Multiple sequence alignment - TraesCS6B01G359000

Loading Multiple Alignment...

Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS6B01G359000 chr6B 100.000 2324 0 0 1 2324 630505998 630503675 0.000000e+00 4292.0
1 TraesCS6B01G359000 chr6B 95.720 701 26 4 1625 2324 67946237 67945540 0.000000e+00 1125.0
2 TraesCS6B01G359000 chr6B 90.148 406 30 2 976 1375 630529582 630529181 9.520000e-144 520.0
3 TraesCS6B01G359000 chr6B 86.842 456 41 8 968 1415 630465947 630465503 2.070000e-135 492.0
4 TraesCS6B01G359000 chr6B 87.379 412 42 5 976 1381 630514592 630514185 4.520000e-127 464.0
5 TraesCS6B01G359000 chr6B 81.452 496 42 26 454 941 630466461 630466008 6.100000e-96 361.0
6 TraesCS6B01G359000 chr6B 75.649 308 48 14 513 797 630532527 630532224 6.740000e-26 128.0
7 TraesCS6B01G359000 chr6B 87.179 78 10 0 1500 1577 630511437 630511360 3.180000e-14 89.8
8 TraesCS6B01G359000 chr6B 87.143 70 2 2 234 296 4592590 4592659 3.200000e-09 73.1
9 TraesCS6B01G359000 chr6A 90.789 1140 63 13 304 1413 560817494 560816367 0.000000e+00 1485.0
10 TraesCS6B01G359000 chr6A 88.403 457 32 11 968 1415 560753663 560753219 4.400000e-147 531.0
11 TraesCS6B01G359000 chr6A 87.773 458 39 5 971 1415 560829437 560828984 9.520000e-144 520.0
12 TraesCS6B01G359000 chr6A 80.473 338 33 16 454 787 560754141 560753833 6.460000e-56 228.0
13 TraesCS6B01G359000 chr6A 92.593 108 7 1 1484 1591 560815189 560815083 1.110000e-33 154.0
14 TraesCS6B01G359000 chr1B 96.291 701 23 2 1624 2324 561625277 561625974 0.000000e+00 1147.0
15 TraesCS6B01G359000 chr1B 95.763 708 25 5 1621 2323 17337319 17338026 0.000000e+00 1136.0
16 TraesCS6B01G359000 chr1B 95.571 700 29 2 1625 2324 295769567 295768870 0.000000e+00 1120.0
17 TraesCS6B01G359000 chrUn 95.898 707 25 4 1621 2323 317006978 317006272 0.000000e+00 1142.0
18 TraesCS6B01G359000 chr2B 95.994 699 26 2 1626 2324 316104083 316103387 0.000000e+00 1134.0
19 TraesCS6B01G359000 chr2B 95.733 703 27 2 1624 2324 296027163 296026462 0.000000e+00 1129.0
20 TraesCS6B01G359000 chr3B 95.857 700 26 3 1625 2324 734166414 734165718 0.000000e+00 1129.0
21 TraesCS6B01G359000 chr3B 93.464 153 10 0 1 153 753215484 753215636 6.460000e-56 228.0
22 TraesCS6B01G359000 chr3A 95.435 701 28 4 1624 2324 676074009 676073313 0.000000e+00 1114.0
23 TraesCS6B01G359000 chr6D 88.146 852 64 20 304 1135 418463659 418462825 0.000000e+00 979.0
24 TraesCS6B01G359000 chr6D 83.537 984 97 33 454 1415 418313667 418312727 0.000000e+00 859.0
25 TraesCS6B01G359000 chr6D 89.670 455 35 5 971 1415 418530981 418530529 9.320000e-159 569.0
26 TraesCS6B01G359000 chr6D 89.116 441 34 4 976 1410 418524221 418523789 9.450000e-149 536.0
27 TraesCS6B01G359000 chr6D 89.865 296 12 3 1124 1413 418461021 418460738 4.720000e-97 364.0
28 TraesCS6B01G359000 chr6D 97.500 40 1 0 1586 1625 418459518 418459479 4.140000e-08 69.4
29 TraesCS6B01G359000 chr4D 91.096 146 13 0 304 449 439697906 439697761 5.070000e-47 198.0
30 TraesCS6B01G359000 chr2D 82.969 229 30 2 1 228 476968817 476968597 5.070000e-47 198.0
31 TraesCS6B01G359000 chr5B 82.533 229 29 5 1 227 498842857 498842638 8.480000e-45 191.0
32 TraesCS6B01G359000 chr5B 87.218 133 17 0 314 446 35451898 35452030 4.000000e-33 152.0
33 TraesCS6B01G359000 chr5B 85.235 149 19 3 301 446 35369124 35369272 1.440000e-32 150.0
34 TraesCS6B01G359000 chr5B 84.932 146 22 0 301 446 35455098 35455243 5.170000e-32 148.0
35 TraesCS6B01G359000 chr7D 88.889 153 17 0 301 453 440561074 440561226 3.050000e-44 189.0
36 TraesCS6B01G359000 chr7D 81.739 230 31 4 1 228 45203066 45202846 5.100000e-42 182.0
37 TraesCS6B01G359000 chr7B 88.235 153 18 0 301 453 458340962 458341114 1.420000e-42 183.0
38 TraesCS6B01G359000 chr7A 88.235 153 18 0 301 453 492238930 492239082 1.420000e-42 183.0
39 TraesCS6B01G359000 chr4B 88.000 125 14 1 1 124 602239177 602239053 1.860000e-31 147.0
40 TraesCS6B01G359000 chr5A 79.039 229 29 8 1 228 44110718 44110508 3.110000e-29 139.0


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 TraesCS6B01G359000 chr6B 630503675 630505998 2323 True 4292.0 4292 100.0000 1 2324 1 chr6B.!!$R2 2323
1 TraesCS6B01G359000 chr6B 67945540 67946237 697 True 1125.0 1125 95.7200 1625 2324 1 chr6B.!!$R1 699
2 TraesCS6B01G359000 chr6B 630465503 630466461 958 True 426.5 492 84.1470 454 1415 2 chr6B.!!$R3 961
3 TraesCS6B01G359000 chr6B 630529181 630532527 3346 True 324.0 520 82.8985 513 1375 2 chr6B.!!$R5 862
4 TraesCS6B01G359000 chr6B 630511360 630514592 3232 True 276.9 464 87.2790 976 1577 2 chr6B.!!$R4 601
5 TraesCS6B01G359000 chr6A 560815083 560817494 2411 True 819.5 1485 91.6910 304 1591 2 chr6A.!!$R3 1287
6 TraesCS6B01G359000 chr6A 560753219 560754141 922 True 379.5 531 84.4380 454 1415 2 chr6A.!!$R2 961
7 TraesCS6B01G359000 chr1B 561625277 561625974 697 False 1147.0 1147 96.2910 1624 2324 1 chr1B.!!$F2 700
8 TraesCS6B01G359000 chr1B 17337319 17338026 707 False 1136.0 1136 95.7630 1621 2323 1 chr1B.!!$F1 702
9 TraesCS6B01G359000 chr1B 295768870 295769567 697 True 1120.0 1120 95.5710 1625 2324 1 chr1B.!!$R1 699
