Multiple sequence alignment - TraesCS6A01G217200

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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 TraesCS6A01G217200 chr6A 100.000 9000 0 0 1 9000 399832476 399841475 0.000000e+00 16620.0
1 TraesCS6A01G217200 chr6A 90.087 575 40 11 8438 9000 274870556 274871125 0.000000e+00 730.0
2 TraesCS6A01G217200 chr6A 87.231 603 38 14 8433 9000 273899907 273900505 0.000000e+00 651.0
3 TraesCS6A01G217200 chr6A 85.956 591 52 24 8431 9000 397467412 397467992 3.590000e-168 603.0
4 TraesCS6A01G217200 chr6A 86.592 537 32 25 8433 8951 273486406 273486920 2.840000e-154 556.0
5 TraesCS6A01G217200 chr6A 90.389 437 20 8 8392 8806 399875127 399875563 1.020000e-153 555.0
6 TraesCS6A01G217200 chr6A 86.735 490 41 19 4034 4514 294645215 294645689 2.880000e-144 523.0
7 TraesCS6A01G217200 chr6A 92.188 192 13 2 7099 7290 121719467 121719278 4.140000e-68 270.0
8 TraesCS6A01G217200 chr6A 79.612 206 32 7 6189 6389 105294581 105294381 1.220000e-28 139.0
9 TraesCS6A01G217200 chr6B 94.854 3673 93 19 4565 8226 438102221 438098634 0.000000e+00 5648.0
10 TraesCS6A01G217200 chr6B 93.499 2015 103 20 1 2005 438111044 438109048 0.000000e+00 2970.0
11 TraesCS6A01G217200 chr6B 95.318 1602 44 10 2008 3594 438108988 438107403 0.000000e+00 2514.0
12 TraesCS6A01G217200 chr6B 94.298 684 33 3 3584 4262 438103598 438102916 0.000000e+00 1042.0
13 TraesCS6A01G217200 chr6B 87.321 489 44 13 4034 4514 377933155 377933633 2.210000e-150 544.0
14 TraesCS6A01G217200 chr6B 96.040 303 12 0 4259 4561 438102495 438102193 2.260000e-135 494.0
15 TraesCS6A01G217200 chr6B 95.597 159 6 1 8224 8382 438098589 438098432 4.170000e-63 254.0
16 TraesCS6A01G217200 chr6D 96.571 3179 82 17 4562 7726 276144377 276141212 0.000000e+00 5241.0
17 TraesCS6A01G217200 chr6D 94.828 3287 100 26 571 3837 276148581 276145345 0.000000e+00 5064.0
18 TraesCS6A01G217200 chr6D 96.328 708 20 2 3860 4561 276145052 276144345 0.000000e+00 1158.0
19 TraesCS6A01G217200 chr6D 93.381 423 16 9 7811 8226 276140990 276140573 4.620000e-172 616.0
20 TraesCS6A01G217200 chr6D 86.967 422 37 12 4101 4514 211670788 211671199 8.230000e-125 459.0
21 TraesCS6A01G217200 chr6D 96.774 155 4 1 8224 8378 276140528 276140375 3.220000e-64 257.0
22 TraesCS6A01G217200 chr6D 78.922 204 35 7 6189 6389 87365389 87365191 2.040000e-26 132.0
23 TraesCS6A01G217200 chr1B 91.653 623 40 8 6596 7214 169949662 169949048 0.000000e+00 852.0
24 TraesCS6A01G217200 chr1B 93.229 192 11 2 7099 7290 146941868 146941679 1.910000e-71 281.0
25 TraesCS6A01G217200 chr1B 92.188 192 13 2 7099 7290 116256379 116256568 4.140000e-68 270.0
26 TraesCS6A01G217200 chr1D 91.475 610 43 7 6610 7214 90553614 90553009 0.000000e+00 830.0
27 TraesCS6A01G217200 chr5B 91.074 605 48 5 6612 7214 92203981 92203381 0.000000e+00 813.0
28 TraesCS6A01G217200 chr7A 90.732 615 48 7 6602 7214 54589891 54589284 0.000000e+00 811.0
29 TraesCS6A01G217200 chr7A 84.122 296 33 6 8452 8733 357857265 357857560 3.200000e-69 274.0
30 TraesCS6A01G217200 chr7A 86.364 66 7 2 8392 8456 346514216 346514280 4.510000e-08 71.3
31 TraesCS6A01G217200 chr7A 86.364 66 7 2 8392 8456 346545653 346545717 4.510000e-08 71.3
32 TraesCS6A01G217200 chr7A 94.444 36 1 1 8135 8170 699261893 699261859 5.000000e-03 54.7
33 TraesCS6A01G217200 chr3B 89.474 608 48 9 6610 7214 62717131 62716537 0.000000e+00 754.0
34 TraesCS6A01G217200 chr3B 92.023 514 27 6 6596 7109 550786945 550787444 0.000000e+00 710.0
35 TraesCS6A01G217200 chr3B 84.663 489 52 15 4031 4514 332931534 332932004 4.920000e-127 466.0
36 TraesCS6A01G217200 chr3B 83.450 429 54 13 4095 4514 489348407 489347987 5.100000e-102 383.0
37 TraesCS6A01G217200 chr3B 94.444 72 4 0 4791 4862 736670181 736670110 2.660000e-20 111.0
38 TraesCS6A01G217200 chr1A 90.256 585 40 8 8431 9000 170831783 170831201 0.000000e+00 749.0
39 TraesCS6A01G217200 chr1A 89.673 581 45 11 8433 9000 173044979 173044401 0.000000e+00 726.0
40 TraesCS6A01G217200 chr1A 89.304 589 37 14 8431 9000 174353036 174353617 0.000000e+00 715.0
41 TraesCS6A01G217200 chr1A 89.446 578 38 15 8438 9000 180395237 180394668 0.000000e+00 708.0
42 TraesCS6A01G217200 chr1A 90.278 432 24 11 8438 8854 180382701 180382273 4.750000e-152 549.0
43 TraesCS6A01G217200 chr1A 82.923 568 66 28 8433 8978 216624910 216624352 4.890000e-132 483.0
44 TraesCS6A01G217200 chr1A 79.878 492 68 13 5848 6322 537534740 537535217 1.870000e-86 331.0
45 TraesCS6A01G217200 chr5A 89.573 585 35 15 8433 9000 257161801 257162376 0.000000e+00 719.0
46 TraesCS6A01G217200 chr5A 89.041 584 46 10 8433 9000 256528736 256529317 0.000000e+00 708.0
47 TraesCS6A01G217200 chr5A 89.078 586 42 14 8433 9000 260965598 260966179 0.000000e+00 708.0
48 TraesCS6A01G217200 chr5A 88.723 603 32 14 8431 9000 57425800 57426399 0.000000e+00 704.0
49 TraesCS6A01G217200 chr5A 87.200 250 16 7 8468 8701 262620153 262620402 4.140000e-68 270.0
50 TraesCS6A01G217200 chr2A 89.365 583 45 11 8433 8999 353669356 353669937 0.000000e+00 717.0
