Multiple sequence alignment - TraesCS1D01G198500

Loading Multiple Alignment...

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 TraesCS1D01G198500 chr1D 100.000 4902 0 0 1 4902 279950999 279946098 0.000000e+00 9053.0
1 TraesCS1D01G198500 chr1D 97.059 34 1 0 4048 4081 279946884 279946851 1.910000e-04 58.4
2 TraesCS1D01G198500 chr1D 97.059 34 1 0 4116 4149 279946952 279946919 1.910000e-04 58.4
3 TraesCS1D01G198500 chr1B 90.025 2787 118 55 104 2851 380471363 380468698 0.000000e+00 3459.0
4 TraesCS1D01G198500 chr1B 94.715 1192 42 9 2841 4027 380468678 380467503 0.000000e+00 1832.0
5 TraesCS1D01G198500 chr1B 94.511 583 19 5 4094 4664 380467359 380466778 0.000000e+00 887.0
6 TraesCS1D01G198500 chr1B 98.742 159 2 0 4744 4902 380466781 380466623 2.890000e-72 283.0
7 TraesCS1D01G198500 chr1A 88.520 1716 94 40 2403 4052 351884581 351882903 0.000000e+00 1982.0
8 TraesCS1D01G198500 chr1A 93.333 1230 49 14 290 1501 351886883 351885669 0.000000e+00 1786.0
9 TraesCS1D01G198500 chr1A 90.616 682 22 15 1607 2261 351885354 351884688 0.000000e+00 867.0
10 TraesCS1D01G198500 chr1A 90.306 588 27 16 4094 4664 351882894 351882320 0.000000e+00 743.0
11 TraesCS1D01G198500 chr1A 89.928 278 24 1 24 297 351887469 351887192 6.040000e-94 355.0
12 TraesCS1D01G198500 chr1A 99.371 159 1 0 4744 4902 351882323 351882165 6.210000e-74 289.0
13 TraesCS1D01G198500 chr5A 94.898 98 5 0 4651 4748 801625 801722 2.360000e-33 154.0
14 TraesCS1D01G198500 chr4B 92.453 106 7 1 4651 4755 29271932 29271827 3.060000e-32 150.0
15 TraesCS1D01G198500 chr7D 95.652 92 4 0 4656 4747 342585474 342585383 1.100000e-31 148.0
16 TraesCS1D01G198500 chr7D 93.814 97 6 0 4656 4752 629185850 629185754 3.950000e-31 147.0
17 TraesCS1D01G198500 chr4A 95.652 92 4 0 4657 4748 708630107 708630016 1.100000e-31 148.0
18 TraesCS1D01G198500 chr3D 94.737 95 5 0 4658 4752 129678092 129677998 1.100000e-31 148.0
19 TraesCS1D01G198500 chr3A 94.792 96 3 2 4654 4749 54716870 54716963 1.100000e-31 148.0
20 TraesCS1D01G198500 chr3A 100.000 28 0 0 1518 1545 691318178 691318151 9.000000e-03 52.8
21 TraesCS1D01G198500 chr5D 94.681 94 5 0 4660 4753 228556520 228556427 3.950000e-31 147.0
22 TraesCS1D01G198500 chr2B 91.346 104 9 0 4660 4763 157060986 157061089 5.110000e-30 143.0


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 TraesCS1D01G198500 chr1D 279946098 279950999 4901 True 9053.000000 9053 100.000000 1 4902 1 chr1D.!!$R1 4901
1 TraesCS1D01G198500 chr1B 380466623 380471363 4740 True 1615.250000 3459 94.498250 104 4902 4 chr1B.!!$R1 4798
2 TraesCS1D01G198500 chr1A 351882165 351887469 5304 True 1003.666667 1982 92.012333 24 4902 6 chr1A.!!$R1 4878

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
390 713 0.250467 GGTGGTGCTGCTGAAGAAGA 60.250 55.0 0.00 0.00 0.00 2.87 F
1694 2263 0.174845 TAGTGCCGTACCACTGCATC 59.825 55.0 13.25 2.16 45.17 3.91 F
1935 2515 0.098728 GCTTCACCACACACACACAC 59.901 55.0 0.00 0.00 0.00 3.82 F
1939 2519 0.167908 CACCACACACACACACACAC 59.832 55.0 0.00 0.00 0.00 3.82 F
2362 2983 0.245539 CCCAGCAAGCACTTGAATGG 59.754 55.0 20.13 20.13 43.10 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1936 2516 0.253044 AGAACCAGCTGTGTGTGTGT 59.747 50.000 13.81 0.0 0.00 3.72 R
2835 3491 0.036448 AGAGGACCAGTTCTCGTCGA 59.964 55.000 0.37 0.0 35.34 4.20 R
2836 3492 0.169230 CAGAGGACCAGTTCTCGTCG 59.831 60.000 0.37 0.0 35.34 5.12 R
2875 3561 0.389948 CCAACGAGTAGGACACTGCC 60.390 60.000 0.00 0.0 37.72 4.85 R
4293 5153 1.668751 GGAACGCTTCTTTGTGTGTCA 59.331 47.619 0.00 0.0 0.00 3.58 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
17 18 2.262915 CCCGAGAGTGAGCACCAC 59.737 66.667 0.00 1.51 46.03 4.16
41 42 0.953960 GTACAAAGGGGCACGACCTG 60.954 60.000 0.00 0.00 38.63 4.00
68 69 3.068732 TCGAGAGGGCATCAAGAATAGTG 59.931 47.826 0.58 0.00 0.00 2.74
98 103 4.653868 ACTGAGTCTCTTCCTCGTTTCTA 58.346 43.478 0.65 0.00 0.00 2.10
158 163 2.507769 GTACGTACGTGGCTGCCC 60.508 66.667 30.25 6.66 0.00 5.36
167 172 3.329889 TGGCTGCCCGAAGACCAT 61.330 61.111 17.53 0.00 0.00 3.55
186 191 3.375299 CCATTTGAGATCACCTCGTTTCC 59.625 47.826 0.00 0.00 44.92 3.13
219 224 1.065551 GTATGGCCATCCTTGCGAAAC 59.934 52.381 24.80 7.70 0.00 2.78
