Multiple sequence alignment - TraesCS2A01G250900

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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 TraesCS2A01G250900 chr2A 100.000 5456 0 0 1 5456 378859064 378853609 0.000000e+00 10076.0
1 TraesCS2A01G250900 chr2A 85.477 241 24 5 528 758 105600289 105600528 1.960000e-59 241.0
2 TraesCS2A01G250900 chr2D 93.501 4601 173 43 918 5456 301824324 301819788 0.000000e+00 6724.0
3 TraesCS2A01G250900 chr2D 89.162 489 50 2 9 495 301853639 301853152 1.680000e-169 606.0
4 TraesCS2A01G250900 chr2D 88.750 160 3 3 785 929 301853152 301852993 1.210000e-41 182.0
5 TraesCS2A01G250900 chr2B 92.836 4690 179 46 840 5456 356601727 356597122 0.000000e+00 6654.0
6 TraesCS2A01G250900 chr2B 80.861 209 38 1 3112 3320 707729725 707729931 4.370000e-36 163.0
7 TraesCS2A01G250900 chr7D 83.405 464 54 12 3523 3973 48544258 48543805 5.090000e-110 409.0
8 TraesCS2A01G250900 chr4A 83.153 463 57 12 3520 3973 464566974 464567424 2.370000e-108 403.0
9 TraesCS2A01G250900 chr4A 85.849 318 42 2 3148 3465 464566663 464566977 8.760000e-88 335.0
10 TraesCS2A01G250900 chr4A 86.957 276 24 2 495 758 162228736 162229011 3.190000e-77 300.0
11 TraesCS2A01G250900 chr4A 81.618 136 20 3 3855 3985 36475888 36475753 2.080000e-19 108.0
12 TraesCS2A01G250900 chr4D 82.684 462 55 11 3523 3973 113153072 113152625 2.380000e-103 387.0
13 TraesCS2A01G250900 chr4D 82.799 343 52 5 3122 3461 63233696 63233358 3.190000e-77 300.0
14 TraesCS2A01G250900 chr5A 87.248 298 29 3 495 784 25862611 25862315 1.130000e-86 331.0
15 TraesCS2A01G250900 chr5A 86.260 262 27 3 528 780 613460625 613460886 5.380000e-70 276.0
16 TraesCS2A01G250900 chr5A 82.168 286 25 7 499 758 671411913 671412198 7.110000e-54 222.0
17 TraesCS2A01G250900 chr5A 84.536 194 10 5 607 780 608858979 608858786 2.020000e-39 174.0
18 TraesCS2A01G250900 chr6A 85.294 306 24 10 499 784 79193573 79193269 4.130000e-76 296.0
19 TraesCS2A01G250900 chr6A 83.007 306 31 11 499 784 79169236 79168932 1.950000e-64 257.0
20 TraesCS2A01G250900 chr6A 84.259 108 16 1 3866 3972 4161116 4161009 2.690000e-18 104.0
21 TraesCS2A01G250900 chr7A 85.053 281 21 12 528 788 663287913 663287634 3.240000e-67 267.0
22 TraesCS2A01G250900 chr7A 84.307 274 22 8 531 784 207090415 207090143 1.170000e-61 248.0
23 TraesCS2A01G250900 chr7A 83.333 252 26 6 540 780 262851802 262852048 9.200000e-53 219.0
24 TraesCS2A01G250900 chr7A 81.651 218 33 7 3121 3336 185980969 185980757 2.020000e-39 174.0
25 TraesCS2A01G250900 chr1B 83.566 286 40 4 3126 3408 428540184 428539903 1.510000e-65 261.0
26 TraesCS2A01G250900 chr1B 85.455 220 30 2 3733 3951 428539041 428538823 1.530000e-55 228.0
27 TraesCS2A01G250900 chr3A 84.583 240 24 5 528 754 511824345 511824106 5.500000e-55 226.0
28 TraesCS2A01G250900 chr3A 78.964 309 37 10 494 781 691340117 691340418 9.330000e-43 185.0
29 TraesCS2A01G250900 chr4B 81.498 227 36 4 3112 3335 285435338 285435115 1.210000e-41 182.0
30 TraesCS2A01G250900 chr5B 82.075 212 34 3 3123 3333 538709284 538709076 1.560000e-40 178.0
31 TraesCS2A01G250900 chr5B 83.740 123 15 4 3870 3989 459469660 459469540 1.610000e-20 111.0
32 TraesCS2A01G250900 chr5D 78.400 250 32 10 544 780 437356452 437356212 5.700000e-30 143.0
33 TraesCS2A01G250900 chr6B 80.000 150 30 0 537 686 713977416 713977565 1.610000e-20 111.0
34 TraesCS2A01G250900 chr3B 100.000 29 0 0 3959 3987 761684888 761684916 3.000000e-03 54.7


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 TraesCS2A01G250900 chr2A 378853609 378859064 5455 True 10076.0 10076 100.0000 1 5456 1 chr2A.!!$R1 5455
1 TraesCS2A01G250900 chr2D 301819788 301824324 4536 True 6724.0 6724 93.5010 918 5456 1 chr2D.!!$R1 4538
2 TraesCS2A01G250900 chr2D 301852993 301853639 646 True 394.0 606 88.9560 9 929 2 chr2D.!!$R2 920
3 TraesCS2A01G250900 chr2B 356597122 356601727 4605 True 6654.0 6654 92.8360 840 5456 1 chr2B.!!$R1 4616
4 TraesCS2A01G250900 chr4A 464566663 464567424 761 False 369.0 403 84.5010 3148 3973 2 chr4A.!!$F2 825
5 TraesCS2A01G250900 chr1B 428538823 428540184 1361 True 244.5 261 84.5105 3126 3951 2 chr1B.!!$R1 825

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
747 750 0.033228 TTTGCATCGGGCTTTGGTTG 59.967 50.0 0.00 0.0 45.15 3.77 F
1444 1484 0.035056 GCCTTGATGTGCCAGTACCT 60.035 55.0 0.00 0.0 0.00 3.08 F
1588 1628 0.038892 GTTAACGTCCGTGCCTGAGA 60.039 55.0 0.00 0.0 0.00 3.27 F
1589 1629 0.242825 TTAACGTCCGTGCCTGAGAG 59.757 55.0 0.00 0.0 0.00 3.20 F
2433 2475 0.670162 GTACTTATGGTAGCGGCGGA 59.330 55.0 9.78 0.0 0.00 5.54 F
3712 4235 0.599991 TGACATCGAGCTTGTGCGTT 60.600 50.0 0.00 0.0 45.42 4.84 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2080 2122 1.273327 CCAGATGGTGGTTTGAAAGGC 59.727 52.381 0.00 0.0 42.17 4.35 R
3314 3394 1.460743 CTCGTTCTTTTCGCATGCTCA 59.539 47.619 17.13 0.0 0.00 4.26 R
3528 3771 0.679002 GCCAGTCCATCATGCACAGT 60.679 55.000 0.00 0.0 0.00 3.55 R
3554 3797 1.002624 GGAACGGCTTGGTCATCCA 60.003 57.895 0.00 0.0 42.66 3.41 R
4419 5124 0.184692 TGTCCCATGAGTTGTTGGCA 59.815 50.000 0.00 0.0 0.00 4.92 R
5149 5860 0.038166 TCAGACATGTTTCCTGGGGC 59.962 55.000 11.83 0.0 0.00 5.80 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
24 25 1.537638 CCATCCTCTATCTCGTCGGTG 59.462 57.143 0.00 0.00 0.00 4.94
55 56 4.552365 CATCTCCGCCACCGCCAT 62.552 66.667 0.00 0.00 0.00 4.40
56 57 3.797353 ATCTCCGCCACCGCCATT 61.797 61.111 0.00 0.00 0.00 3.16
