Multiple sequence alignment - TraesCS3D01G461000

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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 TraesCS3D01G461000 chr3D 100.000 6884 0 0 2008 8891 565662758 565669641 0.000000e+00 12713.0
1 TraesCS3D01G461000 chr3D 100.000 1787 0 0 1 1787 565660751 565662537 0.000000e+00 3301.0
2 TraesCS3D01G461000 chr3D 84.407 2065 250 44 6128 8163 565626946 565628967 0.000000e+00 1964.0
3 TraesCS3D01G461000 chr3D 83.580 810 99 17 873 1658 565617511 565618310 0.000000e+00 728.0
4 TraesCS3D01G461000 chr3D 88.439 173 19 1 2009 2181 565620972 565621143 3.250000e-49 207.0
5 TraesCS3D01G461000 chr3B 91.780 3613 226 26 5298 8891 753806372 753809932 0.000000e+00 4961.0
6 TraesCS3D01G461000 chr3B 90.871 3341 226 29 2009 5299 753803023 753806334 0.000000e+00 4407.0
7 TraesCS3D01G461000 chr3B 93.726 1801 95 11 4 1787 753801186 753802985 0.000000e+00 2684.0
8 TraesCS3D01G461000 chr3B 83.727 2034 242 49 6128 8134 753734466 753736437 0.000000e+00 1840.0
9 TraesCS3D01G461000 chr3B 93.907 837 43 5 4 833 753769063 753769898 0.000000e+00 1256.0
10 TraesCS3D01G461000 chr3B 90.250 800 37 16 8095 8891 753769999 753770760 0.000000e+00 1007.0
11 TraesCS3D01G461000 chr3B 80.750 800 112 28 873 1658 753727714 753728485 3.580000e-163 586.0
12 TraesCS3D01G461000 chr3B 89.595 173 17 1 2009 2181 753731146 753731317 1.500000e-52 219.0
13 TraesCS3D01G461000 chr3B 94.000 50 3 0 5442 5491 124437611 124437562 9.570000e-10 76.8
14 TraesCS3D01G461000 chr3B 93.750 48 2 1 5553 5599 753806986 753807033 4.450000e-08 71.3
15 TraesCS3D01G461000 chr3A 94.298 3227 151 12 2009 5218 699892993 699896203 0.000000e+00 4909.0
16 TraesCS3D01G461000 chr3A 97.317 1118 28 1 1 1116 699891188 699892305 0.000000e+00 1897.0
17 TraesCS3D01G461000 chr3A 96.330 654 16 5 1142 1787 699892302 699892955 0.000000e+00 1068.0
18 TraesCS3D01G461000 chr3A 83.602 1055 120 35 6647 7678 699851843 699852867 0.000000e+00 941.0
19 TraesCS3D01G461000 chr3A 80.952 861 119 27 873 1707 699842587 699843428 2.710000e-179 640.0
20 TraesCS3D01G461000 chr3A 86.146 397 44 3 6128 6524 699851006 699851391 1.380000e-112 418.0
21 TraesCS3D01G461000 chr3A 86.389 360 45 3 2009 2367 699846021 699846377 3.010000e-104 390.0
22 TraesCS3D01G461000 chrUn 92.703 1987 119 16 6121 8093 360808069 360806095 0.000000e+00 2843.0
23 TraesCS3D01G461000 chrUn 92.699 1986 120 17 6121 8093 360841367 360843340 0.000000e+00 2841.0
24 TraesCS3D01G461000 chrUn 91.298 2034 136 15 3289 5299 318348375 318346360 0.000000e+00 2737.0
25 TraesCS3D01G461000 chrUn 91.178 1825 124 14 2188 3985 370089125 370087311 0.000000e+00 2444.0
26 TraesCS3D01G461000 chrUn 90.654 1530 105 13 3791 5299 358023194 358021682 0.000000e+00 1999.0
27 TraesCS3D01G461000 chrUn 93.490 1321 84 2 5298 6617 318346322 318345003 0.000000e+00 1962.0
28 TraesCS3D01G461000 chrUn 89.993 1339 93 14 2773 4085 411655526 411654203 0.000000e+00 1692.0
29 TraesCS3D01G461000 chrUn 92.392 999 65 8 7096 8093 453714186 453713198 0.000000e+00 1413.0
30 TraesCS3D01G461000 chrUn 93.154 964 54 6 835 1787 429961097 429962059 0.000000e+00 1404.0
31 TraesCS3D01G461000 chrUn 91.093 988 57 11 3988 4961 455448048 455447078 0.000000e+00 1308.0
32 TraesCS3D01G461000 chrUn 94.550 844 41 5 6121 6961 464008330 464007489 0.000000e+00 1299.0
33 TraesCS3D01G461000 chrUn 93.787 837 44 5 4 833 303428109 303428944 0.000000e+00 1251.0
34 TraesCS3D01G461000 chrUn 91.986 886 61 5 2188 3067 461980172 461979291 0.000000e+00 1234.0
35 TraesCS3D01G461000 chrUn 92.437 476 35 1 5298 5773 358021644 358021170 0.000000e+00 678.0
36 TraesCS3D01G461000 chrUn 94.318 176 8 2 2009 2184 429962097 429962270 1.470000e-67 268.0
37 TraesCS3D01G461000 chrUn 93.750 48 2 1 5553 5599 318345708 318345661 4.450000e-08 71.3
38 TraesCS3D01G461000 chr5A 91.379 58 5 0 5442 5499 143467510 143467453 7.400000e-11 80.5
39 TraesCS3D01G461000 chr7A 97.778 45 1 0 1210 1254 124856640 124856596 2.660000e-10 78.7
40 TraesCS3D01G461000 chr2A 80.392 102 18 2 1192 1292 707110458 707110558 9.570000e-10 76.8
41 TraesCS3D01G461000 chr2A 97.222 36 0 1 4724 4759 362869754 362869720 9.640000e-05 60.2
42 TraesCS3D01G461000 chr4A 90.909 55 5 0 5442 5496 393322408 393322462 3.440000e-09 75.0
43 TraesCS3D01G461000 chr4A 97.222 36 0 1 4724 4759 369220373 369220407 9.640000e-05 60.2
44 TraesCS3D01G461000 chr1B 91.228 57 2 3 5437 5493 105066007 105065954 3.440000e-09 75.0
45 TraesCS3D01G461000 chr7D 100.000 39 0 0 1216 1254 38619374 38619336 1.240000e-08 73.1
46 TraesCS3D01G461000 chr6B 89.655 58 3 2 5441 5497 453995860 453995915 4.450000e-08 71.3
47 TraesCS3D01G461000 chr6A 89.474 57 5 1 5441 5497 181317507 181317452 4.450000e-08 71.3
48 TraesCS3D01G461000 chr6A 92.857 42 3 0 1211 1252 502672405 502672364 2.680000e-05 62.1
49 TraesCS3D01G461000 chr1D 84.722 72 10 1 1222 1292 293296735 293296664 4.450000e-08 71.3
50 TraesCS3D01G461000 chr4B 87.302 63 2 5 4697 4759 63073300 63073244 5.760000e-07 67.6
51 TraesCS3D01G461000 chr5B 89.796 49 2 3 4711 4759 565441265 565441310 9.640000e-05 60.2


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 TraesCS3D01G461000 chr3D 565660751 565669641 8890 False 8007.000000 12713 100.000000 1 8891 2 chr3D.!!$F3 8890
1 TraesCS3D01G461000 chr3D 565626946 565628967 2021 False 1964.000000 1964 84.407000 6128 8163 1 chr3D.!!$F1 2035
