Multiple sequence alignment - TraesCS1D01G017900

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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 TraesCS1D01G017900 chr1D 100.000 4302 0 0 1 4302 7900155 7895854 0.000000e+00 7945.0
1 TraesCS1D01G017900 chr1D 91.768 1968 124 20 58 1998 7877818 7875862 0.000000e+00 2702.0
2 TraesCS1D01G017900 chr1D 91.249 1657 120 16 2026 3660 7875794 7874141 0.000000e+00 2233.0
3 TraesCS1D01G017900 chr1D 91.840 1152 88 2 2158 3303 7353009 7354160 0.000000e+00 1602.0
4 TraesCS1D01G017900 chr1D 91.493 1152 95 1 2164 3312 7210747 7211898 0.000000e+00 1581.0
5 TraesCS1D01G017900 chr1D 86.207 899 101 14 965 1851 7209248 7210135 0.000000e+00 952.0
6 TraesCS1D01G017900 chr1D 83.924 734 105 10 967 1695 7351453 7352178 0.000000e+00 689.0
7 TraesCS1D01G017900 chr1D 86.717 399 41 5 886 1278 7208066 7208458 2.380000e-117 433.0
8 TraesCS1D01G017900 chr1D 80.864 486 66 21 3812 4278 7874036 7873559 1.470000e-94 357.0
9 TraesCS1D01G017900 chr1D 82.843 408 49 6 60 467 7350476 7350862 3.180000e-91 346.0
10 TraesCS1D01G017900 chr1D 82.899 345 52 3 1198 1538 7237916 7238257 1.940000e-78 303.0
11 TraesCS1D01G017900 chr1D 81.818 264 39 5 1884 2143 7352685 7352943 3.370000e-51 213.0
12 TraesCS1D01G017900 chr1D 97.500 40 1 0 4062 4101 7896015 7895976 7.720000e-08 69.4
13 TraesCS1D01G017900 chr1D 97.500 40 1 0 4141 4180 7896094 7896055 7.720000e-08 69.4
14 TraesCS1D01G017900 chr1B 88.556 3740 291 71 57 3715 9596274 9599957 0.000000e+00 4409.0
15 TraesCS1D01G017900 chr1B 88.422 2902 248 46 886 3713 10082225 10079338 0.000000e+00 3417.0
16 TraesCS1D01G017900 chr1B 91.384 1474 109 7 2019 3478 10069049 10067580 0.000000e+00 2002.0
17 TraesCS1D01G017900 chr1B 88.056 720 55 10 5 712 10083569 10082869 0.000000e+00 824.0
18 TraesCS1D01G017900 chr1B 84.672 685 71 19 1381 2035 10069746 10069066 0.000000e+00 652.0
19 TraesCS1D01G017900 chr1B 89.813 481 45 2 886 1365 10070290 10069813 7.910000e-172 614.0
20 TraesCS1D01G017900 chr1B 88.759 427 42 2 53 479 10073289 10072869 6.380000e-143 518.0
21 TraesCS1D01G017900 chr1B 86.897 290 29 7 3781 4065 10067197 10066912 2.500000e-82 316.0
22 TraesCS1D01G017900 chr1B 91.589 107 6 2 790 893 10070913 10070807 1.250000e-30 145.0
23 TraesCS1D01G017900 chr1B 97.333 75 1 1 710 784 10070424 10070351 4.520000e-25 126.0
24 TraesCS1D01G017900 chr1B 97.222 72 1 1 713 784 10082356 10082286 2.100000e-23 121.0
25 TraesCS1D01G017900 chr1A 89.943 1571 138 18 2154 3713 9550379 9548818 0.000000e+00 2008.0
26 TraesCS1D01G017900 chr1A 91.809 1172 94 1 2141 3312 9356531 9355362 0.000000e+00 1631.0
27 TraesCS1D01G017900 chr1A 87.818 903 87 12 892 1781 9358077 9357185 0.000000e+00 1037.0
28 TraesCS1D01G017900 chr1A 86.157 968 103 16 886 1838 9551863 9550912 0.000000e+00 1016.0
29 TraesCS1D01G017900 chr1A 87.470 423 38 3 57 479 9359623 9359216 1.400000e-129 473.0
30 TraesCS1D01G017900 chr1A 87.411 421 36 6 53 472 9554396 9553992 6.510000e-128 468.0
31 TraesCS1D01G017900 chr1A 78.802 217 46 0 1879 2095 9550693 9550477 3.470000e-31 147.0
32 TraesCS1D01G017900 chr1A 88.158 76 5 3 713 788 9358210 9358139 2.130000e-13 87.9
33 TraesCS1D01G017900 chr3B 82.835 1037 165 10 2171 3202 13966269 13967297 0.000000e+00 917.0


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 TraesCS1D01G017900 chr1D 7895854 7900155 4301 True 7945.000000 7945 100.000000 1 4302 1 chr1D.!!$R1 4301
1 TraesCS1D01G017900 chr1D 7873559 7877818 4259 True 1764.000000 2702 87.960333 58 4278 3 chr1D.!!$R2 4220
2 TraesCS1D01G017900 chr1D 7208066 7211898 3832 False 988.666667 1581 88.139000 886 3312 3 chr1D.!!$F2 2426
3 TraesCS1D01G017900 chr1D 7350476 7354160 3684 False 712.500000 1602 85.106250 60 3303 4 chr1D.!!$F3 3243
4 TraesCS1D01G017900 chr1B 9596274 9599957 3683 False 4409.000000 4409 88.556000 57 3715 1 chr1B.!!$F1 3658
5 TraesCS1D01G017900 chr1B 10079338 10083569 4231 True 1454.000000 3417 91.233333 5 3713 3 chr1B.!!$R2 3708
6 TraesCS1D01G017900 chr1B 10066912 10073289 6377 True 624.714286 2002 90.063857 53 4065 7 chr1B.!!$R1 4012