61 62 2.111043 CGCCACCGCCATTCCTAT 59.889 61.111 0.00 0.00 0.00 2.57
95 96 1.817099 CCCTCATCTCTGCCGCAAC 60.817 63.158 0.00 0.00 0.00 4.17
96 97 1.220206 CCTCATCTCTGCCGCAACT 59.780 57.895 0.00 0.00 0.00 3.16
114 115 3.474570 GCCGCCCTCCTCATCACT 61.475 66.667 0.00 0.00 0.00 3.41
126 127 0.615331 TCATCACTGCCTTGTCTCCC 59.385 55.000 0.00 0.00 0.00 4.30
165 166 1.454201 CGATAGCTAGATGCCGAGGA 58.546 55.000 0.00 0.00 44.23 3.71
179 180 0.168128 CGAGGATTTGCGGTGGAAAC 59.832 55.000 0.00 0.00 0.00 2.78
183 184 0.589223 GATTTGCGGTGGAAACGACA 59.411 50.000 0.00 0.00 0.00 4.35
207 208 1.304547 CCTCCTAGATCCGCCGGAT 60.305 63.158 20.53 20.53 46.28 4.18
208 209 0.900647 CCTCCTAGATCCGCCGGATT 60.901 60.000 21.39 12.45 43.27 3.01
226 227 4.312443 GGATTGTAGAGGAAACAACGTGA 58.688 43.478 0.00 0.00 39.51 4.35
227 228 4.753107 GGATTGTAGAGGAAACAACGTGAA 59.247 41.667 0.00 0.00 39.51 3.18
232 233 0.179067 AGGAAACAACGTGAAGGCGA 60.179 50.000 0.00 0.00 35.59 5.54
255 256 3.414700 CCACGCGTTCAGTGCTCC 61.415 66.667 10.22 0.00 38.22 4.70
261 262 2.811317 GTTCAGTGCTCCGGCGAG 60.811 66.667 9.30 5.11 42.25 5.03
287 288 2.591915 GGAGAGGGAATCACCGTGA 58.408 57.895 3.10 3.10 40.11 4.35
289 290 0.179134 GAGAGGGAATCACCGTGACG 60.179 60.000 2.57 0.00 40.11 4.35
296 297 0.246360 AATCACCGTGACGAGATGCA 59.754 50.000 6.54 0.00 0.00 3.96
314 315 2.173356 TGCAGTGGGGAATGGATAAGAG 59.827 50.000 0.00 0.00 0.00 2.85
319 320 2.021042 TGGGGAATGGATAAGAGGAGGT 60.021 50.000 0.00 0.00 0.00 3.85
343 344 1.674322 CGGCGAGTGGGTGGAAAAT 60.674 57.895 0.00 0.00 0.00 1.82
355 356 1.892474 GTGGAAAATAAGTGGGCTGCA 59.108 47.619 0.50 0.00 0.00 4.41
374 375 3.000041 GCATTGTGTCTCGTTCACCATA 59.000 45.455 0.00 0.00 35.25 2.74
386 387 0.120377 TCACCATACACCTCCCCCTT 59.880 55.000 0.00 0.00 0.00 3.95
417 420 1.296715 GCTGACGTGAGGGGTCAAT 59.703 57.895 3.66 0.00 43.27 2.57
433 436 1.199789 TCAATGTGCGCCAAGATTCAC 59.800 47.619 4.18 0.00 0.00 3.18
441 444 2.574322 CGCCAAGATTCACGTTTTCAG 58.426 47.619 0.00 0.00 0.00 3.02
447 450 4.813296 AGATTCACGTTTTCAGTCCAAC 57.187 40.909 0.00 0.00 0.00 3.77
458 461 0.036010 CAGTCCAACGGGAGATGCTT 60.036 55.000 0.00 0.00 46.12 3.91
460 463 0.744771 GTCCAACGGGAGATGCTTCC 60.745 60.000 0.00 0.00 46.12 3.46
492 495 4.074970 GTTGAAGGGAAAAGATGCTCTGA 58.925 43.478 0.00 0.00 0.00 3.27
495 498 6.065976 TGAAGGGAAAAGATGCTCTGATTA 57.934 37.500 0.00 0.00 0.00 1.75
496 499 6.666678 TGAAGGGAAAAGATGCTCTGATTAT 58.333 36.000 0.00 0.00 0.00 1.28
497 500 7.805163 TGAAGGGAAAAGATGCTCTGATTATA 58.195 34.615 0.00 0.00 0.00 0.98
498 501 7.716998 TGAAGGGAAAAGATGCTCTGATTATAC 59.283 37.037 0.00 0.00 0.00 1.47
499 502 6.538263 AGGGAAAAGATGCTCTGATTATACC 58.462 40.000 0.00 0.00 0.00 2.73
500 503 6.331307 AGGGAAAAGATGCTCTGATTATACCT 59.669 38.462 0.00 0.00 0.00 3.08
501 504 6.429385 GGGAAAAGATGCTCTGATTATACCTG 59.571 42.308 0.00 0.00 0.00 4.00
502 505 6.429385 GGAAAAGATGCTCTGATTATACCTGG 59.571 42.308 0.00 0.00 0.00 4.45
503 506 6.506538 AAAGATGCTCTGATTATACCTGGT 57.493 37.500 4.05 4.05 0.00 4.00
504 507 5.736951 AGATGCTCTGATTATACCTGGTC 57.263 43.478 0.63 0.00 0.00 4.02
505 508 5.150715 AGATGCTCTGATTATACCTGGTCA 58.849 41.667 0.63 0.00 0.00 4.02
506 509 5.784390 AGATGCTCTGATTATACCTGGTCAT 59.216 40.000 0.63 0.00 0.00 3.06
507 510 5.219343 TGCTCTGATTATACCTGGTCATG 57.781 43.478 0.63 0.00 0.00 3.07
508 511 4.040829 TGCTCTGATTATACCTGGTCATGG 59.959 45.833 0.63 0.00 0.00 3.66
509 512 4.040952 GCTCTGATTATACCTGGTCATGGT 59.959 45.833 0.63 0.00 41.28 3.55
510 513 5.788450 CTCTGATTATACCTGGTCATGGTC 58.212 45.833 0.63 0.00 38.88 4.02
511 514 5.215845 TCTGATTATACCTGGTCATGGTCA 58.784 41.667 0.63 2.31 38.88 4.02
512 515 5.305386 TCTGATTATACCTGGTCATGGTCAG 59.695 44.000 0.63 11.92 38.88 3.51
513 516 3.838244 TTATACCTGGTCATGGTCAGC 57.162 47.619 0.63 0.00 38.88 4.26
514 517 0.839946 ATACCTGGTCATGGTCAGCC 59.160 55.000 0.63 0.00 38.88 4.85
515 518 1.271840 TACCTGGTCATGGTCAGCCC 61.272 60.000 0.63 0.00 38.88 5.19
516 519 2.124983 CTGGTCATGGTCAGCCCG 60.125 66.667 0.00 0.00 35.15 6.13
517 520 2.606213 TGGTCATGGTCAGCCCGA 60.606 61.111 0.00 0.00 35.15 5.14
518 521 2.125106 GGTCATGGTCAGCCCGAC 60.125 66.667 0.00 0.00 44.57 4.79
551 554 2.751436 CGACCCGGTCCGACCTTA 60.751 66.667 14.39 0.00 35.66 2.69
552 555 2.123428 CGACCCGGTCCGACCTTAT 61.123 63.158 14.39 0.14 35.66 1.73
553 556 1.738432 GACCCGGTCCGACCTTATC 59.262 63.158 14.39 6.10 35.66 1.75
554 557 1.742324 GACCCGGTCCGACCTTATCC 61.742 65.000 14.39 0.00 35.66 2.59
555 558 1.759299 CCCGGTCCGACCTTATCCA 60.759 63.158 14.39 0.00 35.66 3.41
556 559 1.119574 CCCGGTCCGACCTTATCCAT 61.120 60.000 14.39 0.00 35.66 3.41
557 560 0.033504 CCGGTCCGACCTTATCCATG 59.966 60.000 14.39 0.00 35.66 3.66
558 561 0.033504 CGGTCCGACCTTATCCATGG 59.966 60.000 15.70 4.97 35.66 3.66
559 562 0.396811 GGTCCGACCTTATCCATGGG 59.603 60.000 13.02 0.00 34.73 4.00
560 563 1.129058 GTCCGACCTTATCCATGGGT 58.871 55.000 13.02 7.52 35.89 4.51
561 564 1.070289 GTCCGACCTTATCCATGGGTC 59.930 57.143 13.02 9.88 44.16 4.46
564 567 0.396811 GACCTTATCCATGGGTCGGG 59.603 60.000 13.02 12.98 39.80 5.14
565 568 1.073199 CCTTATCCATGGGTCGGGC 59.927 63.158 13.02 0.00 0.00 6.13
566 569 1.418908 CCTTATCCATGGGTCGGGCT 61.419 60.000 13.02 0.00 0.00 5.19
567 570 0.035458 CTTATCCATGGGTCGGGCTC 59.965 60.000 13.02 0.00 0.00 4.70
568 571 1.754380 TTATCCATGGGTCGGGCTCG 61.754 60.000 13.02 0.00 37.82 5.03
582 585 3.243128 GCTCGGGCCTAAGTTTTGA 57.757 52.632 0.84 0.00 0.00 2.69