2 TraesCS3D01G461000 chr3D 565617511 565621143 3632 False 467.500000 728 86.009500 873 2181 2 chr3D.!!$F2 1308
3 TraesCS3D01G461000 chr3B 753801186 753809932 8746 False 3030.825000 4961 92.531750 4 8891 4 chr3B.!!$F3 8887
4 TraesCS3D01G461000 chr3B 753769063 753770760 1697 False 1131.500000 1256 92.078500 4 8891 2 chr3B.!!$F2 8887
5 TraesCS3D01G461000 chr3B 753727714 753736437 8723 False 881.666667 1840 84.690667 873 8134 3 chr3B.!!$F1 7261
6 TraesCS3D01G461000 chr3A 699891188 699896203 5015 False 2624.666667 4909 95.981667 1 5218 3 chr3A.!!$F3 5217
7 TraesCS3D01G461000 chr3A 699851006 699852867 1861 False 679.500000 941 84.874000 6128 7678 2 chr3A.!!$F2 1550
8 TraesCS3D01G461000 chr3A 699842587 699846377 3790 False 515.000000 640 83.670500 873 2367 2 chr3A.!!$F1 1494
9 TraesCS3D01G461000 chrUn 360806095 360808069 1974 True 2843.000000 2843 92.703000 6121 8093 1 chrUn.!!$R1 1972
10 TraesCS3D01G461000 chrUn 360841367 360843340 1973 False 2841.000000 2841 92.699000 6121 8093 1 chrUn.!!$F2 1972
11 TraesCS3D01G461000 chrUn 370087311 370089125 1814 True 2444.000000 2444 91.178000 2188 3985 1 chrUn.!!$R2 1797
12 TraesCS3D01G461000 chrUn 411654203 411655526 1323 True 1692.000000 1692 89.993000 2773 4085 1 chrUn.!!$R3 1312
13 TraesCS3D01G461000 chrUn 318345003 318348375 3372 True 1590.100000 2737 92.846000 3289 6617 3 chrUn.!!$R8 3328
14 TraesCS3D01G461000 chrUn 453713198 453714186 988 True 1413.000000 1413 92.392000 7096 8093 1 chrUn.!!$R4 997
15 TraesCS3D01G461000 chrUn 358021170 358023194 2024 True 1338.500000 1999 91.545500 3791 5773 2 chrUn.!!$R9 1982
16 TraesCS3D01G461000 chrUn 455447078 455448048 970 True 1308.000000 1308 91.093000 3988 4961 1 chrUn.!!$R5 973
17 TraesCS3D01G461000 chrUn 464007489 464008330 841 True 1299.000000 1299 94.550000 6121 6961 1 chrUn.!!$R7 840
18 TraesCS3D01G461000 chrUn 303428109 303428944 835 False 1251.000000 1251 93.787000 4 833 1 chrUn.!!$F1 829
19 TraesCS3D01G461000 chrUn 461979291 461980172 881 True 1234.000000 1234 91.986000 2188 3067 1 chrUn.!!$R6 879
20 TraesCS3D01G461000 chrUn 429961097 429962270 1173 False 836.000000 1404 93.736000 835 2184 2 chrUn.!!$F3 1349

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
578 581 0.767375 ACTCTTCTTTGAGCTGCCCA 59.233 50.000 0.00 0.00 37.58 5.36 F
2468 7765 0.681733 GGATGGAGGCTGCTCGATTA 59.318 55.000 7.74 0.00 0.00 1.75 F
3681 9003 0.179089 ACATGCAGAGCCGTCTCATC 60.179 55.000 0.00 0.00 41.81 2.92 F
4647 9987 1.051812 CAGAGGGGCTTGGATATCGT 58.948 55.000 0.00 0.00 0.00 3.73 F
4679 10019 1.134699 TGGTGGCATTCGAGCTAGAAG 60.135 52.381 14.74 8.18 33.19 2.85 F
4765 10105 1.462616 TGCAATTCTTGGGTGATCCG 58.537 50.000 0.00 0.00 38.76 4.18 F
5914 11296 1.755179 AGTCGGAATTTGGCTGATGG 58.245 50.000 0.00 0.00 0.00 3.51 F
6147 11529 0.108424 TGTGCCAACAAACCTGCAAC 60.108 50.000 0.00 0.00 35.16 4.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2562 7859 0.178967 TCAGCAATTGGGAACAGGCA 60.179 50.000 7.72 0.0 44.54 4.75 R
4292 9632 0.174845 AGCGTGCTGGCGTAGATTAA 59.825 50.000 0.00 0.0 38.18 1.40 R
5541 10923 0.253044 CCCATGACAACCAGACGGAT 59.747 55.000 0.00 0.0 35.59 4.18 R
5544 10926 0.606401 AAGCCCATGACAACCAGACG 60.606 55.000 0.00 0.0 0.00 4.18 R
5546 10928 0.770499 TCAAGCCCATGACAACCAGA 59.230 50.000 0.00 0.0 0.00 3.86 R
5981 11363 1.100510 TGGTAGTTGATCGGAGTCGG 58.899 55.000 0.00 0.0 36.95 4.79 R
7409 13147 1.299976 CGCTGGCCTAAGGTCCTTT 59.700 57.895 10.04 0.0 0.00 3.11 R
8037 13787 0.400213 CCCAAAGCAGGGTCACACTA 59.600 55.000 0.99 0.0 44.24 2.74 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
31 32 1.403249 CGAGGAAAGGCAAAGGCATTG 60.403 52.381 0.00 0.00 44.37 2.82
199 202 8.204160 ACTTGGGAAGATAGAAAAACAAAAAGG 58.796 33.333 0.00 0.00 0.00 3.11
227 230 1.691976 TGTGACCGATGACAGGTTCTT 59.308 47.619 0.00 0.00 43.01 2.52
273 276 6.080969 ACTAACTCTCTAGGAGACAATGGA 57.919 41.667 13.28 0.00 44.45 3.41
348 351 8.147058 TCTAAATATCTCATTGGAAGAGCAGAC 58.853 37.037 0.00 0.00 33.15 3.51
404 407 2.031870 GTGCAAGATATTTCCCACCCC 58.968 52.381 0.00 0.00 0.00 4.95
473 476 5.125900 TGTCTTGCCATGGTGATTTATCTTG 59.874 40.000 14.67 0.00 0.00 3.02
578 581 0.767375 ACTCTTCTTTGAGCTGCCCA 59.233 50.000 0.00 0.00 37.58 5.36
699 702 7.822161 TGGGAATCCACTTATGTTTATCATG 57.178 36.000 0.09 0.00 38.32 3.07
766 773 1.481772 GGCCATAAGCTTTTCCATGCA 59.518 47.619 3.20 0.00 43.05 3.96
777 785 4.573201 GCTTTTCCATGCATGCATTGTTAT 59.427 37.500 30.32 6.96 33.90 1.89
797 805 1.148027 TCTCCTGGGCGATAATCCTCT 59.852 52.381 0.00 0.00 0.00 3.69
997 1005 2.033194 GGTGTAGTTGCGTGGCTCC 61.033 63.158 0.00 0.00 0.00 4.70
1144 1153 9.559958 CTTGTTCATGTTTGTAAATACATCTCC 57.440 33.333 0.00 0.00 35.89 3.71
1175 1184 8.374728 TGTTAGTACGTTTTGAATTACTATGCG 58.625 33.333 0.00 0.00 29.35 4.73
1285 1296 6.627395 TGGTAAACTATGACCAAGTTTGTG 57.373 37.500 10.61 0.00 44.67 3.33
1292 1324 6.306987 ACTATGACCAAGTTTGTGGAGAAAT 58.693 36.000 0.00 0.00 41.65 2.17
1300 1332 8.704668 ACCAAGTTTGTGGAGAAATTTTCTAAT 58.295 29.630 11.55 0.00 41.65 1.73
1307 1339 8.225603 TGTGGAGAAATTTTCTAATATGAGGC 57.774 34.615 11.55 0.00 40.87 4.70
1328 1368 8.037166 TGAGGCATATATCAACAGATACATCAC 58.963 37.037 0.00 0.00 0.00 3.06
1668 1718 9.052759 GTATTTACTCAGTTTCTCTTGGTTTCA 57.947 33.333 0.00 0.00 0.00 2.69
2130 4707 8.909708 TTGTTTTATGCCGATAAATCAAGAAG 57.090 30.769 8.09 0.00 38.08 2.85
