Multiple sequence alignment - TraesCS5A01G071700

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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 TraesCS5A01G071700 chr5A 100.000 4194 0 0 1 4194 81498729 81502922 0.000000e+00 7745.0
1 TraesCS5A01G071700 chr5A 98.276 58 1 0 555 612 81499225 81499282 7.420000e-18 102.0
2 TraesCS5A01G071700 chr5A 98.276 58 1 0 497 554 81499283 81499340 7.420000e-18 102.0
3 TraesCS5A01G071700 chr5B 92.755 3230 176 27 714 3916 93827469 93830667 0.000000e+00 4615.0
4 TraesCS5A01G071700 chr5B 79.294 821 142 17 1007 1804 94044001 94043186 2.200000e-152 549.0
5 TraesCS5A01G071700 chr5B 92.166 217 17 0 3911 4127 93839738 93839954 1.460000e-79 307.0
6 TraesCS5A01G071700 chr5B 100.000 33 0 0 4162 4194 243487506 243487474 1.260000e-05 62.1
7 TraesCS5A01G071700 chr5D 95.058 1821 77 5 555 2370 88362852 88364664 0.000000e+00 2852.0
8 TraesCS5A01G071700 chr5D 93.333 1770 94 8 2369 4127 88365431 88367187 0.000000e+00 2593.0
9 TraesCS5A01G071700 chr5D 86.691 541 38 20 4 536 88362377 88362891 1.690000e-158 569.0
10 TraesCS5A01G071700 chr5D 79.531 811 146 11 1007 1804 88460892 88460089 1.020000e-155 560.0
11 TraesCS5A01G071700 chr5D 94.737 38 2 0 4157 4194 457697356 457697319 4.530000e-05 60.2
12 TraesCS5A01G071700 chr5D 100.000 29 0 0 380 408 541379164 541379136 2.000000e-03 54.7
13 TraesCS5A01G071700 chr4B 78.036 387 63 18 3758 4127 63012657 63012276 1.520000e-54 224.0
14 TraesCS5A01G071700 chr4B 94.872 39 1 1 4157 4194 20795691 20795653 4.530000e-05 60.2
15 TraesCS5A01G071700 chr4D 79.331 329 47 14 3807 4116 43416455 43416781 1.180000e-50 211.0
16 TraesCS5A01G071700 chr4D 86.170 94 11 2 374 465 63955936 63955843 2.670000e-17 100.0
17 TraesCS5A01G071700 chr3D 82.249 169 26 3 372 538 341677687 341677521 4.370000e-30 143.0
18 TraesCS5A01G071700 chr7D 97.368 38 0 1 4158 4194 396016201 396016164 3.500000e-06 63.9
19 TraesCS5A01G071700 chr6A 97.143 35 1 0 4160 4194 1576315 1576281 4.530000e-05 60.2
20 TraesCS5A01G071700 chr6A 94.872 39 1 1 4157 4194 527679115 527679153 4.530000e-05 60.2
21 TraesCS5A01G071700 chr4A 94.737 38 2 0 4157 4194 122227924 122227887 4.530000e-05 60.2
22 TraesCS5A01G071700 chr2B 94.872 39 1 1 4157 4194 94947901 94947939 4.530000e-05 60.2
23 TraesCS5A01G071700 chr2B 88.000 50 6 0 381 430 237636552 237636503 4.530000e-05 60.2
24 TraesCS5A01G071700 chr2B 100.000 30 0 0 384 413 184593534 184593505 5.860000e-04 56.5
25 TraesCS5A01G071700 chr2B 92.500 40 2 1 4155 4194 626709267 626709305 5.860000e-04 56.5
26 TraesCS5A01G071700 chr2D 96.875 32 1 0 385 416 28769527 28769496 2.000000e-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 TraesCS5A01G071700 chr5A 81498729 81502922 4193 False 2649.666667 7745 98.850667 1 4194 3 chr5A.!!$F1 4193
1 TraesCS5A01G071700 chr5B 93827469 93830667 3198 False 4615.000000 4615 92.755000 714 3916 1 chr5B.!!$F1 3202
2 TraesCS5A01G071700 chr5B 94043186 94044001 815 True 549.000000 549 79.294000 1007 1804 1 chr5B.!!$R1 797
3 TraesCS5A01G071700 chr5D 88362377 88367187 4810 False 2004.666667 2852 91.694000 4 4127 3 chr5D.!!$F1 4123
4 TraesCS5A01G071700 chr5D 88460089 88460892 803 True 560.000000 560 79.531000 1007 1804 1 chr5D.!!$R1 797

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
554 561 0.107703 CTAAACGAGAGGCATGCCCA 60.108 55.000 33.14 7.34 36.58 5.36 F
568 575 0.256752 TGCCCAATGATGCAGTAGCT 59.743 50.000 0.00 0.00 42.74 3.32 F
822 832 0.409092 ATGCAACATGACCAGGGGAA 59.591 50.000 0.00 0.00 0.00 3.97 F
1428 1468 1.007734 CCGTATCGCTACCGTGCAT 60.008 57.895 0.00 0.00 35.54 3.96 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1543 1592 0.806884 ACAAACTCGAACGCCGTGAA 60.807 50.0 0.00 0.00 39.75 3.18 R
1926 1975 0.946221 CACTCACCAGGCAAGTCGTC 60.946 60.0 0.00 0.00 0.00 4.20 R
2634 3455 0.586319 CTTCGCCTTTGCAAGAACGA 59.414 50.0 13.54 13.54 37.32 3.85 R
3259 4080 1.014044 ATGCGCGTAGACAAGGTGTG 61.014 55.0 8.43 0.00 0.00 3.82 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
57 58 2.164422 GCTCCCAAATGAACAGTAAGGC 59.836 50.000 0.00 0.00 0.00 4.35
59 60 4.082125 CTCCCAAATGAACAGTAAGGCTT 58.918 43.478 4.58 4.58 0.00 4.35
98 99 5.927689 TGGCATTAAAGATGCTTGAGTTTTG 59.072 36.000 10.43 0.00 44.02 2.44
101 102 7.761249 GGCATTAAAGATGCTTGAGTTTTGTAT 59.239 33.333 10.43 0.00 44.02 2.29
112 113 7.018826 GCTTGAGTTTTGTATATGCGTGTAAA 58.981 34.615 0.00 0.00 0.00 2.01
113 114 7.535940 GCTTGAGTTTTGTATATGCGTGTAAAA 59.464 33.333 0.00 0.00 0.00 1.52
143 145 5.212532 GTCATATGACATTGGAGAGCTCT 57.787 43.478 27.33 18.28 44.18 4.09
144 146 4.989797 GTCATATGACATTGGAGAGCTCTG 59.010 45.833 27.33 9.88 44.18 3.35
177 182 4.600692 ATGCTCCAAAACCCAAGTTTAC 57.399 40.909 0.00 0.00 45.54 2.01
181 186 4.261867 GCTCCAAAACCCAAGTTTACGAAT 60.262 41.667 0.00 0.00 45.54 3.34
195 200 7.647907 AGTTTACGAATCTTTTTCGAAGCTA 57.352 32.000 13.98 0.00 43.97 3.32
