Multiple sequence alignment - TraesCS2B01G322400

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS2B01G322400 chr2B 100.000 4879 0 0 1 4879 460827886 460823008 0.000000e+00 9010
1 TraesCS2B01G322400 chr2B 76.180 445 74 18 1 422 217153616 217154051 7.110000e-49 206
2 TraesCS2B01G322400 chr2B 100.000 111 0 0 5306 5416 460822581 460822471 7.110000e-49 206
3 TraesCS2B01G322400 chrUn 94.407 2253 78 22 803 3034 291230716 291232941 0.000000e+00 3419
4 TraesCS2B01G322400 chr2A 94.407 2253 78 23 803 3034 525627190 525624965 0.000000e+00 3419
5 TraesCS2B01G322400 chr2A 94.959 1845 76 13 3030 4859 525617930 525616088 0.000000e+00 2876
6 TraesCS2B01G322400 chr2A 94.959 1845 76 10 3030 4859 525633127 525631285 0.000000e+00 2876
7 TraesCS2B01G322400 chr2A 98.198 111 2 0 5306 5416 525616042 525615932 1.540000e-45 195
8 TraesCS2B01G322400 chr2A 98.198 111 2 0 5306 5416 525631239 525631129 1.540000e-45 195
9 TraesCS2B01G322400 chr2D 91.146 2304 152 31 2006 4298 388833654 388831392 0.000000e+00 3077
10 TraesCS2B01G322400 chr2D 87.128 1243 96 28 686 1891 388835960 388834745 0.000000e+00 1351
11 TraesCS2B01G322400 chr2D 89.011 546 24 14 4347 4859 388831384 388830842 1.270000e-180 643
12 TraesCS2B01G322400 chr2D 99.099 111 1 0 5306 5416 388830778 388830668 3.310000e-47 200
13 TraesCS2B01G322400 chr6A 94.959 1845 76 10 3030 4859 422936971 422935129 0.000000e+00 2876
14 TraesCS2B01G322400 chr6A 98.198 111 2 0 5306 5416 422935083 422934973 1.540000e-45 195
15 TraesCS2B01G322400 chr3D 85.057 522 60 8 1 513 560082789 560082277 2.890000e-142 516
16 TraesCS2B01G322400 chr3B 82.510 526 63 13 1 504 161448968 161448450 8.330000e-118 435
17 TraesCS2B01G322400 chr3B 95.402 87 3 1 1910 1996 399973115 399973200 2.630000e-28 137
18 TraesCS2B01G322400 chr6D 84.108 409 49 11 3635 4037 470743847 470744245 1.100000e-101 381
19 TraesCS2B01G322400 chr5B 92.157 102 4 4 1896 1996 479726819 479726917 2.030000e-29 141
20 TraesCS2B01G322400 chr5D 95.455 88 3 1 1909 1996 399614518 399614604 7.310000e-29 139
21 TraesCS2B01G322400 chr4D 94.318 88 4 1 1909 1996 32019448 32019534 3.400000e-27 134
22 TraesCS2B01G322400 chr4D 94.318 88 4 1 1909 1996 32019630 32019716 3.400000e-27 134
23 TraesCS2B01G322400 chr3A 94.253 87 4 1 1910 1996 405691505 405691590 1.220000e-26 132
24 TraesCS2B01G322400 chr1B 94.253 87 4 1 1909 1995 264358060 264358145 1.220000e-26 132


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 TraesCS2B01G322400 chr2B 460822471 460827886 5415 True 4608.000000 9010 100.000000 1 5416 2 chr2B.!!$R1 5415
1 TraesCS2B01G322400 chrUn 291230716 291232941 2225 False 3419.000000 3419 94.407000 803 3034 1 chrUn.!!$F1 2231
2 TraesCS2B01G322400 chr2A 525624965 525633127 8162 True 2163.333333 3419 95.854667 803 5416 3 chr2A.!!$R2 4613
3 TraesCS2B01G322400 chr2A 525615932 525617930 1998 True 1535.500000 2876 96.578500 3030 5416 2 chr2A.!!$R1 2386
4 TraesCS2B01G322400 chr2D 388830668 388835960 5292 True 1317.750000 3077 91.596000 686 5416 4 chr2D.!!$R1 4730
5 TraesCS2B01G322400 chr6A 422934973 422936971 1998 True 1535.500000 2876 96.578500 3030 5416 2 chr6A.!!$R1 2386
6 TraesCS2B01G322400 chr3D 560082277 560082789 512 True 516.000000 516 85.057000 1 513 1 chr3D.!!$R1 512
7 TraesCS2B01G322400 chr3B 161448450 161448968 518 True 435.000000 435 82.510000 1 504 1 chr3B.!!$R1 503

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
205 206 0.035820 GGGAGGTTACCATGCGACAA 60.036 55.000 3.51 0.0 0.0 3.18 F
681 703 0.035820 TAAACCCTAGCCGCCAAGTG 60.036 55.000 0.00 0.0 0.0 3.16 F
830 852 0.996762 ACCAACCAACCTCTTCCCCA 60.997 55.000 0.00 0.0 0.0 4.96 F
991 1013 1.053424 TACTCTCACCAACCCACCAC 58.947 55.000 0.00 0.0 0.0 4.16 F
1303 1325 1.067416 GCGATCGGTGAGGTGCATA 59.933 57.895 18.30 0.0 0.0 3.14 F
2751 3804 0.890996 GTCTGACCTTTGCCCCACTG 60.891 60.000 0.00 0.0 0.0 3.66 F
3409 4465 0.253327 CACTTGGAAGGTCTAGGCCC 59.747 60.000 10.56 0.0 0.0 5.80 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1399 1421 0.317938 GCCGTGTCGCTATGAGGTAG 60.318 60.000 0.00 0.00 0.00 3.18 R
1583 1612 0.817634 TTGCGGTTTGTCCAGTGGAG 60.818 55.000 13.61 0.05 35.57 3.86 R
2511 3564 1.135859 GCTCCATGCTTCAGTTCAACG 60.136 52.381 0.00 0.00 38.95 4.10 R
2743 3796 1.689273 CCTAGACAGATACAGTGGGGC 59.311 57.143 0.00 0.00 0.00 5.80 R
3011 4064 0.036010 AGCAGTCAGGGGATGTTTCG 60.036 55.000 0.00 0.00 0.00 3.46 R
4182 5239 0.390492 CATGAGCCTCCGCATAGTCA 59.610 55.000 0.00 0.00 37.52 3.41 R
4609 5694 0.671781 CACCAAGCTGGAGAGGAACG 60.672 60.000 8.91 0.00 40.96 3.95 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
93 94 0.962356 CATCCTGGAAACGCAAGCCT 60.962 55.000 0.00 0.00 45.62 4.58
143 144 3.114809 CGACAATCAAAGCAAGCAACAA 58.885 40.909 0.00 0.00 0.00 2.83
147 148 0.822811 TCAAAGCAAGCAACAAGGCA 59.177 45.000 0.00 0.00 35.83 4.75
154 155 1.954362 AAGCAACAAGGCAACGGCAA 61.954 50.000 0.00 0.00 43.71 4.52
171 172 1.133853 GCAAGAAGATGGAGCAGGGAT 60.134 52.381 0.00 0.00 0.00 3.85
175 176 0.851469 AAGATGGAGCAGGGATGCAT 59.149 50.000 0.00 0.00 31.76 3.96
182 183 1.820519 GAGCAGGGATGCATCAACAAA 59.179 47.619 27.25 0.00 37.25 2.83
