Multiple sequence alignment - TraesCS7D01G241300

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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 TraesCS7D01G241300 chr7D 100.000 5275 0 0 1 5275 205722566 205727840 0.000000e+00 9742.0
1 TraesCS7D01G241300 chr7D 94.702 151 8 0 1 151 478798973 478798823 8.830000e-58 235.0
2 TraesCS7D01G241300 chr7A 93.766 4347 194 37 152 4464 218025952 218030255 0.000000e+00 6455.0
3 TraesCS7D01G241300 chr7A 91.374 2817 173 30 1678 4464 213818721 213815945 0.000000e+00 3792.0
4 TraesCS7D01G241300 chr7A 93.822 437 25 1 935 1371 213820349 213819915 0.000000e+00 656.0
5 TraesCS7D01G241300 chr7A 94.539 293 14 2 1360 1650 213819012 213818720 8.060000e-123 451.0
6 TraesCS7D01G241300 chr7A 80.729 576 75 18 4670 5218 679742625 679742059 2.940000e-112 416.0
7 TraesCS7D01G241300 chr7B 92.994 4011 171 42 99 4063 196661008 196657062 0.000000e+00 5749.0
8 TraesCS7D01G241300 chr7B 90.364 1235 97 13 3235 4464 197475736 197474519 0.000000e+00 1602.0
9 TraesCS7D01G241300 chr7B 90.598 1170 62 20 624 1777 197486791 197485654 0.000000e+00 1507.0
10 TraesCS7D01G241300 chr7B 92.068 1059 69 5 2061 3107 197476793 197475738 0.000000e+00 1476.0
11 TraesCS7D01G241300 chr7B 95.813 406 12 3 4062 4464 196656788 196656385 0.000000e+00 651.0
12 TraesCS7D01G241300 chr7B 83.306 617 60 23 325 900 172568528 172569142 3.620000e-146 529.0
13 TraesCS7D01G241300 chr7B 95.057 263 12 1 1772 2034 197484954 197484693 3.800000e-111 412.0
14 TraesCS7D01G241300 chr7B 93.233 266 16 2 1125 1390 197487202 197486939 1.780000e-104 390.0
15 TraesCS7D01G241300 chr7B 92.202 218 17 0 920 1137 197490411 197490194 5.130000e-80 309.0
16 TraesCS7D01G241300 chr7B 95.395 152 6 1 1 151 706480051 706480202 1.900000e-59 241.0
17 TraesCS7D01G241300 chr7B 94.702 151 8 0 1 151 657535707 657535557 8.830000e-58 235.0
18 TraesCS7D01G241300 chr7B 89.116 147 11 3 4457 4600 570579057 570579201 1.510000e-40 178.0
19 TraesCS7D01G241300 chr5A 83.253 621 51 24 4671 5241 407932921 407932304 6.050000e-144 521.0
20 TraesCS7D01G241300 chr3D 83.139 599 61 15 4649 5235 116337848 116337278 1.310000e-140 510.0
21 TraesCS7D01G241300 chr3D 82.523 555 59 21 4716 5241 532234556 532235101 2.240000e-123 453.0
22 TraesCS7D01G241300 chr3B 82.208 607 80 15 4647 5233 169927413 169926815 1.020000e-136 497.0
23 TraesCS7D01G241300 chr3B 89.796 147 10 4 4457 4600 604820152 604820008 3.240000e-42 183.0
24 TraesCS7D01G241300 chr3B 89.116 147 11 4 4457 4600 553848927 553848783 1.510000e-40 178.0
25 TraesCS7D01G241300 chr3B 90.323 124 9 3 5118 5239 573365296 573365418 5.470000e-35 159.0
26 TraesCS7D01G241300 chr3A 80.960 625 84 22 4647 5242 667495529 667496147 3.720000e-126 462.0
27 TraesCS7D01G241300 chr2A 81.229 602 82 20 4665 5242 502339315 502339909 1.730000e-124 457.0
28 TraesCS7D01G241300 chr2A 82.495 457 56 17 4647 5085 324638356 324638806 3.860000e-101 379.0
29 TraesCS7D01G241300 chr2A 88.889 153 12 3 4451 4600 758586567 758586717 3.240000e-42 183.0
30 TraesCS7D01G241300 chr4D 88.056 360 36 7 4684 5039 478034403 478034759 2.270000e-113 420.0
31 TraesCS7D01G241300 chr4D 79.093 397 61 20 4853 5241 470199994 470200376 2.440000e-63 254.0
32 TraesCS7D01G241300 chr4D 87.903 124 14 1 5118 5240 478034800 478034923 1.530000e-30 145.0
33 TraesCS7D01G241300 chr4A 80.526 570 65 29 4691 5241 485289810 485290352 3.830000e-106 396.0
34 TraesCS7D01G241300 chr4A 93.750 160 9 1 1 160 670559525 670559683 6.830000e-59 239.0
35 TraesCS7D01G241300 chr2D 76.589 645 87 44 4640 5241 492297921 492298544 3.990000e-76 296.0
36 TraesCS7D01G241300 chr2D 76.592 628 78 48 4652 5239 340274109 340273511 1.120000e-71 281.0
37 TraesCS7D01G241300 chr2B 81.543 363 58 5 4667 5024 383065413 383065771 1.860000e-74 291.0
38 TraesCS7D01G241300 chr2B 94.702 151 8 0 1 151 175454454 175454604 8.830000e-58 235.0
39 TraesCS7D01G241300 chr2B 89.796 147 10 3 4457 4600 62601144 62601000 3.240000e-42 183.0
40 TraesCS7D01G241300 chr2B 90.141 142 10 2 4463 4600 361574993 361574852 1.170000e-41 182.0
41 TraesCS7D01G241300 chr1D 77.867 497 77 24 4762 5233 33337685 33337197 1.450000e-70 278.0
42 TraesCS7D01G241300 chr4B 95.333 150 7 0 1 150 649682164 649682313 6.830000e-59 239.0
43 TraesCS7D01G241300 chr4B 95.333 150 7 0 1 150 665293968 665293819 6.830000e-59 239.0
44 TraesCS7D01G241300 chrUn 94.771 153 7 1 1 152 50438187 50438339 2.460000e-58 237.0
45 TraesCS7D01G241300 chrUn 94.771 153 7 1 1 152 263185444 263185292 2.460000e-58 237.0
46 TraesCS7D01G241300 chr6B 90.476 147 9 3 4457 4600 15042425 15042281 6.970000e-44 189.0