196 201 8.252964 AGTTTACGAATCTTTTTCGAAGCTAT 57.747 30.769 13.98 0.00 43.97 2.97
236 241 2.804527 CCTCACATGACATATCGCCAAG 59.195 50.000 0.00 0.00 0.00 3.61
256 261 6.261826 GCCAAGATATTGCACACTCTTTAGAT 59.738 38.462 0.00 0.00 0.00 1.98
285 291 4.971220 CAGCATTTTTGTGCCATTGTTTTC 59.029 37.500 0.00 0.00 46.19 2.29
296 302 5.229678 GTGCCATTGTTTTCATTTTGTTTGC 59.770 36.000 0.00 0.00 0.00 3.68
297 303 4.739228 GCCATTGTTTTCATTTTGTTTGCC 59.261 37.500 0.00 0.00 0.00 4.52
311 318 9.922305 CATTTTGTTTGCCGTTTTTAGAATTTA 57.078 25.926 0.00 0.00 0.00 1.40
318 325 7.028926 TGCCGTTTTTAGAATTTACTGTTCA 57.971 32.000 0.00 0.00 0.00 3.18
344 351 6.436847 TCATAGATGGAGATGAACTCAGGATC 59.563 42.308 0.00 0.00 46.54 3.36
375 382 6.146510 CGCCACGCCTCTATATTACATTTTAA 59.853 38.462 0.00 0.00 0.00 1.52
397 404 8.964476 TTAAGGGTTTGCTAATTCTCATCTAG 57.036 34.615 0.00 0.00 0.00 2.43
402 409 7.716998 GGGTTTGCTAATTCTCATCTAGATGAA 59.283 37.037 30.28 20.06 46.10 2.57
433 440 6.212388 ACAAAGTCTCATCTGACTCCTACATT 59.788 38.462 0.00 0.00 45.49 2.71
435 442 7.962995 AAGTCTCATCTGACTCCTACATTAA 57.037 36.000 0.00 0.00 45.49 1.40
482 489 8.837788 AAAAGAAAAATCCCACATGAATCTTC 57.162 30.769 0.00 0.00 0.00 2.87
536 543 5.794894 ACGAGACTTGGTTATTTCACATCT 58.205 37.500 0.00 0.00 0.00 2.90
537 544 6.931838 ACGAGACTTGGTTATTTCACATCTA 58.068 36.000 0.00 0.00 0.00 1.98
538 545 7.383687 ACGAGACTTGGTTATTTCACATCTAA 58.616 34.615 0.00 0.00 0.00 2.10
539 546 7.876068 ACGAGACTTGGTTATTTCACATCTAAA 59.124 33.333 0.00 0.00 0.00 1.85
540 547 8.169268 CGAGACTTGGTTATTTCACATCTAAAC 58.831 37.037 0.00 0.00 0.00 2.01
541 548 8.029642 AGACTTGGTTATTTCACATCTAAACG 57.970 34.615 0.00 0.00 0.00 3.60
542 549 7.876068 AGACTTGGTTATTTCACATCTAAACGA 59.124 33.333 0.00 0.00 0.00 3.85
543 550 8.029642 ACTTGGTTATTTCACATCTAAACGAG 57.970 34.615 0.00 0.00 32.22 4.18
544 551 7.876068 ACTTGGTTATTTCACATCTAAACGAGA 59.124 33.333 0.00 0.00 39.01 4.04
545 552 7.827819 TGGTTATTTCACATCTAAACGAGAG 57.172 36.000 0.00 0.00 37.70 3.20
546 553 6.816640 TGGTTATTTCACATCTAAACGAGAGG 59.183 38.462 0.00 0.00 41.91 3.69
547 554 6.238130 GGTTATTTCACATCTAAACGAGAGGC 60.238 42.308 0.00 0.00 39.71 4.70
548 555 3.953712 TTCACATCTAAACGAGAGGCA 57.046 42.857 0.00 0.00 39.71 4.75
549 556 4.471904 TTCACATCTAAACGAGAGGCAT 57.528 40.909 0.00 0.00 39.71 4.40
550 557 3.785486 TCACATCTAAACGAGAGGCATG 58.215 45.455 0.00 0.00 39.71 4.06
551 558 2.286294 CACATCTAAACGAGAGGCATGC 59.714 50.000 9.90 9.90 39.71 4.06
552 559 1.869767 CATCTAAACGAGAGGCATGCC 59.130 52.381 30.12 30.12 37.70 4.40
553 560 0.178068 TCTAAACGAGAGGCATGCCC 59.822 55.000 33.14 23.29 36.58 5.36
554 561 0.107703 CTAAACGAGAGGCATGCCCA 60.108 55.000 33.14 7.34 36.58 5.36
555 562 0.326595 TAAACGAGAGGCATGCCCAA 59.673 50.000 33.14 6.95 36.58 4.12
556 563 0.323725 AAACGAGAGGCATGCCCAAT 60.324 50.000 33.14 19.19 36.58 3.16
557 564 1.033746 AACGAGAGGCATGCCCAATG 61.034 55.000 33.14 22.10 39.49 2.82
558 565 1.153107 CGAGAGGCATGCCCAATGA 60.153 57.895 33.14 0.00 38.72 2.57
559 566 0.536687 CGAGAGGCATGCCCAATGAT 60.537 55.000 33.14 13.92 38.72 2.45
560 567 0.959553 GAGAGGCATGCCCAATGATG 59.040 55.000 33.14 0.00 38.72 3.07
561 568 1.113517 AGAGGCATGCCCAATGATGC 61.114 55.000 33.14 11.98 43.60 3.91
562 569 1.382009 AGGCATGCCCAATGATGCA 60.382 52.632 33.14 4.15 45.70 3.96
563 570 1.069090 GGCATGCCCAATGATGCAG 59.931 57.895 27.24 0.77 45.70 4.41
564 571 1.682451 GGCATGCCCAATGATGCAGT 61.682 55.000 27.24 0.00 45.70 4.40
565 572 1.034356 GCATGCCCAATGATGCAGTA 58.966 50.000 6.36 0.00 43.75 2.74
566 573 1.000607 GCATGCCCAATGATGCAGTAG 60.001 52.381 6.36 0.00 43.75 2.57
567 574 1.000607 CATGCCCAATGATGCAGTAGC 60.001 52.381 0.00 0.00 41.46 3.58
568 575 0.256752 TGCCCAATGATGCAGTAGCT 59.743 50.000 0.00 0.00 42.74 3.32
569 576 1.490069 TGCCCAATGATGCAGTAGCTA 59.510 47.619 0.00 0.00 42.74 3.32
570 577 2.149578 GCCCAATGATGCAGTAGCTAG 58.850 52.381 0.00 0.00 42.74 3.42
571 578 2.224378 GCCCAATGATGCAGTAGCTAGA 60.224 50.000 0.00 0.00 42.74 2.43
572 579 3.397482 CCCAATGATGCAGTAGCTAGAC 58.603 50.000 0.00 0.00 42.74 2.59
573 580 3.055591 CCAATGATGCAGTAGCTAGACG 58.944 50.000 0.00 0.00 42.74 4.18
574 581 3.243535 CCAATGATGCAGTAGCTAGACGA 60.244 47.826 0.00 0.00 42.74 4.20
575 582 3.913548 ATGATGCAGTAGCTAGACGAG 57.086 47.619 0.00 0.00 42.74 4.18
576 583 2.919228 TGATGCAGTAGCTAGACGAGA 58.081 47.619 0.00 0.00 42.74 4.04
577 584 2.614520 TGATGCAGTAGCTAGACGAGAC 59.385 50.000 0.00 0.00 42.74 3.36
578 585 2.404923 TGCAGTAGCTAGACGAGACT 57.595 50.000 0.00 0.00 42.74 3.24
579 586 2.712709 TGCAGTAGCTAGACGAGACTT 58.287 47.619 0.00 0.00 42.74 3.01
580 587 2.420372 TGCAGTAGCTAGACGAGACTTG 59.580 50.000 0.00 0.00 42.74 3.16
581 588 2.223386 GCAGTAGCTAGACGAGACTTGG 60.223 54.545 0.00 0.00 37.91 3.61
582 589 3.011119 CAGTAGCTAGACGAGACTTGGT 58.989 50.000 0.00 0.00 0.00 3.67
583 590 3.440872 CAGTAGCTAGACGAGACTTGGTT 59.559 47.826 0.00 0.00 0.00 3.67
