Multiple sequence alignment - TraesCS3D01G220400

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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 TraesCS3D01G220400 chr3D 100.000 8008 0 0 1 8008 300770683 300778690 0.000000e+00 14789.0
1 TraesCS3D01G220400 chr3D 96.703 91 3 0 4797 4887 570848758 570848668 1.390000e-32 152.0
2 TraesCS3D01G220400 chr3D 97.619 42 0 1 7475 7515 300777908 300777949 4.010000e-08 71.3
3 TraesCS3D01G220400 chr3D 97.619 42 0 1 7226 7267 300778157 300778197 4.010000e-08 71.3
4 TraesCS3D01G220400 chr3A 93.400 2985 87 18 1870 4781 434619222 434616275 0.000000e+00 4320.0
5 TraesCS3D01G220400 chr3A 94.511 2569 87 22 4889 7438 434616278 434613745 0.000000e+00 3914.0
6 TraesCS3D01G220400 chr3A 92.607 1596 70 20 1 1580 434621004 434619441 0.000000e+00 2250.0
7 TraesCS3D01G220400 chr3A 93.697 238 7 4 1595 1832 434619457 434619228 4.600000e-92 350.0
8 TraesCS3D01G220400 chr3A 86.928 153 18 2 7739 7890 466791159 466791008 3.840000e-38 171.0
9 TraesCS3D01G220400 chr3A 81.955 133 14 7 372 504 467093857 467093735 3.950000e-18 104.0
10 TraesCS3D01G220400 chr3A 97.619 42 0 1 7475 7515 434613958 434613917 4.010000e-08 71.3
11 TraesCS3D01G220400 chr3B 94.452 2145 52 14 1595 3692 420413773 420411649 0.000000e+00 3240.0
12 TraesCS3D01G220400 chr3B 97.632 1436 26 5 4886 6319 420410234 420408805 0.000000e+00 2457.0
13 TraesCS3D01G220400 chr3B 93.557 1490 50 13 1 1459 420415518 420414044 0.000000e+00 2178.0
14 TraesCS3D01G220400 chr3B 97.809 502 10 1 3899 4399 420411401 420410900 0.000000e+00 865.0
15 TraesCS3D01G220400 chr3B 89.645 705 34 14 7306 8008 420406353 420405686 0.000000e+00 861.0
16 TraesCS3D01G220400 chr3B 98.044 409 8 0 4397 4805 420410643 420410235 0.000000e+00 712.0
17 TraesCS3D01G220400 chr3B 88.403 595 30 22 6306 6889 420408702 420408136 0.000000e+00 680.0
18 TraesCS3D01G220400 chr3B 93.468 444 10 4 6875 7314 420408110 420407682 6.780000e-180 641.0
19 TraesCS3D01G220400 chr3B 98.361 122 2 0 1459 1580 420413878 420413757 1.750000e-51 215.0
20 TraesCS3D01G220400 chr3B 92.053 151 4 6 3752 3902 420411656 420411514 1.050000e-48 206.0
21 TraesCS3D01G220400 chr3B 87.248 149 17 2 7748 7895 647175922 647176069 1.380000e-37 169.0
22 TraesCS3D01G220400 chr3B 90.789 76 7 0 1133 1208 473395874 473395949 1.420000e-17 102.0
23 TraesCS3D01G220400 chr7D 87.421 159 16 4 7734 7890 436961951 436961795 6.380000e-41 180.0
24 TraesCS3D01G220400 chr7D 95.789 95 3 1 4800 4894 519264633 519264540 1.390000e-32 152.0
25 TraesCS3D01G220400 chr7D 94.845 97 4 1 4803 4898 485090878 485090974 5.010000e-32 150.0
26 TraesCS3D01G220400 chr7D 92.157 102 6 2 4797 4896 226690436 226690335 8.380000e-30 143.0
27 TraesCS3D01G220400 chr7D 90.741 108 6 4 4781 4887 448336942 448337046 3.010000e-29 141.0
28 TraesCS3D01G220400 chr7B 87.421 159 16 4 7734 7890 453623446 453623290 6.380000e-41 180.0
29 TraesCS3D01G220400 chr7B 85.714 161 20 3 7734 7892 72998329 72998488 4.970000e-37 167.0
30 TraesCS3D01G220400 chr7B 86.275 102 9 2 1118 1219 355697606 355697510 1.100000e-18 106.0
31 TraesCS3D01G220400 chr7A 86.792 159 17 4 7734 7890 486930096 486929940 2.970000e-39 174.0
32 TraesCS3D01G220400 chr7A 85.625 160 20 3 7738 7895 609383564 609383406 1.790000e-36 165.0
33 TraesCS3D01G220400 chr4B 86.364 154 19 2 7738 7890 106227409 106227561 4.970000e-37 167.0
34 TraesCS3D01G220400 chr6B 95.699 93 4 0 4800 4892 216509755 216509847 5.010000e-32 150.0
35 TraesCS3D01G220400 chr6B 85.185 108 10 3 1112 1219 536852419 536852318 1.100000e-18 106.0
36 TraesCS3D01G220400 chr5D 93.878 98 4 2 4801 4897 250069626 250069722 6.480000e-31 147.0
37 TraesCS3D01G220400 chr1D 93.000 100 5 2 4793 4891 355171669 355171571 2.330000e-30 145.0
38 TraesCS3D01G220400 chr1D 81.295 139 25 1 618 755 348007214 348007076 2.360000e-20 111.0
39 TraesCS3D01G220400 chr1D 82.400 125 21 1 615 738 348004150 348004026 3.060000e-19 108.0
40 TraesCS3D01G220400 chr2D 90.000 110 7 4 4780 4887 164992661 164992768 1.080000e-28 139.0
41 TraesCS3D01G220400 chr4D 87.755 98 7 2 1122 1219 289345730 289345638 8.500000e-20 110.0
42 TraesCS3D01G220400 chr2A 100.000 29 0 0 369 397 158182765 158182793 4.000000e-03 54.7
43 TraesCS3D01G220400 chr2A 100.000 29 0 0 369 397 158245871 158245899 4.000000e-03 54.7


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS3D01G220400 chr3D 300770683 300778690 8007 False 4977.20 14789 98.412667 1 8008 3 chr3D.!!$F1 8007
1 TraesCS3D01G220400 chr3A 434613745 434621004 7259 True 2181.06 4320 94.366800 1 7515 5 chr3A.!!$R3 7514
2 TraesCS3D01G220400 chr3B 420405686 420415518 9832 True 1205.50 3240 94.342400 1 8008 10 chr3B.!!$R1 8007

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
361 364 0.528684 GAAGTGGGCGATTCGAGAGG 60.529 60.000 10.88 0.0 0.00 3.69 F
1344 1397 0.033208 TGTCTGGGAATGGATTGCCC 60.033 55.000 7.38 0.0 46.44 5.36 F
1588 1809 0.821711 CAGTGTGGCTCCCCGAAAAA 60.822 55.000 0.00 0.0 0.00 1.94 F
2407 2692 1.258982 CATTCCTCGTTGCTATGTCGC 59.741 52.381 0.00 0.0 0.00 5.19 F
3713 4004 0.478072 ATGCACCAAAGGACTCACCA 59.522 50.000 0.00 0.0 42.04 4.17 F
4816 5509 0.032714 ACTACTACCCCCTCCGTTCC 60.033 60.000 0.00 0.0 0.00 3.62 F
4817 5510 0.032813 CTACTACCCCCTCCGTTCCA 60.033 60.000 0.00 0.0 0.00 3.53 F
6093 6788 0.250901 ACAAGATTGGGCAAGTCGCT 60.251 50.000 0.00 0.0 41.91 4.93 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1596 1817 0.036010 ACCATGAGCCACACTGTAGC 60.036 55.000 0.00 0.0 0.00 3.58 R
