Multiple sequence alignment - TraesCS6B01G230700

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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 TraesCS6B01G230700 chr6B 100.000 7893 0 0 1 7893 374974775 374966883 0.000000e+00 14576.0
1 TraesCS6B01G230700 chr6B 100.000 144 0 0 7033 7176 42772483 42772340 4.700000e-67 267.0
2 TraesCS6B01G230700 chr6B 97.973 148 3 0 7035 7182 226144899 226145046 2.830000e-64 257.0
3 TraesCS6B01G230700 chr6B 98.039 102 2 0 3754 3855 374970920 374970819 2.260000e-40 178.0
4 TraesCS6B01G230700 chr6B 98.039 102 2 0 3856 3957 374971022 374970921 2.260000e-40 178.0
5 TraesCS6B01G230700 chr6B 89.474 114 12 0 4355 4468 41441813 41441700 2.300000e-30 145.0
6 TraesCS6B01G230700 chr6A 96.643 5004 118 18 806 5784 317150908 317155886 0.000000e+00 8264.0
7 TraesCS6B01G230700 chr6A 95.540 1166 46 3 5873 7035 317157429 317158591 0.000000e+00 1860.0
8 TraesCS6B01G230700 chr6A 91.444 374 19 7 7211 7581 317158662 317159025 1.180000e-137 501.0
9 TraesCS6B01G230700 chr6A 88.705 363 31 5 281 636 317147727 317148086 1.220000e-117 435.0
10 TraesCS6B01G230700 chr6A 82.288 271 12 15 7648 7892 317159159 317159419 1.340000e-47 202.0
11 TraesCS6B01G230700 chr6A 98.039 102 2 0 3856 3957 317153840 317153941 2.260000e-40 178.0
12 TraesCS6B01G230700 chr6A 98.039 102 2 0 3754 3855 317153942 317154043 2.260000e-40 178.0
13 TraesCS6B01G230700 chr6A 78.623 276 38 11 2880 3135 317154419 317154693 6.340000e-36 163.0
14 TraesCS6B01G230700 chr6D 96.519 3936 75 28 731 4633 237813431 237817337 0.000000e+00 6453.0
15 TraesCS6B01G230700 chr6D 96.243 2422 73 7 4630 7035 237821354 237823773 0.000000e+00 3952.0
16 TraesCS6B01G230700 chr6D 92.188 448 17 8 7205 7647 237823838 237824272 1.130000e-172 617.0
17 TraesCS6B01G230700 chr6D 83.508 382 54 6 281 655 48675180 48674801 1.630000e-91 348.0
18 TraesCS6B01G230700 chr6D 83.246 382 51 7 281 655 128074358 128073983 9.810000e-89 339.0
19 TraesCS6B01G230700 chr6D 93.805 226 12 1 7648 7871 237824382 237824607 9.810000e-89 339.0
20 TraesCS6B01G230700 chr6D 87.895 190 22 1 4336 4525 355872465 355872653 1.030000e-53 222.0
21 TraesCS6B01G230700 chr6D 100.000 102 0 0 3754 3855 237816566 237816667 1.050000e-43 189.0
22 TraesCS6B01G230700 chr6D 97.059 102 3 0 3856 3957 237816464 237816565 1.050000e-38 172.0
23 TraesCS6B01G230700 chr6D 87.273 110 11 2 4359 4468 25635531 25635425 1.080000e-23 122.0
24 TraesCS6B01G230700 chr2B 85.981 428 50 8 1976 2393 451827398 451827825 4.340000e-122 449.0
25 TraesCS6B01G230700 chr2B 95.082 61 2 1 2885 2944 323081502 323081562 2.340000e-15 95.3
26 TraesCS6B01G230700 chr5A 87.404 389 40 4 1977 2356 356500795 356500407 9.400000e-119 438.0
27 TraesCS6B01G230700 chr5A 100.000 144 0 0 7033 7176 394523308 394523165 4.700000e-67 267.0
28 TraesCS6B01G230700 chr5A 100.000 142 0 0 7035 7176 533846761 533846620 6.070000e-66 263.0
29 TraesCS6B01G230700 chr5B 87.147 389 39 6 1977 2356 304628395 304628009 1.570000e-116 431.0
30 TraesCS6B01G230700 chr5B 86.005 393 41 10 1976 2357 248402268 248401879 7.370000e-110 409.0
31 TraesCS6B01G230700 chr7D 85.612 417 50 5 1976 2383 466053385 466053800 5.660000e-116 429.0
32 TraesCS6B01G230700 chr7D 79.625 373 70 6 281 651 410133863 410134231 6.070000e-66 263.0
33 TraesCS6B01G230700 chr7D 74.742 194 40 6 4746 4933 10550300 10550490 2.360000e-10 78.7
34 TraesCS6B01G230700 chr1B 92.384 302 20 3 3 302 527256245 527255945 2.040000e-115 427.0
35 TraesCS6B01G230700 chr1B 100.000 146 0 0 7031 7176 550418429 550418284 3.630000e-68 270.0
36 TraesCS6B01G230700 chr1B 88.043 92 9 2 1974 2064 572911140 572911230 3.010000e-19 108.0
37 TraesCS6B01G230700 chr1B 80.992 121 23 0 178 298 29592123 29592003 6.520000e-16 97.1
38 TraesCS6B01G230700 chr1B 81.579 114 19 2 186 298 529494482 529494370 8.430000e-15 93.5
39 TraesCS6B01G230700 chr4A 92.308 299 21 2 1 298 621118378 621118675 2.630000e-114 424.0
40 TraesCS6B01G230700 chr4A 86.335 161 20 2 96 255 621118096 621118255 2.930000e-39 174.0
41 TraesCS6B01G230700 chr7B 84.652 417 54 5 1976 2382 490602545 490602961 2.650000e-109 407.0
42 TraesCS6B01G230700 chr7B 80.890 382 64 6 281 655 407185640 407185261 7.750000e-75 292.0
43 TraesCS6B01G230700 chr7B 99.306 144 1 0 7033 7176 699165147 699165004 2.180000e-65 261.0
44 TraesCS6B01G230700 chr3B 91.497 294 23 2 2 294 794667761 794668053 3.430000e-108 403.0
45 TraesCS6B01G230700 chr3B 100.000 144 0 0 7035 7178 19040884 19041027 4.700000e-67 267.0
46 TraesCS6B01G230700 chr3B 100.000 142 0 0 7035 7176 508926902 508926761 6.070000e-66 263.0
47 TraesCS6B01G230700 chr3B 79.430 316 39 17 2887 3198 417495631 417495338 4.830000e-47 200.0
48 TraesCS6B01G230700 chr3B 92.929 99 7 0 200 298 794668050 794668148 2.300000e-30 145.0
49 TraesCS6B01G230700 chr2D 90.365 301 24 4 1 299 10052183 10052480 2.670000e-104 390.0
50 TraesCS6B01G230700 chr2D 82.415 381 59 6 281 655 136674307 136674685 7.640000e-85 326.0
51 TraesCS6B01G230700 chr2D 81.967 366 58 8 295 654 624546456 624546819 3.580000e-78 303.0
52 TraesCS6B01G230700 chr2D 80.739 379 66 5 281 654 228751888 228751512 1.000000e-73 289.0
53 TraesCS6B01G230700 chr2A 83.488 430 59 8 1976 2393 505083225 505083654 2.670000e-104 390.0
54 TraesCS6B01G230700 chr2A 81.102 381 54 14 281 654 563222674 563223043 1.000000e-73 289.0