10 TraesCS6B01G359000 chrUn 317006272 317006978 706 True 1142.0 1142 95.8980 1621 2323 1 chrUn.!!$R1 702
11 TraesCS6B01G359000 chr2B 316103387 316104083 696 True 1134.0 1134 95.9940 1626 2324 1 chr2B.!!$R2 698
12 TraesCS6B01G359000 chr2B 296026462 296027163 701 True 1129.0 1129 95.7330 1624 2324 1 chr2B.!!$R1 700
13 TraesCS6B01G359000 chr3B 734165718 734166414 696 True 1129.0 1129 95.8570 1625 2324 1 chr3B.!!$R1 699
14 TraesCS6B01G359000 chr3A 676073313 676074009 696 True 1114.0 1114 95.4350 1624 2324 1 chr3A.!!$R1 700
15 TraesCS6B01G359000 chr6D 418312727 418313667 940 True 859.0 859 83.5370 454 1415 1 chr6D.!!$R1 961
16 TraesCS6B01G359000 chr6D 418459479 418463659 4180 True 470.8 979 91.8370 304 1625 3 chr6D.!!$R4 1321

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
124 125 0.034896 TGGAGGGCTTGAGTTCGAAC 59.965 55.0 20.71 20.71 0.0 3.95 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1456 8348 1.478916 TGCATGCCATATGCCATATGC 59.521 47.619 17.52 13.49 43.55 3.14 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
44 45 9.109393 TCCATGATATTATTATTAAGGCTTCGC 57.891 33.333 1.30 0.00 0.00 4.70
45 46 9.113838 CCATGATATTATTATTAAGGCTTCGCT 57.886 33.333 1.30 0.00 0.00 4.93
48 49 9.371136 TGATATTATTATTAAGGCTTCGCTCTG 57.629 33.333 1.30 0.00 0.00 3.35
49 50 5.924475 TTATTATTAAGGCTTCGCTCTGC 57.076 39.130 1.30 0.00 0.00 4.26
55 56 3.895025 GCTTCGCTCTGCCATGAA 58.105 55.556 0.00 0.00 0.00 2.57
56 57 1.720301 GCTTCGCTCTGCCATGAAG 59.280 57.895 0.00 0.00 40.54 3.02
57 58 1.023513 GCTTCGCTCTGCCATGAAGT 61.024 55.000 0.00 0.00 39.91 3.01
58 59 1.005340 CTTCGCTCTGCCATGAAGTC 58.995 55.000 0.00 0.00 34.54 3.01
59 60 0.321346 TTCGCTCTGCCATGAAGTCA 59.679 50.000 0.00 0.00 0.00 3.41
60 61 0.321346 TCGCTCTGCCATGAAGTCAA 59.679 50.000 0.00 0.00 0.00 3.18
61 62 1.159285 CGCTCTGCCATGAAGTCAAA 58.841 50.000 0.00 0.00 0.00 2.69
62 63 1.536766 CGCTCTGCCATGAAGTCAAAA 59.463 47.619 0.00 0.00 0.00 2.44
63 64 2.030893 CGCTCTGCCATGAAGTCAAAAA 60.031 45.455 0.00 0.00 0.00 1.94
64 65 3.366679 CGCTCTGCCATGAAGTCAAAAAT 60.367 43.478 0.00 0.00 0.00 1.82
65 66 3.924686 GCTCTGCCATGAAGTCAAAAATG 59.075 43.478 0.00 0.00 0.00 2.32
66 67 3.916761 TCTGCCATGAAGTCAAAAATGC 58.083 40.909 0.00 0.00 0.00 3.56
67 68 3.575256 TCTGCCATGAAGTCAAAAATGCT 59.425 39.130 0.00 0.00 0.00 3.79
68 69 3.655486 TGCCATGAAGTCAAAAATGCTG 58.345 40.909 0.00 0.00 0.00 4.41
69 70 3.069872 TGCCATGAAGTCAAAAATGCTGT 59.930 39.130 0.00 0.00 0.00 4.40
70 71 3.676646 GCCATGAAGTCAAAAATGCTGTC 59.323 43.478 0.00 0.00 0.00 3.51
71 72 4.560108 GCCATGAAGTCAAAAATGCTGTCT 60.560 41.667 0.00 0.00 0.00 3.41
72 73 5.335897 GCCATGAAGTCAAAAATGCTGTCTA 60.336 40.000 0.00 0.00 0.00 2.59
73 74 6.320171 CCATGAAGTCAAAAATGCTGTCTAG 58.680 40.000 0.00 0.00 0.00 2.43
74 75 5.947228 TGAAGTCAAAAATGCTGTCTAGG 57.053 39.130 0.00 0.00 0.00 3.02
75 76 4.216257 TGAAGTCAAAAATGCTGTCTAGGC 59.784 41.667 0.00 0.00 0.00 3.93
76 77 2.744202 AGTCAAAAATGCTGTCTAGGCG 59.256 45.455 0.00 0.00 0.00 5.52
77 78 2.742053 GTCAAAAATGCTGTCTAGGCGA 59.258 45.455 0.00 0.00 0.00 5.54
78 79 3.002791 TCAAAAATGCTGTCTAGGCGAG 58.997 45.455 0.00 0.00 0.00 5.03
79 80 1.373570 AAAATGCTGTCTAGGCGAGC 58.626 50.000 10.64 10.64 0.00 5.03
80 81 0.539051 AAATGCTGTCTAGGCGAGCT 59.461 50.000 16.25 0.00 33.66 4.09
81 82 0.179089 AATGCTGTCTAGGCGAGCTG 60.179 55.000 16.25 0.00 33.66 4.24
82 83 2.025767 ATGCTGTCTAGGCGAGCTGG 62.026 60.000 16.25 0.00 33.66 4.85
83 84 2.716017 GCTGTCTAGGCGAGCTGGT 61.716 63.158 10.37 0.00 0.00 4.00
84 85 1.893786 CTGTCTAGGCGAGCTGGTT 59.106 57.895 0.00 0.00 0.00 3.67
85 86 0.459237 CTGTCTAGGCGAGCTGGTTG 60.459 60.000 0.00 0.00 0.00 3.77
86 87 1.185618 TGTCTAGGCGAGCTGGTTGT 61.186 55.000 0.00 0.00 0.00 3.32
87 88 0.815734 GTCTAGGCGAGCTGGTTGTA 59.184 55.000 0.00 0.00 0.00 2.41
88 89 1.103803 TCTAGGCGAGCTGGTTGTAG 58.896 55.000 0.00 0.00 0.00 2.74
89 90 0.528684 CTAGGCGAGCTGGTTGTAGC 60.529 60.000 0.00 0.00 44.01 3.58
90 91 1.254975 TAGGCGAGCTGGTTGTAGCA 61.255 55.000 0.00 0.00 46.07 3.49
91 92 2.391389 GGCGAGCTGGTTGTAGCAC 61.391 63.158 0.00 0.00 46.07 4.40
93 94 4.675404 GAGCTGGTTGTAGCACGT 57.325 55.556 0.00 0.00 46.07 4.49
94 95 2.914379 GAGCTGGTTGTAGCACGTT 58.086 52.632 0.00 0.00 46.07 3.99
95 96 1.226746 GAGCTGGTTGTAGCACGTTT 58.773 50.000 0.00 0.00 46.07 3.60
96 97 0.944386 AGCTGGTTGTAGCACGTTTG 59.056 50.000 0.00 0.00 46.07 2.93
97 98 0.941542 GCTGGTTGTAGCACGTTTGA 59.058 50.000 0.00 0.00 43.17 2.69
98 99 1.332375 GCTGGTTGTAGCACGTTTGAA 59.668 47.619 0.00 0.00 43.17 2.69
99 100 2.602217 GCTGGTTGTAGCACGTTTGAAG 60.602 50.000 0.00 0.00 43.17 3.02
100 101 2.869801 CTGGTTGTAGCACGTTTGAAGA 59.130 45.455 0.00 0.00 0.00 2.87
101 102 3.271729 TGGTTGTAGCACGTTTGAAGAA 58.728 40.909 0.00 0.00 0.00 2.52
102 103 3.880490 TGGTTGTAGCACGTTTGAAGAAT 59.120 39.130 0.00 0.00 0.00 2.40
103 104 4.336993 TGGTTGTAGCACGTTTGAAGAATT 59.663 37.500 0.00 0.00 0.00 2.17
116 117 3.356529 GAAGAATTCTGGAGGGCTTGA 57.643 47.619 9.17 0.00 43.23 3.02
117 118 3.277715 GAAGAATTCTGGAGGGCTTGAG 58.722 50.000 9.17 0.00 43.23 3.02
