Multiple sequence alignment - TraesCS1A01G029200

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 TraesCS1A01G029200 chr1A 100.000 7754 0 0 1 7754 13677212 13669459 0.000000e+00 14320.0
1 TraesCS1A01G029200 chr1A 93.080 289 15 4 7096 7381 13420451 13420165 1.200000e-112 418.0
2 TraesCS1A01G029200 chr1A 93.820 178 9 2 7577 7753 13419783 13419607 4.610000e-67 267.0
3 TraesCS1A01G029200 chr1A 85.263 190 13 11 7383 7570 13420075 13419899 1.720000e-41 182.0
4 TraesCS1A01G029200 chr1D 92.298 2415 94 30 5008 7381 11546272 11543909 0.000000e+00 3345.0
5 TraesCS1A01G029200 chr1D 89.981 2126 147 28 1984 4078 11549594 11547504 0.000000e+00 2686.0
6 TraesCS1A01G029200 chr1D 89.268 1435 66 22 468 1846 11551073 11549671 0.000000e+00 1716.0
7 TraesCS1A01G029200 chr1D 97.988 845 17 0 4165 5009 11547278 11546434 0.000000e+00 1467.0
8 TraesCS1A01G029200 chr1D 83.043 460 51 19 1 440 11551524 11551072 7.290000e-105 392.0
9 TraesCS1A01G029200 chr1D 93.048 187 11 2 7384 7570 11543775 11543591 9.910000e-69 272.0
10 TraesCS1A01G029200 chr1D 93.714 175 11 0 7580 7754 11543474 11543300 5.970000e-66 263.0
11 TraesCS1A01G029200 chr1B 89.204 2501 152 45 1192 3633 17358275 17355834 0.000000e+00 3014.0
12 TraesCS1A01G029200 chr1B 95.159 1570 48 11 5831 7377 17353217 17351653 0.000000e+00 2453.0
13 TraesCS1A01G029200 chr1B 93.860 1482 64 14 5916 7377 16851518 16850044 0.000000e+00 2207.0
14 TraesCS1A01G029200 chr1B 94.804 1174 37 10 6230 7381 16914927 16913756 0.000000e+00 1808.0
15 TraesCS1A01G029200 chr1B 84.425 1252 117 46 4653 5843 17354772 17353538 0.000000e+00 1160.0
16 TraesCS1A01G029200 chr1B 95.397 630 26 1 3007 3633 16922342 16921713 0.000000e+00 1000.0
17 TraesCS1A01G029200 chr1B 93.770 610 22 7 5639 6234 16919680 16919073 0.000000e+00 902.0
18 TraesCS1A01G029200 chr1B 91.993 587 28 6 4980 5549 16920286 16919702 0.000000e+00 806.0
19 TraesCS1A01G029200 chr1B 92.371 485 26 7 4165 4649 17355496 17355023 0.000000e+00 680.0
20 TraesCS1A01G029200 chr1B 92.181 486 28 6 4165 4649 16921375 16920899 0.000000e+00 678.0
21 TraesCS1A01G029200 chr1B 86.754 536 51 13 520 1037 17359125 17358592 5.220000e-161 579.0
22 TraesCS1A01G029200 chr1B 94.118 289 12 4 7096 7381 16742470 16742184 1.190000e-117 435.0
23 TraesCS1A01G029200 chr1B 82.167 443 56 11 1 437 17359604 17359179 7.400000e-95 359.0
24 TraesCS1A01G029200 chr1B 87.000 300 21 3 3875 4170 16921712 16921427 9.710000e-84 322.0
25 TraesCS1A01G029200 chr1B 86.667 300 22 3 3875 4170 17355833 17355548 4.520000e-82 316.0
26 TraesCS1A01G029200 chr1B 94.413 179 9 1 7577 7754 17351254 17351076 2.760000e-69 274.0
27 TraesCS1A01G029200 chr1B 93.714 175 11 0 7580 7754 16913287 16913113 5.970000e-66 263.0
28 TraesCS1A01G029200 chr1B 91.444 187 12 4 7384 7570 16913623 16913441 3.590000e-63 254.0
29 TraesCS1A01G029200 chr1B 85.714 189 14 9 7383 7570 16742094 16741918 3.690000e-43 187.0
30 TraesCS1A01G029200 chr3A 85.908 589 51 20 6816 7381 750729541 750728962 4.000000e-167 599.0
31 TraesCS1A01G029200 chr3A 79.179 341 54 12 4308 4643 740353087 740352759 3.640000e-53 220.0
32 TraesCS1A01G029200 chr3A 78.694 291 36 16 1000 1286 740356497 740356229 3.720000e-38 171.0
33 TraesCS1A01G029200 chr3A 87.023 131 13 4 6669 6798 750730107 750729980 2.250000e-30 145.0
34 TraesCS1A01G029200 chr3A 80.571 175 34 0 6456 6630 609956039 609956213 1.360000e-27 135.0
35 TraesCS1A01G029200 chr3A 80.702 171 29 4 5687 5856 681463149 681463316 6.310000e-26 130.0
36 TraesCS1A01G029200 chr3A 86.441 118 11 3 6402 6517 750730365 750730251 2.940000e-24 124.0
37 TraesCS1A01G029200 chr3A 79.769 173 30 5 5687 5856 683193783 683193953 3.800000e-23 121.0
38 TraesCS1A01G029200 chr3A 92.105 38 3 0 6557 6594 750730244 750730207 4.000000e-03 54.7
39 TraesCS1A01G029200 chr4B 95.154 227 9 2 5156 5382 406211170 406211394 2.660000e-94 357.0
40 TraesCS1A01G029200 chr4B 84.772 197 22 4 4938 5128 406210979 406211173 2.860000e-44 191.0
41 TraesCS1A01G029200 chr3D 81.057 454 64 15 5056 5508 608068148 608067716 7.450000e-90 342.0
42 TraesCS1A01G029200 chr3D 78.299 341 57 15 4308 4643 608069118 608068790 3.670000e-48 204.0
43 TraesCS1A01G029200 chr3D 76.771 353 50 21 1000 1348 608072581 608072257 1.340000e-37 169.0
44 TraesCS1A01G029200 chr3D 79.070 172 32 4 5687 5856 546337986 546338155 1.770000e-21 115.0
45 TraesCS1A01G029200 chr3B 89.778 225 23 0 5056 5280 817823882 817823658 9.840000e-74 289.0
46 TraesCS1A01G029200 chr3B 78.299 341 57 15 4308 4643 817824704 817824376 3.670000e-48 204.0
47 TraesCS1A01G029200 chr3B 78.187 353 48 22 1000 1348 817828165 817827838 1.710000e-46 198.0
48 TraesCS1A01G029200 chr2B 83.626 171 22 6 5688 5856 740319119 740319285 1.040000e-33 156.0
49 TraesCS1A01G029200 chr2A 80.473 169 30 3 5687 5854 17812637 17812471 8.170000e-25 126.0
50 TraesCS1A01G029200 chr2D 79.290 169 32 3 5687 5854 15837560 15837394 1.770000e-21 115.0
