Multiple sequence alignment - TraesCS2D01G429000

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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 TraesCS2D01G429000 chr2D 100.000 3886 0 0 1 3886 540835313 540839198 0.000000e+00 7177.0
1 TraesCS2D01G429000 chr2D 87.500 376 43 3 2320 2692 540952755 540953129 7.710000e-117 431.0
2 TraesCS2D01G429000 chr2B 96.680 3042 76 15 848 3886 646453032 646456051 0.000000e+00 5035.0
3 TraesCS2D01G429000 chr2B 89.276 373 38 2 2320 2691 646594784 646595155 2.110000e-127 466.0
4 TraesCS2D01G429000 chr2B 88.684 380 36 7 3196 3571 484121460 484121084 1.270000e-124 457.0
5 TraesCS2D01G429000 chr2B 88.360 378 40 4 3195 3570 103846981 103846606 5.920000e-123 451.0
6 TraesCS2D01G429000 chr2B 83.541 401 36 9 1 392 646417472 646417851 7.990000e-92 348.0
7 TraesCS2D01G429000 chr2B 85.621 153 19 3 3572 3722 367783900 367783749 1.450000e-34 158.0
8 TraesCS2D01G429000 chr2A 94.898 1568 72 7 1548 3113 684270032 684271593 0.000000e+00 2446.0
9 TraesCS2D01G429000 chr2A 87.548 522 42 11 805 1321 684269313 684269816 2.010000e-162 582.0
10 TraesCS2D01G429000 chr2A 89.008 373 40 1 2320 2692 684402013 684402384 9.840000e-126 460.0
11 TraesCS2D01G429000 chr2A 88.116 345 34 4 2350 2692 684419407 684419746 1.680000e-108 403.0
12 TraesCS2D01G429000 chr2A 76.578 491 55 26 160 623 684268730 684269187 8.460000e-52 215.0
13 TraesCS2D01G429000 chr6A 88.918 379 36 6 3196 3571 552716730 552716355 2.740000e-126 462.0
14 TraesCS2D01G429000 chr6A 91.379 58 5 0 3119 3176 368099312 368099255 3.220000e-11 80.5
15 TraesCS2D01G429000 chr6A 100.000 28 0 0 2994 3021 595990343 595990370 7.000000e-03 52.8
16 TraesCS2D01G429000 chr7A 88.654 379 39 4 3195 3571 162765103 162765479 3.540000e-125 459.0
17 TraesCS2D01G429000 chr7A 88.624 378 38 5 3196 3571 162762374 162762748 4.580000e-124 455.0
18 TraesCS2D01G429000 chr7A 81.166 446 64 12 2019 2457 465754459 465754027 1.340000e-89 340.0
19 TraesCS2D01G429000 chr4D 88.684 380 38 4 3195 3571 128921213 128921590 3.540000e-125 459.0
20 TraesCS2D01G429000 chr4D 84.483 116 18 0 552 667 366287774 366287659 8.820000e-22 115.0
21 TraesCS2D01G429000 chr4D 84.483 116 18 0 552 667 366311145 366311030 8.820000e-22 115.0
22 TraesCS2D01G429000 chr4D 88.235 68 6 2 3110 3176 454900758 454900824 3.220000e-11 80.5
23 TraesCS2D01G429000 chr4A 88.684 380 36 7 3195 3571 607328832 607329207 1.270000e-124 457.0
24 TraesCS2D01G429000 chr4A 86.667 150 19 1 3573 3721 311306569 311306718 8.640000e-37 165.0
25 TraesCS2D01G429000 chr4A 83.036 112 19 0 553 664 98774076 98774187 6.870000e-18 102.0
26 TraesCS2D01G429000 chr1A 88.654 379 38 5 3195 3571 7329094 7329469 1.270000e-124 457.0
27 TraesCS2D01G429000 chr1A 91.026 78 7 0 570 647 343470925 343471002 5.310000e-19 106.0
28 TraesCS2D01G429000 chr7B 83.123 397 49 12 2069 2457 62404574 62404188 2.870000e-91 346.0
29 TraesCS2D01G429000 chr7B 80.761 447 62 13 2019 2457 633920239 633920669 1.040000e-85 327.0
30 TraesCS2D01G429000 chr7B 89.706 68 5 2 3110 3176 427545232 427545298 6.920000e-13 86.1
31 TraesCS2D01G429000 chr7B 100.000 28 0 0 2993 3020 479490905 479490878 7.000000e-03 52.8
32 TraesCS2D01G429000 chr5D 88.995 209 20 3 3679 3886 125812995 125812789 4.980000e-64 255.0
33 TraesCS2D01G429000 chr5D 90.728 151 14 0 3572 3722 235836662 235836812 6.580000e-48 202.0
34 TraesCS2D01G429000 chr5D 100.000 29 0 0 2994 3022 468836874 468836902 2.000000e-03 54.7
35 TraesCS2D01G429000 chr5B 92.308 143 9 1 3572 3714 269300814 269300674 6.580000e-48 202.0
36 TraesCS2D01G429000 chr6D 88.816 152 16 1 3572 3722 455137336 455137487 6.630000e-43 185.0
37 TraesCS2D01G429000 chr6D 90.805 87 6 2 3110 3195 455137255 455137340 8.820000e-22 115.0
38 TraesCS2D01G429000 chr6B 86.755 151 16 4 3572 3720 692341603 692341751 8.640000e-37 165.0
39 TraesCS2D01G429000 chr6B 91.011 89 6 2 3108 3195 692341520 692341607 6.820000e-23 119.0
40 TraesCS2D01G429000 chr6B 88.235 68 6 2 3110 3176 397682302 397682368 3.220000e-11 80.5
41 TraesCS2D01G429000 chr1D 85.333 150 21 1 3572 3720 293358230 293358379 1.870000e-33 154.0
42 TraesCS2D01G429000 chr7D 85.714 133 19 0 3590 3722 242844214 242844346 1.460000e-29 141.0
43 TraesCS2D01G429000 chr4B 81.897 116 19 1 552 667 450887193 450887080 3.200000e-16 97.1
44 TraesCS2D01G429000 chr4B 89.706 68 5 2 3110 3176 374020628 374020694 6.920000e-13 86.1
45 TraesCS2D01G429000 chr4B 91.379 58 5 0 3119 3176 475737778 475737721 3.220000e-11 80.5
46 TraesCS2D01G429000 chr3B 94.872 39 1 1 2985 3022 571760471 571760433 4.190000e-05 60.2


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 TraesCS2D01G429000 chr2D 540835313 540839198 3885 False 7177 7177 100.000000 1 3886 1 chr2D.!!$F1 3885
1 TraesCS2D01G429000 chr2B 646453032 646456051 3019 False 5035 5035 96.680000 848 3886 1 chr2B.!!$F2 3038
2 TraesCS2D01G429000 chr2A 684268730 684271593 2863 False 1081 2446 86.341333 160 3113 3 chr2A.!!$F3 2953