2263 5127 9.298774 GAAGAGAAGAAAAATGCTGATTATTGG 57.701 33.333 0.00 0.00 0.00 3.16
2468 7765 0.681733 GGATGGAGGCTGCTCGATTA 59.318 55.000 7.74 0.00 0.00 1.75
2562 7859 1.202698 GCACCAGTCTGTCTTGAAGGT 60.203 52.381 0.00 0.00 0.00 3.50
2696 7993 7.784633 TGATATTCGTCATGTTATTGCTTCA 57.215 32.000 0.00 0.00 0.00 3.02
2819 8116 2.124151 AATCCTCATGTGGGCCGC 60.124 61.111 10.94 10.94 0.00 6.53
2851 8148 4.643387 GCCACCTTGTCAGGGCGT 62.643 66.667 0.00 0.00 46.01 5.68
2908 8205 1.888436 GATCTGACTCCACCACGCCA 61.888 60.000 0.00 0.00 0.00 5.69
2921 8218 0.179100 CACGCCACGAAGATCCATCT 60.179 55.000 0.00 0.00 39.22 2.90
2945 8242 2.906389 TGCCTGAAGATGTTCACCTAGT 59.094 45.455 0.23 0.00 37.79 2.57
2987 8284 1.076350 CACCAGGATGTTTAACCCCCA 59.924 52.381 0.00 0.00 0.00 4.96
3067 8364 2.957402 TGCCATAGGATGATTGACCC 57.043 50.000 0.00 0.00 0.00 4.46
3173 8489 3.663198 AGGGGATATTCTGAGTGCTTCT 58.337 45.455 0.00 0.00 0.00 2.85
3175 8491 5.219739 AGGGGATATTCTGAGTGCTTCTAA 58.780 41.667 0.00 0.00 0.00 2.10
3177 8493 7.019388 AGGGGATATTCTGAGTGCTTCTAATA 58.981 38.462 0.00 0.00 0.00 0.98
3210 8526 4.278170 CCTTGTGTTTTAGTCTGAATGGCA 59.722 41.667 0.00 0.00 0.00 4.92
3213 8529 5.316167 TGTGTTTTAGTCTGAATGGCATCT 58.684 37.500 0.00 0.00 0.00 2.90
3260 8576 2.430332 CCAAACCTGAAACTTGGCTTGA 59.570 45.455 0.00 0.00 32.80 3.02
3261 8577 3.070015 CCAAACCTGAAACTTGGCTTGAT 59.930 43.478 0.00 0.00 32.80 2.57
3262 8578 4.443315 CCAAACCTGAAACTTGGCTTGATT 60.443 41.667 0.00 0.00 32.80 2.57
3271 8590 8.806429 TGAAACTTGGCTTGATTATTATCTCA 57.194 30.769 0.00 0.00 0.00 3.27
3275 8594 8.092521 ACTTGGCTTGATTATTATCTCATTCG 57.907 34.615 0.00 0.00 0.00 3.34
3315 8634 4.032960 TGGTGTTGCTATGAATCACCTT 57.967 40.909 12.66 0.00 45.82 3.50
3518 8840 5.655394 AGTATATCCAGAGATGGGCTACAA 58.345 41.667 0.00 0.00 33.67 2.41
3553 8875 4.262121 GCAAGGCATCATATATTGCAACCA 60.262 41.667 0.00 0.00 44.32 3.67
3629 8951 0.320596 CAAACGGCCATGCAAATGGT 60.321 50.000 2.24 0.00 43.53 3.55
3681 9003 0.179089 ACATGCAGAGCCGTCTCATC 60.179 55.000 0.00 0.00 41.81 2.92
3773 9095 1.375908 GAAGATGGTGTCAGCGGCA 60.376 57.895 1.45 0.00 33.94 5.69
3835 9157 5.548056 AGGAAACCAGAAGAAAGAGTGGATA 59.452 40.000 0.00 0.00 33.95 2.59
3849 9171 5.021458 AGAGTGGATACCTCGTAAAAAGGA 58.979 41.667 0.00 0.00 38.47 3.36
3963 9285 1.399791 GCAGTGCATGGCTCTAAAGAC 59.600 52.381 11.09 0.00 30.96 3.01
4042 9368 2.304180 AGGAGGATGACCAAGACAACTG 59.696 50.000 0.00 0.00 38.94 3.16
4118 9444 3.432252 GTGTGCATAAGCTTTGTAGTCGT 59.568 43.478 3.20 0.00 42.74 4.34
4200 9526 9.177608 TCCATTACTTTTGATTAGTTGGATCAG 57.822 33.333 0.00 0.00 35.17 2.90
4213 9539 2.910199 TGGATCAGCTAGTGCATGTTC 58.090 47.619 0.00 0.00 42.74 3.18
4292 9632 2.799126 TGGCGACAATGGGATAAACT 57.201 45.000 0.00 0.00 37.44 2.66
4350 9690 4.536090 TCCCTTATCCAAGTTGAGTGTGAT 59.464 41.667 3.87 0.69 0.00 3.06
4352 9692 5.338708 CCCTTATCCAAGTTGAGTGTGATCT 60.339 44.000 3.87 0.00 0.00 2.75
4391 9731 1.925255 TGATCCCATGAAAGAAGCCCT 59.075 47.619 0.00 0.00 0.00 5.19
4610 9950 6.757897 TTACTATCTTTGGCAATGTCAAGG 57.242 37.500 3.14 3.14 0.00 3.61
4647 9987 1.051812 CAGAGGGGCTTGGATATCGT 58.948 55.000 0.00 0.00 0.00 3.73
4679 10019 1.134699 TGGTGGCATTCGAGCTAGAAG 60.135 52.381 14.74 8.18 33.19 2.85
4699 10039 4.116747 AGAATACAAGAAGACCGCAGAG 57.883 45.455 0.00 0.00 0.00 3.35
4700 10040 3.511934 AGAATACAAGAAGACCGCAGAGT 59.488 43.478 0.00 0.00 0.00 3.24
4765 10105 1.462616 TGCAATTCTTGGGTGATCCG 58.537 50.000 0.00 0.00 38.76 4.18
4798 10138 8.265055 ACATTAATACTTACCAGCAAGCTTCTA 58.735 33.333 0.00 0.00 0.00 2.10
4823 10163 3.591527 TGGATTGGTTTAGGTGATCCACT 59.408 43.478 0.00 0.00 40.85 4.00
4848 10188 7.496346 AAGTACCTCTCATTGTCTTCCATAA 57.504 36.000 0.00 0.00 0.00 1.90
4973 10313 7.412063 GGTTAAGCTTGTCGTTCTTTTTCTTA 58.588 34.615 9.86 0.00 0.00 2.10
4979 10319 6.750501 GCTTGTCGTTCTTTTTCTTAAGGTTT 59.249 34.615 1.85 0.00 0.00 3.27
5006 10346 3.655276 TCCTCTCGGTACAACTTGTTC 57.345 47.619 0.00 0.00 0.00 3.18
5036 10376 5.924825 AGCAATTTCTTCAAACTCATTCAGC 59.075 36.000 0.00 0.00 0.00 4.26
5055 10395 3.057736 CAGCTGATGTTCAACCTTCTTGG 60.058 47.826 8.42 0.00 42.93 3.61
5077 10420 4.501743 GGTTTTCAGTCGAGTCTCCTTCTT 60.502 45.833 0.00 0.00 0.00 2.52
5089 10432 2.164624 TCTCCTTCTTGTTCGCTAGCTC 59.835 50.000 13.93 3.91 0.00 4.09
5122 10465 2.035312 CAGAGCCTTGGCCAGCTT 59.965 61.111 19.61 8.08 40.11 3.74
5149 10492 3.136443 TCTTTTGCCTCCAGTCTCTTTCA 59.864 43.478 0.00 0.00 0.00 2.69
5158 10501 5.310409 TCCAGTCTCTTTCAGATGGTTTT 57.690 39.130 0.00 0.00 34.13 2.43
5167 10510 6.446318 TCTTTCAGATGGTTTTTGCACATAC 58.554 36.000 0.00 0.00 0.00 2.39
5194 10537 7.824289 TCAATTCTCTAGTTGGTTGGTCAATAG 59.176 37.037 0.00 0.00 0.00 1.73
5220 10563 4.350368 TTTTCAGCAGGTGTATCTGTCA 57.650 40.909 0.00 0.00 37.12 3.58
5241 10584 4.406972 TCAGAATCAGTTAGGACAGGGATG 59.593 45.833 0.00 0.00 0.00 3.51
5251 10594 6.100424 AGTTAGGACAGGGATGAGAAATAAGG 59.900 42.308 0.00 0.00 0.00 2.69
5327 10709 7.398332 AGTTAAGATGCAATTGATCCCTTTTCT 59.602 33.333 10.34 5.69 0.00 2.52
5332 10714 3.930848 GCAATTGATCCCTTTTCTGCAAG 59.069 43.478 10.34 0.00 0.00 4.01
5343 10725 5.221224 CCCTTTTCTGCAAGTCATTGTACAA 60.221 40.000 11.41 11.41 38.76 2.41
5352 10734 5.220739 GCAAGTCATTGTACAAGCTCATAGG 60.221 44.000 14.65 1.19 38.76 2.57
5386 10768 9.541143 TTCAAACAGAAGATGAAAATTAAACCC 57.459 29.630 0.00 0.00 30.60 4.11
