Multiple sequence alignment - TraesCS3B01G316500

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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 TraesCS3B01G316500 chr3B 100.000 5780 0 0 1 5780 508256985 508251206 0.000000e+00 10674.0
1 TraesCS3B01G316500 chr3B 100.000 37 0 0 5307 5343 508251643 508251607 1.040000e-07 69.4
2 TraesCS3B01G316500 chr3B 100.000 37 0 0 5343 5379 508251679 508251643 1.040000e-07 69.4
3 TraesCS3B01G316500 chr3D 92.697 2314 82 28 3065 5343 390667585 390665324 0.000000e+00 3256.0
4 TraesCS3B01G316500 chr3D 98.170 1694 25 5 1373 3066 390669311 390667624 0.000000e+00 2952.0
5 TraesCS3B01G316500 chr3D 93.990 1381 51 16 12 1375 390670960 390669595 0.000000e+00 2061.0
6 TraesCS3B01G316500 chr3D 89.427 227 16 2 5441 5667 390665030 390664812 4.410000e-71 279.0
7 TraesCS3B01G316500 chr3D 93.902 82 5 0 5343 5424 390665360 390665279 2.190000e-24 124.0
8 TraesCS3B01G316500 chr3D 96.875 32 1 0 1591 1622 292001078 292001047 3.000000e-03 54.7
9 TraesCS3B01G316500 chr3A 95.028 1770 37 25 1304 3066 511078127 511076402 0.000000e+00 2734.0
10 TraesCS3B01G316500 chr3A 95.068 1541 41 7 3065 4601 511076363 511074854 0.000000e+00 2392.0
11 TraesCS3B01G316500 chr3A 91.600 1250 69 16 17 1239 511079379 511078139 0.000000e+00 1694.0
12 TraesCS3B01G316500 chr3A 92.206 757 27 11 4587 5343 511074829 511074105 0.000000e+00 1042.0
13 TraesCS3B01G316500 chr3A 92.378 328 18 4 5343 5667 511074141 511073818 1.470000e-125 460.0
14 TraesCS3B01G316500 chr1D 78.408 741 111 36 2123 2834 439026835 439026115 2.470000e-118 436.0
15 TraesCS3B01G316500 chr1D 100.000 32 0 0 1592 1623 24929041 24929072 6.250000e-05 60.2
16 TraesCS3B01G316500 chr1D 94.444 36 2 0 1590 1625 382633931 382633896 8.090000e-04 56.5
17 TraesCS3B01G316500 chr1D 96.875 32 0 1 1590 1621 465459495 465459525 1.000000e-02 52.8
18 TraesCS3B01G316500 chr1B 80.516 426 68 11 2417 2834 595182507 595182089 4.350000e-81 313.0
19 TraesCS3B01G316500 chr1B 87.940 199 19 4 2123 2318 595182807 595182611 4.500000e-56 230.0
20 TraesCS3B01G316500 chr1B 92.500 40 1 2 1590 1629 98724160 98724123 8.090000e-04 56.5
21 TraesCS3B01G316500 chr1A 80.471 425 69 11 2417 2834 535316581 535316164 4.350000e-81 313.0
22 TraesCS3B01G316500 chr1A 87.437 199 20 4 2123 2318 535316882 535316686 2.100000e-54 224.0
23 TraesCS3B01G316500 chr4B 94.444 36 2 0 1590 1625 640002201 640002236 8.090000e-04 56.5
24 TraesCS3B01G316500 chr5A 96.970 33 0 1 1590 1622 397253496 397253527 3.000000e-03 54.7


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS3B01G316500 chr3B 508251206 508256985 5779 True 10674.0 10674 100.0000 1 5780 1 chr3B.!!$R1 5779
1 TraesCS3B01G316500 chr3D 390664812 390670960 6148 True 1734.4 3256 93.6372 12 5667 5 chr3D.!!$R2 5655
2 TraesCS3B01G316500 chr3A 511073818 511079379 5561 True 1664.4 2734 93.2560 17 5667 5 chr3A.!!$R1 5650
3 TraesCS3B01G316500 chr1D 439026115 439026835 720 True 436.0 436 78.4080 2123 2834 1 chr1D.!!$R2 711
4 TraesCS3B01G316500 chr1B 595182089 595182807 718 True 271.5 313 84.2280 2123 2834 2 chr1B.!!$R2 711
5 TraesCS3B01G316500 chr1A 535316164 535316882 718 True 268.5 313 83.9540 2123 2834 2 chr1A.!!$R1 711

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
893 916 0.166814 GGAACAGCTAGCGTGCTTTG 59.833 55.000 9.55 3.28 41.98 2.77 F
1401 1719 0.036388 TCCCTGTGATTCAGCCGTTC 60.036 55.000 0.00 0.00 42.38 3.95 F
1402 1720 0.321564 CCCTGTGATTCAGCCGTTCA 60.322 55.000 0.00 0.00 42.38 3.18 F
2359 2678 1.667724 GACAGAAAGGACATGGCATCG 59.332 52.381 0.00 0.00 0.00 3.84 F
3348 3717 0.856641 TTACGTTCTGTTGTCTGCGC 59.143 50.000 0.00 0.00 0.00 6.09 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2439 2765 0.609957 CATCAACTTCAGGCCCAGCA 60.610 55.0 0.00 0.0 0.00 4.41 R
3347 3716 2.367030 TTTGCACATAACAGGCATGC 57.633 45.0 9.90 9.9 37.39 4.06 R
3348 3717 5.004630 CGTTAATTTGCACATAACAGGCATG 59.995 40.0 0.00 0.0 37.39 4.06 R
4139 4508 1.136828 TGAGGGGTGCTACACTGTTT 58.863 50.0 0.00 0.0 34.40 2.83 R
5346 5771 0.721718 GCTGTACTGATTGACCACGC 59.278 55.0 3.61 0.0 0.00 5.34 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
29 30 9.653287 TTCATTGTAGTAGTAATTTGGTCTCTG 57.347 33.333 0.00 0.00 0.00 3.35
58 59 5.116377 GTCAGATATTCTCTCGCGCTAAAAG 59.884 44.000 5.56 0.00 29.16 2.27
365 372 2.604139 GAATCGAATCTCTCCTCCCCT 58.396 52.381 0.00 0.00 0.00 4.79
366 373 2.302587 ATCGAATCTCTCCTCCCCTC 57.697 55.000 0.00 0.00 0.00 4.30
369 376 0.565674 GAATCTCTCCTCCCCTCCCT 59.434 60.000 0.00 0.00 0.00 4.20
523 536 2.365635 GTAGGGGAGCCTGCCTCA 60.366 66.667 1.05 0.00 42.62 3.86
591 604 1.079405 CGCGAGGCTCTTGGGTTTA 60.079 57.895 13.50 0.00 0.00 2.01
690 703 0.596083 CTCCCGAGCTTAGCATGTCG 60.596 60.000 7.07 7.19 0.00 4.35
815 838 0.814010 CTTTTATCCCCAGCCGTCGG 60.814 60.000 6.99 6.99 0.00 4.79
848 871 0.664166 GTTGCAATTCAGCACACGGG 60.664 55.000 0.59 0.00 45.61 5.28
866 889 1.050988 GGCCAGCTGGATCTGTCCTA 61.051 60.000 37.21 0.00 45.32 2.94
872 895 4.162320 CCAGCTGGATCTGTCCTACTTAAA 59.838 45.833 29.88 0.00 45.32 1.52
893 916 0.166814 GGAACAGCTAGCGTGCTTTG 59.833 55.000 9.55 3.28 41.98 2.77