51 TraesCS1A01G029200 chr5D 78.912 147 27 4 4312 4456 383778009 383777865 6.400000e-16 97.1
52 TraesCS1A01G029200 chr5A 78.912 147 27 4 4312 4456 484080641 484080497 6.400000e-16 97.1
53 TraesCS1A01G029200 chr5B 78.231 147 28 4 4312 4456 460267527 460267383 2.980000e-14 91.6


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 TraesCS1A01G029200 chr1A 13669459 13677212 7753 True 14320.000000 14320 100.000000 1 7754 1 chr1A.!!$R1 7753
1 TraesCS1A01G029200 chr1A 13419607 13420451 844 True 289.000000 418 90.721000 7096 7753 3 chr1A.!!$R2 657
2 TraesCS1A01G029200 chr1D 11543300 11551524 8224 True 1448.714286 3345 91.334286 1 7754 7 chr1D.!!$R1 7753
3 TraesCS1A01G029200 chr1B 16850044 16851518 1474 True 2207.000000 2207 93.860000 5916 7377 1 chr1B.!!$R1 1461
4 TraesCS1A01G029200 chr1B 17351076 17359604 8528 True 1104.375000 3014 88.895000 1 7754 8 chr1B.!!$R5 7753
5 TraesCS1A01G029200 chr1B 16913113 16914927 1814 True 775.000000 1808 93.320667 6230 7754 3 chr1B.!!$R3 1524
6 TraesCS1A01G029200 chr1B 16919073 16922342 3269 True 741.600000 1000 92.068200 3007 6234 5 chr1B.!!$R4 3227
7 TraesCS1A01G029200 chr1B 16741918 16742470 552 True 311.000000 435 89.916000 7096 7570 2 chr1B.!!$R2 474
8 TraesCS1A01G029200 chr3A 750728962 750730365 1403 True 230.675000 599 87.869250 6402 7381 4 chr3A.!!$R2 979
9 TraesCS1A01G029200 chr3D 608067716 608072581 4865 True 238.333333 342 78.709000 1000 5508 3 chr3D.!!$R1 4508
10 TraesCS1A01G029200 chr3B 817823658 817828165 4507 True 230.333333 289 82.088000 1000 5280 3 chr3B.!!$R1 4280

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
464 483 0.027194 CCTGATCTGATTGCAACGCG 59.973 55.000 3.53 3.53 0.00 6.01 F
485 504 0.249280 CGACCTGCAAAAACCCAACC 60.249 55.000 0.00 0.00 0.00 3.77 F
509 533 0.323725 TCCATTTCCAGCCAAGGAGC 60.324 55.000 0.00 0.00 39.25 4.70 F
920 981 0.449388 GGCTGCGGAGATCTTGTTTG 59.551 55.000 8.65 0.00 0.00 2.93 F
1812 2104 0.543277 CTCATAGCTTGCAGGGTGGA 59.457 55.000 11.20 7.34 0.00 4.02 F
2420 3790 0.602562 CCAACCACAACCGCAATGAT 59.397 50.000 0.00 0.00 0.00 2.45 F
2469 3839 1.067084 CTGCATCGCGAGACTGGAT 59.933 57.895 16.66 0.00 46.97 3.41 F
2603 3973 1.138568 CATCCCCTGATCCTGAGCTT 58.861 55.000 0.00 0.00 0.00 3.74 F
3029 4411 1.404851 GGCTATGCTTCGCCTAGGATC 60.405 57.143 14.75 0.00 42.98 3.36 F
3907 5305 1.754803 TGCATCGTACAGTCTTAGGGG 59.245 52.381 0.00 0.00 0.00 4.79 F
5031 7304 1.003580 TGGCTGGAAGAGTAAAGGCAG 59.996 52.381 0.00 0.00 39.94 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1495 1765 0.676782 GCACTGCCGAACCAATACCT 60.677 55.000 0.00 0.0 0.00 3.08 R
1970 2266 0.739112 CAGGAACCTCAGCGCTTCTC 60.739 60.000 7.50 0.0 0.00 2.87 R
2250 3007 2.292016 CGCAGTTGTAACATGGAACCAA 59.708 45.455 0.00 0.0 0.00 3.67 R
2705 4075 0.947244 CAGGTTCACCAACAGCAGAC 59.053 55.000 0.00 0.0 38.89 3.51 R
3663 5060 0.250081 TGGTGCGCTTGTGTGATACA 60.250 50.000 9.73 0.0 37.56 2.29 R
4017 5419 0.035152 ACATGCGCATTTGAGAGGGA 60.035 50.000 22.81 0.0 0.00 4.20 R
4181 5722 1.975660 GGTCAGTACCCTGTGCAAAA 58.024 50.000 0.00 0.0 40.21 2.44 R
4818 6710 2.814336 GCTAGTGGAAAGAGGTGGTTTG 59.186 50.000 0.00 0.0 0.00 2.93 R
5031 7304 6.910972 CACATGTATCATCAAATGACTCAAGC 59.089 38.462 0.00 0.0 43.01 4.01 R
6025 8694 2.256117 AAGCAAACGGTAAGCAGTCT 57.744 45.000 7.36 0.0 0.00 3.24 R
6878 10017 2.297315 TGTACACTCTCTCCAGTGCAAG 59.703 50.000 0.00 0.0 46.81 4.01 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
24 26 1.912001 TACCCGACGAACATAAAGCG 58.088 50.000 0.00 0.00 0.00 4.68
27 29 0.650512 CCGACGAACATAAAGCGCAT 59.349 50.000 11.47 0.00 0.00 4.73
37 39 4.956085 ACATAAAGCGCATGGTGTATCTA 58.044 39.130 11.47 0.00 0.00 1.98
40 42 3.543680 AAGCGCATGGTGTATCTAAGT 57.456 42.857 11.47 0.00 0.00 2.24
45 47 4.094294 GCGCATGGTGTATCTAAGTTTCAA 59.906 41.667 0.30 0.00 0.00 2.69
46 48 5.220854 GCGCATGGTGTATCTAAGTTTCAAT 60.221 40.000 0.30 0.00 0.00 2.57
49 51 8.394877 CGCATGGTGTATCTAAGTTTCAATAAA 58.605 33.333 0.00 0.00 0.00 1.40
97 99 3.409026 AACACTCATGAAGGGTCACTC 57.591 47.619 0.00 0.00 42.32 3.51
114 116 0.594602 CTCTTGACCCGTCACGTACA 59.405 55.000 0.00 0.00 39.66 2.90
129 131 3.305094 CACGTACACCCATTTATCGACAC 59.695 47.826 0.00 0.00 0.00 3.67
137 139 2.350498 CCATTTATCGACACGACAACCC 59.650 50.000 0.00 0.00 39.18 4.11
141 143 1.792006 ATCGACACGACAACCCTTTC 58.208 50.000 0.00 0.00 39.18 2.62
150 152 1.266989 GACAACCCTTTCCTCAAAGCG 59.733 52.381 0.00 0.00 38.19 4.68
166 168 5.457140 TCAAAGCGAATCAACAAATACACC 58.543 37.500 0.00 0.00 0.00 4.16
202 204 4.145807 TGCCTATTTCGAAGACCCAAAAA 58.854 39.130 0.00 0.00 34.32 1.94
221 230 4.419522 AAAACTGCAATCACACGGTATC 57.580 40.909 0.00 0.00 0.00 2.24
222 231 3.334583 AACTGCAATCACACGGTATCT 57.665 42.857 0.00 0.00 0.00 1.98
236 245 4.509970 CACGGTATCTCAAGTTCAACAACA 59.490 41.667 0.00 0.00 34.60 3.33
240 249 5.007332 GGTATCTCAAGTTCAACAACACGTT 59.993 40.000 0.00 0.00 38.83 3.99
268 286 9.921637 TTTGTACCATTGATAACAAAAATCTCC 57.078 29.630 8.01 0.00 38.50 3.71
