Multiple sequence alignment - TraesCS2D01G132600

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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 TraesCS2D01G132600 chr2D 100.000 6299 0 0 1 6299 77384571 77378273 0.000000e+00 11633.0
1 TraesCS2D01G132600 chr2D 80.676 621 44 28 61 659 77458406 77457840 4.540000e-111 412.0
2 TraesCS2D01G132600 chr2D 86.378 323 22 7 980 1282 78009152 78008832 3.640000e-87 333.0
3 TraesCS2D01G132600 chr2D 80.562 463 36 32 555 986 78010437 78009998 2.210000e-79 307.0
4 TraesCS2D01G132600 chr2D 87.054 224 17 7 205 426 102715220 102715007 6.310000e-60 243.0
5 TraesCS2D01G132600 chr2D 94.853 136 4 1 5 140 77400670 77400538 6.400000e-50 209.0
6 TraesCS2D01G132600 chr2D 90.698 129 12 0 1073 1201 77449982 77449854 8.400000e-39 172.0
7 TraesCS2D01G132600 chr2D 96.154 52 2 0 485 536 78010542 78010491 1.130000e-12 86.1
8 TraesCS2D01G132600 chr2D 94.340 53 3 0 1232 1284 77449852 77449800 1.460000e-11 82.4
9 TraesCS2D01G132600 chr2B 92.949 4269 180 49 6 4213 119635089 119630881 0.000000e+00 6104.0
10 TraesCS2D01G132600 chr2B 87.293 1873 123 59 4405 6243 119630578 119628787 0.000000e+00 2034.0
11 TraesCS2D01G132600 chr2B 88.112 1245 99 28 1272 2495 456699990 456698774 0.000000e+00 1434.0
12 TraesCS2D01G132600 chr2B 87.871 1245 102 28 1272 2495 693044171 693042955 0.000000e+00 1417.0
13 TraesCS2D01G132600 chr2B 88.540 1178 101 20 1339 2495 123135794 123136958 0.000000e+00 1397.0
14 TraesCS2D01G132600 chr2B 84.597 857 77 26 1338 2176 14600452 14599633 0.000000e+00 800.0
15 TraesCS2D01G132600 chr2B 90.385 416 26 6 5 419 120185246 120184844 9.290000e-148 534.0
16 TraesCS2D01G132600 chr2B 86.898 374 31 6 928 1284 120182303 120181931 2.730000e-108 403.0
17 TraesCS2D01G132600 chr2B 82.400 500 39 16 814 1284 120532566 120532087 2.130000e-104 390.0
18 TraesCS2D01G132600 chr2B 87.346 324 18 11 11 321 120533787 120533474 3.610000e-92 350.0
19 TraesCS2D01G132600 chr2B 76.658 377 43 23 524 887 120182656 120182312 3.910000e-37 167.0
20 TraesCS2D01G132600 chr2B 86.466 133 8 6 466 598 120533454 120533332 3.060000e-28 137.0
21 TraesCS2D01G132600 chr2A 91.396 4254 192 78 57 4213 78559408 78563584 0.000000e+00 5668.0
22 TraesCS2D01G132600 chr2A 87.460 1874 142 48 4369 6192 78563848 78565678 0.000000e+00 2073.0
23 TraesCS2D01G132600 chr2A 90.600 500 35 8 2006 2495 465363706 465363209 0.000000e+00 652.0
24 TraesCS2D01G132600 chr2A 87.674 430 29 12 1338 1763 465364119 465363710 4.420000e-131 479.0
25 TraesCS2D01G132600 chr4D 90.090 1221 97 18 1286 2495 456261533 456260326 0.000000e+00 1563.0
26 TraesCS2D01G132600 chr7B 87.952 1245 101 27 1272 2495 25067212 25068428 0.000000e+00 1423.0
27 TraesCS2D01G132600 chr1B 88.455 1178 101 21 1339 2495 345335096 345336259 0.000000e+00 1389.0
28 TraesCS2D01G132600 chr1D 89.070 430 31 7 1338 1763 163479426 163479843 2.600000e-143 520.0
29 TraesCS2D01G132600 chr4B 76.141 679 124 22 2749 3426 252979981 252979340 7.880000e-84 322.0
30 TraesCS2D01G132600 chr4B 77.160 162 36 1 3555 3716 172775238 172775398 6.720000e-15 93.5
31 TraesCS2D01G132600 chr4A 75.785 669 119 24 2758 3422 389990847 389990218 1.330000e-76 298.0
32 TraesCS2D01G132600 chr3A 80.496 282 49 5 3808 4088 746084869 746084593 1.780000e-50 211.0
33 TraesCS2D01G132600 chr3D 78.878 303 50 10 3787 4088 611160775 611160486 6.440000e-45 193.0


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 TraesCS2D01G132600 chr2D 77378273 77384571 6298 True 11633.000000 11633 100.000 1 6299 1 chr2D.!!$R1 6298
1 TraesCS2D01G132600 chr2D 77457840 77458406 566 True 412.000000 412 80.676 61 659 1 chr2D.!!$R3 598
2 TraesCS2D01G132600 chr2D 78008832 78010542 1710 True 242.033333 333 87.698 485 1282 3 chr2D.!!$R6 797
3 TraesCS2D01G132600 chr2B 119628787 119635089 6302 True 4069.000000 6104 90.121 6 6243 2 chr2B.!!$R4 6237
4 TraesCS2D01G132600 chr2B 456698774 456699990 1216 True 1434.000000 1434 88.112 1272 2495 1 chr2B.!!$R2 1223
5 TraesCS2D01G132600 chr2B 693042955 693044171 1216 True 1417.000000 1417 87.871 1272 2495 1 chr2B.!!$R3 1223
6 TraesCS2D01G132600 chr2B 123135794 123136958 1164 False 1397.000000 1397 88.540 1339 2495 1 chr2B.!!$F1 1156
7 TraesCS2D01G132600 chr2B 14599633 14600452 819 True 800.000000 800 84.597 1338 2176 1 chr2B.!!$R1 838
8 TraesCS2D01G132600 chr2B 120181931 120185246 3315 True 368.000000 534 84.647 5 1284 3 chr2B.!!$R5 1279
9 TraesCS2D01G132600 chr2B 120532087 120533787 1700 True 292.333333 390 85.404 11 1284 3 chr2B.!!$R6 1273
10 TraesCS2D01G132600 chr2A 78559408 78565678 6270 False 3870.500000 5668 89.428 57 6192 2 chr2A.!!$F1 6135