923 946 1.372499 CCGTCGTGTCCGTGTGAAT 60.372 57.895 0.00 0.00 35.01 2.57
926 949 1.136721 CGTCGTGTCCGTGTGAATTTC 60.137 52.381 0.00 0.00 35.01 2.17
927 950 2.132762 GTCGTGTCCGTGTGAATTTCT 58.867 47.619 0.00 0.00 35.01 2.52
928 951 2.542595 GTCGTGTCCGTGTGAATTTCTT 59.457 45.455 0.00 0.00 35.01 2.52
929 952 3.737266 GTCGTGTCCGTGTGAATTTCTTA 59.263 43.478 0.00 0.00 35.01 2.10
930 953 3.737266 TCGTGTCCGTGTGAATTTCTTAC 59.263 43.478 0.00 0.00 35.01 2.34
933 956 5.060569 CGTGTCCGTGTGAATTTCTTACTAG 59.939 44.000 0.00 0.00 0.00 2.57
936 959 7.758528 GTGTCCGTGTGAATTTCTTACTAGTAT 59.241 37.037 2.79 0.00 0.00 2.12
951 974 8.639761 TCTTACTAGTATTAGTGATTTCCCAGC 58.360 37.037 8.10 0.00 40.33 4.85
956 979 4.591321 ATTAGTGATTTCCCAGCCTTCA 57.409 40.909 0.00 0.00 0.00 3.02
1192 1219 3.401033 AAGGTTGGTAATTTGGCTTGC 57.599 42.857 0.00 0.00 0.00 4.01
1279 1311 9.927668 CATAATTAGTTTCTTTGTGGGATGTTT 57.072 29.630 0.00 0.00 0.00 2.83
1315 1347 9.745880 GTAATGTGCTAAACTAGTATTCTGCTA 57.254 33.333 0.00 0.00 0.00 3.49
1401 1719 0.036388 TCCCTGTGATTCAGCCGTTC 60.036 55.000 0.00 0.00 42.38 3.95
1402 1720 0.321564 CCCTGTGATTCAGCCGTTCA 60.322 55.000 0.00 0.00 42.38 3.18
1663 1981 7.951530 AAATGAAGCACTCCAGTTATTTTTG 57.048 32.000 0.00 0.00 0.00 2.44
1664 1982 6.655078 ATGAAGCACTCCAGTTATTTTTGT 57.345 33.333 0.00 0.00 0.00 2.83
1667 1985 7.327214 TGAAGCACTCCAGTTATTTTTGTTTT 58.673 30.769 0.00 0.00 0.00 2.43
1668 1986 7.277539 TGAAGCACTCCAGTTATTTTTGTTTTG 59.722 33.333 0.00 0.00 0.00 2.44
1947 2265 4.765856 TCAGCGTCCTAGTTTCTAAACTCT 59.234 41.667 11.21 0.00 45.65 3.24
2127 2446 6.403855 CGGGTTACTTTGTTTTCTGTCTTTGA 60.404 38.462 0.00 0.00 0.00 2.69
2359 2678 1.667724 GACAGAAAGGACATGGCATCG 59.332 52.381 0.00 0.00 0.00 3.84
2924 3252 3.561143 AGTTATGCCAAATATTCCGCCA 58.439 40.909 4.71 0.00 0.00 5.69
3347 3716 3.579147 TTTTACGTTCTGTTGTCTGCG 57.421 42.857 0.00 0.00 0.00 5.18
3348 3717 0.856641 TTACGTTCTGTTGTCTGCGC 59.143 50.000 0.00 0.00 0.00 6.09
3517 3886 1.064017 TGTTCACTTGTTTGCCTCCCT 60.064 47.619 0.00 0.00 0.00 4.20
4127 4496 5.518847 GCATGAGTACTTATGCGTGTCTTTA 59.481 40.000 29.83 0.00 41.55 1.85
4139 4508 4.081365 TGCGTGTCTTTATCCTGATGGTTA 60.081 41.667 0.00 0.00 34.23 2.85
4140 4509 4.873827 GCGTGTCTTTATCCTGATGGTTAA 59.126 41.667 0.00 0.00 34.23 2.01
4141 4510 5.353123 GCGTGTCTTTATCCTGATGGTTAAA 59.647 40.000 0.00 0.00 35.99 1.52
4142 4511 6.674760 GCGTGTCTTTATCCTGATGGTTAAAC 60.675 42.308 0.00 0.00 34.40 2.01
4143 4512 6.370442 CGTGTCTTTATCCTGATGGTTAAACA 59.630 38.462 0.00 0.00 34.40 2.83
4144 4513 7.413000 CGTGTCTTTATCCTGATGGTTAAACAG 60.413 40.741 0.00 0.00 34.40 3.16
4145 4514 7.390718 GTGTCTTTATCCTGATGGTTAAACAGT 59.609 37.037 0.00 0.00 34.40 3.55
4146 4515 7.390440 TGTCTTTATCCTGATGGTTAAACAGTG 59.610 37.037 0.00 0.00 34.40 3.66
4147 4516 7.390718 GTCTTTATCCTGATGGTTAAACAGTGT 59.609 37.037 0.00 0.00 34.40 3.55
4148 4517 8.598916 TCTTTATCCTGATGGTTAAACAGTGTA 58.401 33.333 0.00 0.00 34.40 2.90
4149 4518 8.786826 TTTATCCTGATGGTTAAACAGTGTAG 57.213 34.615 0.00 0.00 34.40 2.74
4150 4519 4.575885 TCCTGATGGTTAAACAGTGTAGC 58.424 43.478 0.00 0.00 34.23 3.58
4151 4520 4.041075 TCCTGATGGTTAAACAGTGTAGCA 59.959 41.667 0.00 0.00 34.23 3.49
4152 4521 4.154195 CCTGATGGTTAAACAGTGTAGCAC 59.846 45.833 0.00 0.00 34.10 4.40
4153 4522 4.069304 TGATGGTTAAACAGTGTAGCACC 58.931 43.478 0.00 3.43 34.49 5.01
4154 4523 2.853705 TGGTTAAACAGTGTAGCACCC 58.146 47.619 12.79 4.29 34.49 4.61
4155 4524 2.156917 GGTTAAACAGTGTAGCACCCC 58.843 52.381 0.00 0.00 34.49 4.95
4156 4525 2.224695 GGTTAAACAGTGTAGCACCCCT 60.225 50.000 0.00 0.00 34.49 4.79
4157 4526 3.072211 GTTAAACAGTGTAGCACCCCTC 58.928 50.000 0.00 0.00 34.49 4.30
4158 4527 1.136828 AAACAGTGTAGCACCCCTCA 58.863 50.000 0.00 0.00 34.49 3.86
4159 4528 1.136828 AACAGTGTAGCACCCCTCAA 58.863 50.000 0.00 0.00 34.49 3.02
4160 4529 1.136828 ACAGTGTAGCACCCCTCAAA 58.863 50.000 0.00 0.00 34.49 2.69
4161 4530 1.493022 ACAGTGTAGCACCCCTCAAAA 59.507 47.619 0.00 0.00 34.49 2.44
4162 4531 2.092103 ACAGTGTAGCACCCCTCAAAAA 60.092 45.455 0.00 0.00 34.49 1.94
4341 4711 7.014134 TCCTGCATGTCTTTTACTTTGAAATCA 59.986 33.333 0.00 0.00 0.00 2.57
4462 4834 8.181904 TGATGTCTATTGCAGTCACTATCATA 57.818 34.615 0.00 0.00 0.00 2.15
4501 4873 2.614057 CTCCCATTATTTGCGTCACCTC 59.386 50.000 0.00 0.00 0.00 3.85
4532 4906 6.809507 AGTTGTGCACTTGATGGTGATCCA 62.810 45.833 19.41 0.00 39.61 3.41
4548 4922 0.545071 TCCAGATGTGCCTCCACTCA 60.545 55.000 0.00 0.00 42.54 3.41
4551 4925 1.451028 GATGTGCCTCCACTCAGCC 60.451 63.158 0.00 0.00 42.54 4.85
4553 4927 1.569030 ATGTGCCTCCACTCAGCCAT 61.569 55.000 0.00 0.00 42.54 4.40
4555 4929 0.179062 GTGCCTCCACTCAGCCATAG 60.179 60.000 0.00 0.00 38.93 2.23
4592 5005 7.970384 TCACAAACCTATACGATTGAAATCAC 58.030 34.615 4.06 0.00 35.11 3.06
4601 5014 9.254133 CTATACGATTGAAATCACATGTTCTCT 57.746 33.333 0.00 0.00 35.11 3.10
4611 5024 3.932710 TCACATGTTCTCTTTATCCGTGC 59.067 43.478 0.00 0.00 0.00 5.34
4617 5030 2.826428 TCTCTTTATCCGTGCTGCATC 58.174 47.619 5.27 0.00 0.00 3.91
4651 5064 7.776933 TGTCTCTGTATTTCTGATATTGCAC 57.223 36.000 0.00 0.00 0.00 4.57
