Multiple sequence alignment - TraesCS7B01G144000

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 TraesCS7B01G144000 chr7B 100.000 3401 0 0 977 4377 185292072 185295472 0.000000e+00 6281.0
1 TraesCS7B01G144000 chr7B 100.000 733 0 0 1 733 185291096 185291828 0.000000e+00 1354.0
2 TraesCS7B01G144000 chr7B 92.047 767 58 3 3614 4377 213386371 213385605 0.000000e+00 1075.0
3 TraesCS7B01G144000 chr4B 97.662 2139 38 3 1396 3524 244775507 244773371 0.000000e+00 3663.0
4 TraesCS7B01G144000 chr4B 95.380 909 38 3 1605 2512 11743948 11743043 0.000000e+00 1443.0
5 TraesCS7B01G144000 chr4B 92.578 768 53 4 3613 4377 542081316 542082082 0.000000e+00 1099.0
6 TraesCS7B01G144000 chr4B 92.448 768 55 3 3613 4377 542104408 542105175 0.000000e+00 1094.0
7 TraesCS7B01G144000 chr4B 91.927 768 59 3 3613 4377 598100656 598099889 0.000000e+00 1072.0
8 TraesCS7B01G144000 chr4B 97.996 549 3 4 977 1525 244776045 244775505 0.000000e+00 946.0
9 TraesCS7B01G144000 chr4B 91.533 437 13 5 297 733 244776494 244776082 8.160000e-162 580.0
10 TraesCS7B01G144000 chr4B 84.091 88 9 5 3538 3622 624160498 624160583 3.630000e-11 80.5
11 TraesCS7B01G144000 chr6B 97.350 1019 17 1 2516 3524 684271124 684270106 0.000000e+00 1724.0
12 TraesCS7B01G144000 chr6B 97.350 1019 17 1 2516 3524 684280116 684279098 0.000000e+00 1724.0
13 TraesCS7B01G144000 chr6B 92.782 762 49 5 3613 4371 599924436 599925194 0.000000e+00 1098.0
14 TraesCS7B01G144000 chr6B 95.560 563 18 5 977 1532 77095169 77094607 0.000000e+00 894.0
15 TraesCS7B01G144000 chr6B 95.871 557 16 5 977 1526 77545905 77546461 0.000000e+00 894.0
16 TraesCS7B01G144000 chr6B 99.120 341 3 0 1192 1532 684272308 684271968 8.050000e-172 614.0
17 TraesCS7B01G144000 chr6B 99.120 341 3 0 1192 1532 684281300 684280960 8.050000e-172 614.0
18 TraesCS7B01G144000 chr6B 99.048 210 2 0 524 733 77095394 77095185 1.150000e-100 377.0
19 TraesCS7B01G144000 chr6B 99.048 210 2 0 524 733 77545680 77545889 1.150000e-100 377.0
20 TraesCS7B01G144000 chr6B 97.143 210 5 1 524 733 77096628 77096420 1.940000e-93 353.0
21 TraesCS7B01G144000 chr6B 98.837 86 1 0 3530 3615 684270129 684270044 2.110000e-33 154.0
22 TraesCS7B01G144000 chr6B 98.837 86 1 0 3530 3615 684279121 684279036 2.110000e-33 154.0
23 TraesCS7B01G144000 chr7D 95.736 1032 20 5 2516 3524 459012350 459011320 0.000000e+00 1640.0
24 TraesCS7B01G144000 chr7D 97.619 84 2 0 3530 3613 459011343 459011260 1.270000e-30 145.0
25 TraesCS7B01G144000 chr4D 94.124 970 48 4 1544 2512 6587915 6586954 0.000000e+00 1467.0
26 TraesCS7B01G144000 chr4D 89.535 172 8 2 297 458 23282486 23282315 4.440000e-50 209.0
27 TraesCS7B01G144000 chr4D 86.047 86 8 2 3538 3620 42178791 42178875 6.030000e-14 89.8
28 TraesCS7B01G144000 chr4A 93.750 960 50 4 1553 2512 596819056 596820005 0.000000e+00 1432.0
29 TraesCS7B01G144000 chr3B 94.450 919 40 7 1595 2512 550799012 550798104 0.000000e+00 1404.0
30 TraesCS7B01G144000 chr3B 92.057 768 55 6 3614 4377 443656764 443657529 0.000000e+00 1075.0
31 TraesCS7B01G144000 chr3B 98.649 296 4 0 1 296 743138618 743138913 3.880000e-145 525.0
32 TraesCS7B01G144000 chr3B 98.007 301 6 0 1 301 581652785 581653085 1.390000e-144 523.0
33 TraesCS7B01G144000 chr5B 92.057 768 56 5 3614 4377 339460223 339459457 0.000000e+00 1075.0
34 TraesCS7B01G144000 chr5B 86.940 513 40 14 1595 2097 487483051 487482556 6.400000e-153 551.0
35 TraesCS7B01G144000 chr5B 98.653 297 4 0 1 297 551513592 551513296 1.080000e-145 527.0
36 TraesCS7B01G144000 chr5B 86.179 123 12 2 2393 2511 487482364 487482243 1.280000e-25 128.0
37 TraesCS7B01G144000 chr2B 92.047 767 58 3 3614 4377 625911070 625911836 0.000000e+00 1075.0
38 TraesCS7B01G144000 chr2B 85.605 521 37 10 2516 3008 763622838 763623348 3.020000e-141 512.0
39 TraesCS7B01G144000 chr2B 87.376 404 38 4 3000 3390 763623410 763623813 6.680000e-123 451.0
40 TraesCS7B01G144000 chr1B 91.917 767 58 4 3614 4377 390439385 390440150 0.000000e+00 1070.0
41 TraesCS7B01G144000 chr1B 92.208 231 10 1 297 527 51401130 51401352 1.960000e-83 320.0
42 TraesCS7B01G144000 chr1B 83.938 193 22 8 2823 3009 675755121 675754932 4.500000e-40 176.0
43 TraesCS7B01G144000 chr7A 98.990 297 3 0 1 297 577959752 577959456 2.320000e-147 532.0
44 TraesCS7B01G144000 chr7A 98.000 300 6 0 1 300 442623562 442623263 5.020000e-144 521.0
45 TraesCS7B01G144000 chr7A 87.500 80 10 0 3541 3620 692684932 692684853 4.660000e-15 93.5
46 TraesCS7B01G144000 chr2A 98.990 297 3 0 1 297 141394859 141394563 2.320000e-147 532.0
47 TraesCS7B01G144000 chr2A 98.322 298 5 0 1 298 397428433 397428730 1.390000e-144 523.0
48 TraesCS7B01G144000 chr2A 98.007 301 6 0 1 301 424165670 424165970 1.390000e-144 523.0
49 TraesCS7B01G144000 chr2A 98.000 300 6 0 1 300 455680846 455680547 5.020000e-144 521.0
