Multiple sequence alignment - TraesCS3B01G436600

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 TraesCS3B01G436600 chr3B 100.000 5706 0 0 1 5706 675046488 675040783 0.000000e+00 10538.0
1 TraesCS3B01G436600 chr3D 93.460 3624 131 44 2119 5706 512672365 512675918 0.000000e+00 5282.0
2 TraesCS3B01G436600 chr3D 90.867 1511 83 31 635 2119 512670852 512672333 0.000000e+00 1975.0
3 TraesCS3B01G436600 chr3D 79.854 412 51 21 1 388 512670328 512670731 7.280000e-69 272.0
4 TraesCS3B01G436600 chr3A 94.017 3443 136 35 2119 5524 648259769 648263178 0.000000e+00 5153.0
5 TraesCS3B01G436600 chr3A 90.136 1612 93 40 540 2113 648258147 648259730 0.000000e+00 2036.0
6 TraesCS3B01G436600 chr3A 75.668 337 38 26 86 386 648257772 648258100 1.670000e-25 128.0
7 TraesCS3B01G436600 chr3A 93.333 75 5 0 5632 5706 648263369 648263443 1.680000e-20 111.0
8 TraesCS3B01G436600 chr7A 85.946 185 15 8 3040 3213 39211290 39211474 2.710000e-43 187.0
9 TraesCS3B01G436600 chr1A 90.909 66 6 0 5641 5706 455819274 455819339 7.870000e-14 89.8
10 TraesCS3B01G436600 chr1D 89.394 66 7 0 5641 5706 355470501 355470566 3.660000e-12 84.2
11 TraesCS3B01G436600 chr2D 89.474 57 4 2 5651 5706 398668252 398668307 2.850000e-08 71.3
12 TraesCS3B01G436600 chr2B 89.474 57 4 2 5651 5706 471322432 471322377 2.850000e-08 71.3
13 TraesCS3B01G436600 chr2A 89.474 57 4 2 5651 5706 535836629 535836684 2.850000e-08 71.3
14 TraesCS3B01G436600 chr6D 88.000 50 6 0 5272 5321 127138102 127138151 6.170000e-05 60.2
15 TraesCS3B01G436600 chr6B 88.000 50 6 0 5272 5321 226187665 226187714 6.170000e-05 60.2
16 TraesCS3B01G436600 chr6A 94.737 38 2 0 5284 5321 151491463 151491426 6.170000e-05 60.2


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 TraesCS3B01G436600 chr3B 675040783 675046488 5705 True 10538.000000 10538 100.000000 1 5706 1 chr3B.!!$R1 5705
1 TraesCS3B01G436600 chr3D 512670328 512675918 5590 False 2509.666667 5282 88.060333 1 5706 3 chr3D.!!$F1 5705
2 TraesCS3B01G436600 chr3A 648257772 648263443 5671 False 1857.000000 5153 88.288500 86 5706 4 chr3A.!!$F1 5620

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
738 798 0.179062 GCGAATCATCAGAGTGGGCT 60.179 55.000 0.00 0.0 0.00 5.19 F
1121 1201 0.326264 CACCTCAGCCAGCCTTAACT 59.674 55.000 0.00 0.0 0.00 2.24 F
2717 2847 0.457851 ACGCAGAGACTGACATAGGC 59.542 55.000 2.81 0.0 32.44 3.93 F
3577 3725 1.541588 GAGAAAGGTGGACAACATGGC 59.458 52.381 0.00 0.0 0.00 4.40 F
4296 4449 1.537202 GGTGTGCCTGATCTTGTTGTC 59.463 52.381 0.00 0.0 0.00 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2429 2559 1.682344 AAATTCCTTGAGGGCCGCC 60.682 57.895 4.35 0.0 35.41 6.13 R
3002 3132 3.190118 GCATACTTCAAAGAAGCAGCACT 59.810 43.478 6.67 0.0 0.00 4.40 R
4029 4182 0.103208 ATCTGAGCCGGAATCGTGTC 59.897 55.000 5.05 0.0 33.95 3.67 R
4396 4553 0.108186 CATGCTGCAAGGTAGGTCGA 60.108 55.000 6.36 0.0 0.00 4.20 R
5383 5554 0.248289 GCAGGCAGCCATGTTTTCAT 59.752 50.000 15.80 0.0 41.78 2.57 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
23 24 5.423886 TGTTGGTTTTTCTGGTTCCATTTC 58.576 37.500 0.00 0.00 0.00 2.17
25 26 4.294347 TGGTTTTTCTGGTTCCATTTCCT 58.706 39.130 0.00 0.00 0.00 3.36
38 39 8.590204 TGGTTCCATTTCCTTACTTTTTATTCC 58.410 33.333 0.00 0.00 0.00 3.01
67 72 6.895782 TCTTTCTTTCTTCTTCACTAACCCA 58.104 36.000 0.00 0.00 0.00 4.51
163 168 9.981114 TTGGATTTATTTTGTCCTTCTCTTTTC 57.019 29.630 0.00 0.00 33.15 2.29
164 169 8.585018 TGGATTTATTTTGTCCTTCTCTTTTCC 58.415 33.333 0.00 0.00 33.15 3.13
274 319 6.693315 AGCCGTAATATTTTACAACAGCAT 57.307 33.333 6.83 0.00 38.06 3.79
310 355 8.958175 ATGCAATGCAATTCAAATAGTTTTTG 57.042 26.923 13.45 0.03 43.62 2.44
322 367 7.044181 TCAAATAGTTTTTGAACATGCCAACA 58.956 30.769 6.31 0.00 35.69 3.33
423 469 8.621532 ACATTTTGAAGAACTATGTTAGCTCA 57.378 30.769 0.00 0.00 0.00 4.26
424 470 8.725148 ACATTTTGAAGAACTATGTTAGCTCAG 58.275 33.333 0.00 0.00 0.00 3.35
425 471 8.939929 CATTTTGAAGAACTATGTTAGCTCAGA 58.060 33.333 0.00 0.00 0.00 3.27
427 473 7.891183 TTGAAGAACTATGTTAGCTCAGAAC 57.109 36.000 0.00 0.00 0.00 3.01
428 474 6.398918 TGAAGAACTATGTTAGCTCAGAACC 58.601 40.000 0.00 0.00 0.00 3.62
429 475 5.000012 AGAACTATGTTAGCTCAGAACCG 58.000 43.478 0.00 0.00 0.00 4.44
430 476 4.705507 AGAACTATGTTAGCTCAGAACCGA 59.294 41.667 0.00 0.00 0.00 4.69
