Multiple sequence alignment - TraesCS5D01G336900

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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 TraesCS5D01G336900 chr5D 100.000 3623 0 0 1 3623 426013952 426017574 0.000000e+00 6691.0
1 TraesCS5D01G336900 chr5D 91.566 1577 117 10 1759 3326 426036566 426038135 0.000000e+00 2161.0
2 TraesCS5D01G336900 chr5D 94.004 467 15 2 1005 1468 426035871 426036327 0.000000e+00 695.0
3 TraesCS5D01G336900 chr5D 93.960 149 9 0 3475 3623 426038252 426038400 3.640000e-55 226.0
4 TraesCS5D01G336900 chr5D 91.667 84 7 0 3324 3407 426038173 426038256 2.290000e-22 117.0
5 TraesCS5D01G336900 chr5A 90.165 1698 136 20 1638 3325 540320696 540322372 0.000000e+00 2182.0
6 TraesCS5D01G336900 chr5A 89.323 768 61 12 797 1553 540319910 540320667 0.000000e+00 944.0
7 TraesCS5D01G336900 chr5A 86.093 302 39 3 3324 3623 540322411 540322711 4.510000e-84 322.0
8 TraesCS5D01G336900 chr5B 94.628 968 47 4 1739 2703 515587622 515588587 0.000000e+00 1495.0
9 TraesCS5D01G336900 chr5B 94.609 946 31 6 569 1514 515586607 515587532 0.000000e+00 1447.0
10 TraesCS5D01G336900 chr5B 90.726 496 35 2 2728 3223 515588867 515589351 0.000000e+00 651.0
11 TraesCS5D01G336900 chr5B 90.863 394 17 9 1 388 515585852 515586232 8.970000e-141 510.0
12 TraesCS5D01G336900 chr5B 90.604 149 14 0 3475 3623 515699854 515700002 7.930000e-47 198.0
13 TraesCS5D01G336900 chr5B 79.612 206 36 3 1534 1734 253175145 253175349 3.770000e-30 143.0
14 TraesCS5D01G336900 chr2B 92.344 209 16 0 1030 1238 406098764 406098972 7.610000e-77 298.0
15 TraesCS5D01G336900 chr2B 82.439 205 27 8 1533 1734 416816027 416815829 1.730000e-38 171.0
16 TraesCS5D01G336900 chr2B 78.378 111 20 4 2042 2150 507911660 507911552 6.490000e-08 69.4
17 TraesCS5D01G336900 chr2B 85.965 57 6 2 2042 2098 508214147 508214093 3.910000e-05 60.2
18 TraesCS5D01G336900 chr2A 92.344 209 16 0 1030 1238 451013629 451013421 7.610000e-77 298.0
19 TraesCS5D01G336900 chr2A 89.202 213 23 0 1026 1238 555883349 555883561 2.140000e-67 267.0
20 TraesCS5D01G336900 chr2A 89.202 213 23 0 1026 1238 556986389 556986601 2.140000e-67 267.0
21 TraesCS5D01G336900 chr2A 80.189 212 30 5 1236 1447 555887768 555887967 8.110000e-32 148.0
22 TraesCS5D01G336900 chr2D 89.952 209 21 0 1030 1238 340270381 340270589 1.660000e-68 270.0
23 TraesCS5D01G336900 chr2D 89.202 213 23 0 1026 1238 430441955 430441743 2.140000e-67 267.0
24 TraesCS5D01G336900 chr2D 86.928 153 15 1 1533 1680 539169765 539169613 2.240000e-37 167.0
25 TraesCS5D01G336900 chr2D 81.863 204 30 6 1533 1734 350746805 350746607 8.050000e-37 165.0
26 TraesCS5D01G336900 chr2D 83.544 79 9 3 2047 2123 430021983 430021907 1.800000e-08 71.3
27 TraesCS5D01G336900 chr6B 85.256 156 20 3 1538 1691 210610867 210611021 1.350000e-34 158.0
28 TraesCS5D01G336900 chr4A 80.751 213 32 4 1533 1740 708426470 708426678 1.350000e-34 158.0
29 TraesCS5D01G336900 chr1D 81.463 205 24 5 1533 1724 45133328 45133125 4.840000e-34 156.0
30 TraesCS5D01G336900 chr1A 78.899 218 37 4 1533 1743 9856431 9856216 4.880000e-29 139.0
31 TraesCS5D01G336900 chr7D 79.327 208 33 8 1535 1734 16394436 16394231 1.750000e-28 137.0
32 TraesCS5D01G336900 chr4D 90.909 55 4 1 1686 1740 400328932 400328879 5.020000e-09 73.1


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS5D01G336900 chr5D 426013952 426017574 3622 False 6691.000000 6691 100.00000 1 3623 1 chr5D.!!$F1 3622
1 TraesCS5D01G336900 chr5D 426035871 426038400 2529 False 799.750000 2161 92.79925 1005 3623 4 chr5D.!!$F2 2618
2 TraesCS5D01G336900 chr5A 540319910 540322711 2801 False 1149.333333 2182 88.52700 797 3623 3 chr5A.!!$F1 2826
3 TraesCS5D01G336900 chr5B 515585852 515589351 3499 False 1025.750000 1495 92.70650 1 3223 4 chr5B.!!$F3 3222

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
543 550 0.035317 ATGCTGACCTGTGAAAGCGA 59.965 50.0 0.0 0.0 38.53 4.93 F
552 559 0.107410 TGTGAAAGCGACTTGGTGGT 60.107 50.0 0.0 0.0 0.00 4.16 F
554 561 0.179234 TGAAAGCGACTTGGTGGTCA 59.821 50.0 0.0 0.0 36.12 4.02 F
766 1001 0.462047 ACGATGGGGAGCGAACAATC 60.462 55.0 0.0 0.0 0.00 2.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2409 2856 0.034186 GGCACACATCATTCCCCTGA 60.034 55.000 0.0 0.0 0.0 3.86 R
2418 2865 0.255604 CTGGTATGGGGCACACATCA 59.744 55.000 0.0 0.0 0.0 3.07 R
2547 2994 3.387699 TCAGGAAATCATGGTAGCGATCA 59.612 43.478 0.0 0.0 0.0 2.92 R
2680 3129 0.178992 CACACACACACCCCTTCCAT 60.179 55.000 0.0 0.0 0.0 3.41 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
21 22 2.280389 CGAGGCGCCTATGCATGT 60.280 61.111 32.97 4.00 37.32 3.21
22 23 1.889105 CGAGGCGCCTATGCATGTT 60.889 57.895 32.97 3.02 37.32 2.71
23 24 1.835483 CGAGGCGCCTATGCATGTTC 61.835 60.000 32.97 13.08 37.32 3.18
24 25 0.533755 GAGGCGCCTATGCATGTTCT 60.534 55.000 32.97 1.35 37.32 3.01
144 148 0.166814 GATTCAGTGCCTTGCGTGAC 59.833 55.000 0.00 0.00 0.00 3.67
166 170 3.290776 GTCAAAGGCTGACGACTGT 57.709 52.632 0.00 0.00 44.95 3.55
205 209 2.759973 TAGACCCAGCCTCGGCAG 60.760 66.667 11.02 1.58 44.88 4.85