5393 10775 5.816682 AGATGAAAATTAAACCCGGAGAGT 58.183 37.500 0.73 0.00 0.00 3.24
5409 10791 4.260456 CGGAGAGTAGTTCATTCGAGACTC 60.260 50.000 0.00 0.00 34.77 3.36
5428 10810 7.246171 AGACTCCAACACTAACTGATTACAT 57.754 36.000 0.00 0.00 0.00 2.29
5429 10811 7.099764 AGACTCCAACACTAACTGATTACATG 58.900 38.462 0.00 0.00 0.00 3.21
5504 10886 4.327680 CCACTGGAAGAAAAGTCCTAAGG 58.672 47.826 0.00 0.00 37.43 2.69
5505 10887 4.041691 CCACTGGAAGAAAAGTCCTAAGGA 59.958 45.833 0.00 0.00 37.43 3.36
5508 10890 6.717084 CACTGGAAGAAAAGTCCTAAGGAAAT 59.283 38.462 0.00 0.00 37.43 2.17
5600 10982 5.631096 GCCAAGTCTATGAAGTTCAAAAAGC 59.369 40.000 10.14 1.99 0.00 3.51
5628 11010 6.927294 AATTCTAATTCAGTCGGTTCATCC 57.073 37.500 0.00 0.00 0.00 3.51
5721 11103 2.262423 AGAGACTTTGACCAACTGCC 57.738 50.000 0.00 0.00 0.00 4.85
5741 11123 2.159099 CCAGCAGTTAATCGTAGCCTCA 60.159 50.000 0.00 0.00 0.00 3.86
5742 11124 3.521560 CAGCAGTTAATCGTAGCCTCAA 58.478 45.455 0.00 0.00 0.00 3.02
5810 11192 3.806316 AGCACAAACTAAATTCGGTCG 57.194 42.857 0.00 0.00 0.00 4.79
5813 11195 3.666111 GCACAAACTAAATTCGGTCGGAC 60.666 47.826 0.00 0.00 0.00 4.79
5850 11232 2.832201 GCCATGGGCTTGGAGCTC 60.832 66.667 15.13 4.71 46.69 4.09
5914 11296 1.755179 AGTCGGAATTTGGCTGATGG 58.245 50.000 0.00 0.00 0.00 3.51
5931 11313 3.145551 GCCATGGGCTTGGAGCTG 61.146 66.667 15.13 0.00 46.69 4.24
5950 11332 3.243501 GCTGAGAGAGCTAAGTCCATGAG 60.244 52.174 0.00 0.00 45.21 2.90
5951 11333 3.953612 CTGAGAGAGCTAAGTCCATGAGT 59.046 47.826 0.00 0.00 0.00 3.41
5987 11369 4.768583 TCCTACTTCTACTCTTCCGACTC 58.231 47.826 0.00 0.00 0.00 3.36
6001 11383 1.475280 CCGACTCCGATCAACTACCAA 59.525 52.381 0.00 0.00 38.22 3.67
6010 11392 7.280205 ACTCCGATCAACTACCAACAATTAATC 59.720 37.037 0.00 0.00 0.00 1.75
6018 11400 6.055588 ACTACCAACAATTAATCGGATCCTG 58.944 40.000 10.75 3.62 0.00 3.86
6029 11411 1.457831 GGATCCTGAGGGGCTACGT 60.458 63.158 3.84 0.00 34.39 3.57
6035 11417 0.395311 CTGAGGGGCTACGTCCACTA 60.395 60.000 0.00 0.00 40.70 2.74
6046 11428 2.748388 ACGTCCACTAGGGCTAGAAAT 58.252 47.619 0.00 0.00 37.38 2.17
6047 11429 3.105283 ACGTCCACTAGGGCTAGAAATT 58.895 45.455 0.00 0.00 37.38 1.82
6054 11436 5.355350 CCACTAGGGCTAGAAATTCACAAAG 59.645 44.000 0.00 0.00 36.97 2.77
6061 11443 7.669722 AGGGCTAGAAATTCACAAAGTAATTCA 59.330 33.333 0.00 0.00 0.00 2.57
6063 11445 7.486232 GGCTAGAAATTCACAAAGTAATTCAGC 59.514 37.037 0.00 0.00 0.00 4.26
6069 11451 5.092554 TCACAAAGTAATTCAGCCGGATA 57.907 39.130 5.05 0.00 0.00 2.59
6085 11467 1.895798 GGATATCTGGCATCCGAGTGA 59.104 52.381 2.05 0.00 33.03 3.41
6094 11476 3.389656 TGGCATCCGAGTGATTACCAATA 59.610 43.478 0.00 0.00 35.25 1.90
6111 11493 4.162509 ACCAATAGGCTTGGACTAAGAGAC 59.837 45.833 12.14 0.00 42.06 3.36
6147 11529 0.108424 TGTGCCAACAAACCTGCAAC 60.108 50.000 0.00 0.00 35.16 4.17
6318 11700 3.388676 TGTTACGACCTCCTTTTCCTCAA 59.611 43.478 0.00 0.00 0.00 3.02
6423 11805 4.787551 ACTTGATTGACTGGTGGTACAAA 58.212 39.130 0.00 0.00 44.16 2.83
6544 12054 7.779798 CCCCTTTCATGAAATCAAATACCTAGA 59.220 37.037 20.76 0.00 0.00 2.43
6591 12104 6.902224 ATTGTTTTGTCAAAAGGTTAGCAC 57.098 33.333 11.03 0.00 0.00 4.40
6636 12149 5.009010 CACATTAGGGTTGGAGTATGAATGC 59.991 44.000 0.00 0.00 0.00 3.56
6754 12471 7.489160 AGTTATTTCTTGTTTTGACTTGGACC 58.511 34.615 0.00 0.00 0.00 4.46
6963 12685 5.480422 TGATCCTTAGTGCTAAGTCACAAGA 59.520 40.000 15.34 6.91 40.59 3.02
7018 12752 5.601313 ACTAGGAGAAGAACCACAACTGTAA 59.399 40.000 0.00 0.00 0.00 2.41
7058 12792 5.352846 GTGTTGTTGGTACCAAATTTTGCTT 59.647 36.000 28.67 0.00 37.70 3.91
7116 12850 2.325484 AGTATGACGGGTATGGCATCA 58.675 47.619 1.65 0.00 0.00 3.07
7130 12864 4.354893 TGGCATCAAAAAGAAGGCAATT 57.645 36.364 0.00 0.00 45.77 2.32
7190 12926 5.616658 CACACATGGTTTGTTGTTTTGTTC 58.383 37.500 0.00 0.00 36.00 3.18
7194 12930 5.573669 ACATGGTTTGTTGTTTTGTTCGTAC 59.426 36.000 0.00 0.00 33.74 3.67
7372 13110 8.134202 TGTCTACAGATAATTTGTCCTGAGAA 57.866 34.615 0.00 0.00 0.00 2.87
7409 13147 0.463654 GATGTTGGGCTGCCGATACA 60.464 55.000 13.40 15.89 0.00 2.29
7456 13194 2.168496 GCCCCTCTTAAAAGGTTGGAC 58.832 52.381 0.00 0.00 34.34 4.02
7494 13233 5.916661 GGTAACTGGACTCTCATTCACTA 57.083 43.478 0.00 0.00 0.00 2.74
7565 13307 3.562557 AGTTTTTCGAATACCAACGTGCT 59.437 39.130 0.00 0.00 0.00 4.40
7571 13313 4.496360 TCGAATACCAACGTGCTCATTTA 58.504 39.130 0.00 0.00 0.00 1.40
7609 13353 9.491675 AAAATCATGTGCAATTAACAAGATTCA 57.508 25.926 17.39 0.00 42.18 2.57
7612 13356 7.660112 TCATGTGCAATTAACAAGATTCAACT 58.340 30.769 0.00 0.00 0.00 3.16
7685 13431 2.751166 ACGCAGTGAGCTAAATGAGT 57.249 45.000 1.72 1.67 42.51 3.41
7734 13480 5.365605 ACCCTTTTTGTTTCCCTAAAGAAGG 59.634 40.000 0.00 0.00 46.09 3.46
7811 13557 7.780064 TGTTCTCAATCTTCCATTTTGTTCAA 58.220 30.769 0.00 0.00 0.00 2.69
7857 13603 8.272176 GTGTTTCATTTGATGCGAAATTTACAA 58.728 29.630 0.00 0.00 31.78 2.41
7891 13637 7.961326 ATAATTGGTTGTCAGGCTTTCTAAT 57.039 32.000 0.00 0.00 0.00 1.73
7893 13639 5.452078 TTGGTTGTCAGGCTTTCTAATTG 57.548 39.130 0.00 0.00 0.00 2.32
7895 13641 3.826729 GGTTGTCAGGCTTTCTAATTGGT 59.173 43.478 0.00 0.00 0.00 3.67
7933 13679 7.922811 AGGATTCTTGTTTGTTGAAGTTGAATC 59.077 33.333 0.00 0.00 37.56 2.52
7934 13680 7.169813 GGATTCTTGTTTGTTGAAGTTGAATCC 59.830 37.037 12.96 12.96 45.21 3.01
7935 13681 6.522625 TCTTGTTTGTTGAAGTTGAATCCA 57.477 33.333 0.00 0.00 0.00 3.41
