Multiple sequence alignment - TraesCS2D01G473700

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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 TraesCS2D01G473700 chr2D 100.000 8558 0 0 1 8558 577159953 577151396 0.000000e+00 15804.0
1 TraesCS2D01G473700 chr2B 92.247 7120 300 132 569 7577 694061366 694054388 0.000000e+00 9858.0
2 TraesCS2D01G473700 chr2B 91.860 1032 35 22 7555 8558 694054138 694053128 0.000000e+00 1395.0
3 TraesCS2D01G473700 chr2B 93.286 566 34 3 2 564 694061985 694061421 0.000000e+00 832.0
4 TraesCS2D01G473700 chr2A 91.209 5119 251 88 3513 8558 715340893 715335901 0.000000e+00 6776.0
5 TraesCS2D01G473700 chr2A 92.718 2925 107 59 575 3415 715343945 715341043 0.000000e+00 4124.0
6 TraesCS2D01G473700 chr2A 96.309 569 13 5 2 564 715344576 715344010 0.000000e+00 928.0
7 TraesCS2D01G473700 chr2A 84.259 108 8 5 3501 3604 715340999 715340897 7.070000e-16 97.1
8 TraesCS2D01G473700 chr7A 77.248 545 84 26 6376 6914 436697404 436697914 5.060000e-72 283.0
9 TraesCS2D01G473700 chr7A 87.179 234 28 2 4744 4976 436696046 436696278 1.830000e-66 265.0
10 TraesCS2D01G473700 chr7A 81.712 257 47 0 6009 6265 436697131 436697387 1.870000e-51 215.0
11 TraesCS2D01G473700 chr7A 75.991 454 83 19 5457 5888 436696658 436697107 2.420000e-50 211.0
12 TraesCS2D01G473700 chr7A 87.302 126 13 3 4110 4233 436695809 436695933 3.220000e-29 141.0
13 TraesCS2D01G473700 chr7A 93.182 44 2 1 7244 7287 436698531 436698573 7.170000e-06 63.9
14 TraesCS2D01G473700 chr7B 76.854 553 83 26 6376 6911 381827678 381828202 3.940000e-68 270.0
15 TraesCS2D01G473700 chr7B 86.752 234 29 2 4744 4976 381826317 381826549 8.520000e-65 259.0
16 TraesCS2D01G473700 chr7B 84.016 244 39 0 6022 6265 381827418 381827661 1.440000e-57 235.0
17 TraesCS2D01G473700 chr7B 75.877 456 83 19 5457 5888 381826929 381827381 3.130000e-49 207.0
18 TraesCS2D01G473700 chr7B 87.302 126 13 3 4110 4233 381826104 381826228 3.220000e-29 141.0
19 TraesCS2D01G473700 chr7B 93.182 44 2 1 7244 7287 381828806 381828848 7.170000e-06 63.9
20 TraesCS2D01G473700 chr7D 76.534 554 88 24 6376 6914 386728955 386729481 1.830000e-66 265.0
21 TraesCS2D01G473700 chr7D 76.600 453 82 17 5457 5888 386728209 386728658 2.400000e-55 228.0
22 TraesCS2D01G473700 chr7D 81.323 257 48 0 6009 6265 386728682 386728938 8.710000e-50 209.0
23 TraesCS2D01G473700 chr7D 87.302 126 13 3 4110 4233 386727362 386727486 3.220000e-29 141.0
24 TraesCS2D01G473700 chr7D 97.222 36 0 1 7252 7287 386730094 386730128 9.280000e-05 60.2
25 TraesCS2D01G473700 chr6A 87.302 63 7 1 2966 3027 558788759 558788697 4.290000e-08 71.3
26 TraesCS2D01G473700 chr6B 87.097 62 7 1 2966 3026 623084250 623084189 1.540000e-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 TraesCS2D01G473700 chr2D 577151396 577159953 8557 True 15804.000000 15804 100.000000 1 8558 1 chr2D.!!$R1 8557
1 TraesCS2D01G473700 chr2B 694053128 694061985 8857 True 4028.333333 9858 92.464333 2 8558 3 chr2B.!!$R1 8556
2 TraesCS2D01G473700 chr2A 715335901 715344576 8675 True 2981.275000 6776 91.123750 2 8558 4 chr2A.!!$R1 8556

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
925 1003 0.107654 ATTGCACTACGCCTTCCTCC 60.108 55.000 0.00 0.00 41.33 4.30 F
1271 1351 1.447489 GATCTGCTGCTGCTCGTGT 60.447 57.895 17.00 0.00 40.48 4.49 F
2065 2165 1.287730 CCAGAGTTCAGAGCACACGC 61.288 60.000 0.00 0.00 38.99 5.34 F
3038 3177 0.169672 GCGTACGCCTACTCAACTCA 59.830 55.000 29.51 0.00 34.56 3.41 F
3683 3962 0.108186 TGTGGATGTGGATGAGCGTC 60.108 55.000 0.00 0.00 0.00 5.19 F
4585 4947 0.032130 ACGTGTACAGTGACCAGCTG 59.968 55.000 6.78 6.78 39.67 4.24 F
4587 4949 0.034059 GTGTACAGTGACCAGCTGCT 59.966 55.000 8.66 0.00 37.47 4.24 F
6043 6449 0.030705 AGGGGAGGAAGAGCATGCTA 60.031 55.000 22.74 0.00 0.00 3.49 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2017 2117 1.347378 TCTATGTGTGAACAGCAGCCA 59.653 47.619 0.00 0.0 0.00 4.75 R
2141 2241 1.353022 AGTGAAGTCTCCCTCTCTCGT 59.647 52.381 0.00 0.0 0.00 4.18 R
3668 3947 0.030773 TAGCGACGCTCATCCACATC 59.969 55.000 28.21 0.0 40.44 3.06 R
4525 4887 0.039035 TGTGGGGTTTGACTATGGGC 59.961 55.000 0.00 0.0 0.00 5.36 R
5439 5841 1.491563 CGCGTACTGGTTCTGCAAC 59.508 57.895 0.00 0.0 0.00 4.17 R
5787 6193 0.384309 CGACCAGCGGCTTGTAGATA 59.616 55.000 6.71 0.0 36.03 1.98 R
6184 6590 0.606401 CGTTGAGGACAATGCCTGGT 60.606 55.000 1.11 0.0 38.73 4.00 R
7863 8582 0.035056 CTGGGATCTGGGTGGTGTTC 60.035 60.000 0.00 0.0 0.00 3.18 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
101 105 4.142271 CCAAGTGCACCTTAGTGTTTTGAA 60.142 41.667 14.63 0.00 46.35 2.69
236 243 6.136071 GGTTGTCACGATTGATACATATTGC 58.864 40.000 0.00 0.00 33.11 3.56
407 416 0.961753 CACCCAAGAAGCTCCAAACC 59.038 55.000 0.00 0.00 0.00 3.27
511 521 7.927629 CCAAGGAATTCAAAACAAAGATCTTCA 59.072 33.333 8.78 0.00 0.00 3.02
