Multiple sequence alignment - TraesCS5A01G522800

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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 TraesCS5A01G522800 chr5A 100.000 3520 0 0 1 3520 683947181 683943662 0.000000e+00 6501
1 TraesCS5A01G522800 chr4B 97.200 1500 35 4 849 2345 668006896 668005401 0.000000e+00 2531
2 TraesCS5A01G522800 chr4B 91.273 275 17 3 268 535 585644690 585644964 5.550000e-98 368
3 TraesCS5A01G522800 chr4B 83.582 134 7 6 2453 2579 668005284 668005159 1.030000e-20 111
4 TraesCS5A01G522800 chrUn 95.021 1406 42 10 947 2342 29715855 29717242 0.000000e+00 2183
5 TraesCS5A01G522800 chrUn 99.043 209 2 0 1 209 240285711 240285503 3.320000e-100 375
6 TraesCS5A01G522800 chrUn 89.474 190 10 5 2341 2525 29717436 29717620 7.600000e-57 231
7 TraesCS5A01G522800 chr6D 92.737 950 55 7 2580 3520 296757735 296758679 0.000000e+00 1360
8 TraesCS5A01G522800 chr6D 90.506 948 77 6 2580 3517 121799526 121800470 0.000000e+00 1240
9 TraesCS5A01G522800 chr6D 96.380 221 8 0 1 221 345048645 345048425 7.180000e-97 364
10 TraesCS5A01G522800 chr7A 89.474 950 87 10 2575 3515 222636113 222635168 0.000000e+00 1188
11 TraesCS5A01G522800 chr4D 88.000 950 97 13 2579 3520 46425780 46424840 0.000000e+00 1107
12 TraesCS5A01G522800 chr1D 86.792 954 108 17 2577 3517 455550274 455551222 0.000000e+00 1048
13 TraesCS5A01G522800 chr7B 86.715 956 105 15 2577 3520 4601740 4600795 0.000000e+00 1042
14 TraesCS5A01G522800 chr7B 86.243 945 111 9 2584 3517 589367503 589368439 0.000000e+00 1007
15 TraesCS5A01G522800 chr7B 94.921 315 14 1 541 853 12148818 12149132 3.160000e-135 492
16 TraesCS5A01G522800 chr2B 86.526 950 116 6 2579 3517 30311239 30310291 0.000000e+00 1035
17 TraesCS5A01G522800 chr2B 94.888 313 14 1 541 851 636430316 636430628 4.080000e-134 488
18 TraesCS5A01G522800 chr2B 95.745 282 10 2 571 851 152706381 152706661 1.490000e-123 453
19 TraesCS5A01G522800 chr2B 92.926 311 17 1 541 851 58782549 58782244 6.930000e-122 448
20 TraesCS5A01G522800 chr2B 90.441 272 13 9 271 535 58783788 58783523 2.600000e-91 346
21 TraesCS5A01G522800 chr7D 86.254 953 107 18 2579 3517 25900164 25899222 0.000000e+00 1013
22 TraesCS5A01G522800 chr7D 98.565 209 3 0 1 209 211868268 211868476 1.540000e-98 370
23 TraesCS5A01G522800 chr3A 85.385 520 58 15 2579 3086 150795945 150795432 1.120000e-144 523
24 TraesCS5A01G522800 chr1B 95.208 313 13 1 541 851 540151360 540151048 8.780000e-136 494
25 TraesCS5A01G522800 chr1B 92.971 313 20 1 541 851 595179051 595178739 4.140000e-124 455
26 TraesCS5A01G522800 chr4A 93.930 313 17 1 541 851 659246780 659247092 4.110000e-129 472
27 TraesCS5A01G522800 chr4A 93.610 313 17 2 541 851 701265166 701264855 6.880000e-127 464
28 TraesCS5A01G522800 chr4A 92.473 279 13 3 265 535 701267746 701267468 3.290000e-105 392
29 TraesCS5A01G522800 chr4A 91.273 275 17 2 268 535 659232063 659232337 5.550000e-98 368
30 TraesCS5A01G522800 chr5B 92.484 306 14 8 551 851 637117254 637116953 2.510000e-116 429
31 TraesCS5A01G522800 chr5B 89.781 274 17 6 271 535 270434776 270434505 1.210000e-89 340
32 TraesCS5A01G522800 chr6B 98.565 209 3 0 1 209 676484463 676484671 1.540000e-98 370
33 TraesCS5A01G522800 chr6B 89.781 274 19 5 269 535 56065543 56065272 3.360000e-90 342
34 TraesCS5A01G522800 chr3D 98.565 209 3 0 1 209 12368988 12368780 1.540000e-98 370
35 TraesCS5A01G522800 chr3B 98.565 209 3 0 1 209 160630573 160630365 1.540000e-98 370
36 TraesCS5A01G522800 chr3B 90.876 274 18 3 269 535 593865530 593865803 9.290000e-96 361
37 TraesCS5A01G522800 chr3B 90.511 274 21 3 266 534 1417399 1417672 1.200000e-94 357
38 TraesCS5A01G522800 chr3B 88.971 272 23 2 271 535 8022256 8021985 2.620000e-86 329
39 TraesCS5A01G522800 chr2D 98.104 211 4 0 1 211 591307308 591307098 5.550000e-98 368
40 TraesCS5A01G522800 chr2A 97.209 215 5 1 1 215 30175352 30175565 2.580000e-96 363
41 TraesCS5A01G522800 chr5D 95.982 224 6 2 1 224 360025816 360026036 9.290000e-96 361


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 TraesCS5A01G522800 chr5A 683943662 683947181 3519 True 6501 6501 100.0000 1 3520 1 chr5A.!!$R1 3519
1 TraesCS5A01G522800 chr4B 668005159 668006896 1737 True 1321 2531 90.3910 849 2579 2 chr4B.!!$R1 1730
2 TraesCS5A01G522800 chrUn 29715855 29717620 1765 False 1207 2183 92.2475 947 2525 2 chrUn.!!$F1 1578
