Multiple sequence alignment - TraesCS7D01G271500

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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 TraesCS7D01G271500 chr7D 100.000 3062 0 0 1 3062 260726959 260723898 0.000000e+00 5655.0
1 TraesCS7D01G271500 chr7D 100.000 30 0 0 2543 2572 260724333 260724304 4.270000e-04 56.5
2 TraesCS7D01G271500 chr7D 100.000 30 0 0 2627 2656 260724417 260724388 4.270000e-04 56.5
3 TraesCS7D01G271500 chr7B 95.634 1397 41 5 900 2295 240023101 240021724 0.000000e+00 2224.0
4 TraesCS7D01G271500 chr7B 82.812 448 59 12 2338 2775 149679810 149679371 4.790000e-103 385.0
5 TraesCS7D01G271500 chr7B 85.906 298 33 7 2769 3062 149678686 149678394 2.970000e-80 309.0
6 TraesCS7D01G271500 chr7B 87.132 272 30 4 2779 3050 29630879 29631145 1.380000e-78 303.0
7 TraesCS7D01G271500 chr7A 96.209 1319 29 9 990 2306 284112728 284111429 0.000000e+00 2139.0
8 TraesCS7D01G271500 chr7A 84.800 375 48 6 2678 3050 95120042 95120409 4.820000e-98 368.0
9 TraesCS7D01G271500 chr1A 83.085 739 78 28 2338 3062 267177473 267176768 2.000000e-176 628.0
10 TraesCS7D01G271500 chr4D 84.640 625 61 15 312 903 110253473 110254095 9.460000e-165 590.0
11 TraesCS7D01G271500 chr4D 84.554 628 60 17 310 904 110252690 110253313 3.400000e-164 588.0
12 TraesCS7D01G271500 chr4D 84.477 612 64 20 310 903 131332181 131331583 2.650000e-160 575.0
13 TraesCS7D01G271500 chr4D 83.121 628 62 18 310 904 473827540 473828156 1.620000e-147 532.0
14 TraesCS7D01G271500 chr4D 85.632 174 17 4 1 167 110253903 110254075 3.140000e-40 176.0
15 TraesCS7D01G271500 chr4D 88.571 140 13 3 173 310 110252487 110252625 1.890000e-37 167.0
16 TraesCS7D01G271500 chrUn 84.477 612 64 20 310 903 216304548 216303950 2.650000e-160 575.0
17 TraesCS7D01G271500 chr4B 84.026 626 64 20 310 902 599655910 599655288 1.230000e-158 569.0
18 TraesCS7D01G271500 chr4B 88.976 127 13 1 184 310 599656099 599655974 4.090000e-34 156.0
19 TraesCS7D01G271500 chr6B 83.866 626 67 18 310 903 640670383 640669760 1.590000e-157 566.0
20 TraesCS7D01G271500 chr6B 89.340 197 15 5 2869 3062 487799976 487799783 3.050000e-60 243.0
21 TraesCS7D01G271500 chr6B 88.571 140 14 2 173 310 640670587 640670448 5.250000e-38 169.0
22 TraesCS7D01G271500 chr6B 87.597 129 16 0 182 310 210573717 210573589 1.900000e-32 150.0
23 TraesCS7D01G271500 chr6B 90.351 114 10 1 183 295 279085023 279085136 6.840000e-32 148.0
24 TraesCS7D01G271500 chr2A 83.797 611 77 14 310 901 419257414 419258021 7.410000e-156 560.0
25 TraesCS7D01G271500 chr2A 89.667 300 29 2 310 609 81590198 81590495 6.200000e-102 381.0
26 TraesCS7D01G271500 chr2A 77.547 530 88 21 385 903 502931630 502932139 1.070000e-74 291.0
27 TraesCS7D01G271500 chr2A 81.707 328 36 13 1 310 502917863 502918184 5.070000e-63 252.0
28 TraesCS7D01G271500 chr2A 86.228 167 19 2 1 167 419257841 419258003 8.720000e-41 178.0
29 TraesCS7D01G271500 chr2A 86.585 164 18 2 4 167 438429889 438429730 8.720000e-41 178.0
30 TraesCS7D01G271500 chr3B 82.353 612 65 17 2338 2939 650054119 650053541 2.740000e-135 492.0
31 TraesCS7D01G271500 chr3B 87.425 167 18 1 1 167 10723749 10723912 4.030000e-44 189.0
32 TraesCS7D01G271500 chr3B 78.414 227 33 7 574 787 194267878 194267655 1.920000e-27 134.0
33 TraesCS7D01G271500 chr1B 80.914 613 77 17 312 901 579932127 579931532 6.020000e-122 448.0
34 TraesCS7D01G271500 chr1B 88.603 272 26 4 2779 3050 107521751 107522017 2.940000e-85 326.0
35 TraesCS7D01G271500 chr1B 84.839 310 38 6 1 310 579932494 579932194 1.380000e-78 303.0
36 TraesCS7D01G271500 chr1B 80.597 335 40 10 1 310 675458367 675458701 5.100000e-58 235.0
37 TraesCS7D01G271500 chr1B 85.119 168 19 4 1 167 579931712 579931550 1.890000e-37 167.0
38 TraesCS7D01G271500 chr1B 89.844 128 13 0 183 310 579933119 579932992 6.790000e-37 165.0
39 TraesCS7D01G271500 chr1D 86.856 388 45 5 2676 3062 348121270 348120888 2.180000e-116 429.0
40 TraesCS7D01G271500 chr1D 81.366 322 36 6 1 298 60179973 60180294 1.100000e-59 241.0
41 TraesCS7D01G271500 chr2D 84.529 446 46 13 2627 3062 645281373 645280941 1.310000e-113 420.0
42 TraesCS7D01G271500 chr2D 83.456 272 37 6 2338 2602 645281584 645281314 2.360000e-61 246.0
43 TraesCS7D01G271500 chr2B 87.879 330 20 6 1 310 791123738 791123409 1.340000e-98 370.0
44 TraesCS7D01G271500 chr2B 86.822 129 16 1 183 310 791124374 791124246 3.180000e-30 143.0
45 TraesCS7D01G271500 chr5B 81.416 226 33 6 556 773 644652804 644652580 3.140000e-40 176.0
46 TraesCS7D01G271500 chr3A 82.778 180 28 3 609 787 151651027 151650850 1.140000e-34 158.0
47 TraesCS7D01G271500 chr5A 74.082 463 78 25 461 901 511970062 511969620 5.290000e-33 152.0
48 TraesCS7D01G271500 chr5A 77.308 260 32 11 69 310 470160331 470160581 8.910000e-26 128.0


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 TraesCS7D01G271500 chr7D 260723898 260726959 3061 True 1922.666667 5655 100.00000 1 3062 3 chr7D.!!$R1 3061
