Multiple sequence alignment - TraesCS7B01G093200

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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 TraesCS7B01G093200 chr7B 100.000 4037 0 0 1 4037 106861430 106857394 0.000000e+00 7456.0
1 TraesCS7B01G093200 chr7B 83.351 931 130 20 2154 3068 114394810 114395731 0.000000e+00 837.0
2 TraesCS7B01G093200 chr7B 82.549 659 104 8 2384 3032 498086225 498085568 1.630000e-158 569.0
3 TraesCS7B01G093200 chr7B 82.781 453 56 13 1617 2065 114394231 114394665 6.330000e-103 385.0
4 TraesCS7B01G093200 chr7B 89.313 262 24 4 1248 1506 114393891 114394151 3.890000e-85 326.0
5 TraesCS7B01G093200 chr7B 84.400 250 20 15 3586 3820 106827141 106826896 1.130000e-55 228.0
6 TraesCS7B01G093200 chr7B 91.667 60 3 2 3250 3307 641143330 641143271 9.300000e-12 82.4
7 TraesCS7B01G093200 chr7D 93.420 2067 80 25 1220 3247 141560976 141563025 0.000000e+00 3013.0
8 TraesCS7B01G093200 chr7D 83.704 945 132 16 2154 3083 152219358 152220295 0.000000e+00 872.0
9 TraesCS7B01G093200 chr7D 85.570 596 59 14 3311 3888 141563019 141563605 2.080000e-167 599.0
10 TraesCS7B01G093200 chr7D 90.314 382 10 7 793 1157 141560600 141560971 3.650000e-130 475.0
11 TraesCS7B01G093200 chr7D 84.410 449 52 8 1617 2065 152218768 152219198 3.730000e-115 425.0
12 TraesCS7B01G093200 chr7D 92.150 293 18 3 252 541 141559854 141560144 3.760000e-110 409.0
13 TraesCS7B01G093200 chr7D 89.683 252 25 1 1256 1506 152218437 152218688 1.810000e-83 320.0
14 TraesCS7B01G093200 chr7D 84.375 352 19 15 3534 3851 141572181 141572530 3.030000e-81 313.0
15 TraesCS7B01G093200 chr7D 85.375 253 15 6 567 802 141560203 141560450 4.030000e-60 243.0
16 TraesCS7B01G093200 chr7D 88.824 170 16 2 255 422 141649074 141648906 5.290000e-49 206.0
17 TraesCS7B01G093200 chr7D 80.296 203 25 6 3059 3249 141571987 141572186 5.440000e-29 139.0
18 TraesCS7B01G093200 chr7D 93.103 58 3 1 3251 3307 220211237 220211180 2.590000e-12 84.2
19 TraesCS7B01G093200 chr7D 92.453 53 4 0 41 93 141559525 141559577 4.330000e-10 76.8
20 TraesCS7B01G093200 chr7D 97.143 35 0 1 3878 3911 141565109 141565143 1.570000e-04 58.4
21 TraesCS7B01G093200 chr7A 90.108 1395 68 36 693 2072 144172498 144171159 0.000000e+00 1748.0
22 TraesCS7B01G093200 chr7A 94.266 1151 43 12 2115 3248 144171146 144170002 0.000000e+00 1738.0
23 TraesCS7B01G093200 chr7A 84.667 900 108 14 2154 3038 152833545 152834429 0.000000e+00 870.0
24 TraesCS7B01G093200 chr7A 81.633 833 93 28 1243 2065 152832541 152833323 1.580000e-178 636.0
25 TraesCS7B01G093200 chr7A 82.353 340 28 14 3533 3851 144137217 144136889 2.390000e-67 267.0
26 TraesCS7B01G093200 chr7A 92.308 143 11 0 565 707 144172656 144172514 1.900000e-48 204.0
27 TraesCS7B01G093200 chr7A 88.535 157 10 5 3763 3911 144168148 144167992 2.480000e-42 183.0
28 TraesCS7B01G093200 chr7A 88.667 150 7 6 3632 3772 144168446 144168298 1.490000e-39 174.0
29 TraesCS7B01G093200 chr7A 90.984 122 6 2 3916 4037 144167766 144167650 4.180000e-35 159.0
30 TraesCS7B01G093200 chr7A 95.745 47 1 1 3558 3604 144168491 144168446 1.560000e-09 75.0
31 TraesCS7B01G093200 chr2D 88.739 666 71 4 2390 3052 574656799 574657463 0.000000e+00 811.0
32 TraesCS7B01G093200 chr2D 86.408 309 40 2 2732 3039 574979053 574978746 1.800000e-88 337.0
33 TraesCS7B01G093200 chr2D 89.041 219 24 0 1835 2053 575162109 575161891 5.140000e-69 272.0
34 TraesCS7B01G093200 chr2D 86.498 237 31 1 1265 1500 574655782 574656018 4.000000e-65 259.0
35 TraesCS7B01G093200 chr2D 86.184 152 17 2 2157 2304 574656656 574656807 1.160000e-35 161.0
36 TraesCS7B01G093200 chr2D 91.262 103 8 1 1831 1933 574656109 574656210 5.440000e-29 139.0
37 TraesCS7B01G093200 chr2B 88.438 666 73 4 2390 3052 690931108 690931772 0.000000e+00 800.0
38 TraesCS7B01G093200 chr2B 90.826 218 20 0 1835 2052 690930751 690930968 3.950000e-75 292.0
39 TraesCS7B01G093200 chr2B 88.608 237 26 1 1265 1500 690930420 690930656 1.840000e-73 287.0
40 TraesCS7B01G093200 chr2A 88.497 652 69 3 2390 3038 713016598 713017246 0.000000e+00 784.0
41 TraesCS7B01G093200 chr2A 81.028 506 73 13 2477 2961 713204241 713203738 8.190000e-102 381.0
42 TraesCS7B01G093200 chr2A 92.694 219 16 0 1834 2052 713016240 713016458 2.340000e-82 316.0
43 TraesCS7B01G093200 chr2A 88.608 237 26 1 1265 1500 713015910 713016146 1.840000e-73 287.0
44 TraesCS7B01G093200 chr2A 94.643 56 2 1 3251 3306 155072900 155072954 7.190000e-13 86.1