230 235 2.345641 CCTTGCGAAACGTAGAGTGATG 59.654 50.000 0.00 0.00 0.00 3.07
261 266 2.281276 ACCTGTTCGGGCGGAAAC 60.281 61.111 9.21 5.01 36.14 2.78
350 673 1.014044 CCTGATGCGTGCGTGTAACT 61.014 55.000 0.00 0.00 31.75 2.24
389 712 0.535780 TGGTGGTGCTGCTGAAGAAG 60.536 55.000 0.00 0.00 0.00 2.85
390 713 0.250467 GGTGGTGCTGCTGAAGAAGA 60.250 55.000 0.00 0.00 0.00 2.87
391 714 1.597742 GTGGTGCTGCTGAAGAAGAA 58.402 50.000 0.00 0.00 0.00 2.52
423 746 4.564110 GGGGGAAGGAATCGCGGG 62.564 72.222 6.13 0.00 41.73 6.13
486 810 4.761739 TCTCACCAAACCAAGCTAAATCTG 59.238 41.667 0.00 0.00 0.00 2.90
604 928 3.139469 GGACGGAGGGAGACGGAC 61.139 72.222 0.00 0.00 0.00 4.79
728 1056 2.284699 ACCTGACCCTCTTCCCCG 60.285 66.667 0.00 0.00 0.00 5.73
758 1090 3.741476 CAGCCAAGCCAAGTCCGC 61.741 66.667 0.00 0.00 0.00 5.54
791 1123 0.457851 ATCTTTCGCTCCTGAGACCG 59.542 55.000 0.00 0.00 0.00 4.79
1015 1351 1.098050 CCCATCACCAGTAAAGCAGC 58.902 55.000 0.00 0.00 0.00 5.25
1075 1411 3.894947 GCTCTCTCGGACGCTCCC 61.895 72.222 0.00 0.00 31.13 4.30
1434 1782 3.685139 ACGTGAGTTGATCCAATCACT 57.315 42.857 20.75 8.85 46.40 3.41
1446 1794 4.927267 TCCAATCACTAATCACAACCCT 57.073 40.909 0.00 0.00 0.00 4.34
1451 1799 4.993705 TCACTAATCACAACCCTTCCTT 57.006 40.909 0.00 0.00 0.00 3.36
1531 1884 6.010850 AGAAAGAATCATGGATGGATGGATG 58.989 40.000 0.00 0.00 0.00 3.51
1532 1885 4.317530 AGAATCATGGATGGATGGATGG 57.682 45.455 0.00 0.00 0.00 3.51
1533 1886 3.920841 AGAATCATGGATGGATGGATGGA 59.079 43.478 0.00 0.00 0.00 3.41
1534 1887 4.544559 AGAATCATGGATGGATGGATGGAT 59.455 41.667 0.00 0.00 0.00 3.41
1535 1888 4.521536 ATCATGGATGGATGGATGGATC 57.478 45.455 0.00 0.00 0.00 3.36
1536 1889 2.237893 TCATGGATGGATGGATGGATCG 59.762 50.000 0.00 0.00 0.00 3.69
1537 1890 2.028561 TGGATGGATGGATGGATCGA 57.971 50.000 0.00 0.00 0.00 3.59
1540 1893 2.482664 GGATGGATGGATGGATCGATCG 60.483 54.545 18.81 9.36 41.27 3.69
1579 1943 4.349365 GGGTTGATTGATTCTTTACCCCA 58.651 43.478 0.00 0.00 36.21 4.96
1581 1945 5.016831 GGTTGATTGATTCTTTACCCCAGT 58.983 41.667 0.00 0.00 0.00 4.00
1590 2155 8.798975 TGATTCTTTACCCCAGTATCTATTCT 57.201 34.615 0.00 0.00 0.00 2.40
1603 2168 2.160205 TCTATTCTCGATCGCCGGATT 58.840 47.619 11.09 7.54 39.14 3.01
1604 2169 2.161808 TCTATTCTCGATCGCCGGATTC 59.838 50.000 11.09 0.00 39.14 2.52
1605 2170 0.962489 ATTCTCGATCGCCGGATTCT 59.038 50.000 11.09 0.00 39.14 2.40
1606 2171 0.311165 TTCTCGATCGCCGGATTCTC 59.689 55.000 11.09 0.00 39.14 2.87
1607 2172 1.441182 CTCGATCGCCGGATTCTCG 60.441 63.158 11.09 7.78 39.14 4.04
1631 2196 1.831286 GCCTGCCAGCCATATTGCT 60.831 57.895 0.00 0.00 44.00 3.91
1692 2261 1.589630 CTAGTGCCGTACCACTGCA 59.410 57.895 13.25 3.08 45.17 4.41
1693 2262 0.175760 CTAGTGCCGTACCACTGCAT 59.824 55.000 13.25 0.64 45.17 3.96
1694 2263 0.174845 TAGTGCCGTACCACTGCATC 59.825 55.000 13.25 2.16 45.17 3.91
1695 2264 1.375396 GTGCCGTACCACTGCATCA 60.375 57.895 0.00 0.00 40.32 3.07
1696 2265 1.079197 TGCCGTACCACTGCATCAG 60.079 57.895 0.00 0.00 33.42 2.90
1697 2266 2.464459 GCCGTACCACTGCATCAGC 61.464 63.158 0.00 0.00 42.57 4.26
1730 2299 3.634448 ACAGCTAGTCGTTGAGCATCTAT 59.366 43.478 7.69 0.00 41.36 1.98
1731 2300 4.822350 ACAGCTAGTCGTTGAGCATCTATA 59.178 41.667 7.69 0.00 41.36 1.31
1732 2301 5.150683 CAGCTAGTCGTTGAGCATCTATAC 58.849 45.833 7.69 0.00 41.36 1.47
1733 2302 5.049060 CAGCTAGTCGTTGAGCATCTATACT 60.049 44.000 7.69 0.00 41.36 2.12
1734 2303 6.147985 CAGCTAGTCGTTGAGCATCTATACTA 59.852 42.308 7.69 0.00 41.36 1.82
1735 2304 6.370442 AGCTAGTCGTTGAGCATCTATACTAG 59.630 42.308 0.00 0.00 39.65 2.57
1736 2305 6.148150 GCTAGTCGTTGAGCATCTATACTAGT 59.852 42.308 0.00 0.00 39.29 2.57
1737 2306 7.331440 GCTAGTCGTTGAGCATCTATACTAGTA 59.669 40.741 4.77 4.77 39.29 1.82
1738 2307 7.661127 AGTCGTTGAGCATCTATACTAGTAG 57.339 40.000 8.85 0.00 34.92 2.57
1739 2308 7.218614 AGTCGTTGAGCATCTATACTAGTAGT 58.781 38.462 8.85 8.14 34.92 2.73
1823 2392 2.285368 CTGCCCCCTCCACCACTA 60.285 66.667 0.00 0.00 0.00 2.74
1935 2515 0.098728 GCTTCACCACACACACACAC 59.901 55.000 0.00 0.00 0.00 3.82
1936 2516 1.447945 CTTCACCACACACACACACA 58.552 50.000 0.00 0.00 0.00 3.72
1937 2517 1.130373 CTTCACCACACACACACACAC 59.870 52.381 0.00 0.00 0.00 3.82