431 477 4.640789 ACTATGTTAGCTCAGAACCGAG 57.359 45.455 0.00 0.00 36.02 4.63
432 478 2.969628 ATGTTAGCTCAGAACCGAGG 57.030 50.000 0.00 0.00 33.36 4.63
433 479 1.919240 TGTTAGCTCAGAACCGAGGA 58.081 50.000 0.00 0.00 33.36 3.71
434 480 2.457598 TGTTAGCTCAGAACCGAGGAT 58.542 47.619 0.00 0.00 33.36 3.24
435 481 2.832129 TGTTAGCTCAGAACCGAGGATT 59.168 45.455 0.00 0.00 33.36 3.01
436 482 3.260884 TGTTAGCTCAGAACCGAGGATTT 59.739 43.478 0.00 0.00 33.36 2.17
437 483 4.464951 TGTTAGCTCAGAACCGAGGATTTA 59.535 41.667 0.00 0.00 33.36 1.40
438 484 5.046878 TGTTAGCTCAGAACCGAGGATTTAA 60.047 40.000 0.00 0.00 33.36 1.52
439 485 4.130286 AGCTCAGAACCGAGGATTTAAG 57.870 45.455 0.00 0.00 33.36 1.85
440 486 3.769844 AGCTCAGAACCGAGGATTTAAGA 59.230 43.478 0.00 0.00 33.36 2.10
441 487 4.407296 AGCTCAGAACCGAGGATTTAAGAT 59.593 41.667 0.00 0.00 33.36 2.40
442 488 4.509600 GCTCAGAACCGAGGATTTAAGATG 59.490 45.833 0.00 0.00 33.36 2.90
443 489 5.665459 CTCAGAACCGAGGATTTAAGATGT 58.335 41.667 0.00 0.00 0.00 3.06
444 490 5.419542 TCAGAACCGAGGATTTAAGATGTG 58.580 41.667 0.00 0.00 0.00 3.21
445 491 5.046591 TCAGAACCGAGGATTTAAGATGTGT 60.047 40.000 0.00 0.00 0.00 3.72
446 492 5.063944 CAGAACCGAGGATTTAAGATGTGTG 59.936 44.000 0.00 0.00 0.00 3.82
447 493 4.553330 ACCGAGGATTTAAGATGTGTGT 57.447 40.909 0.00 0.00 0.00 3.72
448 494 4.906618 ACCGAGGATTTAAGATGTGTGTT 58.093 39.130 0.00 0.00 0.00 3.32
449 495 6.045072 ACCGAGGATTTAAGATGTGTGTTA 57.955 37.500 0.00 0.00 0.00 2.41
450 496 6.106673 ACCGAGGATTTAAGATGTGTGTTAG 58.893 40.000 0.00 0.00 0.00 2.34
451 497 5.006746 CCGAGGATTTAAGATGTGTGTTAGC 59.993 44.000 0.00 0.00 0.00 3.09
452 498 5.276395 CGAGGATTTAAGATGTGTGTTAGCG 60.276 44.000 0.00 0.00 0.00 4.26
453 499 4.876107 AGGATTTAAGATGTGTGTTAGCGG 59.124 41.667 0.00 0.00 0.00 5.52
454 500 4.873827 GGATTTAAGATGTGTGTTAGCGGA 59.126 41.667 0.00 0.00 0.00 5.54
455 501 5.006746 GGATTTAAGATGTGTGTTAGCGGAG 59.993 44.000 0.00 0.00 0.00 4.63
456 502 4.794278 TTAAGATGTGTGTTAGCGGAGA 57.206 40.909 0.00 0.00 0.00 3.71
457 503 2.656560 AGATGTGTGTTAGCGGAGAC 57.343 50.000 0.00 0.00 0.00 3.36
458 504 2.171840 AGATGTGTGTTAGCGGAGACT 58.828 47.619 0.00 0.00 0.00 3.24
459 505 2.563179 AGATGTGTGTTAGCGGAGACTT 59.437 45.455 0.00 0.00 0.00 3.01
460 506 2.148916 TGTGTGTTAGCGGAGACTTG 57.851 50.000 0.00 0.00 0.00 3.16
461 507 0.790814 GTGTGTTAGCGGAGACTTGC 59.209 55.000 0.00 0.00 0.00 4.01
462 508 0.391228 TGTGTTAGCGGAGACTTGCA 59.609 50.000 3.81 0.00 0.00 4.08
463 509 1.001974 TGTGTTAGCGGAGACTTGCAT 59.998 47.619 0.00 0.00 0.00 3.96
464 510 1.661112 GTGTTAGCGGAGACTTGCATC 59.339 52.381 0.00 0.00 0.00 3.91
465 511 0.924090 GTTAGCGGAGACTTGCATCG 59.076 55.000 0.00 0.00 0.00 3.84
466 512 0.530744 TTAGCGGAGACTTGCATCGT 59.469 50.000 0.00 0.00 0.00 3.73
467 513 0.530744 TAGCGGAGACTTGCATCGTT 59.469 50.000 0.00 0.00 0.00 3.85
468 514 0.737715 AGCGGAGACTTGCATCGTTC 60.738 55.000 0.00 0.00 0.00 3.95
469 515 0.737715 GCGGAGACTTGCATCGTTCT 60.738 55.000 0.00 0.00 0.00 3.01
470 516 1.714794 CGGAGACTTGCATCGTTCTT 58.285 50.000 0.00 0.00 0.00 2.52
471 517 2.876091 CGGAGACTTGCATCGTTCTTA 58.124 47.619 0.00 0.00 0.00 2.10
472 518 2.854777 CGGAGACTTGCATCGTTCTTAG 59.145 50.000 0.00 0.00 0.00 2.18
473 519 3.673594 CGGAGACTTGCATCGTTCTTAGT 60.674 47.826 0.00 0.00 0.00 2.24
474 520 4.246458 GGAGACTTGCATCGTTCTTAGTT 58.754 43.478 0.00 0.00 0.00 2.24
475 521 5.408356 GGAGACTTGCATCGTTCTTAGTTA 58.592 41.667 0.00 0.00 0.00 2.24
476 522 5.867716 GGAGACTTGCATCGTTCTTAGTTAA 59.132 40.000 0.00 0.00 0.00 2.01
477 523 6.535508 GGAGACTTGCATCGTTCTTAGTTAAT 59.464 38.462 0.00 0.00 0.00 1.40
478 524 7.064728 GGAGACTTGCATCGTTCTTAGTTAATT 59.935 37.037 0.00 0.00 0.00 1.40
479 525 8.324163 AGACTTGCATCGTTCTTAGTTAATTT 57.676 30.769 0.00 0.00 0.00 1.82
480 526 9.431887 AGACTTGCATCGTTCTTAGTTAATTTA 57.568 29.630 0.00 0.00 0.00 1.40
481 527 9.690434 GACTTGCATCGTTCTTAGTTAATTTAG 57.310 33.333 0.00 0.00 0.00 1.85
482 528 8.175716 ACTTGCATCGTTCTTAGTTAATTTAGC 58.824 33.333 0.00 0.00 0.00 3.09
483 529 7.843490 TGCATCGTTCTTAGTTAATTTAGCT 57.157 32.000 0.00 0.00 0.00 3.32
484 530 7.906160 TGCATCGTTCTTAGTTAATTTAGCTC 58.094 34.615 0.00 0.00 0.00 4.09
485 531 7.547722 TGCATCGTTCTTAGTTAATTTAGCTCA 59.452 33.333 0.00 0.00 0.00 4.26
486 532 8.058915 GCATCGTTCTTAGTTAATTTAGCTCAG 58.941 37.037 0.00 0.00 0.00 3.35
