Multiple sequence alignment - TraesCS2B01G125400

Loading Multiple Alignment...

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 TraesCS2B01G125400 chr2B 100.000 4184 0 0 1 4184 93708052 93703869 0.000000e+00 7727.0
1 TraesCS2B01G125400 chr2B 91.133 203 16 2 365 566 206287187 206286986 1.480000e-69 274.0
2 TraesCS2B01G125400 chr2B 87.554 233 29 0 3298 3530 94155834 94155602 1.920000e-68 270.0
3 TraesCS2B01G125400 chr2B 90.594 202 18 1 373 574 457730436 457730236 2.480000e-67 267.0
4 TraesCS2B01G125400 chr2B 81.457 151 25 3 369 518 347076895 347076747 2.040000e-23 121.0
5 TraesCS2B01G125400 chr2B 100.000 30 0 0 575 604 150082753 150082724 5.840000e-04 56.5
6 TraesCS2B01G125400 chr2D 90.349 3554 230 46 692 4184 60029563 60026062 0.000000e+00 4558.0
7 TraesCS2B01G125400 chr2D 89.882 425 39 4 1853 2274 60020015 60019592 1.020000e-150 544.0
8 TraesCS2B01G125400 chr2D 90.186 377 32 4 1 376 60030019 60029647 1.750000e-133 486.0
9 TraesCS2B01G125400 chr2D 81.851 562 50 15 3619 4179 60025033 60024523 3.870000e-115 425.0
10 TraesCS2B01G125400 chr2A 93.627 1020 58 3 1268 2287 59988793 59987781 0.000000e+00 1517.0
11 TraesCS2B01G125400 chr2A 91.148 836 54 10 2283 3108 59986735 59985910 0.000000e+00 1116.0
12 TraesCS2B01G125400 chr2A 88.656 908 66 18 3100 4001 59985703 59984827 0.000000e+00 1072.0
13 TraesCS2B01G125400 chr2A 86.591 880 63 19 3230 4096 59884466 59883629 0.000000e+00 920.0
14 TraesCS2B01G125400 chr2A 83.738 535 60 13 1741 2274 59878059 59877551 8.140000e-132 481.0
15 TraesCS2B01G125400 chr2A 88.830 376 20 4 1 376 60065718 60065365 3.840000e-120 442.0
16 TraesCS2B01G125400 chr2A 92.691 301 22 0 976 1276 59990615 59990315 6.420000e-118 435.0
17 TraesCS2B01G125400 chr2A 82.979 470 50 7 3711 4179 59882515 59882075 8.430000e-107 398.0
18 TraesCS2B01G125400 chr2A 90.526 95 7 2 4087 4180 59883601 59883508 1.580000e-24 124.0
19 TraesCS2B01G125400 chr2A 78.102 137 24 5 2108 2244 734587241 734587371 9.640000e-12 82.4
20 TraesCS2B01G125400 chr2A 100.000 29 0 0 575 603 364684764 364684792 2.000000e-03 54.7
21 TraesCS2B01G125400 chr7A 76.404 1140 233 27 1122 2252 624966979 624965867 2.170000e-162 582.0
22 TraesCS2B01G125400 chr1A 90.732 205 17 2 371 574 562620976 562621179 5.330000e-69 272.0
23 TraesCS2B01G125400 chr7B 91.753 194 15 1 374 566 436122546 436122739 6.890000e-68 268.0
24 TraesCS2B01G125400 chr5A 91.710 193 16 0 374 566 628789833 628790025 6.890000e-68 268.0
25 TraesCS2B01G125400 chr3D 91.753 194 15 1 370 563 306028956 306029148 6.890000e-68 268.0
26 TraesCS2B01G125400 chr6D 90.547 201 19 0 374 574 363243444 363243644 2.480000e-67 267.0
27 TraesCS2B01G125400 chr5D 91.710 193 15 1 374 566 193046765 193046956 2.480000e-67 267.0
28 TraesCS2B01G125400 chr3B 91.237 194 17 0 373 566 175672257 175672064 8.920000e-67 265.0
29 TraesCS2B01G125400 chr4B 83.495 103 16 1 366 467 30438833 30438731 1.240000e-15 95.3
30 TraesCS2B01G125400 chr6B 74.854 171 35 4 2072 2241 647693470 647693633 2.090000e-08 71.3
31 TraesCS2B01G125400 chr6B 100.000 30 0 0 575 604 657062033 657062004 5.840000e-04 56.5
32 TraesCS2B01G125400 chr6A 73.810 168 36 4 2072 2238 574914080 574914240 4.520000e-05 60.2
33 TraesCS2B01G125400 chr6A 100.000 29 0 0 575 603 125839365 125839337 2.000000e-03 54.7
34 TraesCS2B01G125400 chr3A 96.970 33 0 1 577 609 7989846 7989815 2.000000e-03 54.7
35 TraesCS2B01G125400 chrUn 96.875 32 0 1 575 606 10167713 10167743 8.000000e-03 52.8
36 TraesCS2B01G125400 chr1D 96.875 32 0 1 575 605 378325054 378325085 8.000000e-03 52.8


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 TraesCS2B01G125400 chr2B 93703869 93708052 4183 True 7727.000000 7727 100.000000 1 4184 1 chr2B.!!$R1 4183
1 TraesCS2B01G125400 chr2D 60024523 60030019 5496 True 1823.000000 4558 87.462000 1 4184 3 chr2D.!!$R2 4183
2 TraesCS2B01G125400 chr2A 59984827 59990615 5788 True 1035.000000 1517 91.530500 976 4001 4 chr2A.!!$R4 3025
3 TraesCS2B01G125400 chr2A 59877551 59878059 508 True 481.000000 481 83.738000 1741 2274 1 chr2A.!!$R1 533
4 TraesCS2B01G125400 chr2A 59882075 59884466 2391 True 480.666667 920 86.698667 3230 4180 3 chr2A.!!$R3 950
5 TraesCS2B01G125400 chr7A 624965867 624966979 1112 True 582.000000 582 76.404000 1122 2252 1 chr7A.!!$R1 1130

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
286 288 0.750249 AAAGACAAAAACCTGGCCCG 59.250 50.0 0.00 0.00 0.00 6.13 F
1635 3229 0.326238 TCCTCCGCTTGGTAAGGGAT 60.326 55.0 7.14 0.00 43.53 3.85 F
