Multiple sequence alignment - TraesCS7B01G001700

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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 TraesCS7B01G001700 chr7B 100.000 3371 0 0 1 3371 640124 643494 0.000000e+00 6226.0
1 TraesCS7B01G001700 chr7B 96.875 96 1 2 361 455 528017286 528017192 3.480000e-35 159.0
2 TraesCS7B01G001700 chr5D 86.403 2221 143 72 604 2719 562064670 562062504 0.000000e+00 2281.0
3 TraesCS7B01G001700 chr5D 87.368 570 46 15 2821 3371 562062441 562061879 6.140000e-177 630.0
4 TraesCS7B01G001700 chr5D 83.268 257 13 19 2 248 562065370 562065134 3.410000e-50 209.0
5 TraesCS7B01G001700 chr5D 94.175 103 2 4 363 462 312854069 312853968 1.620000e-33 154.0
6 TraesCS7B01G001700 chr5D 88.182 110 4 4 482 591 562065050 562064950 4.570000e-24 122.0
7 TraesCS7B01G001700 chr5B 89.089 1833 115 33 954 2753 712438040 712436260 0.000000e+00 2198.0
8 TraesCS7B01G001700 chr5B 82.456 456 47 15 2750 3189 712435984 712435546 5.310000e-98 368.0
9 TraesCS7B01G001700 chr5B 78.947 228 27 12 528 737 712438567 712438343 5.870000e-28 135.0
10 TraesCS7B01G001700 chr5B 78.829 222 10 17 148 369 712438869 712438685 7.640000e-22 115.0
11 TraesCS7B01G001700 chr5B 96.000 50 2 0 890 939 712438156 712438107 7.750000e-12 82.4
12 TraesCS7B01G001700 chr6A 97.826 92 1 1 363 454 74241833 74241743 1.250000e-34 158.0
13 TraesCS7B01G001700 chr3B 95.876 97 2 2 358 453 20433630 20433725 4.500000e-34 156.0
14 TraesCS7B01G001700 chr3B 92.727 110 5 3 363 472 85623776 85623882 4.500000e-34 156.0
15 TraesCS7B01G001700 chr3B 93.137 102 5 1 365 466 488986800 488986701 7.540000e-32 148.0
16 TraesCS7B01G001700 chr3B 87.705 122 10 5 354 472 13813688 13813807 1.630000e-28 137.0
17 TraesCS7B01G001700 chrUn 93.939 99 6 0 355 453 48472296 48472394 2.100000e-32 150.0
18 TraesCS7B01G001700 chr2A 91.743 109 6 3 349 456 565275802 565275696 7.540000e-32 148.0
19 TraesCS7B01G001700 chr2B 86.869 99 10 3 2660 2755 693095026 693094928 1.280000e-19 108.0
20 TraesCS7B01G001700 chr2D 94.872 39 2 0 2163 2201 120107464 120107426 1.010000e-05 62.1
21 TraesCS7B01G001700 chr1D 94.737 38 2 0 2322 2359 191861268 191861305 3.630000e-05 60.2
22 TraesCS7B01G001700 chr1B 94.737 38 2 0 2322 2359 265648385 265648422 3.630000e-05 60.2
23 TraesCS7B01G001700 chr1A 94.737 38 2 0 2322 2359 237746066 237746103 3.630000e-05 60.2
24 TraesCS7B01G001700 chr4B 92.500 40 3 0 2320 2359 543399191 543399152 1.310000e-04 58.4
25 TraesCS7B01G001700 chr4D 94.286 35 2 0 2325 2359 439291816 439291782 2.000000e-03 54.7
26 TraesCS7B01G001700 chr4A 94.286 35 2 0 2325 2359 28600744 28600710 2.000000e-03 54.7


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 TraesCS7B01G001700 chr7B 640124 643494 3370 False 6226.00 6226 100.00000 1 3371 1 chr7B.!!$F1 3370
1 TraesCS7B01G001700 chr5D 562061879 562065370 3491 True 810.50 2281 86.30525 2 3371 4 chr5D.!!$R2 3369
2 TraesCS7B01G001700 chr5B 712435546 712438869 3323 True 579.68 2198 85.06420 148 3189 5 chr5B.!!$R1 3041

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
373 387 0.106894 GGGTGCTGCATACTACTCCC 59.893 60.0 5.27 6.01 0.0 4.30 F
1107 1581 0.037975 CCCTGCTGTGACCAATTTGC 60.038 55.0 0.00 0.00 0.0 3.68 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1758 2244 0.034767 TCCGTCGGTGGATGTACTCT 60.035 55.0 11.88 0.0 31.53 3.24 R
2835 3661 0.033366 ATTTGCCAACTTTCCACCGC 59.967 50.0 0.00 0.0 0.00 5.68 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
76 84 9.817365 GTATGTATATACATTTGCTCTTGCTTG 57.183 33.333 28.62 0.00 43.99 4.01
79 87 2.433868 ACATTTGCTCTTGCTTGCAG 57.566 45.000 0.00 0.00 40.46 4.41
98 106 2.676839 CAGCACTTGCATAACTCTCTGG 59.323 50.000 3.62 0.00 45.16 3.86
99 107 2.304180 AGCACTTGCATAACTCTCTGGT 59.696 45.455 3.62 0.00 45.16 4.00
100 108 2.675348 GCACTTGCATAACTCTCTGGTC 59.325 50.000 0.00 0.00 41.59 4.02
101 109 3.618507 GCACTTGCATAACTCTCTGGTCT 60.619 47.826 0.00 0.00 41.59 3.85
102 110 4.573900 CACTTGCATAACTCTCTGGTCTT 58.426 43.478 0.00 0.00 0.00 3.01
103 111 4.999950 CACTTGCATAACTCTCTGGTCTTT 59.000 41.667 0.00 0.00 0.00 2.52
104 112 4.999950 ACTTGCATAACTCTCTGGTCTTTG 59.000 41.667 0.00 0.00 0.00 2.77
105 113 3.338249 TGCATAACTCTCTGGTCTTTGC 58.662 45.455 0.00 0.00 0.00 3.68
106 114 3.008375 TGCATAACTCTCTGGTCTTTGCT 59.992 43.478 0.00 0.00 0.00 3.91
107 115 3.620821 GCATAACTCTCTGGTCTTTGCTC 59.379 47.826 0.00 0.00 0.00 4.26
108 116 4.622695 GCATAACTCTCTGGTCTTTGCTCT 60.623 45.833 0.00 0.00 0.00 4.09
109 117 3.676291 AACTCTCTGGTCTTTGCTCTC 57.324 47.619 0.00 0.00 0.00 3.20
110 118 1.899142 ACTCTCTGGTCTTTGCTCTCC 59.101 52.381 0.00 0.00 0.00 3.71
155 163 6.284459 GTGTACTACTGGATACTACGTAGGT 58.716 44.000 25.63 14.26 37.08 3.08
156 164 7.434492 GTGTACTACTGGATACTACGTAGGTA 58.566 42.308 25.63 15.14 37.08 3.08
161 169 8.317679 ACTACTGGATACTACGTAGGTATAAGG 58.682 40.741 25.63 12.32 37.08 2.69
174 182 5.209685 AGGTATAAGGGGAGTATCTAGCC 57.790 47.826 0.00 0.00 33.73 3.93
175 183 3.952967 GGTATAAGGGGAGTATCTAGCCG 59.047 52.174 0.00 0.00 33.73 5.52
176 184 4.324874 GGTATAAGGGGAGTATCTAGCCGA 60.325 50.000 0.00 0.00 33.73 5.54
205 213 8.394971 AGAGAGATTGAGATGTAGACATGTAG 57.605 38.462 0.00 0.00 36.57 2.74
244 258 1.533299 CAATGCAATGCAAAAGCAGCA 59.467 42.857 13.45 6.81 43.62 4.41