536 546 9.932699 CATAGTAACACTAGTACACTGATACAC 57.067 37.037 11.52 0.00 33.66 2.90
557 567 6.054941 ACACAAATCTCAATGTATATCGCCA 58.945 36.000 0.00 0.00 0.00 5.69
625 689 6.040166 CCCAAGGATCTCCAAACAATATCTTG 59.960 42.308 0.00 0.00 38.89 3.02
679 743 4.082026 TCACATCATATATCGCCCAGAGTG 60.082 45.833 0.00 0.00 0.00 3.51
840 918 3.558006 CCGAGTGAAAATACACACACACA 59.442 43.478 0.00 0.00 42.45 3.72
841 919 4.514506 CGAGTGAAAATACACACACACAC 58.485 43.478 0.00 0.00 42.45 3.82
842 920 4.033472 CGAGTGAAAATACACACACACACA 59.967 41.667 0.00 0.00 42.45 3.72
845 923 5.588246 AGTGAAAATACACACACACACATCA 59.412 36.000 0.00 0.00 42.45 3.07
847 925 5.588246 TGAAAATACACACACACACATCACT 59.412 36.000 0.00 0.00 0.00 3.41
848 926 5.422666 AAATACACACACACACATCACTG 57.577 39.130 0.00 0.00 0.00 3.66
849 927 1.016627 ACACACACACACATCACTGC 58.983 50.000 0.00 0.00 0.00 4.40
850 928 1.302366 CACACACACACATCACTGCT 58.698 50.000 0.00 0.00 0.00 4.24
851 929 1.262417 CACACACACACATCACTGCTC 59.738 52.381 0.00 0.00 0.00 4.26
855 933 1.377725 CACACATCACTGCTCCCCC 60.378 63.158 0.00 0.00 0.00 5.40
925 1003 0.107654 ATTGCACTACGCCTTCCTCC 60.108 55.000 0.00 0.00 41.33 4.30
1144 1224 3.793144 CGCAGCGCAACTCCTTCC 61.793 66.667 11.47 0.00 0.00 3.46
1221 1301 7.180229 ACGATTCTCATCCTAGATCTCTCTCTA 59.820 40.741 0.00 0.00 32.66 2.43
1271 1351 1.447489 GATCTGCTGCTGCTCGTGT 60.447 57.895 17.00 0.00 40.48 4.49
1348 1428 2.912956 AGCACTATCTTTGTTGGAGGGA 59.087 45.455 0.00 0.00 0.00 4.20
1350 1430 3.691609 GCACTATCTTTGTTGGAGGGAAG 59.308 47.826 0.00 0.00 0.00 3.46
1442 1534 2.211250 TCGGTGTTAGACAGGCTAGT 57.789 50.000 0.00 0.00 0.00 2.57
1578 1671 7.553044 GCCAGGTATATGTTTTGTATATCTCCC 59.447 40.741 0.00 0.00 0.00 4.30
1792 1886 9.874205 CCTTAATGATTTGCTCCTTTAATTTCA 57.126 29.630 0.00 0.00 0.00 2.69
1795 1889 6.036577 TGATTTGCTCCTTTAATTTCACCC 57.963 37.500 0.00 0.00 0.00 4.61
2017 2117 1.755783 CCTCCGGGTACTTAGGCGT 60.756 63.158 0.00 0.00 0.00 5.68
2065 2165 1.287730 CCAGAGTTCAGAGCACACGC 61.288 60.000 0.00 0.00 38.99 5.34
2121 2221 4.705507 ACGGAGCAGATAAAGAAGACTACA 59.294 41.667 0.00 0.00 0.00 2.74
2124 2224 5.163457 GGAGCAGATAAAGAAGACTACAGCT 60.163 44.000 0.00 0.00 0.00 4.24
2376 2506 5.248640 TGAGACATCAATCAAGGGAGAAAC 58.751 41.667 0.00 0.00 30.61 2.78
2377 2507 5.013495 TGAGACATCAATCAAGGGAGAAACT 59.987 40.000 0.00 0.00 30.61 2.66
2426 2560 5.690865 TGATCCCCGATTTGTAGCTTTTAT 58.309 37.500 0.00 0.00 0.00 1.40
2593 2729 9.199982 TCTGGCTACTAATTAATTAATACGCAC 57.800 33.333 11.07 0.92 0.00 5.34
2660 2796 7.531871 CGTAATTGAATGGATTAATCGCTTCTG 59.468 37.037 20.43 7.77 0.00 3.02
2708 2844 2.483106 GACGGACCTTAACTTTGCTTCC 59.517 50.000 0.00 0.00 0.00 3.46
2709 2845 2.105993 ACGGACCTTAACTTTGCTTCCT 59.894 45.455 0.00 0.00 0.00 3.36
3026 3165 0.872021 CAGGAGATGGAAGCGTACGC 60.872 60.000 32.17 32.17 42.33 4.42
3027 3166 1.591863 GGAGATGGAAGCGTACGCC 60.592 63.158 34.88 21.18 43.17 5.68
3031 3170 0.384669 GATGGAAGCGTACGCCTACT 59.615 55.000 34.88 18.15 43.17 2.57
3033 3172 0.961857 TGGAAGCGTACGCCTACTCA 60.962 55.000 34.88 22.37 43.17 3.41
3034 3173 0.171903 GGAAGCGTACGCCTACTCAA 59.828 55.000 34.88 0.00 43.17 3.02
3035 3174 1.266466 GAAGCGTACGCCTACTCAAC 58.734 55.000 34.88 14.19 43.17 3.18
3036 3175 0.886563 AAGCGTACGCCTACTCAACT 59.113 50.000 34.88 11.89 43.17 3.16
3037 3176 0.450983 AGCGTACGCCTACTCAACTC 59.549 55.000 34.88 4.79 43.17 3.01
3038 3177 0.169672 GCGTACGCCTACTCAACTCA 59.830 55.000 29.51 0.00 34.56 3.41
3048 3187 4.081420 GCCTACTCAACTCAAATCTCCTCA 60.081 45.833 0.00 0.00 0.00 3.86
3091 3233 8.670135 CACTGTGTATATATACTCTCCTAGTGC 58.330 40.741 20.80 0.00 39.39 4.40
3120 3268 8.604640 ATTAGTCTCATATCAAGTGCTCATTG 57.395 34.615 0.00 0.00 0.00 2.82
3149 3297 3.684788 AGTGCTACTCCTTAATTTGTGCG 59.315 43.478 0.00 0.00 0.00 5.34
3156 3304 4.022416 ACTCCTTAATTTGTGCGCAATTCA 60.022 37.500 14.00 2.47 34.18 2.57
3161 3309 6.237648 CCTTAATTTGTGCGCAATTCATTCTC 60.238 38.462 14.00 0.00 34.18 2.87
3213 3362 9.113838 GTTCTTGAATTGAGAAGGAAGCATATA 57.886 33.333 2.02 0.00 34.05 0.86
3214 3363 9.857656 TTCTTGAATTGAGAAGGAAGCATATAT 57.142 29.630 0.00 0.00 0.00 0.86
3240 3389 8.880991 ATATACGTTGATATACACTCTCCCTT 57.119 34.615 0.00 0.00 0.00 3.95
3298 3464 3.924114 TCTGTAGTCAGAGAGCTAGCT 57.076 47.619 19.45 19.45 44.58 3.32
3413 3588 9.905713 TTAATTGCAATTAGATGGAAGTCTACT 57.094 29.630 26.27 3.23 34.01 2.57
3449 3628 8.514330 TTTACCCAAGGAATGAATACATACAC 57.486 34.615 0.00 0.00 35.50 2.90
3492 3672 9.578439 GCTCATTTATTTCTTGCTATTGAAAGT 57.422 29.630 0.00 0.00 35.93 2.66
3667 3946 2.706636 CAGTGTGGGTGGAACTGTG 58.293 57.895 0.00 0.00 37.20 3.66
3668 3947 0.819259 CAGTGTGGGTGGAACTGTGG 60.819 60.000 0.00 0.00 37.20 4.17
3669 3948 0.986019 AGTGTGGGTGGAACTGTGGA 60.986 55.000 0.00 0.00 36.74 4.02