1 TraesCS7D01G271500 chr7B 240021724 240023101 1377 True 2224.000000 2224 95.63400 900 2295 1 chr7B.!!$R1 1395
2 TraesCS7D01G271500 chr7B 149678394 149679810 1416 True 347.000000 385 84.35900 2338 3062 2 chr7B.!!$R2 724
3 TraesCS7D01G271500 chr7A 284111429 284112728 1299 True 2139.000000 2139 96.20900 990 2306 1 chr7A.!!$R1 1316
4 TraesCS7D01G271500 chr1A 267176768 267177473 705 True 628.000000 628 83.08500 2338 3062 1 chr1A.!!$R1 724
5 TraesCS7D01G271500 chr4D 131331583 131332181 598 True 575.000000 575 84.47700 310 903 1 chr4D.!!$R1 593
6 TraesCS7D01G271500 chr4D 473827540 473828156 616 False 532.000000 532 83.12100 310 904 1 chr4D.!!$F1 594
7 TraesCS7D01G271500 chr4D 110252487 110254095 1608 False 380.250000 590 85.84925 1 904 4 chr4D.!!$F2 903
8 TraesCS7D01G271500 chrUn 216303950 216304548 598 True 575.000000 575 84.47700 310 903 1 chrUn.!!$R1 593
9 TraesCS7D01G271500 chr4B 599655288 599656099 811 True 362.500000 569 86.50100 184 902 2 chr4B.!!$R1 718
10 TraesCS7D01G271500 chr6B 640669760 640670587 827 True 367.500000 566 86.21850 173 903 2 chr6B.!!$R3 730
11 TraesCS7D01G271500 chr2A 419257414 419258021 607 False 369.000000 560 85.01250 1 901 2 chr2A.!!$F4 900
12 TraesCS7D01G271500 chr2A 502931630 502932139 509 False 291.000000 291 77.54700 385 903 1 chr2A.!!$F3 518
13 TraesCS7D01G271500 chr3B 650053541 650054119 578 True 492.000000 492 82.35300 2338 2939 1 chr3B.!!$R2 601
14 TraesCS7D01G271500 chr1B 579931532 579933119 1587 True 270.750000 448 85.17900 1 901 4 chr1B.!!$R1 900
15 TraesCS7D01G271500 chr2D 645280941 645281584 643 True 333.000000 420 83.99250 2338 3062 2 chr2D.!!$R1 724
16 TraesCS7D01G271500 chr2B 791123409 791124374 965 True 256.500000 370 87.35050 1 310 2 chr2B.!!$R1 309

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
467 544 0.029035 CTGGCATTCTCAAGCATCGC 59.971 55.0 0.0 0.0 0.0 4.58 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2409 3591 0.377203 CACGCGGGAAAGGAAATAGC 59.623 55.0 12.47 0.0 0.0 2.97 R

All possible primers

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

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
27 28 9.859427 ATTGTTTACGTGATTGAATTGAATCAT 57.141 25.926 20.89 10.45 42.78 2.45
28 29 8.894409 TGTTTACGTGATTGAATTGAATCATC 57.106 30.769 20.89 14.03 42.78 2.92
29 30 8.510505 TGTTTACGTGATTGAATTGAATCATCA 58.489 29.630 20.89 11.69 42.78 3.07
30 31 8.788813 GTTTACGTGATTGAATTGAATCATCAC 58.211 33.333 20.89 10.76 42.78 3.06
31 32 5.883661 ACGTGATTGAATTGAATCATCACC 58.116 37.500 20.89 9.13 42.78 4.02
32 33 5.649395 ACGTGATTGAATTGAATCATCACCT 59.351 36.000 20.89 0.73 42.78 4.00
33 34 6.823182 ACGTGATTGAATTGAATCATCACCTA 59.177 34.615 20.89 0.00 42.78 3.08
34 35 7.128331 CGTGATTGAATTGAATCATCACCTAC 58.872 38.462 20.89 7.59 42.78 3.18
35 36 7.420800 GTGATTGAATTGAATCATCACCTACC 58.579 38.462 20.89 4.64 42.78 3.18
36 37 7.067372 GTGATTGAATTGAATCATCACCTACCA 59.933 37.037 20.89 0.00 42.78 3.25
37 38 7.614974 TGATTGAATTGAATCATCACCTACCAA 59.385 33.333 15.27 0.00 37.41 3.67
38 39 7.959658 TTGAATTGAATCATCACCTACCAAT 57.040 32.000 0.00 0.00 34.61 3.16
39 40 7.337480 TGAATTGAATCATCACCTACCAATG 57.663 36.000 0.00 0.00 34.61 2.82
40 41 6.321945 TGAATTGAATCATCACCTACCAATGG 59.678 38.462 0.00 0.00 34.61 3.16
41 42 5.449297 TTGAATCATCACCTACCAATGGA 57.551 39.130 6.16 0.00 34.61 3.41
42 43 5.449297 TGAATCATCACCTACCAATGGAA 57.551 39.130 6.16 0.00 0.00 3.53
43 44 5.439721 TGAATCATCACCTACCAATGGAAG 58.560 41.667 6.16 0.00 0.00 3.46
44 45 3.281727 TCATCACCTACCAATGGAAGC 57.718 47.619 6.16 0.00 0.00 3.86
45 46 2.575735 TCATCACCTACCAATGGAAGCA 59.424 45.455 6.16 0.00 0.00 3.91
46 47 2.489938 TCACCTACCAATGGAAGCAC 57.510 50.000 6.16 0.00 0.00 4.40
47 48 1.004277 TCACCTACCAATGGAAGCACC 59.996 52.381 6.16 0.00 39.54 5.01
58 59 2.238521 TGGAAGCACCAAACAAGATCC 58.761 47.619 0.11 0.00 46.75 3.36
59 60 1.546029 GGAAGCACCAAACAAGATCCC 59.454 52.381 0.00 0.00 38.79 3.85
60 61 1.546029 GAAGCACCAAACAAGATCCCC 59.454 52.381 0.00 0.00 0.00 4.81
61 62 0.251787 AGCACCAAACAAGATCCCCC 60.252 55.000 0.00 0.00 0.00 5.40
62 63 0.251787 GCACCAAACAAGATCCCCCT 60.252 55.000 0.00 0.00 0.00 4.79
63 64 1.827245 GCACCAAACAAGATCCCCCTT 60.827 52.381 0.00 0.00 0.00 3.95
64 65 2.556559 GCACCAAACAAGATCCCCCTTA 60.557 50.000 0.00 0.00 0.00 2.69
65 66 3.881713 GCACCAAACAAGATCCCCCTTAT 60.882 47.826 0.00 0.00 0.00 1.73
66 67 4.352893 CACCAAACAAGATCCCCCTTATT 58.647 43.478 0.00 0.00 0.00 1.40
67 68 4.777366 CACCAAACAAGATCCCCCTTATTT 59.223 41.667 0.00 0.00 0.00 1.40
68 69 4.777366 ACCAAACAAGATCCCCCTTATTTG 59.223 41.667 0.00 0.00 39.16 2.32
69 70 5.343307 CAAACAAGATCCCCCTTATTTGG 57.657 43.478 0.00 0.00 37.07 3.28
70 71 4.965283 AACAAGATCCCCCTTATTTGGA 57.035 40.909 0.00 0.00 0.00 3.53