583 586 1.087501 GCTCGGGCCTAAGTTTTGAG 58.912 55.000 0.84 0.00 0.00 3.02
584 587 1.087501 CTCGGGCCTAAGTTTTGAGC 58.912 55.000 0.84 0.00 0.00 4.26
585 588 0.322187 TCGGGCCTAAGTTTTGAGCC 60.322 55.000 0.84 0.00 43.09 4.70
587 590 2.180674 GGCCTAAGTTTTGAGCCCG 58.819 57.895 0.00 0.00 37.66 6.13
588 591 0.322187 GGCCTAAGTTTTGAGCCCGA 60.322 55.000 0.00 0.00 37.66 5.14
589 592 1.530323 GCCTAAGTTTTGAGCCCGAA 58.470 50.000 0.00 0.00 0.00 4.30
590 593 1.468914 GCCTAAGTTTTGAGCCCGAAG 59.531 52.381 0.00 0.00 0.00 3.79
591 594 1.468914 CCTAAGTTTTGAGCCCGAAGC 59.531 52.381 0.00 0.00 44.25 3.86
627 630 3.262686 GAGCCCGTCGATTTCGCC 61.263 66.667 0.00 0.00 39.60 5.54
628 631 4.077184 AGCCCGTCGATTTCGCCA 62.077 61.111 0.00 0.00 39.60 5.69
629 632 2.895372 GCCCGTCGATTTCGCCAT 60.895 61.111 0.00 0.00 39.60 4.40
630 633 2.469516 GCCCGTCGATTTCGCCATT 61.470 57.895 0.00 0.00 39.60 3.16
631 634 1.988834 GCCCGTCGATTTCGCCATTT 61.989 55.000 0.00 0.00 39.60 2.32
632 635 1.292061 CCCGTCGATTTCGCCATTTA 58.708 50.000 0.00 0.00 39.60 1.40
633 636 1.666700 CCCGTCGATTTCGCCATTTAA 59.333 47.619 0.00 0.00 39.60 1.52
634 637 2.286184 CCCGTCGATTTCGCCATTTAAG 60.286 50.000 0.00 0.00 39.60 1.85
635 638 2.286184 CCGTCGATTTCGCCATTTAAGG 60.286 50.000 0.00 0.00 39.60 2.69
636 639 2.605818 CGTCGATTTCGCCATTTAAGGA 59.394 45.455 0.00 0.00 39.60 3.36
637 640 3.062909 CGTCGATTTCGCCATTTAAGGAA 59.937 43.478 0.00 0.00 39.60 3.36
638 641 4.588278 GTCGATTTCGCCATTTAAGGAAG 58.412 43.478 0.00 0.00 39.60 3.46
639 642 4.331717 GTCGATTTCGCCATTTAAGGAAGA 59.668 41.667 0.00 0.00 39.60 2.87
640 643 4.570772 TCGATTTCGCCATTTAAGGAAGAG 59.429 41.667 0.00 0.00 39.60 2.85
641 644 4.260784 CGATTTCGCCATTTAAGGAAGAGG 60.261 45.833 0.00 0.00 0.00 3.69
642 645 2.038387 TCGCCATTTAAGGAAGAGGC 57.962 50.000 0.00 0.00 38.39 4.70
643 646 1.025041 CGCCATTTAAGGAAGAGGCC 58.975 55.000 0.00 0.00 38.48 5.19
644 647 1.408822 CGCCATTTAAGGAAGAGGCCT 60.409 52.381 3.86 3.86 38.48 5.19
645 648 2.027385 GCCATTTAAGGAAGAGGCCTG 58.973 52.381 12.00 0.00 38.58 4.85
646 649 2.659428 CCATTTAAGGAAGAGGCCTGG 58.341 52.381 12.00 0.00 38.58 4.45
647 650 2.027385 CATTTAAGGAAGAGGCCTGGC 58.973 52.381 12.00 11.05 38.58 4.85
674 677 3.536956 CCTGACGGGCTTTTAGTATGA 57.463 47.619 0.00 0.00 0.00 2.15
675 678 4.073293 CCTGACGGGCTTTTAGTATGAT 57.927 45.455 0.00 0.00 0.00 2.45
676 679 3.809832 CCTGACGGGCTTTTAGTATGATG 59.190 47.826 0.00 0.00 0.00 3.07
677 680 3.804036 TGACGGGCTTTTAGTATGATGG 58.196 45.455 0.00 0.00 0.00 3.51
678 681 3.139077 GACGGGCTTTTAGTATGATGGG 58.861 50.000 0.00 0.00 0.00 4.00
679 682 1.880027 CGGGCTTTTAGTATGATGGGC 59.120 52.381 0.00 0.00 0.00 5.36
680 683 2.239400 GGGCTTTTAGTATGATGGGCC 58.761 52.381 0.00 0.00 37.82 5.80
681 684 1.880027 GGCTTTTAGTATGATGGGCCG 59.120 52.381 0.00 0.00 0.00 6.13
682 685 1.880027 GCTTTTAGTATGATGGGCCGG 59.120 52.381 0.00 0.00 0.00 6.13
683 686 2.504367 CTTTTAGTATGATGGGCCGGG 58.496 52.381 2.18 0.00 0.00 5.73
684 687 0.109723 TTTAGTATGATGGGCCGGGC 59.890 55.000 22.00 22.00 0.00 6.13
685 688 0.766674 TTAGTATGATGGGCCGGGCT 60.767 55.000 28.80 9.11 0.00 5.19
686 689 1.192146 TAGTATGATGGGCCGGGCTC 61.192 60.000 28.80 16.93 0.00 4.70
687 690 3.625897 TATGATGGGCCGGGCTCG 61.626 66.667 28.80 0.00 0.00 5.03
744 747 3.603144 TTTTTGCATCGGGCTTTGG 57.397 47.368 0.00 0.00 45.15 3.28
745 748 0.755686 TTTTTGCATCGGGCTTTGGT 59.244 45.000 0.00 0.00 45.15 3.67
746 749 0.755686 TTTTGCATCGGGCTTTGGTT 59.244 45.000 0.00 0.00 45.15 3.67
747 750 0.033228 TTTGCATCGGGCTTTGGTTG 59.967 50.000 0.00 0.00 45.15 3.77
748 751 1.814772 TTGCATCGGGCTTTGGTTGG 61.815 55.000 0.00 0.00 45.15 3.77
749 752 2.573340 CATCGGGCTTTGGTTGGC 59.427 61.111 0.00 0.00 0.00 4.52
750 753 2.679996 ATCGGGCTTTGGTTGGCC 60.680 61.111 0.00 0.00 46.89 5.36
775 778 4.883354 GCCCGAGGAATGGCCAGG 62.883 72.222 13.05 6.01 41.97 4.45
776 779 3.411517 CCCGAGGAATGGCCAGGT 61.412 66.667 13.05 0.12 40.02 4.00
777 780 2.070039 CCCGAGGAATGGCCAGGTA 61.070 63.158 13.05 0.00 40.02 3.08
778 781 1.418908 CCCGAGGAATGGCCAGGTAT 61.419 60.000 13.05 0.00 40.02 2.73
779 782 1.348064 CCGAGGAATGGCCAGGTATA 58.652 55.000 13.05 0.00 40.02 1.47
780 783 1.276421 CCGAGGAATGGCCAGGTATAG 59.724 57.143 13.05 0.92 40.02 1.31
781 784 1.338200 CGAGGAATGGCCAGGTATAGC 60.338 57.143 13.05 0.00 40.02 2.97
782 785 1.981495 GAGGAATGGCCAGGTATAGCT 59.019 52.381 13.05 0.00 40.02 3.32
783 786 1.981495 AGGAATGGCCAGGTATAGCTC 59.019 52.381 13.05 0.00 40.02 4.09
784 787 1.981495 GGAATGGCCAGGTATAGCTCT 59.019 52.381 13.05 0.00 36.34 4.09
785 788 2.289945 GGAATGGCCAGGTATAGCTCTG 60.290 54.545 13.05 0.00 36.34 3.35
786 789 2.405618 ATGGCCAGGTATAGCTCTGA 57.594 50.000 13.05 0.00 33.11 3.27
833 836 1.447489 CAGCCGAGAAGCAGGACTG 60.447 63.158 0.00 0.00 34.23 3.51
930 947 5.112129 AGGGGACATATATAAAATCGGCC 57.888 43.478 0.00 0.00 0.00 6.13
1094 1123 5.177696 CCTCGATTAATTTCTCCGATTCCAC 59.822 44.000 0.00 0.00 0.00 4.02
1125 1154 2.354773 CGTAGCGGAGGATTCGGC 60.355 66.667 0.00 0.00 46.63 5.54
1218 1247 2.143122 GATGTTTCACGCTGTTGGAGA 58.857 47.619 0.00 0.00 0.00 3.71
1353 1393 3.358111 TCGATTTGGTAGGAATTGGCA 57.642 42.857 0.00 0.00 0.00 4.92
1354 1394 3.278574 TCGATTTGGTAGGAATTGGCAG 58.721 45.455 0.00 0.00 0.00 4.85
1418 1458 2.754002 GTTAGTAGTTCGAGCTGTCCCT 59.246 50.000 12.54 5.14 0.00 4.20
1444 1484 0.035056 GCCTTGATGTGCCAGTACCT 60.035 55.000 0.00 0.00 0.00 3.08
1546 1586 2.094675 CCAGAGTTTTGCATACCCTGG 58.905 52.381 13.28 13.28 34.52 4.45
