Multiple sequence alignment - TraesCS1B01G401900

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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 TraesCS1B01G401900 chr1B 100.000 6191 0 0 1 6191 632008565 632002375 0.000000e+00 11433.0
1 TraesCS1B01G401900 chr1B 91.582 297 14 6 1263 1549 400359168 400359463 3.480000e-107 399.0
2 TraesCS1B01G401900 chr1B 90.572 297 17 4 1263 1549 240663660 240663955 3.500000e-102 383.0
3 TraesCS1B01G401900 chr1B 79.406 471 49 30 1036 1466 173133144 173132682 7.850000e-74 289.0
4 TraesCS1B01G401900 chr1B 96.875 32 1 0 5054 5085 428722547 428722516 3.000000e-03 54.7
5 TraesCS1B01G401900 chr1A 97.602 1793 33 8 2246 4033 551609285 551607498 0.000000e+00 3064.0
6 TraesCS1B01G401900 chr1A 90.401 1271 54 27 4032 5264 551607464 551606224 0.000000e+00 1609.0
7 TraesCS1B01G401900 chr1A 92.182 550 16 13 1027 1549 551611085 551610536 0.000000e+00 752.0
8 TraesCS1B01G401900 chr1A 98.357 426 6 1 1822 2247 551609821 551609397 0.000000e+00 747.0
9 TraesCS1B01G401900 chr1A 85.944 683 33 14 5509 6186 551606204 551605580 0.000000e+00 671.0
10 TraesCS1B01G401900 chr1A 93.989 183 11 0 1547 1729 551610001 551609819 1.700000e-70 278.0
11 TraesCS1B01G401900 chr1A 75.327 612 132 12 26 625 521052577 521051973 6.110000e-70 276.0
12 TraesCS1B01G401900 chr1A 77.754 472 69 28 1015 1466 121137738 121137283 2.210000e-64 257.0
13 TraesCS1B01G401900 chr1A 98.039 102 2 0 1723 1824 157352237 157352136 1.770000e-40 178.0
14 TraesCS1B01G401900 chr1D 97.706 1700 29 8 2246 3940 459894246 459892552 0.000000e+00 2915.0
15 TraesCS1B01G401900 chr1D 90.743 713 28 16 5489 6186 459891572 459890883 0.000000e+00 917.0
16 TraesCS1B01G401900 chr1D 98.357 426 6 1 1822 2247 459894782 459894358 0.000000e+00 747.0
17 TraesCS1B01G401900 chr1D 86.034 580 52 20 637 1202 459896428 459895864 4.130000e-166 595.0
18 TraesCS1B01G401900 chr1D 92.708 384 12 6 4388 4755 459892561 459892178 1.960000e-149 540.0
19 TraesCS1B01G401900 chr1D 83.673 441 40 19 1015 1428 459896027 459895592 2.710000e-103 387.0
20 TraesCS1B01G401900 chr1D 83.377 385 30 14 4744 5118 459892152 459891792 5.980000e-85 326.0
21 TraesCS1B01G401900 chr1D 95.652 184 7 1 1547 1729 459894963 459894780 1.690000e-75 294.0
22 TraesCS1B01G401900 chr1D 100.000 88 0 0 5318 5405 459891667 459891580 4.970000e-36 163.0
23 TraesCS1B01G401900 chr1D 96.970 33 1 0 5054 5086 128529119 128529151 8.670000e-04 56.5
24 TraesCS1B01G401900 chr7A 91.443 1566 78 27 2246 3792 206718825 206717297 0.000000e+00 2098.0
25 TraesCS1B01G401900 chr7A 86.059 746 60 15 4034 4755 206717169 206716444 0.000000e+00 761.0
26 TraesCS1B01G401900 chr7A 87.838 444 35 11 1824 2250 206719376 206718935 2.580000e-138 503.0
27 TraesCS1B01G401900 chr7A 88.926 298 19 6 1263 1549 297786578 297786284 7.630000e-94 355.0
28 TraesCS1B01G401900 chr7A 86.220 254 19 8 5402 5655 206714546 206714309 1.710000e-65 261.0
29 TraesCS1B01G401900 chr7A 74.902 510 109 13 26 523 393248209 393247707 1.350000e-51 215.0
30 TraesCS1B01G401900 chr7A 83.913 230 19 7 4744 4973 206716418 206716207 2.930000e-48 204.0
31 TraesCS1B01G401900 chr7A 93.130 131 9 0 1597 1727 206719508 206719378 6.330000e-45 193.0
32 TraesCS1B01G401900 chr7A 94.393 107 6 0 1727 1833 68887575 68887681 1.380000e-36 165.0
33 TraesCS1B01G401900 chr7A 95.455 88 4 0 5318 5405 206714686 206714599 2.330000e-29 141.0
34 TraesCS1B01G401900 chr7D 91.390 1568 76 23 2246 3792 197306768 197305239 0.000000e+00 2093.0
35 TraesCS1B01G401900 chr7D 84.697 758 58 18 4034 4755 197304791 197304056 0.000000e+00 704.0
36 TraesCS1B01G401900 chr7D 87.810 443 35 11 1822 2247 197307320 197306880 9.260000e-138 501.0
37 TraesCS1B01G401900 chr7D 93.798 258 10 4 3780 4033 197305082 197304827 3.500000e-102 383.0
38 TraesCS1B01G401900 chr7D 83.651 367 37 13 1202 1549 578491168 578490806 2.150000e-84 324.0
39 TraesCS1B01G401900 chr7D 79.310 464 60 25 1015 1466 94211376 94210937 6.070000e-75 292.0
40 TraesCS1B01G401900 chr7D 87.109 256 17 7 5400 5655 197302166 197301927 6.110000e-70 276.0
41 TraesCS1B01G401900 chr7D 83.838 297 30 9 1249 1530 541325506 541325799 3.680000e-67 267.0
42 TraesCS1B01G401900 chr7D 75.309 567 120 16 40 594 234331999 234331441 2.860000e-63 254.0
43 TraesCS1B01G401900 chr7D 87.978 183 21 1 1547 1729 197307499 197307318 1.350000e-51 215.0
44 TraesCS1B01G401900 chr7D 96.117 103 4 0 1722 1824 162222204 162222306 1.070000e-37 169.0
45 TraesCS1B01G401900 chr7D 85.714 154 18 4 1016 1165 578491296 578491143 6.420000e-35 159.0
46 TraesCS1B01G401900 chr7D 96.591 88 3 0 5318 5405 197302306 197302219 5.000000e-31 147.0
47 TraesCS1B01G401900 chr7D 100.000 30 0 0 5058 5087 382727390 382727419 8.670000e-04 56.5
48 TraesCS1B01G401900 chr7B 90.741 1566 88 29 2246 3792 161656650 161655123 0.000000e+00 2036.0
49 TraesCS1B01G401900 chr7B 84.288 751 74 19 4034 4755 161654673 161653938 0.000000e+00 693.0
50 TraesCS1B01G401900 chr7B 88.688 442 32 7 1824 2247 161657652 161657211 1.980000e-144 523.0
51 TraesCS1B01G401900 chr7B 91.854 356 17 5 2246 2590 161657099 161656745 2.590000e-133 486.0
52 TraesCS1B01G401900 chr7B 94.186 258 11 2 3780 4033 161654966 161654709 2.090000e-104 390.0
53 TraesCS1B01G401900 chr7B 86.614 254 16 7 5402 5655 161652842 161652607 1.320000e-66 265.0
54 TraesCS1B01G401900 chr7B 86.147 231 22 4 4744 4974 161653912 161653692 2.230000e-59 241.0
55 TraesCS1B01G401900 chr7B 88.950 181 17 2 1547 1727 161657831 161657654 2.910000e-53 220.0