4652 5065 7.559486 TGTCTCTGTATTTCTGATATTGCACT 58.441 34.615 0.00 0.00 0.00 4.40
4653 5066 7.708322 TGTCTCTGTATTTCTGATATTGCACTC 59.292 37.037 0.00 0.00 0.00 3.51
4654 5067 7.170658 GTCTCTGTATTTCTGATATTGCACTCC 59.829 40.741 0.00 0.00 0.00 3.85
4655 5068 6.888105 TCTGTATTTCTGATATTGCACTCCA 58.112 36.000 0.00 0.00 0.00 3.86
4656 5069 7.512130 TCTGTATTTCTGATATTGCACTCCAT 58.488 34.615 0.00 0.00 0.00 3.41
4657 5070 7.658982 TCTGTATTTCTGATATTGCACTCCATC 59.341 37.037 0.00 0.00 0.00 3.51
4658 5071 6.712095 TGTATTTCTGATATTGCACTCCATCC 59.288 38.462 0.00 0.00 0.00 3.51
4659 5072 3.391506 TCTGATATTGCACTCCATCCG 57.608 47.619 0.00 0.00 0.00 4.18
4660 5073 2.965147 TCTGATATTGCACTCCATCCGA 59.035 45.455 0.00 0.00 0.00 4.55
4661 5074 3.580022 TCTGATATTGCACTCCATCCGAT 59.420 43.478 0.00 0.00 0.00 4.18
4662 5075 3.667360 TGATATTGCACTCCATCCGATG 58.333 45.455 0.93 0.93 0.00 3.84
4663 5076 1.882912 TATTGCACTCCATCCGATGC 58.117 50.000 2.53 0.00 38.59 3.91
4664 5077 0.107066 ATTGCACTCCATCCGATGCA 60.107 50.000 2.53 0.00 45.94 3.96
4713 5126 1.897802 CTTCTGGATTTGCAAAGGGCT 59.102 47.619 18.19 0.00 45.15 5.19
4737 5150 0.531753 GGCCGCATCTCCTCTTTCTC 60.532 60.000 0.00 0.00 0.00 2.87
4755 5168 0.032130 TCGATCTATGTGCCGCCTTC 59.968 55.000 0.00 0.00 0.00 3.46
4776 5189 1.949525 CTAGCTCAGCTGAGAGTCCTC 59.050 57.143 41.20 24.51 44.74 3.71
4810 5223 1.670811 GCCCGAGGAATGTATGTTGTG 59.329 52.381 0.00 0.00 0.00 3.33
4864 5277 0.109597 CAGCGGATCAAAGTTGTGGC 60.110 55.000 0.00 0.00 0.00 5.01
4878 5291 3.056107 AGTTGTGGCGTATGTAGACATGT 60.056 43.478 0.00 0.00 37.15 3.21
4934 5353 1.284785 TGAATTTAGACCTGGCAGGGG 59.715 52.381 35.34 15.00 40.58 4.79
4954 5373 1.006922 GGGCAAGTGAAGCAAGCAC 60.007 57.895 0.00 0.00 36.53 4.40
4963 5382 3.056107 AGTGAAGCAAGCACGGAACTATA 60.056 43.478 0.00 0.00 41.04 1.31
5137 5558 6.090358 ACCACGTACACGAATAATTTCTTCAG 59.910 38.462 9.04 0.00 43.02 3.02
5172 5593 0.948141 GAAAGCTGAGCTGCTGACGT 60.948 55.000 8.16 0.00 43.24 4.34
5269 5694 3.258228 CATTGATTGCAAAGCAGCATGA 58.742 40.909 1.71 0.00 46.13 3.07
5334 5759 2.368548 TGGTCAATCAGTACAGCTGTGT 59.631 45.455 29.57 13.63 45.23 3.72
5335 5760 2.996621 GGTCAATCAGTACAGCTGTGTC 59.003 50.000 29.57 20.49 45.23 3.67
5336 5761 3.554960 GGTCAATCAGTACAGCTGTGTCA 60.555 47.826 29.57 6.67 45.23 3.58
5337 5762 4.248859 GTCAATCAGTACAGCTGTGTCAT 58.751 43.478 29.57 12.45 45.23 3.06
5338 5763 4.692625 GTCAATCAGTACAGCTGTGTCATT 59.307 41.667 29.57 17.26 45.23 2.57
5339 5764 4.692155 TCAATCAGTACAGCTGTGTCATTG 59.308 41.667 29.57 25.67 45.23 2.82
5340 5765 3.044235 TCAGTACAGCTGTGTCATTGG 57.956 47.619 29.57 11.20 45.23 3.16
5341 5766 1.466167 CAGTACAGCTGTGTCATTGGC 59.534 52.381 29.57 8.63 40.27 4.52
5342 5767 1.349026 AGTACAGCTGTGTCATTGGCT 59.651 47.619 29.57 10.59 38.19 4.75
5343 5768 2.154462 GTACAGCTGTGTCATTGGCTT 58.846 47.619 29.57 0.00 38.19 4.35
5344 5769 1.696063 ACAGCTGTGTCATTGGCTTT 58.304 45.000 20.97 0.00 32.30 3.51
5345 5770 2.862541 ACAGCTGTGTCATTGGCTTTA 58.137 42.857 20.97 0.00 32.30 1.85
5346 5771 2.816087 ACAGCTGTGTCATTGGCTTTAG 59.184 45.455 20.97 0.00 32.30 1.85
5347 5772 1.815003 AGCTGTGTCATTGGCTTTAGC 59.185 47.619 0.00 0.00 41.14 3.09
5348 5773 1.466360 GCTGTGTCATTGGCTTTAGCG 60.466 52.381 0.00 0.00 43.26 4.26
5349 5774 1.806542 CTGTGTCATTGGCTTTAGCGT 59.193 47.619 0.00 0.00 43.26 5.07
5350 5775 1.535028 TGTGTCATTGGCTTTAGCGTG 59.465 47.619 0.00 0.00 43.26 5.34
5351 5776 1.135689 GTGTCATTGGCTTTAGCGTGG 60.136 52.381 0.00 0.00 43.26 4.94
5352 5777 1.165270 GTCATTGGCTTTAGCGTGGT 58.835 50.000 0.00 0.00 43.26 4.16
5353 5778 1.130561 GTCATTGGCTTTAGCGTGGTC 59.869 52.381 0.00 0.00 43.26 4.02
5354 5779 1.164411 CATTGGCTTTAGCGTGGTCA 58.836 50.000 0.00 0.00 43.26 4.02
5355 5780 1.539388 CATTGGCTTTAGCGTGGTCAA 59.461 47.619 0.00 0.00 43.26 3.18
5356 5781 1.904287 TTGGCTTTAGCGTGGTCAAT 58.096 45.000 0.00 0.00 43.26 2.57
5357 5782 1.448985 TGGCTTTAGCGTGGTCAATC 58.551 50.000 0.00 0.00 43.26 2.67
5358 5783 1.271108 TGGCTTTAGCGTGGTCAATCA 60.271 47.619 0.00 0.00 43.26 2.57
5359 5784 1.398390 GGCTTTAGCGTGGTCAATCAG 59.602 52.381 0.00 0.00 43.26 2.90
5360 5785 2.076863 GCTTTAGCGTGGTCAATCAGT 58.923 47.619 0.00 0.00 0.00 3.41
5361 5786 3.259064 GCTTTAGCGTGGTCAATCAGTA 58.741 45.455 0.00 0.00 0.00 2.74
5362 5787 3.062234 GCTTTAGCGTGGTCAATCAGTAC 59.938 47.826 0.00 0.00 0.00 2.73
5363 5788 3.945981 TTAGCGTGGTCAATCAGTACA 57.054 42.857 0.00 0.00 0.00 2.90
5364 5789 2.370281 AGCGTGGTCAATCAGTACAG 57.630 50.000 0.00 0.00 0.00 2.74
5365 5790 0.721718 GCGTGGTCAATCAGTACAGC 59.278 55.000 0.00 0.00 0.00 4.40
5366 5791 1.673033 GCGTGGTCAATCAGTACAGCT 60.673 52.381 0.00 0.00 0.00 4.24
5367 5792 1.995484 CGTGGTCAATCAGTACAGCTG 59.005 52.381 13.48 13.48 46.34 4.24
5368 5793 2.610479 CGTGGTCAATCAGTACAGCTGT 60.610 50.000 25.12 25.12 45.23 4.40
5369 5794 2.738846 GTGGTCAATCAGTACAGCTGTG 59.261 50.000 29.57 13.08 45.23 3.66
5370 5795 2.368548 TGGTCAATCAGTACAGCTGTGT 59.631 45.455 29.57 13.63 45.23 3.72
5417 5844 0.178998 CCATGGAAGGAGGCATGGAG 60.179 60.000 5.56 0.00 45.40 3.86
5421 5848 0.329596 GGAAGGAGGCATGGAGTGTT 59.670 55.000 0.00 0.00 0.00 3.32