2661 2946 0.398318 GGTGGCTTCAGTCAAGGAGT 59.602 55.000 0.00 0.0 31.94 3.85 R
2911 3202 6.398918 GGTGAGTAGCTCAACTATTTTCTCA 58.601 40.000 6.91 0.0 44.06 3.27 R
3730 4021 1.502163 GCCTGCCACTATGCGATCAC 61.502 60.000 0.00 0.0 0.00 3.06 R
5486 6181 0.250424 GCCAAGCCCTGCACAAAAAT 60.250 50.000 0.00 0.0 0.00 1.82 R
6073 6768 0.109597 GCGACTTGCCCAATCTTGTG 60.110 55.000 0.00 0.0 37.76 3.33 R
6774 7592 3.096092 AGCAACAAGAGGGTTTGTGAAA 58.904 40.909 0.00 0.0 40.24 2.69 R
7500 9709 2.800544 GTTAGCACTTTGTCGAGAAGCA 59.199 45.455 7.59 0.0 0.00 3.91 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
50 52 2.433604 GAGACCATCTCTGAGCCATTGA 59.566 50.000 0.00 0.00 40.30 2.57
219 222 3.205338 TGACTCATGACAGTTTGTGTGG 58.795 45.455 0.00 0.00 40.56 4.17
311 314 4.709886 TGTGATTCTATCCGACTTCCTGAA 59.290 41.667 0.00 0.00 0.00 3.02
361 364 0.528684 GAAGTGGGCGATTCGAGAGG 60.529 60.000 10.88 0.00 0.00 3.69
424 427 6.265196 ACTTTATTGCAGAACTCCATGTTTGA 59.735 34.615 0.00 0.00 39.30 2.69
488 491 7.045354 GCGCTCAAATATTCGCACAATATAATC 60.045 37.037 12.75 0.00 45.99 1.75
504 507 8.362639 ACAATATAATCATGGACAAAGGAATGC 58.637 33.333 0.00 0.00 0.00 3.56
570 573 5.654497 GATGAGAAAATTTGGGTGTCCATC 58.346 41.667 0.00 0.00 43.63 3.51
579 582 7.552050 AATTTGGGTGTCCATCTTGATTTTA 57.448 32.000 0.00 0.00 43.63 1.52
585 588 8.093927 TGGGTGTCCATCTTGATTTTATTTTTC 58.906 33.333 0.00 0.00 38.32 2.29
593 623 9.143631 CATCTTGATTTTATTTTTCTGGTCCAC 57.856 33.333 0.00 0.00 0.00 4.02
642 672 3.353836 CAAGCCCGACAACCCACG 61.354 66.667 0.00 0.00 0.00 4.94
659 689 2.280797 GCGCAGGTGGTTCACTCA 60.281 61.111 0.30 0.00 34.40 3.41
664 694 1.271054 GCAGGTGGTTCACTCACTGAT 60.271 52.381 0.00 0.00 35.61 2.90
782 816 2.176055 CACGTCCGTCGACAGAGG 59.824 66.667 17.16 17.38 42.86 3.69
876 912 1.003118 TGATTTTCTCGTCCCCACTGG 59.997 52.381 0.00 0.00 0.00 4.00
917 968 2.743928 CCAGCGCCACCACTTCTC 60.744 66.667 2.29 0.00 0.00 2.87
918 969 2.743928 CAGCGCCACCACTTCTCC 60.744 66.667 2.29 0.00 0.00 3.71
919 970 2.925170 AGCGCCACCACTTCTCCT 60.925 61.111 2.29 0.00 0.00 3.69
920 971 2.435059 GCGCCACCACTTCTCCTC 60.435 66.667 0.00 0.00 0.00 3.71
921 972 2.266055 CGCCACCACTTCTCCTCC 59.734 66.667 0.00 0.00 0.00 4.30
922 973 2.266055 GCCACCACTTCTCCTCCG 59.734 66.667 0.00 0.00 0.00 4.63
923 974 2.266055 CCACCACTTCTCCTCCGC 59.734 66.667 0.00 0.00 0.00 5.54
924 975 2.286523 CCACCACTTCTCCTCCGCT 61.287 63.158 0.00 0.00 0.00 5.52
925 976 1.216710 CACCACTTCTCCTCCGCTC 59.783 63.158 0.00 0.00 0.00 5.03
926 977 1.228894 ACCACTTCTCCTCCGCTCA 60.229 57.895 0.00 0.00 0.00 4.26
927 978 1.216710 CCACTTCTCCTCCGCTCAC 59.783 63.158 0.00 0.00 0.00 3.51
928 979 1.254284 CCACTTCTCCTCCGCTCACT 61.254 60.000 0.00 0.00 0.00 3.41
984 1035 2.261671 CCTCCGGAACTCCACACG 59.738 66.667 5.23 0.00 35.14 4.49
1089 1140 3.816524 CTCGCCGCTCCTCGTCTT 61.817 66.667 0.00 0.00 36.19 3.01
1110 1161 1.275573 GGTACGAGCCTCTTTGAAGGT 59.724 52.381 0.00 0.00 38.79 3.50
1114 1167 2.618709 ACGAGCCTCTTTGAAGGTTTTG 59.381 45.455 0.00 0.00 38.79 2.44
1186 1239 1.374758 GTGCGGACTGAGAGTTGGG 60.375 63.158 0.00 0.00 0.00 4.12
1276 1329 0.951040 CAGCGACCACTCTTGTTCCC 60.951 60.000 0.00 0.00 0.00 3.97
1282 1335 0.944386 CCACTCTTGTTCCCGTTGTG 59.056 55.000 0.00 0.00 0.00 3.33
1297 1350 5.071250 TCCCGTTGTGAGGTATAATGCTAAT 59.929 40.000 0.00 0.00 0.00 1.73
1298 1351 5.763204 CCCGTTGTGAGGTATAATGCTAATT 59.237 40.000 0.00 0.00 0.00 1.40
1299 1352 6.293407 CCCGTTGTGAGGTATAATGCTAATTG 60.293 42.308 0.00 0.00 0.00 2.32
1300 1353 6.136071 CGTTGTGAGGTATAATGCTAATTGC 58.864 40.000 0.00 0.00 43.25 3.56
1301 1354 6.017934 CGTTGTGAGGTATAATGCTAATTGCT 60.018 38.462 0.00 0.00 43.37 3.91
1302 1355 7.170828 CGTTGTGAGGTATAATGCTAATTGCTA 59.829 37.037 0.00 0.00 43.37 3.49
1303 1356 8.836413 GTTGTGAGGTATAATGCTAATTGCTAA 58.164 33.333 0.00 0.00 43.37 3.09
1344 1397 0.033208 TGTCTGGGAATGGATTGCCC 60.033 55.000 7.38 0.00 46.44 5.36
1440 1494 6.125860 TGTGAGGTAGGGGAGTTCTATATTCT 60.126 42.308 0.00 0.00 0.00 2.40
1445 1499 4.893829 GGGGAGTTCTATATTCTCACCC 57.106 50.000 1.68 0.00 43.63 4.61
1452 1506 7.354751 AGTTCTATATTCTCACCCTCAACTC 57.645 40.000 0.00 0.00 0.00 3.01
1456 1510 8.871629 TCTATATTCTCACCCTCAACTCTATC 57.128 38.462 0.00 0.00 0.00 2.08
1582 1803 2.269241 GCTACAGTGTGGCTCCCC 59.731 66.667 23.03 0.00 37.08 4.81
1583 1804 2.579201 CTACAGTGTGGCTCCCCG 59.421 66.667 5.88 0.00 0.00 5.73
1584 1805 1.982395 CTACAGTGTGGCTCCCCGA 60.982 63.158 5.88 0.00 0.00 5.14
1585 1806 1.534476 TACAGTGTGGCTCCCCGAA 60.534 57.895 5.88 0.00 0.00 4.30
1586 1807 1.122632 TACAGTGTGGCTCCCCGAAA 61.123 55.000 5.88 0.00 0.00 3.46
1587 1808 1.228124 CAGTGTGGCTCCCCGAAAA 60.228 57.895 0.00 0.00 0.00 2.29
1588 1809 0.821711 CAGTGTGGCTCCCCGAAAAA 60.822 55.000 0.00 0.00 0.00 1.94
1771 1992 5.639506 GTGACTGCAGTGAAATGTATACAGT 59.360 40.000 27.27 5.77 39.67 3.55
1772 1993 6.147821 GTGACTGCAGTGAAATGTATACAGTT 59.852 38.462 27.27 17.82 37.26 3.16
1773 1994 7.330946 GTGACTGCAGTGAAATGTATACAGTTA 59.669 37.037 27.27 5.12 37.26 2.24
1774 1995 8.040727 TGACTGCAGTGAAATGTATACAGTTAT 58.959 33.333 27.27 5.48 37.26 1.89
1775 1996 9.529325 GACTGCAGTGAAATGTATACAGTTATA 57.471 33.333 27.27 8.21 37.26 0.98
1776 1997 9.534565 ACTGCAGTGAAATGTATACAGTTATAG 57.465 33.333 20.97 11.82 34.01 1.31
1777 1998 8.365399 TGCAGTGAAATGTATACAGTTATAGC 57.635 34.615 17.81 17.75 34.01 2.97
