1769 5673 1.208293 GTGCTTACCTGAGAGGAAGGG 59.792 57.143 0.00 0.00 37.67 3.95
1805 6004 1.000385 CATTCCGCAGTCAAGCCAAAA 60.000 47.619 0.00 0.00 0.00 2.44
1852 6051 1.523758 GGCGTTCAGAAACAGACCAT 58.476 50.000 0.00 0.00 34.93 3.55
1871 6098 1.097232 TGCTCCAAAGGATTGATGCG 58.903 50.000 0.00 0.00 38.94 4.73
1872 6099 2.494870 AGTTGCTCCAAAGGATTGATGC 59.505 45.455 0.00 0.00 38.94 3.91
1910 6137 6.922957 ACAGGCACTTGTTAATTTTGTATGTG 59.077 34.615 0.00 0.00 34.60 3.21
1934 6161 8.016801 GCCTCAGATAGTCGTTCTAAGTATTAC 58.983 40.741 0.00 0.00 31.94 1.89
1988 6307 8.246180 ACAATTCTCAAAGCAATGGTACTATTG 58.754 33.333 23.49 23.49 40.25 1.90
2027 6438 9.850628 CCATAGATGCATAATTAATCCAACAAG 57.149 33.333 0.00 0.00 0.00 3.16
2028 6439 8.805175 CCCATAGATGCATAATTAATCCAACAA 58.195 33.333 0.00 0.00 0.00 2.83
2030 6441 8.579850 TCCCATAGATGCATAATTAATCCAAC 57.420 34.615 0.00 0.00 0.00 3.77
2032 6443 8.756486 CATCCCATAGATGCATAATTAATCCA 57.244 34.615 0.00 0.00 45.76 3.41
2057 6468 3.181473 TGCAATTTGATCCTGCTAATGGC 60.181 43.478 0.00 0.00 42.22 4.40
2058 6469 4.659111 TGCAATTTGATCCTGCTAATGG 57.341 40.909 0.00 0.00 37.00 3.16
2059 6470 6.085555 AGATGCAATTTGATCCTGCTAATG 57.914 37.500 0.00 0.00 37.00 1.90
2063 6474 5.045012 TCTAGATGCAATTTGATCCTGCT 57.955 39.130 0.00 0.00 37.00 4.24
2064 6475 5.472478 TGATCTAGATGCAATTTGATCCTGC 59.528 40.000 10.74 0.00 36.60 4.85
2065 6476 6.072618 GGTGATCTAGATGCAATTTGATCCTG 60.073 42.308 10.74 0.00 30.81 3.86
2066 6477 6.002704 GGTGATCTAGATGCAATTTGATCCT 58.997 40.000 10.74 0.00 30.81 3.24
2068 6479 6.709397 TGAGGTGATCTAGATGCAATTTGATC 59.291 38.462 10.74 14.10 31.76 2.92
2071 6482 5.587443 TGTGAGGTGATCTAGATGCAATTTG 59.413 40.000 10.74 0.00 0.00 2.32
2072 6483 5.748402 TGTGAGGTGATCTAGATGCAATTT 58.252 37.500 10.74 0.00 0.00 1.82
2074 6485 5.121811 GTTGTGAGGTGATCTAGATGCAAT 58.878 41.667 10.74 1.18 0.00 3.56
2077 6488 4.128925 TGTTGTGAGGTGATCTAGATGC 57.871 45.455 10.74 2.64 0.00 3.91
2080 6491 5.245977 TGTTCATGTTGTGAGGTGATCTAGA 59.754 40.000 0.00 0.00 38.29 2.43
2081 6492 5.482006 TGTTCATGTTGTGAGGTGATCTAG 58.518 41.667 0.00 0.00 38.29 2.43
2083 6494 4.040829 TCTGTTCATGTTGTGAGGTGATCT 59.959 41.667 0.00 0.00 38.29 2.75
2084 6495 4.318332 TCTGTTCATGTTGTGAGGTGATC 58.682 43.478 0.00 0.00 38.29 2.92
2085 6496 4.040829 TCTCTGTTCATGTTGTGAGGTGAT 59.959 41.667 0.00 0.00 38.29 3.06
2086 6497 3.387699 TCTCTGTTCATGTTGTGAGGTGA 59.612 43.478 0.00 0.00 38.29 4.02
2087 6498 3.732212 TCTCTGTTCATGTTGTGAGGTG 58.268 45.455 0.00 0.00 38.29 4.00
2088 6499 4.384056 CTTCTCTGTTCATGTTGTGAGGT 58.616 43.478 0.00 0.00 38.29 3.85
2089 6500 3.750130 CCTTCTCTGTTCATGTTGTGAGG 59.250 47.826 0.00 0.00 38.29 3.86
2095 6781 6.012508 TCCCTAAATCCTTCTCTGTTCATGTT 60.013 38.462 0.00 0.00 0.00 2.71