1588 1628 0.038892 GTTAACGTCCGTGCCTGAGA 60.039 55.000 0.00 0.00 0.00 3.27
1589 1629 0.242825 TTAACGTCCGTGCCTGAGAG 59.757 55.000 0.00 0.00 0.00 3.20
1671 1711 3.333219 CCTTCCTGGGAGGCAGCA 61.333 66.667 8.45 0.00 34.61 4.41
1872 1914 4.199310 TGGCCATTCTTCAGTATTGTAGC 58.801 43.478 0.00 0.00 0.00 3.58
2080 2122 2.202703 GGAACATCCGGTCCGTCG 60.203 66.667 11.06 0.16 0.00 5.12
2171 2213 2.119801 AACCATTGCTGCTACAGAGG 57.880 50.000 0.00 0.00 32.44 3.69
2288 2330 2.146920 ACTGTACTGACCTAGAGCCC 57.853 55.000 6.77 0.00 0.00 5.19
2433 2475 0.670162 GTACTTATGGTAGCGGCGGA 59.330 55.000 9.78 0.00 0.00 5.54
2469 2511 1.319541 TGTACTCGAGCTATGGAGGC 58.680 55.000 13.61 6.42 35.71 4.70
2561 2603 1.566703 TGGTGGTTATGGTATGGGTGG 59.433 52.381 0.00 0.00 0.00 4.61
2562 2604 1.567175 GGTGGTTATGGTATGGGTGGT 59.433 52.381 0.00 0.00 0.00 4.16
2563 2605 2.778850 GGTGGTTATGGTATGGGTGGTA 59.221 50.000 0.00 0.00 0.00 3.25
2564 2606 3.396611 GGTGGTTATGGTATGGGTGGTAT 59.603 47.826 0.00 0.00 0.00 2.73
2565 2607 4.394729 GTGGTTATGGTATGGGTGGTATG 58.605 47.826 0.00 0.00 0.00 2.39
2566 2608 3.396276 TGGTTATGGTATGGGTGGTATGG 59.604 47.826 0.00 0.00 0.00 2.74
2567 2609 3.245122 GGTTATGGTATGGGTGGTATGGG 60.245 52.174 0.00 0.00 0.00 4.00
2568 2610 0.777446 ATGGTATGGGTGGTATGGGC 59.223 55.000 0.00 0.00 0.00 5.36
2569 2611 1.072505 GGTATGGGTGGTATGGGCG 59.927 63.158 0.00 0.00 0.00 6.13
2570 2612 1.072505 GTATGGGTGGTATGGGCGG 59.927 63.158 0.00 0.00 0.00 6.13
2571 2613 2.824880 TATGGGTGGTATGGGCGGC 61.825 63.158 0.00 0.00 0.00 6.53
2573 2615 4.204028 GGGTGGTATGGGCGGCAT 62.204 66.667 12.47 5.20 0.00 4.40
2574 2616 2.906897 GGTGGTATGGGCGGCATG 60.907 66.667 12.47 0.00 0.00 4.06
2575 2617 2.906897 GTGGTATGGGCGGCATGG 60.907 66.667 12.47 0.00 0.00 3.66
2576 2618 4.202574 TGGTATGGGCGGCATGGG 62.203 66.667 12.47 0.00 0.00 4.00
2577 2619 4.204028 GGTATGGGCGGCATGGGT 62.204 66.667 12.47 0.00 0.00 4.51
2578 2620 2.906897 GTATGGGCGGCATGGGTG 60.907 66.667 12.47 0.00 0.00 4.61
2579 2621 4.202574 TATGGGCGGCATGGGTGG 62.203 66.667 12.47 0.00 0.00 4.61
2582 2624 4.204028 GGGCGGCATGGGTGGTAT 62.204 66.667 12.47 0.00 0.00 2.73
2583 2625 2.906897 GGCGGCATGGGTGGTATG 60.907 66.667 3.07 0.00 0.00 2.39
2584 2626 2.906897 GCGGCATGGGTGGTATGG 60.907 66.667 0.00 0.00 0.00 2.74
2585 2627 2.203337 CGGCATGGGTGGTATGGG 60.203 66.667 0.00 0.00 0.00 4.00
2586 2628 2.521708 GGCATGGGTGGTATGGGC 60.522 66.667 0.00 0.00 0.00 5.36
2587 2629 2.906897 GCATGGGTGGTATGGGCG 60.907 66.667 0.00 0.00 0.00 6.13
2790 2860 3.133183 TGCACATTGAAGCATGCCATAAT 59.867 39.130 15.66 9.46 37.26 1.28
2826 2903 8.868916 GTTCATTAATGCGAAATGTTTGGTTAT 58.131 29.630 10.76 0.00 36.07 1.89
2884 2961 7.122055 TGTTTACTGTTTCTTCATCCAGTTGTT 59.878 33.333 0.00 0.00 38.91 2.83
2933 3010 5.207768 GCTGTTGTGAGTTTCTATGTTGTG 58.792 41.667 0.00 0.00 0.00 3.33
3111 3190 8.028540 TGTGTGAAGTTACATGTCATTCATAC 57.971 34.615 24.71 24.71 40.37 2.39
3112 3191 7.659390 TGTGTGAAGTTACATGTCATTCATACA 59.341 33.333 27.41 27.41 44.41 2.29
3116 3195 9.230122 TGAAGTTACATGTCATTCATACAACAT 57.770 29.630 0.00 0.00 34.56 2.71
3130 3209 1.841277 ACAACATATGAAGGCCCCGTA 59.159 47.619 10.38 0.00 0.00 4.02
3302 3382 1.074951 CCAACAACCCTGGACCTCC 59.925 63.158 0.00 0.00 35.85 4.30
3307 3387 2.424793 ACAACCCTGGACCTCCTTTTA 58.575 47.619 0.00 0.00 36.82 1.52
3380 3463 2.486370 CCTGTTGTGTGTGGATGGTGTA 60.486 50.000 0.00 0.00 0.00 2.90
3481 3724 1.753073 CCGTGTTCCCTCCGTTACTAT 59.247 52.381 0.00 0.00 0.00 2.12
3585 3828 2.592287 GTTCCCGTCAACCCGCAA 60.592 61.111 0.00 0.00 0.00 4.85
3627 3870 2.822399 GGCATAGCCGTGTAGCCT 59.178 61.111 0.00 0.00 39.62 4.58
3644 3887 1.447317 CCTTGTTGCAGAGCGTGGTT 61.447 55.000 0.00 0.00 0.00 3.67
3688 4206 4.337274 TGTAAGTTCGATTGCTCCTCGATA 59.663 41.667 6.66 0.00 43.93 2.92
3712 4235 0.599991 TGACATCGAGCTTGTGCGTT 60.600 50.000 0.00 0.00 45.42 4.84
3762 4448 2.046988 CATGCCGGTGCTCTGTGA 60.047 61.111 1.90 0.00 38.71 3.58
3987 4692 6.430925 TCAATACTTTGCTATCAAACACAGCT 59.569 34.615 0.00 0.00 37.28 4.24
4090 4795 4.136796 GGATTTGCTACAGATGCATGGTA 58.863 43.478 2.46 5.76 40.34 3.25
4092 4797 2.620251 TGCTACAGATGCATGGTACC 57.380 50.000 2.46 4.43 35.31 3.34
4204 4909 8.838365 TGTTATTTTAAGTTTTCCTCGCTTGTA 58.162 29.630 0.00 0.00 0.00 2.41
4419 5124 2.742856 GCTTTTTGAGGCACCAAAAGCT 60.743 45.455 27.08 0.00 43.99 3.74
4460 5165 3.842007 TGTTTGGGGAAACTAAGACGA 57.158 42.857 0.00 0.00 33.95 4.20
4462 5167 2.810274 GTTTGGGGAAACTAAGACGACC 59.190 50.000 0.00 0.00 0.00 4.79
4507 5212 9.595823 TGAACTTATAGAAACATACAGTTAGCC 57.404 33.333 0.00 0.00 40.26 3.93
4535 5241 6.200286 GGAAAGATTATGAAAGCATGCATGTG 59.800 38.462 26.79 5.68 35.94 3.21
4548 5254 3.775661 TGCATGTGAGCAATCAATCAG 57.224 42.857 0.00 0.00 42.46 2.90
4563 5269 4.887748 TCAATCAGAAAGCGAAGAAGAGT 58.112 39.130 0.00 0.00 0.00 3.24
4577 5283 2.680352 GAGTGCCCAGTCGGAGGA 60.680 66.667 0.00 0.00 0.00 3.71
4582 5288 1.065709 GTGCCCAGTCGGAGGAAATTA 60.066 52.381 0.00 0.00 0.00 1.40
4781 5488 7.370383 AGAATGAAGCGAAATGTATTGTGTTT 58.630 30.769 0.00 0.00 0.00 2.83
4819 5526 6.530019 AGTTTGATTTTCAACTGAAGGTGT 57.470 33.333 0.00 0.00 35.89 4.16
4825 5532 4.916983 TTTCAACTGAAGGTGTCATTGG 57.083 40.909 0.00 0.00 35.07 3.16
4892 5602 5.460419 GTGTCACAGAAGTACAGACTTGAAG 59.540 44.000 0.00 0.00 46.23 3.02
4934 5644 6.422100 GCTGACTGAGGTACATGTATTATGTG 59.578 42.308 9.18 1.60 33.76 3.21
4984 5694 3.004752 ACATTGACATGGGTTAGGCTC 57.995 47.619 0.00 0.00 34.27 4.70
