Multiple sequence alignment - TraesCS6D01G095100

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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 TraesCS6D01G095100 chr6D 100.000 2546 0 0 1 2546 59337613 59340158 0.000000e+00 4702.0
1 TraesCS6D01G095100 chr6D 87.387 222 14 7 352 561 417519139 417519358 2.530000e-60 243.0
2 TraesCS6D01G095100 chr6D 89.041 73 7 1 481 552 144876574 144876502 3.490000e-14 89.8
3 TraesCS6D01G095100 chr6B 92.680 1612 90 8 939 2526 132711093 132712700 0.000000e+00 2298.0
4 TraesCS6D01G095100 chr6B 91.213 1286 74 8 991 2241 132706443 132707724 0.000000e+00 1712.0
5 TraesCS6D01G095100 chr6A 94.722 720 20 5 939 1651 75371918 75372626 0.000000e+00 1103.0
6 TraesCS6D01G095100 chr6A 90.971 731 41 10 1698 2409 75372636 75373360 0.000000e+00 961.0
7 TraesCS6D01G095100 chr6A 89.157 249 18 6 3 246 75371280 75371524 4.120000e-78 302.0
8 TraesCS6D01G095100 chr7B 87.273 220 17 4 352 561 439648239 439648457 9.100000e-60 241.0
9 TraesCS6D01G095100 chr3B 86.099 223 20 3 352 563 486385190 486385412 1.970000e-56 230.0
10 TraesCS6D01G095100 chr5A 85.068 221 21 5 352 561 456625083 456624864 5.520000e-52 215.0
11 TraesCS6D01G095100 chr5A 83.258 221 25 8 352 561 52739463 52739682 2.580000e-45 193.0
12 TraesCS6D01G095100 chr5A 82.558 172 17 5 352 512 574317693 574317862 3.420000e-29 139.0
13 TraesCS6D01G095100 chr4B 83.784 222 23 5 352 561 663072696 663072916 5.560000e-47 198.0
14 TraesCS6D01G095100 chr3A 85.465 172 13 5 352 512 594979345 594979175 4.360000e-38 169.0
15 TraesCS6D01G095100 chr2B 83.721 172 16 5 352 512 678399207 678399037 4.390000e-33 152.0
16 TraesCS6D01G095100 chr2B 90.909 66 6 0 290 355 678399369 678399304 3.490000e-14 89.8
17 TraesCS6D01G095100 chr7D 76.493 268 39 18 1026 1287 77419061 77418812 9.560000e-25 124.0
18 TraesCS6D01G095100 chr7A 83.704 135 19 3 996 1130 81125319 81125188 9.560000e-25 124.0
19 TraesCS6D01G095100 chr7A 90.141 71 7 0 1019 1089 70819328 70819258 2.700000e-15 93.5
20 TraesCS6D01G095100 chr2D 96.491 57 2 0 842 898 570156991 570156935 7.500000e-16 95.3
21 TraesCS6D01G095100 chr5B 100.000 35 0 0 475 509 656135877 656135911 5.880000e-07 65.8
22 TraesCS6D01G095100 chr1A 100.000 31 0 0 480 510 506495707 506495737 9.840000e-05 58.4


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 TraesCS6D01G095100 chr6D 59337613 59340158 2545 False 4702.000000 4702 100.000000 1 2546 1 chr6D.!!$F1 2545
1 TraesCS6D01G095100 chr6B 132706443 132712700 6257 False 2005.000000 2298 91.946500 939 2526 2 chr6B.!!$F1 1587
2 TraesCS6D01G095100 chr6A 75371280 75373360 2080 False 788.666667 1103 91.616667 3 2409 3 chr6A.!!$F1 2406

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
467 500 0.030908 GCTACTTCGTCCATCTCCCG 59.969 60.0 0.00 0.0 0.0 5.14 F
620 653 0.030908 CCGACGAGGATTCCTGCTAC 59.969 60.0 10.74 0.0 45.0 3.58 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1537 5267 0.176680 GTGCGTCACCATCAGGAGAT 59.823 55.0 0.0 0.0 36.86 2.75 R
2349 6117 0.532573 TGTCTCCTTCCATCGCAGAC 59.467 55.0 0.0 0.0 42.51 3.51 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
31 35 6.946340 TCTGATGCATAGTAGAACTTTCCAA 58.054 36.000 0.00 0.00 0.00 3.53
32 36 7.044181 TCTGATGCATAGTAGAACTTTCCAAG 58.956 38.462 0.00 0.00 0.00 3.61
47 51 6.450545 ACTTTCCAAGTTACCGAGTTAGTAC 58.549 40.000 0.00 0.00 39.04 2.73
88 93 4.824479 TGGACATCTGTCTTGCTTATGA 57.176 40.909 9.98 0.00 44.20 2.15
157 162 2.751806 GCTCTGCCTAGCATTTTGACTT 59.248 45.455 2.69 0.00 42.30 3.01
173 178 7.621832 TTTTGACTTACTTGATTGAAATGCG 57.378 32.000 0.00 0.00 0.00 4.73
178 183 7.333174 TGACTTACTTGATTGAAATGCGTGATA 59.667 33.333 0.00 0.00 0.00 2.15
223 229 9.618410 GTTGTGAGATTAAAACAACGAAAAATG 57.382 29.630 2.52 0.00 42.84 2.32
248 254 8.511321 TGTACATAATTTTGAACTGTGACATCC 58.489 33.333 2.69 0.00 0.00 3.51
252 258 6.423776 AATTTTGAACTGTGACATCCCAAT 57.576 33.333 0.00 0.00 0.00 3.16
264 270 2.292794 ATCCCAATGTCGTAGCGCGT 62.293 55.000 8.43 0.00 42.13 6.01
265 271 2.514013 CCCAATGTCGTAGCGCGTC 61.514 63.158 8.43 0.00 42.13 5.19
268 274 0.227234 CAATGTCGTAGCGCGTCATC 59.773 55.000 8.43 0.00 45.57 2.92
269 275 0.100682 AATGTCGTAGCGCGTCATCT 59.899 50.000 8.43 0.00 45.57 2.90
270 276 0.100682 ATGTCGTAGCGCGTCATCTT 59.899 50.000 8.43 0.00 43.63 2.40
271 277 0.109458 TGTCGTAGCGCGTCATCTTT 60.109 50.000 8.43 0.00 42.13 2.52
272 278 0.989890 GTCGTAGCGCGTCATCTTTT 59.010 50.000 8.43 0.00 42.13 2.27
273 279 1.389106 GTCGTAGCGCGTCATCTTTTT 59.611 47.619 8.43 0.00 42.13 1.94
275 281 1.526986 CGTAGCGCGTCATCTTTTTGG 60.527 52.381 8.43 0.00 35.54 3.28
276 282 1.463444 GTAGCGCGTCATCTTTTTGGT 59.537 47.619 8.43 0.00 0.00 3.67
277 283 1.803334 AGCGCGTCATCTTTTTGGTA 58.197 45.000 8.43 0.00 0.00 3.25
278 284 2.147958 AGCGCGTCATCTTTTTGGTAA 58.852 42.857 8.43 0.00 0.00 2.85
280 286 2.727916 GCGCGTCATCTTTTTGGTAAGG 60.728 50.000 8.43 0.00 0.00 2.69
282 288 3.078837 GCGTCATCTTTTTGGTAAGGGA 58.921 45.455 0.00 0.00 0.00 4.20
283 289 3.504520 GCGTCATCTTTTTGGTAAGGGAA 59.495 43.478 0.00 0.00 0.00 3.97
284 290 4.022676 GCGTCATCTTTTTGGTAAGGGAAA 60.023 41.667 0.00 0.00 0.00 3.13
285 291 5.458015 CGTCATCTTTTTGGTAAGGGAAAC 58.542 41.667 0.00 0.00 0.00 2.78
286 292 5.458015 GTCATCTTTTTGGTAAGGGAAACG 58.542 41.667 0.00 0.00 0.00 3.60
287 293 5.009310 GTCATCTTTTTGGTAAGGGAAACGT 59.991 40.000 0.00 0.00 0.00 3.99
