Multiple sequence alignment - TraesCS5B01G149600

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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 TraesCS5B01G149600 chr5B 100.000 7088 0 0 1 7088 277644220 277637133 0.000000e+00 13090.0
1 TraesCS5B01G149600 chr5A 92.510 3124 133 34 4034 7088 328721018 328717927 0.000000e+00 4379.0
2 TraesCS5B01G149600 chr5A 97.116 2011 48 7 2032 4035 328725716 328723709 0.000000e+00 3384.0
3 TraesCS5B01G149600 chr5A 88.920 2139 124 52 1 2072 328727804 328725712 0.000000e+00 2532.0
4 TraesCS5B01G149600 chr5D 96.957 1972 43 10 2032 3990 244373915 244371948 0.000000e+00 3293.0
5 TraesCS5B01G149600 chr5D 93.280 1890 78 23 4080 5937 244371934 244370062 0.000000e+00 2741.0
6 TraesCS5B01G149600 chr5D 89.995 2129 128 39 1 2072 244376047 244373947 0.000000e+00 2673.0
7 TraesCS5B01G149600 chr5D 92.797 944 48 8 6157 7087 244369631 244368695 0.000000e+00 1349.0
8 TraesCS5B01G149600 chr5D 93.023 215 9 4 5935 6147 244369982 244369772 6.910000e-80 309.0
9 TraesCS5B01G149600 chr3B 87.755 49 6 0 2533 2581 738314540 738314588 2.760000e-04 58.4


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 TraesCS5B01G149600 chr5B 277637133 277644220 7087 True 13090.000000 13090 100.000000 1 7088 1 chr5B.!!$R1 7087
1 TraesCS5B01G149600 chr5A 328717927 328727804 9877 True 3431.666667 4379 92.848667 1 7088 3 chr5A.!!$R1 7087
2 TraesCS5B01G149600 chr5D 244368695 244376047 7352 True 2073.000000 3293 93.210400 1 7087 5 chr5D.!!$R1 7086

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
62 63 0.173481 CCGATCGTGCTTCTTCTCCA 59.827 55.000 15.09 0.00 0.00 3.86 F
374 400 0.251354 TGCCTTCTTCTGCTGCTAGG 59.749 55.000 0.00 0.00 0.00 3.02 F
525 591 0.319900 AGACGTTGAGTTGCGCAGAT 60.320 50.000 11.31 2.44 0.00 2.90 F
537 603 0.446222 GCGCAGATTTTTGGTCGCTA 59.554 50.000 0.30 0.00 39.51 4.26 F
617 687 0.900182 GGGCTTCAAAGGGGAAGGTG 60.900 60.000 5.22 0.00 43.54 4.00 F
709 779 1.005097 TCTCATGTGCCAATGCTTCCT 59.995 47.619 0.00 0.00 38.71 3.36 F
1510 1613 1.551883 AGCAATGGCAAATTCTGTCCC 59.448 47.619 0.00 0.00 44.61 4.46 F
3364 3550 0.850100 TTCTTGGTGGTGGTGATGGT 59.150 50.000 0.00 0.00 0.00 3.55 F
3566 3752 0.037975 CTGGAGTTGGTTTGCATGGC 60.038 55.000 0.00 0.00 0.00 4.40 F
4908 7800 0.729140 GCGGTTTCAATGGCGTTCAG 60.729 55.000 0.00 0.00 0.00 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1081 1183 0.252479 ACAGCTCCAAGATCCTGCAG 59.748 55.000 6.78 6.78 0.00 4.41 R
1888 1991 0.884704 CAGGAGGTGGTGTTGGTTCG 60.885 60.000 0.00 0.00 0.00 3.95 R
2230 2405 1.211703 TCTGGTGGTGTCTCTTTGCAA 59.788 47.619 0.00 0.00 0.00 4.08 R
2463 2638 2.290896 CCACAGTGCCCCTCAAGAAATA 60.291 50.000 0.00 0.00 0.00 1.40 R
2598 2773 2.357323 GACGGTAGTAACCCTGTAGCTC 59.643 54.545 0.00 0.00 43.54 4.09 R
2642 2817 4.690748 TGAAGCTGTTTGAAGGAGTATTCG 59.309 41.667 0.00 0.00 31.52 3.34 R
3405 3591 0.622665 AGGGAGGCCATCAAAGACTG 59.377 55.000 5.01 0.00 0.00 3.51 R
4525 7414 0.179018 AAGCAGTGGAGACCAACACC 60.179 55.000 0.00 0.00 38.34 4.16 R
5474 8373 0.106149 ATTTACGCTGATCCCCCGTC 59.894 55.000 5.80 0.00 36.51 4.79 R
6645 9806 0.884704 AACGACCGCTTTCTGCACAT 60.885 50.000 0.00 0.00 43.06 3.21 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
39 40 2.529744 GCCTGTCTCCACCCAACCT 61.530 63.158 0.00 0.00 0.00 3.50
62 63 0.173481 CCGATCGTGCTTCTTCTCCA 59.827 55.000 15.09 0.00 0.00 3.86
64 65 1.646189 GATCGTGCTTCTTCTCCACC 58.354 55.000 0.00 0.00 0.00 4.61
66 67 1.118965 TCGTGCTTCTTCTCCACCCA 61.119 55.000 0.00 0.00 0.00 4.51
68 69 0.606673 GTGCTTCTTCTCCACCCACC 60.607 60.000 0.00 0.00 0.00 4.61
69 70 1.002011 GCTTCTTCTCCACCCACCC 60.002 63.158 0.00 0.00 0.00 4.61
70 71 1.492993 GCTTCTTCTCCACCCACCCT 61.493 60.000 0.00 0.00 0.00 4.34
71 72 0.615850 CTTCTTCTCCACCCACCCTC 59.384 60.000 0.00 0.00 0.00 4.30
73 74 2.204090 TTCTCCACCCACCCTCCC 60.204 66.667 0.00 0.00 0.00 4.30
74 75 3.883822 TTCTCCACCCACCCTCCCC 62.884 68.421 0.00 0.00 0.00 4.81
78 79 4.029809 CACCCACCCTCCCCGAAC 62.030 72.222 0.00 0.00 0.00 3.95
79 80 4.265507 ACCCACCCTCCCCGAACT 62.266 66.667 0.00 0.00 0.00 3.01
80 81 3.717294 CCCACCCTCCCCGAACTG 61.717 72.222 0.00 0.00 0.00 3.16
81 82 4.410400 CCACCCTCCCCGAACTGC 62.410 72.222 0.00 0.00 0.00 4.40
82 83 3.322466 CACCCTCCCCGAACTGCT 61.322 66.667 0.00 0.00 0.00 4.24
83 84 2.529389 ACCCTCCCCGAACTGCTT 60.529 61.111 0.00 0.00 0.00 3.91
84 85 2.269241 CCCTCCCCGAACTGCTTC 59.731 66.667 0.00 0.00 0.00 3.86
85 86 2.269241 CCTCCCCGAACTGCTTCC 59.731 66.667 0.00 0.00 0.00 3.46
86 87 2.269241 CTCCCCGAACTGCTTCCC 59.731 66.667 0.00 0.00 0.00 3.97
87 88 2.528127 TCCCCGAACTGCTTCCCA 60.528 61.111 0.00 0.00 0.00 4.37