584 591 4.634883 CAGTAGCTAGACGAGACTTGGTTA 59.365 45.833 0.00 0.00 0.00 2.85
585 592 5.297278 CAGTAGCTAGACGAGACTTGGTTAT 59.703 44.000 0.00 0.00 0.00 1.89
586 593 5.887035 AGTAGCTAGACGAGACTTGGTTATT 59.113 40.000 0.00 0.00 0.00 1.40
587 594 5.662674 AGCTAGACGAGACTTGGTTATTT 57.337 39.130 0.00 0.00 0.00 1.40
588 595 5.652518 AGCTAGACGAGACTTGGTTATTTC 58.347 41.667 0.00 0.00 0.00 2.17
589 596 5.185249 AGCTAGACGAGACTTGGTTATTTCA 59.815 40.000 0.00 0.00 0.00 2.69
590 597 5.288952 GCTAGACGAGACTTGGTTATTTCAC 59.711 44.000 0.00 0.00 0.00 3.18
591 598 5.209818 AGACGAGACTTGGTTATTTCACA 57.790 39.130 0.00 0.00 0.00 3.58
592 599 5.794894 AGACGAGACTTGGTTATTTCACAT 58.205 37.500 0.00 0.00 0.00 3.21
593 600 5.869888 AGACGAGACTTGGTTATTTCACATC 59.130 40.000 0.00 0.00 0.00 3.06
594 601 5.794894 ACGAGACTTGGTTATTTCACATCT 58.205 37.500 0.00 0.00 0.00 2.90
595 602 6.931838 ACGAGACTTGGTTATTTCACATCTA 58.068 36.000 0.00 0.00 0.00 1.98
596 603 7.383687 ACGAGACTTGGTTATTTCACATCTAA 58.616 34.615 0.00 0.00 0.00 2.10
597 604 7.876068 ACGAGACTTGGTTATTTCACATCTAAA 59.124 33.333 0.00 0.00 0.00 1.85
598 605 8.169268 CGAGACTTGGTTATTTCACATCTAAAC 58.831 37.037 0.00 0.00 0.00 2.01
599 606 8.029642 AGACTTGGTTATTTCACATCTAAACG 57.970 34.615 0.00 0.00 0.00 3.60
621 628 2.026636 AGAGGCACGCCCTACATTTTAA 60.027 45.455 3.95 0.00 46.60 1.52
625 632 2.099098 GCACGCCCTACATTTTAATGCT 59.901 45.455 2.46 0.00 40.04 3.79
632 639 5.068987 GCCCTACATTTTAATGCTGGAATCA 59.931 40.000 12.82 0.00 40.04 2.57
646 653 3.763360 CTGGAATCAAGCCACACCAATAA 59.237 43.478 0.00 0.00 0.00 1.40
652 659 7.363793 GGAATCAAGCCACACCAATAACTATTT 60.364 37.037 0.00 0.00 0.00 1.40
752 761 9.956720 AGTGACTTCAATTTTTAATCTTGACAG 57.043 29.630 0.00 0.00 0.00 3.51
822 832 0.409092 ATGCAACATGACCAGGGGAA 59.591 50.000 0.00 0.00 0.00 3.97
823 833 0.409092 TGCAACATGACCAGGGGAAT 59.591 50.000 0.00 0.00 0.00 3.01
971 990 8.576442 CCAGAAAAAGTCTACATAAACACCAAT 58.424 33.333 0.00 0.00 33.56 3.16
986 1005 7.769272 AAACACCAATACATTGTTGAACTTG 57.231 32.000 6.50 0.00 34.33 3.16
996 1015 5.301551 ACATTGTTGAACTTGATGCACCTTA 59.698 36.000 0.00 0.00 0.00 2.69
1428 1468 1.007734 CCGTATCGCTACCGTGCAT 60.008 57.895 0.00 0.00 35.54 3.96
1580 1629 3.118905 TGTTGTCAACGTGATCATGGA 57.881 42.857 18.97 4.93 0.00 3.41
1734 1783 4.434354 ACGAGGAGGAGGCTCGCT 62.434 66.667 8.69 6.82 43.48 4.93
1845 1894 2.941333 GAGGACACGACGTCGACA 59.059 61.111 41.52 0.00 46.42 4.35
1993 2042 4.102649 CAAGTGTCAGTATGCATGCATTG 58.897 43.478 36.23 28.09 37.82 2.82
2202 2253 9.921637 TTTGGTAGTGACAATAATTCAATTTCC 57.078 29.630 0.00 0.00 0.00 3.13
2440 3259 4.705507 ACGATAAGAGTCATATACCCGCAT 59.294 41.667 0.00 0.00 0.00 4.73
2482 3303 2.620115 CACTCACACTTGCCTTGATTGT 59.380 45.455 0.00 0.00 0.00 2.71
2494 3315 2.604914 CCTTGATTGTCTGTTCGATCGG 59.395 50.000 16.41 0.00 32.52 4.18
2634 3455 5.248477 TGGCTCTTCTACTTAACAATCCACT 59.752 40.000 0.00 0.00 0.00 4.00
2719 3540 2.824546 GATCTCGCATGCCTCCCA 59.175 61.111 13.15 0.00 0.00 4.37
2734 3555 2.213499 CTCCCATACCTTCGTTGCATC 58.787 52.381 0.00 0.00 0.00 3.91
2830 3651 2.158638 TGCTGGCAGGCAATACATCATA 60.159 45.455 17.64 0.00 39.43 2.15
2834 3655 1.815003 GCAGGCAATACATCATAGCCC 59.185 52.381 0.00 0.00 46.35 5.19
2848 3669 1.615165 TAGCCCGCGGAACAATGGTA 61.615 55.000 30.73 15.79 0.00 3.25
2937 3758 2.158475 AGAGGTTTGAGGTTGGCATTGA 60.158 45.455 0.00 0.00 0.00 2.57
2947 3768 0.327924 TTGGCATTGATGAGGACGGT 59.672 50.000 0.00 0.00 0.00 4.83
2980 3801 0.839277 TCAGGATGATGCCATTCGGT 59.161 50.000 0.00 0.00 42.56 4.69
3026 3847 1.635817 GGGGCTAGCATGGAGGACAA 61.636 60.000 18.24 0.00 0.00 3.18
3085 3906 1.153147 GGAGCGGATGGGGAAAGAC 60.153 63.158 0.00 0.00 0.00 3.01
3098 3919 1.676014 GGAAAGACGAGGTGGACATGG 60.676 57.143 0.00 0.00 0.00 3.66
3160 3981 2.047939 GCAATGTGCCAACCCTGC 60.048 61.111 0.00 0.00 37.42 4.85
3170 3991 1.533625 CCAACCCTGCGAAGAAATGA 58.466 50.000 0.00 0.00 0.00 2.57
3248 4069 6.650390 GCAAGGCCAATCAAAGAAGAAAATAA 59.350 34.615 5.01 0.00 0.00 1.40
3340 4161 3.706594 TGTTCAAGGCCACCAAACATAAA 59.293 39.130 5.01 0.00 0.00 1.40
3344 4165 6.865834 TCAAGGCCACCAAACATAAATTAT 57.134 33.333 5.01 0.00 0.00 1.28
3381 4202 6.158598 TCAAAAGCAATTGTAGGATCAAAGC 58.841 36.000 7.40 0.00 34.78 3.51
3387 4208 5.345702 CAATTGTAGGATCAAAGCATGTGG 58.654 41.667 0.00 0.00 0.00 4.17
3391 4212 2.719739 AGGATCAAAGCATGTGGACTG 58.280 47.619 0.00 0.00 0.00 3.51
3442 4270 8.970691 ATTTCTTCGAAAACCACAAATATCTG 57.029 30.769 0.00 0.00 0.00 2.90
3443 4271 7.737972 TTCTTCGAAAACCACAAATATCTGA 57.262 32.000 0.00 0.00 0.00 3.27
3444 4272 7.737972 TCTTCGAAAACCACAAATATCTGAA 57.262 32.000 0.00 0.00 0.00 3.02
3445 4273 7.581476 TCTTCGAAAACCACAAATATCTGAAC 58.419 34.615 0.00 0.00 0.00 3.18
3446 4274 6.869315 TCGAAAACCACAAATATCTGAACA 57.131 33.333 0.00 0.00 0.00 3.18
3447 4275 6.664515 TCGAAAACCACAAATATCTGAACAC 58.335 36.000 0.00 0.00 0.00 3.32
