Multiple sequence alignment - TraesCS1B01G309800

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 TraesCS1B01G309800 chr1B 100.000 4058 0 0 1 4058 532406162 532402105 0.000000e+00 7494
1 TraesCS1B01G309800 chr1A 94.396 3301 109 14 775 4058 494719720 494716479 0.000000e+00 5001
2 TraesCS1B01G309800 chr1A 83.403 476 66 6 1 463 494720284 494719809 2.900000e-116 429
3 TraesCS1B01G309800 chr1A 87.838 222 19 3 3816 4035 74940929 74940714 1.870000e-63 254
4 TraesCS1B01G309800 chr1A 88.679 212 18 3 3816 4027 542363996 542364201 1.870000e-63 254
5 TraesCS1B01G309800 chr1D 93.389 3343 136 34 754 4058 397180940 397177645 0.000000e+00 4870
6 TraesCS1B01G309800 chr1D 83.893 447 59 4 3 437 439108766 439108321 8.110000e-112 414
7 TraesCS1B01G309800 chr1D 92.830 265 17 2 465 727 481920951 481920687 2.290000e-102 383
8 TraesCS1B01G309800 chr1D 81.920 448 60 6 3 437 211630250 211629811 3.860000e-95 359
9 TraesCS1B01G309800 chr3A 85.821 536 64 7 1148 1680 707384296 707384822 3.540000e-155 558
10 TraesCS1B01G309800 chr6D 83.226 465 60 6 3 450 431854959 431854496 1.050000e-110 411
11 TraesCS1B01G309800 chr6D 83.628 452 57 5 3 437 451958162 451957711 3.780000e-110 409
12 TraesCS1B01G309800 chr6D 91.304 161 8 3 3898 4058 299602027 299601873 8.830000e-52 215
13 TraesCS1B01G309800 chr6D 89.441 161 11 2 3898 4058 240562898 240563052 8.900000e-47 198
14 TraesCS1B01G309800 chr7D 83.519 449 58 6 3 437 91779203 91778757 4.880000e-109 405
15 TraesCS1B01G309800 chr7D 83.073 449 57 7 3 437 91748868 91748425 1.370000e-104 390
16 TraesCS1B01G309800 chr7D 91.633 251 12 5 3809 4058 637025458 637025216 5.020000e-89 339
17 TraesCS1B01G309800 chr3D 83.592 451 54 10 3 437 584115311 584114865 4.880000e-109 405
18 TraesCS1B01G309800 chr3D 81.250 448 70 4 3 437 29493830 29493384 2.320000e-92 350
19 TraesCS1B01G309800 chr3D 81.250 448 70 4 3 437 29528759 29528313 2.320000e-92 350
20 TraesCS1B01G309800 chr3D 91.016 256 11 8 3805 4058 500873619 500873864 6.500000e-88 335
21 TraesCS1B01G309800 chr2B 83.482 448 58 5 3 434 690213224 690213671 1.760000e-108 403
22 TraesCS1B01G309800 chr2B 93.284 268 15 2 463 727 396285383 396285116 3.800000e-105 392
23 TraesCS1B01G309800 chr2B 92.830 265 17 1 465 727 36443811 36444075 2.290000e-102 383
24 TraesCS1B01G309800 chr2B 92.193 269 19 1 461 727 10524069 10523801 2.960000e-101 379
25 TraesCS1B01G309800 chr2B 92.222 270 17 3 461 727 741246392 741246660 2.960000e-101 379
26 TraesCS1B01G309800 chr4B 92.857 266 15 3 465 727 670246648 670246912 2.290000e-102 383
27 TraesCS1B01G309800 chr7B 92.481 266 18 1 464 727 145192871 145192606 2.960000e-101 379
28 TraesCS1B01G309800 chrUn 91.941 273 17 3 454 722 351169013 351169284 1.060000e-100 377
29 TraesCS1B01G309800 chrUn 81.473 448 69 4 3 437 223002177 223001731 4.990000e-94 355
30 TraesCS1B01G309800 chrUn 76.134 419 78 20 988 1399 213326996 213327399 2.470000e-47 200
31 TraesCS1B01G309800 chr7A 92.481 266 17 2 459 722 45687771 45687507 1.060000e-100 377
32 TraesCS1B01G309800 chr7A 89.837 246 18 3 3813 4058 98519947 98519709 3.940000e-80 309
33 TraesCS1B01G309800 chr7A 89.431 246 19 3 3813 4058 596241866 596241628 1.830000e-78 303
34 TraesCS1B01G309800 chr6A 81.562 461 62 10 3 450 545885600 545886050 3.860000e-95 359
35 TraesCS1B01G309800 chr6A 90.094 212 15 2 3816 4027 102586884 102587089 1.860000e-68 270
36 TraesCS1B01G309800 chr6A 88.739 222 17 3 3816 4035 379567295 379567080 8.650000e-67 265
37 TraesCS1B01G309800 chr6A 89.623 212 16 2 3816 4027 606163263 606163468 8.650000e-67 265
38 TraesCS1B01G309800 chr6A 89.151 212 17 2 3816 4027 136354004 136354209 4.020000e-65 259
39 TraesCS1B01G309800 chr6A 89.151 212 17 2 3816 4027 402028982 402029187 4.020000e-65 259
40 TraesCS1B01G309800 chr4A 82.396 409 53 6 40 434 688390846 688390443 5.020000e-89 339
41 TraesCS1B01G309800 chr5D 81.499 427 63 9 4 416 395694146 395693722 1.810000e-88 337
42 TraesCS1B01G309800 chr2D 90.980 255 14 5 3805 4058 473951768 473952014 6.500000e-88 335
43 TraesCS1B01G309800 chr2D 79.673 428 62 11 3 414 515830236 515829818 6.640000e-73 285
44 TraesCS1B01G309800 chr2D 85.646 209 17 3 3 199 451378027 451377820 1.480000e-49 207
45 TraesCS1B01G309800 chr5B 91.165 249 14 5 3805 4052 155250402 155250161 8.410000e-87 331
46 TraesCS1B01G309800 chr4D 89.804 255 17 5 3805 4058 484990157 484989911 6.550000e-83 318
47 TraesCS1B01G309800 chr5A 88.739 222 17 3 3816 4035 506085972 506085757 8.650000e-67 265
48 TraesCS1B01G309800 chr3B 83.333 210 23 8 5 202 543465396 543465605 2.490000e-42 183


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 TraesCS1B01G309800 chr1B 532402105 532406162 4057 True 7494 7494 100.0000 1 4058 1 chr1B.!!$R1 4057
