Multiple sequence alignment - TraesCS2D01G087400

Loading Multiple Alignment...

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 TraesCS2D01G087400 chr2D 100.000 6916 0 0 1 6916 37607958 37614873 0.000000e+00 12772.0
1 TraesCS2D01G087400 chr2D 77.033 209 38 10 1102 1305 168597341 168597544 2.040000e-20 111.0
2 TraesCS2D01G087400 chr2D 87.500 96 11 1 3616 3710 70629289 70629194 7.330000e-20 110.0
3 TraesCS2D01G087400 chr2D 87.234 94 11 1 3617 3709 369468604 369468511 9.490000e-19 106.0
4 TraesCS2D01G087400 chr2D 94.118 51 2 1 3561 3610 575354207 575354257 7.440000e-10 76.8
5 TraesCS2D01G087400 chr2D 100.000 34 0 0 4794 4827 37612703 37612670 5.790000e-06 63.9
6 TraesCS2D01G087400 chr2D 100.000 34 0 0 4713 4746 37612784 37612751 5.790000e-06 63.9
7 TraesCS2D01G087400 chr2A 95.073 1928 47 11 4858 6753 42475084 42476995 0.000000e+00 2990.0
8 TraesCS2D01G087400 chr2A 94.271 1344 62 8 2230 3563 42472436 42473774 0.000000e+00 2041.0
9 TraesCS2D01G087400 chr2A 93.810 1260 24 12 3565 4789 42473819 42475059 0.000000e+00 1845.0
10 TraesCS2D01G087400 chr2A 86.357 1400 92 28 9 1373 42469980 42471315 0.000000e+00 1435.0
11 TraesCS2D01G087400 chr2A 88.760 605 48 10 1649 2248 42471667 42472256 0.000000e+00 723.0
12 TraesCS2D01G087400 chr2A 95.789 95 4 0 6822 6916 42478997 42479091 3.340000e-33 154.0
13 TraesCS2D01G087400 chr2A 78.010 191 32 10 1120 1305 181848647 181848462 2.040000e-20 111.0
14 TraesCS2D01G087400 chr2A 88.298 94 10 1 3617 3709 500525411 500525318 2.040000e-20 111.0
15 TraesCS2D01G087400 chr2A 88.298 94 10 1 3617 3709 500525868 500525775 2.040000e-20 111.0
16 TraesCS2D01G087400 chr2A 97.436 39 1 0 6449 6487 445358442 445358404 4.480000e-07 67.6
17 TraesCS2D01G087400 chr2A 100.000 34 0 0 4794 4827 42475016 42474983 5.790000e-06 63.9
18 TraesCS2D01G087400 chr2B 91.246 1268 73 21 977 2220 65370548 65371801 0.000000e+00 1692.0
19 TraesCS2D01G087400 chr2B 92.229 785 44 7 4856 5633 65374455 65375229 0.000000e+00 1096.0
20 TraesCS2D01G087400 chr2B 90.553 741 42 7 5572 6286 65375123 65375861 0.000000e+00 955.0
21 TraesCS2D01G087400 chr2B 83.028 654 64 15 3779 4386 65372073 65372725 3.650000e-152 549.0
22 TraesCS2D01G087400 chr2B 87.190 484 51 5 6437 6916 65408457 65408933 2.190000e-149 540.0
23 TraesCS2D01G087400 chr2B 86.214 486 36 15 239 703 65369965 65370440 1.340000e-136 497.0
24 TraesCS2D01G087400 chr2B 85.000 260 29 7 3305 3562 65371787 65372038 8.900000e-64 255.0
25 TraesCS2D01G087400 chr2B 79.772 351 58 8 6549 6892 65494014 65494358 6.930000e-60 243.0
26 TraesCS2D01G087400 chr2B 79.494 356 60 8 6549 6897 65409122 65409471 2.490000e-59 241.0
27 TraesCS2D01G087400 chr2B 92.414 145 9 1 6273 6415 65376108 65376252 9.090000e-49 206.0
28 TraesCS2D01G087400 chr2B 84.000 150 22 2 6652 6800 65492301 65492449 7.230000e-30 143.0
29 TraesCS2D01G087400 chr2B 91.176 102 7 1 6817 6916 65493724 65493825 3.360000e-28 137.0
30 TraesCS2D01G087400 chr2B 94.186 86 5 0 793 878 65370440 65370525 1.570000e-26 132.0
31 TraesCS2D01G087400 chr2B 77.368 190 35 8 1120 1305 229622163 229621978 9.490000e-19 106.0
32 TraesCS2D01G087400 chr7D 89.158 867 86 6 2447 3309 232354298 232353436 0.000000e+00 1074.0
33 TraesCS2D01G087400 chr7D 90.948 232 17 4 2219 2448 232354558 232354329 6.740000e-80 309.0
34 TraesCS2D01G087400 chr7D 95.238 42 2 0 6446 6487 414103028 414102987 4.480000e-07 67.6
35 TraesCS2D01G087400 chr3A 82.222 1125 142 31 4858 5978 649821725 649822795 0.000000e+00 917.0
36 TraesCS2D01G087400 chr3A 82.899 690 81 13 976 1638 649819122 649819801 2.780000e-163 586.0
37 TraesCS2D01G087400 chr3A 88.077 260 25 6 2218 2474 659623056 659622800 3.130000e-78 303.0
38 TraesCS2D01G087400 chr3A 85.859 99 12 2 3613 3709 474969435 474969533 3.410000e-18 104.0
39 TraesCS2D01G087400 chr3A 86.154 65 5 3 3542 3605 564342517 564342456 4.480000e-07 67.6
40 TraesCS2D01G087400 chr3B 82.028 1124 145 30 4858 5978 678021003 678022072 0.000000e+00 904.0
41 TraesCS2D01G087400 chr3B 83.090 686 81 14 976 1638 678018320 678018993 5.970000e-165 592.0
42 TraesCS2D01G087400 chr3B 90.638 235 18 4 2219 2451 693468669 693468437 6.740000e-80 309.0
43 TraesCS2D01G087400 chr3B 82.199 191 20 7 4583 4773 678020819 678020995 1.200000e-32 152.0
44 TraesCS2D01G087400 chr3B 94.643 56 3 0 793 848 114087516 114087571 3.440000e-13 87.9
45 TraesCS2D01G087400 chr3B 100.000 28 0 0 4795 4822 678020967 678020940 1.300000e-02 52.8
46 TraesCS2D01G087400 chr3D 81.940 1124 146 30 4858 5978 515552867 515553936 0.000000e+00 898.0
47 TraesCS2D01G087400 chr3D 82.085 614 86 18 1032 1629 515550510 515551115 2.880000e-138 503.0
48 TraesCS2D01G087400 chr3D 89.922 258 21 5 2219 2474 525537079 525536825 1.860000e-85 327.0
49 TraesCS2D01G087400 chr3D 82.320 362 48 8 4416 4773 515552510 515552859 4.050000e-77 300.0
50 TraesCS2D01G087400 chr3D 88.710 62 3 3 3542 3602 424659615 424659673 9.620000e-09 73.1
