Multiple sequence alignment - TraesCS2D01G086600

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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 TraesCS2D01G086600 chr2D 100.000 4502 0 0 1 4502 37254827 37250326 0.000000e+00 8314.0
1 TraesCS2D01G086600 chr2D 81.938 227 35 4 2669 2894 285064581 285064360 2.140000e-43 187.0
2 TraesCS2D01G086600 chr2D 79.518 166 26 6 45 208 542973726 542973567 1.320000e-20 111.0
3 TraesCS2D01G086600 chr2D 75.983 229 36 11 2911 3139 285064281 285064072 2.870000e-17 100.0
4 TraesCS2D01G086600 chr2D 95.238 42 2 0 923 964 398308042 398308001 2.910000e-07 67.6
5 TraesCS2D01G086600 chr2B 90.054 3348 200 60 451 3737 64990810 64987535 0.000000e+00 4215.0
6 TraesCS2D01G086600 chr2B 91.280 539 29 6 3206 3739 64949609 64949084 0.000000e+00 719.0
7 TraesCS2D01G086600 chr2B 90.909 462 29 6 4049 4500 64986144 64985686 3.850000e-170 608.0
8 TraesCS2D01G086600 chr2B 83.110 598 83 12 3343 3936 64955718 64955135 3.080000e-146 529.0
9 TraesCS2D01G086600 chr2B 92.713 247 14 4 4042 4284 64948505 64948259 1.990000e-93 353.0
10 TraesCS2D01G086600 chr2B 90.119 253 22 3 4035 4284 64954565 64954313 4.340000e-85 326.0
11 TraesCS2D01G086600 chr2B 83.929 280 34 6 4089 4363 64886759 64886486 1.610000e-64 257.0
12 TraesCS2D01G086600 chr2B 95.192 104 5 0 3113 3216 64950497 64950394 1.000000e-36 165.0
13 TraesCS2D01G086600 chr2B 82.105 95 14 1 923 1017 263847344 263847435 1.340000e-10 78.7
14 TraesCS2D01G086600 chr2B 97.368 38 1 0 1770 1807 467553323 467553286 1.050000e-06 65.8
15 TraesCS2D01G086600 chr2A 86.942 3829 302 100 1 3728 42155951 42152220 0.000000e+00 4119.0
16 TraesCS2D01G086600 chr2A 85.150 734 60 28 1060 1769 597070030 597070738 0.000000e+00 706.0
17 TraesCS2D01G086600 chr2A 84.218 735 66 28 1060 1769 596882863 596883572 0.000000e+00 669.0
18 TraesCS2D01G086600 chr2A 92.748 262 16 2 4026 4284 42150490 42150229 4.250000e-100 375.0
19 TraesCS2D01G086600 chr2A 80.870 115 16 4 923 1037 193696321 193696213 8.020000e-13 86.1
20 TraesCS2D01G086600 chr6B 87.500 824 51 21 967 1772 267740685 267741474 0.000000e+00 904.0
21 TraesCS2D01G086600 chr6B 83.284 670 63 29 1124 1769 76737260 76736616 5.050000e-159 571.0
22 TraesCS2D01G086600 chr6B 83.159 671 63 29 1124 1769 91949171 91949816 6.540000e-158 568.0
23 TraesCS2D01G086600 chr6B 84.186 215 28 4 2669 2882 199961595 199961804 2.120000e-48 204.0
24 TraesCS2D01G086600 chr6B 81.034 174 23 5 3071 3241 30286380 30286546 3.650000e-26 130.0
25 TraesCS2D01G086600 chr6B 75.536 233 36 12 2908 3139 199961892 199962104 1.330000e-15 95.3
26 TraesCS2D01G086600 chr7A 84.762 735 62 28 1060 1769 633536895 633536186 0.000000e+00 691.0
27 TraesCS2D01G086600 chr7A 84.511 736 62 28 1060 1769 633542278 633541569 0.000000e+00 680.0
28 TraesCS2D01G086600 chr3B 83.982 668 58 29 1126 1769 693620039 693619397 3.000000e-166 595.0
29 TraesCS2D01G086600 chr3B 83.756 671 59 27 1124 1769 690613925 690614570 1.390000e-164 590.0
30 TraesCS2D01G086600 chr3B 76.087 230 34 12 2911 3139 691503305 691503096 2.870000e-17 100.0
31 TraesCS2D01G086600 chr3B 84.444 90 11 3 928 1017 215620827 215620913 8.020000e-13 86.1
32 TraesCS2D01G086600 chr4B 77.436 585 110 14 2911 3487 415121900 415122470 3.360000e-86 329.0
33 TraesCS2D01G086600 chr4D 76.831 587 113 14 2911 3487 336841148 336841721 4.370000e-80 309.0
34 TraesCS2D01G086600 chr4D 80.769 156 24 5 53 208 368870023 368870172 2.850000e-22 117.0
35 TraesCS2D01G086600 chr4D 80.645 155 22 5 56 206 462801127 462801277 3.680000e-21 113.0
36 TraesCS2D01G086600 chr4A 75.932 590 119 14 2911 3490 136617413 136616837 9.530000e-72 281.0
37 TraesCS2D01G086600 chr4A 82.468 154 21 6 56 208 96018820 96018672 3.650000e-26 130.0
38 TraesCS2D01G086600 chr1B 84.681 235 30 6 4057 4288 666072883 666073114 3.500000e-56 230.0
39 TraesCS2D01G086600 chr1B 83.043 230 35 4 4051 4278 665494638 665494865 5.900000e-49 206.0
40 TraesCS2D01G086600 chr1B 78.205 156 30 3 56 211 156849621 156849772 3.710000e-16 97.1
41 TraesCS2D01G086600 chr1A 84.388 237 28 9 4057 4289 574488886 574489117 1.630000e-54 224.0
42 TraesCS2D01G086600 chr1A 83.478 115 13 3 923 1037 435406457 435406565 7.970000e-18 102.0
43 TraesCS2D01G086600 chr1D 83.691 233 30 7 4061 4289 478273893 478274121 3.530000e-51 213.0
