Multiple sequence alignment - TraesCS4A01G359700

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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 TraesCS4A01G359700 chr4A 100.000 2752 0 0 1 2752 632938984 632941735 0.000000e+00 5083.0
1 TraesCS4A01G359700 chr4A 78.339 2216 333 86 328 2448 616618700 616616537 0.000000e+00 1297.0
2 TraesCS4A01G359700 chr4A 79.115 1786 250 83 692 2448 616791310 616789619 0.000000e+00 1118.0
3 TraesCS4A01G359700 chr4A 81.740 931 92 33 1580 2448 616236837 616235923 0.000000e+00 706.0
4 TraesCS4A01G359700 chr4A 76.061 589 109 15 334 897 616840652 616840071 7.510000e-71 278.0
5 TraesCS4A01G359700 chr4A 86.420 243 28 2 2503 2741 616789633 616789392 7.560000e-66 261.0
6 TraesCS4A01G359700 chr4A 86.638 232 31 0 306 537 624486000 624485769 9.780000e-65 257.0
7 TraesCS4A01G359700 chr4A 85.537 242 23 4 287 516 616886015 616885774 2.740000e-60 243.0
8 TraesCS4A01G359700 chr4A 76.048 501 86 19 345 828 616871852 616871369 2.130000e-56 230.0
9 TraesCS4A01G359700 chr4A 82.143 196 13 7 2503 2698 625545059 625545232 6.140000e-32 148.0
10 TraesCS4A01G359700 chr5B 91.993 1711 89 18 199 1876 677811912 677813607 0.000000e+00 2357.0
11 TraesCS4A01G359700 chr5B 91.182 1066 68 12 813 1876 677751024 677749983 0.000000e+00 1424.0
12 TraesCS4A01G359700 chr5B 79.033 1593 258 43 328 1880 703529371 703530927 0.000000e+00 1022.0
13 TraesCS4A01G359700 chr5B 79.232 1406 221 45 306 1676 703634096 703635465 0.000000e+00 913.0
14 TraesCS4A01G359700 chr5B 78.922 1428 217 40 615 1993 703523257 703524649 0.000000e+00 893.0
15 TraesCS4A01G359700 chr5B 82.871 1010 151 17 864 1861 699437465 699438464 0.000000e+00 887.0
16 TraesCS4A01G359700 chr5B 77.244 1560 283 44 282 1805 685499442 685500965 0.000000e+00 848.0
17 TraesCS4A01G359700 chr5B 79.845 1161 197 24 614 1756 699998180 699999321 0.000000e+00 813.0
18 TraesCS4A01G359700 chr5B 81.497 935 94 37 1577 2448 699274542 699275460 0.000000e+00 695.0
19 TraesCS4A01G359700 chr5B 82.496 697 48 27 1813 2448 677813606 677814289 6.700000e-151 544.0
20 TraesCS4A01G359700 chr5B 76.221 942 177 34 952 1876 699432985 699433896 3.230000e-124 455.0
21 TraesCS4A01G359700 chr5B 92.713 247 15 2 2503 2749 677814275 677814518 1.210000e-93 353.0
22 TraesCS4A01G359700 chr5B 90.551 254 17 4 2503 2752 677749372 677749122 2.040000e-86 329.0
23 TraesCS4A01G359700 chr5B 78.585 523 47 27 1813 2292 677749984 677749484 4.490000e-73 285.0
24 TraesCS4A01G359700 chr5B 85.409 281 26 10 249 517 698256473 698256750 7.510000e-71 278.0
25 TraesCS4A01G359700 chr5B 75.777 611 112 29 337 927 685543835 685544429 2.700000e-70 276.0
26 TraesCS4A01G359700 chr5B 91.803 122 10 0 2327 2448 677749479 677749358 1.310000e-38 171.0
27 TraesCS4A01G359700 chr5B 89.320 103 10 1 2503 2605 685253974 685253873 8.000000e-26 128.0
28 TraesCS4A01G359700 chr5B 80.769 104 18 2 622 724 703497052 703497154 2.270000e-11 80.5
29 TraesCS4A01G359700 chr5D 93.530 711 31 6 1175 1876 537216840 537217544 0.000000e+00 1044.0
30 TraesCS4A01G359700 chr5D 78.772 1319 192 52 311 1584 552051653 552050378 0.000000e+00 804.0
31 TraesCS4A01G359700 chr5D 83.059 850 102 26 1151 1966 552394901 552394060 0.000000e+00 734.0
32 TraesCS4A01G359700 chr5D 81.818 935 90 42 1577 2448 552050126 552049209 0.000000e+00 712.0
33 TraesCS4A01G359700 chr5D 76.803 1220 204 52 294 1470 552422827 552421644 1.810000e-171 612.0
34 TraesCS4A01G359700 chr5D 77.136 831 116 34 1669 2448 551612892 551613699 5.480000e-112 414.0
35 TraesCS4A01G359700 chr5D 92.713 247 15 2 2503 2749 537218101 537218344 1.210000e-93 353.0
36 TraesCS4A01G359700 chr5D 76.613 620 108 18 328 926 551611479 551612082 9.570000e-80 307.0
37 TraesCS4A01G359700 chr5D 91.743 218 10 3 2239 2448 537217898 537218115 2.070000e-76 296.0
38 TraesCS4A01G359700 chr5D 89.202 213 23 0 308 520 552458397 552458185 1.620000e-67 267.0
39 TraesCS4A01G359700 chr5D 79.076 368 31 20 1813 2147 537217543 537217897 7.720000e-51 211.0
40 TraesCS4A01G359700 chr5D 74.413 383 79 14 681 1058 551081983 551082351 2.210000e-31 147.0
41 TraesCS4A01G359700 chr5D 90.291 103 9 1 2503 2605 543462493 543462392 1.720000e-27 134.0
42 TraesCS4A01G359700 chr5D 94.872 39 2 0 622 660 552352585 552352547 8.230000e-06 62.1
43 TraesCS4A01G359700 chr1A 75.368 950 174 34 306 1225 569738566 569739485 1.190000e-108 403.0
44 TraesCS4A01G359700 chr1B 76.389 576 85 29 281 821 115748937 115749496 2.100000e-66 263.0
45 TraesCS4A01G359700 chr4B 75.966 466 76 21 282 724 581073627 581073175 9.990000e-50 207.0
46 TraesCS4A01G359700 chr6D 90.647 139 12 1 1 138 473425345 473425483 1.680000e-42 183.0
47 TraesCS4A01G359700 chr7A 88.430 121 14 0 18 138 134592049 134592169 2.210000e-31 147.0
48 TraesCS4A01G359700 chr7B 81.046 153 29 0 365 517 854347 854499 3.720000e-24 122.0
