Multiple sequence alignment - TraesCS2A01G183600

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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 TraesCS2A01G183600 chr2A 100.000 2498 0 0 1 2498 143277770 143275273 0.000000e+00 4614.0
1 TraesCS2A01G183600 chr2A 89.984 629 52 7 1 620 138087249 138087875 0.000000e+00 802.0
2 TraesCS2A01G183600 chr2A 89.888 623 57 6 1 620 83433321 83433940 0.000000e+00 797.0
3 TraesCS2A01G183600 chr2A 87.791 172 19 2 620 790 585703943 585704113 1.520000e-47 200.0
4 TraesCS2A01G183600 chr2A 86.765 68 7 2 2113 2180 562095164 562095099 9.580000e-10 75.0
5 TraesCS2A01G183600 chr2D 92.408 1304 54 18 809 2111 135486000 135484741 0.000000e+00 1818.0
6 TraesCS2A01G183600 chr2D 94.017 234 13 1 2265 2498 135484745 135484513 1.100000e-93 353.0
7 TraesCS2A01G183600 chr2D 92.982 57 1 3 2124 2180 436111328 436111381 2.060000e-11 80.5
8 TraesCS2A01G183600 chr2D 87.500 72 4 5 2113 2180 53145699 53145769 7.410000e-11 78.7
9 TraesCS2A01G183600 chr2D 92.727 55 3 1 1921 1975 548076847 548076794 7.410000e-11 78.7
10 TraesCS2A01G183600 chr2B 91.532 1299 75 18 846 2140 193211046 193209779 0.000000e+00 1757.0
11 TraesCS2A01G183600 chr2B 95.527 313 14 0 2186 2498 193209781 193209469 3.710000e-138 501.0
12 TraesCS2A01G183600 chr2B 81.594 527 64 21 116 627 493519544 493519036 2.990000e-109 405.0
13 TraesCS2A01G183600 chr2B 93.464 153 10 0 638 790 33847349 33847501 6.950000e-56 228.0
14 TraesCS2A01G183600 chr2B 90.000 170 16 1 621 790 776250776 776250608 4.180000e-53 219.0
15 TraesCS2A01G183600 chr2B 88.235 68 6 2 1918 1984 707603469 707603535 2.060000e-11 80.5
16 TraesCS2A01G183600 chr6A 92.160 625 44 5 1 622 81262038 81261416 0.000000e+00 878.0
17 TraesCS2A01G183600 chr6A 89.137 626 62 4 1 620 493578128 493578753 0.000000e+00 774.0
18 TraesCS2A01G183600 chr6A 80.566 530 66 22 115 625 66418803 66419314 8.440000e-100 374.0
19 TraesCS2A01G183600 chr6A 93.464 153 10 0 638 790 127170892 127171044 6.950000e-56 228.0
20 TraesCS2A01G183600 chr6A 83.529 170 26 2 622 790 540321393 540321225 9.250000e-35 158.0
21 TraesCS2A01G183600 chr6A 92.105 38 3 0 1934 1971 594532798 594532761 1.000000e-03 54.7
22 TraesCS2A01G183600 chr3A 91.083 628 47 5 1 620 8651322 8650696 0.000000e+00 841.0
23 TraesCS2A01G183600 chr3A 91.477 528 42 3 98 622 691659284 691658757 0.000000e+00 723.0
24 TraesCS2A01G183600 chr3A 84.848 66 8 1 1910 1973 536635243 536635308 5.770000e-07 65.8
25 TraesCS2A01G183600 chr7A 89.952 627 54 7 1 620 538564453 538563829 0.000000e+00 800.0
26 TraesCS2A01G183600 chr7A 89.406 623 61 5 1 620 49704037 49703417 0.000000e+00 780.0
27 TraesCS2A01G183600 chr7A 88.480 625 62 7 1 620 457468532 457467913 0.000000e+00 747.0
28 TraesCS2A01G183600 chr7A 92.857 56 3 1 2125 2180 162920319 162920373 2.060000e-11 80.5
29 TraesCS2A01G183600 chr4A 90.253 513 33 6 132 627 29002108 29001596 0.000000e+00 654.0
30 TraesCS2A01G183600 chr4A 94.079 152 9 0 638 789 121152243 121152394 5.370000e-57 231.0
31 TraesCS2A01G183600 chr1A 85.940 633 65 13 1 620 589503418 589504039 0.000000e+00 654.0
32 TraesCS2A01G183600 chr5A 84.462 650 77 13 1 636 681057960 681058599 9.810000e-174 619.0
33 TraesCS2A01G183600 chr5A 86.240 516 60 8 115 626 476021487 476020979 1.310000e-152 549.0
34 TraesCS2A01G183600 chr5A 93.464 153 10 0 638 790 60444047 60443895 6.950000e-56 228.0
35 TraesCS2A01G183600 chr5A 93.464 153 10 0 638 790 304003431 304003279 6.950000e-56 228.0
36 TraesCS2A01G183600 chr5D 80.633 537 56 17 115 627 282486876 282487388 3.030000e-99 372.0
37 TraesCS2A01G183600 chr5D 96.078 51 2 0 2130 2180 438373579 438373629 1.590000e-12 84.2
38 TraesCS2A01G183600 chr5D 97.872 47 0 1 2135 2180 62715246 62715200 2.060000e-11 80.5
39 TraesCS2A01G183600 chr5D 92.857 56 1 3 2126 2178 53759199 53759144 7.410000e-11 78.7
40 TraesCS2A01G183600 chr5D 91.071 56 4 1 1920 1975 256458100 256458046 9.580000e-10 75.0
41 TraesCS2A01G183600 chr5D 95.349 43 2 0 1918 1960 354256765 354256807 4.460000e-08 69.4
42 TraesCS2A01G183600 chr4D 82.891 339 42 13 310 643 450362514 450362187 8.740000e-75 291.0
43 TraesCS2A01G183600 chr4D 97.959 49 1 0 2139 2187 121077001 121076953 4.430000e-13 86.1
44 TraesCS2A01G183600 chr4B 93.464 153 10 0 638 790 382202670 382202518 6.950000e-56 228.0
45 TraesCS2A01G183600 chr4B 89.231 65 3 4 2127 2187 433644320 433644384 7.410000e-11 78.7
46 TraesCS2A01G183600 chr1B 93.464 153 10 0 638 790 635509280 635509432 6.950000e-56 228.0
47 TraesCS2A01G183600 chr1B 88.889 63 3 4 1918 1979 156852508 156852567 9.580000e-10 75.0
48 TraesCS2A01G183600 chr3B 92.357 157 12 0 634 790 8463031 8462875 8.990000e-55 224.0
49 TraesCS2A01G183600 chr3B 90.741 54 3 1 1922 1973 308385750 308385697 1.240000e-08 71.3
50 TraesCS2A01G183600 chr5B 89.759 166 15 2 625 790 518809251 518809414 7.000000e-51 211.0
51 TraesCS2A01G183600 chr7D 88.785 107 8 3 518 622 596594599 596594703 7.250000e-26 128.0
52 TraesCS2A01G183600 chr7D 94.545 55 1 2 2127 2180 41837668 41837721 1.590000e-12 84.2
53 TraesCS2A01G183600 chr7D 94.545 55 0 3 2128 2180 519264641 519264588 5.730000e-12 82.4
