Multiple sequence alignment - TraesCS7D01G141100

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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 TraesCS7D01G141100 chr7D 100.000 6118 0 0 1 6118 90000573 90006690 0.000000e+00 11298.0
1 TraesCS7D01G141100 chr7D 85.178 506 56 11 4783 5286 90037914 90038402 9.160000e-138 501.0
2 TraesCS7D01G141100 chr7D 95.370 108 4 1 6011 6118 490208679 490208573 2.930000e-38 171.0
3 TraesCS7D01G141100 chr7D 84.722 144 20 2 3 144 162116490 162116347 6.390000e-30 143.0
4 TraesCS7D01G141100 chr7B 92.002 4051 199 51 406 4404 41167633 41171610 0.000000e+00 5570.0
5 TraesCS7D01G141100 chr7B 92.951 1064 63 7 4403 5458 41171704 41172763 0.000000e+00 1539.0
6 TraesCS7D01G141100 chr7B 86.265 648 64 13 4044 4679 41188681 41189315 0.000000e+00 680.0
7 TraesCS7D01G141100 chr7B 83.130 575 67 12 4714 5288 41191378 41191922 1.180000e-136 497.0
8 TraesCS7D01G141100 chr7B 84.252 254 33 3 5747 5993 41185791 41186044 2.200000e-59 241.0
9 TraesCS7D01G141100 chr7B 90.850 153 6 5 144 290 41167392 41167542 1.350000e-46 198.0
10 TraesCS7D01G141100 chr7B 85.795 176 23 1 1083 1258 708741461 708741288 1.050000e-42 185.0
11 TraesCS7D01G141100 chr7A 92.854 2015 99 16 381 2372 91508814 91510806 0.000000e+00 2881.0
12 TraesCS7D01G141100 chr7A 95.837 1081 30 9 3318 4391 91511662 91512734 0.000000e+00 1733.0
13 TraesCS7D01G141100 chr7A 94.884 1075 41 10 4393 5458 91515636 91516705 0.000000e+00 1668.0
14 TraesCS7D01G141100 chr7A 95.657 875 20 3 2420 3287 91510801 91511664 0.000000e+00 1389.0
15 TraesCS7D01G141100 chr7A 84.006 669 82 16 4044 4689 91518899 91519565 2.420000e-173 619.0
16 TraesCS7D01G141100 chr7A 81.875 640 69 22 1051 1667 696954892 696954277 4.260000e-136 496.0
17 TraesCS7D01G141100 chr7A 87.708 301 21 8 4992 5288 91535818 91536106 2.730000e-88 337.0
18 TraesCS7D01G141100 chr7A 75.208 722 116 35 5305 6007 91536247 91536924 3.610000e-72 283.0
19 TraesCS7D01G141100 chr7A 84.286 140 20 2 3 140 163778797 163778936 1.070000e-27 135.0
20 TraesCS7D01G141100 chr3B 82.803 628 73 19 1047 1667 104267056 104267655 4.200000e-146 529.0
21 TraesCS7D01G141100 chr3B 94.643 112 4 2 6008 6118 796839941 796839831 8.150000e-39 172.0
22 TraesCS7D01G141100 chr5A 81.366 644 71 21 1047 1667 419861469 419862086 4.290000e-131 479.0
23 TraesCS7D01G141100 chr1A 80.901 644 74 22 1047 1667 47874486 47875103 4.320000e-126 462.0
24 TraesCS7D01G141100 chr2B 80.123 649 76 20 1047 1667 660183007 660182384 9.420000e-118 435.0
25 TraesCS7D01G141100 chr6A 82.134 403 47 11 1059 1451 326794908 326794521 7.650000e-84 322.0
26 TraesCS7D01G141100 chr6A 83.740 123 18 2 19 140 602896295 602896416 1.390000e-21 115.0
27 TraesCS7D01G141100 chr1D 84.969 326 38 7 1115 1434 371676096 371676416 2.750000e-83 320.0
28 TraesCS7D01G141100 chr1D 93.860 114 6 1 6005 6118 326551034 326551146 2.930000e-38 171.0
29 TraesCS7D01G141100 chr4D 95.495 111 4 1 6008 6118 107724923 107725032 6.300000e-40 176.0
30 TraesCS7D01G141100 chr6D 94.690 113 5 1 6006 6118 178817899 178817788 2.270000e-39 174.0
31 TraesCS7D01G141100 chr6D 94.595 111 5 1 6008 6118 238979375 238979266 2.930000e-38 171.0
32 TraesCS7D01G141100 chr6D 82.979 141 16 5 3 140 82197522 82197387 3.000000e-23 121.0
33 TraesCS7D01G141100 chr6D 80.000 125 23 2 28 151 100345546 100345669 2.350000e-14 91.6