49 TraesCS4A01G359700 chr1D 74.888 223 39 12 624 842 22968647 22968438 4.880000e-13 86.1


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 TraesCS4A01G359700 chr4A 632938984 632941735 2751 False 5083.000000 5083 100.000000 1 2752 1 chr4A.!!$F2 2751
1 TraesCS4A01G359700 chr4A 616616537 616618700 2163 True 1297.000000 1297 78.339000 328 2448 1 chr4A.!!$R2 2120
2 TraesCS4A01G359700 chr4A 616235923 616236837 914 True 706.000000 706 81.740000 1580 2448 1 chr4A.!!$R1 868
3 TraesCS4A01G359700 chr4A 616789392 616791310 1918 True 689.500000 1118 82.767500 692 2741 2 chr4A.!!$R7 2049
4 TraesCS4A01G359700 chr4A 616840071 616840652 581 True 278.000000 278 76.061000 334 897 1 chr4A.!!$R3 563
5 TraesCS4A01G359700 chr5B 677811912 677814518 2606 False 1084.666667 2357 89.067333 199 2749 3 chr5B.!!$F10 2550
6 TraesCS4A01G359700 chr5B 703529371 703530927 1556 False 1022.000000 1022 79.033000 328 1880 1 chr5B.!!$F8 1552
7 TraesCS4A01G359700 chr5B 703634096 703635465 1369 False 913.000000 913 79.232000 306 1676 1 chr5B.!!$F9 1370
8 TraesCS4A01G359700 chr5B 703523257 703524649 1392 False 893.000000 893 78.922000 615 1993 1 chr5B.!!$F7 1378
9 TraesCS4A01G359700 chr5B 685499442 685500965 1523 False 848.000000 848 77.244000 282 1805 1 chr5B.!!$F1 1523
10 TraesCS4A01G359700 chr5B 699998180 699999321 1141 False 813.000000 813 79.845000 614 1756 1 chr5B.!!$F5 1142
11 TraesCS4A01G359700 chr5B 699274542 699275460 918 False 695.000000 695 81.497000 1577 2448 1 chr5B.!!$F4 871
12 TraesCS4A01G359700 chr5B 699432985 699438464 5479 False 671.000000 887 79.546000 864 1876 2 chr5B.!!$F11 1012
13 TraesCS4A01G359700 chr5B 677749122 677751024 1902 True 552.250000 1424 88.030250 813 2752 4 chr5B.!!$R2 1939
14 TraesCS4A01G359700 chr5B 685543835 685544429 594 False 276.000000 276 75.777000 337 927 1 chr5B.!!$F2 590
15 TraesCS4A01G359700 chr5D 552049209 552051653 2444 True 758.000000 804 80.295000 311 2448 2 chr5D.!!$R6 2137
16 TraesCS4A01G359700 chr5D 552394060 552394901 841 True 734.000000 734 83.059000 1151 1966 1 chr5D.!!$R3 815
17 TraesCS4A01G359700 chr5D 552421644 552422827 1183 True 612.000000 612 76.803000 294 1470 1 chr5D.!!$R4 1176
18 TraesCS4A01G359700 chr5D 537216840 537218344 1504 False 476.000000 1044 89.265500 1175 2749 4 chr5D.!!$F2 1574
19 TraesCS4A01G359700 chr5D 551611479 551613699 2220 False 360.500000 414 76.874500 328 2448 2 chr5D.!!$F3 2120
20 TraesCS4A01G359700 chr1A 569738566 569739485 919 False 403.000000 403 75.368000 306 1225 1 chr1A.!!$F1 919
21 TraesCS4A01G359700 chr1B 115748937 115749496 559 False 263.000000 263 76.389000 281 821 1 chr1B.!!$F1 540

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
680 745 0.099436 GAGAACATGTTGCCCATCGC 59.901 55.0 17.58 0.0 38.31 4.58 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2559 6933 0.669619 TTGCATTGCACTGTGACCAG 59.33 50.0 11.66 0.0 44.68 4.0 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
17 18 4.082523 ATCGTGCTGTCCGTGGGG 62.083 66.667 0.00 0.00 0.00 4.96
20 21 4.699522 GTGCTGTCCGTGGGGGTC 62.700 72.222 0.00 0.00 37.00 4.46
23 24 3.391382 CTGTCCGTGGGGGTCCTC 61.391 72.222 0.00 0.00 37.00 3.71
25 26 3.391382 GTCCGTGGGGGTCCTCTG 61.391 72.222 0.00 0.00 37.00 3.35
26 27 3.596799 TCCGTGGGGGTCCTCTGA 61.597 66.667 0.00 0.00 37.00 3.27
27 28 2.606519 CCGTGGGGGTCCTCTGAA 60.607 66.667 0.00 0.00 0.00 3.02
28 29 2.221299 CCGTGGGGGTCCTCTGAAA 61.221 63.158 0.00 0.00 0.00 2.69
29 30 1.562672 CCGTGGGGGTCCTCTGAAAT 61.563 60.000 0.00 0.00 0.00 2.17
31 32 1.134491 CGTGGGGGTCCTCTGAAATAC 60.134 57.143 0.00 0.00 0.00 1.89
32 33 1.134491 GTGGGGGTCCTCTGAAATACG 60.134 57.143 0.00 0.00 0.00 3.06
33 34 0.179054 GGGGGTCCTCTGAAATACGC 60.179 60.000 0.00 0.00 0.00 4.42
34 35 0.539986 GGGGTCCTCTGAAATACGCA 59.460 55.000 0.00 0.00 0.00 5.24
35 36 1.141053 GGGGTCCTCTGAAATACGCAT 59.859 52.381 0.00 0.00 0.00 4.73
36 37 2.367567 GGGGTCCTCTGAAATACGCATA 59.632 50.000 0.00 0.00 0.00 3.14
37 38 3.008049 GGGGTCCTCTGAAATACGCATAT 59.992 47.826 0.00 0.00 0.00 1.78
38 39 4.222145 GGGGTCCTCTGAAATACGCATATA 59.778 45.833 0.00 0.00 0.00 0.86
39 40 5.169295 GGGTCCTCTGAAATACGCATATAC 58.831 45.833 0.00 0.00 0.00 1.47
40 41 4.857588 GGTCCTCTGAAATACGCATATACG 59.142 45.833 0.00 0.00 39.50 3.06
41 42 4.323868 GTCCTCTGAAATACGCATATACGC 59.676 45.833 0.00 0.00 36.19 4.42
42 43 4.217767 TCCTCTGAAATACGCATATACGCT 59.782 41.667 0.00 0.00 36.19 5.07
44 45 5.512082 CCTCTGAAATACGCATATACGCTAC 59.488 44.000 0.00 0.00 36.19 3.58
45 46 6.004408 TCTGAAATACGCATATACGCTACA 57.996 37.500 0.00 0.00 36.19 2.74
46 47 6.617879 TCTGAAATACGCATATACGCTACAT 58.382 36.000 0.00 0.00 36.19 2.29
48 49 8.403236 TCTGAAATACGCATATACGCTACATAT 58.597 33.333 0.00 0.00 36.19 1.78