3670 3949 0.110486 GTGTGGGTGGAACTGTGGAT 59.890 55.000 0.00 0.00 36.74 3.41
3671 3950 0.110295 TGTGGGTGGAACTGTGGATG 59.890 55.000 0.00 0.00 36.74 3.51
3680 3959 2.012673 GAACTGTGGATGTGGATGAGC 58.987 52.381 0.00 0.00 0.00 4.26
3683 3962 0.108186 TGTGGATGTGGATGAGCGTC 60.108 55.000 0.00 0.00 0.00 5.19
3754 4033 2.119495 AGTGTGGAGTGGACAAAGAGT 58.881 47.619 0.00 0.00 0.00 3.24
3928 4213 2.596631 ACACTTGCTGCTGCTGGG 60.597 61.111 17.00 12.57 40.48 4.45
3932 4217 2.987547 TTGCTGCTGCTGGGCTTC 60.988 61.111 17.00 0.00 40.48 3.86
3933 4218 3.795731 TTGCTGCTGCTGGGCTTCA 62.796 57.895 17.00 0.00 40.48 3.02
3937 4222 1.228644 TGCTGCTGGGCTTCATTGT 60.229 52.632 0.00 0.00 0.00 2.71
4075 4360 8.449251 TGCATGATGTAATGTGTATGTATTGT 57.551 30.769 0.00 0.00 0.00 2.71
4076 4361 9.553064 TGCATGATGTAATGTGTATGTATTGTA 57.447 29.630 0.00 0.00 0.00 2.41
4077 4362 9.811655 GCATGATGTAATGTGTATGTATTGTAC 57.188 33.333 0.00 0.00 0.00 2.90
4236 4530 7.344134 AGGACCCAAATGAAGGTACTAATTAC 58.656 38.462 0.00 0.00 46.02 1.89
4237 4531 7.184022 AGGACCCAAATGAAGGTACTAATTACT 59.816 37.037 0.00 0.00 46.02 2.24
4238 4532 7.282450 GGACCCAAATGAAGGTACTAATTACTG 59.718 40.741 0.00 0.00 38.49 2.74
4239 4533 7.116736 ACCCAAATGAAGGTACTAATTACTGG 58.883 38.462 0.00 0.00 38.49 4.00
4240 4534 7.116736 CCCAAATGAAGGTACTAATTACTGGT 58.883 38.462 0.00 0.00 38.49 4.00
4241 4535 7.614192 CCCAAATGAAGGTACTAATTACTGGTT 59.386 37.037 0.00 0.00 38.49 3.67
4242 4536 9.675464 CCAAATGAAGGTACTAATTACTGGTTA 57.325 33.333 0.00 0.00 38.49 2.85
4247 4541 9.715121 TGAAGGTACTAATTACTGGTTACTTTG 57.285 33.333 0.00 0.00 38.49 2.77
4304 4627 1.215382 GAGAAATTTGGTGGCGGCC 59.785 57.895 13.32 13.32 0.00 6.13
4305 4628 2.126110 GAAATTTGGTGGCGGCCG 60.126 61.111 24.05 24.05 0.00 6.13
4306 4629 3.641159 GAAATTTGGTGGCGGCCGG 62.641 63.158 29.38 8.95 0.00 6.13
4320 4643 4.390048 CCGGCCGGAAAGAAAGAA 57.610 55.556 41.82 0.00 37.50 2.52
4321 4644 2.171635 CCGGCCGGAAAGAAAGAAG 58.828 57.895 41.82 6.81 37.50 2.85
4322 4645 0.321298 CCGGCCGGAAAGAAAGAAGA 60.321 55.000 41.82 0.00 37.50 2.87
4323 4646 1.079503 CGGCCGGAAAGAAAGAAGAG 58.920 55.000 20.10 0.00 0.00 2.85
4324 4647 1.337823 CGGCCGGAAAGAAAGAAGAGA 60.338 52.381 20.10 0.00 0.00 3.10
4325 4648 2.678190 CGGCCGGAAAGAAAGAAGAGAT 60.678 50.000 20.10 0.00 0.00 2.75
4326 4649 2.939756 GGCCGGAAAGAAAGAAGAGATC 59.060 50.000 5.05 0.00 0.00 2.75
4327 4650 2.605366 GCCGGAAAGAAAGAAGAGATCG 59.395 50.000 5.05 0.00 0.00 3.69
4328 4651 3.676324 GCCGGAAAGAAAGAAGAGATCGA 60.676 47.826 5.05 0.00 0.00 3.59
4329 4652 4.495422 CCGGAAAGAAAGAAGAGATCGAA 58.505 43.478 0.00 0.00 0.00 3.71
4330 4653 4.564769 CCGGAAAGAAAGAAGAGATCGAAG 59.435 45.833 0.00 0.00 0.00 3.79
4331 4654 4.564769 CGGAAAGAAAGAAGAGATCGAAGG 59.435 45.833 0.00 0.00 0.00 3.46
4332 4655 4.331443 GGAAAGAAAGAAGAGATCGAAGGC 59.669 45.833 0.00 0.00 0.00 4.35
4581 4943 0.599558 GCCTACGTGTACAGTGACCA 59.400 55.000 0.00 0.00 0.00 4.02
4582 4944 1.402456 GCCTACGTGTACAGTGACCAG 60.402 57.143 0.00 0.00 0.00 4.00
4583 4945 1.402456 CCTACGTGTACAGTGACCAGC 60.402 57.143 0.00 0.00 0.00 4.85
4584 4946 1.540267 CTACGTGTACAGTGACCAGCT 59.460 52.381 0.00 0.00 0.00 4.24
4585 4947 0.032130 ACGTGTACAGTGACCAGCTG 59.968 55.000 6.78 6.78 39.67 4.24
4586 4948 1.284982 CGTGTACAGTGACCAGCTGC 61.285 60.000 8.66 0.00 37.47 5.25
4587 4949 0.034059 GTGTACAGTGACCAGCTGCT 59.966 55.000 8.66 0.00 37.47 4.24
4588 4950 0.318441 TGTACAGTGACCAGCTGCTC 59.682 55.000 8.66 4.89 37.47 4.26
4589 4951 0.318441 GTACAGTGACCAGCTGCTCA 59.682 55.000 8.66 8.11 37.47 4.26
4590 4952 1.066573 GTACAGTGACCAGCTGCTCAT 60.067 52.381 14.63 2.26 37.47 2.90
4591 4953 0.036577 ACAGTGACCAGCTGCTCATC 60.037 55.000 14.63 8.75 37.47 2.92
4592 4954 0.036671 CAGTGACCAGCTGCTCATCA 60.037 55.000 14.63 9.16 0.00 3.07
4593 4955 0.036577 AGTGACCAGCTGCTCATCAC 60.037 55.000 24.98 24.98 39.99 3.06
4594 4956 1.023513 GTGACCAGCTGCTCATCACC 61.024 60.000 23.15 11.45 34.83 4.02
4595 4957 1.451028 GACCAGCTGCTCATCACCC 60.451 63.158 8.66 0.00 0.00 4.61
4600 4962 4.864334 CTGCTCATCACCCGGCCC 62.864 72.222 0.00 0.00 0.00 5.80
4641 5003 4.783621 ATGCACCGTCAGCCGCAT 62.784 61.111 0.00 0.00 40.18 4.73
4690 5087 2.350388 CCACCTGTAAATGCAACGTGTC 60.350 50.000 0.00 0.00 0.00 3.67
5125 5522 4.687215 GTCGAGCTGGCTGTGGCA 62.687 66.667 0.00 0.00 40.87 4.92
5221 5618 0.755698 TGGACGAGGAGGAGTATGCC 60.756 60.000 0.00 0.00 0.00 4.40
5367 5766 4.787083 CGTCGTAAGTACTCAACACTCATC 59.213 45.833 0.00 0.00 39.48 2.92
5370 5769 5.179929 TCGTAAGTACTCAACACTCATCGAA 59.820 40.000 0.00 0.00 39.48 3.71
5378 5777 5.406780 ACTCAACACTCATCGAACATTTCTC 59.593 40.000 0.00 0.00 0.00 2.87
5380 5779 4.271696 ACACTCATCGAACATTTCTCCA 57.728 40.909 0.00 0.00 0.00 3.86
5395 5797 5.627499 TTTCTCCACTTTTTCCGATCATG 57.373 39.130 0.00 0.00 0.00 3.07