34 TraesCS7D01G141100 chr3A 94.690 113 4 2 6007 6118 747328709 747328820 2.270000e-39 174.0
35 TraesCS7D01G141100 chr5B 93.103 116 6 2 6004 6118 406940698 406940584 1.050000e-37 169.0
36 TraesCS7D01G141100 chr6B 91.667 120 8 2 6000 6118 195831062 195831180 1.360000e-36 165.0
37 TraesCS7D01G141100 chr4A 89.344 122 12 1 20 140 501246626 501246747 1.060000e-32 152.0
38 TraesCS7D01G141100 chr2A 84.173 139 21 1 3 140 33561734 33561872 3.850000e-27 134.0
39 TraesCS7D01G141100 chrUn 80.508 118 21 2 25 140 33957199 33957082 8.450000e-14 89.8
40 TraesCS7D01G141100 chr2D 87.342 79 8 2 68 145 559401242 559401319 8.450000e-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 TraesCS7D01G141100 chr7D 90000573 90006690 6117 False 11298.000000 11298 100.000000 1 6118 1 chr7D.!!$F1 6117
1 TraesCS7D01G141100 chr7B 41167392 41172763 5371 False 2435.666667 5570 91.934333 144 5458 3 chr7B.!!$F1 5314
2 TraesCS7D01G141100 chr7B 41185791 41191922 6131 False 472.666667 680 84.549000 4044 5993 3 chr7B.!!$F2 1949
3 TraesCS7D01G141100 chr7A 91508814 91519565 10751 False 1658.000000 2881 92.647600 381 5458 5 chr7A.!!$F2 5077
4 TraesCS7D01G141100 chr7A 696954277 696954892 615 True 496.000000 496 81.875000 1051 1667 1 chr7A.!!$R1 616
5 TraesCS7D01G141100 chr7A 91535818 91536924 1106 False 310.000000 337 81.458000 4992 6007 2 chr7A.!!$F3 1015
6 TraesCS7D01G141100 chr3B 104267056 104267655 599 False 529.000000 529 82.803000 1047 1667 1 chr3B.!!$F1 620
7 TraesCS7D01G141100 chr5A 419861469 419862086 617 False 479.000000 479 81.366000 1047 1667 1 chr5A.!!$F1 620
8 TraesCS7D01G141100 chr1A 47874486 47875103 617 False 462.000000 462 80.901000 1047 1667 1 chr1A.!!$F1 620
9 TraesCS7D01G141100 chr2B 660182384 660183007 623 True 435.000000 435 80.123000 1047 1667 1 chr2B.!!$R1 620

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
366 396 0.034477 CGGCCTGGTTAAATGGTCCT 60.034 55.000 0.00 0.0 0.00 3.85 F
588 618 0.804544 TTCGCCACTGCACTATACGC 60.805 55.000 0.00 0.0 37.32 4.42 F
1781 1891 0.956410 CCACCCGTGATAACGCCAAA 60.956 55.000 0.00 0.0 0.00 3.28 F
3026 3155 1.074566 CTTTCCCCTGACTCCTTGCTT 59.925 52.381 0.00 0.0 0.00 3.91 F
3307 3436 1.337728 TGTTATGGACACAGTGGAGCG 60.338 52.381 5.31 0.0 32.00 5.03 F
4374 4520 0.107897 TTGGCAGTGTGTGTCGTCTT 60.108 50.000 0.00 0.0 31.02 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2058 2168 0.031178 GTCCCAAAGCAGTGCAGTTG 59.969 55.000 19.20 19.35 0.00 3.16 R
2411 2525 1.068055 GCCAGAGGACATGCACAAAAG 60.068 52.381 0.00 0.00 0.00 2.27 R
3446 3575 3.317993 ACCAAAGCACAAAAGAACGCTAT 59.682 39.130 0.00 0.00 33.45 2.97 R
4307 4452 1.485210 GGCCCATAGGTACCCTCTGAT 60.485 57.143 8.74 0.00 34.61 2.90 R
4818 10009 3.965470 AGTAGGAACCCTGGTTTGTTT 57.035 42.857 2.55 0.00 38.60 2.83 R
6054 11554 0.107165 ATGAAAACTAGAGGCGGGGC 60.107 55.000 0.00 0.00 0.00 5.80 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
21 22 4.422546 AACCGAAAACACGTGAGAAAAA 57.577 36.364 25.01 0.00 0.00 1.94
62 63 1.002868 AGCACCCAGAGCATGACAC 60.003 57.895 0.00 0.00 0.00 3.67
65 66 0.246360 CACCCAGAGCATGACACGTA 59.754 55.000 0.00 0.00 0.00 3.57
67 68 1.337823 ACCCAGAGCATGACACGTAAC 60.338 52.381 0.00 0.00 0.00 2.50
68 69 0.992072 CCAGAGCATGACACGTAACG 59.008 55.000 0.00 0.00 0.00 3.18
69 70 1.402325 CCAGAGCATGACACGTAACGA 60.402 52.381 0.00 0.00 0.00 3.85