1 TraesCS1B01G309800 chr1A 494716479 494720284 3805 True 2715 5001 88.8995 1 4058 2 chr1A.!!$R2 4057
2 TraesCS1B01G309800 chr1D 397177645 397180940 3295 True 4870 4870 93.3890 754 4058 1 chr1D.!!$R2 3304
3 TraesCS1B01G309800 chr3A 707384296 707384822 526 False 558 558 85.8210 1148 1680 1 chr3A.!!$F1 532

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
858 902 0.109723 TTAGTGCCTTGGTCCCACAC 59.890 55.000 0.0 0.0 32.09 3.82 F
1924 2011 1.286880 CCACTGCCGCTTCCAAAAG 59.713 57.895 0.0 0.0 35.47 2.27 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1980 2067 1.064758 ACAAGAACCAGCAAGACCACA 60.065 47.619 0.00 0.0 0.0 4.17 R
3743 3835 0.250295 CAGGCCAAAACTGTCTCGGA 60.250 55.000 5.01 0.0 0.0 4.55 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
34 35 1.948104 TGTTGTCACTCTTTCACCCG 58.052 50.000 0.00 0.00 0.00 5.28
38 39 1.300620 TCACTCTTTCACCCGCACG 60.301 57.895 0.00 0.00 0.00 5.34
46 47 1.149987 TTCACCCGCACGAACATTAC 58.850 50.000 0.00 0.00 0.00 1.89
55 56 5.180492 CCCGCACGAACATTACCAATAATAT 59.820 40.000 0.00 0.00 29.44 1.28
85 86 1.515521 CGCCTTAATTCGCCCATCCC 61.516 60.000 0.00 0.00 0.00 3.85
110 111 2.441001 AGATGGGAAGCCTTGATCGATT 59.559 45.455 0.00 0.00 0.00 3.34
113 114 3.541632 TGGGAAGCCTTGATCGATTAAC 58.458 45.455 0.00 0.00 0.00 2.01
117 118 5.179555 GGGAAGCCTTGATCGATTAACATAC 59.820 44.000 0.00 0.00 0.00 2.39
122 123 5.758296 GCCTTGATCGATTAACATACTTGGA 59.242 40.000 0.00 0.00 0.00 3.53
130 143 6.095300 TCGATTAACATACTTGGACCGTAGAA 59.905 38.462 0.74 0.00 0.00 2.10
136 149 1.623811 ACTTGGACCGTAGAAGTGCAT 59.376 47.619 0.00 0.00 35.38 3.96
142 155 1.000506 ACCGTAGAAGTGCATGTCGTT 59.999 47.619 0.00 0.00 0.00 3.85
143 156 1.654105 CCGTAGAAGTGCATGTCGTTC 59.346 52.381 0.00 0.00 0.00 3.95
148 161 3.402110 AGAAGTGCATGTCGTTCAATCA 58.598 40.909 0.00 0.00 0.00 2.57
157 170 6.642540 TGCATGTCGTTCAATCACTATATCTC 59.357 38.462 0.00 0.00 0.00 2.75
160 173 6.504398 TGTCGTTCAATCACTATATCTCCAC 58.496 40.000 0.00 0.00 0.00 4.02
167 180 7.016296 TCAATCACTATATCTCCACCATGGTA 58.984 38.462 19.28 1.36 39.03 3.25
201 214 4.437682 TTCACCTCCACAAAGAATCAGT 57.562 40.909 0.00 0.00 0.00 3.41
206 219 5.047021 CACCTCCACAAAGAATCAGTCTAGA 60.047 44.000 0.00 0.00 34.56 2.43
264 277 8.076781 CAGATCTGAATAATTGAATCTGCAAGG 58.923 37.037 18.34 0.00 0.00 3.61
266 279 7.325660 TCTGAATAATTGAATCTGCAAGGAC 57.674 36.000 0.00 0.00 0.00 3.85
277 290 2.105477 TCTGCAAGGACAGAAAGCTCTT 59.895 45.455 0.00 0.00 43.59 2.85
288 301 6.038050 GGACAGAAAGCTCTTTAATCTCATGG 59.962 42.308 0.00 0.00 32.11 3.66
292 305 4.500499 AGCTCTTTAATCTCATGGCACT 57.500 40.909 0.00 0.00 0.00 4.40
294 307 3.243002 GCTCTTTAATCTCATGGCACTGC 60.243 47.826 0.00 0.00 0.00 4.40
303 316 3.753272 TCTCATGGCACTGCTAAAAGAAC 59.247 43.478 0.00 0.00 0.00 3.01
308 321 3.003480 GGCACTGCTAAAAGAACGAGAT 58.997 45.455 0.00 0.00 0.00 2.75
309 322 3.181516 GGCACTGCTAAAAGAACGAGATG 60.182 47.826 0.00 0.00 0.00 2.90
310 323 3.181516 GCACTGCTAAAAGAACGAGATGG 60.182 47.826 0.00 0.00 0.00 3.51
316 329 7.606456 ACTGCTAAAAGAACGAGATGGAATTTA 59.394 33.333 0.00 0.00 0.00 1.40
377 391 8.430801 AAGAATATTGAAGTCTTGAAGATCCG 57.569 34.615 0.00 0.00 30.48 4.18
380 394 5.667539 ATTGAAGTCTTGAAGATCCGAGA 57.332 39.130 0.00 0.00 0.00 4.04
394 408 1.075970 CGAGATCCCCCACCTCTCA 60.076 63.158 0.00 0.00 36.11 3.27
405 419 1.088340 CACCTCTCAGCGCCAAGATG 61.088 60.000 2.29 7.08 37.65 2.90
451 465 1.384989 TTTTCTTTTGACGGCGGCCA 61.385 50.000 20.71 4.99 0.00 5.36
458 472 1.534336 TTGACGGCGGCCAAGTACTA 61.534 55.000 20.71 0.00 0.00 1.82
463 477 2.093553 ACGGCGGCCAAGTACTATTTAA 60.094 45.455 20.71 0.00 0.00 1.52
464 478 3.135994 CGGCGGCCAAGTACTATTTAAT 58.864 45.455 20.71 0.00 0.00 1.40
465 479 3.562557 CGGCGGCCAAGTACTATTTAATT 59.437 43.478 20.71 0.00 0.00 1.40
468 482 5.993441 GGCGGCCAAGTACTATTTAATTAGA 59.007 40.000 15.62 0.00 0.00 2.10
469 483 6.073385 GGCGGCCAAGTACTATTTAATTAGAC 60.073 42.308 15.62 5.56 0.00 2.59
470 484 6.704937 GCGGCCAAGTACTATTTAATTAGACT 59.295 38.462 2.24 7.26 0.00 3.24
471 485 7.869429 GCGGCCAAGTACTATTTAATTAGACTA 59.131 37.037 2.24 0.00 0.00 2.59
472 486 9.408069 CGGCCAAGTACTATTTAATTAGACTAG 57.592 37.037 2.24 0.00 0.00 2.57
473 487 9.205719 GGCCAAGTACTATTTAATTAGACTAGC 57.794 37.037 10.59 12.92 0.00 3.42
474 488 9.205719 GCCAAGTACTATTTAATTAGACTAGCC 57.794 37.037 10.59 0.00 0.00 3.93
484 498 9.851686 ATTTAATTAGACTAGCCACAATGATCA 57.148 29.630 0.00 0.00 0.00 2.92
485 499 8.893219 TTAATTAGACTAGCCACAATGATCAG 57.107 34.615 0.09 0.00 0.00 2.90
486 500 5.939764 TTAGACTAGCCACAATGATCAGT 57.060 39.130 0.09 0.00 0.00 3.41
487 501 7.603180 ATTAGACTAGCCACAATGATCAGTA 57.397 36.000 0.09 0.00 0.00 2.74
488 502 5.939764 AGACTAGCCACAATGATCAGTAA 57.060 39.130 0.09 0.00 0.00 2.24
489 503 5.665459 AGACTAGCCACAATGATCAGTAAC 58.335 41.667 0.09 0.00 0.00 2.50