71 72 5.487861 AACAAGATCCCCCTTATTTGGAT 57.512 39.130 0.00 0.00 41.54 3.41
72 73 5.487861 ACAAGATCCCCCTTATTTGGATT 57.512 39.130 0.00 0.00 38.98 3.01
73 74 5.853700 ACAAGATCCCCCTTATTTGGATTT 58.146 37.500 0.00 0.00 38.98 2.17
74 75 5.662657 ACAAGATCCCCCTTATTTGGATTTG 59.337 40.000 0.00 0.00 38.98 2.32
75 76 4.819610 AGATCCCCCTTATTTGGATTTGG 58.180 43.478 0.00 0.00 38.98 3.28
76 77 4.235164 AGATCCCCCTTATTTGGATTTGGT 59.765 41.667 0.00 0.00 38.98 3.67
77 78 4.427956 TCCCCCTTATTTGGATTTGGTT 57.572 40.909 0.00 0.00 0.00 3.67
78 79 4.769050 TCCCCCTTATTTGGATTTGGTTT 58.231 39.130 0.00 0.00 0.00 3.27
79 80 5.166407 TCCCCCTTATTTGGATTTGGTTTT 58.834 37.500 0.00 0.00 0.00 2.43
80 81 5.613116 TCCCCCTTATTTGGATTTGGTTTTT 59.387 36.000 0.00 0.00 0.00 1.94
100 101 6.428083 TTTTTAATGGGAGGGAGAAAAACC 57.572 37.500 0.00 0.00 0.00 3.27
101 102 4.750833 TTAATGGGAGGGAGAAAAACCA 57.249 40.909 0.00 0.00 0.00 3.67
102 103 2.907458 ATGGGAGGGAGAAAAACCAG 57.093 50.000 0.00 0.00 0.00 4.00
103 104 1.529744 TGGGAGGGAGAAAAACCAGT 58.470 50.000 0.00 0.00 0.00 4.00
104 105 1.144913 TGGGAGGGAGAAAAACCAGTG 59.855 52.381 0.00 0.00 0.00 3.66
105 106 1.423921 GGGAGGGAGAAAAACCAGTGA 59.576 52.381 0.00 0.00 0.00 3.41
106 107 2.553247 GGGAGGGAGAAAAACCAGTGAG 60.553 54.545 0.00 0.00 0.00 3.51
107 108 2.372172 GGAGGGAGAAAAACCAGTGAGA 59.628 50.000 0.00 0.00 0.00 3.27
108 109 3.558109 GGAGGGAGAAAAACCAGTGAGAG 60.558 52.174 0.00 0.00 0.00 3.20
109 110 2.373502 AGGGAGAAAAACCAGTGAGAGG 59.626 50.000 0.00 0.00 0.00 3.69
110 111 2.553247 GGGAGAAAAACCAGTGAGAGGG 60.553 54.545 0.00 0.00 0.00 4.30
111 112 2.553247 GGAGAAAAACCAGTGAGAGGGG 60.553 54.545 0.00 0.00 0.00 4.79
112 113 1.425448 AGAAAAACCAGTGAGAGGGGG 59.575 52.381 0.00 0.00 0.00 5.40
113 114 1.145119 GAAAAACCAGTGAGAGGGGGT 59.855 52.381 0.00 0.00 34.43 4.95
114 115 0.478507 AAAACCAGTGAGAGGGGGTG 59.521 55.000 0.00 0.00 33.00 4.61
115 116 1.427072 AAACCAGTGAGAGGGGGTGG 61.427 60.000 0.00 0.00 33.00 4.61
116 117 3.721706 CCAGTGAGAGGGGGTGGC 61.722 72.222 0.00 0.00 0.00 5.01
117 118 4.087892 CAGTGAGAGGGGGTGGCG 62.088 72.222 0.00 0.00 0.00 5.69
137 138 1.392510 GGGACGAAGAAAAATCGGACG 59.607 52.381 0.00 0.00 44.32 4.79
138 139 2.331194 GGACGAAGAAAAATCGGACGA 58.669 47.619 0.00 0.00 44.32 4.20
139 140 2.733026 GGACGAAGAAAAATCGGACGAA 59.267 45.455 0.00 0.00 44.32 3.85
140 141 3.184986 GGACGAAGAAAAATCGGACGAAA 59.815 43.478 0.00 0.00 44.32 3.46
141 142 4.318974 GGACGAAGAAAAATCGGACGAAAA 60.319 41.667 0.00 0.00 44.32 2.29
142 143 5.352643 ACGAAGAAAAATCGGACGAAAAT 57.647 34.783 0.00 0.00 44.32 1.82
143 144 6.401367 GGACGAAGAAAAATCGGACGAAAATA 60.401 38.462 0.00 0.00 44.32 1.40
144 145 6.890558 ACGAAGAAAAATCGGACGAAAATAA 58.109 32.000 0.00 0.00 44.32 1.40
145 146 6.793680 ACGAAGAAAAATCGGACGAAAATAAC 59.206 34.615 0.00 0.00 44.32 1.89
146 147 6.247791 CGAAGAAAAATCGGACGAAAATAACC 59.752 38.462 0.00 0.00 36.68 2.85
147 148 5.946298 AGAAAAATCGGACGAAAATAACCC 58.054 37.500 0.00 0.00 0.00 4.11
148 149 5.708697 AGAAAAATCGGACGAAAATAACCCT 59.291 36.000 0.00 0.00 0.00 4.34
149 150 5.970317 AAAATCGGACGAAAATAACCCTT 57.030 34.783 0.00 0.00 0.00 3.95
150 151 7.391275 AGAAAAATCGGACGAAAATAACCCTTA 59.609 33.333 0.00 0.00 0.00 2.69
151 152 6.426980 AAATCGGACGAAAATAACCCTTAC 57.573 37.500 0.00 0.00 0.00 2.34
152 153 3.510719 TCGGACGAAAATAACCCTTACG 58.489 45.455 0.00 0.00 0.00 3.18
153 154 3.192422 TCGGACGAAAATAACCCTTACGA 59.808 43.478 0.00 0.00 0.00 3.43
154 155 3.549070 CGGACGAAAATAACCCTTACGAG 59.451 47.826 0.00 0.00 0.00 4.18
155 156 3.867493 GGACGAAAATAACCCTTACGAGG 59.133 47.826 0.00 0.00 43.15 4.63
156 157 3.264947 ACGAAAATAACCCTTACGAGGC 58.735 45.455 0.00 0.00 42.09 4.70
157 158 3.055602 ACGAAAATAACCCTTACGAGGCT 60.056 43.478 0.00 0.00 42.09 4.58
158 159 4.160252 ACGAAAATAACCCTTACGAGGCTA 59.840 41.667 0.00 0.00 42.09 3.93
159 160 4.505556 CGAAAATAACCCTTACGAGGCTAC 59.494 45.833 0.00 0.00 42.09 3.58
160 161 5.668471 GAAAATAACCCTTACGAGGCTACT 58.332 41.667 0.00 0.00 42.09 2.57
161 162 6.460123 CGAAAATAACCCTTACGAGGCTACTA 60.460 42.308 0.00 0.00 42.09 1.82
162 163 6.796785 AAATAACCCTTACGAGGCTACTAA 57.203 37.500 0.00 0.00 42.09 2.24
163 164 6.402456 AATAACCCTTACGAGGCTACTAAG 57.598 41.667 0.00 0.00 42.09 2.18
164 165 3.378861 ACCCTTACGAGGCTACTAAGT 57.621 47.619 8.93 0.00 42.09 2.24
165 166 3.022406 ACCCTTACGAGGCTACTAAGTG 58.978 50.000 8.93 2.29 42.09 3.16
166 167 2.223758 CCCTTACGAGGCTACTAAGTGC 60.224 54.545 8.93 0.00 42.09 4.40
167 168 2.426024 CCTTACGAGGCTACTAAGTGCA 59.574 50.000 8.93 0.00 35.94 4.57
168 169 3.068307 CCTTACGAGGCTACTAAGTGCAT 59.932 47.826 0.00 0.00 35.94 3.96
169 170 4.441634 CCTTACGAGGCTACTAAGTGCATT 60.442 45.833 0.00 0.00 35.94 3.56
170 171 5.221185 CCTTACGAGGCTACTAAGTGCATTA 60.221 44.000 0.00 0.00 35.94 1.90
171 172 4.730949 ACGAGGCTACTAAGTGCATTAA 57.269 40.909 0.00 0.00 0.00 1.40