91 92 2.348998 CGAACTGCTTCCCAGCCT 59.651 61.111 0.00 0.00 46.74 4.58
110 111 1.377725 GCCTTGCCTGCTCTTGCTA 60.378 57.895 0.00 0.00 40.48 3.49
115 116 2.111582 GCCTGCTCTTGCTACTGCC 61.112 63.158 0.00 0.00 40.48 4.85
123 130 1.066573 TCTTGCTACTGCCTCTGCTTC 60.067 52.381 0.00 0.00 38.71 3.86
151 172 0.392595 GGGGCGTCTCTTCGGATTTT 60.393 55.000 0.00 0.00 0.00 1.82
186 207 1.537202 GGGATTGCGCAATGTAGGATC 59.463 52.381 38.34 22.79 0.00 3.36
213 234 2.709475 GAATTAGGGCGCGTGCTG 59.291 61.111 21.89 0.00 42.25 4.41
214 235 2.823829 GAATTAGGGCGCGTGCTGG 61.824 63.158 21.89 0.00 42.25 4.85
231 252 1.869132 GGCATTTGCATCACGCGAC 60.869 57.895 15.93 0.00 46.97 5.19
241 262 2.635229 ATCACGCGACTGATGCCCTC 62.635 60.000 15.93 0.00 29.23 4.30
272 298 2.791383 TTTTCCTGTTGTGAATGCGG 57.209 45.000 0.00 0.00 0.00 5.69
273 299 0.958091 TTTCCTGTTGTGAATGCGGG 59.042 50.000 0.00 0.00 0.00 6.13
277 303 1.529226 CTGTTGTGAATGCGGGGTTA 58.471 50.000 0.00 0.00 0.00 2.85
279 305 1.815613 TGTTGTGAATGCGGGGTTATG 59.184 47.619 0.00 0.00 0.00 1.90
357 383 3.608662 TGCTTGCCCTGTTGCTGC 61.609 61.111 0.00 0.00 34.01 5.25
373 399 1.654317 CTGCCTTCTTCTGCTGCTAG 58.346 55.000 0.00 0.00 0.00 3.42
374 400 0.251354 TGCCTTCTTCTGCTGCTAGG 59.749 55.000 0.00 0.00 0.00 3.02
384 411 3.811083 TCTGCTGCTAGGACTAGTACTC 58.189 50.000 12.02 0.00 35.65 2.59
402 429 1.804748 CTCGTAGCTTGTTTGGTTCCC 59.195 52.381 0.00 0.00 0.00 3.97
403 430 1.141254 TCGTAGCTTGTTTGGTTCCCA 59.859 47.619 0.00 0.00 0.00 4.37
404 431 2.159382 CGTAGCTTGTTTGGTTCCCAT 58.841 47.619 0.00 0.00 31.53 4.00
405 432 2.161609 CGTAGCTTGTTTGGTTCCCATC 59.838 50.000 0.00 0.00 31.53 3.51
406 433 2.380064 AGCTTGTTTGGTTCCCATCA 57.620 45.000 0.00 0.00 31.53 3.07
408 435 3.242011 AGCTTGTTTGGTTCCCATCATT 58.758 40.909 0.00 0.00 31.53 2.57
410 437 4.837860 AGCTTGTTTGGTTCCCATCATTAA 59.162 37.500 0.00 0.00 31.53 1.40
411 438 4.929211 GCTTGTTTGGTTCCCATCATTAAC 59.071 41.667 0.00 0.00 31.53 2.01
412 439 5.279456 GCTTGTTTGGTTCCCATCATTAACT 60.279 40.000 0.00 0.00 31.53 2.24
413 440 5.720371 TGTTTGGTTCCCATCATTAACTG 57.280 39.130 0.00 0.00 31.53 3.16
422 452 2.542205 CCATCATTAACTGTGCCATGCG 60.542 50.000 0.00 0.00 0.00 4.73
433 463 2.821366 CCATGCGGTCTCAGGTGC 60.821 66.667 0.00 0.00 0.00 5.01
436 466 1.376424 ATGCGGTCTCAGGTGCAAG 60.376 57.895 0.00 0.00 41.22 4.01
471 507 8.774183 AGTATGAGGTGATATAGGAGTAGTAGG 58.226 40.741 0.00 0.00 0.00 3.18
472 508 6.390048 TGAGGTGATATAGGAGTAGTAGGG 57.610 45.833 0.00 0.00 0.00 3.53
485 521 4.047125 TAGGGCTGGGGCTTGCAC 62.047 66.667 0.00 0.00 38.73 4.57
509 575 9.938670 CACTAATTATGTCTAGTGTACTGAGAC 57.061 37.037 12.65 12.65 40.01 3.36
515 581 4.451435 TGTCTAGTGTACTGAGACGTTGAG 59.549 45.833 13.89 0.00 42.10 3.02
520 586 1.714460 GTACTGAGACGTTGAGTTGCG 59.286 52.381 0.00 0.00 0.00 4.85
521 587 1.215655 ACTGAGACGTTGAGTTGCGC 61.216 55.000 0.00 0.00 0.00 6.09
522 588 1.215014 CTGAGACGTTGAGTTGCGCA 61.215 55.000 5.66 5.66 0.00 6.09
523 589 1.215014 TGAGACGTTGAGTTGCGCAG 61.215 55.000 11.31 0.00 0.00 5.18
524 590 0.939577 GAGACGTTGAGTTGCGCAGA 60.940 55.000 11.31 0.00 0.00 4.26
525 591 0.319900 AGACGTTGAGTTGCGCAGAT 60.320 50.000 11.31 2.44 0.00 2.90
526 592 0.512952 GACGTTGAGTTGCGCAGATT 59.487 50.000 11.31 0.00 0.00 2.40
527 593 0.944386 ACGTTGAGTTGCGCAGATTT 59.056 45.000 11.31 0.00 0.00 2.17
528 594 1.333619 ACGTTGAGTTGCGCAGATTTT 59.666 42.857 11.31 0.00 0.00 1.82
529 595 2.223479 ACGTTGAGTTGCGCAGATTTTT 60.223 40.909 11.31 0.00 0.00 1.94
530 596 2.151736 CGTTGAGTTGCGCAGATTTTTG 59.848 45.455 11.31 0.00 0.00 2.44
531 597 2.420628 TGAGTTGCGCAGATTTTTGG 57.579 45.000 11.31 0.00 0.00 3.28
532 598 1.680735 TGAGTTGCGCAGATTTTTGGT 59.319 42.857 11.31 0.00 0.00 3.67
533 599 2.287547 TGAGTTGCGCAGATTTTTGGTC 60.288 45.455 11.31 0.00 0.00 4.02
534 600 1.052287 GTTGCGCAGATTTTTGGTCG 58.948 50.000 11.31 0.00 0.00 4.79
535 601 0.662970 TTGCGCAGATTTTTGGTCGC 60.663 50.000 11.31 0.00 42.47 5.19
536 602 1.210155 GCGCAGATTTTTGGTCGCT 59.790 52.632 0.30 0.00 39.51 4.93
537 603 0.446222 GCGCAGATTTTTGGTCGCTA 59.554 50.000 0.30 0.00 39.51 4.26
538 604 1.790481 GCGCAGATTTTTGGTCGCTAC 60.790 52.381 0.30 0.00 39.51 3.58
539 605 1.463056 CGCAGATTTTTGGTCGCTACA 59.537 47.619 0.00 0.00 0.00 2.74
553 619 3.744426 GTCGCTACACTACATGTTTGGTT 59.256 43.478 2.30 0.00 43.19 3.67
559 625 5.243426 ACACTACATGTTTGGTTGTTCAC 57.757 39.130 2.30 0.00 38.98 3.18
561 627 5.065988 ACACTACATGTTTGGTTGTTCACTC 59.934 40.000 2.30 0.00 38.98 3.51
576 642 3.914426 TCACTCCCCTTTATTGCTCTC 57.086 47.619 0.00 0.00 0.00 3.20
579 645 5.219739 TCACTCCCCTTTATTGCTCTCTAT 58.780 41.667 0.00 0.00 0.00 1.98