50 TraesCS7B01G144000 chr2A 88.158 76 9 0 3539 3614 672997900 672997825 1.680000e-14 91.6
51 TraesCS7B01G144000 chr5D 89.016 437 36 9 1669 2097 406419813 406419381 8.340000e-147 531.0
52 TraesCS7B01G144000 chr5D 82.422 512 63 14 2516 3009 493992327 493991825 5.230000e-114 422.0
53 TraesCS7B01G144000 chr5D 87.719 171 14 4 2346 2511 406419180 406419012 4.470000e-45 193.0
54 TraesCS7B01G144000 chr1A 80.355 733 85 29 2516 3229 72542213 72542905 6.540000e-138 501.0
55 TraesCS7B01G144000 chr5A 89.757 371 30 5 1735 2097 512064746 512064376 6.630000e-128 468.0
56 TraesCS7B01G144000 chr5A 94.643 56 2 1 2346 2400 512064182 512064127 7.800000e-13 86.1
57 TraesCS7B01G144000 chrUn 92.050 239 10 3 297 527 215733528 215733291 1.170000e-85 327.0
58 TraesCS7B01G144000 chrUn 88.312 77 6 2 3539 3613 22556964 22556889 6.030000e-14 89.8
59 TraesCS7B01G144000 chr2D 86.008 243 10 6 297 528 634882128 634882357 5.660000e-59 239.0
60 TraesCS7B01G144000 chr1D 84.615 221 32 2 3012 3230 359496995 359496775 7.370000e-53 219.0
61 TraesCS7B01G144000 chr1D 88.000 75 9 0 3539 3613 359496503 359496429 6.030000e-14 89.8
62 TraesCS7B01G144000 chr6A 88.889 180 9 6 297 466 572023588 572023410 1.230000e-50 211.0


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 TraesCS7B01G144000 chr7B 185291096 185295472 4376 False 3817.500000 6281 100.000000 1 4377 2 chr7B.!!$F1 4376
1 TraesCS7B01G144000 chr7B 213385605 213386371 766 True 1075.000000 1075 92.047000 3614 4377 1 chr7B.!!$R1 763
2 TraesCS7B01G144000 chr4B 244773371 244776494 3123 True 1729.666667 3663 95.730333 297 3524 3 chr4B.!!$R3 3227
3 TraesCS7B01G144000 chr4B 11743043 11743948 905 True 1443.000000 1443 95.380000 1605 2512 1 chr4B.!!$R1 907
4 TraesCS7B01G144000 chr4B 542081316 542082082 766 False 1099.000000 1099 92.578000 3613 4377 1 chr4B.!!$F1 764
5 TraesCS7B01G144000 chr4B 542104408 542105175 767 False 1094.000000 1094 92.448000 3613 4377 1 chr4B.!!$F2 764
6 TraesCS7B01G144000 chr4B 598099889 598100656 767 True 1072.000000 1072 91.927000 3613 4377 1 chr4B.!!$R2 764
7 TraesCS7B01G144000 chr6B 599924436 599925194 758 False 1098.000000 1098 92.782000 3613 4371 1 chr6B.!!$F1 758
8 TraesCS7B01G144000 chr6B 684270044 684272308 2264 True 830.666667 1724 98.435667 1192 3615 3 chr6B.!!$R2 2423
9 TraesCS7B01G144000 chr6B 684279036 684281300 2264 True 830.666667 1724 98.435667 1192 3615 3 chr6B.!!$R3 2423
10 TraesCS7B01G144000 chr6B 77545680 77546461 781 False 635.500000 894 97.459500 524 1526 2 chr6B.!!$F2 1002
11 TraesCS7B01G144000 chr6B 77094607 77096628 2021 True 541.333333 894 97.250333 524 1532 3 chr6B.!!$R1 1008
12 TraesCS7B01G144000 chr7D 459011260 459012350 1090 True 892.500000 1640 96.677500 2516 3613 2 chr7D.!!$R1 1097
13 TraesCS7B01G144000 chr4D 6586954 6587915 961 True 1467.000000 1467 94.124000 1544 2512 1 chr4D.!!$R1 968
14 TraesCS7B01G144000 chr4A 596819056 596820005 949 False 1432.000000 1432 93.750000 1553 2512 1 chr4A.!!$F1 959
15 TraesCS7B01G144000 chr3B 550798104 550799012 908 True 1404.000000 1404 94.450000 1595 2512 1 chr3B.!!$R1 917
16 TraesCS7B01G144000 chr3B 443656764 443657529 765 False 1075.000000 1075 92.057000 3614 4377 1 chr3B.!!$F1 763
17 TraesCS7B01G144000 chr5B 339459457 339460223 766 True 1075.000000 1075 92.057000 3614 4377 1 chr5B.!!$R1 763
18 TraesCS7B01G144000 chr5B 487482243 487483051 808 True 339.500000 551 86.559500 1595 2511 2 chr5B.!!$R3 916
19 TraesCS7B01G144000 chr2B 625911070 625911836 766 False 1075.000000 1075 92.047000 3614 4377 1 chr2B.!!$F1 763
20 TraesCS7B01G144000 chr2B 763622838 763623813 975 False 481.500000 512 86.490500 2516 3390 2 chr2B.!!$F2 874
21 TraesCS7B01G144000 chr1B 390439385 390440150 765 False 1070.000000 1070 91.917000 3614 4377 1 chr1B.!!$F2 763
22 TraesCS7B01G144000 chr5D 493991825 493992327 502 True 422.000000 422 82.422000 2516 3009 1 chr5D.!!$R1 493
23 TraesCS7B01G144000 chr5D 406419012 406419813 801 True 362.000000 531 88.367500 1669 2511 2 chr5D.!!$R2 842
24 TraesCS7B01G144000 chr1A 72542213 72542905 692 False 501.000000 501 80.355000 2516 3229 1 chr1A.!!$F1 713
25 TraesCS7B01G144000 chr5A 512064127 512064746 619 True 277.050000 468 92.200000 1735 2400 2 chr5A.!!$R1 665

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
326 327 0.108041 CGGTTAATACAGCACCCCGT 60.108 55.000 0.0 0.0 0.0 5.28 F
452 453 0.257328 TCTCTCCGGCATGTCTCTCT 59.743 55.000 0.0 0.0 0.0 3.10 F
454 455 0.257328 TCTCCGGCATGTCTCTCTCT 59.743 55.000 0.0 0.0 0.0 3.10 F
456 457 0.257328 TCCGGCATGTCTCTCTCTCT 59.743 55.000 0.0 0.0 0.0 3.10 F
691 1403 0.560193 CTCCCCTCCCATCTCTCTCA 59.440 60.000 0.0 0.0 0.0 3.27 F
2383 3595 1.521457 GCTATGTGTGCCGCAGCTA 60.521 57.895 0.0 0.0 40.8 3.32 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1454 2173 1.908483 GACCCGGGAAGAAGCAGAT 59.092 57.895 32.02 0.0 0.00 2.90 R
