Multiple sequence alignment - TraesCS4D01G159700

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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 TraesCS4D01G159700 chr4D 100.000 7692 0 0 1 7692 230911306 230903615 0.000000e+00 14205.0
1 TraesCS4D01G159700 chr4D 86.898 374 38 6 4164 4526 508914162 508914535 7.190000e-110 409.0
2 TraesCS4D01G159700 chr4D 87.619 105 10 3 4525 4627 399960668 399960771 1.360000e-22 119.0
3 TraesCS4D01G159700 chr4A 95.551 6293 186 30 541 6774 335516770 335510513 0.000000e+00 9984.0
4 TraesCS4D01G159700 chr4A 90.753 465 37 4 3700 4159 387108616 387108153 3.940000e-172 616.0
5 TraesCS4D01G159700 chr4A 94.864 331 10 1 6766 7096 335509829 335509506 1.910000e-140 510.0
6 TraesCS4D01G159700 chr4A 86.523 371 36 8 29 387 335520387 335520019 5.590000e-106 396.0
7 TraesCS4D01G159700 chr4A 90.551 127 8 3 7118 7242 335508402 335508278 1.720000e-36 165.0
8 TraesCS4D01G159700 chr4A 94.937 79 4 0 4871 4949 389240172 389240250 2.910000e-24 124.0
9 TraesCS4D01G159700 chr4B 96.322 3399 73 16 3464 6822 324424523 324421137 0.000000e+00 5537.0
10 TraesCS4D01G159700 chr4B 95.745 3126 69 25 53 3162 324427591 324424514 0.000000e+00 4977.0
11 TraesCS4D01G159700 chr4B 93.135 437 15 10 6818 7239 324421009 324420573 1.820000e-175 627.0
12 TraesCS4D01G159700 chr4B 92.661 436 28 2 3257 3688 600207058 600207493 6.550000e-175 625.0
13 TraesCS4D01G159700 chr4B 85.829 374 42 4 4164 4526 5375623 5375996 3.370000e-103 387.0
14 TraesCS4D01G159700 chr4B 94.872 39 2 0 5289 5327 432813781 432813743 2.320000e-05 62.1
15 TraesCS4D01G159700 chr4B 96.970 33 1 0 435 467 27973532 27973564 1.000000e-03 56.5
16 TraesCS4D01G159700 chr7B 93.651 441 25 2 7242 7681 122422087 122422525 0.000000e+00 656.0
17 TraesCS4D01G159700 chr7B 92.431 436 29 2 3257 3688 432903161 432903596 3.050000e-173 619.0
18 TraesCS4D01G159700 chr7B 92.202 436 30 3 3257 3688 629250810 629251245 1.420000e-171 614.0
19 TraesCS4D01G159700 chr7B 85.714 126 16 2 4521 4644 524718971 524719096 1.740000e-26 132.0
20 TraesCS4D01G159700 chr7B 85.246 122 16 2 4525 4644 301599157 301599036 2.910000e-24 124.0
21 TraesCS4D01G159700 chr7B 100.000 28 0 0 435 462 62852521 62852548 1.400000e-02 52.8
22 TraesCS4D01G159700 chr3A 93.651 441 24 3 7242 7681 688457740 688457303 0.000000e+00 656.0
23 TraesCS4D01G159700 chr3A 85.054 368 44 7 4168 4524 630794691 630794324 1.580000e-96 364.0
24 TraesCS4D01G159700 chr3A 87.245 196 23 2 4761 4955 333325302 333325496 1.000000e-53 222.0
25 TraesCS4D01G159700 chr2B 93.622 439 25 2 7244 7681 357152331 357151895 0.000000e+00 652.0
26 TraesCS4D01G159700 chr2B 93.298 373 23 2 7309 7681 70260660 70260290 4.060000e-152 549.0
27 TraesCS4D01G159700 chr2B 82.313 147 18 8 5048 5189 18270928 18271071 3.770000e-23 121.0
28 TraesCS4D01G159700 chr1D 91.164 464 37 2 3700 4159 114011755 114012218 1.820000e-175 627.0
29 TraesCS4D01G159700 chr1D 93.765 417 22 3 7266 7681 468406642 468406229 2.360000e-174 623.0
30 TraesCS4D01G159700 chr1D 96.970 33 1 0 435 467 377800759 377800791 1.000000e-03 56.5
31 TraesCS4D01G159700 chr5D 92.325 443 28 5 7242 7681 22527034 22526595 6.550000e-175 625.0
32 TraesCS4D01G159700 chr5D 90.909 462 39 2 3700 4159 270204947 270205407 1.100000e-172 617.0
33 TraesCS4D01G159700 chr5D 90.598 468 39 3 3700 4162 319130855 319131322 3.940000e-172 616.0
34 TraesCS4D01G159700 chr5D 100.000 31 0 0 437 467 406986201 406986171 3.000000e-04 58.4
35 TraesCS4D01G159700 chr6B 92.431 436 32 1 3257 3691 404381499 404381064 8.480000e-174 621.0
36 TraesCS4D01G159700 chr6B 86.898 374 38 6 4164 4526 526939278 526938905 7.190000e-110 409.0
37 TraesCS4D01G159700 chr6B 86.364 374 40 5 4164 4526 58845144 58845517 1.560000e-106 398.0
38 TraesCS4D01G159700 chr6B 96.970 33 1 0 435 467 177336747 177336779 1.000000e-03 56.5
39 TraesCS4D01G159700 chr6B 100.000 28 0 0 438 465 68920994 68921021 1.400000e-02 52.8
40 TraesCS4D01G159700 chr6A 92.610 433 31 1 3257 3688 58016307 58016739 8.480000e-174 621.0
41 TraesCS4D01G159700 chr6A 84.426 122 17 2 4525 4644 115345792 115345671 1.360000e-22 119.0
42 TraesCS4D01G159700 chr3B 92.431 436 32 1 3257 3691 76512894 76512459 8.480000e-174 621.0
43 TraesCS4D01G159700 chr3B 88.083 193 19 2 4761 4953 312157323 312157135 7.770000e-55 226.0
44 TraesCS4D01G159700 chr3B 84.252 127 14 4 4521 4644 791284166 791284289 1.360000e-22 119.0
45 TraesCS4D01G159700 chr3B 92.308 39 3 0 6 44 9075984 9076022 1.000000e-03 56.5
46 TraesCS4D01G159700 chr1A 90.948 464 38 2 3700 4159 112938775 112938312 8.480000e-174 621.0
47 TraesCS4D01G159700 chr1A 86.898 374 38 6 4164 4526 491265240 491264867 7.190000e-110 409.0
48 TraesCS4D01G159700 chr1A 86.631 374 38 7 4164 4526 517047918 517048290 3.340000e-108 403.0
49 TraesCS4D01G159700 chr1A 77.872 235 38 14 5008 5233 239903329 239903558 4.840000e-27 134.0
50 TraesCS4D01G159700 chr1A 83.051 118 13 6 4869 4983 86962139 86962252 4.910000e-17 100.0
51 TraesCS4D01G159700 chr1A 82.353 119 12 8 4869 4983 374619883 374619770 2.290000e-15 95.3
52 TraesCS4D01G159700 chr7D 90.733 464 39 2 3700 4159 437411508 437411971 3.940000e-172 616.0