617 687 0.900182 GGGCTTCAAAGGGGAAGGTG 60.900 60.000 5.22 0.00 43.54 4.00
638 708 6.071447 AGGTGTTATTGAAAGTGCATGCATTA 60.071 34.615 25.64 4.57 0.00 1.90
641 711 6.979817 TGTTATTGAAAGTGCATGCATTATCC 59.020 34.615 25.64 10.61 0.00 2.59
653 723 5.335426 GCATGCATTATCCTCGAATCATTGT 60.335 40.000 14.21 0.00 0.00 2.71
675 745 4.384846 GTGTGTCCTCAACGTACAATGTAG 59.615 45.833 0.00 0.00 0.00 2.74
676 746 4.038282 TGTGTCCTCAACGTACAATGTAGT 59.962 41.667 0.00 0.00 0.00 2.73
677 747 5.241285 TGTGTCCTCAACGTACAATGTAGTA 59.759 40.000 0.00 0.00 0.00 1.82
678 748 5.570589 GTGTCCTCAACGTACAATGTAGTAC 59.429 44.000 0.00 0.00 40.68 2.73
680 750 6.016024 TGTCCTCAACGTACAATGTAGTACTT 60.016 38.462 0.00 0.00 41.65 2.24
681 751 6.307318 GTCCTCAACGTACAATGTAGTACTTG 59.693 42.308 0.00 6.43 41.65 3.16
682 752 6.016024 TCCTCAACGTACAATGTAGTACTTGT 60.016 38.462 16.87 16.87 41.65 3.16
683 753 7.174772 TCCTCAACGTACAATGTAGTACTTGTA 59.825 37.037 0.00 15.48 41.65 2.41
687 757 8.740369 CAACGTACAATGTAGTACTTGTATAGC 58.260 37.037 19.33 11.39 41.65 2.97
703 773 4.818005 TGTATAGCTTCTCATGTGCCAATG 59.182 41.667 0.00 0.00 0.00 2.82
708 778 1.466856 TCTCATGTGCCAATGCTTCC 58.533 50.000 0.00 0.00 38.71 3.46
709 779 1.005097 TCTCATGTGCCAATGCTTCCT 59.995 47.619 0.00 0.00 38.71 3.36
731 801 6.723977 TCCTTTCTTACTAAAAATGGTGCCAT 59.276 34.615 0.00 0.00 38.46 4.40
777 849 4.201647 CGGATGAAATTTTTGCATGCAGAC 60.202 41.667 21.50 4.66 31.69 3.51
794 886 4.101585 TGCAGACAGGGGATTCACTAATAG 59.898 45.833 0.00 0.00 0.00 1.73
827 919 5.002464 ACAACTTGCTTCATATCAATGCC 57.998 39.130 0.00 0.00 32.76 4.40
852 944 5.380043 AGACAATGTTCACTGAACCTTCAT 58.620 37.500 17.51 6.28 41.35 2.57
856 948 6.205464 ACAATGTTCACTGAACCTTCATACAG 59.795 38.462 17.51 5.62 41.35 2.74
892 994 4.092383 AGTTAAATGATGCGACGGTGTTAC 59.908 41.667 0.00 0.00 0.00 2.50
901 1003 2.222445 GCGACGGTGTTACTTGATTTGT 59.778 45.455 0.00 0.00 0.00 2.83
954 1056 9.659830 GTTTATGACTAAACAACTTCAATTCGT 57.340 29.630 3.92 0.00 44.05 3.85
978 1080 6.421801 GTGCTGCACTTTGTTTAATCATTTCT 59.578 34.615 24.68 0.00 0.00 2.52
983 1085 7.169645 TGCACTTTGTTTAATCATTTCTGCTTC 59.830 33.333 0.00 0.00 0.00 3.86
1081 1183 3.569701 TGTTCCTGCAAGAAATCTTCCAC 59.430 43.478 0.00 0.00 34.07 4.02
1213 1315 9.143155 TGTTATAAGCCCTTTCTTTTTCTTTCT 57.857 29.630 0.00 0.00 0.00 2.52
1233 1335 6.861065 TTCTTACAAAGAAGTGACATGTCC 57.139 37.500 22.85 13.88 42.31 4.02
1279 1382 6.939622 TCTCCATTTGATGCATCTACGATAT 58.060 36.000 26.32 7.64 0.00 1.63
1367 1470 9.098355 GTCTGTTGAATCATGCACTAACTTATA 57.902 33.333 0.00 0.00 0.00 0.98
1379 1482 7.639039 TGCACTAACTTATATAACTTGCATGC 58.361 34.615 11.82 11.82 32.73 4.06
1474 1577 1.878088 GATGATCGCAGATTGCATGGT 59.122 47.619 1.69 0.00 45.36 3.55
1510 1613 1.551883 AGCAATGGCAAATTCTGTCCC 59.448 47.619 0.00 0.00 44.61 4.46
1578 1681 4.636249 CCTGCTCAGGTATCATCCTTTAC 58.364 47.826 7.75 0.00 43.61 2.01
1607 1710 2.328099 GCCACCTTGCTCAACCTCG 61.328 63.158 0.00 0.00 0.00 4.63
1630 1733 6.884295 TCGATAAAATGACTCAAAGGGAACAT 59.116 34.615 0.00 0.00 0.00 2.71
1984 2087 4.035091 GTGTCATATGCAGATGCGGTAAAA 59.965 41.667 16.53 0.00 45.83 1.52
2036 2139 4.302067 ACTAAGAGATGTGGATGATGGGT 58.698 43.478 0.00 0.00 0.00 4.51
2062 2201 2.743664 CAATGAGTGGAACAATGAGCGA 59.256 45.455 0.00 0.00 44.16 4.93
2338 2513 4.456911 CAGGAAAATGAGCTTAGCTTCACA 59.543 41.667 8.58 1.91 39.88 3.58
2463 2638 6.485171 AGGACATGCAAGAAGTTAAAGGTAT 58.515 36.000 0.00 0.00 0.00 2.73
2548 2723 6.582253 TGGGAGCATTCCAGTTTGCTACTT 62.582 45.833 7.05 0.00 40.56 2.24
2598 2773 9.871238 TTCAGAAGCTAAGGTTAGTTATAACAG 57.129 33.333 17.65 5.57 42.66 3.16
2625 2800 5.129368 ACAGGGTTACTACCGTCCTTATA 57.871 43.478 0.00 0.00 46.04 0.98
2634 2809 9.277783 GTTACTACCGTCCTTATATCTTGTCTA 57.722 37.037 0.00 0.00 0.00 2.59
2635 2810 9.851686 TTACTACCGTCCTTATATCTTGTCTAA 57.148 33.333 0.00 0.00 0.00 2.10
2667 2842 6.535150 CGAATACTCCTTCAAACAGCTTCATA 59.465 38.462 0.00 0.00 0.00 2.15
2691 2866 9.698309 ATATCTATGTATTCCAACTTTCTCACG 57.302 33.333 0.00 0.00 0.00 4.35
2773 2948 2.690497 TGGAGAAGAAGCAGGTATCTCG 59.310 50.000 0.00 0.00 37.89 4.04
2865 3042 6.697455 TGAATCAGTAAGTTGATCATAGCGTC 59.303 38.462 0.00 0.00 36.81 5.19
2970 3152 8.924691 CATTTTGTATGTAAATGTTGGGAACTG 58.075 33.333 0.00 0.00 37.90 3.16
3124 3310 7.428826 AGAACACAGTGAAGAATTTGAATTCC 58.571 34.615 7.81 0.75 44.55 3.01
3216 3402 6.757897 TGTCATTTATCTCATTGGTGGTTC 57.242 37.500 0.00 0.00 0.00 3.62
3364 3550 0.850100 TTCTTGGTGGTGGTGATGGT 59.150 50.000 0.00 0.00 0.00 3.55
3405 3591 5.049405 CAGGTACTCATTGGTTTCTGTGTTC 60.049 44.000 0.00 0.00 34.60 3.18
3566 3752 0.037975 CTGGAGTTGGTTTGCATGGC 60.038 55.000 0.00 0.00 0.00 4.40