44 TraesCS2D01G086600 chrUn 84.516 155 20 4 55 209 50619842 50619992 2.810000e-32 150.0
45 TraesCS2D01G086600 chr3A 82.803 157 22 4 56 211 714331308 714331460 7.860000e-28 135.0
46 TraesCS2D01G086600 chr3A 80.620 129 17 5 923 1049 708354937 708354815 4.800000e-15 93.5
47 TraesCS2D01G086600 chr5D 81.529 157 23 5 56 208 8028442 8028288 1.700000e-24 124.0
48 TraesCS2D01G086600 chr3D 79.739 153 26 5 57 208 534118666 534118518 6.160000e-19 106.0
49 TraesCS2D01G086600 chr3D 84.211 95 12 1 923 1017 497764181 497764090 6.200000e-14 89.8


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 TraesCS2D01G086600 chr2D 37250326 37254827 4501 True 8314.0 8314 100.0000 1 4502 1 chr2D.!!$R1 4501
1 TraesCS2D01G086600 chr2B 64985686 64990810 5124 True 2411.5 4215 90.4815 451 4500 2 chr2B.!!$R4 4049
2 TraesCS2D01G086600 chr2B 64948259 64955718 7459 True 418.4 719 90.4828 3113 4284 5 chr2B.!!$R3 1171
3 TraesCS2D01G086600 chr2A 42150229 42155951 5722 True 2247.0 4119 89.8450 1 4284 2 chr2A.!!$R2 4283
4 TraesCS2D01G086600 chr2A 597070030 597070738 708 False 706.0 706 85.1500 1060 1769 1 chr2A.!!$F2 709
5 TraesCS2D01G086600 chr2A 596882863 596883572 709 False 669.0 669 84.2180 1060 1769 1 chr2A.!!$F1 709
6 TraesCS2D01G086600 chr6B 267740685 267741474 789 False 904.0 904 87.5000 967 1772 1 chr6B.!!$F3 805
7 TraesCS2D01G086600 chr6B 76736616 76737260 644 True 571.0 571 83.2840 1124 1769 1 chr6B.!!$R1 645
8 TraesCS2D01G086600 chr6B 91949171 91949816 645 False 568.0 568 83.1590 1124 1769 1 chr6B.!!$F2 645
9 TraesCS2D01G086600 chr7A 633536186 633536895 709 True 691.0 691 84.7620 1060 1769 1 chr7A.!!$R1 709
10 TraesCS2D01G086600 chr7A 633541569 633542278 709 True 680.0 680 84.5110 1060 1769 1 chr7A.!!$R2 709
11 TraesCS2D01G086600 chr3B 693619397 693620039 642 True 595.0 595 83.9820 1126 1769 1 chr3B.!!$R2 643
12 TraesCS2D01G086600 chr3B 690613925 690614570 645 False 590.0 590 83.7560 1124 1769 1 chr3B.!!$F2 645
13 TraesCS2D01G086600 chr4B 415121900 415122470 570 False 329.0 329 77.4360 2911 3487 1 chr4B.!!$F1 576
14 TraesCS2D01G086600 chr4D 336841148 336841721 573 False 309.0 309 76.8310 2911 3487 1 chr4D.!!$F1 576
15 TraesCS2D01G086600 chr4A 136616837 136617413 576 True 281.0 281 75.9320 2911 3490 1 chr4A.!!$R2 579

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
365 369 0.108851 AATCCGAATTGGCAAACGGC 60.109 50.0 30.37 11.45 44.19 5.68 F
537 551 0.615331 TCATCTCCTTTGCTTCGCCT 59.385 50.0 0.00 0.00 0.00 5.52 F
2045 2189 0.463295 CATCACCATCGCCTTCAGCT 60.463 55.0 0.00 0.00 40.39 4.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1211 1275 0.313043 CTGCACAAACCAAGAGCAGG 59.687 55.0 0.00 0.0 43.81 4.85 R
2403 2553 0.035458 CTGACCGCTTCAAGGAAGGT 59.965 55.0 7.97 0.0 39.76 3.50 R
3515 6424 0.036010 AGAAATGGACTGGACTGCCG 60.036 55.0 0.00 0.0 36.79 5.69 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
43 44 0.255890 TCAATAAGGAGGTGGCTGGC 59.744 55.000 0.00 0.00 0.00 4.85
54 55 2.191641 GGCTGGCTCTCATCCACC 59.808 66.667 0.00 0.00 32.15 4.61
70 71 1.616159 CACCCCCTTCGTTCACAAAT 58.384 50.000 0.00 0.00 0.00 2.32
74 75 4.944930 CACCCCCTTCGTTCACAAATATAA 59.055 41.667 0.00 0.00 0.00 0.98
77 78 6.062095 CCCCCTTCGTTCACAAATATAAGAT 58.938 40.000 0.00 0.00 0.00 2.40
124 127 7.298507 TGTTGTAATACGGACTGAAATTAGC 57.701 36.000 0.00 0.00 0.00 3.09
129 132 3.806316 ACGGACTGAAATTAGCAAACG 57.194 42.857 0.00 0.00 0.00 3.60
134 137 4.909880 GGACTGAAATTAGCAAACGAACAC 59.090 41.667 0.00 0.00 0.00 3.32
143 146 4.688511 AGCAAACGAACACACTAAAACA 57.311 36.364 0.00 0.00 0.00 2.83
152 155 6.704493 ACGAACACACTAAAACATGACTACAT 59.296 34.615 0.00 0.00 37.19 2.29
153 156 7.868922 ACGAACACACTAAAACATGACTACATA 59.131 33.333 0.00 0.00 35.09 2.29
156 159 9.502091 AACACACTAAAACATGACTACATACAT 57.498 29.630 0.00 0.00 35.09 2.29
157 160 9.151471 ACACACTAAAACATGACTACATACATC 57.849 33.333 0.00 0.00 35.09 3.06
160 163 9.586435 CACTAAAACATGACTACATACATCTGA 57.414 33.333 0.00 0.00 35.09 3.27
164 167 9.671279 AAAACATGACTACATACATCTGATTCA 57.329 29.630 0.00 0.00 35.09 2.57
166 169 7.785033 ACATGACTACATACATCTGATTCACA 58.215 34.615 0.00 0.00 35.09 3.58
167 170 8.260114 ACATGACTACATACATCTGATTCACAA 58.740 33.333 0.00 0.00 35.09 3.33
201 204 8.964476 AGAACATCTTGTATTTATGAACGGAT 57.036 30.769 0.00 0.00 0.00 4.18
229 232 4.759782 AGATGAGAATCACCTTTACACCG 58.240 43.478 0.00 0.00 32.33 4.94