3448 4276 6.261158 TCGAAAACCACAAATATCTGAACACA 59.739 34.615 0.00 0.00 0.00 3.72
3449 4277 6.915300 CGAAAACCACAAATATCTGAACACAA 59.085 34.615 0.00 0.00 0.00 3.33
3450 4278 7.096640 CGAAAACCACAAATATCTGAACACAAC 60.097 37.037 0.00 0.00 0.00 3.32
3451 4279 6.707440 AACCACAAATATCTGAACACAACA 57.293 33.333 0.00 0.00 0.00 3.33
3455 4283 6.238731 CCACAAATATCTGAACACAACACTGT 60.239 38.462 0.00 0.00 35.63 3.55
3658 4486 6.908870 TCAGATATGAAGAACAAATCACCG 57.091 37.500 0.00 0.00 0.00 4.94
3661 4489 7.606073 TCAGATATGAAGAACAAATCACCGAAA 59.394 33.333 0.00 0.00 0.00 3.46
3678 4506 4.642885 ACCGAAAAAGAACACAATGAAGGA 59.357 37.500 0.00 0.00 0.00 3.36
3680 4508 5.449862 CCGAAAAAGAACACAATGAAGGACA 60.450 40.000 0.00 0.00 0.00 4.02
3697 4525 9.739276 ATGAAGGACAACTCAATAGAATGTAAA 57.261 29.630 0.00 0.00 0.00 2.01
3780 4608 3.574396 TGTCCTACCAGTTCACTCTTCTG 59.426 47.826 0.00 0.00 0.00 3.02
3782 4610 2.564947 CCTACCAGTTCACTCTTCTGCT 59.435 50.000 0.00 0.00 0.00 4.24
3825 4654 4.320494 GGAGTGCCTTGTAAATGAACACAG 60.320 45.833 0.00 0.00 0.00 3.66
3827 4656 5.072741 AGTGCCTTGTAAATGAACACAGAT 58.927 37.500 0.00 0.00 0.00 2.90
3842 4671 2.027377 CACAGATGCAAACCTCTCTCCT 60.027 50.000 0.00 0.00 0.00 3.69
3853 4682 4.193240 ACCTCTCTCCTTCCTATTCTCC 57.807 50.000 0.00 0.00 0.00 3.71
3869 4698 2.036387 TCTCCTCAACGTGAAGTTCCA 58.964 47.619 0.00 0.00 42.02 3.53
3900 4729 5.523916 GCAGTTGATTTCACTCGTGGTATAT 59.476 40.000 0.00 0.00 0.00 0.86
3926 4755 4.735369 TCAAGGCAATCTCCAAACCTTTA 58.265 39.130 0.00 0.00 38.67 1.85
3929 4758 4.082125 AGGCAATCTCCAAACCTTTACAG 58.918 43.478 0.00 0.00 0.00 2.74
3979 4808 2.542020 TGGTTGCTCAAGATTGACGA 57.458 45.000 0.00 0.00 32.90 4.20
4010 4839 0.878416 AGAGTGACAGCTCTCACGAC 59.122 55.000 15.33 13.35 44.61 4.34
4019 4848 2.359214 CAGCTCTCACGACTAATAGGCA 59.641 50.000 0.00 0.00 0.00 4.75
4033 4862 7.517417 CGACTAATAGGCACAAGCTAATTCAAG 60.517 40.741 0.00 0.00 41.70 3.02
4034 4863 4.907879 ATAGGCACAAGCTAATTCAAGC 57.092 40.909 0.00 0.00 43.11 4.01
4071 4900 3.818773 GCTCAACCACTAAGTTTTGGCTA 59.181 43.478 3.61 0.00 36.20 3.93
4073 4902 5.619981 GCTCAACCACTAAGTTTTGGCTATG 60.620 44.000 3.61 2.12 36.20 2.23
4107 4936 7.456725 TCTCAAAGGATTCACTCAAATCTCTT 58.543 34.615 0.00 0.00 36.19 2.85
4131 4960 2.368439 GCAGGGTGCTCAAACATATCA 58.632 47.619 0.00 0.00 40.96 2.15
4132 4961 2.357009 GCAGGGTGCTCAAACATATCAG 59.643 50.000 0.00 0.00 40.96 2.90
4133 4962 3.614092 CAGGGTGCTCAAACATATCAGT 58.386 45.455 0.00 0.00 0.00 3.41
4134 4963 4.769688 CAGGGTGCTCAAACATATCAGTA 58.230 43.478 0.00 0.00 0.00 2.74
4135 4964 4.813161 CAGGGTGCTCAAACATATCAGTAG 59.187 45.833 0.00 0.00 0.00 2.57
4136 4965 3.561725 GGGTGCTCAAACATATCAGTAGC 59.438 47.826 0.00 0.00 0.00 3.58
4137 4966 4.191544 GGTGCTCAAACATATCAGTAGCA 58.808 43.478 0.00 0.00 36.23 3.49
4138 4967 4.635765 GGTGCTCAAACATATCAGTAGCAA 59.364 41.667 0.00 0.00 39.91 3.91
4139 4968 5.220739 GGTGCTCAAACATATCAGTAGCAAG 60.221 44.000 0.00 0.00 39.91 4.01
4140 4969 4.877823 TGCTCAAACATATCAGTAGCAAGG 59.122 41.667 0.00 0.00 35.70 3.61
4141 4970 5.118990 GCTCAAACATATCAGTAGCAAGGA 58.881 41.667 0.00 0.00 0.00 3.36
4142 4971 5.762218 GCTCAAACATATCAGTAGCAAGGAT 59.238 40.000 0.00 0.00 0.00 3.24
4143 4972 6.261826 GCTCAAACATATCAGTAGCAAGGATT 59.738 38.462 0.00 0.00 0.00 3.01
4154 4983 2.785868 CAAGGATTGGGAAGGAGCG 58.214 57.895 0.00 0.00 43.94 5.03
4155 4984 0.253044 CAAGGATTGGGAAGGAGCGA 59.747 55.000 0.00 0.00 43.94 4.93
4156 4985 0.253327 AAGGATTGGGAAGGAGCGAC 59.747 55.000 0.00 0.00 0.00 5.19
4157 4986 0.618968 AGGATTGGGAAGGAGCGACT 60.619 55.000 0.00 0.00 0.00 4.18
4158 4987 1.120530 GGATTGGGAAGGAGCGACTA 58.879 55.000 0.00 0.00 0.00 2.59
4159 4988 1.694696 GGATTGGGAAGGAGCGACTAT 59.305 52.381 0.00 0.00 0.00 2.12
4160 4989 2.104963 GGATTGGGAAGGAGCGACTATT 59.895 50.000 0.00 0.00 0.00 1.73
4161 4990 3.433740 GGATTGGGAAGGAGCGACTATTT 60.434 47.826 0.00 0.00 0.00 1.40
4162 4991 4.202326 GGATTGGGAAGGAGCGACTATTTA 60.202 45.833 0.00 0.00 0.00 1.40
4163 4992 5.513267 GGATTGGGAAGGAGCGACTATTTAT 60.513 44.000 0.00 0.00 0.00 1.40
4164 4993 4.336889 TGGGAAGGAGCGACTATTTATG 57.663 45.455 0.00 0.00 0.00 1.90
4165 4994 3.964688 TGGGAAGGAGCGACTATTTATGA 59.035 43.478 0.00 0.00 0.00 2.15
4166 4995 4.593206 TGGGAAGGAGCGACTATTTATGAT 59.407 41.667 0.00 0.00 0.00 2.45
4167 4996 4.932200 GGGAAGGAGCGACTATTTATGATG 59.068 45.833 0.00 0.00 0.00 3.07
4168 4997 4.932200 GGAAGGAGCGACTATTTATGATGG 59.068 45.833 0.00 0.00 0.00 3.51
4169 4998 5.279506 GGAAGGAGCGACTATTTATGATGGA 60.280 44.000 0.00 0.00 0.00 3.41
4170 4999 5.808366 AGGAGCGACTATTTATGATGGAA 57.192 39.130 0.00 0.00 0.00 3.53
4171 5000 6.174720 AGGAGCGACTATTTATGATGGAAA 57.825 37.500 0.00 0.00 0.00 3.13
4172 5001 6.773638 AGGAGCGACTATTTATGATGGAAAT 58.226 36.000 0.00 0.00 0.00 2.17
4173 5002 7.907389 AGGAGCGACTATTTATGATGGAAATA 58.093 34.615 0.00 0.00 0.00 1.40
4174 5003 8.543774 AGGAGCGACTATTTATGATGGAAATAT 58.456 33.333 0.00 0.00 30.41 1.28