51 TraesCS2D01G087400 chr5B 78.891 469 83 13 4978 5438 612682104 612682564 3.130000e-78 303.0
52 TraesCS2D01G087400 chr5B 85.043 234 35 0 1075 1308 612679817 612680050 8.960000e-59 239.0
53 TraesCS2D01G087400 chr5B 100.000 38 0 0 6446 6483 473787243 473787206 3.460000e-08 71.3
54 TraesCS2D01G087400 chr5A 78.540 452 90 6 4978 5427 619691880 619692326 2.440000e-74 291.0
55 TraesCS2D01G087400 chr5A 80.000 220 44 0 1089 1308 581488141 581487922 5.550000e-36 163.0
56 TraesCS2D01G087400 chr5A 97.826 46 1 0 3565 3610 552307861 552307906 5.750000e-11 80.5
57 TraesCS2D01G087400 chr5D 78.319 452 89 9 4978 5426 495628121 495628566 4.080000e-72 283.0
58 TraesCS2D01G087400 chr5D 84.016 244 38 1 1065 1308 495626181 495626423 4.170000e-57 233.0
59 TraesCS2D01G087400 chr5D 89.796 98 8 2 3616 3712 393909990 393909894 2.620000e-24 124.0
60 TraesCS2D01G087400 chr4A 80.913 241 36 10 1074 1308 19622545 19622309 1.530000e-41 182.0
61 TraesCS2D01G087400 chr4A 81.967 122 18 4 3607 3726 579421883 579421764 4.410000e-17 100.0
62 TraesCS2D01G087400 chr1B 91.579 95 6 1 3617 3709 249519974 249519880 5.630000e-26 130.0
63 TraesCS2D01G087400 chr7B 100.000 45 0 0 3565 3609 525000417 525000373 4.450000e-12 84.2
64 TraesCS2D01G087400 chr7A 97.826 46 1 0 3565 3610 24857495 24857450 5.750000e-11 80.5
65 TraesCS2D01G087400 chr7A 97.826 46 1 0 3565 3610 675337613 675337658 5.750000e-11 80.5
66 TraesCS2D01G087400 chr6D 92.453 53 4 0 3565 3617 245495141 245495089 7.440000e-10 76.8
67 TraesCS2D01G087400 chr1D 95.556 45 1 1 6438 6481 426932676 426932720 3.460000e-08 71.3
68 TraesCS2D01G087400 chr6A 93.333 45 2 1 6439 6483 124429275 124429318 1.610000e-06 65.8
69 TraesCS2D01G087400 chr6A 93.333 45 2 1 6439 6483 124911417 124911374 1.610000e-06 65.8
70 TraesCS2D01G087400 chr4B 93.023 43 3 0 6446 6488 633579233 633579191 5.790000e-06 63.9


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 TraesCS2D01G087400 chr2D 37607958 37614873 6915 False 12772.000000 12772 100.000000 1 6916 1 chr2D.!!$F1 6915
1 TraesCS2D01G087400 chr2A 42469980 42479091 9111 False 1531.333333 2990 92.343333 9 6916 6 chr2A.!!$F1 6907
2 TraesCS2D01G087400 chr2B 65369965 65376252 6287 False 672.750000 1692 89.358750 239 6415 8 chr2B.!!$F1 6176
3 TraesCS2D01G087400 chr2B 65408457 65409471 1014 False 390.500000 540 83.342000 6437 6916 2 chr2B.!!$F2 479
4 TraesCS2D01G087400 chr7D 232353436 232354558 1122 True 691.500000 1074 90.053000 2219 3309 2 chr7D.!!$R2 1090
5 TraesCS2D01G087400 chr3A 649819122 649822795 3673 False 751.500000 917 82.560500 976 5978 2 chr3A.!!$F2 5002
6 TraesCS2D01G087400 chr3B 678018320 678022072 3752 False 549.333333 904 82.439000 976 5978 3 chr3B.!!$F2 5002
7 TraesCS2D01G087400 chr3D 515550510 515553936 3426 False 567.000000 898 82.115000 1032 5978 3 chr3D.!!$F2 4946
8 TraesCS2D01G087400 chr5B 612679817 612682564 2747 False 271.000000 303 81.967000 1075 5438 2 chr5B.!!$F1 4363
9 TraesCS2D01G087400 chr5D 495626181 495628566 2385 False 258.000000 283 81.167500 1065 5426 2 chr5D.!!$F1 4361

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
218 219 0.415429 AGGGCTGAGAAAGAGAGGGA 59.585 55.0 0.00 0.0 0.00 4.20 F
577 592 0.548510 CATCCTCCTCCAAACCCCTC 59.451 60.0 0.00 0.0 0.00 4.30 F
703 735 0.742990 CCGCCGCAAACTTCTCCATA 60.743 55.0 0.00 0.0 0.00 2.74 F
2612 4112 0.597568 CGCTGGTGAGCCATTCAAAA 59.402 50.0 0.00 0.0 45.05 2.44 F
3120 4623 0.405973 GGTGAAGGAGAAGGCCCTTT 59.594 55.0 0.00 0.0 43.59 3.11 F
3804 5368 0.820074 CCGGCTCAGTATCTCGGAGT 60.820 60.0 4.69 0.0 42.94 3.85 F
5459 8998 0.103937 CTAGTAGCAGCAGCCTGGAC 59.896 60.0 0.00 0.0 43.56 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1254 1309 2.287248 GGAGAAGTTGCTGTGCTTGAAC 60.287 50.000 0.00 0.0 0.00 3.18 R
2574 4074 1.923227 GCTAAAGCGAACTGGGCCAC 61.923 60.000 0.00 0.0 0.00 5.01 R
2752 4254 0.865769 CGTAGACACTTTGTGGTGGC 59.134 55.000 2.72 0.0 44.95 5.01 R
3775 5339 0.036732 ACTGAGCCGGCAAATCTTGA 59.963 50.000 31.54 0.0 0.00 3.02 R
4799 8252 2.158623 TGTTGCAGTTCCATCTCTTGGT 60.159 45.455 0.00 0.0 46.52 3.67 R
5576 9121 0.461961 GGATCTCGTCACCAAGGAGG 59.538 60.000 0.00 0.0 39.78 4.30 R
6681 10541 0.443869 CAACACTAGTGCGATGCCAC 59.556 55.000 22.90 0.0 35.98 5.01 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
54 55 0.955905 TGAAGTCATGGACGACGACA 59.044 50.000 0.00 0.00 40.98 4.35
68 69 2.729467 CGACGACAAAAAGTTGCAACCA 60.729 45.455 25.62 0.00 38.39 3.67
72 73 3.701241 GACAAAAAGTTGCAACCATCGA 58.299 40.909 25.62 0.00 38.39 3.59
74 75 5.446143 ACAAAAAGTTGCAACCATCGATA 57.554 34.783 25.62 0.00 38.39 2.92
87 88 4.009675 ACCATCGATAGCAAAAGCTTCAA 58.990 39.130 0.00 0.00 0.00 2.69
90 91 5.294306 CCATCGATAGCAAAAGCTTCAACTA 59.706 40.000 0.00 1.95 0.00 2.24
97 98 6.147864 AGCAAAAGCTTCAACTAACATTGA 57.852 33.333 0.00 0.00 36.80 2.57
186 187 1.153289 GCTGTGATGACGAGGGCAT 60.153 57.895 0.00 0.00 0.00 4.40
