Multiple sequence alignment - TraesCS2A01G375500

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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 TraesCS2A01G375500 chr2A 100.000 2740 0 0 1 2740 617845278 617848017 0.000000e+00 5060
1 TraesCS2A01G375500 chr2A 97.576 165 4 0 771 935 617850572 617850408 1.610000e-72 283
2 TraesCS2A01G375500 chr5B 95.097 1917 44 14 870 2740 280458297 280456385 0.000000e+00 2974
3 TraesCS2A01G375500 chr5B 97.026 1715 21 10 774 2458 3572770 3571056 0.000000e+00 2857
4 TraesCS2A01G375500 chr2B 92.775 1744 43 19 1074 2740 231244489 231242752 0.000000e+00 2446
5 TraesCS2A01G375500 chr2B 95.602 773 31 1 1 773 556698347 556699116 0.000000e+00 1236
6 TraesCS2A01G375500 chr2B 90.215 838 44 13 1074 1898 326312110 326312922 0.000000e+00 1059
7 TraesCS2A01G375500 chr2B 94.769 497 23 1 2244 2740 326313383 326313876 0.000000e+00 771
8 TraesCS2A01G375500 chr2B 93.131 495 30 2 2247 2740 76499618 76499127 0.000000e+00 723
9 TraesCS2A01G375500 chr2B 93.681 364 15 3 771 1126 231244840 231244477 3.100000e-149 538
10 TraesCS2A01G375500 chr2B 93.213 221 15 0 773 993 326310864 326311084 2.630000e-85 326
11 TraesCS2A01G375500 chr2B 92.121 165 12 1 2081 2245 326313182 326313345 5.900000e-57 231
12 TraesCS2A01G375500 chr2B 100.000 53 0 0 1887 1939 326312932 326312984 6.240000e-17 99
13 TraesCS2A01G375500 chr6D 84.321 2041 140 90 784 2740 391887057 391885113 0.000000e+00 1831
14 TraesCS2A01G375500 chr2D 83.979 1729 127 81 1074 2740 630786816 630785176 0.000000e+00 1520
15 TraesCS2A01G375500 chr2D 95.876 776 28 1 2 773 476023484 476024259 0.000000e+00 1253
16 TraesCS2A01G375500 chr2D 88.076 369 29 8 772 1126 630787171 630786804 9.070000e-115 424
17 TraesCS2A01G375500 chr6B 95.684 811 10 5 774 1559 60118491 60117681 0.000000e+00 1280
18 TraesCS2A01G375500 chr6B 96.970 165 5 0 771 935 60114702 60114866 7.470000e-71 278
19 TraesCS2A01G375500 chr1A 86.486 925 53 29 1076 1980 290127796 290128668 0.000000e+00 950
20 TraesCS2A01G375500 chr1A 92.727 495 31 3 2247 2740 290128945 290129435 0.000000e+00 710
21 TraesCS2A01G375500 chr6A 86.255 924 53 30 1074 1976 582805459 582806329 0.000000e+00 935
22 TraesCS2A01G375500 chr6A 92.000 400 28 2 2292 2691 582806649 582807044 2.380000e-155 558
23 TraesCS2A01G375500 chr6A 89.344 366 31 6 769 1126 582805106 582805471 1.160000e-123 453
24 TraesCS2A01G375500 chr4D 83.816 587 58 21 1117 1695 477005968 477005411 8.690000e-145 523
25 TraesCS2A01G375500 chr4D 88.235 357 37 2 2384 2740 477004483 477004132 3.260000e-114 422


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 TraesCS2A01G375500 chr2A 617845278 617848017 2739 False 5060.000000 5060 100.000000 1 2740 1 chr2A.!!$F1 2739
1 TraesCS2A01G375500 chr5B 280456385 280458297 1912 True 2974.000000 2974 95.097000 870 2740 1 chr5B.!!$R2 1870
2 TraesCS2A01G375500 chr5B 3571056 3572770 1714 True 2857.000000 2857 97.026000 774 2458 1 chr5B.!!$R1 1684
3 TraesCS2A01G375500 chr2B 231242752 231244840 2088 True 1492.000000 2446 93.228000 771 2740 2 chr2B.!!$R2 1969
4 TraesCS2A01G375500 chr2B 556698347 556699116 769 False 1236.000000 1236 95.602000 1 773 1 chr2B.!!$F1 772
5 TraesCS2A01G375500 chr2B 326310864 326313876 3012 False 497.200000 1059 94.063600 773 2740 5 chr2B.!!$F2 1967
6 TraesCS2A01G375500 chr6D 391885113 391887057 1944 True 1831.000000 1831 84.321000 784 2740 1 chr6D.!!$R1 1956
7 TraesCS2A01G375500 chr2D 476023484 476024259 775 False 1253.000000 1253 95.876000 2 773 1 chr2D.!!$F1 771
8 TraesCS2A01G375500 chr2D 630785176 630787171 1995 True 972.000000 1520 86.027500 772 2740 2 chr2D.!!$R1 1968
9 TraesCS2A01G375500 chr6B 60117681 60118491 810 True 1280.000000 1280 95.684000 774 1559 1 chr6B.!!$R1 785
10 TraesCS2A01G375500 chr1A 290127796 290129435 1639 False 830.000000 950 89.606500 1076 2740 2 chr1A.!!$F1 1664
11 TraesCS2A01G375500 chr6A 582805106 582807044 1938 False 648.666667 935 89.199667 769 2691 3 chr6A.!!$F1 1922
12 TraesCS2A01G375500 chr4D 477004132 477005968 1836 True 472.500000 523 86.025500 1117 2740 2 chr4D.!!$R1 1623

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
749 750 0.035317 TGTGGTGATGTGCTGTCCTC 59.965 55.0 0.0 0.0 0.0 3.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2492 4368 0.321919 CCAGAAACAGGCTGCTGCTA 60.322 55.0 15.89 0.0 39.59 3.49 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
22 23 1.093159 CAGAGGTTTCAGCCATGAGC 58.907 55.000 0.00 0.00 44.25 4.26
75 76 2.682494 GGCCACCACCCTCTCGTA 60.682 66.667 0.00 0.00 0.00 3.43
143 144 1.135315 GCCGACGCGAACTACTACA 59.865 57.895 15.93 0.00 0.00 2.74
154 155 0.822532 ACTACTACATCCTCCCGGCG 60.823 60.000 0.00 0.00 0.00 6.46
259 260 3.261951 CGCGATGGCTTACCCGTG 61.262 66.667 0.00 0.00 36.88 4.94
260 261 3.573491 GCGATGGCTTACCCGTGC 61.573 66.667 0.00 0.00 35.87 5.34
261 262 3.261951 CGATGGCTTACCCGTGCG 61.262 66.667 0.00 0.00 35.87 5.34
262 263 3.573491 GATGGCTTACCCGTGCGC 61.573 66.667 0.00 0.00 35.87 6.09
263 264 4.402528 ATGGCTTACCCGTGCGCA 62.403 61.111 5.66 5.66 35.87 6.09
264 265 3.697439 ATGGCTTACCCGTGCGCAT 62.697 57.895 15.91 0.00 35.87 4.73