53 TraesCS4D01G159700 chr7D 82.713 376 42 7 4160 4524 199353379 199353742 5.800000e-81 313.0
54 TraesCS4D01G159700 chr7D 90.000 60 5 1 4465 4524 71311612 71311670 8.280000e-10 76.8
55 TraesCS4D01G159700 chr7D 100.000 29 0 0 435 463 375975928 375975900 4.000000e-03 54.7
56 TraesCS4D01G159700 chr5B 90.733 464 39 2 3700 4159 217610802 217610339 3.940000e-172 616.0
57 TraesCS4D01G159700 chr5B 78.947 361 57 13 4159 4505 708396685 708397040 2.160000e-55 228.0
58 TraesCS4D01G159700 chr5B 82.927 123 17 4 4525 4645 43249603 43249483 2.940000e-19 108.0
59 TraesCS4D01G159700 chr3D 92.027 439 31 2 3257 3691 545326947 545326509 1.420000e-171 614.0
60 TraesCS4D01G159700 chr3D 77.200 500 81 16 4159 4644 525733751 525733271 2.130000e-65 261.0
61 TraesCS4D01G159700 chr3D 86.842 190 24 1 4764 4953 250919124 250918936 2.170000e-50 211.0
62 TraesCS4D01G159700 chr3D 100.000 36 0 0 9 44 597211080 597211045 4.980000e-07 67.6
63 TraesCS4D01G159700 chr7A 88.736 435 43 4 7242 7675 524200401 524200830 1.900000e-145 527.0
64 TraesCS4D01G159700 chr7A 81.003 379 38 20 4160 4524 209153171 209153529 3.540000e-68 270.0
65 TraesCS4D01G159700 chr7A 91.304 46 1 3 423 467 416470626 416470583 8.340000e-05 60.2
66 TraesCS4D01G159700 chr5A 87.417 453 49 8 7238 7687 568804372 568803925 1.480000e-141 514.0
67 TraesCS4D01G159700 chr5A 81.818 121 15 6 4869 4986 247511599 247511715 2.290000e-15 95.3
68 TraesCS4D01G159700 chr5A 96.774 31 1 0 17 47 692537809 692537779 1.400000e-02 52.8
69 TraesCS4D01G159700 chr1B 87.816 435 47 5 7242 7676 502249844 502250272 8.910000e-139 505.0
70 TraesCS4D01G159700 chr1B 86.631 374 39 6 4164 4526 32881072 32880699 3.340000e-108 403.0
71 TraesCS4D01G159700 chr1B 82.228 377 54 5 4159 4524 370026697 370027071 5.800000e-81 313.0
72 TraesCS4D01G159700 chr2A 83.573 347 41 11 4193 4526 521667883 521668226 2.080000e-80 311.0
73 TraesCS4D01G159700 chr2A 84.946 93 6 6 7148 7235 767147459 767147370 3.820000e-13 87.9
74 TraesCS4D01G159700 chr6D 97.368 38 1 0 430 467 440650479 440650442 1.790000e-06 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 TraesCS4D01G159700 chr4D 230903615 230911306 7691 True 14205.000000 14205 100.000000 1 7692 1 chr4D.!!$R1 7691
1 TraesCS4D01G159700 chr4A 335508278 335520387 12109 True 2763.750000 9984 91.872250 29 7242 4 chr4A.!!$R2 7213
2 TraesCS4D01G159700 chr4B 324420573 324427591 7018 True 3713.666667 5537 95.067333 53 7239 3 chr4B.!!$R2 7186

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
566 3707 1.006832 GAACGATTCCGGTCCACATG 58.993 55.000 0.00 0.00 46.22 3.21 F
1357 4498 1.444836 TTTATCGGGCAACGTCAAGG 58.555 50.000 0.00 0.00 44.69 3.61 F
3303 6444 0.753867 TGGCATTCCGCGGTATCTTA 59.246 50.000 27.15 0.06 43.84 2.10 F
4589 7754 0.813610 CTCGCCAAGTCACACAACCA 60.814 55.000 0.00 0.00 0.00 3.67 F
5012 8196 1.932564 GACACAAACGCGCACACAC 60.933 57.895 5.73 0.00 0.00 3.82 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2377 5518 0.107643 TTCTGTGCGGTGAATGTGGA 59.892 50.000 0.00 0.0 0.00 4.02 R
3337 6478 0.185901 AAGGAGCAAAAGGACCTGCA 59.814 50.000 6.94 0.0 41.17 4.41 R
4988 8172 0.249114 TGCGCGTTTGTGTCTCTGTA 60.249 50.000 8.43 0.0 0.00 2.74 R
5415 8609 2.882927 TGATACAAACCGAGCGCTAT 57.117 45.000 11.50 0.0 0.00 2.97 R
6698 9899 3.557185 GCAGACTCGCACATCAATATCAA 59.443 43.478 0.00 0.0 0.00 2.57 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
74 76 7.047460 ACTATGTGTTATTTAGGTCCCGTAG 57.953 40.000 0.00 0.00 0.00 3.51
234 236 3.966665 AGGCTCATTTGGTTTGGAGAAAA 59.033 39.130 0.00 0.00 0.00 2.29
246 248 8.117813 TGGTTTGGAGAAAATTTGTAGGATAC 57.882 34.615 0.00 0.00 43.42 2.24
345 354 6.825721 AGGAAAATAGACATTAGCCTTGACTG 59.174 38.462 0.00 0.00 28.47 3.51
427 3064 9.182214 AGAATTTGAGATGCATAACATGTACTT 57.818 29.630 0.00 0.00 39.84 2.24
431 3068 6.653020 TGAGATGCATAACATGTACTTCCTT 58.347 36.000 0.00 0.00 39.84 3.36
432 3069 6.539826 TGAGATGCATAACATGTACTTCCTTG 59.460 38.462 0.00 0.00 39.84 3.61
433 3070 6.653020 AGATGCATAACATGTACTTCCTTGA 58.347 36.000 0.00 0.00 39.84 3.02
450 3087 9.398921 ACTTCCTTGATCCCATAATATAAGACT 57.601 33.333 0.00 0.00 0.00 3.24
473 3110 3.637998 TTTGACACTACACTCCGTCTC 57.362 47.619 0.00 0.00 0.00 3.36
485 3620 9.001542 ACTACACTCCGTCTCATAATATAAGAC 57.998 37.037 0.00 0.00 36.82 3.01
489 3624 9.186323 CACTCCGTCTCATAATATAAGACTTTG 57.814 37.037 2.40 0.00 37.79 2.77
490 3625 9.132923 ACTCCGTCTCATAATATAAGACTTTGA 57.867 33.333 2.40 0.00 37.79 2.69
552 3693 7.232188 AGAACAGAGGGATATAGTATGAACGA 58.768 38.462 0.00 0.00 0.00 3.85
566 3707 1.006832 GAACGATTCCGGTCCACATG 58.993 55.000 0.00 0.00 46.22 3.21
671 3812 1.698506 TTGTCCCCATTTTCGCTGTT 58.301 45.000 0.00 0.00 0.00 3.16
751 3892 1.831726 TGACGTGTCCCCGTTGGTA 60.832 57.895 0.00 0.00 41.98 3.25
1357 4498 1.444836 TTTATCGGGCAACGTCAAGG 58.555 50.000 0.00 0.00 44.69 3.61
1905 5046 9.746711 CACTTTCGACACTCTTTATGAATTAAG 57.253 33.333 0.00 0.00 0.00 1.85
2125 5266 4.889409 TGGATATTGATGTTTGCCTCCTTC 59.111 41.667 0.00 0.00 0.00 3.46
2377 5518 3.618351 CCAGATGCAGAGGACAAATCTT 58.382 45.455 0.00 0.00 0.00 2.40