51 TraesCS6A01G217200 chr2A 84.929 491 55 14 4034 4511 179292625 179292141 6.320000e-131 479.0
52 TraesCS6A01G217200 chr2A 85.922 206 20 7 4034 4233 705878035 705877833 2.550000e-50 211.0
53 TraesCS6A01G217200 chr2A 75.738 305 41 19 8456 8733 342199362 342199064 1.230000e-23 122.0
54 TraesCS6A01G217200 chr2A 86.567 67 7 2 8392 8457 332204321 332204386 1.250000e-08 73.1
55 TraesCS6A01G217200 chr2A 86.364 66 7 2 8392 8456 352365714 352365650 4.510000e-08 71.3
56 TraesCS6A01G217200 chr3A 89.312 552 45 10 6596 7145 638853800 638853261 0.000000e+00 680.0
57 TraesCS6A01G217200 chr3A 85.111 497 52 15 4034 4517 275289767 275289280 1.050000e-133 488.0
58 TraesCS6A01G217200 chr3A 83.567 499 56 15 4034 4513 264032196 264031705 2.310000e-120 444.0
59 TraesCS6A01G217200 chr3A 81.373 204 29 6 6188 6386 416165475 416165674 3.360000e-34 158.0
60 TraesCS6A01G217200 chr3A 94.444 72 4 0 4791 4862 12465454 12465383 2.660000e-20 111.0
61 TraesCS6A01G217200 chr3A 94.444 72 4 0 4791 4862 416165374 416165445 2.660000e-20 111.0
62 TraesCS6A01G217200 chr2D 85.772 492 51 13 4034 4511 170616623 170617109 3.750000e-138 503.0
63 TraesCS6A01G217200 chr2B 83.700 454 55 14 4034 4474 226696937 226696490 2.340000e-110 411.0
64 TraesCS6A01G217200 chr4A 75.355 564 79 36 8448 8959 467424506 467425061 5.470000e-52 217.0
65 TraesCS6A01G217200 chr4A 94.444 36 2 0 1840 1875 583703416 583703451 1.000000e-03 56.5
66 TraesCS6A01G217200 chrUn 94.444 72 4 0 4791 4862 479938297 479938226 2.660000e-20 111.0
67 TraesCS6A01G217200 chr7B 94.444 72 4 0 4791 4862 327255199 327255128 2.660000e-20 111.0
68 TraesCS6A01G217200 chr3D 88.525 61 6 1 5701 5761 505557798 505557739 1.250000e-08 73.1
69 TraesCS6A01G217200 chr4D 94.118 34 2 0 1840 1873 16818409 16818376 1.600000e-02 52.8


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 TraesCS6A01G217200 chr6A 399832476 399841475 8999 False 16620.000000 16620 100.000000 1 9000 1 chr6A.!!$F6 8999
1 TraesCS6A01G217200 chr6A 274870556 274871125 569 False 730.000000 730 90.087000 8438 9000 1 chr6A.!!$F3 562
2 TraesCS6A01G217200 chr6A 273899907 273900505 598 False 651.000000 651 87.231000 8433 9000 1 chr6A.!!$F2 567
3 TraesCS6A01G217200 chr6A 397467412 397467992 580 False 603.000000 603 85.956000 8431 9000 1 chr6A.!!$F5 569
4 TraesCS6A01G217200 chr6A 273486406 273486920 514 False 556.000000 556 86.592000 8433 8951 1 chr6A.!!$F1 518
5 TraesCS6A01G217200 chr6B 438098432 438111044 12612 True 2153.666667 5648 94.934333 1 8382 6 chr6B.!!$R1 8381
6 TraesCS6A01G217200 chr6D 276140375 276148581 8206 True 2467.200000 5241 95.576400 571 8378 5 chr6D.!!$R2 7807
7 TraesCS6A01G217200 chr1B 169949048 169949662 614 True 852.000000 852 91.653000 6596 7214 1 chr1B.!!$R2 618
8 TraesCS6A01G217200 chr1D 90553009 90553614 605 True 830.000000 830 91.475000 6610 7214 1 chr1D.!!$R1 604
9 TraesCS6A01G217200 chr5B 92203381 92203981 600 True 813.000000 813 91.074000 6612 7214 1 chr5B.!!$R1 602
10 TraesCS6A01G217200 chr7A 54589284 54589891 607 True 811.000000 811 90.732000 6602 7214 1 chr7A.!!$R1 612
11 TraesCS6A01G217200 chr3B 62716537 62717131 594 True 754.000000 754 89.474000 6610 7214 1 chr3B.!!$R1 604
12 TraesCS6A01G217200 chr1A 170831201 170831783 582 True 749.000000 749 90.256000 8431 9000 1 chr1A.!!$R1 569
13 TraesCS6A01G217200 chr1A 173044401 173044979 578 True 726.000000 726 89.673000 8433 9000 1 chr1A.!!$R2 567
14 TraesCS6A01G217200 chr1A 174353036 174353617 581 False 715.000000 715 89.304000 8431 9000 1 chr1A.!!$F1 569
15 TraesCS6A01G217200 chr1A 180394668 180395237 569 True 708.000000 708 89.446000 8438 9000 1 chr1A.!!$R4 562
16 TraesCS6A01G217200 chr1A 216624352 216624910 558 True 483.000000 483 82.923000 8433 8978 1 chr1A.!!$R5 545
17 TraesCS6A01G217200 chr5A 257161801 257162376 575 False 719.000000 719 89.573000 8433 9000 1 chr5A.!!$F3 567
18 TraesCS6A01G217200 chr5A 256528736 256529317 581 False 708.000000 708 89.041000 8433 9000 1 chr5A.!!$F2 567
19 TraesCS6A01G217200 chr5A 260965598 260966179 581 False 708.000000 708 89.078000 8433 9000 1 chr5A.!!$F4 567
20 TraesCS6A01G217200 chr5A 57425800 57426399 599 False 704.000000 704 88.723000 8431 9000 1 chr5A.!!$F1 569
21 TraesCS6A01G217200 chr2A 353669356 353669937 581 False 717.000000 717 89.365000 8433 8999 1 chr2A.!!$F2 566
22 TraesCS6A01G217200 chr3A 638853261 638853800 539 True 680.000000 680 89.312000 6596 7145 1 chr3A.!!$R4 549
23 TraesCS6A01G217200 chr4A 467424506 467425061 555 False 217.000000 217 75.355000 8448 8959 1 chr4A.!!$F1 511

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
202 203 0.394216 TGTTGGCAGTGACACAAGCT 60.394 50.000 18.56 0.0 0.00 3.74 F
298 299 2.006888 CTTGAACCGACAACACTGTGT 58.993 47.619 7.80 7.8 35.30 3.72 F
1320 1330 0.537143 TGCTGATTGGCTGAAACGGT 60.537 50.000 0.00 0.0 0.00 4.83 F
2276 2351 1.250328 TGGCTTCTTGCTCCAATGTG 58.750 50.000 0.00 0.0 42.39 3.21 F
2487 2580 1.406539 AGGCAAACTTTGTCACAGCAG 59.593 47.619 8.78 0.0 37.85 4.24 F
3637 7545 1.600485 CCAAAGTGTCGTTTAGGCGTT 59.400 47.619 0.00 0.0 0.00 4.84 F