5032 5742 6.405176 CGCATGACCAGCATTCTCTATCTATA 60.405 42.308 0.00 0.00 34.15 1.31
5037 5747 9.716531 TGACCAGCATTCTCTATCTATATTTTG 57.283 33.333 0.00 0.00 0.00 2.44
5079 5790 2.079925 GCTTTGAAGATTCTGGCGACT 58.920 47.619 0.00 0.00 0.00 4.18
5103 5814 6.779860 TGTTGAGGATGATGATGATGATGAT 58.220 36.000 0.00 0.00 0.00 2.45
5104 5815 6.655003 TGTTGAGGATGATGATGATGATGATG 59.345 38.462 0.00 0.00 0.00 3.07
5105 5816 6.620877 TGAGGATGATGATGATGATGATGA 57.379 37.500 0.00 0.00 0.00 2.92
5106 5817 7.200434 TGAGGATGATGATGATGATGATGAT 57.800 36.000 0.00 0.00 0.00 2.45
5107 5818 7.050377 TGAGGATGATGATGATGATGATGATG 58.950 38.462 0.00 0.00 0.00 3.07
5109 5820 6.069381 AGGATGATGATGATGATGATGATGGT 60.069 38.462 0.00 0.00 0.00 3.55
5110 5821 6.038714 GGATGATGATGATGATGATGATGGTG 59.961 42.308 0.00 0.00 0.00 4.17
5111 5822 4.700213 TGATGATGATGATGATGATGGTGC 59.300 41.667 0.00 0.00 0.00 5.01
5112 5823 4.093472 TGATGATGATGATGATGGTGCA 57.907 40.909 0.00 0.00 0.00 4.57
5113 5824 4.072131 TGATGATGATGATGATGGTGCAG 58.928 43.478 0.00 0.00 0.00 4.41
5114 5825 3.849563 TGATGATGATGATGGTGCAGA 57.150 42.857 0.00 0.00 0.00 4.26
5115 5826 4.367039 TGATGATGATGATGGTGCAGAT 57.633 40.909 0.00 0.00 0.00 2.90
5116 5827 5.492855 TGATGATGATGATGGTGCAGATA 57.507 39.130 0.00 0.00 0.00 1.98
5117 5828 6.062258 TGATGATGATGATGGTGCAGATAT 57.938 37.500 0.00 0.00 0.00 1.63
5118 5829 6.113411 TGATGATGATGATGGTGCAGATATC 58.887 40.000 0.00 0.00 0.00 1.63
5119 5830 5.492855 TGATGATGATGGTGCAGATATCA 57.507 39.130 5.32 9.18 35.52 2.15
5120 5831 6.062258 TGATGATGATGGTGCAGATATCAT 57.938 37.500 16.05 16.05 42.50 2.45
5121 5832 6.481643 TGATGATGATGGTGCAGATATCATT 58.518 36.000 16.78 6.66 40.56 2.57
5162 5873 2.649816 AGAAAGTAGCCCCAGGAAACAT 59.350 45.455 0.00 0.00 0.00 2.71
5307 6034 1.474320 CGAGGGGATAAATGTGGCGAA 60.474 52.381 0.00 0.00 0.00 4.70
5407 6134 2.587060 TCTCATCCATACAACCCCCT 57.413 50.000 0.00 0.00 0.00 4.79
5408 6135 2.408565 TCTCATCCATACAACCCCCTC 58.591 52.381 0.00 0.00 0.00 4.30
5409 6136 2.126882 CTCATCCATACAACCCCCTCA 58.873 52.381 0.00 0.00 0.00 3.86
5410 6137 2.713167 CTCATCCATACAACCCCCTCAT 59.287 50.000 0.00 0.00 0.00 2.90
5411 6138 2.711009 TCATCCATACAACCCCCTCATC 59.289 50.000 0.00 0.00 0.00 2.92
5412 6139 2.587060 TCCATACAACCCCCTCATCT 57.413 50.000 0.00 0.00 0.00 2.90
5413 6140 2.408565 TCCATACAACCCCCTCATCTC 58.591 52.381 0.00 0.00 0.00 2.75
5414 6141 2.022035 TCCATACAACCCCCTCATCTCT 60.022 50.000 0.00 0.00 0.00 3.10
5415 6142 2.370189 CCATACAACCCCCTCATCTCTC 59.630 54.545 0.00 0.00 0.00 3.20
5416 6143 3.312890 CATACAACCCCCTCATCTCTCT 58.687 50.000 0.00 0.00 0.00 3.10
5417 6144 1.872773 ACAACCCCCTCATCTCTCTC 58.127 55.000 0.00 0.00 0.00 3.20
5418 6145 1.364328 ACAACCCCCTCATCTCTCTCT 59.636 52.381 0.00 0.00 0.00 3.10
5419 6146 2.038659 CAACCCCCTCATCTCTCTCTC 58.961 57.143 0.00 0.00 0.00 3.20
5434 6167 3.008923 TCTCTCTCTCTCTCTCAACTGCA 59.991 47.826 0.00 0.00 0.00 4.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.955178 ACGAGATAGAGGATGGCACG 59.045 55.000 0.00 0.00 0.00 5.34
1 2 1.068885 CGACGAGATAGAGGATGGCAC 60.069 57.143 0.00 0.00 0.00 5.01
3 4 0.523966 CCGACGAGATAGAGGATGGC 59.476 60.000 0.00 0.00 0.00 4.40
4 5 1.537638 CACCGACGAGATAGAGGATGG 59.462 57.143 0.00 0.00 0.00 3.51
5 6 1.537638 CCACCGACGAGATAGAGGATG 59.462 57.143 0.00 0.00 0.00 3.51
6 7 1.898902 CCACCGACGAGATAGAGGAT 58.101 55.000 0.00 0.00 0.00 3.24
7 8 0.818445 GCCACCGACGAGATAGAGGA 60.818 60.000 0.00 0.00 0.00 3.71
31 32 3.531207 TGGCGGAGATGAGGCGAG 61.531 66.667 0.00 0.00 35.52 5.03
95 96 3.473647 TGATGAGGAGGGCGGCAG 61.474 66.667 12.47 0.00 0.00 4.85
96 97 3.785859 GTGATGAGGAGGGCGGCA 61.786 66.667 12.47 0.00 0.00 5.69
104 105 1.552337 GAGACAAGGCAGTGATGAGGA 59.448 52.381 0.00 0.00 0.00 3.71
126 127 2.840102 CCACTAGGAGGAGGCCCG 60.840 72.222 0.00 0.00 36.89 6.13
138 139 2.750166 GCATCTAGCTATCGCTCCACTA 59.250 50.000 0.00 0.00 45.15 2.74
149 150 2.289072 GCAAATCCTCGGCATCTAGCTA 60.289 50.000 0.00 0.00 44.79 3.32
150 151 1.542108 GCAAATCCTCGGCATCTAGCT 60.542 52.381 0.00 0.00 44.79 3.32
151 152 0.871057 GCAAATCCTCGGCATCTAGC 59.129 55.000 0.00 0.00 44.65 3.42
165 166 1.025812 TTGTCGTTTCCACCGCAAAT 58.974 45.000 0.00 0.00 0.00 2.32
179 180 2.290093 GGATCTAGGAGGTACGTTGTCG 59.710 54.545 0.00 0.00 43.34 4.35
183 184 1.316651 GCGGATCTAGGAGGTACGTT 58.683 55.000 0.00 0.00 0.00 3.99
187 188 1.074423 CCGGCGGATCTAGGAGGTA 59.926 63.158 24.41 0.00 0.00 3.08
188 189 2.082836 ATCCGGCGGATCTAGGAGGT 62.083 60.000 34.54 11.59 38.09 3.85
207 208 4.124238 CCTTCACGTTGTTTCCTCTACAA 58.876 43.478 0.00 0.00 33.37 2.41
208 209 3.724374 CCTTCACGTTGTTTCCTCTACA 58.276 45.455 0.00 0.00 0.00 2.74
246 247 2.989253 TTCTCGCCGGAGCACTGA 60.989 61.111 5.05 0.00 40.26 3.41
269 270 0.175989 GTCACGGTGATTCCCTCTCC 59.824 60.000 14.78 0.00 34.71 3.71
272 273 0.179134 CTCGTCACGGTGATTCCCTC 60.179 60.000 14.78 0.00 0.00 4.30
287 288 0.107508 CATTCCCCACTGCATCTCGT 60.108 55.000 0.00 0.00 0.00 4.18
289 290 0.548031 TCCATTCCCCACTGCATCTC 59.452 55.000 0.00 0.00 0.00 2.75
296 297 3.321950 CTCCTCTTATCCATTCCCCACT 58.678 50.000 0.00 0.00 0.00 4.00
314 315 2.336809 CTCGCCGATGCTACCTCC 59.663 66.667 0.00 0.00 34.43 4.30
319 320 2.758327 ACCCACTCGCCGATGCTA 60.758 61.111 0.00 0.00 34.43 3.49
343 344 1.073763 AGACACAATGCAGCCCACTTA 59.926 47.619 0.00 0.00 0.00 2.24
355 356 3.994392 GTGTATGGTGAACGAGACACAAT 59.006 43.478 15.56 0.00 43.24 2.71
374 375 4.974438 TCGCCAAGGGGGAGGTGT 62.974 66.667 3.15 0.00 39.75 4.16