5416 5818 0.107066 ATCGTGCATTGCCCTGATGA 60.107 50.000 6.12 0.00 0.00 2.92
5431 5833 5.415701 GCCCTGATGATCAACTTCACTTTTA 59.584 40.000 0.00 0.00 0.00 1.52
5435 5837 8.180267 CCTGATGATCAACTTCACTTTTATGTC 58.820 37.037 0.00 0.00 0.00 3.06
5439 5841 6.430925 TGATCAACTTCACTTTTATGTCTGGG 59.569 38.462 0.00 0.00 0.00 4.45
5440 5842 5.690865 TCAACTTCACTTTTATGTCTGGGT 58.309 37.500 0.00 0.00 0.00 4.51
5787 6193 1.667830 CGACAGGTCCGTGCACAAT 60.668 57.895 18.64 0.00 0.00 2.71
5898 6304 1.683025 CATGGCCAGCAACATCCCA 60.683 57.895 13.05 0.00 0.00 4.37
5907 6313 1.315257 GCAACATCCCAACCAGCGAT 61.315 55.000 0.00 0.00 0.00 4.58
5923 6329 2.211952 GCGATATCGGAGGTACGTCCT 61.212 57.143 27.29 15.30 44.20 3.85
5924 6330 2.932622 GCGATATCGGAGGTACGTCCTA 60.933 54.545 27.29 19.65 42.68 2.94
5925 6331 4.234180 GCGATATCGGAGGTACGTCCTAT 61.234 52.174 27.29 24.10 42.68 2.57
5926 6332 4.975432 GCGATATCGGAGGTACGTCCTATA 60.975 50.000 27.29 25.20 42.68 1.31
5995 6401 0.888619 CTAACAGAGGTGCTCCACGA 59.111 55.000 7.70 0.00 34.83 4.35
5996 6402 1.478510 CTAACAGAGGTGCTCCACGAT 59.521 52.381 7.70 0.00 34.83 3.73
5998 6404 1.142748 CAGAGGTGCTCCACGATCC 59.857 63.158 7.70 0.00 34.83 3.36
5999 6405 1.305297 AGAGGTGCTCCACGATCCA 60.305 57.895 7.70 0.00 34.83 3.41
6000 6406 0.689080 AGAGGTGCTCCACGATCCAT 60.689 55.000 7.70 0.00 34.83 3.41
6001 6407 0.179000 GAGGTGCTCCACGATCCATT 59.821 55.000 7.70 0.00 34.83 3.16
6043 6449 0.030705 AGGGGAGGAAGAGCATGCTA 60.031 55.000 22.74 0.00 0.00 3.49
6064 6470 0.825840 AGCTAGCGGAGAGGATGGTC 60.826 60.000 9.55 0.00 0.00 4.02
6121 6527 1.302431 CCAATGGACCACGCTGTCA 60.302 57.895 0.00 0.00 36.97 3.58
6226 6632 2.285743 ACCTCCTTCTGGCTCCCC 60.286 66.667 0.00 0.00 0.00 4.81
6297 6703 4.062677 GTGAGGTACACACTTTACACCA 57.937 45.455 12.91 0.00 46.16 4.17
6298 6704 4.638304 GTGAGGTACACACTTTACACCAT 58.362 43.478 12.91 0.00 46.16 3.55
6299 6705 4.451096 GTGAGGTACACACTTTACACCATG 59.549 45.833 12.91 0.00 46.16 3.66
6302 6712 5.686753 AGGTACACACTTTACACCATGAAA 58.313 37.500 0.00 0.00 0.00 2.69
6309 6719 7.094634 ACACACTTTACACCATGAAAGATCATC 60.095 37.037 10.62 0.00 44.53 2.92
6311 6721 6.313658 CACTTTACACCATGAAAGATCATCGA 59.686 38.462 10.62 0.00 44.53 3.59
6315 6725 4.633126 ACACCATGAAAGATCATCGACAAG 59.367 41.667 0.00 0.00 44.53 3.16
6322 6732 6.223120 TGAAAGATCATCGACAAGTTCTTGA 58.777 36.000 17.75 0.00 0.00 3.02
6329 6739 5.181245 TCATCGACAAGTTCTTGAAAATCCC 59.819 40.000 17.75 0.14 0.00 3.85
6341 6751 5.837979 TCTTGAAAATCCCAAGGTTGATGAA 59.162 36.000 0.00 0.00 40.88 2.57
6342 6752 5.467035 TGAAAATCCCAAGGTTGATGAAC 57.533 39.130 0.00 0.00 0.00 3.18
6344 6754 4.871933 AAATCCCAAGGTTGATGAACAC 57.128 40.909 0.00 0.00 33.27 3.32
6345 6755 3.814504 ATCCCAAGGTTGATGAACACT 57.185 42.857 0.00 0.00 33.27 3.55
6346 6756 3.140325 TCCCAAGGTTGATGAACACTC 57.860 47.619 0.00 0.00 33.27 3.51
6347 6757 2.711009 TCCCAAGGTTGATGAACACTCT 59.289 45.455 0.00 0.00 33.27 3.24
6349 6759 4.349636 TCCCAAGGTTGATGAACACTCTTA 59.650 41.667 0.00 0.00 33.27 2.10
6350 6760 4.455877 CCCAAGGTTGATGAACACTCTTAC 59.544 45.833 0.00 0.00 33.27 2.34
6351 6761 5.063204 CCAAGGTTGATGAACACTCTTACA 58.937 41.667 0.00 0.00 33.27 2.41
6352 6762 5.049405 CCAAGGTTGATGAACACTCTTACAC 60.049 44.000 0.00 0.00 33.27 2.90
6353 6763 5.552870 AGGTTGATGAACACTCTTACACT 57.447 39.130 0.00 0.00 33.27 3.55
6354 6764 5.542779 AGGTTGATGAACACTCTTACACTC 58.457 41.667 0.00 0.00 33.27 3.51
6355 6765 5.070446 AGGTTGATGAACACTCTTACACTCA 59.930 40.000 0.00 0.00 33.27 3.41
6356 6766 5.934625 GGTTGATGAACACTCTTACACTCAT 59.065 40.000 0.00 0.00 33.27 2.90
6455 6865 2.743752 CCATGGCAACTGCGTCTCG 61.744 63.158 0.00 0.00 43.26 4.04
6483 6893 5.224888 TCCGTGTCAATGTAAGTACAAGAC 58.775 41.667 15.22 15.22 41.56 3.01
6520 6933 6.728200 CAATAACCTCATGCGTGTGATAATT 58.272 36.000 9.53 3.45 0.00 1.40
6534 6947 7.680827 GCGTGTGATAATTGAATTAACCATGGA 60.681 37.037 21.47 0.00 0.00 3.41
6535 6948 8.352201 CGTGTGATAATTGAATTAACCATGGAT 58.648 33.333 21.47 9.83 0.00 3.41
6613 7026 1.302271 CCTGCAAGAGAGCTGCACA 60.302 57.895 1.02 0.00 34.07 4.57
6622 7035 4.284860 AGCTGCACAGACGCGTCA 62.285 61.111 37.85 18.88 33.35 4.35
6652 7065 4.203076 ATCTACGCGCCGGTGGAC 62.203 66.667 18.41 0.00 29.81 4.02
6703 7116 2.099831 GACCCAGACTACGTCGCG 59.900 66.667 0.00 0.00 37.67 5.87
6957 7370 1.687494 CCGCAGTAGCTTCGCTCAAC 61.687 60.000 0.00 0.00 40.44 3.18
6965 7378 2.072298 AGCTTCGCTCAACTCATCAAC 58.928 47.619 0.00 0.00 30.62 3.18
7014 7427 3.795877 CCTGCAACCAAAACTGTTCATT 58.204 40.909 0.00 0.00 0.00 2.57
7216 7631 2.933906 ACTTCTTCGTTTCGTGCAAGAA 59.066 40.909 11.22 11.22 34.47 2.52
7608 8308 4.021981 GCAAATGTTAGTTCCTTGAGGCTT 60.022 41.667 0.00 0.00 34.44 4.35
7629 8329 5.184671 GCTTGAGGACTGAATCATTTCCTTT 59.815 40.000 13.06 0.00 38.67 3.11