118 119 2.273619 AGAATTCTGGAGGGCTTGAGT 58.726 47.619 7.30 0.00 0.00 3.41
119 120 2.646798 AGAATTCTGGAGGGCTTGAGTT 59.353 45.455 7.30 0.00 0.00 3.01
120 121 2.797177 ATTCTGGAGGGCTTGAGTTC 57.203 50.000 0.00 0.00 0.00 3.01
121 122 0.321671 TTCTGGAGGGCTTGAGTTCG 59.678 55.000 0.00 0.00 0.00 3.95
122 123 0.541998 TCTGGAGGGCTTGAGTTCGA 60.542 55.000 0.00 0.00 0.00 3.71
123 124 0.321671 CTGGAGGGCTTGAGTTCGAA 59.678 55.000 0.00 0.00 0.00 3.71
124 125 0.034896 TGGAGGGCTTGAGTTCGAAC 59.965 55.000 20.71 20.71 0.00 3.95
125 126 0.321996 GGAGGGCTTGAGTTCGAACT 59.678 55.000 30.12 30.12 43.16 3.01
134 135 3.196613 AGTTCGAACTCTTGCCGTC 57.803 52.632 24.93 0.00 32.86 4.79
135 136 0.663568 AGTTCGAACTCTTGCCGTCG 60.664 55.000 24.93 0.00 32.86 5.12
136 137 0.938168 GTTCGAACTCTTGCCGTCGT 60.938 55.000 20.97 0.00 0.00 4.34
137 138 0.592637 TTCGAACTCTTGCCGTCGTA 59.407 50.000 0.00 0.00 0.00 3.43
138 139 0.167470 TCGAACTCTTGCCGTCGTAG 59.833 55.000 0.00 0.00 0.00 3.51
139 140 0.109873 CGAACTCTTGCCGTCGTAGT 60.110 55.000 0.00 0.00 0.00 2.73
140 141 1.665161 CGAACTCTTGCCGTCGTAGTT 60.665 52.381 0.00 0.00 33.26 2.24
141 142 2.401351 GAACTCTTGCCGTCGTAGTTT 58.599 47.619 0.00 0.00 30.83 2.66
142 143 2.521105 ACTCTTGCCGTCGTAGTTTT 57.479 45.000 0.00 0.00 0.00 2.43
143 144 3.648339 ACTCTTGCCGTCGTAGTTTTA 57.352 42.857 0.00 0.00 0.00 1.52
144 145 4.184079 ACTCTTGCCGTCGTAGTTTTAT 57.816 40.909 0.00 0.00 0.00 1.40
145 146 4.563061 ACTCTTGCCGTCGTAGTTTTATT 58.437 39.130 0.00 0.00 0.00 1.40
146 147 4.992951 ACTCTTGCCGTCGTAGTTTTATTT 59.007 37.500 0.00 0.00 0.00 1.40
147 148 5.467735 ACTCTTGCCGTCGTAGTTTTATTTT 59.532 36.000 0.00 0.00 0.00 1.82
148 149 6.017687 ACTCTTGCCGTCGTAGTTTTATTTTT 60.018 34.615 0.00 0.00 0.00 1.94
149 150 6.137415 TCTTGCCGTCGTAGTTTTATTTTTG 58.863 36.000 0.00 0.00 0.00 2.44
150 151 5.670149 TGCCGTCGTAGTTTTATTTTTGA 57.330 34.783 0.00 0.00 0.00 2.69
151 152 6.057627 TGCCGTCGTAGTTTTATTTTTGAA 57.942 33.333 0.00 0.00 0.00 2.69
152 153 6.137415 TGCCGTCGTAGTTTTATTTTTGAAG 58.863 36.000 0.00 0.00 0.00 3.02
153 154 5.058856 GCCGTCGTAGTTTTATTTTTGAAGC 59.941 40.000 0.00 0.00 0.00 3.86
154 155 5.279751 CCGTCGTAGTTTTATTTTTGAAGCG 59.720 40.000 0.00 0.00 0.00 4.68
155 156 5.219533 CGTCGTAGTTTTATTTTTGAAGCGC 60.220 40.000 0.00 0.00 0.00 5.92
156 157 5.849604 GTCGTAGTTTTATTTTTGAAGCGCT 59.150 36.000 2.64 2.64 0.00 5.92
157 158 5.849081 TCGTAGTTTTATTTTTGAAGCGCTG 59.151 36.000 12.58 0.00 0.00 5.18
158 159 5.849081 CGTAGTTTTATTTTTGAAGCGCTGA 59.151 36.000 12.58 0.00 0.00 4.26
159 160 6.358558 CGTAGTTTTATTTTTGAAGCGCTGAA 59.641 34.615 12.58 3.93 0.00 3.02
160 161 6.753897 AGTTTTATTTTTGAAGCGCTGAAG 57.246 33.333 12.58 0.00 0.00 3.02
161 162 5.175673 AGTTTTATTTTTGAAGCGCTGAAGC 59.824 36.000 12.58 1.17 37.78 3.86
172 173 1.849306 GCTGAAGCGCTGCTATACG 59.151 57.895 18.27 1.01 38.25 3.06
179 180 3.867723 CGCTGCTATACGCTACCTT 57.132 52.632 0.00 0.00 40.11 3.50
180 181 2.983402 CGCTGCTATACGCTACCTTA 57.017 50.000 0.00 0.00 40.11 2.69
181 182 3.278367 CGCTGCTATACGCTACCTTAA 57.722 47.619 0.00 0.00 40.11 1.85
182 183 3.834610 CGCTGCTATACGCTACCTTAAT 58.165 45.455 0.00 0.00 40.11 1.40
183 184 3.608506 CGCTGCTATACGCTACCTTAATG 59.391 47.826 0.00 0.00 40.11 1.90
184 185 3.927142 GCTGCTATACGCTACCTTAATGG 59.073 47.826 0.00 0.00 40.11 3.16
185 186 4.495422 CTGCTATACGCTACCTTAATGGG 58.505 47.826 0.00 0.00 38.90 4.00
186 187 3.259902 GCTATACGCTACCTTAATGGGC 58.740 50.000 0.00 0.00 36.37 5.36
187 188 2.853235 ATACGCTACCTTAATGGGCC 57.147 50.000 0.00 0.00 41.11 5.80
188 189 0.390124 TACGCTACCTTAATGGGCCG 59.610 55.000 0.00 0.00 41.11 6.13
189 190 1.597027 CGCTACCTTAATGGGCCGG 60.597 63.158 0.00 0.00 41.11 6.13
190 191 1.897137 GCTACCTTAATGGGCCGGC 60.897 63.158 21.18 21.18 41.11 6.13
191 192 1.228154 CTACCTTAATGGGCCGGCC 60.228 63.158 38.57 38.57 41.11 6.13
212 213 2.826428 CAATCGGTGGACTCCTGTATG 58.174 52.381 0.00 0.00 0.00 2.39
213 214 2.160721 ATCGGTGGACTCCTGTATGT 57.839 50.000 0.00 0.00 0.00 2.29
214 215 2.812836 TCGGTGGACTCCTGTATGTA 57.187 50.000 0.00 0.00 0.00 2.29
215 216 3.308035 TCGGTGGACTCCTGTATGTAT 57.692 47.619 0.00 0.00 0.00 2.29
216 217 4.442401 TCGGTGGACTCCTGTATGTATA 57.558 45.455 0.00 0.00 0.00 1.47
217 218 4.139786 TCGGTGGACTCCTGTATGTATAC 58.860 47.826 0.00 0.00 0.00 1.47
218 219 3.058432 CGGTGGACTCCTGTATGTATACG 60.058 52.174 0.00 0.00 36.06 3.06
219 220 3.887716 GGTGGACTCCTGTATGTATACGT 59.112 47.826 2.56 2.56 36.06 3.57
220 221 4.023365 GGTGGACTCCTGTATGTATACGTC 60.023 50.000 0.00 0.00 36.06 4.34
221 222 4.023365 GTGGACTCCTGTATGTATACGTCC 60.023 50.000 12.69 12.69 38.96 4.79
222 223 4.139786 GGACTCCTGTATGTATACGTCCA 58.860 47.826 14.01 4.30 38.66 4.02
223 224 4.215827 GGACTCCTGTATGTATACGTCCAG 59.784 50.000 10.02 10.02 38.66 3.86
224 225 3.568853 ACTCCTGTATGTATACGTCCAGC 59.431 47.826 11.23 0.00 36.06 4.85
226 227 2.351447 CCTGTATGTATACGTCCAGCGG 60.351 54.545 11.23 0.00 46.52 5.52
227 228 1.610038 TGTATGTATACGTCCAGCGGG 59.390 52.381 0.00 0.00 46.52 6.13
228 229 1.068055 GTATGTATACGTCCAGCGGGG 60.068 57.143 2.05 0.00 46.52 5.73
229 230 1.469335 ATGTATACGTCCAGCGGGGG 61.469 60.000 2.05 0.00 46.52 5.40