55 TraesCS6B01G230700 chr2A 79.634 383 67 8 280 655 302267148 302266770 1.690000e-66 265.0
56 TraesCS6B01G230700 chr1A 100.000 147 0 0 7030 7176 576882606 576882752 1.010000e-68 272.0
57 TraesCS6B01G230700 chr1A 83.636 110 10 5 699 800 16417569 16417678 6.520000e-16 97.1
58 TraesCS6B01G230700 chr5D 83.648 159 20 4 4329 4485 469065525 469065371 2.300000e-30 145.0
59 TraesCS6B01G230700 chr7A 75.566 221 40 12 89 298 657082601 657082818 6.520000e-16 97.1
60 TraesCS6B01G230700 chr3D 80.952 84 10 4 701 779 226968358 226968440 2.380000e-05 62.1


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 TraesCS6B01G230700 chr6B 374966883 374974775 7892 True 4977.333333 14576 98.692667 1 7893 3 chr6B.!!$R3 7892
1 TraesCS6B01G230700 chr6A 317147727 317159419 11692 False 1472.625000 8264 91.165125 281 7892 8 chr6A.!!$F1 7611
2 TraesCS6B01G230700 chr6D 237813431 237817337 3906 False 2271.333333 6453 97.859333 731 4633 3 chr6D.!!$F2 3902
3 TraesCS6B01G230700 chr6D 237821354 237824607 3253 False 1636.000000 3952 94.078667 4630 7871 3 chr6D.!!$F3 3241
4 TraesCS6B01G230700 chr4A 621118096 621118675 579 False 299.000000 424 89.321500 1 298 2 chr4A.!!$F1 297

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
371 654 0.033208 TCCCACTTGATCCCAATGGC 60.033 55.000 0.00 0.0 0.0 4.40 F
1255 4199 0.606096 TCGAATTCCACTCCGCTTCA 59.394 50.000 0.00 0.0 0.0 3.02 F
1935 4881 0.248539 GACGGCCACTCATCGACTAC 60.249 60.000 2.24 0.0 0.0 2.73 F
3206 6154 0.544697 ACTGTGAACCCTTTGTCCGT 59.455 50.000 0.00 0.0 0.0 4.69 F
3261 6209 1.066257 AAGCTGCTTGTTGTTGGCG 59.934 52.632 15.16 0.0 0.0 5.69 F
4104 7056 1.066587 GCTCTTCGTGCGCCTCTAT 59.933 57.895 4.18 0.0 0.0 1.98 F
5902 10324 0.629058 ATGAACCCGCCCCAGTATTT 59.371 50.000 0.00 0.0 0.0 1.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1879 4825 1.339055 GGCATCCTGTGTGCTCTTGTA 60.339 52.381 0.00 0.00 42.16 2.41 R
2871 5819 0.383590 TCACAACAATTGCCCACACG 59.616 50.000 5.05 0.00 0.00 4.49 R
3723 6674 0.040067 GGACGTTGGCTCAAGCAAAG 60.040 55.000 4.13 2.28 44.36 2.77 R
4389 7341 1.003355 AATCCCTCACAGCCACACG 60.003 57.895 0.00 0.00 0.00 4.49 R
4936 7896 1.118838 GGGAGGAGTCCATGACAGAG 58.881 60.000 12.86 0.00 46.07 3.35 R
5918 10340 1.965414 TAGTCCCTTGGCATGGAGAA 58.035 50.000 20.21 3.35 0.00 2.87 R
7159 11584 0.108281 GTAAGGGCCTGTTCGGACTC 60.108 60.000 6.92 0.00 42.26 3.36 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
34 317 4.473520 ATGGGAAGAGCCGCCACG 62.474 66.667 0.00 0.00 37.63 4.94
57 340 2.812619 GGGAAGGATGGGAGGCGAG 61.813 68.421 0.00 0.00 0.00 5.03
99 382 1.748879 GGCTGCAACGGGCTCATTA 60.749 57.895 0.50 0.00 45.15 1.90
142 425 1.529244 AAAAAGCCGCCAGAGCAGT 60.529 52.632 0.00 0.00 39.83 4.40
163 446 3.147595 CCAGGACGGGAGCGATCA 61.148 66.667 1.84 0.00 0.00 2.92
164 447 2.502492 CCAGGACGGGAGCGATCAT 61.502 63.158 1.84 0.00 0.00 2.45
181 464 4.929211 CGATCATTTGATAGCGGGTGATTA 59.071 41.667 0.00 0.00 34.37 1.75
202 485 7.549134 TGATTAGTAACGATTCACAGCAAATCT 59.451 33.333 0.00 0.00 32.15 2.40
246 529 9.965824 AAAATCAATGATCCAACGGATATAAAC 57.034 29.630 0.00 0.00 43.27 2.01
256 539 5.333798 CCAACGGATATAAACGCTAATGGTG 60.334 44.000 0.01 0.00 0.00 4.17
258 541 6.088016 ACGGATATAAACGCTAATGGTGTA 57.912 37.500 0.01 0.00 37.73 2.90
267 550 2.565841 GCTAATGGTGTAAGAGGGCTG 58.434 52.381 0.00 0.00 0.00 4.85
279 562 1.301677 GAGGGCTGGAAAAGTGCTCG 61.302 60.000 0.00 0.00 31.56 5.03
323 606 3.788227 TGGACCAACATGTAAGCTCTT 57.212 42.857 0.00 0.00 0.00 2.85
347 630 9.743057 CTTCCTCTATCTCACTACAATAAAGTG 57.257 37.037 0.00 0.00 44.66 3.16
355 638 4.007659 CACTACAATAAAGTGTGGGTCCC 58.992 47.826 0.00 0.00 39.61 4.46
368 651 0.631212 GGGTCCCACTTGATCCCAAT 59.369 55.000 1.78 0.00 38.15 3.16
369 652 1.686115 GGGTCCCACTTGATCCCAATG 60.686 57.143 1.78 0.00 38.15 2.82
371 654 0.033208 TCCCACTTGATCCCAATGGC 60.033 55.000 0.00 0.00 0.00 4.40
410 693 7.618442 TCTAAAATTATTCGCTTGCTTACTCG 58.382 34.615 0.00 0.00 0.00 4.18
426 709 2.171840 ACTCGTGACAAGTGGAGCTAT 58.828 47.619 0.00 0.00 0.00 2.97
452 735 4.935352 ACCATTGTGAGATAGAGAGAGC 57.065 45.455 0.00 0.00 0.00 4.09
463 746 5.700183 AGATAGAGAGAGCTAACATGTGGA 58.300 41.667 0.00 0.00 0.00 4.02
466 749 3.196685 AGAGAGAGCTAACATGTGGAACC 59.803 47.826 0.00 0.00 34.36 3.62
472 755 1.633432 CTAACATGTGGAACCAGGGGA 59.367 52.381 0.00 0.00 34.36 4.81
479 762 4.200447 TGTGGAACCAGGGGAATTTTTA 57.800 40.909 0.00 0.00 34.36 1.52
517 800 7.931578 TCAACGGGTTTGACTTGATAATAAT 57.068 32.000 0.00 0.00 39.45 1.28
523 806 8.070171 CGGGTTTGACTTGATAATAATGATGTC 58.930 37.037 0.00 0.00 0.00 3.06
617 906 5.768317 TCTCCCAAAACGATGACATTTTTC 58.232 37.500 0.00 0.00 0.00 2.29
620 909 5.068460 TCCCAAAACGATGACATTTTTCAGT 59.932 36.000 0.00 0.00 0.00 3.41
621 910 5.752955 CCCAAAACGATGACATTTTTCAGTT 59.247 36.000 0.00 0.00 0.00 3.16
629 918 7.643764 ACGATGACATTTTTCAGTTGTTGTAAG 59.356 33.333 0.00 0.00 0.00 2.34
654 3171 5.481105 TGTAATGGTAAAACCGAGTAGTGG 58.519 41.667 0.00 0.00 42.58 4.00
655 3172 2.460757 TGGTAAAACCGAGTAGTGGC 57.539 50.000 0.00 0.00 42.58 5.01
663 3180 3.194005 ACCGAGTAGTGGCCATAAATG 57.806 47.619 9.72 0.00 0.00 2.32
677 3194 9.660180 GTGGCCATAAATGATAAAAACCTAAAA 57.340 29.630 9.72 0.00 0.00 1.52
800 3726 9.800433 ATTTTGTATGTAATCGCATTGAAATCA 57.200 25.926 0.00 0.00 0.00 2.57