7638 8338 7.834803 ACTGAATCATTTCCTTTCAAATCTCC 58.165 34.615 0.00 0.00 0.00 3.71
7639 8339 7.452501 ACTGAATCATTTCCTTTCAAATCTCCA 59.547 33.333 0.00 0.00 0.00 3.86
7656 8356 4.843728 TCTCCACGCTCCAATAAGAATTT 58.156 39.130 0.00 0.00 0.00 1.82
7753 8467 7.993101 ACAAATGTGAACCATCAGATATCTTG 58.007 34.615 1.33 0.00 38.52 3.02
7779 8494 2.301346 CAACACTGCTTCCCTTTCAGT 58.699 47.619 0.00 0.00 41.29 3.41
7780 8495 3.118038 ACAACACTGCTTCCCTTTCAGTA 60.118 43.478 0.00 0.00 38.85 2.74
7781 8496 3.409026 ACACTGCTTCCCTTTCAGTAG 57.591 47.619 0.00 0.00 38.85 2.57
7782 8497 2.972713 ACACTGCTTCCCTTTCAGTAGA 59.027 45.455 0.00 0.00 38.85 2.59
7819 8534 9.669353 GACAAATCATTCCATGTATACAACATC 57.331 33.333 10.14 0.00 46.15 3.06
7831 8546 1.148310 ACAACATCGAGCGTTTCTGG 58.852 50.000 0.47 0.00 0.00 3.86
7833 8548 1.126846 CAACATCGAGCGTTTCTGGAC 59.873 52.381 0.47 0.00 32.22 4.02
7848 8563 0.178888 TGGACACCATCTACACCCCA 60.179 55.000 0.00 0.00 0.00 4.96
7849 8564 0.541863 GGACACCATCTACACCCCAG 59.458 60.000 0.00 0.00 0.00 4.45
7853 8568 2.039879 ACACCATCTACACCCCAGAAAC 59.960 50.000 0.00 0.00 0.00 2.78
7854 8569 2.305927 CACCATCTACACCCCAGAAACT 59.694 50.000 0.00 0.00 0.00 2.66
7855 8570 2.305927 ACCATCTACACCCCAGAAACTG 59.694 50.000 0.00 0.00 0.00 3.16
7856 8571 2.359900 CATCTACACCCCAGAAACTGC 58.640 52.381 0.00 0.00 0.00 4.40
7857 8572 1.429930 TCTACACCCCAGAAACTGCA 58.570 50.000 0.00 0.00 0.00 4.41
7863 8582 1.688197 ACCCCAGAAACTGCAACAATG 59.312 47.619 0.00 0.00 0.00 2.82
7866 8585 3.383761 CCCAGAAACTGCAACAATGAAC 58.616 45.455 0.00 0.00 0.00 3.18
7871 8590 2.869233 ACTGCAACAATGAACACCAC 57.131 45.000 0.00 0.00 0.00 4.16
7923 8642 1.303236 CATCAGACCAACGGGCCAA 60.303 57.895 4.39 0.00 37.90 4.52
7931 8650 1.106944 CCAACGGGCCAACACTTCTT 61.107 55.000 4.39 0.00 0.00 2.52
7935 8654 1.247567 CGGGCCAACACTTCTTGATT 58.752 50.000 4.39 0.00 0.00 2.57
7941 8660 5.299949 GGCCAACACTTCTTGATTGAAAAT 58.700 37.500 0.00 0.00 0.00 1.82
7964 8684 4.000988 TGAACTGGATAAAAGAAGGCGTC 58.999 43.478 0.00 0.00 0.00 5.19
7965 8685 3.695830 ACTGGATAAAAGAAGGCGTCA 57.304 42.857 2.69 0.00 0.00 4.35
7966 8686 4.222124 ACTGGATAAAAGAAGGCGTCAT 57.778 40.909 2.69 0.00 0.00 3.06
7968 8688 3.194861 TGGATAAAAGAAGGCGTCATCG 58.805 45.455 2.69 0.00 40.37 3.84
7969 8689 3.118920 TGGATAAAAGAAGGCGTCATCGA 60.119 43.478 2.69 0.00 39.71 3.59
7970 8690 3.245519 GGATAAAAGAAGGCGTCATCGAC 59.754 47.826 2.69 0.00 46.75 4.20
8230 8951 8.048534 AGGAGAAATAACACAACATGAAGATG 57.951 34.615 0.00 0.00 35.49 2.90
8233 8954 9.897744 GAGAAATAACACAACATGAAGATGAAA 57.102 29.630 0.00 0.00 33.36 2.69
8261 8982 6.429385 ACACAGATCATCTTTTCCTTCAGAAC 59.571 38.462 0.00 0.00 32.95 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.316588 TCTTGGCGATGTATCTCACTCTC 59.683 47.826 0.00 0.00 0.00 3.20
101 105 8.674263 TCCAAAAATAGCAATTTTGACATGTT 57.326 26.923 17.79 0.00 45.96 2.71
236 243 7.860613 TGTAACATAATTTGACGGCATAGATG 58.139 34.615 0.00 0.00 0.00 2.90
407 416 9.973450 ATGTACTAGTATTGCTACAAAGATCTG 57.027 33.333 5.75 0.00 0.00 2.90
511 521 9.676861 TGTGTATCAGTGTACTAGTGTTACTAT 57.323 33.333 5.39 4.99 36.51 2.12
518 528 8.244113 TGAGATTTGTGTATCAGTGTACTAGTG 58.756 37.037 5.39 0.00 0.00 2.74
536 546 7.172190 ACTCTTGGCGATATACATTGAGATTTG 59.828 37.037 0.00 0.00 0.00 2.32
557 567 8.862325 TTAATTGTGATACATTGACCACTCTT 57.138 30.769 0.00 0.00 0.00 2.85
673 737 3.494626 AGCGTGTGTGTATTTTCACTCTG 59.505 43.478 0.00 0.00 38.90 3.35
679 743 3.603770 GCAATCAGCGTGTGTGTATTTTC 59.396 43.478 0.00 0.00 0.00 2.29
855 933 2.593026 GTAGAGTCAGAGGGGAGATGG 58.407 57.143 0.00 0.00 0.00 3.51
863 941 2.838637 AGAAGGGGTAGAGTCAGAGG 57.161 55.000 0.00 0.00 0.00 3.69
1059 1138 1.146152 AGATCTAGAGGAAGGGGACGG 59.854 57.143 0.00 0.00 0.00 4.79
1144 1224 0.604780 CTCCCTGTGGCTTGTGTCTG 60.605 60.000 0.00 0.00 0.00 3.51
1207 1287 6.601332 AGGAACTTGGTAGAGAGAGATCTAG 58.399 44.000 0.00 0.00 27.25 2.43
1348 1428 2.244510 TCTGCATCTCTCTCTCTCCCTT 59.755 50.000 0.00 0.00 0.00 3.95
1350 1430 2.363306 TCTGCATCTCTCTCTCTCCC 57.637 55.000 0.00 0.00 0.00 4.30
1442 1534 5.125367 TCATGGTACTCTCTACCTTGCTA 57.875 43.478 7.30 0.00 40.50 3.49
1792 1886 6.016276 CAGTACTTGCAAATAGAAACAAGGGT 60.016 38.462 0.00 0.00 42.97 4.34
1795 1889 7.272084 GCATCAGTACTTGCAAATAGAAACAAG 59.728 37.037 13.51 0.00 43.99 3.16
1883 1977 6.672266 TCAAGTACTTGTCTCTTCCATCTT 57.328 37.500 29.83 0.00 41.16 2.40
2017 2117 1.347378 TCTATGTGTGAACAGCAGCCA 59.653 47.619 0.00 0.00 0.00 4.75
2065 2165 1.460504 GGTCTTAAAGAAAGGGGGCG 58.539 55.000 0.00 0.00 35.75 6.13
2121 2221 2.544768 CCCCCAACCTATAGCAGCT 58.455 57.895 0.00 0.00 0.00 4.24
2141 2241 1.353022 AGTGAAGTCTCCCTCTCTCGT 59.647 52.381 0.00 0.00 0.00 4.18
2142 2242 2.014128 GAGTGAAGTCTCCCTCTCTCG 58.986 57.143 0.00 0.00 0.00 4.04
2145 2245 4.196971 GAGTAGAGTGAAGTCTCCCTCTC 58.803 52.174 0.00 0.00 35.89 3.20