224 228 3.552684 GCAGTTCAGCATGTAAAAGGCAA 60.553 43.478 0.00 0.00 38.31 4.52
235 239 3.636300 TGTAAAAGGCAACAGAGTTGCAT 59.364 39.130 29.06 22.82 46.58 3.96
243 249 5.355350 AGGCAACAGAGTTGCATATTTACTC 59.645 40.000 29.06 13.23 46.58 2.59
246 252 6.676456 GCAACAGAGTTGCATATTTACTCCTG 60.676 42.308 25.02 10.83 44.34 3.86
260 266 6.662865 TTTACTCCTGGAATCAAAATGCAA 57.337 33.333 0.00 0.00 0.00 4.08
305 312 5.689835 TGCCCAGTGTATTATAGCAAATCA 58.310 37.500 0.00 0.00 0.00 2.57
314 321 9.640963 GTGTATTATAGCAAATCAGTACTAGGG 57.359 37.037 0.00 0.00 0.00 3.53
315 322 9.596308 TGTATTATAGCAAATCAGTACTAGGGA 57.404 33.333 0.00 0.00 0.00 4.20
317 324 8.728596 ATTATAGCAAATCAGTACTAGGGAGT 57.271 34.615 0.00 0.00 39.92 3.85
318 325 9.824216 ATTATAGCAAATCAGTACTAGGGAGTA 57.176 33.333 0.00 0.00 37.10 2.59
341 348 3.340814 AGCGATGACTTGGAGAAACAT 57.659 42.857 0.00 0.00 0.00 2.71
347 354 5.004821 CGATGACTTGGAGAAACATAAGACG 59.995 44.000 0.00 0.00 0.00 4.18
367 374 3.879932 GTTGCAGAAACGCTCTAAACT 57.120 42.857 0.00 0.00 31.56 2.66
368 375 4.210832 GTTGCAGAAACGCTCTAAACTT 57.789 40.909 0.00 0.00 31.56 2.66
369 376 3.878086 TGCAGAAACGCTCTAAACTTG 57.122 42.857 0.00 0.00 31.12 3.16
370 377 2.548057 TGCAGAAACGCTCTAAACTTGG 59.452 45.455 0.00 0.00 31.12 3.61
371 378 2.548480 GCAGAAACGCTCTAAACTTGGT 59.452 45.455 0.00 0.00 31.12 3.67
372 379 3.607078 GCAGAAACGCTCTAAACTTGGTG 60.607 47.826 0.00 0.00 31.12 4.17
373 380 3.807622 CAGAAACGCTCTAAACTTGGTGA 59.192 43.478 0.00 0.00 31.12 4.02
374 381 3.808174 AGAAACGCTCTAAACTTGGTGAC 59.192 43.478 0.00 0.00 30.22 3.67
375 382 2.902705 ACGCTCTAAACTTGGTGACA 57.097 45.000 0.00 0.00 39.83 3.58
376 383 3.402628 ACGCTCTAAACTTGGTGACAT 57.597 42.857 0.00 0.00 42.32 3.06
377 384 3.326747 ACGCTCTAAACTTGGTGACATC 58.673 45.455 0.00 0.00 42.32 3.06
378 385 3.006967 ACGCTCTAAACTTGGTGACATCT 59.993 43.478 0.00 0.00 42.32 2.90
379 386 3.997021 CGCTCTAAACTTGGTGACATCTT 59.003 43.478 0.00 0.00 42.32 2.40
380 387 4.452455 CGCTCTAAACTTGGTGACATCTTT 59.548 41.667 0.00 0.00 42.32 2.52
381 388 5.049405 CGCTCTAAACTTGGTGACATCTTTT 60.049 40.000 0.00 0.00 42.32 2.27
382 389 6.145535 GCTCTAAACTTGGTGACATCTTTTG 58.854 40.000 0.00 0.00 42.32 2.44
383 390 6.238759 GCTCTAAACTTGGTGACATCTTTTGT 60.239 38.462 0.00 0.00 42.32 2.83
384 391 7.026631 TCTAAACTTGGTGACATCTTTTGTG 57.973 36.000 0.00 0.00 42.32 3.33
385 392 5.913137 AAACTTGGTGACATCTTTTGTGA 57.087 34.783 0.00 0.00 42.32 3.58
386 393 6.469782 AAACTTGGTGACATCTTTTGTGAT 57.530 33.333 0.00 0.00 42.32 3.06
387 394 7.581213 AAACTTGGTGACATCTTTTGTGATA 57.419 32.000 0.00 0.00 42.32 2.15
388 395 7.581213 AACTTGGTGACATCTTTTGTGATAA 57.419 32.000 0.00 0.00 42.32 1.75
389 396 7.581213 ACTTGGTGACATCTTTTGTGATAAA 57.419 32.000 0.00 0.00 42.32 1.40
390 397 8.006298 ACTTGGTGACATCTTTTGTGATAAAA 57.994 30.769 0.00 0.00 42.32 1.52
391 398 7.920682 ACTTGGTGACATCTTTTGTGATAAAAC 59.079 33.333 0.00 0.00 42.32 2.43
392 399 6.434596 TGGTGACATCTTTTGTGATAAAACG 58.565 36.000 0.00 0.00 39.18 3.60
393 400 5.342259 GGTGACATCTTTTGTGATAAAACGC 59.658 40.000 0.00 0.00 39.18 4.84
394 401 6.142817 GTGACATCTTTTGTGATAAAACGCT 58.857 36.000 0.00 0.00 39.18 5.07
395 402 6.303259 GTGACATCTTTTGTGATAAAACGCTC 59.697 38.462 0.00 0.00 39.18 5.03
398 405 8.094798 ACATCTTTTGTGATAAAACGCTCTAA 57.905 30.769 0.00 0.00 37.11 2.10
403 410 8.555166 TTTTGTGATAAAACGCTCTAAACTTG 57.445 30.769 0.00 0.00 0.00 3.16
416 423 5.121768 GCTCTAAACTTGGCGACATCTTTTA 59.878 40.000 0.00 0.00 42.32 1.52
423 430 7.426929 ACTTGGCGACATCTTTTATGATATC 57.573 36.000 0.00 0.00 42.32 1.63
424 431 6.146184 ACTTGGCGACATCTTTTATGATATCG 59.854 38.462 0.00 1.48 43.63 2.92
426 433 6.683715 TGGCGACATCTTTTATGATATCGTA 58.316 36.000 0.20 0.20 42.99 3.43
428 435 6.237227 GGCGACATCTTTTATGATATCGTACG 60.237 42.308 9.53 9.53 42.99 3.67
430 437 7.479603 GCGACATCTTTTATGATATCGTACGTA 59.520 37.037 16.05 7.55 42.99 3.57
432 439 9.603298 GACATCTTTTATGATATCGTACGTACA 57.397 33.333 24.50 12.54 0.00 2.90
435 442 8.870242 TCTTTTATGATATCGTACGTACATCG 57.130 34.615 24.50 11.75 46.00 3.84
436 443 8.711457 TCTTTTATGATATCGTACGTACATCGA 58.289 33.333 24.50 16.59 42.86 3.59
437 444 8.645649 TTTTATGATATCGTACGTACATCGAC 57.354 34.615 24.50 12.88 42.86 4.20
446 453 2.182904 CGTACATCGACGGTGAATCA 57.817 50.000 16.46 0.00 42.86 2.57
447 454 2.727777 CGTACATCGACGGTGAATCAT 58.272 47.619 16.46 0.00 42.86 2.45
449 456 4.473199 CGTACATCGACGGTGAATCATAT 58.527 43.478 16.46 0.00 42.86 1.78
450 457 4.320953 CGTACATCGACGGTGAATCATATG 59.679 45.833 16.46 0.00 42.86 1.78
452 459 5.139435 ACATCGACGGTGAATCATATGAT 57.861 39.130 16.46 12.62 36.07 2.45
453 460 4.925646 ACATCGACGGTGAATCATATGATG 59.074 41.667 18.85 8.50 37.35 3.07
454 461 4.846779 TCGACGGTGAATCATATGATGA 57.153 40.909 18.85 6.30 44.55 2.92
455 462 4.798574 TCGACGGTGAATCATATGATGAG 58.201 43.478 18.85 10.73 43.53 2.90
456 463 4.518970 TCGACGGTGAATCATATGATGAGA 59.481 41.667 18.85 8.35 43.53 3.27
457 464 4.855937 CGACGGTGAATCATATGATGAGAG 59.144 45.833 18.85 11.67 43.53 3.20
