Multiple sequence alignment - TraesCS4B01G310600

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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 TraesCS4B01G310600 chr4B 100.000 4675 0 0 1 4675 600674253 600669579 0.000000e+00 8634.0
1 TraesCS4B01G310600 chr4B 87.500 832 94 9 2 828 51814835 51815661 0.000000e+00 952.0
2 TraesCS4B01G310600 chr4B 89.037 675 70 4 3 674 166849540 166848867 0.000000e+00 833.0
3 TraesCS4B01G310600 chr4B 84.375 64 9 1 4268 4330 4707067 4707004 1.400000e-05 62.1
4 TraesCS4B01G310600 chr4D 96.434 1935 51 9 830 2757 476318074 476316151 0.000000e+00 3175.0
5 TraesCS4B01G310600 chr4D 96.852 1239 31 5 2755 3988 476316066 476314831 0.000000e+00 2065.0
6 TraesCS4B01G310600 chr4D 97.143 70 2 0 4115 4184 476314729 476314660 8.220000e-23 119.0
7 TraesCS4B01G310600 chr4A 91.204 1262 74 20 2755 3989 683500255 683499004 0.000000e+00 1681.0
8 TraesCS4B01G310600 chr4A 87.629 873 48 24 1906 2758 683501171 683500339 0.000000e+00 959.0
9 TraesCS4B01G310600 chr4A 92.530 589 32 3 1325 1909 683501844 683501264 0.000000e+00 833.0
10 TraesCS4B01G310600 chr4A 93.213 442 24 5 821 1258 683502573 683502134 0.000000e+00 645.0
11 TraesCS4B01G310600 chr4A 89.815 216 18 4 4115 4329 683498896 683498684 1.660000e-69 274.0
12 TraesCS4B01G310600 chr4A 81.176 255 21 13 4448 4675 683498674 683498420 3.720000e-41 180.0
13 TraesCS4B01G310600 chr4A 77.778 234 28 18 2869 3099 41899173 41899385 6.350000e-24 122.0
14 TraesCS4B01G310600 chr5D 87.886 842 84 10 2 829 463969145 463969982 0.000000e+00 974.0
15 TraesCS4B01G310600 chr5D 90.640 641 56 3 2 641 408756903 408756266 0.000000e+00 848.0
16 TraesCS4B01G310600 chr5D 89.189 111 10 2 4340 4449 439260123 439260232 2.270000e-28 137.0
17 TraesCS4B01G310600 chr5D 77.872 235 28 16 2869 3099 34271944 34271730 1.770000e-24 124.0
18 TraesCS4B01G310600 chr5D 93.023 86 4 2 4017 4102 416973418 416973501 1.770000e-24 124.0
19 TraesCS4B01G310600 chr5D 84.375 64 9 1 4268 4330 310276715 310276652 1.400000e-05 62.1
20 TraesCS4B01G310600 chr1D 88.384 792 84 6 3 789 345832614 345833402 0.000000e+00 946.0
21 TraesCS4B01G310600 chr1D 90.351 114 11 0 4336 4449 29961351 29961238 2.910000e-32 150.0
22 TraesCS4B01G310600 chr1D 88.889 117 10 2 4336 4449 479763137 479763021 1.750000e-29 141.0
23 TraesCS4B01G310600 chr1D 97.143 35 0 1 4297 4330 245217223 245217257 1.820000e-04 58.4
24 TraesCS4B01G310600 chr2A 87.356 783 86 11 7 783 510801047 510800272 0.000000e+00 885.0
25 TraesCS4B01G310600 chr2A 78.298 235 27 15 2869 3099 554014473 554014259 3.800000e-26 130.0
26 TraesCS4B01G310600 chr2A 87.037 108 12 2 2139 2246 149211774 149211669 2.280000e-23 121.0
27 TraesCS4B01G310600 chr2A 87.500 64 7 1 4268 4330 695156855 695156792 6.490000e-09 73.1
28 TraesCS4B01G310600 chr1A 88.451 736 75 8 6 740 430228523 430229249 0.000000e+00 880.0
29 TraesCS4B01G310600 chr1A 97.222 36 0 1 4297 4331 306569161 306569196 5.050000e-05 60.2
30 TraesCS4B01G310600 chr1A 97.143 35 0 1 4297 4330 527180458 527180424 1.820000e-04 58.4
31 TraesCS4B01G310600 chr6A 86.717 798 91 9 6 794 66299309 66298518 0.000000e+00 872.0
32 TraesCS4B01G310600 chr6A 85.938 64 7 2 4268 4330 575302633 575302695 3.020000e-07 67.6
33 TraesCS4B01G310600 chr5A 86.076 790 83 15 4 784 387251703 387252474 0.000000e+00 824.0
34 TraesCS4B01G310600 chr5A 91.667 84 6 1 4019 4102 564175468 564175550 1.060000e-21 115.0
35 TraesCS4B01G310600 chr5A 86.316 95 9 4 4009 4102 640739801 640739710 2.980000e-17 100.0
36 TraesCS4B01G310600 chr3A 83.430 344 25 12 1399 1742 323691 323380 1.650000e-74 291.0
37 TraesCS4B01G310600 chr3A 84.937 239 25 7 2094 2329 402084069 402083839 1.010000e-56 231.0
38 TraesCS4B01G310600 chr7D 83.810 315 27 8 1456 1747 575915241 575914928 1.280000e-70 278.0
39 TraesCS4B01G310600 chr3B 82.661 248 36 7 2087 2329 42700332 42700087 3.660000e-51 213.0
40 TraesCS4B01G310600 chr3B 100.000 28 0 0 3992 4019 429973611 429973584 8.000000e-03 52.8
41 TraesCS4B01G310600 chr2D 78.495 279 40 14 3422 3693 433218912 433219177 1.040000e-36 165.0
42 TraesCS4B01G310600 chr2D 84.967 153 10 8 2091 2241 152095749 152095890 4.880000e-30 143.0
43 TraesCS4B01G310600 chr2D 77.872 235 30 14 2869 3099 433218663 433218879 4.910000e-25 126.0
44 TraesCS4B01G310600 chr5B 90.179 112 11 0 4336 4447 664418069 664418180 3.770000e-31 147.0
45 TraesCS4B01G310600 chr2B 84.713 157 11 5 2091 2246 210454936 210455080 1.360000e-30 145.0
46 TraesCS4B01G310600 chr6B 94.118 85 4 1 4017 4101 22555600 22555683 1.370000e-25 128.0
47 TraesCS4B01G310600 chr6B 88.043 92 9 2 4014 4104 615187030 615186940 1.780000e-19 108.0
48 TraesCS4B01G310600 chr3D 93.023 86 4 2 4017 4102 317739458 317739375 1.770000e-24 124.0
49 TraesCS4B01G310600 chr3D 100.000 28 0 0 3992 4019 613017389 613017362 8.000000e-03 52.8
50 TraesCS4B01G310600 chr6D 92.857 84 5 1 4018 4101 177794273 177794191 2.280000e-23 121.0
51 TraesCS4B01G310600 chr6D 86.957 92 10 2 4014 4104 409547376 409547286 8.280000e-18 102.0
52 TraesCS4B01G310600 chr7B 86.517 89 10 2 4014 4101 561753556 561753469 3.850000e-16 97.1
53 TraesCS4B01G310600 chr7B 85.714 63 7 2 4268 4329 28687748 28687809 1.090000e-06 65.8
54 TraesCS4B01G310600 chr7B 96.875 32 1 0 3988 4019 135716516 135716547 2.000000e-03 54.7
55 TraesCS4B01G310600 chr7B 100.000 28 0 0 3992 4019 56386863 56386836 8.000000e-03 52.8