184 185 2.232941 AGCAGGGATGCATCAACAAAAG 59.767 45.455 27.25 10.75 37.25 2.27
188 189 1.207811 GGATGCATCAACAAAAGGGGG 59.792 52.381 27.25 0.00 0.00 5.40
192 193 1.827245 GCATCAACAAAAGGGGGAGGT 60.827 52.381 0.00 0.00 0.00 3.85
198 199 2.078611 ACAAAAGGGGGAGGTTACCAT 58.921 47.619 3.51 0.00 0.00 3.55
205 206 0.035820 GGGAGGTTACCATGCGACAA 60.036 55.000 3.51 0.00 0.00 3.18
210 211 2.147958 GGTTACCATGCGACAACAGAA 58.852 47.619 0.00 0.00 0.00 3.02
214 215 1.070758 ACCATGCGACAACAGAAGAGT 59.929 47.619 0.00 0.00 0.00 3.24
215 216 1.462283 CCATGCGACAACAGAAGAGTG 59.538 52.381 0.00 0.00 0.00 3.51
223 224 2.300437 ACAACAGAAGAGTGAGGCTACC 59.700 50.000 0.00 0.00 0.00 3.18
230 231 1.415659 AGAGTGAGGCTACCATGCATC 59.584 52.381 0.00 0.00 43.12 3.91
235 236 3.137446 GAGGCTACCATGCATCAAGAT 57.863 47.619 0.00 0.00 42.47 2.40
238 252 3.117776 AGGCTACCATGCATCAAGATCAA 60.118 43.478 0.00 0.00 34.04 2.57
248 262 4.202010 TGCATCAAGATCAACATGCATCAG 60.202 41.667 17.03 0.00 45.19 2.90
291 313 2.882324 GGCACCAACGAAAAACTTGAA 58.118 42.857 0.00 0.00 0.00 2.69
293 315 2.857748 GCACCAACGAAAAACTTGAAGG 59.142 45.455 0.00 0.00 0.00 3.46
295 317 4.739195 CACCAACGAAAAACTTGAAGGAA 58.261 39.130 0.00 0.00 0.00 3.36
296 318 4.798387 CACCAACGAAAAACTTGAAGGAAG 59.202 41.667 0.00 0.00 37.73 3.46
297 319 4.142249 ACCAACGAAAAACTTGAAGGAAGG 60.142 41.667 0.00 0.00 35.78 3.46
299 321 5.273944 CAACGAAAAACTTGAAGGAAGGAG 58.726 41.667 0.00 0.00 35.78 3.69
300 322 4.777463 ACGAAAAACTTGAAGGAAGGAGA 58.223 39.130 0.00 0.00 35.78 3.71
301 323 4.816925 ACGAAAAACTTGAAGGAAGGAGAG 59.183 41.667 0.00 0.00 35.78 3.20
302 324 4.816925 CGAAAAACTTGAAGGAAGGAGAGT 59.183 41.667 0.00 0.00 35.78 3.24
303 325 5.989777 CGAAAAACTTGAAGGAAGGAGAGTA 59.010 40.000 0.00 0.00 35.78 2.59
304 326 6.482308 CGAAAAACTTGAAGGAAGGAGAGTAA 59.518 38.462 0.00 0.00 35.78 2.24
305 327 7.518529 CGAAAAACTTGAAGGAAGGAGAGTAAC 60.519 40.741 0.00 0.00 35.78 2.50
336 358 3.048602 CGACGAGGAACCAGTGGT 58.951 61.111 9.70 9.70 37.65 4.16
506 528 4.910585 CGGCGGGGTATGCACTCC 62.911 72.222 0.00 0.00 42.59 3.85
513 535 1.301009 GGTATGCACTCCGCCTAGC 60.301 63.158 0.00 0.00 41.33 3.42
514 536 1.301009 GTATGCACTCCGCCTAGCC 60.301 63.158 0.00 0.00 41.33 3.93
515 537 2.507854 TATGCACTCCGCCTAGCCC 61.508 63.158 0.00 0.00 41.33 5.19
516 538 2.946988 TATGCACTCCGCCTAGCCCT 62.947 60.000 0.00 0.00 41.33 5.19
517 539 4.228567 GCACTCCGCCTAGCCCTC 62.229 72.222 0.00 0.00 32.94 4.30
518 540 2.759973 CACTCCGCCTAGCCCTCA 60.760 66.667 0.00 0.00 0.00 3.86
519 541 2.760385 ACTCCGCCTAGCCCTCAC 60.760 66.667 0.00 0.00 0.00 3.51
520 542 2.443016 CTCCGCCTAGCCCTCACT 60.443 66.667 0.00 0.00 0.00 3.41
521 543 2.038975 TCCGCCTAGCCCTCACTT 59.961 61.111 0.00 0.00 0.00 3.16
522 544 0.755698 CTCCGCCTAGCCCTCACTTA 60.756 60.000 0.00 0.00 0.00 2.24
523 545 0.105658 TCCGCCTAGCCCTCACTTAT 60.106 55.000 0.00 0.00 0.00 1.73
524 546 1.146359 TCCGCCTAGCCCTCACTTATA 59.854 52.381 0.00 0.00 0.00 0.98
525 547 2.180276 CCGCCTAGCCCTCACTTATAT 58.820 52.381 0.00 0.00 0.00 0.86
526 548 3.010920 TCCGCCTAGCCCTCACTTATATA 59.989 47.826 0.00 0.00 0.00 0.86
527 549 3.381908 CCGCCTAGCCCTCACTTATATAG 59.618 52.174 0.00 0.00 0.00 1.31
528 550 3.181485 CGCCTAGCCCTCACTTATATAGC 60.181 52.174 0.00 0.00 0.00 2.97
529 551 3.769844 GCCTAGCCCTCACTTATATAGCA 59.230 47.826 0.00 0.00 0.00 3.49
530 552 4.407296 GCCTAGCCCTCACTTATATAGCAT 59.593 45.833 0.00 0.00 0.00 3.79
531 553 5.598830 GCCTAGCCCTCACTTATATAGCATA 59.401 44.000 0.00 0.00 0.00 3.14
532 554 6.268847 GCCTAGCCCTCACTTATATAGCATAT 59.731 42.308 0.00 0.00 0.00 1.78
533 555 7.451877 GCCTAGCCCTCACTTATATAGCATATA 59.548 40.741 0.00 0.00 0.00 0.86
534 556 9.368416 CCTAGCCCTCACTTATATAGCATATAA 57.632 37.037 7.77 7.77 0.00 0.98
551 573 8.206325 AGCATATAATTGAGACACTTCAACTG 57.794 34.615 0.00 0.00 39.68 3.16
552 574 8.043113 AGCATATAATTGAGACACTTCAACTGA 58.957 33.333 0.00 0.00 39.68 3.41
553 575 8.668353 GCATATAATTGAGACACTTCAACTGAA 58.332 33.333 0.00 0.00 39.68 3.02
556 578 6.757897 AATTGAGACACTTCAACTGAAACA 57.242 33.333 0.00 0.00 39.68 2.83
557 579 6.757897 ATTGAGACACTTCAACTGAAACAA 57.242 33.333 0.00 0.00 39.68 2.83
558 580 5.545658 TGAGACACTTCAACTGAAACAAC 57.454 39.130 0.00 0.00 33.07 3.32
559 581 5.000591 TGAGACACTTCAACTGAAACAACA 58.999 37.500 0.00 0.00 33.07 3.33
560 582 5.647658 TGAGACACTTCAACTGAAACAACAT 59.352 36.000 0.00 0.00 33.07 2.71
561 583 6.821160 TGAGACACTTCAACTGAAACAACATA 59.179 34.615 0.00 0.00 33.07 2.29
562 584 7.011389 TGAGACACTTCAACTGAAACAACATAG 59.989 37.037 0.00 0.00 33.07 2.23
563 585 5.821204 ACACTTCAACTGAAACAACATAGC 58.179 37.500 0.00 0.00 33.07 2.97
564 586 5.356751 ACACTTCAACTGAAACAACATAGCA 59.643 36.000 0.00 0.00 33.07 3.49
565 587 6.039717 ACACTTCAACTGAAACAACATAGCAT 59.960 34.615 0.00 0.00 33.07 3.79
566 588 6.919662 CACTTCAACTGAAACAACATAGCATT 59.080 34.615 0.00 0.00 33.07 3.56
567 589 6.919662 ACTTCAACTGAAACAACATAGCATTG 59.080 34.615 0.00 0.00 33.07 2.82
568 590 6.389830 TCAACTGAAACAACATAGCATTGT 57.610 33.333 0.00 0.00 42.07 2.71
579 601 8.391075 ACAACATAGCATTGTTTGTAGTTACT 57.609 30.769 1.89 0.00 36.93 2.24
580 602 8.846211 ACAACATAGCATTGTTTGTAGTTACTT 58.154 29.630 1.89 0.00 36.93 2.24