490 504 5.187772 AGACTAGCCACAATGATCAGTAACA 59.812 40.000 0.09 0.00 0.00 2.41
491 505 5.994250 ACTAGCCACAATGATCAGTAACAT 58.006 37.500 0.09 0.00 0.00 2.71
492 506 7.069950 AGACTAGCCACAATGATCAGTAACATA 59.930 37.037 0.09 0.00 0.00 2.29
493 507 6.986817 ACTAGCCACAATGATCAGTAACATAC 59.013 38.462 0.09 0.00 0.00 2.39
494 508 5.744171 AGCCACAATGATCAGTAACATACA 58.256 37.500 0.09 0.00 0.00 2.29
495 509 6.359804 AGCCACAATGATCAGTAACATACAT 58.640 36.000 0.09 0.00 0.00 2.29
496 510 6.830324 AGCCACAATGATCAGTAACATACATT 59.170 34.615 0.09 0.00 0.00 2.71
497 511 7.992608 AGCCACAATGATCAGTAACATACATTA 59.007 33.333 0.09 0.00 0.00 1.90
498 512 8.285394 GCCACAATGATCAGTAACATACATTAG 58.715 37.037 0.09 0.00 0.00 1.73
499 513 9.330063 CCACAATGATCAGTAACATACATTAGT 57.670 33.333 0.09 0.00 0.00 2.24
532 546 9.871238 CACATATTCCTATACTATGTTACCACC 57.129 37.037 0.00 0.00 34.66 4.61
533 547 9.839185 ACATATTCCTATACTATGTTACCACCT 57.161 33.333 0.00 0.00 33.42 4.00
536 550 8.792830 ATTCCTATACTATGTTACCACCTTCA 57.207 34.615 0.00 0.00 0.00 3.02
537 551 8.792830 TTCCTATACTATGTTACCACCTTCAT 57.207 34.615 0.00 0.00 0.00 2.57
538 552 9.886337 TTCCTATACTATGTTACCACCTTCATA 57.114 33.333 0.00 0.00 0.00 2.15
539 553 9.529823 TCCTATACTATGTTACCACCTTCATAG 57.470 37.037 8.77 8.77 42.80 2.23
551 565 5.670792 CACCTTCATAGTGGGTAGTAACA 57.329 43.478 0.00 0.00 0.00 2.41
552 566 6.235231 CACCTTCATAGTGGGTAGTAACAT 57.765 41.667 0.00 0.00 0.00 2.71
553 567 7.356089 CACCTTCATAGTGGGTAGTAACATA 57.644 40.000 0.00 0.00 0.00 2.29
554 568 7.788026 CACCTTCATAGTGGGTAGTAACATAA 58.212 38.462 0.00 0.00 0.00 1.90
555 569 7.926555 CACCTTCATAGTGGGTAGTAACATAAG 59.073 40.741 0.00 0.00 0.00 1.73
556 570 7.622479 ACCTTCATAGTGGGTAGTAACATAAGT 59.378 37.037 0.00 0.00 0.00 2.24
557 571 7.926555 CCTTCATAGTGGGTAGTAACATAAGTG 59.073 40.741 0.00 0.00 0.00 3.16
558 572 7.966339 TCATAGTGGGTAGTAACATAAGTGT 57.034 36.000 0.00 0.00 41.28 3.55
559 573 7.778083 TCATAGTGGGTAGTAACATAAGTGTG 58.222 38.462 0.00 0.00 38.92 3.82
560 574 5.416271 AGTGGGTAGTAACATAAGTGTGG 57.584 43.478 0.00 0.00 38.92 4.17
561 575 4.842380 AGTGGGTAGTAACATAAGTGTGGT 59.158 41.667 0.00 0.00 38.92 4.16
562 576 6.018469 AGTGGGTAGTAACATAAGTGTGGTA 58.982 40.000 0.00 0.00 38.92 3.25
563 577 6.497954 AGTGGGTAGTAACATAAGTGTGGTAA 59.502 38.462 0.00 0.00 38.92 2.85
564 578 6.591448 GTGGGTAGTAACATAAGTGTGGTAAC 59.409 42.308 0.00 0.00 38.92 2.50
579 593 4.870123 TGGTAACATGCAAAGCTTCATT 57.130 36.364 0.00 0.00 46.17 2.57
580 594 5.212532 TGGTAACATGCAAAGCTTCATTT 57.787 34.783 0.00 1.04 46.17 2.32
581 595 6.338214 TGGTAACATGCAAAGCTTCATTTA 57.662 33.333 0.00 0.18 46.17 1.40
582 596 6.934056 TGGTAACATGCAAAGCTTCATTTAT 58.066 32.000 0.00 0.00 46.17 1.40
583 597 7.385267 TGGTAACATGCAAAGCTTCATTTATT 58.615 30.769 0.00 0.00 46.17 1.40
584 598 8.526978 TGGTAACATGCAAAGCTTCATTTATTA 58.473 29.630 0.00 0.00 46.17 0.98
585 599 9.023967 GGTAACATGCAAAGCTTCATTTATTAG 57.976 33.333 0.00 0.00 0.00 1.73
586 600 9.023967 GTAACATGCAAAGCTTCATTTATTAGG 57.976 33.333 0.00 0.00 0.00 2.69
587 601 7.174107 ACATGCAAAGCTTCATTTATTAGGT 57.826 32.000 0.00 0.00 0.00 3.08
588 602 7.614494 ACATGCAAAGCTTCATTTATTAGGTT 58.386 30.769 0.00 0.00 0.00 3.50
589 603 8.748412 ACATGCAAAGCTTCATTTATTAGGTTA 58.252 29.630 0.00 0.00 0.00 2.85
590 604 9.754382 CATGCAAAGCTTCATTTATTAGGTTAT 57.246 29.630 0.00 0.00 0.00 1.89
610 624 8.874156 AGGTTATAGACTCATATTGCATTGAGA 58.126 33.333 21.77 6.70 41.53 3.27
611 625 8.930760 GGTTATAGACTCATATTGCATTGAGAC 58.069 37.037 21.77 17.18 41.53 3.36
612 626 9.481340 GTTATAGACTCATATTGCATTGAGACA 57.519 33.333 21.77 10.72 41.53 3.41
614 628 6.862711 AGACTCATATTGCATTGAGACATG 57.137 37.500 21.77 5.67 41.53 3.21
615 629 6.354938 AGACTCATATTGCATTGAGACATGT 58.645 36.000 21.77 0.00 41.53 3.21
616 630 6.260271 AGACTCATATTGCATTGAGACATGTG 59.740 38.462 21.77 5.93 41.53 3.21
617 631 6.117488 ACTCATATTGCATTGAGACATGTGA 58.883 36.000 21.77 9.32 41.53 3.58
618 632 6.771267 ACTCATATTGCATTGAGACATGTGAT 59.229 34.615 21.77 0.00 41.53 3.06
619 633 6.966021 TCATATTGCATTGAGACATGTGATG 58.034 36.000 1.15 3.48 0.00 3.07
621 635 5.654603 ATTGCATTGAGACATGTGATGTT 57.345 34.783 1.15 0.00 45.03 2.71
622 636 6.762702 ATTGCATTGAGACATGTGATGTTA 57.237 33.333 1.15 0.00 45.03 2.41
623 637 5.550232 TGCATTGAGACATGTGATGTTAC 57.450 39.130 1.15 0.00 45.03 2.50
624 638 5.002516 TGCATTGAGACATGTGATGTTACA 58.997 37.500 1.15 0.00 45.03 2.41
625 639 5.122711 TGCATTGAGACATGTGATGTTACAG 59.877 40.000 1.15 0.00 45.03 2.74
626 640 5.122869 GCATTGAGACATGTGATGTTACAGT 59.877 40.000 1.15 0.00 45.03 3.55
627 641 6.313658 GCATTGAGACATGTGATGTTACAGTA 59.686 38.462 1.15 0.00 45.03 2.74
628 642 7.148423 GCATTGAGACATGTGATGTTACAGTAA 60.148 37.037 1.15 0.00 45.03 2.24
