Multiple sequence alignment - TraesCS5B01G069000

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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 TraesCS5B01G069000 chr5B 100.000 6733 0 0 1 6733 78713926 78707194 0.000000e+00 12434.0
1 TraesCS5B01G069000 chr5D 89.903 5863 409 93 904 6666 73794542 73800321 0.000000e+00 7378.0
2 TraesCS5B01G069000 chr5D 92.084 758 25 6 1 724 73770985 73771741 0.000000e+00 1035.0
3 TraesCS5B01G069000 chr5D 95.556 45 2 0 6689 6733 73800325 73800369 9.370000e-09 73.1
4 TraesCS5B01G069000 chr5A 88.536 2111 141 49 4110 6171 68935085 68937143 0.000000e+00 2464.0
5 TraesCS5B01G069000 chr5A 88.988 1689 99 41 2481 4113 68933077 68934734 0.000000e+00 2008.0
6 TraesCS5B01G069000 chr5A 94.129 528 26 4 1959 2483 68932429 68932954 0.000000e+00 798.0
7 TraesCS5B01G069000 chr5A 92.171 562 39 2 943 1499 68931414 68931975 0.000000e+00 789.0
8 TraesCS5B01G069000 chr5A 93.686 491 27 2 6247 6733 68941144 68941634 0.000000e+00 732.0
9 TraesCS5B01G069000 chr5A 82.185 595 51 27 374 940 68930538 68931105 1.710000e-125 460.0
10 TraesCS5B01G069000 chr5A 84.978 446 49 13 1482 1914 68931988 68932428 2.880000e-118 436.0
11 TraesCS5B01G069000 chr5A 89.922 258 21 3 121 376 68930180 68930434 1.810000e-85 327.0
12 TraesCS5B01G069000 chr6B 93.103 638 34 4 1002 1631 247209165 247209800 0.000000e+00 926.0


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 TraesCS5B01G069000 chr5B 78707194 78713926 6732 True 12434.000000 12434 100.000000 1 6733 1 chr5B.!!$R1 6732
1 TraesCS5B01G069000 chr5D 73794542 73800369 5827 False 3725.550000 7378 92.729500 904 6733 2 chr5D.!!$F2 5829
2 TraesCS5B01G069000 chr5D 73770985 73771741 756 False 1035.000000 1035 92.084000 1 724 1 chr5D.!!$F1 723
3 TraesCS5B01G069000 chr5A 68930180 68937143 6963 False 1040.285714 2464 88.701286 121 6171 7 chr5A.!!$F2 6050
4 TraesCS5B01G069000 chr6B 247209165 247209800 635 False 926.000000 926 93.103000 1002 1631 1 chr6B.!!$F1 629

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
971 1422 0.042581 TGCCACCTATCCTGTCCTCA 59.957 55.0 0.00 0.00 0.00 3.86 F
1866 2384 0.302890 CCGTTCGATCAGCTCATTGC 59.697 55.0 0.00 0.00 43.29 3.56 F
2024 2542 0.167908 TTTCACGATGTGCGCCAATC 59.832 50.0 4.18 7.17 46.04 2.67 F
3768 4468 0.107361 CGGTTAACACCCCCATCCTC 60.107 60.0 8.10 0.00 40.52 3.71 F
3771 4471 0.623723 TTAACACCCCCATCCTCTGC 59.376 55.0 0.00 0.00 0.00 4.26 F
4071 4775 1.109323 ACAACCAGCTCCCAAAGTGC 61.109 55.0 0.00 0.00 35.13 4.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2005 2523 0.167908 GATTGGCGCACATCGTGAAA 59.832 50.000 10.83 0.00 41.07 2.69 R
3315 3993 0.674895 GGAGCCGATGTTCTGCAAGT 60.675 55.000 0.00 0.00 33.76 3.16 R
3935 4638 0.909610 TGGTAAGTGGAGGCAGGAGG 60.910 60.000 0.00 0.00 0.00 4.30 R
5030 6130 2.168106 CCAGACAGAGCAGCTCTTACAT 59.832 50.000 23.18 8.51 38.99 2.29 R
5201 6314 2.348472 TCCAGGTCAGAATTTGGTCCT 58.652 47.619 0.00 0.00 33.88 3.85 R
5862 6996 0.036765 TCCCGTCACCAAATCTTCCG 60.037 55.000 0.00 0.00 0.00 4.30 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
24 25 7.368198 TGACTTAAAAACTAGGCCCAAAAAT 57.632 32.000 0.00 0.00 0.00 1.82
62 70 2.031919 CCCACGCCACAGCTAACA 59.968 61.111 0.00 0.00 36.60 2.41
81 89 5.852282 AACAACAGAATTAGTGGCTTGTT 57.148 34.783 0.00 0.00 0.00 2.83
189 197 4.107051 GCATGCTCACACGCCACC 62.107 66.667 11.37 0.00 0.00 4.61
297 307 7.317970 CGCGTGATTAATATGATTGTGTGTAAC 59.682 37.037 0.00 0.00 37.35 2.50
308 318 6.969366 TGATTGTGTGTAACCATTTCTTCAG 58.031 36.000 0.00 0.00 34.36 3.02
313 323 6.704493 TGTGTGTAACCATTTCTTCAGTAGTC 59.296 38.462 0.00 0.00 34.36 2.59
528 651 8.084590 AGTGTTTCTGAGGTAAAAATAAGTCG 57.915 34.615 0.00 0.00 0.00 4.18
679 820 5.011738 TGAGATTTAAGTGAGTTCGGGAAGT 59.988 40.000 0.00 0.00 0.00 3.01
695 836 4.374399 GGGAAGTCTTGTGTCGAGTTTTA 58.626 43.478 0.00 0.00 0.00 1.52
751 894 3.686016 TGGGTCATGAAAACTAGCCTTC 58.314 45.455 0.00 0.00 0.00 3.46
753 896 3.335579 GGTCATGAAAACTAGCCTTCGT 58.664 45.455 0.00 0.00 0.00 3.85
762 905 4.994907 AACTAGCCTTCGTTTTGGTTTT 57.005 36.364 0.00 0.00 0.00 2.43
763 906 4.301637 ACTAGCCTTCGTTTTGGTTTTG 57.698 40.909 0.00 0.00 0.00 2.44
764 907 3.949113 ACTAGCCTTCGTTTTGGTTTTGA 59.051 39.130 0.00 0.00 0.00 2.69
767 910 4.368315 AGCCTTCGTTTTGGTTTTGATTC 58.632 39.130 0.00 0.00 0.00 2.52
773 916 3.801594 CGTTTTGGTTTTGATTCACCCTG 59.198 43.478 0.00 0.00 31.24 4.45
774 917 4.126437 GTTTTGGTTTTGATTCACCCTGG 58.874 43.478 0.00 0.00 31.24 4.45
775 918 3.320610 TTGGTTTTGATTCACCCTGGA 57.679 42.857 0.00 0.00 31.24 3.86
779 922 3.255888 GGTTTTGATTCACCCTGGAAGTC 59.744 47.826 0.00 0.00 0.00 3.01
793 936 5.581085 CCCTGGAAGTCTATCGTTAAGTTTG 59.419 44.000 0.00 0.00 0.00 2.93
801 944 8.967552 AGTCTATCGTTAAGTTTGTTACAGAG 57.032 34.615 0.00 0.00 0.00 3.35
807 950 8.697846 TCGTTAAGTTTGTTACAGAGGATATG 57.302 34.615 0.00 0.00 0.00 1.78