2037 3631 0.318441 TGTTCGAGGAGCTCAACCAG 59.682 55.0 17.19 1.84 0.00 4.00 F
2860 5512 0.602638 TGGTTATCATCATCGGCGGC 60.603 55.0 7.21 0.00 0.00 6.53 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1734 3328 0.247460 CTTCATCGAGGGTGAGCACA 59.753 55.0 0.00 0.00 0.00 4.57 R
2751 5403 0.031314 CCTCGATGGTCACCTCGATG 59.969 60.0 15.86 11.06 42.45 3.84 R
3094 5746 0.106569 CATATGCCCTGCAACTCCCA 60.107 55.0 0.00 0.00 43.62 4.37 R
4118 8474 0.250252 TCCATTCAGCAGTGCGACAA 60.250 50.0 10.00 4.15 0.00 3.18 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
29 30 6.621316 TGCTAATAAAGTCCACGAAAACAA 57.379 33.333 0.00 0.00 0.00 2.83
33 34 7.481798 GCTAATAAAGTCCACGAAAACAATGAG 59.518 37.037 0.00 0.00 0.00 2.90
36 37 5.362556 AAGTCCACGAAAACAATGAGATG 57.637 39.130 0.00 0.00 0.00 2.90
42 43 7.382218 GTCCACGAAAACAATGAGATGAAATTT 59.618 33.333 0.00 0.00 0.00 1.82
80 81 8.298729 TGTATATGTATCTAGGGAGATTGCAG 57.701 38.462 0.00 0.00 39.56 4.41
128 129 9.998106 TTAAGAAGGGACAATATACATTAGAGC 57.002 33.333 0.00 0.00 0.00 4.09
155 157 6.672593 AGCTTCAAAGGATGGACCATTATTA 58.327 36.000 8.78 0.00 42.04 0.98
158 160 7.449704 GCTTCAAAGGATGGACCATTATTAGAT 59.550 37.037 8.78 0.00 42.04 1.98
159 161 9.359653 CTTCAAAGGATGGACCATTATTAGATT 57.640 33.333 8.78 0.00 42.04 2.40
160 162 9.713684 TTCAAAGGATGGACCATTATTAGATTT 57.286 29.630 8.78 0.44 42.04 2.17
161 163 9.713684 TCAAAGGATGGACCATTATTAGATTTT 57.286 29.630 8.78 0.00 42.04 1.82
286 288 0.750249 AAAGACAAAAACCTGGCCCG 59.250 50.000 0.00 0.00 0.00 6.13
302 304 3.263261 GGCCCGAAAACAACAAAGAAAA 58.737 40.909 0.00 0.00 0.00 2.29
329 331 1.623163 TTTTGGGCGGGGTAGAAAAG 58.377 50.000 0.00 0.00 0.00 2.27
381 383 8.927675 TTTTTGTGTACATTACATACTCCCTT 57.072 30.769 0.00 0.00 41.34 3.95
382 384 8.556213 TTTTGTGTACATTACATACTCCCTTC 57.444 34.615 0.00 0.00 41.34 3.46
383 385 5.898174 TGTGTACATTACATACTCCCTTCG 58.102 41.667 0.00 0.00 41.34 3.79
384 386 5.419788 TGTGTACATTACATACTCCCTTCGT 59.580 40.000 0.00 0.00 41.34 3.85
385 387 6.071221 TGTGTACATTACATACTCCCTTCGTT 60.071 38.462 0.00 0.00 41.34 3.85
386 388 6.815142 GTGTACATTACATACTCCCTTCGTTT 59.185 38.462 0.00 0.00 41.34 3.60
387 389 7.009907 GTGTACATTACATACTCCCTTCGTTTC 59.990 40.741 0.00 0.00 41.34 2.78
388 390 6.295719 ACATTACATACTCCCTTCGTTTCT 57.704 37.500 0.00 0.00 0.00 2.52
389 391 6.708285 ACATTACATACTCCCTTCGTTTCTT 58.292 36.000 0.00 0.00 0.00 2.52
390 392 7.166167 ACATTACATACTCCCTTCGTTTCTTT 58.834 34.615 0.00 0.00 0.00 2.52
391 393 7.664318 ACATTACATACTCCCTTCGTTTCTTTT 59.336 33.333 0.00 0.00 0.00 2.27
392 394 8.512138 CATTACATACTCCCTTCGTTTCTTTTT 58.488 33.333 0.00 0.00 0.00 1.94
393 395 9.729281 ATTACATACTCCCTTCGTTTCTTTTTA 57.271 29.630 0.00 0.00 0.00 1.52
394 396 7.668525 ACATACTCCCTTCGTTTCTTTTTAG 57.331 36.000 0.00 0.00 0.00 1.85
395 397 7.222161 ACATACTCCCTTCGTTTCTTTTTAGT 58.778 34.615 0.00 0.00 0.00 2.24
396 398 7.387122 ACATACTCCCTTCGTTTCTTTTTAGTC 59.613 37.037 0.00 0.00 0.00 2.59
397 399 4.748600 ACTCCCTTCGTTTCTTTTTAGTCG 59.251 41.667 0.00 0.00 0.00 4.18
398 400 4.060205 TCCCTTCGTTTCTTTTTAGTCGG 58.940 43.478 0.00 0.00 0.00 4.79
399 401 3.364664 CCCTTCGTTTCTTTTTAGTCGGC 60.365 47.826 0.00 0.00 0.00 5.54
400 402 3.249080 CCTTCGTTTCTTTTTAGTCGGCA 59.751 43.478 0.00 0.00 0.00 5.69
401 403 4.083484 CCTTCGTTTCTTTTTAGTCGGCAT 60.083 41.667 0.00 0.00 0.00 4.40
402 404 5.121142 CCTTCGTTTCTTTTTAGTCGGCATA 59.879 40.000 0.00 0.00 0.00 3.14
403 405 6.183360 CCTTCGTTTCTTTTTAGTCGGCATAT 60.183 38.462 0.00 0.00 0.00 1.78
404 406 7.010738 CCTTCGTTTCTTTTTAGTCGGCATATA 59.989 37.037 0.00 0.00 0.00 0.86
405 407 7.830940 TCGTTTCTTTTTAGTCGGCATATAA 57.169 32.000 0.00 0.00 0.00 0.98
406 408 7.902032 TCGTTTCTTTTTAGTCGGCATATAAG 58.098 34.615 0.00 0.00 0.00 1.73
407 409 7.760794 TCGTTTCTTTTTAGTCGGCATATAAGA 59.239 33.333 0.00 0.00 0.00 2.10
408 410 8.548721 CGTTTCTTTTTAGTCGGCATATAAGAT 58.451 33.333 0.00 0.00 0.00 2.40
412 414 9.607988 TCTTTTTAGTCGGCATATAAGATTTGA 57.392 29.630 0.00 0.00 0.00 2.69
415 417 9.554395 TTTTAGTCGGCATATAAGATTTGATCA 57.446 29.630 0.00 0.00 0.00 2.92
416 418 9.554395 TTTAGTCGGCATATAAGATTTGATCAA 57.446 29.630 3.38 3.38 0.00 2.57
417 419 9.554395 TTAGTCGGCATATAAGATTTGATCAAA 57.446 29.630 22.52 22.52 34.46 2.69
418 420 8.092521 AGTCGGCATATAAGATTTGATCAAAG 57.907 34.615 24.17 10.49 33.32 2.77
419 421 7.716998 AGTCGGCATATAAGATTTGATCAAAGT 59.283 33.333 24.17 14.86 33.32 2.66
420 422 8.012241 GTCGGCATATAAGATTTGATCAAAGTC 58.988 37.037 24.17 19.70 33.32 3.01
421 423 7.714813 TCGGCATATAAGATTTGATCAAAGTCA 59.285 33.333 24.17 11.02 33.32 3.41