2110 6796 6.486993 GTGACATGTAAAGGATCCCTAAATCC 59.513 42.308 8.55 0.00 44.81 3.01
2111 6797 6.202954 CGTGACATGTAAAGGATCCCTAAATC 59.797 42.308 8.55 0.00 31.13 2.17
2113 6799 5.424757 CGTGACATGTAAAGGATCCCTAAA 58.575 41.667 8.55 0.00 31.13 1.85
2115 6801 3.386726 CCGTGACATGTAAAGGATCCCTA 59.613 47.826 9.50 0.00 31.13 3.53
2116 6802 2.170607 CCGTGACATGTAAAGGATCCCT 59.829 50.000 9.50 0.00 33.87 4.20
2117 6803 2.561569 CCGTGACATGTAAAGGATCCC 58.438 52.381 9.50 0.00 0.00 3.85
2118 6804 2.169769 TCCCGTGACATGTAAAGGATCC 59.830 50.000 16.28 2.48 0.00 3.36
2122 6808 2.346803 CACTCCCGTGACATGTAAAGG 58.653 52.381 8.17 8.17 43.97 3.11
2123 6809 2.028476 TCCACTCCCGTGACATGTAAAG 60.028 50.000 0.00 0.00 43.97 1.85
2124 6810 1.972075 TCCACTCCCGTGACATGTAAA 59.028 47.619 0.00 0.00 43.97 2.01
2126 6812 0.892755 GTCCACTCCCGTGACATGTA 59.107 55.000 0.00 0.00 43.97 2.29
2127 6813 1.118965 TGTCCACTCCCGTGACATGT 61.119 55.000 0.00 0.00 43.97 3.21
2128 6814 0.250234 ATGTCCACTCCCGTGACATG 59.750 55.000 3.75 0.00 43.97 3.21
2129 6815 0.250234 CATGTCCACTCCCGTGACAT 59.750 55.000 0.00 0.00 43.97 3.06
2131 6817 0.537188 ATCATGTCCACTCCCGTGAC 59.463 55.000 0.00 0.00 43.97 3.67
2134 6820 1.816537 CGATCATGTCCACTCCCGT 59.183 57.895 0.00 0.00 0.00 5.28
2135 6821 1.592669 GCGATCATGTCCACTCCCG 60.593 63.158 0.00 0.00 0.00 5.14
2136 6822 1.227674 GGCGATCATGTCCACTCCC 60.228 63.158 0.00 0.00 0.00 4.30
2137 6823 0.531532 CAGGCGATCATGTCCACTCC 60.532 60.000 0.00 0.00 0.00 3.85
2138 6824 1.156645 GCAGGCGATCATGTCCACTC 61.157 60.000 0.00 0.00 0.00 3.51
2139 6825 1.153289 GCAGGCGATCATGTCCACT 60.153 57.895 0.00 0.00 0.00 4.00
2140 6826 1.153289 AGCAGGCGATCATGTCCAC 60.153 57.895 0.00 0.00 0.00 4.02
2141 6827 1.144716 GAGCAGGCGATCATGTCCA 59.855 57.895 0.00 0.00 0.00 4.02
2142 6828 1.953138 CGAGCAGGCGATCATGTCC 60.953 63.158 0.00 0.00 0.00 4.02
2143 6829 1.953138 CCGAGCAGGCGATCATGTC 60.953 63.158 0.00 0.00 0.00 3.06
2144 6830 2.107750 CCGAGCAGGCGATCATGT 59.892 61.111 0.00 0.00 0.00 3.21
2146 6832 2.107750 CACCGAGCAGGCGATCAT 59.892 61.111 0.00 0.00 46.52 2.45
2147 6833 4.819761 GCACCGAGCAGGCGATCA 62.820 66.667 0.00 0.00 46.52 2.92
2157 6843 3.190849 CATCACGCCTGCACCGAG 61.191 66.667 8.82 1.62 0.00 4.63
2160 6846 3.807538 CTGCATCACGCCTGCACC 61.808 66.667 3.31 0.00 44.30 5.01
2166 6852 3.704231 ATCACCCCTGCATCACGCC 62.704 63.158 0.00 0.00 41.33 5.68
2168 6854 2.475466 GCATCACCCCTGCATCACG 61.475 63.158 0.00 0.00 39.46 4.35
2169 6855 1.378911 TGCATCACCCCTGCATCAC 60.379 57.895 0.00 0.00 44.30 3.06
2174 6860 2.753043 CCACTGCATCACCCCTGC 60.753 66.667 0.00 0.00 40.10 4.85
2176 6862 1.687612 CTTCCACTGCATCACCCCT 59.312 57.895 0.00 0.00 0.00 4.79
2177 6863 2.048603 GCTTCCACTGCATCACCCC 61.049 63.158 0.00 0.00 0.00 4.95