629 643 7.652300 TTGAGACATGTGATGTTACAGTAAC 57.348 36.000 15.58 15.58 45.03 2.50
630 644 6.993079 TGAGACATGTGATGTTACAGTAACT 58.007 36.000 21.56 9.41 45.03 2.24
631 645 8.117813 TGAGACATGTGATGTTACAGTAACTA 57.882 34.615 21.56 10.50 45.03 2.24
632 646 8.244113 TGAGACATGTGATGTTACAGTAACTAG 58.756 37.037 21.56 8.25 45.03 2.57
633 647 7.036220 AGACATGTGATGTTACAGTAACTAGC 58.964 38.462 21.56 12.59 45.03 3.42
634 648 6.936279 ACATGTGATGTTACAGTAACTAGCT 58.064 36.000 21.56 6.57 41.63 3.32
635 649 8.063200 ACATGTGATGTTACAGTAACTAGCTA 57.937 34.615 21.56 4.25 41.63 3.32
636 650 8.528643 ACATGTGATGTTACAGTAACTAGCTAA 58.471 33.333 21.56 3.59 41.63 3.09
637 651 9.025020 CATGTGATGTTACAGTAACTAGCTAAG 57.975 37.037 21.56 6.36 39.38 2.18
638 652 8.118976 TGTGATGTTACAGTAACTAGCTAAGT 57.881 34.615 21.56 0.00 41.49 2.24
655 669 6.947644 GCTAAGTTACTAGCTACCTCTCTT 57.052 41.667 0.00 0.00 41.01 2.85
656 670 6.962686 GCTAAGTTACTAGCTACCTCTCTTC 58.037 44.000 0.00 0.00 41.01 2.87
657 671 6.769341 GCTAAGTTACTAGCTACCTCTCTTCT 59.231 42.308 0.00 0.00 41.01 2.85
658 672 7.041576 GCTAAGTTACTAGCTACCTCTCTTCTC 60.042 44.444 0.00 0.00 41.01 2.87
659 673 6.316280 AGTTACTAGCTACCTCTCTTCTCA 57.684 41.667 0.00 0.00 0.00 3.27
660 674 6.906848 AGTTACTAGCTACCTCTCTTCTCAT 58.093 40.000 0.00 0.00 0.00 2.90
661 675 7.351166 AGTTACTAGCTACCTCTCTTCTCATT 58.649 38.462 0.00 0.00 0.00 2.57
662 676 8.496088 AGTTACTAGCTACCTCTCTTCTCATTA 58.504 37.037 0.00 0.00 0.00 1.90
663 677 9.122779 GTTACTAGCTACCTCTCTTCTCATTAA 57.877 37.037 0.00 0.00 0.00 1.40
664 678 7.576861 ACTAGCTACCTCTCTTCTCATTAAC 57.423 40.000 0.00 0.00 0.00 2.01
665 679 7.351166 ACTAGCTACCTCTCTTCTCATTAACT 58.649 38.462 0.00 0.00 0.00 2.24
666 680 7.837187 ACTAGCTACCTCTCTTCTCATTAACTT 59.163 37.037 0.00 0.00 0.00 2.66
667 681 9.344772 CTAGCTACCTCTCTTCTCATTAACTTA 57.655 37.037 0.00 0.00 0.00 2.24
668 682 8.776061 AGCTACCTCTCTTCTCATTAACTTAT 57.224 34.615 0.00 0.00 0.00 1.73
669 683 9.207868 AGCTACCTCTCTTCTCATTAACTTATT 57.792 33.333 0.00 0.00 0.00 1.40
670 684 9.255304 GCTACCTCTCTTCTCATTAACTTATTG 57.745 37.037 0.00 0.00 0.00 1.90
673 687 8.816894 ACCTCTCTTCTCATTAACTTATTGTCA 58.183 33.333 0.00 0.00 0.00 3.58
674 688 9.092876 CCTCTCTTCTCATTAACTTATTGTCAC 57.907 37.037 0.00 0.00 0.00 3.67
675 689 9.645059 CTCTCTTCTCATTAACTTATTGTCACA 57.355 33.333 0.00 0.00 0.00 3.58
681 695 9.665719 TCTCATTAACTTATTGTCACATAAGCA 57.334 29.630 11.53 2.67 34.60 3.91
713 727 5.545658 AGTTGTACTCAATGTTATTGCCG 57.454 39.130 0.00 0.00 35.92 5.69
714 728 5.242434 AGTTGTACTCAATGTTATTGCCGA 58.758 37.500 0.00 0.00 35.92 5.54
715 729 5.703592 AGTTGTACTCAATGTTATTGCCGAA 59.296 36.000 0.00 0.00 35.92 4.30
716 730 5.794687 TGTACTCAATGTTATTGCCGAAG 57.205 39.130 0.00 0.00 0.00 3.79
717 731 5.242434 TGTACTCAATGTTATTGCCGAAGT 58.758 37.500 0.00 0.00 0.00 3.01
718 732 5.703592 TGTACTCAATGTTATTGCCGAAGTT 59.296 36.000 0.00 0.00 0.00 2.66
719 733 6.874664 TGTACTCAATGTTATTGCCGAAGTTA 59.125 34.615 0.00 0.00 0.00 2.24
720 734 6.178239 ACTCAATGTTATTGCCGAAGTTAC 57.822 37.500 0.00 0.00 0.00 2.50
721 735 5.938125 ACTCAATGTTATTGCCGAAGTTACT 59.062 36.000 0.00 0.00 0.00 2.24
722 736 6.092259 ACTCAATGTTATTGCCGAAGTTACTC 59.908 38.462 0.00 0.00 0.00 2.59
723 737 5.353123 TCAATGTTATTGCCGAAGTTACTCC 59.647 40.000 0.00 0.00 0.00 3.85
724 738 3.602483 TGTTATTGCCGAAGTTACTCCC 58.398 45.455 0.00 0.00 0.00 4.30
725 739 3.008157 TGTTATTGCCGAAGTTACTCCCA 59.992 43.478 0.00 0.00 0.00 4.37
726 740 2.109425 ATTGCCGAAGTTACTCCCAC 57.891 50.000 0.00 0.00 0.00 4.61
741 755 0.958822 CCCACCGCTACTTTTGCTTT 59.041 50.000 0.00 0.00 0.00 3.51
745 759 3.243401 CCACCGCTACTTTTGCTTTTCTT 60.243 43.478 0.00 0.00 0.00 2.52
746 760 4.359706 CACCGCTACTTTTGCTTTTCTTT 58.640 39.130 0.00 0.00 0.00 2.52
751 765 5.687285 CGCTACTTTTGCTTTTCTTTGATGT 59.313 36.000 0.00 0.00 0.00 3.06
793 837 8.574251 AAATAACAACATAACAGTAGGCATCA 57.426 30.769 0.00 0.00 0.00 3.07
822 866 0.601057 ACAATGCGTTTAAGGCCCAC 59.399 50.000 0.00 0.00 0.00 4.61
858 902 0.109723 TTAGTGCCTTGGTCCCACAC 59.890 55.000 0.00 0.00 32.09 3.82
948 1008 1.362584 CCCTTCTTCCTCCCCCAAATT 59.637 52.381 0.00 0.00 0.00 1.82
994 1054 4.143333 GGAGAACCTAGCCGCGCA 62.143 66.667 8.75 0.00 0.00 6.09
1813 1891 3.432588 ACGTCGTCGAGAGCTGGG 61.433 66.667 9.47 0.00 40.62 4.45
1924 2011 1.286880 CCACTGCCGCTTCCAAAAG 59.713 57.895 0.00 0.00 35.47 2.27
1960 2047 4.957954 ACCATAACCTATTCTACACGGTGA 59.042 41.667 16.29 0.00 0.00 4.02
2021 2108 6.737720 TGTGGTCATCAGCTCTATTCTATT 57.262 37.500 0.00 0.00 0.00 1.73
2032 2119 6.370994 CAGCTCTATTCTATTGATTCGCCATT 59.629 38.462 0.00 0.00 0.00 3.16
2182 2269 2.353376 CTGGCGCGGTTGTGTTTG 60.353 61.111 8.83 0.00 0.00 2.93
2676 2763 3.503363 GGTGTGGCATCAGAGCGC 61.503 66.667 0.00 0.00 34.64 5.92