187 188 1.434622 GCTGTGATGACGAGGGCATG 61.435 60.000 0.00 0.00 0.00 4.06
193 194 1.072331 GATGACGAGGGCATGGGTATT 59.928 52.381 0.00 0.00 0.00 1.89
194 195 0.468226 TGACGAGGGCATGGGTATTC 59.532 55.000 0.00 0.00 0.00 1.75
196 197 1.301716 CGAGGGCATGGGTATTCCG 60.302 63.158 0.00 0.00 38.76 4.30
218 219 0.415429 AGGGCTGAGAAAGAGAGGGA 59.585 55.000 0.00 0.00 0.00 4.20
228 229 4.247380 GAGAGGGAGGCGCCATGG 62.247 72.222 31.54 7.63 38.95 3.66
265 270 1.002250 CAAGCGCAACTCGTACTCGT 61.002 55.000 11.47 0.00 41.07 4.18
276 281 3.001414 CTCGTACTCGTGAGAAAGGAGA 58.999 50.000 3.44 0.00 42.34 3.71
283 288 5.017490 ACTCGTGAGAAAGGAGAAGGATTA 58.983 41.667 3.44 0.00 42.34 1.75
306 313 2.417933 CCTGCACGAGAAAAGATCCAAG 59.582 50.000 0.00 0.00 0.00 3.61
309 316 3.262420 GCACGAGAAAAGATCCAAGCTA 58.738 45.455 0.00 0.00 0.00 3.32
316 323 6.578919 CGAGAAAAGATCCAAGCTAAACAAAC 59.421 38.462 0.00 0.00 0.00 2.93
324 331 8.253113 AGATCCAAGCTAAACAAACATTATTGG 58.747 33.333 0.00 0.00 36.78 3.16
344 351 2.202479 GAATCAAACGGCTGGCGC 60.202 61.111 24.07 0.00 0.00 6.53
401 408 4.327357 CGCCTATCACTCGCCATTAATAAG 59.673 45.833 0.00 0.00 0.00 1.73
406 413 8.836413 CCTATCACTCGCCATTAATAAGAAAAA 58.164 33.333 0.00 0.00 0.00 1.94
577 592 0.548510 CATCCTCCTCCAAACCCCTC 59.451 60.000 0.00 0.00 0.00 4.30
612 627 2.086610 AGCAATCTCTCTCCTCTCCC 57.913 55.000 0.00 0.00 0.00 4.30
614 629 1.690845 GCAATCTCTCTCCTCTCCCCA 60.691 57.143 0.00 0.00 0.00 4.96
698 730 3.050275 GCTCCGCCGCAAACTTCT 61.050 61.111 0.00 0.00 0.00 2.85
699 731 3.028366 GCTCCGCCGCAAACTTCTC 62.028 63.158 0.00 0.00 0.00 2.87
700 732 2.358247 TCCGCCGCAAACTTCTCC 60.358 61.111 0.00 0.00 0.00 3.71
701 733 2.668212 CCGCCGCAAACTTCTCCA 60.668 61.111 0.00 0.00 0.00 3.86
702 734 2.040544 CCGCCGCAAACTTCTCCAT 61.041 57.895 0.00 0.00 0.00 3.41
703 735 0.742990 CCGCCGCAAACTTCTCCATA 60.743 55.000 0.00 0.00 0.00 2.74
704 736 1.083489 CGCCGCAAACTTCTCCATAA 58.917 50.000 0.00 0.00 0.00 1.90
705 737 1.062587 CGCCGCAAACTTCTCCATAAG 59.937 52.381 0.00 0.00 0.00 1.73
706 738 1.401905 GCCGCAAACTTCTCCATAAGG 59.598 52.381 0.00 0.00 0.00 2.69
707 739 1.401905 CCGCAAACTTCTCCATAAGGC 59.598 52.381 0.00 0.00 33.74 4.35
708 740 1.401905 CGCAAACTTCTCCATAAGGCC 59.598 52.381 0.00 0.00 33.74 5.19
713 745 1.307517 TTCTCCATAAGGCCCCCGT 60.308 57.895 0.00 0.00 33.74 5.28
736 768 3.353836 GCTCCGCTTCGTTTGCCA 61.354 61.111 0.00 0.00 0.00 4.92
737 769 2.863153 CTCCGCTTCGTTTGCCAG 59.137 61.111 0.00 0.00 0.00 4.85
738 770 1.961277 CTCCGCTTCGTTTGCCAGT 60.961 57.895 0.00 0.00 0.00 4.00
739 771 1.901650 CTCCGCTTCGTTTGCCAGTC 61.902 60.000 0.00 0.00 0.00 3.51
842 874 4.451900 GGTGGGAGTGATACGATTTTGAT 58.548 43.478 0.00 0.00 0.00 2.57
898 930 4.475444 CTCCCCTCCCCGTGCCTA 62.475 72.222 0.00 0.00 0.00 3.93
992 1041 2.160853 GTGGGAGGGTTCTTGGGGT 61.161 63.158 0.00 0.00 0.00 4.95
1017 1069 2.731571 TATGGACCCAGTGCCGAGC 61.732 63.158 0.00 0.00 0.00 5.03
1322 1378 1.075374 TGTAAGCCACCAAGCCTGATT 59.925 47.619 0.00 0.00 0.00 2.57
1396 1455 1.290324 CCGCTGTGAGTGTAGCTGT 59.710 57.895 0.00 0.00 37.78 4.40
1441 1501 2.602878 CAAATGCAATGCTGTGAGACC 58.397 47.619 6.82 0.00 0.00 3.85
1500 1590 7.541122 AGACAAGTACAGAAAAAGAGTCAAC 57.459 36.000 0.00 0.00 0.00 3.18
1510 1600 4.795970 AAAAGAGTCAACTACAACTGCG 57.204 40.909 0.00 0.00 0.00 5.18
1575 1667 6.333416 TCTCTTGTTCTTCATGATTAGGACG 58.667 40.000 0.00 0.00 31.42 4.79
1613 1705 9.582648 AGAAAATTGGTGGTATTACACTAAACT 57.417 29.630 0.00 0.00 43.48 2.66
1732 2115 3.807622 TCAGTTAAGAAGAAGCCAACACG 59.192 43.478 0.00 0.00 0.00 4.49
1735 2118 5.235616 CAGTTAAGAAGAAGCCAACACGTTA 59.764 40.000 0.00 0.00 0.00 3.18
1756 2141 3.762407 ACAAAATTTACCTGTTGGGCC 57.238 42.857 0.00 0.00 39.10 5.80
1764 2149 2.034066 CTGTTGGGCCGGATGTGT 59.966 61.111 5.05 0.00 0.00 3.72
1780 2287 5.505654 CGGATGTGTTGGATAAACCTTATGC 60.506 44.000 0.00 0.00 38.06 3.14
1797 2308 8.593945 ACCTTATGCCATCATTAAGAGAAAAA 57.406 30.769 0.00 0.00 34.22 1.94
1835 2349 9.387123 GAAAGTTTATTCTGTCTGTTTCACATC 57.613 33.333 0.00 0.00 0.00 3.06
1847 2488 7.448161 TGTCTGTTTCACATCCATTTATCTGTT 59.552 33.333 0.00 0.00 0.00 3.16
1848 2489 8.946085 GTCTGTTTCACATCCATTTATCTGTTA 58.054 33.333 0.00 0.00 0.00 2.41
1852 2493 8.730680 GTTTCACATCCATTTATCTGTTAGTGT 58.269 33.333 0.00 0.00 0.00 3.55
1927 2585 7.413644 TCTTGTATGTGTTGTACAATTGTGTG 58.586 34.615 21.42 0.00 43.77 3.82
2029 3157 2.889045 ACTTCTTTGTGAGCATGTGCAT 59.111 40.909 7.83 0.00 45.16 3.96
2030 3158 3.319972 ACTTCTTTGTGAGCATGTGCATT 59.680 39.130 7.83 0.00 45.16 3.56
2032 3160 1.724623 CTTTGTGAGCATGTGCATTGC 59.275 47.619 14.75 14.75 45.16 3.56
2033 3161 0.963225 TTGTGAGCATGTGCATTGCT 59.037 45.000 22.56 22.56 45.16 3.91
2050 3178 1.075374 TGCTTGGTGCCATCTTAGGTT 59.925 47.619 0.00 0.00 42.00 3.50
2128 3389 2.284754 TACCTGCTTTCACCATGCAA 57.715 45.000 0.00 0.00 35.23 4.08
2292 3755 8.163408 TGTTATATTAATCAAGGATCAGGGGTG 58.837 37.037 0.00 0.00 0.00 4.61