50 51 8.185505 TGAAATACGCATATACGCTACATATCA 58.814 33.333 0.00 0.00 36.19 2.15
51 52 7.909777 AATACGCATATACGCTACATATCAC 57.090 36.000 0.00 0.00 36.19 3.06
52 53 5.562506 ACGCATATACGCTACATATCACT 57.437 39.130 0.00 0.00 36.19 3.41
53 54 5.570344 ACGCATATACGCTACATATCACTC 58.430 41.667 0.00 0.00 36.19 3.51
54 55 5.354513 ACGCATATACGCTACATATCACTCT 59.645 40.000 0.00 0.00 36.19 3.24
57 58 6.183360 GCATATACGCTACATATCACTCTCCA 60.183 42.308 0.00 0.00 0.00 3.86
58 59 5.888691 ATACGCTACATATCACTCTCCAG 57.111 43.478 0.00 0.00 0.00 3.86
59 60 3.821748 ACGCTACATATCACTCTCCAGA 58.178 45.455 0.00 0.00 0.00 3.86
60 61 3.566322 ACGCTACATATCACTCTCCAGAC 59.434 47.826 0.00 0.00 0.00 3.51
63 64 4.036971 GCTACATATCACTCTCCAGACGTT 59.963 45.833 0.00 0.00 0.00 3.99
65 66 3.065510 ACATATCACTCTCCAGACGTTCG 59.934 47.826 0.00 0.00 0.00 3.95
66 67 0.171455 ATCACTCTCCAGACGTTCGC 59.829 55.000 0.00 0.00 0.00 4.70
67 68 1.444553 CACTCTCCAGACGTTCGCC 60.445 63.158 0.00 0.00 0.00 5.54
69 70 0.322277 ACTCTCCAGACGTTCGCCTA 60.322 55.000 0.00 0.00 0.00 3.93
70 71 1.025812 CTCTCCAGACGTTCGCCTAT 58.974 55.000 0.00 0.00 0.00 2.57
72 73 1.945394 TCTCCAGACGTTCGCCTATAC 59.055 52.381 0.00 0.00 0.00 1.47
73 74 1.948145 CTCCAGACGTTCGCCTATACT 59.052 52.381 0.00 0.00 0.00 2.12
74 75 1.945394 TCCAGACGTTCGCCTATACTC 59.055 52.381 0.00 0.00 0.00 2.59
76 77 1.674441 CAGACGTTCGCCTATACTCCA 59.326 52.381 0.00 0.00 0.00 3.86
77 78 2.098607 CAGACGTTCGCCTATACTCCAA 59.901 50.000 0.00 0.00 0.00 3.53
78 79 2.957006 AGACGTTCGCCTATACTCCAAT 59.043 45.455 0.00 0.00 0.00 3.16
79 80 3.383825 AGACGTTCGCCTATACTCCAATT 59.616 43.478 0.00 0.00 0.00 2.32
80 81 4.581824 AGACGTTCGCCTATACTCCAATTA 59.418 41.667 0.00 0.00 0.00 1.40
81 82 4.868067 ACGTTCGCCTATACTCCAATTAG 58.132 43.478 0.00 0.00 0.00 1.73
85 86 3.639561 TCGCCTATACTCCAATTAGCACA 59.360 43.478 0.00 0.00 0.00 4.57
87 88 4.997395 CGCCTATACTCCAATTAGCACATT 59.003 41.667 0.00 0.00 0.00 2.71
88 89 5.120830 CGCCTATACTCCAATTAGCACATTC 59.879 44.000 0.00 0.00 0.00 2.67
89 90 5.997746 GCCTATACTCCAATTAGCACATTCA 59.002 40.000 0.00 0.00 0.00 2.57
93 94 3.693085 ACTCCAATTAGCACATTCAGCTG 59.307 43.478 7.63 7.63 43.33 4.24
94 95 3.689347 TCCAATTAGCACATTCAGCTGT 58.311 40.909 14.67 0.00 43.33 4.40
95 96 4.081406 TCCAATTAGCACATTCAGCTGTT 58.919 39.130 14.67 0.00 43.33 3.16
96 97 4.156556 TCCAATTAGCACATTCAGCTGTTC 59.843 41.667 14.67 0.00 43.33 3.18
97 98 4.093514 CAATTAGCACATTCAGCTGTTCG 58.906 43.478 14.67 5.56 43.33 3.95
98 99 2.741759 TAGCACATTCAGCTGTTCGA 57.258 45.000 14.67 0.00 43.33 3.71
99 100 1.882912 AGCACATTCAGCTGTTCGAA 58.117 45.000 14.67 0.06 41.61 3.71
100 101 2.430465 AGCACATTCAGCTGTTCGAAT 58.570 42.857 14.67 2.86 41.61 3.34
101 102 2.417933 AGCACATTCAGCTGTTCGAATC 59.582 45.455 14.67 0.00 41.61 2.52
103 104 1.394917 ACATTCAGCTGTTCGAATCGC 59.605 47.619 14.67 7.34 29.38 4.58
104 105 0.647410 ATTCAGCTGTTCGAATCGCG 59.353 50.000 14.67 0.00 42.69 5.87
112 113 4.601315 TCGAATCGCGATGGTACG 57.399 55.556 24.47 23.15 45.59 3.67
130 131 3.842126 CGCACCGTCGATGCACTG 61.842 66.667 13.03 0.00 43.57 3.66
131 132 4.152625 GCACCGTCGATGCACTGC 62.153 66.667 6.73 4.79 42.88 4.40
132 133 3.842126 CACCGTCGATGCACTGCG 61.842 66.667 0.00 0.00 0.00 5.18
133 134 4.357947 ACCGTCGATGCACTGCGT 62.358 61.111 0.00 0.00 0.00 5.24
134 135 3.842126 CCGTCGATGCACTGCGTG 61.842 66.667 0.00 4.61 36.51 5.34
151 152 1.300963 TGCAGGGATGCACTTCTCC 59.699 57.895 0.00 0.00 40.23 3.71
152 153 1.300963 GCAGGGATGCACTTCTCCA 59.699 57.895 6.42 0.00 32.90 3.86
154 155 1.887956 GCAGGGATGCACTTCTCCAAA 60.888 52.381 6.42 0.00 32.90 3.28
155 156 2.517959 CAGGGATGCACTTCTCCAAAA 58.482 47.619 6.42 0.00 32.90 2.44
182 183 1.337118 GGAAACCAAGCATCCAACCA 58.663 50.000 0.00 0.00 33.30 3.67
183 184 1.273327 GGAAACCAAGCATCCAACCAG 59.727 52.381 0.00 0.00 33.30 4.00
184 185 0.681175 AAACCAAGCATCCAACCAGC 59.319 50.000 0.00 0.00 0.00 4.85
185 186 1.187567 AACCAAGCATCCAACCAGCC 61.188 55.000 0.00 0.00 0.00 4.85
186 187 2.703798 CCAAGCATCCAACCAGCCG 61.704 63.158 0.00 0.00 0.00 5.52
187 188 3.064324 AAGCATCCAACCAGCCGC 61.064 61.111 0.00 0.00 0.00 6.53
190 191 4.431131 CATCCAACCAGCCGCCCT 62.431 66.667 0.00 0.00 0.00 5.19
194 195 4.335647 CAACCAGCCGCCCTCACT 62.336 66.667 0.00 0.00 0.00 3.41
195 196 4.335647 AACCAGCCGCCCTCACTG 62.336 66.667 0.00 0.00 0.00 3.66
202 203 3.775654 CGCCCTCACTGTCCTCCC 61.776 72.222 0.00 0.00 0.00 4.30
229 230 3.818121 CTGTCGGAAACCCCACGCA 62.818 63.158 0.00 0.00 34.14 5.24
252 253 2.029964 GGCTGAACCGAACCGTGA 59.970 61.111 0.00 0.00 0.00 4.35
271 272 3.249189 AGCAACCGCCTTCCTCCA 61.249 61.111 0.00 0.00 39.83 3.86
302 304 2.092323 CTCAAAATTTCCCCTCCCGAC 58.908 52.381 0.00 0.00 0.00 4.79
523 554 2.477245 TGCTGGGCTTCCTTCATAGTA 58.523 47.619 0.00 0.00 0.00 1.82
537 568 0.941963 ATAGTACCTGGCTGGAGGGA 59.058 55.000 18.12 0.00 37.45 4.20
