Multiple sequence alignment - TraesCS2D01G361700

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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 TraesCS2D01G361700 chr2D 100.000 3430 0 0 1 3430 466808551 466811980 0.000000e+00 6335.0
1 TraesCS2D01G361700 chr2B 92.216 2351 116 27 783 3096 545432360 545434680 0.000000e+00 3265.0
2 TraesCS2D01G361700 chr2B 89.456 294 30 1 3130 3422 545434683 545434976 1.500000e-98 370.0
3 TraesCS2D01G361700 chr2B 82.667 150 19 5 3143 3286 223244664 223244516 3.590000e-25 126.0
4 TraesCS2D01G361700 chr2A 94.214 2022 71 14 806 2813 607876947 607874958 0.000000e+00 3044.0
5 TraesCS2D01G361700 chr6B 87.371 483 57 4 1926 2406 457310687 457311167 5.000000e-153 551.0
6 TraesCS2D01G361700 chr6B 76.700 794 150 25 1063 1834 457309813 457310593 3.190000e-110 409.0
7 TraesCS2D01G361700 chr6D 87.164 483 58 4 1926 2406 292783295 292783775 2.330000e-151 545.0
8 TraesCS2D01G361700 chr6D 76.671 793 152 24 1063 1834 292782425 292783205 3.190000e-110 409.0
9 TraesCS2D01G361700 chr6A 86.804 485 60 4 1924 2406 428302328 428301846 3.890000e-149 538.0
10 TraesCS2D01G361700 chr6A 76.797 793 151 24 1063 1834 428303205 428302425 6.850000e-112 414.0
11 TraesCS2D01G361700 chr6A 81.518 303 40 12 435 731 594380625 594380917 5.720000e-58 235.0
12 TraesCS2D01G361700 chr5B 83.280 311 40 11 435 735 513969743 513970051 3.370000e-70 276.0
13 TraesCS2D01G361700 chr3D 82.675 329 39 16 426 745 308788596 308788277 3.370000e-70 276.0
14 TraesCS2D01G361700 chr3D 84.000 225 26 9 519 736 568043621 568043400 1.250000e-49 207.0
15 TraesCS2D01G361700 chr3D 79.861 144 16 7 2928 3070 270459846 270459715 3.640000e-15 93.5
16 TraesCS2D01G361700 chr3D 94.118 51 2 1 391 441 2628305 2628256 3.670000e-10 76.8
17 TraesCS2D01G361700 chr3B 83.972 287 31 14 426 704 412721570 412721849 9.440000e-66 261.0
18 TraesCS2D01G361700 chr3B 81.944 144 22 4 3145 3286 146777884 146777743 6.010000e-23 119.0
19 TraesCS2D01G361700 chr1A 81.847 314 44 12 426 736 331521146 331521449 5.680000e-63 252.0
20 TraesCS2D01G361700 chr5D 80.268 299 49 9 440 736 67016444 67016154 2.070000e-52 217.0
21 TraesCS2D01G361700 chr5D 79.798 297 42 15 456 745 497017811 497018096 2.090000e-47 200.0
22 TraesCS2D01G361700 chr3A 80.064 311 46 12 437 736 1397813 1397508 2.070000e-52 217.0
23 TraesCS2D01G361700 chr3A 82.432 148 21 5 3142 3286 689201150 689201295 1.290000e-24 124.0
24 TraesCS2D01G361700 chr3A 73.684 228 42 9 301 513 656973002 656972778 4.750000e-09 73.1
25 TraesCS2D01G361700 chrUn 75.154 487 86 24 261 736 90114152 90113690 2.700000e-46 196.0
26 TraesCS2D01G361700 chr4A 84.564 149 17 6 1682 1827 691133250 691133395 3.570000e-30 143.0
27 TraesCS2D01G361700 chr7B 83.673 147 18 5 3145 3286 696343283 696343138 2.150000e-27 134.0
28 TraesCS2D01G361700 chr7B 81.507 146 22 4 3144 3286 232696088 232695945 7.780000e-22 115.0
29 TraesCS2D01G361700 chr4B 83.562 146 20 4 3144 3286 228050534 228050390 2.150000e-27 134.0
30 TraesCS2D01G361700 chr7A 82.313 147 19 7 3144 3286 256509045 256508902 1.670000e-23 121.0
31 TraesCS2D01G361700 chr7A 81.379 145 22 5 3145 3286 256516713 256516571 2.800000e-21 113.0
32 TraesCS2D01G361700 chr1D 94.545 55 3 0 391 445 302892319 302892373 6.100000e-13 86.1
33 TraesCS2D01G361700 chr1D 90.196 51 4 1 397 446 307671735 307671685 7.950000e-07 65.8


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 TraesCS2D01G361700 chr2D 466808551 466811980 3429 False 6335.0 6335 100.0000 1 3430 1 chr2D.!!$F1 3429
1 TraesCS2D01G361700 chr2B 545432360 545434976 2616 False 1817.5 3265 90.8360 783 3422 2 chr2B.!!$F1 2639
2 TraesCS2D01G361700 chr2A 607874958 607876947 1989 True 3044.0 3044 94.2140 806 2813 1 chr2A.!!$R1 2007
3 TraesCS2D01G361700 chr6B 457309813 457311167 1354 False 480.0 551 82.0355 1063 2406 2 chr6B.!!$F1 1343
4 TraesCS2D01G361700 chr6D 292782425 292783775 1350 False 477.0 545 81.9175 1063 2406 2 chr6D.!!$F1 1343
5 TraesCS2D01G361700 chr6A 428301846 428303205 1359 True 476.0 538 81.8005 1063 2406 2 chr6A.!!$R1 1343

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
25 26 0.454196 GCCACCGTTGACTTTGTGTT 59.546 50.000 0.00 0.00 0.00 3.32 F
54 55 0.685097 GGCACACACTCCTTGAGGTA 59.315 55.000 0.00 0.00 33.35 3.08 F
55 56 1.071699 GGCACACACTCCTTGAGGTAA 59.928 52.381 0.00 0.00 33.35 2.85 F
985 991 2.202570 CCGACCTTGGTAGCGTCG 60.203 66.667 12.14 12.14 41.07 5.12 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1209 1215 0.619255 TGAAGCCCATTAGACCGGGA 60.619 55.000 6.32 0.0 46.34 5.14 R
1269 1275 1.892862 CTCCTCGGCGTACTCGGAT 60.893 63.158 6.85 0.0 37.56 4.18 R
1934 1976 1.982612 TCATCAGCACGTTCTTCTCG 58.017 50.000 0.00 0.0 0.00 4.04 R
2555 2613 0.037232 AGCTCCGTGCAAGAAGGTAC 60.037 55.000 0.00 0.0 45.94 3.34 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
17 18 4.012895 CACTGCGCCACCGTTGAC 62.013 66.667 4.18 0.00 36.67 3.18
18 19 4.235762 ACTGCGCCACCGTTGACT 62.236 61.111 4.18 0.00 36.67 3.41
19 20 2.972505 CTGCGCCACCGTTGACTT 60.973 61.111 4.18 0.00 36.67 3.01
20 21 2.515057 TGCGCCACCGTTGACTTT 60.515 55.556 4.18 0.00 36.67 2.66
21 22 2.051345 GCGCCACCGTTGACTTTG 60.051 61.111 0.00 0.00 36.67 2.77
22 23 2.830285 GCGCCACCGTTGACTTTGT 61.830 57.895 0.00 0.00 36.67 2.83
23 24 1.010125 CGCCACCGTTGACTTTGTG 60.010 57.895 0.00 0.00 0.00 3.33
24 25 1.711060 CGCCACCGTTGACTTTGTGT 61.711 55.000 0.00 0.00 0.00 3.72
