Multiple sequence alignment - TraesCS7A01G127300

Loading Multiple Alignment...

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 TraesCS7A01G127300 chr7A 100.000 4442 0 0 1 4442 81779073 81774632 0.000000e+00 8203.0
1 TraesCS7A01G127300 chr7A 89.067 1436 142 11 2038 3469 81641243 81639819 0.000000e+00 1768.0
2 TraesCS7A01G127300 chr7A 87.709 1432 159 12 2043 3472 81768829 81767413 0.000000e+00 1653.0
3 TraesCS7A01G127300 chr7A 82.426 1047 160 13 1007 2047 81642304 81641276 0.000000e+00 893.0
4 TraesCS7A01G127300 chr7A 82.086 882 142 10 1168 2047 81769734 81768867 0.000000e+00 739.0
5 TraesCS7A01G127300 chr7A 76.218 349 44 22 4004 4320 81766902 81766561 9.950000e-32 148.0
6 TraesCS7A01G127300 chr7B 93.567 2456 125 15 1004 3450 25886444 25888875 0.000000e+00 3629.0
7 TraesCS7A01G127300 chr7B 95.648 1103 48 0 1673 2775 25664572 25663470 0.000000e+00 1772.0
8 TraesCS7A01G127300 chr7B 86.838 1436 172 13 2038 3469 25631212 25629790 0.000000e+00 1589.0
9 TraesCS7A01G127300 chr7B 87.500 1312 155 7 2156 3466 25654583 25653280 0.000000e+00 1506.0
10 TraesCS7A01G127300 chr7B 91.975 947 51 14 2805 3739 25663476 25662543 0.000000e+00 1304.0
11 TraesCS7A01G127300 chr7B 92.457 822 41 11 838 1654 25669172 25668367 0.000000e+00 1155.0
12 TraesCS7A01G127300 chr7B 83.565 359 25 8 304 636 25670018 25669668 5.580000e-79 305.0
13 TraesCS7A01G127300 chr7B 87.709 179 16 1 636 808 25669619 25669441 2.090000e-48 204.0
14 TraesCS7A01G127300 chr7B 88.506 174 9 6 139 303 25670292 25670121 2.710000e-47 200.0
15 TraesCS7A01G127300 chr7B 100.000 44 0 0 4000 4043 25660534 25660491 1.020000e-11 82.4
16 TraesCS7A01G127300 chr7B 95.238 42 2 0 1645 1686 25667008 25666967 2.870000e-07 67.6
17 TraesCS7A01G127300 chr7D 93.840 2419 125 13 1032 3450 78309145 78306751 0.000000e+00 3620.0
18 TraesCS7A01G127300 chr7D 86.820 1434 178 8 2038 3469 78210045 78208621 0.000000e+00 1591.0
19 TraesCS7A01G127300 chr7D 87.348 1312 157 8 2156 3466 78301436 78300133 0.000000e+00 1495.0
20 TraesCS7A01G127300 chr7D 85.507 345 32 10 304 636 78310140 78309802 1.180000e-90 344.0
21 TraesCS7A01G127300 chr7D 95.146 103 5 0 1580 1682 78322239 78322137 3.560000e-36 163.0
22 TraesCS7A01G127300 chr7D 95.833 96 4 0 156 251 78310364 78310269 5.950000e-34 156.0
23 TraesCS7A01G127300 chr7D 76.271 295 30 12 4004 4258 78305442 78305148 2.170000e-23 121.0
24 TraesCS7A01G127300 chr7D 97.368 38 0 1 914 951 78309230 78309194 3.710000e-06 63.9
25 TraesCS7A01G127300 chr4A 94.326 141 8 0 1 141 626007075 626007215 2.690000e-52 217.0
26 TraesCS7A01G127300 chr4A 91.608 143 12 0 1 143 164519366 164519224 9.750000e-47 198.0
27 TraesCS7A01G127300 chr6A 93.662 142 9 0 1 142 29831880 29831739 3.480000e-51 213.0
28 TraesCS7A01G127300 chr2A 93.571 140 9 0 1 140 613986719 613986580 4.500000e-50 209.0
29 TraesCS7A01G127300 chr2A 92.857 140 10 0 1 140 34152759 34152620 2.090000e-48 204.0
30 TraesCS7A01G127300 chr2A 91.608 143 12 0 1 143 698794921 698794779 9.750000e-47 198.0
31 TraesCS7A01G127300 chr5A 92.414 145 11 0 1 145 598054421 598054277 1.620000e-49 207.0
32 TraesCS7A01G127300 chr5A 91.667 144 12 0 1 144 85777853 85777710 2.710000e-47 200.0
33 TraesCS7A01G127300 chr3A 91.667 144 12 0 1 144 739954381 739954524 2.710000e-47 200.0
34 TraesCS7A01G127300 chr2D 82.390 159 15 7 136 284 585639386 585639541 4.660000e-25 126.0
35 TraesCS7A01G127300 chr3B 86.916 107 12 2 136 242 560164773 560164877 7.810000e-23 119.0


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS7A01G127300 chr7A 81774632 81779073 4441 True 8203.000000 8203 100.000000 1 4442 1 chr7A.!!$R1 4441
1 TraesCS7A01G127300 chr7A 81639819 81642304 2485 True 1330.500000 1768 85.746500 1007 3469 2 chr7A.!!$R2 2462
2 TraesCS7A01G127300 chr7A 81766561 81769734 3173 True 846.666667 1653 82.004333 1168 4320 3 chr7A.!!$R3 3152
3 TraesCS7A01G127300 chr7B 25886444 25888875 2431 False 3629.000000 3629 93.567000 1004 3450 1 chr7B.!!$F1 2446
4 TraesCS7A01G127300 chr7B 25629790 25631212 1422 True 1589.000000 1589 86.838000 2038 3469 1 chr7B.!!$R1 1431
5 TraesCS7A01G127300 chr7B 25653280 25654583 1303 True 1506.000000 1506 87.500000 2156 3466 1 chr7B.!!$R2 1310
6 TraesCS7A01G127300 chr7B 25660491 25670292 9801 True 636.250000 1772 91.887250 139 4043 8 chr7B.!!$R3 3904
7 TraesCS7A01G127300 chr7D 78208621 78210045 1424 True 1591.000000 1591 86.820000 2038 3469 1 chr7D.!!$R1 1431
8 TraesCS7A01G127300 chr7D 78300133 78310364 10231 True 966.650000 3620 89.361167 156 4258 6 chr7D.!!$R3 4102

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
780 987 0.035056 CCTGGAACCATCGCCTTTCT 60.035 55.0 0.00 0.00 0.00 2.52 F
1068 1756 0.108898 CACTCCTTCTCCTGCTGACG 60.109 60.0 0.00 0.00 0.00 4.35 F
1069 1757 0.251386 ACTCCTTCTCCTGCTGACGA 60.251 55.0 0.00 0.00 0.00 4.20 F