54 TraesCS2A01G183600 chr7D 91.379 58 4 1 2122 2178 141292071 141292128 7.410000e-11 78.7
55 TraesCS2A01G183600 chr6D 94.595 74 3 1 634 706 463193745 463193672 2.030000e-21 113.0
56 TraesCS2A01G183600 chr6D 97.917 48 0 1 2134 2180 177788379 177788426 5.730000e-12 82.4
57 TraesCS2A01G183600 chr6D 97.826 46 1 0 2135 2180 78520578 78520533 2.060000e-11 80.5
58 TraesCS2A01G183600 chr6D 96.000 50 1 1 2131 2180 157587500 157587452 2.060000e-11 80.5
59 TraesCS2A01G183600 chr6D 92.982 57 1 3 2134 2188 288470113 288470168 2.060000e-11 80.5
60 TraesCS2A01G183600 chr6D 97.826 46 1 0 2135 2180 387885987 387886032 2.060000e-11 80.5
61 TraesCS2A01G183600 chr6D 100.000 42 0 0 2139 2180 78083162 78083121 7.410000e-11 78.7
62 TraesCS2A01G183600 chr6D 94.000 50 3 0 2138 2187 20296606 20296557 2.660000e-10 76.8
63 TraesCS2A01G183600 chr6D 89.655 58 4 1 2139 2194 255527348 255527291 3.450000e-09 73.1
64 TraesCS2A01G183600 chr3D 94.737 57 2 1 1919 1975 219571968 219572023 1.230000e-13 87.9
65 TraesCS2A01G183600 chr3D 93.750 48 0 2 1936 1983 273466389 273466433 4.460000e-08 69.4
66 TraesCS2A01G183600 chr1D 94.643 56 1 2 2127 2180 114366402 114366347 4.430000e-13 86.1
67 TraesCS2A01G183600 chr1D 92.857 56 2 2 2124 2178 440050456 440050402 2.060000e-11 80.5
68 TraesCS2A01G183600 chr1D 95.918 49 1 1 2132 2180 431958019 431958066 7.410000e-11 78.7
69 TraesCS2A01G183600 chr1D 90.164 61 2 3 2120 2178 23423842 23423900 2.660000e-10 76.8
70 TraesCS2A01G183600 chr1D 90.000 60 2 3 1921 1979 95867032 95866976 9.580000e-10 75.0
71 TraesCS2A01G183600 chr6B 92.857 56 4 0 2125 2180 183717435 183717380 5.730000e-12 82.4
72 TraesCS2A01G183600 chrUn 100.000 43 0 0 2139 2181 19086530 19086488 2.060000e-11 80.5
73 TraesCS2A01G183600 chrUn 97.826 46 1 0 2135 2180 65138956 65138911 2.060000e-11 80.5
74 TraesCS2A01G183600 chrUn 100.000 42 0 0 2139 2180 31861293 31861252 7.410000e-11 78.7
75 TraesCS2A01G183600 chrUn 100.000 42 0 0 2139 2180 84435464 84435423 7.410000e-11 78.7
76 TraesCS2A01G183600 chrUn 100.000 42 0 0 2139 2180 104668809 104668850 7.410000e-11 78.7
77 TraesCS2A01G183600 chrUn 97.727 44 0 1 2136 2178 68883355 68883312 9.580000e-10 75.0
78 TraesCS2A01G183600 chrUn 100.000 40 0 0 2139 2178 176719711 176719672 9.580000e-10 75.0
79 TraesCS2A01G183600 chrUn 100.000 40 0 0 2139 2178 355020726 355020687 9.580000e-10 75.0
80 TraesCS2A01G183600 chrUn 100.000 40 0 0 2139 2178 359477395 359477356 9.580000e-10 75.0
81 TraesCS2A01G183600 chrUn 94.000 50 1 1 2131 2178 386553477 386553526 9.580000e-10 75.0
82 TraesCS2A01G183600 chrUn 90.741 54 4 1 2123 2176 65136678 65136730 1.240000e-08 71.3
83 TraesCS2A01G183600 chrUn 100.000 31 0 0 1940 1970 176717930 176717900 9.650000e-05 58.4
84 TraesCS2A01G183600 chrUn 100.000 31 0 0 1940 1970 176752133 176752103 9.650000e-05 58.4
85 TraesCS2A01G183600 chrUn 100.000 31 0 0 1940 1970 397363684 397363654 9.650000e-05 58.4
86 TraesCS2A01G183600 chrUn 100.000 31 0 0 1940 1970 449383608 449383578 9.650000e-05 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 TraesCS2A01G183600 chr2A 143275273 143277770 2497 True 4614.0 4614 100.0000 1 2498 1 chr2A.!!$R1 2497
1 TraesCS2A01G183600 chr2A 138087249 138087875 626 False 802.0 802 89.9840 1 620 1 chr2A.!!$F2 619
2 TraesCS2A01G183600 chr2A 83433321 83433940 619 False 797.0 797 89.8880 1 620 1 chr2A.!!$F1 619
3 TraesCS2A01G183600 chr2D 135484513 135486000 1487 True 1085.5 1818 93.2125 809 2498 2 chr2D.!!$R2 1689
4 TraesCS2A01G183600 chr2B 193209469 193211046 1577 True 1129.0 1757 93.5295 846 2498 2 chr2B.!!$R3 1652
5 TraesCS2A01G183600 chr2B 493519036 493519544 508 True 405.0 405 81.5940 116 627 1 chr2B.!!$R1 511
6 TraesCS2A01G183600 chr6A 81261416 81262038 622 True 878.0 878 92.1600 1 622 1 chr6A.!!$R1 621
7 TraesCS2A01G183600 chr6A 493578128 493578753 625 False 774.0 774 89.1370 1 620 1 chr6A.!!$F3 619
8 TraesCS2A01G183600 chr6A 66418803 66419314 511 False 374.0 374 80.5660 115 625 1 chr6A.!!$F1 510
9 TraesCS2A01G183600 chr3A 8650696 8651322 626 True 841.0 841 91.0830 1 620 1 chr3A.!!$R1 619
10 TraesCS2A01G183600 chr3A 691658757 691659284 527 True 723.0 723 91.4770 98 622 1 chr3A.!!$R2 524
11 TraesCS2A01G183600 chr7A 538563829 538564453 624 True 800.0 800 89.9520 1 620 1 chr7A.!!$R3 619
12 TraesCS2A01G183600 chr7A 49703417 49704037 620 True 780.0 780 89.4060 1 620 1 chr7A.!!$R1 619
13 TraesCS2A01G183600 chr7A 457467913 457468532 619 True 747.0 747 88.4800 1 620 1 chr7A.!!$R2 619
14 TraesCS2A01G183600 chr4A 29001596 29002108 512 True 654.0 654 90.2530 132 627 1 chr4A.!!$R1 495
15 TraesCS2A01G183600 chr1A 589503418 589504039 621 False 654.0 654 85.9400 1 620 1 chr1A.!!$F1 619
16 TraesCS2A01G183600 chr5A 681057960 681058599 639 False 619.0 619 84.4620 1 636 1 chr5A.!!$F1 635
17 TraesCS2A01G183600 chr5A 476020979 476021487 508 True 549.0 549 86.2400 115 626 1 chr5A.!!$R3 511
18 TraesCS2A01G183600 chr5D 282486876 282487388 512 False 372.0 372 80.6330 115 627 1 chr5D.!!$F1 512

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