244 245 2.922779 GGGGGTTGTACGACTTGTG 58.077 57.895 13.01 0.00 0.00 3.33
245 246 0.393820 GGGGGTTGTACGACTTGTGA 59.606 55.000 13.01 0.00 0.00 3.58
246 247 1.202675 GGGGGTTGTACGACTTGTGAA 60.203 52.381 13.01 0.00 0.00 3.18
247 248 2.563702 GGGGTTGTACGACTTGTGAAA 58.436 47.619 13.01 0.00 0.00 2.69
248 249 3.143728 GGGGTTGTACGACTTGTGAAAT 58.856 45.455 13.01 0.00 0.00 2.17
249 250 3.566742 GGGGTTGTACGACTTGTGAAATT 59.433 43.478 13.01 0.00 0.00 1.82
250 251 4.756135 GGGGTTGTACGACTTGTGAAATTA 59.244 41.667 13.01 0.00 0.00 1.40
251 252 5.334337 GGGGTTGTACGACTTGTGAAATTAC 60.334 44.000 13.01 0.00 0.00 1.89
252 253 5.467735 GGGTTGTACGACTTGTGAAATTACT 59.532 40.000 13.01 0.00 0.00 2.24
253 254 6.646240 GGGTTGTACGACTTGTGAAATTACTA 59.354 38.462 13.01 0.00 0.00 1.82
254 255 7.332678 GGGTTGTACGACTTGTGAAATTACTAT 59.667 37.037 13.01 0.00 0.00 2.12
255 256 9.357652 GGTTGTACGACTTGTGAAATTACTATA 57.642 33.333 13.01 0.00 0.00 1.31
276 277 9.259832 ACTATATTACCTTTTATACGTAGGGGG 57.740 37.037 6.29 4.28 33.22 5.40
277 278 9.259832 CTATATTACCTTTTATACGTAGGGGGT 57.740 37.037 6.29 9.23 33.22 4.95
278 279 6.829985 ATTACCTTTTATACGTAGGGGGTT 57.170 37.500 6.29 0.00 33.22 4.11
279 280 4.492494 ACCTTTTATACGTAGGGGGTTG 57.508 45.455 6.29 0.00 33.22 3.77
280 281 3.845992 ACCTTTTATACGTAGGGGGTTGT 59.154 43.478 6.29 0.00 33.22 3.32
281 282 5.029474 ACCTTTTATACGTAGGGGGTTGTA 58.971 41.667 6.29 0.00 33.22 2.41
282 283 5.104941 ACCTTTTATACGTAGGGGGTTGTAC 60.105 44.000 6.29 0.00 33.22 2.90
283 284 5.351948 TTTTATACGTAGGGGGTTGTACC 57.648 43.478 0.08 0.00 37.60 3.34
284 285 2.854736 ATACGTAGGGGGTTGTACCT 57.145 50.000 0.08 0.00 38.64 3.08
285 286 3.971468 ATACGTAGGGGGTTGTACCTA 57.029 47.619 0.08 0.00 38.64 3.08
286 287 2.621556 ACGTAGGGGGTTGTACCTAA 57.378 50.000 0.00 0.00 40.80 2.69
287 288 2.460669 ACGTAGGGGGTTGTACCTAAG 58.539 52.381 0.00 0.00 40.80 2.18
288 289 1.137675 CGTAGGGGGTTGTACCTAAGC 59.862 57.143 0.00 0.00 40.80 3.09
289 290 1.137675 GTAGGGGGTTGTACCTAAGCG 59.862 57.143 0.00 0.00 40.80 4.68
290 291 1.222661 GGGGGTTGTACCTAAGCGG 59.777 63.158 0.00 0.00 38.64 5.52
291 292 1.222661 GGGGTTGTACCTAAGCGGG 59.777 63.158 0.00 0.00 38.64 6.13
292 293 1.556373 GGGGTTGTACCTAAGCGGGT 61.556 60.000 4.64 4.64 42.86 5.28
293 294 0.107993 GGGTTGTACCTAAGCGGGTC 60.108 60.000 2.53 0.00 40.48 4.46
294 295 0.900421 GGTTGTACCTAAGCGGGTCT 59.100 55.000 2.53 0.00 40.48 3.85
295 296 1.134877 GGTTGTACCTAAGCGGGTCTC 60.135 57.143 2.53 0.30 40.48 3.36
296 297 0.813184 TTGTACCTAAGCGGGTCTCG 59.187 55.000 2.53 0.00 40.48 4.04
297 298 0.322816 TGTACCTAAGCGGGTCTCGT 60.323 55.000 0.00 0.00 40.48 4.18
298 299 0.813821 GTACCTAAGCGGGTCTCGTT 59.186 55.000 0.00 0.00 40.48 3.85
299 300 1.203287 GTACCTAAGCGGGTCTCGTTT 59.797 52.381 0.00 0.00 44.23 3.60
300 301 0.245813 ACCTAAGCGGGTCTCGTTTC 59.754 55.000 0.00 0.00 41.26 2.78
301 302 0.245539 CCTAAGCGGGTCTCGTTTCA 59.754 55.000 0.00 0.00 41.26 2.69
302 303 1.347320 CTAAGCGGGTCTCGTTTCAC 58.653 55.000 0.00 0.00 41.26 3.18
348 349 1.615392 GGAAGAAACTGCCATGTTGCT 59.385 47.619 0.00 0.00 37.41 3.91
370 371 1.642762 AGAGAAAATGCCACCCCTCAT 59.357 47.619 0.00 0.00 0.00 2.90
397 398 2.948979 CCTCACAACTAAAACTGCCACA 59.051 45.455 0.00 0.00 0.00 4.17
431 432 4.547367 CCATCCTCCCCGGCGAAC 62.547 72.222 9.30 0.00 0.00 3.95
560 565 2.789409 GGACAAATCCTGTGCCTAGT 57.211 50.000 0.00 0.00 42.45 2.57
661 673 3.694734 CAGCACACACGAAACAGAAATT 58.305 40.909 0.00 0.00 0.00 1.82
680 695 1.031571 TGAAAGGCCCAAGCATAGCG 61.032 55.000 0.00 0.00 42.56 4.26
769 793 1.550130 CCTCCGCTACCCTCCAAACA 61.550 60.000 0.00 0.00 0.00 2.83
776 800 2.704572 CTACCCTCCAAACAGCTGAAG 58.295 52.381 23.35 9.25 0.00 3.02
777 801 1.140312 ACCCTCCAAACAGCTGAAGA 58.860 50.000 23.35 9.92 0.00 2.87
801 828 0.776080 ATCCCAACACCCACCTTCCT 60.776 55.000 0.00 0.00 0.00 3.36
802 829 0.104356 TCCCAACACCCACCTTCCTA 60.104 55.000 0.00 0.00 0.00 2.94
803 830 0.328258 CCCAACACCCACCTTCCTAG 59.672 60.000 0.00 0.00 0.00 3.02
804 831 1.064825 CCAACACCCACCTTCCTAGT 58.935 55.000 0.00 0.00 0.00 2.57
805 832 1.423921 CCAACACCCACCTTCCTAGTT 59.576 52.381 0.00 0.00 0.00 2.24
806 833 2.552373 CCAACACCCACCTTCCTAGTTC 60.552 54.545 0.00 0.00 0.00 3.01
807 834 1.359168 ACACCCACCTTCCTAGTTCC 58.641 55.000 0.00 0.00 0.00 3.62
868 1854 2.159448 TCCACAAAAACAACAGACTGCG 60.159 45.455 1.25 0.00 0.00 5.18
879 3440 0.389166 CAGACTGCGACAACCTCCTC 60.389 60.000 0.00 0.00 0.00 3.71
925 3497 2.334977 TCTTCCACTCCTTACCAGCAA 58.665 47.619 0.00 0.00 0.00 3.91
943 3515 0.250727 AACAGGCAAGTGCATACGGT 60.251 50.000 5.52 0.00 44.36 4.83
956 3528 2.351726 GCATACGGTAAGGAAGCAACAG 59.648 50.000 0.00 0.00 0.00 3.16
958 3530 0.763035 ACGGTAAGGAAGCAACAGGT 59.237 50.000 0.00 0.00 0.00 4.00
961 3533 2.289195 CGGTAAGGAAGCAACAGGTACA 60.289 50.000 0.00 0.00 0.00 2.90
1203 5631 2.997897 GGGACGTGCTCTGGGTCT 60.998 66.667 7.11 0.00 0.00 3.85
1334 5768 3.703420 ACTACAACTGATATTCGTCGGC 58.297 45.455 0.00 0.00 0.00 5.54
1335 5769 2.665649 ACAACTGATATTCGTCGGCA 57.334 45.000 0.00 0.00 0.00 5.69