56 TraesCS4B01G310600 chr7A 94.118 34 2 0 3986 4019 44884945 44884978 8.000000e-03 52.8
57 TraesCS4B01G310600 chr1B 100.000 28 0 0 3992 4019 137449221 137449194 8.000000e-03 52.8


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 TraesCS4B01G310600 chr4B 600669579 600674253 4674 True 8634.000000 8634 100.000000 1 4675 1 chr4B.!!$R3 4674
1 TraesCS4B01G310600 chr4B 51814835 51815661 826 False 952.000000 952 87.500000 2 828 1 chr4B.!!$F1 826
2 TraesCS4B01G310600 chr4B 166848867 166849540 673 True 833.000000 833 89.037000 3 674 1 chr4B.!!$R2 671
3 TraesCS4B01G310600 chr4D 476314660 476318074 3414 True 1786.333333 3175 96.809667 830 4184 3 chr4D.!!$R1 3354
4 TraesCS4B01G310600 chr4A 683498420 683502573 4153 True 762.000000 1681 89.261167 821 4675 6 chr4A.!!$R1 3854
5 TraesCS4B01G310600 chr5D 463969145 463969982 837 False 974.000000 974 87.886000 2 829 1 chr5D.!!$F3 827
6 TraesCS4B01G310600 chr5D 408756266 408756903 637 True 848.000000 848 90.640000 2 641 1 chr5D.!!$R3 639
7 TraesCS4B01G310600 chr1D 345832614 345833402 788 False 946.000000 946 88.384000 3 789 1 chr1D.!!$F2 786
8 TraesCS4B01G310600 chr2A 510800272 510801047 775 True 885.000000 885 87.356000 7 783 1 chr2A.!!$R2 776
9 TraesCS4B01G310600 chr1A 430228523 430229249 726 False 880.000000 880 88.451000 6 740 1 chr1A.!!$F2 734
10 TraesCS4B01G310600 chr6A 66298518 66299309 791 True 872.000000 872 86.717000 6 794 1 chr6A.!!$R1 788
11 TraesCS4B01G310600 chr5A 387251703 387252474 771 False 824.000000 824 86.076000 4 784 1 chr5A.!!$F1 780

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
960 997 0.035176 TAGGTTTTTCGTCCCCGTGG 59.965 55.0 0.00 0.00 35.01 4.94 F
2150 2513 0.881796 GGTAAGAGTTGGCTTGCCAC 59.118 55.0 14.52 9.59 46.18 5.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2898 3367 1.709147 CCTGCACGCAAGGTAGATGC 61.709 60.0 0.0 0.0 46.39 3.91 R
4086 4583 0.106116 ACATCTACTCCCTCCGTCCC 60.106 60.0 0.0 0.0 0.00 4.46 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
27 28 2.034939 TGCAGTGCTCAAATGTCTTTGG 59.965 45.455 17.60 0.00 41.74 3.28
64 65 3.031013 TCATGCTCCTCCGATGAACTTA 58.969 45.455 0.00 0.00 0.00 2.24
67 68 2.427453 TGCTCCTCCGATGAACTTAGAC 59.573 50.000 0.00 0.00 0.00 2.59
105 106 7.949006 CCACTACAATAAGGGATACTACCTAGT 59.051 40.741 0.00 0.00 37.35 2.57
157 158 5.560722 TTGTGAAGACTATCTCAAACCCA 57.439 39.130 0.00 0.00 31.85 4.51
171 173 1.142688 AACCCAGTCCAGGAGGCAAT 61.143 55.000 0.00 0.00 33.74 3.56
214 216 0.465278 GGAGGCTTGCAGGAAGGATC 60.465 60.000 0.00 0.00 31.56 3.36
353 356 0.109342 ATTATTGGGAGCGAGCAGGG 59.891 55.000 0.00 0.00 0.00 4.45
426 429 0.249120 TTGATCACCAGGTACCAGCG 59.751 55.000 15.94 2.83 0.00 5.18
470 473 0.464735 CGTCAGGAGATCCGAGACCT 60.465 60.000 16.67 0.00 40.44 3.85
489 492 5.246203 AGACCTACAAGTGCATCAAGAACTA 59.754 40.000 0.00 0.00 33.87 2.24
534 537 0.823356 GAAGGCTCAAGGGCAACACA 60.823 55.000 0.00 0.00 43.56 3.72
577 581 3.539563 CGTGTTTGAATTATGAGCTTGCG 59.460 43.478 0.00 0.00 0.00 4.85
578 582 3.301642 GTGTTTGAATTATGAGCTTGCGC 59.698 43.478 0.00 0.00 0.00 6.09
688 694 2.542020 TTGTGCCGAATCTGAGTTGA 57.458 45.000 0.00 0.00 0.00 3.18
743 765 3.319198 GGAACCAGAGCCCCGACA 61.319 66.667 0.00 0.00 0.00 4.35
754 786 1.485066 AGCCCCGACATCGAAAATAGT 59.515 47.619 2.09 0.00 43.02 2.12
766 798 1.810151 GAAAATAGTGCCGACAAGCCA 59.190 47.619 0.00 0.00 0.00 4.75
773 805 2.617274 GCCGACAAGCCACCAAGAC 61.617 63.158 0.00 0.00 0.00 3.01
798 830 3.427098 GCTATTTTCCGCCTAAAAACGCT 60.427 43.478 0.00 0.00 32.42 5.07
799 831 2.691984 TTTTCCGCCTAAAAACGCTC 57.308 45.000 0.00 0.00 0.00 5.03
800 832 0.876399 TTTCCGCCTAAAAACGCTCC 59.124 50.000 0.00 0.00 0.00 4.70
804 838 3.047718 GCCTAAAAACGCTCCGGGC 62.048 63.158 0.00 2.69 37.64 6.13
832 866 1.327303 CTCGAGATGCTCTTAGGGCT 58.673 55.000 6.58 0.00 0.00 5.19
857 891 9.762381 CTAGGATGACCTAACTATCTATTTCCT 57.238 37.037 0.00 0.00 46.59 3.36
859 893 7.038658 AGGATGACCTAACTATCTATTTCCTGC 60.039 40.741 0.00 0.00 45.83 4.85
960 997 0.035176 TAGGTTTTTCGTCCCCGTGG 59.965 55.000 0.00 0.00 35.01 4.94
1414 1674 7.751047 TGTTTCAGCGTATAGTTTAGTGATC 57.249 36.000 0.00 0.00 0.00 2.92
1439 1699 2.359900 CTGAACCTATGGCCTTGTCAC 58.640 52.381 3.32 0.00 0.00 3.67
1440 1700 1.985159 TGAACCTATGGCCTTGTCACT 59.015 47.619 3.32 0.00 0.00 3.41
1441 1701 2.375174 TGAACCTATGGCCTTGTCACTT 59.625 45.455 3.32 0.00 0.00 3.16
1442 1702 2.496899 ACCTATGGCCTTGTCACTTG 57.503 50.000 3.32 0.00 0.00 3.16
1443 1703 1.705186 ACCTATGGCCTTGTCACTTGT 59.295 47.619 3.32 0.00 0.00 3.16
1444 1704 2.290323 ACCTATGGCCTTGTCACTTGTC 60.290 50.000 3.32 0.00 0.00 3.18
1445 1705 2.290260 CCTATGGCCTTGTCACTTGTCA 60.290 50.000 3.32 0.00 0.00 3.58
1516 1776 4.273235 GTGTTGGATGATTGCGATGTATGA 59.727 41.667 0.00 0.00 0.00 2.15
1569 1829 1.202794 TGTGTGCTTCCATCAGCTCAA 60.203 47.619 0.00 0.00 43.13 3.02
1596 1856 4.389374 CCAGGAGCAAAGTCTTCACTTAA 58.611 43.478 0.00 0.00 42.45 1.85
1725 1985 1.948611 GCGACTTAACCTGCCAATGGA 60.949 52.381 2.05 0.00 0.00 3.41
1773 2033 1.878953 CCATCCGGGTAATGCTGTAC 58.121 55.000 0.00 0.00 0.00 2.90
1852 2116 7.736447 ACAAAATGTTTGTTGGAGAAAAACA 57.264 28.000 0.54 3.00 45.08 2.83
1925 2287 9.911788 AGATGATATTTGTCTATCAGTTGGTTT 57.088 29.630 0.00 0.00 40.48 3.27
1946 2308 9.092876 TGGTTTTCTAAAATTAGCAAAACACAG 57.907 29.630 23.52 0.00 38.20 3.66