458 465 4.564041 ACGGTGAATCATATGATGAGAGC 58.436 43.478 18.85 13.19 43.53 4.09
459 466 4.282957 ACGGTGAATCATATGATGAGAGCT 59.717 41.667 18.85 1.93 43.53 4.09
460 467 5.478332 ACGGTGAATCATATGATGAGAGCTA 59.522 40.000 18.85 0.00 43.53 3.32
462 469 6.870439 CGGTGAATCATATGATGAGAGCTAAA 59.130 38.462 18.85 0.00 43.53 1.85
463 470 7.063191 CGGTGAATCATATGATGAGAGCTAAAG 59.937 40.741 18.85 0.80 43.53 1.85
464 471 8.093307 GGTGAATCATATGATGAGAGCTAAAGA 58.907 37.037 18.85 0.00 43.53 2.52
465 472 9.486497 GTGAATCATATGATGAGAGCTAAAGAA 57.514 33.333 18.85 0.00 43.53 2.52
470 477 7.818446 TCATATGATGAGAGCTAAAGAATCTGC 59.182 37.037 0.00 0.00 33.59 4.26
471 478 5.349061 TGATGAGAGCTAAAGAATCTGCA 57.651 39.130 0.00 0.00 0.00 4.41
472 479 5.114780 TGATGAGAGCTAAAGAATCTGCAC 58.885 41.667 0.00 0.00 0.00 4.57
474 481 4.248859 TGAGAGCTAAAGAATCTGCACAC 58.751 43.478 0.00 0.00 0.00 3.82
475 482 4.020751 TGAGAGCTAAAGAATCTGCACACT 60.021 41.667 0.00 0.00 0.00 3.55
476 483 5.185828 TGAGAGCTAAAGAATCTGCACACTA 59.814 40.000 0.00 0.00 0.00 2.74
479 486 4.467795 AGCTAAAGAATCTGCACACTAGGA 59.532 41.667 0.00 0.00 0.00 2.94
480 487 5.130145 AGCTAAAGAATCTGCACACTAGGAT 59.870 40.000 0.00 0.00 0.00 3.24
481 488 5.465056 GCTAAAGAATCTGCACACTAGGATC 59.535 44.000 0.00 0.00 0.00 3.36
483 490 5.426689 AAGAATCTGCACACTAGGATCAA 57.573 39.130 0.00 0.00 0.00 2.57
484 491 4.764172 AGAATCTGCACACTAGGATCAAC 58.236 43.478 0.00 0.00 0.00 3.18
485 492 4.223700 AGAATCTGCACACTAGGATCAACA 59.776 41.667 0.00 0.00 0.00 3.33
486 493 4.767578 ATCTGCACACTAGGATCAACAT 57.232 40.909 0.00 0.00 0.00 2.71
498 505 4.336889 GGATCAACATCCGTCCTCATAA 57.663 45.455 0.00 0.00 39.52 1.90
499 506 4.703897 GGATCAACATCCGTCCTCATAAA 58.296 43.478 0.00 0.00 39.52 1.40
500 507 5.123227 GGATCAACATCCGTCCTCATAAAA 58.877 41.667 0.00 0.00 39.52 1.52
501 508 5.007724 GGATCAACATCCGTCCTCATAAAAC 59.992 44.000 0.00 0.00 39.52 2.43
502 509 4.900684 TCAACATCCGTCCTCATAAAACA 58.099 39.130 0.00 0.00 0.00 2.83
503 510 4.935205 TCAACATCCGTCCTCATAAAACAG 59.065 41.667 0.00 0.00 0.00 3.16
504 511 4.819105 ACATCCGTCCTCATAAAACAGA 57.181 40.909 0.00 0.00 0.00 3.41
505 512 5.160607 ACATCCGTCCTCATAAAACAGAA 57.839 39.130 0.00 0.00 0.00 3.02
506 513 5.178797 ACATCCGTCCTCATAAAACAGAAG 58.821 41.667 0.00 0.00 0.00 2.85
507 514 3.596214 TCCGTCCTCATAAAACAGAAGC 58.404 45.455 0.00 0.00 0.00 3.86
508 515 3.007506 TCCGTCCTCATAAAACAGAAGCA 59.992 43.478 0.00 0.00 0.00 3.91
509 516 3.751175 CCGTCCTCATAAAACAGAAGCAA 59.249 43.478 0.00 0.00 0.00 3.91
510 517 4.142816 CCGTCCTCATAAAACAGAAGCAAG 60.143 45.833 0.00 0.00 0.00 4.01
511 518 4.670221 CGTCCTCATAAAACAGAAGCAAGC 60.670 45.833 0.00 0.00 0.00 4.01
512 519 4.216257 GTCCTCATAAAACAGAAGCAAGCA 59.784 41.667 0.00 0.00 0.00 3.91
514 521 5.048504 TCCTCATAAAACAGAAGCAAGCAAG 60.049 40.000 0.00 0.00 0.00 4.01
516 523 4.826733 TCATAAAACAGAAGCAAGCAAGGA 59.173 37.500 0.00 0.00 0.00 3.36
517 524 5.301551 TCATAAAACAGAAGCAAGCAAGGAA 59.698 36.000 0.00 0.00 0.00 3.36
518 525 3.722728 AAACAGAAGCAAGCAAGGAAG 57.277 42.857 0.00 0.00 0.00 3.46
519 526 2.645838 ACAGAAGCAAGCAAGGAAGA 57.354 45.000 0.00 0.00 0.00 2.87
520 527 2.936202 ACAGAAGCAAGCAAGGAAGAA 58.064 42.857 0.00 0.00 0.00 2.52
522 529 3.701040 ACAGAAGCAAGCAAGGAAGAAAA 59.299 39.130 0.00 0.00 0.00 2.29
523 530 4.160252 ACAGAAGCAAGCAAGGAAGAAAAA 59.840 37.500 0.00 0.00 0.00 1.94
541 548 3.375782 AAAATGCTGACCTGTGAAAGC 57.624 42.857 0.00 0.00 36.18 3.51
543 550 0.035317 ATGCTGACCTGTGAAAGCGA 59.965 50.000 0.00 0.00 38.53 4.93
544 551 0.880278 TGCTGACCTGTGAAAGCGAC 60.880 55.000 0.00 0.00 38.53 5.19
545 552 0.601311 GCTGACCTGTGAAAGCGACT 60.601 55.000 0.00 0.00 0.00 4.18
546 553 1.871080 CTGACCTGTGAAAGCGACTT 58.129 50.000 0.00 0.00 0.00 3.01
548 555 0.868406 GACCTGTGAAAGCGACTTGG 59.132 55.000 0.00 0.00 0.00 3.61
549 556 0.180406 ACCTGTGAAAGCGACTTGGT 59.820 50.000 0.00 0.00 0.00 3.67
550 557 0.588252 CCTGTGAAAGCGACTTGGTG 59.412 55.000 0.00 0.00 0.00 4.17
552 559 0.107410 TGTGAAAGCGACTTGGTGGT 60.107 50.000 0.00 0.00 0.00 4.16
553 560 0.586802 GTGAAAGCGACTTGGTGGTC 59.413 55.000 0.00 0.00 0.00 4.02
554 561 0.179234 TGAAAGCGACTTGGTGGTCA 59.821 50.000 0.00 0.00 36.12 4.02
555 562 1.202758 TGAAAGCGACTTGGTGGTCAT 60.203 47.619 0.00 0.00 36.12 3.06
556 563 1.880027 GAAAGCGACTTGGTGGTCATT 59.120 47.619 0.00 0.00 36.12 2.57
558 565 1.210155 GCGACTTGGTGGTCATTGC 59.790 57.895 0.00 0.00 36.12 3.56
559 566 1.514678 GCGACTTGGTGGTCATTGCA 61.515 55.000 0.00 0.00 36.12 4.08
560 567 0.950836 CGACTTGGTGGTCATTGCAA 59.049 50.000 0.00 0.00 36.12 4.08
561 568 1.336440 CGACTTGGTGGTCATTGCAAA 59.664 47.619 1.71 0.00 36.12 3.68
562 569 2.223688 CGACTTGGTGGTCATTGCAAAA 60.224 45.455 1.71 0.00 36.12 2.44
650 885 0.478507 CACCAACCCCACTTTCCTCT 59.521 55.000 0.00 0.00 0.00 3.69
656 891 5.133221 CCAACCCCACTTTCCTCTATATTG 58.867 45.833 0.00 0.00 0.00 1.90
718 953 5.855045 AGAAACACTTGAACTTCTCCGTAT 58.145 37.500 0.00 0.00 0.00 3.06
766 1001 0.462047 ACGATGGGGAGCGAACAATC 60.462 55.000 0.00 0.00 0.00 2.67