538 569 0.714180 TAGTACCTGGCTGGAGGGAA 59.286 55.000 18.12 0.00 37.45 3.97
540 571 0.696501 GTACCTGGCTGGAGGGAAAA 59.303 55.000 18.12 0.00 37.45 2.29
545 576 1.563410 CTGGCTGGAGGGAAAAGATCT 59.437 52.381 0.00 0.00 0.00 2.75
597 656 4.477975 CCCGACGAGGACGACTGC 62.478 72.222 0.00 0.00 45.00 4.40
598 657 4.813526 CCGACGAGGACGACTGCG 62.814 72.222 0.00 0.00 45.00 5.18
600 659 4.477975 GACGAGGACGACTGCGGG 62.478 72.222 0.00 0.00 43.17 6.13
602 661 4.180946 CGAGGACGACTGCGGGAG 62.181 72.222 0.00 0.00 43.17 4.30
625 690 1.986698 GTACCACAAGTACGATGCGT 58.013 50.000 0.00 0.00 41.94 5.24
626 691 1.652124 GTACCACAAGTACGATGCGTG 59.348 52.381 2.33 0.00 41.94 5.34
627 692 2.078226 CCACAAGTACGATGCGTGG 58.922 57.895 2.33 7.49 41.39 4.94
628 693 1.358725 CCACAAGTACGATGCGTGGG 61.359 60.000 2.33 0.00 42.79 4.61
629 694 0.389296 CACAAGTACGATGCGTGGGA 60.389 55.000 2.33 0.00 41.39 4.37
630 695 0.389426 ACAAGTACGATGCGTGGGAC 60.389 55.000 2.33 0.00 41.39 4.46
632 697 0.108804 AAGTACGATGCGTGGGACTG 60.109 55.000 6.57 0.00 41.39 3.51
633 698 2.165301 GTACGATGCGTGGGACTGC 61.165 63.158 2.33 0.00 41.39 4.40
653 718 4.473520 CCATGGCCGCGTTCTCCT 62.474 66.667 4.92 0.00 0.00 3.69
654 719 2.436646 CATGGCCGCGTTCTCCTT 60.437 61.111 4.92 0.00 0.00 3.36
655 720 2.436646 ATGGCCGCGTTCTCCTTG 60.437 61.111 4.92 0.00 0.00 3.61
657 722 4.388499 GGCCGCGTTCTCCTTGGA 62.388 66.667 4.92 0.00 0.00 3.53
658 723 2.815647 GCCGCGTTCTCCTTGGAG 60.816 66.667 4.92 10.28 0.00 3.86
660 725 1.446272 CCGCGTTCTCCTTGGAGAC 60.446 63.158 18.03 12.32 0.00 3.36
662 727 1.585006 GCGTTCTCCTTGGAGACGA 59.415 57.895 28.28 13.51 32.00 4.20
663 728 0.456995 GCGTTCTCCTTGGAGACGAG 60.457 60.000 28.28 19.72 41.95 4.18
665 730 1.540267 CGTTCTCCTTGGAGACGAGAA 59.460 52.381 23.87 8.99 45.46 2.87
667 732 2.287977 TCTCCTTGGAGACGAGAACA 57.712 50.000 14.79 0.00 45.46 3.18
668 733 2.808919 TCTCCTTGGAGACGAGAACAT 58.191 47.619 14.79 0.00 45.46 2.71
669 734 2.493675 TCTCCTTGGAGACGAGAACATG 59.506 50.000 14.79 0.00 45.46 3.21
672 737 2.738846 CCTTGGAGACGAGAACATGTTG 59.261 50.000 17.58 4.18 45.46 3.33
674 739 1.079503 GGAGACGAGAACATGTTGCC 58.920 55.000 17.58 6.28 0.00 4.52
675 740 1.079503 GAGACGAGAACATGTTGCCC 58.920 55.000 17.58 1.22 0.00 5.36
676 741 0.396435 AGACGAGAACATGTTGCCCA 59.604 50.000 17.58 0.00 0.00 5.36
677 742 1.003580 AGACGAGAACATGTTGCCCAT 59.996 47.619 17.58 0.00 0.00 4.00
678 743 1.398390 GACGAGAACATGTTGCCCATC 59.602 52.381 17.58 0.00 0.00 3.51
679 744 0.374758 CGAGAACATGTTGCCCATCG 59.625 55.000 17.58 12.96 0.00 3.84
680 745 0.099436 GAGAACATGTTGCCCATCGC 59.901 55.000 17.58 0.00 38.31 4.58
681 746 1.226379 GAACATGTTGCCCATCGCG 60.226 57.895 17.58 0.00 42.08 5.87
682 747 2.597117 GAACATGTTGCCCATCGCGG 62.597 60.000 17.58 0.00 42.08 6.46
683 748 3.133464 CATGTTGCCCATCGCGGT 61.133 61.111 6.13 0.00 42.08 5.68
684 749 2.824041 ATGTTGCCCATCGCGGTC 60.824 61.111 6.13 0.00 42.08 4.79
690 755 4.789075 CCCATCGCGGTCGTCGTT 62.789 66.667 6.13 0.00 41.72 3.85
691 756 2.807895 CCATCGCGGTCGTCGTTT 60.808 61.111 6.13 0.00 41.72 3.60
692 757 2.390288 CATCGCGGTCGTCGTTTG 59.610 61.111 6.13 0.00 41.72 2.93
693 758 2.807895 ATCGCGGTCGTCGTTTGG 60.808 61.111 6.13 0.00 41.72 3.28
696 761 3.408851 GCGGTCGTCGTTTGGGAC 61.409 66.667 0.00 0.00 41.72 4.46
697 762 2.735857 CGGTCGTCGTTTGGGACC 60.736 66.667 0.00 0.00 45.34 4.46
698 763 2.357881 GGTCGTCGTTTGGGACCC 60.358 66.667 2.45 2.45 43.51 4.46
699 764 2.357881 GTCGTCGTTTGGGACCCC 60.358 66.667 8.45 2.69 33.30 4.95
700 765 2.843411 TCGTCGTTTGGGACCCCA 60.843 61.111 8.45 3.10 45.63 4.96
703 768 1.377229 GTCGTTTGGGACCCCATGA 59.623 57.895 8.45 2.63 46.64 3.07
704 769 0.958876 GTCGTTTGGGACCCCATGAC 60.959 60.000 8.45 11.85 46.64 3.06
706 771 1.677633 GTTTGGGACCCCATGACGG 60.678 63.158 8.45 0.00 46.64 4.79
730 795 4.475135 GGAAGGACCTGCCGGAGC 62.475 72.222 5.05 0.00 43.43 4.70
731 796 4.475135 GAAGGACCTGCCGGAGCC 62.475 72.222 5.05 1.77 43.43 4.70
749 814 2.734723 CGACCTGGTGCACGACAG 60.735 66.667 11.45 13.10 34.54 3.51
755 820 3.799753 GGTGCACGACAGCTATGG 58.200 61.111 11.45 0.00 43.65 2.74
756 821 2.464459 GGTGCACGACAGCTATGGC 61.464 63.158 11.45 0.00 43.65 4.40
816 881 4.424711 TGTCATGCGGGCCCCTTC 62.425 66.667 18.66 6.27 0.00 3.46
825 890 4.048470 GGCCCCTTCCAGGTGGTC 62.048 72.222 0.00 0.00 31.93 4.02
828 893 2.081585 GCCCCTTCCAGGTGGTCTTT 62.082 60.000 0.00 0.00 31.93 2.52
829 894 0.251341 CCCCTTCCAGGTGGTCTTTG 60.251 60.000 0.00 0.00 31.93 2.77
830 895 0.478507 CCCTTCCAGGTGGTCTTTGT 59.521 55.000 0.00 0.00 31.93 2.83
832 897 1.956477 CCTTCCAGGTGGTCTTTGTTG 59.044 52.381 0.00 0.00 36.34 3.33
836 901 0.468029 CAGGTGGTCTTTGTTGGCCT 60.468 55.000 3.32 0.00 0.00 5.19
837 902 0.468029 AGGTGGTCTTTGTTGGCCTG 60.468 55.000 3.32 0.00 0.00 4.85
838 903 1.463553 GGTGGTCTTTGTTGGCCTGG 61.464 60.000 3.32 0.00 0.00 4.45