7985 13735 8.816640 ATTTATTTCTTCGCAAGTCACAAAAT 57.183 26.923 0.00 0.00 39.48 1.82
8017 13767 6.619801 ATGCTAGTTGGGATATTTTCGTTC 57.380 37.500 0.00 0.00 0.00 3.95
8019 13769 4.807304 GCTAGTTGGGATATTTTCGTTCGA 59.193 41.667 0.00 0.00 0.00 3.71
8026 13776 6.664515 TGGGATATTTTCGTTCGATTAATGC 58.335 36.000 0.00 0.00 0.00 3.56
8037 13787 6.929049 TCGTTCGATTAATGCTAATGGATTCT 59.071 34.615 0.00 0.00 33.72 2.40
8096 13846 0.179020 TGCCCCTTCTCACTGTTGTG 60.179 55.000 0.00 0.00 45.07 3.33
8238 13993 7.996098 TTATAAGCAAGAGCAACCTTTTACT 57.004 32.000 0.00 0.00 45.49 2.24
8239 13994 4.837896 AAGCAAGAGCAACCTTTTACTC 57.162 40.909 0.00 0.00 45.49 2.59
8249 14004 5.009710 AGCAACCTTTTACTCCTTAGTTTGC 59.990 40.000 0.00 0.00 40.13 3.68
8307 14062 4.866327 TTTTACCGTCCCCTTATTCCAT 57.134 40.909 0.00 0.00 0.00 3.41
8313 14068 4.970640 ACCGTCCCCTTATTCCATAGTTTA 59.029 41.667 0.00 0.00 0.00 2.01
8357 14112 3.682858 CCTTACGTGGTTTAGTGTCATGG 59.317 47.826 0.00 0.00 0.00 3.66
8362 14117 1.173913 GGTTTAGTGTCATGGGGCAC 58.826 55.000 0.00 0.33 35.98 5.01
8390 14145 9.249053 TGATAGCCTATGGAATAAAACACAAAA 57.751 29.630 0.00 0.00 0.00 2.44
8393 14148 6.873605 AGCCTATGGAATAAAACACAAAAAGC 59.126 34.615 0.00 0.00 0.00 3.51
8394 14149 6.092122 GCCTATGGAATAAAACACAAAAAGCC 59.908 38.462 0.00 0.00 0.00 4.35
8395 14150 7.386059 CCTATGGAATAAAACACAAAAAGCCT 58.614 34.615 0.00 0.00 0.00 4.58
8396 14151 8.527810 CCTATGGAATAAAACACAAAAAGCCTA 58.472 33.333 0.00 0.00 0.00 3.93
8398 14153 8.776376 ATGGAATAAAACACAAAAAGCCTATG 57.224 30.769 0.00 0.00 0.00 2.23
8399 14154 7.158021 TGGAATAAAACACAAAAAGCCTATGG 58.842 34.615 0.00 0.00 0.00 2.74
8400 14155 7.015682 TGGAATAAAACACAAAAAGCCTATGGA 59.984 33.333 0.00 0.00 0.00 3.41
8401 14156 7.875554 GGAATAAAACACAAAAAGCCTATGGAA 59.124 33.333 0.00 0.00 0.00 3.53
8402 14157 9.435688 GAATAAAACACAAAAAGCCTATGGAAT 57.564 29.630 0.00 0.00 0.00 3.01
8406 14161 9.620259 AAAACACAAAAAGCCTATGGAATAAAA 57.380 25.926 0.00 0.00 0.00 1.52
8407 14162 8.601845 AACACAAAAAGCCTATGGAATAAAAC 57.398 30.769 0.00 0.00 0.00 2.43
8408 14163 7.731054 ACACAAAAAGCCTATGGAATAAAACA 58.269 30.769 0.00 0.00 0.00 2.83
8409 14164 7.655732 ACACAAAAAGCCTATGGAATAAAACAC 59.344 33.333 0.00 0.00 0.00 3.32
8410 14165 7.655328 CACAAAAAGCCTATGGAATAAAACACA 59.345 33.333 0.00 0.00 0.00 3.72
8411 14166 8.207545 ACAAAAAGCCTATGGAATAAAACACAA 58.792 29.630 0.00 0.00 0.00 3.33
8412 14167 9.050601 CAAAAAGCCTATGGAATAAAACACAAA 57.949 29.630 0.00 0.00 0.00 2.83
8504 14259 4.294416 TGTTGAAAATTACACACGTGGG 57.706 40.909 18.21 18.21 34.19 4.61
8540 14295 8.328864 CCAACGAGATATAAAAAGTCTACTTGC 58.671 37.037 0.00 0.00 36.12 4.01
8563 14318 3.521937 CCCCCTTAGGTTATGTGTTCTGA 59.478 47.826 0.00 0.00 0.00 3.27
8651 14406 4.391830 AGTGTTGACATGTATTAGTTGCCG 59.608 41.667 0.00 0.00 0.00 5.69
8729 14484 3.717392 ACTCTCTTTATCCCTAAAGCCCC 59.283 47.826 1.17 0.00 42.35 5.80
8732 14487 4.166144 TCTCTTTATCCCTAAAGCCCCAAG 59.834 45.833 1.17 0.00 42.35 3.61
8745 14500 2.177888 AGCCCCAAGAAAGGAAGAAAGT 59.822 45.455 0.00 0.00 0.00 2.66
8800 14555 4.020662 TGGCAAAATAACCCTCAAACATCC 60.021 41.667 0.00 0.00 0.00 3.51
8801 14556 4.020662 GGCAAAATAACCCTCAAACATCCA 60.021 41.667 0.00 0.00 0.00 3.41
8877 14632 4.111577 AGGGGAAGACAATCATACAAGGA 58.888 43.478 0.00 0.00 0.00 3.36
8878 14633 4.728860 AGGGGAAGACAATCATACAAGGAT 59.271 41.667 0.00 0.00 0.00 3.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
31 32 4.754114 ACTGAAACAAGATCTCAAGCTCAC 59.246 41.667 0.00 0.00 0.00 3.51
197 200 3.941483 GTCATCGGTCACAAATCAATCCT 59.059 43.478 0.00 0.00 0.00 3.24
199 202 4.201851 CCTGTCATCGGTCACAAATCAATC 60.202 45.833 0.00 0.00 0.00 2.67
227 230 2.918345 GCATGGTTCTTGCCACGCA 61.918 57.895 0.00 0.00 45.89 5.24
273 276 6.240894 TGAGGCTAAAGATCAAGACATGTTT 58.759 36.000 0.00 0.00 0.00 2.83
348 351 4.764172 ACTCCCTCATTTTCTTCATCTCG 58.236 43.478 0.00 0.00 0.00 4.04
404 407 3.997021 CAGCTAGTATTTTAGGGATGCCG 59.003 47.826 0.00 0.00 0.00 5.69
473 476 2.235898 AGATGAGGGCAAGAGTCAGAAC 59.764 50.000 0.00 0.00 0.00 3.01
578 581 3.279434 GGTCAAGACACCACAAGAACTT 58.721 45.455 2.29 0.00 36.32 2.66
663 666 5.638133 AGTGGATTCCCAAGATATCAATGG 58.362 41.667 16.74 16.74 45.59 3.16
699 702 5.106317 TGGCATCGAAGACCATTAAGAAAAC 60.106 40.000 0.00 0.00 42.51 2.43
766 773 2.590821 GCCCAGGAGATAACAATGCAT 58.409 47.619 0.00 0.00 0.00 3.96
777 785 1.148027 AGAGGATTATCGCCCAGGAGA 59.852 52.381 0.00 0.00 0.00 3.71
797 805 1.371183 CTCCCACGAAGGTGCTTCA 59.629 57.895 0.00 0.00 43.00 3.02
1144 1153 8.562052 AGTAATTCAAAACGTACTAACAAAGGG 58.438 33.333 0.00 0.00 0.00 3.95
1175 1184 9.370126 GAAAGTATCATGTATGAAAATACGTGC 57.630 33.333 11.52 1.53 41.45 5.34
1301 1333 8.765517 TGATGTATCTGTTGATATATGCCTCAT 58.234 33.333 0.00 0.00 37.20 2.90
1303 1335 7.221645 CGTGATGTATCTGTTGATATATGCCTC 59.778 40.741 0.00 0.00 37.20 4.70
1305 1337 7.035612 TCGTGATGTATCTGTTGATATATGCC 58.964 38.462 0.00 0.00 37.20 4.40
1307 1339 7.221645 GGCTCGTGATGTATCTGTTGATATATG 59.778 40.741 0.00 0.00 37.20 1.78
1316 1356 1.781786 AGGGCTCGTGATGTATCTGT 58.218 50.000 0.00 0.00 0.00 3.41
1668 1718 9.260002 GAATGCAATGGAATTAATACCGATTTT 57.740 29.630 0.00 0.00 32.46 1.82
2007 4584 7.550712 GGTGAGCTGGAAATAAAATTGAGATT 58.449 34.615 0.00 0.00 0.00 2.40
2068 4645 9.063484 TCATCTGGATAGTCTATATACTCCACT 57.937 37.037 0.00 0.00 0.00 4.00
