Multiple sequence alignment - TraesCS1D01G367900

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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 TraesCS1D01G367900 chr1D 100.000 3228 0 0 1 3228 447669520 447666293 0.000000e+00 5962.0
1 TraesCS1D01G367900 chr3B 88.013 1852 148 37 698 2515 15101004 15099193 0.000000e+00 2122.0
2 TraesCS1D01G367900 chr3B 88.349 1708 142 35 822 2512 15138319 15139986 0.000000e+00 1999.0
3 TraesCS1D01G367900 chr3B 87.905 1265 122 16 1261 2516 15150113 15151355 0.000000e+00 1459.0
4 TraesCS1D01G367900 chr3B 92.144 611 20 10 1 607 15101649 15101063 0.000000e+00 837.0
5 TraesCS1D01G367900 chr3B 87.150 428 52 3 2729 3155 15165732 15166157 1.740000e-132 483.0
6 TraesCS1D01G367900 chr3B 86.417 427 54 2 2729 3155 26058652 26058230 6.310000e-127 464.0
7 TraesCS1D01G367900 chr3B 86.183 427 55 2 2729 3155 25922529 25922107 2.930000e-125 459.0
8 TraesCS1D01G367900 chr3B 86.183 427 55 2 2729 3155 26400819 26400397 2.930000e-125 459.0
9 TraesCS1D01G367900 chr3B 85.714 427 59 2 2729 3155 26431479 26431055 1.770000e-122 449.0
10 TraesCS1D01G367900 chr3B 90.661 257 18 3 2088 2339 15165015 15165270 1.430000e-88 337.0
11 TraesCS1D01G367900 chr3B 83.730 252 18 9 2498 2728 15151367 15151616 1.950000e-52 217.0
12 TraesCS1D01G367900 chr3B 90.000 120 11 1 2612 2730 15099046 15098927 1.550000e-33 154.0
13 TraesCS1D01G367900 chr3B 90.000 120 11 1 2612 2730 15140136 15140255 1.550000e-33 154.0
14 TraesCS1D01G367900 chr3B 76.294 367 41 18 2392 2717 26431916 26431555 1.550000e-33 154.0
15 TraesCS1D01G367900 chr3B 83.465 127 19 2 2390 2515 15165282 15165407 2.030000e-22 117.0
16 TraesCS1D01G367900 chr3B 84.000 125 15 4 2392 2515 25922971 25922851 7.320000e-22 115.0
17 TraesCS1D01G367900 chr3B 84.000 125 15 4 2392 2515 26059095 26058975 7.320000e-22 115.0
18 TraesCS1D01G367900 chr3B 84.000 125 15 4 2392 2515 26401262 26401142 7.320000e-22 115.0
19 TraesCS1D01G367900 chr3D 85.929 1400 139 34 1029 2405 10824202 10822838 0.000000e+00 1441.0
20 TraesCS1D01G367900 chr3D 95.763 472 11 4 1 465 10840218 10840687 0.000000e+00 752.0
21 TraesCS1D01G367900 chr3D 87.822 427 51 1 2729 3155 10808756 10808331 1.730000e-137 499.0
22 TraesCS1D01G367900 chr3D 86.885 427 55 1 2729 3155 10822083 10821658 8.100000e-131 477.0
23 TraesCS1D01G367900 chr3D 84.043 282 26 10 753 1034 10824498 10824236 1.490000e-63 254.0
24 TraesCS1D01G367900 chr3D 82.988 241 32 5 2497 2730 10822398 10822160 3.260000e-50 209.0
25 TraesCS1D01G367900 chr3D 82.787 244 31 3 2497 2730 10809075 10808833 1.170000e-49 207.0
26 TraesCS1D01G367900 chr3D 82.895 228 19 9 2178 2405 10809722 10809515 1.530000e-43 187.0
27 TraesCS1D01G367900 chr3D 76.891 238 49 6 1193 1424 10837613 10837850 2.610000e-26 130.0
28 TraesCS1D01G367900 chrUn 87.822 427 51 1 2729 3155 314623103 314622678 1.730000e-137 499.0
29 TraesCS1D01G367900 chrUn 82.895 228 19 9 2178 2405 335936736 335936529 1.530000e-43 187.0
30 TraesCS1D01G367900 chrUn 85.950 121 15 1 2612 2730 314623300 314623180 9.400000e-26 128.0
31 TraesCS1D01G367900 chr3A 87.822 427 50 2 2729 3155 17448291 17448715 1.730000e-137 499.0
32 TraesCS1D01G367900 chr3A 79.572 421 52 20 2344 2730 17447794 17448214 1.480000e-68 270.0
33 TraesCS1D01G367900 chr5A 84.746 177 25 2 68 243 472992371 472992546 3.310000e-40 176.0
34 TraesCS1D01G367900 chr5A 87.143 70 5 3 4 71 562490835 562490902 3.450000e-10 76.8
35 TraesCS1D01G367900 chr4B 82.635 167 27 2 67 231 665267060 665267226 2.600000e-31 147.0


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 TraesCS1D01G367900 chr1D 447666293 447669520 3227 True 5962.000000 5962 100.000000 1 3228 1 chr1D.!!$R1 3227
1 TraesCS1D01G367900 chr3B 15138319 15140255 1936 False 1076.500000 1999 89.174500 822 2730 2 chr3B.!!$F1 1908
2 TraesCS1D01G367900 chr3B 15098927 15101649 2722 True 1037.666667 2122 90.052333 1 2730 3 chr3B.!!$R1 2729
3 TraesCS1D01G367900 chr3B 15150113 15151616 1503 False 838.000000 1459 85.817500 1261 2728 2 chr3B.!!$F2 1467
4 TraesCS1D01G367900 chr3B 15165015 15166157 1142 False 312.333333 483 87.092000 2088 3155 3 chr3B.!!$F3 1067
5 TraesCS1D01G367900 chr3B 26431055 26431916 861 True 301.500000 449 81.004000 2392 3155 2 chr3B.!!$R5 763
6 TraesCS1D01G367900 chr3B 26058230 26059095 865 True 289.500000 464 85.208500 2392 3155 2 chr3B.!!$R3 763
7 TraesCS1D01G367900 chr3B 25922107 25922971 864 True 287.000000 459 85.091500 2392 3155 2 chr3B.!!$R2 763
8 TraesCS1D01G367900 chr3B 26400397 26401262 865 True 287.000000 459 85.091500 2392 3155 2 chr3B.!!$R4 763