1778 1999 7.441157 TGCAGTGAAATGTATACAGTTATAGCC 59.559 37.037 17.81 6.64 34.01 3.93
1811 2032 7.276438 GTGCAATGGAATTCATTTACCTCTTTC 59.724 37.037 7.93 0.00 43.04 2.62
1819 2040 6.648879 TTCATTTACCTCTTTCCAAACTGG 57.351 37.500 0.00 0.00 39.43 4.00
1834 2061 5.009610 TCCAAACTGGTTGCACTTATCTTTC 59.990 40.000 0.00 0.00 39.03 2.62
1909 2137 9.896263 TTTTCCGTTTTGTATTAATAACTGGTC 57.104 29.630 0.00 0.00 0.00 4.02
1910 2138 8.618702 TTCCGTTTTGTATTAATAACTGGTCA 57.381 30.769 0.00 0.00 0.00 4.02
2130 2388 5.449553 AGATAAGAATTGGTAGGGGCTTTG 58.550 41.667 0.00 0.00 0.00 2.77
2407 2692 1.258982 CATTCCTCGTTGCTATGTCGC 59.741 52.381 0.00 0.00 0.00 5.19
2427 2712 6.366604 TGTCGCGACATCTTCAGTTTTTATTA 59.633 34.615 36.40 8.51 36.21 0.98
2557 2842 6.365247 CCCGTATAGTTTCGTATGAAGATTGG 59.635 42.308 0.00 0.82 35.06 3.16
2633 2918 5.064441 ACCATCTTAGCTGTGATTTTTGC 57.936 39.130 0.00 0.00 0.00 3.68
2935 3226 6.398918 TGAGAAAATAGTTGAGCTACTCACC 58.601 40.000 0.00 0.00 40.46 4.02
3004 3295 9.503427 AAAATTTCAGTTCTCTTGTCTTTAACG 57.497 29.630 0.00 0.00 0.00 3.18
3258 3549 1.587066 TTACCGTGGGCCTAGGATTT 58.413 50.000 21.58 5.08 0.00 2.17
3511 3802 7.233632 TCAAACCAATGCTAGGATATGCTATT 58.766 34.615 4.23 0.00 0.00 1.73
3597 3888 6.307800 GTGATTGTGGATGTTTAAATTCGTGG 59.692 38.462 0.00 0.00 0.00 4.94
3613 3904 6.604735 ATTCGTGGTGAATAGTCTTATTGC 57.395 37.500 0.00 0.00 45.51 3.56
3708 3999 3.766545 ACAATGTATGCACCAAAGGACT 58.233 40.909 0.00 0.00 0.00 3.85
3709 4000 3.758554 ACAATGTATGCACCAAAGGACTC 59.241 43.478 0.00 0.00 0.00 3.36
3713 4004 0.478072 ATGCACCAAAGGACTCACCA 59.522 50.000 0.00 0.00 42.04 4.17
3730 4021 7.206981 ACTCACCAATGTAAAGTTTGATCAG 57.793 36.000 0.00 0.00 0.00 2.90
3819 4110 8.195436 TCTTTATACATGAGTAGCAAGTGTACC 58.805 37.037 0.00 0.00 32.86 3.34
3820 4111 5.932619 ATACATGAGTAGCAAGTGTACCA 57.067 39.130 0.00 0.00 32.86 3.25
3821 4112 4.617253 ACATGAGTAGCAAGTGTACCAA 57.383 40.909 0.00 0.00 0.00 3.67
3822 4113 5.165961 ACATGAGTAGCAAGTGTACCAAT 57.834 39.130 0.00 0.00 0.00 3.16
3823 4114 5.178797 ACATGAGTAGCAAGTGTACCAATC 58.821 41.667 0.00 0.00 0.00 2.67
3824 4115 5.046304 ACATGAGTAGCAAGTGTACCAATCT 60.046 40.000 0.00 0.00 0.00 2.40
3825 4116 4.820897 TGAGTAGCAAGTGTACCAATCTG 58.179 43.478 0.00 0.00 0.00 2.90
3826 4117 4.283467 TGAGTAGCAAGTGTACCAATCTGT 59.717 41.667 0.00 0.00 0.00 3.41
3827 4118 5.221641 TGAGTAGCAAGTGTACCAATCTGTT 60.222 40.000 0.00 0.00 0.00 3.16
3828 4119 4.997395 AGTAGCAAGTGTACCAATCTGTTG 59.003 41.667 0.00 0.00 35.05 3.33
3829 4120 4.085357 AGCAAGTGTACCAATCTGTTGA 57.915 40.909 0.00 0.00 37.53 3.18
3830 4121 4.460263 AGCAAGTGTACCAATCTGTTGAA 58.540 39.130 0.00 0.00 37.53 2.69
3831 4122 4.275936 AGCAAGTGTACCAATCTGTTGAAC 59.724 41.667 0.00 0.00 37.53 3.18
4032 4455 1.900545 CGAGGACTTCCCAGTTCCCC 61.901 65.000 0.00 0.00 37.41 4.81
4036 4459 1.652947 GACTTCCCAGTTCCCCTGTA 58.347 55.000 0.00 0.00 39.74 2.74
4037 4460 1.982958 GACTTCCCAGTTCCCCTGTAA 59.017 52.381 0.00 0.00 39.74 2.41
4038 4461 2.374170 GACTTCCCAGTTCCCCTGTAAA 59.626 50.000 0.00 0.00 39.74 2.01
4039 4462 2.375509 ACTTCCCAGTTCCCCTGTAAAG 59.624 50.000 0.00 0.00 39.74 1.85
4040 4463 2.127651 TCCCAGTTCCCCTGTAAAGT 57.872 50.000 0.00 0.00 39.74 2.66
4041 4464 2.424793 TCCCAGTTCCCCTGTAAAGTT 58.575 47.619 0.00 0.00 39.74 2.66
4042 4465 2.787035 TCCCAGTTCCCCTGTAAAGTTT 59.213 45.455 0.00 0.00 39.74 2.66
4043 4466 3.982052 TCCCAGTTCCCCTGTAAAGTTTA 59.018 43.478 0.00 0.00 39.74 2.01
4044 4467 4.604490 TCCCAGTTCCCCTGTAAAGTTTAT 59.396 41.667 0.00 0.00 39.74 1.40
4045 4468 5.791664 TCCCAGTTCCCCTGTAAAGTTTATA 59.208 40.000 0.00 0.00 39.74 0.98
4050 4473 9.292195 CAGTTCCCCTGTAAAGTTTATAAAAGA 57.708 33.333 0.00 0.00 36.37 2.52
4167 4601 7.041721 GGTTTCAAACTTTCTGATGTTTCCTT 58.958 34.615 0.00 0.00 34.60 3.36
4326 4760 9.512435 CTCTTTGTTCATGGCTAATCTATTTTG 57.488 33.333 0.00 0.00 0.00 2.44
4333 4767 8.593945 TCATGGCTAATCTATTTTGAAACCTT 57.406 30.769 0.00 0.00 0.00 3.50
4658 5351 4.087182 TGTACCTCCGTCTCTCTTGAATT 58.913 43.478 0.00 0.00 0.00 2.17
4727 5420 9.595823 GTTGCAGTTATTAGAATTCCACTAGTA 57.404 33.333 0.65 0.00 0.00 1.82
4789 5482 9.613428 CACAGAATTTGGGTTATTCTACTATGA 57.387 33.333 0.00 0.00 39.65 2.15
4792 5485 9.343539 AGAATTTGGGTTATTCTACTATGAAGC 57.656 33.333 0.00 0.00 39.82 3.86
4805 5498 9.558396 TTCTACTATGAAGCTAGAACTACTACC 57.442 37.037 0.00 0.00 0.00 3.18
4806 5499 8.156165 TCTACTATGAAGCTAGAACTACTACCC 58.844 40.741 0.00 0.00 0.00 3.69
4807 5500 6.069994 ACTATGAAGCTAGAACTACTACCCC 58.930 44.000 0.00 0.00 0.00 4.95
4808 5501 3.639952 TGAAGCTAGAACTACTACCCCC 58.360 50.000 0.00 0.00 0.00 5.40
4809 5502 3.271490 TGAAGCTAGAACTACTACCCCCT 59.729 47.826 0.00 0.00 0.00 4.79
4810 5503 3.598693 AGCTAGAACTACTACCCCCTC 57.401 52.381 0.00 0.00 0.00 4.30
4811 5504 2.177451 AGCTAGAACTACTACCCCCTCC 59.823 54.545 0.00 0.00 0.00 4.30
4812 5505 2.861274 CTAGAACTACTACCCCCTCCG 58.139 57.143 0.00 0.00 0.00 4.63
4813 5506 1.006020 AGAACTACTACCCCCTCCGT 58.994 55.000 0.00 0.00 0.00 4.69
4814 5507 1.360507 AGAACTACTACCCCCTCCGTT 59.639 52.381 0.00 0.00 0.00 4.44
4815 5508 1.753649 GAACTACTACCCCCTCCGTTC 59.246 57.143 0.00 0.00 0.00 3.95
4816 5509 0.032714 ACTACTACCCCCTCCGTTCC 60.033 60.000 0.00 0.00 0.00 3.62
4817 5510 0.032813 CTACTACCCCCTCCGTTCCA 60.033 60.000 0.00 0.00 0.00 3.53
4818 5511 0.638292 TACTACCCCCTCCGTTCCAT 59.362 55.000 0.00 0.00 0.00 3.41