3 TraesCS2D01G429000 chr7A 162762374 162765479 3105 False 457 459 88.639000 3195 3571 2 chr7A.!!$F1 376

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
681 709 0.032815 TCGTTCGTCAGGACAATGCA 59.967 50.0 0.00 0.0 0.00 3.96 F
792 827 0.107263 TGTGGACAAGCACTGCAAGA 60.107 50.0 3.30 0.0 37.43 3.02 F
820 875 0.322997 TTGCGAAATCGACCCCCATT 60.323 50.0 7.06 0.0 43.02 3.16 F
822 877 0.380733 GCGAAATCGACCCCCATTTC 59.619 55.0 7.06 0.0 43.02 2.17 F
842 897 0.389296 ATGTCATCGTCGTGGCGAAA 60.389 50.0 0.00 0.0 44.38 3.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2444 2549 4.085210 GGCAAACGTATTATCAGCGAGTAC 60.085 45.833 0.00 0.00 0.00 2.73 R
2603 2708 4.501229 CCTGTAGAGCTGCTCCATTAGAAG 60.501 50.000 25.09 12.94 33.31 2.85 R
2812 2917 8.512966 TTATGACACCGGATGAAAAATTGATA 57.487 30.769 9.46 0.00 0.00 2.15 R
2826 2931 2.159254 CCCTGCAAAATTATGACACCGG 60.159 50.000 0.00 0.00 0.00 5.28 R
3103 3209 4.570772 GGAAGCGCACTCTATAATTTGACA 59.429 41.667 11.47 0.00 0.00 3.58 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
25 26 8.560576 ACATTGTTCGTAAAATTCAAAGTCTG 57.439 30.769 0.00 0.00 0.00 3.51
26 27 7.647715 ACATTGTTCGTAAAATTCAAAGTCTGG 59.352 33.333 0.00 0.00 0.00 3.86
27 28 6.687081 TGTTCGTAAAATTCAAAGTCTGGT 57.313 33.333 0.00 0.00 0.00 4.00
28 29 7.789273 TGTTCGTAAAATTCAAAGTCTGGTA 57.211 32.000 0.00 0.00 0.00 3.25
29 30 8.385898 TGTTCGTAAAATTCAAAGTCTGGTAT 57.614 30.769 0.00 0.00 0.00 2.73
31 32 9.113876 GTTCGTAAAATTCAAAGTCTGGTATTG 57.886 33.333 0.00 0.00 0.00 1.90
32 33 8.610248 TCGTAAAATTCAAAGTCTGGTATTGA 57.390 30.769 0.00 0.00 0.00 2.57
34 35 9.672086 CGTAAAATTCAAAGTCTGGTATTGAAA 57.328 29.630 4.51 0.00 43.79 2.69
41 42 8.335532 TCAAAGTCTGGTATTGAAAATAGTGG 57.664 34.615 0.00 0.00 30.60 4.00
42 43 8.160765 TCAAAGTCTGGTATTGAAAATAGTGGA 58.839 33.333 0.00 0.00 30.60 4.02
43 44 8.454106 CAAAGTCTGGTATTGAAAATAGTGGAG 58.546 37.037 0.00 0.00 0.00 3.86
44 45 6.116126 AGTCTGGTATTGAAAATAGTGGAGC 58.884 40.000 0.00 0.00 0.00 4.70
46 47 4.196193 TGGTATTGAAAATAGTGGAGCGG 58.804 43.478 0.00 0.00 0.00 5.52
47 48 3.003378 GGTATTGAAAATAGTGGAGCGGC 59.997 47.826 0.00 0.00 0.00 6.53
48 49 1.459450 TTGAAAATAGTGGAGCGGCC 58.541 50.000 0.00 0.00 37.10 6.13
49 50 0.326595 TGAAAATAGTGGAGCGGCCA 59.673 50.000 2.24 0.00 46.96 5.36
56 57 2.033448 TGGAGCGGCCAACGAATT 59.967 55.556 2.24 0.00 45.87 2.17
57 58 1.602323 TGGAGCGGCCAACGAATTT 60.602 52.632 2.24 0.00 45.87 1.82
58 59 1.861542 TGGAGCGGCCAACGAATTTG 61.862 55.000 2.24 0.00 45.87 2.32
62 63 3.171911 GGCCAACGAATTTGCGCG 61.172 61.111 0.00 0.00 34.13 6.86
63 64 3.171911 GCCAACGAATTTGCGCGG 61.172 61.111 8.83 0.00 33.34 6.46
64 65 3.171911 CCAACGAATTTGCGCGGC 61.172 61.111 8.83 0.00 33.34 6.53
65 66 2.126888 CAACGAATTTGCGCGGCT 60.127 55.556 8.83 0.00 33.86 5.52
66 67 1.133664 CAACGAATTTGCGCGGCTA 59.866 52.632 8.83 0.00 33.86 3.93
67 68 0.248054 CAACGAATTTGCGCGGCTAT 60.248 50.000 8.83 0.00 33.86 2.97
69 70 1.508632 ACGAATTTGCGCGGCTATAT 58.491 45.000 8.83 0.00 33.86 0.86
70 71 1.871039 ACGAATTTGCGCGGCTATATT 59.129 42.857 8.83 2.18 33.86 1.28
72 73 2.651703 CGAATTTGCGCGGCTATATTTG 59.348 45.455 8.83 2.80 0.00 2.32
73 74 2.050477 ATTTGCGCGGCTATATTTGC 57.950 45.000 8.83 0.00 0.00 3.68
74 75 1.021202 TTTGCGCGGCTATATTTGCT 58.979 45.000 8.83 0.00 0.00 3.91
75 76 0.307453 TTGCGCGGCTATATTTGCTG 59.693 50.000 8.83 5.23 39.61 4.41
77 78 0.307760 GCGCGGCTATATTTGCTGTT 59.692 50.000 8.83 0.00 38.90 3.16
78 79 1.660333 GCGCGGCTATATTTGCTGTTC 60.660 52.381 8.83 1.41 38.90 3.18
79 80 1.867233 CGCGGCTATATTTGCTGTTCT 59.133 47.619 0.00 0.00 38.90 3.01
80 81 2.287915 CGCGGCTATATTTGCTGTTCTT 59.712 45.455 0.00 0.00 38.90 2.52
81 82 3.621794 GCGGCTATATTTGCTGTTCTTG 58.378 45.455 9.84 0.00 38.90 3.02
82 83 3.312421 GCGGCTATATTTGCTGTTCTTGA 59.688 43.478 9.84 0.00 38.90 3.02
83 84 4.201910 GCGGCTATATTTGCTGTTCTTGAA 60.202 41.667 9.84 0.00 38.90 2.69
84 85 5.266242 CGGCTATATTTGCTGTTCTTGAAC 58.734 41.667 6.56 6.56 32.57 3.18
86 87 6.403636 CGGCTATATTTGCTGTTCTTGAACTT 60.404 38.462 13.65 0.00 32.57 2.66
88 89 8.624776 GGCTATATTTGCTGTTCTTGAACTTAT 58.375 33.333 13.65 4.29 0.00 1.73
96 97 7.083858 TGCTGTTCTTGAACTTATTACAATGC 58.916 34.615 13.65 0.00 0.00 3.56
97 98 7.083858 GCTGTTCTTGAACTTATTACAATGCA 58.916 34.615 13.65 0.00 0.00 3.96
99 100 9.282247 CTGTTCTTGAACTTATTACAATGCATC 57.718 33.333 13.65 0.00 0.00 3.91
101 102 8.462016 GTTCTTGAACTTATTACAATGCATCCT 58.538 33.333 0.00 0.00 0.00 3.24
102 103 7.988737 TCTTGAACTTATTACAATGCATCCTG 58.011 34.615 0.00 0.00 0.00 3.86
103 104 7.611467 TCTTGAACTTATTACAATGCATCCTGT 59.389 33.333 8.95 8.95 0.00 4.00
104 105 7.701539 TGAACTTATTACAATGCATCCTGTT 57.298 32.000 9.22 2.74 0.00 3.16
105 106 8.800370 TGAACTTATTACAATGCATCCTGTTA 57.200 30.769 9.22 1.28 0.00 2.41
106 107 9.237187 TGAACTTATTACAATGCATCCTGTTAA 57.763 29.630 9.22 3.20 0.00 2.01
116 117 6.645790 ATGCATCCTGTTAATTGAAGGATC 57.354 37.500 12.88 9.84 45.76 3.36
