Multiple sequence alignment - TraesCS7D01G391400

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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 TraesCS7D01G391400 chr7D 100.000 5493 0 0 1 5493 506674060 506679552 0.000000e+00 10144.0
1 TraesCS7D01G391400 chr7D 85.352 908 99 10 2539 3415 515397459 515396555 0.000000e+00 909.0
2 TraesCS7D01G391400 chr7D 83.716 958 126 13 2483 3415 477655543 477656495 0.000000e+00 878.0
3 TraesCS7D01G391400 chr7D 95.098 102 2 2 5373 5474 604292591 604292689 2.050000e-34 158.0
4 TraesCS7D01G391400 chr7D 91.525 59 5 0 3740 3798 283343784 283343842 1.270000e-11 82.4
5 TraesCS7D01G391400 chr7B 89.030 1732 108 45 813 2487 535241297 535243003 0.000000e+00 2071.0
6 TraesCS7D01G391400 chr7B 93.854 960 41 5 4107 5058 535243001 535243950 0.000000e+00 1430.0
7 TraesCS7D01G391400 chr7B 90.965 808 65 4 6 811 659253982 659253181 0.000000e+00 1081.0
8 TraesCS7D01G391400 chr7B 93.103 580 14 2 4220 4799 535246274 535246827 0.000000e+00 826.0
9 TraesCS7D01G391400 chr7B 94.175 412 22 2 4967 5378 535253206 535253615 1.300000e-175 627.0
10 TraesCS7D01G391400 chr7B 88.922 334 31 6 5045 5376 535245306 535245635 1.840000e-109 407.0
11 TraesCS7D01G391400 chr7B 97.541 122 3 0 4851 4972 535250115 535250236 5.580000e-50 209.0
12 TraesCS7D01G391400 chr7B 97.403 77 2 0 4107 4183 535246196 535246272 1.240000e-26 132.0
13 TraesCS7D01G391400 chr7B 98.305 59 1 0 4795 4853 535249934 535249992 2.710000e-18 104.0
14 TraesCS7D01G391400 chr7A 92.522 1150 51 12 815 1934 574097468 574098612 0.000000e+00 1615.0
15 TraesCS7D01G391400 chr7A 91.842 809 60 5 1 808 519167485 519168288 0.000000e+00 1123.0
16 TraesCS7D01G391400 chr7A 94.636 522 28 0 1926 2447 574109066 574109587 0.000000e+00 809.0
17 TraesCS7D01G391400 chr7A 82.633 904 136 17 2517 3408 531102477 531103371 0.000000e+00 780.0
18 TraesCS7D01G391400 chr7A 83.811 593 60 11 4095 4684 574109617 574110176 1.050000e-146 531.0
19 TraesCS7D01G391400 chr7A 90.674 193 14 2 4804 4994 574110300 574110490 2.540000e-63 254.0
20 TraesCS7D01G391400 chr7A 90.909 88 8 0 4706 4793 574110173 574110260 9.670000e-23 119.0
21 TraesCS7D01G391400 chr2D 94.957 813 39 2 1 811 143235177 143234365 0.000000e+00 1273.0
22 TraesCS7D01G391400 chr2D 82.919 966 121 27 2484 3415 512907804 512908759 0.000000e+00 830.0
23 TraesCS7D01G391400 chr2D 84.783 828 109 13 2594 3415 111499664 111500480 0.000000e+00 815.0
24 TraesCS7D01G391400 chr2D 78.551 704 123 22 3427 4109 95181962 95182658 6.530000e-119 438.0
25 TraesCS7D01G391400 chr2D 95.192 104 3 1 5372 5475 83966681 83966782 4.400000e-36 163.0
26 TraesCS7D01G391400 chr2D 81.395 172 30 2 3940 4110 555934432 555934262 7.420000e-29 139.0
27 TraesCS7D01G391400 chr6D 93.086 810 51 3 1 808 445691372 445690566 0.000000e+00 1181.0
28 TraesCS7D01G391400 chr6D 85.714 140 15 4 5353 5487 410399820 410399959 5.740000e-30 143.0
29 TraesCS7D01G391400 chr6D 79.787 94 10 6 3837 3922 399695604 399695696 5.940000e-05 60.2
30 TraesCS7D01G391400 chr5D 92.822 808 53 3 1 806 84673151 84673955 0.000000e+00 1166.0
31 TraesCS7D01G391400 chr5D 92.469 810 56 3 1 808 305584927 305584121 0.000000e+00 1153.0
32 TraesCS7D01G391400 chr5D 82.460 935 139 11 2504 3415 352845994 352845062 0.000000e+00 795.0
33 TraesCS7D01G391400 chr5D 80.126 634 98 23 3425 4037 341684865 341685491 1.090000e-121 448.0
34 TraesCS7D01G391400 chr5D 89.655 116 6 2 5360 5474 134780489 134780599 5.740000e-30 143.0
35 TraesCS7D01G391400 chr5D 90.654 107 7 3 5371 5477 24356330 24356433 7.420000e-29 139.0
36 TraesCS7D01G391400 chr5D 91.176 102 8 1 1031 1131 379387300 379387199 2.670000e-28 137.0
37 TraesCS7D01G391400 chr5D 90.099 101 10 0 1035 1135 378956658 378956758 1.240000e-26 132.0
38 TraesCS7D01G391400 chr3D 92.383 814 49 8 1 811 603585279 603584476 0.000000e+00 1147.0
39 TraesCS7D01G391400 chr3D 90.965 819 60 4 1 808 508430253 508431068 0.000000e+00 1090.0
40 TraesCS7D01G391400 chr3D 81.923 697 101 19 3424 4103 302226121 302226809 2.870000e-157 566.0
41 TraesCS7D01G391400 chr3D 80.250 719 116 11 3424 4123 96444361 96443650 8.160000e-143 518.0
42 TraesCS7D01G391400 chr3D 78.042 674 116 21 3452 4107 170077556 170078215 3.990000e-106 396.0
43 TraesCS7D01G391400 chr3D 82.703 370 61 2 3739 4106 160632039 160632407 5.310000e-85 326.0
44 TraesCS7D01G391400 chr3D 86.802 197 20 6 2485 2680 398414155 398414346 1.200000e-51 215.0
45 TraesCS7D01G391400 chr3D 75.503 298 60 12 3742 4035 420307450 420307162 3.450000e-27 134.0
46 TraesCS7D01G391400 chr3D 78.698 169 28 5 3946 4108 516849147 516849313 7.530000e-19 106.0