72 73 2.923655 AGAGCATGACACGTAACGAATG 59.076 45.455 0.00 0.00 0.00 2.67
73 74 2.921121 GAGCATGACACGTAACGAATGA 59.079 45.455 0.00 0.00 0.00 2.57
74 75 2.666508 AGCATGACACGTAACGAATGAC 59.333 45.455 0.00 0.00 0.00 3.06
75 76 2.666508 GCATGACACGTAACGAATGACT 59.333 45.455 0.00 0.00 0.00 3.41
77 78 3.629438 TGACACGTAACGAATGACTGA 57.371 42.857 0.00 0.00 0.00 3.41
78 79 3.561503 TGACACGTAACGAATGACTGAG 58.438 45.455 0.00 0.00 0.00 3.35
79 80 3.251487 TGACACGTAACGAATGACTGAGA 59.749 43.478 0.00 0.00 0.00 3.27
84 85 1.073216 AACGAATGACTGAGAGCGCG 61.073 55.000 0.00 0.00 0.00 6.86
87 88 1.354337 GAATGACTGAGAGCGCGCAA 61.354 55.000 35.10 14.66 0.00 4.85
89 90 2.431601 GACTGAGAGCGCGCAAGT 60.432 61.111 35.10 27.94 41.68 3.16
101 102 2.875080 GCGCAAGTGACTTTAATCGT 57.125 45.000 0.30 0.00 41.68 3.73
103 104 2.902484 GCGCAAGTGACTTTAATCGTTG 59.098 45.455 0.30 0.00 41.68 4.10
105 106 2.902484 GCAAGTGACTTTAATCGTTGCG 59.098 45.455 0.00 0.00 33.81 4.85
106 107 3.363575 GCAAGTGACTTTAATCGTTGCGA 60.364 43.478 0.00 0.00 41.13 5.10
107 108 4.386230 CAAGTGACTTTAATCGTTGCGAG 58.614 43.478 0.00 0.00 39.91 5.03
110 111 3.673809 GTGACTTTAATCGTTGCGAGACT 59.326 43.478 0.00 0.00 39.91 3.24
112 113 3.251571 ACTTTAATCGTTGCGAGACTCC 58.748 45.455 0.00 0.00 39.91 3.85
114 115 2.561733 TAATCGTTGCGAGACTCCTG 57.438 50.000 0.00 0.00 39.91 3.86
116 117 0.888619 ATCGTTGCGAGACTCCTGAA 59.111 50.000 0.00 0.00 39.91 3.02
117 118 0.241213 TCGTTGCGAGACTCCTGAAG 59.759 55.000 0.00 0.00 0.00 3.02
118 119 0.734253 CGTTGCGAGACTCCTGAAGG 60.734 60.000 0.00 0.00 0.00 3.46
128 129 2.746697 TCCTGAAGGAGTGCTCGTT 58.253 52.632 6.82 6.82 39.78 3.85
130 131 2.244695 TCCTGAAGGAGTGCTCGTTAA 58.755 47.619 7.06 0.20 39.78 2.01
132 133 2.028930 CCTGAAGGAGTGCTCGTTAACT 60.029 50.000 3.71 0.00 37.75 2.24
133 134 3.192844 CCTGAAGGAGTGCTCGTTAACTA 59.807 47.826 3.71 0.00 37.75 2.24
134 135 4.416620 CTGAAGGAGTGCTCGTTAACTAG 58.583 47.826 3.71 3.24 37.75 2.57
135 136 3.825014 TGAAGGAGTGCTCGTTAACTAGT 59.175 43.478 8.74 0.00 37.75 2.57
136 137 4.280174 TGAAGGAGTGCTCGTTAACTAGTT 59.720 41.667 13.68 13.68 37.75 2.24
137 138 4.175787 AGGAGTGCTCGTTAACTAGTTG 57.824 45.455 18.56 1.62 0.00 3.16
138 139 2.666994 GGAGTGCTCGTTAACTAGTTGC 59.333 50.000 18.56 12.57 0.00 4.17
139 140 3.576648 GAGTGCTCGTTAACTAGTTGCT 58.423 45.455 18.56 4.94 0.00 3.91
141 142 4.377897 AGTGCTCGTTAACTAGTTGCTTT 58.622 39.130 18.56 2.78 0.00 3.51
142 143 4.448060 AGTGCTCGTTAACTAGTTGCTTTC 59.552 41.667 18.56 7.51 0.00 2.62
159 160 2.838637 TTCCTGTTTTTGGGGTCACT 57.161 45.000 0.00 0.00 0.00 3.41
211 213 8.785329 TTTTGTCTTTTGAGCCAATAACTTTT 57.215 26.923 0.00 0.00 0.00 2.27
290 296 1.004595 CAGACGAGCATGACACATGG 58.995 55.000 12.56 0.74 0.00 3.66
291 297 0.742281 AGACGAGCATGACACATGGC 60.742 55.000 12.56 6.12 0.00 4.40
299 329 3.086733 TGACACATGGCGTTTGTCA 57.913 47.368 21.42 21.42 45.71 3.58
326 356 2.033194 GCCAGGCTGGTTACGTGTC 61.033 63.158 32.80 11.39 40.46 3.67
332 362 1.079405 CTGGTTACGTGTCGGGCAT 60.079 57.895 0.00 0.00 0.00 4.40
333 363 1.358725 CTGGTTACGTGTCGGGCATG 61.359 60.000 0.00 0.00 39.90 4.06
337 367 0.175989 TTACGTGTCGGGCATGCATA 59.824 50.000 21.36 0.21 37.62 3.14
338 368 0.528901 TACGTGTCGGGCATGCATAC 60.529 55.000 21.36 14.10 37.62 2.39
345 375 1.775039 CGGGCATGCATACTCGTTGG 61.775 60.000 21.36 0.00 0.00 3.77