2551 5692 4.347360 AAACAGGTACAGTGGAACCTAC 57.653 45.455 16.58 0.00 44.43 3.18
2908 6049 5.415701 TGGTACATTCTTGCTCATTTTCTCC 59.584 40.000 0.00 0.00 0.00 3.71
3203 6344 3.737263 ACACTAGGGAGGCCTTTAGATT 58.263 45.455 20.45 8.56 0.00 2.40
3222 6363 5.314529 AGATTGTGCTCATTCCCATCTATG 58.685 41.667 6.96 0.00 0.00 2.23
3273 6414 4.576463 AGCTACACTTTGTGTTTCTCCAAG 59.424 41.667 8.67 0.24 45.08 3.61
3276 6417 2.031870 ACTTTGTGTTTCTCCAAGGCC 58.968 47.619 0.00 0.00 0.00 5.19
3293 6434 3.199551 CCACCACATGGCATTCCG 58.800 61.111 0.00 0.00 43.24 4.30
3303 6444 0.753867 TGGCATTCCGCGGTATCTTA 59.246 50.000 27.15 0.06 43.84 2.10
3333 6474 3.503748 CCTTCTCCAAGTCAATGAACACC 59.496 47.826 0.00 0.00 0.00 4.16
3337 6478 6.065976 TCTCCAAGTCAATGAACACCATAT 57.934 37.500 0.00 0.00 34.45 1.78
3372 6513 4.039730 TGCTCCTTGTATCTCTCCATAAGC 59.960 45.833 0.00 0.00 0.00 3.09
3400 6541 1.483415 CCAGGAAAATGGCTTCCATGG 59.517 52.381 4.97 4.97 44.40 3.66
3429 6570 1.135024 CCAGGCATGAAACCGAAATGG 60.135 52.381 0.00 0.00 46.41 3.16
3460 6601 4.152402 TCACGCTTGTCATTCTTCTTAAGC 59.848 41.667 0.00 0.00 37.69 3.09
3469 6610 2.370281 TCTTCTTAAGCGGTGCTCAG 57.630 50.000 0.00 0.00 38.25 3.35
3607 6756 2.092429 TCTTCTGACACCTTGTTTGCCT 60.092 45.455 0.00 0.00 0.00 4.75
3693 6843 4.209538 CTCAATGGGGATGCAATAAGACA 58.790 43.478 0.00 0.00 0.00 3.41
3823 6973 2.452813 CCCGCAAGACACGAATCCG 61.453 63.158 0.00 0.00 43.02 4.18
3951 7101 4.758674 CACAATCAATCAGGAGTGTTGACT 59.241 41.667 14.28 0.00 42.83 3.41
3967 7117 7.432059 AGTGTTGACTACTACTAAAAGTCACC 58.568 38.462 4.00 0.00 46.85 4.02
3973 7123 6.631962 ACTACTACTAAAAGTCACCAGATGC 58.368 40.000 0.00 0.00 0.00 3.91
4157 7310 2.159043 CCTATGAAGAGCTTCTCGCCAA 60.159 50.000 11.16 0.00 40.14 4.52
4166 7319 1.324736 GCTTCTCGCCAATAGTTGTCG 59.675 52.381 0.00 0.00 0.00 4.35
4213 7366 1.219393 CTCCACCTCCTTCGCCTTC 59.781 63.158 0.00 0.00 0.00 3.46
4315 7469 1.677820 CCTGTTAAGGGCCCTACGTTG 60.678 57.143 28.96 15.57 40.27 4.10
4457 7611 4.446413 GGATGCGACGACCCGGTT 62.446 66.667 0.00 0.00 0.00 4.44
4458 7612 3.186047 GATGCGACGACCCGGTTG 61.186 66.667 0.00 2.91 0.00 3.77
4528 7693 2.890945 CCGACCCTTGTCCATTTTCTTT 59.109 45.455 0.00 0.00 38.32 2.52
4539 7704 4.021456 GTCCATTTTCTTTCGGGTTCCATT 60.021 41.667 0.00 0.00 0.00 3.16
4541 7706 5.071115 TCCATTTTCTTTCGGGTTCCATTTT 59.929 36.000 0.00 0.00 0.00 1.82
4586 7751 1.891919 GGCTCGCCAAGTCACACAA 60.892 57.895 2.41 0.00 35.81 3.33
4587 7752 1.279840 GCTCGCCAAGTCACACAAC 59.720 57.895 0.00 0.00 0.00 3.32
4588 7753 1.941812 CTCGCCAAGTCACACAACC 59.058 57.895 0.00 0.00 0.00 3.77
4589 7754 0.813610 CTCGCCAAGTCACACAACCA 60.814 55.000 0.00 0.00 0.00 3.67
4602 7769 4.141287 CACACAACCATTCTCCTTTACCA 58.859 43.478 0.00 0.00 0.00 3.25
4634 7801 4.816385 CACCGGCTATGTTGAGATAACATT 59.184 41.667 0.00 0.00 40.87 2.71
4721 7900 6.721318 TGTAGATGGCTCTCCTAAAAATGTT 58.279 36.000 0.00 0.00 32.66 2.71
4731 7910 8.730680 GCTCTCCTAAAAATGTTGATAAAGTCA 58.269 33.333 0.00 0.00 34.25 3.41
5005 8189 4.896562 TTAATACAGAGACACAAACGCG 57.103 40.909 3.53 3.53 0.00 6.01
5011 8195 2.031044 GAGACACAAACGCGCACACA 62.031 55.000 5.73 0.00 0.00 3.72
5012 8196 1.932564 GACACAAACGCGCACACAC 60.933 57.895 5.73 0.00 0.00 3.82
5213 8398 6.426937 TCGCAGCCCTTAGTTTGAATAATATC 59.573 38.462 0.00 0.00 0.00 1.63
5215 8400 6.490040 GCAGCCCTTAGTTTGAATAATATCCA 59.510 38.462 0.00 0.00 0.00 3.41
6237 9437 3.023119 TGATTCAATAAATGCACCGCCT 58.977 40.909 0.00 0.00 0.00 5.52
6293 9493 2.175931 TGGTTACAGGTGTGGGATGTTT 59.824 45.455 0.00 0.00 0.00 2.83
6698 9899 7.839680 AGTCCAACCAAGAAATGAAGTTTAT 57.160 32.000 0.00 0.00 0.00 1.40
6795 10688 4.100084 CATGCCCGGTGAGCTCCA 62.100 66.667 12.15 0.30 0.00 3.86
6803 10696 1.671742 GGTGAGCTCCAGTCCGAAA 59.328 57.895 12.15 0.00 0.00 3.46
7065 11092 4.143659 GCTACACTTTTTGACTACGACGAC 60.144 45.833 0.00 0.00 0.00 4.34
7087 11114 3.130633 GGCATACGCATGTATTCTGTGA 58.869 45.455 0.00 0.00 39.28 3.58
7102 11139 8.146412 TGTATTCTGTGAGATTAGATCATGTGG 58.854 37.037 0.00 0.00 0.00 4.17
7146 12255 5.267587 ACGTGTTTATAAGTACTCCCTCCT 58.732 41.667 0.00 0.00 0.00 3.69
7154 12265 6.954352 ATAAGTACTCCCTCCTGTCTTTTT 57.046 37.500 0.00 0.00 0.00 1.94
7258 12374 7.457024 AAAATTAACTAGTACAAATGCCCGT 57.543 32.000 0.00 0.00 0.00 5.28
7259 12375 6.431198 AATTAACTAGTACAAATGCCCGTG 57.569 37.500 0.00 0.00 0.00 4.94
7260 12376 1.734163 ACTAGTACAAATGCCCGTGC 58.266 50.000 0.00 0.00 38.26 5.34
7261 12377 0.650512 CTAGTACAAATGCCCGTGCG 59.349 55.000 0.00 0.00 41.78 5.34
7262 12378 0.037139 TAGTACAAATGCCCGTGCGT 60.037 50.000 0.00 0.00 41.78 5.24
7264 12380 0.797542 GTACAAATGCCCGTGCGTTA 59.202 50.000 0.00 0.00 45.88 3.18
7265 12381 0.797542 TACAAATGCCCGTGCGTTAC 59.202 50.000 0.00 0.00 45.88 2.50
7266 12382 1.167155 ACAAATGCCCGTGCGTTACA 61.167 50.000 0.00 0.00 45.88 2.41
7267 12383 0.727793 CAAATGCCCGTGCGTTACAC 60.728 55.000 0.00 0.00 45.88 2.90
7268 12384 1.858372 AAATGCCCGTGCGTTACACC 61.858 55.000 0.00 0.00 45.88 4.16
7274 12390 2.356553 GTGCGTTACACCAGGCGA 60.357 61.111 0.00 0.00 44.02 5.54
7275 12391 1.957186 GTGCGTTACACCAGGCGAA 60.957 57.895 0.00 0.00 44.02 4.70
7276 12392 1.227586 TGCGTTACACCAGGCGAAA 60.228 52.632 0.00 0.00 0.00 3.46