2130 4707 9.691362 TCAACAGAAGAAACTAATTTTATTGGC 57.309 29.630 0.00 0.00 28.51 4.52
2249 5113 4.340381 GCCTTGACTCCAATAATCAGCATT 59.660 41.667 0.00 0.00 0.00 3.56
2508 7805 1.696832 GGACGCGCCATCAAGTTCTC 61.697 60.000 5.73 0.00 36.34 2.87
2562 7859 0.178967 TCAGCAATTGGGAACAGGCA 60.179 50.000 7.72 0.00 44.54 4.75
2600 7897 3.210223 TTGCATTGCGGTGTGCTGG 62.210 57.895 3.84 0.00 46.63 4.85
2602 7899 2.646719 CTTGCATTGCGGTGTGCT 59.353 55.556 3.84 0.00 46.63 4.40
2668 7965 6.936335 AGCAATAACATGACGAATATCATCCA 59.064 34.615 0.00 0.00 37.20 3.41
2705 8002 3.779759 TGTCACATTTTGTCACAAAGCC 58.220 40.909 2.58 0.00 0.00 4.35
2819 8116 1.134907 GGTGGCAAAGCATTGGATCTG 60.135 52.381 3.55 0.00 37.02 2.90
2851 8148 5.249622 ACATCACTAGATCGAGGAGGAGATA 59.750 44.000 7.79 0.00 30.20 1.98
2908 8205 1.556911 AGGCACAAGATGGATCTTCGT 59.443 47.619 0.00 0.08 44.84 3.85
2921 8218 2.158623 AGGTGAACATCTTCAGGCACAA 60.159 45.455 0.00 0.00 37.06 3.33
2945 8242 2.543848 GCGAGGTGAATAATCATTGCGA 59.456 45.455 0.00 0.00 38.01 5.10
2987 8284 2.500098 ACGTGGTGAGTAGCCATAACAT 59.500 45.455 0.00 0.00 38.40 2.71
3067 8364 2.103094 TCAATCATCCCTGCTTAGGACG 59.897 50.000 0.00 0.00 35.85 4.79
3173 8489 9.238368 CTAAAACACAAGGGACCTGAAATATTA 57.762 33.333 0.00 0.00 0.00 0.98
3175 8491 7.238710 ACTAAAACACAAGGGACCTGAAATAT 58.761 34.615 0.00 0.00 0.00 1.28
3177 8493 5.454966 ACTAAAACACAAGGGACCTGAAAT 58.545 37.500 0.00 0.00 0.00 2.17
3210 8526 8.731275 TTTCGTTGTATTTATCACCATCAGAT 57.269 30.769 0.00 0.00 0.00 2.90
3213 8529 9.781834 GAATTTTCGTTGTATTTATCACCATCA 57.218 29.630 0.00 0.00 0.00 3.07
3260 8576 7.448161 TGCAACCAATCCGAATGAGATAATAAT 59.552 33.333 0.00 0.00 0.00 1.28
3261 8577 6.770303 TGCAACCAATCCGAATGAGATAATAA 59.230 34.615 0.00 0.00 0.00 1.40
3262 8578 6.295249 TGCAACCAATCCGAATGAGATAATA 58.705 36.000 0.00 0.00 0.00 0.98
3271 8590 2.198827 TCACTGCAACCAATCCGAAT 57.801 45.000 0.00 0.00 0.00 3.34
3275 8594 2.100252 CCATCATCACTGCAACCAATCC 59.900 50.000 0.00 0.00 0.00 3.01
3315 8634 2.930019 CCCTCCAGCACCAGTGGA 60.930 66.667 18.40 0.00 42.06 4.02
3354 8673 4.440127 CCATTGGGCGGCAAGTGC 62.440 66.667 12.47 0.00 41.14 4.40
3425 8747 1.207089 TCCATCAGGACGCTTGTAAGG 59.793 52.381 0.00 0.00 39.61 2.69
3569 8891 0.468029 AGGTGCCAACTTCCAAGTGG 60.468 55.000 0.00 0.00 39.66 4.00
3571 8893 1.402787 CAAGGTGCCAACTTCCAAGT 58.597 50.000 0.00 0.00 42.04 3.16
3629 8951 1.338136 GGATTCGCTCCTCTTCCCCA 61.338 60.000 0.00 0.00 41.29 4.96
3681 9003 5.065731 GCCCTGACTGATTGTTATTCTTCTG 59.934 44.000 0.00 0.00 0.00 3.02
3736 9058 1.651240 CCCATCTGACTTGCGCTTGG 61.651 60.000 9.73 0.61 0.00 3.61
3835 9157 2.158726 TGTGGCTTCCTTTTTACGAGGT 60.159 45.455 0.00 0.00 35.71 3.85
3849 9171 4.521146 CAGAATATCACCTTCTGTGGCTT 58.479 43.478 5.16 0.00 45.48 4.35
3951 9273 1.816835 ACATCGTCGTCTTTAGAGCCA 59.183 47.619 0.00 0.00 0.00 4.75
3963 9285 0.439985 CAACTTGCCTGACATCGTCG 59.560 55.000 0.00 0.00 34.95 5.12
4042 9368 3.003480 ACGCTTTGCTCTCTCAAATACC 58.997 45.455 0.00 0.00 35.64 2.73
4087 9413 2.878406 AGCTTATGCACACGTTTTGACT 59.122 40.909 3.16 0.00 42.74 3.41
4118 9444 3.579335 TTACGACGACATTCACATCCA 57.421 42.857 0.00 0.00 0.00 3.41
4193 9519 2.502947 AGAACATGCACTAGCTGATCCA 59.497 45.455 0.00 0.00 42.74 3.41
4200 9526 3.791245 AGCTCTTAGAACATGCACTAGC 58.209 45.455 0.00 0.00 42.57 3.42
4213 9539 6.811253 AGTGGATCTACGATTAGCTCTTAG 57.189 41.667 3.29 0.00 0.00 2.18
4292 9632 0.174845 AGCGTGCTGGCGTAGATTAA 59.825 50.000 0.00 0.00 38.18 1.40
4350 9690 4.020307 TCACTTCATGGAACTGCATGTAGA 60.020 41.667 18.40 8.40 32.76 2.59
4352 9692 4.284829 TCACTTCATGGAACTGCATGTA 57.715 40.909 10.51 1.35 0.00 2.29
4391 9731 3.850173 AGGTAATTAGCCCCAAAGACTCA 59.150 43.478 10.99 0.00 0.00 3.41
4610 9950 2.169352 TCTGCAGGCAATTCTCTACTCC 59.831 50.000 15.13 0.00 0.00 3.85
4679 10019 3.851098 ACTCTGCGGTCTTCTTGTATTC 58.149 45.455 0.00 0.00 0.00 1.75
4699 10039 2.887783 TCTCGAAGATGGATCAGCCTAC 59.112 50.000 0.00 0.00 37.63 3.18
4700 10040 3.229697 TCTCGAAGATGGATCAGCCTA 57.770 47.619 0.00 0.00 37.63 3.93
4765 10105 8.263940 TGCTGGTAAGTATTAATGTTTCAGTC 57.736 34.615 0.00 2.52 28.70 3.51
4798 10138 4.044065 TGGATCACCTAAACCAATCCACTT 59.956 41.667 0.00 0.00 40.64 3.16
4823 10163 8.475639 GTTATGGAAGACAATGAGAGGTACTTA 58.524 37.037 0.00 0.00 41.55 2.24
4848 10188 6.319048 AGACATAGAAAGAATCACCCATGT 57.681 37.500 0.00 0.00 0.00 3.21
5006 10346 8.807667 ATGAGTTTGAAGAAATTGCTAAACTG 57.192 30.769 16.08 0.00 38.17 3.16
5055 10395 4.245845 AGAAGGAGACTCGACTGAAAAC 57.754 45.455 0.00 0.00 42.68 2.43
5077 10420 1.226974 GATGCCGAGCTAGCGAACA 60.227 57.895 9.55 7.14 0.00 3.18
5089 10432 1.045350 TCTGAAGGAGAGGGATGCCG 61.045 60.000 0.00 0.00 0.00 5.69
5122 10465 2.373169 AGACTGGAGGCAAAAGATGTCA 59.627 45.455 0.00 0.00 35.54 3.58
5149 10492 6.594788 ATTGAGTATGTGCAAAAACCATCT 57.405 33.333 0.00 0.00 0.00 2.90
5158 10501 6.595326 CCAACTAGAGAATTGAGTATGTGCAA 59.405 38.462 0.00 0.00 0.00 4.08
5167 10510 5.551233 TGACCAACCAACTAGAGAATTGAG 58.449 41.667 0.00 0.00 0.00 3.02
5194 10537 6.109359 ACAGATACACCTGCTGAAAATAGAC 58.891 40.000 0.00 0.00 37.68 2.59
5220 10563 4.624913 TCATCCCTGTCCTAACTGATTCT 58.375 43.478 0.00 0.00 0.00 2.40
5267 10610 4.590918 TGGCGGTAAGTTCCATAAATCAA 58.409 39.130 0.00 0.00 0.00 2.57
5268 10611 4.223556 TGGCGGTAAGTTCCATAAATCA 57.776 40.909 0.00 0.00 0.00 2.57