1955 6434 0.032540 GGCAAAAACACCCTCTGCAG 59.967 55.0 7.63 7.63 34.66 4.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1691 6170 0.321564 CCTGTGATTGACAAGCGGGA 60.322 55.000 8.55 0.00 32.80 5.14 R
1946 6425 0.759346 GGGTATGTACCTGCAGAGGG 59.241 60.000 17.39 1.11 44.84 4.30 R
2851 7373 1.280133 CCATTGGAGCACAGGAGAAGA 59.720 52.381 0.00 0.00 0.00 2.87 R
3840 8588 0.674895 GCCTAGCACCTGGTGAACTG 60.675 60.000 30.23 15.31 35.23 3.16 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
24 25 4.845177 CACGCGTTGGACTACGTA 57.155 55.556 10.22 0.00 43.22 3.57
25 26 3.317608 CACGCGTTGGACTACGTAT 57.682 52.632 10.22 0.00 43.22 3.06
26 27 0.911856 CACGCGTTGGACTACGTATG 59.088 55.000 10.22 0.00 43.22 2.39
27 28 0.799534 ACGCGTTGGACTACGTATGC 60.800 55.000 5.58 0.00 43.22 3.14
28 29 1.477030 CGCGTTGGACTACGTATGCC 61.477 60.000 0.00 1.02 43.22 4.40
29 30 1.477030 GCGTTGGACTACGTATGCCG 61.477 60.000 0.00 0.00 43.22 5.69
64 65 4.451150 CGCCCGCTGGAGCAACTA 62.451 66.667 0.00 0.00 42.21 2.24
65 66 2.190578 GCCCGCTGGAGCAACTAT 59.809 61.111 0.00 0.00 42.21 2.12
66 67 1.452108 GCCCGCTGGAGCAACTATT 60.452 57.895 0.00 0.00 42.21 1.73
67 68 1.440145 GCCCGCTGGAGCAACTATTC 61.440 60.000 0.00 0.00 42.21 1.75
68 69 0.815615 CCCGCTGGAGCAACTATTCC 60.816 60.000 0.00 0.00 42.21 3.01
69 70 1.154205 CCGCTGGAGCAACTATTCCG 61.154 60.000 0.00 0.00 42.21 4.30
70 71 1.154205 CGCTGGAGCAACTATTCCGG 61.154 60.000 0.00 0.00 41.82 5.14
71 72 0.107654 GCTGGAGCAACTATTCCGGT 60.108 55.000 0.00 0.00 41.13 5.28
72 73 1.679032 GCTGGAGCAACTATTCCGGTT 60.679 52.381 0.00 0.00 41.13 4.44
73 74 2.009774 CTGGAGCAACTATTCCGGTTG 58.990 52.381 0.00 0.00 44.60 3.77
77 78 1.060308 CAACTATTCCGGTTGCGCG 59.940 57.895 0.00 0.00 37.76 6.86
78 79 2.746803 AACTATTCCGGTTGCGCGC 61.747 57.895 27.26 27.26 0.00 6.86
79 80 4.279535 CTATTCCGGTTGCGCGCG 62.280 66.667 28.44 28.44 0.00 6.86
86 87 4.377661 GGTTGCGCGCGTGCTAAA 62.378 61.111 40.02 26.85 39.65 1.85
87 88 2.426098 GTTGCGCGCGTGCTAAAA 60.426 55.556 40.02 26.14 39.65 1.52
88 89 2.426098 TTGCGCGCGTGCTAAAAC 60.426 55.556 40.02 15.40 39.65 2.43
89 90 4.711193 TGCGCGCGTGCTAAAACG 62.711 61.111 40.02 19.10 46.30 3.60
94 95 3.658048 GCGTGCTAAAACGGGGAA 58.342 55.556 0.00 0.00 43.75 3.97
95 96 2.177044 GCGTGCTAAAACGGGGAAT 58.823 52.632 0.00 0.00 43.75 3.01
96 97 0.524414 GCGTGCTAAAACGGGGAATT 59.476 50.000 0.00 0.00 43.75 2.17
97 98 1.068125 GCGTGCTAAAACGGGGAATTT 60.068 47.619 0.00 0.00 43.75 1.82
98 99 2.608506 GCGTGCTAAAACGGGGAATTTT 60.609 45.455 0.00 0.00 43.75 1.82
99 100 2.983803 CGTGCTAAAACGGGGAATTTTG 59.016 45.455 0.00 0.00 39.89 2.44
100 101 2.734606 GTGCTAAAACGGGGAATTTTGC 59.265 45.455 0.00 0.00 31.79 3.68
101 102 1.989864 GCTAAAACGGGGAATTTTGCG 59.010 47.619 0.00 0.00 31.79 4.85
102 103 2.601804 CTAAAACGGGGAATTTTGCGG 58.398 47.619 0.00 0.00 31.79 5.69
103 104 0.601576 AAAACGGGGAATTTTGCGGC 60.602 50.000 0.00 0.00 0.00 6.53
104 105 2.757155 AAACGGGGAATTTTGCGGCG 62.757 55.000 0.51 0.51 0.00 6.46
126 127 4.794241 GCTAGTTTGGCGCGCGTG 62.794 66.667 32.35 16.86 0.00 5.34
127 128 3.411351 CTAGTTTGGCGCGCGTGT 61.411 61.111 32.35 10.14 0.00 4.49
128 129 2.950172 CTAGTTTGGCGCGCGTGTT 61.950 57.895 32.35 11.84 0.00 3.32
129 130 3.230005 TAGTTTGGCGCGCGTGTTG 62.230 57.895 32.35 2.67 0.00 3.33
135 136 4.505217 GCGCGCGTGTTGGAGATG 62.505 66.667 32.35 0.00 0.00 2.90
136 137 4.505217 CGCGCGTGTTGGAGATGC 62.505 66.667 24.19 0.00 0.00 3.91
137 138 3.121030 GCGCGTGTTGGAGATGCT 61.121 61.111 8.43 0.00 0.00 3.79
258 267 1.992277 CTCTAGCTGGCCAGGGTGT 60.992 63.158 33.46 4.66 0.00 4.16
264 273 1.915266 CTGGCCAGGGTGTCTCTCA 60.915 63.158 26.14 0.00 0.00 3.27
278 287 2.625790 GTCTCTCAGGTTGTCTGACAGT 59.374 50.000 10.77 0.00 46.71 3.55
291 300 4.184629 GTCTGACAGTCTCTCTCTCTCTC 58.815 52.174 2.24 0.00 0.00 3.20
293 302 4.160439 TCTGACAGTCTCTCTCTCTCTCTC 59.840 50.000 1.59 0.00 0.00 3.20
420 544 3.064324 GCAGCGGCCATTGGAAGT 61.064 61.111 6.95 0.00 0.00 3.01
421 545 3.056313 GCAGCGGCCATTGGAAGTC 62.056 63.158 6.95 0.00 0.00 3.01
423 547 2.746277 GCGGCCATTGGAAGTCGT 60.746 61.111 6.95 0.00 0.00 4.34
424 548 2.750888 GCGGCCATTGGAAGTCGTC 61.751 63.158 6.95 0.00 0.00 4.20
493 642 5.520376 TTCTTTCTTTCTTTCTTGCCAGG 57.480 39.130 0.00 0.00 0.00 4.45
519 668 5.575606 CACAGCATTTCTCAGGCTAAATTTG 59.424 40.000 0.00 0.00 35.82 2.32
520 669 5.477984 ACAGCATTTCTCAGGCTAAATTTGA 59.522 36.000 0.00 0.00 35.82 2.69
554 704 6.318628 TGAAACTGTTATCACACAACACAAC 58.681 36.000 0.00 0.00 32.64 3.32
622 773 1.020437 GCACAAGAGGAATGCTAGCC 58.980 55.000 13.29 0.00 36.40 3.93
739 946 0.588252 CAAGACAAGCCACGGTCAAG 59.412 55.000 0.00 0.00 36.50 3.02
760 967 1.588824 TTGCCGGCTCTTGCTCAATG 61.589 55.000 29.70 0.00 39.59 2.82
775 982 1.754234 AATGCCTGGAACCATCGCC 60.754 57.895 0.00 0.00 0.00 5.54
778 985 1.678970 GCCTGGAACCATCGCCTTT 60.679 57.895 0.00 0.00 0.00 3.11
780 987 0.035056 CCTGGAACCATCGCCTTTCT 60.035 55.000 0.00 0.00 0.00 2.52