288 294 5.595133 TCATCTTTTTGGTAAGGGAAACGTT 59.405 36.000 0.00 0.00 42.03 3.99
289 295 5.503662 TCTTTTTGGTAAGGGAAACGTTC 57.496 39.130 0.00 0.00 39.53 3.95
296 302 3.733960 GGGAAACGTTCGCTGGGC 61.734 66.667 0.00 0.00 39.31 5.36
298 304 4.084888 GAAACGTTCGCTGGGCCG 62.085 66.667 0.00 0.00 0.00 6.13
331 337 3.082579 GCGAGGCTCCTCCAATCGT 62.083 63.158 9.32 0.00 39.77 3.73
335 341 2.010497 GAGGCTCCTCCAATCGTTTTC 58.990 52.381 2.15 0.00 37.11 2.29
336 342 1.630878 AGGCTCCTCCAATCGTTTTCT 59.369 47.619 0.00 0.00 37.29 2.52
338 344 2.420372 GGCTCCTCCAATCGTTTTCTTC 59.580 50.000 0.00 0.00 34.01 2.87
339 345 3.339141 GCTCCTCCAATCGTTTTCTTCT 58.661 45.455 0.00 0.00 0.00 2.85
344 350 4.563580 CCTCCAATCGTTTTCTTCTCCTGA 60.564 45.833 0.00 0.00 0.00 3.86
347 353 4.319177 CAATCGTTTTCTTCTCCTGAGGT 58.681 43.478 0.00 0.00 0.00 3.85
350 356 2.037251 CGTTTTCTTCTCCTGAGGTGGA 59.963 50.000 0.00 0.00 34.52 4.02
352 358 4.657013 GTTTTCTTCTCCTGAGGTGGATT 58.343 43.478 0.00 0.00 35.30 3.01
354 360 3.481559 TCTTCTCCTGAGGTGGATTCT 57.518 47.619 0.00 0.00 35.30 2.40
356 362 3.772025 TCTTCTCCTGAGGTGGATTCTTC 59.228 47.826 0.00 0.00 35.30 2.87
357 363 2.472029 TCTCCTGAGGTGGATTCTTCC 58.528 52.381 0.00 0.00 42.94 3.46
360 366 1.635487 CCTGAGGTGGATTCTTCCCAA 59.365 52.381 0.00 0.00 41.83 4.12
361 367 2.619074 CCTGAGGTGGATTCTTCCCAAC 60.619 54.545 0.00 0.00 41.83 3.77
364 370 2.130272 GGTGGATTCTTCCCAACTCC 57.870 55.000 0.00 0.00 41.83 3.85
365 371 1.354368 GGTGGATTCTTCCCAACTCCA 59.646 52.381 0.00 0.00 41.83 3.86
368 374 1.354368 GGATTCTTCCCAACTCCACCA 59.646 52.381 0.00 0.00 35.84 4.17
370 376 2.656947 TTCTTCCCAACTCCACCAAG 57.343 50.000 0.00 0.00 0.00 3.61
372 378 0.178992 CTTCCCAACTCCACCAAGCA 60.179 55.000 0.00 0.00 0.00 3.91
373 379 0.178992 TTCCCAACTCCACCAAGCAG 60.179 55.000 0.00 0.00 0.00 4.24
374 380 1.604593 CCCAACTCCACCAAGCAGG 60.605 63.158 0.00 0.00 45.67 4.85
375 381 2.270986 CCAACTCCACCAAGCAGGC 61.271 63.158 0.00 0.00 43.14 4.85
377 383 1.073897 AACTCCACCAAGCAGGCTC 59.926 57.895 0.00 0.00 43.14 4.70
378 384 1.422161 AACTCCACCAAGCAGGCTCT 61.422 55.000 0.00 0.00 43.14 4.09
380 386 1.834856 CTCCACCAAGCAGGCTCTCA 61.835 60.000 0.00 0.00 43.14 3.27
383 389 1.030488 CACCAAGCAGGCTCTCATGG 61.030 60.000 7.92 7.92 43.14 3.66
384 390 2.119655 CCAAGCAGGCTCTCATGGC 61.120 63.158 0.00 0.00 0.00 4.40
385 391 1.378119 CAAGCAGGCTCTCATGGCA 60.378 57.895 0.00 0.00 34.73 4.92
406 439 2.626780 GCCCCAAGCTCGTCCAAAC 61.627 63.158 0.00 0.00 38.99 2.93
409 442 2.556287 CAAGCTCGTCCAAACCGC 59.444 61.111 0.00 0.00 0.00 5.68
410 443 2.668550 AAGCTCGTCCAAACCGCC 60.669 61.111 0.00 0.00 0.00 6.13
411 444 3.469863 AAGCTCGTCCAAACCGCCA 62.470 57.895 0.00 0.00 0.00 5.69
413 446 2.332654 GCTCGTCCAAACCGCCATT 61.333 57.895 0.00 0.00 0.00 3.16
414 447 1.501741 CTCGTCCAAACCGCCATTG 59.498 57.895 0.00 0.00 0.00 2.82
420 453 1.373246 CAAACCGCCATTGGCTGTG 60.373 57.895 23.22 14.66 44.98 3.66
421 454 1.530419 AAACCGCCATTGGCTGTGA 60.530 52.632 23.22 0.00 44.98 3.58
425 458 2.964978 GCCATTGGCTGTGACCAC 59.035 61.111 20.66 0.00 46.69 4.16
426 459 2.639327 GCCATTGGCTGTGACCACC 61.639 63.158 20.66 0.00 46.69 4.61
427 460 2.334946 CCATTGGCTGTGACCACCG 61.335 63.158 0.00 0.00 40.19 4.94
428 461 2.672996 ATTGGCTGTGACCACCGC 60.673 61.111 7.84 7.84 40.19 5.68
433 466 4.363990 CTGTGACCACCGCGAGCT 62.364 66.667 8.23 0.00 0.00 4.09
434 467 2.986979 TGTGACCACCGCGAGCTA 60.987 61.111 8.23 0.00 0.00 3.32
435 468 2.506438 GTGACCACCGCGAGCTAC 60.506 66.667 8.23 0.00 0.00 3.58
437 470 2.102553 GACCACCGCGAGCTACTC 59.897 66.667 8.23 0.00 0.00 2.59
438 471 3.412879 GACCACCGCGAGCTACTCC 62.413 68.421 8.23 0.00 0.00 3.85
439 472 3.449227 CCACCGCGAGCTACTCCA 61.449 66.667 8.23 0.00 0.00 3.86
440 473 2.786495 CCACCGCGAGCTACTCCAT 61.786 63.158 8.23 0.00 0.00 3.41
441 474 1.589993 CACCGCGAGCTACTCCATG 60.590 63.158 8.23 0.00 0.00 3.66
442 475 1.753078 ACCGCGAGCTACTCCATGA 60.753 57.895 8.23 0.00 0.00 3.07
444 477 1.299468 CGCGAGCTACTCCATGACC 60.299 63.158 0.00 0.00 0.00 4.02
446 479 0.528684 GCGAGCTACTCCATGACCAC 60.529 60.000 0.00 0.00 0.00 4.16
448 481 1.202348 CGAGCTACTCCATGACCACAG 60.202 57.143 0.00 0.00 0.00 3.66
449 482 0.539051 AGCTACTCCATGACCACAGC 59.461 55.000 0.00 0.00 0.00 4.40
450 483 0.539051 GCTACTCCATGACCACAGCT 59.461 55.000 0.00 0.00 0.00 4.24
451 484 1.757118 GCTACTCCATGACCACAGCTA 59.243 52.381 0.00 0.00 0.00 3.32
453 486 1.944177 ACTCCATGACCACAGCTACT 58.056 50.000 0.00 0.00 0.00 2.57
455 488 2.234908 ACTCCATGACCACAGCTACTTC 59.765 50.000 0.00 0.00 0.00 3.01
458 491 2.263077 CATGACCACAGCTACTTCGTC 58.737 52.381 0.00 0.00 0.00 4.20
460 493 0.601558 GACCACAGCTACTTCGTCCA 59.398 55.000 0.00 0.00 0.00 4.02
461 494 1.204941 GACCACAGCTACTTCGTCCAT 59.795 52.381 0.00 0.00 0.00 3.41
462 495 1.204941 ACCACAGCTACTTCGTCCATC 59.795 52.381 0.00 0.00 0.00 3.51
463 496 1.478510 CCACAGCTACTTCGTCCATCT 59.521 52.381 0.00 0.00 0.00 2.90
464 497 2.480416 CCACAGCTACTTCGTCCATCTC 60.480 54.545 0.00 0.00 0.00 2.75
467 500 0.030908 GCTACTTCGTCCATCTCCCG 59.969 60.000 0.00 0.00 0.00 5.14
468 501 0.669077 CTACTTCGTCCATCTCCCGG 59.331 60.000 0.00 0.00 0.00 5.73
470 503 2.363795 TTCGTCCATCTCCCGGCT 60.364 61.111 0.00 0.00 0.00 5.52
471 504 2.356818 CTTCGTCCATCTCCCGGCTC 62.357 65.000 0.00 0.00 0.00 4.70
472 505 3.917760 CGTCCATCTCCCGGCTCC 61.918 72.222 0.00 0.00 0.00 4.70
474 507 3.767268 TCCATCTCCCGGCTCCCT 61.767 66.667 0.00 0.00 0.00 4.20