25 26 0.454196 GCCACCGTTGACTTTGTGTT 59.546 50.000 0.00 0.00 0.00 3.32
26 27 1.135228 GCCACCGTTGACTTTGTGTTT 60.135 47.619 0.00 0.00 0.00 2.83
27 28 2.097791 GCCACCGTTGACTTTGTGTTTA 59.902 45.455 0.00 0.00 0.00 2.01
28 29 3.687200 CCACCGTTGACTTTGTGTTTAC 58.313 45.455 0.00 0.00 0.00 2.01
29 30 3.127203 CCACCGTTGACTTTGTGTTTACA 59.873 43.478 0.00 0.00 34.31 2.41
30 31 4.201970 CCACCGTTGACTTTGTGTTTACAT 60.202 41.667 0.00 0.00 36.53 2.29
31 32 5.007823 CCACCGTTGACTTTGTGTTTACATA 59.992 40.000 0.00 0.00 36.53 2.29
32 33 6.133392 CACCGTTGACTTTGTGTTTACATAG 58.867 40.000 0.00 0.00 40.41 2.23
33 34 5.237779 ACCGTTGACTTTGTGTTTACATAGG 59.762 40.000 0.00 0.00 39.34 2.57
34 35 5.237779 CCGTTGACTTTGTGTTTACATAGGT 59.762 40.000 0.00 0.00 39.34 3.08
35 36 6.133392 CGTTGACTTTGTGTTTACATAGGTG 58.867 40.000 0.00 0.00 39.34 4.00
36 37 6.435428 GTTGACTTTGTGTTTACATAGGTGG 58.565 40.000 0.00 0.00 39.34 4.61
37 38 4.517453 TGACTTTGTGTTTACATAGGTGGC 59.483 41.667 0.00 0.00 39.34 5.01
38 39 4.465886 ACTTTGTGTTTACATAGGTGGCA 58.534 39.130 0.00 0.00 39.34 4.92
39 40 4.277423 ACTTTGTGTTTACATAGGTGGCAC 59.723 41.667 9.70 9.70 39.34 5.01
40 41 3.493767 TGTGTTTACATAGGTGGCACA 57.506 42.857 20.82 0.00 34.39 4.57
52 53 1.451504 TGGCACACACTCCTTGAGG 59.548 57.895 0.00 0.00 33.35 3.86
53 54 1.344953 TGGCACACACTCCTTGAGGT 61.345 55.000 0.00 0.00 33.35 3.85
54 55 0.685097 GGCACACACTCCTTGAGGTA 59.315 55.000 0.00 0.00 33.35 3.08
55 56 1.071699 GGCACACACTCCTTGAGGTAA 59.928 52.381 0.00 0.00 33.35 2.85
56 57 2.486548 GGCACACACTCCTTGAGGTAAA 60.487 50.000 0.00 0.00 33.35 2.01
57 58 2.548480 GCACACACTCCTTGAGGTAAAC 59.452 50.000 0.00 0.00 33.35 2.01
58 59 3.804036 CACACACTCCTTGAGGTAAACA 58.196 45.455 0.00 0.00 33.35 2.83
59 60 4.389374 CACACACTCCTTGAGGTAAACAT 58.611 43.478 0.00 0.00 33.35 2.71
60 61 4.452455 CACACACTCCTTGAGGTAAACATC 59.548 45.833 0.00 0.00 33.35 3.06
61 62 3.679980 CACACTCCTTGAGGTAAACATCG 59.320 47.826 0.00 0.00 33.35 3.84
62 63 3.262420 CACTCCTTGAGGTAAACATCGG 58.738 50.000 0.00 0.00 33.35 4.18
63 64 3.056107 CACTCCTTGAGGTAAACATCGGA 60.056 47.826 0.00 0.00 33.35 4.55
64 65 3.195825 ACTCCTTGAGGTAAACATCGGAG 59.804 47.826 13.66 13.66 39.24 4.63
65 66 3.170717 TCCTTGAGGTAAACATCGGAGT 58.829 45.455 0.00 0.00 36.34 3.85
66 67 3.581332 TCCTTGAGGTAAACATCGGAGTT 59.419 43.478 0.00 0.00 36.34 3.01
67 68 4.041198 TCCTTGAGGTAAACATCGGAGTTT 59.959 41.667 10.22 10.22 43.58 2.66
68 69 4.760204 CCTTGAGGTAAACATCGGAGTTTT 59.240 41.667 10.54 2.53 41.58 2.43
69 70 5.240844 CCTTGAGGTAAACATCGGAGTTTTT 59.759 40.000 10.54 0.50 41.58 1.94
93 94 9.567776 TTTTTATTTCTCCATTTCCCCTTTTTC 57.432 29.630 0.00 0.00 0.00 2.29
94 95 8.504811 TTTATTTCTCCATTTCCCCTTTTTCT 57.495 30.769 0.00 0.00 0.00 2.52
95 96 8.504811 TTATTTCTCCATTTCCCCTTTTTCTT 57.495 30.769 0.00 0.00 0.00 2.52
96 97 6.823286 TTTCTCCATTTCCCCTTTTTCTTT 57.177 33.333 0.00 0.00 0.00 2.52
97 98 6.823286 TTCTCCATTTCCCCTTTTTCTTTT 57.177 33.333 0.00 0.00 0.00 2.27
98 99 6.419484 TCTCCATTTCCCCTTTTTCTTTTC 57.581 37.500 0.00 0.00 0.00 2.29
99 100 6.143206 TCTCCATTTCCCCTTTTTCTTTTCT 58.857 36.000 0.00 0.00 0.00 2.52
100 101 6.615316 TCTCCATTTCCCCTTTTTCTTTTCTT 59.385 34.615 0.00 0.00 0.00 2.52
101 102 7.127186 TCTCCATTTCCCCTTTTTCTTTTCTTT 59.873 33.333 0.00 0.00 0.00 2.52
102 103 8.325477 TCCATTTCCCCTTTTTCTTTTCTTTA 57.675 30.769 0.00 0.00 0.00 1.85
103 104 8.773216 TCCATTTCCCCTTTTTCTTTTCTTTAA 58.227 29.630 0.00 0.00 0.00 1.52
104 105 9.573166 CCATTTCCCCTTTTTCTTTTCTTTAAT 57.427 29.630 0.00 0.00 0.00 1.40
134 135 7.871853 TCCTTGGTTTTCTTATTTTTCTCTCG 58.128 34.615 0.00 0.00 0.00 4.04
135 136 6.582672 CCTTGGTTTTCTTATTTTTCTCTCGC 59.417 38.462 0.00 0.00 0.00 5.03
136 137 6.877611 TGGTTTTCTTATTTTTCTCTCGCT 57.122 33.333 0.00 0.00 0.00 4.93
137 138 7.272037 TGGTTTTCTTATTTTTCTCTCGCTT 57.728 32.000 0.00 0.00 0.00 4.68
138 139 7.712797 TGGTTTTCTTATTTTTCTCTCGCTTT 58.287 30.769 0.00 0.00 0.00 3.51
139 140 7.860872 TGGTTTTCTTATTTTTCTCTCGCTTTC 59.139 33.333 0.00 0.00 0.00 2.62
140 141 8.076781 GGTTTTCTTATTTTTCTCTCGCTTTCT 58.923 33.333 0.00 0.00 0.00 2.52
141 142 9.452065 GTTTTCTTATTTTTCTCTCGCTTTCTT 57.548 29.630 0.00 0.00 0.00 2.52
292 293 9.944663 AGTTTTCTTTGTTTCTTTTGGTTTTTC 57.055 25.926 0.00 0.00 0.00 2.29
293 294 9.723447 GTTTTCTTTGTTTCTTTTGGTTTTTCA 57.277 25.926 0.00 0.00 0.00 2.69
296 297 9.890352 TTCTTTGTTTCTTTTGGTTTTTCATTG 57.110 25.926 0.00 0.00 0.00 2.82
297 298 9.061435 TCTTTGTTTCTTTTGGTTTTTCATTGT 57.939 25.926 0.00 0.00 0.00 2.71
300 301 8.833231 TGTTTCTTTTGGTTTTTCATTGTACA 57.167 26.923 0.00 0.00 0.00 2.90
301 302 9.442047 TGTTTCTTTTGGTTTTTCATTGTACAT 57.558 25.926 0.00 0.00 0.00 2.29
337 338 9.897744 ATGTCAACAACAGTTTTCTAATACATG 57.102 29.630 0.00 0.00 42.37 3.21
338 339 8.898761 TGTCAACAACAGTTTTCTAATACATGT 58.101 29.630 2.69 2.69 32.81 3.21
339 340 9.730420 GTCAACAACAGTTTTCTAATACATGTT 57.270 29.630 2.30 0.00 0.00 2.71
450 451 8.524870 AATACAAGATGAACATTTTTCTGTGC 57.475 30.769 0.00 0.00 0.00 4.57
451 452 5.904941 ACAAGATGAACATTTTTCTGTGCA 58.095 33.333 0.00 0.00 39.02 4.57
452 453 5.750067 ACAAGATGAACATTTTTCTGTGCAC 59.250 36.000 10.75 10.75 37.51 4.57
453 454 5.518848 AGATGAACATTTTTCTGTGCACA 57.481 34.783 20.37 20.37 37.51 4.57
454 455 6.092955 AGATGAACATTTTTCTGTGCACAT 57.907 33.333 22.00 0.89 37.51 3.21
455 456 6.518493 AGATGAACATTTTTCTGTGCACATT 58.482 32.000 22.00 9.01 37.51 2.71