823 1058 3.181510 CCTGCGGCACAAATAGTTAAGAC 60.182 47.826 0.00 0.00 0.00 3.01
930 1169 2.123589 TCTTCCCCAGTTCACTCAACA 58.876 47.619 0.00 0.00 37.48 3.33
985 1224 1.301009 GAGCCGATTAGCCTTCCGG 60.301 63.158 0.00 0.00 44.34 5.14
986 1225 2.029307 GAGCCGATTAGCCTTCCGGT 62.029 60.000 0.00 0.00 43.51 5.28
1296 1539 1.448540 CAAGTTCGGCATCCTCGCT 60.449 57.895 0.00 0.00 0.00 4.93
1468 1901 2.104963 GAGTCAACCTCAGTTCAACCCT 59.895 50.000 0.00 0.00 40.17 4.34
1479 1912 2.236395 AGTTCAACCCTATCCCGTTGAG 59.764 50.000 3.20 0.00 46.54 3.02
1494 1927 3.249013 GTTGAGTAGTCAAACCAACGC 57.751 47.619 14.56 0.00 44.44 4.84
1528 1961 0.944311 CACCAAACTGAGACCCGACG 60.944 60.000 0.00 0.00 0.00 5.12
1547 1980 2.806244 ACGGTGGAAAAGTCAAATCTCG 59.194 45.455 0.00 0.00 0.00 4.04
1553 1986 7.368059 GGTGGAAAAGTCAAATCTCGTAAATT 58.632 34.615 0.00 0.00 0.00 1.82
1554 1987 7.865889 GGTGGAAAAGTCAAATCTCGTAAATTT 59.134 33.333 0.00 0.00 0.00 1.82
1590 2023 9.919416 TTATGGAGAAAATCATTTACATCTGGA 57.081 29.630 0.00 0.00 0.00 3.86
1591 2024 8.827832 ATGGAGAAAATCATTTACATCTGGAA 57.172 30.769 0.00 0.00 0.00 3.53
1592 2025 8.827832 TGGAGAAAATCATTTACATCTGGAAT 57.172 30.769 0.00 0.00 0.00 3.01
1593 2026 8.689061 TGGAGAAAATCATTTACATCTGGAATG 58.311 33.333 0.00 0.00 33.24 2.67
1594 2027 8.689972 GGAGAAAATCATTTACATCTGGAATGT 58.310 33.333 0.00 0.00 33.60 2.71
1595 2028 9.727627 GAGAAAATCATTTACATCTGGAATGTC 57.272 33.333 0.00 1.58 33.60 3.06
1596 2029 9.246670 AGAAAATCATTTACATCTGGAATGTCA 57.753 29.630 0.00 0.00 33.60 3.58
1597 2030 9.859427 GAAAATCATTTACATCTGGAATGTCAA 57.141 29.630 0.00 0.00 33.60 3.18
1599 2032 9.643693 AAATCATTTACATCTGGAATGTCAAAC 57.356 29.630 0.00 0.00 33.60 2.93
1600 2033 7.757941 TCATTTACATCTGGAATGTCAAACA 57.242 32.000 0.00 0.00 33.60 2.83
1601 2034 7.592938 TCATTTACATCTGGAATGTCAAACAC 58.407 34.615 0.00 0.00 33.60 3.32
1602 2035 6.951062 TTTACATCTGGAATGTCAAACACA 57.049 33.333 0.00 0.00 40.18 3.72
1615 2048 7.615582 ATGTCAAACACATTAGATTCGTCAT 57.384 32.000 0.00 0.00 43.89 3.06
1616 2049 8.716646 ATGTCAAACACATTAGATTCGTCATA 57.283 30.769 0.00 0.00 43.89 2.15
1617 2050 8.541133 TGTCAAACACATTAGATTCGTCATAA 57.459 30.769 0.00 0.00 0.00 1.90
1618 2051 8.655970 TGTCAAACACATTAGATTCGTCATAAG 58.344 33.333 0.00 0.00 0.00 1.73
1619 2052 8.869897 GTCAAACACATTAGATTCGTCATAAGA 58.130 33.333 0.00 0.00 0.00 2.10
1620 2053 9.599866 TCAAACACATTAGATTCGTCATAAGAT 57.400 29.630 0.00 0.00 0.00 2.40
1624 2057 9.684448 ACACATTAGATTCGTCATAAGATACAG 57.316 33.333 0.00 0.00 0.00 2.74
1625 2058 9.684448 CACATTAGATTCGTCATAAGATACAGT 57.316 33.333 0.00 0.00 0.00 3.55
1635 2068 9.692749 TCGTCATAAGATACAGTTTCATATTCC 57.307 33.333 0.00 0.00 0.00 3.01
1636 2069 9.476202 CGTCATAAGATACAGTTTCATATTCCA 57.524 33.333 0.00 0.00 0.00 3.53
1773 2211 6.072508 TCCATGAGAGAAATTTACACACTTGC 60.073 38.462 0.00 0.00 0.00 4.01
1974 2415 3.126171 GCAGGTACGTACATTTTCATGCA 59.874 43.478 26.02 0.00 33.05 3.96
2182 2629 1.099689 GTCTGCCTACTTCGCTCTCT 58.900 55.000 0.00 0.00 0.00 3.10
2183 2630 1.064952 GTCTGCCTACTTCGCTCTCTC 59.935 57.143 0.00 0.00 0.00 3.20
2194 2641 3.406728 TCGCTCTCTCGTGTATTTGAG 57.593 47.619 0.00 0.00 0.00 3.02
2630 3077 1.531578 GAAGGCCGAGTGACAACTTTC 59.468 52.381 0.00 0.00 36.52 2.62
2651 3098 3.328343 TCCGTGGGAACTGGAATAAAAGA 59.672 43.478 0.00 0.00 33.51 2.52
2676 3125 6.912591 AGTTGCTTGTTTCTTAATTTCTCGTG 59.087 34.615 0.00 0.00 0.00 4.35
2680 3129 5.759506 TGTTTCTTAATTTCTCGTGCCAA 57.240 34.783 0.00 0.00 0.00 4.52
2732 3436 1.265365 TGTGTGTGTGTGTGTGTGTTG 59.735 47.619 0.00 0.00 0.00 3.33
2742 3446 3.066064 TGTGTGTGTGTTGGCTTGATTAC 59.934 43.478 0.00 0.00 0.00 1.89
2758 3462 5.862678 TGATTACTCATGTTGTATCCCGA 57.137 39.130 0.00 0.00 0.00 5.14
2775 3479 1.065701 CCGAGAAGTACTGTGATCCGG 59.934 57.143 0.00 0.00 0.00 5.14
2780 3484 3.695060 AGAAGTACTGTGATCCGGTGTAG 59.305 47.826 0.00 0.00 33.63 2.74
2861 3569 2.110899 TCCATCTGTTAAAAAGGGCCCA 59.889 45.455 27.56 0.00 0.00 5.36
2905 3613 4.321601 CCGAATGCAAAATAACTCCCAACA 60.322 41.667 0.00 0.00 0.00 3.33
2914 3622 4.796110 ATAACTCCCAACACATATGGCT 57.204 40.909 7.80 0.00 36.58 4.75
2930 3638 1.843851 TGGCTCCTTTATCCGAACCAT 59.156 47.619 0.00 0.00 0.00 3.55
2954 3662 3.438087 CAGTTGCTCCGAGATTGTTGAAT 59.562 43.478 0.00 0.00 0.00 2.57
3081 3790 5.589855 TGATACAACTGATACAATGCCCAAG 59.410 40.000 0.00 0.00 0.00 3.61
3083 3792 4.012374 ACAACTGATACAATGCCCAAGAG 58.988 43.478 0.00 0.00 0.00 2.85
3110 3829 0.109964 CACCCACCGCAATTACAACG 60.110 55.000 0.00 0.00 0.00 4.10
3111 3830 0.250381 ACCCACCGCAATTACAACGA 60.250 50.000 0.00 0.00 0.00 3.85
3112 3831 0.167251 CCCACCGCAATTACAACGAC 59.833 55.000 0.00 0.00 0.00 4.34
3113 3832 0.869068 CCACCGCAATTACAACGACA 59.131 50.000 0.00 0.00 0.00 4.35
3114 3833 1.399215 CCACCGCAATTACAACGACAC 60.399 52.381 0.00 0.00 0.00 3.67
3115 3834 1.261885 CACCGCAATTACAACGACACA 59.738 47.619 0.00 0.00 0.00 3.72
3116 3835 1.262151 ACCGCAATTACAACGACACAC 59.738 47.619 0.00 0.00 0.00 3.82
3117 3836 1.261885 CCGCAATTACAACGACACACA 59.738 47.619 0.00 0.00 0.00 3.72