803 3729 7.984391 TGTATGTAATCGCATTGAAATCACTT 58.016 30.769 0.00 0.00 0.00 3.16
804 3730 8.122330 TGTATGTAATCGCATTGAAATCACTTC 58.878 33.333 0.00 0.00 34.31 3.01
879 3822 1.298788 CACAACCGGAAACAACGCC 60.299 57.895 9.46 0.00 0.00 5.68
1255 4199 0.606096 TCGAATTCCACTCCGCTTCA 59.394 50.000 0.00 0.00 0.00 3.02
1426 4370 1.005037 GTGTCACGGCTCCATCACA 60.005 57.895 0.00 0.00 0.00 3.58
1614 4558 1.741145 GGCCATTACAACCTAACACCG 59.259 52.381 0.00 0.00 0.00 4.94
1718 4664 2.507110 ATCTTCCGACACGTGGCTGG 62.507 60.000 21.24 21.46 0.00 4.85
1836 4782 2.370445 CCCCTCTGTGTAGGCCAGG 61.370 68.421 5.01 0.00 35.09 4.45
1935 4881 0.248539 GACGGCCACTCATCGACTAC 60.249 60.000 2.24 0.00 0.00 2.73
2122 5068 2.626743 GCCGTTCTATAGACCTGCCTTA 59.373 50.000 0.67 0.00 0.00 2.69
2243 5189 0.694771 TCCTTCTGCAGCATTGACCT 59.305 50.000 9.47 0.00 0.00 3.85
2333 5279 0.973632 ACCGCACCTCATGTACTTGA 59.026 50.000 10.70 10.70 0.00 3.02
2368 5314 9.968743 CTACTAAGCCTAAAAACATTAGTTTCG 57.031 33.333 1.69 0.00 46.79 3.46
2639 5587 9.415544 TGAGATTTCATATGTAGATTGTGATCG 57.584 33.333 1.90 0.00 37.37 3.69
2694 5642 1.478631 TGGTGTGGACAATGTTGCAA 58.521 45.000 0.00 0.00 0.00 4.08
2696 5644 2.223994 TGGTGTGGACAATGTTGCAATG 60.224 45.455 0.59 0.00 0.00 2.82
2718 5666 6.761099 TGCTTTTACACCTGTTCTTTGTTA 57.239 33.333 0.00 0.00 0.00 2.41
2729 5677 5.238006 TGTTCTTTGTTAACAACTTCCGG 57.762 39.130 20.43 0.00 34.04 5.14
3017 5965 3.135994 GTTCTTCCTTGCCTCAAACGTA 58.864 45.455 0.00 0.00 0.00 3.57
3080 6028 7.691993 TGACCTCTCCTAATAAGGCTTAAAT 57.308 36.000 11.59 6.14 43.31 1.40
3206 6154 0.544697 ACTGTGAACCCTTTGTCCGT 59.455 50.000 0.00 0.00 0.00 4.69
3256 6204 1.312815 GTCCTCAAGCTGCTTGTTGT 58.687 50.000 33.94 3.52 41.66 3.32
3261 6209 1.066257 AAGCTGCTTGTTGTTGGCG 59.934 52.632 15.16 0.00 0.00 5.69
3379 6327 9.570468 CAGGTACAACTTGTATATCTCTAGGTA 57.430 37.037 4.93 0.00 35.05 3.08
3394 6342 6.982899 TCTCTAGGTAACCCTGATACTTCTT 58.017 40.000 0.00 0.00 42.67 2.52
3409 6359 6.843333 TGATACTTCTTTGAGATCCTCTCCAT 59.157 38.462 1.90 0.00 42.73 3.41
3600 6551 3.636764 GGAGCCAATACGAATCCCATTTT 59.363 43.478 0.00 0.00 0.00 1.82
3615 6566 5.649557 TCCCATTTTATTTGTTCTCATGCG 58.350 37.500 0.00 0.00 0.00 4.73
3616 6567 4.268405 CCCATTTTATTTGTTCTCATGCGC 59.732 41.667 0.00 0.00 0.00 6.09
3723 6674 3.315191 ACACATGCACACAGAACTAAACC 59.685 43.478 0.00 0.00 0.00 3.27
3733 6684 5.066505 ACACAGAACTAAACCTTTGCTTGAG 59.933 40.000 0.00 0.00 0.00 3.02
3750 6701 2.187599 GAGCCAACGTCCACACATGC 62.188 60.000 0.00 0.00 0.00 4.06
3933 6884 1.407989 CCCTTTTCTAGCCTGCCTCAG 60.408 57.143 0.00 0.00 0.00 3.35
3940 6891 4.400961 GCCTGCCTCAGCCGTTCT 62.401 66.667 0.00 0.00 38.69 3.01
3970 6921 9.362539 GAAGATGATTTTGTTGATGCTGTTATT 57.637 29.630 0.00 0.00 0.00 1.40
3983 6934 4.140536 TGCTGTTATTCATGGTTGTGTCA 58.859 39.130 0.00 0.00 0.00 3.58
4013 6964 2.654877 GCAATGCTGCTGTGCCTT 59.345 55.556 14.59 0.00 45.74 4.35
4028 6979 1.350684 TGCCTTGTTGCTCCTATGTCA 59.649 47.619 0.00 0.00 0.00 3.58
4104 7056 1.066587 GCTCTTCGTGCGCCTCTAT 59.933 57.895 4.18 0.00 0.00 1.98
4294 7246 3.365364 GCGTTGAACTCTTCCATGAAAGG 60.365 47.826 0.00 0.00 0.00 3.11
4389 7341 2.271800 CGTGTTGAAGATAGCCAGACC 58.728 52.381 0.00 0.00 0.00 3.85
4674 7629 1.301677 GACCAAGGTGCAGCTGTAGC 61.302 60.000 24.23 24.23 42.49 3.58
4695 7650 3.051479 CTGCATGCACACGCCTCA 61.051 61.111 18.46 0.00 37.32 3.86
4786 7741 1.771255 GGGCATATTGACTGGAGGAGT 59.229 52.381 0.00 0.00 37.76 3.85
4869 7829 7.431376 CGAGTCGAAATACTTCTAATTACTGCA 59.569 37.037 6.73 0.00 0.00 4.41
4875 7835 9.326413 GAAATACTTCTAATTACTGCAGCCTTA 57.674 33.333 15.27 8.22 0.00 2.69
5012 7972 5.116983 GTCCACAACAAAAGTATTGCATTCG 59.883 40.000 0.00 0.00 0.00 3.34
5039 7999 4.839121 ACACCTCTTCTTTGTGTACAACA 58.161 39.130 0.00 0.00 41.18 3.33
5056 8016 8.230486 GTGTACAACATCAGACCAATTTAGAAG 58.770 37.037 0.00 0.00 0.00 2.85
5105 8065 8.293699 ACAAACTAGTTGGATTTTCTTCTTGT 57.706 30.769 17.18 6.01 41.97 3.16
5200 8164 3.646162 TGCTCTTAAGTCCAAGGACAAGA 59.354 43.478 20.52 18.22 46.76 3.02
5238 8202 3.513750 AAAGCCTGACCCTGCCACC 62.514 63.158 0.00 0.00 0.00 4.61
5316 8280 2.025037 TGCTCTTAGGAAACATGCCCAT 60.025 45.455 0.00 0.00 0.00 4.00
5598 8566 6.985188 TGCTTTCTCCATGTACTTGTTATC 57.015 37.500 7.86 0.00 0.00 1.75
5611 8579 9.959721 ATGTACTTGTTATCCTTTTCTGTACAT 57.040 29.630 0.00 0.00 41.35 2.29
5778 8746 5.395546 GGGCTTTGGCATTTCAATCATTCTA 60.396 40.000 0.00 0.00 40.87 2.10
5785 8753 8.303780 TGGCATTTCAATCATTCTATTGGTTA 57.696 30.769 0.00 0.00 37.44 2.85
5830 8798 5.314923 TCTATCCAGCAAGCACATTTTTC 57.685 39.130 0.00 0.00 0.00 2.29
5893 10315 1.906105 TACCTGGACATGAACCCGCC 61.906 60.000 0.00 0.00 0.00 6.13
5894 10316 2.438434 CTGGACATGAACCCGCCC 60.438 66.667 0.00 0.00 0.00 6.13
5902 10324 0.629058 ATGAACCCGCCCCAGTATTT 59.371 50.000 0.00 0.00 0.00 1.40
5918 10340 6.127253 CCCAGTATTTTCTGCAATCCAAGAAT 60.127 38.462 0.00 0.00 34.47 2.40
5927 10349 3.131577 TGCAATCCAAGAATTCTCCATGC 59.868 43.478 8.78 14.64 0.00 4.06
5935 10357 2.027385 GAATTCTCCATGCCAAGGGAC 58.973 52.381 0.00 0.00 31.54 4.46
5940 10362 3.664320 TCTCCATGCCAAGGGACTATAA 58.336 45.455 0.00 0.00 38.49 0.98
5993 10415 5.587388 AATGTTAACATGCTCATTCTGGG 57.413 39.130 21.46 0.00 36.56 4.45
5997 10419 0.700564 ACATGCTCATTCTGGGGTGT 59.299 50.000 0.00 0.00 0.00 4.16