7277 12393 0.814410 TGCGTTACACCAGGCGAAAA 60.814 50.000 0.00 0.00 0.00 2.29
7278 12394 0.308376 GCGTTACACCAGGCGAAAAA 59.692 50.000 0.00 0.00 0.00 1.94
7279 12395 1.662026 GCGTTACACCAGGCGAAAAAG 60.662 52.381 0.00 0.00 0.00 2.27
7280 12396 1.868498 CGTTACACCAGGCGAAAAAGA 59.132 47.619 0.00 0.00 0.00 2.52
7281 12397 2.096417 CGTTACACCAGGCGAAAAAGAG 60.096 50.000 0.00 0.00 0.00 2.85
7282 12398 2.178912 TACACCAGGCGAAAAAGAGG 57.821 50.000 0.00 0.00 0.00 3.69
7283 12399 1.172812 ACACCAGGCGAAAAAGAGGC 61.173 55.000 0.00 0.00 0.00 4.70
7284 12400 1.150536 ACCAGGCGAAAAAGAGGCA 59.849 52.632 0.00 0.00 35.18 4.75
7285 12401 1.172812 ACCAGGCGAAAAAGAGGCAC 61.173 55.000 0.00 0.00 35.18 5.01
7286 12402 1.172180 CCAGGCGAAAAAGAGGCACA 61.172 55.000 0.00 0.00 35.18 4.57
7287 12403 0.667993 CAGGCGAAAAAGAGGCACAA 59.332 50.000 0.00 0.00 35.18 3.33
7288 12404 0.668535 AGGCGAAAAAGAGGCACAAC 59.331 50.000 0.00 0.00 35.18 3.32
7289 12405 0.318699 GGCGAAAAAGAGGCACAACC 60.319 55.000 0.00 0.00 39.61 3.77
7303 12419 5.581126 GGCACAACCTGATTCATATTTCA 57.419 39.130 0.00 0.00 34.51 2.69
7304 12420 6.152932 GGCACAACCTGATTCATATTTCAT 57.847 37.500 0.00 0.00 34.51 2.57
7305 12421 6.211515 GGCACAACCTGATTCATATTTCATC 58.788 40.000 0.00 0.00 34.51 2.92
7306 12422 5.911280 GCACAACCTGATTCATATTTCATCG 59.089 40.000 0.00 0.00 0.00 3.84
7307 12423 6.458751 GCACAACCTGATTCATATTTCATCGT 60.459 38.462 0.00 0.00 0.00 3.73
7308 12424 6.908820 CACAACCTGATTCATATTTCATCGTG 59.091 38.462 0.00 0.00 0.00 4.35
7309 12425 5.679734 ACCTGATTCATATTTCATCGTGC 57.320 39.130 0.00 0.00 0.00 5.34
7310 12426 5.125356 ACCTGATTCATATTTCATCGTGCA 58.875 37.500 0.00 0.00 0.00 4.57
7311 12427 5.008019 ACCTGATTCATATTTCATCGTGCAC 59.992 40.000 6.82 6.82 0.00 4.57
7312 12428 5.422666 TGATTCATATTTCATCGTGCACC 57.577 39.130 12.15 0.00 0.00 5.01
7313 12429 4.880696 TGATTCATATTTCATCGTGCACCA 59.119 37.500 12.15 0.00 0.00 4.17
7314 12430 5.532032 TGATTCATATTTCATCGTGCACCAT 59.468 36.000 12.15 0.00 0.00 3.55
7315 12431 5.833406 TTCATATTTCATCGTGCACCATT 57.167 34.783 12.15 0.00 0.00 3.16
7316 12432 5.833406 TCATATTTCATCGTGCACCATTT 57.167 34.783 12.15 0.00 0.00 2.32
7317 12433 6.206395 TCATATTTCATCGTGCACCATTTT 57.794 33.333 12.15 0.00 0.00 1.82
7318 12434 7.326968 TCATATTTCATCGTGCACCATTTTA 57.673 32.000 12.15 0.00 0.00 1.52
7319 12435 7.939782 TCATATTTCATCGTGCACCATTTTAT 58.060 30.769 12.15 1.49 0.00 1.40
7320 12436 9.061435 TCATATTTCATCGTGCACCATTTTATA 57.939 29.630 12.15 3.75 0.00 0.98
7321 12437 9.844790 CATATTTCATCGTGCACCATTTTATAT 57.155 29.630 12.15 5.88 0.00 0.86
7325 12441 7.609760 TCATCGTGCACCATTTTATATATCC 57.390 36.000 12.15 0.00 0.00 2.59
7326 12442 7.164803 TCATCGTGCACCATTTTATATATCCA 58.835 34.615 12.15 0.00 0.00 3.41
7327 12443 7.663493 TCATCGTGCACCATTTTATATATCCAA 59.337 33.333 12.15 0.00 0.00 3.53
7328 12444 7.994425 TCGTGCACCATTTTATATATCCAAT 57.006 32.000 12.15 0.00 0.00 3.16
7329 12445 8.402798 TCGTGCACCATTTTATATATCCAATT 57.597 30.769 12.15 0.00 0.00 2.32
7330 12446 8.855110 TCGTGCACCATTTTATATATCCAATTT 58.145 29.630 12.15 0.00 0.00 1.82
7331 12447 9.474920 CGTGCACCATTTTATATATCCAATTTT 57.525 29.630 12.15 0.00 0.00 1.82
7401 12517 8.090831 AGAATTAATTTTGGACAAGAAGAAGCC 58.909 33.333 1.43 0.00 0.00 4.35
7402 12518 6.723298 TTAATTTTGGACAAGAAGAAGCCA 57.277 33.333 0.00 0.00 0.00 4.75
7403 12519 5.612725 AATTTTGGACAAGAAGAAGCCAA 57.387 34.783 0.00 0.00 36.88 4.52
7404 12520 4.385358 TTTTGGACAAGAAGAAGCCAAC 57.615 40.909 0.00 0.00 38.26 3.77
7405 12521 3.297134 TTGGACAAGAAGAAGCCAACT 57.703 42.857 0.00 0.00 33.96 3.16
7406 12522 3.297134 TGGACAAGAAGAAGCCAACTT 57.703 42.857 0.00 0.00 39.43 2.66
7407 12523 4.431416 TGGACAAGAAGAAGCCAACTTA 57.569 40.909 0.00 0.00 35.82 2.24
7408 12524 4.389374 TGGACAAGAAGAAGCCAACTTAG 58.611 43.478 0.00 0.00 35.82 2.18
7409 12525 3.189495 GGACAAGAAGAAGCCAACTTAGC 59.811 47.826 0.00 0.00 35.82 3.09
7410 12526 3.815401 GACAAGAAGAAGCCAACTTAGCA 59.185 43.478 0.00 0.00 35.82 3.49
7411 12527 4.401925 ACAAGAAGAAGCCAACTTAGCAT 58.598 39.130 0.00 0.00 35.82 3.79
7412 12528 4.829492 ACAAGAAGAAGCCAACTTAGCATT 59.171 37.500 0.00 0.00 35.82 3.56
7413 12529 5.048434 ACAAGAAGAAGCCAACTTAGCATTC 60.048 40.000 0.00 0.00 35.82 2.67
7414 12530 4.916183 AGAAGAAGCCAACTTAGCATTCT 58.084 39.130 0.00 0.00 35.82 2.40
7415 12531 5.320277 AGAAGAAGCCAACTTAGCATTCTT 58.680 37.500 0.00 0.00 38.86 2.52
7416 12532 5.414144 AGAAGAAGCCAACTTAGCATTCTTC 59.586 40.000 19.01 19.01 44.27 2.87
7417 12533 4.655963 AGAAGCCAACTTAGCATTCTTCA 58.344 39.130 0.00 0.00 35.82 3.02
7418 12534 5.259632 AGAAGCCAACTTAGCATTCTTCAT 58.740 37.500 0.00 0.00 35.82 2.57
7419 12535 5.356470 AGAAGCCAACTTAGCATTCTTCATC 59.644 40.000 0.00 0.00 35.82 2.92
7420 12536 4.592942 AGCCAACTTAGCATTCTTCATCA 58.407 39.130 0.00 0.00 0.00 3.07
7421 12537 4.639310 AGCCAACTTAGCATTCTTCATCAG 59.361 41.667 0.00 0.00 0.00 2.90
7422 12538 4.637534 GCCAACTTAGCATTCTTCATCAGA 59.362 41.667 0.00 0.00 0.00 3.27
7423 12539 5.298777 GCCAACTTAGCATTCTTCATCAGAT 59.701 40.000 0.00 0.00 0.00 2.90
7424 12540 6.726230 CCAACTTAGCATTCTTCATCAGATG 58.274 40.000 3.71 3.71 0.00 2.90