172 173 5.277857 ACGAGGCTACTAAGTGCATTAAT 57.722 39.130 0.00 0.00 0.00 1.40
173 174 5.050490 ACGAGGCTACTAAGTGCATTAATG 58.950 41.667 11.27 11.27 0.00 1.90
174 175 5.163447 ACGAGGCTACTAAGTGCATTAATGA 60.163 40.000 19.73 1.75 0.00 2.57
175 176 5.175856 CGAGGCTACTAAGTGCATTAATGAC 59.824 44.000 19.73 13.37 0.00 3.06
176 177 6.240549 AGGCTACTAAGTGCATTAATGACT 57.759 37.500 19.73 15.22 0.00 3.41
177 178 6.284459 AGGCTACTAAGTGCATTAATGACTC 58.716 40.000 19.73 10.79 0.00 3.36
178 179 5.175856 GGCTACTAAGTGCATTAATGACTCG 59.824 44.000 19.73 14.23 0.00 4.18
179 180 5.977725 GCTACTAAGTGCATTAATGACTCGA 59.022 40.000 19.73 9.81 0.00 4.04
180 181 6.642950 GCTACTAAGTGCATTAATGACTCGAT 59.357 38.462 19.73 7.52 0.00 3.59
181 182 6.834959 ACTAAGTGCATTAATGACTCGATG 57.165 37.500 19.73 11.40 0.00 3.84
224 225 8.621532 ATGGACTTAATTGATTGCATACGTAT 57.378 30.769 1.14 1.14 0.00 3.06
330 396 7.304735 TGAATCTTGACATTTAAATGGACACG 58.695 34.615 27.43 22.29 40.70 4.49
347 413 4.398247 GACACGCTTGATTTGAGAATGTC 58.602 43.478 0.00 0.00 0.00 3.06
426 503 2.522436 TCTCCCACCACGGTCGTT 60.522 61.111 0.00 0.00 0.00 3.85
428 505 3.584868 CTCCCACCACGGTCGTTCC 62.585 68.421 0.00 0.00 0.00 3.62
467 544 0.029035 CTGGCATTCTCAAGCATCGC 59.971 55.000 0.00 0.00 0.00 4.58
673 1550 7.661847 AGGTTGTCGAGAAAAATCTTATGTCTT 59.338 33.333 0.00 0.00 0.00 3.01
691 1568 5.560724 TGTCTTTCTTTTAGGAGGGTGATG 58.439 41.667 0.00 0.00 0.00 3.07
707 1584 7.202075 GGAGGGTGATGTCATATATATGATGCT 60.202 40.741 24.62 14.11 43.82 3.79
747 1624 8.547091 AATTATTTGTTGATTACGCGATTGAG 57.453 30.769 15.93 0.00 0.00 3.02
751 1628 3.124466 TGTTGATTACGCGATTGAGTTGG 59.876 43.478 15.93 0.00 0.00 3.77
791 1670 4.323257 GGAAGAACGAAACAAGATCCCCTA 60.323 45.833 0.00 0.00 0.00 3.53
793 1672 5.437191 AGAACGAAACAAGATCCCCTAAT 57.563 39.130 0.00 0.00 0.00 1.73
794 1673 5.186198 AGAACGAAACAAGATCCCCTAATG 58.814 41.667 0.00 0.00 0.00 1.90
798 1677 5.133221 CGAAACAAGATCCCCTAATGGATT 58.867 41.667 0.00 0.00 45.25 3.01
820 1719 6.494666 TTTGGGAGAAAAACTAGTGAGAGA 57.505 37.500 0.00 0.00 0.00 3.10
821 1720 5.730296 TGGGAGAAAAACTAGTGAGAGAG 57.270 43.478 0.00 0.00 0.00 3.20
823 1722 4.773149 GGGAGAAAAACTAGTGAGAGAGGA 59.227 45.833 0.00 0.00 0.00 3.71
829 1728 4.323569 AACTAGTGAGAGAGGATGGTGA 57.676 45.455 0.00 0.00 0.00 4.02
833 1732 2.580322 AGTGAGAGAGGATGGTGAGAGA 59.420 50.000 0.00 0.00 0.00 3.10
924 1835 8.969260 ATTAAAAGATCACTGATGCACTGATA 57.031 30.769 0.00 0.00 0.00 2.15
931 1842 3.309138 CACTGATGCACTGATAGTTGCTC 59.691 47.826 0.00 0.00 0.00 4.26
933 1844 1.863454 GATGCACTGATAGTTGCTCCG 59.137 52.381 0.00 0.00 0.00 4.63
992 1903 0.307146 CCGCGCCTAGTACTCACTAC 59.693 60.000 0.00 0.00 36.14 2.73
1015 1926 1.820906 CGCATGTCCACCATCCCAG 60.821 63.158 0.00 0.00 0.00 4.45
1031 1942 1.639298 CCAGTCGCCAAAGCTGTAGC 61.639 60.000 0.00 0.00 42.49 3.58
1052 1963 3.521995 CACCGAGTGTGCAAGAGAT 57.478 52.632 0.00 0.00 38.34 2.75
1649 2560 3.133014 CATCGATCTGAGCCCCGT 58.867 61.111 0.00 0.00 0.00 5.28
2046 2957 0.248743 TTCGCGATTTCGTATCCGCT 60.249 50.000 10.88 0.00 44.77 5.52
2048 2959 1.853319 GCGATTTCGTATCCGCTGG 59.147 57.895 0.00 0.00 43.75 4.85
2075 2986 0.731417 GCTTGATGCTTGACGCTGAT 59.269 50.000 0.00 0.00 40.11 2.90
2076 2987 1.267932 GCTTGATGCTTGACGCTGATC 60.268 52.381 0.00 0.00 40.11 2.92
2077 2988 2.277969 CTTGATGCTTGACGCTGATCT 58.722 47.619 0.00 0.00 40.11 2.75
2078 2989 1.648504 TGATGCTTGACGCTGATCTG 58.351 50.000 0.00 0.00 40.11 2.90
2079 2990 1.205417 TGATGCTTGACGCTGATCTGA 59.795 47.619 3.42 0.00 40.11 3.27
2080 2991 1.859703 GATGCTTGACGCTGATCTGAG 59.140 52.381 3.42 2.57 40.11 3.35
2081 2992 0.605083 TGCTTGACGCTGATCTGAGT 59.395 50.000 8.67 8.67 40.11 3.41
2082 2993 0.997932 GCTTGACGCTGATCTGAGTG 59.002 55.000 13.43 3.01 35.14 3.51
2083 2994 0.997932 CTTGACGCTGATCTGAGTGC 59.002 55.000 13.43 6.40 0.00 4.40
2086 2997 3.260483 CGCTGATCTGAGTGCGCC 61.260 66.667 4.18 0.00 41.85 6.53
2304 3285 8.816894 ACTCTAAAATCTCATGGAGTAACTTGA 58.183 33.333 0.00 0.00 33.13 3.02
2305 3286 9.311916 CTCTAAAATCTCATGGAGTAACTTGAG 57.688 37.037 0.00 0.00 37.52 3.02
2307 3288 6.627087 AAATCTCATGGAGTAACTTGAGGA 57.373 37.500 8.58 0.00 36.95 3.71
2308 3289 5.867903 ATCTCATGGAGTAACTTGAGGAG 57.132 43.478 8.58 0.00 36.95 3.69
2310 3291 2.501723 TCATGGAGTAACTTGAGGAGCC 59.498 50.000 0.00 0.00 0.00 4.70
2313 3294 2.501723 TGGAGTAACTTGAGGAGCCATC 59.498 50.000 0.00 0.00 0.00 3.51
2315 3296 3.431486 GGAGTAACTTGAGGAGCCATCAG 60.431 52.174 0.00 0.00 0.00 2.90
2316 3297 3.177228 AGTAACTTGAGGAGCCATCAGT 58.823 45.455 0.00 0.00 0.00 3.41
2317 3298 3.584848 AGTAACTTGAGGAGCCATCAGTT 59.415 43.478 0.00 0.00 0.00 3.16
2319 3300 4.640771 AACTTGAGGAGCCATCAGTTAA 57.359 40.909 0.00 0.00 0.00 2.01
2320 3301 3.944087 ACTTGAGGAGCCATCAGTTAAC 58.056 45.455 0.00 0.00 0.00 2.01
2323 3304 3.942829 TGAGGAGCCATCAGTTAACAAG 58.057 45.455 8.61 0.00 0.00 3.16