5504 6163 0.179020 CTCAGCTTTGGACACCACCA 60.179 55.000 0.00 0.00 38.24 4.17
5505 6164 0.465460 TCAGCTTTGGACACCACCAC 60.465 55.000 0.00 0.00 39.85 4.16
5506 6165 1.152756 AGCTTTGGACACCACCACC 60.153 57.895 0.00 0.00 39.85 4.61
5595 6255 2.034878 TGCAGATACTCTCCATTCGCT 58.965 47.619 0.00 0.00 0.00 4.93
5607 6267 2.030893 TCCATTCGCTTGTTCTTGCTTG 60.031 45.455 0.00 0.00 0.00 4.01
5635 6295 1.026182 GCACCGGTCATCATCAAGCA 61.026 55.000 2.59 0.00 0.00 3.91
5664 6324 9.639601 GCTATTAAAGGCTTGTTAATTTGAACT 57.360 29.630 0.00 0.00 34.02 3.01
5667 6327 8.865590 TTAAAGGCTTGTTAATTTGAACTGTC 57.134 30.769 0.00 0.00 0.00 3.51
5668 6328 6.715347 AAGGCTTGTTAATTTGAACTGTCT 57.285 33.333 0.00 0.00 0.00 3.41
5669 6329 6.715347 AGGCTTGTTAATTTGAACTGTCTT 57.285 33.333 0.00 0.00 0.00 3.01
5670 6330 7.112452 AGGCTTGTTAATTTGAACTGTCTTT 57.888 32.000 0.00 0.00 0.00 2.52
5671 6331 7.555965 AGGCTTGTTAATTTGAACTGTCTTTT 58.444 30.769 0.00 0.00 0.00 2.27
5672 6332 8.040727 AGGCTTGTTAATTTGAACTGTCTTTTT 58.959 29.630 0.00 0.00 0.00 1.94
5673 6333 8.328146 GGCTTGTTAATTTGAACTGTCTTTTTC 58.672 33.333 0.00 0.00 0.00 2.29
5674 6334 9.087424 GCTTGTTAATTTGAACTGTCTTTTTCT 57.913 29.630 0.00 0.00 0.00 2.52
5676 6336 9.581099 TTGTTAATTTGAACTGTCTTTTTCTCC 57.419 29.630 0.00 0.00 0.00 3.71
5677 6337 8.966868 TGTTAATTTGAACTGTCTTTTTCTCCT 58.033 29.630 0.00 0.00 0.00 3.69
5678 6338 9.803315 GTTAATTTGAACTGTCTTTTTCTCCTT 57.197 29.630 0.00 0.00 0.00 3.36
5681 6341 8.707938 ATTTGAACTGTCTTTTTCTCCTTTTG 57.292 30.769 0.00 0.00 0.00 2.44
5682 6342 6.834168 TGAACTGTCTTTTTCTCCTTTTGT 57.166 33.333 0.00 0.00 0.00 2.83
5683 6343 7.931578 TGAACTGTCTTTTTCTCCTTTTGTA 57.068 32.000 0.00 0.00 0.00 2.41
5684 6344 8.343168 TGAACTGTCTTTTTCTCCTTTTGTAA 57.657 30.769 0.00 0.00 0.00 2.41
5685 6345 8.798402 TGAACTGTCTTTTTCTCCTTTTGTAAA 58.202 29.630 0.00 0.00 0.00 2.01
5686 6346 9.803315 GAACTGTCTTTTTCTCCTTTTGTAAAT 57.197 29.630 0.00 0.00 0.00 1.40
5691 6351 9.856488 GTCTTTTTCTCCTTTTGTAAATATCCC 57.144 33.333 0.00 0.00 0.00 3.85
5692 6352 9.031537 TCTTTTTCTCCTTTTGTAAATATCCCC 57.968 33.333 0.00 0.00 0.00 4.81
5693 6353 8.966155 TTTTTCTCCTTTTGTAAATATCCCCT 57.034 30.769 0.00 0.00 0.00 4.79
5694 6354 7.954666 TTTCTCCTTTTGTAAATATCCCCTG 57.045 36.000 0.00 0.00 0.00 4.45
5695 6355 5.445964 TCTCCTTTTGTAAATATCCCCTGC 58.554 41.667 0.00 0.00 0.00 4.85
5696 6356 5.044476 TCTCCTTTTGTAAATATCCCCTGCA 60.044 40.000 0.00 0.00 0.00 4.41
5697 6357 5.776358 TCCTTTTGTAAATATCCCCTGCAT 58.224 37.500 0.00 0.00 0.00 3.96
5698 6358 5.833131 TCCTTTTGTAAATATCCCCTGCATC 59.167 40.000 0.00 0.00 0.00 3.91
5699 6359 5.278463 CCTTTTGTAAATATCCCCTGCATCG 60.278 44.000 0.00 0.00 0.00 3.84
5700 6360 2.778299 TGTAAATATCCCCTGCATCGC 58.222 47.619 0.00 0.00 0.00 4.58
5701 6361 1.732259 GTAAATATCCCCTGCATCGCG 59.268 52.381 0.00 0.00 0.00 5.87
5702 6362 0.108585 AAATATCCCCTGCATCGCGT 59.891 50.000 5.77 0.00 0.00 6.01
5703 6363 0.108585 AATATCCCCTGCATCGCGTT 59.891 50.000 5.77 0.00 0.00 4.84
5704 6364 0.603707 ATATCCCCTGCATCGCGTTG 60.604 55.000 12.78 12.78 0.00 4.10
5712 6372 2.816083 CATCGCGTTGCCCCGTTA 60.816 61.111 5.77 0.00 0.00 3.18
5713 6373 2.816520 ATCGCGTTGCCCCGTTAC 60.817 61.111 5.77 0.00 0.00 2.50
5714 6374 3.305177 ATCGCGTTGCCCCGTTACT 62.305 57.895 5.77 0.00 0.00 2.24
5715 6375 3.784412 CGCGTTGCCCCGTTACTG 61.784 66.667 0.00 0.00 0.00 2.74
5716 6376 2.667199 GCGTTGCCCCGTTACTGT 60.667 61.111 0.00 0.00 0.00 3.55
5717 6377 2.255881 GCGTTGCCCCGTTACTGTT 61.256 57.895 0.00 0.00 0.00 3.16
5718 6378 1.572447 CGTTGCCCCGTTACTGTTG 59.428 57.895 0.00 0.00 0.00 3.33
5719 6379 1.847890 CGTTGCCCCGTTACTGTTGG 61.848 60.000 0.00 0.00 0.00 3.77
5720 6380 0.820482 GTTGCCCCGTTACTGTTGGT 60.820 55.000 0.00 0.00 0.00 3.67
5721 6381 0.106619 TTGCCCCGTTACTGTTGGTT 60.107 50.000 0.00 0.00 0.00 3.67
5722 6382 0.106619 TGCCCCGTTACTGTTGGTTT 60.107 50.000 0.00 0.00 0.00 3.27
5723 6383 0.594602 GCCCCGTTACTGTTGGTTTC 59.405 55.000 0.00 0.00 0.00 2.78
5724 6384 1.970092 CCCCGTTACTGTTGGTTTCA 58.030 50.000 0.00 0.00 0.00 2.69
5725 6385 1.877443 CCCCGTTACTGTTGGTTTCAG 59.123 52.381 0.00 0.00 38.68 3.02
5726 6386 1.877443 CCCGTTACTGTTGGTTTCAGG 59.123 52.381 0.00 0.00 37.25 3.86
5727 6387 2.485835 CCCGTTACTGTTGGTTTCAGGA 60.486 50.000 0.00 0.00 37.25 3.86
5728 6388 3.207778 CCGTTACTGTTGGTTTCAGGAA 58.792 45.455 0.00 0.00 37.25 3.36
5729 6389 3.628487 CCGTTACTGTTGGTTTCAGGAAA 59.372 43.478 0.00 0.00 37.47 3.13
5730 6390 4.277423 CCGTTACTGTTGGTTTCAGGAAAT 59.723 41.667 0.00 0.00 37.47 2.17
5731 6391 5.212194 CGTTACTGTTGGTTTCAGGAAATG 58.788 41.667 0.00 0.00 37.47 2.32
5732 6392 5.220970 CGTTACTGTTGGTTTCAGGAAATGT 60.221 40.000 0.00 0.00 37.47 2.71
5733 6393 6.569780 GTTACTGTTGGTTTCAGGAAATGTT 58.430 36.000 0.00 0.00 37.47 2.71
5734 6394 5.009854 ACTGTTGGTTTCAGGAAATGTTG 57.990 39.130 0.00 0.00 37.25 3.33
5735 6395 3.791245 TGTTGGTTTCAGGAAATGTTGC 58.209 40.909 0.00 0.00 32.36 4.17
5736 6396 3.196469 TGTTGGTTTCAGGAAATGTTGCA 59.804 39.130 0.00 0.00 32.36 4.08
5737 6397 4.187694 GTTGGTTTCAGGAAATGTTGCAA 58.812 39.130 0.00 0.00 32.36 4.08
5738 6398 4.478206 TGGTTTCAGGAAATGTTGCAAA 57.522 36.364 0.00 0.00 32.36 3.68