47 TraesCS7D01G241300 chr6B 89.116 147 11 5 4457 4600 495568074 495567930 1.510000e-40 178.0
48 TraesCS7D01G241300 chr5B 89.116 147 11 3 4457 4600 270079481 270079625 1.510000e-40 178.0
49 TraesCS7D01G241300 chr1B 96.875 32 1 0 5239 5270 495959670 495959701 3.000000e-03 54.7


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 TraesCS7D01G241300 chr7D 205722566 205727840 5274 False 9742.0 9742 100.0000 1 5275 1 chr7D.!!$F1 5274
1 TraesCS7D01G241300 chr7A 218025952 218030255 4303 False 6455.0 6455 93.7660 152 4464 1 chr7A.!!$F1 4312
2 TraesCS7D01G241300 chr7A 213815945 213820349 4404 True 1633.0 3792 93.2450 935 4464 3 chr7A.!!$R2 3529
3 TraesCS7D01G241300 chr7A 679742059 679742625 566 True 416.0 416 80.7290 4670 5218 1 chr7A.!!$R1 548
4 TraesCS7D01G241300 chr7B 196656385 196661008 4623 True 3200.0 5749 94.4035 99 4464 2 chr7B.!!$R2 4365
5 TraesCS7D01G241300 chr7B 197474519 197476793 2274 True 1539.0 1602 91.2160 2061 4464 2 chr7B.!!$R3 2403
6 TraesCS7D01G241300 chr7B 197484693 197490411 5718 True 654.5 1507 92.7725 624 2034 4 chr7B.!!$R4 1410
7 TraesCS7D01G241300 chr7B 172568528 172569142 614 False 529.0 529 83.3060 325 900 1 chr7B.!!$F1 575
8 TraesCS7D01G241300 chr5A 407932304 407932921 617 True 521.0 521 83.2530 4671 5241 1 chr5A.!!$R1 570
9 TraesCS7D01G241300 chr3D 116337278 116337848 570 True 510.0 510 83.1390 4649 5235 1 chr3D.!!$R1 586
10 TraesCS7D01G241300 chr3D 532234556 532235101 545 False 453.0 453 82.5230 4716 5241 1 chr3D.!!$F1 525
11 TraesCS7D01G241300 chr3B 169926815 169927413 598 True 497.0 497 82.2080 4647 5233 1 chr3B.!!$R1 586
12 TraesCS7D01G241300 chr3A 667495529 667496147 618 False 462.0 462 80.9600 4647 5242 1 chr3A.!!$F1 595
13 TraesCS7D01G241300 chr2A 502339315 502339909 594 False 457.0 457 81.2290 4665 5242 1 chr2A.!!$F2 577
14 TraesCS7D01G241300 chr4D 478034403 478034923 520 False 282.5 420 87.9795 4684 5240 2 chr4D.!!$F2 556
15 TraesCS7D01G241300 chr4A 485289810 485290352 542 False 396.0 396 80.5260 4691 5241 1 chr4A.!!$F1 550
16 TraesCS7D01G241300 chr2D 492297921 492298544 623 False 296.0 296 76.5890 4640 5241 1 chr2D.!!$F1 601
17 TraesCS7D01G241300 chr2D 340273511 340274109 598 True 281.0 281 76.5920 4652 5239 1 chr2D.!!$R1 587

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
45 46 0.040958 CTTGCGTTGGTGTCAAGCTC 60.041 55.0 0.00 0.0 32.92 4.09 F
1251 4274 0.179137 TCAGTGAGGTAAGATGCGCG 60.179 55.0 0.00 0.0 0.00 6.86 F
1573 5510 0.769386 ACCCGGGGTTGAGGTTAGTT 60.769 55.0 27.92 0.0 27.29 2.24 F
2366 7030 0.998928 TGGCACCAGTGGGATATGTT 59.001 50.0 15.21 0.0 38.05 2.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1643 5581 0.250727 CGGGGTCCAAGAAGAGCAAA 60.251 55.000 0.00 0.00 35.95 3.68 R
2953 7631 1.156736 CCCAAGCTTGTAACCGACAG 58.843 55.000 24.35 6.18 39.88 3.51 R
2961 7639 1.213296 GATCCTCCCCCAAGCTTGTA 58.787 55.000 24.35 6.77 0.00 2.41 R
4345 9301 1.325640 CATTCTCATCGCACAAGACCG 59.674 52.381 0.00 0.00 0.00 4.79 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
29 30 2.046892 CCGGAGGCAGGTGACTTG 60.047 66.667 0.00 0.00 46.14 3.16
30 31 2.743928 CGGAGGCAGGTGACTTGC 60.744 66.667 11.57 11.57 40.21 4.01
31 32 2.743928 GGAGGCAGGTGACTTGCG 60.744 66.667 13.59 0.00 40.21 4.85
33 34 1.598130 GAGGCAGGTGACTTGCGTT 60.598 57.895 15.77 5.73 40.21 4.84
34 35 1.845809 GAGGCAGGTGACTTGCGTTG 61.846 60.000 15.77 0.00 40.21 4.10
35 36 2.639286 GCAGGTGACTTGCGTTGG 59.361 61.111 3.35 0.00 40.21 3.77
36 37 2.186826 GCAGGTGACTTGCGTTGGT 61.187 57.895 3.35 0.00 40.21 3.67
37 38 1.648720 CAGGTGACTTGCGTTGGTG 59.351 57.895 0.00 0.00 40.21 4.17
38 39 1.095228 CAGGTGACTTGCGTTGGTGT 61.095 55.000 0.00 0.00 40.21 4.16
41 42 0.730265 GTGACTTGCGTTGGTGTCAA 59.270 50.000 0.00 0.00 40.47 3.18
42 43 1.013596 TGACTTGCGTTGGTGTCAAG 58.986 50.000 0.00 0.00 41.99 3.02
43 44 0.317020 GACTTGCGTTGGTGTCAAGC 60.317 55.000 0.00 0.00 40.45 4.01
44 45 0.748005 ACTTGCGTTGGTGTCAAGCT 60.748 50.000 0.00 0.00 40.45 3.74
45 46 0.040958 CTTGCGTTGGTGTCAAGCTC 60.041 55.000 0.00 0.00 32.92 4.09
47 48 1.159713 TGCGTTGGTGTCAAGCTCAG 61.160 55.000 0.00 0.00 32.92 3.35
48 49 0.880278 GCGTTGGTGTCAAGCTCAGA 60.880 55.000 0.00 0.00 32.92 3.27
51 52 2.611473 CGTTGGTGTCAAGCTCAGAGAT 60.611 50.000 0.00 0.00 32.92 2.75
52 53 2.740981 GTTGGTGTCAAGCTCAGAGATG 59.259 50.000 0.00 0.00 32.92 2.90
53 54 1.973515 TGGTGTCAAGCTCAGAGATGT 59.026 47.619 0.00 0.00 0.00 3.06
54 55 2.369860 TGGTGTCAAGCTCAGAGATGTT 59.630 45.455 0.00 0.00 0.00 2.71
55 56 2.999355 GGTGTCAAGCTCAGAGATGTTC 59.001 50.000 0.00 0.00 0.00 3.18
56 57 3.306641 GGTGTCAAGCTCAGAGATGTTCT 60.307 47.826 0.00 0.00 36.25 3.01