45 TraesCS7B01G093200 chr5A 93.548 62 3 1 3246 3306 513230899 513230960 1.550000e-14 91.6
46 TraesCS7B01G093200 chr4A 93.220 59 2 2 3250 3308 664228291 664228235 7.190000e-13 86.1
47 TraesCS7B01G093200 chr3A 94.643 56 2 1 3250 3304 686989695 686989750 7.190000e-13 86.1
48 TraesCS7B01G093200 chr5D 92.982 57 3 1 3252 3307 319144772 319144716 9.300000e-12 82.4


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 TraesCS7B01G093200 chr7B 106857394 106861430 4036 True 7456.000000 7456 100.000000 1 4037 1 chr7B.!!$R2 4036
1 TraesCS7B01G093200 chr7B 498085568 498086225 657 True 569.000000 569 82.549000 2384 3032 1 chr7B.!!$R3 648
2 TraesCS7B01G093200 chr7B 114393891 114395731 1840 False 516.000000 837 85.148333 1248 3068 3 chr7B.!!$F1 1820
3 TraesCS7B01G093200 chr7D 141559525 141565143 5618 False 696.314286 3013 90.917857 41 3911 7 chr7D.!!$F1 3870
4 TraesCS7B01G093200 chr7D 152218437 152220295 1858 False 539.000000 872 85.932333 1256 3083 3 chr7D.!!$F3 1827
5 TraesCS7B01G093200 chr7D 141571987 141572530 543 False 226.000000 313 82.335500 3059 3851 2 chr7D.!!$F2 792
6 TraesCS7B01G093200 chr7A 152832541 152834429 1888 False 753.000000 870 83.150000 1243 3038 2 chr7A.!!$F1 1795
7 TraesCS7B01G093200 chr7A 144167650 144172656 5006 True 611.571429 1748 91.516143 565 4037 7 chr7A.!!$R2 3472
8 TraesCS7B01G093200 chr2D 574655782 574657463 1681 False 342.500000 811 88.170750 1265 3052 4 chr2D.!!$F1 1787
9 TraesCS7B01G093200 chr2B 690930420 690931772 1352 False 459.666667 800 89.290667 1265 3052 3 chr2B.!!$F1 1787
10 TraesCS7B01G093200 chr2A 713015910 713017246 1336 False 462.333333 784 89.933000 1265 3038 3 chr2A.!!$F2 1773
11 TraesCS7B01G093200 chr2A 713203738 713204241 503 True 381.000000 381 81.028000 2477 2961 1 chr2A.!!$R1 484

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
271 408 0.106167 ACTAGCTATCAGCCGGTCCA 60.106 55.0 1.9 0.0 43.77 4.02 F
1160 1564 0.535102 CTCCCTCTCTCTCTCGCTCC 60.535 65.0 0.0 0.0 0.00 4.70 F
1225 1629 0.166814 GCGTTGTGCAGACCAATCTC 59.833 55.0 0.0 0.0 45.45 2.75 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1205 1609 0.250467 AGATTGGTCTGCACAACGCT 60.250 50.000 0.00 0.0 43.06 5.07 R
2334 3275 0.743345 GACCGTGACTTATGGGTGCC 60.743 60.000 0.00 0.0 39.98 5.01 R
3195 4180 1.066858 GGAGACTCAACGGCATCAAGA 60.067 52.381 4.53 0.0 0.00 3.02 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
48 49 3.964909 AGTCTTAAAAGGCTTTGCGTTG 58.035 40.909 14.19 3.16 37.85 4.10
83 84 7.715249 AGTTGCTCTTAACATGTCTTCACTTTA 59.285 33.333 0.00 0.00 33.02 1.85
121 129 3.038352 CACGATTGTGCGGATTACAAG 57.962 47.619 0.00 0.00 40.92 3.16
122 130 2.415168 CACGATTGTGCGGATTACAAGT 59.585 45.455 0.00 0.00 40.92 3.16
123 131 2.671396 ACGATTGTGCGGATTACAAGTC 59.329 45.455 0.00 0.00 40.92 3.01
124 132 2.670905 CGATTGTGCGGATTACAAGTCA 59.329 45.455 0.00 0.00 40.92 3.41
125 133 3.309682 CGATTGTGCGGATTACAAGTCAT 59.690 43.478 0.00 0.00 40.92 3.06
126 134 4.506288 CGATTGTGCGGATTACAAGTCATA 59.494 41.667 0.00 0.00 40.92 2.15
131 139 3.621268 TGCGGATTACAAGTCATAGCAAC 59.379 43.478 0.00 0.00 0.00 4.17
132 140 3.302480 GCGGATTACAAGTCATAGCAACG 60.302 47.826 0.00 0.00 0.00 4.10
133 141 3.863424 CGGATTACAAGTCATAGCAACGT 59.137 43.478 0.00 0.00 0.00 3.99
144 152 3.454574 GCAACGTGCATGCATGTG 58.545 55.556 38.72 31.10 44.45 3.21
145 153 1.372004 GCAACGTGCATGCATGTGT 60.372 52.632 38.72 26.78 44.45 3.72
147 155 0.730155 CAACGTGCATGCATGTGTCC 60.730 55.000 38.72 18.47 44.45 4.02
148 156 1.865788 AACGTGCATGCATGTGTCCC 61.866 55.000 38.72 17.77 44.45 4.46
150 158 2.751036 TGCATGCATGTGTCCCCG 60.751 61.111 26.79 0.03 0.00 5.73
151 159 4.197498 GCATGCATGTGTCCCCGC 62.197 66.667 26.79 7.09 0.00 6.13
152 160 2.751036 CATGCATGTGTCCCCGCA 60.751 61.111 18.91 0.00 39.01 5.69
153 161 2.035469 ATGCATGTGTCCCCGCAA 59.965 55.556 0.00 0.00 38.01 4.85
154 162 1.606025 ATGCATGTGTCCCCGCAAA 60.606 52.632 0.00 0.00 38.01 3.68
155 163 1.184322 ATGCATGTGTCCCCGCAAAA 61.184 50.000 0.00 0.00 38.01 2.44
156 164 1.365633 GCATGTGTCCCCGCAAAAA 59.634 52.632 0.00 0.00 34.15 1.94
192 200 2.010145 TGTGGATGCGTTTAGAGAGC 57.990 50.000 0.00 0.00 0.00 4.09
193 201 1.275010 TGTGGATGCGTTTAGAGAGCA 59.725 47.619 0.00 0.00 45.46 4.26
194 202 1.929836 GTGGATGCGTTTAGAGAGCAG 59.070 52.381 0.00 0.00 44.55 4.24
197 205 0.807667 ATGCGTTTAGAGAGCAGGCG 60.808 55.000 0.00 0.00 44.55 5.52
224 239 2.274747 CGCTACGTACACGCTACGC 61.275 63.158 11.96 0.00 43.97 4.42