456 457 6.987992 AGATGAACATTTTTCTGTGCACATTT 59.012 30.769 22.00 3.63 37.51 2.32
457 458 6.981762 TGAACATTTTTCTGTGCACATTTT 57.018 29.167 22.00 3.27 29.39 1.82
458 459 8.659925 ATGAACATTTTTCTGTGCACATTTTA 57.340 26.923 22.00 5.64 37.51 1.52
459 460 7.904094 TGAACATTTTTCTGTGCACATTTTAC 58.096 30.769 22.00 5.40 29.39 2.01
460 461 7.547019 TGAACATTTTTCTGTGCACATTTTACA 59.453 29.630 22.00 3.56 29.39 2.41
461 462 8.436046 AACATTTTTCTGTGCACATTTTACAT 57.564 26.923 22.00 5.89 0.00 2.29
462 463 8.436046 ACATTTTTCTGTGCACATTTTACATT 57.564 26.923 22.00 0.00 0.00 2.71
463 464 8.891720 ACATTTTTCTGTGCACATTTTACATTT 58.108 25.926 22.00 0.00 0.00 2.32
464 465 9.160576 CATTTTTCTGTGCACATTTTACATTTG 57.839 29.630 22.00 4.42 0.00 2.32
465 466 5.903764 TTCTGTGCACATTTTACATTTGC 57.096 34.783 22.00 0.00 0.00 3.68
466 467 4.305769 TCTGTGCACATTTTACATTTGCC 58.694 39.130 22.00 0.00 31.94 4.52
467 468 4.056740 CTGTGCACATTTTACATTTGCCA 58.943 39.130 22.00 0.00 31.94 4.92
468 469 4.445453 TGTGCACATTTTACATTTGCCAA 58.555 34.783 17.42 0.00 31.94 4.52
469 470 5.061853 TGTGCACATTTTACATTTGCCAAT 58.938 33.333 17.42 0.00 31.94 3.16
470 471 5.178996 TGTGCACATTTTACATTTGCCAATC 59.821 36.000 17.42 0.00 31.94 2.67
471 472 4.388165 TGCACATTTTACATTTGCCAATCG 59.612 37.500 0.00 0.00 31.94 3.34
472 473 4.724602 GCACATTTTACATTTGCCAATCGC 60.725 41.667 0.00 0.00 38.31 4.58
473 474 4.626604 CACATTTTACATTTGCCAATCGCT 59.373 37.500 0.00 0.00 38.78 4.93
474 475 5.120519 CACATTTTACATTTGCCAATCGCTT 59.879 36.000 0.00 0.00 38.78 4.68
475 476 5.120519 ACATTTTACATTTGCCAATCGCTTG 59.879 36.000 0.00 0.00 38.78 4.01
476 477 4.511617 TTTACATTTGCCAATCGCTTGA 57.488 36.364 0.00 0.00 38.78 3.02
477 478 4.717233 TTACATTTGCCAATCGCTTGAT 57.283 36.364 0.00 0.00 38.78 2.57
478 479 3.598019 ACATTTGCCAATCGCTTGATT 57.402 38.095 0.00 0.00 43.08 2.57
479 480 4.717233 ACATTTGCCAATCGCTTGATTA 57.283 36.364 0.00 0.00 40.34 1.75
480 481 5.070770 ACATTTGCCAATCGCTTGATTAA 57.929 34.783 0.00 0.00 40.34 1.40
481 482 4.864247 ACATTTGCCAATCGCTTGATTAAC 59.136 37.500 0.00 0.00 40.34 2.01
482 483 4.511617 TTTGCCAATCGCTTGATTAACA 57.488 36.364 0.00 0.00 40.34 2.41
483 484 4.717233 TTGCCAATCGCTTGATTAACAT 57.283 36.364 0.00 0.00 40.34 2.71
484 485 4.717233 TGCCAATCGCTTGATTAACATT 57.283 36.364 0.00 0.00 40.34 2.71
485 486 5.070770 TGCCAATCGCTTGATTAACATTT 57.929 34.783 0.00 0.00 40.34 2.32
486 487 5.477510 TGCCAATCGCTTGATTAACATTTT 58.522 33.333 0.00 0.00 40.34 1.82
487 488 5.931146 TGCCAATCGCTTGATTAACATTTTT 59.069 32.000 0.00 0.00 40.34 1.94
488 489 6.090628 TGCCAATCGCTTGATTAACATTTTTC 59.909 34.615 0.00 0.00 40.34 2.29
489 490 6.090628 GCCAATCGCTTGATTAACATTTTTCA 59.909 34.615 0.00 0.00 40.34 2.69
490 491 7.359933 GCCAATCGCTTGATTAACATTTTTCAA 60.360 33.333 0.00 0.00 40.34 2.69
491 492 8.494347 CCAATCGCTTGATTAACATTTTTCAAA 58.506 29.630 0.00 0.00 40.34 2.69
492 493 9.305110 CAATCGCTTGATTAACATTTTTCAAAC 57.695 29.630 0.00 0.00 40.34 2.93
493 494 7.993821 TCGCTTGATTAACATTTTTCAAACA 57.006 28.000 0.00 0.00 0.00 2.83
494 495 7.836512 TCGCTTGATTAACATTTTTCAAACAC 58.163 30.769 0.00 0.00 0.00 3.32
495 496 7.704472 TCGCTTGATTAACATTTTTCAAACACT 59.296 29.630 0.00 0.00 0.00 3.55
496 497 8.327429 CGCTTGATTAACATTTTTCAAACACTT 58.673 29.630 0.00 0.00 0.00 3.16
645 646 8.994429 AACATTGTTCAAATACTTGTTCAACA 57.006 26.923 0.00 0.00 33.17 3.33
646 647 9.598517 AACATTGTTCAAATACTTGTTCAACAT 57.401 25.926 0.00 0.00 30.96 2.71
647 648 9.598517 ACATTGTTCAAATACTTGTTCAACATT 57.401 25.926 0.00 0.00 30.96 2.71
657 658 9.934190 AATACTTGTTCAACATTTTTCAAATGC 57.066 25.926 8.77 0.00 0.00 3.56
658 659 7.614124 ACTTGTTCAACATTTTTCAAATGCT 57.386 28.000 8.77 0.00 0.00 3.79
659 660 8.042944 ACTTGTTCAACATTTTTCAAATGCTT 57.957 26.923 8.77 1.68 0.00 3.91
660 661 7.964011 ACTTGTTCAACATTTTTCAAATGCTTG 59.036 29.630 8.77 11.36 0.00 4.01
661 662 7.606858 TGTTCAACATTTTTCAAATGCTTGA 57.393 28.000 15.56 15.56 39.87 3.02
662 663 8.211116 TGTTCAACATTTTTCAAATGCTTGAT 57.789 26.923 17.89 0.00 41.22 2.57
663 664 8.675504 TGTTCAACATTTTTCAAATGCTTGATT 58.324 25.926 17.89 3.70 41.22 2.57
953 959 2.432628 CACCCTCTCCGCACGAAC 60.433 66.667 0.00 0.00 0.00 3.95
985 991 2.202570 CCGACCTTGGTAGCGTCG 60.203 66.667 12.14 12.14 41.07 5.12
1269 1275 4.956085 TCTTCTTCAAGATCACCAACGAA 58.044 39.130 0.00 0.00 33.38 3.85
1292 1304 2.821366 GTACGCCGAGGAGACCGA 60.821 66.667 0.00 0.00 0.00 4.69
1359 1371 2.892425 CTCAAGGACATCGGGCGC 60.892 66.667 0.00 0.00 0.00 6.53
1564 1582 3.015312 GCCTCCTCCGTGGTGTACC 62.015 68.421 0.00 0.00 37.07 3.34
1934 1976 4.802051 TGGGGAATGCAGGAGCGC 62.802 66.667 0.00 0.00 46.23 5.92
2364 2406 2.134789 GAGGAACCCGTACCTCTACA 57.865 55.000 0.00 0.00 46.28 2.74
2430 2472 3.194542 AGAGGGAACGTTTGAGATCTGAG 59.805 47.826 0.00 0.00 0.00 3.35
2431 2473 3.165875 AGGGAACGTTTGAGATCTGAGA 58.834 45.455 0.00 0.00 0.00 3.27
2432 2474 3.056465 AGGGAACGTTTGAGATCTGAGAC 60.056 47.826 0.00 0.00 0.00 3.36
2509 2564 4.058817 CCGTCTCTGCTCTAAGTTTTGTT 58.941 43.478 0.00 0.00 0.00 2.83
2510 2565 4.511826 CCGTCTCTGCTCTAAGTTTTGTTT 59.488 41.667 0.00 0.00 0.00 2.83
2511 2566 5.007724 CCGTCTCTGCTCTAAGTTTTGTTTT 59.992 40.000 0.00 0.00 0.00 2.43
2512 2567 5.904080 CGTCTCTGCTCTAAGTTTTGTTTTG 59.096 40.000 0.00 0.00 0.00 2.44
2513 2568 6.456988 CGTCTCTGCTCTAAGTTTTGTTTTGT 60.457 38.462 0.00 0.00 0.00 2.83