581 603 9.677567 CAACATAGCATTGTTTGTAGTTACTTT 57.322 29.630 1.89 0.00 37.73 2.66
601 623 7.611213 ACTTTACATATGTTCTTACCACTGC 57.389 36.000 14.77 0.00 0.00 4.40
602 624 7.394816 ACTTTACATATGTTCTTACCACTGCT 58.605 34.615 14.77 0.00 0.00 4.24
603 625 7.883311 ACTTTACATATGTTCTTACCACTGCTT 59.117 33.333 14.77 0.00 0.00 3.91
604 626 8.630054 TTTACATATGTTCTTACCACTGCTTT 57.370 30.769 14.77 0.00 0.00 3.51
605 627 6.500684 ACATATGTTCTTACCACTGCTTTG 57.499 37.500 1.41 0.00 0.00 2.77
606 628 5.415701 ACATATGTTCTTACCACTGCTTTGG 59.584 40.000 1.41 2.85 43.04 3.28
607 629 3.569194 TGTTCTTACCACTGCTTTGGA 57.431 42.857 10.77 0.00 39.24 3.53
608 630 3.211045 TGTTCTTACCACTGCTTTGGAC 58.789 45.455 10.77 0.00 39.24 4.02
609 631 3.118038 TGTTCTTACCACTGCTTTGGACT 60.118 43.478 10.77 0.00 39.24 3.85
610 632 3.126001 TCTTACCACTGCTTTGGACTG 57.874 47.619 10.77 1.41 39.24 3.51
611 633 2.438021 TCTTACCACTGCTTTGGACTGT 59.562 45.455 10.77 0.00 39.24 3.55
612 634 3.644265 TCTTACCACTGCTTTGGACTGTA 59.356 43.478 10.77 0.00 39.24 2.74
613 635 4.101898 TCTTACCACTGCTTTGGACTGTAA 59.898 41.667 10.77 0.00 39.24 2.41
614 636 3.508845 ACCACTGCTTTGGACTGTAAT 57.491 42.857 10.77 0.00 39.24 1.89
615 637 4.634012 ACCACTGCTTTGGACTGTAATA 57.366 40.909 10.77 0.00 39.24 0.98
616 638 4.980573 ACCACTGCTTTGGACTGTAATAA 58.019 39.130 10.77 0.00 39.24 1.40
617 639 5.381757 ACCACTGCTTTGGACTGTAATAAA 58.618 37.500 10.77 0.00 39.24 1.40
618 640 5.473504 ACCACTGCTTTGGACTGTAATAAAG 59.526 40.000 10.77 0.00 39.24 1.85
621 643 4.371855 GCTTTGGACTGTAATAAAGCCC 57.628 45.455 17.81 0.00 45.56 5.19
622 644 4.017126 GCTTTGGACTGTAATAAAGCCCT 58.983 43.478 17.81 0.00 45.56 5.19
623 645 4.142381 GCTTTGGACTGTAATAAAGCCCTG 60.142 45.833 17.81 0.00 45.56 4.45
624 646 4.919774 TTGGACTGTAATAAAGCCCTGA 57.080 40.909 0.00 0.00 0.00 3.86
625 647 4.919774 TGGACTGTAATAAAGCCCTGAA 57.080 40.909 0.00 0.00 0.00 3.02
626 648 5.450818 TGGACTGTAATAAAGCCCTGAAT 57.549 39.130 0.00 0.00 0.00 2.57
627 649 5.826643 TGGACTGTAATAAAGCCCTGAATT 58.173 37.500 0.00 0.00 0.00 2.17
628 650 6.252995 TGGACTGTAATAAAGCCCTGAATTT 58.747 36.000 0.00 0.00 0.00 1.82
629 651 6.377146 TGGACTGTAATAAAGCCCTGAATTTC 59.623 38.462 0.00 0.00 0.00 2.17
630 652 6.377146 GGACTGTAATAAAGCCCTGAATTTCA 59.623 38.462 0.00 0.00 0.00 2.69
631 653 7.396540 ACTGTAATAAAGCCCTGAATTTCAG 57.603 36.000 17.78 17.78 43.91 3.02
632 654 6.948309 ACTGTAATAAAGCCCTGAATTTCAGT 59.052 34.615 21.75 8.30 42.80 3.41
633 655 7.451566 ACTGTAATAAAGCCCTGAATTTCAGTT 59.548 33.333 21.75 13.30 42.80 3.16
634 656 8.871629 TGTAATAAAGCCCTGAATTTCAGTTA 57.128 30.769 21.75 14.74 42.80 2.24
635 657 8.736244 TGTAATAAAGCCCTGAATTTCAGTTAC 58.264 33.333 21.75 19.54 42.80 2.50
636 658 4.766404 AAAGCCCTGAATTTCAGTTACG 57.234 40.909 21.75 8.95 42.80 3.18
637 659 3.418684 AGCCCTGAATTTCAGTTACGT 57.581 42.857 21.75 0.00 42.80 3.57
638 660 3.751518 AGCCCTGAATTTCAGTTACGTT 58.248 40.909 21.75 5.07 42.80 3.99
639 661 3.502211 AGCCCTGAATTTCAGTTACGTTG 59.498 43.478 21.75 7.42 42.80 4.10
640 662 3.365969 GCCCTGAATTTCAGTTACGTTGG 60.366 47.826 21.75 15.39 42.80 3.77
641 663 3.190535 CCCTGAATTTCAGTTACGTTGGG 59.809 47.826 21.75 12.22 42.80 4.12
642 664 3.365969 CCTGAATTTCAGTTACGTTGGGC 60.366 47.826 21.75 0.00 42.80 5.36
643 665 3.215151 TGAATTTCAGTTACGTTGGGCA 58.785 40.909 0.00 0.00 0.00 5.36
644 666 3.823873 TGAATTTCAGTTACGTTGGGCAT 59.176 39.130 0.00 0.00 0.00 4.40
645 667 4.083003 TGAATTTCAGTTACGTTGGGCATC 60.083 41.667 0.00 0.00 0.00 3.91
646 668 1.434555 TTCAGTTACGTTGGGCATCG 58.565 50.000 0.00 0.00 0.00 3.84
647 669 1.017177 TCAGTTACGTTGGGCATCGC 61.017 55.000 0.00 0.00 0.00 4.58
648 670 1.004320 AGTTACGTTGGGCATCGCA 60.004 52.632 0.00 0.00 0.00 5.10
649 671 0.392461 AGTTACGTTGGGCATCGCAT 60.392 50.000 0.00 0.00 0.00 4.73
650 672 0.450184 GTTACGTTGGGCATCGCATT 59.550 50.000 0.00 0.00 0.00 3.56
651 673 0.449786 TTACGTTGGGCATCGCATTG 59.550 50.000 0.00 0.00 0.00 2.82
652 674 0.675208 TACGTTGGGCATCGCATTGT 60.675 50.000 0.00 0.00 0.00 2.71
653 675 0.675208 ACGTTGGGCATCGCATTGTA 60.675 50.000 0.00 0.00 0.00 2.41
654 676 0.449786 CGTTGGGCATCGCATTGTAA 59.550 50.000 0.00 0.00 0.00 2.41
655 677 1.065401 CGTTGGGCATCGCATTGTAAT 59.935 47.619 0.00 0.00 0.00 1.89
656 678 2.731217 GTTGGGCATCGCATTGTAATC 58.269 47.619 0.00 0.00 0.00 1.75
657 679 2.049888 TGGGCATCGCATTGTAATCA 57.950 45.000 0.00 0.00 0.00 2.57
658 680 1.948834 TGGGCATCGCATTGTAATCAG 59.051 47.619 0.00 0.00 0.00 2.90
659 681 1.267806 GGGCATCGCATTGTAATCAGG 59.732 52.381 0.00 0.00 0.00 3.86
660 682 1.949525 GGCATCGCATTGTAATCAGGT 59.050 47.619 0.00 0.00 0.00 4.00
661 683 3.138304 GGCATCGCATTGTAATCAGGTA 58.862 45.455 0.00 0.00 0.00 3.08
662 684 3.753272 GGCATCGCATTGTAATCAGGTAT 59.247 43.478 0.00 0.00 0.00 2.73
663 685 4.935205 GGCATCGCATTGTAATCAGGTATA 59.065 41.667 0.00 0.00 0.00 1.47
664 686 5.411361 GGCATCGCATTGTAATCAGGTATAA 59.589 40.000 0.00 0.00 0.00 0.98
665 687 6.072728 GGCATCGCATTGTAATCAGGTATAAA 60.073 38.462 0.00 0.00 0.00 1.40
666 688 6.797033 GCATCGCATTGTAATCAGGTATAAAC 59.203 38.462 0.00 0.00 0.00 2.01
676 698 3.620061 GGTATAAACCCTAGCCGCC 57.380 57.895 0.00 0.00 40.21 6.13
677 699 0.760572 GGTATAAACCCTAGCCGCCA 59.239 55.000 0.00 0.00 40.21 5.69