276 294 1.250840 ACAAAAATCTCCGGCAGCCC 61.251 55.000 5.63 0.00 0.00 5.19
283 301 0.541764 TCTCCGGCAGCCCAAAAATT 60.542 50.000 5.63 0.00 0.00 1.82
286 304 1.273886 TCCGGCAGCCCAAAAATTAAC 59.726 47.619 5.63 0.00 0.00 2.01
288 306 1.068194 CGGCAGCCCAAAAATTAACGA 60.068 47.619 5.63 0.00 0.00 3.85
289 307 2.606108 GGCAGCCCAAAAATTAACGAG 58.394 47.619 0.00 0.00 0.00 4.18
300 318 9.301153 CCCAAAAATTAACGAGGAAATAATGAG 57.699 33.333 0.00 0.00 0.00 2.90
301 319 9.301153 CCAAAAATTAACGAGGAAATAATGAGG 57.699 33.333 0.00 0.00 0.00 3.86
354 373 8.608185 AAAGAGGAAGAAGAAGATACTCTGAT 57.392 34.615 0.00 0.00 34.39 2.90
440 459 4.520492 GCTTGAAGAGGAATTTGACCTGAA 59.480 41.667 0.00 0.00 37.93 3.02
441 460 5.335504 GCTTGAAGAGGAATTTGACCTGAAG 60.336 44.000 0.00 0.00 37.93 3.02
442 461 4.074970 TGAAGAGGAATTTGACCTGAAGC 58.925 43.478 0.00 0.00 37.93 3.86
443 462 3.078891 AGAGGAATTTGACCTGAAGCC 57.921 47.619 0.00 0.00 37.93 4.35
444 463 2.646798 AGAGGAATTTGACCTGAAGCCT 59.353 45.455 0.00 0.00 37.93 4.58
445 464 3.013219 GAGGAATTTGACCTGAAGCCTC 58.987 50.000 0.00 0.00 37.93 4.70
446 465 2.095461 GGAATTTGACCTGAAGCCTCC 58.905 52.381 0.00 0.00 0.00 4.30
447 466 2.291217 GGAATTTGACCTGAAGCCTCCT 60.291 50.000 0.00 0.00 0.00 3.69
448 467 2.503895 ATTTGACCTGAAGCCTCCTG 57.496 50.000 0.00 0.00 0.00 3.86
449 468 1.434188 TTTGACCTGAAGCCTCCTGA 58.566 50.000 0.00 0.00 0.00 3.86
450 469 1.661463 TTGACCTGAAGCCTCCTGAT 58.339 50.000 0.00 0.00 0.00 2.90
451 470 1.198713 TGACCTGAAGCCTCCTGATC 58.801 55.000 0.00 0.00 0.00 2.92
452 471 1.273495 TGACCTGAAGCCTCCTGATCT 60.273 52.381 0.00 0.00 0.00 2.75
453 472 1.138661 GACCTGAAGCCTCCTGATCTG 59.861 57.143 0.00 0.00 0.00 2.90
454 473 1.273495 ACCTGAAGCCTCCTGATCTGA 60.273 52.381 0.38 0.00 0.00 3.27
455 474 2.048601 CCTGAAGCCTCCTGATCTGAT 58.951 52.381 0.38 0.00 0.00 2.90
456 475 2.438763 CCTGAAGCCTCCTGATCTGATT 59.561 50.000 0.38 0.00 0.00 2.57
457 476 3.468770 CTGAAGCCTCCTGATCTGATTG 58.531 50.000 0.38 0.00 0.00 2.67
458 477 2.220313 GAAGCCTCCTGATCTGATTGC 58.780 52.381 0.38 0.76 0.00 3.56
459 478 1.210538 AGCCTCCTGATCTGATTGCA 58.789 50.000 0.38 0.00 0.00 4.08
460 479 1.562942 AGCCTCCTGATCTGATTGCAA 59.437 47.619 0.00 0.00 0.00 4.08
461 480 1.674962 GCCTCCTGATCTGATTGCAAC 59.325 52.381 0.00 0.00 0.00 4.17
462 481 1.938577 CCTCCTGATCTGATTGCAACG 59.061 52.381 0.00 0.00 0.00 4.10
463 482 1.329906 CTCCTGATCTGATTGCAACGC 59.670 52.381 0.00 0.00 0.00 4.84
464 483 0.027194 CCTGATCTGATTGCAACGCG 59.973 55.000 3.53 3.53 0.00 6.01
465 484 0.027194 CTGATCTGATTGCAACGCGG 59.973 55.000 12.47 2.04 0.00 6.46
466 485 1.297893 GATCTGATTGCAACGCGGC 60.298 57.895 12.47 5.57 0.00 6.53
467 486 2.954756 GATCTGATTGCAACGCGGCG 62.955 60.000 22.36 22.36 36.28 6.46
468 487 3.787676 CTGATTGCAACGCGGCGA 61.788 61.111 30.94 6.23 36.28 5.54
485 504 0.249280 CGACCTGCAAAAACCCAACC 60.249 55.000 0.00 0.00 0.00 3.77
509 533 0.323725 TCCATTTCCAGCCAAGGAGC 60.324 55.000 0.00 0.00 39.25 4.70
555 589 3.961414 GCCCAAACCCCTCCGTCA 61.961 66.667 0.00 0.00 0.00 4.35
556 590 2.840576 CCCAAACCCCTCCGTCAA 59.159 61.111 0.00 0.00 0.00 3.18
567 601 4.770874 CCGTCAAATCCCGGCCGT 62.771 66.667 26.12 1.61 37.43 5.68
568 602 2.744709 CGTCAAATCCCGGCCGTT 60.745 61.111 26.12 9.34 0.00 4.44
592 626 3.900892 CGGATCCGACGGTCCAGG 61.901 72.222 30.62 12.94 42.83 4.45
630 664 0.821711 TTAACACAGCCGCCTTGCTT 60.822 50.000 0.00 0.00 40.32 3.91
889 950 3.514362 GTAATGGCGGCGGGGTTG 61.514 66.667 9.78 0.00 0.00 3.77
920 981 0.449388 GGCTGCGGAGATCTTGTTTG 59.551 55.000 8.65 0.00 0.00 2.93
922 983 1.813513 CTGCGGAGATCTTGTTTGGT 58.186 50.000 0.00 0.00 0.00 3.67
935 996 4.686554 TCTTGTTTGGTTTCGTTTGTTTGG 59.313 37.500 0.00 0.00 0.00 3.28
962 1023 0.759060 GGTGGTGGGGCTGTTTCTTT 60.759 55.000 0.00 0.00 0.00 2.52
965 1026 1.063266 TGGTGGGGCTGTTTCTTTCTT 60.063 47.619 0.00 0.00 0.00 2.52
968 1029 1.332195 GGGGCTGTTTCTTTCTTGCT 58.668 50.000 0.00 0.00 0.00 3.91
1479 1749 6.685403 TCTCGTTTTTCATCTTTCGTTTTCAC 59.315 34.615 0.00 0.00 0.00 3.18
1486 1756 3.624326 TCTTTCGTTTTCACCATGCTG 57.376 42.857 0.00 0.00 0.00 4.41
1493 1763 6.176975 TCGTTTTCACCATGCTGTTATTAG 57.823 37.500 0.00 0.00 0.00 1.73
1494 1764 5.703592 TCGTTTTCACCATGCTGTTATTAGT 59.296 36.000 0.00 0.00 0.00 2.24
1495 1765 6.874664 TCGTTTTCACCATGCTGTTATTAGTA 59.125 34.615 0.00 0.00 0.00 1.82
1496 1766 7.064134 TCGTTTTCACCATGCTGTTATTAGTAG 59.936 37.037 0.00 0.00 0.00 2.57
1507 1777 6.982141 TGCTGTTATTAGTAGGTATTGGTTCG 59.018 38.462 0.00 0.00 0.00 3.95
1540 1810 5.063944 GTGTGTTATGACTTGCTATGAGTGG 59.936 44.000 0.00 0.00 0.00 4.00
1554 1824 1.416401 TGAGTGGAGTGGACTGGAAAC 59.584 52.381 0.00 0.00 0.00 2.78
1592 1862 3.600388 GGTGGTCAACTGAATAGTCCAG 58.400 50.000 0.00 0.00 35.69 3.86
1685 1968 7.573096 CGGTTAACTGAATAGTGCAAAGTTCAT 60.573 37.037 8.90 0.56 37.19 2.57
1686 1969 8.726988 GGTTAACTGAATAGTGCAAAGTTCATA 58.273 33.333 5.42 0.00 37.19 2.15
1687 1970 9.760660 GTTAACTGAATAGTGCAAAGTTCATAG 57.239 33.333 8.72 3.04 37.19 2.23