2449 3948 1.766496 GGTCGATTATGAACCCCCTCA 59.234 52.381 0.00 0.00 0.00 3.86
2494 3994 2.356125 CCAAGATCCATGGAGAACGGTT 60.356 50.000 21.33 0.15 40.56 4.44
2495 3995 3.347216 CAAGATCCATGGAGAACGGTTT 58.653 45.455 21.33 0.00 0.00 3.27
2496 3996 3.721087 AGATCCATGGAGAACGGTTTT 57.279 42.857 21.33 0.00 0.00 2.43
2612 4112 0.597568 CGCTGGTGAGCCATTCAAAA 59.402 50.000 0.00 0.00 45.05 2.44
2674 4176 2.899339 GAGCTGCGAAGGGGCATC 60.899 66.667 0.00 0.00 42.99 3.91
2774 4276 0.756903 ACCACAAAGTGTCTACGGCT 59.243 50.000 0.00 0.00 0.00 5.52
2802 4304 0.904865 TCCTGGTGTTGAGCCGATCT 60.905 55.000 0.00 0.00 0.00 2.75
2956 4458 3.597255 CAGCTATAGGACCATGCATCAG 58.403 50.000 0.00 0.00 0.00 2.90
2980 4482 1.200483 CGCCGTGTTGATGTAGCTAG 58.800 55.000 0.00 0.00 0.00 3.42
3014 4517 2.045536 GAGCTGGCCACTTCCTGG 60.046 66.667 0.00 0.00 44.08 4.45
3032 4535 2.203480 TGGGCTTGGGCAGACAAC 60.203 61.111 0.00 0.00 40.87 3.32
3047 4550 1.719780 GACAACGGTAAGCAGAAGACG 59.280 52.381 0.00 0.00 0.00 4.18
3048 4551 1.068474 CAACGGTAAGCAGAAGACGG 58.932 55.000 0.00 0.00 0.00 4.79
3120 4623 0.405973 GGTGAAGGAGAAGGCCCTTT 59.594 55.000 0.00 0.00 43.59 3.11
3133 4636 2.567169 AGGCCCTTTGGTATTTTTCTGC 59.433 45.455 0.00 0.00 0.00 4.26
3310 4813 6.878923 TCATTGTAGTAAGTGTTCCAGATTGG 59.121 38.462 0.00 0.00 39.43 3.16
3526 5046 8.529911 GTCGAAGTTAAAATATCGAAGATCGTT 58.470 33.333 0.00 0.00 44.79 3.85
3563 5083 7.497249 AGCTTCACTTATTTGTGATATGGAGTC 59.503 37.037 0.00 0.00 45.03 3.36
3583 5146 7.448777 TGGAGTCTGATCTAAACGCTCTTATAT 59.551 37.037 0.00 0.00 0.00 0.86
3673 5236 1.139058 CCACCCGGATTCAAGTCCTAG 59.861 57.143 0.73 0.00 36.07 3.02
3744 5308 4.091509 GCGATTTATTACGAGCCACCTATG 59.908 45.833 0.00 0.00 0.00 2.23
3765 5329 5.970317 TGGTAACGTAGTCAATCTCAAGA 57.030 39.130 0.00 0.00 45.00 3.02
3766 5330 6.525578 TGGTAACGTAGTCAATCTCAAGAT 57.474 37.500 0.00 0.00 45.00 2.40
3767 5331 6.931838 TGGTAACGTAGTCAATCTCAAGATT 58.068 36.000 0.00 0.00 45.00 2.40
3768 5332 7.383687 TGGTAACGTAGTCAATCTCAAGATTT 58.616 34.615 2.47 0.00 45.00 2.17
3769 5333 7.876068 TGGTAACGTAGTCAATCTCAAGATTTT 59.124 33.333 2.47 0.00 45.00 1.82
3770 5334 8.381387 GGTAACGTAGTCAATCTCAAGATTTTC 58.619 37.037 2.47 0.42 45.00 2.29
3771 5335 7.962964 AACGTAGTCAATCTCAAGATTTTCA 57.037 32.000 2.47 0.00 45.00 2.69
3772 5336 7.962964 ACGTAGTCAATCTCAAGATTTTCAA 57.037 32.000 2.47 0.00 42.41 2.69
3773 5337 8.553459 ACGTAGTCAATCTCAAGATTTTCAAT 57.447 30.769 2.47 0.00 42.41 2.57
3774 5338 8.660373 ACGTAGTCAATCTCAAGATTTTCAATC 58.340 33.333 2.47 0.00 42.41 2.67
3775 5339 8.877779 CGTAGTCAATCTCAAGATTTTCAATCT 58.122 33.333 2.47 0.00 42.41 2.40
3777 5341 8.859236 AGTCAATCTCAAGATTTTCAATCTCA 57.141 30.769 2.47 0.00 42.41 3.27
3778 5342 9.293404 AGTCAATCTCAAGATTTTCAATCTCAA 57.707 29.630 2.47 0.00 42.41 3.02
3779 5343 9.557338 GTCAATCTCAAGATTTTCAATCTCAAG 57.443 33.333 2.47 1.80 42.41 3.02
3804 5368 0.820074 CCGGCTCAGTATCTCGGAGT 60.820 60.000 4.69 0.00 42.94 3.85
3871 5435 1.647213 GTACGTGTGTATGCGAGTGTG 59.353 52.381 0.00 0.00 32.11 3.82
3998 5586 4.021981 ACAAGCAGAGCTAATTCCCAAAAC 60.022 41.667 0.00 0.00 38.25 2.43
4005 5593 7.362920 GCAGAGCTAATTCCCAAAACTGAATAA 60.363 37.037 0.00 0.00 0.00 1.40
4006 5594 8.522830 CAGAGCTAATTCCCAAAACTGAATAAA 58.477 33.333 0.00 0.00 0.00 1.40
4044 5673 9.959749 TTGTGCAGAAAACCTTAAGTTAATAAG 57.040 29.630 0.97 0.00 37.88 1.73
4348 5994 1.079888 GGCCAAAAGATTGCACCGG 60.080 57.895 0.00 0.00 35.10 5.28
4373 6020 3.056607 ACCTCATTTTTCCTTCATTGCCG 60.057 43.478 0.00 0.00 0.00 5.69
4793 8246 2.030412 CAGCCTGGTGCACGTGTA 59.970 61.111 18.38 10.46 44.83 2.90
4794 8247 1.596752 CAGCCTGGTGCACGTGTAA 60.597 57.895 18.38 2.89 44.83 2.41
4796 8249 1.890041 GCCTGGTGCACGTGTAACA 60.890 57.895 23.19 23.19 40.77 2.41
4798 8251 0.531974 CCTGGTGCACGTGTAACAGT 60.532 55.000 38.04 0.00 42.78 3.55
4799 8252 1.269883 CCTGGTGCACGTGTAACAGTA 60.270 52.381 38.04 14.31 42.78 2.74
4800 8253 1.790623 CTGGTGCACGTGTAACAGTAC 59.209 52.381 34.93 11.69 40.03 2.73
4801 8254 1.142474 GGTGCACGTGTAACAGTACC 58.858 55.000 17.33 4.87 39.30 3.34
4802 8255 1.538634 GGTGCACGTGTAACAGTACCA 60.539 52.381 17.33 0.00 43.40 3.25
4803 8256 2.203401 GTGCACGTGTAACAGTACCAA 58.797 47.619 18.38 0.00 35.74 3.67
4804 8257 2.220133 GTGCACGTGTAACAGTACCAAG 59.780 50.000 18.38 0.00 35.74 3.61
4805 8258 2.101082 TGCACGTGTAACAGTACCAAGA 59.899 45.455 18.38 0.00 35.74 3.02
4806 8259 2.729882 GCACGTGTAACAGTACCAAGAG 59.270 50.000 18.38 0.00 35.74 2.85
4807 8260 3.551454 GCACGTGTAACAGTACCAAGAGA 60.551 47.826 18.38 0.00 35.74 3.10
4808 8261 4.806330 CACGTGTAACAGTACCAAGAGAT 58.194 43.478 7.58 0.00 35.74 2.75
4809 8262 4.621460 CACGTGTAACAGTACCAAGAGATG 59.379 45.833 7.58 0.00 35.74 2.90
4812 8265 5.566032 CGTGTAACAGTACCAAGAGATGGAA 60.566 44.000 0.67 0.00 45.95 3.53
4813 8266 5.638234 GTGTAACAGTACCAAGAGATGGAAC 59.362 44.000 0.67 0.00 45.20 3.62