245 248 7.169982 CCTTTACACCGTTTGATTTAATGCAAA 59.830 33.333 0.00 0.00 0.00 3.68
250 253 7.116233 ACACCGTTTGATTTAATGCAAAGATTC 59.884 33.333 0.00 0.00 34.95 2.52
251 254 7.116090 CACCGTTTGATTTAATGCAAAGATTCA 59.884 33.333 0.00 0.00 34.95 2.57
253 256 9.299963 CCGTTTGATTTAATGCAAAGATTCATA 57.700 29.630 0.00 0.00 34.95 2.15
309 312 3.057104 TCAATCAAATGAGGCAGCAGTTG 60.057 43.478 12.35 12.35 43.11 3.16
316 319 1.375098 GAGGCAGCAGTTGGATGAGC 61.375 60.000 0.00 0.00 33.82 4.26
317 320 1.378250 GGCAGCAGTTGGATGAGCT 60.378 57.895 0.00 0.00 33.82 4.09
332 336 5.536538 TGGATGAGCTATGTTAGTCCTACAG 59.463 44.000 0.00 0.00 0.00 2.74
357 361 6.959361 ACGAGAATTATCAAATCCGAATTGG 58.041 36.000 0.35 0.00 40.09 3.16
363 367 2.940147 TCAAATCCGAATTGGCAAACG 58.060 42.857 18.41 18.41 37.80 3.60
365 369 0.108851 AATCCGAATTGGCAAACGGC 60.109 50.000 30.37 11.45 44.19 5.68
379 383 1.757682 AACGGCCACAAAAACTCTCA 58.242 45.000 2.24 0.00 0.00 3.27
382 386 3.482436 ACGGCCACAAAAACTCTCAATA 58.518 40.909 2.24 0.00 0.00 1.90
384 388 4.023193 ACGGCCACAAAAACTCTCAATAAG 60.023 41.667 2.24 0.00 0.00 1.73
388 392 6.294731 GGCCACAAAAACTCTCAATAAGTCAT 60.295 38.462 0.00 0.00 0.00 3.06
398 402 8.228035 ACTCTCAATAAGTCATAGTCTACACC 57.772 38.462 0.00 0.00 0.00 4.16
403 407 4.897025 AAGTCATAGTCTACACCGCTAC 57.103 45.455 0.00 0.00 0.00 3.58
411 415 1.079405 TACACCGCTACTTGGCAGC 60.079 57.895 0.00 0.00 35.61 5.25
412 416 1.822114 TACACCGCTACTTGGCAGCA 61.822 55.000 0.00 0.00 39.04 4.41
432 436 2.522638 GGGCATCGGCGTAAACTCG 61.523 63.158 6.85 0.00 42.47 4.18
447 451 3.983044 AACTCGGCTCCAGACTTTTAT 57.017 42.857 0.00 0.00 0.00 1.40
471 485 3.191371 ACCCGTGATTTGCAAATCTTCTC 59.809 43.478 38.33 27.18 43.97 2.87
473 487 4.142315 CCCGTGATTTGCAAATCTTCTCAT 60.142 41.667 38.33 14.36 43.97 2.90
474 488 5.404946 CCGTGATTTGCAAATCTTCTCATT 58.595 37.500 38.33 13.69 43.97 2.57
475 489 5.514204 CCGTGATTTGCAAATCTTCTCATTC 59.486 40.000 38.33 20.56 43.97 2.67
476 490 6.320171 CGTGATTTGCAAATCTTCTCATTCT 58.680 36.000 38.33 12.52 43.97 2.40
522 536 8.776376 TGCTTTAAATGATTCCCTTTTTCATC 57.224 30.769 0.00 0.00 30.03 2.92
534 548 4.479619 CCTTTTTCATCTCCTTTGCTTCG 58.520 43.478 0.00 0.00 0.00 3.79
535 549 3.559238 TTTTCATCTCCTTTGCTTCGC 57.441 42.857 0.00 0.00 0.00 4.70
537 551 0.615331 TCATCTCCTTTGCTTCGCCT 59.385 50.000 0.00 0.00 0.00 5.52
539 553 0.615331 ATCTCCTTTGCTTCGCCTGA 59.385 50.000 0.00 0.00 0.00 3.86
635 652 9.360093 TCAAGAACAACAAAATACGAAACAAAT 57.640 25.926 0.00 0.00 0.00 2.32
770 791 2.585153 GCCGGTCTCTTTCTCCCC 59.415 66.667 1.90 0.00 0.00 4.81
855 885 4.825679 CCACCCTCTCCCCTCCCC 62.826 77.778 0.00 0.00 0.00 4.81
1211 1275 1.538047 TCCAGGTGAGCTGATTTTGC 58.462 50.000 14.03 0.00 0.00 3.68
1212 1280 0.529378 CCAGGTGAGCTGATTTTGCC 59.471 55.000 14.03 0.00 0.00 4.52
1270 1344 4.162690 AGAGGAATGGGGCGCGAC 62.163 66.667 12.10 6.99 0.00 5.19
1273 1347 2.280186 GGAATGGGGCGCGACTAG 60.280 66.667 13.91 0.00 0.00 2.57
1361 1468 9.609950 GTACTATTATTAGTCATGGAGTTCGAC 57.390 37.037 0.62 0.00 39.42 4.20
1431 1547 6.967199 GCAACTGTATAACTGTAAATTGGCTC 59.033 38.462 0.00 0.00 29.85 4.70
1472 1588 4.459390 TGGTGATTCAGCAATGATTTGG 57.541 40.909 15.79 0.00 38.96 3.28
1668 1790 6.258507 ACAAATCTGAATTGGCACTGTTTTTC 59.741 34.615 10.01 0.00 32.02 2.29
1674 1797 8.514594 TCTGAATTGGCACTGTTTTTCTTATAG 58.485 33.333 0.00 0.00 0.00 1.31
1833 1968 2.924454 GCTCACAGTTGAAGAGACGAGG 60.924 54.545 0.00 0.00 0.00 4.63
1847 1982 1.742831 GACGAGGCACCAAATATGCAA 59.257 47.619 0.00 0.00 45.27 4.08
1856 1991 5.418676 GCACCAAATATGCAACCACTAATT 58.581 37.500 0.00 0.00 42.88 1.40
1961 2096 1.152777 CCCACCACAGTTCCTGCAA 60.153 57.895 0.00 0.00 34.37 4.08
1997 2141 2.284258 AGAAGAGCACCCTCGCCT 60.284 61.111 0.00 0.00 43.05 5.52
2045 2189 0.463295 CATCACCATCGCCTTCAGCT 60.463 55.000 0.00 0.00 40.39 4.24
2285 2429 2.040544 CACAGGGTTAAGCGGGCAG 61.041 63.158 0.00 0.00 0.00 4.85
2403 2553 4.735369 ACCAATCATGTTTTCCAGGTGTA 58.265 39.130 0.00 0.00 0.00 2.90
2409 2559 3.217681 TGTTTTCCAGGTGTACCTTCC 57.782 47.619 0.00 0.00 46.09 3.46
2415 2565 2.637872 TCCAGGTGTACCTTCCTTGAAG 59.362 50.000 0.00 0.00 46.09 3.02
2541 2691 5.019498 GCGGTTGTGTCAAGTTTAATATCG 58.981 41.667 0.00 0.00 0.00 2.92
2557 2707 9.813080 GTTTAATATCGTCTAAGAATGATTGGC 57.187 33.333 0.00 0.00 0.00 4.52