11 TraesCS2D01G132600 chr2A 465363209 465364119 910 True 565.500000 652 89.137 1338 2495 2 chr2A.!!$R1 1157
12 TraesCS2D01G132600 chr4D 456260326 456261533 1207 True 1563.000000 1563 90.090 1286 2495 1 chr4D.!!$R1 1209
13 TraesCS2D01G132600 chr7B 25067212 25068428 1216 False 1423.000000 1423 87.952 1272 2495 1 chr7B.!!$F1 1223
14 TraesCS2D01G132600 chr1B 345335096 345336259 1163 False 1389.000000 1389 88.455 1339 2495 1 chr1B.!!$F1 1156
15 TraesCS2D01G132600 chr4B 252979340 252979981 641 True 322.000000 322 76.141 2749 3426 1 chr4B.!!$R1 677
16 TraesCS2D01G132600 chr4A 389990218 389990847 629 True 298.000000 298 75.785 2758 3422 1 chr4A.!!$R1 664

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
605 2795 1.227853 ACCAACAAGACGACCCTGC 60.228 57.895 0.00 0.0 0.00 4.85 F
2392 6106 0.520404 CATCAGGTGTGTTGCTCTGC 59.480 55.000 0.00 0.0 0.00 4.26 F
3049 6792 0.380378 TGCGCAAGTTGTTCAAGGTC 59.620 50.000 8.16 0.0 41.68 3.85 F
3542 7285 1.266989 GCACCCTAACTGTTTGCTGTC 59.733 52.381 0.00 0.0 0.00 3.51 F
4318 8114 1.480137 TGGCTGAAAGTTGGTGGTTTG 59.520 47.619 0.00 0.0 35.30 2.93 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2436 6159 0.250553 TCGAATTCCACGGCCAAAGT 60.251 50.0 2.24 0.0 0.00 2.66 R
3542 7285 0.179145 CGAACCTGGGTAGTAGTGCG 60.179 60.0 0.00 0.0 0.00 5.34 R
4490 8344 0.110486 ATGGTGGGCACGAAAGAACT 59.890 50.0 0.00 0.0 0.00 3.01 R
4491 8345 0.240945 CATGGTGGGCACGAAAGAAC 59.759 55.0 0.00 0.0 0.00 3.01 R
6243 10172 0.040336 CGGATCCACGTCGACTATGG 60.040 60.0 23.20 23.2 34.58 2.74 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
302 349 2.126618 TGCGTCCACGTCGTCATC 60.127 61.111 0.00 0.00 42.22 2.92
344 394 1.811359 GCTGCTGATGGATATGGCTTC 59.189 52.381 0.00 0.00 0.00 3.86
345 395 2.434428 CTGCTGATGGATATGGCTTCC 58.566 52.381 0.00 0.00 0.00 3.46
346 396 2.040012 CTGCTGATGGATATGGCTTCCT 59.960 50.000 3.92 0.00 34.17 3.36
347 397 2.039480 TGCTGATGGATATGGCTTCCTC 59.961 50.000 3.92 1.08 34.17 3.71
384 437 6.116711 ACCTAGGAGAAAGAAAGAAAGACC 57.883 41.667 17.98 0.00 0.00 3.85
432 812 2.294979 CCCCTAAATTAAGCCACGGAC 58.705 52.381 0.00 0.00 0.00 4.79
480 866 1.628846 CTACCACCCTTGTGCTAACCT 59.371 52.381 0.00 0.00 41.35 3.50
605 2795 1.227853 ACCAACAAGACGACCCTGC 60.228 57.895 0.00 0.00 0.00 4.85
634 2825 2.160417 CGCAAGAATCAACCAAGTCTCC 59.840 50.000 0.00 0.00 43.02 3.71
690 2881 6.935771 TCCGGTTGCTAAACTTATTCTGTAAA 59.064 34.615 0.00 0.00 36.48 2.01
691 2882 7.444792 TCCGGTTGCTAAACTTATTCTGTAAAA 59.555 33.333 0.00 0.00 36.48 1.52
746 2979 7.746703 AGACAAAACTAGAACCAGTTTAGGAT 58.253 34.615 0.00 0.00 45.68 3.24
747 2980 7.661847 AGACAAAACTAGAACCAGTTTAGGATG 59.338 37.037 0.00 0.50 45.68 3.51
786 3024 2.822637 CCATGGGACGGATGGGAGG 61.823 68.421 2.85 0.00 37.33 4.30
802 3040 3.263425 TGGGAGGAGTACCAAGTTTCATC 59.737 47.826 0.00 0.00 38.94 2.92
803 3041 3.263425 GGGAGGAGTACCAAGTTTCATCA 59.737 47.826 0.00 0.00 38.94 3.07
808 3059 7.277174 AGGAGTACCAAGTTTCATCAAAAAG 57.723 36.000 0.00 0.00 38.94 2.27
2100 5809 1.745489 GGTGTCCGGGATGAGCAAC 60.745 63.158 0.00 0.00 0.00 4.17
2392 6106 0.520404 CATCAGGTGTGTTGCTCTGC 59.480 55.000 0.00 0.00 0.00 4.26
2436 6159 6.240894 ACTCTGAACTATGCAGATTTTGGAA 58.759 36.000 0.00 0.00 41.20 3.53
2444 6167 2.224257 TGCAGATTTTGGAACTTTGGCC 60.224 45.455 0.00 0.00 0.00 5.36
2525 6248 5.630415 TTACCAGTCTGAATTAGGGGATG 57.370 43.478 0.00 0.00 0.00 3.51
2594 6324 5.739752 TCATGCAATCGTTAGGAAATGAG 57.260 39.130 0.00 0.00 34.16 2.90
2620 6350 2.283532 TGGGTTTGGCCAATCCGG 60.284 61.111 30.57 0.00 39.65 5.14
2635 6365 0.537653 TCCGGTTTCGATACATGGCA 59.462 50.000 0.00 0.00 39.00 4.92
2643 6373 2.016318 TCGATACATGGCAAAGGCTTG 58.984 47.619 0.00 5.17 40.87 4.01
2795 6527 1.136336 CGGTTACGCTTGAGCTGAAAC 60.136 52.381 0.00 3.11 39.32 2.78
3014 6757 5.471556 TCAACATGCCATTTGTTCTGAAT 57.528 34.783 0.00 0.00 35.18 2.57
3049 6792 0.380378 TGCGCAAGTTGTTCAAGGTC 59.620 50.000 8.16 0.00 41.68 3.85
3213 6956 3.662759 TTGTTCTTTGTGGTTCCCTCT 57.337 42.857 0.00 0.00 0.00 3.69
3232 6975 5.365314 CCCTCTTGTCTCTAGGCTTTCTAAT 59.635 44.000 0.00 0.00 0.00 1.73
3234 6977 7.070074 CCCTCTTGTCTCTAGGCTTTCTAATTA 59.930 40.741 0.00 0.00 0.00 1.40
3235 6978 8.478877 CCTCTTGTCTCTAGGCTTTCTAATTAA 58.521 37.037 0.00 0.00 0.00 1.40
3401 7144 3.820557 ACATTGTGTCAAGTTAGCTGGT 58.179 40.909 0.00 0.00 0.00 4.00
3542 7285 1.266989 GCACCCTAACTGTTTGCTGTC 59.733 52.381 0.00 0.00 0.00 3.51
3613 7356 6.471233 TCTCATAATTCTATCCATAGGCGG 57.529 41.667 0.00 0.00 0.00 6.13
4221 8001 6.211184 ACTGGAATGCAATTTTGATCCTTGTA 59.789 34.615 0.00 0.00 36.07 2.41
4223 8003 8.303780 TGGAATGCAATTTTGATCCTTGTATA 57.696 30.769 0.00 0.00 36.07 1.47
4290 8086 5.450818 TGCTAGTTTATGGATCCCTTTGT 57.549 39.130 9.90 0.00 0.00 2.83