9 TraesCS1D01G367900 chr3D 10821658 10824498 2840 True 595.250000 1441 84.961250 753 3155 4 chr3D.!!$R2 2402
10 TraesCS1D01G367900 chr3D 10837613 10840687 3074 False 441.000000 752 86.327000 1 1424 2 chr3D.!!$F1 1423
11 TraesCS1D01G367900 chr3D 10808331 10809722 1391 True 297.666667 499 84.501333 2178 3155 3 chr3D.!!$R1 977
12 TraesCS1D01G367900 chrUn 314622678 314623300 622 True 313.500000 499 86.886000 2612 3155 2 chrUn.!!$R2 543
13 TraesCS1D01G367900 chr3A 17447794 17448715 921 False 384.500000 499 83.697000 2344 3155 2 chr3A.!!$F1 811

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
653 658 0.034767 GGGTGGGTGGGTTAACTAGC 60.035 60.0 5.42 4.97 0.00 3.42 F
713 718 0.803768 CCATCTCAACCACGAGCTCG 60.804 60.0 33.45 33.45 46.33 5.03 F
2069 2282 0.772926 CGTGATAAGATCGCTGACGC 59.227 55.0 0.00 0.00 39.84 5.19 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2069 2282 0.236711 CTGCGAAGGTTGCTGACAAG 59.763 55.0 0.00 0.0 36.16 3.16 R
2096 2309 0.754217 CCGTCCTCCTTCCCGTATGA 60.754 60.0 0.00 0.0 0.00 2.15 R
3179 5315 0.249398 GTCACCGGAGCCACATAACT 59.751 55.0 9.46 0.0 0.00 2.24 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
31 32 6.737254 AGTCTTTGTATCAAATTGTACCGG 57.263 37.500 0.00 0.00 0.00 5.28
58 59 7.360361 GCTGCAAGTTTATGTACTAAAACAGT 58.640 34.615 19.19 8.94 37.92 3.55
104 105 5.083821 AGGCCTTACAAATTAGGAAGCAAA 58.916 37.500 0.00 0.00 33.13 3.68
107 108 6.093404 GCCTTACAAATTAGGAAGCAAAGAC 58.907 40.000 0.00 0.00 33.13 3.01
242 243 8.221944 ACTAGAGTGCTTAGTGTTATAGAGGAT 58.778 37.037 0.00 0.00 0.00 3.24
285 286 3.050275 GTTGGTGCGCTCAGGGTC 61.050 66.667 9.73 0.00 0.00 4.46
312 313 4.722361 TTAAGCGGTTTCCTTGTGTTTT 57.278 36.364 4.64 0.00 0.00 2.43
368 369 5.301551 TGGTGCAGAAAAGAAAAGAAGCATA 59.698 36.000 0.00 0.00 32.98 3.14
381 382 3.505386 AGAAGCATATGAGGGAGACGAT 58.495 45.455 6.97 0.00 0.00 3.73
385 386 2.163509 CATATGAGGGAGACGATCGGT 58.836 52.381 20.98 5.94 0.00 4.69
386 387 2.359981 TATGAGGGAGACGATCGGTT 57.640 50.000 20.98 6.71 0.00 4.44
387 388 1.486211 ATGAGGGAGACGATCGGTTT 58.514 50.000 20.98 3.86 0.00 3.27
388 389 1.263356 TGAGGGAGACGATCGGTTTT 58.737 50.000 20.98 0.00 0.00 2.43
389 390 1.621814 TGAGGGAGACGATCGGTTTTT 59.378 47.619 20.98 0.00 0.00 1.94
407 408 3.806625 TTTTTAGGGATAGACGACCGG 57.193 47.619 0.00 0.00 0.00 5.28
415 416 2.159198 GGATAGACGACCGGCTGTAAAA 60.159 50.000 8.20 0.00 34.01 1.52
437 438 2.108157 TCTTGTCGCGTGCAAGGT 59.892 55.556 29.99 0.00 42.44 3.50
562 563 5.470098 TGGTCTCGAAAGAAAGAAATGAAGG 59.530 40.000 0.00 0.00 41.32 3.46
581 582 3.792401 AGGAAAAAGAAAAGGTTTGGCG 58.208 40.909 0.00 0.00 0.00 5.69
607 612 6.513806 CATGGATGGATGTTTGAAGTTGTA 57.486 37.500 0.00 0.00 0.00 2.41
608 613 5.957842 TGGATGGATGTTTGAAGTTGTAC 57.042 39.130 0.00 0.00 0.00 2.90
609 614 4.454161 TGGATGGATGTTTGAAGTTGTACG 59.546 41.667 0.00 0.00 0.00 3.67
610 615 4.454504 GGATGGATGTTTGAAGTTGTACGT 59.545 41.667 0.00 0.00 0.00 3.57
613 618 5.574082 TGGATGTTTGAAGTTGTACGTTTG 58.426 37.500 0.00 0.00 0.00 2.93
614 619 5.354513 TGGATGTTTGAAGTTGTACGTTTGA 59.645 36.000 0.00 0.00 0.00 2.69
615 620 6.038825 TGGATGTTTGAAGTTGTACGTTTGAT 59.961 34.615 0.00 0.00 0.00 2.57
616 621 6.915843 GGATGTTTGAAGTTGTACGTTTGATT 59.084 34.615 0.00 0.00 0.00 2.57
618 623 6.843208 TGTTTGAAGTTGTACGTTTGATTGA 58.157 32.000 0.00 0.00 0.00 2.57
619 624 7.306213 TGTTTGAAGTTGTACGTTTGATTGAA 58.694 30.769 0.00 0.00 0.00 2.69
620 625 7.808381 TGTTTGAAGTTGTACGTTTGATTGAAA 59.192 29.630 0.00 0.00 0.00 2.69
621 626 7.728580 TTGAAGTTGTACGTTTGATTGAAAC 57.271 32.000 0.00 0.00 40.65 2.78
629 634 2.148558 TTTGATTGAAACGGCGGGGC 62.149 55.000 13.24 0.00 0.00 5.80
630 635 3.059386 GATTGAAACGGCGGGGCA 61.059 61.111 13.24 2.36 0.00 5.36
631 636 3.051392 GATTGAAACGGCGGGGCAG 62.051 63.158 13.24 0.00 0.00 4.85
649 654 2.441959 GGGGGTGGGTGGGTTAAC 59.558 66.667 0.00 0.00 0.00 2.01
650 655 2.164967 GGGGGTGGGTGGGTTAACT 61.165 63.158 5.42 0.00 0.00 2.24
651 656 0.845985 GGGGGTGGGTGGGTTAACTA 60.846 60.000 5.42 0.00 0.00 2.24
652 657 0.622136 GGGGTGGGTGGGTTAACTAG 59.378 60.000 5.42 0.00 0.00 2.57
653 658 0.034767 GGGTGGGTGGGTTAACTAGC 60.035 60.000 5.42 4.97 0.00 3.42
654 659 0.989602 GGTGGGTGGGTTAACTAGCT 59.010 55.000 5.42 0.00 0.00 3.32
655 660 2.190538 GGTGGGTGGGTTAACTAGCTA 58.809 52.381 5.42 0.00 0.00 3.32
656 661 2.169978 GGTGGGTGGGTTAACTAGCTAG 59.830 54.545 19.44 19.44 0.00 3.42
657 662 2.836372 GTGGGTGGGTTAACTAGCTAGT 59.164 50.000 20.95 20.95 38.39 2.57
661 666 4.382793 GGGTGGGTTAACTAGCTAGTTGAG 60.383 50.000 37.89 13.65 45.44 3.02