3 TraesCS5A01G522800 chr6D 296757735 296758679 944 False 1360 1360 92.7370 2580 3520 1 chr6D.!!$F2 940
4 TraesCS5A01G522800 chr6D 121799526 121800470 944 False 1240 1240 90.5060 2580 3517 1 chr6D.!!$F1 937
5 TraesCS5A01G522800 chr7A 222635168 222636113 945 True 1188 1188 89.4740 2575 3515 1 chr7A.!!$R1 940
6 TraesCS5A01G522800 chr4D 46424840 46425780 940 True 1107 1107 88.0000 2579 3520 1 chr4D.!!$R1 941
7 TraesCS5A01G522800 chr1D 455550274 455551222 948 False 1048 1048 86.7920 2577 3517 1 chr1D.!!$F1 940
8 TraesCS5A01G522800 chr7B 4600795 4601740 945 True 1042 1042 86.7150 2577 3520 1 chr7B.!!$R1 943
9 TraesCS5A01G522800 chr7B 589367503 589368439 936 False 1007 1007 86.2430 2584 3517 1 chr7B.!!$F2 933
10 TraesCS5A01G522800 chr2B 30310291 30311239 948 True 1035 1035 86.5260 2579 3517 1 chr2B.!!$R1 938
11 TraesCS5A01G522800 chr2B 58782244 58783788 1544 True 397 448 91.6835 271 851 2 chr2B.!!$R2 580
12 TraesCS5A01G522800 chr7D 25899222 25900164 942 True 1013 1013 86.2540 2579 3517 1 chr7D.!!$R1 938
13 TraesCS5A01G522800 chr3A 150795432 150795945 513 True 523 523 85.3850 2579 3086 1 chr3A.!!$R1 507
14 TraesCS5A01G522800 chr4A 701264855 701267746 2891 True 428 464 93.0415 265 851 2 chr4A.!!$R1 586

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
148 149 0.035152 ATGCGAGCACCAGGATTTGA 60.035 50.0 0.0 0.0 0.0 2.69 F
150 151 0.169009 GCGAGCACCAGGATTTGAAC 59.831 55.0 0.0 0.0 0.0 3.18 F
1820 4240 0.177836 CACCCACAGCATACGGATCA 59.822 55.0 0.0 0.0 0.0 2.92 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1988 4411 0.867753 CGTAGCATGTCCTCGCAGAC 60.868 60.000 0.00 0.0 37.28 3.51 R
2132 4555 3.055602 TGATCCAAGTCATCTGGTGTCAG 60.056 47.826 0.00 0.0 42.21 3.51 R
2865 5533 0.452184 ATGTGGTCGCTACTCACTCG 59.548 55.000 10.01 0.0 31.73 4.18 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 3.520402 CCTCCGAGAGACTGAGCC 58.480 66.667 0.00 0.00 0.00 4.70
18 19 2.477176 CCTCCGAGAGACTGAGCCG 61.477 68.421 0.00 0.00 0.00 5.52
19 20 2.438614 TCCGAGAGACTGAGCCGG 60.439 66.667 0.00 0.00 41.36 6.13
20 21 4.200283 CCGAGAGACTGAGCCGGC 62.200 72.222 21.89 21.89 33.47 6.13
21 22 3.443925 CGAGAGACTGAGCCGGCA 61.444 66.667 31.54 7.98 0.00 5.69
22 23 2.780094 CGAGAGACTGAGCCGGCAT 61.780 63.158 31.54 14.28 0.00 4.40
23 24 1.448119 CGAGAGACTGAGCCGGCATA 61.448 60.000 31.54 16.21 0.00 3.14
24 25 0.965439 GAGAGACTGAGCCGGCATAT 59.035 55.000 31.54 8.11 0.00 1.78
25 26 0.965439 AGAGACTGAGCCGGCATATC 59.035 55.000 31.54 18.63 0.00 1.63
26 27 0.676184 GAGACTGAGCCGGCATATCA 59.324 55.000 31.54 22.44 0.00 2.15
27 28 1.274728 GAGACTGAGCCGGCATATCAT 59.725 52.381 31.54 13.17 0.00 2.45
28 29 1.274728 AGACTGAGCCGGCATATCATC 59.725 52.381 31.54 19.98 0.00 2.92
29 30 1.274728 GACTGAGCCGGCATATCATCT 59.725 52.381 31.54 11.40 0.00 2.90
30 31 1.696336 ACTGAGCCGGCATATCATCTT 59.304 47.619 31.54 3.33 0.00 2.40
31 32 2.074576 CTGAGCCGGCATATCATCTTG 58.925 52.381 31.54 7.95 0.00 3.02
32 33 1.693606 TGAGCCGGCATATCATCTTGA 59.306 47.619 31.54 0.00 0.00 3.02
33 34 2.289257 TGAGCCGGCATATCATCTTGAG 60.289 50.000 31.54 0.00 0.00 3.02
34 35 1.973515 AGCCGGCATATCATCTTGAGA 59.026 47.619 31.54 0.00 0.00 3.27
35 36 2.570752 AGCCGGCATATCATCTTGAGAT 59.429 45.455 31.54 0.00 34.56 2.75
36 37 3.008813 AGCCGGCATATCATCTTGAGATT 59.991 43.478 31.54 0.00 31.21 2.40
37 38 3.755378 GCCGGCATATCATCTTGAGATTT 59.245 43.478 24.80 0.00 31.21 2.17
38 39 4.937620 GCCGGCATATCATCTTGAGATTTA 59.062 41.667 24.80 0.00 31.21 1.40
39 40 5.163814 GCCGGCATATCATCTTGAGATTTAC 60.164 44.000 24.80 0.00 31.21 2.01
40 41 5.062683 CCGGCATATCATCTTGAGATTTACG 59.937 44.000 0.00 0.00 31.21 3.18
41 42 5.863935 CGGCATATCATCTTGAGATTTACGA 59.136 40.000 0.00 0.00 31.21 3.43
42 43 6.366061 CGGCATATCATCTTGAGATTTACGAA 59.634 38.462 0.00 0.00 31.21 3.85
43 44 7.411264 CGGCATATCATCTTGAGATTTACGAAG 60.411 40.741 0.00 0.00 31.21 3.79
44 45 7.232994 GCATATCATCTTGAGATTTACGAAGC 58.767 38.462 0.00 0.00 31.21 3.86
45 46 7.095481 GCATATCATCTTGAGATTTACGAAGCA 60.095 37.037 0.00 0.00 31.21 3.91
46 47 8.768019 CATATCATCTTGAGATTTACGAAGCAA 58.232 33.333 0.00 0.00 31.21 3.91
47 48 6.408858 TCATCTTGAGATTTACGAAGCAAC 57.591 37.500 0.00 0.00 31.21 4.17
48 49 5.351465 TCATCTTGAGATTTACGAAGCAACC 59.649 40.000 0.00 0.00 31.21 3.77
49 50 3.678072 TCTTGAGATTTACGAAGCAACCG 59.322 43.478 0.00 0.00 0.00 4.44
50 51 3.034721 TGAGATTTACGAAGCAACCGT 57.965 42.857 0.00 0.00 43.26 4.83
51 52 4.177165 TGAGATTTACGAAGCAACCGTA 57.823 40.909 0.00 0.00 40.95 4.02
