Multiple sequence alignment - TraesCS4D01G218100

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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 TraesCS4D01G218100 chr4D 100.000 4927 0 0 1 4927 373813388 373808462 0.000000e+00 9099.0
1 TraesCS4D01G218100 chr4B 92.676 4069 175 39 694 4710 459925379 459921382 0.000000e+00 5749.0
2 TraesCS4D01G218100 chr4B 95.082 183 8 1 4694 4875 459920660 459920478 2.240000e-73 287.0
3 TraesCS4D01G218100 chr4B 83.537 328 17 12 364 673 459925751 459925443 6.280000e-69 272.0
4 TraesCS4D01G218100 chr4A 92.432 3105 152 31 698 3771 90786014 90789066 0.000000e+00 4355.0
5 TraesCS4D01G218100 chr4A 87.936 1119 64 24 3803 4875 90789066 90790159 0.000000e+00 1253.0
6 TraesCS4D01G218100 chr4A 80.282 142 12 7 486 626 90780457 90780583 5.250000e-15 93.5
7 TraesCS4D01G218100 chr1D 95.068 365 16 2 1 365 350655167 350654805 1.540000e-159 573.0
8 TraesCS4D01G218100 chr6A 94.886 352 17 1 11 362 601959612 601959962 2.590000e-152 549.0
9 TraesCS4D01G218100 chr6A 88.764 356 38 2 1 356 447583740 447584093 7.570000e-118 435.0
10 TraesCS4D01G218100 chr6A 82.203 118 16 4 1353 1469 470415790 470415903 4.060000e-16 97.1
11 TraesCS4D01G218100 chr6B 92.394 355 23 3 11 362 647845642 647845995 2.050000e-138 503.0
12 TraesCS4D01G218100 chr1B 93.678 174 9 2 1 174 194531489 194531660 4.890000e-65 259.0
13 TraesCS4D01G218100 chr1B 81.053 190 28 4 1289 1477 594111636 594111818 1.430000e-30 145.0
14 TraesCS4D01G218100 chr7B 81.090 312 49 7 53 356 652297378 652297069 1.770000e-59 241.0
15 TraesCS4D01G218100 chr7B 79.100 311 51 9 53 356 521200030 521200333 8.360000e-48 202.0
16 TraesCS4D01G218100 chr7A 80.707 311 45 10 53 356 58215252 58215554 1.380000e-55 228.0
17 TraesCS4D01G218100 chr2B 82.069 145 20 2 53 194 665452454 665452313 8.660000e-23 119.0
18 TraesCS4D01G218100 chr3B 82.114 123 17 4 1353 1474 349977231 349977113 3.140000e-17 100.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS4D01G218100 chr4D 373808462 373813388 4926 True 9099.000000 9099 100.000000 1 4927 1 chr4D.!!$R1 4926
1 TraesCS4D01G218100 chr4B 459920478 459925751 5273 True 2102.666667 5749 90.431667 364 4875 3 chr4B.!!$R1 4511
2 TraesCS4D01G218100 chr4A 90786014 90790159 4145 False 2804.000000 4355 90.184000 698 4875 2 chr4A.!!$F2 4177

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
524 533 0.034896 GGAGGGCTTGAAACTGACGA 59.965 55.0 0.00 0.0 0.0 4.20 F
554 563 0.035458 CTGTTCCCTGACTGTCACCC 59.965 60.0 6.36 0.0 0.0 4.61 F
692 723 0.185901 ACATTGGCTGGTCACAACCT 59.814 50.0 0.00 0.0 46.6 3.50 F
1326 1412 0.252696 TGGGCTACTGTCTCCACCAT 60.253 55.0 0.00 0.0 0.0 3.55 F
2965 3087 0.179936 GGACAAGGAGAGGAGCATGG 59.820 60.0 0.00 0.0 0.0 3.66 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2419 2538 0.035630 ACCTCATGCTCTGCTTCACC 60.036 55.000 0.00 0.0 0.00 4.02 R
2474 2593 0.604780 TTCGTCCTCCTCGTTCTCGT 60.605 55.000 0.00 0.0 38.33 4.18 R
2685 2804 1.299468 CTCCAGCTCGGCGTACATC 60.299 63.158 6.85 0.0 33.14 3.06 R
3123 3245 0.389817 CGGTGTTCTCTTGATCCGCA 60.390 55.000 0.00 0.0 0.00 5.69 R
4389 4554 0.034756 TCAAAACTGGCTAGAGCGCA 59.965 50.000 11.47 0.0 43.26 6.09 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
36 37 3.175240 CAGCGGCGAACTCACGAG 61.175 66.667 12.98 0.00 35.09 4.18
39 40 2.733218 CGGCGAACTCACGAGCAA 60.733 61.111 0.00 0.00 35.09 3.91
40 41 2.720758 CGGCGAACTCACGAGCAAG 61.721 63.158 0.00 0.00 35.09 4.01
41 42 2.383527 GGCGAACTCACGAGCAAGG 61.384 63.158 0.00 0.00 35.09 3.61
42 43 2.383527 GCGAACTCACGAGCAAGGG 61.384 63.158 0.00 0.00 35.09 3.95
43 44 1.289066 CGAACTCACGAGCAAGGGA 59.711 57.895 0.00 0.00 35.09 4.20
44 45 1.009389 CGAACTCACGAGCAAGGGAC 61.009 60.000 0.00 0.00 35.09 4.46
45 46 0.670854 GAACTCACGAGCAAGGGACC 60.671 60.000 0.00 0.00 0.00 4.46
46 47 1.122019 AACTCACGAGCAAGGGACCT 61.122 55.000 0.00 0.00 0.00 3.85
47 48 1.216710 CTCACGAGCAAGGGACCTC 59.783 63.158 0.00 0.00 0.00 3.85
48 49 2.232298 CTCACGAGCAAGGGACCTCC 62.232 65.000 0.00 0.00 0.00 4.30
49 50 3.382832 ACGAGCAAGGGACCTCCG 61.383 66.667 0.00 0.00 41.52 4.63
50 51 3.068691 CGAGCAAGGGACCTCCGA 61.069 66.667 0.00 0.00 41.52 4.55
51 52 2.579738 GAGCAAGGGACCTCCGAC 59.420 66.667 0.00 0.00 41.52 4.79
52 53 3.003763 AGCAAGGGACCTCCGACC 61.004 66.667 0.00 0.00 41.52 4.79
53 54 3.003763 GCAAGGGACCTCCGACCT 61.004 66.667 0.00 0.00 41.52 3.85
54 55 2.982130 CAAGGGACCTCCGACCTG 59.018 66.667 0.00 0.00 41.52 4.00
55 56 2.284699 AAGGGACCTCCGACCTGG 60.285 66.667 0.00 0.00 41.52 4.45
57 58 3.075641 GGGACCTCCGACCTGGAC 61.076 72.222 0.00 0.00 43.74 4.02
58 59 2.037527 GGACCTCCGACCTGGACT 59.962 66.667 0.00 0.00 43.74 3.85
59 60 2.053277 GGACCTCCGACCTGGACTC 61.053 68.421 0.00 0.00 43.74 3.36
60 61 2.361357 ACCTCCGACCTGGACTCG 60.361 66.667 0.00 0.00 43.74 4.18
64 65 4.753662 CCGACCTGGACTCGGGGA 62.754 72.222 15.87 0.00 45.90 4.81
65 66 2.678934 CGACCTGGACTCGGGGAA 60.679 66.667 0.00 0.00 43.79 3.97
66 67 2.711922 CGACCTGGACTCGGGGAAG 61.712 68.421 0.00 0.00 43.79 3.46
67 68 3.003763 ACCTGGACTCGGGGAAGC 61.004 66.667 0.00 0.00 43.79 3.86