4302 8098 7.102518 TGGATCCCTTTGTTTATATATGGCT 57.897 36.000 9.90 0.00 0.00 4.75
4307 8103 8.463930 TCCCTTTGTTTATATATGGCTGAAAG 57.536 34.615 0.00 0.00 0.00 2.62
4311 8107 9.520204 CTTTGTTTATATATGGCTGAAAGTTGG 57.480 33.333 0.00 0.00 35.30 3.77
4312 8108 8.588290 TTGTTTATATATGGCTGAAAGTTGGT 57.412 30.769 0.00 0.00 35.30 3.67
4313 8109 7.995289 TGTTTATATATGGCTGAAAGTTGGTG 58.005 34.615 0.00 0.00 35.30 4.17
4316 8112 2.086610 ATGGCTGAAAGTTGGTGGTT 57.913 45.000 0.00 0.00 35.30 3.67
4317 8113 1.859302 TGGCTGAAAGTTGGTGGTTT 58.141 45.000 0.00 0.00 35.30 3.27
4318 8114 1.480137 TGGCTGAAAGTTGGTGGTTTG 59.520 47.619 0.00 0.00 35.30 2.93
4322 8118 3.370672 GCTGAAAGTTGGTGGTTTGTTTG 59.629 43.478 0.00 0.00 35.30 2.93
4323 8119 3.330267 TGAAAGTTGGTGGTTTGTTTGC 58.670 40.909 0.00 0.00 0.00 3.68
4324 8120 3.007398 TGAAAGTTGGTGGTTTGTTTGCT 59.993 39.130 0.00 0.00 0.00 3.91
4325 8121 3.694043 AAGTTGGTGGTTTGTTTGCTT 57.306 38.095 0.00 0.00 0.00 3.91
4326 8122 2.971307 AGTTGGTGGTTTGTTTGCTTG 58.029 42.857 0.00 0.00 0.00 4.01
4327 8123 2.564947 AGTTGGTGGTTTGTTTGCTTGA 59.435 40.909 0.00 0.00 0.00 3.02
4328 8124 3.197549 AGTTGGTGGTTTGTTTGCTTGAT 59.802 39.130 0.00 0.00 0.00 2.57
4330 8126 4.314740 TGGTGGTTTGTTTGCTTGATAC 57.685 40.909 0.00 0.00 0.00 2.24
4331 8127 3.957497 TGGTGGTTTGTTTGCTTGATACT 59.043 39.130 0.00 0.00 0.00 2.12
4374 8226 8.937634 TTTAATTCTAAGTCAATAGGGACGTC 57.062 34.615 7.13 7.13 42.62 4.34
4381 8233 8.844244 TCTAAGTCAATAGGGACGTCTAATTAC 58.156 37.037 16.46 5.81 42.62 1.89
4385 8237 8.316214 AGTCAATAGGGACGTCTAATTACAAAA 58.684 33.333 16.46 0.00 42.62 2.44
4386 8238 8.601476 GTCAATAGGGACGTCTAATTACAAAAG 58.399 37.037 16.46 1.17 0.00 2.27
4391 8243 8.315391 AGGGACGTCTAATTACAAAAGTTAAC 57.685 34.615 16.46 0.00 0.00 2.01
4455 8309 4.514441 GCCATCGATGTGATCATTCTTCTT 59.486 41.667 23.27 0.00 34.13 2.52
4489 8343 9.611284 TTCAATTTCAAATTCTAGAATGTGTCG 57.389 29.630 27.51 15.98 37.32 4.35
4490 8344 8.998377 TCAATTTCAAATTCTAGAATGTGTCGA 58.002 29.630 27.51 17.82 37.32 4.20
4491 8345 9.270576 CAATTTCAAATTCTAGAATGTGTCGAG 57.729 33.333 27.51 15.25 37.32 4.04
4492 8346 7.962964 TTTCAAATTCTAGAATGTGTCGAGT 57.037 32.000 27.51 5.98 37.32 4.18
4493 8347 7.962964 TTCAAATTCTAGAATGTGTCGAGTT 57.037 32.000 27.51 11.05 37.32 3.01
4494 8348 7.582435 TCAAATTCTAGAATGTGTCGAGTTC 57.418 36.000 27.51 0.00 37.32 3.01
4495 8349 7.378966 TCAAATTCTAGAATGTGTCGAGTTCT 58.621 34.615 27.51 4.22 37.32 3.01
4496 8350 7.872993 TCAAATTCTAGAATGTGTCGAGTTCTT 59.127 33.333 27.51 9.40 37.32 2.52
4497 8351 8.499162 CAAATTCTAGAATGTGTCGAGTTCTTT 58.501 33.333 22.77 6.73 32.63 2.52
4498 8352 7.820044 ATTCTAGAATGTGTCGAGTTCTTTC 57.180 36.000 17.26 5.31 34.33 2.62
4527 8381 4.336433 CACCATGGCTTATTTCTACACCTG 59.664 45.833 13.04 0.00 0.00 4.00
4528 8382 3.885297 CCATGGCTTATTTCTACACCTGG 59.115 47.826 0.00 0.00 0.00 4.45
4550 8404 4.468868 GGACCCTAGCTGTTCTTACCTTTA 59.531 45.833 0.00 0.00 0.00 1.85
4551 8405 5.395435 GGACCCTAGCTGTTCTTACCTTTAG 60.395 48.000 0.00 0.00 0.00 1.85
4571 8425 7.168135 CCTTTAGATTCATATTTTTCAAGCGGC 59.832 37.037 0.00 0.00 0.00 6.53
4573 8427 3.518634 TTCATATTTTTCAAGCGGCCC 57.481 42.857 0.00 0.00 0.00 5.80
4575 8429 2.426738 TCATATTTTTCAAGCGGCCCTG 59.573 45.455 0.00 0.00 0.00 4.45
4576 8430 0.530288 TATTTTTCAAGCGGCCCTGC 59.470 50.000 0.00 0.00 0.00 4.85
4585 8439 3.202001 CGGCCCTGCATACGGTTG 61.202 66.667 0.00 0.00 0.00 3.77
4586 8440 3.518068 GGCCCTGCATACGGTTGC 61.518 66.667 0.00 5.02 43.07 4.17
4608 8469 4.701765 CATAGGCTGTCAACTAGCTGAAT 58.298 43.478 0.00 0.00 40.92 2.57
4616 8477 6.039493 GCTGTCAACTAGCTGAATAGTAGGTA 59.961 42.308 0.00 0.00 34.90 3.08
4617 8478 7.569639 TGTCAACTAGCTGAATAGTAGGTAG 57.430 40.000 0.00 9.05 46.43 3.18
4618 8479 6.546403 TGTCAACTAGCTGAATAGTAGGTAGG 59.454 42.308 13.67 0.61 45.71 3.18
4619 8480 6.771749 GTCAACTAGCTGAATAGTAGGTAGGA 59.228 42.308 13.67 2.54 45.71 2.94
4620 8481 6.999272 TCAACTAGCTGAATAGTAGGTAGGAG 59.001 42.308 13.67 7.24 45.71 3.69
4621 8482 6.518516 ACTAGCTGAATAGTAGGTAGGAGT 57.481 41.667 13.67 0.00 45.71 3.85
4622 8483 7.630005 ACTAGCTGAATAGTAGGTAGGAGTA 57.370 40.000 13.67 0.00 45.71 2.59
4638 8499 8.925338 AGGTAGGAGTAGTAAATATCCACAAAG 58.075 37.037 0.00 0.00 34.08 2.77
4639 8500 8.702819 GGTAGGAGTAGTAAATATCCACAAAGT 58.297 37.037 0.00 0.00 34.08 2.66
4653 8514 6.773976 TCCACAAAGTTGAACTTTCAAGAT 57.226 33.333 19.53 0.00 44.47 2.40
4662 8523 6.013293 AGTTGAACTTTCAAGATAGGGCTACT 60.013 38.462 4.61 0.00 46.80 2.57
4665 8526 6.013725 TGAACTTTCAAGATAGGGCTACTGAA 60.014 38.462 0.00 0.00 33.55 3.02
4666 8527 5.983540 ACTTTCAAGATAGGGCTACTGAAG 58.016 41.667 0.00 0.00 0.00 3.02