1939 2519 0.167908 CACCACACACACACACACAC 59.832 55.000 0.00 0.00 0.00 3.82
2015 2599 3.521937 TGGGTGCTACTAGCTGGTTAATT 59.478 43.478 8.46 0.00 42.97 1.40
2056 2644 1.380302 GATGGTGGTGCAGGAGGTT 59.620 57.895 0.00 0.00 0.00 3.50
2126 2714 1.888436 GCAGACGGTGACCATGGAGA 61.888 60.000 21.47 0.13 0.00 3.71
2181 2772 1.371558 GGAAGGACGACCACAAGCT 59.628 57.895 6.71 0.00 38.94 3.74
2182 2773 0.951040 GGAAGGACGACCACAAGCTG 60.951 60.000 6.71 0.00 38.94 4.24
2194 2785 1.961277 CAAGCTGGTCGACGCCTTT 60.961 57.895 9.92 0.00 0.00 3.11
2278 2869 3.341043 CCATCGCCCGCTCATTCG 61.341 66.667 0.00 0.00 0.00 3.34
2319 2940 2.365293 GCTTCTTTCTTTTGGGGCAAGA 59.635 45.455 0.00 0.00 0.00 3.02
2354 2975 3.426568 GCGAGACCCAGCAAGCAC 61.427 66.667 0.00 0.00 0.00 4.40
2355 2976 2.345244 CGAGACCCAGCAAGCACT 59.655 61.111 0.00 0.00 0.00 4.40
2357 2978 1.572085 CGAGACCCAGCAAGCACTTG 61.572 60.000 6.01 6.01 43.14 3.16
2358 2979 0.250467 GAGACCCAGCAAGCACTTGA 60.250 55.000 14.44 0.00 42.93 3.02
2360 2981 1.202976 AGACCCAGCAAGCACTTGAAT 60.203 47.619 14.44 0.00 42.93 2.57
2361 2982 0.963962 ACCCAGCAAGCACTTGAATG 59.036 50.000 14.44 10.89 42.93 2.67
2362 2983 0.245539 CCCAGCAAGCACTTGAATGG 59.754 55.000 20.13 20.13 43.10 3.16
2460 3081 1.966451 CACGGAAAGAAAGCGGGCT 60.966 57.895 0.00 0.00 0.00 5.19
2517 3138 2.349532 GCTCTTGGCGTTAATTATCCGC 60.350 50.000 17.17 17.17 46.28 5.54
2624 3272 5.326069 TGAGACTAGTAAGAACTGGCTTCT 58.674 41.667 0.00 0.00 41.39 2.85
2656 3304 7.330700 GTGAAGATTAAGACACAGAAAGAGAGG 59.669 40.741 0.00 0.00 34.05 3.69
2686 3337 2.005960 CTAGTCGTCCCCCGCAAGAG 62.006 65.000 0.00 0.00 43.02 2.85
2830 3486 4.081642 TGCTCCAGCTACTTATTTCTCGTT 60.082 41.667 0.00 0.00 42.66 3.85
2835 3491 7.159372 TCCAGCTACTTATTTCTCGTTCTTTT 58.841 34.615 0.00 0.00 0.00 2.27
2836 3492 7.331193 TCCAGCTACTTATTTCTCGTTCTTTTC 59.669 37.037 0.00 0.00 0.00 2.29
2837 3493 7.167481 CAGCTACTTATTTCTCGTTCTTTTCG 58.833 38.462 0.00 0.00 0.00 3.46
2875 3561 4.080695 TCTGTTCCTGAATTCTGATGGGAG 60.081 45.833 13.45 0.00 0.00 4.30
2889 3575 0.614979 TGGGAGGCAGTGTCCTACTC 60.615 60.000 13.51 6.58 37.60 2.59
2902 3588 1.146263 CTACTCGTTGGGGCCATCC 59.854 63.158 4.39 0.00 0.00 3.51
2903 3589 1.613928 TACTCGTTGGGGCCATCCA 60.614 57.895 4.39 0.00 37.22 3.41
2904 3590 1.906105 TACTCGTTGGGGCCATCCAC 61.906 60.000 4.39 0.00 36.38 4.02
2905 3591 2.933287 TCGTTGGGGCCATCCACT 60.933 61.111 4.39 0.00 36.47 4.00
2906 3592 1.613928 TCGTTGGGGCCATCCACTA 60.614 57.895 4.39 0.00 36.47 2.74
2907 3593 1.451387 CGTTGGGGCCATCCACTAC 60.451 63.158 4.39 0.00 38.01 2.73
2908 3594 1.688811 GTTGGGGCCATCCACTACA 59.311 57.895 4.39 0.00 40.56 2.74
3063 3749 6.183360 CCTTTAGGACACCGCAATTAATTGAT 60.183 38.462 28.33 12.16 37.38 2.57
3065 3751 7.490962 TTAGGACACCGCAATTAATTGATAG 57.509 36.000 28.33 18.06 40.14 2.08
3067 3753 6.588204 AGGACACCGCAATTAATTGATAGTA 58.412 36.000 28.33 0.00 40.14 1.82
3068 3754 6.706270 AGGACACCGCAATTAATTGATAGTAG 59.294 38.462 28.33 15.25 40.14 2.57
3073 3759 9.687210 CACCGCAATTAATTGATAGTAGTAGTA 57.313 33.333 28.33 0.00 40.14 1.82
3074 3760 9.909644 ACCGCAATTAATTGATAGTAGTAGTAG 57.090 33.333 28.33 8.37 40.14 2.57
3075 3761 8.861101 CCGCAATTAATTGATAGTAGTAGTAGC 58.139 37.037 28.33 9.29 40.14 3.58
3076 3762 9.406828 CGCAATTAATTGATAGTAGTAGTAGCA 57.593 33.333 28.33 0.00 40.14 3.49
3375 4093 2.350522 CGCTACCTCTGCTTCAACAAT 58.649 47.619 0.00 0.00 0.00 2.71
3385 4103 1.268488 GCTTCAACAATGTCGTGTGCA 60.268 47.619 0.00 0.00 0.00 4.57
3390 4108 1.968017 CAATGTCGTGTGCAGGCCT 60.968 57.895 0.00 0.00 0.00 5.19
3411 4129 4.070552 GACGCCCTCCAGTTCGCT 62.071 66.667 0.00 0.00 0.00 4.93
3459 4177 2.340809 CCGCCAAGGTACACACGA 59.659 61.111 0.00 0.00 34.51 4.35
3477 4206 3.910170 CACGAGTCAATGAACAGCATTTG 59.090 43.478 0.00 0.00 44.68 2.32
3507 4236 8.504005 TCGAAAATTCTAAGAAAATCCAGTGAC 58.496 33.333 0.00 0.00 0.00 3.67
4020 4761 6.099341 ACCACATGAAACTGAAACTTTTGAC 58.901 36.000 0.00 0.00 0.00 3.18
4024 4765 7.951565 CACATGAAACTGAAACTTTTGACAAAC 59.048 33.333 0.00 0.00 0.00 2.93
4027 4768 9.921637 ATGAAACTGAAACTTTTGACAAACTTA 57.078 25.926 0.00 0.00 0.00 2.24
4052 4903 5.184096 AGTGTACATGGTTTCACAAACAACA 59.816 36.000 0.00 0.00 43.15 3.33