118 119 6.131264 TGCATCCTGTTAATTGAAGGATCAT 58.869 36.000 12.88 0.00 45.76 2.45
119 120 6.608405 TGCATCCTGTTAATTGAAGGATCATT 59.392 34.615 12.88 0.00 45.76 2.57
120 121 7.124599 TGCATCCTGTTAATTGAAGGATCATTT 59.875 33.333 12.88 0.00 45.76 2.32
122 123 8.689061 CATCCTGTTAATTGAAGGATCATTTGA 58.311 33.333 12.88 0.00 45.76 2.69
124 125 7.340232 TCCTGTTAATTGAAGGATCATTTGAGG 59.660 37.037 0.00 0.00 35.14 3.86
125 126 6.866480 TGTTAATTGAAGGATCATTTGAGGC 58.134 36.000 0.00 0.00 34.96 4.70
126 127 6.664816 TGTTAATTGAAGGATCATTTGAGGCT 59.335 34.615 0.00 0.00 34.96 4.58
127 128 7.833682 TGTTAATTGAAGGATCATTTGAGGCTA 59.166 33.333 0.00 0.00 34.96 3.93
130 131 5.635278 TGAAGGATCATTTGAGGCTATCA 57.365 39.130 0.00 0.00 35.62 2.15
131 132 5.618236 TGAAGGATCATTTGAGGCTATCAG 58.382 41.667 0.00 0.00 39.68 2.90
132 133 5.367644 TGAAGGATCATTTGAGGCTATCAGA 59.632 40.000 0.00 0.00 39.68 3.27
133 134 6.044054 TGAAGGATCATTTGAGGCTATCAGAT 59.956 38.462 0.00 0.00 39.68 2.90
134 135 7.236225 TGAAGGATCATTTGAGGCTATCAGATA 59.764 37.037 0.00 0.00 39.68 1.98
135 136 7.752518 AGGATCATTTGAGGCTATCAGATAT 57.247 36.000 0.00 0.00 39.68 1.63
136 137 8.160434 AGGATCATTTGAGGCTATCAGATATT 57.840 34.615 0.00 0.00 39.68 1.28
140 141 7.738847 TCATTTGAGGCTATCAGATATTCACA 58.261 34.615 0.00 0.00 39.68 3.58
141 142 8.380867 TCATTTGAGGCTATCAGATATTCACAT 58.619 33.333 0.00 0.00 39.68 3.21
142 143 7.974482 TTTGAGGCTATCAGATATTCACATG 57.026 36.000 0.00 0.00 39.68 3.21
143 144 6.923199 TGAGGCTATCAGATATTCACATGA 57.077 37.500 0.00 0.00 32.77 3.07
144 145 6.695429 TGAGGCTATCAGATATTCACATGAC 58.305 40.000 0.00 0.00 32.77 3.06
145 146 6.268387 TGAGGCTATCAGATATTCACATGACA 59.732 38.462 0.00 0.00 32.77 3.58
146 147 6.699366 AGGCTATCAGATATTCACATGACAG 58.301 40.000 0.00 0.00 0.00 3.51
149 150 7.278203 GGCTATCAGATATTCACATGACAGATG 59.722 40.741 0.00 0.00 0.00 2.90
150 151 7.818446 GCTATCAGATATTCACATGACAGATGT 59.182 37.037 0.00 0.00 0.00 3.06
151 152 9.708092 CTATCAGATATTCACATGACAGATGTT 57.292 33.333 0.00 0.00 0.00 2.71
152 153 8.975663 ATCAGATATTCACATGACAGATGTTT 57.024 30.769 0.00 0.00 0.00 2.83
153 154 8.797350 TCAGATATTCACATGACAGATGTTTT 57.203 30.769 0.00 0.00 0.00 2.43
154 155 8.671028 TCAGATATTCACATGACAGATGTTTTG 58.329 33.333 0.00 0.00 0.00 2.44
155 156 8.456471 CAGATATTCACATGACAGATGTTTTGT 58.544 33.333 0.00 0.00 0.00 2.83
156 157 9.671279 AGATATTCACATGACAGATGTTTTGTA 57.329 29.630 0.00 0.00 0.00 2.41
158 159 6.934048 TTCACATGACAGATGTTTTGTACA 57.066 33.333 0.00 0.00 41.97 2.90
165 166 9.299963 CATGACAGATGTTTTGTACAAGAAAAA 57.700 29.630 8.56 0.00 40.89 1.94
168 169 9.736023 GACAGATGTTTTGTACAAGAAAAATCT 57.264 29.630 15.58 15.58 40.89 2.40
183 185 0.613777 AATCTTCACCTGTCCCGGTC 59.386 55.000 0.00 0.00 34.29 4.79
209 221 4.388499 GGCGTCACACGATGGGGT 62.388 66.667 0.00 0.00 46.05 4.95
269 282 1.456518 CTCCAGCCGATCTCCCTCA 60.457 63.158 0.00 0.00 0.00 3.86
283 296 2.507854 CCTCACCACCGCCGGATAT 61.508 63.158 11.71 0.00 0.00 1.63
329 351 1.876156 CAACAGGTCTTCAGAAGGTGC 59.124 52.381 10.42 1.65 0.00 5.01
330 352 0.398318 ACAGGTCTTCAGAAGGTGCC 59.602 55.000 10.42 10.07 0.00 5.01
332 354 2.035442 GGTCTTCAGAAGGTGCCGC 61.035 63.158 10.42 0.00 0.00 6.53
338 360 3.626924 AGAAGGTGCCGCGGTTCT 61.627 61.111 28.70 23.57 0.00 3.01
381 403 2.590073 CTTGTTTGCACACACGAACAA 58.410 42.857 4.89 8.45 46.68 2.83
382 404 2.254918 TGTTTGCACACACGAACAAG 57.745 45.000 0.45 0.00 40.24 3.16
390 412 1.525197 ACACACGAACAAGCGTACATG 59.475 47.619 0.00 0.00 43.59 3.21
391 413 0.511221 ACACGAACAAGCGTACATGC 59.489 50.000 0.00 0.00 43.59 4.06
411 433 5.512753 TGCTTCACATGTACAAACATTGT 57.487 34.783 0.00 0.00 44.07 2.71
416 438 7.429340 GCTTCACATGTACAAACATTGTATAGC 59.571 37.037 0.00 7.78 44.07 2.97
418 440 6.881602 TCACATGTACAAACATTGTATAGCCA 59.118 34.615 0.00 1.13 44.07 4.75
446 468 4.473444 CATTTGGCAGGTACATATTCCCT 58.527 43.478 0.00 0.00 0.00 4.20
448 470 2.054799 TGGCAGGTACATATTCCCTCC 58.945 52.381 0.00 0.00 0.00 4.30
450 472 1.692519 GCAGGTACATATTCCCTCCGT 59.307 52.381 0.00 0.00 0.00 4.69
452 474 3.728845 CAGGTACATATTCCCTCCGTTG 58.271 50.000 0.00 0.00 0.00 4.10
461 489 4.657814 ATTCCCTCCGTTGCCATAATAT 57.342 40.909 0.00 0.00 0.00 1.28
501 529 5.933790 TCAACATACTTTGCGTTATTGACC 58.066 37.500 0.00 0.00 0.00 4.02
504 532 5.001232 ACATACTTTGCGTTATTGACCTGT 58.999 37.500 0.00 0.00 0.00 4.00
509 537 3.052455 TGCGTTATTGACCTGTCATGT 57.948 42.857 0.03 0.00 39.64 3.21
525 553 8.502738 ACCTGTCATGTTTTATACTCCCATTAT 58.497 33.333 0.00 0.00 0.00 1.28
526 554 9.354673 CCTGTCATGTTTTATACTCCCATTATT 57.645 33.333 0.00 0.00 0.00 1.40
558 586 8.429739 TTTTTAGCGACTGTTTATTTTCATCG 57.570 30.769 0.00 0.00 0.00 3.84
561 589 6.715344 AGCGACTGTTTATTTTCATCGTAA 57.285 33.333 0.00 0.00 0.00 3.18
563 591 6.367969 AGCGACTGTTTATTTTCATCGTAACT 59.632 34.615 0.00 0.00 0.00 2.24
601 629 6.595716 GCAGATACCAAACTAGTCAATTCACT 59.404 38.462 0.00 0.00 0.00 3.41