56 TraesCS1B01G401900 chr7B 74.354 542 121 13 40 569 50798609 50799144 1.350000e-51 215.0
57 TraesCS1B01G401900 chr7B 97.059 102 3 0 1727 1828 159510698 159510597 8.250000e-39 172.0
58 TraesCS1B01G401900 chr7B 97.727 88 2 0 5318 5405 161652982 161652895 1.070000e-32 152.0
59 TraesCS1B01G401900 chr2B 92.256 297 11 7 1263 1549 358756582 358756876 1.610000e-110 411.0
60 TraesCS1B01G401900 chr2B 98.969 97 1 0 1727 1823 25123326 25123230 2.290000e-39 174.0
61 TraesCS1B01G401900 chr2B 83.333 66 9 2 5661 5725 767154314 767154378 6.700000e-05 60.2
62 TraesCS1B01G401900 chr3B 90.789 304 14 8 1257 1549 604141902 604141602 1.620000e-105 394.0
63 TraesCS1B01G401900 chr3B 76.179 424 86 11 36 448 409994085 409994504 6.290000e-50 209.0
64 TraesCS1B01G401900 chr4B 89.803 304 17 7 1257 1549 535284546 535284846 1.630000e-100 377.0
65 TraesCS1B01G401900 chr4B 89.803 304 16 11 1257 1549 449517004 449517303 5.860000e-100 375.0
66 TraesCS1B01G401900 chr4B 74.532 534 117 12 26 547 600325303 600325829 1.350000e-51 215.0
67 TraesCS1B01G401900 chr4B 100.000 30 0 0 5058 5087 469505184 469505155 8.670000e-04 56.5
68 TraesCS1B01G401900 chr5D 88.235 306 20 8 1257 1549 420017648 420017950 9.870000e-93 351.0
69 TraesCS1B01G401900 chr5D 74.267 614 134 16 26 625 337349601 337348998 2.880000e-58 237.0
70 TraesCS1B01G401900 chr4D 76.766 637 132 12 1 625 55967841 55968473 5.940000e-90 342.0
71 TraesCS1B01G401900 chrUn 83.386 319 31 15 1249 1549 254427846 254428160 6.110000e-70 276.0
72 TraesCS1B01G401900 chrUn 74.468 564 129 11 20 572 110579503 110580062 4.830000e-56 230.0
73 TraesCS1B01G401900 chr2D 84.068 295 27 13 1252 1530 6544814 6544524 3.680000e-67 267.0
74 TraesCS1B01G401900 chr2D 73.675 604 139 15 33 623 562942328 562942924 3.760000e-52 217.0
75 TraesCS1B01G401900 chr2D 85.000 220 17 13 994 1203 88287546 88287759 6.290000e-50 209.0
76 TraesCS1B01G401900 chr2D 85.496 131 17 2 4627 4755 106999396 106999526 1.080000e-27 135.0
77 TraesCS1B01G401900 chr3A 74.756 614 131 16 26 625 218042223 218041620 2.860000e-63 254.0
78 TraesCS1B01G401900 chr3A 96.117 103 3 1 1726 1828 692869667 692869566 3.840000e-37 167.0
79 TraesCS1B01G401900 chr3A 100.000 29 0 0 5058 5086 494729264 494729236 3.000000e-03 54.7
80 TraesCS1B01G401900 chr2A 85.106 235 19 14 993 1213 88661626 88661858 6.240000e-55 226.0
81 TraesCS1B01G401900 chr2A 98.980 98 1 0 1726 1823 689713781 689713878 6.380000e-40 176.0
82 TraesCS1B01G401900 chr2A 97.143 35 1 0 5053 5087 168984227 168984193 6.700000e-05 60.2
83 TraesCS1B01G401900 chr2A 83.333 66 9 2 5661 5725 683147495 683147559 6.700000e-05 60.2
84 TraesCS1B01G401900 chr5B 82.090 268 30 12 1019 1269 694527323 694527057 4.860000e-51 213.0
85 TraesCS1B01G401900 chr5A 74.044 497 111 12 110 594 363229767 363230257 2.950000e-43 187.0
86 TraesCS1B01G401900 chr6D 95.370 108 4 1 1726 1832 35700723 35700830 2.970000e-38 171.0
87 TraesCS1B01G401900 chr6D 95.283 106 4 1 1726 1830 389999795 389999690 3.840000e-37 167.0


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 TraesCS1B01G401900 chr1B 632002375 632008565 6190 True 11433.000000 11433 100.000000 1 6191 1 chr1B.!!$R3 6190
1 TraesCS1B01G401900 chr1A 551605580 551611085 5505 True 1186.833333 3064 93.079167 1027 6186 6 chr1A.!!$R4 5159
2 TraesCS1B01G401900 chr1A 521051973 521052577 604 True 276.000000 276 75.327000 26 625 1 chr1A.!!$R3 599
3 TraesCS1B01G401900 chr1D 459890883 459896428 5545 True 764.888889 2915 92.027778 637 6186 9 chr1D.!!$R1 5549
4 TraesCS1B01G401900 chr7A 206714309 206719508 5199 True 594.428571 2098 89.151143 1597 5655 7 chr7A.!!$R3 4058
5 TraesCS1B01G401900 chr7A 393247707 393248209 502 True 215.000000 215 74.902000 26 523 1 chr7A.!!$R2 497
6 TraesCS1B01G401900 chr7D 197301927 197307499 5572 True 617.000000 2093 89.910429 1547 5655 7 chr7D.!!$R3 4108
7 TraesCS1B01G401900 chr7D 234331441 234331999 558 True 254.000000 254 75.309000 40 594 1 chr7D.!!$R2 554
8 TraesCS1B01G401900 chr7B 161652607 161657831 5224 True 556.222222 2036 89.910556 1547 5655 9 chr7B.!!$R2 4108
9 TraesCS1B01G401900 chr7B 50798609 50799144 535 False 215.000000 215 74.354000 40 569 1 chr7B.!!$F1 529
10 TraesCS1B01G401900 chr4B 600325303 600325829 526 False 215.000000 215 74.532000 26 547 1 chr4B.!!$F3 521
11 TraesCS1B01G401900 chr5D 337348998 337349601 603 True 237.000000 237 74.267000 26 625 1 chr5D.!!$R1 599
12 TraesCS1B01G401900 chr4D 55967841 55968473 632 False 342.000000 342 76.766000 1 625 1 chr4D.!!$F1 624
13 TraesCS1B01G401900 chrUn 110579503 110580062 559 False 230.000000 230 74.468000 20 572 1 chrUn.!!$F1 552
14 TraesCS1B01G401900 chr2D 562942328 562942924 596 False 217.000000 217 73.675000 33 623 1 chr2D.!!$F3 590
15 TraesCS1B01G401900 chr3A 218041620 218042223 603 True 254.000000 254 74.756000 26 625 1 chr3A.!!$R1 599

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
410 420 0.182061 GAGGCCCAGCTTGATCATGA 59.818 55.000 12.54 0.00 0.0 3.07 F
467 477 0.247301 GATAAGCACACGCGTGAAGC 60.247 55.000 42.94 38.79 46.8 3.86 F
1373 1460 0.267356 ATCCCTCTTCCTCTCCCCTG 59.733 60.000 0.00 0.00 0.0 4.45 F
1742 2454 0.410663 TCCTACTCCCTCCGTTCCAA 59.589 55.000 0.00 0.00 0.0 3.53 F
1743 2455 1.203212 TCCTACTCCCTCCGTTCCAAA 60.203 52.381 0.00 0.00 0.0 3.28 F
1744 2456 1.626825 CCTACTCCCTCCGTTCCAAAA 59.373 52.381 0.00 0.00 0.0 2.44 F
2859 4164 2.101917 GCCACTACTCTTATTACGCCCA 59.898 50.000 0.00 0.00 0.0 5.36 F
4004 5496 1.027357 GCGGTCTGATTTGCATCCAT 58.973 50.000 0.00 0.00 0.0 3.41 F