47 TraesCS7D01G391400 chr3D 89.474 57 5 1 3744 3799 558880140 558880196 2.750000e-08 71.3
48 TraesCS7D01G391400 chr2A 91.320 818 59 6 1 812 12583401 12582590 0.000000e+00 1107.0
49 TraesCS7D01G391400 chr2A 95.000 100 4 1 5375 5474 746253397 746253495 7.370000e-34 156.0
50 TraesCS7D01G391400 chr2A 90.566 106 8 2 5369 5474 746253500 746253397 7.420000e-29 139.0
51 TraesCS7D01G391400 chr4B 84.153 915 133 8 2510 3415 491091314 491090403 0.000000e+00 876.0
52 TraesCS7D01G391400 chr4B 80.828 459 74 7 3424 3874 135205984 135205532 1.130000e-91 348.0
53 TraesCS7D01G391400 chr4B 84.722 216 27 5 2482 2694 416545018 416545230 1.550000e-50 211.0
54 TraesCS7D01G391400 chr4B 93.069 101 5 1 5374 5474 11736927 11736829 4.430000e-31 147.0
55 TraesCS7D01G391400 chr4B 92.157 102 7 1 5374 5475 544445277 544445377 5.740000e-30 143.0
56 TraesCS7D01G391400 chr4D 84.424 886 106 10 2554 3415 95776726 95775849 0.000000e+00 843.0
57 TraesCS7D01G391400 chr4D 79.349 707 116 16 3425 4105 57470634 57471336 2.320000e-128 470.0
58 TraesCS7D01G391400 chr4D 78.551 690 115 16 3426 4108 95775754 95775091 1.830000e-114 424.0
59 TraesCS7D01G391400 chr4D 86.383 235 26 6 3900 4133 303845847 303845618 9.130000e-63 252.0
60 TraesCS7D01G391400 chr4D 79.109 359 65 9 3750 4104 343063046 343063398 7.110000e-59 239.0
61 TraesCS7D01G391400 chr4D 86.449 214 24 5 2482 2692 337426006 337426217 4.280000e-56 230.0
62 TraesCS7D01G391400 chr6B 81.789 950 150 17 2482 3415 462176483 462177425 0.000000e+00 774.0
63 TraesCS7D01G391400 chr6A 77.904 706 122 26 3426 4109 186523578 186522885 5.120000e-110 409.0
64 TraesCS7D01G391400 chr1A 81.310 519 81 6 3418 3929 280504728 280505237 1.840000e-109 407.0
65 TraesCS7D01G391400 chr1A 92.473 93 7 0 1039 1131 586720493 586720401 3.450000e-27 134.0
66 TraesCS7D01G391400 chr1D 78.549 648 103 25 3424 4053 109785769 109786398 1.430000e-105 394.0
67 TraesCS7D01G391400 chr1D 87.895 190 20 3 2485 2672 221023616 221023428 2.580000e-53 220.0
68 TraesCS7D01G391400 chr1D 81.221 213 34 6 3896 4106 25363468 25363676 3.400000e-37 167.0
69 TraesCS7D01G391400 chr5A 78.756 579 105 15 3426 3990 677669278 677668704 6.720000e-99 372.0
70 TraesCS7D01G391400 chr5A 88.235 119 12 2 1014 1131 479397649 479397532 2.060000e-29 141.0
71 TraesCS7D01G391400 chr5A 91.176 102 8 1 1031 1131 480089986 480089885 2.670000e-28 137.0
72 TraesCS7D01G391400 chr3B 88.835 206 19 4 2487 2689 703030088 703030292 3.290000e-62 250.0
73 TraesCS7D01G391400 chr3B 87.000 100 12 1 4010 4109 411290191 411290093 1.620000e-20 111.0
74 TraesCS7D01G391400 chr5B 92.473 93 7 0 1039 1131 455147775 455147683 3.450000e-27 134.0
75 TraesCS7D01G391400 chr5B 90.196 102 9 1 1031 1131 455294736 455294635 1.240000e-26 132.0
76 TraesCS7D01G391400 chr3A 89.655 58 6 0 3742 3799 706435701 706435758 2.120000e-09 75.0
77 TraesCS7D01G391400 chr3A 94.444 36 2 0 3841 3876 247360817 247360782 7.690000e-04 56.5
78 TraesCS7D01G391400 chr2B 94.444 36 2 0 3841 3876 765158775 765158740 7.690000e-04 56.5


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 TraesCS7D01G391400 chr7D 506674060 506679552 5492 False 10144.00 10144 100.000000 1 5493 1 chr7D.!!$F3 5492
1 TraesCS7D01G391400 chr7D 515396555 515397459 904 True 909.00 909 85.352000 2539 3415 1 chr7D.!!$R1 876
2 TraesCS7D01G391400 chr7D 477655543 477656495 952 False 878.00 878 83.716000 2483 3415 1 chr7D.!!$F2 932
3 TraesCS7D01G391400 chr7B 659253181 659253982 801 True 1081.00 1081 90.965000 6 811 1 chr7B.!!$R1 805
4 TraesCS7D01G391400 chr7B 535241297 535253615 12318 False 725.75 2071 94.041625 813 5378 8 chr7B.!!$F1 4565
5 TraesCS7D01G391400 chr7A 574097468 574098612 1144 False 1615.00 1615 92.522000 815 1934 1 chr7A.!!$F3 1119
6 TraesCS7D01G391400 chr7A 519167485 519168288 803 False 1123.00 1123 91.842000 1 808 1 chr7A.!!$F1 807
7 TraesCS7D01G391400 chr7A 531102477 531103371 894 False 780.00 780 82.633000 2517 3408 1 chr7A.!!$F2 891
8 TraesCS7D01G391400 chr7A 574109066 574110490 1424 False 428.25 809 90.007500 1926 4994 4 chr7A.!!$F4 3068
9 TraesCS7D01G391400 chr2D 143234365 143235177 812 True 1273.00 1273 94.957000 1 811 1 chr2D.!!$R1 810
10 TraesCS7D01G391400 chr2D 512907804 512908759 955 False 830.00 830 82.919000 2484 3415 1 chr2D.!!$F4 931
11 TraesCS7D01G391400 chr2D 111499664 111500480 816 False 815.00 815 84.783000 2594 3415 1 chr2D.!!$F3 821
12 TraesCS7D01G391400 chr2D 95181962 95182658 696 False 438.00 438 78.551000 3427 4109 1 chr2D.!!$F2 682