4819 5512 0.638292 ACTACCCCCTCCGTTCCATA 59.362 55.000 0.00 0.00 0.00 2.74
4820 5513 1.008693 ACTACCCCCTCCGTTCCATAA 59.991 52.381 0.00 0.00 0.00 1.90
4821 5514 2.335933 CTACCCCCTCCGTTCCATAAT 58.664 52.381 0.00 0.00 0.00 1.28
4822 5515 2.500269 ACCCCCTCCGTTCCATAATA 57.500 50.000 0.00 0.00 0.00 0.98
4823 5516 2.999928 ACCCCCTCCGTTCCATAATAT 58.000 47.619 0.00 0.00 0.00 1.28
4824 5517 4.150516 ACCCCCTCCGTTCCATAATATA 57.849 45.455 0.00 0.00 0.00 0.86
4825 5518 4.505367 ACCCCCTCCGTTCCATAATATAA 58.495 43.478 0.00 0.00 0.00 0.98
4826 5519 4.534897 ACCCCCTCCGTTCCATAATATAAG 59.465 45.833 0.00 0.00 0.00 1.73
4827 5520 4.781087 CCCCCTCCGTTCCATAATATAAGA 59.219 45.833 0.00 0.00 0.00 2.10
4828 5521 5.104900 CCCCCTCCGTTCCATAATATAAGAG 60.105 48.000 0.00 0.00 0.00 2.85
4829 5522 5.420409 CCCTCCGTTCCATAATATAAGAGC 58.580 45.833 0.00 0.00 0.00 4.09
4830 5523 5.103000 CCTCCGTTCCATAATATAAGAGCG 58.897 45.833 3.06 3.06 33.46 5.03
4831 5524 5.336531 CCTCCGTTCCATAATATAAGAGCGT 60.337 44.000 7.53 0.00 32.01 5.07
4832 5525 6.092955 TCCGTTCCATAATATAAGAGCGTT 57.907 37.500 7.53 0.00 32.01 4.84
4833 5526 6.518493 TCCGTTCCATAATATAAGAGCGTTT 58.482 36.000 7.53 0.00 32.01 3.60
4834 5527 6.987992 TCCGTTCCATAATATAAGAGCGTTTT 59.012 34.615 7.53 0.00 32.01 2.43
4835 5528 7.496591 TCCGTTCCATAATATAAGAGCGTTTTT 59.503 33.333 7.53 0.00 32.01 1.94
4836 5529 7.586300 CCGTTCCATAATATAAGAGCGTTTTTG 59.414 37.037 7.53 0.00 32.01 2.44
4837 5530 8.332464 CGTTCCATAATATAAGAGCGTTTTTGA 58.668 33.333 0.00 0.00 0.00 2.69
4838 5531 9.434559 GTTCCATAATATAAGAGCGTTTTTGAC 57.565 33.333 0.00 0.00 0.00 3.18
4839 5532 8.725405 TCCATAATATAAGAGCGTTTTTGACA 57.275 30.769 0.00 0.00 0.00 3.58
4840 5533 8.609176 TCCATAATATAAGAGCGTTTTTGACAC 58.391 33.333 0.00 0.00 0.00 3.67
4841 5534 8.612619 CCATAATATAAGAGCGTTTTTGACACT 58.387 33.333 0.00 0.00 0.00 3.55
4844 5537 8.542497 AATATAAGAGCGTTTTTGACACTACA 57.458 30.769 0.00 0.00 0.00 2.74
4845 5538 4.531659 AAGAGCGTTTTTGACACTACAC 57.468 40.909 0.00 0.00 0.00 2.90
4846 5539 3.793559 AGAGCGTTTTTGACACTACACT 58.206 40.909 0.00 0.00 0.00 3.55
4847 5540 4.940463 AGAGCGTTTTTGACACTACACTA 58.060 39.130 0.00 0.00 0.00 2.74
4848 5541 4.982916 AGAGCGTTTTTGACACTACACTAG 59.017 41.667 0.00 0.00 0.00 2.57
4849 5542 4.690122 AGCGTTTTTGACACTACACTAGT 58.310 39.130 0.00 0.00 40.28 2.57
4862 5555 4.743644 ACTACACTAGTGTCAAAAACGCTC 59.256 41.667 31.11 0.00 45.69 5.03
4863 5556 3.793559 ACACTAGTGTCAAAAACGCTCT 58.206 40.909 22.95 0.00 45.69 4.09
4864 5557 4.189231 ACACTAGTGTCAAAAACGCTCTT 58.811 39.130 22.95 0.00 45.69 2.85
4865 5558 5.353938 ACACTAGTGTCAAAAACGCTCTTA 58.646 37.500 22.95 0.00 45.69 2.10
4866 5559 5.989777 ACACTAGTGTCAAAAACGCTCTTAT 59.010 36.000 22.95 0.00 45.69 1.73
4867 5560 7.149973 ACACTAGTGTCAAAAACGCTCTTATA 58.850 34.615 22.95 0.00 45.69 0.98
4868 5561 7.817962 ACACTAGTGTCAAAAACGCTCTTATAT 59.182 33.333 22.95 0.00 45.69 0.86
4869 5562 8.656849 CACTAGTGTCAAAAACGCTCTTATATT 58.343 33.333 15.06 0.00 45.69 1.28
4870 5563 9.865321 ACTAGTGTCAAAAACGCTCTTATATTA 57.135 29.630 0.00 0.00 45.69 0.98
4873 5566 8.612619 AGTGTCAAAAACGCTCTTATATTATGG 58.387 33.333 0.00 0.00 45.69 2.74
4874 5567 7.855904 GTGTCAAAAACGCTCTTATATTATGGG 59.144 37.037 0.00 0.00 35.42 4.00
4875 5568 7.771361 TGTCAAAAACGCTCTTATATTATGGGA 59.229 33.333 0.00 0.00 0.00 4.37
4876 5569 8.784043 GTCAAAAACGCTCTTATATTATGGGAT 58.216 33.333 0.00 0.00 0.00 3.85
4877 5570 8.783093 TCAAAAACGCTCTTATATTATGGGATG 58.217 33.333 0.00 0.00 0.00 3.51
4878 5571 7.687941 AAAACGCTCTTATATTATGGGATGG 57.312 36.000 0.00 0.00 0.00 3.51
4879 5572 6.620877 AACGCTCTTATATTATGGGATGGA 57.379 37.500 0.00 0.00 0.00 3.41
4880 5573 6.227298 ACGCTCTTATATTATGGGATGGAG 57.773 41.667 0.00 0.00 0.00 3.86
4881 5574 5.129485 ACGCTCTTATATTATGGGATGGAGG 59.871 44.000 0.00 0.00 0.00 4.30
4882 5575 5.453903 CGCTCTTATATTATGGGATGGAGGG 60.454 48.000 0.00 0.00 0.00 4.30
4883 5576 5.667626 GCTCTTATATTATGGGATGGAGGGA 59.332 44.000 0.00 0.00 0.00 4.20
4884 5577 6.183361 GCTCTTATATTATGGGATGGAGGGAG 60.183 46.154 0.00 0.00 0.00 4.30
4934 5627 7.741785 TCTACATTGGTTATGGATATTTCCGT 58.258 34.615 2.28 2.28 45.89 4.69
5154 5847 7.164122 TGTCAAGCATGAGATTCTTCTAGTTT 58.836 34.615 0.00 0.00 35.88 2.66
5308 6003 6.864342 TCTGCTTCCAGTACTATTCTAACAC 58.136 40.000 0.00 0.00 40.09 3.32
5566 6261 6.712998 TCGTTGGAGGTGAATCTTAATTGAAA 59.287 34.615 0.00 0.00 0.00 2.69
5632 6327 7.289587 TGACATATGTTGTGACACTATTTCG 57.710 36.000 10.30 0.00 39.18 3.46
6093 6788 0.250901 ACAAGATTGGGCAAGTCGCT 60.251 50.000 0.00 0.00 41.91 4.93
6264 6959 7.066163 CAGGTACACAGATATTCAAATGCTCAA 59.934 37.037 0.00 0.00 0.00 3.02
6327 7138 9.702253 TGGCCTTTAATAACATTATGGTTCTTA 57.298 29.630 3.32 0.00 32.29 2.10
6395 7206 2.873170 TTAATGCAGTCTTTCGTGCG 57.127 45.000 0.00 0.00 42.96 5.34
6409 7220 0.989890 CGTGCGCTACCTGTTTAGAC 59.010 55.000 9.73 0.00 0.00 2.59
6545 7356 7.913789 TGTCTAGGTTTACATTATCAACACCT 58.086 34.615 0.00 0.00 37.02 4.00
6640 7452 4.579340 AGAATGTGCATTAGCTGGATTGAG 59.421 41.667 0.00 0.00 42.74 3.02
6649 7461 6.293135 GCATTAGCTGGATTGAGTTTACTAGC 60.293 42.308 0.00 0.00 37.91 3.42
6765 7583 1.648681 GCGCTTGGATTTTTACTTGCG 59.351 47.619 0.00 0.00 44.10 4.85
6873 7691 6.326583 CCCCCTCATAATTCTGTAGTCACTAA 59.673 42.308 0.00 0.00 0.00 2.24
6898 7762 0.808125 TATTGCGTGGTGGTTCATGC 59.192 50.000 2.46 2.46 46.61 4.06
7051 7916 3.018149 CTCCAGCTTCTAGTCGTTACCT 58.982 50.000 0.00 0.00 0.00 3.08