5269 10612 5.067283 ACAATGGCGGTAAGTTCCATAAATC 59.933 40.000 0.00 0.00 39.51 2.17
5327 10709 3.475575 TGAGCTTGTACAATGACTTGCA 58.524 40.909 9.13 0.62 35.69 4.08
5332 10714 6.743575 AAACCTATGAGCTTGTACAATGAC 57.256 37.500 9.13 2.10 0.00 3.06
5343 10725 5.827797 TGTTTGAACAGAAAACCTATGAGCT 59.172 36.000 0.00 0.00 36.82 4.09
5384 10766 2.022195 TCGAATGAACTACTCTCCGGG 58.978 52.381 0.00 0.00 0.00 5.73
5385 10767 2.943690 TCTCGAATGAACTACTCTCCGG 59.056 50.000 0.00 0.00 0.00 5.14
5386 10768 3.623960 AGTCTCGAATGAACTACTCTCCG 59.376 47.826 0.00 0.00 0.00 4.63
5393 10775 4.523173 AGTGTTGGAGTCTCGAATGAACTA 59.477 41.667 0.24 0.00 0.00 2.24
5428 10810 2.014857 CCGAGACTCCGAGTGATTACA 58.985 52.381 5.57 0.00 0.00 2.41
5429 10811 1.334243 CCCGAGACTCCGAGTGATTAC 59.666 57.143 5.57 0.00 0.00 1.89
5438 10820 3.217743 GTAGCCCCCGAGACTCCG 61.218 72.222 0.00 0.00 0.00 4.63
5474 10856 3.636231 CTTCCAGTGGGGGCACGA 61.636 66.667 9.92 0.00 37.22 4.35
5537 10919 1.052617 TGACAACCAGACGGATTCCA 58.947 50.000 3.09 0.00 35.59 3.53
5539 10921 2.009774 CCATGACAACCAGACGGATTC 58.990 52.381 0.00 0.00 35.59 2.52
5541 10923 0.253044 CCCATGACAACCAGACGGAT 59.747 55.000 0.00 0.00 35.59 4.18
5542 10924 1.676968 CCCATGACAACCAGACGGA 59.323 57.895 0.00 0.00 35.59 4.69
5544 10926 0.606401 AAGCCCATGACAACCAGACG 60.606 55.000 0.00 0.00 0.00 4.18
5546 10928 0.770499 TCAAGCCCATGACAACCAGA 59.230 50.000 0.00 0.00 0.00 3.86
5692 11074 7.391275 AGTTGGTCAAAGTCTCTAGAGTAGTAC 59.609 40.741 19.21 10.11 0.00 2.73
5700 11082 3.244215 TGGCAGTTGGTCAAAGTCTCTAG 60.244 47.826 0.00 0.00 0.00 2.43
5703 11085 1.876156 CTGGCAGTTGGTCAAAGTCTC 59.124 52.381 6.28 0.00 0.00 3.36
5721 11103 3.165058 TGAGGCTACGATTAACTGCTG 57.835 47.619 0.00 0.00 0.00 4.41
5775 11157 5.529060 AGTTTGTGCTTTTCTTCTAGTGGAG 59.471 40.000 0.00 0.00 0.00 3.86
5778 11160 9.736023 AATTTAGTTTGTGCTTTTCTTCTAGTG 57.264 29.630 0.00 0.00 0.00 2.74
5810 11192 1.741706 TCTGTTAGATGTCCGTCGTCC 59.258 52.381 0.00 0.00 32.85 4.79
5813 11195 3.556513 GCTATCTGTTAGATGTCCGTCG 58.443 50.000 1.71 0.00 35.37 5.12
5850 11232 2.082231 CTTCATGGACTTGGCACTCTG 58.918 52.381 0.00 0.00 0.00 3.35
5931 11313 5.105554 TGAAACTCATGGACTTAGCTCTCTC 60.106 44.000 0.00 0.00 0.00 3.20
5981 11363 1.100510 TGGTAGTTGATCGGAGTCGG 58.899 55.000 0.00 0.00 36.95 4.79
5987 11369 6.418956 CGATTAATTGTTGGTAGTTGATCGG 58.581 40.000 0.00 0.00 36.81 4.18
6001 11383 3.073062 CCCCTCAGGATCCGATTAATTGT 59.927 47.826 5.98 0.00 38.24 2.71
6010 11392 2.565645 CGTAGCCCCTCAGGATCCG 61.566 68.421 5.98 1.36 38.24 4.18
6018 11400 1.108132 CCTAGTGGACGTAGCCCCTC 61.108 65.000 0.00 0.00 34.57 4.30
6029 11411 4.101114 TGTGAATTTCTAGCCCTAGTGGA 58.899 43.478 2.53 0.00 35.39 4.02
6035 11417 7.669722 TGAATTACTTTGTGAATTTCTAGCCCT 59.330 33.333 0.00 0.00 0.00 5.19
6046 11428 3.745799 TCCGGCTGAATTACTTTGTGAA 58.254 40.909 0.00 0.00 0.00 3.18
6047 11429 3.410631 TCCGGCTGAATTACTTTGTGA 57.589 42.857 0.00 0.00 0.00 3.58
6054 11436 3.003480 GCCAGATATCCGGCTGAATTAC 58.997 50.000 20.79 0.00 45.29 1.89
6069 11451 2.037772 GGTAATCACTCGGATGCCAGAT 59.962 50.000 0.00 0.00 36.02 2.90
6085 11467 6.615726 TCTCTTAGTCCAAGCCTATTGGTAAT 59.384 38.462 6.53 0.00 40.40 1.89
6094 11476 1.203313 TGGGTCTCTTAGTCCAAGCCT 60.203 52.381 0.00 0.00 33.94 4.58
6111 11493 2.862140 GCACAACTTTCACGGAATTGGG 60.862 50.000 0.00 0.00 0.00 4.12
6147 11529 4.150627 CAGTCTCGGATAAATTATGTGCCG 59.849 45.833 5.55 5.55 40.06 5.69
6318 11700 5.135020 AGGAATATCATTCTCCCAACACCAT 59.865 40.000 0.00 0.00 0.00 3.55
6423 11805 2.957402 TGCCAGTCCAGAAACAATCT 57.043 45.000 0.00 0.00 39.68 2.40
6511 12021 1.259609 TTCATGAAAGGGGCAAGCTG 58.740 50.000 5.45 0.00 0.00 4.24
6564 12074 9.092876 TGCTAACCTTTTGACAAAACAATTAAG 57.907 29.630 9.30 4.51 0.00 1.85
6718 12434 5.682943 CAAGAAATAACTTGTTCCGGTCA 57.317 39.130 0.00 0.00 41.32 4.02
6754 12471 6.860023 GCAGATATAGCAAGCATAAAACTTGG 59.140 38.462 5.72 0.00 43.81 3.61
6861 12578 1.666700 GCACCAGTACGACACAACAAA 59.333 47.619 0.00 0.00 0.00 2.83
6900 12617 7.362802 ACTTACAACTTGTAGTCCTTTCTCT 57.637 36.000 1.95 0.00 33.92 3.10
7018 12752 6.767902 CCAACAACACTAGTGGCAGATATATT 59.232 38.462 26.12 5.84 34.19 1.28
7058 12792 7.254556 CGCTCTCAATTTTTCATCTATAGCACA 60.255 37.037 0.00 0.00 0.00 4.57
7094 12828 2.902705 TGCCATACCCGTCATACTTC 57.097 50.000 0.00 0.00 0.00 3.01
7103 12837 3.181487 CCTTCTTTTTGATGCCATACCCG 60.181 47.826 0.00 0.00 0.00 5.28
7143 12877 8.677300 GTGCATAGAGACATTCAAATCCTTTTA 58.323 33.333 0.00 0.00 0.00 1.52
7372 13110 3.333680 ACATCCACCTTCACCTATTGGTT 59.666 43.478 0.00 0.00 46.05 3.67
7409 13147 1.299976 CGCTGGCCTAAGGTCCTTT 59.700 57.895 10.04 0.00 0.00 3.11
7437 13175 2.803956 GGTCCAACCTTTTAAGAGGGG 58.196 52.381 16.01 8.67 41.31 4.79
7456 13194 2.045926 CCTGTGAAAGAGGGGCGG 60.046 66.667 0.00 0.00 45.29 6.13
7480 13218 8.539770 TTTTCATCAAGTAGTGAATGAGAGTC 57.460 34.615 0.00 0.00 40.50 3.36
7484 13222 9.565213 GGAATTTTTCATCAAGTAGTGAATGAG 57.435 33.333 0.00 0.00 40.50 2.90
7571 13313 6.344500 TGCACATGATTTTACAAACCTTGTT 58.656 32.000 0.00 0.00 42.22 2.83
7609 13353 9.019656 TGCATATGACCTTTAACAAATGTAGTT 57.980 29.630 6.97 0.00 0.00 2.24
7612 13356 9.019656 AGTTGCATATGACCTTTAACAAATGTA 57.980 29.630 6.97 0.00 0.00 2.29
7783 13529 8.463930 AACAAAATGGAAGATTGAGAACAGTA 57.536 30.769 0.00 0.00 0.00 2.74
7784 13530 6.966534 ACAAAATGGAAGATTGAGAACAGT 57.033 33.333 0.00 0.00 0.00 3.55