7 TraesCS1D01G017900 chr1A 9548818 9554396 5578 True 909.750000 2008 85.578250 53 3713 4 chr1A.!!$R2 3660
8 TraesCS1D01G017900 chr1A 9355362 9359623 4261 True 807.225000 1631 88.813750 57 3312 4 chr1A.!!$R1 3255
9 TraesCS1D01G017900 chr3B 13966269 13967297 1028 False 917.000000 917 82.835000 2171 3202 1 chr3B.!!$F1 1031

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
826 3915 1.135053 GGTCGTCTTCTGTTCCTAGCC 60.135 57.143 0.00 0.0 0.00 3.93 F
1796 5356 0.107165 CCCTTCCATTTCCTCCCGAC 60.107 60.000 0.00 0.0 0.00 4.79 F
2899 6929 0.108804 CCAGCAAGTCCGACGTGTAT 60.109 55.000 14.74 3.1 30.18 2.29 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2785 6815 1.812686 CGAAACTGTCACCCCTCGGA 61.813 60.0 0.00 0.0 0.00 4.55 R
3272 7305 0.178973 TCTTCCTCGGACACCACAGA 60.179 55.0 0.00 0.0 0.00 3.41 R
4066 8376 0.029300 GTTGCACGCACAAGTGACAT 59.971 50.0 4.04 0.0 44.43 3.06 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
37 38 2.473816 TGAGAATTGCCGATCACGATC 58.526 47.619 0.00 0.00 42.66 3.69
38 39 2.159114 TGAGAATTGCCGATCACGATCA 60.159 45.455 7.75 0.00 42.66 2.92
101 102 2.886081 CAGTTTCTGGAGATGACGAGG 58.114 52.381 0.00 0.00 0.00 4.63
134 135 2.132686 ACCAAACAGGGGTCTACAAGT 58.867 47.619 0.00 0.00 43.89 3.16
237 238 2.302733 TCTTGACCAGAGCATGCTAACA 59.697 45.455 22.74 13.18 0.00 2.41
250 257 4.022849 GCATGCTAACATCCTGGTTAATCC 60.023 45.833 11.37 0.00 32.87 3.01
257 264 1.817941 CCTGGTTAATCCGCCGGTG 60.818 63.158 8.42 8.42 39.52 4.94
258 265 2.437002 TGGTTAATCCGCCGGTGC 60.437 61.111 10.27 0.00 39.52 5.01
413 432 1.410083 GCCATGGCCAAGTAGATTCCA 60.410 52.381 27.24 0.00 34.56 3.53
415 434 3.569491 CCATGGCCAAGTAGATTCCATT 58.431 45.455 10.96 0.00 35.51 3.16
826 3915 1.135053 GGTCGTCTTCTGTTCCTAGCC 60.135 57.143 0.00 0.00 0.00 3.93
834 3923 3.334583 TCTGTTCCTAGCCACACAATC 57.665 47.619 0.00 0.00 0.00 2.67
920 4042 6.126940 ACAGCTGGATATGATCAACTAGTTGT 60.127 38.462 29.83 19.45 41.16 3.32
1374 4896 6.485648 ACATTCCTTACTTTGGATATTACGGC 59.514 38.462 0.00 0.00 33.09 5.68
1375 4897 4.624015 TCCTTACTTTGGATATTACGGCG 58.376 43.478 4.80 4.80 0.00 6.46
1376 4898 4.341806 TCCTTACTTTGGATATTACGGCGA 59.658 41.667 16.62 0.00 0.00 5.54
1427 4949 5.985781 TCGTTATTTGCTCACTCAAAGTTC 58.014 37.500 0.00 0.00 39.06 3.01
1433 4955 2.626266 TGCTCACTCAAAGTTCCTACGA 59.374 45.455 0.00 0.00 0.00 3.43
1444 4966 5.767816 AAGTTCCTACGAAGCATGTTTTT 57.232 34.783 0.00 0.00 0.00 1.94
1445 4967 5.108385 AGTTCCTACGAAGCATGTTTTTG 57.892 39.130 0.00 0.00 0.00 2.44
1477 4999 7.797038 TCACGAGCAGTAACAGATAATAGTA 57.203 36.000 0.00 0.00 0.00 1.82
1478 5000 7.862648 TCACGAGCAGTAACAGATAATAGTAG 58.137 38.462 0.00 0.00 0.00 2.57
1516 5038 1.547372 GCCTGAGTGCCAACAATTCAT 59.453 47.619 0.00 0.00 0.00 2.57
1538 5060 3.417069 TGTTTATGTCTGGGTGTCTGG 57.583 47.619 0.00 0.00 0.00 3.86
1599 5127 1.483415 CTGGCCAAGATTCCATTTGGG 59.517 52.381 7.01 0.00 43.23 4.12
1602 5139 2.401568 GCCAAGATTCCATTTGGGGAT 58.598 47.619 5.51 0.00 43.23 3.85
1615 5152 5.339530 CCATTTGGGGATGAGTACTCTTCTT 60.340 44.000 28.20 11.72 35.05 2.52
1661 5198 4.074259 AGTTATGCAGAAATCACACAGCA 58.926 39.130 0.00 0.00 36.34 4.41
1665 5202 2.624364 TGCAGAAATCACACAGCACATT 59.376 40.909 0.00 0.00 0.00 2.71
1666 5203 3.068448 TGCAGAAATCACACAGCACATTT 59.932 39.130 0.00 0.00 0.00 2.32
1667 5204 3.671928 GCAGAAATCACACAGCACATTTC 59.328 43.478 0.00 0.00 36.07 2.17
1686 5223 4.903045 TTCTAAGGGGTTTACTGTCCAG 57.097 45.455 0.00 0.00 0.00 3.86
1695 5232 3.813724 GGTTTACTGTCCAGTTTCCTGTC 59.186 47.826 5.10 0.00 42.54 3.51
1696 5233 3.764237 TTACTGTCCAGTTTCCTGTCC 57.236 47.619 5.10 0.00 42.54 4.02
1697 5234 0.765510 ACTGTCCAGTTTCCTGTCCC 59.234 55.000 0.00 0.00 38.83 4.46
1698 5235 0.320771 CTGTCCAGTTTCCTGTCCCG 60.321 60.000 0.00 0.00 36.95 5.14
1700 5237 1.460689 TCCAGTTTCCTGTCCCGGT 60.461 57.895 0.00 0.00 36.95 5.28
1701 5238 1.057851 TCCAGTTTCCTGTCCCGGTT 61.058 55.000 0.00 0.00 36.95 4.44
1702 5239 0.179001 CCAGTTTCCTGTCCCGGTTT 60.179 55.000 0.00 0.00 36.95 3.27