228 243 0.452618 TACGTACACGCTACGCACAC 60.453 55.000 11.96 0.00 43.97 3.82
239 254 2.864968 CTACGCACACCAAGACTAGTC 58.135 52.381 15.41 15.41 0.00 2.59
243 258 3.257375 ACGCACACCAAGACTAGTCAATA 59.743 43.478 24.44 0.00 0.00 1.90
244 259 3.859961 CGCACACCAAGACTAGTCAATAG 59.140 47.826 24.44 12.22 37.53 1.73
249 264 7.251994 CACACCAAGACTAGTCAATAGTACTC 58.748 42.308 24.44 0.00 45.06 2.59
271 408 0.106167 ACTAGCTATCAGCCGGTCCA 60.106 55.000 1.90 0.00 43.77 4.02
279 416 2.047274 AGCCGGTCCATGTTCACG 60.047 61.111 1.90 0.00 0.00 4.35
281 418 1.964373 GCCGGTCCATGTTCACGTT 60.964 57.895 1.90 0.00 0.00 3.99
287 424 1.806542 GTCCATGTTCACGTTGCAGAT 59.193 47.619 0.00 0.00 0.00 2.90
303 440 3.095898 GATAGCGGCCGTGTGTTGC 62.096 63.158 28.70 7.85 0.00 4.17
339 476 7.062957 TCTTTCTCCTCCAGTTTCAGAAAAAT 58.937 34.615 0.00 0.00 33.72 1.82
341 478 8.760980 TTTCTCCTCCAGTTTCAGAAAAATAA 57.239 30.769 0.00 0.00 31.64 1.40
342 479 8.940397 TTCTCCTCCAGTTTCAGAAAAATAAT 57.060 30.769 0.00 0.00 0.00 1.28
366 503 3.259625 AGAAGAAAACTCTTCCTCCTCCG 59.740 47.826 10.51 0.00 45.25 4.63
372 509 2.756283 CTTCCTCCTCCGAGCGGT 60.756 66.667 8.96 0.00 34.49 5.68
423 560 4.778415 CCGCGGACTCTGTGACGG 62.778 72.222 24.07 0.00 0.00 4.79
437 574 1.450134 GACGGAGACATGGCATGCA 60.450 57.895 26.70 6.13 0.00 3.96
448 585 3.817084 ACATGGCATGCATGTCACTATAC 59.183 43.478 34.69 11.83 46.22 1.47
451 588 2.483876 GCATGCATGTCACTATACGGT 58.516 47.619 26.79 0.00 0.00 4.83
522 662 6.849085 ACAGTCAGATGTAGTCATTCTCTT 57.151 37.500 0.00 0.00 34.06 2.85
526 666 8.655092 CAGTCAGATGTAGTCATTCTCTTTTTC 58.345 37.037 0.00 0.00 34.06 2.29
527 667 8.592809 AGTCAGATGTAGTCATTCTCTTTTTCT 58.407 33.333 0.00 0.00 34.06 2.52
528 668 8.868916 GTCAGATGTAGTCATTCTCTTTTTCTC 58.131 37.037 0.00 0.00 34.06 2.87
529 669 8.811017 TCAGATGTAGTCATTCTCTTTTTCTCT 58.189 33.333 0.00 0.00 34.06 3.10
530 670 9.434420 CAGATGTAGTCATTCTCTTTTTCTCTT 57.566 33.333 0.00 0.00 34.06 2.85
611 804 7.478667 CGTTCTGATCTTTTAAATCCGAAACTG 59.521 37.037 0.00 0.00 31.13 3.16
626 819 4.261405 CCGAAACTGGCAAAAACTGTATCA 60.261 41.667 0.00 0.00 0.00 2.15
636 829 7.984050 TGGCAAAAACTGTATCAATCTTTTTGA 59.016 29.630 14.86 0.00 41.31 2.69
647 840 5.560724 TCAATCTTTTTGATCGAGTTCCCT 58.439 37.500 0.00 0.00 33.57 4.20
707 900 8.824783 TGGCCCTAACTAACTAACAACTATAAA 58.175 33.333 0.00 0.00 0.00 1.40
745 969 6.015180 CCGGGATTAACCAATCAATCATCAAT 60.015 38.462 0.00 0.00 42.10 2.57
746 970 7.086376 CGGGATTAACCAATCAATCATCAATC 58.914 38.462 0.29 0.00 42.10 2.67
747 971 7.255555 CGGGATTAACCAATCAATCATCAATCA 60.256 37.037 0.29 0.00 42.10 2.57
748 972 8.423349 GGGATTAACCAATCAATCATCAATCAA 58.577 33.333 0.29 0.00 42.10 2.57
749 973 9.820725 GGATTAACCAATCAATCATCAATCAAA 57.179 29.630 0.29 0.00 42.10 2.69
894 1280 4.467084 GGCAACTGGGCCGATCGA 62.467 66.667 18.66 0.00 45.40 3.59
895 1281 2.203070 GCAACTGGGCCGATCGAT 60.203 61.111 18.66 0.00 0.00 3.59
904 1290 0.671781 GGCCGATCGATTCCATCCAG 60.672 60.000 18.66 0.00 0.00 3.86
924 1310 9.853177 CATCCAGGAAGTAATAAAGGAGTAAAT 57.147 33.333 0.00 0.00 0.00 1.40
926 1312 8.202137 TCCAGGAAGTAATAAAGGAGTAAATCG 58.798 37.037 0.00 0.00 0.00 3.34
927 1313 7.441458 CCAGGAAGTAATAAAGGAGTAAATCGG 59.559 40.741 0.00 0.00 0.00 4.18
1138 1542 2.130073 GACAGGCAAGCCAAACCGAC 62.130 60.000 14.40 0.00 38.92 4.79
1141 1545 3.680786 GCAAGCCAAACCGACCCC 61.681 66.667 0.00 0.00 0.00 4.95
1144 1548 3.205851 AAGCCAAACCGACCCCTCC 62.206 63.158 0.00 0.00 0.00 4.30
1146 1550 2.933834 CCAAACCGACCCCTCCCT 60.934 66.667 0.00 0.00 0.00 4.20
1150 1554 2.108208 AAACCGACCCCTCCCTCTCT 62.108 60.000 0.00 0.00 0.00 3.10
1158 1562 1.531748 CCTCCCTCTCTCTCTCGCT 59.468 63.158 0.00 0.00 0.00 4.93
1160 1564 0.535102 CTCCCTCTCTCTCTCGCTCC 60.535 65.000 0.00 0.00 0.00 4.70
1166 1570 0.880278 CTCTCTCTCGCTCCCTCTCG 60.880 65.000 0.00 0.00 0.00 4.04
1167 1571 2.515057 TCTCTCGCTCCCTCTCGC 60.515 66.667 0.00 0.00 0.00 5.03
1173 1577 2.261671 GCTCCCTCTCGCGACAAA 59.738 61.111 3.71 0.00 0.00 2.83
1174 1578 1.153549 GCTCCCTCTCGCGACAAAT 60.154 57.895 3.71 0.00 0.00 2.32
1175 1579 1.148759 GCTCCCTCTCGCGACAAATC 61.149 60.000 3.71 0.00 0.00 2.17
1184 1588 4.851114 CGACAAATCGCGCCGCTG 62.851 66.667 7.78 0.07 42.43 5.18
1185 1589 4.520846 GACAAATCGCGCCGCTGG 62.521 66.667 7.78 0.00 0.00 4.85
1225 1629 0.166814 GCGTTGTGCAGACCAATCTC 59.833 55.000 0.00 0.00 45.45 2.75
1227 1632 0.798776 GTTGTGCAGACCAATCTCGG 59.201 55.000 0.00 0.00 30.42 4.63
