Multiple sequence alignment - TraesCS1D01G090300

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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 TraesCS1D01G090300 chr1D 100.000 5530 0 0 1 5530 76786658 76792187 0.000000e+00 10213.0
1 TraesCS1D01G090300 chr1D 98.361 122 2 0 4469 4590 76791003 76791124 1.210000e-51 215.0
2 TraesCS1D01G090300 chr1D 98.361 122 2 0 4346 4467 76791126 76791247 1.210000e-51 215.0
3 TraesCS1D01G090300 chr1D 86.331 139 16 2 4865 5003 377372599 377372734 1.240000e-31 148.0
4 TraesCS1D01G090300 chr1D 82.192 146 24 2 4875 5020 347198674 347198531 2.090000e-24 124.0
5 TraesCS1D01G090300 chr1B 96.130 2687 62 12 1809 4467 120396850 120399522 0.000000e+00 4348.0
6 TraesCS1D01G090300 chr1B 92.909 1100 47 14 852 1946 120395718 120396791 0.000000e+00 1570.0
7 TraesCS1D01G090300 chr1B 92.376 564 39 3 4469 5032 120399402 120399961 0.000000e+00 800.0
8 TraesCS1D01G090300 chr1B 87.872 470 43 8 383 848 120393209 120393668 1.750000e-149 540.0
9 TraesCS1D01G090300 chr1B 93.220 118 7 1 5220 5337 120401684 120401800 7.360000e-39 172.0
10 TraesCS1D01G090300 chr1B 85.106 94 13 1 4910 5003 634016299 634016391 1.640000e-15 95.3
11 TraesCS1D01G090300 chr1B 100.000 35 0 0 1784 1818 120396795 120396829 1.290000e-06 65.8
12 TraesCS1D01G090300 chr1A 97.010 1505 39 3 2968 4467 108073061 108074564 0.000000e+00 2525.0
13 TraesCS1D01G090300 chr1A 97.737 1193 26 1 1784 2976 108071753 108072944 0.000000e+00 2052.0
14 TraesCS1D01G090300 chr1A 92.179 1317 81 15 362 1668 108070064 108071368 0.000000e+00 1842.0
15 TraesCS1D01G090300 chr1A 94.394 553 26 3 4469 5017 108074444 108074995 0.000000e+00 845.0
16 TraesCS1D01G090300 chr1A 96.797 281 7 1 1666 1946 108071471 108071749 8.390000e-128 468.0
17 TraesCS1D01G090300 chr1A 84.848 462 34 16 5099 5530 108074995 108075450 3.060000e-117 433.0
18 TraesCS1D01G090300 chr1A 91.667 168 14 0 136 303 108069277 108069444 3.330000e-57 233.0
19 TraesCS1D01G090300 chr1A 91.304 138 12 0 1 138 108068892 108069029 7.310000e-44 189.0
20 TraesCS1D01G090300 chr1A 83.051 177 21 6 436 610 367025288 367025119 9.590000e-33 152.0
21 TraesCS1D01G090300 chr1A 83.133 166 20 2 440 604 291255980 291255822 1.610000e-30 145.0
22 TraesCS1D01G090300 chr1A 92.754 69 4 1 305 372 108069978 108070046 1.270000e-16 99.0
23 TraesCS1D01G090300 chr1A 81.000 100 15 4 4905 5002 184033329 184033426 5.940000e-10 76.8
24 TraesCS1D01G090300 chr4A 84.524 168 18 5 437 604 469243057 469242898 5.730000e-35 159.0
25 TraesCS1D01G090300 chr4A 82.143 168 20 8 437 601 574285256 574285416 9.660000e-28 135.0
26 TraesCS1D01G090300 chr4A 95.238 42 1 1 4967 5007 673412839 673412798 1.290000e-06 65.8
27 TraesCS1D01G090300 chr4A 90.476 42 2 2 565 606 221373480 221373519 3.000000e-03 54.7
28 TraesCS1D01G090300 chr5D 87.050 139 17 1 4865 5003 138409236 138409099 7.420000e-34 156.0
29 TraesCS1D01G090300 chr5D 84.800 125 17 2 446 568 59886365 59886241 2.090000e-24 124.0
30 TraesCS1D01G090300 chr3A 83.140 172 21 2 436 606 681178049 681178213 3.450000e-32 150.0
31 TraesCS1D01G090300 chr4D 82.738 168 19 8 437 601 29317169 29317009 2.080000e-29 141.0
32 TraesCS1D01G090300 chr5B 85.271 129 16 3 436 562 570905737 570905864 4.500000e-26 130.0
33 TraesCS1D01G090300 chr6A 81.065 169 24 4 437 604 21556681 21556842 1.620000e-25 128.0
34 TraesCS1D01G090300 chrUn 87.952 83 8 2 4862 4943 74889901 74889982 4.560000e-16 97.1
35 TraesCS1D01G090300 chrUn 87.952 83 8 2 4862 4943 75347093 75347174 4.560000e-16 97.1
36 TraesCS1D01G090300 chrUn 87.952 83 8 2 4862 4943 326635197 326635278 4.560000e-16 97.1
37 TraesCS1D01G090300 chr6D 87.952 83 8 2 4862 4943 471622503 471622584 4.560000e-16 97.1
38 TraesCS1D01G090300 chr7A 91.935 62 3 2 4947 5007 353964881 353964821 9.870000e-13 86.1
39 TraesCS1D01G090300 chr2A 100.000 28 0 0 579 606 72434593 72434620 1.000000e-02 52.8


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 TraesCS1D01G090300 chr1D 76786658 76792187 5529 False 3547.666667 10213 98.907333 1 5530 3 chr1D.!!$F2 5529
1 TraesCS1D01G090300 chr1B 120393209 120401800 8591 False 1249.300000 4348 93.751167 383 5337 6 chr1B.!!$F2 4954
2 TraesCS1D01G090300 chr1A 108068892 108075450 6558 False 965.111111 2525 93.187778 1 5530 9 chr1A.!!$F2 5529

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
106 107 0.321564 TGGAGACCGCAAGATGTTGG 60.322 55.000 4.57 0.00 43.02 3.77 F
132 133 0.461961 GAGCTGACGAGGGCTACAAT 59.538 55.000 0.00 0.00 39.05 2.71 F
1160 4028 0.618458 ATTAGCTCCGTGGGCTTCAA 59.382 50.000 3.53 0.00 40.74 2.69 F
1416 4284 0.811616 GCATGCGGAGGGTAAGTGAG 60.812 60.000 0.00 0.00 0.00 3.51 F
1482 4350 2.036098 TCTGGCCATGGTGCTTGG 59.964 61.111 14.67 0.00 37.31 3.61 F
1948 5117 2.304751 GGTTACCACCGTCTGTATGG 57.695 55.000 0.00 0.00 39.57 2.74 F
2102 5271 3.338249 CTGCTCCCGATGAAAAAGAAGA 58.662 45.455 0.00 0.00 0.00 2.87 F
2480 5649 3.623510 GTGAATTCACTGGCTTACCTAGC 59.376 47.826 27.66 0.00 44.96 3.42 F
3942 7236 0.798159 TTGACAGCATGCGACATGAC 59.202 50.000 19.56 6.12 42.53 3.06 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1888 4863 0.036732 GTGACATGGGAAGCCACAGA 59.963 55.000 0.00 0.0 0.00 3.41 R
1948 5117 7.923878 TCATTTTAGCCCTTTTACTTGTGAAAC 59.076 33.333 0.00 0.0 37.35 2.78 R