6015 10437 3.307059 GGTGTCAGTTACCAGCAAGAGAT 60.307 47.826 0.00 0.00 38.12 2.75
6025 10447 3.244215 ACCAGCAAGAGATTTCTTCACGA 60.244 43.478 0.00 0.00 41.71 4.35
6100 10523 7.394359 ACTTTGTAACTGATGGATAAGTGCAAT 59.606 33.333 0.00 0.00 0.00 3.56
6118 10541 4.186159 GCAATGCAGCAAATTGGTATTCT 58.814 39.130 0.00 0.00 35.88 2.40
6122 10545 3.374988 TGCAGCAAATTGGTATTCTCTCG 59.625 43.478 0.00 0.00 0.00 4.04
6128 10551 7.011389 CAGCAAATTGGTATTCTCTCGTCATAA 59.989 37.037 0.00 0.00 0.00 1.90
6130 10553 8.012241 GCAAATTGGTATTCTCTCGTCATAATC 58.988 37.037 0.00 0.00 0.00 1.75
6365 10788 4.717233 ATTTGTCAGTTGCAACTTGTCA 57.283 36.364 29.23 22.59 37.08 3.58
6471 10896 3.557595 CCTCATAACACAGCGAAATCTCC 59.442 47.826 0.00 0.00 0.00 3.71
6556 10981 4.433615 AGGCATACATTCACGAGTACAAG 58.566 43.478 0.00 0.00 0.00 3.16
6569 10994 4.113354 CGAGTACAAGCTTAACCTCCATC 58.887 47.826 0.00 0.00 0.00 3.51
6597 11022 1.710809 AGAGCACCCCAACCACTATTT 59.289 47.619 0.00 0.00 0.00 1.40
6637 11062 4.742201 CCGTCGAGGGGCACAGTG 62.742 72.222 16.51 0.00 35.97 3.66
6732 11157 2.082140 TATACGGTGCCATCTCCAGT 57.918 50.000 0.00 0.00 0.00 4.00
6745 11170 2.467880 TCTCCAGTTGTCAGTATCCCC 58.532 52.381 0.00 0.00 0.00 4.81
6759 11184 1.229209 TCCCCGAGGAGCTTCAGTT 60.229 57.895 0.00 0.00 37.19 3.16
6765 11190 1.831580 GAGGAGCTTCAGTTGCCAAT 58.168 50.000 0.00 0.00 0.00 3.16
6911 11336 0.254178 AGAGCTATGGGTTGCTGTGG 59.746 55.000 0.00 0.00 39.91 4.17
6931 11356 3.449377 TGGACATAGTTTATGAGCACCGA 59.551 43.478 3.26 0.00 39.45 4.69
7014 11439 0.988063 TTGTGGGCTGCATGTAGGTA 59.012 50.000 13.03 0.00 0.00 3.08
7046 11471 1.940613 GGCTATTAAGGCTGTGTTCGG 59.059 52.381 0.00 0.00 44.73 4.30
7047 11472 2.629051 GCTATTAAGGCTGTGTTCGGT 58.371 47.619 0.00 0.00 0.00 4.69
7048 11473 3.431207 GGCTATTAAGGCTGTGTTCGGTA 60.431 47.826 0.00 0.00 44.73 4.02
7049 11474 3.802685 GCTATTAAGGCTGTGTTCGGTAG 59.197 47.826 0.00 0.00 0.00 3.18
7050 11475 2.088950 TTAAGGCTGTGTTCGGTAGC 57.911 50.000 0.00 0.00 36.74 3.58
7053 11478 2.663196 GCTGTGTTCGGTAGCCCT 59.337 61.111 0.00 0.00 0.00 5.19
7054 11479 1.448013 GCTGTGTTCGGTAGCCCTC 60.448 63.158 0.00 0.00 0.00 4.30
7055 11480 1.218316 CTGTGTTCGGTAGCCCTCC 59.782 63.158 0.00 0.00 0.00 4.30
7056 11481 1.534476 TGTGTTCGGTAGCCCTCCA 60.534 57.895 0.00 0.00 0.00 3.86
7057 11482 1.079336 GTGTTCGGTAGCCCTCCAC 60.079 63.158 0.00 0.00 0.00 4.02
7058 11483 1.229082 TGTTCGGTAGCCCTCCACT 60.229 57.895 0.00 0.00 0.00 4.00
7059 11484 1.255667 TGTTCGGTAGCCCTCCACTC 61.256 60.000 0.00 0.00 0.00 3.51
7060 11485 1.684734 TTCGGTAGCCCTCCACTCC 60.685 63.158 0.00 0.00 0.00 3.85
7061 11486 2.042843 CGGTAGCCCTCCACTCCT 60.043 66.667 0.00 0.00 0.00 3.69
7062 11487 2.128507 CGGTAGCCCTCCACTCCTC 61.129 68.421 0.00 0.00 0.00 3.71
7063 11488 1.762858 GGTAGCCCTCCACTCCTCC 60.763 68.421 0.00 0.00 0.00 4.30
7064 11489 1.001760 GTAGCCCTCCACTCCTCCA 59.998 63.158 0.00 0.00 0.00 3.86
7065 11490 0.399233 GTAGCCCTCCACTCCTCCAT 60.399 60.000 0.00 0.00 0.00 3.41
7066 11491 0.343372 TAGCCCTCCACTCCTCCATT 59.657 55.000 0.00 0.00 0.00 3.16
7067 11492 0.985490 AGCCCTCCACTCCTCCATTC 60.985 60.000 0.00 0.00 0.00 2.67
7068 11493 1.274703 GCCCTCCACTCCTCCATTCA 61.275 60.000 0.00 0.00 0.00 2.57
7069 11494 0.835941 CCCTCCACTCCTCCATTCAG 59.164 60.000 0.00 0.00 0.00 3.02
7070 11495 0.835941 CCTCCACTCCTCCATTCAGG 59.164 60.000 0.00 0.00 39.47 3.86
7071 11496 1.623557 CCTCCACTCCTCCATTCAGGA 60.624 57.143 0.00 0.00 46.75 3.86
7078 11503 2.903357 TCCATTCAGGAGCGGAGC 59.097 61.111 0.00 0.00 46.33 4.70
7103 11528 4.873746 TGGAGTACCATATTAGCAGCTC 57.126 45.455 0.00 0.00 41.77 4.09
7104 11529 3.578716 TGGAGTACCATATTAGCAGCTCC 59.421 47.826 0.00 0.00 41.77 4.70
7105 11530 3.835395 GGAGTACCATATTAGCAGCTCCT 59.165 47.826 0.00 0.00 38.47 3.69
7106 11531 4.081917 GGAGTACCATATTAGCAGCTCCTC 60.082 50.000 0.00 0.00 38.47 3.71
7107 11532 4.483950 AGTACCATATTAGCAGCTCCTCA 58.516 43.478 0.00 0.00 0.00 3.86
7108 11533 4.901849 AGTACCATATTAGCAGCTCCTCAA 59.098 41.667 0.00 0.00 0.00 3.02
7109 11534 4.778213 ACCATATTAGCAGCTCCTCAAA 57.222 40.909 0.00 0.00 0.00 2.69
7110 11535 5.316158 ACCATATTAGCAGCTCCTCAAAT 57.684 39.130 0.00 0.00 0.00 2.32
7111 11536 5.699143 ACCATATTAGCAGCTCCTCAAATT 58.301 37.500 0.00 0.00 0.00 1.82
7112 11537 6.841601 ACCATATTAGCAGCTCCTCAAATTA 58.158 36.000 0.00 0.00 0.00 1.40
7113 11538 7.290061 ACCATATTAGCAGCTCCTCAAATTAA 58.710 34.615 0.00 0.00 0.00 1.40
7114 11539 7.229506 ACCATATTAGCAGCTCCTCAAATTAAC 59.770 37.037 0.00 0.00 0.00 2.01
7115 11540 7.229306 CCATATTAGCAGCTCCTCAAATTAACA 59.771 37.037 0.00 0.00 0.00 2.41
7116 11541 5.880054 TTAGCAGCTCCTCAAATTAACAC 57.120 39.130 0.00 0.00 0.00 3.32
7117 11542 4.026356 AGCAGCTCCTCAAATTAACACT 57.974 40.909 0.00 0.00 0.00 3.55
7118 11543 3.755378 AGCAGCTCCTCAAATTAACACTG 59.245 43.478 0.00 0.00 0.00 3.66
7119 11544 3.671702 GCAGCTCCTCAAATTAACACTGC 60.672 47.826 0.00 0.00 40.89 4.40
7120 11545 3.503363 CAGCTCCTCAAATTAACACTGCA 59.497 43.478 0.00 0.00 0.00 4.41
7121 11546 4.157289 CAGCTCCTCAAATTAACACTGCAT 59.843 41.667 0.00 0.00 0.00 3.96
7122 11547 4.157289 AGCTCCTCAAATTAACACTGCATG 59.843 41.667 0.00 0.00 0.00 4.06
7123 11548 4.082571 GCTCCTCAAATTAACACTGCATGT 60.083 41.667 0.00 0.00 46.42 3.21
7130 11555 3.659334 ACACTGCATGTTGCTCCG 58.341 55.556 0.75 0.00 45.31 4.63