619 647 2.814919 CACTCGAGACTAGTGACACCTT 59.185 50.000 21.68 0.00 45.89 3.50
620 648 2.814919 ACTCGAGACTAGTGACACCTTG 59.185 50.000 21.68 0.00 0.00 3.61
621 649 3.075148 CTCGAGACTAGTGACACCTTGA 58.925 50.000 6.58 0.00 0.00 3.02
622 650 3.075148 TCGAGACTAGTGACACCTTGAG 58.925 50.000 0.00 0.00 0.00 3.02
633 661 2.051334 CACCTTGAGTGTGACCCAAA 57.949 50.000 0.00 0.00 41.93 3.28
650 678 5.003804 ACCCAAACACTCATCATAACACTC 58.996 41.667 0.00 0.00 0.00 3.51
652 680 4.436050 CCAAACACTCATCATAACACTCGC 60.436 45.833 0.00 0.00 0.00 5.03
653 681 2.893637 ACACTCATCATAACACTCGCC 58.106 47.619 0.00 0.00 0.00 5.54
654 682 2.497675 ACACTCATCATAACACTCGCCT 59.502 45.455 0.00 0.00 0.00 5.52
657 685 2.791560 CTCATCATAACACTCGCCTTCG 59.208 50.000 0.00 0.00 0.00 3.79
658 686 1.258982 CATCATAACACTCGCCTTCGC 59.741 52.381 0.00 0.00 35.26 4.70
659 687 0.530744 TCATAACACTCGCCTTCGCT 59.469 50.000 0.00 0.00 35.26 4.93
662 690 0.032952 TAACACTCGCCTTCGCTGTT 59.967 50.000 0.00 0.00 38.73 3.16
663 691 1.222115 AACACTCGCCTTCGCTGTTC 61.222 55.000 0.00 0.00 33.78 3.18
664 692 2.430921 ACTCGCCTTCGCTGTTCG 60.431 61.111 0.00 0.00 40.15 3.95
665 693 2.430921 CTCGCCTTCGCTGTTCGT 60.431 61.111 0.00 0.00 39.67 3.85
666 694 2.022129 CTCGCCTTCGCTGTTCGTT 61.022 57.895 0.00 0.00 39.67 3.85
668 696 2.470286 GCCTTCGCTGTTCGTTCG 59.530 61.111 0.00 0.00 39.67 3.95
669 697 2.308039 GCCTTCGCTGTTCGTTCGT 61.308 57.895 0.00 0.00 39.67 3.85
670 698 1.773496 CCTTCGCTGTTCGTTCGTC 59.227 57.895 0.00 0.00 39.67 4.20
671 699 0.937699 CCTTCGCTGTTCGTTCGTCA 60.938 55.000 0.00 0.00 39.67 4.35
672 700 0.431233 CTTCGCTGTTCGTTCGTCAG 59.569 55.000 12.33 12.33 39.67 3.51
673 701 0.937699 TTCGCTGTTCGTTCGTCAGG 60.938 55.000 15.83 9.80 39.67 3.86
674 702 1.371267 CGCTGTTCGTTCGTCAGGA 60.371 57.895 15.83 0.00 0.00 3.86
675 703 1.606350 CGCTGTTCGTTCGTCAGGAC 61.606 60.000 15.83 0.00 0.00 3.85
676 704 0.596600 GCTGTTCGTTCGTCAGGACA 60.597 55.000 15.83 0.00 0.00 4.02
678 706 2.404215 CTGTTCGTTCGTCAGGACAAT 58.596 47.619 0.00 0.00 0.00 2.71
679 707 2.131972 TGTTCGTTCGTCAGGACAATG 58.868 47.619 0.00 0.17 0.00 2.82
680 708 1.136336 GTTCGTTCGTCAGGACAATGC 60.136 52.381 0.00 0.00 0.00 3.56
681 709 0.032815 TCGTTCGTCAGGACAATGCA 59.967 50.000 0.00 0.00 0.00 3.96
682 710 0.865111 CGTTCGTCAGGACAATGCAA 59.135 50.000 0.00 0.00 0.00 4.08
683 711 1.262950 CGTTCGTCAGGACAATGCAAA 59.737 47.619 0.00 0.00 0.00 3.68
684 712 2.650608 GTTCGTCAGGACAATGCAAAC 58.349 47.619 0.00 0.00 0.00 2.93
686 714 3.394674 TCGTCAGGACAATGCAAACTA 57.605 42.857 0.00 0.00 0.00 2.24
687 715 3.734463 TCGTCAGGACAATGCAAACTAA 58.266 40.909 0.00 0.00 0.00 2.24
690 718 4.393062 CGTCAGGACAATGCAAACTAAGAT 59.607 41.667 0.00 0.00 0.00 2.40
692 720 6.092122 CGTCAGGACAATGCAAACTAAGATAA 59.908 38.462 0.00 0.00 0.00 1.75
694 722 9.109393 GTCAGGACAATGCAAACTAAGATAATA 57.891 33.333 0.00 0.00 0.00 0.98
695 723 9.109393 TCAGGACAATGCAAACTAAGATAATAC 57.891 33.333 0.00 0.00 0.00 1.89
696 724 9.113838 CAGGACAATGCAAACTAAGATAATACT 57.886 33.333 0.00 0.00 0.00 2.12
697 725 9.686683 AGGACAATGCAAACTAAGATAATACTT 57.313 29.630 0.00 0.00 0.00 2.24
699 727 9.226345 GACAATGCAAACTAAGATAATACTTGC 57.774 33.333 0.00 0.00 38.48 4.01
704 732 8.879759 TGCAAACTAAGATAATACTTGCAGTAC 58.120 33.333 2.65 0.00 41.82 2.73
705 733 8.879759 GCAAACTAAGATAATACTTGCAGTACA 58.120 33.333 0.00 0.00 38.03 2.90
708 736 9.587772 AACTAAGATAATACTTGCAGTACACTG 57.412 33.333 4.96 4.96 46.40 3.66
709 737 8.750298 ACTAAGATAATACTTGCAGTACACTGT 58.250 33.333 10.87 0.00 45.45 3.55
710 738 7.834068 AAGATAATACTTGCAGTACACTGTG 57.166 36.000 6.19 6.19 45.45 3.66
711 739 6.936279 AGATAATACTTGCAGTACACTGTGT 58.064 36.000 18.51 18.51 45.45 3.72
712 740 7.036220 AGATAATACTTGCAGTACACTGTGTC 58.964 38.462 17.99 9.26 45.45 3.67
713 741 4.873746 ATACTTGCAGTACACTGTGTCT 57.126 40.909 17.99 11.37 45.45 3.41
714 742 3.543680 ACTTGCAGTACACTGTGTCTT 57.456 42.857 17.99 3.95 45.45 3.01
717 745 3.819564 TGCAGTACACTGTGTCTTCTT 57.180 42.857 17.99 0.00 45.45 2.52
719 747 4.513442 TGCAGTACACTGTGTCTTCTTTT 58.487 39.130 17.99 0.00 45.45 2.27
757 785 8.784043 AGTAAATTGTGTTTCAATCAGTCCTAC 58.216 33.333 0.00 0.00 44.85 3.18
758 786 7.823745 AAATTGTGTTTCAATCAGTCCTACT 57.176 32.000 0.00 0.00 44.85 2.57
759 787 8.918202 AAATTGTGTTTCAATCAGTCCTACTA 57.082 30.769 0.00 0.00 44.85 1.82
776 808 5.478332 TCCTACTAGCAGGACATCATATGTG 59.522 44.000 7.70 3.41 45.03 3.21
785 817 3.313526 GGACATCATATGTGGACAAGCAC 59.686 47.826 1.90 0.00 45.03 4.40
792 827 0.107263 TGTGGACAAGCACTGCAAGA 60.107 50.000 3.30 0.00 37.43 3.02
819 874 1.029947 GTTGCGAAATCGACCCCCAT 61.030 55.000 7.06 0.00 43.02 4.00
820 875 0.322997 TTGCGAAATCGACCCCCATT 60.323 50.000 7.06 0.00 43.02 3.16
822 877 0.380733 GCGAAATCGACCCCCATTTC 59.619 55.000 7.06 0.00 43.02 2.17
824 879 2.297701 CGAAATCGACCCCCATTTCAT 58.702 47.619 0.00 0.00 43.02 2.57
842 897 0.389296 ATGTCATCGTCGTGGCGAAA 60.389 50.000 0.00 0.00 44.38 3.46
950 1007 3.036959 AAACCCACCCCACCCCAA 61.037 61.111 0.00 0.00 0.00 4.12