2549 5718 1.342175 GGAGCTGGTAGGTCTGGTAGT 60.342 57.143 0.00 0.0 42.10 2.73 R
3297 6591 0.102481 GCTCGTCTATGGCTCGGAAA 59.898 55.000 0.00 0.0 0.00 3.13 R
3300 6594 1.007964 CTGCTCGTCTATGGCTCGG 60.008 63.158 0.00 0.0 0.00 4.63 R
3877 7171 1.293498 GCCTCTCCTTGTCGAAGCA 59.707 57.895 0.00 0.0 0.00 3.91 R
3898 7192 2.037772 GCCGAGGATGTTCATCAGGTAT 59.962 50.000 13.64 0.0 0.00 2.73 R
4462 7784 0.108945 GGAATCAAGCAGCAACTGGC 60.109 55.000 0.00 0.0 45.30 4.85 R
5407 10361 0.030504 CCGAGCATTGCACAACACAA 59.969 50.000 11.91 0.0 0.00 3.33 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
31 32 4.260620 GCGGATGTTGTACCAACACATATC 60.261 45.833 11.62 6.03 34.61 1.63
37 38 7.441890 TGTTGTACCAACACATATCGAAAAT 57.558 32.000 5.73 0.00 34.61 1.82
50 51 9.352784 CACATATCGAAAATGCCTAAAAAGAAA 57.647 29.630 10.20 0.00 0.00 2.52
55 56 5.387342 CGAAAATGCCTAAAAAGAAAGTGCG 60.387 40.000 0.00 0.00 0.00 5.34
60 61 3.795488 GCCTAAAAAGAAAGTGCGCTTGT 60.795 43.478 14.36 3.83 34.71 3.16
67 68 2.225019 AGAAAGTGCGCTTGTGAAGATG 59.775 45.455 14.36 0.00 34.71 2.90
76 77 0.865111 TTGTGAAGATGCGAACCACG 59.135 50.000 0.00 0.00 45.66 4.94
94 95 0.669625 CGTCCCTTTCGTTGGAGACC 60.670 60.000 0.00 0.00 0.00 3.85
97 98 1.301401 CCTTTCGTTGGAGACCGCA 60.301 57.895 0.00 0.00 0.00 5.69
106 107 0.321564 TGGAGACCGCAAGATGTTGG 60.322 55.000 4.57 0.00 43.02 3.77
121 122 0.737715 GTTGGCCACTAGAGCTGACG 60.738 60.000 3.88 0.00 0.00 4.35
132 133 0.461961 GAGCTGACGAGGGCTACAAT 59.538 55.000 0.00 0.00 39.05 2.71
163 414 6.929606 AGAACTAAAACAACAACGCTAGATCT 59.070 34.615 0.00 0.00 0.00 2.75
164 415 6.707599 ACTAAAACAACAACGCTAGATCTC 57.292 37.500 0.00 0.00 0.00 2.75
175 426 8.359060 ACAACGCTAGATCTCAAAAGAATATC 57.641 34.615 0.00 0.00 34.49 1.63
179 430 9.553064 ACGCTAGATCTCAAAAGAATATCAAAT 57.447 29.630 0.00 0.00 34.49 2.32
189 440 9.075519 TCAAAAGAATATCAAATGCGAACATTC 57.924 29.630 0.00 0.00 45.90 2.67
199 450 6.533012 TCAAATGCGAACATTCTGTTGAAAAA 59.467 30.769 0.00 0.00 45.90 1.94
205 456 6.506357 GCGAACATTCTGTTGAAAAAGTGAAC 60.506 38.462 0.00 0.00 41.28 3.18
217 468 6.900189 TGAAAAAGTGAACTGTTGAAACGTA 58.100 32.000 0.00 0.00 0.00 3.57
272 523 7.953005 AAAACTCAAACATTTTTGGGGAAAT 57.047 28.000 8.98 0.00 46.22 2.17
451 1262 6.752815 CAGAATCTAGTACTCCCTTCGTTTTC 59.247 42.308 0.00 0.00 0.00 2.29
462 1273 6.715264 ACTCCCTTCGTTTTCAAACATAAGAT 59.285 34.615 12.74 0.00 38.81 2.40
463 1274 7.230712 ACTCCCTTCGTTTTCAAACATAAGATT 59.769 33.333 12.74 0.00 38.81 2.40
551 1362 7.712639 TCACTCATTTTGCTTCATATCTAGTCC 59.287 37.037 0.00 0.00 0.00 3.85
553 1364 6.582636 TCATTTTGCTTCATATCTAGTCCGT 58.417 36.000 0.00 0.00 0.00 4.69
594 1406 8.794553 TCTCTAAAAGCCTTATATCTAGGAACG 58.205 37.037 7.77 0.00 34.56 3.95
848 1663 3.195610 TGGAGGACTACAGTGTAATGCTG 59.804 47.826 10.66 0.00 39.67 4.41
883 3744 4.767255 GGCAGGCTGACGGTGGAG 62.767 72.222 20.86 0.00 0.00 3.86
930 3791 1.396996 CCAACGGATGGTAAAAGCTCG 59.603 52.381 0.00 0.00 44.85 5.03
1151 4019 2.487532 CCCCGTCGATTAGCTCCGT 61.488 63.158 0.00 0.00 0.00 4.69
1160 4028 0.618458 ATTAGCTCCGTGGGCTTCAA 59.382 50.000 3.53 0.00 40.74 2.69
1281 4149 1.402896 CGAGCAAGGGGAGGAGCATA 61.403 60.000 0.00 0.00 0.00 3.14
1416 4284 0.811616 GCATGCGGAGGGTAAGTGAG 60.812 60.000 0.00 0.00 0.00 3.51
1482 4350 2.036098 TCTGGCCATGGTGCTTGG 59.964 61.111 14.67 0.00 37.31 3.61
1514 4382 4.425520 CTGTGATCCGTCTCCTTTTCTAC 58.574 47.826 0.00 0.00 0.00 2.59
1519 4387 3.437213 TCCGTCTCCTTTTCTACCATGA 58.563 45.455 0.00 0.00 0.00 3.07
1560 4428 6.494893 TGAACTGCTGTAATTTATGGTGAC 57.505 37.500 0.00 0.00 0.00 3.67
1633 4501 3.252458 GTCAATGCTAAACGAAAGGGTGT 59.748 43.478 0.00 0.00 0.00 4.16
1888 4863 7.064728 CAGCTAACTCCGCTAGAAATTTAAGTT 59.935 37.037 0.00 0.00 35.63 2.66
1948 5117 2.304751 GGTTACCACCGTCTGTATGG 57.695 55.000 0.00 0.00 39.57 2.74
2102 5271 3.338249 CTGCTCCCGATGAAAAAGAAGA 58.662 45.455 0.00 0.00 0.00 2.87
2170 5339 7.939782 TGGTCATAAACGTATTATTCTCCGTA 58.060 34.615 0.00 0.00 32.49 4.02
2480 5649 3.623510 GTGAATTCACTGGCTTACCTAGC 59.376 47.826 27.66 0.00 44.96 3.42
2549 5718 8.902540 TTCTACAAAAGCTCAAGAAGTATGAA 57.097 30.769 0.00 0.00 0.00 2.57
2952 6121 7.116376 TGTTTGTAGTTCTCATTTAGCTTCTCG 59.884 37.037 0.00 0.00 0.00 4.04
3139 6433 4.641396 TGGATAATGGAGTTTGCTATCCG 58.359 43.478 0.00 0.00 40.57 4.18
3877 7171 3.721575 TGATGGCAGGGATAGTATGGTTT 59.278 43.478 0.00 0.00 0.00 3.27
3898 7192 1.137086 GCTTCGACAAGGAGAGGCATA 59.863 52.381 0.00 0.00 38.99 3.14
3942 7236 0.798159 TTGACAGCATGCGACATGAC 59.202 50.000 19.56 6.12 42.53 3.06
3972 7266 3.334583 TCCAGTCACAGGCAGAATTAC 57.665 47.619 0.00 0.00 0.00 1.89
4325 7647 2.270352 TGTTTTTCGTGGGAGCATCT 57.730 45.000 0.00 0.00 33.73 2.90
4335 7657 0.901124 GGGAGCATCTGTCTCAGTGT 59.099 55.000 0.00 0.00 33.73 3.55
4359 7681 0.955428 GACGGTGCTGCTTGATTCCA 60.955 55.000 0.00 0.00 0.00 3.53
4441 7763 2.587322 TAGTTGGCGCATCCCCGAAG 62.587 60.000 10.83 0.00 0.00 3.79
4453 7775 2.815647 CCGAAGGCCGAAGCAGTC 60.816 66.667 0.00 0.00 46.14 3.51
4454 7776 2.262915 CGAAGGCCGAAGCAGTCT 59.737 61.111 0.00 0.00 42.56 3.24
4455 7777 2.097038 CGAAGGCCGAAGCAGTCTG 61.097 63.158 0.00 0.00 42.56 3.51
4456 7778 2.359230 AAGGCCGAAGCAGTCTGC 60.359 61.111 17.48 17.48 45.46 4.26
4459 7781 3.123620 GCCGAAGCAGTCTGCCAG 61.124 66.667 21.32 12.30 46.52 4.85