2813 2900 1.073548 TTGATGCAGCAGACCAGCA 59.926 52.632 4.20 0.00 43.14 4.41
2826 2913 2.345244 CAGCAGCTTCAGGGACGT 59.655 61.111 0.00 0.00 0.00 4.34
2952 3039 1.553248 GGTAGTGCACCCATGACACTA 59.447 52.381 14.63 11.42 42.07 2.74
3215 3305 9.821662 CATTAGATATGTGTGAATGTTGCATAG 57.178 33.333 0.00 0.00 0.00 2.23
3258 3348 3.244526 ACTGGTGCACTATCAATGACACA 60.245 43.478 17.98 0.16 0.00 3.72
3382 3472 9.774742 GGTGTCATTTATGTGAAGATAGTTTTC 57.225 33.333 0.00 0.00 0.00 2.29
3514 3605 3.988379 AGCTGATTTTGTTTTCGCAGA 57.012 38.095 0.00 0.00 0.00 4.26
3518 3609 3.631144 TGATTTTGTTTTCGCAGAGCAG 58.369 40.909 0.00 0.00 38.43 4.24
3563 3654 7.682787 AGATATAACAGAATTGTCTCCCTGT 57.317 36.000 0.00 0.00 41.14 4.00
3575 3666 6.887626 TTGTCTCCCTGTGTTTATTTTACC 57.112 37.500 0.00 0.00 0.00 2.85
3603 3694 6.216801 TGGTATTCGCTCTACACTGTTTAT 57.783 37.500 0.00 0.00 0.00 1.40
3613 3704 7.043986 CGCTCTACACTGTTTATGTCTATTGAC 60.044 40.741 0.00 0.00 43.20 3.18
3625 3716 2.609459 GTCTATTGACACATGGAAGGCG 59.391 50.000 2.19 0.00 42.48 5.52
3631 3722 2.034053 TGACACATGGAAGGCGAAAAAC 59.966 45.455 0.00 0.00 0.00 2.43
3635 3726 2.223711 ACATGGAAGGCGAAAAACACAC 60.224 45.455 0.00 0.00 0.00 3.82
3639 3730 1.673920 GAAGGCGAAAAACACACTCCA 59.326 47.619 0.00 0.00 0.00 3.86
3650 3741 7.308589 CGAAAAACACACTCCATTTCCTATTCT 60.309 37.037 0.00 0.00 0.00 2.40
3662 3753 8.933653 TCCATTTCCTATTCTTGTTTTCCTTTT 58.066 29.630 0.00 0.00 0.00 2.27
3698 3789 9.636789 ATGATCCAAACATTTCTTATCATCTGA 57.363 29.630 0.00 0.00 28.99 3.27
3743 3835 4.686091 CGCGTGTCATAAGTCCATGATTAT 59.314 41.667 0.00 0.00 37.28 1.28
3746 3838 5.346011 CGTGTCATAAGTCCATGATTATCCG 59.654 44.000 0.00 0.00 37.28 4.18
3765 3857 2.615493 CCGAGACAGTTTTGGCCTGTAT 60.615 50.000 3.32 0.00 43.00 2.29
3831 3924 7.383300 GCACCCATTTCTCTTGATTAATTATGC 59.617 37.037 0.00 0.00 0.00 3.14
3859 3953 6.108687 TGTGTGTGACAATTTAAAATTGCCA 58.891 32.000 0.00 0.00 32.55 4.92
3893 3987 4.974645 AGTGTTAACCATCACTTCTGGA 57.025 40.909 2.48 0.00 41.33 3.86
3952 4046 3.550437 AGCTGCATAGTACTTTCCCTG 57.450 47.619 0.00 0.00 0.00 4.45
3955 4049 2.171448 CTGCATAGTACTTTCCCTGGCT 59.829 50.000 0.00 0.00 0.00 4.75
3961 4055 4.388577 AGTACTTTCCCTGGCTTGATTT 57.611 40.909 0.00 0.00 0.00 2.17
3977 4071 5.556947 GCTTGATTTTTGTTTTGAGCTTCCG 60.557 40.000 0.00 0.00 0.00 4.30
4027 4121 4.518211 CAGGGATCAATTAGACCAGATTGC 59.482 45.833 0.00 0.00 34.15 3.56
4052 4146 7.523293 TCTTCTTCAGCATTTCACCATTTTA 57.477 32.000 0.00 0.00 0.00 1.52
4054 4148 8.587608 TCTTCTTCAGCATTTCACCATTTTATT 58.412 29.630 0.00 0.00 0.00 1.40
4055 4149 8.537049 TTCTTCAGCATTTCACCATTTTATTG 57.463 30.769 0.00 0.00 0.00 1.90
4056 4150 7.894708 TCTTCAGCATTTCACCATTTTATTGA 58.105 30.769 0.00 0.00 0.00 2.57
4057 4151 8.533657 TCTTCAGCATTTCACCATTTTATTGAT 58.466 29.630 0.00 0.00 0.00 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
74 75 1.473258 CATCTTTTGGGATGGGCGAA 58.527 50.000 0.00 0.00 39.33 4.70
85 86 3.181493 CGATCAAGGCTTCCCATCTTTTG 60.181 47.826 0.00 0.00 0.00 2.44
99 100 6.202954 GGTCCAAGTATGTTAATCGATCAAGG 59.797 42.308 0.00 0.00 0.00 3.61
110 111 5.622914 GCACTTCTACGGTCCAAGTATGTTA 60.623 44.000 4.76 0.00 0.00 2.41
113 114 3.187700 GCACTTCTACGGTCCAAGTATG 58.812 50.000 4.76 0.00 0.00 2.39
117 118 2.002586 CATGCACTTCTACGGTCCAAG 58.997 52.381 0.00 0.00 0.00 3.61
122 123 0.601558 ACGACATGCACTTCTACGGT 59.398 50.000 0.00 0.00 0.00 4.83
130 143 2.771089 AGTGATTGAACGACATGCACT 58.229 42.857 0.00 3.46 37.94 4.40
136 149 6.461092 GGTGGAGATATAGTGATTGAACGACA 60.461 42.308 0.00 0.00 0.00 4.35
142 155 5.846164 ACCATGGTGGAGATATAGTGATTGA 59.154 40.000 18.99 0.00 40.96 2.57
143 156 6.119240 ACCATGGTGGAGATATAGTGATTG 57.881 41.667 18.99 0.00 40.96 2.67
148 161 5.827756 TCGATACCATGGTGGAGATATAGT 58.172 41.667 28.17 0.00 40.96 2.12
157 170 4.071961 TCTTTCATCGATACCATGGTGG 57.928 45.455 28.17 15.96 45.02 4.61
160 173 6.866010 TGAAATCTTTCATCGATACCATGG 57.134 37.500 11.19 11.19 41.88 3.66
252 265 2.816087 GCTTTCTGTCCTTGCAGATTCA 59.184 45.455 0.00 0.00 43.99 2.57
254 267 3.080319 GAGCTTTCTGTCCTTGCAGATT 58.920 45.455 0.00 0.00 43.99 2.40
259 272 5.414144 AGATTAAAGAGCTTTCTGTCCTTGC 59.586 40.000 0.00 0.00 34.23 4.01
264 277 6.458070 GCCATGAGATTAAAGAGCTTTCTGTC 60.458 42.308 0.00 0.00 34.23 3.51
266 279 5.356190 TGCCATGAGATTAAAGAGCTTTCTG 59.644 40.000 0.00 0.00 34.23 3.02
272 285 3.243002 GCAGTGCCATGAGATTAAAGAGC 60.243 47.826 2.85 0.00 0.00 4.09
277 290 6.179756 TCTTTTAGCAGTGCCATGAGATTAA 58.820 36.000 12.58 0.00 0.00 1.40
288 301 3.181516 CCATCTCGTTCTTTTAGCAGTGC 60.182 47.826 7.13 7.13 0.00 4.40
292 305 6.817765 AAATTCCATCTCGTTCTTTTAGCA 57.182 33.333 0.00 0.00 0.00 3.49
343 356 8.896744 CAAGACTTCAATATTCTTGCCATTCTA 58.103 33.333 2.06 0.00 39.75 2.10
345 358 7.765307 TCAAGACTTCAATATTCTTGCCATTC 58.235 34.615 8.60 0.00 43.96 2.67