662 667 4.222366 GGTGGGTTAACTAGCTAGTTGAGT 59.778 45.833 37.89 21.57 45.44 3.41
663 668 5.169295 GTGGGTTAACTAGCTAGTTGAGTG 58.831 45.833 37.89 10.46 45.44 3.51
664 669 5.047519 GTGGGTTAACTAGCTAGTTGAGTGA 60.048 44.000 37.89 21.77 45.44 3.41
665 670 5.185249 TGGGTTAACTAGCTAGTTGAGTGAG 59.815 44.000 37.89 10.76 45.44 3.51
666 671 5.185442 GGGTTAACTAGCTAGTTGAGTGAGT 59.815 44.000 37.89 19.32 45.44 3.41
667 672 6.094061 GGTTAACTAGCTAGTTGAGTGAGTG 58.906 44.000 37.89 7.88 45.44 3.51
668 673 6.294620 GGTTAACTAGCTAGTTGAGTGAGTGT 60.295 42.308 37.89 18.05 45.44 3.55
669 674 5.793030 AACTAGCTAGTTGAGTGAGTGTT 57.207 39.130 33.09 9.18 44.30 3.32
670 675 5.127693 ACTAGCTAGTTGAGTGAGTGTTG 57.872 43.478 20.95 0.00 31.13 3.33
671 676 4.585162 ACTAGCTAGTTGAGTGAGTGTTGT 59.415 41.667 20.95 0.00 31.13 3.32
672 677 5.768662 ACTAGCTAGTTGAGTGAGTGTTGTA 59.231 40.000 20.95 0.00 31.13 2.41
673 678 5.531122 AGCTAGTTGAGTGAGTGTTGTAA 57.469 39.130 0.00 0.00 0.00 2.41
674 679 5.914033 AGCTAGTTGAGTGAGTGTTGTAAA 58.086 37.500 0.00 0.00 0.00 2.01
675 680 6.346096 AGCTAGTTGAGTGAGTGTTGTAAAA 58.654 36.000 0.00 0.00 0.00 1.52
676 681 6.992715 AGCTAGTTGAGTGAGTGTTGTAAAAT 59.007 34.615 0.00 0.00 0.00 1.82
677 682 7.499232 AGCTAGTTGAGTGAGTGTTGTAAAATT 59.501 33.333 0.00 0.00 0.00 1.82
678 683 8.129211 GCTAGTTGAGTGAGTGTTGTAAAATTT 58.871 33.333 0.00 0.00 0.00 1.82
679 684 9.438291 CTAGTTGAGTGAGTGTTGTAAAATTTG 57.562 33.333 0.00 0.00 0.00 2.32
680 685 8.050778 AGTTGAGTGAGTGTTGTAAAATTTGA 57.949 30.769 0.00 0.00 0.00 2.69
681 686 8.519526 AGTTGAGTGAGTGTTGTAAAATTTGAA 58.480 29.630 0.00 0.00 0.00 2.69
682 687 8.798153 GTTGAGTGAGTGTTGTAAAATTTGAAG 58.202 33.333 0.00 0.00 0.00 3.02
683 688 8.275015 TGAGTGAGTGTTGTAAAATTTGAAGA 57.725 30.769 0.00 0.00 0.00 2.87
684 689 8.735315 TGAGTGAGTGTTGTAAAATTTGAAGAA 58.265 29.630 0.00 0.00 0.00 2.52
685 690 9.567848 GAGTGAGTGTTGTAAAATTTGAAGAAA 57.432 29.630 0.00 0.00 0.00 2.52
686 691 9.921637 AGTGAGTGTTGTAAAATTTGAAGAAAA 57.078 25.926 0.00 0.00 0.00 2.29
709 714 1.276421 AGGAACCATCTCAACCACGAG 59.724 52.381 0.00 0.00 0.00 4.18
713 718 0.803768 CCATCTCAACCACGAGCTCG 60.804 60.000 33.45 33.45 46.33 5.03
729 734 4.016706 CGCCTCCCACGTCCCTTT 62.017 66.667 0.00 0.00 0.00 3.11
887 910 2.364970 CAAGAGCCTCTCCATCTTCGAT 59.635 50.000 0.00 0.00 30.99 3.59
921 944 6.538742 CCATAAATACATATTCGATCGGCCTT 59.461 38.462 16.41 0.33 0.00 4.35
931 960 2.053259 GATCGGCCTTCCCCCTAACC 62.053 65.000 0.00 0.00 0.00 2.85
942 971 1.425448 CCCCCTAACCTTCATCCCATC 59.575 57.143 0.00 0.00 0.00 3.51
944 973 2.513738 CCCCTAACCTTCATCCCATCAA 59.486 50.000 0.00 0.00 0.00 2.57
949 978 2.187958 ACCTTCATCCCATCAACTCGA 58.812 47.619 0.00 0.00 0.00 4.04
964 993 1.006220 TCGATCACAAGCACGCACT 60.006 52.632 0.00 0.00 0.00 4.40
967 996 1.428448 GATCACAAGCACGCACTGTA 58.572 50.000 0.00 0.00 0.00 2.74
1013 1042 1.472878 CAGACCGATGGAGAAGAACGA 59.527 52.381 0.00 0.00 0.00 3.85
1131 1199 3.057596 ACACATATGTTGCCGTTCTTTGG 60.058 43.478 5.37 0.00 34.46 3.28
1252 1335 1.889530 GACCTCCCGGACAAGGACAG 61.890 65.000 20.35 0.00 36.46 3.51
1258 1341 2.358737 GGACAAGGACAGGTGCGG 60.359 66.667 0.00 0.00 0.00 5.69
1584 1673 2.424246 GACGTCGGGAAGAAGAAGATCT 59.576 50.000 0.00 0.00 32.54 2.75
1585 1674 2.164624 ACGTCGGGAAGAAGAAGATCTG 59.835 50.000 0.00 0.00 32.54 2.90
1586 1675 2.164624 CGTCGGGAAGAAGAAGATCTGT 59.835 50.000 0.00 0.00 0.00 3.41
1588 1677 3.193691 GTCGGGAAGAAGAAGATCTGTGA 59.806 47.826 0.00 0.00 0.00 3.58
1599 1688 4.713814 AGAAGATCTGTGATAGTGGCAAGA 59.286 41.667 0.00 0.00 0.00 3.02
1602 1691 1.901833 TCTGTGATAGTGGCAAGAGCA 59.098 47.619 0.00 0.00 44.61 4.26
1614 1703 3.019564 GGCAAGAGCACAATGGTAAGAT 58.980 45.455 0.00 0.00 44.61 2.40
1616 1705 3.691118 GCAAGAGCACAATGGTAAGATGA 59.309 43.478 0.00 0.00 41.58 2.92
1617 1706 4.156556 GCAAGAGCACAATGGTAAGATGAA 59.843 41.667 0.00 0.00 41.58 2.57
1624 1713 4.016444 ACAATGGTAAGATGAACGCCAAT 58.984 39.130 0.00 0.00 32.54 3.16
1628 1717 4.580868 TGGTAAGATGAACGCCAATAACA 58.419 39.130 0.00 0.00 0.00 2.41
1643 1732 5.531634 CCAATAACATGGGGAATTTGATCG 58.468 41.667 0.00 0.00 36.79 3.69
1646 1735 3.085952 ACATGGGGAATTTGATCGTGT 57.914 42.857 0.00 0.00 0.00 4.49
1652 1741 5.257262 TGGGGAATTTGATCGTGTTGATTA 58.743 37.500 0.00 0.00 37.47 1.75
1657 1746 9.965824 GGGAATTTGATCGTGTTGATTAATATT 57.034 29.630 0.00 0.00 37.47 1.28
1752 1841 1.476891 GTTAGGGAGACGAGCATGTCA 59.523 52.381 10.47 0.00 41.41 3.58
1788 1877 1.115326 TCGAGGTCATCATCCGCCAT 61.115 55.000 0.00 0.00 0.00 4.40