1950 2312 6.212955 TCTAAAATTAGCAAAACACAGGCAC 58.787 36.000 0.00 0.00 0.00 5.01
2054 2417 8.056407 AGTTTGGGAATCTTAGCTTGTTTATC 57.944 34.615 0.00 0.00 0.00 1.75
2150 2513 0.881796 GGTAAGAGTTGGCTTGCCAC 59.118 55.000 14.52 9.59 46.18 5.01
2200 2563 6.407299 CCTCATTTGGCCAACTATTTAGCAAT 60.407 38.462 20.35 1.33 0.00 3.56
2286 2649 1.949525 CCAAGATTTGATAGGCACCCG 59.050 52.381 0.00 0.00 0.00 5.28
2322 2690 2.236489 AGTATGGGCAGCAAACCAAT 57.764 45.000 0.00 0.00 40.73 3.16
2402 2779 6.014156 CCCCTTGTGGTGATTTTTATGGTTAA 60.014 38.462 0.00 0.00 0.00 2.01
2598 2976 8.362639 GGATGCATATCTTTCATGGTTATTGTT 58.637 33.333 0.00 0.00 33.68 2.83
2740 3120 2.098607 CCATATTGCTGCACTGGTTCAG 59.901 50.000 0.00 0.00 37.52 3.02
2898 3367 2.165167 CACCTGGCATGCTTATATGGG 58.835 52.381 18.92 11.20 0.00 4.00
3176 3661 3.119316 ACAGGCTTCACTGAGATAGTTCG 60.119 47.826 0.00 0.00 40.97 3.95
3288 3773 2.036346 TGACCACTCGATCATATGCCAG 59.964 50.000 0.00 0.00 0.00 4.85
3405 3890 1.238439 CATGGACACCGTCAAGCTTT 58.762 50.000 0.00 0.00 33.68 3.51
3425 3910 4.233635 CTCGAAGCTGGCGCATGC 62.234 66.667 10.83 13.16 39.10 4.06
3441 3926 2.423373 GCATGCCCCAAGAAGGAGAATA 60.423 50.000 6.36 0.00 41.22 1.75
3491 3976 2.033049 CGATCAAGATACCGAAGTCCGT 59.967 50.000 0.00 0.00 36.31 4.69
3534 4019 2.029020 GTCGAGGCCAGCATACATATGA 60.029 50.000 10.38 0.00 35.75 2.15
3543 4028 4.683320 CCAGCATACATATGACGAACTGAG 59.317 45.833 10.38 1.92 35.75 3.35
3598 4086 1.632409 AGTCATGATGAGTGGGCAGTT 59.368 47.619 1.21 0.00 0.00 3.16
3705 4194 3.027412 TGGAGTTATCTGCAGAGAGGAC 58.973 50.000 22.96 13.46 37.12 3.85
3706 4195 3.027412 GGAGTTATCTGCAGAGAGGACA 58.973 50.000 22.96 0.00 32.20 4.02
3707 4196 3.640967 GGAGTTATCTGCAGAGAGGACAT 59.359 47.826 22.96 5.74 32.20 3.06
3777 4271 3.406764 AGGCACAATCAGTTGAACTCTC 58.593 45.455 0.00 0.00 38.71 3.20
3778 4272 3.141398 GGCACAATCAGTTGAACTCTCA 58.859 45.455 0.00 0.00 38.71 3.27
3779 4273 3.755378 GGCACAATCAGTTGAACTCTCAT 59.245 43.478 0.00 0.00 38.71 2.90
3780 4274 4.217118 GGCACAATCAGTTGAACTCTCATT 59.783 41.667 0.00 0.00 38.71 2.57
3781 4275 5.412594 GGCACAATCAGTTGAACTCTCATTA 59.587 40.000 0.00 0.00 38.71 1.90
3828 4325 5.533154 TCTTACCCTTGCGAGAATTTTGAAA 59.467 36.000 1.22 0.00 0.00 2.69
3837 4334 7.176285 TGCGAGAATTTTGAAAAAGGAAATG 57.824 32.000 0.00 0.00 0.00 2.32
3878 4375 6.092807 CCTGAGACTGAATTGCTTAAGTTACC 59.907 42.308 4.02 0.00 0.00 2.85
3881 4378 4.648651 ACTGAATTGCTTAAGTTACCCGT 58.351 39.130 4.02 0.00 0.00 5.28
3965 4462 5.344743 TCTTATGTGTTTGGTGGCAAAAA 57.655 34.783 0.00 0.00 0.00 1.94
4012 4509 9.916360 AAAAATACTCCCTCCGTAAAGAAATAT 57.084 29.630 0.00 0.00 0.00 1.28
4016 4513 7.909485 ACTCCCTCCGTAAAGAAATATAAGA 57.091 36.000 0.00 0.00 0.00 2.10
4017 4514 7.724287 ACTCCCTCCGTAAAGAAATATAAGAC 58.276 38.462 0.00 0.00 0.00 3.01
4019 4516 7.949434 TCCCTCCGTAAAGAAATATAAGACTC 58.051 38.462 0.00 0.00 0.00 3.36
4020 4517 7.015001 TCCCTCCGTAAAGAAATATAAGACTCC 59.985 40.741 0.00 0.00 0.00 3.85
4021 4518 7.153315 CCTCCGTAAAGAAATATAAGACTCCC 58.847 42.308 0.00 0.00 0.00 4.30
4022 4519 7.015389 CCTCCGTAAAGAAATATAAGACTCCCT 59.985 40.741 0.00 0.00 0.00 4.20
4024 4521 8.419442 TCCGTAAAGAAATATAAGACTCCCTTC 58.581 37.037 0.00 0.00 36.34 3.46
4027 4524 9.247126 GTAAAGAAATATAAGACTCCCTTCGTC 57.753 37.037 0.00 0.00 36.34 4.20
4028 4525 7.663043 AAGAAATATAAGACTCCCTTCGTCT 57.337 36.000 0.00 0.00 43.20 4.18
4029 4526 7.279750 AGAAATATAAGACTCCCTTCGTCTC 57.720 40.000 0.00 0.00 40.65 3.36
4030 4527 6.834451 AGAAATATAAGACTCCCTTCGTCTCA 59.166 38.462 0.00 0.00 40.65 3.27
4031 4528 7.507616 AGAAATATAAGACTCCCTTCGTCTCAT 59.492 37.037 0.00 0.00 40.65 2.90
4032 4529 8.707796 AAATATAAGACTCCCTTCGTCTCATA 57.292 34.615 0.00 0.00 40.65 2.15
4033 4530 8.707796 AATATAAGACTCCCTTCGTCTCATAA 57.292 34.615 0.00 0.00 40.65 1.90
4035 4532 9.976776 ATATAAGACTCCCTTCGTCTCATAATA 57.023 33.333 0.00 0.00 40.65 0.98
4036 4533 8.887264 ATAAGACTCCCTTCGTCTCATAATAT 57.113 34.615 0.00 0.00 40.65 1.28
4039 4536 8.343168 AGACTCCCTTCGTCTCATAATATAAG 57.657 38.462 0.00 0.00 37.13 1.73
4040 4537 8.164733 AGACTCCCTTCGTCTCATAATATAAGA 58.835 37.037 0.00 0.00 37.13 2.10
4041 4538 8.707796 ACTCCCTTCGTCTCATAATATAAGAA 57.292 34.615 0.00 0.00 0.00 2.52
4092 4589 5.806366 AACGTTCTTATATTTTGGGACGG 57.194 39.130 0.00 0.00 0.00 4.79
4093 4590 5.088680 ACGTTCTTATATTTTGGGACGGA 57.911 39.130 0.00 0.00 0.00 4.69
4094 4591 5.114081 ACGTTCTTATATTTTGGGACGGAG 58.886 41.667 0.00 0.00 0.00 4.63
4095 4592 4.510340 CGTTCTTATATTTTGGGACGGAGG 59.490 45.833 0.00 0.00 0.00 4.30
4096 4593 4.699925 TCTTATATTTTGGGACGGAGGG 57.300 45.455 0.00 0.00 0.00 4.30
4097 4594 4.300345 TCTTATATTTTGGGACGGAGGGA 58.700 43.478 0.00 0.00 0.00 4.20
4098 4595 4.347000 TCTTATATTTTGGGACGGAGGGAG 59.653 45.833 0.00 0.00 0.00 4.30
4099 4596 1.961133 TATTTTGGGACGGAGGGAGT 58.039 50.000 0.00 0.00 0.00 3.85
4100 4597 1.961133 ATTTTGGGACGGAGGGAGTA 58.039 50.000 0.00 0.00 0.00 2.59
4101 4598 1.272807 TTTTGGGACGGAGGGAGTAG 58.727 55.000 0.00 0.00 0.00 2.57
4102 4599 0.410663 TTTGGGACGGAGGGAGTAGA 59.589 55.000 0.00 0.00 0.00 2.59
4103 4600 0.635009 TTGGGACGGAGGGAGTAGAT 59.365 55.000 0.00 0.00 0.00 1.98
4104 4601 0.106167 TGGGACGGAGGGAGTAGATG 60.106 60.000 0.00 0.00 0.00 2.90
4105 4602 0.106116 GGGACGGAGGGAGTAGATGT 60.106 60.000 0.00 0.00 0.00 3.06
4106 4603 1.320507 GGACGGAGGGAGTAGATGTC 58.679 60.000 0.00 0.00 0.00 3.06
4107 4604 1.409802 GGACGGAGGGAGTAGATGTCA 60.410 57.143 0.00 0.00 0.00 3.58