808 951 8.525316 TCGTTAAGTTTGTTACAGAGGATATGA 58.475 33.333 0.00 0.00 0.00 2.15
845 988 6.604735 AGTTTAATAAAGCTAGCCATGACG 57.395 37.500 12.13 0.00 0.00 4.35
846 989 6.346096 AGTTTAATAAAGCTAGCCATGACGA 58.654 36.000 12.13 0.00 0.00 4.20
847 990 6.992715 AGTTTAATAAAGCTAGCCATGACGAT 59.007 34.615 12.13 0.00 0.00 3.73
848 991 7.171678 AGTTTAATAAAGCTAGCCATGACGATC 59.828 37.037 12.13 0.00 0.00 3.69
856 999 2.625737 AGCCATGACGATCTTCAACTG 58.374 47.619 5.94 1.19 0.00 3.16
892 1037 7.882179 TCAAAGAATAGAAAACAAAGGGCTAC 58.118 34.615 0.00 0.00 0.00 3.58
900 1045 3.706600 AACAAAGGGCTACGGTGATAA 57.293 42.857 0.00 0.00 0.00 1.75
902 1047 5.362105 AACAAAGGGCTACGGTGATAATA 57.638 39.130 0.00 0.00 0.00 0.98
940 1085 1.408822 GGAGGAAACCCATCGCATCTT 60.409 52.381 0.00 0.00 0.00 2.40
971 1422 0.042581 TGCCACCTATCCTGTCCTCA 59.957 55.000 0.00 0.00 0.00 3.86
975 1426 2.035632 CACCTATCCTGTCCTCACTCC 58.964 57.143 0.00 0.00 0.00 3.85
1021 1472 2.043450 CGGCTCTCTCCCTGTCCT 60.043 66.667 0.00 0.00 0.00 3.85
1022 1473 2.422231 CGGCTCTCTCCCTGTCCTG 61.422 68.421 0.00 0.00 0.00 3.86
1333 1789 5.164606 TGGACGAAGCTTTTGTTTAGTTC 57.835 39.130 0.00 0.00 29.90 3.01
1341 1797 7.432252 CGAAGCTTTTGTTTAGTTCAGTTTCAT 59.568 33.333 0.00 0.00 0.00 2.57
1421 1883 7.176340 GGTAGTACCTATCACGAAGGAATATGT 59.824 40.741 12.41 0.00 37.57 2.29
1559 2051 6.206634 AGTCGCTCCATTTTGAAATAGACAAA 59.793 34.615 0.00 0.00 35.81 2.83
1590 2082 0.528017 TGAGATGACACGCTCTCCAC 59.472 55.000 8.21 0.00 37.66 4.02
1598 2090 1.740285 ACGCTCTCCACGTGTCTTT 59.260 52.632 15.65 0.00 43.23 2.52
1599 2091 0.956633 ACGCTCTCCACGTGTCTTTA 59.043 50.000 15.65 0.00 43.23 1.85
1600 2092 1.338973 ACGCTCTCCACGTGTCTTTAA 59.661 47.619 15.65 0.00 43.23 1.52
1608 2101 5.697633 TCTCCACGTGTCTTTAACAATTACC 59.302 40.000 15.65 0.00 40.31 2.85
1616 2110 7.698970 CGTGTCTTTAACAATTACCTTTTGTGT 59.301 33.333 0.00 0.00 40.31 3.72
1617 2111 8.803799 GTGTCTTTAACAATTACCTTTTGTGTG 58.196 33.333 0.00 0.00 40.31 3.82
1680 2179 6.515272 AACAACTATCCATGACAAATCCAC 57.485 37.500 0.00 0.00 0.00 4.02
1691 2198 7.502226 TCCATGACAAATCCACTTATATTCACC 59.498 37.037 0.00 0.00 0.00 4.02
1699 2206 5.925509 TCCACTTATATTCACCTTACCAGC 58.074 41.667 0.00 0.00 0.00 4.85
1714 2221 5.180492 CCTTACCAGCATTTACGAACTGAAA 59.820 40.000 0.00 0.00 31.67 2.69
1718 2225 6.149633 ACCAGCATTTACGAACTGAAAAATC 58.850 36.000 0.00 0.00 31.67 2.17
1778 2286 7.614124 ATTCAAAGTTTGACTGCATGTTTTT 57.386 28.000 17.85 0.00 39.87 1.94
1865 2383 1.645034 ACCGTTCGATCAGCTCATTG 58.355 50.000 0.00 0.00 0.00 2.82
1866 2384 0.302890 CCGTTCGATCAGCTCATTGC 59.697 55.000 0.00 0.00 43.29 3.56
1869 2387 2.031314 CGTTCGATCAGCTCATTGCATT 59.969 45.455 0.00 0.00 45.94 3.56
1870 2388 3.360533 GTTCGATCAGCTCATTGCATTG 58.639 45.455 2.08 2.08 45.94 2.82
1872 2390 3.011818 TCGATCAGCTCATTGCATTGTT 58.988 40.909 8.36 0.00 45.94 2.83
1874 2392 4.818005 TCGATCAGCTCATTGCATTGTTAT 59.182 37.500 8.36 0.00 45.94 1.89
1875 2393 5.297527 TCGATCAGCTCATTGCATTGTTATT 59.702 36.000 8.36 0.00 45.94 1.40
1983 2501 6.704289 TGAATGGATGAATCTTGAATGGTC 57.296 37.500 0.00 0.00 0.00 4.02
1990 2508 2.698855 ATCTTGAATGGTCACTCGGG 57.301 50.000 0.00 0.00 31.90 5.14
2005 2523 4.954202 TCACTCGGGTTTATCTCAGTATGT 59.046 41.667 0.00 0.00 37.40 2.29
2017 2535 3.926527 TCTCAGTATGTTTCACGATGTGC 59.073 43.478 0.00 0.00 37.40 4.57
2024 2542 0.167908 TTTCACGATGTGCGCCAATC 59.832 50.000 4.18 7.17 46.04 2.67
2025 2543 0.952984 TTCACGATGTGCGCCAATCA 60.953 50.000 16.76 7.08 46.04 2.57
2087 2606 7.739477 CACTGTGTTTTTGTTGTTGTTTATGTG 59.261 33.333 0.00 0.00 0.00 3.21
2153 2672 3.612681 CACCGGTGGTCGTGGAGT 61.613 66.667 27.57 0.00 37.11 3.85
2167 2686 2.529744 GGAGTTGGTGGCTCAGGGT 61.530 63.158 0.00 0.00 34.83 4.34
2176 2695 1.380302 GGCTCAGGGTGTCATTGGT 59.620 57.895 0.00 0.00 0.00 3.67
2316 2835 4.700700 TCTACATCATTGACCTGCATCTG 58.299 43.478 0.00 0.00 0.00 2.90
2385 2904 3.186119 GAGAACTATGCTGTGTGCTCTC 58.814 50.000 0.00 0.00 43.37 3.20
2419 2939 7.345422 CCATATTGTGGTACCAAAATGATGA 57.655 36.000 32.44 17.87 43.44 2.92
2572 3219 6.647229 AGATATCACTGAGAATGCTTTGTGA 58.353 36.000 5.32 10.81 39.30 3.58
2677 3324 0.457035 CCAATTGATCGTGGGCCTTG 59.543 55.000 7.12 0.00 0.00 3.61
2712 3359 7.159372 GTGTTAAGTTCTTGAAGACATCCCTA 58.841 38.462 0.00 0.00 0.00 3.53
2801 3456 9.381038 TCAGCTGGACTAATTATTACTATCCTT 57.619 33.333 15.13 0.00 0.00 3.36
2951 3628 6.035112 GTGTTACTTCTACTGCAGCAATACTC 59.965 42.308 15.27 0.00 0.00 2.59
2956 3633 5.089970 TCTACTGCAGCAATACTCACATT 57.910 39.130 15.27 0.00 0.00 2.71
2962 3639 4.080919 TGCAGCAATACTCACATTAGTCCT 60.081 41.667 0.00 0.00 0.00 3.85
3000 3678 7.701539 TTTCTGGATGCATATTTACACTGTT 57.298 32.000 0.00 0.00 0.00 3.16
3082 3760 5.699915 TGAAAAGAAAGAGAGCAGACATGAG 59.300 40.000 0.00 0.00 0.00 2.90