2634 2692 3.122780 TCAAAGTTCATGCACATACGTCG 59.877 43.478 0.00 0.00 0.00 5.12
2641 2699 1.520564 GCACATACGTCGCCCATGA 60.521 57.895 0.00 0.00 0.00 3.07
2644 2702 1.327460 CACATACGTCGCCCATGAAAG 59.673 52.381 0.00 0.00 0.00 2.62
2732 2792 3.695830 AACAGATCCGCTAAAACCTCA 57.304 42.857 0.00 0.00 0.00 3.86
2741 2801 2.459202 CTAAAACCTCACCGGCCCGT 62.459 60.000 0.00 0.00 35.61 5.28
2750 2810 0.961358 CACCGGCCCGTAAAATTCCA 60.961 55.000 0.00 0.00 0.00 3.53
2751 2811 0.251253 ACCGGCCCGTAAAATTCCAA 60.251 50.000 0.00 0.00 0.00 3.53
2754 2814 0.171679 GGCCCGTAAAATTCCAACCG 59.828 55.000 0.00 0.00 0.00 4.44
2820 2880 4.483243 CCGCCGGCCCATACAAGT 62.483 66.667 23.46 0.00 0.00 3.16
2821 2881 2.437716 CGCCGGCCCATACAAGTT 60.438 61.111 23.46 0.00 0.00 2.66
2822 2882 2.043980 CGCCGGCCCATACAAGTTT 61.044 57.895 23.46 0.00 0.00 2.66
2823 2883 1.591504 CGCCGGCCCATACAAGTTTT 61.592 55.000 23.46 0.00 0.00 2.43
2824 2884 0.606096 GCCGGCCCATACAAGTTTTT 59.394 50.000 18.11 0.00 0.00 1.94
2825 2885 1.671556 GCCGGCCCATACAAGTTTTTG 60.672 52.381 18.11 0.00 40.24 2.44
2826 2886 1.889829 CCGGCCCATACAAGTTTTTGA 59.110 47.619 0.00 0.00 37.73 2.69
2827 2887 2.094752 CCGGCCCATACAAGTTTTTGAG 60.095 50.000 0.00 0.00 37.73 3.02
2828 2888 2.817258 CGGCCCATACAAGTTTTTGAGA 59.183 45.455 0.00 0.00 37.73 3.27
2829 2889 3.365969 CGGCCCATACAAGTTTTTGAGAC 60.366 47.826 0.00 0.00 37.73 3.36
2833 2893 4.083484 CCCATACAAGTTTTTGAGACGACC 60.083 45.833 0.00 0.00 37.73 4.79
2842 2902 3.996150 TTTGAGACGACCCGTATATCC 57.004 47.619 0.00 0.00 41.37 2.59
2844 2904 0.167689 GAGACGACCCGTATATCCGC 59.832 60.000 0.00 0.00 41.37 5.54
2850 2910 2.356780 CCCGTATATCCGCCCCTCC 61.357 68.421 0.00 0.00 0.00 4.30
2851 2911 2.707849 CCGTATATCCGCCCCTCCG 61.708 68.421 0.00 0.00 0.00 4.63
2861 2921 1.679898 GCCCCTCCGCTGCTATATT 59.320 57.895 0.00 0.00 0.00 1.28
2865 2925 2.607187 CCCTCCGCTGCTATATTTACG 58.393 52.381 0.00 0.00 0.00 3.18
2870 2930 2.093658 CCGCTGCTATATTTACGGGGAT 60.094 50.000 0.00 0.00 37.04 3.85
2872 2932 3.368013 CGCTGCTATATTTACGGGGATGA 60.368 47.826 0.00 0.00 0.00 2.92
2874 2934 4.759782 CTGCTATATTTACGGGGATGAGG 58.240 47.826 0.00 0.00 0.00 3.86
2880 2940 0.917333 TTACGGGGATGAGGGCCTTT 60.917 55.000 7.89 0.00 0.00 3.11
2886 2946 1.288037 GGGATGAGGGCCTTTTAGGTT 59.712 52.381 7.89 0.00 37.80 3.50
2896 2956 2.629051 CCTTTTAGGTTAGCAGACCGG 58.371 52.381 0.00 0.00 44.62 5.28
2900 2960 5.395990 CCTTTTAGGTTAGCAGACCGGATAA 60.396 44.000 9.46 0.00 44.62 1.75
2902 2962 1.413077 AGGTTAGCAGACCGGATAAGC 59.587 52.381 9.46 6.64 44.62 3.09
2923 2983 4.278419 AGCTTCACCGCAAAAATACTTCTT 59.722 37.500 0.00 0.00 0.00 2.52
2927 2987 5.938322 TCACCGCAAAAATACTTCTTCATC 58.062 37.500 0.00 0.00 0.00 2.92
2928 2988 4.788100 CACCGCAAAAATACTTCTTCATCG 59.212 41.667 0.00 0.00 0.00 3.84
2971 3031 2.125673 AATTAGCCGCACGTCGCT 60.126 55.556 6.55 6.55 39.08 4.93
2975 3035 3.678717 TAGCCGCACGTCGCTTCTC 62.679 63.158 6.62 0.00 39.08 2.87
2982 3042 1.398578 GCACGTCGCTTCTCCTTTTTC 60.399 52.381 0.00 0.00 37.77 2.29
2983 3043 1.136611 CACGTCGCTTCTCCTTTTTCG 60.137 52.381 0.00 0.00 0.00 3.46
2989 3049 0.438830 CTTCTCCTTTTTCGCCGTCG 59.561 55.000 0.00 0.00 0.00 5.12
2990 3050 0.947180 TTCTCCTTTTTCGCCGTCGG 60.947 55.000 6.99 6.99 36.13 4.79
3004 3064 1.062525 GTCGGCGACAAATCCATGC 59.937 57.895 33.07 2.90 32.09 4.06
3056 3116 2.669569 CAACACTGGTGGAGGCCG 60.670 66.667 0.00 0.00 34.19 6.13
3096 3156 2.202566 GGCGAGCAAGGTTAGTACATC 58.797 52.381 0.00 0.00 0.00 3.06
3097 3157 2.159085 GGCGAGCAAGGTTAGTACATCT 60.159 50.000 0.00 0.00 0.00 2.90
3098 3158 2.860735 GCGAGCAAGGTTAGTACATCTG 59.139 50.000 0.00 0.00 0.00 2.90
3100 3160 3.198872 GAGCAAGGTTAGTACATCTGGC 58.801 50.000 0.00 0.00 0.00 4.85
3101 3161 2.092914 AGCAAGGTTAGTACATCTGGCC 60.093 50.000 0.00 0.00 0.00 5.36
3102 3162 2.355716 GCAAGGTTAGTACATCTGGCCA 60.356 50.000 4.71 4.71 0.00 5.36
3103 3163 3.872240 GCAAGGTTAGTACATCTGGCCAA 60.872 47.826 7.01 0.00 0.00 4.52
3104 3164 4.331968 CAAGGTTAGTACATCTGGCCAAA 58.668 43.478 7.01 0.00 0.00 3.28
3105 3165 4.650972 AGGTTAGTACATCTGGCCAAAA 57.349 40.909 7.01 0.00 0.00 2.44
3107 3167 5.580022 AGGTTAGTACATCTGGCCAAAATT 58.420 37.500 7.01 0.00 0.00 1.82
3108 3168 6.016555 AGGTTAGTACATCTGGCCAAAATTT 58.983 36.000 7.01 0.00 0.00 1.82
3109 3169 6.496911 AGGTTAGTACATCTGGCCAAAATTTT 59.503 34.615 7.01 0.00 0.00 1.82
3110 3170 6.589907 GGTTAGTACATCTGGCCAAAATTTTG 59.410 38.462 21.65 21.65 37.90 2.44
3111 3171 5.806654 AGTACATCTGGCCAAAATTTTGT 57.193 34.783 25.25 10.77 36.45 2.83
3112 3172 5.783111 AGTACATCTGGCCAAAATTTTGTC 58.217 37.500 25.25 15.67 36.45 3.18
3113 3173 4.006780 ACATCTGGCCAAAATTTTGTCC 57.993 40.909 25.25 23.37 36.76 4.02
3114 3174 3.390639 ACATCTGGCCAAAATTTTGTCCA 59.609 39.130 27.06 27.06 43.20 4.02
3117 3177 3.922171 TGGCCAAAATTTTGTCCAGTT 57.078 38.095 25.68 0.00 40.85 3.16
3118 3178 4.227864 TGGCCAAAATTTTGTCCAGTTT 57.772 36.364 25.68 0.00 40.85 2.66
3119 3179 3.944015 TGGCCAAAATTTTGTCCAGTTTG 59.056 39.130 25.68 11.26 40.85 2.93
3120 3180 4.195416 GGCCAAAATTTTGTCCAGTTTGA 58.805 39.130 22.79 0.00 36.28 2.69
3121 3181 4.035091 GGCCAAAATTTTGTCCAGTTTGAC 59.965 41.667 22.79 7.69 36.28 3.18
3122 3182 4.260172 GCCAAAATTTTGTCCAGTTTGACG 60.260 41.667 25.25 9.73 38.11 4.35
3123 3183 4.867608 CCAAAATTTTGTCCAGTTTGACGT 59.132 37.500 25.25 0.00 38.11 4.34
3124 3184 5.005299 CCAAAATTTTGTCCAGTTTGACGTC 59.995 40.000 25.25 9.11 38.11 4.34