265 266 3.573491 GGCTTACCCGTGCGCATC 61.573 66.667 15.91 6.64 0.00 3.91
266 267 3.925238 GCTTACCCGTGCGCATCG 61.925 66.667 15.91 18.89 0.00 3.84
301 302 3.255379 GCGCCGTCCGACAAGATC 61.255 66.667 0.00 0.00 40.02 2.75
302 303 2.180769 CGCCGTCCGACAAGATCA 59.819 61.111 0.00 0.00 40.02 2.92
303 304 1.226974 CGCCGTCCGACAAGATCAT 60.227 57.895 0.00 0.00 40.02 2.45
304 305 1.209275 CGCCGTCCGACAAGATCATC 61.209 60.000 0.00 0.00 40.02 2.92
305 306 0.876342 GCCGTCCGACAAGATCATCC 60.876 60.000 0.00 0.00 0.00 3.51
306 307 0.595053 CCGTCCGACAAGATCATCCG 60.595 60.000 0.00 0.00 0.00 4.18
307 308 0.595053 CGTCCGACAAGATCATCCGG 60.595 60.000 0.00 0.00 41.36 5.14
308 309 0.876342 GTCCGACAAGATCATCCGGC 60.876 60.000 0.00 3.92 39.96 6.13
309 310 1.043116 TCCGACAAGATCATCCGGCT 61.043 55.000 0.00 0.00 39.96 5.52
310 311 0.877649 CCGACAAGATCATCCGGCTG 60.878 60.000 0.00 0.00 33.47 4.85
311 312 0.179100 CGACAAGATCATCCGGCTGT 60.179 55.000 5.00 0.00 0.00 4.40
312 313 1.576356 GACAAGATCATCCGGCTGTC 58.424 55.000 5.00 2.76 0.00 3.51
313 314 0.179100 ACAAGATCATCCGGCTGTCG 60.179 55.000 5.00 0.00 38.88 4.35
314 315 0.103026 CAAGATCATCCGGCTGTCGA 59.897 55.000 1.87 0.00 42.43 4.20
315 316 0.103208 AAGATCATCCGGCTGTCGAC 59.897 55.000 9.11 9.11 42.43 4.20
316 317 1.300233 GATCATCCGGCTGTCGACC 60.300 63.158 14.12 0.00 42.43 4.79
327 328 4.471726 GTCGACCGACGTCCGCAT 62.472 66.667 10.58 0.00 43.13 4.73
328 329 4.170062 TCGACCGACGTCCGCATC 62.170 66.667 10.58 1.57 43.13 3.91
329 330 4.175489 CGACCGACGTCCGCATCT 62.175 66.667 10.58 0.00 35.40 2.90
330 331 2.278013 GACCGACGTCCGCATCTC 60.278 66.667 10.58 0.00 36.84 2.75
331 332 3.753070 GACCGACGTCCGCATCTCC 62.753 68.421 10.58 0.00 36.84 3.71
332 333 3.518998 CCGACGTCCGCATCTCCT 61.519 66.667 10.58 0.00 36.84 3.69
333 334 2.490217 CGACGTCCGCATCTCCTT 59.510 61.111 10.58 0.00 0.00 3.36
334 335 1.586564 CGACGTCCGCATCTCCTTC 60.587 63.158 10.58 0.00 0.00 3.46
335 336 1.227002 GACGTCCGCATCTCCTTCC 60.227 63.158 3.51 0.00 0.00 3.46
336 337 2.278857 CGTCCGCATCTCCTTCCG 60.279 66.667 0.00 0.00 0.00 4.30
337 338 2.586357 GTCCGCATCTCCTTCCGC 60.586 66.667 0.00 0.00 0.00 5.54
338 339 4.207281 TCCGCATCTCCTTCCGCG 62.207 66.667 0.00 0.00 46.96 6.46
341 342 4.537433 GCATCTCCTTCCGCGCCT 62.537 66.667 0.00 0.00 0.00 5.52
342 343 3.129300 CATCTCCTTCCGCGCCTA 58.871 61.111 0.00 0.00 0.00 3.93
343 344 1.300233 CATCTCCTTCCGCGCCTAC 60.300 63.158 0.00 0.00 0.00 3.18
344 345 1.756950 ATCTCCTTCCGCGCCTACA 60.757 57.895 0.00 0.00 0.00 2.74
345 346 2.017559 ATCTCCTTCCGCGCCTACAC 62.018 60.000 0.00 0.00 0.00 2.90
346 347 4.124351 TCCTTCCGCGCCTACACG 62.124 66.667 0.00 0.00 0.00 4.49
347 348 4.124351 CCTTCCGCGCCTACACGA 62.124 66.667 0.00 0.00 34.06 4.35
348 349 2.879462 CTTCCGCGCCTACACGAC 60.879 66.667 0.00 0.00 34.06 4.34
349 350 4.764336 TTCCGCGCCTACACGACG 62.764 66.667 0.00 0.00 34.06 5.12
363 364 3.753539 GACGTGCGTGCAGTCGAC 61.754 66.667 7.70 7.70 0.00 4.20
366 367 4.994201 GTGCGTGCAGTCGACCGA 62.994 66.667 13.01 0.00 0.00 4.69
367 368 4.700365 TGCGTGCAGTCGACCGAG 62.700 66.667 13.01 3.77 0.00 4.63
368 369 4.702081 GCGTGCAGTCGACCGAGT 62.702 66.667 13.01 0.00 0.00 4.18
369 370 2.801162 CGTGCAGTCGACCGAGTG 60.801 66.667 19.53 19.53 45.58 3.51
370 371 2.430921 GTGCAGTCGACCGAGTGG 60.431 66.667 23.42 9.73 43.66 4.00
371 372 4.357947 TGCAGTCGACCGAGTGGC 62.358 66.667 23.42 17.14 43.66 5.01
372 373 4.357947 GCAGTCGACCGAGTGGCA 62.358 66.667 23.42 0.00 43.66 4.92
373 374 2.430921 CAGTCGACCGAGTGGCAC 60.431 66.667 13.01 10.29 40.75 5.01
374 375 2.910479 AGTCGACCGAGTGGCACA 60.910 61.111 21.41 0.00 39.70 4.57
375 376 2.261671 GTCGACCGAGTGGCACAT 59.738 61.111 21.41 4.74 44.52 3.21
376 377 1.805945 GTCGACCGAGTGGCACATC 60.806 63.158 21.41 12.99 44.52 3.06
377 378 2.880879 CGACCGAGTGGCACATCG 60.881 66.667 21.41 22.69 44.52 3.84
378 379 2.571757 GACCGAGTGGCACATCGA 59.428 61.111 28.55 0.00 44.52 3.59
379 380 1.805945 GACCGAGTGGCACATCGAC 60.806 63.158 28.55 20.90 44.52 4.20
380 381 2.261361 CCGAGTGGCACATCGACA 59.739 61.111 28.55 0.00 44.52 4.35
381 382 1.807165 CCGAGTGGCACATCGACAG 60.807 63.158 28.55 15.56 44.52 3.51
382 383 2.447887 CGAGTGGCACATCGACAGC 61.448 63.158 25.09 0.00 44.52 4.40
383 384 2.433145 AGTGGCACATCGACAGCG 60.433 61.111 21.41 0.00 44.52 5.18
454 455 4.821589 CCGAGCGGCAGGGAGAAC 62.822 72.222 1.45 0.00 0.00 3.01
459 460 4.394712 CGGCAGGGAGAACGCCTT 62.395 66.667 0.00 0.00 43.95 4.35
460 461 2.436824 GGCAGGGAGAACGCCTTC 60.437 66.667 0.00 0.00 42.78 3.46
461 462 2.436824 GCAGGGAGAACGCCTTCC 60.437 66.667 0.00 0.00 41.22 3.46
462 463 2.125512 CAGGGAGAACGCCTTCCG 60.126 66.667 0.00 0.00 45.87 4.30
463 464 4.083862 AGGGAGAACGCCTTCCGC 62.084 66.667 0.00 0.00 45.87 5.54
464 465 4.388499 GGGAGAACGCCTTCCGCA 62.388 66.667 0.00 0.00 41.76 5.69
465 466 2.125106 GGAGAACGCCTTCCGCAT 60.125 61.111 0.00 0.00 41.76 4.73
466 467 2.174319 GGAGAACGCCTTCCGCATC 61.174 63.158 0.00 0.00 41.76 3.91
467 468 2.509336 AGAACGCCTTCCGCATCG 60.509 61.111 0.00 0.00 41.76 3.84
468 469 2.508439 GAACGCCTTCCGCATCGA 60.508 61.111 0.00 0.00 41.76 3.59
469 470 2.509336 AACGCCTTCCGCATCGAG 60.509 61.111 0.00 0.00 41.76 4.04