3600 3786 2.484062 GGCGGTGGAGATGGCATTG 61.484 63.158 0.00 0.00 0.00 2.82
3657 3843 3.202151 TCAGGGAAAGTGGACAAAGAGTT 59.798 43.478 0.00 0.00 0.00 3.01
3726 3912 5.183713 TGATTCAACTTACCTTCATTGCAGG 59.816 40.000 0.34 0.34 37.45 4.85
3909 4097 7.852945 CCATTTTCAATACAAAGACGAGATAGC 59.147 37.037 0.00 0.00 0.00 2.97
3980 4168 9.601217 GAAATCCTAAGCAGTTACAGATAAGAA 57.399 33.333 0.00 0.00 0.00 2.52
4007 4195 3.026707 TGTCGGAGAATGGTCCATAGA 57.973 47.619 4.33 0.00 39.69 1.98
4079 6959 5.836358 TGTTGCTGGGTATTTTTCCTACTTT 59.164 36.000 0.00 0.00 0.00 2.66
4085 6965 7.392393 GCTGGGTATTTTTCCTACTTTTAGTCA 59.608 37.037 0.00 0.00 0.00 3.41
4092 6973 7.672983 TTTTCCTACTTTTAGTCAGCATCTG 57.327 36.000 0.00 0.00 0.00 2.90
4205 7094 6.377327 CCATAAGTTGGCCTAACATTGTAG 57.623 41.667 16.93 5.23 41.88 2.74
4219 7108 7.667219 CCTAACATTGTAGCATCTTATCCCAAT 59.333 37.037 0.00 0.00 0.00 3.16
4381 7270 6.996282 CAGGGTTAAGTCTTCTGTAAGGAAAA 59.004 38.462 0.00 0.00 33.22 2.29
4382 7271 7.501225 CAGGGTTAAGTCTTCTGTAAGGAAAAA 59.499 37.037 0.00 0.00 33.22 1.94
4398 7287 2.197324 AAAAACAGGGGCTCCGCA 59.803 55.556 0.00 0.00 38.33 5.69
4405 7294 1.678970 AGGGGCTCCGCAAATTCAC 60.679 57.895 0.00 0.00 38.33 3.18
4525 7414 8.682936 ATGAACATAAATAACTTCTAGGCTGG 57.317 34.615 0.00 0.00 0.00 4.85
4526 7415 7.054124 TGAACATAAATAACTTCTAGGCTGGG 58.946 38.462 0.00 0.00 0.00 4.45
4816 7708 6.335471 TGTGATGATTGCTTTTGTCTGAAT 57.665 33.333 0.00 0.00 0.00 2.57
4825 7717 6.258230 TGCTTTTGTCTGAATAATCTGTGG 57.742 37.500 0.00 0.00 0.00 4.17
4860 7752 1.813513 GCTTTTCTCTAGCTGGTGCA 58.186 50.000 0.00 0.00 42.74 4.57
4907 7799 1.284408 GCGGTTTCAATGGCGTTCA 59.716 52.632 0.00 0.00 0.00 3.18
4908 7800 0.729140 GCGGTTTCAATGGCGTTCAG 60.729 55.000 0.00 0.00 0.00 3.02
5018 7910 6.727824 AGTAAGTAGTTTAGTGCAGCAATG 57.272 37.500 5.38 0.00 0.00 2.82
5045 7937 3.754965 TGCAAAAGTCCTAGAGCACATT 58.245 40.909 0.00 0.00 0.00 2.71
5202 8101 2.991190 GGCTTGCATGACAATGAACTTG 59.009 45.455 3.33 0.00 37.72 3.16
5225 8124 8.801715 TTGTTATTTCTTCAAAGTGAGAATGC 57.198 30.769 0.00 0.00 0.00 3.56
5344 8243 6.717997 TGAGTACAGTAAGAGGTTGTCATACA 59.282 38.462 0.00 0.00 32.66 2.29
5375 8274 7.009999 CAGTGCTTGATGAGAAGATGTAAGTAC 59.990 40.741 0.00 0.00 32.09 2.73
5411 8310 1.678627 CAGATCAGGACGGTCCACTAG 59.321 57.143 27.87 14.72 39.61 2.57
5423 8322 5.476614 ACGGTCCACTAGAAATTGTAGAAC 58.523 41.667 4.07 0.17 0.00 3.01
5471 8370 6.018994 GGTATAGCTCTTTGTGGTAAATCACG 60.019 42.308 0.00 0.00 40.31 4.35
5472 8371 3.074412 AGCTCTTTGTGGTAAATCACGG 58.926 45.455 0.00 0.00 40.31 4.94
5473 8372 2.161609 GCTCTTTGTGGTAAATCACGGG 59.838 50.000 0.00 0.00 40.31 5.28
5474 8373 2.747446 CTCTTTGTGGTAAATCACGGGG 59.253 50.000 0.00 0.00 40.31 5.73
5475 8374 2.372504 TCTTTGTGGTAAATCACGGGGA 59.627 45.455 0.00 0.00 40.31 4.81
5476 8375 2.188062 TTGTGGTAAATCACGGGGAC 57.812 50.000 0.00 0.00 40.31 4.46
5500 8399 4.583073 GGGGGATCAGCGTAAATTTTGTAT 59.417 41.667 0.00 0.00 0.00 2.29
5516 8415 1.229428 GTATGATGTCGGCCCATGTG 58.771 55.000 0.00 0.00 0.00 3.21
5520 8419 0.886490 GATGTCGGCCCATGTGATCC 60.886 60.000 0.00 0.00 0.00 3.36
5749 8649 2.721971 CTTCAGCTGTGCTCGGTGGT 62.722 60.000 14.67 0.00 36.40 4.16
5833 8755 3.429410 GCTACACCCAGATGCAATTTTCC 60.429 47.826 0.00 0.00 0.00 3.13
5864 8788 2.772077 TACGGCTGCTAACATCCAAA 57.228 45.000 0.00 0.00 31.11 3.28
5868 8792 3.206150 CGGCTGCTAACATCCAAACTAT 58.794 45.455 0.00 0.00 31.11 2.12
5870 8794 4.211374 CGGCTGCTAACATCCAAACTATAC 59.789 45.833 0.00 0.00 31.11 1.47
5885 8809 9.075678 TCCAAACTATACTACTGCCTAGATTAC 57.924 37.037 0.00 0.00 0.00 1.89
5954 8959 8.902806 TGATGTGTAGTTTCTCAGAAAAATTGT 58.097 29.630 0.00 0.00 0.00 2.71
5974 8979 3.242706 TGTGCTGATCAACTGTTGAAACG 60.243 43.478 25.26 16.61 43.95 3.60
5975 8980 2.286950 TGCTGATCAACTGTTGAAACGC 60.287 45.455 25.26 23.81 43.95 4.84
6103 9116 1.878656 CTGACCGACCGGCTTTCTCT 61.879 60.000 8.55 0.00 39.32 3.10
6118 9133 4.381079 GCTTTCTCTGATCTACGGACACTT 60.381 45.833 0.00 0.00 0.00 3.16
6136 9151 6.204495 GGACACTTCGAACCTATACCTACTAG 59.796 46.154 0.00 0.00 0.00 2.57
6137 9152 6.657875 ACACTTCGAACCTATACCTACTAGT 58.342 40.000 0.00 0.00 0.00 2.57
6138 9153 7.796054 ACACTTCGAACCTATACCTACTAGTA 58.204 38.462 1.89 1.89 0.00 1.82
6222 9368 1.150135 TGGAGGGTCCTCTCTTTGTCT 59.850 52.381 15.74 0.00 42.38 3.41
6250 9396 3.328931 TGAATTCAGAAGCCCTTGTCTCT 59.671 43.478 3.38 0.00 0.00 3.10
6265 9418 3.463944 TGTCTCTTGAACCGAGAAAACC 58.536 45.455 0.00 0.00 39.08 3.27
6274 9427 1.202651 ACCGAGAAAACCACTGTCCAG 60.203 52.381 0.00 0.00 0.00 3.86
6318 9471 4.201940 TGGATCTTAATTCACAATGCAGCG 60.202 41.667 0.00 0.00 0.00 5.18