649 714 0.041312 GCGCACACGAATCAACTTGT 60.041 50.0 0.3 0.0 43.93 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2137 2206 1.424638 ATTATGGGACGGAGGGAGTG 58.575 55.0 0.0 0.0 0.0 3.51 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
25 26 2.348665 ACGCCGGTGAAGAAGTAGT 58.651 52.632 24.59 0.00 0.00 2.73
171 172 4.093952 CACTTTGCAGAGCGCCGG 62.094 66.667 2.29 0.00 41.33 6.13
426 486 6.377327 AATATATGTCCAAGTTTGCCGAAG 57.623 37.500 0.00 0.00 0.00 3.79
457 518 0.109597 TAGCCGAACTTCGTCGAACC 60.110 55.000 2.90 0.00 43.86 3.62
551 613 0.896226 AACTCGCCCCTAGACTCAAC 59.104 55.000 0.00 0.00 0.00 3.18
627 692 2.356125 GCTGGAGATGCTCTAAAACCCA 60.356 50.000 0.00 0.00 0.00 4.51
631 696 2.620585 GAGATGCTCTAAAACCCATGGC 59.379 50.000 6.09 0.00 0.00 4.40
636 701 0.250945 TCTAAAACCCATGGCGCACA 60.251 50.000 10.83 5.20 0.00 4.57
637 702 0.109319 CTAAAACCCATGGCGCACAC 60.109 55.000 10.83 0.00 0.00 3.82
638 703 1.857318 TAAAACCCATGGCGCACACG 61.857 55.000 10.83 0.00 44.07 4.49
639 704 4.634703 AACCCATGGCGCACACGA 62.635 61.111 10.83 0.00 43.93 4.35
640 705 4.634703 ACCCATGGCGCACACGAA 62.635 61.111 10.83 0.00 43.93 3.85
641 706 3.133464 CCCATGGCGCACACGAAT 61.133 61.111 10.83 0.00 43.93 3.34
642 707 2.404789 CCATGGCGCACACGAATC 59.595 61.111 10.83 0.00 43.93 2.52
643 708 2.397754 CCATGGCGCACACGAATCA 61.398 57.895 10.83 0.00 43.93 2.57
644 709 1.501292 CATGGCGCACACGAATCAA 59.499 52.632 10.83 0.00 43.93 2.57
645 710 0.794229 CATGGCGCACACGAATCAAC 60.794 55.000 10.83 0.00 43.93 3.18
646 711 0.955428 ATGGCGCACACGAATCAACT 60.955 50.000 10.83 0.00 43.93 3.16
647 712 1.163420 TGGCGCACACGAATCAACTT 61.163 50.000 10.83 0.00 43.93 2.66
648 713 0.725784 GGCGCACACGAATCAACTTG 60.726 55.000 10.83 0.00 43.93 3.16
649 714 0.041312 GCGCACACGAATCAACTTGT 60.041 50.000 0.30 0.00 43.93 3.16
650 715 1.662360 CGCACACGAATCAACTTGTG 58.338 50.000 0.00 0.00 43.93 3.33
651 716 1.660052 CGCACACGAATCAACTTGTGG 60.660 52.381 0.00 0.00 43.93 4.17
652 717 1.333619 GCACACGAATCAACTTGTGGT 59.666 47.619 0.00 0.00 39.37 4.16
653 718 2.223479 GCACACGAATCAACTTGTGGTT 60.223 45.455 0.00 0.00 39.37 3.67
665 730 3.551846 ACTTGTGGTTGAGTTGGTTAGG 58.448 45.455 0.00 0.00 0.00 2.69
666 731 3.053917 ACTTGTGGTTGAGTTGGTTAGGT 60.054 43.478 0.00 0.00 0.00 3.08
667 732 2.925724 TGTGGTTGAGTTGGTTAGGTG 58.074 47.619 0.00 0.00 0.00 4.00
668 733 2.227194 GTGGTTGAGTTGGTTAGGTGG 58.773 52.381 0.00 0.00 0.00 4.61
669 734 2.128535 TGGTTGAGTTGGTTAGGTGGA 58.871 47.619 0.00 0.00 0.00 4.02
670 735 2.158726 TGGTTGAGTTGGTTAGGTGGAC 60.159 50.000 0.00 0.00 0.00 4.02
671 736 2.158726 GGTTGAGTTGGTTAGGTGGACA 60.159 50.000 0.00 0.00 0.00 4.02
672 737 3.139077 GTTGAGTTGGTTAGGTGGACAG 58.861 50.000 0.00 0.00 0.00 3.51
673 738 2.404559 TGAGTTGGTTAGGTGGACAGT 58.595 47.619 0.00 0.00 0.00 3.55
674 739 2.104111 TGAGTTGGTTAGGTGGACAGTG 59.896 50.000 0.00 0.00 0.00 3.66
675 740 2.367567 GAGTTGGTTAGGTGGACAGTGA 59.632 50.000 0.00 0.00 0.00 3.41
676 741 2.979678 AGTTGGTTAGGTGGACAGTGAT 59.020 45.455 0.00 0.00 0.00 3.06
677 742 4.164981 AGTTGGTTAGGTGGACAGTGATA 58.835 43.478 0.00 0.00 0.00 2.15
678 743 4.783227 AGTTGGTTAGGTGGACAGTGATAT 59.217 41.667 0.00 0.00 0.00 1.63
679 744 5.104900 AGTTGGTTAGGTGGACAGTGATATC 60.105 44.000 0.00 0.00 0.00 1.63
680 745 3.709653 TGGTTAGGTGGACAGTGATATCC 59.290 47.826 0.00 0.00 0.00 2.59
681 746 3.071167 GGTTAGGTGGACAGTGATATCCC 59.929 52.174 0.00 0.00 0.00 3.85
682 747 1.807814 AGGTGGACAGTGATATCCCC 58.192 55.000 0.00 0.00 0.00 4.81
683 748 1.009552 AGGTGGACAGTGATATCCCCA 59.990 52.381 0.00 0.00 0.00 4.96
684 749 1.843851 GGTGGACAGTGATATCCCCAA 59.156 52.381 0.00 0.00 0.00 4.12
685 750 2.421529 GGTGGACAGTGATATCCCCAAC 60.422 54.545 0.00 0.00 0.00 3.77
686 751 1.843851 TGGACAGTGATATCCCCAACC 59.156 52.381 0.00 0.00 0.00 3.77
687 752 1.143073 GGACAGTGATATCCCCAACCC 59.857 57.143 0.00 0.00 0.00 4.11
688 753 1.843851 GACAGTGATATCCCCAACCCA 59.156 52.381 0.00 0.00 0.00 4.51
689 754 1.564348 ACAGTGATATCCCCAACCCAC 59.436 52.381 0.00 0.00 0.00 4.61
690 755 1.133792 CAGTGATATCCCCAACCCACC 60.134 57.143 0.00 0.00 0.00 4.61
691 756 0.923358 GTGATATCCCCAACCCACCA 59.077 55.000 0.00 0.00 0.00 4.17
692 757 1.133792 GTGATATCCCCAACCCACCAG 60.134 57.143 0.00 0.00 0.00 4.00
693 758 0.478507 GATATCCCCAACCCACCAGG 59.521 60.000 0.00 0.00 43.78 4.45
711 776 3.010200 AGGGTTCAAATCCTGATGCTC 57.990 47.619 0.00 0.00 38.36 4.26
712 777 1.672881 GGGTTCAAATCCTGATGCTCG 59.327 52.381 0.00 0.00 32.78 5.03
713 778 1.064654 GGTTCAAATCCTGATGCTCGC 59.935 52.381 0.00 0.00 32.78 5.03
714 779 1.739466 GTTCAAATCCTGATGCTCGCA 59.261 47.619 0.00 0.00 32.78 5.10
715 780 2.336945 TCAAATCCTGATGCTCGCAT 57.663 45.000 3.70 3.70 39.69 4.73
716 781 2.646930 TCAAATCCTGATGCTCGCATT 58.353 42.857 5.79 0.00 36.70 3.56
717 782 3.807553 TCAAATCCTGATGCTCGCATTA 58.192 40.909 5.79 0.89 36.70 1.90
718 783 4.392047 TCAAATCCTGATGCTCGCATTAT 58.608 39.130 5.79 0.00 36.70 1.28
719 784 4.823442 TCAAATCCTGATGCTCGCATTATT 59.177 37.500 5.79 2.29 36.70 1.40
720 785 5.049198 TCAAATCCTGATGCTCGCATTATTC 60.049 40.000 5.79 0.00 36.70 1.75
721 786 2.771089 TCCTGATGCTCGCATTATTCC 58.229 47.619 5.79 0.00 36.70 3.01