951 1008 3.398365 AAACCCACCCCACCCCAAC 62.398 63.158 0.00 0.00 0.00 3.77
971 1032 4.379243 CCCACCACGCGAGCTTCT 62.379 66.667 15.93 0.00 0.00 2.85
976 1037 1.515952 CCACGCGAGCTTCTCTCAG 60.516 63.158 15.93 0.00 41.98 3.35
977 1038 1.211449 CACGCGAGCTTCTCTCAGT 59.789 57.895 15.93 0.00 41.98 3.41
978 1039 0.796491 CACGCGAGCTTCTCTCAGTC 60.796 60.000 15.93 0.00 41.98 3.51
979 1040 1.582424 CGCGAGCTTCTCTCAGTCG 60.582 63.158 0.00 0.00 41.98 4.18
980 1041 4.375723 CGAGCTTCTCTCAGTCGC 57.624 61.111 0.00 0.00 41.98 5.19
981 1042 1.226547 CGAGCTTCTCTCAGTCGCC 60.227 63.158 0.00 0.00 41.98 5.54
982 1043 1.886585 GAGCTTCTCTCAGTCGCCA 59.113 57.895 0.00 0.00 41.51 5.69
989 1050 0.970937 CTCTCAGTCGCCACCCCTTA 60.971 60.000 0.00 0.00 0.00 2.69
991 1052 1.534476 TCAGTCGCCACCCCTTACA 60.534 57.895 0.00 0.00 0.00 2.41
1062 1123 2.677875 CCCAGCAAGAACAGGGGC 60.678 66.667 0.00 0.00 37.66 5.80
1088 1155 4.779733 GCGTCCTCCTCCCCCTCA 62.780 72.222 0.00 0.00 0.00 3.86
1143 1210 1.142778 CGTTCGCTGCTCCTCTAAGC 61.143 60.000 0.00 0.00 42.82 3.09
1298 1365 6.342338 AGCTCAGAGAAGAATTTTTGCAAT 57.658 33.333 0.00 0.00 0.00 3.56
1369 1436 2.562738 CCCCAAGAAAAATCACCCACTC 59.437 50.000 0.00 0.00 0.00 3.51
1538 1605 1.899814 TCCCGCAATCTGTACTCTGTT 59.100 47.619 0.00 0.00 0.00 3.16
1902 2005 3.511934 GGATACCTAGTACATGCTCCCTG 59.488 52.174 0.00 0.00 0.00 4.45
2603 2708 4.453136 TGAACCACCAAGTCGCTTTAATAC 59.547 41.667 0.00 0.00 0.00 1.89
2812 2917 7.578310 ATGTTTGCTGCTAATTGTGATATCT 57.422 32.000 3.98 0.00 0.00 1.98
3220 3326 1.148310 AATAAATCCGAGGCGCATCG 58.852 50.000 34.96 34.96 42.36 3.84
3337 3443 2.300967 GCTCCTCCCCATGACACCA 61.301 63.158 0.00 0.00 0.00 4.17
3453 3559 5.072600 TGTGTCCACCCCCTCATTATATAAC 59.927 44.000 0.00 0.00 0.00 1.89
3469 3575 9.295825 CATTATATAACAGGCCAAGGATACAAA 57.704 33.333 5.01 0.00 41.41 2.83
3508 3614 9.298250 ACACGTCTCTATATCCTATTTACACAT 57.702 33.333 0.00 0.00 0.00 3.21
3589 3695 4.618920 ACACAAGTAAGGGTTAGGTCTG 57.381 45.455 0.00 0.00 0.00 3.51
3617 3723 6.618287 TCACAAGAAATACACAAGGAACAG 57.382 37.500 0.00 0.00 0.00 3.16
3682 3788 2.880890 CAAGTCTGTGTTGGAAGGAAGG 59.119 50.000 0.00 0.00 0.00 3.46
3740 3846 3.552478 GGGCTTTATGACGAGGTAGTAGC 60.552 52.174 0.00 0.00 0.00 3.58
3860 3966 5.460091 TGAAATGATATGACGAAGAAGCTCG 59.540 40.000 0.00 0.00 44.50 5.03
3868 3974 3.190744 TGACGAAGAAGCTCGACATAAGT 59.809 43.478 0.00 0.00 41.44 2.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 7.647715 CCAGACTTTGAATTTTACGAACAATGT 59.352 33.333 0.00 0.00 33.73 2.71
1 2 7.647715 ACCAGACTTTGAATTTTACGAACAATG 59.352 33.333 0.00 0.00 0.00 2.82
2 3 7.712797 ACCAGACTTTGAATTTTACGAACAAT 58.287 30.769 0.00 0.00 0.00 2.71
4 5 6.687081 ACCAGACTTTGAATTTTACGAACA 57.313 33.333 0.00 0.00 0.00 3.18
6 7 9.058174 TCAATACCAGACTTTGAATTTTACGAA 57.942 29.630 0.00 0.00 0.00 3.85
7 8 8.610248 TCAATACCAGACTTTGAATTTTACGA 57.390 30.769 0.00 0.00 0.00 3.43
8 9 9.672086 TTTCAATACCAGACTTTGAATTTTACG 57.328 29.630 1.82 0.00 38.68 3.18
15 16 8.792633 CCACTATTTTCAATACCAGACTTTGAA 58.207 33.333 0.00 0.00 37.53 2.69
16 17 8.160765 TCCACTATTTTCAATACCAGACTTTGA 58.839 33.333 0.00 0.00 0.00 2.69
17 18 8.335532 TCCACTATTTTCAATACCAGACTTTG 57.664 34.615 0.00 0.00 0.00 2.77
18 19 7.121315 GCTCCACTATTTTCAATACCAGACTTT 59.879 37.037 0.00 0.00 0.00 2.66
19 20 6.599638 GCTCCACTATTTTCAATACCAGACTT 59.400 38.462 0.00 0.00 0.00 3.01
20 21 6.116126 GCTCCACTATTTTCAATACCAGACT 58.884 40.000 0.00 0.00 0.00 3.24
21 22 5.006746 CGCTCCACTATTTTCAATACCAGAC 59.993 44.000 0.00 0.00 0.00 3.51
24 25 4.196193 CCGCTCCACTATTTTCAATACCA 58.804 43.478 0.00 0.00 0.00 3.25
25 26 3.003378 GCCGCTCCACTATTTTCAATACC 59.997 47.826 0.00 0.00 0.00 2.73
26 27 3.003378 GGCCGCTCCACTATTTTCAATAC 59.997 47.826 0.00 0.00 34.01 1.89
27 28 3.211045 GGCCGCTCCACTATTTTCAATA 58.789 45.455 0.00 0.00 34.01 1.90
28 29 2.024414 GGCCGCTCCACTATTTTCAAT 58.976 47.619 0.00 0.00 34.01 2.57
29 30 1.271652 TGGCCGCTCCACTATTTTCAA 60.272 47.619 0.00 0.00 40.72 2.69
31 32 1.132453 GTTGGCCGCTCCACTATTTTC 59.868 52.381 0.00 0.00 46.55 2.29
32 33 1.173913 GTTGGCCGCTCCACTATTTT 58.826 50.000 0.00 0.00 46.55 1.82
34 35 1.449601 CGTTGGCCGCTCCACTATT 60.450 57.895 0.00 0.00 46.55 1.73
35 36 1.895020 TTCGTTGGCCGCTCCACTAT 61.895 55.000 0.00 0.00 46.55 2.12
36 37 1.895020 ATTCGTTGGCCGCTCCACTA 61.895 55.000 0.00 0.00 46.55 2.74
39 40 1.602323 AAATTCGTTGGCCGCTCCA 60.602 52.632 0.00 0.00 44.85 3.86
40 41 1.154035 CAAATTCGTTGGCCGCTCC 60.154 57.895 0.00 0.00 36.19 4.70
41 42 1.801512 GCAAATTCGTTGGCCGCTC 60.802 57.895 0.00 0.00 37.73 5.03
42 43 2.258286 GCAAATTCGTTGGCCGCT 59.742 55.556 0.00 0.00 37.73 5.52
43 44 3.171911 CGCAAATTCGTTGGCCGC 61.172 61.111 0.00 0.00 37.73 6.53
44 45 3.171911 GCGCAAATTCGTTGGCCG 61.172 61.111 0.30 0.00 37.73 6.13
46 47 3.171911 CCGCGCAAATTCGTTGGC 61.172 61.111 8.75 0.00 37.73 4.52
47 48 2.246993 TAGCCGCGCAAATTCGTTGG 62.247 55.000 8.75 0.00 37.73 3.77