839 904 1.152567 TGGTCTTTGTTGGCCTGGG 60.153 57.895 3.32 0.00 0.00 4.45
840 905 2.574018 GGTCTTTGTTGGCCTGGGC 61.574 63.158 14.23 14.23 41.06 5.36
841 906 1.832167 GTCTTTGTTGGCCTGGGCA 60.832 57.895 20.19 20.19 44.11 5.36
842 907 1.155859 TCTTTGTTGGCCTGGGCAT 59.844 52.632 24.56 0.00 44.11 4.40
843 908 1.186917 TCTTTGTTGGCCTGGGCATG 61.187 55.000 24.56 11.66 44.11 4.06
844 909 2.175035 CTTTGTTGGCCTGGGCATGG 62.175 60.000 24.56 8.62 44.11 3.66
845 910 4.700448 TGTTGGCCTGGGCATGGG 62.700 66.667 24.56 0.00 44.11 4.00
846 911 4.702274 GTTGGCCTGGGCATGGGT 62.702 66.667 24.56 0.00 44.11 4.51
861 926 1.619654 TGGGTGCAGATTTTGACTGG 58.380 50.000 0.00 0.00 36.09 4.00
862 927 1.144708 TGGGTGCAGATTTTGACTGGA 59.855 47.619 0.00 0.00 36.09 3.86
863 928 2.238521 GGGTGCAGATTTTGACTGGAA 58.761 47.619 0.00 0.00 37.45 3.53
865 930 3.367703 GGGTGCAGATTTTGACTGGAATG 60.368 47.826 0.00 0.00 37.45 2.67
866 931 3.367703 GGTGCAGATTTTGACTGGAATGG 60.368 47.826 0.00 0.00 37.45 3.16
867 932 3.256631 GTGCAGATTTTGACTGGAATGGT 59.743 43.478 0.00 0.00 37.45 3.55
941 4613 0.956410 TGCCCCGTGTTTGATAACCG 60.956 55.000 0.00 0.00 33.15 4.44
1137 4816 2.045438 CTTGTGGGGCGTGGCATA 60.045 61.111 0.00 0.00 0.00 3.14
1173 4852 1.056125 TCATGGCGATGGAGGATGGT 61.056 55.000 8.98 0.00 0.00 3.55
1404 5086 4.569943 AGATTAATGTCAAGTCACAGCGT 58.430 39.130 0.00 0.00 0.00 5.07
1825 5983 2.097825 GATGACAAGCTTGGAGGCAAT 58.902 47.619 29.18 13.13 34.17 3.56
1846 6004 6.016777 GCAATAGGGGTCTTGTGATGAATTAG 60.017 42.308 0.00 0.00 0.00 1.73
1920 6216 5.929697 TTGTCAGTGAGCTTGATAGTTTG 57.070 39.130 0.00 0.00 0.00 2.93
1996 6308 1.753073 GCAGCTGCAATAGGAACCATT 59.247 47.619 33.36 0.00 41.59 3.16
2030 6361 2.568956 TCTGCAGGCAGTACTCAAGAAT 59.431 45.455 19.75 0.00 43.96 2.40
2036 6367 2.482142 GGCAGTACTCAAGAATCGGAGG 60.482 54.545 9.18 0.00 35.45 4.30
2055 6386 5.532557 GGAGGTTTTTCTGTCCATTTTGAG 58.467 41.667 0.00 0.00 0.00 3.02
2150 6488 8.874156 AGTTGATAATAATGGCATGTCTAGAGA 58.126 33.333 0.00 0.00 0.00 3.10
2200 6538 3.945921 AGACATGATGATGGTTTCTGCAG 59.054 43.478 7.63 7.63 33.39 4.41
2218 6560 1.209019 CAGGCTGGCTCACTAATCTGT 59.791 52.381 6.61 0.00 0.00 3.41
2264 6619 8.194104 TCTTTTTAGCAAAGCAATGTTACTGAA 58.806 29.630 0.00 0.00 0.00 3.02
2303 6666 8.443953 AAACTGAATCTTGAGCTATATGTTCC 57.556 34.615 0.00 0.00 0.00 3.62
2404 6774 3.840666 TGCAGGGAAGATCTTGAGTAGTT 59.159 43.478 14.00 0.00 0.00 2.24
2405 6775 4.287067 TGCAGGGAAGATCTTGAGTAGTTT 59.713 41.667 14.00 0.00 0.00 2.66
2448 6822 3.118738 GGCCTACAGTGCACATACTAGTT 60.119 47.826 21.04 0.00 0.00 2.24
2449 6823 4.504858 GCCTACAGTGCACATACTAGTTT 58.495 43.478 21.04 0.00 0.00 2.66
2450 6824 4.935808 GCCTACAGTGCACATACTAGTTTT 59.064 41.667 21.04 0.00 0.00 2.43
2451 6825 5.411669 GCCTACAGTGCACATACTAGTTTTT 59.588 40.000 21.04 0.00 0.00 1.94
2566 6944 3.813443 AGATGTTCATATGCCTGGTCAC 58.187 45.455 0.00 0.00 0.00 3.67
2577 6955 1.174078 CCTGGTCACAGTGCAATGCA 61.174 55.000 15.18 2.72 43.36 3.96
2656 7035 9.757227 ACAGATTTTCCTTCTTAGATAAGATCG 57.243 33.333 3.25 0.00 41.52 3.69
2686 7065 9.467258 ACTAAAAATCATGAACACACATTTCTG 57.533 29.630 0.00 0.00 0.00 3.02
2738 7121 8.616076 CATGAAAGAAGTATGGTTCTATTCCAC 58.384 37.037 0.00 0.00 35.65 4.02
2743 7126 7.633789 AGAAGTATGGTTCTATTCCACATGTT 58.366 34.615 0.00 0.00 37.81 2.71
2749 7132 8.821686 ATGGTTCTATTCCACATGTTTCATAA 57.178 30.769 0.00 0.00 37.81 1.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.082523 CCCCACGGACAGCACGAT 62.083 66.667 0.00 0.00 34.93 3.73
9 10 2.682928 TTTCAGAGGACCCCCACGGA 62.683 60.000 0.00 0.00 34.64 4.69
10 11 1.562672 ATTTCAGAGGACCCCCACGG 61.563 60.000 0.00 0.00 37.81 4.94
11 12 1.134491 GTATTTCAGAGGACCCCCACG 60.134 57.143 0.00 0.00 33.88 4.94
12 13 1.134491 CGTATTTCAGAGGACCCCCAC 60.134 57.143 0.00 0.00 33.88 4.61
13 14 1.200519 CGTATTTCAGAGGACCCCCA 58.799 55.000 0.00 0.00 33.88 4.96
15 16 0.539986 TGCGTATTTCAGAGGACCCC 59.460 55.000 0.00 0.00 0.00 4.95
16 17 2.622064 ATGCGTATTTCAGAGGACCC 57.378 50.000 0.00 0.00 0.00 4.46
17 18 4.857588 CGTATATGCGTATTTCAGAGGACC 59.142 45.833 3.23 0.00 0.00 4.46
18 19 4.323868 GCGTATATGCGTATTTCAGAGGAC 59.676 45.833 14.75 0.00 0.00 3.85
19 20 4.217767 AGCGTATATGCGTATTTCAGAGGA 59.782 41.667 14.75 0.00 40.67 3.71
20 21 4.486090 AGCGTATATGCGTATTTCAGAGG 58.514 43.478 14.75 0.00 40.67 3.69
21 22 6.084277 TGTAGCGTATATGCGTATTTCAGAG 58.916 40.000 14.75 0.00 40.67 3.35
22 23 6.004408 TGTAGCGTATATGCGTATTTCAGA 57.996 37.500 14.75 0.00 40.67 3.27
23 24 6.871044 ATGTAGCGTATATGCGTATTTCAG 57.129 37.500 14.75 0.00 40.67 3.02
25 26 8.469902 GTGATATGTAGCGTATATGCGTATTTC 58.530 37.037 14.75 11.14 40.67 2.17
26 27 8.188799 AGTGATATGTAGCGTATATGCGTATTT 58.811 33.333 14.75 3.26 40.67 1.40
27 28 7.704271 AGTGATATGTAGCGTATATGCGTATT 58.296 34.615 14.75 4.03 40.67 1.89