7287 8159 8.042515 ACAAAGCAGTAATTCGTTTATAGGGTA 58.957 33.333 0.00 0.00 0.00 3.69
7293 8165 8.280497 CAGTAATTCGTTTATAGGGTATTGTGC 58.720 37.037 0.00 0.00 0.00 4.57
7315 9524 5.067674 TGCAGTAGGCCATATTTGTTGATTC 59.932 40.000 5.01 0.00 43.89 2.52
7318 9527 3.897239 AGGCCATATTTGTTGATTCGGA 58.103 40.909 5.01 0.00 0.00 4.55
7427 9636 0.403271 ATCCTGCATCCATACCTGGC 59.597 55.000 0.00 0.00 42.80 4.85
7429 9638 1.533219 CTGCATCCATACCTGGCCA 59.467 57.895 4.71 4.71 42.80 5.36
7430 9639 0.536687 CTGCATCCATACCTGGCCAG 60.537 60.000 26.87 26.87 42.80 4.85
7431 9640 1.900498 GCATCCATACCTGGCCAGC 60.900 63.158 28.39 9.86 42.80 4.85
7432 9641 1.842007 CATCCATACCTGGCCAGCT 59.158 57.895 28.39 17.23 42.80 4.24
7433 9642 0.536687 CATCCATACCTGGCCAGCTG 60.537 60.000 28.39 21.57 42.80 4.24
7435 9644 2.377810 CCATACCTGGCCAGCTGGA 61.378 63.158 37.21 15.88 35.23 3.86
7436 9645 1.609239 CATACCTGGCCAGCTGGAA 59.391 57.895 37.21 21.71 37.39 3.53
7437 9646 0.034186 CATACCTGGCCAGCTGGAAA 60.034 55.000 37.21 21.33 37.39 3.13
7438 9647 0.929244 ATACCTGGCCAGCTGGAAAT 59.071 50.000 37.21 17.59 37.39 2.17
7439 9648 0.034186 TACCTGGCCAGCTGGAAATG 60.034 55.000 37.21 21.98 37.39 2.32
7440 9649 1.304713 CCTGGCCAGCTGGAAATGT 60.305 57.895 37.21 0.00 37.39 2.71
7441 9650 0.901580 CCTGGCCAGCTGGAAATGTT 60.902 55.000 37.21 0.00 37.39 2.71
7442 9651 0.971386 CTGGCCAGCTGGAAATGTTT 59.029 50.000 37.21 0.00 37.39 2.83
7443 9652 2.170166 CTGGCCAGCTGGAAATGTTTA 58.830 47.619 37.21 10.70 37.39 2.01
7444 9653 2.762327 CTGGCCAGCTGGAAATGTTTAT 59.238 45.455 37.21 0.00 37.39 1.40
7445 9654 2.760092 TGGCCAGCTGGAAATGTTTATC 59.240 45.455 37.21 13.87 37.39 1.75
7446 9655 2.760092 GGCCAGCTGGAAATGTTTATCA 59.240 45.455 37.21 0.00 37.39 2.15
7447 9656 3.429410 GGCCAGCTGGAAATGTTTATCAC 60.429 47.826 37.21 13.11 37.39 3.06
7448 9657 3.429410 GCCAGCTGGAAATGTTTATCACC 60.429 47.826 37.21 9.26 37.39 4.02
7449 9658 3.131046 CCAGCTGGAAATGTTTATCACCC 59.869 47.826 29.88 0.00 37.39 4.61
7450 9659 3.763360 CAGCTGGAAATGTTTATCACCCA 59.237 43.478 5.57 0.00 0.00 4.51
7451 9660 3.763897 AGCTGGAAATGTTTATCACCCAC 59.236 43.478 0.00 0.00 0.00 4.61
7452 9661 3.763897 GCTGGAAATGTTTATCACCCACT 59.236 43.478 0.00 0.00 0.00 4.00
7453 9662 4.220602 GCTGGAAATGTTTATCACCCACTT 59.779 41.667 0.00 0.00 0.00 3.16
7454 9663 5.713025 CTGGAAATGTTTATCACCCACTTG 58.287 41.667 0.00 0.00 0.00 3.16
7455 9664 5.389520 TGGAAATGTTTATCACCCACTTGA 58.610 37.500 0.00 0.00 0.00 3.02
7456 9665 6.015918 TGGAAATGTTTATCACCCACTTGAT 58.984 36.000 0.00 0.00 39.61 2.57
7457 9666 7.178573 TGGAAATGTTTATCACCCACTTGATA 58.821 34.615 0.00 0.00 37.42 2.15
7458 9667 7.671819 TGGAAATGTTTATCACCCACTTGATAA 59.328 33.333 2.16 2.16 43.60 1.75
7539 9748 6.034683 GTGCTAACTGTTAATGGTCTAGTTCG 59.965 42.308 1.46 0.00 33.93 3.95
7575 9784 6.782298 TGATGAAAATGTAACGTCCGTTTA 57.218 33.333 10.61 1.38 39.31 2.01
7612 9821 0.316841 GGCGTGGCATTTTCCAAAGA 59.683 50.000 0.00 0.00 37.96 2.52
7642 9851 6.038271 ACACTCTTCATGTTTACTGTGTTTCC 59.962 38.462 0.00 0.00 34.32 3.13
7669 9878 9.952030 AAGTTAAAAGAAAATCCCACTTTTTCA 57.048 25.926 0.00 0.00 42.72 2.69
7684 9893 4.830600 ACTTTTTCAAAGGATAGCCGGAAA 59.169 37.500 5.05 9.49 39.96 3.13
7757 9966 5.326200 AGTACTCCCTTCGTTCACTATTG 57.674 43.478 0.00 0.00 0.00 1.90
7765 9974 6.993902 TCCCTTCGTTCACTATTGTAAAAGTT 59.006 34.615 0.00 0.00 0.00 2.66
7766 9975 8.149647 TCCCTTCGTTCACTATTGTAAAAGTTA 58.850 33.333 0.00 0.00 0.00 2.24
7767 9976 8.943002 CCCTTCGTTCACTATTGTAAAAGTTAT 58.057 33.333 0.00 0.00 0.00 1.89
7820 10029 5.287513 ACAACATTTTAGCGTGTTTGTTCAC 59.712 36.000 0.00 0.00 36.48 3.18
7845 10054 8.816894 ACTCATTTCAATCCGTATATAGTCCAT 58.183 33.333 0.00 0.00 0.00 3.41
7872 10081 6.119536 TGAAGTATCCAAAACGCCTTATGAT 58.880 36.000 0.00 0.00 0.00 2.45
7891 10100 4.543689 TGATAGTGAACGGAGGGAGTAAT 58.456 43.478 0.00 0.00 0.00 1.89
7904 10113 5.714806 GGAGGGAGTAATTTTGAATTGTCCA 59.285 40.000 13.88 0.00 0.00 4.02
7958 10168 9.281371 CTTGATTTCACATCATACATGTCCTAT 57.719 33.333 0.00 0.00 0.00 2.57
7979 10189 8.359642 TCCTATAACATGAAAATAATGCAAGGC 58.640 33.333 0.00 0.00 0.00 4.35
7980 10190 7.326789 CCTATAACATGAAAATAATGCAAGGCG 59.673 37.037 0.00 0.00 0.00 5.52
7988 10198 7.660112 TGAAAATAATGCAAGGCGATGATTAT 58.340 30.769 0.00 0.00 0.00 1.28
7995 10205 8.743085 AATGCAAGGCGATGATTATAGATATT 57.257 30.769 0.00 0.00 0.00 1.28
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
219 222 6.262944 TCCTCCACAATTACATTATGCATGAC 59.737 38.462 10.16 0.00 36.24 3.06
311 314 5.163642 ACGAGTATTTGTCGCTAGATTCTGT 60.164 40.000 0.00 0.00 41.26 3.41
464 467 9.778993 ATGATTATATTGTGCGAATATTTGAGC 57.221 29.630 6.89 5.82 0.00 4.26
488 491 2.549633 GACGCATTCCTTTGTCCATG 57.450 50.000 0.00 0.00 0.00 3.66
546 549 3.505680 TGGACACCCAAATTTTCTCATCG 59.494 43.478 0.00 0.00 40.09 3.84
570 573 9.546428 AAAGTGGACCAGAAAAATAAAATCAAG 57.454 29.630 0.00 0.00 0.00 3.02
579 582 5.147032 TCCATCAAAGTGGACCAGAAAAAT 58.853 37.500 0.00 0.00 43.20 1.82
593 623 2.223203 GCAGCATTCTCGTCCATCAAAG 60.223 50.000 0.00 0.00 0.00 2.77
607 637 0.036164 TGACCCGTGTAAGCAGCATT 59.964 50.000 0.00 0.00 0.00 3.56
642 672 2.280797 TGAGTGAACCACCTGCGC 60.281 61.111 0.00 0.00 34.49 6.09
643 673 1.069765 AGTGAGTGAACCACCTGCG 59.930 57.895 0.00 0.00 34.49 5.18
659 689 1.692042 CCTCAGGCCCAGGATCAGT 60.692 63.158 12.44 0.00 31.91 3.41
664 694 2.040606 GTACCCTCAGGCCCAGGA 59.959 66.667 18.51 4.63 36.11 3.86