476 509 2.378634 CCATCTCCCGGCTCCCTTT 61.379 63.158 0.00 0.00 0.00 3.11
478 511 0.034089 CATCTCCCGGCTCCCTTTTT 60.034 55.000 0.00 0.00 0.00 1.94
496 529 1.904287 TTTGCTACAACCGGCTTCAT 58.096 45.000 0.00 0.00 0.00 2.57
497 530 1.904287 TTGCTACAACCGGCTTCATT 58.096 45.000 0.00 0.00 0.00 2.57
498 531 1.904287 TGCTACAACCGGCTTCATTT 58.096 45.000 0.00 0.00 0.00 2.32
499 532 2.235016 TGCTACAACCGGCTTCATTTT 58.765 42.857 0.00 0.00 0.00 1.82
500 533 2.625790 TGCTACAACCGGCTTCATTTTT 59.374 40.909 0.00 0.00 0.00 1.94
518 551 1.975660 TTTGCTACAACCGGCTTCTT 58.024 45.000 0.00 0.00 0.00 2.52
540 573 5.828299 TTTTTGCTATAAACCGAGGATGG 57.172 39.130 0.00 0.00 0.00 3.51
541 574 2.543777 TGCTATAAACCGAGGATGGC 57.456 50.000 0.00 0.00 0.00 4.40
543 576 1.000506 GCTATAAACCGAGGATGGCGA 59.999 52.381 0.00 0.00 0.00 5.54
544 577 2.927014 GCTATAAACCGAGGATGGCGAG 60.927 54.545 0.00 0.00 0.00 5.03
545 578 0.249911 ATAAACCGAGGATGGCGAGC 60.250 55.000 0.00 0.00 0.00 5.03
547 580 2.257409 AAACCGAGGATGGCGAGCAT 62.257 55.000 0.00 0.00 0.00 3.79
549 582 2.664185 CGAGGATGGCGAGCATGG 60.664 66.667 0.00 0.00 0.00 3.66
550 583 2.507944 GAGGATGGCGAGCATGGT 59.492 61.111 0.00 0.00 0.00 3.55
551 584 1.890979 GAGGATGGCGAGCATGGTG 60.891 63.158 0.00 0.00 0.00 4.17
555 588 2.874648 GATGGCGAGCATGGTGACCA 62.875 60.000 6.84 6.84 38.19 4.02
556 589 3.127533 GGCGAGCATGGTGACCAC 61.128 66.667 6.40 0.00 35.80 4.16
557 590 3.490759 GCGAGCATGGTGACCACG 61.491 66.667 6.40 7.29 35.80 4.94
558 591 3.490759 CGAGCATGGTGACCACGC 61.491 66.667 15.80 15.80 43.62 5.34
559 592 2.358615 GAGCATGGTGACCACGCA 60.359 61.111 25.35 0.00 45.90 5.24
562 595 3.422303 CATGGTGACCACGCACGG 61.422 66.667 6.40 0.00 39.66 4.94
563 596 3.936203 ATGGTGACCACGCACGGT 61.936 61.111 6.40 0.00 43.91 4.83
564 597 2.575893 ATGGTGACCACGCACGGTA 61.576 57.895 6.40 0.00 40.22 4.02
565 598 2.431942 GGTGACCACGCACGGTAG 60.432 66.667 0.00 0.00 40.22 3.18
567 600 3.299977 TGACCACGCACGGTAGCT 61.300 61.111 0.00 0.00 40.22 3.32
569 602 3.569049 GACCACGCACGGTAGCTGT 62.569 63.158 0.00 0.00 40.22 4.40
570 603 2.203972 GACCACGCACGGTAGCTGTA 62.204 60.000 0.00 0.00 40.22 2.74
571 604 1.080366 CCACGCACGGTAGCTGTAA 60.080 57.895 0.00 0.00 0.00 2.41
572 605 1.076533 CCACGCACGGTAGCTGTAAG 61.077 60.000 0.00 0.00 0.00 2.34
573 606 1.076533 CACGCACGGTAGCTGTAAGG 61.077 60.000 0.00 0.00 0.00 2.69
575 608 0.389426 CGCACGGTAGCTGTAAGGTT 60.389 55.000 0.00 0.00 46.63 3.50
577 610 1.076332 CACGGTAGCTGTAAGGTTGC 58.924 55.000 0.00 0.00 46.63 4.17
578 611 0.682852 ACGGTAGCTGTAAGGTTGCA 59.317 50.000 0.00 0.00 46.63 4.08
579 612 1.278127 ACGGTAGCTGTAAGGTTGCAT 59.722 47.619 0.00 0.00 46.63 3.96
580 613 2.498481 ACGGTAGCTGTAAGGTTGCATA 59.502 45.455 0.00 0.00 46.63 3.14
584 617 2.893637 AGCTGTAAGGTTGCATACGAG 58.106 47.619 0.00 0.00 46.63 4.18
585 618 1.933853 GCTGTAAGGTTGCATACGAGG 59.066 52.381 0.00 0.00 0.00 4.63
586 619 2.677037 GCTGTAAGGTTGCATACGAGGT 60.677 50.000 0.00 0.00 0.00 3.85
587 620 3.596214 CTGTAAGGTTGCATACGAGGTT 58.404 45.455 0.00 0.00 0.00 3.50
588 621 4.000988 CTGTAAGGTTGCATACGAGGTTT 58.999 43.478 0.00 0.00 0.00 3.27
589 622 4.391155 TGTAAGGTTGCATACGAGGTTTT 58.609 39.130 0.00 0.00 0.00 2.43
590 623 4.822896 TGTAAGGTTGCATACGAGGTTTTT 59.177 37.500 0.00 0.00 0.00 1.94
592 625 2.817844 AGGTTGCATACGAGGTTTTTCC 59.182 45.455 0.00 0.00 0.00 3.13
606 639 2.342279 TTCCTGCTGGAACCGACG 59.658 61.111 20.15 0.00 46.57 5.12
607 640 2.204461 TTCCTGCTGGAACCGACGA 61.204 57.895 20.15 0.00 46.57 4.20
608 641 2.125912 CCTGCTGGAACCGACGAG 60.126 66.667 2.92 0.00 34.57 4.18
609 642 3.649277 CCTGCTGGAACCGACGAGG 62.649 68.421 2.92 0.00 40.29 4.63
610 643 2.599281 TGCTGGAACCGACGAGGA 60.599 61.111 8.56 0.00 45.00 3.71
611 644 1.949847 CTGCTGGAACCGACGAGGAT 61.950 60.000 8.56 0.00 45.00 3.24
613 646 0.806492 GCTGGAACCGACGAGGATTC 60.806 60.000 8.56 8.04 45.00 2.52
615 648 0.613853 TGGAACCGACGAGGATTCCT 60.614 55.000 22.08 4.44 45.00 3.36
616 649 0.179108 GGAACCGACGAGGATTCCTG 60.179 60.000 10.74 5.33 45.00 3.86
617 650 0.806492 GAACCGACGAGGATTCCTGC 60.806 60.000 10.74 1.12 45.00 4.85
618 651 1.258445 AACCGACGAGGATTCCTGCT 61.258 55.000 10.74 0.00 45.00 4.24
620 653 0.030908 CCGACGAGGATTCCTGCTAC 59.969 60.000 10.74 0.00 45.00 3.58
621 654 0.738975 CGACGAGGATTCCTGCTACA 59.261 55.000 10.74 0.00 31.76 2.74
622 655 1.134367 CGACGAGGATTCCTGCTACAA 59.866 52.381 10.74 0.00 31.76 2.41
635 668 1.709147 GCTACAAGCACCATGGAGCG 61.709 60.000 25.68 16.30 44.30 5.03
637 670 1.836999 TACAAGCACCATGGAGCGGT 61.837 55.000 27.38 27.38 36.83 5.68
638 671 1.973281 CAAGCACCATGGAGCGGTT 60.973 57.895 25.68 17.59 36.83 4.44
639 672 1.228552 AAGCACCATGGAGCGGTTT 60.229 52.632 25.68 13.86 36.83 3.27
641 674 0.827507 AGCACCATGGAGCGGTTTTT 60.828 50.000 25.68 7.00 36.83 1.94
655 688 4.160928 TTTTTCCGAACACGGGGG 57.839 55.556 8.75 0.00 45.88 5.40
656 689 1.226822 TTTTTCCGAACACGGGGGT 59.773 52.632 8.75 0.00 45.88 4.95
657 690 1.102222 TTTTTCCGAACACGGGGGTG 61.102 55.000 8.75 0.00 45.88 4.61
658 691 2.962142 TTTTCCGAACACGGGGGTGG 62.962 60.000 8.75 0.00 45.88 4.61
659 692 4.938074 TCCGAACACGGGGGTGGA 62.938 66.667 8.75 0.00 45.88 4.02
660 693 4.388499 CCGAACACGGGGGTGGAG 62.388 72.222 0.00 0.00 42.66 3.86
661 694 3.307906 CGAACACGGGGGTGGAGA 61.308 66.667 0.00 0.00 0.00 3.71
662 695 2.656069 CGAACACGGGGGTGGAGAT 61.656 63.158 0.00 0.00 0.00 2.75
