Multiple sequence alignment - TraesCS1A01G122400

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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 TraesCS1A01G122400 chr1A 100.000 3160 0 0 1 3160 137413518 137410359 0.000000e+00 5836.0
1 TraesCS1A01G122400 chr1A 100.000 29 0 0 1073 1101 137412389 137412361 2.000000e-03 54.7
2 TraesCS1A01G122400 chr1A 100.000 29 0 0 1130 1158 137412446 137412418 2.000000e-03 54.7
3 TraesCS1A01G122400 chr1D 92.532 2437 99 23 664 3054 124920166 124917767 0.000000e+00 3415.0
4 TraesCS1A01G122400 chr1D 91.857 307 22 3 25 330 459519618 459519922 2.910000e-115 425.0
5 TraesCS1A01G122400 chr1D 86.517 178 19 4 1315 1492 427826920 427827092 1.160000e-44 191.0
6 TraesCS1A01G122400 chr1D 97.273 110 3 0 3051 3160 124917731 124917622 1.500000e-43 187.0
7 TraesCS1A01G122400 chr1D 88.966 145 14 2 471 615 124920417 124920275 9.010000e-41 178.0
8 TraesCS1A01G122400 chr1D 83.065 124 18 3 326 447 12331978 12331856 3.330000e-20 110.0
9 TraesCS1A01G122400 chr1D 100.000 29 0 0 1130 1158 124919780 124919752 2.000000e-03 54.7
10 TraesCS1A01G122400 chr1B 96.754 1294 40 2 1065 2357 188914019 188912727 0.000000e+00 2156.0
11 TraesCS1A01G122400 chr1B 96.124 516 15 3 2390 2905 188912727 188912217 0.000000e+00 837.0
12 TraesCS1A01G122400 chr1B 85.512 635 51 19 472 1079 188916605 188915985 2.680000e-175 625.0
13 TraesCS1A01G122400 chr1B 95.122 164 8 0 2891 3054 188909311 188909148 3.130000e-65 259.0
14 TraesCS1A01G122400 chr1B 88.636 176 13 3 1315 1489 314565538 314565707 1.150000e-49 207.0
15 TraesCS1A01G122400 chr1B 88.166 169 19 1 1315 1483 592646808 592646641 1.920000e-47 200.0
16 TraesCS1A01G122400 chr1B 99.091 110 1 0 3051 3160 188909113 188909004 6.910000e-47 198.0
17 TraesCS1A01G122400 chr1B 86.592 179 17 5 1315 1493 24349051 24349222 1.160000e-44 191.0
18 TraesCS1A01G122400 chr1B 100.000 33 0 0 990 1022 188916128 188916096 9.460000e-06 62.1
19 TraesCS1A01G122400 chr1B 100.000 29 0 0 1130 1158 188914011 188913983 2.000000e-03 54.7
20 TraesCS1A01G122400 chr4A 91.290 310 24 2 21 330 699937918 699937612 1.360000e-113 420.0
21 TraesCS1A01G122400 chr4A 90.523 306 28 1 25 330 4498206 4497902 1.370000e-108 403.0
22 TraesCS1A01G122400 chr5B 88.856 341 33 5 23 360 467949751 467949413 6.310000e-112 414.0
23 TraesCS1A01G122400 chr4D 90.252 318 29 2 23 340 438105206 438105521 6.310000e-112 414.0
24 TraesCS1A01G122400 chr4D 90.615 309 28 1 22 330 7927921 7927614 2.930000e-110 409.0
25 TraesCS1A01G122400 chr4D 85.000 120 12 2 328 447 135171093 135170980 1.990000e-22 117.0
26 TraesCS1A01G122400 chr6B 90.909 308 27 1 23 330 524969312 524969618 2.270000e-111 412.0
27 TraesCS1A01G122400 chr6B 82.192 146 19 5 475 617 321256059 321255918 5.540000e-23 119.0
28 TraesCS1A01G122400 chr5D 90.615 309 26 3 23 330 481804126 481803820 1.060000e-109 407.0
29 TraesCS1A01G122400 chr5D 94.118 68 4 0 331 398 240505272 240505339 1.550000e-18 104.0
30 TraesCS1A01G122400 chr2D 89.655 319 32 1 12 330 247054652 247054969 3.800000e-109 405.0
31 TraesCS1A01G122400 chr2D 89.820 167 11 2 1318 1483 524963640 524963801 3.190000e-50 209.0
32 TraesCS1A01G122400 chr2D 87.719 114 13 1 330 443 31733413 31733301 7.110000e-27 132.0
33 TraesCS1A01G122400 chr2D 83.871 124 8 6 331 444 551849964 551850085 1.200000e-19 108.0
34 TraesCS1A01G122400 chr2D 94.203 69 4 0 331 399 45322999 45323067 4.310000e-19 106.0
35 TraesCS1A01G122400 chr2D 90.000 70 5 1 375 444 555111906 555111973 4.340000e-14 89.8
36 TraesCS1A01G122400 chr2B 87.571 177 16 2 1307 1482 453265438 453265609 1.920000e-47 200.0
37 TraesCS1A01G122400 chr2B 91.176 68 2 2 382 448 1285633 1285569 4.340000e-14 89.8
38 TraesCS1A01G122400 chr7A 87.429 175 18 3 1317 1491 540770403 540770573 6.910000e-47 198.0
39 TraesCS1A01G122400 chr7A 84.536 97 14 1 611 707 43796738 43796643 9.330000e-16 95.3
40 TraesCS1A01G122400 chr7A 85.526 76 8 2 375 447 118239574 118239499 3.380000e-10 76.8
41 TraesCS1A01G122400 chr6D 87.611 113 11 1 331 443 47226607 47226498 9.200000e-26 128.0
42 TraesCS1A01G122400 chr4B 94.521 73 4 0 328 400 663740601 663740673 2.580000e-21 113.0