349 379 0.930310 CATGCATACTCGTTGGTCGG 59.070 55.000 0.00 0.00 40.32 4.79
354 384 1.956629 ATACTCGTTGGTCGGCCTGG 61.957 60.000 7.97 0.00 40.32 4.45
356 386 3.530910 CTCGTTGGTCGGCCTGGTT 62.531 63.158 7.97 0.00 40.32 3.67
357 387 2.162338 CTCGTTGGTCGGCCTGGTTA 62.162 60.000 7.97 0.00 40.32 2.85
358 388 1.301874 CGTTGGTCGGCCTGGTTAA 60.302 57.895 7.97 0.00 35.71 2.01
359 389 0.885596 CGTTGGTCGGCCTGGTTAAA 60.886 55.000 7.97 0.00 35.71 1.52
360 390 1.541379 GTTGGTCGGCCTGGTTAAAT 58.459 50.000 7.97 0.00 35.27 1.40
361 391 1.201414 GTTGGTCGGCCTGGTTAAATG 59.799 52.381 7.97 0.00 35.27 2.32
362 392 0.322997 TGGTCGGCCTGGTTAAATGG 60.323 55.000 7.97 0.00 35.27 3.16
363 393 0.323087 GGTCGGCCTGGTTAAATGGT 60.323 55.000 0.00 0.00 0.00 3.55
364 394 1.092348 GTCGGCCTGGTTAAATGGTC 58.908 55.000 0.00 0.00 0.00 4.02
365 395 0.034863 TCGGCCTGGTTAAATGGTCC 60.035 55.000 0.00 0.00 0.00 4.46
366 396 0.034477 CGGCCTGGTTAAATGGTCCT 60.034 55.000 0.00 0.00 0.00 3.85
367 397 1.763968 GGCCTGGTTAAATGGTCCTC 58.236 55.000 0.00 0.00 0.00 3.71
368 398 1.005450 GGCCTGGTTAAATGGTCCTCA 59.995 52.381 0.00 0.00 0.00 3.86
369 399 2.358195 GGCCTGGTTAAATGGTCCTCAT 60.358 50.000 0.00 0.00 37.79 2.90
370 400 2.952310 GCCTGGTTAAATGGTCCTCATC 59.048 50.000 0.00 0.00 34.44 2.92
372 402 4.202441 CCTGGTTAAATGGTCCTCATCAG 58.798 47.826 0.00 0.00 34.44 2.90
373 403 3.620488 TGGTTAAATGGTCCTCATCAGC 58.380 45.455 0.00 0.00 34.44 4.26
374 404 3.266772 TGGTTAAATGGTCCTCATCAGCT 59.733 43.478 0.00 0.00 34.44 4.24
375 405 4.263905 TGGTTAAATGGTCCTCATCAGCTT 60.264 41.667 0.00 0.00 34.44 3.74
376 406 4.336713 GGTTAAATGGTCCTCATCAGCTTC 59.663 45.833 0.00 0.00 34.44 3.86
378 408 0.842635 ATGGTCCTCATCAGCTTCCC 59.157 55.000 0.00 0.00 0.00 3.97
379 409 1.144936 GGTCCTCATCAGCTTCCCG 59.855 63.158 0.00 0.00 0.00 5.14
493 523 8.336806 TCAATTTTCAGAATTTGCAATGTTCAC 58.663 29.630 20.56 4.05 0.00 3.18
530 560 5.812642 CACATAGCAGTCTCGACCTAAATTT 59.187 40.000 0.00 0.00 0.00 1.82
588 618 0.804544 TTCGCCACTGCACTATACGC 60.805 55.000 0.00 0.00 37.32 4.42
613 643 4.321008 CGTTTATTAGGAGAGCGCTATGGA 60.321 45.833 10.44 0.00 0.00 3.41
655 685 2.859273 CTTCATCCCGCTCCGTGCTT 62.859 60.000 0.00 0.00 40.11 3.91
757 796 8.591312 CGCAATTTTTACGTATCCATGAAAAAT 58.409 29.630 8.97 8.97 39.93 1.82
791 830 6.043243 GGAGATGGTCTAAATAATGGGTCTCA 59.957 42.308 0.00 0.00 32.23 3.27
822 863 1.961277 GGATTGCATAGTCGGGCCG 60.961 63.158 22.51 22.51 0.00 6.13
1338 1421 2.258726 GCCCGCCTCTCGTTGTTTT 61.259 57.895 0.00 0.00 36.19 2.43
1434 1523 1.859080 GACCTCGGATGCACGTAATTC 59.141 52.381 0.00 0.00 34.94 2.17
1440 1529 1.069906 GGATGCACGTAATTCATCGGC 60.070 52.381 0.00 0.00 37.93 5.54
1447 1536 4.607955 CACGTAATTCATCGGCTCTCTAA 58.392 43.478 0.00 0.00 0.00 2.10
1724 1833 2.431454 CCCAGAGGTTTGCTCTTCTTC 58.569 52.381 0.00 0.00 0.00 2.87
1737 1846 6.560253 TGCTCTTCTTCTTCATTTTGTACC 57.440 37.500 0.00 0.00 0.00 3.34
1751 1860 3.386768 TTGTACCACTCTTCTCACTGC 57.613 47.619 0.00 0.00 0.00 4.40
1768 1878 0.969894 TGCCAAAATTAACCCACCCG 59.030 50.000 0.00 0.00 0.00 5.28
1778 1888 2.512974 CCCACCCGTGATAACGCC 60.513 66.667 0.00 0.00 0.00 5.68
1781 1891 0.956410 CCACCCGTGATAACGCCAAA 60.956 55.000 0.00 0.00 0.00 3.28
1829 1939 7.678947 AACTGAAGAGAATAACTGTGATTGG 57.321 36.000 0.00 0.00 0.00 3.16
1830 1940 7.009179 ACTGAAGAGAATAACTGTGATTGGA 57.991 36.000 0.00 0.00 0.00 3.53