2383 3595 0.322546 GAAATGGCCTGGAACTCCGT 60.323 55.000 3.32 0.0 39.43 4.69 R
2444 3656 3.764434 CCCGACATCTGTAGCAGGTATAT 59.236 47.826 0.00 0.0 31.51 0.86 R
2462 3678 0.699399 TAAAATGCCCTGGAACCCGA 59.301 50.000 0.00 0.0 0.00 5.14 R
2512 3728 7.568199 ACATCACAGTAAATATAAACTGCCC 57.432 36.000 14.33 0.0 45.65 5.36 R
3694 5036 1.140652 CAACACATGCCCCCTGTTTTT 59.859 47.619 0.00 0.0 0.00 1.94 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
22 23 4.429108 CAACAGATGAATCAATGCATGCA 58.571 39.130 25.04 25.04 0.00 3.96
23 24 4.937201 ACAGATGAATCAATGCATGCAT 57.063 36.364 27.46 27.46 38.46 3.96
24 25 6.212955 CAACAGATGAATCAATGCATGCATA 58.787 36.000 32.36 19.13 35.31 3.14
25 26 6.590234 ACAGATGAATCAATGCATGCATAT 57.410 33.333 32.36 20.78 35.31 1.78
26 27 7.696992 ACAGATGAATCAATGCATGCATATA 57.303 32.000 32.36 22.88 35.31 0.86
28 29 9.403583 ACAGATGAATCAATGCATGCATATATA 57.596 29.630 32.36 18.08 35.31 0.86
29 30 9.665264 CAGATGAATCAATGCATGCATATATAC 57.335 33.333 32.36 22.19 35.31 1.47
30 31 9.628500 AGATGAATCAATGCATGCATATATACT 57.372 29.630 32.36 19.48 35.31 2.12
80 81 9.944663 TGTGTAAAATAGAATGTGTTTTGAGTC 57.055 29.630 0.00 0.00 0.00 3.36
81 82 9.944663 GTGTAAAATAGAATGTGTTTTGAGTCA 57.055 29.630 0.00 0.00 0.00 3.41
91 92 8.659925 AATGTGTTTTGAGTCATAAATTTGCA 57.340 26.923 0.00 0.00 0.00 4.08
92 93 8.659925 ATGTGTTTTGAGTCATAAATTTGCAA 57.340 26.923 0.00 0.00 0.00 4.08
93 94 8.484641 TGTGTTTTGAGTCATAAATTTGCAAA 57.515 26.923 15.44 15.44 0.00 3.68
94 95 9.107177 TGTGTTTTGAGTCATAAATTTGCAAAT 57.893 25.926 18.99 18.99 0.00 2.32
95 96 9.934190 GTGTTTTGAGTCATAAATTTGCAAATT 57.066 25.926 27.73 27.73 40.15 1.82
122 123 3.262135 ACGTCATTTTCAAATTCGCGT 57.738 38.095 5.77 0.00 31.15 6.01
124 125 3.222361 CGTCATTTTCAAATTCGCGTCA 58.778 40.909 5.77 0.00 0.00 4.35
125 126 3.661728 CGTCATTTTCAAATTCGCGTCAA 59.338 39.130 5.77 0.00 0.00 3.18
126 127 4.429812 CGTCATTTTCAAATTCGCGTCAAC 60.430 41.667 5.77 0.00 0.00 3.18
127 128 4.675114 GTCATTTTCAAATTCGCGTCAACT 59.325 37.500 5.77 0.00 0.00 3.16
128 129 5.173131 GTCATTTTCAAATTCGCGTCAACTT 59.827 36.000 5.77 0.00 0.00 2.66
129 130 5.746245 TCATTTTCAAATTCGCGTCAACTTT 59.254 32.000 5.77 0.00 0.00 2.66
130 131 5.368552 TTTTCAAATTCGCGTCAACTTTG 57.631 34.783 5.77 10.10 0.00 2.77
131 132 2.993545 TCAAATTCGCGTCAACTTTGG 58.006 42.857 5.77 0.00 0.00 3.28
132 133 2.356382 TCAAATTCGCGTCAACTTTGGT 59.644 40.909 5.77 0.00 0.00 3.67
133 134 3.112580 CAAATTCGCGTCAACTTTGGTT 58.887 40.909 5.77 0.00 35.86 3.67
134 135 3.430333 AATTCGCGTCAACTTTGGTTT 57.570 38.095 5.77 0.00 32.73 3.27
135 136 2.923605 TTCGCGTCAACTTTGGTTTT 57.076 40.000 5.77 0.00 32.73 2.43
137 138 4.352600 TTCGCGTCAACTTTGGTTTTTA 57.647 36.364 5.77 0.00 32.73 1.52
138 139 4.555348 TCGCGTCAACTTTGGTTTTTAT 57.445 36.364 5.77 0.00 32.73 1.40
139 140 4.283678 TCGCGTCAACTTTGGTTTTTATG 58.716 39.130 5.77 0.00 32.73 1.90
140 141 3.423867 CGCGTCAACTTTGGTTTTTATGG 59.576 43.478 0.00 0.00 32.73 2.74
141 142 4.364860 GCGTCAACTTTGGTTTTTATGGT 58.635 39.130 0.00 0.00 32.73 3.55
142 143 5.521544 GCGTCAACTTTGGTTTTTATGGTA 58.478 37.500 0.00 0.00 32.73 3.25
143 144 6.153756 GCGTCAACTTTGGTTTTTATGGTAT 58.846 36.000 0.00 0.00 32.73 2.73
145 146 7.971722 GCGTCAACTTTGGTTTTTATGGTATAT 59.028 33.333 0.00 0.00 32.73 0.86
149 150 9.724839 CAACTTTGGTTTTTATGGTATATACCG 57.275 33.333 23.82 9.53 40.37 4.02
150 151 9.683870 AACTTTGGTTTTTATGGTATATACCGA 57.316 29.630 23.82 13.54 39.83 4.69
161 162 5.643379 GGTATATACCGAAACCATACCGA 57.357 43.478 16.11 0.00 36.50 4.69
162 163 6.024552 GGTATATACCGAAACCATACCGAA 57.975 41.667 16.11 0.00 36.50 4.30
163 164 6.454795 GGTATATACCGAAACCATACCGAAA 58.545 40.000 16.11 0.00 36.50 3.46
164 165 7.099120 GGTATATACCGAAACCATACCGAAAT 58.901 38.462 16.11 0.00 36.50 2.17
165 166 8.250332 GGTATATACCGAAACCATACCGAAATA 58.750 37.037 16.11 0.00 36.50 1.40
166 167 9.638239 GTATATACCGAAACCATACCGAAATAA 57.362 33.333 1.02 0.00 0.00 1.40
168 169 9.729281 ATATACCGAAACCATACCGAAATAATT 57.271 29.630 0.00 0.00 0.00 1.40
169 170 6.762702 ACCGAAACCATACCGAAATAATTT 57.237 33.333 0.00 0.00 0.00 1.82
170 171 6.557110 ACCGAAACCATACCGAAATAATTTG 58.443 36.000 0.00 0.00 0.00 2.32
171 172 5.974751 CCGAAACCATACCGAAATAATTTGG 59.025 40.000 0.00 0.00 44.62 3.28
192 193 3.243401 GGTATATACCGAAACCGAACCGT 60.243 47.826 16.11 0.00 36.50 4.83
193 194 4.023536 GGTATATACCGAAACCGAACCGTA 60.024 45.833 16.11 0.00 36.50 4.02
194 195 4.853924 ATATACCGAAACCGAACCGTAT 57.146 40.909 0.00 0.00 0.00 3.06
195 196 3.525268 ATACCGAAACCGAACCGTATT 57.475 42.857 0.00 0.00 0.00 1.89
196 197 2.168326 ACCGAAACCGAACCGTATTT 57.832 45.000 0.00 0.00 0.00 1.40
197 198 2.493035 ACCGAAACCGAACCGTATTTT 58.507 42.857 0.00 0.00 0.00 1.82
198 199 3.658709 ACCGAAACCGAACCGTATTTTA 58.341 40.909 0.00 0.00 0.00 1.52