43 TraesCS1A01G122400 chr3A 93.056 72 5 0 327 398 638069852 638069923 4.310000e-19 106.0
44 TraesCS1A01G122400 chr7B 85.714 91 12 1 617 707 737316879 737316790 9.330000e-16 95.3
45 TraesCS1A01G122400 chr7B 85.714 91 12 1 617 707 737708473 737708384 9.330000e-16 95.3
46 TraesCS1A01G122400 chr7B 85.714 91 12 1 617 707 737725736 737725647 9.330000e-16 95.3
47 TraesCS1A01G122400 chr7B 85.714 91 12 1 617 707 737743501 737743412 9.330000e-16 95.3
48 TraesCS1A01G122400 chr7B 87.654 81 8 2 366 444 640921047 640921127 3.360000e-15 93.5
49 TraesCS1A01G122400 chr7B 84.615 91 13 1 617 707 737016385 737016296 4.340000e-14 89.8
50 TraesCS1A01G122400 chr7B 84.615 91 13 1 617 707 737357694 737357605 4.340000e-14 89.8
51 TraesCS1A01G122400 chr7B 84.615 91 13 1 617 707 737611374 737611285 4.340000e-14 89.8


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 TraesCS1A01G122400 chr1A 137410359 137413518 3159 True 1981.800000 5836 100.000000 1 3160 3 chr1A.!!$R1 3159
1 TraesCS1A01G122400 chr1D 124917622 124920417 2795 True 958.675000 3415 94.692750 471 3160 4 chr1D.!!$R2 2689
2 TraesCS1A01G122400 chr1B 188909004 188916605 7601 True 598.828571 2156 96.086143 472 3160 7 chr1B.!!$R2 2688

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
985 1058 0.178801 AAGGGGGAAAGAGGGTCCAT 60.179 55.0 0.0 0.0 36.83 3.41 F
1288 3339 0.469892 TCTGAGTCACTGCCTCACCA 60.470 55.0 0.0 0.0 35.23 4.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1857 3909 0.603975 GGTTGACTGACCTGCTGTCC 60.604 60.000 4.79 0.00 43.78 4.02 R
2707 4784 1.324736 GAGTTTAGATTGACGCAGGCG 59.675 52.381 12.71 12.71 46.03 5.52 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
26 27 3.264666 GAGCACATCTCTGTAGCCG 57.735 57.895 0.00 0.00 38.78 5.52
27 28 0.249238 GAGCACATCTCTGTAGCCGG 60.249 60.000 0.00 0.00 38.78 6.13
28 29 0.684479 AGCACATCTCTGTAGCCGGA 60.684 55.000 5.05 0.00 33.14 5.14
29 30 0.390860 GCACATCTCTGTAGCCGGAT 59.609 55.000 5.05 0.00 33.14 4.18
30 31 1.604185 GCACATCTCTGTAGCCGGATC 60.604 57.143 5.05 0.00 33.14 3.36
31 32 1.000283 CACATCTCTGTAGCCGGATCC 60.000 57.143 5.05 0.00 33.14 3.36
32 33 1.133325 ACATCTCTGTAGCCGGATCCT 60.133 52.381 5.05 0.00 32.49 3.24
33 34 1.543802 CATCTCTGTAGCCGGATCCTC 59.456 57.143 5.05 1.17 0.00 3.71
34 35 0.847373 TCTCTGTAGCCGGATCCTCT 59.153 55.000 5.05 9.28 0.00 3.69
35 36 2.055579 TCTCTGTAGCCGGATCCTCTA 58.944 52.381 5.05 8.25 0.00 2.43
36 37 2.442126 TCTCTGTAGCCGGATCCTCTAA 59.558 50.000 5.05 2.49 0.00 2.10
37 38 2.554893 CTCTGTAGCCGGATCCTCTAAC 59.445 54.545 5.05 3.83 0.00 2.34
38 39 2.175069 TCTGTAGCCGGATCCTCTAACT 59.825 50.000 5.05 2.35 0.00 2.24
39 40 2.959707 CTGTAGCCGGATCCTCTAACTT 59.040 50.000 5.05 0.00 0.00 2.66
40 41 4.141321 TCTGTAGCCGGATCCTCTAACTTA 60.141 45.833 5.05 0.00 0.00 2.24
41 42 4.539726 TGTAGCCGGATCCTCTAACTTAA 58.460 43.478 5.05 0.00 0.00 1.85
42 43 4.957954 TGTAGCCGGATCCTCTAACTTAAA 59.042 41.667 5.05 0.00 0.00 1.52
43 44 4.674281 AGCCGGATCCTCTAACTTAAAG 57.326 45.455 5.05 0.00 0.00 1.85
44 45 4.287552 AGCCGGATCCTCTAACTTAAAGA 58.712 43.478 5.05 0.00 0.00 2.52
45 46 4.715297 AGCCGGATCCTCTAACTTAAAGAA 59.285 41.667 5.05 0.00 0.00 2.52
46 47 5.051153 GCCGGATCCTCTAACTTAAAGAAG 58.949 45.833 5.05 0.00 38.76 2.85
47 48 5.602628 CCGGATCCTCTAACTTAAAGAAGG 58.397 45.833 10.75 0.00 36.95 3.46
48 49 5.453480 CCGGATCCTCTAACTTAAAGAAGGG 60.453 48.000 10.75 0.00 36.95 3.95
49 50 5.363005 CGGATCCTCTAACTTAAAGAAGGGA 59.637 44.000 10.75 0.00 36.95 4.20
50 51 6.127140 CGGATCCTCTAACTTAAAGAAGGGAA 60.127 42.308 10.75 0.00 36.95 3.97
51 52 7.276658 GGATCCTCTAACTTAAAGAAGGGAAG 58.723 42.308 3.84 0.00 36.95 3.46
52 53 7.092802 GGATCCTCTAACTTAAAGAAGGGAAGT 60.093 40.741 3.84 0.00 36.95 3.01
53 54 7.242322 TCCTCTAACTTAAAGAAGGGAAGTC 57.758 40.000 0.00 0.00 36.95 3.01
54 55 6.785963 TCCTCTAACTTAAAGAAGGGAAGTCA 59.214 38.462 0.00 0.00 36.95 3.41
55 56 6.874664 CCTCTAACTTAAAGAAGGGAAGTCAC 59.125 42.308 0.00 0.00 36.95 3.67
56 57 7.256368 CCTCTAACTTAAAGAAGGGAAGTCACT 60.256 40.741 0.00 0.00 36.95 3.41
57 58 8.716674 TCTAACTTAAAGAAGGGAAGTCACTA 57.283 34.615 0.00 0.00 36.95 2.74
58 59 9.322769 TCTAACTTAAAGAAGGGAAGTCACTAT 57.677 33.333 0.00 0.00 36.95 2.12
59 60 9.372369 CTAACTTAAAGAAGGGAAGTCACTATG 57.628 37.037 0.00 0.00 36.95 2.23