3118 3837 2.286477 CCGCAATTACAACGACACACAA 60.286 45.455 0.00 0.00 0.00 3.33
3119 3838 2.711964 CGCAATTACAACGACACACAAC 59.288 45.455 0.00 0.00 0.00 3.32
3189 3908 3.057315 CGGAAGCATGAACAAAACTCCAT 60.057 43.478 0.00 0.00 0.00 3.41
3237 3956 1.455032 TTGGCGCCTAGGAGATCGA 60.455 57.895 29.70 4.50 0.00 3.59
3294 4013 1.246056 TGTCGTCCAAGAGGTACCGG 61.246 60.000 6.18 0.00 35.89 5.28
3312 4031 0.032130 GGCGACGAGGATGCAGATAA 59.968 55.000 0.00 0.00 0.00 1.75
3314 4033 1.536072 GCGACGAGGATGCAGATAACA 60.536 52.381 0.00 0.00 0.00 2.41
3348 4108 3.296709 CTACGTGAGCCCGCCAAGT 62.297 63.158 0.00 0.00 0.00 3.16
3388 4148 1.064906 TCCGGTAAACACCACAACCAA 60.065 47.619 0.00 0.00 32.04 3.67
3398 4158 0.314935 CCACAACCAACCATGCAGTC 59.685 55.000 0.00 0.00 0.00 3.51
3414 4175 0.977395 AGTCCTTCCAAGAAGGGTCG 59.023 55.000 20.45 0.00 37.99 4.79
3419 4180 4.394712 CCAAGAAGGGTCGCCGCT 62.395 66.667 0.00 0.00 34.93 5.52
3435 4196 2.359107 CTGCACTGCCACCATCGT 60.359 61.111 0.00 0.00 0.00 3.73
3436 4197 2.358615 TGCACTGCCACCATCGTC 60.359 61.111 0.00 0.00 0.00 4.20
3458 4219 2.486966 CCGACGAACCGGTCCTAC 59.513 66.667 8.04 0.00 44.23 3.18
3460 4221 2.390599 CGACGAACCGGTCCTACGA 61.391 63.158 22.84 0.00 35.47 3.43
3467 4228 1.332889 ACCGGTCCTACGATTTCCCC 61.333 60.000 0.00 0.00 35.47 4.81
3470 4231 1.472728 CGGTCCTACGATTTCCCCTTG 60.473 57.143 0.00 0.00 35.47 3.61
3527 4289 2.422803 CCAAAGAGGAGAACACCCACAA 60.423 50.000 0.00 0.00 41.22 3.33
3553 4315 4.034510 GTCACCATTATCTGCAACTGCTAC 59.965 45.833 2.95 0.00 42.66 3.58
3580 4342 2.532250 GGATTTCTCCCCAACCATGT 57.468 50.000 0.00 0.00 35.28 3.21
3582 4344 2.017049 GATTTCTCCCCAACCATGTCG 58.983 52.381 0.00 0.00 0.00 4.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 8.511604 AAACAGGGAATCAAGTATAGAACATG 57.488 34.615 0.00 0.00 0.00 3.21
166 170 2.417651 CGGCTTTGGTTATCTCACCGTA 60.418 50.000 0.00 0.00 40.09 4.02
205 209 3.976169 TGTTGCCTTTTACATGCTGAAC 58.024 40.909 0.00 0.00 0.00 3.18
224 228 5.189736 TCCAGGAGTAAATATGCAACTCTGT 59.810 40.000 13.66 1.54 39.65 3.41
235 239 7.953005 TGCATTTTGATTCCAGGAGTAAATA 57.047 32.000 0.00 0.00 0.00 1.40
243 249 2.355007 GGGGTTGCATTTTGATTCCAGG 60.355 50.000 0.00 0.00 0.00 4.45
246 252 2.038295 TGTGGGGTTGCATTTTGATTCC 59.962 45.455 0.00 0.00 0.00 3.01
260 266 2.815158 ACTTCTTTGTTGTTGTGGGGT 58.185 42.857 0.00 0.00 0.00 4.95
312 319 2.271800 CAAGTCATCGCTTGTACTCCC 58.728 52.381 0.00 0.00 40.52 4.30
313 320 2.094182 TCCAAGTCATCGCTTGTACTCC 60.094 50.000 0.00 0.00 43.03 3.85
314 321 3.119459 TCTCCAAGTCATCGCTTGTACTC 60.119 47.826 0.00 0.00 43.03 2.59
315 322 2.826128 TCTCCAAGTCATCGCTTGTACT 59.174 45.455 0.00 0.00 43.03 2.73
316 323 3.232213 TCTCCAAGTCATCGCTTGTAC 57.768 47.619 5.30 0.00 43.03 2.90
317 324 3.953712 TTCTCCAAGTCATCGCTTGTA 57.046 42.857 5.30 0.00 43.03 2.41
318 325 2.808543 GTTTCTCCAAGTCATCGCTTGT 59.191 45.455 5.30 0.00 43.03 3.16
319 326 2.807967 TGTTTCTCCAAGTCATCGCTTG 59.192 45.455 0.00 0.00 43.88 4.01
320 327 3.126001 TGTTTCTCCAAGTCATCGCTT 57.874 42.857 0.00 0.00 0.00 4.68
321 328 2.839486 TGTTTCTCCAAGTCATCGCT 57.161 45.000 0.00 0.00 0.00 4.93
322 329 4.870426 TCTTATGTTTCTCCAAGTCATCGC 59.130 41.667 0.00 0.00 0.00 4.58
323 330 5.004821 CGTCTTATGTTTCTCCAAGTCATCG 59.995 44.000 0.00 0.00 0.00 3.84
347 354 3.879932 AGTTTAGAGCGTTTCTGCAAC 57.120 42.857 0.00 5.35 36.61 4.17
361 368 7.026631 TCACAAAAGATGTCACCAAGTTTAG 57.973 36.000 0.00 0.00 41.46 1.85
362 369 7.581213 ATCACAAAAGATGTCACCAAGTTTA 57.419 32.000 0.00 0.00 41.46 2.01
363 370 5.913137 TCACAAAAGATGTCACCAAGTTT 57.087 34.783 0.00 0.00 41.46 2.66
364 371 7.581213 TTATCACAAAAGATGTCACCAAGTT 57.419 32.000 0.00 0.00 41.46 2.66
365 372 7.581213 TTTATCACAAAAGATGTCACCAAGT 57.419 32.000 0.00 0.00 41.46 3.16
366 373 7.113404 CGTTTTATCACAAAAGATGTCACCAAG 59.887 37.037 0.00 0.00 41.46 3.61
367 374 6.915300 CGTTTTATCACAAAAGATGTCACCAA 59.085 34.615 0.00 0.00 41.46 3.67
368 375 6.434596 CGTTTTATCACAAAAGATGTCACCA 58.565 36.000 0.00 0.00 41.46 4.17
369 376 5.342259 GCGTTTTATCACAAAAGATGTCACC 59.658 40.000 0.00 0.00 41.46 4.02
370 377 6.142817 AGCGTTTTATCACAAAAGATGTCAC 58.857 36.000 0.00 0.00 41.46 3.67
371 378 6.204688 AGAGCGTTTTATCACAAAAGATGTCA 59.795 34.615 0.00 0.00 41.46 3.58
372 379 6.603095 AGAGCGTTTTATCACAAAAGATGTC 58.397 36.000 0.00 0.00 41.46 3.06
373 380 6.560253 AGAGCGTTTTATCACAAAAGATGT 57.440 33.333 0.00 0.00 45.34 3.06
374 381 8.840867 GTTTAGAGCGTTTTATCACAAAAGATG 58.159 33.333 0.00 0.00 0.00 2.90
375 382 8.784043 AGTTTAGAGCGTTTTATCACAAAAGAT 58.216 29.630 0.00 0.00 0.00 2.40
376 383 8.149973 AGTTTAGAGCGTTTTATCACAAAAGA 57.850 30.769 0.00 0.00 0.00 2.52
377 384 8.682016 CAAGTTTAGAGCGTTTTATCACAAAAG 58.318 33.333 0.00 0.00 0.00 2.27
378 385 7.646130 CCAAGTTTAGAGCGTTTTATCACAAAA 59.354 33.333 0.00 0.00 0.00 2.44
379 386 7.136119 CCAAGTTTAGAGCGTTTTATCACAAA 58.864 34.615 0.00 0.00 0.00 2.83
380 387 6.664515 CCAAGTTTAGAGCGTTTTATCACAA 58.335 36.000 0.00 0.00 0.00 3.33
381 388 5.334569 GCCAAGTTTAGAGCGTTTTATCACA 60.335 40.000 0.00 0.00 0.00 3.58
382 389 5.086727 GCCAAGTTTAGAGCGTTTTATCAC 58.913 41.667 0.00 0.00 0.00 3.06