4481 6038 1.002888 GATGGTGGATCCGAGCATCAT 59.997 52.381 30.59 18.34 44.3 2.45 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1806 2518 0.115745 AGGTACTCCCTCCGTTCCAA 59.884 55.000 0.00 0.00 40.71 3.53 R
1808 2520 1.273759 AAAGGTACTCCCTCCGTTCC 58.726 55.000 0.00 0.00 45.47 3.62 R
2419 3717 2.879907 CGAACAATGCCTGCCAGG 59.120 61.111 6.32 6.32 38.80 4.45 R
3499 4817 1.214589 CAAACAGGATGGCAGCAGC 59.785 57.895 4.64 0.00 43.62 5.25 R
3761 5079 9.914131 AGCCACAAAGATTAAGAAAAGAAATAC 57.086 29.630 0.00 0.00 0.00 1.89 R
3875 5365 4.613437 AGGGCATATGACTTCCAAAATGT 58.387 39.130 8.85 0.00 0.00 2.71 R
4464 6021 0.394192 TCATGATGCTCGGATCCACC 59.606 55.000 13.41 0.00 0.00 4.61 R
5027 7505 0.708802 ACGGAGGGAGTAGGGAGAAA 59.291 55.000 0.00 0.00 0.00 2.52 R
5312 8665 0.889186 TGCTTTCCCAGAAAGGCGAC 60.889 55.000 16.54 0.00 34.23 5.19 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
59 60 3.780173 AGCTGGCGCTTCTCCTCC 61.780 66.667 7.64 0.00 46.47 4.30
61 62 3.764466 CTGGCGCTTCTCCTCCGT 61.764 66.667 7.64 0.00 0.00 4.69
62 63 3.997064 CTGGCGCTTCTCCTCCGTG 62.997 68.421 7.64 0.00 0.00 4.94
68 69 0.532573 GCTTCTCCTCCGTGATGACA 59.467 55.000 0.00 0.00 0.00 3.58
75 77 1.276421 CCTCCGTGATGACAAGGACTT 59.724 52.381 0.00 0.00 46.40 3.01
94 96 4.660938 ACCAACTTGGAGCCGGCC 62.661 66.667 26.15 15.07 40.96 6.13
130 132 2.854963 GACTTTTTGTAGTCCCCGGTT 58.145 47.619 0.00 0.00 38.88 4.44
166 175 0.689080 TTGGGGCCTGCAACTTCAAA 60.689 50.000 0.84 0.00 0.00 2.69
186 195 1.563924 TAGGCGTAATGTGGGACTGT 58.436 50.000 0.00 0.00 0.00 3.55
187 196 0.690762 AGGCGTAATGTGGGACTGTT 59.309 50.000 0.00 0.00 0.00 3.16
229 238 1.302192 GCCCAAGAGTGCGTGGTAA 60.302 57.895 0.00 0.00 41.44 2.85
279 288 0.725117 ATTGGTTCGCGACGGAAATC 59.275 50.000 9.15 0.00 0.00 2.17
285 294 3.176578 GCGACGGAAATCACGCGA 61.177 61.111 15.93 0.00 41.49 5.87
329 339 0.972471 GACCTTGCCAATTGGGGAGG 60.972 60.000 25.73 7.24 38.72 4.30
338 348 0.725133 AATTGGGGAGGAGGAGAGGA 59.275 55.000 0.00 0.00 0.00 3.71
367 377 3.367743 CCGTGGAAGGTCGTCCGA 61.368 66.667 0.00 0.00 40.96 4.55
370 380 1.080705 GTGGAAGGTCGTCCGACTG 60.081 63.158 18.17 0.00 44.04 3.51
373 383 1.975407 GAAGGTCGTCCGACTGGGA 60.975 63.158 18.17 0.00 44.04 4.37
410 420 0.182061 GAGGCCCAGCTTGATCATGA 59.818 55.000 12.54 0.00 0.00 3.07
454 464 3.330853 CTGCCGCCGTCGATAAGC 61.331 66.667 0.00 0.00 38.10 3.09
457 467 2.202690 CCGCCGTCGATAAGCACA 60.203 61.111 0.00 0.00 38.10 4.57
467 477 0.247301 GATAAGCACACGCGTGAAGC 60.247 55.000 42.94 38.79 46.80 3.86
468 478 0.948623 ATAAGCACACGCGTGAAGCA 60.949 50.000 39.86 29.50 46.80 3.91
550 563 3.004354 ATTACGGCCGGGTGGTCA 61.004 61.111 31.76 4.77 41.18 4.02
575 588 1.450312 CTCCATGTGACCGGCTTCC 60.450 63.158 0.00 0.00 0.00 3.46
576 589 2.184020 CTCCATGTGACCGGCTTCCA 62.184 60.000 0.00 0.00 0.00 3.53
577 590 1.746615 CCATGTGACCGGCTTCCAG 60.747 63.158 0.00 0.00 0.00 3.86
602 615 3.014623 CAATGCATGGACTGATGAGTGT 58.985 45.455 0.00 0.00 30.16 3.55
604 617 1.284657 GCATGGACTGATGAGTGTCG 58.715 55.000 0.00 0.00 34.31 4.35
631 645 4.814294 GCGTTCACCTCGCGGGAT 62.814 66.667 8.08 0.00 43.94 3.85
632 646 2.582498 CGTTCACCTCGCGGGATC 60.582 66.667 8.08 0.00 38.76 3.36
633 647 2.582498 GTTCACCTCGCGGGATCG 60.582 66.667 8.08 0.00 38.76 3.69
666 680 1.883084 GCCATGCTTACCTCGGTCG 60.883 63.158 0.00 0.00 0.00 4.79
668 682 1.883084 CATGCTTACCTCGGTCGGC 60.883 63.158 0.00 0.00 0.00 5.54
671 685 3.446570 CTTACCTCGGTCGGCGGT 61.447 66.667 7.21 0.00 34.86 5.68
685 699 2.112815 GCGGTGCCATCCTGTAACC 61.113 63.158 0.00 0.00 0.00 2.85
688 702 2.125310 TGCCATCCTGTAACCGCG 60.125 61.111 0.00 0.00 0.00 6.46
730 744 2.847234 TGGTTGTCTGGCCGAGGT 60.847 61.111 0.00 0.00 0.00 3.85
735 749 4.803426 GTCTGGCCGAGGTGAGCG 62.803 72.222 0.00 0.00 0.00 5.03
796 810 4.778143 CCTCCCCGCCGTTTCCAG 62.778 72.222 0.00 0.00 0.00 3.86
848 862 2.029844 GTGTCAGCCCGAGAAGTGC 61.030 63.158 0.00 0.00 0.00 4.40
879 893 5.874261 CCCCGTAGACCTAAAAATCGTTAAA 59.126 40.000 0.00 0.00 0.00 1.52
884 898 8.257841 CGTAGACCTAAAAATCGTTAAATCTCG 58.742 37.037 0.00 0.00 0.00 4.04
885 899 9.294030 GTAGACCTAAAAATCGTTAAATCTCGA 57.706 33.333 0.00 0.00 40.28 4.04
888 902 7.916552 ACCTAAAAATCGTTAAATCTCGATGG 58.083 34.615 0.10 0.44 44.29 3.51
889 903 7.767198 ACCTAAAAATCGTTAAATCTCGATGGA 59.233 33.333 0.10 0.00 44.29 3.41
894 908 5.434352 TCGTTAAATCTCGATGGACCTAG 57.566 43.478 0.00 0.00 0.00 3.02
897 913 2.016905 AATCTCGATGGACCTAGGGG 57.983 55.000 14.81 0.00 38.88 4.79
926 942 2.159841 CCACTGACAGCGTTATTTGTCG 60.160 50.000 1.25 0.00 45.12 4.35
943 959 3.190878 GCAATCTGCGAAGGTGGG 58.809 61.111 0.00 0.00 31.71 4.61
944 960 1.377202 GCAATCTGCGAAGGTGGGA 60.377 57.895 0.00 0.00 31.71 4.37
954 970 2.622436 CGAAGGTGGGAGTGATCTTTC 58.378 52.381 0.00 0.00 0.00 2.62
959 975 3.395941 AGGTGGGAGTGATCTTTCAAACT 59.604 43.478 0.00 0.00 32.48 2.66
1005 1026 4.508128 CCACGCCCGTATCGCTGT 62.508 66.667 0.00 0.00 0.00 4.40
1053 1075 3.314331 CCTCCCACTCAGGTGCGT 61.314 66.667 0.00 0.00 41.75 5.24
1156 1182 1.988956 CTCCTCTCCTGCACAGCCT 60.989 63.158 0.00 0.00 0.00 4.58
1162 1195 4.031129 CCTGCACAGCCTGCCTCT 62.031 66.667 0.00 0.00 46.51 3.69
1173 1206 1.326213 CCTGCCTCTCTCCACATCGT 61.326 60.000 0.00 0.00 0.00 3.73
1240 1317 1.767088 CCTCTCTTCCATGGATCTGCA 59.233 52.381 17.06 0.00 0.00 4.41
1292 1369 2.274542 TCTGCAGGATACAAGGGGAAA 58.725 47.619 15.13 0.00 41.41 3.13
1296 1373 3.181423 TGCAGGATACAAGGGGAAAAAGT 60.181 43.478 0.00 0.00 41.41 2.66
1373 1460 0.267356 ATCCCTCTTCCTCTCCCCTG 59.733 60.000 0.00 0.00 0.00 4.45