60 61 6.174049 ACTTAAAGAAGGGAAGTCACTATGC 58.826 40.000 0.00 0.00 36.95 3.14
61 62 4.917906 AAAGAAGGGAAGTCACTATGCT 57.082 40.909 0.00 0.00 0.00 3.79
62 63 7.180408 ACTTAAAGAAGGGAAGTCACTATGCTA 59.820 37.037 0.00 0.00 36.95 3.49
63 64 5.346181 AAGAAGGGAAGTCACTATGCTAC 57.654 43.478 0.00 0.00 0.00 3.58
64 65 4.353777 AGAAGGGAAGTCACTATGCTACA 58.646 43.478 0.00 0.00 0.00 2.74
65 66 4.404073 AGAAGGGAAGTCACTATGCTACAG 59.596 45.833 0.00 0.00 0.00 2.74
66 67 3.714144 AGGGAAGTCACTATGCTACAGT 58.286 45.455 0.00 0.00 0.00 3.55
67 68 3.449018 AGGGAAGTCACTATGCTACAGTG 59.551 47.826 6.59 6.59 43.92 3.66
68 69 3.190874 GGAAGTCACTATGCTACAGTGC 58.809 50.000 7.72 4.54 42.58 4.40
69 70 3.118956 GGAAGTCACTATGCTACAGTGCT 60.119 47.826 7.72 6.22 42.58 4.40
70 71 3.791973 AGTCACTATGCTACAGTGCTC 57.208 47.619 7.72 4.80 42.58 4.26
71 72 2.098280 AGTCACTATGCTACAGTGCTCG 59.902 50.000 7.72 0.00 42.58 5.03
72 73 2.092323 TCACTATGCTACAGTGCTCGT 58.908 47.619 7.72 0.00 42.58 4.18
73 74 2.097629 TCACTATGCTACAGTGCTCGTC 59.902 50.000 7.72 0.00 42.58 4.20
74 75 2.098280 CACTATGCTACAGTGCTCGTCT 59.902 50.000 0.00 0.00 37.22 4.18
75 76 3.312697 CACTATGCTACAGTGCTCGTCTA 59.687 47.826 0.00 0.00 37.22 2.59
76 77 3.945921 ACTATGCTACAGTGCTCGTCTAA 59.054 43.478 0.00 0.00 0.00 2.10
77 78 4.580995 ACTATGCTACAGTGCTCGTCTAAT 59.419 41.667 0.00 0.00 0.00 1.73
78 79 3.150848 TGCTACAGTGCTCGTCTAATG 57.849 47.619 0.00 0.00 0.00 1.90
79 80 2.492088 TGCTACAGTGCTCGTCTAATGT 59.508 45.455 0.00 0.00 0.00 2.71
80 81 3.692593 TGCTACAGTGCTCGTCTAATGTA 59.307 43.478 0.00 0.00 0.00 2.29
81 82 4.157105 TGCTACAGTGCTCGTCTAATGTAA 59.843 41.667 0.00 0.00 0.00 2.41
82 83 5.100259 GCTACAGTGCTCGTCTAATGTAAA 58.900 41.667 0.00 0.00 0.00 2.01
83 84 5.575606 GCTACAGTGCTCGTCTAATGTAAAA 59.424 40.000 0.00 0.00 0.00 1.52
84 85 6.255887 GCTACAGTGCTCGTCTAATGTAAAAT 59.744 38.462 0.00 0.00 0.00 1.82
85 86 6.408858 ACAGTGCTCGTCTAATGTAAAATG 57.591 37.500 0.00 0.00 0.00 2.32
86 87 6.163476 ACAGTGCTCGTCTAATGTAAAATGA 58.837 36.000 0.00 0.00 0.00 2.57
87 88 6.649141 ACAGTGCTCGTCTAATGTAAAATGAA 59.351 34.615 0.00 0.00 0.00 2.57
88 89 7.148573 ACAGTGCTCGTCTAATGTAAAATGAAG 60.149 37.037 0.00 0.00 0.00 3.02
89 90 7.063426 CAGTGCTCGTCTAATGTAAAATGAAGA 59.937 37.037 0.00 0.00 0.00 2.87
90 91 7.602644 AGTGCTCGTCTAATGTAAAATGAAGAA 59.397 33.333 0.00 0.00 0.00 2.52
91 92 7.900352 GTGCTCGTCTAATGTAAAATGAAGAAG 59.100 37.037 0.00 0.00 0.00 2.85
92 93 7.064609 TGCTCGTCTAATGTAAAATGAAGAAGG 59.935 37.037 0.00 0.00 0.00 3.46
93 94 7.277981 GCTCGTCTAATGTAAAATGAAGAAGGA 59.722 37.037 0.00 0.00 0.00 3.36
94 95 9.151471 CTCGTCTAATGTAAAATGAAGAAGGAA 57.849 33.333 0.00 0.00 0.00 3.36
95 96 9.667107 TCGTCTAATGTAAAATGAAGAAGGAAT 57.333 29.630 0.00 0.00 0.00 3.01
96 97 9.708222 CGTCTAATGTAAAATGAAGAAGGAATG 57.292 33.333 0.00 0.00 0.00 2.67
187 188 9.480053 AATTTTATCTCACCATCAACTTGTTTG 57.520 29.630 0.00 0.00 36.42 2.93
188 189 7.581213 TTTATCTCACCATCAACTTGTTTGT 57.419 32.000 0.00 0.00 36.49 2.83
189 190 8.684386 TTTATCTCACCATCAACTTGTTTGTA 57.316 30.769 0.00 0.00 36.49 2.41
190 191 8.862325 TTATCTCACCATCAACTTGTTTGTAT 57.138 30.769 0.00 0.00 36.49 2.29
191 192 6.558771 TCTCACCATCAACTTGTTTGTATG 57.441 37.500 0.00 0.00 36.49 2.39
192 193 6.061441 TCTCACCATCAACTTGTTTGTATGT 58.939 36.000 0.00 0.00 36.49 2.29
193 194 7.220740 TCTCACCATCAACTTGTTTGTATGTA 58.779 34.615 0.00 0.00 36.49 2.29
194 195 7.717436 TCTCACCATCAACTTGTTTGTATGTAA 59.283 33.333 0.00 0.00 36.49 2.41
195 196 8.402798 TCACCATCAACTTGTTTGTATGTAAT 57.597 30.769 0.00 0.00 36.49 1.89
196 197 8.855110 TCACCATCAACTTGTTTGTATGTAATT 58.145 29.630 0.00 0.00 36.49 1.40
222 223 8.187913 ACTATGAATGTGCATACTAGATCTGT 57.812 34.615 5.18 4.31 0.00 3.41
223 224 9.301897 ACTATGAATGTGCATACTAGATCTGTA 57.698 33.333 5.18 6.49 0.00 2.74
227 228 9.836864 TGAATGTGCATACTAGATCTGTAATTT 57.163 29.630 5.18 0.00 0.00 1.82
276 277 9.167311 AGCCTTAGTTGTATGAATTAACAGAAG 57.833 33.333 0.00 0.00 0.00 2.85
277 278 8.398665 GCCTTAGTTGTATGAATTAACAGAAGG 58.601 37.037 12.84 12.84 39.80 3.46
278 279 9.667107 CCTTAGTTGTATGAATTAACAGAAGGA 57.333 33.333 12.26 0.00 39.52 3.36
282 283 9.574516 AGTTGTATGAATTAACAGAAGGAAAGT 57.425 29.630 0.00 0.00 0.00 2.66