422 424 8.344831 CGGCATATAAGATTTGATCAAAGTCAA 58.655 33.333 24.17 11.64 36.38 3.18
430 432 9.671279 AAGATTTGATCAAAGTCAAACCTTTTT 57.329 25.926 24.17 4.59 45.33 1.94
434 436 9.936759 TTTGATCAAAGTCAAACCTTTTTAACT 57.063 25.926 16.91 0.00 41.70 2.24
435 437 9.936759 TTGATCAAAGTCAAACCTTTTTAACTT 57.063 25.926 5.45 0.00 35.31 2.66
436 438 9.936759 TGATCAAAGTCAAACCTTTTTAACTTT 57.063 25.926 0.00 0.00 37.41 2.66
492 494 8.760103 TCACAATATGAAATCAACATTGTTGG 57.240 30.769 25.16 10.51 37.65 3.77
493 495 8.583296 TCACAATATGAAATCAACATTGTTGGA 58.417 29.630 25.16 14.50 37.65 3.53
494 496 9.373603 CACAATATGAAATCAACATTGTTGGAT 57.626 29.630 25.16 15.83 37.65 3.41
495 497 9.373603 ACAATATGAAATCAACATTGTTGGATG 57.626 29.630 25.16 14.26 36.66 3.51
496 498 8.332464 CAATATGAAATCAACATTGTTGGATGC 58.668 33.333 25.16 15.20 0.00 3.91
497 499 5.211174 TGAAATCAACATTGTTGGATGCA 57.789 34.783 25.16 17.19 0.00 3.96
498 500 5.795972 TGAAATCAACATTGTTGGATGCAT 58.204 33.333 25.16 0.00 0.00 3.96
499 501 5.870433 TGAAATCAACATTGTTGGATGCATC 59.130 36.000 25.16 18.81 0.00 3.91
500 502 5.408880 AATCAACATTGTTGGATGCATCA 57.591 34.783 27.25 11.43 0.00 3.07
501 503 5.607939 ATCAACATTGTTGGATGCATCAT 57.392 34.783 27.25 9.69 0.00 2.45
502 504 4.749976 TCAACATTGTTGGATGCATCATG 58.250 39.130 27.25 21.91 0.00 3.07
503 505 4.463186 TCAACATTGTTGGATGCATCATGA 59.537 37.500 27.25 10.11 0.00 3.07
504 506 4.649088 ACATTGTTGGATGCATCATGAG 57.351 40.909 27.25 12.37 0.00 2.90
505 507 4.274978 ACATTGTTGGATGCATCATGAGA 58.725 39.130 27.25 10.87 0.00 3.27
506 508 4.893524 ACATTGTTGGATGCATCATGAGAT 59.106 37.500 27.25 12.57 33.87 2.75
507 509 5.362717 ACATTGTTGGATGCATCATGAGATT 59.637 36.000 27.25 4.37 30.20 2.40
508 510 6.548251 ACATTGTTGGATGCATCATGAGATTA 59.452 34.615 27.25 5.83 30.20 1.75
509 511 7.068962 ACATTGTTGGATGCATCATGAGATTAA 59.931 33.333 27.25 11.32 30.20 1.40
510 512 7.591421 TTGTTGGATGCATCATGAGATTAAT 57.409 32.000 27.25 0.00 30.20 1.40
511 513 7.591421 TGTTGGATGCATCATGAGATTAATT 57.409 32.000 27.25 0.00 30.20 1.40
512 514 8.014070 TGTTGGATGCATCATGAGATTAATTT 57.986 30.769 27.25 0.00 30.20 1.82
513 515 8.479689 TGTTGGATGCATCATGAGATTAATTTT 58.520 29.630 27.25 0.00 30.20 1.82
514 516 8.975439 GTTGGATGCATCATGAGATTAATTTTC 58.025 33.333 27.25 5.38 30.20 2.29
515 517 8.240267 TGGATGCATCATGAGATTAATTTTCA 57.760 30.769 27.25 7.90 30.20 2.69
516 518 8.866093 TGGATGCATCATGAGATTAATTTTCAT 58.134 29.630 27.25 9.42 30.20 2.57
520 522 9.134055 TGCATCATGAGATTAATTTTCATACCA 57.866 29.630 13.09 7.72 30.77 3.25
583 585 6.509418 AAAGTTTGACTTTGTGCAGACTAA 57.491 33.333 5.34 0.00 45.83 2.24
584 586 6.509418 AAGTTTGACTTTGTGCAGACTAAA 57.491 33.333 0.00 0.00 34.11 1.85
585 587 6.509418 AGTTTGACTTTGTGCAGACTAAAA 57.491 33.333 0.00 0.00 28.95 1.52
586 588 6.919721 AGTTTGACTTTGTGCAGACTAAAAA 58.080 32.000 0.00 0.00 28.95 1.94
587 589 7.547227 AGTTTGACTTTGTGCAGACTAAAAAT 58.453 30.769 0.00 0.00 28.95 1.82
588 590 8.682710 AGTTTGACTTTGTGCAGACTAAAAATA 58.317 29.630 0.00 0.00 28.95 1.40
589 591 9.296400 GTTTGACTTTGTGCAGACTAAAAATAA 57.704 29.630 0.00 0.00 0.00 1.40
590 592 9.862371 TTTGACTTTGTGCAGACTAAAAATAAA 57.138 25.926 0.00 0.00 0.00 1.40
591 593 8.850454 TGACTTTGTGCAGACTAAAAATAAAC 57.150 30.769 0.00 0.00 0.00 2.01
592 594 7.642194 TGACTTTGTGCAGACTAAAAATAAACG 59.358 33.333 0.00 0.00 0.00 3.60
593 595 6.915843 ACTTTGTGCAGACTAAAAATAAACGG 59.084 34.615 0.00 0.00 0.00 4.44
594 596 6.621316 TTGTGCAGACTAAAAATAAACGGA 57.379 33.333 0.00 0.00 0.00 4.69
595 597 6.236017 TGTGCAGACTAAAAATAAACGGAG 57.764 37.500 0.00 0.00 0.00 4.63
596 598 5.180492 TGTGCAGACTAAAAATAAACGGAGG 59.820 40.000 0.00 0.00 0.00 4.30
597 599 4.698304 TGCAGACTAAAAATAAACGGAGGG 59.302 41.667 0.00 0.00 0.00 4.30
598 600 4.939439 GCAGACTAAAAATAAACGGAGGGA 59.061 41.667 0.00 0.00 0.00 4.20
599 601 5.064834 GCAGACTAAAAATAAACGGAGGGAG 59.935 44.000 0.00 0.00 0.00 4.30
600 602 6.171213 CAGACTAAAAATAAACGGAGGGAGT 58.829 40.000 0.00 0.00 0.00 3.85
601 603 7.325694 CAGACTAAAAATAAACGGAGGGAGTA 58.674 38.462 0.00 0.00 0.00 2.59
602 604 7.277319 CAGACTAAAAATAAACGGAGGGAGTAC 59.723 40.741 0.00 0.00 0.00 2.73
603 605 7.179872 AGACTAAAAATAAACGGAGGGAGTACT 59.820 37.037 0.00 0.00 0.00 2.73
604 606 8.366359 ACTAAAAATAAACGGAGGGAGTACTA 57.634 34.615 0.00 0.00 0.00 1.82
605 607 8.815912 ACTAAAAATAAACGGAGGGAGTACTAA 58.184 33.333 0.00 0.00 0.00 2.24
606 608 9.828039 CTAAAAATAAACGGAGGGAGTACTAAT 57.172 33.333 0.00 0.00 0.00 1.73
649 651 8.996988 TGAAATTTTATACGTTTATCATCCGC 57.003 30.769 0.00 0.00 0.00 5.54