781 988 1.209504 CCTGGAACCATCGCCTTTCTA 59.790 52.381 0.00 0.00 0.00 2.10
787 994 2.711542 ACCATCGCCTTTCTAACCTTG 58.288 47.619 0.00 0.00 0.00 3.61
798 1231 5.578727 CCTTTCTAACCTTGATCTTCACTCG 59.421 44.000 0.00 0.00 0.00 4.18
808 1241 7.861372 ACCTTGATCTTCACTCGTTATTATACG 59.139 37.037 0.00 0.00 42.68 3.06
831 1320 5.105837 CGAGATCCATAGCATGAGAGATTGA 60.106 44.000 0.00 0.00 0.00 2.57
832 1321 6.288941 AGATCCATAGCATGAGAGATTGAG 57.711 41.667 0.00 0.00 0.00 3.02
833 1322 5.781306 AGATCCATAGCATGAGAGATTGAGT 59.219 40.000 0.00 0.00 0.00 3.41
835 1324 6.338214 TCCATAGCATGAGAGATTGAGTAC 57.662 41.667 0.00 0.00 0.00 2.73
836 1325 6.073981 TCCATAGCATGAGAGATTGAGTACT 58.926 40.000 0.00 0.00 0.00 2.73
899 1572 1.558233 AGGCCCTGTACTGTACACTC 58.442 55.000 16.26 8.30 34.46 3.51
989 1674 7.808856 CAGTAGAACTACAAGTTAGAACCAGAC 59.191 40.741 13.34 0.00 38.80 3.51
990 1675 6.099159 AGAACTACAAGTTAGAACCAGACC 57.901 41.667 0.00 0.00 38.80 3.85
1067 1755 1.204467 CTCACTCCTTCTCCTGCTGAC 59.796 57.143 0.00 0.00 0.00 3.51
1068 1756 0.108898 CACTCCTTCTCCTGCTGACG 60.109 60.000 0.00 0.00 0.00 4.35
1069 1757 0.251386 ACTCCTTCTCCTGCTGACGA 60.251 55.000 0.00 0.00 0.00 4.20
1144 1841 2.187946 CCTCGGTGTCCATCCAGC 59.812 66.667 0.00 0.00 0.00 4.85
1146 1843 1.153489 CTCGGTGTCCATCCAGCAG 60.153 63.158 0.00 0.00 33.13 4.24
1147 1844 1.892819 CTCGGTGTCCATCCAGCAGT 61.893 60.000 0.00 0.00 33.13 4.40
1148 1845 0.613572 TCGGTGTCCATCCAGCAGTA 60.614 55.000 0.00 0.00 33.13 2.74
1150 1847 0.460284 GGTGTCCATCCAGCAGTACG 60.460 60.000 0.00 0.00 33.13 3.67
1151 1848 0.460284 GTGTCCATCCAGCAGTACGG 60.460 60.000 0.00 0.00 0.00 4.02
1153 1850 2.203070 CCATCCAGCAGTACGGCC 60.203 66.667 14.67 0.00 0.00 6.13
1157 1854 4.473520 CCAGCAGTACGGCCCCAG 62.474 72.222 14.67 2.69 0.00 4.45
1283 1986 4.697756 CTCGGCGGCCAAGACCAA 62.698 66.667 20.71 0.00 0.00 3.67
1284 1987 4.697756 TCGGCGGCCAAGACCAAG 62.698 66.667 20.71 0.00 0.00 3.61
1285 1988 4.697756 CGGCGGCCAAGACCAAGA 62.698 66.667 20.71 0.00 0.00 3.02
1286 1989 3.056328 GGCGGCCAAGACCAAGAC 61.056 66.667 15.62 0.00 0.00 3.01
1287 1990 3.056328 GCGGCCAAGACCAAGACC 61.056 66.667 2.24 0.00 0.00 3.85
1288 1991 2.742372 CGGCCAAGACCAAGACCG 60.742 66.667 2.24 0.00 0.00 4.79
1289 1992 2.430367 GGCCAAGACCAAGACCGT 59.570 61.111 0.00 0.00 0.00 4.83
1451 2154 2.179517 CACGGAGCTCCTCGACAC 59.820 66.667 29.73 2.36 0.00 3.67
1582 2285 4.767255 CTGCGTCTGCCAGGGGTC 62.767 72.222 0.00 0.00 41.78 4.46
1598 2301 1.326951 GGTCTGCTCTCCTCAGGGTC 61.327 65.000 0.00 0.00 32.63 4.46
1691 6170 1.384191 GGCCTGACCCTTTCACCAT 59.616 57.895 0.00 0.00 0.00 3.55
1827 6306 4.487714 TCATGTTATGAGGAGGTTGACC 57.512 45.455 0.00 0.00 33.59 4.02
1946 6425 0.317854 GGACTCTGCGGCAAAAACAC 60.318 55.000 3.44 0.00 0.00 3.32
1955 6434 0.032540 GGCAAAAACACCCTCTGCAG 59.967 55.000 7.63 7.63 34.66 4.41
1974 6453 2.220479 GGTACATACCCAAGCTCGAC 57.780 55.000 0.00 0.00 40.53 4.20
1978 6457 1.141881 ATACCCAAGCTCGACTGCG 59.858 57.895 0.00 0.00 38.13 5.18
2288 6809 3.366052 TTATCTCAAAGTTCCCAGGGC 57.634 47.619 0.00 0.00 0.00 5.19
2322 6843 3.369147 CGTCAGAATTGGCTTCTACAGTG 59.631 47.826 0.00 0.00 42.48 3.66
2843 7365 3.552890 GCCACAGTTCTTTTTGATCACCC 60.553 47.826 0.00 0.00 0.00 4.61
2850 7372 2.552315 TCTTTTTGATCACCCGAGCAAC 59.448 45.455 0.00 0.00 46.69 4.17
2851 7373 2.270352 TTTTGATCACCCGAGCAACT 57.730 45.000 0.00 0.00 46.69 3.16
2852 7374 1.808411 TTTGATCACCCGAGCAACTC 58.192 50.000 0.00 0.00 46.69 3.01
2928 7450 1.346068 GGACTGGCCTATCTCCATCAC 59.654 57.143 3.32 0.00 32.37 3.06
3190 7712 0.672711 GAAGGGGGTTCGTCTTTCCG 60.673 60.000 0.00 0.00 0.00 4.30
3232 7754 0.890683 GGAGGTTGAAATGGCTGGTG 59.109 55.000 0.00 0.00 0.00 4.17
3240 7762 1.678101 GAAATGGCTGGTGTATGCTCC 59.322 52.381 0.00 0.00 0.00 4.70
3246 7768 1.945394 GCTGGTGTATGCTCCATTGAG 59.055 52.381 5.00 0.00 41.84 3.02
3340 7862 3.441572 AGAATTCAACCATTCAGAAGCGG 59.558 43.478 8.44 0.60 35.85 5.52
3342 7864 1.522668 TCAACCATTCAGAAGCGGTG 58.477 50.000 7.64 0.20 0.00 4.94
3450 7972 6.801539 TCACTTGTGGAATAATGTTCAGTC 57.198 37.500 0.64 0.00 0.00 3.51
3451 7973 6.295249 TCACTTGTGGAATAATGTTCAGTCA 58.705 36.000 0.64 0.00 0.00 3.41
3452 7974 6.427853 TCACTTGTGGAATAATGTTCAGTCAG 59.572 38.462 0.64 0.00 0.00 3.51
3453 7975 6.205464 CACTTGTGGAATAATGTTCAGTCAGT 59.795 38.462 0.00 0.00 0.00 3.41
3555 8080 7.458409 AATACTCTGTGATGTTGCAGAAAAT 57.542 32.000 0.00 0.00 40.68 1.82
3588 8113 1.506025 TGTCCCTGCCATATGTAGCA 58.494 50.000 1.24 4.29 37.46 3.49
3600 8248 4.489810 CATATGTAGCAACTCTCCGGATC 58.510 47.826 3.57 0.00 0.00 3.36
3608 8256 3.551863 GCAACTCTCCGGATCTGTATCAG 60.552 52.174 3.57 0.00 33.41 2.90
3613 8261 4.142790 TCTCCGGATCTGTATCAGTAACC 58.857 47.826 3.57 0.00 33.41 2.85
3617 8265 4.825634 CCGGATCTGTATCAGTAACCAGTA 59.174 45.833 0.00 0.00 33.41 2.74