401 404 0.034756 CACATTGACCCCTCACGTCA 59.965 55.000 0.00 0.00 38.46 4.35
408 411 3.505790 TTGGCGCACATTGACCCCT 62.506 57.895 10.83 0.00 0.00 4.79
409 412 2.988684 TTGGCGCACATTGACCCC 60.989 61.111 10.83 0.00 0.00 4.95
417 420 1.163420 AACGTGAATCTTGGCGCACA 61.163 50.000 10.83 1.22 0.00 4.57
433 436 0.865769 CTCCCGTTGGACTGAAAACG 59.134 55.000 1.17 1.17 46.61 3.60
441 444 0.744771 GGAAGCATCTCCCGTTGGAC 60.745 60.000 0.00 0.00 35.03 4.02
492 495 3.073062 GGCTGACCATGACCAGGTATAAT 59.927 47.826 13.64 0.00 40.09 1.28
495 498 0.839946 GGCTGACCATGACCAGGTAT 59.160 55.000 13.64 0.00 40.09 2.73
496 499 1.271840 GGGCTGACCATGACCAGGTA 61.272 60.000 13.64 0.00 40.09 3.08
497 500 2.606587 GGGCTGACCATGACCAGGT 61.607 63.158 13.64 0.00 43.46 4.00
498 501 2.273449 GGGCTGACCATGACCAGG 59.727 66.667 13.64 0.00 39.85 4.45
499 502 2.124983 CGGGCTGACCATGACCAG 60.125 66.667 0.00 1.89 40.22 4.00
500 503 2.606213 TCGGGCTGACCATGACCA 60.606 61.111 0.00 0.00 40.22 4.02
501 504 2.125106 GTCGGGCTGACCATGACC 60.125 66.667 15.76 0.00 42.04 4.02
534 537 2.068277 GATAAGGTCGGACCGGGTCG 62.068 65.000 20.87 15.30 44.90 4.79
535 538 1.738432 GATAAGGTCGGACCGGGTC 59.262 63.158 20.87 19.06 44.90 4.46
536 539 1.759692 GGATAAGGTCGGACCGGGT 60.760 63.158 20.87 12.91 44.90 5.28
537 540 1.119574 ATGGATAAGGTCGGACCGGG 61.120 60.000 20.87 0.00 44.90 5.73
538 541 0.033504 CATGGATAAGGTCGGACCGG 59.966 60.000 20.87 0.00 44.90 5.28
539 542 0.033504 CCATGGATAAGGTCGGACCG 59.966 60.000 20.87 7.84 44.90 4.79
540 543 0.396811 CCCATGGATAAGGTCGGACC 59.603 60.000 19.61 19.61 38.99 4.46
541 544 1.070289 GACCCATGGATAAGGTCGGAC 59.930 57.143 15.22 0.00 40.65 4.79
542 545 1.420430 GACCCATGGATAAGGTCGGA 58.580 55.000 15.22 0.00 40.65 4.55
545 548 0.396811 CCCGACCCATGGATAAGGTC 59.603 60.000 15.22 10.66 45.49 3.85
546 549 1.705997 GCCCGACCCATGGATAAGGT 61.706 60.000 15.22 0.83 36.31 3.50
547 550 1.073199 GCCCGACCCATGGATAAGG 59.927 63.158 15.22 9.87 0.00 2.69
548 551 0.035458 GAGCCCGACCCATGGATAAG 59.965 60.000 15.22 0.00 0.00 1.73
549 552 1.754380 CGAGCCCGACCCATGGATAA 61.754 60.000 15.22 0.00 38.22 1.75
550 553 2.207229 CGAGCCCGACCCATGGATA 61.207 63.158 15.22 0.00 38.22 2.59
551 554 3.550431 CGAGCCCGACCCATGGAT 61.550 66.667 15.22 0.00 38.22 3.41
564 567 1.087501 CTCAAAACTTAGGCCCGAGC 58.912 55.000 0.00 0.00 38.76 5.03
565 568 1.087501 GCTCAAAACTTAGGCCCGAG 58.912 55.000 0.00 0.00 0.00 4.63
566 569 0.322187 GGCTCAAAACTTAGGCCCGA 60.322 55.000 0.00 0.00 37.12 5.14
567 570 2.180674 GGCTCAAAACTTAGGCCCG 58.819 57.895 0.00 0.00 37.12 6.13
570 573 1.468914 CTTCGGGCTCAAAACTTAGGC 59.531 52.381 0.00 0.00 37.55 3.93
571 574 1.468914 GCTTCGGGCTCAAAACTTAGG 59.531 52.381 0.00 0.00 38.06 2.69
572 575 2.902065 GCTTCGGGCTCAAAACTTAG 57.098 50.000 0.00 0.00 38.06 2.18
606 609 4.832608 AAATCGACGGGCTCGGGC 62.833 66.667 12.42 0.00 43.16 6.13
607 610 2.585247 GAAATCGACGGGCTCGGG 60.585 66.667 12.42 0.86 43.16 5.14
608 611 2.954868 CGAAATCGACGGGCTCGG 60.955 66.667 12.42 0.00 43.16 4.63
609 612 3.617538 GCGAAATCGACGGGCTCG 61.618 66.667 3.27 3.27 44.44 5.03
610 613 3.262686 GGCGAAATCGACGGGCTC 61.263 66.667 7.06 0.00 43.02 4.70
617 620 4.509616 TCTTCCTTAAATGGCGAAATCGA 58.490 39.130 7.06 0.00 43.02 3.59
618 621 4.260784 CCTCTTCCTTAAATGGCGAAATCG 60.261 45.833 0.00 0.00 43.27 3.34
619 622 4.498177 GCCTCTTCCTTAAATGGCGAAATC 60.498 45.833 0.00 0.00 30.28 2.17
620 623 3.381590 GCCTCTTCCTTAAATGGCGAAAT 59.618 43.478 0.00 0.00 30.28 2.17
621 624 2.752903 GCCTCTTCCTTAAATGGCGAAA 59.247 45.455 0.00 0.00 30.28 3.46
622 625 2.365582 GCCTCTTCCTTAAATGGCGAA 58.634 47.619 0.00 0.00 30.28 4.70
623 626 1.408266 GGCCTCTTCCTTAAATGGCGA 60.408 52.381 0.00 0.00 37.30 5.54
624 627 1.025041 GGCCTCTTCCTTAAATGGCG 58.975 55.000 0.00 0.00 37.30 5.69
625 628 2.027385 CAGGCCTCTTCCTTAAATGGC 58.973 52.381 0.00 0.00 36.32 4.40
626 629 2.659428 CCAGGCCTCTTCCTTAAATGG 58.341 52.381 0.00 0.00 33.25 3.16
627 630 2.027385 GCCAGGCCTCTTCCTTAAATG 58.973 52.381 0.00 0.00 33.25 2.32
628 631 1.063642 GGCCAGGCCTCTTCCTTAAAT 60.064 52.381 24.99 0.00 46.69 1.40
629 632 0.331616 GGCCAGGCCTCTTCCTTAAA 59.668 55.000 24.99 0.00 46.69 1.52
630 633 1.999346 GGCCAGGCCTCTTCCTTAA 59.001 57.895 24.99 0.00 46.69 1.85
631 634 3.741325 GGCCAGGCCTCTTCCTTA 58.259 61.111 24.99 0.00 46.69 2.69
654 657 3.536956 TCATACTAAAAGCCCGTCAGG 57.463 47.619 0.00 0.00 39.47 3.86
655 658 3.809832 CCATCATACTAAAAGCCCGTCAG 59.190 47.826 0.00 0.00 0.00 3.51
656 659 3.433031 CCCATCATACTAAAAGCCCGTCA 60.433 47.826 0.00 0.00 0.00 4.35
657 660 3.139077 CCCATCATACTAAAAGCCCGTC 58.861 50.000 0.00 0.00 0.00 4.79
658 661 2.748465 GCCCATCATACTAAAAGCCCGT 60.748 50.000 0.00 0.00 0.00 5.28
659 662 1.880027 GCCCATCATACTAAAAGCCCG 59.120 52.381 0.00 0.00 0.00 6.13
660 663 2.239400 GGCCCATCATACTAAAAGCCC 58.761 52.381 0.00 0.00 32.93 5.19
661 664 1.880027 CGGCCCATCATACTAAAAGCC 59.120 52.381 0.00 0.00 35.78 4.35
662 665 1.880027 CCGGCCCATCATACTAAAAGC 59.120 52.381 0.00 0.00 0.00 3.51
663 666 2.504367 CCCGGCCCATCATACTAAAAG 58.496 52.381 0.00 0.00 0.00 2.27
664 667 1.477923 GCCCGGCCCATCATACTAAAA 60.478 52.381 0.00 0.00 0.00 1.52
665 668 0.109723 GCCCGGCCCATCATACTAAA 59.890 55.000 0.00 0.00 0.00 1.85
666 669 0.766674 AGCCCGGCCCATCATACTAA 60.767 55.000 5.55 0.00 0.00 2.24
667 670 1.152118 AGCCCGGCCCATCATACTA 60.152 57.895 5.55 0.00 0.00 1.82
668 671 2.448542 AGCCCGGCCCATCATACT 60.449 61.111 5.55 0.00 0.00 2.12