1336 5770 2.540515 ACAACTGATATTCGTCGGCAG 58.459 47.619 0.00 0.00 0.00 4.85
1337 5771 1.860950 CAACTGATATTCGTCGGCAGG 59.139 52.381 0.00 0.00 0.00 4.85
1415 7430 6.094048 GTGTATATGCAACATGTTCACTCCTT 59.906 38.462 8.48 0.00 0.00 3.36
1416 7431 5.824904 ATATGCAACATGTTCACTCCTTC 57.175 39.130 8.48 0.00 0.00 3.46
1418 7433 3.141398 TGCAACATGTTCACTCCTTCTC 58.859 45.455 8.48 0.00 0.00 2.87
1421 8313 4.129380 CAACATGTTCACTCCTTCTCACA 58.871 43.478 8.48 0.00 0.00 3.58
1424 8316 5.192927 ACATGTTCACTCCTTCTCACAAAA 58.807 37.500 0.00 0.00 0.00 2.44
1425 8317 5.297776 ACATGTTCACTCCTTCTCACAAAAG 59.702 40.000 0.00 0.00 0.00 2.27
1426 8318 4.199310 TGTTCACTCCTTCTCACAAAAGG 58.801 43.478 0.00 0.00 43.94 3.11
1429 8321 5.623956 TCACTCCTTCTCACAAAAGGTTA 57.376 39.130 2.10 0.00 43.22 2.85
1432 8324 7.386851 TCACTCCTTCTCACAAAAGGTTATAG 58.613 38.462 2.10 0.00 43.22 1.31
1435 8327 7.878644 ACTCCTTCTCACAAAAGGTTATAGAAC 59.121 37.037 2.10 0.00 43.22 3.01
1437 8329 8.437575 TCCTTCTCACAAAAGGTTATAGAACTT 58.562 33.333 0.00 0.00 43.22 2.66
1438 8330 8.507249 CCTTCTCACAAAAGGTTATAGAACTTG 58.493 37.037 0.00 0.14 38.79 3.16
1442 8334 8.177119 TCACAAAAGGTTATAGAACTTGCATT 57.823 30.769 0.00 0.00 35.74 3.56
1443 8335 8.637986 TCACAAAAGGTTATAGAACTTGCATTT 58.362 29.630 0.00 0.00 35.74 2.32
1444 8336 9.260002 CACAAAAGGTTATAGAACTTGCATTTT 57.740 29.630 0.00 0.00 35.74 1.82
1457 8349 7.761249 AGAACTTGCATTTTATTCCATACTTGC 59.239 33.333 0.00 0.00 0.00 4.01
1461 8353 9.701098 CTTGCATTTTATTCCATACTTGCATAT 57.299 29.630 0.00 0.00 38.50 1.78
1462 8354 9.478768 TTGCATTTTATTCCATACTTGCATATG 57.521 29.630 0.00 0.00 38.50 1.78
1479 8371 3.135027 TGGCATATGGCATGCACAT 57.865 47.368 26.67 20.91 46.12 3.21
1480 8372 2.289592 TGGCATATGGCATGCACATA 57.710 45.000 26.67 22.25 46.12 2.29
1481 8373 2.810164 TGGCATATGGCATGCACATAT 58.190 42.857 26.67 24.41 46.12 1.78
1525 8735 3.297736 TCCAAATCATGTGCATGCCATA 58.702 40.909 16.68 1.17 38.65 2.74
1584 8794 3.149196 ACGATTATTGATCCATGTGCCC 58.851 45.455 0.00 0.00 0.00 5.36
1618 8847 7.916914 ATTTCAGTTTACCACGTATAGCTTT 57.083 32.000 0.00 0.00 0.00 3.51
1833 9062 5.619309 CGACGAGATCTTCAAAACTAGACCA 60.619 44.000 0.00 0.00 0.00 4.02
1881 9119 1.136695 CTTTTGCCAGAAGTTGCCACA 59.863 47.619 0.00 0.00 0.00 4.17
2037 9276 3.249917 GAACCATGGCAATTTTACGTGG 58.750 45.455 13.04 9.41 44.81 4.94
2091 9330 8.635765 TCATGGCAAGTCTAGTTTCTTAATTT 57.364 30.769 0.00 0.00 0.00 1.82
2092 9331 9.077885 TCATGGCAAGTCTAGTTTCTTAATTTT 57.922 29.630 0.00 0.00 0.00 1.82
2167 9406 3.379372 ACATATCATGGCAACTTCAGTGC 59.621 43.478 0.00 0.00 37.61 4.40
2212 9451 6.389091 TGCAATAGACATGGCAACTTTTAAG 58.611 36.000 0.00 0.00 38.19 1.85
2277 9517 2.919228 TCGAAGATCTCATCACGAGGA 58.081 47.619 0.00 0.00 42.55 3.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
39 40 1.005340 GACTTCATGGCAGAGCGAAG 58.995 55.000 13.83 13.83 40.54 3.79
40 41 0.321346 TGACTTCATGGCAGAGCGAA 59.679 50.000 0.00 0.00 0.00 4.70
41 42 0.321346 TTGACTTCATGGCAGAGCGA 59.679 50.000 0.00 0.00 33.66 4.93
42 43 1.159285 TTTGACTTCATGGCAGAGCG 58.841 50.000 0.00 0.00 33.66 5.03
43 44 3.648339 TTTTTGACTTCATGGCAGAGC 57.352 42.857 0.00 0.00 33.66 4.09
44 45 3.924686 GCATTTTTGACTTCATGGCAGAG 59.075 43.478 0.00 0.00 33.66 3.35
45 46 3.575256 AGCATTTTTGACTTCATGGCAGA 59.425 39.130 0.00 0.00 33.66 4.26
46 47 3.678072 CAGCATTTTTGACTTCATGGCAG 59.322 43.478 0.00 0.00 33.66 4.85
47 48 3.069872 ACAGCATTTTTGACTTCATGGCA 59.930 39.130 0.00 0.00 0.00 4.92
48 49 3.656559 ACAGCATTTTTGACTTCATGGC 58.343 40.909 0.00 0.00 0.00 4.40
49 50 5.130292 AGACAGCATTTTTGACTTCATGG 57.870 39.130 0.00 0.00 0.00 3.66
50 51 6.320171 CCTAGACAGCATTTTTGACTTCATG 58.680 40.000 0.00 0.00 0.00 3.07
51 52 5.105997 GCCTAGACAGCATTTTTGACTTCAT 60.106 40.000 0.00 0.00 0.00 2.57
52 53 4.216257 GCCTAGACAGCATTTTTGACTTCA 59.784 41.667 0.00 0.00 0.00 3.02
53 54 4.670221 CGCCTAGACAGCATTTTTGACTTC 60.670 45.833 0.00 0.00 0.00 3.01
54 55 3.189287 CGCCTAGACAGCATTTTTGACTT 59.811 43.478 0.00 0.00 0.00 3.01
55 56 2.744202 CGCCTAGACAGCATTTTTGACT 59.256 45.455 0.00 0.00 0.00 3.41
56 57 2.742053 TCGCCTAGACAGCATTTTTGAC 59.258 45.455 0.00 0.00 0.00 3.18
57 58 3.002791 CTCGCCTAGACAGCATTTTTGA 58.997 45.455 0.00 0.00 0.00 2.69
58 59 2.476854 GCTCGCCTAGACAGCATTTTTG 60.477 50.000 0.00 0.00 0.00 2.44
59 60 1.740025 GCTCGCCTAGACAGCATTTTT 59.260 47.619 0.00 0.00 0.00 1.94
60 61 1.065854 AGCTCGCCTAGACAGCATTTT 60.066 47.619 9.40 0.00 0.00 1.82
61 62 0.539051 AGCTCGCCTAGACAGCATTT 59.461 50.000 9.40 0.00 0.00 2.32
62 63 0.179089 CAGCTCGCCTAGACAGCATT 60.179 55.000 9.40 0.00 0.00 3.56
63 64 1.440893 CAGCTCGCCTAGACAGCAT 59.559 57.895 9.40 0.00 0.00 3.79
64 65 2.714991 CCAGCTCGCCTAGACAGCA 61.715 63.158 9.40 0.00 0.00 4.41
65 66 2.105930 CCAGCTCGCCTAGACAGC 59.894 66.667 0.00 0.00 0.00 4.40
66 67 0.459237 CAACCAGCTCGCCTAGACAG 60.459 60.000 0.00 0.00 0.00 3.51
67 68 1.185618 ACAACCAGCTCGCCTAGACA 61.186 55.000 0.00 0.00 0.00 3.41
68 69 0.815734 TACAACCAGCTCGCCTAGAC 59.184 55.000 0.00 0.00 0.00 2.59
69 70 1.103803 CTACAACCAGCTCGCCTAGA 58.896 55.000 0.00 0.00 0.00 2.43