6330 9483 3.181503 ACAATGCAGCGAACATCTGATTC 60.182 43.478 0.00 0.00 33.54 2.52
6404 9565 3.773860 TTTGTTGCCGTATGCTTATGG 57.226 42.857 12.51 12.51 42.00 2.74
6419 9580 3.608474 GCTTATGGTCGTTTTTCGCTGTT 60.608 43.478 0.00 0.00 39.67 3.16
6479 9640 2.105477 ACCAGACACAGCAAGAGAACAT 59.895 45.455 0.00 0.00 0.00 2.71
6483 9644 2.740981 GACACAGCAAGAGAACATCAGG 59.259 50.000 0.00 0.00 0.00 3.86
6537 9698 6.427547 TGCCATGATCCTTGATTTTTCAAAAC 59.572 34.615 0.00 0.00 0.00 2.43
6641 9802 2.307098 AGAACTGTAGAAGCAGGGCAAT 59.693 45.455 0.00 0.00 40.59 3.56
6642 9803 3.519510 AGAACTGTAGAAGCAGGGCAATA 59.480 43.478 0.00 0.00 40.59 1.90
6643 9804 4.164988 AGAACTGTAGAAGCAGGGCAATAT 59.835 41.667 0.00 0.00 40.59 1.28
6644 9805 3.813443 ACTGTAGAAGCAGGGCAATATG 58.187 45.455 0.00 0.00 40.59 1.78
6645 9806 3.455910 ACTGTAGAAGCAGGGCAATATGA 59.544 43.478 0.00 0.00 40.59 2.15
6646 9807 4.103785 ACTGTAGAAGCAGGGCAATATGAT 59.896 41.667 0.00 0.00 40.59 2.45
6689 9857 2.726832 AGTAAAGAGGACGTGCAGAC 57.273 50.000 10.52 0.03 0.00 3.51
6924 10098 0.322456 CCCCGTGCCTTTTCATCTCA 60.322 55.000 0.00 0.00 0.00 3.27
6949 10123 2.766229 GCCACTCCTCCCTCTCCC 60.766 72.222 0.00 0.00 0.00 4.30
6954 10128 3.695825 TCCTCCCTCTCCCACCCC 61.696 72.222 0.00 0.00 0.00 4.95
7010 10184 3.732849 GCCACCCTCCTCCCCTTG 61.733 72.222 0.00 0.00 0.00 3.61
7038 10212 3.701604 CTTCTTCTCGTCCCGCCGG 62.702 68.421 0.00 0.00 0.00 6.13
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
13 14 3.692406 GGAGACAGGCGTCCCGTT 61.692 66.667 5.98 0.00 43.73 4.44
15 16 4.436998 GTGGAGACAGGCGTCCCG 62.437 72.222 5.98 0.00 43.73 5.14
17 18 4.083862 GGGTGGAGACAGGCGTCC 62.084 72.222 5.98 0.00 43.73 4.79
25 26 2.047179 GCGAGGTTGGGTGGAGAC 60.047 66.667 0.00 0.00 0.00 3.36
62 63 4.265507 AGTTCGGGGAGGGTGGGT 62.266 66.667 0.00 0.00 0.00 4.51
64 65 4.410400 GCAGTTCGGGGAGGGTGG 62.410 72.222 0.00 0.00 0.00 4.61
66 67 2.529389 AAGCAGTTCGGGGAGGGT 60.529 61.111 0.00 0.00 0.00 4.34
68 69 2.269241 GGAAGCAGTTCGGGGAGG 59.731 66.667 0.00 0.00 32.92 4.30
69 70 2.269241 GGGAAGCAGTTCGGGGAG 59.731 66.667 0.00 0.00 32.92 4.30
70 71 2.528127 TGGGAAGCAGTTCGGGGA 60.528 61.111 0.00 0.00 32.92 4.81
71 72 2.045926 CTGGGAAGCAGTTCGGGG 60.046 66.667 0.00 0.00 32.92 5.73
73 74 2.747855 GGCTGGGAAGCAGTTCGG 60.748 66.667 0.00 0.00 36.33 4.30
74 75 2.037136 CAGGCTGGGAAGCAGTTCG 61.037 63.158 6.61 0.00 36.33 3.95
75 76 2.338785 GCAGGCTGGGAAGCAGTTC 61.339 63.158 17.64 0.00 36.33 3.01
76 77 2.282745 GCAGGCTGGGAAGCAGTT 60.283 61.111 17.64 0.00 36.33 3.16
77 78 4.357279 GGCAGGCTGGGAAGCAGT 62.357 66.667 17.64 0.00 36.33 4.40
78 79 3.580604 AAGGCAGGCTGGGAAGCAG 62.581 63.158 17.64 0.00 36.33 4.24
79 80 3.583380 AAGGCAGGCTGGGAAGCA 61.583 61.111 17.64 0.00 36.33 3.91
80 81 3.066814 CAAGGCAGGCTGGGAAGC 61.067 66.667 17.64 0.11 0.00 3.86
81 82 3.066814 GCAAGGCAGGCTGGGAAG 61.067 66.667 17.64 0.00 0.00 3.46
82 83 4.684134 GGCAAGGCAGGCTGGGAA 62.684 66.667 17.64 0.00 0.00 3.97
87 88 4.737177 GAGCAGGCAAGGCAGGCT 62.737 66.667 11.46 11.46 46.40 4.58
88 89 4.737177 AGAGCAGGCAAGGCAGGC 62.737 66.667 0.00 0.00 0.00 4.85
91 92 2.128290 TAGCAAGAGCAGGCAAGGCA 62.128 55.000 0.00 0.00 45.49 4.75
110 111 2.345244 CCACGAAGCAGAGGCAGT 59.655 61.111 0.00 0.00 44.61 4.40
115 116 3.114616 CACCGCCACGAAGCAGAG 61.115 66.667 0.00 0.00 0.00 3.35
138 159 3.348647 TGCATGGAAAATCCGAAGAGA 57.651 42.857 0.00 0.00 40.17 3.10
151 172 2.142356 ATCCCGTTGATTTGCATGGA 57.858 45.000 0.00 0.00 0.00 3.41
186 207 1.152756 CCCTAATTCCCCCGCTTGG 60.153 63.158 0.00 0.00 0.00 3.61
213 234 1.869132 GTCGCGTGATGCAAATGCC 60.869 57.895 5.77 0.00 46.97 4.40
214 235 1.129879 CAGTCGCGTGATGCAAATGC 61.130 55.000 5.77 6.84 46.97 3.56
231 252 0.305922 GCGAAAATCGAGGGCATCAG 59.694 55.000 3.61 0.00 43.74 2.90
260 286 1.816224 ACATAACCCCGCATTCACAAC 59.184 47.619 0.00 0.00 0.00 3.32
271 297 2.922740 TGCTAATCGGACATAACCCC 57.077 50.000 0.00 0.00 0.00 4.95
272 298 3.805207 ACTTGCTAATCGGACATAACCC 58.195 45.455 0.00 0.00 0.00 4.11
273 299 4.748600 GGTACTTGCTAATCGGACATAACC 59.251 45.833 0.00 0.00 0.00 2.85
277 303 2.802057 GCGGTACTTGCTAATCGGACAT 60.802 50.000 3.79 0.00 0.00 3.06
279 305 1.206523 GCGGTACTTGCTAATCGGAC 58.793 55.000 3.79 0.00 0.00 4.79
288 314 3.431725 GCACCCTGCGGTACTTGC 61.432 66.667 4.03 4.03 42.04 4.01
310 336 2.283173 AAGGGAGGGCCTTTTGCG 60.283 61.111 7.89 0.00 42.61 4.85
318 344 1.751437 GTGATAACACAAGGGAGGGC 58.249 55.000 0.00 0.00 45.32 5.19
357 383 1.830477 AGTCCTAGCAGCAGAAGAAGG 59.170 52.381 0.00 0.00 0.00 3.46
373 399 4.961435 AACAAGCTACGAGTACTAGTCC 57.039 45.455 12.24 5.39 0.00 3.85
374 400 5.094134 CCAAACAAGCTACGAGTACTAGTC 58.906 45.833 12.24 0.00 0.00 2.59