3618 8266 5.301045 CCGGATCTGTATCAGTAACCAGTAA 59.699 44.000 0.00 0.00 33.41 2.24
3619 8267 6.439599 CGGATCTGTATCAGTAACCAGTAAG 58.560 44.000 0.00 0.00 33.41 2.34
3640 8322 9.000486 AGTAAGTAGTATTTCACTTTTGCCTTC 58.000 33.333 0.00 0.00 38.80 3.46
3662 8344 2.749621 CTGTTTGGATGCTTAGGTCCAC 59.250 50.000 0.00 0.00 43.85 4.02
3663 8345 2.092323 GTTTGGATGCTTAGGTCCACC 58.908 52.381 0.00 0.00 43.85 4.61
3716 8398 7.821359 TCTGAAGAAATGTTTGATCCTAGTGAG 59.179 37.037 0.00 0.00 0.00 3.51
3717 8399 6.372659 TGAAGAAATGTTTGATCCTAGTGAGC 59.627 38.462 0.00 0.00 0.00 4.26
3718 8400 6.059787 AGAAATGTTTGATCCTAGTGAGCT 57.940 37.500 0.00 0.00 0.00 4.09
3721 8403 6.798427 AATGTTTGATCCTAGTGAGCTAGA 57.202 37.500 0.00 0.00 45.77 2.43
3741 8423 8.306038 AGCTAGATAGATTGATAGCAAACAGAG 58.694 37.037 0.00 0.00 42.45 3.35
3752 8434 8.201554 TGATAGCAAACAGAGATGTATCAAAC 57.798 34.615 0.00 0.00 0.00 2.93
3756 8438 5.182001 GCAAACAGAGATGTATCAAACCTGT 59.818 40.000 0.00 0.00 0.00 4.00
3757 8439 6.621596 GCAAACAGAGATGTATCAAACCTGTC 60.622 42.308 0.00 0.00 0.00 3.51
3776 8500 5.001237 TGTCAATTTATCATGCAGCCAAG 57.999 39.130 0.00 0.00 0.00 3.61
3788 8512 4.240881 TGCAGCCAAGAGATTAAGGAAT 57.759 40.909 0.00 0.00 0.00 3.01
3840 8588 8.715998 CAATATACAGTAGAATCAGCAATGACC 58.284 37.037 0.00 0.00 0.00 4.02
3841 8589 4.558226 ACAGTAGAATCAGCAATGACCA 57.442 40.909 0.00 0.00 0.00 4.02
3843 8591 4.019860 ACAGTAGAATCAGCAATGACCAGT 60.020 41.667 0.00 0.00 0.00 4.00
3844 8592 4.940046 CAGTAGAATCAGCAATGACCAGTT 59.060 41.667 0.00 0.00 0.00 3.16
3845 8593 5.064452 CAGTAGAATCAGCAATGACCAGTTC 59.936 44.000 0.00 0.00 0.00 3.01
3847 8595 3.755378 AGAATCAGCAATGACCAGTTCAC 59.245 43.478 0.00 0.00 36.92 3.18
3848 8596 1.896220 TCAGCAATGACCAGTTCACC 58.104 50.000 0.00 0.00 36.92 4.02
3849 8597 1.142667 TCAGCAATGACCAGTTCACCA 59.857 47.619 0.00 0.00 36.92 4.17
3850 8598 1.538512 CAGCAATGACCAGTTCACCAG 59.461 52.381 0.00 0.00 36.92 4.00
3851 8599 0.883833 GCAATGACCAGTTCACCAGG 59.116 55.000 0.00 0.00 36.92 4.45
3852 8600 1.819305 GCAATGACCAGTTCACCAGGT 60.819 52.381 0.00 0.00 36.92 4.00
3853 8601 1.881973 CAATGACCAGTTCACCAGGTG 59.118 52.381 14.19 14.19 36.92 4.00
3855 8603 1.344953 TGACCAGTTCACCAGGTGCT 61.345 55.000 15.64 4.18 35.36 4.40
3857 8605 0.687354 ACCAGTTCACCAGGTGCTAG 59.313 55.000 15.64 2.98 33.57 3.42
3858 8606 0.036010 CCAGTTCACCAGGTGCTAGG 60.036 60.000 15.64 9.92 32.98 3.02
3859 8607 0.674895 CAGTTCACCAGGTGCTAGGC 60.675 60.000 15.64 2.96 32.98 3.93
3860 8608 1.741770 GTTCACCAGGTGCTAGGCG 60.742 63.158 15.64 0.00 32.98 5.52
3861 8609 2.954684 TTCACCAGGTGCTAGGCGG 61.955 63.158 15.64 0.00 32.98 6.13
3862 8610 4.473520 CACCAGGTGCTAGGCGGG 62.474 72.222 6.67 0.00 0.00 6.13
3892 9327 1.443194 CGCTCATTGTTGCTGCCAC 60.443 57.895 0.00 0.00 0.00 5.01
3893 9328 1.080298 GCTCATTGTTGCTGCCACC 60.080 57.895 1.07 0.00 0.00 4.61
3895 9330 1.228094 TCATTGTTGCTGCCACCGA 60.228 52.632 1.07 0.00 0.00 4.69
3896 9331 1.210931 CATTGTTGCTGCCACCGAG 59.789 57.895 1.07 0.00 0.00 4.63
3934 9386 3.798639 CTTGTGCGCGGCGTTGAAA 62.799 57.895 24.46 12.13 0.00 2.69
3935 9387 3.798639 TTGTGCGCGGCGTTGAAAG 62.799 57.895 24.46 0.00 0.00 2.62
3938 9390 4.445545 GCGCGGCGTTGAAAGGAG 62.446 66.667 24.46 0.00 0.00 3.69
3939 9391 4.445545 CGCGGCGTTGAAAGGAGC 62.446 66.667 15.36 0.00 0.00 4.70
3940 9392 4.103103 GCGGCGTTGAAAGGAGCC 62.103 66.667 9.37 0.00 45.67 4.70
3942 9394 3.431725 GGCGTTGAAAGGAGCCGG 61.432 66.667 0.00 0.00 40.17 6.13
3943 9395 3.431725 GCGTTGAAAGGAGCCGGG 61.432 66.667 2.18 0.00 0.00 5.73
3944 9396 3.431725 CGTTGAAAGGAGCCGGGC 61.432 66.667 12.11 12.11 0.00 6.13
3945 9397 2.282180 GTTGAAAGGAGCCGGGCA 60.282 61.111 23.09 0.00 0.00 5.36
3946 9398 2.282180 TTGAAAGGAGCCGGGCAC 60.282 61.111 23.09 15.59 0.00 5.01
3961 9413 4.358841 CACCACCGCCCCATGGAA 62.359 66.667 15.22 0.00 39.46 3.53
3962 9414 4.360405 ACCACCGCCCCATGGAAC 62.360 66.667 15.22 3.27 39.46 3.62
3970 9422 4.047125 CCCATGGAACGGCACCCT 62.047 66.667 15.22 0.00 0.00 4.34
3971 9423 2.751436 CCATGGAACGGCACCCTG 60.751 66.667 5.56 0.00 0.00 4.45
3972 9424 2.350895 CATGGAACGGCACCCTGA 59.649 61.111 0.00 0.00 0.00 3.86
3973 9425 1.303236 CATGGAACGGCACCCTGAA 60.303 57.895 0.00 0.00 0.00 3.02
3974 9426 0.680921 CATGGAACGGCACCCTGAAT 60.681 55.000 0.00 0.00 0.00 2.57
3975 9427 0.680921 ATGGAACGGCACCCTGAATG 60.681 55.000 0.00 0.00 0.00 2.67
3976 9428 1.002624 GGAACGGCACCCTGAATGA 60.003 57.895 0.00 0.00 0.00 2.57
4065 11347 1.260538 TGCTCCAGCTCCTGTACAGG 61.261 60.000 32.61 32.61 43.70 4.00
4077 11359 0.830444 TGTACAGGGACGACAGCCTT 60.830 55.000 0.00 0.00 0.00 4.35
4080 11362 1.258445 ACAGGGACGACAGCCTTAGG 61.258 60.000 0.00 0.00 0.00 2.69
4091 11382 2.494918 CCTTAGGACCTCGCGGTG 59.505 66.667 0.00 0.00 45.73 4.94
4143 11444 4.821589 CGGCCACGAGCTTCCCTC 62.822 72.222 2.24 0.00 44.60 4.30
4154 11455 4.348495 TTCCCTCCCCGGCCTTCT 62.348 66.667 0.00 0.00 0.00 2.85