4108 4605 1.950909 GACGGAGGGAGTAGATGTCAG 59.049 57.143 0.00 0.00 0.00 3.51
4109 4606 1.564818 ACGGAGGGAGTAGATGTCAGA 59.435 52.381 0.00 0.00 0.00 3.27
4110 4607 2.226330 CGGAGGGAGTAGATGTCAGAG 58.774 57.143 0.00 0.00 0.00 3.35
4111 4608 2.158740 CGGAGGGAGTAGATGTCAGAGA 60.159 54.545 0.00 0.00 0.00 3.10
4112 4609 3.486383 GGAGGGAGTAGATGTCAGAGAG 58.514 54.545 0.00 0.00 0.00 3.20
4113 4610 3.486383 GAGGGAGTAGATGTCAGAGAGG 58.514 54.545 0.00 0.00 0.00 3.69
4137 4635 6.017400 ACATTGGAAAGAGCAGTAATGTTG 57.983 37.500 0.00 0.00 35.83 3.33
4140 4638 6.463995 TTGGAAAGAGCAGTAATGTTGTTT 57.536 33.333 1.92 1.92 0.00 2.83
4181 4679 5.867903 TGGTTCAATGTTTTCCATGTCTT 57.132 34.783 0.00 0.00 32.82 3.01
4238 4736 4.836125 TGTTGAAATCTTGCTGGAACTC 57.164 40.909 0.00 0.00 0.00 3.01
4245 4743 7.394016 TGAAATCTTGCTGGAACTCTGTATAA 58.606 34.615 0.00 0.00 0.00 0.98
4249 4747 7.615582 TCTTGCTGGAACTCTGTATAAAATG 57.384 36.000 0.00 0.00 0.00 2.32
4251 4749 5.252547 TGCTGGAACTCTGTATAAAATGCA 58.747 37.500 0.00 0.00 0.00 3.96
4333 4831 8.910351 AAGTAATGATCTAAATGTCTTAGGCC 57.090 34.615 0.00 0.00 0.00 5.19
4334 4832 7.454225 AGTAATGATCTAAATGTCTTAGGCCC 58.546 38.462 0.00 0.00 0.00 5.80
4335 4833 6.521527 AATGATCTAAATGTCTTAGGCCCT 57.478 37.500 0.00 0.00 0.00 5.19
4336 4834 5.552870 TGATCTAAATGTCTTAGGCCCTC 57.447 43.478 0.00 0.00 0.00 4.30
4337 4835 4.968719 TGATCTAAATGTCTTAGGCCCTCA 59.031 41.667 0.00 0.00 0.00 3.86
4338 4836 5.608437 TGATCTAAATGTCTTAGGCCCTCAT 59.392 40.000 0.00 0.00 0.00 2.90
4339 4837 5.552870 TCTAAATGTCTTAGGCCCTCATC 57.447 43.478 0.00 0.00 0.00 2.92
4340 4838 4.968719 TCTAAATGTCTTAGGCCCTCATCA 59.031 41.667 0.00 0.00 0.00 3.07
4341 4839 4.591321 AAATGTCTTAGGCCCTCATCAA 57.409 40.909 0.00 0.00 0.00 2.57
4342 4840 4.591321 AATGTCTTAGGCCCTCATCAAA 57.409 40.909 0.00 0.00 0.00 2.69
4343 4841 4.591321 ATGTCTTAGGCCCTCATCAAAA 57.409 40.909 0.00 0.00 0.00 2.44
4344 4842 3.955471 TGTCTTAGGCCCTCATCAAAAG 58.045 45.455 0.00 0.00 0.00 2.27
4345 4843 2.685388 GTCTTAGGCCCTCATCAAAAGC 59.315 50.000 0.00 0.00 0.00 3.51
4346 4844 2.027385 CTTAGGCCCTCATCAAAAGCC 58.973 52.381 0.00 0.00 44.20 4.35
4347 4845 0.998928 TAGGCCCTCATCAAAAGCCA 59.001 50.000 0.00 0.00 46.35 4.75
4348 4846 0.337428 AGGCCCTCATCAAAAGCCAT 59.663 50.000 0.00 0.00 46.35 4.40
4349 4847 1.570501 AGGCCCTCATCAAAAGCCATA 59.429 47.619 0.00 0.00 46.35 2.74
4350 4848 2.024080 AGGCCCTCATCAAAAGCCATAA 60.024 45.455 0.00 0.00 46.35 1.90
4351 4849 2.765699 GGCCCTCATCAAAAGCCATAAA 59.234 45.455 0.00 0.00 43.32 1.40
4352 4850 3.197549 GGCCCTCATCAAAAGCCATAAAA 59.802 43.478 0.00 0.00 43.32 1.52
4353 4851 4.436332 GCCCTCATCAAAAGCCATAAAAG 58.564 43.478 0.00 0.00 0.00 2.27
4354 4852 4.436332 CCCTCATCAAAAGCCATAAAAGC 58.564 43.478 0.00 0.00 0.00 3.51
4355 4853 4.436332 CCTCATCAAAAGCCATAAAAGCC 58.564 43.478 0.00 0.00 0.00 4.35
4356 4854 4.436332 CTCATCAAAAGCCATAAAAGCCC 58.564 43.478 0.00 0.00 0.00 5.19
4357 4855 3.197549 TCATCAAAAGCCATAAAAGCCCC 59.802 43.478 0.00 0.00 0.00 5.80
4358 4856 2.614259 TCAAAAGCCATAAAAGCCCCA 58.386 42.857 0.00 0.00 0.00 4.96
4359 4857 2.975489 TCAAAAGCCATAAAAGCCCCAA 59.025 40.909 0.00 0.00 0.00 4.12
4360 4858 3.392616 TCAAAAGCCATAAAAGCCCCAAA 59.607 39.130 0.00 0.00 0.00 3.28
4361 4859 4.140536 CAAAAGCCATAAAAGCCCCAAAA 58.859 39.130 0.00 0.00 0.00 2.44
4362 4860 3.701205 AAGCCATAAAAGCCCCAAAAG 57.299 42.857 0.00 0.00 0.00 2.27
4363 4861 2.901291 AGCCATAAAAGCCCCAAAAGA 58.099 42.857 0.00 0.00 0.00 2.52
4364 4862 3.247162 AGCCATAAAAGCCCCAAAAGAA 58.753 40.909 0.00 0.00 0.00 2.52
4365 4863 3.845992 AGCCATAAAAGCCCCAAAAGAAT 59.154 39.130 0.00 0.00 0.00 2.40
4366 4864 4.080919 AGCCATAAAAGCCCCAAAAGAATC 60.081 41.667 0.00 0.00 0.00 2.52
4367 4865 4.080919 GCCATAAAAGCCCCAAAAGAATCT 60.081 41.667 0.00 0.00 0.00 2.40
4368 4866 5.128663 GCCATAAAAGCCCCAAAAGAATCTA 59.871 40.000 0.00 0.00 0.00 1.98
4369 4867 6.183361 GCCATAAAAGCCCCAAAAGAATCTAT 60.183 38.462 0.00 0.00 0.00 1.98
4370 4868 7.635750 GCCATAAAAGCCCCAAAAGAATCTATT 60.636 37.037 0.00 0.00 0.00 1.73
4371 4869 8.267183 CCATAAAAGCCCCAAAAGAATCTATTT 58.733 33.333 0.00 0.00 0.00 1.40
4374 4872 7.423844 AAAGCCCCAAAAGAATCTATTTAGG 57.576 36.000 0.00 0.00 0.00 2.69
4375 4873 6.341408 AGCCCCAAAAGAATCTATTTAGGA 57.659 37.500 4.83 0.00 0.00 2.94
4376 4874 6.368805 AGCCCCAAAAGAATCTATTTAGGAG 58.631 40.000 4.83 0.00 0.00 3.69
4377 4875 5.010112 GCCCCAAAAGAATCTATTTAGGAGC 59.990 44.000 4.83 0.00 0.00 4.70
4378 4876 6.368805 CCCCAAAAGAATCTATTTAGGAGCT 58.631 40.000 0.00 0.00 0.00 4.09
4379 4877 6.836007 CCCCAAAAGAATCTATTTAGGAGCTT 59.164 38.462 0.00 0.00 0.00 3.74
4380 4878 7.343057 CCCCAAAAGAATCTATTTAGGAGCTTT 59.657 37.037 0.00 0.00 0.00 3.51
4381 4879 8.753133 CCCAAAAGAATCTATTTAGGAGCTTTT 58.247 33.333 0.00 0.00 34.60 2.27
4394 4892 7.833285 TTAGGAGCTTTTATGTCTTTTTGGT 57.167 32.000 0.00 0.00 0.00 3.67
4395 4893 6.332735 AGGAGCTTTTATGTCTTTTTGGTC 57.667 37.500 0.00 0.00 0.00 4.02
4396 4894 5.833131 AGGAGCTTTTATGTCTTTTTGGTCA 59.167 36.000 0.00 0.00 0.00 4.02
4397 4895 6.323739 AGGAGCTTTTATGTCTTTTTGGTCAA 59.676 34.615 0.00 0.00 0.00 3.18
4398 4896 6.983890 GGAGCTTTTATGTCTTTTTGGTCAAA 59.016 34.615 0.00 0.00 0.00 2.69
4399 4897 7.494298 GGAGCTTTTATGTCTTTTTGGTCAAAA 59.506 33.333 4.92 4.92 38.40 2.44
4400 4898 8.962884 AGCTTTTATGTCTTTTTGGTCAAAAT 57.037 26.923 9.32 0.00 39.69 1.82