311 312 9.950496 AGATAATGTAGTTTGTCAAACATCTCT 57.050 29.630 26.19 15.37 43.79 3.10
314 315 7.807977 ATGTAGTTTGTCAAACATCTCTTGT 57.192 32.000 26.19 8.97 43.79 3.16
315 316 8.902540 ATGTAGTTTGTCAAACATCTCTTGTA 57.097 30.769 26.19 8.10 43.79 2.41
316 317 8.902540 TGTAGTTTGTCAAACATCTCTTGTAT 57.097 30.769 26.19 7.72 43.79 2.29
317 318 9.990360 TGTAGTTTGTCAAACATCTCTTGTATA 57.010 29.630 26.19 6.86 43.79 1.47
320 321 9.507329 AGTTTGTCAAACATCTCTTGTATATGT 57.493 29.630 26.19 1.36 43.79 2.29
336 337 9.930693 CTTGTATATGTTAAAGGATCTACTCCC 57.069 37.037 0.00 0.00 46.27 4.30
337 338 9.670442 TTGTATATGTTAAAGGATCTACTCCCT 57.330 33.333 0.00 0.00 46.27 4.20
338 339 9.310449 TGTATATGTTAAAGGATCTACTCCCTC 57.690 37.037 0.00 0.00 46.27 4.30
339 340 7.800300 ATATGTTAAAGGATCTACTCCCTCC 57.200 40.000 0.00 0.00 46.27 4.30
340 341 3.958798 TGTTAAAGGATCTACTCCCTCCG 59.041 47.826 0.00 0.00 46.27 4.63
341 342 2.850695 AAAGGATCTACTCCCTCCGT 57.149 50.000 0.00 0.00 46.27 4.69
342 343 2.368311 AAGGATCTACTCCCTCCGTC 57.632 55.000 0.00 0.00 46.27 4.79
343 344 0.479378 AGGATCTACTCCCTCCGTCC 59.521 60.000 0.00 0.00 46.27 4.79
344 345 0.479378 GGATCTACTCCCTCCGTCCT 59.521 60.000 0.00 0.00 38.19 3.85
345 346 1.704070 GGATCTACTCCCTCCGTCCTA 59.296 57.143 0.00 0.00 38.19 2.94
346 347 2.309458 GGATCTACTCCCTCCGTCCTAT 59.691 54.545 0.00 0.00 38.19 2.57
347 348 3.522750 GGATCTACTCCCTCCGTCCTATA 59.477 52.174 0.00 0.00 38.19 1.31
348 349 4.018597 GGATCTACTCCCTCCGTCCTATAA 60.019 50.000 0.00 0.00 38.19 0.98
349 350 5.340194 GGATCTACTCCCTCCGTCCTATAAT 60.340 48.000 0.00 0.00 38.19 1.28
350 351 6.126536 GGATCTACTCCCTCCGTCCTATAATA 60.127 46.154 0.00 0.00 38.19 0.98
351 352 6.905067 TCTACTCCCTCCGTCCTATAATAT 57.095 41.667 0.00 0.00 0.00 1.28
352 353 8.578593 ATCTACTCCCTCCGTCCTATAATATA 57.421 38.462 0.00 0.00 0.00 0.86
353 354 8.397951 TCTACTCCCTCCGTCCTATAATATAA 57.602 38.462 0.00 0.00 0.00 0.98
354 355 8.492782 TCTACTCCCTCCGTCCTATAATATAAG 58.507 40.741 0.00 0.00 0.00 1.73
355 356 7.281366 ACTCCCTCCGTCCTATAATATAAGA 57.719 40.000 0.00 0.00 0.00 2.10
356 357 7.348033 ACTCCCTCCGTCCTATAATATAAGAG 58.652 42.308 0.00 0.00 0.00 2.85
357 358 6.127793 TCCCTCCGTCCTATAATATAAGAGC 58.872 44.000 0.00 0.00 0.00 4.09
358 359 5.008811 CCCTCCGTCCTATAATATAAGAGCG 59.991 48.000 0.00 0.00 0.00 5.03
359 360 5.589452 CCTCCGTCCTATAATATAAGAGCGT 59.411 44.000 0.00 0.00 0.00 5.07
360 361 6.095160 CCTCCGTCCTATAATATAAGAGCGTT 59.905 42.308 0.00 0.00 0.00 4.84
361 362 7.362747 CCTCCGTCCTATAATATAAGAGCGTTT 60.363 40.741 0.00 0.00 0.00 3.60
362 363 7.889469 TCCGTCCTATAATATAAGAGCGTTTT 58.111 34.615 0.00 0.00 0.00 2.43
363 364 8.362639 TCCGTCCTATAATATAAGAGCGTTTTT 58.637 33.333 0.00 0.00 0.00 1.94
364 365 9.630098 CCGTCCTATAATATAAGAGCGTTTTTA 57.370 33.333 0.00 0.00 0.00 1.52
435 436 9.689501 AAAAACTTTCTTATATTATGGGACGGA 57.310 29.630 0.00 0.00 0.00 4.69
436 437 8.904099 AAACTTTCTTATATTATGGGACGGAG 57.096 34.615 0.00 0.00 0.00 4.63
437 438 7.005709 ACTTTCTTATATTATGGGACGGAGG 57.994 40.000 0.00 0.00 0.00 4.30
438 439 6.013639 ACTTTCTTATATTATGGGACGGAGGG 60.014 42.308 0.00 0.00 0.00 4.30
439 440 5.279562 TCTTATATTATGGGACGGAGGGA 57.720 43.478 0.00 0.00 0.00 4.20
440 441 5.269991 TCTTATATTATGGGACGGAGGGAG 58.730 45.833 0.00 0.00 0.00 4.30
441 442 3.562108 ATATTATGGGACGGAGGGAGT 57.438 47.619 0.00 0.00 0.00 3.85
442 443 4.687262 ATATTATGGGACGGAGGGAGTA 57.313 45.455 0.00 0.00 0.00 2.59
443 444 2.376695 TTATGGGACGGAGGGAGTAG 57.623 55.000 0.00 0.00 0.00 2.57
444 445 1.229131 TATGGGACGGAGGGAGTAGT 58.771 55.000 0.00 0.00 0.00 2.73
445 446 0.338814 ATGGGACGGAGGGAGTAGTT 59.661 55.000 0.00 0.00 0.00 2.24
446 447 0.324091 TGGGACGGAGGGAGTAGTTC 60.324 60.000 0.00 0.00 0.00 3.01
447 448 1.042003 GGGACGGAGGGAGTAGTTCC 61.042 65.000 0.00 0.00 46.00 3.62
457 458 2.753247 GGAGTAGTTCCCACATCTCCT 58.247 52.381 0.00 0.00 40.37 3.69
458 459 3.912248 GGAGTAGTTCCCACATCTCCTA 58.088 50.000 0.00 0.00 40.37 2.94
459 460 3.892588 GGAGTAGTTCCCACATCTCCTAG 59.107 52.174 0.00 0.00 40.37 3.02
460 461 3.892588 GAGTAGTTCCCACATCTCCTAGG 59.107 52.174 0.82 0.82 0.00 3.02
461 462 2.950990 AGTTCCCACATCTCCTAGGT 57.049 50.000 9.08 0.00 0.00 3.08