1489 1661 8.462589 TTGCAATATGTGGTGATGTGTAATAT 57.537 30.769 0.00 0.00 0.00 1.28
1543 1715 8.811378 GGTCAAGAAGATGAACAAAAGAAAAAG 58.189 33.333 0.00 0.00 36.99 2.27
1545 1717 8.748412 TCAAGAAGATGAACAAAAGAAAAAGGA 58.252 29.630 0.00 0.00 0.00 3.36
1546 1718 9.538508 CAAGAAGATGAACAAAAGAAAAAGGAT 57.461 29.630 0.00 0.00 0.00 3.24
1547 1719 9.538508 AAGAAGATGAACAAAAGAAAAAGGATG 57.461 29.630 0.00 0.00 0.00 3.51
1549 1721 6.226052 AGATGAACAAAAGAAAAAGGATGGC 58.774 36.000 0.00 0.00 0.00 4.40
1550 1722 4.702831 TGAACAAAAGAAAAAGGATGGCC 58.297 39.130 0.00 0.00 0.00 5.36
1551 1723 3.385193 ACAAAAGAAAAAGGATGGCCG 57.615 42.857 0.00 0.00 39.96 6.13
1645 2357 1.609210 TGTGTGCCTCGGAGATGGA 60.609 57.895 6.58 0.00 33.89 3.41
1651 2363 3.209812 CTCGGAGATGGACGGCGA 61.210 66.667 16.62 0.00 33.89 5.54
1705 2417 2.338500 GTCGACATCCAAGTGAGGAAC 58.662 52.381 11.55 0.00 41.92 3.62
1729 2441 3.312890 CTCCACATCCCTCAATCCTACT 58.687 50.000 0.00 0.00 0.00 2.57
1730 2442 3.309296 TCCACATCCCTCAATCCTACTC 58.691 50.000 0.00 0.00 0.00 2.59
1731 2443 2.370189 CCACATCCCTCAATCCTACTCC 59.630 54.545 0.00 0.00 0.00 3.85
1732 2444 2.370189 CACATCCCTCAATCCTACTCCC 59.630 54.545 0.00 0.00 0.00 4.30
1733 2445 2.251338 ACATCCCTCAATCCTACTCCCT 59.749 50.000 0.00 0.00 0.00 4.20
1734 2446 2.777459 TCCCTCAATCCTACTCCCTC 57.223 55.000 0.00 0.00 0.00 4.30
1735 2447 1.220750 TCCCTCAATCCTACTCCCTCC 59.779 57.143 0.00 0.00 0.00 4.30
1736 2448 1.333177 CCTCAATCCTACTCCCTCCG 58.667 60.000 0.00 0.00 0.00 4.63
1737 2449 1.411787 CCTCAATCCTACTCCCTCCGT 60.412 57.143 0.00 0.00 0.00 4.69
1738 2450 2.389715 CTCAATCCTACTCCCTCCGTT 58.610 52.381 0.00 0.00 0.00 4.44
1739 2451 2.362717 CTCAATCCTACTCCCTCCGTTC 59.637 54.545 0.00 0.00 0.00 3.95
1740 2452 1.413077 CAATCCTACTCCCTCCGTTCC 59.587 57.143 0.00 0.00 0.00 3.62
1741 2453 0.635009 ATCCTACTCCCTCCGTTCCA 59.365 55.000 0.00 0.00 0.00 3.53
1742 2454 0.410663 TCCTACTCCCTCCGTTCCAA 59.589 55.000 0.00 0.00 0.00 3.53
1743 2455 1.203212 TCCTACTCCCTCCGTTCCAAA 60.203 52.381 0.00 0.00 0.00 3.28
1744 2456 1.626825 CCTACTCCCTCCGTTCCAAAA 59.373 52.381 0.00 0.00 0.00 2.44
1745 2457 2.238898 CCTACTCCCTCCGTTCCAAAAT 59.761 50.000 0.00 0.00 0.00 1.82
1746 2458 3.453353 CCTACTCCCTCCGTTCCAAAATA 59.547 47.826 0.00 0.00 0.00 1.40
1747 2459 3.629142 ACTCCCTCCGTTCCAAAATAG 57.371 47.619 0.00 0.00 0.00 1.73
1748 2460 3.178865 ACTCCCTCCGTTCCAAAATAGA 58.821 45.455 0.00 0.00 0.00 1.98
1749 2461 3.780850 ACTCCCTCCGTTCCAAAATAGAT 59.219 43.478 0.00 0.00 0.00 1.98
1750 2462 4.130118 CTCCCTCCGTTCCAAAATAGATG 58.870 47.826 0.00 0.00 0.00 2.90
1751 2463 3.778075 TCCCTCCGTTCCAAAATAGATGA 59.222 43.478 0.00 0.00 0.00 2.92
1752 2464 3.877508 CCCTCCGTTCCAAAATAGATGAC 59.122 47.826 0.00 0.00 0.00 3.06
1753 2465 3.877508 CCTCCGTTCCAAAATAGATGACC 59.122 47.826 0.00 0.00 0.00 4.02
1754 2466 3.877508 CTCCGTTCCAAAATAGATGACCC 59.122 47.826 0.00 0.00 0.00 4.46
1755 2467 3.264706 TCCGTTCCAAAATAGATGACCCA 59.735 43.478 0.00 0.00 0.00 4.51
1756 2468 4.013728 CCGTTCCAAAATAGATGACCCAA 58.986 43.478 0.00 0.00 0.00 4.12
1757 2469 4.644685 CCGTTCCAAAATAGATGACCCAAT 59.355 41.667 0.00 0.00 0.00 3.16
1758 2470 5.127031 CCGTTCCAAAATAGATGACCCAATT 59.873 40.000 0.00 0.00 0.00 2.32
1759 2471 6.350949 CCGTTCCAAAATAGATGACCCAATTT 60.351 38.462 0.00 0.00 0.00 1.82
1760 2472 7.096551 CGTTCCAAAATAGATGACCCAATTTT 58.903 34.615 0.00 0.00 33.07 1.82
1761 2473 7.063308 CGTTCCAAAATAGATGACCCAATTTTG 59.937 37.037 10.80 10.80 43.77 2.44
1762 2474 7.552050 TCCAAAATAGATGACCCAATTTTGT 57.448 32.000 14.67 0.00 43.14 2.83
1763 2475 8.657387 TCCAAAATAGATGACCCAATTTTGTA 57.343 30.769 14.67 1.18 43.14 2.41
1764 2476 8.527810 TCCAAAATAGATGACCCAATTTTGTAC 58.472 33.333 14.67 0.00 43.14 2.90
1765 2477 8.531146 CCAAAATAGATGACCCAATTTTGTACT 58.469 33.333 14.67 0.00 43.14 2.73
1766 2478 9.573133 CAAAATAGATGACCCAATTTTGTACTC 57.427 33.333 9.93 0.00 41.26 2.59
1767 2479 8.877864 AAATAGATGACCCAATTTTGTACTCA 57.122 30.769 0.00 0.00 0.00 3.41
1768 2480 7.865706 ATAGATGACCCAATTTTGTACTCAC 57.134 36.000 0.00 0.00 0.00 3.51
1769 2481 5.880901 AGATGACCCAATTTTGTACTCACT 58.119 37.500 0.00 0.00 0.00 3.41
1770 2482 6.306987 AGATGACCCAATTTTGTACTCACTT 58.693 36.000 0.00 0.00 0.00 3.16
1771 2483 6.777580 AGATGACCCAATTTTGTACTCACTTT 59.222 34.615 0.00 0.00 0.00 2.66
1772 2484 6.142818 TGACCCAATTTTGTACTCACTTTG 57.857 37.500 0.00 0.00 0.00 2.77
1773 2485 5.654650 TGACCCAATTTTGTACTCACTTTGT 59.345 36.000 0.00 0.00 0.00 2.83
1774 2486 6.829298 TGACCCAATTTTGTACTCACTTTGTA 59.171 34.615 0.00 0.00 0.00 2.41
1775 2487 7.034685 ACCCAATTTTGTACTCACTTTGTAC 57.965 36.000 0.00 0.00 40.27 2.90
1776 2488 6.831868 ACCCAATTTTGTACTCACTTTGTACT 59.168 34.615 0.00 0.00 40.44 2.73
1777 2489 7.994334 ACCCAATTTTGTACTCACTTTGTACTA 59.006 33.333 0.00 0.00 40.44 1.82
1778 2490 8.842280 CCCAATTTTGTACTCACTTTGTACTAA 58.158 33.333 0.00 0.00 40.44 2.24
1809 2521 9.003658 AGTACAAAGTTGAGTCATCTATTTTGG 57.996 33.333 14.35 0.00 40.00 3.28
1810 2522 8.999431 GTACAAAGTTGAGTCATCTATTTTGGA 58.001 33.333 14.35 6.88 40.00 3.53
1811 2523 8.463930 ACAAAGTTGAGTCATCTATTTTGGAA 57.536 30.769 14.35 0.00 40.00 3.53
1812 2524 8.352942 ACAAAGTTGAGTCATCTATTTTGGAAC 58.647 33.333 14.35 0.00 40.00 3.62
1813 2525 6.727824 AGTTGAGTCATCTATTTTGGAACG 57.272 37.500 1.70 0.00 0.00 3.95
1814 2526 5.643777 AGTTGAGTCATCTATTTTGGAACGG 59.356 40.000 1.70 0.00 0.00 4.44
1815 2527 5.414789 TGAGTCATCTATTTTGGAACGGA 57.585 39.130 0.00 0.00 0.00 4.69
1816 2528 5.419542 TGAGTCATCTATTTTGGAACGGAG 58.580 41.667 0.00 0.00 0.00 4.63