669 672 2.032681 GAGCCCGGCCCATCATAC 59.967 66.667 5.55 0.00 0.00 2.39
670 673 3.625897 CGAGCCCGGCCCATCATA 61.626 66.667 5.55 0.00 0.00 2.15
726 729 0.755686 ACCAAAGCCCGATGCAAAAA 59.244 45.000 0.00 0.00 44.83 1.94
727 730 0.755686 AACCAAAGCCCGATGCAAAA 59.244 45.000 0.00 0.00 44.83 2.44
728 731 0.033228 CAACCAAAGCCCGATGCAAA 59.967 50.000 0.00 0.00 44.83 3.68
729 732 1.664873 CAACCAAAGCCCGATGCAA 59.335 52.632 0.00 0.00 44.83 4.08
730 733 2.274645 CCAACCAAAGCCCGATGCA 61.275 57.895 0.00 0.00 44.83 3.96
731 734 2.573340 CCAACCAAAGCCCGATGC 59.427 61.111 0.00 0.00 41.71 3.91
732 735 2.573340 GCCAACCAAAGCCCGATG 59.427 61.111 0.00 0.00 0.00 3.84
733 736 2.679996 GGCCAACCAAAGCCCGAT 60.680 61.111 0.00 0.00 43.76 4.18
759 762 1.418908 ATACCTGGCCATTCCTCGGG 61.419 60.000 5.51 4.26 35.26 5.14
760 763 1.276421 CTATACCTGGCCATTCCTCGG 59.724 57.143 5.51 5.16 35.26 4.63
761 764 1.338200 GCTATACCTGGCCATTCCTCG 60.338 57.143 5.51 0.00 35.26 4.63
762 765 1.981495 AGCTATACCTGGCCATTCCTC 59.019 52.381 5.51 0.00 35.26 3.71
763 766 1.981495 GAGCTATACCTGGCCATTCCT 59.019 52.381 5.51 0.00 35.26 3.36
764 767 1.981495 AGAGCTATACCTGGCCATTCC 59.019 52.381 5.51 0.00 0.00 3.01
765 768 2.634940 TCAGAGCTATACCTGGCCATTC 59.365 50.000 5.51 0.00 0.00 2.67
766 769 2.694397 TCAGAGCTATACCTGGCCATT 58.306 47.619 5.51 0.00 0.00 3.16
767 770 2.405618 TCAGAGCTATACCTGGCCAT 57.594 50.000 5.51 0.00 0.00 4.40
768 771 2.369860 CAATCAGAGCTATACCTGGCCA 59.630 50.000 4.71 4.71 0.00 5.36
769 772 2.634940 TCAATCAGAGCTATACCTGGCC 59.365 50.000 0.00 0.00 0.00 5.36
770 773 4.550076 ATCAATCAGAGCTATACCTGGC 57.450 45.455 0.00 0.00 0.00 4.85
771 774 5.167121 CGAATCAATCAGAGCTATACCTGG 58.833 45.833 0.72 0.00 0.00 4.45
772 775 5.167121 CCGAATCAATCAGAGCTATACCTG 58.833 45.833 0.00 0.00 0.00 4.00
773 776 4.322349 GCCGAATCAATCAGAGCTATACCT 60.322 45.833 0.00 0.00 0.00 3.08
774 777 3.929610 GCCGAATCAATCAGAGCTATACC 59.070 47.826 0.00 0.00 0.00 2.73
775 778 4.560128 TGCCGAATCAATCAGAGCTATAC 58.440 43.478 0.00 0.00 0.00 1.47
776 779 4.871933 TGCCGAATCAATCAGAGCTATA 57.128 40.909 0.00 0.00 0.00 1.31
777 780 3.758755 TGCCGAATCAATCAGAGCTAT 57.241 42.857 0.00 0.00 0.00 2.97
778 781 3.198068 GTTGCCGAATCAATCAGAGCTA 58.802 45.455 0.00 0.00 0.00 3.32
779 782 2.012673 GTTGCCGAATCAATCAGAGCT 58.987 47.619 0.00 0.00 0.00 4.09
780 783 1.267732 CGTTGCCGAATCAATCAGAGC 60.268 52.381 0.00 0.00 35.63 4.09
781 784 2.002586 ACGTTGCCGAATCAATCAGAG 58.997 47.619 0.00 0.00 37.88 3.35
782 785 1.731709 CACGTTGCCGAATCAATCAGA 59.268 47.619 0.00 0.00 37.88 3.27
783 786 1.731709 TCACGTTGCCGAATCAATCAG 59.268 47.619 0.00 0.00 37.88 2.90
784 787 1.463056 GTCACGTTGCCGAATCAATCA 59.537 47.619 0.00 0.00 37.88 2.57
785 788 1.202031 GGTCACGTTGCCGAATCAATC 60.202 52.381 0.00 0.00 37.88 2.67
786 789 0.802494 GGTCACGTTGCCGAATCAAT 59.198 50.000 0.00 0.00 37.88 2.57
833 836 2.663630 TTCTCTATCCGAGCGCGTGC 62.664 60.000 14.39 14.39 39.70 5.34
1094 1123 3.659089 CTACGGGGTGGACTTGGCG 62.659 68.421 0.00 0.00 0.00 5.69
1137 1166 1.069636 CAAGCGGAACTGAGCAAGAAC 60.070 52.381 0.00 0.00 35.48 3.01
1218 1247 4.363991 ACAGAAGCACCTCAAATCTCTT 57.636 40.909 0.00 0.00 0.00 2.85
1353 1393 4.595538 TTCGCACGAACCGCCACT 62.596 61.111 0.49 0.00 0.00 4.00
1354 1394 4.072088 CTTCGCACGAACCGCCAC 62.072 66.667 0.49 0.00 0.00 5.01
1418 1458 0.394762 GGCACATCAAGGCATCTCCA 60.395 55.000 0.00 0.00 37.29 3.86
1468 1508 6.798482 TGAATCATGCCAATCAACATAGAAC 58.202 36.000 0.00 0.00 0.00 3.01
1520 1560 1.148310 ATGCAAAACTCTGGTCGACG 58.852 50.000 9.92 0.00 0.00 5.12
1546 1586 2.961526 TCGTAGAACATCAAGAGCCC 57.038 50.000 0.00 0.00 0.00 5.19
1607 1647 6.959639 AATGACCAGTGTACTTTGACAAAT 57.040 33.333 0.05 0.00 0.00 2.32
1671 1711 8.686334 GGTATATGATCAAATGCCCGATTTTAT 58.314 33.333 0.00 0.00 31.41 1.40
1872 1914 1.367599 GGCAGTGAGCTAGCAGCAAG 61.368 60.000 18.83 11.31 45.56 4.01
2080 2122 1.273327 CCAGATGGTGGTTTGAAAGGC 59.727 52.381 0.00 0.00 42.17 4.35
2171 2213 1.549203 ACATTGGCAGACATGTTCCC 58.451 50.000 0.00 1.44 0.00 3.97
2288 2330 5.267776 CAAAAGGCAAACAAGCTTCAAATG 58.732 37.500 0.00 0.00 34.17 2.32
2433 2475 5.184096 CGAGTACATGCTATTCCCATAGAGT 59.816 44.000 0.00 0.00 35.20 3.24
2469 2511 4.609018 CCATAGAGGCCGCCACCG 62.609 72.222 13.15 0.00 33.69 4.94
2561 2603 2.906897 CACCCATGCCGCCCATAC 60.907 66.667 0.00 0.00 31.47 2.39
2562 2604 4.202574 CCACCCATGCCGCCCATA 62.203 66.667 0.00 0.00 31.47 2.74
2565 2607 4.204028 ATACCACCCATGCCGCCC 62.204 66.667 0.00 0.00 0.00 6.13
2566 2608 2.906897 CATACCACCCATGCCGCC 60.907 66.667 0.00 0.00 0.00 6.13
2567 2609 2.906897 CCATACCACCCATGCCGC 60.907 66.667 0.00 0.00 0.00 6.53
2568 2610 2.203337 CCCATACCACCCATGCCG 60.203 66.667 0.00 0.00 0.00 5.69
2569 2611 2.521708 GCCCATACCACCCATGCC 60.522 66.667 0.00 0.00 0.00 4.40
2570 2612 2.906897 CGCCCATACCACCCATGC 60.907 66.667 0.00 0.00 0.00 4.06
2571 2613 2.203337 CCGCCCATACCACCCATG 60.203 66.667 0.00 0.00 0.00 3.66
2572 2614 4.204028 GCCGCCCATACCACCCAT 62.204 66.667 0.00 0.00 0.00 4.00
2574 2616 4.204028 ATGCCGCCCATACCACCC 62.204 66.667 0.00 0.00 30.69 4.61
2575 2617 2.906897 CATGCCGCCCATACCACC 60.907 66.667 0.00 0.00 31.47 4.61
2576 2618 2.906897 CCATGCCGCCCATACCAC 60.907 66.667 0.00 0.00 31.47 4.16
2577 2619 4.202574 CCCATGCCGCCCATACCA 62.203 66.667 0.00 0.00 31.47 3.25
2578 2620 4.204028 ACCCATGCCGCCCATACC 62.204 66.667 0.00 0.00 31.47 2.73
2579 2621 2.906897 CACCCATGCCGCCCATAC 60.907 66.667 0.00 0.00 31.47 2.39