1703 5240 1.072648 CCAGTTTCCTGTCCCGGTTTA 59.927 52.381 0.00 0.00 36.95 2.01
1704 5241 2.148768 CAGTTTCCTGTCCCGGTTTAC 58.851 52.381 0.00 0.00 33.80 2.01
1705 5242 2.052468 AGTTTCCTGTCCCGGTTTACT 58.948 47.619 0.00 0.00 0.00 2.24
1710 5253 1.072648 CCTGTCCCGGTTTACTTGGAA 59.927 52.381 0.00 0.00 0.00 3.53
1719 5262 3.219281 GGTTTACTTGGAACCTTCTGCA 58.781 45.455 0.00 0.00 42.58 4.41
1724 5267 2.373169 ACTTGGAACCTTCTGCATCTGA 59.627 45.455 0.00 0.00 0.00 3.27
1726 5269 1.339438 TGGAACCTTCTGCATCTGAGC 60.339 52.381 0.00 0.00 0.00 4.26
1746 5289 6.959361 TGAGCAGTTAAGAAAGAACATCAAC 58.041 36.000 0.00 0.00 0.00 3.18
1796 5356 0.107165 CCCTTCCATTTCCTCCCGAC 60.107 60.000 0.00 0.00 0.00 4.79
1828 5388 5.045578 TCTCACCTCCCTATTCTTTTGAAGG 60.046 44.000 0.00 0.00 42.30 3.46
1843 5403 1.004745 TGAAGGATTGACTTGGGGCTC 59.995 52.381 0.00 0.00 0.00 4.70
1939 5878 4.646040 AGCAAATATCTGGCACAAGCATTA 59.354 37.500 0.00 0.00 44.61 1.90
1999 5974 3.510388 TCTTAGAATGCGTGACTCAGG 57.490 47.619 0.00 0.00 0.00 3.86
2001 5976 3.701542 TCTTAGAATGCGTGACTCAGGAT 59.298 43.478 2.83 0.00 0.00 3.24
2003 5978 1.134580 AGAATGCGTGACTCAGGATGG 60.135 52.381 2.83 0.00 36.16 3.51
2014 5992 3.096852 ACTCAGGATGGTAACGATCACA 58.903 45.455 0.00 0.00 42.51 3.58
2015 5993 3.706594 ACTCAGGATGGTAACGATCACAT 59.293 43.478 0.00 0.00 42.51 3.21
2023 6001 2.930040 GGTAACGATCACATCCACACAG 59.070 50.000 0.00 0.00 0.00 3.66
2125 6104 9.828852 TGTATACGCATTTTACTTTCGAAAAAT 57.171 25.926 12.41 5.92 30.03 1.82
2812 6842 1.539496 GGTGACAGTTTCGTGCCACTA 60.539 52.381 0.00 0.00 0.00 2.74
2899 6929 0.108804 CCAGCAAGTCCGACGTGTAT 60.109 55.000 14.74 3.10 30.18 2.29
3210 7243 2.652382 TTCTGCGACGAAGGGCACAA 62.652 55.000 2.22 0.00 36.23 3.33
3231 7264 2.225650 ACCATGTGGAGGACTCTTACCT 60.226 50.000 5.96 0.00 40.80 3.08
3237 7270 4.040461 TGTGGAGGACTCTTACCTTTTCAG 59.960 45.833 0.00 0.00 37.93 3.02
3269 7302 3.066233 GCGGTCTCGGAGGAGGAAC 62.066 68.421 4.96 0.00 40.85 3.62
3272 7305 0.612453 GGTCTCGGAGGAGGAACTGT 60.612 60.000 4.96 0.00 41.55 3.55
3283 7316 0.759346 AGGAACTGTCTGTGGTGTCC 59.241 55.000 0.00 0.00 37.18 4.02
3317 7350 7.759886 ACGATGTGTGAGGTATATATACAATGC 59.240 37.037 21.56 10.93 34.98 3.56
3337 7370 9.991906 ACAATGCGTGGTACTATAATTTAGTAT 57.008 29.630 9.34 0.00 33.23 2.12
3372 7420 4.942761 GTATCATGGGGTGATGCAATTT 57.057 40.909 0.00 0.00 46.85 1.82
3380 7442 6.219417 TGGGGTGATGCAATTTATTTGTAG 57.781 37.500 0.00 0.00 37.65 2.74
3382 7444 5.049828 GGGTGATGCAATTTATTTGTAGCC 58.950 41.667 0.00 0.00 35.73 3.93
3405 7469 6.037391 GCCGTACCAACAGTATAAATGCTTTA 59.963 38.462 0.00 0.00 32.28 1.85
3425 7489 1.397672 TACAAACTGCCTTGCTTGCA 58.602 45.000 0.00 0.00 37.17 4.08
3505 7751 8.920665 CATTACTCTCGATAAATTCTGATGGAC 58.079 37.037 0.00 0.00 0.00 4.02
3558 7817 6.407202 ACATATAAGTTTGTGAGAGGTGACC 58.593 40.000 0.00 0.00 0.00 4.02
3566 7825 0.768221 TGAGAGGTGACCAAAGGCCT 60.768 55.000 3.63 0.00 0.00 5.19
3568 7827 2.070639 GAGGTGACCAAAGGCCTCT 58.929 57.895 5.23 0.00 42.99 3.69
3623 7882 3.763097 TGTATTTCAATTCTGCTGGCG 57.237 42.857 0.00 0.00 0.00 5.69
3627 7886 1.448985 TTCAATTCTGCTGGCGGTAC 58.551 50.000 0.00 0.00 0.00 3.34
3664 7926 2.028112 AGCATTGTCACCGAGAAGCTAA 60.028 45.455 0.00 0.00 0.00 3.09
3716 7978 9.818270 ATGATAGATCCATAACACCATTGATTT 57.182 29.630 0.00 0.00 0.00 2.17
3723 7985 8.514330 TCCATAACACCATTGATTTACTTACC 57.486 34.615 0.00 0.00 0.00 2.85
3724 7986 8.333235 TCCATAACACCATTGATTTACTTACCT 58.667 33.333 0.00 0.00 0.00 3.08
3725 7987 8.405531 CCATAACACCATTGATTTACTTACCTG 58.594 37.037 0.00 0.00 0.00 4.00
3726 7988 5.897377 ACACCATTGATTTACTTACCTGC 57.103 39.130 0.00 0.00 0.00 4.85
3727 7989 5.321102 ACACCATTGATTTACTTACCTGCA 58.679 37.500 0.00 0.00 0.00 4.41
3728 7990 5.951747 ACACCATTGATTTACTTACCTGCAT 59.048 36.000 0.00 0.00 0.00 3.96
3729 7991 6.095440 ACACCATTGATTTACTTACCTGCATC 59.905 38.462 0.00 0.00 0.00 3.91
3730 7992 5.594317 ACCATTGATTTACTTACCTGCATCC 59.406 40.000 0.00 0.00 0.00 3.51
3731 7993 5.593909 CCATTGATTTACTTACCTGCATCCA 59.406 40.000 0.00 0.00 0.00 3.41