678 700 1.141455 GGTATAAACCCTAGCCGCCAA 59.859 52.381 0.00 0.00 40.21 4.52
679 701 2.490991 GTATAAACCCTAGCCGCCAAG 58.509 52.381 0.00 0.00 0.00 3.61
680 702 0.916809 ATAAACCCTAGCCGCCAAGT 59.083 50.000 0.00 0.00 0.00 3.16
681 703 0.035820 TAAACCCTAGCCGCCAAGTG 60.036 55.000 0.00 0.00 0.00 3.16
682 704 2.764637 AAACCCTAGCCGCCAAGTGG 62.765 60.000 0.00 0.00 36.10 4.00
683 705 3.717294 CCCTAGCCGCCAAGTGGT 61.717 66.667 0.00 0.00 35.34 4.16
684 706 2.351276 CCTAGCCGCCAAGTGGTT 59.649 61.111 0.00 0.00 35.34 3.67
705 727 4.243793 TGGTCCACTTTCCTTTTCTTGA 57.756 40.909 0.00 0.00 0.00 3.02
706 728 3.951680 TGGTCCACTTTCCTTTTCTTGAC 59.048 43.478 0.00 0.00 0.00 3.18
745 767 1.368374 TTTCCCTCCAATTCGGGTCT 58.632 50.000 4.40 0.00 41.40 3.85
830 852 0.996762 ACCAACCAACCTCTTCCCCA 60.997 55.000 0.00 0.00 0.00 4.96
841 863 4.995058 TTCCCCAACCCCGAGCCT 62.995 66.667 0.00 0.00 0.00 4.58
947 969 3.160047 CCGCAGCTCCTCCCTCAT 61.160 66.667 0.00 0.00 0.00 2.90
991 1013 1.053424 TACTCTCACCAACCCACCAC 58.947 55.000 0.00 0.00 0.00 4.16
992 1014 1.073199 CTCTCACCAACCCACCACC 59.927 63.158 0.00 0.00 0.00 4.61
993 1015 2.115266 CTCACCAACCCACCACCC 59.885 66.667 0.00 0.00 0.00 4.61
994 1016 2.696504 TCACCAACCCACCACCCA 60.697 61.111 0.00 0.00 0.00 4.51
995 1017 2.080336 CTCACCAACCCACCACCCAT 62.080 60.000 0.00 0.00 0.00 4.00
996 1018 1.606313 CACCAACCCACCACCCATC 60.606 63.158 0.00 0.00 0.00 3.51
997 1019 2.088096 ACCAACCCACCACCCATCA 61.088 57.895 0.00 0.00 0.00 3.07
1177 1199 4.787280 CTCGGCCCTCCCAGGTCT 62.787 72.222 0.00 0.00 31.93 3.85
1184 1206 2.650116 CCTCCCAGGTCTGTGTCGG 61.650 68.421 0.00 0.00 0.00 4.79
1303 1325 1.067416 GCGATCGGTGAGGTGCATA 59.933 57.895 18.30 0.00 0.00 3.14
1399 1421 1.420138 CACCCCATCCTGGTATGGTAC 59.580 57.143 18.02 0.00 44.29 3.34
1400 1422 1.297141 ACCCCATCCTGGTATGGTACT 59.703 52.381 18.02 3.92 44.29 2.73
1401 1423 2.525310 ACCCCATCCTGGTATGGTACTA 59.475 50.000 18.02 0.00 44.29 1.82
1442 1464 2.169769 TGGCACGCTTTTAGGCTACTAT 59.830 45.455 0.00 0.00 0.00 2.12
1443 1465 3.385433 TGGCACGCTTTTAGGCTACTATA 59.615 43.478 0.00 0.00 0.00 1.31
1444 1466 3.739810 GGCACGCTTTTAGGCTACTATAC 59.260 47.826 0.00 0.00 0.00 1.47
1445 1467 4.501058 GGCACGCTTTTAGGCTACTATACT 60.501 45.833 0.00 0.00 0.00 2.12
1446 1468 5.278660 GGCACGCTTTTAGGCTACTATACTA 60.279 44.000 0.00 0.00 0.00 1.82
1447 1469 5.857517 GCACGCTTTTAGGCTACTATACTAG 59.142 44.000 0.00 0.00 0.00 2.57
1448 1470 6.380190 CACGCTTTTAGGCTACTATACTAGG 58.620 44.000 0.00 0.00 0.00 3.02
1583 1612 6.572519 TCAAAAAGGCTTGCCAACATATATC 58.427 36.000 14.54 0.00 0.00 1.63
1759 1806 6.085416 AGCCTAGCCCTACTATACTGAAAAT 58.915 40.000 0.00 0.00 0.00 1.82
1766 1813 7.661847 AGCCCTACTATACTGAAAATGTTATGC 59.338 37.037 0.00 0.00 0.00 3.14
1850 1909 8.595362 TCAGGATATGAGAAGACTTCAGTTAA 57.405 34.615 17.34 0.00 32.77 2.01
1863 1922 8.045176 AGACTTCAGTTAATTAGCCATCAAAC 57.955 34.615 0.00 0.00 0.00 2.93
1974 2340 2.504175 TGGGGAAGGGAATTTCTAGACG 59.496 50.000 0.00 0.00 0.00 4.18
1975 2341 2.770232 GGGGAAGGGAATTTCTAGACGA 59.230 50.000 0.00 0.00 0.00 4.20
1976 2342 3.199289 GGGGAAGGGAATTTCTAGACGAA 59.801 47.826 0.00 0.00 0.00 3.85
1980 2346 5.489249 GAAGGGAATTTCTAGACGAACCTT 58.511 41.667 12.28 12.28 37.19 3.50
2051 3086 4.604843 ATGTTGCATCGACATTACACAG 57.395 40.909 0.00 0.00 35.15 3.66
2080 3116 6.538021 AGAGCATTATCAACTGCACTCTTTAG 59.462 38.462 0.00 0.00 40.88 1.85
2081 3117 6.176183 AGCATTATCAACTGCACTCTTTAGT 58.824 36.000 0.00 0.00 40.88 2.24
2083 3119 6.314896 GCATTATCAACTGCACTCTTTAGTCT 59.685 38.462 0.00 0.00 38.28 3.24
2084 3120 7.148340 GCATTATCAACTGCACTCTTTAGTCTT 60.148 37.037 0.00 0.00 38.28 3.01
2085 3121 8.725148 CATTATCAACTGCACTCTTTAGTCTTT 58.275 33.333 0.00 0.00 31.97 2.52
2087 3123 9.944376 TTATCAACTGCACTCTTTAGTCTTTAT 57.056 29.630 0.00 0.00 31.97 1.40
2088 3124 7.658179 TCAACTGCACTCTTTAGTCTTTATG 57.342 36.000 0.00 0.00 31.97 1.90
2090 3126 5.551233 ACTGCACTCTTTAGTCTTTATGCA 58.449 37.500 0.00 0.00 31.97 3.96
2091 3127 5.641209 ACTGCACTCTTTAGTCTTTATGCAG 59.359 40.000 18.52 18.52 44.61 4.41
2092 3128 5.793817 TGCACTCTTTAGTCTTTATGCAGA 58.206 37.500 0.00 0.00 31.97 4.26
2093 3129 5.639506 TGCACTCTTTAGTCTTTATGCAGAC 59.360 40.000 0.00 0.00 43.26 3.51
2192 3238 2.727123 TCTTTCCAGTTGGCAGTCAA 57.273 45.000 0.00 0.00 34.44 3.18
2241 3287 3.181493 CCATCTGTCCAAATAAGCACTGC 60.181 47.826 0.00 0.00 0.00 4.40
2317 3363 3.758023 TGCAACTACTTAGTGCAATGCAT 59.242 39.130 12.38 3.24 39.81 3.96
2341 3387 3.259625 GGTACAGGGCCATTTTTGCTTTA 59.740 43.478 6.18 0.00 0.00 1.85
2487 3540 3.612247 CTGGCCAGAACGAGGTGGG 62.612 68.421 29.88 0.00 34.06 4.61
2511 3564 7.258441 GGGCTAATGGAAGTTTAAGATTTGAC 58.742 38.462 0.00 0.00 0.00 3.18
2560 3613 3.273434 GGTACGGTTACCTGGATTTTCC 58.727 50.000 0.00 0.00 44.24 3.13
2562 3615 1.339342 ACGGTTACCTGGATTTTCCCG 60.339 52.381 0.00 5.64 35.03 5.14
2662 3715 1.882623 GCTCTAAAGCTTGTGCAACCT 59.117 47.619 0.00 0.00 45.55 3.50
2751 3804 0.890996 GTCTGACCTTTGCCCCACTG 60.891 60.000 0.00 0.00 0.00 3.66
2926 3979 3.948473 GGGAAGCTTCCTGGTTAGAAATC 59.052 47.826 37.72 17.61 46.72 2.17
2939 3992 5.769662 TGGTTAGAAATCTTGTTCACTGCAT 59.230 36.000 0.00 0.00 0.00 3.96