413 440 2.821366 CCTGAGACCGCATGGCAC 60.821 66.667 0.00 0.00 39.70 5.01
422 452 0.394565 ACTCACTTGCACCTGAGACC 59.605 55.000 21.50 0.00 37.85 3.85
433 463 9.823647 ATATCACCTCATACTAAAACTCACTTG 57.176 33.333 0.00 0.00 0.00 3.16
436 466 9.915629 CCTATATCACCTCATACTAAAACTCAC 57.084 37.037 0.00 0.00 0.00 3.51
461 497 2.141448 GCCCCAGCCCTACTACTCC 61.141 68.421 0.00 0.00 0.00 3.85
464 500 1.527370 CAAGCCCCAGCCCTACTAC 59.473 63.158 0.00 0.00 41.25 2.73
467 503 4.047125 TGCAAGCCCCAGCCCTAC 62.047 66.667 0.00 0.00 41.25 3.18
468 504 4.047125 GTGCAAGCCCCAGCCCTA 62.047 66.667 0.00 0.00 41.25 3.53
470 506 2.861271 ATTAGTGCAAGCCCCAGCCC 62.861 60.000 0.00 0.00 41.25 5.19
471 507 0.972471 AATTAGTGCAAGCCCCAGCC 60.972 55.000 0.00 0.00 41.25 4.85
472 508 1.762708 TAATTAGTGCAAGCCCCAGC 58.237 50.000 0.00 0.00 40.32 4.85
485 521 8.828644 ACGTCTCAGTACACTAGACATAATTAG 58.171 37.037 17.26 6.41 39.69 1.73
509 575 2.036556 AAAATCTGCGCAACTCAACG 57.963 45.000 13.05 0.00 0.00 4.10
515 581 1.052287 CGACCAAAAATCTGCGCAAC 58.948 50.000 13.05 0.00 0.00 4.17
520 586 2.484264 AGTGTAGCGACCAAAAATCTGC 59.516 45.455 0.00 0.00 0.00 4.26
521 587 4.688879 TGTAGTGTAGCGACCAAAAATCTG 59.311 41.667 0.00 0.00 0.00 2.90
522 588 4.890088 TGTAGTGTAGCGACCAAAAATCT 58.110 39.130 0.00 0.00 0.00 2.40
523 589 5.121768 ACATGTAGTGTAGCGACCAAAAATC 59.878 40.000 0.00 0.00 39.91 2.17
524 590 5.001232 ACATGTAGTGTAGCGACCAAAAAT 58.999 37.500 0.00 0.00 39.91 1.82
525 591 4.382291 ACATGTAGTGTAGCGACCAAAAA 58.618 39.130 0.00 0.00 39.91 1.94
526 592 3.997762 ACATGTAGTGTAGCGACCAAAA 58.002 40.909 0.00 0.00 39.91 2.44
527 593 3.671008 ACATGTAGTGTAGCGACCAAA 57.329 42.857 0.00 0.00 39.91 3.28
528 594 3.671008 AACATGTAGTGTAGCGACCAA 57.329 42.857 0.00 0.00 41.14 3.67
529 595 3.322369 CAAACATGTAGTGTAGCGACCA 58.678 45.455 0.00 0.00 41.14 4.02
530 596 2.671396 CCAAACATGTAGTGTAGCGACC 59.329 50.000 0.00 0.00 41.14 4.79
531 597 3.323243 ACCAAACATGTAGTGTAGCGAC 58.677 45.455 0.00 0.00 41.14 5.19
532 598 3.671008 ACCAAACATGTAGTGTAGCGA 57.329 42.857 0.00 0.00 41.14 4.93
533 599 3.496884 ACAACCAAACATGTAGTGTAGCG 59.503 43.478 0.00 0.00 41.14 4.26
534 600 5.008217 TGAACAACCAAACATGTAGTGTAGC 59.992 40.000 0.00 0.00 41.14 3.58
535 601 6.260050 AGTGAACAACCAAACATGTAGTGTAG 59.740 38.462 0.00 0.00 41.14 2.74
536 602 6.116806 AGTGAACAACCAAACATGTAGTGTA 58.883 36.000 0.00 0.00 41.14 2.90
537 603 4.947388 AGTGAACAACCAAACATGTAGTGT 59.053 37.500 0.00 0.00 44.84 3.55
538 604 5.499139 AGTGAACAACCAAACATGTAGTG 57.501 39.130 0.00 0.00 0.00 2.74
539 605 4.578928 GGAGTGAACAACCAAACATGTAGT 59.421 41.667 0.00 0.00 0.00 2.73
553 619 3.330701 AGAGCAATAAAGGGGAGTGAACA 59.669 43.478 0.00 0.00 0.00 3.18
559 625 6.671779 AGGATATAGAGAGCAATAAAGGGGAG 59.328 42.308 0.00 0.00 0.00 4.30
561 627 6.882768 AGGATATAGAGAGCAATAAAGGGG 57.117 41.667 0.00 0.00 0.00 4.79
576 642 7.342026 AGCCCCAAACTTACAAAAAGGATATAG 59.658 37.037 0.00 0.00 0.00 1.31
579 645 5.399113 AGCCCCAAACTTACAAAAAGGATA 58.601 37.500 0.00 0.00 0.00 2.59
617 687 7.205297 AGGATAATGCATGCACTTTCAATAAC 58.795 34.615 25.37 3.68 0.00 1.89
638 708 3.198635 AGGACACACAATGATTCGAGGAT 59.801 43.478 0.00 0.00 0.00 3.24
641 711 3.588955 TGAGGACACACAATGATTCGAG 58.411 45.455 0.00 0.00 0.00 4.04
653 723 3.462483 ACATTGTACGTTGAGGACACA 57.538 42.857 0.00 0.00 44.92 3.72
675 745 5.463724 GGCACATGAGAAGCTATACAAGTAC 59.536 44.000 0.00 0.00 0.00 2.73
676 746 5.128663 TGGCACATGAGAAGCTATACAAGTA 59.871 40.000 0.00 0.00 0.00 2.24
677 747 4.080919 TGGCACATGAGAAGCTATACAAGT 60.081 41.667 0.00 0.00 0.00 3.16
678 748 4.445453 TGGCACATGAGAAGCTATACAAG 58.555 43.478 0.00 0.00 0.00 3.16
680 750 4.486125 TTGGCACATGAGAAGCTATACA 57.514 40.909 0.00 0.00 39.30 2.29
681 751 4.320057 GCATTGGCACATGAGAAGCTATAC 60.320 45.833 0.00 0.00 39.30 1.47
682 752 3.817084 GCATTGGCACATGAGAAGCTATA 59.183 43.478 0.00 0.00 39.30 1.31
683 753 2.621998 GCATTGGCACATGAGAAGCTAT 59.378 45.455 0.00 0.00 39.30 2.97
687 757 2.159282 GGAAGCATTGGCACATGAGAAG 60.159 50.000 0.00 0.00 44.61 2.85
703 773 6.586463 GCACCATTTTTAGTAAGAAAGGAAGC 59.414 38.462 12.84 11.76 0.00 3.86
731 801 7.618117 TCCGGAACATCATATAAAGAGCCTATA 59.382 37.037 0.00 0.00 0.00 1.31
748 819 4.892433 TGCAAAAATTTCATCCGGAACAT 58.108 34.783 9.01 0.00 34.56 2.71
749 820 4.327982 TGCAAAAATTTCATCCGGAACA 57.672 36.364 9.01 0.00 34.56 3.18
777 849 4.999950 GCATGACTATTAGTGAATCCCCTG 59.000 45.833 0.00 0.00 0.00 4.45
794 886 3.923017 AGCAAGTTGTTTAGGCATGAC 57.077 42.857 4.48 0.00 0.00 3.06
827 919 5.991606 TGAAGGTTCAGTGAACATTGTCTAG 59.008 40.000 33.50 0.00 44.61 2.43
872 964 3.852286 AGTAACACCGTCGCATCATTTA 58.148 40.909 0.00 0.00 0.00 1.40