4670 8531 6.374417 TCAAGATAGGGCTACTGAAGTTTT 57.626 37.500 0.00 0.00 0.00 2.43
4690 8551 7.679783 AGTTTTTCTTCCCCATAAAATTCTGG 58.320 34.615 0.00 0.00 0.00 3.86
4695 8556 8.909423 TTCTTCCCCATAAAATTCTGGTTTAT 57.091 30.769 0.00 0.00 32.58 1.40
4705 8566 3.552604 TTCTGGTTTATGCTGTTTCGC 57.447 42.857 0.00 0.00 0.00 4.70
4706 8567 2.778299 TCTGGTTTATGCTGTTTCGCT 58.222 42.857 0.00 0.00 0.00 4.93
4712 8573 7.282224 TCTGGTTTATGCTGTTTCGCTATTTAT 59.718 33.333 0.00 0.00 0.00 1.40
4749 8610 6.950842 TCTGAATATCTGTGAATGAACAGGT 58.049 36.000 7.90 4.09 46.27 4.00
4814 8675 2.159170 GCTGACTGCTAGGAAGAACGAT 60.159 50.000 0.00 0.00 38.95 3.73
4991 8852 1.067821 GATCCAAGGCAGTACTCGAGG 59.932 57.143 18.41 0.00 0.00 4.63
5119 8983 0.394080 GGAAAGCTCAGCCTCTGCAT 60.394 55.000 0.00 0.00 41.13 3.96
5146 9010 1.673337 GGGGTGCCCGAACTTGTAC 60.673 63.158 0.54 0.00 36.85 2.90
5150 9014 2.357760 GCCCGAACTTGTACGCCA 60.358 61.111 0.00 0.00 0.00 5.69
5181 9046 2.039746 TGGTACAAGGATGGTTGAGTGG 59.960 50.000 0.00 0.00 31.92 4.00
5240 9107 2.579684 GAAATGGTCCGGCTCTCGCT 62.580 60.000 0.00 0.00 37.59 4.93
5246 9113 1.653151 GTCCGGCTCTCGCTTAAATT 58.347 50.000 0.00 0.00 37.59 1.82
5321 9191 4.620086 TTTGTAGGGTAGGAGATGGAGA 57.380 45.455 0.00 0.00 0.00 3.71
5413 9284 6.142817 CGGGAGTTGTAAATGTCTCTTTTTG 58.857 40.000 0.00 0.00 0.00 2.44
5415 9286 6.918022 GGGAGTTGTAAATGTCTCTTTTTGTG 59.082 38.462 0.00 0.00 0.00 3.33
5417 9288 7.973944 GGAGTTGTAAATGTCTCTTTTTGTGTT 59.026 33.333 0.00 0.00 0.00 3.32
5418 9289 9.353999 GAGTTGTAAATGTCTCTTTTTGTGTTT 57.646 29.630 0.00 0.00 0.00 2.83
5420 9291 9.134734 GTTGTAAATGTCTCTTTTTGTGTTTCA 57.865 29.630 0.00 0.00 0.00 2.69
5421 9292 8.682128 TGTAAATGTCTCTTTTTGTGTTTCAC 57.318 30.769 0.00 0.00 34.56 3.18
5422 9293 7.757624 TGTAAATGTCTCTTTTTGTGTTTCACC 59.242 33.333 0.00 0.00 32.73 4.02
5578 9452 1.876497 CGTTTGGGACCTGGCATTGG 61.876 60.000 0.00 0.00 0.00 3.16
5581 9455 0.541764 TTGGGACCTGGCATTGGAAC 60.542 55.000 0.00 0.00 0.00 3.62
5582 9456 1.076549 GGGACCTGGCATTGGAACA 59.923 57.895 0.00 0.00 0.00 3.18
5589 9468 1.236616 TGGCATTGGAACACAGAGCG 61.237 55.000 0.00 0.00 39.29 5.03
5591 9470 1.503542 CATTGGAACACAGAGCGGC 59.496 57.895 0.00 0.00 39.29 6.53
5727 9616 3.200593 GTGGCAGCTGAGGCATCG 61.201 66.667 20.43 0.00 46.23 3.84
5818 9707 4.679373 AATTGGGTGTAATGTTTGCACA 57.321 36.364 9.99 0.00 46.35 4.57
5871 9765 3.004839 GTGACAGATTCATCGGCTAGCTA 59.995 47.826 15.72 3.53 36.32 3.32
5875 9774 3.006323 CAGATTCATCGGCTAGCTAGGTT 59.994 47.826 22.10 0.00 0.00 3.50
5877 9776 0.952280 TCATCGGCTAGCTAGGTTCG 59.048 55.000 22.10 8.59 0.00 3.95
5882 9781 1.403780 CGGCTAGCTAGGTTCGTGTTT 60.404 52.381 22.10 0.00 0.00 2.83
5945 9848 3.733337 ACTAGAAGGAACTGCAACAGTG 58.267 45.455 0.15 0.00 44.62 3.66
5947 9850 3.838244 AGAAGGAACTGCAACAGTGTA 57.162 42.857 0.00 0.00 44.62 2.90
5969 9872 8.118607 GTGTATCTGATAACAACATCACATGTG 58.881 37.037 20.18 20.18 44.07 3.21
6004 9907 0.609131 CAGATCCGGGCCACTGTTTT 60.609 55.000 4.39 0.00 0.00 2.43
6006 9909 1.644786 GATCCGGGCCACTGTTTTCG 61.645 60.000 4.39 0.00 0.00 3.46
6119 10033 2.747822 GCATGTCTGCCTGACTGCG 61.748 63.158 3.32 0.00 45.54 5.18
6147 10061 1.413767 CCTTTCAGTCGCGGTCATCG 61.414 60.000 6.13 0.00 42.76 3.84
6151 10076 1.583967 CAGTCGCGGTCATCGAGTC 60.584 63.158 6.13 0.00 42.43 3.36
6152 10077 2.038837 AGTCGCGGTCATCGAGTCA 61.039 57.895 6.13 0.00 42.43 3.41
6155 10080 1.064134 CGCGGTCATCGAGTCATGA 59.936 57.895 0.00 0.00 42.43 3.07
6156 10081 0.932123 CGCGGTCATCGAGTCATGAG 60.932 60.000 0.00 0.00 42.43 2.90
6157 10082 0.382158 GCGGTCATCGAGTCATGAGA 59.618 55.000 0.00 0.00 42.43 3.27
6158 10083 1.000827 GCGGTCATCGAGTCATGAGAT 60.001 52.381 0.00 0.00 42.43 2.75
6159 10084 2.659387 CGGTCATCGAGTCATGAGATG 58.341 52.381 14.36 14.36 42.43 2.90
6160 10085 2.033927 CGGTCATCGAGTCATGAGATGT 59.966 50.000 18.03 0.00 41.63 3.06
6161 10086 3.489908 CGGTCATCGAGTCATGAGATGTT 60.490 47.826 18.03 0.00 41.63 2.71
6162 10087 4.437239 GGTCATCGAGTCATGAGATGTTT 58.563 43.478 18.03 0.00 41.63 2.83
6180 10105 7.809238 AGATGTTTTGGATCTGGATCTTGATA 58.191 34.615 9.96 0.00 37.92 2.15
6188 10113 9.650714 TTGGATCTGGATCTTGATATTTTTCAT 57.349 29.630 9.96 0.00 37.92 2.57
6209 10137 3.663176 GTGCTGCTGCGCCTTTGA 61.663 61.111 17.42 0.00 43.34 2.69
6216 10144 1.308069 GCTGCGCCTTTGATCTGGAA 61.308 55.000 4.18 0.00 0.00 3.53
6217 10145 0.731417 CTGCGCCTTTGATCTGGAAG 59.269 55.000 4.18 0.00 0.00 3.46
6233 10162 4.019411 TCTGGAAGTAGCAATGATTGGACA 60.019 41.667 7.35 0.00 33.76 4.02
6243 10172 4.142600 GCAATGATTGGACAGTGTTAGGTC 60.143 45.833 7.35 0.00 38.00 3.85
6251 10180 4.030134 GACAGTGTTAGGTCCATAGTCG 57.970 50.000 0.00 0.00 0.00 4.18