462 463 2.753247 AGTTCCCACATCTCCTAGGTC 58.247 52.381 9.08 0.00 0.00 3.85
463 464 1.763545 GTTCCCACATCTCCTAGGTCC 59.236 57.143 9.08 0.00 0.00 4.46
464 465 1.015609 TCCCACATCTCCTAGGTCCA 58.984 55.000 9.08 0.00 0.00 4.02
465 466 1.364678 TCCCACATCTCCTAGGTCCAA 59.635 52.381 9.08 0.00 0.00 3.53
466 467 2.022035 TCCCACATCTCCTAGGTCCAAT 60.022 50.000 9.08 0.00 0.00 3.16
467 468 2.780010 CCCACATCTCCTAGGTCCAATT 59.220 50.000 9.08 0.00 0.00 2.32
468 469 3.434167 CCCACATCTCCTAGGTCCAATTG 60.434 52.174 9.08 0.00 0.00 2.32
469 470 3.200825 CCACATCTCCTAGGTCCAATTGT 59.799 47.826 9.08 3.04 0.00 2.71
553 554 5.855395 GCTACTTGCAGATTTTGAGACAAAG 59.145 40.000 0.00 0.00 42.31 2.77
555 556 6.069684 ACTTGCAGATTTTGAGACAAAGAG 57.930 37.500 0.00 0.00 0.00 2.85
617 619 6.041182 ACACCAAAAGTTACCCTAAAATGTCC 59.959 38.462 0.00 0.00 0.00 4.02
618 620 5.242171 ACCAAAAGTTACCCTAAAATGTCCG 59.758 40.000 0.00 0.00 0.00 4.79
640 674 3.795150 GCAGCTCCGTTTCACATGAAAAA 60.795 43.478 8.58 0.00 44.58 1.94
644 678 6.808212 CAGCTCCGTTTCACATGAAAAATATT 59.192 34.615 8.58 0.00 44.58 1.28
647 681 9.944663 GCTCCGTTTCACATGAAAAATATTATA 57.055 29.630 8.58 0.00 44.58 0.98
673 707 3.548014 GCTTGCGACACTAACACAAACAT 60.548 43.478 0.00 0.00 0.00 2.71
680 714 5.918576 CGACACTAACACAAACATCTACAGA 59.081 40.000 0.00 0.00 0.00 3.41
681 715 6.419710 CGACACTAACACAAACATCTACAGAA 59.580 38.462 0.00 0.00 0.00 3.02
682 716 7.116376 CGACACTAACACAAACATCTACAGAAT 59.884 37.037 0.00 0.00 0.00 2.40
683 717 8.677148 ACACTAACACAAACATCTACAGAATT 57.323 30.769 0.00 0.00 0.00 2.17
930 995 2.280389 CGATCTCGGGCCATGGTG 60.280 66.667 14.67 3.93 35.37 4.17
931 996 2.911143 GATCTCGGGCCATGGTGT 59.089 61.111 14.67 0.00 0.00 4.16
932 997 1.227674 GATCTCGGGCCATGGTGTC 60.228 63.158 14.67 3.46 0.00 3.67
933 998 1.971505 GATCTCGGGCCATGGTGTCA 61.972 60.000 14.67 0.00 0.00 3.58
934 999 1.348008 ATCTCGGGCCATGGTGTCAT 61.348 55.000 14.67 0.00 0.00 3.06
981 1054 2.648304 GTTTCTAAGGGGGAAAGAGGGT 59.352 50.000 0.00 0.00 34.02 4.34
982 1055 2.265526 TCTAAGGGGGAAAGAGGGTC 57.734 55.000 0.00 0.00 0.00 4.46
983 1056 1.214217 CTAAGGGGGAAAGAGGGTCC 58.786 60.000 0.00 0.00 0.00 4.46
984 1057 0.499147 TAAGGGGGAAAGAGGGTCCA 59.501 55.000 0.00 0.00 36.83 4.02
985 1058 0.178801 AAGGGGGAAAGAGGGTCCAT 60.179 55.000 0.00 0.00 36.83 3.41
986 1059 0.921256 AGGGGGAAAGAGGGTCCATG 60.921 60.000 0.00 0.00 36.83 3.66
987 1060 1.615262 GGGGAAAGAGGGTCCATGG 59.385 63.158 4.97 4.97 36.83 3.66
988 1061 1.076705 GGGAAAGAGGGTCCATGGC 60.077 63.158 6.96 1.78 36.83 4.40
1243 3294 9.855361 CTTAGAAAAATATAAGCATGTGTCTCG 57.145 33.333 0.00 0.00 0.00 4.04
1247 3298 1.945387 ATAAGCATGTGTCTCGCCAG 58.055 50.000 0.00 0.00 0.00 4.85
1288 3339 0.469892 TCTGAGTCACTGCCTCACCA 60.470 55.000 0.00 0.00 35.23 4.17
1307 3358 2.159128 CCAGCTGTGTCGATCTCATCTT 60.159 50.000 13.81 0.00 0.00 2.40
1378 3429 6.150641 TCCAATATAGACTACATACGGAGCAC 59.849 42.308 0.00 0.00 0.00 4.40
1620 3672 8.865090 TCAATGATTGTGGTACTTGGTTAAATT 58.135 29.630 4.93 0.00 0.00 1.82
1702 3754 1.423921 CCAGGAGTACCCAAACCAACT 59.576 52.381 3.60 0.00 37.41 3.16
1857 3909 3.935203 ACTCACAACTTCACTGTGTTGAG 59.065 43.478 14.26 14.39 44.29 3.02
2211 4270 1.882623 CAGAAGCCAAGTTCAGGGAAC 59.117 52.381 0.94 0.94 42.25 3.62
2335 4394 4.015872 TCACCAACATTCTAGTTCCACC 57.984 45.455 0.00 0.00 0.00 4.61
2704 4781 9.489084 CACCGGATATTTATTCTATCAACAGAA 57.511 33.333 9.46 0.00 38.84 3.02
2828 4913 3.133542 TGTCATGGAGAAGTAGAGGCATG 59.866 47.826 0.00 0.00 0.00 4.06
2940 7952 7.695480 TTCTGTGTAGCAGGCAAATAATTTA 57.305 32.000 0.00 0.00 45.08 1.40
3031 8043 6.943718 ACAATAGAAGATTTAAAACCGGTCCA 59.056 34.615 8.04 0.00 0.00 4.02
3038 8050 7.770366 AGATTTAAAACCGGTCCATAAAACT 57.230 32.000 8.04 14.27 0.00 2.66
3049 8061 6.017440 CCGGTCCATAAAACTACACATAATGG 60.017 42.308 0.00 0.00 0.00 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 0.249238 CCGGCTACAGAGATGTGCTC 60.249 60.000 0.00 0.00 44.29 4.26
9 10 0.684479 TCCGGCTACAGAGATGTGCT 60.684 55.000 0.00 0.00 0.00 4.40
10 11 0.390860 ATCCGGCTACAGAGATGTGC 59.609 55.000 0.00 0.00 0.00 4.57
11 12 1.000283 GGATCCGGCTACAGAGATGTG 60.000 57.143 0.00 0.00 0.00 3.21