70 71 0.528684 GCTACAACCAGCTCGCCTAG 60.529 60.000 0.00 0.00 38.57 3.02
71 72 1.254975 TGCTACAACCAGCTCGCCTA 61.255 55.000 0.00 0.00 42.30 3.93
72 73 2.266055 GCTACAACCAGCTCGCCT 59.734 61.111 0.00 0.00 38.57 5.52
73 74 2.047274 TGCTACAACCAGCTCGCC 60.047 61.111 0.00 0.00 42.30 5.54
74 75 3.169198 GTGCTACAACCAGCTCGC 58.831 61.111 0.00 0.00 42.30 5.03
76 77 1.069906 CAAACGTGCTACAACCAGCTC 60.070 52.381 0.00 0.00 42.30 4.09
77 78 0.944386 CAAACGTGCTACAACCAGCT 59.056 50.000 0.00 0.00 42.30 4.24
78 79 0.941542 TCAAACGTGCTACAACCAGC 59.058 50.000 0.00 0.00 42.15 4.85
79 80 2.869801 TCTTCAAACGTGCTACAACCAG 59.130 45.455 0.00 0.00 0.00 4.00
80 81 2.907634 TCTTCAAACGTGCTACAACCA 58.092 42.857 0.00 0.00 0.00 3.67
81 82 3.955771 TTCTTCAAACGTGCTACAACC 57.044 42.857 0.00 0.00 0.00 3.77
82 83 5.621228 CAGAATTCTTCAAACGTGCTACAAC 59.379 40.000 4.86 0.00 0.00 3.32
83 84 5.277779 CCAGAATTCTTCAAACGTGCTACAA 60.278 40.000 4.86 0.00 0.00 2.41
84 85 4.213270 CCAGAATTCTTCAAACGTGCTACA 59.787 41.667 4.86 0.00 0.00 2.74
85 86 4.451096 TCCAGAATTCTTCAAACGTGCTAC 59.549 41.667 4.86 0.00 0.00 3.58
86 87 4.637276 TCCAGAATTCTTCAAACGTGCTA 58.363 39.130 4.86 0.00 0.00 3.49
87 88 3.476552 TCCAGAATTCTTCAAACGTGCT 58.523 40.909 4.86 0.00 0.00 4.40
88 89 3.365364 CCTCCAGAATTCTTCAAACGTGC 60.365 47.826 4.86 0.00 0.00 5.34
89 90 3.189287 CCCTCCAGAATTCTTCAAACGTG 59.811 47.826 4.86 0.00 0.00 4.49
90 91 3.412386 CCCTCCAGAATTCTTCAAACGT 58.588 45.455 4.86 0.00 0.00 3.99
91 92 2.162408 GCCCTCCAGAATTCTTCAAACG 59.838 50.000 4.86 0.00 0.00 3.60
92 93 3.425659 AGCCCTCCAGAATTCTTCAAAC 58.574 45.455 4.86 0.00 0.00 2.93
93 94 3.814504 AGCCCTCCAGAATTCTTCAAA 57.185 42.857 4.86 0.00 0.00 2.69
94 95 3.074390 TCAAGCCCTCCAGAATTCTTCAA 59.926 43.478 4.86 0.00 0.00 2.69
95 96 2.644299 TCAAGCCCTCCAGAATTCTTCA 59.356 45.455 4.86 0.00 0.00 3.02
96 97 3.277715 CTCAAGCCCTCCAGAATTCTTC 58.722 50.000 4.86 0.00 0.00 2.87
97 98 2.646798 ACTCAAGCCCTCCAGAATTCTT 59.353 45.455 4.86 0.00 0.00 2.52
98 99 2.273619 ACTCAAGCCCTCCAGAATTCT 58.726 47.619 0.88 0.88 0.00 2.40
99 100 2.797177 ACTCAAGCCCTCCAGAATTC 57.203 50.000 0.00 0.00 0.00 2.17
100 101 2.616510 CGAACTCAAGCCCTCCAGAATT 60.617 50.000 0.00 0.00 0.00 2.17
101 102 1.065854 CGAACTCAAGCCCTCCAGAAT 60.066 52.381 0.00 0.00 0.00 2.40
102 103 0.321671 CGAACTCAAGCCCTCCAGAA 59.678 55.000 0.00 0.00 0.00 3.02
103 104 0.541998 TCGAACTCAAGCCCTCCAGA 60.542 55.000 0.00 0.00 0.00 3.86
104 105 0.321671 TTCGAACTCAAGCCCTCCAG 59.678 55.000 0.00 0.00 0.00 3.86
105 106 0.034896 GTTCGAACTCAAGCCCTCCA 59.965 55.000 20.97 0.00 0.00 3.86
106 107 0.321996 AGTTCGAACTCAAGCCCTCC 59.678 55.000 24.93 0.00 32.86 4.30
107 108 3.917072 AGTTCGAACTCAAGCCCTC 57.083 52.632 24.93 0.00 32.86 4.30
116 117 0.663568 CGACGGCAAGAGTTCGAACT 60.664 55.000 30.12 30.12 43.16 3.01
117 118 0.938168 ACGACGGCAAGAGTTCGAAC 60.938 55.000 20.71 20.71 0.00 3.95
118 119 0.592637 TACGACGGCAAGAGTTCGAA 59.407 50.000 0.00 0.00 0.00 3.71
119 120 0.167470 CTACGACGGCAAGAGTTCGA 59.833 55.000 0.00 0.00 0.00 3.71
120 121 0.109873 ACTACGACGGCAAGAGTTCG 60.110 55.000 0.00 0.00 0.00 3.95
121 122 2.061740 AACTACGACGGCAAGAGTTC 57.938 50.000 0.00 0.00 0.00 3.01
122 123 2.521105 AAACTACGACGGCAAGAGTT 57.479 45.000 0.00 0.00 31.79 3.01
123 124 2.521105 AAAACTACGACGGCAAGAGT 57.479 45.000 0.00 0.00 0.00 3.24
124 125 5.526010 AAATAAAACTACGACGGCAAGAG 57.474 39.130 0.00 0.00 0.00 2.85
125 126 5.927954 AAAATAAAACTACGACGGCAAGA 57.072 34.783 0.00 0.00 0.00 3.02
126 127 6.137415 TCAAAAATAAAACTACGACGGCAAG 58.863 36.000 0.00 0.00 0.00 4.01
127 128 6.057627 TCAAAAATAAAACTACGACGGCAA 57.942 33.333 0.00 0.00 0.00 4.52
128 129 5.670149 TCAAAAATAAAACTACGACGGCA 57.330 34.783 0.00 0.00 0.00 5.69
129 130 5.058856 GCTTCAAAAATAAAACTACGACGGC 59.941 40.000 0.00 0.00 0.00 5.68
130 131 5.279751 CGCTTCAAAAATAAAACTACGACGG 59.720 40.000 0.00 0.00 0.00 4.79
131 132 5.219533 GCGCTTCAAAAATAAAACTACGACG 60.220 40.000 0.00 0.00 0.00 5.12
132 133 5.849604 AGCGCTTCAAAAATAAAACTACGAC 59.150 36.000 2.64 0.00 0.00 4.34
133 134 5.849081 CAGCGCTTCAAAAATAAAACTACGA 59.151 36.000 7.50 0.00 0.00 3.43
134 135 5.849081 TCAGCGCTTCAAAAATAAAACTACG 59.151 36.000 7.50 0.00 0.00 3.51
135 136 7.617325 GCTTCAGCGCTTCAAAAATAAAACTAC 60.617 37.037 7.50 0.00 0.00 2.73
136 137 6.362283 GCTTCAGCGCTTCAAAAATAAAACTA 59.638 34.615 7.50 0.00 0.00 2.24
137 138 5.175673 GCTTCAGCGCTTCAAAAATAAAACT 59.824 36.000 7.50 0.00 0.00 2.66
138 139 5.365942 GCTTCAGCGCTTCAAAAATAAAAC 58.634 37.500 7.50 0.00 0.00 2.43
139 140 5.574815 GCTTCAGCGCTTCAAAAATAAAA 57.425 34.783 7.50 0.00 0.00 1.52
154 155 1.849306 CGTATAGCAGCGCTTCAGC 59.151 57.895 7.50 9.05 40.44 4.26
162 163 5.151326 CCCATTAAGGTAGCGTATAGCAGC 61.151 50.000 0.00 0.00 42.14 5.25
163 164 4.495422 CCCATTAAGGTAGCGTATAGCAG 58.505 47.826 0.00 0.00 42.14 4.24
164 165 3.306502 GCCCATTAAGGTAGCGTATAGCA 60.307 47.826 0.00 0.00 42.14 3.49
165 166 3.259902 GCCCATTAAGGTAGCGTATAGC 58.740 50.000 0.00 0.00 40.61 2.97
166 167 3.675228 CGGCCCATTAAGGTAGCGTATAG 60.675 52.174 0.00 0.00 34.66 1.31
167 168 2.231964 CGGCCCATTAAGGTAGCGTATA 59.768 50.000 0.00 0.00 34.66 1.47