3157 3835 1.813513 AGTGTCAAATTCCAGGAGCG 58.186 50.000 0.00 0.00 0.00 5.03
3255 3933 6.873605 TGAATATTCGATGTTGACACTTCTGT 59.126 34.615 10.80 0.00 0.00 3.41
3346 4024 0.108186 TCGGCTCCTGTTGCTACATG 60.108 55.000 0.34 0.00 32.86 3.21
3354 4032 5.677091 GCTCCTGTTGCTACATGGTTATTTG 60.677 44.000 0.34 0.00 32.86 2.32
3358 4036 5.649557 TGTTGCTACATGGTTATTTGCATC 58.350 37.500 0.00 0.00 0.00 3.91
3452 4135 7.491372 TCAAGACAGAATATTTACAGCCTTACG 59.509 37.037 0.00 0.00 0.00 3.18
3463 4146 4.281898 ACAGCCTTACGTAACTGGATTT 57.718 40.909 22.60 7.53 34.40 2.17
3470 4153 6.526674 GCCTTACGTAACTGGATTTGAAATTG 59.473 38.462 15.75 0.00 0.00 2.32
3479 4162 4.823157 TGGATTTGAAATTGGTGCAGATG 58.177 39.130 0.00 0.00 0.00 2.90
3482 4165 6.380560 TGGATTTGAAATTGGTGCAGATGATA 59.619 34.615 0.00 0.00 0.00 2.15
3494 4177 4.450419 GTGCAGATGATACCTATCAGTTGC 59.550 45.833 18.22 18.22 45.01 4.17
3503 4186 4.423625 ACCTATCAGTTGCCTCATAACC 57.576 45.455 0.00 0.00 0.00 2.85
3535 4218 3.786048 CGTGTGCAGTTTTCTTTCTGAAC 59.214 43.478 0.00 0.00 39.81 3.18
3587 4278 2.266689 CCCATGGCTGCCAAAAGC 59.733 61.111 27.24 0.00 42.75 3.51
3647 4338 9.859427 TTTGTTATTTGCAGATTTCTAATGGAG 57.141 29.630 0.00 0.00 0.00 3.86
3648 4339 7.483307 TGTTATTTGCAGATTTCTAATGGAGC 58.517 34.615 0.00 0.00 0.00 4.70
3728 4420 3.495331 ACATTTGTGTTAGGGCATGACA 58.505 40.909 0.00 0.00 0.00 3.58
3729 4421 3.255642 ACATTTGTGTTAGGGCATGACAC 59.744 43.478 18.69 18.69 46.03 3.67
3763 4463 0.845337 AAAGACGGTTAACACCCCCA 59.155 50.000 8.10 0.00 40.52 4.96
3764 4464 1.069775 AAGACGGTTAACACCCCCAT 58.930 50.000 8.10 0.00 40.52 4.00
3766 4466 0.393402 GACGGTTAACACCCCCATCC 60.393 60.000 8.10 0.00 40.52 3.51
3768 4468 0.107361 CGGTTAACACCCCCATCCTC 60.107 60.000 8.10 0.00 40.52 3.71
3769 4469 1.296002 GGTTAACACCCCCATCCTCT 58.704 55.000 8.10 0.00 37.03 3.69
3770 4470 1.064685 GGTTAACACCCCCATCCTCTG 60.065 57.143 8.10 0.00 37.03 3.35
3771 4471 0.623723 TTAACACCCCCATCCTCTGC 59.376 55.000 0.00 0.00 0.00 4.26
3774 4474 1.150081 CACCCCCATCCTCTGCATC 59.850 63.158 0.00 0.00 0.00 3.91
3780 4480 1.278413 CCCATCCTCTGCATCGATGAT 59.722 52.381 29.20 9.33 36.33 2.45
3830 4530 8.632679 TCTTATTTGCCATCTTGGAATGTAATC 58.367 33.333 0.00 0.00 40.96 1.75
3839 4539 7.227314 CCATCTTGGAATGTAATCGATTTCTCA 59.773 37.037 17.19 13.31 40.96 3.27
3971 4674 3.045601 ACCACTGAGCACTGTTATGTC 57.954 47.619 0.00 0.00 0.00 3.06
3972 4675 2.289694 ACCACTGAGCACTGTTATGTCC 60.290 50.000 0.00 0.00 0.00 4.02
3978 4681 2.225491 GAGCACTGTTATGTCCGCAAAA 59.775 45.455 0.00 0.00 0.00 2.44
4015 4718 6.715280 AGATGAGTTATGAACCACTGTCATT 58.285 36.000 0.00 0.00 0.00 2.57
4032 4735 4.155063 TCATTCATACATGACACCCCTG 57.845 45.455 0.00 0.00 36.36 4.45
4059 4763 4.009675 ACATATGCACCTTGTACAACCAG 58.990 43.478 3.59 0.00 0.00 4.00
4071 4775 1.109323 ACAACCAGCTCCCAAAGTGC 61.109 55.000 0.00 0.00 35.13 4.40
4082 4786 2.708861 TCCCAAAGTGCCAGAGTTCTAA 59.291 45.455 0.00 0.00 0.00 2.10
4084 4788 3.244561 CCCAAAGTGCCAGAGTTCTAAGA 60.245 47.826 0.00 0.00 0.00 2.10
4198 5259 2.540361 GCACATCATCGTTCCTGCATTC 60.540 50.000 0.00 0.00 0.00 2.67
4234 5296 4.944962 TTGGTTGAAACTAGATGCATCG 57.055 40.909 20.67 10.34 0.00 3.84
4273 5335 7.204496 ACTAAGTCTGTGAACTAGTGTGTAG 57.796 40.000 0.00 0.00 0.00 2.74
4277 5339 5.828859 AGTCTGTGAACTAGTGTGTAGTCTT 59.171 40.000 0.00 0.00 0.00 3.01
4288 5368 3.372206 GTGTGTAGTCTTCATGGTGCATC 59.628 47.826 0.00 0.00 0.00 3.91
4349 5429 8.806146 ACATTTTCTGGTACTTCATTAATTGCT 58.194 29.630 0.00 0.00 0.00 3.91
4355 5435 8.677300 TCTGGTACTTCATTAATTGCTTCAATC 58.323 33.333 0.00 0.00 32.43 2.67
4359 5439 9.508567 GTACTTCATTAATTGCTTCAATCTTCC 57.491 33.333 0.00 0.00 32.43 3.46
4371 5451 5.829924 GCTTCAATCTTCCATAAATCCCTGA 59.170 40.000 0.00 0.00 0.00 3.86
4438 5519 4.405358 TGATGGTGAACAAGAAAAGCCTTT 59.595 37.500 0.00 0.00 0.00 3.11
4439 5520 4.122143 TGGTGAACAAGAAAAGCCTTTG 57.878 40.909 0.00 0.00 0.00 2.77
4572 5672 4.783560 TCTGTGATGATGGATTGATGGT 57.216 40.909 0.00 0.00 0.00 3.55
4634 5734 9.026121 ACATTAACAGACATAGTTCACTAGACT 57.974 33.333 0.00 0.00 0.00 3.24
4643 5743 9.856488 GACATAGTTCACTAGACTCATTAACAA 57.144 33.333 0.00 0.00 0.00 2.83
4717 5817 6.588373 GGAAGAGTGCTTCTTGAAGTAGTTAG 59.412 42.308 11.41 0.00 46.12 2.34
4718 5818 5.474825 AGAGTGCTTCTTGAAGTAGTTAGC 58.525 41.667 11.41 0.00 29.61 3.09
4736 5836 7.693969 AGTTAGCTTATTTGGATATCCATGC 57.306 36.000 25.07 20.84 46.97 4.06
4741 5841 5.244626 GCTTATTTGGATATCCATGCCAACT 59.755 40.000 25.07 6.85 46.97 3.16
4768 5868 6.976934 AGTTTCCCAATCTTTTGAGCTAAA 57.023 33.333 0.00 0.00 34.60 1.85
4966 6066 7.770897 AGATATGTTGGACTCCTGAAATAACAC 59.229 37.037 0.00 0.00 30.51 3.32
5030 6130 9.847224 GGAATATCCTTAATTACTTTGGTCTGA 57.153 33.333 0.00 0.00 32.53 3.27
5048 6148 3.130164 TCTGATGTAAGAGCTGCTCTGTC 59.870 47.826 31.03 24.63 40.28 3.51
5059 6159 2.481952 GCTGCTCTGTCTGGTTTGTAAG 59.518 50.000 0.00 0.00 0.00 2.34