2947 4000 3.691118 TCTTGTTCACTGCATATTCCAGC 59.309 43.478 0.00 0.00 33.65 4.85
2950 4003 2.229675 TCACTGCATATTCCAGCTCG 57.770 50.000 0.00 0.00 33.65 5.03
2952 4005 2.093500 TCACTGCATATTCCAGCTCGTT 60.093 45.455 0.00 0.00 33.65 3.85
2957 4010 2.420022 GCATATTCCAGCTCGTTGTGTT 59.580 45.455 0.00 0.00 0.00 3.32
2958 4011 3.485877 GCATATTCCAGCTCGTTGTGTTC 60.486 47.826 0.00 0.00 0.00 3.18
3101 4156 2.296752 CCATCACCACATCAAAAGCACA 59.703 45.455 0.00 0.00 0.00 4.57
3322 4378 1.202675 CCTGTTTGCCCATGCTGTTTT 60.203 47.619 0.00 0.00 38.71 2.43
3349 4405 1.071502 CGTTGTTGAGCTGTGTGTACG 60.072 52.381 0.00 0.00 0.00 3.67
3409 4465 0.253327 CACTTGGAAGGTCTAGGCCC 59.747 60.000 10.56 0.00 0.00 5.80
3477 4533 8.896320 TGCTGTTCTTAACTTTTCTGTGTATA 57.104 30.769 0.00 0.00 0.00 1.47
3576 4632 9.935241 TGCTGGAAATTTGCATACTTAAAATTA 57.065 25.926 13.13 0.00 33.51 1.40
3610 4666 1.896220 TTGGGAACTAGCTGTGCTTG 58.104 50.000 0.00 0.00 40.44 4.01
3666 4722 7.615582 TCTTAGCCTTTGTTTACATCTGATG 57.384 36.000 15.83 15.83 0.00 3.07
3687 4743 4.847198 TGGTGTCAGTTGAGATATGCAAT 58.153 39.130 0.00 0.00 0.00 3.56
3688 4744 5.255687 TGGTGTCAGTTGAGATATGCAATT 58.744 37.500 0.00 0.00 0.00 2.32
3689 4745 5.711506 TGGTGTCAGTTGAGATATGCAATTT 59.288 36.000 0.00 0.00 0.00 1.82
3690 4746 6.209192 TGGTGTCAGTTGAGATATGCAATTTT 59.791 34.615 0.00 0.00 0.00 1.82
3691 4747 7.092716 GGTGTCAGTTGAGATATGCAATTTTT 58.907 34.615 0.00 0.00 0.00 1.94
3735 4791 3.584834 ACCCGCTTCAAAACATTAATGC 58.415 40.909 15.48 0.00 0.00 3.56
4091 5148 2.625790 GTTCTCGGCATCCTATGAGAGT 59.374 50.000 10.48 0.00 38.59 3.24
4117 5174 7.828717 TGAAATAATTCCTGAACTGACTGCATA 59.171 33.333 0.00 0.00 34.49 3.14
4354 5414 6.248433 TCTCTGCTTTTGATCCAACCTTATT 58.752 36.000 0.00 0.00 0.00 1.40
4476 5536 5.385198 ACACACTTCCAAAAGGTACATCAT 58.615 37.500 0.00 0.00 36.78 2.45
4482 5542 4.116113 TCCAAAAGGTACATCATACCCCT 58.884 43.478 0.00 0.00 38.33 4.79
4585 5670 1.758514 GATCCCTCGCAGGACCAGA 60.759 63.158 4.00 0.00 39.24 3.86
4609 5694 2.747446 ACGGCACAACTTAATCACCATC 59.253 45.455 0.00 0.00 0.00 3.51
4702 5787 9.103861 GTACAAGATAGAGATTTTCCTTTCCAG 57.896 37.037 0.00 0.00 0.00 3.86
4800 5893 0.037326 TGTGAACCTGCTCCGATGAC 60.037 55.000 0.00 0.00 0.00 3.06
4859 5953 2.124193 TGCCTGTGCAGTGCTGTT 60.124 55.556 17.60 0.00 44.23 3.16
4860 5954 2.188829 TGCCTGTGCAGTGCTGTTC 61.189 57.895 17.60 5.08 44.23 3.18
4861 5955 2.912624 GCCTGTGCAGTGCTGTTCC 61.913 63.158 17.60 0.00 37.47 3.62
4866 5960 4.030452 GCAGTGCTGTTCCGTGCC 62.030 66.667 8.18 0.00 0.00 5.01
4869 5963 4.012895 GTGCTGTTCCGTGCCGTG 62.013 66.667 0.00 0.00 0.00 4.94
4872 5966 3.716006 CTGTTCCGTGCCGTGCTG 61.716 66.667 0.00 0.00 0.00 4.41
4874 5968 3.712881 GTTCCGTGCCGTGCTGTC 61.713 66.667 0.00 0.00 0.00 3.51
4875 5969 4.228567 TTCCGTGCCGTGCTGTCA 62.229 61.111 0.00 0.00 0.00 3.58
4876 5970 3.529341 TTCCGTGCCGTGCTGTCAT 62.529 57.895 0.00 0.00 0.00 3.06
4878 5972 2.616330 CCGTGCCGTGCTGTCATTT 61.616 57.895 0.00 0.00 0.00 2.32
5360 6454 2.201830 CATAAACCCCTGGACCCTACA 58.798 52.381 0.00 0.00 0.00 2.74
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
19 20 2.124529 TGTTGCTGGTCGTTGCCA 60.125 55.556 0.00 0.00 36.97 4.92
20 21 2.639286 CTGTTGCTGGTCGTTGCC 59.361 61.111 0.00 0.00 0.00 4.52
24 25 2.031163 GAGGCTGTTGCTGGTCGT 59.969 61.111 0.00 0.00 39.59 4.34
106 107 1.913262 TCGCTCTGGTGGACCATGT 60.913 57.895 0.00 0.00 46.46 3.21
111 112 0.037326 TGATTGTCGCTCTGGTGGAC 60.037 55.000 0.00 0.00 0.00 4.02
118 119 1.198637 GCTTGCTTTGATTGTCGCTCT 59.801 47.619 0.00 0.00 0.00 4.09
143 144 0.962356 CCATCTTCTTGCCGTTGCCT 60.962 55.000 0.00 0.00 36.33 4.75
147 148 0.036732 TGCTCCATCTTCTTGCCGTT 59.963 50.000 0.00 0.00 0.00 4.44
154 155 0.473326 GCATCCCTGCTCCATCTTCT 59.527 55.000 0.00 0.00 45.32 2.85
171 172 1.631405 CTCCCCCTTTTGTTGATGCA 58.369 50.000 0.00 0.00 0.00 3.96
175 176 2.158430 GGTAACCTCCCCCTTTTGTTGA 60.158 50.000 0.00 0.00 0.00 3.18
182 183 1.921869 CGCATGGTAACCTCCCCCTT 61.922 60.000 0.00 0.00 0.00 3.95
184 185 2.192175 CGCATGGTAACCTCCCCC 59.808 66.667 0.00 0.00 0.00 5.40
188 189 1.732259 CTGTTGTCGCATGGTAACCTC 59.268 52.381 0.00 0.00 0.00 3.85
192 193 3.244078 ACTCTTCTGTTGTCGCATGGTAA 60.244 43.478 0.00 0.00 0.00 2.85
198 199 1.269778 CCTCACTCTTCTGTTGTCGCA 60.270 52.381 0.00 0.00 0.00 5.10
205 206 2.310779 TGGTAGCCTCACTCTTCTGT 57.689 50.000 0.00 0.00 0.00 3.41
210 211 1.415659 GATGCATGGTAGCCTCACTCT 59.584 52.381 2.46 0.00 0.00 3.24
214 215 1.839354 TCTTGATGCATGGTAGCCTCA 59.161 47.619 2.46 0.00 37.37 3.86
215 216 2.627515 TCTTGATGCATGGTAGCCTC 57.372 50.000 2.46 0.00 0.00 4.70
223 224 4.040445 TGCATGTTGATCTTGATGCATG 57.960 40.909 2.46 11.84 44.75 4.06
230 231 2.223735 GCCCTGATGCATGTTGATCTTG 60.224 50.000 2.46 0.00 0.00 3.02
235 236 0.322366 TTCGCCCTGATGCATGTTGA 60.322 50.000 2.46 0.00 0.00 3.18
238 252 1.660560 GCTTTCGCCCTGATGCATGT 61.661 55.000 2.46 0.00 0.00 3.21
248 262 2.114670 TATGCAGCAGCTTTCGCCC 61.115 57.895 0.00 0.00 42.74 6.13
265 287 0.183014 TTTTCGTTGGTGCCCAGGTA 59.817 50.000 0.00 0.00 33.81 3.08
287 309 5.399991 TGGTAGTTACTCTCCTTCCTTCAA 58.600 41.667 7.71 0.00 0.00 2.69
291 313 3.367321 GCTGGTAGTTACTCTCCTTCCT 58.633 50.000 7.71 0.00 0.00 3.36