199 200 4.252878 ACCGAAACCGAACCGTATTTTAT 58.747 39.130 0.00 0.00 0.00 1.40
200 201 4.093261 ACCGAAACCGAACCGTATTTTATG 59.907 41.667 0.00 0.00 0.00 1.90
202 203 5.390779 CCGAAACCGAACCGTATTTTATGTT 60.391 40.000 0.00 0.00 0.00 2.71
203 204 5.729424 CGAAACCGAACCGTATTTTATGTTC 59.271 40.000 0.00 0.00 35.03 3.18
204 205 6.557291 AAACCGAACCGTATTTTATGTTCA 57.443 33.333 0.00 0.00 37.53 3.18
205 206 6.746745 AACCGAACCGTATTTTATGTTCAT 57.253 33.333 0.00 0.00 37.53 2.57
206 207 7.846644 AACCGAACCGTATTTTATGTTCATA 57.153 32.000 0.00 0.00 37.53 2.15
209 210 6.349426 CGAACCGTATTTTATGTTCATACCG 58.651 40.000 0.00 0.00 37.53 4.02
210 211 6.019640 CGAACCGTATTTTATGTTCATACCGT 60.020 38.462 0.00 0.00 37.53 4.83
211 212 7.167302 CGAACCGTATTTTATGTTCATACCGTA 59.833 37.037 0.00 0.00 37.53 4.02
212 213 8.891671 AACCGTATTTTATGTTCATACCGTAT 57.108 30.769 0.00 0.00 0.00 3.06
213 214 8.891671 ACCGTATTTTATGTTCATACCGTATT 57.108 30.769 0.00 0.00 0.00 1.89
219 220 8.939201 TTTTATGTTCATACCGTATTTACCGA 57.061 30.769 0.00 0.00 0.00 4.69
220 221 8.939201 TTTATGTTCATACCGTATTTACCGAA 57.061 30.769 0.00 0.00 0.00 4.30
221 222 8.578308 TTATGTTCATACCGTATTTACCGAAG 57.422 34.615 0.00 0.00 0.00 3.79
223 224 7.094508 TGTTCATACCGTATTTACCGAAGTA 57.905 36.000 0.00 0.00 0.00 2.24
225 226 8.196771 TGTTCATACCGTATTTACCGAAGTATT 58.803 33.333 0.00 0.00 0.00 1.89
226 227 9.677567 GTTCATACCGTATTTACCGAAGTATTA 57.322 33.333 0.00 0.00 0.00 0.98
232 233 7.807907 ACCGTATTTACCGAAGTATTAATACCG 59.192 37.037 19.74 16.55 32.90 4.02
233 234 7.807907 CCGTATTTACCGAAGTATTAATACCGT 59.192 37.037 19.74 13.65 32.90 4.83
234 235 9.820229 CGTATTTACCGAAGTATTAATACCGTA 57.180 33.333 19.74 12.84 32.90 4.02
241 242 8.177663 ACCGAAGTATTAATACCGTACATATCG 58.822 37.037 19.74 15.30 33.79 2.92
243 244 9.759259 CGAAGTATTAATACCGTACATATCGAA 57.241 33.333 19.74 0.00 33.79 3.71
249 250 6.515043 AATACCGTACATATCGAAAAACCG 57.485 37.500 0.00 0.00 0.00 4.44
250 251 3.848726 ACCGTACATATCGAAAAACCGT 58.151 40.909 0.00 0.00 0.00 4.83
251 252 4.992688 ACCGTACATATCGAAAAACCGTA 58.007 39.130 0.00 0.00 0.00 4.02
252 253 5.591099 ACCGTACATATCGAAAAACCGTAT 58.409 37.500 0.00 0.00 0.00 3.06
253 254 6.734137 ACCGTACATATCGAAAAACCGTATA 58.266 36.000 0.00 0.00 0.00 1.47
256 257 8.702438 CCGTACATATCGAAAAACCGTATAAAT 58.298 33.333 0.00 0.00 0.00 1.40
257 258 9.717844 CGTACATATCGAAAAACCGTATAAATC 57.282 33.333 0.00 0.00 0.00 2.17
258 259 9.717844 GTACATATCGAAAAACCGTATAAATCG 57.282 33.333 0.00 0.00 0.00 3.34
259 260 8.578308 ACATATCGAAAAACCGTATAAATCGA 57.422 30.769 0.00 0.00 41.36 3.59
263 264 7.522901 TCGAAAAACCGTATAAATCGAATCA 57.477 32.000 0.00 0.00 35.22 2.57
264 265 8.133754 TCGAAAAACCGTATAAATCGAATCAT 57.866 30.769 0.00 0.00 35.22 2.45
265 266 8.059502 TCGAAAAACCGTATAAATCGAATCATG 58.940 33.333 0.00 0.00 35.22 3.07
266 267 7.849026 CGAAAAACCGTATAAATCGAATCATGT 59.151 33.333 0.00 0.00 0.00 3.21
270 271 9.925268 AAACCGTATAAATCGAATCATGTAAAC 57.075 29.630 0.00 0.00 0.00 2.01
271 272 8.080083 ACCGTATAAATCGAATCATGTAAACC 57.920 34.615 0.00 0.00 0.00 3.27
272 273 7.095940 ACCGTATAAATCGAATCATGTAAACCG 60.096 37.037 0.00 0.00 0.00 4.44
273 274 7.115236 CCGTATAAATCGAATCATGTAAACCGA 59.885 37.037 0.00 0.00 0.00 4.69
274 275 8.481641 CGTATAAATCGAATCATGTAAACCGAA 58.518 33.333 0.00 0.00 0.00 4.30
279 280 9.498307 AAATCGAATCATGTAAACCGAATAAAC 57.502 29.630 0.00 0.00 0.00 2.01
280 281 7.007313 TCGAATCATGTAAACCGAATAAACC 57.993 36.000 0.00 0.00 0.00 3.27
281 282 5.899696 CGAATCATGTAAACCGAATAAACCG 59.100 40.000 0.00 0.00 0.00 4.44
282 283 6.237888 CGAATCATGTAAACCGAATAAACCGA 60.238 38.462 0.00 0.00 0.00 4.69
283 284 6.988622 ATCATGTAAACCGAATAAACCGAA 57.011 33.333 0.00 0.00 0.00 4.30
284 285 6.168164 TCATGTAAACCGAATAAACCGAAC 57.832 37.500 0.00 0.00 0.00 3.95
285 286 4.644044 TGTAAACCGAATAAACCGAACG 57.356 40.909 0.00 0.00 0.00 3.95
288 289 1.729284 ACCGAATAAACCGAACGCAT 58.271 45.000 0.00 0.00 0.00 4.73
290 291 2.861935 ACCGAATAAACCGAACGCATAG 59.138 45.455 0.00 0.00 0.00 2.23
291 292 2.220133 CCGAATAAACCGAACGCATAGG 59.780 50.000 0.00 0.00 0.00 2.57
292 293 2.220133 CGAATAAACCGAACGCATAGGG 59.780 50.000 0.00 0.00 0.00 3.53
293 294 1.589803 ATAAACCGAACGCATAGGGC 58.410 50.000 0.00 0.00 39.90 5.19
295 296 0.538118 AAACCGAACGCATAGGGCTA 59.462 50.000 0.00 0.00 41.67 3.93
326 327 0.108041 CGGTTAATACAGCACCCCGT 60.108 55.000 0.00 0.00 0.00 5.28
372 373 4.636435 CCGGTGGAACGTGCCCTT 62.636 66.667 11.01 0.00 38.12 3.95
384 385 2.124695 GCCCTTTCCCGATTCGCT 60.125 61.111 0.00 0.00 0.00 4.93
400 401 2.683465 GCTGCCCTCTCCCCAATCA 61.683 63.158 0.00 0.00 0.00 2.57
436 437 1.178276 TTGACCTCTCCTCGCTTCTC 58.822 55.000 0.00 0.00 0.00 2.87
440 441 1.444119 CCTCTCCTCGCTTCTCTCCG 61.444 65.000 0.00 0.00 0.00 4.63