4460 7782 2.345244 CCGAAGCAGTCTGCCAGT 59.655 61.111 21.32 7.09 46.52 4.00
4461 7783 1.302033 CCGAAGCAGTCTGCCAGTT 60.302 57.895 21.32 9.33 46.52 3.16
4462 7784 1.572085 CCGAAGCAGTCTGCCAGTTG 61.572 60.000 21.32 10.53 46.52 3.16
4463 7785 1.578423 GAAGCAGTCTGCCAGTTGC 59.422 57.895 21.32 13.53 46.52 4.17
4464 7786 1.860484 GAAGCAGTCTGCCAGTTGCC 61.860 60.000 21.32 0.00 46.52 4.52
4465 7787 2.595463 GCAGTCTGCCAGTTGCCA 60.595 61.111 14.27 0.00 37.42 4.92
4466 7788 2.623915 GCAGTCTGCCAGTTGCCAG 61.624 63.158 14.27 0.00 37.42 4.85
4467 7789 1.228063 CAGTCTGCCAGTTGCCAGT 60.228 57.895 0.00 0.00 40.16 4.00
4468 7790 0.820891 CAGTCTGCCAGTTGCCAGTT 60.821 55.000 0.00 0.00 40.16 3.16
4469 7791 0.820891 AGTCTGCCAGTTGCCAGTTG 60.821 55.000 0.00 0.00 40.16 3.16
4470 7792 2.195567 TCTGCCAGTTGCCAGTTGC 61.196 57.895 0.00 0.00 40.16 4.17
4471 7793 2.123769 TGCCAGTTGCCAGTTGCT 60.124 55.556 0.00 0.00 42.00 3.91
4472 7794 2.337532 GCCAGTTGCCAGTTGCTG 59.662 61.111 0.00 0.00 42.00 4.41
4473 7795 2.337532 CCAGTTGCCAGTTGCTGC 59.662 61.111 0.00 0.00 42.00 5.25
4474 7796 2.198287 CCAGTTGCCAGTTGCTGCT 61.198 57.895 0.00 0.00 42.00 4.24
4475 7797 1.737816 CAGTTGCCAGTTGCTGCTT 59.262 52.632 0.00 0.00 42.00 3.91
4476 7798 0.596600 CAGTTGCCAGTTGCTGCTTG 60.597 55.000 0.00 0.00 42.00 4.01
4477 7799 0.752743 AGTTGCCAGTTGCTGCTTGA 60.753 50.000 0.00 0.00 42.00 3.02
4478 7800 0.316204 GTTGCCAGTTGCTGCTTGAT 59.684 50.000 0.00 0.00 42.00 2.57
4479 7801 1.042229 TTGCCAGTTGCTGCTTGATT 58.958 45.000 0.00 0.00 42.00 2.57
4480 7802 0.599558 TGCCAGTTGCTGCTTGATTC 59.400 50.000 0.00 0.00 42.00 2.52
4481 7803 0.108945 GCCAGTTGCTGCTTGATTCC 60.109 55.000 0.00 0.00 36.87 3.01
4482 7804 1.250328 CCAGTTGCTGCTTGATTCCA 58.750 50.000 0.00 0.00 0.00 3.53
4483 7805 1.614903 CCAGTTGCTGCTTGATTCCAA 59.385 47.619 0.00 0.00 0.00 3.53
4484 7806 2.608752 CCAGTTGCTGCTTGATTCCAAC 60.609 50.000 0.00 0.00 36.83 3.77
4485 7807 1.615392 AGTTGCTGCTTGATTCCAACC 59.385 47.619 0.00 0.00 37.17 3.77
4486 7808 1.615392 GTTGCTGCTTGATTCCAACCT 59.385 47.619 0.00 0.00 31.96 3.50
4487 7809 1.250328 TGCTGCTTGATTCCAACCTG 58.750 50.000 0.00 0.00 0.00 4.00
4488 7810 1.202915 TGCTGCTTGATTCCAACCTGA 60.203 47.619 0.00 0.00 0.00 3.86
4489 7811 1.200948 GCTGCTTGATTCCAACCTGAC 59.799 52.381 0.00 0.00 0.00 3.51
4490 7812 2.507484 CTGCTTGATTCCAACCTGACA 58.493 47.619 0.00 0.00 0.00 3.58
4491 7813 3.087031 CTGCTTGATTCCAACCTGACAT 58.913 45.455 0.00 0.00 0.00 3.06
4492 7814 3.084039 TGCTTGATTCCAACCTGACATC 58.916 45.455 0.00 0.00 0.00 3.06
4493 7815 3.084039 GCTTGATTCCAACCTGACATCA 58.916 45.455 0.00 0.00 0.00 3.07
4494 7816 3.698040 GCTTGATTCCAACCTGACATCAT 59.302 43.478 0.00 0.00 0.00 2.45
4495 7817 4.439700 GCTTGATTCCAACCTGACATCATG 60.440 45.833 0.00 0.00 0.00 3.07
4496 7818 3.018856 TGATTCCAACCTGACATCATGC 58.981 45.455 0.00 0.00 0.00 4.06
4497 7819 2.885135 TTCCAACCTGACATCATGCT 57.115 45.000 0.00 0.00 0.00 3.79
4498 7820 2.118313 TCCAACCTGACATCATGCTG 57.882 50.000 0.00 0.00 0.00 4.41
4499 7821 1.100510 CCAACCTGACATCATGCTGG 58.899 55.000 1.02 4.24 0.00 4.85
4500 7822 1.100510 CAACCTGACATCATGCTGGG 58.899 55.000 1.02 0.00 0.00 4.45
4501 7823 0.700564 AACCTGACATCATGCTGGGT 59.299 50.000 1.02 0.00 0.00 4.51
4502 7824 0.700564 ACCTGACATCATGCTGGGTT 59.299 50.000 1.02 0.00 0.00 4.11
4503 7825 1.100510 CCTGACATCATGCTGGGTTG 58.899 55.000 1.02 0.00 0.00 3.77
4504 7826 1.100510 CTGACATCATGCTGGGTTGG 58.899 55.000 1.02 0.00 0.00 3.77
4505 7827 0.323633 TGACATCATGCTGGGTTGGG 60.324 55.000 1.02 0.00 0.00 4.12
4506 7828 0.323725 GACATCATGCTGGGTTGGGT 60.324 55.000 1.02 0.00 0.00 4.51
4507 7829 0.612732 ACATCATGCTGGGTTGGGTG 60.613 55.000 1.02 0.00 0.00 4.61
4508 7830 1.683365 ATCATGCTGGGTTGGGTGC 60.683 57.895 0.00 0.00 0.00 5.01
4509 7831 2.159101 ATCATGCTGGGTTGGGTGCT 62.159 55.000 0.00 0.00 0.00 4.40
4510 7832 2.036256 ATGCTGGGTTGGGTGCTC 59.964 61.111 0.00 0.00 0.00 4.26
4511 7833 2.844195 ATGCTGGGTTGGGTGCTCA 61.844 57.895 0.00 0.00 0.00 4.26
4512 7834 2.036256 GCTGGGTTGGGTGCTCAT 59.964 61.111 0.00 0.00 0.00 2.90
4513 7835 1.302949 GCTGGGTTGGGTGCTCATA 59.697 57.895 0.00 0.00 0.00 2.15
4514 7836 0.323360 GCTGGGTTGGGTGCTCATAA 60.323 55.000 0.00 0.00 0.00 1.90
4515 7837 1.890573 GCTGGGTTGGGTGCTCATAAA 60.891 52.381 0.00 0.00 0.00 1.40
4516 7838 2.738743 CTGGGTTGGGTGCTCATAAAT 58.261 47.619 0.00 0.00 0.00 1.40
4517 7839 2.428171 CTGGGTTGGGTGCTCATAAATG 59.572 50.000 0.00 0.00 0.00 2.32
4518 7840 2.042297 TGGGTTGGGTGCTCATAAATGA 59.958 45.455 0.00 0.00 35.16 2.57
4519 7841 3.299503 GGGTTGGGTGCTCATAAATGAT 58.700 45.455 0.00 0.00 36.02 2.45
4520 7842 3.706086 GGGTTGGGTGCTCATAAATGATT 59.294 43.478 0.00 0.00 36.02 2.57
4521 7843 4.441913 GGGTTGGGTGCTCATAAATGATTG 60.442 45.833 0.00 0.00 36.02 2.67
4522 7844 4.160252 GGTTGGGTGCTCATAAATGATTGT 59.840 41.667 0.00 0.00 36.02 2.71
4523 7845 5.337491 GGTTGGGTGCTCATAAATGATTGTT 60.337 40.000 0.00 0.00 36.02 2.83
4524 7846 5.999205 TGGGTGCTCATAAATGATTGTTT 57.001 34.783 0.00 0.00 36.02 2.83
4525 7847 5.722263 TGGGTGCTCATAAATGATTGTTTG 58.278 37.500 0.00 0.00 36.02 2.93
4526 7848 5.479724 TGGGTGCTCATAAATGATTGTTTGA 59.520 36.000 0.00 0.00 36.02 2.69
4527 7849 6.014755 TGGGTGCTCATAAATGATTGTTTGAA 60.015 34.615 0.00 0.00 36.02 2.69
4528 7850 7.043565 GGGTGCTCATAAATGATTGTTTGAAT 58.956 34.615 0.00 0.00 36.02 2.57