12 13 1.133325 AGGATCCGGCTACAGAGATGT 60.133 52.381 5.98 0.00 0.00 3.06
13 14 1.543802 GAGGATCCGGCTACAGAGATG 59.456 57.143 5.98 0.00 0.00 2.90
14 15 1.427368 AGAGGATCCGGCTACAGAGAT 59.573 52.381 5.98 0.00 33.66 2.75
15 16 0.847373 AGAGGATCCGGCTACAGAGA 59.153 55.000 5.98 0.00 33.66 3.10
16 17 2.554893 GTTAGAGGATCCGGCTACAGAG 59.445 54.545 14.60 0.00 33.66 3.35
17 18 2.175069 AGTTAGAGGATCCGGCTACAGA 59.825 50.000 14.60 1.53 33.66 3.41
18 19 2.588620 AGTTAGAGGATCCGGCTACAG 58.411 52.381 14.60 0.00 33.66 2.74
19 20 2.750141 AGTTAGAGGATCCGGCTACA 57.250 50.000 14.60 6.31 33.66 2.74
20 21 5.301298 TCTTTAAGTTAGAGGATCCGGCTAC 59.699 44.000 14.60 8.84 33.66 3.58
21 22 5.452255 TCTTTAAGTTAGAGGATCCGGCTA 58.548 41.667 5.98 9.58 33.66 3.93
22 23 4.287552 TCTTTAAGTTAGAGGATCCGGCT 58.712 43.478 5.98 10.63 33.66 5.52
23 24 4.667519 TCTTTAAGTTAGAGGATCCGGC 57.332 45.455 5.98 2.53 33.66 6.13
24 25 5.453480 CCCTTCTTTAAGTTAGAGGATCCGG 60.453 48.000 5.98 0.00 33.66 5.14
25 26 5.363005 TCCCTTCTTTAAGTTAGAGGATCCG 59.637 44.000 5.98 0.00 33.66 4.18
26 27 6.809976 TCCCTTCTTTAAGTTAGAGGATCC 57.190 41.667 2.48 2.48 33.66 3.36
27 28 7.853299 ACTTCCCTTCTTTAAGTTAGAGGATC 58.147 38.462 0.91 0.00 29.25 3.36
28 29 7.458170 TGACTTCCCTTCTTTAAGTTAGAGGAT 59.542 37.037 0.91 0.00 33.72 3.24
29 30 6.785963 TGACTTCCCTTCTTTAAGTTAGAGGA 59.214 38.462 0.91 0.00 33.72 3.71
30 31 6.874664 GTGACTTCCCTTCTTTAAGTTAGAGG 59.125 42.308 0.91 0.13 33.72 3.69
31 32 7.672240 AGTGACTTCCCTTCTTTAAGTTAGAG 58.328 38.462 0.00 0.00 33.72 2.43
32 33 7.613551 AGTGACTTCCCTTCTTTAAGTTAGA 57.386 36.000 0.00 0.00 33.72 2.10
33 34 9.372369 CATAGTGACTTCCCTTCTTTAAGTTAG 57.628 37.037 0.00 0.00 33.72 2.34
34 35 7.822822 GCATAGTGACTTCCCTTCTTTAAGTTA 59.177 37.037 0.00 0.00 33.72 2.24
35 36 6.655425 GCATAGTGACTTCCCTTCTTTAAGTT 59.345 38.462 0.00 0.00 33.72 2.66
36 37 6.013293 AGCATAGTGACTTCCCTTCTTTAAGT 60.013 38.462 0.00 0.00 36.20 2.24
37 38 6.410540 AGCATAGTGACTTCCCTTCTTTAAG 58.589 40.000 0.00 0.00 0.00 1.85
38 39 6.374417 AGCATAGTGACTTCCCTTCTTTAA 57.626 37.500 0.00 0.00 0.00 1.52
39 40 6.439375 TGTAGCATAGTGACTTCCCTTCTTTA 59.561 38.462 0.00 0.00 0.00 1.85
40 41 4.917906 AGCATAGTGACTTCCCTTCTTT 57.082 40.909 0.00 0.00 0.00 2.52
41 42 4.777896 TGTAGCATAGTGACTTCCCTTCTT 59.222 41.667 0.00 0.00 0.00 2.52
42 43 4.353777 TGTAGCATAGTGACTTCCCTTCT 58.646 43.478 0.00 0.00 0.00 2.85
43 44 4.160626 ACTGTAGCATAGTGACTTCCCTTC 59.839 45.833 0.00 0.00 0.00 3.46
44 45 4.081420 CACTGTAGCATAGTGACTTCCCTT 60.081 45.833 8.75 0.00 46.52 3.95
45 46 3.449018 CACTGTAGCATAGTGACTTCCCT 59.551 47.826 8.75 0.00 46.52 4.20
46 47 3.786635 CACTGTAGCATAGTGACTTCCC 58.213 50.000 8.75 0.00 46.52 3.97
47 48 3.118956 AGCACTGTAGCATAGTGACTTCC 60.119 47.826 16.18 1.89 46.52 3.46
48 49 4.109050 GAGCACTGTAGCATAGTGACTTC 58.891 47.826 16.18 8.24 46.52 3.01
49 50 3.428180 CGAGCACTGTAGCATAGTGACTT 60.428 47.826 16.18 3.96 46.52 3.01
50 51 2.098280 CGAGCACTGTAGCATAGTGACT 59.902 50.000 16.18 12.61 46.52 3.41
51 52 2.159366 ACGAGCACTGTAGCATAGTGAC 60.159 50.000 16.18 9.15 46.52 3.67
52 53 2.092323 ACGAGCACTGTAGCATAGTGA 58.908 47.619 16.18 0.00 46.52 3.41
53 54 2.098280 AGACGAGCACTGTAGCATAGTG 59.902 50.000 9.76 9.76 46.37 2.74
54 55 2.370349 AGACGAGCACTGTAGCATAGT 58.630 47.619 0.00 0.00 36.85 2.12
55 56 4.553756 TTAGACGAGCACTGTAGCATAG 57.446 45.455 0.00 0.00 36.85 2.23
56 57 4.338400 ACATTAGACGAGCACTGTAGCATA 59.662 41.667 0.00 0.00 36.85 3.14
57 58 3.131223 ACATTAGACGAGCACTGTAGCAT 59.869 43.478 0.00 0.00 36.85 3.79
58 59 2.492088 ACATTAGACGAGCACTGTAGCA 59.508 45.455 0.00 0.00 36.85 3.49
59 60 3.152261 ACATTAGACGAGCACTGTAGC 57.848 47.619 0.00 0.00 0.00 3.58
60 61 7.488150 TCATTTTACATTAGACGAGCACTGTAG 59.512 37.037 0.00 0.00 0.00 2.74
61 62 7.317390 TCATTTTACATTAGACGAGCACTGTA 58.683 34.615 0.00 0.00 0.00 2.74
62 63 6.163476 TCATTTTACATTAGACGAGCACTGT 58.837 36.000 0.00 0.00 0.00 3.55
63 64 6.647212 TCATTTTACATTAGACGAGCACTG 57.353 37.500 0.00 0.00 0.00 3.66
64 65 7.097192 TCTTCATTTTACATTAGACGAGCACT 58.903 34.615 0.00 0.00 0.00 4.40
65 66 7.290857 TCTTCATTTTACATTAGACGAGCAC 57.709 36.000 0.00 0.00 0.00 4.40
66 67 7.064609 CCTTCTTCATTTTACATTAGACGAGCA 59.935 37.037 0.00 0.00 0.00 4.26