2146 2246 3.589735 TGAGTAGAGTGAAGTCTCCCTCT 59.410 47.826 12.44 0.00 37.93 3.69
2147 2247 3.945285 CTGAGTAGAGTGAAGTCTCCCTC 59.055 52.174 0.00 0.44 35.44 4.30
2148 2248 3.332485 ACTGAGTAGAGTGAAGTCTCCCT 59.668 47.826 0.00 0.00 35.28 4.20
2164 2269 3.812053 GTGTGCAAGATCAAGAACTGAGT 59.188 43.478 0.00 0.00 37.52 3.41
2376 2506 6.293680 GGGAGAAGAAGTGAAGCAACTTTTAG 60.294 42.308 1.61 0.00 40.48 1.85
2377 2507 5.531287 GGGAGAAGAAGTGAAGCAACTTTTA 59.469 40.000 1.61 0.00 40.48 1.52
2426 2560 2.025321 GGGGTGGAATGGAAAAGCTAGA 60.025 50.000 0.00 0.00 0.00 2.43
2494 2630 3.788333 ACCATCCGAAAATTCATGCTG 57.212 42.857 0.00 0.00 0.00 4.41
2507 2643 6.757026 AAAATTTCGTGTAAAAACCATCCG 57.243 33.333 0.00 0.00 0.00 4.18
2708 2844 5.591877 AGGTTTGGCTGCAATTTATAGAGAG 59.408 40.000 0.50 0.00 0.00 3.20
2709 2845 5.357878 CAGGTTTGGCTGCAATTTATAGAGA 59.642 40.000 0.50 0.00 0.00 3.10
3026 3165 5.667539 TGAGGAGATTTGAGTTGAGTAGG 57.332 43.478 0.00 0.00 0.00 3.18
3027 3166 6.459066 TGTTGAGGAGATTTGAGTTGAGTAG 58.541 40.000 0.00 0.00 0.00 2.57
3031 3170 7.068593 ACAAAATGTTGAGGAGATTTGAGTTGA 59.931 33.333 1.62 0.00 38.20 3.18
3033 3172 7.352079 ACAAAATGTTGAGGAGATTTGAGTT 57.648 32.000 1.62 0.00 38.20 3.01
3034 3173 6.966534 ACAAAATGTTGAGGAGATTTGAGT 57.033 33.333 1.62 0.00 38.20 3.41
3035 3174 9.918630 ATTAACAAAATGTTGAGGAGATTTGAG 57.081 29.630 1.62 0.00 41.30 3.02
3077 3219 7.294584 AGACTAATCAAGCACTAGGAGAGTAT 58.705 38.462 0.00 0.00 35.64 2.12
3127 3275 3.684788 CGCACAAATTAAGGAGTAGCACT 59.315 43.478 0.00 0.00 0.00 4.40
3149 3297 7.020914 AGGAAAGATAACGAGAATGAATTGC 57.979 36.000 0.00 0.00 0.00 3.56
3161 3309 6.314784 AGCGAAAATTCAAGGAAAGATAACG 58.685 36.000 0.00 0.00 0.00 3.18
3214 3363 9.970553 AAGGGAGAGTGTATATCAACGTATATA 57.029 33.333 0.00 0.00 0.00 0.86
3215 3364 8.880991 AAGGGAGAGTGTATATCAACGTATAT 57.119 34.615 0.00 0.00 0.00 0.86
3216 3365 9.797642 TTAAGGGAGAGTGTATATCAACGTATA 57.202 33.333 0.00 0.00 0.00 1.47
3291 3457 6.591750 TGAACAGAAAAGTAGTAGCTAGCT 57.408 37.500 23.12 23.12 0.00 3.32
3295 3461 8.910351 AAGAATTGAACAGAAAAGTAGTAGCT 57.090 30.769 0.00 0.00 0.00 3.32
3412 3587 8.850156 CATTCCTTGGGTAAAATGAAGGTATAG 58.150 37.037 0.00 0.00 36.98 1.31
3413 3588 8.561769 TCATTCCTTGGGTAAAATGAAGGTATA 58.438 33.333 0.00 0.00 35.72 1.47
3414 3589 7.418378 TCATTCCTTGGGTAAAATGAAGGTAT 58.582 34.615 0.00 0.00 35.72 2.73
3415 3590 6.795590 TCATTCCTTGGGTAAAATGAAGGTA 58.204 36.000 0.00 0.00 35.72 3.08
3416 3591 5.650283 TCATTCCTTGGGTAAAATGAAGGT 58.350 37.500 0.00 0.00 35.72 3.50
3666 3945 1.141665 CGACGCTCATCCACATCCA 59.858 57.895 0.00 0.00 0.00 3.41
3667 3946 2.240500 GCGACGCTCATCCACATCC 61.241 63.158 13.73 0.00 0.00 3.51
3668 3947 0.030773 TAGCGACGCTCATCCACATC 59.969 55.000 28.21 0.00 40.44 3.06
3669 3948 0.031314 CTAGCGACGCTCATCCACAT 59.969 55.000 28.21 0.98 40.44 3.21
3670 3949 1.433471 CTAGCGACGCTCATCCACA 59.567 57.895 28.21 5.76 40.44 4.17
3671 3950 1.946650 GCTAGCGACGCTCATCCAC 60.947 63.158 28.21 6.77 40.44 4.02
3712 3991 7.155328 CACTACTAGGACTCAATTTGACTTGT 58.845 38.462 0.00 2.15 0.00 3.16
3834 4117 4.676951 TTGGGGAAGGGCGCAAGG 62.677 66.667 10.83 0.00 38.28 3.61
3867 4150 2.163010 CCTTGAATGAATGCTGCGTCTT 59.837 45.455 0.00 0.00 0.00 3.01
3868 4151 1.741706 CCTTGAATGAATGCTGCGTCT 59.258 47.619 0.00 0.00 0.00 4.18
4031 4316 3.509184 TGCATCGTCCCAATTTTCAATGA 59.491 39.130 0.00 0.00 0.00 2.57
4272 4566 4.440839 AATTTCTCAGCCGAAATGGTTC 57.559 40.909 6.91 0.00 41.42 3.62
4273 4567 4.559153 CAAATTTCTCAGCCGAAATGGTT 58.441 39.130 6.91 0.00 41.42 3.67
4304 4627 1.079503 CTCTTCTTTCTTTCCGGCCG 58.920 55.000 21.04 21.04 0.00 6.13
4305 4628 2.474410 TCTCTTCTTTCTTTCCGGCC 57.526 50.000 0.00 0.00 0.00 6.13
4306 4629 2.605366 CGATCTCTTCTTTCTTTCCGGC 59.395 50.000 0.00 0.00 0.00 6.13
4307 4630 4.111375 TCGATCTCTTCTTTCTTTCCGG 57.889 45.455 0.00 0.00 0.00 5.14
4308 4631 4.564769 CCTTCGATCTCTTCTTTCTTTCCG 59.435 45.833 0.00 0.00 0.00 4.30
4309 4632 4.331443 GCCTTCGATCTCTTCTTTCTTTCC 59.669 45.833 0.00 0.00 0.00 3.13
4310 4633 4.331443 GGCCTTCGATCTCTTCTTTCTTTC 59.669 45.833 0.00 0.00 0.00 2.62
4311 4634 4.257731 GGCCTTCGATCTCTTCTTTCTTT 58.742 43.478 0.00 0.00 0.00 2.52
4312 4635 3.677424 CGGCCTTCGATCTCTTCTTTCTT 60.677 47.826 0.00 0.00 42.43 2.52
4313 4636 2.159170 CGGCCTTCGATCTCTTCTTTCT 60.159 50.000 0.00 0.00 42.43 2.52
4314 4637 2.197577 CGGCCTTCGATCTCTTCTTTC 58.802 52.381 0.00 0.00 42.43 2.62
4315 4638 1.134670 CCGGCCTTCGATCTCTTCTTT 60.135 52.381 0.00 0.00 42.43 2.52
4316 4639 0.461961 CCGGCCTTCGATCTCTTCTT 59.538 55.000 0.00 0.00 42.43 2.52
4317 4640 2.022240 GCCGGCCTTCGATCTCTTCT 62.022 60.000 18.11 0.00 42.43 2.85
4318 4641 1.592939 GCCGGCCTTCGATCTCTTC 60.593 63.158 18.11 0.00 42.43 2.87
4319 4642 2.501610 GCCGGCCTTCGATCTCTT 59.498 61.111 18.11 0.00 42.43 2.85