293 315 2.099427 CGGCTGGTAGTTACTCTCCTTC 59.901 54.545 7.71 1.32 0.00 3.46
295 317 1.685491 CCGGCTGGTAGTTACTCTCCT 60.685 57.143 2.29 0.00 0.00 3.69
296 318 0.745468 CCGGCTGGTAGTTACTCTCC 59.255 60.000 2.29 0.00 0.00 3.71
297 319 0.102663 GCCGGCTGGTAGTTACTCTC 59.897 60.000 22.15 0.00 37.67 3.20
299 321 1.226888 CGCCGGCTGGTAGTTACTC 60.227 63.158 26.68 0.00 37.67 2.59
300 322 2.718073 CCGCCGGCTGGTAGTTACT 61.718 63.158 26.68 0.00 37.67 2.24
301 323 2.202837 CCGCCGGCTGGTAGTTAC 60.203 66.667 26.68 0.00 37.67 2.50
302 324 4.151582 GCCGCCGGCTGGTAGTTA 62.152 66.667 29.37 0.00 46.69 2.24
330 352 2.357034 CCGTTCCGACCACCACTG 60.357 66.667 0.00 0.00 0.00 3.66
336 358 1.865788 CGTTAGACCCGTTCCGACCA 61.866 60.000 0.00 0.00 0.00 4.02
366 388 1.480219 GCTACGGTGTGCACTATCGC 61.480 60.000 19.41 9.27 0.00 4.58
370 392 1.589630 CCAGCTACGGTGTGCACTA 59.410 57.895 19.41 1.23 0.00 2.74
371 393 2.343758 CCAGCTACGGTGTGCACT 59.656 61.111 19.41 0.00 0.00 4.40
414 436 3.723348 GCCACCAAACCGTCGCTC 61.723 66.667 0.00 0.00 0.00 5.03
504 526 0.105658 ATAAGTGAGGGCTAGGCGGA 60.106 55.000 10.58 0.00 0.00 5.54
505 527 1.629043 TATAAGTGAGGGCTAGGCGG 58.371 55.000 10.58 0.00 0.00 6.13
506 528 3.181485 GCTATATAAGTGAGGGCTAGGCG 60.181 52.174 10.58 0.00 0.00 5.52
507 529 3.769844 TGCTATATAAGTGAGGGCTAGGC 59.230 47.826 8.00 8.00 0.00 3.93
525 547 9.317936 CAGTTGAAGTGTCTCAATTATATGCTA 57.682 33.333 0.00 0.00 37.63 3.49
526 548 8.043113 TCAGTTGAAGTGTCTCAATTATATGCT 58.957 33.333 0.00 0.00 37.63 3.79
527 549 8.201554 TCAGTTGAAGTGTCTCAATTATATGC 57.798 34.615 0.00 0.00 37.63 3.14
530 552 9.554395 TGTTTCAGTTGAAGTGTCTCAATTATA 57.446 29.630 0.00 0.00 37.63 0.98
531 553 8.450578 TGTTTCAGTTGAAGTGTCTCAATTAT 57.549 30.769 0.00 0.00 37.63 1.28
532 554 7.857734 TGTTTCAGTTGAAGTGTCTCAATTA 57.142 32.000 0.00 0.00 37.63 1.40
533 555 6.757897 TGTTTCAGTTGAAGTGTCTCAATT 57.242 33.333 0.00 0.00 37.63 2.32
534 556 6.150976 TGTTGTTTCAGTTGAAGTGTCTCAAT 59.849 34.615 0.00 0.00 37.63 2.57
535 557 5.471797 TGTTGTTTCAGTTGAAGTGTCTCAA 59.528 36.000 0.00 2.14 35.21 3.02
536 558 5.000591 TGTTGTTTCAGTTGAAGTGTCTCA 58.999 37.500 0.00 0.00 35.21 3.27
537 559 5.545658 TGTTGTTTCAGTTGAAGTGTCTC 57.454 39.130 0.00 0.00 35.21 3.36
538 560 6.238484 GCTATGTTGTTTCAGTTGAAGTGTCT 60.238 38.462 0.00 0.00 35.21 3.41
539 561 5.909610 GCTATGTTGTTTCAGTTGAAGTGTC 59.090 40.000 0.00 0.00 35.21 3.67
540 562 5.356751 TGCTATGTTGTTTCAGTTGAAGTGT 59.643 36.000 0.00 0.00 35.21 3.55
541 563 5.820131 TGCTATGTTGTTTCAGTTGAAGTG 58.180 37.500 0.00 0.00 35.21 3.16
542 564 6.639632 ATGCTATGTTGTTTCAGTTGAAGT 57.360 33.333 0.00 0.00 35.21 3.01
543 565 6.919662 ACAATGCTATGTTGTTTCAGTTGAAG 59.080 34.615 0.00 0.00 36.44 3.02
544 566 6.804677 ACAATGCTATGTTGTTTCAGTTGAA 58.195 32.000 0.00 0.00 36.44 2.69
545 567 6.389830 ACAATGCTATGTTGTTTCAGTTGA 57.610 33.333 0.00 0.00 36.44 3.18
554 576 8.391075 AGTAACTACAAACAATGCTATGTTGT 57.609 30.769 8.18 10.22 42.49 3.32
555 577 9.677567 AAAGTAACTACAAACAATGCTATGTTG 57.322 29.630 8.18 6.01 42.49 3.33
575 597 9.158233 GCAGTGGTAAGAACATATGTAAAGTAA 57.842 33.333 9.21 0.00 0.00 2.24
576 598 8.537016 AGCAGTGGTAAGAACATATGTAAAGTA 58.463 33.333 9.21 0.00 0.00 2.24
577 599 7.394816 AGCAGTGGTAAGAACATATGTAAAGT 58.605 34.615 9.21 0.00 0.00 2.66
578 600 7.849804 AGCAGTGGTAAGAACATATGTAAAG 57.150 36.000 9.21 0.00 0.00 1.85
579 601 8.511321 CAAAGCAGTGGTAAGAACATATGTAAA 58.489 33.333 9.21 0.00 0.00 2.01
580 602 7.120579 CCAAAGCAGTGGTAAGAACATATGTAA 59.879 37.037 9.21 0.00 33.63 2.41
581 603 6.597672 CCAAAGCAGTGGTAAGAACATATGTA 59.402 38.462 9.21 0.00 33.63 2.29
582 604 5.415701 CCAAAGCAGTGGTAAGAACATATGT 59.584 40.000 1.41 1.41 33.63 2.29
583 605 5.647658 TCCAAAGCAGTGGTAAGAACATATG 59.352 40.000 0.00 0.00 39.88 1.78
584 606 5.648092 GTCCAAAGCAGTGGTAAGAACATAT 59.352 40.000 0.00 0.00 39.88 1.78
585 607 5.001232 GTCCAAAGCAGTGGTAAGAACATA 58.999 41.667 0.00 0.00 39.88 2.29
586 608 3.821033 GTCCAAAGCAGTGGTAAGAACAT 59.179 43.478 0.00 0.00 39.88 2.71
587 609 3.118038 AGTCCAAAGCAGTGGTAAGAACA 60.118 43.478 0.00 0.00 39.88 3.18
588 610 3.251004 CAGTCCAAAGCAGTGGTAAGAAC 59.749 47.826 0.00 0.00 39.88 3.01
589 611 3.118038 ACAGTCCAAAGCAGTGGTAAGAA 60.118 43.478 0.00 0.00 39.88 2.52
590 612 2.438021 ACAGTCCAAAGCAGTGGTAAGA 59.562 45.455 0.00 0.00 39.88 2.10
591 613 2.851195 ACAGTCCAAAGCAGTGGTAAG 58.149 47.619 0.00 0.00 39.88 2.34
592 614 4.425180 TTACAGTCCAAAGCAGTGGTAA 57.575 40.909 0.00 0.00 39.88 2.85
593 615 4.634012 ATTACAGTCCAAAGCAGTGGTA 57.366 40.909 0.00 0.00 39.88 3.25
594 616 3.508845 ATTACAGTCCAAAGCAGTGGT 57.491 42.857 5.66 0.00 39.88 4.16
595 617 5.942872 CTTTATTACAGTCCAAAGCAGTGG 58.057 41.667 0.00 0.00 40.33 4.00
601 623 5.253330 TCAGGGCTTTATTACAGTCCAAAG 58.747 41.667 3.45 0.00 38.65 2.77
602 624 5.249780 TCAGGGCTTTATTACAGTCCAAA 57.750 39.130 3.45 0.00 38.65 3.28
603 625 4.919774 TCAGGGCTTTATTACAGTCCAA 57.080 40.909 3.45 0.00 38.65 3.53
604 626 4.919774 TTCAGGGCTTTATTACAGTCCA 57.080 40.909 3.45 0.00 38.65 4.02
605 627 6.377146 TGAAATTCAGGGCTTTATTACAGTCC 59.623 38.462 0.00 0.00 36.12 3.85
606 628 7.391148 TGAAATTCAGGGCTTTATTACAGTC 57.609 36.000 0.00 0.00 0.00 3.51