2613 2765 0.391793 GCTGCCACTGACCTCCTTAC 60.392 60.000 0.00 0.00 0.00 2.34
2674 2828 2.766263 ACGGCTATGGTTTCAGATCTCA 59.234 45.455 0.00 0.00 0.00 3.27
2776 2930 3.438781 TGGTGTTTGAATATGCTCCGAAC 59.561 43.478 0.00 0.00 0.00 3.95
2782 2936 1.068741 GAATATGCTCCGAACGGGACT 59.931 52.381 13.29 0.00 40.94 3.85
2866 3027 7.448161 TGTCAACAGAATGATTCCTACAATGTT 59.552 33.333 0.75 2.30 39.69 2.71
2869 3030 7.383102 ACAGAATGATTCCTACAATGTTCAC 57.617 36.000 0.75 0.00 39.69 3.18
2882 3045 5.160641 ACAATGTTCACACACTTCAACAAC 58.839 37.500 0.00 0.00 35.03 3.32
3054 3217 3.307059 GCTCAACAACTATCCACCTCACT 60.307 47.826 0.00 0.00 0.00 3.41
3117 5227 1.303309 GCACCAAGGGATCTGATTCG 58.697 55.000 0.00 0.00 0.00 3.34
3222 6127 1.840635 GTACCCTTCCCTGAGCAAGAT 59.159 52.381 0.00 0.00 0.00 2.40
3534 6443 0.036010 CGGCAGTCCAGTCCATTTCT 60.036 55.000 0.00 0.00 0.00 2.52
3562 6471 6.244654 TGTTGTGATGATGGATTCTTTGGTA 58.755 36.000 0.00 0.00 0.00 3.25
3618 6527 1.597937 GGCTTTGAGCTTGAACGTGTG 60.598 52.381 0.00 0.00 41.99 3.82
3671 6583 3.008375 TGCCAGCAAATCTAGTGAGAGTT 59.992 43.478 0.00 0.00 40.57 3.01
3710 6622 5.092781 GGTTTACGCAATGTTTGTCTATGG 58.907 41.667 0.00 0.00 0.00 2.74
3718 6630 5.512788 GCAATGTTTGTCTATGGTTTGATCG 59.487 40.000 0.00 0.00 0.00 3.69
3737 6649 5.525012 TGATCGATTCTTAGGCAAACATCTG 59.475 40.000 0.00 0.00 0.00 2.90
3741 6653 4.365514 TTCTTAGGCAAACATCTGGTGA 57.634 40.909 0.00 0.00 0.00 4.02
3742 6654 3.942829 TCTTAGGCAAACATCTGGTGAG 58.057 45.455 0.00 0.00 0.00 3.51
3743 6655 2.113860 TAGGCAAACATCTGGTGAGC 57.886 50.000 0.00 0.00 0.00 4.26
3744 6656 0.111061 AGGCAAACATCTGGTGAGCA 59.889 50.000 0.00 0.00 0.00 4.26
3745 6657 0.524862 GGCAAACATCTGGTGAGCAG 59.475 55.000 5.07 5.07 0.00 4.24
3746 6658 0.109412 GCAAACATCTGGTGAGCAGC 60.109 55.000 6.80 0.00 0.00 5.25
3747 6659 0.524862 CAAACATCTGGTGAGCAGCC 59.475 55.000 6.80 0.00 0.00 4.85
3749 6661 0.322277 AACATCTGGTGAGCAGCCTG 60.322 55.000 6.80 9.33 0.00 4.85
3750 6662 2.113433 CATCTGGTGAGCAGCCTGC 61.113 63.158 9.13 9.13 45.46 4.85
3766 6678 3.855689 CCTGCAATAGGTTTGTTGAGG 57.144 47.619 0.00 0.00 42.00 3.86
3768 6680 2.557924 CTGCAATAGGTTTGTTGAGGCA 59.442 45.455 0.00 0.00 0.00 4.75
3769 6681 2.961741 TGCAATAGGTTTGTTGAGGCAA 59.038 40.909 0.00 0.00 0.00 4.52
3777 6689 3.731652 TTTGTTGAGGCAAACATCTGG 57.268 42.857 6.60 0.00 39.68 3.86
3779 6691 1.955778 TGTTGAGGCAAACATCTGGTG 59.044 47.619 2.06 0.00 35.16 4.17
3780 6692 2.229792 GTTGAGGCAAACATCTGGTGA 58.770 47.619 0.00 0.00 0.00 4.02
3781 6693 2.189594 TGAGGCAAACATCTGGTGAG 57.810 50.000 0.00 0.00 0.00 3.51
3782 6694 0.807496 GAGGCAAACATCTGGTGAGC 59.193 55.000 0.00 0.00 0.00 4.26
3783 6695 0.957395 AGGCAAACATCTGGTGAGCG 60.957 55.000 0.00 0.00 0.00 5.03
3787 6699 0.322975 AAACATCTGGTGAGCGCTCT 59.677 50.000 35.27 13.88 0.00 4.09
3788 6700 0.390866 AACATCTGGTGAGCGCTCTG 60.391 55.000 35.27 25.90 0.00 3.35
3814 6853 5.499313 TGTGATACAAGATCAAATCCAGCA 58.501 37.500 0.00 0.00 0.00 4.41
3816 6855 6.433716 TGTGATACAAGATCAAATCCAGCAAA 59.566 34.615 0.00 0.00 0.00 3.68
3817 6856 7.039853 TGTGATACAAGATCAAATCCAGCAAAA 60.040 33.333 0.00 0.00 0.00 2.44
3819 6858 5.534207 ACAAGATCAAATCCAGCAAAACA 57.466 34.783 0.00 0.00 0.00 2.83
3820 6859 6.105397 ACAAGATCAAATCCAGCAAAACAT 57.895 33.333 0.00 0.00 0.00 2.71
3821 6860 6.161381 ACAAGATCAAATCCAGCAAAACATC 58.839 36.000 0.00 0.00 0.00 3.06
3822 6861 5.334724 AGATCAAATCCAGCAAAACATCC 57.665 39.130 0.00 0.00 0.00 3.51
3823 6862 3.959535 TCAAATCCAGCAAAACATCCC 57.040 42.857 0.00 0.00 0.00 3.85
3824 6863 3.237746 TCAAATCCAGCAAAACATCCCA 58.762 40.909 0.00 0.00 0.00 4.37
3825 6864 3.645212 TCAAATCCAGCAAAACATCCCAA 59.355 39.130 0.00 0.00 0.00 4.12
3826 6865 4.102210 TCAAATCCAGCAAAACATCCCAAA 59.898 37.500 0.00 0.00 0.00 3.28
3827 6866 4.703379 AATCCAGCAAAACATCCCAAAA 57.297 36.364 0.00 0.00 0.00 2.44
3828 6867 4.703379 ATCCAGCAAAACATCCCAAAAA 57.297 36.364 0.00 0.00 0.00 1.94
3829 6868 3.802866 TCCAGCAAAACATCCCAAAAAC 58.197 40.909 0.00 0.00 0.00 2.43
3830 6869 3.454082 TCCAGCAAAACATCCCAAAAACT 59.546 39.130 0.00 0.00 0.00 2.66
3831 6870 4.080638 TCCAGCAAAACATCCCAAAAACTT 60.081 37.500 0.00 0.00 0.00 2.66
3832 6871 5.129485 TCCAGCAAAACATCCCAAAAACTTA 59.871 36.000 0.00 0.00 0.00 2.24
3833 6872 5.819901 CCAGCAAAACATCCCAAAAACTTAA 59.180 36.000 0.00 0.00 0.00 1.85