4529 7851 7.550196 GGGTGCTCATAAATGATTGTTTGAATT 59.450 33.333 0.00 0.00 36.02 2.17
4530 7852 8.385111 GGTGCTCATAAATGATTGTTTGAATTG 58.615 33.333 0.00 0.00 36.02 2.32
4531 7853 7.901377 GTGCTCATAAATGATTGTTTGAATTGC 59.099 33.333 0.00 0.00 36.02 3.56
4532 7854 7.114920 GCTCATAAATGATTGTTTGAATTGCG 58.885 34.615 0.00 0.00 36.02 4.85
4533 7855 7.201461 GCTCATAAATGATTGTTTGAATTGCGT 60.201 33.333 0.00 0.00 36.02 5.24
4534 7856 8.172159 TCATAAATGATTGTTTGAATTGCGTC 57.828 30.769 0.00 0.00 0.00 5.19
4535 7857 8.028354 TCATAAATGATTGTTTGAATTGCGTCT 58.972 29.630 0.00 0.00 0.00 4.18
4536 7858 6.695292 AAATGATTGTTTGAATTGCGTCTC 57.305 33.333 0.00 0.00 0.00 3.36
4537 7859 4.159377 TGATTGTTTGAATTGCGTCTCC 57.841 40.909 0.00 0.00 0.00 3.71
4538 7860 3.567585 TGATTGTTTGAATTGCGTCTCCA 59.432 39.130 0.00 0.00 0.00 3.86
4539 7861 4.037327 TGATTGTTTGAATTGCGTCTCCAA 59.963 37.500 0.00 0.00 0.00 3.53
4540 7862 4.377839 TTGTTTGAATTGCGTCTCCAAA 57.622 36.364 0.00 0.00 0.00 3.28
4541 7863 4.582701 TGTTTGAATTGCGTCTCCAAAT 57.417 36.364 0.00 0.00 0.00 2.32
4542 7864 5.697473 TGTTTGAATTGCGTCTCCAAATA 57.303 34.783 0.00 0.00 0.00 1.40
4543 7865 6.266168 TGTTTGAATTGCGTCTCCAAATAT 57.734 33.333 0.00 0.00 0.00 1.28
4544 7866 6.092092 TGTTTGAATTGCGTCTCCAAATATG 58.908 36.000 0.00 0.00 0.00 1.78
4545 7867 5.895636 TTGAATTGCGTCTCCAAATATGT 57.104 34.783 0.00 0.00 0.00 2.29
4546 7868 6.993786 TTGAATTGCGTCTCCAAATATGTA 57.006 33.333 0.00 0.00 0.00 2.29
4547 7869 6.603237 TGAATTGCGTCTCCAAATATGTAG 57.397 37.500 0.00 0.00 0.00 2.74
4548 7870 6.112734 TGAATTGCGTCTCCAAATATGTAGT 58.887 36.000 0.00 0.00 0.00 2.73
4549 7871 6.597672 TGAATTGCGTCTCCAAATATGTAGTT 59.402 34.615 0.00 0.00 0.00 2.24
4550 7872 5.794687 TTGCGTCTCCAAATATGTAGTTG 57.205 39.130 0.00 0.00 0.00 3.16
4551 7873 5.079689 TGCGTCTCCAAATATGTAGTTGA 57.920 39.130 2.11 0.00 33.49 3.18
4552 7874 4.868171 TGCGTCTCCAAATATGTAGTTGAC 59.132 41.667 2.11 0.00 33.49 3.18
4553 7875 4.026804 GCGTCTCCAAATATGTAGTTGACG 60.027 45.833 0.00 0.00 34.44 4.35
4554 7876 4.026804 CGTCTCCAAATATGTAGTTGACGC 60.027 45.833 0.00 0.00 33.49 5.19
4555 7877 4.868171 GTCTCCAAATATGTAGTTGACGCA 59.132 41.667 2.11 0.00 33.49 5.24
4556 7878 5.523916 GTCTCCAAATATGTAGTTGACGCAT 59.476 40.000 2.11 0.00 33.49 4.73
4557 7879 5.753438 TCTCCAAATATGTAGTTGACGCATC 59.247 40.000 2.11 0.00 33.49 3.91
4558 7880 4.814234 TCCAAATATGTAGTTGACGCATCC 59.186 41.667 2.11 0.00 33.49 3.51
4559 7881 4.024048 CCAAATATGTAGTTGACGCATCCC 60.024 45.833 2.11 0.00 33.49 3.85
4560 7882 2.902705 TATGTAGTTGACGCATCCCC 57.097 50.000 0.00 0.00 0.00 4.81
4561 7883 0.179084 ATGTAGTTGACGCATCCCCG 60.179 55.000 0.00 0.00 0.00 5.73
4562 7884 1.252215 TGTAGTTGACGCATCCCCGA 61.252 55.000 0.00 0.00 0.00 5.14
4563 7885 0.108520 GTAGTTGACGCATCCCCGAA 60.109 55.000 0.00 0.00 0.00 4.30
4641 7966 3.360867 TGGTGTTGAATGTTGTCCTTGT 58.639 40.909 0.00 0.00 0.00 3.16
4676 8001 1.666189 GCAGTTTGATAGGTCGAAGGC 59.334 52.381 0.00 0.00 0.00 4.35
4703 8028 4.192317 GGTGGTTCTACACATCTGAATCC 58.808 47.826 0.00 0.00 43.08 3.01
4895 8221 5.972327 TTATTGGTCCCCTCCGTATTTTA 57.028 39.130 0.00 0.00 0.00 1.52
4912 8238 8.327429 CCGTATTTTATGCCAAATTTTGATCAC 58.673 33.333 10.72 0.00 0.00 3.06
5024 8350 8.556213 TTTTGTGATGTATAACTTGTACTCCC 57.444 34.615 0.00 0.00 0.00 4.30
5025 8351 7.490657 TTGTGATGTATAACTTGTACTCCCT 57.509 36.000 0.00 0.00 0.00 4.20
5026 8352 7.108841 TGTGATGTATAACTTGTACTCCCTC 57.891 40.000 0.00 0.00 0.00 4.30
5027 8353 6.097839 TGTGATGTATAACTTGTACTCCCTCC 59.902 42.308 0.00 0.00 0.00 4.30
5028 8354 5.301045 TGATGTATAACTTGTACTCCCTCCG 59.699 44.000 0.00 0.00 0.00 4.63
5029 8355 4.603131 TGTATAACTTGTACTCCCTCCGT 58.397 43.478 0.00 0.00 0.00 4.69
5030 8356 5.018809 TGTATAACTTGTACTCCCTCCGTT 58.981 41.667 0.00 0.00 0.00 4.44
5031 8357 5.481473 TGTATAACTTGTACTCCCTCCGTTT 59.519 40.000 0.00 0.00 0.00 3.60
5032 8358 3.397849 AACTTGTACTCCCTCCGTTTC 57.602 47.619 0.00 0.00 0.00 2.78
5033 8359 2.322658 ACTTGTACTCCCTCCGTTTCA 58.677 47.619 0.00 0.00 0.00 2.69
5034 8360 2.904434 ACTTGTACTCCCTCCGTTTCAT 59.096 45.455 0.00 0.00 0.00 2.57
5035 8361 4.091549 ACTTGTACTCCCTCCGTTTCATA 58.908 43.478 0.00 0.00 0.00 2.15
5036 8362 4.159879 ACTTGTACTCCCTCCGTTTCATAG 59.840 45.833 0.00 0.00 0.00 2.23
5037 8363 3.705051 TGTACTCCCTCCGTTTCATAGT 58.295 45.455 0.00 0.00 0.00 2.12
5038 8364 4.858850 TGTACTCCCTCCGTTTCATAGTA 58.141 43.478 0.00 0.00 0.00 1.82
5039 8365 5.452255 TGTACTCCCTCCGTTTCATAGTAT 58.548 41.667 0.00 0.00 0.00 2.12
5040 8366 6.604171 TGTACTCCCTCCGTTTCATAGTATA 58.396 40.000 0.00 0.00 0.00 1.47
5041 8367 6.713903 TGTACTCCCTCCGTTTCATAGTATAG 59.286 42.308 0.00 0.00 0.00 1.31
5042 8368 5.078256 ACTCCCTCCGTTTCATAGTATAGG 58.922 45.833 0.00 0.00 0.00 2.57
5043 8369 5.163012 ACTCCCTCCGTTTCATAGTATAGGA 60.163 44.000 0.00 0.00 0.00 2.94
5044 8370 5.322754 TCCCTCCGTTTCATAGTATAGGAG 58.677 45.833 1.89 1.89 42.36 3.69
5045 8371 5.078256 CCCTCCGTTTCATAGTATAGGAGT 58.922 45.833 7.67 0.00 41.44 3.85
5046 8372 5.047943 CCCTCCGTTTCATAGTATAGGAGTG 60.048 48.000 7.67 0.00 41.44 3.51
5047 8373 5.535406 CCTCCGTTTCATAGTATAGGAGTGT 59.465 44.000 7.67 0.00 41.44 3.55
5048 8374 6.040616 CCTCCGTTTCATAGTATAGGAGTGTT 59.959 42.308 7.67 0.00 41.44 3.32
5049 8375 7.414222 TCCGTTTCATAGTATAGGAGTGTTT 57.586 36.000 0.00 0.00 30.70 2.83