68 69 3.003173 CCTGGACTCGGGGAAGCA 61.003 66.667 0.00 0.00 35.76 3.91
69 70 2.581354 CTGGACTCGGGGAAGCAG 59.419 66.667 0.00 0.00 0.00 4.24
70 71 1.984570 CTGGACTCGGGGAAGCAGA 60.985 63.158 0.00 0.00 0.00 4.26
71 72 1.954362 CTGGACTCGGGGAAGCAGAG 61.954 65.000 0.00 0.00 37.96 3.35
72 73 2.726351 GGACTCGGGGAAGCAGAGG 61.726 68.421 0.00 0.00 36.40 3.69
73 74 1.682684 GACTCGGGGAAGCAGAGGA 60.683 63.158 0.00 0.00 36.40 3.71
74 75 1.671901 GACTCGGGGAAGCAGAGGAG 61.672 65.000 0.00 0.00 36.40 3.69
75 76 1.380515 CTCGGGGAAGCAGAGGAGA 60.381 63.158 0.00 0.00 0.00 3.71
76 77 1.671901 CTCGGGGAAGCAGAGGAGAC 61.672 65.000 0.00 0.00 0.00 3.36
77 78 2.726351 CGGGGAAGCAGAGGAGACC 61.726 68.421 0.00 0.00 0.00 3.85
78 79 1.613630 GGGGAAGCAGAGGAGACCA 60.614 63.158 0.00 0.00 0.00 4.02
79 80 1.599576 GGGAAGCAGAGGAGACCAC 59.400 63.158 0.00 0.00 0.00 4.16
80 81 1.216710 GGAAGCAGAGGAGACCACG 59.783 63.158 0.00 0.00 0.00 4.94
81 82 1.216710 GAAGCAGAGGAGACCACGG 59.783 63.158 0.00 0.00 0.00 4.94
82 83 2.844072 GAAGCAGAGGAGACCACGGC 62.844 65.000 0.00 0.00 0.00 5.68
83 84 3.695606 GCAGAGGAGACCACGGCA 61.696 66.667 0.00 0.00 0.00 5.69
84 85 2.262915 CAGAGGAGACCACGGCAC 59.737 66.667 0.00 0.00 0.00 5.01
85 86 2.997897 AGAGGAGACCACGGCACC 60.998 66.667 0.00 0.00 0.00 5.01
86 87 4.436998 GAGGAGACCACGGCACCG 62.437 72.222 7.71 7.71 46.03 4.94
87 88 4.988716 AGGAGACCACGGCACCGA 62.989 66.667 17.40 0.00 42.83 4.69
88 89 4.436998 GGAGACCACGGCACCGAG 62.437 72.222 17.40 7.94 42.83 4.63
103 104 3.207354 GAGCCCTTGACGGATCGA 58.793 61.111 0.00 0.00 33.16 3.59
104 105 1.227002 GAGCCCTTGACGGATCGAC 60.227 63.158 0.00 0.00 33.16 4.20
105 106 2.582498 GCCCTTGACGGATCGACG 60.582 66.667 0.00 0.00 40.31 5.12
106 107 2.582498 CCCTTGACGGATCGACGC 60.582 66.667 0.00 0.00 37.37 5.19
107 108 2.180769 CCTTGACGGATCGACGCA 59.819 61.111 0.00 0.00 37.37 5.24
108 109 1.874019 CCTTGACGGATCGACGCAG 60.874 63.158 0.00 0.00 37.37 5.18
109 110 1.136774 CTTGACGGATCGACGCAGA 59.863 57.895 0.00 0.00 37.37 4.26
110 111 1.134530 CTTGACGGATCGACGCAGAC 61.135 60.000 0.00 0.00 37.37 3.51
112 113 4.175489 ACGGATCGACGCAGACGG 62.175 66.667 0.00 0.00 46.86 4.79
144 145 3.429141 CTGCAGCAGCGGTGGAAG 61.429 66.667 17.54 0.15 46.23 3.46
145 146 3.889134 CTGCAGCAGCGGTGGAAGA 62.889 63.158 17.54 0.00 46.23 2.87
146 147 3.426568 GCAGCAGCGGTGGAAGAC 61.427 66.667 17.54 0.00 0.00 3.01
147 148 3.114616 CAGCAGCGGTGGAAGACG 61.115 66.667 17.54 0.00 0.00 4.18
148 149 3.303135 AGCAGCGGTGGAAGACGA 61.303 61.111 17.54 0.00 0.00 4.20
149 150 3.112709 GCAGCGGTGGAAGACGAC 61.113 66.667 17.54 0.00 0.00 4.34
150 151 2.805353 CAGCGGTGGAAGACGACG 60.805 66.667 6.74 0.00 0.00 5.12
152 153 4.719369 GCGGTGGAAGACGACGCT 62.719 66.667 0.00 0.00 46.02 5.07
153 154 2.805353 CGGTGGAAGACGACGCTG 60.805 66.667 0.00 0.00 0.00 5.18
154 155 2.432628 GGTGGAAGACGACGCTGG 60.433 66.667 0.00 0.00 0.00 4.85
155 156 2.649034 GTGGAAGACGACGCTGGA 59.351 61.111 0.00 0.00 0.00 3.86
156 157 1.215647 GTGGAAGACGACGCTGGAT 59.784 57.895 0.00 0.00 0.00 3.41
157 158 0.802607 GTGGAAGACGACGCTGGATC 60.803 60.000 0.00 0.00 0.00 3.36
158 159 1.586564 GGAAGACGACGCTGGATCG 60.587 63.158 0.00 0.00 45.17 3.69
159 160 1.586564 GAAGACGACGCTGGATCGG 60.587 63.158 0.00 0.00 43.95 4.18
185 186 4.122515 GCAGACGTTCGCGACAGC 62.123 66.667 9.15 1.43 44.71 4.40
210 211 4.200283 CTGGGCGAGCCGAGAGAC 62.200 72.222 19.41 0.00 43.43 3.36
239 240 3.685459 CGAGTCTGTCGTTGGAGAG 57.315 57.895 0.00 0.00 44.20 3.20
240 241 0.455295 CGAGTCTGTCGTTGGAGAGC 60.455 60.000 0.00 0.00 44.20 4.09
241 242 0.598562 GAGTCTGTCGTTGGAGAGCA 59.401 55.000 0.00 0.00 33.72 4.26
242 243 0.315568 AGTCTGTCGTTGGAGAGCAC 59.684 55.000 0.00 0.00 33.72 4.40
243 244 1.004277 GTCTGTCGTTGGAGAGCACG 61.004 60.000 0.00 0.00 33.72 5.34
244 245 1.007271 CTGTCGTTGGAGAGCACGT 60.007 57.895 0.00 0.00 37.66 4.49
245 246 1.004277 CTGTCGTTGGAGAGCACGTC 61.004 60.000 0.00 0.00 37.66 4.34
246 247 2.081212 GTCGTTGGAGAGCACGTCG 61.081 63.158 0.00 0.00 37.66 5.12
247 248 3.470567 CGTTGGAGAGCACGTCGC 61.471 66.667 0.00 2.28 42.91 5.19
260 261 4.500116 GTCGCGGGGAGCTCAGAC 62.500 72.222 17.19 12.06 45.59 3.51
266 267 3.775654 GGGAGCTCAGACCCGGTG 61.776 72.222 17.19 0.00 36.56 4.94
267 268 2.997897 GGAGCTCAGACCCGGTGT 60.998 66.667 17.19 0.00 0.00 4.16
268 269 2.574399 GAGCTCAGACCCGGTGTC 59.426 66.667 9.40 13.42 44.82 3.67
292 293 4.796231 CGCAACGGAGGTCGGAGG 62.796 72.222 0.00 0.00 44.45 4.30
304 305 3.610669 CGGAGGCCGGAGATCCAG 61.611 72.222 5.05 1.73 44.15 3.86
305 306 3.237741 GGAGGCCGGAGATCCAGG 61.238 72.222 5.05 2.86 35.14 4.45
362 363 0.577269 GCAAGAGCGCCATAGTTACG 59.423 55.000 2.29 0.00 0.00 3.18
363 364 1.209128 CAAGAGCGCCATAGTTACGG 58.791 55.000 2.29 0.00 0.00 4.02
364 365 0.104304 AAGAGCGCCATAGTTACGGG 59.896 55.000 2.29 0.00 0.00 5.28
365 366 0.754217 AGAGCGCCATAGTTACGGGA 60.754 55.000 2.29 0.00 0.00 5.14
366 367 0.317479 GAGCGCCATAGTTACGGGAT 59.683 55.000 2.29 0.00 0.00 3.85
382 383 2.632996 CGGGATCCTAGCTGGTTTATCA 59.367 50.000 12.58 0.00 37.07 2.15
396 397 2.906182 TTATCACTGAGCCGCTGCCG 62.906 60.000 0.00 0.00 38.69 5.69