4814 8267 6.518537 GTGTAACAGTACCAAGAGATGGAACT 60.519 42.308 0.67 0.00 45.20 3.01
4815 8268 8.477604 GTGTAACAGTACCAAGAGATGGAACTG 61.478 44.444 0.67 0.00 45.20 3.16
4821 8274 3.826236 CAAGAGATGGAACTGCAACAG 57.174 47.619 0.00 0.00 37.52 3.16
4822 8275 3.405831 CAAGAGATGGAACTGCAACAGA 58.594 45.455 0.78 0.00 35.18 3.41
4823 8276 3.331478 AGAGATGGAACTGCAACAGAG 57.669 47.619 0.78 0.00 35.18 3.35
4824 8277 2.636893 AGAGATGGAACTGCAACAGAGT 59.363 45.455 0.78 0.00 35.18 3.24
4825 8278 3.834813 AGAGATGGAACTGCAACAGAGTA 59.165 43.478 0.78 0.00 35.18 2.59
4826 8279 4.469227 AGAGATGGAACTGCAACAGAGTAT 59.531 41.667 0.78 0.00 35.18 2.12
4827 8280 5.658634 AGAGATGGAACTGCAACAGAGTATA 59.341 40.000 0.78 0.00 35.18 1.47
4828 8281 6.155221 AGAGATGGAACTGCAACAGAGTATAA 59.845 38.462 0.78 0.00 35.18 0.98
4829 8282 6.711277 AGATGGAACTGCAACAGAGTATAAA 58.289 36.000 0.78 0.00 35.18 1.40
4830 8283 6.595716 AGATGGAACTGCAACAGAGTATAAAC 59.404 38.462 0.78 0.00 35.18 2.01
4831 8284 5.001232 TGGAACTGCAACAGAGTATAAACC 58.999 41.667 0.78 0.00 35.18 3.27
4832 8285 5.221843 TGGAACTGCAACAGAGTATAAACCT 60.222 40.000 0.78 0.00 35.18 3.50
4833 8286 5.351740 GGAACTGCAACAGAGTATAAACCTC 59.648 44.000 0.78 0.00 35.18 3.85
4834 8287 5.746990 ACTGCAACAGAGTATAAACCTCT 57.253 39.130 0.78 0.00 39.87 3.69
4835 8288 6.115448 ACTGCAACAGAGTATAAACCTCTT 57.885 37.500 0.78 0.00 37.18 2.85
4836 8289 5.934625 ACTGCAACAGAGTATAAACCTCTTG 59.065 40.000 0.78 0.00 37.18 3.02
4837 8290 4.695455 TGCAACAGAGTATAAACCTCTTGC 59.305 41.667 7.00 7.00 40.64 4.01
4838 8291 4.938226 GCAACAGAGTATAAACCTCTTGCT 59.062 41.667 6.78 0.00 38.70 3.91
4839 8292 5.163814 GCAACAGAGTATAAACCTCTTGCTG 60.164 44.000 6.78 0.00 38.70 4.41
4840 8293 5.746990 ACAGAGTATAAACCTCTTGCTGT 57.253 39.130 0.00 0.00 37.18 4.40
4841 8294 6.852420 ACAGAGTATAAACCTCTTGCTGTA 57.148 37.500 0.00 0.00 37.18 2.74
4842 8295 7.425224 ACAGAGTATAAACCTCTTGCTGTAT 57.575 36.000 0.00 0.00 37.18 2.29
4843 8296 7.493367 ACAGAGTATAAACCTCTTGCTGTATC 58.507 38.462 0.00 0.00 37.18 2.24
4844 8297 7.343316 ACAGAGTATAAACCTCTTGCTGTATCT 59.657 37.037 0.00 0.00 37.18 1.98
4845 8298 8.200792 CAGAGTATAAACCTCTTGCTGTATCTT 58.799 37.037 0.00 0.00 37.18 2.40
4846 8299 8.417884 AGAGTATAAACCTCTTGCTGTATCTTC 58.582 37.037 0.00 0.00 35.80 2.87
4847 8300 8.079211 AGTATAAACCTCTTGCTGTATCTTCA 57.921 34.615 0.00 0.00 0.00 3.02
4848 8301 7.982354 AGTATAAACCTCTTGCTGTATCTTCAC 59.018 37.037 0.00 0.00 0.00 3.18
4849 8302 4.899352 AACCTCTTGCTGTATCTTCACT 57.101 40.909 0.00 0.00 0.00 3.41
4850 8303 6.360370 AAACCTCTTGCTGTATCTTCACTA 57.640 37.500 0.00 0.00 0.00 2.74
4851 8304 5.331876 ACCTCTTGCTGTATCTTCACTAC 57.668 43.478 0.00 0.00 0.00 2.73
4852 8305 4.772624 ACCTCTTGCTGTATCTTCACTACA 59.227 41.667 0.00 0.00 0.00 2.74
4853 8306 5.423610 ACCTCTTGCTGTATCTTCACTACAT 59.576 40.000 0.00 0.00 0.00 2.29
4854 8307 6.070538 ACCTCTTGCTGTATCTTCACTACATT 60.071 38.462 0.00 0.00 0.00 2.71
4936 8390 5.994250 TCCAAGCTTGCATTATAAGTCTCT 58.006 37.500 21.43 0.00 0.00 3.10
5459 8998 0.103937 CTAGTAGCAGCAGCCTGGAC 59.896 60.000 0.00 0.00 43.56 4.02
5538 9083 1.228154 GTGCCGGTGGAACTCCTTT 60.228 57.895 1.90 0.00 40.32 3.11
5576 9121 0.908198 ATCTGGAAGGCTCAGTGGAC 59.092 55.000 3.45 0.00 34.15 4.02
5584 9129 1.298014 GCTCAGTGGACCTCCTTGG 59.702 63.158 0.00 0.00 42.93 3.61
5940 9502 7.703621 AGTTCCATTTCATTCTATCAAATTGCG 59.296 33.333 0.00 0.00 0.00 4.85
6130 9700 6.710597 ATATAGCCTCGTCAGTCTGTAAAA 57.289 37.500 0.00 0.00 0.00 1.52
6137 9707 0.669318 TCAGTCTGTAAAAGCGGGCG 60.669 55.000 0.00 0.00 0.00 6.13
6150 9720 3.503363 GGGCGCTGCTAGCTGTTG 61.503 66.667 21.03 15.22 39.60 3.33
6184 9754 6.039047 TGTTCTGATCTATACCGTGTAAGACC 59.961 42.308 0.00 0.00 0.00 3.85
6212 9782 4.612264 TGTGGACTAAAGTTGTACTCCC 57.388 45.455 0.00 0.00 0.00 4.30
6224 9794 4.081807 AGTTGTACTCCCGTCTGGATTTAC 60.082 45.833 0.00 0.00 44.07 2.01
6228 9798 1.139058 CTCCCGTCTGGATTTACAGGG 59.861 57.143 0.00 0.00 44.07 4.45
6356 10212 9.716507 AATGAAGTTTGGAATCGTATATTTTCG 57.283 29.630 0.00 0.00 0.00 3.46
6397 10253 8.749354 ACATTTAGGTATTCAAATCAAAGACCC 58.251 33.333 0.00 0.00 38.49 4.46
6433 10291 6.363065 CACACCCTGGATAGAACTAGTAGTA 58.637 44.000 2.50 0.00 0.00 1.82
6457 10315 9.583765 GTATTTACTCCCTCTGTACTAAAGTTG 57.416 37.037 0.00 0.00 0.00 3.16
6458 10316 7.844493 TTTACTCCCTCTGTACTAAAGTTGA 57.156 36.000 0.00 0.00 0.00 3.18
6459 10317 5.986501 ACTCCCTCTGTACTAAAGTTGAG 57.013 43.478 0.00 0.00 0.00 3.02
6483 10343 6.159398 AGACACTTATTTTGAGATGGAGGGAT 59.841 38.462 0.00 0.00 0.00 3.85
6505 10365 6.712095 GGATCATTGTAGATGACCTTGCATAA 59.288 38.462 0.00 0.00 0.00 1.90
6516 10376 4.754618 TGACCTTGCATAATAGGCATAACG 59.245 41.667 0.00 0.00 41.58 3.18
6581 10441 8.702438 ACATTTGATTTTTCATAGTTTTCGCAG 58.298 29.630 0.00 0.00 0.00 5.18
6657 10517 2.891112 CCACTTGTGTTGTGTTGCAAT 58.109 42.857 0.59 0.00 39.55 3.56
6711 10571 4.142924 CGCACTAGTGTTGCAACAATGATA 60.143 41.667 35.44 22.56 41.21 2.15