446 447 2.185350 CGCTTCTCTCCGGCATGT 59.815 61.111 0.00 0.00 0.00 3.21
447 448 1.880340 CGCTTCTCTCCGGCATGTC 60.880 63.158 0.00 0.00 0.00 3.06
448 449 1.519719 GCTTCTCTCCGGCATGTCT 59.480 57.895 0.00 0.00 0.00 3.41
450 451 1.110442 CTTCTCTCCGGCATGTCTCT 58.890 55.000 0.00 0.00 0.00 3.10
452 453 0.257328 TCTCTCCGGCATGTCTCTCT 59.743 55.000 0.00 0.00 0.00 3.10
454 455 0.257328 TCTCCGGCATGTCTCTCTCT 59.743 55.000 0.00 0.00 0.00 3.10
455 456 0.667993 CTCCGGCATGTCTCTCTCTC 59.332 60.000 0.00 0.00 0.00 3.20
456 457 0.257328 TCCGGCATGTCTCTCTCTCT 59.743 55.000 0.00 0.00 0.00 3.10
458 459 1.679139 CGGCATGTCTCTCTCTCTCT 58.321 55.000 0.00 0.00 0.00 3.10
459 460 1.603802 CGGCATGTCTCTCTCTCTCTC 59.396 57.143 0.00 0.00 0.00 3.20
462 463 3.434167 GGCATGTCTCTCTCTCTCTCTCT 60.434 52.174 0.00 0.00 0.00 3.10
464 465 4.444022 GCATGTCTCTCTCTCTCTCTCTCT 60.444 50.000 0.00 0.00 0.00 3.10
466 467 4.614475 TGTCTCTCTCTCTCTCTCTCTCT 58.386 47.826 0.00 0.00 0.00 3.10
467 468 4.646945 TGTCTCTCTCTCTCTCTCTCTCTC 59.353 50.000 0.00 0.00 0.00 3.20
468 469 4.892934 GTCTCTCTCTCTCTCTCTCTCTCT 59.107 50.000 0.00 0.00 0.00 3.10
691 1403 0.560193 CTCCCCTCCCATCTCTCTCA 59.440 60.000 0.00 0.00 0.00 3.27
1135 1847 2.176148 GGAGGGAGACTAGCTAGGAGTT 59.824 54.545 24.35 3.34 0.00 3.01
1136 1848 3.373329 GGAGGGAGACTAGCTAGGAGTTT 60.373 52.174 24.35 2.94 0.00 2.66
1140 1852 2.960384 GAGACTAGCTAGGAGTTTCCCC 59.040 54.545 24.35 4.55 37.19 4.81
1454 2173 3.379445 GACCAACGCTCCTCCGGA 61.379 66.667 2.93 2.93 0.00 5.14
1664 2782 2.545946 GCGGAAAGTCATAGAAGATGGC 59.454 50.000 0.00 0.00 0.00 4.40
1744 2862 4.391216 CGCAGAAGTGAAAGATGAAGATGT 59.609 41.667 0.00 0.00 0.00 3.06
1795 2913 9.167311 AGCTGAACTTAAATGGTTAGAATACAG 57.833 33.333 0.00 0.00 0.00 2.74
2383 3595 1.521457 GCTATGTGTGCCGCAGCTA 60.521 57.895 0.00 0.00 40.80 3.32
2444 3656 2.997315 CAGACGCCTCCACCTGGA 60.997 66.667 0.00 0.00 43.08 3.86
2462 3678 4.774726 CCTGGATATACCTGCTACAGATGT 59.225 45.833 0.00 0.00 39.86 3.06
2512 3728 1.586028 CAACCATTGGCGGTTCCAG 59.414 57.895 1.54 0.00 46.60 3.86
2913 4172 2.227194 CTAAAAGGGGCAAAGTGTCGT 58.773 47.619 0.00 0.00 0.00 4.34
3064 4393 2.826128 TCGCTTGGACTTATCTCACACT 59.174 45.455 0.00 0.00 0.00 3.55
3390 4732 3.058224 GCGCTTGGACAATAAGTTGAGTT 60.058 43.478 0.00 0.00 38.71 3.01
3430 4772 2.087501 TTGGTGTATGGCACTGTACG 57.912 50.000 0.00 0.00 46.86 3.67
3489 4831 2.274542 TCCTTGGGCCAGTTCATAGAA 58.725 47.619 6.23 0.00 0.00 2.10
3492 4834 3.445096 CCTTGGGCCAGTTCATAGAAAAG 59.555 47.826 6.23 0.00 0.00 2.27
3500 4842 5.649831 GCCAGTTCATAGAAAAGGATTCTGT 59.350 40.000 1.10 0.00 0.00 3.41
3501 4843 6.823689 GCCAGTTCATAGAAAAGGATTCTGTA 59.176 38.462 1.10 0.00 0.00 2.74
3502 4844 7.201652 GCCAGTTCATAGAAAAGGATTCTGTAC 60.202 40.741 1.10 0.00 0.00 2.90
3503 4845 8.043710 CCAGTTCATAGAAAAGGATTCTGTACT 58.956 37.037 1.10 0.00 0.00 2.73
3511 4853 8.312669 AGAAAAGGATTCTGTACTATAGCTGT 57.687 34.615 0.00 0.00 0.00 4.40
3512 4854 9.422681 AGAAAAGGATTCTGTACTATAGCTGTA 57.577 33.333 0.00 0.00 0.00 2.74
3518 4860 9.938670 GGATTCTGTACTATAGCTGTATTATCG 57.061 37.037 0.00 0.00 0.00 2.92
3519 4861 9.938670 GATTCTGTACTATAGCTGTATTATCGG 57.061 37.037 0.00 0.00 0.00 4.18
3520 4862 9.682465 ATTCTGTACTATAGCTGTATTATCGGA 57.318 33.333 0.00 0.00 0.00 4.55
3521 4863 9.682465 TTCTGTACTATAGCTGTATTATCGGAT 57.318 33.333 0.00 0.00 0.00 4.18
3522 4864 9.682465 TCTGTACTATAGCTGTATTATCGGATT 57.318 33.333 0.00 0.00 0.00 3.01
3523 4865 9.723447 CTGTACTATAGCTGTATTATCGGATTG 57.277 37.037 0.00 0.00 0.00 2.67
3524 4866 9.239551 TGTACTATAGCTGTATTATCGGATTGT 57.760 33.333 0.00 0.00 0.00 2.71
3525 4867 9.719279 GTACTATAGCTGTATTATCGGATTGTC 57.281 37.037 0.00 0.00 0.00 3.18
3526 4868 8.349568 ACTATAGCTGTATTATCGGATTGTCA 57.650 34.615 0.00 0.00 0.00 3.58
3527 4869 8.972127 ACTATAGCTGTATTATCGGATTGTCAT 58.028 33.333 0.00 0.00 0.00 3.06
3572 4914 0.463654 GATATGACAGTGCCCGGCAA 60.464 55.000 15.39 0.00 41.47 4.52
3650 4992 3.322541 TGGAGTGTTGACATCGTCCTTAA 59.677 43.478 9.92 0.00 0.00 1.85
3699 5041 2.476018 GCACACAAGCTTTGCCAAAAAC 60.476 45.455 9.98 0.00 0.00 2.43
3700 5042 2.740981 CACACAAGCTTTGCCAAAAACA 59.259 40.909 0.00 0.00 0.00 2.83
3799 5143 9.443323 TCTTCATGAAAGATTTCCGTATTGTTA 57.557 29.630 9.88 0.00 39.12 2.41
3850 5194 2.100916 ACCGTCCGATTTCATCTCGAAT 59.899 45.455 0.00 0.00 38.38 3.34
3946 5290 7.812191 TGACCTCAAATGGAAAAATGATTTACG 59.188 33.333 0.00 0.00 0.00 3.18
4012 5357 2.228582 TCGTCCAAATCCGAGTTCGTAA 59.771 45.455 0.48 0.00 37.74 3.18
4037 5382 5.277538 GCAAAAGTTAGAGCCATCGGAATAG 60.278 44.000 0.00 0.00 0.00 1.73
4062 5407 2.575532 CTGTCAGGAGGCAAAAACTGA 58.424 47.619 0.00 0.00 37.61 3.41
4148 5493 6.183360 CGATTTGACCCTCAAGATTACCTCTA 60.183 42.308 0.00 0.00 37.70 2.43
4224 5570 4.189231 GCTTTTAGGCTCGTTTCCATCTA 58.811 43.478 0.00 0.00 0.00 1.98
