Multiple sequence alignment - TraesCS7A01G409800

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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 TraesCS7A01G409800 chr7A 100.000 6025 0 0 1 6025 596683866 596689890 0.000000e+00 11127.0
1 TraesCS7A01G409800 chr7A 85.392 664 56 21 3019 3667 651433101 651433738 0.000000e+00 651.0
2 TraesCS7A01G409800 chr7D 95.579 3099 87 18 1803 4893 520387365 520390421 0.000000e+00 4918.0
3 TraesCS7A01G409800 chr7D 93.300 1791 89 20 26 1804 520385500 520387271 0.000000e+00 2614.0
4 TraesCS7A01G409800 chr7D 91.297 563 28 6 4892 5448 520390775 520391322 0.000000e+00 749.0
5 TraesCS7A01G409800 chr7D 81.265 427 55 17 5466 5878 520391439 520391854 7.530000e-84 322.0
6 TraesCS7A01G409800 chr7D 89.286 56 5 1 5441 5496 299594570 299594516 1.080000e-07 69.4
7 TraesCS7A01G409800 chr7B 94.801 3020 126 19 1872 4881 553443212 553446210 0.000000e+00 4678.0
8 TraesCS7A01G409800 chr7B 89.695 1834 116 34 26 1811 553440700 553442508 0.000000e+00 2272.0
9 TraesCS7A01G409800 chr7B 91.814 904 48 13 4892 5787 553446299 553447184 0.000000e+00 1236.0
10 TraesCS7A01G409800 chr7B 98.387 62 1 0 1810 1871 553442618 553442679 6.380000e-20 110.0
11 TraesCS7A01G409800 chr3D 88.825 2962 215 67 2263 5160 191097589 191100498 0.000000e+00 3530.0
12 TraesCS7A01G409800 chr3D 89.858 917 58 13 829 1723 191095293 191096196 0.000000e+00 1146.0
13 TraesCS7A01G409800 chr3D 92.212 321 20 2 1910 2229 191097270 191097586 3.310000e-122 449.0
14 TraesCS7A01G409800 chr3D 80.000 280 26 13 5173 5429 191100560 191100832 4.800000e-41 180.0
15 TraesCS7A01G409800 chr3D 91.358 81 6 1 5909 5989 545256791 545256712 6.380000e-20 110.0
16 TraesCS7A01G409800 chr3D 93.478 46 3 0 5451 5496 324311119 324311164 1.080000e-07 69.4
17 TraesCS7A01G409800 chr3B 89.191 2831 219 54 2258 5028 277032028 277034831 0.000000e+00 3452.0
18 TraesCS7A01G409800 chr3B 91.349 786 59 5 941 1723 277029330 277030109 0.000000e+00 1066.0
19 TraesCS7A01G409800 chr3B 87.195 656 46 21 3019 3667 755228339 755228963 0.000000e+00 712.0
20 TraesCS7A01G409800 chr3B 84.821 672 62 21 3019 3681 449163374 449162734 1.830000e-179 640.0
21 TraesCS7A01G409800 chr3B 92.260 323 20 2 1910 2231 277031714 277032032 2.560000e-123 453.0
22 TraesCS7A01G409800 chr3B 89.381 226 22 2 2353 2578 96859540 96859763 3.550000e-72 283.0
23 TraesCS7A01G409800 chr3A 89.409 2030 160 34 1910 3908 266691110 266693115 0.000000e+00 2507.0
24 TraesCS7A01G409800 chr3A 91.325 853 60 6 874 1723 266689190 266690031 0.000000e+00 1153.0
25 TraesCS7A01G409800 chr3A 91.938 583 41 5 3932 4510 266693230 266693810 0.000000e+00 811.0
26 TraesCS7A01G409800 chr3A 84.816 652 50 30 4534 5160 266693798 266694425 1.440000e-170 610.0
27 TraesCS7A01G409800 chr3A 85.437 515 39 21 3019 3526 725881200 725881685 2.510000e-138 503.0
28 TraesCS7A01G409800 chr3A 84.599 474 38 18 3139 3605 365962900 365962455 7.170000e-119 438.0
29 TraesCS7A01G409800 chr3A 90.132 304 27 2 3926 4229 629690725 629691025 5.660000e-105 392.0
30 TraesCS7A01G409800 chr3A 90.361 83 5 2 5905 5986 492044049 492043969 8.260000e-19 106.0
31 TraesCS7A01G409800 chr2D 87.827 764 68 15 3596 4352 278879476 278880221 0.000000e+00 872.0
32 TraesCS7A01G409800 chr2D 85.285 333 37 7 4354 4684 278880297 278880619 3.480000e-87 333.0
33 TraesCS7A01G409800 chr2D 92.308 78 4 1 5909 5986 564703810 564703885 6.380000e-20 110.0
34 TraesCS7A01G409800 chr2D 88.608 79 6 2 5909 5986 20847354 20847278 6.430000e-15 93.5
35 TraesCS7A01G409800 chr2D 93.478 46 3 0 5451 5496 159688991 159688946 1.080000e-07 69.4
36 TraesCS7A01G409800 chr2D 95.238 42 2 0 5455 5496 608027269 608027310 3.900000e-07 67.6
37 TraesCS7A01G409800 chr2D 100.000 30 0 0 5987 6016 564703904 564703933 8.440000e-04 56.5
38 TraesCS7A01G409800 chr4B 86.509 593 43 23 3019 3604 462782774 462782212 8.580000e-173 617.0
39 TraesCS7A01G409800 chr2B 89.506 324 31 3 2353 2676 770585705 770586025 2.020000e-109 407.0
40 TraesCS7A01G409800 chr2B 92.157 51 2 2 5447 5497 729493747 729493795 3.010000e-08 71.3
41 TraesCS7A01G409800 chr1B 88.889 324 32 4 2353 2676 345535819 345535500 4.380000e-106 396.0
42 TraesCS7A01G409800 chr5D 90.837 251 22 1 2515 2765 333076590 333076839 9.680000e-88 335.0
43 TraesCS7A01G409800 chr5D 89.615 260 23 4 2515 2772 492284771 492284514 1.620000e-85 327.0
44 TraesCS7A01G409800 chr5D 87.912 91 11 0 2353 2443 492284853 492284763 2.300000e-19 108.0
45 TraesCS7A01G409800 chr5D 89.610 77 5 2 5909 5984 439230667 439230741 1.790000e-15 95.3
46 TraesCS7A01G409800 chr1D 90.244 82 8 0 5908 5989 33857243 33857324 2.300000e-19 108.0
47 TraesCS7A01G409800 chr6A 90.123 81 6 2 5909 5989 606095569 606095647 2.970000e-18 104.0
48 TraesCS7A01G409800 chr6A 100.000 28 0 0 5989 6016 606095667 606095694 1.100000e-02 52.8
49 TraesCS7A01G409800 chr5B 89.157 83 7 2 5904 5986 394675001 394675081 1.070000e-17 102.0