1791 1880 2.263741 GGTCATCATCCGCCATGGC 61.264 63.158 27.67 27.67 37.80 4.40
1839 1962 2.351276 GAGCGGAAGGGCAAGGAA 59.649 61.111 0.00 0.00 34.64 3.36
1894 2017 2.522436 CCGCCCCGGTAGGTATCA 60.522 66.667 0.00 0.00 42.73 2.15
1905 2028 2.294233 GGTAGGTATCACGTCGCCATTA 59.706 50.000 0.00 0.00 0.00 1.90
1914 2037 2.160615 CACGTCGCCATTAATTTCCACA 59.839 45.455 0.00 0.00 0.00 4.17
1934 2064 4.079970 ACAATCTCGAGACTAGTGTTGGA 58.920 43.478 19.30 0.42 0.00 3.53
1939 2069 3.752665 TCGAGACTAGTGTTGGACTCTT 58.247 45.455 0.00 0.00 35.96 2.85
1940 2070 3.502595 TCGAGACTAGTGTTGGACTCTTG 59.497 47.826 0.00 0.00 35.96 3.02
1943 2073 3.574826 AGACTAGTGTTGGACTCTTGGTC 59.425 47.826 0.00 0.00 43.79 4.02
1944 2074 3.574826 GACTAGTGTTGGACTCTTGGTCT 59.425 47.826 0.00 0.00 43.97 3.85
1945 2075 3.574826 ACTAGTGTTGGACTCTTGGTCTC 59.425 47.826 0.00 0.00 43.97 3.36
1946 2076 2.683768 AGTGTTGGACTCTTGGTCTCT 58.316 47.619 0.00 0.00 43.97 3.10
1947 2077 2.630580 AGTGTTGGACTCTTGGTCTCTC 59.369 50.000 0.00 0.00 43.97 3.20
1948 2078 2.630580 GTGTTGGACTCTTGGTCTCTCT 59.369 50.000 0.00 0.00 43.97 3.10
1949 2079 2.630098 TGTTGGACTCTTGGTCTCTCTG 59.370 50.000 0.00 0.00 43.97 3.35
1950 2080 2.630580 GTTGGACTCTTGGTCTCTCTGT 59.369 50.000 0.00 0.00 43.97 3.41
1951 2081 2.964209 TGGACTCTTGGTCTCTCTGTT 58.036 47.619 0.00 0.00 43.97 3.16
1952 2082 2.894126 TGGACTCTTGGTCTCTCTGTTC 59.106 50.000 0.00 0.00 43.97 3.18
1953 2083 2.894126 GGACTCTTGGTCTCTCTGTTCA 59.106 50.000 0.00 0.00 43.97 3.18
1954 2084 3.322254 GGACTCTTGGTCTCTCTGTTCAA 59.678 47.826 0.00 0.00 43.97 2.69
1955 2085 4.303282 GACTCTTGGTCTCTCTGTTCAAC 58.697 47.826 0.00 0.00 41.46 3.18
1965 2103 6.017852 GGTCTCTCTGTTCAACCTACTTTTTG 60.018 42.308 0.00 0.00 0.00 2.44
1973 2111 6.147985 TGTTCAACCTACTTTTTGGTTTTTGC 59.852 34.615 0.00 0.00 43.27 3.68
2045 2258 1.349688 ACTACGGCCAATTCAAGGACA 59.650 47.619 2.24 0.00 31.91 4.02
2046 2259 1.737793 CTACGGCCAATTCAAGGACAC 59.262 52.381 2.24 0.00 31.91 3.67
2053 2266 2.224079 CCAATTCAAGGACACTGTCGTG 59.776 50.000 5.16 5.35 46.63 4.35
2069 2282 0.772926 CGTGATAAGATCGCTGACGC 59.227 55.000 0.00 0.00 39.84 5.19
2096 2309 2.580601 AACCTTCGCAGCTACGGGT 61.581 57.895 6.49 3.89 0.00 5.28
2223 2436 5.220931 GCACCTATGTGAAGATGGACAATTC 60.221 44.000 1.92 0.00 45.76 2.17
2255 2503 2.578786 CATGGTGCATGCCAGATCTAA 58.421 47.619 16.68 0.00 42.47 2.10
2284 2532 5.514559 CGCATACATGAGATGAGCATACTAC 59.485 44.000 14.11 0.00 0.00 2.73
2285 2533 6.624642 CGCATACATGAGATGAGCATACTACT 60.625 42.308 14.11 0.00 0.00 2.57
2286 2534 6.751425 GCATACATGAGATGAGCATACTACTC 59.249 42.308 14.11 0.00 34.62 2.59
2300 2553 7.800092 AGCATACTACTCCTGATTCTGAATTT 58.200 34.615 4.11 0.00 0.00 1.82
2302 2555 9.547753 GCATACTACTCCTGATTCTGAATTTTA 57.452 33.333 4.11 0.00 0.00 1.52
2341 2594 0.548031 ATGCCGGTTGATGGACAGAT 59.452 50.000 1.90 0.00 0.00 2.90
2342 2595 1.199615 TGCCGGTTGATGGACAGATA 58.800 50.000 1.90 0.00 0.00 1.98
2490 3061 8.024145 AGGTTTCCTAATTCTCTGAATACGAT 57.976 34.615 0.00 0.00 28.47 3.73
2492 3063 9.110502 GGTTTCCTAATTCTCTGAATACGATTT 57.889 33.333 0.00 0.00 0.00 2.17
2502 3105 7.145323 TCTCTGAATACGATTTATGCGATCAA 58.855 34.615 0.00 0.00 0.00 2.57
2517 3120 5.181009 TGCGATCAATTTGAGATTCTCTGT 58.819 37.500 14.54 0.00 0.00 3.41
2537 3140 5.472137 TCTGTATACTTTGGTTTGTGCTTCC 59.528 40.000 4.17 0.00 0.00 3.46
2602 3205 5.520288 GCAGTTAGCTTGATCGATCAGTAAA 59.480 40.000 25.95 16.48 41.15 2.01
2686 3315 7.945109 AGAGGAGGCTTGAACTAAAACTAAAAT 59.055 33.333 0.00 0.00 0.00 1.82
2750 3636 6.334102 TCTTCTGTTCAAGTCTCTTACTCC 57.666 41.667 0.00 0.00 37.50 3.85
2844 4327 4.124238 TCTGTGTTTATATGTTAGCGGCC 58.876 43.478 0.00 0.00 0.00 6.13
2847 4330 5.860611 TGTGTTTATATGTTAGCGGCCTAT 58.139 37.500 0.00 0.00 0.00 2.57
2951 4434 3.975168 ACTGGACCTTACATACACCAC 57.025 47.619 0.00 0.00 0.00 4.16
2953 4436 3.007614 ACTGGACCTTACATACACCACAC 59.992 47.826 0.00 0.00 0.00 3.82
2954 4437 2.973406 TGGACCTTACATACACCACACA 59.027 45.455 0.00 0.00 0.00 3.72
3014 4497 2.819115 AGATCAGTGCTACAATCAGCG 58.181 47.619 0.00 0.00 44.88 5.18
3021 4504 0.729116 GCTACAATCAGCGCACACAT 59.271 50.000 11.47 0.00 0.00 3.21
3022 4505 1.530441 GCTACAATCAGCGCACACATG 60.530 52.381 11.47 4.29 0.00 3.21
3023 4506 1.733912 CTACAATCAGCGCACACATGT 59.266 47.619 11.47 10.54 0.00 3.21
3037 4520 4.858692 GCACACATGTTTAAGCACCATAAG 59.141 41.667 0.00 0.00 0.00 1.73
3098 5160 4.678256 TGCCCTGGTAAATTAATTGGTCA 58.322 39.130 0.39 0.17 0.00 4.02
3124 5260 2.353889 ACATTGCTCGCTAGAATTGCAG 59.646 45.455 0.00 0.00 35.02 4.41