52 53 4.171005 TGAGATTTACGAAGCAACCGTAG 58.829 43.478 0.00 0.00 42.42 3.51
65 66 4.883300 CGTAGGCGCCTCGTCGTC 62.883 72.222 36.73 15.88 36.23 4.20
66 67 4.883300 GTAGGCGCCTCGTCGTCG 62.883 72.222 36.73 0.00 39.34 5.12
87 88 4.115270 GGAACGTCTCCTCCCACT 57.885 61.111 8.87 0.00 41.61 4.00
88 89 1.592223 GGAACGTCTCCTCCCACTG 59.408 63.158 8.87 0.00 41.61 3.66
89 90 0.898789 GGAACGTCTCCTCCCACTGA 60.899 60.000 8.87 0.00 41.61 3.41
90 91 0.966920 GAACGTCTCCTCCCACTGAA 59.033 55.000 0.00 0.00 0.00 3.02
91 92 1.343465 GAACGTCTCCTCCCACTGAAA 59.657 52.381 0.00 0.00 0.00 2.69
92 93 0.969894 ACGTCTCCTCCCACTGAAAG 59.030 55.000 0.00 0.00 42.29 2.62
93 94 0.390472 CGTCTCCTCCCACTGAAAGC 60.390 60.000 0.00 0.00 37.60 3.51
94 95 0.390472 GTCTCCTCCCACTGAAAGCG 60.390 60.000 0.00 0.00 37.60 4.68
95 96 1.743252 CTCCTCCCACTGAAAGCGC 60.743 63.158 0.00 0.00 37.60 5.92
96 97 2.032528 CCTCCCACTGAAAGCGCA 59.967 61.111 11.47 0.00 37.60 6.09
97 98 1.377725 CCTCCCACTGAAAGCGCAT 60.378 57.895 11.47 0.00 37.60 4.73
98 99 1.372087 CCTCCCACTGAAAGCGCATC 61.372 60.000 11.47 8.39 37.60 3.91
99 100 1.699656 CTCCCACTGAAAGCGCATCG 61.700 60.000 11.47 6.82 37.60 3.84
110 111 2.588877 CGCATCGCCGGAAATCCT 60.589 61.111 5.05 0.00 0.00 3.24
111 112 2.885676 CGCATCGCCGGAAATCCTG 61.886 63.158 5.05 0.00 0.00 3.86
112 113 1.523711 GCATCGCCGGAAATCCTGA 60.524 57.895 5.05 0.00 0.00 3.86
113 114 1.095228 GCATCGCCGGAAATCCTGAA 61.095 55.000 5.05 0.00 0.00 3.02
114 115 1.378531 CATCGCCGGAAATCCTGAAA 58.621 50.000 5.05 0.00 0.00 2.69
115 116 1.949525 CATCGCCGGAAATCCTGAAAT 59.050 47.619 5.05 0.00 0.00 2.17
116 117 2.992124 TCGCCGGAAATCCTGAAATA 57.008 45.000 5.05 0.00 0.00 1.40
117 118 3.269538 TCGCCGGAAATCCTGAAATAA 57.730 42.857 5.05 0.00 0.00 1.40
118 119 3.611970 TCGCCGGAAATCCTGAAATAAA 58.388 40.909 5.05 0.00 0.00 1.40
119 120 4.204012 TCGCCGGAAATCCTGAAATAAAT 58.796 39.130 5.05 0.00 0.00 1.40
120 121 4.274950 TCGCCGGAAATCCTGAAATAAATC 59.725 41.667 5.05 0.00 0.00 2.17
121 122 4.556699 CGCCGGAAATCCTGAAATAAATCC 60.557 45.833 5.05 0.00 0.00 3.01
122 123 4.340950 GCCGGAAATCCTGAAATAAATCCA 59.659 41.667 5.05 0.00 0.00 3.41
123 124 5.507985 GCCGGAAATCCTGAAATAAATCCAG 60.508 44.000 5.05 0.00 0.00 3.86
124 125 5.010012 CCGGAAATCCTGAAATAAATCCAGG 59.990 44.000 0.00 0.00 46.64 4.45
134 135 7.815840 TGAAATAAATCCAGGAATAATGCGA 57.184 32.000 0.00 0.00 0.00 5.10
135 136 7.874940 TGAAATAAATCCAGGAATAATGCGAG 58.125 34.615 0.00 0.00 0.00 5.03
136 137 5.886960 ATAAATCCAGGAATAATGCGAGC 57.113 39.130 0.00 0.00 0.00 5.03
137 138 2.936919 ATCCAGGAATAATGCGAGCA 57.063 45.000 0.00 0.00 0.00 4.26
138 139 1.953559 TCCAGGAATAATGCGAGCAC 58.046 50.000 0.00 0.00 0.00 4.40
139 140 0.947244 CCAGGAATAATGCGAGCACC 59.053 55.000 0.00 0.00 0.00 5.01
140 141 1.667236 CAGGAATAATGCGAGCACCA 58.333 50.000 0.00 0.00 0.00 4.17
141 142 1.600957 CAGGAATAATGCGAGCACCAG 59.399 52.381 0.00 0.00 0.00 4.00
142 143 0.947244 GGAATAATGCGAGCACCAGG 59.053 55.000 0.00 0.00 0.00 4.45
143 144 1.475034 GGAATAATGCGAGCACCAGGA 60.475 52.381 0.00 0.00 0.00 3.86
144 145 2.498167 GAATAATGCGAGCACCAGGAT 58.502 47.619 0.00 0.00 0.00 3.24
145 146 2.645838 ATAATGCGAGCACCAGGATT 57.354 45.000 0.00 0.00 33.17 3.01
146 147 2.418368 TAATGCGAGCACCAGGATTT 57.582 45.000 0.00 0.00 31.11 2.17
147 148 0.813184 AATGCGAGCACCAGGATTTG 59.187 50.000 0.00 0.00 0.00 2.32
148 149 0.035152 ATGCGAGCACCAGGATTTGA 60.035 50.000 0.00 0.00 0.00 2.69
149 150 0.250684 TGCGAGCACCAGGATTTGAA 60.251 50.000 0.00 0.00 0.00 2.69
150 151 0.169009 GCGAGCACCAGGATTTGAAC 59.831 55.000 0.00 0.00 0.00 3.18
151 152 0.804989 CGAGCACCAGGATTTGAACC 59.195 55.000 0.00 0.00 0.00 3.62
152 153 1.177401 GAGCACCAGGATTTGAACCC 58.823 55.000 0.00 0.00 0.00 4.11
153 154 0.779997 AGCACCAGGATTTGAACCCT 59.220 50.000 0.00 0.00 0.00 4.34
158 159 1.549203 CAGGATTTGAACCCTGGTGG 58.451 55.000 0.00 0.00 44.68 4.61
184 185 3.538634 GGATACCACTGTCCACCTAAC 57.461 52.381 0.00 0.00 34.57 2.34
185 186 2.169978 GGATACCACTGTCCACCTAACC 59.830 54.545 0.00 0.00 34.57 2.85
186 187 2.402182 TACCACTGTCCACCTAACCA 57.598 50.000 0.00 0.00 0.00 3.67
187 188 1.742308 ACCACTGTCCACCTAACCAT 58.258 50.000 0.00 0.00 0.00 3.55
188 189 1.628846 ACCACTGTCCACCTAACCATC 59.371 52.381 0.00 0.00 0.00 3.51
189 190 1.909302 CCACTGTCCACCTAACCATCT 59.091 52.381 0.00 0.00 0.00 2.90
190 191 2.093447 CCACTGTCCACCTAACCATCTC 60.093 54.545 0.00 0.00 0.00 2.75