71 72 7.333921 CAGAGATGTTCTGCTATCTTTTCAGTT 59.666 37.037 0.00 0.00 46.30 3.16
72 73 7.882271 AGAGATGTTCTGCTATCTTTTCAGTTT 59.118 33.333 0.00 0.00 33.97 2.66
73 74 8.401490 AGATGTTCTGCTATCTTTTCAGTTTT 57.599 30.769 0.00 0.00 29.64 2.43
75 76 7.333528 TGTTCTGCTATCTTTTCAGTTTTGT 57.666 32.000 0.00 0.00 0.00 2.83
76 77 7.417612 TGTTCTGCTATCTTTTCAGTTTTGTC 58.582 34.615 0.00 0.00 0.00 3.18
77 78 7.066887 TGTTCTGCTATCTTTTCAGTTTTGTCA 59.933 33.333 0.00 0.00 0.00 3.58
78 79 7.750229 TCTGCTATCTTTTCAGTTTTGTCAT 57.250 32.000 0.00 0.00 0.00 3.06
80 81 9.453572 TCTGCTATCTTTTCAGTTTTGTCATAT 57.546 29.630 0.00 0.00 0.00 1.78
81 82 9.713740 CTGCTATCTTTTCAGTTTTGTCATATC 57.286 33.333 0.00 0.00 0.00 1.63
82 83 8.390354 TGCTATCTTTTCAGTTTTGTCATATCG 58.610 33.333 0.00 0.00 0.00 2.92
84 85 7.687941 ATCTTTTCAGTTTTGTCATATCGGT 57.312 32.000 0.00 0.00 0.00 4.69
85 86 7.504924 TCTTTTCAGTTTTGTCATATCGGTT 57.495 32.000 0.00 0.00 0.00 4.44
86 87 7.581476 TCTTTTCAGTTTTGTCATATCGGTTC 58.419 34.615 0.00 0.00 0.00 3.62
87 88 7.444183 TCTTTTCAGTTTTGTCATATCGGTTCT 59.556 33.333 0.00 0.00 0.00 3.01
88 89 7.504924 TTTCAGTTTTGTCATATCGGTTCTT 57.495 32.000 0.00 0.00 0.00 2.52
90 91 7.591006 TCAGTTTTGTCATATCGGTTCTTAC 57.409 36.000 0.00 0.00 0.00 2.34
91 92 6.309494 TCAGTTTTGTCATATCGGTTCTTACG 59.691 38.462 0.00 0.00 0.00 3.18
92 93 6.090358 CAGTTTTGTCATATCGGTTCTTACGT 59.910 38.462 0.00 0.00 0.00 3.57
93 94 6.090358 AGTTTTGTCATATCGGTTCTTACGTG 59.910 38.462 0.00 0.00 0.00 4.49
94 95 4.968812 TGTCATATCGGTTCTTACGTGA 57.031 40.909 0.00 0.00 0.00 4.35
95 96 4.665212 TGTCATATCGGTTCTTACGTGAC 58.335 43.478 0.00 0.00 36.26 3.67
96 97 4.397103 TGTCATATCGGTTCTTACGTGACT 59.603 41.667 0.00 0.00 36.57 3.41
97 98 4.968788 GTCATATCGGTTCTTACGTGACTC 59.031 45.833 0.00 0.00 33.74 3.36
113 114 6.686130 CGTGACTCGTACTTTGTTCTTTAT 57.314 37.500 0.00 0.00 34.52 1.40
168 182 3.692791 AAAGTTCAGAAGGCGTGTTTC 57.307 42.857 0.00 0.00 0.00 2.78
199 213 3.742369 CGGAGGCGTAAACTTGTTCTTAA 59.258 43.478 0.00 0.00 0.00 1.85
200 214 4.376717 CGGAGGCGTAAACTTGTTCTTAAC 60.377 45.833 0.00 0.00 0.00 2.01
202 216 4.711399 AGGCGTAAACTTGTTCTTAACCT 58.289 39.130 0.00 0.00 0.00 3.50
203 217 4.753610 AGGCGTAAACTTGTTCTTAACCTC 59.246 41.667 0.00 0.00 0.00 3.85
204 218 4.512571 GGCGTAAACTTGTTCTTAACCTCA 59.487 41.667 0.00 0.00 0.00 3.86
205 219 5.333875 GGCGTAAACTTGTTCTTAACCTCAG 60.334 44.000 0.00 0.00 0.00 3.35
314 328 2.126424 GCGCTCTCGAACGTTCCT 60.126 61.111 22.07 0.00 38.10 3.36
337 351 1.884497 CGCCTCCAAATAACCCACACA 60.884 52.381 0.00 0.00 0.00 3.72
339 353 2.167662 CCTCCAAATAACCCACACACC 58.832 52.381 0.00 0.00 0.00 4.16
340 354 2.225017 CCTCCAAATAACCCACACACCT 60.225 50.000 0.00 0.00 0.00 4.00
347 361 1.065997 AACCCACACACCTAAGGGCT 61.066 55.000 0.00 0.00 45.45 5.19
368 382 3.329542 GAGGCGGCCCATCACTTCA 62.330 63.158 17.02 0.00 0.00 3.02
375 389 2.390599 CCCATCACTTCACCGCGTG 61.391 63.158 4.92 3.64 34.45 5.34
607 627 0.322546 GTCGAATTGGGGGCAGTCTT 60.323 55.000 0.00 0.00 0.00 3.01
608 628 1.065709 GTCGAATTGGGGGCAGTCTTA 60.066 52.381 0.00 0.00 0.00 2.10
670 3668 7.900782 TTTGTATGTCTAGTTTTCTACAGCC 57.099 36.000 0.00 0.00 0.00 4.85
672 3670 7.241042 TGTATGTCTAGTTTTCTACAGCCTT 57.759 36.000 0.00 0.00 0.00 4.35
682 3680 7.004691 AGTTTTCTACAGCCTTGGTAAAGATT 58.995 34.615 0.00 0.00 35.19 2.40
708 3707 5.304686 TGGAAGTATTGGGGTAGCAATAG 57.695 43.478 0.00 0.00 0.00 1.73
743 3742 2.050442 CCTTTTGGTTGCGCGGAC 60.050 61.111 8.83 3.71 34.07 4.79
781 3781 6.484288 TCCAATATTTTCCTCTGCTTCTGAA 58.516 36.000 0.00 0.00 0.00 3.02
813 3826 6.381994 TCGGGAATTAGGAGTAGTGTAATTGT 59.618 38.462 0.00 0.00 0.00 2.71
817 3830 9.227777 GGAATTAGGAGTAGTGTAATTGTGTTT 57.772 33.333 0.00 0.00 0.00 2.83
903 3923 3.591527 TCCCTTCCCACTGATAACATTGT 59.408 43.478 0.00 0.00 0.00 2.71
914 3934 7.094677 CCACTGATAACATTGTTGAGATGACAA 60.095 37.037 12.30 0.00 40.86 3.18
919 3939 8.797350 ATAACATTGTTGAGATGACAATCTGA 57.203 30.769 12.30 0.00 43.75 3.27
1109 4132 2.296945 TTTGGGCAACTGCTCCAGGT 62.297 55.000 0.00 0.00 41.95 4.00
1113 4136 1.616159 GGCAACTGCTCCAGGTTTTA 58.384 50.000 1.06 0.00 41.70 1.52
1200 4223 3.588842 TGATCAGTCCATTTTCAGACCCT 59.411 43.478 0.00 0.00 33.29 4.34
1251 4274 0.179137 TCAGTGAGGTAAGATGCGCG 60.179 55.000 0.00 0.00 0.00 6.86
1329 4352 4.510038 ACATCATTTCTGTGCACCTTTC 57.490 40.909 15.69 0.00 0.00 2.62
1330 4353 4.147321 ACATCATTTCTGTGCACCTTTCT 58.853 39.130 15.69 0.00 0.00 2.52
1423 5360 6.096001 GGAAGTATCAGACAATGGCAAAAGAT 59.904 38.462 0.00 0.00 0.00 2.40
1573 5510 0.769386 ACCCGGGGTTGAGGTTAGTT 60.769 55.000 27.92 0.00 27.29 2.24
1587 5524 7.086685 TGAGGTTAGTTAATTTTCTGACCCT 57.913 36.000 15.00 7.52 39.95 4.34