1832 1942 7.389053 ACTGAAGAGAATAACTGTGATTGGAAC 59.611 37.037 0.00 0.00 0.00 3.62
1834 1944 7.388776 TGAAGAGAATAACTGTGATTGGAACTG 59.611 37.037 0.00 0.00 0.00 3.16
1835 1945 5.645497 AGAGAATAACTGTGATTGGAACTGC 59.355 40.000 0.00 0.00 0.00 4.40
1836 1946 5.316167 AGAATAACTGTGATTGGAACTGCA 58.684 37.500 0.00 0.00 0.00 4.41
1837 1947 5.182001 AGAATAACTGTGATTGGAACTGCAC 59.818 40.000 0.00 0.00 0.00 4.57
1838 1948 2.645838 ACTGTGATTGGAACTGCACT 57.354 45.000 0.00 0.00 32.69 4.40
1840 1950 2.158769 ACTGTGATTGGAACTGCACTGA 60.159 45.455 0.00 0.00 35.20 3.41
1841 1951 3.079578 CTGTGATTGGAACTGCACTGAT 58.920 45.455 0.00 0.00 33.69 2.90
1842 1952 3.489355 TGTGATTGGAACTGCACTGATT 58.511 40.909 0.00 0.00 32.69 2.57
1894 2004 8.402472 CAAATGACCCAGCTTATATTTTTCGTA 58.598 33.333 0.00 0.00 0.00 3.43
2041 2151 6.923508 TGATCACAACACACTTACTAGTTGAG 59.076 38.462 0.00 2.36 42.87 3.02
2057 2167 4.739046 GTTGAGGAGAACAACTGTGATG 57.261 45.455 0.00 0.00 42.63 3.07
2058 2168 2.771089 TGAGGAGAACAACTGTGATGC 58.229 47.619 0.00 0.00 0.00 3.91
2088 2199 2.152016 GCTTTGGGACTGTAGGTTGAC 58.848 52.381 0.00 0.00 0.00 3.18
2181 2295 9.435688 AATTTTGGTGTTCTAATTCTAATTGCC 57.564 29.630 0.00 0.00 0.00 4.52
2377 2491 7.580910 AGTTAGAATCCATCCATGTCATTCTT 58.419 34.615 12.79 0.00 37.06 2.52
2378 2492 7.501559 AGTTAGAATCCATCCATGTCATTCTTG 59.498 37.037 12.79 0.00 37.06 3.02
2420 2534 2.688477 AGAATTTCCCCCTTTTGTGCA 58.312 42.857 0.00 0.00 0.00 4.57
2422 2536 3.008266 AGAATTTCCCCCTTTTGTGCATG 59.992 43.478 0.00 0.00 0.00 4.06
2491 2613 5.047235 AGGTGATAGCTTGGACCGTAATATC 60.047 44.000 0.00 0.00 33.39 1.63
2551 2673 7.499200 TCTGGTAAGGCTTGGTTAATAACTA 57.501 36.000 10.69 0.00 0.00 2.24
2604 2726 5.948992 ACCTTCAGAACTTCACTATTTGC 57.051 39.130 0.00 0.00 0.00 3.68
3026 3155 1.074566 CTTTCCCCTGACTCCTTGCTT 59.925 52.381 0.00 0.00 0.00 3.91
3212 3341 8.840200 TCTATTTAACTCCAACTAGACCATCT 57.160 34.615 0.00 0.00 0.00 2.90
3307 3436 1.337728 TGTTATGGACACAGTGGAGCG 60.338 52.381 5.31 0.00 32.00 5.03
3446 3575 9.196552 CATCTGAGCGATATTGTAGTTTGAATA 57.803 33.333 0.00 0.00 0.00 1.75
3585 3714 2.048444 AGTAGCCTGGCATGTTCATG 57.952 50.000 22.65 8.26 0.00 3.07
3599 3728 5.122869 GCATGTTCATGTGTGTCTAATCAGT 59.877 40.000 13.24 0.00 0.00 3.41
3654 3783 4.265073 CATTTGGAAGTTAGCCTAGCTGT 58.735 43.478 0.00 0.00 40.10 4.40
3708 3837 3.393089 ACTCTGTGCCTAAAGTCAGTG 57.607 47.619 0.00 0.00 0.00 3.66
3738 3867 4.084011 TGGTGTGTGAATGTTGATCAGA 57.916 40.909 0.00 0.00 0.00 3.27
3816 3946 4.729868 ACAGACCTAAAGCATTTCAACCT 58.270 39.130 0.00 0.00 40.09 3.50
3885 4021 2.224572 GGGACTAGGTCTCGCTGATCTA 60.225 54.545 0.00 0.00 37.35 1.98
3999 4135 8.534333 TGTAATTGCCGAGATTCAGTTATATC 57.466 34.615 0.00 0.00 0.00 1.63
4179 4322 2.095059 CCTCTCAAACAATTTGGCTCGG 60.095 50.000 0.78 0.00 40.98 4.63
4374 4520 0.107897 TTGGCAGTGTGTGTCGTCTT 60.108 50.000 0.00 0.00 31.02 3.01
4434 7575 4.156556 GCAGGATCAGCAGTTTGAATGTTA 59.843 41.667 4.68 0.00 0.00 2.41
4443 7584 6.808212 CAGCAGTTTGAATGTTACAATTAGGG 59.192 38.462 0.00 0.00 0.00 3.53
4473 7614 3.738982 TCTTGGTCGATCAAAAGCTCAA 58.261 40.909 13.02 0.00 0.00 3.02
4500 7641 5.221322 GGTTTTCTTGGTTGATCAGAAGCTT 60.221 40.000 0.00 0.00 0.00 3.74
4798 9989 5.628134 GTGCTTAAAGACCAAAACCTATCG 58.372 41.667 0.00 0.00 0.00 2.92
4817 10008 6.875195 CCTATCGTTTTTGGGTCTTTGTACTA 59.125 38.462 0.00 0.00 0.00 1.82