50 TraesCS7A01G409800 chr5B 88.608 79 7 2 5909 5986 494034701 494034624 1.790000e-15 95.3
51 TraesCS7A01G409800 chr5B 94.595 37 2 0 5989 6025 394675103 394675139 2.350000e-04 58.4
52 TraesCS7A01G409800 chr5A 90.789 76 5 1 3608 3681 565381987 565381912 3.840000e-17 100.0
53 TraesCS7A01G409800 chr6D 88.462 78 8 1 5906 5983 392524769 392524845 6.430000e-15 93.5
54 TraesCS7A01G409800 chr6D 93.478 46 3 0 5451 5496 318346682 318346637 1.080000e-07 69.4
55 TraesCS7A01G409800 chr2A 87.805 82 7 2 5906 5986 752398399 752398478 6.430000e-15 93.5
56 TraesCS7A01G409800 chr2A 87.097 62 6 2 5964 6025 528266153 528266094 1.080000e-07 69.4
57 TraesCS7A01G409800 chr6B 85.714 70 5 5 5451 5519 505802616 505802681 1.080000e-07 69.4


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS7A01G409800 chr7A 596683866 596689890 6024 False 11127.00 11127 100.000000 1 6025 1 chr7A.!!$F1 6024
1 TraesCS7A01G409800 chr7A 651433101 651433738 637 False 651.00 651 85.392000 3019 3667 1 chr7A.!!$F2 648
2 TraesCS7A01G409800 chr7D 520385500 520391854 6354 False 2150.75 4918 90.360250 26 5878 4 chr7D.!!$F1 5852
3 TraesCS7A01G409800 chr7B 553440700 553447184 6484 False 2074.00 4678 93.674250 26 5787 4 chr7B.!!$F1 5761
4 TraesCS7A01G409800 chr3D 191095293 191100832 5539 False 1326.25 3530 87.723750 829 5429 4 chr3D.!!$F2 4600
5 TraesCS7A01G409800 chr3B 277029330 277034831 5501 False 1657.00 3452 90.933333 941 5028 3 chr3B.!!$F3 4087
6 TraesCS7A01G409800 chr3B 755228339 755228963 624 False 712.00 712 87.195000 3019 3667 1 chr3B.!!$F2 648
7 TraesCS7A01G409800 chr3B 449162734 449163374 640 True 640.00 640 84.821000 3019 3681 1 chr3B.!!$R1 662
8 TraesCS7A01G409800 chr3A 266689190 266694425 5235 False 1270.25 2507 89.372000 874 5160 4 chr3A.!!$F3 4286
9 TraesCS7A01G409800 chr2D 278879476 278880619 1143 False 602.50 872 86.556000 3596 4684 2 chr2D.!!$F2 1088
10 TraesCS7A01G409800 chr4B 462782212 462782774 562 True 617.00 617 86.509000 3019 3604 1 chr4B.!!$R1 585

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
281 294 0.036306 CAGGTCCAGGCGTTAAGGTT 59.964 55.000 0.00 0.0 0.00 3.50 F
482 507 0.105778 GATCCGGGCTTCTTCTCAGG 59.894 60.000 0.00 0.0 0.00 3.86 F
484 509 1.219393 CCGGGCTTCTTCTCAGGTC 59.781 63.158 0.00 0.0 0.00 3.85 F
929 983 2.271944 AGGGGGCTTACGATTTATGC 57.728 50.000 0.00 0.0 0.00 3.14 F
1915 4075 2.697761 GCTGACAGTGGCCTGCATG 61.698 63.158 3.32 0.0 42.81 4.06 F
2754 4963 0.110056 GCACAAGTGTCCTGCGAATG 60.110 55.000 1.79 0.0 0.00 2.67 F
3706 5941 1.522569 CCGCTTTCTCTCCCCGAAT 59.477 57.895 0.00 0.0 0.00 3.34 F
4451 6862 1.493022 GTCACAGGTATAATGCCCCCA 59.507 52.381 0.00 0.0 0.00 4.96 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1224 1281 0.034089 GGAACCCATCAGAACCAGGG 60.034 60.000 0.00 0.00 46.96 4.45 R
1664 1728 1.148310 TTAGCTGCTTTGCGTCTGAC 58.852 50.000 7.79 0.00 38.13 3.51 R
2311 4503 5.529581 TCTGGAATGAAAACAAAGGGAAC 57.470 39.130 0.00 0.00 0.00 3.62 R
2525 4731 5.508489 GGGTGCATTATTCATGTGAATCAGG 60.508 44.000 11.24 4.64 43.17 3.86 R
3689 5924 1.136305 TGTATTCGGGGAGAGAAAGCG 59.864 52.381 0.00 0.00 0.00 4.68 R
4306 6642 0.400213 ACATGAAAACCGGAGCTGGA 59.600 50.000 9.46 0.00 0.00 3.86 R
4628 7135 0.836606 TGACTGAAGGGAAGTGTGCA 59.163 50.000 0.00 0.00 0.00 4.57 R
5933 9000 0.032952 TTCGTACAGTGGTGTGGAGC 59.967 55.000 0.00 0.00 37.52 4.70 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
90 92 3.285215 GGGATCTCGCGCCTCGTA 61.285 66.667 0.00 0.00 39.67 3.43
92 94 1.154188 GGATCTCGCGCCTCGTATC 60.154 63.158 0.00 0.00 39.67 2.24
94 96 0.179210 GATCTCGCGCCTCGTATCTC 60.179 60.000 0.00 0.00 39.67 2.75
95 97 0.885150 ATCTCGCGCCTCGTATCTCA 60.885 55.000 0.00 0.00 39.67 3.27
97 99 0.248498 CTCGCGCCTCGTATCTCAAA 60.248 55.000 0.00 0.00 39.67 2.69
111 115 5.127031 CGTATCTCAAATTTTGGGTGGGAAT 59.873 40.000 8.80 0.00 31.46 3.01
194 207 3.663233 CGCGAGCTTTGTTTCGTATTTGA 60.663 43.478 0.00 0.00 38.96 2.69
212 225 3.365265 CGGGTTGCTGCCTTGTCC 61.365 66.667 0.00 0.00 0.00 4.02
234 247 1.473278 GTGTGTTTTGTCGGTTTGGGA 59.527 47.619 0.00 0.00 0.00 4.37
239 252 2.249844 TTTGTCGGTTTGGGACTCTC 57.750 50.000 0.00 0.00 35.45 3.20
281 294 0.036306 CAGGTCCAGGCGTTAAGGTT 59.964 55.000 0.00 0.00 0.00 3.50
314 329 7.196331 AGTTGCCGCTATAAAAATTGATCTTC 58.804 34.615 0.00 0.00 0.00 2.87
325 340 6.786967 AAAATTGATCTTCAGGGATCTTGG 57.213 37.500 0.00 0.00 41.72 3.61
334 349 0.609131 AGGGATCTTGGTGCAAACGG 60.609 55.000 0.00 0.00 0.00 4.44
337 352 0.804989 GATCTTGGTGCAAACGGAGG 59.195 55.000 0.00 0.00 0.00 4.30
399 423 1.209504 CTCTTGGAGGGGCGAACATAA 59.790 52.381 0.00 0.00 0.00 1.90
405 429 3.949113 TGGAGGGGCGAACATAATTTAAC 59.051 43.478 0.00 0.00 0.00 2.01
406 430 3.949113 GGAGGGGCGAACATAATTTAACA 59.051 43.478 0.00 0.00 0.00 2.41
407 431 4.201980 GGAGGGGCGAACATAATTTAACAC 60.202 45.833 0.00 0.00 0.00 3.32
408 432 3.375922 AGGGGCGAACATAATTTAACACG 59.624 43.478 0.00 0.00 0.00 4.49