1699 1982 7.065085 GTGCAAAGTTCATAGTACATCATGAGT 59.935 37.037 0.09 2.37 32.96 3.41
1709 1992 6.707440 AGTACATCATGAGTCTAGTCTTGG 57.293 41.667 0.09 0.00 0.00 3.61
1741 2025 5.163663 GCTGTTTGATTTATCGATTGGGTGA 60.164 40.000 1.71 0.00 0.00 4.02
1770 2054 4.274214 TGCTTCTCAGTGTGATTTGAAGTG 59.726 41.667 0.00 0.00 32.22 3.16
1786 2078 8.585471 ATTTGAAGTGGCATATATAGGAATGG 57.415 34.615 0.00 0.00 0.00 3.16
1809 2101 2.169352 CTGTACTCATAGCTTGCAGGGT 59.831 50.000 5.64 5.64 0.00 4.34
1810 2102 2.093500 TGTACTCATAGCTTGCAGGGTG 60.093 50.000 11.20 0.00 0.00 4.61
1812 2104 0.543277 CTCATAGCTTGCAGGGTGGA 59.457 55.000 11.20 7.34 0.00 4.02
1813 2105 0.991146 TCATAGCTTGCAGGGTGGAA 59.009 50.000 11.20 0.00 0.00 3.53
1814 2106 1.098050 CATAGCTTGCAGGGTGGAAC 58.902 55.000 11.20 0.00 0.00 3.62
1815 2107 0.698238 ATAGCTTGCAGGGTGGAACA 59.302 50.000 11.20 0.00 39.98 3.18
1819 2113 1.691196 CTTGCAGGGTGGAACAAAGA 58.309 50.000 0.00 0.00 44.16 2.52
1821 2115 0.843309 TGCAGGGTGGAACAAAGAGA 59.157 50.000 0.00 0.00 44.16 3.10
1822 2116 1.239347 GCAGGGTGGAACAAAGAGAC 58.761 55.000 0.00 0.00 44.16 3.36
1840 2134 4.021894 AGAGACGCTATTCAGTTTGAGTGT 60.022 41.667 0.00 0.00 35.43 3.55
1853 2147 6.821160 TCAGTTTGAGTGTTGAATAGTGTTGA 59.179 34.615 0.00 0.00 0.00 3.18
1854 2148 7.498900 TCAGTTTGAGTGTTGAATAGTGTTGAT 59.501 33.333 0.00 0.00 0.00 2.57
1859 2153 8.394971 TGAGTGTTGAATAGTGTTGATTGATT 57.605 30.769 0.00 0.00 0.00 2.57
1878 2174 7.707624 TTGATTTATGAATTCTCAGCCAGTT 57.292 32.000 7.05 0.00 34.23 3.16
1899 2195 8.073768 CCAGTTTTTCTTTCTTTCGTAGCATTA 58.926 33.333 0.00 0.00 0.00 1.90
1933 2229 9.439500 TGGGTTATTGTAACTGTTATCACTAAC 57.561 33.333 19.95 19.95 38.17 2.34
1947 2243 9.098355 TGTTATCACTAACAGTTGCTGAATATC 57.902 33.333 2.91 0.00 41.73 1.63
1954 2250 6.899393 AACAGTTGCTGAATATCCTTTTCA 57.101 33.333 2.91 0.00 35.18 2.69
1959 2255 9.459640 CAGTTGCTGAATATCCTTTTCATATTG 57.540 33.333 0.00 0.00 32.94 1.90
1962 2258 8.985315 TGCTGAATATCCTTTTCATATTGACT 57.015 30.769 0.00 0.00 32.94 3.41
1970 2266 7.812690 TCCTTTTCATATTGACTGGATCATG 57.187 36.000 0.00 0.00 37.11 3.07
1977 2273 2.591571 TGACTGGATCATGAGAAGCG 57.408 50.000 0.09 0.00 29.99 4.68
1979 2275 0.829333 ACTGGATCATGAGAAGCGCT 59.171 50.000 2.64 2.64 0.00 5.92
1990 2286 2.348998 AAGCGCTGAGGTTCCTGG 59.651 61.111 12.58 0.00 35.29 4.45
2025 2321 9.117183 TCTGAATTTACTGGATCATGAGAAATG 57.883 33.333 0.09 0.00 0.00 2.32
2172 2691 2.565841 CCTGCATTAGGCCAGTAGAAC 58.434 52.381 5.01 0.00 43.89 3.01
2176 2695 2.608090 GCATTAGGCCAGTAGAACGAAC 59.392 50.000 5.01 0.00 36.11 3.95
2187 2706 4.448060 CAGTAGAACGAACCTTCCAAACTC 59.552 45.833 0.00 0.00 0.00 3.01
2189 2708 3.467803 AGAACGAACCTTCCAAACTCTG 58.532 45.455 0.00 0.00 0.00 3.35
2194 2713 2.278332 ACCTTCCAAACTCTGGCTTC 57.722 50.000 0.00 0.00 45.98 3.86
2197 2716 2.431454 CTTCCAAACTCTGGCTTCCTC 58.569 52.381 0.00 0.00 45.98 3.71
2198 2717 1.434188 TCCAAACTCTGGCTTCCTCA 58.566 50.000 0.00 0.00 45.98 3.86
2199 2718 1.072331 TCCAAACTCTGGCTTCCTCAC 59.928 52.381 0.00 0.00 45.98 3.51
2200 2719 1.528129 CAAACTCTGGCTTCCTCACC 58.472 55.000 0.00 0.00 0.00 4.02
2210 2729 4.816126 TGGCTTCCTCACCAGTATATACT 58.184 43.478 9.71 9.71 36.90 2.12
2283 3040 7.197071 TGTTACAACTGCGAACAATCTAATT 57.803 32.000 0.00 0.00 30.37 1.40
2310 3603 9.219603 TGGACAGTTCTATTTCTATTCAGTTTG 57.780 33.333 0.00 0.00 0.00 2.93
2420 3790 0.602562 CCAACCACAACCGCAATGAT 59.397 50.000 0.00 0.00 0.00 2.45
2469 3839 1.067084 CTGCATCGCGAGACTGGAT 59.933 57.895 16.66 0.00 46.97 3.41
2546 3916 3.120095 ACAATGAGTTGTCATCACATGCG 60.120 43.478 0.00 0.00 45.14 4.73
2567 3937 1.453633 ATGCATCTATTCTGGGGCCT 58.546 50.000 0.84 0.00 0.00 5.19
2603 3973 1.138568 CATCCCCTGATCCTGAGCTT 58.861 55.000 0.00 0.00 0.00 3.74
2705 4075 2.227968 CTTCTTTCCGCCGCAGTTCG 62.228 60.000 0.00 0.00 38.08 3.95
2774 4144 2.105128 CTGTCATCGTCGAGGGCC 59.895 66.667 9.23 0.00 0.00 5.80
2928 4310 3.143010 CCTGAGGGGTATTCGGCTA 57.857 57.895 0.00 0.00 0.00 3.93
2929 4311 1.420430 CCTGAGGGGTATTCGGCTAA 58.580 55.000 0.00 0.00 0.00 3.09
2933 4315 3.042682 TGAGGGGTATTCGGCTAATTCA 58.957 45.455 0.00 0.00 0.00 2.57
2934 4316 3.071023 TGAGGGGTATTCGGCTAATTCAG 59.929 47.826 0.00 0.00 0.00 3.02
2936 4318 3.071167 AGGGGTATTCGGCTAATTCAGTC 59.929 47.826 0.00 0.00 0.00 3.51
3029 4411 1.404851 GGCTATGCTTCGCCTAGGATC 60.405 57.143 14.75 0.00 42.98 3.36
3086 4468 5.079643 AGACAAAATTTAGGTGGTGCATCT 58.920 37.500 0.00 0.00 0.00 2.90
3095 4477 2.906354 GGTGGTGCATCTAACTACCTG 58.094 52.381 0.00 0.00 43.72 4.00
3134 4516 2.202866 TCCGACTGGAGCATCTTCC 58.797 57.895 0.00 0.00 40.17 3.46
3341 4735 2.043664 TGGATTTGGCCTTGGTTATGGA 59.956 45.455 3.32 0.00 0.00 3.41
3554 4948 5.175090 AGAGCAACAAAAGCAGAACTTAC 57.825 39.130 0.00 0.00 37.75 2.34
3572 4966 2.483583 ACGAGCTCTCTGAAATAGCG 57.516 50.000 12.85 0.00 41.19 4.26
3614 5008 6.149308 TCAGGTACACTTCTGCATTTAATGTG 59.851 38.462 6.81 0.00 0.00 3.21