7425 12541 6.238676 CCAACTTAGCATTCTTCATCAGATGG 60.239 42.308 10.67 0.00 0.00 3.51
7426 12542 6.244552 ACTTAGCATTCTTCATCAGATGGA 57.755 37.500 10.67 0.16 0.00 3.41
7427 12543 6.656902 ACTTAGCATTCTTCATCAGATGGAA 58.343 36.000 10.67 7.46 0.00 3.53
7428 12544 7.114754 ACTTAGCATTCTTCATCAGATGGAAA 58.885 34.615 10.67 3.46 0.00 3.13
7429 12545 7.613022 ACTTAGCATTCTTCATCAGATGGAAAA 59.387 33.333 10.67 0.00 0.00 2.29
7430 12546 6.452494 AGCATTCTTCATCAGATGGAAAAG 57.548 37.500 10.67 7.20 0.00 2.27
7431 12547 5.041940 GCATTCTTCATCAGATGGAAAAGC 58.958 41.667 10.67 10.97 0.00 3.51
7432 12548 5.393787 GCATTCTTCATCAGATGGAAAAGCA 60.394 40.000 10.67 0.00 0.00 3.91
7433 12549 5.892160 TTCTTCATCAGATGGAAAAGCAG 57.108 39.130 10.67 0.00 0.00 4.24
7434 12550 4.914983 TCTTCATCAGATGGAAAAGCAGT 58.085 39.130 10.67 0.00 0.00 4.40
7435 12551 5.319453 TCTTCATCAGATGGAAAAGCAGTT 58.681 37.500 10.67 0.00 0.00 3.16
7436 12552 5.771666 TCTTCATCAGATGGAAAAGCAGTTT 59.228 36.000 10.67 0.00 0.00 2.66
7437 12553 6.266103 TCTTCATCAGATGGAAAAGCAGTTTT 59.734 34.615 10.67 0.00 38.65 2.43
7438 12554 5.775686 TCATCAGATGGAAAAGCAGTTTTG 58.224 37.500 10.67 0.00 35.94 2.44
7454 12570 6.695292 CAGTTTTGCATGGAATAGTTTGTC 57.305 37.500 0.00 0.00 0.00 3.18
7455 12571 6.215121 CAGTTTTGCATGGAATAGTTTGTCA 58.785 36.000 0.00 0.00 0.00 3.58
7456 12572 6.700960 CAGTTTTGCATGGAATAGTTTGTCAA 59.299 34.615 0.00 0.00 0.00 3.18
7457 12573 7.385752 CAGTTTTGCATGGAATAGTTTGTCAAT 59.614 33.333 0.00 0.00 0.00 2.57
7458 12574 7.599998 AGTTTTGCATGGAATAGTTTGTCAATC 59.400 33.333 0.00 0.00 0.00 2.67
7459 12575 6.587206 TTGCATGGAATAGTTTGTCAATCA 57.413 33.333 0.00 0.00 0.00 2.57
7460 12576 6.778834 TGCATGGAATAGTTTGTCAATCAT 57.221 33.333 0.00 0.00 0.00 2.45
7461 12577 7.172868 TGCATGGAATAGTTTGTCAATCATT 57.827 32.000 0.00 0.00 0.00 2.57
7462 12578 7.613585 TGCATGGAATAGTTTGTCAATCATTT 58.386 30.769 0.00 0.00 0.00 2.32
7463 12579 8.095792 TGCATGGAATAGTTTGTCAATCATTTT 58.904 29.630 0.00 0.00 0.00 1.82
7464 12580 8.938906 GCATGGAATAGTTTGTCAATCATTTTT 58.061 29.630 0.00 0.00 0.00 1.94
7485 12601 6.434018 TTTTTGGCTTTTCTGGAAAACATG 57.566 33.333 4.61 0.00 35.57 3.21
7486 12602 5.350504 TTTGGCTTTTCTGGAAAACATGA 57.649 34.783 0.00 0.00 35.57 3.07
7487 12603 5.350504 TTGGCTTTTCTGGAAAACATGAA 57.649 34.783 0.00 0.00 35.57 2.57
7488 12604 5.350504 TGGCTTTTCTGGAAAACATGAAA 57.649 34.783 0.00 0.00 35.57 2.69
7489 12605 5.738909 TGGCTTTTCTGGAAAACATGAAAA 58.261 33.333 0.00 0.00 35.57 2.29
7490 12606 6.355747 TGGCTTTTCTGGAAAACATGAAAAT 58.644 32.000 0.00 0.00 36.53 1.82
7491 12607 6.827762 TGGCTTTTCTGGAAAACATGAAAATT 59.172 30.769 0.00 0.00 36.53 1.82
7492 12608 7.338957 TGGCTTTTCTGGAAAACATGAAAATTT 59.661 29.630 0.00 0.00 36.53 1.82
7493 12609 7.857389 GGCTTTTCTGGAAAACATGAAAATTTC 59.143 33.333 0.00 0.00 36.53 2.17
7686 12802 9.825109 TTTAGTAAAAATGGAACTTTTCTTGGG 57.175 29.630 0.00 0.00 0.00 4.12
7687 12803 7.669089 AGTAAAAATGGAACTTTTCTTGGGA 57.331 32.000 0.00 0.00 0.00 4.37
7688 12804 8.084985 AGTAAAAATGGAACTTTTCTTGGGAA 57.915 30.769 0.00 0.00 0.00 3.97
7689 12805 7.985184 AGTAAAAATGGAACTTTTCTTGGGAAC 59.015 33.333 0.00 0.00 0.00 3.62
7690 12806 6.560003 AAAATGGAACTTTTCTTGGGAACT 57.440 33.333 0.00 0.00 0.00 3.01
7691 12807 6.560003 AAATGGAACTTTTCTTGGGAACTT 57.440 33.333 0.00 0.00 0.00 2.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
44 46 9.841295 GGGACCTAAATAACACATAGTCAAATA 57.159 33.333 0.00 0.00 0.00 1.40
48 50 5.422970 ACGGGACCTAAATAACACATAGTCA 59.577 40.000 0.00 0.00 0.00 3.41
54 56 4.095946 ACCTACGGGACCTAAATAACACA 58.904 43.478 0.00 0.00 36.25 3.72
57 59 5.104776 AGGAAACCTACGGGACCTAAATAAC 60.105 44.000 0.00 0.00 34.64 1.89
60 62 3.457836 AGGAAACCTACGGGACCTAAAT 58.542 45.455 0.00 0.00 34.64 1.40
64 66 1.738474 AAAGGAAACCTACGGGACCT 58.262 50.000 0.00 0.00 36.47 3.85
190 192 1.371558 GGCTCTTTGAGTCACGGGT 59.628 57.895 0.00 0.00 34.02 5.28
395 3032 7.868775 TGTTATGCATCTCAAATTCTATGAGC 58.131 34.615 0.19 0.00 43.19 4.26
465 3102 9.967346 TTCAAAGTCTTATATTATGAGACGGAG 57.033 33.333 17.91 13.13 46.84 4.63
525 3666 8.361139 CGTTCATACTATATCCCTCTGTTCTTT 58.639 37.037 0.00 0.00 0.00 2.52
527 3668 7.232188 TCGTTCATACTATATCCCTCTGTTCT 58.768 38.462 0.00 0.00 0.00 3.01
528 3669 7.450124 TCGTTCATACTATATCCCTCTGTTC 57.550 40.000 0.00 0.00 0.00 3.18
529 3670 8.423906 AATCGTTCATACTATATCCCTCTGTT 57.576 34.615 0.00 0.00 0.00 3.16
530 3671 7.122948 GGAATCGTTCATACTATATCCCTCTGT 59.877 40.741 1.25 0.00 0.00 3.41
531 3672 7.484975 GGAATCGTTCATACTATATCCCTCTG 58.515 42.308 1.25 0.00 0.00 3.35
532 3673 6.319152 CGGAATCGTTCATACTATATCCCTCT 59.681 42.308 0.00 0.00 0.00 3.69
533 3674 6.459848 CCGGAATCGTTCATACTATATCCCTC 60.460 46.154 0.00 0.00 33.95 4.30
534 3675 5.360144 CCGGAATCGTTCATACTATATCCCT 59.640 44.000 0.00 0.00 33.95 4.20
535 3676 5.126707 ACCGGAATCGTTCATACTATATCCC 59.873 44.000 9.46 0.00 33.95 3.85
536 3677 6.205101 ACCGGAATCGTTCATACTATATCC 57.795 41.667 9.46 0.00 33.95 2.59
537 3678 6.127814 TGGACCGGAATCGTTCATACTATATC 60.128 42.308 9.46 0.00 28.96 1.63
552 3693 0.833287 CTCCTCATGTGGACCGGAAT 59.167 55.000 9.46 0.00 31.94 3.01