5739 6399 5.033589 TGGTTTCAGGAAATGTTGCAAAT 57.966 34.783 0.00 0.00 32.36 2.32
5740 6400 5.055812 TGGTTTCAGGAAATGTTGCAAATC 58.944 37.500 0.00 0.00 32.36 2.17
5741 6401 4.452114 GGTTTCAGGAAATGTTGCAAATCC 59.548 41.667 0.00 7.21 32.36 3.01
5742 6402 3.574284 TCAGGAAATGTTGCAAATCCG 57.426 42.857 0.00 4.43 35.31 4.18
5743 6403 3.153130 TCAGGAAATGTTGCAAATCCGA 58.847 40.909 0.00 6.51 35.31 4.55
5744 6404 3.057596 TCAGGAAATGTTGCAAATCCGAC 60.058 43.478 0.00 0.00 35.31 4.79
5745 6405 2.095263 AGGAAATGTTGCAAATCCGACG 60.095 45.455 0.00 0.00 35.31 5.12
5746 6406 2.351350 GGAAATGTTGCAAATCCGACGT 60.351 45.455 0.00 0.00 0.00 4.34
5747 6407 3.305110 GAAATGTTGCAAATCCGACGTT 58.695 40.909 0.00 0.00 31.28 3.99
5748 6408 4.468643 GAAATGTTGCAAATCCGACGTTA 58.531 39.130 0.00 0.00 30.16 3.18
5749 6409 3.740044 ATGTTGCAAATCCGACGTTAG 57.260 42.857 0.00 0.00 0.00 2.34
5750 6410 2.756829 TGTTGCAAATCCGACGTTAGA 58.243 42.857 0.00 0.00 0.00 2.10
5751 6411 3.331150 TGTTGCAAATCCGACGTTAGAT 58.669 40.909 0.00 0.00 0.00 1.98
5752 6412 3.749088 TGTTGCAAATCCGACGTTAGATT 59.251 39.130 0.00 7.88 34.18 2.40
5753 6413 4.214545 TGTTGCAAATCCGACGTTAGATTT 59.785 37.500 16.61 16.61 42.08 2.17
5754 6414 5.151389 GTTGCAAATCCGACGTTAGATTTT 58.849 37.500 18.69 6.99 39.97 1.82
5755 6415 4.717991 TGCAAATCCGACGTTAGATTTTG 58.282 39.130 18.69 15.58 39.97 2.44
5756 6416 4.452795 TGCAAATCCGACGTTAGATTTTGA 59.547 37.500 18.69 9.48 39.97 2.69
5757 6417 5.049336 TGCAAATCCGACGTTAGATTTTGAA 60.049 36.000 18.69 10.14 39.97 2.69
5758 6418 5.283012 GCAAATCCGACGTTAGATTTTGAAC 59.717 40.000 18.69 9.27 39.97 3.18
5759 6419 6.367421 CAAATCCGACGTTAGATTTTGAACA 58.633 36.000 18.69 0.00 39.97 3.18
5760 6420 4.977741 TCCGACGTTAGATTTTGAACAC 57.022 40.909 0.00 0.00 0.00 3.32
5761 6421 4.624015 TCCGACGTTAGATTTTGAACACT 58.376 39.130 0.00 0.00 0.00 3.55
5762 6422 5.771469 TCCGACGTTAGATTTTGAACACTA 58.229 37.500 0.00 0.00 0.00 2.74
5763 6423 6.215121 TCCGACGTTAGATTTTGAACACTAA 58.785 36.000 0.00 0.00 0.00 2.24
5764 6424 6.700960 TCCGACGTTAGATTTTGAACACTAAA 59.299 34.615 0.00 0.00 0.00 1.85
5765 6425 7.224362 TCCGACGTTAGATTTTGAACACTAAAA 59.776 33.333 0.00 0.00 0.00 1.52
5766 6426 7.851963 CCGACGTTAGATTTTGAACACTAAAAA 59.148 33.333 0.00 0.00 31.54 1.94
5767 6427 9.377383 CGACGTTAGATTTTGAACACTAAAAAT 57.623 29.630 0.00 0.00 38.39 1.82
5769 6429 9.673454 ACGTTAGATTTTGAACACTAAAAATCC 57.327 29.630 14.17 2.96 46.70 3.01
5770 6430 9.672086 CGTTAGATTTTGAACACTAAAAATCCA 57.328 29.630 14.17 2.27 46.70 3.41
5774 6434 8.912988 AGATTTTGAACACTAAAAATCCAGTGA 58.087 29.630 14.17 0.00 46.70 3.41
5775 6435 8.871686 ATTTTGAACACTAAAAATCCAGTGAC 57.128 30.769 8.61 3.56 43.99 3.67
5776 6436 6.385649 TTGAACACTAAAAATCCAGTGACC 57.614 37.500 8.61 1.22 43.99 4.02
5777 6437 5.441500 TGAACACTAAAAATCCAGTGACCA 58.558 37.500 8.61 3.49 43.99 4.02
5778 6438 5.530915 TGAACACTAAAAATCCAGTGACCAG 59.469 40.000 8.61 0.00 43.99 4.00
5779 6439 5.304686 ACACTAAAAATCCAGTGACCAGA 57.695 39.130 8.61 0.00 43.99 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 9.653287 CAGAGACCAAATTACTACTACAATGAA 57.347 33.333 0.00 0.00 0.00 2.57
4 5 7.764443 GCAGAGACCAAATTACTACTACAATGA 59.236 37.037 0.00 0.00 0.00 2.57
5 6 7.766278 AGCAGAGACCAAATTACTACTACAATG 59.234 37.037 0.00 0.00 0.00 2.82
6 7 7.766278 CAGCAGAGACCAAATTACTACTACAAT 59.234 37.037 0.00 0.00 0.00 2.71
7 8 7.097192 CAGCAGAGACCAAATTACTACTACAA 58.903 38.462 0.00 0.00 0.00 2.41
8 9 6.210784 ACAGCAGAGACCAAATTACTACTACA 59.789 38.462 0.00 0.00 0.00 2.74
9 10 6.531948 CACAGCAGAGACCAAATTACTACTAC 59.468 42.308 0.00 0.00 0.00 2.73
10 11 6.210784 ACACAGCAGAGACCAAATTACTACTA 59.789 38.462 0.00 0.00 0.00 1.82
11 12 5.012148 ACACAGCAGAGACCAAATTACTACT 59.988 40.000 0.00 0.00 0.00 2.57
12 13 5.238583 ACACAGCAGAGACCAAATTACTAC 58.761 41.667 0.00 0.00 0.00 2.73
13 14 5.011635 TGACACAGCAGAGACCAAATTACTA 59.988 40.000 0.00 0.00 0.00 1.82
14 15 4.202357 TGACACAGCAGAGACCAAATTACT 60.202 41.667 0.00 0.00 0.00 2.24
15 16 4.065088 TGACACAGCAGAGACCAAATTAC 58.935 43.478 0.00 0.00 0.00 1.89
29 30 3.049206 GCGAGAGAATATCTGACACAGC 58.951 50.000 0.00 0.00 38.84 4.40
58 59 0.737019 TGCGATTAACGTCCGGGTTC 60.737 55.000 0.00 0.00 44.60 3.62
201 208 2.743179 GGGACGGGGAGGATTCCAC 61.743 68.421 5.29 0.00 45.98 4.02
225 232 0.798776 CAATCAGACAACGGGCAGAC 59.201 55.000 0.00 0.00 0.00 3.51
566 579 1.153349 AAGAGCCTCGCGGAATTCC 60.153 57.895 15.01 15.01 0.00 3.01
581 594 1.356398 GGTCCACCCATAAACCCAAGA 59.644 52.381 0.00 0.00 0.00 3.02
602 615 3.423645 GGAGCGATGAAACGAAAACTCAG 60.424 47.826 0.00 0.00 35.09 3.35
636 649 1.623163 GCTAGGTAGGGAGCGAATCT 58.377 55.000 0.00 0.00 0.00 2.40
646 659 0.972883 GGATCTGCAGGCTAGGTAGG 59.027 60.000 15.13 0.00 0.00 3.18
688 701 1.154093 CGCCGAAAGACTAGCACGA 60.154 57.895 0.00 0.00 0.00 4.35
690 703 0.924090 CATCGCCGAAAGACTAGCAC 59.076 55.000 0.00 0.00 0.00 4.40
698 711 2.753966 CCCACAGCATCGCCGAAAG 61.754 63.158 0.00 0.00 0.00 2.62
701 714 4.451150 GACCCACAGCATCGCCGA 62.451 66.667 0.00 0.00 0.00 5.54
820 843 1.212751 GAATTGCAACTGTCCCCGC 59.787 57.895 0.00 0.00 0.00 6.13
821 844 0.523072 CTGAATTGCAACTGTCCCCG 59.477 55.000 0.00 0.00 0.00 5.73