881 983 3.794536 CACAAATCAAGTAACACCGTCG 58.205 45.455 0.00 0.00 0.00 5.12
938 1040 3.115554 GCAGCACGAATTGAAGTTGTTT 58.884 40.909 0.00 0.00 0.00 2.83
954 1056 6.421501 CAGAAATGATTAAACAAAGTGCAGCA 59.578 34.615 0.00 0.00 0.00 4.41
978 1080 3.678289 TGCATTAAGCTGAGAAGAAGCA 58.322 40.909 0.00 0.00 45.94 3.91
983 1085 4.397103 TGACCATTGCATTAAGCTGAGAAG 59.603 41.667 0.00 0.00 45.94 2.85
1081 1183 0.252479 ACAGCTCCAAGATCCTGCAG 59.748 55.000 6.78 6.78 0.00 4.41
1186 1288 9.758651 GAAAGAAAAAGAAAGGGCTTATAACAA 57.241 29.630 0.00 0.00 0.00 2.83
1213 1315 4.699637 ACGGACATGTCACTTCTTTGTAA 58.300 39.130 26.47 0.00 0.00 2.41
1249 1352 1.820519 TGCATCAAATGGAGAAGGCAC 59.179 47.619 0.00 0.00 0.00 5.01
1279 1382 9.467258 CATGAAAGAAGAATTTTTAGCACAAGA 57.533 29.630 0.00 0.00 0.00 3.02
1367 1470 1.479323 CAAGCCTGGCATGCAAGTTAT 59.521 47.619 22.65 3.30 0.00 1.89
1390 1493 7.781056 TGTGTACATATGAGAGATGTGCTTTA 58.219 34.615 10.38 0.00 39.72 1.85
1474 1577 4.239304 CATTGCTTGCAGCTTCATAAACA 58.761 39.130 9.12 0.00 42.97 2.83
1510 1613 7.306925 CCATTATTTGTCCATGCATTTGATTCG 60.307 37.037 0.00 0.00 0.00 3.34
1578 1681 3.812053 GAGCAAGGTGGCATATACAAGAG 59.188 47.826 0.00 0.00 35.83 2.85
1607 1710 8.306761 ACAATGTTCCCTTTGAGTCATTTTATC 58.693 33.333 0.00 0.00 31.59 1.75
1630 1733 7.769044 GCAACCTAGATAATTGGAAGAGTACAA 59.231 37.037 0.00 0.00 0.00 2.41
1888 1991 0.884704 CAGGAGGTGGTGTTGGTTCG 60.885 60.000 0.00 0.00 0.00 3.95
1984 2087 3.131046 CCTCAACCTCAAACTTGCTTTGT 59.869 43.478 0.00 0.00 40.35 2.83
2036 2139 4.468713 TCATTGTTCCACTCATTGTTCCA 58.531 39.130 0.00 0.00 0.00 3.53
2062 2201 2.639065 TCTGGTTTGAGCTCGTTGTTT 58.361 42.857 9.64 0.00 0.00 2.83
2230 2405 1.211703 TCTGGTGGTGTCTCTTTGCAA 59.788 47.619 0.00 0.00 0.00 4.08
2463 2638 2.290896 CCACAGTGCCCCTCAAGAAATA 60.291 50.000 0.00 0.00 0.00 1.40
2598 2773 2.357323 GACGGTAGTAACCCTGTAGCTC 59.643 54.545 0.00 0.00 43.54 4.09
2634 2809 9.367444 CTGTTTGAAGGAGTATTCGTATTAGTT 57.633 33.333 0.00 0.00 31.52 2.24
2635 2810 7.491696 GCTGTTTGAAGGAGTATTCGTATTAGT 59.508 37.037 0.00 0.00 31.52 2.24
2642 2817 4.690748 TGAAGCTGTTTGAAGGAGTATTCG 59.309 41.667 0.00 0.00 31.52 3.34
2653 2828 9.494271 GGAATACATAGATATGAAGCTGTTTGA 57.506 33.333 6.84 0.00 37.15 2.69
2667 2842 6.986817 CCGTGAGAAAGTTGGAATACATAGAT 59.013 38.462 0.00 0.00 0.00 1.98
2718 2893 1.348064 TCGGACAGTCCTTTGACCAT 58.652 50.000 17.95 0.00 42.81 3.55
2723 2898 2.427232 TACGTTCGGACAGTCCTTTG 57.573 50.000 17.95 7.17 33.30 2.77
2773 2948 8.139989 AGGCATTTGAAGATATTACAGCATTTC 58.860 33.333 0.00 0.00 0.00 2.17
2847 3024 7.234187 TGAATTGACGCTATGATCAACTTAC 57.766 36.000 0.00 0.00 37.64 2.34
2865 3042 4.220693 TCCTGTAGGTCACCATGAATTG 57.779 45.455 0.00 0.00 36.34 2.32
2970 3152 6.361748 CAGAACACTAAAGAAGCTGAATTTGC 59.638 38.462 0.00 0.00 0.00 3.68
3216 3402 3.129113 TGACAAAAATGAGATGCCATCGG 59.871 43.478 0.00 0.00 0.00 4.18
3364 3550 2.161855 CCTGTATCAAACCAGCAAGCA 58.838 47.619 0.00 0.00 0.00 3.91
3405 3591 0.622665 AGGGAGGCCATCAAAGACTG 59.377 55.000 5.01 0.00 0.00 3.51
3457 3643 6.105333 CAGTCAACTTCAGGAGAAAGGATAG 58.895 44.000 0.00 0.00 32.35 2.08
3458 3644 5.544176 ACAGTCAACTTCAGGAGAAAGGATA 59.456 40.000 0.00 0.00 32.35 2.59
3566 3752 4.437121 CCACCGCCAAATGCATAAATTTTG 60.437 41.667 0.00 0.61 41.33 2.44
3600 3786 2.354259 CTCCATGTCAGAGAAACAGCC 58.646 52.381 0.00 0.00 32.86 4.85
3657 3843 7.040201 CGTATGTACCTTTTCTAGCATAGGGTA 60.040 40.741 4.12 0.92 39.78 3.69
3792 3978 6.734104 TTCTCTTTACGGTGTAGTACTCTC 57.266 41.667 0.00 0.00 0.00 3.20
3793 3979 7.516198 TTTTCTCTTTACGGTGTAGTACTCT 57.484 36.000 0.00 0.00 0.00 3.24
3909 4097 7.331934 TCGAGAATGAAGAGATAAAAGTTGGTG 59.668 37.037 0.00 0.00 0.00 4.17
4007 4195 9.892130 AGATCGAAGAGTTACTTTTTCCATATT 57.108 29.630 0.00 0.00 43.63 1.28
4028 4216 5.885352 AGAGGAGACCATCACATATAGATCG 59.115 44.000 0.00 0.00 0.00 3.69
4092 6973 1.152546 AAGGTGTGGTTTCCCCAGC 60.153 57.895 0.00 0.00 46.45 4.85
4204 7093 6.252599 TCTACAACATTGGGATAAGATGCT 57.747 37.500 0.00 0.00 0.00 3.79
4205 7094 7.516198 AATCTACAACATTGGGATAAGATGC 57.484 36.000 0.00 0.00 0.00 3.91
4522 7411 0.250467 CAGTGGAGACCAACACCCAG 60.250 60.000 0.00 0.00 38.34 4.45
4523 7412 1.836391 CAGTGGAGACCAACACCCA 59.164 57.895 0.00 0.00 38.34 4.51
4524 7413 1.600916 GCAGTGGAGACCAACACCC 60.601 63.158 0.00 0.00 38.34 4.61
4525 7414 0.179018 AAGCAGTGGAGACCAACACC 60.179 55.000 0.00 0.00 38.34 4.16
4526 7415 2.543777 TAAGCAGTGGAGACCAACAC 57.456 50.000 0.00 0.00 34.18 3.32
4574 7463 5.813672 ACTAACGAGTTTTGCTAGTCAACAA 59.186 36.000 0.00 0.00 33.73 2.83
4816 7708 4.211125 TGAAAACCAAGCACCACAGATTA 58.789 39.130 0.00 0.00 0.00 1.75