383 390 4.142988 CGCCAAGTTTAGAGCGTTTTATCA 60.143 41.667 0.00 0.00 43.45 2.15
384 391 4.331962 CGCCAAGTTTAGAGCGTTTTATC 58.668 43.478 0.00 0.00 43.45 1.75
385 392 4.336532 CGCCAAGTTTAGAGCGTTTTAT 57.663 40.909 0.00 0.00 43.45 1.40
386 393 3.799137 CGCCAAGTTTAGAGCGTTTTA 57.201 42.857 0.00 0.00 43.45 1.52
387 394 2.681152 CGCCAAGTTTAGAGCGTTTT 57.319 45.000 0.00 0.00 43.45 2.43
392 399 2.622436 AGATGTCGCCAAGTTTAGAGC 58.378 47.619 0.00 0.00 0.00 4.09
393 400 5.613358 AAAAGATGTCGCCAAGTTTAGAG 57.387 39.130 0.00 0.00 0.00 2.43
394 401 6.876789 TCATAAAAGATGTCGCCAAGTTTAGA 59.123 34.615 0.00 0.00 0.00 2.10
395 402 7.072177 TCATAAAAGATGTCGCCAAGTTTAG 57.928 36.000 0.00 0.00 0.00 1.85
398 405 7.307396 CGATATCATAAAAGATGTCGCCAAGTT 60.307 37.037 9.48 0.00 46.96 2.66
406 413 9.603298 TGTACGTACGATATCATAAAAGATGTC 57.397 33.333 24.41 0.00 34.10 3.06
416 423 4.201656 CCGTCGATGTACGTACGATATCAT 60.202 45.833 24.41 18.15 42.83 2.45
423 430 0.369931 TCACCGTCGATGTACGTACG 59.630 55.000 20.18 15.01 41.27 3.67
424 431 2.525750 TTCACCGTCGATGTACGTAC 57.474 50.000 18.90 18.90 41.27 3.67
426 433 1.469703 TGATTCACCGTCGATGTACGT 59.530 47.619 3.52 0.00 41.27 3.57
428 435 5.458015 TCATATGATTCACCGTCGATGTAC 58.542 41.667 0.00 0.00 0.00 2.90
430 437 4.584327 TCATATGATTCACCGTCGATGT 57.416 40.909 0.00 0.00 0.00 3.06
432 439 5.183904 TCTCATCATATGATTCACCGTCGAT 59.816 40.000 15.74 0.00 38.85 3.59
434 441 4.798574 TCTCATCATATGATTCACCGTCG 58.201 43.478 15.74 2.55 38.85 5.12
435 442 4.624882 GCTCTCATCATATGATTCACCGTC 59.375 45.833 15.74 0.00 38.85 4.79
436 443 4.282957 AGCTCTCATCATATGATTCACCGT 59.717 41.667 15.74 0.00 38.85 4.83
437 444 4.818642 AGCTCTCATCATATGATTCACCG 58.181 43.478 15.74 4.67 38.85 4.94
438 445 8.093307 TCTTTAGCTCTCATCATATGATTCACC 58.907 37.037 15.74 4.15 38.85 4.02
439 446 9.486497 TTCTTTAGCTCTCATCATATGATTCAC 57.514 33.333 15.74 4.48 38.85 3.18
443 450 9.878667 CAGATTCTTTAGCTCTCATCATATGAT 57.121 33.333 12.62 12.62 38.85 2.45
444 451 7.818446 GCAGATTCTTTAGCTCTCATCATATGA 59.182 37.037 8.10 8.10 37.76 2.15
446 453 7.603404 GTGCAGATTCTTTAGCTCTCATCATAT 59.397 37.037 0.00 0.00 0.00 1.78
447 454 6.927936 GTGCAGATTCTTTAGCTCTCATCATA 59.072 38.462 0.00 0.00 0.00 2.15
449 456 5.114780 GTGCAGATTCTTTAGCTCTCATCA 58.885 41.667 0.00 0.00 0.00 3.07
450 457 5.006552 GTGTGCAGATTCTTTAGCTCTCATC 59.993 44.000 0.00 0.00 0.00 2.92
452 459 4.020751 AGTGTGCAGATTCTTTAGCTCTCA 60.021 41.667 0.00 0.00 0.00 3.27
453 460 4.502962 AGTGTGCAGATTCTTTAGCTCTC 58.497 43.478 0.00 0.00 0.00 3.20
454 461 4.550076 AGTGTGCAGATTCTTTAGCTCT 57.450 40.909 0.00 0.00 0.00 4.09
455 462 4.808364 CCTAGTGTGCAGATTCTTTAGCTC 59.192 45.833 0.00 0.00 0.00 4.09
456 463 4.467795 TCCTAGTGTGCAGATTCTTTAGCT 59.532 41.667 0.00 0.00 0.00 3.32
457 464 4.759782 TCCTAGTGTGCAGATTCTTTAGC 58.240 43.478 0.00 0.00 0.00 3.09
458 465 6.577103 TGATCCTAGTGTGCAGATTCTTTAG 58.423 40.000 0.00 0.00 0.00 1.85
459 466 6.544928 TGATCCTAGTGTGCAGATTCTTTA 57.455 37.500 0.00 0.00 0.00 1.85
460 467 5.426689 TGATCCTAGTGTGCAGATTCTTT 57.573 39.130 0.00 0.00 0.00 2.52
462 469 4.223700 TGTTGATCCTAGTGTGCAGATTCT 59.776 41.667 0.00 0.00 0.00 2.40
463 470 4.507710 TGTTGATCCTAGTGTGCAGATTC 58.492 43.478 0.00 0.00 0.00 2.52
464 471 4.558226 TGTTGATCCTAGTGTGCAGATT 57.442 40.909 0.00 0.00 0.00 2.40
465 472 4.444022 GGATGTTGATCCTAGTGTGCAGAT 60.444 45.833 0.00 0.00 44.58 2.90
466 473 3.118629 GGATGTTGATCCTAGTGTGCAGA 60.119 47.826 0.00 0.00 44.58 4.26
467 474 3.201290 GGATGTTGATCCTAGTGTGCAG 58.799 50.000 0.00 0.00 44.58 4.41
470 477 3.448686 GACGGATGTTGATCCTAGTGTG 58.551 50.000 0.00 0.00 45.68 3.82
471 478 2.431057 GGACGGATGTTGATCCTAGTGT 59.569 50.000 0.00 0.00 45.68 3.55
472 479 2.695666 AGGACGGATGTTGATCCTAGTG 59.304 50.000 0.00 0.00 45.68 2.74
474 481 2.959030 TGAGGACGGATGTTGATCCTAG 59.041 50.000 0.00 0.00 45.68 3.02
475 482 3.026707 TGAGGACGGATGTTGATCCTA 57.973 47.619 0.00 0.00 45.68 2.94
476 483 1.866015 TGAGGACGGATGTTGATCCT 58.134 50.000 0.00 0.00 45.68 3.24
479 486 5.496556 TGTTTTATGAGGACGGATGTTGAT 58.503 37.500 0.00 0.00 0.00 2.57
480 487 4.900684 TGTTTTATGAGGACGGATGTTGA 58.099 39.130 0.00 0.00 0.00 3.18
481 488 4.935205 TCTGTTTTATGAGGACGGATGTTG 59.065 41.667 0.00 0.00 0.00 3.33
483 490 4.819105 TCTGTTTTATGAGGACGGATGT 57.181 40.909 0.00 0.00 0.00 3.06
484 491 4.034510 GCTTCTGTTTTATGAGGACGGATG 59.965 45.833 0.00 0.00 0.00 3.51
485 492 4.192317 GCTTCTGTTTTATGAGGACGGAT 58.808 43.478 0.00 0.00 0.00 4.18
486 493 3.007506 TGCTTCTGTTTTATGAGGACGGA 59.992 43.478 0.00 0.00 0.00 4.69
488 495 4.670221 GCTTGCTTCTGTTTTATGAGGACG 60.670 45.833 0.00 0.00 0.00 4.79
489 496 4.216257 TGCTTGCTTCTGTTTTATGAGGAC 59.784 41.667 0.00 0.00 0.00 3.85
490 497 4.397420 TGCTTGCTTCTGTTTTATGAGGA 58.603 39.130 0.00 0.00 0.00 3.71
492 499 5.048504 TCCTTGCTTGCTTCTGTTTTATGAG 60.049 40.000 0.00 0.00 0.00 2.90
493 500 4.826733 TCCTTGCTTGCTTCTGTTTTATGA 59.173 37.500 0.00 0.00 0.00 2.15
494 501 5.125100 TCCTTGCTTGCTTCTGTTTTATG 57.875 39.130 0.00 0.00 0.00 1.90