3834 6873 6.317391 CCAGCAAAACATCCCAAAAACTTAAA 59.683 34.615 0.00 0.00 0.00 1.52
3835 6874 7.148171 CCAGCAAAACATCCCAAAAACTTAAAA 60.148 33.333 0.00 0.00 0.00 1.52
3836 6875 8.404765 CAGCAAAACATCCCAAAAACTTAAAAT 58.595 29.630 0.00 0.00 0.00 1.82
3837 6876 8.620416 AGCAAAACATCCCAAAAACTTAAAATC 58.380 29.630 0.00 0.00 0.00 2.17
3838 6877 7.860373 GCAAAACATCCCAAAAACTTAAAATCC 59.140 33.333 0.00 0.00 0.00 3.01
3839 6878 8.897752 CAAAACATCCCAAAAACTTAAAATCCA 58.102 29.630 0.00 0.00 0.00 3.41
3840 6879 8.675705 AAACATCCCAAAAACTTAAAATCCAG 57.324 30.769 0.00 0.00 0.00 3.86
3841 6880 7.610580 ACATCCCAAAAACTTAAAATCCAGA 57.389 32.000 0.00 0.00 0.00 3.86
3842 6881 7.670364 ACATCCCAAAAACTTAAAATCCAGAG 58.330 34.615 0.00 0.00 0.00 3.35
3843 6882 6.096673 TCCCAAAAACTTAAAATCCAGAGC 57.903 37.500 0.00 0.00 0.00 4.09
3844 6883 4.923281 CCCAAAAACTTAAAATCCAGAGCG 59.077 41.667 0.00 0.00 0.00 5.03
3845 6884 4.385748 CCAAAAACTTAAAATCCAGAGCGC 59.614 41.667 0.00 0.00 0.00 5.92
3936 8486 5.680229 CAGCGAAATAAGCAATGTCAGATTC 59.320 40.000 0.00 0.00 37.01 2.52
3939 8489 7.227314 AGCGAAATAAGCAATGTCAGATTCATA 59.773 33.333 0.00 0.00 37.01 2.15
3972 8542 0.257039 ATTCAATCTGCTCCCGGCTT 59.743 50.000 0.00 0.00 42.39 4.35
3974 8544 0.908910 TCAATCTGCTCCCGGCTTAA 59.091 50.000 0.00 0.00 42.39 1.85
3985 8555 4.379186 GCTCCCGGCTTAACTTAGAAAAAC 60.379 45.833 0.00 0.00 38.06 2.43
3988 8558 4.377738 CCCGGCTTAACTTAGAAAAACGTC 60.378 45.833 0.00 0.00 0.00 4.34
3990 8560 5.135330 CGGCTTAACTTAGAAAAACGTCAC 58.865 41.667 0.00 0.00 0.00 3.67
3991 8561 5.050567 CGGCTTAACTTAGAAAAACGTCACT 60.051 40.000 0.00 0.00 0.00 3.41
3995 8565 5.494632 AACTTAGAAAAACGTCACTTGGG 57.505 39.130 0.00 0.00 0.00 4.12
3996 8566 3.881089 ACTTAGAAAAACGTCACTTGGGG 59.119 43.478 0.00 0.00 0.00 4.96
4004 8574 2.124085 TCACTTGGGGACGGGGAT 59.876 61.111 0.00 0.00 0.00 3.85
4033 8615 2.413796 CGCCTGCAGTTTATTTACGTCA 59.586 45.455 13.81 0.00 0.00 4.35
4073 9845 5.708877 AAATTTGAATTTGCATTGTGGGG 57.291 34.783 1.14 0.00 37.24 4.96
4078 9850 0.841594 ATTTGCATTGTGGGGCCCTT 60.842 50.000 25.93 2.81 0.00 3.95
4321 10096 2.388494 TTCGATCGATCTCCCACGCG 62.388 60.000 20.18 3.53 0.00 6.01
4340 10115 2.556287 CGGCCTCGACAGCAAAAC 59.444 61.111 0.00 0.00 39.00 2.43
4382 10161 2.041265 CTAGGACTGGGCCTGGGT 59.959 66.667 15.36 6.24 39.08 4.51
4387 10166 2.040606 ACTGGGCCTGGGTACGAT 59.959 61.111 15.36 0.00 0.00 3.73
4399 10178 1.733912 GGGTACGATTGAACCGGAAAC 59.266 52.381 9.46 0.00 36.57 2.78
4403 10182 0.802494 CGATTGAACCGGAAACCTGG 59.198 55.000 9.46 0.00 0.00 4.45
4415 10194 2.310930 AAACCTGGCTGGGCTTGGAA 62.311 55.000 15.36 0.00 41.11 3.53
4438 10217 4.267452 ACAGCGTTGTTTGCTTGTTTATTG 59.733 37.500 0.00 0.00 41.72 1.90
4439 10218 4.267452 CAGCGTTGTTTGCTTGTTTATTGT 59.733 37.500 0.00 0.00 41.72 2.71
4440 10219 4.867608 AGCGTTGTTTGCTTGTTTATTGTT 59.132 33.333 0.00 0.00 40.48 2.83
4441 10220 6.020281 CAGCGTTGTTTGCTTGTTTATTGTTA 60.020 34.615 0.00 0.00 41.72 2.41
4442 10221 6.198216 AGCGTTGTTTGCTTGTTTATTGTTAG 59.802 34.615 0.00 0.00 40.48 2.34
4443 10222 6.561350 GCGTTGTTTGCTTGTTTATTGTTAGG 60.561 38.462 0.00 0.00 0.00 2.69
4445 10224 5.293560 TGTTTGCTTGTTTATTGTTAGGCC 58.706 37.500 0.00 0.00 0.00 5.19
4446 10225 5.069781 TGTTTGCTTGTTTATTGTTAGGCCT 59.930 36.000 11.78 11.78 0.00 5.19
4447 10226 5.385509 TTGCTTGTTTATTGTTAGGCCTC 57.614 39.130 9.68 0.00 0.00 4.70
4448 10227 3.438781 TGCTTGTTTATTGTTAGGCCTCG 59.561 43.478 9.68 0.00 0.00 4.63
4449 10228 3.181500 GCTTGTTTATTGTTAGGCCTCGG 60.181 47.826 9.68 0.00 0.00 4.63
4466 10245 4.495844 GCCTCGGTAAGAAAATCGAATTGG 60.496 45.833 0.00 0.00 0.00 3.16
4473 10252 9.991388 CGGTAAGAAAATCGAATTGGTAAAATA 57.009 29.630 0.00 0.00 0.00 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 8.840321 CTTATTGAGAATAACGTGGAAATCCAT 58.160 33.333 5.27 0.00 37.49 3.41
23 24 1.748591 GCCAGCCACCTCCTTATTGAG 60.749 57.143 0.00 0.00 0.00 3.02
26 27 0.548510 GAGCCAGCCACCTCCTTATT 59.451 55.000 0.00 0.00 0.00 1.40
27 28 0.327000 AGAGCCAGCCACCTCCTTAT 60.327 55.000 0.00 0.00 0.00 1.73
28 29 0.978146 GAGAGCCAGCCACCTCCTTA 60.978 60.000 0.00 0.00 0.00 2.69
43 44 0.978146 ACGAAGGGGGTGGATGAGAG 60.978 60.000 0.00 0.00 0.00 3.20
54 55 6.542370 ACATCTTATATTTGTGAACGAAGGGG 59.458 38.462 0.00 0.00 0.00 4.79
99 101 7.551262 TGCTAATTTCAGTCCGTATTACAACAT 59.449 33.333 0.00 0.00 0.00 2.71