566 3707 3.967335 CGGATCGGTCGGCTCCTC 61.967 72.222 9.79 0.00 0.00 3.71
596 3737 2.496817 GGCGTGGTTTGGTGCAAA 59.503 55.556 0.00 0.00 0.00 3.68
1905 5046 3.871006 TCACTCGATACAATTGGCATGAC 59.129 43.478 10.83 0.00 0.00 3.06
1967 5108 1.376543 CATGCTCACCCATCACACTC 58.623 55.000 0.00 0.00 0.00 3.51
2125 5266 2.824341 AGGCATCCAAGAGCAAGAAAAG 59.176 45.455 0.00 0.00 0.00 2.27
2377 5518 0.107643 TTCTGTGCGGTGAATGTGGA 59.892 50.000 0.00 0.00 0.00 4.02
2551 5692 7.630242 TGAGTAATTAAAGCCATTCAAGGAG 57.370 36.000 0.00 0.00 0.00 3.69
2787 5928 7.119846 AGCCAACACATTAAACAGAAGAGATAC 59.880 37.037 0.00 0.00 0.00 2.24
2908 6049 8.543774 GGAAGAGATAACATACATTCTTGTTCG 58.456 37.037 0.00 0.00 37.29 3.95
3160 6301 8.292448 AGTGTAGTTGTGAATCAAATGTTCATC 58.708 33.333 0.00 0.00 37.84 2.92
3203 6344 3.497103 CCATAGATGGGAATGAGCACA 57.503 47.619 0.10 0.00 44.31 4.57
3222 6363 2.765699 TGGGGTCTACGTATGGTAAACC 59.234 50.000 0.00 0.00 40.86 3.27
3234 6375 1.068250 GCTGCGATCTGGGGTCTAC 59.932 63.158 0.00 0.00 0.00 2.59
3303 6444 0.544595 ACTTGGAGAAGGCCTACGGT 60.545 55.000 5.16 0.00 32.95 4.83
3333 6474 2.360165 GGAGCAAAAGGACCTGCATATG 59.640 50.000 6.94 0.00 41.17 1.78
3337 6478 0.185901 AAGGAGCAAAAGGACCTGCA 59.814 50.000 6.94 0.00 41.17 4.41
3372 6513 1.094785 CCATTTTCCTGGTACGGCAG 58.905 55.000 0.00 0.00 0.00 4.85
3400 6541 2.436646 CATGCCTGGGTGGTCGAC 60.437 66.667 7.13 7.13 38.35 4.20
3407 6548 0.178975 TTTCGGTTTCATGCCTGGGT 60.179 50.000 0.00 0.00 0.00 4.51
3429 6570 2.553079 TGACAAGCGTGACCAAAAAC 57.447 45.000 6.65 0.00 0.00 2.43
3460 6601 0.170116 GAGAGAGTCACTGAGCACCG 59.830 60.000 0.00 0.00 0.00 4.94
3469 6610 3.027412 TGAAGCTATGGGAGAGAGTCAC 58.973 50.000 0.00 0.00 0.00 3.67
3693 6843 1.306568 GGGAGGAAGGAGGTGCTCT 60.307 63.158 0.00 0.00 36.32 4.09
3823 6973 0.591659 GGTGGCTGACTTCCGTTTTC 59.408 55.000 0.00 0.00 0.00 2.29
3951 7101 5.416639 TCGCATCTGGTGACTTTTAGTAGTA 59.583 40.000 0.00 0.00 0.00 1.82
3967 7117 7.968246 TCTTTAAAAAGAGAGAATCGCATCTG 58.032 34.615 1.00 0.00 39.95 2.90
4157 7310 0.889994 TGGTACACGGCGACAACTAT 59.110 50.000 16.62 0.00 0.00 2.12
4213 7366 2.171003 GAAACCAAATGGAGGGGACAG 58.829 52.381 6.42 0.00 38.94 3.51
4266 7420 3.259876 ACGGGAGCTAGTTGATACAACAA 59.740 43.478 15.29 0.00 0.00 2.83
4354 7508 3.104512 TCGATGTATGTGAAGGGGAAGT 58.895 45.455 0.00 0.00 0.00 3.01
4358 7512 2.430694 TGACTCGATGTATGTGAAGGGG 59.569 50.000 0.00 0.00 0.00 4.79
4528 7693 4.457603 CACACTTATGAAAATGGAACCCGA 59.542 41.667 0.00 0.00 0.00 5.14
4539 7704 5.592282 TCAAAACTCAGCCACACTTATGAAA 59.408 36.000 0.00 0.00 0.00 2.69
4541 7706 4.713553 TCAAAACTCAGCCACACTTATGA 58.286 39.130 0.00 0.00 0.00 2.15
4581 7746 4.447138 TGGTAAAGGAGAATGGTTGTGT 57.553 40.909 0.00 0.00 0.00 3.72
4582 7747 5.376854 CTTGGTAAAGGAGAATGGTTGTG 57.623 43.478 0.00 0.00 0.00 3.33
4607 7774 1.078497 TCAACATAGCCGGTGCCAG 60.078 57.895 1.90 0.00 38.69 4.85
4634 7801 1.418637 AGTGGTAGAAAAACTCCGCCA 59.581 47.619 0.00 0.00 31.52 5.69
4822 8005 1.531149 CCGAAGCCCATAGTTTATGCG 59.469 52.381 0.00 0.00 34.85 4.73
4988 8172 0.249114 TGCGCGTTTGTGTCTCTGTA 60.249 50.000 8.43 0.00 0.00 2.74
5003 8187 2.277247 GTGTGTGTGTGTGTGCGC 60.277 61.111 0.00 0.00 0.00 6.09
5005 8189 0.454285 GTGTGTGTGTGTGTGTGTGC 60.454 55.000 0.00 0.00 0.00 4.57
5011 8195 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
5012 8196 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
5415 8609 2.882927 TGATACAAACCGAGCGCTAT 57.117 45.000 11.50 0.00 0.00 2.97
5420 8614 3.684788 ACACATCTTGATACAAACCGAGC 59.315 43.478 0.00 0.00 0.00 5.03
6293 9493 3.819245 CCACTTCCTGGTTGGACAA 57.181 52.632 6.03 0.00 46.14 3.18
6698 9899 3.557185 GCAGACTCGCACATCAATATCAA 59.443 43.478 0.00 0.00 0.00 2.57
6803 10696 5.715753 ACTCATCCTTAAGAGTAAACCGACT 59.284 40.000 3.36 0.00 42.92 4.18
7065 11092 2.096762 CACAGAATACATGCGTATGCCG 60.097 50.000 13.82 0.00 38.37 5.69
7087 11114 5.826737 CCTTTTCAGCCACATGATCTAATCT 59.173 40.000 0.00 0.00 0.00 2.40
7102 11139 0.109132 CCACGCCAATCCTTTTCAGC 60.109 55.000 0.00 0.00 0.00 4.26
7154 12265 9.695526 TTTAGACAAAACTTATACGCAGACTAA 57.304 29.630 0.00 0.00 0.00 2.24
7155 12266 9.350357 CTTTAGACAAAACTTATACGCAGACTA 57.650 33.333 0.00 0.00 0.00 2.59
7159 12270 8.014322 TGACTTTAGACAAAACTTATACGCAG 57.986 34.615 0.00 0.00 0.00 5.18
7239 12355 3.264104 GCACGGGCATTTGTACTAGTTA 58.736 45.455 3.77 0.00 40.72 2.24
7242 12358 0.650512 CGCACGGGCATTTGTACTAG 59.349 55.000 11.77 0.00 41.24 2.57
7243 12359 0.037139 ACGCACGGGCATTTGTACTA 60.037 50.000 11.77 0.00 41.24 1.82
7244 12360 0.887387 AACGCACGGGCATTTGTACT 60.887 50.000 11.77 0.00 41.24 2.73
7245 12361 0.797542 TAACGCACGGGCATTTGTAC 59.202 50.000 11.77 0.00 41.24 2.90
7246 12362 0.797542 GTAACGCACGGGCATTTGTA 59.202 50.000 11.77 0.00 41.24 2.41
7247 12363 1.167155 TGTAACGCACGGGCATTTGT 61.167 50.000 11.77 0.00 41.24 2.83
7248 12364 0.727793 GTGTAACGCACGGGCATTTG 60.728 55.000 11.77 0.00 41.24 2.32
7249 12365 1.577421 GTGTAACGCACGGGCATTT 59.423 52.632 11.77 4.27 41.24 2.32
7250 12366 3.259930 GTGTAACGCACGGGCATT 58.740 55.556 11.77 1.95 41.24 3.56
7257 12373 1.500512 TTTCGCCTGGTGTAACGCAC 61.501 55.000 7.20 0.00 46.97 5.34