650 652 8.613482 TGAAATTTTATACGTTTATCATCCGCA 58.387 29.630 0.00 0.00 0.00 5.69
651 653 9.440784 GAAATTTTATACGTTTATCATCCGCAA 57.559 29.630 0.00 0.00 0.00 4.85
652 654 9.790389 AAATTTTATACGTTTATCATCCGCAAA 57.210 25.926 0.00 0.00 0.00 3.68
653 655 9.790389 AATTTTATACGTTTATCATCCGCAAAA 57.210 25.926 0.00 0.00 0.00 2.44
654 656 9.790389 ATTTTATACGTTTATCATCCGCAAAAA 57.210 25.926 0.00 0.00 0.00 1.94
780 818 4.794278 TGATTCGGCTCGCCTATATTTA 57.206 40.909 6.35 0.00 0.00 1.40
781 819 4.744570 TGATTCGGCTCGCCTATATTTAG 58.255 43.478 6.35 0.00 0.00 1.85
782 820 4.219944 TGATTCGGCTCGCCTATATTTAGT 59.780 41.667 6.35 0.00 0.00 2.24
783 821 3.570926 TCGGCTCGCCTATATTTAGTG 57.429 47.619 6.35 0.00 0.00 2.74
786 824 3.305813 CGGCTCGCCTATATTTAGTGGAA 60.306 47.826 6.35 0.00 0.00 3.53
787 825 4.638304 GGCTCGCCTATATTTAGTGGAAA 58.362 43.478 0.00 0.00 0.00 3.13
788 826 4.451435 GGCTCGCCTATATTTAGTGGAAAC 59.549 45.833 0.00 0.00 0.00 2.78
789 827 5.054477 GCTCGCCTATATTTAGTGGAAACA 58.946 41.667 0.00 0.00 38.70 2.83
815 865 7.726738 ACACCTATTGTAAGTAACCAAACCAAT 59.273 33.333 0.00 0.00 36.32 3.16
872 923 5.359194 AATCGGAATCTTGTGTCATAGGT 57.641 39.130 0.00 0.00 0.00 3.08
874 925 3.118775 TCGGAATCTTGTGTCATAGGTGG 60.119 47.826 0.00 0.00 0.00 4.61
886 937 1.134699 CATAGGTGGCACGTGTCATCT 60.135 52.381 35.62 35.62 44.38 2.90
922 973 1.366366 CCGAACACTTCTCCGTGGT 59.634 57.895 0.00 0.00 39.19 4.16
949 1000 2.430921 CGTGTCTCCTGCCACGTC 60.431 66.667 4.17 0.00 46.87 4.34
1048 1112 1.316706 CGTCCTCGGCTTCCTCTTCT 61.317 60.000 0.00 0.00 0.00 2.85
1194 1258 1.175983 GCTCCATCGAGATCGTCCCT 61.176 60.000 1.70 0.00 38.52 4.20
1344 2938 4.003788 CTGGGACGGCGGTTCAGT 62.004 66.667 13.24 0.00 0.00 3.41
1455 3049 2.661866 GACGTGCGGTTGCTCAGT 60.662 61.111 0.00 0.00 43.34 3.41
1573 3167 3.359523 ACTACACCGACGCGCAGA 61.360 61.111 5.73 0.00 0.00 4.26
1635 3229 0.326238 TCCTCCGCTTGGTAAGGGAT 60.326 55.000 7.14 0.00 43.53 3.85
1843 3437 2.182030 GCTACTTCGCCGAGCTGT 59.818 61.111 0.00 0.00 33.28 4.40
2037 3631 0.318441 TGTTCGAGGAGCTCAACCAG 59.682 55.000 17.19 1.84 0.00 4.00
2327 4970 1.366319 ACTTGTTCTGCCTCCCTCAT 58.634 50.000 0.00 0.00 0.00 2.90
2352 4995 8.322906 TCTTGACAAGATTTTTATGACGATGT 57.677 30.769 13.99 0.00 31.20 3.06
2366 5009 5.147330 TGACGATGTGGTTAAGACTCAAT 57.853 39.130 0.00 0.00 0.00 2.57
2538 5182 3.925630 AAGCGGACCACCATGGCAG 62.926 63.158 13.04 5.77 42.67 4.85
2644 5288 7.872993 TGCAAGGTTAGCTAGCTATTAACATAG 59.127 37.037 24.69 14.64 36.20 2.23
2676 5320 2.156098 CCTAGCTACTCCGAGATCACC 58.844 57.143 1.33 0.00 0.00 4.02
2680 5324 1.271102 GCTACTCCGAGATCACCCATC 59.729 57.143 1.33 0.00 0.00 3.51
2715 5360 7.589587 TGTCAATTTGTAACACGAATCATTCAC 59.410 33.333 0.00 0.00 31.20 3.18
2736 5388 2.677902 CGATGGGCGCAGTATATGGAAT 60.678 50.000 10.83 0.00 0.00 3.01
2751 5403 1.753078 GAATTGGGGAAGGCGGGAC 60.753 63.158 0.00 0.00 0.00 4.46
2856 5508 4.186926 CCAGCTATGGTTATCATCATCGG 58.813 47.826 0.00 0.00 42.17 4.18
2860 5512 0.602638 TGGTTATCATCATCGGCGGC 60.603 55.000 7.21 0.00 0.00 6.53
2875 5527 1.599606 GCGGCTGAGTCAGGAAGAGA 61.600 60.000 21.54 0.00 31.21 3.10
2877 5529 1.480137 CGGCTGAGTCAGGAAGAGATT 59.520 52.381 21.54 0.00 31.21 2.40
2999 5651 1.413445 CATGGAGCTGGAGGAGAAGAG 59.587 57.143 0.00 0.00 0.00 2.85
3060 5712 1.009389 GGCTCGACGGAAACACAGAG 61.009 60.000 0.00 0.00 0.00 3.35
3094 5746 3.304829 GGGGACTATGAGAAGAAGCTCT 58.695 50.000 0.00 0.00 35.91 4.09
3096 5748 3.069443 GGGACTATGAGAAGAAGCTCTGG 59.931 52.174 0.00 0.00 35.91 3.86
3109 5976 2.853542 TCTGGGAGTTGCAGGGCA 60.854 61.111 0.00 0.00 36.47 5.36
3111 5978 0.913934 TCTGGGAGTTGCAGGGCATA 60.914 55.000 0.00 0.00 38.76 3.14
3152 6019 1.001181 CATGCAAACAAGGTTGGGAGG 59.999 52.381 0.00 0.00 0.00 4.30
3226 6093 6.648725 GCCCTGAAAATAACAATTGTTAGCAA 59.351 34.615 29.25 14.15 42.94 3.91
3286 6154 6.817184 ACTACTAGCTAAATACCCACACATG 58.183 40.000 0.00 0.00 0.00 3.21
3302 6170 4.025360 ACACATGGCCACATAACAATCAT 58.975 39.130 8.16 0.00 34.99 2.45
3333 6201 7.491372 TCAGTTTTACACGATAGAGGCATTAAG 59.509 37.037 0.00 0.00 41.38 1.85
3397 6268 4.022503 TCAATCGTGATTGCAATTGGTTGA 60.023 37.500 21.93 21.93 45.77 3.18
3406 6277 2.226200 TGCAATTGGTTGACATGTCTCG 59.774 45.455 25.55 7.10 37.53 4.04
3413 6284 4.329392 TGGTTGACATGTCTCGTACTCTA 58.671 43.478 25.55 0.00 0.00 2.43
3414 6285 4.763279 TGGTTGACATGTCTCGTACTCTAA 59.237 41.667 25.55 6.40 0.00 2.10
3421 6292 7.272731 TGACATGTCTCGTACTCTAATTTTTCG 59.727 37.037 25.55 0.00 0.00 3.46