1817 2529 4.770795 AGTCATCTATTTTGGAACGGAGG 58.229 43.478 0.00 0.00 0.00 4.30
1818 2530 3.877508 GTCATCTATTTTGGAACGGAGGG 59.122 47.826 0.00 0.00 0.00 4.30
1819 2531 3.778075 TCATCTATTTTGGAACGGAGGGA 59.222 43.478 0.00 0.00 0.00 4.20
1820 2532 3.906720 TCTATTTTGGAACGGAGGGAG 57.093 47.619 0.00 0.00 0.00 4.30
1821 2533 3.178865 TCTATTTTGGAACGGAGGGAGT 58.821 45.455 0.00 0.00 0.00 3.85
1822 2534 4.355549 TCTATTTTGGAACGGAGGGAGTA 58.644 43.478 0.00 0.00 0.00 2.59
1823 2535 2.845363 TTTTGGAACGGAGGGAGTAC 57.155 50.000 0.00 0.00 0.00 2.73
1995 2709 5.835113 AATCCCATTTTGGAAGTGATACG 57.165 39.130 0.00 0.00 40.96 3.06
2274 3567 6.658831 TCTAATTCTGTTTTTGTCTTCAGCG 58.341 36.000 0.00 0.00 0.00 5.18
2343 3641 8.216453 GTGCAAGCAGTTTTTGTTTATGAATAG 58.784 33.333 0.00 0.00 0.00 1.73
2419 3717 2.497107 AGTCATTGTTTGCACACTGC 57.503 45.000 4.37 0.00 45.29 4.40
2859 4164 2.101917 GCCACTACTCTTATTACGCCCA 59.898 50.000 0.00 0.00 0.00 5.36
3016 4327 8.298030 GCTGTCTTAACTGCATGTTAAAAATT 57.702 30.769 16.79 0.00 46.60 1.82
3017 4328 8.427774 GCTGTCTTAACTGCATGTTAAAAATTC 58.572 33.333 16.79 9.67 46.60 2.17
3041 4352 9.847224 TTCAAAACTTGAAGTTAGTCCTATCTT 57.153 29.630 11.43 0.00 44.21 2.40
3203 4514 4.910456 GCGAATGCATCTTTGATGATCTTC 59.090 41.667 11.25 1.67 42.15 2.87
3384 4702 3.256631 AGTTTAATTGGCTGCCTGTCAAG 59.743 43.478 21.03 0.00 44.09 3.02
3499 4817 5.995282 TGCTTCCCATCTATACAAATTACGG 59.005 40.000 0.00 0.00 0.00 4.02
3761 5079 8.294577 TGTCAACAATCTTGATTCTTGATCTTG 58.705 33.333 14.00 0.00 35.69 3.02
3875 5365 7.817418 ACTTCTTTCTGCATGTTACCTTTAA 57.183 32.000 0.00 0.00 0.00 1.52
3922 5412 5.592688 ACTTTGAGGGAAATTTCGAGAACAA 59.407 36.000 11.95 10.29 0.00 2.83
4004 5496 1.027357 GCGGTCTGATTTGCATCCAT 58.973 50.000 0.00 0.00 0.00 3.41
4160 5690 5.484173 TCATTTGCATCTCATTTCCGTAC 57.516 39.130 0.00 0.00 0.00 3.67
4235 5765 4.147322 GCGTGAATGGCGTCGGTG 62.147 66.667 0.00 0.00 0.00 4.94
4250 5780 2.601763 GTCGGTGCCGTTTCTAGTTATG 59.398 50.000 10.60 0.00 40.74 1.90
4301 5831 4.159135 CCATTATTTCATGGCTAGGCATCC 59.841 45.833 27.63 2.79 37.51 3.51
4315 5868 4.770874 ATCCGCACCGTTTCCCCG 62.771 66.667 0.00 0.00 0.00 5.73
4341 5894 9.882996 GGAATGAATTTGGTTTCAATTTCTTTC 57.117 29.630 19.82 19.82 44.25 2.62
4415 5972 6.919721 TGTGCTTTACTGTCAATTTTATCCC 58.080 36.000 0.00 0.00 0.00 3.85
4464 6021 2.565841 GCTGCTAACCCAGGTAAGATG 58.434 52.381 0.00 0.00 33.44 2.90
4481 6038 1.002888 GATGGTGGATCCGAGCATCAT 59.997 52.381 30.59 18.34 44.30 2.45
4651 6228 5.711506 TGATGTGATGCTATTTCCTTGTGTT 59.288 36.000 0.00 0.00 0.00 3.32
4781 6399 8.635765 AGTTATTGAATTTACTTTCAGCCTGA 57.364 30.769 0.00 0.00 36.97 3.86
4782 6400 8.734386 AGTTATTGAATTTACTTTCAGCCTGAG 58.266 33.333 0.00 0.00 36.97 3.35
4783 6401 8.515414 GTTATTGAATTTACTTTCAGCCTGAGT 58.485 33.333 0.00 0.00 36.97 3.41
4784 6402 6.560253 TTGAATTTACTTTCAGCCTGAGTC 57.440 37.500 0.00 0.00 36.97 3.36
5015 7493 2.233605 TATTGGACGGGCCTGTGTCG 62.234 60.000 25.51 9.77 35.95 4.35
5024 7502 1.672356 GCCTGTGTCGGTGCAGAAT 60.672 57.895 0.00 0.00 34.87 2.40
5027 7505 1.608590 CCTGTGTCGGTGCAGAATTTT 59.391 47.619 0.00 0.00 34.87 1.82
5094 7582 5.637006 ACGGATGTATCTAGATCAAGAGC 57.363 43.478 8.95 0.00 0.00 4.09
5255 8600 1.504359 CGAACGGCAAACAGTTCCTA 58.496 50.000 3.99 0.00 42.57 2.94
5292 8637 1.736126 AGTTCACGAATGCTGCTCATG 59.264 47.619 0.00 0.00 35.13 3.07
5303 8656 0.596577 CTGCTCATGCTTGCACAACT 59.403 50.000 0.00 0.00 40.48 3.16
5408 9134 3.326880 TGGAAACCTAAGGAAGAGTGACC 59.673 47.826 0.00 0.00 0.00 4.02
5418 9144 2.159085 GGAAGAGTGACCAATCCTACCG 60.159 54.545 0.00 0.00 0.00 4.02
5445 9171 7.149569 TCATTTGACCTCTCAACATCATTTC 57.850 36.000 0.00 0.00 36.06 2.17
5476 9202 1.541147 CATGTGTTTGTACAGCCCTGG 59.459 52.381 0.00 0.00 34.24 4.45
5500 9226 6.640907 GGCAACACAATGAAAAGGTTAAGTAG 59.359 38.462 0.00 0.00 0.00 2.57
5501 9227 7.200455 GCAACACAATGAAAAGGTTAAGTAGT 58.800 34.615 0.00 0.00 0.00 2.73
5502 9228 8.347035 GCAACACAATGAAAAGGTTAAGTAGTA 58.653 33.333 0.00 0.00 0.00 1.82
5519 9245 6.978674 AGTAGTAGCTCCATGTTAGCATAA 57.021 37.500 16.91 2.66 42.62 1.90
5520 9246 7.546250 AGTAGTAGCTCCATGTTAGCATAAT 57.454 36.000 16.91 9.52 42.62 1.28
5521 9247 8.651589 AGTAGTAGCTCCATGTTAGCATAATA 57.348 34.615 16.91 8.81 42.62 0.98
5522 9248 9.261035 AGTAGTAGCTCCATGTTAGCATAATAT 57.739 33.333 16.91 1.32 42.62 1.28
5560 9290 5.467902 GAGCAGAGCAATTTCTGTTCTAG 57.532 43.478 13.71 0.00 46.03 2.43
5602 9337 9.950680 CCACCAGCTTTAACAAATTATATACTG 57.049 33.333 0.00 0.00 0.00 2.74
5688 9423 0.735287 GGAGAACACCGGCGAGTAAC 60.735 60.000 9.30 5.09 0.00 2.50
5700 9435 1.547372 GCGAGTAACTAGGGGTGAACA 59.453 52.381 0.00 0.00 0.00 3.18
5730 9465 0.102481 CGAGACGTGTAAGATGGGGG 59.898 60.000 0.00 0.00 0.00 5.40
5826 9561 4.771114 ATGGGACTCGAAATACCATTGA 57.229 40.909 7.20 0.00 38.73 2.57
5829 9564 4.019681 TGGGACTCGAAATACCATTGAACT 60.020 41.667 0.00 0.00 0.00 3.01
5917 9652 9.719355 CTATTTAGGCCTTAACAAAAATTTGGT 57.281 29.630 12.58 6.27 42.34 3.67
5938 9673 6.423182 TGGTTCAATCTTGTAGAAATAGGGG 58.577 40.000 0.00 0.00 0.00 4.79
6030 9770 6.981722 ACTTATCACCTGAATTTGTGGTTTC 58.018 36.000 4.52 0.00 33.29 2.78
6065 9805 1.406539 CACAACAAGCTGCCCCATATC 59.593 52.381 0.00 0.00 0.00 1.63
6094 9834 9.936329 ACTCACCCTAAAATCATATTACCATTT 57.064 29.630 0.00 0.00 0.00 2.32
6129 9874 0.605319 TCCACATTGGCCGTGTTCTC 60.605 55.000 10.61 0.00 37.47 2.87
6142 9887 1.301479 GTTCTCAAGGACGCGGGTT 60.301 57.895 12.47 0.00 0.00 4.11
6186 9931 1.416030 ACGCCACATCATGCCTACATA 59.584 47.619 0.00 0.00 33.67 2.29