4190 11491 4.179599 GGGGAGAGGGGAGGAGGG 62.180 77.778 0.00 0.00 0.00 4.30
4221 11537 3.708220 CTCTCGGTGAGGAAGGCGC 62.708 68.421 0.00 0.00 39.08 6.53
4222 11538 4.821589 CTCGGTGAGGAAGGCGCC 62.822 72.222 21.89 21.89 0.00 6.53
4239 11555 3.330720 CCAAGGGCGAGGAGGGTT 61.331 66.667 0.00 0.00 0.00 4.11
4258 11574 4.735599 GGGACGGGAGGAAGGGGT 62.736 72.222 0.00 0.00 0.00 4.95
4259 11575 3.400054 GGACGGGAGGAAGGGGTG 61.400 72.222 0.00 0.00 0.00 4.61
4265 11581 1.392534 GGAGGAAGGGGTGAGAGGA 59.607 63.158 0.00 0.00 0.00 3.71
4268 11584 1.306568 GGAAGGGGTGAGAGGAGCT 60.307 63.158 0.00 0.00 0.00 4.09
4273 11589 3.791586 GGTGAGAGGAGCTGGCCC 61.792 72.222 0.00 0.00 0.00 5.80
4274 11590 2.686835 GTGAGAGGAGCTGGCCCT 60.687 66.667 0.00 0.00 36.57 5.19
4341 11693 2.760385 GGCGCTAGGAGGGACAGT 60.760 66.667 7.64 0.00 36.01 3.55
4343 11695 3.082579 GCGCTAGGAGGGACAGTGG 62.083 68.421 0.00 0.00 0.00 4.00
4344 11696 1.379977 CGCTAGGAGGGACAGTGGA 60.380 63.158 0.00 0.00 0.00 4.02
4345 11697 1.388065 CGCTAGGAGGGACAGTGGAG 61.388 65.000 0.00 0.00 0.00 3.86
4347 11699 1.770294 CTAGGAGGGACAGTGGAGAC 58.230 60.000 0.00 0.00 0.00 3.36
4348 11700 1.286553 CTAGGAGGGACAGTGGAGACT 59.713 57.143 0.00 0.00 0.00 3.24
4357 11709 0.040351 CAGTGGAGACTGGAGAGGGA 59.960 60.000 0.00 0.00 45.26 4.20
4358 11710 0.334676 AGTGGAGACTGGAGAGGGAG 59.665 60.000 0.00 0.00 0.00 4.30
4359 11711 0.333312 GTGGAGACTGGAGAGGGAGA 59.667 60.000 0.00 0.00 0.00 3.71
4360 11712 0.333312 TGGAGACTGGAGAGGGAGAC 59.667 60.000 0.00 0.00 0.00 3.36
4361 11713 0.750182 GGAGACTGGAGAGGGAGACG 60.750 65.000 0.00 0.00 0.00 4.18
4362 11714 1.379309 AGACTGGAGAGGGAGACGC 60.379 63.158 0.00 0.00 0.00 5.19
4363 11715 2.752238 ACTGGAGAGGGAGACGCG 60.752 66.667 3.53 3.53 0.00 6.01
4364 11716 4.200283 CTGGAGAGGGAGACGCGC 62.200 72.222 5.73 0.00 0.00 6.86
4366 11718 4.500116 GGAGAGGGAGACGCGCAC 62.500 72.222 5.73 0.00 0.00 5.34
4369 11721 4.803426 GAGGGAGACGCGCACCTG 62.803 72.222 14.87 0.00 32.42 4.00
4373 11725 3.044305 GAGACGCGCACCTGCTTT 61.044 61.111 5.73 0.00 39.32 3.51
4374 11726 2.591715 AGACGCGCACCTGCTTTT 60.592 55.556 5.73 0.00 39.32 2.27
4375 11727 2.117941 GAGACGCGCACCTGCTTTTT 62.118 55.000 5.73 0.00 39.32 1.94
4402 15361 2.674084 GCAGTTGTACCCGGCGAAC 61.674 63.158 9.30 4.07 0.00 3.95
4404 15363 2.356194 GTTGTACCCGGCGAACGT 60.356 61.111 9.30 3.72 42.24 3.99
4425 15384 0.099436 CGCTGTAAGGAATGGCAAGC 59.901 55.000 0.00 0.00 0.00 4.01
4427 15386 1.545582 GCTGTAAGGAATGGCAAGCAA 59.454 47.619 0.00 0.00 0.00 3.91
4428 15387 2.029110 GCTGTAAGGAATGGCAAGCAAA 60.029 45.455 0.00 0.00 0.00 3.68
4429 15388 3.578688 CTGTAAGGAATGGCAAGCAAAC 58.421 45.455 0.00 0.00 0.00 2.93
4431 15390 1.422531 AAGGAATGGCAAGCAAACCA 58.577 45.000 0.00 0.00 41.06 3.67
4433 15392 1.551883 AGGAATGGCAAGCAAACCATC 59.448 47.619 5.04 0.66 46.04 3.51
4434 15393 1.551883 GGAATGGCAAGCAAACCATCT 59.448 47.619 5.04 0.00 46.04 2.90
4435 15394 2.027837 GGAATGGCAAGCAAACCATCTT 60.028 45.455 5.04 0.00 46.04 2.40
4436 15395 3.557686 GGAATGGCAAGCAAACCATCTTT 60.558 43.478 5.04 0.00 46.04 2.52
4440 15399 2.611224 GGCAAGCAAACCATCTTTCCTG 60.611 50.000 0.00 0.00 0.00 3.86
4441 15400 2.036346 GCAAGCAAACCATCTTTCCTGT 59.964 45.455 0.00 0.00 0.00 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 0.911856 CATACGTAGTCCAACGCGTG 59.088 55.000 14.98 7.16 46.71 5.34
8 9 0.799534 GCATACGTAGTCCAACGCGT 60.800 55.000 5.58 5.58 46.71 6.01
9 10 1.477030 GGCATACGTAGTCCAACGCG 61.477 60.000 3.53 3.53 46.71 6.01
10 11 1.477030 CGGCATACGTAGTCCAACGC 61.477 60.000 14.03 3.19 46.71 4.84
47 48 3.740128 ATAGTTGCTCCAGCGGGCG 62.740 63.158 0.00 0.00 45.83 6.13
48 49 1.440145 GAATAGTTGCTCCAGCGGGC 61.440 60.000 0.00 0.00 45.83 6.13
49 50 0.815615 GGAATAGTTGCTCCAGCGGG 60.816 60.000 0.00 0.00 45.83 6.13
50 51 1.154205 CGGAATAGTTGCTCCAGCGG 61.154 60.000 0.00 0.00 45.83 5.52
51 52 1.154205 CCGGAATAGTTGCTCCAGCG 61.154 60.000 0.00 0.00 45.83 5.18
52 53 0.107654 ACCGGAATAGTTGCTCCAGC 60.108 55.000 9.46 0.00 42.50 4.85
53 54 2.009774 CAACCGGAATAGTTGCTCCAG 58.990 52.381 9.46 0.00 38.31 3.86
54 55 2.107950 CAACCGGAATAGTTGCTCCA 57.892 50.000 9.46 0.00 38.31 3.86
59 60 1.060308 CGCGCAACCGGAATAGTTG 59.940 57.895 9.46 2.17 45.92 3.16
60 61 2.746803 GCGCGCAACCGGAATAGTT 61.747 57.895 29.10 0.00 34.32 2.24
61 62 3.192922 GCGCGCAACCGGAATAGT 61.193 61.111 29.10 0.00 34.32 2.12
62 63 4.279535 CGCGCGCAACCGGAATAG 62.280 66.667 32.61 6.38 34.32 1.73
69 70 3.865502 TTTTAGCACGCGCGCAACC 62.866 57.895 32.58 17.53 45.49 3.77
70 71 2.426098 TTTTAGCACGCGCGCAAC 60.426 55.556 32.58 19.71 45.49 4.17
71 72 2.426098 GTTTTAGCACGCGCGCAA 60.426 55.556 32.58 14.81 45.49 4.85
72 73 4.711193 CGTTTTAGCACGCGCGCA 62.711 61.111 32.58 8.18 45.49 6.09
74 75 4.787299 CCCGTTTTAGCACGCGCG 62.787 66.667 30.96 30.96 45.49 6.86
75 76 4.454717 CCCCGTTTTAGCACGCGC 62.455 66.667 5.73 0.00 38.93 6.86