409 433 3.103007 GGGCGAACATAATTTAACACGC 58.897 45.455 0.00 0.00 43.19 5.34
410 434 3.426426 GGGCGAACATAATTTAACACGCA 60.426 43.478 0.00 0.00 45.17 5.24
411 435 3.783943 GGCGAACATAATTTAACACGCAG 59.216 43.478 0.00 0.00 45.17 5.18
412 436 3.237433 GCGAACATAATTTAACACGCAGC 59.763 43.478 0.00 0.00 43.35 5.25
453 478 0.523072 AAATGTGCTGGTGCGTCATC 59.477 50.000 0.00 0.00 43.34 2.92
470 495 1.945394 CATCTTTGCTTGAGATCCGGG 59.055 52.381 0.00 0.00 31.66 5.73
482 507 0.105778 GATCCGGGCTTCTTCTCAGG 59.894 60.000 0.00 0.00 0.00 3.86
484 509 1.219393 CCGGGCTTCTTCTCAGGTC 59.781 63.158 0.00 0.00 0.00 3.85
658 685 9.525826 CTTATAGGGATCAAGCAATTTAATCCT 57.474 33.333 0.00 0.00 36.84 3.24
684 716 4.823989 AGATTCTTGGAGTGTCCTGTTTTG 59.176 41.667 0.00 0.00 37.46 2.44
708 740 5.156355 GCAGTATTCACAACAGTGATTTGG 58.844 41.667 0.00 0.00 41.56 3.28
719 752 4.215109 ACAGTGATTTGGCACTAGGTTTT 58.785 39.130 0.00 0.00 46.80 2.43
720 753 5.381757 ACAGTGATTTGGCACTAGGTTTTA 58.618 37.500 0.00 0.00 46.80 1.52
721 754 5.240844 ACAGTGATTTGGCACTAGGTTTTAC 59.759 40.000 0.00 0.00 46.80 2.01
726 759 5.616488 TTTGGCACTAGGTTTTACGAATC 57.384 39.130 0.00 0.00 0.00 2.52
736 769 6.627395 AGGTTTTACGAATCAAATGTCACA 57.373 33.333 0.00 0.00 0.00 3.58
743 776 3.181497 CGAATCAAATGTCACATGGACCC 60.181 47.826 10.60 0.00 46.38 4.46
820 855 9.373603 AGGTGTTTATTTTTGTAGTTTTTGTCC 57.626 29.630 0.00 0.00 0.00 4.02
896 950 6.823689 TCTTCCATTCTATTCTGGTACTTTGC 59.176 38.462 0.00 0.00 34.03 3.68
929 983 2.271944 AGGGGGCTTACGATTTATGC 57.728 50.000 0.00 0.00 0.00 3.14
962 1018 9.557338 GAATAGTAGCTATTACTGTGGTTATCG 57.443 37.037 0.00 0.00 42.57 2.92
966 1022 5.770417 AGCTATTACTGTGGTTATCGTAGC 58.230 41.667 0.00 0.00 0.00 3.58
1111 1167 8.783660 TGACTTCCTCTGTGGTATATATTCTT 57.216 34.615 0.00 0.00 37.07 2.52
1117 1173 9.702253 TCCTCTGTGGTATATATTCTTCCTATC 57.298 37.037 0.00 0.00 37.07 2.08
1118 1174 8.625651 CCTCTGTGGTATATATTCTTCCTATCG 58.374 40.741 0.00 0.00 0.00 2.92
1224 1281 4.380233 CCTTCTGTTGCTGGAATCATCAAC 60.380 45.833 6.25 6.25 45.20 3.18
1396 1453 4.521943 GCAGTTTGCTAGCTCAATATTCG 58.478 43.478 17.23 0.00 40.96 3.34
1399 1456 4.034510 AGTTTGCTAGCTCAATATTCGTGC 59.965 41.667 17.23 0.00 0.00 5.34
1400 1457 3.177997 TGCTAGCTCAATATTCGTGCA 57.822 42.857 17.23 0.00 0.00 4.57
1519 1583 5.692204 CGGAGGTTAGTTACAGCATTGATAG 59.308 44.000 0.00 0.00 0.00 2.08
1530 1594 4.708909 ACAGCATTGATAGTCTGTCTGAGA 59.291 41.667 0.00 0.00 35.05 3.27
1915 4075 2.697761 GCTGACAGTGGCCTGCATG 61.698 63.158 3.32 0.00 42.81 4.06
2103 4263 5.109210 TGTGTCTAAATCGGTATGCTTCAG 58.891 41.667 0.00 0.00 0.00 3.02
2362 4555 8.092068 TCCACTTCTTTAATTTGACGACTGATA 58.908 33.333 0.00 0.00 0.00 2.15
2525 4731 9.853555 TGTGAATAAATGTAAATGTCACATTCC 57.146 29.630 2.74 0.00 43.94 3.01
2752 4961 3.731136 GCACAAGTGTCCTGCGAA 58.269 55.556 1.79 0.00 0.00 4.70
2753 4962 2.247790 GCACAAGTGTCCTGCGAAT 58.752 52.632 1.79 0.00 0.00 3.34
2754 4963 0.110056 GCACAAGTGTCCTGCGAATG 60.110 55.000 1.79 0.00 0.00 2.67
2845 5054 9.748708 CACATCCTTTTTGTCTTCTAATTTTCA 57.251 29.630 0.00 0.00 0.00 2.69
2975 5184 6.942005 TCACGATAATTCCATTCCTGCATTAT 59.058 34.615 0.00 0.00 0.00 1.28
3059 5270 6.553100 AGGTTAAAATGATGGTTGTTCTTGGA 59.447 34.615 0.00 0.00 0.00 3.53
3241 5462 3.930336 TCTGGTGAGCTGAACAATACAG 58.070 45.455 0.00 0.00 38.27 2.74
3263 5484 3.372206 GTCAGTATGCACAGATGTGGTTC 59.628 47.826 14.44 0.00 45.72 3.62
3689 5924 3.430790 GCTTGATAATTGTCCTTTGCCCC 60.431 47.826 0.00 0.00 0.00 5.80
3706 5941 1.522569 CCGCTTTCTCTCCCCGAAT 59.477 57.895 0.00 0.00 0.00 3.34
4119 6453 3.265791 CTTGGTATCTGGTGAGCTTGTC 58.734 50.000 0.00 0.00 0.00 3.18
4161 6495 6.170506 CCTGTACCATTATGTACACAACAGT 58.829 40.000 0.00 0.00 44.53 3.55
4334 6671 5.682943 TCCGGTTTTCATGTGTTTCTTAG 57.317 39.130 0.00 0.00 0.00 2.18
4445 6856 5.047566 TGGGATTGGTCACAGGTATAATG 57.952 43.478 0.00 0.00 31.32 1.90
4451 6862 1.493022 GTCACAGGTATAATGCCCCCA 59.507 52.381 0.00 0.00 0.00 4.96
4488 6993 4.634199 ACTTGCACCTGAAAATGGATTTG 58.366 39.130 0.00 0.00 0.00 2.32
4595 7102 3.152341 CAAAAGCAGAGACAACAGGGAT 58.848 45.455 0.00 0.00 0.00 3.85
4628 7135 6.095860 TGCAGCTTTTACAGAAATATGCTCAT 59.904 34.615 0.00 0.00 32.76 2.90
4721 7228 8.550710 CCAACAATTTGGTTATGAATGTTGAT 57.449 30.769 15.11 0.00 46.63 2.57
4733 7240 2.890474 GTTGATGGCGCGATCGGT 60.890 61.111 24.51 0.00 35.95 4.69
4736 7243 2.279517 GATGGCGCGATCGGTTCT 60.280 61.111 16.80 0.00 35.95 3.01
4786 7293 3.365767 GGAATGTTCAGCAAGCAAGAGAC 60.366 47.826 0.00 0.00 0.00 3.36
4881 7388 8.704234 GGTAAGTCTCGCTCTTTTATAATGATG 58.296 37.037 0.00 0.00 0.00 3.07
4884 7391 8.948631 AGTCTCGCTCTTTTATAATGATGAAA 57.051 30.769 0.00 0.00 0.00 2.69
4885 7392 9.553064 AGTCTCGCTCTTTTATAATGATGAAAT 57.447 29.630 0.00 0.00 0.00 2.17
4886 7393 9.804547 GTCTCGCTCTTTTATAATGATGAAATC 57.195 33.333 0.00 0.00 45.83 2.17