3658 7566 1.600916 GGCAGTCTTGGGTGGTGAC 60.601 63.158 0.00 0.0 0.00 3.67 F
3997 8175 2.035321 TCACTGCATGTCGTAGTTGTCA 59.965 45.455 0.00 0.0 38.70 3.58 F
4552 9159 0.028642 ATGGCTGGTATCCCCTCCTT 60.029 55.000 0.00 0.0 0.00 3.36 F
4662 9270 0.107459 GAGCAGGGTTGAGGTGGATC 60.107 60.000 0.00 0.0 0.00 3.36 F
4668 9276 0.535335 GGTTGAGGTGGATCACGCTA 59.465 55.000 0.00 0.0 34.83 4.26 F
5260 9869 1.439353 CTGCGGGCGATACAGCATTT 61.439 55.000 0.00 0.0 39.02 2.32 F
6034 10646 3.748083 TGAGGCCAGATATGAGCATTTC 58.252 45.455 5.01 0.0 0.00 2.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1303 1313 0.109597 GCACCGTTTCAGCCAATCAG 60.110 55.000 0.00 0.0 0.0 2.90 R
1544 1554 0.740868 CGAGGAGGAATTTGAGCGCA 60.741 55.000 11.47 0.0 0.0 6.09 R
2581 2674 2.205911 GCGAATAAGAAGTGAGGAGCC 58.794 52.381 0.00 0.0 0.0 4.70 R
3838 7746 0.402121 AGAACTGCTTCCCTCAACCC 59.598 55.000 0.00 0.0 0.0 4.11 R
4370 8977 1.600957 CAATATGGCAGCAGGAGTTCG 59.399 52.381 0.00 0.0 0.0 3.95 R
4547 9154 0.323178 ATGGTGGCAGCTGAAAGGAG 60.323 55.000 20.43 0.0 0.0 3.69 R
4548 9155 0.609957 CATGGTGGCAGCTGAAAGGA 60.610 55.000 20.43 0.0 0.0 3.36 R
5842 10454 0.107831 TCCCTGCCCGTATAACATGC 59.892 55.000 0.00 0.0 0.0 4.06 R
5908 10520 0.267960 ATACCCGACTCCCATCCCTT 59.732 55.000 0.00 0.0 0.0 3.95 R
6655 11271 4.165779 CAATAATTCACCTGGTTTGTCGC 58.834 43.478 0.00 0.0 0.0 5.19 R
6729 11345 8.322906 ACAAACTGATCAAAATTCATACTCGA 57.677 30.769 0.00 0.0 0.0 4.04 R
6730 11346 8.446273 AGACAAACTGATCAAAATTCATACTCG 58.554 33.333 0.00 0.0 0.0 4.18 R
8004 12776 1.348064 AAGGATTCAGACGGTCACCA 58.652 50.000 11.27 0.0 0.0 4.17 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
31 32 6.291849 CGATGTAGATAGAAAGGCAAAACTCG 60.292 42.308 0.00 0.00 0.00 4.18
35 36 6.038997 AGATAGAAAGGCAAAACTCGTACT 57.961 37.500 0.00 0.00 0.00 2.73
66 67 4.699257 ACATGGTTCAAGCTCTTCTTCATC 59.301 41.667 0.00 0.00 31.27 2.92
67 68 4.630644 TGGTTCAAGCTCTTCTTCATCT 57.369 40.909 0.00 0.00 31.27 2.90
83 84 5.249163 TCTTCATCTGAGTGAATTTCCCTCA 59.751 40.000 10.56 10.56 37.47 3.86
112 113 1.218316 CCTAGCGGTGTGAGGGTTC 59.782 63.158 0.00 0.00 0.00 3.62
155 156 3.081804 GTCGGGGATGTTTCTTTGATGT 58.918 45.455 0.00 0.00 0.00 3.06
157 158 3.505680 TCGGGGATGTTTCTTTGATGTTG 59.494 43.478 0.00 0.00 0.00 3.33
158 159 3.588955 GGGGATGTTTCTTTGATGTTGC 58.411 45.455 0.00 0.00 0.00 4.17
187 188 3.425577 TGAGCTTTTCTGTTGCTGTTG 57.574 42.857 0.00 0.00 37.16 3.33
202 203 0.394216 TGTTGGCAGTGACACAAGCT 60.394 50.000 18.56 0.00 0.00 3.74
298 299 2.006888 CTTGAACCGACAACACTGTGT 58.993 47.619 7.80 7.80 35.30 3.72
342 343 8.294341 ACACGAAATTGATACCACTATATTCG 57.706 34.615 0.00 0.00 41.86 3.34
410 411 7.816031 TCCTTGTCTTAACGAAACCTAATACAG 59.184 37.037 0.00 0.00 0.00 2.74
420 421 7.533426 ACGAAACCTAATACAGCCTATATACG 58.467 38.462 0.00 0.00 0.00 3.06
425 426 8.278729 ACCTAATACAGCCTATATACGAGAAC 57.721 38.462 0.00 0.00 0.00 3.01
562 567 3.536158 TGATCAAAGCTGCGTTTGTAC 57.464 42.857 17.71 14.39 38.38 2.90
901 910 5.204409 TCTGCAAGTGAGCAAATCAAATT 57.796 34.783 0.00 0.00 45.13 1.82
1288 1298 4.667573 TCCGCTCTTCTATCCAGTCATAT 58.332 43.478 0.00 0.00 0.00 1.78
1303 1313 1.669115 ATATCCGATGCGCCACTGC 60.669 57.895 4.18 0.00 0.00 4.40
1320 1330 0.537143 TGCTGATTGGCTGAAACGGT 60.537 50.000 0.00 0.00 0.00 4.83
1324 1334 1.573829 GATTGGCTGAAACGGTGCGA 61.574 55.000 0.00 0.00 0.00 5.10
1325 1335 1.852067 ATTGGCTGAAACGGTGCGAC 61.852 55.000 0.00 0.00 0.00 5.19
1544 1554 3.243975 ACAAGATAACGTCCAAGTTCCGT 60.244 43.478 0.00 0.00 35.70 4.69
1746 1756 2.816087 CTGCATGCTTCAGTTAGTTGGT 59.184 45.455 20.33 0.00 0.00 3.67
1820 1830 8.462016 GTGTCAAAATATGAGGCTTATTTCACT 58.538 33.333 0.00 0.00 39.19 3.41
1902 1913 7.532546 TCGTATTGAAAAAGTACTTGCGATTTG 59.467 33.333 9.34 4.36 0.00 2.32
1903 1914 7.322699 CGTATTGAAAAAGTACTTGCGATTTGT 59.677 33.333 9.34 0.00 0.00 2.83
1905 1916 7.901874 TTGAAAAAGTACTTGCGATTTGTAC 57.098 32.000 9.34 0.00 37.42 2.90
1906 1917 6.432107 TGAAAAAGTACTTGCGATTTGTACC 58.568 36.000 9.34 0.00 37.76 3.34
2023 2094 8.476657 AGTTACTTTCTTACGATTAGCTTTCC 57.523 34.615 0.00 0.00 0.00 3.13
2024 2095 8.092687 AGTTACTTTCTTACGATTAGCTTTCCA 58.907 33.333 0.00 0.00 0.00 3.53
2074 2145 6.817765 TTCTTGCGAAAGATAATCCAAGTT 57.182 33.333 6.69 0.00 32.08 2.66
2202 2277 5.212194 CCCATCAGTGTTAACTTTTTGACG 58.788 41.667 7.22 0.00 32.98 4.35
2276 2351 1.250328 TGGCTTCTTGCTCCAATGTG 58.750 50.000 0.00 0.00 42.39 3.21
2367 2442 6.531923 CATATCTTGTCTGGATGGTTCTGAT 58.468 40.000 0.00 0.00 0.00 2.90
2438 2531 9.104965 GCATAACACATGTAGTTATTCCTGTAA 57.895 33.333 21.16 4.85 39.46 2.41
2487 2580 1.406539 AGGCAAACTTTGTCACAGCAG 59.593 47.619 8.78 0.00 37.85 4.24
2511 2604 6.323739 AGACTGTTTGGAAATTTGTGTACCAT 59.676 34.615 0.00 0.00 0.00 3.55
2513 2606 6.983890 ACTGTTTGGAAATTTGTGTACCATTC 59.016 34.615 0.00 0.00 0.00 2.67
2520 2613 9.921637 TGGAAATTTGTGTACCATTCTATTTTC 57.078 29.630 0.00 0.00 0.00 2.29
2581 2674 6.753180 TGTTGATGGCTTCTCTATAGCTTAG 58.247 40.000 0.00 0.00 38.67 2.18
2762 2855 5.584251 TGTGTTCATATCATTGCGTGTATGT 59.416 36.000 0.00 0.00 0.00 2.29