3732 7994 6.460123 CCATTGATTTACTTACCTGCATCCAC 60.460 42.308 0.00 0.00 0.00 4.02
3733 7995 5.172687 TGATTTACTTACCTGCATCCACA 57.827 39.130 0.00 0.00 0.00 4.17
3734 7996 5.754782 TGATTTACTTACCTGCATCCACAT 58.245 37.500 0.00 0.00 0.00 3.21
3735 7997 6.186957 TGATTTACTTACCTGCATCCACATT 58.813 36.000 0.00 0.00 0.00 2.71
3736 7998 7.342581 TGATTTACTTACCTGCATCCACATTA 58.657 34.615 0.00 0.00 0.00 1.90
3737 7999 7.831690 TGATTTACTTACCTGCATCCACATTAA 59.168 33.333 0.00 0.00 0.00 1.40
3738 8000 8.588290 ATTTACTTACCTGCATCCACATTAAA 57.412 30.769 0.00 0.00 0.00 1.52
3739 8001 7.624360 TTACTTACCTGCATCCACATTAAAG 57.376 36.000 0.00 0.00 0.00 1.85
3740 8002 5.815581 ACTTACCTGCATCCACATTAAAGA 58.184 37.500 0.00 0.00 0.00 2.52
3741 8003 6.426587 ACTTACCTGCATCCACATTAAAGAT 58.573 36.000 0.00 0.00 0.00 2.40
3742 8004 6.891908 ACTTACCTGCATCCACATTAAAGATT 59.108 34.615 0.00 0.00 0.00 2.40
3743 8005 5.587388 ACCTGCATCCACATTAAAGATTG 57.413 39.130 0.00 0.00 0.00 2.67
3744 8006 5.263599 ACCTGCATCCACATTAAAGATTGA 58.736 37.500 0.00 0.00 0.00 2.57
3745 8007 5.126061 ACCTGCATCCACATTAAAGATTGAC 59.874 40.000 0.00 0.00 0.00 3.18
3746 8008 5.125900 CCTGCATCCACATTAAAGATTGACA 59.874 40.000 0.00 0.00 0.00 3.58
3747 8009 6.183360 CCTGCATCCACATTAAAGATTGACAT 60.183 38.462 0.00 0.00 0.00 3.06
3769 8031 0.806102 ATTCTGATTCCGGTGCGACG 60.806 55.000 0.00 0.00 0.00 5.12
3785 8047 3.430895 TGCGACGGATAAGACAAGTTTTC 59.569 43.478 0.00 0.00 0.00 2.29
3786 8048 3.181523 GCGACGGATAAGACAAGTTTTCC 60.182 47.826 0.00 0.00 0.00 3.13
3791 8060 6.735130 ACGGATAAGACAAGTTTTCCTTTTG 58.265 36.000 0.00 0.00 0.00 2.44
3801 8070 5.728637 AGTTTTCCTTTTGGCTGGATAAG 57.271 39.130 0.00 0.00 40.12 1.73
3880 8185 6.910536 AGTTTAAAGCAACATATCTCTCCG 57.089 37.500 0.00 0.00 0.00 4.63
3894 8200 2.108168 CTCTCCGGGTTGACCAATCTA 58.892 52.381 0.00 0.00 40.22 1.98
3910 8216 7.448161 TGACCAATCTATCATGAACAAAGTTGT 59.552 33.333 0.00 0.00 44.72 3.32
3927 8237 2.512485 TGTGCATGCCAAAGAAACTG 57.488 45.000 16.68 0.00 0.00 3.16
3943 8253 5.306394 AGAAACTGGCTAGGTAACAGAAAC 58.694 41.667 0.85 0.00 41.41 2.78
3945 8255 6.269307 AGAAACTGGCTAGGTAACAGAAACTA 59.731 38.462 0.85 0.00 41.41 2.24
3946 8256 5.662674 ACTGGCTAGGTAACAGAAACTAG 57.337 43.478 0.85 0.00 41.41 2.57
3958 8268 8.175716 GGTAACAGAAACTAGACACATATTTGC 58.824 37.037 0.00 0.00 0.00 3.68
3960 8270 7.133891 ACAGAAACTAGACACATATTTGCAC 57.866 36.000 0.00 0.00 0.00 4.57
3963 8273 6.936900 AGAAACTAGACACATATTTGCACTGT 59.063 34.615 0.00 0.00 0.00 3.55
3987 8297 2.556114 GCATAGCCTGCCATATTCCCTT 60.556 50.000 0.00 0.00 45.66 3.95
3991 8301 2.245806 AGCCTGCCATATTCCCTTCTTT 59.754 45.455 0.00 0.00 0.00 2.52
3992 8302 2.363359 GCCTGCCATATTCCCTTCTTTG 59.637 50.000 0.00 0.00 0.00 2.77
4010 8320 2.672996 GGTCTGTGCACCGCCAAT 60.673 61.111 15.69 0.00 0.00 3.16
4020 8330 2.126502 CCGCCAATCACGCAAACC 60.127 61.111 0.00 0.00 0.00 3.27
4022 8332 1.442520 CGCCAATCACGCAAACCTG 60.443 57.895 0.00 0.00 0.00 4.00
4024 8334 0.878416 GCCAATCACGCAAACCTGTA 59.122 50.000 0.00 0.00 0.00 2.74
4029 8339 0.941542 TCACGCAAACCTGTAGTTGC 59.058 50.000 0.00 0.00 39.19 4.17
4049 8359 4.863491 TGCTTTTCTTCTTTGCAGCTAAG 58.137 39.130 10.08 10.08 0.00 2.18
4065 8375 2.666508 GCTAAGAAATCGTCGCAGTCAA 59.333 45.455 0.00 0.00 0.00 3.18
4066 8376 3.122948 GCTAAGAAATCGTCGCAGTCAAA 59.877 43.478 0.00 0.00 0.00 2.69
4067 8377 4.201724 GCTAAGAAATCGTCGCAGTCAAAT 60.202 41.667 0.00 0.00 0.00 2.32
4068 8378 3.729526 AGAAATCGTCGCAGTCAAATG 57.270 42.857 0.00 0.00 0.00 2.32
4069 8379 3.067106 AGAAATCGTCGCAGTCAAATGT 58.933 40.909 0.00 0.00 0.00 2.71
4070 8380 3.123621 AGAAATCGTCGCAGTCAAATGTC 59.876 43.478 0.00 0.00 0.00 3.06
4071 8381 2.078849 ATCGTCGCAGTCAAATGTCA 57.921 45.000 0.00 0.00 0.00 3.58
4072 8382 1.136690 TCGTCGCAGTCAAATGTCAC 58.863 50.000 0.00 0.00 0.00 3.67
4073 8383 1.139989 CGTCGCAGTCAAATGTCACT 58.860 50.000 0.00 0.00 0.00 3.41
4076 8386 2.287915 GTCGCAGTCAAATGTCACTTGT 59.712 45.455 0.00 0.00 0.00 3.16
4077 8387 2.287644 TCGCAGTCAAATGTCACTTGTG 59.712 45.455 0.00 0.00 0.00 3.33
4078 8388 2.388121 GCAGTCAAATGTCACTTGTGC 58.612 47.619 0.00 0.00 0.00 4.57