4401 4899 8.829612 AGCTTTTATGTCTTTTTGGTCAAAATG 58.170 29.630 9.32 11.29 39.69 2.32
4402 4900 8.825745 GCTTTTATGTCTTTTTGGTCAAAATGA 58.174 29.630 15.92 15.92 39.69 2.57
4407 4905 7.608308 TGTCTTTTTGGTCAAAATGAAAAGG 57.392 32.000 19.36 0.00 42.29 3.11
4408 4906 6.093357 TGTCTTTTTGGTCAAAATGAAAAGGC 59.907 34.615 19.36 11.82 42.29 4.35
4409 4907 5.588246 TCTTTTTGGTCAAAATGAAAAGGCC 59.412 36.000 16.93 0.00 39.73 5.19
4410 4908 2.810439 TGGTCAAAATGAAAAGGCCG 57.190 45.000 0.00 0.00 0.00 6.13
4411 4909 1.270041 TGGTCAAAATGAAAAGGCCGC 60.270 47.619 0.00 0.00 0.00 6.53
4412 4910 1.270041 GGTCAAAATGAAAAGGCCGCA 60.270 47.619 0.00 0.00 0.00 5.69
4413 4911 2.478831 GTCAAAATGAAAAGGCCGCAA 58.521 42.857 0.00 0.00 0.00 4.85
4414 4912 2.869192 GTCAAAATGAAAAGGCCGCAAA 59.131 40.909 0.00 0.00 0.00 3.68
4415 4913 3.311048 GTCAAAATGAAAAGGCCGCAAAA 59.689 39.130 0.00 0.00 0.00 2.44
4416 4914 3.559242 TCAAAATGAAAAGGCCGCAAAAG 59.441 39.130 0.00 0.00 0.00 2.27
4417 4915 1.511850 AATGAAAAGGCCGCAAAAGC 58.488 45.000 0.00 0.00 0.00 3.51
4418 4916 0.392336 ATGAAAAGGCCGCAAAAGCA 59.608 45.000 0.00 0.00 0.00 3.91
4419 4917 0.176680 TGAAAAGGCCGCAAAAGCAA 59.823 45.000 0.00 0.00 0.00 3.91
4420 4918 1.294857 GAAAAGGCCGCAAAAGCAAA 58.705 45.000 0.00 0.00 0.00 3.68
4421 4919 1.668237 GAAAAGGCCGCAAAAGCAAAA 59.332 42.857 0.00 0.00 0.00 2.44
4422 4920 1.298602 AAAGGCCGCAAAAGCAAAAG 58.701 45.000 0.00 0.00 0.00 2.27
4423 4921 1.159713 AAGGCCGCAAAAGCAAAAGC 61.160 50.000 0.00 0.00 0.00 3.51
4424 4922 1.886777 GGCCGCAAAAGCAAAAGCA 60.887 52.632 0.00 0.00 0.00 3.91
4425 4923 1.566077 GCCGCAAAAGCAAAAGCAG 59.434 52.632 0.00 0.00 0.00 4.24
4426 4924 0.875474 GCCGCAAAAGCAAAAGCAGA 60.875 50.000 0.00 0.00 0.00 4.26
4427 4925 1.569708 CCGCAAAAGCAAAAGCAGAA 58.430 45.000 0.00 0.00 0.00 3.02
4428 4926 1.523934 CCGCAAAAGCAAAAGCAGAAG 59.476 47.619 0.00 0.00 0.00 2.85
4429 4927 1.071041 CGCAAAAGCAAAAGCAGAAGC 60.071 47.619 0.00 0.00 42.56 3.86
4430 4928 1.262417 GCAAAAGCAAAAGCAGAAGCC 59.738 47.619 0.00 0.00 43.56 4.35
4431 4929 1.869132 CAAAAGCAAAAGCAGAAGCCC 59.131 47.619 0.00 0.00 43.56 5.19
4432 4930 1.122227 AAAGCAAAAGCAGAAGCCCA 58.878 45.000 0.00 0.00 43.56 5.36
4433 4931 1.122227 AAGCAAAAGCAGAAGCCCAA 58.878 45.000 0.00 0.00 43.56 4.12
4434 4932 1.122227 AGCAAAAGCAGAAGCCCAAA 58.878 45.000 0.00 0.00 43.56 3.28
4435 4933 1.202568 AGCAAAAGCAGAAGCCCAAAC 60.203 47.619 0.00 0.00 43.56 2.93
4436 4934 1.473080 GCAAAAGCAGAAGCCCAAACA 60.473 47.619 0.00 0.00 43.56 2.83
4437 4935 2.903798 CAAAAGCAGAAGCCCAAACAA 58.096 42.857 0.00 0.00 43.56 2.83
4438 4936 3.269178 CAAAAGCAGAAGCCCAAACAAA 58.731 40.909 0.00 0.00 43.56 2.83
4439 4937 2.602257 AAGCAGAAGCCCAAACAAAC 57.398 45.000 0.00 0.00 43.56 2.93
4440 4938 1.484038 AGCAGAAGCCCAAACAAACA 58.516 45.000 0.00 0.00 43.56 2.83
4441 4939 1.410153 AGCAGAAGCCCAAACAAACAG 59.590 47.619 0.00 0.00 43.56 3.16
4442 4940 1.538849 GCAGAAGCCCAAACAAACAGG 60.539 52.381 0.00 0.00 33.58 4.00
4443 4941 1.069049 CAGAAGCCCAAACAAACAGGG 59.931 52.381 0.00 0.00 45.68 4.45
4446 4944 4.293610 CCCAAACAAACAGGGCCT 57.706 55.556 0.00 0.00 35.44 5.19
4453 4951 3.306472 AACAAACAGGGCCTTACAGAA 57.694 42.857 1.32 0.00 0.00 3.02
4454 4952 3.306472 ACAAACAGGGCCTTACAGAAA 57.694 42.857 1.32 0.00 0.00 2.52
4458 4956 2.339769 ACAGGGCCTTACAGAAAGAGT 58.660 47.619 1.32 0.00 37.38 3.24
4460 4958 3.261137 ACAGGGCCTTACAGAAAGAGTAC 59.739 47.826 1.32 0.00 37.38 2.73
4480 4978 3.167485 ACATGATTGTGGTGGCATTCTT 58.833 40.909 0.00 0.00 33.85 2.52
4508 5006 4.015872 TCAGGAATGAAGTAACCACACC 57.984 45.455 0.00 0.00 0.00 4.16
4509 5007 3.392947 TCAGGAATGAAGTAACCACACCA 59.607 43.478 0.00 0.00 0.00 4.17
4544 5045 5.710513 TGCTATCAAACAAAATGTCAGCT 57.289 34.783 0.00 0.00 31.52 4.24
4545 5046 6.088016 TGCTATCAAACAAAATGTCAGCTT 57.912 33.333 0.00 0.00 31.52 3.74
4547 5048 5.346822 GCTATCAAACAAAATGTCAGCTTGG 59.653 40.000 0.00 0.00 0.00 3.61
4548 5049 3.456280 TCAAACAAAATGTCAGCTTGGC 58.544 40.909 0.00 0.00 0.00 4.52
4565 5084 3.736483 CATGGATGCTACCACGCC 58.264 61.111 4.71 0.00 43.03 5.68
4583 5108 2.555325 CGCCAATAGGTATGTACTCGGA 59.445 50.000 0.00 0.00 37.19 4.55
4595 5120 4.217836 TGTACTCGGACATGTCTAGAGT 57.782 45.455 35.72 35.72 43.71 3.24
4600 5125 1.745653 CGGACATGTCTAGAGTCAGCA 59.254 52.381 24.50 0.00 34.04 4.41
4631 5156 0.402121 AGAACAAGGGTGAGAAGGCC 59.598 55.000 0.00 0.00 0.00 5.19
4641 5166 0.817634 TGAGAAGGCCACCAAACACG 60.818 55.000 5.01 0.00 0.00 4.49
4669 5194 2.089980 GTTCACTAGGCGTGGAGTCTA 58.910 52.381 0.00 0.00 43.94 2.59
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.068748 CATTTGAGCACTGCAGGACAC 60.069 52.381 19.93 8.62 0.00 3.67
27 28 2.669364 CATGACCTTCAACAAGCTTGC 58.331 47.619 26.27 7.87 0.00 4.01
64 65 4.015406 TGGCGCCCATTGACGTCT 62.015 61.111 26.77 0.00 34.36 4.18
67 68 2.125310 TAGTGGCGCCCATTGACG 60.125 61.111 26.77 0.00 35.28 4.35
157 158 1.840635 GGAGTTATTGCCTCCTGGACT 59.159 52.381 0.00 0.00 44.29 3.85
171 173 6.295123 CCTGACACTTAGCAAAGTAGGAGTTA 60.295 42.308 1.04 0.00 44.28 2.24
214 216 2.436646 ACCAAATGCCCGCTCGAG 60.437 61.111 8.45 8.45 0.00 4.04
273 275 5.118990 CACATCTGATATTTCGACCAGGTT 58.881 41.667 0.00 0.00 0.00 3.50
353 356 1.279840 GTGTCAAACACTGGCTCGC 59.720 57.895 3.03 0.00 45.27 5.03
441 444 4.695928 CGGATCTCCTGACGTATATTGAGA 59.304 45.833 0.00 0.00 33.78 3.27
470 473 6.018262 GTGTTGTAGTTCTTGATGCACTTGTA 60.018 38.462 0.00 0.00 0.00 2.41