824 847 1.337703 TGTGCTGAATTGCAACTGTCC 59.662 47.619 0.00 0.00 45.12 4.02
825 848 2.388121 GTGTGCTGAATTGCAACTGTC 58.612 47.619 0.00 0.00 45.12 3.51
826 849 1.268692 CGTGTGCTGAATTGCAACTGT 60.269 47.619 0.00 0.00 45.12 3.55
827 850 1.401530 CGTGTGCTGAATTGCAACTG 58.598 50.000 0.00 0.00 45.12 3.16
866 889 3.684788 CACGCTAGCTGTTCCATTTAAGT 59.315 43.478 13.93 0.00 0.00 2.24
872 895 0.036010 AAGCACGCTAGCTGTTCCAT 60.036 50.000 13.93 0.00 45.89 3.41
882 905 0.521291 GGCATGAACAAAGCACGCTA 59.479 50.000 0.00 0.00 0.00 4.26
912 935 8.699283 AATACTAGTAAGAAATTCACACGGAC 57.301 34.615 6.70 0.00 0.00 4.79
926 949 7.873505 GGCTGGGAAATCACTAATACTAGTAAG 59.126 40.741 6.70 3.34 36.14 2.34
927 950 7.567622 AGGCTGGGAAATCACTAATACTAGTAA 59.432 37.037 6.70 0.00 36.14 2.24
928 951 7.073854 AGGCTGGGAAATCACTAATACTAGTA 58.926 38.462 4.77 4.77 36.14 1.82
929 952 5.905913 AGGCTGGGAAATCACTAATACTAGT 59.094 40.000 0.00 0.00 39.04 2.57
930 953 6.426646 AGGCTGGGAAATCACTAATACTAG 57.573 41.667 0.00 0.00 0.00 2.57
933 956 5.437060 TGAAGGCTGGGAAATCACTAATAC 58.563 41.667 0.00 0.00 0.00 1.89
936 959 4.591321 ATGAAGGCTGGGAAATCACTAA 57.409 40.909 0.00 0.00 0.00 2.24
956 979 5.299279 CACACCAAACTACACTTCAGGAAAT 59.701 40.000 0.00 0.00 0.00 2.17
1279 1311 7.768807 AGTTTAGCACATTACCCAATAAACA 57.231 32.000 0.00 0.00 0.00 2.83
1329 1361 5.643379 TGTCAACTTTCCATTTATGAGCC 57.357 39.130 0.00 0.00 0.00 4.70
1629 1947 5.774690 TGGAGTGCTTCATTTTAGACCAAAT 59.225 36.000 0.00 0.00 0.00 2.32
1972 2290 4.799564 AGTGGCAAACAAGAACAGAAAA 57.200 36.364 0.00 0.00 0.00 2.29
1973 2291 4.799564 AAGTGGCAAACAAGAACAGAAA 57.200 36.364 0.00 0.00 0.00 2.52
2359 2678 3.477530 AGTCTGGGAACAAAGCTACAAC 58.522 45.455 0.00 0.00 42.06 3.32
2415 2740 8.989980 GCATACAGTTTTCCAGATATAACCTAC 58.010 37.037 0.00 0.00 0.00 3.18
2439 2765 0.609957 CATCAACTTCAGGCCCAGCA 60.610 55.000 0.00 0.00 0.00 4.41
2559 2885 7.975058 CCATTCAAATGCAGACAACACATATAA 59.025 33.333 0.00 0.00 35.08 0.98
3347 3716 2.367030 TTTGCACATAACAGGCATGC 57.633 45.000 9.90 9.90 37.39 4.06
3348 3717 5.004630 CGTTAATTTGCACATAACAGGCATG 59.995 40.000 0.00 0.00 37.39 4.06
3517 3886 7.148573 GCAGTCAGAAGATTAAAACAGAATCGA 60.149 37.037 0.00 0.00 38.18 3.59
3678 4047 2.229784 GCTGGAAAATGTGGTCTCAAGG 59.770 50.000 0.00 0.00 0.00 3.61
4127 4496 5.186198 GCTACACTGTTTAACCATCAGGAT 58.814 41.667 0.00 0.00 38.69 3.24
4139 4508 1.136828 TGAGGGGTGCTACACTGTTT 58.863 50.000 0.00 0.00 34.40 2.83
4140 4509 1.136828 TTGAGGGGTGCTACACTGTT 58.863 50.000 0.00 0.00 34.40 3.16
4141 4510 1.136828 TTTGAGGGGTGCTACACTGT 58.863 50.000 0.00 0.00 34.40 3.55
4142 4511 2.270352 TTTTGAGGGGTGCTACACTG 57.730 50.000 0.00 0.00 34.40 3.66
4162 4531 4.335594 GTCAAGGTCTGCTACACTGTTTTT 59.664 41.667 0.00 0.00 0.00 1.94
4163 4532 3.877508 GTCAAGGTCTGCTACACTGTTTT 59.122 43.478 0.00 0.00 0.00 2.43
4297 4666 7.071069 TGCAGGATATGTGAAGAGTTATCAT 57.929 36.000 0.00 0.00 0.00 2.45
4462 4834 6.729690 TGGGAGTTGAATTTCAGTTTTCAT 57.270 33.333 0.00 0.00 32.27 2.57
4491 4863 1.961394 ACTGAAGTAAGAGGTGACGCA 59.039 47.619 0.00 0.00 0.00 5.24
4501 4873 5.446709 CATCAAGTGCACAACTGAAGTAAG 58.553 41.667 21.04 4.78 39.81 2.34
4532 4906 1.601171 GCTGAGTGGAGGCACATCT 59.399 57.895 0.00 0.00 0.00 2.90
4555 4929 9.646336 CGTATAGGTTTGTGAATTATGTAAAGC 57.354 33.333 0.00 0.00 0.00 3.51
4570 4944 8.397906 ACATGTGATTTCAATCGTATAGGTTTG 58.602 33.333 0.00 9.10 38.26 2.93
4589 5002 3.932710 GCACGGATAAAGAGAACATGTGA 59.067 43.478 0.00 0.00 0.00 3.58
4592 5005 3.242543 GCAGCACGGATAAAGAGAACATG 60.243 47.826 0.00 0.00 0.00 3.21
4601 5014 2.092968 AGAAGGATGCAGCACGGATAAA 60.093 45.455 3.51 0.00 0.00 1.40
4611 5024 4.869297 CAGAGACAACTAAGAAGGATGCAG 59.131 45.833 0.00 0.00 0.00 4.41
4617 5030 8.307483 TCAGAAATACAGAGACAACTAAGAAGG 58.693 37.037 0.00 0.00 0.00 3.46
4652 5065 1.209261 TGTAAAGCTGCATCGGATGGA 59.791 47.619 18.96 15.47 0.00 3.41
4653 5066 1.667236 TGTAAAGCTGCATCGGATGG 58.333 50.000 18.96 5.13 0.00 3.51
4654 5067 3.763097 TTTGTAAAGCTGCATCGGATG 57.237 42.857 13.63 13.63 0.00 3.51
4655 5068 3.505680 TGTTTTGTAAAGCTGCATCGGAT 59.494 39.130 1.02 0.00 0.00 4.18
4656 5069 2.881513 TGTTTTGTAAAGCTGCATCGGA 59.118 40.909 1.02 0.00 0.00 4.55
4657 5070 3.281341 TGTTTTGTAAAGCTGCATCGG 57.719 42.857 1.02 0.00 0.00 4.18
4658 5071 4.536065 TCTTGTTTTGTAAAGCTGCATCG 58.464 39.130 1.02 0.00 0.00 3.84
4659 5072 5.762045 TCTCTTGTTTTGTAAAGCTGCATC 58.238 37.500 1.02 0.00 0.00 3.91
4660 5073 5.772825 TCTCTTGTTTTGTAAAGCTGCAT 57.227 34.783 1.02 0.00 0.00 3.96
4661 5074 5.299028 TCATCTCTTGTTTTGTAAAGCTGCA 59.701 36.000 1.02 0.00 0.00 4.41
4662 5075 5.762045 TCATCTCTTGTTTTGTAAAGCTGC 58.238 37.500 0.00 0.00 0.00 5.25
4663 5076 7.194607 TCTCATCTCTTGTTTTGTAAAGCTG 57.805 36.000 0.00 0.00 0.00 4.24
4664 5077 7.807977 TTCTCATCTCTTGTTTTGTAAAGCT 57.192 32.000 0.00 0.00 0.00 3.74
4737 5150 0.946221 GGAAGGCGGCACATAGATCG 60.946 60.000 13.08 0.00 0.00 3.69
4755 5168 1.032014 GGACTCTCAGCTGAGCTAGG 58.968 60.000 34.48 24.72 41.80 3.02
4776 5189 0.752658 TCGGGCACATCTGGTATCAG 59.247 55.000 0.00 0.00 42.21 2.90
4810 5223 9.587772 TTGCTATTTACATCTCTTTAGAGTGAC 57.412 33.333 6.65 0.00 42.60 3.67