2178 6864 1.303561 TGCTTCCACTGCATCACCC 60.304 57.895 0.00 0.00 35.31 4.61
2179 6865 0.321919 TCTGCTTCCACTGCATCACC 60.322 55.000 0.00 0.00 39.86 4.02
2180 6866 1.085091 CTCTGCTTCCACTGCATCAC 58.915 55.000 0.00 0.00 39.86 3.06
2181 6867 0.035725 CCTCTGCTTCCACTGCATCA 60.036 55.000 0.00 0.00 39.86 3.07
2182 6868 0.035630 ACCTCTGCTTCCACTGCATC 60.036 55.000 0.00 0.00 39.86 3.91
2183 6869 0.403271 AACCTCTGCTTCCACTGCAT 59.597 50.000 0.00 0.00 39.86 3.96
2184 6870 0.250467 GAACCTCTGCTTCCACTGCA 60.250 55.000 0.00 0.00 38.81 4.41
2185 6871 0.036022 AGAACCTCTGCTTCCACTGC 59.964 55.000 0.00 0.00 0.00 4.40
2186 6872 1.338579 GGAGAACCTCTGCTTCCACTG 60.339 57.143 0.00 0.00 31.63 3.66
2187 6873 0.980423 GGAGAACCTCTGCTTCCACT 59.020 55.000 0.00 0.00 31.63 4.00
2188 6874 0.980423 AGGAGAACCTCTGCTTCCAC 59.020 55.000 0.00 0.00 42.83 4.02
2189 6875 3.483352 AGGAGAACCTCTGCTTCCA 57.517 52.632 0.00 0.00 42.83 3.53
2199 6885 2.814280 TCAAGACGTCAAGGAGAACC 57.186 50.000 19.50 0.00 0.00 3.62
2200 6886 3.680458 GGAATCAAGACGTCAAGGAGAAC 59.320 47.826 19.50 7.22 0.00 3.01
2201 6887 3.578716 AGGAATCAAGACGTCAAGGAGAA 59.421 43.478 19.50 0.00 0.00 2.87
2203 6889 3.601443 AGGAATCAAGACGTCAAGGAG 57.399 47.619 19.50 2.41 0.00 3.69
2204 6890 3.323691 TGAAGGAATCAAGACGTCAAGGA 59.676 43.478 19.50 12.07 34.30 3.36
2205 6891 3.664107 TGAAGGAATCAAGACGTCAAGG 58.336 45.455 19.50 6.56 34.30 3.61
2206 6892 3.681897 CCTGAAGGAATCAAGACGTCAAG 59.318 47.826 19.50 9.67 37.67 3.02
2207 6893 3.323691 TCCTGAAGGAATCAAGACGTCAA 59.676 43.478 19.50 2.80 42.18 3.18
2208 6894 2.897326 TCCTGAAGGAATCAAGACGTCA 59.103 45.455 19.50 0.00 42.18 4.35
2209 6895 3.594603 TCCTGAAGGAATCAAGACGTC 57.405 47.619 7.70 7.70 42.18 4.34
2225 9632 4.096003 AATCCCGGTGGCGTCCTG 62.096 66.667 0.00 0.00 0.00 3.86
2258 10677 4.208686 GACCTACTCCAGCCGCCG 62.209 72.222 0.00 0.00 0.00 6.46
2265 10684 0.679002 CGACGGGAAGACCTACTCCA 60.679 60.000 0.00 0.00 36.97 3.86
2266 10685 2.002509 GCGACGGGAAGACCTACTCC 62.003 65.000 0.00 0.00 36.97 3.85
2268 10687 1.001145 AGCGACGGGAAGACCTACT 60.001 57.895 0.00 0.00 36.97 2.57
2270 10689 2.707849 GCAGCGACGGGAAGACCTA 61.708 63.158 0.00 0.00 36.97 3.08
2271 10690 4.070552 GCAGCGACGGGAAGACCT 62.071 66.667 0.00 0.00 36.97 3.85
2272 10691 4.373116 TGCAGCGACGGGAAGACC 62.373 66.667 0.00 0.00 0.00 3.85
2274 10693 4.742201 GCTGCAGCGACGGGAAGA 62.742 66.667 25.23 0.00 0.00 2.87
2287 10706 4.925861 GATCAGGGGGAGCGCTGC 62.926 72.222 22.03 22.03 0.00 5.25
2292 10711 2.746359 CATCCGATCAGGGGGAGC 59.254 66.667 0.00 0.00 41.52 4.70
2293 10712 2.219875 CCCATCCGATCAGGGGGAG 61.220 68.421 10.39 2.91 42.32 4.30
2294 10713 2.122413 CCCATCCGATCAGGGGGA 60.122 66.667 10.39 1.72 42.32 4.81


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

AutoCloner maintained by Alex Coulton.