663 696 1.683441 GAACACGGGGGTGGAGATT 59.317 57.895 0.00 0.00 0.00 2.40
664 697 0.676782 GAACACGGGGGTGGAGATTG 60.677 60.000 0.00 0.00 0.00 2.67
665 698 1.423794 AACACGGGGGTGGAGATTGT 61.424 55.000 0.00 0.00 0.00 2.71
666 699 1.377202 CACGGGGGTGGAGATTGTG 60.377 63.158 0.00 0.00 0.00 3.33
667 700 2.438434 CGGGGGTGGAGATTGTGC 60.438 66.667 0.00 0.00 0.00 4.57
669 702 2.763215 GGGGTGGAGATTGTGCCA 59.237 61.111 0.00 0.00 0.00 4.92
671 704 1.379044 GGGTGGAGATTGTGCCAGG 60.379 63.158 0.00 0.00 34.22 4.45
673 706 2.048603 GTGGAGATTGTGCCAGGGC 61.049 63.158 2.62 2.62 42.35 5.19
674 707 2.825836 GGAGATTGTGCCAGGGCG 60.826 66.667 5.74 0.00 45.51 6.13
675 708 2.825836 GAGATTGTGCCAGGGCGG 60.826 66.667 5.74 0.00 45.51 6.13
677 710 3.443045 GATTGTGCCAGGGCGGTG 61.443 66.667 5.74 0.00 45.51 4.94
804 837 4.899239 GAGCTGCGGATCACGGGG 62.899 72.222 5.77 0.00 44.51 5.73
810 843 4.899239 CGGATCACGGGGCTGCTC 62.899 72.222 0.00 0.00 39.42 4.26
811 844 3.474570 GGATCACGGGGCTGCTCT 61.475 66.667 0.00 0.00 0.00 4.09
812 845 2.202987 GATCACGGGGCTGCTCTG 60.203 66.667 6.84 6.84 0.00 3.35
816 849 3.790437 ACGGGGCTGCTCTGGATG 61.790 66.667 13.85 0.00 0.00 3.51
817 850 3.473647 CGGGGCTGCTCTGGATGA 61.474 66.667 0.00 0.00 0.00 2.92
818 851 3.001514 GGGGCTGCTCTGGATGAA 58.998 61.111 0.00 0.00 0.00 2.57
819 852 1.452833 GGGGCTGCTCTGGATGAAC 60.453 63.158 0.00 0.00 0.00 3.18
820 853 1.300963 GGGCTGCTCTGGATGAACA 59.699 57.895 0.00 0.00 0.00 3.18
821 854 0.106819 GGGCTGCTCTGGATGAACAT 60.107 55.000 0.00 0.00 0.00 2.71
822 855 1.022735 GGCTGCTCTGGATGAACATG 58.977 55.000 0.00 0.00 0.00 3.21
824 857 0.656259 CTGCTCTGGATGAACATGCG 59.344 55.000 0.00 0.00 31.21 4.73
829 862 2.313717 CTGGATGAACATGCGCCGTG 62.314 60.000 4.18 6.65 31.21 4.94
830 863 2.404789 GATGAACATGCGCCGTGG 59.595 61.111 4.18 0.00 0.00 4.94
831 864 3.739782 GATGAACATGCGCCGTGGC 62.740 63.158 4.18 0.00 37.85 5.01
834 867 3.267597 GAACATGCGCCGTGGCTTT 62.268 57.895 4.18 0.00 39.32 3.51
835 868 2.747507 GAACATGCGCCGTGGCTTTT 62.748 55.000 4.18 0.00 39.32 2.27
836 869 2.049248 CATGCGCCGTGGCTTTTT 60.049 55.556 4.18 0.00 39.32 1.94
868 901 1.160137 CGAAGCAGTTGAGGGAAAGG 58.840 55.000 0.00 0.00 0.00 3.11
869 902 1.543429 CGAAGCAGTTGAGGGAAAGGT 60.543 52.381 0.00 0.00 0.00 3.50
871 904 3.619979 CGAAGCAGTTGAGGGAAAGGTAT 60.620 47.826 0.00 0.00 0.00 2.73
872 905 3.636153 AGCAGTTGAGGGAAAGGTATC 57.364 47.619 0.00 0.00 0.00 2.24
873 906 3.185455 AGCAGTTGAGGGAAAGGTATCT 58.815 45.455 0.00 0.00 0.00 1.98
874 907 3.054802 AGCAGTTGAGGGAAAGGTATCTG 60.055 47.826 0.00 0.00 0.00 2.90
875 908 3.274288 CAGTTGAGGGAAAGGTATCTGC 58.726 50.000 0.00 0.00 0.00 4.26
876 909 2.093447 AGTTGAGGGAAAGGTATCTGCG 60.093 50.000 0.00 0.00 0.00 5.18
877 910 0.830648 TGAGGGAAAGGTATCTGCGG 59.169 55.000 0.00 0.00 0.00 5.69
878 911 0.533085 GAGGGAAAGGTATCTGCGGC 60.533 60.000 0.00 0.00 0.00 6.53
879 912 0.983378 AGGGAAAGGTATCTGCGGCT 60.983 55.000 0.00 0.00 0.00 5.52
880 913 0.756903 GGGAAAGGTATCTGCGGCTA 59.243 55.000 0.00 0.00 0.00 3.93
881 914 1.348036 GGGAAAGGTATCTGCGGCTAT 59.652 52.381 0.00 0.00 0.00 2.97
882 915 2.224548 GGGAAAGGTATCTGCGGCTATT 60.225 50.000 0.00 0.00 0.00 1.73
884 917 4.504340 GGGAAAGGTATCTGCGGCTATTAA 60.504 45.833 0.00 0.00 0.00 1.40
885 918 4.451435 GGAAAGGTATCTGCGGCTATTAAC 59.549 45.833 0.00 0.00 0.00 2.01
886 919 4.682778 AAGGTATCTGCGGCTATTAACA 57.317 40.909 0.00 0.00 0.00 2.41
887 920 4.258702 AGGTATCTGCGGCTATTAACAG 57.741 45.455 0.00 0.00 0.00 3.16
889 922 2.620251 ATCTGCGGCTATTAACAGCA 57.380 45.000 8.22 0.00 43.67 4.41
890 923 2.394930 TCTGCGGCTATTAACAGCAA 57.605 45.000 8.22 0.00 43.67 3.91
891 924 2.705730 TCTGCGGCTATTAACAGCAAA 58.294 42.857 8.22 0.00 43.67 3.68
892 925 3.278574 TCTGCGGCTATTAACAGCAAAT 58.721 40.909 8.22 0.00 43.67 2.32
893 926 3.312421 TCTGCGGCTATTAACAGCAAATC 59.688 43.478 8.22 0.00 43.67 2.17
895 928 2.031683 GCGGCTATTAACAGCAAATCGT 59.968 45.455 8.22 0.00 43.67 3.73
896 929 3.246699 GCGGCTATTAACAGCAAATCGTA 59.753 43.478 8.22 0.00 43.67 3.43
898 931 4.605354 CGGCTATTAACAGCAAATCGTACG 60.605 45.833 9.53 9.53 43.67 3.67
899 932 4.269363 GGCTATTAACAGCAAATCGTACGT 59.731 41.667 16.05 0.00 43.67 3.57
900 933 5.421203 GCTATTAACAGCAAATCGTACGTC 58.579 41.667 16.05 1.04 41.40 4.34
901 934 4.852609 ATTAACAGCAAATCGTACGTCC 57.147 40.909 16.05 0.57 0.00 4.79
902 935 2.157834 AACAGCAAATCGTACGTCCA 57.842 45.000 16.05 0.00 0.00 4.02
903 936 1.425412 ACAGCAAATCGTACGTCCAC 58.575 50.000 16.05 2.71 0.00 4.02
904 937 0.365523 CAGCAAATCGTACGTCCACG 59.634 55.000 16.05 4.49 46.33 4.94
933 966 3.272334 CACCGGCGCCTATTGCTC 61.272 66.667 26.68 0.00 38.05 4.26
934 967 4.891727 ACCGGCGCCTATTGCTCG 62.892 66.667 26.68 8.26 38.05 5.03
938 971 2.029073 GCGCCTATTGCTCGCCTA 59.971 61.111 0.00 0.00 42.71 3.93
939 972 1.374758 GCGCCTATTGCTCGCCTAT 60.375 57.895 0.00 0.00 42.71 2.57
940 973 1.630244 GCGCCTATTGCTCGCCTATG 61.630 60.000 0.00 0.00 42.71 2.23
941 974 0.038251 CGCCTATTGCTCGCCTATGA 60.038 55.000 0.00 0.00 38.05 2.15
942 975 1.404717 CGCCTATTGCTCGCCTATGAT 60.405 52.381 0.00 0.00 38.05 2.45
949 4672 4.600692 TTGCTCGCCTATGATAAAGCTA 57.399 40.909 0.00 0.00 0.00 3.32
955 4678 3.243336 GCCTATGATAAAGCTACCGTCG 58.757 50.000 0.00 0.00 0.00 5.12
1003 4726 4.403432 CCCACAAAGAATCATTAGCCATGT 59.597 41.667 0.00 0.00 34.06 3.21
1673 5420 1.804372 CGGAGATACAAGGAGCTGTGC 60.804 57.143 0.00 0.00 0.00 4.57