4320 4643 3.541713 GGCCGGCCTTCGATCTCT 61.542 66.667 38.76 0.00 42.43 3.10
4321 4644 3.798954 CTGGCCGGCCTTCGATCTC 62.799 68.421 43.34 16.73 42.43 2.75
4322 4645 3.854669 CTGGCCGGCCTTCGATCT 61.855 66.667 43.34 0.00 42.43 2.75
4525 4887 0.039035 TGTGGGGTTTGACTATGGGC 59.961 55.000 0.00 0.00 0.00 5.36
4581 4943 4.479993 GCCGGGTGATGAGCAGCT 62.480 66.667 2.18 0.00 44.32 4.24
4583 4945 4.864334 GGGCCGGGTGATGAGCAG 62.864 72.222 2.18 0.00 0.00 4.24
4690 5087 3.378112 ACGCCATCAGATTAACAACCATG 59.622 43.478 0.00 0.00 0.00 3.66
5221 5618 1.656652 GTGGGTCGATGAACATCCTG 58.343 55.000 8.87 0.00 34.40 3.86
5367 5766 4.024387 TCGGAAAAAGTGGAGAAATGTTCG 60.024 41.667 0.00 0.00 34.02 3.95
5370 5769 5.070001 TGATCGGAAAAAGTGGAGAAATGT 58.930 37.500 0.00 0.00 0.00 2.71
5378 5777 3.699067 GATGCATGATCGGAAAAAGTGG 58.301 45.455 2.46 0.00 0.00 4.00
5395 5797 1.731433 ATCAGGGCAATGCACGATGC 61.731 55.000 7.79 11.44 45.29 3.91
5409 5811 8.048534 ACATAAAAGTGAAGTTGATCATCAGG 57.951 34.615 6.55 0.00 0.00 3.86
5416 5818 6.306987 ACCCAGACATAAAAGTGAAGTTGAT 58.693 36.000 0.00 0.00 0.00 2.57
5439 5841 1.491563 CGCGTACTGGTTCTGCAAC 59.508 57.895 0.00 0.00 0.00 4.17
5440 5842 1.666553 CCGCGTACTGGTTCTGCAA 60.667 57.895 4.92 0.00 0.00 4.08
5787 6193 0.384309 CGACCAGCGGCTTGTAGATA 59.616 55.000 6.71 0.00 36.03 1.98
5898 6304 1.612463 GTACCTCCGATATCGCTGGTT 59.388 52.381 30.84 20.47 41.20 3.67
5932 6338 8.237267 CGAGCAGATGAACTATGTATGTGTATA 58.763 37.037 0.00 0.00 0.00 1.47
5941 6347 4.098501 TGATCACGAGCAGATGAACTATGT 59.901 41.667 0.00 0.00 0.00 2.29
5995 6401 3.693807 AGTGATCACTGCACAAATGGAT 58.306 40.909 27.37 0.00 40.75 3.41
5996 6402 3.144657 AGTGATCACTGCACAAATGGA 57.855 42.857 27.37 0.00 40.75 3.41
5998 6404 3.688185 AGCTAGTGATCACTGCACAAATG 59.312 43.478 33.76 15.65 42.52 2.32
5999 6405 3.937706 GAGCTAGTGATCACTGCACAAAT 59.062 43.478 33.76 19.10 42.52 2.32
6000 6406 3.329386 GAGCTAGTGATCACTGCACAAA 58.671 45.455 33.76 15.04 42.52 2.83
6001 6407 2.672195 CGAGCTAGTGATCACTGCACAA 60.672 50.000 33.76 15.73 42.52 3.33
6043 6449 0.755686 CCATCCTCTCCGCTAGCTTT 59.244 55.000 13.93 0.00 0.00 3.51
6106 6512 2.665000 CCTGACAGCGTGGTCCAT 59.335 61.111 0.00 0.00 36.97 3.41
6184 6590 0.606401 CGTTGAGGACAATGCCTGGT 60.606 55.000 1.11 0.00 38.73 4.00
6193 6599 4.980805 GTGGCGGCGTTGAGGACA 62.981 66.667 9.37 0.00 0.00 4.02
6226 6632 4.430765 ACGCGCTTAGGTGGGACG 62.431 66.667 5.73 0.00 38.89 4.79
6277 6683 4.345547 TCATGGTGTAAAGTGTGTACCTCA 59.654 41.667 0.00 0.00 32.68 3.86
6289 6695 6.169800 TGTCGATGATCTTTCATGGTGTAAA 58.830 36.000 0.00 0.00 42.73 2.01
6291 6697 5.337578 TGTCGATGATCTTTCATGGTGTA 57.662 39.130 0.00 0.00 42.73 2.90
6293 6699 4.633126 ACTTGTCGATGATCTTTCATGGTG 59.367 41.667 0.00 0.00 42.73 4.17
6294 6700 4.836825 ACTTGTCGATGATCTTTCATGGT 58.163 39.130 0.00 0.00 42.73 3.55
6295 6701 5.583854 AGAACTTGTCGATGATCTTTCATGG 59.416 40.000 0.00 0.00 42.73 3.66
6296 6702 6.659361 AGAACTTGTCGATGATCTTTCATG 57.341 37.500 0.00 0.00 42.73 3.07
6297 6703 6.875726 TCAAGAACTTGTCGATGATCTTTCAT 59.124 34.615 13.15 0.00 41.88 2.57
6298 6704 6.223120 TCAAGAACTTGTCGATGATCTTTCA 58.777 36.000 13.15 0.00 41.16 2.69
6299 6705 6.712241 TCAAGAACTTGTCGATGATCTTTC 57.288 37.500 13.15 0.00 41.16 2.62
6302 6712 7.148340 GGATTTTCAAGAACTTGTCGATGATCT 60.148 37.037 13.15 0.00 41.16 2.75
6309 6719 4.829064 TGGGATTTTCAAGAACTTGTCG 57.171 40.909 13.15 0.00 41.16 4.35
6311 6721 4.962362 ACCTTGGGATTTTCAAGAACTTGT 59.038 37.500 13.15 0.00 42.94 3.16
6315 6725 5.529581 TCAACCTTGGGATTTTCAAGAAC 57.470 39.130 5.51 0.00 42.94 3.01
6322 6732 4.901250 AGTGTTCATCAACCTTGGGATTTT 59.099 37.500 0.00 0.00 0.00 1.82
6329 6739 5.760253 AGTGTAAGAGTGTTCATCAACCTTG 59.240 40.000 0.00 0.00 0.00 3.61
6341 6751 8.417106 CACCAAGATATATGAGTGTAAGAGTGT 58.583 37.037 0.00 0.00 0.00 3.55
6342 6752 8.417106 ACACCAAGATATATGAGTGTAAGAGTG 58.583 37.037 4.34 0.00 36.73 3.51
6344 6754 9.254133 CAACACCAAGATATATGAGTGTAAGAG 57.746 37.037 6.19 0.00 37.47 2.85
6345 6755 8.204160 CCAACACCAAGATATATGAGTGTAAGA 58.796 37.037 6.19 0.00 37.47 2.10
6346 6756 7.041780 GCCAACACCAAGATATATGAGTGTAAG 60.042 40.741 6.19 3.39 37.47 2.34
6347 6757 6.765989 GCCAACACCAAGATATATGAGTGTAA 59.234 38.462 6.19 0.00 37.47 2.41
6349 6759 5.126067 GCCAACACCAAGATATATGAGTGT 58.874 41.667 0.00 0.97 39.99 3.55
6350 6760 5.125356 TGCCAACACCAAGATATATGAGTG 58.875 41.667 0.00 0.00 0.00 3.51
6351 6761 5.104360 ACTGCCAACACCAAGATATATGAGT 60.104 40.000 0.00 0.00 0.00 3.41
6352 6762 5.237996 CACTGCCAACACCAAGATATATGAG 59.762 44.000 0.00 0.00 0.00 2.90
6353 6763 5.125356 CACTGCCAACACCAAGATATATGA 58.875 41.667 0.00 0.00 0.00 2.15
6354 6764 4.276678 CCACTGCCAACACCAAGATATATG 59.723 45.833 0.00 0.00 0.00 1.78
6355 6765 4.464008 CCACTGCCAACACCAAGATATAT 58.536 43.478 0.00 0.00 0.00 0.86