13 TraesCS7D01G391400 chr6D 445690566 445691372 806 True 1181.00 1181 93.086000 1 808 1 chr6D.!!$R1 807
14 TraesCS7D01G391400 chr5D 84673151 84673955 804 False 1166.00 1166 92.822000 1 806 1 chr5D.!!$F2 805
15 TraesCS7D01G391400 chr5D 305584121 305584927 806 True 1153.00 1153 92.469000 1 808 1 chr5D.!!$R1 807
16 TraesCS7D01G391400 chr5D 352845062 352845994 932 True 795.00 795 82.460000 2504 3415 1 chr5D.!!$R2 911
17 TraesCS7D01G391400 chr5D 341684865 341685491 626 False 448.00 448 80.126000 3425 4037 1 chr5D.!!$F4 612
18 TraesCS7D01G391400 chr3D 603584476 603585279 803 True 1147.00 1147 92.383000 1 811 1 chr3D.!!$R3 810
19 TraesCS7D01G391400 chr3D 508430253 508431068 815 False 1090.00 1090 90.965000 1 808 1 chr3D.!!$F5 807
20 TraesCS7D01G391400 chr3D 302226121 302226809 688 False 566.00 566 81.923000 3424 4103 1 chr3D.!!$F3 679
21 TraesCS7D01G391400 chr3D 96443650 96444361 711 True 518.00 518 80.250000 3424 4123 1 chr3D.!!$R1 699
22 TraesCS7D01G391400 chr3D 170077556 170078215 659 False 396.00 396 78.042000 3452 4107 1 chr3D.!!$F2 655
23 TraesCS7D01G391400 chr2A 12582590 12583401 811 True 1107.00 1107 91.320000 1 812 1 chr2A.!!$R1 811
24 TraesCS7D01G391400 chr4B 491090403 491091314 911 True 876.00 876 84.153000 2510 3415 1 chr4B.!!$R3 905
25 TraesCS7D01G391400 chr4D 95775091 95776726 1635 True 633.50 843 81.487500 2554 4108 2 chr4D.!!$R2 1554
26 TraesCS7D01G391400 chr4D 57470634 57471336 702 False 470.00 470 79.349000 3425 4105 1 chr4D.!!$F1 680
27 TraesCS7D01G391400 chr6B 462176483 462177425 942 False 774.00 774 81.789000 2482 3415 1 chr6B.!!$F1 933
28 TraesCS7D01G391400 chr6A 186522885 186523578 693 True 409.00 409 77.904000 3426 4109 1 chr6A.!!$R1 683
29 TraesCS7D01G391400 chr1A 280504728 280505237 509 False 407.00 407 81.310000 3418 3929 1 chr1A.!!$F1 511
30 TraesCS7D01G391400 chr1D 109785769 109786398 629 False 394.00 394 78.549000 3424 4053 1 chr1D.!!$F2 629
31 TraesCS7D01G391400 chr5A 677668704 677669278 574 True 372.00 372 78.756000 3426 3990 1 chr5A.!!$R3 564

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
808 827 0.101579 GGTCCGCTAGAGTTGCTCTC 59.898 60.0 1.54 2.14 40.34 3.20 F
811 830 0.527385 CCGCTAGAGTTGCTCTCAGC 60.527 60.0 1.54 13.77 44.98 4.26 F
2764 2916 0.176449 CGTGTCATCCTCCATCTGCA 59.824 55.0 0.00 0.00 0.00 4.41 F
3054 3208 0.030369 CGTCCACGATACCTGTAGCC 59.970 60.0 0.00 0.00 43.02 3.93 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2764 2916 0.744414 CGCCGGTGGTCATGAAGATT 60.744 55.000 7.26 0.00 0.00 2.40 R
2775 2927 2.279252 CGGTCTTATCGCCGGTGG 60.279 66.667 16.49 1.03 43.85 4.61 R
4351 4685 1.341080 CTTGGACAACCCTGCCATTT 58.659 50.000 0.00 0.00 35.38 2.32 R
4542 4876 4.058124 GCTCATTATCGGCACAGTAATCA 58.942 43.478 0.00 0.00 0.00 2.57 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
186 187 1.874345 GCTCGTTCCGGTGAAGAGGA 61.874 60.000 18.81 6.34 31.72 3.71
240 241 4.545706 GATGCGTCATCGGGCCCA 62.546 66.667 24.92 9.77 37.56 5.36
537 548 4.499696 GCTCAATTTTGTTGTAGTGGTGCT 60.500 41.667 0.00 0.00 0.00 4.40
567 578 1.969923 GCCCTGTCTAGCATCTCTGAT 59.030 52.381 0.00 0.00 0.00 2.90
618 632 7.772332 ACGAACTTATTATGCGAAGAAGAAT 57.228 32.000 11.29 1.98 0.00 2.40
676 690 0.231279 TTTCTCGCGCGAAACAACTC 59.769 50.000 33.99 0.00 0.00 3.01
731 749 1.372748 CTGCCGCCGCAATTTTCAA 60.373 52.632 0.47 0.00 46.66 2.69
793 812 4.128388 CGGCAAAATGCGGGGTCC 62.128 66.667 2.33 0.00 46.21 4.46
808 827 0.101579 GGTCCGCTAGAGTTGCTCTC 59.898 60.000 1.54 2.14 40.34 3.20
811 830 0.527385 CCGCTAGAGTTGCTCTCAGC 60.527 60.000 1.54 13.77 44.98 4.26
915 937 2.173669 CGTGCTCCAATAGTGGGCG 61.174 63.158 9.77 5.77 46.01 6.13
941 967 1.280746 CGCGCCATCAAATAGCTGG 59.719 57.895 0.00 0.00 36.57 4.85
985 1011 1.079543 CCTGCGACACTCTTCCCTG 60.080 63.158 0.00 0.00 0.00 4.45
1030 1059 4.157958 GGAGGACGACGACGACGG 62.158 72.222 22.36 6.21 44.46 4.79
1031 1060 4.808238 GAGGACGACGACGACGGC 62.808 72.222 22.36 19.95 45.02 5.68
1145 1184 2.210341 GACCCCGGTGAGTTCTCGAC 62.210 65.000 0.00 0.00 0.00 4.20
1412 1453 1.362584 CCCCTTTCCCATTTCCCTCTT 59.637 52.381 0.00 0.00 0.00 2.85
1456 1497 1.560611 TCAATAAACGGGTACAGGGGG 59.439 52.381 0.00 0.00 0.00 5.40
1458 1499 1.969713 ATAAACGGGTACAGGGGGAA 58.030 50.000 0.00 0.00 0.00 3.97
1459 1500 0.983467 TAAACGGGTACAGGGGGAAC 59.017 55.000 0.00 0.00 0.00 3.62
1460 1501 1.061324 AAACGGGTACAGGGGGAACA 61.061 55.000 0.00 0.00 0.00 3.18
1461 1502 1.771783 AACGGGTACAGGGGGAACAC 61.772 60.000 0.00 0.00 0.00 3.32
1462 1503 2.666812 GGGTACAGGGGGAACACG 59.333 66.667 0.00 0.00 40.46 4.49