245 259 1.438651 ATGCAATGCAAAAGCAGCAG 58.561 45.000 13.45 0.00 46.36 4.24
246 260 1.225376 TGCAATGCAAAAGCAGCAGC 61.225 50.000 5.01 0.00 46.36 5.25
247 261 3.570547 TGCAATGCAAAAGCAGCAGCT 62.571 47.619 5.01 0.00 45.13 4.24
271 285 7.623925 GCTGGTACACTAGCTACGAATATACTC 60.624 44.444 10.16 0.00 45.52 2.59
273 287 7.881751 TGGTACACTAGCTACGAATATACTCAT 59.118 37.037 0.00 0.00 0.00 2.90
276 290 8.392372 ACACTAGCTACGAATATACTCATCAA 57.608 34.615 0.00 0.00 0.00 2.57
277 291 8.291032 ACACTAGCTACGAATATACTCATCAAC 58.709 37.037 0.00 0.00 0.00 3.18
282 296 9.069082 AGCTACGAATATACTCATCAACTTACT 57.931 33.333 0.00 0.00 0.00 2.24
333 347 5.143660 CGATGATGCTAGAAAGACGACTAG 58.856 45.833 0.00 0.00 39.05 2.57
369 383 1.942657 CATGTGGGTGCTGCATACTAC 59.057 52.381 5.27 10.91 0.00 2.73
370 384 1.275666 TGTGGGTGCTGCATACTACT 58.724 50.000 18.87 0.00 0.00 2.57
371 385 1.207089 TGTGGGTGCTGCATACTACTC 59.793 52.381 18.87 3.37 0.00 2.59
372 386 0.830648 TGGGTGCTGCATACTACTCC 59.169 55.000 5.27 0.00 0.00 3.85
373 387 0.106894 GGGTGCTGCATACTACTCCC 59.893 60.000 5.27 6.01 0.00 4.30
374 388 1.123928 GGTGCTGCATACTACTCCCT 58.876 55.000 5.27 0.00 0.00 4.20
375 389 1.069358 GGTGCTGCATACTACTCCCTC 59.931 57.143 5.27 0.00 0.00 4.30
376 390 1.032794 TGCTGCATACTACTCCCTCG 58.967 55.000 0.00 0.00 0.00 4.63
377 391 0.315568 GCTGCATACTACTCCCTCGG 59.684 60.000 0.00 0.00 0.00 4.63
378 392 1.693627 CTGCATACTACTCCCTCGGT 58.306 55.000 0.00 0.00 0.00 4.69
380 394 2.029623 TGCATACTACTCCCTCGGTTC 58.970 52.381 0.00 0.00 0.00 3.62
381 395 1.340568 GCATACTACTCCCTCGGTTCC 59.659 57.143 0.00 0.00 0.00 3.62
382 396 2.662866 CATACTACTCCCTCGGTTCCA 58.337 52.381 0.00 0.00 0.00 3.53
384 398 2.019807 ACTACTCCCTCGGTTCCAAA 57.980 50.000 0.00 0.00 0.00 3.28
385 399 2.332117 ACTACTCCCTCGGTTCCAAAA 58.668 47.619 0.00 0.00 0.00 2.44
386 400 2.910977 ACTACTCCCTCGGTTCCAAAAT 59.089 45.455 0.00 0.00 0.00 1.82
387 401 4.098894 ACTACTCCCTCGGTTCCAAAATA 58.901 43.478 0.00 0.00 0.00 1.40
388 402 3.629142 ACTCCCTCGGTTCCAAAATAG 57.371 47.619 0.00 0.00 0.00 1.73
390 404 3.780850 ACTCCCTCGGTTCCAAAATAGAT 59.219 43.478 0.00 0.00 0.00 1.98
391 405 4.130118 CTCCCTCGGTTCCAAAATAGATG 58.870 47.826 0.00 0.00 0.00 2.90
393 407 3.877508 CCCTCGGTTCCAAAATAGATGAC 59.122 47.826 0.00 0.00 0.00 3.06
394 408 3.877508 CCTCGGTTCCAAAATAGATGACC 59.122 47.826 0.00 0.00 0.00 4.02
395 409 3.877508 CTCGGTTCCAAAATAGATGACCC 59.122 47.826 0.00 0.00 0.00 4.46
396 410 3.264706 TCGGTTCCAAAATAGATGACCCA 59.735 43.478 0.00 0.00 0.00 4.51
397 411 4.013728 CGGTTCCAAAATAGATGACCCAA 58.986 43.478 0.00 0.00 0.00 4.12
399 413 5.016831 GGTTCCAAAATAGATGACCCAACT 58.983 41.667 0.00 0.00 0.00 3.16
400 414 5.480422 GGTTCCAAAATAGATGACCCAACTT 59.520 40.000 0.00 0.00 0.00 2.66
405 419 9.403583 TCCAAAATAGATGACCCAACTTTATAC 57.596 33.333 0.00 0.00 0.00 1.47
406 420 9.408648 CCAAAATAGATGACCCAACTTTATACT 57.591 33.333 0.00 0.00 0.00 2.12
443 457 7.611213 AAGTTGGGTCATCTATTTTAGAACG 57.389 36.000 0.00 0.00 38.50 3.95
444 458 6.113411 AGTTGGGTCATCTATTTTAGAACGG 58.887 40.000 0.00 0.00 38.50 4.44
445 459 5.943349 TGGGTCATCTATTTTAGAACGGA 57.057 39.130 0.00 0.00 38.50 4.69
446 460 5.914033 TGGGTCATCTATTTTAGAACGGAG 58.086 41.667 0.00 0.00 38.50 4.63
447 461 5.163343 TGGGTCATCTATTTTAGAACGGAGG 60.163 44.000 0.00 0.00 38.50 4.30
448 462 5.298347 GGTCATCTATTTTAGAACGGAGGG 58.702 45.833 0.00 0.00 38.50 4.30
449 463 5.070047 GGTCATCTATTTTAGAACGGAGGGA 59.930 44.000 0.00 0.00 38.50 4.20
450 464 6.217294 GTCATCTATTTTAGAACGGAGGGAG 58.783 44.000 0.00 0.00 38.50 4.30
451 465 5.897824 TCATCTATTTTAGAACGGAGGGAGT 59.102 40.000 0.00 0.00 38.50 3.85
452 466 7.014038 GTCATCTATTTTAGAACGGAGGGAGTA 59.986 40.741 0.00 0.00 38.50 2.59
453 467 6.705863 TCTATTTTAGAACGGAGGGAGTAC 57.294 41.667 0.00 0.00 0.00 2.73
454 468 6.430007 TCTATTTTAGAACGGAGGGAGTACT 58.570 40.000 0.00 0.00 0.00 2.73
455 469 7.577303 TCTATTTTAGAACGGAGGGAGTACTA 58.423 38.462 0.00 0.00 0.00 1.82
456 470 5.904362 TTTTAGAACGGAGGGAGTACTAC 57.096 43.478 0.00 0.00 0.00 2.73
457 471 4.574674 TTAGAACGGAGGGAGTACTACA 57.425 45.455 7.57 0.00 0.00 2.74
458 472 3.002038 AGAACGGAGGGAGTACTACAG 57.998 52.381 7.57 0.00 0.00 2.74
459 473 2.308275 AGAACGGAGGGAGTACTACAGT 59.692 50.000 7.57 0.00 0.00 3.55
460 474 3.521126 AGAACGGAGGGAGTACTACAGTA 59.479 47.826 7.57 0.00 0.00 2.74
461 475 4.165758 AGAACGGAGGGAGTACTACAGTAT 59.834 45.833 7.57 0.00 32.54 2.12
462 476 5.367937 AGAACGGAGGGAGTACTACAGTATA 59.632 44.000 7.57 0.00 32.54 1.47
463 477 5.839517 ACGGAGGGAGTACTACAGTATAT 57.160 43.478 7.57 0.00 32.54 0.86
464 478 5.803552 ACGGAGGGAGTACTACAGTATATC 58.196 45.833 7.57 0.00 32.54 1.63
465 479 5.547276 ACGGAGGGAGTACTACAGTATATCT 59.453 44.000 7.57 0.00 32.54 1.98
466 480 6.728164 ACGGAGGGAGTACTACAGTATATCTA 59.272 42.308 7.57 0.00 32.54 1.98
467 481 7.402650 ACGGAGGGAGTACTACAGTATATCTAT 59.597 40.741 7.57 0.00 32.54 1.98
468 482 8.922237 CGGAGGGAGTACTACAGTATATCTATA 58.078 40.741 7.57 0.00 32.54 1.31
511 536 1.409427 GTGGAATCCTCCCTCACGTAG 59.591 57.143 0.00 0.00 41.64 3.51
514 539 2.885894 GGAATCCTCCCTCACGTAGTAG 59.114 54.545 0.00 0.00 34.80 2.57
517 542 4.997545 ATCCTCCCTCACGTAGTAGTAT 57.002 45.455 0.00 0.00 41.61 2.12