489 492 0.320771 GCTCCACCAGATCGTGTTGT 60.321 55.000 0.89 0.00 31.47 3.32
534 537 9.959749 AACACGAATTAAAACACATCAAACTAT 57.040 25.926 0.00 0.00 0.00 2.12
555 559 3.539563 CGCAAGCTCATAATTCAAACACG 59.460 43.478 0.00 0.00 0.00 4.49
637 643 6.454795 ACACTTCGGCACAAATTCAATAAAT 58.545 32.000 0.00 0.00 0.00 1.40
708 720 2.672996 CAGCCGTCCCCCAAGTTG 60.673 66.667 0.00 0.00 0.00 3.16
740 762 2.927477 TGTCGGCACTATTTTCGATGTC 59.073 45.455 0.00 0.00 34.13 3.06
741 763 2.967362 TGTCGGCACTATTTTCGATGT 58.033 42.857 0.00 0.00 34.13 3.06
743 765 2.351726 GCTTGTCGGCACTATTTTCGAT 59.648 45.455 0.00 0.00 34.13 3.59
766 798 1.084289 GGAAAATAGCGCGTCTTGGT 58.916 50.000 8.43 0.00 0.00 3.67
773 805 0.653636 TTTAGGCGGAAAATAGCGCG 59.346 50.000 0.00 0.00 0.00 6.86
832 866 9.535170 CAGGAAATAGATAGTTAGGTCATCCTA 57.465 37.037 0.00 0.00 44.58 2.94
857 891 5.833406 ACGGAACAAAATGATCATATGCA 57.167 34.783 9.04 0.00 0.00 3.96
868 904 5.692204 CGCTCTAGATCATACGGAACAAAAT 59.308 40.000 0.00 0.00 0.00 1.82
873 909 3.900388 ACGCTCTAGATCATACGGAAC 57.100 47.619 0.00 0.00 0.00 3.62
960 997 4.870158 GTCGAGACTTGTGTCGAGAGCC 62.870 59.091 20.41 7.79 45.41 4.70
1439 1699 1.079127 AACCCGATCCGCTGACAAG 60.079 57.895 0.00 0.00 0.00 3.16
1440 1700 1.375396 CAACCCGATCCGCTGACAA 60.375 57.895 0.00 0.00 0.00 3.18
1441 1701 1.252215 TACAACCCGATCCGCTGACA 61.252 55.000 0.00 0.00 0.00 3.58
1442 1702 0.104304 ATACAACCCGATCCGCTGAC 59.896 55.000 0.00 0.00 0.00 3.51
1443 1703 0.828022 AATACAACCCGATCCGCTGA 59.172 50.000 0.00 0.00 0.00 4.26
1444 1704 1.663695 AAATACAACCCGATCCGCTG 58.336 50.000 0.00 0.00 0.00 5.18
1445 1705 2.093128 AGAAAATACAACCCGATCCGCT 60.093 45.455 0.00 0.00 0.00 5.52
1516 1776 1.021968 GAAGCGACCCAAACACAACT 58.978 50.000 0.00 0.00 0.00 3.16
1569 1829 1.366319 AGACTTTGCTCCTGGGTCAT 58.634 50.000 0.00 0.00 0.00 3.06
1596 1856 2.682594 TGCATCCTAGTGCTACTGGAT 58.317 47.619 6.85 11.05 45.27 3.41
1925 2287 6.699642 GTGCCTGTGTTTTGCTAATTTTAGAA 59.300 34.615 1.52 0.00 32.47 2.10
1926 2288 6.040391 AGTGCCTGTGTTTTGCTAATTTTAGA 59.960 34.615 1.52 0.00 32.47 2.10
1946 2308 4.271696 AGGATGGCTTTTAAAAAGTGCC 57.728 40.909 18.24 18.24 38.75 5.01
2054 2417 2.858344 GCAAGCATAGCAAGCAATTCAG 59.142 45.455 0.00 0.00 32.47 3.02
2200 2563 4.162320 GTCCACCATTCCTCTCACAGATTA 59.838 45.833 0.00 0.00 0.00 1.75
2322 2690 2.278245 ACATTCATGGGGAAGGTCTGA 58.722 47.619 0.00 0.00 46.84 3.27
2520 2898 7.063426 GCAATAGCATTTCCCTTGTTTAAGTTC 59.937 37.037 0.00 0.00 41.58 3.01
2598 2976 6.227298 AGACAAACTTGAAGAGAGAACTCA 57.773 37.500 0.00 0.00 44.79 3.41
2689 3068 5.181811 CACACTGAGATGGTTAGCAATCAAA 59.818 40.000 0.00 0.00 0.00 2.69
2690 3069 4.696877 CACACTGAGATGGTTAGCAATCAA 59.303 41.667 0.00 0.00 0.00 2.57
2740 3120 4.681483 GGCATGTTTTAGCAACAAGACTTC 59.319 41.667 0.00 0.00 33.42 3.01
2898 3367 1.709147 CCTGCACGCAAGGTAGATGC 61.709 60.000 0.00 0.00 46.39 3.91
3288 3773 1.798283 TGCTGCAAAATCAACATGGC 58.202 45.000 0.00 0.00 0.00 4.40
3405 3890 4.986645 TGCGCCAGCTTCGAGCAA 62.987 61.111 4.18 0.00 45.56 3.91
3425 3910 3.069729 CGTAGGTATTCTCCTTCTTGGGG 59.930 52.174 0.00 0.00 38.86 4.96
3491 3976 1.602323 CTTGGCGGTTAACAGGGCA 60.602 57.895 17.42 17.42 34.16 5.36
3534 4019 0.898320 CAGGTCCATCCTCAGTTCGT 59.102 55.000 0.00 0.00 46.24 3.85
3543 4028 0.976073 TTCCTCCGACAGGTCCATCC 60.976 60.000 0.00 0.00 43.95 3.51
3705 4194 2.564062 AGGGCAAATGGAGAAACACATG 59.436 45.455 0.00 0.00 0.00 3.21
3706 4195 2.893424 AGGGCAAATGGAGAAACACAT 58.107 42.857 0.00 0.00 0.00 3.21
3707 4196 2.380064 AGGGCAAATGGAGAAACACA 57.620 45.000 0.00 0.00 0.00 3.72
3828 4325 4.582656 TGTCATGGACGAAACATTTCCTTT 59.417 37.500 0.00 0.00 34.95 3.11
3837 4334 2.480419 CTCAGGTTGTCATGGACGAAAC 59.520 50.000 0.00 0.00 34.95 2.78
3878 4375 3.959975 CCACCAAACACGCCACGG 61.960 66.667 0.00 0.00 0.00 4.94
3881 4378 1.525077 GACTCCACCAAACACGCCA 60.525 57.895 0.00 0.00 0.00 5.69
3990 4487 9.597681 TCTTATATTTCTTTACGGAGGGAGTAT 57.402 33.333 0.00 0.00 0.00 2.12
3992 4489 7.564292 AGTCTTATATTTCTTTACGGAGGGAGT 59.436 37.037 0.00 0.00 0.00 3.85
3993 4490 7.953752 AGTCTTATATTTCTTTACGGAGGGAG 58.046 38.462 0.00 0.00 0.00 4.30
3995 4492 7.153315 GGAGTCTTATATTTCTTTACGGAGGG 58.847 42.308 0.00 0.00 0.00 4.30
3996 4493 7.015389 AGGGAGTCTTATATTTCTTTACGGAGG 59.985 40.741 0.00 0.00 0.00 4.30
3997 4494 7.953752 AGGGAGTCTTATATTTCTTTACGGAG 58.046 38.462 0.00 0.00 0.00 4.63
3999 4496 7.381678 CGAAGGGAGTCTTATATTTCTTTACGG 59.618 40.741 0.00 0.00 35.50 4.02
4000 4497 7.919621 ACGAAGGGAGTCTTATATTTCTTTACG 59.080 37.037 0.00 0.00 35.50 3.18
4001 4498 9.247126 GACGAAGGGAGTCTTATATTTCTTTAC 57.753 37.037 0.00 0.00 35.50 2.01
4002 4499 9.198475 AGACGAAGGGAGTCTTATATTTCTTTA 57.802 33.333 0.00 0.00 45.74 1.85
4003 4500 8.080363 AGACGAAGGGAGTCTTATATTTCTTT 57.920 34.615 0.00 0.00 45.74 2.52
4015 4512 8.338072 TCTTATATTATGAGACGAAGGGAGTC 57.662 38.462 0.00 0.00 38.81 3.36
4016 4513 8.707796 TTCTTATATTATGAGACGAAGGGAGT 57.292 34.615 0.00 0.00 0.00 3.85
4067 4564 7.040548 TCCGTCCCAAAATATAAGAACGTTTTT 60.041 33.333 9.22 9.22 0.00 1.94
4068 4565 6.430616 TCCGTCCCAAAATATAAGAACGTTTT 59.569 34.615 0.46 0.00 0.00 2.43
4069 4566 5.939296 TCCGTCCCAAAATATAAGAACGTTT 59.061 36.000 0.46 0.00 0.00 3.60
4070 4567 5.490159 TCCGTCCCAAAATATAAGAACGTT 58.510 37.500 0.00 0.00 0.00 3.99
4071 4568 5.088680 TCCGTCCCAAAATATAAGAACGT 57.911 39.130 0.00 0.00 0.00 3.99