5050 8376 7.844009 TCCGTTTCATAGTATAGGAGTGTTTT 58.156 34.615 0.00 0.00 30.70 2.43
5051 8377 8.316214 TCCGTTTCATAGTATAGGAGTGTTTTT 58.684 33.333 0.00 0.00 30.70 1.94
5052 8378 8.388103 CCGTTTCATAGTATAGGAGTGTTTTTG 58.612 37.037 0.00 0.00 30.70 2.44
5053 8379 9.146984 CGTTTCATAGTATAGGAGTGTTTTTGA 57.853 33.333 0.00 0.00 30.70 2.69
5068 8394 6.358118 TGTTTTTGACACTAGTGTGATGTC 57.642 37.500 32.51 17.72 46.55 3.06
5075 8401 6.319229 GACACTAGTGTGATGTCAATAACG 57.681 41.667 32.51 0.00 46.55 3.18
5076 8402 4.625742 ACACTAGTGTGATGTCAATAACGC 59.374 41.667 27.41 0.00 46.55 4.84
5077 8403 4.864806 CACTAGTGTGATGTCAATAACGCT 59.135 41.667 15.06 0.00 46.55 5.07
5078 8404 5.004821 CACTAGTGTGATGTCAATAACGCTC 59.995 44.000 15.06 0.00 46.55 5.03
5079 8405 4.193826 AGTGTGATGTCAATAACGCTCT 57.806 40.909 0.00 0.00 33.33 4.09
5080 8406 4.569943 AGTGTGATGTCAATAACGCTCTT 58.430 39.130 0.00 0.00 33.33 2.85
5081 8407 5.720202 AGTGTGATGTCAATAACGCTCTTA 58.280 37.500 0.00 0.00 33.33 2.10
5082 8408 6.341316 AGTGTGATGTCAATAACGCTCTTAT 58.659 36.000 0.00 0.00 33.33 1.73
5083 8409 7.489160 AGTGTGATGTCAATAACGCTCTTATA 58.511 34.615 0.00 0.00 33.33 0.98
5084 8410 8.144478 AGTGTGATGTCAATAACGCTCTTATAT 58.856 33.333 0.00 0.00 33.33 0.86
5085 8411 9.406828 GTGTGATGTCAATAACGCTCTTATATA 57.593 33.333 0.00 0.00 0.00 0.86
5086 8412 9.626045 TGTGATGTCAATAACGCTCTTATATAG 57.374 33.333 0.00 0.00 0.00 1.31
5087 8413 9.077674 GTGATGTCAATAACGCTCTTATATAGG 57.922 37.037 0.00 0.00 0.00 2.57
5088 8414 9.020731 TGATGTCAATAACGCTCTTATATAGGA 57.979 33.333 0.00 0.00 0.00 2.94
5089 8415 9.291664 GATGTCAATAACGCTCTTATATAGGAC 57.708 37.037 0.00 0.00 0.00 3.85
5090 8416 7.303261 TGTCAATAACGCTCTTATATAGGACG 58.697 38.462 12.11 12.11 0.00 4.79
5091 8417 7.173735 TGTCAATAACGCTCTTATATAGGACGA 59.826 37.037 17.29 3.79 0.00 4.20
5092 8418 8.019669 GTCAATAACGCTCTTATATAGGACGAA 58.980 37.037 17.29 9.47 0.00 3.85
5093 8419 8.235226 TCAATAACGCTCTTATATAGGACGAAG 58.765 37.037 17.29 0.63 0.00 3.79
5094 8420 5.373981 AACGCTCTTATATAGGACGAAGG 57.626 43.478 17.29 0.72 0.00 3.46
5095 8421 3.757493 ACGCTCTTATATAGGACGAAGGG 59.243 47.826 17.29 8.29 0.00 3.95
5096 8422 4.008330 CGCTCTTATATAGGACGAAGGGA 58.992 47.826 9.60 0.00 0.00 4.20
5097 8423 4.095185 CGCTCTTATATAGGACGAAGGGAG 59.905 50.000 9.60 0.00 0.00 4.30
5098 8424 5.011586 GCTCTTATATAGGACGAAGGGAGT 58.988 45.833 0.00 0.00 0.00 3.85
5135 8972 8.739972 AGCGAAAATTCTGGTTAAAATATGACT 58.260 29.630 0.00 0.00 0.00 3.41
5155 8993 5.307196 TGACTCTAAATATGAGGGGGCTAAC 59.693 44.000 0.00 0.00 35.98 2.34
5235 10184 5.879777 TGATCATAAAGTTTCGCCTCAATGA 59.120 36.000 0.00 0.00 0.00 2.57
5261 10210 2.935481 TGGGCAGGGACAGGAAGG 60.935 66.667 0.00 0.00 0.00 3.46
5352 10305 4.436113 TTGATTGATAGGGCATGTGCTA 57.564 40.909 4.84 0.00 41.70 3.49
5358 10311 1.567357 TAGGGCATGTGCTAGTGACA 58.433 50.000 4.84 0.00 41.70 3.58
5379 10332 4.463879 CGGGTGAGGCTGCTCTGG 62.464 72.222 0.00 0.00 0.00 3.86
5381 10334 2.596851 GGGTGAGGCTGCTCTGGAA 61.597 63.158 0.00 0.00 0.00 3.53
5407 10361 4.528076 TCTCCACCTATCTACTCAAGCT 57.472 45.455 0.00 0.00 0.00 3.74
5412 10366 4.081420 CCACCTATCTACTCAAGCTTGTGT 60.081 45.833 30.44 30.44 38.34 3.72
5417 10371 2.872245 TCTACTCAAGCTTGTGTTGTGC 59.128 45.455 32.13 0.00 36.44 4.57
5418 10372 1.462616 ACTCAAGCTTGTGTTGTGCA 58.537 45.000 24.62 4.38 31.51 4.57
5419 10373 1.818060 ACTCAAGCTTGTGTTGTGCAA 59.182 42.857 24.62 3.69 31.51 4.08
5420 10374 2.428171 ACTCAAGCTTGTGTTGTGCAAT 59.572 40.909 24.62 3.66 31.51 3.56
5421 10375 2.792674 CTCAAGCTTGTGTTGTGCAATG 59.207 45.455 25.19 0.00 0.00 2.82
5422 10376 1.259507 CAAGCTTGTGTTGTGCAATGC 59.740 47.619 18.65 0.00 0.00 3.56
5478 10432 0.912486 GTGCCTGATAGTGGGGAAGT 59.088 55.000 0.00 0.00 0.00 3.01
5482 10436 2.972713 GCCTGATAGTGGGGAAGTCATA 59.027 50.000 0.00 0.00 0.00 2.15
5494 10448 3.617263 GGGAAGTCATAAACTAGTGCACG 59.383 47.826 12.01 0.00 37.17 5.34
5507 10461 2.280797 GCACGAAGGGCAGACACA 60.281 61.111 0.00 0.00 0.00 3.72
5510 10464 0.946221 CACGAAGGGCAGACACAGAC 60.946 60.000 0.00 0.00 0.00 3.51
5515 10469 2.574955 GGGCAGACACAGACCGAGT 61.575 63.158 0.00 0.00 0.00 4.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
31 32 5.387342 CGCACTTTCTTTTTAGGCATTTTCG 60.387 40.000 0.00 0.00 0.00 3.46
37 38 1.953686 AGCGCACTTTCTTTTTAGGCA 59.046 42.857 11.47 0.00 0.00 4.75
50 51 1.871772 GCATCTTCACAAGCGCACT 59.128 52.632 11.47 0.00 0.00 4.40
55 56 0.874390 TGGTTCGCATCTTCACAAGC 59.126 50.000 0.00 0.00 0.00 4.01
60 61 0.669318 GGACGTGGTTCGCATCTTCA 60.669 55.000 0.00 0.00 44.19 3.02
67 68 2.664436 CGAAAGGGACGTGGTTCGC 61.664 63.158 0.00 0.00 44.19 4.70
76 77 0.669625 CGGTCTCCAACGAAAGGGAC 60.670 60.000 0.00 0.00 0.00 4.46
94 95 0.729116 CTAGTGGCCAACATCTTGCG 59.271 55.000 7.24 0.00 0.00 4.85
97 98 1.912043 AGCTCTAGTGGCCAACATCTT 59.088 47.619 7.24 0.00 0.00 2.40
106 107 1.435515 CCTCGTCAGCTCTAGTGGC 59.564 63.158 0.00 3.03 0.00 5.01
157 408 9.546428 TCGCATTTGATATTCTTTTGAGATCTA 57.454 29.630 0.00 0.00 0.00 1.98
163 414 8.984891 AATGTTCGCATTTGATATTCTTTTGA 57.015 26.923 0.00 0.00 44.77 2.69
164 415 9.079833 AGAATGTTCGCATTTGATATTCTTTTG 57.920 29.630 0.00 0.00 46.84 2.44
189 440 7.501515 GTTTCAACAGTTCACTTTTTCAACAG 58.498 34.615 0.00 0.00 0.00 3.16
244 495 9.467796 TTCCCCAAAAATGTTTGAGTTTTAAAT 57.532 25.926 10.09 0.00 45.99 1.40