3424 6295 7.736031 TGTCTCGTACTCTAATTTTTCGATG 57.264 36.000 0.00 0.00 0.00 3.84
3478 6350 6.811634 TTATACCCGACCTCCAGATAAAAA 57.188 37.500 0.00 0.00 0.00 1.94
3508 6380 3.002348 GCGATAAAAGGGTAGACATGCAC 59.998 47.826 0.00 0.00 0.00 4.57
3530 6402 6.254157 GCACGCATTTCATTGATCAAAAGTAT 59.746 34.615 13.09 1.73 0.00 2.12
3569 6441 1.999735 GCGTTCGTCAGAATGGATCAA 59.000 47.619 0.00 0.00 42.22 2.57
3630 6502 0.035317 TGATCTCGCACTTGGCACTT 59.965 50.000 0.00 0.00 45.17 3.16
3655 6527 1.078759 CACTTGGTAGAAGGCTCGCG 61.079 60.000 0.00 0.00 0.00 5.87
3853 6742 0.839477 CGTGCTGCTCGTTTGTTTTG 59.161 50.000 15.22 0.00 0.00 2.44
3882 6771 1.568612 CGAACGTGAGGCTTGTGCAT 61.569 55.000 0.00 0.00 41.91 3.96
3914 6806 4.237445 CCTCAAGGCCTCATGCTG 57.763 61.111 5.23 0.00 40.92 4.41
3915 6807 1.605992 CCTCAAGGCCTCATGCTGA 59.394 57.895 5.23 4.51 40.92 4.26
3923 6815 2.599032 CTCATGCTGATGGGGCCA 59.401 61.111 4.39 0.00 0.00 5.36
3951 6843 1.522580 GAATGCTGGAGGCGAGTCC 60.523 63.158 0.00 0.00 45.43 3.85
3956 6848 2.284625 TGGAGGCGAGTCCCATGT 60.285 61.111 1.34 0.00 35.49 3.21
3957 6849 1.903877 CTGGAGGCGAGTCCCATGTT 61.904 60.000 1.34 0.00 35.49 2.71
3958 6850 0.616395 TGGAGGCGAGTCCCATGTTA 60.616 55.000 1.34 0.00 35.49 2.41
3959 6851 0.539986 GGAGGCGAGTCCCATGTTAA 59.460 55.000 0.00 0.00 34.51 2.01
3979 8335 9.826574 ATGTTAATTAGTAGGCGACATTTAGAA 57.173 29.630 0.00 0.00 0.00 2.10
4022 8378 0.955919 GACGGAAGAAGCCCAAGTGG 60.956 60.000 0.00 0.00 37.09 4.00
4023 8379 1.073199 CGGAAGAAGCCCAAGTGGT 59.927 57.895 0.00 0.00 36.04 4.16
4025 8381 0.178990 GGAAGAAGCCCAAGTGGTGT 60.179 55.000 0.00 0.00 36.04 4.16
4026 8382 0.954452 GAAGAAGCCCAAGTGGTGTG 59.046 55.000 0.00 0.00 36.04 3.82
4027 8383 0.258774 AAGAAGCCCAAGTGGTGTGT 59.741 50.000 0.00 0.00 36.04 3.72
4028 8384 0.466189 AGAAGCCCAAGTGGTGTGTG 60.466 55.000 0.00 0.00 36.04 3.82
4029 8385 0.465460 GAAGCCCAAGTGGTGTGTGA 60.465 55.000 0.00 0.00 36.04 3.58
4036 8392 2.289072 CCAAGTGGTGTGTGACTAGAGG 60.289 54.545 0.00 0.00 0.00 3.69
4063 8419 1.441732 GGCCCAAACTGTTTCGTCGT 61.442 55.000 2.13 0.00 0.00 4.34
4072 8428 0.319986 TGTTTCGTCGTAGGCATGCA 60.320 50.000 21.36 0.00 0.00 3.96
4075 8431 0.459899 TTCGTCGTAGGCATGCATCT 59.540 50.000 21.36 10.94 0.00 2.90
4080 8436 1.206849 TCGTAGGCATGCATCTGAACA 59.793 47.619 21.36 0.00 0.00 3.18
4092 8448 1.079543 CTGAACAGAGTGCCCCTCG 60.080 63.158 0.00 0.00 45.44 4.63
4099 8455 3.655810 GAGTGCCCCTCGACTGCAG 62.656 68.421 13.48 13.48 35.33 4.41
4118 8474 5.005740 TGCAGTACAGAGCATGAAAGAAAT 58.994 37.500 0.00 0.00 35.51 2.17
4123 8479 5.039480 ACAGAGCATGAAAGAAATTGTCG 57.961 39.130 0.00 0.00 0.00 4.35
4155 8511 4.001618 TGGAATCGTGTCACTTTCATCA 57.998 40.909 14.06 4.96 0.00 3.07
4179 10091 1.949525 ACAACCTGTGTGCAAGATGAC 59.050 47.619 0.00 0.00 39.72 3.06
4180 10092 2.224606 CAACCTGTGTGCAAGATGACT 58.775 47.619 0.00 0.00 0.00 3.41
4181 10093 3.181455 ACAACCTGTGTGCAAGATGACTA 60.181 43.478 0.00 0.00 39.72 2.59
4182 10094 3.045601 ACCTGTGTGCAAGATGACTAC 57.954 47.619 0.00 0.00 0.00 2.73
4183 10095 1.995484 CCTGTGTGCAAGATGACTACG 59.005 52.381 0.00 0.00 0.00 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 7.504924 TCTCATTGTTTTCGTGGACTTTATT 57.495 32.000 0.00 0.00 0.00 1.40
13 14 5.530915 TCATCTCATTGTTTTCGTGGACTTT 59.469 36.000 0.00 0.00 0.00 2.66
19 20 8.542132 ACAAAATTTCATCTCATTGTTTTCGTG 58.458 29.630 0.00 0.00 0.00 4.35
58 59 8.621126 AATCTGCAATCTCCCTAGATACATAT 57.379 34.615 0.00 0.00 41.81 1.78
60 61 6.949117 AATCTGCAATCTCCCTAGATACAT 57.051 37.500 0.00 0.00 41.81 2.29
66 67 6.115446 TGTTACAAATCTGCAATCTCCCTAG 58.885 40.000 0.00 0.00 0.00 3.02
123 124 3.118482 CCATCCTTTGAAGCTCTGCTCTA 60.118 47.826 0.00 0.00 38.25 2.43
128 129 2.290514 TGGTCCATCCTTTGAAGCTCTG 60.291 50.000 0.00 0.00 37.07 3.35
186 188 9.516546 AGAACATGTATGCATATCATCTTTGAT 57.483 29.630 10.16 1.06 44.76 2.57
286 288 9.891828 AAAAAGGACATTTTCTTTGTTGTTTTC 57.108 25.926 0.00 0.00 40.27 2.29
359 361 6.071221 ACGAAGGGAGTATGTAATGTACACAA 60.071 38.462 0.00 0.00 42.23 3.33
368 370 9.211485 CTAAAAAGAAACGAAGGGAGTATGTAA 57.789 33.333 0.00 0.00 0.00 2.41
369 371 8.370182 ACTAAAAAGAAACGAAGGGAGTATGTA 58.630 33.333 0.00 0.00 0.00 2.29
376 378 4.060205 CCGACTAAAAAGAAACGAAGGGA 58.940 43.478 0.00 0.00 0.00 4.20
377 379 3.364664 GCCGACTAAAAAGAAACGAAGGG 60.365 47.826 0.00 0.00 0.00 3.95
378 380 3.249080 TGCCGACTAAAAAGAAACGAAGG 59.751 43.478 0.00 0.00 0.00 3.46
380 382 6.730960 ATATGCCGACTAAAAAGAAACGAA 57.269 33.333 0.00 0.00 0.00 3.85
381 383 7.760794 TCTTATATGCCGACTAAAAAGAAACGA 59.239 33.333 0.00 0.00 0.00 3.85