48 49 0.248054 ATAGCCGCGCAAATTCGTTG 60.248 50.000 8.75 0.00 40.50 4.10
49 50 1.292061 TATAGCCGCGCAAATTCGTT 58.708 45.000 8.75 0.00 0.00 3.85
50 51 1.508632 ATATAGCCGCGCAAATTCGT 58.491 45.000 8.75 0.00 0.00 3.85
51 52 2.594529 AATATAGCCGCGCAAATTCG 57.405 45.000 8.75 0.00 0.00 3.34
52 53 2.405025 GCAAATATAGCCGCGCAAATTC 59.595 45.455 8.75 0.00 0.00 2.17
53 54 2.034558 AGCAAATATAGCCGCGCAAATT 59.965 40.909 8.75 0.00 0.00 1.82
54 55 1.608590 AGCAAATATAGCCGCGCAAAT 59.391 42.857 8.75 0.00 0.00 2.32
55 56 1.021202 AGCAAATATAGCCGCGCAAA 58.979 45.000 8.75 0.00 0.00 3.68
56 57 0.307453 CAGCAAATATAGCCGCGCAA 59.693 50.000 8.75 0.00 0.00 4.85
57 58 0.813610 ACAGCAAATATAGCCGCGCA 60.814 50.000 8.75 0.00 0.00 6.09
58 59 0.307760 AACAGCAAATATAGCCGCGC 59.692 50.000 0.00 0.00 0.00 6.86
59 60 1.867233 AGAACAGCAAATATAGCCGCG 59.133 47.619 0.00 0.00 0.00 6.46
60 61 3.312421 TCAAGAACAGCAAATATAGCCGC 59.688 43.478 0.00 0.00 0.00 6.53
61 62 5.065218 AGTTCAAGAACAGCAAATATAGCCG 59.935 40.000 14.69 0.00 43.47 5.52
62 63 6.442513 AGTTCAAGAACAGCAAATATAGCC 57.557 37.500 14.69 0.00 43.47 3.93
69 70 9.462174 CATTGTAATAAGTTCAAGAACAGCAAA 57.538 29.630 14.69 1.63 43.47 3.68
70 71 7.594758 GCATTGTAATAAGTTCAAGAACAGCAA 59.405 33.333 14.69 9.73 43.47 3.91
72 73 7.083858 TGCATTGTAATAAGTTCAAGAACAGC 58.916 34.615 14.69 4.25 43.47 4.40
73 74 9.282247 GATGCATTGTAATAAGTTCAAGAACAG 57.718 33.333 14.69 0.00 43.47 3.16
74 75 8.243426 GGATGCATTGTAATAAGTTCAAGAACA 58.757 33.333 14.69 0.00 43.47 3.18
75 76 8.462016 AGGATGCATTGTAATAAGTTCAAGAAC 58.538 33.333 0.00 4.82 41.45 3.01
77 78 7.611467 ACAGGATGCATTGTAATAAGTTCAAGA 59.389 33.333 0.00 0.00 42.53 3.02
78 79 7.765307 ACAGGATGCATTGTAATAAGTTCAAG 58.235 34.615 0.00 0.00 42.53 3.02
79 80 7.701539 ACAGGATGCATTGTAATAAGTTCAA 57.298 32.000 0.00 0.00 42.53 2.69
80 81 7.701539 AACAGGATGCATTGTAATAAGTTCA 57.298 32.000 0.00 0.00 42.53 3.18
88 89 7.395772 TCCTTCAATTAACAGGATGCATTGTAA 59.604 33.333 0.00 0.00 42.53 2.41
89 90 6.889177 TCCTTCAATTAACAGGATGCATTGTA 59.111 34.615 0.00 0.00 42.53 2.41
91 92 6.211587 TCCTTCAATTAACAGGATGCATTG 57.788 37.500 0.00 0.00 42.53 2.82
92 93 6.608405 TGATCCTTCAATTAACAGGATGCATT 59.392 34.615 14.23 0.00 45.81 3.56
96 97 8.689061 TCAAATGATCCTTCAATTAACAGGATG 58.311 33.333 14.23 4.73 45.81 3.51
99 100 7.486647 CCTCAAATGATCCTTCAATTAACAGG 58.513 38.462 0.00 0.00 34.96 4.00
101 102 6.664816 AGCCTCAAATGATCCTTCAATTAACA 59.335 34.615 0.00 0.00 34.96 2.41
102 103 7.105241 AGCCTCAAATGATCCTTCAATTAAC 57.895 36.000 0.00 0.00 34.96 2.01
103 104 9.071276 GATAGCCTCAAATGATCCTTCAATTAA 57.929 33.333 0.00 0.00 34.96 1.40
104 105 8.219868 TGATAGCCTCAAATGATCCTTCAATTA 58.780 33.333 0.00 0.00 34.96 1.40
105 106 7.064866 TGATAGCCTCAAATGATCCTTCAATT 58.935 34.615 0.00 0.00 34.96 2.32
106 107 6.607970 TGATAGCCTCAAATGATCCTTCAAT 58.392 36.000 0.00 0.00 34.96 2.57
107 108 6.005066 TGATAGCCTCAAATGATCCTTCAA 57.995 37.500 0.00 0.00 34.96 2.69
108 109 5.367644 TCTGATAGCCTCAAATGATCCTTCA 59.632 40.000 0.00 0.00 32.49 3.02
110 111 5.901413 TCTGATAGCCTCAAATGATCCTT 57.099 39.130 0.00 0.00 32.14 3.36
111 112 7.752518 ATATCTGATAGCCTCAAATGATCCT 57.247 36.000 3.48 0.00 32.14 3.24
112 113 8.045507 TGAATATCTGATAGCCTCAAATGATCC 58.954 37.037 3.48 0.00 32.14 3.36
115 116 7.738847 TGTGAATATCTGATAGCCTCAAATGA 58.261 34.615 3.48 0.00 32.14 2.57
116 117 7.974482 TGTGAATATCTGATAGCCTCAAATG 57.026 36.000 3.48 0.00 32.14 2.32
118 119 7.658982 GTCATGTGAATATCTGATAGCCTCAAA 59.341 37.037 3.48 2.42 32.14 2.69
119 120 7.157347 GTCATGTGAATATCTGATAGCCTCAA 58.843 38.462 3.48 0.04 32.14 3.02
120 121 6.268387 TGTCATGTGAATATCTGATAGCCTCA 59.732 38.462 3.48 3.73 0.00 3.86
122 123 6.496218 TCTGTCATGTGAATATCTGATAGCCT 59.504 38.462 3.48 0.00 29.87 4.58
124 125 7.818446 ACATCTGTCATGTGAATATCTGATAGC 59.182 37.037 3.48 0.00 29.87 2.97
125 126 9.708092 AACATCTGTCATGTGAATATCTGATAG 57.292 33.333 3.48 0.00 31.80 2.08
127 128 8.975663 AAACATCTGTCATGTGAATATCTGAT 57.024 30.769 0.00 0.00 31.80 2.90
130 131 8.571461 ACAAAACATCTGTCATGTGAATATCT 57.429 30.769 0.00 0.00 31.80 1.98
131 132 9.708222 GTACAAAACATCTGTCATGTGAATATC 57.292 33.333 9.80 0.00 31.86 1.63
132 133 9.230122 TGTACAAAACATCTGTCATGTGAATAT 57.770 29.630 0.00 0.00 31.43 1.28
133 134 8.614469 TGTACAAAACATCTGTCATGTGAATA 57.386 30.769 0.00 0.00 31.43 1.75
134 135 7.509141 TGTACAAAACATCTGTCATGTGAAT 57.491 32.000 0.00 0.00 31.43 2.57
135 136 6.934048 TGTACAAAACATCTGTCATGTGAA 57.066 33.333 0.00 0.00 31.43 3.18
136 137 6.765512 TCTTGTACAAAACATCTGTCATGTGA 59.234 34.615 10.03 0.00 38.10 3.58
141 142 9.515020 GATTTTTCTTGTACAAAACATCTGTCA 57.485 29.630 10.03 0.00 38.10 3.58
142 143 9.736023 AGATTTTTCTTGTACAAAACATCTGTC 57.264 29.630 15.85 6.98 38.10 3.51
149 150 8.807581 CAGGTGAAGATTTTTCTTGTACAAAAC 58.192 33.333 10.03 0.00 0.00 2.43
150 151 8.527810 ACAGGTGAAGATTTTTCTTGTACAAAA 58.472 29.630 10.03 1.20 0.00 2.44
151 152 8.062065 ACAGGTGAAGATTTTTCTTGTACAAA 57.938 30.769 10.03 0.00 0.00 2.83