487 533 9.088512 CATCGTTCTTAGTTAATTTAGCTCAGT 57.911 33.333 0.00 0.00 0.00 3.41
489 535 9.784680 TCGTTCTTAGTTAATTTAGCTCAGTAG 57.215 33.333 0.00 0.00 0.00 2.57
685 737 2.814280 CGGTTATCGGGCTAGAACAT 57.186 50.000 0.00 0.00 34.75 2.71
703 763 3.469739 ACATACCGAACAACGAAAACCT 58.530 40.909 0.00 0.00 45.77 3.50
710 770 3.308866 CGAACAACGAAAACCTCTCAAGT 59.691 43.478 0.00 0.00 45.77 3.16
715 775 1.993370 CGAAAACCTCTCAAGTAGCGG 59.007 52.381 0.00 0.00 36.06 5.52
738 798 0.179062 GCGAATCATCAGAGTGGGCT 60.179 55.000 0.00 0.00 0.00 5.19
841 913 4.161295 CCGCTGCCTTCCCATCGA 62.161 66.667 0.00 0.00 0.00 3.59
842 914 2.892425 CGCTGCCTTCCCATCGAC 60.892 66.667 0.00 0.00 0.00 4.20
843 915 2.514824 GCTGCCTTCCCATCGACC 60.515 66.667 0.00 0.00 0.00 4.79
849 921 3.447025 CTTCCCATCGACCCCTCGC 62.447 68.421 0.00 0.00 39.96 5.03
922 1001 2.760385 CCTCGACCACCTCCTCCC 60.760 72.222 0.00 0.00 0.00 4.30
931 1010 1.053264 CACCTCCTCCCCTCCATCTG 61.053 65.000 0.00 0.00 0.00 2.90
932 1011 2.146061 CCTCCTCCCCTCCATCTGC 61.146 68.421 0.00 0.00 0.00 4.26
934 1013 2.040043 CCTCCCCTCCATCTGCCT 60.040 66.667 0.00 0.00 0.00 4.75
1118 1198 1.195115 CTACACCTCAGCCAGCCTTA 58.805 55.000 0.00 0.00 0.00 2.69
1121 1201 0.326264 CACCTCAGCCAGCCTTAACT 59.674 55.000 0.00 0.00 0.00 2.24
1285 1369 2.971330 TGTGGTTTGGGAAATTGATGCT 59.029 40.909 0.00 0.00 0.00 3.79
1344 1428 2.197577 GATTAGCGTTCTCAGGCAGTC 58.802 52.381 0.00 0.00 36.16 3.51
1384 1468 1.139520 CGTGGGCTGCCATTTAAGC 59.860 57.895 22.05 1.06 38.76 3.09
1413 1497 1.140852 TGGGTCTGAACTTCACACAGG 59.859 52.381 0.00 0.00 33.19 4.00
1469 1553 8.729805 TGTCATGCACAATATCAATAGTTGTA 57.270 30.769 0.00 0.00 34.55 2.41
1540 1624 2.935849 TGGCTGCAGTAATGTAATGTCG 59.064 45.455 16.64 0.00 0.00 4.35
1545 1629 4.816392 TGCAGTAATGTAATGTCGACTGT 58.184 39.130 17.92 6.95 37.28 3.55
1550 1634 5.862323 AGTAATGTAATGTCGACTGTGTGTC 59.138 40.000 17.92 1.92 42.06 3.67
1567 1651 3.948473 TGTGTCGAAAAATTCAAGGTCCA 59.052 39.130 0.00 0.00 0.00 4.02
1628 1712 8.103305 TGTTAGAGCTCAGTATTCTTTGGAAAT 58.897 33.333 17.77 0.00 34.90 2.17
1660 1744 9.664332 TCAAATGGATTATATTGTTTGGTTTGG 57.336 29.630 0.00 0.00 0.00 3.28
1797 1892 3.308053 AGTCATTGATGTCGAATCTTGCG 59.692 43.478 0.00 0.00 0.00 4.85
1844 1939 6.835174 TCTGGATTATCATAGCTGCTTTTCT 58.165 36.000 7.79 0.00 0.00 2.52
1917 2013 3.504520 TCCTCGCCATAAAAACTTTGGTC 59.495 43.478 0.00 0.00 32.90 4.02
2051 2147 9.338622 GGTTGTTATCCTGTGCTTTACTTATAT 57.661 33.333 0.00 0.00 0.00 0.86
2105 2201 4.385405 GCGAGCCACTGCCTGTCT 62.385 66.667 0.00 0.00 38.69 3.41
2107 2203 2.031516 CGAGCCACTGCCTGTCTTG 61.032 63.158 0.00 0.00 38.69 3.02
2108 2204 2.282040 AGCCACTGCCTGTCTTGC 60.282 61.111 0.00 0.00 38.69 4.01
2110 2206 2.433446 CCACTGCCTGTCTTGCCT 59.567 61.111 0.00 0.00 0.00 4.75
2111 2207 1.970114 CCACTGCCTGTCTTGCCTG 60.970 63.158 0.00 0.00 0.00 4.85
2112 2208 1.228063 CACTGCCTGTCTTGCCTGT 60.228 57.895 0.00 0.00 0.00 4.00
2113 2209 1.228063 ACTGCCTGTCTTGCCTGTG 60.228 57.895 0.00 0.00 0.00 3.66
2114 2210 2.595463 TGCCTGTCTTGCCTGTGC 60.595 61.111 0.00 0.00 38.26 4.57
2115 2211 2.282040 GCCTGTCTTGCCTGTGCT 60.282 61.111 0.00 0.00 38.71 4.40
2117 2213 1.458639 GCCTGTCTTGCCTGTGCTTT 61.459 55.000 0.00 0.00 38.71 3.51
2175 2305 7.447374 TCTAAACACCCAATCATGTAAACAG 57.553 36.000 0.00 0.00 0.00 3.16
2418 2548 2.907042 AGGAGCTTTAACTGGCTGTACT 59.093 45.455 0.00 0.00 39.05 2.73
2429 2559 3.119459 ACTGGCTGTACTTATCACGACTG 60.119 47.826 0.00 0.00 0.00 3.51
2483 2613 6.211384 AGGTTTTTGCATGGCTATACTTTTCT 59.789 34.615 0.00 0.00 0.00 2.52
2485 2615 8.032451 GGTTTTTGCATGGCTATACTTTTCTTA 58.968 33.333 0.00 0.00 0.00 2.10
2486 2616 9.418045 GTTTTTGCATGGCTATACTTTTCTTAA 57.582 29.630 0.00 0.00 0.00 1.85
2717 2847 0.457851 ACGCAGAGACTGACATAGGC 59.542 55.000 2.81 0.00 32.44 3.93
2890 3020 7.682787 ACCCTCTCTTATCATCATTACACTT 57.317 36.000 0.00 0.00 0.00 3.16
2934 3064 8.930760 CATTCTTCGTTTCTCTCTTTCTTGTAT 58.069 33.333 0.00 0.00 0.00 2.29
3140 3271 3.181452 ACATGCCTTCAAACTGCCATTTT 60.181 39.130 0.00 0.00 0.00 1.82
3287 3430 6.535150 ACGATGATGAAACTGTTACGATGATT 59.465 34.615 0.00 0.00 0.00 2.57
3572 3720 4.957296 TCTTACAGAGAAAGGTGGACAAC 58.043 43.478 0.00 0.00 0.00 3.32
3577 3725 1.541588 GAGAAAGGTGGACAACATGGC 59.458 52.381 0.00 0.00 0.00 4.40