722 787 2.369860 TCCTGATGCTCGCATTATTCCT 59.630 45.455 5.79 0.00 36.70 3.36
723 788 2.483106 CCTGATGCTCGCATTATTCCTG 59.517 50.000 5.79 0.00 36.70 3.86
724 789 3.396560 CTGATGCTCGCATTATTCCTGA 58.603 45.455 5.79 0.00 36.70 3.86
725 790 3.807553 TGATGCTCGCATTATTCCTGAA 58.192 40.909 5.79 0.00 36.70 3.02
726 791 4.392047 TGATGCTCGCATTATTCCTGAAT 58.608 39.130 5.79 0.00 36.70 2.57
727 792 4.823442 TGATGCTCGCATTATTCCTGAATT 59.177 37.500 5.79 0.00 36.70 2.17
728 793 5.300034 TGATGCTCGCATTATTCCTGAATTT 59.700 36.000 5.79 0.00 36.70 1.82
729 794 6.486320 TGATGCTCGCATTATTCCTGAATTTA 59.514 34.615 5.79 0.00 36.70 1.40
730 795 6.882610 TGCTCGCATTATTCCTGAATTTAT 57.117 33.333 0.00 0.00 32.50 1.40
731 796 7.275888 TGCTCGCATTATTCCTGAATTTATT 57.724 32.000 0.00 0.00 32.50 1.40
732 797 7.715657 TGCTCGCATTATTCCTGAATTTATTT 58.284 30.769 0.00 0.00 32.50 1.40
733 798 8.196771 TGCTCGCATTATTCCTGAATTTATTTT 58.803 29.630 0.00 0.00 32.50 1.82
734 799 8.482429 GCTCGCATTATTCCTGAATTTATTTTG 58.518 33.333 0.00 0.00 32.50 2.44
735 800 8.870160 TCGCATTATTCCTGAATTTATTTTGG 57.130 30.769 0.00 0.00 32.50 3.28
736 801 8.690884 TCGCATTATTCCTGAATTTATTTTGGA 58.309 29.630 0.00 0.00 32.50 3.53
737 802 9.311916 CGCATTATTCCTGAATTTATTTTGGAA 57.688 29.630 0.00 10.40 36.57 3.53
744 809 8.770438 TCCTGAATTTATTTTGGAATTTTCGG 57.230 30.769 0.00 0.00 0.00 4.30
745 810 7.333174 TCCTGAATTTATTTTGGAATTTTCGGC 59.667 33.333 0.00 0.00 0.00 5.54
746 811 7.054855 TGAATTTATTTTGGAATTTTCGGCG 57.945 32.000 0.00 0.00 0.00 6.46
747 812 6.868864 TGAATTTATTTTGGAATTTTCGGCGA 59.131 30.769 4.99 4.99 0.00 5.54
748 813 7.547370 TGAATTTATTTTGGAATTTTCGGCGAT 59.453 29.630 11.76 0.00 0.00 4.58
749 814 8.934507 AATTTATTTTGGAATTTTCGGCGATA 57.065 26.923 11.76 2.15 0.00 2.92
750 815 9.541143 AATTTATTTTGGAATTTTCGGCGATAT 57.459 25.926 11.76 4.65 0.00 1.63
751 816 7.922505 TTATTTTGGAATTTTCGGCGATATG 57.077 32.000 11.76 0.00 0.00 1.78
752 817 3.347958 TTGGAATTTTCGGCGATATGC 57.652 42.857 11.76 6.18 45.38 3.14
753 818 2.571212 TGGAATTTTCGGCGATATGCT 58.429 42.857 11.76 0.00 45.43 3.79
754 819 2.948979 TGGAATTTTCGGCGATATGCTT 59.051 40.909 11.76 0.07 45.43 3.91
755 820 3.380004 TGGAATTTTCGGCGATATGCTTT 59.620 39.130 11.76 0.00 45.43 3.51
756 821 3.975035 GGAATTTTCGGCGATATGCTTTC 59.025 43.478 11.76 8.48 45.43 2.62
757 822 4.497340 GGAATTTTCGGCGATATGCTTTCA 60.497 41.667 11.76 0.00 45.43 2.69
758 823 3.673746 TTTTCGGCGATATGCTTTCAG 57.326 42.857 11.76 0.00 45.43 3.02
759 824 2.309528 TTCGGCGATATGCTTTCAGT 57.690 45.000 11.76 0.00 45.43 3.41
760 825 2.309528 TCGGCGATATGCTTTCAGTT 57.690 45.000 4.99 0.00 45.43 3.16
761 826 1.933181 TCGGCGATATGCTTTCAGTTG 59.067 47.619 4.99 0.00 45.43 3.16
762 827 1.003545 CGGCGATATGCTTTCAGTTGG 60.004 52.381 0.00 0.00 45.43 3.77
763 828 2.288666 GGCGATATGCTTTCAGTTGGA 58.711 47.619 0.00 0.00 45.43 3.53
764 829 2.289002 GGCGATATGCTTTCAGTTGGAG 59.711 50.000 0.00 0.00 45.43 3.86
765 830 2.289002 GCGATATGCTTTCAGTTGGAGG 59.711 50.000 0.00 0.00 41.73 4.30
766 831 3.797039 CGATATGCTTTCAGTTGGAGGA 58.203 45.455 0.00 0.00 0.00 3.71
767 832 3.806521 CGATATGCTTTCAGTTGGAGGAG 59.193 47.826 0.00 0.00 0.00 3.69
768 833 4.442052 CGATATGCTTTCAGTTGGAGGAGA 60.442 45.833 0.00 0.00 0.00 3.71
769 834 2.550830 TGCTTTCAGTTGGAGGAGAC 57.449 50.000 0.00 0.00 0.00 3.36
770 835 1.270305 TGCTTTCAGTTGGAGGAGACG 60.270 52.381 0.00 0.00 0.00 4.18
771 836 1.270358 GCTTTCAGTTGGAGGAGACGT 60.270 52.381 0.00 0.00 0.00 4.34
772 837 2.807108 GCTTTCAGTTGGAGGAGACGTT 60.807 50.000 0.00 0.00 0.00 3.99
773 838 2.814280 TTCAGTTGGAGGAGACGTTC 57.186 50.000 0.00 0.00 0.00 3.95
774 839 1.996798 TCAGTTGGAGGAGACGTTCT 58.003 50.000 0.00 0.00 0.00 3.01
775 840 1.887198 TCAGTTGGAGGAGACGTTCTC 59.113 52.381 0.00 0.00 42.66 2.87
776 841 0.882474 AGTTGGAGGAGACGTTCTCG 59.118 55.000 0.00 0.00 44.28 4.04
794 859 2.506217 TCGACGACGAGGCAATGC 60.506 61.111 5.75 0.00 43.81 3.56
795 860 2.507102 CGACGACGAGGCAATGCT 60.507 61.111 4.82 0.00 42.66 3.79
796 861 1.226575 CGACGACGAGGCAATGCTA 60.227 57.895 4.82 0.00 42.66 3.49
797 862 0.800683 CGACGACGAGGCAATGCTAA 60.801 55.000 4.82 0.00 42.66 3.09
798 863 1.355971 GACGACGAGGCAATGCTAAA 58.644 50.000 4.82 0.00 0.00 1.85
799 864 1.730064 GACGACGAGGCAATGCTAAAA 59.270 47.619 4.82 0.00 0.00 1.52
800 865 2.147958 ACGACGAGGCAATGCTAAAAA 58.852 42.857 4.82 0.00 0.00 1.94
920 985 0.398318 AGTCTCCAACCCACAGAAGC 59.602 55.000 0.00 0.00 0.00 3.86
985 1053 4.767892 CCCCCTCCCCCTTGCTCT 62.768 72.222 0.00 0.00 0.00 4.09
986 1054 3.093172 CCCCTCCCCCTTGCTCTC 61.093 72.222 0.00 0.00 0.00 3.20
987 1055 3.093172 CCCTCCCCCTTGCTCTCC 61.093 72.222 0.00 0.00 0.00 3.71
1061 1129 2.436646 CGCGCCCACTGAATCCTT 60.437 61.111 0.00 0.00 0.00 3.36
1071 1139 2.508439 GAATCCTTCGCCGACGCA 60.508 61.111 0.00 0.00 39.84 5.24
1551 1619 3.258872 AGTGCTGCTATTTTGGCATTTCA 59.741 39.130 0.00 0.00 39.07 2.69
1601 1669 9.796120 CTACTACTTTATTAGAGATGCCTATGC 57.204 37.037 0.00 0.00 38.26 3.14
1752 1820 2.821307 GCAGTAGATTGCAAGCAGAC 57.179 50.000 18.24 13.99 43.53 3.51
1770 1838 6.653020 AGCAGACTGTACCAATGAATATTCA 58.347 36.000 20.07 20.07 42.14 2.57