5065 6165 3.327757 TCTGTCTGGTTTGTAAGCCTCAT 59.672 43.478 0.00 0.00 0.00 2.90
5066 6166 3.411446 TGTCTGGTTTGTAAGCCTCATG 58.589 45.455 0.00 0.00 0.00 3.07
5067 6167 3.072330 TGTCTGGTTTGTAAGCCTCATGA 59.928 43.478 0.00 0.00 0.00 3.07
5068 6168 4.072131 GTCTGGTTTGTAAGCCTCATGAA 58.928 43.478 0.00 0.00 0.00 2.57
5069 6169 4.072131 TCTGGTTTGTAAGCCTCATGAAC 58.928 43.478 0.00 0.00 0.00 3.18
5070 6170 3.820467 CTGGTTTGTAAGCCTCATGAACA 59.180 43.478 0.00 0.00 0.00 3.18
5071 6171 4.211125 TGGTTTGTAAGCCTCATGAACAA 58.789 39.130 5.92 5.92 0.00 2.83
5072 6172 4.832266 TGGTTTGTAAGCCTCATGAACAAT 59.168 37.500 9.99 0.00 30.76 2.71
5073 6173 6.007076 TGGTTTGTAAGCCTCATGAACAATA 58.993 36.000 9.99 1.22 30.76 1.90
5074 6174 6.072175 TGGTTTGTAAGCCTCATGAACAATAC 60.072 38.462 9.99 10.40 30.76 1.89
5075 6175 6.151144 GGTTTGTAAGCCTCATGAACAATACT 59.849 38.462 9.99 0.00 30.76 2.12
5076 6176 6.741992 TTGTAAGCCTCATGAACAATACTG 57.258 37.500 5.92 0.00 0.00 2.74
5077 6177 5.185454 TGTAAGCCTCATGAACAATACTGG 58.815 41.667 0.00 0.00 0.00 4.00
5201 6314 7.503521 TGATAACACTGAAAGCACAAATACA 57.496 32.000 0.00 0.00 37.60 2.29
5342 6455 5.416013 TGTTGTTGACTCCACATGTTTACAA 59.584 36.000 0.00 0.00 0.00 2.41
5343 6456 6.071896 TGTTGTTGACTCCACATGTTTACAAA 60.072 34.615 0.00 0.00 0.00 2.83
5402 6515 2.196997 TCCGGCCTGGAATGTTCCTG 62.197 60.000 13.07 11.60 46.38 3.86
5474 6590 6.647334 TTGAAATGAGCACATTAGTTTCCA 57.353 33.333 9.89 0.00 44.67 3.53
5481 6597 7.377766 TGAGCACATTAGTTTCCATTAAGTC 57.622 36.000 0.00 0.00 0.00 3.01
5486 6602 9.556030 GCACATTAGTTTCCATTAAGTCTTTAC 57.444 33.333 0.00 0.00 0.00 2.01
5499 6615 9.262472 CATTAAGTCTTTACGAGTTTACATTGC 57.738 33.333 0.00 0.00 36.66 3.56
5500 6616 5.857822 AGTCTTTACGAGTTTACATTGCC 57.142 39.130 0.00 0.00 0.00 4.52
5510 6626 6.128117 ACGAGTTTACATTGCCGTAATTCAAT 60.128 34.615 0.00 0.00 31.65 2.57
5526 6642 7.647715 CGTAATTCAATTTCTTCAACTTGTGGT 59.352 33.333 0.00 0.00 0.00 4.16
5527 6643 9.959749 GTAATTCAATTTCTTCAACTTGTGGTA 57.040 29.630 0.00 0.00 0.00 3.25
5612 6728 2.911484 GGTGAGCTACCTTCATTCCAG 58.089 52.381 0.00 0.00 46.51 3.86
5614 6730 3.307762 GGTGAGCTACCTTCATTCCAGTT 60.308 47.826 0.00 0.00 46.51 3.16
5636 6752 7.336931 CAGTTAACTATAAGTTGCCCTGAATGT 59.663 37.037 8.04 0.00 39.11 2.71
5654 6770 3.593442 TGTCACCCTTGTCTGGAAAAT 57.407 42.857 0.00 0.00 0.00 1.82
5655 6771 4.715534 TGTCACCCTTGTCTGGAAAATA 57.284 40.909 0.00 0.00 0.00 1.40
5657 6773 5.640147 TGTCACCCTTGTCTGGAAAATAAT 58.360 37.500 0.00 0.00 0.00 1.28
5660 6776 7.070571 TGTCACCCTTGTCTGGAAAATAATTTT 59.929 33.333 0.00 0.00 35.12 1.82
5709 6825 6.767524 AGGTACATCAAACAACACTGAAAA 57.232 33.333 0.00 0.00 0.00 2.29
5732 6848 4.927267 TCTTCAGGAAATGGCCTTCTAA 57.073 40.909 3.32 0.00 35.66 2.10
5737 6853 4.706476 TCAGGAAATGGCCTTCTAATGTTG 59.294 41.667 3.32 0.00 35.66 3.33
5773 6891 9.935682 AGTCATATACAATACAAAAATGAAGCG 57.064 29.630 0.00 0.00 0.00 4.68
5812 6946 7.682787 AGCTATCGGGATATTTTCTCCATAT 57.317 36.000 0.00 0.00 34.24 1.78
5813 6947 8.783660 AGCTATCGGGATATTTTCTCCATATA 57.216 34.615 0.00 0.00 34.24 0.86
5830 6964 9.159254 TCTCCATATATAACTTGTTGATGAGGT 57.841 33.333 0.00 0.00 0.00 3.85
5831 6965 9.212641 CTCCATATATAACTTGTTGATGAGGTG 57.787 37.037 0.00 0.00 0.00 4.00
5832 6966 8.713971 TCCATATATAACTTGTTGATGAGGTGT 58.286 33.333 0.00 0.00 0.00 4.16
5833 6967 8.777413 CCATATATAACTTGTTGATGAGGTGTG 58.223 37.037 0.00 0.00 0.00 3.82
5834 6968 9.330063 CATATATAACTTGTTGATGAGGTGTGT 57.670 33.333 0.00 0.00 0.00 3.72
5835 6969 9.905713 ATATATAACTTGTTGATGAGGTGTGTT 57.094 29.630 0.00 0.00 0.00 3.32
5836 6970 4.900635 AACTTGTTGATGAGGTGTGTTC 57.099 40.909 0.00 0.00 0.00 3.18
5869 7003 1.747355 CTGCAAAATGGAGCGGAAGAT 59.253 47.619 0.00 0.00 39.47 2.40
5870 7004 2.165030 CTGCAAAATGGAGCGGAAGATT 59.835 45.455 0.00 0.00 39.47 2.40
5871 7005 2.562298 TGCAAAATGGAGCGGAAGATTT 59.438 40.909 0.00 0.00 0.00 2.17
5878 7012 0.721718 GAGCGGAAGATTTGGTGACG 59.278 55.000 0.00 0.00 0.00 4.35
5895 7029 4.432741 GGGAGCACCTGAAGGCCC 62.433 72.222 0.00 0.00 39.32 5.80
5916 7050 3.933332 CCAACGATTACTTCCAGTCTTCC 59.067 47.826 0.00 0.00 0.00 3.46
5943 7077 2.864343 GGGTACTGTTGTATCATCACGC 59.136 50.000 0.00 0.00 31.60 5.34
5952 7086 0.179148 TATCATCACGCGCAGACGTT 60.179 50.000 5.73 0.00 45.75 3.99
5993 7127 4.037923 TGGAAACTTGAAAGGAGCACAATC 59.962 41.667 0.00 0.00 0.00 2.67
6056 7194 9.209175 AGTAGTGCTTTTTGAAGACATTACTAG 57.791 33.333 12.34 0.00 32.96 2.57
6229 7378 2.086869 TCCCTCGTAGTCGGTAACTTG 58.913 52.381 0.00 0.00 39.55 3.16
6230 7379 1.468736 CCCTCGTAGTCGGTAACTTGC 60.469 57.143 0.00 0.00 39.55 4.01
6231 7380 1.200716 CCTCGTAGTCGGTAACTTGCA 59.799 52.381 0.00 0.00 39.55 4.08
6307 7456 6.012658 TGAGTGAAGACATTATTTGTTGCC 57.987 37.500 0.00 0.00 39.18 4.52
6308 7457 5.048083 TGAGTGAAGACATTATTTGTTGCCC 60.048 40.000 0.00 0.00 39.18 5.36