4864 5277 3.181486 ACAGCTCCACATGTCTACATACG 60.181 47.826 0.00 0.00 34.26 3.06
4878 5291 2.566833 ATAAGCACACAACAGCTCCA 57.433 45.000 0.00 0.00 40.90 3.86
4934 5353 2.256461 CTTGCTTCACTTGCCCGC 59.744 61.111 0.00 0.00 0.00 6.13
4954 5373 3.753294 AACCTGATGGCTATAGTTCCG 57.247 47.619 0.84 0.00 36.63 4.30
4963 5382 2.243221 AGCTGGAAATAACCTGATGGCT 59.757 45.455 0.00 0.00 36.63 4.75
5051 5470 4.608948 AAAACAGCAGCAGAGTAGTACT 57.391 40.909 1.37 1.37 0.00 2.73
5052 5471 5.471257 AGTAAAACAGCAGCAGAGTAGTAC 58.529 41.667 0.00 0.00 0.00 2.73
5053 5472 5.723672 AGTAAAACAGCAGCAGAGTAGTA 57.276 39.130 0.00 0.00 0.00 1.82
5054 5473 4.608948 AGTAAAACAGCAGCAGAGTAGT 57.391 40.909 0.00 0.00 0.00 2.73
5055 5474 4.377841 GCAAGTAAAACAGCAGCAGAGTAG 60.378 45.833 0.00 0.00 0.00 2.57
5137 5558 6.101332 TCAGCTTTCATTAACCATTGCAATC 58.899 36.000 9.53 0.00 0.00 2.67
5172 5593 4.664150 TGATATACGATTGTCTGTGGCA 57.336 40.909 0.00 0.00 0.00 4.92
5211 5632 5.788450 AGATCAGGCACCTCGAATTATTAG 58.212 41.667 0.00 0.00 0.00 1.73
5212 5633 5.540337 AGAGATCAGGCACCTCGAATTATTA 59.460 40.000 0.00 0.00 32.52 0.98
5213 5634 4.346418 AGAGATCAGGCACCTCGAATTATT 59.654 41.667 0.00 0.00 32.52 1.40
5214 5635 3.900601 AGAGATCAGGCACCTCGAATTAT 59.099 43.478 0.00 0.00 32.52 1.28
5227 5648 2.545532 GGACGCATCAGAAGAGATCAGG 60.546 54.545 0.00 0.00 0.00 3.86
5269 5694 2.609737 GGAAGATTCTCAACGGACGTGT 60.610 50.000 0.00 0.00 0.00 4.49
5334 5759 1.271108 TGACCACGCTAAAGCCAATGA 60.271 47.619 0.00 0.00 37.91 2.57
5335 5760 1.164411 TGACCACGCTAAAGCCAATG 58.836 50.000 0.00 0.00 37.91 2.82
5336 5761 1.904287 TTGACCACGCTAAAGCCAAT 58.096 45.000 0.00 0.00 37.91 3.16
5337 5762 1.810151 GATTGACCACGCTAAAGCCAA 59.190 47.619 0.00 0.00 37.91 4.52
5338 5763 1.271108 TGATTGACCACGCTAAAGCCA 60.271 47.619 0.00 0.00 37.91 4.75
5339 5764 1.398390 CTGATTGACCACGCTAAAGCC 59.602 52.381 0.00 0.00 37.91 4.35
5340 5765 2.076863 ACTGATTGACCACGCTAAAGC 58.923 47.619 0.00 0.00 37.78 3.51
5341 5766 4.242475 TGTACTGATTGACCACGCTAAAG 58.758 43.478 0.00 0.00 0.00 1.85
5342 5767 4.242475 CTGTACTGATTGACCACGCTAAA 58.758 43.478 0.00 0.00 0.00 1.85
5343 5768 3.845178 CTGTACTGATTGACCACGCTAA 58.155 45.455 0.00 0.00 0.00 3.09
5344 5769 2.416836 GCTGTACTGATTGACCACGCTA 60.417 50.000 3.61 0.00 0.00 4.26
5345 5770 1.673033 GCTGTACTGATTGACCACGCT 60.673 52.381 3.61 0.00 0.00 5.07
5346 5771 0.721718 GCTGTACTGATTGACCACGC 59.278 55.000 3.61 0.00 0.00 5.34
5347 5772 2.370281 AGCTGTACTGATTGACCACG 57.630 50.000 3.61 0.00 0.00 4.94
5358 5783 1.349026 AGCCAATGACACAGCTGTACT 59.651 47.619 21.20 7.57 33.41 2.73
5359 5784 1.466167 CAGCCAATGACACAGCTGTAC 59.534 52.381 21.20 16.78 46.00 2.90
5360 5785 1.812235 CAGCCAATGACACAGCTGTA 58.188 50.000 21.20 4.30 46.00 2.74
5361 5786 2.637521 CAGCCAATGACACAGCTGT 58.362 52.632 15.25 15.25 46.00 4.40
5363 5788 0.689055 TCTCAGCCAATGACACAGCT 59.311 50.000 0.00 0.00 33.22 4.24
5364 5789 1.198637 GTTCTCAGCCAATGACACAGC 59.801 52.381 0.00 0.00 33.22 4.40
5365 5790 2.497138 TGTTCTCAGCCAATGACACAG 58.503 47.619 0.00 0.00 33.22 3.66
5366 5791 2.636647 TGTTCTCAGCCAATGACACA 57.363 45.000 0.00 0.00 33.22 3.72
5367 5792 3.829948 CATTGTTCTCAGCCAATGACAC 58.170 45.455 10.00 0.00 46.93 3.67
5368 5793 2.229543 GCATTGTTCTCAGCCAATGACA 59.770 45.455 16.75 0.00 46.93 3.58
5369 5794 2.730090 CGCATTGTTCTCAGCCAATGAC 60.730 50.000 16.75 9.52 46.93 3.06
5370 5795 1.469703 CGCATTGTTCTCAGCCAATGA 59.530 47.619 16.75 0.00 46.93 2.57
5417 5844 1.087501 GGCAGCTTACTAGGCAACAC 58.912 55.000 0.00 0.00 41.41 3.32
5421 5848 0.541863 GGAAGGCAGCTTACTAGGCA 59.458 55.000 0.00 0.00 0.00 4.75
5484 6143 0.108585 GGTGGTGTCCAAAGCTGAGA 59.891 55.000 0.00 0.00 34.18 3.27
5504 6163 3.717294 GTGCCCTCCCATCGTGGT 61.717 66.667 3.82 0.00 35.17 4.16
5505 6164 2.876368 GAAGTGCCCTCCCATCGTGG 62.876 65.000 0.00 0.00 37.25 4.94
5506 6165 1.450312 GAAGTGCCCTCCCATCGTG 60.450 63.158 0.00 0.00 0.00 4.35
5547 6207 4.092968 GCGTTTTCTCCTACTACCAACATG 59.907 45.833 0.00 0.00 0.00 3.21
5595 6255 2.297701 GTGGACTCCAAGCAAGAACAA 58.702 47.619 0.00 0.00 34.18 2.83
5607 6267 4.736896 GACCGGTGCGTGGACTCC 62.737 72.222 14.63 0.00 0.00 3.85
5667 6327 9.035890 AGGGGATATTTACAAAAGGAGAAAAAG 57.964 33.333 0.00 0.00 0.00 2.27
5668 6328 8.811994 CAGGGGATATTTACAAAAGGAGAAAAA 58.188 33.333 0.00 0.00 0.00 1.94
5669 6329 7.093509 GCAGGGGATATTTACAAAAGGAGAAAA 60.094 37.037 0.00 0.00 0.00 2.29
5670 6330 6.379988 GCAGGGGATATTTACAAAAGGAGAAA 59.620 38.462 0.00 0.00 0.00 2.52
5671 6331 5.891551 GCAGGGGATATTTACAAAAGGAGAA 59.108 40.000 0.00 0.00 0.00 2.87
5672 6332 5.044476 TGCAGGGGATATTTACAAAAGGAGA 60.044 40.000 0.00 0.00 0.00 3.71
5673 6333 5.200483 TGCAGGGGATATTTACAAAAGGAG 58.800 41.667 0.00 0.00 0.00 3.69
5674 6334 5.199982 TGCAGGGGATATTTACAAAAGGA 57.800 39.130 0.00 0.00 0.00 3.36
5675 6335 5.278463 CGATGCAGGGGATATTTACAAAAGG 60.278 44.000 0.00 0.00 0.00 3.11
5676 6336 5.762045 CGATGCAGGGGATATTTACAAAAG 58.238 41.667 0.00 0.00 0.00 2.27
5677 6337 4.037446 GCGATGCAGGGGATATTTACAAAA 59.963 41.667 0.00 0.00 0.00 2.44
5678 6338 3.568007 GCGATGCAGGGGATATTTACAAA 59.432 43.478 0.00 0.00 0.00 2.83