1512 1553 1.065199 CCTCCATGTTTCTGCAGGCTA 60.065 52.381 15.13 0.00 0.00 3.93
1520 1561 7.559533 TCCATGTTTCTGCAGGCTAATTTAATA 59.440 33.333 15.13 0.00 0.00 0.98
1571 1612 0.607489 TGAAAGCTTGCTCTGAGGCC 60.607 55.000 5.89 0.00 0.00 5.19
1610 1651 2.049063 GTGTCTTCCGTCGCTGCT 60.049 61.111 0.00 0.00 0.00 4.24
1739 1796 5.379827 CGAGTCATGATCGTAGCGTAATTA 58.620 41.667 15.20 0.00 35.48 1.40
1740 1797 5.849604 CGAGTCATGATCGTAGCGTAATTAA 59.150 40.000 15.20 0.00 35.48 1.40
1743 1800 8.589335 AGTCATGATCGTAGCGTAATTAATTT 57.411 30.769 5.91 0.00 0.00 1.82
1744 1801 9.042008 AGTCATGATCGTAGCGTAATTAATTTT 57.958 29.630 5.91 0.00 0.00 1.82
1745 1802 9.646336 GTCATGATCGTAGCGTAATTAATTTTT 57.354 29.630 5.91 0.00 0.00 1.94
1803 1889 4.631813 GTGCTAGAAAGTGTACAGGGATTG 59.368 45.833 0.00 0.00 0.00 2.67
1859 1945 5.215160 GCGTTTCAAACATCATTTCAGTCT 58.785 37.500 0.22 0.00 0.00 3.24
2068 2155 2.431601 GTGAACGCGAGCAGCTCT 60.432 61.111 20.39 0.72 45.59 4.09
2106 2193 2.875933 TGAAAGGTTACCTCACTTTGCG 59.124 45.455 3.62 0.00 34.82 4.85
2129 2216 5.506483 CGACACCGATCTGAAATAGTCATCT 60.506 44.000 0.00 0.00 34.85 2.90
2136 2223 6.293680 CGATCTGAAATAGTCATCTCCGAAGA 60.294 42.308 0.00 0.00 35.07 2.87
2206 2293 7.716998 ACCTGCTTCAGACATTAGTATATTTGG 59.283 37.037 0.00 0.00 32.44 3.28
2240 2327 0.969917 TCCTCTGACTCTCTGCAGGC 60.970 60.000 15.13 0.00 33.05 4.85
2261 2348 4.212214 GGCGATAATGAGGTAAAGAGCAAG 59.788 45.833 0.00 0.00 0.00 4.01
2285 2372 2.157668 CAGAAACTTCGTGGATGTTCGG 59.842 50.000 0.00 0.00 30.49 4.30
2324 2411 2.483014 TCTTGGTGTATGAAACCCCG 57.517 50.000 0.00 0.00 36.83 5.73
2343 2430 1.542767 CGGAGGTCTCTGGACGCTATA 60.543 57.143 0.00 0.00 42.97 1.31
2394 2481 4.026052 TGATGTCATAGACCTGCTGAAGA 58.974 43.478 0.00 0.00 0.00 2.87
2435 2522 1.327303 TTGCCAACAAGTAAGCCTGG 58.673 50.000 0.00 0.00 0.00 4.45
2473 2562 7.272084 GCATATTCAGCCGCTTATAATTGAAAG 59.728 37.037 0.00 0.00 0.00 2.62
2480 2569 5.681543 GCCGCTTATAATTGAAAGTTAGTGC 59.318 40.000 0.00 0.00 0.00 4.40
2496 2585 3.039252 AGTGCTAGTTAGGGCATCTCT 57.961 47.619 0.00 0.00 40.66 3.10
2498 2588 4.148838 AGTGCTAGTTAGGGCATCTCTAG 58.851 47.826 6.29 6.29 40.66 2.43
2501 2591 3.500654 GCTAGTTAGGGCATCTCTAGGGA 60.501 52.174 0.00 0.00 31.72 4.20
2640 2741 3.569701 ACCAGATGAAATTCGTGCAAACT 59.430 39.130 0.00 0.00 0.00 2.66
2726 2878 1.332144 AAACCTATCCTACGGCGGCA 61.332 55.000 13.24 0.00 0.00 5.69
2764 2916 0.176449 CGTGTCATCCTCCATCTGCA 59.824 55.000 0.00 0.00 0.00 4.41
2775 2927 3.564644 CCTCCATCTGCAATCTTCATGAC 59.435 47.826 0.00 0.00 0.00 3.06
2839 2991 3.057736 CGAGAAAGAGTAGAACACGGGAA 60.058 47.826 0.00 0.00 0.00 3.97
2899 3051 1.101635 CGTGGCCTACTCATCCTCGA 61.102 60.000 3.32 0.00 38.65 4.04
3040 3193 1.300620 CTGGCGTTGTTCTCGTCCA 60.301 57.895 0.00 0.00 35.00 4.02
3054 3208 0.030369 CGTCCACGATACCTGTAGCC 59.970 60.000 0.00 0.00 43.02 3.93
3138 3292 3.793144 GCTGCTCCGCAACGAAGG 61.793 66.667 0.00 0.00 38.41 3.46
3189 3343 2.429236 CTTCGCTCACACGCTCGT 60.429 61.111 0.00 0.00 0.00 4.18
3236 3390 3.164024 TTGCTCCAGGAGGAACAGA 57.836 52.632 19.16 0.00 45.19 3.41
3247 3401 2.429610 GGAGGAACAGATTGTACCGCTA 59.570 50.000 0.00 0.00 0.00 4.26
3250 3404 5.099042 AGGAACAGATTGTACCGCTATTT 57.901 39.130 0.00 0.00 0.00 1.40
3321 3479 2.125310 CCATGGCGGCGTTGTAGA 60.125 61.111 9.37 0.00 0.00 2.59
3415 3575 1.029681 CTCCATCGTGGTATCGTCCA 58.970 55.000 4.33 0.00 39.03 4.02
3416 3576 1.001268 CTCCATCGTGGTATCGTCCAG 60.001 57.143 4.33 0.00 39.03 3.86
3421 3665 1.065928 GTGGTATCGTCCAGAGCCG 59.934 63.158 0.00 0.00 38.23 5.52
3422 3666 2.125326 TGGTATCGTCCAGAGCCGG 61.125 63.158 0.00 0.00 32.59 6.13
3475 3719 2.464459 ATAGCTTCGCCGCTTGCAC 61.464 57.895 0.00 0.00 41.30 4.57
3477 3721 2.220615 TAGCTTCGCCGCTTGCACTA 62.221 55.000 0.00 0.00 41.30 2.74
3490 3734 1.356624 GCACTAATGGCGGATGCAC 59.643 57.895 0.00 0.00 45.35 4.57
3543 3788 2.214216 TGCTGTGGAGTTAGCCGGT 61.214 57.895 1.90 0.00 39.15 5.28
3626 3871 1.898154 CCGGAGTGGGTTTCTCGAT 59.102 57.895 0.00 0.00 33.26 3.59
3633 3878 1.877165 GGGTTTCTCGATCGGCGAC 60.877 63.158 13.76 5.50 45.59 5.19
3643 3888 1.152383 GATCGGCGACCCTGCTTAAC 61.152 60.000 13.76 0.00 34.52 2.01
3685 3930 1.857364 CACTGAACGGGCGTTGTAC 59.143 57.895 0.00 0.00 38.60 2.90
3693 3938 0.249155 CGGGCGTTGTACATATCCGT 60.249 55.000 14.98 0.00 0.00 4.69
3694 3939 1.494824 GGGCGTTGTACATATCCGTC 58.505 55.000 0.00 0.00 0.00 4.79
3695 3940 1.494824 GGCGTTGTACATATCCGTCC 58.505 55.000 0.00 0.41 0.00 4.79
3696 3941 1.494824 GCGTTGTACATATCCGTCCC 58.505 55.000 0.00 0.00 0.00 4.46
3697 3942 1.762419 CGTTGTACATATCCGTCCCG 58.238 55.000 0.00 0.00 0.00 5.14