7131 11556 2.177531 CACTGCATGTTGCTCCGC 59.822 61.111 0.75 0.00 45.31 5.54
7132 11557 2.033141 ACTGCATGTTGCTCCGCT 59.967 55.556 0.75 0.00 45.31 5.52
7133 11558 2.037136 ACTGCATGTTGCTCCGCTC 61.037 57.895 0.75 0.00 45.31 5.03
7134 11559 2.747460 TGCATGTTGCTCCGCTCC 60.747 61.111 0.75 0.00 45.31 4.70
7135 11560 3.869272 GCATGTTGCTCCGCTCCG 61.869 66.667 0.00 0.00 40.96 4.63
7151 11576 2.492090 CGGAGCGGAGTTGGAGAG 59.508 66.667 0.00 0.00 0.00 3.20
7152 11577 2.185608 GGAGCGGAGTTGGAGAGC 59.814 66.667 0.00 0.00 0.00 4.09
7153 11578 2.202676 GAGCGGAGTTGGAGAGCG 60.203 66.667 0.00 0.00 0.00 5.03
7154 11579 3.708220 GAGCGGAGTTGGAGAGCGG 62.708 68.421 0.00 0.00 0.00 5.52
7155 11580 4.821589 GCGGAGTTGGAGAGCGGG 62.822 72.222 0.00 0.00 0.00 6.13
7156 11581 3.068691 CGGAGTTGGAGAGCGGGA 61.069 66.667 0.00 0.00 0.00 5.14
7157 11582 2.896443 GGAGTTGGAGAGCGGGAG 59.104 66.667 0.00 0.00 0.00 4.30
7158 11583 2.726351 GGAGTTGGAGAGCGGGAGG 61.726 68.421 0.00 0.00 0.00 4.30
7159 11584 2.685380 AGTTGGAGAGCGGGAGGG 60.685 66.667 0.00 0.00 0.00 4.30
7160 11585 2.683933 GTTGGAGAGCGGGAGGGA 60.684 66.667 0.00 0.00 0.00 4.20
7161 11586 2.364317 TTGGAGAGCGGGAGGGAG 60.364 66.667 0.00 0.00 0.00 4.30
7162 11587 3.239627 TTGGAGAGCGGGAGGGAGT 62.240 63.158 0.00 0.00 0.00 3.85
7163 11588 2.835895 GGAGAGCGGGAGGGAGTC 60.836 72.222 0.00 0.00 0.00 3.36
7164 11589 2.835895 GAGAGCGGGAGGGAGTCC 60.836 72.222 0.00 0.00 46.10 3.85
7171 11596 3.300013 GGAGGGAGTCCGAACAGG 58.700 66.667 2.26 0.00 42.97 4.00
7172 11597 2.579738 GAGGGAGTCCGAACAGGC 59.420 66.667 2.26 0.00 40.77 4.85
7173 11598 3.003763 AGGGAGTCCGAACAGGCC 61.004 66.667 2.26 0.00 40.77 5.19
7178 11603 0.108281 GAGTCCGAACAGGCCCTTAC 60.108 60.000 0.00 0.00 40.77 2.34
7231 11686 2.161410 GTGTTGACAATGCGGCTATCAA 59.839 45.455 0.00 3.33 0.00 2.57
7295 11752 3.030652 CCAGGTGACGTGCAAACC 58.969 61.111 0.00 0.00 0.00 3.27
7463 11921 8.198778 TGCATCAACTATAGTATTAAACCGACA 58.801 33.333 5.65 0.00 0.00 4.35
7467 11925 9.524106 TCAACTATAGTATTAAACCGACATGTG 57.476 33.333 1.15 0.00 0.00 3.21
7468 11926 9.524106 CAACTATAGTATTAAACCGACATGTGA 57.476 33.333 1.15 0.00 0.00 3.58
7469 11927 9.525409 AACTATAGTATTAAACCGACATGTGAC 57.475 33.333 1.15 0.00 0.00 3.67
7470 11928 7.859377 ACTATAGTATTAAACCGACATGTGACG 59.141 37.037 1.15 0.54 0.00 4.35
7471 11929 4.813027 AGTATTAAACCGACATGTGACGT 58.187 39.130 1.15 0.00 0.00 4.34
7472 11930 4.624024 AGTATTAAACCGACATGTGACGTG 59.376 41.667 1.15 2.72 0.00 4.49
7473 11931 2.512485 TAAACCGACATGTGACGTGT 57.488 45.000 10.68 10.68 0.00 4.49
7474 11932 2.512485 AAACCGACATGTGACGTGTA 57.488 45.000 10.87 0.00 0.00 2.90
7475 11933 1.774639 AACCGACATGTGACGTGTAC 58.225 50.000 10.87 4.13 0.00 2.90
7476 11934 0.669619 ACCGACATGTGACGTGTACA 59.330 50.000 10.87 0.00 0.00 2.90
7477 11935 1.057636 CCGACATGTGACGTGTACAC 58.942 55.000 16.32 16.32 38.55 2.90
7532 11990 2.550699 TTTGCGGCCCCAGGATGTAG 62.551 60.000 0.00 0.00 0.00 2.74
7539 11997 2.042301 GCCCCAGGATGTAGGATCACT 61.042 57.143 0.00 0.00 29.59 3.41
7613 12071 3.702048 TTCTCCCCGGCGAACCAG 61.702 66.667 9.30 0.00 34.57 4.00
7642 12103 0.038744 AACCATGCCTCAACCTGGAG 59.961 55.000 0.00 0.00 32.92 3.86
7650 12223 2.104170 CCTCAACCTGGAGTCTACCTC 58.896 57.143 0.00 0.00 39.67 3.85
7667 12240 1.202582 CCTCGATCTCACCAAGTCGTT 59.797 52.381 0.00 0.00 35.71 3.85
7668 12241 2.254459 CTCGATCTCACCAAGTCGTTG 58.746 52.381 0.00 0.00 35.71 4.10
7721 12297 0.032615 AGCATCTCCTTCGGTCCTCT 60.033 55.000 0.00 0.00 0.00 3.69
7730 12306 2.516460 CGGTCCTCTCGTCGGGAT 60.516 66.667 0.00 0.00 33.89 3.85
7812 12412 6.263842 TCATCTTTTTCACTGCTGTTCATCTT 59.736 34.615 0.00 0.00 0.00 2.40
7856 12456 1.713078 ACTTTTGGGAGGAGCCTCATT 59.287 47.619 17.68 0.00 44.40 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
14 297 4.115199 GGCGGCTCTTCCCATGGT 62.115 66.667 11.73 0.00 0.00 3.55
34 317 2.768344 TCCCATCCTTCCCCTCGC 60.768 66.667 0.00 0.00 0.00 5.03
46 329 3.933722 CCATCGCTCGCCTCCCAT 61.934 66.667 0.00 0.00 0.00 4.00
73 356 3.188786 CGTTGCAGCCTCCGCTAC 61.189 66.667 0.00 0.00 46.25 3.58
99 382 0.255033 GTCTCGGGTTAATTGGGCCT 59.745 55.000 4.53 0.00 0.00 5.19
134 417 3.324930 TCCTGGGCCACTGCTCTG 61.325 66.667 0.00 0.00 39.40 3.35
157 440 1.195448 CACCCGCTATCAAATGATCGC 59.805 52.381 9.23 9.23 39.14 4.58
158 441 2.754472 TCACCCGCTATCAAATGATCG 58.246 47.619 0.00 0.00 36.05 3.69
159 442 5.934625 ACTAATCACCCGCTATCAAATGATC 59.065 40.000 0.00 0.00 36.05 2.92
160 443 5.869579 ACTAATCACCCGCTATCAAATGAT 58.130 37.500 1.01 1.01 38.51 2.45
161 444 5.290493 ACTAATCACCCGCTATCAAATGA 57.710 39.130 0.00 0.00 0.00 2.57
162 445 6.346598 CGTTACTAATCACCCGCTATCAAATG 60.347 42.308 0.00 0.00 0.00 2.32
163 446 5.694910 CGTTACTAATCACCCGCTATCAAAT 59.305 40.000 0.00 0.00 0.00 2.32
164 447 5.045215 CGTTACTAATCACCCGCTATCAAA 58.955 41.667 0.00 0.00 0.00 2.69
174 457 4.868171 TGCTGTGAATCGTTACTAATCACC 59.132 41.667 3.24 0.00 39.64 4.02
181 464 5.120830 GTCAGATTTGCTGTGAATCGTTACT 59.879 40.000 0.00 0.00 45.14 2.24
202 485 1.035923 TTGAGCATTTTTGGCCGTCA 58.964 45.000 0.00 0.00 0.00 4.35
246 529 1.139058 AGCCCTCTTACACCATTAGCG 59.861 52.381 0.00 0.00 0.00 4.26
256 539 1.813178 GCACTTTTCCAGCCCTCTTAC 59.187 52.381 0.00 0.00 0.00 2.34
258 541 0.480252 AGCACTTTTCCAGCCCTCTT 59.520 50.000 0.00 0.00 0.00 2.85
267 550 5.813080 ACATTATAACCGAGCACTTTTCC 57.187 39.130 0.00 0.00 0.00 3.13