4053 4904 5.864474 GTGTACATGGTTTCACAAACAACAA 59.136 36.000 0.00 0.00 43.15 2.83
4056 4907 5.486526 ACATGGTTTCACAAACAACAACAT 58.513 33.333 0.00 0.00 43.15 2.71
4059 4910 7.768120 ACATGGTTTCACAAACAACAACATATT 59.232 29.630 0.00 0.00 43.15 1.28
4060 4911 7.763172 TGGTTTCACAAACAACAACATATTC 57.237 32.000 1.78 0.00 43.15 1.75
4061 4912 7.323420 TGGTTTCACAAACAACAACATATTCA 58.677 30.769 1.78 0.00 43.15 2.57
4062 4913 7.984050 TGGTTTCACAAACAACAACATATTCAT 59.016 29.630 1.78 0.00 43.15 2.57
4063 4914 8.487176 GGTTTCACAAACAACAACATATTCATC 58.513 33.333 1.78 0.00 43.15 2.92
4064 4915 9.248291 GTTTCACAAACAACAACATATTCATCT 57.752 29.630 0.00 0.00 41.04 2.90
4065 4916 9.462174 TTTCACAAACAACAACATATTCATCTC 57.538 29.630 0.00 0.00 0.00 2.75
4066 4917 8.164058 TCACAAACAACAACATATTCATCTCA 57.836 30.769 0.00 0.00 0.00 3.27
4067 4918 8.075574 TCACAAACAACAACATATTCATCTCAC 58.924 33.333 0.00 0.00 0.00 3.51
4068 4919 7.861872 CACAAACAACAACATATTCATCTCACA 59.138 33.333 0.00 0.00 0.00 3.58
4069 4920 8.412456 ACAAACAACAACATATTCATCTCACAA 58.588 29.630 0.00 0.00 0.00 3.33
4070 4921 9.247126 CAAACAACAACATATTCATCTCACAAA 57.753 29.630 0.00 0.00 0.00 2.83
4071 4922 9.814899 AAACAACAACATATTCATCTCACAAAA 57.185 25.926 0.00 0.00 0.00 2.44
4072 4923 9.814899 AACAACAACATATTCATCTCACAAAAA 57.185 25.926 0.00 0.00 0.00 1.94
4073 4924 9.467258 ACAACAACATATTCATCTCACAAAAAG 57.533 29.630 0.00 0.00 0.00 2.27
4074 4925 8.430063 CAACAACATATTCATCTCACAAAAAGC 58.570 33.333 0.00 0.00 0.00 3.51
4075 4926 7.092716 ACAACATATTCATCTCACAAAAAGCC 58.907 34.615 0.00 0.00 0.00 4.35
4076 4927 6.839124 ACATATTCATCTCACAAAAAGCCA 57.161 33.333 0.00 0.00 0.00 4.75
4077 4928 7.414222 ACATATTCATCTCACAAAAAGCCAT 57.586 32.000 0.00 0.00 0.00 4.40
4078 4929 7.486647 ACATATTCATCTCACAAAAAGCCATC 58.513 34.615 0.00 0.00 0.00 3.51
4079 4930 4.789012 TTCATCTCACAAAAAGCCATCC 57.211 40.909 0.00 0.00 0.00 3.51
4080 4931 4.038271 TCATCTCACAAAAAGCCATCCT 57.962 40.909 0.00 0.00 0.00 3.24
4081 4932 4.012374 TCATCTCACAAAAAGCCATCCTC 58.988 43.478 0.00 0.00 0.00 3.71
4082 4933 3.507162 TCTCACAAAAAGCCATCCTCA 57.493 42.857 0.00 0.00 0.00 3.86
4083 4934 4.038271 TCTCACAAAAAGCCATCCTCAT 57.962 40.909 0.00 0.00 0.00 2.90
4084 4935 5.178096 TCTCACAAAAAGCCATCCTCATA 57.822 39.130 0.00 0.00 0.00 2.15
4085 4936 4.943705 TCTCACAAAAAGCCATCCTCATAC 59.056 41.667 0.00 0.00 0.00 2.39
4086 4937 4.661222 TCACAAAAAGCCATCCTCATACA 58.339 39.130 0.00 0.00 0.00 2.29
4087 4938 5.263599 TCACAAAAAGCCATCCTCATACAT 58.736 37.500 0.00 0.00 0.00 2.29
4088 4939 5.716228 TCACAAAAAGCCATCCTCATACATT 59.284 36.000 0.00 0.00 0.00 2.71
4089 4940 5.808540 CACAAAAAGCCATCCTCATACATTG 59.191 40.000 0.00 0.00 0.00 2.82
4090 4941 5.716228 ACAAAAAGCCATCCTCATACATTGA 59.284 36.000 0.00 0.00 0.00 2.57
4091 4942 6.211184 ACAAAAAGCCATCCTCATACATTGAA 59.789 34.615 0.00 0.00 32.78 2.69
4092 4943 6.461110 AAAAGCCATCCTCATACATTGAAG 57.539 37.500 0.00 0.00 32.78 3.02
4133 4984 7.205992 TCAGCTGACAACTACATATTCATCTC 58.794 38.462 13.74 0.00 0.00 2.75
4293 5153 7.643528 CATCATTGCATACGTCATACTACTT 57.356 36.000 0.00 0.00 0.00 2.24
4380 5240 2.239907 GTTCAATCCTAGGCTCCAAGGT 59.760 50.000 2.96 0.00 34.30 3.50
4394 5254 3.515901 CTCCAAGGTACCCATAGATAGGC 59.484 52.174 8.74 0.00 0.00 3.93
4602 5477 3.840666 AGGCAAGAGAAACACATCTCCTA 59.159 43.478 0.90 0.00 45.70 2.94
4638 5515 1.611977 GTTTGGAAACTGTAGCACCCC 59.388 52.381 0.00 0.00 36.03 4.95
4643 5520 2.290960 GGAAACTGTAGCACCCCAGATT 60.291 50.000 0.00 0.00 32.93 2.40
4652 5529 0.179048 CACCCCAGATTCTGCGCATA 60.179 55.000 12.24 0.00 0.00 3.14
4660 5537 5.450965 CCCAGATTCTGCGCATAAAATTTCT 60.451 40.000 12.24 7.06 0.00 2.52
4661 5538 6.238731 CCCAGATTCTGCGCATAAAATTTCTA 60.239 38.462 12.24 0.00 0.00 2.10
4662 5539 6.634436 CCAGATTCTGCGCATAAAATTTCTAC 59.366 38.462 12.24 0.00 0.00 2.59
4663 5540 7.412853 CAGATTCTGCGCATAAAATTTCTACT 58.587 34.615 12.24 1.99 0.00 2.57
4664 5541 7.585573 CAGATTCTGCGCATAAAATTTCTACTC 59.414 37.037 12.24 1.02 0.00 2.59
4665 5542 5.734855 TCTGCGCATAAAATTTCTACTCC 57.265 39.130 12.24 0.00 0.00 3.85
4666 5543 4.574828 TCTGCGCATAAAATTTCTACTCCC 59.425 41.667 12.24 0.00 0.00 4.30