346 359 7.707624 TCAAGACTTCAATATTCTTGCCATT 57.292 32.000 8.60 0.00 43.96 3.16
350 363 8.127954 GGATCTTCAAGACTTCAATATTCTTGC 58.872 37.037 8.60 0.00 43.96 4.01
360 374 4.098654 GGATCTCGGATCTTCAAGACTTCA 59.901 45.833 11.91 0.00 0.00 3.02
367 381 1.343985 TGGGGGATCTCGGATCTTCAA 60.344 52.381 11.91 0.00 0.00 2.69
369 383 0.682292 GTGGGGGATCTCGGATCTTC 59.318 60.000 11.91 6.56 0.00 2.87
372 386 1.152226 AGGTGGGGGATCTCGGATC 60.152 63.158 5.59 5.59 0.00 3.36
377 391 1.406860 GCTGAGAGGTGGGGGATCTC 61.407 65.000 0.00 0.00 39.93 2.75
380 394 2.765807 CGCTGAGAGGTGGGGGAT 60.766 66.667 0.00 0.00 0.00 3.85
398 412 2.515523 CTCCGGCTGCCATCTTGG 60.516 66.667 20.29 11.34 41.55 3.61
412 426 0.927029 ATTTAGGTCCCCTTGCCTCC 59.073 55.000 0.00 0.00 36.38 4.30
416 430 5.483685 AAGAAAAATTTAGGTCCCCTTGC 57.516 39.130 0.00 0.00 34.61 4.01
437 451 1.227883 TACTTGGCCGCCGTCAAAA 60.228 52.632 4.58 0.00 0.00 2.44
438 452 1.962306 GTACTTGGCCGCCGTCAAA 60.962 57.895 4.58 0.00 0.00 2.69
439 453 1.534336 TAGTACTTGGCCGCCGTCAA 61.534 55.000 0.00 0.00 0.00 3.18
442 456 0.251073 AAATAGTACTTGGCCGCCGT 59.749 50.000 0.00 0.00 0.00 5.68
458 472 9.851686 TGATCATTGTGGCTAGTCTAATTAAAT 57.148 29.630 0.00 0.00 0.00 1.40
463 477 6.491714 ACTGATCATTGTGGCTAGTCTAAT 57.508 37.500 0.00 0.00 0.00 1.73
464 478 5.939764 ACTGATCATTGTGGCTAGTCTAA 57.060 39.130 0.00 0.00 0.00 2.10
465 479 6.379988 TGTTACTGATCATTGTGGCTAGTCTA 59.620 38.462 0.00 0.00 0.00 2.59
468 482 5.420725 TGTTACTGATCATTGTGGCTAGT 57.579 39.130 0.00 0.00 0.00 2.57
469 483 6.986231 TGTATGTTACTGATCATTGTGGCTAG 59.014 38.462 0.00 0.00 0.00 3.42
470 484 6.883744 TGTATGTTACTGATCATTGTGGCTA 58.116 36.000 0.00 0.00 0.00 3.93
471 485 5.744171 TGTATGTTACTGATCATTGTGGCT 58.256 37.500 0.00 0.00 0.00 4.75
472 486 6.624352 ATGTATGTTACTGATCATTGTGGC 57.376 37.500 0.00 0.00 0.00 5.01
473 487 9.330063 ACTAATGTATGTTACTGATCATTGTGG 57.670 33.333 0.00 0.00 0.00 4.17
523 537 8.189915 TTACTACCCACTATGAAGGTGGTAACA 61.190 40.741 11.80 0.00 46.42 2.41
524 538 6.155049 TTACTACCCACTATGAAGGTGGTAAC 59.845 42.308 11.80 0.00 46.42 2.50
529 543 5.670792 TGTTACTACCCACTATGAAGGTG 57.329 43.478 0.00 0.00 35.02 4.00
530 544 7.622479 ACTTATGTTACTACCCACTATGAAGGT 59.378 37.037 0.00 0.00 37.69 3.50
531 545 7.926555 CACTTATGTTACTACCCACTATGAAGG 59.073 40.741 0.00 0.00 0.00 3.46
532 546 8.475639 ACACTTATGTTACTACCCACTATGAAG 58.524 37.037 0.00 0.00 34.46 3.02
533 547 8.255206 CACACTTATGTTACTACCCACTATGAA 58.745 37.037 0.00 0.00 36.72 2.57
534 548 7.147794 CCACACTTATGTTACTACCCACTATGA 60.148 40.741 0.00 0.00 36.72 2.15
535 549 6.984474 CCACACTTATGTTACTACCCACTATG 59.016 42.308 0.00 0.00 36.72 2.23
536 550 6.670902 ACCACACTTATGTTACTACCCACTAT 59.329 38.462 0.00 0.00 36.72 2.12
537 551 6.018469 ACCACACTTATGTTACTACCCACTA 58.982 40.000 0.00 0.00 36.72 2.74
538 552 4.842380 ACCACACTTATGTTACTACCCACT 59.158 41.667 0.00 0.00 36.72 4.00
539 553 5.156608 ACCACACTTATGTTACTACCCAC 57.843 43.478 0.00 0.00 36.72 4.61
540 554 6.269538 TGTTACCACACTTATGTTACTACCCA 59.730 38.462 0.00 0.00 36.72 4.51
541 555 6.700352 TGTTACCACACTTATGTTACTACCC 58.300 40.000 0.00 0.00 36.72 3.69
542 556 7.201582 GCATGTTACCACACTTATGTTACTACC 60.202 40.741 0.00 0.00 36.72 3.18
543 557 7.332430 TGCATGTTACCACACTTATGTTACTAC 59.668 37.037 0.00 0.00 36.72 2.73
544 558 7.387643 TGCATGTTACCACACTTATGTTACTA 58.612 34.615 0.00 0.00 36.72 1.82
545 559 6.234920 TGCATGTTACCACACTTATGTTACT 58.765 36.000 0.00 0.00 36.72 2.24
546 560 6.489127 TGCATGTTACCACACTTATGTTAC 57.511 37.500 0.00 0.00 36.72 2.50
547 561 7.511959 TTTGCATGTTACCACACTTATGTTA 57.488 32.000 0.00 0.00 36.72 2.41
548 562 6.398234 TTTGCATGTTACCACACTTATGTT 57.602 33.333 0.00 0.00 36.72 2.71
549 563 5.564651 GCTTTGCATGTTACCACACTTATGT 60.565 40.000 0.00 0.00 40.80 2.29
550 564 4.858692 GCTTTGCATGTTACCACACTTATG 59.141 41.667 0.00 0.00 35.03 1.90
551 565 4.766891 AGCTTTGCATGTTACCACACTTAT 59.233 37.500 0.00 0.00 35.03 1.73
552 566 4.141287 AGCTTTGCATGTTACCACACTTA 58.859 39.130 0.00 0.00 35.03 2.24
553 567 2.958355 AGCTTTGCATGTTACCACACTT 59.042 40.909 0.00 0.00 35.03 3.16
554 568 2.586425 AGCTTTGCATGTTACCACACT 58.414 42.857 0.00 0.00 35.03 3.55
555 569 3.243367 TGAAGCTTTGCATGTTACCACAC 60.243 43.478 0.00 0.00 35.03 3.82
556 570 2.954989 TGAAGCTTTGCATGTTACCACA 59.045 40.909 0.00 0.00 37.31 4.17
557 571 3.641437 TGAAGCTTTGCATGTTACCAC 57.359 42.857 0.00 0.00 0.00 4.16
558 572 4.870123 AATGAAGCTTTGCATGTTACCA 57.130 36.364 0.00 0.00 0.00 3.25
559 573 7.832503 AATAAATGAAGCTTTGCATGTTACC 57.167 32.000 0.00 0.00 0.00 2.85
560 574 9.023967 CCTAATAAATGAAGCTTTGCATGTTAC 57.976 33.333 0.00 0.00 0.00 2.50
561 575 8.748412 ACCTAATAAATGAAGCTTTGCATGTTA 58.252 29.630 0.00 3.50 0.00 2.41