152 153 7.201785 GGACAGGTGAAGATTTTTCTTGTACAA 60.202 37.037 8.28 8.28 0.00 2.41
153 154 6.262273 GGACAGGTGAAGATTTTTCTTGTACA 59.738 38.462 0.00 0.00 0.00 2.90
154 155 6.294010 GGGACAGGTGAAGATTTTTCTTGTAC 60.294 42.308 0.00 0.00 0.00 2.90
155 156 5.768164 GGGACAGGTGAAGATTTTTCTTGTA 59.232 40.000 0.00 0.00 0.00 2.41
156 157 4.584743 GGGACAGGTGAAGATTTTTCTTGT 59.415 41.667 0.00 0.00 0.00 3.16
158 159 3.821033 CGGGACAGGTGAAGATTTTTCTT 59.179 43.478 0.00 0.00 0.00 2.52
165 166 0.252284 AGACCGGGACAGGTGAAGAT 60.252 55.000 6.32 0.00 46.09 2.40
168 169 0.113776 AGTAGACCGGGACAGGTGAA 59.886 55.000 6.32 0.00 46.09 3.18
183 185 4.063967 TGTGACGCCGGGCAGTAG 62.064 66.667 20.71 4.85 0.00 2.57
202 204 2.750237 GCCGGTGTTCACCCCATC 60.750 66.667 15.20 0.34 0.00 3.51
203 205 4.715523 CGCCGGTGTTCACCCCAT 62.716 66.667 15.20 0.00 0.00 4.00
220 232 0.759436 TAGACGAGGAATCAGGCCCC 60.759 60.000 0.00 0.00 0.00 5.80
235 248 4.202274 GGCTGGAGAAGAAATACCCTAGAC 60.202 50.000 0.00 0.00 0.00 2.59
269 282 0.111832 TAGAGATATCCGGCGGTGGT 59.888 55.000 27.32 15.51 0.00 4.16
283 296 3.755628 GGCCACGCACGGTAGAGA 61.756 66.667 0.00 0.00 0.00 3.10
309 331 1.876156 GCACCTTCTGAAGACCTGTTG 59.124 52.381 18.68 2.81 0.00 3.33
311 333 0.398318 GGCACCTTCTGAAGACCTGT 59.602 55.000 18.68 5.20 0.00 4.00
316 338 2.048222 CGCGGCACCTTCTGAAGA 60.048 61.111 18.68 0.00 0.00 2.87
329 351 0.591170 ATGTCAACAAAGAACCGCGG 59.409 50.000 26.86 26.86 0.00 6.46
330 352 2.399396 AATGTCAACAAAGAACCGCG 57.601 45.000 0.00 0.00 0.00 6.46
332 354 5.518812 TGATGAAATGTCAACAAAGAACCG 58.481 37.500 0.00 0.00 37.30 4.44
371 393 1.721489 GCATGTACGCTTGTTCGTGTG 60.721 52.381 0.00 0.00 43.21 3.82
402 424 5.893687 TGCTTGATGGCTATACAATGTTTG 58.106 37.500 0.00 0.00 0.00 2.93
403 425 6.720112 ATGCTTGATGGCTATACAATGTTT 57.280 33.333 0.00 0.00 0.00 2.83
404 426 6.720112 AATGCTTGATGGCTATACAATGTT 57.280 33.333 0.00 0.00 0.00 2.71
406 428 5.924254 CCAAATGCTTGATGGCTATACAATG 59.076 40.000 0.00 0.00 34.14 2.82
407 429 6.092955 CCAAATGCTTGATGGCTATACAAT 57.907 37.500 0.00 0.00 34.14 2.71
408 430 5.518848 CCAAATGCTTGATGGCTATACAA 57.481 39.130 0.00 0.00 34.14 2.41
416 438 0.899720 ACCTGCCAAATGCTTGATGG 59.100 50.000 1.46 1.46 42.00 3.51
418 440 2.806434 TGTACCTGCCAAATGCTTGAT 58.194 42.857 0.00 0.00 42.00 2.57
431 453 3.728845 CAACGGAGGGAATATGTACCTG 58.271 50.000 0.00 0.00 34.02 4.00
441 463 4.447138 AATATTATGGCAACGGAGGGAA 57.553 40.909 0.00 0.00 42.51 3.97
443 465 6.882140 TGTATTAATATTATGGCAACGGAGGG 59.118 38.462 0.00 0.00 42.51 4.30
446 468 9.647797 CTAGTGTATTAATATTATGGCAACGGA 57.352 33.333 0.00 0.00 42.51 4.69
448 470 9.647797 TCCTAGTGTATTAATATTATGGCAACG 57.352 33.333 0.00 0.00 42.51 4.10
480 508 5.472137 ACAGGTCAATAACGCAAAGTATGTT 59.528 36.000 0.00 0.00 0.00 2.71
490 518 4.419522 AAACATGACAGGTCAATAACGC 57.580 40.909 6.17 0.00 43.58 4.84
533 561 8.071368 ACGATGAAAATAAACAGTCGCTAAAAA 58.929 29.630 0.00 0.00 0.00 1.94
536 564 6.715344 ACGATGAAAATAAACAGTCGCTAA 57.285 33.333 0.00 0.00 0.00 3.09
537 565 7.543172 AGTTACGATGAAAATAAACAGTCGCTA 59.457 33.333 0.00 0.00 0.00 4.26
538 566 6.367969 AGTTACGATGAAAATAAACAGTCGCT 59.632 34.615 0.00 0.00 0.00 4.93
554 582 6.036470 TGCAAGACTTGAGATAGTTACGATG 58.964 40.000 19.51 0.00 0.00 3.84
556 584 5.414765 TCTGCAAGACTTGAGATAGTTACGA 59.585 40.000 19.51 0.00 38.67 3.43
601 629 3.075148 CTCAAGGTGTCACTAGTCTCGA 58.925 50.000 2.35 0.00 0.00 4.04
622 650 2.571212 TGATGAGTGTTTGGGTCACAC 58.429 47.619 0.00 0.00 44.25 3.82
624 652 4.759693 TGTTATGATGAGTGTTTGGGTCAC 59.240 41.667 0.00 0.00 36.22 3.67
626 654 5.003804 AGTGTTATGATGAGTGTTTGGGTC 58.996 41.667 0.00 0.00 0.00 4.46
627 655 4.985538 AGTGTTATGATGAGTGTTTGGGT 58.014 39.130 0.00 0.00 0.00 4.51
628 656 4.093408 CGAGTGTTATGATGAGTGTTTGGG 59.907 45.833 0.00 0.00 0.00 4.12
629 657 4.436050 GCGAGTGTTATGATGAGTGTTTGG 60.436 45.833 0.00 0.00 0.00 3.28
631 659 3.684788 GGCGAGTGTTATGATGAGTGTTT 59.315 43.478 0.00 0.00 0.00 2.83
633 661 2.497675 AGGCGAGTGTTATGATGAGTGT 59.502 45.455 0.00 0.00 0.00 3.55
639 667 1.137086 AGCGAAGGCGAGTGTTATGAT 59.863 47.619 0.00 0.00 46.35 2.45
650 678 2.470286 GAACGAACAGCGAAGGCG 59.530 61.111 0.00 0.00 46.35 5.52
652 680 0.937699 TGACGAACGAACAGCGAAGG 60.938 55.000 0.14 0.00 44.57 3.46
653 681 0.431233 CTGACGAACGAACAGCGAAG 59.569 55.000 0.14 0.00 44.57 3.79
654 682 0.937699 CCTGACGAACGAACAGCGAA 60.938 55.000 15.24 0.00 44.57 4.70
657 685 0.596600 TGTCCTGACGAACGAACAGC 60.597 55.000 15.24 7.89 0.00 4.40
658 686 1.847818 TTGTCCTGACGAACGAACAG 58.152 50.000 0.14 9.53 0.00 3.16
659 687 2.131972 CATTGTCCTGACGAACGAACA 58.868 47.619 0.14 0.62 0.00 3.18
662 690 0.032815 TGCATTGTCCTGACGAACGA 59.967 50.000 0.14 0.00 0.00 3.85
663 691 0.865111 TTGCATTGTCCTGACGAACG 59.135 50.000 0.00 0.00 0.00 3.95
664 692 2.290641 AGTTTGCATTGTCCTGACGAAC 59.709 45.455 0.00 0.00 0.00 3.95
665 693 2.571212 AGTTTGCATTGTCCTGACGAA 58.429 42.857 0.00 0.00 0.00 3.85