6187 9932 1.800586 CGCCACATCATGCCTACATAC 59.199 52.381 0.00 0.00 33.67 2.39
6188 9933 2.806382 CGCCACATCATGCCTACATACA 60.806 50.000 0.00 0.00 33.67 2.29
6189 9934 3.415212 GCCACATCATGCCTACATACAT 58.585 45.455 0.00 0.00 33.67 2.29
6190 9935 3.438087 GCCACATCATGCCTACATACATC 59.562 47.826 0.00 0.00 33.67 3.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
28 29 3.910490 AGCTCGATCGGCTCCTGC 61.910 66.667 20.77 13.16 34.70 4.85
31 32 4.959596 GCCAGCTCGATCGGCTCC 62.960 72.222 22.80 15.18 42.78 4.70
59 60 2.069273 GGTCAAGTCCTTGTCATCACG 58.931 52.381 6.90 0.00 41.16 4.35
61 62 3.136443 AGTTGGTCAAGTCCTTGTCATCA 59.864 43.478 6.90 0.00 41.16 3.07
62 63 3.744660 AGTTGGTCAAGTCCTTGTCATC 58.255 45.455 6.90 6.54 41.16 2.92
68 69 2.749800 GCTCCAAGTTGGTCAAGTCCTT 60.750 50.000 21.35 0.00 39.03 3.36
75 77 2.429930 CCGGCTCCAAGTTGGTCA 59.570 61.111 21.35 2.32 39.03 4.02
130 132 0.390603 CAAGGGCGTCATCACCGTAA 60.391 55.000 0.00 0.00 0.00 3.18
166 175 2.116238 ACAGTCCCACATTACGCCTAT 58.884 47.619 0.00 0.00 0.00 2.57
186 195 2.101783 CCATGCTGGCCAAGTTCATAA 58.898 47.619 7.01 0.00 0.00 1.90
187 196 1.685803 CCCATGCTGGCCAAGTTCATA 60.686 52.381 7.01 0.00 35.79 2.15
217 226 1.014564 GCAGTCCTTACCACGCACTC 61.015 60.000 0.00 0.00 0.00 3.51
229 238 1.915769 GGTGGACCTGAGCAGTCCT 60.916 63.158 11.01 0.00 38.07 3.85
271 280 1.800315 CGACTCGCGTGATTTCCGT 60.800 57.895 16.04 0.00 34.64 4.69
285 294 1.226603 GACGTGCTATTCGGCGACT 60.227 57.895 10.16 7.15 34.52 4.18
329 339 3.827898 CGTGCCGGTCCTCTCCTC 61.828 72.222 1.90 0.00 0.00 3.71
359 369 0.381089 CTACATCCCAGTCGGACGAC 59.619 60.000 16.39 16.39 46.09 4.34
367 377 2.237392 GGAGAAGCAACTACATCCCAGT 59.763 50.000 0.00 0.00 0.00 4.00
370 380 3.055094 TCAAGGAGAAGCAACTACATCCC 60.055 47.826 0.00 0.00 0.00 3.85
373 383 3.620966 GCCTCAAGGAGAAGCAACTACAT 60.621 47.826 0.00 0.00 37.39 2.29
375 385 2.351455 GCCTCAAGGAGAAGCAACTAC 58.649 52.381 0.00 0.00 37.39 2.73
376 386 1.279271 GGCCTCAAGGAGAAGCAACTA 59.721 52.381 0.00 0.00 37.39 2.24
410 420 2.165641 TCAACATTCTCTACCGCGACAT 59.834 45.455 8.23 0.00 0.00 3.06
457 467 4.609018 ACCTGCTGCTTCACGCGT 62.609 61.111 5.58 5.58 43.27 6.01
467 477 0.662619 TTCGAAAAGTGCACCTGCTG 59.337 50.000 14.63 1.05 42.66 4.41
468 478 0.947244 CTTCGAAAAGTGCACCTGCT 59.053 50.000 14.63 0.00 42.66 4.24
502 515 1.520666 CGGTTATGCCCTCGTCCTT 59.479 57.895 0.00 0.00 0.00 3.36
523 536 2.435234 GCCGTAATGCCCACGACA 60.435 61.111 3.69 0.00 41.91 4.35
535 548 3.463585 GATGACCACCCGGCCGTA 61.464 66.667 26.12 1.12 34.57 4.02
550 563 0.253044 CGGTCACATGGAGTTGGGAT 59.747 55.000 0.00 0.00 30.30 3.85
575 588 1.100510 CAGTCCATGCATTGGTCCTG 58.899 55.000 0.00 9.21 46.52 3.86
576 589 0.994247 TCAGTCCATGCATTGGTCCT 59.006 50.000 0.00 1.01 46.52 3.85
577 590 1.679680 CATCAGTCCATGCATTGGTCC 59.320 52.381 0.00 0.00 46.52 4.46
590 603 0.179124 GCCCTCGACACTCATCAGTC 60.179 60.000 0.00 0.00 0.00 3.51
634 648 3.723235 ATGGCTACAGCGCGTCCAG 62.723 63.158 8.43 1.09 43.26 3.86
635 649 3.770040 ATGGCTACAGCGCGTCCA 61.770 61.111 8.43 8.39 43.26 4.02
639 653 1.882625 TAAGCATGGCTACAGCGCG 60.883 57.895 0.00 0.00 38.25 6.86
642 656 1.587547 GAGGTAAGCATGGCTACAGC 58.412 55.000 0.00 0.00 38.25 4.40
649 663 1.227263 CCGACCGAGGTAAGCATGG 60.227 63.158 0.00 0.00 0.00 3.66
668 682 4.218722 GGTTACAGGATGGCACCG 57.781 61.111 0.00 0.00 43.62 4.94
671 685 2.125310 CGCGGTTACAGGATGGCA 60.125 61.111 0.00 0.00 43.62 4.92
673 687 2.125310 TGCGCGGTTACAGGATGG 60.125 61.111 8.83 0.00 43.62 3.51
703 717 2.214920 AGACAACCAGACCGTCCCC 61.215 63.158 0.00 0.00 0.00 4.81
707 721 2.426023 GCCAGACAACCAGACCGT 59.574 61.111 0.00 0.00 0.00 4.83
708 722 2.358737 GGCCAGACAACCAGACCG 60.359 66.667 0.00 0.00 0.00 4.79
835 849 2.359230 GCAAGCACTTCTCGGGCT 60.359 61.111 0.00 0.00 40.14 5.19
848 862 4.832608 GGTCTACGGGGCGGCAAG 62.833 72.222 12.47 6.32 0.00 4.01
879 893 0.115349 CCCCCTAGGTCCATCGAGAT 59.885 60.000 8.29 0.00 0.00 2.75
901 917 3.610040 AATAACGCTGTCAGTGGATGA 57.390 42.857 17.46 0.45 34.79 2.92
905 921 2.159841 CGACAAATAACGCTGTCAGTGG 60.160 50.000 17.46 5.06 41.71 4.00
926 942 1.372087 CTCCCACCTTCGCAGATTGC 61.372 60.000 0.00 0.00 40.69 3.56
927 943 0.036010 ACTCCCACCTTCGCAGATTG 60.036 55.000 0.00 0.00 35.04 2.67
928 944 0.036010 CACTCCCACCTTCGCAGATT 60.036 55.000 0.00 0.00 35.04 2.40
929 945 0.904865 TCACTCCCACCTTCGCAGAT 60.905 55.000 0.00 0.00 35.04 2.90
930 946 0.904865 ATCACTCCCACCTTCGCAGA 60.905 55.000 0.00 0.00 0.00 4.26
931 947 0.460987 GATCACTCCCACCTTCGCAG 60.461 60.000 0.00 0.00 0.00 5.18
932 948 0.904865 AGATCACTCCCACCTTCGCA 60.905 55.000 0.00 0.00 0.00 5.10
933 949 0.250513 AAGATCACTCCCACCTTCGC 59.749 55.000 0.00 0.00 0.00 4.70
934 950 2.028112 TGAAAGATCACTCCCACCTTCG 60.028 50.000 0.00 0.00 0.00 3.79
935 951 3.703001 TGAAAGATCACTCCCACCTTC 57.297 47.619 0.00 0.00 0.00 3.46
936 952 4.141158 AGTTTGAAAGATCACTCCCACCTT 60.141 41.667 0.00 0.00 34.61 3.50
937 953 3.395941 AGTTTGAAAGATCACTCCCACCT 59.604 43.478 0.00 0.00 34.61 4.00
938 954 3.756117 AGTTTGAAAGATCACTCCCACC 58.244 45.455 0.00 0.00 34.61 4.61
939 955 7.824779 AGTATTAGTTTGAAAGATCACTCCCAC 59.175 37.037 0.00 0.00 34.61 4.61
940 956 7.918076 AGTATTAGTTTGAAAGATCACTCCCA 58.082 34.615 0.00 0.00 34.61 4.37
941 957 7.496263 GGAGTATTAGTTTGAAAGATCACTCCC 59.504 40.741 11.59 0.00 33.49 4.30
942 958 8.261522 AGGAGTATTAGTTTGAAAGATCACTCC 58.738 37.037 13.51 13.51 36.96 3.85
983 1004 3.520862 GATACGGGCGTGGGACGA 61.521 66.667 0.00 0.00 46.05 4.20
984 1005 4.918129 CGATACGGGCGTGGGACG 62.918 72.222 0.00 0.00 45.88 4.79