4667 5544 4.523083 TGCGCATAAAATTTCTACTCCCT 58.477 39.130 5.66 0.00 0.00 4.20
4668 5545 4.574828 TGCGCATAAAATTTCTACTCCCTC 59.425 41.667 5.66 0.00 0.00 4.30
4669 5546 4.816925 GCGCATAAAATTTCTACTCCCTCT 59.183 41.667 0.30 0.00 0.00 3.69
4670 5547 5.277538 GCGCATAAAATTTCTACTCCCTCTG 60.278 44.000 0.30 0.00 0.00 3.35
4671 5548 5.817816 CGCATAAAATTTCTACTCCCTCTGT 59.182 40.000 0.00 0.00 0.00 3.41
4672 5549 6.984474 CGCATAAAATTTCTACTCCCTCTGTA 59.016 38.462 0.00 0.00 0.00 2.74
4673 5550 7.494625 CGCATAAAATTTCTACTCCCTCTGTAA 59.505 37.037 0.00 0.00 0.00 2.41
4674 5551 9.174166 GCATAAAATTTCTACTCCCTCTGTAAA 57.826 33.333 0.00 0.00 0.00 2.01
4687 5564 8.862085 ACTCCCTCTGTAAACTAATATAAGAGC 58.138 37.037 0.00 0.00 0.00 4.09
4688 5565 7.883217 TCCCTCTGTAAACTAATATAAGAGCG 58.117 38.462 0.00 0.00 0.00 5.03
4689 5566 7.504911 TCCCTCTGTAAACTAATATAAGAGCGT 59.495 37.037 0.00 0.00 0.00 5.07
4690 5567 8.142551 CCCTCTGTAAACTAATATAAGAGCGTT 58.857 37.037 0.00 0.00 0.00 4.84
4691 5568 9.530633 CCTCTGTAAACTAATATAAGAGCGTTT 57.469 33.333 0.00 0.00 0.00 3.60
4707 5584 8.828688 AAGAGCGTTTAGAACACTAAAATAGT 57.171 30.769 0.00 0.00 37.69 2.12
4741 5618 9.710818 ACACTCTTATATTAGTTTACAGAGGGA 57.289 33.333 2.59 0.00 34.50 4.20
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.262915 GTGGTGCTCACTCTCGGG 59.737 66.667 0.00 0.00 42.86 5.14
1 2 1.080230 CTGTGGTGCTCACTCTCGG 60.080 63.158 11.00 0.00 46.20 4.63
2 3 1.735920 GCTGTGGTGCTCACTCTCG 60.736 63.158 11.00 0.00 46.20 4.04
3 4 0.669932 CTGCTGTGGTGCTCACTCTC 60.670 60.000 11.00 2.98 46.20 3.20
4 5 1.370437 CTGCTGTGGTGCTCACTCT 59.630 57.895 11.00 0.00 46.20 3.24
5 6 0.318441 TACTGCTGTGGTGCTCACTC 59.682 55.000 6.48 5.11 46.20 3.51
6 7 0.034059 GTACTGCTGTGGTGCTCACT 59.966 55.000 6.48 0.00 46.20 3.41
7 8 0.249868 TGTACTGCTGTGGTGCTCAC 60.250 55.000 6.48 4.23 46.23 3.51
8 9 0.467804 TTGTACTGCTGTGGTGCTCA 59.532 50.000 6.48 0.00 0.00 4.26
9 10 1.532868 CTTTGTACTGCTGTGGTGCTC 59.467 52.381 6.48 0.00 0.00 4.26
10 11 1.597742 CTTTGTACTGCTGTGGTGCT 58.402 50.000 6.48 0.00 0.00 4.40
11 12 0.593128 CCTTTGTACTGCTGTGGTGC 59.407 55.000 6.48 0.00 0.00 5.01
12 13 1.238439 CCCTTTGTACTGCTGTGGTG 58.762 55.000 6.48 0.00 0.00 4.17
13 14 0.110486 CCCCTTTGTACTGCTGTGGT 59.890 55.000 6.48 0.00 0.00 4.16
14 15 1.244019 GCCCCTTTGTACTGCTGTGG 61.244 60.000 6.48 0.00 0.00 4.17
15 16 0.537143 TGCCCCTTTGTACTGCTGTG 60.537 55.000 6.48 0.00 0.00 3.66
16 17 0.537371 GTGCCCCTTTGTACTGCTGT 60.537 55.000 0.66 0.66 0.00 4.40
17 18 1.577328 CGTGCCCCTTTGTACTGCTG 61.577 60.000 0.00 0.00 0.00 4.41
18 19 1.302511 CGTGCCCCTTTGTACTGCT 60.303 57.895 0.00 0.00 0.00 4.24
19 20 1.302192 TCGTGCCCCTTTGTACTGC 60.302 57.895 0.00 0.00 0.00 4.40
20 21 0.953960 GGTCGTGCCCCTTTGTACTG 60.954 60.000 0.00 0.00 0.00 2.74
21 22 1.125711 AGGTCGTGCCCCTTTGTACT 61.126 55.000 0.00 0.00 38.26 2.73
22 23 0.953960 CAGGTCGTGCCCCTTTGTAC 60.954 60.000 0.00 0.00 38.26 2.90
41 42 0.032130 TTGATGCCCTCTCGATACGC 59.968 55.000 0.00 0.00 0.00 4.42
43 44 3.735237 TTCTTGATGCCCTCTCGATAC 57.265 47.619 0.00 0.00 0.00 2.24
45 46 3.900601 ACTATTCTTGATGCCCTCTCGAT 59.099 43.478 0.00 0.00 0.00 3.59
47 48 3.181471 ACACTATTCTTGATGCCCTCTCG 60.181 47.826 0.00 0.00 0.00 4.04
158 163 3.866651 AGGTGATCTCAAATGGTCTTCG 58.133 45.455 0.00 0.00 0.00 3.79
167 172 2.370519 TGGGAAACGAGGTGATCTCAAA 59.629 45.455 0.00 0.00 42.55 2.69
186 191 3.355378 TGGCCATACTCTGTTTTCATGG 58.645 45.455 0.00 0.00 0.00 3.66
219 224 4.214332 TCATTCGATCCTCATCACTCTACG 59.786 45.833 0.00 0.00 0.00 3.51
230 235 2.969628 ACAGGTGTCATTCGATCCTC 57.030 50.000 0.00 0.00 0.00 3.71
261 266 4.860072 TCTCGTATGGATCATCAAACTCG 58.140 43.478 0.00 0.00 0.00 4.18
389 712 1.004862 CCCCCACCCTCTTTCTTCTTC 59.995 57.143 0.00 0.00 0.00 2.87
390 713 1.076438 CCCCCACCCTCTTTCTTCTT 58.924 55.000 0.00 0.00 0.00 2.52
391 714 2.792635 CCCCCACCCTCTTTCTTCT 58.207 57.895 0.00 0.00 0.00 2.85
534 858 3.680786 CCTCACCTGCGACGGACA 61.681 66.667 0.00 0.00 0.00 4.02
538 862 3.939837 ATGCACCTCACCTGCGACG 62.940 63.158 0.00 0.00 37.46 5.12
728 1056 4.448976 GGCTGGGGAAGGGGAAGC 62.449 72.222 0.00 0.00 0.00 3.86
758 1090 0.539051 AAAGATGAGGGAGGACGCAG 59.461 55.000 0.00 0.00 0.00 5.18