4887 7394 9.770097 TCTCGCTCTTTTATAATGATGAAATCT 57.230 29.630 0.00 0.00 45.81 2.40
5029 7898 2.027192 TCCTCTACACCAAATGAGGCAC 60.027 50.000 0.00 0.00 44.09 5.01
5031 7914 1.086696 CTACACCAAATGAGGCACCG 58.913 55.000 0.00 0.00 0.00 4.94
5087 7970 9.783256 AAAAATAAAATCGAGCATAACTACACC 57.217 29.630 0.00 0.00 0.00 4.16
5088 7971 8.500753 AAATAAAATCGAGCATAACTACACCA 57.499 30.769 0.00 0.00 0.00 4.17
5089 7972 8.500753 AATAAAATCGAGCATAACTACACCAA 57.499 30.769 0.00 0.00 0.00 3.67
5090 7973 6.811253 AAAATCGAGCATAACTACACCAAA 57.189 33.333 0.00 0.00 0.00 3.28
5091 7974 7.391148 AAAATCGAGCATAACTACACCAAAT 57.609 32.000 0.00 0.00 0.00 2.32
5092 7975 5.991328 ATCGAGCATAACTACACCAAATG 57.009 39.130 0.00 0.00 0.00 2.32
5093 7976 5.079689 TCGAGCATAACTACACCAAATGA 57.920 39.130 0.00 0.00 0.00 2.57
5094 7977 5.109210 TCGAGCATAACTACACCAAATGAG 58.891 41.667 0.00 0.00 0.00 2.90
5337 8279 4.177537 TCCCCATCACAAAACTCTGAAA 57.822 40.909 0.00 0.00 0.00 2.69
5454 8410 2.771943 CCCCGTCATGGCTACCATATAT 59.228 50.000 0.00 0.00 43.15 0.86
5574 8631 3.046087 CAGCACCAGTCACTGCCG 61.046 66.667 0.00 0.00 33.57 5.69
5611 8668 4.458164 GCATGTGCGTGCTTTACC 57.542 55.556 8.95 0.00 41.82 2.85
5629 8686 1.335872 ACCGCGCCATTTTCTTCTTTG 60.336 47.619 0.00 0.00 0.00 2.77
5745 8803 5.221048 GCCTGGTTTAGTGATGCGATTTATT 60.221 40.000 0.00 0.00 0.00 1.40
5771 8829 8.246908 TGTTTTAACCTTACGACATGTCTATG 57.753 34.615 22.95 10.64 40.24 2.23
5787 8845 8.972127 ACATGTCTATGTTGAGTTCTACAGTAT 58.028 33.333 0.00 0.00 45.01 2.12
5795 8853 7.258441 TGTTGAGTTCTACAGTATATCACAGC 58.742 38.462 0.00 0.00 0.00 4.40
5809 8867 2.842457 TCACAGCTATAGCATGCCTTG 58.158 47.619 26.07 16.20 45.16 3.61
5814 8872 1.000938 GCTATAGCATGCCTTGGTTGC 60.001 52.381 20.01 6.46 41.59 4.17
5829 8887 0.250901 GTTGCTCCTGGTGTGGTGAT 60.251 55.000 0.00 0.00 0.00 3.06
5830 8888 1.003118 GTTGCTCCTGGTGTGGTGATA 59.997 52.381 0.00 0.00 0.00 2.15
5831 8889 0.904649 TGCTCCTGGTGTGGTGATAG 59.095 55.000 0.00 0.00 0.00 2.08
5832 8890 0.462759 GCTCCTGGTGTGGTGATAGC 60.463 60.000 0.00 0.00 0.00 2.97
5855 8922 5.170270 GCGCTTCAATTTATTGTTGAGATCG 59.830 40.000 0.00 0.00 36.96 3.69
5857 8924 6.742718 CGCTTCAATTTATTGTTGAGATCGTT 59.257 34.615 2.66 0.00 36.96 3.85
5858 8925 7.253092 CGCTTCAATTTATTGTTGAGATCGTTG 60.253 37.037 2.66 0.00 36.96 4.10
5859 8926 7.461938 GCTTCAATTTATTGTTGAGATCGTTGC 60.462 37.037 2.66 0.00 36.96 4.17
5861 8928 5.895636 ATTTATTGTTGAGATCGTTGCCA 57.104 34.783 0.00 0.00 0.00 4.92
5862 8929 4.678509 TTATTGTTGAGATCGTTGCCAC 57.321 40.909 0.00 0.00 0.00 5.01
5873 8940 1.298859 CGTTGCCACTTGCTAGGGAC 61.299 60.000 0.00 0.00 42.00 4.46
5878 8945 3.313791 TGCCACTTGCTAGGGACATATA 58.686 45.455 0.00 0.00 42.00 0.86
5879 8946 3.909995 TGCCACTTGCTAGGGACATATAT 59.090 43.478 0.00 0.00 42.00 0.86
5880 8947 5.090845 TGCCACTTGCTAGGGACATATATA 58.909 41.667 0.00 0.00 42.00 0.86
5881 8948 5.726308 TGCCACTTGCTAGGGACATATATAT 59.274 40.000 0.00 0.00 42.00 0.86
5882 8949 6.051717 GCCACTTGCTAGGGACATATATATG 58.948 44.000 19.21 19.21 37.04 1.78
5883 8950 6.586344 CCACTTGCTAGGGACATATATATGG 58.414 44.000 23.44 8.42 38.00 2.74
5884 8951 6.051717 CACTTGCTAGGGACATATATATGGC 58.948 44.000 23.44 21.33 41.05 4.40
5885 8952 5.726308 ACTTGCTAGGGACATATATATGGCA 59.274 40.000 26.35 19.84 43.61 4.92
5886 8953 5.876651 TGCTAGGGACATATATATGGCAG 57.123 43.478 26.35 17.42 43.61 4.85
5887 8954 5.280499 TGCTAGGGACATATATATGGCAGT 58.720 41.667 26.35 16.37 43.61 4.40
5888 8955 6.440354 TGCTAGGGACATATATATGGCAGTA 58.560 40.000 26.35 16.58 43.61 2.74
5889 8956 6.323996 TGCTAGGGACATATATATGGCAGTAC 59.676 42.308 26.35 14.73 43.61 2.73
5890 8957 6.551601 GCTAGGGACATATATATGGCAGTACT 59.448 42.308 26.35 19.72 43.61 2.73
5891 8958 7.724506 GCTAGGGACATATATATGGCAGTACTA 59.275 40.741 26.35 19.76 43.61 1.82
5892 8959 9.642343 CTAGGGACATATATATGGCAGTACTAA 57.358 37.037 26.35 6.80 43.61 2.24
5893 8960 8.911018 AGGGACATATATATGGCAGTACTAAA 57.089 34.615 26.35 0.00 43.61 1.85
5894 8961 9.507381 AGGGACATATATATGGCAGTACTAAAT 57.493 33.333 26.35 2.84 43.61 1.40
5895 8962 9.547753 GGGACATATATATGGCAGTACTAAATG 57.452 37.037 26.35 1.41 43.61 2.32
5896 8963 9.046296 GGACATATATATGGCAGTACTAAATGC 57.954 37.037 26.35 4.48 43.61 3.56
5897 8964 8.648557 ACATATATATGGCAGTACTAAATGCG 57.351 34.615 23.44 0.00 43.49 4.73
5898 8965 7.224753 ACATATATATGGCAGTACTAAATGCGC 59.775 37.037 23.44 0.00 43.49 6.09
5899 8966 2.036958 ATGGCAGTACTAAATGCGCA 57.963 45.000 14.96 14.96 43.49 6.09
5900 8967 1.083489 TGGCAGTACTAAATGCGCAC 58.917 50.000 14.90 0.00 43.49 5.34
5901 8968 0.377203 GGCAGTACTAAATGCGCACC 59.623 55.000 14.90 0.22 43.49 5.01
5902 8969 0.377203 GCAGTACTAAATGCGCACCC 59.623 55.000 14.90 0.00 31.87 4.61
5903 8970 1.732941 CAGTACTAAATGCGCACCCA 58.267 50.000 14.90 0.00 0.00 4.51
5904 8971 2.080693 CAGTACTAAATGCGCACCCAA 58.919 47.619 14.90 0.00 0.00 4.12
5905 8972 2.081462 AGTACTAAATGCGCACCCAAC 58.919 47.619 14.90 6.79 0.00 3.77