1228 1633 0.321564 TTGTGCAGACCAATCTCGGG 60.322 55.000 0.00 0.00 30.42 5.14
1241 1646 4.065088 CAATCTCGGGTTTCTTGACTGAA 58.935 43.478 0.00 0.00 0.00 3.02
1242 1647 4.559862 ATCTCGGGTTTCTTGACTGAAT 57.440 40.909 0.00 0.00 0.00 2.57
1507 1913 1.452651 TCCCTCCTAGGTACGCACG 60.453 63.158 9.08 0.00 31.93 5.34
1509 1915 2.024305 CTCCTAGGTACGCACGCG 59.976 66.667 9.08 10.36 46.03 6.01
1510 1916 3.465296 CTCCTAGGTACGCACGCGG 62.465 68.421 16.70 0.00 44.69 6.46
1536 1942 2.750657 CCTCCACCCCATGCCTCTC 61.751 68.421 0.00 0.00 0.00 3.20
1661 2071 1.585006 CGGCCTCTGTCAGTACGTT 59.415 57.895 0.00 0.00 0.00 3.99
1712 2122 2.785540 TTACAGCATCCATCAGTGCA 57.214 45.000 0.00 0.00 43.63 4.57
1724 2140 0.667487 TCAGTGCAGCGTAAGTCAGC 60.667 55.000 0.00 0.00 41.68 4.26
1725 2141 0.668706 CAGTGCAGCGTAAGTCAGCT 60.669 55.000 0.00 0.00 45.74 4.24
1953 2706 0.253347 TCTTCTCCCAGCTCCCCAAT 60.253 55.000 0.00 0.00 0.00 3.16
2093 3018 4.037208 CCCACCAAGAGATCAATGCATTAC 59.963 45.833 12.53 6.95 0.00 1.89
2134 3059 4.282068 GTGTAACTTTGTGTCTGCATGTG 58.718 43.478 0.00 0.00 0.00 3.21
2135 3060 3.944650 TGTAACTTTGTGTCTGCATGTGT 59.055 39.130 0.00 0.00 0.00 3.72
2181 3106 1.613255 CCTACGGGCAAGACAACCATT 60.613 52.381 0.00 0.00 0.00 3.16
2202 3127 1.586028 CGGCACTCAAATTGGGGTG 59.414 57.895 8.64 8.64 0.00 4.61
2302 3230 9.057089 CCATGGTTCTTATAGAAATTCAGGTAC 57.943 37.037 2.57 0.00 35.75 3.34
2360 3306 4.957954 ACCCATAAGTCACGGTCACTAATA 59.042 41.667 0.00 0.00 0.00 0.98
2377 3323 8.129840 GTCACTAATAGCGTCTATATATGTGGG 58.870 40.741 0.00 0.00 0.00 4.61
2704 3654 1.968017 TTCGTCGTCCGGCAGTACT 60.968 57.895 0.00 0.00 37.11 2.73
2745 3704 2.113860 GCCTCAACATGTTCAGGCTA 57.886 50.000 37.60 7.90 46.88 3.93
2961 3932 2.028484 TGCTTCGTGGTCACCGTC 59.972 61.111 0.00 0.00 0.00 4.79
3038 4009 3.127895 CCGTTCAAGACCAAGTTGTGAAA 59.872 43.478 7.89 0.00 30.49 2.69
3039 4010 4.202010 CCGTTCAAGACCAAGTTGTGAAAT 60.202 41.667 7.89 0.00 30.49 2.17
3089 4060 9.705290 AATTCTTTGACTTGTGTTTGTTTAAGT 57.295 25.926 0.00 0.00 36.18 2.24
3153 4130 7.660112 TGTGTGCTTGATGTTTTTAGATGAAT 58.340 30.769 0.00 0.00 0.00 2.57
3154 4131 7.595875 TGTGTGCTTGATGTTTTTAGATGAATG 59.404 33.333 0.00 0.00 0.00 2.67
3160 4137 9.880157 CTTGATGTTTTTAGATGAATGGGAAAT 57.120 29.630 0.00 0.00 0.00 2.17
3161 4138 9.874205 TTGATGTTTTTAGATGAATGGGAAATC 57.126 29.630 0.00 0.00 0.00 2.17
3185 4170 5.104360 CCAATGGATGGTAGGACTATATGGG 60.104 48.000 0.00 0.00 44.85 4.00
3234 4219 1.009078 CGTTCCATGCATGATCACGT 58.991 50.000 28.31 0.00 0.00 4.49
3235 4220 1.267682 CGTTCCATGCATGATCACGTG 60.268 52.381 28.31 9.94 36.24 4.49
3236 4221 2.009051 GTTCCATGCATGATCACGTGA 58.991 47.619 28.31 22.48 35.25 4.35
3237 4222 1.944032 TCCATGCATGATCACGTGAG 58.056 50.000 28.31 11.20 35.25 3.51
3239 4224 1.865340 CCATGCATGATCACGTGAGAG 59.135 52.381 28.31 13.68 35.25 3.20
3241 4226 3.391049 CATGCATGATCACGTGAGAGAT 58.609 45.455 24.41 12.11 44.19 2.75
3242 4227 3.531934 TGCATGATCACGTGAGAGATT 57.468 42.857 24.41 6.33 41.55 2.40
3244 4229 4.363138 TGCATGATCACGTGAGAGATTAC 58.637 43.478 24.41 10.13 41.55 1.89
3245 4230 4.098501 TGCATGATCACGTGAGAGATTACT 59.901 41.667 24.41 3.83 41.55 2.24
3247 4232 5.521735 GCATGATCACGTGAGAGATTACTTT 59.478 40.000 24.41 2.19 41.55 2.66
3248 4233 6.036517 GCATGATCACGTGAGAGATTACTTTT 59.963 38.462 24.41 1.61 41.55 2.27
3249 4234 7.616673 CATGATCACGTGAGAGATTACTTTTC 58.383 38.462 24.41 11.88 41.55 2.29
3250 4235 6.687604 TGATCACGTGAGAGATTACTTTTCA 58.312 36.000 24.41 14.32 41.55 2.69
3251 4236 6.808704 TGATCACGTGAGAGATTACTTTTCAG 59.191 38.462 24.41 0.00 41.55 3.02
3252 4237 6.085555 TCACGTGAGAGATTACTTTTCAGT 57.914 37.500 15.76 0.00 36.99 3.41
3253 4238 6.513180 TCACGTGAGAGATTACTTTTCAGTT 58.487 36.000 15.76 0.00 34.06 3.16
3254 4239 6.984474 TCACGTGAGAGATTACTTTTCAGTTT 59.016 34.615 15.76 0.00 34.06 2.66
3255 4240 7.042725 TCACGTGAGAGATTACTTTTCAGTTTG 60.043 37.037 15.76 0.00 34.06 2.93
3256 4241 6.761714 ACGTGAGAGATTACTTTTCAGTTTGT 59.238 34.615 0.00 0.00 34.06 2.83
3257 4242 7.042658 ACGTGAGAGATTACTTTTCAGTTTGTC 60.043 37.037 0.00 0.00 34.06 3.18
3258 4243 7.169982 CGTGAGAGATTACTTTTCAGTTTGTCT 59.830 37.037 0.00 0.00 34.06 3.41
3259 4244 9.477484 GTGAGAGATTACTTTTCAGTTTGTCTA 57.523 33.333 0.00 0.00 34.06 2.59
3305 4290 9.554395 TTAAGAATGTCACATCTAAACTTCACA 57.446 29.630 0.00 0.00 0.00 3.58
3306 4291 8.450578 AAGAATGTCACATCTAAACTTCACAA 57.549 30.769 0.00 0.00 0.00 3.33