191 192 2.567169 CACTGTCCACCTAACCATCTCA 59.433 50.000 0.00 0.00 0.00 3.27
192 193 3.007940 CACTGTCCACCTAACCATCTCAA 59.992 47.826 0.00 0.00 0.00 3.02
193 194 3.008049 ACTGTCCACCTAACCATCTCAAC 59.992 47.826 0.00 0.00 0.00 3.18
194 195 2.304761 TGTCCACCTAACCATCTCAACC 59.695 50.000 0.00 0.00 0.00 3.77
195 196 2.304761 GTCCACCTAACCATCTCAACCA 59.695 50.000 0.00 0.00 0.00 3.67
196 197 2.304761 TCCACCTAACCATCTCAACCAC 59.695 50.000 0.00 0.00 0.00 4.16
197 198 2.039746 CCACCTAACCATCTCAACCACA 59.960 50.000 0.00 0.00 0.00 4.17
198 199 3.338249 CACCTAACCATCTCAACCACAG 58.662 50.000 0.00 0.00 0.00 3.66
199 200 2.305927 ACCTAACCATCTCAACCACAGG 59.694 50.000 0.00 0.00 0.00 4.00
200 201 2.305927 CCTAACCATCTCAACCACAGGT 59.694 50.000 0.00 0.00 37.65 4.00
209 210 3.725754 AACCACAGGTTGATTCGCT 57.274 47.368 0.00 0.00 45.07 4.93
210 211 2.851263 AACCACAGGTTGATTCGCTA 57.149 45.000 0.00 0.00 45.07 4.26
211 212 2.851263 ACCACAGGTTGATTCGCTAA 57.149 45.000 0.00 0.00 27.29 3.09
212 213 3.134574 ACCACAGGTTGATTCGCTAAA 57.865 42.857 0.00 0.00 27.29 1.85
213 214 3.074412 ACCACAGGTTGATTCGCTAAAG 58.926 45.455 0.00 0.00 27.29 1.85
214 215 3.244422 ACCACAGGTTGATTCGCTAAAGA 60.244 43.478 0.00 0.00 27.29 2.52
215 216 3.372206 CCACAGGTTGATTCGCTAAAGAG 59.628 47.826 0.00 0.00 0.00 2.85
216 217 4.245660 CACAGGTTGATTCGCTAAAGAGA 58.754 43.478 0.00 0.00 0.00 3.10
217 218 4.872691 CACAGGTTGATTCGCTAAAGAGAT 59.127 41.667 0.00 0.00 0.00 2.75
218 219 6.042777 CACAGGTTGATTCGCTAAAGAGATA 58.957 40.000 0.00 0.00 0.00 1.98
219 220 6.535150 CACAGGTTGATTCGCTAAAGAGATAA 59.465 38.462 0.00 0.00 0.00 1.75
220 221 7.064609 CACAGGTTGATTCGCTAAAGAGATAAA 59.935 37.037 0.00 0.00 0.00 1.40
221 222 7.278868 ACAGGTTGATTCGCTAAAGAGATAAAG 59.721 37.037 0.00 0.00 0.00 1.85
222 223 7.492669 CAGGTTGATTCGCTAAAGAGATAAAGA 59.507 37.037 0.00 0.00 0.00 2.52
223 224 8.207545 AGGTTGATTCGCTAAAGAGATAAAGAT 58.792 33.333 0.00 0.00 0.00 2.40
224 225 9.477484 GGTTGATTCGCTAAAGAGATAAAGATA 57.523 33.333 0.00 0.00 0.00 1.98
236 237 7.981102 AGAGATAAAGATATAAAAACGGGGC 57.019 36.000 0.00 0.00 0.00 5.80
237 238 6.649557 AGAGATAAAGATATAAAAACGGGGCG 59.350 38.462 0.00 0.00 0.00 6.13
238 239 6.527423 AGATAAAGATATAAAAACGGGGCGA 58.473 36.000 0.00 0.00 0.00 5.54
239 240 6.993902 AGATAAAGATATAAAAACGGGGCGAA 59.006 34.615 0.00 0.00 0.00 4.70
240 241 5.900865 AAAGATATAAAAACGGGGCGAAA 57.099 34.783 0.00 0.00 0.00 3.46
241 242 5.494632 AAGATATAAAAACGGGGCGAAAG 57.505 39.130 0.00 0.00 0.00 2.62
431 439 2.339556 GCGCAGTGTATTTGGGGCA 61.340 57.895 0.30 0.00 38.83 5.36
565 2971 5.606348 TTGGGCATGAACTTTTAGTTTGT 57.394 34.783 0.00 0.00 38.80 2.83
710 3116 0.239879 CGCACGCCCTGTATTTTTGT 59.760 50.000 0.00 0.00 0.00 2.83
851 3259 0.809241 CGGCTGTTGGAGATGCTCTC 60.809 60.000 5.01 5.01 42.66 3.20
882 3290 5.640189 ACATGTACTCCGTATATGCTACC 57.360 43.478 0.00 0.00 39.91 3.18
1820 4240 0.177836 CACCCACAGCATACGGATCA 59.822 55.000 0.00 0.00 0.00 2.92
1834 4254 1.493950 GGATCAACGGCATGAGAGCG 61.494 60.000 0.00 0.00 34.64 5.03
1846 4266 0.756294 TGAGAGCGGAGGTGTTCAAA 59.244 50.000 0.00 0.00 39.88 2.69
1988 4411 1.134461 CCATGGAGAGACTCAAGCTGG 60.134 57.143 5.56 2.80 31.08 4.85
2000 4423 2.210013 AAGCTGGTCTGCGAGGACA 61.210 57.895 9.69 0.00 37.91 4.02
2132 4555 2.359900 CAACCACACTAGATCAAGCCC 58.640 52.381 0.00 0.00 0.00 5.19
2180 4603 1.889170 CCAAAACCTGCCCTTCTCTTC 59.111 52.381 0.00 0.00 0.00 2.87
2244 4667 2.813754 TCAACAATGAAAAGCCGGAGAG 59.186 45.455 5.05 0.00 30.99 3.20
2295 4718 2.029844 GAGCACCGACACCAAGCTC 61.030 63.158 0.00 0.00 43.95 4.09
2353 4988 3.556423 CCGCTCCAACAACCTAAACTAGT 60.556 47.826 0.00 0.00 0.00 2.57
2379 5014 6.738649 GCGTGACATGAGTTAAATCTTCTTTC 59.261 38.462 0.00 0.00 0.00 2.62
2525 5165 5.741388 AATTGATCAGTGCGAGGTTTATC 57.259 39.130 0.00 0.00 0.00 1.75
2526 5166 4.471904 TTGATCAGTGCGAGGTTTATCT 57.528 40.909 0.00 0.00 0.00 1.98
2527 5167 4.046938 TGATCAGTGCGAGGTTTATCTC 57.953 45.455 0.00 0.00 0.00 2.75
2528 5168 3.447229 TGATCAGTGCGAGGTTTATCTCA 59.553 43.478 0.00 0.00 33.59 3.27
2529 5169 4.100035 TGATCAGTGCGAGGTTTATCTCAT 59.900 41.667 0.00 0.00 33.59 2.90
2530 5170 4.471904 TCAGTGCGAGGTTTATCTCATT 57.528 40.909 0.00 0.00 33.59 2.57
2531 5171 4.183865 TCAGTGCGAGGTTTATCTCATTG 58.816 43.478 0.00 0.00 33.59 2.82
2558 5198 4.343231 TGAGCTCAAATTCTTGCCCATTA 58.657 39.130 15.67 0.00 32.14 1.90