782 816 2.284995 AGGTCAGGTGGCTCCTCC 60.285 66.667 4.85 5.19 46.24 4.30
783 817 0.980231 ATCAGGTCAGGTGGCTCCTC 60.980 60.000 4.85 0.00 46.24 3.71
862 898 3.311110 GCACCAGTGGGGACGAGA 61.311 66.667 18.10 0.00 41.15 4.04
876 912 4.477975 CGTCGACGGGGAGAGCAC 62.478 72.222 29.70 0.00 35.37 4.40
914 965 0.038310 TTGAGAGTGAGCGGAGGAGA 59.962 55.000 0.00 0.00 0.00 3.71
915 966 0.455410 CTTGAGAGTGAGCGGAGGAG 59.545 60.000 0.00 0.00 0.00 3.69
916 967 0.038310 TCTTGAGAGTGAGCGGAGGA 59.962 55.000 0.00 0.00 0.00 3.71
917 968 0.455410 CTCTTGAGAGTGAGCGGAGG 59.545 60.000 0.00 0.00 37.40 4.30
927 978 5.245075 AGTGAGGGTTTAAGACTCTTGAGAG 59.755 44.000 6.48 6.48 39.90 3.20
928 979 5.148502 AGTGAGGGTTTAAGACTCTTGAGA 58.851 41.667 4.49 0.00 39.90 3.27
984 1035 2.753296 GCCATGTCTGACAGAGATAGC 58.247 52.381 15.28 15.28 31.63 2.97
1089 1140 1.275291 CCTTCAAAGAGGCTCGTACCA 59.725 52.381 9.22 0.00 0.00 3.25
1110 1161 1.228429 CGGAGAAGTGGGGGCAAAA 60.228 57.895 0.00 0.00 0.00 2.44
1114 1167 1.971695 CAAACGGAGAAGTGGGGGC 60.972 63.158 0.00 0.00 0.00 5.80
1231 1284 2.788640 CGCAATGGCCAATCCCCAG 61.789 63.158 10.96 0.00 35.48 4.45
1276 1329 6.136071 GCAATTAGCATTATACCTCACAACG 58.864 40.000 0.00 0.00 44.79 4.10
1297 1350 4.888326 ATTTCACAAGCCCAATTAGCAA 57.112 36.364 2.79 0.00 0.00 3.91
1298 1351 4.282957 TCAATTTCACAAGCCCAATTAGCA 59.717 37.500 2.79 0.00 0.00 3.49
1299 1352 4.819769 TCAATTTCACAAGCCCAATTAGC 58.180 39.130 0.00 0.00 0.00 3.09
1300 1353 5.745294 CGATCAATTTCACAAGCCCAATTAG 59.255 40.000 0.00 0.00 0.00 1.73
1301 1354 5.184864 ACGATCAATTTCACAAGCCCAATTA 59.815 36.000 0.00 0.00 0.00 1.40
1302 1355 4.021192 ACGATCAATTTCACAAGCCCAATT 60.021 37.500 0.00 0.00 0.00 2.32
1303 1356 3.511146 ACGATCAATTTCACAAGCCCAAT 59.489 39.130 0.00 0.00 0.00 3.16
1344 1397 6.857777 TGACAAAATAAAACCCAGCAATTG 57.142 33.333 0.00 0.00 0.00 2.32
1559 1780 2.005451 GAGCCACACTGTAGCTTGATG 58.995 52.381 3.48 0.00 36.87 3.07
1591 1812 2.930950 TGAGCCACACTGTAGCTTTTT 58.069 42.857 3.48 0.00 36.87 1.94
1592 1813 2.638480 TGAGCCACACTGTAGCTTTT 57.362 45.000 3.48 0.00 36.87 2.27
1593 1814 2.430465 CATGAGCCACACTGTAGCTTT 58.570 47.619 3.48 0.00 36.87 3.51
1594 1815 1.339438 CCATGAGCCACACTGTAGCTT 60.339 52.381 3.48 0.00 36.87 3.74
1595 1816 0.251354 CCATGAGCCACACTGTAGCT 59.749 55.000 1.31 1.31 40.24 3.32
1596 1817 0.036010 ACCATGAGCCACACTGTAGC 60.036 55.000 0.00 0.00 0.00 3.58
1597 1818 1.276138 TGACCATGAGCCACACTGTAG 59.724 52.381 0.00 0.00 0.00 2.74
1598 1819 1.347062 TGACCATGAGCCACACTGTA 58.653 50.000 0.00 0.00 0.00 2.74
1599 1820 0.694771 ATGACCATGAGCCACACTGT 59.305 50.000 0.00 0.00 0.00 3.55
1600 1821 1.092348 CATGACCATGAGCCACACTG 58.908 55.000 4.03 0.00 41.20 3.66
1601 1822 0.679002 GCATGACCATGAGCCACACT 60.679 55.000 13.67 0.00 41.20 3.55
1602 1823 0.679002 AGCATGACCATGAGCCACAC 60.679 55.000 13.67 0.00 41.20 3.82
1603 1824 0.393402 GAGCATGACCATGAGCCACA 60.393 55.000 13.67 0.00 41.20 4.17
1604 1825 0.393402 TGAGCATGACCATGAGCCAC 60.393 55.000 13.67 0.00 41.20 5.01
1605 1826 0.328926 TTGAGCATGACCATGAGCCA 59.671 50.000 13.67 5.10 41.20 4.75
1606 1827 1.688772 ATTGAGCATGACCATGAGCC 58.311 50.000 13.67 2.81 41.20 4.70
1607 1828 3.444916 CAAATTGAGCATGACCATGAGC 58.555 45.455 13.67 5.17 41.20 4.26
1608 1829 3.446161 ACCAAATTGAGCATGACCATGAG 59.554 43.478 13.67 0.00 41.20 2.90
1771 1992 6.696042 TCCATTGCACCTATAAGGCTATAA 57.304 37.500 0.00 0.00 39.63 0.98
1772 1993 6.696042 TTCCATTGCACCTATAAGGCTATA 57.304 37.500 0.00 0.00 39.63 1.31
1773 1994 5.582950 TTCCATTGCACCTATAAGGCTAT 57.417 39.130 0.00 0.00 39.63 2.97
1774 1995 5.582950 ATTCCATTGCACCTATAAGGCTA 57.417 39.130 0.00 0.00 39.63 3.93
1775 1996 3.951563 TTCCATTGCACCTATAAGGCT 57.048 42.857 0.00 0.00 39.63 4.58
1776 1997 4.584325 TGAATTCCATTGCACCTATAAGGC 59.416 41.667 2.27 0.00 39.63 4.35
1777 1998 6.906157 ATGAATTCCATTGCACCTATAAGG 57.094 37.500 2.27 0.00 34.79 2.69
1778 1999 9.683069 GTAAATGAATTCCATTGCACCTATAAG 57.317 33.333 2.27 0.00 44.28 1.73
1811 2032 4.853924 AAGATAAGTGCAACCAGTTTGG 57.146 40.909 0.00 0.00 45.02 3.28
1819 2040 5.103290 TCAAACCGAAAGATAAGTGCAAC 57.897 39.130 0.00 0.00 0.00 4.17
1834 2061 3.848272 AATGGCATGTACTTCAAACCG 57.152 42.857 0.00 0.00 0.00 4.44
1906 2134 2.941720 TGGCAAAGCAACAATTTTGACC 59.058 40.909 0.00 3.01 40.74 4.02
1907 2135 4.816786 ATGGCAAAGCAACAATTTTGAC 57.183 36.364 0.00 0.00 41.60 3.18
1908 2136 6.054295 ACTAATGGCAAAGCAACAATTTTGA 58.946 32.000 0.00 0.00 36.61 2.69
1909 2137 6.303021 ACTAATGGCAAAGCAACAATTTTG 57.697 33.333 0.00 0.00 37.35 2.44
1910 2138 5.469760 GGACTAATGGCAAAGCAACAATTTT 59.530 36.000 0.00 0.00 0.00 1.82
2130 2388 2.158755 AGTATTGGTAGGCAGGCATGAC 60.159 50.000 0.62 0.00 32.98 3.06
2407 2692 8.324567 GCTCTCTAATAAAAACTGAAGATGTCG 58.675 37.037 0.00 0.00 0.00 4.35
2427 2712 8.634444 AGTTACAAATAGTCGATAATGCTCTCT 58.366 33.333 0.00 0.00 0.00 3.10
2461 2746 7.434307 AGCTATCAAAATTGATCAGCGAAATTG 59.566 33.333 11.69 0.00 44.17 2.32
2557 2842 8.844244 AGTTAATGCTATTTGATGATGGTTCTC 58.156 33.333 0.00 0.00 0.00 2.87
2603 2888 1.667724 CAGCTAAGATGGTTCTTGCGG 59.332 52.381 0.00 0.00 42.25 5.69
2661 2946 0.398318 GGTGGCTTCAGTCAAGGAGT 59.602 55.000 0.00 0.00 31.94 3.85
2911 3202 6.398918 GGTGAGTAGCTCAACTATTTTCTCA 58.601 40.000 6.91 0.00 44.06 3.27
3258 3549 7.402054 ATGTTAGTCCCATTGACAACATTAGA 58.598 34.615 12.83 0.00 44.29 2.10
3708 3999 6.770303 TCACTGATCAAACTTTACATTGGTGA 59.230 34.615 0.00 0.00 0.00 4.02