416 421 3.290308 GTCCTCTACGGTAGATGCATG 57.710 52.381 17.63 6.39 33.66 4.06
424 429 0.183492 GGTAGATGCATGCAGGGGAA 59.817 55.000 26.69 6.71 0.00 3.97
431 436 2.044946 ATGCAGGGGAAGCGGAAC 60.045 61.111 0.00 0.00 33.85 3.62
434 439 2.335712 GCAGGGGAAGCGGAACTTG 61.336 63.158 0.00 0.00 39.29 3.16
442 447 2.767697 GCGGAACTTGTACGCGAC 59.232 61.111 15.93 7.50 43.98 5.19
446 451 0.782384 GGAACTTGTACGCGACACAG 59.218 55.000 15.93 14.16 37.96 3.66
467 472 2.412770 GCATGCCGAAATGTTTGAAAGG 59.587 45.455 6.36 0.00 0.00 3.11
479 484 5.514274 TGTTTGAAAGGAGTAAAAGCCAG 57.486 39.130 0.00 0.00 0.00 4.85
480 485 4.202111 TGTTTGAAAGGAGTAAAAGCCAGC 60.202 41.667 0.00 0.00 0.00 4.85
481 486 2.514803 TGAAAGGAGTAAAAGCCAGCC 58.485 47.619 0.00 0.00 0.00 4.85
482 487 2.158534 TGAAAGGAGTAAAAGCCAGCCA 60.159 45.455 0.00 0.00 0.00 4.75
496 501 4.603131 AGCCAGCCATTTTAATTCTCTGA 58.397 39.130 0.00 0.00 0.00 3.27
524 533 0.034896 GGAGGGCTTGAAACTGACGA 59.965 55.000 0.00 0.00 0.00 4.20
548 557 5.413309 AGACTAAATCTGTTCCCTGACTG 57.587 43.478 0.00 0.00 35.81 3.51
549 558 4.841246 AGACTAAATCTGTTCCCTGACTGT 59.159 41.667 0.00 0.00 35.81 3.55
550 559 5.046950 AGACTAAATCTGTTCCCTGACTGTC 60.047 44.000 0.00 0.00 35.81 3.51
551 560 4.593206 ACTAAATCTGTTCCCTGACTGTCA 59.407 41.667 10.50 10.50 0.00 3.58
552 561 3.409026 AATCTGTTCCCTGACTGTCAC 57.591 47.619 6.36 0.00 0.00 3.67
553 562 1.048601 TCTGTTCCCTGACTGTCACC 58.951 55.000 6.36 0.00 0.00 4.02
554 563 0.035458 CTGTTCCCTGACTGTCACCC 59.965 60.000 6.36 0.00 0.00 4.61
673 691 2.485903 CAAGTAACCCAAGCACGTACA 58.514 47.619 0.00 0.00 0.00 2.90
674 692 2.159327 AGTAACCCAAGCACGTACAC 57.841 50.000 0.00 0.00 0.00 2.90
676 694 2.038033 AGTAACCCAAGCACGTACACAT 59.962 45.455 0.00 0.00 0.00 3.21
684 715 1.234615 GCACGTACACATTGGCTGGT 61.235 55.000 0.00 0.00 0.00 4.00
692 723 0.185901 ACATTGGCTGGTCACAACCT 59.814 50.000 0.00 0.00 46.60 3.50
855 920 4.039357 ACACGACTCGTCCAGCCG 62.039 66.667 0.00 0.00 38.32 5.52
989 1072 4.971125 GGCACTAGGGATCGCGCC 62.971 72.222 0.00 9.96 0.00 6.53
991 1074 2.815308 CACTAGGGATCGCGCCTT 59.185 61.111 9.10 0.69 0.00 4.35
1317 1403 1.762460 CTCCGGGATGGGCTACTGT 60.762 63.158 0.00 0.00 38.76 3.55
1326 1412 0.252696 TGGGCTACTGTCTCCACCAT 60.253 55.000 0.00 0.00 0.00 3.55
1394 1480 3.772025 TCTTCTTGGAAGAGGGAGATGAC 59.228 47.826 5.96 0.00 36.22 3.06
1469 1555 3.570926 ACAGATTACTTCTTCACGCGA 57.429 42.857 15.93 0.00 29.93 5.87
1504 1611 1.292223 GTACACGAGAAGGCAGCCA 59.708 57.895 15.80 0.00 0.00 4.75
1548 1655 4.038162 GGCTACGTTCTACTGGATCAAGAT 59.962 45.833 3.42 0.00 0.00 2.40
1560 1667 3.118992 TGGATCAAGATGACCACGAAGAG 60.119 47.826 0.00 0.00 0.00 2.85
1596 1703 1.266989 CAAAACGAAGAGGAAGCCCAC 59.733 52.381 0.00 0.00 33.88 4.61
1735 1842 1.737838 TGAGATGACAATTGCCGACC 58.262 50.000 5.05 0.00 0.00 4.79
2008 2115 5.299531 GGTAATAACCTCTCCATTTGCTTCC 59.700 44.000 0.00 0.00 43.08 3.46
2124 2237 1.617947 AATCGGCAGAGGTGGAGACC 61.618 60.000 0.00 0.00 43.52 3.85
2170 2283 1.449246 ATCTGCGAGCAGGAGCAAC 60.449 57.895 22.93 0.00 45.49 4.17
2172 2285 2.666190 TGCGAGCAGGAGCAACAC 60.666 61.111 0.00 0.00 45.49 3.32
2181 2294 4.120331 GAGCAACACGGCCATGCC 62.120 66.667 14.15 0.00 46.75 4.40
2220 2333 2.817396 GCGCTGGAGGAGCTGTTC 60.817 66.667 0.00 0.00 46.64 3.18
2241 2354 5.635278 TCTCTCCATTGGAATATGCAGAA 57.365 39.130 6.88 0.00 0.00 3.02
2245 2358 5.131642 TCTCCATTGGAATATGCAGAAGACT 59.868 40.000 6.88 0.00 0.00 3.24
2375 2489 2.063156 CAGTGACTCTGTCTGTCTGC 57.937 55.000 0.00 0.00 39.17 4.26
2474 2593 6.049149 GGAGATTTGAGTACCAATCGAATGA 58.951 40.000 0.94 0.00 32.12 2.57
2529 2648 1.074951 ACCCACCTACAGCTTTGCC 59.925 57.895 0.00 0.00 0.00 4.52
2541 2660 1.739049 CTTTGCCGCCCAAAACTCA 59.261 52.632 1.96 0.00 42.51 3.41
2601 2720 1.180456 TGTCCTTGGACGGAAGCGTA 61.180 55.000 14.24 0.00 34.20 4.42
2661 2780 2.510012 CTGAGATCCGCGCTGCAA 60.510 61.111 5.56 0.00 0.00 4.08
2718 2837 1.139947 GGAGGAAGAGAGGAACGCG 59.860 63.158 3.53 3.53 0.00 6.01
2769 2888 1.377202 GATCAACCGGCTGCAGGAA 60.377 57.895 25.53 10.37 0.00 3.36
2951 3070 0.391228 TTGCTGCAGTACGAGGACAA 59.609 50.000 16.64 5.31 0.00 3.18
2961 3080 0.968393 ACGAGGACAAGGAGAGGAGC 60.968 60.000 0.00 0.00 0.00 4.70
2965 3087 0.179936 GGACAAGGAGAGGAGCATGG 59.820 60.000 0.00 0.00 0.00 3.66
2973 3095 2.044252 AGGAGCATGGCAGCCTTG 60.044 61.111 20.82 20.82 33.10 3.61
3057 3179 2.976509 CGATGAGAATTCCGATGACTCG 59.023 50.000 0.65 0.00 44.62 4.18
3123 3245 2.993853 GCTGCTCTTAGCCCCAGT 59.006 61.111 0.00 0.00 41.51 4.00
3222 3344 1.078567 GGAGGAGCTCAAGGCACTG 60.079 63.158 17.19 0.00 44.79 3.66
3247 3369 0.739112 GAGGCTCTTCACGCTGGAAG 60.739 60.000 7.40 7.66 44.46 3.46
3249 3371 1.016653 GGCTCTTCACGCTGGAAGAC 61.017 60.000 11.53 9.25 46.16 3.01
3307 3429 0.734889 TTCCTCGGACGATTACGGTC 59.265 55.000 0.00 0.00 44.46 4.79
3315 3437 0.172803 ACGATTACGGTCTGTCAGCC 59.827 55.000 0.00 0.00 44.46 4.85
3615 3737 3.560025 GCATCAAGTCCCTCAAGAAAGGA 60.560 47.826 0.00 0.00 38.87 3.36
3792 3921 3.888811 TGCCCTTGCAGCCATTTT 58.111 50.000 0.00 0.00 44.23 1.82