1156 1182 1.323271 GGACGATGTGGAGAGAGGCA 61.323 60.000 0.00 0.00 0.00 4.75
1162 1195 1.475403 GAAGAGGGACGATGTGGAGA 58.525 55.000 0.00 0.00 0.00 3.71
1173 1206 1.162951 AAGGGAGGGAGGAAGAGGGA 61.163 60.000 0.00 0.00 0.00 4.20
1240 1317 4.564406 GGATGAGATGAATAAGCCGTCCAT 60.564 45.833 0.00 0.00 31.78 3.41
1292 1369 0.984995 GCACCTAGACCCCTGACTTT 59.015 55.000 0.00 0.00 0.00 2.66
1296 1373 1.008403 AGTAGCACCTAGACCCCTGA 58.992 55.000 0.00 0.00 0.00 3.86
1373 1460 2.918712 ACTGGACAGCAGCATATACC 57.081 50.000 0.00 0.00 0.00 2.73
1489 1661 8.468399 TCTACAATTGATGCATGCTATCAAAAA 58.532 29.630 31.01 19.31 44.83 1.94
1549 1721 2.498056 AAACAAACTGCTGGGCCGG 61.498 57.895 8.39 8.39 0.00 6.13
1550 1722 1.300080 CAAACAAACTGCTGGGCCG 60.300 57.895 0.00 0.00 0.00 6.13
1551 1723 1.000274 CTACAAACAAACTGCTGGGCC 60.000 52.381 0.00 0.00 0.00 5.80
1645 2357 1.722011 ATCGAAAAATGACTCGCCGT 58.278 45.000 0.00 0.00 35.04 5.68
1651 2363 6.318900 GGAAACCATCCTATCGAAAAATGACT 59.681 38.462 0.00 0.00 45.56 3.41
1705 2417 1.133976 GGATTGAGGGATGTGGAGGTG 60.134 57.143 0.00 0.00 0.00 4.00
1729 2441 3.778075 TCATCTATTTTGGAACGGAGGGA 59.222 43.478 0.00 0.00 0.00 4.20
1730 2442 3.877508 GTCATCTATTTTGGAACGGAGGG 59.122 47.826 0.00 0.00 0.00 4.30
1731 2443 3.877508 GGTCATCTATTTTGGAACGGAGG 59.122 47.826 0.00 0.00 0.00 4.30
1732 2444 3.877508 GGGTCATCTATTTTGGAACGGAG 59.122 47.826 0.00 0.00 0.00 4.63
1733 2445 3.264706 TGGGTCATCTATTTTGGAACGGA 59.735 43.478 0.00 0.00 0.00 4.69
1734 2446 3.616219 TGGGTCATCTATTTTGGAACGG 58.384 45.455 0.00 0.00 0.00 4.44
1735 2447 5.835113 ATTGGGTCATCTATTTTGGAACG 57.165 39.130 0.00 0.00 0.00 3.95
1736 2448 7.877612 ACAAAATTGGGTCATCTATTTTGGAAC 59.122 33.333 19.76 0.00 45.43 3.62
1737 2449 7.972301 ACAAAATTGGGTCATCTATTTTGGAA 58.028 30.769 19.76 0.00 45.43 3.53
1738 2450 7.552050 ACAAAATTGGGTCATCTATTTTGGA 57.448 32.000 19.76 0.00 45.43 3.53
1739 2451 8.531146 AGTACAAAATTGGGTCATCTATTTTGG 58.469 33.333 19.76 9.08 45.43 3.28
1740 2452 9.573133 GAGTACAAAATTGGGTCATCTATTTTG 57.427 33.333 16.57 16.57 46.06 2.44
1741 2453 9.308000 TGAGTACAAAATTGGGTCATCTATTTT 57.692 29.630 0.00 0.00 32.14 1.82
1742 2454 8.739972 GTGAGTACAAAATTGGGTCATCTATTT 58.260 33.333 0.00 0.00 0.00 1.40
1743 2455 8.109634 AGTGAGTACAAAATTGGGTCATCTATT 58.890 33.333 0.00 0.00 0.00 1.73
1744 2456 7.633789 AGTGAGTACAAAATTGGGTCATCTAT 58.366 34.615 0.00 0.00 0.00 1.98
1745 2457 7.016153 AGTGAGTACAAAATTGGGTCATCTA 57.984 36.000 0.00 0.00 0.00 1.98
1746 2458 5.880901 AGTGAGTACAAAATTGGGTCATCT 58.119 37.500 0.00 0.00 0.00 2.90
1747 2459 6.575162 AAGTGAGTACAAAATTGGGTCATC 57.425 37.500 0.00 0.00 0.00 2.92
1748 2460 6.323739 ACAAAGTGAGTACAAAATTGGGTCAT 59.676 34.615 0.00 0.00 0.00 3.06
1749 2461 5.654650 ACAAAGTGAGTACAAAATTGGGTCA 59.345 36.000 0.00 0.00 0.00 4.02
1750 2462 6.144078 ACAAAGTGAGTACAAAATTGGGTC 57.856 37.500 0.00 0.00 0.00 4.46
1751 2463 6.831868 AGTACAAAGTGAGTACAAAATTGGGT 59.168 34.615 6.30 0.00 43.24 4.51
1752 2464 7.272037 AGTACAAAGTGAGTACAAAATTGGG 57.728 36.000 6.30 0.00 43.24 4.12
1783 2495 9.003658 CCAAAATAGATGACTCAACTTTGTACT 57.996 33.333 0.00 0.00 0.00 2.73
1784 2496 8.999431 TCCAAAATAGATGACTCAACTTTGTAC 58.001 33.333 0.00 0.00 0.00 2.90
1785 2497 9.567776 TTCCAAAATAGATGACTCAACTTTGTA 57.432 29.630 0.00 0.00 0.00 2.41
1786 2498 8.352942 GTTCCAAAATAGATGACTCAACTTTGT 58.647 33.333 0.00 0.00 0.00 2.83
1787 2499 7.535258 CGTTCCAAAATAGATGACTCAACTTTG 59.465 37.037 0.00 0.00 0.00 2.77
1788 2500 7.308589 CCGTTCCAAAATAGATGACTCAACTTT 60.309 37.037 0.00 0.00 0.00 2.66
1789 2501 6.149474 CCGTTCCAAAATAGATGACTCAACTT 59.851 38.462 0.00 0.00 0.00 2.66
1790 2502 5.643777 CCGTTCCAAAATAGATGACTCAACT 59.356 40.000 0.00 0.00 0.00 3.16
1791 2503 5.642063 TCCGTTCCAAAATAGATGACTCAAC 59.358 40.000 0.00 0.00 0.00 3.18
1792 2504 5.800296 TCCGTTCCAAAATAGATGACTCAA 58.200 37.500 0.00 0.00 0.00 3.02
1793 2505 5.414789 TCCGTTCCAAAATAGATGACTCA 57.585 39.130 0.00 0.00 0.00 3.41
1794 2506 4.811557 CCTCCGTTCCAAAATAGATGACTC 59.188 45.833 0.00 0.00 0.00 3.36
1795 2507 4.384208 CCCTCCGTTCCAAAATAGATGACT 60.384 45.833 0.00 0.00 0.00 3.41
1796 2508 3.877508 CCCTCCGTTCCAAAATAGATGAC 59.122 47.826 0.00 0.00 0.00 3.06
1797 2509 3.778075 TCCCTCCGTTCCAAAATAGATGA 59.222 43.478 0.00 0.00 0.00 2.92
1798 2510 4.130118 CTCCCTCCGTTCCAAAATAGATG 58.870 47.826 0.00 0.00 0.00 2.90
1799 2511 3.780850 ACTCCCTCCGTTCCAAAATAGAT 59.219 43.478 0.00 0.00 0.00 1.98
1800 2512 3.178865 ACTCCCTCCGTTCCAAAATAGA 58.821 45.455 0.00 0.00 0.00 1.98
1801 2513 3.629142 ACTCCCTCCGTTCCAAAATAG 57.371 47.619 0.00 0.00 0.00 1.73
1802 2514 3.198417 GGTACTCCCTCCGTTCCAAAATA 59.802 47.826 0.00 0.00 0.00 1.40
1803 2515 2.026542 GGTACTCCCTCCGTTCCAAAAT 60.027 50.000 0.00 0.00 0.00 1.82
1804 2516 1.348696 GGTACTCCCTCCGTTCCAAAA 59.651 52.381 0.00 0.00 0.00 2.44
1805 2517 0.978907 GGTACTCCCTCCGTTCCAAA 59.021 55.000 0.00 0.00 0.00 3.28
1806 2518 0.115745 AGGTACTCCCTCCGTTCCAA 59.884 55.000 0.00 0.00 40.71 3.53
1807 2519 0.115745 AAGGTACTCCCTCCGTTCCA 59.884 55.000 0.00 0.00 45.47 3.53
1808 2520 1.273759 AAAGGTACTCCCTCCGTTCC 58.726 55.000 0.00 0.00 45.47 3.62
1809 2521 3.513119 ACTAAAAGGTACTCCCTCCGTTC 59.487 47.826 0.00 0.00 45.47 3.95
1810 2522 3.514539 ACTAAAAGGTACTCCCTCCGTT 58.485 45.455 0.00 0.00 45.47 4.44
1811 2523 3.181393 ACTAAAAGGTACTCCCTCCGT 57.819 47.619 0.00 0.00 45.47 4.69
1812 2524 3.768215 AGAACTAAAAGGTACTCCCTCCG 59.232 47.826 0.00 0.00 45.47 4.63
1813 2525 7.434927 AATAGAACTAAAAGGTACTCCCTCC 57.565 40.000 0.00 0.00 45.47 4.30