298 581 5.045578 AGAGCTTACATGTTGGTCCATAAGT 60.046 40.000 19.92 2.72 0.00 2.24
300 583 5.435686 AGAGCTTACATGTTGGTCCATAA 57.564 39.130 19.92 1.34 0.00 1.90
305 588 3.935828 GAGGAAGAGCTTACATGTTGGTC 59.064 47.826 17.45 17.45 0.00 4.02
308 591 6.815089 AGATAGAGGAAGAGCTTACATGTTG 58.185 40.000 2.30 0.00 0.00 3.33
323 606 8.687242 CACACTTTATTGTAGTGAGATAGAGGA 58.313 37.037 9.74 0.00 44.52 3.71
355 638 1.753073 GAAGGCCATTGGGATCAAGTG 59.247 52.381 5.01 0.00 36.19 3.16
368 651 8.664669 AATTTTAGAGGAAAATAAGAAGGCCA 57.335 30.769 5.01 0.00 45.21 5.36
397 680 1.125021 CTTGTCACGAGTAAGCAAGCG 59.875 52.381 0.00 0.00 31.72 4.68
410 693 5.105473 TGGTAAGTATAGCTCCACTTGTCAC 60.105 44.000 18.51 11.14 35.79 3.67
426 709 7.229707 GCTCTCTCTATCTCACAATGGTAAGTA 59.770 40.741 0.00 0.00 0.00 2.24
452 735 1.633432 TCCCCTGGTTCCACATGTTAG 59.367 52.381 0.00 0.00 0.00 2.34
479 762 8.160765 TCAAACCCGTTGACCATATTATATGAT 58.839 33.333 13.29 0.00 41.47 2.45
601 890 6.811170 ACAACAACTGAAAAATGTCATCGTTT 59.189 30.769 0.00 0.00 34.68 3.60
617 906 9.790389 TTTTACCATTACAACTTACAACAACTG 57.210 29.630 0.00 0.00 0.00 3.16
620 909 7.914346 CGGTTTTACCATTACAACTTACAACAA 59.086 33.333 0.00 0.00 38.47 2.83
621 910 7.281774 TCGGTTTTACCATTACAACTTACAACA 59.718 33.333 0.00 0.00 38.47 3.33
629 918 6.128472 CCACTACTCGGTTTTACCATTACAAC 60.128 42.308 0.00 0.00 38.47 3.32
780 3700 7.011016 ACGAAGTGATTTCAATGCGATTACATA 59.989 33.333 14.70 0.00 44.98 2.29
781 3701 6.183360 ACGAAGTGATTTCAATGCGATTACAT 60.183 34.615 14.70 0.00 44.98 2.29
784 3704 5.794687 ACGAAGTGATTTCAATGCGATTA 57.205 34.783 14.70 0.00 44.98 1.75
785 3705 4.685169 ACGAAGTGATTTCAATGCGATT 57.315 36.364 14.70 0.00 44.98 3.34
825 3768 2.938798 AATGGGTGCCGGGAAGGA 60.939 61.111 2.18 0.00 45.00 3.36
1083 4026 0.610785 TTCGGATTTGGTCTTGGGGC 60.611 55.000 0.00 0.00 0.00 5.80
1084 4027 2.024414 GATTCGGATTTGGTCTTGGGG 58.976 52.381 0.00 0.00 0.00 4.96
1085 4028 3.004752 AGATTCGGATTTGGTCTTGGG 57.995 47.619 0.00 0.00 0.00 4.12
1086 4029 3.378427 GGAAGATTCGGATTTGGTCTTGG 59.622 47.826 0.00 0.00 29.89 3.61
1087 4030 3.378427 GGGAAGATTCGGATTTGGTCTTG 59.622 47.826 0.00 0.00 29.89 3.02
1088 4031 3.267031 AGGGAAGATTCGGATTTGGTCTT 59.733 43.478 0.00 0.00 32.23 3.01
1255 4199 6.350445 GCAAATAGTTCAGATCCAAACCACAT 60.350 38.462 4.62 0.00 0.00 3.21
1426 4370 2.416547 GCACGATGACACTAAGCAACAT 59.583 45.455 0.00 0.00 0.00 2.71
1468 4412 8.472007 ACCACAATAACAACCAAAGAAAGATA 57.528 30.769 0.00 0.00 0.00 1.98
1614 4558 2.035530 AGTTGCTATCTTGCTGGAGC 57.964 50.000 0.00 0.00 42.50 4.70
1718 4664 3.005684 TCATGACAAACATTTCCACTGGC 59.994 43.478 0.00 0.00 37.07 4.85
1879 4825 1.339055 GGCATCCTGTGTGCTCTTGTA 60.339 52.381 0.00 0.00 42.16 2.41
2122 5068 4.887071 TGACAAGAGTGCCACAAAAGTTAT 59.113 37.500 0.00 0.00 0.00 1.89
2195 5141 7.789026 TGATATCGATGAAGATATGAGCCATT 58.211 34.615 8.54 0.00 42.15 3.16
2243 5189 7.230747 TCAGAAGGACACCTTTCAATATTTGA 58.769 34.615 4.51 0.00 44.82 2.69
2296 5242 3.181478 GCGGTTTCAGTACTACTAGGCAT 60.181 47.826 0.00 0.00 0.00 4.40
2368 5314 4.799564 AGAGTTGTGGAGAGAGACATTC 57.200 45.455 0.00 0.00 0.00 2.67
2694 5642 5.852282 ACAAAGAACAGGTGTAAAAGCAT 57.148 34.783 0.00 0.00 0.00 3.79
2696 5644 7.030768 TGTTAACAAAGAACAGGTGTAAAAGC 58.969 34.615 5.64 0.00 33.03 3.51
2718 5666 4.721132 TCCTAAATTGTCCGGAAGTTGTT 58.279 39.130 5.23 0.00 0.00 2.83
2729 5677 7.538575 ACATTGCATGTAACTCCTAAATTGTC 58.461 34.615 0.00 0.00 42.78 3.18
2764 5712 5.590663 AGAGAACGCATCACTAGACTAATGA 59.409 40.000 0.00 0.00 0.00 2.57
2870 5818 0.597118 CACAACAATTGCCCACACGG 60.597 55.000 5.05 0.00 0.00 4.94
2871 5819 0.383590 TCACAACAATTGCCCACACG 59.616 50.000 5.05 0.00 0.00 4.49
3017 5965 5.819379 CGTTATATAAGGATGGCATGCATCT 59.181 40.000 21.36 7.73 0.00 2.90
3080 6028 5.617252 AGAGTCCAATCGTACAAGGAAAAA 58.383 37.500 0.00 0.00 0.00 1.94
3206 6154 2.841881 GTCCAGGAGGGGTGTAATGTTA 59.158 50.000 0.00 0.00 37.22 2.41
3256 6204 1.378514 GGAATTCAGCCCTCGCCAA 60.379 57.895 7.93 0.00 34.57 4.52
3261 6209 3.145286 GCTATGAAGGAATTCAGCCCTC 58.855 50.000 7.93 0.00 34.02 4.30
3379 6327 5.728741 AGGATCTCAAAGAAGTATCAGGGTT 59.271 40.000 0.00 0.00 0.00 4.11
3409 6359 7.394923 ACATAATAAGGGACGTTCCAAATTTCA 59.605 33.333 17.22 0.62 38.64 2.69
3600 6551 1.082690 TGCGCGCATGAGAACAAATA 58.917 45.000 33.09 1.22 0.00 1.40
3615 6566 3.795561 AGCACGAGAATTATTATGCGC 57.204 42.857 0.00 0.00 38.12 6.09
3616 6567 6.422223 AGAAAAGCACGAGAATTATTATGCG 58.578 36.000 0.00 0.00 38.12 4.73
3723 6674 0.040067 GGACGTTGGCTCAAGCAAAG 60.040 55.000 4.13 2.28 44.36 2.77
3733 6684 1.865788 ATGCATGTGTGGACGTTGGC 61.866 55.000 0.00 0.00 0.00 4.52
3750 6701 3.305131 CGAAATTGATCTGGGCCATCATG 60.305 47.826 6.72 0.00 30.26 3.07
3933 6884 5.122396 ACAAAATCATCTTCAGTAGAACGGC 59.878 40.000 0.00 0.00 36.22 5.68
3940 6891 7.175467 ACAGCATCAACAAAATCATCTTCAGTA 59.825 33.333 0.00 0.00 0.00 2.74
3983 6934 1.021390 GCATTGCTAGCGACAGTGGT 61.021 55.000 6.86 0.00 0.00 4.16
4013 6964 2.497675 GAGGAGTGACATAGGAGCAACA 59.502 50.000 0.00 0.00 0.00 3.33
4028 6979 3.826157 GCTACAGATGCAGATAGAGGAGT 59.174 47.826 0.00 0.00 0.00 3.85
4373 7325 1.899814 ACACGGTCTGGCTATCTTCAA 59.100 47.619 0.00 0.00 0.00 2.69
4389 7341 1.003355 AATCCCTCACAGCCACACG 60.003 57.895 0.00 0.00 0.00 4.49
4674 7629 2.500369 GCGTGTGCATGCAGTTCG 60.500 61.111 23.41 24.28 42.66 3.95