1643 5581 6.041182 CCATTGGATAACAATCATGACACCAT 59.959 38.462 0.00 0.00 46.67 3.55
1646 5584 6.865411 TGGATAACAATCATGACACCATTTG 58.135 36.000 0.00 0.00 30.61 2.32
1647 5585 5.750067 GGATAACAATCATGACACCATTTGC 59.250 40.000 0.00 0.00 28.38 3.68
1648 5586 4.877378 AACAATCATGACACCATTTGCT 57.123 36.364 0.00 0.00 28.38 3.91
1649 5587 4.445452 ACAATCATGACACCATTTGCTC 57.555 40.909 0.00 0.00 28.38 4.26
1650 5588 4.084287 ACAATCATGACACCATTTGCTCT 58.916 39.130 0.00 0.00 28.38 4.09
1652 5590 4.978083 ATCATGACACCATTTGCTCTTC 57.022 40.909 0.00 0.00 0.00 2.87
1731 5670 8.528044 TTGTACCTTTACATTTTTGGTCTTCT 57.472 30.769 0.00 0.00 38.05 2.85
1881 6525 5.435291 AGAGCATAGAAGACCCAAAATCAG 58.565 41.667 0.00 0.00 0.00 2.90
1882 6526 5.045286 AGAGCATAGAAGACCCAAAATCAGT 60.045 40.000 0.00 0.00 0.00 3.41
1885 6529 6.494835 AGCATAGAAGACCCAAAATCAGTTTT 59.505 34.615 0.00 0.00 38.03 2.43
2199 6861 5.124457 GGAAGCTCTGAAAAGAATGCACATA 59.876 40.000 0.00 0.00 0.00 2.29
2366 7030 0.998928 TGGCACCAGTGGGATATGTT 59.001 50.000 15.21 0.00 38.05 2.71
2804 7482 4.576463 CCAGCTGTTTACTTTGACTTCACT 59.424 41.667 13.81 0.00 0.00 3.41
2942 7620 8.868522 ATGAAGATGAGTTTGATTTAGAACCA 57.131 30.769 0.00 0.00 0.00 3.67
2953 7631 4.637534 TGATTTAGAACCAGAAGCTCATGC 59.362 41.667 0.00 0.00 40.05 4.06
2981 7659 0.846427 ACAAGCTTGGGGGAGGATCA 60.846 55.000 29.18 0.00 36.25 2.92
3099 7777 6.926313 AGTGTTACTAAATCTGTGGAGAGAC 58.074 40.000 0.00 0.00 0.00 3.36
3146 7824 0.954449 CTGATCCGGATGATGCTGGC 60.954 60.000 24.82 4.99 32.41 4.85
3194 7872 0.108138 CGGAACCAGACCCAGATGAC 60.108 60.000 0.00 0.00 0.00 3.06
3197 7875 2.427506 GAACCAGACCCAGATGACAAC 58.572 52.381 0.00 0.00 0.00 3.32
3308 7986 1.399440 CCTGTTCCTGATGATGTTGCG 59.601 52.381 0.00 0.00 0.00 4.85
3384 8062 4.183865 TGACATGCTTAACAAGGAGATCG 58.816 43.478 0.00 0.00 30.29 3.69
3409 8087 4.202441 GGTGAGCATGATAATGAACCTGT 58.798 43.478 0.00 0.00 0.00 4.00
3615 8293 3.261933 GCTGTGGAGCTGTTCTGC 58.738 61.111 0.00 0.00 42.52 4.26
3632 8310 7.325660 TGTTCTGCAATCTGGAAATAAGATC 57.674 36.000 0.00 0.00 33.17 2.75
3705 8383 1.224075 CCCTGACGATAATGCTGCTG 58.776 55.000 0.00 0.00 0.00 4.41
3707 8385 1.863454 CCTGACGATAATGCTGCTGAC 59.137 52.381 0.00 0.00 0.00 3.51
3978 8656 9.425248 AATTATTGCTAATCCTCATCCTTTTCA 57.575 29.630 0.00 0.00 0.00 2.69
3987 8665 4.584325 TCCTCATCCTTTTCACCAAACTTG 59.416 41.667 0.00 0.00 0.00 3.16
4223 9179 2.094649 CCTGGTACTGAAGAGGAACGAC 60.095 54.545 0.00 0.00 0.00 4.34
4345 9301 3.059665 GTGCTGCAAAAATGGTTTAGTGC 60.060 43.478 2.77 0.00 35.51 4.40
4380 9337 7.516470 GCGATGAGAATGAGAACATGAAACTAG 60.516 40.741 0.00 0.00 36.79 2.57
4387 9344 4.515191 TGAGAACATGAAACTAGGTGTTGC 59.485 41.667 0.00 0.00 39.13 4.17
4403 9360 2.157738 GTTGCCTGTCAGCTTCTCAAT 58.842 47.619 0.00 0.00 0.00 2.57
4436 9395 5.866159 ATATGTGATTGCAGAGAGACTCA 57.134 39.130 5.02 0.00 32.06 3.41
4464 9423 2.170607 TCTTGTCTGGGGCTTATGCTAC 59.829 50.000 0.13 0.00 39.59 3.58
4465 9424 1.879575 TGTCTGGGGCTTATGCTACT 58.120 50.000 0.13 0.00 39.59 2.57
4466 9425 1.762957 TGTCTGGGGCTTATGCTACTC 59.237 52.381 0.13 0.00 39.59 2.59
4467 9426 1.070914 GTCTGGGGCTTATGCTACTCC 59.929 57.143 0.13 0.00 39.59 3.85
4468 9427 0.398318 CTGGGGCTTATGCTACTCCC 59.602 60.000 5.90 5.90 37.43 4.30
4469 9428 0.030092 TGGGGCTTATGCTACTCCCT 60.030 55.000 12.04 0.00 37.68 4.20
4470 9429 0.687920 GGGGCTTATGCTACTCCCTC 59.312 60.000 0.13 0.00 39.59 4.30
4471 9430 0.687920 GGGCTTATGCTACTCCCTCC 59.312 60.000 0.13 0.00 39.59 4.30
4472 9431 0.318762 GGCTTATGCTACTCCCTCCG 59.681 60.000 0.13 0.00 39.59 4.63
4473 9432 1.041437 GCTTATGCTACTCCCTCCGT 58.959 55.000 0.00 0.00 36.03 4.69
4474 9433 1.413077 GCTTATGCTACTCCCTCCGTT 59.587 52.381 0.00 0.00 36.03 4.44
4475 9434 2.546162 GCTTATGCTACTCCCTCCGTTC 60.546 54.545 0.00 0.00 36.03 3.95
4476 9435 1.700955 TATGCTACTCCCTCCGTTCC 58.299 55.000 0.00 0.00 0.00 3.62
4477 9436 0.032017 ATGCTACTCCCTCCGTTCCT 60.032 55.000 0.00 0.00 0.00 3.36
4478 9437 0.627451 TGCTACTCCCTCCGTTCCTA 59.373 55.000 0.00 0.00 0.00 2.94
4479 9438 1.006281 TGCTACTCCCTCCGTTCCTAA 59.994 52.381 0.00 0.00 0.00 2.69
4480 9439 2.105766 GCTACTCCCTCCGTTCCTAAA 58.894 52.381 0.00 0.00 0.00 1.85
4481 9440 2.699321 GCTACTCCCTCCGTTCCTAAAT 59.301 50.000 0.00 0.00 0.00 1.40
4482 9441 3.893813 GCTACTCCCTCCGTTCCTAAATA 59.106 47.826 0.00 0.00 0.00 1.40
4483 9442 4.261952 GCTACTCCCTCCGTTCCTAAATAC 60.262 50.000 0.00 0.00 0.00 1.89
4484 9443 3.716431 ACTCCCTCCGTTCCTAAATACA 58.284 45.455 0.00 0.00 0.00 2.29
4485 9444 4.098894 ACTCCCTCCGTTCCTAAATACAA 58.901 43.478 0.00 0.00 0.00 2.41