817 1153 3.860605 TGTGGGTGCGTGCTCTGT 61.861 61.111 0.00 0.00 0.00 3.41
1015 1351 1.379527 GGCGGGAGTGGAATTACTTG 58.620 55.000 0.00 0.00 0.00 3.16
1075 1411 2.166007 GCTTTTGCTTGTACGTATGCG 58.834 47.619 0.19 0.19 43.35 4.73
1406 1751 3.414700 CAACTCACGTCGCAGCCC 61.415 66.667 0.00 0.00 0.00 5.19
1434 1782 5.321927 GAAGGAAAGGAAGGGTTGTGATTA 58.678 41.667 0.00 0.00 0.00 1.75
1446 1794 2.378886 GGGAGGAAAGGAAGGAAAGGAA 59.621 50.000 0.00 0.00 0.00 3.36
1451 1799 1.276622 CGAGGGAGGAAAGGAAGGAA 58.723 55.000 0.00 0.00 0.00 3.36
1579 1943 2.678836 CCGGCGATCGAGAATAGATACT 59.321 50.000 21.57 0.00 42.43 2.12
1581 1945 2.981898 TCCGGCGATCGAGAATAGATA 58.018 47.619 21.57 0.00 42.43 1.98
1590 2155 2.637589 CGAGAATCCGGCGATCGA 59.362 61.111 21.57 0.00 42.43 3.59
1604 2169 4.598894 CTGGCAGGCCGATCCGAG 62.599 72.222 6.61 0.00 40.77 4.63
1626 2191 2.234414 CCAACCAATTAGCCACAGCAAT 59.766 45.455 0.00 0.00 43.56 3.56
1631 2196 5.186256 TCTTATCCAACCAATTAGCCACA 57.814 39.130 0.00 0.00 0.00 4.17
1692 2261 2.828520 AGCTGTACTGTACTGTGCTGAT 59.171 45.455 23.75 17.94 32.58 2.90
1693 2262 2.239400 AGCTGTACTGTACTGTGCTGA 58.761 47.619 23.75 6.48 32.58 4.26
1694 2263 2.732412 AGCTGTACTGTACTGTGCTG 57.268 50.000 22.39 18.53 32.58 4.41
1695 2264 3.422796 ACTAGCTGTACTGTACTGTGCT 58.577 45.455 24.51 24.51 35.74 4.40
1696 2265 3.728268 CGACTAGCTGTACTGTACTGTGC 60.728 52.174 21.03 18.84 0.00 4.57
1697 2266 3.436015 ACGACTAGCTGTACTGTACTGTG 59.564 47.826 21.03 15.18 0.00 3.66
1737 2306 7.608376 GCCAAGGAGAAAGAAAGAAATAGTACT 59.392 37.037 0.00 0.00 0.00 2.73
1738 2307 7.413109 CGCCAAGGAGAAAGAAAGAAATAGTAC 60.413 40.741 0.00 0.00 0.00 2.73
1739 2308 6.594159 CGCCAAGGAGAAAGAAAGAAATAGTA 59.406 38.462 0.00 0.00 0.00 1.82
1823 2392 3.261897 AGTTAATGCTGCACTGGAGTACT 59.738 43.478 3.57 0.00 0.00 2.73
1935 2515 0.378257 GAACCAGCTGTGTGTGTGTG 59.622 55.000 13.81 0.00 0.00 3.82
1936 2516 0.253044 AGAACCAGCTGTGTGTGTGT 59.747 50.000 13.81 0.00 0.00 3.72
1937 2517 2.238942 TAGAACCAGCTGTGTGTGTG 57.761 50.000 13.81 0.00 0.00 3.82
1939 2519 3.402110 TGATTAGAACCAGCTGTGTGTG 58.598 45.455 13.81 0.00 0.00 3.82
1973 2553 1.062525 CGGTCTGCTTAATTGGCGC 59.937 57.895 0.00 0.00 0.00 6.53
2032 2616 2.034532 TGCACCACCATCAGCCAG 59.965 61.111 0.00 0.00 0.00 4.85
2056 2644 0.326238 GGACCTCCACCTCCACCATA 60.326 60.000 0.00 0.00 35.64 2.74
2181 2772 2.355363 CGTCAAAGGCGTCGACCA 60.355 61.111 10.58 0.00 0.00 4.02
2182 2773 2.049802 TCGTCAAAGGCGTCGACC 60.050 61.111 10.58 2.55 0.00 4.79
2194 2785 1.587043 CGCTCCAGTTCCTCTCGTCA 61.587 60.000 0.00 0.00 0.00 4.35
2278 2869 2.995482 CGGTGCTCGCGTATGAAC 59.005 61.111 5.77 2.39 0.00 3.18
2319 2940 2.159099 TCGCAACAAGACTGTCTCAGTT 60.159 45.455 11.31 15.24 45.44 3.16
2354 2975 3.558505 CTGCTTTTCGTGTCCATTCAAG 58.441 45.455 0.00 0.00 0.00 3.02
2355 2976 2.293122 CCTGCTTTTCGTGTCCATTCAA 59.707 45.455 0.00 0.00 0.00 2.69
2357 2978 2.151202 TCCTGCTTTTCGTGTCCATTC 58.849 47.619 0.00 0.00 0.00 2.67
2358 2979 2.154462 CTCCTGCTTTTCGTGTCCATT 58.846 47.619 0.00 0.00 0.00 3.16
2360 2981 0.756294 TCTCCTGCTTTTCGTGTCCA 59.244 50.000 0.00 0.00 0.00 4.02
2361 2982 1.433534 CTCTCCTGCTTTTCGTGTCC 58.566 55.000 0.00 0.00 0.00 4.02
2362 2983 0.793250 GCTCTCCTGCTTTTCGTGTC 59.207 55.000 0.00 0.00 0.00 3.67
2385 3006 2.420129 GGATTCGTAACAGGACAGGCAT 60.420 50.000 0.00 0.00 0.00 4.40
2460 3081 1.440618 TGCTTTCTTGGGGTCTGGTA 58.559 50.000 0.00 0.00 0.00 3.25
2517 3138 0.301687 CTAGGCGCTTGTATTGCACG 59.698 55.000 7.64 0.00 0.00 5.34
2558 3198 7.892609 ACACTTACAGGTTTTTGACTCTTTTT 58.107 30.769 0.00 0.00 0.00 1.94
2559 3199 7.175990 TGACACTTACAGGTTTTTGACTCTTTT 59.824 33.333 0.00 0.00 0.00 2.27
2560 3200 6.657541 TGACACTTACAGGTTTTTGACTCTTT 59.342 34.615 0.00 0.00 0.00 2.52
2561 3201 6.177610 TGACACTTACAGGTTTTTGACTCTT 58.822 36.000 0.00 0.00 0.00 2.85
2562 3202 5.741011 TGACACTTACAGGTTTTTGACTCT 58.259 37.500 0.00 0.00 0.00 3.24
2563 3203 6.431198 TTGACACTTACAGGTTTTTGACTC 57.569 37.500 0.00 0.00 0.00 3.36
2569 3209 4.345854 TGGGTTTGACACTTACAGGTTTT 58.654 39.130 0.00 0.00 0.00 2.43
2579 3219 4.447138 TCCACTTATTGGGTTTGACACT 57.553 40.909 0.00 0.00 46.92 3.55
2656 3304 5.536260 GGGGGACGACTAGATTATTTGTAC 58.464 45.833 0.00 0.00 0.00 2.90