382 384 7.902032 TCTTATATGCCGACTAAAAAGAAACG 58.098 34.615 0.00 0.00 0.00 3.60
386 388 9.607988 TCAAATCTTATATGCCGACTAAAAAGA 57.392 29.630 0.00 0.00 0.00 2.52
389 391 9.554395 TGATCAAATCTTATATGCCGACTAAAA 57.446 29.630 0.00 0.00 0.00 1.52
390 392 9.554395 TTGATCAAATCTTATATGCCGACTAAA 57.446 29.630 5.45 0.00 0.00 1.85
391 393 9.554395 TTTGATCAAATCTTATATGCCGACTAA 57.446 29.630 16.91 0.00 0.00 2.24
392 394 9.208022 CTTTGATCAAATCTTATATGCCGACTA 57.792 33.333 20.76 0.00 0.00 2.59
393 395 7.716998 ACTTTGATCAAATCTTATATGCCGACT 59.283 33.333 20.76 0.00 0.00 4.18
394 396 7.865707 ACTTTGATCAAATCTTATATGCCGAC 58.134 34.615 20.76 0.00 0.00 4.79
395 397 7.714813 TGACTTTGATCAAATCTTATATGCCGA 59.285 33.333 20.76 0.00 0.00 5.54
396 398 7.864686 TGACTTTGATCAAATCTTATATGCCG 58.135 34.615 20.76 7.58 0.00 5.69
408 410 9.936759 AGTTAAAAAGGTTTGACTTTGATCAAA 57.063 25.926 19.45 19.45 39.78 2.69
409 411 9.936759 AAGTTAAAAAGGTTTGACTTTGATCAA 57.063 25.926 3.38 3.38 46.02 2.57
466 468 9.205719 CCAACAATGTTGATTTCATATTGTGAA 57.794 29.630 25.93 0.00 44.87 3.18
467 469 8.583296 TCCAACAATGTTGATTTCATATTGTGA 58.417 29.630 25.93 8.01 40.18 3.58
468 470 8.760103 TCCAACAATGTTGATTTCATATTGTG 57.240 30.769 25.93 5.86 40.18 3.33
469 471 9.373603 CATCCAACAATGTTGATTTCATATTGT 57.626 29.630 25.93 13.53 41.49 2.71
470 472 8.332464 GCATCCAACAATGTTGATTTCATATTG 58.668 33.333 25.93 6.53 37.09 1.90
471 473 8.041919 TGCATCCAACAATGTTGATTTCATATT 58.958 29.630 25.93 0.00 0.00 1.28
472 474 7.557724 TGCATCCAACAATGTTGATTTCATAT 58.442 30.769 25.93 6.16 0.00 1.78
473 475 6.932947 TGCATCCAACAATGTTGATTTCATA 58.067 32.000 25.93 4.83 0.00 2.15
474 476 5.795972 TGCATCCAACAATGTTGATTTCAT 58.204 33.333 25.93 7.88 0.00 2.57
475 477 5.211174 TGCATCCAACAATGTTGATTTCA 57.789 34.783 25.93 15.03 0.00 2.69
476 478 5.870433 TGATGCATCCAACAATGTTGATTTC 59.130 36.000 25.93 12.91 0.00 2.17
477 479 5.795972 TGATGCATCCAACAATGTTGATTT 58.204 33.333 25.93 8.39 0.00 2.17
478 480 5.408880 TGATGCATCCAACAATGTTGATT 57.591 34.783 25.93 10.78 0.00 2.57
479 481 5.128008 TCATGATGCATCCAACAATGTTGAT 59.872 36.000 25.93 14.60 0.00 2.57
480 482 4.463186 TCATGATGCATCCAACAATGTTGA 59.537 37.500 25.93 13.07 0.00 3.18
481 483 4.749976 TCATGATGCATCCAACAATGTTG 58.250 39.130 23.67 18.45 0.00 3.33
482 484 4.707934 TCTCATGATGCATCCAACAATGTT 59.292 37.500 23.67 0.00 0.00 2.71
483 485 4.274978 TCTCATGATGCATCCAACAATGT 58.725 39.130 23.67 0.00 0.00 2.71
484 486 4.911514 TCTCATGATGCATCCAACAATG 57.088 40.909 23.67 18.57 0.00 2.82
485 487 7.591421 TTAATCTCATGATGCATCCAACAAT 57.409 32.000 23.67 7.42 32.44 2.71
486 488 7.591421 ATTAATCTCATGATGCATCCAACAA 57.409 32.000 23.67 5.13 32.44 2.83
487 489 7.591421 AATTAATCTCATGATGCATCCAACA 57.409 32.000 23.67 6.24 32.44 3.33
488 490 8.882415 AAAATTAATCTCATGATGCATCCAAC 57.118 30.769 23.67 0.00 32.44 3.77
489 491 8.697292 TGAAAATTAATCTCATGATGCATCCAA 58.303 29.630 23.67 6.72 32.44 3.53
490 492 8.240267 TGAAAATTAATCTCATGATGCATCCA 57.760 30.769 23.67 12.20 32.44 3.41
494 496 9.134055 TGGTATGAAAATTAATCTCATGATGCA 57.866 29.630 17.36 0.00 32.22 3.96
561 563 6.509418 TTTAGTCTGCACAAAGTCAAACTT 57.491 33.333 0.00 0.00 40.80 2.66
562 564 6.509418 TTTTAGTCTGCACAAAGTCAAACT 57.491 33.333 0.00 0.00 0.00 2.66
563 565 7.755582 ATTTTTAGTCTGCACAAAGTCAAAC 57.244 32.000 0.00 0.00 0.00 2.93
564 566 9.862371 TTTATTTTTAGTCTGCACAAAGTCAAA 57.138 25.926 0.00 0.00 0.00 2.69
565 567 9.296400 GTTTATTTTTAGTCTGCACAAAGTCAA 57.704 29.630 0.00 0.00 0.00 3.18
566 568 7.642194 CGTTTATTTTTAGTCTGCACAAAGTCA 59.358 33.333 0.00 0.00 0.00 3.41
567 569 7.112984 CCGTTTATTTTTAGTCTGCACAAAGTC 59.887 37.037 0.00 0.00 0.00 3.01
568 570 6.915843 CCGTTTATTTTTAGTCTGCACAAAGT 59.084 34.615 0.00 0.00 0.00 2.66
569 571 7.136119 TCCGTTTATTTTTAGTCTGCACAAAG 58.864 34.615 0.00 0.00 0.00 2.77
570 572 7.028926 TCCGTTTATTTTTAGTCTGCACAAA 57.971 32.000 0.00 0.00 0.00 2.83
571 573 6.293735 CCTCCGTTTATTTTTAGTCTGCACAA 60.294 38.462 0.00 0.00 0.00 3.33
572 574 5.180492 CCTCCGTTTATTTTTAGTCTGCACA 59.820 40.000 0.00 0.00 0.00 4.57
573 575 5.391629 CCCTCCGTTTATTTTTAGTCTGCAC 60.392 44.000 0.00 0.00 0.00 4.57
574 576 4.698304 CCCTCCGTTTATTTTTAGTCTGCA 59.302 41.667 0.00 0.00 0.00 4.41
575 577 4.939439 TCCCTCCGTTTATTTTTAGTCTGC 59.061 41.667 0.00 0.00 0.00 4.26
576 578 6.171213 ACTCCCTCCGTTTATTTTTAGTCTG 58.829 40.000 0.00 0.00 0.00 3.51
577 579 6.370186 ACTCCCTCCGTTTATTTTTAGTCT 57.630 37.500 0.00 0.00 0.00 3.24
578 580 7.326454 AGTACTCCCTCCGTTTATTTTTAGTC 58.674 38.462 0.00 0.00 0.00 2.59