6323 7474 2.732619 GCCCCCTAGGTCCAACTCG 61.733 68.421 8.29 0.00 38.26 4.18
6601 7753 0.035725 GTTCCTCCCCGAATCCGTTT 60.036 55.000 0.00 0.00 0.00 3.60
6632 7784 0.030369 ATCCGACGAGGTTATCACGC 59.970 55.000 0.00 0.00 41.99 5.34
6633 7785 1.588139 CCGACGAGGTTATCACGCC 60.588 63.158 0.00 0.00 34.51 5.68
6653 7805 2.048127 AGTTCTTCCGCTCCGCAC 60.048 61.111 0.00 0.00 0.00 5.34
6655 7807 4.388499 TTCTTCCGCTCCGCACCC 62.388 66.667 0.00 0.00 0.00 4.61
6681 7833 4.478195 CGATCGACGGTTCTGCTT 57.522 55.556 10.26 0.00 38.46 3.91
6682 7834 2.279469 CGATCGACGGTTCTGCTTC 58.721 57.895 10.26 0.00 38.46 3.86
6683 7835 1.464429 CGATCGACGGTTCTGCTTCG 61.464 60.000 10.26 0.00 38.46 3.79
6684 7836 0.456312 GATCGACGGTTCTGCTTCGT 60.456 55.000 0.00 0.00 39.99 3.85
6685 7837 0.456312 ATCGACGGTTCTGCTTCGTC 60.456 55.000 0.00 0.00 46.52 4.20
6686 7838 3.857909 GACGGTTCTGCTTCGTCC 58.142 61.111 0.00 0.00 44.96 4.79
6687 7839 1.737008 GACGGTTCTGCTTCGTCCC 60.737 63.158 0.00 0.00 44.96 4.46
6719 7871 0.880718 GCCAAGGGGATTCGATCGTC 60.881 60.000 15.94 6.07 35.59 4.20
6721 7873 1.269831 CCAAGGGGATTCGATCGTCTC 60.270 57.143 15.94 12.43 35.59 3.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
19 20 9.874215 GTTTTCTCACGCTACTAGTTTATTTTT 57.126 29.630 0.00 0.00 0.00 1.94
21 22 7.118825 GGGTTTTCTCACGCTACTAGTTTATTT 59.881 37.037 0.00 0.00 0.00 1.40
24 25 5.010922 TGGGTTTTCTCACGCTACTAGTTTA 59.989 40.000 0.00 0.00 0.00 2.01
62 70 6.942576 AGACATAACAAGCCACTAATTCTGTT 59.057 34.615 0.00 0.00 0.00 3.16
81 89 0.392461 GGAGGCGTGCCAAAGACATA 60.392 55.000 14.29 0.00 38.92 2.29
180 188 1.525077 AATGTTGTCGGTGGCGTGT 60.525 52.632 0.00 0.00 0.00 4.49
189 197 2.154963 CGTCACCAGTACAATGTTGTCG 59.845 50.000 0.99 0.00 42.35 4.35
492 614 7.511959 ACCTCAGAAACACTATTTTTCTTCC 57.488 36.000 0.00 0.00 40.59 3.46
502 624 9.199982 CGACTTATTTTTACCTCAGAAACACTA 57.800 33.333 0.00 0.00 0.00 2.74
528 651 6.976349 TCTTATGCACATCAAAAAGCATCATC 59.024 34.615 1.65 0.00 43.67 2.92
602 743 7.985184 AGTTAATTGTCTACGGATTGCAATAGA 59.015 33.333 12.97 8.75 0.00 1.98
648 789 4.759782 ACTCACTTAAATCTCATCCACGG 58.240 43.478 0.00 0.00 0.00 4.94
679 820 8.786826 ATTCCATTATAAAACTCGACACAAGA 57.213 30.769 0.00 0.00 0.00 3.02
695 836 4.706842 AACACGCCCTAGATTCCATTAT 57.293 40.909 0.00 0.00 0.00 1.28
729 872 3.356529 AGGCTAGTTTTCATGACCCAG 57.643 47.619 0.00 0.00 0.00 4.45
751 894 3.801594 CAGGGTGAATCAAAACCAAAACG 59.198 43.478 3.34 0.00 38.27 3.60
753 896 4.033709 TCCAGGGTGAATCAAAACCAAAA 58.966 39.130 3.34 0.00 38.27 2.44
762 905 3.384789 CGATAGACTTCCAGGGTGAATCA 59.615 47.826 0.00 0.00 39.76 2.57
763 906 3.385111 ACGATAGACTTCCAGGGTGAATC 59.615 47.826 0.00 0.00 41.38 2.52
764 907 3.375699 ACGATAGACTTCCAGGGTGAAT 58.624 45.455 0.00 0.00 41.38 2.57
767 910 4.159879 ACTTAACGATAGACTTCCAGGGTG 59.840 45.833 0.00 0.00 41.38 4.61
773 916 8.524870 TGTAACAAACTTAACGATAGACTTCC 57.475 34.615 0.00 0.00 41.38 3.46
774 917 9.403110 TCTGTAACAAACTTAACGATAGACTTC 57.597 33.333 0.00 0.00 41.38 3.01
775 918 9.408069 CTCTGTAACAAACTTAACGATAGACTT 57.592 33.333 0.00 0.00 41.38 3.01
779 922 8.928270 ATCCTCTGTAACAAACTTAACGATAG 57.072 34.615 0.00 0.00 46.19 2.08
820 963 7.982919 TCGTCATGGCTAGCTTTATTAAACTTA 59.017 33.333 15.72 0.00 0.00 2.24
821 964 6.821665 TCGTCATGGCTAGCTTTATTAAACTT 59.178 34.615 15.72 0.00 0.00 2.66
822 965 6.346096 TCGTCATGGCTAGCTTTATTAAACT 58.654 36.000 15.72 0.00 0.00 2.66
823 966 6.598753 TCGTCATGGCTAGCTTTATTAAAC 57.401 37.500 15.72 2.16 0.00 2.01
824 967 7.217200 AGATCGTCATGGCTAGCTTTATTAAA 58.783 34.615 15.72 0.00 0.00 1.52
825 968 6.759272 AGATCGTCATGGCTAGCTTTATTAA 58.241 36.000 15.72 0.00 0.00 1.40
829 972 4.099419 TGAAGATCGTCATGGCTAGCTTTA 59.901 41.667 15.72 0.00 0.00 1.85
831 974 2.432146 TGAAGATCGTCATGGCTAGCTT 59.568 45.455 15.72 1.56 0.00 3.74
832 975 2.034878 TGAAGATCGTCATGGCTAGCT 58.965 47.619 15.72 0.00 0.00 3.32
833 976 2.515926 TGAAGATCGTCATGGCTAGC 57.484 50.000 6.04 6.04 0.00 3.42
834 977 3.801050 CAGTTGAAGATCGTCATGGCTAG 59.199 47.826 12.25 3.87 0.00 3.42
836 979 2.234661 TCAGTTGAAGATCGTCATGGCT 59.765 45.455 12.25 8.28 0.00 4.75
866 1009 7.544804 AGCCCTTTGTTTTCTATTCTTTGAT 57.455 32.000 0.00 0.00 0.00 2.57
875 1018 3.071312 TCACCGTAGCCCTTTGTTTTCTA 59.929 43.478 0.00 0.00 0.00 2.10
877 1020 2.223745 TCACCGTAGCCCTTTGTTTTC 58.776 47.619 0.00 0.00 0.00 2.29
912 1057 1.368374 TGGGTTTCCTCCTTTCCGAT 58.632 50.000 0.00 0.00 0.00 4.18
923 1068 1.025041 GGAAGATGCGATGGGTTTCC 58.975 55.000 0.00 0.00 0.00 3.13
951 1402 0.466124 GAGGACAGGATAGGTGGCAC 59.534 60.000 9.70 9.70 0.00 5.01
983 1434 1.002868 ATGGCTTTGCTCTGCTCGT 60.003 52.632 0.00 0.00 0.00 4.18
1102 1553 2.772691 GGCAGACGACGAGGGTAGG 61.773 68.421 0.00 0.00 0.00 3.18
1172 1623 2.283388 ACTTAGCGGGGTCGTCCA 60.283 61.111 0.04 0.00 38.89 4.02