2767 2860 7.313951 TCATATCATTGCGTGTATGTTTTCA 57.686 32.000 0.00 0.00 0.00 2.69
2776 2869 6.036470 TGCGTGTATGTTTTCATTTTCAACA 58.964 32.000 0.00 0.00 41.25 3.33
2865 2958 5.303165 CCCCCAATATTACGTTTCTACTCC 58.697 45.833 0.00 0.00 0.00 3.85
2889 2982 8.893560 TCCCCCTATACCCATACTTAAAAATAC 58.106 37.037 0.00 0.00 0.00 1.89
3219 3312 6.611613 TTCTTGTCCTACTCAGATGTCATT 57.388 37.500 0.00 0.00 0.00 2.57
3220 3313 5.970592 TCTTGTCCTACTCAGATGTCATTG 58.029 41.667 0.00 0.00 0.00 2.82
3358 3451 7.571080 TTCAGGTAAGGTTGACGTTTAAATT 57.429 32.000 0.00 0.00 0.00 1.82
3516 3610 7.230108 ACCTGCCTCATTTTACATGATCTATTG 59.770 37.037 0.00 0.00 0.00 1.90
3556 3650 7.806960 GGAATATTAAGAAGCATTGATCAGTGC 59.193 37.037 29.92 29.92 43.34 4.40
3637 7545 1.600485 CCAAAGTGTCGTTTAGGCGTT 59.400 47.619 0.00 0.00 0.00 4.84
3657 7565 1.768684 GAGGCAGTCTTGGGTGGTGA 61.769 60.000 0.00 0.00 0.00 4.02
3658 7566 1.600916 GGCAGTCTTGGGTGGTGAC 60.601 63.158 0.00 0.00 0.00 3.67
3734 7642 3.023949 GCGAGGCAGGTGATGAGGT 62.024 63.158 0.00 0.00 0.00 3.85
3900 8078 2.281970 CTCCACTGGCTTGCTGCA 60.282 61.111 0.00 0.00 45.15 4.41
3997 8175 2.035321 TCACTGCATGTCGTAGTTGTCA 59.965 45.455 0.00 0.00 38.70 3.58
4056 8234 6.477053 TGATGAGGAACAATAGAGAGAAGG 57.523 41.667 0.00 0.00 0.00 3.46
4058 8236 3.131223 TGAGGAACAATAGAGAGAAGGCG 59.869 47.826 0.00 0.00 0.00 5.52
4194 8372 8.341173 CCATGAGTAGAATGTTGAATCTTAAGC 58.659 37.037 0.00 0.00 0.00 3.09
4264 8871 4.093743 CCCAAAGCCCTGTAAATTAGGTT 58.906 43.478 0.00 0.00 33.31 3.50
4317 8924 7.012607 TGTACCCCACTACCTATAATAGAACC 58.987 42.308 0.00 0.00 0.00 3.62
4319 8926 6.082707 ACCCCACTACCTATAATAGAACCTG 58.917 44.000 0.00 0.00 0.00 4.00
4355 8962 3.895232 TCTTGGACTAGATCTTGTGCC 57.105 47.619 22.03 17.77 0.00 5.01
4370 8977 5.428253 TCTTGTGCCCTATGAGTTTGTATC 58.572 41.667 0.00 0.00 0.00 2.24
4548 9155 4.008453 CCATGGCTGGTATCCCCT 57.992 61.111 0.00 0.00 37.79 4.79
4549 9156 1.763770 CCATGGCTGGTATCCCCTC 59.236 63.158 0.00 0.00 37.79 4.30
4550 9157 1.763770 CATGGCTGGTATCCCCTCC 59.236 63.158 0.00 0.00 0.00 4.30
4551 9158 0.769776 CATGGCTGGTATCCCCTCCT 60.770 60.000 0.00 0.00 0.00 3.69
4552 9159 0.028642 ATGGCTGGTATCCCCTCCTT 60.029 55.000 0.00 0.00 0.00 3.36
4553 9160 0.253630 TGGCTGGTATCCCCTCCTTT 60.254 55.000 0.00 0.00 0.00 3.11
4554 9161 0.474614 GGCTGGTATCCCCTCCTTTC 59.525 60.000 0.00 0.00 0.00 2.62
4555 9162 1.213296 GCTGGTATCCCCTCCTTTCA 58.787 55.000 0.00 0.00 0.00 2.69
4556 9163 1.141858 GCTGGTATCCCCTCCTTTCAG 59.858 57.143 0.00 0.00 0.00 3.02
4557 9164 1.141858 CTGGTATCCCCTCCTTTCAGC 59.858 57.143 0.00 0.00 0.00 4.26
4558 9165 1.274416 TGGTATCCCCTCCTTTCAGCT 60.274 52.381 0.00 0.00 0.00 4.24
4559 9166 1.141858 GGTATCCCCTCCTTTCAGCTG 59.858 57.143 7.63 7.63 0.00 4.24
4560 9167 0.839946 TATCCCCTCCTTTCAGCTGC 59.160 55.000 9.47 0.00 0.00 5.25
4561 9168 1.931007 ATCCCCTCCTTTCAGCTGCC 61.931 60.000 9.47 0.00 0.00 4.85
4562 9169 2.759114 CCCTCCTTTCAGCTGCCA 59.241 61.111 9.47 0.00 0.00 4.92
4563 9170 1.676967 CCCTCCTTTCAGCTGCCAC 60.677 63.158 9.47 0.00 0.00 5.01
4564 9171 1.676967 CCTCCTTTCAGCTGCCACC 60.677 63.158 9.47 0.00 0.00 4.61
4565 9172 1.073722 CTCCTTTCAGCTGCCACCA 59.926 57.895 9.47 0.00 0.00 4.17
4566 9173 0.323178 CTCCTTTCAGCTGCCACCAT 60.323 55.000 9.47 0.00 0.00 3.55
4567 9174 0.609957 TCCTTTCAGCTGCCACCATG 60.610 55.000 9.47 0.00 0.00 3.66
4568 9175 1.601419 CCTTTCAGCTGCCACCATGG 61.601 60.000 11.19 11.19 41.55 3.66
4662 9270 0.107459 GAGCAGGGTTGAGGTGGATC 60.107 60.000 0.00 0.00 0.00 3.36
4668 9276 0.535335 GGTTGAGGTGGATCACGCTA 59.465 55.000 0.00 0.00 34.83 4.26
4697 9305 5.394443 GCTATGATTGCCATTTCAACCTTGA 60.394 40.000 0.00 0.00 36.71 3.02
4733 9341 7.362662 CGGGACACCATTTTATCATCTAATTG 58.637 38.462 0.00 0.00 36.13 2.32
4736 9344 9.520204 GGACACCATTTTATCATCTAATTGTTG 57.480 33.333 0.00 0.00 0.00 3.33
4738 9346 7.981225 ACACCATTTTATCATCTAATTGTTGCC 59.019 33.333 0.00 0.00 0.00 4.52
4748 9356 6.597672 TCATCTAATTGTTGCCGTACAAGATT 59.402 34.615 0.00 3.15 40.99 2.40
4765 9373 4.246712 AGATTGGAATGTCATGCCTTCT 57.753 40.909 11.41 10.08 0.00 2.85
4785 9393 4.800023 TCTGTGCCTAGTAGGTGCTATAA 58.200 43.478 17.69 0.00 37.80 0.98
4943 9552 4.040952 AGAATATTGGCTAGGTACAGGCTG 59.959 45.833 14.16 14.16 41.51 4.85
5007 9616 7.147983 TGGTTATGTGGTTGATTTATTGGCTAC 60.148 37.037 0.00 0.00 0.00 3.58
5046 9655 2.149973 ATGGTTGGGAAATGAGGAGC 57.850 50.000 0.00 0.00 0.00 4.70
5056 9665 3.007398 GGAAATGAGGAGCGATAGTGGAT 59.993 47.826 0.00 0.00 39.35 3.41
5060 9669 4.060038 TGAGGAGCGATAGTGGATTTTC 57.940 45.455 0.00 0.00 39.35 2.29
5062 9671 2.135933 GGAGCGATAGTGGATTTTCCG 58.864 52.381 0.00 0.00 40.17 4.30
5092 9701 7.326454 TCTAAGCATATCTGAGCATAATGACC 58.674 38.462 0.00 0.00 0.00 4.02
5098 9707 4.142609 TCTGAGCATAATGACCAAGGAC 57.857 45.455 0.00 0.00 0.00 3.85
5099 9708 3.519107 TCTGAGCATAATGACCAAGGACA 59.481 43.478 0.00 0.00 0.00 4.02
5100 9709 4.019411 TCTGAGCATAATGACCAAGGACAA 60.019 41.667 0.00 0.00 0.00 3.18
5106 9715 5.713025 CATAATGACCAAGGACAAAAGGTG 58.287 41.667 0.00 0.00 33.77 4.00