6252 10181 3.693085 GACAGTGTTAGGTCCATAGTCGA 59.307 47.826 0.00 0.00 0.00 4.20
6253 10182 3.442977 ACAGTGTTAGGTCCATAGTCGAC 59.557 47.826 7.70 7.70 0.00 4.20
6254 10183 2.681848 AGTGTTAGGTCCATAGTCGACG 59.318 50.000 10.46 0.00 0.00 5.12
6255 10184 2.421424 GTGTTAGGTCCATAGTCGACGT 59.579 50.000 10.46 0.00 33.28 4.34
6256 10185 2.421073 TGTTAGGTCCATAGTCGACGTG 59.579 50.000 10.46 12.96 31.30 4.49
6257 10186 1.671979 TAGGTCCATAGTCGACGTGG 58.328 55.000 27.19 27.19 31.30 4.94
6258 10187 0.034767 AGGTCCATAGTCGACGTGGA 60.035 55.000 29.89 29.89 39.61 4.02
6259 10188 1.030457 GGTCCATAGTCGACGTGGAT 58.970 55.000 33.37 15.97 43.38 3.41
6260 10189 1.001597 GGTCCATAGTCGACGTGGATC 60.002 57.143 33.37 30.96 43.38 3.36
6261 10190 1.001597 GTCCATAGTCGACGTGGATCC 60.002 57.143 33.37 23.52 43.38 3.36
6262 10191 0.040336 CCATAGTCGACGTGGATCCG 60.040 60.000 28.42 9.12 34.94 4.18
6263 10192 0.942252 CATAGTCGACGTGGATCCGA 59.058 55.000 10.46 0.00 0.00 4.55
6264 10193 1.069838 CATAGTCGACGTGGATCCGAG 60.070 57.143 10.46 5.97 32.65 4.63
6265 10194 0.107993 TAGTCGACGTGGATCCGAGT 60.108 55.000 10.46 11.18 39.09 4.18
6266 10195 0.959372 AGTCGACGTGGATCCGAGTT 60.959 55.000 10.46 0.00 32.76 3.01
6267 10196 0.522915 GTCGACGTGGATCCGAGTTC 60.523 60.000 7.39 0.00 32.65 3.01
6268 10197 1.582937 CGACGTGGATCCGAGTTCG 60.583 63.158 7.39 8.73 39.44 3.95
6269 10198 1.505353 GACGTGGATCCGAGTTCGT 59.495 57.895 7.39 12.10 37.74 3.85
6270 10199 0.797249 GACGTGGATCCGAGTTCGTG 60.797 60.000 18.11 1.99 37.74 4.35
6271 10200 1.516386 CGTGGATCCGAGTTCGTGG 60.516 63.158 7.39 0.00 37.74 4.94
6272 10201 1.888018 GTGGATCCGAGTTCGTGGA 59.112 57.895 7.39 0.00 38.95 4.02
6274 10203 0.459899 TGGATCCGAGTTCGTGGATG 59.540 55.000 7.39 0.00 44.92 3.51
6275 10204 0.249489 GGATCCGAGTTCGTGGATGG 60.249 60.000 0.00 0.00 44.92 3.51
6276 10205 0.744874 GATCCGAGTTCGTGGATGGA 59.255 55.000 0.00 0.00 44.92 3.41
6277 10206 1.136305 GATCCGAGTTCGTGGATGGAA 59.864 52.381 0.00 0.00 44.92 3.53
6278 10207 0.530744 TCCGAGTTCGTGGATGGAAG 59.469 55.000 0.48 0.00 37.74 3.46
6279 10208 0.530744 CCGAGTTCGTGGATGGAAGA 59.469 55.000 0.48 0.00 37.74 2.87
6280 10209 1.067142 CCGAGTTCGTGGATGGAAGAA 60.067 52.381 0.48 0.00 37.74 2.52
6281 10210 2.263077 CGAGTTCGTGGATGGAAGAAG 58.737 52.381 0.00 0.00 34.11 2.85
6282 10211 2.352814 CGAGTTCGTGGATGGAAGAAGT 60.353 50.000 0.00 0.00 34.11 3.01
6283 10212 3.665190 GAGTTCGTGGATGGAAGAAGTT 58.335 45.455 0.00 0.00 0.00 2.66
6284 10213 4.617530 CGAGTTCGTGGATGGAAGAAGTTA 60.618 45.833 0.00 0.00 34.11 2.24
6285 10214 5.223449 AGTTCGTGGATGGAAGAAGTTAA 57.777 39.130 0.00 0.00 0.00 2.01
6286 10215 4.995487 AGTTCGTGGATGGAAGAAGTTAAC 59.005 41.667 0.00 0.00 0.00 2.01
6287 10216 4.610605 TCGTGGATGGAAGAAGTTAACA 57.389 40.909 8.61 0.00 0.00 2.41
6288 10217 5.160607 TCGTGGATGGAAGAAGTTAACAT 57.839 39.130 8.61 0.00 0.00 2.71
6289 10218 5.175859 TCGTGGATGGAAGAAGTTAACATC 58.824 41.667 8.61 5.47 37.73 3.06
6290 10219 5.046591 TCGTGGATGGAAGAAGTTAACATCT 60.047 40.000 7.53 7.53 38.33 2.90
6291 10220 5.643777 CGTGGATGGAAGAAGTTAACATCTT 59.356 40.000 22.43 22.43 38.33 2.40
6292 10221 6.183360 CGTGGATGGAAGAAGTTAACATCTTC 60.183 42.308 31.50 31.50 45.07 2.87
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.409064 CAATCTGCAGCCGTACTCCTA 59.591 52.381 9.47 0.00 0.00 2.94
1 2 0.176680 CAATCTGCAGCCGTACTCCT 59.823 55.000 9.47 0.00 0.00 3.69
2 3 1.432270 GCAATCTGCAGCCGTACTCC 61.432 60.000 9.47 0.00 44.26 3.85
3 4 2.009888 GCAATCTGCAGCCGTACTC 58.990 57.895 9.47 0.00 44.26 2.59
23 24 1.064463 TCCCTTGTCAATGCCTCATCC 60.064 52.381 0.00 0.00 0.00 3.51
84 86 3.998156 CTGGTGCATTCAGCTGCT 58.002 55.556 9.47 0.00 45.94 4.24
195 233 8.190784 CAGTTTACTTGACAATTCAACCTCTTT 58.809 33.333 0.00 0.00 36.79 2.52
247 291 9.907576 CACGAATCAGTTTTACAGAGATTAATC 57.092 33.333 7.41 7.41 0.00 1.75
302 349 0.909843 GAAACCGACGACGTATTCCG 59.090 55.000 0.00 0.00 44.03 4.30
344 394 0.890996 GGTTTCCACTGCACAGGAGG 60.891 60.000 2.21 4.01 34.91 4.30
345 395 0.109342 AGGTTTCCACTGCACAGGAG 59.891 55.000 2.21 0.00 34.91 3.69
346 396 1.347707 CTAGGTTTCCACTGCACAGGA 59.652 52.381 2.21 0.00 0.00 3.86
347 397 1.611673 CCTAGGTTTCCACTGCACAGG 60.612 57.143 0.00 0.00 0.00 4.00
384 437 1.525923 CCATGAGCCTCCTGTCCTG 59.474 63.158 0.00 0.00 0.00 3.86
432 812 5.431765 ACCACTAGCCAACTAATCAATCAG 58.568 41.667 0.00 0.00 0.00 2.90
605 2795 5.856126 TGGTTGATTCTTGCGTTTACTAG 57.144 39.130 0.00 0.00 0.00 2.57
720 2948 7.571025 TCCTAAACTGGTTCTAGTTTTGTCTT 58.429 34.615 16.72 0.00 45.85 3.01
732 2961 2.235402 TCCGTCCATCCTAAACTGGTTC 59.765 50.000 0.00 0.00 34.03 3.62
746 2979 3.770040 CGTGATGGCCTCCGTCCA 61.770 66.667 3.32 0.00 38.69 4.02