7258 12374 0.814410 TTTTCGCCTGGTGTAACGCA 60.814 50.000 7.20 0.00 38.12 5.24
7259 12375 0.308376 TTTTTCGCCTGGTGTAACGC 59.692 50.000 7.20 0.00 38.12 4.84
7260 12376 1.868498 TCTTTTTCGCCTGGTGTAACG 59.132 47.619 7.20 0.00 38.12 3.18
7261 12377 2.225727 CCTCTTTTTCGCCTGGTGTAAC 59.774 50.000 7.20 0.00 0.00 2.50
7262 12378 2.500229 CCTCTTTTTCGCCTGGTGTAA 58.500 47.619 7.20 0.65 0.00 2.41
7263 12379 1.880646 GCCTCTTTTTCGCCTGGTGTA 60.881 52.381 7.20 0.00 0.00 2.90
7264 12380 1.172812 GCCTCTTTTTCGCCTGGTGT 61.173 55.000 7.20 0.00 0.00 4.16
7265 12381 1.172180 TGCCTCTTTTTCGCCTGGTG 61.172 55.000 0.00 0.00 0.00 4.17
7266 12382 1.150536 TGCCTCTTTTTCGCCTGGT 59.849 52.632 0.00 0.00 0.00 4.00
7267 12383 1.172180 TGTGCCTCTTTTTCGCCTGG 61.172 55.000 0.00 0.00 0.00 4.45
7268 12384 0.667993 TTGTGCCTCTTTTTCGCCTG 59.332 50.000 0.00 0.00 0.00 4.85
7269 12385 0.668535 GTTGTGCCTCTTTTTCGCCT 59.331 50.000 0.00 0.00 0.00 5.52
7270 12386 0.318699 GGTTGTGCCTCTTTTTCGCC 60.319 55.000 0.00 0.00 0.00 5.54
7271 12387 0.668535 AGGTTGTGCCTCTTTTTCGC 59.331 50.000 0.00 0.00 46.96 4.70
7272 12388 1.946768 TCAGGTTGTGCCTCTTTTTCG 59.053 47.619 0.00 0.00 46.96 3.46
7273 12389 4.037923 TGAATCAGGTTGTGCCTCTTTTTC 59.962 41.667 0.00 0.00 46.96 2.29
7274 12390 3.960102 TGAATCAGGTTGTGCCTCTTTTT 59.040 39.130 0.00 0.00 46.96 1.94
7275 12391 3.565307 TGAATCAGGTTGTGCCTCTTTT 58.435 40.909 0.00 0.00 46.96 2.27
7276 12392 3.228188 TGAATCAGGTTGTGCCTCTTT 57.772 42.857 0.00 0.00 46.96 2.52
7277 12393 2.957402 TGAATCAGGTTGTGCCTCTT 57.043 45.000 0.00 0.00 46.96 2.85
7278 12394 4.785346 ATATGAATCAGGTTGTGCCTCT 57.215 40.909 0.00 0.00 46.96 3.69
7279 12395 5.357878 TGAAATATGAATCAGGTTGTGCCTC 59.642 40.000 0.00 0.00 46.96 4.70
7281 12397 5.581126 TGAAATATGAATCAGGTTGTGCC 57.419 39.130 0.00 0.00 37.58 5.01
7282 12398 5.911280 CGATGAAATATGAATCAGGTTGTGC 59.089 40.000 0.00 0.00 0.00 4.57
7283 12399 6.908820 CACGATGAAATATGAATCAGGTTGTG 59.091 38.462 0.00 0.00 0.00 3.33
7284 12400 6.458751 GCACGATGAAATATGAATCAGGTTGT 60.459 38.462 0.00 0.00 0.00 3.32
7285 12401 5.911280 GCACGATGAAATATGAATCAGGTTG 59.089 40.000 0.00 0.00 0.00 3.77
7286 12402 5.589855 TGCACGATGAAATATGAATCAGGTT 59.410 36.000 0.00 0.00 0.00 3.50
7287 12403 5.008019 GTGCACGATGAAATATGAATCAGGT 59.992 40.000 0.00 0.00 0.00 4.00
7288 12404 5.446709 GTGCACGATGAAATATGAATCAGG 58.553 41.667 0.00 0.00 0.00 3.86
7289 12405 5.007921 TGGTGCACGATGAAATATGAATCAG 59.992 40.000 11.45 0.00 0.00 2.90
7290 12406 4.880696 TGGTGCACGATGAAATATGAATCA 59.119 37.500 11.45 0.00 0.00 2.57
7291 12407 5.422666 TGGTGCACGATGAAATATGAATC 57.577 39.130 11.45 0.00 0.00 2.52
7292 12408 6.395426 AATGGTGCACGATGAAATATGAAT 57.605 33.333 15.55 0.00 0.00 2.57
7293 12409 5.833406 AATGGTGCACGATGAAATATGAA 57.167 34.783 15.55 0.00 0.00 2.57
7294 12410 5.833406 AAATGGTGCACGATGAAATATGA 57.167 34.783 15.55 0.00 0.00 2.15
7295 12411 9.844790 ATATAAAATGGTGCACGATGAAATATG 57.155 29.630 15.55 0.00 0.00 1.78
7299 12415 8.511321 GGATATATAAAATGGTGCACGATGAAA 58.489 33.333 15.55 4.10 0.00 2.69
7300 12416 7.663493 TGGATATATAAAATGGTGCACGATGAA 59.337 33.333 15.55 4.46 0.00 2.57
7301 12417 7.164803 TGGATATATAAAATGGTGCACGATGA 58.835 34.615 15.55 4.59 0.00 2.92
7302 12418 7.376435 TGGATATATAAAATGGTGCACGATG 57.624 36.000 15.55 0.00 0.00 3.84
7303 12419 7.994425 TTGGATATATAAAATGGTGCACGAT 57.006 32.000 11.45 10.06 0.00 3.73
7304 12420 7.994425 ATTGGATATATAAAATGGTGCACGA 57.006 32.000 11.45 7.55 0.00 4.35
7305 12421 9.474920 AAAATTGGATATATAAAATGGTGCACG 57.525 29.630 11.45 0.00 0.00 5.34
7375 12491 8.090831 GGCTTCTTCTTGTCCAAAATTAATTCT 58.909 33.333 0.10 0.00 0.00 2.40
7376 12492 7.872483 TGGCTTCTTCTTGTCCAAAATTAATTC 59.128 33.333 0.10 0.00 0.00 2.17
7377 12493 7.734942 TGGCTTCTTCTTGTCCAAAATTAATT 58.265 30.769 0.00 0.00 0.00 1.40
7378 12494 7.301868 TGGCTTCTTCTTGTCCAAAATTAAT 57.698 32.000 0.00 0.00 0.00 1.40
7379 12495 6.723298 TGGCTTCTTCTTGTCCAAAATTAA 57.277 33.333 0.00 0.00 0.00 1.40
7380 12496 6.323739 AGTTGGCTTCTTCTTGTCCAAAATTA 59.676 34.615 0.00 0.00 38.39 1.40
7381 12497 5.129320 AGTTGGCTTCTTCTTGTCCAAAATT 59.871 36.000 0.00 0.00 38.39 1.82
7382 12498 4.651045 AGTTGGCTTCTTCTTGTCCAAAAT 59.349 37.500 0.00 0.00 38.39 1.82
7383 12499 4.023291 AGTTGGCTTCTTCTTGTCCAAAA 58.977 39.130 0.00 0.00 38.39 2.44
7384 12500 3.631250 AGTTGGCTTCTTCTTGTCCAAA 58.369 40.909 0.00 0.00 38.39 3.28
7385 12501 3.297134 AGTTGGCTTCTTCTTGTCCAA 57.703 42.857 0.00 0.00 34.73 3.53
7386 12502 3.297134 AAGTTGGCTTCTTCTTGTCCA 57.703 42.857 0.00 0.00 0.00 4.02
7387 12503 3.189495 GCTAAGTTGGCTTCTTCTTGTCC 59.811 47.826 3.61 0.00 36.22 4.02
7388 12504 3.815401 TGCTAAGTTGGCTTCTTCTTGTC 59.185 43.478 12.78 0.00 36.22 3.18
7389 12505 3.820557 TGCTAAGTTGGCTTCTTCTTGT 58.179 40.909 12.78 0.00 36.22 3.16
7390 12506 5.182760 AGAATGCTAAGTTGGCTTCTTCTTG 59.817 40.000 12.78 0.00 36.22 3.02
7391 12507 5.320277 AGAATGCTAAGTTGGCTTCTTCTT 58.680 37.500 12.78 0.00 36.22 2.52
7392 12508 4.916183 AGAATGCTAAGTTGGCTTCTTCT 58.084 39.130 12.78 13.58 36.22 2.85
7393 12509 5.182001 TGAAGAATGCTAAGTTGGCTTCTTC 59.818 40.000 31.39 31.39 43.64 2.87