519 544 6.639590 ATCCTCCCTCACGTAGTAGTATAT 57.360 41.667 0.00 0.00 41.61 0.86
520 545 6.047511 TCCTCCCTCACGTAGTAGTATATC 57.952 45.833 0.00 0.00 41.61 1.63
521 546 5.784390 TCCTCCCTCACGTAGTAGTATATCT 59.216 44.000 0.00 0.00 41.61 1.98
523 548 6.372103 CCTCCCTCACGTAGTAGTATATCTTG 59.628 46.154 0.00 0.00 41.61 3.02
525 550 7.966812 TCCCTCACGTAGTAGTATATCTTGTA 58.033 38.462 0.00 0.00 41.61 2.41
526 551 8.093307 TCCCTCACGTAGTAGTATATCTTGTAG 58.907 40.741 0.00 0.00 41.61 2.74
595 633 6.770746 TTCTCATCACCAAGTACTAGTACC 57.229 41.667 25.97 11.01 36.75 3.34
596 634 5.823312 TCTCATCACCAAGTACTAGTACCA 58.177 41.667 25.97 7.04 36.75 3.25
597 635 5.651139 TCTCATCACCAAGTACTAGTACCAC 59.349 44.000 25.97 7.75 36.75 4.16
660 989 1.340308 CCATCTCCAACTCCATGCACA 60.340 52.381 0.00 0.00 0.00 4.57
680 1009 1.613836 CCGGCCGGAATAGTAGTAGT 58.386 55.000 41.82 0.00 37.50 2.73
681 1010 2.783135 CCGGCCGGAATAGTAGTAGTA 58.217 52.381 41.82 0.00 37.50 1.82
682 1011 2.485814 CCGGCCGGAATAGTAGTAGTAC 59.514 54.545 41.82 0.00 37.50 2.73
683 1012 3.141398 CGGCCGGAATAGTAGTAGTACA 58.859 50.000 20.10 0.00 0.00 2.90
684 1013 3.755378 CGGCCGGAATAGTAGTAGTACAT 59.245 47.826 20.10 0.00 0.00 2.29
685 1014 4.142730 CGGCCGGAATAGTAGTAGTACATC 60.143 50.000 20.10 5.34 0.00 3.06
686 1015 5.008980 GGCCGGAATAGTAGTAGTACATCT 58.991 45.833 5.05 3.09 0.00 2.90
690 1019 7.551974 GCCGGAATAGTAGTAGTACATCTATCA 59.448 40.741 5.05 0.00 0.00 2.15
761 1111 4.767409 AGCCACCTACCTTTGAATTTCTTC 59.233 41.667 0.00 0.00 0.00 2.87
770 1121 2.729028 TGAATTTCTTCGGGGATCCC 57.271 50.000 23.95 23.95 41.09 3.85
792 1143 3.920231 TCCATATGCTTCTGCTTCTGT 57.080 42.857 0.00 0.00 40.48 3.41
793 1144 4.226427 TCCATATGCTTCTGCTTCTGTT 57.774 40.909 0.00 0.00 40.48 3.16
794 1145 4.194640 TCCATATGCTTCTGCTTCTGTTC 58.805 43.478 0.00 0.00 40.48 3.18
795 1146 4.080695 TCCATATGCTTCTGCTTCTGTTCT 60.081 41.667 0.00 0.00 40.48 3.01
796 1147 4.035324 CCATATGCTTCTGCTTCTGTTCTG 59.965 45.833 0.00 0.00 40.48 3.02
797 1148 2.916702 TGCTTCTGCTTCTGTTCTGA 57.083 45.000 0.00 0.00 40.48 3.27
798 1149 2.763933 TGCTTCTGCTTCTGTTCTGAG 58.236 47.619 0.00 0.00 40.48 3.35
799 1150 2.103771 TGCTTCTGCTTCTGTTCTGAGT 59.896 45.455 0.00 0.00 40.48 3.41
800 1151 3.321968 TGCTTCTGCTTCTGTTCTGAGTA 59.678 43.478 0.00 0.00 40.48 2.59
813 1186 7.539436 TCTGTTCTGAGTAGCACTATAAGTTG 58.461 38.462 0.00 0.00 0.00 3.16
814 1187 6.631016 TGTTCTGAGTAGCACTATAAGTTGG 58.369 40.000 0.00 0.00 0.00 3.77
815 1188 6.436218 TGTTCTGAGTAGCACTATAAGTTGGA 59.564 38.462 0.00 0.00 0.00 3.53
816 1189 6.452494 TCTGAGTAGCACTATAAGTTGGAC 57.548 41.667 0.00 0.00 0.00 4.02
843 1216 3.971702 GCCTCCACACCCCAAGCT 61.972 66.667 0.00 0.00 0.00 3.74
844 1217 2.602676 GCCTCCACACCCCAAGCTA 61.603 63.158 0.00 0.00 0.00 3.32
845 1218 1.604378 CCTCCACACCCCAAGCTAG 59.396 63.158 0.00 0.00 0.00 3.42
846 1219 1.078143 CTCCACACCCCAAGCTAGC 60.078 63.158 6.62 6.62 0.00 3.42
849 1222 1.380302 CACACCCCAAGCTAGCCTT 59.620 57.895 12.13 2.15 0.00 4.35
897 1299 5.590259 GCCTCTAGCAACTCAATTCCATTTA 59.410 40.000 0.00 0.00 42.97 1.40
899 1301 6.238211 CCTCTAGCAACTCAATTCCATTTACG 60.238 42.308 0.00 0.00 0.00 3.18
982 1442 2.733956 AGCTTCACCTCCAACACAAAA 58.266 42.857 0.00 0.00 0.00 2.44
1027 1501 1.450025 GCAAGTAGCCACCAAGGTAC 58.550 55.000 0.00 0.00 40.61 3.34
1028 1502 1.722011 CAAGTAGCCACCAAGGTACG 58.278 55.000 0.00 0.00 40.61 3.67
1032 1506 3.102204 AGTAGCCACCAAGGTACGTAAT 58.898 45.455 0.00 0.00 40.61 1.89
1036 1510 4.256110 AGCCACCAAGGTACGTAATTAAC 58.744 43.478 0.00 0.00 40.61 2.01
1037 1511 4.019950 AGCCACCAAGGTACGTAATTAACT 60.020 41.667 0.00 0.00 40.61 2.24
1041 1515 7.099120 CCACCAAGGTACGTAATTAACTAACT 58.901 38.462 0.00 0.00 0.00 2.24
1042 1516 8.250332 CCACCAAGGTACGTAATTAACTAACTA 58.750 37.037 0.00 0.00 0.00 2.24
1043 1517 9.076596 CACCAAGGTACGTAATTAACTAACTAC 57.923 37.037 0.00 0.00 0.00 2.73
1044 1518 8.802267 ACCAAGGTACGTAATTAACTAACTACA 58.198 33.333 0.00 0.00 0.00 2.74
1045 1519 9.076596 CCAAGGTACGTAATTAACTAACTACAC 57.923 37.037 0.00 0.00 0.00 2.90
1048 1522 9.626045 AGGTACGTAATTAACTAACTACACAAC 57.374 33.333 0.00 0.00 0.00 3.32
1050 1524 7.889589 ACGTAATTAACTAACTACACAACCC 57.110 36.000 0.00 0.00 0.00 4.11
1058 1532 6.947376 ACTAACTACACAACCCCTAATCTT 57.053 37.500 0.00 0.00 0.00 2.40
1060 1534 7.392418 ACTAACTACACAACCCCTAATCTTTC 58.608 38.462 0.00 0.00 0.00 2.62
1061 1535 5.175388 ACTACACAACCCCTAATCTTTCC 57.825 43.478 0.00 0.00 0.00 3.13
1062 1536 4.600111 ACTACACAACCCCTAATCTTTCCA 59.400 41.667 0.00 0.00 0.00 3.53
1064 1538 4.600062 ACACAACCCCTAATCTTTCCATC 58.400 43.478 0.00 0.00 0.00 3.51
1065 1539 4.044065 ACACAACCCCTAATCTTTCCATCA 59.956 41.667 0.00 0.00 0.00 3.07
1066 1540 5.203528 CACAACCCCTAATCTTTCCATCAT 58.796 41.667 0.00 0.00 0.00 2.45
1067 1541 6.069088 ACACAACCCCTAATCTTTCCATCATA 60.069 38.462 0.00 0.00 0.00 2.15
1068 1542 7.006509 CACAACCCCTAATCTTTCCATCATAT 58.993 38.462 0.00 0.00 0.00 1.78
1069 1543 8.163408 CACAACCCCTAATCTTTCCATCATATA 58.837 37.037 0.00 0.00 0.00 0.86
1070 1544 8.164070 ACAACCCCTAATCTTTCCATCATATAC 58.836 37.037 0.00 0.00 0.00 1.47
1072 1546 7.922382 ACCCCTAATCTTTCCATCATATACTG 58.078 38.462 0.00 0.00 0.00 2.74
1091 1565 5.242795 ACTGTATTTGTTACTTGCTCCCT 57.757 39.130 0.00 0.00 0.00 4.20