2324 3305 2.680339 GAGGAGCCATCAGTTAACAAGC 59.320 50.000 8.61 3.05 0.00 4.01
2325 3306 1.398390 GGAGCCATCAGTTAACAAGCG 59.602 52.381 8.61 0.00 0.00 4.68
2326 3307 0.804989 AGCCATCAGTTAACAAGCGC 59.195 50.000 8.61 0.00 0.00 5.92
2327 3308 0.804989 GCCATCAGTTAACAAGCGCT 59.195 50.000 2.64 2.64 0.00 5.92
2328 3309 1.200020 GCCATCAGTTAACAAGCGCTT 59.800 47.619 18.98 18.98 0.00 4.68
2329 3310 2.729156 GCCATCAGTTAACAAGCGCTTC 60.729 50.000 22.21 8.85 0.00 3.86
2330 3311 2.744202 CCATCAGTTAACAAGCGCTTCT 59.256 45.455 22.21 11.35 0.00 2.85
2331 3312 3.189287 CCATCAGTTAACAAGCGCTTCTT 59.811 43.478 22.21 18.18 34.78 2.52
2333 3314 2.475111 TCAGTTAACAAGCGCTTCTTCG 59.525 45.455 22.21 11.93 31.27 3.79
2334 3315 2.475111 CAGTTAACAAGCGCTTCTTCGA 59.525 45.455 22.21 4.86 31.27 3.71
2335 3316 3.059868 CAGTTAACAAGCGCTTCTTCGAA 60.060 43.478 22.21 4.39 31.27 3.71
2336 3317 3.558418 AGTTAACAAGCGCTTCTTCGAAA 59.442 39.130 22.21 3.60 31.27 3.46
2353 3442 2.706952 AAAACGGGGCTTGCCTGCTA 62.707 55.000 11.71 0.00 0.00 3.49
2356 3445 4.047125 GGGGCTTGCCTGCTACCA 62.047 66.667 11.71 0.00 32.90 3.25
2391 3573 0.652592 CGTGCTCCCTTCGCTAATTG 59.347 55.000 0.00 0.00 0.00 2.32
2406 3588 3.059800 GCTAATTGTTTATCGGACGGCTC 60.060 47.826 0.00 0.00 0.00 4.70
2407 3589 1.567504 ATTGTTTATCGGACGGCTCG 58.432 50.000 0.00 0.00 0.00 5.03
2409 3591 2.278336 TTTATCGGACGGCTCGCG 60.278 61.111 0.00 0.00 0.00 5.87
2420 3603 1.429148 CGGCTCGCGCTATTTCCTTT 61.429 55.000 5.56 0.00 36.09 3.11
2480 3742 1.933853 CCCGTATTTCTCTTTGCCTCG 59.066 52.381 0.00 0.00 0.00 4.63
2644 3912 2.894387 GAGTGGATCGGCTGCAGC 60.894 66.667 30.88 30.88 41.14 5.25
2697 3971 4.776322 CGCCCGTCCCAGATTGCA 62.776 66.667 0.00 0.00 0.00 4.08
2705 3979 0.619832 TCCCAGATTGCAGCCTCTCT 60.620 55.000 0.00 0.00 0.00 3.10
2744 4018 0.456142 CCTCTTGATTCGTCGTCGCA 60.456 55.000 0.00 0.00 36.96 5.10
2751 4025 0.599204 ATTCGTCGTCGCACCAAAGT 60.599 50.000 0.00 0.00 36.96 2.66
2775 4049 0.809241 GTCTTGGAGATGCCTGCGAG 60.809 60.000 0.00 0.00 41.93 5.03
2803 4768 2.039624 ATGGTGGAGCTCGGGTCT 59.960 61.111 7.83 0.00 0.00 3.85
2825 4793 0.118346 ATAGTGGAGGTGGTGGTGGA 59.882 55.000 0.00 0.00 0.00 4.02
2841 4809 2.690778 GGATGTTGTGCCGCCACTC 61.691 63.158 0.00 0.00 42.54 3.51
2846 4814 1.597854 TTGTGCCGCCACTCAAGAG 60.598 57.895 0.00 0.00 42.54 2.85
2953 4921 4.070552 GGCTGCCGACCTCGACTT 62.071 66.667 1.35 0.00 43.02 3.01
2954 4922 2.811317 GCTGCCGACCTCGACTTG 60.811 66.667 0.00 0.00 43.02 3.16
2955 4923 2.125912 CTGCCGACCTCGACTTGG 60.126 66.667 0.00 0.00 43.02 3.61
2956 4924 4.373116 TGCCGACCTCGACTTGGC 62.373 66.667 9.05 9.05 45.91 4.52
2957 4925 4.373116 GCCGACCTCGACTTGGCA 62.373 66.667 10.63 0.00 45.06 4.92
2958 4926 2.579201 CCGACCTCGACTTGGCAT 59.421 61.111 0.00 0.00 43.02 4.40
2959 4927 1.811266 CCGACCTCGACTTGGCATG 60.811 63.158 0.00 0.00 43.02 4.06
2960 4928 2.456119 CGACCTCGACTTGGCATGC 61.456 63.158 9.90 9.90 43.02 4.06
2961 4929 1.375908 GACCTCGACTTGGCATGCA 60.376 57.895 21.36 2.54 0.00 3.96
2990 4958 1.229082 TACGGCAACTCACCCTCCT 60.229 57.895 0.00 0.00 0.00 3.69
3000 4968 1.003696 CTCACCCTCCTTCCCTTTCAC 59.996 57.143 0.00 0.00 0.00 3.18
3052 5021 3.829601 AGATGTCTCCTCTGTTTCTTCGT 59.170 43.478 0.00 0.00 0.00 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 7.967854 GGTGATGATTCAATTCAATCACGTAAA 59.032 33.333 6.92 0.00 43.88 2.01
6 7 7.336679 AGGTGATGATTCAATTCAATCACGTAA 59.663 33.333 6.92 0.00 43.88 3.18
7 8 6.823182 AGGTGATGATTCAATTCAATCACGTA 59.177 34.615 6.92 0.00 43.88 3.57
8 9 5.649395 AGGTGATGATTCAATTCAATCACGT 59.351 36.000 6.92 6.03 43.88 4.49
9 10 6.127810 AGGTGATGATTCAATTCAATCACG 57.872 37.500 6.92 0.00 43.88 4.35
10 11 7.067372 TGGTAGGTGATGATTCAATTCAATCAC 59.933 37.037 6.92 6.86 43.88 3.06
11 12 7.118060 TGGTAGGTGATGATTCAATTCAATCA 58.882 34.615 7.24 7.24 44.90 2.57
12 13 7.572523 TGGTAGGTGATGATTCAATTCAATC 57.427 36.000 0.00 0.00 32.48 2.67
13 14 7.959658 TTGGTAGGTGATGATTCAATTCAAT 57.040 32.000 0.00 0.00 32.48 2.57
14 15 7.147863 CCATTGGTAGGTGATGATTCAATTCAA 60.148 37.037 0.00 0.00 32.48 2.69
15 16 6.321945 CCATTGGTAGGTGATGATTCAATTCA 59.678 38.462 0.00 0.00 32.48 2.57
16 17 6.547141 TCCATTGGTAGGTGATGATTCAATTC 59.453 38.462 1.86 0.00 32.48 2.17
17 18 6.434302 TCCATTGGTAGGTGATGATTCAATT 58.566 36.000 1.86 0.00 32.48 2.32
18 19 6.017211 TCCATTGGTAGGTGATGATTCAAT 57.983 37.500 1.86 0.00 32.48 2.57
19 20 5.449297 TCCATTGGTAGGTGATGATTCAA 57.551 39.130 1.86 0.00 32.48 2.69
20 21 5.439721 CTTCCATTGGTAGGTGATGATTCA 58.560 41.667 1.86 0.00 0.00 2.57
21 22 4.276926 GCTTCCATTGGTAGGTGATGATTC 59.723 45.833 10.90 0.00 0.00 2.52
22 23 4.210331 GCTTCCATTGGTAGGTGATGATT 58.790 43.478 10.90 0.00 0.00 2.57
23 24 3.202818 TGCTTCCATTGGTAGGTGATGAT 59.797 43.478 10.90 0.00 0.00 2.45
24 25 2.575735 TGCTTCCATTGGTAGGTGATGA 59.424 45.455 10.90 0.00 0.00 2.92