168 169 1.001633 CGGCCCATTAAGGTAGCGTAT 59.998 52.381 0.00 0.00 34.66 3.06
169 170 0.390124 CGGCCCATTAAGGTAGCGTA 59.610 55.000 0.00 0.00 34.66 4.42
170 171 1.145377 CGGCCCATTAAGGTAGCGT 59.855 57.895 0.00 0.00 34.66 5.07
171 172 1.597027 CCGGCCCATTAAGGTAGCG 60.597 63.158 0.00 0.00 34.66 4.26
172 173 1.897137 GCCGGCCCATTAAGGTAGC 60.897 63.158 18.11 0.00 34.66 3.58
173 174 1.228154 GGCCGGCCCATTAAGGTAG 60.228 63.158 36.64 0.00 34.66 3.18
174 175 2.920636 GGCCGGCCCATTAAGGTA 59.079 61.111 36.64 0.00 34.66 3.08
190 191 1.221840 CAGGAGTCCACCGATTGGG 59.778 63.158 12.86 0.00 46.92 4.12
191 192 9.603357 GTATACATACAGGAGTCCACCGATTGG 62.603 48.148 12.86 0.00 38.73 3.16
192 193 2.168521 ACATACAGGAGTCCACCGATTG 59.831 50.000 12.86 1.80 34.73 2.67
193 194 2.467880 ACATACAGGAGTCCACCGATT 58.532 47.619 12.86 0.00 34.73 3.34
194 195 2.160721 ACATACAGGAGTCCACCGAT 57.839 50.000 12.86 0.00 34.73 4.18
195 196 2.812836 TACATACAGGAGTCCACCGA 57.187 50.000 12.86 0.00 34.73 4.69
196 197 3.058432 CGTATACATACAGGAGTCCACCG 60.058 52.174 12.86 1.55 32.87 4.94
197 198 3.887716 ACGTATACATACAGGAGTCCACC 59.112 47.826 12.86 0.00 32.87 4.61
198 199 4.023365 GGACGTATACATACAGGAGTCCAC 60.023 50.000 12.86 0.00 38.66 4.02
199 200 4.139786 GGACGTATACATACAGGAGTCCA 58.860 47.826 12.86 0.00 38.66 4.02
200 201 4.139786 TGGACGTATACATACAGGAGTCC 58.860 47.826 0.00 0.00 38.96 3.85
201 202 4.320348 GCTGGACGTATACATACAGGAGTC 60.320 50.000 12.89 4.36 32.87 3.36
202 203 3.568853 GCTGGACGTATACATACAGGAGT 59.431 47.826 12.89 0.00 32.87 3.85
203 204 3.365064 CGCTGGACGTATACATACAGGAG 60.365 52.174 12.89 0.00 36.87 3.69
204 205 2.551032 CGCTGGACGTATACATACAGGA 59.449 50.000 12.89 0.00 36.87 3.86
205 206 2.351447 CCGCTGGACGTATACATACAGG 60.351 54.545 12.89 3.47 41.42 4.00
206 207 2.351447 CCCGCTGGACGTATACATACAG 60.351 54.545 6.81 6.81 41.42 2.74
207 208 1.610038 CCCGCTGGACGTATACATACA 59.390 52.381 3.32 0.00 41.42 2.29
208 209 1.068055 CCCCGCTGGACGTATACATAC 60.068 57.143 3.32 0.00 41.42 2.39
209 210 1.250328 CCCCGCTGGACGTATACATA 58.750 55.000 3.32 0.00 41.42 2.29
210 211 1.469335 CCCCCGCTGGACGTATACAT 61.469 60.000 3.32 0.00 41.42 2.29
211 212 2.129146 CCCCCGCTGGACGTATACA 61.129 63.158 3.32 0.00 41.42 2.29
212 213 2.732658 CCCCCGCTGGACGTATAC 59.267 66.667 0.00 0.00 41.42 1.47
226 227 0.393820 TCACAAGTCGTACAACCCCC 59.606 55.000 0.00 0.00 0.00 5.40
227 228 2.243602 TTCACAAGTCGTACAACCCC 57.756 50.000 0.00 0.00 0.00 4.95
228 229 4.823790 AATTTCACAAGTCGTACAACCC 57.176 40.909 0.00 0.00 0.00 4.11
229 230 6.535274 AGTAATTTCACAAGTCGTACAACC 57.465 37.500 0.00 0.00 0.00 3.77
250 251 9.259832 CCCCCTACGTATAAAAGGTAATATAGT 57.740 37.037 0.00 0.00 0.00 2.12
251 252 9.259832 ACCCCCTACGTATAAAAGGTAATATAG 57.740 37.037 0.00 0.00 0.00 1.31
252 253 9.614269 AACCCCCTACGTATAAAAGGTAATATA 57.386 33.333 0.00 0.00 0.00 0.86
253 254 8.377799 CAACCCCCTACGTATAAAAGGTAATAT 58.622 37.037 0.00 0.00 0.00 1.28
254 255 7.346960 ACAACCCCCTACGTATAAAAGGTAATA 59.653 37.037 0.00 0.00 0.00 0.98
255 256 6.158520 ACAACCCCCTACGTATAAAAGGTAAT 59.841 38.462 0.00 0.00 0.00 1.89
256 257 5.487131 ACAACCCCCTACGTATAAAAGGTAA 59.513 40.000 0.00 0.00 0.00 2.85
257 258 5.029474 ACAACCCCCTACGTATAAAAGGTA 58.971 41.667 0.00 0.00 0.00 3.08
258 259 3.845992 ACAACCCCCTACGTATAAAAGGT 59.154 43.478 0.00 0.00 0.00 3.50
259 260 4.492494 ACAACCCCCTACGTATAAAAGG 57.508 45.455 0.00 0.00 0.00 3.11
260 261 5.129320 AGGTACAACCCCCTACGTATAAAAG 59.871 44.000 0.00 0.00 39.75 2.27
261 262 5.029474 AGGTACAACCCCCTACGTATAAAA 58.971 41.667 0.00 0.00 39.75 1.52
262 263 4.619679 AGGTACAACCCCCTACGTATAAA 58.380 43.478 0.00 0.00 39.75 1.40
263 264 4.264373 AGGTACAACCCCCTACGTATAA 57.736 45.455 0.00 0.00 39.75 0.98
264 265 3.971468 AGGTACAACCCCCTACGTATA 57.029 47.619 0.00 0.00 39.75 1.47
265 266 2.854736 AGGTACAACCCCCTACGTAT 57.145 50.000 0.00 0.00 39.75 3.06
266 267 3.631250 CTTAGGTACAACCCCCTACGTA 58.369 50.000 0.00 0.00 39.75 3.57
267 268 2.460669 CTTAGGTACAACCCCCTACGT 58.539 52.381 0.00 0.00 39.75 3.57
268 269 1.137675 GCTTAGGTACAACCCCCTACG 59.862 57.143 0.00 0.00 39.75 3.51
269 270 1.137675 CGCTTAGGTACAACCCCCTAC 59.862 57.143 0.00 0.00 39.75 3.18
270 271 1.488390 CGCTTAGGTACAACCCCCTA 58.512 55.000 0.00 0.00 39.75 3.53
271 272 1.269703 CCGCTTAGGTACAACCCCCT 61.270 60.000 0.00 0.00 39.75 4.79
272 273 1.222661 CCGCTTAGGTACAACCCCC 59.777 63.158 0.00 0.00 39.75 5.40
273 274 1.222661 CCCGCTTAGGTACAACCCC 59.777 63.158 0.00 0.00 39.75 4.95
274 275 0.107993 GACCCGCTTAGGTACAACCC 60.108 60.000 0.00 0.00 41.42 4.11
275 276 0.900421 AGACCCGCTTAGGTACAACC 59.100 55.000 0.00 0.00 41.42 3.77
276 277 1.468736 CGAGACCCGCTTAGGTACAAC 60.469 57.143 0.00 0.00 41.42 3.32
277 278 0.813184 CGAGACCCGCTTAGGTACAA 59.187 55.000 0.00 0.00 41.42 2.41
278 279 0.322816 ACGAGACCCGCTTAGGTACA 60.323 55.000 0.00 0.00 41.42 2.90
279 280 0.813821 AACGAGACCCGCTTAGGTAC 59.186 55.000 0.00 0.00 41.42 3.34
280 281 1.474077 GAAACGAGACCCGCTTAGGTA 59.526 52.381 0.00 0.00 41.42 3.08
281 282 0.245813 GAAACGAGACCCGCTTAGGT 59.754 55.000 0.00 0.00 45.12 3.08