3307 4292 7.865707 AGAATGTCACATCTAAACTTCACAAC 58.134 34.615 0.00 0.00 0.00 3.32
3308 4293 6.560253 ATGTCACATCTAAACTTCACAACC 57.440 37.500 0.00 0.00 0.00 3.77
3309 4294 4.819630 TGTCACATCTAAACTTCACAACCC 59.180 41.667 0.00 0.00 0.00 4.11
3325 4310 7.461182 TCACAACCCATTACTTTTATCCAAG 57.539 36.000 0.00 0.00 0.00 3.61
3350 4335 2.073117 AATATCACACGTGTCGCACA 57.927 45.000 20.49 2.72 33.40 4.57
3353 4338 0.581529 ATCACACGTGTCGCACAAAG 59.418 50.000 20.49 5.03 33.40 2.77
3360 4345 0.310543 GTGTCGCACAAAGCAATCCA 59.689 50.000 5.30 0.00 46.13 3.41
3362 4347 0.730494 GTCGCACAAAGCAATCCAGC 60.730 55.000 0.00 0.00 46.13 4.85
3366 4351 1.838112 CACAAAGCAATCCAGCCCTA 58.162 50.000 0.00 0.00 34.23 3.53
3368 4353 2.094545 CACAAAGCAATCCAGCCCTAAC 60.095 50.000 0.00 0.00 34.23 2.34
3372 4357 2.659428 AGCAATCCAGCCCTAACATTC 58.341 47.619 0.00 0.00 34.23 2.67
3373 4358 2.025037 AGCAATCCAGCCCTAACATTCA 60.025 45.455 0.00 0.00 34.23 2.57
3458 4443 5.718146 TGAAAACAAAGTTGTCATGCTTGA 58.282 33.333 0.00 0.00 41.31 3.02
3469 4454 8.220755 AGTTGTCATGCTTGAAACTAAAGTTA 57.779 30.769 19.19 0.00 37.25 2.24
3471 4456 8.905702 GTTGTCATGCTTGAAACTAAAGTTATG 58.094 33.333 3.51 0.00 37.25 1.90
3472 4457 7.592938 TGTCATGCTTGAAACTAAAGTTATGG 58.407 34.615 3.51 0.00 37.25 2.74
3482 4467 8.212312 TGAAACTAAAGTTATGGTCCTTACACA 58.788 33.333 0.00 0.00 37.25 3.72
3484 4469 8.617290 AACTAAAGTTATGGTCCTTACACAAG 57.383 34.615 0.00 0.00 36.32 3.16
3518 4503 1.385528 AAAACGTCCCTGGTTGTCAC 58.614 50.000 0.00 0.00 0.00 3.67
3519 4504 0.464916 AAACGTCCCTGGTTGTCACC 60.465 55.000 0.00 0.00 44.56 4.02
3524 4509 1.228245 CCCTGGTTGTCACCTGTGG 60.228 63.158 0.00 0.00 44.61 4.17
3526 4511 2.203139 TGGTTGTCACCTGTGGCG 60.203 61.111 0.00 0.00 44.61 5.69
3618 5913 2.446341 GCGTCAAGCTACAGTGGTC 58.554 57.895 0.00 0.00 44.04 4.02
3695 5995 3.252701 GGAAACGACAGTGACAGTCTAGA 59.747 47.826 6.56 0.00 33.89 2.43
3697 5997 5.455056 AAACGACAGTGACAGTCTAGAAT 57.545 39.130 6.56 0.00 33.89 2.40
3699 5999 5.548706 ACGACAGTGACAGTCTAGAATAC 57.451 43.478 6.56 0.00 33.89 1.89
3700 6000 4.093115 ACGACAGTGACAGTCTAGAATACG 59.907 45.833 6.56 2.53 33.89 3.06
3736 6036 4.342772 CGTGCATGCACCTTAATTAACTC 58.657 43.478 37.92 14.53 43.49 3.01
3739 6039 4.640201 TGCATGCACCTTAATTAACTCCTC 59.360 41.667 18.46 0.00 0.00 3.71
3740 6040 4.884164 GCATGCACCTTAATTAACTCCTCT 59.116 41.667 14.21 0.00 0.00 3.69
3808 6278 0.657077 CATGCACAACGGACAACACG 60.657 55.000 0.00 0.00 37.36 4.49
3837 6313 6.467723 AATACTTGTTTAGCTGTTCTGACG 57.532 37.500 0.00 0.00 0.00 4.35
3866 6342 6.800408 CACTGTTCAGCACAAGATTGAAATAG 59.200 38.462 0.00 0.00 33.87 1.73
3991 8203 6.804534 CTCGAGTAGCAACAGAAAGATAAG 57.195 41.667 3.62 0.00 0.00 1.73
3992 8204 6.268825 TCGAGTAGCAACAGAAAGATAAGT 57.731 37.500 0.00 0.00 0.00 2.24
3993 8205 7.387119 TCGAGTAGCAACAGAAAGATAAGTA 57.613 36.000 0.00 0.00 0.00 2.24
3994 8206 7.473366 TCGAGTAGCAACAGAAAGATAAGTAG 58.527 38.462 0.00 0.00 0.00 2.57
3995 8207 7.336176 TCGAGTAGCAACAGAAAGATAAGTAGA 59.664 37.037 0.00 0.00 0.00 2.59
3996 8208 7.968956 CGAGTAGCAACAGAAAGATAAGTAGAA 59.031 37.037 0.00 0.00 0.00 2.10
3997 8209 9.810545 GAGTAGCAACAGAAAGATAAGTAGAAT 57.189 33.333 0.00 0.00 0.00 2.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
18 19 8.864024 GCAAAGCCTTTTAAGACTTATGATTTC 58.136 33.333 0.00 0.00 28.18 2.17
19 20 7.542130 CGCAAAGCCTTTTAAGACTTATGATTT 59.458 33.333 0.00 0.00 28.18 2.17
20 21 7.029563 CGCAAAGCCTTTTAAGACTTATGATT 58.970 34.615 0.00 0.00 28.18 2.57
21 22 6.151144 ACGCAAAGCCTTTTAAGACTTATGAT 59.849 34.615 0.00 0.00 28.18 2.45
22 23 5.472137 ACGCAAAGCCTTTTAAGACTTATGA 59.528 36.000 0.00 0.00 28.18 2.15
23 24 5.699839 ACGCAAAGCCTTTTAAGACTTATG 58.300 37.500 0.00 0.00 28.18 1.90
24 25 5.959618 ACGCAAAGCCTTTTAAGACTTAT 57.040 34.783 0.00 0.00 28.18 1.73
25 26 5.066764 ACAACGCAAAGCCTTTTAAGACTTA 59.933 36.000 0.00 0.00 28.18 2.24
26 27 4.142249 ACAACGCAAAGCCTTTTAAGACTT 60.142 37.500 0.00 0.00 29.47 3.01
27 28 3.380320 ACAACGCAAAGCCTTTTAAGACT 59.620 39.130 0.00 0.00 0.00 3.24
28 29 3.702330 ACAACGCAAAGCCTTTTAAGAC 58.298 40.909 0.00 0.00 0.00 3.01
29 30 3.630312 AGACAACGCAAAGCCTTTTAAGA 59.370 39.130 0.00 0.00 0.00 2.10
30 31 3.730715 CAGACAACGCAAAGCCTTTTAAG 59.269 43.478 0.00 0.00 0.00 1.85
31 32 3.701241 CAGACAACGCAAAGCCTTTTAA 58.299 40.909 0.00 0.00 0.00 1.52
32 33 2.542824 GCAGACAACGCAAAGCCTTTTA 60.543 45.455 0.00 0.00 0.00 1.52