4175 5004 8.607459 GGAGCGACTATTTATGATGGAAATATG 58.393 37.037 0.00 0.00 30.41 1.78
4176 5005 7.978982 AGCGACTATTTATGATGGAAATATGC 58.021 34.615 0.00 0.00 30.41 3.14
4177 5006 7.066284 AGCGACTATTTATGATGGAAATATGCC 59.934 37.037 0.00 0.00 30.41 4.40
4178 5007 7.679638 GCGACTATTTATGATGGAAATATGCCC 60.680 40.741 0.00 0.00 30.41 5.36
4179 5008 7.554118 CGACTATTTATGATGGAAATATGCCCT 59.446 37.037 0.00 0.00 30.41 5.19
4180 5009 9.905713 GACTATTTATGATGGAAATATGCCCTA 57.094 33.333 0.00 0.00 30.41 3.53
4181 5010 9.911788 ACTATTTATGATGGAAATATGCCCTAG 57.088 33.333 0.00 0.00 30.41 3.02
4184 5013 4.916041 TGATGGAAATATGCCCTAGAGG 57.084 45.455 0.00 0.00 39.47 3.69
4185 5014 4.502415 TGATGGAAATATGCCCTAGAGGA 58.498 43.478 0.00 0.00 38.24 3.71
4186 5015 4.913355 TGATGGAAATATGCCCTAGAGGAA 59.087 41.667 0.00 0.00 38.24 3.36
4187 5016 5.372363 TGATGGAAATATGCCCTAGAGGAAA 59.628 40.000 0.00 0.00 38.24 3.13
4188 5017 5.930209 TGGAAATATGCCCTAGAGGAAAT 57.070 39.130 0.00 0.00 38.24 2.17
4189 5018 7.239563 TGATGGAAATATGCCCTAGAGGAAATA 59.760 37.037 0.00 0.00 38.24 1.40
4190 5019 7.401060 TGGAAATATGCCCTAGAGGAAATAA 57.599 36.000 0.00 0.00 38.24 1.40
4191 5020 8.000171 TGGAAATATGCCCTAGAGGAAATAAT 58.000 34.615 0.00 0.00 38.24 1.28
4192 5021 9.122954 TGGAAATATGCCCTAGAGGAAATAATA 57.877 33.333 0.00 0.00 38.24 0.98
4193 5022 9.975218 GGAAATATGCCCTAGAGGAAATAATAA 57.025 33.333 0.00 0.00 38.24 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
20 21 2.501316 GGGAGCAAACATTTTGGGCTAT 59.499 45.455 1.07 0.00 34.44 2.97
32 33 3.733443 ACTGTTCATTTGGGAGCAAAC 57.267 42.857 0.00 0.00 0.00 2.93
68 69 5.695816 TCAAGCATCTTTAATGCCAACAAAC 59.304 36.000 6.40 0.00 45.59 2.93
69 70 5.851720 TCAAGCATCTTTAATGCCAACAAA 58.148 33.333 6.40 0.00 45.59 2.83
70 71 5.010922 ACTCAAGCATCTTTAATGCCAACAA 59.989 36.000 6.40 0.00 45.59 2.83
71 72 4.523943 ACTCAAGCATCTTTAATGCCAACA 59.476 37.500 6.40 0.00 45.59 3.33
72 73 5.064441 ACTCAAGCATCTTTAATGCCAAC 57.936 39.130 6.40 0.00 45.59 3.77
73 74 5.726980 AACTCAAGCATCTTTAATGCCAA 57.273 34.783 6.40 0.00 45.59 4.52
98 99 9.119329 TGACAACAAAATTTTACACGCATATAC 57.881 29.630 2.44 0.00 0.00 1.47
101 102 9.847706 ATATGACAACAAAATTTTACACGCATA 57.152 25.926 2.44 9.49 0.00 3.14
103 104 7.862873 TCATATGACAACAAAATTTTACACGCA 59.137 29.630 2.44 0.77 0.00 5.24
153 158 4.871933 AACTTGGGTTTTGGAGCATTAG 57.128 40.909 0.00 0.00 30.55 1.73
177 182 8.606727 AAAATCATAGCTTCGAAAAAGATTCG 57.393 30.769 0.00 4.32 42.74 3.34
205 210 7.653311 CGATATGTCATGTGAGGAATTCTGTAA 59.347 37.037 5.23 0.00 0.00 2.41
206 211 7.147976 CGATATGTCATGTGAGGAATTCTGTA 58.852 38.462 5.23 0.00 0.00 2.74
209 214 4.993584 GCGATATGTCATGTGAGGAATTCT 59.006 41.667 5.23 0.00 0.00 2.40
210 215 4.153117 GGCGATATGTCATGTGAGGAATTC 59.847 45.833 0.00 0.00 0.00 2.17
211 216 4.067896 GGCGATATGTCATGTGAGGAATT 58.932 43.478 0.00 0.00 0.00 2.17
212 217 3.071457 TGGCGATATGTCATGTGAGGAAT 59.929 43.478 0.00 0.00 0.00 3.01
213 218 2.433970 TGGCGATATGTCATGTGAGGAA 59.566 45.455 0.00 0.00 0.00 3.36
214 219 2.038659 TGGCGATATGTCATGTGAGGA 58.961 47.619 0.00 0.00 0.00 3.71
215 220 2.531522 TGGCGATATGTCATGTGAGG 57.468 50.000 0.00 0.00 0.00 3.86
216 221 3.721035 TCTTGGCGATATGTCATGTGAG 58.279 45.455 0.00 0.00 27.93 3.51
217 222 3.817709 TCTTGGCGATATGTCATGTGA 57.182 42.857 0.00 0.00 27.93 3.58
218 223 6.540205 CAATATCTTGGCGATATGTCATGTG 58.460 40.000 0.00 0.00 43.00 3.21
219 224 5.122869 GCAATATCTTGGCGATATGTCATGT 59.877 40.000 0.00 0.00 43.00 3.21
220 225 5.122711 TGCAATATCTTGGCGATATGTCATG 59.877 40.000 0.00 0.00 43.00 3.07
242 247 6.045318 TGCTGAGATTATCTAAAGAGTGTGC 58.955 40.000 8.16 0.00 0.00 4.57
243 248 8.659925 AATGCTGAGATTATCTAAAGAGTGTG 57.340 34.615 8.16 0.00 0.00 3.82
244 249 9.678260 AAAATGCTGAGATTATCTAAAGAGTGT 57.322 29.630 8.16 0.00 0.00 3.55
285 291 8.833976 AAATTCTAAAAACGGCAAACAAAATG 57.166 26.923 0.00 0.00 0.00 2.32
296 302 9.840427 ATGATGAACAGTAAATTCTAAAAACGG 57.160 29.630 0.00 0.00 0.00 4.44
311 318 6.990908 TCATCTCCATCTATGATGAACAGT 57.009 37.500 8.91 0.00 42.15 3.55
318 325 6.321321 TCCTGAGTTCATCTCCATCTATGAT 58.679 40.000 0.00 0.00 42.12 2.45
326 333 3.986435 TCAGATCCTGAGTTCATCTCCA 58.014 45.455 0.00 0.00 42.12 3.86
337 344 0.389817 CGTGGCGTTTCAGATCCTGA 60.390 55.000 0.00 0.00 38.87 3.86
344 351 0.460284 ATAGAGGCGTGGCGTTTCAG 60.460 55.000 0.00 0.00 0.00 3.02
375 382 6.814954 TCTAGATGAGAATTAGCAAACCCT 57.185 37.500 0.00 0.00 0.00 4.34
491 498 7.210174 TCGTCTAGCTACTGCATCATTTAATT 58.790 34.615 0.00 0.00 42.74 1.40
492 499 6.749139 TCGTCTAGCTACTGCATCATTTAAT 58.251 36.000 0.00 0.00 42.74 1.40
500 507 2.925724 AGTCTCGTCTAGCTACTGCAT 58.074 47.619 0.00 0.00 42.74 3.96
514 521 7.827819 TTAGATGTGAAATAACCAAGTCTCG 57.172 36.000 0.00 0.00 0.00 4.04
536 543 0.326595 TTGGGCATGCCTCTCGTTTA 59.673 50.000 34.70 9.67 36.10 2.01
537 544 0.323725 ATTGGGCATGCCTCTCGTTT 60.324 50.000 34.70 11.28 36.10 3.60