1804 1872 4.747810 CCAATTGTATGCTTGTTCCTTCC 58.252 43.478 4.43 0.00 0.00 3.46
1812 1880 1.002792 GCTTGTTCCTTCCGTGTTGAC 60.003 52.381 0.00 0.00 0.00 3.18
1828 1896 4.004314 TGTTGACTTTGTTCTCGTTTGGA 58.996 39.130 0.00 0.00 0.00 3.53
1834 1902 1.234821 TGTTCTCGTTTGGATGGTGC 58.765 50.000 0.00 0.00 0.00 5.01
1841 1909 1.533625 GTTTGGATGGTGCAGCAGTA 58.466 50.000 24.45 9.89 0.00 2.74
1843 1911 1.753930 TTGGATGGTGCAGCAGTATG 58.246 50.000 24.45 0.00 40.87 2.39
1860 1928 5.156355 CAGTATGTGCTTTCGCTCATTTTT 58.844 37.500 7.10 0.00 45.22 1.94
1877 1945 6.919721 TCATTTTTACCTTATGCACTTGGAC 58.080 36.000 7.57 0.00 0.00 4.02
1910 1978 8.877195 AGTTCTTAGGTAGGTTTCATTCTGTTA 58.123 33.333 0.00 0.00 0.00 2.41
1930 1998 9.546909 TCTGTTAAATAGTACGTTTTAGAGACG 57.453 33.333 0.00 0.00 45.46 4.18
2009 2077 8.474831 TGCTGAGCTGATTAAGTAAATACTACA 58.525 33.333 5.83 0.00 34.99 2.74
2055 2123 9.423061 GTTGAAAATAGGCACATATTGTTTTCT 57.577 29.630 0.00 0.00 35.95 2.52
2073 2141 7.036829 TGTTTTCTAAAAGTAAAAGGCCACAC 58.963 34.615 5.01 0.00 0.00 3.82
2074 2142 7.093684 TGTTTTCTAAAAGTAAAAGGCCACACT 60.094 33.333 5.01 0.00 0.00 3.55
2079 2147 6.575162 AAAAGTAAAAGGCCACACTCATAG 57.425 37.500 5.01 0.00 0.00 2.23
2084 2153 6.879458 AGTAAAAGGCCACACTCATAGTTTAG 59.121 38.462 5.01 0.00 0.00 1.85
2142 2211 8.837389 ACTACAGTTGTTTTTCTAAATCACTCC 58.163 33.333 0.00 0.00 0.00 3.85
2143 2212 7.039313 ACAGTTGTTTTTCTAAATCACTCCC 57.961 36.000 0.00 0.00 0.00 4.30
2144 2213 6.833933 ACAGTTGTTTTTCTAAATCACTCCCT 59.166 34.615 0.00 0.00 0.00 4.20
2145 2214 7.013369 ACAGTTGTTTTTCTAAATCACTCCCTC 59.987 37.037 0.00 0.00 0.00 4.30
2146 2215 6.490381 AGTTGTTTTTCTAAATCACTCCCTCC 59.510 38.462 0.00 0.00 0.00 4.30
2147 2216 5.001232 TGTTTTTCTAAATCACTCCCTCCG 58.999 41.667 0.00 0.00 0.00 4.63
2148 2217 4.903045 TTTTCTAAATCACTCCCTCCGT 57.097 40.909 0.00 0.00 0.00 4.69
2149 2218 4.467198 TTTCTAAATCACTCCCTCCGTC 57.533 45.455 0.00 0.00 0.00 4.79
2150 2219 2.385803 TCTAAATCACTCCCTCCGTCC 58.614 52.381 0.00 0.00 0.00 4.79
2151 2220 1.413077 CTAAATCACTCCCTCCGTCCC 59.587 57.143 0.00 0.00 0.00 4.46
2152 2221 0.546747 AAATCACTCCCTCCGTCCCA 60.547 55.000 0.00 0.00 0.00 4.37
2153 2222 0.326618 AATCACTCCCTCCGTCCCAT 60.327 55.000 0.00 0.00 0.00 4.00
2154 2223 0.561184 ATCACTCCCTCCGTCCCATA 59.439 55.000 0.00 0.00 0.00 2.74
2155 2224 0.337082 TCACTCCCTCCGTCCCATAA 59.663 55.000 0.00 0.00 0.00 1.90
2156 2225 1.062428 TCACTCCCTCCGTCCCATAAT 60.062 52.381 0.00 0.00 0.00 1.28
2157 2226 2.178325 TCACTCCCTCCGTCCCATAATA 59.822 50.000 0.00 0.00 0.00 0.98
2158 2227 3.173965 CACTCCCTCCGTCCCATAATAT 58.826 50.000 0.00 0.00 0.00 1.28
2159 2228 4.044952 TCACTCCCTCCGTCCCATAATATA 59.955 45.833 0.00 0.00 0.00 0.86
2160 2229 4.775780 CACTCCCTCCGTCCCATAATATAA 59.224 45.833 0.00 0.00 0.00 0.98
2161 2230 5.024118 ACTCCCTCCGTCCCATAATATAAG 58.976 45.833 0.00 0.00 0.00 1.73
2162 2231 5.222484 ACTCCCTCCGTCCCATAATATAAGA 60.222 44.000 0.00 0.00 0.00 2.10
2163 2232 5.269991 TCCCTCCGTCCCATAATATAAGAG 58.730 45.833 0.00 0.00 0.00 2.85
2164 2233 4.141914 CCCTCCGTCCCATAATATAAGAGC 60.142 50.000 0.00 0.00 0.00 4.09
2165 2234 4.440250 CCTCCGTCCCATAATATAAGAGCG 60.440 50.000 0.00 0.00 0.00 5.03
2166 2235 4.084287 TCCGTCCCATAATATAAGAGCGT 58.916 43.478 0.00 0.00 0.00 5.07
2167 2236 4.525487 TCCGTCCCATAATATAAGAGCGTT 59.475 41.667 0.00 0.00 0.00 4.84
2168 2237 5.011329 TCCGTCCCATAATATAAGAGCGTTT 59.989 40.000 0.00 0.00 0.00 3.60
2169 2238 5.699458 CCGTCCCATAATATAAGAGCGTTTT 59.301 40.000 0.00 0.00 0.00 2.43
2170 2239 6.204108 CCGTCCCATAATATAAGAGCGTTTTT 59.796 38.462 0.00 0.00 0.00 1.94
2171 2240 7.069569 CGTCCCATAATATAAGAGCGTTTTTG 58.930 38.462 0.00 0.00 0.00 2.44
2172 2241 7.042321 CGTCCCATAATATAAGAGCGTTTTTGA 60.042 37.037 0.00 0.00 0.00 2.69
2173 2242 8.068380 GTCCCATAATATAAGAGCGTTTTTGAC 58.932 37.037 0.00 0.00 0.00 3.18
2174 2243 7.771361 TCCCATAATATAAGAGCGTTTTTGACA 59.229 33.333 0.00 0.00 0.00 3.58
2175 2244 7.855904 CCCATAATATAAGAGCGTTTTTGACAC 59.144 37.037 0.00 0.00 0.00 3.67
2176 2245 8.612619 CCATAATATAAGAGCGTTTTTGACACT 58.387 33.333 0.00 0.00 0.00 3.55
2179 2248 8.542497 AATATAAGAGCGTTTTTGACACTACA 57.458 30.769 0.00 0.00 0.00 2.74
2180 2249 4.795970 AAGAGCGTTTTTGACACTACAG 57.204 40.909 0.00 0.00 0.00 2.74
2181 2250 3.131396 AGAGCGTTTTTGACACTACAGG 58.869 45.455 0.00 0.00 0.00 4.00
2182 2251 2.218603 AGCGTTTTTGACACTACAGGG 58.781 47.619 0.00 0.00 0.00 4.45
2183 2252 2.158871 AGCGTTTTTGACACTACAGGGA 60.159 45.455 0.00 0.00 0.00 4.20
2184 2253 2.223377 GCGTTTTTGACACTACAGGGAG 59.777 50.000 0.00 0.00 0.00 4.30
2236 2305 1.134580 TGACTGAATGGAGCTGCTAGC 60.135 52.381 8.10 8.10 42.84 3.42
2237 2306 0.907486 ACTGAATGGAGCTGCTAGCA 59.093 50.000 18.22 18.22 45.56 3.49
2243 2312 0.322726 TGGAGCTGCTAGCATTGCAA 60.323 50.000 25.52 0.00 45.56 4.08
2248 2317 1.734707 GCTGCTAGCATTGCAACCAAG 60.735 52.381 19.72 3.24 41.89 3.61
2272 2341 8.029642 AGACAACAACTAACATAGTAACATGC 57.970 34.615 0.00 0.00 38.26 4.06
2324 2393 1.340991 ACCCGATTGCAATGCTAGGTT 60.341 47.619 18.59 0.34 0.00 3.50
2375 2444 9.860898 ACAGAATTGAGCCATTTTAATTTAGTC 57.139 29.630 0.00 0.00 0.00 2.59