4786 7741 2.227149 CAGCATGCAGTCACTAAAAGCA 59.773 45.455 21.98 0.00 39.79 3.91
4936 7896 1.118838 GGGAGGAGTCCATGACAGAG 58.881 60.000 12.86 0.00 46.07 3.35
5012 7972 7.311364 TGTACACAAAGAAGAGGTGTAAAAC 57.689 36.000 5.54 0.00 46.14 2.43
5039 7999 6.176183 CACCTGACTTCTAAATTGGTCTGAT 58.824 40.000 0.00 0.00 32.14 2.90
5056 8016 4.201950 CCTTATTGCTACATTGCACCTGAC 60.202 45.833 2.57 0.00 43.20 3.51
5105 8065 6.067263 AGCTAAACTAAAACGCAAACATGA 57.933 33.333 0.00 0.00 0.00 3.07
5169 8133 2.079925 GACTTAAGAGCAGCCAACCTG 58.920 52.381 10.09 0.00 44.67 4.00
5200 8164 2.662309 CAGTGCATGCCCCTTCTTT 58.338 52.632 16.68 0.00 0.00 2.52
5238 8202 3.686726 AGCTGCATAAGAAAAGAACCTCG 59.313 43.478 1.02 0.00 0.00 4.63
5316 8280 2.934932 TGCCTCTCCCCATGCACA 60.935 61.111 0.00 0.00 0.00 4.57
5349 8313 2.509548 CAATACCTTCCCACATCCCTCA 59.490 50.000 0.00 0.00 0.00 3.86
5748 8716 2.825532 TGAAATGCCAAAGCCCTAGAAC 59.174 45.455 0.00 0.00 38.69 3.01
5750 8718 2.897271 TGAAATGCCAAAGCCCTAGA 57.103 45.000 0.00 0.00 38.69 2.43
5830 8798 8.347035 TGCATGTGAAATTCATATGATGTACAG 58.653 33.333 28.72 7.29 45.26 2.74
5893 10315 4.706476 TCTTGGATTGCAGAAAATACTGGG 59.294 41.667 0.00 0.00 38.22 4.45
5894 10316 5.902613 TCTTGGATTGCAGAAAATACTGG 57.097 39.130 0.00 0.00 38.22 4.00
5902 10324 4.665451 TGGAGAATTCTTGGATTGCAGAA 58.335 39.130 9.87 0.00 33.55 3.02
5918 10340 1.965414 TAGTCCCTTGGCATGGAGAA 58.035 50.000 20.21 3.35 0.00 2.87
5993 10415 2.037251 TCTCTTGCTGGTAACTGACACC 59.963 50.000 0.00 0.00 37.83 4.16
5997 10419 5.489792 AGAAATCTCTTGCTGGTAACTGA 57.510 39.130 0.00 0.00 37.83 3.41
6100 10523 3.374988 CGAGAGAATACCAATTTGCTGCA 59.625 43.478 0.00 0.00 0.00 4.41
6118 10541 4.368315 CCAAATCCACGATTATGACGAGA 58.632 43.478 0.00 0.00 31.46 4.04
6122 10545 4.881850 AGTTCCCAAATCCACGATTATGAC 59.118 41.667 0.00 0.00 31.46 3.06
6128 10551 3.282021 CATGAGTTCCCAAATCCACGAT 58.718 45.455 0.00 0.00 0.00 3.73
6130 10553 1.745087 CCATGAGTTCCCAAATCCACG 59.255 52.381 0.00 0.00 0.00 4.94
6365 10788 8.818622 TGTAGTCTTGTGAGTATAGGTTATGT 57.181 34.615 0.00 0.00 31.55 2.29
6471 10896 0.107081 TGGAACTGGTGGTGTTACCG 59.893 55.000 0.00 0.00 42.58 4.02
6556 10981 5.491982 TCTTTCTTCAGATGGAGGTTAAGC 58.508 41.667 0.00 0.00 0.00 3.09
6569 10994 1.882623 GTTGGGGTGCTCTTTCTTCAG 59.117 52.381 0.00 0.00 0.00 3.02
6597 11022 1.676635 GCTTGAGCACCAGCATCCA 60.677 57.895 2.26 0.00 45.49 3.41
6637 11062 2.858941 GCTTCTACGGGAATTCTTCGAC 59.141 50.000 21.75 0.37 33.01 4.20
6732 11157 1.776662 CTCCTCGGGGATACTGACAA 58.223 55.000 3.31 0.00 41.36 3.18
6745 11170 0.603707 TTGGCAACTGAAGCTCCTCG 60.604 55.000 0.00 0.00 37.61 4.63
6753 11178 2.665165 ACACCTTCATTGGCAACTGAA 58.335 42.857 17.84 17.84 37.61 3.02
6759 11184 1.876799 CGTACAACACCTTCATTGGCA 59.123 47.619 0.00 0.00 0.00 4.92
6765 11190 4.594123 TCATCTTCGTACAACACCTTCA 57.406 40.909 0.00 0.00 0.00 3.02
6799 11224 4.033709 CAAGGTTATCTCCCTCTTCCTCA 58.966 47.826 0.00 0.00 0.00 3.86
6858 11283 0.658368 CGTCTCCTCATCGTCATCGT 59.342 55.000 0.00 0.00 38.33 3.73
6911 11336 5.005779 CAGTTCGGTGCTCATAAACTATGTC 59.994 44.000 0.00 0.00 37.45 3.06
6931 11356 9.189156 ACATGTATGCAAAACTATAATCCAGTT 57.811 29.630 0.00 0.00 37.85 3.16
7014 11439 8.001292 ACAGCCTTAATAGCCTTAAATTGAGAT 58.999 33.333 0.00 0.00 0.00 2.75
7036 11461 1.448013 GAGGGCTACCGAACACAGC 60.448 63.158 0.00 0.00 43.47 4.40
7037 11462 1.218316 GGAGGGCTACCGAACACAG 59.782 63.158 0.00 0.00 43.47 3.66
7038 11463 1.534476 TGGAGGGCTACCGAACACA 60.534 57.895 0.00 0.00 43.47 3.72
7039 11464 1.079336 GTGGAGGGCTACCGAACAC 60.079 63.158 0.00 0.00 43.47 3.32
7040 11465 1.229082 AGTGGAGGGCTACCGAACA 60.229 57.895 0.00 0.00 43.47 3.18
7041 11466 1.516423 GAGTGGAGGGCTACCGAAC 59.484 63.158 0.00 0.00 43.47 3.95
7042 11467 1.684734 GGAGTGGAGGGCTACCGAA 60.685 63.158 0.00 0.00 43.47 4.30
7043 11468 2.043248 GGAGTGGAGGGCTACCGA 60.043 66.667 0.00 0.00 43.47 4.69
7044 11469 2.042843 AGGAGTGGAGGGCTACCG 60.043 66.667 0.00 0.00 43.47 4.02
7045 11470 1.762858 GGAGGAGTGGAGGGCTACC 60.763 68.421 0.00 0.00 0.00 3.18
7046 11471 0.399233 ATGGAGGAGTGGAGGGCTAC 60.399 60.000 0.00 0.00 0.00 3.58
7047 11472 0.343372 AATGGAGGAGTGGAGGGCTA 59.657 55.000 0.00 0.00 0.00 3.93
7048 11473 0.985490 GAATGGAGGAGTGGAGGGCT 60.985 60.000 0.00 0.00 0.00 5.19
7049 11474 1.274703 TGAATGGAGGAGTGGAGGGC 61.275 60.000 0.00 0.00 0.00 5.19
7050 11475 0.835941 CTGAATGGAGGAGTGGAGGG 59.164 60.000 0.00 0.00 0.00 4.30
7051 11476 0.835941 CCTGAATGGAGGAGTGGAGG 59.164 60.000 0.00 0.00 38.35 4.30
7052 11477 1.871418 TCCTGAATGGAGGAGTGGAG 58.129 55.000 0.00 0.00 40.56 3.86
7061 11486 2.903357 GCTCCGCTCCTGAATGGA 59.097 61.111 0.00 0.00 43.86 3.41
7062 11487 2.587194 CGCTCCGCTCCTGAATGG 60.587 66.667 0.00 0.00 37.10 3.16
7063 11488 2.587194 CCGCTCCGCTCCTGAATG 60.587 66.667 0.00 0.00 0.00 2.67
7064 11489 3.854669 CCCGCTCCGCTCCTGAAT 61.855 66.667 0.00 0.00 0.00 2.57
7071 11496 4.753662 TACTCCACCCGCTCCGCT 62.754 66.667 0.00 0.00 0.00 5.52
7072 11497 4.509737 GTACTCCACCCGCTCCGC 62.510 72.222 0.00 0.00 0.00 5.54
7073 11498 3.834799 GGTACTCCACCCGCTCCG 61.835 72.222 0.00 0.00 42.07 4.63
7083 11508 3.835395 AGGAGCTGCTAATATGGTACTCC 59.165 47.826 5.69 0.00 42.25 3.85
7084 11509 4.524714 TGAGGAGCTGCTAATATGGTACTC 59.475 45.833 8.12 0.00 39.02 2.59