3826 3955 6.749923 ATCTTGTCTTCCTTAACTGCATTC 57.250 37.500 0.00 0.00 0.00 2.67
3869 3998 4.558496 GCTGTTTAATTACCTGCAGCAACA 60.558 41.667 8.66 6.95 45.83 3.33
3938 4067 3.190744 GGCTATGGTGAGTCGATCGATTA 59.809 47.826 22.50 7.93 0.00 1.75
3951 4080 3.990469 CGATCGATTAGAATGGTCCAAGG 59.010 47.826 10.26 0.00 0.00 3.61
3990 4122 1.216678 TCCCTTTCCCTTGTGCAAGAA 59.783 47.619 12.99 0.00 40.79 2.52
4033 4165 4.704833 TTGCTCGTCTGGCCTGCC 62.705 66.667 3.32 0.00 0.00 4.85
4157 4293 3.189376 TTCGGAGGCATGCACACCA 62.189 57.895 21.36 7.39 0.00 4.17
4158 4294 3.434319 CGGAGGCATGCACACCAC 61.434 66.667 21.36 0.00 0.00 4.16
4159 4295 3.064324 GGAGGCATGCACACCACC 61.064 66.667 21.36 6.20 0.00 4.61
4160 4296 2.034687 GAGGCATGCACACCACCT 59.965 61.111 21.36 4.91 0.00 4.00
4161 4297 2.034687 AGGCATGCACACCACCTC 59.965 61.111 21.36 0.00 0.00 3.85
4162 4298 2.282391 GGCATGCACACCACCTCA 60.282 61.111 21.36 0.00 0.00 3.86
4186 4338 1.552337 TCAACAGGACAGATGGAGAGC 59.448 52.381 0.00 0.00 0.00 4.09
4191 4343 1.133513 AGGACAGATGGAGAGCGAGAT 60.134 52.381 0.00 0.00 0.00 2.75
4280 4437 7.254117 CGCTTCTTTTTCCCTTTTCTTTCTTTC 60.254 37.037 0.00 0.00 0.00 2.62
4312 4470 3.953612 TCAGATTTGTTTGTGCAGAGGTT 59.046 39.130 0.00 0.00 0.00 3.50
4316 4474 1.679139 TGTTTGTGCAGAGGTTGAGG 58.321 50.000 0.00 0.00 0.00 3.86
4317 4475 1.211703 TGTTTGTGCAGAGGTTGAGGA 59.788 47.619 0.00 0.00 0.00 3.71
4323 4481 0.033504 GCAGAGGTTGAGGACGTTCA 59.966 55.000 0.00 0.00 0.00 3.18
4389 4554 4.311606 GTGTGGTTTGGTCTTTGTTTTGT 58.688 39.130 0.00 0.00 0.00 2.83
4390 4555 4.151512 GTGTGGTTTGGTCTTTGTTTTGTG 59.848 41.667 0.00 0.00 0.00 3.33
4392 4557 2.347150 GGTTTGGTCTTTGTTTTGTGCG 59.653 45.455 0.00 0.00 0.00 5.34
4393 4558 1.634702 TTGGTCTTTGTTTTGTGCGC 58.365 45.000 0.00 0.00 0.00 6.09
4395 4560 1.202245 TGGTCTTTGTTTTGTGCGCTC 60.202 47.619 9.73 5.51 0.00 5.03
4460 4630 4.280677 TCCTGTTTCATTTGACATGGTTCC 59.719 41.667 0.00 0.00 0.00 3.62
4474 4644 0.615850 GGTTCCCTCTGGTCCTTGAG 59.384 60.000 5.75 5.75 0.00 3.02
4602 4783 4.025360 TCAATTATGCTGGCTTTGATGGT 58.975 39.130 0.00 0.00 0.00 3.55
4651 4833 3.821219 GCCCTGGGAAGATAGAGAGCTAT 60.821 52.174 19.27 0.00 40.00 2.97
4652 4834 4.424842 CCCTGGGAAGATAGAGAGCTATT 58.575 47.826 7.01 0.00 37.45 1.73
4660 4842 8.616942 GGGAAGATAGAGAGCTATTTTTCAAAC 58.383 37.037 0.00 0.00 37.45 2.93
4729 5649 6.376299 CCAATGATTTTCAGGACATCTTCTGA 59.624 38.462 0.00 0.00 38.14 3.27
4782 5702 2.203800 TAGCCGTGAAATGACTAGCG 57.796 50.000 0.00 0.00 0.00 4.26
4786 5706 1.852895 CCGTGAAATGACTAGCGCTAC 59.147 52.381 14.45 5.48 0.00 3.58
4875 5796 7.750229 ATCAAGAAAGCATACTTCAACTTGA 57.250 32.000 17.28 17.28 44.47 3.02
4876 5797 7.566760 TCAAGAAAGCATACTTCAACTTGAA 57.433 32.000 14.73 4.16 41.61 2.69
4889 5810 6.826893 TTCAACTTGAAGTAAAATGCAAGC 57.173 33.333 0.00 0.00 40.94 4.01
4890 5811 4.975502 TCAACTTGAAGTAAAATGCAAGCG 59.024 37.500 0.00 0.00 40.94 4.68
4891 5812 3.308530 ACTTGAAGTAAAATGCAAGCGC 58.691 40.909 0.00 0.00 40.94 5.92
4892 5813 1.962412 TGAAGTAAAATGCAAGCGCG 58.038 45.000 0.00 0.00 42.97 6.86
4893 5814 1.259316 GAAGTAAAATGCAAGCGCGG 58.741 50.000 8.83 0.00 42.97 6.46
4894 5815 0.596082 AAGTAAAATGCAAGCGCGGT 59.404 45.000 4.23 4.23 42.97 5.68
4895 5816 0.596082 AGTAAAATGCAAGCGCGGTT 59.404 45.000 19.31 19.31 42.97 4.44
4896 5817 0.981956 GTAAAATGCAAGCGCGGTTC 59.018 50.000 22.37 15.94 42.97 3.62
4897 5818 0.878416 TAAAATGCAAGCGCGGTTCT 59.122 45.000 22.37 6.00 42.97 3.01
4898 5819 0.878416 AAAATGCAAGCGCGGTTCTA 59.122 45.000 22.37 13.30 42.97 2.10
4899 5820 0.878416 AAATGCAAGCGCGGTTCTAA 59.122 45.000 22.37 9.92 42.97 2.10
4900 5821 1.094785 AATGCAAGCGCGGTTCTAAT 58.905 45.000 22.37 11.87 42.97 1.73
4901 5822 1.094785 ATGCAAGCGCGGTTCTAATT 58.905 45.000 22.37 0.00 42.97 1.40
4902 5823 0.446222 TGCAAGCGCGGTTCTAATTC 59.554 50.000 22.37 6.76 42.97 2.17
4903 5824 0.727398 GCAAGCGCGGTTCTAATTCT 59.273 50.000 22.37 0.00 0.00 2.40
4904 5825 1.130561 GCAAGCGCGGTTCTAATTCTT 59.869 47.619 22.37 1.92 0.00 2.52
4905 5826 2.414161 GCAAGCGCGGTTCTAATTCTTT 60.414 45.455 22.37 0.00 0.00 2.52
4906 5827 3.821841 CAAGCGCGGTTCTAATTCTTTT 58.178 40.909 22.37 0.00 0.00 2.27
4907 5828 3.741805 AGCGCGGTTCTAATTCTTTTC 57.258 42.857 4.23 0.00 0.00 2.29
4908 5829 2.418976 AGCGCGGTTCTAATTCTTTTCC 59.581 45.455 4.23 0.00 0.00 3.13
4909 5830 2.160813 GCGCGGTTCTAATTCTTTTCCA 59.839 45.455 8.83 0.00 0.00 3.53
4910 5831 3.365565 GCGCGGTTCTAATTCTTTTCCAA 60.366 43.478 8.83 0.00 0.00 3.53
4911 5832 4.789784 CGCGGTTCTAATTCTTTTCCAAA 58.210 39.130 0.00 0.00 0.00 3.28
4912 5833 4.851558 CGCGGTTCTAATTCTTTTCCAAAG 59.148 41.667 0.00 0.00 0.00 2.77
4913 5834 5.562113 CGCGGTTCTAATTCTTTTCCAAAGT 60.562 40.000 0.00 0.00 0.00 2.66
4914 5835 5.629435 GCGGTTCTAATTCTTTTCCAAAGTG 59.371 40.000 0.00 0.00 0.00 3.16
4915 5836 6.734871 GCGGTTCTAATTCTTTTCCAAAGTGT 60.735 38.462 0.00 0.00 0.00 3.55
4916 5837 6.856426 CGGTTCTAATTCTTTTCCAAAGTGTC 59.144 38.462 0.00 0.00 0.00 3.67
4917 5838 6.856426 GGTTCTAATTCTTTTCCAAAGTGTCG 59.144 38.462 0.00 0.00 0.00 4.35
4918 5839 7.255001 GGTTCTAATTCTTTTCCAAAGTGTCGA 60.255 37.037 0.00 0.00 0.00 4.20