1094 1568 2.656947 TTTGTTACTTGCTCCCTGCT 57.343 45.000 0.00 0.00 43.37 4.24
1096 1570 0.764890 TGTTACTTGCTCCCTGCTGT 59.235 50.000 0.00 0.00 43.37 4.40
1097 1571 1.160137 GTTACTTGCTCCCTGCTGTG 58.840 55.000 0.00 0.00 43.37 3.66
1098 1572 1.055849 TTACTTGCTCCCTGCTGTGA 58.944 50.000 0.00 0.00 43.37 3.58
1099 1573 0.321671 TACTTGCTCCCTGCTGTGAC 59.678 55.000 0.00 0.00 43.37 3.67
1100 1574 1.673665 CTTGCTCCCTGCTGTGACC 60.674 63.158 0.00 0.00 43.37 4.02
1101 1575 2.401699 CTTGCTCCCTGCTGTGACCA 62.402 60.000 0.00 0.00 43.37 4.02
1102 1576 1.993701 TTGCTCCCTGCTGTGACCAA 61.994 55.000 0.00 0.00 43.37 3.67
1103 1577 1.001641 GCTCCCTGCTGTGACCAAT 60.002 57.895 0.00 0.00 38.95 3.16
1106 1580 1.542915 CTCCCTGCTGTGACCAATTTG 59.457 52.381 0.00 0.00 0.00 2.32
1107 1581 0.037975 CCCTGCTGTGACCAATTTGC 60.038 55.000 0.00 0.00 0.00 3.68
1109 1583 1.603678 CCTGCTGTGACCAATTTGCAC 60.604 52.381 0.00 0.00 0.00 4.57
1110 1584 1.067364 CTGCTGTGACCAATTTGCACA 59.933 47.619 8.81 8.81 39.95 4.57
1112 1586 1.860326 GCTGTGACCAATTTGCACAAC 59.140 47.619 9.96 4.01 41.45 3.32
1114 1588 1.474478 TGTGACCAATTTGCACAACGT 59.526 42.857 7.20 0.00 39.36 3.99
1115 1589 2.683362 TGTGACCAATTTGCACAACGTA 59.317 40.909 7.20 0.00 39.36 3.57
1117 1591 2.946329 TGACCAATTTGCACAACGTACT 59.054 40.909 0.00 0.00 0.00 2.73
1119 1593 4.575236 TGACCAATTTGCACAACGTACTAA 59.425 37.500 0.00 0.00 0.00 2.24
1120 1594 5.103290 ACCAATTTGCACAACGTACTAAG 57.897 39.130 0.00 0.00 0.00 2.18
1122 1596 5.144359 CCAATTTGCACAACGTACTAAGTC 58.856 41.667 0.00 0.00 0.00 3.01
1123 1597 5.144359 CAATTTGCACAACGTACTAAGTCC 58.856 41.667 0.00 0.00 0.00 3.85
1124 1598 3.455990 TTGCACAACGTACTAAGTCCA 57.544 42.857 0.00 0.00 0.00 4.02
1135 1609 6.708285 ACGTACTAAGTCCATCTCCAAATTT 58.292 36.000 0.00 0.00 0.00 1.82
1137 1611 8.483758 ACGTACTAAGTCCATCTCCAAATTTAT 58.516 33.333 0.00 0.00 0.00 1.40
1141 1615 8.214364 ACTAAGTCCATCTCCAAATTTATCCTC 58.786 37.037 0.00 0.00 0.00 3.71
1142 1616 5.946486 AGTCCATCTCCAAATTTATCCTCC 58.054 41.667 0.00 0.00 0.00 4.30
1145 1619 4.106987 CCATCTCCAAATTTATCCTCCCCT 59.893 45.833 0.00 0.00 0.00 4.79
1146 1620 4.796110 TCTCCAAATTTATCCTCCCCTG 57.204 45.455 0.00 0.00 0.00 4.45
1147 1621 3.463329 TCTCCAAATTTATCCTCCCCTGG 59.537 47.826 0.00 0.00 0.00 4.45
1175 1649 0.315251 GAGGCCAACAACAAGGAAGC 59.685 55.000 5.01 0.00 0.00 3.86
1179 1653 1.666888 GCCAACAACAAGGAAGCATCG 60.667 52.381 0.00 0.00 0.00 3.84
1242 1716 1.118838 CGGCAGAGGAGAAGAAGGAT 58.881 55.000 0.00 0.00 0.00 3.24
1296 1770 1.062488 ACAAGGAGGAACCACCAGCT 61.062 55.000 9.72 0.00 42.04 4.24
1533 2019 2.106332 ATCTCGCCTTTACCGCCG 59.894 61.111 0.00 0.00 0.00 6.46
1673 2159 2.026542 AGCTGCAGACCAAGATGATGAA 60.027 45.455 20.43 0.00 0.00 2.57
1689 2175 0.698238 TGAAGATGAAGGGGGTGGTG 59.302 55.000 0.00 0.00 0.00 4.17
1692 2178 0.178861 AGATGAAGGGGGTGGTGAGT 60.179 55.000 0.00 0.00 0.00 3.41
1741 2227 2.264794 CCCTCAGTACCACCGTGC 59.735 66.667 0.00 0.00 0.00 5.34
1749 2235 0.739813 GTACCACCGTGCAGGATGAC 60.740 60.000 8.24 0.00 45.00 3.06
1758 2244 3.261580 CGTGCAGGATGACAAGATTGTA 58.738 45.455 0.00 0.00 42.43 2.41
2070 2562 2.486191 GGAGATGATGAAGCGGATGGTT 60.486 50.000 0.00 0.00 38.83 3.67
2121 2613 0.449388 GCATCCACTACAAGCTGCAC 59.551 55.000 1.02 0.00 0.00 4.57
2219 2735 1.024579 CACAACCCCTACGCCATGAC 61.025 60.000 0.00 0.00 0.00 3.06
2220 2736 1.451387 CAACCCCTACGCCATGACC 60.451 63.158 0.00 0.00 0.00 4.02
2221 2737 1.921346 AACCCCTACGCCATGACCA 60.921 57.895 0.00 0.00 0.00 4.02
2222 2738 1.279025 AACCCCTACGCCATGACCAT 61.279 55.000 0.00 0.00 0.00 3.55
2223 2739 1.227943 CCCCTACGCCATGACCATG 60.228 63.158 0.00 3.11 38.51 3.66
2224 2740 1.695114 CCCCTACGCCATGACCATGA 61.695 60.000 11.28 0.00 41.20 3.07
2355 2871 2.029964 GACGAGAACCCCAACGCA 59.970 61.111 0.00 0.00 0.00 5.24
2399 2927 1.524621 CTCGGATCACCACATGGGC 60.525 63.158 2.32 0.00 42.05 5.36
2494 3022 2.854777 CTCCGATTATATACTGCTGCGC 59.145 50.000 0.00 0.00 0.00 6.09
2635 3168 4.563140 TGGATCGCCCTACTTTTAGTTT 57.437 40.909 0.00 0.00 35.38 2.66
2647 3180 7.136119 CCTACTTTTAGTTTGCGAACAATTCA 58.864 34.615 19.01 0.00 38.26 2.57
2704 3237 9.710900 ATGCTATATTCGTTTGATCTTGTATGA 57.289 29.630 0.00 0.00 0.00 2.15
2746 3279 9.475620 TTTCTTCTAGTTTTTCCTTTTCCTCTT 57.524 29.630 0.00 0.00 0.00 2.85
2747 3280 8.451908 TCTTCTAGTTTTTCCTTTTCCTCTTG 57.548 34.615 0.00 0.00 0.00 3.02
2748 3281 8.053355 TCTTCTAGTTTTTCCTTTTCCTCTTGT 58.947 33.333 0.00 0.00 0.00 3.16
2749 3282 9.338622 CTTCTAGTTTTTCCTTTTCCTCTTGTA 57.661 33.333 0.00 0.00 0.00 2.41
2750 3283 9.862149 TTCTAGTTTTTCCTTTTCCTCTTGTAT 57.138 29.630 0.00 0.00 0.00 2.29
2801 3611 4.300189 GTCACTGAGACATAGCCAGTAG 57.700 50.000 0.15 0.00 46.77 2.57
2802 3612 2.690497 TCACTGAGACATAGCCAGTAGC 59.310 50.000 0.00 0.00 38.93 3.58
2803 3613 2.035632 ACTGAGACATAGCCAGTAGCC 58.964 52.381 0.00 0.00 45.47 3.93
2808 3618 0.541863 ACATAGCCAGTAGCCACACC 59.458 55.000 0.00 0.00 45.47 4.16
2833 3659 7.172190 CCGAAAGAGTATATTGCAACATGATCT 59.828 37.037 0.00 0.62 0.00 2.75
2835 3661 7.741027 AAGAGTATATTGCAACATGATCTGG 57.259 36.000 0.00 0.00 0.00 3.86
2836 3662 5.704515 AGAGTATATTGCAACATGATCTGGC 59.295 40.000 0.00 0.00 0.00 4.85
2861 3687 4.280929 GTGGAAAGTTGGCAAATCCTTACT 59.719 41.667 21.47 5.01 33.72 2.24