3660 5057 9.838975 CAGCATGTAAACTGTAATGATTTGTAA 57.161 29.630 0.00 0.00 0.00 2.41
3662 5059 9.840427 GCATGTAAACTGTAATGATTTGTAAGT 57.160 29.630 0.00 0.00 0.00 2.24
3691 5088 2.677836 CACAAGCGCACCATACAGTTAT 59.322 45.455 11.47 0.00 0.00 1.89
3701 5098 6.475207 GCACCATACAGTTATTGTTACTTCG 58.525 40.000 0.00 0.00 41.29 3.79
3708 5105 9.784680 ATACAGTTATTGTTACTTCGTAGTCAG 57.215 33.333 0.00 0.00 41.29 3.51
3714 5111 6.866010 TTGTTACTTCGTAGTCAGTAGTCA 57.134 37.500 0.00 0.00 35.78 3.41
3728 5125 7.543756 AGTCAGTAGTCAGAGCTATTTCTTTC 58.456 38.462 0.00 0.00 0.00 2.62
3773 5170 8.091385 TGAACTGCTATATTGCATACATGAAG 57.909 34.615 12.26 1.33 42.48 3.02
3858 5256 8.709308 AGATTGTTTCTACAGCCTAGTGATAAT 58.291 33.333 0.00 0.00 35.28 1.28
3907 5305 1.754803 TGCATCGTACAGTCTTAGGGG 59.245 52.381 0.00 0.00 0.00 4.79
3942 5340 4.633565 CAGAAAGCACACTAATCCTCCTTC 59.366 45.833 0.00 0.00 0.00 3.46
4030 5432 3.563390 GCTTCTATGTCCCTCTCAAATGC 59.437 47.826 0.00 0.00 0.00 3.56
4064 5466 2.033299 GCACACACATACTGCACAAAGT 59.967 45.455 0.00 0.00 0.00 2.66
4078 5480 8.673626 ACTGCACAAAGTCGATAAAAATTATG 57.326 30.769 0.00 0.00 0.00 1.90
4525 6148 6.269307 GGTACTTATCCTTATGGTCTGCCTTA 59.731 42.308 0.00 0.00 35.27 2.69
4897 6791 5.012239 AGCTGTTATTTCAGAAGGCATCAA 58.988 37.500 0.00 0.00 37.61 2.57
5031 7304 1.003580 TGGCTGGAAGAGTAAAGGCAG 59.996 52.381 0.00 0.00 39.94 4.85
5317 7605 5.070847 ACATGCCCCCTTGATAAATTCATTC 59.929 40.000 0.00 0.00 33.34 2.67
5366 7656 7.468141 AATCTACCTCGCTCATTATCATGTA 57.532 36.000 0.00 0.00 0.00 2.29
5549 7839 6.013293 ACCTTGAACTTATCCAAGCTTCTACT 60.013 38.462 0.00 0.00 38.65 2.57
5550 7840 6.314896 CCTTGAACTTATCCAAGCTTCTACTG 59.685 42.308 0.00 0.00 38.65 2.74
5552 7842 7.476540 TGAACTTATCCAAGCTTCTACTGTA 57.523 36.000 0.00 0.00 34.94 2.74
5553 7843 8.079211 TGAACTTATCCAAGCTTCTACTGTAT 57.921 34.615 0.00 0.00 34.94 2.29
5604 7912 7.615582 TCATCTGAAGGTTATCATGTTGTTC 57.384 36.000 0.00 0.00 0.00 3.18
5659 7967 5.648330 AGTTTTCCTTTTGTACTCCCTCT 57.352 39.130 0.00 0.00 0.00 3.69
5799 8110 6.629128 TCGGCATTGTGAATGTTGATATTTT 58.371 32.000 0.00 0.00 41.01 1.82
5955 8604 4.216411 TCTGTTTTGGGTAGTAGCATCC 57.784 45.455 1.13 0.00 0.00 3.51
6044 8713 2.256117 AGACTGCTTACCGTTTGCTT 57.744 45.000 0.00 0.00 0.00 3.91
6535 9214 3.489355 TCAGCAGAGAGAGATGATCCTC 58.511 50.000 3.62 3.62 0.00 3.71
7301 10471 6.030228 GCATGAGTTAGTTTATGTTCTTGCC 58.970 40.000 0.00 0.00 32.70 4.52
7342 10517 8.477256 CCAAGATTCATGGTGTTTGGTATTTAT 58.523 33.333 0.00 0.00 32.44 1.40
7413 10719 9.964354 AGGCTATGCATATCAGATAAAATGTTA 57.036 29.630 6.92 0.00 0.00 2.41
7532 10839 1.763545 GTAGGAGGGTAGGCTCAAAGG 59.236 57.143 0.00 0.00 0.00 3.11
7553 10860 6.502136 AGGAAGTAACTGAGCTAAAATTGC 57.498 37.500 0.00 0.00 0.00 3.56
7567 10874 1.732941 AATTGCGGCGATGAACTGTA 58.267 45.000 12.98 0.00 0.00 2.74
7570 10877 0.319986 TGCGGCGATGAACTGTACAA 60.320 50.000 12.98 0.00 0.00 2.41
7572 10879 1.195900 GCGGCGATGAACTGTACAAAA 59.804 47.619 12.98 0.00 0.00 2.44
7574 10881 2.478894 CGGCGATGAACTGTACAAAACT 59.521 45.455 0.00 0.00 0.00 2.66
7576 10883 4.219033 GGCGATGAACTGTACAAAACTTG 58.781 43.478 0.00 0.00 0.00 3.16
7577 10884 3.664025 GCGATGAACTGTACAAAACTTGC 59.336 43.478 0.00 0.00 0.00 4.01
7578 10885 4.788201 GCGATGAACTGTACAAAACTTGCA 60.788 41.667 0.00 0.00 0.00 4.08
7707 11158 2.258286 GCAATGTTGTCCCCACGC 59.742 61.111 0.00 0.00 0.00 5.34
7722 11173 1.153168 ACGCGCTTAGGGCATTCAT 60.153 52.632 20.69 0.00 41.67 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 12 1.396996 ACCATGCGCTTTATGTTCGTC 59.603 47.619 9.73 0.00 0.00 4.20
12 14 1.130373 ACACCATGCGCTTTATGTTCG 59.870 47.619 9.73 0.00 0.00 3.95
24 26 9.722056 CTTTATTGAAACTTAGATACACCATGC 57.278 33.333 0.00 0.00 0.00 4.06
27 29 9.226606 CCACTTTATTGAAACTTAGATACACCA 57.773 33.333 0.00 0.00 0.00 4.17
79 81 3.007290 TCAAGAGTGACCCTTCATGAGTG 59.993 47.826 0.00 0.00 33.11 3.51
81 83 3.969287 TCAAGAGTGACCCTTCATGAG 57.031 47.619 0.00 0.00 33.11 2.90
94 96 0.595095 GTACGTGACGGGTCAAGAGT 59.405 55.000 19.10 13.86 41.85 3.24
97 99 0.665369 GGTGTACGTGACGGGTCAAG 60.665 60.000 10.66 12.20 41.85 3.02
114 116 2.997986 GTTGTCGTGTCGATAAATGGGT 59.002 45.455 3.28 0.00 38.54 4.51
129 131 1.266989 GCTTTGAGGAAAGGGTTGTCG 59.733 52.381 0.00 0.00 39.29 4.35
137 139 4.488126 TGTTGATTCGCTTTGAGGAAAG 57.512 40.909 0.00 0.00 41.49 2.62
141 143 5.569059 GTGTATTTGTTGATTCGCTTTGAGG 59.431 40.000 0.00 0.00 0.00 3.86
150 152 4.776795 AACGGGGTGTATTTGTTGATTC 57.223 40.909 0.00 0.00 0.00 2.52
202 204 3.262420 GAGATACCGTGTGATTGCAGTT 58.738 45.455 0.00 0.00 0.00 3.16
204 206 2.892374 TGAGATACCGTGTGATTGCAG 58.108 47.619 0.00 0.00 0.00 4.41
205 207 3.261580 CTTGAGATACCGTGTGATTGCA 58.738 45.455 0.00 0.00 0.00 4.08
206 208 3.262420 ACTTGAGATACCGTGTGATTGC 58.738 45.455 0.00 0.00 0.00 3.56
207 209 4.929211 TGAACTTGAGATACCGTGTGATTG 59.071 41.667 0.00 0.00 0.00 2.67
210 219 4.202172 TGTTGAACTTGAGATACCGTGTGA 60.202 41.667 0.00 0.00 0.00 3.58