3125 3185 4.974368 AATTTTGTCCAGTTTGACGTCA 57.026 36.364 15.76 15.76 38.11 4.35
3126 3186 5.514274 AATTTTGTCCAGTTTGACGTCAT 57.486 34.783 20.80 0.76 38.11 3.06
3127 3187 4.545823 TTTTGTCCAGTTTGACGTCATC 57.454 40.909 20.80 15.32 38.11 2.92
3128 3188 2.900716 TGTCCAGTTTGACGTCATCA 57.099 45.000 20.80 6.46 38.11 3.07
3129 3189 3.401033 TGTCCAGTTTGACGTCATCAT 57.599 42.857 20.80 5.03 37.11 2.45
3130 3190 3.066380 TGTCCAGTTTGACGTCATCATG 58.934 45.455 20.80 16.74 37.11 3.07
3131 3191 2.416547 GTCCAGTTTGACGTCATCATGG 59.583 50.000 25.93 25.93 37.11 3.66
3132 3192 2.038426 TCCAGTTTGACGTCATCATGGT 59.962 45.455 28.35 9.39 37.11 3.55
3133 3193 2.160219 CCAGTTTGACGTCATCATGGTG 59.840 50.000 20.80 10.84 37.11 4.17
3134 3194 2.807967 CAGTTTGACGTCATCATGGTGT 59.192 45.455 20.80 0.00 37.11 4.16
3135 3195 3.250762 CAGTTTGACGTCATCATGGTGTT 59.749 43.478 20.80 0.00 37.11 3.32
3136 3196 3.250762 AGTTTGACGTCATCATGGTGTTG 59.749 43.478 20.80 2.28 37.11 3.33
3145 3205 5.156355 GTCATCATGGTGTTGTTTTAGCTG 58.844 41.667 5.73 0.00 0.00 4.24
3147 3207 6.000840 TCATCATGGTGTTGTTTTAGCTGTA 58.999 36.000 5.73 0.00 0.00 2.74
3155 3215 4.214545 TGTTGTTTTAGCTGTAACATCCCG 59.785 41.667 13.95 0.00 34.52 5.14
3198 3258 8.655901 AGATTTATTTTCAAAAAGTAGGGCCAA 58.344 29.630 6.18 0.00 0.00 4.52
3201 3261 9.634021 TTTATTTTCAAAAAGTAGGGCCAAAAT 57.366 25.926 6.18 8.36 0.00 1.82
3202 3262 9.634021 TTATTTTCAAAAAGTAGGGCCAAAATT 57.366 25.926 6.18 0.00 0.00 1.82
3203 3263 7.946381 TTTTCAAAAAGTAGGGCCAAAATTT 57.054 28.000 6.18 1.99 0.00 1.82
3204 3264 7.946381 TTTCAAAAAGTAGGGCCAAAATTTT 57.054 28.000 6.18 8.76 0.00 1.82
3295 3355 6.765915 AATGCCAACCTTAATCTTCTTCTC 57.234 37.500 0.00 0.00 0.00 2.87
3315 3375 4.770010 TCTCAGTTGGGTTGTTTTCTTTGT 59.230 37.500 0.00 0.00 0.00 2.83
3331 3391 6.515272 TTCTTTGTCTTGGGCATCTTAATC 57.485 37.500 0.00 0.00 0.00 1.75
3335 3395 3.633525 TGTCTTGGGCATCTTAATCATGC 59.366 43.478 9.94 9.94 45.13 4.06
3337 3397 2.636647 TGGGCATCTTAATCATGCGA 57.363 45.000 11.49 1.54 46.55 5.10
3351 3411 8.661352 TTAATCATGCGACTATGAATTCTTGA 57.339 30.769 7.05 0.00 40.21 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.012895 GTCAACGGTGGCGCAGTG 62.013 66.667 10.83 0.00 0.00 3.66
1 2 3.750373 AAGTCAACGGTGGCGCAGT 62.750 57.895 10.83 0.00 33.27 4.40
2 3 2.542907 AAAGTCAACGGTGGCGCAG 61.543 57.895 10.83 0.00 33.27 5.18
3 4 2.515057 AAAGTCAACGGTGGCGCA 60.515 55.556 10.83 0.00 33.27 6.09
4 5 2.051345 CAAAGTCAACGGTGGCGC 60.051 61.111 0.00 0.00 33.27 6.53
5 6 1.010125 CACAAAGTCAACGGTGGCG 60.010 57.895 0.00 0.00 33.27 5.69
6 7 0.454196 AACACAAAGTCAACGGTGGC 59.546 50.000 0.00 0.00 35.62 5.01
7 8 2.931512 AAACACAAAGTCAACGGTGG 57.068 45.000 0.00 0.00 35.62 4.61
8 9 4.343811 TGTAAACACAAAGTCAACGGTG 57.656 40.909 0.00 0.00 37.29 4.94
9 10 5.237779 CCTATGTAAACACAAAGTCAACGGT 59.762 40.000 0.00 0.00 0.00 4.83
10 11 5.237779 ACCTATGTAAACACAAAGTCAACGG 59.762 40.000 0.00 0.00 0.00 4.44
11 12 6.133392 CACCTATGTAAACACAAAGTCAACG 58.867 40.000 0.00 0.00 0.00 4.10
12 13 6.435428 CCACCTATGTAAACACAAAGTCAAC 58.565 40.000 0.00 0.00 0.00 3.18
13 14 5.009210 GCCACCTATGTAAACACAAAGTCAA 59.991 40.000 0.00 0.00 0.00 3.18
14 15 4.517453 GCCACCTATGTAAACACAAAGTCA 59.483 41.667 0.00 0.00 0.00 3.41
15 16 4.517453 TGCCACCTATGTAAACACAAAGTC 59.483 41.667 0.00 0.00 0.00 3.01
16 17 4.277423 GTGCCACCTATGTAAACACAAAGT 59.723 41.667 0.00 0.00 0.00 2.66
17 18 4.277174 TGTGCCACCTATGTAAACACAAAG 59.723 41.667 0.00 0.00 33.94 2.77
18 19 4.036971 GTGTGCCACCTATGTAAACACAAA 59.963 41.667 0.00 0.00 38.19 2.83
19 20 3.566322 GTGTGCCACCTATGTAAACACAA 59.434 43.478 0.00 0.00 38.19 3.33
20 21 3.142951 GTGTGCCACCTATGTAAACACA 58.857 45.455 0.00 0.00 34.43 3.72
21 22 3.058501 GTGTGTGCCACCTATGTAAACAC 60.059 47.826 0.00 0.00 38.18 3.32
22 23 3.142951 GTGTGTGCCACCTATGTAAACA 58.857 45.455 0.00 0.00 38.18 2.83
23 24 3.408634 AGTGTGTGCCACCTATGTAAAC 58.591 45.455 0.00 0.00 45.74 2.01
24 25 3.558321 GGAGTGTGTGCCACCTATGTAAA 60.558 47.826 0.00 0.00 45.74 2.01
25 26 2.027561 GGAGTGTGTGCCACCTATGTAA 60.028 50.000 0.00 0.00 45.74 2.41
26 27 1.553248 GGAGTGTGTGCCACCTATGTA 59.447 52.381 0.00 0.00 45.74 2.29
27 28 0.324943 GGAGTGTGTGCCACCTATGT 59.675 55.000 0.00 0.00 45.74 2.29
28 29 0.615331 AGGAGTGTGTGCCACCTATG 59.385 55.000 0.00 0.00 45.74 2.23
29 30 1.003580 CAAGGAGTGTGTGCCACCTAT 59.996 52.381 0.00 0.00 45.74 2.57
30 31 0.396435 CAAGGAGTGTGTGCCACCTA 59.604 55.000 0.00 0.00 45.74 3.08
31 32 1.149174 CAAGGAGTGTGTGCCACCT 59.851 57.895 0.00 0.00 45.74 4.00
32 33 0.886490 CTCAAGGAGTGTGTGCCACC 60.886 60.000 0.00 0.00 45.74 4.61
33 34 0.886490 CCTCAAGGAGTGTGTGCCAC 60.886 60.000 0.00 0.00 44.89 5.01
34 35 1.344953 ACCTCAAGGAGTGTGTGCCA 61.345 55.000 2.30 0.00 38.94 4.92
35 36 0.685097 TACCTCAAGGAGTGTGTGCC 59.315 55.000 2.30 0.00 38.94 5.01
36 37 2.543777 TTACCTCAAGGAGTGTGTGC 57.456 50.000 2.30 0.00 38.94 4.57
37 38 3.804036 TGTTTACCTCAAGGAGTGTGTG 58.196 45.455 2.30 0.00 38.94 3.82
38 39 4.642429 GATGTTTACCTCAAGGAGTGTGT 58.358 43.478 2.30 0.00 38.94 3.72
39 40 3.679980 CGATGTTTACCTCAAGGAGTGTG 59.320 47.826 2.30 0.00 38.94 3.82
40 41 3.306780 CCGATGTTTACCTCAAGGAGTGT 60.307 47.826 2.30 0.00 38.94 3.55
41 42 3.056107 TCCGATGTTTACCTCAAGGAGTG 60.056 47.826 2.30 0.00 38.94 3.51
42 43 3.170717 TCCGATGTTTACCTCAAGGAGT 58.829 45.455 2.30 0.00 38.94 3.85