470 471 2.884087 GAACGCCTTCCGCATCGAGA 62.884 60.000 0.00 0.00 41.76 4.04
471 472 2.202743 CGCCTTCCGCATCGAGAA 60.203 61.111 0.00 0.00 37.30 2.87
472 473 2.233654 CGCCTTCCGCATCGAGAAG 61.234 63.158 5.41 5.41 39.38 2.85
473 474 1.153549 GCCTTCCGCATCGAGAAGT 60.154 57.895 10.25 0.00 38.24 3.01
474 475 0.102481 GCCTTCCGCATCGAGAAGTA 59.898 55.000 10.25 0.00 38.24 2.24
475 476 1.841450 CCTTCCGCATCGAGAAGTAC 58.159 55.000 10.25 0.00 38.24 2.73
476 477 1.134367 CCTTCCGCATCGAGAAGTACA 59.866 52.381 10.25 0.00 38.24 2.90
477 478 2.455032 CTTCCGCATCGAGAAGTACAG 58.545 52.381 0.00 0.00 35.75 2.74
478 479 0.100682 TCCGCATCGAGAAGTACAGC 59.899 55.000 0.00 0.00 0.00 4.40
479 480 1.202973 CCGCATCGAGAAGTACAGCG 61.203 60.000 0.00 0.00 42.93 5.18
480 481 1.202973 CGCATCGAGAAGTACAGCGG 61.203 60.000 0.00 0.00 40.00 5.52
481 482 1.483424 GCATCGAGAAGTACAGCGGC 61.483 60.000 0.00 0.00 0.00 6.53
482 483 1.064296 ATCGAGAAGTACAGCGGCG 59.936 57.895 0.51 0.51 0.00 6.46
483 484 2.938539 ATCGAGAAGTACAGCGGCGC 62.939 60.000 26.86 26.86 0.00 6.53
484 485 3.248171 GAGAAGTACAGCGGCGCG 61.248 66.667 27.59 22.69 0.00 6.86
485 486 4.796231 AGAAGTACAGCGGCGCGG 62.796 66.667 29.46 29.46 0.00 6.46
486 487 4.789075 GAAGTACAGCGGCGCGGA 62.789 66.667 36.69 21.07 0.00 5.54
487 488 4.796231 AAGTACAGCGGCGCGGAG 62.796 66.667 36.69 26.50 0.00 4.63
498 499 4.111016 CGCGGAGGTGCACGAGTA 62.111 66.667 11.45 0.00 34.15 2.59
499 500 2.506438 GCGGAGGTGCACGAGTAC 60.506 66.667 11.45 0.00 34.15 2.73
500 501 2.959372 CGGAGGTGCACGAGTACA 59.041 61.111 11.45 0.00 31.27 2.90
501 502 1.287815 CGGAGGTGCACGAGTACAA 59.712 57.895 11.45 0.00 31.27 2.41
502 503 0.732880 CGGAGGTGCACGAGTACAAG 60.733 60.000 11.45 0.00 31.27 3.16
503 504 1.014564 GGAGGTGCACGAGTACAAGC 61.015 60.000 11.45 0.00 31.27 4.01
504 505 0.038159 GAGGTGCACGAGTACAAGCT 60.038 55.000 11.45 0.00 31.27 3.74
505 506 0.038159 AGGTGCACGAGTACAAGCTC 60.038 55.000 11.45 0.00 31.27 4.09
506 507 0.319555 GGTGCACGAGTACAAGCTCA 60.320 55.000 11.45 0.00 35.33 4.26
507 508 1.673033 GGTGCACGAGTACAAGCTCAT 60.673 52.381 11.45 0.00 35.33 2.90
508 509 1.391485 GTGCACGAGTACAAGCTCATG 59.609 52.381 0.00 0.00 35.33 3.07
509 510 1.002366 GCACGAGTACAAGCTCATGG 58.998 55.000 0.00 0.00 35.33 3.66
510 511 1.002366 CACGAGTACAAGCTCATGGC 58.998 55.000 0.00 0.00 42.19 4.40
532 533 4.083862 GGGGACTCGTGCCAGGAC 62.084 72.222 9.84 0.00 43.56 3.85
533 534 4.083862 GGGACTCGTGCCAGGACC 62.084 72.222 2.47 0.00 41.16 4.46
534 535 2.997897 GGACTCGTGCCAGGACCT 60.998 66.667 0.00 0.00 0.00 3.85
535 536 2.574399 GACTCGTGCCAGGACCTC 59.426 66.667 0.00 0.00 0.00 3.85
536 537 3.343788 GACTCGTGCCAGGACCTCG 62.344 68.421 0.00 0.00 0.00 4.63
537 538 4.135153 CTCGTGCCAGGACCTCGG 62.135 72.222 0.00 0.00 0.00 4.63
543 544 4.003788 CCAGGACCTCGGCGTGTT 62.004 66.667 6.85 0.00 0.00 3.32
544 545 2.432628 CAGGACCTCGGCGTGTTC 60.433 66.667 6.85 1.60 0.00 3.18
545 546 2.915659 AGGACCTCGGCGTGTTCA 60.916 61.111 6.85 0.00 0.00 3.18
546 547 2.432628 GGACCTCGGCGTGTTCAG 60.433 66.667 6.85 0.00 0.00 3.02
547 548 2.432628 GACCTCGGCGTGTTCAGG 60.433 66.667 6.85 8.56 0.00 3.86
548 549 3.934391 GACCTCGGCGTGTTCAGGG 62.934 68.421 14.98 6.51 0.00 4.45
549 550 3.691342 CCTCGGCGTGTTCAGGGA 61.691 66.667 6.85 0.00 0.00 4.20
550 551 2.432628 CTCGGCGTGTTCAGGGAC 60.433 66.667 6.85 0.00 0.00 4.46
551 552 3.934391 CTCGGCGTGTTCAGGGACC 62.934 68.421 6.85 0.00 0.00 4.46
552 553 4.003788 CGGCGTGTTCAGGGACCT 62.004 66.667 0.00 0.00 0.00 3.85
553 554 2.047179 GGCGTGTTCAGGGACCTC 60.047 66.667 0.00 0.00 0.00 3.85
554 555 2.741092 GCGTGTTCAGGGACCTCA 59.259 61.111 0.00 0.00 0.00 3.86
555 556 1.070786 GCGTGTTCAGGGACCTCAA 59.929 57.895 0.00 0.00 0.00 3.02
556 557 0.951040 GCGTGTTCAGGGACCTCAAG 60.951 60.000 0.00 0.00 0.00 3.02
557 558 0.320771 CGTGTTCAGGGACCTCAAGG 60.321 60.000 0.00 0.00 42.17 3.61
558 559 0.036875 GTGTTCAGGGACCTCAAGGG 59.963 60.000 0.29 0.00 40.27 3.95
559 560 1.002011 GTTCAGGGACCTCAAGGGC 60.002 63.158 0.29 0.00 44.61 5.19
560 561 2.592993 TTCAGGGACCTCAAGGGCG 61.593 63.158 0.29 0.00 47.00 6.13
561 562 4.101448 CAGGGACCTCAAGGGCGG 62.101 72.222 0.29 0.00 47.00 6.13
595 596 4.157120 GCCACCGAGCCGTACCAT 62.157 66.667 0.00 0.00 0.00 3.55
596 597 2.202878 CCACCGAGCCGTACCATG 60.203 66.667 0.00 0.00 0.00 3.66
597 598 2.577059 CACCGAGCCGTACCATGT 59.423 61.111 0.00 0.00 0.00 3.21
598 599 1.518572 CACCGAGCCGTACCATGTC 60.519 63.158 0.00 0.00 0.00 3.06
599 600 1.980232 ACCGAGCCGTACCATGTCA 60.980 57.895 0.00 0.00 0.00 3.58
600 601 1.327690 ACCGAGCCGTACCATGTCAT 61.328 55.000 0.00 0.00 0.00 3.06
601 602 0.597637 CCGAGCCGTACCATGTCATC 60.598 60.000 0.00 0.00 0.00 2.92
602 603 0.934901 CGAGCCGTACCATGTCATCG 60.935 60.000 0.00 0.00 0.00 3.84
603 604 0.102481 GAGCCGTACCATGTCATCGT 59.898 55.000 0.00 0.00 0.00 3.73
604 605 0.179111 AGCCGTACCATGTCATCGTG 60.179 55.000 0.00 0.00 0.00 4.35
605 606 0.459585 GCCGTACCATGTCATCGTGT 60.460 55.000 0.00 0.00 0.00 4.49
606 607 2.004583 CCGTACCATGTCATCGTGTT 57.995 50.000 0.00 0.00 0.00 3.32
607 608 1.924524 CCGTACCATGTCATCGTGTTC 59.075 52.381 0.00 0.00 0.00 3.18
608 609 2.601804 CGTACCATGTCATCGTGTTCA 58.398 47.619 0.00 0.00 0.00 3.18