2873 3699 5.468409 GCAAATCCTTACTCTTCTAGCCATC 59.532 44.000 0.00 0.00 0.00 3.51
2903 3733 5.378985 TCATTCCTCCTATAAGTCCTACCCT 59.621 44.000 0.00 0.00 0.00 4.34
2908 3738 3.330110 TCCTATAAGTCCTACCCTCTCCG 59.670 52.174 0.00 0.00 0.00 4.63
2953 3786 1.668101 CCTGACCTGTAGCTCGGACC 61.668 65.000 0.00 0.00 0.00 4.46
2954 3787 0.681564 CTGACCTGTAGCTCGGACCT 60.682 60.000 0.00 0.00 0.00 3.85
2996 3829 7.222872 ACTATCTAGAAAGATGCCAAATGGAG 58.777 38.462 2.98 0.00 42.60 3.86
3018 3853 6.227298 AGGATGAAGTGTGAGAATAACGAT 57.773 37.500 0.00 0.00 0.00 3.73
3020 3855 7.429633 AGGATGAAGTGTGAGAATAACGATAG 58.570 38.462 0.00 0.00 46.19 2.08
3026 3861 3.452990 TGTGAGAATAACGATAGGCCCAA 59.547 43.478 0.00 0.00 43.77 4.12
3037 3872 3.507233 CGATAGGCCCAATGTTGCAATAT 59.493 43.478 0.59 1.59 0.00 1.28
3066 3901 5.067273 CGATACCCTGATTCTACTCTGAGT 58.933 45.833 15.57 15.57 0.00 3.41
3072 3907 4.648762 CCTGATTCTACTCTGAGTGGATGT 59.351 45.833 22.14 14.84 35.60 3.06
3079 3914 2.289320 ACTCTGAGTGGATGTTGCTCAC 60.289 50.000 10.00 0.00 35.65 3.51
3092 3927 0.036164 TGCTCACGTGGCCAAACTAT 59.964 50.000 17.00 0.00 0.00 2.12
3103 3938 1.064060 GCCAAACTATAAGCGGTGCTG 59.936 52.381 0.00 0.00 39.62 4.41
3123 3958 1.407437 GGACTCCTTCATGGCGAACAT 60.407 52.381 0.00 0.00 41.57 2.71
3145 3981 1.478654 GGCCTCACCCTCAACTTTGAA 60.479 52.381 0.00 0.00 36.64 2.69
3151 3987 5.068987 CCTCACCCTCAACTTTGAAAAATGA 59.931 40.000 0.00 0.00 36.64 2.57
3155 3991 6.203338 CACCCTCAACTTTGAAAAATGAATGG 59.797 38.462 0.00 6.42 36.64 3.16
3176 4012 1.522668 TGTTCCTCAACATCTTGCCG 58.477 50.000 0.00 0.00 37.61 5.69
3224 4060 4.428845 GGGTGTCCGGTGACTAGA 57.571 61.111 0.00 0.00 42.28 2.43
3226 4062 1.192428 GGGTGTCCGGTGACTAGATT 58.808 55.000 0.00 0.00 42.28 2.40
3235 4071 3.186909 CGGTGACTAGATTTTCGCATCA 58.813 45.455 0.00 0.00 0.00 3.07
3255 4091 2.898472 ATACCTTGGGCTCCCGCTCT 62.898 60.000 0.00 0.00 37.58 4.09
3256 4092 3.721706 CCTTGGGCTCCCGCTCTT 61.722 66.667 0.00 0.00 37.58 2.85
3292 4128 0.176680 ATCGCTGACCTTAGCACCAG 59.823 55.000 0.00 0.00 43.87 4.00
3317 4153 3.591527 AGGTAGGGTTGACAAATGGATCA 59.408 43.478 0.00 0.00 0.00 2.92
3320 4156 3.424703 AGGGTTGACAAATGGATCACTG 58.575 45.455 0.00 0.00 0.00 3.66
3325 4161 2.108075 TGACAAATGGATCACTGGGTGT 59.892 45.455 0.00 0.00 34.79 4.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
26 28 8.415192 ACATTGGTGTACAAATACATAGTACG 57.585 34.615 0.00 0.00 43.21 3.67
29 31 9.899661 ACATACATTGGTGTACAAATACATAGT 57.100 29.630 0.00 0.23 43.21 2.12
54 60 6.728200 TGCAAGCAAGAGCAAATGTATATAC 58.272 36.000 5.89 5.89 45.49 1.47
79 87 2.675348 GACCAGAGAGTTATGCAAGTGC 59.325 50.000 0.00 0.00 42.50 4.40
87 95 4.161377 GGAGAGCAAAGACCAGAGAGTTAT 59.839 45.833 0.00 0.00 0.00 1.89
89 97 2.301583 GGAGAGCAAAGACCAGAGAGTT 59.698 50.000 0.00 0.00 0.00 3.01
90 98 1.899142 GGAGAGCAAAGACCAGAGAGT 59.101 52.381 0.00 0.00 0.00 3.24
91 99 1.898472 TGGAGAGCAAAGACCAGAGAG 59.102 52.381 0.00 0.00 0.00 3.20
92 100 1.620819 GTGGAGAGCAAAGACCAGAGA 59.379 52.381 0.00 0.00 32.89 3.10
93 101 1.671261 CGTGGAGAGCAAAGACCAGAG 60.671 57.143 0.00 0.00 32.89 3.35
94 102 0.318441 CGTGGAGAGCAAAGACCAGA 59.682 55.000 0.00 0.00 32.89 3.86
95 103 0.034059 ACGTGGAGAGCAAAGACCAG 59.966 55.000 0.00 0.00 32.89 4.00
96 104 0.249868 CACGTGGAGAGCAAAGACCA 60.250 55.000 7.95 0.00 0.00 4.02
97 105 0.249911 ACACGTGGAGAGCAAAGACC 60.250 55.000 21.57 0.00 0.00 3.85
98 106 2.059541 GTACACGTGGAGAGCAAAGAC 58.940 52.381 21.57 0.00 0.00 3.01
99 107 1.335597 CGTACACGTGGAGAGCAAAGA 60.336 52.381 21.57 0.00 34.11 2.52
100 108 1.060713 CGTACACGTGGAGAGCAAAG 58.939 55.000 21.57 0.00 34.11 2.77
101 109 3.188773 CGTACACGTGGAGAGCAAA 57.811 52.632 21.57 0.00 34.11 3.68
102 110 4.957266 CGTACACGTGGAGAGCAA 57.043 55.556 21.57 0.00 34.11 3.91
155 163 4.786994 TCTCGGCTAGATACTCCCCTTATA 59.213 45.833 0.00 0.00 0.00 0.98
156 164 3.592427 TCTCGGCTAGATACTCCCCTTAT 59.408 47.826 0.00 0.00 0.00 1.73
161 169 2.303600 TCTCTCTCGGCTAGATACTCCC 59.696 54.545 0.00 0.00 32.41 4.30
174 182 6.146184 GTCTACATCTCAATCTCTCTCTCTCG 59.854 46.154 0.00 0.00 0.00 4.04
175 183 6.992123 TGTCTACATCTCAATCTCTCTCTCTC 59.008 42.308 0.00 0.00 0.00 3.20
176 184 6.899089 TGTCTACATCTCAATCTCTCTCTCT 58.101 40.000 0.00 0.00 0.00 3.10
245 259 3.712091 ATTCGTAGCTAGTGTACCAGC 57.288 47.619 0.00 3.65 38.09 4.85
246 260 7.387122 TGAGTATATTCGTAGCTAGTGTACCAG 59.613 40.741 0.00 0.00 0.00 4.00
247 261 7.219322 TGAGTATATTCGTAGCTAGTGTACCA 58.781 38.462 0.00 0.00 0.00 3.25
248 262 7.664082 TGAGTATATTCGTAGCTAGTGTACC 57.336 40.000 0.00 0.00 0.00 3.34
249 263 8.933807 TGATGAGTATATTCGTAGCTAGTGTAC 58.066 37.037 0.00 0.00 0.00 2.90
250 264 9.498176 TTGATGAGTATATTCGTAGCTAGTGTA 57.502 33.333 0.00 0.00 0.00 2.90
251 265 7.981102 TGATGAGTATATTCGTAGCTAGTGT 57.019 36.000 0.00 0.00 0.00 3.55
252 266 8.508062 AGTTGATGAGTATATTCGTAGCTAGTG 58.492 37.037 0.00 0.00 0.00 2.74
253 267 8.624367 AGTTGATGAGTATATTCGTAGCTAGT 57.376 34.615 0.00 0.00 0.00 2.57
256 270 9.069082 AGTAAGTTGATGAGTATATTCGTAGCT 57.931 33.333 0.00 0.00 0.00 3.32
285 299 8.893727 CGGTCCAAGAATATCTTTATGTTTTCT 58.106 33.333 0.00 0.00 33.78 2.52
286 300 8.889717 TCGGTCCAAGAATATCTTTATGTTTTC 58.110 33.333 0.00 0.00 33.78 2.29
287 301 8.801882 TCGGTCCAAGAATATCTTTATGTTTT 57.198 30.769 0.00 0.00 33.78 2.43