76 77 1.641123 ATTCCCCGTTTTAGCACGCG 61.641 55.000 3.53 3.53 38.93 6.01
77 78 0.524414 AATTCCCCGTTTTAGCACGC 59.476 50.000 0.00 0.00 38.93 5.34
78 79 2.983803 CAAAATTCCCCGTTTTAGCACG 59.016 45.455 0.00 0.00 40.02 5.34
79 80 2.734606 GCAAAATTCCCCGTTTTAGCAC 59.265 45.455 0.00 0.00 0.00 4.40
80 81 2.608261 CGCAAAATTCCCCGTTTTAGCA 60.608 45.455 0.00 0.00 0.00 3.49
81 82 1.989864 CGCAAAATTCCCCGTTTTAGC 59.010 47.619 0.00 0.00 0.00 3.09
82 83 2.601804 CCGCAAAATTCCCCGTTTTAG 58.398 47.619 0.00 0.00 0.00 1.85
83 84 1.336980 GCCGCAAAATTCCCCGTTTTA 60.337 47.619 0.00 0.00 0.00 1.52
84 85 0.601576 GCCGCAAAATTCCCCGTTTT 60.602 50.000 0.00 0.00 0.00 2.43
85 86 1.005512 GCCGCAAAATTCCCCGTTT 60.006 52.632 0.00 0.00 0.00 3.60
86 87 2.654289 GCCGCAAAATTCCCCGTT 59.346 55.556 0.00 0.00 0.00 4.44
87 88 3.743636 CGCCGCAAAATTCCCCGT 61.744 61.111 0.00 0.00 0.00 5.28
109 110 4.794241 CACGCGCGCCAAACTAGC 62.794 66.667 32.58 0.00 0.00 3.42
110 111 2.950172 AACACGCGCGCCAAACTAG 61.950 57.895 32.58 12.27 0.00 2.57
111 112 2.968156 AACACGCGCGCCAAACTA 60.968 55.556 32.58 0.00 0.00 2.24
112 113 4.605967 CAACACGCGCGCCAAACT 62.606 61.111 32.58 6.00 0.00 2.66
118 119 4.505217 CATCTCCAACACGCGCGC 62.505 66.667 32.58 23.91 0.00 6.86
119 120 4.505217 GCATCTCCAACACGCGCG 62.505 66.667 30.96 30.96 0.00 6.86
120 121 3.088500 GAGCATCTCCAACACGCGC 62.089 63.158 5.73 0.00 0.00 6.86
121 122 3.084579 GAGCATCTCCAACACGCG 58.915 61.111 3.53 3.53 0.00 6.01
132 133 4.577693 TCATCAACCAAGCATAAGAGCATC 59.422 41.667 0.00 0.00 36.85 3.91
133 134 4.337555 GTCATCAACCAAGCATAAGAGCAT 59.662 41.667 0.00 0.00 36.85 3.79
134 135 3.691118 GTCATCAACCAAGCATAAGAGCA 59.309 43.478 0.00 0.00 36.85 4.26
135 136 3.691118 TGTCATCAACCAAGCATAAGAGC 59.309 43.478 0.00 0.00 0.00 4.09
136 137 5.821470 AGATGTCATCAACCAAGCATAAGAG 59.179 40.000 15.20 0.00 0.00 2.85
137 138 5.587443 CAGATGTCATCAACCAAGCATAAGA 59.413 40.000 15.20 0.00 0.00 2.10
215 222 1.005340 CAAGAACGATCCTCTGCAGC 58.995 55.000 9.47 0.00 0.00 5.25
264 273 3.153919 GAGAGAGACTGTCAGACAACCT 58.846 50.000 10.88 4.45 0.00 3.50
278 287 2.195727 TGGCAGAGAGAGAGAGAGAGA 58.804 52.381 0.00 0.00 0.00 3.10
291 300 1.754234 CCCCCGGAAAATGGCAGAG 60.754 63.158 0.73 0.00 0.00 3.35
293 302 0.323908 TTACCCCCGGAAAATGGCAG 60.324 55.000 0.73 0.00 0.00 4.85
369 493 2.281345 ACGGACGACTGGACGAGT 60.281 61.111 0.00 0.00 37.76 4.18
378 502 4.090354 TCAAATTAAACGATCACGGACGAC 59.910 41.667 0.00 0.00 44.46 4.34
421 545 4.767255 GTGCAGAGGCCAGGGACG 62.767 72.222 5.01 0.00 40.13 4.79
425 549 3.965539 CTTCGGTGCAGAGGCCAGG 62.966 68.421 5.01 0.00 40.13 4.45
427 551 4.020617 CCTTCGGTGCAGAGGCCA 62.021 66.667 5.01 0.00 40.13 5.36
428 552 3.672295 CTCCTTCGGTGCAGAGGCC 62.672 68.421 0.00 0.00 40.13 5.19
429 553 2.125350 CTCCTTCGGTGCAGAGGC 60.125 66.667 0.00 0.00 41.68 4.70
430 554 1.216710 GTCTCCTTCGGTGCAGAGG 59.783 63.158 0.00 0.00 0.00 3.69
431 555 0.108898 CAGTCTCCTTCGGTGCAGAG 60.109 60.000 0.00 0.00 0.00 3.35
454 578 8.561738 AAGAAAGAAAGTCTTGTCTGTAAACA 57.438 30.769 0.00 0.00 36.71 2.83
473 610 4.339247 TGACCTGGCAAGAAAGAAAGAAAG 59.661 41.667 0.00 0.00 0.00 2.62
476 613 3.214328 GTGACCTGGCAAGAAAGAAAGA 58.786 45.455 0.00 0.00 0.00 2.52
493 642 1.818642 AGCCTGAGAAATGCTGTGAC 58.181 50.000 0.00 0.00 33.23 3.67
538 688 2.614520 CGGTGGTTGTGTTGTGTGATAA 59.385 45.455 0.00 0.00 0.00 1.75
541 691 0.036294 TCGGTGGTTGTGTTGTGTGA 60.036 50.000 0.00 0.00 0.00 3.58
622 773 1.944676 GTGATAGAACCGAGCGGCG 60.945 63.158 9.14 0.51 39.32 6.46
688 888 1.975363 GCACGTGCTCAGCTTCATCC 61.975 60.000 32.55 0.00 38.21 3.51
712 913 2.139118 GTGGCTTGTCTTGAGTGAGAC 58.861 52.381 0.00 0.00 44.97 3.36
739 946 3.808656 GAGCAAGAGCCGGCAAGC 61.809 66.667 31.54 24.85 43.56 4.01
760 967 1.657751 GAAAGGCGATGGTTCCAGGC 61.658 60.000 8.52 8.52 0.00 4.85
775 982 6.159988 ACGAGTGAAGATCAAGGTTAGAAAG 58.840 40.000 0.00 0.00 0.00 2.62
778 985 5.723672 AACGAGTGAAGATCAAGGTTAGA 57.276 39.130 0.00 0.00 0.00 2.10
781 988 9.530633 GTATAATAACGAGTGAAGATCAAGGTT 57.469 33.333 0.00 0.00 0.00 3.50
798 1231 9.457110 CTCATGCTATGGATCTCGTATAATAAC 57.543 37.037 0.00 0.00 0.00 1.89
808 1241 6.071221 ACTCAATCTCTCATGCTATGGATCTC 60.071 42.308 0.00 0.00 0.00 2.75
809 1242 5.781306 ACTCAATCTCTCATGCTATGGATCT 59.219 40.000 0.00 0.00 0.00 2.75
810 1243 6.040209 ACTCAATCTCTCATGCTATGGATC 57.960 41.667 0.00 0.00 0.00 3.36
860 1533 1.595382 GGCTCACGTGTCAAGCTGT 60.595 57.895 22.38 0.00 36.29 4.40
863 1536 1.571460 CTTGGCTCACGTGTCAAGC 59.429 57.895 23.97 21.08 31.73 4.01
990 1675 2.512286 ATCGCCATGGCAGTCGTG 60.512 61.111 34.93 18.32 42.06 4.35
1067 1755 4.891727 CGAGGGCAACGGGGATCG 62.892 72.222 0.00 0.00 45.88 3.69
1092 1780 2.677524 CTGGTGCCATGGGTGTGG 60.678 66.667 15.13 0.00 42.35 4.17
1144 1841 4.778143 GGTGCTGGGGCCGTACTG 62.778 72.222 0.00 0.00 37.74 2.74
1281 1984 3.458579 CACGCGACGACGGTCTTG 61.459 66.667 15.93 0.00 41.16 3.02