609 610 2.990514 CGTACCATGTCATCGTGTTCAA 59.009 45.455 0.00 0.00 0.00 2.69
610 611 3.060761 CGTACCATGTCATCGTGTTCAAG 59.939 47.826 0.00 0.00 0.00 3.02
611 612 3.401033 ACCATGTCATCGTGTTCAAGA 57.599 42.857 0.00 0.00 0.00 3.02
612 613 3.738982 ACCATGTCATCGTGTTCAAGAA 58.261 40.909 0.00 0.00 0.00 2.52
613 614 3.748048 ACCATGTCATCGTGTTCAAGAAG 59.252 43.478 0.00 0.00 0.00 2.85
614 615 3.125829 CCATGTCATCGTGTTCAAGAAGG 59.874 47.826 0.00 0.00 0.00 3.46
615 616 2.143122 TGTCATCGTGTTCAAGAAGGC 58.857 47.619 0.00 0.00 0.00 4.35
616 617 1.126846 GTCATCGTGTTCAAGAAGGCG 59.873 52.381 0.00 0.00 0.00 5.52
617 618 0.179215 CATCGTGTTCAAGAAGGCGC 60.179 55.000 0.00 0.00 0.00 6.53
618 619 1.298859 ATCGTGTTCAAGAAGGCGCC 61.299 55.000 21.89 21.89 0.00 6.53
619 620 1.961277 CGTGTTCAAGAAGGCGCCT 60.961 57.895 27.08 27.08 0.00 5.52
620 621 1.869690 GTGTTCAAGAAGGCGCCTC 59.130 57.895 32.93 22.64 0.00 4.70
621 622 1.302511 TGTTCAAGAAGGCGCCTCC 60.303 57.895 32.93 20.17 0.00 4.30
622 623 2.041115 GTTCAAGAAGGCGCCTCCC 61.041 63.158 32.93 24.22 34.51 4.30
623 624 3.605749 TTCAAGAAGGCGCCTCCCG 62.606 63.158 32.93 18.65 40.75 5.14
635 636 2.765807 CTCCCGCCTGAGGTCCAT 60.766 66.667 0.00 0.00 0.00 3.41
636 637 3.083349 TCCCGCCTGAGGTCCATG 61.083 66.667 0.00 0.00 0.00 3.66
637 638 4.864334 CCCGCCTGAGGTCCATGC 62.864 72.222 0.00 0.00 33.75 4.06
642 643 4.457496 CTGAGGTCCATGCGGCGT 62.457 66.667 9.37 0.00 0.00 5.68
643 644 4.758251 TGAGGTCCATGCGGCGTG 62.758 66.667 15.20 15.20 0.00 5.34
644 645 4.451150 GAGGTCCATGCGGCGTGA 62.451 66.667 23.18 6.97 0.00 4.35
645 646 3.740128 GAGGTCCATGCGGCGTGAT 62.740 63.158 23.18 6.35 0.00 3.06
646 647 3.576356 GGTCCATGCGGCGTGATG 61.576 66.667 23.18 11.24 0.00 3.07
647 648 3.576356 GTCCATGCGGCGTGATGG 61.576 66.667 25.27 25.27 40.61 3.51
670 671 3.864686 GCCCGTAGCGTGCATGTG 61.865 66.667 7.93 0.00 29.43 3.21
671 672 2.434185 CCCGTAGCGTGCATGTGT 60.434 61.111 7.93 0.00 0.00 3.72
672 673 2.739704 CCCGTAGCGTGCATGTGTG 61.740 63.158 7.93 0.00 0.00 3.82
686 687 3.961182 CATGTGTGCATCTGAATAAGGC 58.039 45.455 0.00 0.00 31.99 4.35
687 688 3.354948 TGTGTGCATCTGAATAAGGCT 57.645 42.857 0.00 0.00 0.00 4.58
688 689 3.011818 TGTGTGCATCTGAATAAGGCTG 58.988 45.455 0.00 0.00 0.00 4.85
689 690 2.357009 GTGTGCATCTGAATAAGGCTGG 59.643 50.000 0.00 0.00 0.00 4.85
690 691 1.336125 GTGCATCTGAATAAGGCTGGC 59.664 52.381 0.00 0.00 0.00 4.85
691 692 0.957362 GCATCTGAATAAGGCTGGCC 59.043 55.000 3.00 3.00 0.00 5.36
692 693 1.233019 CATCTGAATAAGGCTGGCCG 58.767 55.000 5.93 0.00 41.95 6.13
693 694 1.131638 ATCTGAATAAGGCTGGCCGA 58.868 50.000 5.93 0.00 41.95 5.54
694 695 0.908910 TCTGAATAAGGCTGGCCGAA 59.091 50.000 5.93 0.00 41.95 4.30
695 696 1.280710 TCTGAATAAGGCTGGCCGAAA 59.719 47.619 5.93 0.00 41.95 3.46
696 697 1.401905 CTGAATAAGGCTGGCCGAAAC 59.598 52.381 5.93 0.00 41.95 2.78
697 698 1.271652 TGAATAAGGCTGGCCGAAACA 60.272 47.619 5.93 2.41 41.95 2.83
698 699 1.401905 GAATAAGGCTGGCCGAAACAG 59.598 52.381 5.93 0.00 41.95 3.16
699 700 0.328258 ATAAGGCTGGCCGAAACAGT 59.672 50.000 5.93 0.00 41.95 3.55
700 701 0.605319 TAAGGCTGGCCGAAACAGTG 60.605 55.000 5.93 0.00 41.95 3.66
701 702 2.594592 GGCTGGCCGAAACAGTGT 60.595 61.111 0.00 0.00 38.22 3.55
702 703 2.639286 GCTGGCCGAAACAGTGTG 59.361 61.111 0.00 0.00 38.22 3.82
703 704 2.639286 CTGGCCGAAACAGTGTGC 59.361 61.111 0.00 0.00 0.00 4.57
704 705 1.893808 CTGGCCGAAACAGTGTGCT 60.894 57.895 0.00 0.00 0.00 4.40
717 718 3.945179 CAGTGTGCTGTTTTTGTCTCTC 58.055 45.455 0.00 0.00 37.92 3.20
718 719 3.624861 CAGTGTGCTGTTTTTGTCTCTCT 59.375 43.478 0.00 0.00 37.92 3.10
719 720 4.095483 CAGTGTGCTGTTTTTGTCTCTCTT 59.905 41.667 0.00 0.00 37.92 2.85
720 721 5.294306 CAGTGTGCTGTTTTTGTCTCTCTTA 59.706 40.000 0.00 0.00 37.92 2.10
721 722 5.525378 AGTGTGCTGTTTTTGTCTCTCTTAG 59.475 40.000 0.00 0.00 0.00 2.18
722 723 5.523916 GTGTGCTGTTTTTGTCTCTCTTAGA 59.476 40.000 0.00 0.00 0.00 2.10
736 737 6.925211 TCTCTCTTAGACAATAAGTGTGGTG 58.075 40.000 0.00 0.00 41.96 4.17
737 738 6.719829 TCTCTCTTAGACAATAAGTGTGGTGA 59.280 38.462 0.00 0.00 41.96 4.02
738 739 7.397476 TCTCTCTTAGACAATAAGTGTGGTGAT 59.603 37.037 0.00 0.00 41.96 3.06
739 740 7.323420 TCTCTTAGACAATAAGTGTGGTGATG 58.677 38.462 0.00 0.00 41.96 3.07
740 741 7.004555 TCTTAGACAATAAGTGTGGTGATGT 57.995 36.000 0.00 0.00 41.96 3.06
741 742 6.873605 TCTTAGACAATAAGTGTGGTGATGTG 59.126 38.462 0.00 0.00 41.96 3.21
742 743 3.753272 AGACAATAAGTGTGGTGATGTGC 59.247 43.478 0.00 0.00 41.96 4.57
743 744 3.753272 GACAATAAGTGTGGTGATGTGCT 59.247 43.478 0.00 0.00 41.96 4.40
744 745 3.503363 ACAATAAGTGTGGTGATGTGCTG 59.497 43.478 0.00 0.00 39.72 4.41
745 746 2.928801 TAAGTGTGGTGATGTGCTGT 57.071 45.000 0.00 0.00 0.00 4.40
746 747 1.597742 AAGTGTGGTGATGTGCTGTC 58.402 50.000 0.00 0.00 0.00 3.51
747 748 0.250467 AGTGTGGTGATGTGCTGTCC 60.250 55.000 0.00 0.00 0.00 4.02
748 749 0.250467 GTGTGGTGATGTGCTGTCCT 60.250 55.000 0.00 0.00 0.00 3.85
749 750 0.035317 TGTGGTGATGTGCTGTCCTC 59.965 55.000 0.00 0.00 0.00 3.71
750 751 0.035317 GTGGTGATGTGCTGTCCTCA 59.965 55.000 0.00 0.00 0.00 3.86
751 752 0.035317 TGGTGATGTGCTGTCCTCAC 59.965 55.000 0.00 0.00 37.79 3.51