288 302 8.840321 CATCGGTCCAAGAATATCTTTATGTTT 58.160 33.333 0.00 0.00 33.78 2.83
289 303 8.210946 TCATCGGTCCAAGAATATCTTTATGTT 58.789 33.333 0.00 0.00 33.78 2.71
290 304 7.735917 TCATCGGTCCAAGAATATCTTTATGT 58.264 34.615 0.00 0.00 33.78 2.29
291 305 8.663025 CATCATCGGTCCAAGAATATCTTTATG 58.337 37.037 0.00 0.00 33.78 1.90
292 306 7.335422 GCATCATCGGTCCAAGAATATCTTTAT 59.665 37.037 0.00 0.00 33.78 1.40
293 307 6.650807 GCATCATCGGTCCAAGAATATCTTTA 59.349 38.462 0.00 0.00 33.78 1.85
297 311 4.573900 AGCATCATCGGTCCAAGAATATC 58.426 43.478 0.00 0.00 0.00 1.63
309 323 3.046390 GTCGTCTTTCTAGCATCATCGG 58.954 50.000 0.00 0.00 0.00 4.18
333 347 0.095935 CATGCACGCAACTACTCTGC 59.904 55.000 0.00 0.00 36.41 4.26
334 348 1.127397 CACATGCACGCAACTACTCTG 59.873 52.381 0.00 0.00 0.00 3.35
335 349 1.432514 CACATGCACGCAACTACTCT 58.567 50.000 0.00 0.00 0.00 3.24
336 350 0.443869 CCACATGCACGCAACTACTC 59.556 55.000 0.00 0.00 0.00 2.59
337 351 0.955428 CCCACATGCACGCAACTACT 60.955 55.000 0.00 0.00 0.00 2.57
369 383 3.906720 TCTATTTTGGAACCGAGGGAG 57.093 47.619 0.00 0.00 0.00 4.30
370 384 3.778075 TCATCTATTTTGGAACCGAGGGA 59.222 43.478 0.00 0.00 0.00 4.20
371 385 3.877508 GTCATCTATTTTGGAACCGAGGG 59.122 47.826 0.00 0.00 0.00 4.30
372 386 3.877508 GGTCATCTATTTTGGAACCGAGG 59.122 47.826 0.00 0.00 0.00 4.63
373 387 3.877508 GGGTCATCTATTTTGGAACCGAG 59.122 47.826 0.00 0.00 0.00 4.63
374 388 3.264706 TGGGTCATCTATTTTGGAACCGA 59.735 43.478 0.00 0.00 40.06 4.69
375 389 3.616219 TGGGTCATCTATTTTGGAACCG 58.384 45.455 0.00 0.00 40.06 4.44
376 390 5.016831 AGTTGGGTCATCTATTTTGGAACC 58.983 41.667 0.00 0.00 37.64 3.62
377 391 6.590234 AAGTTGGGTCATCTATTTTGGAAC 57.410 37.500 0.00 0.00 0.00 3.62
378 392 8.893563 ATAAAGTTGGGTCATCTATTTTGGAA 57.106 30.769 0.00 0.00 0.00 3.53
380 394 9.408648 AGTATAAAGTTGGGTCATCTATTTTGG 57.591 33.333 0.00 0.00 0.00 3.28
417 431 9.158233 CGTTCTAAAATAGATGACCCAACTTTA 57.842 33.333 0.00 0.00 34.22 1.85
418 432 7.120726 CCGTTCTAAAATAGATGACCCAACTTT 59.879 37.037 0.00 0.00 34.22 2.66
419 433 6.598064 CCGTTCTAAAATAGATGACCCAACTT 59.402 38.462 0.00 0.00 34.22 2.66
420 434 6.070424 TCCGTTCTAAAATAGATGACCCAACT 60.070 38.462 0.00 0.00 34.22 3.16
421 435 6.110707 TCCGTTCTAAAATAGATGACCCAAC 58.889 40.000 0.00 0.00 34.22 3.77
422 436 6.302535 TCCGTTCTAAAATAGATGACCCAA 57.697 37.500 0.00 0.00 34.22 4.12
423 437 5.163343 CCTCCGTTCTAAAATAGATGACCCA 60.163 44.000 0.00 0.00 34.22 4.51
424 438 5.298347 CCTCCGTTCTAAAATAGATGACCC 58.702 45.833 0.00 0.00 34.22 4.46
425 439 5.070047 TCCCTCCGTTCTAAAATAGATGACC 59.930 44.000 0.00 0.00 34.22 4.02
426 440 6.158023 TCCCTCCGTTCTAAAATAGATGAC 57.842 41.667 0.00 0.00 34.22 3.06
427 441 5.897824 ACTCCCTCCGTTCTAAAATAGATGA 59.102 40.000 0.00 0.00 34.22 2.92
428 442 6.163135 ACTCCCTCCGTTCTAAAATAGATG 57.837 41.667 0.00 0.00 34.22 2.90
429 443 7.068061 AGTACTCCCTCCGTTCTAAAATAGAT 58.932 38.462 0.00 0.00 34.22 1.98
430 444 6.430007 AGTACTCCCTCCGTTCTAAAATAGA 58.570 40.000 0.00 0.00 0.00 1.98
431 445 6.712179 AGTACTCCCTCCGTTCTAAAATAG 57.288 41.667 0.00 0.00 0.00 1.73
432 446 7.118723 TGTAGTACTCCCTCCGTTCTAAAATA 58.881 38.462 0.00 0.00 0.00 1.40
433 447 5.954150 TGTAGTACTCCCTCCGTTCTAAAAT 59.046 40.000 0.00 0.00 0.00 1.82
434 448 5.324409 TGTAGTACTCCCTCCGTTCTAAAA 58.676 41.667 0.00 0.00 0.00 1.52
435 449 4.922206 TGTAGTACTCCCTCCGTTCTAAA 58.078 43.478 0.00 0.00 0.00 1.85
436 450 4.018960 ACTGTAGTACTCCCTCCGTTCTAA 60.019 45.833 0.00 0.00 0.00 2.10
437 451 3.521126 ACTGTAGTACTCCCTCCGTTCTA 59.479 47.826 0.00 0.00 0.00 2.10
438 452 2.308275 ACTGTAGTACTCCCTCCGTTCT 59.692 50.000 0.00 0.00 0.00 3.01
439 453 2.720915 ACTGTAGTACTCCCTCCGTTC 58.279 52.381 0.00 0.00 0.00 3.95
440 454 2.895242 ACTGTAGTACTCCCTCCGTT 57.105 50.000 0.00 0.00 0.00 4.44
441 455 5.547276 AGATATACTGTAGTACTCCCTCCGT 59.453 44.000 0.00 0.00 32.72 4.69
442 456 6.052405 AGATATACTGTAGTACTCCCTCCG 57.948 45.833 0.00 0.00 32.72 4.63
469 483 9.728100 TCCACATCCATCCATATGATACTAATA 57.272 33.333 3.65 0.00 34.84 0.98
470 484 8.628368 TCCACATCCATCCATATGATACTAAT 57.372 34.615 3.65 0.00 34.84 1.73
471 485 8.448068 TTCCACATCCATCCATATGATACTAA 57.552 34.615 3.65 0.00 34.84 2.24
474 488 6.769822 GGATTCCACATCCATCCATATGATAC 59.230 42.308 3.65 0.00 37.10 2.24
481 495 2.377869 GGAGGATTCCACATCCATCCAT 59.622 50.000 5.29 0.00 43.45 3.41
482 496 1.776667 GGAGGATTCCACATCCATCCA 59.223 52.381 5.29 0.00 43.45 3.41
492 506 1.006758 ACTACGTGAGGGAGGATTCCA 59.993 52.381 5.29 0.00 45.98 3.53
526 551 9.180678 GCATGTACCAACTGCATAAAATAATAC 57.819 33.333 0.00 0.00 35.96 1.89
600 638 5.008980 ACAAGGACTGGACTAGTGTAGTAC 58.991 45.833 0.00 5.12 40.53 2.73
602 640 4.115398 ACAAGGACTGGACTAGTGTAGT 57.885 45.455 0.00 4.00 40.53 2.73
608 913 4.261197 GCAAACAAACAAGGACTGGACTAG 60.261 45.833 0.00 0.00 0.00 2.57
660 989 1.133668 ACTACTACTATTCCGGCCGGT 60.134 52.381 41.57 27.50 36.47 5.28
679 1008 8.487668 GATGATCGATCGATTGATAGATGTAC 57.512 38.462 29.89 13.81 44.07 2.90
741 1083 4.156008 CCCGAAGAAATTCAAAGGTAGGTG 59.844 45.833 0.00 0.00 0.00 4.00
770 1121 4.197750 ACAGAAGCAGAAGCATATGGAAG 58.802 43.478 4.56 0.00 45.49 3.46
776 1127 4.020751 ACTCAGAACAGAAGCAGAAGCATA 60.021 41.667 0.00 0.00 45.49 3.14