6730 10590 2.342279 CGGCGAGTGGTCCTTTGA 59.658 61.111 0.00 0.00 0.00 2.69
6760 10620 4.210328 CACTTGTGTTGTGTTGCTACGATA 59.790 41.667 0.00 0.00 0.00 2.92
6761 10621 4.447724 ACTTGTGTTGTGTTGCTACGATAG 59.552 41.667 0.00 0.00 46.19 2.08
6773 10633 2.889617 CGATAGTGGTCACGGGCA 59.110 61.111 0.00 0.00 36.20 5.36
6780 10640 0.535335 GTGGTCACGGGCAGATAAGA 59.465 55.000 0.00 0.00 0.00 2.10
6868 12704 2.674177 CGTGTAGTGGTGAATCAGACCC 60.674 54.545 0.00 0.00 31.84 4.46
6884 12720 2.727544 CCGTGCAAGGTGGTTTGG 59.272 61.111 10.93 0.00 0.00 3.28
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
48 49 2.869897 TGGTTGCAACTTTTTGTCGTC 58.130 42.857 27.64 8.66 34.90 4.20
54 55 4.022416 TGCTATCGATGGTTGCAACTTTTT 60.022 37.500 27.64 11.07 0.00 1.94
102 103 5.449588 CGCTCATATGAAATGGTTGAAGCTT 60.450 40.000 6.90 0.00 0.00 3.74
113 114 2.079158 CATCGGCCGCTCATATGAAAT 58.921 47.619 23.51 0.61 0.00 2.17
166 167 1.520342 GCCCTCGTCATCACAGCTC 60.520 63.158 0.00 0.00 0.00 4.09
179 180 1.600916 GCGGAATACCCATGCCCTC 60.601 63.158 0.00 0.00 34.14 4.30
180 181 2.515901 GCGGAATACCCATGCCCT 59.484 61.111 0.00 0.00 34.14 5.19
186 187 3.857038 GCCCTCGCGGAATACCCA 61.857 66.667 6.13 0.00 34.14 4.51
187 188 3.547513 AGCCCTCGCGGAATACCC 61.548 66.667 6.13 0.00 41.18 3.69
193 194 2.994995 TTTCTCAGCCCTCGCGGA 60.995 61.111 6.13 0.00 41.18 5.54
194 195 2.510238 CTTTCTCAGCCCTCGCGG 60.510 66.667 6.13 0.00 41.18 6.46
196 197 0.179113 CTCTCTTTCTCAGCCCTCGC 60.179 60.000 0.00 0.00 0.00 5.03
206 207 2.363172 GGCGCCTCCCTCTCTTTCT 61.363 63.158 22.15 0.00 0.00 2.52
228 229 1.598130 GACACACAGGCACACTCCC 60.598 63.158 0.00 0.00 0.00 4.30
229 230 0.463654 TTGACACACAGGCACACTCC 60.464 55.000 0.00 0.00 32.34 3.85
230 231 0.940126 CTTGACACACAGGCACACTC 59.060 55.000 0.00 0.00 32.34 3.51
238 239 0.041839 GAGTTGCGCTTGACACACAG 60.042 55.000 9.73 0.00 0.00 3.66
265 270 5.571658 GCAGGTTAATCCTTCTCCTTTCTCA 60.572 44.000 0.00 0.00 45.67 3.27
276 281 3.695830 TTCTCGTGCAGGTTAATCCTT 57.304 42.857 6.26 0.00 45.67 3.36
283 288 2.224523 TGGATCTTTTCTCGTGCAGGTT 60.225 45.455 6.26 0.00 0.00 3.50
306 313 4.739195 TCGCCCAATAATGTTTGTTTAGC 58.261 39.130 0.00 0.00 0.00 3.09
309 316 5.788450 TGATTCGCCCAATAATGTTTGTTT 58.212 33.333 0.00 0.00 0.00 2.83
316 323 3.371168 CCGTTTGATTCGCCCAATAATG 58.629 45.455 0.00 0.00 0.00 1.90
324 331 2.485122 CCAGCCGTTTGATTCGCC 59.515 61.111 0.00 0.00 0.00 5.54
347 354 1.531739 GCCCAAATTTGAGCCGGTCA 61.532 55.000 19.86 2.59 0.00 4.02
406 413 2.355818 GGGAGCGGTCAGGTTATTCTTT 60.356 50.000 17.59 0.00 0.00 2.52
407 414 1.209747 GGGAGCGGTCAGGTTATTCTT 59.790 52.381 17.59 0.00 0.00 2.52
408 415 0.831307 GGGAGCGGTCAGGTTATTCT 59.169 55.000 17.59 0.00 0.00 2.40
409 416 0.179054 GGGGAGCGGTCAGGTTATTC 60.179 60.000 17.59 0.00 0.00 1.75
410 417 0.912487 TGGGGAGCGGTCAGGTTATT 60.912 55.000 17.59 0.00 0.00 1.40
548 563 1.613630 AGGAGGATGAAGGGCACGT 60.614 57.895 0.00 0.00 0.00 4.49
551 566 0.549902 TTGGAGGAGGATGAAGGGCA 60.550 55.000 0.00 0.00 0.00 5.36
552 567 0.625849 TTTGGAGGAGGATGAAGGGC 59.374 55.000 0.00 0.00 0.00 5.19
577 592 4.897670 AGATTGCTATTTTGGGAATGGAGG 59.102 41.667 0.00 0.00 0.00 4.30
614 629 4.467107 GAGGGGAGGAGGAGCGGT 62.467 72.222 0.00 0.00 0.00 5.68
658 685 2.982130 CCGGGATGGGATCGATCC 59.018 66.667 32.57 32.57 46.41 3.36
698 730 2.770904 GGACGGGGGCCTTATGGA 60.771 66.667 0.84 0.00 34.57 3.41
699 731 4.250305 CGGACGGGGGCCTTATGG 62.250 72.222 0.84 0.00 0.00 2.74
700 732 4.929707 GCGGACGGGGGCCTTATG 62.930 72.222 0.84 0.00 0.00 1.90
728 760 0.384725 CGAGCTTTGACTGGCAAACG 60.385 55.000 4.15 3.80 41.37 3.60
729 761 0.661483 GCGAGCTTTGACTGGCAAAC 60.661 55.000 4.15 2.72 41.37 2.93
730 762 1.654220 GCGAGCTTTGACTGGCAAA 59.346 52.632 8.63 8.63 43.89 3.68
736 768 3.106407 GCGTCGCGAGCTTTGACT 61.106 61.111 10.24 0.00 0.00 3.41
783 815 2.603953 GAAAGCAGCTGAAAGATTGCC 58.396 47.619 20.43 0.00 44.08 4.52
842 874 1.074319 GAAATCGCGCTACGGACACA 61.074 55.000 5.56 0.00 43.89 3.72
892 924 1.571773 AAGGTGGGTGGGATAGGCAC 61.572 60.000 0.00 0.00 0.00 5.01
893 925 1.230149 AAGGTGGGTGGGATAGGCA 60.230 57.895 0.00 0.00 0.00 4.75
894 926 0.988678 AGAAGGTGGGTGGGATAGGC 60.989 60.000 0.00 0.00 0.00 3.93
897 929 1.335132 GCGAGAAGGTGGGTGGGATA 61.335 60.000 0.00 0.00 0.00 2.59
898 930 2.670148 GCGAGAAGGTGGGTGGGAT 61.670 63.158 0.00 0.00 0.00 3.85
970 1007 1.550130 CCAAGAACCCTCCCACGCTA 61.550 60.000 0.00 0.00 0.00 4.26
971 1008 2.750350 CAAGAACCCTCCCACGCT 59.250 61.111 0.00 0.00 0.00 5.07
1017 1069 0.980231 CCTCCTCCTCCTTGACCAGG 60.980 65.000 0.00 0.00 45.64 4.45
1254 1309 2.287248 GGAGAAGTTGCTGTGCTTGAAC 60.287 50.000 0.00 0.00 0.00 3.18
1322 1378 3.074390 TCTGCAAGAGGAATCAAGGGAAA 59.926 43.478 0.00 0.00 38.67 3.13
1396 1455 4.410492 GCTTCGAGAAGATGCAAAAGAA 57.590 40.909 16.23 0.00 45.93 2.52
1441 1501 3.728864 GCAACACAATCTCAATGGCTACG 60.729 47.826 0.00 0.00 0.00 3.51