4079 8389 2.642995 CAGTCAAATGTCACTTGTGCG 58.357 47.619 0.00 0.00 0.00 5.34
4081 8391 2.032054 AGTCAAATGTCACTTGTGCGTG 59.968 45.455 0.00 0.00 36.25 5.34
4082 8392 1.122849 CAAATGTCACTTGTGCGTGC 58.877 50.000 0.00 0.00 34.92 5.34
4084 8394 0.737804 AATGTCACTTGTGCGTGCAA 59.262 45.000 0.00 0.00 34.92 4.08
4085 8395 0.029300 ATGTCACTTGTGCGTGCAAC 59.971 50.000 0.00 0.00 34.92 4.17
4086 8396 1.024046 TGTCACTTGTGCGTGCAACT 61.024 50.000 0.00 0.00 34.92 3.16
4087 8397 0.098728 GTCACTTGTGCGTGCAACTT 59.901 50.000 0.00 0.00 34.92 2.66
4088 8398 0.098552 TCACTTGTGCGTGCAACTTG 59.901 50.000 0.00 0.00 34.92 3.16
4089 8399 0.866906 CACTTGTGCGTGCAACTTGG 60.867 55.000 0.00 0.00 31.75 3.61
4090 8400 1.299316 CTTGTGCGTGCAACTTGGG 60.299 57.895 0.00 0.00 31.75 4.12
4091 8401 2.682256 CTTGTGCGTGCAACTTGGGG 62.682 60.000 0.00 0.00 31.75 4.96
4092 8402 4.645921 GTGCGTGCAACTTGGGGC 62.646 66.667 0.00 0.00 31.75 5.80
4095 8405 4.025401 CGTGCAACTTGGGGCGTC 62.025 66.667 0.00 0.00 31.75 5.19
4096 8406 4.025401 GTGCAACTTGGGGCGTCG 62.025 66.667 0.00 0.00 0.00 5.12
4099 8409 2.978010 CAACTTGGGGCGTCGCTT 60.978 61.111 18.11 0.00 0.00 4.68
4100 8410 2.978010 AACTTGGGGCGTCGCTTG 60.978 61.111 18.11 5.66 0.00 4.01
4101 8411 3.767630 AACTTGGGGCGTCGCTTGT 62.768 57.895 18.11 6.27 0.00 3.16
4102 8412 3.726517 CTTGGGGCGTCGCTTGTG 61.727 66.667 18.11 0.49 0.00 3.33
4121 8431 3.067320 TGTGCGTGTTGATTTGATGGAAA 59.933 39.130 0.00 0.00 0.00 3.13
4148 8488 1.946768 CCGTGTTGTCCTGTCAAATGT 59.053 47.619 0.00 0.00 0.00 2.71
4165 8505 1.024046 TGTCACTTGTGCGTGCAACT 61.024 50.000 0.00 0.00 34.92 3.16
4166 8506 0.098728 GTCACTTGTGCGTGCAACTT 59.901 50.000 0.00 0.00 34.92 2.66
4170 8510 2.682256 CTTGTGCGTGCAACTTGGGG 62.682 60.000 0.00 0.00 31.75 4.96
4186 8526 2.559330 GGCGTCGCGTGGAAATTT 59.441 55.556 11.75 0.00 0.00 1.82
4187 8527 1.511254 GGCGTCGCGTGGAAATTTC 60.511 57.895 11.75 9.83 0.00 2.17
4195 8535 1.786579 GCGTGGAAATTTCAGCAACAC 59.213 47.619 19.49 15.25 0.00 3.32
4206 8546 1.151221 AGCAACACTGACATGGCCA 59.849 52.632 8.56 8.56 0.00 5.36
4207 8547 0.251474 AGCAACACTGACATGGCCAT 60.251 50.000 14.09 14.09 0.00 4.40
4208 8548 0.108992 GCAACACTGACATGGCCATG 60.109 55.000 38.53 38.53 44.15 3.66
4225 8568 0.994247 ATGCCTGGAGAATGTGTGGA 59.006 50.000 0.00 0.00 0.00 4.02
4262 8605 2.744494 GCAGATGGGGCAGAAGAGTAAG 60.744 54.545 0.00 0.00 0.00 2.34
4264 8607 1.210478 GATGGGGCAGAAGAGTAAGCA 59.790 52.381 0.00 0.00 0.00 3.91
4288 8631 8.519492 CAAAAGTCTTTTGTTTGAAGTTCTGA 57.481 30.769 24.18 0.00 43.77 3.27
4289 8632 9.143631 CAAAAGTCTTTTGTTTGAAGTTCTGAT 57.856 29.630 24.18 0.00 43.77 2.90
4290 8633 8.917415 AAAGTCTTTTGTTTGAAGTTCTGATC 57.083 30.769 4.17 0.00 0.00 2.92
4291 8634 7.872113 AGTCTTTTGTTTGAAGTTCTGATCT 57.128 32.000 4.17 0.00 0.00 2.75
4292 8635 7.701445 AGTCTTTTGTTTGAAGTTCTGATCTG 58.299 34.615 4.17 0.00 0.00 2.90
4293 8636 7.554118 AGTCTTTTGTTTGAAGTTCTGATCTGA 59.446 33.333 4.17 0.00 0.00 3.27
4294 8637 7.641802 GTCTTTTGTTTGAAGTTCTGATCTGAC 59.358 37.037 4.17 0.00 0.00 3.51
4295 8638 7.336679 TCTTTTGTTTGAAGTTCTGATCTGACA 59.663 33.333 4.17 0.00 0.00 3.58
4296 8639 7.572523 TTTGTTTGAAGTTCTGATCTGACAT 57.427 32.000 4.17 0.00 0.00 3.06
4297 8640 8.675705 TTTGTTTGAAGTTCTGATCTGACATA 57.324 30.769 4.17 0.00 0.00 2.29
4298 8641 8.853077 TTGTTTGAAGTTCTGATCTGACATAT 57.147 30.769 4.17 0.00 0.00 1.78
4299 8642 8.853077 TGTTTGAAGTTCTGATCTGACATATT 57.147 30.769 4.17 0.00 0.00 1.28
4300 8643 8.724229 TGTTTGAAGTTCTGATCTGACATATTG 58.276 33.333 4.17 0.00 0.00 1.90
4301 8644 8.725148 GTTTGAAGTTCTGATCTGACATATTGT 58.275 33.333 4.17 0.00 0.00 2.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 7.922278 GCAATTCTCAATTTGGTCATATAGCAA 59.078 33.333 0.00 0.00 43.65 3.91
2 3 6.865205 GGCAATTCTCAATTTGGTCATATAGC 59.135 38.462 0.00 0.00 0.00 2.97
3 4 7.041167 TCGGCAATTCTCAATTTGGTCATATAG 60.041 37.037 0.00 0.00 0.00 1.31
7 8 3.763360 TCGGCAATTCTCAATTTGGTCAT 59.237 39.130 0.00 0.00 0.00 3.06
84 85 3.056536 CAGAACCTCGTCATCTCCAGAAA 60.057 47.826 0.00 0.00 0.00 2.52