103 105 7.412129 CGTTTGCTAATTTCAGTCCGTATTACA 60.412 37.037 0.00 0.00 0.00 2.41
114 117 5.510671 AGTGTGTTCGTTTGCTAATTTCAG 58.489 37.500 0.00 0.00 0.00 3.02
121 124 5.798015 TGTTTTAGTGTGTTCGTTTGCTA 57.202 34.783 0.00 0.00 0.00 3.49
122 125 4.688511 TGTTTTAGTGTGTTCGTTTGCT 57.311 36.364 0.00 0.00 0.00 3.91
124 127 6.255215 AGTCATGTTTTAGTGTGTTCGTTTG 58.745 36.000 0.00 0.00 0.00 2.93
129 132 8.984764 TGTATGTAGTCATGTTTTAGTGTGTTC 58.015 33.333 0.00 0.00 35.70 3.18
134 137 9.586435 TCAGATGTATGTAGTCATGTTTTAGTG 57.414 33.333 0.00 0.00 35.70 2.74
143 146 8.699130 TCTTGTGAATCAGATGTATGTAGTCAT 58.301 33.333 0.00 0.00 38.00 3.06
153 156 9.730705 TTCTATCTTTTCTTGTGAATCAGATGT 57.269 29.630 0.00 0.00 35.30 3.06
156 159 9.730705 ATGTTCTATCTTTTCTTGTGAATCAGA 57.269 29.630 0.00 0.00 31.56 3.27
157 160 9.985318 GATGTTCTATCTTTTCTTGTGAATCAG 57.015 33.333 0.00 0.00 31.56 2.90
161 164 9.342308 ACAAGATGTTCTATCTTTTCTTGTGAA 57.658 29.630 13.54 0.00 46.79 3.18
162 165 8.908786 ACAAGATGTTCTATCTTTTCTTGTGA 57.091 30.769 13.54 0.00 46.79 3.58
176 179 8.830580 CATCCGTTCATAAATACAAGATGTTCT 58.169 33.333 0.00 0.00 0.00 3.01
186 189 8.304596 TCATCTACTCCATCCGTTCATAAATAC 58.695 37.037 0.00 0.00 0.00 1.89
191 194 5.631119 TCTCATCTACTCCATCCGTTCATA 58.369 41.667 0.00 0.00 0.00 2.15
201 204 6.667848 TGTAAAGGTGATTCTCATCTACTCCA 59.332 38.462 0.00 0.00 36.70 3.86
299 302 0.107508 TAGCTCATCCAACTGCTGCC 60.108 55.000 0.00 0.00 37.02 4.85
309 312 5.770663 TCTGTAGGACTAACATAGCTCATCC 59.229 44.000 0.00 0.00 0.00 3.51
316 319 6.922247 TTCTCGTCTGTAGGACTAACATAG 57.078 41.667 0.00 0.00 42.44 2.23
317 320 7.876936 AATTCTCGTCTGTAGGACTAACATA 57.123 36.000 0.00 0.00 42.44 2.29
332 336 7.072030 CCAATTCGGATTTGATAATTCTCGTC 58.928 38.462 12.81 0.00 36.56 4.20
357 361 0.927537 GAGTTTTTGTGGCCGTTTGC 59.072 50.000 0.00 0.00 40.16 3.68
363 367 5.009610 TGACTTATTGAGAGTTTTTGTGGCC 59.990 40.000 0.00 0.00 0.00 5.36
365 369 9.003658 ACTATGACTTATTGAGAGTTTTTGTGG 57.996 33.333 0.00 0.00 0.00 4.17
379 383 6.771749 AGTAGCGGTGTAGACTATGACTTATT 59.228 38.462 0.00 0.00 0.00 1.40
382 386 4.525024 AGTAGCGGTGTAGACTATGACTT 58.475 43.478 0.00 0.00 0.00 3.01
384 388 4.497674 CCAAGTAGCGGTGTAGACTATGAC 60.498 50.000 0.00 0.00 0.00 3.06
388 392 1.747355 GCCAAGTAGCGGTGTAGACTA 59.253 52.381 0.00 0.00 0.00 2.59
396 400 2.046892 CTGCTGCCAAGTAGCGGT 60.047 61.111 5.45 0.00 43.95 5.68
398 402 2.821366 CCCTGCTGCCAAGTAGCG 60.821 66.667 0.00 0.00 43.95 4.26
403 407 3.145551 GATGCCCCTGCTGCCAAG 61.146 66.667 0.00 0.00 38.71 3.61
411 415 2.124901 TTTACGCCGATGCCCCTG 60.125 61.111 0.00 0.00 0.00 4.45
412 416 2.124860 GTTTACGCCGATGCCCCT 60.125 61.111 0.00 0.00 0.00 4.79
432 436 3.203716 CGGGTTATAAAAGTCTGGAGCC 58.796 50.000 0.00 0.00 0.00 4.70
437 441 6.027749 GCAAATCACGGGTTATAAAAGTCTG 58.972 40.000 0.00 0.00 0.00 3.51
447 451 4.764823 AGAAGATTTGCAAATCACGGGTTA 59.235 37.500 39.58 8.61 45.59 2.85
607 621 8.918961 TGTTTCGTATTTTGTTGTTCTTGATT 57.081 26.923 0.00 0.00 0.00 2.57
631 648 3.723835 GCTGGACGCGTTAACACTATTTG 60.724 47.826 15.53 1.80 0.00 2.32
635 652 0.388907 GGCTGGACGCGTTAACACTA 60.389 55.000 15.53 0.00 40.44 2.74
638 655 0.533308 AAAGGCTGGACGCGTTAACA 60.533 50.000 15.53 12.62 45.21 2.41
855 885 0.322098 TATGGTGGTTTGGTGGCGAG 60.322 55.000 0.00 0.00 0.00 5.03
1211 1275 0.313043 CTGCACAAACCAAGAGCAGG 59.687 55.000 0.00 0.00 43.81 4.85
1212 1280 3.859650 CTGCACAAACCAAGAGCAG 57.140 52.632 0.00 0.00 42.53 4.24
1270 1344 2.029666 CGGAAGCGGCATCCCTAG 59.970 66.667 17.77 1.19 33.13 3.02
1273 1347 3.508840 CAACGGAAGCGGCATCCC 61.509 66.667 17.77 6.92 33.13 3.85
1361 1468 3.503748 AGAAAATTCGAACCCAAGCTCTG 59.496 43.478 0.00 0.00 0.00 3.35
1431 1547 1.672356 CCAAGAACACCCAGGAGCG 60.672 63.158 0.00 0.00 0.00 5.03
1472 1588 1.146263 CCGATAAGCCAGACCACCC 59.854 63.158 0.00 0.00 0.00 4.61
1780 1915 7.073342 ACACTTGAGTAAGAAACACTTTGAC 57.927 36.000 0.00 0.00 39.72 3.18
1833 1968 4.448537 TTAGTGGTTGCATATTTGGTGC 57.551 40.909 0.00 0.00 42.81 5.01
1847 1982 6.547510 AGCAGAACAAAGAGAAAATTAGTGGT 59.452 34.615 0.00 0.00 0.00 4.16
1856 1991 5.734220 GCACATGAAGCAGAACAAAGAGAAA 60.734 40.000 0.00 0.00 0.00 2.52
1961 2096 3.321648 TGATGCCTGTGCCTCGGT 61.322 61.111 0.00 0.00 35.15 4.69
2192 2336 0.747283 CTGCCATGACAAGGAGAGCC 60.747 60.000 0.00 0.00 0.00 4.70
2225 2369 0.462047 CTTTCTTCGCCCGGCAGTAT 60.462 55.000 10.77 0.00 0.00 2.12