5130 9739 4.864704 TGGAAAGTGCCATAAAAGTTCC 57.135 40.909 0.00 0.00 34.83 3.62
5254 9863 4.830765 GCACCTGCGGGCGATACA 62.831 66.667 12.89 0.00 35.63 2.29
5260 9869 1.439353 CTGCGGGCGATACAGCATTT 61.439 55.000 0.00 0.00 39.02 2.32
5829 10441 5.130350 GCCCAGTATTTTTATGCTAGGTGA 58.870 41.667 0.00 0.00 0.00 4.02
5908 10520 4.580167 AGTGCTTTCTTAGTTGTGCAATCA 59.420 37.500 0.00 0.00 32.10 2.57
6034 10646 3.748083 TGAGGCCAGATATGAGCATTTC 58.252 45.455 5.01 0.00 0.00 2.17
6138 10751 4.611310 AGCATCTGTTCATGAAATGTCG 57.389 40.909 10.35 0.48 46.80 4.35
6327 10940 6.238648 CAGGTAAATGTTCTACCTTCCAGTT 58.761 40.000 0.00 0.00 45.70 3.16
6655 11271 7.113658 TCTCACCTATAGCTAAAGTCAAAGG 57.886 40.000 0.00 0.00 0.00 3.11
6729 11345 8.803235 GGTAAGTTTCTATCCTTTCAAATGGTT 58.197 33.333 0.00 0.00 0.00 3.67
6730 11346 9.841880 GTAAGTTTCTATCCTTTCAAATGGTTC 57.158 33.333 0.00 0.00 0.00 3.62
7233 11859 7.117667 TGCGTACGCTCATGATATTTGAATTAT 59.882 33.333 36.99 0.00 42.51 1.28
7339 11965 5.097529 GGAAAATATGTGCAGACATGTGTG 58.902 41.667 18.25 18.25 43.03 3.82
7492 12118 4.624913 TGGGCCCCACAATTATATTTTCA 58.375 39.130 22.27 0.00 0.00 2.69
7532 12158 3.614150 CGTAGAAGTAACTTGAGCCTGCA 60.614 47.826 0.00 0.00 0.00 4.41
7560 12186 5.515797 TCTATCTGTAACTCACCAATCCG 57.484 43.478 0.00 0.00 0.00 4.18
7574 12200 5.536916 TCACCAATCCGGAATTAAGTTTGTT 59.463 36.000 9.01 0.00 38.63 2.83
7584 12210 6.581166 CGGAATTAAGTTTGTTAAGAAGCCAC 59.419 38.462 0.00 0.00 0.00 5.01
7653 12279 4.251103 TCTGCAGGTAGGATAGAAGACA 57.749 45.455 15.13 0.00 0.00 3.41
7654 12280 3.954904 TCTGCAGGTAGGATAGAAGACAC 59.045 47.826 15.13 0.00 0.00 3.67
7700 12328 1.270550 GGGGACAGCAGATTTTGTGTG 59.729 52.381 0.00 0.00 0.00 3.82
7734 12362 9.903682 GAGTGAAATAAACTACTGTACACTGTA 57.096 33.333 0.00 0.00 36.45 2.74
7794 12423 3.628832 TTTCATTCTTTTGGAGGGGGT 57.371 42.857 0.00 0.00 0.00 4.95
7795 12424 2.603075 TCATTCTTTTGGAGGGGGTG 57.397 50.000 0.00 0.00 0.00 4.61
7796 12425 0.897621 CATTCTTTTGGAGGGGGTGC 59.102 55.000 0.00 0.00 0.00 5.01
7797 12426 0.611896 ATTCTTTTGGAGGGGGTGCG 60.612 55.000 0.00 0.00 0.00 5.34
7798 12427 2.002018 TTCTTTTGGAGGGGGTGCGT 62.002 55.000 0.00 0.00 0.00 5.24
7799 12428 1.971695 CTTTTGGAGGGGGTGCGTC 60.972 63.158 0.00 0.00 0.00 5.19
7800 12429 3.501040 TTTTGGAGGGGGTGCGTCC 62.501 63.158 0.00 0.00 0.00 4.79
7840 12605 5.120830 GCGCATGATAACTTGGATAGTAAGG 59.879 44.000 0.30 0.00 35.54 2.69
7904 12669 4.840115 AGAAATTCATTTTTCCCTGGAGCA 59.160 37.500 0.00 0.00 36.47 4.26
7922 12687 2.993545 GCATGTTGCGTACAGTCAAAA 58.006 42.857 0.00 0.00 40.83 2.44
8003 12775 5.499004 ACTTGGTTCTTCTGGTGCTTATA 57.501 39.130 0.00 0.00 0.00 0.98
8004 12776 6.067217 ACTTGGTTCTTCTGGTGCTTATAT 57.933 37.500 0.00 0.00 0.00 0.86
8099 12871 6.801575 TGTTTCATGTTTGAACCTAAGAACC 58.198 36.000 0.00 0.00 41.50 3.62
8112 12884 4.343239 ACCTAAGAACCGTTGTTACTCAGT 59.657 41.667 0.00 0.00 33.97 3.41
8124 12896 4.737578 TGTTACTCAGTAGGACAGGAAGT 58.262 43.478 0.00 0.00 0.00 3.01
8148 12920 3.835395 AGAATTACTCCCTCCGATCCATC 59.165 47.826 0.00 0.00 0.00 3.51
8275 13094 3.953612 TGAGGTGCAGTTTGTTTGAAGAT 59.046 39.130 0.00 0.00 0.00 2.40
8330 13149 5.012239 GCAGCCCATTAAGATGATATCCAA 58.988 41.667 0.00 0.00 35.16 3.53
8348 13167 9.071276 GATATCCAATGCAATTTCTCTAGGAAA 57.929 33.333 8.30 8.30 46.33 3.13
8378 13197 8.563123 ACCATAGATAAGCAGATTTCATCATG 57.437 34.615 0.00 0.00 0.00 3.07
8382 13201 6.010850 AGATAAGCAGATTTCATCATGGCAT 58.989 36.000 0.00 0.00 0.00 4.40
8383 13202 6.493802 AGATAAGCAGATTTCATCATGGCATT 59.506 34.615 0.00 0.00 0.00 3.56
8384 13203 7.668469 AGATAAGCAGATTTCATCATGGCATTA 59.332 33.333 0.00 0.00 0.00 1.90
8385 13204 5.707242 AGCAGATTTCATCATGGCATTAG 57.293 39.130 0.00 0.00 0.00 1.73
8386 13205 4.523173 AGCAGATTTCATCATGGCATTAGG 59.477 41.667 0.00 0.00 0.00 2.69
8387 13206 4.321750 GCAGATTTCATCATGGCATTAGGG 60.322 45.833 0.00 0.00 0.00 3.53
8388 13207 4.831155 CAGATTTCATCATGGCATTAGGGT 59.169 41.667 0.00 0.00 0.00 4.34
8389 13208 4.831155 AGATTTCATCATGGCATTAGGGTG 59.169 41.667 0.00 0.00 0.00 4.61
8390 13209 2.662535 TCATCATGGCATTAGGGTGG 57.337 50.000 0.00 0.00 0.00 4.61
8391 13210 2.134354 TCATCATGGCATTAGGGTGGA 58.866 47.619 0.00 0.00 0.00 4.02
8392 13211 2.718062 TCATCATGGCATTAGGGTGGAT 59.282 45.455 0.00 0.00 0.00 3.41
8393 13212 2.957402 TCATGGCATTAGGGTGGATC 57.043 50.000 0.00 0.00 0.00 3.36
8394 13213 1.072173 TCATGGCATTAGGGTGGATCG 59.928 52.381 0.00 0.00 0.00 3.69
8395 13214 0.401738 ATGGCATTAGGGTGGATCGG 59.598 55.000 0.00 0.00 0.00 4.18
8396 13215 1.600916 GGCATTAGGGTGGATCGGC 60.601 63.158 0.00 0.00 0.00 5.54
8397 13216 1.600916 GCATTAGGGTGGATCGGCC 60.601 63.158 0.00 0.00 37.10 6.13
8398 13217 1.301716 CATTAGGGTGGATCGGCCG 60.302 63.158 22.12 22.12 40.66 6.13
8399 13218 1.458777 ATTAGGGTGGATCGGCCGA 60.459 57.895 33.12 33.12 40.66 5.54
8400 13219 0.836400 ATTAGGGTGGATCGGCCGAT 60.836 55.000 39.64 39.64 40.66 4.18
8408 13227 2.217112 GATCGGCCGATCTTTCACG 58.783 57.895 45.74 12.74 45.42 4.35
8409 13228 0.248907 GATCGGCCGATCTTTCACGA 60.249 55.000 45.74 18.68 45.42 4.35
8410 13229 0.174845 ATCGGCCGATCTTTCACGAA 59.825 50.000 34.60 5.94 33.86 3.85