3807 4073 2.264794 GGTCGCGTCCACCTTGAT 59.735 61.111 17.72 0.00 0.00 2.57
3898 4210 2.867855 GCGGGCGAGGTATGATGGA 61.868 63.158 0.00 0.00 0.00 3.41
3909 4221 2.965147 GGTATGATGGATTTTGGTGGGG 59.035 50.000 0.00 0.00 0.00 4.96
4351 4685 6.201226 TGATGCGTATTTTTGCTCCAAATA 57.799 33.333 0.00 0.00 33.19 1.40
4488 4822 0.605860 AAGGCTGCAGCTGTCTTGAG 60.606 55.000 35.82 5.16 41.70 3.02
4550 4884 3.813596 GCCGGTGGCTGATTACTG 58.186 61.111 1.90 0.00 46.69 2.74
4638 4972 5.794945 TCGAGCTTCGCTTGAATAAAATTTG 59.205 36.000 3.39 0.00 44.93 2.32
4639 4973 5.794945 CGAGCTTCGCTTGAATAAAATTTGA 59.205 36.000 0.00 0.00 42.27 2.69
4668 5002 6.183360 TGCGCATCAAAATGATTCAGAATACT 60.183 34.615 5.66 0.00 34.28 2.12
4800 8261 7.787725 AACCGAATTTCTATAGTGATTCACC 57.212 36.000 13.14 0.00 34.49 4.02
4802 8263 6.986817 ACCGAATTTCTATAGTGATTCACCTG 59.013 38.462 13.14 2.06 34.49 4.00
4919 11616 4.821805 GCTATGGCTAGCTTTATGGTTCAA 59.178 41.667 15.72 0.00 45.78 2.69
5059 14729 7.864108 TTCAGTATGGTTTAGAATGATGTGG 57.136 36.000 0.00 0.00 36.16 4.17
5061 14731 4.816385 AGTATGGTTTAGAATGATGTGGCG 59.184 41.667 0.00 0.00 0.00 5.69
5062 14732 2.364632 TGGTTTAGAATGATGTGGCGG 58.635 47.619 0.00 0.00 0.00 6.13
5071 14741 4.100963 AGAATGATGTGGCGGTAGTATTCA 59.899 41.667 0.00 0.00 0.00 2.57
5212 14882 4.216902 CACTGCAAGAAATCTGTTGATCCA 59.783 41.667 0.00 0.00 37.43 3.41
5227 14897 4.387026 TGATCCATTATGGTCCCAATCC 57.613 45.455 11.39 0.00 39.03 3.01
5265 14935 8.130307 TGCAAAACTTTGAGATTTTAGAAAGC 57.870 30.769 6.37 0.00 40.55 3.51
5378 15048 6.990798 AGTTAAGGTTCCTTGTGTAGTACTC 58.009 40.000 13.64 0.00 0.00 2.59
5379 15049 4.886496 AAGGTTCCTTGTGTAGTACTCC 57.114 45.455 0.00 0.00 0.00 3.85
5380 15050 3.171528 AGGTTCCTTGTGTAGTACTCCC 58.828 50.000 0.00 0.00 0.00 4.30
5381 15051 3.171528 GGTTCCTTGTGTAGTACTCCCT 58.828 50.000 0.00 0.00 0.00 4.20
5382 15052 3.195182 GGTTCCTTGTGTAGTACTCCCTC 59.805 52.174 0.00 0.00 0.00 4.30
5383 15053 3.097342 TCCTTGTGTAGTACTCCCTCC 57.903 52.381 0.00 0.00 0.00 4.30
5384 15054 1.749634 CCTTGTGTAGTACTCCCTCCG 59.250 57.143 0.00 0.00 0.00 4.63
5385 15055 2.444421 CTTGTGTAGTACTCCCTCCGT 58.556 52.381 0.00 0.00 0.00 4.69
5386 15056 3.614092 CTTGTGTAGTACTCCCTCCGTA 58.386 50.000 0.00 0.00 0.00 4.02
5387 15057 3.719268 TGTGTAGTACTCCCTCCGTAA 57.281 47.619 0.00 0.00 0.00 3.18
5388 15058 4.032960 TGTGTAGTACTCCCTCCGTAAA 57.967 45.455 0.00 0.00 0.00 2.01
5389 15059 4.012374 TGTGTAGTACTCCCTCCGTAAAG 58.988 47.826 0.00 0.00 0.00 1.85
5390 15060 4.263462 TGTGTAGTACTCCCTCCGTAAAGA 60.263 45.833 0.00 0.00 0.00 2.52
5391 15061 4.702131 GTGTAGTACTCCCTCCGTAAAGAA 59.298 45.833 0.00 0.00 0.00 2.52
5392 15062 5.183904 GTGTAGTACTCCCTCCGTAAAGAAA 59.816 44.000 0.00 0.00 0.00 2.52
5393 15063 5.954150 TGTAGTACTCCCTCCGTAAAGAAAT 59.046 40.000 0.00 0.00 0.00 2.17
5394 15064 5.340439 AGTACTCCCTCCGTAAAGAAATG 57.660 43.478 0.00 0.00 0.00 2.32
5395 15065 4.776308 AGTACTCCCTCCGTAAAGAAATGT 59.224 41.667 0.00 0.00 0.00 2.71
5396 15066 5.954150 AGTACTCCCTCCGTAAAGAAATGTA 59.046 40.000 0.00 0.00 0.00 2.29
5397 15067 5.750352 ACTCCCTCCGTAAAGAAATGTAA 57.250 39.130 0.00 0.00 0.00 2.41
5398 15068 5.731591 ACTCCCTCCGTAAAGAAATGTAAG 58.268 41.667 0.00 0.00 0.00 2.34
5399 15069 5.482878 ACTCCCTCCGTAAAGAAATGTAAGA 59.517 40.000 0.00 0.00 0.00 2.10
5400 15070 5.974108 TCCCTCCGTAAAGAAATGTAAGAG 58.026 41.667 0.00 0.00 0.00 2.85
5401 15071 4.571176 CCCTCCGTAAAGAAATGTAAGAGC 59.429 45.833 0.00 0.00 0.00 4.09
5402 15072 4.267928 CCTCCGTAAAGAAATGTAAGAGCG 59.732 45.833 0.00 0.00 0.00 5.03
5403 15073 4.813027 TCCGTAAAGAAATGTAAGAGCGT 58.187 39.130 0.00 0.00 0.00 5.07
5404 15074 5.232463 TCCGTAAAGAAATGTAAGAGCGTT 58.768 37.500 0.00 0.00 0.00 4.84
5405 15075 5.697633 TCCGTAAAGAAATGTAAGAGCGTTT 59.302 36.000 0.00 0.00 0.00 3.60
5406 15076 6.867816 TCCGTAAAGAAATGTAAGAGCGTTTA 59.132 34.615 0.00 0.00 0.00 2.01
5407 15077 7.062605 TCCGTAAAGAAATGTAAGAGCGTTTAG 59.937 37.037 0.00 0.00 0.00 1.85
5408 15078 7.062605 CCGTAAAGAAATGTAAGAGCGTTTAGA 59.937 37.037 0.00 0.00 0.00 2.10
5409 15079 8.592998 CGTAAAGAAATGTAAGAGCGTTTAGAT 58.407 33.333 0.00 0.00 0.00 1.98
5410 15080 9.903185 GTAAAGAAATGTAAGAGCGTTTAGATC 57.097 33.333 0.00 0.00 35.01 2.75
5411 15081 8.547967 AAAGAAATGTAAGAGCGTTTAGATCA 57.452 30.769 0.00 0.00 37.82 2.92
5412 15082 7.527084 AGAAATGTAAGAGCGTTTAGATCAC 57.473 36.000 0.00 0.00 37.82 3.06
5413 15083 7.324178 AGAAATGTAAGAGCGTTTAGATCACT 58.676 34.615 0.00 0.00 37.82 3.41
5414 15084 8.467598 AGAAATGTAAGAGCGTTTAGATCACTA 58.532 33.333 0.00 0.00 37.82 2.74