747 2980 4.530857 CCGTGATGGCCTCCGTCC 62.531 72.222 3.32 0.00 38.69 4.79
786 3024 7.363431 CCTCTTTTTGATGAAACTTGGTACTC 58.637 38.462 0.00 0.00 0.00 2.59
802 3040 6.207417 TCCTCTGTTTTATCTGCCTCTTTTTG 59.793 38.462 0.00 0.00 0.00 2.44
803 3041 6.306987 TCCTCTGTTTTATCTGCCTCTTTTT 58.693 36.000 0.00 0.00 0.00 1.94
808 3059 5.473504 TGTTTTCCTCTGTTTTATCTGCCTC 59.526 40.000 0.00 0.00 0.00 4.70
1042 4697 0.315568 GTGGATCTAGCTAGCACCGG 59.684 60.000 18.83 0.00 0.00 5.28
1405 5089 3.267118 GTATTTCCCGGCGCCGTC 61.267 66.667 43.12 21.37 37.81 4.79
1419 5103 2.056223 CCCGTCCGTCCACAGGTAT 61.056 63.158 0.00 0.00 0.00 2.73
2392 6106 0.322975 CGCTAATGGAGGGAGATGGG 59.677 60.000 0.00 0.00 40.59 4.00
2436 6159 0.250553 TCGAATTCCACGGCCAAAGT 60.251 50.000 2.24 0.00 0.00 2.66
2444 6167 0.650512 CCGGTTGATCGAATTCCACG 59.349 55.000 0.00 0.00 0.00 4.94
2525 6248 2.236395 ACCACTGACAGGGTAATACTGC 59.764 50.000 12.40 0.00 39.55 4.40
2594 6324 1.691434 TGGCCAAACCCACAATTCTTC 59.309 47.619 0.61 0.00 37.83 2.87
2620 6350 2.423538 AGCCTTTGCCATGTATCGAAAC 59.576 45.455 0.00 0.00 38.69 2.78
2635 6365 3.525800 ATCCACAAGGTACAAGCCTTT 57.474 42.857 0.00 0.00 45.91 3.11
2643 6373 5.705441 TGTTGATTGAGAATCCACAAGGTAC 59.295 40.000 0.00 0.00 39.66 3.34
2756 6488 0.110486 GGACCTTGCTTCCCAACTGA 59.890 55.000 0.00 0.00 0.00 3.41
3049 6792 3.957671 AACATGTAATCAGCAGCATCG 57.042 42.857 0.00 0.00 0.00 3.84
3235 6978 8.574737 GCTTCTGGAATTATTTATGATGAAGCT 58.425 33.333 0.82 0.00 45.00 3.74
3283 7026 7.594758 TCAAAAGCATCTGTAATGTTAACAAGC 59.405 33.333 13.23 6.44 0.00 4.01
3293 7036 6.770746 AGCATCTTCAAAAGCATCTGTAAT 57.229 33.333 0.00 0.00 0.00 1.89
3401 7144 5.620206 TCACTAACCTTCTTCTGATTTGCA 58.380 37.500 0.00 0.00 0.00 4.08
3496 7239 9.426837 CAAGTTTTGAACATTGGACATAATGAT 57.573 29.630 5.58 0.00 39.79 2.45
3505 7248 3.431486 GGGTGCAAGTTTTGAACATTGGA 60.431 43.478 2.60 0.00 41.21 3.53
3542 7285 0.179145 CGAACCTGGGTAGTAGTGCG 60.179 60.000 0.00 0.00 0.00 5.34
3613 7356 3.330267 AGACGAGCCTTTCAGATCAAAC 58.670 45.455 0.00 0.00 0.00 2.93
3804 7547 7.765360 ACATTATGGACTAAATGCACAAATTGG 59.235 33.333 0.00 0.00 36.72 3.16
4190 7933 6.154203 TCAAAATTGCATTCCAGTACAACA 57.846 33.333 0.00 0.00 0.00 3.33
4193 7936 5.716228 AGGATCAAAATTGCATTCCAGTACA 59.284 36.000 0.00 0.00 0.00 2.90
4197 7940 5.484715 ACAAGGATCAAAATTGCATTCCAG 58.515 37.500 0.00 6.52 0.00 3.86
4230 8010 5.839063 TGCTAGTATGAAGCCACCTAATACT 59.161 40.000 0.00 0.00 39.30 2.12
4268 8049 5.450818 ACAAAGGGATCCATAAACTAGCA 57.549 39.130 15.23 0.00 0.00 3.49
4277 8058 7.616935 CAGCCATATATAAACAAAGGGATCCAT 59.383 37.037 15.23 2.55 0.00 3.41
4278 8059 6.947733 CAGCCATATATAAACAAAGGGATCCA 59.052 38.462 15.23 0.00 0.00 3.41
4290 8086 7.122715 ACCACCAACTTTCAGCCATATATAAA 58.877 34.615 0.00 0.00 0.00 1.40
4300 8096 2.959507 ACAAACCACCAACTTTCAGC 57.040 45.000 0.00 0.00 0.00 4.26
4302 8098 3.007398 AGCAAACAAACCACCAACTTTCA 59.993 39.130 0.00 0.00 0.00 2.69
4307 8103 2.966050 TCAAGCAAACAAACCACCAAC 58.034 42.857 0.00 0.00 0.00 3.77
4311 8107 5.831997 AGAAGTATCAAGCAAACAAACCAC 58.168 37.500 0.00 0.00 0.00 4.16
4312 8108 6.463995 AAGAAGTATCAAGCAAACAAACCA 57.536 33.333 0.00 0.00 0.00 3.67
4313 8109 7.203218 AGAAAGAAGTATCAAGCAAACAAACC 58.797 34.615 0.00 0.00 0.00 3.27
4316 8112 9.950680 CTTAAGAAAGAAGTATCAAGCAAACAA 57.049 29.630 0.00 0.00 34.37 2.83
4317 8113 8.076178 GCTTAAGAAAGAAGTATCAAGCAAACA 58.924 33.333 6.67 0.00 37.63 2.83
4318 8114 8.076178 TGCTTAAGAAAGAAGTATCAAGCAAAC 58.924 33.333 6.67 0.00 42.82 2.93
4322 8118 6.128172 TGCTGCTTAAGAAAGAAGTATCAAGC 60.128 38.462 6.67 0.00 40.20 4.01
4323 8119 7.369803 TGCTGCTTAAGAAAGAAGTATCAAG 57.630 36.000 6.67 0.00 40.20 3.02
4324 8120 7.928307 ATGCTGCTTAAGAAAGAAGTATCAA 57.072 32.000 6.67 0.00 38.89 2.57
4325 8121 7.928307 AATGCTGCTTAAGAAAGAAGTATCA 57.072 32.000 6.67 0.00 41.46 2.15
4360 8170 8.483307 TTTTGTAATTAGACGTCCCTATTGAC 57.517 34.615 13.01 2.96 0.00 3.18
4361 8171 8.316214 ACTTTTGTAATTAGACGTCCCTATTGA 58.684 33.333 13.01 0.00 0.00 2.57
4362 8172 8.488651 ACTTTTGTAATTAGACGTCCCTATTG 57.511 34.615 13.01 0.08 0.00 1.90
4365 8175 9.423061 GTTAACTTTTGTAATTAGACGTCCCTA 57.577 33.333 13.01 0.00 0.00 3.53
4366 8176 7.933033 TGTTAACTTTTGTAATTAGACGTCCCT 59.067 33.333 13.01 0.00 0.00 4.20
4367 8177 8.086851 TGTTAACTTTTGTAATTAGACGTCCC 57.913 34.615 13.01 0.00 0.00 4.46
4385 8237 9.120538 AGTTGTTATGACTGTTGATTGTTAACT 57.879 29.630 7.22 0.00 0.00 2.24
4386 8238 9.169468 CAGTTGTTATGACTGTTGATTGTTAAC 57.831 33.333 0.00 0.00 39.66 2.01
4391 8243 8.908678 CATTTCAGTTGTTATGACTGTTGATTG 58.091 33.333 4.40 0.00 43.80 2.67
4426 8280 6.487668 AGAATGATCACATCGATGGCATTTAA 59.512 34.615 28.09 8.83 35.50 1.52