245 254 7.193595 CCGGAGATTTTTGTTATCAATGGTAC 58.806 38.462 0.00 0.00 33.32 3.34
247 256 5.394115 GCCGGAGATTTTTGTTATCAATGGT 60.394 40.000 5.05 0.00 33.32 3.55
250 259 5.679638 GCTGCCGGAGATTTTTGTTATCAAT 60.680 40.000 5.05 0.00 33.32 2.57
252 261 3.128589 GCTGCCGGAGATTTTTGTTATCA 59.871 43.478 5.05 0.00 0.00 2.15
253 262 3.489229 GGCTGCCGGAGATTTTTGTTATC 60.489 47.826 5.05 0.00 0.00 1.75
254 263 2.427095 GGCTGCCGGAGATTTTTGTTAT 59.573 45.455 5.05 0.00 0.00 1.89
255 264 1.816224 GGCTGCCGGAGATTTTTGTTA 59.184 47.619 5.05 0.00 0.00 2.41
256 265 0.603065 GGCTGCCGGAGATTTTTGTT 59.397 50.000 5.05 0.00 0.00 2.83
258 267 1.250154 TGGGCTGCCGGAGATTTTTG 61.250 55.000 13.40 0.00 0.00 2.44
259 268 0.541764 TTGGGCTGCCGGAGATTTTT 60.542 50.000 13.40 0.00 0.00 1.94
268 286 1.068194 TCGTTAATTTTTGGGCTGCCG 60.068 47.619 13.40 0.00 0.00 5.69
286 304 7.387948 ACGGAATAATTCCTCATTATTTCCTCG 59.612 37.037 0.00 6.55 44.81 4.63
288 306 8.217799 TGACGGAATAATTCCTCATTATTTCCT 58.782 33.333 0.00 0.00 44.81 3.36
289 307 8.391075 TGACGGAATAATTCCTCATTATTTCC 57.609 34.615 0.00 0.00 44.81 3.13
300 318 5.859495 AGAGGAGATTGACGGAATAATTCC 58.141 41.667 0.00 0.00 46.62 3.01
301 319 6.516718 TGAGAGGAGATTGACGGAATAATTC 58.483 40.000 0.00 0.00 0.00 2.17
302 320 6.485830 TGAGAGGAGATTGACGGAATAATT 57.514 37.500 0.00 0.00 0.00 1.40
354 373 8.934825 GCTAATTTTGGCAATGTGATCTTTTTA 58.065 29.630 0.00 0.00 34.50 1.52
440 459 1.210538 TGCAATCAGATCAGGAGGCT 58.789 50.000 0.00 0.00 0.00 4.58
441 460 1.674962 GTTGCAATCAGATCAGGAGGC 59.325 52.381 0.59 1.62 0.00 4.70
442 461 1.938577 CGTTGCAATCAGATCAGGAGG 59.061 52.381 0.59 0.00 0.00 4.30
443 462 1.329906 GCGTTGCAATCAGATCAGGAG 59.670 52.381 0.59 0.00 0.00 3.69
444 463 1.372582 GCGTTGCAATCAGATCAGGA 58.627 50.000 0.59 0.00 0.00 3.86
445 464 0.027194 CGCGTTGCAATCAGATCAGG 59.973 55.000 0.59 0.00 0.00 3.86
446 465 0.027194 CCGCGTTGCAATCAGATCAG 59.973 55.000 0.59 0.00 0.00 2.90
447 466 1.980951 GCCGCGTTGCAATCAGATCA 61.981 55.000 0.59 0.00 0.00 2.92
448 467 1.297893 GCCGCGTTGCAATCAGATC 60.298 57.895 0.59 0.00 0.00 2.75
449 468 2.793946 GCCGCGTTGCAATCAGAT 59.206 55.556 0.59 0.00 0.00 2.90
450 469 3.787676 CGCCGCGTTGCAATCAGA 61.788 61.111 0.59 0.00 0.00 3.27
451 470 3.787676 TCGCCGCGTTGCAATCAG 61.788 61.111 13.39 0.00 0.00 2.90
452 471 4.083600 GTCGCCGCGTTGCAATCA 62.084 61.111 13.39 0.00 0.00 2.57
453 472 4.811761 GGTCGCCGCGTTGCAATC 62.812 66.667 13.39 0.00 0.00 2.67
461 480 4.320928 TTTTTGCAGGTCGCCGCG 62.321 61.111 6.39 6.39 41.33 6.46
462 481 2.729491 GTTTTTGCAGGTCGCCGC 60.729 61.111 0.00 6.03 41.33 6.53
463 482 2.050442 GGTTTTTGCAGGTCGCCG 60.050 61.111 0.00 0.00 41.33 6.46
464 483 2.022240 TTGGGTTTTTGCAGGTCGCC 62.022 55.000 0.00 0.00 41.33 5.54
465 484 0.874175 GTTGGGTTTTTGCAGGTCGC 60.874 55.000 0.00 0.00 42.89 5.19
466 485 0.249280 GGTTGGGTTTTTGCAGGTCG 60.249 55.000 0.00 0.00 0.00 4.79
467 486 0.827368 TGGTTGGGTTTTTGCAGGTC 59.173 50.000 0.00 0.00 0.00 3.85
468 487 0.829990 CTGGTTGGGTTTTTGCAGGT 59.170 50.000 0.00 0.00 0.00 4.00
485 504 2.028748 CCTTGGCTGGAAATGGAAACTG 60.029 50.000 0.00 0.00 0.00 3.16
509 533 1.933247 TTGAGGCCGCAAAGTTTTTG 58.067 45.000 20.47 0.00 0.00 2.44
553 587 2.435234 CGAACGGCCGGGATTTGA 60.435 61.111 31.76 0.00 0.00 2.69
630 664 1.657804 GTGGGGGAAGAAGAGAAGGA 58.342 55.000 0.00 0.00 0.00 3.36
734 777 2.824041 CAGACCGCCGGAAATGGG 60.824 66.667 11.71 0.00 0.00 4.00
889 950 1.371558 CGCAGCCTTATCCCCCTAC 59.628 63.158 0.00 0.00 0.00 3.18
920 981 2.668945 CACCAACCAAACAAACGAAACC 59.331 45.455 0.00 0.00 0.00 3.27
922 983 3.318017 CACACCAACCAAACAAACGAAA 58.682 40.909 0.00 0.00 0.00 3.46
935 996 2.520741 CCCCACCACCACACCAAC 60.521 66.667 0.00 0.00 0.00 3.77
986 1047 0.319900 CACCATCGGATCGATCACCC 60.320 60.000 25.93 9.55 45.19 4.61
1158 1234 3.695606 TCGTCCAGCAGCACCTCC 61.696 66.667 0.00 0.00 0.00 4.30
1479 1749 7.224297 ACCAATACCTACTAATAACAGCATGG 58.776 38.462 0.00 0.00 43.62 3.66
1486 1756 6.282930 TGCCGAACCAATACCTACTAATAAC 58.717 40.000 0.00 0.00 0.00 1.89
1493 1763 2.277084 CACTGCCGAACCAATACCTAC 58.723 52.381 0.00 0.00 0.00 3.18
1494 1764 1.406341 GCACTGCCGAACCAATACCTA 60.406 52.381 0.00 0.00 0.00 3.08
1495 1765 0.676782 GCACTGCCGAACCAATACCT 60.677 55.000 0.00 0.00 0.00 3.08
1496 1766 0.676782 AGCACTGCCGAACCAATACC 60.677 55.000 0.00 0.00 0.00 2.73
1507 1777 1.197721 GTCATAACACACAGCACTGCC 59.802 52.381 0.00 0.00 0.00 4.85
1540 1810 1.543429 CCCAGTGTTTCCAGTCCACTC 60.543 57.143 0.00 0.00 37.34 3.51
1570 1840 2.028476 TGGACTATTCAGTTGACCACCG 60.028 50.000 0.00 0.00 34.21 4.94
1572 1842 3.008049 ACCTGGACTATTCAGTTGACCAC 59.992 47.826 0.00 0.00 34.21 4.16
1685 1968 7.347252 ACCAAGACTAGACTCATGATGTACTA 58.653 38.462 0.00 0.00 0.00 1.82
1686 1969 6.191315 ACCAAGACTAGACTCATGATGTACT 58.809 40.000 0.00 0.00 0.00 2.73
1687 1970 6.320164 AGACCAAGACTAGACTCATGATGTAC 59.680 42.308 0.00 0.00 0.00 2.90
1699 1982 2.028658 CAGCTGCAAGACCAAGACTAGA 60.029 50.000 0.00 0.00 34.07 2.43