1282 1985 4.695231 CCACGCGACGACGGTCTT 62.695 66.667 15.93 0.00 41.16 3.01
1377 2080 2.817834 GCCGCGCCATTGTAGTCA 60.818 61.111 0.00 0.00 0.00 3.41
1435 2138 3.063084 GGTGTCGAGGAGCTCCGT 61.063 66.667 26.95 15.37 42.08 4.69
1582 2285 0.394488 TACGACCCTGAGGAGAGCAG 60.394 60.000 0.00 0.00 36.73 4.24
1598 2301 9.083080 TGTCATTGTCAAAGTAGAATGTATACG 57.917 33.333 0.00 0.00 0.00 3.06
1691 6170 0.321564 CCTGTGATTGACAAGCGGGA 60.322 55.000 8.55 0.00 32.80 5.14
1827 6306 1.134098 AGGTTGCCATCGTAATCCAGG 60.134 52.381 0.00 0.00 0.00 4.45
1946 6425 0.759346 GGGTATGTACCTGCAGAGGG 59.241 60.000 17.39 1.11 44.84 4.30
1955 6434 1.755380 AGTCGAGCTTGGGTATGTACC 59.245 52.381 0.00 0.40 45.71 3.34
1974 6453 2.818714 CCTCTGAGGCAAGCGCAG 60.819 66.667 11.42 2.01 41.24 5.18
2231 6752 4.261867 GGTTTGGAAAGTTCTTGCCGTTAT 60.262 41.667 5.25 0.00 0.00 1.89
2288 6809 1.847818 TTCTGACGAAGACAACACCG 58.152 50.000 0.00 0.00 33.46 4.94
2322 6843 3.940209 TGAACTTTGCATTCATGGGTC 57.060 42.857 0.00 0.00 31.11 4.46
2386 6907 5.998363 AGTAGCCAAACTTGAAGTTAGAAGG 59.002 40.000 11.43 11.68 37.47 3.46
2843 7365 1.707632 CACAGGAGAAGAGTTGCTCG 58.292 55.000 0.00 0.00 35.36 5.03
2850 7372 2.630158 CATTGGAGCACAGGAGAAGAG 58.370 52.381 0.00 0.00 0.00 2.85
2851 7373 1.280133 CCATTGGAGCACAGGAGAAGA 59.720 52.381 0.00 0.00 0.00 2.87
2852 7374 1.681166 CCCATTGGAGCACAGGAGAAG 60.681 57.143 3.62 0.00 0.00 2.85
2928 7450 3.425359 GCACAATCCATTCAAGACACTCG 60.425 47.826 0.00 0.00 0.00 4.18
3190 7712 4.512914 GCCCTCAGCCACCCATCC 62.513 72.222 0.00 0.00 34.35 3.51
3232 7754 7.220030 TCTTTAAGGATCTCAATGGAGCATAC 58.780 38.462 0.00 0.00 41.13 2.39
3240 7762 9.780413 GCTAGTTTTTCTTTAAGGATCTCAATG 57.220 33.333 0.00 0.00 0.00 2.82
3246 7768 6.556212 GCCTGCTAGTTTTTCTTTAAGGATC 58.444 40.000 0.00 0.00 0.00 3.36
3555 8080 1.741525 GGACAAGGCTTGCAGCAAA 59.258 52.632 26.45 0.00 44.75 3.68
3570 8095 2.158755 AGTTGCTACATATGGCAGGGAC 60.159 50.000 7.80 3.80 43.99 4.46
3588 8113 3.904717 ACTGATACAGATCCGGAGAGTT 58.095 45.455 11.34 0.00 35.18 3.01
3613 8261 8.324163 AGGCAAAAGTGAAATACTACTTACTG 57.676 34.615 0.00 0.00 39.18 2.74
3617 8265 7.004691 AGGAAGGCAAAAGTGAAATACTACTT 58.995 34.615 0.00 0.00 39.18 2.24
3618 8266 6.431234 CAGGAAGGCAAAAGTGAAATACTACT 59.569 38.462 0.00 0.00 39.18 2.57
3619 8267 6.206829 ACAGGAAGGCAAAAGTGAAATACTAC 59.793 38.462 0.00 0.00 39.18 2.73
3640 8322 2.290896 TGGACCTAAGCATCCAAACAGG 60.291 50.000 0.00 0.00 42.14 4.00
3667 8349 9.003658 CAGATAACTGAAGGTAGATGTGTTTTT 57.996 33.333 0.00 0.00 46.03 1.94
3691 8373 7.413877 GCTCACTAGGATCAAACATTTCTTCAG 60.414 40.741 0.00 0.00 0.00 3.02
3701 8383 7.753309 TCTATCTAGCTCACTAGGATCAAAC 57.247 40.000 0.00 0.00 45.20 2.93
3716 8398 8.303156 TCTCTGTTTGCTATCAATCTATCTAGC 58.697 37.037 0.00 0.00 37.65 3.42
3752 8434 3.382227 TGGCTGCATGATAAATTGACAGG 59.618 43.478 0.50 0.00 0.00 4.00
3756 8438 5.195185 TCTCTTGGCTGCATGATAAATTGA 58.805 37.500 0.50 0.00 0.00 2.57
3757 8439 5.509716 TCTCTTGGCTGCATGATAAATTG 57.490 39.130 0.50 0.00 0.00 2.32
3817 8565 7.069950 ACTGGTCATTGCTGATTCTACTGTATA 59.930 37.037 0.00 0.00 32.98 1.47
3818 8566 6.126940 ACTGGTCATTGCTGATTCTACTGTAT 60.127 38.462 0.00 0.00 32.98 2.29
3819 8567 5.187772 ACTGGTCATTGCTGATTCTACTGTA 59.812 40.000 0.00 0.00 32.98 2.74
3820 8568 4.019860 ACTGGTCATTGCTGATTCTACTGT 60.020 41.667 0.00 0.00 32.98 3.55
3821 8569 4.511527 ACTGGTCATTGCTGATTCTACTG 58.488 43.478 0.00 0.00 32.98 2.74
3822 8570 4.833478 ACTGGTCATTGCTGATTCTACT 57.167 40.909 0.00 0.00 32.98 2.57
3823 8571 4.937620 TGAACTGGTCATTGCTGATTCTAC 59.062 41.667 0.00 0.00 32.98 2.59
3824 8572 4.937620 GTGAACTGGTCATTGCTGATTCTA 59.062 41.667 0.00 0.00 38.90 2.10
3840 8588 0.674895 GCCTAGCACCTGGTGAACTG 60.675 60.000 30.23 15.31 35.23 3.16
3841 8589 1.679898 GCCTAGCACCTGGTGAACT 59.320 57.895 30.23 19.68 35.23 3.01
3843 8591 2.662596 CGCCTAGCACCTGGTGAA 59.337 61.111 30.23 15.61 35.23 3.18
3844 8592 3.390521 CCGCCTAGCACCTGGTGA 61.391 66.667 30.23 9.54 35.23 4.02
3845 8593 4.473520 CCCGCCTAGCACCTGGTG 62.474 72.222 22.46 22.46 36.51 4.17
3863 8611 0.933097 CAATGAGCGATTGGAGGACG 59.067 55.000 4.11 0.00 38.27 4.79
3864 8612 2.029838 ACAATGAGCGATTGGAGGAC 57.970 50.000 13.90 0.00 45.20 3.85
3867 8615 1.741706 AGCAACAATGAGCGATTGGAG 59.258 47.619 13.90 8.11 45.20 3.86
3868 8616 1.469703 CAGCAACAATGAGCGATTGGA 59.530 47.619 13.90 0.00 45.20 3.53
3872 8620 0.961857 TGGCAGCAACAATGAGCGAT 60.962 50.000 0.00 0.00 35.48 4.58
3875 9297 1.080298 GGTGGCAGCAACAATGAGC 60.080 57.895 12.58 0.00 0.00 4.26
3899 9334 3.567797 GACAATCTGCCGCTCGCC 61.568 66.667 0.00 0.00 36.24 5.54
3900 9335 2.103042 AAGACAATCTGCCGCTCGC 61.103 57.895 0.00 0.00 38.31 5.03
3910 9362 2.202349 GCCGCGCACAAGACAATC 60.202 61.111 8.75 0.00 0.00 2.67
3944 9396 4.358841 TTCCATGGGGCGGTGGTG 62.359 66.667 13.02 0.00 36.84 4.17