4427 8281 5.999600 AGAATGATCACATCGATGGCATTTA 59.000 36.000 28.09 10.98 35.50 1.40
4433 8287 6.259387 TCAAAGAAGAATGATCACATCGATGG 59.741 38.462 28.09 17.13 35.50 3.51
4434 8288 7.124471 GTCAAAGAAGAATGATCACATCGATG 58.876 38.462 23.68 23.68 35.50 3.84
4437 8291 5.583854 AGGTCAAAGAAGAATGATCACATCG 59.416 40.000 0.00 0.00 35.50 3.84
4475 8329 5.856986 CGAAAGAACTCGACACATTCTAGAA 59.143 40.000 7.82 7.82 41.44 2.10
4482 8336 1.792949 GCACGAAAGAACTCGACACAT 59.207 47.619 0.00 0.00 41.44 3.21
4486 8340 0.599204 TGGGCACGAAAGAACTCGAC 60.599 55.000 0.00 0.00 41.44 4.20
4487 8341 0.599204 GTGGGCACGAAAGAACTCGA 60.599 55.000 0.00 0.00 41.44 4.04
4488 8342 1.566018 GGTGGGCACGAAAGAACTCG 61.566 60.000 0.00 0.00 44.50 4.18
4489 8343 0.534203 TGGTGGGCACGAAAGAACTC 60.534 55.000 0.00 0.00 0.00 3.01
4490 8344 0.110486 ATGGTGGGCACGAAAGAACT 59.890 50.000 0.00 0.00 0.00 3.01
4491 8345 0.240945 CATGGTGGGCACGAAAGAAC 59.759 55.000 0.00 0.00 0.00 3.01
4492 8346 0.893270 CCATGGTGGGCACGAAAGAA 60.893 55.000 2.57 0.00 32.67 2.52
4493 8347 1.303236 CCATGGTGGGCACGAAAGA 60.303 57.895 2.57 0.00 32.67 2.52
4494 8348 3.277133 CCATGGTGGGCACGAAAG 58.723 61.111 2.57 0.00 32.67 2.62
4515 8369 2.772515 GCTAGGGTCCAGGTGTAGAAAT 59.227 50.000 0.00 0.00 0.00 2.17
4521 8375 1.158705 ACAGCTAGGGTCCAGGTGT 59.841 57.895 7.97 7.97 46.85 4.16
4527 8381 2.468915 AGGTAAGAACAGCTAGGGTCC 58.531 52.381 0.00 0.00 0.00 4.46
4528 8382 4.554960 AAAGGTAAGAACAGCTAGGGTC 57.445 45.455 0.00 0.00 0.00 4.46
4550 8404 4.202151 GGGCCGCTTGAAAAATATGAATCT 60.202 41.667 0.00 0.00 0.00 2.40
4551 8405 4.051237 GGGCCGCTTGAAAAATATGAATC 58.949 43.478 0.00 0.00 0.00 2.52
4564 8418 3.576356 CGTATGCAGGGCCGCTTG 61.576 66.667 18.47 4.54 0.00 4.01
4569 8423 3.518068 GCAACCGTATGCAGGGCC 61.518 66.667 0.00 0.00 45.70 5.80
4575 8429 0.588252 CAGCCTATGCAACCGTATGC 59.412 55.000 0.00 2.94 46.58 3.14
4576 8430 1.867233 GACAGCCTATGCAACCGTATG 59.133 52.381 0.00 0.00 41.13 2.39
4585 8439 2.159043 TCAGCTAGTTGACAGCCTATGC 60.159 50.000 5.01 0.00 39.99 3.14
4586 8440 3.808466 TCAGCTAGTTGACAGCCTATG 57.192 47.619 5.01 0.00 39.99 2.23
4589 8443 3.772025 ACTATTCAGCTAGTTGACAGCCT 59.228 43.478 9.01 0.00 39.99 4.58
4590 8444 4.130286 ACTATTCAGCTAGTTGACAGCC 57.870 45.455 9.01 0.00 39.99 4.85
4616 8477 8.822805 TCAACTTTGTGGATATTTACTACTCCT 58.177 33.333 0.00 0.00 0.00 3.69
4617 8478 9.444600 TTCAACTTTGTGGATATTTACTACTCC 57.555 33.333 0.00 0.00 0.00 3.85
4638 8499 6.092807 CAGTAGCCCTATCTTGAAAGTTCAAC 59.907 42.308 2.32 0.00 41.88 3.18
4639 8500 6.013725 TCAGTAGCCCTATCTTGAAAGTTCAA 60.014 38.462 6.33 6.33 44.31 2.69
4641 8502 5.978814 TCAGTAGCCCTATCTTGAAAGTTC 58.021 41.667 0.00 0.00 0.00 3.01
4644 8505 5.983540 ACTTCAGTAGCCCTATCTTGAAAG 58.016 41.667 0.00 0.00 0.00 2.62
4665 8526 7.292356 ACCAGAATTTTATGGGGAAGAAAAACT 59.708 33.333 8.69 0.00 43.69 2.66
4666 8527 7.450074 ACCAGAATTTTATGGGGAAGAAAAAC 58.550 34.615 8.69 0.00 43.69 2.43
4670 8531 8.757877 CATAAACCAGAATTTTATGGGGAAGAA 58.242 33.333 8.69 0.00 43.69 2.52
4675 8536 6.127083 ACAGCATAAACCAGAATTTTATGGGG 60.127 38.462 8.69 0.00 43.69 4.96
4676 8537 6.877236 ACAGCATAAACCAGAATTTTATGGG 58.123 36.000 8.69 0.00 43.69 4.00
4677 8538 8.776376 AAACAGCATAAACCAGAATTTTATGG 57.224 30.769 13.84 2.48 43.05 2.74
4678 8539 8.586273 CGAAACAGCATAAACCAGAATTTTATG 58.414 33.333 9.49 9.49 44.54 1.90
4679 8540 7.275560 GCGAAACAGCATAAACCAGAATTTTAT 59.724 33.333 0.00 0.00 37.05 1.40
4686 8547 2.778299 AGCGAAACAGCATAAACCAGA 58.222 42.857 0.00 0.00 40.15 3.86
4690 8551 9.284594 TCAAATAAATAGCGAAACAGCATAAAC 57.715 29.630 0.00 0.00 40.15 2.01
4695 8556 6.735678 TCTCAAATAAATAGCGAAACAGCA 57.264 33.333 0.00 0.00 40.15 4.41
4723 8584 8.708378 ACCTGTTCATTCACAGATATTCAGATA 58.292 33.333 2.32 0.00 46.29 1.98
4734 8595 6.618287 TTTAGACAACCTGTTCATTCACAG 57.382 37.500 0.00 0.00 43.46 3.66
4742 8603 6.851330 CGAGTTTGATTTTAGACAACCTGTTC 59.149 38.462 0.00 0.00 0.00 3.18
4749 8610 5.369833 TGTCCCGAGTTTGATTTTAGACAA 58.630 37.500 0.00 0.00 0.00 3.18
4793 8654 1.202582 TCGTTCTTCCTAGCAGTCAGC 59.797 52.381 0.00 0.00 46.19 4.26
4991 8852 8.743099 GCTTTGTATATGAAATCCTTAAAACGC 58.257 33.333 0.00 0.00 0.00 4.84
5174 9039 2.032528 CGCTGAAGCCCCACTCAA 59.967 61.111 0.00 0.00 37.91 3.02
5270 9137 9.566530 CAGTGAGCTCTATGTATTGTATGTATC 57.433 37.037 16.19 0.00 0.00 2.24
5288 9158 5.305644 CCTACCCTACAAATATCAGTGAGCT 59.694 44.000 0.00 0.00 0.00 4.09
5321 9191 9.388506 CTTGAATCACTAAGTTAACATCTCCAT 57.611 33.333 8.61 0.00 0.00 3.41
5357 9227 1.608283 GCGCTTGGTTACAACTCTCCT 60.608 52.381 0.00 0.00 32.14 3.69
5421 9292 1.147824 CATGCTGCCTACCCTCAGG 59.852 63.158 0.00 0.00 38.86 3.86
5422 9293 0.463295 CACATGCTGCCTACCCTCAG 60.463 60.000 0.00 0.00 0.00 3.35