2580 2622 4.202574 CCACCCATGCCGCCCATA 62.203 66.667 0.00 0.00 31.47 2.74
2790 2860 8.809159 TTTCGCATTAATGAACATTCAGAAAA 57.191 26.923 19.73 1.63 41.08 2.29
2973 3050 6.341316 ACCATGATGACACACTAGAATGTAC 58.659 40.000 0.00 0.00 0.00 2.90
3111 3190 2.631160 TACGGGGCCTTCATATGTTG 57.369 50.000 0.84 0.00 0.00 3.33
3112 3191 2.708861 TCATACGGGGCCTTCATATGTT 59.291 45.455 0.84 0.00 0.00 2.71
3116 3195 2.500098 GCTATCATACGGGGCCTTCATA 59.500 50.000 0.84 0.00 0.00 2.15
3187 3267 6.952773 AACAGCTCACAGTAATTAAAACCA 57.047 33.333 0.00 0.00 0.00 3.67
3314 3394 1.460743 CTCGTTCTTTTCGCATGCTCA 59.539 47.619 17.13 0.00 0.00 4.26
3380 3463 2.440796 CCATGGCCGCTGACCAAT 60.441 61.111 0.00 0.00 41.49 3.16
3481 3724 6.071560 CCCACACACCTTCGCTATATAAGATA 60.072 42.308 0.00 0.00 0.00 1.98
3521 3764 4.022589 AGTCCATCATGCACAGTGAAAAAG 60.023 41.667 4.15 0.00 0.00 2.27
3528 3771 0.679002 GCCAGTCCATCATGCACAGT 60.679 55.000 0.00 0.00 0.00 3.55
3554 3797 1.002624 GGAACGGCTTGGTCATCCA 60.003 57.895 0.00 0.00 42.66 3.41
3627 3870 0.463654 AGAACCACGCTCTGCAACAA 60.464 50.000 0.00 0.00 0.00 2.83
3644 3887 0.240145 CGTACTGACACGGAGCAAGA 59.760 55.000 0.00 0.00 38.26 3.02
3688 4206 2.138320 CACAAGCTCGATGTCACACTT 58.862 47.619 0.00 0.00 0.00 3.16
3712 4235 4.330944 ACGACCACAGACTAATTGAACA 57.669 40.909 0.00 0.00 0.00 3.18
3762 4448 1.470098 GCAAGCTGATGAACGGACATT 59.530 47.619 0.00 0.00 0.00 2.71
4090 4795 1.164041 CGCCCAAAGAAACTGACGGT 61.164 55.000 0.00 0.00 0.00 4.83
4092 4797 0.512952 CTCGCCCAAAGAAACTGACG 59.487 55.000 0.00 0.00 0.00 4.35
4122 4827 3.006323 AGGCTTGTGTGTTTTGTTCAACA 59.994 39.130 0.00 0.00 34.15 3.33
4188 4893 3.081804 CCCAATACAAGCGAGGAAAACT 58.918 45.455 0.00 0.00 0.00 2.66
4192 4897 2.817258 CAAACCCAATACAAGCGAGGAA 59.183 45.455 0.00 0.00 0.00 3.36
4204 4909 5.421693 TGTAAGCATGCTATTCAAACCCAAT 59.578 36.000 23.00 2.44 0.00 3.16
4419 5124 0.184692 TGTCCCATGAGTTGTTGGCA 59.815 50.000 0.00 0.00 0.00 4.92
4460 5165 0.965363 CGGCACATAAAAGGGCAGGT 60.965 55.000 0.00 0.00 0.00 4.00
4462 5167 0.887933 AACGGCACATAAAAGGGCAG 59.112 50.000 0.00 0.00 0.00 4.85
4507 5212 6.334989 TGCATGCTTTCATAATCTTTCCTTG 58.665 36.000 20.33 0.00 0.00 3.61
4535 5241 4.093998 TCTTCGCTTTCTGATTGATTGCTC 59.906 41.667 0.00 0.00 0.00 4.26
4547 5253 1.609320 GGGCACTCTTCTTCGCTTTCT 60.609 52.381 0.00 0.00 0.00 2.52
4548 5254 0.799393 GGGCACTCTTCTTCGCTTTC 59.201 55.000 0.00 0.00 0.00 2.62
4563 5269 1.281419 TAATTTCCTCCGACTGGGCA 58.719 50.000 0.00 0.00 35.24 5.36
4577 5283 9.431887 TCTTTCGCTAACTACAACAGATAATTT 57.568 29.630 0.00 0.00 0.00 1.82
4582 5288 6.145696 GTGTTCTTTCGCTAACTACAACAGAT 59.854 38.462 0.00 0.00 0.00 2.90
4645 5351 2.159043 ACTGGACATCATTAGGCTCACG 60.159 50.000 0.00 0.00 0.00 4.35
4740 5447 8.180267 CGCTTCATTCTTTTCAAGATAACAGAT 58.820 33.333 0.00 0.00 37.38 2.90
4741 5448 7.387673 TCGCTTCATTCTTTTCAAGATAACAGA 59.612 33.333 0.00 0.00 37.38 3.41
4819 5526 5.357878 GCACTTCATTTACCATCTCCAATGA 59.642 40.000 0.00 0.00 34.54 2.57
4825 5532 6.012658 TGTTTGCACTTCATTTACCATCTC 57.987 37.500 0.00 0.00 0.00 2.75
4934 5644 0.670162 TGGCTGCTTTGACTTCTTGC 59.330 50.000 0.00 0.00 0.00 4.01
4984 5694 8.543774 TGCGACCAACAATTAAAGTTATTTTTG 58.456 29.630 0.00 0.00 0.00 2.44
5007 5717 2.229675 TAGAGAATGCTGGTCATGCG 57.770 50.000 0.00 0.00 35.77 4.73
5037 5747 7.269477 AGCCAGCTTCATCAGTTATTAATTC 57.731 36.000 0.00 0.00 0.00 2.17
5056 5766 1.131883 CGCCAGAATCTTCAAAGCCAG 59.868 52.381 0.00 0.00 0.00 4.85
5079 5790 6.182507 TCATCATCATCATCATCCTCAACA 57.817 37.500 0.00 0.00 0.00 3.33
5103 5814 7.455891 AGACAATAATGATATCTGCACCATCA 58.544 34.615 3.98 3.35 33.47 3.07
5104 5815 7.918536 AGACAATAATGATATCTGCACCATC 57.081 36.000 3.98 0.00 0.00 3.51
5105 5816 7.722728 ACAAGACAATAATGATATCTGCACCAT 59.277 33.333 3.98 0.00 0.00 3.55
5106 5817 7.056006 ACAAGACAATAATGATATCTGCACCA 58.944 34.615 3.98 0.00 0.00 4.17
5107 5818 7.443575 AGACAAGACAATAATGATATCTGCACC 59.556 37.037 3.98 0.00 0.00 5.01
5109 5820 7.658982 GGAGACAAGACAATAATGATATCTGCA 59.341 37.037 3.98 0.00 0.00 4.41
5110 5821 7.658982 TGGAGACAAGACAATAATGATATCTGC 59.341 37.037 3.98 0.00 37.44 4.26
5149 5860 0.038166 TCAGACATGTTTCCTGGGGC 59.962 55.000 11.83 0.00 0.00 5.80
5162 5873 0.615331 GATCAGGGGTGCTTCAGACA 59.385 55.000 0.00 0.00 0.00 3.41
5307 6034 2.311841 CAACCCTCCCTTCCCTACAAAT 59.688 50.000 0.00 0.00 0.00 2.32
5407 6134 5.426509 AGTTGAGAGAGAGAGAGAGAGATGA 59.573 44.000 0.00 0.00 0.00 2.92
5408 6135 5.526479 CAGTTGAGAGAGAGAGAGAGAGATG 59.474 48.000 0.00 0.00 0.00 2.90
5409 6136 5.678583 CAGTTGAGAGAGAGAGAGAGAGAT 58.321 45.833 0.00 0.00 0.00 2.75
5410 6137 4.623886 GCAGTTGAGAGAGAGAGAGAGAGA 60.624 50.000 0.00 0.00 0.00 3.10
5411 6138 3.624861 GCAGTTGAGAGAGAGAGAGAGAG 59.375 52.174 0.00 0.00 0.00 3.20
5412 6139 3.008923 TGCAGTTGAGAGAGAGAGAGAGA 59.991 47.826 0.00 0.00 0.00 3.10
5413 6140 3.127548 GTGCAGTTGAGAGAGAGAGAGAG 59.872 52.174 0.00 0.00 0.00 3.20
5414 6141 3.081061 GTGCAGTTGAGAGAGAGAGAGA 58.919 50.000 0.00 0.00 0.00 3.10
5415 6142 2.819019 TGTGCAGTTGAGAGAGAGAGAG 59.181 50.000 0.00 0.00 0.00 3.20
5416 6143 2.868899 TGTGCAGTTGAGAGAGAGAGA 58.131 47.619 0.00 0.00 0.00 3.10
5417 6144 3.657015 TTGTGCAGTTGAGAGAGAGAG 57.343 47.619 0.00 0.00 0.00 3.20
5418 6145 4.613925 AATTGTGCAGTTGAGAGAGAGA 57.386 40.909 0.00 0.00 0.00 3.10
5419 6146 6.817641 AGAATAATTGTGCAGTTGAGAGAGAG 59.182 38.462 0.00 0.00 0.00 3.20


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

AutoCloner maintained by Alex Coulton.