5906 8973 1.807742 GTACTAAATGCGCACCCAACA 59.192 47.619 14.90 0.00 0.00 3.33
5907 8974 1.323412 ACTAAATGCGCACCCAACAA 58.677 45.000 14.90 0.00 0.00 2.83
5908 8975 1.269448 ACTAAATGCGCACCCAACAAG 59.731 47.619 14.90 6.20 0.00 3.16
5909 8976 0.600557 TAAATGCGCACCCAACAAGG 59.399 50.000 14.90 0.00 37.03 3.61
5910 8977 1.112315 AAATGCGCACCCAACAAGGA 61.112 50.000 14.90 0.00 41.22 3.36
5911 8978 1.805428 AATGCGCACCCAACAAGGAC 61.805 55.000 14.90 0.00 41.22 3.85
5912 8979 4.025401 GCGCACCCAACAAGGACG 62.025 66.667 0.30 0.00 41.22 4.79
5913 8980 2.280524 CGCACCCAACAAGGACGA 60.281 61.111 0.00 0.00 41.22 4.20
5914 8981 2.317609 CGCACCCAACAAGGACGAG 61.318 63.158 0.00 0.00 41.22 4.18
5915 8982 1.966451 GCACCCAACAAGGACGAGG 60.966 63.158 0.00 0.00 41.22 4.63
5916 8983 1.752198 CACCCAACAAGGACGAGGA 59.248 57.895 0.00 0.00 41.22 3.71
5917 8984 0.324943 CACCCAACAAGGACGAGGAT 59.675 55.000 0.00 0.00 41.22 3.24
5918 8985 1.064825 ACCCAACAAGGACGAGGATT 58.935 50.000 0.00 0.00 41.22 3.01
5919 8986 1.423921 ACCCAACAAGGACGAGGATTT 59.576 47.619 0.00 0.00 41.22 2.17
5920 8987 1.812571 CCCAACAAGGACGAGGATTTG 59.187 52.381 0.00 0.00 41.22 2.32
5921 8988 1.812571 CCAACAAGGACGAGGATTTGG 59.187 52.381 0.00 0.00 41.22 3.28
5922 8989 2.552155 CCAACAAGGACGAGGATTTGGA 60.552 50.000 0.00 0.00 41.22 3.53
5923 8990 2.744202 CAACAAGGACGAGGATTTGGAG 59.256 50.000 0.00 0.00 0.00 3.86
5924 8991 1.339151 ACAAGGACGAGGATTTGGAGC 60.339 52.381 0.00 0.00 0.00 4.70
5925 8992 0.984230 AAGGACGAGGATTTGGAGCA 59.016 50.000 0.00 0.00 0.00 4.26
5926 8993 0.250513 AGGACGAGGATTTGGAGCAC 59.749 55.000 0.00 0.00 0.00 4.40
5927 8994 0.250513 GGACGAGGATTTGGAGCACT 59.749 55.000 0.00 0.00 0.00 4.40
5928 8995 1.646189 GACGAGGATTTGGAGCACTC 58.354 55.000 0.00 0.00 0.00 3.51
5929 8996 2.670635 CGAGGATTTGGAGCACTCG 58.329 57.895 0.00 0.00 43.85 4.18
5930 8997 0.807667 CGAGGATTTGGAGCACTCGG 60.808 60.000 0.00 0.00 45.11 4.63
5931 8998 0.462759 GAGGATTTGGAGCACTCGGG 60.463 60.000 0.00 0.00 0.00 5.14
5932 8999 1.201429 AGGATTTGGAGCACTCGGGT 61.201 55.000 0.00 0.00 0.00 5.28
5933 9000 1.026718 GGATTTGGAGCACTCGGGTG 61.027 60.000 12.23 12.23 45.53 4.61
5949 9016 2.914379 GTGCTCCACACCACTGTAC 58.086 57.895 0.00 0.00 44.02 2.90
5950 9017 0.944311 GTGCTCCACACCACTGTACG 60.944 60.000 0.00 0.00 44.02 3.67
5951 9018 1.110518 TGCTCCACACCACTGTACGA 61.111 55.000 0.00 0.00 0.00 3.43
5952 9019 0.032952 GCTCCACACCACTGTACGAA 59.967 55.000 0.00 0.00 0.00 3.85
5953 9020 1.779569 CTCCACACCACTGTACGAAC 58.220 55.000 0.00 0.00 0.00 3.95
5954 9021 1.067974 CTCCACACCACTGTACGAACA 59.932 52.381 0.00 0.00 0.00 3.18
5955 9022 1.481363 TCCACACCACTGTACGAACAA 59.519 47.619 0.00 0.00 34.49 2.83
5956 9023 2.103432 TCCACACCACTGTACGAACAAT 59.897 45.455 0.00 0.00 34.49 2.71
5957 9024 2.875933 CCACACCACTGTACGAACAATT 59.124 45.455 0.00 0.00 34.49 2.32
5958 9025 3.314080 CCACACCACTGTACGAACAATTT 59.686 43.478 0.00 0.00 34.49 1.82
5959 9026 4.512198 CCACACCACTGTACGAACAATTTA 59.488 41.667 0.00 0.00 34.49 1.40
5960 9027 5.180492 CCACACCACTGTACGAACAATTTAT 59.820 40.000 0.00 0.00 34.49 1.40
5961 9028 6.293735 CCACACCACTGTACGAACAATTTATT 60.294 38.462 0.00 0.00 34.49 1.40
5962 9029 6.795114 CACACCACTGTACGAACAATTTATTC 59.205 38.462 0.00 0.00 34.49 1.75
5963 9030 6.483974 ACACCACTGTACGAACAATTTATTCA 59.516 34.615 0.00 0.00 34.49 2.57
5964 9031 7.012515 ACACCACTGTACGAACAATTTATTCAA 59.987 33.333 0.00 0.00 34.49 2.69
5965 9032 7.858382 CACCACTGTACGAACAATTTATTCAAA 59.142 33.333 0.00 0.00 34.49 2.69
5966 9033 8.407064 ACCACTGTACGAACAATTTATTCAAAA 58.593 29.630 0.00 0.00 34.49 2.44
5967 9034 9.239002 CCACTGTACGAACAATTTATTCAAAAA 57.761 29.630 0.00 0.00 34.49 1.94
5993 9060 8.853077 ATATGCCGAGAAATTTGAGAATATCA 57.147 30.769 0.00 0.00 35.62 2.15
5994 9061 7.572523 ATGCCGAGAAATTTGAGAATATCAA 57.427 32.000 0.00 0.00 46.31 2.57
6004 9071 5.873179 TTGAGAATATCAAACGTGGGTTC 57.127 39.130 0.00 0.00 45.00 3.62
6005 9072 4.258543 TGAGAATATCAAACGTGGGTTCC 58.741 43.478 0.00 0.00 34.62 3.62
6006 9073 3.617284 AGAATATCAAACGTGGGTTCCC 58.383 45.455 0.12 0.12 34.62 3.97
6007 9074 2.032680 ATATCAAACGTGGGTTCCCG 57.967 50.000 3.27 0.00 34.62 5.14
6008 9075 0.975135 TATCAAACGTGGGTTCCCGA 59.025 50.000 3.27 0.00 34.62 5.14
6009 9076 0.326927 ATCAAACGTGGGTTCCCGAT 59.673 50.000 3.27 0.00 34.62 4.18
6010 9077 0.320946 TCAAACGTGGGTTCCCGATC 60.321 55.000 3.27 0.00 34.62 3.69
6011 9078 0.321298 CAAACGTGGGTTCCCGATCT 60.321 55.000 3.27 0.00 34.62 2.75
6012 9079 1.066716 CAAACGTGGGTTCCCGATCTA 60.067 52.381 3.27 0.00 34.62 1.98
6013 9080 0.533951 AACGTGGGTTCCCGATCTAC 59.466 55.000 3.27 0.00 0.00 2.59
6014 9081 0.324091 ACGTGGGTTCCCGATCTACT 60.324 55.000 3.27 0.00 0.00 2.57
6015 9082 0.384669 CGTGGGTTCCCGATCTACTC 59.615 60.000 3.27 0.00 0.00 2.59
6016 9083 1.777941 GTGGGTTCCCGATCTACTCT 58.222 55.000 3.27 0.00 0.00 3.24
6017 9084 2.108970 GTGGGTTCCCGATCTACTCTT 58.891 52.381 3.27 0.00 0.00 2.85