33 34 1.802508 GCAGACAACGCAAAGCCTTTT 60.803 47.619 0.00 0.00 0.00 2.27
34 35 0.249031 GCAGACAACGCAAAGCCTTT 60.249 50.000 0.00 0.00 0.00 3.11
35 36 1.103398 AGCAGACAACGCAAAGCCTT 61.103 50.000 0.00 0.00 0.00 4.35
36 37 1.526917 AGCAGACAACGCAAAGCCT 60.527 52.632 0.00 0.00 0.00 4.58
37 38 1.370900 CAGCAGACAACGCAAAGCC 60.371 57.895 0.00 0.00 0.00 4.35
38 39 1.370900 CCAGCAGACAACGCAAAGC 60.371 57.895 0.00 0.00 0.00 3.51
39 40 0.236711 CTCCAGCAGACAACGCAAAG 59.763 55.000 0.00 0.00 0.00 2.77
40 41 0.463654 ACTCCAGCAGACAACGCAAA 60.464 50.000 0.00 0.00 0.00 3.68
41 42 0.463654 AACTCCAGCAGACAACGCAA 60.464 50.000 0.00 0.00 0.00 4.85
42 43 1.146041 AACTCCAGCAGACAACGCA 59.854 52.632 0.00 0.00 0.00 5.24
43 44 1.571460 CAACTCCAGCAGACAACGC 59.429 57.895 0.00 0.00 0.00 4.84
44 45 0.882042 AGCAACTCCAGCAGACAACG 60.882 55.000 0.00 0.00 0.00 4.10
45 46 0.871057 GAGCAACTCCAGCAGACAAC 59.129 55.000 0.00 0.00 0.00 3.32
46 47 0.761187 AGAGCAACTCCAGCAGACAA 59.239 50.000 0.00 0.00 0.00 3.18
47 48 0.761187 AAGAGCAACTCCAGCAGACA 59.239 50.000 0.00 0.00 0.00 3.41
48 49 2.739379 GTTAAGAGCAACTCCAGCAGAC 59.261 50.000 0.00 0.00 0.00 3.51
83 84 8.999431 ACAATCGTGTTTCTACTTCAAACATAT 58.001 29.630 1.60 0.00 43.74 1.78
100 105 2.087501 TGTAATCCGCACAATCGTGT 57.912 45.000 0.00 0.00 45.50 4.49
101 106 2.415168 ACTTGTAATCCGCACAATCGTG 59.585 45.455 0.00 0.00 46.56 4.35
104 109 4.882671 ATGACTTGTAATCCGCACAATC 57.117 40.909 0.00 0.00 35.46 2.67
111 119 3.863424 ACGTTGCTATGACTTGTAATCCG 59.137 43.478 0.00 0.00 0.00 4.18
115 123 3.394719 TGCACGTTGCTATGACTTGTAA 58.605 40.909 10.54 0.00 45.31 2.41
120 128 0.729116 GCATGCACGTTGCTATGACT 59.271 50.000 14.21 0.00 45.31 3.41
121 129 0.447406 TGCATGCACGTTGCTATGAC 59.553 50.000 18.46 9.35 45.31 3.06
122 130 1.064357 CATGCATGCACGTTGCTATGA 59.936 47.619 25.37 0.00 45.31 2.15
123 131 1.202211 ACATGCATGCACGTTGCTATG 60.202 47.619 25.37 17.00 45.31 2.23
124 132 1.097232 ACATGCATGCACGTTGCTAT 58.903 45.000 25.37 0.38 45.31 2.97
125 133 0.168568 CACATGCATGCACGTTGCTA 59.831 50.000 25.37 0.00 45.31 3.49
126 134 1.081041 CACATGCATGCACGTTGCT 60.081 52.632 25.37 2.19 45.31 3.91
131 139 2.486504 GGGACACATGCATGCACG 59.513 61.111 25.37 19.13 0.00 5.34
132 140 2.887360 GGGGACACATGCATGCAC 59.113 61.111 25.37 16.57 0.00 4.57
133 141 2.751036 CGGGGACACATGCATGCA 60.751 61.111 26.53 25.04 0.00 3.96
137 145 1.395045 TTTTTGCGGGGACACATGCA 61.395 50.000 0.00 0.00 35.15 3.96
138 146 1.365633 TTTTTGCGGGGACACATGC 59.634 52.632 0.00 0.00 0.00 4.06
158 166 4.484236 CATCCACATGCATACACGTTTTT 58.516 39.130 0.00 0.00 0.00 1.94
159 167 4.095410 CATCCACATGCATACACGTTTT 57.905 40.909 0.00 0.00 0.00 2.43
160 168 3.763097 CATCCACATGCATACACGTTT 57.237 42.857 0.00 0.00 0.00 3.60
177 185 0.933796 GCCTGCTCTCTAAACGCATC 59.066 55.000 0.00 0.00 32.62 3.91
186 194 2.813901 GCTGATCGCCTGCTCTCT 59.186 61.111 0.00 0.00 36.86 3.10
197 205 0.027194 TGTACGTAGCGTCGCTGATC 59.973 55.000 29.43 17.29 41.54 2.92
203 211 0.916762 GTAGCGTGTACGTAGCGTCG 60.917 60.000 17.15 11.08 41.54 5.12
224 239 7.159322 AGTACTATTGACTAGTCTTGGTGTG 57.841 40.000 23.01 9.55 41.10 3.82
228 243 7.994334 AGTAGGAGTACTATTGACTAGTCTTGG 59.006 40.741 23.01 14.50 41.10 3.61
239 254 7.066525 GGCTGATAGCTAGTAGGAGTACTATTG 59.933 44.444 0.00 0.00 40.33 1.90
243 258 4.563993 CGGCTGATAGCTAGTAGGAGTACT 60.564 50.000 0.00 0.00 41.99 2.73
244 259 3.685756 CGGCTGATAGCTAGTAGGAGTAC 59.314 52.174 0.00 0.00 41.99 2.73
249 264 1.813786 GACCGGCTGATAGCTAGTAGG 59.186 57.143 0.00 0.00 41.99 3.18
271 408 1.660607 CGCTATCTGCAACGTGAACAT 59.339 47.619 0.00 0.00 43.06 2.71
279 416 2.511600 ACGGCCGCTATCTGCAAC 60.512 61.111 28.58 0.00 43.06 4.17
281 418 3.770040 ACACGGCCGCTATCTGCA 61.770 61.111 28.58 0.00 43.06 4.41
303 440 1.014564 GGAGAAAGAGTTGACCGCGG 61.015 60.000 26.86 26.86 0.00 6.46
348 485 2.675603 GCTCGGAGGAGGAAGAGTTTTC 60.676 54.545 7.20 0.00 40.80 2.29
349 486 1.276705 GCTCGGAGGAGGAAGAGTTTT 59.723 52.381 7.20 0.00 40.80 2.43
366 503 0.175760 TAGCTCATGAACCACCGCTC 59.824 55.000 8.04 0.00 0.00 5.03
372 509 2.424601 GCATTGCTTAGCTCATGAACCA 59.575 45.455 17.21 0.00 0.00 3.67
437 574 0.756903 GGCCCACCGTATAGTGACAT 59.243 55.000 0.00 0.00 40.34 3.06
451 588 4.161295 CGGAGAAGATGCGGCCCA 62.161 66.667 0.00 0.00 39.39 5.36
604 797 4.854399 TGATACAGTTTTTGCCAGTTTCG 58.146 39.130 0.00 0.00 0.00 3.46
611 804 8.364129 TCAAAAAGATTGATACAGTTTTTGCC 57.636 30.769 11.80 0.00 43.21 4.52