43 44 3.195825 ACTCCGATGTTTACCTCAAGGAG 59.804 47.826 2.30 14.39 43.07 3.69
44 45 3.170717 ACTCCGATGTTTACCTCAAGGA 58.829 45.455 2.30 0.00 38.94 3.36
45 46 3.611766 ACTCCGATGTTTACCTCAAGG 57.388 47.619 0.00 0.00 42.17 3.61
46 47 5.941948 AAAACTCCGATGTTTACCTCAAG 57.058 39.130 6.25 0.00 38.98 3.02
67 68 9.567776 GAAAAAGGGGAAATGGAGAAATAAAAA 57.432 29.630 0.00 0.00 0.00 1.94
68 69 8.944138 AGAAAAAGGGGAAATGGAGAAATAAAA 58.056 29.630 0.00 0.00 0.00 1.52
69 70 8.504811 AGAAAAAGGGGAAATGGAGAAATAAA 57.495 30.769 0.00 0.00 0.00 1.40
70 71 8.504811 AAGAAAAAGGGGAAATGGAGAAATAA 57.495 30.769 0.00 0.00 0.00 1.40
71 72 8.504811 AAAGAAAAAGGGGAAATGGAGAAATA 57.495 30.769 0.00 0.00 0.00 1.40
72 73 7.392766 AAAGAAAAAGGGGAAATGGAGAAAT 57.607 32.000 0.00 0.00 0.00 2.17
73 74 6.823286 AAAGAAAAAGGGGAAATGGAGAAA 57.177 33.333 0.00 0.00 0.00 2.52
74 75 6.615316 AGAAAAGAAAAAGGGGAAATGGAGAA 59.385 34.615 0.00 0.00 0.00 2.87
75 76 6.143206 AGAAAAGAAAAAGGGGAAATGGAGA 58.857 36.000 0.00 0.00 0.00 3.71
76 77 6.425210 AGAAAAGAAAAAGGGGAAATGGAG 57.575 37.500 0.00 0.00 0.00 3.86
77 78 6.823286 AAGAAAAGAAAAAGGGGAAATGGA 57.177 33.333 0.00 0.00 0.00 3.41
78 79 8.972458 TTAAAGAAAAGAAAAAGGGGAAATGG 57.028 30.769 0.00 0.00 0.00 3.16
108 109 8.349983 CGAGAGAAAAATAAGAAAACCAAGGAA 58.650 33.333 0.00 0.00 0.00 3.36
109 110 7.521585 GCGAGAGAAAAATAAGAAAACCAAGGA 60.522 37.037 0.00 0.00 0.00 3.36
110 111 6.582672 GCGAGAGAAAAATAAGAAAACCAAGG 59.417 38.462 0.00 0.00 0.00 3.61
111 112 7.363431 AGCGAGAGAAAAATAAGAAAACCAAG 58.637 34.615 0.00 0.00 0.00 3.61
112 113 7.272037 AGCGAGAGAAAAATAAGAAAACCAA 57.728 32.000 0.00 0.00 0.00 3.67
113 114 6.877611 AGCGAGAGAAAAATAAGAAAACCA 57.122 33.333 0.00 0.00 0.00 3.67
114 115 8.076781 AGAAAGCGAGAGAAAAATAAGAAAACC 58.923 33.333 0.00 0.00 0.00 3.27
115 116 9.452065 AAGAAAGCGAGAGAAAAATAAGAAAAC 57.548 29.630 0.00 0.00 0.00 2.43
266 267 9.944663 GAAAAACCAAAAGAAACAAAGAAAACT 57.055 25.926 0.00 0.00 0.00 2.66
267 268 9.723447 TGAAAAACCAAAAGAAACAAAGAAAAC 57.277 25.926 0.00 0.00 0.00 2.43
270 271 9.890352 CAATGAAAAACCAAAAGAAACAAAGAA 57.110 25.926 0.00 0.00 0.00 2.52
271 272 9.061435 ACAATGAAAAACCAAAAGAAACAAAGA 57.939 25.926 0.00 0.00 0.00 2.52
274 275 9.273016 TGTACAATGAAAAACCAAAAGAAACAA 57.727 25.926 0.00 0.00 0.00 2.83
275 276 8.833231 TGTACAATGAAAAACCAAAAGAAACA 57.167 26.923 0.00 0.00 0.00 2.83
311 312 9.897744 CATGTATTAGAAAACTGTTGTTGACAT 57.102 29.630 0.00 0.00 37.69 3.06
312 313 8.898761 ACATGTATTAGAAAACTGTTGTTGACA 58.101 29.630 0.00 0.00 36.39 3.58
313 314 9.730420 AACATGTATTAGAAAACTGTTGTTGAC 57.270 29.630 0.00 0.00 36.39 3.18
424 425 8.981647 GCACAGAAAAATGTTCATCTTGTATTT 58.018 29.630 0.00 0.00 0.00 1.40
425 426 8.143193 TGCACAGAAAAATGTTCATCTTGTATT 58.857 29.630 0.00 0.00 0.00 1.89
426 427 7.596248 GTGCACAGAAAAATGTTCATCTTGTAT 59.404 33.333 13.17 0.00 29.23 2.29
427 428 6.917477 GTGCACAGAAAAATGTTCATCTTGTA 59.083 34.615 13.17 0.00 29.23 2.41
428 429 5.750067 GTGCACAGAAAAATGTTCATCTTGT 59.250 36.000 13.17 0.00 29.23 3.16
429 430 5.749588 TGTGCACAGAAAAATGTTCATCTTG 59.250 36.000 17.42 0.00 29.23 3.02
430 431 5.904941 TGTGCACAGAAAAATGTTCATCTT 58.095 33.333 17.42 0.00 29.23 2.40
431 432 5.518848 TGTGCACAGAAAAATGTTCATCT 57.481 34.783 17.42 0.00 29.23 2.90
432 433 6.774354 AATGTGCACAGAAAAATGTTCATC 57.226 33.333 25.84 0.00 29.23 2.92
433 434 7.556733 AAAATGTGCACAGAAAAATGTTCAT 57.443 28.000 25.84 0.00 29.23 2.57
434 435 6.981762 AAAATGTGCACAGAAAAATGTTCA 57.018 29.167 25.84 0.00 0.00 3.18
435 436 7.904094 TGTAAAATGTGCACAGAAAAATGTTC 58.096 30.769 25.84 8.08 0.00 3.18
436 437 7.840342 TGTAAAATGTGCACAGAAAAATGTT 57.160 28.000 25.84 10.85 0.00 2.71
437 438 8.436046 AATGTAAAATGTGCACAGAAAAATGT 57.564 26.923 25.84 2.15 0.00 2.71
438 439 9.160576 CAAATGTAAAATGTGCACAGAAAAATG 57.839 29.630 25.84 11.39 0.00 2.32
439 440 7.856894 GCAAATGTAAAATGTGCACAGAAAAAT 59.143 29.630 25.84 11.23 35.28 1.82
440 441 7.185453 GCAAATGTAAAATGTGCACAGAAAAA 58.815 30.769 25.84 9.36 35.28 1.94
441 442 6.238320 GGCAAATGTAAAATGTGCACAGAAAA 60.238 34.615 25.84 8.12 36.93 2.29
442 443 5.236047 GGCAAATGTAAAATGTGCACAGAAA 59.764 36.000 25.84 7.74 36.93 2.52
443 444 4.749099 GGCAAATGTAAAATGTGCACAGAA 59.251 37.500 25.84 7.38 36.93 3.02
444 445 4.202192 TGGCAAATGTAAAATGTGCACAGA 60.202 37.500 25.84 7.54 36.93 3.41
445 446 4.056740 TGGCAAATGTAAAATGTGCACAG 58.943 39.130 25.84 8.32 36.93 3.66
446 447 4.063998 TGGCAAATGTAAAATGTGCACA 57.936 36.364 24.08 24.08 36.93 4.57
447 448 5.610235 ATTGGCAAATGTAAAATGTGCAC 57.390 34.783 10.75 10.75 36.93 4.57
448 449 4.388165 CGATTGGCAAATGTAAAATGTGCA 59.612 37.500 3.01 0.00 36.93 4.57
449 450 4.724602 GCGATTGGCAAATGTAAAATGTGC 60.725 41.667 3.01 0.00 42.87 4.57
450 451 4.884707 GCGATTGGCAAATGTAAAATGTG 58.115 39.130 3.01 0.00 42.87 3.21
464 465 6.090628 TGAAAAATGTTAATCAAGCGATTGGC 59.909 34.615 14.27 0.28 42.00 4.52
465 466 7.579589 TGAAAAATGTTAATCAAGCGATTGG 57.420 32.000 14.27 0.00 42.00 3.16
466 467 9.305110 GTTTGAAAAATGTTAATCAAGCGATTG 57.695 29.630 7.17 7.17 42.00 2.67
467 468 9.039870 TGTTTGAAAAATGTTAATCAAGCGATT 57.960 25.926 0.00 0.00 44.24 3.34
468 469 8.487176 GTGTTTGAAAAATGTTAATCAAGCGAT 58.513 29.630 0.00 0.00 36.27 4.58
469 470 7.704472 AGTGTTTGAAAAATGTTAATCAAGCGA 59.296 29.630 0.00 0.00 36.27 4.93
470 471 7.840489 AGTGTTTGAAAAATGTTAATCAAGCG 58.160 30.769 0.00 0.00 36.27 4.68
620 621 8.994429 TGTTGAACAAGTATTTGAACAATGTT 57.006 26.923 4.81 0.00 37.73 2.71