4263 5609 4.047822 CAAAAATTACTCGCAAGGTGCAA 58.952 39.130 0.61 0.00 45.36 4.08
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 4.729227 TGCATGCATTGATTCATCTGTT 57.271 36.364 18.46 0.00 0.00 3.16
2 3 4.937201 ATGCATGCATTGATTCATCTGT 57.063 36.364 27.46 1.07 31.82 3.41
4 5 9.628500 AGTATATATGCATGCATTGATTCATCT 57.372 29.630 36.23 20.28 37.82 2.90
54 55 9.944663 GACTCAAAACACATTCTATTTTACACA 57.055 29.630 0.00 0.00 0.00 3.72
55 56 9.944663 TGACTCAAAACACATTCTATTTTACAC 57.055 29.630 0.00 0.00 0.00 2.90
64 65 8.981647 GCAAATTTATGACTCAAAACACATTCT 58.018 29.630 0.00 0.00 0.00 2.40
65 66 8.763356 TGCAAATTTATGACTCAAAACACATTC 58.237 29.630 0.00 0.00 0.00 2.67
66 67 8.659925 TGCAAATTTATGACTCAAAACACATT 57.340 26.923 0.00 0.00 0.00 2.71
67 68 8.659925 TTGCAAATTTATGACTCAAAACACAT 57.340 26.923 0.00 0.00 0.00 3.21
68 69 8.484641 TTTGCAAATTTATGACTCAAAACACA 57.515 26.923 8.05 0.00 0.00 3.72
69 70 9.934190 AATTTGCAAATTTATGACTCAAAACAC 57.066 25.926 27.73 0.00 35.16 3.32
95 96 9.149556 CGCGAATTTGAAAATGACGTAATAATA 57.850 29.630 0.00 0.00 34.20 0.98
96 97 7.694784 ACGCGAATTTGAAAATGACGTAATAAT 59.305 29.630 15.93 0.00 33.31 1.28
97 98 7.016466 ACGCGAATTTGAAAATGACGTAATAA 58.984 30.769 15.93 0.00 33.31 1.40
98 99 6.535811 ACGCGAATTTGAAAATGACGTAATA 58.464 32.000 15.93 0.00 33.31 0.98
100 101 4.774586 ACGCGAATTTGAAAATGACGTAA 58.225 34.783 15.93 0.00 33.31 3.18
101 102 4.084485 TGACGCGAATTTGAAAATGACGTA 60.084 37.500 15.93 0.00 34.40 3.57
102 103 3.223157 GACGCGAATTTGAAAATGACGT 58.777 40.909 15.93 9.40 35.85 4.34
103 104 3.222361 TGACGCGAATTTGAAAATGACG 58.778 40.909 15.93 9.63 34.53 4.35
104 105 4.675114 AGTTGACGCGAATTTGAAAATGAC 59.325 37.500 15.93 0.00 0.00 3.06
105 106 4.854399 AGTTGACGCGAATTTGAAAATGA 58.146 34.783 15.93 0.00 0.00 2.57
107 108 5.051106 CCAAAGTTGACGCGAATTTGAAAAT 60.051 36.000 15.93 0.00 33.69 1.82
108 109 4.266502 CCAAAGTTGACGCGAATTTGAAAA 59.733 37.500 15.93 0.00 33.69 2.29
110 111 3.181495 ACCAAAGTTGACGCGAATTTGAA 60.181 39.130 15.93 0.00 33.69 2.69
111 112 2.356382 ACCAAAGTTGACGCGAATTTGA 59.644 40.909 15.93 0.00 33.69 2.69
112 113 2.726633 ACCAAAGTTGACGCGAATTTG 58.273 42.857 15.93 12.71 0.00 2.32
114 115 3.430333 AAACCAAAGTTGACGCGAATT 57.570 38.095 15.93 0.00 35.97 2.17
115 116 3.430333 AAAACCAAAGTTGACGCGAAT 57.570 38.095 15.93 0.00 35.97 3.34
116 117 2.923605 AAAACCAAAGTTGACGCGAA 57.076 40.000 15.93 0.00 35.97 4.70
117 118 2.923605 AAAAACCAAAGTTGACGCGA 57.076 40.000 15.93 0.00 35.97 5.87
118 119 3.423867 CCATAAAAACCAAAGTTGACGCG 59.576 43.478 3.53 3.53 35.97 6.01
124 125 9.683870 TCGGTATATACCATAAAAACCAAAGTT 57.316 29.630 27.58 0.00 46.80 2.66
125 126 9.683870 TTCGGTATATACCATAAAAACCAAAGT 57.316 29.630 27.58 0.00 46.80 2.66
128 129 8.901793 GGTTTCGGTATATACCATAAAAACCAA 58.098 33.333 33.00 15.19 46.80 3.67
129 130 8.449251 GGTTTCGGTATATACCATAAAAACCA 57.551 34.615 33.00 15.64 46.80 3.67
130 131 8.449251 TGGTTTCGGTATATACCATAAAAACC 57.551 34.615 32.31 32.31 46.80 3.27
138 139 5.076182 TCGGTATGGTTTCGGTATATACCA 58.924 41.667 27.58 13.16 46.80 3.25
139 140 5.643379 TCGGTATGGTTTCGGTATATACC 57.357 43.478 20.39 20.39 42.98 2.73
140 141 9.638239 TTATTTCGGTATGGTTTCGGTATATAC 57.362 33.333 4.14 4.14 0.00 1.47
142 143 9.729281 AATTATTTCGGTATGGTTTCGGTATAT 57.271 29.630 0.00 0.00 0.00 0.86
143 144 9.558396 AAATTATTTCGGTATGGTTTCGGTATA 57.442 29.630 0.00 0.00 0.00 1.47
145 146 7.201714 CCAAATTATTTCGGTATGGTTTCGGTA 60.202 37.037 0.00 0.00 0.00 4.02
146 147 6.404954 CCAAATTATTTCGGTATGGTTTCGGT 60.405 38.462 0.00 0.00 0.00 4.69
147 148 5.974751 CCAAATTATTTCGGTATGGTTTCGG 59.025 40.000 0.00 0.00 0.00 4.30
157 158 9.558396 TTTCGGTATATACCAAATTATTTCGGT 57.442 29.630 27.58 13.35 46.80 4.69
158 159 9.815936 GTTTCGGTATATACCAAATTATTTCGG 57.184 33.333 27.58 9.93 46.80 4.30
159 160 9.815936 GGTTTCGGTATATACCAAATTATTTCG 57.184 33.333 27.58 12.15 46.80 3.46
160 161 9.815936 CGGTTTCGGTATATACCAAATTATTTC 57.184 33.333 27.58 14.34 46.80 2.17
161 162 9.558396 TCGGTTTCGGTATATACCAAATTATTT 57.442 29.630 27.58 0.00 46.80 1.40
162 163 9.558396 TTCGGTTTCGGTATATACCAAATTATT 57.442 29.630 27.58 0.00 46.80 1.40
163 164 8.992073 GTTCGGTTTCGGTATATACCAAATTAT 58.008 33.333 27.58 0.00 46.80 1.28
164 165 7.440856 GGTTCGGTTTCGGTATATACCAAATTA 59.559 37.037 27.58 14.29 46.80 1.40
165 166 6.260714 GGTTCGGTTTCGGTATATACCAAATT 59.739 38.462 27.58 0.00 46.80 1.82
166 167 5.759763 GGTTCGGTTTCGGTATATACCAAAT 59.240 40.000 27.58 0.00 46.80 2.32
167 168 5.115480 GGTTCGGTTTCGGTATATACCAAA 58.885 41.667 27.58 22.18 46.80 3.28
168 169 4.692228 GGTTCGGTTTCGGTATATACCAA 58.308 43.478 27.58 18.57 46.80 3.67
169 170 3.243367 CGGTTCGGTTTCGGTATATACCA 60.243 47.826 27.58 14.40 46.80 3.25
170 171 3.243401 ACGGTTCGGTTTCGGTATATACC 60.243 47.826 20.39 20.39 42.98 2.73
171 172 3.964909 ACGGTTCGGTTTCGGTATATAC 58.035 45.455 4.14 4.14 36.95 1.47