3709 4000 6.969366 TCACTGATCAAACTTTACATTGGTG 58.031 36.000 0.00 0.00 0.00 4.17
3713 4004 6.149308 TGCGATCACTGATCAAACTTTACATT 59.851 34.615 17.43 0.00 38.84 2.71
3730 4021 1.502163 GCCTGCCACTATGCGATCAC 61.502 60.000 0.00 0.00 0.00 3.06
3819 4110 6.135290 TGAAACAGGAAGTTCAACAGATTG 57.865 37.500 5.01 0.00 40.26 2.67
3820 4111 6.774656 AGATGAAACAGGAAGTTCAACAGATT 59.225 34.615 5.01 0.00 40.26 2.40
3821 4112 6.302269 AGATGAAACAGGAAGTTCAACAGAT 58.698 36.000 5.01 0.00 40.26 2.90
3822 4113 5.684704 AGATGAAACAGGAAGTTCAACAGA 58.315 37.500 5.01 0.00 40.26 3.41
3823 4114 6.382869 AAGATGAAACAGGAAGTTCAACAG 57.617 37.500 5.01 0.00 40.26 3.16
3824 4115 6.773976 AAAGATGAAACAGGAAGTTCAACA 57.226 33.333 5.01 0.00 40.26 3.33
3825 4116 8.406297 ACTAAAAGATGAAACAGGAAGTTCAAC 58.594 33.333 5.01 0.00 40.26 3.18
3826 4117 8.519799 ACTAAAAGATGAAACAGGAAGTTCAA 57.480 30.769 5.01 0.00 40.26 2.69
3827 4118 8.519799 AACTAAAAGATGAAACAGGAAGTTCA 57.480 30.769 5.01 0.00 40.26 3.18
3828 4119 9.803315 AAAACTAAAAGATGAAACAGGAAGTTC 57.197 29.630 0.00 0.00 40.26 3.01
4013 4436 1.597461 GGGAACTGGGAAGTCCTCG 59.403 63.158 0.00 0.00 36.20 4.63
4050 4473 8.695456 AGCCATTTATCCTCGTTTTCATTTAAT 58.305 29.630 0.00 0.00 0.00 1.40
4326 4760 7.437862 TCATTTGTACAAGCAATTCAAGGTTTC 59.562 33.333 8.56 0.00 0.00 2.78
4406 5099 6.796785 AATAGGAAAGCAAATTAGGTGCAT 57.203 33.333 3.58 0.00 44.74 3.96
4727 5420 6.144402 CAGCGAATTTTGAAAACAGTTAGCAT 59.856 34.615 9.19 0.00 0.00 3.79
4789 5482 3.373987 GGAGGGGGTAGTAGTTCTAGCTT 60.374 52.174 0.00 0.00 43.99 3.74
4792 5485 2.174424 ACGGAGGGGGTAGTAGTTCTAG 59.826 54.545 0.00 0.00 0.00 2.43
4805 5498 5.627040 GCTCTTATATTATGGAACGGAGGGG 60.627 48.000 0.00 0.00 0.00 4.79
4806 5499 5.420409 GCTCTTATATTATGGAACGGAGGG 58.580 45.833 0.00 0.00 0.00 4.30
4807 5500 5.103000 CGCTCTTATATTATGGAACGGAGG 58.897 45.833 0.00 0.00 0.00 4.30
4808 5501 5.710984 ACGCTCTTATATTATGGAACGGAG 58.289 41.667 0.00 0.00 0.00 4.63
4809 5502 5.717078 ACGCTCTTATATTATGGAACGGA 57.283 39.130 0.00 0.00 0.00 4.69
4810 5503 6.780706 AAACGCTCTTATATTATGGAACGG 57.219 37.500 0.00 0.00 0.00 4.44
4811 5504 8.332464 TCAAAAACGCTCTTATATTATGGAACG 58.668 33.333 0.00 0.00 0.00 3.95
4812 5505 9.434559 GTCAAAAACGCTCTTATATTATGGAAC 57.565 33.333 0.00 0.00 0.00 3.62
4813 5506 9.168451 TGTCAAAAACGCTCTTATATTATGGAA 57.832 29.630 0.00 0.00 0.00 3.53
4814 5507 8.609176 GTGTCAAAAACGCTCTTATATTATGGA 58.391 33.333 0.00 0.00 35.42 3.41
4815 5508 8.612619 AGTGTCAAAAACGCTCTTATATTATGG 58.387 33.333 0.00 0.00 45.69 2.74
4818 5511 9.642327 TGTAGTGTCAAAAACGCTCTTATATTA 57.358 29.630 0.00 0.00 45.69 0.98
4819 5512 8.440833 GTGTAGTGTCAAAAACGCTCTTATATT 58.559 33.333 0.00 0.00 45.69 1.28
4820 5513 7.817962 AGTGTAGTGTCAAAAACGCTCTTATAT 59.182 33.333 0.00 0.00 45.69 0.86
4821 5514 7.149973 AGTGTAGTGTCAAAAACGCTCTTATA 58.850 34.615 0.00 0.00 45.69 0.98
4822 5515 5.989777 AGTGTAGTGTCAAAAACGCTCTTAT 59.010 36.000 0.00 0.00 45.69 1.73
4823 5516 5.353938 AGTGTAGTGTCAAAAACGCTCTTA 58.646 37.500 0.00 0.00 45.69 2.10
4824 5517 4.189231 AGTGTAGTGTCAAAAACGCTCTT 58.811 39.130 0.00 0.00 45.69 2.85
4825 5518 3.793559 AGTGTAGTGTCAAAAACGCTCT 58.206 40.909 0.00 0.00 45.69 4.09
4826 5519 4.743644 ACTAGTGTAGTGTCAAAAACGCTC 59.256 41.667 0.00 0.00 45.69 5.03
4839 5532 4.690122 AGCGTTTTTGACACTAGTGTAGT 58.310 39.130 27.98 6.32 45.05 2.73
4840 5533 4.982916 AGAGCGTTTTTGACACTAGTGTAG 59.017 41.667 27.98 13.76 45.05 2.74
4841 5534 4.940463 AGAGCGTTTTTGACACTAGTGTA 58.060 39.130 27.98 11.50 45.05 2.90
4843 5536 4.795970 AAGAGCGTTTTTGACACTAGTG 57.204 40.909 21.44 21.44 0.00 2.74
4844 5537 8.773404 AATATAAGAGCGTTTTTGACACTAGT 57.227 30.769 0.00 0.00 0.00 2.57
4847 5540 8.612619 CCATAATATAAGAGCGTTTTTGACACT 58.387 33.333 0.00 0.00 0.00 3.55
4848 5541 7.855904 CCCATAATATAAGAGCGTTTTTGACAC 59.144 37.037 0.00 0.00 0.00 3.67
4849 5542 7.771361 TCCCATAATATAAGAGCGTTTTTGACA 59.229 33.333 0.00 0.00 0.00 3.58
4850 5543 8.149973 TCCCATAATATAAGAGCGTTTTTGAC 57.850 34.615 0.00 0.00 0.00 3.18
4851 5544 8.783093 CATCCCATAATATAAGAGCGTTTTTGA 58.217 33.333 0.00 0.00 0.00 2.69
4852 5545 8.023128 CCATCCCATAATATAAGAGCGTTTTTG 58.977 37.037 0.00 0.00 0.00 2.44
4853 5546 7.942341 TCCATCCCATAATATAAGAGCGTTTTT 59.058 33.333 0.00 0.00 0.00 1.94
4854 5547 7.458397 TCCATCCCATAATATAAGAGCGTTTT 58.542 34.615 0.00 0.00 0.00 2.43
4855 5548 7.016153 TCCATCCCATAATATAAGAGCGTTT 57.984 36.000 0.00 0.00 0.00 3.60
4856 5549 6.352222 CCTCCATCCCATAATATAAGAGCGTT 60.352 42.308 0.00 0.00 0.00 4.84
4857 5550 5.129485 CCTCCATCCCATAATATAAGAGCGT 59.871 44.000 0.00 0.00 0.00 5.07
4858 5551 5.453903 CCCTCCATCCCATAATATAAGAGCG 60.454 48.000 0.00 0.00 0.00 5.03
4859 5552 5.667626 TCCCTCCATCCCATAATATAAGAGC 59.332 44.000 0.00 0.00 0.00 4.09
4860 5553 6.905776 ACTCCCTCCATCCCATAATATAAGAG 59.094 42.308 0.00 0.00 0.00 2.85
4861 5554 6.826727 ACTCCCTCCATCCCATAATATAAGA 58.173 40.000 0.00 0.00 0.00 2.10
4862 5555 7.846823 ACTACTCCCTCCATCCCATAATATAAG 59.153 40.741 0.00 0.00 0.00 1.73
4863 5556 7.729350 ACTACTCCCTCCATCCCATAATATAA 58.271 38.462 0.00 0.00 0.00 0.98
4864 5557 7.312162 ACTACTCCCTCCATCCCATAATATA 57.688 40.000 0.00 0.00 0.00 0.86
4865 5558 6.185677 ACTACTCCCTCCATCCCATAATAT 57.814 41.667 0.00 0.00 0.00 1.28
4866 5559 5.633473 ACTACTCCCTCCATCCCATAATA 57.367 43.478 0.00 0.00 0.00 0.98
4867 5560 4.510303 ACTACTCCCTCCATCCCATAAT 57.490 45.455 0.00 0.00 0.00 1.28