4486 9445 4.161754 ACTCCCTCCGTTCCTAAATACAAG 59.838 45.833 0.00 0.00 0.00 3.16
4487 9446 4.098894 TCCCTCCGTTCCTAAATACAAGT 58.901 43.478 0.00 0.00 0.00 3.16
4488 9447 4.161001 TCCCTCCGTTCCTAAATACAAGTC 59.839 45.833 0.00 0.00 0.00 3.01
4489 9448 4.439968 CCTCCGTTCCTAAATACAAGTCC 58.560 47.826 0.00 0.00 0.00 3.85
4490 9449 4.161754 CCTCCGTTCCTAAATACAAGTCCT 59.838 45.833 0.00 0.00 0.00 3.85
4491 9450 5.338137 CCTCCGTTCCTAAATACAAGTCCTT 60.338 44.000 0.00 0.00 0.00 3.36
4492 9451 6.117975 TCCGTTCCTAAATACAAGTCCTTT 57.882 37.500 0.00 0.00 0.00 3.11
4493 9452 6.536447 TCCGTTCCTAAATACAAGTCCTTTT 58.464 36.000 0.00 0.00 0.00 2.27
4494 9453 7.678837 TCCGTTCCTAAATACAAGTCCTTTTA 58.321 34.615 0.00 0.00 0.00 1.52
4495 9454 7.820872 TCCGTTCCTAAATACAAGTCCTTTTAG 59.179 37.037 0.00 0.00 33.47 1.85
4496 9455 7.820872 CCGTTCCTAAATACAAGTCCTTTTAGA 59.179 37.037 0.00 0.00 34.90 2.10
4497 9456 8.870879 CGTTCCTAAATACAAGTCCTTTTAGAG 58.129 37.037 0.00 0.00 34.90 2.43
4498 9457 9.939802 GTTCCTAAATACAAGTCCTTTTAGAGA 57.060 33.333 0.00 0.00 34.90 3.10
4530 9489 9.692749 ATATGGACTACATACGTAAAATGAGTG 57.307 33.333 0.00 0.00 44.41 3.51
4531 9490 7.160547 TGGACTACATACGTAAAATGAGTGA 57.839 36.000 0.00 0.00 0.00 3.41
4532 9491 7.604549 TGGACTACATACGTAAAATGAGTGAA 58.395 34.615 0.00 0.00 0.00 3.18
4533 9492 8.255206 TGGACTACATACGTAAAATGAGTGAAT 58.745 33.333 0.00 0.00 0.00 2.57
4534 9493 8.753175 GGACTACATACGTAAAATGAGTGAATC 58.247 37.037 0.00 0.00 0.00 2.52
4535 9494 9.517609 GACTACATACGTAAAATGAGTGAATCT 57.482 33.333 0.00 0.00 0.00 2.40
4539 9498 9.084164 ACATACGTAAAATGAGTGAATCTACAC 57.916 33.333 0.00 0.00 40.60 2.90
4552 9511 7.493367 AGTGAATCTACACTCTAAACTATGGC 58.507 38.462 0.00 0.00 46.36 4.40
4553 9512 7.343316 AGTGAATCTACACTCTAAACTATGGCT 59.657 37.037 0.00 0.00 46.36 4.75
4554 9513 8.630917 GTGAATCTACACTCTAAACTATGGCTA 58.369 37.037 0.00 0.00 37.73 3.93
4555 9514 9.368416 TGAATCTACACTCTAAACTATGGCTAT 57.632 33.333 0.00 0.00 0.00 2.97
4564 9523 8.904834 ACTCTAAACTATGGCTATATACATCCG 58.095 37.037 0.00 0.00 0.00 4.18
4565 9524 8.818622 TCTAAACTATGGCTATATACATCCGT 57.181 34.615 0.00 0.00 0.00 4.69
4566 9525 9.910267 TCTAAACTATGGCTATATACATCCGTA 57.090 33.333 0.00 0.00 0.00 4.02
4610 9569 2.304221 AAAAACTTACAGCCTCCCCC 57.696 50.000 0.00 0.00 0.00 5.40
4634 9593 3.826822 CCCCACCACCACCACCAA 61.827 66.667 0.00 0.00 0.00 3.67
4635 9594 2.280416 CCCACCACCACCACCAAA 59.720 61.111 0.00 0.00 0.00 3.28
4636 9595 2.131067 CCCACCACCACCACCAAAC 61.131 63.158 0.00 0.00 0.00 2.93
4637 9596 1.380515 CCACCACCACCACCAAACA 60.381 57.895 0.00 0.00 0.00 2.83
4638 9597 1.391157 CCACCACCACCACCAAACAG 61.391 60.000 0.00 0.00 0.00 3.16
4639 9598 1.756561 ACCACCACCACCAAACAGC 60.757 57.895 0.00 0.00 0.00 4.40
4640 9599 2.498056 CCACCACCACCAAACAGCC 61.498 63.158 0.00 0.00 0.00 4.85
4641 9600 2.123468 ACCACCACCAAACAGCCC 60.123 61.111 0.00 0.00 0.00 5.19
4642 9601 2.917227 CCACCACCAAACAGCCCC 60.917 66.667 0.00 0.00 0.00 5.80
4643 9602 2.198426 CACCACCAAACAGCCCCT 59.802 61.111 0.00 0.00 0.00 4.79
4644 9603 1.457455 CACCACCAAACAGCCCCTT 60.457 57.895 0.00 0.00 0.00 3.95
4645 9604 1.457455 ACCACCAAACAGCCCCTTG 60.457 57.895 0.00 0.00 0.00 3.61
4646 9605 1.152567 CCACCAAACAGCCCCTTGA 60.153 57.895 0.00 0.00 0.00 3.02
4647 9606 0.758685 CCACCAAACAGCCCCTTGAA 60.759 55.000 0.00 0.00 0.00 2.69
4708 9668 2.685388 GCACCCCTAGAAGCTCATTTTC 59.315 50.000 0.00 0.00 0.00 2.29
4816 9800 4.671590 TGGACCCGCCGAGTCAGA 62.672 66.667 0.14 0.00 40.66 3.27
4985 9996 1.676635 ATGCGTCCACATTGCTGCT 60.677 52.632 0.00 0.00 0.00 4.24
5054 10071 0.178068 TTGCCATAACCGCTCTCTCC 59.822 55.000 0.00 0.00 0.00 3.71
5055 10072 1.069935 GCCATAACCGCTCTCTCCC 59.930 63.158 0.00 0.00 0.00 4.30
5092 10115 1.003696 TCTCTCTCTCTCGCCACTGAA 59.996 52.381 0.00 0.00 0.00 3.02
5145 10215 1.595357 GTTTCCCCGACGATGGAGT 59.405 57.895 0.00 0.00 30.91 3.85
5243 10314 3.803082 CGACATGCGGGTGCCAAG 61.803 66.667 0.00 0.00 41.78 3.61
5244 10315 2.359850 GACATGCGGGTGCCAAGA 60.360 61.111 0.00 0.00 41.78 3.02
5245 10316 1.750399 GACATGCGGGTGCCAAGAT 60.750 57.895 0.00 0.00 41.78 2.40
5246 10317 1.718757 GACATGCGGGTGCCAAGATC 61.719 60.000 0.00 0.00 41.78 2.75
5247 10318 2.514592 ATGCGGGTGCCAAGATCG 60.515 61.111 0.00 0.00 41.78 3.69
5255 10326 4.656558 GCCAAGATCGCGCGCATC 62.657 66.667 32.61 28.52 0.00 3.91
5256 10327 3.264159 CCAAGATCGCGCGCATCA 61.264 61.111 32.61 14.82 0.00 3.07
5257 10328 2.244669 CAAGATCGCGCGCATCAG 59.755 61.111 32.61 21.71 0.00 2.90
5258 10329 2.963854 AAGATCGCGCGCATCAGG 60.964 61.111 32.61 14.68 0.00 3.86
5259 10330 3.723235 AAGATCGCGCGCATCAGGT 62.723 57.895 32.61 11.13 0.00 4.00