28 29 7.226918 AGAGTGATATGTAGCGTATATGCGTAT 59.773 37.037 14.75 3.47 40.67 3.06
29 30 6.537660 AGAGTGATATGTAGCGTATATGCGTA 59.462 38.462 14.75 3.65 40.67 4.42
31 32 5.811588 AGAGTGATATGTAGCGTATATGCG 58.188 41.667 9.01 9.01 40.67 4.73
32 33 6.183360 TGGAGAGTGATATGTAGCGTATATGC 60.183 42.308 9.00 9.00 0.00 3.14
33 34 7.281100 TCTGGAGAGTGATATGTAGCGTATATG 59.719 40.741 0.00 0.00 0.00 1.78
34 35 7.281324 GTCTGGAGAGTGATATGTAGCGTATAT 59.719 40.741 0.00 0.00 0.00 0.86
35 36 6.594547 GTCTGGAGAGTGATATGTAGCGTATA 59.405 42.308 0.00 0.00 0.00 1.47
36 37 5.413213 GTCTGGAGAGTGATATGTAGCGTAT 59.587 44.000 0.00 0.00 0.00 3.06
37 38 4.755629 GTCTGGAGAGTGATATGTAGCGTA 59.244 45.833 0.00 0.00 0.00 4.42
38 39 3.566322 GTCTGGAGAGTGATATGTAGCGT 59.434 47.826 0.00 0.00 0.00 5.07
39 40 3.364465 CGTCTGGAGAGTGATATGTAGCG 60.364 52.174 0.00 0.00 0.00 4.26
40 41 3.566322 ACGTCTGGAGAGTGATATGTAGC 59.434 47.826 0.00 0.00 0.00 3.58
41 42 5.559225 CGAACGTCTGGAGAGTGATATGTAG 60.559 48.000 0.00 0.00 0.00 2.74
42 43 4.272748 CGAACGTCTGGAGAGTGATATGTA 59.727 45.833 0.00 0.00 0.00 2.29
44 45 3.622828 CGAACGTCTGGAGAGTGATATG 58.377 50.000 0.00 0.00 0.00 1.78
45 46 2.033550 GCGAACGTCTGGAGAGTGATAT 59.966 50.000 0.00 0.00 0.00 1.63
46 47 1.400846 GCGAACGTCTGGAGAGTGATA 59.599 52.381 0.00 0.00 0.00 2.15
48 49 1.579932 GCGAACGTCTGGAGAGTGA 59.420 57.895 0.00 0.00 0.00 3.41
50 51 0.322277 TAGGCGAACGTCTGGAGAGT 60.322 55.000 11.57 0.00 0.00 3.24
51 52 1.025812 ATAGGCGAACGTCTGGAGAG 58.974 55.000 11.57 0.00 0.00 3.20
52 53 1.945394 GTATAGGCGAACGTCTGGAGA 59.055 52.381 11.57 0.00 0.00 3.71
53 54 1.948145 AGTATAGGCGAACGTCTGGAG 59.052 52.381 11.57 0.00 0.00 3.86
54 55 1.945394 GAGTATAGGCGAACGTCTGGA 59.055 52.381 11.57 0.00 0.00 3.86
57 58 2.048444 TGGAGTATAGGCGAACGTCT 57.952 50.000 6.56 6.56 0.00 4.18
58 59 2.857592 TTGGAGTATAGGCGAACGTC 57.142 50.000 0.00 0.00 0.00 4.34
59 60 3.814005 AATTGGAGTATAGGCGAACGT 57.186 42.857 0.00 0.00 0.00 3.99
60 61 3.673809 GCTAATTGGAGTATAGGCGAACG 59.326 47.826 0.00 0.00 0.00 3.95
63 64 3.639561 TGTGCTAATTGGAGTATAGGCGA 59.360 43.478 0.00 0.00 0.00 5.54
65 66 5.997746 TGAATGTGCTAATTGGAGTATAGGC 59.002 40.000 0.00 0.00 0.00 3.93
66 67 6.148480 GCTGAATGTGCTAATTGGAGTATAGG 59.852 42.308 0.00 0.00 0.00 2.57
67 68 6.933521 AGCTGAATGTGCTAATTGGAGTATAG 59.066 38.462 0.00 0.00 39.21 1.31
69 70 5.530171 CAGCTGAATGTGCTAATTGGAGTAT 59.470 40.000 8.42 0.00 38.92 2.12
70 71 4.877823 CAGCTGAATGTGCTAATTGGAGTA 59.122 41.667 8.42 0.00 38.92 2.59
72 73 3.693085 ACAGCTGAATGTGCTAATTGGAG 59.307 43.478 23.35 0.00 38.92 3.86
73 74 3.689347 ACAGCTGAATGTGCTAATTGGA 58.311 40.909 23.35 0.00 38.92 3.53
74 75 4.418392 GAACAGCTGAATGTGCTAATTGG 58.582 43.478 23.35 0.00 38.92 3.16
76 77 4.002982 TCGAACAGCTGAATGTGCTAATT 58.997 39.130 23.35 0.00 38.92 1.40
77 78 3.599343 TCGAACAGCTGAATGTGCTAAT 58.401 40.909 23.35 0.00 38.92 1.73
78 79 3.038788 TCGAACAGCTGAATGTGCTAA 57.961 42.857 23.35 0.00 38.92 3.09
79 80 2.741759 TCGAACAGCTGAATGTGCTA 57.258 45.000 23.35 0.00 38.92 3.49
80 81 1.882912 TTCGAACAGCTGAATGTGCT 58.117 45.000 23.35 0.00 42.06 4.40
81 82 2.778659 GATTCGAACAGCTGAATGTGC 58.221 47.619 23.35 0.00 35.06 4.57
85 86 0.647410 CGCGATTCGAACAGCTGAAT 59.353 50.000 23.35 9.59 41.67 2.57
87 88 1.211709 TCGCGATTCGAACAGCTGA 59.788 52.632 23.35 16.18 45.36 4.26
88 89 3.767301 TCGCGATTCGAACAGCTG 58.233 55.556 13.48 13.48 45.36 4.24
96 97 2.837280 GCGTACCATCGCGATTCG 59.163 61.111 21.14 20.67 46.31 3.34
104 105 3.252484 GACGGTGCGCGTACCATC 61.252 66.667 38.96 32.84 40.89 3.51
107 108 4.842091 ATCGACGGTGCGCGTACC 62.842 66.667 33.25 33.25 37.37 3.34
108 109 3.604202 CATCGACGGTGCGCGTAC 61.604 66.667 19.68 19.68 0.00 3.67
113 114 3.842126 CAGTGCATCGACGGTGCG 61.842 66.667 26.56 10.18 45.37 5.34
114 115 4.152625 GCAGTGCATCGACGGTGC 62.153 66.667 25.86 25.86 42.81 5.01
115 116 3.842126 CGCAGTGCATCGACGGTG 61.842 66.667 16.83 3.04 0.00 4.94
116 117 4.357947 ACGCAGTGCATCGACGGT 62.358 61.111 16.83 0.00 42.51 4.83
136 137 2.978156 TTTTGGAGAAGTGCATCCCT 57.022 45.000 1.64 0.00 34.47 4.20
154 155 0.758734 GCTTGGTTTCCCTGCCTTTT 59.241 50.000 0.00 0.00 0.00 2.27
155 156 0.398381 TGCTTGGTTTCCCTGCCTTT 60.398 50.000 0.00 0.00 32.45 3.11
157 158 0.613012 GATGCTTGGTTTCCCTGCCT 60.613 55.000 0.00 0.00 32.45 4.75
158 159 1.607801 GGATGCTTGGTTTCCCTGCC 61.608 60.000 0.00 0.00 32.45 4.85
160 161 1.273327 GTTGGATGCTTGGTTTCCCTG 59.727 52.381 0.00 0.00 0.00 4.45
161 162 1.632589 GTTGGATGCTTGGTTTCCCT 58.367 50.000 0.00 0.00 0.00 4.20
162 163 0.608130 GGTTGGATGCTTGGTTTCCC 59.392 55.000 0.00 0.00 0.00 3.97
164 165 1.337167 GCTGGTTGGATGCTTGGTTTC 60.337 52.381 0.00 0.00 0.00 2.78
165 166 0.681175 GCTGGTTGGATGCTTGGTTT 59.319 50.000 0.00 0.00 0.00 3.27
166 167 1.187567 GGCTGGTTGGATGCTTGGTT 61.188 55.000 0.00 0.00 0.00 3.67