7394 12510 5.072741 TGAAGAATGCTAAGTTGGCTTCTT 58.927 37.500 24.58 24.58 38.50 2.52
7395 12511 4.655963 TGAAGAATGCTAAGTTGGCTTCT 58.344 39.130 12.78 14.29 36.22 2.85
7396 12512 5.124457 TGATGAAGAATGCTAAGTTGGCTTC 59.876 40.000 12.78 12.51 36.22 3.86
7397 12513 5.012239 TGATGAAGAATGCTAAGTTGGCTT 58.988 37.500 12.78 3.15 38.66 4.35
7398 12514 4.592942 TGATGAAGAATGCTAAGTTGGCT 58.407 39.130 12.78 0.00 0.00 4.75
7399 12515 4.637534 TCTGATGAAGAATGCTAAGTTGGC 59.362 41.667 3.92 3.92 29.54 4.52
7400 12516 6.238676 CCATCTGATGAAGAATGCTAAGTTGG 60.239 42.308 18.92 0.00 38.79 3.77
7401 12517 6.541278 TCCATCTGATGAAGAATGCTAAGTTG 59.459 38.462 18.92 0.00 38.79 3.16
7402 12518 6.656902 TCCATCTGATGAAGAATGCTAAGTT 58.343 36.000 18.92 0.00 38.79 2.66
7403 12519 6.244552 TCCATCTGATGAAGAATGCTAAGT 57.755 37.500 18.92 0.00 38.79 2.24
7404 12520 7.563888 TTTCCATCTGATGAAGAATGCTAAG 57.436 36.000 18.92 0.00 38.79 2.18
7405 12521 7.415989 GCTTTTCCATCTGATGAAGAATGCTAA 60.416 37.037 18.92 5.58 38.79 3.09
7406 12522 6.039047 GCTTTTCCATCTGATGAAGAATGCTA 59.961 38.462 18.92 0.00 38.79 3.49
7407 12523 5.163540 GCTTTTCCATCTGATGAAGAATGCT 60.164 40.000 18.92 0.00 38.79 3.79
7408 12524 5.041940 GCTTTTCCATCTGATGAAGAATGC 58.958 41.667 18.92 16.62 38.79 3.56
7409 12525 6.127703 ACTGCTTTTCCATCTGATGAAGAATG 60.128 38.462 18.92 12.06 38.79 2.67
7410 12526 5.950549 ACTGCTTTTCCATCTGATGAAGAAT 59.049 36.000 18.92 2.16 38.79 2.40
7411 12527 5.319453 ACTGCTTTTCCATCTGATGAAGAA 58.681 37.500 18.92 11.45 38.79 2.52
7412 12528 4.914983 ACTGCTTTTCCATCTGATGAAGA 58.085 39.130 18.92 5.91 39.94 2.87
7413 12529 5.640189 AACTGCTTTTCCATCTGATGAAG 57.360 39.130 18.92 14.49 0.00 3.02
7414 12530 6.218019 CAAAACTGCTTTTCCATCTGATGAA 58.782 36.000 18.92 8.50 0.00 2.57
7415 12531 5.775686 CAAAACTGCTTTTCCATCTGATGA 58.224 37.500 18.92 2.75 0.00 2.92
7416 12532 4.387862 GCAAAACTGCTTTTCCATCTGATG 59.612 41.667 10.71 10.71 0.00 3.07
7417 12533 4.039488 TGCAAAACTGCTTTTCCATCTGAT 59.961 37.500 0.00 0.00 35.49 2.90
7418 12534 3.384146 TGCAAAACTGCTTTTCCATCTGA 59.616 39.130 0.00 0.00 35.49 3.27
7419 12535 3.719924 TGCAAAACTGCTTTTCCATCTG 58.280 40.909 0.00 0.00 35.49 2.90
7420 12536 4.312443 CATGCAAAACTGCTTTTCCATCT 58.688 39.130 0.00 0.00 35.49 2.90
7421 12537 3.434299 CCATGCAAAACTGCTTTTCCATC 59.566 43.478 0.00 0.00 35.49 3.51
7422 12538 3.071312 TCCATGCAAAACTGCTTTTCCAT 59.929 39.130 0.00 0.00 35.49 3.41
7423 12539 2.433604 TCCATGCAAAACTGCTTTTCCA 59.566 40.909 0.00 0.00 35.49 3.53
7424 12540 3.110447 TCCATGCAAAACTGCTTTTCC 57.890 42.857 0.00 0.00 35.49 3.13
7425 12541 5.928264 ACTATTCCATGCAAAACTGCTTTTC 59.072 36.000 0.00 0.00 35.49 2.29
7426 12542 5.857268 ACTATTCCATGCAAAACTGCTTTT 58.143 33.333 0.00 0.00 35.49 2.27
7427 12543 5.473066 ACTATTCCATGCAAAACTGCTTT 57.527 34.783 0.00 0.00 35.49 3.51
7428 12544 5.473066 AACTATTCCATGCAAAACTGCTT 57.527 34.783 0.00 0.00 35.49 3.91
7429 12545 5.221501 ACAAACTATTCCATGCAAAACTGCT 60.222 36.000 0.00 0.00 35.49 4.24
7430 12546 4.990426 ACAAACTATTCCATGCAAAACTGC 59.010 37.500 0.00 0.00 0.00 4.40
7431 12547 6.215121 TGACAAACTATTCCATGCAAAACTG 58.785 36.000 0.00 0.00 0.00 3.16
7432 12548 6.403866 TGACAAACTATTCCATGCAAAACT 57.596 33.333 0.00 0.00 0.00 2.66
7433 12549 7.384660 TGATTGACAAACTATTCCATGCAAAAC 59.615 33.333 0.00 0.00 0.00 2.43
7434 12550 7.440198 TGATTGACAAACTATTCCATGCAAAA 58.560 30.769 0.00 0.00 0.00 2.44
7435 12551 6.990798 TGATTGACAAACTATTCCATGCAAA 58.009 32.000 0.00 0.00 0.00 3.68
7436 12552 6.587206 TGATTGACAAACTATTCCATGCAA 57.413 33.333 0.00 0.00 0.00 4.08
7437 12553 6.778834 ATGATTGACAAACTATTCCATGCA 57.221 33.333 0.00 0.00 0.00 3.96
7438 12554 8.483307 AAAATGATTGACAAACTATTCCATGC 57.517 30.769 0.00 0.00 0.00 4.06
7462 12578 6.176183 TCATGTTTTCCAGAAAAGCCAAAAA 58.824 32.000 5.82 0.00 40.53 1.94
7463 12579 5.738909 TCATGTTTTCCAGAAAAGCCAAAA 58.261 33.333 5.82 0.00 40.53 2.44
7464 12580 5.350504 TCATGTTTTCCAGAAAAGCCAAA 57.649 34.783 5.82 0.00 40.53 3.28
7465 12581 5.350504 TTCATGTTTTCCAGAAAAGCCAA 57.649 34.783 5.82 0.00 40.53 4.52
7466 12582 5.350504 TTTCATGTTTTCCAGAAAAGCCA 57.649 34.783 5.82 2.79 40.53 4.75
7467 12583 6.866010 ATTTTCATGTTTTCCAGAAAAGCC 57.134 33.333 5.82 0.00 41.53 4.35
7468 12584 7.857389 GGAAATTTTCATGTTTTCCAGAAAAGC 59.143 33.333 18.57 3.03 45.02 3.51
7660 12776 9.825109 CCCAAGAAAAGTTCCATTTTTACTAAA 57.175 29.630 0.00 0.00 32.62 1.85
7661 12777 9.203163 TCCCAAGAAAAGTTCCATTTTTACTAA 57.797 29.630 0.00 0.00 32.62 2.24
7662 12778 8.770010 TCCCAAGAAAAGTTCCATTTTTACTA 57.230 30.769 0.00 0.00 32.62 1.82
7663 12779 7.669089 TCCCAAGAAAAGTTCCATTTTTACT 57.331 32.000 0.00 0.00 32.62 2.24
7664 12780 7.985184 AGTTCCCAAGAAAAGTTCCATTTTTAC 59.015 33.333 0.00 0.00 32.62 2.01
7665 12781 8.084985 AGTTCCCAAGAAAAGTTCCATTTTTA 57.915 30.769 0.00 0.00 32.62 1.52
7666 12782 6.957631 AGTTCCCAAGAAAAGTTCCATTTTT 58.042 32.000 0.00 0.00 32.62 1.94
7667 12783 6.560003 AGTTCCCAAGAAAAGTTCCATTTT 57.440 33.333 0.00 0.00 35.12 1.82
7668 12784 6.560003 AAGTTCCCAAGAAAAGTTCCATTT 57.440 33.333 0.00 0.00 32.58 2.32


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

AutoCloner maintained by Alex Coulton.