495 502 5.536161 TCTTCCTTGCTTGCTTCTGTTTTAT 59.464 36.000 0.00 0.00 0.00 1.40
497 504 3.701040 TCTTCCTTGCTTGCTTCTGTTTT 59.299 39.130 0.00 0.00 0.00 2.43
498 505 3.290710 TCTTCCTTGCTTGCTTCTGTTT 58.709 40.909 0.00 0.00 0.00 2.83
499 506 2.936202 TCTTCCTTGCTTGCTTCTGTT 58.064 42.857 0.00 0.00 0.00 3.16
500 507 2.645838 TCTTCCTTGCTTGCTTCTGT 57.354 45.000 0.00 0.00 0.00 3.41
501 508 3.996150 TTTCTTCCTTGCTTGCTTCTG 57.004 42.857 0.00 0.00 0.00 3.02
520 527 3.721035 GCTTTCACAGGTCAGCATTTTT 58.279 40.909 0.00 0.00 32.17 1.94
522 529 1.267806 CGCTTTCACAGGTCAGCATTT 59.732 47.619 0.00 0.00 32.17 2.32
523 530 0.877071 CGCTTTCACAGGTCAGCATT 59.123 50.000 0.00 0.00 32.17 3.56
524 531 0.035317 TCGCTTTCACAGGTCAGCAT 59.965 50.000 0.00 0.00 32.17 3.79
525 532 0.880278 GTCGCTTTCACAGGTCAGCA 60.880 55.000 0.00 0.00 32.17 4.41
526 533 0.601311 AGTCGCTTTCACAGGTCAGC 60.601 55.000 0.00 0.00 0.00 4.26
528 535 1.581934 CAAGTCGCTTTCACAGGTCA 58.418 50.000 0.00 0.00 0.00 4.02
529 536 0.868406 CCAAGTCGCTTTCACAGGTC 59.132 55.000 0.00 0.00 0.00 3.85
530 537 0.180406 ACCAAGTCGCTTTCACAGGT 59.820 50.000 0.00 0.00 0.00 4.00
531 538 0.588252 CACCAAGTCGCTTTCACAGG 59.412 55.000 0.00 0.00 0.00 4.00
532 539 0.588252 CCACCAAGTCGCTTTCACAG 59.412 55.000 0.00 0.00 0.00 3.66
533 540 0.107410 ACCACCAAGTCGCTTTCACA 60.107 50.000 0.00 0.00 0.00 3.58
535 542 0.179234 TGACCACCAAGTCGCTTTCA 59.821 50.000 0.00 0.00 39.77 2.69
536 543 1.523758 ATGACCACCAAGTCGCTTTC 58.476 50.000 0.00 0.00 39.77 2.62
537 544 1.608590 CAATGACCACCAAGTCGCTTT 59.391 47.619 0.00 0.00 39.77 3.51
539 546 1.237285 GCAATGACCACCAAGTCGCT 61.237 55.000 0.00 0.00 39.77 4.93
541 548 0.950836 TTGCAATGACCACCAAGTCG 59.049 50.000 0.00 0.00 39.77 4.18
543 550 3.902881 TTTTTGCAATGACCACCAAGT 57.097 38.095 0.00 0.00 0.00 3.16
561 568 9.581099 CCAAAGCCGTCTTGTTATTAATATTTT 57.419 29.630 0.00 0.00 31.78 1.82
562 569 8.745590 ACCAAAGCCGTCTTGTTATTAATATTT 58.254 29.630 0.00 0.00 31.78 1.40
564 571 7.201785 CCACCAAAGCCGTCTTGTTATTAATAT 60.202 37.037 0.00 0.00 31.78 1.28
565 572 6.094325 CCACCAAAGCCGTCTTGTTATTAATA 59.906 38.462 0.00 0.00 31.78 0.98
566 573 5.105917 CCACCAAAGCCGTCTTGTTATTAAT 60.106 40.000 0.00 0.00 31.78 1.40
585 820 2.421952 GCATTATCTTCCAGCTCCACCA 60.422 50.000 0.00 0.00 0.00 4.17
650 885 7.295672 AGTTCTCCTGATTGGGGATTCAATATA 59.704 37.037 0.00 0.00 46.45 0.86
656 891 3.549794 CAGTTCTCCTGATTGGGGATTC 58.450 50.000 0.00 0.00 46.45 2.52
704 939 4.637276 TGCAAAAGATACGGAGAAGTTCA 58.363 39.130 5.50 0.00 0.00 3.18
766 1001 1.535462 CTTTAATAATGGCGGCTCCGG 59.465 52.381 11.43 0.00 40.19 5.14
823 1058 3.463505 CTGCTAAGCACCGTCGTG 58.536 61.111 0.00 0.00 43.35 4.35
912 1151 3.138283 AGATTGTTGAGTGAACTGGGGAA 59.862 43.478 0.00 0.00 35.37 3.97
930 1169 4.716784 TCAGCCACTGTACTGGATTAGATT 59.283 41.667 5.35 0.00 34.57 2.40
985 1224 1.883021 CCATTGCAGGTTCCGGAAC 59.117 57.895 34.71 34.71 40.45 3.62
986 1225 1.976474 GCCATTGCAGGTTCCGGAA 60.976 57.895 14.35 14.35 37.47 4.30
1248 1491 4.617595 ACCTTGCCCCTCACCCCT 62.618 66.667 0.00 0.00 0.00 4.79
1380 1623 3.570550 GGTAGTAGAGGTCGATGCATTCT 59.429 47.826 0.00 1.37 0.00 2.40
1468 1901 3.833650 TGGTTTGACTACTCAACGGGATA 59.166 43.478 0.00 0.00 36.06 2.59
1479 1912 1.154727 CGCGCGTTGGTTTGACTAC 60.155 57.895 24.19 0.00 0.00 2.73
1494 1927 1.729131 GGTGCATTTGGTCAACGCG 60.729 57.895 3.53 3.53 0.00 6.01
1528 1961 5.934935 TTACGAGATTTGACTTTTCCACC 57.065 39.130 0.00 0.00 0.00 4.61
1565 1998 9.919416 TTCCAGATGTAAATGATTTTCTCCATA 57.081 29.630 0.00 0.00 0.00 2.74
1567 2000 8.689061 CATTCCAGATGTAAATGATTTTCTCCA 58.311 33.333 0.00 0.00 33.22 3.86
1568 2001 8.689972 ACATTCCAGATGTAAATGATTTTCTCC 58.310 33.333 0.00 0.00 35.03 3.71
1570 2003 9.246670 TGACATTCCAGATGTAAATGATTTTCT 57.753 29.630 0.00 0.00 35.03 2.52
1573 2006 9.643693 GTTTGACATTCCAGATGTAAATGATTT 57.356 29.630 10.45 0.00 35.03 2.17
1574 2007 8.805175 TGTTTGACATTCCAGATGTAAATGATT 58.195 29.630 10.45 0.00 35.03 2.57
1576 2009 7.230309 TGTGTTTGACATTCCAGATGTAAATGA 59.770 33.333 10.45 0.00 35.03 2.57
1577 2010 7.369607 TGTGTTTGACATTCCAGATGTAAATG 58.630 34.615 0.00 0.00 36.64 2.32
1578 2011 7.523293 TGTGTTTGACATTCCAGATGTAAAT 57.477 32.000 0.00 0.00 31.52 1.40
1592 2025 8.541133 TTATGACGAATCTAATGTGTTTGACA 57.459 30.769 0.00 0.00 39.53 3.58
1593 2026 8.869897 TCTTATGACGAATCTAATGTGTTTGAC 58.130 33.333 0.00 0.00 0.00 3.18
1594 2027 8.996024 TCTTATGACGAATCTAATGTGTTTGA 57.004 30.769 0.00 0.00 0.00 2.69
1598 2031 9.684448 CTGTATCTTATGACGAATCTAATGTGT 57.316 33.333 0.00 0.00 0.00 3.72
1599 2032 9.684448 ACTGTATCTTATGACGAATCTAATGTG 57.316 33.333 0.00 0.00 0.00 3.21
1609 2042 9.692749 GGAATATGAAACTGTATCTTATGACGA 57.307 33.333 0.00 0.00 0.00 4.20
1610 2043 9.476202 TGGAATATGAAACTGTATCTTATGACG 57.524 33.333 0.00 0.00 0.00 4.35
1694 2127 9.569167 TGTAGTGTGTATAGATTTTTCGAAGAG 57.431 33.333 0.00 0.00 38.43 2.85
1713 2147 7.680730 ACTTTCTCTGTTCCATAATGTAGTGT 58.319 34.615 0.00 0.00 0.00 3.55
1730 2164 7.397476 TCTCATGGATAGTGTTGTACTTTCTCT 59.603 37.037 0.00 0.00 40.89 3.10