1333 1789 7.042051 TGTTCTAAAAGACGAAGGATGAAACTG 60.042 37.037 0.00 0.00 0.00 3.16
1341 1797 6.342906 TGAAACTGTTCTAAAAGACGAAGGA 58.657 36.000 0.00 0.00 34.60 3.36
1421 1883 5.975344 CGAGAATCATAGTAACTGCCGTTTA 59.025 40.000 0.00 0.00 32.46 2.01
1559 2051 8.668510 AGCGTGTCATCTCAATATCTAAAAAT 57.331 30.769 0.00 0.00 0.00 1.82
1568 2060 3.023832 TGGAGAGCGTGTCATCTCAATA 58.976 45.455 4.74 0.00 43.11 1.90
1582 2074 2.750948 TGTTAAAGACACGTGGAGAGC 58.249 47.619 21.57 3.59 32.00 4.09
1590 2082 7.698970 ACACAAAAGGTAATTGTTAAAGACACG 59.301 33.333 0.00 0.00 38.90 4.49
1598 2090 8.580720 ACATATGCACACAAAAGGTAATTGTTA 58.419 29.630 1.58 0.00 38.90 2.41
1599 2091 7.441017 ACATATGCACACAAAAGGTAATTGTT 58.559 30.769 1.58 0.00 38.90 2.83
1600 2092 6.991938 ACATATGCACACAAAAGGTAATTGT 58.008 32.000 1.58 0.00 41.50 2.71
1678 2177 7.807977 AATGCTGGTAAGGTGAATATAAGTG 57.192 36.000 0.00 0.00 0.00 3.16
1680 2179 8.495949 CGTAAATGCTGGTAAGGTGAATATAAG 58.504 37.037 0.00 0.00 0.00 1.73
1691 2198 5.856126 TTCAGTTCGTAAATGCTGGTAAG 57.144 39.130 0.00 0.00 0.00 2.34
1699 2206 7.374754 TGTTCGTGATTTTTCAGTTCGTAAATG 59.625 33.333 0.00 0.00 0.00 2.32
1714 2221 2.828877 TCAGACCGTTGTTCGTGATTT 58.171 42.857 0.00 0.00 37.94 2.17
1718 2225 3.571571 TCTATTCAGACCGTTGTTCGTG 58.428 45.455 0.00 0.00 37.94 4.35
1818 2335 9.729281 AAAATGTGCCAATTCATCTAAAGAAAT 57.271 25.926 0.00 0.00 0.00 2.17
1983 2501 5.263968 ACATACTGAGATAAACCCGAGTG 57.736 43.478 0.00 0.00 0.00 3.51
1990 2508 8.110612 CACATCGTGAAACATACTGAGATAAAC 58.889 37.037 0.00 0.00 35.23 2.01
2005 2523 0.167908 GATTGGCGCACATCGTGAAA 59.832 50.000 10.83 0.00 41.07 2.69
2017 2535 2.029970 GCAGCAAATTCAATGATTGGCG 59.970 45.455 5.20 0.00 40.22 5.69
2024 2542 3.250744 CTCACAGGCAGCAAATTCAATG 58.749 45.455 0.00 0.00 0.00 2.82
2025 2543 2.232941 CCTCACAGGCAGCAAATTCAAT 59.767 45.455 0.00 0.00 0.00 2.57
2087 2606 4.839121 TCCATCTACAACACCACCAATAC 58.161 43.478 0.00 0.00 0.00 1.89
2145 2664 2.099652 CTGAGCCACCAACTCCACGA 62.100 60.000 0.00 0.00 32.98 4.35
2153 2672 1.426251 ATGACACCCTGAGCCACCAA 61.426 55.000 0.00 0.00 0.00 3.67
2167 2686 6.157820 TCTCATCAACCCTATTACCAATGACA 59.842 38.462 0.00 0.00 0.00 3.58
2176 2695 6.268617 CAGACTCCATCTCATCAACCCTATTA 59.731 42.308 0.00 0.00 34.41 0.98
2316 2835 6.002062 ACGGAATGTTCATTCAGAAAAGAC 57.998 37.500 24.13 7.84 38.13 3.01
2408 2927 8.840321 AGATAAACCGATAGTTCATCATTTTGG 58.160 33.333 0.00 0.00 35.77 3.28
2419 2939 9.712305 CATAATTGGAGAGATAAACCGATAGTT 57.288 33.333 0.00 0.00 41.81 2.24
2572 3219 5.422650 GTGGACTTCAGAGTTACCCTATTCT 59.577 44.000 0.00 0.00 35.88 2.40
2677 3324 6.228258 TCAAGAACTTAACACATACCCAGAC 58.772 40.000 0.00 0.00 0.00 3.51
2712 3359 5.502153 TCAAATTGCAGCAAAGCATTTTT 57.498 30.435 12.97 4.08 45.19 1.94
2749 3396 5.181748 ACAGTGCCTCAGAATATCTTTCAC 58.818 41.667 0.00 0.00 0.00 3.18
2801 3456 9.609346 GGGAAGTAGAAAAAGCTTATACATGTA 57.391 33.333 8.27 8.27 0.00 2.29
2802 3457 8.329502 AGGGAAGTAGAAAAAGCTTATACATGT 58.670 33.333 2.69 2.69 0.00 3.21
2803 3458 8.738645 AGGGAAGTAGAAAAAGCTTATACATG 57.261 34.615 0.00 0.00 0.00 3.21
2831 3508 4.380444 CGCTGCCATTGTAAAACTGGTATT 60.380 41.667 0.00 0.00 32.42 1.89
2982 3660 6.771076 TCGTCAAACAGTGTAAATATGCATC 58.229 36.000 0.19 0.00 0.00 3.91
2995 3673 1.215655 GCGCAGACTCGTCAAACAGT 61.216 55.000 0.30 0.00 0.00 3.55
3000 3678 1.149361 AAAACGCGCAGACTCGTCAA 61.149 50.000 5.73 0.00 35.91 3.18
3157 3835 6.475727 CCTGATTTGCAATGTCATTGAGATTC 59.524 38.462 26.36 17.74 42.83 2.52
3237 3915 4.848562 AGTACAGAAGTGTCAACATCGA 57.151 40.909 0.00 0.00 38.19 3.59
3242 3920 7.271653 CGAGAATCTAAGTACAGAAGTGTCAAC 59.728 40.741 0.00 0.00 38.19 3.18
3315 3993 0.674895 GGAGCCGATGTTCTGCAAGT 60.675 55.000 0.00 0.00 33.76 3.16
3370 4048 6.203915 TGTTCATTTGCGACATGTAACTAACT 59.796 34.615 0.00 0.00 0.00 2.24
3452 4135 5.537188 TGCACCAATTTCAAATCCAGTTAC 58.463 37.500 0.00 0.00 0.00 2.50
3463 4146 4.858850 AGGTATCATCTGCACCAATTTCA 58.141 39.130 0.00 0.00 34.62 2.69
3470 4153 4.881019 ACTGATAGGTATCATCTGCACC 57.119 45.455 0.13 0.00 41.46 5.01
3519 4202 8.230486 AGTTATATGCGTTCAGAAAGAAAACTG 58.770 33.333 0.00 0.00 38.13 3.16
3763 4463 3.324268 AGTTCATCATCGATGCAGAGGAT 59.676 43.478 20.81 4.87 41.63 3.24
3764 4464 2.697229 AGTTCATCATCGATGCAGAGGA 59.303 45.455 20.81 8.14 39.63 3.71
3766 4466 5.981915 TCTAAAGTTCATCATCGATGCAGAG 59.018 40.000 20.81 9.75 39.63 3.35
3768 4468 6.347483 CCATCTAAAGTTCATCATCGATGCAG 60.347 42.308 20.81 14.57 39.63 4.41
3769 4469 5.467735 CCATCTAAAGTTCATCATCGATGCA 59.532 40.000 20.81 10.01 39.63 3.96
3770 4470 5.468072 ACCATCTAAAGTTCATCATCGATGC 59.532 40.000 20.81 6.20 39.63 3.91
3771 4471 7.488187 AACCATCTAAAGTTCATCATCGATG 57.512 36.000 19.61 19.61 41.00 3.84
3774 4474 7.751732 TCAAAACCATCTAAAGTTCATCATCG 58.248 34.615 0.00 0.00 0.00 3.84
3780 4480 8.966868 AGAAAGTTCAAAACCATCTAAAGTTCA 58.033 29.630 0.00 0.00 0.00 3.18