3156 5292 1.047002 TGTTTGCCCAAAGGTCCATG 58.953 50.000 0.00 0.00 34.57 3.66
3157 5293 0.321346 GTTTGCCCAAAGGTCCATGG 59.679 55.000 4.97 4.97 36.42 3.66
3158 5294 0.105246 TTTGCCCAAAGGTCCATGGT 60.105 50.000 12.58 0.00 34.79 3.55
3159 5295 0.780637 TTGCCCAAAGGTCCATGGTA 59.219 50.000 12.58 0.00 34.79 3.25
3160 5296 0.331278 TGCCCAAAGGTCCATGGTAG 59.669 55.000 12.58 0.00 34.79 3.18
3161 5297 0.331616 GCCCAAAGGTCCATGGTAGT 59.668 55.000 12.58 0.00 34.79 2.73
3163 5299 1.340991 CCCAAAGGTCCATGGTAGTGG 60.341 57.143 12.58 12.68 40.76 4.00
3164 5300 1.463674 CAAAGGTCCATGGTAGTGGC 58.536 55.000 12.58 0.00 39.19 5.01
3165 5301 1.072266 AAAGGTCCATGGTAGTGGCA 58.928 50.000 12.58 0.00 39.19 4.92
3166 5302 1.298953 AAGGTCCATGGTAGTGGCAT 58.701 50.000 12.58 0.00 39.19 4.40
3167 5303 2.190398 AGGTCCATGGTAGTGGCATA 57.810 50.000 12.58 0.00 39.19 3.14
3168 5304 2.050144 AGGTCCATGGTAGTGGCATAG 58.950 52.381 12.58 0.00 39.19 2.23
3169 5305 2.047061 GGTCCATGGTAGTGGCATAGA 58.953 52.381 12.58 0.00 39.19 1.98
3171 5307 3.118038 GGTCCATGGTAGTGGCATAGAAA 60.118 47.826 12.58 0.00 39.19 2.52
3172 5308 4.523083 GTCCATGGTAGTGGCATAGAAAA 58.477 43.478 12.58 0.00 39.19 2.29
3173 5309 5.133221 GTCCATGGTAGTGGCATAGAAAAT 58.867 41.667 12.58 0.00 39.19 1.82
3174 5310 5.009010 GTCCATGGTAGTGGCATAGAAAATG 59.991 44.000 12.58 0.00 39.19 2.32
3176 5312 5.360714 CCATGGTAGTGGCATAGAAAATGTT 59.639 40.000 2.57 0.00 31.43 2.71
3177 5313 5.895636 TGGTAGTGGCATAGAAAATGTTG 57.104 39.130 0.00 0.00 0.00 3.33
3179 5315 6.007076 TGGTAGTGGCATAGAAAATGTTGAA 58.993 36.000 0.00 0.00 0.00 2.69
3180 5316 6.150976 TGGTAGTGGCATAGAAAATGTTGAAG 59.849 38.462 0.00 0.00 0.00 3.02
3181 5317 6.151144 GGTAGTGGCATAGAAAATGTTGAAGT 59.849 38.462 0.00 0.00 0.00 3.01
3182 5318 6.655078 AGTGGCATAGAAAATGTTGAAGTT 57.345 33.333 0.00 0.00 0.00 2.66
3185 5321 8.246180 AGTGGCATAGAAAATGTTGAAGTTATG 58.754 33.333 0.00 0.00 0.00 1.90
3186 5322 8.028938 GTGGCATAGAAAATGTTGAAGTTATGT 58.971 33.333 0.00 0.00 0.00 2.29
3187 5323 8.028354 TGGCATAGAAAATGTTGAAGTTATGTG 58.972 33.333 0.00 0.00 0.00 3.21
3188 5324 7.489113 GGCATAGAAAATGTTGAAGTTATGTGG 59.511 37.037 0.00 0.00 0.00 4.17
3189 5325 7.009540 GCATAGAAAATGTTGAAGTTATGTGGC 59.990 37.037 0.00 0.00 0.00 5.01
3190 5326 6.655078 AGAAAATGTTGAAGTTATGTGGCT 57.345 33.333 0.00 0.00 0.00 4.75
3191 5327 6.681777 AGAAAATGTTGAAGTTATGTGGCTC 58.318 36.000 0.00 0.00 0.00 4.70
3192 5328 5.391312 AAATGTTGAAGTTATGTGGCTCC 57.609 39.130 0.00 0.00 0.00 4.70
3195 5331 0.981183 TGAAGTTATGTGGCTCCGGT 59.019 50.000 0.00 0.00 0.00 5.28
3196 5332 1.338674 TGAAGTTATGTGGCTCCGGTG 60.339 52.381 0.00 0.00 0.00 4.94
3197 5333 0.981183 AAGTTATGTGGCTCCGGTGA 59.019 50.000 7.92 0.00 0.00 4.02
3198 5334 0.249398 AGTTATGTGGCTCCGGTGAC 59.751 55.000 7.92 4.69 0.00 3.67
3200 5336 0.981183 TTATGTGGCTCCGGTGACTT 59.019 50.000 11.34 0.43 0.00 3.01
3202 5338 0.606401 ATGTGGCTCCGGTGACTTTG 60.606 55.000 11.34 0.00 0.00 2.77
3204 5340 2.144078 TGGCTCCGGTGACTTTGGA 61.144 57.895 11.34 0.00 0.00 3.53
3206 5342 1.371558 GCTCCGGTGACTTTGGACT 59.628 57.895 7.92 0.00 0.00 3.85
3207 5343 0.606604 GCTCCGGTGACTTTGGACTA 59.393 55.000 7.92 0.00 0.00 2.59
3208 5344 1.001633 GCTCCGGTGACTTTGGACTAA 59.998 52.381 7.92 0.00 0.00 2.24
3210 5346 3.868754 GCTCCGGTGACTTTGGACTAATT 60.869 47.826 7.92 0.00 0.00 1.40
3213 5349 5.134661 TCCGGTGACTTTGGACTAATTTTT 58.865 37.500 0.00 0.00 0.00 1.94
3215 5351 5.009210 CCGGTGACTTTGGACTAATTTTTGA 59.991 40.000 0.00 0.00 0.00 2.69
3216 5352 6.460399 CCGGTGACTTTGGACTAATTTTTGAA 60.460 38.462 0.00 0.00 0.00 2.69
3218 5354 6.700081 GGTGACTTTGGACTAATTTTTGAACC 59.300 38.462 0.00 0.00 0.00 3.62
3219 5355 6.416750 GTGACTTTGGACTAATTTTTGAACCG 59.583 38.462 0.00 0.00 0.00 4.44
3220 5356 5.838529 ACTTTGGACTAATTTTTGAACCGG 58.161 37.500 0.00 0.00 0.00 5.28
3221 5357 5.361571 ACTTTGGACTAATTTTTGAACCGGT 59.638 36.000 0.00 0.00 0.00 5.28
3223 5359 6.956202 TTGGACTAATTTTTGAACCGGTAA 57.044 33.333 8.00 0.00 0.00 2.85
3225 5361 6.297582 TGGACTAATTTTTGAACCGGTAAGA 58.702 36.000 8.00 0.00 0.00 2.10
3226 5362 6.771749 TGGACTAATTTTTGAACCGGTAAGAA 59.228 34.615 8.00 0.73 0.00 2.52
3227 5363 7.040961 TGGACTAATTTTTGAACCGGTAAGAAG 60.041 37.037 8.00 2.27 0.00 2.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 4.339429 CGCCGGTACAATTTGATACAAAG 58.661 43.478 1.90 0.00 0.00 2.77
31 32 4.593597 TTAGTACATAAACTTGCAGCGC 57.406 40.909 0.00 0.00 0.00 5.92
131 132 7.229707 TCGGGTCAAACATTTCTCAAAGATTTA 59.770 33.333 0.00 0.00 0.00 1.40
171 172 3.089284 GGGTCTTCAATTGGAATTCGGT 58.911 45.455 5.42 0.00 34.32 4.69