8411 13230 0.038067 TCGGCCGATCTTTCACGAAA 60.038 50.000 27.28 0.00 0.00 3.46
8412 13231 0.370273 CGGCCGATCTTTCACGAAAG 59.630 55.000 24.07 12.40 46.82 2.62
8413 13232 0.727398 GGCCGATCTTTCACGAAAGG 59.273 55.000 17.23 5.63 45.80 3.11
8414 13233 1.674817 GGCCGATCTTTCACGAAAGGA 60.675 52.381 17.23 6.84 45.80 3.36
8415 13234 1.661112 GCCGATCTTTCACGAAAGGAG 59.339 52.381 17.23 9.96 45.80 3.69
8416 13235 2.931320 GCCGATCTTTCACGAAAGGAGT 60.931 50.000 17.23 6.29 45.80 3.85
8417 13236 2.668457 CCGATCTTTCACGAAAGGAGTG 59.332 50.000 17.23 7.15 45.80 3.51
8418 13237 2.668457 CGATCTTTCACGAAAGGAGTGG 59.332 50.000 17.23 4.61 45.80 4.00
8419 13238 2.543777 TCTTTCACGAAAGGAGTGGG 57.456 50.000 17.23 0.00 45.80 4.61
8420 13239 1.766496 TCTTTCACGAAAGGAGTGGGT 59.234 47.619 17.23 0.00 45.80 4.51
8421 13240 2.143925 CTTTCACGAAAGGAGTGGGTC 58.856 52.381 11.02 0.00 42.96 4.46
8422 13241 5.375674 TCTTTCACGAAAGGAGTGGGTCC 62.376 52.174 17.23 0.00 45.80 4.46
8432 13251 3.055209 GGAGTGGGTCCTGTAAAGAAC 57.945 52.381 0.00 0.00 42.99 3.01
8433 13252 2.370849 GGAGTGGGTCCTGTAAAGAACA 59.629 50.000 0.00 0.00 42.99 3.18
8434 13253 3.400255 GAGTGGGTCCTGTAAAGAACAC 58.600 50.000 0.00 0.00 33.45 3.32
8435 13254 2.140717 GTGGGTCCTGTAAAGAACACG 58.859 52.381 0.00 0.00 33.45 4.49
8436 13255 2.040939 TGGGTCCTGTAAAGAACACGA 58.959 47.619 0.00 0.00 33.45 4.35
8439 13258 2.298163 GGTCCTGTAAAGAACACGAGGA 59.702 50.000 0.00 0.00 33.45 3.71
8469 13289 4.569162 CGAGAGAAACACTAAACCAACACA 59.431 41.667 0.00 0.00 0.00 3.72
8471 13291 6.436843 AGAGAAACACTAAACCAACACAAG 57.563 37.500 0.00 0.00 0.00 3.16
8514 13346 3.893200 TCCTCGAATACATGGAACGGTAT 59.107 43.478 7.79 0.00 33.82 2.73
8554 13391 5.579511 CGATACAATGGTAACGGTCTTCTTT 59.420 40.000 2.10 0.00 40.72 2.52
8785 13647 3.233980 ACTGTGCGCAGACAGGGA 61.234 61.111 32.90 0.00 46.56 4.20
8888 13822 3.839432 CTCTCGGGTTCGGAGGGC 61.839 72.222 3.32 0.00 36.95 5.19
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 6.407202 ACGAGTTTTGCCTTTCTATCTACAT 58.593 36.000 0.00 0.00 0.00 2.29
31 32 4.380841 TGAACCATGTATCGTGGAGTAC 57.619 45.455 13.94 0.00 42.73 2.73
35 36 2.236146 AGCTTGAACCATGTATCGTGGA 59.764 45.455 13.94 0.00 42.73 4.02
48 49 5.120519 CACTCAGATGAAGAAGAGCTTGAAC 59.879 44.000 0.00 0.00 36.83 3.18
83 84 2.645567 CGCTAGGACCGCATCGAT 59.354 61.111 0.00 0.00 0.00 3.59
112 113 0.826672 ATCGTAGGTTCCCCTAGCCG 60.827 60.000 0.00 0.00 44.14 5.52
129 130 2.403252 AGAAACATCCCCGACACATC 57.597 50.000 0.00 0.00 0.00 3.06
133 134 2.940994 TCAAAGAAACATCCCCGACA 57.059 45.000 0.00 0.00 0.00 4.35
155 156 3.638160 AGAAAAGCTCATGTCCTTTGCAA 59.362 39.130 16.07 0.00 30.50 4.08
157 158 3.005155 ACAGAAAAGCTCATGTCCTTTGC 59.995 43.478 11.97 10.69 32.06 3.68
158 159 4.843220 ACAGAAAAGCTCATGTCCTTTG 57.157 40.909 11.97 5.80 32.06 2.77
187 188 2.099756 AGAAAAAGCTTGTGTCACTGCC 59.900 45.455 0.00 3.53 0.00 4.85
202 203 8.908903 TCATAACTCCAAACTAAGCAAGAAAAA 58.091 29.630 0.00 0.00 0.00 1.94
390 391 6.290294 AGGCTGTATTAGGTTTCGTTAAGA 57.710 37.500 0.00 0.00 0.00 2.10
410 411 5.869753 TTACTCCGTTCTCGTATATAGGC 57.130 43.478 0.00 0.00 35.01 3.93
541 546 3.424829 CGTACAAACGCAGCTTTGATCAT 60.425 43.478 18.55 4.74 43.12 2.45
562 567 4.668576 AGTACTTGACAATGTTGCATCG 57.331 40.909 0.00 0.00 0.00 3.84
732 737 3.090210 TCATGTGGATTTCAGTGCCAT 57.910 42.857 0.00 0.00 33.66 4.40
901 910 5.579047 TCTGCCCTTTTGGATCTTTTGATA 58.421 37.500 0.00 0.00 44.07 2.15
950 959 9.144747 GTATTTATATACTGCTCATGTCACTGG 57.855 37.037 0.00 0.00 34.92 4.00
1303 1313 0.109597 GCACCGTTTCAGCCAATCAG 60.110 55.000 0.00 0.00 0.00 2.90
1320 1330 1.751351 AGCATTACTAGAGCAGTCGCA 59.249 47.619 0.00 0.00 42.27 5.10
1324 1334 3.133721 CCCAGAAGCATTACTAGAGCAGT 59.866 47.826 0.00 0.00 41.62 4.40
1325 1335 3.386078 TCCCAGAAGCATTACTAGAGCAG 59.614 47.826 0.00 0.00 0.00 4.24
1544 1554 0.740868 CGAGGAGGAATTTGAGCGCA 60.741 55.000 11.47 0.00 0.00 6.09
1746 1756 4.643463 TGCATGTAACGTTAAAGAAGGGA 58.357 39.130 10.11 0.00 0.00 4.20
1902 1913 5.994887 TTGATACATGGTTTATGCGGTAC 57.005 39.130 0.00 0.00 40.59 3.34
1903 1914 7.446769 ACTATTGATACATGGTTTATGCGGTA 58.553 34.615 0.00 0.00 40.59 4.02
1905 1916 6.801539 ACTATTGATACATGGTTTATGCGG 57.198 37.500 0.00 0.00 40.59 5.69
1975 1989 6.964086 ACTTACTAGTCCCTCTATCCCAAAAA 59.036 38.462 0.00 0.00 0.00 1.94
2074 2145 5.658634 ACCTAATCATGAACACAGCTCTCTA 59.341 40.000 0.00 0.00 0.00 2.43
2202 2277 4.686091 GCAAAGATAACTTTTGCAACCTCC 59.314 41.667 15.47 0.00 43.41 4.30
2276 2351 3.680789 GGCGTACATGCACAATAGAAAC 58.319 45.455 0.00 0.00 36.28 2.78
2438 2531 7.444487 GGTGATAGGTGAGTAAAGAACTTTTGT 59.556 37.037 5.14 0.00 39.07 2.83
2487 2580 5.897050 TGGTACACAAATTTCCAAACAGTC 58.103 37.500 0.00 0.00 0.00 3.51
2511 2604 7.725397 AGCTATTATGCACCATGGAAAATAGAA 59.275 33.333 21.47 3.90 34.99 2.10
2513 2606 7.310664 CAGCTATTATGCACCATGGAAAATAG 58.689 38.462 21.47 20.41 34.99 1.73
2581 2674 2.205911 GCGAATAAGAAGTGAGGAGCC 58.794 52.381 0.00 0.00 0.00 4.70
2776 2869 7.444299 ACAAAAATACCAAGCACTGATTCAAT 58.556 30.769 0.00 0.00 0.00 2.57