538 545 1.033746 CATTGGGCATGCCTCTCGTT 61.034 55.000 34.70 12.32 36.10 3.85
539 546 1.452651 CATTGGGCATGCCTCTCGT 60.453 57.895 34.70 14.72 36.10 4.18
540 547 0.536687 ATCATTGGGCATGCCTCTCG 60.537 55.000 34.70 20.97 36.10 4.04
541 548 0.959553 CATCATTGGGCATGCCTCTC 59.040 55.000 34.70 19.75 36.10 3.20
542 549 1.113517 GCATCATTGGGCATGCCTCT 61.114 55.000 34.70 17.47 39.70 3.69
543 550 1.366366 GCATCATTGGGCATGCCTC 59.634 57.895 34.70 24.58 39.70 4.70
544 551 1.382009 TGCATCATTGGGCATGCCT 60.382 52.632 34.70 14.32 44.15 4.75
545 552 1.069090 CTGCATCATTGGGCATGCC 59.931 57.895 29.47 29.47 44.15 4.40
546 553 1.000607 CTACTGCATCATTGGGCATGC 60.001 52.381 9.90 9.90 44.87 4.06
547 554 1.000607 GCTACTGCATCATTGGGCATG 60.001 52.381 4.74 0.00 39.65 4.06
548 555 1.133575 AGCTACTGCATCATTGGGCAT 60.134 47.619 4.74 0.35 42.74 4.40
549 556 0.256752 AGCTACTGCATCATTGGGCA 59.743 50.000 0.00 4.32 42.74 5.36
550 557 2.149578 CTAGCTACTGCATCATTGGGC 58.850 52.381 0.00 0.00 42.74 5.36
551 558 3.397482 GTCTAGCTACTGCATCATTGGG 58.603 50.000 0.00 0.00 42.74 4.12
552 559 3.055591 CGTCTAGCTACTGCATCATTGG 58.944 50.000 0.00 0.00 42.74 3.16
553 560 3.969899 TCGTCTAGCTACTGCATCATTG 58.030 45.455 0.00 0.00 42.74 2.82
554 561 3.885901 TCTCGTCTAGCTACTGCATCATT 59.114 43.478 0.00 0.00 42.74 2.57
555 562 3.252215 GTCTCGTCTAGCTACTGCATCAT 59.748 47.826 0.00 0.00 42.74 2.45
556 563 2.614520 GTCTCGTCTAGCTACTGCATCA 59.385 50.000 0.00 0.00 42.74 3.07
557 564 2.875933 AGTCTCGTCTAGCTACTGCATC 59.124 50.000 0.00 0.00 42.74 3.91
558 565 2.925724 AGTCTCGTCTAGCTACTGCAT 58.074 47.619 0.00 0.00 42.74 3.96
559 566 2.404923 AGTCTCGTCTAGCTACTGCA 57.595 50.000 0.00 0.00 42.74 4.41
560 567 2.223386 CCAAGTCTCGTCTAGCTACTGC 60.223 54.545 0.00 0.00 40.05 4.40
561 568 3.011119 ACCAAGTCTCGTCTAGCTACTG 58.989 50.000 0.00 0.00 0.00 2.74
562 569 3.353370 ACCAAGTCTCGTCTAGCTACT 57.647 47.619 0.00 0.00 0.00 2.57
563 570 5.754543 ATAACCAAGTCTCGTCTAGCTAC 57.245 43.478 0.00 0.00 0.00 3.58
564 571 6.376299 TGAAATAACCAAGTCTCGTCTAGCTA 59.624 38.462 0.00 0.00 0.00 3.32
565 572 5.185249 TGAAATAACCAAGTCTCGTCTAGCT 59.815 40.000 0.00 0.00 0.00 3.32
566 573 5.288952 GTGAAATAACCAAGTCTCGTCTAGC 59.711 44.000 0.00 0.00 0.00 3.42
567 574 6.387465 TGTGAAATAACCAAGTCTCGTCTAG 58.613 40.000 0.00 0.00 0.00 2.43
568 575 6.335471 TGTGAAATAACCAAGTCTCGTCTA 57.665 37.500 0.00 0.00 0.00 2.59
569 576 5.209818 TGTGAAATAACCAAGTCTCGTCT 57.790 39.130 0.00 0.00 0.00 4.18
570 577 5.869888 AGATGTGAAATAACCAAGTCTCGTC 59.130 40.000 0.00 0.00 0.00 4.20
571 578 5.794894 AGATGTGAAATAACCAAGTCTCGT 58.205 37.500 0.00 0.00 0.00 4.18
572 579 7.827819 TTAGATGTGAAATAACCAAGTCTCG 57.172 36.000 0.00 0.00 0.00 4.04
573 580 8.169268 CGTTTAGATGTGAAATAACCAAGTCTC 58.831 37.037 0.00 0.00 0.00 3.36
574 581 7.876068 TCGTTTAGATGTGAAATAACCAAGTCT 59.124 33.333 0.00 0.00 0.00 3.24
575 582 8.025243 TCGTTTAGATGTGAAATAACCAAGTC 57.975 34.615 0.00 0.00 0.00 3.01
576 583 7.876068 TCTCGTTTAGATGTGAAATAACCAAGT 59.124 33.333 0.00 0.00 0.00 3.16
577 584 8.251750 TCTCGTTTAGATGTGAAATAACCAAG 57.748 34.615 0.00 0.00 0.00 3.61
578 585 7.333423 CCTCTCGTTTAGATGTGAAATAACCAA 59.667 37.037 0.00 0.00 32.41 3.67
579 586 6.816640 CCTCTCGTTTAGATGTGAAATAACCA 59.183 38.462 0.00 0.00 32.41 3.67
580 587 6.238130 GCCTCTCGTTTAGATGTGAAATAACC 60.238 42.308 0.00 0.00 32.41 2.85
581 588 6.312918 TGCCTCTCGTTTAGATGTGAAATAAC 59.687 38.462 0.00 0.00 32.41 1.89
582 589 6.312918 GTGCCTCTCGTTTAGATGTGAAATAA 59.687 38.462 0.00 0.00 32.41 1.40
583 590 5.810587 GTGCCTCTCGTTTAGATGTGAAATA 59.189 40.000 0.00 0.00 32.41 1.40
584 591 4.631813 GTGCCTCTCGTTTAGATGTGAAAT 59.368 41.667 0.00 0.00 32.41 2.17
585 592 3.994392 GTGCCTCTCGTTTAGATGTGAAA 59.006 43.478 0.00 0.00 32.41 2.69
586 593 3.585862 GTGCCTCTCGTTTAGATGTGAA 58.414 45.455 0.00 0.00 32.41 3.18
587 594 2.415491 CGTGCCTCTCGTTTAGATGTGA 60.415 50.000 0.00 0.00 32.41 3.58
588 595 1.920574 CGTGCCTCTCGTTTAGATGTG 59.079 52.381 0.00 0.00 32.41 3.21
589 596 1.736032 GCGTGCCTCTCGTTTAGATGT 60.736 52.381 0.00 0.00 32.41 3.06
590 597 0.924090 GCGTGCCTCTCGTTTAGATG 59.076 55.000 0.00 0.00 32.41 2.90
591 598 0.179108 GGCGTGCCTCTCGTTTAGAT 60.179 55.000 2.98 0.00 32.41 1.98
592 599 1.214589 GGCGTGCCTCTCGTTTAGA 59.785 57.895 2.98 0.00 0.00 2.10
593 600 1.810030 GGGCGTGCCTCTCGTTTAG 60.810 63.158 11.25 0.00 36.10 1.85
594 601 0.966875 TAGGGCGTGCCTCTCGTTTA 60.967 55.000 11.25 0.00 36.10 2.01
595 602 2.280552 TAGGGCGTGCCTCTCGTTT 61.281 57.895 11.25 0.00 36.10 3.60
596 603 2.678934 TAGGGCGTGCCTCTCGTT 60.679 61.111 11.25 0.00 36.10 3.85
597 604 3.450115 GTAGGGCGTGCCTCTCGT 61.450 66.667 11.25 0.00 36.10 4.18
598 605 2.298158 AATGTAGGGCGTGCCTCTCG 62.298 60.000 11.25 0.00 36.10 4.04
599 606 0.107654 AAATGTAGGGCGTGCCTCTC 60.108 55.000 11.25 2.22 36.10 3.20
621 628 1.180029 GTGTGGCTTGATTCCAGCAT 58.820 50.000 11.44 0.00 33.63 3.79