621 622 9.598517 AATGTTGAACAAGTATTTGAACAATGT 57.401 25.926 0.62 0.00 34.35 2.71
631 632 9.934190 GCATTTGAAAAATGTTGAACAAGTATT 57.066 25.926 0.62 0.00 0.00 1.89
632 633 9.328845 AGCATTTGAAAAATGTTGAACAAGTAT 57.671 25.926 0.62 0.00 0.00 2.12
633 634 8.715191 AGCATTTGAAAAATGTTGAACAAGTA 57.285 26.923 0.62 0.00 0.00 2.24
634 635 7.614124 AGCATTTGAAAAATGTTGAACAAGT 57.386 28.000 0.62 0.00 0.00 3.16
635 636 8.176365 TCAAGCATTTGAAAAATGTTGAACAAG 58.824 29.630 18.04 4.03 40.26 3.16
636 637 8.037382 TCAAGCATTTGAAAAATGTTGAACAA 57.963 26.923 18.04 0.00 40.26 2.83
637 638 7.606858 TCAAGCATTTGAAAAATGTTGAACA 57.393 28.000 18.04 0.00 40.26 3.18
762 763 9.812347 TCCCATATAAAAATGTCAATCTAGCAT 57.188 29.630 0.00 0.00 0.00 3.79
763 764 9.812347 ATCCCATATAAAAATGTCAATCTAGCA 57.188 29.630 0.00 0.00 0.00 3.49
767 768 9.768662 GCAAATCCCATATAAAAATGTCAATCT 57.231 29.630 0.00 0.00 0.00 2.40
768 769 8.702438 CGCAAATCCCATATAAAAATGTCAATC 58.298 33.333 0.00 0.00 0.00 2.67
769 770 8.203485 ACGCAAATCCCATATAAAAATGTCAAT 58.797 29.630 0.00 0.00 0.00 2.57
770 771 7.551585 ACGCAAATCCCATATAAAAATGTCAA 58.448 30.769 0.00 0.00 0.00 3.18
771 772 7.106439 ACGCAAATCCCATATAAAAATGTCA 57.894 32.000 0.00 0.00 0.00 3.58
772 773 7.096640 CGAACGCAAATCCCATATAAAAATGTC 60.097 37.037 0.00 0.00 0.00 3.06
773 774 6.695278 CGAACGCAAATCCCATATAAAAATGT 59.305 34.615 0.00 0.00 0.00 2.71
774 775 6.695278 ACGAACGCAAATCCCATATAAAAATG 59.305 34.615 0.00 0.00 0.00 2.32
775 776 6.695278 CACGAACGCAAATCCCATATAAAAAT 59.305 34.615 0.00 0.00 0.00 1.82
776 777 6.030849 CACGAACGCAAATCCCATATAAAAA 58.969 36.000 0.00 0.00 0.00 1.94
777 778 5.124138 ACACGAACGCAAATCCCATATAAAA 59.876 36.000 0.00 0.00 0.00 1.52
778 779 4.636648 ACACGAACGCAAATCCCATATAAA 59.363 37.500 0.00 0.00 0.00 1.40
779 780 4.193090 ACACGAACGCAAATCCCATATAA 58.807 39.130 0.00 0.00 0.00 0.98
780 781 3.799366 ACACGAACGCAAATCCCATATA 58.201 40.909 0.00 0.00 0.00 0.86
781 782 2.612212 GACACGAACGCAAATCCCATAT 59.388 45.455 0.00 0.00 0.00 1.78
953 959 3.095278 CGGGTTCGTGTCACGTCG 61.095 66.667 23.82 18.22 43.14 5.12
985 991 0.037790 GCCATGGAGGATCGAGCTAC 60.038 60.000 18.40 0.00 41.22 3.58
1009 1015 4.963428 GGCGGCGAGGAATACGGG 62.963 72.222 12.98 0.00 0.00 5.28
1209 1215 0.619255 TGAAGCCCATTAGACCGGGA 60.619 55.000 6.32 0.00 46.34 5.14
1215 1221 4.237843 AGATGAGGATGAAGCCCATTAGA 58.762 43.478 0.00 0.00 35.17 2.10
1218 1224 2.107901 GGAGATGAGGATGAAGCCCATT 59.892 50.000 0.00 0.00 35.17 3.16
1269 1275 1.892862 CTCCTCGGCGTACTCGGAT 60.893 63.158 6.85 0.00 37.56 4.18
1292 1304 4.400961 GCGGGCAGAAGGAGCTGT 62.401 66.667 0.00 0.00 38.17 4.40
1861 1885 3.343617 CCCTCATGTGTTGGTCGTTATT 58.656 45.455 0.00 0.00 0.00 1.40
1862 1886 2.355716 CCCCTCATGTGTTGGTCGTTAT 60.356 50.000 0.00 0.00 0.00 1.89
1934 1976 1.982612 TCATCAGCACGTTCTTCTCG 58.017 50.000 0.00 0.00 0.00 4.04
2364 2406 0.970937 TCTTCCTCCTCGTCCGCAAT 60.971 55.000 0.00 0.00 0.00 3.56
2414 2456 3.566523 GTCGTCTCAGATCTCAAACGTT 58.433 45.455 15.81 0.00 0.00 3.99
2430 2472 1.148157 CTCCATGCATCCACGTCGTC 61.148 60.000 0.00 0.00 0.00 4.20
2431 2473 1.153568 CTCCATGCATCCACGTCGT 60.154 57.895 0.00 0.00 0.00 4.34
2432 2474 1.884464 CCTCCATGCATCCACGTCG 60.884 63.158 0.00 0.00 0.00 5.12
2555 2613 0.037232 AGCTCCGTGCAAGAAGGTAC 60.037 55.000 0.00 0.00 45.94 3.34
2634 2692 4.692155 CCTGAATGTTTTTCTTTCATGGGC 59.308 41.667 0.00 0.00 38.76 5.36
2641 2699 5.948742 TGAACCCCTGAATGTTTTTCTTT 57.051 34.783 0.00 0.00 0.00 2.52
2644 2702 6.101650 AGATTGAACCCCTGAATGTTTTTC 57.898 37.500 0.00 0.00 0.00 2.29
2704 2764 5.854010 TTTAGCGGATCTGTTAGAGATGT 57.146 39.130 2.89 0.00 41.91 3.06
2713 2773 2.354805 GGTGAGGTTTTAGCGGATCTGT 60.355 50.000 2.89 0.00 0.00 3.41
2732 2792 0.251253 TTGGAATTTTACGGGCCGGT 60.251 50.000 31.78 20.77 0.00 5.28
2741 2801 5.420409 ACTTGCAAAACGGTTGGAATTTTA 58.580 33.333 0.00 0.00 0.00 1.52
2750 2810 1.656594 GCGAAAACTTGCAAAACGGTT 59.343 42.857 0.00 0.00 0.00 4.44
2751 2811 1.135228 AGCGAAAACTTGCAAAACGGT 60.135 42.857 0.00 5.08 0.00 4.83
2779 2839 5.124617 GGCTTTTAGCAGATATATTCAGGCC 59.875 44.000 0.00 0.00 44.75 5.19
2789 2849 0.531974 CGGCGGGCTTTTAGCAGATA 60.532 55.000 0.00 0.00 44.75 1.98
2790 2850 1.819632 CGGCGGGCTTTTAGCAGAT 60.820 57.895 0.00 0.00 44.75 2.90
2813 2873 3.744426 CGGGTCGTCTCAAAAACTTGTAT 59.256 43.478 0.00 0.00 0.00 2.29
2816 2876 1.937899 ACGGGTCGTCTCAAAAACTTG 59.062 47.619 0.00 0.00 33.69 3.16
2820 2880 4.685924 GGATATACGGGTCGTCTCAAAAA 58.314 43.478 0.00 0.00 41.54 1.94
2821 2881 3.243168 CGGATATACGGGTCGTCTCAAAA 60.243 47.826 0.00 0.00 41.54 2.44
2822 2882 2.291465 CGGATATACGGGTCGTCTCAAA 59.709 50.000 0.00 0.00 41.54 2.69
2823 2883 1.875514 CGGATATACGGGTCGTCTCAA 59.124 52.381 0.00 0.00 41.54 3.02
2824 2884 1.516161 CGGATATACGGGTCGTCTCA 58.484 55.000 0.00 0.00 41.54 3.27
2825 2885 0.167689 GCGGATATACGGGTCGTCTC 59.832 60.000 9.89 0.00 41.54 3.36
2826 2886 1.239968 GGCGGATATACGGGTCGTCT 61.240 60.000 9.89 0.00 41.54 4.18
2827 2887 1.211190 GGCGGATATACGGGTCGTC 59.789 63.158 9.89 0.00 41.54 4.20
2828 2888 2.270986 GGGCGGATATACGGGTCGT 61.271 63.158 9.89 0.00 44.35 4.34
2829 2889 2.570181 GGGCGGATATACGGGTCG 59.430 66.667 9.89 0.00 0.00 4.79
2833 2893 2.707849 CGGAGGGGCGGATATACGG 61.708 68.421 9.89 0.00 0.00 4.02
2842 2902 2.172483 AATATAGCAGCGGAGGGGCG 62.172 60.000 0.00 0.00 38.18 6.13