607 629 7.396540 CTGAAATTCAGGGCTTTATTACAGT 57.603 36.000 14.85 0.00 40.71 3.55
622 644 3.215151 TGCCCAACGTAACTGAAATTCA 58.785 40.909 0.00 0.00 0.00 2.57
623 645 3.907894 TGCCCAACGTAACTGAAATTC 57.092 42.857 0.00 0.00 0.00 2.17
624 646 3.119990 CGATGCCCAACGTAACTGAAATT 60.120 43.478 0.00 0.00 0.00 1.82
625 647 2.418628 CGATGCCCAACGTAACTGAAAT 59.581 45.455 0.00 0.00 0.00 2.17
626 648 1.801771 CGATGCCCAACGTAACTGAAA 59.198 47.619 0.00 0.00 0.00 2.69
627 649 1.434555 CGATGCCCAACGTAACTGAA 58.565 50.000 0.00 0.00 0.00 3.02
628 650 1.017177 GCGATGCCCAACGTAACTGA 61.017 55.000 0.00 0.00 0.00 3.41
629 651 1.295357 TGCGATGCCCAACGTAACTG 61.295 55.000 0.00 0.00 0.00 3.16
630 652 0.392461 ATGCGATGCCCAACGTAACT 60.392 50.000 0.00 0.00 0.00 2.24
631 653 0.450184 AATGCGATGCCCAACGTAAC 59.550 50.000 0.00 0.00 0.00 2.50
632 654 0.449786 CAATGCGATGCCCAACGTAA 59.550 50.000 0.00 0.00 0.00 3.18
633 655 0.675208 ACAATGCGATGCCCAACGTA 60.675 50.000 0.00 0.00 0.00 3.57
634 656 0.675208 TACAATGCGATGCCCAACGT 60.675 50.000 0.00 0.00 0.00 3.99
635 657 0.449786 TTACAATGCGATGCCCAACG 59.550 50.000 0.00 0.00 0.00 4.10
636 658 2.098934 TGATTACAATGCGATGCCCAAC 59.901 45.455 0.00 0.00 0.00 3.77
637 659 2.358582 CTGATTACAATGCGATGCCCAA 59.641 45.455 0.00 0.00 0.00 4.12
638 660 1.948834 CTGATTACAATGCGATGCCCA 59.051 47.619 0.00 0.00 0.00 5.36
639 661 1.267806 CCTGATTACAATGCGATGCCC 59.732 52.381 0.00 0.00 0.00 5.36
640 662 1.949525 ACCTGATTACAATGCGATGCC 59.050 47.619 0.00 0.00 0.00 4.40
641 663 6.480524 TTATACCTGATTACAATGCGATGC 57.519 37.500 0.00 0.00 0.00 3.91
642 664 7.298122 GGTTTATACCTGATTACAATGCGATG 58.702 38.462 0.00 0.00 41.53 3.84
643 665 6.430000 GGGTTTATACCTGATTACAATGCGAT 59.570 38.462 2.17 0.00 44.38 4.58
644 666 5.761234 GGGTTTATACCTGATTACAATGCGA 59.239 40.000 2.17 0.00 44.38 5.10
645 667 5.763204 AGGGTTTATACCTGATTACAATGCG 59.237 40.000 2.17 0.00 44.38 4.73
646 668 7.094762 GCTAGGGTTTATACCTGATTACAATGC 60.095 40.741 2.17 0.00 44.38 3.56
647 669 7.390718 GGCTAGGGTTTATACCTGATTACAATG 59.609 40.741 2.17 0.00 44.38 2.82
648 670 7.459234 GGCTAGGGTTTATACCTGATTACAAT 58.541 38.462 2.17 0.00 44.38 2.71
649 671 6.463331 CGGCTAGGGTTTATACCTGATTACAA 60.463 42.308 2.17 0.00 44.38 2.41
650 672 5.011329 CGGCTAGGGTTTATACCTGATTACA 59.989 44.000 2.17 0.00 44.38 2.41
651 673 5.476614 CGGCTAGGGTTTATACCTGATTAC 58.523 45.833 2.17 0.00 44.38 1.89
652 674 4.020839 GCGGCTAGGGTTTATACCTGATTA 60.021 45.833 2.17 0.00 44.38 1.75
653 675 3.244457 GCGGCTAGGGTTTATACCTGATT 60.244 47.826 2.17 0.00 44.38 2.57
654 676 2.302157 GCGGCTAGGGTTTATACCTGAT 59.698 50.000 2.17 0.00 44.38 2.90
655 677 1.690352 GCGGCTAGGGTTTATACCTGA 59.310 52.381 2.17 0.00 44.38 3.86
656 678 1.270678 GGCGGCTAGGGTTTATACCTG 60.271 57.143 0.00 0.00 44.38 4.00
657 679 1.054231 GGCGGCTAGGGTTTATACCT 58.946 55.000 0.00 0.00 44.38 3.08
658 680 0.760572 TGGCGGCTAGGGTTTATACC 59.239 55.000 11.43 0.00 44.22 2.73
659 681 2.158856 ACTTGGCGGCTAGGGTTTATAC 60.159 50.000 23.01 0.00 0.00 1.47
660 682 2.121129 ACTTGGCGGCTAGGGTTTATA 58.879 47.619 23.01 0.00 0.00 0.98
661 683 0.916809 ACTTGGCGGCTAGGGTTTAT 59.083 50.000 23.01 0.00 0.00 1.40
662 684 0.035820 CACTTGGCGGCTAGGGTTTA 60.036 55.000 23.01 0.00 0.00 2.01
663 685 1.303317 CACTTGGCGGCTAGGGTTT 60.303 57.895 23.01 0.49 0.00 3.27
664 686 2.351276 CACTTGGCGGCTAGGGTT 59.649 61.111 23.01 0.86 0.00 4.11
665 687 3.717294 CCACTTGGCGGCTAGGGT 61.717 66.667 23.01 7.94 0.00 4.34
666 688 3.268103 AACCACTTGGCGGCTAGGG 62.268 63.158 23.01 19.55 39.32 3.53
667 689 2.040544 CAACCACTTGGCGGCTAGG 61.041 63.158 23.01 14.99 39.32 3.02
668 690 2.040544 CCAACCACTTGGCGGCTAG 61.041 63.158 18.31 18.31 40.79 3.42
669 691 2.033448 CCAACCACTTGGCGGCTA 59.967 61.111 11.43 0.46 40.79 3.93
681 703 3.296854 AGAAAAGGAAAGTGGACCAACC 58.703 45.455 0.00 0.00 39.54 3.77
682 704 4.401202 TCAAGAAAAGGAAAGTGGACCAAC 59.599 41.667 0.00 0.00 0.00 3.77
683 705 4.401202 GTCAAGAAAAGGAAAGTGGACCAA 59.599 41.667 0.00 0.00 0.00 3.67
684 706 3.951680 GTCAAGAAAAGGAAAGTGGACCA 59.048 43.478 0.00 0.00 0.00 4.02
705 727 0.953003 GCTCGCTAGGGTTCTATCGT 59.047 55.000 6.70 0.00 36.72 3.73
706 728 1.240256 AGCTCGCTAGGGTTCTATCG 58.760 55.000 6.70 0.00 36.70 2.92
721 743 1.745653 CCGAATTGGAGGGAAAAGCTC 59.254 52.381 0.00 0.00 42.00 4.09
947 969 1.128809 TAGACCGTGGCCCTTTGGAA 61.129 55.000 0.00 0.00 0.00 3.53
971 993 1.418637 GTGGTGGGTTGGTGAGAGTAA 59.581 52.381 0.00 0.00 0.00 2.24
993 1015 3.646976 CGCTCGGCCATGCTGATG 61.647 66.667 13.96 0.00 43.40 3.07
994 1016 4.166888 ACGCTCGGCCATGCTGAT 62.167 61.111 13.96 0.00 43.40 2.90
995 1017 4.819761 GACGCTCGGCCATGCTGA 62.820 66.667 13.96 0.00 42.08 4.26
996 1018 4.827087 AGACGCTCGGCCATGCTG 62.827 66.667 13.96 10.17 36.06 4.41
997 1019 4.521062 GAGACGCTCGGCCATGCT 62.521 66.667 13.96 2.79 0.00 3.79
1177 1199 1.667151 CCCGAACCTAACCGACACA 59.333 57.895 0.00 0.00 0.00 3.72
1399 1421 0.317938 GCCGTGTCGCTATGAGGTAG 60.318 60.000 0.00 0.00 0.00 3.18
1400 1422 1.731700 GCCGTGTCGCTATGAGGTA 59.268 57.895 0.00 0.00 0.00 3.08
1401 1423 2.494918 GCCGTGTCGCTATGAGGT 59.505 61.111 0.00 0.00 0.00 3.85
1583 1612 0.817634 TTGCGGTTTGTCCAGTGGAG 60.818 55.000 13.61 0.05 35.57 3.86