5679 6339 3.146066 GCGATGCAGGGGATATTTACAA 58.854 45.455 0.00 0.00 0.00 2.41
5680 6340 2.778299 GCGATGCAGGGGATATTTACA 58.222 47.619 0.00 0.00 0.00 2.41
5681 6341 1.732259 CGCGATGCAGGGGATATTTAC 59.268 52.381 0.00 0.00 0.00 2.01
5682 6342 1.346395 ACGCGATGCAGGGGATATTTA 59.654 47.619 15.93 0.00 0.00 1.40
5683 6343 0.108585 ACGCGATGCAGGGGATATTT 59.891 50.000 15.93 0.00 0.00 1.40
5684 6344 0.108585 AACGCGATGCAGGGGATATT 59.891 50.000 15.93 0.00 0.00 1.28
5685 6345 0.603707 CAACGCGATGCAGGGGATAT 60.604 55.000 15.93 0.00 0.00 1.63
5686 6346 1.227527 CAACGCGATGCAGGGGATA 60.228 57.895 15.93 0.00 0.00 2.59
5687 6347 2.514592 CAACGCGATGCAGGGGAT 60.515 61.111 15.93 0.00 0.00 3.85
5700 6360 1.572447 CAACAGTAACGGGGCAACG 59.428 57.895 0.00 0.00 40.31 4.10
5701 6361 0.820482 ACCAACAGTAACGGGGCAAC 60.820 55.000 0.00 0.00 0.00 4.17
5702 6362 0.106619 AACCAACAGTAACGGGGCAA 60.107 50.000 0.00 0.00 0.00 4.52
5703 6363 0.106619 AAACCAACAGTAACGGGGCA 60.107 50.000 0.00 0.00 0.00 5.36
5704 6364 0.594602 GAAACCAACAGTAACGGGGC 59.405 55.000 0.00 0.00 0.00 5.80
5705 6365 1.877443 CTGAAACCAACAGTAACGGGG 59.123 52.381 0.00 0.00 0.00 5.73
5706 6366 1.877443 CCTGAAACCAACAGTAACGGG 59.123 52.381 0.00 0.00 34.04 5.28
5707 6367 2.841215 TCCTGAAACCAACAGTAACGG 58.159 47.619 0.00 0.00 34.04 4.44
5708 6368 4.886247 TTTCCTGAAACCAACAGTAACG 57.114 40.909 0.00 0.00 34.04 3.18
5709 6369 6.144078 ACATTTCCTGAAACCAACAGTAAC 57.856 37.500 0.00 0.00 34.04 2.50
5710 6370 6.568869 CAACATTTCCTGAAACCAACAGTAA 58.431 36.000 0.00 0.00 34.04 2.24
5711 6371 5.451242 GCAACATTTCCTGAAACCAACAGTA 60.451 40.000 0.00 0.00 34.04 2.74
5712 6372 4.680440 GCAACATTTCCTGAAACCAACAGT 60.680 41.667 0.00 0.00 34.04 3.55
5713 6373 3.803778 GCAACATTTCCTGAAACCAACAG 59.196 43.478 0.00 0.00 32.51 3.16
5714 6374 3.196469 TGCAACATTTCCTGAAACCAACA 59.804 39.130 0.00 0.00 32.51 3.33
5715 6375 3.791245 TGCAACATTTCCTGAAACCAAC 58.209 40.909 0.00 0.00 32.51 3.77
5716 6376 4.478206 TTGCAACATTTCCTGAAACCAA 57.522 36.364 0.00 0.00 32.51 3.67
5717 6377 4.478206 TTTGCAACATTTCCTGAAACCA 57.522 36.364 0.00 0.00 32.51 3.67
5718 6378 4.452114 GGATTTGCAACATTTCCTGAAACC 59.548 41.667 0.00 0.00 32.51 3.27
5719 6379 4.150451 CGGATTTGCAACATTTCCTGAAAC 59.850 41.667 0.00 0.00 32.51 2.78
5720 6380 4.038522 TCGGATTTGCAACATTTCCTGAAA 59.961 37.500 0.00 0.00 34.46 2.69
5721 6381 3.571828 TCGGATTTGCAACATTTCCTGAA 59.428 39.130 0.00 0.00 0.00 3.02
5722 6382 3.057596 GTCGGATTTGCAACATTTCCTGA 60.058 43.478 0.00 3.55 0.00 3.86
5723 6383 3.244976 GTCGGATTTGCAACATTTCCTG 58.755 45.455 0.00 1.37 0.00 3.86
5724 6384 2.095263 CGTCGGATTTGCAACATTTCCT 60.095 45.455 0.00 0.00 0.00 3.36
5725 6385 2.250188 CGTCGGATTTGCAACATTTCC 58.750 47.619 0.00 2.71 0.00 3.13
5726 6386 2.928694 ACGTCGGATTTGCAACATTTC 58.071 42.857 0.00 0.00 0.00 2.17
5727 6387 3.363341 AACGTCGGATTTGCAACATTT 57.637 38.095 0.00 0.00 0.00 2.32
5728 6388 3.749088 TCTAACGTCGGATTTGCAACATT 59.251 39.130 0.00 0.00 0.00 2.71
5729 6389 3.331150 TCTAACGTCGGATTTGCAACAT 58.669 40.909 0.00 0.00 0.00 2.71
5730 6390 2.756829 TCTAACGTCGGATTTGCAACA 58.243 42.857 0.00 0.00 0.00 3.33
5731 6391 4.336532 AATCTAACGTCGGATTTGCAAC 57.663 40.909 0.00 0.00 0.00 4.17
5732 6392 5.049336 TCAAAATCTAACGTCGGATTTGCAA 60.049 36.000 21.23 0.00 40.58 4.08
5733 6393 4.452795 TCAAAATCTAACGTCGGATTTGCA 59.547 37.500 21.23 12.62 40.58 4.08
5734 6394 4.965062 TCAAAATCTAACGTCGGATTTGC 58.035 39.130 21.23 0.00 40.58 3.68
5735 6395 6.302313 GTGTTCAAAATCTAACGTCGGATTTG 59.698 38.462 21.23 14.49 40.58 2.32
5736 6396 6.204108 AGTGTTCAAAATCTAACGTCGGATTT 59.796 34.615 17.35 17.35 41.92 2.17
5737 6397 5.699458 AGTGTTCAAAATCTAACGTCGGATT 59.301 36.000 9.28 9.28 34.14 3.01
5738 6398 5.235516 AGTGTTCAAAATCTAACGTCGGAT 58.764 37.500 0.00 0.00 0.00 4.18
5739 6399 4.624015 AGTGTTCAAAATCTAACGTCGGA 58.376 39.130 0.00 0.00 0.00 4.55
5740 6400 4.985044 AGTGTTCAAAATCTAACGTCGG 57.015 40.909 0.00 0.00 0.00 4.79
5741 6401 8.756376 TTTTTAGTGTTCAAAATCTAACGTCG 57.244 30.769 0.00 0.00 0.00 5.12
5743 6403 9.673454 GGATTTTTAGTGTTCAAAATCTAACGT 57.327 29.630 14.05 0.00 44.03 3.99
5744 6404 9.672086 TGGATTTTTAGTGTTCAAAATCTAACG 57.328 29.630 14.05 0.00 44.03 3.18
5748 6408 8.912988 TCACTGGATTTTTAGTGTTCAAAATCT 58.087 29.630 14.05 0.00 44.03 2.40
5749 6409 8.968242 GTCACTGGATTTTTAGTGTTCAAAATC 58.032 33.333 8.29 8.29 43.92 2.17
5750 6410 7.926018 GGTCACTGGATTTTTAGTGTTCAAAAT 59.074 33.333 0.00 0.00 43.59 1.82
5751 6411 7.093727 TGGTCACTGGATTTTTAGTGTTCAAAA 60.094 33.333 0.00 0.00 43.59 2.44
5752 6412 6.378564 TGGTCACTGGATTTTTAGTGTTCAAA 59.621 34.615 0.00 0.00 43.59 2.69
5753 6413 5.888724 TGGTCACTGGATTTTTAGTGTTCAA 59.111 36.000 0.00 0.00 43.59 2.69
5754 6414 5.441500 TGGTCACTGGATTTTTAGTGTTCA 58.558 37.500 0.00 0.00 43.59 3.18
5755 6415 5.763204 TCTGGTCACTGGATTTTTAGTGTTC 59.237 40.000 0.00 0.00 43.59 3.18
5756 6416 5.690865 TCTGGTCACTGGATTTTTAGTGTT 58.309 37.500 0.00 0.00 43.59 3.32
5757 6417 5.304686 TCTGGTCACTGGATTTTTAGTGT 57.695 39.130 0.00 0.00 43.59 3.55


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

AutoCloner maintained by Alex Coulton.