2559 5199 4.957954 TGAGCTCAAATTCTTGCCCATTAT 59.042 37.500 15.67 0.00 32.14 1.28
2582 5229 5.622770 ATTGGGATGTCGTGTAAGTTTTC 57.377 39.130 0.00 0.00 0.00 2.29
2586 5233 5.237779 TGGGATGTCGTGTAAGTTTTCTTTC 59.762 40.000 0.00 0.00 40.91 2.62
2798 5466 1.377463 CCGCCATCCAAACCGGTTA 60.377 57.895 22.60 5.30 36.18 2.85
2806 5474 5.336929 GCCATCCAAACCGGTTAAAAATAGT 60.337 40.000 22.60 0.00 35.57 2.12
2865 5533 3.844090 GCTCTCTGGCCTCCGTCC 61.844 72.222 3.32 0.00 0.00 4.79
2895 5563 1.470979 GCGACCACATACGGATCAACT 60.471 52.381 0.00 0.00 0.00 3.16
2905 5573 0.247460 CGGATCAACTCAGTGGCTCA 59.753 55.000 0.00 0.00 0.00 4.26
3002 5671 8.091449 GCTCATAATAAAGCACATACTCCTACT 58.909 37.037 0.00 0.00 38.42 2.57
3008 5677 6.710597 AAAGCACATACTCCTACTCGAATA 57.289 37.500 0.00 0.00 0.00 1.75
3032 5701 4.113354 GTCTCGCTGTTTCGGAATCTATT 58.887 43.478 0.00 0.00 0.00 1.73
3102 5771 9.555727 GAGTAATATTAAAGGCTATGTGAACCA 57.444 33.333 0.00 0.00 0.00 3.67
3108 5777 0.463654 GGCTATGTGAACCATCCGCA 60.464 55.000 0.00 0.00 33.86 5.69
3298 5970 7.558444 AGGTACTTTGACTTTCCAACATGTTTA 59.442 33.333 8.77 0.00 27.25 2.01
3331 6003 9.935241 GGAATAGAGCTAGAATTGATAACATCA 57.065 33.333 0.00 0.00 37.55 3.07
3374 6046 6.632035 CGTAAACTCTCCATTACTAGTTAGCG 59.368 42.308 0.00 0.00 32.09 4.26
3441 6113 2.235898 GTCTTCTCACAAGATGGAGCCT 59.764 50.000 0.00 0.00 0.00 4.58
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.477176 CGGCTCAGTCTCTCGGAGG 61.477 68.421 4.96 0.00 38.48 4.30
1 2 2.477176 CCGGCTCAGTCTCTCGGAG 61.477 68.421 0.00 0.00 42.94 4.63
3 4 4.200283 GCCGGCTCAGTCTCTCGG 62.200 72.222 22.15 0.00 43.13 4.63
5 6 0.965439 ATATGCCGGCTCAGTCTCTC 59.035 55.000 29.70 0.00 0.00 3.20
7 8 0.676184 TGATATGCCGGCTCAGTCTC 59.324 55.000 29.70 15.31 0.00 3.36
8 9 1.274728 GATGATATGCCGGCTCAGTCT 59.725 52.381 29.70 8.26 0.00 3.24
9 10 1.274728 AGATGATATGCCGGCTCAGTC 59.725 52.381 29.70 19.55 0.00 3.51
10 11 1.346062 AGATGATATGCCGGCTCAGT 58.654 50.000 29.70 13.44 0.00 3.41
11 12 2.074576 CAAGATGATATGCCGGCTCAG 58.925 52.381 29.70 7.35 0.00 3.35
12 13 1.693606 TCAAGATGATATGCCGGCTCA 59.306 47.619 29.70 23.34 0.00 4.26
13 14 2.028658 TCTCAAGATGATATGCCGGCTC 60.029 50.000 29.70 17.89 0.00 4.70
14 15 1.973515 TCTCAAGATGATATGCCGGCT 59.026 47.619 29.70 15.76 0.00 5.52
15 16 2.462456 TCTCAAGATGATATGCCGGC 57.538 50.000 22.73 22.73 0.00 6.13
16 17 5.062683 CGTAAATCTCAAGATGATATGCCGG 59.937 44.000 0.00 0.00 34.49 6.13
17 18 5.863935 TCGTAAATCTCAAGATGATATGCCG 59.136 40.000 0.00 0.00 34.49 5.69
18 19 7.623089 GCTTCGTAAATCTCAAGATGATATGCC 60.623 40.741 0.00 0.00 34.49 4.40
19 20 7.095481 TGCTTCGTAAATCTCAAGATGATATGC 60.095 37.037 0.00 0.00 34.49 3.14
20 21 8.302965 TGCTTCGTAAATCTCAAGATGATATG 57.697 34.615 0.00 0.00 34.49 1.78
21 22 8.768955 GTTGCTTCGTAAATCTCAAGATGATAT 58.231 33.333 0.00 0.00 34.49 1.63
22 23 7.224753 GGTTGCTTCGTAAATCTCAAGATGATA 59.775 37.037 0.00 0.00 34.49 2.15
23 24 6.037610 GGTTGCTTCGTAAATCTCAAGATGAT 59.962 38.462 0.00 0.00 34.49 2.45
24 25 5.351465 GGTTGCTTCGTAAATCTCAAGATGA 59.649 40.000 0.00 0.00 34.49 2.92
25 26 5.563842 GGTTGCTTCGTAAATCTCAAGATG 58.436 41.667 0.00 0.00 34.49 2.90
26 27 4.330074 CGGTTGCTTCGTAAATCTCAAGAT 59.670 41.667 0.00 0.00 36.07 2.40
27 28 3.678072 CGGTTGCTTCGTAAATCTCAAGA 59.322 43.478 0.00 0.00 0.00 3.02
28 29 3.432252 ACGGTTGCTTCGTAAATCTCAAG 59.568 43.478 0.00 0.00 39.22 3.02
29 30 3.395639 ACGGTTGCTTCGTAAATCTCAA 58.604 40.909 0.00 0.00 39.22 3.02
30 31 3.034721 ACGGTTGCTTCGTAAATCTCA 57.965 42.857 0.00 0.00 39.22 3.27
31 32 3.550678 CCTACGGTTGCTTCGTAAATCTC 59.449 47.826 7.80 0.00 41.62 2.75
32 33 3.518590 CCTACGGTTGCTTCGTAAATCT 58.481 45.455 7.80 0.00 41.62 2.40
33 34 2.030091 GCCTACGGTTGCTTCGTAAATC 59.970 50.000 7.80 0.00 41.62 2.17
34 35 2.004733 GCCTACGGTTGCTTCGTAAAT 58.995 47.619 7.80 0.00 41.62 1.40
35 36 1.431496 GCCTACGGTTGCTTCGTAAA 58.569 50.000 7.80 0.00 41.62 2.01
36 37 0.733566 CGCCTACGGTTGCTTCGTAA 60.734 55.000 7.80 0.00 41.62 3.18
37 38 1.153978 CGCCTACGGTTGCTTCGTA 60.154 57.895 6.60 6.60 41.38 3.43
38 39 2.431942 CGCCTACGGTTGCTTCGT 60.432 61.111 5.13 5.13 43.64 3.85
39 40 3.849953 GCGCCTACGGTTGCTTCG 61.850 66.667 0.00 0.00 40.57 3.79
40 41 3.497031 GGCGCCTACGGTTGCTTC 61.497 66.667 22.15 0.00 40.57 3.86
41 42 3.952628 GAGGCGCCTACGGTTGCTT 62.953 63.158 32.97 2.04 40.57 3.91
42 43 4.452733 GAGGCGCCTACGGTTGCT 62.453 66.667 32.97 3.02 40.57 3.91