242 243 3.567585 TGACAACAAAATCCAAGCATCGA 59.432 39.130 0.00 0.00 0.00 3.59
312 313 3.197766 AGTGTGACCTCTCTCAAAACACA 59.802 43.478 5.90 0.00 39.05 3.72
368 369 1.486211 AAACCGATCGTCTCCCTCAT 58.514 50.000 15.09 0.00 0.00 2.90
387 388 2.159057 GCCGGTCGTCTATCCCTAAAAA 60.159 50.000 1.90 0.00 0.00 1.94
388 389 1.410153 GCCGGTCGTCTATCCCTAAAA 59.590 52.381 1.90 0.00 0.00 1.52
389 390 1.035139 GCCGGTCGTCTATCCCTAAA 58.965 55.000 1.90 0.00 0.00 1.85
390 391 0.184451 AGCCGGTCGTCTATCCCTAA 59.816 55.000 1.90 0.00 0.00 2.69
391 392 0.536687 CAGCCGGTCGTCTATCCCTA 60.537 60.000 1.90 0.00 0.00 3.53
392 393 1.828660 CAGCCGGTCGTCTATCCCT 60.829 63.158 1.90 0.00 0.00 4.20
393 394 0.820891 TACAGCCGGTCGTCTATCCC 60.821 60.000 1.90 0.00 0.00 3.85
394 395 1.027357 TTACAGCCGGTCGTCTATCC 58.973 55.000 1.90 0.00 0.00 2.59
395 396 2.857592 TTTACAGCCGGTCGTCTATC 57.142 50.000 1.90 0.00 0.00 2.08
396 397 2.494870 ACTTTTACAGCCGGTCGTCTAT 59.505 45.455 1.90 0.00 0.00 1.98
397 398 1.888512 ACTTTTACAGCCGGTCGTCTA 59.111 47.619 1.90 0.00 0.00 2.59
398 399 0.677842 ACTTTTACAGCCGGTCGTCT 59.322 50.000 1.90 0.00 0.00 4.18
399 400 1.193874 CAACTTTTACAGCCGGTCGTC 59.806 52.381 1.90 0.00 0.00 4.20
400 401 1.223187 CAACTTTTACAGCCGGTCGT 58.777 50.000 1.90 2.77 0.00 4.34
401 402 1.193874 GACAACTTTTACAGCCGGTCG 59.806 52.381 1.90 0.00 0.00 4.79
402 403 2.490991 AGACAACTTTTACAGCCGGTC 58.509 47.619 1.90 0.00 0.00 4.79
403 404 2.616842 CAAGACAACTTTTACAGCCGGT 59.383 45.455 1.90 0.00 33.70 5.28
404 405 2.616842 ACAAGACAACTTTTACAGCCGG 59.383 45.455 0.00 0.00 33.70 6.13
405 406 3.603857 CGACAAGACAACTTTTACAGCCG 60.604 47.826 0.00 0.00 33.70 5.52
406 407 3.848554 GCGACAAGACAACTTTTACAGCC 60.849 47.826 0.00 0.00 33.70 4.85
407 408 3.289076 GCGACAAGACAACTTTTACAGC 58.711 45.455 0.00 0.00 33.70 4.40
415 416 1.087202 TTGCACGCGACAAGACAACT 61.087 50.000 15.93 0.00 0.00 3.16
493 494 0.999228 CTCAGCATATCGTCGCCGTC 60.999 60.000 0.00 0.00 35.01 4.79
533 534 1.554042 TTTCTTTCGAGACCACGCGC 61.554 55.000 5.73 0.00 39.03 6.86
539 540 5.701290 TCCTTCATTTCTTTCTTTCGAGACC 59.299 40.000 0.00 0.00 0.00 3.85
562 563 3.554324 GGACGCCAAACCTTTTCTTTTTC 59.446 43.478 0.00 0.00 0.00 2.29
573 574 1.809207 CATCCATGGACGCCAAACC 59.191 57.895 18.99 0.00 36.95 3.27
609 614 0.388006 CCCCGCCGTTTCAATCAAAC 60.388 55.000 0.00 0.00 41.08 2.93
610 615 1.960612 CCCCGCCGTTTCAATCAAA 59.039 52.632 0.00 0.00 0.00 2.69
613 618 3.051392 CTGCCCCGCCGTTTCAATC 62.051 63.158 0.00 0.00 0.00 2.67
614 619 3.061848 CTGCCCCGCCGTTTCAAT 61.062 61.111 0.00 0.00 0.00 2.57
632 637 0.845985 TAGTTAACCCACCCACCCCC 60.846 60.000 0.88 0.00 0.00 5.40
633 638 0.622136 CTAGTTAACCCACCCACCCC 59.378 60.000 0.88 0.00 0.00 4.95
634 639 0.034767 GCTAGTTAACCCACCCACCC 60.035 60.000 0.88 0.00 0.00 4.61
635 640 0.989602 AGCTAGTTAACCCACCCACC 59.010 55.000 0.88 0.00 0.00 4.61
636 641 2.836372 ACTAGCTAGTTAACCCACCCAC 59.164 50.000 20.95 0.00 31.13 4.61
640 645 5.047519 TCACTCAACTAGCTAGTTAACCCAC 60.048 44.000 33.06 0.00 44.19 4.61
643 648 6.094061 CACTCACTCAACTAGCTAGTTAACC 58.906 44.000 33.06 0.00 44.19 2.85
644 649 6.679843 ACACTCACTCAACTAGCTAGTTAAC 58.320 40.000 33.06 0.00 44.19 2.01
645 650 6.896021 ACACTCACTCAACTAGCTAGTTAA 57.104 37.500 33.06 22.04 44.19 2.01
646 651 6.264744 ACAACACTCACTCAACTAGCTAGTTA 59.735 38.462 33.06 21.38 44.19 2.24
647 652 5.069251 ACAACACTCACTCAACTAGCTAGTT 59.931 40.000 29.48 29.48 46.76 2.24
649 654 5.127693 ACAACACTCACTCAACTAGCTAG 57.872 43.478 19.44 19.44 0.00 3.42
650 655 6.644248 TTACAACACTCACTCAACTAGCTA 57.356 37.500 0.00 0.00 0.00 3.32
651 656 5.531122 TTACAACACTCACTCAACTAGCT 57.469 39.130 0.00 0.00 0.00 3.32
652 657 6.598753 TTTTACAACACTCACTCAACTAGC 57.401 37.500 0.00 0.00 0.00 3.42
653 658 9.438291 CAAATTTTACAACACTCACTCAACTAG 57.562 33.333 0.00 0.00 0.00 2.57
654 659 9.168451 TCAAATTTTACAACACTCACTCAACTA 57.832 29.630 0.00 0.00 0.00 2.24
655 660 8.050778 TCAAATTTTACAACACTCACTCAACT 57.949 30.769 0.00 0.00 0.00 3.16
656 661 8.682128 TTCAAATTTTACAACACTCACTCAAC 57.318 30.769 0.00 0.00 0.00 3.18
657 662 8.735315 TCTTCAAATTTTACAACACTCACTCAA 58.265 29.630 0.00 0.00 0.00 3.02
658 663 8.275015 TCTTCAAATTTTACAACACTCACTCA 57.725 30.769 0.00 0.00 0.00 3.41
685 690 3.317993 CGTGGTTGAGATGGTTCCTTTTT 59.682 43.478 0.00 0.00 0.00 1.94
686 691 2.884639 CGTGGTTGAGATGGTTCCTTTT 59.115 45.455 0.00 0.00 0.00 2.27
687 692 2.105821 TCGTGGTTGAGATGGTTCCTTT 59.894 45.455 0.00 0.00 0.00 3.11
688 693 1.697432 TCGTGGTTGAGATGGTTCCTT 59.303 47.619 0.00 0.00 0.00 3.36
689 694 1.276421 CTCGTGGTTGAGATGGTTCCT 59.724 52.381 0.00 0.00 38.28 3.36