4919 5840 7.979444 TCTAATTCTTTTCCAAAGTGTCGAT 57.021 32.000 0.00 0.00 0.00 3.59
4920 5841 8.391075 TCTAATTCTTTTCCAAAGTGTCGATT 57.609 30.769 0.00 0.00 0.00 3.34
4921 5842 8.289618 TCTAATTCTTTTCCAAAGTGTCGATTG 58.710 33.333 0.00 0.00 0.00 2.67
4922 5843 4.829064 TCTTTTCCAAAGTGTCGATTGG 57.171 40.909 8.90 8.90 46.03 3.16
4923 5844 3.568007 TCTTTTCCAAAGTGTCGATTGGG 59.432 43.478 14.05 0.33 44.99 4.12
4924 5845 2.649531 TTCCAAAGTGTCGATTGGGT 57.350 45.000 14.05 0.00 44.99 4.51
4925 5846 2.178912 TCCAAAGTGTCGATTGGGTC 57.821 50.000 14.05 0.00 44.99 4.46
4926 5847 1.418264 TCCAAAGTGTCGATTGGGTCA 59.582 47.619 14.05 0.00 44.99 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
19 20 3.175240 CTCGTGAGTTCGCCGCTG 61.175 66.667 0.00 0.00 0.00 5.18
22 23 2.720758 CTTGCTCGTGAGTTCGCCG 61.721 63.158 0.00 0.00 0.00 6.46
23 24 2.383527 CCTTGCTCGTGAGTTCGCC 61.384 63.158 0.00 0.00 0.00 5.54
24 25 2.383527 CCCTTGCTCGTGAGTTCGC 61.384 63.158 0.00 0.00 0.00 4.70
25 26 1.009389 GTCCCTTGCTCGTGAGTTCG 61.009 60.000 0.00 0.00 0.00 3.95
26 27 0.670854 GGTCCCTTGCTCGTGAGTTC 60.671 60.000 0.00 0.00 0.00 3.01
27 28 1.122019 AGGTCCCTTGCTCGTGAGTT 61.122 55.000 0.00 0.00 0.00 3.01
28 29 1.534235 AGGTCCCTTGCTCGTGAGT 60.534 57.895 0.00 0.00 0.00 3.41
29 30 1.216710 GAGGTCCCTTGCTCGTGAG 59.783 63.158 0.00 0.00 0.00 3.51
30 31 2.283529 GGAGGTCCCTTGCTCGTGA 61.284 63.158 0.00 0.00 0.00 4.35
31 32 2.266055 GGAGGTCCCTTGCTCGTG 59.734 66.667 0.00 0.00 0.00 4.35
32 33 3.382832 CGGAGGTCCCTTGCTCGT 61.383 66.667 0.00 0.00 0.00 4.18
33 34 3.068691 TCGGAGGTCCCTTGCTCG 61.069 66.667 0.00 0.00 0.00 5.03
34 35 2.579738 GTCGGAGGTCCCTTGCTC 59.420 66.667 0.00 0.00 0.00 4.26
35 36 3.003763 GGTCGGAGGTCCCTTGCT 61.004 66.667 0.00 0.00 0.00 3.91
36 37 3.003763 AGGTCGGAGGTCCCTTGC 61.004 66.667 0.00 0.00 0.00 4.01
37 38 2.660064 CCAGGTCGGAGGTCCCTTG 61.660 68.421 0.00 0.00 36.56 3.61
38 39 2.284699 CCAGGTCGGAGGTCCCTT 60.285 66.667 0.00 0.00 36.56 3.95
39 40 3.273654 TCCAGGTCGGAGGTCCCT 61.274 66.667 0.00 0.00 39.64 4.20
48 49 2.678934 TTCCCCGAGTCCAGGTCG 60.679 66.667 0.00 0.00 37.17 4.79
49 50 3.020237 GCTTCCCCGAGTCCAGGTC 62.020 68.421 0.00 0.00 0.00 3.85
50 51 3.003763 GCTTCCCCGAGTCCAGGT 61.004 66.667 0.00 0.00 0.00 4.00
51 52 3.003173 TGCTTCCCCGAGTCCAGG 61.003 66.667 0.00 0.00 0.00 4.45
52 53 1.954362 CTCTGCTTCCCCGAGTCCAG 61.954 65.000 0.00 0.00 0.00 3.86
53 54 1.984570 CTCTGCTTCCCCGAGTCCA 60.985 63.158 0.00 0.00 0.00 4.02
54 55 2.726351 CCTCTGCTTCCCCGAGTCC 61.726 68.421 0.00 0.00 0.00 3.85
55 56 1.671901 CTCCTCTGCTTCCCCGAGTC 61.672 65.000 0.00 0.00 0.00 3.36
56 57 1.684049 CTCCTCTGCTTCCCCGAGT 60.684 63.158 0.00 0.00 0.00 4.18
57 58 1.380515 TCTCCTCTGCTTCCCCGAG 60.381 63.158 0.00 0.00 0.00 4.63
58 59 1.682684 GTCTCCTCTGCTTCCCCGA 60.683 63.158 0.00 0.00 0.00 5.14
59 60 2.726351 GGTCTCCTCTGCTTCCCCG 61.726 68.421 0.00 0.00 0.00 5.73
60 61 1.613630 TGGTCTCCTCTGCTTCCCC 60.614 63.158 0.00 0.00 0.00 4.81
61 62 1.599576 GTGGTCTCCTCTGCTTCCC 59.400 63.158 0.00 0.00 0.00 3.97
62 63 1.216710 CGTGGTCTCCTCTGCTTCC 59.783 63.158 0.00 0.00 0.00 3.46
63 64 1.216710 CCGTGGTCTCCTCTGCTTC 59.783 63.158 0.00 0.00 0.00 3.86
64 65 2.948720 GCCGTGGTCTCCTCTGCTT 61.949 63.158 0.00 0.00 0.00 3.91
65 66 3.386237 GCCGTGGTCTCCTCTGCT 61.386 66.667 0.00 0.00 0.00 4.24
66 67 3.695606 TGCCGTGGTCTCCTCTGC 61.696 66.667 0.00 0.00 0.00 4.26
67 68 2.262915 GTGCCGTGGTCTCCTCTG 59.737 66.667 0.00 0.00 0.00 3.35
68 69 2.997897 GGTGCCGTGGTCTCCTCT 60.998 66.667 0.00 0.00 0.00 3.69
69 70 4.436998 CGGTGCCGTGGTCTCCTC 62.437 72.222 1.93 0.00 34.35 3.71
70 71 4.988716 TCGGTGCCGTGGTCTCCT 62.989 66.667 10.60 0.00 40.74 3.69
71 72 4.436998 CTCGGTGCCGTGGTCTCC 62.437 72.222 10.60 0.00 40.74 3.71
82 83 2.907897 GATCCGTCAAGGGCTCGGTG 62.908 65.000 0.00 0.00 43.94 4.94
83 84 2.683933 ATCCGTCAAGGGCTCGGT 60.684 61.111 0.00 0.00 43.94 4.69
84 85 2.107141 GATCCGTCAAGGGCTCGG 59.893 66.667 0.00 0.00 44.76 4.63
85 86 2.278857 CGATCCGTCAAGGGCTCG 60.279 66.667 1.24 1.24 41.52 5.03
86 87 1.227002 GTCGATCCGTCAAGGGCTC 60.227 63.158 0.00 0.00 41.52 4.70
87 88 2.893398 GTCGATCCGTCAAGGGCT 59.107 61.111 0.00 0.00 41.52 5.19
88 89 2.582498 CGTCGATCCGTCAAGGGC 60.582 66.667 0.00 0.00 41.52 5.19
89 90 2.582498 GCGTCGATCCGTCAAGGG 60.582 66.667 0.00 0.00 41.52 3.95
90 91 1.874019 CTGCGTCGATCCGTCAAGG 60.874 63.158 0.00 0.00 42.97 3.61
91 92 1.134530 GTCTGCGTCGATCCGTCAAG 61.135 60.000 0.00 0.00 0.00 3.02
92 93 1.154093 GTCTGCGTCGATCCGTCAA 60.154 57.895 0.00 0.00 0.00 3.18
93 94 2.483745 GTCTGCGTCGATCCGTCA 59.516 61.111 0.00 0.00 0.00 4.35
94 95 2.648102 CGTCTGCGTCGATCCGTC 60.648 66.667 0.00 0.00 0.00 4.79
95 96 4.175489 CCGTCTGCGTCGATCCGT 62.175 66.667 0.00 0.00 36.15 4.69
125 126 4.687215 TCCACCGCTGCTGCAGTC 62.687 66.667 28.50 19.70 39.64 3.51
126 127 4.254709 TTCCACCGCTGCTGCAGT 62.255 61.111 28.50 9.31 39.64 4.40
127 128 3.429141 CTTCCACCGCTGCTGCAG 61.429 66.667 24.80 24.80 39.64 4.41
128 129 3.939939 TCTTCCACCGCTGCTGCA 61.940 61.111 16.29 0.88 39.64 4.41