5260 10331 3.696426 GATCGCGCGCATCAGGTC 61.696 66.667 32.61 16.66 0.00 3.85
5267 10338 3.250323 CGCATCAGGTCGTCGCTG 61.250 66.667 0.00 0.00 0.00 5.18
5268 10339 3.558411 GCATCAGGTCGTCGCTGC 61.558 66.667 0.00 0.00 0.00 5.25
5269 10340 2.887568 CATCAGGTCGTCGCTGCC 60.888 66.667 0.00 0.00 0.00 4.85
5270 10341 3.381983 ATCAGGTCGTCGCTGCCA 61.382 61.111 0.00 0.00 0.00 4.92
5271 10342 2.942796 ATCAGGTCGTCGCTGCCAA 61.943 57.895 0.00 0.00 0.00 4.52
5272 10343 2.449031 ATCAGGTCGTCGCTGCCAAA 62.449 55.000 0.00 0.00 0.00 3.28
5273 10344 2.357517 AGGTCGTCGCTGCCAAAG 60.358 61.111 0.00 0.00 0.00 2.77
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 2.046892 CAAGTCACCTGCCTCCGG 60.047 66.667 0.00 0.00 0.00 5.14
13 14 2.743928 GCAAGTCACCTGCCTCCG 60.744 66.667 0.00 0.00 0.00 4.63
14 15 2.743928 CGCAAGTCACCTGCCTCC 60.744 66.667 0.00 0.00 0.00 4.30
26 27 0.040958 GAGCTTGACACCAACGCAAG 60.041 55.000 0.00 0.00 41.36 4.01
28 29 1.153269 TGAGCTTGACACCAACGCA 60.153 52.632 0.00 0.00 32.57 5.24
29 30 0.880278 TCTGAGCTTGACACCAACGC 60.880 55.000 0.00 0.00 0.00 4.84
30 31 1.143305 CTCTGAGCTTGACACCAACG 58.857 55.000 0.00 0.00 0.00 4.10
31 32 2.533266 TCTCTGAGCTTGACACCAAC 57.467 50.000 0.00 0.00 0.00 3.77
33 34 1.973515 ACATCTCTGAGCTTGACACCA 59.026 47.619 12.47 0.00 0.00 4.17
34 35 2.758736 ACATCTCTGAGCTTGACACC 57.241 50.000 12.47 0.00 0.00 4.16
35 36 3.924144 AGAACATCTCTGAGCTTGACAC 58.076 45.455 12.47 5.44 31.12 3.67
47 48 7.608308 AACTGAAAAGATAGCAGAACATCTC 57.392 36.000 0.00 0.00 33.94 2.75
48 49 7.992754 AAACTGAAAAGATAGCAGAACATCT 57.007 32.000 0.00 0.00 33.94 2.90
51 52 7.066887 TGACAAAACTGAAAAGATAGCAGAACA 59.933 33.333 0.00 0.00 33.94 3.18
52 53 7.417612 TGACAAAACTGAAAAGATAGCAGAAC 58.582 34.615 0.00 0.00 33.94 3.01
53 54 7.566760 TGACAAAACTGAAAAGATAGCAGAA 57.433 32.000 0.00 0.00 33.94 3.02
54 55 7.750229 ATGACAAAACTGAAAAGATAGCAGA 57.250 32.000 0.00 0.00 33.94 4.26
55 56 9.713740 GATATGACAAAACTGAAAAGATAGCAG 57.286 33.333 0.00 0.00 35.81 4.24
56 57 8.390354 CGATATGACAAAACTGAAAAGATAGCA 58.610 33.333 0.00 0.00 0.00 3.49
57 58 7.852945 CCGATATGACAAAACTGAAAAGATAGC 59.147 37.037 0.00 0.00 0.00 2.97
58 59 8.883731 ACCGATATGACAAAACTGAAAAGATAG 58.116 33.333 0.00 0.00 0.00 2.08
59 60 8.786826 ACCGATATGACAAAACTGAAAAGATA 57.213 30.769 0.00 0.00 0.00 1.98
60 61 7.687941 ACCGATATGACAAAACTGAAAAGAT 57.312 32.000 0.00 0.00 0.00 2.40
62 63 7.584987 AGAACCGATATGACAAAACTGAAAAG 58.415 34.615 0.00 0.00 0.00 2.27
63 64 7.504924 AGAACCGATATGACAAAACTGAAAA 57.495 32.000 0.00 0.00 0.00 2.29
67 68 6.090358 ACGTAAGAACCGATATGACAAAACTG 59.910 38.462 0.00 0.00 43.62 3.16
68 69 6.090358 CACGTAAGAACCGATATGACAAAACT 59.910 38.462 0.00 0.00 43.62 2.66
71 72 5.574055 GTCACGTAAGAACCGATATGACAAA 59.426 40.000 0.00 0.00 43.62 2.83
72 73 5.097529 GTCACGTAAGAACCGATATGACAA 58.902 41.667 0.00 0.00 43.62 3.18
73 74 4.397103 AGTCACGTAAGAACCGATATGACA 59.603 41.667 0.00 0.00 38.11 3.58
75 76 4.260497 CGAGTCACGTAAGAACCGATATGA 60.260 45.833 0.00 0.00 43.62 2.15
76 77 3.966844 CGAGTCACGTAAGAACCGATATG 59.033 47.826 0.00 0.00 43.62 1.78
77 78 4.206698 CGAGTCACGTAAGAACCGATAT 57.793 45.455 0.00 0.00 43.62 1.63
78 79 3.663464 CGAGTCACGTAAGAACCGATA 57.337 47.619 0.00 0.00 43.62 2.92
91 92 7.633361 TCATAAAGAACAAAGTACGAGTCAC 57.367 36.000 0.00 0.00 0.00 3.67
168 182 2.486636 TTACGCCTCCGTCTGCACAG 62.487 60.000 0.00 0.00 46.39 3.66
172 186 0.669625 AAGTTTACGCCTCCGTCTGC 60.670 55.000 0.00 0.00 46.39 4.26
202 216 4.147449 CATCGCTGACGGGGCTGA 62.147 66.667 0.00 0.00 40.63 4.26
203 217 4.147449 TCATCGCTGACGGGGCTG 62.147 66.667 0.00 0.00 40.63 4.85
204 218 4.148825 GTCATCGCTGACGGGGCT 62.149 66.667 3.30 0.00 42.24 5.19
262 276 4.986587 CGACGTCGGCGGTCACAA 62.987 66.667 29.70 0.00 43.45 3.33
314 328 1.065709 GTGGGTTATTTGGAGGCGAGA 60.066 52.381 0.00 0.00 0.00 4.04
337 351 2.692741 GCCTCCCAGCCCTTAGGT 60.693 66.667 0.00 0.00 34.57 3.08
339 353 3.866582 CCGCCTCCCAGCCCTTAG 61.867 72.222 0.00 0.00 0.00 2.18
375 389 2.115291 GGGTGCTTCCGGAATCTGC 61.115 63.158 19.21 18.24 37.00 4.26
672 3670 7.777910 CCCAATACTTCCATGTAATCTTTACCA 59.222 37.037 0.00 0.00 0.00 3.25
682 3680 4.041464 TGCTACCCCAATACTTCCATGTA 58.959 43.478 0.00 0.00 0.00 2.29
708 3707 2.054453 GGGGCAGAATTCCCACTGC 61.054 63.158 10.14 10.14 46.92 4.40
781 3781 3.930035 ACTCCTAATTCCCGAGATTCCT 58.070 45.455 3.97 0.00 0.00 3.36
842 3856 5.163488 CCATGAAAATAAGCTCAAGGCATCA 60.163 40.000 0.00 0.00 44.79 3.07
1109 4132 7.440856 ACGTCTCCGGTTTAACATTAGTTAAAA 59.559 33.333 13.27 0.73 46.33 1.52
1113 4136 4.886579 ACGTCTCCGGTTTAACATTAGTT 58.113 39.130 0.00 0.00 39.00 2.24
1128 4151 3.512033 ACTATGAGCTTCAACGTCTCC 57.488 47.619 0.00 0.00 0.00 3.71