25 26 2.684881 GTGCTTCCATTGGTAGGTGATG 59.315 50.000 10.90 0.00 0.00 3.07
26 27 2.357154 GGTGCTTCCATTGGTAGGTGAT 60.357 50.000 10.90 0.00 35.97 3.06
27 28 1.004277 GGTGCTTCCATTGGTAGGTGA 59.996 52.381 10.90 0.00 35.97 4.02
28 29 1.271871 TGGTGCTTCCATTGGTAGGTG 60.272 52.381 10.90 0.00 41.93 4.00
29 30 1.072266 TGGTGCTTCCATTGGTAGGT 58.928 50.000 10.90 0.00 41.93 3.08
30 31 2.214376 TTGGTGCTTCCATTGGTAGG 57.786 50.000 10.90 0.74 46.60 3.18
31 32 2.890311 TGTTTGGTGCTTCCATTGGTAG 59.110 45.455 5.02 5.02 46.60 3.18
32 33 2.950781 TGTTTGGTGCTTCCATTGGTA 58.049 42.857 1.86 0.00 46.60 3.25
33 34 1.786937 TGTTTGGTGCTTCCATTGGT 58.213 45.000 1.86 0.00 46.60 3.67
34 35 2.364970 TCTTGTTTGGTGCTTCCATTGG 59.635 45.455 0.00 0.00 46.60 3.16
35 36 3.731652 TCTTGTTTGGTGCTTCCATTG 57.268 42.857 2.36 0.00 46.60 2.82
36 37 3.259123 GGATCTTGTTTGGTGCTTCCATT 59.741 43.478 2.36 0.00 46.60 3.16
37 38 2.827921 GGATCTTGTTTGGTGCTTCCAT 59.172 45.455 2.36 0.00 46.60 3.41
38 39 2.238521 GGATCTTGTTTGGTGCTTCCA 58.761 47.619 0.00 0.00 45.60 3.53
39 40 1.546029 GGGATCTTGTTTGGTGCTTCC 59.454 52.381 0.00 0.00 0.00 3.46
40 41 1.546029 GGGGATCTTGTTTGGTGCTTC 59.454 52.381 0.00 0.00 0.00 3.86
41 42 1.632589 GGGGATCTTGTTTGGTGCTT 58.367 50.000 0.00 0.00 0.00 3.91
42 43 0.251787 GGGGGATCTTGTTTGGTGCT 60.252 55.000 0.00 0.00 0.00 4.40
43 44 0.251787 AGGGGGATCTTGTTTGGTGC 60.252 55.000 0.00 0.00 0.00 5.01
44 45 2.309136 AAGGGGGATCTTGTTTGGTG 57.691 50.000 0.00 0.00 0.00 4.17
45 46 4.692523 AATAAGGGGGATCTTGTTTGGT 57.307 40.909 0.00 0.00 0.00 3.67
46 47 5.343307 CAAATAAGGGGGATCTTGTTTGG 57.657 43.478 14.64 2.58 44.59 3.28
47 48 5.022787 TCCAAATAAGGGGGATCTTGTTTG 58.977 41.667 15.17 15.17 46.21 2.93
48 49 5.283876 TCCAAATAAGGGGGATCTTGTTT 57.716 39.130 0.00 0.00 38.16 2.83
49 50 4.965283 TCCAAATAAGGGGGATCTTGTT 57.035 40.909 0.00 0.00 31.01 2.83
50 51 5.487861 AATCCAAATAAGGGGGATCTTGT 57.512 39.130 0.00 0.00 40.46 3.16
51 52 5.070847 CCAAATCCAAATAAGGGGGATCTTG 59.929 44.000 0.00 0.00 40.46 3.02
52 53 5.218959 CCAAATCCAAATAAGGGGGATCTT 58.781 41.667 0.00 0.00 40.46 2.40
53 54 4.235164 ACCAAATCCAAATAAGGGGGATCT 59.765 41.667 0.00 0.00 40.46 2.75
54 55 4.556697 ACCAAATCCAAATAAGGGGGATC 58.443 43.478 0.00 0.00 40.46 3.36
55 56 4.642489 ACCAAATCCAAATAAGGGGGAT 57.358 40.909 0.00 0.00 43.12 3.85
56 57 4.427956 AACCAAATCCAAATAAGGGGGA 57.572 40.909 0.00 0.00 34.70 4.81
57 58 5.512942 AAAACCAAATCCAAATAAGGGGG 57.487 39.130 0.00 0.00 0.00 5.40
77 78 5.905913 TGGTTTTTCTCCCTCCCATTAAAAA 59.094 36.000 0.00 0.00 0.00 1.94
78 79 5.468658 TGGTTTTTCTCCCTCCCATTAAAA 58.531 37.500 0.00 0.00 0.00 1.52
79 80 5.081315 TGGTTTTTCTCCCTCCCATTAAA 57.919 39.130 0.00 0.00 0.00 1.52
80 81 4.107311 ACTGGTTTTTCTCCCTCCCATTAA 59.893 41.667 0.00 0.00 0.00 1.40
81 82 3.660669 ACTGGTTTTTCTCCCTCCCATTA 59.339 43.478 0.00 0.00 0.00 1.90
82 83 2.450886 ACTGGTTTTTCTCCCTCCCATT 59.549 45.455 0.00 0.00 0.00 3.16
83 84 2.073776 ACTGGTTTTTCTCCCTCCCAT 58.926 47.619 0.00 0.00 0.00 4.00
84 85 1.144913 CACTGGTTTTTCTCCCTCCCA 59.855 52.381 0.00 0.00 0.00 4.37
85 86 1.423921 TCACTGGTTTTTCTCCCTCCC 59.576 52.381 0.00 0.00 0.00 4.30
86 87 2.372172 TCTCACTGGTTTTTCTCCCTCC 59.628 50.000 0.00 0.00 0.00 4.30
87 88 3.558109 CCTCTCACTGGTTTTTCTCCCTC 60.558 52.174 0.00 0.00 0.00 4.30
88 89 2.373502 CCTCTCACTGGTTTTTCTCCCT 59.626 50.000 0.00 0.00 0.00 4.20
89 90 2.553247 CCCTCTCACTGGTTTTTCTCCC 60.553 54.545 0.00 0.00 0.00 4.30
90 91 2.553247 CCCCTCTCACTGGTTTTTCTCC 60.553 54.545 0.00 0.00 0.00 3.71
91 92 2.553247 CCCCCTCTCACTGGTTTTTCTC 60.553 54.545 0.00 0.00 0.00 2.87
92 93 1.425448 CCCCCTCTCACTGGTTTTTCT 59.575 52.381 0.00 0.00 0.00 2.52
93 94 1.145119 ACCCCCTCTCACTGGTTTTTC 59.855 52.381 0.00 0.00 0.00 2.29
94 95 1.133482 CACCCCCTCTCACTGGTTTTT 60.133 52.381 0.00 0.00 0.00 1.94
95 96 0.478507 CACCCCCTCTCACTGGTTTT 59.521 55.000 0.00 0.00 0.00 2.43
96 97 1.427072 CCACCCCCTCTCACTGGTTT 61.427 60.000 0.00 0.00 0.00 3.27
97 98 1.847968 CCACCCCCTCTCACTGGTT 60.848 63.158 0.00 0.00 0.00 3.67
98 99 2.203998 CCACCCCCTCTCACTGGT 60.204 66.667 0.00 0.00 0.00 4.00
99 100 3.721706 GCCACCCCCTCTCACTGG 61.722 72.222 0.00 0.00 0.00 4.00
100 101 4.087892 CGCCACCCCCTCTCACTG 62.088 72.222 0.00 0.00 0.00 3.66
110 111 3.540367 TTTCTTCGTCCCGCCACCC 62.540 63.158 0.00 0.00 0.00 4.61
111 112 1.167781 TTTTTCTTCGTCCCGCCACC 61.168 55.000 0.00 0.00 0.00 4.61
112 113 0.879090 ATTTTTCTTCGTCCCGCCAC 59.121 50.000 0.00 0.00 0.00 5.01
113 114 1.161843 GATTTTTCTTCGTCCCGCCA 58.838 50.000 0.00 0.00 0.00 5.69
114 115 0.096454 CGATTTTTCTTCGTCCCGCC 59.904 55.000 0.00 0.00 32.08 6.13
115 116 0.096454 CCGATTTTTCTTCGTCCCGC 59.904 55.000 0.00 0.00 34.85 6.13
116 117 1.392510 GTCCGATTTTTCTTCGTCCCG 59.607 52.381 0.00 0.00 34.85 5.14
117 118 1.392510 CGTCCGATTTTTCTTCGTCCC 59.607 52.381 0.00 0.00 34.85 4.46