3656 3804 2.158475 TCTGGTGCCTTGGACAAAGAAT 60.158 45.455 0.00 0.00 38.24 2.40
3761 3909 8.245701 ACGAGTTTCTCATTTTGAAGATCTAC 57.754 34.615 0.00 0.00 0.00 2.59
3817 3966 7.986553 TTTGGTTAATGTTGATAATGGGGAT 57.013 32.000 0.00 0.00 0.00 3.85
3863 4012 4.273969 ACAATGCACTTTTTGAAGGCAATG 59.726 37.500 4.82 12.14 40.29 2.82
3943 4095 7.395645 TCATGTGCAGTCGTATTAATTTTACG 58.604 34.615 12.10 12.10 42.83 3.18
4029 4182 5.357314 AGTTCATTGATGAGAATGCTGAAGG 59.643 40.000 0.00 0.00 38.19 3.46
4157 4310 9.717942 AGGTATTGATCTGCATCTAAATACTTC 57.282 33.333 15.95 6.57 32.91 3.01
4208 4361 1.945394 CACTGCCAAGCTATCATCCAC 59.055 52.381 0.00 0.00 0.00 4.02
4215 4368 4.467769 CCAAGCTATCATCCACCAGATTT 58.532 43.478 0.00 0.00 30.59 2.17
4229 4382 6.486657 TCCACCAGATTTAGTTTTCTCAGTTG 59.513 38.462 0.00 0.00 0.00 3.16
4243 4396 5.424121 TCTCAGTTGCTAGTTTTTGAAGC 57.576 39.130 0.00 0.00 0.00 3.86
4296 4449 1.537202 GGTGTGCCTGATCTTGTTGTC 59.463 52.381 0.00 0.00 0.00 3.18
4318 4471 8.217131 TGTCATGGATTCAGATAAACATGAAG 57.783 34.615 0.00 0.00 44.10 3.02
4396 4553 9.851686 TTATCAATGGATATTGCTTACTTCTGT 57.148 29.630 0.00 0.00 42.71 3.41
4397 4554 7.792374 TCAATGGATATTGCTTACTTCTGTC 57.208 36.000 0.00 0.00 42.71 3.51
4400 4557 5.348986 TGGATATTGCTTACTTCTGTCGAC 58.651 41.667 9.11 9.11 0.00 4.20
4450 4607 1.522668 CCAGTGGCGAGAACAAATCA 58.477 50.000 0.00 0.00 0.00 2.57
4453 4610 2.549754 CAGTGGCGAGAACAAATCAACT 59.450 45.455 0.00 0.00 0.00 3.16
4520 4677 2.202260 GCGACGACGACGATGACA 60.202 61.111 22.94 0.00 42.66 3.58
4521 4678 1.794785 GCGACGACGACGATGACAA 60.795 57.895 22.94 0.00 42.66 3.18
4522 4679 1.971336 CGACGACGACGATGACAAC 59.029 57.895 15.32 0.00 42.66 3.32
4657 4814 3.203716 GAACGCTTACAAGGATAAGGGG 58.796 50.000 12.46 0.00 45.01 4.79
4769 4926 1.282875 GTTTGGTGCGGTCTTGAGC 59.717 57.895 0.00 0.00 0.00 4.26
4770 4927 1.896660 TTTGGTGCGGTCTTGAGCC 60.897 57.895 0.00 0.00 0.00 4.70
4772 4929 4.329545 GGTGCGGTCTTGAGCCCA 62.330 66.667 0.00 0.00 0.00 5.36
5001 5163 2.991866 GGTGTAACTAGTTGCCGTTCTC 59.008 50.000 18.56 3.65 36.74 2.87
5002 5164 2.660236 GTGTAACTAGTTGCCGTTCTCG 59.340 50.000 18.56 0.00 0.00 4.04
5026 5188 5.391097 GCGCTAGATCGTGTCTTACTGATAT 60.391 44.000 0.00 0.00 38.42 1.63
5045 5207 9.334947 ACTGATATATGACACTTCAATCTTTGG 57.665 33.333 0.00 0.00 34.61 3.28
5046 5208 9.334947 CTGATATATGACACTTCAATCTTTGGT 57.665 33.333 0.00 0.00 34.61 3.67
5051 5213 6.377327 TGACACTTCAATCTTTGGTTCTTC 57.623 37.500 0.00 0.00 0.00 2.87
5052 5214 6.122277 TGACACTTCAATCTTTGGTTCTTCT 58.878 36.000 0.00 0.00 0.00 2.85
5053 5215 6.038603 TGACACTTCAATCTTTGGTTCTTCTG 59.961 38.462 0.00 0.00 0.00 3.02
5054 5216 5.300286 ACACTTCAATCTTTGGTTCTTCTGG 59.700 40.000 0.00 0.00 0.00 3.86
5055 5217 4.279420 ACTTCAATCTTTGGTTCTTCTGGC 59.721 41.667 0.00 0.00 0.00 4.85
5056 5218 3.157087 TCAATCTTTGGTTCTTCTGGCC 58.843 45.455 0.00 0.00 0.00 5.36
5057 5219 1.826385 ATCTTTGGTTCTTCTGGCCG 58.174 50.000 0.00 0.00 0.00 6.13
5058 5220 0.472471 TCTTTGGTTCTTCTGGCCGT 59.528 50.000 0.00 0.00 0.00 5.68
5059 5221 0.593128 CTTTGGTTCTTCTGGCCGTG 59.407 55.000 0.00 0.00 0.00 4.94
5060 5222 1.452145 TTTGGTTCTTCTGGCCGTGC 61.452 55.000 0.00 0.00 0.00 5.34
5061 5223 2.281484 GGTTCTTCTGGCCGTGCA 60.281 61.111 0.00 0.00 0.00 4.57
5062 5224 2.617274 GGTTCTTCTGGCCGTGCAC 61.617 63.158 6.82 6.82 0.00 4.57
5179 5350 1.233285 GCGGCAGCATCCTTGGATAG 61.233 60.000 3.18 0.00 44.35 2.08
5337 5508 0.107508 CTGGATGACGACCCTGCAAT 60.108 55.000 0.00 0.00 0.00 3.56
5356 5527 3.922171 ATCAAAGGGCAAAACCAACAA 57.078 38.095 0.00 0.00 42.05 2.83
5382 5553 4.693095 GTCTTTGAGCCTGAACCTTAGAAG 59.307 45.833 0.00 0.00 0.00 2.85
5383 5554 4.593206 TCTTTGAGCCTGAACCTTAGAAGA 59.407 41.667 0.00 0.00 0.00 2.87
5384 5555 5.249393 TCTTTGAGCCTGAACCTTAGAAGAT 59.751 40.000 0.00 0.00 0.00 2.40
5413 5591 1.881602 CTGCCTGCTTCTTCTTGGC 59.118 57.895 0.00 0.00 43.49 4.52
5418 5598 1.891150 CCTGCTTCTTCTTGGCAATGT 59.109 47.619 0.00 0.00 35.49 2.71
5429 5609 4.401022 TCTTGGCAATGTGAAGAGTGAAT 58.599 39.130 0.00 0.00 0.00 2.57
5437 5617 2.295070 TGTGAAGAGTGAATCGACGGAA 59.705 45.455 0.00 0.00 0.00 4.30
5438 5618 2.917971 GTGAAGAGTGAATCGACGGAAG 59.082 50.000 0.00 0.00 0.00 3.46
5439 5619 1.921230 GAAGAGTGAATCGACGGAAGC 59.079 52.381 0.00 0.00 0.00 3.86