3812 4512 5.695851 AATCGATTACATTCCAAGATGGC 57.304 39.130 9.39 0.00 37.47 4.40
3830 4530 5.853282 GTCAAAAGTTGGACATGAGAAATCG 59.147 40.000 0.00 0.00 34.22 3.34
3839 4539 4.709397 TCAAACAGGTCAAAAGTTGGACAT 59.291 37.500 9.41 0.84 35.74 3.06
3885 4585 6.183360 TGCTGATATGAACTTGAACTATCCGA 60.183 38.462 0.00 0.00 0.00 4.55
3935 4638 0.909610 TGGTAAGTGGAGGCAGGAGG 60.910 60.000 0.00 0.00 0.00 4.30
3971 4674 3.052036 CTCCAAAATGTCAGTTTTGCGG 58.948 45.455 0.00 0.00 44.02 5.69
3972 4675 3.963665 TCTCCAAAATGTCAGTTTTGCG 58.036 40.909 0.00 0.00 44.02 4.85
3978 4681 7.397221 TCATAACTCATCTCCAAAATGTCAGT 58.603 34.615 0.00 0.00 0.00 3.41
4032 4735 7.281324 TGGTTGTACAAGGTGCATATGTTATAC 59.719 37.037 8.98 0.00 0.00 1.47
4059 4763 0.538287 AACTCTGGCACTTTGGGAGC 60.538 55.000 0.00 0.00 0.00 4.70
4071 4775 4.756642 TGCAAACACATCTTAGAACTCTGG 59.243 41.667 0.00 0.00 0.00 3.86
4082 4786 1.806542 GACCACGATGCAAACACATCT 59.193 47.619 0.00 0.00 43.54 2.90
4084 4788 1.896220 AGACCACGATGCAAACACAT 58.104 45.000 0.00 0.00 0.00 3.21
4198 5259 5.381174 TCAACCAATTTCAGAGCATCAAG 57.619 39.130 0.00 0.00 37.82 3.02
4234 5296 8.276325 CACAGACTTAGTTTAGTCATTTGTGAC 58.724 37.037 14.44 0.44 43.92 3.67
4273 5335 3.965292 CAGATGATGCACCATGAAGAC 57.035 47.619 0.00 0.00 0.00 3.01
4288 5368 6.367686 TGCTAGTGTTGATAATTGCAGATG 57.632 37.500 0.00 0.00 0.00 2.90
4349 5429 7.006509 GGATCAGGGATTTATGGAAGATTGAA 58.993 38.462 0.00 0.00 0.00 2.69
4355 5435 7.607615 AAAATGGATCAGGGATTTATGGAAG 57.392 36.000 0.00 0.00 0.00 3.46
4359 5439 8.241497 TCTCAAAAATGGATCAGGGATTTATG 57.759 34.615 0.00 0.00 0.00 1.90
4438 5519 5.483231 TGGAATTCTAAATGGCATTTGGACA 59.517 36.000 30.86 23.65 39.09 4.02
4439 5520 5.976458 TGGAATTCTAAATGGCATTTGGAC 58.024 37.500 30.86 21.82 39.09 4.02
4520 5620 9.797642 AGTATCAATTCAGATGGCATGTATTTA 57.202 29.630 3.81 0.00 0.00 1.40
4614 5714 7.710676 AATGAGTCTAGTGAACTATGTCTGT 57.289 36.000 0.00 0.00 0.00 3.41
4736 5836 8.802267 TCAAAAGATTGGGAAACTATTAGTTGG 58.198 33.333 9.78 0.00 36.50 3.77
4741 5841 9.747898 TTAGCTCAAAAGATTGGGAAACTATTA 57.252 29.630 0.00 0.00 39.55 0.98
4768 5868 6.405508 CCATTGACTGCAGCAATAGAGAAAAT 60.406 38.462 25.62 8.30 34.41 1.82
4966 6066 7.315142 ACACATGGTATTAAAGATTGCAACTG 58.685 34.615 0.00 0.00 0.00 3.16
5030 6130 2.168106 CCAGACAGAGCAGCTCTTACAT 59.832 50.000 23.18 8.51 38.99 2.29
5048 6148 3.820467 TGTTCATGAGGCTTACAAACCAG 59.180 43.478 0.00 0.00 0.00 4.00
5059 6159 3.609853 TCACCAGTATTGTTCATGAGGC 58.390 45.455 0.00 0.00 0.00 4.70
5065 6165 4.133820 CACCTGTTCACCAGTATTGTTCA 58.866 43.478 0.00 0.00 39.74 3.18
5066 6166 4.385825 TCACCTGTTCACCAGTATTGTTC 58.614 43.478 0.00 0.00 39.74 3.18
5067 6167 4.431416 TCACCTGTTCACCAGTATTGTT 57.569 40.909 0.00 0.00 39.74 2.83
5068 6168 4.134563 GTTCACCTGTTCACCAGTATTGT 58.865 43.478 0.00 0.00 39.74 2.71
5069 6169 4.389374 AGTTCACCTGTTCACCAGTATTG 58.611 43.478 0.00 0.00 39.74 1.90
5070 6170 4.706842 AGTTCACCTGTTCACCAGTATT 57.293 40.909 0.00 0.00 39.74 1.89
5071 6171 4.348168 AGAAGTTCACCTGTTCACCAGTAT 59.652 41.667 5.50 0.00 39.74 2.12
5072 6172 3.709653 AGAAGTTCACCTGTTCACCAGTA 59.290 43.478 5.50 0.00 39.74 2.74
5073 6173 2.505819 AGAAGTTCACCTGTTCACCAGT 59.494 45.455 5.50 0.00 39.74 4.00
5074 6174 3.199880 AGAAGTTCACCTGTTCACCAG 57.800 47.619 5.50 0.00 41.15 4.00
5075 6175 3.054728 TCAAGAAGTTCACCTGTTCACCA 60.055 43.478 5.50 0.00 0.00 4.17
5076 6176 3.541632 TCAAGAAGTTCACCTGTTCACC 58.458 45.455 5.50 0.00 0.00 4.02
5077 6177 3.002759 GCTCAAGAAGTTCACCTGTTCAC 59.997 47.826 5.50 0.00 0.00 3.18
5201 6314 2.348472 TCCAGGTCAGAATTTGGTCCT 58.652 47.619 0.00 0.00 33.88 3.85
5302 6415 6.017109 GTCAACAACAGTCTGGTTCAATGTAT 60.017 38.462 4.53 0.00 0.00 2.29
5342 6455 4.994217 CCCGTTGCATTTTCCTAATGTTTT 59.006 37.500 0.00 0.00 0.00 2.43
5343 6456 4.565022 CCCGTTGCATTTTCCTAATGTTT 58.435 39.130 0.00 0.00 0.00 2.83
5402 6515 7.501844 AGCATAATACCTTAGAAACTGTCTCC 58.498 38.462 0.00 0.00 37.84 3.71
5462 6578 9.715121 TCGTAAAGACTTAATGGAAACTAATGT 57.285 29.630 0.00 0.00 0.00 2.71
5474 6590 8.448615 GGCAATGTAAACTCGTAAAGACTTAAT 58.551 33.333 0.00 0.00 0.00 1.40
5481 6597 4.657075 ACGGCAATGTAAACTCGTAAAG 57.343 40.909 0.00 0.00 0.00 1.85
5486 6602 5.211266 TGAATTACGGCAATGTAAACTCG 57.789 39.130 0.46 0.00 37.81 4.18
5499 6615 7.114811 CCACAAGTTGAAGAAATTGAATTACGG 59.885 37.037 10.54 0.00 39.07 4.02
5500 6616 7.647715 ACCACAAGTTGAAGAAATTGAATTACG 59.352 33.333 10.54 0.00 39.07 3.18
5510 6626 7.996644 AGACCTTATTACCACAAGTTGAAGAAA 59.003 33.333 10.54 0.00 0.00 2.52
5526 6642 7.497595 CATATATGCCGCCTAAGACCTTATTA 58.502 38.462 0.00 0.00 0.00 0.98
5527 6643 4.910458 ATATGCCGCCTAAGACCTTATT 57.090 40.909 0.00 0.00 0.00 1.40
5528 6644 5.918608 CATATATGCCGCCTAAGACCTTAT 58.081 41.667 0.00 0.00 0.00 1.73
5612 6728 7.335924 TGACATTCAGGGCAACTTATAGTTAAC 59.664 37.037 0.00 0.00 36.03 2.01