625 632 2.307496 ATTGGTGTGGCTTGATTCCA 57.693 45.000 0.00 0.00 0.00 3.53
680 687 8.818141 ATGGTGATACTGATACTGATTAAACG 57.182 34.615 0.00 0.00 0.00 3.60
694 701 3.738982 TCCGGCATTAATGGTGATACTG 58.261 45.455 17.02 4.28 0.00 2.74
822 832 1.305549 CCAGGCCAAAGCAAGGGAT 60.306 57.895 5.01 0.00 42.56 3.85
823 833 2.118076 CCAGGCCAAAGCAAGGGA 59.882 61.111 5.01 0.00 42.56 4.20
871 881 7.550196 ACCATAGTGTTCCGTACGATTTTAAAT 59.450 33.333 18.76 0.00 0.00 1.40
874 884 5.806502 CACCATAGTGTTCCGTACGATTTTA 59.193 40.000 18.76 1.93 39.30 1.52
891 903 2.061773 GCTGCTATGCGTACACCATAG 58.938 52.381 19.06 19.06 43.09 2.23
971 990 4.826733 AGGTGCATCAAGTTCAACAATGTA 59.173 37.500 0.00 0.00 0.00 2.29
986 1005 3.266510 TGACCATGAGTAAGGTGCATC 57.733 47.619 0.00 0.00 38.50 3.91
996 1015 2.114616 GAGACCTCCATGACCATGAGT 58.885 52.381 11.28 5.92 41.20 3.41
1023 1051 1.674962 GAAGCTAAGAGCAAGGCATGG 59.325 52.381 0.64 0.00 45.56 3.66
1129 1169 2.801631 GGAGATGGAGGTGGCCGAG 61.802 68.421 0.00 0.00 0.00 4.63
1404 1444 2.256591 GGTAGCGATACGGCGGAGA 61.257 63.158 13.24 0.00 38.18 3.71
1413 1453 4.336581 GCATGCACGGTAGCGATA 57.663 55.556 22.88 6.85 37.31 2.92
1543 1592 0.806884 ACAAACTCGAACGCCGTGAA 60.807 50.000 0.00 0.00 39.75 3.18
1580 1629 4.778143 GCCTTCCCGCGACCATGT 62.778 66.667 8.23 0.00 0.00 3.21
1926 1975 0.946221 CACTCACCAGGCAAGTCGTC 60.946 60.000 0.00 0.00 0.00 4.20
1931 1980 2.031516 CGCTCACTCACCAGGCAAG 61.032 63.158 0.00 0.00 0.00 4.01
2076 2125 8.621286 ACAAAGTTGAAAGTACACTAATTGAGG 58.379 33.333 0.00 0.00 0.00 3.86
2081 2130 7.417612 CAGCACAAAGTTGAAAGTACACTAAT 58.582 34.615 0.00 0.00 0.00 1.73
2357 2408 7.921787 TGGTTAACATTGTTATATTCGCGATT 58.078 30.769 10.88 9.61 0.00 3.34
2482 3303 1.805943 TGAACGTACCGATCGAACAGA 59.194 47.619 18.66 0.00 31.45 3.41
2634 3455 0.586319 CTTCGCCTTTGCAAGAACGA 59.414 50.000 13.54 13.54 37.32 3.85
2719 3540 3.206150 GGTGATGATGCAACGAAGGTAT 58.794 45.455 0.00 0.00 0.00 2.73
2734 3555 2.636009 ATCCGAAGGGTCTCGGTGATG 61.636 57.143 11.48 0.00 28.78 3.07
2785 3606 1.881903 CGCAGTCAGAGGAGGCTTGA 61.882 60.000 0.00 0.00 0.00 3.02
2830 3651 2.265467 ATACCATTGTTCCGCGGGCT 62.265 55.000 27.83 2.37 0.00 5.19
2834 3655 1.091537 ACCAATACCATTGTTCCGCG 58.908 50.000 0.00 0.00 0.00 6.46
2848 3669 3.696051 GCATGGAGTACACATCAACCAAT 59.304 43.478 0.00 0.00 0.00 3.16
2937 3758 1.270839 CCTGTTTGTCACCGTCCTCAT 60.271 52.381 0.00 0.00 0.00 2.90
2947 3768 1.208706 TCCTGACCACCTGTTTGTCA 58.791 50.000 0.00 0.00 37.45 3.58
2980 3801 4.169696 CACTTCCGCCGGCCCATA 62.170 66.667 23.46 2.61 0.00 2.74
3026 3847 2.316586 CCCCAAGTGCTACCCCCAT 61.317 63.158 0.00 0.00 0.00 4.00
3085 3906 3.723235 CTCGCCCATGTCCACCTCG 62.723 68.421 0.00 0.00 0.00 4.63
3098 3919 4.097361 GAACCCTGACCCCTCGCC 62.097 72.222 0.00 0.00 0.00 5.54
3158 3979 6.912082 TGAGAATTTCATTCATTTCTTCGCA 58.088 32.000 0.00 0.00 41.71 5.10
3160 3981 9.275231 CTCTTGAGAATTTCATTCATTTCTTCG 57.725 33.333 0.00 0.00 41.71 3.79
3208 4029 1.203052 CCTTGCAAGGGTACAATGCTG 59.797 52.381 34.08 7.04 42.66 4.41
3248 4069 4.998051 AGACAAGGTGTGGGATGTAAATT 58.002 39.130 0.00 0.00 0.00 1.82
3258 4079 2.380410 GCGCGTAGACAAGGTGTGG 61.380 63.158 8.43 0.00 0.00 4.17
3259 4080 1.014044 ATGCGCGTAGACAAGGTGTG 61.014 55.000 8.43 0.00 0.00 3.82
3310 4131 2.231235 GGTGGCCTTGAACAATGTTAGG 59.769 50.000 3.32 9.92 0.00 2.69
3344 4165 9.177608 ACAATTGCTTTTGAGCTTAGATATACA 57.822 29.630 5.05 0.00 35.49 2.29
3381 4202 3.001514 CCCCCTCCAGTCCACATG 58.998 66.667 0.00 0.00 0.00 3.21
3426 4254 7.491048 GTGTTGTGTTCAGATATTTGTGGTTTT 59.509 33.333 0.00 0.00 0.00 2.43
3430 4258 6.144854 CAGTGTTGTGTTCAGATATTTGTGG 58.855 40.000 0.00 0.00 0.00 4.17
3445 4273 7.860576 GCTTACTGCTTTTTCACAGTGTTGTG 61.861 42.308 5.93 1.35 46.31 3.33
3446 4274 5.637006 TTACTGCTTTTTCACAGTGTTGT 57.363 34.783 5.93 0.00 46.31 3.32
3447 4275 4.500477 GCTTACTGCTTTTTCACAGTGTTG 59.500 41.667 5.93 0.00 46.31 3.33
3448 4276 4.157656 TGCTTACTGCTTTTTCACAGTGTT 59.842 37.500 5.93 0.00 46.31 3.32
3449 4277 3.694072 TGCTTACTGCTTTTTCACAGTGT 59.306 39.130 5.93 0.00 46.31 3.55
3450 4278 4.035558 TCTGCTTACTGCTTTTTCACAGTG 59.964 41.667 5.93 0.00 46.31 3.66
3455 4283 2.032030 GCGTCTGCTTACTGCTTTTTCA 60.032 45.455 0.00 0.00 43.37 2.69
3462 4290 0.440371 GAACTGCGTCTGCTTACTGC 59.560 55.000 0.00 0.00 43.34 4.40
3474 4302 6.952935 AGTTTATCTTCAAGTAGAACTGCG 57.047 37.500 2.65 0.00 31.61 5.18
3534 4362 7.598869 GTGTGTTCACATGTTCTTCATCTACTA 59.401 37.037 8.87 0.00 43.37 1.82
3612 4440 3.287867 AGCATTTCCATCTGTACCAGG 57.712 47.619 0.00 0.00 31.51 4.45
3613 4441 6.057533 TGATTAGCATTTCCATCTGTACCAG 58.942 40.000 0.00 0.00 0.00 4.00
3614 4442 6.000246 TGATTAGCATTTCCATCTGTACCA 58.000 37.500 0.00 0.00 0.00 3.25
3633 4461 7.770433 TCGGTGATTTGTTCTTCATATCTGATT 59.230 33.333 0.00 0.00 36.15 2.57
3658 4486 7.035612 AGTTGTCCTTCATTGTGTTCTTTTTC 58.964 34.615 0.00 0.00 0.00 2.29
3661 4489 5.652014 TGAGTTGTCCTTCATTGTGTTCTTT 59.348 36.000 0.00 0.00 0.00 2.52