4072 4569 4.510340 CCTCCGTCCCAAAATATAAGAACG 59.490 45.833 0.00 0.00 0.00 3.95
4073 4570 4.820173 CCCTCCGTCCCAAAATATAAGAAC 59.180 45.833 0.00 0.00 0.00 3.01
4074 4571 4.722781 TCCCTCCGTCCCAAAATATAAGAA 59.277 41.667 0.00 0.00 0.00 2.52
4077 4574 4.042174 ACTCCCTCCGTCCCAAAATATAA 58.958 43.478 0.00 0.00 0.00 0.98
4079 4576 2.488836 ACTCCCTCCGTCCCAAAATAT 58.511 47.619 0.00 0.00 0.00 1.28
4080 4577 1.961133 ACTCCCTCCGTCCCAAAATA 58.039 50.000 0.00 0.00 0.00 1.40
4083 4580 0.410663 TCTACTCCCTCCGTCCCAAA 59.589 55.000 0.00 0.00 0.00 3.28
4085 4582 0.106167 CATCTACTCCCTCCGTCCCA 60.106 60.000 0.00 0.00 0.00 4.37
4086 4583 0.106116 ACATCTACTCCCTCCGTCCC 60.106 60.000 0.00 0.00 0.00 4.46
4088 4585 1.950909 CTGACATCTACTCCCTCCGTC 59.049 57.143 0.00 0.00 0.00 4.79
4090 4587 2.158740 TCTCTGACATCTACTCCCTCCG 60.159 54.545 0.00 0.00 0.00 4.63
4091 4588 3.486383 CTCTCTGACATCTACTCCCTCC 58.514 54.545 0.00 0.00 0.00 4.30
4092 4589 3.137544 TCCTCTCTGACATCTACTCCCTC 59.862 52.174 0.00 0.00 0.00 4.30
4093 4590 3.117663 GTCCTCTCTGACATCTACTCCCT 60.118 52.174 0.00 0.00 35.29 4.20
4094 4591 3.219281 GTCCTCTCTGACATCTACTCCC 58.781 54.545 0.00 0.00 35.29 4.30
4095 4592 3.892284 TGTCCTCTCTGACATCTACTCC 58.108 50.000 0.00 0.00 40.22 3.85
4104 4601 4.502962 CTCTTTCCAATGTCCTCTCTGAC 58.497 47.826 0.00 0.00 35.77 3.51
4105 4602 3.055530 GCTCTTTCCAATGTCCTCTCTGA 60.056 47.826 0.00 0.00 0.00 3.27
4106 4603 3.269178 GCTCTTTCCAATGTCCTCTCTG 58.731 50.000 0.00 0.00 0.00 3.35
4107 4604 2.909006 TGCTCTTTCCAATGTCCTCTCT 59.091 45.455 0.00 0.00 0.00 3.10
4108 4605 3.269178 CTGCTCTTTCCAATGTCCTCTC 58.731 50.000 0.00 0.00 0.00 3.20
4109 4606 2.641815 ACTGCTCTTTCCAATGTCCTCT 59.358 45.455 0.00 0.00 0.00 3.69
4110 4607 3.064900 ACTGCTCTTTCCAATGTCCTC 57.935 47.619 0.00 0.00 0.00 3.71
4111 4608 4.640771 TTACTGCTCTTTCCAATGTCCT 57.359 40.909 0.00 0.00 0.00 3.85
4112 4609 4.702131 ACATTACTGCTCTTTCCAATGTCC 59.298 41.667 0.00 0.00 32.65 4.02
4113 4610 5.886960 ACATTACTGCTCTTTCCAATGTC 57.113 39.130 0.00 0.00 32.65 3.06
4137 4635 5.691754 CCAAGTATCAAAGAACAAGGCAAAC 59.308 40.000 0.00 0.00 0.00 2.93
4140 4638 4.469657 ACCAAGTATCAAAGAACAAGGCA 58.530 39.130 0.00 0.00 0.00 4.75
4318 4816 5.296151 TGATGAGGGCCTAAGACATTTAG 57.704 43.478 5.73 0.00 0.00 1.85
4319 4817 5.708736 TTGATGAGGGCCTAAGACATTTA 57.291 39.130 5.73 0.00 0.00 1.40
4323 4821 3.873801 GCTTTTGATGAGGGCCTAAGACA 60.874 47.826 5.73 0.00 0.00 3.41
4324 4822 2.685388 GCTTTTGATGAGGGCCTAAGAC 59.315 50.000 5.73 0.00 0.00 3.01
4325 4823 2.357154 GGCTTTTGATGAGGGCCTAAGA 60.357 50.000 5.73 0.00 39.68 2.10
4326 4824 2.027385 GGCTTTTGATGAGGGCCTAAG 58.973 52.381 5.73 6.57 39.68 2.18
4327 4825 1.357420 TGGCTTTTGATGAGGGCCTAA 59.643 47.619 5.73 0.00 42.84 2.69
4329 4827 0.337428 ATGGCTTTTGATGAGGGCCT 59.663 50.000 5.25 5.25 42.84 5.19
4330 4828 2.071778 TATGGCTTTTGATGAGGGCC 57.928 50.000 0.00 0.00 42.73 5.80
4331 4829 4.436332 CTTTTATGGCTTTTGATGAGGGC 58.564 43.478 0.00 0.00 0.00 5.19
4332 4830 4.436332 GCTTTTATGGCTTTTGATGAGGG 58.564 43.478 0.00 0.00 0.00 4.30
4333 4831 4.436332 GGCTTTTATGGCTTTTGATGAGG 58.564 43.478 0.00 0.00 0.00 3.86
4334 4832 4.436332 GGGCTTTTATGGCTTTTGATGAG 58.564 43.478 0.00 0.00 0.00 2.90
4335 4833 3.197549 GGGGCTTTTATGGCTTTTGATGA 59.802 43.478 0.00 0.00 0.00 2.92
4336 4834 3.055240 TGGGGCTTTTATGGCTTTTGATG 60.055 43.478 0.00 0.00 0.00 3.07
4337 4835 3.180507 TGGGGCTTTTATGGCTTTTGAT 58.819 40.909 0.00 0.00 0.00 2.57
4338 4836 2.614259 TGGGGCTTTTATGGCTTTTGA 58.386 42.857 0.00 0.00 0.00 2.69
4339 4837 3.415457 TTGGGGCTTTTATGGCTTTTG 57.585 42.857 0.00 0.00 0.00 2.44
4340 4838 4.103943 TCTTTTGGGGCTTTTATGGCTTTT 59.896 37.500 0.00 0.00 0.00 2.27
4341 4839 3.650461 TCTTTTGGGGCTTTTATGGCTTT 59.350 39.130 0.00 0.00 0.00 3.51
4342 4840 3.247162 TCTTTTGGGGCTTTTATGGCTT 58.753 40.909 0.00 0.00 0.00 4.35
4343 4841 2.901291 TCTTTTGGGGCTTTTATGGCT 58.099 42.857 0.00 0.00 0.00 4.75
4344 4842 3.694043 TTCTTTTGGGGCTTTTATGGC 57.306 42.857 0.00 0.00 0.00 4.40
4345 4843 5.682234 AGATTCTTTTGGGGCTTTTATGG 57.318 39.130 0.00 0.00 0.00 2.74
4348 4846 8.977412 CCTAAATAGATTCTTTTGGGGCTTTTA 58.023 33.333 12.05 0.00 31.78 1.52
4349 4847 7.678171 TCCTAAATAGATTCTTTTGGGGCTTTT 59.322 33.333 16.27 0.00 35.03 2.27
4350 4848 7.189087 TCCTAAATAGATTCTTTTGGGGCTTT 58.811 34.615 16.27 0.00 35.03 3.51
4351 4849 6.741724 TCCTAAATAGATTCTTTTGGGGCTT 58.258 36.000 16.27 0.00 35.03 4.35
4352 4850 6.341408 TCCTAAATAGATTCTTTTGGGGCT 57.659 37.500 16.27 0.00 35.03 5.19
4353 4851 5.010112 GCTCCTAAATAGATTCTTTTGGGGC 59.990 44.000 16.27 12.48 43.96 5.80
4354 4852 6.368805 AGCTCCTAAATAGATTCTTTTGGGG 58.631 40.000 16.27 8.18 35.03 4.96
4355 4853 7.888250 AAGCTCCTAAATAGATTCTTTTGGG 57.112 36.000 12.97 12.97 35.45 4.12
4368 4866 8.870116 ACCAAAAAGACATAAAAGCTCCTAAAT 58.130 29.630 0.00 0.00 0.00 1.40
4369 4867 8.245195 ACCAAAAAGACATAAAAGCTCCTAAA 57.755 30.769 0.00 0.00 0.00 1.85
4370 4868 7.504238 TGACCAAAAAGACATAAAAGCTCCTAA 59.496 33.333 0.00 0.00 0.00 2.69
4371 4869 7.001674 TGACCAAAAAGACATAAAAGCTCCTA 58.998 34.615 0.00 0.00 0.00 2.94
4372 4870 5.833131 TGACCAAAAAGACATAAAAGCTCCT 59.167 36.000 0.00 0.00 0.00 3.69
4373 4871 6.084326 TGACCAAAAAGACATAAAAGCTCC 57.916 37.500 0.00 0.00 0.00 4.70
4374 4872 8.419076 TTTTGACCAAAAAGACATAAAAGCTC 57.581 30.769 5.53 0.00 37.35 4.09