129 130 3.426568 GTCTTCCACCGCTGCTGC 61.427 66.667 5.34 5.34 0.00 5.25
130 131 3.114616 CGTCTTCCACCGCTGCTG 61.115 66.667 0.00 0.00 0.00 4.41
131 132 3.303135 TCGTCTTCCACCGCTGCT 61.303 61.111 0.00 0.00 0.00 4.24
132 133 3.112709 GTCGTCTTCCACCGCTGC 61.113 66.667 0.00 0.00 0.00 5.25
133 134 2.805353 CGTCGTCTTCCACCGCTG 60.805 66.667 0.00 0.00 0.00 5.18
134 135 4.719369 GCGTCGTCTTCCACCGCT 62.719 66.667 0.00 0.00 41.06 5.52
135 136 4.719369 AGCGTCGTCTTCCACCGC 62.719 66.667 0.00 0.00 44.35 5.68
136 137 2.805353 CAGCGTCGTCTTCCACCG 60.805 66.667 0.00 0.00 0.00 4.94
137 138 2.227089 ATCCAGCGTCGTCTTCCACC 62.227 60.000 0.00 0.00 0.00 4.61
138 139 0.802607 GATCCAGCGTCGTCTTCCAC 60.803 60.000 0.00 0.00 0.00 4.02
139 140 1.511305 GATCCAGCGTCGTCTTCCA 59.489 57.895 0.00 0.00 0.00 3.53
140 141 1.586564 CGATCCAGCGTCGTCTTCC 60.587 63.158 0.00 0.00 34.56 3.46
141 142 1.586564 CCGATCCAGCGTCGTCTTC 60.587 63.158 0.00 0.00 37.39 2.87
142 143 2.490217 CCGATCCAGCGTCGTCTT 59.510 61.111 0.00 0.00 37.39 3.01
143 144 4.194720 GCCGATCCAGCGTCGTCT 62.195 66.667 0.00 0.00 37.39 4.18
168 169 4.122515 GCTGTCGCGAACGTCTGC 62.123 66.667 12.06 10.62 42.52 4.26
193 194 4.200283 GTCTCTCGGCTCGCCCAG 62.200 72.222 1.72 0.00 0.00 4.45
222 223 0.598562 TGCTCTCCAACGACAGACTC 59.401 55.000 0.00 0.00 0.00 3.36
223 224 0.315568 GTGCTCTCCAACGACAGACT 59.684 55.000 0.00 0.00 0.00 3.24
224 225 1.004277 CGTGCTCTCCAACGACAGAC 61.004 60.000 0.00 0.00 0.00 3.51
225 226 1.285950 CGTGCTCTCCAACGACAGA 59.714 57.895 0.00 0.00 0.00 3.41
226 227 1.004277 GACGTGCTCTCCAACGACAG 61.004 60.000 0.00 0.00 0.00 3.51
227 228 1.007734 GACGTGCTCTCCAACGACA 60.008 57.895 0.00 0.00 0.00 4.35
228 229 2.081212 CGACGTGCTCTCCAACGAC 61.081 63.158 0.00 0.00 0.00 4.34
229 230 2.254350 CGACGTGCTCTCCAACGA 59.746 61.111 0.00 0.00 0.00 3.85
230 231 3.470567 GCGACGTGCTCTCCAACG 61.471 66.667 0.00 0.00 41.73 4.10
231 232 3.470567 CGCGACGTGCTCTCCAAC 61.471 66.667 0.00 0.00 43.27 3.77
232 233 4.717629 CCGCGACGTGCTCTCCAA 62.718 66.667 8.23 0.00 43.27 3.53
243 244 4.500116 GTCTGAGCTCCCCGCGAC 62.500 72.222 8.23 6.38 45.59 5.19
249 250 3.775654 CACCGGGTCTGAGCTCCC 61.776 72.222 12.15 4.48 40.26 4.30
250 251 2.997897 ACACCGGGTCTGAGCTCC 60.998 66.667 12.15 0.00 0.00 4.70
251 252 2.574399 GACACCGGGTCTGAGCTC 59.426 66.667 6.82 6.82 43.46 4.09
252 253 3.374402 CGACACCGGGTCTGAGCT 61.374 66.667 17.48 0.00 44.68 4.09
275 276 4.796231 CCTCCGACCTCCGTTGCG 62.796 72.222 0.00 0.00 36.31 4.85
277 278 4.452733 GGCCTCCGACCTCCGTTG 62.453 72.222 0.00 0.00 36.31 4.10
288 289 3.237741 CCTGGATCTCCGGCCTCC 61.238 72.222 0.00 0.00 41.13 4.30
289 290 3.934962 GCCTGGATCTCCGGCCTC 61.935 72.222 16.45 0.00 44.35 4.70
343 344 0.577269 CGTAACTATGGCGCTCTTGC 59.423 55.000 7.64 0.00 0.00 4.01
344 345 1.209128 CCGTAACTATGGCGCTCTTG 58.791 55.000 7.64 0.00 0.00 3.02
345 346 0.104304 CCCGTAACTATGGCGCTCTT 59.896 55.000 7.64 0.00 0.00 2.85
346 347 0.754217 TCCCGTAACTATGGCGCTCT 60.754 55.000 7.64 0.00 0.00 4.09
347 348 0.317479 ATCCCGTAACTATGGCGCTC 59.683 55.000 7.64 0.00 0.00 5.03
348 349 0.317479 GATCCCGTAACTATGGCGCT 59.683 55.000 7.64 0.00 0.00 5.92
349 350 0.669625 GGATCCCGTAACTATGGCGC 60.670 60.000 0.00 0.00 0.00 6.53
350 351 0.966920 AGGATCCCGTAACTATGGCG 59.033 55.000 8.55 0.00 0.00 5.69
351 352 2.094130 GCTAGGATCCCGTAACTATGGC 60.094 54.545 8.55 0.00 0.00 4.40
352 353 3.193691 CAGCTAGGATCCCGTAACTATGG 59.806 52.174 8.55 0.00 0.00 2.74
353 354 3.193691 CCAGCTAGGATCCCGTAACTATG 59.806 52.174 8.55 0.00 41.22 2.23
354 355 3.181420 ACCAGCTAGGATCCCGTAACTAT 60.181 47.826 8.55 0.00 41.22 2.12
355 356 2.176364 ACCAGCTAGGATCCCGTAACTA 59.824 50.000 8.55 0.00 41.22 2.24
356 357 1.063114 ACCAGCTAGGATCCCGTAACT 60.063 52.381 8.55 0.00 41.22 2.24
357 358 1.411041 ACCAGCTAGGATCCCGTAAC 58.589 55.000 8.55 0.00 41.22 2.50
358 359 2.170012 AACCAGCTAGGATCCCGTAA 57.830 50.000 8.55 0.00 41.22 3.18
359 360 2.170012 AAACCAGCTAGGATCCCGTA 57.830 50.000 8.55 0.00 41.22 4.02
360 361 2.170012 TAAACCAGCTAGGATCCCGT 57.830 50.000 8.55 0.00 41.22 5.28
361 362 2.632996 TGATAAACCAGCTAGGATCCCG 59.367 50.000 8.55 0.53 41.22 5.14
362 363 3.648545 AGTGATAAACCAGCTAGGATCCC 59.351 47.826 8.55 0.00 41.22 3.85
363 364 4.345257 TCAGTGATAAACCAGCTAGGATCC 59.655 45.833 2.48 2.48 41.22 3.36
364 365 5.537188 CTCAGTGATAAACCAGCTAGGATC 58.463 45.833 8.91 3.30 41.22 3.36
365 366 4.202305 GCTCAGTGATAAACCAGCTAGGAT 60.202 45.833 8.91 0.00 41.22 3.24
366 367 3.133003 GCTCAGTGATAAACCAGCTAGGA 59.867 47.826 8.91 0.00 41.22 2.94
396 397 2.608261 GCATGCATCTACCGTAGAGGAC 60.608 54.545 21.48 13.66 45.00 3.85
397 398 1.613925 GCATGCATCTACCGTAGAGGA 59.386 52.381 21.48 11.55 45.00 3.71
399 400 2.608998 CCTGCATGCATCTACCGTAGAG 60.609 54.545 22.97 4.42 38.38 2.43
414 419 2.044946 GTTCCGCTTCCCCTGCAT 60.045 61.111 0.00 0.00 0.00 3.96
416 421 2.034221 AAGTTCCGCTTCCCCTGC 59.966 61.111 0.00 0.00 30.06 4.85
424 429 1.731969 GTCGCGTACAAGTTCCGCT 60.732 57.895 5.77 0.00 44.92 5.52
431 436 0.093535 CATGCTGTGTCGCGTACAAG 59.906 55.000 16.88 14.10 40.63 3.16
434 439 2.395690 GCATGCTGTGTCGCGTAC 59.604 61.111 11.37 7.70 0.00 3.67