3945 9397 4.360405 GTTCCATGGGGCGGTGGT 62.360 66.667 13.02 0.00 36.84 4.16
3953 9405 4.047125 AGGGTGCCGTTCCATGGG 62.047 66.667 13.02 0.00 0.00 4.00
3954 9406 2.751436 CAGGGTGCCGTTCCATGG 60.751 66.667 4.97 4.97 33.78 3.66
3955 9407 0.680921 ATTCAGGGTGCCGTTCCATG 60.681 55.000 0.00 0.00 37.99 3.66
3956 9408 0.680921 CATTCAGGGTGCCGTTCCAT 60.681 55.000 0.00 0.00 0.00 3.41
3957 9409 1.303236 CATTCAGGGTGCCGTTCCA 60.303 57.895 0.00 0.00 0.00 3.53
3958 9410 1.002624 TCATTCAGGGTGCCGTTCC 60.003 57.895 0.00 0.00 0.00 3.62
3959 9411 1.648467 GCTCATTCAGGGTGCCGTTC 61.648 60.000 0.00 0.00 0.00 3.95
3960 9412 1.675641 GCTCATTCAGGGTGCCGTT 60.676 57.895 0.00 0.00 0.00 4.44
3961 9413 2.045926 GCTCATTCAGGGTGCCGT 60.046 61.111 0.00 0.00 0.00 5.68
3962 9414 2.825836 GGCTCATTCAGGGTGCCG 60.826 66.667 0.00 0.00 33.96 5.69
3963 9415 1.751927 CTGGCTCATTCAGGGTGCC 60.752 63.158 0.00 0.00 43.49 5.01
3964 9416 2.413142 GCTGGCTCATTCAGGGTGC 61.413 63.158 0.00 0.00 33.16 5.01
3965 9417 2.110967 CGCTGGCTCATTCAGGGTG 61.111 63.158 0.00 0.00 39.41 4.61
3966 9418 2.270205 CGCTGGCTCATTCAGGGT 59.730 61.111 0.00 0.00 39.41 4.34
3967 9419 3.207669 GCGCTGGCTCATTCAGGG 61.208 66.667 0.00 0.00 44.65 4.45
3968 9420 2.437180 TGCGCTGGCTCATTCAGG 60.437 61.111 9.73 0.00 40.82 3.86
3969 9421 2.470362 CCTGCGCTGGCTCATTCAG 61.470 63.158 21.02 0.00 40.82 3.02
3970 9422 2.437180 CCTGCGCTGGCTCATTCA 60.437 61.111 21.02 0.00 40.82 2.57
3971 9423 2.124983 TCCTGCGCTGGCTCATTC 60.125 61.111 27.02 0.00 40.82 2.67
3972 9424 2.124819 CTCCTGCGCTGGCTCATT 60.125 61.111 27.02 0.00 40.82 2.57
3973 9425 4.853050 GCTCCTGCGCTGGCTCAT 62.853 66.667 27.02 0.00 40.82 2.90
4065 11347 0.971447 AGGTCCTAAGGCTGTCGTCC 60.971 60.000 0.00 0.00 0.00 4.79
4141 11442 2.506472 GCTTAGAAGGCCGGGGAG 59.494 66.667 2.18 0.00 0.00 4.30
4142 11443 3.467226 CGCTTAGAAGGCCGGGGA 61.467 66.667 2.18 0.00 0.00 4.81
4168 11469 2.285180 CTCCCCTCTCCCCTCCTG 59.715 72.222 0.00 0.00 0.00 3.86
4190 11491 3.462678 GAGAGTCCGGCACCTCCC 61.463 72.222 0.00 0.00 0.00 4.30
4203 11519 2.492090 CGCCTTCCTCACCGAGAG 59.508 66.667 0.00 0.00 44.31 3.20
4210 11526 4.033776 CCTTGGGCGCCTTCCTCA 62.034 66.667 28.56 12.88 0.00 3.86
4222 11538 3.330720 AACCCTCCTCGCCCTTGG 61.331 66.667 0.00 0.00 0.00 3.61
4224 11540 3.330720 CCAACCCTCCTCGCCCTT 61.331 66.667 0.00 0.00 0.00 3.95
4239 11555 4.733725 CCCTTCCTCCCGTCCCCA 62.734 72.222 0.00 0.00 0.00 4.96
4258 11574 1.075674 CTAGGGCCAGCTCCTCTCA 60.076 63.158 6.18 0.00 35.92 3.27
4259 11575 0.827507 CTCTAGGGCCAGCTCCTCTC 60.828 65.000 6.18 0.00 35.92 3.20
4265 11581 0.397816 CACTACCTCTAGGGCCAGCT 60.398 60.000 6.18 0.00 40.27 4.24
4268 11584 0.032416 GACCACTACCTCTAGGGCCA 60.032 60.000 6.18 0.00 40.27 5.36
4273 11589 0.395311 TGCCCGACCACTACCTCTAG 60.395 60.000 0.00 0.00 0.00 2.43
4274 11590 0.395311 CTGCCCGACCACTACCTCTA 60.395 60.000 0.00 0.00 0.00 2.43
4329 11681 1.006043 CAGTCTCCACTGTCCCTCCTA 59.994 57.143 0.00 0.00 44.63 2.94
4330 11682 0.252012 CAGTCTCCACTGTCCCTCCT 60.252 60.000 0.00 0.00 44.63 3.69
4331 11683 2.281830 CAGTCTCCACTGTCCCTCC 58.718 63.158 0.00 0.00 44.63 4.30
4339 11691 0.334676 CTCCCTCTCCAGTCTCCACT 59.665 60.000 0.00 0.00 0.00 4.00
4341 11693 0.333312 GTCTCCCTCTCCAGTCTCCA 59.667 60.000 0.00 0.00 0.00 3.86
4343 11695 1.381165 GCGTCTCCCTCTCCAGTCTC 61.381 65.000 0.00 0.00 0.00 3.36
4344 11696 1.379309 GCGTCTCCCTCTCCAGTCT 60.379 63.158 0.00 0.00 0.00 3.24
4345 11697 2.766400 CGCGTCTCCCTCTCCAGTC 61.766 68.421 0.00 0.00 0.00 3.51
4347 11699 4.200283 GCGCGTCTCCCTCTCCAG 62.200 72.222 8.43 0.00 0.00 3.86
4377 11729 3.024431 GGGTACAACTGCCCGAAAA 57.976 52.632 0.00 0.00 34.90 2.29
4378 11730 4.804806 GGGTACAACTGCCCGAAA 57.195 55.556 0.00 0.00 34.90 3.46
4383 11735 3.887335 TTCGCCGGGTACAACTGCC 62.887 63.158 2.18 0.00 0.00 4.85
4384 11736 2.357760 TTCGCCGGGTACAACTGC 60.358 61.111 2.18 0.00 0.00 4.40
4385 11737 2.377310 CGTTCGCCGGGTACAACTG 61.377 63.158 2.18 0.00 0.00 3.16
4388 11740 1.664333 GAACGTTCGCCGGGTACAA 60.664 57.895 13.36 0.00 42.24 2.41
4389 11741 2.049248 GAACGTTCGCCGGGTACA 60.049 61.111 13.36 0.00 42.24 2.90
4390 11742 3.174573 CGAACGTTCGCCGGGTAC 61.175 66.667 34.54 2.69 44.26 3.34
4399 15358 2.093783 CCATTCCTTACAGCGAACGTTC 59.906 50.000 18.47 18.47 0.00 3.95
4402 15361 0.373716 GCCATTCCTTACAGCGAACG 59.626 55.000 0.00 0.00 0.00 3.95
4404 15363 2.083774 CTTGCCATTCCTTACAGCGAA 58.916 47.619 0.00 0.00 0.00 4.70
4407 15366 1.176527 TGCTTGCCATTCCTTACAGC 58.823 50.000 0.00 0.00 0.00 4.40
4410 15369 2.298729 TGGTTTGCTTGCCATTCCTTAC 59.701 45.455 0.00 0.00 0.00 2.34
4412 15371 1.422531 TGGTTTGCTTGCCATTCCTT 58.577 45.000 0.00 0.00 0.00 3.36
4413 15372 1.551883 GATGGTTTGCTTGCCATTCCT 59.448 47.619 7.67 0.00 44.73 3.36
4414 15373 1.551883 AGATGGTTTGCTTGCCATTCC 59.448 47.619 7.67 0.00 44.73 3.01


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

AutoCloner maintained by Alex Coulton.