2721 3376 3.698040 GCAAGGATGATCTTTGTGTGGAT 59.302 43.478 16.99 0.00 36.07 3.41
2830 3486 2.288030 GGACCAGTTCTCGTCGAAAAGA 60.288 50.000 0.00 0.00 32.41 2.52
2835 3491 0.036448 AGAGGACCAGTTCTCGTCGA 59.964 55.000 0.37 0.00 35.34 4.20
2836 3492 0.169230 CAGAGGACCAGTTCTCGTCG 59.831 60.000 0.37 0.00 35.34 5.12
2837 3493 1.249407 ACAGAGGACCAGTTCTCGTC 58.751 55.000 0.37 0.00 35.34 4.20
2858 3544 1.213678 TGCCTCCCATCAGAATTCAGG 59.786 52.381 8.44 4.85 0.00 3.86
2875 3561 0.389948 CCAACGAGTAGGACACTGCC 60.390 60.000 0.00 0.00 37.72 4.85
2889 3575 1.451387 GTAGTGGATGGCCCCAACG 60.451 63.158 0.00 0.00 38.06 4.10
2902 3588 0.736325 GGCCGCTGTAGTGTGTAGTG 60.736 60.000 0.00 0.00 0.00 2.74
2903 3589 1.590147 GGCCGCTGTAGTGTGTAGT 59.410 57.895 0.00 0.00 0.00 2.73
2904 3590 1.153628 GGGCCGCTGTAGTGTGTAG 60.154 63.158 0.00 0.00 0.00 2.74
2905 3591 2.652095 GGGGCCGCTGTAGTGTGTA 61.652 63.158 13.57 0.00 0.00 2.90
2906 3592 4.016706 GGGGCCGCTGTAGTGTGT 62.017 66.667 13.57 0.00 0.00 3.72
2907 3593 3.329542 ATGGGGCCGCTGTAGTGTG 62.330 63.158 21.80 0.00 0.00 3.82
2908 3594 3.009115 ATGGGGCCGCTGTAGTGT 61.009 61.111 21.80 0.00 0.00 3.55
3065 3751 9.905171 AGTAAAACAAACTACTGCTACTACTAC 57.095 33.333 0.00 0.00 0.00 2.73
3073 3759 8.502105 AACAGTAAGTAAAACAAACTACTGCT 57.498 30.769 6.90 0.00 34.94 4.24
3074 3760 9.642312 GTAACAGTAAGTAAAACAAACTACTGC 57.358 33.333 6.90 0.00 34.94 4.40
3327 4045 3.702048 GTGGGGCACTCGTAGGCA 61.702 66.667 0.00 0.00 0.00 4.75
3375 4093 3.519973 CTCAGGCCTGCACACGACA 62.520 63.158 28.91 7.14 0.00 4.35
3411 4129 2.359169 GGACGGGGTGAGCATCTGA 61.359 63.158 0.00 0.00 34.92 3.27
3459 4177 3.825014 AGCTCAAATGCTGTTCATTGACT 59.175 39.130 0.00 0.00 44.23 3.41
3477 4206 7.752695 TGGATTTTCTTAGAATTTTCGAGCTC 58.247 34.615 2.73 2.73 0.00 4.09
3507 4236 2.736721 CAGTTACAGGAACACACCATCG 59.263 50.000 0.00 0.00 40.86 3.84
3933 4674 5.697633 GCTTTCAACATTTGTTCACCATCAT 59.302 36.000 0.00 0.00 35.83 2.45
3934 4675 5.049167 GCTTTCAACATTTGTTCACCATCA 58.951 37.500 0.00 0.00 35.83 3.07
3935 4676 5.291971 AGCTTTCAACATTTGTTCACCATC 58.708 37.500 0.00 0.00 35.83 3.51
3936 4677 5.280654 AGCTTTCAACATTTGTTCACCAT 57.719 34.783 0.00 0.00 35.83 3.55
3937 4678 4.734398 AGCTTTCAACATTTGTTCACCA 57.266 36.364 0.00 0.00 35.83 4.17
3938 4679 5.108517 TGAAGCTTTCAACATTTGTTCACC 58.891 37.500 0.00 0.00 36.59 4.02
3939 4680 6.237915 CCTTGAAGCTTTCAACATTTGTTCAC 60.238 38.462 0.00 0.00 44.21 3.18
4000 4741 8.243289 AGTTTGTCAAAAGTTTCAGTTTCATG 57.757 30.769 0.00 0.00 0.00 3.07
4020 4761 7.476667 TGTGAAACCATGTACACTTAAGTTTG 58.523 34.615 5.07 0.00 34.36 2.93
4024 4765 7.476667 TGTTTGTGAAACCATGTACACTTAAG 58.523 34.615 0.00 0.00 40.67 1.85
4027 4768 5.906113 TGTTTGTGAAACCATGTACACTT 57.094 34.783 0.00 0.00 40.67 3.16
4052 4903 7.230849 TGGCTTTTTGTGAGATGAATATGTT 57.769 32.000 0.00 0.00 0.00 2.71
4053 4904 6.839124 TGGCTTTTTGTGAGATGAATATGT 57.161 33.333 0.00 0.00 0.00 2.29
4056 4907 6.189859 AGGATGGCTTTTTGTGAGATGAATA 58.810 36.000 0.00 0.00 0.00 1.75
4059 4910 4.012374 GAGGATGGCTTTTTGTGAGATGA 58.988 43.478 0.00 0.00 0.00 2.92
4060 4911 3.760151 TGAGGATGGCTTTTTGTGAGATG 59.240 43.478 0.00 0.00 0.00 2.90
4061 4912 4.038271 TGAGGATGGCTTTTTGTGAGAT 57.962 40.909 0.00 0.00 0.00 2.75
4062 4913 3.507162 TGAGGATGGCTTTTTGTGAGA 57.493 42.857 0.00 0.00 0.00 3.27
4063 4914 4.701651 TGTATGAGGATGGCTTTTTGTGAG 59.298 41.667 0.00 0.00 0.00 3.51
4064 4915 4.661222 TGTATGAGGATGGCTTTTTGTGA 58.339 39.130 0.00 0.00 0.00 3.58
4065 4916 5.587388 ATGTATGAGGATGGCTTTTTGTG 57.413 39.130 0.00 0.00 0.00 3.33
4066 4917 5.716228 TCAATGTATGAGGATGGCTTTTTGT 59.284 36.000 0.00 0.00 33.04 2.83
4067 4918 6.211587 TCAATGTATGAGGATGGCTTTTTG 57.788 37.500 0.00 0.00 33.04 2.44
4068 4919 6.664816 TCTTCAATGTATGAGGATGGCTTTTT 59.335 34.615 0.00 0.00 39.06 1.94
4069 4920 6.189859 TCTTCAATGTATGAGGATGGCTTTT 58.810 36.000 0.00 0.00 39.06 2.27
4070 4921 5.759059 TCTTCAATGTATGAGGATGGCTTT 58.241 37.500 0.00 0.00 39.06 3.51
4071 4922 5.378230 TCTTCAATGTATGAGGATGGCTT 57.622 39.130 0.00 0.00 39.06 4.35
4072 4923 5.128919 GTTCTTCAATGTATGAGGATGGCT 58.871 41.667 0.00 0.00 42.96 4.75
4073 4924 4.883585 TGTTCTTCAATGTATGAGGATGGC 59.116 41.667 0.00 0.00 42.96 4.40