134 135 0.250234 CTTCGGTGAAGCTCATCCCA 59.750 55.000 0.00 0.00 32.78 4.37
237 238 1.342672 ACCGGCGGATTAACCAGGAT 61.343 55.000 35.78 1.21 38.90 3.24
257 264 0.870393 CATCATGTGGATGTAGCGGC 59.130 55.000 0.00 0.00 46.81 6.53
413 432 2.366533 CTGCTGCCTCTGATCAACAAT 58.633 47.619 0.00 0.00 0.00 2.71
415 434 0.675837 GCTGCTGCCTCTGATCAACA 60.676 55.000 3.85 0.00 0.00 3.33
826 3915 6.511416 AGGAAGATATTCTCTCGATTGTGTG 58.489 40.000 0.00 0.00 31.03 3.82
834 3923 6.695278 GTGTGAAAGAGGAAGATATTCTCTCG 59.305 42.308 0.00 0.00 36.93 4.04
920 4042 0.981277 GGAGGGGAAGGGATCGACAA 60.981 60.000 0.00 0.00 0.00 3.18
1351 4801 5.699458 CGCCGTAATATCCAAAGTAAGGAAT 59.301 40.000 0.00 0.00 38.93 3.01
1375 4897 3.251004 GGTGGTGAAACTGAATCAGTGTC 59.749 47.826 23.16 23.16 44.62 3.67
1376 4898 3.117888 AGGTGGTGAAACTGAATCAGTGT 60.118 43.478 17.46 11.79 44.62 3.55
1427 4949 6.861055 ACAATTACAAAAACATGCTTCGTAGG 59.139 34.615 0.00 0.00 0.00 3.18
1433 4955 6.754209 TCGTGAACAATTACAAAAACATGCTT 59.246 30.769 0.00 0.00 0.00 3.91
1444 4966 5.051153 TGTTACTGCTCGTGAACAATTACA 58.949 37.500 0.00 0.00 0.00 2.41
1445 4967 5.404366 TCTGTTACTGCTCGTGAACAATTAC 59.596 40.000 0.00 0.00 31.76 1.89
1516 5038 4.534500 ACCAGACACCCAGACATAAACATA 59.466 41.667 0.00 0.00 0.00 2.29
1538 5060 5.239306 TCAAGATCTTCAACCACACATGAAC 59.761 40.000 4.57 0.00 32.46 3.18
1599 5127 4.985409 CGCCAATAAGAAGAGTACTCATCC 59.015 45.833 24.44 12.41 0.00 3.51
1602 5139 4.461431 TGTCGCCAATAAGAAGAGTACTCA 59.539 41.667 24.44 3.92 0.00 3.41
1615 5152 3.457234 CATTCTGTAGCTGTCGCCAATA 58.543 45.455 0.00 0.00 36.60 1.90
1650 5187 4.460382 CCCTTAGAAATGTGCTGTGTGATT 59.540 41.667 0.00 0.00 0.00 2.57
1659 5196 4.765339 ACAGTAAACCCCTTAGAAATGTGC 59.235 41.667 0.00 0.00 0.00 4.57
1661 5198 5.073965 TGGACAGTAAACCCCTTAGAAATGT 59.926 40.000 0.00 0.00 0.00 2.71
1665 5202 4.237018 ACTGGACAGTAAACCCCTTAGAA 58.763 43.478 2.58 0.00 40.43 2.10
1666 5203 3.865571 ACTGGACAGTAAACCCCTTAGA 58.134 45.455 2.58 0.00 40.43 2.10
1667 5204 4.635699 AACTGGACAGTAAACCCCTTAG 57.364 45.455 5.25 0.00 41.58 2.18
1686 5223 2.551032 CAAGTAAACCGGGACAGGAAAC 59.449 50.000 6.32 0.00 34.73 2.78
1698 5235 3.219281 TGCAGAAGGTTCCAAGTAAACC 58.781 45.455 0.00 0.00 45.41 3.27
1700 5237 4.761739 CAGATGCAGAAGGTTCCAAGTAAA 59.238 41.667 0.00 0.00 0.00 2.01
1701 5238 4.041567 TCAGATGCAGAAGGTTCCAAGTAA 59.958 41.667 0.00 0.00 0.00 2.24
1702 5239 3.582647 TCAGATGCAGAAGGTTCCAAGTA 59.417 43.478 0.00 0.00 0.00 2.24
1703 5240 2.373169 TCAGATGCAGAAGGTTCCAAGT 59.627 45.455 0.00 0.00 0.00 3.16
1704 5241 3.008330 CTCAGATGCAGAAGGTTCCAAG 58.992 50.000 0.00 0.00 0.00 3.61
1705 5242 2.877300 GCTCAGATGCAGAAGGTTCCAA 60.877 50.000 0.00 0.00 0.00 3.53
1719 5262 7.164122 TGATGTTCTTTCTTAACTGCTCAGAT 58.836 34.615 3.60 0.00 0.00 2.90
1724 5267 7.573968 AAGTTGATGTTCTTTCTTAACTGCT 57.426 32.000 0.00 0.00 0.00 4.24
1726 5269 9.334693 GCATAAGTTGATGTTCTTTCTTAACTG 57.665 33.333 0.00 0.00 0.00 3.16
1746 5289 6.127535 ACCTGATTGAATTGTTGAGGCATAAG 60.128 38.462 0.00 0.00 0.00 1.73
1796 5356 7.189079 AGAATAGGGAGGTGAGAAACTAAAG 57.811 40.000 0.00 0.00 0.00 1.85
1828 5388 2.685388 GCTTAAGAGCCCCAAGTCAATC 59.315 50.000 6.67 0.00 43.29 2.67
1893 5832 4.397103 TCCTTGAAGTAGCTGCAAATCATG 59.603 41.667 4.12 7.66 27.38 3.07
1939 5878 8.636213 CCAGAAAATAGCATGAGTCCAATTAAT 58.364 33.333 0.00 0.00 0.00 1.40
1999 5974 3.555956 GTGTGGATGTGATCGTTACCATC 59.444 47.826 0.00 0.00 34.35 3.51
2001 5976 2.300437 TGTGTGGATGTGATCGTTACCA 59.700 45.455 0.00 0.00 0.00 3.25
2003 5978 2.348666 GCTGTGTGGATGTGATCGTTAC 59.651 50.000 0.00 0.00 0.00 2.50
2014 5992 2.071778 ACCAACTTTGCTGTGTGGAT 57.928 45.000 0.00 0.00 0.00 3.41
2015 5993 1.846007 AACCAACTTTGCTGTGTGGA 58.154 45.000 0.00 0.00 0.00 4.02
2017 5995 3.583806 TCAAAACCAACTTTGCTGTGTG 58.416 40.909 0.00 0.00 36.44 3.82
2023 6001 4.142730 TGCAACAATCAAAACCAACTTTGC 60.143 37.500 0.00 0.00 36.44 3.68
2785 6815 1.812686 CGAAACTGTCACCCCTCGGA 61.813 60.000 0.00 0.00 0.00 4.55
2812 6842 2.676471 GTTCCCCGCATGGCACTT 60.676 61.111 0.00 0.00 0.00 3.16