6356 6766 3.371487 CCCACTGCCAACACCAAGATATA 60.371 47.826 0.00 0.00 0.00 0.86
6455 6865 2.271800 CTTACATTGACACGGAGGAGC 58.728 52.381 0.00 0.00 0.00 4.70
6483 6893 6.628919 TGAGGTTATTGCATGATCAGATTG 57.371 37.500 0.09 0.00 0.00 2.67
6534 6947 9.734620 GCACATAAACACACAATATGTCAATAT 57.265 29.630 0.00 0.00 40.64 1.28
6535 6948 8.734386 TGCACATAAACACACAATATGTCAATA 58.266 29.630 0.00 0.00 40.64 1.90
6536 6949 7.600960 TGCACATAAACACACAATATGTCAAT 58.399 30.769 0.00 0.00 40.64 2.57
6537 6950 6.974965 TGCACATAAACACACAATATGTCAA 58.025 32.000 0.00 0.00 40.64 3.18
6538 6951 6.429385 TCTGCACATAAACACACAATATGTCA 59.571 34.615 0.00 0.00 40.64 3.58
6539 6952 6.841119 TCTGCACATAAACACACAATATGTC 58.159 36.000 0.00 0.00 40.64 3.06
6540 6953 6.623549 GCTCTGCACATAAACACACAATATGT 60.624 38.462 0.00 0.00 44.81 2.29
6541 6954 5.740569 GCTCTGCACATAAACACACAATATG 59.259 40.000 0.00 0.00 34.08 1.78
6613 7026 2.045242 TAGGAGCCTGACGCGTCT 60.045 61.111 36.27 19.29 44.76 4.18
6622 7035 1.595466 CGTAGATGACGTAGGAGCCT 58.405 55.000 0.00 0.00 46.86 4.58
6652 7065 2.668212 ACGTTCATGGCCACCACG 60.668 61.111 24.52 24.52 35.80 4.94
6957 7370 5.738909 ACAGAACATAGGAAGGTTGATGAG 58.261 41.667 0.00 0.00 27.75 2.90
6965 7378 5.600484 ACCTCTGATACAGAACATAGGAAGG 59.400 44.000 0.00 4.50 40.18 3.46
7000 7413 7.385752 ACATGCATTTCTAATGAACAGTTTTGG 59.614 33.333 0.00 0.00 31.02 3.28
7014 7427 5.543507 AAAACCCAACACATGCATTTCTA 57.456 34.783 0.00 0.00 0.00 2.10
7216 7631 5.500825 GCATCTTGTTTTCGCAAATGTTTT 58.499 33.333 0.00 0.00 0.00 2.43
7608 8308 5.879763 TGAAAGGAAATGATTCAGTCCTCA 58.120 37.500 17.68 11.95 37.29 3.86
7629 8329 2.787473 ATTGGAGCGTGGAGATTTGA 57.213 45.000 0.00 0.00 0.00 2.69
7638 8338 9.573133 AATTTCTAAAATTCTTATTGGAGCGTG 57.427 29.630 0.00 0.00 0.00 5.34
7723 8425 4.516321 TCTGATGGTTCACATTTGTCAGTG 59.484 41.667 0.00 0.00 40.72 3.66
7725 8427 5.892160 ATCTGATGGTTCACATTTGTCAG 57.108 39.130 0.00 0.00 40.72 3.51
7726 8428 7.341030 AGATATCTGATGGTTCACATTTGTCA 58.659 34.615 3.89 0.00 40.72 3.58
7727 8429 7.798596 AGATATCTGATGGTTCACATTTGTC 57.201 36.000 3.89 0.00 40.72 3.18
7731 8445 8.991783 AATCAAGATATCTGATGGTTCACATT 57.008 30.769 5.86 0.00 40.72 2.71
7737 8451 9.685276 TGTTGTAAATCAAGATATCTGATGGTT 57.315 29.630 5.86 1.37 36.66 3.67
7753 8467 5.009610 TGAAAGGGAAGCAGTGTTGTAAATC 59.990 40.000 0.00 0.00 0.00 2.17
7779 8494 9.764363 GGAATGATTTGTCAGTGTATGTATCTA 57.236 33.333 0.00 0.00 0.00 1.98
7780 8495 8.267183 TGGAATGATTTGTCAGTGTATGTATCT 58.733 33.333 0.00 0.00 0.00 1.98
7781 8496 8.437360 TGGAATGATTTGTCAGTGTATGTATC 57.563 34.615 0.00 0.00 0.00 2.24
7782 8497 8.985315 ATGGAATGATTTGTCAGTGTATGTAT 57.015 30.769 0.00 0.00 0.00 2.29
7819 8534 0.670546 ATGGTGTCCAGAAACGCTCG 60.671 55.000 0.00 0.00 36.75 5.03
7831 8546 1.568504 TCTGGGGTGTAGATGGTGTC 58.431 55.000 0.00 0.00 0.00 3.67
7833 8548 2.305927 AGTTTCTGGGGTGTAGATGGTG 59.694 50.000 0.00 0.00 0.00 4.17
7848 8563 3.446873 TGGTGTTCATTGTTGCAGTTTCT 59.553 39.130 0.00 0.00 0.00 2.52
7849 8564 3.551485 GTGGTGTTCATTGTTGCAGTTTC 59.449 43.478 0.00 0.00 0.00 2.78
7853 8568 1.269726 GGGTGGTGTTCATTGTTGCAG 60.270 52.381 0.00 0.00 0.00 4.41
7854 8569 0.749649 GGGTGGTGTTCATTGTTGCA 59.250 50.000 0.00 0.00 0.00 4.08
7855 8570 0.749649 TGGGTGGTGTTCATTGTTGC 59.250 50.000 0.00 0.00 0.00 4.17
7856 8571 2.305928 TCTGGGTGGTGTTCATTGTTG 58.694 47.619 0.00 0.00 0.00 3.33
7857 8572 2.746279 TCTGGGTGGTGTTCATTGTT 57.254 45.000 0.00 0.00 0.00 2.83
7863 8582 0.035056 CTGGGATCTGGGTGGTGTTC 60.035 60.000 0.00 0.00 0.00 3.18
7866 8585 0.698238 TTTCTGGGATCTGGGTGGTG 59.302 55.000 0.00 0.00 0.00 4.17
7871 8590 3.009033 TGTTGTAGTTTCTGGGATCTGGG 59.991 47.826 0.00 0.00 0.00 4.45
7923 8642 7.707893 CCAGTTCAATTTTCAATCAAGAAGTGT 59.292 33.333 0.00 0.00 34.70 3.55
7935 8654 7.872483 GCCTTCTTTTATCCAGTTCAATTTTCA 59.128 33.333 0.00 0.00 0.00 2.69
7941 8660 4.394729 ACGCCTTCTTTTATCCAGTTCAA 58.605 39.130 0.00 0.00 0.00 2.69
7964 8684 2.145958 AGATGATCCAAGCGTCGATG 57.854 50.000 0.00 0.00 0.00 3.84
7965 8685 2.101415 TGAAGATGATCCAAGCGTCGAT 59.899 45.455 0.00 0.00 0.00 3.59
7966 8686 1.476488 TGAAGATGATCCAAGCGTCGA 59.524 47.619 0.00 0.00 0.00 4.20
7968 8688 1.596727 GCTGAAGATGATCCAAGCGTC 59.403 52.381 0.00 0.00 0.00 5.19
7969 8689 1.065926 TGCTGAAGATGATCCAAGCGT 60.066 47.619 6.99 0.00 0.00 5.07
7970 8690 1.598132 CTGCTGAAGATGATCCAAGCG 59.402 52.381 6.99 0.00 0.00 4.68
7971 8691 1.948145 CCTGCTGAAGATGATCCAAGC 59.052 52.381 5.06 5.06 0.00 4.01
7976 8696 4.268797 TCATAGCCTGCTGAAGATGATC 57.731 45.455 0.97 0.00 0.00 2.92
8230 8951 9.780413 GAAGGAAAAGATGATCTGTGTAATTTC 57.220 33.333 0.00 1.26 0.00 2.17
8233 8954 8.324306 TCTGAAGGAAAAGATGATCTGTGTAAT 58.676 33.333 0.00 0.00 0.00 1.89


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

AutoCloner maintained by Alex Coulton.