666 694 2.254546 AGTTTGCATTGTCCTGACGA 57.745 45.000 0.00 0.00 0.00 4.20
668 696 5.886960 ATCTTAGTTTGCATTGTCCTGAC 57.113 39.130 0.00 0.00 0.00 3.51
669 697 9.109393 GTATTATCTTAGTTTGCATTGTCCTGA 57.891 33.333 0.00 0.00 0.00 3.86
670 698 9.113838 AGTATTATCTTAGTTTGCATTGTCCTG 57.886 33.333 0.00 0.00 0.00 3.86
671 699 9.686683 AAGTATTATCTTAGTTTGCATTGTCCT 57.313 29.630 0.00 0.00 0.00 3.85
672 700 9.722056 CAAGTATTATCTTAGTTTGCATTGTCC 57.278 33.333 0.00 0.00 0.00 4.02
673 701 9.226345 GCAAGTATTATCTTAGTTTGCATTGTC 57.774 33.333 0.00 0.00 0.00 3.18
674 702 8.739039 TGCAAGTATTATCTTAGTTTGCATTGT 58.261 29.630 5.03 0.00 0.00 2.71
675 703 9.229784 CTGCAAGTATTATCTTAGTTTGCATTG 57.770 33.333 9.10 0.00 0.00 2.82
723 751 0.596082 ACACAATTTACTGCACCCGC 59.404 50.000 0.00 0.00 39.24 6.13
725 753 4.314740 TGAAACACAATTTACTGCACCC 57.685 40.909 0.00 0.00 0.00 4.61
757 785 4.039609 TGTCCACATATGATGTCCTGCTAG 59.960 45.833 10.38 0.00 42.70 3.42
758 786 3.966665 TGTCCACATATGATGTCCTGCTA 59.033 43.478 10.38 0.00 42.70 3.49
759 787 2.773661 TGTCCACATATGATGTCCTGCT 59.226 45.455 10.38 0.00 42.70 4.24
772 804 0.956633 CTTGCAGTGCTTGTCCACAT 59.043 50.000 17.60 0.00 38.18 3.21
776 808 1.597742 TTCTCTTGCAGTGCTTGTCC 58.402 50.000 17.60 0.00 0.00 4.02
785 817 2.032054 TCGCAACACTTTTCTCTTGCAG 59.968 45.455 0.00 0.00 39.19 4.41
792 827 3.303791 GGTCGATTTCGCAACACTTTTCT 60.304 43.478 0.00 0.00 39.60 2.52
819 874 1.075542 GCCACGACGATGACATGAAA 58.924 50.000 0.00 0.00 0.00 2.69
820 875 1.075979 CGCCACGACGATGACATGAA 61.076 55.000 0.00 0.00 34.06 2.57
822 877 1.075979 TTCGCCACGACGATGACATG 61.076 55.000 0.00 0.00 42.54 3.21
824 879 1.006825 CTTTCGCCACGACGATGACA 61.007 55.000 0.00 0.00 42.54 3.58
842 897 1.677820 CGTATTTTTGTCGGAGGGGCT 60.678 52.381 0.00 0.00 0.00 5.19
888 944 3.169512 TGGGAAGAAGATGAAAACCCC 57.830 47.619 0.00 0.00 35.48 4.95
971 1032 1.077805 TAAGGGGTGGCGACTGAGA 59.922 57.895 0.00 0.00 0.00 3.27
976 1037 0.179081 GAGATGTAAGGGGTGGCGAC 60.179 60.000 0.00 0.00 0.00 5.19
977 1038 1.335132 GGAGATGTAAGGGGTGGCGA 61.335 60.000 0.00 0.00 0.00 5.54
978 1039 1.146263 GGAGATGTAAGGGGTGGCG 59.854 63.158 0.00 0.00 0.00 5.69
979 1040 0.470341 GAGGAGATGTAAGGGGTGGC 59.530 60.000 0.00 0.00 0.00 5.01
980 1041 1.132500 GGAGGAGATGTAAGGGGTGG 58.868 60.000 0.00 0.00 0.00 4.61
981 1042 1.879575 TGGAGGAGATGTAAGGGGTG 58.120 55.000 0.00 0.00 0.00 4.61
982 1043 2.412591 CATGGAGGAGATGTAAGGGGT 58.587 52.381 0.00 0.00 0.00 4.95
1080 1147 0.031111 CTGTACCAGGATGAGGGGGA 60.031 60.000 0.00 0.00 39.69 4.81
1081 1148 1.700042 GCTGTACCAGGATGAGGGGG 61.700 65.000 0.00 0.00 39.69 5.40
1082 1149 1.700042 GGCTGTACCAGGATGAGGGG 61.700 65.000 0.00 0.00 39.69 4.79
1083 1150 0.692419 AGGCTGTACCAGGATGAGGG 60.692 60.000 0.00 0.00 43.14 4.30
1084 1151 0.755686 GAGGCTGTACCAGGATGAGG 59.244 60.000 0.00 0.00 43.14 3.86
1088 1155 0.912486 GGTTGAGGCTGTACCAGGAT 59.088 55.000 9.21 0.00 43.14 3.24
1107 1174 0.328258 ACGGAGAAATGGTGAAGGGG 59.672 55.000 0.00 0.00 0.00 4.79
1143 1210 6.042093 TGGTGAGAATATTAGGACAGCTTAGG 59.958 42.308 0.00 0.00 0.00 2.69
1298 1365 7.873719 TGTTGAGGATAACTGAACTGAAAAA 57.126 32.000 0.00 0.00 0.00 1.94
1369 1436 1.608590 ACCGGAGAAACAATTGCACAG 59.391 47.619 9.46 0.00 0.00 3.66
1459 1526 7.686438 TCTGCTGTCTTGCTCAATTAAATTA 57.314 32.000 0.00 0.00 0.00 1.40
1902 2005 8.589629 CACGGTACAGTAAAACAATATAGTGAC 58.410 37.037 7.27 0.00 0.00 3.67
2444 2549 4.085210 GGCAAACGTATTATCAGCGAGTAC 60.085 45.833 0.00 0.00 0.00 2.73
2603 2708 4.501229 CCTGTAGAGCTGCTCCATTAGAAG 60.501 50.000 25.09 12.94 33.31 2.85
2812 2917 8.512966 TTATGACACCGGATGAAAAATTGATA 57.487 30.769 9.46 0.00 0.00 2.15
2826 2931 2.159254 CCCTGCAAAATTATGACACCGG 60.159 50.000 0.00 0.00 0.00 5.28
3103 3209 4.570772 GGAAGCGCACTCTATAATTTGACA 59.429 41.667 11.47 0.00 0.00 3.58
3116 3222 1.267806 CAAGAACATTGGAAGCGCACT 59.732 47.619 11.47 0.00 0.00 4.40
3119 3225 2.053627 CAACAAGAACATTGGAAGCGC 58.946 47.619 0.00 0.00 0.00 5.92
3120 3226 3.624326 TCAACAAGAACATTGGAAGCG 57.376 42.857 0.00 0.00 0.00 4.68
3220 3326 2.930682 GCTTGGAACTTGGTAGATCGAC 59.069 50.000 0.00 0.00 0.00 4.20
3307 3413 2.678934 AGGAGCGCCCGTAGTCAA 60.679 61.111 2.29 0.00 40.87 3.18
3337 3443 0.108520 CCGGTGTGCGGTATTGTAGT 60.109 55.000 0.00 0.00 0.00 2.73
3453 3559 2.689983 GGACATTTGTATCCTTGGCCTG 59.310 50.000 3.32 0.00 34.24 4.85
3589 3695 7.672983 TCCTTGTGTATTTCTTGTGATCTTC 57.327 36.000 0.00 0.00 0.00 2.87
3617 3723 8.023706 CCTTAAGTTCCTTGCTATTCTTGAAAC 58.976 37.037 0.97 0.00 0.00 2.78
3714 3820 0.830648 CCTCGTCATAAAGCCCCTCA 59.169 55.000 0.00 0.00 0.00 3.86
3740 3846 7.372714 TCTTTCATTTTGATCATGTCACCTTG 58.627 34.615 0.00 0.00 36.32 3.61
3842 3948 3.953766 TGTCGAGCTTCTTCGTCATATC 58.046 45.455 0.00 0.00 41.22 1.63
3860 3966 6.887376 TTGACGATGAGCTAAACTTATGTC 57.113 37.500 0.00 0.00 0.00 3.06


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

AutoCloner maintained by Alex Coulton.