2899 6929 1.144716 CAGCAGCATCCCGAAGCTA 59.855 57.895 0.00 0.00 39.50 3.32
3210 7243 2.188817 GGTAAGAGTCCTCCACATGGT 58.811 52.381 0.00 0.00 36.34 3.55
3231 7264 1.497991 CGTCAGCTCGGAACTGAAAA 58.502 50.000 12.35 0.00 45.32 2.29
3269 7302 1.179174 TCCTCGGACACCACAGACAG 61.179 60.000 0.00 0.00 0.00 3.51
3272 7305 0.178973 TCTTCCTCGGACACCACAGA 60.179 55.000 0.00 0.00 0.00 3.41
3283 7316 1.468224 CCTCACACATCGTCTTCCTCG 60.468 57.143 0.00 0.00 0.00 4.63
3347 7395 2.175284 TGCATCACCCCATGATACACAT 59.825 45.455 0.00 0.00 46.96 3.21
3349 7397 2.346766 TGCATCACCCCATGATACAC 57.653 50.000 0.00 0.00 46.96 2.90
3360 7408 4.739716 CGGCTACAAATAAATTGCATCACC 59.260 41.667 0.00 0.00 43.13 4.02
3369 7417 5.941647 ACTGTTGGTACGGCTACAAATAAAT 59.058 36.000 0.00 0.00 33.73 1.40
3372 7420 4.540359 ACTGTTGGTACGGCTACAAATA 57.460 40.909 0.00 0.00 33.73 1.40
3373 7421 3.412237 ACTGTTGGTACGGCTACAAAT 57.588 42.857 0.00 0.00 33.73 2.32
3380 7442 3.875134 AGCATTTATACTGTTGGTACGGC 59.125 43.478 0.00 0.00 33.73 5.68
3405 7469 1.962807 TGCAAGCAAGGCAGTTTGTAT 59.037 42.857 7.97 0.00 36.11 2.29
3425 7489 4.392940 ACTTATTGAAGTTGCTCTGCACT 58.607 39.130 0.00 0.00 43.70 4.40
3537 7796 6.428083 TTGGTCACCTCTCACAAACTTATA 57.572 37.500 0.00 0.00 0.00 0.98
3611 7870 1.682849 TGGTACCGCCAGCAGAATT 59.317 52.632 7.57 0.00 43.61 2.17
3705 7967 5.895636 TGCAGGTAAGTAAATCAATGGTG 57.104 39.130 0.00 0.00 0.00 4.17
3715 7977 7.398829 TCTTTAATGTGGATGCAGGTAAGTAA 58.601 34.615 0.00 0.00 0.00 2.24
3716 7978 6.953101 TCTTTAATGTGGATGCAGGTAAGTA 58.047 36.000 0.00 0.00 0.00 2.24
3717 7979 5.815581 TCTTTAATGTGGATGCAGGTAAGT 58.184 37.500 0.00 0.00 0.00 2.24
3718 7980 6.949352 ATCTTTAATGTGGATGCAGGTAAG 57.051 37.500 0.00 0.00 0.00 2.34
3719 7981 6.889177 TCAATCTTTAATGTGGATGCAGGTAA 59.111 34.615 0.00 0.00 0.00 2.85
3720 7982 6.318648 GTCAATCTTTAATGTGGATGCAGGTA 59.681 38.462 0.00 0.00 0.00 3.08
3721 7983 5.126061 GTCAATCTTTAATGTGGATGCAGGT 59.874 40.000 0.00 0.00 0.00 4.00
3722 7984 5.125900 TGTCAATCTTTAATGTGGATGCAGG 59.874 40.000 0.00 0.00 0.00 4.85
3723 7985 6.198650 TGTCAATCTTTAATGTGGATGCAG 57.801 37.500 0.00 0.00 0.00 4.41
3724 7986 6.778834 ATGTCAATCTTTAATGTGGATGCA 57.221 33.333 0.00 0.00 0.00 3.96
3725 7987 7.706159 TGTATGTCAATCTTTAATGTGGATGC 58.294 34.615 0.00 0.00 0.00 3.91
3728 7990 9.685276 AGAATGTATGTCAATCTTTAATGTGGA 57.315 29.630 0.00 0.00 32.99 4.02
3729 7991 9.726232 CAGAATGTATGTCAATCTTTAATGTGG 57.274 33.333 0.00 0.00 34.44 4.17
3735 7997 9.045223 CGGAATCAGAATGTATGTCAATCTTTA 57.955 33.333 0.00 0.00 34.44 1.85
3736 7998 7.012704 CCGGAATCAGAATGTATGTCAATCTTT 59.987 37.037 0.00 0.00 34.44 2.52
3737 7999 6.484643 CCGGAATCAGAATGTATGTCAATCTT 59.515 38.462 0.00 0.00 34.44 2.40
3738 8000 5.994054 CCGGAATCAGAATGTATGTCAATCT 59.006 40.000 0.00 0.00 36.82 2.40
3739 8001 5.760253 ACCGGAATCAGAATGTATGTCAATC 59.240 40.000 9.46 0.00 37.40 2.67
3740 8002 5.528690 CACCGGAATCAGAATGTATGTCAAT 59.471 40.000 9.46 0.00 37.40 2.57
3741 8003 4.875536 CACCGGAATCAGAATGTATGTCAA 59.124 41.667 9.46 0.00 37.40 3.18
3742 8004 4.441792 CACCGGAATCAGAATGTATGTCA 58.558 43.478 9.46 0.00 37.40 3.58
3743 8005 3.248602 GCACCGGAATCAGAATGTATGTC 59.751 47.826 9.46 0.00 37.40 3.06
3744 8006 3.206150 GCACCGGAATCAGAATGTATGT 58.794 45.455 9.46 0.00 37.40 2.29
3745 8007 2.221749 CGCACCGGAATCAGAATGTATG 59.778 50.000 9.46 0.00 37.40 2.39
3746 8008 2.102420 TCGCACCGGAATCAGAATGTAT 59.898 45.455 9.46 0.00 37.40 2.29
3747 8009 1.478916 TCGCACCGGAATCAGAATGTA 59.521 47.619 9.46 0.00 37.40 2.29
3769 8031 5.926542 GCCAAAAGGAAAACTTGTCTTATCC 59.073 40.000 0.00 0.00 39.96 2.59
3776 8038 3.103742 TCCAGCCAAAAGGAAAACTTGT 58.896 40.909 0.00 0.00 39.96 3.16
3785 8047 3.379688 GCTTCTCTTATCCAGCCAAAAGG 59.620 47.826 0.00 0.00 0.00 3.11
3786 8048 4.012374 TGCTTCTCTTATCCAGCCAAAAG 58.988 43.478 0.00 0.00 0.00 2.27
3791 8060 2.680339 GTTGTGCTTCTCTTATCCAGCC 59.320 50.000 0.00 0.00 0.00 4.85
3801 8070 0.957888 GGGGCTGAGTTGTGCTTCTC 60.958 60.000 0.00 0.00 0.00 2.87
3863 8168 2.119495 ACCCGGAGAGATATGTTGCTT 58.881 47.619 0.73 0.00 0.00 3.91