1575 1667 5.220643 CCACCAATTTTCTGAAGTGCAAAAC 60.221 40.000 0.00 0.00 0.00 2.43
1613 1705 5.371526 CATTTCTGGGATTTAGCTCTGCTA 58.628 41.667 0.00 0.00 40.44 3.49
1672 2055 4.462483 GGATTCCCATGCACTTTTCTACAA 59.538 41.667 0.00 0.00 0.00 2.41
1732 2115 5.467399 GGCCCAACAGGTAAATTTTGTTAAC 59.533 40.000 6.45 0.00 38.26 2.01
1735 2118 3.493524 CGGCCCAACAGGTAAATTTTGTT 60.494 43.478 0.00 0.00 38.26 2.83
1756 2141 5.505654 GCATAAGGTTTATCCAACACATCCG 60.506 44.000 0.00 0.00 37.07 4.18
1764 2149 8.774546 TTAATGATGGCATAAGGTTTATCCAA 57.225 30.769 0.00 0.00 34.58 3.53
1797 2308 5.535030 AGAATAAACTTTCCTCGGCAACTTT 59.465 36.000 0.00 0.00 0.00 2.66
1898 2556 9.862371 ACAATTGTACAACACATACAAGAAAAA 57.138 25.926 11.22 0.00 43.76 1.94
1907 2565 6.038714 TGAAGCACACAATTGTACAACACATA 59.961 34.615 11.22 0.00 36.90 2.29
1927 2585 4.155644 GGCTCTAATATGAAGGCATGAAGC 59.844 45.833 0.00 0.00 44.65 3.86
2032 3160 6.299141 ACATATAACCTAAGATGGCACCAAG 58.701 40.000 0.00 0.00 0.00 3.61
2033 3161 6.126623 TGACATATAACCTAAGATGGCACCAA 60.127 38.462 0.00 0.00 32.33 3.67
2226 3488 3.435275 TCTCCTACAGTCATTCACAGCT 58.565 45.455 0.00 0.00 0.00 4.24
2449 3948 3.716872 TCAGGAGGTTCAAGGAAGACTTT 59.283 43.478 0.00 0.00 37.29 2.66
2574 4074 1.923227 GCTAAAGCGAACTGGGCCAC 61.923 60.000 0.00 0.00 0.00 5.01
2752 4254 0.865769 CGTAGACACTTTGTGGTGGC 59.134 55.000 2.72 0.00 44.95 5.01
2774 4276 3.411446 CTCAACACCAGGAACATGCTTA 58.589 45.455 0.00 0.00 0.00 3.09
2802 4304 7.112122 AGATGTTTGCATGGTTATTACTCTCA 58.888 34.615 0.00 0.00 35.07 3.27
2956 4458 1.011968 TACATCAACACGGCGACTGC 61.012 55.000 16.62 0.00 41.71 4.40
3014 4517 2.203480 TTGTCTGCCCAAGCCCAC 60.203 61.111 0.00 0.00 38.69 4.61
3032 4535 2.158959 CGCCGTCTTCTGCTTACCG 61.159 63.158 0.00 0.00 0.00 4.02
3047 4550 0.884704 TGACCAGCTCTTTGAACGCC 60.885 55.000 0.00 0.00 0.00 5.68
3048 4551 0.514691 CTGACCAGCTCTTTGAACGC 59.485 55.000 0.00 0.00 0.00 4.84
3120 4623 5.708948 CCAAATCTTCGCAGAAAAATACCA 58.291 37.500 0.00 0.00 45.90 3.25
3133 4636 2.639970 TGGTGTGGCCAAATCTTCG 58.360 52.632 7.24 0.00 45.94 3.79
3310 4813 2.292267 CATGGAGGGAGCAACATACAC 58.708 52.381 0.00 0.00 0.00 2.90
3516 5036 5.289675 AGCTTAGACATTGAAACGATCTTCG 59.710 40.000 0.00 0.00 46.93 3.79
3526 5046 9.066892 ACAAATAAGTGAAGCTTAGACATTGAA 57.933 29.630 0.00 0.00 42.34 2.69
3583 5146 7.486407 AGTTAATACTCCCTCCGTAAAGAAA 57.514 36.000 0.00 0.00 0.00 2.52
3714 5278 3.558418 GCTCGTAATAAATCGCCAGGAAA 59.442 43.478 0.00 0.00 0.00 3.13
3744 5308 7.829378 AAATCTTGAGATTGACTACGTTACC 57.171 36.000 6.98 0.00 43.41 2.85
3765 5329 5.413499 CCGGCAAATCTTGAGATTGAAAAT 58.587 37.500 6.98 0.00 43.41 1.82
3766 5330 4.808558 CCGGCAAATCTTGAGATTGAAAA 58.191 39.130 6.98 0.00 43.41 2.29
3767 5331 3.367292 GCCGGCAAATCTTGAGATTGAAA 60.367 43.478 24.80 0.00 43.41 2.69
3768 5332 2.164219 GCCGGCAAATCTTGAGATTGAA 59.836 45.455 24.80 0.00 43.41 2.69
3769 5333 1.745087 GCCGGCAAATCTTGAGATTGA 59.255 47.619 24.80 0.00 43.41 2.57
3770 5334 1.747355 AGCCGGCAAATCTTGAGATTG 59.253 47.619 31.54 3.69 43.41 2.67
3771 5335 2.019984 GAGCCGGCAAATCTTGAGATT 58.980 47.619 31.54 1.45 45.91 2.40
3772 5336 1.065199 TGAGCCGGCAAATCTTGAGAT 60.065 47.619 31.54 1.71 36.07 2.75
3773 5337 0.324614 TGAGCCGGCAAATCTTGAGA 59.675 50.000 31.54 0.00 0.00 3.27
3774 5338 0.731417 CTGAGCCGGCAAATCTTGAG 59.269 55.000 31.54 6.14 0.00 3.02
3775 5339 0.036732 ACTGAGCCGGCAAATCTTGA 59.963 50.000 31.54 0.00 0.00 3.02
3776 5340 1.737838 TACTGAGCCGGCAAATCTTG 58.262 50.000 31.54 16.07 0.00 3.02
3777 5341 2.171448 AGATACTGAGCCGGCAAATCTT 59.829 45.455 31.54 6.18 0.00 2.40
3778 5342 1.765314 AGATACTGAGCCGGCAAATCT 59.235 47.619 31.54 23.03 0.00 2.40
3779 5343 2.139118 GAGATACTGAGCCGGCAAATC 58.861 52.381 31.54 21.27 0.00 2.17
3804 5368 4.064768 CCCTGCCCCCATGAGCAA 62.065 66.667 0.00 0.00 38.82 3.91
3871 5435 8.455598 TTTTTAGAAACACAGTACAAAAGCAC 57.544 30.769 0.00 0.00 0.00 4.40
4044 5673 4.878397 ACTAGAGTTTGTCAATATGCTGCC 59.122 41.667 0.00 0.00 0.00 4.85
4348 5994 4.248058 CAATGAAGGAAAAATGAGGTGGC 58.752 43.478 0.00 0.00 0.00 5.01
4373 6020 2.856557 GACGTATGGAGGTTTCGTTAGC 59.143 50.000 0.00 0.00 34.93 3.09
4427 7444 4.087182 TGAACGACTAAACAGGGAGATCT 58.913 43.478 0.00 0.00 0.00 2.75
4549 7584 5.824243 AATAAAAGAACTGTCGACTCGTG 57.176 39.130 17.92 6.97 0.00 4.35
4789 8242 5.401531 TCCATCTCTTGGTACTGTTACAC 57.598 43.478 0.00 0.00 46.52 2.90
4798 8251 3.072330 TGTTGCAGTTCCATCTCTTGGTA 59.928 43.478 0.00 0.00 46.52 3.25
4799 8252 2.158623 TGTTGCAGTTCCATCTCTTGGT 60.159 45.455 0.00 0.00 46.52 3.67
4800 8253 3.808265 TCTGTTGCAGTTCCATCTCTTGG 60.808 47.826 0.00 0.00 38.59 3.61
4801 8254 3.405831 TCTGTTGCAGTTCCATCTCTTG 58.594 45.455 0.00 0.00 32.61 3.02
4802 8255 3.072184 ACTCTGTTGCAGTTCCATCTCTT 59.928 43.478 0.00 0.00 32.61 2.85
4803 8256 2.636893 ACTCTGTTGCAGTTCCATCTCT 59.363 45.455 0.00 0.00 32.61 3.10
4804 8257 3.051081 ACTCTGTTGCAGTTCCATCTC 57.949 47.619 0.00 0.00 32.61 2.75