5440 5620 0.179161 AGAGTGAATCGACGGAAGCG 60.179 55.000 0.00 0.00 0.00 4.68
5441 5621 0.179171 GAGTGAATCGACGGAAGCGA 60.179 55.000 0.00 0.00 42.00 4.93
5531 5711 2.095263 CGTAGGTGGTCTTGCAAATTGG 60.095 50.000 0.00 0.00 0.00 3.16
5532 5712 2.086610 AGGTGGTCTTGCAAATTGGT 57.913 45.000 0.00 0.00 0.00 3.67
5538 5718 3.323403 TGGTCTTGCAAATTGGTAAAGGG 59.677 43.478 0.00 0.00 0.00 3.95
5539 5719 3.576550 GGTCTTGCAAATTGGTAAAGGGA 59.423 43.478 0.00 0.00 0.00 4.20
5580 5763 4.100035 CAGTTAGTCACTAGCATCCATCCA 59.900 45.833 1.08 0.00 32.76 3.41
5581 5764 4.904251 AGTTAGTCACTAGCATCCATCCAT 59.096 41.667 1.08 0.00 31.97 3.41
5582 5765 5.011533 AGTTAGTCACTAGCATCCATCCATC 59.988 44.000 1.08 0.00 31.97 3.51
5583 5766 2.636893 AGTCACTAGCATCCATCCATCC 59.363 50.000 0.00 0.00 0.00 3.51
5584 5767 2.369860 GTCACTAGCATCCATCCATCCA 59.630 50.000 0.00 0.00 0.00 3.41
5585 5768 3.008813 GTCACTAGCATCCATCCATCCAT 59.991 47.826 0.00 0.00 0.00 3.41
5586 5769 3.262660 TCACTAGCATCCATCCATCCATC 59.737 47.826 0.00 0.00 0.00 3.51
5588 5771 1.452540 AGCATCCATCCATCCATCCA 58.547 50.000 0.00 0.00 0.00 3.41
5589 5772 2.000803 AGCATCCATCCATCCATCCAT 58.999 47.619 0.00 0.00 0.00 3.41
5590 5773 2.025226 AGCATCCATCCATCCATCCATC 60.025 50.000 0.00 0.00 0.00 3.51
5592 5775 2.136974 TCCATCCATCCATCCATCCA 57.863 50.000 0.00 0.00 0.00 3.41
5593 5776 2.651190 TCCATCCATCCATCCATCCAT 58.349 47.619 0.00 0.00 0.00 3.41
5594 5777 2.579400 TCCATCCATCCATCCATCCATC 59.421 50.000 0.00 0.00 0.00 3.51
5595 5778 2.357881 CCATCCATCCATCCATCCATCC 60.358 54.545 0.00 0.00 0.00 3.51
5596 5779 2.136974 TCCATCCATCCATCCATCCA 57.863 50.000 0.00 0.00 0.00 3.41
5597 5780 2.651190 TCCATCCATCCATCCATCCAT 58.349 47.619 0.00 0.00 0.00 3.41
5642 5911 4.193826 TGATACTTTGCAGAGGACACTC 57.806 45.455 9.34 0.00 44.31 3.51
5645 5914 1.486310 ACTTTGCAGAGGACACTCACA 59.514 47.619 9.34 0.00 46.44 3.58
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 8.590204 GGAATAAAAAGTAAGGAAATGGAACCA 58.410 33.333 0.00 0.00 0.00 3.67
40 41 8.683615 GGGTTAGTGAAGAAGAAAGAAAGAAAA 58.316 33.333 0.00 0.00 0.00 2.29
48 53 6.693315 TTTGTGGGTTAGTGAAGAAGAAAG 57.307 37.500 0.00 0.00 0.00 2.62
164 169 9.640952 TGATTAGTAAATAGAGAAAAATGGGGG 57.359 33.333 0.00 0.00 0.00 5.40
232 243 9.856488 TTACGGCTAAAAATATAAAATGTGCAA 57.144 25.926 0.00 0.00 0.00 4.08
251 262 6.317642 TCATGCTGTTGTAAAATATTACGGCT 59.682 34.615 16.34 4.08 43.59 5.52
252 263 6.491394 TCATGCTGTTGTAAAATATTACGGC 58.509 36.000 10.82 10.82 43.59 5.68
253 264 8.341903 TCATCATGCTGTTGTAAAATATTACGG 58.658 33.333 0.00 0.00 43.59 4.02
254 265 9.715123 TTCATCATGCTGTTGTAAAATATTACG 57.285 29.630 0.00 0.00 43.59 3.18
269 314 6.018343 TGCATTGCATAAATTTCATCATGCTG 60.018 34.615 19.32 13.39 43.30 4.41
271 316 6.293713 TGCATTGCATAAATTTCATCATGC 57.706 33.333 7.38 14.16 43.22 4.06
274 319 8.494016 TGAATTGCATTGCATAAATTTCATCA 57.506 26.923 12.95 1.54 38.76 3.07
310 355 7.599630 ATTGTTCAAATATGTTGGCATGTTC 57.400 32.000 0.00 0.00 35.77 3.18
399 445 8.939929 TCTGAGCTAACATAGTTCTTCAAAATG 58.060 33.333 0.00 0.00 37.01 2.32
405 451 5.517054 CGGTTCTGAGCTAACATAGTTCTTC 59.483 44.000 0.56 0.00 37.01 2.87
408 454 4.995124 TCGGTTCTGAGCTAACATAGTTC 58.005 43.478 0.56 0.00 36.67 3.01
411 457 3.632604 TCCTCGGTTCTGAGCTAACATAG 59.367 47.826 3.35 0.00 34.56 2.23
414 460 1.919240 TCCTCGGTTCTGAGCTAACA 58.081 50.000 3.35 0.00 34.56 2.41
416 462 5.421056 TCTTAAATCCTCGGTTCTGAGCTAA 59.579 40.000 3.35 0.00 34.56 3.09
417 463 4.954202 TCTTAAATCCTCGGTTCTGAGCTA 59.046 41.667 3.35 0.00 34.56 3.32
419 465 4.124851 TCTTAAATCCTCGGTTCTGAGC 57.875 45.455 3.35 0.00 34.56 4.26
422 468 5.063944 CACACATCTTAAATCCTCGGTTCTG 59.936 44.000 0.00 0.00 0.00 3.02
423 469 5.178797 CACACATCTTAAATCCTCGGTTCT 58.821 41.667 0.00 0.00 0.00 3.01
424 470 4.935808 ACACACATCTTAAATCCTCGGTTC 59.064 41.667 0.00 0.00 0.00 3.62
425 471 4.906618 ACACACATCTTAAATCCTCGGTT 58.093 39.130 0.00 0.00 0.00 4.44
427 473 5.006746 GCTAACACACATCTTAAATCCTCGG 59.993 44.000 0.00 0.00 0.00 4.63
428 474 5.276395 CGCTAACACACATCTTAAATCCTCG 60.276 44.000 0.00 0.00 0.00 4.63
429 475 5.006746 CCGCTAACACACATCTTAAATCCTC 59.993 44.000 0.00 0.00 0.00 3.71
430 476 4.876107 CCGCTAACACACATCTTAAATCCT 59.124 41.667 0.00 0.00 0.00 3.24
431 477 4.873827 TCCGCTAACACACATCTTAAATCC 59.126 41.667 0.00 0.00 0.00 3.01