1715 5462 1.602237 GCCCGAGATGACCTGGAAA 59.398 57.895 0.00 0.00 0.00 3.13
1778 5525 4.867599 GCGGCTAGGCGCGTTAGT 62.868 66.667 41.74 0.00 40.44 2.24
1798 5545 4.065789 AGTGAATTCTTGAAGTCGTTCCC 58.934 43.478 7.05 0.00 0.00 3.97
1800 5547 1.439679 ATTCTTGAAGTCGTTCCCGC 58.560 50.000 0.00 0.00 0.00 6.13
1825 5572 2.812619 GGCTTCCTGGGGATCTCCG 61.813 68.421 7.25 1.55 36.71 4.63
1902 5649 2.032634 GCGGACGTCATTGAAGGCA 61.033 57.895 18.91 0.00 0.00 4.75
1912 5659 2.577563 TCATTGAAGGCATGAGGAAGGA 59.422 45.455 0.00 0.00 0.00 3.36
2122 5889 3.312697 GGTCTGTTCACAACTTCAGAACC 59.687 47.826 0.00 0.00 40.58 3.62
2148 5915 9.284594 CGAACTTGTTTTGTTTTCTGAGATTTA 57.715 29.630 0.00 0.00 0.00 1.40
2163 5931 8.954950 TCTGAGATTTAGAAGTTTGATGATCC 57.045 34.615 0.00 0.00 0.00 3.36
2190 5958 6.409524 TCCAAAGAGCAGAATGAAAAACAT 57.590 33.333 0.00 0.00 39.69 2.71
2191 5959 6.218019 TCCAAAGAGCAGAATGAAAAACATG 58.782 36.000 0.00 0.00 39.69 3.21
2199 5967 6.147164 AGCAGAATGAAAAACATGCAGATTTG 59.853 34.615 0.00 0.00 39.69 2.32
2205 5973 6.717413 TGAAAAACATGCAGATTTGAAAAGC 58.283 32.000 0.00 0.00 0.00 3.51
2297 6065 3.181487 CGAATTACAAGCAGAAATGGGGG 60.181 47.826 0.00 0.00 0.00 5.40
2301 6069 0.685458 CAAGCAGAAATGGGGGAGGG 60.685 60.000 0.00 0.00 0.00 4.30
2349 6117 1.342082 CGTGGCCACTAGTCGTTTCG 61.342 60.000 32.28 12.39 0.00 3.46
2354 6122 1.337821 CCACTAGTCGTTTCGTCTGC 58.662 55.000 0.00 0.00 0.00 4.26
2407 6177 3.313526 ACACATTCATTAAGCTCATCGGC 59.686 43.478 0.00 0.00 0.00 5.54
2463 6233 0.452184 AGAGATCGTGTGCCACTACG 59.548 55.000 11.78 11.78 41.38 3.51
2510 6280 6.851222 ATAGCAACGAATGATCTTTACTGG 57.149 37.500 0.00 0.00 0.00 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 6.754209 AGTTCTACTATGCATCAGAAAAGACG 59.246 38.462 15.87 0.00 0.00 4.18
1 2 8.485976 AAGTTCTACTATGCATCAGAAAAGAC 57.514 34.615 15.87 7.96 0.00 3.01
7 8 6.544928 TGGAAAGTTCTACTATGCATCAGA 57.455 37.500 0.19 1.59 0.00 3.27
31 35 6.211515 CAACAACTGTACTAACTCGGTAACT 58.788 40.000 0.00 0.00 0.00 2.24
32 36 5.403466 CCAACAACTGTACTAACTCGGTAAC 59.597 44.000 0.00 0.00 0.00 2.50
34 38 4.584325 ACCAACAACTGTACTAACTCGGTA 59.416 41.667 0.00 0.00 0.00 4.02
35 39 3.385755 ACCAACAACTGTACTAACTCGGT 59.614 43.478 0.00 0.00 0.00 4.69
36 40 3.739300 CACCAACAACTGTACTAACTCGG 59.261 47.826 0.00 0.00 0.00 4.63
37 41 4.365723 ACACCAACAACTGTACTAACTCG 58.634 43.478 0.00 0.00 0.00 4.18
38 42 6.509039 CGAAACACCAACAACTGTACTAACTC 60.509 42.308 0.00 0.00 0.00 3.01
39 43 5.292589 CGAAACACCAACAACTGTACTAACT 59.707 40.000 0.00 0.00 0.00 2.24
41 45 5.177326 ACGAAACACCAACAACTGTACTAA 58.823 37.500 0.00 0.00 0.00 2.24
42 46 4.757594 ACGAAACACCAACAACTGTACTA 58.242 39.130 0.00 0.00 0.00 1.82
43 47 3.602483 ACGAAACACCAACAACTGTACT 58.398 40.909 0.00 0.00 0.00 2.73
47 51 3.366422 CCAAAACGAAACACCAACAACTG 59.634 43.478 0.00 0.00 0.00 3.16
88 93 2.287788 CCGCACATTCAGCAGAAAACTT 60.288 45.455 0.00 0.00 37.29 2.66
143 148 9.897744 TTTCAATCAAGTAAGTCAAAATGCTAG 57.102 29.630 0.00 0.00 0.00 3.42
149 154 7.167302 CACGCATTTCAATCAAGTAAGTCAAAA 59.833 33.333 0.00 0.00 0.00 2.44
153 158 5.927030 TCACGCATTTCAATCAAGTAAGTC 58.073 37.500 0.00 0.00 0.00 3.01
157 162 9.487790 TCATATATCACGCATTTCAATCAAGTA 57.512 29.630 0.00 0.00 0.00 2.24
223 229 7.968405 GGGATGTCACAGTTCAAAATTATGTAC 59.032 37.037 0.00 0.00 0.00 2.90
228 234 6.968263 TTGGGATGTCACAGTTCAAAATTA 57.032 33.333 0.00 0.00 0.00 1.40
257 263 1.803334 ACCAAAAAGATGACGCGCTA 58.197 45.000 5.73 0.00 0.00 4.26
258 264 1.803334 TACCAAAAAGATGACGCGCT 58.197 45.000 5.73 0.00 0.00 5.92
259 265 2.505866 CTTACCAAAAAGATGACGCGC 58.494 47.619 5.73 0.00 0.00 6.86
264 270 5.134661 ACGTTTCCCTTACCAAAAAGATGA 58.865 37.500 0.00 0.00 0.00 2.92
265 271 5.447624 ACGTTTCCCTTACCAAAAAGATG 57.552 39.130 0.00 0.00 0.00 2.90
267 273 4.035441 CGAACGTTTCCCTTACCAAAAAGA 59.965 41.667 0.46 0.00 0.00 2.52
268 274 4.284485 CGAACGTTTCCCTTACCAAAAAG 58.716 43.478 0.46 0.00 0.00 2.27
269 275 3.488890 GCGAACGTTTCCCTTACCAAAAA 60.489 43.478 0.46 0.00 0.00 1.94
270 276 2.033174 GCGAACGTTTCCCTTACCAAAA 59.967 45.455 0.46 0.00 0.00 2.44
271 277 1.603326 GCGAACGTTTCCCTTACCAAA 59.397 47.619 0.46 0.00 0.00 3.28
272 278 1.202675 AGCGAACGTTTCCCTTACCAA 60.203 47.619 0.46 0.00 0.00 3.67
273 279 0.393820 AGCGAACGTTTCCCTTACCA 59.606 50.000 0.46 0.00 0.00 3.25
275 281 0.794473 CCAGCGAACGTTTCCCTTAC 59.206 55.000 0.46 0.00 0.00 2.34
276 282 0.320946 CCCAGCGAACGTTTCCCTTA 60.321 55.000 0.46 0.00 0.00 2.69
277 283 1.599797 CCCAGCGAACGTTTCCCTT 60.600 57.895 0.46 0.00 0.00 3.95
278 284 2.032071 CCCAGCGAACGTTTCCCT 59.968 61.111 0.46 0.00 0.00 4.20
280 286 3.733960 GGCCCAGCGAACGTTTCC 61.734 66.667 0.46 0.00 0.00 3.13
310 316 2.691674 GATTGGAGGAGCCTCGCGAG 62.692 65.000 29.06 29.06 43.59 5.03
311 317 2.759973 ATTGGAGGAGCCTCGCGA 60.760 61.111 9.26 9.26 43.59 5.87
312 318 2.279784 GATTGGAGGAGCCTCGCG 60.280 66.667 10.25 0.00 43.59 5.87
313 319 2.279784 CGATTGGAGGAGCCTCGC 60.280 66.667 10.25 4.59 43.59 5.03
314 320 0.108138 AAACGATTGGAGGAGCCTCG 60.108 55.000 10.25 2.36 43.59 4.63
318 324 3.339141 AGAAGAAAACGATTGGAGGAGC 58.661 45.455 0.00 0.00 0.00 4.70
319 325 3.935828 GGAGAAGAAAACGATTGGAGGAG 59.064 47.826 0.00 0.00 0.00 3.69
320 326 3.583086 AGGAGAAGAAAACGATTGGAGGA 59.417 43.478 0.00 0.00 0.00 3.71
321 327 3.686726 CAGGAGAAGAAAACGATTGGAGG 59.313 47.826 0.00 0.00 0.00 4.30
324 330 3.686726 CCTCAGGAGAAGAAAACGATTGG 59.313 47.826 0.00 0.00 0.00 3.16