562 576 7.614494 ACCTAATAAATGAAGCTTTGCATGTT 58.386 30.769 0.00 1.51 0.00 2.71
563 577 7.174107 ACCTAATAAATGAAGCTTTGCATGT 57.826 32.000 0.00 0.00 0.00 3.21
564 578 9.754382 ATAACCTAATAAATGAAGCTTTGCATG 57.246 29.630 0.00 0.00 0.00 4.06
584 598 8.874156 TCTCAATGCAATATGAGTCTATAACCT 58.126 33.333 20.36 0.00 42.86 3.50
585 599 8.930760 GTCTCAATGCAATATGAGTCTATAACC 58.069 37.037 20.36 4.05 42.86 2.85
586 600 9.481340 TGTCTCAATGCAATATGAGTCTATAAC 57.519 33.333 20.36 13.54 42.86 1.89
588 602 9.649167 CATGTCTCAATGCAATATGAGTCTATA 57.351 33.333 20.36 6.88 42.86 1.31
589 603 8.155510 ACATGTCTCAATGCAATATGAGTCTAT 58.844 33.333 20.36 13.30 42.86 1.98
590 604 7.440255 CACATGTCTCAATGCAATATGAGTCTA 59.560 37.037 20.36 12.13 42.86 2.59
591 605 6.260271 CACATGTCTCAATGCAATATGAGTCT 59.740 38.462 20.36 9.05 42.86 3.24
592 606 6.259387 TCACATGTCTCAATGCAATATGAGTC 59.741 38.462 20.36 16.98 42.86 3.36
593 607 6.117488 TCACATGTCTCAATGCAATATGAGT 58.883 36.000 20.36 5.71 42.86 3.41
594 608 6.613755 TCACATGTCTCAATGCAATATGAG 57.386 37.500 17.01 17.01 43.51 2.90
595 609 6.544564 ACATCACATGTCTCAATGCAATATGA 59.455 34.615 0.00 0.00 39.92 2.15
596 610 6.735130 ACATCACATGTCTCAATGCAATATG 58.265 36.000 0.00 0.00 39.92 1.78
597 611 6.954487 ACATCACATGTCTCAATGCAATAT 57.046 33.333 0.00 0.00 39.92 1.28
598 612 6.762702 AACATCACATGTCTCAATGCAATA 57.237 33.333 0.00 0.00 44.07 1.90
599 613 5.654603 AACATCACATGTCTCAATGCAAT 57.345 34.783 0.00 0.00 44.07 3.56
600 614 5.472820 TGTAACATCACATGTCTCAATGCAA 59.527 36.000 0.00 0.00 44.07 4.08
601 615 5.002516 TGTAACATCACATGTCTCAATGCA 58.997 37.500 0.00 0.00 44.07 3.96
602 616 5.122869 ACTGTAACATCACATGTCTCAATGC 59.877 40.000 0.00 0.00 44.07 3.56
603 617 6.732531 ACTGTAACATCACATGTCTCAATG 57.267 37.500 0.00 0.45 44.07 2.82
604 618 8.097038 AGTTACTGTAACATCACATGTCTCAAT 58.903 33.333 27.12 3.45 44.07 2.57
605 619 7.441836 AGTTACTGTAACATCACATGTCTCAA 58.558 34.615 27.12 0.00 44.07 3.02
606 620 6.993079 AGTTACTGTAACATCACATGTCTCA 58.007 36.000 27.12 0.00 44.07 3.27
607 621 7.221067 GCTAGTTACTGTAACATCACATGTCTC 59.779 40.741 27.12 1.55 44.07 3.36
608 622 7.036220 GCTAGTTACTGTAACATCACATGTCT 58.964 38.462 27.12 9.43 44.07 3.41
609 623 7.036220 AGCTAGTTACTGTAACATCACATGTC 58.964 38.462 27.12 9.51 44.07 3.06
611 625 8.926715 TTAGCTAGTTACTGTAACATCACATG 57.073 34.615 27.12 12.57 41.07 3.21
612 626 8.750298 ACTTAGCTAGTTACTGTAACATCACAT 58.250 33.333 27.12 11.85 41.07 3.21
613 627 8.118976 ACTTAGCTAGTTACTGTAACATCACA 57.881 34.615 27.12 10.61 41.07 3.58
614 628 8.983307 AACTTAGCTAGTTACTGTAACATCAC 57.017 34.615 27.12 15.70 45.22 3.06
632 646 6.769341 AGAAGAGAGGTAGCTAGTAACTTAGC 59.231 42.308 0.00 0.00 45.05 3.09
633 647 7.988599 TGAGAAGAGAGGTAGCTAGTAACTTAG 59.011 40.741 0.00 0.00 0.00 2.18
634 648 7.859540 TGAGAAGAGAGGTAGCTAGTAACTTA 58.140 38.462 0.00 0.00 0.00 2.24
635 649 6.723339 TGAGAAGAGAGGTAGCTAGTAACTT 58.277 40.000 0.00 0.00 0.00 2.66
636 650 6.316280 TGAGAAGAGAGGTAGCTAGTAACT 57.684 41.667 0.00 0.00 0.00 2.24
637 651 7.576861 AATGAGAAGAGAGGTAGCTAGTAAC 57.423 40.000 0.00 0.00 0.00 2.50
638 652 9.122779 GTTAATGAGAAGAGAGGTAGCTAGTAA 57.877 37.037 0.00 0.00 0.00 2.24
639 653 8.496088 AGTTAATGAGAAGAGAGGTAGCTAGTA 58.504 37.037 0.00 0.00 0.00 1.82
640 654 7.351166 AGTTAATGAGAAGAGAGGTAGCTAGT 58.649 38.462 0.00 0.00 0.00 2.57
641 655 7.817418 AGTTAATGAGAAGAGAGGTAGCTAG 57.183 40.000 0.00 0.00 0.00 3.42
642 656 9.869667 ATAAGTTAATGAGAAGAGAGGTAGCTA 57.130 33.333 0.00 0.00 0.00 3.32
643 657 8.776061 ATAAGTTAATGAGAAGAGAGGTAGCT 57.224 34.615 0.00 0.00 0.00 3.32
644 658 9.255304 CAATAAGTTAATGAGAAGAGAGGTAGC 57.745 37.037 0.00 0.00 0.00 3.58
647 661 8.816894 TGACAATAAGTTAATGAGAAGAGAGGT 58.183 33.333 4.94 0.00 0.00 3.85
648 662 9.092876 GTGACAATAAGTTAATGAGAAGAGAGG 57.907 37.037 4.94 0.00 0.00 3.69
649 663 9.645059 TGTGACAATAAGTTAATGAGAAGAGAG 57.355 33.333 4.94 0.00 0.00 3.20
655 669 9.665719 TGCTTATGTGACAATAAGTTAATGAGA 57.334 29.630 4.94 0.00 40.70 3.27
690 704 5.350365 TCGGCAATAACATTGAGTACAACTC 59.650 40.000 3.11 0.01 45.26 3.01
691 705 5.242434 TCGGCAATAACATTGAGTACAACT 58.758 37.500 3.11 0.00 38.90 3.16
692 706 5.539582 TCGGCAATAACATTGAGTACAAC 57.460 39.130 3.11 0.00 38.90 3.32
693 707 5.703592 ACTTCGGCAATAACATTGAGTACAA 59.296 36.000 3.11 0.00 40.42 2.41
694 708 5.242434 ACTTCGGCAATAACATTGAGTACA 58.758 37.500 3.11 0.00 0.00 2.90
695 709 5.796350 ACTTCGGCAATAACATTGAGTAC 57.204 39.130 3.11 0.00 0.00 2.73
696 710 7.101054 AGTAACTTCGGCAATAACATTGAGTA 58.899 34.615 3.11 0.00 0.00 2.59
697 711 5.938125 AGTAACTTCGGCAATAACATTGAGT 59.062 36.000 3.11 0.00 0.00 3.41
698 712 6.422776 AGTAACTTCGGCAATAACATTGAG 57.577 37.500 3.11 0.00 0.00 3.02
699 713 5.353123 GGAGTAACTTCGGCAATAACATTGA 59.647 40.000 3.11 0.00 0.00 2.57
700 714 5.448632 GGGAGTAACTTCGGCAATAACATTG 60.449 44.000 0.00 0.00 0.00 2.82