2395 2464 1.935873 CGGTCATGTGTTGCTAGATGG 59.064 52.381 0.00 0.00 0.00 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
80 81 1.889573 GCTATGGAGTCCTTGCGCC 60.890 63.158 11.33 0.00 0.00 6.53
197 199 1.444383 GTCGCTGTCGCAGATGACA 60.444 57.895 18.38 0.00 46.15 3.58
426 486 4.916099 AGTTCGGCTAAACACGATAAAC 57.084 40.909 0.00 0.00 39.06 2.01
457 518 7.851822 AATTTATATAGCAAATTTCGGCACG 57.148 32.000 3.62 0.00 39.50 5.34
551 613 1.576421 GGGTGAGTCAGCGCAAAAG 59.424 57.895 11.47 0.00 32.08 2.27
627 692 0.955428 AGTTGATTCGTGTGCGCCAT 60.955 50.000 4.18 0.00 38.14 4.40
631 696 1.660052 CCACAAGTTGATTCGTGTGCG 60.660 52.381 10.54 0.00 42.96 5.34
643 708 3.951680 CCTAACCAACTCAACCACAAGTT 59.048 43.478 0.00 0.00 40.16 2.66
644 709 3.053917 ACCTAACCAACTCAACCACAAGT 60.054 43.478 0.00 0.00 0.00 3.16
645 710 3.315191 CACCTAACCAACTCAACCACAAG 59.685 47.826 0.00 0.00 0.00 3.16
646 711 3.283751 CACCTAACCAACTCAACCACAA 58.716 45.455 0.00 0.00 0.00 3.33
647 712 2.422235 CCACCTAACCAACTCAACCACA 60.422 50.000 0.00 0.00 0.00 4.17
648 713 2.158726 TCCACCTAACCAACTCAACCAC 60.159 50.000 0.00 0.00 0.00 4.16
649 714 2.128535 TCCACCTAACCAACTCAACCA 58.871 47.619 0.00 0.00 0.00 3.67
650 715 2.158726 TGTCCACCTAACCAACTCAACC 60.159 50.000 0.00 0.00 0.00 3.77
651 716 3.139077 CTGTCCACCTAACCAACTCAAC 58.861 50.000 0.00 0.00 0.00 3.18
652 717 2.775384 ACTGTCCACCTAACCAACTCAA 59.225 45.455 0.00 0.00 0.00 3.02
653 718 2.104111 CACTGTCCACCTAACCAACTCA 59.896 50.000 0.00 0.00 0.00 3.41
654 719 2.367567 TCACTGTCCACCTAACCAACTC 59.632 50.000 0.00 0.00 0.00 3.01
655 720 2.404559 TCACTGTCCACCTAACCAACT 58.595 47.619 0.00 0.00 0.00 3.16
656 721 2.922740 TCACTGTCCACCTAACCAAC 57.077 50.000 0.00 0.00 0.00 3.77
657 722 4.163458 GGATATCACTGTCCACCTAACCAA 59.837 45.833 4.83 0.00 33.05 3.67
658 723 3.709653 GGATATCACTGTCCACCTAACCA 59.290 47.826 4.83 0.00 33.05 3.67
659 724 3.071167 GGGATATCACTGTCCACCTAACC 59.929 52.174 4.83 0.00 34.44 2.85
660 725 3.071167 GGGGATATCACTGTCCACCTAAC 59.929 52.174 4.65 0.00 34.44 2.34
661 726 3.311028 TGGGGATATCACTGTCCACCTAA 60.311 47.826 4.65 0.00 35.25 2.69
662 727 2.248950 TGGGGATATCACTGTCCACCTA 59.751 50.000 4.65 0.00 35.25 3.08
663 728 1.009552 TGGGGATATCACTGTCCACCT 59.990 52.381 4.65 0.00 35.25 4.00
664 729 1.507140 TGGGGATATCACTGTCCACC 58.493 55.000 4.65 0.00 35.25 4.61
665 730 2.421529 GGTTGGGGATATCACTGTCCAC 60.422 54.545 4.65 0.00 36.63 4.02
666 731 1.843851 GGTTGGGGATATCACTGTCCA 59.156 52.381 4.65 1.40 34.44 4.02
667 732 1.143073 GGGTTGGGGATATCACTGTCC 59.857 57.143 4.65 4.82 32.06 4.02
668 733 1.843851 TGGGTTGGGGATATCACTGTC 59.156 52.381 4.65 0.00 0.00 3.51
669 734 1.564348 GTGGGTTGGGGATATCACTGT 59.436 52.381 4.65 0.00 0.00 3.55
670 735 1.133792 GGTGGGTTGGGGATATCACTG 60.134 57.143 4.65 0.00 0.00 3.66
671 736 1.222567 GGTGGGTTGGGGATATCACT 58.777 55.000 4.65 0.00 0.00 3.41
672 737 0.923358 TGGTGGGTTGGGGATATCAC 59.077 55.000 4.83 0.00 0.00 3.06
673 738 1.221635 CTGGTGGGTTGGGGATATCA 58.778 55.000 4.83 0.00 0.00 2.15
674 739 0.478507 CCTGGTGGGTTGGGGATATC 59.521 60.000 0.00 0.00 0.00 1.63
675 740 2.645604 CCTGGTGGGTTGGGGATAT 58.354 57.895 0.00 0.00 0.00 1.63
676 741 4.179896 CCTGGTGGGTTGGGGATA 57.820 61.111 0.00 0.00 0.00 2.59
686 751 1.549203 CAGGATTTGAACCCTGGTGG 58.451 55.000 0.00 0.00 44.68 4.61
691 756 2.681976 CGAGCATCAGGATTTGAACCCT 60.682 50.000 0.00 0.00 39.77 4.34
692 757 1.672881 CGAGCATCAGGATTTGAACCC 59.327 52.381 0.00 0.00 39.77 4.11
693 758 1.064654 GCGAGCATCAGGATTTGAACC 59.935 52.381 0.00 0.00 39.77 3.62
694 759 1.739466 TGCGAGCATCAGGATTTGAAC 59.261 47.619 0.00 0.00 39.77 3.18
695 760 2.112380 TGCGAGCATCAGGATTTGAA 57.888 45.000 0.00 0.00 39.77 2.69
696 761 2.336945 ATGCGAGCATCAGGATTTGA 57.663 45.000 4.52 0.00 40.85 2.69
697 762 4.761235 ATAATGCGAGCATCAGGATTTG 57.239 40.909 11.26 0.00 35.31 2.32
698 763 4.217118 GGAATAATGCGAGCATCAGGATTT 59.783 41.667 11.26 0.00 35.31 2.17
699 764 3.755378 GGAATAATGCGAGCATCAGGATT 59.245 43.478 11.26 8.63 35.31 3.01
700 765 3.008813 AGGAATAATGCGAGCATCAGGAT 59.991 43.478 11.26 0.00 35.31 3.24
701 766 2.369860 AGGAATAATGCGAGCATCAGGA 59.630 45.455 11.26 0.00 35.31 3.86
702 767 2.483106 CAGGAATAATGCGAGCATCAGG 59.517 50.000 11.26 0.00 35.31 3.86
703 768 3.396560 TCAGGAATAATGCGAGCATCAG 58.603 45.455 11.26 0.00 35.31 2.90
704 769 3.473923 TCAGGAATAATGCGAGCATCA 57.526 42.857 11.26 0.00 35.31 3.07
705 770 5.368256 AATTCAGGAATAATGCGAGCATC 57.632 39.130 11.26 0.00 35.31 3.91
706 771 5.779529 AAATTCAGGAATAATGCGAGCAT 57.220 34.783 4.52 4.52 38.46 3.79
707 772 6.882610 ATAAATTCAGGAATAATGCGAGCA 57.117 33.333 0.00 0.00 0.00 4.26
708 773 8.482429 CAAAATAAATTCAGGAATAATGCGAGC 58.518 33.333 0.00 0.00 0.00 5.03
709 774 8.971321 CCAAAATAAATTCAGGAATAATGCGAG 58.029 33.333 0.00 0.00 0.00 5.03
710 775 8.690884 TCCAAAATAAATTCAGGAATAATGCGA 58.309 29.630 0.00 0.00 0.00 5.10
711 776 8.870160 TCCAAAATAAATTCAGGAATAATGCG 57.130 30.769 0.00 0.00 0.00 4.73
718 783 9.213799 CCGAAAATTCCAAAATAAATTCAGGAA 57.786 29.630 9.76 9.76 37.17 3.36
719 784 7.333174 GCCGAAAATTCCAAAATAAATTCAGGA 59.667 33.333 0.00 0.00 0.00 3.86