626 819 6.371825 GTGTAGGGAACTCGATCAAAAAGATT 59.628 38.462 0.00 0.00 43.67 2.40
636 829 0.683504 AGCCGTGTAGGGAACTCGAT 60.684 55.000 1.59 0.00 45.57 3.59
638 831 1.139095 GAGCCGTGTAGGGAACTCG 59.861 63.158 0.00 0.00 43.67 4.18
647 840 4.013702 GGGTCTCTGAGCCGTGTA 57.986 61.111 0.00 0.00 40.45 2.90
707 900 3.570912 AATCCCGGATTCCGTTGTTAT 57.429 42.857 22.83 6.69 46.80 1.89
811 1194 1.227853 GAGCCGTGTCCAACTTGGT 60.228 57.895 7.72 0.00 39.03 3.67
904 1290 7.168804 CGACCGATTTACTCCTTTATTACTTCC 59.831 40.741 0.00 0.00 0.00 3.46
909 1295 5.981315 CAGCGACCGATTTACTCCTTTATTA 59.019 40.000 0.00 0.00 0.00 0.98
911 1297 4.369182 CAGCGACCGATTTACTCCTTTAT 58.631 43.478 0.00 0.00 0.00 1.40
924 1310 0.734309 TCTTATAACGCAGCGACCGA 59.266 50.000 24.65 5.88 0.00 4.69
925 1311 0.844503 GTCTTATAACGCAGCGACCG 59.155 55.000 24.65 3.44 0.00 4.79
926 1312 1.206523 GGTCTTATAACGCAGCGACC 58.793 55.000 24.65 13.06 34.79 4.79
927 1313 0.844503 CGGTCTTATAACGCAGCGAC 59.155 55.000 24.65 6.93 31.47 5.19
1138 1542 1.150536 CGAGAGAGAGAGGGAGGGG 59.849 68.421 0.00 0.00 0.00 4.79
1141 1545 0.535102 GGAGCGAGAGAGAGAGGGAG 60.535 65.000 0.00 0.00 0.00 4.30
1144 1548 0.535102 GAGGGAGCGAGAGAGAGAGG 60.535 65.000 0.00 0.00 0.00 3.69
1146 1550 0.468226 GAGAGGGAGCGAGAGAGAGA 59.532 60.000 0.00 0.00 0.00 3.10
1150 1554 2.515057 GCGAGAGGGAGCGAGAGA 60.515 66.667 0.00 0.00 0.00 3.10
1167 1571 4.851114 CAGCGGCGCGATTTGTCG 62.851 66.667 27.59 4.10 0.00 4.35
1168 1572 4.520846 CCAGCGGCGCGATTTGTC 62.521 66.667 27.59 0.00 0.00 3.18
1202 1606 4.077188 GGTCTGCACAACGCTCGC 62.077 66.667 0.00 0.00 43.06 5.03
1205 1609 0.250467 AGATTGGTCTGCACAACGCT 60.250 50.000 0.00 0.00 43.06 5.07
1208 1612 0.798776 CCGAGATTGGTCTGCACAAC 59.201 55.000 0.00 0.00 33.97 3.32
1210 1614 1.296392 CCCGAGATTGGTCTGCACA 59.704 57.895 0.00 0.00 33.97 4.57
1212 1616 0.400213 AAACCCGAGATTGGTCTGCA 59.600 50.000 0.00 0.00 34.15 4.41
1225 1629 1.732259 CCGATTCAGTCAAGAAACCCG 59.268 52.381 0.00 0.00 0.00 5.28
1227 1632 1.468914 GGCCGATTCAGTCAAGAAACC 59.531 52.381 0.00 0.00 0.00 3.27
1228 1633 1.128692 CGGCCGATTCAGTCAAGAAAC 59.871 52.381 24.07 0.00 0.00 2.78
1661 2071 3.531538 GATTGCAGTCCCAACGAGATTA 58.468 45.455 0.00 0.00 0.00 1.75
1712 2122 0.969894 AAGGTCAGCTGACTTACGCT 59.030 50.000 38.17 26.36 44.20 5.07
1724 2140 1.338864 ACTGCATCAGAGCAAGGTCAG 60.339 52.381 0.29 0.00 45.13 3.51
1725 2141 0.689055 ACTGCATCAGAGCAAGGTCA 59.311 50.000 0.29 0.00 45.13 4.02
2093 3018 1.153086 CGGGCAAGAGAGAATGGGG 60.153 63.158 0.00 0.00 0.00 4.96
2134 3059 4.044426 GCCAATTGCCAATTAGATCGAAC 58.956 43.478 1.66 0.00 0.00 3.95
2135 3060 3.698539 TGCCAATTGCCAATTAGATCGAA 59.301 39.130 1.66 0.00 40.16 3.71
2181 3106 2.274645 CCCAATTTGAGTGCCGCCA 61.275 57.895 0.00 0.00 0.00 5.69
2202 3127 3.934391 CTGGGCCGAAGTGACGTCC 62.934 68.421 14.12 4.42 0.00 4.79
2259 3187 3.305676 CCATGGAGTATGAGTAGGCGAAG 60.306 52.174 5.56 0.00 39.21 3.79
2302 3230 4.153986 GCACTGAATCTTTGTGACATTCG 58.846 43.478 0.00 0.00 33.95 3.34
2334 3275 0.743345 GACCGTGACTTATGGGTGCC 60.743 60.000 0.00 0.00 39.98 5.01
2360 3306 6.605471 TCAATTCCCACATATATAGACGCT 57.395 37.500 0.00 0.00 0.00 5.07
2369 3315 3.568443 TGCAGCATCAATTCCCACATAT 58.432 40.909 0.00 0.00 0.00 1.78
2377 3323 1.202110 CGTGTCCTGCAGCATCAATTC 60.202 52.381 8.66 0.00 0.00 2.17
2418 3364 2.427506 GCCTTCCTCATCGTCTTGTTT 58.572 47.619 0.00 0.00 0.00 2.83
2745 3704 3.222354 GAACGCCGTCCTCCACACT 62.222 63.158 0.00 0.00 0.00 3.55
3038 4009 5.835819 TCTACTCACAGCTAAGCTAATCCAT 59.164 40.000 0.00 0.00 36.40 3.41
3039 4010 5.201243 TCTACTCACAGCTAAGCTAATCCA 58.799 41.667 0.00 0.00 36.40 3.41
3163 4140 5.676125 ACCCATATAGTCCTACCATCCATT 58.324 41.667 0.00 0.00 0.00 3.16
3165 4142 4.777877 ACCCATATAGTCCTACCATCCA 57.222 45.455 0.00 0.00 0.00 3.41
3166 4143 6.326843 GGATAACCCATATAGTCCTACCATCC 59.673 46.154 0.00 0.00 34.14 3.51
3168 4145 6.822374 TGGATAACCCATATAGTCCTACCAT 58.178 40.000 0.00 0.00 40.82 3.55
3181 4166 3.749954 GCATCAAGAGCTGGATAACCCAT 60.750 47.826 0.00 0.00 45.57 4.00
3182 4167 2.421952 GCATCAAGAGCTGGATAACCCA 60.422 50.000 0.00 0.00 44.25 4.51
3185 4170 1.869767 CGGCATCAAGAGCTGGATAAC 59.130 52.381 0.00 0.00 34.75 1.89
3195 4180 1.066858 GGAGACTCAACGGCATCAAGA 60.067 52.381 4.53 0.00 0.00 3.02
3279 4264 9.554395 TGTGAAGTTTAGATGTGACATTCTTAA 57.446 29.630 0.00 0.00 0.00 1.85
3280 4265 9.554395 TTGTGAAGTTTAGATGTGACATTCTTA 57.446 29.630 0.00 0.00 0.00 2.10