4818 10009 7.388500 CCTATCGTTTTTGGGTCTTTGTACTAA 59.612 37.037 0.00 0.00 0.00 2.24
4841 10033 2.781174 ACAAACCAGGGTTCCTACTTCA 59.219 45.455 3.82 0.00 37.35 3.02
5132 10324 3.376935 ATGAGCGGAAGGACCAGCG 62.377 63.158 0.00 0.00 40.86 5.18
5227 10429 2.835764 AGGCAGCCAATGTGAATGAATT 59.164 40.909 15.80 0.00 0.00 2.17
5319 10645 6.513230 GCATACTTCATTCACAGTTGACACAA 60.513 38.462 0.00 0.00 0.00 3.33
5343 10669 3.967987 AGTGTAGAAGAACAACCTGACCT 59.032 43.478 0.00 0.00 0.00 3.85
5360 10686 6.156256 ACCTGACCTGACTGTATAAGCATTTA 59.844 38.462 0.00 0.00 0.00 1.40
5376 10702 6.594788 AGCATTTATGTTTTCATGGACACT 57.405 33.333 0.00 0.00 41.09 3.55
5409 10737 1.608283 CGACTTCTTCAGGTCAACCCC 60.608 57.143 0.00 0.00 36.42 4.95
5411 10739 0.321653 CTTCTTCAGGTCAACCCCCG 60.322 60.000 0.00 0.00 36.42 5.73
5412 10740 1.774894 TTCTTCAGGTCAACCCCCGG 61.775 60.000 0.00 0.00 36.42 5.73
5440 10768 0.749454 GCTGCCATGGACGAATTCCT 60.749 55.000 18.40 0.00 46.10 3.36
5479 10944 4.922206 AGTGAACAAAATGCCCATCTCTA 58.078 39.130 0.00 0.00 0.00 2.43
5481 10946 5.359009 AGTGAACAAAATGCCCATCTCTATG 59.641 40.000 0.00 0.00 0.00 2.23
5509 10975 4.423732 GGCATTGTAAATCTTGCACGAAT 58.576 39.130 0.00 0.00 36.82 3.34
5523 10989 2.031682 GCACGAATATTGGATCCACAGC 60.032 50.000 15.91 5.99 0.00 4.40
5527 10993 3.059597 CGAATATTGGATCCACAGCGTTC 60.060 47.826 15.91 13.05 0.00 3.95
5576 11045 2.375509 TCCGCCTAGTCCATCTCTGATA 59.624 50.000 0.00 0.00 0.00 2.15
5581 11050 5.621104 CGCCTAGTCCATCTCTGATATGAAC 60.621 48.000 4.74 0.00 0.00 3.18
5607 11076 3.323243 CGTTTGTCCGAGACTATTGGTT 58.677 45.455 5.77 0.00 33.54 3.67
5625 11094 2.903855 CGTGGGCATCCATGGAGC 60.904 66.667 21.33 21.32 46.09 4.70
5626 11095 2.599597 GTGGGCATCCATGGAGCT 59.400 61.111 25.57 8.76 46.09 4.09
5628 11097 2.002407 TGGGCATCCATGGAGCTCA 61.002 57.895 25.78 25.78 38.32 4.26
5632 11101 0.534652 GCATCCATGGAGCTCAGACC 60.535 60.000 21.33 0.00 0.00 3.85
5654 11123 2.501610 GCTACTTGGAGGAGGCCG 59.498 66.667 0.00 0.00 0.00 6.13
5666 11135 1.540435 GGAGGCCGGCCAAAATGAAA 61.540 55.000 45.13 0.00 38.92 2.69
5667 11136 0.108662 GAGGCCGGCCAAAATGAAAG 60.109 55.000 45.13 0.00 38.92 2.62
5680 11149 8.264347 GGCCAAAATGAAAGGGAAGAATATTAA 58.736 33.333 0.00 0.00 0.00 1.40
5684 11153 7.914427 AATGAAAGGGAAGAATATTAACCCC 57.086 36.000 15.89 12.80 41.26 4.95
5685 11154 6.668133 TGAAAGGGAAGAATATTAACCCCT 57.332 37.500 15.89 14.38 45.49 4.79
5687 11156 6.218730 TGAAAGGGAAGAATATTAACCCCTGA 59.781 38.462 17.10 6.49 42.95 3.86
5689 11158 5.297799 AGGGAAGAATATTAACCCCTGACT 58.702 41.667 16.14 0.79 42.23 3.41
5691 11160 6.559157 AGGGAAGAATATTAACCCCTGACTAG 59.441 42.308 16.14 0.00 42.23 2.57
5692 11161 6.231951 GGAAGAATATTAACCCCTGACTAGC 58.768 44.000 0.00 0.00 0.00 3.42
5693 11162 6.183361 GGAAGAATATTAACCCCTGACTAGCA 60.183 42.308 0.00 0.00 0.00 3.49
5694 11163 6.426646 AGAATATTAACCCCTGACTAGCAG 57.573 41.667 7.07 7.07 44.49 4.24
5751 11222 4.665451 TCAATTGACTGACCACATGGAAT 58.335 39.130 3.38 0.00 38.94 3.01
5783 11254 4.248058 GGTTGGCAATCTTCAAAATCCAG 58.752 43.478 1.92 0.00 0.00 3.86
5788 11259 6.189859 TGGCAATCTTCAAAATCCAGTATCT 58.810 36.000 0.00 0.00 0.00 1.98
5790 11261 7.148018 TGGCAATCTTCAAAATCCAGTATCTTC 60.148 37.037 0.00 0.00 0.00 2.87
5808 11279 1.009675 CACACTTGACCTTGCGCAC 60.010 57.895 11.12 0.00 0.00 5.34