67 68 7.277981 TCCTTCTTCATTTTACATTAGACGAGC 59.722 37.037 0.00 0.00 0.00 5.03
68 69 8.703604 TCCTTCTTCATTTTACATTAGACGAG 57.296 34.615 0.00 0.00 0.00 4.18
69 70 9.667107 ATTCCTTCTTCATTTTACATTAGACGA 57.333 29.630 0.00 0.00 0.00 4.20
70 71 9.708222 CATTCCTTCTTCATTTTACATTAGACG 57.292 33.333 0.00 0.00 0.00 4.18
161 162 9.480053 CAAACAAGTTGATGGTGAGATAAAATT 57.520 29.630 10.54 0.00 39.87 1.82
162 163 8.641541 ACAAACAAGTTGATGGTGAGATAAAAT 58.358 29.630 10.54 0.00 39.87 1.82
163 164 8.006298 ACAAACAAGTTGATGGTGAGATAAAA 57.994 30.769 10.54 0.00 39.87 1.52
164 165 7.581213 ACAAACAAGTTGATGGTGAGATAAA 57.419 32.000 10.54 0.00 39.87 1.40
165 166 8.729756 CATACAAACAAGTTGATGGTGAGATAA 58.270 33.333 10.54 0.00 39.87 1.75
166 167 7.882791 ACATACAAACAAGTTGATGGTGAGATA 59.117 33.333 10.54 0.00 39.87 1.98
167 168 6.716628 ACATACAAACAAGTTGATGGTGAGAT 59.283 34.615 10.54 0.00 39.87 2.75
168 169 6.061441 ACATACAAACAAGTTGATGGTGAGA 58.939 36.000 10.54 0.00 39.87 3.27
169 170 6.317789 ACATACAAACAAGTTGATGGTGAG 57.682 37.500 10.54 1.60 39.87 3.51
170 171 7.809546 TTACATACAAACAAGTTGATGGTGA 57.190 32.000 10.54 0.00 39.87 4.02
196 197 9.301897 ACAGATCTAGTATGCACATTCATAGTA 57.698 33.333 0.00 0.00 35.09 1.82
197 198 8.187913 ACAGATCTAGTATGCACATTCATAGT 57.812 34.615 0.00 0.00 36.73 2.12
201 202 9.836864 AAATTACAGATCTAGTATGCACATTCA 57.163 29.630 0.00 0.00 0.00 2.57
250 251 9.167311 CTTCTGTTAATTCATACAACTAAGGCT 57.833 33.333 0.00 0.00 0.00 4.58
251 252 8.398665 CCTTCTGTTAATTCATACAACTAAGGC 58.601 37.037 8.52 0.00 33.44 4.35
252 253 9.667107 TCCTTCTGTTAATTCATACAACTAAGG 57.333 33.333 12.15 12.15 37.36 2.69
256 257 9.574516 ACTTTCCTTCTGTTAATTCATACAACT 57.425 29.630 0.00 0.00 0.00 3.16
285 286 9.950496 AGAGATGTTTGACAAACTACATTATCT 57.050 29.630 26.80 23.39 41.90 1.98
288 289 9.337396 ACAAGAGATGTTTGACAAACTACATTA 57.663 29.630 26.80 10.13 40.06 1.90
289 290 8.225603 ACAAGAGATGTTTGACAAACTACATT 57.774 30.769 26.80 16.81 40.06 2.71
290 291 7.807977 ACAAGAGATGTTTGACAAACTACAT 57.192 32.000 26.80 16.06 40.06 2.29
291 292 8.902540 ATACAAGAGATGTTTGACAAACTACA 57.097 30.769 26.80 12.24 43.63 2.74
294 295 9.507329 ACATATACAAGAGATGTTTGACAAACT 57.493 29.630 26.80 15.18 36.57 2.66
326 327 3.724732 ATAGGACGGAGGGAGTAGATC 57.275 52.381 0.00 0.00 0.00 2.75
327 328 5.799978 ATTATAGGACGGAGGGAGTAGAT 57.200 43.478 0.00 0.00 0.00 1.98
328 329 6.905067 ATATTATAGGACGGAGGGAGTAGA 57.095 41.667 0.00 0.00 0.00 2.59
329 330 8.492782 TCTTATATTATAGGACGGAGGGAGTAG 58.507 40.741 0.00 0.00 0.00 2.57
330 331 8.397951 TCTTATATTATAGGACGGAGGGAGTA 57.602 38.462 0.00 0.00 0.00 2.59
331 332 7.281366 TCTTATATTATAGGACGGAGGGAGT 57.719 40.000 0.00 0.00 0.00 3.85
332 333 6.263617 GCTCTTATATTATAGGACGGAGGGAG 59.736 46.154 0.00 0.00 0.00 4.30
333 334 6.127793 GCTCTTATATTATAGGACGGAGGGA 58.872 44.000 0.00 0.00 0.00 4.20
334 335 5.008811 CGCTCTTATATTATAGGACGGAGGG 59.991 48.000 0.00 0.00 0.00 4.30
335 336 5.589452 ACGCTCTTATATTATAGGACGGAGG 59.411 44.000 15.28 1.51 0.00 4.30
336 337 6.680874 ACGCTCTTATATTATAGGACGGAG 57.319 41.667 15.28 0.00 0.00 4.63
337 338 7.458409 AAACGCTCTTATATTATAGGACGGA 57.542 36.000 15.28 0.00 0.00 4.69
338 339 8.530269 AAAAACGCTCTTATATTATAGGACGG 57.470 34.615 15.28 5.50 0.00 4.79
409 410 9.689501 TCCGTCCCATAATATAAGAAAGTTTTT 57.310 29.630 0.00 0.00 0.00 1.94
410 411 9.338622 CTCCGTCCCATAATATAAGAAAGTTTT 57.661 33.333 0.00 0.00 0.00 2.43
411 412 7.937394 CCTCCGTCCCATAATATAAGAAAGTTT 59.063 37.037 0.00 0.00 0.00 2.66
412 413 7.450903 CCTCCGTCCCATAATATAAGAAAGTT 58.549 38.462 0.00 0.00 0.00 2.66
413 414 6.013639 CCCTCCGTCCCATAATATAAGAAAGT 60.014 42.308 0.00 0.00 0.00 2.66
414 415 6.212791 TCCCTCCGTCCCATAATATAAGAAAG 59.787 42.308 0.00 0.00 0.00 2.62
415 416 6.086095 TCCCTCCGTCCCATAATATAAGAAA 58.914 40.000 0.00 0.00 0.00 2.52
416 417 5.657446 TCCCTCCGTCCCATAATATAAGAA 58.343 41.667 0.00 0.00 0.00 2.52
417 418 5.222484 ACTCCCTCCGTCCCATAATATAAGA 60.222 44.000 0.00 0.00 0.00 2.10
418 419 5.024118 ACTCCCTCCGTCCCATAATATAAG 58.976 45.833 0.00 0.00 0.00 1.73
419 420 5.019657 ACTCCCTCCGTCCCATAATATAA 57.980 43.478 0.00 0.00 0.00 0.98
420 421 4.687262 ACTCCCTCCGTCCCATAATATA 57.313 45.455 0.00 0.00 0.00 0.86