1709 1992 4.790140 CGATAAATCAAACAGCTGCAAGAC 59.210 41.667 15.27 0.00 34.07 3.01
1741 2025 1.072806 TCACACTGAGAAGCATGCCTT 59.927 47.619 15.66 8.13 36.19 4.35
1770 2054 7.124298 TGAGTACAGACCATTCCTATATATGCC 59.876 40.741 0.00 0.00 0.00 4.40
1786 2078 3.452474 CCTGCAAGCTATGAGTACAGAC 58.548 50.000 0.00 0.00 0.00 3.51
1809 2101 4.245660 CTGAATAGCGTCTCTTTGTTCCA 58.754 43.478 0.00 0.00 0.00 3.53
1810 2102 4.246458 ACTGAATAGCGTCTCTTTGTTCC 58.754 43.478 0.00 0.00 0.00 3.62
1812 2104 5.758296 TCAAACTGAATAGCGTCTCTTTGTT 59.242 36.000 0.00 0.00 0.00 2.83
1813 2105 5.297547 TCAAACTGAATAGCGTCTCTTTGT 58.702 37.500 0.00 0.00 0.00 2.83
1814 2106 5.406780 ACTCAAACTGAATAGCGTCTCTTTG 59.593 40.000 0.00 0.00 0.00 2.77
1815 2107 5.406780 CACTCAAACTGAATAGCGTCTCTTT 59.593 40.000 0.00 0.00 0.00 2.52
1819 2113 4.258702 ACACTCAAACTGAATAGCGTCT 57.741 40.909 0.00 0.00 0.00 4.18
1821 2115 4.377021 TCAACACTCAAACTGAATAGCGT 58.623 39.130 0.00 0.00 0.00 5.07
1822 2116 4.990543 TCAACACTCAAACTGAATAGCG 57.009 40.909 0.00 0.00 0.00 4.26
1853 2147 7.893124 ACTGGCTGAGAATTCATAAATCAAT 57.107 32.000 8.44 0.00 31.68 2.57
1854 2148 7.707624 AACTGGCTGAGAATTCATAAATCAA 57.292 32.000 8.44 0.00 31.68 2.57
1859 2153 7.765695 AGAAAAACTGGCTGAGAATTCATAA 57.234 32.000 8.44 0.00 31.68 1.90
1899 2195 3.454812 AGTTACAATAACCCATCCGAGCT 59.545 43.478 0.00 0.00 0.00 4.09
1903 2199 6.764085 TGATAACAGTTACAATAACCCATCCG 59.236 38.462 0.00 0.00 0.00 4.18
1933 2229 9.459640 CAATATGAAAAGGATATTCAGCAACTG 57.540 33.333 0.00 0.00 39.92 3.16
1938 2234 8.295288 CCAGTCAATATGAAAAGGATATTCAGC 58.705 37.037 0.00 0.00 39.92 4.26
1947 2243 7.718314 TCTCATGATCCAGTCAATATGAAAAGG 59.282 37.037 0.00 0.00 40.97 3.11
1954 2250 5.236282 CGCTTCTCATGATCCAGTCAATAT 58.764 41.667 0.00 0.00 40.97 1.28
1959 2255 1.202510 AGCGCTTCTCATGATCCAGTC 60.203 52.381 2.64 0.00 0.00 3.51
1962 2258 0.826062 TCAGCGCTTCTCATGATCCA 59.174 50.000 7.50 0.00 0.00 3.41
1970 2266 0.739112 CAGGAACCTCAGCGCTTCTC 60.739 60.000 7.50 0.00 0.00 2.87
1977 2273 2.333688 GGTTATCCAGGAACCTCAGC 57.666 55.000 3.23 0.00 42.68 4.26
1998 2294 9.863650 ATTTCTCATGATCCAGTAAATTCAGAT 57.136 29.630 0.00 0.00 0.00 2.90
2025 2321 6.706270 TGAAACATTGTGAAGACCTAGAGAAC 59.294 38.462 0.00 0.00 0.00 3.01
2164 2683 4.377897 AGTTTGGAAGGTTCGTTCTACTG 58.622 43.478 5.47 0.00 0.00 2.74
2189 2708 5.810080 AAGTATATACTGGTGAGGAAGCC 57.190 43.478 16.11 0.00 36.50 4.35
2190 2709 7.527568 AGTAAGTATATACTGGTGAGGAAGC 57.472 40.000 16.11 0.00 36.50 3.86
2194 2713 8.466617 AGTGAAGTAAGTATATACTGGTGAGG 57.533 38.462 16.11 0.00 36.28 3.86
2207 2726 9.201989 ACATGATCAGGAATAGTGAAGTAAGTA 57.798 33.333 15.42 0.00 0.00 2.24
2208 2727 8.083828 ACATGATCAGGAATAGTGAAGTAAGT 57.916 34.615 15.42 0.00 0.00 2.24
2250 3007 2.292016 CGCAGTTGTAACATGGAACCAA 59.708 45.455 0.00 0.00 0.00 3.67
2283 3040 9.793259 AAACTGAATAGAAATAGAACTGTCCAA 57.207 29.630 0.00 0.00 0.00 3.53
2301 3201 6.441274 CGCCTTGCATAATATCAAACTGAAT 58.559 36.000 0.00 0.00 0.00 2.57
2310 3603 4.878397 AGATAAGCCGCCTTGCATAATATC 59.122 41.667 0.00 0.00 32.47 1.63
2420 3790 4.019174 GCATTCCAGAAGAATCCAGGAAA 58.981 43.478 0.00 0.00 43.63 3.13
2469 3839 2.817424 CTGCAGGCCGCTCATAGA 59.183 61.111 18.14 0.00 43.06 1.98
2546 3916 2.307098 AGGCCCCAGAATAGATGCATAC 59.693 50.000 0.00 0.00 0.00 2.39
2567 3937 3.449018 GGGATGCACTTCTAGAGAGTGAA 59.551 47.826 26.05 20.59 35.75 3.18
2603 3973 1.640917 GACTTGGTACCCTCCTCACA 58.359 55.000 10.07 0.00 0.00 3.58
2618 3988 4.021925 GGAGGCAGGCACGGACTT 62.022 66.667 0.00 0.00 40.62 3.01
2705 4075 0.947244 CAGGTTCACCAACAGCAGAC 59.053 55.000 0.00 0.00 38.89 3.51
2774 4144 1.202758 TCCATAGCTTGCCCATTACCG 60.203 52.381 0.00 0.00 0.00 4.02
3086 4468 3.709653 CTCCATTGTAGCCCAGGTAGTTA 59.290 47.826 0.00 0.00 0.00 2.24
3095 4477 2.290960 ACTTCCAACTCCATTGTAGCCC 60.291 50.000 0.00 0.00 36.47 5.19
3134 4516 2.416566 CGGATCGATAGGCATCTGAAGG 60.417 54.545 0.00 0.00 0.00 3.46
3554 4948 1.601663 CCCGCTATTTCAGAGAGCTCG 60.602 57.143 8.37 0.00 33.91 5.03
3572 4966 0.605319 TGAACTCAACGACATGCCCC 60.605 55.000 0.00 0.00 0.00 5.80
3636 5033 9.840427 ACTTACAAATCATTACAGTTTACATGC 57.160 29.630 0.00 0.00 0.00 4.06
3651 5048 7.359595 GCTTGTGTGATACAACTTACAAATCA 58.640 34.615 0.00 0.00 44.07 2.57
3652 5049 6.519761 CGCTTGTGTGATACAACTTACAAATC 59.480 38.462 0.00 0.00 44.07 2.17
3653 5050 6.370593 CGCTTGTGTGATACAACTTACAAAT 58.629 36.000 0.00 0.00 44.07 2.32
3654 5051 5.743467 CGCTTGTGTGATACAACTTACAAA 58.257 37.500 0.00 0.00 44.07 2.83
3655 5052 4.319190 GCGCTTGTGTGATACAACTTACAA 60.319 41.667 0.00 0.00 44.07 2.41
3656 5053 3.185594 GCGCTTGTGTGATACAACTTACA 59.814 43.478 0.00 0.00 44.07 2.41
3657 5054 3.185594 TGCGCTTGTGTGATACAACTTAC 59.814 43.478 9.73 0.00 44.07 2.34
3658 5055 3.185594 GTGCGCTTGTGTGATACAACTTA 59.814 43.478 9.73 0.00 44.07 2.24
3659 5056 2.032030 GTGCGCTTGTGTGATACAACTT 60.032 45.455 9.73 0.00 44.07 2.66
3660 5057 1.531149 GTGCGCTTGTGTGATACAACT 59.469 47.619 9.73 0.00 44.07 3.16