5810 11281 3.649986 ACTTGACCTTGCGCACGC 61.650 61.111 11.12 8.33 42.35 5.34
5850 11322 3.217626 CTCCTGCCATCCTTGGAAATAC 58.782 50.000 0.00 0.00 46.92 1.89
5892 11390 3.019799 TCAGTCCCTGTCACTCTATCC 57.980 52.381 0.00 0.00 32.61 2.59
5924 11422 6.093082 TCGATCACGATAAGAAGTACAGTTCA 59.907 38.462 0.00 0.00 43.81 3.18
5931 11429 6.412362 CGATAAGAAGTACAGTTCAGATCACG 59.588 42.308 0.00 0.00 0.00 4.35
5936 11434 0.036952 ACAGTTCAGATCACGGCAGG 60.037 55.000 0.00 0.00 0.00 4.85
5942 11440 1.145598 AGATCACGGCAGGCAGATG 59.854 57.895 3.88 0.00 0.00 2.90
5944 11442 2.599645 GATCACGGCAGGCAGATGGT 62.600 60.000 3.88 0.00 0.00 3.55
5982 11480 2.421073 TCCAATCATCTTTGCTTCTGCG 59.579 45.455 0.00 0.00 43.34 5.18
6007 11507 0.036105 TGTGCAGATGCGTCAGGATT 60.036 50.000 8.99 0.00 45.83 3.01
6008 11508 0.376152 GTGCAGATGCGTCAGGATTG 59.624 55.000 8.99 0.00 45.83 2.67
6009 11509 0.036105 TGCAGATGCGTCAGGATTGT 60.036 50.000 8.99 0.00 45.83 2.71
6010 11510 1.089920 GCAGATGCGTCAGGATTGTT 58.910 50.000 8.99 0.00 0.00 2.83
6011 11511 1.202110 GCAGATGCGTCAGGATTGTTG 60.202 52.381 8.99 0.00 0.00 3.33
6013 11513 2.743664 CAGATGCGTCAGGATTGTTGAA 59.256 45.455 8.99 0.00 0.00 2.69
6014 11514 2.744202 AGATGCGTCAGGATTGTTGAAC 59.256 45.455 8.99 0.00 0.00 3.18
6015 11515 1.960417 TGCGTCAGGATTGTTGAACA 58.040 45.000 0.00 0.00 0.00 3.18
6016 11516 2.503331 TGCGTCAGGATTGTTGAACAT 58.497 42.857 0.00 0.00 0.00 2.71
6017 11517 3.669536 TGCGTCAGGATTGTTGAACATA 58.330 40.909 0.00 0.00 0.00 2.29
6018 11518 4.260985 TGCGTCAGGATTGTTGAACATAT 58.739 39.130 0.00 0.00 0.00 1.78
6019 11519 4.332543 TGCGTCAGGATTGTTGAACATATC 59.667 41.667 0.00 5.52 0.00 1.63
6020 11520 4.332543 GCGTCAGGATTGTTGAACATATCA 59.667 41.667 16.47 0.00 35.85 2.15
6021 11521 5.008019 GCGTCAGGATTGTTGAACATATCAT 59.992 40.000 16.47 10.37 38.03 2.45
6024 11524 7.191551 GTCAGGATTGTTGAACATATCATGTG 58.808 38.462 21.91 15.13 44.07 3.21
6026 11526 5.653330 AGGATTGTTGAACATATCATGTGCA 59.347 36.000 16.47 0.00 46.90 4.57
6036 11536 9.729281 TGAACATATCATGTGCATATATCTGTT 57.271 29.630 0.00 4.40 43.79 3.16
6039 11539 9.828039 ACATATCATGTGCATATATCTGTTAGG 57.172 33.333 0.00 0.00 43.01 2.69
6048 11548 9.757227 GTGCATATATCTGTTAGGATAATCTCC 57.243 37.037 0.00 0.00 45.33 3.71
6057 11557 0.903236 GGATAATCTCCTACCGGCCC 59.097 60.000 0.00 0.00 41.29 5.80
6059 11559 0.903454 ATAATCTCCTACCGGCCCCG 60.903 60.000 0.00 0.00 39.44 5.73
6071 11571 1.451567 GGCCCCGCCTCTAGTTTTC 60.452 63.158 0.00 0.00 46.69 2.29
6072 11572 1.298667 GCCCCGCCTCTAGTTTTCA 59.701 57.895 0.00 0.00 0.00 2.69
6073 11573 0.107165 GCCCCGCCTCTAGTTTTCAT 60.107 55.000 0.00 0.00 0.00 2.57
6074 11574 1.668419 CCCCGCCTCTAGTTTTCATG 58.332 55.000 0.00 0.00 0.00 3.07
6075 11575 1.065418 CCCCGCCTCTAGTTTTCATGT 60.065 52.381 0.00 0.00 0.00 3.21
6076 11576 2.169769 CCCCGCCTCTAGTTTTCATGTA 59.830 50.000 0.00 0.00 0.00 2.29
6077 11577 3.181454 CCCCGCCTCTAGTTTTCATGTAT 60.181 47.826 0.00 0.00 0.00 2.29
6079 11579 5.230942 CCCGCCTCTAGTTTTCATGTATAG 58.769 45.833 0.00 0.00 0.00 1.31
6080 11580 5.010719 CCCGCCTCTAGTTTTCATGTATAGA 59.989 44.000 0.00 0.00 0.00 1.98
6082 11582 6.587990 CCGCCTCTAGTTTTCATGTATAGATG 59.412 42.308 3.46 3.46 0.00 2.90
6085 11585 7.816995 GCCTCTAGTTTTCATGTATAGATGAGG 59.183 40.741 11.94 8.80 38.19 3.86
6087 11587 8.484214 TCTAGTTTTCATGTATAGATGAGGCT 57.516 34.615 11.94 12.80 33.86 4.58