1200 4223 7.566760 TTCTTTCAGTGTTAAGCTTGAATGA 57.433 32.000 9.86 8.45 0.00 2.57
1319 4342 2.825532 AGAGAGAGAGAGAAAGGTGCAC 59.174 50.000 8.80 8.80 0.00 4.57
1329 4352 3.567576 TGCACGAAAAGAGAGAGAGAG 57.432 47.619 0.00 0.00 0.00 3.20
1330 4353 3.507622 TGATGCACGAAAAGAGAGAGAGA 59.492 43.478 0.00 0.00 0.00 3.10
1423 5360 4.897509 ATCCAATTATCCGCAGATCTGA 57.102 40.909 27.04 5.94 33.67 3.27
1598 5535 3.321968 TGGATCTGTCTCATATGAACCGG 59.678 47.826 6.90 0.00 0.00 5.28
1643 5581 0.250727 CGGGGTCCAAGAAGAGCAAA 60.251 55.000 0.00 0.00 35.95 3.68
1646 5584 0.831307 ATACGGGGTCCAAGAAGAGC 59.169 55.000 0.00 0.00 0.00 4.09
1647 5585 3.641906 ACATATACGGGGTCCAAGAAGAG 59.358 47.826 0.00 0.00 0.00 2.85
1648 5586 3.640029 GACATATACGGGGTCCAAGAAGA 59.360 47.826 0.00 0.00 0.00 2.87
1649 5587 3.386726 TGACATATACGGGGTCCAAGAAG 59.613 47.826 0.00 0.00 0.00 2.85
1650 5588 3.376636 TGACATATACGGGGTCCAAGAA 58.623 45.455 0.00 0.00 0.00 2.52
1652 5590 3.463944 GTTGACATATACGGGGTCCAAG 58.536 50.000 0.00 0.00 0.00 3.61
1688 5627 4.277515 ACAAAGTAGCATGAGCAGAAGA 57.722 40.909 0.00 0.00 45.49 2.87
1731 5670 8.408601 GGAAAGAGCATAGAATTATTCAAGCAA 58.591 33.333 7.74 0.00 0.00 3.91
1935 6579 7.437713 AGTTAGTGGTATGAGATGGAAATGA 57.562 36.000 0.00 0.00 0.00 2.57
2123 6784 6.777526 AAAAGCAAATAAGCGCACAATTTA 57.222 29.167 11.47 0.00 40.15 1.40
2155 6817 3.328382 CGAAGGTGGTGGATTCAACTA 57.672 47.619 0.00 0.00 31.05 2.24
2199 6861 1.604593 GCCAGGGTCACATGCAAGT 60.605 57.895 0.00 0.00 0.00 3.16
2366 7030 2.552599 TGCATTTCGGACTAACACCA 57.447 45.000 0.00 0.00 0.00 4.17
2564 7229 5.136105 AGTTCATGGAGCAGAGTTTTCTTT 58.864 37.500 0.00 0.00 0.00 2.52
2644 7309 2.089201 AGCCCATAACCGTAGCAAAAC 58.911 47.619 0.00 0.00 0.00 2.43
2653 7318 4.007659 AGACAAGTAAAAGCCCATAACCG 58.992 43.478 0.00 0.00 0.00 4.44
2654 7319 7.338449 TGAATAGACAAGTAAAAGCCCATAACC 59.662 37.037 0.00 0.00 0.00 2.85
2659 7324 6.945435 TCAATGAATAGACAAGTAAAAGCCCA 59.055 34.615 0.00 0.00 0.00 5.36
2870 7548 3.890756 TCAGCACATGTCCACTTGATTTT 59.109 39.130 0.00 0.00 0.00 1.82
2953 7631 1.156736 CCCAAGCTTGTAACCGACAG 58.843 55.000 24.35 6.18 39.88 3.51
2961 7639 1.213296 GATCCTCCCCCAAGCTTGTA 58.787 55.000 24.35 6.77 0.00 2.41
3099 7777 4.156556 AGCTTGTGTACCTTGCACATTATG 59.843 41.667 0.00 0.00 44.91 1.90
3146 7824 7.839907 TCACATTTTCCTGAATAAAATCCTGG 58.160 34.615 0.00 0.00 35.00 4.45
3194 7872 1.948834 TCAATAGGCATGGCATCGTTG 59.051 47.619 22.64 17.99 0.00 4.10
3197 7875 2.156917 ACATCAATAGGCATGGCATCG 58.843 47.619 22.64 6.84 0.00 3.84
3233 7911 2.224744 TGCTACAAAACCTGCTGATCCA 60.225 45.455 0.00 0.00 0.00 3.41
3308 7986 3.375642 GCAACCAACAGAGCTTTTCTTC 58.624 45.455 0.00 0.00 32.41 2.87
3384 8062 5.048921 CAGGTTCATTATCATGCTCACCATC 60.049 44.000 0.00 0.00 31.54 3.51
3409 8087 7.437713 AATTCACTAGTACCATCATCAGGAA 57.562 36.000 0.00 0.00 0.00 3.36
3553 8231 2.380941 CCATGTGCTTCCCATCAATGA 58.619 47.619 0.00 0.00 0.00 2.57
3615 8293 5.278169 CCGCTTGGATCTTATTTCCAGATTG 60.278 44.000 0.00 0.00 43.87 2.67
3632 8310 2.045045 TGCCCAATCTCCGCTTGG 60.045 61.111 0.00 0.00 42.36 3.61
3978 8656 4.104102 TGAGGATTGGTCTACAAGTTTGGT 59.896 41.667 0.00 0.00 43.48 3.67
3987 8665 5.358160 CCTTTGGAAATGAGGATTGGTCTAC 59.642 44.000 0.00 0.00 32.11 2.59
4223 9179 3.815407 AAGCCACAGCAACCCAGGG 62.815 63.158 2.85 2.85 43.56 4.45
4345 9301 1.325640 CATTCTCATCGCACAAGACCG 59.674 52.381 0.00 0.00 0.00 4.79
4380 9337 0.536006 AGAAGCTGACAGGCAACACC 60.536 55.000 4.26 0.00 41.41 4.16
4387 9344 6.988580 TGATATACAATTGAGAAGCTGACAGG 59.011 38.462 13.59 0.00 0.00 4.00
4418 9375 5.871524 TGTTTATGAGTCTCTCTGCAATCAC 59.128 40.000 0.65 0.00 0.00 3.06
4429 9388 5.814705 CCCAGACAAGATGTTTATGAGTCTC 59.185 44.000 0.00 0.00 33.01 3.36
4436 9395 4.322057 AAGCCCCAGACAAGATGTTTAT 57.678 40.909 0.00 0.00 0.00 1.40
4464 9423 4.161754 ACTTGTATTTAGGAACGGAGGGAG 59.838 45.833 0.00 0.00 0.00 4.30
4465 9424 4.098894 ACTTGTATTTAGGAACGGAGGGA 58.901 43.478 0.00 0.00 0.00 4.20
4466 9425 4.439968 GACTTGTATTTAGGAACGGAGGG 58.560 47.826 0.00 0.00 0.00 4.30
4467 9426 4.161754 AGGACTTGTATTTAGGAACGGAGG 59.838 45.833 0.00 0.00 0.00 4.30
4468 9427 5.340439 AGGACTTGTATTTAGGAACGGAG 57.660 43.478 0.00 0.00 0.00 4.63
4469 9428 5.750352 AAGGACTTGTATTTAGGAACGGA 57.250 39.130 0.00 0.00 0.00 4.69
4470 9429 6.812879 AAAAGGACTTGTATTTAGGAACGG 57.187 37.500 0.00 0.00 0.00 4.44
4471 9430 8.767478 TCTAAAAGGACTTGTATTTAGGAACG 57.233 34.615 0.00 0.00 36.48 3.95
4472 9431 9.939802 TCTCTAAAAGGACTTGTATTTAGGAAC 57.060 33.333 0.00 0.00 36.48 3.62
4504 9463 9.692749 CACTCATTTTACGTATGTAGTCCATAT 57.307 33.333 0.00 0.00 38.29 1.78