5415 15085 7.988904 AATGTAAGAGCGTTTAGATCACTAC 57.011 36.000 0.00 0.00 37.82 2.73
5416 15086 6.754702 TGTAAGAGCGTTTAGATCACTACT 57.245 37.500 0.00 0.00 37.82 2.57
5417 15087 7.154435 TGTAAGAGCGTTTAGATCACTACTT 57.846 36.000 0.00 0.00 37.82 2.24
5418 15088 7.600065 TGTAAGAGCGTTTAGATCACTACTTT 58.400 34.615 0.00 0.00 37.82 2.66
5419 15089 8.733458 TGTAAGAGCGTTTAGATCACTACTTTA 58.267 33.333 0.00 0.00 37.82 1.85
5420 15090 9.224058 GTAAGAGCGTTTAGATCACTACTTTAG 57.776 37.037 0.00 0.00 37.82 1.85
5421 15091 7.393841 AGAGCGTTTAGATCACTACTTTAGT 57.606 36.000 0.00 0.00 37.82 2.24
5447 15117 9.084164 TGATCTAAAAAGTAGTGATCTAAACGC 57.916 33.333 0.00 0.00 35.77 4.84
5448 15118 9.303537 GATCTAAAAAGTAGTGATCTAAACGCT 57.696 33.333 0.00 0.00 33.03 5.07
5449 15119 8.684973 TCTAAAAAGTAGTGATCTAAACGCTC 57.315 34.615 0.00 0.00 0.00 5.03
5450 15120 8.521176 TCTAAAAAGTAGTGATCTAAACGCTCT 58.479 33.333 0.00 0.00 0.00 4.09
5451 15121 7.964604 AAAAAGTAGTGATCTAAACGCTCTT 57.035 32.000 0.00 0.00 0.00 2.85
5453 15123 9.654663 AAAAAGTAGTGATCTAAACGCTCTTAT 57.345 29.630 0.00 0.00 0.00 1.73
5468 15138 8.649973 AACGCTCTTATATTTCTTTACAGAGG 57.350 34.615 0.00 0.00 0.00 3.69
5469 15139 7.210873 ACGCTCTTATATTTCTTTACAGAGGG 58.789 38.462 8.36 8.36 42.53 4.30
5470 15140 7.069578 ACGCTCTTATATTTCTTTACAGAGGGA 59.930 37.037 14.96 0.00 40.49 4.20
5471 15141 7.596995 CGCTCTTATATTTCTTTACAGAGGGAG 59.403 40.741 4.76 0.00 40.49 4.30
5472 15142 8.425703 GCTCTTATATTTCTTTACAGAGGGAGT 58.574 37.037 0.00 0.00 0.00 3.85
5479 15149 6.793505 TTCTTTACAGAGGGAGTATCTTCC 57.206 41.667 0.00 0.00 36.46 3.46
5480 15150 5.838955 TCTTTACAGAGGGAGTATCTTCCA 58.161 41.667 0.00 0.00 39.09 3.53
5481 15151 6.261435 TCTTTACAGAGGGAGTATCTTCCAA 58.739 40.000 0.00 0.00 39.09 3.53
5482 15152 6.729100 TCTTTACAGAGGGAGTATCTTCCAAA 59.271 38.462 0.00 0.00 39.09 3.28
5483 15153 6.945636 TTACAGAGGGAGTATCTTCCAAAA 57.054 37.500 0.00 0.00 39.09 2.44
5484 15154 5.843019 ACAGAGGGAGTATCTTCCAAAAA 57.157 39.130 0.00 0.00 39.09 1.94
5485 15155 6.394345 ACAGAGGGAGTATCTTCCAAAAAT 57.606 37.500 0.00 0.00 39.09 1.82
5486 15156 7.510675 ACAGAGGGAGTATCTTCCAAAAATA 57.489 36.000 0.00 0.00 39.09 1.40
5487 15157 8.107196 ACAGAGGGAGTATCTTCCAAAAATAT 57.893 34.615 0.00 0.00 39.09 1.28
5488 15158 8.560903 ACAGAGGGAGTATCTTCCAAAAATATT 58.439 33.333 0.00 0.00 39.09 1.28
5489 15159 9.413734 CAGAGGGAGTATCTTCCAAAAATATTT 57.586 33.333 0.00 0.00 39.09 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
225 226 4.776322 CTTGGGCCCGATGACGCA 62.776 66.667 19.37 0.00 38.29 5.24
240 241 2.367378 CCGGGGGAGGTAGTCCTT 59.633 66.667 0.00 0.00 46.06 3.36
353 355 2.046864 CCGTCTCGAGGAAGAGCCA 61.047 63.158 13.56 0.00 40.02 4.75
390 392 2.125552 CCTCCTTCGATGCGTGCA 60.126 61.111 0.00 0.00 0.00 4.57
537 548 0.256752 TAGACAGGGCCTACGCTACA 59.743 55.000 5.28 0.00 37.30 2.74
567 578 7.929245 ACACGCCACATACATACATATTAAAGA 59.071 33.333 0.00 0.00 0.00 2.52
618 632 0.239613 GAGCTCGCTCGCATAGATGA 59.760 55.000 0.00 0.00 33.06 2.92
704 718 1.740296 GCGGCGGCAGACTAGAAAA 60.740 57.895 9.78 0.00 39.62 2.29
731 749 4.856801 CGGGGCGCTTATGCAGGT 62.857 66.667 7.64 0.00 39.64 4.00
793 812 0.527385 GGCTGAGAGCAACTCTAGCG 60.527 60.000 18.37 0.00 44.75 4.26
808 827 0.606604 AGCTGGCAAATTTGAGGCTG 59.393 50.000 22.31 12.46 31.49 4.85
811 830 3.317430 GGATAGAGCTGGCAAATTTGAGG 59.683 47.826 22.31 10.97 0.00 3.86
915 937 2.470801 TTTGATGGCGCGCTGGTTTC 62.471 55.000 32.29 19.37 0.00 2.78
960 986 2.493414 AGAGTGTCGCAGGTACTACT 57.507 50.000 0.00 0.00 36.02 2.57
1125 1163 2.572284 GAGAACTCACCGGGGTCG 59.428 66.667 2.12 0.00 0.00 4.79
1145 1184 0.036765 TCACGGAAGAATCCAACGGG 60.037 55.000 0.00 0.00 46.97 5.28
1391 1430 0.032117 GAGGGAAATGGGAAAGGGGG 60.032 60.000 0.00 0.00 0.00 5.40
1412 1453 7.011828 ACTGAATTTCGAAGAAGAAAACGAA 57.988 32.000 0.00 0.00 45.90 3.85
1458 1499 1.299541 CAAGAACAGAACAGGCGTGT 58.700 50.000 6.15 6.15 39.19 4.49
1459 1500 1.299541 ACAAGAACAGAACAGGCGTG 58.700 50.000 4.53 4.53 0.00 5.34
1460 1501 2.902705 TACAAGAACAGAACAGGCGT 57.097 45.000 0.00 0.00 0.00 5.68
1461 1502 3.125316 GGATTACAAGAACAGAACAGGCG 59.875 47.826 0.00 0.00 0.00 5.52
1462 1503 4.072131 TGGATTACAAGAACAGAACAGGC 58.928 43.478 0.00 0.00 0.00 4.85
1535 1576 0.460109 TCAGGACATTCATCGTGCCG 60.460 55.000 0.00 0.00 35.03 5.69
1547 1588 1.417517 TCAGAGCAAGCTTTCAGGACA 59.582 47.619 0.00 0.00 0.00 4.02
1571 1612 2.638480 TCACAACCCTCTTGACCTTG 57.362 50.000 0.00 0.00 0.00 3.61
1610 1651 1.003839 GCTGGGGTTCGTCATGACA 60.004 57.895 24.93 9.94 0.00 3.58