4074 4925 6.600822 ACTTGTTCTTCAATGTATGAGGATGG 59.399 38.462 0.00 0.00 42.96 3.51
4075 4926 7.335171 TCACTTGTTCTTCAATGTATGAGGATG 59.665 37.037 0.00 0.00 42.96 3.51
4076 4927 7.397221 TCACTTGTTCTTCAATGTATGAGGAT 58.603 34.615 0.00 0.00 42.96 3.24
4077 4928 6.768483 TCACTTGTTCTTCAATGTATGAGGA 58.232 36.000 0.00 0.00 41.91 3.71
4078 4929 7.335171 TGATCACTTGTTCTTCAATGTATGAGG 59.665 37.037 0.00 0.00 39.77 3.86
4079 4930 8.260270 TGATCACTTGTTCTTCAATGTATGAG 57.740 34.615 0.00 0.00 39.77 2.90
4080 4931 8.620116 TTGATCACTTGTTCTTCAATGTATGA 57.380 30.769 0.00 0.00 35.35 2.15
4081 4932 9.681692 TTTTGATCACTTGTTCTTCAATGTATG 57.318 29.630 0.00 0.00 35.35 2.39
4083 4934 9.897744 GATTTTGATCACTTGTTCTTCAATGTA 57.102 29.630 0.00 0.00 35.35 2.29
4084 4935 8.415553 TGATTTTGATCACTTGTTCTTCAATGT 58.584 29.630 0.00 0.00 35.35 2.71
4085 4936 8.806177 TGATTTTGATCACTTGTTCTTCAATG 57.194 30.769 0.00 0.00 35.35 2.82
4086 4937 7.597743 GCTGATTTTGATCACTTGTTCTTCAAT 59.402 33.333 0.00 0.00 35.35 2.57
4087 4938 6.919662 GCTGATTTTGATCACTTGTTCTTCAA 59.080 34.615 0.00 0.00 34.61 2.69
4088 4939 6.263842 AGCTGATTTTGATCACTTGTTCTTCA 59.736 34.615 0.00 0.00 0.00 3.02
4089 4940 6.581542 CAGCTGATTTTGATCACTTGTTCTTC 59.418 38.462 8.42 0.00 0.00 2.87
4090 4941 6.263842 TCAGCTGATTTTGATCACTTGTTCTT 59.736 34.615 13.74 0.00 0.00 2.52
4091 4942 5.766670 TCAGCTGATTTTGATCACTTGTTCT 59.233 36.000 13.74 0.00 0.00 3.01
4092 4943 5.855395 GTCAGCTGATTTTGATCACTTGTTC 59.145 40.000 21.47 0.00 0.00 3.18
4133 4984 4.996122 TGCAATTTAGGATGGCTTTTTGTG 59.004 37.500 0.00 0.00 0.00 3.33
4141 4992 4.339247 ACTGTGTATGCAATTTAGGATGGC 59.661 41.667 0.00 0.00 0.00 4.40
4293 5153 1.668751 GGAACGCTTCTTTGTGTGTCA 59.331 47.619 0.00 0.00 0.00 3.58
4380 5240 3.076032 TGCTCTCTGCCTATCTATGGGTA 59.924 47.826 0.00 0.00 42.00 3.69
4394 5254 1.349026 TCCACTCCCTTTTGCTCTCTG 59.651 52.381 0.00 0.00 0.00 3.35
4602 5477 2.556114 CCAAACTTTCTGGCTCCCTCAT 60.556 50.000 0.00 0.00 0.00 2.90
4638 5515 7.412853 AGTAGAAATTTTATGCGCAGAATCTG 58.587 34.615 22.35 5.78 34.12 2.90
4643 5520 4.574828 GGGAGTAGAAATTTTATGCGCAGA 59.425 41.667 18.32 9.06 0.00 4.26
4661 5538 8.862085 GCTCTTATATTAGTTTACAGAGGGAGT 58.138 37.037 0.00 0.00 0.00 3.85
4662 5539 8.024285 CGCTCTTATATTAGTTTACAGAGGGAG 58.976 40.741 4.76 0.00 40.49 4.30
4663 5540 7.504911 ACGCTCTTATATTAGTTTACAGAGGGA 59.495 37.037 14.96 0.00 40.49 4.20
4664 5541 7.659186 ACGCTCTTATATTAGTTTACAGAGGG 58.341 38.462 8.36 8.36 42.53 4.30
4665 5542 9.530633 AAACGCTCTTATATTAGTTTACAGAGG 57.469 33.333 0.00 0.00 31.14 3.69
4715 5592 9.710818 TCCCTCTGTAAACTAATATAAGAGTGT 57.289 33.333 0.00 0.00 0.00 3.55
4717 5594 9.939424 ACTCCCTCTGTAAACTAATATAAGAGT 57.061 33.333 0.00 0.00 0.00 3.24
4726 5603 9.678260 CTAGTAAGTACTCCCTCTGTAAACTAA 57.322 37.037 0.00 0.00 37.73 2.24
4727 5604 8.270744 CCTAGTAAGTACTCCCTCTGTAAACTA 58.729 40.741 0.00 0.00 37.73 2.24
4728 5605 7.118060 CCTAGTAAGTACTCCCTCTGTAAACT 58.882 42.308 0.00 0.00 37.73 2.66
4729 5606 6.183360 GCCTAGTAAGTACTCCCTCTGTAAAC 60.183 46.154 0.00 0.00 37.73 2.01
4730 5607 5.890419 GCCTAGTAAGTACTCCCTCTGTAAA 59.110 44.000 0.00 0.00 37.73 2.01
4731 5608 5.444176 GCCTAGTAAGTACTCCCTCTGTAA 58.556 45.833 0.00 0.00 37.73 2.41
4732 5609 4.444022 CGCCTAGTAAGTACTCCCTCTGTA 60.444 50.000 0.00 0.00 37.73 2.74
4733 5610 3.684981 CGCCTAGTAAGTACTCCCTCTGT 60.685 52.174 0.00 0.00 37.73 3.41
4734 5611 2.879646 CGCCTAGTAAGTACTCCCTCTG 59.120 54.545 0.00 0.00 37.73 3.35
4735 5612 2.749132 GCGCCTAGTAAGTACTCCCTCT 60.749 54.545 0.00 0.00 37.73 3.69
4736 5613 1.608109 GCGCCTAGTAAGTACTCCCTC 59.392 57.143 0.00 0.00 37.73 4.30
4737 5614 1.214923 AGCGCCTAGTAAGTACTCCCT 59.785 52.381 2.29 0.00 37.73 4.20
4738 5615 1.608109 GAGCGCCTAGTAAGTACTCCC 59.392 57.143 2.29 0.00 37.73 4.30
4739 5616 2.291190 CTGAGCGCCTAGTAAGTACTCC 59.709 54.545 2.29 0.00 37.73 3.85
4740 5617 2.944349 ACTGAGCGCCTAGTAAGTACTC 59.056 50.000 11.94 0.00 37.73 2.59
4741 5618 2.683867 CACTGAGCGCCTAGTAAGTACT 59.316 50.000 13.05 0.00 40.24 2.73
4742 5619 2.422832 ACACTGAGCGCCTAGTAAGTAC 59.577 50.000 13.05 0.00 0.00 2.73


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

AutoCloner maintained by Alex Coulton.