2403 2553 0.035458 CTGACCGCTTCAAGGAAGGT 59.965 55.000 7.97 0.00 39.76 3.50
2409 2559 1.018226 CCAGCTCTGACCGCTTCAAG 61.018 60.000 0.00 0.00 35.07 3.02
2415 2565 2.817396 GCTTCCAGCTCTGACCGC 60.817 66.667 0.00 0.00 38.45 5.68
2541 2691 6.515272 TCTTTTGGCCAATCATTCTTAGAC 57.485 37.500 21.26 0.00 0.00 2.59
2557 2707 5.476599 TGTACTGGGATTCACATTCTTTTGG 59.523 40.000 0.00 0.00 0.00 3.28
2627 2781 6.142139 TCAGTCAATGTGTATTTCGCAAAAG 58.858 36.000 0.00 0.00 40.08 2.27
2629 2783 5.681337 TCAGTCAATGTGTATTTCGCAAA 57.319 34.783 0.00 0.00 40.08 3.68
2631 2785 5.448438 GTTTCAGTCAATGTGTATTTCGCA 58.552 37.500 0.00 0.00 40.97 5.10
2632 2786 4.549599 CGTTTCAGTCAATGTGTATTTCGC 59.450 41.667 0.00 0.00 0.00 4.70
2635 2789 4.518970 AGCCGTTTCAGTCAATGTGTATTT 59.481 37.500 0.00 0.00 0.00 1.40
2674 2828 2.897326 GTGGCCCACTTTGGATAAACTT 59.103 45.455 6.63 0.00 40.96 2.66
2782 2936 2.237143 ACCATGGAGATGCTCGAAAAGA 59.763 45.455 21.47 0.00 0.00 2.52
2860 3021 5.401550 AGTTGTTGAAGTGTGTGAACATTG 58.598 37.500 0.00 0.00 0.00 2.82
2866 3027 4.323417 ACTGAAGTTGTTGAAGTGTGTGA 58.677 39.130 0.00 0.00 0.00 3.58
2869 3030 7.471721 TCAAATACTGAAGTTGTTGAAGTGTG 58.528 34.615 6.20 0.00 31.21 3.82
3054 3217 1.617850 ACCTTTGCGGCAAAATCATCA 59.382 42.857 26.28 5.30 32.75 3.07
3117 5227 2.733593 GTGCAGTCGTCGGTGACC 60.734 66.667 0.00 0.00 39.77 4.02
3515 6424 0.036010 AGAAATGGACTGGACTGCCG 60.036 55.000 0.00 0.00 36.79 5.69
3534 6443 3.524789 AGAATCCATCATCACAACAGGGA 59.475 43.478 0.00 0.00 0.00 4.20
3562 6471 4.887071 TCAGTACAAGGAACAACAAAGCAT 59.113 37.500 0.00 0.00 0.00 3.79
3618 6527 2.500392 TACAATGCCACTAACCCACC 57.500 50.000 0.00 0.00 0.00 4.61
3671 6583 1.354101 AACCACACATCTCCCCGTTA 58.646 50.000 0.00 0.00 0.00 3.18
3696 6608 7.630242 ATCGATCAAACCATAGACAAACATT 57.370 32.000 0.00 0.00 0.00 2.71
3710 6622 5.938322 TGTTTGCCTAAGAATCGATCAAAC 58.062 37.500 20.90 20.90 40.97 2.93
3718 6630 4.943705 TCACCAGATGTTTGCCTAAGAATC 59.056 41.667 0.00 0.00 0.00 2.52
3737 6649 1.099879 CCTATTGCAGGCTGCTCACC 61.100 60.000 36.50 11.43 45.31 4.02
3747 6659 2.557924 TGCCTCAACAAACCTATTGCAG 59.442 45.455 0.00 0.00 0.00 4.41
3749 6661 3.658757 TTGCCTCAACAAACCTATTGC 57.341 42.857 0.00 0.00 0.00 3.56
3758 6670 2.361757 CACCAGATGTTTGCCTCAACAA 59.638 45.455 0.00 0.00 0.00 2.83
3761 6673 2.507484 CTCACCAGATGTTTGCCTCAA 58.493 47.619 0.00 0.00 0.00 3.02
3762 6674 1.883638 GCTCACCAGATGTTTGCCTCA 60.884 52.381 0.00 0.00 0.00 3.86
3764 6676 0.957395 CGCTCACCAGATGTTTGCCT 60.957 55.000 0.00 0.00 0.00 4.75
3766 6678 1.154150 GCGCTCACCAGATGTTTGC 60.154 57.895 0.00 0.00 0.00 3.68
3768 6680 0.322975 AGAGCGCTCACCAGATGTTT 59.677 50.000 36.87 11.42 0.00 2.83
3769 6681 0.390866 CAGAGCGCTCACCAGATGTT 60.391 55.000 36.87 12.20 0.00 2.71
3771 6683 2.172372 GCAGAGCGCTCACCAGATG 61.172 63.158 36.87 25.59 37.77 2.90
3772 6684 1.969200 ATGCAGAGCGCTCACCAGAT 61.969 55.000 36.87 18.61 43.06 2.90
3776 6688 2.435586 ACATGCAGAGCGCTCACC 60.436 61.111 36.87 26.37 43.06 4.02
3777 6689 1.088340 ATCACATGCAGAGCGCTCAC 61.088 55.000 36.87 27.96 43.06 3.51
3779 6691 0.857935 GTATCACATGCAGAGCGCTC 59.142 55.000 30.01 30.01 43.06 5.03
3780 6692 0.176449 TGTATCACATGCAGAGCGCT 59.824 50.000 11.27 11.27 43.06 5.92
3781 6693 1.004185 CTTGTATCACATGCAGAGCGC 60.004 52.381 0.00 0.00 42.89 5.92
3782 6694 2.543641 TCTTGTATCACATGCAGAGCG 58.456 47.619 0.00 0.00 0.00 5.03
3783 6695 4.124970 TGATCTTGTATCACATGCAGAGC 58.875 43.478 0.00 0.00 0.00 4.09
3787 6699 5.887035 TGGATTTGATCTTGTATCACATGCA 59.113 36.000 4.78 4.78 35.31 3.96
3788 6700 6.381481 TGGATTTGATCTTGTATCACATGC 57.619 37.500 0.00 0.00 30.50 4.06
3790 6702 6.124340 TGCTGGATTTGATCTTGTATCACAT 58.876 36.000 0.00 0.00 0.00 3.21
3791 6703 5.499313 TGCTGGATTTGATCTTGTATCACA 58.501 37.500 0.00 0.00 0.00 3.58
3793 6705 7.039853 TGTTTTGCTGGATTTGATCTTGTATCA 60.040 33.333 0.00 0.00 0.00 2.15
3794 6706 7.315142 TGTTTTGCTGGATTTGATCTTGTATC 58.685 34.615 0.00 0.00 0.00 2.24
3814 6853 9.119418 CTGGATTTTAAGTTTTTGGGATGTTTT 57.881 29.630 0.00 0.00 0.00 2.43
3816 6855 8.028652 TCTGGATTTTAAGTTTTTGGGATGTT 57.971 30.769 0.00 0.00 0.00 2.71
3817 6856 7.610580 TCTGGATTTTAAGTTTTTGGGATGT 57.389 32.000 0.00 0.00 0.00 3.06
3819 6858 6.572314 CGCTCTGGATTTTAAGTTTTTGGGAT 60.572 38.462 0.00 0.00 0.00 3.85