1803 1889 6.650807 TCACTGTAGACAATCCAATTCTTCAC 59.349 38.462 0.00 0.00 0.00 3.18
1859 1945 4.640201 GCCACATTTCTGCATAACTAAGGA 59.360 41.667 0.00 0.00 0.00 3.36
2065 2152 8.449397 CCTTTCAAGAAATCAACTATGACAGAG 58.551 37.037 0.00 0.00 38.69 3.35
2068 2155 8.463930 AACCTTTCAAGAAATCAACTATGACA 57.536 30.769 0.00 0.00 38.69 3.58
2106 2193 5.837437 AGATGACTATTTCAGATCGGTGTC 58.163 41.667 0.00 0.00 37.77 3.67
2129 2216 3.074412 GGCAAAGAATTCACTCTTCGGA 58.926 45.455 8.44 0.00 34.49 4.55
2136 2223 5.774690 TGGAAACATAGGCAAAGAATTCACT 59.225 36.000 8.44 0.57 33.40 3.41
2204 2291 6.208599 GTCAGAGGATAAAACCATTTCAACCA 59.791 38.462 0.00 0.00 0.00 3.67
2206 2293 7.391833 AGAGTCAGAGGATAAAACCATTTCAAC 59.608 37.037 0.00 0.00 0.00 3.18
2240 2327 6.925718 TGATCTTGCTCTTTACCTCATTATCG 59.074 38.462 0.00 0.00 0.00 2.92
2261 2348 4.201628 CGAACATCCACGAAGTTTCTGATC 60.202 45.833 0.00 0.00 41.61 2.92
2324 2411 2.273538 TATAGCGTCCAGAGACCTCC 57.726 55.000 0.00 0.00 40.12 4.30
2333 2420 4.038642 TGTGAACTGCATATATAGCGTCCA 59.961 41.667 0.00 0.00 33.85 4.02
2453 2542 6.821665 ACTAACTTTCAATTATAAGCGGCTGA 59.178 34.615 1.81 0.00 0.00 4.26
2456 2545 5.681543 GCACTAACTTTCAATTATAAGCGGC 59.318 40.000 0.00 0.00 0.00 6.53
2457 2546 7.016361 AGCACTAACTTTCAATTATAAGCGG 57.984 36.000 0.00 0.00 0.00 5.52
2473 2562 4.342665 AGAGATGCCCTAACTAGCACTAAC 59.657 45.833 0.00 0.00 42.84 2.34
2480 2569 4.390129 TCCCTAGAGATGCCCTAACTAG 57.610 50.000 0.00 0.00 0.00 2.57
2485 2574 2.690840 GGTTTCCCTAGAGATGCCCTA 58.309 52.381 0.00 0.00 0.00 3.53
2496 2585 2.172679 GGAAATTTGCGGGTTTCCCTA 58.827 47.619 12.88 0.00 44.82 3.53
2498 2588 3.525619 GGAAATTTGCGGGTTTCCC 57.474 52.632 12.88 0.00 44.82 3.97
2501 2591 0.973632 GGGAGGAAATTTGCGGGTTT 59.026 50.000 3.87 0.00 0.00 3.27
2640 2741 4.093703 CGTGTTTGTATGAAATCCGGCTTA 59.906 41.667 0.00 0.00 0.00 3.09
2764 2916 0.744414 CGCCGGTGGTCATGAAGATT 60.744 55.000 7.26 0.00 0.00 2.40
2775 2927 2.279252 CGGTCTTATCGCCGGTGG 60.279 66.667 16.49 1.03 43.85 4.61
2839 2991 4.715523 CATGTGGGCCGGTCCGTT 62.716 66.667 22.68 4.19 34.94 4.44
2899 3051 2.028385 ACGGATAGGTCGCAAACTTCTT 60.028 45.455 0.00 0.00 0.00 2.52
3017 3170 2.203195 AGAACAACGCCAGCTGCA 60.203 55.556 8.66 0.00 41.33 4.41
3040 3193 2.719979 CGCGGCTACAGGTATCGT 59.280 61.111 0.00 0.00 0.00 3.73
3171 3325 2.429236 CGAGCGTGTGAGCGAAGT 60.429 61.111 0.00 0.00 43.00 3.01
3173 3327 2.428569 GACGAGCGTGTGAGCGAA 60.429 61.111 0.00 0.00 43.00 4.70
3189 3343 1.528542 CGGAGGGCCAGATCTACGA 60.529 63.158 6.18 0.00 39.52 3.43
3236 3390 3.467803 GCAGGAGAAATAGCGGTACAAT 58.532 45.455 0.00 0.00 0.00 2.71
3247 3401 1.748122 CAGCAGGCGCAGGAGAAAT 60.748 57.895 10.83 0.00 42.27 2.17
3421 3665 2.514824 GGAGATGAAGCACGCCCC 60.515 66.667 0.00 0.00 0.00 5.80
3422 3666 2.892425 CGGAGATGAAGCACGCCC 60.892 66.667 0.00 0.00 0.00 6.13
3475 3719 1.096967 TGCAGTGCATCCGCCATTAG 61.097 55.000 15.37 0.00 37.32 1.73
3477 3721 1.940883 CTTGCAGTGCATCCGCCATT 61.941 55.000 20.50 0.00 38.76 3.16
3490 3734 0.469070 CTCATCCTCCTCCCTTGCAG 59.531 60.000 0.00 0.00 0.00 4.41
3543 3788 2.417239 CGCTATTTAAAGTCGGCCACAA 59.583 45.455 2.24 0.00 0.00 3.33
3552 3797 4.124970 GACCGGAATCCGCTATTTAAAGT 58.875 43.478 17.50 5.09 46.86 2.66
3626 3871 2.263540 GTTAAGCAGGGTCGCCGA 59.736 61.111 0.00 0.00 0.00 5.54
3643 3888 2.864097 GCTGTCCGTCTATATGCCACTG 60.864 54.545 0.00 0.00 0.00 3.66
3773 4039 1.738099 CCTTTCACTGCCTCCGTCG 60.738 63.158 0.00 0.00 0.00 5.12
3803 4069 4.092821 CGCTCAACATTAAAGACGGATCAA 59.907 41.667 0.00 0.00 0.00 2.57
3807 4073 2.343101 CCGCTCAACATTAAAGACGGA 58.657 47.619 0.00 0.00 41.86 4.69
3876 4186 4.969196 CATACCTCGCCCGCGCAT 62.969 66.667 8.75 0.00 39.59 4.73
3890 4201 2.023598 TGCCCCACCAAAATCCATCATA 60.024 45.455 0.00 0.00 0.00 2.15
3898 4210 2.607442 GCCCTGCCCCACCAAAAT 60.607 61.111 0.00 0.00 0.00 1.82
3909 4221 2.125350 CTCTTCTGACCGCCCTGC 60.125 66.667 0.00 0.00 0.00 4.85
3931 4245 2.491022 GGAGTCTGGACCGATCCCG 61.491 68.421 0.00 0.00 45.59 5.14
4018 4341 3.869272 CATCCAACGCGAGCCTGC 61.869 66.667 15.93 0.00 0.00 4.85
4060 4384 3.410628 TCCCTGCATGCATCCGGT 61.411 61.111 22.97 0.00 0.00 5.28
4073 4397 2.115266 CAACCCGCAAACCTCCCT 59.885 61.111 0.00 0.00 0.00 4.20
4351 4685 1.341080 CTTGGACAACCCTGCCATTT 58.659 50.000 0.00 0.00 35.38 2.32
4488 4822 7.985634 ACTACATCAACATTGTTTGTTCAAC 57.014 32.000 11.09 0.00 45.55 3.18
4542 4876 4.058124 GCTCATTATCGGCACAGTAATCA 58.942 43.478 0.00 0.00 0.00 2.57
4638 4972 5.513376 TGAATCATTTTGATGCGCATAGTC 58.487 37.500 25.40 14.83 35.09 2.59
4639 4973 5.297527 TCTGAATCATTTTGATGCGCATAGT 59.702 36.000 25.40 4.53 35.09 2.12