579 581 7.250032 AGTACTCCCTCCGTTTATTTTTAGT 57.750 36.000 0.00 0.00 0.00 2.24
580 582 9.828039 ATTAGTACTCCCTCCGTTTATTTTTAG 57.172 33.333 0.00 0.00 0.00 1.85
588 590 8.931568 ACAAATATATTAGTACTCCCTCCGTTT 58.068 33.333 0.00 0.00 0.00 3.60
589 591 8.488308 ACAAATATATTAGTACTCCCTCCGTT 57.512 34.615 0.00 0.00 0.00 4.44
590 592 9.765295 ATACAAATATATTAGTACTCCCTCCGT 57.235 33.333 0.00 0.00 0.00 4.69
628 630 9.790389 TTTTTGCGGATGATAAACGTATAAAAT 57.210 25.926 0.00 0.00 0.00 1.82
687 689 4.271533 CCAGCGAAAATACTATTTGCGGTA 59.728 41.667 20.99 0.00 0.00 4.02
688 690 3.064820 CCAGCGAAAATACTATTTGCGGT 59.935 43.478 17.36 17.36 0.00 5.68
689 691 3.311322 TCCAGCGAAAATACTATTTGCGG 59.689 43.478 19.32 12.63 0.00 5.69
690 692 4.530094 TCCAGCGAAAATACTATTTGCG 57.470 40.909 15.18 15.18 0.00 4.85
732 766 0.609131 AAGTGCATTTGGGAGACGGG 60.609 55.000 0.00 0.00 0.00 5.28
741 775 3.557577 TCATCGTGGAAAGTGCATTTG 57.442 42.857 0.00 0.00 0.00 2.32
765 803 3.955650 TCCACTAAATATAGGCGAGCC 57.044 47.619 5.89 5.89 33.15 4.70
780 818 5.937111 ACTTACAATAGGTGTGTTTCCACT 58.063 37.500 0.00 0.00 41.89 4.00
781 819 7.308169 GGTTACTTACAATAGGTGTGTTTCCAC 60.308 40.741 0.00 0.00 41.89 4.02
782 820 6.711645 GGTTACTTACAATAGGTGTGTTTCCA 59.288 38.462 0.00 0.00 41.89 3.53
783 821 6.711645 TGGTTACTTACAATAGGTGTGTTTCC 59.288 38.462 0.00 0.00 41.89 3.13
786 824 7.013559 GGTTTGGTTACTTACAATAGGTGTGTT 59.986 37.037 0.00 0.00 41.89 3.32
787 825 6.487668 GGTTTGGTTACTTACAATAGGTGTGT 59.512 38.462 0.00 0.00 41.89 3.72
788 826 6.487331 TGGTTTGGTTACTTACAATAGGTGTG 59.513 38.462 0.00 0.00 41.89 3.82
789 827 6.603224 TGGTTTGGTTACTTACAATAGGTGT 58.397 36.000 0.00 0.00 44.82 4.16
790 828 7.513371 TTGGTTTGGTTACTTACAATAGGTG 57.487 36.000 0.00 0.00 0.00 4.00
791 829 8.715190 AATTGGTTTGGTTACTTACAATAGGT 57.285 30.769 0.00 0.00 0.00 3.08
792 830 9.634163 GAAATTGGTTTGGTTACTTACAATAGG 57.366 33.333 0.00 0.00 0.00 2.57
796 834 9.892130 AATTGAAATTGGTTTGGTTACTTACAA 57.108 25.926 0.00 0.00 0.00 2.41
856 907 3.347216 GTGCCACCTATGACACAAGATT 58.653 45.455 0.00 0.00 33.23 2.40
857 908 2.677902 CGTGCCACCTATGACACAAGAT 60.678 50.000 0.00 0.00 33.23 2.40
863 914 0.037697 GACACGTGCCACCTATGACA 60.038 55.000 17.22 0.00 0.00 3.58
872 923 0.320683 CCAGAAGATGACACGTGCCA 60.321 55.000 17.22 12.24 0.00 4.92
874 925 1.195448 CAACCAGAAGATGACACGTGC 59.805 52.381 17.22 9.30 0.00 5.34
877 928 2.289072 ACTCCAACCAGAAGATGACACG 60.289 50.000 0.00 0.00 0.00 4.49
886 937 1.474320 CGGTGTTCACTCCAACCAGAA 60.474 52.381 2.98 0.00 32.69 3.02
922 973 2.741092 GAGACACGTCCCAAGGCA 59.259 61.111 0.00 0.00 0.00 4.75
1038 1102 2.166664 CGTGAGGGGTAAGAAGAGGAAG 59.833 54.545 0.00 0.00 0.00 3.46
1324 2918 3.782443 GAACCGCCGTCCCAGGAT 61.782 66.667 0.00 0.00 0.00 3.24
1361 2955 2.584391 GGCAAGGTCTCCACGTCCT 61.584 63.158 0.00 0.00 0.00 3.85
1485 3079 1.524621 CGCCCTGTCCATCATGTCC 60.525 63.158 0.00 0.00 0.00 4.02
1515 3109 4.379243 CGCGTGACCTTCCTGCCT 62.379 66.667 0.00 0.00 0.00 4.75
1573 3167 0.464452 GCCTCCTTGGTAGCGTACAT 59.536 55.000 0.00 0.00 38.35 2.29
1657 3251 0.460284 CTATGCTTGTCGAGGCCGTT 60.460 55.000 0.00 0.00 37.05 4.44
1734 3328 0.247460 CTTCATCGAGGGTGAGCACA 59.753 55.000 0.00 0.00 0.00 4.57
1881 3475 4.074526 AGCCTCTGCATCGCGTGT 62.075 61.111 5.77 0.00 41.13 4.49
2037 3631 3.437049 CCATCGTCTTCAAGAAAAGGTCC 59.563 47.826 0.00 0.00 0.00 4.46
2327 4970 8.229811 CACATCGTCATAAAAATCTTGTCAAGA 58.770 33.333 17.46 17.46 42.69 3.02
2382 5025 7.117667 CACGTCAACTATGCCTGCATATAATAA 59.882 37.037 11.94 0.00 38.13 1.40
2383 5026 6.589907 CACGTCAACTATGCCTGCATATAATA 59.410 38.462 11.94 0.00 38.13 0.98
2486 5130 0.392863 TGATGACATGCGTCCCCTTG 60.393 55.000 0.00 0.00 41.85 3.61
2538 5182 0.535335 TCGCCCTCATACACCTTGAC 59.465 55.000 0.00 0.00 0.00 3.18
2644 5288 4.703093 GGAGTAGCTAGGATGTAGGATCAC 59.297 50.000 0.00 0.00 0.00 3.06
2676 5320 9.950680 GTTACAAATTGACAATATGTAGGATGG 57.049 33.333 0.00 0.00 0.00 3.51
2680 5324 8.661257 TCGTGTTACAAATTGACAATATGTAGG 58.339 33.333 0.00 0.00 0.00 3.18
2703 5348 1.299541 GCCCATCGTGAATGATTCGT 58.700 50.000 0.18 0.00 37.59 3.85
2715 5360 0.246360 TCCATATACTGCGCCCATCG 59.754 55.000 4.18 0.00 42.12 3.84
2736 5388 2.938798 ATGTCCCGCCTTCCCCAA 60.939 61.111 0.00 0.00 0.00 4.12
2751 5403 0.031314 CCTCGATGGTCACCTCGATG 59.969 60.000 15.86 11.06 42.45 3.84
2824 5476 0.396435 CCATAGCTGGTATTGGCCGA 59.604 55.000 0.00 0.00 37.79 5.54
2856 5508 1.153667 CTCTTCCTGACTCAGCCGC 60.154 63.158 0.00 0.00 0.00 6.53
2860 5512 3.768406 CGTCAATCTCTTCCTGACTCAG 58.232 50.000 0.00 0.00 37.84 3.35