1734 2168 7.482169 TCTCTCATGGATAGTGTTGTACTTT 57.518 36.000 0.00 0.00 40.89 2.66
1735 2169 7.482169 TTCTCTCATGGATAGTGTTGTACTT 57.518 36.000 0.00 0.00 40.89 2.24
1857 2296 2.278596 GCGTGCGCTCTTCGGATA 60.279 61.111 9.73 0.00 41.52 2.59
1974 2415 8.521170 AAATGATCTTGAGATGTCATGATTGT 57.479 30.769 18.59 10.26 43.96 2.71
2012 2453 4.155826 TGAGCAGGAACAAAATTCATACGG 59.844 41.667 0.00 0.00 0.00 4.02
2182 2629 4.087182 AGAAGGGTCTCTCAAATACACGA 58.913 43.478 0.00 0.00 0.00 4.35
2183 2630 4.425520 GAGAAGGGTCTCTCAAATACACG 58.574 47.826 0.00 0.00 45.99 4.49
2196 2643 6.937465 AGATTTCTTGTACAAAGAGAAGGGTC 59.063 38.462 10.03 8.97 31.67 4.46
2198 2645 7.588512 CAAGATTTCTTGTACAAAGAGAAGGG 58.411 38.462 10.03 0.00 46.11 3.95
2244 2691 7.177392 AGCATTGTTGGCTTAGAAACTTAGAAT 59.823 33.333 0.00 0.00 38.81 2.40
2259 2706 6.966435 ATAAATGTGTTAAGCATTGTTGGC 57.034 33.333 6.10 0.00 36.75 4.52
2271 2718 9.226606 CTTGGTAAGTCCTGAATAAATGTGTTA 57.773 33.333 0.00 0.00 37.07 2.41
2388 2835 1.827789 GTGAACCCAGGCAAGTGCA 60.828 57.895 5.52 0.00 44.36 4.57
2409 2856 0.034186 GGCACACATCATTCCCCTGA 60.034 55.000 0.00 0.00 0.00 3.86
2418 2865 0.255604 CTGGTATGGGGCACACATCA 59.744 55.000 0.00 0.00 0.00 3.07
2547 2994 3.387699 TCAGGAAATCATGGTAGCGATCA 59.612 43.478 0.00 0.00 0.00 2.92
2630 3077 3.681593 TCTTTTATTCCAGTTCCCACGG 58.318 45.455 0.00 0.00 0.00 4.94
2651 3098 6.912591 CACGAGAAATTAAGAAACAAGCAACT 59.087 34.615 0.00 0.00 0.00 3.16
2676 3125 1.228862 ACACACCCCTTCCATTGGC 60.229 57.895 0.00 0.00 0.00 4.52
2680 3129 0.178992 CACACACACACCCCTTCCAT 60.179 55.000 0.00 0.00 0.00 3.41
2732 3436 5.239525 GGGATACAACATGAGTAATCAAGCC 59.760 44.000 0.00 0.00 39.74 4.35
2742 3446 4.392921 ACTTCTCGGGATACAACATGAG 57.607 45.455 0.00 0.00 39.74 2.90
2758 3462 2.526432 ACACCGGATCACAGTACTTCT 58.474 47.619 9.46 0.00 0.00 2.85
2775 3479 4.553330 TTTCCAGAGTCCATTCCTACAC 57.447 45.455 0.00 0.00 0.00 2.90
2780 3484 6.202954 CGTACATTATTTCCAGAGTCCATTCC 59.797 42.308 0.00 0.00 0.00 3.01
2872 3580 1.298157 TTGCATTCGGACTTGCCTCG 61.298 55.000 9.01 0.00 38.08 4.63
2905 3613 4.505039 GGTTCGGATAAAGGAGCCATATGT 60.505 45.833 1.24 0.00 34.12 2.29
2914 3622 3.112263 ACTGGATGGTTCGGATAAAGGA 58.888 45.455 0.00 0.00 0.00 3.36
2930 3638 0.976641 ACAATCTCGGAGCAACTGGA 59.023 50.000 0.00 0.00 0.00 3.86
2967 3675 5.426689 AGTGGATGAGAGAATACAAGCAA 57.573 39.130 0.00 0.00 0.00 3.91
2976 3684 4.982241 AAAGGTGAAGTGGATGAGAGAA 57.018 40.909 0.00 0.00 0.00 2.87
3008 3716 2.501316 TGGTACATCTCTCCATGGTGTG 59.499 50.000 12.58 10.60 0.00 3.82
3087 3796 1.974343 TAATTGCGGTGGGTGTGGC 60.974 57.895 0.00 0.00 0.00 5.01
3099 3808 3.947626 AGTTGTGTGTCGTTGTAATTGC 58.052 40.909 0.00 0.00 0.00 3.56
3110 3829 3.466836 TGGACAAGATGAGTTGTGTGTC 58.533 45.455 0.00 0.00 40.83 3.67
3111 3830 3.558931 TGGACAAGATGAGTTGTGTGT 57.441 42.857 0.00 0.00 40.83 3.72
3112 3831 3.879295 AGTTGGACAAGATGAGTTGTGTG 59.121 43.478 0.00 0.00 40.83 3.82
3113 3832 4.130118 GAGTTGGACAAGATGAGTTGTGT 58.870 43.478 0.00 0.00 40.83 3.72
3114 3833 4.129380 TGAGTTGGACAAGATGAGTTGTG 58.871 43.478 0.00 0.00 40.83 3.33
3115 3834 4.422073 TGAGTTGGACAAGATGAGTTGT 57.578 40.909 0.00 0.00 43.49 3.32
3116 3835 4.320057 GCTTGAGTTGGACAAGATGAGTTG 60.320 45.833 11.08 0.00 44.92 3.16
3117 3836 3.817647 GCTTGAGTTGGACAAGATGAGTT 59.182 43.478 11.08 0.00 44.92 3.01
3118 3837 3.406764 GCTTGAGTTGGACAAGATGAGT 58.593 45.455 11.08 0.00 44.92 3.41
3119 3838 2.746362 GGCTTGAGTTGGACAAGATGAG 59.254 50.000 11.08 0.00 44.92 2.90
3189 3908 1.375908 GCATTGAGTCAGTCGGGCA 60.376 57.895 0.00 0.00 0.00 5.36
3237 3956 5.639506 CGATTGTTTCTTAGTGTCCATCTGT 59.360 40.000 0.00 0.00 0.00 3.41
3294 4013 1.132588 GTTATCTGCATCCTCGTCGC 58.867 55.000 0.00 0.00 0.00 5.19
3308 4027 1.153025 GGGGCCTTCGGGTGTTATC 60.153 63.158 0.84 0.00 37.45 1.75
3312 4031 3.966543 CTTGGGGCCTTCGGGTGT 61.967 66.667 0.84 0.00 37.45 4.16
3332 4092 4.681978 GACTTGGCGGGCTCACGT 62.682 66.667 2.38 0.00 35.98 4.49
3348 4108 0.455410 GTGCAAGCTGGTGTTGTTGA 59.545 50.000 0.00 0.00 0.00 3.18
3388 4148 1.067295 TCTTGGAAGGACTGCATGGT 58.933 50.000 0.00 0.00 0.00 3.55
3398 4158 1.377333 GGCGACCCTTCTTGGAAGG 60.377 63.158 16.79 16.79 38.35 3.46
3419 4180 2.358615 GACGATGGTGGCAGTGCA 60.359 61.111 18.61 0.00 0.00 4.57
3427 4188 3.822192 TCGGAGCCGACGATGGTG 61.822 66.667 7.66 0.00 44.01 4.17
3458 4219 2.406616 CGGGCACAAGGGGAAATCG 61.407 63.158 0.00 0.00 0.00 3.34
3460 4221 1.000896 CTCGGGCACAAGGGGAAAT 60.001 57.895 0.00 0.00 0.00 2.17
3467 4228 3.636231 TGTCCCCTCGGGCACAAG 61.636 66.667 0.00 0.00 39.48 3.16
3527 4289 2.009774 GTTGCAGATAATGGTGACGCT 58.990 47.619 0.00 0.00 0.00 5.07
3553 4315 1.069258 GGGAGAAATCCCTACGCGG 59.931 63.158 12.47 0.00 46.39 6.46
3574 4336 1.303317 GGTTCTTGGCCGACATGGT 60.303 57.895 0.00 0.00 41.21 3.55
3582 4344 3.994204 TTTCTTTAACGGTTCTTGGCC 57.006 42.857 0.00 0.00 0.00 5.36
3597 4359 1.138859 GCAACCCAACCTGCTTTTCTT 59.861 47.619 0.00 0.00 35.62 2.52


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

AutoCloner maintained by Alex Coulton.