720 785 7.463544 GCCGAAAATTCCAAAATAAATTCAGG 58.536 34.615 0.00 0.00 0.00 3.86
721 786 7.062839 TCGCCGAAAATTCCAAAATAAATTCAG 59.937 33.333 0.00 0.00 0.00 3.02
722 787 6.868864 TCGCCGAAAATTCCAAAATAAATTCA 59.131 30.769 0.00 0.00 0.00 2.57
723 788 7.284518 TCGCCGAAAATTCCAAAATAAATTC 57.715 32.000 0.00 0.00 0.00 2.17
724 789 7.841915 ATCGCCGAAAATTCCAAAATAAATT 57.158 28.000 0.00 0.00 0.00 1.82
725 790 8.977505 CATATCGCCGAAAATTCCAAAATAAAT 58.022 29.630 0.00 0.00 0.00 1.40
726 791 7.043059 GCATATCGCCGAAAATTCCAAAATAAA 60.043 33.333 0.00 0.00 32.94 1.40
727 792 6.419413 GCATATCGCCGAAAATTCCAAAATAA 59.581 34.615 0.00 0.00 32.94 1.40
728 793 5.918011 GCATATCGCCGAAAATTCCAAAATA 59.082 36.000 0.00 0.00 32.94 1.40
729 794 4.744631 GCATATCGCCGAAAATTCCAAAAT 59.255 37.500 0.00 0.00 32.94 1.82
730 795 4.109050 GCATATCGCCGAAAATTCCAAAA 58.891 39.130 0.00 0.00 32.94 2.44
731 796 3.380004 AGCATATCGCCGAAAATTCCAAA 59.620 39.130 0.00 0.00 44.04 3.28
732 797 2.948979 AGCATATCGCCGAAAATTCCAA 59.051 40.909 0.00 0.00 44.04 3.53
733 798 2.571212 AGCATATCGCCGAAAATTCCA 58.429 42.857 0.00 0.00 44.04 3.53
734 799 3.626028 AAGCATATCGCCGAAAATTCC 57.374 42.857 0.00 0.00 44.04 3.01
735 800 4.597079 TGAAAGCATATCGCCGAAAATTC 58.403 39.130 0.00 0.00 44.04 2.17
736 801 4.096382 ACTGAAAGCATATCGCCGAAAATT 59.904 37.500 0.00 0.00 44.04 1.82
737 802 3.627577 ACTGAAAGCATATCGCCGAAAAT 59.372 39.130 0.00 0.00 44.04 1.82
738 803 3.006940 ACTGAAAGCATATCGCCGAAAA 58.993 40.909 0.00 0.00 44.04 2.29
739 804 2.627945 ACTGAAAGCATATCGCCGAAA 58.372 42.857 0.00 0.00 44.04 3.46
740 805 2.309528 ACTGAAAGCATATCGCCGAA 57.690 45.000 0.00 0.00 44.04 4.30
741 806 1.933181 CAACTGAAAGCATATCGCCGA 59.067 47.619 0.00 0.00 44.04 5.54
742 807 1.003545 CCAACTGAAAGCATATCGCCG 60.004 52.381 0.00 0.00 44.04 6.46
743 808 2.288666 TCCAACTGAAAGCATATCGCC 58.711 47.619 0.00 0.00 44.04 5.54
744 809 2.289002 CCTCCAACTGAAAGCATATCGC 59.711 50.000 0.00 0.00 37.60 4.58
745 810 3.797039 TCCTCCAACTGAAAGCATATCG 58.203 45.455 0.00 0.00 37.60 2.92
746 811 4.813697 GTCTCCTCCAACTGAAAGCATATC 59.186 45.833 0.00 0.00 37.60 1.63
747 812 4.681781 CGTCTCCTCCAACTGAAAGCATAT 60.682 45.833 0.00 0.00 37.60 1.78
748 813 3.368427 CGTCTCCTCCAACTGAAAGCATA 60.368 47.826 0.00 0.00 37.60 3.14
749 814 2.613977 CGTCTCCTCCAACTGAAAGCAT 60.614 50.000 0.00 0.00 37.60 3.79
750 815 1.270305 CGTCTCCTCCAACTGAAAGCA 60.270 52.381 0.00 0.00 37.60 3.91
751 816 1.270358 ACGTCTCCTCCAACTGAAAGC 60.270 52.381 0.00 0.00 37.60 3.51
752 817 2.821991 ACGTCTCCTCCAACTGAAAG 57.178 50.000 0.00 0.00 42.29 2.62
753 818 2.698797 AGAACGTCTCCTCCAACTGAAA 59.301 45.455 0.00 0.00 0.00 2.69
754 819 2.296471 GAGAACGTCTCCTCCAACTGAA 59.704 50.000 0.00 0.00 37.55 3.02
755 820 1.887198 GAGAACGTCTCCTCCAACTGA 59.113 52.381 0.00 0.00 37.55 3.41
756 821 1.401670 CGAGAACGTCTCCTCCAACTG 60.402 57.143 8.73 0.00 40.34 3.16
757 822 0.882474 CGAGAACGTCTCCTCCAACT 59.118 55.000 8.73 0.00 40.34 3.16
758 823 3.403276 CGAGAACGTCTCCTCCAAC 57.597 57.895 8.73 0.00 40.34 3.77
776 841 2.789203 GCATTGCCTCGTCGTCGAC 61.789 63.158 15.51 15.51 41.35 4.20
777 842 1.650314 TAGCATTGCCTCGTCGTCGA 61.650 55.000 4.70 4.42 44.12 4.20
778 843 0.800683 TTAGCATTGCCTCGTCGTCG 60.801 55.000 4.70 0.00 38.55 5.12
779 844 1.355971 TTTAGCATTGCCTCGTCGTC 58.644 50.000 4.70 0.00 0.00 4.20
780 845 1.803334 TTTTAGCATTGCCTCGTCGT 58.197 45.000 4.70 0.00 0.00 4.34
781 846 2.892373 TTTTTAGCATTGCCTCGTCG 57.108 45.000 4.70 0.00 0.00 5.12
798 863 2.338257 CGTGCGCCATGGGTTTTT 59.662 55.556 15.13 0.00 0.00 1.94
799 864 4.356442 GCGTGCGCCATGGGTTTT 62.356 61.111 15.13 0.00 34.56 2.43
855 920 1.080298 GTCACGGGTGAGGGTTACG 60.080 63.158 0.94 0.00 40.75 3.18
858 923 4.309950 GCGTCACGGGTGAGGGTT 62.310 66.667 19.45 0.00 43.45 4.11
920 985 2.716017 GGGAGGAGAGCGAGGTGTG 61.716 68.421 0.00 0.00 0.00 3.82
982 1050 4.200283 GGCGTGGAGAGCGGAGAG 62.200 72.222 0.00 0.00 35.00 3.20
984 1052 3.842923 ATGGCGTGGAGAGCGGAG 61.843 66.667 0.00 0.00 35.00 4.63
985 1053 4.147449 CATGGCGTGGAGAGCGGA 62.147 66.667 0.00 0.00 35.00 5.54
1081 1149 4.116328 CTTCTCTGCCGACGCCGA 62.116 66.667 0.00 0.00 38.22 5.54
1445 1513 0.109226 CGAACCCTCCGACTCTTCAC 60.109 60.000 0.00 0.00 0.00 3.18
1601 1669 4.454728 AACAAACATCAATTCCCCATCG 57.545 40.909 0.00 0.00 0.00 3.84
1673 1741 3.624777 CTTAAGGACAATGATGCACCCT 58.375 45.455 0.00 0.00 0.00 4.34
1752 1820 9.836076 CATTGCTATGAATATTCATTGGTACAG 57.164 33.333 30.60 22.08 45.13 2.74
1804 1872 3.651562 AACGAGAACAAAGTCAACACG 57.348 42.857 0.00 0.00 0.00 4.49
1812 1880 3.853307 GCACCATCCAAACGAGAACAAAG 60.853 47.826 0.00 0.00 0.00 2.77
1828 1896 2.485677 GCACATACTGCTGCACCAT 58.514 52.632 0.00 0.00 43.33 3.55
1850 1918 5.235305 AGTGCATAAGGTAAAAATGAGCG 57.765 39.130 0.00 0.00 0.00 5.03
1852 1920 7.029563 GTCCAAGTGCATAAGGTAAAAATGAG 58.970 38.462 0.00 0.00 0.00 2.90
1853 1921 6.719370 AGTCCAAGTGCATAAGGTAAAAATGA 59.281 34.615 0.00 0.00 0.00 2.57
1860 1928 2.676750 CGCAGTCCAAGTGCATAAGGTA 60.677 50.000 7.47 0.00 44.55 3.08
1877 1945 4.715527 ACCTACCTAAGAACTAACGCAG 57.284 45.455 0.00 0.00 0.00 5.18