2842 2935 5.303165 GGAGTAGAAACGTAATATTGGGGG 58.697 45.833 0.00 0.00 0.00 5.40
2862 2955 7.396906 TTTTTAAGTATGGGTATAGGGGGAG 57.603 40.000 0.00 0.00 0.00 4.30
2864 2957 8.897692 AGTATTTTTAAGTATGGGTATAGGGGG 58.102 37.037 0.00 0.00 0.00 5.40
3219 3312 8.834749 TGCATACACACTAATACAACTAAACA 57.165 30.769 0.00 0.00 0.00 2.83
3233 3326 9.573166 AAATGGTGTTATATATGCATACACACT 57.427 29.630 24.01 12.26 34.70 3.55
3358 3451 7.801716 AAACTGTAGAAATAACTGCAACAGA 57.198 32.000 14.52 0.00 37.04 3.41
3606 7514 3.009723 CGACACTTTGGTGATGCCTTAT 58.990 45.455 3.06 0.00 45.61 1.73
3637 7545 1.770110 ACCACCCAAGACTGCCTCA 60.770 57.895 0.00 0.00 0.00 3.86
3643 7551 1.909302 CTATGGTCACCACCCAAGACT 59.091 52.381 0.00 0.00 42.99 3.24
3657 7565 2.263153 GCCACAAAACGGCTATGGT 58.737 52.632 0.00 0.00 46.56 3.55
3718 7626 1.028868 GCAACCTCATCACCTGCCTC 61.029 60.000 0.00 0.00 0.00 4.70
3734 7642 1.281867 CCATCCTCCCACTACAAGCAA 59.718 52.381 0.00 0.00 0.00 3.91
3824 7732 1.930520 AACCCAAGGTTGCAGGTCT 59.069 52.632 0.00 0.00 45.07 3.85
3838 7746 0.402121 AGAACTGCTTCCCTCAACCC 59.598 55.000 0.00 0.00 0.00 4.11
3913 8091 3.327600 CCAAGATGTGGTGACAGCA 57.672 52.632 2.50 2.50 41.19 4.41
4264 8871 6.488769 TCTGGTTACAAACTAGAGGTGAAA 57.511 37.500 0.00 0.00 43.02 2.69
4317 8924 7.069331 AGTCCAAGATCTTAGATAGAACACCAG 59.931 40.741 7.86 0.00 36.22 4.00
4319 8926 7.354751 AGTCCAAGATCTTAGATAGAACACC 57.645 40.000 7.86 0.00 36.22 4.16
4370 8977 1.600957 CAATATGGCAGCAGGAGTTCG 59.399 52.381 0.00 0.00 0.00 3.95
4400 9007 5.186256 CCCTAGATATCACTCTAGAGGCA 57.814 47.826 23.50 9.84 45.04 4.75
4540 9147 1.475930 GCAGCTGAAAGGAGGGGATAC 60.476 57.143 20.43 0.00 0.00 2.24
4541 9148 0.839946 GCAGCTGAAAGGAGGGGATA 59.160 55.000 20.43 0.00 0.00 2.59
4542 9149 1.611965 GCAGCTGAAAGGAGGGGAT 59.388 57.895 20.43 0.00 0.00 3.85
4543 9150 2.606587 GGCAGCTGAAAGGAGGGGA 61.607 63.158 20.43 0.00 0.00 4.81
4544 9151 2.044551 GGCAGCTGAAAGGAGGGG 60.045 66.667 20.43 0.00 0.00 4.79
4545 9152 1.676967 GTGGCAGCTGAAAGGAGGG 60.677 63.158 20.43 0.00 0.00 4.30
4546 9153 1.676967 GGTGGCAGCTGAAAGGAGG 60.677 63.158 20.43 0.00 0.00 4.30
4547 9154 0.323178 ATGGTGGCAGCTGAAAGGAG 60.323 55.000 20.43 0.00 0.00 3.69
4548 9155 0.609957 CATGGTGGCAGCTGAAAGGA 60.610 55.000 20.43 0.00 0.00 3.36
4549 9156 1.601419 CCATGGTGGCAGCTGAAAGG 61.601 60.000 20.43 8.41 0.00 3.11
4550 9157 1.888018 CCATGGTGGCAGCTGAAAG 59.112 57.895 20.43 3.19 0.00 2.62
4551 9158 4.100479 CCATGGTGGCAGCTGAAA 57.900 55.556 20.43 0.24 0.00 2.69
4662 9270 2.095567 GCAATCATAGCCCAATAGCGTG 60.096 50.000 0.00 0.00 38.01 5.34
4697 9305 1.144093 TGGTGTCCCGGATGAAAAAGT 59.856 47.619 0.73 0.00 0.00 2.66
4733 9341 3.190535 ACATTCCAATCTTGTACGGCAAC 59.809 43.478 0.00 0.00 32.90 4.17
4736 9344 3.006940 TGACATTCCAATCTTGTACGGC 58.993 45.455 0.00 0.00 0.00 5.68
4738 9346 4.496341 GGCATGACATTCCAATCTTGTACG 60.496 45.833 0.00 0.00 0.00 3.67
4748 9356 2.439409 CACAGAAGGCATGACATTCCA 58.561 47.619 0.00 0.00 0.00 3.53
4765 9373 5.010719 GTCATTATAGCACCTACTAGGCACA 59.989 44.000 1.55 0.00 39.63 4.57
4785 9393 7.168219 TCTTGTAAATAGCTTTGACTGGTCAT 58.832 34.615 4.19 0.00 39.64 3.06
4892 9500 9.467258 CTAATTTATTTGGGATATGCACAACTG 57.533 33.333 0.00 0.00 40.26 3.16
4943 9552 1.598701 GAGGGAACATGGCAAGGCAC 61.599 60.000 0.00 0.00 0.00 5.01
5007 9616 4.569162 CCATTTGTAAGAAATGCATGGCTG 59.431 41.667 0.00 0.00 36.56 4.85
5046 9655 9.504710 CTTAGATATACGGAAAATCCACTATCG 57.495 37.037 0.00 0.00 35.91 2.92
5060 9669 7.032377 TGCTCAGATATGCTTAGATATACGG 57.968 40.000 0.00 0.00 0.00 4.02
5092 9701 1.962807 TCCATGCACCTTTTGTCCTTG 59.037 47.619 0.00 0.00 0.00 3.61
5098 9707 2.137523 GCACTTTCCATGCACCTTTTG 58.862 47.619 0.00 0.00 42.88 2.44
5099 9708 1.070601 GGCACTTTCCATGCACCTTTT 59.929 47.619 0.00 0.00 45.27 2.27
5100 9709 0.681175 GGCACTTTCCATGCACCTTT 59.319 50.000 0.00 0.00 45.27 3.11
5106 9715 4.192429 ACTTTTATGGCACTTTCCATGC 57.808 40.909 5.60 0.00 45.84 4.06
5130 9739 4.926238 AGAAGTTAACATTGCTGAGAGTCG 59.074 41.667 8.61 0.00 0.00 4.18
5254 9863 4.521146 CAGTGATAGGAAGACCAAATGCT 58.479 43.478 0.00 0.00 38.94 3.79
5260 9869 3.570125 CGATAGCAGTGATAGGAAGACCA 59.430 47.826 0.00 0.00 38.94 4.02
5829 10441 8.086522 CCCGTATAACATGCAGTACTTACTATT 58.913 37.037 0.00 0.00 34.13 1.73
5842 10454 0.107831 TCCCTGCCCGTATAACATGC 59.892 55.000 0.00 0.00 0.00 4.06
5908 10520 0.267960 ATACCCGACTCCCATCCCTT 59.732 55.000 0.00 0.00 0.00 3.95
6138 10751 5.180492 TGCACCAACACTTAAGTAGCATTAC 59.820 40.000 8.04 0.00 0.00 1.89
6327 10940 9.482627 AGAACAAACACAATGTACAAAAGAAAA 57.517 25.926 0.00 0.00 0.00 2.29
6655 11271 4.165779 CAATAATTCACCTGGTTTGTCGC 58.834 43.478 0.00 0.00 0.00 5.19
6729 11345 8.322906 ACAAACTGATCAAAATTCATACTCGA 57.677 30.769 0.00 0.00 0.00 4.04
6730 11346 8.446273 AGACAAACTGATCAAAATTCATACTCG 58.554 33.333 0.00 0.00 0.00 4.18
6776 11392 9.958180 TGTATCAAAGTTATCAAGGAATCAAGA 57.042 29.630 0.00 0.00 0.00 3.02
7532 12158 7.973048 TTGGTGAGTTACAGATAGAACCTAT 57.027 36.000 0.00 0.00 0.00 2.57
7560 12186 6.581166 CGTGGCTTCTTAACAAACTTAATTCC 59.419 38.462 0.00 0.00 0.00 3.01