7085 11510 4.483950 TGAGGAGCTGCTAATATGGTACT 58.516 43.478 8.12 0.00 0.00 2.73
7086 11511 4.873746 TGAGGAGCTGCTAATATGGTAC 57.126 45.455 8.12 0.00 0.00 3.34
7087 11512 5.887214 TTTGAGGAGCTGCTAATATGGTA 57.113 39.130 8.12 0.00 0.00 3.25
7088 11513 4.778213 TTTGAGGAGCTGCTAATATGGT 57.222 40.909 8.12 0.00 0.00 3.55
7089 11514 7.229306 TGTTAATTTGAGGAGCTGCTAATATGG 59.771 37.037 8.12 0.00 0.00 2.74
7090 11515 8.072567 GTGTTAATTTGAGGAGCTGCTAATATG 58.927 37.037 8.12 0.00 0.00 1.78
7091 11516 7.995488 AGTGTTAATTTGAGGAGCTGCTAATAT 59.005 33.333 8.12 0.00 0.00 1.28
7092 11517 7.280876 CAGTGTTAATTTGAGGAGCTGCTAATA 59.719 37.037 8.12 0.00 0.00 0.98
7093 11518 6.094603 CAGTGTTAATTTGAGGAGCTGCTAAT 59.905 38.462 8.12 2.08 0.00 1.73
7094 11519 5.412594 CAGTGTTAATTTGAGGAGCTGCTAA 59.587 40.000 8.12 0.00 0.00 3.09
7095 11520 4.937620 CAGTGTTAATTTGAGGAGCTGCTA 59.062 41.667 8.12 0.00 0.00 3.49
7096 11521 3.755378 CAGTGTTAATTTGAGGAGCTGCT 59.245 43.478 7.79 7.79 0.00 4.24
7097 11522 3.671702 GCAGTGTTAATTTGAGGAGCTGC 60.672 47.826 0.00 0.00 39.65 5.25
7098 11523 3.503363 TGCAGTGTTAATTTGAGGAGCTG 59.497 43.478 0.00 0.00 0.00 4.24
7099 11524 3.754965 TGCAGTGTTAATTTGAGGAGCT 58.245 40.909 0.00 0.00 0.00 4.09
7100 11525 4.082571 ACATGCAGTGTTAATTTGAGGAGC 60.083 41.667 0.00 0.00 38.01 4.70
7101 11526 5.633830 ACATGCAGTGTTAATTTGAGGAG 57.366 39.130 0.00 0.00 38.01 3.69
7134 11559 2.492090 CTCTCCAACTCCGCTCCG 59.508 66.667 0.00 0.00 0.00 4.63
7135 11560 2.185608 GCTCTCCAACTCCGCTCC 59.814 66.667 0.00 0.00 0.00 4.70
7136 11561 2.202676 CGCTCTCCAACTCCGCTC 60.203 66.667 0.00 0.00 0.00 5.03
7137 11562 3.764466 CCGCTCTCCAACTCCGCT 61.764 66.667 0.00 0.00 0.00 5.52
7138 11563 4.821589 CCCGCTCTCCAACTCCGC 62.822 72.222 0.00 0.00 0.00 5.54
7139 11564 3.068691 TCCCGCTCTCCAACTCCG 61.069 66.667 0.00 0.00 0.00 4.63
7140 11565 2.726351 CCTCCCGCTCTCCAACTCC 61.726 68.421 0.00 0.00 0.00 3.85
7141 11566 2.726351 CCCTCCCGCTCTCCAACTC 61.726 68.421 0.00 0.00 0.00 3.01
7142 11567 2.685380 CCCTCCCGCTCTCCAACT 60.685 66.667 0.00 0.00 0.00 3.16
7143 11568 2.683933 TCCCTCCCGCTCTCCAAC 60.684 66.667 0.00 0.00 0.00 3.77
7144 11569 2.364317 CTCCCTCCCGCTCTCCAA 60.364 66.667 0.00 0.00 0.00 3.53
7145 11570 3.663815 GACTCCCTCCCGCTCTCCA 62.664 68.421 0.00 0.00 0.00 3.86
7146 11571 2.835895 GACTCCCTCCCGCTCTCC 60.836 72.222 0.00 0.00 0.00 3.71
7147 11572 2.835895 GGACTCCCTCCCGCTCTC 60.836 72.222 0.00 0.00 31.83 3.20
7148 11573 4.824515 CGGACTCCCTCCCGCTCT 62.825 72.222 0.00 0.00 39.22 4.09
7149 11574 4.816984 TCGGACTCCCTCCCGCTC 62.817 72.222 0.00 0.00 44.96 5.03
7150 11575 4.377760 TTCGGACTCCCTCCCGCT 62.378 66.667 0.00 0.00 44.96 5.52
7151 11576 4.144703 GTTCGGACTCCCTCCCGC 62.145 72.222 0.00 0.00 44.96 6.13
7152 11577 2.678934 TGTTCGGACTCCCTCCCG 60.679 66.667 0.00 0.00 46.57 5.14
7153 11578 2.359967 CCTGTTCGGACTCCCTCCC 61.360 68.421 0.00 0.00 35.21 4.30
7154 11579 3.020237 GCCTGTTCGGACTCCCTCC 62.020 68.421 0.00 0.00 35.33 4.30
7155 11580 2.579738 GCCTGTTCGGACTCCCTC 59.420 66.667 0.00 0.00 33.16 4.30
7156 11581 3.003763 GGCCTGTTCGGACTCCCT 61.004 66.667 0.00 0.00 38.04 4.20
7157 11582 4.097361 GGGCCTGTTCGGACTCCC 62.097 72.222 0.84 0.00 42.26 4.30
7158 11583 1.262640 TAAGGGCCTGTTCGGACTCC 61.263 60.000 6.92 0.00 42.26 3.85
7159 11584 0.108281 GTAAGGGCCTGTTCGGACTC 60.108 60.000 6.92 0.00 42.26 3.36
7160 11585 0.544595 AGTAAGGGCCTGTTCGGACT 60.545 55.000 6.92 1.00 42.26 3.85
7161 11586 1.188863 TAGTAAGGGCCTGTTCGGAC 58.811 55.000 6.92 0.00 41.67 4.79
7162 11587 1.829222 CTTAGTAAGGGCCTGTTCGGA 59.171 52.381 6.92 0.00 33.16 4.55
7163 11588 1.829222 TCTTAGTAAGGGCCTGTTCGG 59.171 52.381 6.92 0.00 0.00 4.30
7164 11589 3.522553 CTTCTTAGTAAGGGCCTGTTCG 58.477 50.000 6.92 0.00 0.00 3.95
7165 11590 3.875125 CCTTCTTAGTAAGGGCCTGTTC 58.125 50.000 6.92 0.04 42.08 3.18
7201 11626 3.684305 CGCATTGTCAACACCTCTGATAA 59.316 43.478 0.00 0.00 0.00 1.75
7202 11627 3.261580 CGCATTGTCAACACCTCTGATA 58.738 45.455 0.00 0.00 0.00 2.15
7203 11628 2.079158 CGCATTGTCAACACCTCTGAT 58.921 47.619 0.00 0.00 0.00 2.90
7207 11662 1.210155 GCCGCATTGTCAACACCTC 59.790 57.895 0.00 0.00 0.00 3.85
7209 11664 1.064060 GATAGCCGCATTGTCAACACC 59.936 52.381 0.00 0.00 0.00 4.16
7231 11686 0.464452 GCGCACCCTATGAGTACCTT 59.536 55.000 0.30 0.00 0.00 3.50
7295 11752 2.557056 TGAAGTTGAGACGTGGGACTAG 59.443 50.000 0.00 0.00 0.00 2.57
7357 11814 5.988561 GTCACAAACTTGGATTTTAATGGCA 59.011 36.000 0.00 0.00 0.00 4.92
7470 11928 2.728383 AGCGCGACGTGTGTACAC 60.728 61.111 19.36 19.36 43.15 2.90
7471 11929 2.728015 CAGCGCGACGTGTGTACA 60.728 61.111 12.10 0.00 0.00 2.90
7472 11930 3.467119 CCAGCGCGACGTGTGTAC 61.467 66.667 12.10 0.00 0.00 2.90
7539 11997 4.141620 GCATTTTGAGAGGAGACAGGGATA 60.142 45.833 0.00 0.00 0.00 2.59
7545 12003 4.321718 CAAGAGCATTTTGAGAGGAGACA 58.678 43.478 0.00 0.00 0.00 3.41
7642 12103 3.018149 ACTTGGTGAGATCGAGGTAGAC 58.982 50.000 0.00 0.00 0.00 2.59
7650 12223 1.350193 CCAACGACTTGGTGAGATCG 58.650 55.000 0.00 0.00 42.09 3.69
7745 12321 1.645710 CCTAGAAGTCCCACTGTGGT 58.354 55.000 24.32 6.73 35.17 4.16
7812 12412 8.762645 AGTGAAAATTGGAGTACTCATCTATGA 58.237 33.333 23.91 2.41 35.16 2.15
7856 12456 5.962433 ACGAGAAGTGAAAATCGAGGAATA 58.038 37.500 0.00 0.00 38.50 1.75


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

AutoCloner maintained by Alex Coulton.