2897 5549 4.796231 CCCTGGCGAACTCGTCCG 62.796 72.222 0.63 0.00 44.42 4.79
2918 5570 1.452833 GCCTCCAGCCTAGCTTTGG 60.453 63.158 0.00 0.00 36.40 3.28
2966 5618 3.129502 CCATGTCACCAGCAGCGG 61.130 66.667 2.15 2.15 0.00 5.52
3094 5746 0.106569 CATATGCCCTGCAACTCCCA 60.107 55.000 0.00 0.00 43.62 4.37
3096 5748 1.789078 CGCATATGCCCTGCAACTCC 61.789 60.000 21.77 0.00 43.62 3.85
3109 5976 1.270826 CGAGATGACAGGGTCGCATAT 59.729 52.381 0.00 0.00 34.95 1.78
3111 5978 1.439228 CGAGATGACAGGGTCGCAT 59.561 57.895 0.00 0.00 34.95 4.73
3120 5987 0.322366 TTTGCATGGCCGAGATGACA 60.322 50.000 5.75 1.10 0.00 3.58
3152 6019 2.104267 TCGTAGTCATCGAGGCCAC 58.896 57.895 5.01 0.00 33.38 5.01
3260 6127 8.585881 CATGTGTGGGTATTTAGCTAGTAGTAT 58.414 37.037 0.00 0.00 0.00 2.12
3263 6130 6.223852 CCATGTGTGGGTATTTAGCTAGTAG 58.776 44.000 0.00 0.00 42.11 2.57
3286 6154 6.039717 ACTGACATTATGATTGTTATGTGGCC 59.960 38.462 0.00 0.00 31.76 5.36
3302 6170 6.755141 GCCTCTATCGTGTAAAACTGACATTA 59.245 38.462 0.00 0.00 0.00 1.90
3318 6186 3.434641 CACCATGCTTAATGCCTCTATCG 59.565 47.826 0.00 0.00 42.00 2.92
3333 6201 7.593825 AGACAATAACTTTAGAAACACCATGC 58.406 34.615 0.00 0.00 0.00 4.06
3397 6268 7.310664 TCGAAAAATTAGAGTACGAGACATGT 58.689 34.615 0.00 0.00 0.00 3.21
3406 6277 8.265165 ACCCTTTCATCGAAAAATTAGAGTAC 57.735 34.615 0.00 0.00 30.84 2.73
3413 6284 5.219633 CGTTGACCCTTTCATCGAAAAATT 58.780 37.500 0.00 0.00 46.26 1.82
3414 6285 4.794169 CGTTGACCCTTTCATCGAAAAAT 58.206 39.130 0.00 0.00 46.26 1.82
3421 6292 1.369625 ATCGCGTTGACCCTTTCATC 58.630 50.000 5.77 0.00 32.84 2.92
3424 6295 1.717194 TGTATCGCGTTGACCCTTTC 58.283 50.000 5.77 0.00 0.00 2.62
3453 6324 7.383156 TTTTATCTGGAGGTCGGGTATAATT 57.617 36.000 0.00 0.00 0.00 1.40
3478 6350 3.366052 ACCCTTTTATCGCATTGACCT 57.634 42.857 0.00 0.00 0.00 3.85
3530 6402 5.849357 ACGCGAACAAGTGATTACAAATA 57.151 34.783 15.93 0.00 0.00 1.40
3548 6420 0.572590 GATCCATTCTGACGAACGCG 59.427 55.000 3.53 3.53 44.79 6.01
3549 6421 1.640428 TGATCCATTCTGACGAACGC 58.360 50.000 0.00 0.00 30.67 4.84
3613 6485 0.322975 AGAAGTGCCAAGTGCGAGAT 59.677 50.000 0.00 0.00 45.60 2.75
3630 6502 2.180276 GCCTTCTACCAAGTGGAGAGA 58.820 52.381 3.83 3.64 38.94 3.10
3695 6567 7.529158 CAACACAGATGCTCACATGTTATTTA 58.471 34.615 0.00 0.00 36.35 1.40
3759 6631 7.672983 TTATCTAAAAGAACTGAAGGCACAG 57.327 36.000 9.52 9.52 42.78 3.66
3853 6742 1.945776 CTCACGTTCGCTTTCGCTCC 61.946 60.000 0.00 0.00 35.26 4.70
3882 6771 0.753867 TGAGGCGTGTGTAGTTCCAA 59.246 50.000 0.00 0.00 0.00 3.53
3923 6815 2.915604 CCTCCAGCATTCTATATGGGGT 59.084 50.000 0.00 0.00 30.84 4.95
3928 6820 3.169099 ACTCGCCTCCAGCATTCTATAT 58.831 45.455 0.00 0.00 44.04 0.86
3951 6843 6.861065 AATGTCGCCTACTAATTAACATGG 57.139 37.500 0.00 0.00 0.00 3.66
3956 6848 7.982919 TGCTTCTAAATGTCGCCTACTAATTAA 59.017 33.333 0.00 0.00 0.00 1.40
3957 6849 7.437267 GTGCTTCTAAATGTCGCCTACTAATTA 59.563 37.037 0.00 0.00 0.00 1.40
3958 6850 6.258068 GTGCTTCTAAATGTCGCCTACTAATT 59.742 38.462 0.00 0.00 0.00 1.40
3959 6851 5.753921 GTGCTTCTAAATGTCGCCTACTAAT 59.246 40.000 0.00 0.00 0.00 1.73
3979 8335 1.326951 GGGTGTTGTTGTTGGGTGCT 61.327 55.000 0.00 0.00 0.00 4.40
4022 8378 4.872691 CCAAATCATCCTCTAGTCACACAC 59.127 45.833 0.00 0.00 0.00 3.82
4023 8379 4.623886 GCCAAATCATCCTCTAGTCACACA 60.624 45.833 0.00 0.00 0.00 3.72
4025 8381 3.118261 GGCCAAATCATCCTCTAGTCACA 60.118 47.826 0.00 0.00 0.00 3.58
4026 8382 3.471680 GGCCAAATCATCCTCTAGTCAC 58.528 50.000 0.00 0.00 0.00 3.67
4027 8383 2.439507 GGGCCAAATCATCCTCTAGTCA 59.560 50.000 4.39 0.00 0.00 3.41
4028 8384 2.439507 TGGGCCAAATCATCCTCTAGTC 59.560 50.000 2.13 0.00 0.00 2.59
4029 8385 2.492025 TGGGCCAAATCATCCTCTAGT 58.508 47.619 2.13 0.00 0.00 2.57
4036 8392 3.683365 AACAGTTTGGGCCAAATCATC 57.317 42.857 32.51 20.15 35.74 2.92
4063 8419 2.502947 ACTCTGTTCAGATGCATGCCTA 59.497 45.455 16.68 0.00 0.00 3.93
4072 8428 0.908198 GAGGGGCACTCTGTTCAGAT 59.092 55.000 10.16 0.00 43.14 2.90
4075 8431 1.533033 TCGAGGGGCACTCTGTTCA 60.533 57.895 15.97 0.00 44.33 3.18
4080 8436 3.386237 GCAGTCGAGGGGCACTCT 61.386 66.667 15.97 0.00 44.33 3.24
4092 8448 2.662006 TCATGCTCTGTACTGCAGTC 57.338 50.000 25.56 15.44 45.23 3.51
4099 8455 6.017933 CGACAATTTCTTTCATGCTCTGTAC 58.982 40.000 0.00 0.00 0.00 2.90
4118 8474 0.250252 TCCATTCAGCAGTGCGACAA 60.250 50.000 10.00 4.15 0.00 3.18
4123 8479 1.089920 ACGATTCCATTCAGCAGTGC 58.910 50.000 7.13 7.13 0.00 4.40


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

AutoCloner maintained by Alex Coulton.