331 337 4.599241 AGAATCCACCTCAGGAGAAGAAAA 59.401 41.667 0.00 0.00 41.90 2.29
335 341 3.118445 GGAAGAATCCACCTCAGGAGAAG 60.118 52.174 0.00 0.00 45.79 2.85
336 342 2.840651 GGAAGAATCCACCTCAGGAGAA 59.159 50.000 0.00 0.00 45.79 2.87
338 344 2.998316 GGAAGAATCCACCTCAGGAG 57.002 55.000 0.00 0.00 45.79 3.69
350 356 2.819348 GCTTGGTGGAGTTGGGAAGAAT 60.819 50.000 0.00 0.00 0.00 2.40
352 358 0.110486 GCTTGGTGGAGTTGGGAAGA 59.890 55.000 0.00 0.00 0.00 2.87
354 360 0.178992 CTGCTTGGTGGAGTTGGGAA 60.179 55.000 0.00 0.00 0.00 3.97
356 362 1.604593 CCTGCTTGGTGGAGTTGGG 60.605 63.158 0.00 0.00 31.70 4.12
357 363 2.270986 GCCTGCTTGGTGGAGTTGG 61.271 63.158 0.00 0.00 38.35 3.77
360 366 1.835927 GAGAGCCTGCTTGGTGGAGT 61.836 60.000 0.00 0.00 38.35 3.85
361 367 1.078567 GAGAGCCTGCTTGGTGGAG 60.079 63.158 0.00 0.00 38.35 3.86
362 368 1.203441 ATGAGAGCCTGCTTGGTGGA 61.203 55.000 0.00 0.00 38.35 4.02
363 369 1.030488 CATGAGAGCCTGCTTGGTGG 61.030 60.000 0.00 0.00 38.35 4.61
364 370 1.030488 CCATGAGAGCCTGCTTGGTG 61.030 60.000 0.00 0.00 38.35 4.17
365 371 1.302285 CCATGAGAGCCTGCTTGGT 59.698 57.895 0.00 0.00 38.35 3.67
368 374 0.964358 GTTGCCATGAGAGCCTGCTT 60.964 55.000 0.00 0.00 0.00 3.91
370 376 2.758089 CGTTGCCATGAGAGCCTGC 61.758 63.158 0.00 0.00 0.00 4.85
372 378 2.437359 GCGTTGCCATGAGAGCCT 60.437 61.111 0.00 0.00 0.00 4.58
391 424 2.966309 GCGGTTTGGACGAGCTTGG 61.966 63.158 5.79 0.00 0.00 3.61
396 429 1.501741 CAATGGCGGTTTGGACGAG 59.498 57.895 0.00 0.00 0.00 4.18
409 442 2.334946 CGGTGGTCACAGCCAATGG 61.335 63.158 0.00 0.00 41.98 3.16
410 443 2.981560 GCGGTGGTCACAGCCAATG 61.982 63.158 13.75 0.00 44.78 2.82
411 444 2.672996 GCGGTGGTCACAGCCAAT 60.673 61.111 13.75 0.00 44.78 3.16
417 450 2.986979 TAGCTCGCGGTGGTCACA 60.987 61.111 6.13 0.00 0.00 3.58
420 453 2.102553 GAGTAGCTCGCGGTGGTC 59.897 66.667 6.13 0.56 0.00 4.02
421 454 3.450115 GGAGTAGCTCGCGGTGGT 61.450 66.667 6.13 8.17 0.00 4.16
423 456 1.589993 CATGGAGTAGCTCGCGGTG 60.590 63.158 6.13 0.07 0.00 4.94
424 457 1.753078 TCATGGAGTAGCTCGCGGT 60.753 57.895 6.13 0.00 0.00 5.68
425 458 1.299468 GTCATGGAGTAGCTCGCGG 60.299 63.158 6.13 0.00 0.00 6.46
426 459 1.299468 GGTCATGGAGTAGCTCGCG 60.299 63.158 0.00 0.00 0.00 5.87
427 460 0.528684 GTGGTCATGGAGTAGCTCGC 60.529 60.000 0.00 0.00 0.00 5.03
428 461 0.817654 TGTGGTCATGGAGTAGCTCG 59.182 55.000 0.00 0.00 0.00 5.03
430 463 0.539051 GCTGTGGTCATGGAGTAGCT 59.461 55.000 0.00 0.00 0.00 3.32
431 464 0.539051 AGCTGTGGTCATGGAGTAGC 59.461 55.000 0.00 0.00 0.00 3.58
432 465 3.027412 AGTAGCTGTGGTCATGGAGTAG 58.973 50.000 0.00 0.00 0.00 2.57
433 466 3.101643 AGTAGCTGTGGTCATGGAGTA 57.898 47.619 0.00 0.00 0.00 2.59
434 467 1.944177 AGTAGCTGTGGTCATGGAGT 58.056 50.000 0.00 0.00 0.00 3.85
435 468 2.736719 CGAAGTAGCTGTGGTCATGGAG 60.737 54.545 0.00 0.00 0.00 3.86
437 470 1.066858 ACGAAGTAGCTGTGGTCATGG 60.067 52.381 0.00 0.00 41.94 3.66
438 471 2.370281 ACGAAGTAGCTGTGGTCATG 57.630 50.000 0.00 0.00 41.94 3.07
453 486 2.363795 AGCCGGGAGATGGACGAA 60.364 61.111 2.18 0.00 0.00 3.85
455 488 3.917760 GGAGCCGGGAGATGGACG 61.918 72.222 2.18 0.00 0.00 4.79
458 491 1.926426 AAAAGGGAGCCGGGAGATGG 61.926 60.000 2.18 0.00 0.00 3.51
460 493 2.398919 AAAAAGGGAGCCGGGAGAT 58.601 52.632 2.18 0.00 0.00 2.75
461 494 3.916184 AAAAAGGGAGCCGGGAGA 58.084 55.556 2.18 0.00 0.00 3.71
476 509 1.681538 TGAAGCCGGTTGTAGCAAAA 58.318 45.000 1.90 0.00 0.00 2.44
478 511 1.904287 AATGAAGCCGGTTGTAGCAA 58.096 45.000 1.90 0.00 0.00 3.91
479 512 1.904287 AAATGAAGCCGGTTGTAGCA 58.096 45.000 1.90 0.00 0.00 3.49
480 513 3.297830 AAAAATGAAGCCGGTTGTAGC 57.702 42.857 1.90 0.00 0.00 3.58
497 530 2.303175 AGAAGCCGGTTGTAGCAAAAA 58.697 42.857 1.90 0.00 0.00 1.94
498 531 1.975660 AGAAGCCGGTTGTAGCAAAA 58.024 45.000 1.90 0.00 0.00 2.44
499 532 1.975660 AAGAAGCCGGTTGTAGCAAA 58.024 45.000 1.90 0.00 0.00 3.68
500 533 1.975660 AAAGAAGCCGGTTGTAGCAA 58.024 45.000 1.90 0.00 0.00 3.91
501 534 1.975660 AAAAGAAGCCGGTTGTAGCA 58.024 45.000 1.90 0.00 0.00 3.49
518 551 4.097286 GCCATCCTCGGTTTATAGCAAAAA 59.903 41.667 0.00 0.00 0.00 1.94
524 557 2.927014 GCTCGCCATCCTCGGTTTATAG 60.927 54.545 0.00 0.00 0.00 1.31
525 558 1.000506 GCTCGCCATCCTCGGTTTATA 59.999 52.381 0.00 0.00 0.00 0.98
528 561 2.125106 GCTCGCCATCCTCGGTTT 60.125 61.111 0.00 0.00 0.00 3.27
531 564 2.664185 CATGCTCGCCATCCTCGG 60.664 66.667 0.00 0.00 29.71 4.63
532 565 2.664185 CCATGCTCGCCATCCTCG 60.664 66.667 0.00 0.00 29.71 4.63
536 569 2.182842 GGTCACCATGCTCGCCATC 61.183 63.158 0.00 0.00 29.71 3.51
540 573 3.490759 CGTGGTCACCATGCTCGC 61.491 66.667 2.15 0.00 35.28 5.03
545 578 2.773397 TACCGTGCGTGGTCACCATG 62.773 60.000 12.22 12.22 42.62 3.66
547 580 3.215597 CTACCGTGCGTGGTCACCA 62.216 63.158 2.52 0.00 42.62 4.17
549 582 3.110178 GCTACCGTGCGTGGTCAC 61.110 66.667 2.52 0.00 42.62 3.67
550 583 3.299977 AGCTACCGTGCGTGGTCA 61.300 61.111 2.52 0.00 42.62 4.02
551 584 2.203972 TACAGCTACCGTGCGTGGTC 62.204 60.000 2.52 0.00 42.62 4.02
555 588 1.214589 CCTTACAGCTACCGTGCGT 59.785 57.895 0.00 0.00 38.13 5.24
556 589 0.389426 AACCTTACAGCTACCGTGCG 60.389 55.000 0.00 0.00 38.13 5.34
557 590 1.076332 CAACCTTACAGCTACCGTGC 58.924 55.000 0.00 0.00 0.00 5.34
558 591 1.076332 GCAACCTTACAGCTACCGTG 58.924 55.000 0.00 0.00 0.00 4.94
559 592 0.682852 TGCAACCTTACAGCTACCGT 59.317 50.000 0.00 0.00 0.00 4.83
562 595 3.777478 TCGTATGCAACCTTACAGCTAC 58.223 45.455 0.00 0.00 0.00 3.58