421 422 3.562108 ACTCCCTCCGTCCCATAATAT 57.438 47.619 0.00 0.00 0.00 1.28
422 423 3.400322 ACTACTCCCTCCGTCCCATAATA 59.600 47.826 0.00 0.00 0.00 0.98
423 424 2.179424 ACTACTCCCTCCGTCCCATAAT 59.821 50.000 0.00 0.00 0.00 1.28
424 425 1.572415 ACTACTCCCTCCGTCCCATAA 59.428 52.381 0.00 0.00 0.00 1.90
425 426 1.229131 ACTACTCCCTCCGTCCCATA 58.771 55.000 0.00 0.00 0.00 2.74
426 427 0.338814 AACTACTCCCTCCGTCCCAT 59.661 55.000 0.00 0.00 0.00 4.00
427 428 0.324091 GAACTACTCCCTCCGTCCCA 60.324 60.000 0.00 0.00 0.00 4.37
428 429 1.042003 GGAACTACTCCCTCCGTCCC 61.042 65.000 0.00 0.00 38.44 4.46
429 430 2.502633 GGAACTACTCCCTCCGTCC 58.497 63.158 0.00 0.00 38.44 4.79
437 438 2.753247 AGGAGATGTGGGAACTACTCC 58.247 52.381 0.00 0.00 44.54 3.85
438 439 3.892588 CCTAGGAGATGTGGGAACTACTC 59.107 52.174 1.05 0.00 0.00 2.59
439 440 3.272551 ACCTAGGAGATGTGGGAACTACT 59.727 47.826 17.98 0.00 0.00 2.57
440 441 3.637694 GACCTAGGAGATGTGGGAACTAC 59.362 52.174 17.98 0.00 0.00 2.73
441 442 3.373877 GGACCTAGGAGATGTGGGAACTA 60.374 52.174 17.98 0.00 0.00 2.24
442 443 2.627217 GGACCTAGGAGATGTGGGAACT 60.627 54.545 17.98 0.00 0.00 3.01
443 444 1.763545 GGACCTAGGAGATGTGGGAAC 59.236 57.143 17.98 0.00 0.00 3.62
444 445 1.364678 TGGACCTAGGAGATGTGGGAA 59.635 52.381 17.98 0.00 0.00 3.97
445 446 1.015609 TGGACCTAGGAGATGTGGGA 58.984 55.000 17.98 0.00 0.00 4.37
446 447 1.879575 TTGGACCTAGGAGATGTGGG 58.120 55.000 17.98 0.00 0.00 4.61
447 448 3.200825 ACAATTGGACCTAGGAGATGTGG 59.799 47.826 17.98 2.46 0.00 4.17
448 449 4.494091 ACAATTGGACCTAGGAGATGTG 57.506 45.455 17.98 8.52 0.00 3.21
449 450 5.520748 AAACAATTGGACCTAGGAGATGT 57.479 39.130 17.98 8.50 0.00 3.06
450 451 6.840780 AAAAACAATTGGACCTAGGAGATG 57.159 37.500 17.98 7.87 0.00 2.90
511 512 7.573843 GCAAGTAGCATTTGAATGTGACTAAGT 60.574 37.037 5.68 0.00 44.79 2.24
617 619 1.133253 CATGTGAAACGGAGCTGCG 59.867 57.895 26.95 26.95 42.39 5.18
618 620 0.874390 TTCATGTGAAACGGAGCTGC 59.126 50.000 0.00 0.00 42.39 5.25
640 674 7.655732 TGTTAGTGTCGCAAGCATGTATAATAT 59.344 33.333 0.00 0.00 37.18 1.28
644 678 4.565166 GTGTTAGTGTCGCAAGCATGTATA 59.435 41.667 0.00 0.00 37.18 1.47
647 681 1.531149 GTGTTAGTGTCGCAAGCATGT 59.469 47.619 0.00 0.00 37.18 3.21
916 981 1.995066 ATGACACCATGGCCCGAGA 60.995 57.895 13.04 0.00 0.00 4.04
1014 1087 4.754667 TGCTGCTGCTCCTGCTCG 62.755 66.667 17.00 0.00 40.48 5.03
1015 1088 2.820479 CTGCTGCTGCTCCTGCTC 60.820 66.667 17.00 0.00 40.48 4.26
1019 1092 4.756458 GACGCTGCTGCTGCTCCT 62.756 66.667 25.43 10.59 40.48 3.69
1021 1094 3.786586 GTGACGCTGCTGCTGCTC 61.787 66.667 25.43 20.88 40.48 4.26
1173 3224 4.102524 ACTTCTGGTATATCGCCCATTTCA 59.897 41.667 0.00 0.00 0.00 2.69
1240 3291 2.814919 CACCTAGGTATCTACTGGCGAG 59.185 54.545 15.80 0.00 0.00 5.03
1243 3294 4.153411 ACATCACCTAGGTATCTACTGGC 58.847 47.826 15.80 0.00 0.00 4.85
1247 3298 9.298250 TCAGATTTACATCACCTAGGTATCTAC 57.702 37.037 15.80 0.72 0.00 2.59
1288 3339 3.519579 CAAAGATGAGATCGACACAGCT 58.480 45.455 0.00 0.00 37.42 4.24
1307 3358 2.019807 ACGGAGGGAGTAGTTTCCAA 57.980 50.000 0.00 0.00 39.09 3.53
1685 3737 3.504906 GCTTTAGTTGGTTTGGGTACTCC 59.495 47.826 0.00 0.00 0.00 3.85
1857 3909 0.603975 GGTTGACTGACCTGCTGTCC 60.604 60.000 4.79 0.00 43.78 4.02
2211 4270 6.435430 TTTAGATTCGTCATGTTTCCATGG 57.565 37.500 4.97 4.97 46.96 3.66
2225 4284 3.248602 CGAAGGCCCTGAATTTAGATTCG 59.751 47.826 0.00 0.00 43.75 3.34
2277 4336 6.183360 TGGTGCTGCTGAAAGAATATATTTGG 60.183 38.462 0.00 0.00 34.07 3.28
2335 4394 1.747355 GGCCAATGAGGTGATGACTTG 59.253 52.381 0.00 0.00 40.61 3.16
2575 4642 9.092876 TGTAAAATTTCAACATCAAACTGAACC 57.907 29.630 0.00 0.00 0.00 3.62
2707 4784 1.324736 GAGTTTAGATTGACGCAGGCG 59.675 52.381 12.71 12.71 46.03 5.52
2828 4913 6.929606 GGTAAGAGATATTGTGGGTGACATAC 59.070 42.308 0.00 0.00 33.40 2.39
2919 7931 7.880160 ATCTAAATTATTTGCCTGCTACACA 57.120 32.000 0.00 0.00 0.00 3.72
3038 8050 4.764308 TGTGCTGCTTTTCCATTATGTGTA 59.236 37.500 0.00 0.00 0.00 2.90
3049 8061 5.402270 ACACGATTAAATTGTGCTGCTTTTC 59.598 36.000 0.00 0.00 46.43 2.29
3084 8135 4.326826 TGTCTCTCTGGCCAATTTACTTG 58.673 43.478 7.01 0.00 34.42 3.16


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

AutoCloner maintained by Alex Coulton.