6018 9085 3.294214 GTGGGTTCCCGATCTACTCTTA 58.706 50.000 3.27 0.00 0.00 2.10
6019 9086 3.896272 GTGGGTTCCCGATCTACTCTTAT 59.104 47.826 3.27 0.00 0.00 1.73
6020 9087 3.895656 TGGGTTCCCGATCTACTCTTATG 59.104 47.826 3.27 0.00 0.00 1.90
6021 9088 3.896272 GGGTTCCCGATCTACTCTTATGT 59.104 47.826 0.00 0.00 0.00 2.29
6022 9089 4.262079 GGGTTCCCGATCTACTCTTATGTG 60.262 50.000 0.00 0.00 0.00 3.21
6023 9090 4.583489 GGTTCCCGATCTACTCTTATGTGA 59.417 45.833 0.00 0.00 0.00 3.58
6024 9091 5.068723 GGTTCCCGATCTACTCTTATGTGAA 59.931 44.000 0.00 0.00 0.00 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
61 63 0.970937 GAGATCCCCACGAGACACCA 60.971 60.000 0.00 0.00 0.00 4.17
90 92 4.225717 CCATTCCCACCCAAAATTTGAGAT 59.774 41.667 7.37 0.00 0.00 2.75
92 94 3.307621 CCCATTCCCACCCAAAATTTGAG 60.308 47.826 7.37 0.00 0.00 3.02
94 96 2.374839 ACCCATTCCCACCCAAAATTTG 59.625 45.455 0.00 0.00 0.00 2.32
95 97 2.712384 ACCCATTCCCACCCAAAATTT 58.288 42.857 0.00 0.00 0.00 1.82
97 99 1.984424 CAACCCATTCCCACCCAAAAT 59.016 47.619 0.00 0.00 0.00 1.82
111 115 2.123338 AAGCAAGCAGGCAACCCA 60.123 55.556 2.37 0.00 35.83 4.51
169 182 2.499732 GAAACAAAGCTCGCGCCG 60.500 61.111 0.00 0.00 36.60 6.46
194 207 2.594592 GACAAGGCAGCAACCCGT 60.595 61.111 0.00 0.00 0.00 5.28
196 209 2.116125 AGGACAAGGCAGCAACCC 59.884 61.111 0.00 0.00 0.00 4.11
212 225 2.525055 CCAAACCGACAAAACACACAG 58.475 47.619 0.00 0.00 0.00 3.66
234 247 0.176680 AAATGGATCTGCGCGAGAGT 59.823 50.000 12.10 0.60 32.80 3.24
239 252 0.657312 TAAGCAAATGGATCTGCGCG 59.343 50.000 0.00 0.00 43.51 6.86
292 305 6.238731 CCTGAAGATCAATTTTTATAGCGGCA 60.239 38.462 1.45 0.00 0.00 5.69
295 310 7.496529 TCCCTGAAGATCAATTTTTATAGCG 57.503 36.000 0.00 0.00 0.00 4.26
304 319 5.198965 CACCAAGATCCCTGAAGATCAATT 58.801 41.667 0.00 0.00 44.32 2.32
305 320 4.789807 CACCAAGATCCCTGAAGATCAAT 58.210 43.478 0.00 0.00 44.32 2.57
309 324 1.918262 TGCACCAAGATCCCTGAAGAT 59.082 47.619 0.00 0.00 0.00 2.40
314 329 0.523072 CGTTTGCACCAAGATCCCTG 59.477 55.000 0.00 0.00 0.00 4.45
325 340 2.088950 TACTAAGCCTCCGTTTGCAC 57.911 50.000 0.00 0.00 0.00 4.57
399 423 2.747446 CCCAACTAGCTGCGTGTTAAAT 59.253 45.455 11.57 0.00 0.00 1.40
405 429 3.490759 CGCCCAACTAGCTGCGTG 61.491 66.667 5.76 0.00 41.95 5.34
406 430 2.521958 AATCGCCCAACTAGCTGCGT 62.522 55.000 12.76 0.00 46.57 5.24
408 432 1.026718 ACAATCGCCCAACTAGCTGC 61.027 55.000 0.00 0.00 0.00 5.25
409 433 0.729116 CACAATCGCCCAACTAGCTG 59.271 55.000 0.00 0.00 0.00 4.24
410 434 0.392998 CCACAATCGCCCAACTAGCT 60.393 55.000 0.00 0.00 0.00 3.32
411 435 0.392461 TCCACAATCGCCCAACTAGC 60.392 55.000 0.00 0.00 0.00 3.42
412 436 2.107950 TTCCACAATCGCCCAACTAG 57.892 50.000 0.00 0.00 0.00 2.57
453 478 0.393537 AGCCCGGATCTCAAGCAAAG 60.394 55.000 0.73 0.00 0.00 2.77
470 495 4.264460 TGAGAAAGACCTGAGAAGAAGC 57.736 45.455 0.00 0.00 0.00 3.86
658 685 7.496346 AAACAGGACACTCCAAGAATCTATA 57.504 36.000 0.00 0.00 39.61 1.31
659 686 6.380079 AAACAGGACACTCCAAGAATCTAT 57.620 37.500 0.00 0.00 39.61 1.98
668 700 0.257328 TGCCAAAACAGGACACTCCA 59.743 50.000 0.00 0.00 39.61 3.86
708 740 6.608610 ACATTTGATTCGTAAAACCTAGTGC 58.391 36.000 0.00 0.00 0.00 4.40
719 752 4.634004 GGTCCATGTGACATTTGATTCGTA 59.366 41.667 13.95 0.00 46.38 3.43
720 753 3.440173 GGTCCATGTGACATTTGATTCGT 59.560 43.478 13.95 0.00 46.38 3.85
721 754 3.181497 GGGTCCATGTGACATTTGATTCG 60.181 47.826 13.95 0.00 46.38 3.34
726 759 2.229543 CACTGGGTCCATGTGACATTTG 59.770 50.000 13.95 0.00 46.38 2.32
820 855 3.317149 CCCAGCATCCAACATGATAACTG 59.683 47.826 0.00 0.00 32.17 3.16
875 929 4.273480 CGGCAAAGTACCAGAATAGAATGG 59.727 45.833 0.00 0.00 42.60 3.16
896 950 0.112025 CCCCCTACCCTACTAGTCGG 59.888 65.000 6.46 6.46 0.00 4.79
962 1018 8.837389 CCTGAAAATTAACAGGTATTAGGCTAC 58.163 37.037 17.50 0.00 45.82 3.58
1008 1064 4.515567 GTGGTTTTCGAGAAGATTTGACCT 59.484 41.667 0.00 0.00 0.00 3.85
1017 1073 1.266989 GCTTGGGTGGTTTTCGAGAAG 59.733 52.381 0.00 0.00 0.00 2.85
1111 1167 6.713276 TCCTTTTAAACCAATGACGATAGGA 58.287 36.000 0.00 0.00 43.77 2.94
1116 1172 6.642707 ACAATCCTTTTAAACCAATGACGA 57.357 33.333 0.00 0.00 0.00 4.20
1117 1173 7.707774 AAACAATCCTTTTAAACCAATGACG 57.292 32.000 0.00 0.00 0.00 4.35
1118 1174 9.758651 ACTAAACAATCCTTTTAAACCAATGAC 57.241 29.630 0.00 0.00 0.00 3.06
1224 1281 0.034089 GGAACCCATCAGAACCAGGG 60.034 60.000 0.00 0.00 46.96 4.45
1307 1364 9.076781 TGTTCAATCAAACAAGATAAATGAGGA 57.923 29.630 0.00 0.00 36.25 3.71
1508 1572 5.259832 TCTCAGACAGACTATCAATGCTG 57.740 43.478 0.00 0.00 34.65 4.41
1519 1583 5.871524 TCATGCAGTATTTTCTCAGACAGAC 59.128 40.000 0.00 0.00 0.00 3.51
1530 1594 4.529897 TGCTCCAGATCATGCAGTATTTT 58.470 39.130 0.00 0.00 0.00 1.82
1664 1728 1.148310 TTAGCTGCTTTGCGTCTGAC 58.852 50.000 7.79 0.00 38.13 3.51
1768 2615 9.587772 GTCTTACTCTAAGCACTTTATGATGAA 57.412 33.333 0.00 0.00 35.76 2.57
2311 4503 5.529581 TCTGGAATGAAAACAAAGGGAAC 57.470 39.130 0.00 0.00 0.00 3.62