4805 8258 4.833478 ATACTCTGTTGCAGTTCCATCT 57.167 40.909 0.00 0.00 32.61 2.90
4806 8259 6.183360 GGTTTATACTCTGTTGCAGTTCCATC 60.183 42.308 0.00 0.00 32.61 3.51
4807 8260 5.648092 GGTTTATACTCTGTTGCAGTTCCAT 59.352 40.000 0.00 0.00 32.61 3.41
4808 8261 5.001232 GGTTTATACTCTGTTGCAGTTCCA 58.999 41.667 0.00 0.00 32.61 3.53
4809 8262 5.246307 AGGTTTATACTCTGTTGCAGTTCC 58.754 41.667 0.00 0.00 32.61 3.62
4810 8263 6.166982 AGAGGTTTATACTCTGTTGCAGTTC 58.833 40.000 0.00 0.00 43.35 3.01
4812 8265 5.746990 AGAGGTTTATACTCTGTTGCAGT 57.253 39.130 0.00 0.00 43.35 4.40
4813 8266 6.414408 CAAGAGGTTTATACTCTGTTGCAG 57.586 41.667 0.00 0.00 44.17 4.41
4815 8268 5.223225 GCAAGAGGTTTATACTCTGTTGC 57.777 43.478 15.01 15.01 45.58 4.17
4816 8269 5.934625 ACAGCAAGAGGTTTATACTCTGTTG 59.065 40.000 0.00 0.00 44.17 3.33
4817 8270 6.115448 ACAGCAAGAGGTTTATACTCTGTT 57.885 37.500 0.00 0.00 44.17 3.16
4818 8271 5.746990 ACAGCAAGAGGTTTATACTCTGT 57.253 39.130 0.00 0.00 44.17 3.41
4819 8272 7.721402 AGATACAGCAAGAGGTTTATACTCTG 58.279 38.462 0.00 0.00 44.17 3.35
4820 8273 7.906199 AGATACAGCAAGAGGTTTATACTCT 57.094 36.000 0.00 0.00 46.77 3.24
4821 8274 8.198109 TGAAGATACAGCAAGAGGTTTATACTC 58.802 37.037 0.00 0.00 35.20 2.59
4822 8275 7.982354 GTGAAGATACAGCAAGAGGTTTATACT 59.018 37.037 0.00 0.00 0.00 2.12
4823 8276 7.982354 AGTGAAGATACAGCAAGAGGTTTATAC 59.018 37.037 0.00 0.00 0.00 1.47
4824 8277 8.079211 AGTGAAGATACAGCAAGAGGTTTATA 57.921 34.615 0.00 0.00 0.00 0.98
4825 8278 6.951971 AGTGAAGATACAGCAAGAGGTTTAT 58.048 36.000 0.00 0.00 0.00 1.40
4826 8279 6.360370 AGTGAAGATACAGCAAGAGGTTTA 57.640 37.500 0.00 0.00 0.00 2.01
4827 8280 5.234466 AGTGAAGATACAGCAAGAGGTTT 57.766 39.130 0.00 0.00 0.00 3.27
4828 8281 4.899352 AGTGAAGATACAGCAAGAGGTT 57.101 40.909 0.00 0.00 0.00 3.50
4829 8282 4.772624 TGTAGTGAAGATACAGCAAGAGGT 59.227 41.667 0.00 0.00 0.00 3.85
4830 8283 5.330455 TGTAGTGAAGATACAGCAAGAGG 57.670 43.478 0.00 0.00 0.00 3.69
4831 8284 9.539825 AATAATGTAGTGAAGATACAGCAAGAG 57.460 33.333 0.00 0.00 36.63 2.85
4936 8390 7.013834 ACATACCAGGGAAAATTTACTTCCAA 58.986 34.615 9.15 0.00 43.64 3.53
5262 8801 1.301716 GCTTCTGCTCGGTTCCACA 60.302 57.895 0.00 0.00 36.03 4.17
5538 9083 2.365105 GGGTGGGATCCCGTCAGA 60.365 66.667 26.03 4.80 37.93 3.27
5576 9121 0.461961 GGATCTCGTCACCAAGGAGG 59.538 60.000 0.00 0.00 39.78 4.30
5584 9129 1.517832 CCAGGTGGGATCTCGTCAC 59.482 63.158 0.00 0.00 40.01 3.67
5940 9502 3.896648 TGAAACATGAAGAAAGTCGCC 57.103 42.857 0.00 0.00 0.00 5.54
6137 9707 0.806868 TGCATTCAACAGCTAGCAGC 59.193 50.000 18.83 7.83 42.84 5.25
6150 9720 6.128715 CGGTATAGATCAGAACATGTGCATTC 60.129 42.308 6.60 0.00 0.00 2.67
6184 9754 5.479716 ACAACTTTAGTCCACAAAAGACG 57.520 39.130 2.08 0.00 39.31 4.18
6212 9782 2.158900 AGATGCCCTGTAAATCCAGACG 60.159 50.000 0.00 0.00 34.23 4.18
6224 9794 2.094675 CCTAACCACAAAGATGCCCTG 58.905 52.381 0.00 0.00 0.00 4.45
6228 9798 2.415512 GACGACCTAACCACAAAGATGC 59.584 50.000 0.00 0.00 0.00 3.91
6291 10124 6.263516 ACTCCATTTGAACATGATTCTGTG 57.736 37.500 0.00 1.46 0.00 3.66
6372 10228 8.748412 TGGGTCTTTGATTTGAATACCTAAATG 58.252 33.333 0.00 0.00 0.00 2.32
6397 10253 1.067915 CAGGGTGTGCGGGTATTTTTG 60.068 52.381 0.00 0.00 0.00 2.44
6433 10291 8.431910 TCAACTTTAGTACAGAGGGAGTAAAT 57.568 34.615 0.00 0.00 0.00 1.40
6451 10309 8.571336 CCATCTCAAAATAAGTGTCTCAACTTT 58.429 33.333 0.00 0.00 40.77 2.66
6457 10315 5.819901 CCCTCCATCTCAAAATAAGTGTCTC 59.180 44.000 0.00 0.00 0.00 3.36
6458 10316 5.488919 TCCCTCCATCTCAAAATAAGTGTCT 59.511 40.000 0.00 0.00 0.00 3.41
6459 10317 5.745227 TCCCTCCATCTCAAAATAAGTGTC 58.255 41.667 0.00 0.00 0.00 3.67
6475 10333 3.648067 GGTCATCTACAATGATCCCTCCA 59.352 47.826 0.00 0.00 0.00 3.86
6483 10343 7.879677 CCTATTATGCAAGGTCATCTACAATGA 59.120 37.037 0.00 0.00 0.00 2.57
6577 10437 6.105657 TGTAATTGAATACACATGACTGCG 57.894 37.500 0.00 0.00 31.03 5.18
6657 10517 1.623311 ACCACTCGTGACCATCATTCA 59.377 47.619 0.00 0.00 0.00 2.57
6681 10541 0.443869 CAACACTAGTGCGATGCCAC 59.556 55.000 22.90 0.00 35.98 5.01
6711 10571 3.626924 AAAGGACCACTCGCCGCT 61.627 61.111 0.00 0.00 0.00 5.52
6760 10620 0.537188 CTTATCTGCCCGTGACCACT 59.463 55.000 0.00 0.00 0.00 4.00
6761 10621 0.535335 TCTTATCTGCCCGTGACCAC 59.465 55.000 0.00 0.00 0.00 4.16
6770 10630 3.257393 CCATGCGACTATCTTATCTGCC 58.743 50.000 0.00 0.00 0.00 4.85
6773 10633 6.717540 ACTAAGACCATGCGACTATCTTATCT 59.282 38.462 0.00 0.00 32.82 1.98
6780 10640 3.296854 TGGACTAAGACCATGCGACTAT 58.703 45.455 0.00 0.00 32.03 2.12
6809 10669 3.166560 ACCTAGAGGACTTACCGTTGT 57.833 47.619 1.60 0.00 44.74 3.32
6811 10671 4.044946 AGAACCTAGAGGACTTACCGTT 57.955 45.455 1.60 0.00 44.74 4.44
6868 12704 1.065600 CACCAAACCACCTTGCACG 59.934 57.895 0.00 0.00 0.00 5.34
6884 12720 4.755266 ACAACTAGGGATCACCATACAC 57.245 45.455 0.00 0.00 43.89 2.90


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

AutoCloner maintained by Alex Coulton.