118 119 2.331194 TCGTCCGATTTTTCTTCGTCC 58.669 47.619 0.00 0.00 34.85 4.79
119 120 4.379374 TTTCGTCCGATTTTTCTTCGTC 57.621 40.909 0.00 0.00 34.85 4.20
120 121 4.799419 TTTTCGTCCGATTTTTCTTCGT 57.201 36.364 0.00 0.00 34.85 3.85
121 122 6.247791 GGTTATTTTCGTCCGATTTTTCTTCG 59.752 38.462 0.00 0.00 36.38 3.79
122 123 6.525628 GGGTTATTTTCGTCCGATTTTTCTTC 59.474 38.462 0.00 0.00 0.00 2.87
123 124 6.208007 AGGGTTATTTTCGTCCGATTTTTCTT 59.792 34.615 0.00 0.00 0.00 2.52
124 125 5.708697 AGGGTTATTTTCGTCCGATTTTTCT 59.291 36.000 0.00 0.00 0.00 2.52
125 126 5.946298 AGGGTTATTTTCGTCCGATTTTTC 58.054 37.500 0.00 0.00 0.00 2.29
126 127 5.970317 AGGGTTATTTTCGTCCGATTTTT 57.030 34.783 0.00 0.00 0.00 1.94
127 128 5.970317 AAGGGTTATTTTCGTCCGATTTT 57.030 34.783 0.00 0.00 0.00 1.82
128 129 5.063817 CGTAAGGGTTATTTTCGTCCGATTT 59.936 40.000 0.00 0.00 0.00 2.17
129 130 4.567959 CGTAAGGGTTATTTTCGTCCGATT 59.432 41.667 0.00 0.00 0.00 3.34
130 131 4.114794 CGTAAGGGTTATTTTCGTCCGAT 58.885 43.478 0.00 0.00 0.00 4.18
131 132 3.192422 TCGTAAGGGTTATTTTCGTCCGA 59.808 43.478 0.00 0.00 38.47 4.55
132 133 3.510719 TCGTAAGGGTTATTTTCGTCCG 58.489 45.455 0.00 0.00 38.47 4.79
133 134 3.867493 CCTCGTAAGGGTTATTTTCGTCC 59.133 47.826 0.00 0.00 39.21 4.79
134 135 3.308053 GCCTCGTAAGGGTTATTTTCGTC 59.692 47.826 0.00 0.00 43.58 4.20
135 136 3.264947 GCCTCGTAAGGGTTATTTTCGT 58.735 45.455 0.00 0.00 43.58 3.85
136 137 3.938778 GCCTCGTAAGGGTTATTTTCG 57.061 47.619 0.00 0.00 43.58 3.46
145 146 2.223758 GCACTTAGTAGCCTCGTAAGGG 60.224 54.545 0.00 0.00 43.58 3.95
146 147 2.426024 TGCACTTAGTAGCCTCGTAAGG 59.574 50.000 4.82 0.00 46.44 2.69
147 148 3.777465 TGCACTTAGTAGCCTCGTAAG 57.223 47.619 4.82 0.00 0.00 2.34
148 149 4.730949 AATGCACTTAGTAGCCTCGTAA 57.269 40.909 0.00 0.00 0.00 3.18
149 150 5.840243 TTAATGCACTTAGTAGCCTCGTA 57.160 39.130 0.00 0.00 0.00 3.43
150 151 4.730949 TTAATGCACTTAGTAGCCTCGT 57.269 40.909 0.00 0.00 0.00 4.18
151 152 5.175856 GTCATTAATGCACTTAGTAGCCTCG 59.824 44.000 10.76 0.00 0.00 4.63
152 153 6.284459 AGTCATTAATGCACTTAGTAGCCTC 58.716 40.000 10.76 0.00 0.00 4.70
153 154 6.240549 AGTCATTAATGCACTTAGTAGCCT 57.759 37.500 10.76 0.00 0.00 4.58
154 155 5.175856 CGAGTCATTAATGCACTTAGTAGCC 59.824 44.000 10.76 2.02 0.00 3.93
155 156 5.977725 TCGAGTCATTAATGCACTTAGTAGC 59.022 40.000 10.76 0.00 0.00 3.58
156 157 7.862873 TCATCGAGTCATTAATGCACTTAGTAG 59.137 37.037 10.76 9.66 0.00 2.57
157 158 7.712797 TCATCGAGTCATTAATGCACTTAGTA 58.287 34.615 10.76 3.85 0.00 1.82
158 159 6.573434 TCATCGAGTCATTAATGCACTTAGT 58.427 36.000 10.76 0.00 0.00 2.24
159 160 7.468922 TTCATCGAGTCATTAATGCACTTAG 57.531 36.000 10.76 11.98 0.00 2.18
160 161 7.841915 TTTCATCGAGTCATTAATGCACTTA 57.158 32.000 10.76 8.03 0.00 2.24
161 162 6.741992 TTTCATCGAGTCATTAATGCACTT 57.258 33.333 10.76 0.00 0.00 3.16
162 163 6.741992 TTTTCATCGAGTCATTAATGCACT 57.258 33.333 10.76 13.85 0.00 4.40
211 212 9.953825 GCTACATAGTTAAATACGTATGCAATC 57.046 33.333 9.24 0.00 0.00 2.67
233 234 9.533253 AAACCATTGATGCAATTAATTAGCTAC 57.467 29.630 17.58 13.34 29.05 3.58
330 396 2.421424 AGGCGACATTCTCAAATCAAGC 59.579 45.455 0.00 0.00 0.00 4.01
409 486 2.522436 AACGACCGTGGTGGGAGA 60.522 61.111 6.01 0.00 44.64 3.71
428 505 2.961721 CATGGATCACGGCGTCGG 60.962 66.667 16.39 2.38 41.39 4.79
467 544 2.509336 CGGACCTAACGCTGGCAG 60.509 66.667 10.94 10.94 0.00 4.85
481 558 2.577059 GAAGATGTCGTGGCCGGA 59.423 61.111 5.05 0.00 33.95 5.14
673 1550 5.779241 ATGACATCACCCTCCTAAAAGAA 57.221 39.130 0.00 0.00 0.00 2.52
727 1604 5.143660 CAACTCAATCGCGTAATCAACAAA 58.856 37.500 5.77 0.00 0.00 2.83
734 1611 3.792401 TGATCCAACTCAATCGCGTAAT 58.208 40.909 5.77 0.00 0.00 1.89
740 1617 3.338249 AGGTGTTGATCCAACTCAATCG 58.662 45.455 10.63 0.00 43.85 3.34
747 1624 3.506067 CCTTTGGTAGGTGTTGATCCAAC 59.494 47.826 3.10 3.10 38.73 3.77
751 1628 4.906618 TCTTCCTTTGGTAGGTGTTGATC 58.093 43.478 0.00 0.00 45.03 2.92
791 1670 7.010160 TCACTAGTTTTTCTCCCAAATCCATT 58.990 34.615 0.00 0.00 0.00 3.16
793 1672 5.947663 TCACTAGTTTTTCTCCCAAATCCA 58.052 37.500 0.00 0.00 0.00 3.41
794 1673 6.238648 TCTCACTAGTTTTTCTCCCAAATCC 58.761 40.000 0.00 0.00 0.00 3.01
797 1676 6.464465 CCTCTCTCACTAGTTTTTCTCCCAAA 60.464 42.308 0.00 0.00 0.00 3.28
798 1677 5.012148 CCTCTCTCACTAGTTTTTCTCCCAA 59.988 44.000 0.00 0.00 0.00 4.12
820 1719 1.799933 GTCCCATCTCTCACCATCCT 58.200 55.000 0.00 0.00 0.00 3.24
821 1720 0.390860 CGTCCCATCTCTCACCATCC 59.609 60.000 0.00 0.00 0.00 3.51
823 1722 1.759445 CTTCGTCCCATCTCTCACCAT 59.241 52.381 0.00 0.00 0.00 3.55
829 1728 3.676093 GGTTTTTCTTCGTCCCATCTCT 58.324 45.455 0.00 0.00 0.00 3.10
833 1732 1.072648 TCCGGTTTTTCTTCGTCCCAT 59.927 47.619 0.00 0.00 0.00 4.00
908 1819 3.055602 AGCAACTATCAGTGCATCAGTGA 60.056 43.478 6.78 6.78 46.01 3.41
912 1823 2.739609 CGGAGCAACTATCAGTGCATCA 60.740 50.000 0.00 0.00 0.00 3.07