752 753 0.322975 GGTGATGTGCTGTCCTCACT 59.677 55.000 0.00 0.00 38.41 3.41
753 754 1.436600 GTGATGTGCTGTCCTCACTG 58.563 55.000 0.00 0.00 36.07 3.66
754 755 0.321034 TGATGTGCTGTCCTCACTGC 60.321 55.000 0.00 0.00 45.38 4.40
755 756 0.036577 GATGTGCTGTCCTCACTGCT 60.037 55.000 5.71 0.00 45.39 4.24
756 757 0.399454 ATGTGCTGTCCTCACTGCTT 59.601 50.000 5.71 0.00 45.39 3.91
757 758 1.047801 TGTGCTGTCCTCACTGCTTA 58.952 50.000 5.71 0.00 45.39 3.09
758 759 1.001293 TGTGCTGTCCTCACTGCTTAG 59.999 52.381 5.71 0.00 45.39 2.18
759 760 0.610174 TGCTGTCCTCACTGCTTAGG 59.390 55.000 5.71 0.00 45.39 2.69
760 761 0.610687 GCTGTCCTCACTGCTTAGGT 59.389 55.000 0.00 0.00 42.66 3.08
761 762 1.002544 GCTGTCCTCACTGCTTAGGTT 59.997 52.381 0.00 0.00 42.66 3.50
762 763 2.693069 CTGTCCTCACTGCTTAGGTTG 58.307 52.381 0.00 0.00 34.30 3.77
763 764 2.037772 CTGTCCTCACTGCTTAGGTTGT 59.962 50.000 0.00 0.00 34.30 3.32
764 765 2.438021 TGTCCTCACTGCTTAGGTTGTT 59.562 45.455 0.00 0.00 34.30 2.83
765 766 3.118038 TGTCCTCACTGCTTAGGTTGTTT 60.118 43.478 0.00 0.00 34.30 2.83
766 767 3.883489 GTCCTCACTGCTTAGGTTGTTTT 59.117 43.478 0.00 0.00 34.30 2.43
767 768 3.882888 TCCTCACTGCTTAGGTTGTTTTG 59.117 43.478 0.00 0.00 34.30 2.44
800 801 2.566833 TGCACTGCAGGTACTTGAAT 57.433 45.000 19.93 0.00 34.60 2.57
1066 1975 2.500229 CTAGTTTTGTTCCCCTCGCAA 58.500 47.619 0.00 0.00 0.00 4.85
2273 4051 3.365472 ACATAAGATGGCCAAAAGGACC 58.635 45.455 10.96 0.00 33.60 4.46
2492 4368 3.070734 TCTCTCTCTGCAAGCTTCTTTGT 59.929 43.478 0.00 0.00 0.00 2.83
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
247 248 4.402528 ATGCGCACGGGTAAGCCA 62.403 61.111 14.90 0.00 36.17 4.75
284 285 3.255379 GATCTTGTCGGACGGCGC 61.255 66.667 6.90 0.00 0.00 6.53
285 286 1.209275 GATGATCTTGTCGGACGGCG 61.209 60.000 4.80 4.80 0.00 6.46
286 287 0.876342 GGATGATCTTGTCGGACGGC 60.876 60.000 3.34 0.00 0.00 5.68
287 288 0.595053 CGGATGATCTTGTCGGACGG 60.595 60.000 3.34 0.00 0.00 4.79
288 289 0.595053 CCGGATGATCTTGTCGGACG 60.595 60.000 0.00 0.00 42.94 4.79
289 290 0.876342 GCCGGATGATCTTGTCGGAC 60.876 60.000 5.05 0.00 42.94 4.79
290 291 1.043116 AGCCGGATGATCTTGTCGGA 61.043 55.000 5.05 0.00 42.94 4.55
291 292 0.877649 CAGCCGGATGATCTTGTCGG 60.878 60.000 16.48 12.70 43.13 4.79
292 293 0.179100 ACAGCCGGATGATCTTGTCG 60.179 55.000 29.47 0.00 0.00 4.35
293 294 1.576356 GACAGCCGGATGATCTTGTC 58.424 55.000 29.47 8.52 0.00 3.18
294 295 0.179100 CGACAGCCGGATGATCTTGT 60.179 55.000 29.47 1.19 33.91 3.16
295 296 0.103026 TCGACAGCCGGATGATCTTG 59.897 55.000 29.47 8.33 39.14 3.02
296 297 0.103208 GTCGACAGCCGGATGATCTT 59.897 55.000 29.47 2.62 39.14 2.40
297 298 1.736586 GTCGACAGCCGGATGATCT 59.263 57.895 29.47 3.10 39.14 2.75
298 299 1.300233 GGTCGACAGCCGGATGATC 60.300 63.158 29.47 18.40 39.14 2.92
299 300 2.815308 GGTCGACAGCCGGATGAT 59.185 61.111 29.47 10.95 39.14 2.45
300 301 3.822192 CGGTCGACAGCCGGATGA 61.822 66.667 29.47 0.00 44.98 2.92
306 307 4.773117 GGACGTCGGTCGACAGCC 62.773 72.222 18.91 16.82 44.39 4.85
310 311 4.471726 ATGCGGACGTCGGTCGAC 62.472 66.667 22.19 7.13 44.39 4.20
311 312 4.170062 GATGCGGACGTCGGTCGA 62.170 66.667 22.19 9.03 44.39 4.20
312 313 4.175489 AGATGCGGACGTCGGTCG 62.175 66.667 22.19 15.31 44.39 4.79
313 314 2.278013 GAGATGCGGACGTCGGTC 60.278 66.667 22.19 13.76 42.66 4.79
314 315 3.823330 GGAGATGCGGACGTCGGT 61.823 66.667 22.19 5.52 39.69 4.69
315 316 2.938539 GAAGGAGATGCGGACGTCGG 62.939 65.000 17.98 17.98 39.69 4.79
316 317 1.586564 GAAGGAGATGCGGACGTCG 60.587 63.158 9.92 6.26 42.76 5.12
317 318 1.227002 GGAAGGAGATGCGGACGTC 60.227 63.158 7.13 7.13 0.00 4.34
318 319 2.893398 GGAAGGAGATGCGGACGT 59.107 61.111 0.00 0.00 0.00 4.34
319 320 2.278857 CGGAAGGAGATGCGGACG 60.279 66.667 0.00 0.00 0.00 4.79
320 321 2.586357 GCGGAAGGAGATGCGGAC 60.586 66.667 0.00 0.00 34.46 4.79
321 322 4.207281 CGCGGAAGGAGATGCGGA 62.207 66.667 0.00 0.00 46.31 5.54
324 325 3.151958 TAGGCGCGGAAGGAGATGC 62.152 63.158 8.83 0.00 0.00 3.91
325 326 1.300233 GTAGGCGCGGAAGGAGATG 60.300 63.158 8.83 0.00 0.00 2.90
326 327 1.756950 TGTAGGCGCGGAAGGAGAT 60.757 57.895 8.83 0.00 0.00 2.75
327 328 2.361992 TGTAGGCGCGGAAGGAGA 60.362 61.111 8.83 0.00 0.00 3.71
328 329 2.202756 GTGTAGGCGCGGAAGGAG 60.203 66.667 8.83 0.00 0.00 3.69
329 330 4.124351 CGTGTAGGCGCGGAAGGA 62.124 66.667 8.83 0.00 44.04 3.36
346 347 3.753539 GTCGACTGCACGCACGTC 61.754 66.667 8.70 9.96 0.00 4.34
349 350 4.994201 TCGGTCGACTGCACGCAC 62.994 66.667 19.89 0.00 0.00 5.34
350 351 4.700365 CTCGGTCGACTGCACGCA 62.700 66.667 19.89 0.79 0.00 5.24
351 352 4.702081 ACTCGGTCGACTGCACGC 62.702 66.667 19.89 0.00 0.00 5.34
352 353 2.801162 CACTCGGTCGACTGCACG 60.801 66.667 19.89 12.33 0.00 5.34
353 354 2.430921 CCACTCGGTCGACTGCAC 60.431 66.667 19.89 0.00 0.00 4.57
354 355 4.357947 GCCACTCGGTCGACTGCA 62.358 66.667 19.89 7.82 33.28 4.41
355 356 4.357947 TGCCACTCGGTCGACTGC 62.358 66.667 19.89 10.83 33.28 4.40
356 357 2.430921 GTGCCACTCGGTCGACTG 60.431 66.667 18.66 18.66 33.28 3.51
357 358 2.214181 GATGTGCCACTCGGTCGACT 62.214 60.000 16.46 0.00 33.28 4.18
358 359 1.805945 GATGTGCCACTCGGTCGAC 60.806 63.158 7.13 7.13 33.28 4.20