167 168 1.607467 GGCTGGTTGGATGCTTGGT 60.607 57.895 0.00 0.00 0.00 3.67
168 169 2.703798 CGGCTGGTTGGATGCTTGG 61.704 63.158 0.00 0.00 0.00 3.61
170 171 3.064324 GCGGCTGGTTGGATGCTT 61.064 61.111 0.00 0.00 0.00 3.91
173 174 4.431131 AGGGCGGCTGGTTGGATG 62.431 66.667 9.56 0.00 0.00 3.51
174 175 4.115199 GAGGGCGGCTGGTTGGAT 62.115 66.667 9.56 0.00 0.00 3.41
177 178 4.335647 AGTGAGGGCGGCTGGTTG 62.336 66.667 9.56 0.00 0.00 3.77
178 179 4.335647 CAGTGAGGGCGGCTGGTT 62.336 66.667 9.56 0.00 0.00 3.67
180 181 4.767255 GACAGTGAGGGCGGCTGG 62.767 72.222 9.56 0.00 34.79 4.85
181 182 4.767255 GGACAGTGAGGGCGGCTG 62.767 72.222 9.56 0.47 36.41 4.85
183 184 4.459089 GAGGACAGTGAGGGCGGC 62.459 72.222 0.00 0.00 0.00 6.53
184 185 3.775654 GGAGGACAGTGAGGGCGG 61.776 72.222 0.00 0.00 0.00 6.13
185 186 3.775654 GGGAGGACAGTGAGGGCG 61.776 72.222 0.00 0.00 0.00 6.13
186 187 3.775654 CGGGAGGACAGTGAGGGC 61.776 72.222 0.00 0.00 0.00 5.19
229 230 1.004440 GTTCGGTTCAGCCAGCTCT 60.004 57.895 0.00 0.00 36.97 4.09
237 238 1.009389 GCTCTCACGGTTCGGTTCAG 61.009 60.000 0.00 0.00 0.00 3.02
271 272 3.443976 GAAATTTTGAGCCGTGTTGTGT 58.556 40.909 0.00 0.00 0.00 3.72
302 304 4.899239 GTGGAGGCGGCGAGGATG 62.899 72.222 12.98 0.00 0.00 3.51
523 554 0.772124 TCTTTTCCCTCCAGCCAGGT 60.772 55.000 0.00 0.00 39.02 4.00
537 568 3.138283 TGGTGGGTGTGAAGAGATCTTTT 59.862 43.478 0.00 0.00 36.11 2.27
538 569 2.711009 TGGTGGGTGTGAAGAGATCTTT 59.289 45.455 0.00 0.00 36.11 2.52
540 571 1.625818 GTGGTGGGTGTGAAGAGATCT 59.374 52.381 0.00 0.00 0.00 2.75
545 576 0.542333 TTTCGTGGTGGGTGTGAAGA 59.458 50.000 0.00 0.00 0.00 2.87
597 656 3.659089 CTTGTGGTACCCGCTCCCG 62.659 68.421 10.07 0.00 34.70 5.14
598 657 1.259840 TACTTGTGGTACCCGCTCCC 61.260 60.000 10.07 0.00 34.70 4.30
600 659 0.457337 CGTACTTGTGGTACCCGCTC 60.457 60.000 10.07 0.00 45.76 5.03
601 660 0.895100 TCGTACTTGTGGTACCCGCT 60.895 55.000 10.07 0.00 45.76 5.52
602 661 0.174162 ATCGTACTTGTGGTACCCGC 59.826 55.000 10.07 2.81 45.76 6.13
636 701 3.976701 AAGGAGAACGCGGCCATGG 62.977 63.158 12.47 7.63 0.00 3.66
637 702 2.436646 AAGGAGAACGCGGCCATG 60.437 61.111 12.47 0.00 0.00 3.66
640 705 4.388499 TCCAAGGAGAACGCGGCC 62.388 66.667 12.47 6.24 0.00 6.13
642 707 2.970639 TCTCCAAGGAGAACGCGG 59.029 61.111 16.19 0.00 46.89 6.46
649 714 2.232452 ACATGTTCTCGTCTCCAAGGAG 59.768 50.000 9.90 9.90 43.21 3.69
651 716 2.738846 CAACATGTTCTCGTCTCCAAGG 59.261 50.000 8.48 0.00 0.00 3.61
652 717 2.158449 GCAACATGTTCTCGTCTCCAAG 59.842 50.000 8.48 0.00 0.00 3.61
653 718 2.143122 GCAACATGTTCTCGTCTCCAA 58.857 47.619 8.48 0.00 0.00 3.53
654 719 1.608025 GGCAACATGTTCTCGTCTCCA 60.608 52.381 8.48 0.00 0.00 3.86
655 720 1.079503 GGCAACATGTTCTCGTCTCC 58.920 55.000 8.48 0.00 0.00 3.71
657 722 0.396435 TGGGCAACATGTTCTCGTCT 59.604 50.000 8.48 0.00 39.74 4.18
658 723 1.398390 GATGGGCAACATGTTCTCGTC 59.602 52.381 8.48 10.61 40.72 4.20
660 725 0.374758 CGATGGGCAACATGTTCTCG 59.625 55.000 8.48 8.57 40.72 4.04
662 727 1.647545 CGCGATGGGCAACATGTTCT 61.648 55.000 8.48 0.00 43.84 3.01
663 728 1.226379 CGCGATGGGCAACATGTTC 60.226 57.895 8.48 3.87 43.84 3.18
665 730 3.133464 CCGCGATGGGCAACATGT 61.133 61.111 8.23 0.00 43.84 3.21
674 739 2.807895 AAACGACGACCGCGATGG 60.808 61.111 8.23 0.00 43.32 3.51
675 740 2.390288 CAAACGACGACCGCGATG 59.610 61.111 8.23 0.00 43.32 3.84
676 741 2.807895 CCAAACGACGACCGCGAT 60.808 61.111 8.23 0.00 43.32 4.58
679 744 3.408851 GTCCCAAACGACGACCGC 61.409 66.667 0.00 0.00 43.32 5.68
680 745 2.735857 GGTCCCAAACGACGACCG 60.736 66.667 0.00 0.00 45.44 4.79
681 746 2.357881 GGGTCCCAAACGACGACC 60.358 66.667 1.78 0.00 44.50 4.79
682 747 2.357881 GGGGTCCCAAACGACGAC 60.358 66.667 10.98 0.00 33.30 4.34
683 748 2.843411 TGGGGTCCCAAACGACGA 60.843 61.111 10.98 0.00 44.12 4.20
713 778 4.475135 GCTCCGGCAGGTCCTTCC 62.475 72.222 1.81 0.00 39.05 3.46
714 779 4.475135 GGCTCCGGCAGGTCCTTC 62.475 72.222 1.81 0.00 40.87 3.46
731 796 4.293648 TGTCGTGCACCAGGTCGG 62.294 66.667 12.15 0.00 42.50 4.79
733 798 2.154798 TAGCTGTCGTGCACCAGGTC 62.155 60.000 24.76 10.55 39.83 3.85
735 800 1.086067 CATAGCTGTCGTGCACCAGG 61.086 60.000 20.34 4.76 34.99 4.45
736 801 1.086067 CCATAGCTGTCGTGCACCAG 61.086 60.000 12.15 14.59 34.99 4.00
738 803 2.464459 GCCATAGCTGTCGTGCACC 61.464 63.158 12.15 0.00 35.50 5.01
739 804 2.802667 CGCCATAGCTGTCGTGCAC 61.803 63.158 6.82 6.82 36.60 4.57
740 805 2.509111 CGCCATAGCTGTCGTGCA 60.509 61.111 0.00 0.00 36.60 4.57
741 806 3.929948 GCGCCATAGCTGTCGTGC 61.930 66.667 0.00 0.00 36.60 5.34
743 808 4.873129 CGGCGCCATAGCTGTCGT 62.873 66.667 28.98 0.00 38.63 4.34
799 864 4.424711 GAAGGGGCCCGCATGACA 62.425 66.667 18.95 0.00 0.00 3.58
813 878 1.956477 CCAACAAAGACCACCTGGAAG 59.044 52.381 0.00 0.00 38.94 3.46
814 879 2.026905 GCCAACAAAGACCACCTGGAA 61.027 52.381 0.00 0.00 38.94 3.53