4668 5002 6.281190 TGACTAGGGAAGGATCATCTTCTA 57.719 41.667 10.40 6.50 41.94 2.10
5057 14727 2.100252 GTGCTACTGAATACTACCGCCA 59.900 50.000 0.00 0.00 0.00 5.69
5058 14728 2.100252 TGTGCTACTGAATACTACCGCC 59.900 50.000 0.00 0.00 0.00 6.13
5059 14729 3.431922 TGTGCTACTGAATACTACCGC 57.568 47.619 0.00 0.00 0.00 5.68
5212 14882 2.507886 TGTGACGGATTGGGACCATAAT 59.492 45.455 0.00 0.00 0.00 1.28
5227 14897 2.548057 AGTTTTGCAGTGGTATGTGACG 59.452 45.455 0.00 0.00 0.00 4.35
5265 14935 8.190122 TGTGCATAATAGCCTAAAATCAAGTTG 58.810 33.333 0.00 0.00 0.00 3.16
5345 15015 6.488683 CACAAGGAACCTTAACTTGGTATTCA 59.511 38.462 5.75 0.00 44.35 2.57
5346 15016 6.489022 ACACAAGGAACCTTAACTTGGTATTC 59.511 38.462 5.75 0.00 44.35 1.75
5354 15024 6.014755 GGAGTACTACACAAGGAACCTTAACT 60.015 42.308 0.00 2.44 34.50 2.24
5355 15025 6.162079 GGAGTACTACACAAGGAACCTTAAC 58.838 44.000 0.00 0.00 34.50 2.01
5364 15034 1.749634 CGGAGGGAGTACTACACAAGG 59.250 57.143 7.57 0.00 0.00 3.61
5378 15048 4.571176 GCTCTTACATTTCTTTACGGAGGG 59.429 45.833 0.00 0.00 0.00 4.30
5379 15049 4.267928 CGCTCTTACATTTCTTTACGGAGG 59.732 45.833 0.00 0.00 0.00 4.30
5380 15050 4.863131 ACGCTCTTACATTTCTTTACGGAG 59.137 41.667 0.00 0.00 0.00 4.63
5381 15051 4.813027 ACGCTCTTACATTTCTTTACGGA 58.187 39.130 0.00 0.00 0.00 4.69
5382 15052 5.526010 AACGCTCTTACATTTCTTTACGG 57.474 39.130 0.00 0.00 0.00 4.02
5383 15053 7.946043 TCTAAACGCTCTTACATTTCTTTACG 58.054 34.615 0.00 0.00 0.00 3.18
5384 15054 9.903185 GATCTAAACGCTCTTACATTTCTTTAC 57.097 33.333 0.00 0.00 0.00 2.01
5385 15055 9.647797 TGATCTAAACGCTCTTACATTTCTTTA 57.352 29.630 0.00 0.00 0.00 1.85
5386 15056 8.443937 GTGATCTAAACGCTCTTACATTTCTTT 58.556 33.333 0.00 0.00 0.00 2.52
5387 15057 7.819900 AGTGATCTAAACGCTCTTACATTTCTT 59.180 33.333 0.00 0.00 0.00 2.52
5388 15058 7.324178 AGTGATCTAAACGCTCTTACATTTCT 58.676 34.615 0.00 0.00 0.00 2.52
5389 15059 7.527084 AGTGATCTAAACGCTCTTACATTTC 57.473 36.000 0.00 0.00 0.00 2.17
5390 15060 8.251721 AGTAGTGATCTAAACGCTCTTACATTT 58.748 33.333 0.00 0.00 0.00 2.32
5391 15061 7.773149 AGTAGTGATCTAAACGCTCTTACATT 58.227 34.615 0.00 0.00 0.00 2.71
5392 15062 7.336161 AGTAGTGATCTAAACGCTCTTACAT 57.664 36.000 0.00 0.00 0.00 2.29
5393 15063 6.754702 AGTAGTGATCTAAACGCTCTTACA 57.245 37.500 0.00 0.00 0.00 2.41
5394 15064 9.224058 CTAAAGTAGTGATCTAAACGCTCTTAC 57.776 37.037 0.00 0.00 0.00 2.34
5395 15065 8.954350 ACTAAAGTAGTGATCTAAACGCTCTTA 58.046 33.333 0.00 0.00 37.69 2.10
5396 15066 7.828712 ACTAAAGTAGTGATCTAAACGCTCTT 58.171 34.615 0.00 0.00 37.69 2.85
5397 15067 7.393841 ACTAAAGTAGTGATCTAAACGCTCT 57.606 36.000 0.00 0.00 37.69 4.09
5421 15091 9.084164 GCGTTTAGATCACTACTTTTTAGATCA 57.916 33.333 0.00 0.00 38.00 2.92
5422 15092 9.303537 AGCGTTTAGATCACTACTTTTTAGATC 57.696 33.333 0.00 0.00 36.29 2.75
5423 15093 9.303537 GAGCGTTTAGATCACTACTTTTTAGAT 57.696 33.333 0.00 0.00 34.89 1.98
5424 15094 8.521176 AGAGCGTTTAGATCACTACTTTTTAGA 58.479 33.333 0.00 0.00 37.82 2.10
5425 15095 8.690680 AGAGCGTTTAGATCACTACTTTTTAG 57.309 34.615 0.00 0.00 37.82 1.85
5427 15097 7.964604 AAGAGCGTTTAGATCACTACTTTTT 57.035 32.000 0.00 0.00 37.82 1.94
5442 15112 9.099454 CCTCTGTAAAGAAATATAAGAGCGTTT 57.901 33.333 0.00 0.00 0.00 3.60
5443 15113 7.711339 CCCTCTGTAAAGAAATATAAGAGCGTT 59.289 37.037 0.00 0.00 0.00 4.84
5444 15114 7.069578 TCCCTCTGTAAAGAAATATAAGAGCGT 59.930 37.037 0.00 0.00 0.00 5.07
5445 15115 7.434492 TCCCTCTGTAAAGAAATATAAGAGCG 58.566 38.462 0.00 0.00 0.00 5.03
5446 15116 8.425703 ACTCCCTCTGTAAAGAAATATAAGAGC 58.574 37.037 0.00 0.00 0.00 4.09
5453 15123 8.925338 GGAAGATACTCCCTCTGTAAAGAAATA 58.075 37.037 0.00 0.00 0.00 1.40
5454 15124 7.403231 TGGAAGATACTCCCTCTGTAAAGAAAT 59.597 37.037 0.00 0.00 34.22 2.17
5455 15125 6.729100 TGGAAGATACTCCCTCTGTAAAGAAA 59.271 38.462 0.00 0.00 34.22 2.52
5456 15126 6.261435 TGGAAGATACTCCCTCTGTAAAGAA 58.739 40.000 0.00 0.00 34.22 2.52
5457 15127 5.838955 TGGAAGATACTCCCTCTGTAAAGA 58.161 41.667 0.00 0.00 34.22 2.52
5458 15128 6.546428 TTGGAAGATACTCCCTCTGTAAAG 57.454 41.667 0.00 0.00 34.22 1.85
5459 15129 6.945636 TTTGGAAGATACTCCCTCTGTAAA 57.054 37.500 0.00 0.00 34.22 2.01
5460 15130 6.945636 TTTTGGAAGATACTCCCTCTGTAA 57.054 37.500 0.00 0.00 34.22 2.41
5461 15131 6.945636 TTTTTGGAAGATACTCCCTCTGTA 57.054 37.500 0.00 0.00 34.22 2.74
5462 15132 5.843019 TTTTTGGAAGATACTCCCTCTGT 57.157 39.130 0.00 0.00 34.22 3.41
5463 15133 8.986929 AATATTTTTGGAAGATACTCCCTCTG 57.013 34.615 0.00 0.00 34.22 3.35


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

AutoCloner maintained by Alex Coulton.