5578 9452 0.671781 ATCACTGCCGCTCTGTGTTC 60.672 55.000 10.82 0.00 42.88 3.18
5581 9455 2.747822 GCATCACTGCCGCTCTGTG 61.748 63.158 6.54 6.54 42.88 3.66
5582 9456 2.435586 GCATCACTGCCGCTCTGT 60.436 61.111 0.00 0.00 42.88 3.41
5591 9470 3.567164 AGAACAAAACTGAGGCATCACTG 59.433 43.478 0.00 0.00 0.00 3.66
5727 9616 0.387239 GACGGAGCACACAAAATGCC 60.387 55.000 0.00 0.00 44.53 4.40
5871 9765 4.520179 AGGTTAAACTCAAACACGAACCT 58.480 39.130 0.00 0.00 40.22 3.50
5875 9774 7.711772 TCTGATTTAGGTTAAACTCAAACACGA 59.288 33.333 0.00 0.00 0.00 4.35
5877 9776 9.827411 GATCTGATTTAGGTTAAACTCAAACAC 57.173 33.333 0.00 0.00 0.00 3.32
5909 9812 6.349300 TCCTTCTAGTTAGCACATCCAATTC 58.651 40.000 0.00 0.00 0.00 2.17
5919 9822 4.202315 TGTTGCAGTTCCTTCTAGTTAGCA 60.202 41.667 0.00 0.00 0.00 3.49
5920 9823 4.315803 TGTTGCAGTTCCTTCTAGTTAGC 58.684 43.478 0.00 0.00 0.00 3.09
5945 9848 8.201554 ACACATGTGATGTTGTTATCAGATAC 57.798 34.615 31.94 0.00 42.70 2.24
5947 9850 6.317140 GGACACATGTGATGTTGTTATCAGAT 59.683 38.462 31.94 3.39 42.70 2.90
5969 9872 5.641209 CCGGATCTGATTTAGATTGATGGAC 59.359 44.000 2.08 0.00 46.12 4.02
6004 9907 1.164411 CCACAATTAAGCTGTGCCGA 58.836 50.000 12.80 0.00 42.36 5.54
6006 9909 2.736400 GCATCCACAATTAAGCTGTGCC 60.736 50.000 12.80 1.33 42.36 5.01
6119 10033 2.594592 ACTGAAAGGTGCGGCCAC 60.595 61.111 2.24 0.00 39.30 5.01
6147 10061 5.296283 CCAGATCCAAAACATCTCATGACTC 59.704 44.000 0.00 0.00 0.00 3.36
6151 10076 6.062749 AGATCCAGATCCAAAACATCTCATG 58.937 40.000 4.01 0.00 38.58 3.07
6152 10077 6.263412 AGATCCAGATCCAAAACATCTCAT 57.737 37.500 4.01 0.00 38.58 2.90
6155 10080 6.070951 TCAAGATCCAGATCCAAAACATCT 57.929 37.500 4.01 0.00 38.58 2.90
6156 10081 6.956202 ATCAAGATCCAGATCCAAAACATC 57.044 37.500 4.01 0.00 38.58 3.06
6157 10082 9.430399 AAATATCAAGATCCAGATCCAAAACAT 57.570 29.630 4.01 0.00 38.58 2.71
6158 10083 8.827832 AAATATCAAGATCCAGATCCAAAACA 57.172 30.769 4.01 0.00 38.58 2.83
6161 10086 9.478238 TGAAAAATATCAAGATCCAGATCCAAA 57.522 29.630 4.01 0.00 38.58 3.28
6162 10087 9.650714 ATGAAAAATATCAAGATCCAGATCCAA 57.349 29.630 4.01 0.00 38.58 3.53
6180 10105 3.323243 GCAGCAGCACAAGATGAAAAAT 58.677 40.909 0.00 0.00 41.58 1.82
6209 10137 5.128919 GTCCAATCATTGCTACTTCCAGAT 58.871 41.667 0.00 0.00 0.00 2.90
6216 10144 4.292186 ACACTGTCCAATCATTGCTACT 57.708 40.909 0.00 0.00 0.00 2.57
6217 10145 5.065218 CCTAACACTGTCCAATCATTGCTAC 59.935 44.000 0.00 0.00 0.00 3.58
6233 10162 2.681848 CGTCGACTATGGACCTAACACT 59.318 50.000 14.70 0.00 0.00 3.55
6243 10172 0.040336 CGGATCCACGTCGACTATGG 60.040 60.000 23.20 23.20 34.58 2.74
6244 10173 0.942252 TCGGATCCACGTCGACTATG 59.058 55.000 14.70 11.54 34.94 2.23
6245 10174 1.227639 CTCGGATCCACGTCGACTAT 58.772 55.000 14.70 1.67 34.94 2.12
6246 10175 0.107993 ACTCGGATCCACGTCGACTA 60.108 55.000 14.70 0.00 34.94 2.59
6247 10176 0.959372 AACTCGGATCCACGTCGACT 60.959 55.000 14.70 0.00 34.94 4.18
6248 10177 0.522915 GAACTCGGATCCACGTCGAC 60.523 60.000 13.41 5.18 34.94 4.20
6249 10178 1.798735 GAACTCGGATCCACGTCGA 59.201 57.895 13.41 1.48 34.94 4.20
6250 10179 1.582937 CGAACTCGGATCCACGTCG 60.583 63.158 13.41 10.79 35.37 5.12
6251 10180 0.797249 CACGAACTCGGATCCACGTC 60.797 60.000 13.41 2.17 44.95 4.34
6252 10181 1.211969 CACGAACTCGGATCCACGT 59.788 57.895 13.41 11.62 44.95 4.49
6253 10182 1.516386 CCACGAACTCGGATCCACG 60.516 63.158 13.41 11.01 44.95 4.94
6254 10183 0.460311 ATCCACGAACTCGGATCCAC 59.540 55.000 13.41 0.00 44.95 4.02
6255 10184 0.459899 CATCCACGAACTCGGATCCA 59.540 55.000 13.41 0.00 40.12 3.41
6256 10185 0.249489 CCATCCACGAACTCGGATCC 60.249 60.000 0.00 0.00 40.12 3.36
6257 10186 0.744874 TCCATCCACGAACTCGGATC 59.255 55.000 3.88 0.00 40.12 3.36
6258 10187 1.137086 CTTCCATCCACGAACTCGGAT 59.863 52.381 3.88 0.00 42.96 4.18
6259 10188 0.530744 CTTCCATCCACGAACTCGGA 59.469 55.000 3.88 0.00 44.95 4.55
6260 10189 0.530744 TCTTCCATCCACGAACTCGG 59.469 55.000 3.88 0.00 44.95 4.63
6261 10190 2.263077 CTTCTTCCATCCACGAACTCG 58.737 52.381 0.00 0.00 46.33 4.18
6262 10191 3.320673 ACTTCTTCCATCCACGAACTC 57.679 47.619 0.00 0.00 0.00 3.01
6263 10192 3.771577 AACTTCTTCCATCCACGAACT 57.228 42.857 0.00 0.00 0.00 3.01
6264 10193 4.753107 TGTTAACTTCTTCCATCCACGAAC 59.247 41.667 7.22 0.00 0.00 3.95
6265 10194 4.963373 TGTTAACTTCTTCCATCCACGAA 58.037 39.130 7.22 0.00 0.00 3.85
6266 10195 4.610605 TGTTAACTTCTTCCATCCACGA 57.389 40.909 7.22 0.00 0.00 4.35
6267 10196 5.178797 AGATGTTAACTTCTTCCATCCACG 58.821 41.667 16.18 0.00 33.95 4.94
6268 10197 7.078011 GAAGATGTTAACTTCTTCCATCCAC 57.922 40.000 33.60 19.26 44.63 4.02


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

AutoCloner maintained by Alex Coulton.