336 1120 0.897621 CTCAAAATTCTGGGCCCACC 59.102 55.000 24.45 0.00 40.81 4.61
579 1390 5.572252 ACTCCCTCCGTTCCTAGATATAAG 58.428 45.833 0.00 0.00 0.00 1.73
593 1404 2.530701 AGGATTGCTATACTCCCTCCG 58.469 52.381 0.00 0.00 0.00 4.63
594 1406 4.984146 AAAGGATTGCTATACTCCCTCC 57.016 45.455 0.00 0.00 0.00 4.30
683 1495 8.608844 AAATGACCGGCAAAAATAAAATTACA 57.391 26.923 0.00 0.00 0.00 2.41
698 1510 1.476488 ACAAGGCATAAAATGACCGGC 59.524 47.619 0.00 0.00 39.88 6.13
782 1596 7.687941 TTGACCATCAGACTATTTTTCCTTC 57.312 36.000 0.00 0.00 0.00 3.46
796 1610 3.483574 GCGATTACGTGTTTGACCATCAG 60.484 47.826 0.00 0.00 41.98 2.90
848 1663 4.156008 CCTGCCAGTTGGTTGTAAGAATAC 59.844 45.833 0.00 0.00 37.57 1.89
883 3744 3.302347 CTGTCCACGTGGAGGAGCC 62.302 68.421 37.04 24.35 46.49 4.70
1151 4019 4.659172 CCCACGCCTTGAAGCCCA 62.659 66.667 0.00 0.00 0.00 5.36
1227 4095 2.445845 CATACCCCTCCGCCTCCA 60.446 66.667 0.00 0.00 0.00 3.86
1248 4116 2.791927 CTCGTCGACATCAGCCGA 59.208 61.111 17.16 4.04 0.00 5.54
1281 4149 1.674057 CTTCTCCACCTTGCTCCGT 59.326 57.895 0.00 0.00 0.00 4.69
1416 4284 2.517166 GGAGGAGGAAATGGCGCC 60.517 66.667 22.73 22.73 0.00 6.53
1482 4350 1.596477 GGATCACAGCGAGATGGCC 60.596 63.158 0.00 0.00 0.00 5.36
1514 4382 7.092079 TCAAAACAGCATATCTTGTTTCATGG 58.908 34.615 12.21 5.84 33.94 3.66
1519 4387 6.421801 GCAGTTCAAAACAGCATATCTTGTTT 59.578 34.615 7.83 7.83 42.68 2.83
1560 4428 0.956633 AGCCACACAGTGAGCAAATG 59.043 50.000 18.48 2.13 35.23 2.32
1570 4438 2.430332 TCCCTTTCAAAAAGCCACACAG 59.570 45.455 0.00 0.00 0.00 3.66
1633 4501 6.038382 ACAAATTTCACAATGCAAATGCTTCA 59.962 30.769 6.97 0.00 42.66 3.02
1834 4809 4.927978 TCTGATGAGAGCTAGCCTTTAC 57.072 45.455 12.13 0.00 0.00 2.01
1888 4863 0.036732 GTGACATGGGAAGCCACAGA 59.963 55.000 0.00 0.00 0.00 3.41
1948 5117 7.923878 TCATTTTAGCCCTTTTACTTGTGAAAC 59.076 33.333 0.00 0.00 37.35 2.78
2293 5462 9.628500 GTAATACCCAATTCAGATAGGACTTTT 57.372 33.333 0.00 0.00 0.00 2.27
2379 5548 8.725148 CACAAGTTGAGTAAAGAGAAATATGCT 58.275 33.333 10.54 0.00 0.00 3.79
2480 5649 5.239525 GGCCTGCATAAAGTTAACCAGATAG 59.760 44.000 0.88 0.00 0.00 2.08
2549 5718 1.342175 GGAGCTGGTAGGTCTGGTAGT 60.342 57.143 0.00 0.00 42.10 2.73
2952 6121 5.193679 AGGGTGTATGATCCAAAGCTAAAC 58.806 41.667 0.00 0.00 0.00 2.01
3055 6349 5.913137 TGGACATAGCCCAAAACATTAAG 57.087 39.130 0.00 0.00 0.00 1.85
3297 6591 0.102481 GCTCGTCTATGGCTCGGAAA 59.898 55.000 0.00 0.00 0.00 3.13
3300 6594 1.007964 CTGCTCGTCTATGGCTCGG 60.008 63.158 0.00 0.00 0.00 4.63
3877 7171 1.293498 GCCTCTCCTTGTCGAAGCA 59.707 57.895 0.00 0.00 0.00 3.91
3898 7192 2.037772 GCCGAGGATGTTCATCAGGTAT 59.962 50.000 13.64 0.00 0.00 2.73
3942 7236 2.232452 CCTGTGACTGGAACTACTCCTG 59.768 54.545 1.83 0.00 45.64 3.86
4196 7493 3.751621 TCGTCGGTATTCTTCTTCGTTC 58.248 45.455 0.00 0.00 0.00 3.95
4325 7647 1.282875 CGTCTGCGACACTGAGACA 59.717 57.895 8.91 0.00 41.33 3.41
4359 7681 0.700564 ACCCAGCATGATGTCAGGTT 59.299 50.000 10.55 0.00 39.69 3.50
4442 7764 3.123620 CTGGCAGACTGCTTCGGC 61.124 66.667 25.92 10.28 44.28 5.54
4443 7765 1.302033 AACTGGCAGACTGCTTCGG 60.302 57.895 25.92 17.38 44.28 4.30
4444 7766 1.864862 CAACTGGCAGACTGCTTCG 59.135 57.895 25.92 16.32 44.28 3.79
4445 7767 1.578423 GCAACTGGCAGACTGCTTC 59.422 57.895 27.44 11.73 44.28 3.86
4446 7768 2.629424 TGGCAACTGGCAGACTGCTT 62.629 55.000 30.64 10.79 46.12 3.91
4447 7769 3.124051 TGGCAACTGGCAGACTGCT 62.124 57.895 30.64 4.53 46.12 4.24
4448 7770 2.595463 TGGCAACTGGCAGACTGC 60.595 61.111 27.07 27.07 46.12 4.40
4462 7784 0.108945 GGAATCAAGCAGCAACTGGC 60.109 55.000 0.00 0.00 45.30 4.85
4463 7785 1.250328 TGGAATCAAGCAGCAACTGG 58.750 50.000 0.00 0.00 31.21 4.00
4464 7786 2.669364 GTTGGAATCAAGCAGCAACTG 58.331 47.619 0.00 0.00 32.92 3.16
4473 7795 4.439700 GCATGATGTCAGGTTGGAATCAAG 60.440 45.833 0.00 0.00 32.92 3.02
4474 7796 3.444742 GCATGATGTCAGGTTGGAATCAA 59.555 43.478 0.00 0.00 31.49 2.57
4475 7797 3.018856 GCATGATGTCAGGTTGGAATCA 58.981 45.455 0.00 0.00 0.00 2.57
4476 7798 3.066342 CAGCATGATGTCAGGTTGGAATC 59.934 47.826 1.88 0.00 39.69 2.52
4477 7799 3.021695 CAGCATGATGTCAGGTTGGAAT 58.978 45.455 1.88 0.00 39.69 3.01
4478 7800 2.439409 CAGCATGATGTCAGGTTGGAA 58.561 47.619 1.88 0.00 39.69 3.53
4479 7801 2.118313 CAGCATGATGTCAGGTTGGA 57.882 50.000 1.88 0.00 39.69 3.53
4481 7803 1.100510 CCCAGCATGATGTCAGGTTG 58.899 55.000 10.55 4.81 39.69 3.77
4482 7804 0.700564 ACCCAGCATGATGTCAGGTT 59.299 50.000 10.55 0.00 39.69 3.50
4483 7805 0.700564 AACCCAGCATGATGTCAGGT 59.299 50.000 10.55 7.38 39.69 4.00
4484 7806 1.100510 CAACCCAGCATGATGTCAGG 58.899 55.000 10.55 6.70 39.69 3.86
4485 7807 1.100510 CCAACCCAGCATGATGTCAG 58.899 55.000 10.55 0.75 39.69 3.51
4486 7808 0.323633 CCCAACCCAGCATGATGTCA 60.324 55.000 10.55 0.00 39.69 3.58
4487 7809 0.323725 ACCCAACCCAGCATGATGTC 60.324 55.000 10.55 0.00 39.69 3.06
4488 7810 0.612732 CACCCAACCCAGCATGATGT 60.613 55.000 10.55 0.00 39.69 3.06
4489 7811 1.952102 GCACCCAACCCAGCATGATG 61.952 60.000 3.34 3.34 39.69 3.07
4490 7812 1.683365 GCACCCAACCCAGCATGAT 60.683 57.895 0.00 0.00 39.69 2.45
4491 7813 2.283101 GCACCCAACCCAGCATGA 60.283 61.111 0.00 0.00 39.69 3.07
4492 7814 2.283388 AGCACCCAACCCAGCATG 60.283 61.111 0.00 0.00 0.00 4.06
4493 7815 2.036256 GAGCACCCAACCCAGCAT 59.964 61.111 0.00 0.00 0.00 3.79