3872 8177 1.486726 GATTGGTCAACCCGGAGAGAT 59.513 52.381 0.73 0.00 35.15 2.75
3877 8182 2.473070 TGATAGATTGGTCAACCCGGA 58.527 47.619 0.73 0.00 35.15 5.14
3878 8183 3.141398 CATGATAGATTGGTCAACCCGG 58.859 50.000 0.00 0.00 35.15 5.73
3879 8184 4.071961 TCATGATAGATTGGTCAACCCG 57.928 45.455 0.00 0.00 35.15 5.28
3880 8185 5.192927 TGTTCATGATAGATTGGTCAACCC 58.807 41.667 0.00 0.00 34.29 4.11
3927 8237 5.047519 TGTGTCTAGTTTCTGTTACCTAGCC 60.048 44.000 0.00 0.00 0.00 3.93
3934 8244 8.717821 GTGCAAATATGTGTCTAGTTTCTGTTA 58.282 33.333 0.00 0.00 0.00 2.41
3987 8297 1.227823 CGGTGCACAGACCCAAAGA 60.228 57.895 20.43 0.00 31.57 2.52
3992 8302 4.947147 TTGGCGGTGCACAGACCC 62.947 66.667 20.65 12.99 31.57 4.46
4010 8320 0.941542 GCAACTACAGGTTTGCGTGA 59.058 50.000 0.00 0.00 35.74 4.35
4020 8330 5.581605 TGCAAAGAAGAAAAGCAACTACAG 58.418 37.500 0.00 0.00 31.42 2.74
4022 8332 4.442403 GCTGCAAAGAAGAAAAGCAACTAC 59.558 41.667 0.00 0.00 34.45 2.73
4024 8334 3.131755 AGCTGCAAAGAAGAAAAGCAACT 59.868 39.130 1.02 0.00 34.45 3.16
4029 8339 7.060403 CGATTTCTTAGCTGCAAAGAAGAAAAG 59.940 37.037 22.80 18.09 45.81 2.27
4049 8359 3.120683 TGACATTTGACTGCGACGATTTC 60.121 43.478 0.00 0.00 0.00 2.17
4065 8375 0.737804 TTGCACGCACAAGTGACATT 59.262 45.000 4.04 0.00 44.43 2.71
4066 8376 0.029300 GTTGCACGCACAAGTGACAT 59.971 50.000 4.04 0.00 44.43 3.06
4067 8377 1.024046 AGTTGCACGCACAAGTGACA 61.024 50.000 4.04 0.00 44.43 3.58
4068 8378 0.098728 AAGTTGCACGCACAAGTGAC 59.901 50.000 4.04 0.00 44.43 3.67
4069 8379 0.098552 CAAGTTGCACGCACAAGTGA 59.901 50.000 4.04 0.00 44.43 3.41
4070 8380 0.866906 CCAAGTTGCACGCACAAGTG 60.867 55.000 0.00 0.00 44.47 3.16
4071 8381 1.433064 CCAAGTTGCACGCACAAGT 59.567 52.632 0.00 0.00 34.66 3.16
4072 8382 1.299316 CCCAAGTTGCACGCACAAG 60.299 57.895 0.00 0.00 0.00 3.16
4073 8383 2.780094 CCCCAAGTTGCACGCACAA 61.780 57.895 0.00 0.00 0.00 3.33
4078 8388 4.025401 GACGCCCCAAGTTGCACG 62.025 66.667 0.00 3.22 0.00 5.34
4079 8389 4.025401 CGACGCCCCAAGTTGCAC 62.025 66.667 0.00 0.00 0.00 4.57
4082 8392 2.978010 AAGCGACGCCCCAAGTTG 60.978 61.111 17.79 0.00 0.00 3.16
4084 8394 4.250305 ACAAGCGACGCCCCAAGT 62.250 61.111 17.79 5.32 0.00 3.16
4085 8395 3.726517 CACAAGCGACGCCCCAAG 61.727 66.667 17.79 4.64 0.00 3.61
4096 8406 2.118228 TCAAATCAACACGCACAAGC 57.882 45.000 0.00 0.00 37.42 4.01
4097 8407 2.981805 CCATCAAATCAACACGCACAAG 59.018 45.455 0.00 0.00 0.00 3.16
4098 8408 2.620585 TCCATCAAATCAACACGCACAA 59.379 40.909 0.00 0.00 0.00 3.33
4099 8409 2.225467 TCCATCAAATCAACACGCACA 58.775 42.857 0.00 0.00 0.00 4.57
4100 8410 2.987413 TCCATCAAATCAACACGCAC 57.013 45.000 0.00 0.00 0.00 5.34
4101 8411 3.551863 GGTTTCCATCAAATCAACACGCA 60.552 43.478 0.00 0.00 0.00 5.24
4102 8412 2.986479 GGTTTCCATCAAATCAACACGC 59.014 45.455 0.00 0.00 0.00 5.34
4103 8413 4.229096 CAGGTTTCCATCAAATCAACACG 58.771 43.478 0.00 0.00 0.00 4.49
4104 8414 4.984161 CACAGGTTTCCATCAAATCAACAC 59.016 41.667 0.00 0.00 0.00 3.32
4105 8415 4.501229 GCACAGGTTTCCATCAAATCAACA 60.501 41.667 0.00 0.00 0.00 3.33
4114 8424 0.889186 ACACGGCACAGGTTTCCATC 60.889 55.000 0.00 0.00 0.00 3.51
4121 8431 2.203153 GGACAACACGGCACAGGT 60.203 61.111 0.00 0.00 0.00 4.00
4148 8488 0.098552 CAAGTTGCACGCACAAGTGA 59.901 50.000 4.04 0.00 44.43 3.41
4170 8510 0.789383 CTGAAATTTCCACGCGACGC 60.789 55.000 15.93 10.49 0.00 5.19
4173 8513 0.947960 TTGCTGAAATTTCCACGCGA 59.052 45.000 15.93 11.72 0.00 5.87
4176 8516 3.354089 AGTGTTGCTGAAATTTCCACG 57.646 42.857 15.48 5.45 0.00 4.94
4187 8527 1.174078 TGGCCATGTCAGTGTTGCTG 61.174 55.000 0.00 0.00 46.34 4.41
4206 8546 0.994247 TCCACACATTCTCCAGGCAT 59.006 50.000 0.00 0.00 0.00 4.40
4207 8547 0.036732 GTCCACACATTCTCCAGGCA 59.963 55.000 0.00 0.00 0.00 4.75
4208 8548 0.036732 TGTCCACACATTCTCCAGGC 59.963 55.000 0.00 0.00 0.00 4.85
4225 8568 1.488812 TCTGCTGGGTAACAACAGTGT 59.511 47.619 0.00 0.00 42.54 3.55
4264 8607 9.358872 GATCAGAACTTCAAACAAAAGACTTTT 57.641 29.630 7.38 7.38 0.00 2.27


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

AutoCloner maintained by Alex Coulton.