432 478 5.810587 TCTCCGCTAACACACATCTTAAATC 59.189 40.000 0.00 0.00 0.00 2.17
433 479 5.581085 GTCTCCGCTAACACACATCTTAAAT 59.419 40.000 0.00 0.00 0.00 1.40
434 480 4.927425 GTCTCCGCTAACACACATCTTAAA 59.073 41.667 0.00 0.00 0.00 1.52
435 481 4.219944 AGTCTCCGCTAACACACATCTTAA 59.780 41.667 0.00 0.00 0.00 1.85
436 482 3.762288 AGTCTCCGCTAACACACATCTTA 59.238 43.478 0.00 0.00 0.00 2.10
437 483 2.563179 AGTCTCCGCTAACACACATCTT 59.437 45.455 0.00 0.00 0.00 2.40
438 484 2.171840 AGTCTCCGCTAACACACATCT 58.828 47.619 0.00 0.00 0.00 2.90
439 485 2.656560 AGTCTCCGCTAACACACATC 57.343 50.000 0.00 0.00 0.00 3.06
440 486 2.688507 CAAGTCTCCGCTAACACACAT 58.311 47.619 0.00 0.00 0.00 3.21
441 487 1.872237 GCAAGTCTCCGCTAACACACA 60.872 52.381 0.00 0.00 0.00 3.72
442 488 0.790814 GCAAGTCTCCGCTAACACAC 59.209 55.000 0.00 0.00 0.00 3.82
443 489 0.391228 TGCAAGTCTCCGCTAACACA 59.609 50.000 0.00 0.00 0.00 3.72
444 490 1.661112 GATGCAAGTCTCCGCTAACAC 59.339 52.381 0.00 0.00 0.00 3.32
445 491 1.735700 CGATGCAAGTCTCCGCTAACA 60.736 52.381 0.00 0.00 0.00 2.41
446 492 0.924090 CGATGCAAGTCTCCGCTAAC 59.076 55.000 0.00 0.00 0.00 2.34
447 493 0.530744 ACGATGCAAGTCTCCGCTAA 59.469 50.000 0.00 0.00 0.00 3.09
448 494 0.530744 AACGATGCAAGTCTCCGCTA 59.469 50.000 0.00 0.00 0.00 4.26
449 495 0.737715 GAACGATGCAAGTCTCCGCT 60.738 55.000 0.00 0.00 0.00 5.52
450 496 0.737715 AGAACGATGCAAGTCTCCGC 60.738 55.000 0.00 0.00 0.00 5.54
451 497 1.714794 AAGAACGATGCAAGTCTCCG 58.285 50.000 0.00 0.00 0.00 4.63
452 498 3.851098 ACTAAGAACGATGCAAGTCTCC 58.149 45.455 0.00 0.00 0.00 3.71
453 499 6.946229 TTAACTAAGAACGATGCAAGTCTC 57.054 37.500 0.00 0.00 0.00 3.36
454 500 7.907214 AATTAACTAAGAACGATGCAAGTCT 57.093 32.000 0.00 0.00 0.00 3.24
455 501 9.690434 CTAAATTAACTAAGAACGATGCAAGTC 57.310 33.333 0.00 0.00 0.00 3.01
456 502 8.175716 GCTAAATTAACTAAGAACGATGCAAGT 58.824 33.333 0.00 0.00 0.00 3.16
457 503 8.391106 AGCTAAATTAACTAAGAACGATGCAAG 58.609 33.333 0.00 0.00 0.00 4.01
458 504 8.263940 AGCTAAATTAACTAAGAACGATGCAA 57.736 30.769 0.00 0.00 0.00 4.08
459 505 7.547722 TGAGCTAAATTAACTAAGAACGATGCA 59.452 33.333 0.00 0.00 0.00 3.96
460 506 7.906160 TGAGCTAAATTAACTAAGAACGATGC 58.094 34.615 0.00 0.00 0.00 3.91
461 507 9.088512 ACTGAGCTAAATTAACTAAGAACGATG 57.911 33.333 0.00 0.00 0.00 3.84
463 509 9.784680 CTACTGAGCTAAATTAACTAAGAACGA 57.215 33.333 0.00 0.00 0.00 3.85
464 510 8.533153 GCTACTGAGCTAAATTAACTAAGAACG 58.467 37.037 0.00 0.00 45.98 3.95
520 566 1.136305 TCACTACTAGAACGCCCATGC 59.864 52.381 0.00 0.00 0.00 4.06
521 567 2.427453 ACTCACTACTAGAACGCCCATG 59.573 50.000 0.00 0.00 0.00 3.66
522 568 2.736347 ACTCACTACTAGAACGCCCAT 58.264 47.619 0.00 0.00 0.00 4.00
523 569 2.211250 ACTCACTACTAGAACGCCCA 57.789 50.000 0.00 0.00 0.00 5.36
524 570 4.915158 AATACTCACTACTAGAACGCCC 57.085 45.455 0.00 0.00 0.00 6.13
525 571 8.868635 AATTAAATACTCACTACTAGAACGCC 57.131 34.615 0.00 0.00 0.00 5.68
680 732 4.024641 AGGTTTTCGTTGTTCGGTATGTTC 60.025 41.667 0.00 0.00 40.32 3.18
685 737 3.181477 TGAGAGGTTTTCGTTGTTCGGTA 60.181 43.478 0.00 0.00 40.32 4.02
715 775 0.299895 CACTCTGATGATTCGCGCAC 59.700 55.000 8.75 0.00 0.00 5.34
721 781 1.964552 CCAGCCCACTCTGATGATTC 58.035 55.000 0.00 0.00 36.19 2.52
722 782 0.106819 GCCAGCCCACTCTGATGATT 60.107 55.000 0.00 0.00 36.19 2.57
738 798 2.579657 CCACGAGTGTACTGGGCCA 61.580 63.158 5.85 5.85 0.00 5.36
828 900 3.407967 GGGGTCGATGGGAAGGCA 61.408 66.667 0.00 0.00 0.00 4.75
832 904 3.467226 GCGAGGGGTCGATGGGAA 61.467 66.667 0.00 0.00 34.64 3.97
894 967 2.043852 GTCGAGGAGGAGGAGGCA 60.044 66.667 0.00 0.00 0.00 4.75
922 1001 1.664873 CGCTAGAGGCAGATGGAGG 59.335 63.158 0.00 0.00 41.91 4.30
1118 1198 0.388649 GTCTCACATGGCGTCGAGTT 60.389 55.000 0.00 0.00 0.00 3.01
1121 1201 1.212751 CAGTCTCACATGGCGTCGA 59.787 57.895 0.00 0.00 0.00 4.20
1285 1369 4.258543 GCAGCTAAATACACCTACCACAA 58.741 43.478 0.00 0.00 0.00 3.33
1344 1428 4.618912 CGAACTATCATATCAACTCGCCTG 59.381 45.833 0.00 0.00 0.00 4.85
1384 1468 4.994852 TGAAGTTCAGACCCAACGATTAAG 59.005 41.667 0.08 0.00 0.00 1.85
1413 1497 2.390938 GTGCAAAGCTTAACCGAAACC 58.609 47.619 0.00 0.00 0.00 3.27
1540 1624 4.970003 CCTTGAATTTTTCGACACACAGTC 59.030 41.667 0.00 0.00 44.02 3.51
1545 1629 3.948473 TGGACCTTGAATTTTTCGACACA 59.052 39.130 0.00 0.00 0.00 3.72