172 173 5.957842 ATACGGTTCGGTTTCGGTATATA 57.042 39.130 0.00 0.00 36.95 0.86
174 175 4.647424 AATACGGTTCGGTTTCGGTATA 57.353 40.909 0.00 0.00 36.95 1.47
175 176 3.525268 AATACGGTTCGGTTTCGGTAT 57.475 42.857 0.00 0.00 36.95 2.73
177 178 2.168326 AAATACGGTTCGGTTTCGGT 57.832 45.000 0.00 0.00 36.95 4.69
178 179 4.093261 ACATAAAATACGGTTCGGTTTCGG 59.907 41.667 0.00 0.00 36.95 4.30
180 181 6.601264 TGAACATAAAATACGGTTCGGTTTC 58.399 36.000 0.00 0.00 41.84 2.78
181 182 6.557291 TGAACATAAAATACGGTTCGGTTT 57.443 33.333 0.00 0.00 41.84 3.27
182 183 6.746745 ATGAACATAAAATACGGTTCGGTT 57.253 33.333 0.00 0.00 41.84 4.44
183 184 6.258507 GGTATGAACATAAAATACGGTTCGGT 59.741 38.462 0.00 0.00 41.84 4.69
184 185 6.562640 CGGTATGAACATAAAATACGGTTCGG 60.563 42.308 0.00 0.00 41.84 4.30
185 186 6.019640 ACGGTATGAACATAAAATACGGTTCG 60.020 38.462 0.00 0.00 41.84 3.95
186 187 7.237920 ACGGTATGAACATAAAATACGGTTC 57.762 36.000 0.00 0.00 37.15 3.62
187 188 8.891671 ATACGGTATGAACATAAAATACGGTT 57.108 30.769 0.00 0.00 39.54 4.44
193 194 9.545105 TCGGTAAATACGGTATGAACATAAAAT 57.455 29.630 0.58 0.00 0.00 1.82
194 195 8.939201 TCGGTAAATACGGTATGAACATAAAA 57.061 30.769 0.58 0.00 0.00 1.52
195 196 8.939201 TTCGGTAAATACGGTATGAACATAAA 57.061 30.769 0.58 0.00 0.00 1.40
196 197 8.196771 ACTTCGGTAAATACGGTATGAACATAA 58.803 33.333 0.58 1.80 0.00 1.90
197 198 7.715657 ACTTCGGTAAATACGGTATGAACATA 58.284 34.615 0.58 0.00 0.00 2.29
198 199 6.576185 ACTTCGGTAAATACGGTATGAACAT 58.424 36.000 0.58 0.00 0.00 2.71
199 200 5.964758 ACTTCGGTAAATACGGTATGAACA 58.035 37.500 0.58 0.00 0.00 3.18
200 201 8.579682 AATACTTCGGTAAATACGGTATGAAC 57.420 34.615 0.58 3.37 33.79 3.18
206 207 7.807907 CGGTATTAATACTTCGGTAAATACGGT 59.192 37.037 21.86 0.00 36.24 4.83
215 216 8.177663 CGATATGTACGGTATTAATACTTCGGT 58.822 37.037 21.86 16.68 33.81 4.69
223 224 8.702438 CGGTTTTTCGATATGTACGGTATTAAT 58.298 33.333 0.00 0.00 0.00 1.40
225 226 7.199766 ACGGTTTTTCGATATGTACGGTATTA 58.800 34.615 0.00 0.00 0.00 0.98
226 227 6.042143 ACGGTTTTTCGATATGTACGGTATT 58.958 36.000 0.00 0.00 0.00 1.89
227 228 5.591099 ACGGTTTTTCGATATGTACGGTAT 58.409 37.500 0.00 0.00 0.00 2.73
228 229 4.992688 ACGGTTTTTCGATATGTACGGTA 58.007 39.130 0.00 0.00 0.00 4.02
229 230 3.848726 ACGGTTTTTCGATATGTACGGT 58.151 40.909 0.00 0.00 0.00 4.83
230 231 7.621832 TTATACGGTTTTTCGATATGTACGG 57.378 36.000 0.00 0.00 0.00 4.02
232 233 9.717844 CGATTTATACGGTTTTTCGATATGTAC 57.282 33.333 0.00 0.00 0.00 2.90
233 234 9.676195 TCGATTTATACGGTTTTTCGATATGTA 57.324 29.630 0.00 0.00 0.00 2.29
234 235 8.578308 TCGATTTATACGGTTTTTCGATATGT 57.422 30.769 0.00 0.00 0.00 2.29
238 239 8.133754 TGATTCGATTTATACGGTTTTTCGAT 57.866 30.769 0.00 0.00 34.55 3.59
239 240 7.522901 TGATTCGATTTATACGGTTTTTCGA 57.477 32.000 0.00 0.00 32.89 3.71
240 241 7.849026 ACATGATTCGATTTATACGGTTTTTCG 59.151 33.333 0.00 0.00 0.00 3.46
246 247 7.095940 CGGTTTACATGATTCGATTTATACGGT 60.096 37.037 0.00 0.00 0.00 4.83
247 248 7.115236 TCGGTTTACATGATTCGATTTATACGG 59.885 37.037 0.00 0.00 0.00 4.02
248 249 7.999213 TCGGTTTACATGATTCGATTTATACG 58.001 34.615 0.00 0.00 0.00 3.06
253 254 9.498307 GTTTATTCGGTTTACATGATTCGATTT 57.502 29.630 0.00 0.00 0.00 2.17
256 257 6.237888 CGGTTTATTCGGTTTACATGATTCGA 60.238 38.462 0.00 0.00 0.00 3.71
257 258 5.899696 CGGTTTATTCGGTTTACATGATTCG 59.100 40.000 0.00 0.00 0.00 3.34
258 259 7.007313 TCGGTTTATTCGGTTTACATGATTC 57.993 36.000 0.00 0.00 0.00 2.52
259 260 6.988622 TCGGTTTATTCGGTTTACATGATT 57.011 33.333 0.00 0.00 0.00 2.57
261 262 5.163972 CGTTCGGTTTATTCGGTTTACATGA 60.164 40.000 0.00 0.00 0.00 3.07
262 263 5.016985 CGTTCGGTTTATTCGGTTTACATG 58.983 41.667 0.00 0.00 0.00 3.21
263 264 4.435917 GCGTTCGGTTTATTCGGTTTACAT 60.436 41.667 0.00 0.00 0.00 2.29
264 265 3.120718 GCGTTCGGTTTATTCGGTTTACA 60.121 43.478 0.00 0.00 0.00 2.41
265 266 3.120718 TGCGTTCGGTTTATTCGGTTTAC 60.121 43.478 0.00 0.00 0.00 2.01
266 267 3.062763 TGCGTTCGGTTTATTCGGTTTA 58.937 40.909 0.00 0.00 0.00 2.01
267 268 1.872313 TGCGTTCGGTTTATTCGGTTT 59.128 42.857 0.00 0.00 0.00 3.27
268 269 1.510776 TGCGTTCGGTTTATTCGGTT 58.489 45.000 0.00 0.00 0.00 4.44
269 270 1.729284 ATGCGTTCGGTTTATTCGGT 58.271 45.000 0.00 0.00 0.00 4.69
270 271 2.220133 CCTATGCGTTCGGTTTATTCGG 59.780 50.000 0.00 0.00 0.00 4.30
271 272 2.220133 CCCTATGCGTTCGGTTTATTCG 59.780 50.000 0.00 0.00 0.00 3.34
272 273 2.032290 GCCCTATGCGTTCGGTTTATTC 60.032 50.000 0.00 0.00 0.00 1.75
273 274 1.944709 GCCCTATGCGTTCGGTTTATT 59.055 47.619 0.00 0.00 0.00 1.40
274 275 1.589803 GCCCTATGCGTTCGGTTTAT 58.410 50.000 0.00 0.00 0.00 1.40
275 276 3.068574 GCCCTATGCGTTCGGTTTA 57.931 52.632 0.00 0.00 0.00 2.01
276 277 3.899395 GCCCTATGCGTTCGGTTT 58.101 55.556 0.00 0.00 0.00 3.27
326 327 2.230130 AATCCCAAAATTGCCCTCGA 57.770 45.000 0.00 0.00 0.00 4.04