3740 4568 1.464608 ACAAATGTCTTGTCGCCATCG 59.535 47.619 0.00 0.00 0.00 3.84
3754 4582 4.899502 AGAGTGAACTGGTAGGACAAATG 58.100 43.478 0.00 0.00 0.00 2.32
3761 4589 2.564947 AGCAGAAGAGTGAACTGGTAGG 59.435 50.000 0.00 0.00 39.91 3.18
3793 4622 2.540383 ACAAGGCACTCCATCTAGACA 58.460 47.619 0.00 0.00 38.49 3.41
3806 4635 4.321156 GCATCTGTGTTCATTTACAAGGCA 60.321 41.667 0.00 0.00 0.00 4.75
3825 4654 2.238395 AGGAAGGAGAGAGGTTTGCATC 59.762 50.000 0.00 0.00 0.00 3.91
3827 4656 1.734655 AGGAAGGAGAGAGGTTTGCA 58.265 50.000 0.00 0.00 0.00 4.08
3842 4671 4.527038 ACTTCACGTTGAGGAGAATAGGAA 59.473 41.667 0.00 0.00 0.00 3.36
3869 4698 3.206150 AGTGAAATCAACTGCAGTTCGT 58.794 40.909 28.97 17.23 35.83 3.85
3876 4705 1.873591 ACCACGAGTGAAATCAACTGC 59.126 47.619 4.59 0.00 0.00 4.40
3900 4729 3.573967 GGTTTGGAGATTGCCTTGAAGAA 59.426 43.478 0.00 0.00 0.00 2.52
3926 4755 8.006298 TGTGGTTTATTGAAGACAAAATCTGT 57.994 30.769 0.00 0.00 42.61 3.41
3929 4758 9.528018 TCTTTGTGGTTTATTGAAGACAAAATC 57.472 29.630 0.00 0.00 39.54 2.17
3979 4808 4.080015 AGCTGTCACTCTCTAGATGGTAGT 60.080 45.833 0.00 0.00 0.00 2.73
4005 4834 2.893637 AGCTTGTGCCTATTAGTCGTG 58.106 47.619 0.00 0.00 40.80 4.35
4006 4835 4.730949 TTAGCTTGTGCCTATTAGTCGT 57.269 40.909 0.00 0.00 40.80 4.34
4010 4839 6.433766 GCTTGAATTAGCTTGTGCCTATTAG 58.566 40.000 0.00 0.00 40.80 1.73
4033 4862 0.105778 GAGCATCACAGGGGACTAGC 59.894 60.000 0.00 0.00 34.14 3.42
4034 4863 1.489481 TGAGCATCACAGGGGACTAG 58.511 55.000 0.00 0.00 42.56 2.57
4071 4900 4.682021 ATCCTTTGAGAGAAAACCCCAT 57.318 40.909 0.00 0.00 0.00 4.00
4073 4902 4.218635 GTGAATCCTTTGAGAGAAAACCCC 59.781 45.833 0.00 0.00 0.00 4.95
4127 4956 4.103153 CCTTCCCAATCCTTGCTACTGATA 59.897 45.833 0.00 0.00 0.00 2.15
4128 4957 3.117738 CCTTCCCAATCCTTGCTACTGAT 60.118 47.826 0.00 0.00 0.00 2.90
4129 4958 2.239654 CCTTCCCAATCCTTGCTACTGA 59.760 50.000 0.00 0.00 0.00 3.41
4130 4959 2.239654 TCCTTCCCAATCCTTGCTACTG 59.760 50.000 0.00 0.00 0.00 2.74
4131 4960 2.507471 CTCCTTCCCAATCCTTGCTACT 59.493 50.000 0.00 0.00 0.00 2.57
4132 4961 2.924421 CTCCTTCCCAATCCTTGCTAC 58.076 52.381 0.00 0.00 0.00 3.58
4133 4962 1.212935 GCTCCTTCCCAATCCTTGCTA 59.787 52.381 0.00 0.00 0.00 3.49
4134 4963 0.033699 GCTCCTTCCCAATCCTTGCT 60.034 55.000 0.00 0.00 0.00 3.91
4135 4964 1.379642 CGCTCCTTCCCAATCCTTGC 61.380 60.000 0.00 0.00 0.00 4.01
4136 4965 0.253044 TCGCTCCTTCCCAATCCTTG 59.747 55.000 0.00 0.00 0.00 3.61
4137 4966 0.253327 GTCGCTCCTTCCCAATCCTT 59.747 55.000 0.00 0.00 0.00 3.36
4138 4967 0.618968 AGTCGCTCCTTCCCAATCCT 60.619 55.000 0.00 0.00 0.00 3.24
4139 4968 1.120530 TAGTCGCTCCTTCCCAATCC 58.879 55.000 0.00 0.00 0.00 3.01
4140 4969 3.477210 AATAGTCGCTCCTTCCCAATC 57.523 47.619 0.00 0.00 0.00 2.67
4141 4970 3.933861 AAATAGTCGCTCCTTCCCAAT 57.066 42.857 0.00 0.00 0.00 3.16
4142 4971 4.407621 TCATAAATAGTCGCTCCTTCCCAA 59.592 41.667 0.00 0.00 0.00 4.12
4143 4972 3.964688 TCATAAATAGTCGCTCCTTCCCA 59.035 43.478 0.00 0.00 0.00 4.37
4144 4973 4.602340 TCATAAATAGTCGCTCCTTCCC 57.398 45.455 0.00 0.00 0.00 3.97
4145 4974 4.932200 CCATCATAAATAGTCGCTCCTTCC 59.068 45.833 0.00 0.00 0.00 3.46
4146 4975 5.784177 TCCATCATAAATAGTCGCTCCTTC 58.216 41.667 0.00 0.00 0.00 3.46
4147 4976 5.808366 TCCATCATAAATAGTCGCTCCTT 57.192 39.130 0.00 0.00 0.00 3.36
4148 4977 5.808366 TTCCATCATAAATAGTCGCTCCT 57.192 39.130 0.00 0.00 0.00 3.69
4149 4978 8.607459 CATATTTCCATCATAAATAGTCGCTCC 58.393 37.037 0.00 0.00 33.53 4.70
4150 4979 8.119226 GCATATTTCCATCATAAATAGTCGCTC 58.881 37.037 0.00 0.00 33.53 5.03
4151 4980 7.066284 GGCATATTTCCATCATAAATAGTCGCT 59.934 37.037 0.00 0.00 33.53 4.93
4152 4981 7.189512 GGCATATTTCCATCATAAATAGTCGC 58.810 38.462 0.00 0.00 33.53 5.19
4153 4982 7.554118 AGGGCATATTTCCATCATAAATAGTCG 59.446 37.037 0.00 0.00 33.53 4.18
4154 4983 8.814038 AGGGCATATTTCCATCATAAATAGTC 57.186 34.615 0.00 0.00 33.53 2.59
4155 4984 9.911788 CTAGGGCATATTTCCATCATAAATAGT 57.088 33.333 0.00 0.00 33.53 2.12
4158 4987 8.057623 CCTCTAGGGCATATTTCCATCATAAAT 58.942 37.037 0.00 0.00 0.00 1.40
4159 4988 7.239563 TCCTCTAGGGCATATTTCCATCATAAA 59.760 37.037 0.00 0.00 35.41 1.40
4160 4989 6.735229 TCCTCTAGGGCATATTTCCATCATAA 59.265 38.462 0.00 0.00 35.41 1.90
4161 4990 6.271537 TCCTCTAGGGCATATTTCCATCATA 58.728 40.000 0.00 0.00 35.41 2.15
4162 4991 5.103687 TCCTCTAGGGCATATTTCCATCAT 58.896 41.667 0.00 0.00 35.41 2.45
4163 4992 4.502415 TCCTCTAGGGCATATTTCCATCA 58.498 43.478 0.00 0.00 35.41 3.07
4164 4993 5.505181 TTCCTCTAGGGCATATTTCCATC 57.495 43.478 0.00 0.00 35.41 3.51
4165 4994 5.930209 TTTCCTCTAGGGCATATTTCCAT 57.070 39.130 0.00 0.00 35.41 3.41
4166 4995 5.930209 ATTTCCTCTAGGGCATATTTCCA 57.070 39.130 0.00 0.00 35.41 3.53
4167 4996 9.975218 TTATTATTTCCTCTAGGGCATATTTCC 57.025 33.333 0.00 0.00 35.41 3.13


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

AutoCloner maintained by Alex Coulton.