3820 6859 5.278758 CGCTCTGGATTTTAAGTTTTTGGGA 60.279 40.000 0.00 0.00 0.00 4.37
3821 6860 4.923281 CGCTCTGGATTTTAAGTTTTTGGG 59.077 41.667 0.00 0.00 0.00 4.12
3822 6861 4.385748 GCGCTCTGGATTTTAAGTTTTTGG 59.614 41.667 0.00 0.00 0.00 3.28
3823 6862 5.222631 AGCGCTCTGGATTTTAAGTTTTTG 58.777 37.500 2.64 0.00 0.00 2.44
3824 6863 5.453567 AGCGCTCTGGATTTTAAGTTTTT 57.546 34.783 2.64 0.00 0.00 1.94
3825 6864 5.222631 CAAGCGCTCTGGATTTTAAGTTTT 58.777 37.500 12.06 0.00 0.00 2.43
3826 6865 4.321230 CCAAGCGCTCTGGATTTTAAGTTT 60.321 41.667 25.31 0.00 0.00 2.66
3827 6866 3.191371 CCAAGCGCTCTGGATTTTAAGTT 59.809 43.478 25.31 0.00 0.00 2.66
3828 6867 2.749621 CCAAGCGCTCTGGATTTTAAGT 59.250 45.455 25.31 0.00 0.00 2.24
3829 6868 2.478539 GCCAAGCGCTCTGGATTTTAAG 60.479 50.000 30.45 11.18 0.00 1.85
3830 6869 1.472480 GCCAAGCGCTCTGGATTTTAA 59.528 47.619 30.45 0.00 0.00 1.52
3831 6870 1.094785 GCCAAGCGCTCTGGATTTTA 58.905 50.000 30.45 0.00 0.00 1.52
3832 6871 1.885871 GCCAAGCGCTCTGGATTTT 59.114 52.632 30.45 5.56 0.00 1.82
3833 6872 3.595819 GCCAAGCGCTCTGGATTT 58.404 55.556 30.45 6.27 0.00 2.17
3842 6881 0.591170 TAACTTTCACAGCCAAGCGC 59.409 50.000 0.00 0.00 37.98 5.92
3843 6882 3.347958 TTTAACTTTCACAGCCAAGCG 57.652 42.857 0.00 0.00 0.00 4.68
3844 6883 5.107875 CGAATTTTAACTTTCACAGCCAAGC 60.108 40.000 0.00 0.00 0.00 4.01
3845 6884 5.977129 ACGAATTTTAACTTTCACAGCCAAG 59.023 36.000 0.00 0.00 0.00 3.61
3903 6942 3.919804 TGCTTATTTCGCTGATGTTTTGC 59.080 39.130 0.00 0.00 0.00 3.68
3909 6948 4.912214 TGACATTGCTTATTTCGCTGATG 58.088 39.130 0.00 0.00 0.00 3.07
3910 6949 4.877823 TCTGACATTGCTTATTTCGCTGAT 59.122 37.500 0.00 0.00 0.00 2.90
3951 8501 1.517242 GCCGGGAGCAGATTGAATAG 58.483 55.000 2.18 0.00 42.97 1.73
3962 8512 2.685850 TTCTAAGTTAAGCCGGGAGC 57.314 50.000 2.18 0.00 44.25 4.70
3964 8534 3.747529 CGTTTTTCTAAGTTAAGCCGGGA 59.252 43.478 2.18 0.00 0.00 5.14
3972 8542 5.528320 CCCCAAGTGACGTTTTTCTAAGTTA 59.472 40.000 0.00 0.00 0.00 2.24
3974 8544 3.881089 CCCCAAGTGACGTTTTTCTAAGT 59.119 43.478 0.00 0.00 0.00 2.24
3988 8558 1.378514 CAATCCCCGTCCCCAAGTG 60.379 63.158 0.00 0.00 0.00 3.16
3990 8560 2.440247 GCAATCCCCGTCCCCAAG 60.440 66.667 0.00 0.00 0.00 3.61
3991 8561 3.260888 TGCAATCCCCGTCCCCAA 61.261 61.111 0.00 0.00 0.00 4.12
3995 8565 3.134127 GTGCTGCAATCCCCGTCC 61.134 66.667 2.77 0.00 0.00 4.79
3996 8566 3.499737 CGTGCTGCAATCCCCGTC 61.500 66.667 2.77 0.00 0.00 4.79
4015 8585 6.130723 TCGTTTTGACGTAAATAAACTGCAG 58.869 36.000 13.48 13.48 0.00 4.41
4021 8591 7.566709 GGAGTTCTCGTTTTGACGTAAATAAA 58.433 34.615 0.00 0.00 0.00 1.40
4022 8592 6.129115 CGGAGTTCTCGTTTTGACGTAAATAA 60.129 38.462 0.00 0.00 0.00 1.40
4023 8593 5.343058 CGGAGTTCTCGTTTTGACGTAAATA 59.657 40.000 0.00 0.00 0.00 1.40
4033 8615 7.867752 TCAAATTTTATCGGAGTTCTCGTTTT 58.132 30.769 0.00 0.00 0.00 2.43
4038 8620 8.587111 GCAAATTCAAATTTTATCGGAGTTCTC 58.413 33.333 0.00 0.00 36.52 2.87
4073 9845 2.851045 TTCCCCACAAGGAAGGGC 59.149 61.111 0.00 0.00 44.06 5.19
4330 10105 1.896660 TCGGGCCTGTTTTGCTGTC 60.897 57.895 12.43 0.00 0.00 3.51
4382 10161 2.613474 CCAGGTTTCCGGTTCAATCGTA 60.613 50.000 0.00 0.00 0.00 3.43
4387 10166 0.821711 CAGCCAGGTTTCCGGTTCAA 60.822 55.000 0.00 0.00 0.00 2.69
4399 10178 2.677875 GTTCCAAGCCCAGCCAGG 60.678 66.667 0.00 0.00 37.03 4.45
4403 10182 3.741476 CGCTGTTCCAAGCCCAGC 61.741 66.667 0.00 0.00 46.25 4.85
4415 10194 2.362169 AAACAAGCAAACAACGCTGT 57.638 40.000 0.00 0.00 40.35 4.40
4427 10206 3.181500 CCGAGGCCTAACAATAAACAAGC 60.181 47.826 4.42 0.00 0.00 4.01
4438 10217 3.554731 CGATTTTCTTACCGAGGCCTAAC 59.445 47.826 4.42 0.00 0.00 2.34
4439 10218 3.448301 TCGATTTTCTTACCGAGGCCTAA 59.552 43.478 4.42 0.00 0.00 2.69
4440 10219 3.025978 TCGATTTTCTTACCGAGGCCTA 58.974 45.455 4.42 0.00 0.00 3.93
4441 10220 1.829222 TCGATTTTCTTACCGAGGCCT 59.171 47.619 3.86 3.86 0.00 5.19
4442 10221 2.304751 TCGATTTTCTTACCGAGGCC 57.695 50.000 0.00 0.00 0.00 5.19
4443 10222 4.495844 CCAATTCGATTTTCTTACCGAGGC 60.496 45.833 0.00 0.00 32.41 4.70
4445 10224 5.796350 ACCAATTCGATTTTCTTACCGAG 57.204 39.130 0.00 0.00 32.41 4.63
4446 10225 7.670009 TTTACCAATTCGATTTTCTTACCGA 57.330 32.000 0.00 0.00 0.00 4.69
4447 10226 8.905103 ATTTTACCAATTCGATTTTCTTACCG 57.095 30.769 0.00 0.00 0.00 4.02


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

AutoCloner maintained by Alex Coulton.