359 360 2.571757 GATGTGCCACTCGGTCGA 59.428 61.111 0.00 0.00 33.28 4.20
360 361 2.880879 CGATGTGCCACTCGGTCG 60.881 66.667 8.27 4.19 33.28 4.79
361 362 1.805945 GTCGATGTGCCACTCGGTC 60.806 63.158 13.88 6.83 35.64 4.79
362 363 2.261671 GTCGATGTGCCACTCGGT 59.738 61.111 13.88 0.00 35.64 4.69
363 364 1.807165 CTGTCGATGTGCCACTCGG 60.807 63.158 13.88 0.00 35.64 4.63
364 365 2.447887 GCTGTCGATGTGCCACTCG 61.448 63.158 9.46 9.46 36.25 4.18
365 366 2.447887 CGCTGTCGATGTGCCACTC 61.448 63.158 0.00 0.00 38.10 3.51
366 367 2.433145 CGCTGTCGATGTGCCACT 60.433 61.111 0.00 0.00 38.10 4.00
367 368 2.432456 TCGCTGTCGATGTGCCAC 60.432 61.111 0.00 0.00 40.21 5.01
368 369 2.125952 CTCGCTGTCGATGTGCCA 60.126 61.111 0.00 0.00 44.56 4.92
369 370 3.558411 GCTCGCTGTCGATGTGCC 61.558 66.667 0.00 0.00 44.56 5.01
370 371 2.507992 AGCTCGCTGTCGATGTGC 60.508 61.111 0.00 0.00 44.56 4.57
371 372 2.163390 CCAGCTCGCTGTCGATGTG 61.163 63.158 16.82 0.00 44.56 3.21
372 373 2.182791 CCAGCTCGCTGTCGATGT 59.817 61.111 16.82 0.00 44.56 3.06
373 374 2.163390 CACCAGCTCGCTGTCGATG 61.163 63.158 16.82 6.71 44.56 3.84
374 375 2.182791 CACCAGCTCGCTGTCGAT 59.817 61.111 16.82 0.00 44.56 3.59
375 376 3.268965 GACACCAGCTCGCTGTCGA 62.269 63.158 16.82 0.00 42.15 4.20
376 377 2.807045 GACACCAGCTCGCTGTCG 60.807 66.667 16.82 10.01 42.15 4.35
377 378 2.807045 CGACACCAGCTCGCTGTC 60.807 66.667 16.82 8.56 42.15 3.51
378 379 4.363990 CCGACACCAGCTCGCTGT 62.364 66.667 16.82 0.21 42.15 4.40
437 438 4.821589 GTTCTCCCTGCCGCTCGG 62.822 72.222 3.56 3.56 38.57 4.63
444 445 2.436824 GGAAGGCGTTCTCCCTGC 60.437 66.667 17.90 0.00 31.73 4.85
445 446 2.125512 CGGAAGGCGTTCTCCCTG 60.126 66.667 17.90 0.00 31.73 4.45
446 447 4.083862 GCGGAAGGCGTTCTCCCT 62.084 66.667 17.90 0.00 32.72 4.20
455 456 0.102481 TACTTCTCGATGCGGAAGGC 59.898 55.000 14.47 0.00 42.05 4.35
456 457 1.134367 TGTACTTCTCGATGCGGAAGG 59.866 52.381 14.47 0.62 42.05 3.46
457 458 2.455032 CTGTACTTCTCGATGCGGAAG 58.545 52.381 9.83 9.83 43.02 3.46
458 459 1.469251 GCTGTACTTCTCGATGCGGAA 60.469 52.381 0.00 0.00 0.00 4.30
459 460 0.100682 GCTGTACTTCTCGATGCGGA 59.899 55.000 0.00 0.00 0.00 5.54
460 461 1.202973 CGCTGTACTTCTCGATGCGG 61.203 60.000 0.00 0.00 38.54 5.69
461 462 1.202973 CCGCTGTACTTCTCGATGCG 61.203 60.000 0.00 0.00 41.30 4.73
462 463 1.483424 GCCGCTGTACTTCTCGATGC 61.483 60.000 0.00 0.00 0.00 3.91
463 464 1.202973 CGCCGCTGTACTTCTCGATG 61.203 60.000 0.00 0.00 0.00 3.84
464 465 1.064296 CGCCGCTGTACTTCTCGAT 59.936 57.895 0.00 0.00 0.00 3.59
465 466 2.483745 CGCCGCTGTACTTCTCGA 59.516 61.111 0.00 0.00 0.00 4.04
466 467 3.248171 GCGCCGCTGTACTTCTCG 61.248 66.667 0.00 0.00 0.00 4.04
467 468 3.248171 CGCGCCGCTGTACTTCTC 61.248 66.667 7.78 0.00 0.00 2.87
468 469 4.796231 CCGCGCCGCTGTACTTCT 62.796 66.667 7.78 0.00 0.00 2.85
469 470 4.789075 TCCGCGCCGCTGTACTTC 62.789 66.667 7.78 0.00 0.00 3.01
470 471 4.796231 CTCCGCGCCGCTGTACTT 62.796 66.667 7.78 0.00 0.00 2.24
481 482 4.111016 TACTCGTGCACCTCCGCG 62.111 66.667 12.15 0.00 39.87 6.46
482 483 2.506438 GTACTCGTGCACCTCCGC 60.506 66.667 12.15 0.00 0.00 5.54
483 484 0.732880 CTTGTACTCGTGCACCTCCG 60.733 60.000 12.15 0.00 0.00 4.63
484 485 1.014564 GCTTGTACTCGTGCACCTCC 61.015 60.000 12.15 0.00 0.00 4.30
485 486 0.038159 AGCTTGTACTCGTGCACCTC 60.038 55.000 12.15 0.00 0.00 3.85
486 487 0.038159 GAGCTTGTACTCGTGCACCT 60.038 55.000 12.15 0.00 0.00 4.00
487 488 0.319555 TGAGCTTGTACTCGTGCACC 60.320 55.000 12.15 0.00 39.68 5.01
488 489 1.391485 CATGAGCTTGTACTCGTGCAC 59.609 52.381 6.82 6.82 44.38 4.57
489 490 1.713597 CATGAGCTTGTACTCGTGCA 58.286 50.000 1.16 0.00 44.38 4.57
492 493 0.458543 CGCCATGAGCTTGTACTCGT 60.459 55.000 0.00 0.00 39.68 4.18
493 494 0.458543 ACGCCATGAGCTTGTACTCG 60.459 55.000 0.00 0.00 39.68 4.18
494 495 1.002366 CACGCCATGAGCTTGTACTC 58.998 55.000 0.00 0.00 40.39 2.59
495 496 1.021390 GCACGCCATGAGCTTGTACT 61.021 55.000 12.09 0.00 42.57 2.73
496 497 1.425428 GCACGCCATGAGCTTGTAC 59.575 57.895 12.09 0.00 42.57 2.90
497 498 2.100031 CGCACGCCATGAGCTTGTA 61.100 57.895 12.09 0.00 42.57 2.41
498 499 3.425713 CGCACGCCATGAGCTTGT 61.426 61.111 12.09 0.00 42.57 3.16
499 500 4.170062 CCGCACGCCATGAGCTTG 62.170 66.667 0.00 1.11 43.43 4.01
515 516 4.083862 GTCCTGGCACGAGTCCCC 62.084 72.222 0.00 0.00 0.00 4.81
516 517 4.083862 GGTCCTGGCACGAGTCCC 62.084 72.222 0.00 0.00 0.00 4.46
517 518 2.997897 AGGTCCTGGCACGAGTCC 60.998 66.667 0.00 0.00 0.00 3.85
518 519 2.574399 GAGGTCCTGGCACGAGTC 59.426 66.667 0.00 0.00 0.00 3.36
519 520 3.374402 CGAGGTCCTGGCACGAGT 61.374 66.667 0.00 0.00 0.00 4.18
520 521 4.135153 CCGAGGTCCTGGCACGAG 62.135 72.222 0.00 0.00 0.00 4.18
526 527 3.934391 GAACACGCCGAGGTCCTGG 62.934 68.421 0.00 0.00 0.00 4.45
527 528 2.432628 GAACACGCCGAGGTCCTG 60.433 66.667 0.00 0.00 0.00 3.86
528 529 2.915659 TGAACACGCCGAGGTCCT 60.916 61.111 0.00 0.00 0.00 3.85
529 530 2.432628 CTGAACACGCCGAGGTCC 60.433 66.667 0.00 0.00 0.00 4.46
530 531 2.432628 CCTGAACACGCCGAGGTC 60.433 66.667 0.00 0.00 0.00 3.85
531 532 4.003788 CCCTGAACACGCCGAGGT 62.004 66.667 0.00 0.00 0.00 3.85
532 533 3.691342 TCCCTGAACACGCCGAGG 61.691 66.667 0.00 0.00 0.00 4.63