4825 7717 0.249031 AAGCGCTGAAAACCAAGCAC 60.249 50.000 12.58 0.00 32.90 4.40
4860 7752 7.394359 ACTGCATAAATCACACCATTAAGTTCT 59.606 33.333 0.00 0.00 0.00 3.01
4907 7799 7.296628 GTGAAAGGATATCACCTCAGATACT 57.703 40.000 4.83 0.00 41.02 2.12
5018 7910 2.485814 CTCTAGGACTTTTGCAGGTTGC 59.514 50.000 0.00 0.00 45.29 4.17
5034 7926 6.293298 GCCATGAGTTATGAAATGTGCTCTAG 60.293 42.308 0.00 0.00 39.21 2.43
5045 7937 4.842574 TGCACTAAGCCATGAGTTATGAA 58.157 39.130 0.00 0.00 44.83 2.57
5202 8101 8.976986 ATGCATTCTCACTTTGAAGAAATAAC 57.023 30.769 0.00 0.00 0.00 1.89
5344 8243 0.689055 TCTCATCAAGCACTGCCACT 59.311 50.000 0.00 0.00 0.00 4.00
5375 8274 5.220548 CCTGATCTGTAAAAAGAGATGCACG 60.221 44.000 0.00 0.00 0.00 5.34
5411 8310 3.689649 AGATGCCCACGTTCTACAATTTC 59.310 43.478 0.00 0.00 0.00 2.17
5423 8322 4.747108 CAGAGACTTAATTAGATGCCCACG 59.253 45.833 0.00 0.00 0.00 4.94
5473 8372 1.963464 TTTACGCTGATCCCCCGTCC 61.963 60.000 5.80 0.00 36.51 4.79
5474 8373 0.106149 ATTTACGCTGATCCCCCGTC 59.894 55.000 5.80 0.00 36.51 4.79
5475 8374 0.544697 AATTTACGCTGATCCCCCGT 59.455 50.000 7.41 7.41 38.84 5.28
5476 8375 1.675552 AAATTTACGCTGATCCCCCG 58.324 50.000 0.00 0.00 0.00 5.73
5477 8376 2.758423 ACAAAATTTACGCTGATCCCCC 59.242 45.455 0.00 0.00 0.00 5.40
5500 8399 0.179048 GATCACATGGGCCGACATCA 60.179 55.000 0.00 0.00 0.00 3.07
5516 8415 9.750125 AGAGTCAGTAAAACAAAATTTTGGATC 57.250 29.630 29.37 16.59 42.34 3.36
5520 8419 8.872845 AGCAAGAGTCAGTAAAACAAAATTTTG 58.127 29.630 25.73 25.73 43.62 2.44
5650 8550 1.614903 TCGTACAACTCAACGGTGGAT 59.385 47.619 0.00 0.00 39.52 3.41
5864 8788 7.345958 AGGGTAATCTAGGCAGTAGTATAGT 57.654 40.000 0.00 0.00 0.00 2.12
5868 8792 6.022107 TGAAGGGTAATCTAGGCAGTAGTA 57.978 41.667 0.00 0.00 0.00 1.82
5870 8794 4.896482 ACTGAAGGGTAATCTAGGCAGTAG 59.104 45.833 0.00 0.00 33.99 2.57
5885 8809 1.318576 AAACGGCTGAAACTGAAGGG 58.681 50.000 0.00 0.00 0.00 3.95
5954 8959 2.286950 GCGTTTCAACAGTTGATCAGCA 60.287 45.455 16.89 0.00 39.84 4.41
5974 8979 1.895131 ACAATCCATCCAACACAAGGC 59.105 47.619 0.00 0.00 0.00 4.35
5975 8980 3.156293 TGACAATCCATCCAACACAAGG 58.844 45.455 0.00 0.00 0.00 3.61
6103 9116 2.163010 GGTTCGAAGTGTCCGTAGATCA 59.837 50.000 0.00 0.00 0.00 2.92
6137 9152 8.898761 GCAGCAGCTTAGATAGATACTTAGATA 58.101 37.037 0.00 0.00 37.91 1.98
6138 9153 7.771183 GCAGCAGCTTAGATAGATACTTAGAT 58.229 38.462 0.00 0.00 37.91 1.98
6246 9392 3.134081 AGTGGTTTTCTCGGTTCAAGAGA 59.866 43.478 0.00 0.00 42.39 3.10
6250 9396 2.940410 GACAGTGGTTTTCTCGGTTCAA 59.060 45.455 0.00 0.00 0.00 2.69
6265 9418 3.458189 AGAAACGAGAAACTGGACAGTG 58.542 45.455 5.63 0.00 41.58 3.66
6295 9448 4.201940 CGCTGCATTGTGAATTAAGATCCA 60.202 41.667 0.00 0.00 0.00 3.41
6307 9460 1.465777 TCAGATGTTCGCTGCATTGTG 59.534 47.619 0.00 0.00 33.45 3.33
6311 9464 1.596260 CGAATCAGATGTTCGCTGCAT 59.404 47.619 0.00 0.00 41.43 3.96
6318 9471 6.146184 TCAGTTCAGTTTCGAATCAGATGTTC 59.854 38.462 8.83 0.00 0.00 3.18
6330 9483 3.519908 TCGCATTTCAGTTCAGTTTCG 57.480 42.857 0.00 0.00 0.00 3.46
6404 9565 2.284232 GCAAACAACAGCGAAAAACGAC 60.284 45.455 0.00 0.00 45.77 4.34
6419 9580 4.020543 AGTAAACAACAGGAAGGCAAACA 58.979 39.130 0.00 0.00 0.00 2.83
6479 9640 1.564348 GGGCCTGAATCTAAACCCTGA 59.436 52.381 0.84 0.00 34.34 3.86
6483 9644 1.101635 GCCGGGCCTGAATCTAAACC 61.102 60.000 15.09 0.00 0.00 3.27
6514 9675 7.966246 TGTTTTGAAAAATCAAGGATCATGG 57.034 32.000 0.00 0.00 0.00 3.66
6537 9698 9.136952 GATCTTTTGAAACCATCTTCAAGAATG 57.863 33.333 0.00 0.00 44.06 2.67
6633 9794 2.578786 TCTGCACATCATATTGCCCTG 58.421 47.619 0.00 0.00 38.00 4.45
6641 9802 2.279741 GACCGCTTTCTGCACATCATA 58.720 47.619 0.00 0.00 43.06 2.15
6642 9803 1.089920 GACCGCTTTCTGCACATCAT 58.910 50.000 0.00 0.00 43.06 2.45
6643 9804 1.291184 CGACCGCTTTCTGCACATCA 61.291 55.000 0.00 0.00 43.06 3.07
6644 9805 1.291877 ACGACCGCTTTCTGCACATC 61.292 55.000 0.00 0.00 43.06 3.06
6645 9806 0.884704 AACGACCGCTTTCTGCACAT 60.885 50.000 0.00 0.00 43.06 3.21
6646 9807 1.522806 AACGACCGCTTTCTGCACA 60.523 52.632 0.00 0.00 43.06 4.57
6661 9829 5.029014 CACGTCCTCTTTACTATCTCAACG 58.971 45.833 0.00 0.00 0.00 4.10
6689 9857 2.094338 GGGGACGTGTAAAGGTCAGTAG 60.094 54.545 7.98 0.00 34.87 2.57
6867 10041 1.305623 GTAGTCGGAGAGGGTGGGA 59.694 63.158 0.00 0.00 36.95 4.37
6924 10098 2.066999 GGAGGAGTGGCCGGAGATT 61.067 63.158 5.05 0.00 43.43 2.40
6949 10123 2.284921 TGAGAGGGAGCAGGGGTG 60.285 66.667 0.00 0.00 0.00 4.61
6954 10128 1.120795 GGGGATCTGAGAGGGAGCAG 61.121 65.000 0.00 0.00 0.00 4.24
6993 10167 3.732849 CAAGGGGAGGAGGGTGGC 61.733 72.222 0.00 0.00 0.00 5.01


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

AutoCloner maintained by Alex Coulton.