4505 9464 8.905850 TCACTCATTTTACGTATGTAGTCCATA 58.094 33.333 0.00 0.00 34.86 2.74
4506 9465 7.778083 TCACTCATTTTACGTATGTAGTCCAT 58.222 34.615 0.00 0.00 37.58 3.41
4507 9466 7.160547 TCACTCATTTTACGTATGTAGTCCA 57.839 36.000 0.00 0.00 0.00 4.02
4508 9467 8.644318 ATTCACTCATTTTACGTATGTAGTCC 57.356 34.615 0.00 0.00 0.00 3.85
4509 9468 9.517609 AGATTCACTCATTTTACGTATGTAGTC 57.482 33.333 0.00 0.00 0.00 2.59
4513 9472 9.084164 GTGTAGATTCACTCATTTTACGTATGT 57.916 33.333 0.00 0.00 35.68 2.29
4514 9473 9.302345 AGTGTAGATTCACTCATTTTACGTATG 57.698 33.333 0.00 0.00 44.07 2.39
4528 9487 7.493367 AGCCATAGTTTAGAGTGTAGATTCAC 58.507 38.462 0.00 0.00 38.46 3.18
4529 9488 7.661536 AGCCATAGTTTAGAGTGTAGATTCA 57.338 36.000 0.00 0.00 0.00 2.57
4538 9497 8.904834 CGGATGTATATAGCCATAGTTTAGAGT 58.095 37.037 4.56 0.00 0.00 3.24
4539 9498 8.904834 ACGGATGTATATAGCCATAGTTTAGAG 58.095 37.037 4.56 0.00 0.00 2.43
4540 9499 8.818622 ACGGATGTATATAGCCATAGTTTAGA 57.181 34.615 4.56 0.00 0.00 2.10
4543 9502 8.978472 ACATACGGATGTATATAGCCATAGTTT 58.022 33.333 12.79 0.00 44.77 2.66
4544 9503 8.534954 ACATACGGATGTATATAGCCATAGTT 57.465 34.615 12.79 0.00 44.77 2.24
4545 9504 9.286170 CTACATACGGATGTATATAGCCATAGT 57.714 37.037 20.64 0.00 45.42 2.12
4546 9505 9.286170 ACTACATACGGATGTATATAGCCATAG 57.714 37.037 20.64 9.36 45.42 2.23
4547 9506 9.636789 AACTACATACGGATGTATATAGCCATA 57.363 33.333 20.64 0.00 45.42 2.74
4548 9507 8.534954 AACTACATACGGATGTATATAGCCAT 57.465 34.615 20.64 0.00 45.42 4.40
4549 9508 7.612633 TGAACTACATACGGATGTATATAGCCA 59.387 37.037 20.64 9.72 45.42 4.75
4550 9509 7.993101 TGAACTACATACGGATGTATATAGCC 58.007 38.462 20.64 7.45 45.42 3.93
4591 9550 2.304221 GGGGGAGGCTGTAAGTTTTT 57.696 50.000 0.00 0.00 35.30 1.94
4617 9576 3.381509 TTTGGTGGTGGTGGTGGGG 62.382 63.158 0.00 0.00 0.00 4.96
4618 9577 2.131067 GTTTGGTGGTGGTGGTGGG 61.131 63.158 0.00 0.00 0.00 4.61
4619 9578 1.380515 TGTTTGGTGGTGGTGGTGG 60.381 57.895 0.00 0.00 0.00 4.61
4620 9579 2.015227 GCTGTTTGGTGGTGGTGGTG 62.015 60.000 0.00 0.00 0.00 4.17
4621 9580 1.756561 GCTGTTTGGTGGTGGTGGT 60.757 57.895 0.00 0.00 0.00 4.16
4622 9581 2.498056 GGCTGTTTGGTGGTGGTGG 61.498 63.158 0.00 0.00 0.00 4.61
4623 9582 2.498056 GGGCTGTTTGGTGGTGGTG 61.498 63.158 0.00 0.00 0.00 4.17
4624 9583 2.123468 GGGCTGTTTGGTGGTGGT 60.123 61.111 0.00 0.00 0.00 4.16
4625 9584 2.917227 GGGGCTGTTTGGTGGTGG 60.917 66.667 0.00 0.00 0.00 4.61
4626 9585 1.457455 AAGGGGCTGTTTGGTGGTG 60.457 57.895 0.00 0.00 0.00 4.17
4627 9586 1.457455 CAAGGGGCTGTTTGGTGGT 60.457 57.895 0.00 0.00 0.00 4.16
4628 9587 0.758685 TTCAAGGGGCTGTTTGGTGG 60.759 55.000 0.00 0.00 0.00 4.61
4629 9588 0.675633 CTTCAAGGGGCTGTTTGGTG 59.324 55.000 0.00 0.00 0.00 4.17
4630 9589 1.115326 GCTTCAAGGGGCTGTTTGGT 61.115 55.000 0.00 0.00 0.00 3.67
4631 9590 1.667722 GCTTCAAGGGGCTGTTTGG 59.332 57.895 0.00 0.00 0.00 3.28
4632 9591 1.667722 GGCTTCAAGGGGCTGTTTG 59.332 57.895 0.00 0.00 0.00 2.93
4633 9592 1.533994 GGGCTTCAAGGGGCTGTTT 60.534 57.895 0.00 0.00 0.00 2.83
4634 9593 2.023760 AAGGGCTTCAAGGGGCTGTT 62.024 55.000 0.00 0.00 0.00 3.16
4635 9594 2.023760 AAAGGGCTTCAAGGGGCTGT 62.024 55.000 0.00 0.00 0.00 4.40
4636 9595 0.833409 AAAAGGGCTTCAAGGGGCTG 60.833 55.000 0.00 0.00 0.00 4.85
4637 9596 0.104986 AAAAAGGGCTTCAAGGGGCT 60.105 50.000 0.00 0.00 0.00 5.19
4638 9597 2.452116 AAAAAGGGCTTCAAGGGGC 58.548 52.632 0.00 0.00 0.00 5.80
4968 9968 2.281692 AGCAGCAATGTGGACGCA 60.282 55.556 0.00 0.00 0.00 5.24
4985 9996 1.962321 TTTATAGCGGCGAGTGGGCA 61.962 55.000 12.98 0.00 42.43 5.36
5041 10058 1.614241 GGCAAGGGAGAGAGCGGTTA 61.614 60.000 0.00 0.00 0.00 2.85
5092 10115 2.370633 GAAGGAGAGGAGGGGGCT 59.629 66.667 0.00 0.00 0.00 5.19
5185 10256 1.753463 CGTAGAGGAGACGGGCCTT 60.753 63.158 0.84 0.00 35.44 4.35
5242 10313 4.212913 ACCTGATGCGCGCGATCT 62.213 61.111 37.18 17.15 0.00 2.75
5243 10314 3.696426 GACCTGATGCGCGCGATC 61.696 66.667 37.18 29.66 0.00 3.69
5250 10321 3.250323 CAGCGACGACCTGATGCG 61.250 66.667 0.00 0.00 32.03 4.73
5251 10322 3.558411 GCAGCGACGACCTGATGC 61.558 66.667 0.00 2.40 32.03 3.91
5252 10323 2.887568 GGCAGCGACGACCTGATG 60.888 66.667 0.00 0.00 32.03 3.07
5253 10324 2.449031 TTTGGCAGCGACGACCTGAT 62.449 55.000 0.00 0.00 32.03 2.90
5254 10325 3.158537 TTTGGCAGCGACGACCTGA 62.159 57.895 0.00 0.00 32.03 3.86
5255 10326 2.664851 TTTGGCAGCGACGACCTG 60.665 61.111 0.00 0.00 0.00 4.00
5256 10327 2.357517 CTTTGGCAGCGACGACCT 60.358 61.111 0.00 0.00 0.00 3.85
5257 10328 4.090057 GCTTTGGCAGCGACGACC 62.090 66.667 0.00 0.00 39.29 4.79


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

AutoCloner maintained by Alex Coulton.