1567 1651 3.284617 AGTTGTTTTAAGCCGTGGTCTT 58.715 40.909 2.12 2.12 0.00 3.01
1851 1946 2.943033 CCGAAACCCATCATCTACAACC 59.057 50.000 0.00 0.00 0.00 3.77
1853 1948 2.238646 AGCCGAAACCCATCATCTACAA 59.761 45.455 0.00 0.00 0.00 2.41
1855 1950 2.158957 TGAGCCGAAACCCATCATCTAC 60.159 50.000 0.00 0.00 0.00 2.59
1917 2013 2.159787 CGAAGCAAAGACTCCACGATTG 60.160 50.000 0.00 0.00 0.00 2.67
2013 2109 7.339212 CACAGGATAACAACCATAAATTGAGGA 59.661 37.037 0.00 0.00 0.00 3.71
2019 2115 7.480760 AAAGCACAGGATAACAACCATAAAT 57.519 32.000 0.00 0.00 0.00 1.40
2052 2148 8.947055 ATGTCTTTCTTGTGCAACTTTAAAAT 57.053 26.923 0.00 0.00 38.04 1.82
2093 2189 1.970114 CAGGCAAGACAGGCAGTGG 60.970 63.158 0.00 0.00 36.37 4.00
2105 2201 5.767665 TCTTAATCAAGTAAAGCACAGGCAA 59.232 36.000 0.00 0.00 36.36 4.52
2107 2203 5.880054 TCTTAATCAAGTAAAGCACAGGC 57.120 39.130 0.00 0.00 35.08 4.85
2108 2204 9.185192 CTTTTTCTTAATCAAGTAAAGCACAGG 57.815 33.333 0.00 0.00 34.01 4.00
2175 2305 5.437060 TGATAATCTAGTTTGGTTGGGCTC 58.563 41.667 0.00 0.00 0.00 4.70
2418 2548 2.185867 GGCCGCCAGTCGTGATAA 59.814 61.111 3.91 0.00 36.19 1.75
2429 2559 1.682344 AAATTCCTTGAGGGCCGCC 60.682 57.895 4.35 0.00 35.41 6.13
2438 2568 7.967890 AACCTTCATAAAAGCAAATTCCTTG 57.032 32.000 0.00 0.00 38.15 3.61
2488 2618 9.066892 ACAATTAAGCAGTTAGACAGATCAAAA 57.933 29.630 0.00 0.00 0.00 2.44
2529 2659 5.451798 GCCTTCAAGTGGAATGAGAAAACAA 60.452 40.000 0.00 0.00 34.32 2.83
2881 3011 6.372659 ACAAGCTGACTTATCCAAGTGTAATG 59.627 38.462 0.00 0.00 45.18 1.90
3002 3132 3.190118 GCATACTTCAAAGAAGCAGCACT 59.810 43.478 6.67 0.00 0.00 4.40
3073 3204 6.846283 GCAAATCTTGATAAAGGTTACGATCG 59.154 38.462 14.88 14.88 0.00 3.69
3140 3271 5.417266 TGAAAACACCATTCTGTTCAACTCA 59.583 36.000 0.00 0.00 33.03 3.41
3572 3720 4.196971 TCATCATCAGTTTCAGAGCCATG 58.803 43.478 0.00 0.00 0.00 3.66
3577 3725 6.036191 CACTGTCATCATCATCAGTTTCAGAG 59.964 42.308 0.00 0.00 38.79 3.35
3737 3885 8.244494 TGTAGATCTTCAAAATGAGAAACTCG 57.756 34.615 0.00 0.00 32.35 4.18
3773 3921 6.719370 ACCAAATGACATACTTCTGCCTTTAA 59.281 34.615 0.00 0.00 0.00 1.52
3817 3966 1.484653 CAAGATCCCCGTATGGTCACA 59.515 52.381 0.00 0.00 0.00 3.58
3952 4104 5.221722 GCACTCACCAGGATCTAATTATCCA 60.222 44.000 9.45 0.00 46.81 3.41
3953 4105 5.012561 AGCACTCACCAGGATCTAATTATCC 59.987 44.000 0.00 0.00 45.06 2.59
4029 4182 0.103208 ATCTGAGCCGGAATCGTGTC 59.897 55.000 5.05 0.00 33.95 3.67
4157 4310 6.483640 AGCTTGGTGACACTTTTAAGTTAGAG 59.516 38.462 5.39 0.00 42.67 2.43
4169 4322 1.109323 GGGCAAAGCTTGGTGACACT 61.109 55.000 0.00 0.00 42.67 3.55
4175 4328 2.501602 GCAGTGGGCAAAGCTTGGT 61.502 57.895 0.00 0.00 43.97 3.67
4208 4361 6.566197 AGCAACTGAGAAAACTAAATCTGG 57.434 37.500 0.00 0.00 0.00 3.86
4215 4368 8.500753 TCAAAAACTAGCAACTGAGAAAACTA 57.499 30.769 0.00 0.00 0.00 2.24
4229 4382 5.523552 ACCAAAACATGCTTCAAAAACTAGC 59.476 36.000 0.00 0.00 0.00 3.42
4243 4396 6.071447 TCCTGAACAATATCCACCAAAACATG 60.071 38.462 0.00 0.00 0.00 3.21
4296 4449 7.273320 AGCTTCATGTTTATCTGAATCCATG 57.727 36.000 0.00 0.00 31.39 3.66
4396 4553 0.108186 CATGCTGCAAGGTAGGTCGA 60.108 55.000 6.36 0.00 0.00 4.20
4397 4554 1.709147 GCATGCTGCAAGGTAGGTCG 61.709 60.000 11.37 0.00 44.26 4.79
4450 4607 1.405526 CCATCGTCGGTTGGATCAGTT 60.406 52.381 8.88 0.00 35.40 3.16
4453 4610 1.153449 GCCATCGTCGGTTGGATCA 60.153 57.895 16.37 0.00 35.40 2.92
4520 4677 3.054287 TCCTCAGTATCCTCAGACGAGTT 60.054 47.826 0.00 0.00 37.59 3.01
4521 4678 2.506231 TCCTCAGTATCCTCAGACGAGT 59.494 50.000 0.00 0.00 37.59 4.18
4522 4679 3.201353 TCCTCAGTATCCTCAGACGAG 57.799 52.381 0.00 0.00 39.16 4.18
4612 4769 2.121832 TTGAGGGGCCTTCTCCGA 59.878 61.111 17.30 8.97 0.00 4.55
4657 4814 3.055094 TCTTAGAGTTCATGGTGCCCTTC 60.055 47.826 0.00 0.00 0.00 3.46
4675 4832 1.487976 CAGGCTTGCCTCTGGATCTTA 59.512 52.381 11.72 0.00 0.00 2.10
4772 4929 4.148825 CTAGCAAGCCCGCTCGGT 62.149 66.667 7.59 0.00 42.62 4.69
4781 4938 8.713271 GGAAATATACTCATACAACTAGCAAGC 58.287 37.037 0.00 0.00 0.00 4.01
4784 4941 7.948357 ACGGAAATATACTCATACAACTAGCA 58.052 34.615 0.00 0.00 0.00 3.49
4791 4948 7.778083 ACTGACAACGGAAATATACTCATACA 58.222 34.615 0.00 0.00 0.00 2.29
4876 5038 3.900388 ACGAGATACCAGTATCGCTTC 57.100 47.619 16.24 7.42 44.93 3.86
4877 5039 4.387598 AGTACGAGATACCAGTATCGCTT 58.612 43.478 16.24 11.23 44.93 4.68