3281 4266 8.345565 GTTGTGAAGTTTAGATGTGACATTCTT 58.654 33.333 0.00 0.72 0.00 2.52
3282 4267 7.041098 GGTTGTGAAGTTTAGATGTGACATTCT 60.041 37.037 0.00 1.32 0.00 2.40
3283 4268 7.078228 GGTTGTGAAGTTTAGATGTGACATTC 58.922 38.462 0.00 0.00 0.00 2.67
3284 4269 6.016276 GGGTTGTGAAGTTTAGATGTGACATT 60.016 38.462 0.00 0.00 0.00 2.71
3285 4270 5.473504 GGGTTGTGAAGTTTAGATGTGACAT 59.526 40.000 0.00 0.00 0.00 3.06
3286 4271 4.819630 GGGTTGTGAAGTTTAGATGTGACA 59.180 41.667 0.00 0.00 0.00 3.58
3287 4272 4.819630 TGGGTTGTGAAGTTTAGATGTGAC 59.180 41.667 0.00 0.00 0.00 3.67
3288 4273 5.042463 TGGGTTGTGAAGTTTAGATGTGA 57.958 39.130 0.00 0.00 0.00 3.58
3289 4274 5.964958 ATGGGTTGTGAAGTTTAGATGTG 57.035 39.130 0.00 0.00 0.00 3.21
3290 4275 7.231467 AGTAATGGGTTGTGAAGTTTAGATGT 58.769 34.615 0.00 0.00 0.00 3.06
3291 4276 7.687941 AGTAATGGGTTGTGAAGTTTAGATG 57.312 36.000 0.00 0.00 0.00 2.90
3292 4277 8.706322 AAAGTAATGGGTTGTGAAGTTTAGAT 57.294 30.769 0.00 0.00 0.00 1.98
3293 4278 8.528044 AAAAGTAATGGGTTGTGAAGTTTAGA 57.472 30.769 0.00 0.00 0.00 2.10
3296 4281 8.364894 GGATAAAAGTAATGGGTTGTGAAGTTT 58.635 33.333 0.00 0.00 0.00 2.66
3297 4282 7.507616 TGGATAAAAGTAATGGGTTGTGAAGTT 59.492 33.333 0.00 0.00 0.00 2.66
3298 4283 7.007723 TGGATAAAAGTAATGGGTTGTGAAGT 58.992 34.615 0.00 0.00 0.00 3.01
3299 4284 7.461182 TGGATAAAAGTAATGGGTTGTGAAG 57.539 36.000 0.00 0.00 0.00 3.02
3300 4285 7.507616 ACTTGGATAAAAGTAATGGGTTGTGAA 59.492 33.333 0.00 0.00 38.62 3.18
3301 4286 7.007723 ACTTGGATAAAAGTAATGGGTTGTGA 58.992 34.615 0.00 0.00 38.62 3.58
3302 4287 7.040062 TCACTTGGATAAAAGTAATGGGTTGTG 60.040 37.037 0.00 0.00 38.34 3.33
3303 4288 7.007723 TCACTTGGATAAAAGTAATGGGTTGT 58.992 34.615 0.00 0.00 38.34 3.32
3304 4289 7.461182 TCACTTGGATAAAAGTAATGGGTTG 57.539 36.000 0.00 0.00 38.34 3.77
3305 4290 9.762381 TTATCACTTGGATAAAAGTAATGGGTT 57.238 29.630 0.00 0.00 43.70 4.11
3334 4319 0.581529 CTTTGTGCGACACGTGTGAT 59.418 50.000 28.82 0.00 37.14 3.06
3345 4330 1.444895 GGCTGGATTGCTTTGTGCG 60.445 57.895 0.00 0.00 46.63 5.34
3350 4335 2.603075 TGTTAGGGCTGGATTGCTTT 57.397 45.000 0.00 0.00 0.00 3.51
3353 4338 2.378038 TGAATGTTAGGGCTGGATTGC 58.622 47.619 0.00 0.00 0.00 3.56
3360 4345 8.644374 TTTTAGTTGTAATGAATGTTAGGGCT 57.356 30.769 0.00 0.00 0.00 5.19
3441 4426 7.489113 ACTTTAGTTTCAAGCATGACAACTTTG 59.511 33.333 17.99 13.06 37.69 2.77
3458 4443 8.983702 TTGTGTAAGGACCATAACTTTAGTTT 57.016 30.769 0.00 0.00 39.31 2.66
3469 4454 6.877611 CAAGTTTACTTGTGTAAGGACCAT 57.122 37.500 13.22 0.00 46.11 3.55
3511 4496 2.978010 CCCGCCACAGGTGACAAC 60.978 66.667 0.00 0.00 34.74 3.32
3518 4503 2.748058 AAAGTAGCACCCGCCACAGG 62.748 60.000 0.00 0.00 39.83 4.00
3519 4504 0.889186 AAAAGTAGCACCCGCCACAG 60.889 55.000 0.00 0.00 39.83 3.66
3524 4509 1.329599 CCGATTAAAAGTAGCACCCGC 59.670 52.381 0.00 0.00 38.99 6.13
3526 4511 2.681344 CACCCGATTAAAAGTAGCACCC 59.319 50.000 0.00 0.00 0.00 4.61
3530 4518 3.687698 TCTTGCACCCGATTAAAAGTAGC 59.312 43.478 0.00 0.00 0.00 3.58
3618 5913 3.708563 AATTTCAAGTGGTCACCGTTG 57.291 42.857 2.75 2.75 0.00 4.10
3695 5995 2.733026 ACGCTGCGAAAAACTACGTATT 59.267 40.909 30.47 0.00 0.00 1.89
3697 5997 1.452773 CACGCTGCGAAAAACTACGTA 59.547 47.619 30.47 0.00 0.00 3.57
3699 5999 1.052768 GCACGCTGCGAAAAACTACG 61.053 55.000 30.47 6.01 31.71 3.51
3700 6000 2.696290 GCACGCTGCGAAAAACTAC 58.304 52.632 30.47 4.49 31.71 2.73
3808 6278 5.043189 ACAGCTAAACAAGTATTTTCGCC 57.957 39.130 0.00 0.00 0.00 5.54
3837 6313 2.722130 CTTGTGCTGAACAGTGCCGC 62.722 60.000 3.77 0.00 40.74 6.53
3911 7903 5.163612 CGTGACTCTGTCCATTTAGATGAGA 60.164 44.000 0.00 0.00 35.16 3.27
3912 7904 5.039984 CGTGACTCTGTCCATTTAGATGAG 58.960 45.833 0.00 0.00 35.16 2.90
3914 7906 3.553511 GCGTGACTCTGTCCATTTAGATG 59.446 47.826 0.00 0.00 0.00 2.90
3915 7907 3.195610 TGCGTGACTCTGTCCATTTAGAT 59.804 43.478 0.00 0.00 0.00 1.98
3917 7909 2.926200 CTGCGTGACTCTGTCCATTTAG 59.074 50.000 0.00 0.00 0.00 1.85
3918 7910 2.353704 CCTGCGTGACTCTGTCCATTTA 60.354 50.000 0.00 0.00 0.00 1.40
3919 7911 1.609061 CCTGCGTGACTCTGTCCATTT 60.609 52.381 0.00 0.00 0.00 2.32
3951 8163 0.738389 GAGCCAGAAGAGACTCTCCG 59.262 60.000 5.20 0.00 0.00 4.63
3979 8191 9.771534 GCTGGAATATTCTACTTATCTTTCTGT 57.228 33.333 14.95 0.00 0.00 3.41
4007 8219 7.156876 TCGATTTTTGTAATGAAGGAGCATT 57.843 32.000 0.00 0.00 41.15 3.56


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

AutoCloner maintained by Alex Coulton.