44 45 4.430765 ACGAGGCGCCTACGGTTG 62.431 66.667 34.97 21.03 40.57 3.77
45 46 4.125695 GACGAGGCGCCTACGGTT 62.126 66.667 34.97 23.48 40.57 4.44
48 49 4.883300 GACGACGAGGCGCCTACG 62.883 72.222 32.91 32.91 44.07 3.51
71 72 0.966920 TTCAGTGGGAGGAGACGTTC 59.033 55.000 0.00 0.00 0.00 3.95
72 73 1.344763 CTTTCAGTGGGAGGAGACGTT 59.655 52.381 0.00 0.00 0.00 3.99
73 74 0.969894 CTTTCAGTGGGAGGAGACGT 59.030 55.000 0.00 0.00 0.00 4.34
74 75 0.390472 GCTTTCAGTGGGAGGAGACG 60.390 60.000 0.00 0.00 0.00 4.18
75 76 0.390472 CGCTTTCAGTGGGAGGAGAC 60.390 60.000 0.00 0.00 0.00 3.36
76 77 1.975327 CGCTTTCAGTGGGAGGAGA 59.025 57.895 0.00 0.00 0.00 3.71
77 78 1.743252 GCGCTTTCAGTGGGAGGAG 60.743 63.158 0.00 0.00 0.00 3.69
78 79 1.841302 ATGCGCTTTCAGTGGGAGGA 61.841 55.000 9.73 0.00 0.00 3.71
79 80 1.372087 GATGCGCTTTCAGTGGGAGG 61.372 60.000 9.73 0.00 0.00 4.30
80 81 1.699656 CGATGCGCTTTCAGTGGGAG 61.700 60.000 9.73 0.00 0.00 4.30
81 82 1.741401 CGATGCGCTTTCAGTGGGA 60.741 57.895 9.73 0.00 0.00 4.37
82 83 2.787249 CGATGCGCTTTCAGTGGG 59.213 61.111 9.73 0.00 0.00 4.61
93 94 2.588877 AGGATTTCCGGCGATGCG 60.589 61.111 9.30 0.00 42.08 4.73
94 95 1.095228 TTCAGGATTTCCGGCGATGC 61.095 55.000 9.30 0.00 42.08 3.91
95 96 1.378531 TTTCAGGATTTCCGGCGATG 58.621 50.000 9.30 0.00 42.08 3.84
96 97 2.348411 ATTTCAGGATTTCCGGCGAT 57.652 45.000 9.30 0.00 42.08 4.58
97 98 2.992124 TATTTCAGGATTTCCGGCGA 57.008 45.000 9.30 0.00 42.08 5.54
98 99 4.537015 GATTTATTTCAGGATTTCCGGCG 58.463 43.478 0.00 0.00 42.08 6.46
99 100 4.340950 TGGATTTATTTCAGGATTTCCGGC 59.659 41.667 0.00 0.00 42.08 6.13
100 101 6.076981 CTGGATTTATTTCAGGATTTCCGG 57.923 41.667 0.00 0.00 42.08 5.14
108 109 7.040478 TCGCATTATTCCTGGATTTATTTCAGG 60.040 37.037 0.00 0.00 46.91 3.86
109 110 7.874940 TCGCATTATTCCTGGATTTATTTCAG 58.125 34.615 0.00 0.00 0.00 3.02
110 111 7.522073 GCTCGCATTATTCCTGGATTTATTTCA 60.522 37.037 0.00 0.00 0.00 2.69
111 112 6.803807 GCTCGCATTATTCCTGGATTTATTTC 59.196 38.462 0.00 0.00 0.00 2.17
112 113 6.265196 TGCTCGCATTATTCCTGGATTTATTT 59.735 34.615 0.00 0.00 0.00 1.40
113 114 5.769662 TGCTCGCATTATTCCTGGATTTATT 59.230 36.000 0.00 0.00 0.00 1.40
114 115 5.182001 GTGCTCGCATTATTCCTGGATTTAT 59.818 40.000 0.00 0.00 0.00 1.40
115 116 4.515191 GTGCTCGCATTATTCCTGGATTTA 59.485 41.667 0.00 0.00 0.00 1.40
116 117 3.316308 GTGCTCGCATTATTCCTGGATTT 59.684 43.478 0.00 0.00 0.00 2.17
117 118 2.880890 GTGCTCGCATTATTCCTGGATT 59.119 45.455 0.00 0.00 0.00 3.01
118 119 2.498167 GTGCTCGCATTATTCCTGGAT 58.502 47.619 0.00 0.00 0.00 3.41
119 120 1.475034 GGTGCTCGCATTATTCCTGGA 60.475 52.381 0.00 0.00 0.00 3.86
120 121 0.947244 GGTGCTCGCATTATTCCTGG 59.053 55.000 0.00 0.00 0.00 4.45
121 122 1.600957 CTGGTGCTCGCATTATTCCTG 59.399 52.381 0.00 0.00 0.00 3.86
122 123 1.475751 CCTGGTGCTCGCATTATTCCT 60.476 52.381 0.00 0.00 0.00 3.36
123 124 0.947244 CCTGGTGCTCGCATTATTCC 59.053 55.000 0.00 0.00 0.00 3.01
124 125 1.953559 TCCTGGTGCTCGCATTATTC 58.046 50.000 0.00 0.00 0.00 1.75
125 126 2.645838 ATCCTGGTGCTCGCATTATT 57.354 45.000 0.00 0.00 0.00 1.40
126 127 2.620115 CAAATCCTGGTGCTCGCATTAT 59.380 45.455 0.00 0.00 0.00 1.28
127 128 2.016318 CAAATCCTGGTGCTCGCATTA 58.984 47.619 0.00 0.00 0.00 1.90
128 129 0.813184 CAAATCCTGGTGCTCGCATT 59.187 50.000 0.00 0.00 0.00 3.56
129 130 0.035152 TCAAATCCTGGTGCTCGCAT 60.035 50.000 0.00 0.00 0.00 4.73
130 131 0.250684 TTCAAATCCTGGTGCTCGCA 60.251 50.000 0.00 0.00 0.00 5.10
131 132 0.169009 GTTCAAATCCTGGTGCTCGC 59.831 55.000 0.00 0.00 0.00 5.03
132 133 0.804989 GGTTCAAATCCTGGTGCTCG 59.195 55.000 0.00 0.00 0.00 5.03
133 134 1.177401 GGGTTCAAATCCTGGTGCTC 58.823 55.000 0.00 0.00 0.00 4.26
134 135 0.779997 AGGGTTCAAATCCTGGTGCT 59.220 50.000 0.00 0.00 38.36 4.40
135 136 3.363787 AGGGTTCAAATCCTGGTGC 57.636 52.632 0.00 0.00 38.36 5.01
151 152 1.137697 GGTATCCCTAACCCACCAGG 58.862 60.000 0.00 0.00 43.78 4.45
152 153 1.489230 GTGGTATCCCTAACCCACCAG 59.511 57.143 0.00 0.00 41.20 4.00
153 154 1.081513 AGTGGTATCCCTAACCCACCA 59.918 52.381 4.15 0.00 46.84 4.17
154 155 1.489230 CAGTGGTATCCCTAACCCACC 59.511 57.143 4.15 0.00 46.84 4.61
155 156 2.169978 GACAGTGGTATCCCTAACCCAC 59.830 54.545 0.00 0.00 46.17 4.61
156 157 2.474112 GACAGTGGTATCCCTAACCCA 58.526 52.381 0.00 0.00 36.06 4.51
157 158 1.767088 GGACAGTGGTATCCCTAACCC 59.233 57.143 0.00 0.00 36.06 4.11
158 159 2.169978 GTGGACAGTGGTATCCCTAACC 59.830 54.545 0.00 0.00 37.53 2.85