4375 4873 8.829612 CATTTTGACCAAAAAGACATAAAAGCT 58.170 29.630 11.34 0.00 42.71 3.74
4376 4874 8.825745 TCATTTTGACCAAAAAGACATAAAAGC 58.174 29.630 11.34 0.00 42.71 3.51
4381 4879 9.323985 CCTTTTCATTTTGACCAAAAAGACATA 57.676 29.630 11.34 0.00 42.71 2.29
4382 4880 7.201723 GCCTTTTCATTTTGACCAAAAAGACAT 60.202 33.333 11.34 0.00 42.71 3.06
4383 4881 6.093357 GCCTTTTCATTTTGACCAAAAAGACA 59.907 34.615 11.34 4.13 42.71 3.41
4384 4882 6.458206 GGCCTTTTCATTTTGACCAAAAAGAC 60.458 38.462 11.34 2.12 42.71 3.01
4385 4883 5.588246 GGCCTTTTCATTTTGACCAAAAAGA 59.412 36.000 11.34 9.84 42.71 2.52
4386 4884 5.503846 CGGCCTTTTCATTTTGACCAAAAAG 60.504 40.000 11.34 7.83 42.71 2.27
4387 4885 4.333926 CGGCCTTTTCATTTTGACCAAAAA 59.666 37.500 11.34 0.00 42.71 1.94
4388 4886 3.873952 CGGCCTTTTCATTTTGACCAAAA 59.126 39.130 9.94 9.94 43.48 2.44
4389 4887 3.462021 CGGCCTTTTCATTTTGACCAAA 58.538 40.909 0.00 0.00 0.00 3.28
4390 4888 2.804933 GCGGCCTTTTCATTTTGACCAA 60.805 45.455 0.00 0.00 0.00 3.67
4391 4889 1.270041 GCGGCCTTTTCATTTTGACCA 60.270 47.619 0.00 0.00 0.00 4.02
4392 4890 1.270041 TGCGGCCTTTTCATTTTGACC 60.270 47.619 0.00 0.00 0.00 4.02
4393 4891 2.147436 TGCGGCCTTTTCATTTTGAC 57.853 45.000 0.00 0.00 0.00 3.18
4394 4892 2.898729 TTGCGGCCTTTTCATTTTGA 57.101 40.000 0.00 0.00 0.00 2.69
4395 4893 3.849281 GCTTTTGCGGCCTTTTCATTTTG 60.849 43.478 0.00 0.00 34.86 2.44
4396 4894 2.290367 GCTTTTGCGGCCTTTTCATTTT 59.710 40.909 0.00 0.00 34.86 1.82
4397 4895 1.872952 GCTTTTGCGGCCTTTTCATTT 59.127 42.857 0.00 0.00 34.86 2.32
4398 4896 1.511850 GCTTTTGCGGCCTTTTCATT 58.488 45.000 0.00 0.00 34.86 2.57
4399 4897 3.215642 GCTTTTGCGGCCTTTTCAT 57.784 47.368 0.00 0.00 34.86 2.57
4400 4898 4.748409 GCTTTTGCGGCCTTTTCA 57.252 50.000 0.00 0.00 34.86 2.69
4417 4915 2.600470 TGTTTGGGCTTCTGCTTTTG 57.400 45.000 0.00 0.00 39.59 2.44
4418 4916 3.270027 GTTTGTTTGGGCTTCTGCTTTT 58.730 40.909 0.00 0.00 39.59 2.27
4419 4917 2.235898 TGTTTGTTTGGGCTTCTGCTTT 59.764 40.909 0.00 0.00 39.59 3.51
4420 4918 1.830477 TGTTTGTTTGGGCTTCTGCTT 59.170 42.857 0.00 0.00 39.59 3.91
4421 4919 1.410153 CTGTTTGTTTGGGCTTCTGCT 59.590 47.619 0.00 0.00 39.59 4.24
4422 4920 1.538849 CCTGTTTGTTTGGGCTTCTGC 60.539 52.381 0.00 0.00 38.76 4.26
4423 4921 1.069049 CCCTGTTTGTTTGGGCTTCTG 59.931 52.381 0.00 0.00 33.88 3.02
4424 4922 1.413118 CCCTGTTTGTTTGGGCTTCT 58.587 50.000 0.00 0.00 33.88 2.85
4425 4923 3.986970 CCCTGTTTGTTTGGGCTTC 57.013 52.632 0.00 0.00 33.88 3.86
4429 4927 1.343142 GTAAGGCCCTGTTTGTTTGGG 59.657 52.381 0.00 0.00 43.62 4.12
4430 4928 2.035632 TGTAAGGCCCTGTTTGTTTGG 58.964 47.619 0.00 0.00 0.00 3.28
4431 4929 2.955660 TCTGTAAGGCCCTGTTTGTTTG 59.044 45.455 0.00 0.00 0.00 2.93
4432 4930 3.306472 TCTGTAAGGCCCTGTTTGTTT 57.694 42.857 0.00 0.00 0.00 2.83
4433 4931 3.306472 TTCTGTAAGGCCCTGTTTGTT 57.694 42.857 0.00 0.00 0.00 2.83
4434 4932 3.117663 TCTTTCTGTAAGGCCCTGTTTGT 60.118 43.478 0.00 0.00 34.46 2.83
4435 4933 3.486383 TCTTTCTGTAAGGCCCTGTTTG 58.514 45.455 0.00 0.00 34.46 2.93
4436 4934 3.138468 ACTCTTTCTGTAAGGCCCTGTTT 59.862 43.478 0.00 0.00 34.46 2.83
4437 4935 2.711547 ACTCTTTCTGTAAGGCCCTGTT 59.288 45.455 0.00 0.00 34.46 3.16
4438 4936 2.339769 ACTCTTTCTGTAAGGCCCTGT 58.660 47.619 0.00 0.00 34.46 4.00
4439 4937 3.260884 TGTACTCTTTCTGTAAGGCCCTG 59.739 47.826 0.00 0.00 34.46 4.45
4440 4938 3.517612 TGTACTCTTTCTGTAAGGCCCT 58.482 45.455 0.00 0.00 34.46 5.19
4441 4939 3.975168 TGTACTCTTTCTGTAAGGCCC 57.025 47.619 0.00 0.00 34.46 5.80
4442 4940 5.086104 TCATGTACTCTTTCTGTAAGGCC 57.914 43.478 0.00 0.00 34.46 5.19
4443 4941 6.595716 ACAATCATGTACTCTTTCTGTAAGGC 59.404 38.462 0.00 0.00 38.24 4.35
4444 4942 7.065085 CCACAATCATGTACTCTTTCTGTAAGG 59.935 40.741 0.00 0.00 37.82 2.69
4445 4943 7.604164 ACCACAATCATGTACTCTTTCTGTAAG 59.396 37.037 0.00 0.00 37.82 2.34
4446 4944 7.387673 CACCACAATCATGTACTCTTTCTGTAA 59.612 37.037 0.00 0.00 37.82 2.41
4453 4951 3.244875 TGCCACCACAATCATGTACTCTT 60.245 43.478 0.00 0.00 37.82 2.85
4454 4952 2.305635 TGCCACCACAATCATGTACTCT 59.694 45.455 0.00 0.00 37.82 3.24
4458 4956 3.966979 AGAATGCCACCACAATCATGTA 58.033 40.909 0.00 0.00 37.82 2.29
4460 4958 3.517602 CAAGAATGCCACCACAATCATG 58.482 45.455 0.00 0.00 0.00 3.07
4480 4978 6.318648 GTGGTTACTTCATTCCTGATATTGCA 59.681 38.462 0.00 0.00 0.00 4.08
4497 4995 7.011499 TGTATATGAGTTTGGTGTGGTTACT 57.989 36.000 0.00 0.00 0.00 2.24
4534 5035 1.927487 TCCATGCCAAGCTGACATTT 58.073 45.000 0.00 0.00 0.00 2.32
4537 5038 2.876581 CATCCATGCCAAGCTGACA 58.123 52.632 0.00 0.00 0.00 3.58
4548 5049 0.747644 TTGGCGTGGTAGCATCCATG 60.748 55.000 16.29 12.97 44.65 3.66
4560 5079 3.305964 CGAGTACATACCTATTGGCGTG 58.694 50.000 0.00 0.00 36.63 5.34
4563 5082 3.319972 TGTCCGAGTACATACCTATTGGC 59.680 47.826 0.00 0.00 36.63 4.52
4564 5083 5.010719 ACATGTCCGAGTACATACCTATTGG 59.989 44.000 0.00 0.00 38.01 3.16
4565 5084 6.016192 AGACATGTCCGAGTACATACCTATTG 60.016 42.308 22.21 0.00 38.01 1.90
4595 5120 0.611896 TCTCCACCGAGACATGCTGA 60.612 55.000 0.00 0.00 40.34 4.26
4600 5125 1.276421 CCTTGTTCTCCACCGAGACAT 59.724 52.381 0.00 0.00 45.01 3.06
4631 5156 4.025401 GCGAGGGCGTGTTTGGTG 62.025 66.667 0.00 0.00 40.36 4.17
4641 5166 2.202756 CCTAGTGAACGCGAGGGC 60.203 66.667 15.93 0.00 0.00 5.19
4655 5180 1.776662 AGCAATAGACTCCACGCCTA 58.223 50.000 0.00 0.00 0.00 3.93


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

AutoCloner maintained by Alex Coulton.