4494 7816 1.496444 TATGAGCACCCAACCCAGCA 61.496 55.000 0.00 0.00 0.00 4.41
4495 7817 0.323360 TTATGAGCACCCAACCCAGC 60.323 55.000 0.00 0.00 0.00 4.85
4496 7818 2.214376 TTTATGAGCACCCAACCCAG 57.786 50.000 0.00 0.00 0.00 4.45
4497 7819 2.042297 TCATTTATGAGCACCCAACCCA 59.958 45.455 0.00 0.00 32.11 4.51
4498 7820 2.733956 TCATTTATGAGCACCCAACCC 58.266 47.619 0.00 0.00 32.11 4.11
4499 7821 4.160252 ACAATCATTTATGAGCACCCAACC 59.840 41.667 0.00 0.00 40.64 3.77
4500 7822 5.329035 ACAATCATTTATGAGCACCCAAC 57.671 39.130 0.00 0.00 40.64 3.77
4501 7823 5.999205 AACAATCATTTATGAGCACCCAA 57.001 34.783 0.00 0.00 40.64 4.12
4502 7824 5.479724 TCAAACAATCATTTATGAGCACCCA 59.520 36.000 0.00 0.00 40.64 4.51
4503 7825 5.964758 TCAAACAATCATTTATGAGCACCC 58.035 37.500 0.00 0.00 40.64 4.61
4504 7826 8.385111 CAATTCAAACAATCATTTATGAGCACC 58.615 33.333 0.00 0.00 40.64 5.01
4505 7827 7.901377 GCAATTCAAACAATCATTTATGAGCAC 59.099 33.333 0.00 0.00 40.64 4.40
4506 7828 7.201453 CGCAATTCAAACAATCATTTATGAGCA 60.201 33.333 0.00 0.00 40.64 4.26
4507 7829 7.114920 CGCAATTCAAACAATCATTTATGAGC 58.885 34.615 0.00 0.00 40.64 4.26
4508 7830 8.176814 ACGCAATTCAAACAATCATTTATGAG 57.823 30.769 0.00 0.00 40.64 2.90
4509 7831 8.028354 AGACGCAATTCAAACAATCATTTATGA 58.972 29.630 0.00 0.00 41.70 2.15
4510 7832 8.176814 AGACGCAATTCAAACAATCATTTATG 57.823 30.769 0.00 0.00 0.00 1.90
4511 7833 7.489113 GGAGACGCAATTCAAACAATCATTTAT 59.511 33.333 0.00 0.00 0.00 1.40
4512 7834 6.806249 GGAGACGCAATTCAAACAATCATTTA 59.194 34.615 0.00 0.00 0.00 1.40
4513 7835 5.634859 GGAGACGCAATTCAAACAATCATTT 59.365 36.000 0.00 0.00 0.00 2.32
4514 7836 5.163513 GGAGACGCAATTCAAACAATCATT 58.836 37.500 0.00 0.00 0.00 2.57
4515 7837 4.218200 TGGAGACGCAATTCAAACAATCAT 59.782 37.500 0.00 0.00 0.00 2.45
4516 7838 3.567585 TGGAGACGCAATTCAAACAATCA 59.432 39.130 0.00 0.00 0.00 2.57
4517 7839 4.159377 TGGAGACGCAATTCAAACAATC 57.841 40.909 0.00 0.00 0.00 2.67
4518 7840 4.582701 TTGGAGACGCAATTCAAACAAT 57.417 36.364 0.00 0.00 0.00 2.71
4519 7841 4.377839 TTTGGAGACGCAATTCAAACAA 57.622 36.364 0.00 0.00 0.00 2.83
4520 7842 4.582701 ATTTGGAGACGCAATTCAAACA 57.417 36.364 0.00 0.00 31.42 2.83
4521 7843 6.092748 ACATATTTGGAGACGCAATTCAAAC 58.907 36.000 0.00 0.00 31.42 2.93
4522 7844 6.266168 ACATATTTGGAGACGCAATTCAAA 57.734 33.333 0.00 0.00 0.00 2.69
4523 7845 5.895636 ACATATTTGGAGACGCAATTCAA 57.104 34.783 0.00 0.00 0.00 2.69
4524 7846 6.112734 ACTACATATTTGGAGACGCAATTCA 58.887 36.000 1.97 0.00 35.62 2.57
4525 7847 6.604735 ACTACATATTTGGAGACGCAATTC 57.395 37.500 1.97 0.00 35.62 2.17
4526 7848 6.597672 TCAACTACATATTTGGAGACGCAATT 59.402 34.615 1.97 0.00 35.62 2.32
4527 7849 6.037172 GTCAACTACATATTTGGAGACGCAAT 59.963 38.462 1.97 0.00 35.62 3.56
4528 7850 5.350365 GTCAACTACATATTTGGAGACGCAA 59.650 40.000 1.97 0.00 35.62 4.85
4529 7851 4.868171 GTCAACTACATATTTGGAGACGCA 59.132 41.667 1.97 0.00 35.62 5.24
4530 7852 4.026804 CGTCAACTACATATTTGGAGACGC 60.027 45.833 1.97 0.00 35.62 5.19
4531 7853 4.026804 GCGTCAACTACATATTTGGAGACG 60.027 45.833 15.04 15.04 35.62 4.18
4532 7854 4.868171 TGCGTCAACTACATATTTGGAGAC 59.132 41.667 1.97 0.00 35.62 3.36
4533 7855 5.079689 TGCGTCAACTACATATTTGGAGA 57.920 39.130 1.97 0.00 35.62 3.71
4534 7856 5.050091 GGATGCGTCAACTACATATTTGGAG 60.050 44.000 8.47 0.00 39.96 3.86
4535 7857 4.814234 GGATGCGTCAACTACATATTTGGA 59.186 41.667 8.47 0.00 0.00 3.53
4536 7858 4.024048 GGGATGCGTCAACTACATATTTGG 60.024 45.833 8.47 0.00 0.00 3.28
4537 7859 4.024048 GGGGATGCGTCAACTACATATTTG 60.024 45.833 8.47 0.00 0.00 2.32
4538 7860 4.134563 GGGGATGCGTCAACTACATATTT 58.865 43.478 8.47 0.00 0.00 1.40
4539 7861 3.740115 GGGGATGCGTCAACTACATATT 58.260 45.455 8.47 0.00 0.00 1.28
4540 7862 2.288825 CGGGGATGCGTCAACTACATAT 60.289 50.000 8.47 0.00 0.00 1.78
4541 7863 1.067974 CGGGGATGCGTCAACTACATA 59.932 52.381 8.47 0.00 0.00 2.29
4542 7864 0.179084 CGGGGATGCGTCAACTACAT 60.179 55.000 8.47 0.00 0.00 2.29
4543 7865 1.216977 CGGGGATGCGTCAACTACA 59.783 57.895 8.47 0.00 0.00 2.74
4544 7866 0.108520 TTCGGGGATGCGTCAACTAC 60.109 55.000 8.47 0.00 0.00 2.73
4545 7867 0.174845 CTTCGGGGATGCGTCAACTA 59.825 55.000 8.47 0.00 0.00 2.24
4546 7868 1.079127 CTTCGGGGATGCGTCAACT 60.079 57.895 8.47 0.00 0.00 3.16
4547 7869 2.106683 CCTTCGGGGATGCGTCAAC 61.107 63.158 8.47 0.00 37.23 3.18
4548 7870 2.267642 CCTTCGGGGATGCGTCAA 59.732 61.111 8.47 0.00 37.23 3.18
4549 7871 4.467084 GCCTTCGGGGATGCGTCA 62.467 66.667 8.47 0.00 37.23 4.35
4553 7875 4.483243 TTCGGCCTTCGGGGATGC 62.483 66.667 0.00 0.00 39.77 3.91
4554 7876 2.203070 CTTCGGCCTTCGGGGATG 60.203 66.667 0.00 0.00 39.77 3.51
4555 7877 4.176752 GCTTCGGCCTTCGGGGAT 62.177 66.667 0.00 0.00 39.77 3.85
4558 7880 4.394712 ACTGCTTCGGCCTTCGGG 62.395 66.667 0.00 0.00 40.91 5.14
4559 7881 2.815647 GACTGCTTCGGCCTTCGG 60.816 66.667 0.00 0.00 40.91 4.30
4560 7882 2.097038 CAGACTGCTTCGGCCTTCG 61.097 63.158 0.00 0.00 40.91 3.79
4561 7883 2.394563 GCAGACTGCTTCGGCCTTC 61.395 63.158 20.41 0.00 40.96 3.46
4562 7884 2.359230 GCAGACTGCTTCGGCCTT 60.359 61.111 20.41 0.00 40.96 4.35
4641 7966 2.325583 ACTGCCGAAACACTTTCAGA 57.674 45.000 0.00 0.00 39.63 3.27
4676 8001 2.231478 AGATGTGTAGAACCACCAGACG 59.769 50.000 0.00 0.00 34.35 4.18