1814 2526 7.986320 GGAAATAGAACTAAAAGGTACTCCCTC 59.014 40.741 0.00 0.00 45.47 4.30
1816 2528 6.760298 CGGAAATAGAACTAAAAGGTACTCCC 59.240 42.308 0.00 0.00 38.49 4.30
1817 2529 7.326454 ACGGAAATAGAACTAAAAGGTACTCC 58.674 38.462 0.00 0.00 38.49 3.85
1818 2530 9.295214 GTACGGAAATAGAACTAAAAGGTACTC 57.705 37.037 0.00 0.00 38.49 2.59
1820 2532 8.986477 TGTACGGAAATAGAACTAAAAGGTAC 57.014 34.615 0.00 0.00 0.00 3.34
1821 2533 9.807649 GATGTACGGAAATAGAACTAAAAGGTA 57.192 33.333 0.00 0.00 0.00 3.08
1822 2534 8.537858 AGATGTACGGAAATAGAACTAAAAGGT 58.462 33.333 0.00 0.00 0.00 3.50
1823 2535 8.943909 AGATGTACGGAAATAGAACTAAAAGG 57.056 34.615 0.00 0.00 0.00 3.11
1995 2709 4.508662 ACTTGGCATGCTAAAGAGACTAC 58.491 43.478 28.71 7.70 0.00 2.73
2104 2834 9.725019 ATGACATGTTCAACTTCTTCAACTATA 57.275 29.630 0.00 0.00 37.92 1.31
2107 2837 6.769822 AGATGACATGTTCAACTTCTTCAACT 59.230 34.615 0.00 0.00 33.67 3.16
2183 2914 5.590530 AGAGAATGCCTACAAGTGACTAG 57.409 43.478 0.00 0.00 0.00 2.57
2274 3567 3.736720 AGGGAAGGTTTAGTTCGTTCAC 58.263 45.455 0.00 0.00 34.58 3.18
2343 3641 6.598753 TTATAACCGTCTTTAGAGCAATGC 57.401 37.500 0.00 0.00 0.00 3.56
2419 3717 2.879907 CGAACAATGCCTGCCAGG 59.120 61.111 6.32 6.32 38.80 4.45
2884 4190 7.437713 AACTCATCATCTTATAAGTGACCCA 57.562 36.000 12.19 0.00 0.00 4.51
3203 4514 3.438434 GCAGGTGAAAGAAAAGGCTAGAG 59.562 47.826 0.00 0.00 0.00 2.43
3384 4702 6.038714 AGGAAATCAAAAGTGACAAGTCTGAC 59.961 38.462 0.00 0.00 36.31 3.51
3499 4817 1.214589 CAAACAGGATGGCAGCAGC 59.785 57.895 4.64 0.00 43.62 5.25
3761 5079 9.914131 AGCCACAAAGATTAAGAAAAGAAATAC 57.086 29.630 0.00 0.00 0.00 1.89
3875 5365 4.613437 AGGGCATATGACTTCCAAAATGT 58.387 39.130 8.85 0.00 0.00 2.71
3922 5412 7.285566 ACCATGAGAGCACATAATACAGAAAT 58.714 34.615 0.00 0.00 0.00 2.17
4004 5496 1.609580 GGAGCGGTGGTGTTGTAATCA 60.610 52.381 0.00 0.00 0.00 2.57
4160 5690 1.202557 GCAGAGCAGATCCTTCTCCAG 60.203 57.143 0.00 0.00 0.00 3.86
4235 5765 5.485662 AGCAAATCATAACTAGAAACGGC 57.514 39.130 0.00 0.00 0.00 5.68
4250 5780 4.142469 ACATTAACCACGGCTAAGCAAATC 60.142 41.667 0.00 0.00 0.00 2.17
4315 5868 9.882996 GAAAGAAATTGAAACCAAATTCATTCC 57.117 29.630 10.40 0.00 36.34 3.01
4360 5917 2.497675 AGGTGCAGATAACACGATGAGT 59.502 45.455 0.00 0.00 38.98 3.41
4400 5957 5.448632 GCTGTTACCGGGATAAAATTGACAG 60.449 44.000 6.32 6.44 35.22 3.51
4464 6021 0.394192 TCATGATGCTCGGATCCACC 59.606 55.000 13.41 0.00 0.00 4.61
4481 6038 4.015872 AGGACTTTTGCGGAGTATTTCA 57.984 40.909 0.00 0.00 0.00 2.69
4651 6228 4.020307 TCTGGTCATAGTTGAACTGCATGA 60.020 41.667 8.33 7.37 40.45 3.07
4703 6280 5.424757 TCGGAATACTTGAACCCATACTTG 58.575 41.667 0.00 0.00 0.00 3.16
5027 7505 0.708802 ACGGAGGGAGTAGGGAGAAA 59.291 55.000 0.00 0.00 0.00 2.52
5032 7510 3.528370 CGCACGGAGGGAGTAGGG 61.528 72.222 0.00 0.00 0.00 3.53
5034 7512 2.439701 TCCGCACGGAGGGAGTAG 60.440 66.667 7.89 0.00 39.76 2.57
5155 8457 5.685954 GGTTTTCTGATTCAAAGTTCGTTCC 59.314 40.000 0.00 0.00 0.00 3.62
5265 8610 4.044426 GCAGCATTCGTGAACTTCTTTTT 58.956 39.130 0.00 0.00 0.00 1.94
5266 8611 3.316308 AGCAGCATTCGTGAACTTCTTTT 59.684 39.130 0.00 0.00 0.00 2.27
5267 8612 2.880890 AGCAGCATTCGTGAACTTCTTT 59.119 40.909 0.00 0.00 0.00 2.52
5268 8613 2.481952 GAGCAGCATTCGTGAACTTCTT 59.518 45.455 0.00 0.00 0.00 2.52
5269 8614 2.072298 GAGCAGCATTCGTGAACTTCT 58.928 47.619 0.00 0.00 0.00 2.85
5270 8615 1.800586 TGAGCAGCATTCGTGAACTTC 59.199 47.619 0.00 0.00 0.00 3.01
5271 8616 1.882912 TGAGCAGCATTCGTGAACTT 58.117 45.000 0.00 0.00 0.00 2.66
5312 8665 0.889186 TGCTTTCCCAGAAAGGCGAC 60.889 55.000 16.54 0.00 34.23 5.19
5315 8668 1.747924 GAGATGCTTTCCCAGAAAGGC 59.252 52.381 16.54 10.43 35.39 4.35
5408 9134 4.700213 AGGTCAAATGAAACGGTAGGATTG 59.300 41.667 0.00 0.00 0.00 2.67
5418 9144 6.317789 TGATGTTGAGAGGTCAAATGAAAC 57.682 37.500 0.00 0.00 44.44 2.78
5445 9171 3.091545 ACAAACACATGGATGGCCTAAG 58.908 45.455 3.32 0.00 34.31 2.18
5476 9202 7.200455 ACTACTTAACCTTTTCATTGTGTTGC 58.800 34.615 0.00 0.00 0.00 4.17
5481 9207 7.606839 GGAGCTACTACTTAACCTTTTCATTGT 59.393 37.037 0.00 0.00 0.00 2.71
5536 9266 2.574006 ACAGAAATTGCTCTGCTCCA 57.426 45.000 7.00 0.00 45.72 3.86
5560 9290 5.012561 AGCTGGTGGATATTTCTAGGTCATC 59.987 44.000 0.00 0.00 0.00 2.92
5688 9423 2.039084 AGCTCAAACTGTTCACCCCTAG 59.961 50.000 0.00 0.00 0.00 3.02
5700 9435 0.941463 CACGTCTCGCAGCTCAAACT 60.941 55.000 0.00 0.00 0.00 2.66
5730 9465 1.430992 TTCCGGATAGGGGGATTCAC 58.569 55.000 4.15 0.00 41.52 3.18
5917 9652 7.070696 TCGATCCCCTATTTCTACAAGATTGAA 59.929 37.037 0.00 0.00 0.00 2.69
5938 9673 6.083630 CGAGACAGGAGATAATCTTTCGATC 58.916 44.000 0.00 0.00 0.00 3.69
5949 9684 1.112113 GGGCAACGAGACAGGAGATA 58.888 55.000 0.00 0.00 37.60 1.98
6030 9770 3.566261 GTGCGACCCACATGTCAG 58.434 61.111 0.00 0.00 44.06 3.51
6087 9827 6.480981 GGAAAATATTCTCCGACGAAATGGTA 59.519 38.462 0.00 0.00 35.79 3.25
6088 9828 5.296035 GGAAAATATTCTCCGACGAAATGGT 59.704 40.000 0.00 0.00 35.79 3.55
6090 9830 6.183360 TGTGGAAAATATTCTCCGACGAAATG 60.183 38.462 3.37 0.00 35.79 2.32
6091 9831 5.878116 TGTGGAAAATATTCTCCGACGAAAT 59.122 36.000 3.37 0.00 35.79 2.17
6092 9832 5.239351 TGTGGAAAATATTCTCCGACGAAA 58.761 37.500 3.37 0.00 35.79 3.46
6093 9833 4.823157 TGTGGAAAATATTCTCCGACGAA 58.177 39.130 3.37 0.00 35.79 3.85
6094 9834 4.459390 TGTGGAAAATATTCTCCGACGA 57.541 40.909 3.37 0.00 35.79 4.20
6129 9874 1.429148 GCAGATAACCCGCGTCCTTG 61.429 60.000 4.92 0.00 0.00 3.61


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

AutoCloner maintained by Alex Coulton.