945 1856 1.133946 GTTTTTATGCTCCGCGCTGC 61.134 55.000 5.56 13.36 40.11 5.25
953 1864 1.602191 CGCACACGGTTTTTATGCTC 58.398 50.000 0.00 0.00 34.06 4.26
992 1903 3.680620 ATGGTGGACATGCGACGGG 62.681 63.158 0.00 0.00 38.70 5.28
1015 1926 3.178539 GGCTACAGCTTTGGCGAC 58.821 61.111 1.87 0.00 44.37 5.19
1052 1963 0.604243 TTCCTCGCGGCTTTGCTTTA 60.604 50.000 6.13 0.00 0.00 1.85
1564 2475 2.359850 GCCCATGACGAAGCACCA 60.360 61.111 0.00 0.00 0.00 4.17
1890 2801 1.102154 CTCTCTGCCTGTCGATCAGT 58.898 55.000 12.10 0.00 42.19 3.41
2078 2989 2.813042 GCACTCAGAGGCGCACTC 60.813 66.667 10.83 13.78 46.98 3.51
2085 2996 3.865929 AACACGGCGCACTCAGAGG 62.866 63.158 10.83 0.00 0.00 3.69
2086 2997 2.356313 AACACGGCGCACTCAGAG 60.356 61.111 10.83 0.00 0.00 3.35
2303 3284 2.680339 GCTTGTTAACTGATGGCTCCTC 59.320 50.000 7.22 0.00 0.00 3.71
2304 3285 2.716217 GCTTGTTAACTGATGGCTCCT 58.284 47.619 7.22 0.00 0.00 3.69
2305 3286 1.398390 CGCTTGTTAACTGATGGCTCC 59.602 52.381 7.22 0.00 0.00 4.70
2307 3288 0.804989 GCGCTTGTTAACTGATGGCT 59.195 50.000 7.22 0.00 0.00 4.75
2308 3289 0.804989 AGCGCTTGTTAACTGATGGC 59.195 50.000 2.64 4.40 0.00 4.40
2310 3291 4.398247 GAAGAAGCGCTTGTTAACTGATG 58.602 43.478 29.83 0.00 36.83 3.07
2313 3294 2.475111 TCGAAGAAGCGCTTGTTAACTG 59.525 45.455 29.83 19.70 36.83 3.16
2315 3296 3.515071 TTCGAAGAAGCGCTTGTTAAC 57.485 42.857 29.83 18.37 45.90 2.01
2316 3297 4.276460 GTTTTCGAAGAAGCGCTTGTTAA 58.724 39.130 29.83 19.54 45.90 2.01
2317 3298 3.602946 CGTTTTCGAAGAAGCGCTTGTTA 60.603 43.478 29.83 14.81 45.90 2.41
2319 3300 1.332904 CGTTTTCGAAGAAGCGCTTGT 60.333 47.619 30.47 22.66 45.90 3.16
2320 3301 1.309108 CGTTTTCGAAGAAGCGCTTG 58.691 50.000 30.47 13.53 45.90 4.01
2323 3304 1.154469 CCCGTTTTCGAAGAAGCGC 60.154 57.895 0.00 0.00 45.90 5.92
2324 3305 1.495951 CCCCGTTTTCGAAGAAGCG 59.504 57.895 0.00 0.00 45.90 4.68
2325 3306 1.209383 GCCCCGTTTTCGAAGAAGC 59.791 57.895 0.00 0.00 45.90 3.86
2326 3307 1.069227 CAAGCCCCGTTTTCGAAGAAG 60.069 52.381 0.00 0.00 45.90 2.85
2327 3308 0.948678 CAAGCCCCGTTTTCGAAGAA 59.051 50.000 0.00 0.00 45.90 2.52
2330 3311 2.969300 AGGCAAGCCCCGTTTTCGAA 62.969 55.000 7.62 0.00 43.79 3.71
2331 3312 3.485346 AGGCAAGCCCCGTTTTCGA 62.485 57.895 7.62 0.00 43.79 3.71
2333 3314 2.650778 CAGGCAAGCCCCGTTTTC 59.349 61.111 7.62 0.00 36.58 2.29
2334 3315 2.706952 TAGCAGGCAAGCCCCGTTTT 62.707 55.000 7.62 0.00 36.58 2.43
2335 3316 3.204467 TAGCAGGCAAGCCCCGTTT 62.204 57.895 7.62 0.00 36.58 3.60
2336 3317 3.646715 TAGCAGGCAAGCCCCGTT 61.647 61.111 7.62 0.01 36.58 4.44
2353 3442 1.649271 GGATGGGAGCAGGGAATGGT 61.649 60.000 0.00 0.00 44.02 3.55
2356 3445 1.694169 ACGGATGGGAGCAGGGAAT 60.694 57.895 0.00 0.00 0.00 3.01
2391 3573 2.574222 CGCGAGCCGTCCGATAAAC 61.574 63.158 0.00 0.00 0.00 2.01
2406 3588 1.641677 CGGGAAAGGAAATAGCGCG 59.358 57.895 0.00 0.00 0.00 6.86
2407 3589 1.355563 GCGGGAAAGGAAATAGCGC 59.644 57.895 0.00 0.00 0.00 5.92
2409 3591 0.377203 CACGCGGGAAAGGAAATAGC 59.623 55.000 12.47 0.00 0.00 2.97
2461 3722 2.888594 TCGAGGCAAAGAGAAATACGG 58.111 47.619 0.00 0.00 0.00 4.02
2480 3742 3.907194 CGAAAGAGGAGCGAATACGTATC 59.093 47.826 8.86 2.01 41.98 2.24
2572 3837 4.096003 CCCGTTGGAGGCCACGAT 62.096 66.667 14.42 0.00 32.71 3.73
2677 3951 4.096003 AATCTGGGACGGGCGTGG 62.096 66.667 0.00 0.00 33.92 4.94
2678 3952 2.819595 CAATCTGGGACGGGCGTG 60.820 66.667 0.00 0.00 33.92 5.34
2679 3953 4.778143 GCAATCTGGGACGGGCGT 62.778 66.667 0.00 0.00 33.92 5.68
2697 3971 4.140599 CTTGCGGCGAGAGAGGCT 62.141 66.667 12.98 0.00 34.19 4.58
2705 3979 4.415332 GAGACGGTCTTGCGGCGA 62.415 66.667 12.98 0.00 0.00 5.54
2803 4768 0.118346 ACCACCACCTCCACTATCCA 59.882 55.000 0.00 0.00 0.00 3.41
2825 4793 1.518056 CTTGAGTGGCGGCACAACAT 61.518 55.000 38.86 22.02 0.00 2.71
2900 4868 4.760047 CCCCGAAGACCCGCTGTG 62.760 72.222 0.00 0.00 0.00 3.66
2950 4918 1.228956 ACCATGGTGCATGCCAAGT 60.229 52.632 18.99 6.23 42.48 3.16
2953 4921 1.679641 CTGACCATGGTGCATGCCA 60.680 57.895 25.52 11.96 40.20 4.92
2954 4922 0.394216 TACTGACCATGGTGCATGCC 60.394 55.000 25.52 7.14 40.20 4.40
2955 4923 0.734889 GTACTGACCATGGTGCATGC 59.265 55.000 25.52 11.82 40.20 4.06
2956 4924 1.009078 CGTACTGACCATGGTGCATG 58.991 55.000 25.52 11.53 41.10 4.06
2957 4925 0.107703 CCGTACTGACCATGGTGCAT 60.108 55.000 25.52 9.43 0.00 3.96
2958 4926 1.295101 CCGTACTGACCATGGTGCA 59.705 57.895 25.52 18.28 0.00 4.57
2959 4927 2.106683 GCCGTACTGACCATGGTGC 61.107 63.158 25.52 14.05 0.00 5.01
2960 4928 0.321210 TTGCCGTACTGACCATGGTG 60.321 55.000 25.52 11.85 0.00 4.17
2961 4929 0.321298 GTTGCCGTACTGACCATGGT 60.321 55.000 19.89 19.89 0.00 3.55
2990 4958 1.152271 AGAGAGGAGGGTGAAAGGGAA 59.848 52.381 0.00 0.00 0.00 3.97
3000 4968 3.866449 GCACAAAACAGTAGAGAGGAGGG 60.866 52.174 0.00 0.00 0.00 4.30


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

AutoCloner maintained by Alex Coulton.