792 1143 6.404403 CGTCCAACTTATAGTGCTACTCAGAA 60.404 42.308 0.00 0.00 0.00 3.02
793 1144 5.066117 CGTCCAACTTATAGTGCTACTCAGA 59.934 44.000 0.00 0.00 0.00 3.27
794 1145 5.274718 CGTCCAACTTATAGTGCTACTCAG 58.725 45.833 0.00 0.00 0.00 3.35
795 1146 4.097437 CCGTCCAACTTATAGTGCTACTCA 59.903 45.833 0.00 0.00 0.00 3.41
796 1147 4.337555 TCCGTCCAACTTATAGTGCTACTC 59.662 45.833 0.00 0.00 0.00 2.59
797 1148 4.097589 GTCCGTCCAACTTATAGTGCTACT 59.902 45.833 0.00 0.00 0.00 2.57
798 1149 4.357996 GTCCGTCCAACTTATAGTGCTAC 58.642 47.826 0.00 0.00 0.00 3.58
799 1150 3.382546 GGTCCGTCCAACTTATAGTGCTA 59.617 47.826 0.00 0.00 35.97 3.49
800 1151 2.167900 GGTCCGTCCAACTTATAGTGCT 59.832 50.000 0.00 0.00 35.97 4.40
813 1186 3.462678 GAGGCAGGAGGTCCGTCC 61.463 72.222 0.00 0.00 42.08 4.79
814 1187 3.462678 GGAGGCAGGAGGTCCGTC 61.463 72.222 0.00 0.00 42.08 4.79
815 1188 4.316823 TGGAGGCAGGAGGTCCGT 62.317 66.667 0.00 0.00 42.08 4.69
816 1189 3.775654 GTGGAGGCAGGAGGTCCG 61.776 72.222 0.00 0.00 42.08 4.79
843 1216 2.105477 GGGAATGAGATGAGCAAGGCTA 59.895 50.000 0.00 0.00 39.88 3.93
844 1217 1.133853 GGGAATGAGATGAGCAAGGCT 60.134 52.381 0.00 0.00 43.88 4.58
845 1218 1.133853 AGGGAATGAGATGAGCAAGGC 60.134 52.381 0.00 0.00 0.00 4.35
846 1219 2.486907 GGAGGGAATGAGATGAGCAAGG 60.487 54.545 0.00 0.00 0.00 3.61
849 1222 1.135094 GGGAGGGAATGAGATGAGCA 58.865 55.000 0.00 0.00 0.00 4.26
850 1223 1.433121 AGGGAGGGAATGAGATGAGC 58.567 55.000 0.00 0.00 0.00 4.26
982 1442 3.323691 CCCATGGTGATGCAATTGATGAT 59.676 43.478 10.34 0.00 0.00 2.45
1027 1501 7.099120 AGGGGTTGTGTAGTTAGTTAATTACG 58.901 38.462 0.00 0.00 32.89 3.18
1028 1502 9.942850 TTAGGGGTTGTGTAGTTAGTTAATTAC 57.057 33.333 0.00 0.00 0.00 1.89
1032 1506 8.439964 AGATTAGGGGTTGTGTAGTTAGTTAA 57.560 34.615 0.00 0.00 0.00 2.01
1036 1510 6.822170 GGAAAGATTAGGGGTTGTGTAGTTAG 59.178 42.308 0.00 0.00 0.00 2.34
1037 1511 6.272792 TGGAAAGATTAGGGGTTGTGTAGTTA 59.727 38.462 0.00 0.00 0.00 2.24
1041 1515 5.251932 TGATGGAAAGATTAGGGGTTGTGTA 59.748 40.000 0.00 0.00 0.00 2.90
1042 1516 4.044065 TGATGGAAAGATTAGGGGTTGTGT 59.956 41.667 0.00 0.00 0.00 3.72
1043 1517 4.599041 TGATGGAAAGATTAGGGGTTGTG 58.401 43.478 0.00 0.00 0.00 3.33
1044 1518 4.946160 TGATGGAAAGATTAGGGGTTGT 57.054 40.909 0.00 0.00 0.00 3.32
1045 1519 8.386264 AGTATATGATGGAAAGATTAGGGGTTG 58.614 37.037 0.00 0.00 0.00 3.77
1048 1522 7.922382 ACAGTATATGATGGAAAGATTAGGGG 58.078 38.462 0.00 0.00 0.00 4.79
1064 1538 8.774586 GGGAGCAAGTAACAAATACAGTATATG 58.225 37.037 0.00 0.00 36.94 1.78
1065 1539 8.714906 AGGGAGCAAGTAACAAATACAGTATAT 58.285 33.333 0.00 0.00 36.94 0.86
1066 1540 7.985184 CAGGGAGCAAGTAACAAATACAGTATA 59.015 37.037 0.00 0.00 36.94 1.47
1067 1541 6.823689 CAGGGAGCAAGTAACAAATACAGTAT 59.176 38.462 0.00 0.00 36.94 2.12
1068 1542 6.170506 CAGGGAGCAAGTAACAAATACAGTA 58.829 40.000 0.00 0.00 36.94 2.74
1069 1543 5.003804 CAGGGAGCAAGTAACAAATACAGT 58.996 41.667 0.00 0.00 36.94 3.55
1070 1544 4.142600 GCAGGGAGCAAGTAACAAATACAG 60.143 45.833 0.00 0.00 44.79 2.74
1072 1546 4.357018 GCAGGGAGCAAGTAACAAATAC 57.643 45.455 0.00 0.00 44.79 1.89
1091 1565 1.109609 TGTGCAAATTGGTCACAGCA 58.890 45.000 6.12 0.00 35.99 4.41
1094 1568 1.474478 ACGTTGTGCAAATTGGTCACA 59.526 42.857 6.12 6.12 38.76 3.58
1096 1570 2.946329 AGTACGTTGTGCAAATTGGTCA 59.054 40.909 0.00 0.00 0.00 4.02
1097 1571 3.619233 AGTACGTTGTGCAAATTGGTC 57.381 42.857 0.00 0.00 0.00 4.02
1098 1572 4.577283 ACTTAGTACGTTGTGCAAATTGGT 59.423 37.500 0.00 0.00 0.00 3.67
1099 1573 5.103290 ACTTAGTACGTTGTGCAAATTGG 57.897 39.130 0.00 0.00 0.00 3.16
1100 1574 5.144359 GGACTTAGTACGTTGTGCAAATTG 58.856 41.667 0.00 0.00 0.00 2.32
1101 1575 4.817464 TGGACTTAGTACGTTGTGCAAATT 59.183 37.500 0.00 0.00 0.00 1.82
1102 1576 4.382291 TGGACTTAGTACGTTGTGCAAAT 58.618 39.130 0.00 0.00 0.00 2.32
1103 1577 3.794717 TGGACTTAGTACGTTGTGCAAA 58.205 40.909 0.00 0.00 0.00 3.68
1106 1580 3.846360 AGATGGACTTAGTACGTTGTGC 58.154 45.455 0.00 0.00 0.00 4.57
1107 1581 4.082408 TGGAGATGGACTTAGTACGTTGTG 60.082 45.833 0.00 0.00 0.00 3.33
1109 1583 4.713824 TGGAGATGGACTTAGTACGTTG 57.286 45.455 0.00 0.00 0.00 4.10
1110 1584 5.733620 TTTGGAGATGGACTTAGTACGTT 57.266 39.130 0.00 0.00 0.00 3.99
1112 1586 8.888579 ATAAATTTGGAGATGGACTTAGTACG 57.111 34.615 0.00 0.00 0.00 3.67
1114 1588 9.225682 AGGATAAATTTGGAGATGGACTTAGTA 57.774 33.333 0.00 0.00 0.00 1.82
1115 1589 8.107196 AGGATAAATTTGGAGATGGACTTAGT 57.893 34.615 0.00 0.00 0.00 2.24
1117 1591 7.421382 GGGAGGATAAATTTGGAGATGGACTTA 60.421 40.741 0.00 0.00 0.00 2.24
1119 1593 5.163045 GGGAGGATAAATTTGGAGATGGACT 60.163 44.000 0.00 0.00 0.00 3.85
1120 1594 5.073428 GGGAGGATAAATTTGGAGATGGAC 58.927 45.833 0.00 0.00 0.00 4.02
1122 1596 4.106987 AGGGGAGGATAAATTTGGAGATGG 59.893 45.833 0.00 0.00 0.00 3.51
1123 1597 5.075493 CAGGGGAGGATAAATTTGGAGATG 58.925 45.833 0.00 0.00 0.00 2.90
1124 1598 4.106987 CCAGGGGAGGATAAATTTGGAGAT 59.893 45.833 0.00 0.00 0.00 2.75
1135 1609 4.399764 CTGCACCAGGGGAGGATA 57.600 61.111 0.00 0.00 0.00 2.59
1145 1619 4.980592 TGGCCTCCTCCTGCACCA 62.981 66.667 3.32 0.00 0.00 4.17
1146 1620 3.650950 TTGGCCTCCTCCTGCACC 61.651 66.667 3.32 0.00 0.00 5.01
1147 1621 2.360475 GTTGGCCTCCTCCTGCAC 60.360 66.667 3.32 0.00 0.00 4.57
1242 1716 2.203337 GGTGGTGGTGCTGCTTCA 60.203 61.111 0.00 0.00 0.00 3.02