442 447 1.722464 CAAACATTTCGGCATGCTGTG 59.278 47.619 25.42 18.58 0.00 3.66
446 451 2.412770 CCTTTCAAACATTTCGGCATGC 59.587 45.455 9.90 9.90 0.00 4.06
467 472 7.323420 AGAATTAAAATGGCTGGCTTTTACTC 58.677 34.615 14.02 13.13 0.00 2.59
496 501 5.047092 CAGTTTCAAGCCCTCCATTACAAAT 60.047 40.000 0.00 0.00 0.00 2.32
540 549 2.750350 GTGGGGTGACAGTCAGGG 59.250 66.667 2.53 0.00 0.00 4.45
541 550 2.750350 GGTGGGGTGACAGTCAGG 59.250 66.667 2.53 0.00 0.00 3.86
545 554 2.923035 CTCGGGTGGGGTGACAGT 60.923 66.667 0.00 0.00 0.00 3.55
546 555 2.603473 TCTCGGGTGGGGTGACAG 60.603 66.667 0.00 0.00 0.00 3.51
547 556 2.603473 CTCTCGGGTGGGGTGACA 60.603 66.667 0.00 0.00 0.00 3.58
548 557 4.083862 GCTCTCGGGTGGGGTGAC 62.084 72.222 0.00 0.00 0.00 3.67
604 617 4.457496 ACGACATCGCTGGGCCTG 62.457 66.667 4.53 5.32 44.43 4.85
605 618 4.457496 CACGACATCGCTGGGCCT 62.457 66.667 4.53 0.00 44.43 5.19
673 691 2.732289 GGTTGTGACCAGCCAATGT 58.268 52.632 0.00 0.00 45.77 2.71
684 715 1.521450 GAGGACGGACGAGGTTGTGA 61.521 60.000 0.00 0.00 0.00 3.58
745 807 3.462333 ATGAGAGCGAGCGAGCGAC 62.462 63.158 1.41 0.83 43.00 5.19
789 851 2.002018 TTGTGCGGGGAAAGAAGGGT 62.002 55.000 0.00 0.00 0.00 4.34
792 854 1.602920 GCTTTTGTGCGGGGAAAGAAG 60.603 52.381 6.03 0.00 33.35 2.85
869 934 2.517875 AATCAGGCTGCGGATGGC 60.518 61.111 10.34 0.00 43.96 4.40
870 935 0.465097 AAGAATCAGGCTGCGGATGG 60.465 55.000 10.34 0.00 0.00 3.51
871 936 1.332997 GAAAGAATCAGGCTGCGGATG 59.667 52.381 10.34 0.00 0.00 3.51
872 937 1.211457 AGAAAGAATCAGGCTGCGGAT 59.789 47.619 10.34 0.00 0.00 4.18
873 938 0.615331 AGAAAGAATCAGGCTGCGGA 59.385 50.000 10.34 0.00 0.00 5.54
874 939 1.457346 AAGAAAGAATCAGGCTGCGG 58.543 50.000 10.34 0.00 0.00 5.69
875 940 2.159462 GGAAAGAAAGAATCAGGCTGCG 60.159 50.000 10.34 0.00 0.00 5.18
876 941 3.087781 AGGAAAGAAAGAATCAGGCTGC 58.912 45.455 10.34 0.00 0.00 5.25
879 946 2.680339 CCGAGGAAAGAAAGAATCAGGC 59.320 50.000 0.00 0.00 0.00 4.85
882 949 4.618460 CGAGACCGAGGAAAGAAAGAATCA 60.618 45.833 0.00 0.00 38.22 2.57
922 989 2.577059 GTGCGTGGGAATCGGAGA 59.423 61.111 0.00 0.00 45.75 3.71
976 1048 1.006805 CTGAAGGCGCGATCCCTAG 60.007 63.158 12.10 0.00 30.93 3.02
989 1072 1.817099 GTCGCCATGGCTCCTGAAG 60.817 63.158 33.07 16.54 39.32 3.02
991 1074 4.147449 CGTCGCCATGGCTCCTGA 62.147 66.667 33.07 20.46 39.32 3.86
1504 1611 6.067350 AGCCTTGATCTTGTTCTTCTTCTTT 58.933 36.000 0.00 0.00 0.00 2.52
1548 1655 2.558795 CTCTTCTTCCTCTTCGTGGTCA 59.441 50.000 0.00 0.00 0.00 4.02
1560 1667 2.191128 TTTGCTGCTCCTCTTCTTCC 57.809 50.000 0.00 0.00 0.00 3.46
1596 1703 1.403814 TGATCTCCCCTTGTAGCTCG 58.596 55.000 0.00 0.00 0.00 5.03
1601 1708 2.196595 CCACCTTGATCTCCCCTTGTA 58.803 52.381 0.00 0.00 0.00 2.41
1710 1817 3.703420 GGCAATTGTCATCTCATCAAGC 58.297 45.455 4.85 0.00 0.00 4.01
1713 1820 2.938451 GTCGGCAATTGTCATCTCATCA 59.062 45.455 11.22 0.00 0.00 3.07
1808 1915 2.968574 ACTGCGGTATCAAGATCATCCT 59.031 45.455 0.00 0.00 0.00 3.24
2008 2115 1.131693 GAGTAAAATTGAACGGGCCGG 59.868 52.381 31.78 12.53 0.00 6.13
2064 2171 1.242076 CTTCAGTGGCTGGAACCAAG 58.758 55.000 0.00 0.00 42.70 3.61
2124 2237 0.439985 CGATTGACACCTCGCAGTTG 59.560 55.000 0.00 0.00 0.00 3.16
2181 2294 2.095567 CACCAGTTCTTGAAATGGAGCG 60.096 50.000 28.93 16.26 40.11 5.03
2241 2354 0.979665 CCAGTGGTGATGTCCAGTCT 59.020 55.000 0.00 0.00 38.90 3.24
2245 2358 1.833630 GATCTCCAGTGGTGATGTCCA 59.166 52.381 27.29 1.23 36.26 4.02
2375 2489 9.705290 AAATAAGTAGCAAATTAAAGTTGTGGG 57.295 29.630 4.68 0.00 0.00 4.61
2419 2538 0.035630 ACCTCATGCTCTGCTTCACC 60.036 55.000 0.00 0.00 0.00 4.02
2474 2593 0.604780 TTCGTCCTCCTCGTTCTCGT 60.605 55.000 0.00 0.00 38.33 4.18
2592 2711 1.722852 CTCGCTCGATACGCTTCCG 60.723 63.158 3.29 0.00 41.14 4.30
2601 2720 1.745864 ACACTCGACCTCGCTCGAT 60.746 57.895 0.00 0.00 41.71 3.59
2685 2804 1.299468 CTCCAGCTCGGCGTACATC 60.299 63.158 6.85 0.00 33.14 3.06
2769 2888 3.694058 CTGCATGGCGGCCTTCTCT 62.694 63.158 21.46 0.00 0.00 3.10
2932 3051 0.391228 TTGTCCTCGTACTGCAGCAA 59.609 50.000 15.27 4.24 0.00 3.91
2951 3070 2.744243 GCTGCCATGCTCCTCTCCT 61.744 63.158 0.00 0.00 0.00 3.69
2961 3080 0.609957 TGTCCTTCAAGGCTGCCATG 60.610 55.000 22.65 19.89 34.61 3.66
2973 3095 1.348594 GCTACGCGCATTGTCCTTC 59.651 57.895 5.73 0.00 38.92 3.46
2997 3119 1.001764 CTCAGAGGTGCCATTGCCA 60.002 57.895 0.00 0.00 36.33 4.92
3123 3245 0.389817 CGGTGTTCTCTTGATCCGCA 60.390 55.000 0.00 0.00 0.00 5.69
3222 3344 1.813192 CGTGAAGAGCCTCTCCTCC 59.187 63.158 0.00 0.00 32.17 4.30
3247 3369 1.383120 CCGTTGATATCGTCGTCGTC 58.617 55.000 14.85 0.00 38.33 4.20
3248 3370 0.590732 GCCGTTGATATCGTCGTCGT 60.591 55.000 14.85 0.00 38.33 4.34
3249 3371 0.590481 TGCCGTTGATATCGTCGTCG 60.590 55.000 14.85 0.00 38.55 5.12
3307 3429 4.436998 GGGACCGTCGGCTGACAG 62.437 72.222 24.91 16.64 45.80 3.51
3486 3608 1.082104 CTCTTTCGCAAACACGGCC 60.082 57.895 0.00 0.00 0.00 6.13
3615 3737 0.610232 GAAGGTGCATGCCCTTGTCT 60.610 55.000 32.37 17.10 42.37 3.41
3826 3955 2.665519 GCCACAATAATTCGGCTATGCG 60.666 50.000 0.00 0.00 41.50 4.73