690 695 1.726853 CTCGTGGTTGAGATGGTTCC 58.273 55.000 0.00 0.00 38.28 3.62
691 696 1.079503 GCTCGTGGTTGAGATGGTTC 58.920 55.000 0.00 0.00 38.28 3.62
692 697 0.687354 AGCTCGTGGTTGAGATGGTT 59.313 50.000 0.00 0.00 38.28 3.67
693 698 0.247736 GAGCTCGTGGTTGAGATGGT 59.752 55.000 0.00 0.00 38.28 3.55
694 699 0.803768 CGAGCTCGTGGTTGAGATGG 60.804 60.000 27.79 0.00 38.28 3.51
695 700 1.416813 GCGAGCTCGTGGTTGAGATG 61.417 60.000 34.46 5.25 42.22 2.90
696 701 1.153745 GCGAGCTCGTGGTTGAGAT 60.154 57.895 34.46 0.00 42.22 2.75
713 718 0.255033 ATAAAAGGGACGTGGGAGGC 59.745 55.000 0.00 0.00 0.00 4.70
887 910 8.371699 TCGAATATGTATTTATGGTGATGTGGA 58.628 33.333 0.00 0.00 0.00 4.02
921 944 0.423956 TGGGATGAAGGTTAGGGGGA 59.576 55.000 0.00 0.00 0.00 4.81
931 960 3.806521 GTGATCGAGTTGATGGGATGAAG 59.193 47.826 0.00 0.00 37.47 3.02
942 971 0.179240 GCGTGCTTGTGATCGAGTTG 60.179 55.000 0.00 0.00 0.00 3.16
944 973 1.006220 TGCGTGCTTGTGATCGAGT 60.006 52.632 0.00 0.00 0.00 4.18
949 978 1.148310 GTACAGTGCGTGCTTGTGAT 58.852 50.000 11.14 0.00 0.00 3.06
964 993 4.086457 TGATCTTGCAGTGGAGTAGTACA 58.914 43.478 2.52 0.00 0.00 2.90
967 996 4.202357 TGTTTGATCTTGCAGTGGAGTAGT 60.202 41.667 0.00 0.00 0.00 2.73
1013 1042 2.092323 TGATCATCGTCTCGGAAGTGT 58.908 47.619 0.00 0.00 0.00 3.55
1131 1199 2.338500 CAAGTAGGTGGAGAAACGCTC 58.662 52.381 0.00 0.00 43.17 5.03
1252 1335 4.025401 CAAAGCACGACCCGCACC 62.025 66.667 0.00 0.00 0.00 5.01
1258 1341 0.586802 GGAGTTGACAAAGCACGACC 59.413 55.000 0.00 0.00 0.00 4.79
1326 1409 0.955428 GATTGCAGGACACGCTCCAA 60.955 55.000 2.71 0.00 42.46 3.53
1584 1673 1.347378 TGTGCTCTTGCCACTATCACA 59.653 47.619 0.00 0.00 38.71 3.58
1585 1674 2.099141 TGTGCTCTTGCCACTATCAC 57.901 50.000 0.00 0.00 38.71 3.06
1586 1675 2.857186 TTGTGCTCTTGCCACTATCA 57.143 45.000 0.00 0.00 38.71 2.15
1588 1677 2.291153 ACCATTGTGCTCTTGCCACTAT 60.291 45.455 0.00 0.00 38.71 2.12
1599 1688 2.420022 GCGTTCATCTTACCATTGTGCT 59.580 45.455 0.00 0.00 0.00 4.40
1602 1691 3.066291 TGGCGTTCATCTTACCATTGT 57.934 42.857 0.00 0.00 0.00 2.71
1614 1703 1.004862 TCCCCATGTTATTGGCGTTCA 59.995 47.619 0.00 0.00 35.29 3.18
1616 1705 2.223803 TTCCCCATGTTATTGGCGTT 57.776 45.000 0.00 0.00 35.29 4.84
1617 1706 2.452600 ATTCCCCATGTTATTGGCGT 57.547 45.000 0.00 0.00 35.29 5.68
1624 1713 4.594970 ACACGATCAAATTCCCCATGTTA 58.405 39.130 0.00 0.00 0.00 2.41
1628 1717 3.696045 TCAACACGATCAAATTCCCCAT 58.304 40.909 0.00 0.00 0.00 4.00
1731 1820 1.476891 GACATGCTCGTCTCCCTAACA 59.523 52.381 0.00 0.00 32.92 2.41
1734 1823 1.064685 TCTGACATGCTCGTCTCCCTA 60.065 52.381 7.46 0.00 36.82 3.53
1752 1841 1.471287 TCGACGATTCGGTTGACATCT 59.529 47.619 11.29 0.00 45.90 2.90
1839 1962 3.991051 CACCTGTCGGTCCACGCT 61.991 66.667 0.00 0.00 43.24 5.07
1879 2002 2.080222 GACGTGATACCTACCGGGGC 62.080 65.000 6.32 0.00 40.03 5.80
1894 2017 2.428491 TGTGGAAATTAATGGCGACGT 58.572 42.857 0.00 0.00 0.00 4.34
1905 2028 6.102663 CACTAGTCTCGAGATTGTGGAAATT 58.897 40.000 19.90 0.00 0.00 1.82
1914 2037 4.337145 AGTCCAACACTAGTCTCGAGATT 58.663 43.478 19.90 17.40 31.37 2.40
1934 2064 3.070302 GGTTGAACAGAGAGACCAAGAGT 59.930 47.826 0.00 0.00 0.00 3.24
1939 2069 3.845860 AGTAGGTTGAACAGAGAGACCA 58.154 45.455 0.00 0.00 32.81 4.02
1940 2070 4.875561 AAGTAGGTTGAACAGAGAGACC 57.124 45.455 0.00 0.00 0.00 3.85
1943 2073 5.823045 ACCAAAAAGTAGGTTGAACAGAGAG 59.177 40.000 0.00 0.00 33.39 3.20
1944 2074 5.751586 ACCAAAAAGTAGGTTGAACAGAGA 58.248 37.500 0.00 0.00 33.39 3.10
1945 2075 6.451064 AACCAAAAAGTAGGTTGAACAGAG 57.549 37.500 0.00 0.00 45.91 3.35
1946 2076 6.844097 AAACCAAAAAGTAGGTTGAACAGA 57.156 33.333 0.00 0.00 46.92 3.41
1947 2077 7.623297 GCAAAAACCAAAAAGTAGGTTGAACAG 60.623 37.037 0.00 0.00 46.92 3.16
1948 2078 6.147985 GCAAAAACCAAAAAGTAGGTTGAACA 59.852 34.615 0.00 0.00 46.92 3.18
1949 2079 6.147985 TGCAAAAACCAAAAAGTAGGTTGAAC 59.852 34.615 0.00 0.00 46.92 3.18
1950 2080 6.147985 GTGCAAAAACCAAAAAGTAGGTTGAA 59.852 34.615 0.00 0.00 46.92 2.69
1951 2081 5.639931 GTGCAAAAACCAAAAAGTAGGTTGA 59.360 36.000 0.00 0.00 46.92 3.18
1952 2082 5.445275 CGTGCAAAAACCAAAAAGTAGGTTG 60.445 40.000 0.00 0.00 46.92 3.77
1954 2084 4.177783 CGTGCAAAAACCAAAAAGTAGGT 58.822 39.130 0.00 0.00 40.61 3.08
1955 2085 4.032331 CACGTGCAAAAACCAAAAAGTAGG 59.968 41.667 0.82 0.00 0.00 3.18
2045 2258 2.683362 TCAGCGATCTTATCACGACAGT 59.317 45.455 0.00 0.00 0.00 3.55
2046 2259 3.039405 GTCAGCGATCTTATCACGACAG 58.961 50.000 0.00 0.00 0.00 3.51
2069 2282 0.236711 CTGCGAAGGTTGCTGACAAG 59.763 55.000 0.00 0.00 36.16 3.16