1673 2159 0.178861 ACTCACCACCCCCTTCATCT 60.179 55.000 0.00 0.00 0.00 2.90
1689 2175 2.997897 AGGTCCGTCTGGGCACTC 60.998 66.667 0.00 0.00 43.76 3.51
1725 2211 1.079819 CTGCACGGTGGTACTGAGG 60.080 63.158 10.60 0.00 0.00 3.86
1741 2227 6.867550 TGTACTCTACAATCTTGTCATCCTG 58.132 40.000 0.00 0.00 42.35 3.86
1749 2235 5.043903 CGGTGGATGTACTCTACAATCTTG 58.956 45.833 9.71 0.00 42.76 3.02
1758 2244 0.034767 TCCGTCGGTGGATGTACTCT 60.035 55.000 11.88 0.00 31.53 3.24
1810 2296 3.393970 CTTGGGCGGCTCCAGAGA 61.394 66.667 9.56 0.00 38.17 3.10
1956 2448 2.158081 ACCACCTTCCTTCTTCTCCTCT 60.158 50.000 0.00 0.00 0.00 3.69
2268 2784 1.372582 AGCTGTTGTACATCGGCATG 58.627 50.000 30.13 7.92 38.28 4.06
2355 2871 2.373335 AGGACTAGGAGATGACGCAT 57.627 50.000 0.00 0.00 0.00 4.73
2399 2927 0.957395 GCTCATATCCGTGCCATGGG 60.957 60.000 15.13 0.00 0.00 4.00
2408 2936 2.067013 CACATGCTCAGCTCATATCCG 58.933 52.381 0.00 0.00 0.00 4.18
2519 3047 7.982919 TGTCCTTTAATTTCGTAGCTAATAGCA 59.017 33.333 15.28 0.00 45.56 3.49
2520 3048 8.361592 TGTCCTTTAATTTCGTAGCTAATAGC 57.638 34.615 3.66 3.66 42.84 2.97
2529 3057 6.128499 CGTGACCAATGTCCTTTAATTTCGTA 60.128 38.462 0.00 0.00 41.01 3.43
2604 3137 3.806625 AGGGCGATCCATTGATTTTTG 57.193 42.857 0.00 0.00 38.24 2.44
2635 3168 9.853555 AAGAAAATATACATTGAATTGTTCGCA 57.146 25.926 0.00 0.00 0.00 5.10
2663 3196 7.978414 CGAATATAGCATGGACTGAGACATAAT 59.022 37.037 0.00 0.00 0.00 1.28
2704 3237 9.822185 ACTAGAAGAAAATTTTGCACAAATCTT 57.178 25.926 8.47 2.70 32.05 2.40
2749 3282 9.737427 CGAAGTCTTAGTCAAATGTCATAGTAT 57.263 33.333 0.00 0.00 0.00 2.12
2750 3283 8.737175 ACGAAGTCTTAGTCAAATGTCATAGTA 58.263 33.333 0.00 0.00 29.74 1.82
2751 3284 7.603651 ACGAAGTCTTAGTCAAATGTCATAGT 58.396 34.615 0.00 0.00 29.74 2.12
2774 3584 4.106197 GGCTATGTCTCAGTGACTTAACG 58.894 47.826 4.31 0.00 45.54 3.18
2797 3607 1.339097 ACTCTTTCGGTGTGGCTACT 58.661 50.000 0.64 0.00 0.00 2.57
2798 3608 3.521947 ATACTCTTTCGGTGTGGCTAC 57.478 47.619 0.00 0.00 0.00 3.58
2799 3609 5.597806 CAATATACTCTTTCGGTGTGGCTA 58.402 41.667 0.00 0.00 0.00 3.93
2800 3610 4.442706 CAATATACTCTTTCGGTGTGGCT 58.557 43.478 0.00 0.00 0.00 4.75
2801 3611 3.002348 GCAATATACTCTTTCGGTGTGGC 59.998 47.826 0.00 0.00 0.00 5.01
2802 3612 4.188462 TGCAATATACTCTTTCGGTGTGG 58.812 43.478 0.00 0.00 0.00 4.17
2803 3613 5.121611 TGTTGCAATATACTCTTTCGGTGTG 59.878 40.000 0.59 0.00 0.00 3.82
2808 3618 8.008279 CAGATCATGTTGCAATATACTCTTTCG 58.992 37.037 8.49 0.10 0.00 3.46
2833 3659 2.909965 GCCAACTTTCCACCGCCA 60.910 61.111 0.00 0.00 0.00 5.69
2835 3661 0.033366 ATTTGCCAACTTTCCACCGC 59.967 50.000 0.00 0.00 0.00 5.68
2836 3662 1.336795 GGATTTGCCAACTTTCCACCG 60.337 52.381 0.00 0.00 36.34 4.94
2861 3687 1.063942 TGAGGTCGGATGGCTAGAAGA 60.064 52.381 0.00 0.00 0.00 2.87
2873 3699 4.153411 ACTTATAGGAGGAATGAGGTCGG 58.847 47.826 0.00 0.00 0.00 4.79
2903 3733 1.203025 GGAGAGGTATTAGGGCGGAGA 60.203 57.143 0.00 0.00 0.00 3.71
2908 3738 1.621317 GCAGAGGAGAGGTATTAGGGC 59.379 57.143 0.00 0.00 0.00 5.19
2953 3786 9.352784 CTAGATAGTTGTCAACTTTTGAGAGAG 57.647 37.037 22.81 7.04 42.81 3.20
2954 3787 9.078990 TCTAGATAGTTGTCAACTTTTGAGAGA 57.921 33.333 22.81 14.50 42.81 3.10
2982 3815 3.053095 ACTTCATCCTCCATTTGGCATCT 60.053 43.478 0.00 0.00 34.44 2.90
2996 3829 6.642950 CCTATCGTTATTCTCACACTTCATCC 59.357 42.308 0.00 0.00 0.00 3.51
3018 3853 2.364970 GCATATTGCAACATTGGGCCTA 59.635 45.455 0.00 0.00 44.26 3.93
3020 3855 1.585297 GCATATTGCAACATTGGGCC 58.415 50.000 0.00 0.00 44.26 5.80
3026 3861 1.662517 TCGTCCGCATATTGCAACAT 58.337 45.000 0.00 0.00 45.36 2.71
3037 3872 0.387929 GAATCAGGGTATCGTCCGCA 59.612 55.000 0.00 0.00 0.00 5.69
3066 3901 1.965930 GCCACGTGAGCAACATCCA 60.966 57.895 19.30 0.00 0.00 3.41
3072 3907 0.179043 TAGTTTGGCCACGTGAGCAA 60.179 50.000 19.30 9.69 0.00 3.91
3079 3914 0.655733 CCGCTTATAGTTTGGCCACG 59.344 55.000 3.88 1.43 0.00 4.94
3092 3927 1.192146 AAGGAGTCCAGCACCGCTTA 61.192 55.000 12.86 0.00 36.40 3.09
3103 3938 0.036388 TGTTCGCCATGAAGGAGTCC 60.036 55.000 0.00 0.00 41.22 3.85
3123 3958 0.555769 AAAGTTGAGGGTGAGGCCAA 59.444 50.000 5.01 0.00 39.65 4.52
3176 4012 3.064324 AAATGCACAGCCGCCTCC 61.064 61.111 0.00 0.00 0.00 4.30
3191 4027 1.376683 CCCGAAGACCGATGCCAAA 60.377 57.895 0.00 0.00 41.76 3.28
3224 4060 3.181476 GCCCAAGGTATTGATGCGAAAAT 60.181 43.478 0.00 0.00 38.83 1.82
3226 4062 1.748493 GCCCAAGGTATTGATGCGAAA 59.252 47.619 0.00 0.00 38.83 3.46
3255 4091 0.030092 ATCCGGAGATTGAGGGGGAA 60.030 55.000 11.34 0.00 0.00 3.97
3256 4092 0.471971 GATCCGGAGATTGAGGGGGA 60.472 60.000 11.34 0.00 30.90 4.81
3292 4128 5.367945 TCCATTTGTCAACCCTACCTATC 57.632 43.478 0.00 0.00 0.00 2.08
3301 4137 2.493278 CCCAGTGATCCATTTGTCAACC 59.507 50.000 0.00 0.00 0.00 3.77
3317 4153 1.194781 AGCCGATGAGAACACCCAGT 61.195 55.000 0.00 0.00 0.00 4.00
3320 4156 1.450312 CCAGCCGATGAGAACACCC 60.450 63.158 0.00 0.00 0.00 4.61
3325 4161 1.746615 GCTTGCCAGCCGATGAGAA 60.747 57.895 0.00 0.00 40.61 2.87
3343 4192 2.049433 AACGTCGACAAGAGCCCG 60.049 61.111 17.16 0.88 0.00 6.13
3346 4195 1.452399 GAGAACAACGTCGACAAGAGC 59.548 52.381 17.16 0.00 0.00 4.09


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

AutoCloner maintained by Alex Coulton.