4703 8028 8.543774 GTTCTTACGAATGATCTCATAACAAGG 58.456 37.037 0.00 0.00 35.10 3.61
4895 8221 8.938906 GTTAAATCTGTGATCAAAATTTGGCAT 58.061 29.630 15.98 0.00 0.00 4.40
5004 8330 5.301045 CGGAGGGAGTACAAGTTATACATCA 59.699 44.000 0.00 0.00 0.00 3.07
5005 8331 5.301298 ACGGAGGGAGTACAAGTTATACATC 59.699 44.000 0.00 0.00 0.00 3.06
5017 8343 6.150809 CCTATACTATGAAACGGAGGGAGTAC 59.849 46.154 0.00 0.00 0.00 2.73
5018 8344 6.044754 TCCTATACTATGAAACGGAGGGAGTA 59.955 42.308 0.00 0.00 0.00 2.59
5019 8345 5.078256 CCTATACTATGAAACGGAGGGAGT 58.922 45.833 0.00 0.00 0.00 3.85
5020 8346 5.322754 TCCTATACTATGAAACGGAGGGAG 58.677 45.833 0.00 0.00 0.00 4.30
5021 8347 5.163012 ACTCCTATACTATGAAACGGAGGGA 60.163 44.000 0.00 0.00 40.57 4.20
5022 8348 5.047943 CACTCCTATACTATGAAACGGAGGG 60.048 48.000 0.00 0.00 40.57 4.30
5023 8349 5.535406 ACACTCCTATACTATGAAACGGAGG 59.465 44.000 0.00 0.00 40.57 4.30
5024 8350 6.636562 ACACTCCTATACTATGAAACGGAG 57.363 41.667 0.00 0.00 41.68 4.63
5025 8351 7.414222 AAACACTCCTATACTATGAAACGGA 57.586 36.000 0.00 0.00 0.00 4.69
5026 8352 8.388103 CAAAAACACTCCTATACTATGAAACGG 58.612 37.037 0.00 0.00 0.00 4.44
5027 8353 9.146984 TCAAAAACACTCCTATACTATGAAACG 57.853 33.333 0.00 0.00 0.00 3.60
5045 8371 5.877564 TGACATCACACTAGTGTCAAAAACA 59.122 36.000 25.63 17.10 46.45 2.83
5046 8372 6.358118 TGACATCACACTAGTGTCAAAAAC 57.642 37.500 25.63 14.98 46.45 2.43
5052 8378 5.220228 GCGTTATTGACATCACACTAGTGTC 60.220 44.000 25.63 14.38 46.01 3.67
5053 8379 4.625742 GCGTTATTGACATCACACTAGTGT 59.374 41.667 22.95 22.95 46.01 3.55
5055 8381 5.073311 AGCGTTATTGACATCACACTAGT 57.927 39.130 0.00 0.00 0.00 2.57
5056 8382 5.344066 AGAGCGTTATTGACATCACACTAG 58.656 41.667 0.00 0.00 0.00 2.57
5057 8383 5.324784 AGAGCGTTATTGACATCACACTA 57.675 39.130 0.00 0.00 0.00 2.74
5058 8384 4.193826 AGAGCGTTATTGACATCACACT 57.806 40.909 0.00 0.00 0.00 3.55
5059 8385 4.928661 AAGAGCGTTATTGACATCACAC 57.071 40.909 0.00 0.00 0.00 3.82
5060 8386 9.626045 CTATATAAGAGCGTTATTGACATCACA 57.374 33.333 0.40 0.00 0.00 3.58
5061 8387 9.077674 CCTATATAAGAGCGTTATTGACATCAC 57.922 37.037 0.40 0.00 0.00 3.06
5062 8388 9.020731 TCCTATATAAGAGCGTTATTGACATCA 57.979 33.333 0.40 0.00 0.00 3.07
5063 8389 9.291664 GTCCTATATAAGAGCGTTATTGACATC 57.708 37.037 0.40 0.00 0.00 3.06
5064 8390 7.968956 CGTCCTATATAAGAGCGTTATTGACAT 59.031 37.037 0.40 0.00 0.00 3.06
5065 8391 7.173735 TCGTCCTATATAAGAGCGTTATTGACA 59.826 37.037 0.40 0.00 0.00 3.58
5066 8392 7.524912 TCGTCCTATATAAGAGCGTTATTGAC 58.475 38.462 0.40 0.00 0.00 3.18
5067 8393 7.677454 TCGTCCTATATAAGAGCGTTATTGA 57.323 36.000 0.40 0.00 0.00 2.57
5068 8394 7.485277 CCTTCGTCCTATATAAGAGCGTTATTG 59.515 40.741 0.40 0.00 0.00 1.90
5069 8395 7.362747 CCCTTCGTCCTATATAAGAGCGTTATT 60.363 40.741 0.40 0.00 0.00 1.40
5070 8396 6.095160 CCCTTCGTCCTATATAAGAGCGTTAT 59.905 42.308 0.79 0.79 0.00 1.89
5071 8397 5.413833 CCCTTCGTCCTATATAAGAGCGTTA 59.586 44.000 0.00 0.00 0.00 3.18
5072 8398 4.217983 CCCTTCGTCCTATATAAGAGCGTT 59.782 45.833 0.00 0.00 0.00 4.84
5073 8399 3.757493 CCCTTCGTCCTATATAAGAGCGT 59.243 47.826 0.00 0.00 0.00 5.07
5074 8400 4.008330 TCCCTTCGTCCTATATAAGAGCG 58.992 47.826 0.00 0.00 0.00 5.03
5075 8401 5.011586 ACTCCCTTCGTCCTATATAAGAGC 58.988 45.833 0.00 0.00 0.00 4.09
5085 8411 8.312564 GCTAATAAAATATACTCCCTTCGTCCT 58.687 37.037 0.00 0.00 0.00 3.85
5086 8412 7.275123 CGCTAATAAAATATACTCCCTTCGTCC 59.725 40.741 0.00 0.00 0.00 4.79
5087 8413 8.025445 TCGCTAATAAAATATACTCCCTTCGTC 58.975 37.037 0.00 0.00 0.00 4.20
5088 8414 7.889469 TCGCTAATAAAATATACTCCCTTCGT 58.111 34.615 0.00 0.00 0.00 3.85
5089 8415 8.752766 TTCGCTAATAAAATATACTCCCTTCG 57.247 34.615 0.00 0.00 0.00 3.79
5135 8972 6.362248 GTTTGTTAGCCCCCTCATATTTAGA 58.638 40.000 0.00 0.00 0.00 2.10
5140 8977 2.856231 TGGTTTGTTAGCCCCCTCATAT 59.144 45.455 0.00 0.00 0.00 1.78
5155 8993 1.010125 CAACGCACGTCCTGGTTTG 60.010 57.895 0.00 0.00 0.00 2.93
5187 9025 9.061435 TCATGTAACGATTTATGAAATATGGCA 57.939 29.630 0.00 0.00 0.00 4.92
5216 9054 3.374058 CGGTCATTGAGGCGAAACTTTAT 59.626 43.478 0.00 0.00 0.00 1.40
5261 10210 1.276145 GGAGAACTGTGACGCACGTC 61.276 60.000 15.94 15.94 44.77 4.34
5352 10305 2.279069 CCTCACCCGCTCTGTCACT 61.279 63.158 0.00 0.00 0.00 3.41
5381 10334 6.041523 GCTTGAGTAGATAGGTGGAGAAGAAT 59.958 42.308 0.00 0.00 0.00 2.40
5407 10361 0.030504 CCGAGCATTGCACAACACAA 59.969 50.000 11.91 0.00 0.00 3.33
5412 10366 2.282391 AGCCCGAGCATTGCACAA 60.282 55.556 11.91 0.00 43.56 3.33
5417 10371 1.678635 TTTCCCAGCCCGAGCATTG 60.679 57.895 0.00 0.00 43.56 2.82
5418 10372 1.678970 GTTTCCCAGCCCGAGCATT 60.679 57.895 0.00 0.00 43.56 3.56
5419 10373 2.044946 GTTTCCCAGCCCGAGCAT 60.045 61.111 0.00 0.00 43.56 3.79
5420 10374 3.551496 CTGTTTCCCAGCCCGAGCA 62.551 63.158 0.00 0.00 43.56 4.26
5421 10375 2.747855 CTGTTTCCCAGCCCGAGC 60.748 66.667 0.00 0.00 40.32 5.03
5444 10398 1.595093 GGCACCAACGGCAAATAGCT 61.595 55.000 0.00 0.00 44.79 3.32
5448 10402 0.899717 ATCAGGCACCAACGGCAAAT 60.900 50.000 0.00 0.00 0.00 2.32
5478 10432 3.857052 CCCTTCGTGCACTAGTTTATGA 58.143 45.455 16.19 0.00 0.00 2.15
5482 10436 0.107831 TGCCCTTCGTGCACTAGTTT 59.892 50.000 16.19 0.00 32.85 2.66
5494 10448 1.374758 CGGTCTGTGTCTGCCCTTC 60.375 63.158 0.00 0.00 0.00 3.46


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

AutoCloner maintained by Alex Coulton.