4878 5040 4.005487 AGTACGAGATACCAGTATCGCT 57.995 45.455 16.24 8.47 44.93 4.93
4879 5041 6.419980 AATAGTACGAGATACCAGTATCGC 57.580 41.667 11.21 10.83 44.93 4.58
4880 5042 9.310716 TGATAATAGTACGAGATACCAGTATCG 57.689 37.037 11.21 5.87 44.93 2.92
4934 5096 6.544564 TGGTTTTGCTTTAGTAAACTGCTAGT 59.455 34.615 7.98 0.00 33.44 2.57
4935 5097 6.966021 TGGTTTTGCTTTAGTAAACTGCTAG 58.034 36.000 7.98 0.00 33.44 3.42
4937 5099 5.845391 TGGTTTTGCTTTAGTAAACTGCT 57.155 34.783 7.98 0.00 33.44 4.24
5001 5163 1.003759 AGTAAGACACGATCTAGCGCG 60.004 52.381 0.00 0.00 36.27 6.86
5002 5164 2.031807 TCAGTAAGACACGATCTAGCGC 59.968 50.000 0.00 0.00 36.27 5.92
5026 5188 7.939039 AGAAGAACCAAAGATTGAAGTGTCATA 59.061 33.333 0.00 0.00 32.48 2.15
5042 5204 1.896660 GCACGGCCAGAAGAACCAA 60.897 57.895 2.24 0.00 0.00 3.67
5043 5205 2.281484 GCACGGCCAGAAGAACCA 60.281 61.111 2.24 0.00 0.00 3.67
5044 5206 2.281484 TGCACGGCCAGAAGAACC 60.281 61.111 2.24 0.00 0.00 3.62
5045 5207 2.946762 GTGCACGGCCAGAAGAAC 59.053 61.111 2.24 0.00 0.00 3.01
5046 5208 2.664851 CGTGCACGGCCAGAAGAA 60.665 61.111 31.15 0.00 35.37 2.52
5048 5210 3.114616 CTCGTGCACGGCCAGAAG 61.115 66.667 36.41 22.31 40.29 2.85
5051 5213 4.435436 TAGCTCGTGCACGGCCAG 62.435 66.667 36.41 27.16 42.74 4.85
5052 5214 4.735132 GTAGCTCGTGCACGGCCA 62.735 66.667 36.41 24.54 42.74 5.36
5054 5216 3.934391 AAGGTAGCTCGTGCACGGC 62.934 63.158 36.41 33.90 42.74 5.68
5055 5217 2.094659 CAAGGTAGCTCGTGCACGG 61.095 63.158 36.41 27.12 42.74 4.94
5056 5218 2.094659 CCAAGGTAGCTCGTGCACG 61.095 63.158 32.76 32.76 42.74 5.34
5057 5219 2.391389 GCCAAGGTAGCTCGTGCAC 61.391 63.158 12.58 6.82 42.74 4.57
5058 5220 2.047274 GCCAAGGTAGCTCGTGCA 60.047 61.111 12.58 0.00 42.74 4.57
5059 5221 2.047274 TGCCAAGGTAGCTCGTGC 60.047 61.111 0.07 0.07 40.05 5.34
5060 5222 4.192000 CTGCCAAGGTAGCTCGTG 57.808 61.111 0.00 0.00 0.00 4.35
5179 5350 1.145819 GCCAGGATGAGGACAGAGC 59.854 63.158 0.00 0.00 39.69 4.09
5337 5508 2.569404 AGTTGTTGGTTTTGCCCTTTGA 59.431 40.909 0.00 0.00 36.04 2.69
5356 5527 1.771255 AGGTTCAGGCTCAAAGACAGT 59.229 47.619 0.00 0.00 0.00 3.55
5382 5553 1.738030 GCAGGCAGCCATGTTTTCATC 60.738 52.381 15.80 0.00 38.64 2.92
5383 5554 0.248289 GCAGGCAGCCATGTTTTCAT 59.752 50.000 15.80 0.00 41.78 2.57
5384 5555 1.667151 GCAGGCAGCCATGTTTTCA 59.333 52.632 15.80 0.00 37.23 2.69
5413 5591 3.061295 CCGTCGATTCACTCTTCACATTG 59.939 47.826 0.00 0.00 0.00 2.82
5418 5598 2.671351 GCTTCCGTCGATTCACTCTTCA 60.671 50.000 0.00 0.00 0.00 3.02
5429 5609 3.806422 TCGCATCGCTTCCGTCGA 61.806 61.111 0.00 0.00 40.45 4.20
5439 5619 4.266070 ATCGGGTCGGTCGCATCG 62.266 66.667 0.00 0.00 0.00 3.84
5440 5620 2.658593 CATCGGGTCGGTCGCATC 60.659 66.667 0.00 0.00 0.00 3.91
5441 5621 3.144871 TCATCGGGTCGGTCGCAT 61.145 61.111 0.00 0.00 0.00 4.73
5538 5718 3.694566 ACTGTGTCTCTGTTGGGTTTTTC 59.305 43.478 0.00 0.00 0.00 2.29
5539 5719 3.697166 ACTGTGTCTCTGTTGGGTTTTT 58.303 40.909 0.00 0.00 0.00 1.94
5580 5763 4.606697 AGAAGAATGGATGGATGGATGGAT 59.393 41.667 0.00 0.00 0.00 3.41
5581 5764 3.985452 AGAAGAATGGATGGATGGATGGA 59.015 43.478 0.00 0.00 0.00 3.41
5582 5765 4.383931 AGAAGAATGGATGGATGGATGG 57.616 45.455 0.00 0.00 0.00 3.51
5583 5766 6.550108 AGAAAAGAAGAATGGATGGATGGATG 59.450 38.462 0.00 0.00 0.00 3.51
5584 5767 6.680540 AGAAAAGAAGAATGGATGGATGGAT 58.319 36.000 0.00 0.00 0.00 3.41
5585 5768 6.069206 AGAGAAAAGAAGAATGGATGGATGGA 60.069 38.462 0.00 0.00 0.00 3.41
5586 5769 6.127793 AGAGAAAAGAAGAATGGATGGATGG 58.872 40.000 0.00 0.00 0.00 3.51
5588 5771 7.641249 AGAAGAGAAAAGAAGAATGGATGGAT 58.359 34.615 0.00 0.00 0.00 3.41
5589 5772 7.025520 AGAAGAGAAAAGAAGAATGGATGGA 57.974 36.000 0.00 0.00 0.00 3.41
5590 5773 8.046107 AGTAGAAGAGAAAAGAAGAATGGATGG 58.954 37.037 0.00 0.00 0.00 3.51
5592 5775 8.820831 TCAGTAGAAGAGAAAAGAAGAATGGAT 58.179 33.333 0.00 0.00 0.00 3.41
5593 5776 8.195165 TCAGTAGAAGAGAAAAGAAGAATGGA 57.805 34.615 0.00 0.00 0.00 3.41
5623 5806 3.324846 TGTGAGTGTCCTCTGCAAAGTAT 59.675 43.478 0.00 0.00 38.61 2.12
5642 5911 3.269178 GCTCTTCTTCTGGATCCTTGTG 58.731 50.000 14.23 1.26 0.00 3.33
5645 5914 1.134551 GCGCTCTTCTTCTGGATCCTT 60.135 52.381 14.23 0.00 0.00 3.36


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

AutoCloner maintained by Alex Coulton.