2394 4587 9.349713 AGTAATGGAAGTTCAGTTTGTAATGAA 57.650 29.630 5.01 0.00 33.16 2.57
2525 4731 5.508489 GGGTGCATTATTCATGTGAATCAGG 60.508 44.000 11.24 4.64 43.17 3.86
2685 4891 8.095169 CACTACAGGAAGAAGGTTAACACTATT 58.905 37.037 8.10 0.00 0.00 1.73
2752 4961 9.412460 TCATGCCAGAGAAGAAAAATATAACAT 57.588 29.630 0.00 0.00 0.00 2.71
2753 4962 8.806429 TCATGCCAGAGAAGAAAAATATAACA 57.194 30.769 0.00 0.00 0.00 2.41
2975 5184 2.380064 ATCCAGACTTGGGTTGCAAA 57.620 45.000 0.00 0.00 45.10 3.68
3059 5270 2.500910 CTCATCACTTCCTCCAAGCTCT 59.499 50.000 0.00 0.00 35.17 4.09
3241 5462 2.977914 ACCACATCTGTGCATACTGAC 58.022 47.619 4.77 0.00 44.34 3.51
3465 5695 4.440145 CCCCATTGGTTCCCACTG 57.560 61.111 1.20 0.00 34.54 3.66
3547 5782 6.349300 GCAGTGTTAAGATCCTCAGGAATTA 58.651 40.000 0.00 0.00 34.34 1.40
3548 5783 5.189180 GCAGTGTTAAGATCCTCAGGAATT 58.811 41.667 0.00 0.00 34.34 2.17
3689 5924 1.136305 TGTATTCGGGGAGAGAAAGCG 59.864 52.381 0.00 0.00 0.00 4.68
4119 6453 3.065786 ACAGGTTCGCATGCATCAATTAG 59.934 43.478 19.57 2.58 31.07 1.73
4305 6641 1.004745 ACATGAAAACCGGAGCTGGAT 59.995 47.619 9.46 0.00 0.00 3.41
4306 6642 0.400213 ACATGAAAACCGGAGCTGGA 59.600 50.000 9.46 0.00 0.00 3.86
4307 6643 0.523072 CACATGAAAACCGGAGCTGG 59.477 55.000 9.46 0.00 0.00 4.85
4357 6768 3.372660 GGCGTAAGACCCTAGAATCAG 57.627 52.381 0.00 0.00 42.36 2.90
4445 6856 5.079643 AGTTTATTATGATGTCATGGGGGC 58.920 41.667 5.78 0.00 37.15 5.80
4451 6862 7.557358 TCAGGTGCAAGTTTATTATGATGTCAT 59.443 33.333 0.68 0.68 40.22 3.06
4517 7024 6.867662 AAAGACAACAACATAACTCAGAGG 57.132 37.500 1.53 0.00 0.00 3.69
4595 7102 2.736721 CTGTAAAAGCTGCACTCGCTTA 59.263 45.455 11.61 0.00 46.24 3.09
4628 7135 0.836606 TGACTGAAGGGAAGTGTGCA 59.163 50.000 0.00 0.00 0.00 4.57
4721 7228 2.501223 AAAGAGAACCGATCGCGCCA 62.501 55.000 10.32 0.00 35.83 5.69
4733 7240 7.446625 CCAGAAAGAAGATCCAAGAAAAGAGAA 59.553 37.037 0.00 0.00 0.00 2.87
4736 7243 6.006449 CCCAGAAAGAAGATCCAAGAAAAGA 58.994 40.000 0.00 0.00 0.00 2.52
4786 7293 6.582677 ACCCAATCTCTATAATCTCGTCAG 57.417 41.667 0.00 0.00 0.00 3.51
4884 7391 9.603189 ATGTAACTAGGGTAGCAATAGTTAGAT 57.397 33.333 20.99 20.99 40.71 1.98
4885 7392 9.430399 AATGTAACTAGGGTAGCAATAGTTAGA 57.570 33.333 20.52 19.91 40.71 2.10
5083 7966 9.696917 GAATTTTGAATTCTACTCATTTGGTGT 57.303 29.630 7.05 0.00 0.00 4.16
5175 8107 5.845103 TGCTTTCATGCTTGAATGAAGAAA 58.155 33.333 24.01 6.47 44.96 2.52
5178 8110 6.475727 CCTAATGCTTTCATGCTTGAATGAAG 59.524 38.462 24.01 16.17 44.96 3.02
5181 8113 5.047847 CCCTAATGCTTTCATGCTTGAATG 58.952 41.667 15.04 17.01 41.38 2.67
5375 8330 1.224069 GAGCTCGAAGCAGCAACACA 61.224 55.000 0.00 0.00 45.56 3.72
5402 8358 3.498397 CCAATAAGTTTGGGATCGATCGG 59.502 47.826 18.81 6.28 35.96 4.18
5403 8359 3.058914 GCCAATAAGTTTGGGATCGATCG 60.059 47.826 18.81 9.36 39.90 3.69
5610 8667 1.068610 TCAAAGAAGAAAATGGCGCGG 60.069 47.619 8.83 0.00 0.00 6.46
5611 8668 2.330231 TCAAAGAAGAAAATGGCGCG 57.670 45.000 0.00 0.00 0.00 6.86
5617 8674 7.759433 ACAAACACAACGATCAAAGAAGAAAAT 59.241 29.630 0.00 0.00 0.00 1.82
5701 8759 2.027837 GCCTTCCTGCAAACCAATTCAT 60.028 45.455 0.00 0.00 0.00 2.57
5702 8760 1.344114 GCCTTCCTGCAAACCAATTCA 59.656 47.619 0.00 0.00 0.00 2.57
5703 8761 1.338105 GGCCTTCCTGCAAACCAATTC 60.338 52.381 0.00 0.00 0.00 2.17
5745 8803 8.714179 CATAGACATGTCGTAAGGTTAAAACAA 58.286 33.333 19.85 0.00 38.47 2.83
5771 8829 7.484975 AGCTGTGATATACTGTAGAACTCAAC 58.515 38.462 0.00 0.00 0.00 3.18
5787 8845 4.564199 CCAAGGCATGCTATAGCTGTGATA 60.564 45.833 24.61 4.45 42.66 2.15
5788 8846 3.409570 CAAGGCATGCTATAGCTGTGAT 58.590 45.455 24.61 7.81 42.66 3.06
5790 8848 1.878088 CCAAGGCATGCTATAGCTGTG 59.122 52.381 24.61 21.86 42.66 3.66
5791 8849 1.492176 ACCAAGGCATGCTATAGCTGT 59.508 47.619 24.61 11.34 42.66 4.40
5792 8850 2.267174 ACCAAGGCATGCTATAGCTG 57.733 50.000 24.61 19.50 42.66 4.24
5793 8851 2.579873 CAACCAAGGCATGCTATAGCT 58.420 47.619 24.61 8.42 42.66 3.32
5794 8852 1.000938 GCAACCAAGGCATGCTATAGC 60.001 52.381 18.92 18.18 42.50 2.97
5800 8858 1.980772 AGGAGCAACCAAGGCATGC 60.981 57.895 9.90 9.90 42.04 4.06
5809 8867 1.898574 CACCACACCAGGAGCAACC 60.899 63.158 0.00 0.00 39.35 3.77
5814 8872 0.179100 CGCTATCACCACACCAGGAG 60.179 60.000 0.00 0.00 0.00 3.69
5829 8887 6.735678 TCTCAACAATAAATTGAAGCGCTA 57.264 33.333 12.05 0.00 40.14 4.26
5830 8888 5.627499 TCTCAACAATAAATTGAAGCGCT 57.373 34.783 2.64 2.64 40.14 5.92
5831 8889 5.170270 CGATCTCAACAATAAATTGAAGCGC 59.830 40.000 9.60 0.00 40.14 5.92
5832 8890 6.250819 ACGATCTCAACAATAAATTGAAGCG 58.749 36.000 9.60 6.38 40.14 4.68
5857 8924 9.213780 CCATATATATGTCCCTAGCAAGTGGCA 62.214 44.444 19.11 0.00 37.16 4.92
5858 8925 2.938956 ATATGTCCCTAGCAAGTGGC 57.061 50.000 0.00 0.00 45.30 5.01
5859 8926 6.586344 CCATATATATGTCCCTAGCAAGTGG 58.414 44.000 19.11 0.00 31.82 4.00
5861 8928 5.726308 TGCCATATATATGTCCCTAGCAAGT 59.274 40.000 19.11 0.00 31.82 3.16