3661 5058 1.399727 GGTGCGCTTGTGTGATACAAC 60.400 52.381 9.73 0.00 44.07 3.32
3662 5059 0.871722 GGTGCGCTTGTGTGATACAA 59.128 50.000 9.73 0.00 46.62 2.41
3663 5060 0.250081 TGGTGCGCTTGTGTGATACA 60.250 50.000 9.73 0.00 37.56 2.29
3664 5061 1.086696 ATGGTGCGCTTGTGTGATAC 58.913 50.000 9.73 0.00 0.00 2.24
3665 5062 2.276201 GTATGGTGCGCTTGTGTGATA 58.724 47.619 9.73 0.00 0.00 2.15
3666 5063 1.086696 GTATGGTGCGCTTGTGTGAT 58.913 50.000 9.73 0.00 0.00 3.06
3667 5064 0.250081 TGTATGGTGCGCTTGTGTGA 60.250 50.000 9.73 0.00 0.00 3.58
3671 5068 2.465860 TAACTGTATGGTGCGCTTGT 57.534 45.000 9.73 0.00 0.00 3.16
3676 5073 6.417191 AAGTAACAATAACTGTATGGTGCG 57.583 37.500 0.00 0.00 37.23 5.34
3680 5077 8.922058 ACTACGAAGTAACAATAACTGTATGG 57.078 34.615 0.00 0.00 45.13 2.74
3691 5088 6.707608 TCTGACTACTGACTACGAAGTAACAA 59.292 38.462 0.00 0.00 45.13 2.83
3701 5098 7.562454 AGAAATAGCTCTGACTACTGACTAC 57.438 40.000 0.00 0.00 0.00 2.73
3708 5105 6.481644 CCCATGAAAGAAATAGCTCTGACTAC 59.518 42.308 0.00 0.00 0.00 2.73
3714 5111 5.819991 TGTTCCCATGAAAGAAATAGCTCT 58.180 37.500 0.00 0.00 30.79 4.09
3728 5125 1.766494 TGCTATGCCTTGTTCCCATG 58.234 50.000 0.00 0.00 0.00 3.66
3783 5180 6.009589 TCCTCATTTTTGCTCAGTTTATCCA 58.990 36.000 0.00 0.00 0.00 3.41
3830 5228 5.246203 TCACTAGGCTGTAGAAACAATCTGT 59.754 40.000 0.00 0.00 39.30 3.41
3858 5256 7.398047 TGCACACTAAGGGAGTACTCTTAATAA 59.602 37.037 21.88 3.44 38.43 1.40
3867 5265 4.058817 GCATATGCACACTAAGGGAGTAC 58.941 47.826 22.84 0.00 41.59 2.73
3907 5305 3.243704 TGTGCTTTCTGTTGGGTATTTGC 60.244 43.478 0.00 0.00 0.00 3.68
3942 5340 9.270576 CTTTTCATTATTTGAGTGATCAGAACG 57.729 33.333 0.00 0.00 35.27 3.95
4017 5419 0.035152 ACATGCGCATTTGAGAGGGA 60.035 50.000 22.81 0.00 0.00 4.20
4030 5432 3.285982 TGTGCACCCACACATGCG 61.286 61.111 15.69 0.00 46.51 4.73
4078 5480 8.964150 GTGTTCCACACTACAAAAATATGTTTC 58.036 33.333 0.00 0.00 45.27 2.78
4087 5548 2.357075 TGCGTGTTCCACACTACAAAA 58.643 42.857 5.53 0.00 46.46 2.44
4110 5571 3.503365 AGGTGCCATAATGCATTATGCT 58.497 40.909 37.65 29.46 45.11 3.79
4126 5587 2.231235 CACTGGGGATTTTGTTAGGTGC 59.769 50.000 0.00 0.00 0.00 5.01
4181 5722 1.975660 GGTCAGTACCCTGTGCAAAA 58.024 50.000 0.00 0.00 40.21 2.44
4818 6710 2.814336 GCTAGTGGAAAGAGGTGGTTTG 59.186 50.000 0.00 0.00 0.00 2.93
4897 6791 8.922676 CGACAGTTTACAAGTTAATCTGTACAT 58.077 33.333 0.00 0.00 37.50 2.29
5031 7304 6.910972 CACATGTATCATCAAATGACTCAAGC 59.089 38.462 0.00 0.00 43.01 4.01
5341 7629 7.468141 ACATGATAATGAGCGAGGTAGATTA 57.532 36.000 0.00 0.00 0.00 1.75
5366 7656 2.514458 CCAGCACCCTCTGGTAATTT 57.486 50.000 1.80 0.00 45.57 1.82
5549 7839 7.523219 CACAAAATAGCCGACTACAAAATACA 58.477 34.615 0.00 0.00 0.00 2.29
5550 7840 6.468000 GCACAAAATAGCCGACTACAAAATAC 59.532 38.462 0.00 0.00 0.00 1.89
5552 7842 5.048364 TGCACAAAATAGCCGACTACAAAAT 60.048 36.000 0.00 0.00 0.00 1.82
5553 7843 4.276183 TGCACAAAATAGCCGACTACAAAA 59.724 37.500 0.00 0.00 0.00 2.44
5659 7967 8.962679 ACCTAATATGCGGAATAAAAAGAAACA 58.037 29.630 0.00 0.00 0.00 2.83
5863 8507 6.864685 TGTGTAAAGTCCACGTCTTAGTAATG 59.135 38.462 0.00 0.00 35.56 1.90
6025 8694 2.256117 AAGCAAACGGTAAGCAGTCT 57.744 45.000 7.36 0.00 0.00 3.24
6535 9214 2.486982 CAGGTGAGCTTTGATCCTTGTG 59.513 50.000 0.00 0.00 0.00 3.33
6647 9326 5.100344 AGATCTTCATGCTGAATCTGTGT 57.900 39.130 0.00 0.00 35.59 3.72
6878 10017 2.297315 TGTACACTCTCTCCAGTGCAAG 59.703 50.000 0.00 0.00 46.81 4.01
7227 10385 5.867716 AGACGACACACTCCATTAATACAAC 59.132 40.000 0.00 0.00 0.00 3.32
7301 10471 7.031226 TGAATCTTGGTGAGAGAAAAACTTG 57.969 36.000 0.00 0.00 37.93 3.16
7342 10517 6.425210 ACAGATATGAGTTATGCTTGGCTA 57.575 37.500 0.00 0.00 0.00 3.93
7343 10518 5.301835 ACAGATATGAGTTATGCTTGGCT 57.698 39.130 0.00 0.00 0.00 4.75
7381 10556 4.079253 TCTGATATGCATAGCCTACACGA 58.921 43.478 18.79 3.85 0.00 4.35
7472 10779 4.700268 CTGTGCACAGCCAAACATATTA 57.300 40.909 32.39 0.00 37.15 0.98
7532 10839 5.324697 CCGCAATTTTAGCTCAGTTACTTC 58.675 41.667 0.00 0.00 0.00 3.01
7553 10860 2.478894 AGTTTTGTACAGTTCATCGCCG 59.521 45.455 0.00 0.00 0.00 6.46
7567 10874 7.977853 GGATATGATCTCAAATGCAAGTTTTGT 59.022 33.333 10.26 0.00 35.90 2.83
7570 10877 7.649533 TGGATATGATCTCAAATGCAAGTTT 57.350 32.000 0.00 0.00 0.00 2.66
7572 10879 7.649533 TTTGGATATGATCTCAAATGCAAGT 57.350 32.000 0.00 0.00 32.40 3.16
7574 10881 8.070034 AGTTTTGGATATGATCTCAAATGCAA 57.930 30.769 0.00 0.00 33.03 4.08
7576 10883 7.042925 GCAAGTTTTGGATATGATCTCAAATGC 60.043 37.037 0.00 0.00 32.59 3.56
7577 10884 7.977293 TGCAAGTTTTGGATATGATCTCAAATG 59.023 33.333 0.00 0.00 33.03 2.32
7578 10885 8.070034 TGCAAGTTTTGGATATGATCTCAAAT 57.930 30.769 0.00 0.00 33.03 2.32
7632 11083 3.964031 TGTTGGGGCTGTGTTTCTTAAAT 59.036 39.130 0.00 0.00 0.00 1.40
7722 11173 2.445145 TGAGTCTTGGGGGTTGATTTGA 59.555 45.455 0.00 0.00 0.00 2.69


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

AutoCloner maintained by Alex Coulton.