533 534 2.432628 GTCCCTGAACACGCCGAG 60.433 66.667 0.00 0.00 0.00 4.63
534 535 3.998672 GGTCCCTGAACACGCCGA 61.999 66.667 0.00 0.00 0.00 5.54
535 536 3.934391 GAGGTCCCTGAACACGCCG 62.934 68.421 0.00 0.00 0.00 6.46
536 537 2.047179 GAGGTCCCTGAACACGCC 60.047 66.667 0.00 0.00 0.00 5.68
537 538 0.951040 CTTGAGGTCCCTGAACACGC 60.951 60.000 0.00 0.00 0.00 5.34
538 539 0.320771 CCTTGAGGTCCCTGAACACG 60.321 60.000 0.00 0.00 0.00 4.49
539 540 0.036875 CCCTTGAGGTCCCTGAACAC 59.963 60.000 0.00 0.00 0.00 3.32
540 541 1.779061 GCCCTTGAGGTCCCTGAACA 61.779 60.000 0.00 0.00 38.26 3.18
541 542 1.002011 GCCCTTGAGGTCCCTGAAC 60.002 63.158 0.00 0.00 38.26 3.18
542 543 2.592993 CGCCCTTGAGGTCCCTGAA 61.593 63.158 0.00 0.00 38.26 3.02
543 544 3.003173 CGCCCTTGAGGTCCCTGA 61.003 66.667 0.00 0.00 38.26 3.86
544 545 4.101448 CCGCCCTTGAGGTCCCTG 62.101 72.222 0.00 0.00 38.26 4.45
578 579 4.157120 ATGGTACGGCTCGGTGGC 62.157 66.667 0.00 0.00 37.94 5.01
579 580 2.202878 CATGGTACGGCTCGGTGG 60.203 66.667 0.00 0.00 0.00 4.61
580 581 1.518572 GACATGGTACGGCTCGGTG 60.519 63.158 0.00 0.00 0.00 4.94
581 582 1.327690 ATGACATGGTACGGCTCGGT 61.328 55.000 0.00 0.00 0.00 4.69
582 583 0.597637 GATGACATGGTACGGCTCGG 60.598 60.000 0.00 0.00 0.00 4.63
583 584 0.934901 CGATGACATGGTACGGCTCG 60.935 60.000 0.00 0.00 0.00 5.03
584 585 0.102481 ACGATGACATGGTACGGCTC 59.898 55.000 0.64 0.00 0.00 4.70
585 586 0.179111 CACGATGACATGGTACGGCT 60.179 55.000 2.49 0.00 0.00 5.52
586 587 0.459585 ACACGATGACATGGTACGGC 60.460 55.000 2.49 0.00 0.00 5.68
587 588 1.924524 GAACACGATGACATGGTACGG 59.075 52.381 2.49 0.00 0.00 4.02
588 589 2.601804 TGAACACGATGACATGGTACG 58.398 47.619 2.49 0.00 0.00 3.67
589 590 4.242475 TCTTGAACACGATGACATGGTAC 58.758 43.478 2.49 0.00 0.00 3.34
590 591 4.529109 TCTTGAACACGATGACATGGTA 57.471 40.909 2.49 0.00 0.00 3.25
591 592 3.401033 TCTTGAACACGATGACATGGT 57.599 42.857 0.00 0.00 0.00 3.55
592 593 3.125829 CCTTCTTGAACACGATGACATGG 59.874 47.826 0.00 0.00 0.00 3.66
593 594 3.425359 GCCTTCTTGAACACGATGACATG 60.425 47.826 0.00 0.00 0.00 3.21
594 595 2.744202 GCCTTCTTGAACACGATGACAT 59.256 45.455 0.00 0.00 0.00 3.06
595 596 2.143122 GCCTTCTTGAACACGATGACA 58.857 47.619 0.00 0.00 0.00 3.58
596 597 1.126846 CGCCTTCTTGAACACGATGAC 59.873 52.381 0.00 0.00 0.00 3.06
597 598 1.428448 CGCCTTCTTGAACACGATGA 58.572 50.000 0.00 0.00 0.00 2.92
598 599 0.179215 GCGCCTTCTTGAACACGATG 60.179 55.000 0.00 0.00 0.00 3.84
599 600 1.298859 GGCGCCTTCTTGAACACGAT 61.299 55.000 22.15 0.00 0.00 3.73
600 601 1.959226 GGCGCCTTCTTGAACACGA 60.959 57.895 22.15 0.00 0.00 4.35
601 602 1.901650 GAGGCGCCTTCTTGAACACG 61.902 60.000 33.34 0.00 0.00 4.49
602 603 1.578206 GGAGGCGCCTTCTTGAACAC 61.578 60.000 33.34 14.28 0.00 3.32
603 604 1.302511 GGAGGCGCCTTCTTGAACA 60.303 57.895 33.34 0.00 0.00 3.18
604 605 2.041115 GGGAGGCGCCTTCTTGAAC 61.041 63.158 33.42 17.31 36.66 3.18
605 606 2.351276 GGGAGGCGCCTTCTTGAA 59.649 61.111 33.42 0.00 36.66 2.69
606 607 4.082523 CGGGAGGCGCCTTCTTGA 62.083 66.667 33.42 0.00 36.66 3.02
618 619 2.765807 ATGGACCTCAGGCGGGAG 60.766 66.667 0.00 2.68 34.62 4.30
619 620 3.083349 CATGGACCTCAGGCGGGA 61.083 66.667 0.00 0.00 0.00 5.14
620 621 4.864334 GCATGGACCTCAGGCGGG 62.864 72.222 0.00 0.00 43.41 6.13
625 626 4.457496 ACGCCGCATGGACCTCAG 62.457 66.667 0.00 0.00 37.49 3.35
626 627 4.758251 CACGCCGCATGGACCTCA 62.758 66.667 0.00 0.00 37.49 3.86
627 628 3.740128 ATCACGCCGCATGGACCTC 62.740 63.158 0.00 0.00 37.49 3.85
628 629 3.785859 ATCACGCCGCATGGACCT 61.786 61.111 0.00 0.00 37.49 3.85
629 630 3.576356 CATCACGCCGCATGGACC 61.576 66.667 0.00 0.00 37.49 4.46
630 631 3.576356 CCATCACGCCGCATGGAC 61.576 66.667 9.54 0.00 42.11 4.02
654 655 2.434185 ACACATGCACGCTACGGG 60.434 61.111 0.00 0.00 0.00 5.28
655 656 2.778026 CACACATGCACGCTACGG 59.222 61.111 0.00 0.00 0.00 4.02
665 666 3.630769 AGCCTTATTCAGATGCACACATG 59.369 43.478 0.00 0.00 36.35 3.21
666 667 3.630769 CAGCCTTATTCAGATGCACACAT 59.369 43.478 0.00 0.00 39.98 3.21
667 668 3.011818 CAGCCTTATTCAGATGCACACA 58.988 45.455 0.00 0.00 0.00 3.72
668 669 2.357009 CCAGCCTTATTCAGATGCACAC 59.643 50.000 0.00 0.00 0.00 3.82
669 670 2.646930 CCAGCCTTATTCAGATGCACA 58.353 47.619 0.00 0.00 0.00 4.57
670 671 1.336125 GCCAGCCTTATTCAGATGCAC 59.664 52.381 0.00 0.00 0.00 4.57
671 672 1.683943 GCCAGCCTTATTCAGATGCA 58.316 50.000 0.00 0.00 0.00 3.96
672 673 0.957362 GGCCAGCCTTATTCAGATGC 59.043 55.000 0.00 0.00 0.00 3.91
673 674 1.202687 TCGGCCAGCCTTATTCAGATG 60.203 52.381 2.24 0.00 0.00 2.90
674 675 1.131638 TCGGCCAGCCTTATTCAGAT 58.868 50.000 2.24 0.00 0.00 2.90
675 676 0.908910 TTCGGCCAGCCTTATTCAGA 59.091 50.000 2.24 0.00 0.00 3.27
676 677 1.401905 GTTTCGGCCAGCCTTATTCAG 59.598 52.381 2.24 0.00 0.00 3.02
677 678 1.271652 TGTTTCGGCCAGCCTTATTCA 60.272 47.619 2.24 0.00 0.00 2.57
678 679 1.401905 CTGTTTCGGCCAGCCTTATTC 59.598 52.381 2.24 0.00 0.00 1.75
679 680 1.271926 ACTGTTTCGGCCAGCCTTATT 60.272 47.619 2.24 0.00 33.09 1.40
680 681 0.328258 ACTGTTTCGGCCAGCCTTAT 59.672 50.000 2.24 0.00 33.09 1.73
681 682 0.605319 CACTGTTTCGGCCAGCCTTA 60.605 55.000 2.24 0.00 33.09 2.69
682 683 1.898574 CACTGTTTCGGCCAGCCTT 60.899 57.895 2.24 0.00 33.09 4.35