5614 6730 6.821665 GTGACATTCAGGGCAACTTATAGTTA 59.178 38.462 0.00 0.00 36.03 2.24
5636 6752 7.610580 AAAATTATTTTCCAGACAAGGGTGA 57.389 32.000 0.00 0.00 0.00 4.02
5682 6798 9.733556 TTTCAGTGTTGTTTGATGTACCTATAT 57.266 29.630 0.00 0.00 0.00 0.86
5709 6825 4.328118 AGAAGGCCATTTCCTGAAGAAT 57.672 40.909 5.01 0.00 36.38 2.40
5732 6848 6.993902 TGTATATGACTGATCACATGCAACAT 59.006 34.615 8.65 0.00 32.22 2.71
5737 6853 8.538409 TGTATTGTATATGACTGATCACATGC 57.462 34.615 8.65 1.57 37.79 4.06
5771 6889 1.860326 AGCTTCATTTGTGCAAAACGC 59.140 42.857 1.26 3.01 42.89 4.84
5773 6891 4.324402 CCGATAGCTTCATTTGTGCAAAAC 59.676 41.667 0.00 0.00 33.56 2.43
5785 6903 5.306937 TGGAGAAAATATCCCGATAGCTTCA 59.693 40.000 0.00 0.00 35.86 3.02
5812 6946 7.387673 CAGAACACACCTCATCAACAAGTTATA 59.612 37.037 0.00 0.00 0.00 0.98
5813 6947 6.205464 CAGAACACACCTCATCAACAAGTTAT 59.795 38.462 0.00 0.00 0.00 1.89
5815 6949 4.336433 CAGAACACACCTCATCAACAAGTT 59.664 41.667 0.00 0.00 0.00 2.66
5816 6950 3.879295 CAGAACACACCTCATCAACAAGT 59.121 43.478 0.00 0.00 0.00 3.16
5819 6953 3.134623 ACTCAGAACACACCTCATCAACA 59.865 43.478 0.00 0.00 0.00 3.33
5820 6954 3.733337 ACTCAGAACACACCTCATCAAC 58.267 45.455 0.00 0.00 0.00 3.18
5821 6955 4.422073 AACTCAGAACACACCTCATCAA 57.578 40.909 0.00 0.00 0.00 2.57
5822 6956 4.588951 AGTAACTCAGAACACACCTCATCA 59.411 41.667 0.00 0.00 0.00 3.07
5823 6957 5.140747 AGTAACTCAGAACACACCTCATC 57.859 43.478 0.00 0.00 0.00 2.92
5824 6958 5.300752 CAAGTAACTCAGAACACACCTCAT 58.699 41.667 0.00 0.00 0.00 2.90
5825 6959 4.442893 CCAAGTAACTCAGAACACACCTCA 60.443 45.833 0.00 0.00 0.00 3.86
5826 6960 4.058817 CCAAGTAACTCAGAACACACCTC 58.941 47.826 0.00 0.00 0.00 3.85
5827 6961 3.744530 GCCAAGTAACTCAGAACACACCT 60.745 47.826 0.00 0.00 0.00 4.00
5828 6962 2.548480 GCCAAGTAACTCAGAACACACC 59.452 50.000 0.00 0.00 0.00 4.16
5829 6963 3.248602 CAGCCAAGTAACTCAGAACACAC 59.751 47.826 0.00 0.00 0.00 3.82
5830 6964 3.466836 CAGCCAAGTAACTCAGAACACA 58.533 45.455 0.00 0.00 0.00 3.72
5831 6965 2.224314 GCAGCCAAGTAACTCAGAACAC 59.776 50.000 0.00 0.00 0.00 3.32
5832 6966 2.158827 TGCAGCCAAGTAACTCAGAACA 60.159 45.455 0.00 0.00 0.00 3.18
5833 6967 2.494059 TGCAGCCAAGTAACTCAGAAC 58.506 47.619 0.00 0.00 0.00 3.01
5834 6968 2.928801 TGCAGCCAAGTAACTCAGAA 57.071 45.000 0.00 0.00 0.00 3.02
5835 6969 2.928801 TTGCAGCCAAGTAACTCAGA 57.071 45.000 0.00 0.00 0.00 3.27
5836 6970 3.988379 TTTTGCAGCCAAGTAACTCAG 57.012 42.857 0.00 0.00 31.52 3.35
5862 6996 0.036765 TCCCGTCACCAAATCTTCCG 60.037 55.000 0.00 0.00 0.00 4.30
5878 7012 4.432741 GGGCCTTCAGGTGCTCCC 62.433 72.222 0.84 0.00 37.57 4.30
5916 7050 2.498481 TGATACAACAGTACCCTTCCCG 59.502 50.000 0.00 0.00 0.00 5.14
5951 7085 3.135712 TCCAACTTACTTCTGGACTGCAA 59.864 43.478 0.00 0.00 34.26 4.08
5952 7086 2.703536 TCCAACTTACTTCTGGACTGCA 59.296 45.455 0.00 0.00 34.26 4.41
5980 7114 2.306847 ACCGTTTGATTGTGCTCCTTT 58.693 42.857 0.00 0.00 0.00 3.11
6056 7194 5.105877 GCTTCCAAAACCCTTTCTGGTATAC 60.106 44.000 0.00 0.00 37.76 1.47
6068 7206 3.696548 CAGAATCCTAGCTTCCAAAACCC 59.303 47.826 0.00 0.00 0.00 4.11
6185 7326 2.290008 TGTCGCCACACCTAACATTCAT 60.290 45.455 0.00 0.00 0.00 2.57
6191 7332 1.467342 GGAATTGTCGCCACACCTAAC 59.533 52.381 0.00 0.00 29.76 2.34
6229 7378 2.952714 AGAAAGTGTCTGGGCATGC 58.047 52.632 9.90 9.90 34.29 4.06
6257 7406 8.556213 ACATAAGTGCCGTCTTTCTATAAAAA 57.444 30.769 0.00 0.00 0.00 1.94
6279 7428 9.467258 CAACAAATAATGTCTTCACTCAAACAT 57.533 29.630 0.00 0.00 42.99 2.71
6281 7430 7.096065 GGCAACAAATAATGTCTTCACTCAAAC 60.096 37.037 0.00 0.00 42.99 2.93
6300 7449 1.068943 TTGGACCTAGGGGGCAACAA 61.069 55.000 14.81 5.91 44.19 2.83
6307 7456 2.064581 CCCGAGTTGGACCTAGGGG 61.065 68.421 14.81 1.30 42.09 4.79
6308 7457 2.064581 CCCCGAGTTGGACCTAGGG 61.065 68.421 14.81 0.00 44.57 3.53
6323 7474 0.108662 CAAATCAAAGAAGCCGCCCC 60.109 55.000 0.00 0.00 0.00 5.80
6394 7545 3.477582 TGGATGGTTCTCCGTGCA 58.522 55.556 0.00 0.00 46.26 4.57
6601 7753 3.033773 TCGGATCAGGGAGGGGGA 61.034 66.667 0.00 0.00 0.00 4.81
6666 7818 0.456312 GACGAAGCAGAACCGTCGAT 60.456 55.000 4.67 0.00 42.24 3.59
6667 7819 1.081641 GACGAAGCAGAACCGTCGA 60.082 57.895 4.67 0.00 42.24 4.20
6668 7820 3.449042 GACGAAGCAGAACCGTCG 58.551 61.111 0.00 0.00 42.24 5.12
6670 7822 2.342648 GGGACGAAGCAGAACCGT 59.657 61.111 0.00 0.00 39.41 4.83
6683 7835 0.591659 GGCTTGTTCAGAAACGGGAC 59.408 55.000 0.00 0.00 38.28 4.46
6684 7836 0.181587 TGGCTTGTTCAGAAACGGGA 59.818 50.000 0.00 0.00 38.28 5.14
6685 7837 1.001378 CTTGGCTTGTTCAGAAACGGG 60.001 52.381 0.00 0.00 38.28 5.28
6686 7838 1.001378 CCTTGGCTTGTTCAGAAACGG 60.001 52.381 0.00 0.00 38.28 4.44
6687 7839 1.001378 CCCTTGGCTTGTTCAGAAACG 60.001 52.381 0.00 0.00 38.28 3.60


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

AutoCloner maintained by Alex Coulton.