372 373 3.385749 GAGGGCAGCGAATCGGGAA 62.386 63.158 4.35 0.00 0.00 3.97
384 385 0.332632 CTTTGATTGGGGAGAGGGCA 59.667 55.000 0.00 0.00 0.00 5.36
400 401 1.342174 TCAAACCCTACGCGTCTCTTT 59.658 47.619 18.63 6.66 0.00 2.52
436 437 0.667993 GAGAGAGAGACATGCCGGAG 59.332 60.000 5.05 0.00 0.00 4.63
440 441 2.880890 GAGAGAGAGAGAGAGACATGCC 59.119 54.545 0.00 0.00 0.00 4.40
446 447 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
447 448 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
448 449 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
450 451 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
452 453 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
454 455 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
455 456 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
456 457 5.136068 AGAGAGAGAGAGAGAGAGAGAGA 57.864 47.826 0.00 0.00 0.00 3.10
458 459 3.885901 CGAGAGAGAGAGAGAGAGAGAGA 59.114 52.174 0.00 0.00 0.00 3.10
459 460 3.551863 GCGAGAGAGAGAGAGAGAGAGAG 60.552 56.522 0.00 0.00 0.00 3.20
462 463 2.101415 CTGCGAGAGAGAGAGAGAGAGA 59.899 54.545 0.00 0.00 0.00 3.10
464 465 1.831106 ACTGCGAGAGAGAGAGAGAGA 59.169 52.381 0.00 0.00 0.00 3.10
466 467 1.470805 CGACTGCGAGAGAGAGAGAGA 60.471 57.143 0.00 0.00 40.82 3.10
467 468 0.930310 CGACTGCGAGAGAGAGAGAG 59.070 60.000 0.00 0.00 40.82 3.20
468 469 0.248012 ACGACTGCGAGAGAGAGAGA 59.752 55.000 0.00 0.00 41.64 3.10
1140 1852 3.500289 CCCCAAGAGAGAGATAGAGAGGG 60.500 56.522 0.00 0.00 0.00 4.30
1454 2173 1.908483 GACCCGGGAAGAAGCAGAT 59.092 57.895 32.02 0.00 0.00 2.90
1664 2782 6.183360 CCACTGATCTGTTTGAAGCTAATGAG 60.183 42.308 1.95 0.00 0.00 2.90
1795 2913 5.314923 TGACTTATGCAAGAAGGAAATGC 57.685 39.130 14.32 0.00 40.45 3.56
2130 3301 7.227873 TGGAAACAATTGTCTAGTTACCATCA 58.772 34.615 12.39 0.00 37.44 3.07
2133 3304 5.472137 GCTGGAAACAATTGTCTAGTTACCA 59.528 40.000 12.39 11.86 42.06 3.25
2134 3305 5.106277 GGCTGGAAACAATTGTCTAGTTACC 60.106 44.000 12.39 5.20 42.06 2.85
2383 3595 0.322546 GAAATGGCCTGGAACTCCGT 60.323 55.000 3.32 0.00 39.43 4.69
2444 3656 3.764434 CCCGACATCTGTAGCAGGTATAT 59.236 47.826 0.00 0.00 31.51 0.86
2462 3678 0.699399 TAAAATGCCCTGGAACCCGA 59.301 50.000 0.00 0.00 0.00 5.14
2512 3728 7.568199 ACATCACAGTAAATATAAACTGCCC 57.432 36.000 14.33 0.00 45.65 5.36
2711 3946 7.879160 GCAAGATTAATTCTCTCTGAGATGGAT 59.121 37.037 8.00 0.40 38.56 3.41
2800 4037 1.406069 CCTTGATGAGTGGGACCTTCG 60.406 57.143 0.00 0.00 0.00 3.79
2913 4172 4.505808 TGTCAAAACAGGTAGACAACGAA 58.494 39.130 0.00 0.00 37.99 3.85
3064 4393 1.159285 CAAAGCGAGCCAGATCAACA 58.841 50.000 0.00 0.00 0.00 3.33
3207 4537 6.877611 AAAGGTAAGGCCATCAAATATACG 57.122 37.500 5.01 0.00 40.61 3.06
3283 4625 6.663093 AGTCCAATACAATAAGGTTGCATCAA 59.337 34.615 0.00 0.00 0.00 2.57
3390 4732 1.153449 CAATTCTCGCGGGTGCCTA 60.153 57.895 5.57 0.00 38.08 3.93
3430 4772 2.785679 ACTGCATAAAATTTCTCGCGC 58.214 42.857 0.00 0.00 0.00 6.86
3492 4834 9.938670 CGATAATACAGCTATAGTACAGAATCC 57.061 37.037 0.84 0.00 0.00 3.01
3500 4842 9.457436 TGACAATCCGATAATACAGCTATAGTA 57.543 33.333 0.84 0.00 0.00 1.82
3501 4843 8.349568 TGACAATCCGATAATACAGCTATAGT 57.650 34.615 0.84 0.00 0.00 2.12
3506 4848 8.972127 AGTATATGACAATCCGATAATACAGCT 58.028 33.333 0.00 0.00 0.00 4.24
3514 4856 9.628500 ACAGCTATAGTATATGACAATCCGATA 57.372 33.333 0.84 0.00 0.00 2.92
3515 4857 8.526667 ACAGCTATAGTATATGACAATCCGAT 57.473 34.615 0.84 0.00 0.00 4.18
3516 4858 7.939784 ACAGCTATAGTATATGACAATCCGA 57.060 36.000 0.84 0.00 0.00 4.55
3650 4992 5.649782 AATAACTTGCACATAGCTTGCTT 57.350 34.783 10.10 0.00 45.94 3.91
3694 5036 1.140652 CAACACATGCCCCCTGTTTTT 59.859 47.619 0.00 0.00 0.00 1.94
3699 5041 1.228521 TGTCAACACATGCCCCCTG 60.229 57.895 0.00 0.00 0.00 4.45
3700 5042 1.228552 GTGTCAACACATGCCCCCT 60.229 57.895 8.37 0.00 45.75 4.79
3814 5158 3.139077 GGACGGTGATGACTCAAACTTT 58.861 45.455 0.00 0.00 31.85 2.66
3850 5194 2.778299 ACTTTGAGCATAGTTTCGGCA 58.222 42.857 0.00 0.00 0.00 5.69
3902 5246 1.760613 TCATCTTCGGGGCTTAATCGT 59.239 47.619 0.00 0.00 0.00 3.73
3946 5290 1.914700 GACGAGACGAAGACAATCTGC 59.085 52.381 0.00 0.00 0.00 4.26
4012 5357 2.027192 TCCGATGGCTCTAACTTTTGCT 60.027 45.455 0.00 0.00 0.00 3.91
4037 5382 2.129555 TTTGCCTCCTGACAGGGCTC 62.130 60.000 21.56 10.61 45.45 4.70
4148 5493 6.811170 ACTTTCATGTTGAACGTGTTTTGATT 59.189 30.769 16.31 0.00 37.45 2.57
4197 5543 3.427638 GGAAACGAGCCTAAAAGCAATCC 60.428 47.826 0.00 0.00 34.23 3.01
4224 5570 6.894339 ATTTTTGAGGTGGTAAACGATCTT 57.106 33.333 0.00 0.00 0.00 2.40
4263 5609 5.404096 CAAAACTGTTCGGTTTAAACTGGT 58.596 37.500 23.69 12.72 38.30 4.00
4313 5659 2.806244 CACGTCCAAAACCCTAGTCAAG 59.194 50.000 0.00 0.00 0.00 3.02


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

AutoCloner maintained by Alex Coulton.