683 684 2.281761 CACTGTTTCGGCCAGCCT 60.282 61.111 2.24 0.00 33.09 4.58
684 685 2.594592 ACACTGTTTCGGCCAGCC 60.595 61.111 2.24 0.00 33.09 4.85
685 686 2.639286 CACACTGTTTCGGCCAGC 59.361 61.111 2.24 0.00 33.09 4.85
686 687 1.893808 AGCACACTGTTTCGGCCAG 60.894 57.895 2.24 0.00 36.01 4.85
687 688 2.186160 CAGCACACTGTTTCGGCCA 61.186 57.895 2.24 0.00 39.22 5.36
688 689 2.639286 CAGCACACTGTTTCGGCC 59.361 61.111 0.00 0.00 39.22 6.13
697 698 3.878778 AGAGAGACAAAAACAGCACACT 58.121 40.909 0.00 0.00 0.00 3.55
698 699 4.622701 AAGAGAGACAAAAACAGCACAC 57.377 40.909 0.00 0.00 0.00 3.82
699 700 5.670485 TCTAAGAGAGACAAAAACAGCACA 58.330 37.500 0.00 0.00 0.00 4.57
712 713 6.719829 TCACCACACTTATTGTCTAAGAGAGA 59.280 38.462 0.00 0.00 35.67 3.10
713 714 6.925211 TCACCACACTTATTGTCTAAGAGAG 58.075 40.000 0.00 0.00 35.67 3.20
714 715 6.911250 TCACCACACTTATTGTCTAAGAGA 57.089 37.500 0.00 0.00 35.67 3.10
715 716 7.063898 CACATCACCACACTTATTGTCTAAGAG 59.936 40.741 0.00 0.00 35.67 2.85
716 717 6.873605 CACATCACCACACTTATTGTCTAAGA 59.126 38.462 0.00 0.00 35.67 2.10
717 718 6.402550 GCACATCACCACACTTATTGTCTAAG 60.403 42.308 0.00 0.00 35.67 2.18
718 719 5.411361 GCACATCACCACACTTATTGTCTAA 59.589 40.000 0.00 0.00 35.67 2.10
719 720 4.935205 GCACATCACCACACTTATTGTCTA 59.065 41.667 0.00 0.00 35.67 2.59
720 721 3.753272 GCACATCACCACACTTATTGTCT 59.247 43.478 0.00 0.00 35.67 3.41
721 722 3.753272 AGCACATCACCACACTTATTGTC 59.247 43.478 0.00 0.00 35.67 3.18
722 723 3.503363 CAGCACATCACCACACTTATTGT 59.497 43.478 0.00 0.00 39.97 2.71
723 724 3.503363 ACAGCACATCACCACACTTATTG 59.497 43.478 0.00 0.00 0.00 1.90
724 725 3.753272 GACAGCACATCACCACACTTATT 59.247 43.478 0.00 0.00 0.00 1.40
725 726 3.338249 GACAGCACATCACCACACTTAT 58.662 45.455 0.00 0.00 0.00 1.73
726 727 2.549992 GGACAGCACATCACCACACTTA 60.550 50.000 0.00 0.00 0.00 2.24
727 728 1.597742 GACAGCACATCACCACACTT 58.402 50.000 0.00 0.00 0.00 3.16
728 729 0.250467 GGACAGCACATCACCACACT 60.250 55.000 0.00 0.00 0.00 3.55
729 730 0.250467 AGGACAGCACATCACCACAC 60.250 55.000 0.00 0.00 0.00 3.82
730 731 0.035317 GAGGACAGCACATCACCACA 59.965 55.000 0.00 0.00 0.00 4.17
731 732 0.035317 TGAGGACAGCACATCACCAC 59.965 55.000 0.00 0.00 0.00 4.16
732 733 0.035317 GTGAGGACAGCACATCACCA 59.965 55.000 10.59 0.00 42.99 4.17
733 734 2.846371 GTGAGGACAGCACATCACC 58.154 57.895 10.59 0.00 42.99 4.02
735 736 0.321034 GCAGTGAGGACAGCACATCA 60.321 55.000 0.00 0.00 38.70 3.07
736 737 0.036577 AGCAGTGAGGACAGCACATC 60.037 55.000 0.00 0.00 37.07 3.06
737 738 0.399454 AAGCAGTGAGGACAGCACAT 59.601 50.000 0.00 0.00 37.07 3.21
738 739 1.001293 CTAAGCAGTGAGGACAGCACA 59.999 52.381 0.00 0.00 37.07 4.57
739 740 1.674221 CCTAAGCAGTGAGGACAGCAC 60.674 57.143 0.00 0.00 37.07 4.40
740 741 0.610174 CCTAAGCAGTGAGGACAGCA 59.390 55.000 0.00 0.00 37.07 4.41
741 742 0.610687 ACCTAAGCAGTGAGGACAGC 59.389 55.000 3.44 0.00 36.61 4.40
742 743 2.037772 ACAACCTAAGCAGTGAGGACAG 59.962 50.000 3.44 0.00 36.61 3.51
743 744 2.047061 ACAACCTAAGCAGTGAGGACA 58.953 47.619 3.44 0.00 36.61 4.02
744 745 2.841442 ACAACCTAAGCAGTGAGGAC 57.159 50.000 3.44 0.00 36.61 3.85
745 746 3.857157 AAACAACCTAAGCAGTGAGGA 57.143 42.857 3.44 0.00 36.61 3.71
746 747 3.632145 ACAAAACAACCTAAGCAGTGAGG 59.368 43.478 0.00 0.00 38.92 3.86
747 748 4.335315 TCACAAAACAACCTAAGCAGTGAG 59.665 41.667 0.00 0.00 0.00 3.51
748 749 4.265893 TCACAAAACAACCTAAGCAGTGA 58.734 39.130 0.00 0.00 0.00 3.41
749 750 4.630894 TCACAAAACAACCTAAGCAGTG 57.369 40.909 0.00 0.00 0.00 3.66
750 751 5.417580 TCTTTCACAAAACAACCTAAGCAGT 59.582 36.000 0.00 0.00 0.00 4.40
751 752 5.890334 TCTTTCACAAAACAACCTAAGCAG 58.110 37.500 0.00 0.00 0.00 4.24
752 753 5.417580 ACTCTTTCACAAAACAACCTAAGCA 59.582 36.000 0.00 0.00 0.00 3.91
753 754 5.891451 ACTCTTTCACAAAACAACCTAAGC 58.109 37.500 0.00 0.00 0.00 3.09
754 755 9.849166 TTTTACTCTTTCACAAAACAACCTAAG 57.151 29.630 0.00 0.00 0.00 2.18
756 757 9.796120 CATTTTACTCTTTCACAAAACAACCTA 57.204 29.630 0.00 0.00 0.00 3.08
757 758 7.277760 GCATTTTACTCTTTCACAAAACAACCT 59.722 33.333 0.00 0.00 0.00 3.50
758 759 7.064016 TGCATTTTACTCTTTCACAAAACAACC 59.936 33.333 0.00 0.00 0.00 3.77
759 760 7.897800 GTGCATTTTACTCTTTCACAAAACAAC 59.102 33.333 0.00 0.00 0.00 3.32
760 761 7.816995 AGTGCATTTTACTCTTTCACAAAACAA 59.183 29.630 0.00 0.00 0.00 2.83
761 762 7.275341 CAGTGCATTTTACTCTTTCACAAAACA 59.725 33.333 0.00 0.00 0.00 2.83
762 763 7.612266 CAGTGCATTTTACTCTTTCACAAAAC 58.388 34.615 0.00 0.00 0.00 2.43
763 764 6.255453 GCAGTGCATTTTACTCTTTCACAAAA 59.745 34.615 11.09 0.00 0.00 2.44
764 765 5.748152 GCAGTGCATTTTACTCTTTCACAAA 59.252 36.000 11.09 0.00 0.00 2.83
765 766 5.163571 TGCAGTGCATTTTACTCTTTCACAA 60.164 36.000 15.37 0.00 31.71 3.33
766 767 4.337836 TGCAGTGCATTTTACTCTTTCACA 59.662 37.500 15.37 0.00 31.71 3.58
767 768 4.858935 TGCAGTGCATTTTACTCTTTCAC 58.141 39.130 15.37 0.00 31.71 3.18
2273 4051 6.036517 CTAGTGCTAGAAATGTTAGGCAACTG 59.963 42.308 0.00 0.00 40.96 3.16
2492 4368 0.321919 CCAGAAACAGGCTGCTGCTA 60.322 55.000 15.89 0.00 39.59 3.49


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

AutoCloner maintained by Alex Coulton.