159 160 2.169978 GGTGGACAGTGGTATCCCTAAC 59.830 54.545 0.00 0.00 33.69 2.34
160 161 2.045326 AGGTGGACAGTGGTATCCCTAA 59.955 50.000 0.00 0.00 33.69 2.69
161 162 1.649633 AGGTGGACAGTGGTATCCCTA 59.350 52.381 0.00 0.00 33.69 3.53
162 163 0.417841 AGGTGGACAGTGGTATCCCT 59.582 55.000 0.00 0.00 33.69 4.20
163 164 2.169978 GTTAGGTGGACAGTGGTATCCC 59.830 54.545 0.00 0.00 33.69 3.85
164 165 2.169978 GGTTAGGTGGACAGTGGTATCC 59.830 54.545 0.00 0.00 35.37 2.59
165 166 2.835764 TGGTTAGGTGGACAGTGGTATC 59.164 50.000 0.00 0.00 0.00 2.24
166 167 2.910544 TGGTTAGGTGGACAGTGGTAT 58.089 47.619 0.00 0.00 0.00 2.73
167 168 2.402182 TGGTTAGGTGGACAGTGGTA 57.598 50.000 0.00 0.00 0.00 3.25
168 169 1.628846 GATGGTTAGGTGGACAGTGGT 59.371 52.381 0.00 0.00 0.00 4.16
169 170 1.909302 AGATGGTTAGGTGGACAGTGG 59.091 52.381 0.00 0.00 0.00 4.00
170 171 2.567169 TGAGATGGTTAGGTGGACAGTG 59.433 50.000 0.00 0.00 0.00 3.66
171 172 2.902608 TGAGATGGTTAGGTGGACAGT 58.097 47.619 0.00 0.00 0.00 3.55
172 173 3.600388 GTTGAGATGGTTAGGTGGACAG 58.400 50.000 0.00 0.00 0.00 3.51
173 174 2.304761 GGTTGAGATGGTTAGGTGGACA 59.695 50.000 0.00 0.00 0.00 4.02
174 175 2.304761 TGGTTGAGATGGTTAGGTGGAC 59.695 50.000 0.00 0.00 0.00 4.02
175 176 2.304761 GTGGTTGAGATGGTTAGGTGGA 59.695 50.000 0.00 0.00 0.00 4.02
176 177 2.039746 TGTGGTTGAGATGGTTAGGTGG 59.960 50.000 0.00 0.00 0.00 4.61
177 178 3.338249 CTGTGGTTGAGATGGTTAGGTG 58.662 50.000 0.00 0.00 0.00 4.00
178 179 2.305927 CCTGTGGTTGAGATGGTTAGGT 59.694 50.000 0.00 0.00 0.00 3.08
179 180 2.305927 ACCTGTGGTTGAGATGGTTAGG 59.694 50.000 0.00 0.00 27.29 2.69
180 181 3.703001 ACCTGTGGTTGAGATGGTTAG 57.297 47.619 0.00 0.00 27.29 2.34
192 193 2.851263 TTAGCGAATCAACCTGTGGT 57.149 45.000 0.00 0.00 37.65 4.16
193 194 3.334691 TCTTTAGCGAATCAACCTGTGG 58.665 45.455 0.00 0.00 0.00 4.17
194 195 4.245660 TCTCTTTAGCGAATCAACCTGTG 58.754 43.478 0.00 0.00 0.00 3.66
195 196 4.537135 TCTCTTTAGCGAATCAACCTGT 57.463 40.909 0.00 0.00 0.00 4.00
196 197 7.492669 TCTTTATCTCTTTAGCGAATCAACCTG 59.507 37.037 0.00 0.00 0.00 4.00
197 198 7.556844 TCTTTATCTCTTTAGCGAATCAACCT 58.443 34.615 0.00 0.00 0.00 3.50
198 199 7.772332 TCTTTATCTCTTTAGCGAATCAACC 57.228 36.000 0.00 0.00 0.00 3.77
210 211 8.847196 GCCCCGTTTTTATATCTTTATCTCTTT 58.153 33.333 0.00 0.00 0.00 2.52
211 212 7.172703 CGCCCCGTTTTTATATCTTTATCTCTT 59.827 37.037 0.00 0.00 0.00 2.85
212 213 6.649557 CGCCCCGTTTTTATATCTTTATCTCT 59.350 38.462 0.00 0.00 0.00 3.10
213 214 6.647895 TCGCCCCGTTTTTATATCTTTATCTC 59.352 38.462 0.00 0.00 0.00 2.75
214 215 6.527423 TCGCCCCGTTTTTATATCTTTATCT 58.473 36.000 0.00 0.00 0.00 1.98
215 216 6.790285 TCGCCCCGTTTTTATATCTTTATC 57.210 37.500 0.00 0.00 0.00 1.75
216 217 7.571080 TTTCGCCCCGTTTTTATATCTTTAT 57.429 32.000 0.00 0.00 0.00 1.40
217 218 6.458615 GCTTTCGCCCCGTTTTTATATCTTTA 60.459 38.462 0.00 0.00 0.00 1.85
218 219 5.677852 GCTTTCGCCCCGTTTTTATATCTTT 60.678 40.000 0.00 0.00 0.00 2.52
219 220 4.201980 GCTTTCGCCCCGTTTTTATATCTT 60.202 41.667 0.00 0.00 0.00 2.40
220 221 3.314357 GCTTTCGCCCCGTTTTTATATCT 59.686 43.478 0.00 0.00 0.00 1.98
221 222 3.624900 GCTTTCGCCCCGTTTTTATATC 58.375 45.455 0.00 0.00 0.00 1.63
222 223 3.703286 GCTTTCGCCCCGTTTTTATAT 57.297 42.857 0.00 0.00 0.00 0.86
257 258 5.942236 TGCAGATGCTCTAAGATCTGTTTTT 59.058 36.000 6.35 0.00 45.05 1.94
258 259 5.494724 TGCAGATGCTCTAAGATCTGTTTT 58.505 37.500 6.35 0.00 45.05 2.43
259 260 5.095145 TGCAGATGCTCTAAGATCTGTTT 57.905 39.130 6.35 0.00 45.05 2.83
260 261 4.750021 TGCAGATGCTCTAAGATCTGTT 57.250 40.909 6.35 0.00 45.05 3.16
261 262 4.081254 TGTTGCAGATGCTCTAAGATCTGT 60.081 41.667 6.35 0.00 45.05 3.41
262 263 4.439968 TGTTGCAGATGCTCTAAGATCTG 58.560 43.478 6.35 0.00 45.72 2.90
263 264 4.695396 CTGTTGCAGATGCTCTAAGATCT 58.305 43.478 6.35 0.00 42.66 2.75
264 265 3.248125 GCTGTTGCAGATGCTCTAAGATC 59.752 47.826 6.35 0.00 42.66 2.75
265 266 3.204526 GCTGTTGCAGATGCTCTAAGAT 58.795 45.455 6.35 0.00 42.66 2.40
266 267 2.625737 GCTGTTGCAGATGCTCTAAGA 58.374 47.619 6.35 0.00 42.66 2.10
267 268 1.669779 GGCTGTTGCAGATGCTCTAAG 59.330 52.381 6.35 0.48 42.66 2.18
268 269 1.742761 GGCTGTTGCAGATGCTCTAA 58.257 50.000 6.35 0.00 42.66 2.10
269 270 0.460811 CGGCTGTTGCAGATGCTCTA 60.461 55.000 6.35 0.00 42.66 2.43
279 280 1.632046 TAGTTTAGCGCGGCTGTTGC 61.632 55.000 8.83 3.97 40.10 4.17
417 425 0.611896 GCTGGTGCCCCAAATACACT 60.612 55.000 0.00 0.00 41.27 3.55