3834 3963 8.188139 AGGTAATTAAACAGCCACAATAATTCG 58.812 33.333 0.00 0.00 30.97 3.34
3898 4027 0.725686 CCGAGCAACTGAATCTGCAG 59.274 55.000 7.63 7.63 41.17 4.41
3951 4080 5.276440 AGGGACCATATCATAGATCCACTC 58.724 45.833 0.00 0.00 0.00 3.51
3990 4122 4.500716 CGTTCCCTTAAACACAAGCCATTT 60.501 41.667 0.00 0.00 0.00 2.32
4157 4293 2.771943 TCTGTCCTGTTGAAGTTGAGGT 59.228 45.455 0.00 0.00 0.00 3.85
4158 4294 3.475566 TCTGTCCTGTTGAAGTTGAGG 57.524 47.619 0.00 0.00 0.00 3.86
4159 4295 3.750130 CCATCTGTCCTGTTGAAGTTGAG 59.250 47.826 0.00 0.00 0.00 3.02
4160 4296 3.390967 TCCATCTGTCCTGTTGAAGTTGA 59.609 43.478 0.00 0.00 0.00 3.18
4161 4297 3.743521 TCCATCTGTCCTGTTGAAGTTG 58.256 45.455 0.00 0.00 0.00 3.16
4162 4298 3.648067 TCTCCATCTGTCCTGTTGAAGTT 59.352 43.478 0.00 0.00 0.00 2.66
4186 4338 3.738282 CCTTTTGCCGATTCTCTATCTCG 59.262 47.826 0.00 0.00 0.00 4.04
4191 4343 4.829872 TTACCCTTTTGCCGATTCTCTA 57.170 40.909 0.00 0.00 0.00 2.43
4280 4437 7.062848 GCACAAACAAATCTGAAATTTAACCG 58.937 34.615 0.00 0.00 0.00 4.44
4312 4470 3.754323 ACACAAAAACTTGAACGTCCTCA 59.246 39.130 0.00 0.00 0.00 3.86
4316 4474 8.247774 CGTATAAAACACAAAAACTTGAACGTC 58.752 33.333 0.00 0.00 0.00 4.34
4317 4475 7.961827 TCGTATAAAACACAAAAACTTGAACGT 59.038 29.630 0.00 0.00 0.00 3.99
4323 4481 8.245491 ACAACCTCGTATAAAACACAAAAACTT 58.755 29.630 0.00 0.00 0.00 2.66
4389 4554 0.034756 TCAAAACTGGCTAGAGCGCA 59.965 50.000 11.47 0.00 43.26 6.09
4390 4555 1.063174 CATCAAAACTGGCTAGAGCGC 59.937 52.381 3.17 0.00 43.26 5.92
4392 4557 4.256920 TCTTCATCAAAACTGGCTAGAGC 58.743 43.478 3.17 0.00 41.14 4.09
4393 4558 6.652481 TCTTTCTTCATCAAAACTGGCTAGAG 59.348 38.462 3.17 0.00 0.00 2.43
4395 4560 6.808008 TCTTTCTTCATCAAAACTGGCTAG 57.192 37.500 0.00 0.00 0.00 3.42
4474 4644 4.208666 GGTCGAATAATGTACGAAGAAGCC 59.791 45.833 0.00 0.00 37.77 4.35
4602 4783 4.623932 AGTAATGACAGCTCAAGGACAA 57.376 40.909 0.00 0.00 0.00 3.18
4651 4833 9.248291 GAGTAATGCAAGAATCTGTTTGAAAAA 57.752 29.630 0.00 0.00 0.00 1.94
4652 4834 8.412456 TGAGTAATGCAAGAATCTGTTTGAAAA 58.588 29.630 0.00 0.00 0.00 2.29
4660 4842 6.373779 ACGTTTTGAGTAATGCAAGAATCTG 58.626 36.000 0.00 0.00 0.00 2.90
4662 4844 7.623268 AAACGTTTTGAGTAATGCAAGAATC 57.377 32.000 7.96 0.00 0.00 2.52
4729 5649 1.869342 GCAATGCCGAACTGCTGTTTT 60.869 47.619 10.54 0.00 36.39 2.43
4786 5706 2.926200 CTCATGTTTGTCGGAGCTGTAG 59.074 50.000 0.00 0.00 0.00 2.74
4875 5796 0.596082 ACCGCGCTTGCATTTTACTT 59.404 45.000 5.56 0.00 39.07 2.24
4876 5797 0.596082 AACCGCGCTTGCATTTTACT 59.404 45.000 5.56 0.00 39.07 2.24
4877 5798 0.981956 GAACCGCGCTTGCATTTTAC 59.018 50.000 5.56 0.00 39.07 2.01
4878 5799 0.878416 AGAACCGCGCTTGCATTTTA 59.122 45.000 5.56 0.00 39.07 1.52
4879 5800 0.878416 TAGAACCGCGCTTGCATTTT 59.122 45.000 5.56 0.00 39.07 1.82
4880 5801 0.878416 TTAGAACCGCGCTTGCATTT 59.122 45.000 5.56 0.00 39.07 2.32
4881 5802 1.094785 ATTAGAACCGCGCTTGCATT 58.905 45.000 5.56 0.00 39.07 3.56
4882 5803 1.064060 GAATTAGAACCGCGCTTGCAT 59.936 47.619 5.56 0.00 39.07 3.96
4883 5804 0.446222 GAATTAGAACCGCGCTTGCA 59.554 50.000 5.56 0.00 39.07 4.08
4884 5805 0.727398 AGAATTAGAACCGCGCTTGC 59.273 50.000 5.56 0.00 0.00 4.01
4885 5806 3.471495 AAAGAATTAGAACCGCGCTTG 57.529 42.857 5.56 0.00 0.00 4.01
4886 5807 3.119955 GGAAAAGAATTAGAACCGCGCTT 60.120 43.478 5.56 0.00 0.00 4.68
4887 5808 2.418976 GGAAAAGAATTAGAACCGCGCT 59.581 45.455 5.56 0.00 0.00 5.92
4888 5809 2.160813 TGGAAAAGAATTAGAACCGCGC 59.839 45.455 0.00 0.00 0.00 6.86
4889 5810 4.413495 TTGGAAAAGAATTAGAACCGCG 57.587 40.909 0.00 0.00 0.00 6.46
4890 5811 5.629435 CACTTTGGAAAAGAATTAGAACCGC 59.371 40.000 6.73 0.00 0.00 5.68
4891 5812 6.735130 ACACTTTGGAAAAGAATTAGAACCG 58.265 36.000 6.73 0.00 0.00 4.44
4892 5813 6.856426 CGACACTTTGGAAAAGAATTAGAACC 59.144 38.462 6.73 0.00 0.00 3.62
4893 5814 7.636326 TCGACACTTTGGAAAAGAATTAGAAC 58.364 34.615 6.73 0.00 0.00 3.01
4894 5815 7.795482 TCGACACTTTGGAAAAGAATTAGAA 57.205 32.000 6.73 0.00 0.00 2.10
4895 5816 7.979444 ATCGACACTTTGGAAAAGAATTAGA 57.021 32.000 6.73 1.03 0.00 2.10
4896 5817 7.538678 CCAATCGACACTTTGGAAAAGAATTAG 59.461 37.037 9.49 0.00 44.23 1.73
4897 5818 7.367285 CCAATCGACACTTTGGAAAAGAATTA 58.633 34.615 9.49 0.00 44.23 1.40
4898 5819 6.215845 CCAATCGACACTTTGGAAAAGAATT 58.784 36.000 9.49 0.00 44.23 2.17
4899 5820 5.278957 CCCAATCGACACTTTGGAAAAGAAT 60.279 40.000 15.56 0.00 44.23 2.40
4900 5821 4.037446 CCCAATCGACACTTTGGAAAAGAA 59.963 41.667 15.56 0.00 44.23 2.52
4901 5822 3.568007 CCCAATCGACACTTTGGAAAAGA 59.432 43.478 15.56 0.00 44.23 2.52
4902 5823 3.317993 ACCCAATCGACACTTTGGAAAAG 59.682 43.478 15.56 3.26 44.23 2.27
4903 5824 3.292460 ACCCAATCGACACTTTGGAAAA 58.708 40.909 15.56 0.00 44.23 2.29
4904 5825 2.882137 GACCCAATCGACACTTTGGAAA 59.118 45.455 15.56 0.00 44.23 3.13
4905 5826 2.158740 TGACCCAATCGACACTTTGGAA 60.159 45.455 15.56 0.56 44.23 3.53
4906 5827 1.418264 TGACCCAATCGACACTTTGGA 59.582 47.619 15.56 0.00 44.23 3.53
4907 5828 1.890876 TGACCCAATCGACACTTTGG 58.109 50.000 8.30 8.30 41.71 3.28


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

AutoCloner maintained by Alex Coulton.