7574 12200 3.671008 TCTTAGCAACGTGGCTTCTTA 57.329 42.857 25.12 0.85 42.71 2.10
7584 12210 7.166142 GTGAGCTAGTTAGTATTCTTAGCAACG 59.834 40.741 4.83 0.00 0.00 4.10
7653 12279 2.764010 GTTGGAACCACCTGGAAAAAGT 59.236 45.455 0.00 0.00 39.86 2.66
7654 12280 2.763448 TGTTGGAACCACCTGGAAAAAG 59.237 45.455 0.00 0.00 39.86 2.27
7700 12328 2.484264 AGTTTATTTCACTCGCAGCACC 59.516 45.455 0.00 0.00 0.00 5.01
7734 12362 6.524101 TTTGTAACTTCTGTCTTTGCCTTT 57.476 33.333 0.00 0.00 0.00 3.11
7840 12605 7.147637 GGGGACTTCCTGTGGAGATAATATATC 60.148 44.444 0.00 0.00 35.95 1.63
7904 12669 4.083324 CCTCATTTTGACTGTACGCAACAT 60.083 41.667 0.00 0.00 37.50 2.71
7922 12687 8.575649 AAATTCCGTACAAAAGAATACCTCAT 57.424 30.769 0.00 0.00 30.21 2.90
7979 12751 4.373156 AAGCACCAGAAGAACCAAGTAT 57.627 40.909 0.00 0.00 0.00 2.12
8003 12775 1.573108 AGGATTCAGACGGTCACCAT 58.427 50.000 11.27 0.00 0.00 3.55
8004 12776 1.348064 AAGGATTCAGACGGTCACCA 58.652 50.000 11.27 0.00 0.00 4.17
8033 12805 4.448210 GACTTCAACCTCTTACAACACCA 58.552 43.478 0.00 0.00 0.00 4.17
8034 12806 3.493503 CGACTTCAACCTCTTACAACACC 59.506 47.826 0.00 0.00 0.00 4.16
8063 12835 9.979578 TTCAAACATGAAACAGTGCTATTTTAT 57.020 25.926 0.00 0.00 0.00 1.40
8099 12871 3.504906 TCCTGTCCTACTGAGTAACAACG 59.495 47.826 0.00 0.00 0.00 4.10
8112 12884 5.657302 GGAGTAATTCTGACTTCCTGTCCTA 59.343 44.000 0.00 0.00 44.75 2.94
8124 12896 3.231818 GGATCGGAGGGAGTAATTCTGA 58.768 50.000 0.00 0.00 0.00 3.27
8185 12957 4.523083 TGAGAACCACTTGTAAAACAGCT 58.477 39.130 0.00 0.00 0.00 4.24
8330 13149 6.294731 GGTTGTGTTTCCTAGAGAAATTGCAT 60.295 38.462 8.89 0.00 45.99 3.96
8348 13167 7.112122 TGAAATCTGCTTATCTATGGTTGTGT 58.888 34.615 0.00 0.00 0.00 3.72
8378 13197 1.600916 GCCGATCCACCCTAATGCC 60.601 63.158 0.00 0.00 0.00 4.40
8382 13201 1.458777 ATCGGCCGATCCACCCTAA 60.459 57.895 34.60 6.56 34.01 2.69
8383 13202 1.906824 GATCGGCCGATCCACCCTA 60.907 63.158 44.61 17.90 43.71 3.53
8384 13203 3.234730 GATCGGCCGATCCACCCT 61.235 66.667 44.61 24.48 43.71 4.34
8391 13210 0.174845 TTCGTGAAAGATCGGCCGAT 59.825 50.000 39.64 39.64 37.59 4.18
8392 13211 0.038067 TTTCGTGAAAGATCGGCCGA 60.038 50.000 33.12 33.12 0.00 5.54
8393 13212 2.451693 TTTCGTGAAAGATCGGCCG 58.548 52.632 22.12 22.12 0.00 6.13
8401 13220 2.143925 GACCCACTCCTTTCGTGAAAG 58.856 52.381 14.05 14.05 45.47 2.62
8402 13221 1.202722 GGACCCACTCCTTTCGTGAAA 60.203 52.381 0.00 0.00 35.89 2.69
8403 13222 0.395312 GGACCCACTCCTTTCGTGAA 59.605 55.000 0.00 0.00 35.89 3.18
8404 13223 2.055299 GGACCCACTCCTTTCGTGA 58.945 57.895 0.00 0.00 35.89 4.35
8405 13224 4.695560 GGACCCACTCCTTTCGTG 57.304 61.111 0.00 0.00 35.89 4.35
8412 13231 2.370849 TGTTCTTTACAGGACCCACTCC 59.629 50.000 0.00 0.00 39.81 3.85
8413 13232 3.400255 GTGTTCTTTACAGGACCCACTC 58.600 50.000 0.00 0.00 37.45 3.51
8414 13233 2.224209 CGTGTTCTTTACAGGACCCACT 60.224 50.000 0.00 0.00 43.62 4.00
8415 13234 2.140717 CGTGTTCTTTACAGGACCCAC 58.859 52.381 0.00 0.00 43.62 4.61
8416 13235 2.036733 CTCGTGTTCTTTACAGGACCCA 59.963 50.000 0.00 0.00 44.35 4.51
8417 13236 2.612221 CCTCGTGTTCTTTACAGGACCC 60.612 54.545 0.00 0.00 44.35 4.46
8418 13237 2.298163 TCCTCGTGTTCTTTACAGGACC 59.702 50.000 0.00 0.00 44.35 4.46
8419 13238 3.255149 TCTCCTCGTGTTCTTTACAGGAC 59.745 47.826 0.00 0.00 44.35 3.85
8420 13239 3.493334 TCTCCTCGTGTTCTTTACAGGA 58.507 45.455 0.00 0.00 46.33 3.86
8421 13240 3.936372 TCTCCTCGTGTTCTTTACAGG 57.064 47.619 0.00 0.00 42.57 4.00
8422 13241 5.047847 TGTTTCTCCTCGTGTTCTTTACAG 58.952 41.667 0.00 0.00 37.45 2.74
8423 13242 4.807304 GTGTTTCTCCTCGTGTTCTTTACA 59.193 41.667 0.00 0.00 0.00 2.41
8424 13243 4.085210 CGTGTTTCTCCTCGTGTTCTTTAC 60.085 45.833 0.00 0.00 0.00 2.01
8425 13244 4.046462 CGTGTTTCTCCTCGTGTTCTTTA 58.954 43.478 0.00 0.00 0.00 1.85
8426 13245 2.864343 CGTGTTTCTCCTCGTGTTCTTT 59.136 45.455 0.00 0.00 0.00 2.52
8427 13246 2.100252 TCGTGTTTCTCCTCGTGTTCTT 59.900 45.455 0.00 0.00 0.00 2.52
8428 13247 1.679680 TCGTGTTTCTCCTCGTGTTCT 59.320 47.619 0.00 0.00 0.00 3.01
8429 13248 2.052157 CTCGTGTTTCTCCTCGTGTTC 58.948 52.381 0.00 0.00 0.00 3.18
8430 13249 1.679680 TCTCGTGTTTCTCCTCGTGTT 59.320 47.619 0.00 0.00 0.00 3.32
8431 13250 1.267261 CTCTCGTGTTTCTCCTCGTGT 59.733 52.381 0.00 0.00 0.00 4.49
8432 13251 1.535896 TCTCTCGTGTTTCTCCTCGTG 59.464 52.381 0.00 0.00 0.00 4.35
8433 13252 1.893544 TCTCTCGTGTTTCTCCTCGT 58.106 50.000 0.00 0.00 0.00 4.18
8434 13253 2.981140 GTTTCTCTCGTGTTTCTCCTCG 59.019 50.000 0.00 0.00 0.00 4.63
8435 13254 3.736759 GTGTTTCTCTCGTGTTTCTCCTC 59.263 47.826 0.00 0.00 0.00 3.71
8436 13255 3.385111 AGTGTTTCTCTCGTGTTTCTCCT 59.615 43.478 0.00 0.00 0.00 3.69
8439 13258 5.522824 GGTTTAGTGTTTCTCTCGTGTTTCT 59.477 40.000 0.00 0.00 0.00 2.52
8514 13346 4.707105 TGTATCGTCCCTAGTTGATCGTA 58.293 43.478 0.00 0.00 0.00 3.43
8554 13391 2.964209 AGAACTCAAGACCTCCTCACA 58.036 47.619 0.00 0.00 0.00 3.58
8605 13454 0.754957 CGAGCCTCCACCAGAGATCT 60.755 60.000 0.00 0.00 46.50 2.75


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

AutoCloner maintained by Alex Coulton.