2844 2904 2.674177 CGTAAATATAGCAGCGGAGGGG 60.674 54.545 0.00 0.00 0.00 4.79
2850 2910 2.736144 TCCCCGTAAATATAGCAGCG 57.264 50.000 0.00 0.00 0.00 5.18
2851 2911 4.184629 CTCATCCCCGTAAATATAGCAGC 58.815 47.826 0.00 0.00 0.00 5.25
2861 2921 0.917333 AAAGGCCCTCATCCCCGTAA 60.917 55.000 0.00 0.00 0.00 3.18
2865 2925 0.186143 CCTAAAAGGCCCTCATCCCC 59.814 60.000 0.00 0.00 0.00 4.81
2870 2930 1.989586 TGCTAACCTAAAAGGCCCTCA 59.010 47.619 0.00 0.00 39.63 3.86
2872 2932 2.026169 GTCTGCTAACCTAAAAGGCCCT 60.026 50.000 0.00 0.00 39.63 5.19
2874 2934 2.366533 GGTCTGCTAACCTAAAAGGCC 58.633 52.381 0.00 0.00 39.63 5.19
2880 2940 3.069158 GCTTATCCGGTCTGCTAACCTAA 59.931 47.826 0.00 0.00 37.15 2.69
2886 2946 2.100916 GTGAAGCTTATCCGGTCTGCTA 59.899 50.000 0.00 0.00 33.28 3.49
2896 2956 5.880341 AGTATTTTTGCGGTGAAGCTTATC 58.120 37.500 0.00 0.00 38.13 1.75
2900 2960 3.821033 AGAAGTATTTTTGCGGTGAAGCT 59.179 39.130 0.00 0.00 38.13 3.74
2902 2962 5.757886 TGAAGAAGTATTTTTGCGGTGAAG 58.242 37.500 0.00 0.00 0.00 3.02
2923 2983 3.556999 AGCTCTCTAAACCTAGCGATGA 58.443 45.455 0.00 0.00 39.94 2.92
2927 2987 1.002251 CGGAGCTCTCTAAACCTAGCG 60.002 57.143 14.64 0.00 39.94 4.26
2928 2988 2.033675 GTCGGAGCTCTCTAAACCTAGC 59.966 54.545 14.64 0.00 35.16 3.42
2971 3031 0.947180 CCGACGGCGAAAAAGGAGAA 60.947 55.000 15.16 0.00 40.82 2.87
2983 3043 3.861263 GGATTTGTCGCCGACGGC 61.861 66.667 29.10 29.10 46.48 5.68
2989 3049 2.785425 GGGGCATGGATTTGTCGCC 61.785 63.158 0.00 0.00 42.21 5.54
2990 3050 2.051518 TGGGGCATGGATTTGTCGC 61.052 57.895 0.00 0.00 34.98 5.19
3040 3100 2.847234 TCGGCCTCCACCAGTGTT 60.847 61.111 0.00 0.00 0.00 3.32
3073 3133 2.877360 TACTAACCTTGCTCGCCGCG 62.877 60.000 6.39 6.39 43.27 6.46
3100 3160 4.867608 ACGTCAAACTGGACAAAATTTTGG 59.132 37.500 29.37 16.73 42.34 3.28
3101 3161 5.574830 TGACGTCAAACTGGACAAAATTTTG 59.425 36.000 25.73 25.73 43.62 2.44
3102 3162 5.715070 TGACGTCAAACTGGACAAAATTTT 58.285 33.333 17.62 0.00 37.66 1.82
3103 3163 5.317733 TGACGTCAAACTGGACAAAATTT 57.682 34.783 17.62 0.00 37.66 1.82
3104 3164 4.974368 TGACGTCAAACTGGACAAAATT 57.026 36.364 17.62 0.00 37.66 1.82
3105 3165 4.578516 TGATGACGTCAAACTGGACAAAAT 59.421 37.500 24.13 0.00 37.66 1.82
3107 3167 3.536570 TGATGACGTCAAACTGGACAAA 58.463 40.909 24.13 0.00 37.66 2.83
3108 3168 3.186702 TGATGACGTCAAACTGGACAA 57.813 42.857 24.13 0.00 37.66 3.18
3109 3169 2.900716 TGATGACGTCAAACTGGACA 57.099 45.000 24.13 10.90 37.66 4.02
3110 3170 2.416547 CCATGATGACGTCAAACTGGAC 59.583 50.000 26.95 13.35 40.97 4.02
3111 3171 2.038426 ACCATGATGACGTCAAACTGGA 59.962 45.455 32.85 14.90 40.97 3.86
3112 3172 2.160219 CACCATGATGACGTCAAACTGG 59.840 50.000 28.18 28.18 40.97 4.00
3113 3173 2.807967 ACACCATGATGACGTCAAACTG 59.192 45.455 24.13 18.09 40.97 3.16
3114 3174 3.126001 ACACCATGATGACGTCAAACT 57.874 42.857 24.13 6.01 40.97 2.66
3115 3175 3.003275 ACAACACCATGATGACGTCAAAC 59.997 43.478 24.13 19.15 40.97 2.93
3116 3176 3.210227 ACAACACCATGATGACGTCAAA 58.790 40.909 24.13 14.54 40.97 2.69
3117 3177 2.844946 ACAACACCATGATGACGTCAA 58.155 42.857 24.13 7.48 40.97 3.18
3118 3178 2.542020 ACAACACCATGATGACGTCA 57.458 45.000 22.48 22.48 42.06 4.35
3119 3179 3.896648 AAACAACACCATGATGACGTC 57.103 42.857 9.11 9.11 0.00 4.34
3120 3180 4.320202 GCTAAAACAACACCATGATGACGT 60.320 41.667 0.00 0.00 0.00 4.34
3121 3181 4.083324 AGCTAAAACAACACCATGATGACG 60.083 41.667 0.00 0.00 0.00 4.35
3122 3182 5.156355 CAGCTAAAACAACACCATGATGAC 58.844 41.667 0.00 0.00 0.00 3.06
3123 3183 4.826733 ACAGCTAAAACAACACCATGATGA 59.173 37.500 0.00 0.00 0.00 2.92
3124 3184 5.125100 ACAGCTAAAACAACACCATGATG 57.875 39.130 0.00 0.00 0.00 3.07
3125 3185 6.264292 TGTTACAGCTAAAACAACACCATGAT 59.736 34.615 9.88 0.00 32.86 2.45
3126 3186 5.590663 TGTTACAGCTAAAACAACACCATGA 59.409 36.000 9.88 0.00 32.86 3.07
3127 3187 5.826586 TGTTACAGCTAAAACAACACCATG 58.173 37.500 9.88 0.00 32.86 3.66
3128 3188 6.294508 GGATGTTACAGCTAAAACAACACCAT 60.295 38.462 14.85 0.76 38.95 3.55
3129 3189 5.009210 GGATGTTACAGCTAAAACAACACCA 59.991 40.000 14.85 0.00 38.95 4.17
3130 3190 5.458015 GGATGTTACAGCTAAAACAACACC 58.542 41.667 14.85 13.97 38.95 4.16
3131 3191 5.458015 GGGATGTTACAGCTAAAACAACAC 58.542 41.667 14.85 10.83 38.95 3.32
3132 3192 4.214545 CGGGATGTTACAGCTAAAACAACA 59.785 41.667 14.85 8.21 38.95 3.33
3133 3193 4.453136 TCGGGATGTTACAGCTAAAACAAC 59.547 41.667 14.85 12.52 38.95 3.32
3134 3194 4.643463 TCGGGATGTTACAGCTAAAACAA 58.357 39.130 14.85 0.00 38.95 2.83
3135 3195 4.274602 TCGGGATGTTACAGCTAAAACA 57.725 40.909 13.63 13.63 39.73 2.83
3136 3196 5.156804 CATCGGGATGTTACAGCTAAAAC 57.843 43.478 0.00 3.90 34.23 2.43
3173 3233 8.840833 TTGGCCCTACTTTTTGAAAATAAATC 57.159 30.769 0.00 0.00 0.00 2.17
3178 3238 8.532186 AAATTTTGGCCCTACTTTTTGAAAAT 57.468 26.923 0.00 0.00 0.00 1.82
3256 3316 8.771286 AGGTTGGCATTAATCAAATTAAATCCT 58.229 29.630 0.00 0.00 38.15 3.24
3288 3348 5.261216 AGAAAACAACCCAACTGAGAAGAA 58.739 37.500 0.00 0.00 0.00 2.52
3295 3355 5.072040 AGACAAAGAAAACAACCCAACTG 57.928 39.130 0.00 0.00 0.00 3.16
3315 3375 2.880268 CGCATGATTAAGATGCCCAAGA 59.120 45.455 13.84 0.00 42.80 3.02
3331 3391 8.624701 AAATTTCAAGAATTCATAGTCGCATG 57.375 30.769 8.44 0.00 0.00 4.06
3381 3441 8.885693 AAAGTCTAGAAAATGGATAAAGGCTT 57.114 30.769 0.00 0.00 0.00 4.35


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

AutoCloner maintained by Alex Coulton.