4868 5561 5.633473 ATACTACTCCCTCCATCCCATAA 57.367 43.478 0.00 0.00 0.00 1.90
4869 5562 5.633473 AATACTACTCCCTCCATCCCATA 57.367 43.478 0.00 0.00 0.00 2.74
4870 5563 4.510303 AATACTACTCCCTCCATCCCAT 57.490 45.455 0.00 0.00 0.00 4.00
4871 5564 4.295905 AAATACTACTCCCTCCATCCCA 57.704 45.455 0.00 0.00 0.00 4.37
4872 5565 4.747009 GCAAAATACTACTCCCTCCATCCC 60.747 50.000 0.00 0.00 0.00 3.85
4873 5566 4.141482 TGCAAAATACTACTCCCTCCATCC 60.141 45.833 0.00 0.00 0.00 3.51
4874 5567 5.036117 TGCAAAATACTACTCCCTCCATC 57.964 43.478 0.00 0.00 0.00 3.51
4875 5568 5.653255 ATGCAAAATACTACTCCCTCCAT 57.347 39.130 0.00 0.00 0.00 3.41
4876 5569 6.569127 TTATGCAAAATACTACTCCCTCCA 57.431 37.500 0.00 0.00 0.00 3.86
4877 5570 7.875327 TTTTATGCAAAATACTACTCCCTCC 57.125 36.000 0.00 0.00 0.00 4.30
4878 5571 9.174166 TCTTTTTATGCAAAATACTACTCCCTC 57.826 33.333 0.00 0.00 33.73 4.30
4879 5572 9.700831 ATCTTTTTATGCAAAATACTACTCCCT 57.299 29.630 0.00 0.00 33.73 4.20
4934 5627 5.835819 AGCTAGTACTTATGATGGAAGCAGA 59.164 40.000 0.00 0.00 32.93 4.26
5045 5738 4.143986 AGTAAGTCCTATTTGCAGCCTC 57.856 45.455 0.00 0.00 0.00 4.70
5163 5856 7.972832 TTTCGGCAGAGAAACTTCTATAAAA 57.027 32.000 0.00 0.00 37.73 1.52
5308 6003 5.570589 GCAACTGGAAGATTCAGAAAAATCG 59.429 40.000 0.00 0.00 40.00 3.34
5486 6181 0.250424 GCCAAGCCCTGCACAAAAAT 60.250 50.000 0.00 0.00 0.00 1.82
5566 6261 6.788598 TGCCACAATAATGTACAATGGATT 57.211 33.333 0.00 0.00 37.82 3.01
5632 6327 3.247411 GTGCCAACACTGCAAATTAAACC 59.753 43.478 0.00 0.00 43.85 3.27
6073 6768 0.109597 GCGACTTGCCCAATCTTGTG 60.110 55.000 0.00 0.00 37.76 3.33
6093 6788 4.380444 GCACCTTGAGTTTTCAACACTTCA 60.380 41.667 0.00 0.00 38.37 3.02
6273 6968 6.163135 AGTGCTACGGCTAGATAAGAAAAT 57.837 37.500 0.00 0.00 39.59 1.82
6395 7206 4.221041 AGGAACTGAGTCTAAACAGGTAGC 59.779 45.833 0.00 0.00 37.18 3.58
6409 7220 4.153117 GCAACAACTACATGAGGAACTGAG 59.847 45.833 0.00 0.00 41.55 3.35
6545 7356 4.020928 TCAACTACCTCGGTCAATTAGCAA 60.021 41.667 0.00 0.00 0.00 3.91
6640 7452 8.336080 GCTGTAAACTTCATATGGCTAGTAAAC 58.664 37.037 2.13 6.94 0.00 2.01
6649 7461 7.546358 TCAAAATGGCTGTAAACTTCATATGG 58.454 34.615 2.13 0.00 0.00 2.74
6774 7592 3.096092 AGCAACAAGAGGGTTTGTGAAA 58.904 40.909 0.00 0.00 40.24 2.69
6873 7691 6.349280 GCATGAACCACCACGCAATAATATAT 60.349 38.462 0.00 0.00 0.00 0.86
6898 7762 8.233190 GTGAAGAAAAGAACAGTCAGATATTGG 58.767 37.037 0.00 0.00 0.00 3.16
7051 7916 4.260294 CGTAACCACGCTCAACTAAAACAA 60.260 41.667 0.00 0.00 42.05 2.83
7287 8159 4.280819 ACAAATATGGCCTACTGCACAAT 58.719 39.130 3.32 0.00 43.89 2.71
7293 8165 5.277974 CCGAATCAACAAATATGGCCTACTG 60.278 44.000 3.32 0.00 0.00 2.74
7355 9564 6.780901 ACCAAACAAAACCTCCCTTTAAAAA 58.219 32.000 0.00 0.00 0.00 1.94
7387 9596 4.407496 TTTTGCGTTAGGTAACCGAATG 57.593 40.909 0.00 0.00 32.69 2.67
7427 9636 3.131046 GGGTGATAAACATTTCCAGCTGG 59.869 47.826 27.87 27.87 0.00 4.85
7429 9638 3.763897 GTGGGTGATAAACATTTCCAGCT 59.236 43.478 0.00 0.00 30.99 4.24
7430 9639 3.763897 AGTGGGTGATAAACATTTCCAGC 59.236 43.478 0.00 0.00 30.99 4.85
7431 9640 5.476599 TCAAGTGGGTGATAAACATTTCCAG 59.523 40.000 0.00 0.00 30.99 3.86
7432 9641 5.389520 TCAAGTGGGTGATAAACATTTCCA 58.610 37.500 0.00 0.00 0.00 3.53
7433 9642 5.975693 TCAAGTGGGTGATAAACATTTCC 57.024 39.130 0.00 0.00 0.00 3.13
7500 9709 2.800544 GTTAGCACTTTGTCGAGAAGCA 59.199 45.455 7.59 0.00 0.00 3.91
7507 9716 5.049680 ACCATTAACAGTTAGCACTTTGTCG 60.050 40.000 0.00 0.00 0.00 4.35
7539 9748 9.868277 TTACATTTTCATCAAATTATCCACCAC 57.132 29.630 0.00 0.00 32.24 4.16
7575 9784 2.951642 CGCCATGTATCATTCCAAACCT 59.048 45.455 0.00 0.00 0.00 3.50
7612 9821 5.221382 ACAGTAAACATGAAGAGTGTACGGT 60.221 40.000 0.00 0.00 35.35 4.83
7736 9945 5.069501 ACAATAGTGAACGAAGGGAGTAC 57.930 43.478 0.00 0.00 0.00 2.73
7795 10004 5.864474 TGAACAAACACGCTAAAATGTTGTT 59.136 32.000 0.00 0.00 39.00 2.83
7799 10008 5.163703 TGAGTGAACAAACACGCTAAAATGT 60.164 36.000 0.00 0.00 44.35 2.71
7800 10009 5.270083 TGAGTGAACAAACACGCTAAAATG 58.730 37.500 0.00 0.00 44.35 2.32
7801 10010 5.493133 TGAGTGAACAAACACGCTAAAAT 57.507 34.783 0.00 0.00 44.35 1.82
7803 10012 5.493133 AATGAGTGAACAAACACGCTAAA 57.507 34.783 0.00 0.00 44.35 1.85
7804 10013 5.065346 TGAAATGAGTGAACAAACACGCTAA 59.935 36.000 0.00 0.00 44.35 3.09
7845 10054 7.771361 TCATAAGGCGTTTTGGATACTTCAATA 59.229 33.333 9.25 0.00 37.61 1.90
7852 10061 6.704493 TCACTATCATAAGGCGTTTTGGATAC 59.296 38.462 9.25 0.00 0.00 2.24
7853 10062 6.822442 TCACTATCATAAGGCGTTTTGGATA 58.178 36.000 9.25 7.85 0.00 2.59
7854 10063 5.680619 TCACTATCATAAGGCGTTTTGGAT 58.319 37.500 9.25 7.23 0.00 3.41
7855 10064 5.092554 TCACTATCATAAGGCGTTTTGGA 57.907 39.130 9.25 0.71 0.00 3.53
7856 10065 5.569413 GTTCACTATCATAAGGCGTTTTGG 58.431 41.667 9.25 0.00 0.00 3.28
7857 10066 5.255596 CGTTCACTATCATAAGGCGTTTTG 58.744 41.667 0.00 0.00 0.00 2.44
7872 10081 5.246656 TCAAAATTACTCCCTCCGTTCACTA 59.753 40.000 0.00 0.00 0.00 2.74
7891 10100 6.723298 ACCTTGTATGTGGACAATTCAAAA 57.277 33.333 0.00 0.00 38.60 2.44
7904 10113 2.922740 ACGTGTGGAACCTTGTATGT 57.077 45.000 0.00 0.00 34.36 2.29
7958 10168 6.201226 TCGCCTTGCATTATTTTCATGTTA 57.799 33.333 0.00 0.00 0.00 2.41
7959 10169 5.070770 TCGCCTTGCATTATTTTCATGTT 57.929 34.783 0.00 0.00 0.00 2.71
7979 10189 8.883954 ATGAGCCACAATATCTATAATCATCG 57.116 34.615 0.00 0.00 0.00 3.84


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

AutoCloner maintained by Alex Coulton.