7785 13531 7.428020 TGAACAAAATGGAAGATTGAGAACAG 58.572 34.615 0.00 0.00 0.00 3.16
7828 13574 7.424227 AATTTCGCATCAAATGAAACACAAT 57.576 28.000 0.00 0.00 34.73 2.71
7833 13579 9.810231 AATTGTAAATTTCGCATCAAATGAAAC 57.190 25.926 0.00 0.00 34.73 2.78
7857 13603 9.338622 GCCTGACAACCAATTATAGTTACTAAT 57.661 33.333 0.00 0.00 0.00 1.73
7909 13655 7.706179 TGGATTCAACTTCAACAAACAAGAATC 59.294 33.333 0.00 0.00 38.55 2.52
7933 13679 3.652057 AACACCAAGTATCCTCCATGG 57.348 47.619 4.97 4.97 37.19 3.66
7934 13680 5.982890 AAAAACACCAAGTATCCTCCATG 57.017 39.130 0.00 0.00 0.00 3.66
7957 13703 7.428282 TGTGACTTGCGAAGAAATAAATACA 57.572 32.000 3.37 0.00 0.00 2.29
7985 13735 7.838079 ATATCCCAACTAGCATAATTTTGCA 57.162 32.000 20.75 7.89 45.23 4.08
8013 13763 7.121974 AGAATCCATTAGCATTAATCGAACG 57.878 36.000 0.00 0.00 0.00 3.95
8017 13767 8.438513 CACACTAGAATCCATTAGCATTAATCG 58.561 37.037 0.00 0.00 0.00 3.34
8019 13769 9.277783 GTCACACTAGAATCCATTAGCATTAAT 57.722 33.333 0.00 0.00 0.00 1.40
8026 13776 5.605534 CAGGGTCACACTAGAATCCATTAG 58.394 45.833 0.00 0.00 0.00 1.73
8037 13787 0.400213 CCCAAAGCAGGGTCACACTA 59.600 55.000 0.99 0.00 44.24 2.74
8096 13846 6.199937 AGCATGTCAATGGAATGTTAAGAC 57.800 37.500 0.00 0.00 34.09 3.01
8186 13939 6.821665 ACTTCTAGTAGTGCTCTTCTCTACAG 59.178 42.308 0.59 0.00 41.72 2.74
8187 13940 6.713276 ACTTCTAGTAGTGCTCTTCTCTACA 58.287 40.000 0.59 0.00 41.72 2.74
8188 13941 7.619964 AACTTCTAGTAGTGCTCTTCTCTAC 57.380 40.000 2.42 0.00 40.36 2.59
8218 13973 3.570125 GGAGTAAAAGGTTGCTCTTGCTT 59.430 43.478 4.86 0.00 43.74 3.91
8236 13991 8.352942 CACTCAATAAAAAGCAAACTAAGGAGT 58.647 33.333 0.00 0.00 37.59 3.85
8237 13992 8.352942 ACACTCAATAAAAAGCAAACTAAGGAG 58.647 33.333 0.00 0.00 0.00 3.69
8238 13993 8.232913 ACACTCAATAAAAAGCAAACTAAGGA 57.767 30.769 0.00 0.00 0.00 3.36
8239 13994 8.352942 AGACACTCAATAAAAAGCAAACTAAGG 58.647 33.333 0.00 0.00 0.00 2.69
8293 14048 5.457197 GGGGTAAACTATGGAATAAGGGGAC 60.457 48.000 0.00 0.00 0.00 4.46
8313 14068 6.752091 AGGGATTAAATTTGTTAGATGGGGT 58.248 36.000 0.00 0.00 0.00 4.95
8362 14117 8.394971 TGTGTTTTATTCCATAGGCTATCATG 57.605 34.615 3.47 0.00 0.00 3.07
8376 14131 8.825667 TTCCATAGGCTTTTTGTGTTTTATTC 57.174 30.769 0.00 0.00 0.00 1.75
8390 14145 6.496911 ACCTTTGTGTTTTATTCCATAGGCTT 59.503 34.615 0.00 0.00 31.58 4.35
8391 14146 6.016555 ACCTTTGTGTTTTATTCCATAGGCT 58.983 36.000 0.00 0.00 31.58 4.58
8392 14147 6.071616 TCACCTTTGTGTTTTATTCCATAGGC 60.072 38.462 0.00 0.00 43.26 3.93
8393 14148 7.362920 CCTCACCTTTGTGTTTTATTCCATAGG 60.363 40.741 0.00 0.00 43.26 2.57
8394 14149 7.393234 TCCTCACCTTTGTGTTTTATTCCATAG 59.607 37.037 0.00 0.00 43.26 2.23
8395 14150 7.235079 TCCTCACCTTTGTGTTTTATTCCATA 58.765 34.615 0.00 0.00 43.26 2.74
8396 14151 6.074648 TCCTCACCTTTGTGTTTTATTCCAT 58.925 36.000 0.00 0.00 43.26 3.41
8397 14152 5.450453 TCCTCACCTTTGTGTTTTATTCCA 58.550 37.500 0.00 0.00 43.26 3.53
8398 14153 6.399639 TTCCTCACCTTTGTGTTTTATTCC 57.600 37.500 0.00 0.00 43.26 3.01
8399 14154 8.194769 TCTTTTCCTCACCTTTGTGTTTTATTC 58.805 33.333 0.00 0.00 43.26 1.75
8400 14155 7.979537 GTCTTTTCCTCACCTTTGTGTTTTATT 59.020 33.333 0.00 0.00 43.26 1.40
8401 14156 7.123547 TGTCTTTTCCTCACCTTTGTGTTTTAT 59.876 33.333 0.00 0.00 43.26 1.40
8402 14157 6.434652 TGTCTTTTCCTCACCTTTGTGTTTTA 59.565 34.615 0.00 0.00 43.26 1.52
8403 14158 5.245075 TGTCTTTTCCTCACCTTTGTGTTTT 59.755 36.000 0.00 0.00 43.26 2.43
8404 14159 4.770010 TGTCTTTTCCTCACCTTTGTGTTT 59.230 37.500 0.00 0.00 43.26 2.83
8405 14160 4.340617 TGTCTTTTCCTCACCTTTGTGTT 58.659 39.130 0.00 0.00 43.26 3.32
8406 14161 3.963129 TGTCTTTTCCTCACCTTTGTGT 58.037 40.909 0.00 0.00 43.26 3.72
8407 14162 4.981806 TTGTCTTTTCCTCACCTTTGTG 57.018 40.909 0.00 0.00 44.18 3.33
8408 14163 5.993748 TTTTGTCTTTTCCTCACCTTTGT 57.006 34.783 0.00 0.00 0.00 2.83
8409 14164 6.258507 CCATTTTTGTCTTTTCCTCACCTTTG 59.741 38.462 0.00 0.00 0.00 2.77
8410 14165 6.156083 TCCATTTTTGTCTTTTCCTCACCTTT 59.844 34.615 0.00 0.00 0.00 3.11
8411 14166 5.660864 TCCATTTTTGTCTTTTCCTCACCTT 59.339 36.000 0.00 0.00 0.00 3.50
8412 14167 5.208121 TCCATTTTTGTCTTTTCCTCACCT 58.792 37.500 0.00 0.00 0.00 4.00
8479 14234 6.745450 CCCACGTGTGTAATTTTCAACATATC 59.255 38.462 15.65 0.00 0.00 1.63
8553 14308 1.352352 CCTTGAGGGGTCAGAACACAT 59.648 52.381 0.00 0.00 0.00 3.21
8563 14318 1.132168 AGGGTCTAAACCTTGAGGGGT 60.132 52.381 1.54 0.00 45.66 4.95
8628 14383 4.391830 CGGCAACTAATACATGTCAACACT 59.608 41.667 0.00 0.00 0.00 3.55
8662 14417 4.327982 ACTCAGATCCAACGTGATATGG 57.672 45.455 9.74 4.41 35.26 2.74
8704 14459 5.012251 GGGCTTTAGGGATAAAGAGAGTAGG 59.988 48.000 11.03 0.00 38.88 3.18
8705 14460 5.012251 GGGGCTTTAGGGATAAAGAGAGTAG 59.988 48.000 11.03 0.00 38.88 2.57
8729 14484 7.609532 AGGATGTGATACTTTCTTCCTTTCTTG 59.390 37.037 0.00 0.00 29.87 3.02
8732 14487 7.148171 CCAAGGATGTGATACTTTCTTCCTTTC 60.148 40.741 8.24 0.00 37.08 2.62
8745 14500 4.566278 GGATATGCTGCCAAGGATGTGATA 60.566 45.833 0.00 0.00 34.94 2.15
8771 14526 2.168313 GAGGGTTATTTTGCCACCATGG 59.832 50.000 11.19 11.19 41.55 3.66
8786 14541 2.539302 CCCATTGGATGTTTGAGGGTT 58.461 47.619 3.62 0.00 0.00 4.11
8800 14555 3.432046 GCACCATCCAAATAACCCCATTG 60.432 47.826 0.00 0.00 0.00 2.82
8801 14556 2.771372 GCACCATCCAAATAACCCCATT 59.229 45.455 0.00 0.00 0.00 3.16


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

AutoCloner maintained by Alex Coulton.