563 596 3.181479 CCTCGTATGCAACCTTACAGCTA 60.181 47.826 0.00 0.00 0.00 3.32
564 597 2.418746 CCTCGTATGCAACCTTACAGCT 60.419 50.000 0.00 0.00 0.00 4.24
565 598 1.933853 CCTCGTATGCAACCTTACAGC 59.066 52.381 0.00 0.00 0.00 4.40
567 600 3.688694 AACCTCGTATGCAACCTTACA 57.311 42.857 0.00 0.00 0.00 2.41
569 602 4.456566 GGAAAAACCTCGTATGCAACCTTA 59.543 41.667 0.00 0.00 35.41 2.69
570 603 3.254903 GGAAAAACCTCGTATGCAACCTT 59.745 43.478 0.00 0.00 35.41 3.50
571 604 2.817844 GGAAAAACCTCGTATGCAACCT 59.182 45.455 0.00 0.00 35.41 3.50
572 605 3.211803 GGAAAAACCTCGTATGCAACC 57.788 47.619 0.00 0.00 35.41 3.77
590 623 2.599281 TCGTCGGTTCCAGCAGGA 60.599 61.111 0.00 0.00 43.93 3.86
592 625 1.949847 ATCCTCGTCGGTTCCAGCAG 61.950 60.000 0.00 0.00 0.00 4.24
593 626 1.541310 AATCCTCGTCGGTTCCAGCA 61.541 55.000 0.00 0.00 0.00 4.41
596 629 0.613853 AGGAATCCTCGTCGGTTCCA 60.614 55.000 15.70 0.00 41.53 3.53
597 630 0.179108 CAGGAATCCTCGTCGGTTCC 60.179 60.000 0.00 8.05 40.42 3.62
598 631 0.806492 GCAGGAATCCTCGTCGGTTC 60.806 60.000 0.00 0.00 0.00 3.62
599 632 1.218316 GCAGGAATCCTCGTCGGTT 59.782 57.895 0.00 0.00 0.00 4.44
600 633 0.395311 TAGCAGGAATCCTCGTCGGT 60.395 55.000 0.00 0.00 0.00 4.69
601 634 0.030908 GTAGCAGGAATCCTCGTCGG 59.969 60.000 0.00 0.00 0.00 4.79
602 635 0.738975 TGTAGCAGGAATCCTCGTCG 59.261 55.000 0.00 0.00 0.00 5.12
603 636 2.815478 CTTGTAGCAGGAATCCTCGTC 58.185 52.381 0.00 0.00 0.00 4.20
605 638 1.576356 GCTTGTAGCAGGAATCCTCG 58.424 55.000 0.00 0.00 41.89 4.63
616 649 1.709147 CGCTCCATGGTGCTTGTAGC 61.709 60.000 30.35 20.06 42.82 3.58
617 650 1.091771 CCGCTCCATGGTGCTTGTAG 61.092 60.000 30.35 17.44 33.07 2.74
618 651 1.078497 CCGCTCCATGGTGCTTGTA 60.078 57.895 30.35 2.11 33.07 2.41
620 653 1.526575 AAACCGCTCCATGGTGCTTG 61.527 55.000 30.35 23.90 40.35 4.01
621 654 0.827507 AAAACCGCTCCATGGTGCTT 60.828 50.000 30.35 19.13 40.35 3.91
622 655 0.827507 AAAAACCGCTCCATGGTGCT 60.828 50.000 30.35 14.68 40.35 4.40
644 677 2.180159 AATCTCCACCCCCGTGTTCG 62.180 60.000 0.00 0.00 38.41 3.95
645 678 0.676782 CAATCTCCACCCCCGTGTTC 60.677 60.000 0.00 0.00 38.41 3.18
647 680 1.846124 ACAATCTCCACCCCCGTGT 60.846 57.895 0.00 0.00 38.41 4.49
649 682 3.077907 CACAATCTCCACCCCCGT 58.922 61.111 0.00 0.00 0.00 5.28
651 684 2.043953 GGCACAATCTCCACCCCC 60.044 66.667 0.00 0.00 0.00 5.40
653 686 1.379044 CCTGGCACAATCTCCACCC 60.379 63.158 0.00 0.00 38.70 4.61
654 687 1.379044 CCCTGGCACAATCTCCACC 60.379 63.158 0.00 0.00 38.70 4.61
655 688 2.048603 GCCCTGGCACAATCTCCAC 61.049 63.158 2.58 0.00 38.70 4.02
656 689 2.356278 GCCCTGGCACAATCTCCA 59.644 61.111 2.58 0.00 38.70 3.86
657 690 2.825836 CGCCCTGGCACAATCTCC 60.826 66.667 9.17 0.00 42.06 3.71
658 691 2.825836 CCGCCCTGGCACAATCTC 60.826 66.667 9.17 0.00 42.06 2.75
659 692 3.650950 ACCGCCCTGGCACAATCT 61.651 61.111 9.17 0.00 43.94 2.40
660 693 3.443045 CACCGCCCTGGCACAATC 61.443 66.667 9.17 0.00 43.94 2.67
696 729 4.415332 CCTCGTCACCGGTGGTCG 62.415 72.222 33.40 32.31 31.02 4.79
697 730 4.065281 CCCTCGTCACCGGTGGTC 62.065 72.222 33.40 23.96 31.02 4.02
738 771 4.873129 CCTCATCGCCGGTGGTCG 62.873 72.222 16.49 3.66 38.88 4.79
782 815 4.519437 TGATCCGCAGCTCGCTGG 62.519 66.667 19.42 10.00 43.77 4.85
783 816 3.260483 GTGATCCGCAGCTCGCTG 61.260 66.667 14.30 14.30 46.15 5.18
787 820 4.899239 CCCCGTGATCCGCAGCTC 62.899 72.222 0.00 0.00 34.38 4.09
793 826 4.899239 GAGCAGCCCCGTGATCCG 62.899 72.222 0.00 0.00 0.00 4.18
795 828 2.202987 CAGAGCAGCCCCGTGATC 60.203 66.667 0.00 0.00 32.80 2.92
796 829 3.790437 CCAGAGCAGCCCCGTGAT 61.790 66.667 0.00 0.00 0.00 3.06
799 832 3.790437 CATCCAGAGCAGCCCCGT 61.790 66.667 0.00 0.00 0.00 5.28
800 833 3.035173 TTCATCCAGAGCAGCCCCG 62.035 63.158 0.00 0.00 0.00 5.73
801 834 1.452833 GTTCATCCAGAGCAGCCCC 60.453 63.158 0.00 0.00 0.00 5.80
804 837 0.381089 GCATGTTCATCCAGAGCAGC 59.619 55.000 0.00 0.00 40.95 5.25
805 838 0.656259 CGCATGTTCATCCAGAGCAG 59.344 55.000 0.00 0.00 40.95 4.24
807 840 1.354506 GCGCATGTTCATCCAGAGC 59.645 57.895 0.30 0.00 0.00 4.09
809 842 1.815003 CGGCGCATGTTCATCCAGA 60.815 57.895 10.83 0.00 0.00 3.86
810 843 2.108514 ACGGCGCATGTTCATCCAG 61.109 57.895 10.83 0.00 0.00 3.86
811 844 2.046411 ACGGCGCATGTTCATCCA 60.046 55.556 10.83 0.00 0.00 3.41
812 845 2.404789 CACGGCGCATGTTCATCC 59.595 61.111 10.83 0.00 0.00 3.51
839 872 4.451096 CCTCAACTGCTTCGCTAGTTAAAA 59.549 41.667 0.00 0.00 35.50 1.52
841 874 3.585862 CCTCAACTGCTTCGCTAGTTAA 58.414 45.455 0.00 0.00 35.50 2.01
842 875 2.094182 CCCTCAACTGCTTCGCTAGTTA 60.094 50.000 0.00 0.00 35.50 2.24
844 877 0.247736 CCCTCAACTGCTTCGCTAGT 59.752 55.000 0.00 0.00 0.00 2.57
847 880 0.108585 TTTCCCTCAACTGCTTCGCT 59.891 50.000 0.00 0.00 0.00 4.93
849 882 1.160137 CCTTTCCCTCAACTGCTTCG 58.840 55.000 0.00 0.00 0.00 3.79
851 884 3.589288 AGATACCTTTCCCTCAACTGCTT 59.411 43.478 0.00 0.00 0.00 3.91
852 885 3.054802 CAGATACCTTTCCCTCAACTGCT 60.055 47.826 0.00 0.00 0.00 4.24
853 886 3.274288 CAGATACCTTTCCCTCAACTGC 58.726 50.000 0.00 0.00 0.00 4.40
854 887 3.274288 GCAGATACCTTTCCCTCAACTG 58.726 50.000 0.00 0.00 0.00 3.16
855 888 2.093447 CGCAGATACCTTTCCCTCAACT 60.093 50.000 0.00 0.00 0.00 3.16
856 889 2.280628 CGCAGATACCTTTCCCTCAAC 58.719 52.381 0.00 0.00 0.00 3.18
857 890 1.209504 CCGCAGATACCTTTCCCTCAA 59.790 52.381 0.00 0.00 0.00 3.02
860 893 0.983378 AGCCGCAGATACCTTTCCCT 60.983 55.000 0.00 0.00 0.00 4.20