2096 2309 0.754217 CCGTCCTCCTTCCCGTATGA 60.754 60.000 0.00 0.00 0.00 2.15
2223 2436 1.440850 CACCATGCGCGTGTTCAAG 60.441 57.895 26.86 14.22 0.00 3.02
2255 2503 3.806521 GCTCATCTCATGTATGCGAAACT 59.193 43.478 0.00 0.00 0.00 2.66
2284 2532 7.225538 ACGCACTATAAAATTCAGAATCAGGAG 59.774 37.037 0.00 0.00 0.00 3.69
2285 2533 7.047891 ACGCACTATAAAATTCAGAATCAGGA 58.952 34.615 0.00 0.00 0.00 3.86
2286 2534 7.225538 AGACGCACTATAAAATTCAGAATCAGG 59.774 37.037 0.00 0.00 0.00 3.86
2300 2553 6.598525 CATCAACAAAACAGACGCACTATAA 58.401 36.000 0.00 0.00 0.00 0.98
2302 2555 4.613622 GCATCAACAAAACAGACGCACTAT 60.614 41.667 0.00 0.00 0.00 2.12
2452 3022 2.307686 AGGAAACCTTGGGAAAGCGATA 59.692 45.455 0.00 0.00 0.00 2.92
2517 3120 6.245408 AGATGGAAGCACAAACCAAAGTATA 58.755 36.000 0.00 0.00 37.24 1.47
2537 3140 5.882557 AGGGTCACACTTTGCTTTATAGATG 59.117 40.000 0.00 0.00 0.00 2.90
2686 3315 5.714806 CCAGGTCCTTTTTCAGCCTATTTTA 59.285 40.000 0.00 0.00 0.00 1.52
2818 4008 6.468000 GCCGCTAACATATAAACACAGAAAAC 59.532 38.462 0.00 0.00 0.00 2.43
2951 4434 7.860613 TGTTCATACTCACTGTGTAATTTGTG 58.139 34.615 7.79 0.00 0.00 3.33
2953 4436 9.897744 ATTTGTTCATACTCACTGTGTAATTTG 57.102 29.630 7.79 1.65 0.00 2.32
3009 4492 1.069296 GCTTAAACATGTGTGCGCTGA 60.069 47.619 9.73 0.00 0.00 4.26
3014 4497 2.791383 TGGTGCTTAAACATGTGTGC 57.209 45.000 0.00 2.34 0.00 4.57
3021 4504 4.865776 GTGCAACTTATGGTGCTTAAACA 58.134 39.130 18.38 0.00 0.00 2.83
3124 5260 3.873952 TGGGCAAACATTTGTTAGCAAAC 59.126 39.130 6.91 0.00 45.99 2.93
3156 5292 6.151144 ACTTCAACATTTTCTATGCCACTACC 59.849 38.462 0.00 0.00 0.00 3.18
3157 5293 7.145932 ACTTCAACATTTTCTATGCCACTAC 57.854 36.000 0.00 0.00 0.00 2.73
3158 5294 7.759489 AACTTCAACATTTTCTATGCCACTA 57.241 32.000 0.00 0.00 0.00 2.74
3159 5295 6.655078 AACTTCAACATTTTCTATGCCACT 57.345 33.333 0.00 0.00 0.00 4.00
3160 5296 8.028938 ACATAACTTCAACATTTTCTATGCCAC 58.971 33.333 0.00 0.00 0.00 5.01
3161 5297 8.028354 CACATAACTTCAACATTTTCTATGCCA 58.972 33.333 0.00 0.00 0.00 4.92
3163 5299 7.009540 GCCACATAACTTCAACATTTTCTATGC 59.990 37.037 0.00 0.00 0.00 3.14
3164 5300 8.246180 AGCCACATAACTTCAACATTTTCTATG 58.754 33.333 0.00 0.00 0.00 2.23
3165 5301 8.353423 AGCCACATAACTTCAACATTTTCTAT 57.647 30.769 0.00 0.00 0.00 1.98
3166 5302 7.094377 GGAGCCACATAACTTCAACATTTTCTA 60.094 37.037 0.00 0.00 0.00 2.10
3167 5303 6.294731 GGAGCCACATAACTTCAACATTTTCT 60.295 38.462 0.00 0.00 0.00 2.52
3168 5304 5.863935 GGAGCCACATAACTTCAACATTTTC 59.136 40.000 0.00 0.00 0.00 2.29
3169 5305 5.564651 CGGAGCCACATAACTTCAACATTTT 60.565 40.000 0.00 0.00 0.00 1.82
3171 5307 3.440173 CGGAGCCACATAACTTCAACATT 59.560 43.478 0.00 0.00 0.00 2.71
3172 5308 3.009723 CGGAGCCACATAACTTCAACAT 58.990 45.455 0.00 0.00 0.00 2.71
3173 5309 2.422597 CGGAGCCACATAACTTCAACA 58.577 47.619 0.00 0.00 0.00 3.33
3174 5310 1.737793 CCGGAGCCACATAACTTCAAC 59.262 52.381 0.00 0.00 0.00 3.18
3176 5312 0.981183 ACCGGAGCCACATAACTTCA 59.019 50.000 9.46 0.00 0.00 3.02
3177 5313 1.066430 TCACCGGAGCCACATAACTTC 60.066 52.381 9.46 0.00 0.00 3.01
3179 5315 0.249398 GTCACCGGAGCCACATAACT 59.751 55.000 9.46 0.00 0.00 2.24
3180 5316 0.249398 AGTCACCGGAGCCACATAAC 59.751 55.000 9.46 0.00 0.00 1.89
3181 5317 0.981183 AAGTCACCGGAGCCACATAA 59.019 50.000 9.46 0.00 0.00 1.90
3182 5318 0.981183 AAAGTCACCGGAGCCACATA 59.019 50.000 9.46 0.00 0.00 2.29
3185 5321 1.966451 CCAAAGTCACCGGAGCCAC 60.966 63.158 9.46 0.00 0.00 5.01
3186 5322 2.144078 TCCAAAGTCACCGGAGCCA 61.144 57.895 9.46 0.00 0.00 4.75
3187 5323 1.671379 GTCCAAAGTCACCGGAGCC 60.671 63.158 9.46 0.00 0.00 4.70
3188 5324 0.606604 TAGTCCAAAGTCACCGGAGC 59.393 55.000 9.46 0.00 0.00 4.70
3189 5325 3.611766 ATTAGTCCAAAGTCACCGGAG 57.388 47.619 9.46 0.00 0.00 4.63
3190 5326 4.360951 AAATTAGTCCAAAGTCACCGGA 57.639 40.909 9.46 0.00 0.00 5.14
3191 5327 5.009210 TCAAAAATTAGTCCAAAGTCACCGG 59.991 40.000 0.00 0.00 0.00 5.28
3192 5328 6.067263 TCAAAAATTAGTCCAAAGTCACCG 57.933 37.500 0.00 0.00 0.00 4.94
3195 5331 6.460399 CCGGTTCAAAAATTAGTCCAAAGTCA 60.460 38.462 0.00 0.00 0.00 3.41
3196 5332 5.918576 CCGGTTCAAAAATTAGTCCAAAGTC 59.081 40.000 0.00 0.00 0.00 3.01
3197 5333 5.361571 ACCGGTTCAAAAATTAGTCCAAAGT 59.638 36.000 0.00 0.00 0.00 2.66
3198 5334 5.838529 ACCGGTTCAAAAATTAGTCCAAAG 58.161 37.500 0.00 0.00 0.00 2.77
3200 5336 6.771749 TCTTACCGGTTCAAAAATTAGTCCAA 59.228 34.615 15.04 0.00 0.00 3.53
3202 5338 6.806388 TCTTACCGGTTCAAAAATTAGTCC 57.194 37.500 15.04 0.00 0.00 3.85


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

AutoCloner maintained by Alex Coulton.