816 881 1.463553 GGCCAACAAAGACCACCTGG 61.464 60.000 0.00 0.00 42.17 4.45
817 882 0.468029 AGGCCAACAAAGACCACCTG 60.468 55.000 5.01 0.00 0.00 4.00
818 883 0.468029 CAGGCCAACAAAGACCACCT 60.468 55.000 5.01 0.00 0.00 4.00
820 885 1.463553 CCCAGGCCAACAAAGACCAC 61.464 60.000 5.01 0.00 0.00 4.16
821 886 1.152567 CCCAGGCCAACAAAGACCA 60.153 57.895 5.01 0.00 0.00 4.02
822 887 2.574018 GCCCAGGCCAACAAAGACC 61.574 63.158 5.01 0.00 34.56 3.85
823 888 1.187567 ATGCCCAGGCCAACAAAGAC 61.188 55.000 5.01 0.00 41.09 3.01
825 890 1.294138 CATGCCCAGGCCAACAAAG 59.706 57.895 5.01 0.00 41.09 2.77
828 893 4.700448 CCCATGCCCAGGCCAACA 62.700 66.667 5.01 0.00 41.09 3.33
829 894 4.702274 ACCCATGCCCAGGCCAAC 62.702 66.667 5.01 0.00 41.09 3.77
830 895 4.700448 CACCCATGCCCAGGCCAA 62.700 66.667 5.01 0.00 41.09 4.52
840 905 2.094390 CCAGTCAAAATCTGCACCCATG 60.094 50.000 0.00 0.00 0.00 3.66
841 906 2.173519 CCAGTCAAAATCTGCACCCAT 58.826 47.619 0.00 0.00 0.00 4.00
842 907 1.144708 TCCAGTCAAAATCTGCACCCA 59.855 47.619 0.00 0.00 0.00 4.51
843 908 1.909700 TCCAGTCAAAATCTGCACCC 58.090 50.000 0.00 0.00 0.00 4.61
844 909 3.367703 CCATTCCAGTCAAAATCTGCACC 60.368 47.826 0.00 0.00 0.00 5.01
845 910 3.256631 ACCATTCCAGTCAAAATCTGCAC 59.743 43.478 0.00 0.00 0.00 4.57
846 911 3.499338 ACCATTCCAGTCAAAATCTGCA 58.501 40.909 0.00 0.00 0.00 4.41
849 914 3.057315 CGCAACCATTCCAGTCAAAATCT 60.057 43.478 0.00 0.00 0.00 2.40
850 915 3.244976 CGCAACCATTCCAGTCAAAATC 58.755 45.455 0.00 0.00 0.00 2.17
851 916 2.627699 ACGCAACCATTCCAGTCAAAAT 59.372 40.909 0.00 0.00 0.00 1.82
852 917 2.028130 ACGCAACCATTCCAGTCAAAA 58.972 42.857 0.00 0.00 0.00 2.44
853 918 1.686355 ACGCAACCATTCCAGTCAAA 58.314 45.000 0.00 0.00 0.00 2.69
854 919 1.336440 CAACGCAACCATTCCAGTCAA 59.664 47.619 0.00 0.00 0.00 3.18
857 922 1.659794 GCAACGCAACCATTCCAGT 59.340 52.632 0.00 0.00 0.00 4.00
927 4593 2.156891 CCAGTGACGGTTATCAAACACG 59.843 50.000 0.00 0.00 37.34 4.49
941 4613 4.021925 AAGGCTCGCCCCAGTGAC 62.022 66.667 3.92 0.00 36.58 3.67
1137 4816 3.075005 AGGATAGCGGCACCGTGT 61.075 61.111 11.27 1.12 42.09 4.49
1173 4852 2.363680 CACATGTGCAAACCCCAAACTA 59.636 45.455 13.94 0.00 0.00 2.24
1404 5086 3.070159 CGCTCTTCCATATCTCCTTCCAA 59.930 47.826 0.00 0.00 0.00 3.53
1501 5206 9.054922 ACATTTGTTCCCTAAATCACAAAAATG 57.945 29.630 0.80 0.00 41.26 2.32
1502 5207 9.625747 AACATTTGTTCCCTAAATCACAAAAAT 57.374 25.926 0.80 0.00 41.26 1.82
1825 5983 5.036916 ACCTAATTCATCACAAGACCCCTA 58.963 41.667 0.00 0.00 0.00 3.53
1846 6004 4.489306 AAAGGGCTACTGAATAGTGACC 57.511 45.455 0.00 0.00 37.78 4.02
1906 6202 2.019984 CCTGGGCAAACTATCAAGCTC 58.980 52.381 0.00 0.00 0.00 4.09
2030 6361 3.502123 AATGGACAGAAAAACCTCCGA 57.498 42.857 0.00 0.00 0.00 4.55
2036 6367 8.877808 AGAATTCTCAAAATGGACAGAAAAAC 57.122 30.769 0.88 0.00 0.00 2.43
2055 6386 4.579869 TGGGAGAGCAAACTGTAGAATTC 58.420 43.478 0.00 0.00 0.00 2.17
2122 6460 8.097038 TCTAGACATGCCATTATTATCAACTCC 58.903 37.037 0.00 0.00 0.00 3.85
2150 6488 4.190001 TCTAGAGCGAGACAAACGACTAT 58.810 43.478 0.00 0.00 0.00 2.12
2181 6519 2.223735 GCCTGCAGAAACCATCATCATG 60.224 50.000 17.39 0.00 0.00 3.07
2200 6538 1.484240 AGACAGATTAGTGAGCCAGCC 59.516 52.381 0.00 0.00 0.00 4.85
2303 6666 1.002087 GCCCCATATCTGTAGTTCCCG 59.998 57.143 0.00 0.00 0.00 5.14
2365 6730 2.880890 CTGCAGTTTTGTGGAGCTACTT 59.119 45.455 5.25 0.00 0.00 2.24
2404 6774 6.148480 GGCCAAACATATGCAACAAATAACAA 59.852 34.615 1.58 0.00 0.00 2.83
2405 6775 5.641209 GGCCAAACATATGCAACAAATAACA 59.359 36.000 1.58 0.00 0.00 2.41
2496 6870 9.419297 CAGTCTACTAGTATGTGCACTTAAAAA 57.581 33.333 19.41 0.00 0.00 1.94
2497 6871 7.544566 GCAGTCTACTAGTATGTGCACTTAAAA 59.455 37.037 19.41 6.74 0.00 1.52
2498 6872 7.033791 GCAGTCTACTAGTATGTGCACTTAAA 58.966 38.462 19.41 7.08 0.00 1.52
2499 6873 6.152154 TGCAGTCTACTAGTATGTGCACTTAA 59.848 38.462 21.33 0.00 34.65 1.85
2500 6874 5.650703 TGCAGTCTACTAGTATGTGCACTTA 59.349 40.000 21.33 13.53 34.65 2.24
2501 6875 4.462834 TGCAGTCTACTAGTATGTGCACTT 59.537 41.667 21.33 14.68 34.65 3.16
2502 6876 4.017126 TGCAGTCTACTAGTATGTGCACT 58.983 43.478 21.33 6.22 34.65 4.40
2503 6877 4.371855 TGCAGTCTACTAGTATGTGCAC 57.628 45.455 21.33 10.75 34.65 4.57
2504 6878 5.105351 ACATTGCAGTCTACTAGTATGTGCA 60.105 40.000 21.33 21.33 37.66 4.57
2505 6879 5.352284 ACATTGCAGTCTACTAGTATGTGC 58.648 41.667 17.98 17.98 0.00 4.57
2506 6880 6.800543 AGACATTGCAGTCTACTAGTATGTG 58.199 40.000 6.82 2.82 46.52 3.21
2559 6933 0.669619 TTGCATTGCACTGTGACCAG 59.330 50.000 11.66 0.00 44.68 4.00
2566 6944 3.580731 TGATCATTGTTGCATTGCACTG 58.419 40.909 11.66 7.05 38.71 3.66
2619 6997 7.436933 AGAAGGAAAATCTGTGAAATCAAACC 58.563 34.615 0.00 0.00 0.00 3.27


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

AutoCloner maintained by Alex Coulton.