1759 1806 7.174772 ACAAATGTCTCATGTGTAAGCATAACA 59.825 33.333 4.02 0.00 0.00 2.41
1766 1813 9.897744 AATTACAACAAATGTCTCATGTGTAAG 57.102 29.630 6.06 5.36 42.70 2.34
1811 1862 6.226052 TCATATCCTGATTGGTCAAATCTCG 58.774 40.000 1.62 0.00 44.42 4.04
1850 1909 1.745087 CTGCACGGTTTGATGGCTAAT 59.255 47.619 0.00 0.00 0.00 1.73
1863 1922 2.354821 GCCCTTTAAATACTCTGCACGG 59.645 50.000 0.00 0.00 0.00 4.94
1974 2340 4.082408 GGTTATTGTGCAAGGGTAAGGTTC 60.082 45.833 0.00 0.00 0.00 3.62
1975 2341 3.830178 GGTTATTGTGCAAGGGTAAGGTT 59.170 43.478 0.00 0.00 0.00 3.50
1976 2342 3.427573 GGTTATTGTGCAAGGGTAAGGT 58.572 45.455 0.00 0.00 0.00 3.50
1980 2346 3.332485 AGAAGGGTTATTGTGCAAGGGTA 59.668 43.478 0.00 0.00 0.00 3.69
2051 3086 4.815308 AGTGCAGTTGATAATGCTCTCATC 59.185 41.667 0.00 0.00 41.09 2.92
2080 3116 9.712305 AATGTGGTATATAGTCTGCATAAAGAC 57.288 33.333 0.00 0.00 45.82 3.01
2087 3123 8.046708 ACAAGAAAATGTGGTATATAGTCTGCA 58.953 33.333 0.00 0.00 30.82 4.41
2088 3124 8.438676 ACAAGAAAATGTGGTATATAGTCTGC 57.561 34.615 0.00 0.00 30.82 4.26
2165 3211 6.012745 ACTGCCAACTGGAAAGAAAATATCT 58.987 36.000 0.00 0.00 37.41 1.98
2192 3238 6.911308 TCCCTATCTATGCCTTAAGCTTTTT 58.089 36.000 3.20 0.00 44.23 1.94
2241 3287 3.129638 TCGTTTTGAAAAGTTCCAGTGGG 59.870 43.478 9.92 0.00 0.00 4.61
2317 3363 1.540267 CAAAAATGGCCCTGTACCGA 58.460 50.000 0.00 0.00 0.00 4.69
2361 3408 5.808366 TGGAGCGGATATAGAAAACTGAT 57.192 39.130 0.00 0.00 0.00 2.90
2364 3411 5.871396 TCTTGGAGCGGATATAGAAAACT 57.129 39.130 0.00 0.00 0.00 2.66
2408 3460 2.393764 CCAAACGAACCTTGATGCAAC 58.606 47.619 0.00 0.00 0.00 4.17
2409 3461 1.339610 CCCAAACGAACCTTGATGCAA 59.660 47.619 0.00 0.00 0.00 4.08
2487 3540 6.967199 CGTCAAATCTTAAACTTCCATTAGCC 59.033 38.462 0.00 0.00 0.00 3.93
2511 3564 1.135859 GCTCCATGCTTCAGTTCAACG 60.136 52.381 0.00 0.00 38.95 4.10
2544 3597 2.026542 ACTCGGGAAAATCCAGGTAACC 60.027 50.000 0.00 0.00 38.64 2.85
2560 3613 4.392138 GGAGGAACAAAGAAATGTACTCGG 59.608 45.833 0.00 0.00 37.87 4.63
2562 3615 7.824779 ACATAGGAGGAACAAAGAAATGTACTC 59.175 37.037 0.00 0.00 37.02 2.59
2662 3715 6.989155 ATACTCGGGTATTTGTCCTTGATA 57.011 37.500 0.88 0.00 35.32 2.15
2743 3796 1.689273 CCTAGACAGATACAGTGGGGC 59.311 57.143 0.00 0.00 0.00 5.80
2793 3846 9.847706 GATTGAGAAAAGAAAGGAAATTAGGTC 57.152 33.333 0.00 0.00 0.00 3.85
2926 3979 3.693085 AGCTGGAATATGCAGTGAACAAG 59.307 43.478 0.00 0.00 38.17 3.16
2939 3992 3.244078 ACAGAACACAACGAGCTGGAATA 60.244 43.478 1.44 0.00 0.00 1.75
2947 4000 6.565234 AGAAGGATATACAGAACACAACGAG 58.435 40.000 0.00 0.00 0.00 4.18
2950 4003 7.777095 AGAGAGAAGGATATACAGAACACAAC 58.223 38.462 0.00 0.00 0.00 3.32
2952 4005 7.350382 AGAGAGAGAAGGATATACAGAACACA 58.650 38.462 0.00 0.00 0.00 3.72
2957 4010 8.218423 AGATGAGAGAGAGAAGGATATACAGA 57.782 38.462 0.00 0.00 0.00 3.41
2958 4011 8.868522 AAGATGAGAGAGAGAAGGATATACAG 57.131 38.462 0.00 0.00 0.00 2.74
3011 4064 0.036010 AGCAGTCAGGGGATGTTTCG 60.036 55.000 0.00 0.00 0.00 3.46
3036 4089 7.546667 TGGAGATAACGAATACACTTGGTTTAC 59.453 37.037 0.00 0.00 0.00 2.01
3206 4262 3.005539 ACTCGGGCCAGCATCTGT 61.006 61.111 4.39 0.00 0.00 3.41
3322 4378 3.286751 GCTCAACAACGCCAGCCA 61.287 61.111 0.00 0.00 0.00 4.75
3349 4405 2.555199 ACGATTTCCTGCAGATACAGC 58.445 47.619 17.39 0.00 36.29 4.40
3409 4465 4.760047 CCCCAGCCACTCCGTTCG 62.760 72.222 0.00 0.00 0.00 3.95
3477 4533 7.568128 TTACAACATCCAGGGTAGCATATAT 57.432 36.000 0.00 0.00 0.00 0.86
3489 4545 3.968265 ACCTGGGAATTACAACATCCAG 58.032 45.455 0.00 0.00 40.86 3.86
3576 4632 7.175119 GCTAGTTCCCAAAGAGATTTTAAGTGT 59.825 37.037 0.00 0.00 0.00 3.55
3591 4647 1.142870 ACAAGCACAGCTAGTTCCCAA 59.857 47.619 0.00 0.00 38.25 4.12
3642 4698 6.599244 CCATCAGATGTAAACAAAGGCTAAGA 59.401 38.462 9.64 0.00 0.00 2.10
3666 4722 5.824904 AATTGCATATCTCAACTGACACC 57.175 39.130 0.00 0.00 0.00 4.16
3691 4747 6.265876 GGTACCATAAGGACTGTTTGGAAAAA 59.734 38.462 7.15 0.00 38.69 1.94
3694 4750 4.913784 GGTACCATAAGGACTGTTTGGAA 58.086 43.478 7.15 0.00 38.69 3.53
3744 4800 4.406648 TGTACATCTACATGGAGCAAGG 57.593 45.455 0.00 0.00 33.82 3.61
4091 5148 6.003326 TGCAGTCAGTTCAGGAATTATTTCA 58.997 36.000 0.20 0.00 33.23 2.69
4117 5174 2.554032 CCTGAAAGCGTTGTGGATTCTT 59.446 45.455 0.00 0.00 0.00 2.52
4182 5239 0.390492 CATGAGCCTCCGCATAGTCA 59.610 55.000 0.00 0.00 37.52 3.41
4315 5373 0.967887 AGAGAGCAGAGCAACGCCTA 60.968 55.000 0.00 0.00 0.00 3.93
4317 5375 2.099431 CAGAGAGCAGAGCAACGCC 61.099 63.158 0.00 0.00 0.00 5.68
4426 5486 1.279271 GCTTCAAGGGTTCTCTGGCTA 59.721 52.381 0.00 0.00 0.00 3.93
4476 5536 2.457794 GGGGAGTGGGAAGGGGTA 59.542 66.667 0.00 0.00 0.00 3.69
4482 5542 0.930726 AACAAACTGGGGAGTGGGAA 59.069 50.000 0.00 0.00 0.00 3.97
4515 5575 1.075536 GGATCAAGTGGGTGAAAGGGT 59.924 52.381 0.00 0.00 0.00 4.34
4585 5670 2.423577 GTGATTAAGTTGTGCCGTCCT 58.576 47.619 0.00 0.00 0.00 3.85
4609 5694 0.671781 CACCAAGCTGGAGAGGAACG 60.672 60.000 8.91 0.00 40.96 3.95
4702 5787 5.120674 GCCAAATCTAACAATTTGACCAAGC 59.879 40.000 2.79 2.56 45.40 4.01
5360 6454 3.082701 GGCAGCTCCTCAGAGGCT 61.083 66.667 12.26 3.31 40.79 4.58


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

AutoCloner maintained by Alex Coulton.