861 894 0.756903 TAGCCGCAGATACCTTTCCC 59.243 55.000 0.00 0.00 0.00 3.97
862 895 2.841442 ATAGCCGCAGATACCTTTCC 57.159 50.000 0.00 0.00 0.00 3.13
863 896 5.054477 TGTTAATAGCCGCAGATACCTTTC 58.946 41.667 0.00 0.00 0.00 2.62
864 897 5.031066 TGTTAATAGCCGCAGATACCTTT 57.969 39.130 0.00 0.00 0.00 3.11
865 898 4.632153 CTGTTAATAGCCGCAGATACCTT 58.368 43.478 0.00 0.00 0.00 3.50
866 899 3.555168 GCTGTTAATAGCCGCAGATACCT 60.555 47.826 12.86 0.00 37.73 3.08
867 900 2.737252 GCTGTTAATAGCCGCAGATACC 59.263 50.000 12.86 0.00 37.73 2.73
868 901 3.390135 TGCTGTTAATAGCCGCAGATAC 58.610 45.455 20.01 0.00 43.02 2.24
869 902 3.744238 TGCTGTTAATAGCCGCAGATA 57.256 42.857 20.01 0.00 43.02 1.98
871 904 2.394930 TTGCTGTTAATAGCCGCAGA 57.605 45.000 20.01 0.00 43.02 4.26
872 905 3.621794 GATTTGCTGTTAATAGCCGCAG 58.378 45.455 20.01 3.18 43.02 5.18
873 906 2.031560 CGATTTGCTGTTAATAGCCGCA 59.968 45.455 20.01 5.76 43.02 5.69
874 907 2.031683 ACGATTTGCTGTTAATAGCCGC 59.968 45.455 20.01 7.08 43.02 6.53
875 908 3.944422 ACGATTTGCTGTTAATAGCCG 57.056 42.857 20.01 17.40 43.02 5.52
876 909 4.269363 ACGTACGATTTGCTGTTAATAGCC 59.731 41.667 24.41 5.14 43.02 3.93
877 910 5.385396 ACGTACGATTTGCTGTTAATAGC 57.615 39.130 24.41 16.59 43.95 2.97
878 911 5.517411 TGGACGTACGATTTGCTGTTAATAG 59.483 40.000 24.41 0.00 0.00 1.73
879 912 5.289193 GTGGACGTACGATTTGCTGTTAATA 59.711 40.000 24.41 0.00 0.00 0.98
880 913 4.092383 GTGGACGTACGATTTGCTGTTAAT 59.908 41.667 24.41 0.00 0.00 1.40
881 914 3.429543 GTGGACGTACGATTTGCTGTTAA 59.570 43.478 24.41 0.00 0.00 2.01
882 915 2.988493 GTGGACGTACGATTTGCTGTTA 59.012 45.455 24.41 0.00 0.00 2.41
884 917 1.425412 GTGGACGTACGATTTGCTGT 58.575 50.000 24.41 0.00 0.00 4.40
885 918 0.365523 CGTGGACGTACGATTTGCTG 59.634 55.000 24.41 1.32 46.46 4.41
886 919 2.733127 CGTGGACGTACGATTTGCT 58.267 52.632 24.41 0.00 46.46 3.91
924 957 4.331168 GCTTTATCATAGGCGAGCAATAGG 59.669 45.833 0.00 0.00 0.00 2.57
925 958 5.174395 AGCTTTATCATAGGCGAGCAATAG 58.826 41.667 0.00 0.00 32.78 1.73
926 959 5.152623 AGCTTTATCATAGGCGAGCAATA 57.847 39.130 0.00 0.00 32.78 1.90
927 960 4.013267 AGCTTTATCATAGGCGAGCAAT 57.987 40.909 0.00 0.00 32.78 3.56
928 961 3.475566 AGCTTTATCATAGGCGAGCAA 57.524 42.857 0.00 0.00 32.78 3.91
929 962 3.306088 GGTAGCTTTATCATAGGCGAGCA 60.306 47.826 0.00 0.00 32.78 4.26
930 963 3.254892 GGTAGCTTTATCATAGGCGAGC 58.745 50.000 0.00 0.00 0.00 5.03
931 964 3.057456 ACGGTAGCTTTATCATAGGCGAG 60.057 47.826 0.00 0.00 0.00 5.03
932 965 2.889045 ACGGTAGCTTTATCATAGGCGA 59.111 45.455 0.00 0.00 0.00 5.54
933 966 3.243336 GACGGTAGCTTTATCATAGGCG 58.757 50.000 0.00 0.00 0.00 5.52
934 967 3.057736 TCGACGGTAGCTTTATCATAGGC 60.058 47.826 0.00 0.00 0.00 3.93
935 968 4.761235 TCGACGGTAGCTTTATCATAGG 57.239 45.455 0.00 0.00 0.00 2.57
936 969 5.700846 ACATCGACGGTAGCTTTATCATAG 58.299 41.667 0.00 0.00 0.00 2.23
937 970 5.700722 ACATCGACGGTAGCTTTATCATA 57.299 39.130 0.00 0.00 0.00 2.15
938 971 4.585955 ACATCGACGGTAGCTTTATCAT 57.414 40.909 0.00 0.00 0.00 2.45
939 972 4.023450 CCTACATCGACGGTAGCTTTATCA 60.023 45.833 16.75 0.00 37.49 2.15
940 973 4.214971 TCCTACATCGACGGTAGCTTTATC 59.785 45.833 16.75 0.00 37.49 1.75
941 974 4.139786 TCCTACATCGACGGTAGCTTTAT 58.860 43.478 16.75 0.00 37.49 1.40
942 975 3.544684 TCCTACATCGACGGTAGCTTTA 58.455 45.455 16.75 3.79 37.49 1.85
949 4672 0.533951 GGGTTTCCTACATCGACGGT 59.466 55.000 0.00 0.00 0.00 4.83
1537 5267 0.176680 GTGCGTCACCATCAGGAGAT 59.823 55.000 0.00 0.00 36.86 2.75
1540 5270 1.005037 GTGTGCGTCACCATCAGGA 60.005 57.895 7.38 0.00 40.84 3.86
1541 5271 3.566261 GTGTGCGTCACCATCAGG 58.434 61.111 7.38 0.00 40.84 3.86
1655 5402 1.565305 CGCACAGCTCCTTGTATCTC 58.435 55.000 0.00 0.00 0.00 2.75
1715 5462 1.043673 GCCGGGACATGTACCTCTCT 61.044 60.000 24.90 0.00 0.00 3.10
1825 5572 2.113243 GAGGGGATCATACGGTGGCC 62.113 65.000 0.00 0.00 0.00 5.36
1893 5640 2.091994 CCTCCTTCCTCATGCCTTCAAT 60.092 50.000 0.00 0.00 0.00 2.57
1902 5649 2.739996 CCGCTGCCTCCTTCCTCAT 61.740 63.158 0.00 0.00 0.00 2.90
1984 5731 1.811266 CGCCACTTCTCGTGATGGG 60.811 63.158 8.72 2.97 46.81 4.00
2044 5791 1.890625 CGTTCACCGGTGTCCCCATA 61.891 60.000 32.74 10.28 0.00 2.74
2122 5889 7.740519 AATCTCAGAAAACAAAACAAGTTCG 57.259 32.000 0.00 0.00 0.00 3.95
2148 5915 7.452501 TCTTTGGAATTGGATCATCAAACTTCT 59.547 33.333 0.00 0.00 0.00 2.85
2149 5916 7.605449 TCTTTGGAATTGGATCATCAAACTTC 58.395 34.615 0.00 0.00 0.00 3.01
2163 5931 7.225145 TGTTTTTCATTCTGCTCTTTGGAATTG 59.775 33.333 0.00 0.00 0.00 2.32
2190 5958 7.629222 GCCTTATCTAAGCTTTTCAAATCTGCA 60.629 37.037 3.20 0.00 32.02 4.41
2191 5959 6.694844 GCCTTATCTAAGCTTTTCAAATCTGC 59.305 38.462 3.20 0.00 32.02 4.26
2199 5967 7.851387 ACACTAAGCCTTATCTAAGCTTTTC 57.149 36.000 3.20 0.00 34.22 2.29
2297 6065 1.341913 GGAAGAAGCTCCTCCCCCTC 61.342 65.000 0.00 0.00 32.21 4.30
2301 6069 1.065053 GGAAAGGAAGAAGCTCCTCCC 60.065 57.143 5.33 1.54 45.59 4.30
2349 6117 0.532573 TGTCTCCTTCCATCGCAGAC 59.467 55.000 0.00 0.00 42.51 3.51
2354 6122 1.403814 TAGCCTGTCTCCTTCCATCG 58.596 55.000 0.00 0.00 0.00 3.84
2407 6177 6.354794 TGAAAACTGTATATATCCCCCTCG 57.645 41.667 0.00 0.00 0.00 4.63
2463 6233 7.872163 TTCATTACAATTGTTTCACATCAGC 57.128 32.000 17.78 0.00 0.00 4.26
2521 6293 7.411486 ACATCCCTTCGGAGACTATATATTG 57.589 40.000 0.00 0.00 43.12 1.90


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

AutoCloner maintained by Alex Coulton.