5862 8929 6.126940 ACTGCCATATATATGTCCCTAGCAAG 60.127 42.308 19.11 14.78 31.82 4.01
5873 8940 7.224557 TGCGCATTTAGTACTGCCATATATATG 59.775 37.037 5.66 14.78 34.89 1.78
5878 8945 3.498397 GTGCGCATTTAGTACTGCCATAT 59.502 43.478 15.91 0.00 34.89 1.78
5879 8946 2.869801 GTGCGCATTTAGTACTGCCATA 59.130 45.455 15.91 0.00 34.89 2.74
5880 8947 1.670811 GTGCGCATTTAGTACTGCCAT 59.329 47.619 15.91 0.00 34.89 4.40
5881 8948 1.083489 GTGCGCATTTAGTACTGCCA 58.917 50.000 15.91 0.00 34.89 4.92
5882 8949 0.377203 GGTGCGCATTTAGTACTGCC 59.623 55.000 15.91 1.08 34.89 4.85
5883 8950 0.377203 GGGTGCGCATTTAGTACTGC 59.623 55.000 15.91 0.00 35.02 4.40
5884 8951 1.732941 TGGGTGCGCATTTAGTACTG 58.267 50.000 15.91 0.00 0.00 2.74
5885 8952 2.081462 GTTGGGTGCGCATTTAGTACT 58.919 47.619 15.91 0.00 0.00 2.73
5886 8953 1.807742 TGTTGGGTGCGCATTTAGTAC 59.192 47.619 15.91 8.33 0.00 2.73
5887 8954 2.186532 TGTTGGGTGCGCATTTAGTA 57.813 45.000 15.91 0.00 0.00 1.82
5888 8955 1.269448 CTTGTTGGGTGCGCATTTAGT 59.731 47.619 15.91 0.00 0.00 2.24
5889 8956 1.402720 CCTTGTTGGGTGCGCATTTAG 60.403 52.381 15.91 4.56 0.00 1.85
5890 8957 0.600557 CCTTGTTGGGTGCGCATTTA 59.399 50.000 15.91 0.00 0.00 1.40
5891 8958 1.112315 TCCTTGTTGGGTGCGCATTT 61.112 50.000 15.91 0.00 36.20 2.32
5892 8959 1.530419 TCCTTGTTGGGTGCGCATT 60.530 52.632 15.91 0.00 36.20 3.56
5893 8960 2.115052 TCCTTGTTGGGTGCGCAT 59.885 55.556 15.91 0.00 36.20 4.73
5894 8961 2.904866 GTCCTTGTTGGGTGCGCA 60.905 61.111 5.66 5.66 36.20 6.09
5895 8962 4.025401 CGTCCTTGTTGGGTGCGC 62.025 66.667 0.00 0.00 36.20 6.09
5896 8963 2.280524 TCGTCCTTGTTGGGTGCG 60.281 61.111 0.00 0.00 36.20 5.34
5897 8964 1.966451 CCTCGTCCTTGTTGGGTGC 60.966 63.158 0.00 0.00 36.20 5.01
5898 8965 0.324943 ATCCTCGTCCTTGTTGGGTG 59.675 55.000 0.00 0.00 36.20 4.61
5899 8966 1.064825 AATCCTCGTCCTTGTTGGGT 58.935 50.000 0.00 0.00 36.20 4.51
5900 8967 1.812571 CAAATCCTCGTCCTTGTTGGG 59.187 52.381 0.00 0.00 36.20 4.12
5901 8968 1.812571 CCAAATCCTCGTCCTTGTTGG 59.187 52.381 0.00 0.00 37.10 3.77
5902 8969 2.744202 CTCCAAATCCTCGTCCTTGTTG 59.256 50.000 0.00 0.00 0.00 3.33
5903 8970 2.876079 GCTCCAAATCCTCGTCCTTGTT 60.876 50.000 0.00 0.00 0.00 2.83
5904 8971 1.339151 GCTCCAAATCCTCGTCCTTGT 60.339 52.381 0.00 0.00 0.00 3.16
5905 8972 1.339055 TGCTCCAAATCCTCGTCCTTG 60.339 52.381 0.00 0.00 0.00 3.61
5906 8973 0.984230 TGCTCCAAATCCTCGTCCTT 59.016 50.000 0.00 0.00 0.00 3.36
5907 8974 0.250513 GTGCTCCAAATCCTCGTCCT 59.749 55.000 0.00 0.00 0.00 3.85
5908 8975 0.250513 AGTGCTCCAAATCCTCGTCC 59.749 55.000 0.00 0.00 0.00 4.79
5909 8976 1.646189 GAGTGCTCCAAATCCTCGTC 58.354 55.000 0.00 0.00 0.00 4.20
5910 8977 0.108615 CGAGTGCTCCAAATCCTCGT 60.109 55.000 0.00 0.00 39.96 4.18
5911 8978 0.807667 CCGAGTGCTCCAAATCCTCG 60.808 60.000 0.00 0.00 43.36 4.63
5912 8979 0.462759 CCCGAGTGCTCCAAATCCTC 60.463 60.000 0.00 0.00 0.00 3.71
5913 8980 1.201429 ACCCGAGTGCTCCAAATCCT 61.201 55.000 0.00 0.00 0.00 3.24
5914 8981 1.026718 CACCCGAGTGCTCCAAATCC 61.027 60.000 0.00 0.00 37.14 3.01
5915 8982 2.471255 CACCCGAGTGCTCCAAATC 58.529 57.895 0.00 0.00 37.14 2.17
5916 8983 4.722193 CACCCGAGTGCTCCAAAT 57.278 55.556 0.00 0.00 37.14 2.32
5932 8999 1.110518 TCGTACAGTGGTGTGGAGCA 61.111 55.000 0.00 0.00 37.52 4.26
5933 9000 0.032952 TTCGTACAGTGGTGTGGAGC 59.967 55.000 0.00 0.00 37.52 4.70
5934 9001 1.067974 TGTTCGTACAGTGGTGTGGAG 59.932 52.381 0.00 0.00 37.52 3.86
5935 9002 1.112950 TGTTCGTACAGTGGTGTGGA 58.887 50.000 0.00 0.00 37.52 4.02
5936 9003 1.942677 TTGTTCGTACAGTGGTGTGG 58.057 50.000 0.00 0.00 37.52 4.17
5937 9004 4.545823 AAATTGTTCGTACAGTGGTGTG 57.454 40.909 0.00 0.00 37.52 3.82
5938 9005 6.483974 TGAATAAATTGTTCGTACAGTGGTGT 59.516 34.615 0.00 0.00 41.06 4.16
5939 9006 6.893759 TGAATAAATTGTTCGTACAGTGGTG 58.106 36.000 0.00 0.00 35.28 4.17
5940 9007 7.499321 TTGAATAAATTGTTCGTACAGTGGT 57.501 32.000 0.00 0.00 35.28 4.16
5941 9008 8.789881 TTTTGAATAAATTGTTCGTACAGTGG 57.210 30.769 0.00 0.00 35.28 4.00
5967 9034 9.288576 TGATATTCTCAAATTTCTCGGCATATT 57.711 29.630 0.00 0.00 0.00 1.28
5968 9035 8.853077 TGATATTCTCAAATTTCTCGGCATAT 57.147 30.769 0.00 0.00 0.00 1.78
5969 9036 8.675705 TTGATATTCTCAAATTTCTCGGCATA 57.324 30.769 0.00 0.00 40.92 3.14
5970 9037 7.572523 TTGATATTCTCAAATTTCTCGGCAT 57.427 32.000 0.00 0.00 40.92 4.40
5971 9038 7.389803 TTTGATATTCTCAAATTTCTCGGCA 57.610 32.000 0.00 0.00 46.45 5.69
5981 9048 7.742294 GGGAACCCACGTTTGATATTCTCAAA 61.742 42.308 4.85 0.00 46.85 2.69
5982 9049 4.698304 GGAACCCACGTTTGATATTCTCAA 59.302 41.667 0.00 0.00 42.15 3.02
5983 9050 4.258543 GGAACCCACGTTTGATATTCTCA 58.741 43.478 0.00 0.00 30.30 3.27
5984 9051 4.877323 GGAACCCACGTTTGATATTCTC 57.123 45.455 0.00 0.00 30.30 2.87
6001 9068 5.769484 TCACATAAGAGTAGATCGGGAAC 57.231 43.478 0.00 0.00 0.00 3.62


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

AutoCloner maintained by Alex Coulton.