468 476 0.755327 GGAGGAGAGGAGAGAGTGCC 60.755 65.000 0.00 0.00 0.00 5.01
526 540 3.164268 CCCAAAAGTTCATGTCCATGGA 58.836 45.455 11.44 11.44 39.24 3.41
535 549 4.961438 AAGTTCATGCCCAAAAGTTCAT 57.039 36.364 0.00 0.00 0.00 2.57
536 550 4.751767 AAAGTTCATGCCCAAAAGTTCA 57.248 36.364 0.00 0.00 0.00 3.18
538 552 6.233905 ACTAAAAGTTCATGCCCAAAAGTT 57.766 33.333 0.00 0.00 0.00 2.66
543 2949 5.606348 ACAAACTAAAAGTTCATGCCCAA 57.394 34.783 0.00 0.00 37.47 4.12
565 2971 7.595819 AGTTCATCCAACCAAGTTCAAAATA 57.404 32.000 0.00 0.00 35.28 1.40
694 3100 0.239879 CGCACAAAAATACAGGGCGT 59.760 50.000 0.00 0.00 38.36 5.68
698 3104 1.068333 AGCAGCGCACAAAAATACAGG 60.068 47.619 11.47 0.00 0.00 4.00
882 3290 0.172578 TCGGACAGCCACTCGTATTG 59.827 55.000 0.00 0.00 0.00 1.90
1126 3546 4.023707 CGTTTGGATATGAAAGCCCTGATC 60.024 45.833 0.00 0.00 0.00 2.92
1300 3720 1.079503 GGAAGAAGTCGATGTGCCAC 58.920 55.000 0.00 0.00 0.00 5.01
1783 4203 3.599704 GCGCCCTCCATCATTGGC 61.600 66.667 0.00 0.00 43.29 4.52
1820 4240 2.185350 CTCCGCTCTCATGCCGTT 59.815 61.111 0.00 0.00 0.00 4.44
1834 4254 3.447742 CAGCAAGTTTTTGAACACCTCC 58.552 45.455 0.00 0.00 36.36 4.30
1891 4311 1.733399 GTCGTCTTGGTGCTCCGTC 60.733 63.158 0.00 0.00 36.30 4.79
1892 4312 2.338984 GTCGTCTTGGTGCTCCGT 59.661 61.111 0.00 0.00 36.30 4.69
1893 4313 2.805353 CGTCGTCTTGGTGCTCCG 60.805 66.667 0.00 0.00 36.30 4.63
1894 4314 1.733399 GTCGTCGTCTTGGTGCTCC 60.733 63.158 0.00 0.00 0.00 4.70
1895 4315 2.081212 CGTCGTCGTCTTGGTGCTC 61.081 63.158 0.00 0.00 0.00 4.26
1988 4411 0.867753 CGTAGCATGTCCTCGCAGAC 60.868 60.000 0.00 0.00 37.28 3.51
2132 4555 3.055602 TGATCCAAGTCATCTGGTGTCAG 60.056 47.826 0.00 0.00 42.21 3.51
2244 4667 6.851222 TTCTATTTGATGAAGGAAGCGATC 57.149 37.500 0.00 0.00 0.00 3.69
2353 4988 5.237815 AGAAGATTTAACTCATGTCACGCA 58.762 37.500 0.00 0.00 0.00 5.24
2432 5067 4.999311 TGATTGGCACTGCTATGTATGATC 59.001 41.667 0.00 0.00 0.00 2.92
2435 5070 4.517832 ACATGATTGGCACTGCTATGTATG 59.482 41.667 0.00 4.23 0.00 2.39
2436 5071 4.722220 ACATGATTGGCACTGCTATGTAT 58.278 39.130 0.00 0.00 0.00 2.29
2437 5072 4.155063 ACATGATTGGCACTGCTATGTA 57.845 40.909 0.00 0.00 0.00 2.29
2438 5073 3.008835 ACATGATTGGCACTGCTATGT 57.991 42.857 0.00 2.57 0.00 2.29
2510 5150 3.935203 ACAATGAGATAAACCTCGCACTG 59.065 43.478 0.00 0.00 35.99 3.66
2525 5165 9.073368 CAAGAATTTGAGCTCAATTACAATGAG 57.927 33.333 28.89 10.56 40.67 2.90
2526 5166 7.543172 GCAAGAATTTGAGCTCAATTACAATGA 59.457 33.333 28.89 12.52 36.36 2.57
2527 5167 7.201496 GGCAAGAATTTGAGCTCAATTACAATG 60.201 37.037 28.89 21.86 36.36 2.82
2528 5168 6.815142 GGCAAGAATTTGAGCTCAATTACAAT 59.185 34.615 28.89 16.39 36.36 2.71
2529 5169 6.158598 GGCAAGAATTTGAGCTCAATTACAA 58.841 36.000 28.89 14.76 36.36 2.41
2530 5170 5.336690 GGGCAAGAATTTGAGCTCAATTACA 60.337 40.000 28.89 15.14 36.36 2.41
2531 5171 5.105063 GGGCAAGAATTTGAGCTCAATTAC 58.895 41.667 28.89 20.66 36.36 1.89
2558 5198 7.110155 AGAAAACTTACACGACATCCCAATAT 58.890 34.615 0.00 0.00 0.00 1.28
2559 5199 6.469410 AGAAAACTTACACGACATCCCAATA 58.531 36.000 0.00 0.00 0.00 1.90
2582 5229 0.969149 GGTGCTCCCCCTTTTGAAAG 59.031 55.000 0.00 0.00 35.79 2.62
2627 5275 6.126568 TGCTTTTTAATAAGTATGGCCGTC 57.873 37.500 0.00 0.00 0.00 4.79
2798 5466 5.099042 AGATGGTAGCACGGACTATTTTT 57.901 39.130 0.00 0.00 0.00 1.94
2806 5474 1.957177 GATGAGAGATGGTAGCACGGA 59.043 52.381 0.00 0.00 0.00 4.69
2865 5533 0.452184 ATGTGGTCGCTACTCACTCG 59.548 55.000 10.01 0.00 31.73 4.18
2895 5563 4.326826 CAGGTTATTTTCTGAGCCACTGA 58.673 43.478 0.00 0.00 33.11 3.41
2978 5647 8.297426 CGAGTAGGAGTATGTGCTTTATTATGA 58.703 37.037 0.00 0.00 0.00 2.15
3002 5671 3.105937 CGAAACAGCGAGACATATTCGA 58.894 45.455 0.00 0.00 40.22 3.71
3008 5677 2.093973 AGATTCCGAAACAGCGAGACAT 60.094 45.455 0.00 0.00 0.00 3.06
3032 5701 3.998672 GGGACGTGGCTTGACGGA 61.999 66.667 0.00 0.00 43.84 4.69
3129 5800 5.300286 CCATCAAACACCTCTTTCTTGACTT 59.700 40.000 0.00 0.00 0.00 3.01
3247 5918 7.995463 TTGAAAGTTAAAGTGTTTATGTGGC 57.005 32.000 0.00 0.00 0.00 5.01
3298 5970 9.600432 ATCAATTCTAGCTCTATTCCTAGTTCT 57.400 33.333 0.00 0.00 34.18 3.01
3364 6036 3.069158 AGTTGTGTTGGACGCTAACTAGT 59.931 43.478 0.00 0.00 32.46 2.57
3374 6046 1.156736 CCCGATCAGTTGTGTTGGAC 58.843 55.000 0.00 0.00 0.00 4.02
3441 6113 1.529713 GGAAACCGTTGGGAAGCCA 60.530 57.895 0.00 0.00 36.97 4.75


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

AutoCloner maintained by Alex Coulton.