1930 1998 5.041940 AGACGTTTTAGAGACTTGTGTCAC 58.958 41.667 0.00 0.00 45.20 3.67
1931 1999 5.258456 AGACGTTTTAGAGACTTGTGTCA 57.742 39.130 0.00 0.00 45.20 3.58
1932 2000 7.870588 ATAAGACGTTTTAGAGACTTGTGTC 57.129 36.000 4.75 0.00 43.22 3.67
1933 2001 9.924650 AATATAAGACGTTTTAGAGACTTGTGT 57.075 29.630 4.75 0.00 0.00 3.72
2009 2077 9.762381 TTTCAACCCAAAATAGATGGTACTTAT 57.238 29.630 0.00 0.00 36.14 1.73
2012 2080 8.664669 ATTTTCAACCCAAAATAGATGGTACT 57.335 30.769 0.00 0.00 34.77 2.73
2055 2123 7.228590 ACTATGAGTGTGGCCTTTTACTTTTA 58.771 34.615 3.32 0.00 0.00 1.52
2056 2124 6.068670 ACTATGAGTGTGGCCTTTTACTTTT 58.931 36.000 3.32 0.00 0.00 2.27
2057 2125 5.631119 ACTATGAGTGTGGCCTTTTACTTT 58.369 37.500 3.32 0.00 0.00 2.66
2058 2126 5.242795 ACTATGAGTGTGGCCTTTTACTT 57.757 39.130 3.32 0.00 0.00 2.24
2059 2127 4.910458 ACTATGAGTGTGGCCTTTTACT 57.090 40.909 3.32 2.62 0.00 2.24
2060 2128 5.959618 AAACTATGAGTGTGGCCTTTTAC 57.040 39.130 3.32 0.00 0.00 2.01
2137 2206 1.424638 ATTATGGGACGGAGGGAGTG 58.575 55.000 0.00 0.00 0.00 3.51
2138 2207 3.562108 ATATTATGGGACGGAGGGAGT 57.438 47.619 0.00 0.00 0.00 3.85
2139 2208 5.269991 TCTTATATTATGGGACGGAGGGAG 58.730 45.833 0.00 0.00 0.00 4.30
2140 2209 5.269991 CTCTTATATTATGGGACGGAGGGA 58.730 45.833 0.00 0.00 0.00 4.20
2141 2210 4.141914 GCTCTTATATTATGGGACGGAGGG 60.142 50.000 0.00 0.00 0.00 4.30
2142 2211 4.440250 CGCTCTTATATTATGGGACGGAGG 60.440 50.000 0.00 0.00 0.00 4.30
2143 2212 4.158025 ACGCTCTTATATTATGGGACGGAG 59.842 45.833 0.00 0.00 0.00 4.63
2144 2213 4.084287 ACGCTCTTATATTATGGGACGGA 58.916 43.478 0.00 0.00 0.00 4.69
2145 2214 4.451629 ACGCTCTTATATTATGGGACGG 57.548 45.455 0.00 0.00 0.00 4.79
2146 2215 6.780706 AAAACGCTCTTATATTATGGGACG 57.219 37.500 0.00 0.00 0.00 4.79
2147 2216 8.068380 GTCAAAAACGCTCTTATATTATGGGAC 58.932 37.037 0.00 0.00 0.00 4.46
2148 2217 7.771361 TGTCAAAAACGCTCTTATATTATGGGA 59.229 33.333 0.00 0.00 0.00 4.37
2149 2218 7.855904 GTGTCAAAAACGCTCTTATATTATGGG 59.144 37.037 0.00 0.00 35.42 4.00
2150 2219 8.612619 AGTGTCAAAAACGCTCTTATATTATGG 58.387 33.333 0.00 0.00 45.69 2.74
2153 2222 9.642327 TGTAGTGTCAAAAACGCTCTTATATTA 57.358 29.630 0.00 0.00 45.69 0.98
2154 2223 8.542497 TGTAGTGTCAAAAACGCTCTTATATT 57.458 30.769 0.00 0.00 45.69 1.28
2155 2224 7.277981 CCTGTAGTGTCAAAAACGCTCTTATAT 59.722 37.037 0.00 0.00 45.69 0.86
2156 2225 6.588756 CCTGTAGTGTCAAAAACGCTCTTATA 59.411 38.462 0.00 0.00 45.69 0.98
2157 2226 5.408604 CCTGTAGTGTCAAAAACGCTCTTAT 59.591 40.000 0.00 0.00 45.69 1.73
2158 2227 4.748102 CCTGTAGTGTCAAAAACGCTCTTA 59.252 41.667 0.00 0.00 45.69 2.10
2159 2228 3.560068 CCTGTAGTGTCAAAAACGCTCTT 59.440 43.478 0.00 0.00 45.69 2.85
2160 2229 3.131396 CCTGTAGTGTCAAAAACGCTCT 58.869 45.455 0.00 0.00 45.69 4.09
2161 2230 2.223377 CCCTGTAGTGTCAAAAACGCTC 59.777 50.000 0.00 0.00 45.69 5.03
2163 2232 2.215196 TCCCTGTAGTGTCAAAAACGC 58.785 47.619 0.00 0.00 38.74 4.84
2164 2233 3.463944 ACTCCCTGTAGTGTCAAAAACG 58.536 45.455 0.00 0.00 0.00 3.60
2165 2234 5.362263 TGTACTCCCTGTAGTGTCAAAAAC 58.638 41.667 0.00 0.00 0.00 2.43
2166 2235 5.617528 TGTACTCCCTGTAGTGTCAAAAA 57.382 39.130 0.00 0.00 0.00 1.94
2167 2236 5.617528 TTGTACTCCCTGTAGTGTCAAAA 57.382 39.130 0.00 0.00 0.00 2.44
2168 2237 5.818678 ATTGTACTCCCTGTAGTGTCAAA 57.181 39.130 0.00 0.00 32.61 2.69
2169 2238 6.250711 TCTATTGTACTCCCTGTAGTGTCAA 58.749 40.000 0.00 0.00 33.03 3.18
2170 2239 5.823312 TCTATTGTACTCCCTGTAGTGTCA 58.177 41.667 0.00 0.00 0.00 3.58
2171 2240 6.546403 TGATCTATTGTACTCCCTGTAGTGTC 59.454 42.308 0.00 0.00 0.00 3.67
2172 2241 6.432581 TGATCTATTGTACTCCCTGTAGTGT 58.567 40.000 0.00 0.00 0.00 3.55
2173 2242 6.961360 TGATCTATTGTACTCCCTGTAGTG 57.039 41.667 0.00 0.00 0.00 2.74
2174 2243 7.785028 TCATTGATCTATTGTACTCCCTGTAGT 59.215 37.037 0.00 0.00 0.00 2.73
2175 2244 8.183104 TCATTGATCTATTGTACTCCCTGTAG 57.817 38.462 0.00 0.00 0.00 2.74
2176 2245 8.727100 ATCATTGATCTATTGTACTCCCTGTA 57.273 34.615 0.00 0.00 0.00 2.74
2177 2246 7.623999 ATCATTGATCTATTGTACTCCCTGT 57.376 36.000 0.00 0.00 0.00 4.00
2178 2247 8.811017 ACTATCATTGATCTATTGTACTCCCTG 58.189 37.037 1.55 0.00 0.00 4.45
2179 2248 8.964533 ACTATCATTGATCTATTGTACTCCCT 57.035 34.615 1.55 0.00 0.00 4.20
2180 2249 8.807118 TGACTATCATTGATCTATTGTACTCCC 58.193 37.037 1.55 0.00 0.00 4.30
2236 2305 3.784338 AGTTGTTGTCTTGGTTGCAATG 58.216 40.909 0.59 0.00 0.00 2.82
2237 2306 5.105554 TGTTAGTTGTTGTCTTGGTTGCAAT 60.106 36.000 0.59 0.00 0.00 3.56
2243 2312 7.988599 TGTTACTATGTTAGTTGTTGTCTTGGT 59.011 33.333 0.00 0.00 40.14 3.67
2248 2317 7.744715 GTGCATGTTACTATGTTAGTTGTTGTC 59.255 37.037 0.00 0.00 40.14 3.18
2272 2341 3.762288 TGGAGTGCCAACTACTAGTAGTG 59.238 47.826 31.26 23.76 44.96 2.74
2357 2426 6.431198 TGACCGACTAAATTAAAATGGCTC 57.569 37.500 0.00 0.00 0.00 4.70
2360 2429 7.535139 ACACATGACCGACTAAATTAAAATGG 58.465 34.615 0.00 0.00 0.00 3.16
2375 2444 1.935873 CCATCTAGCAACACATGACCG 59.064 52.381 0.00 0.00 0.00 4.79
2395 2464 5.959618 AGTATTTGGTAAACTGCACTTCC 57.040 39.130 0.00 0.00 0.00 3.46


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

AutoCloner maintained by Alex Coulton.