701 715 4.638865 GGGAGTAACTTCGGCAATAACATT 59.361 41.667 0.00 0.00 0.00 2.71
702 716 4.196971 GGGAGTAACTTCGGCAATAACAT 58.803 43.478 0.00 0.00 0.00 2.71
703 717 3.008157 TGGGAGTAACTTCGGCAATAACA 59.992 43.478 0.00 0.00 0.00 2.41
704 718 3.373130 GTGGGAGTAACTTCGGCAATAAC 59.627 47.826 0.00 0.00 0.00 1.89
705 719 3.602483 GTGGGAGTAACTTCGGCAATAA 58.398 45.455 0.00 0.00 0.00 1.40
706 720 2.093341 GGTGGGAGTAACTTCGGCAATA 60.093 50.000 0.00 0.00 0.00 1.90
707 721 1.339727 GGTGGGAGTAACTTCGGCAAT 60.340 52.381 0.00 0.00 0.00 3.56
708 722 0.035739 GGTGGGAGTAACTTCGGCAA 59.964 55.000 0.00 0.00 0.00 4.52
709 723 1.675219 GGTGGGAGTAACTTCGGCA 59.325 57.895 0.00 0.00 0.00 5.69
710 724 1.447314 CGGTGGGAGTAACTTCGGC 60.447 63.158 0.00 0.00 0.00 5.54
711 725 1.447314 GCGGTGGGAGTAACTTCGG 60.447 63.158 0.00 0.00 0.00 4.30
712 726 0.813184 TAGCGGTGGGAGTAACTTCG 59.187 55.000 0.00 0.00 0.00 3.79
713 727 1.823610 AGTAGCGGTGGGAGTAACTTC 59.176 52.381 0.00 0.00 0.00 3.01
714 728 1.934410 AGTAGCGGTGGGAGTAACTT 58.066 50.000 0.00 0.00 0.00 2.66
715 729 1.934410 AAGTAGCGGTGGGAGTAACT 58.066 50.000 0.00 0.00 0.00 2.24
716 730 2.740447 CAAAAGTAGCGGTGGGAGTAAC 59.260 50.000 0.00 0.00 0.00 2.50
717 731 2.872842 GCAAAAGTAGCGGTGGGAGTAA 60.873 50.000 0.00 0.00 0.00 2.24
718 732 1.338389 GCAAAAGTAGCGGTGGGAGTA 60.338 52.381 0.00 0.00 0.00 2.59
719 733 0.605589 GCAAAAGTAGCGGTGGGAGT 60.606 55.000 0.00 0.00 0.00 3.85
720 734 0.321653 AGCAAAAGTAGCGGTGGGAG 60.322 55.000 0.00 0.00 37.01 4.30
721 735 0.109723 AAGCAAAAGTAGCGGTGGGA 59.890 50.000 0.00 0.00 37.01 4.37
722 736 0.958822 AAAGCAAAAGTAGCGGTGGG 59.041 50.000 0.00 0.00 37.01 4.61
723 737 2.293399 AGAAAAGCAAAAGTAGCGGTGG 59.707 45.455 0.00 0.00 37.01 4.61
724 738 3.626028 AGAAAAGCAAAAGTAGCGGTG 57.374 42.857 0.00 0.00 37.01 4.94
725 739 4.097286 TCAAAGAAAAGCAAAAGTAGCGGT 59.903 37.500 0.00 0.00 37.01 5.68
726 740 4.606961 TCAAAGAAAAGCAAAAGTAGCGG 58.393 39.130 0.00 0.00 37.01 5.52
768 782 8.458843 GTGATGCCTACTGTTATGTTGTTATTT 58.541 33.333 0.00 0.00 0.00 1.40
793 837 1.873698 AACGCATTGTCCAGTAACGT 58.126 45.000 0.00 0.00 0.00 3.99
822 866 3.099141 ACTAATGGGCCCAAACATTCTG 58.901 45.455 32.58 16.47 38.24 3.02
925 980 1.006227 GGGGGAGGAAGAAGGGGAT 59.994 63.158 0.00 0.00 0.00 3.85
972 1032 2.050350 CGGCTAGGTTCTCCGTGGA 61.050 63.158 0.00 0.00 38.47 4.02
1734 1812 2.509166 ACATGTACGTGAGGAGGAGA 57.491 50.000 21.82 0.00 0.00 3.71
1924 2011 2.365582 GTTATGGTGGTGGTGGTGATC 58.634 52.381 0.00 0.00 0.00 2.92
1980 2067 1.064758 ACAAGAACCAGCAAGACCACA 60.065 47.619 0.00 0.00 0.00 4.17
2032 2119 2.899838 ACTTGTGCGGCGCTTTGA 60.900 55.556 33.26 9.91 0.00 2.69
2173 2260 1.954382 GAGAACCCCCTCAAACACAAC 59.046 52.381 0.00 0.00 33.50 3.32
2619 2706 1.330655 CGAGGTATCCCAGTGTGCCT 61.331 60.000 0.00 0.00 0.00 4.75
2676 2763 1.927174 CCGAAGCTGTAAACATCCGAG 59.073 52.381 0.00 0.00 0.00 4.63
2813 2900 1.594331 GACAAAACGTCCCTGAAGCT 58.406 50.000 0.00 0.00 38.85 3.74
2826 2913 1.442769 GCATCTCCTCTGCGACAAAA 58.557 50.000 0.00 0.00 0.00 2.44
3094 3181 7.148641 CAGATAGAACACCACTACATATGGAC 58.851 42.308 7.80 0.00 39.87 4.02
3215 3305 6.459161 CCAGTAGTAACCTTTCCAAACAACAC 60.459 42.308 0.00 0.00 0.00 3.32
3514 3605 4.808414 TCAACAATACAGCTACTCTGCT 57.192 40.909 0.00 0.00 46.76 4.24
3575 3666 5.221263 ACAGTGTAGAGCGAATACCATAAGG 60.221 44.000 0.00 0.00 42.21 2.69
3613 3704 2.223688 TGTGTTTTTCGCCTTCCATGTG 60.224 45.455 0.00 0.00 0.00 3.21
3623 3714 3.049912 GGAAATGGAGTGTGTTTTTCGC 58.950 45.455 0.00 0.00 0.00 4.70
3625 3716 7.886338 AGAATAGGAAATGGAGTGTGTTTTTC 58.114 34.615 0.00 0.00 0.00 2.29
3631 3722 6.824305 AACAAGAATAGGAAATGGAGTGTG 57.176 37.500 0.00 0.00 0.00 3.82
3635 3726 7.709149 AGGAAAACAAGAATAGGAAATGGAG 57.291 36.000 0.00 0.00 0.00 3.86
3662 3753 9.246670 AGAAATGTTTGGATCATCATACAAAGA 57.753 29.630 0.00 0.00 42.56 2.52
3692 3783 5.577945 GGCCACATTGTGTAAAATTCAGATG 59.422 40.000 15.34 0.00 0.00 2.90
3698 3789 3.556843 GGCAGGCCACATTGTGTAAAATT 60.557 43.478 15.34 0.00 35.81 1.82
3702 3793 1.240641 CGGCAGGCCACATTGTGTAA 61.241 55.000 15.34 0.00 35.37 2.41
3743 3835 0.250295 CAGGCCAAAACTGTCTCGGA 60.250 55.000 5.01 0.00 0.00 4.55
3746 3838 2.673368 CGATACAGGCCAAAACTGTCTC 59.327 50.000 5.01 1.23 45.50 3.36
3893 3987 6.952773 TTGAAACACAGCTAAGGTTACAAT 57.047 33.333 0.00 0.00 0.00 2.71
3952 4046 5.277490 GGAAGCTCAAAACAAAAATCAAGCC 60.277 40.000 0.00 0.00 0.00 4.35
3955 4049 5.290643 CACGGAAGCTCAAAACAAAAATCAA 59.709 36.000 0.00 0.00 0.00 2.57
3961 4055 1.474478 TGCACGGAAGCTCAAAACAAA 59.526 42.857 0.00 0.00 34.99 2.83
4027 4121 5.640189 AATGGTGAAATGCTGAAGAAGAG 57.360 39.130 0.00 0.00 0.00 2.85


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

AutoCloner maintained by Alex Coulton.