282 283 0.245539 TGAAACGAGACCCGCTTAGG 59.754 55.000 0.00 0.00 43.32 2.69
283 284 1.067776 AGTGAAACGAGACCCGCTTAG 60.068 52.381 0.00 0.00 45.86 2.18
284 285 0.963962 AGTGAAACGAGACCCGCTTA 59.036 50.000 0.00 0.00 45.86 3.09
285 286 0.106149 AAGTGAAACGAGACCCGCTT 59.894 50.000 0.00 0.00 45.86 4.68
286 287 0.106149 AAAGTGAAACGAGACCCGCT 59.894 50.000 0.00 0.00 45.86 5.52
287 288 0.942252 AAAAGTGAAACGAGACCCGC 59.058 50.000 0.00 0.00 45.86 6.13
288 289 4.799419 TTAAAAAGTGAAACGAGACCCG 57.201 40.909 0.00 0.00 45.86 5.28
296 297 8.172484 AGGCAATTTTCGTTTAAAAAGTGAAAC 58.828 29.630 12.15 3.67 43.33 2.78
297 298 8.257830 AGGCAATTTTCGTTTAAAAAGTGAAA 57.742 26.923 12.15 3.16 43.33 2.69
298 299 7.835634 AGGCAATTTTCGTTTAAAAAGTGAA 57.164 28.000 12.15 0.00 43.33 3.18
299 300 7.762159 AGAAGGCAATTTTCGTTTAAAAAGTGA 59.238 29.630 12.15 0.00 43.33 3.41
300 301 7.905126 AGAAGGCAATTTTCGTTTAAAAAGTG 58.095 30.769 5.47 5.47 43.44 3.16
301 302 7.043656 CGAGAAGGCAATTTTCGTTTAAAAAGT 60.044 33.333 5.88 0.00 40.37 2.66
302 303 7.273659 CGAGAAGGCAATTTTCGTTTAAAAAG 58.726 34.615 5.88 0.00 40.37 2.27
348 349 2.647299 TGAGGGGTGGCATTTTCTCTAA 59.353 45.455 0.00 0.00 0.00 2.10
370 371 4.574828 GCAGTTTTAGTTGTGAGGAAGTGA 59.425 41.667 0.00 0.00 0.00 3.41
397 398 3.304659 GGATGGCATATGCGAACGATTTT 60.305 43.478 21.04 0.36 43.26 1.82
431 432 0.392998 ACCCTGTTAGCTGGCGAATG 60.393 55.000 0.00 0.00 32.98 2.67
483 484 1.270625 TGTAACTGGCCGAAGACTTGG 60.271 52.381 0.00 0.00 0.00 3.61
560 565 1.530441 CGCTACGAGACGAATTCGGAA 60.530 52.381 29.79 8.89 44.95 4.30
600 605 1.771854 TGTGTTTACTCTCCCCTTGCA 59.228 47.619 0.00 0.00 0.00 4.08
661 673 1.031571 CGCTATGCTTGGGCCTTTCA 61.032 55.000 4.53 0.00 37.74 2.69
680 695 2.027751 GCATCCGTCGGCTACTCC 59.972 66.667 6.34 0.00 0.00 3.85
769 793 4.327680 GTGTTGGGATAGTTTCTTCAGCT 58.672 43.478 0.00 0.00 0.00 4.24
776 800 2.041216 AGGTGGGTGTTGGGATAGTTTC 59.959 50.000 0.00 0.00 0.00 2.78
777 801 2.070573 AGGTGGGTGTTGGGATAGTTT 58.929 47.619 0.00 0.00 0.00 2.66
801 828 2.323999 TTCGGGGGTTGTAGGAACTA 57.676 50.000 0.00 0.00 41.75 2.24
802 829 1.437397 TTTCGGGGGTTGTAGGAACT 58.563 50.000 0.00 0.00 46.37 3.01
803 830 2.275134 TTTTCGGGGGTTGTAGGAAC 57.725 50.000 0.00 0.00 0.00 3.62
868 1854 1.668151 GTGTGGCGAGGAGGTTGTC 60.668 63.158 0.00 0.00 0.00 3.18
879 3440 3.055719 GGATGGGTGTGTGTGGCG 61.056 66.667 0.00 0.00 0.00 5.69
925 3497 0.611200 TACCGTATGCACTTGCCTGT 59.389 50.000 0.00 0.00 41.18 4.00
943 3515 4.385825 CTGTTGTACCTGTTGCTTCCTTA 58.614 43.478 0.00 0.00 0.00 2.69
956 3528 0.824759 ATCTCCGGAGCTGTTGTACC 59.175 55.000 27.39 0.00 0.00 3.34
958 3530 2.457598 AGAATCTCCGGAGCTGTTGTA 58.542 47.619 27.39 8.01 0.00 2.41
961 3533 1.065854 CCAAGAATCTCCGGAGCTGTT 60.066 52.381 27.39 19.66 0.00 3.16
1415 7430 6.995686 TGCAAGTTCTATAACCTTTTGTGAGA 59.004 34.615 0.00 0.00 36.15 3.27
1416 7431 7.202016 TGCAAGTTCTATAACCTTTTGTGAG 57.798 36.000 0.00 0.00 36.15 3.51
1418 7433 8.816640 AAATGCAAGTTCTATAACCTTTTGTG 57.183 30.769 0.00 0.00 36.15 3.33
1424 8316 9.474313 TGGAATAAAATGCAAGTTCTATAACCT 57.526 29.630 0.00 0.00 36.15 3.50
1432 8324 7.545265 TGCAAGTATGGAATAAAATGCAAGTTC 59.455 33.333 0.00 0.00 39.41 3.01
1435 8327 9.701098 ATATGCAAGTATGGAATAAAATGCAAG 57.299 29.630 0.97 0.00 42.86 4.01
1456 8348 1.478916 TGCATGCCATATGCCATATGC 59.521 47.619 17.52 13.49 43.55 3.14
1457 8349 2.494073 TGTGCATGCCATATGCCATATG 59.506 45.455 16.68 16.26 43.94 1.78
1461 8353 2.289592 TATGTGCATGCCATATGCCA 57.710 45.000 16.68 7.29 43.94 4.92
1462 8354 2.159156 CCATATGTGCATGCCATATGCC 60.159 50.000 35.02 14.38 45.55 4.40
1464 8356 4.794278 AACCATATGTGCATGCCATATG 57.206 40.909 34.31 34.31 46.07 1.78
1465 8357 7.576403 TCTATAACCATATGTGCATGCCATAT 58.424 34.615 24.41 24.41 36.23 1.78
1466 8358 6.956497 TCTATAACCATATGTGCATGCCATA 58.044 36.000 22.78 22.78 0.00 2.74
1468 8360 5.240013 TCTATAACCATATGTGCATGCCA 57.760 39.130 16.68 13.21 0.00 4.92
1469 8361 5.707298 AGTTCTATAACCATATGTGCATGCC 59.293 40.000 16.68 7.25 36.15 4.40
1470 8362 6.808008 AGTTCTATAACCATATGTGCATGC 57.192 37.500 11.82 11.82 36.15 4.06
1472 8364 6.772233 TGCAAGTTCTATAACCATATGTGCAT 59.228 34.615 1.24 0.00 36.15 3.96
1473 8365 6.118852 TGCAAGTTCTATAACCATATGTGCA 58.881 36.000 1.24 3.73 36.15 4.57
1474 8366 6.618287 TGCAAGTTCTATAACCATATGTGC 57.382 37.500 1.24 1.07 36.15 4.57
1481 8373 9.249053 TGGAATAAAATGCAAGTTCTATAACCA 57.751 29.630 0.00 0.00 36.15 3.67
1564 8774 2.160219 CGGGCACATGGATCAATAATCG 59.840 50.000 0.00 0.00 34.99 3.34
1618 8847 3.866910 GGCGTTAACATTTCCGTAGATGA 59.133 43.478 6.39 0.00 0.00 2.92
1833 9062 9.474920 AAAAATCGTCAAAACATATCAACATGT 57.525 25.926 0.00 0.00 40.90 3.21
1881 9119 2.692557 TGGCAACTGCAGTGTAAACATT 59.307 40.909 22.49 0.00 44.36 2.71
1962 9200 5.840243 TGGAGTTGCCATCATCAAAATAG 57.160 39.130 0.00 0.00 43.33 1.73
2167 9406 5.755861 TGCATATGAATTGCCATGATGTTTG 59.244 36.000 6.97 0.00 39.39 2.93
2228 9467 7.338800 AGATCCCATGTTGATATGTTTTGAC 57.661 36.000 0.00 0.00 0.00 3.18


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

AutoCloner maintained by Alex Coulton.