6088 11588 8.363390 TCTAGTTTTCATGTATAGATGAGGCTG 58.637 37.037 11.94 3.91 33.86 4.85
6090 11590 7.215789 AGTTTTCATGTATAGATGAGGCTGAG 58.784 38.462 11.94 0.00 33.86 3.35
6092 11592 4.092279 TCATGTATAGATGAGGCTGAGGG 58.908 47.826 8.43 0.00 0.00 4.30
6093 11593 2.251818 TGTATAGATGAGGCTGAGGGC 58.748 52.381 0.00 0.00 40.90 5.19
6108 11608 3.970205 GGGCTGCCCTTGTACTTTA 57.030 52.632 30.42 0.00 41.34 1.85
6109 11609 2.437085 GGGCTGCCCTTGTACTTTAT 57.563 50.000 30.42 0.00 41.34 1.40
6110 11610 3.570912 GGGCTGCCCTTGTACTTTATA 57.429 47.619 30.42 0.00 41.34 0.98
6112 11612 5.237236 GGGCTGCCCTTGTACTTTATATA 57.763 43.478 30.42 0.00 41.34 0.86
6113 11613 5.001874 GGGCTGCCCTTGTACTTTATATAC 58.998 45.833 30.42 0.00 41.34 1.47
6114 11614 4.689345 GGCTGCCCTTGTACTTTATATACG 59.311 45.833 7.66 0.00 0.00 3.06
6115 11615 5.295152 GCTGCCCTTGTACTTTATATACGT 58.705 41.667 0.00 0.00 0.00 3.57
6117 11617 5.051816 TGCCCTTGTACTTTATATACGTGC 58.948 41.667 0.00 0.00 0.00 5.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.422546 TTTTTCTCACGTGTTTTCGGTT 57.577 36.364 16.51 0.00 34.94 4.44
25 26 4.159693 GTGCTCCCTCCGGATTTTATTTTT 59.840 41.667 3.57 0.00 37.60 1.94
26 27 3.699538 GTGCTCCCTCCGGATTTTATTTT 59.300 43.478 3.57 0.00 37.60 1.82
27 28 3.288092 GTGCTCCCTCCGGATTTTATTT 58.712 45.455 3.57 0.00 37.60 1.40
28 29 2.422945 GGTGCTCCCTCCGGATTTTATT 60.423 50.000 3.57 0.00 37.60 1.40
30 31 0.544697 GGTGCTCCCTCCGGATTTTA 59.455 55.000 3.57 0.00 37.60 1.52
42 43 1.451028 GTCATGCTCTGGGTGCTCC 60.451 63.158 0.00 0.00 0.00 4.70
43 44 1.023513 GTGTCATGCTCTGGGTGCTC 61.024 60.000 0.00 0.00 0.00 4.26
44 45 1.002868 GTGTCATGCTCTGGGTGCT 60.003 57.895 0.00 0.00 0.00 4.40
45 46 2.393768 CGTGTCATGCTCTGGGTGC 61.394 63.158 0.00 0.00 0.00 5.01
46 47 0.246360 TACGTGTCATGCTCTGGGTG 59.754 55.000 0.00 0.00 0.00 4.61
49 50 0.992072 CGTTACGTGTCATGCTCTGG 59.008 55.000 0.00 0.00 0.00 3.86
50 51 1.977188 TCGTTACGTGTCATGCTCTG 58.023 50.000 4.24 0.00 0.00 3.35
51 52 2.717580 TTCGTTACGTGTCATGCTCT 57.282 45.000 4.24 0.00 0.00 4.09
53 54 2.666508 GTCATTCGTTACGTGTCATGCT 59.333 45.455 4.24 0.00 0.00 3.79
54 55 2.666508 AGTCATTCGTTACGTGTCATGC 59.333 45.455 4.24 1.44 0.00 4.06
55 56 3.917985 TCAGTCATTCGTTACGTGTCATG 59.082 43.478 4.24 3.98 0.00 3.07
57 58 3.251487 TCTCAGTCATTCGTTACGTGTCA 59.749 43.478 4.24 0.00 0.00 3.58
58 59 3.818387 TCTCAGTCATTCGTTACGTGTC 58.182 45.455 4.24 0.00 0.00 3.67
62 63 1.840741 CGCTCTCAGTCATTCGTTACG 59.159 52.381 0.00 0.00 0.00 3.18
65 66 1.073216 CGCGCTCTCAGTCATTCGTT 61.073 55.000 5.56 0.00 0.00 3.85
67 68 2.854214 GCGCGCTCTCAGTCATTCG 61.854 63.158 26.67 0.00 0.00 3.34
68 69 1.354337 TTGCGCGCTCTCAGTCATTC 61.354 55.000 33.29 0.00 0.00 2.67
69 70 1.357258 CTTGCGCGCTCTCAGTCATT 61.357 55.000 33.29 0.00 0.00 2.57
72 73 2.431601 ACTTGCGCGCTCTCAGTC 60.432 61.111 33.29 0.00 0.00 3.51
73 74 2.736236 CACTTGCGCGCTCTCAGT 60.736 61.111 33.29 23.59 0.00 3.41
74 75 2.431430 TCACTTGCGCGCTCTCAG 60.431 61.111 33.29 22.94 0.00 3.35
75 76 2.699576 AAGTCACTTGCGCGCTCTCA 62.700 55.000 33.29 9.09 0.00 3.27
77 78 0.319555 TAAAGTCACTTGCGCGCTCT 60.320 50.000 33.29 16.53 0.00 4.09
78 79 0.511221 TTAAAGTCACTTGCGCGCTC 59.489 50.000 33.29 14.60 0.00 5.03
79 80 1.128692 GATTAAAGTCACTTGCGCGCT 59.871 47.619 33.29 9.55 0.00 5.92
84 85 2.902484 CGCAACGATTAAAGTCACTTGC 59.098 45.455 0.00 0.00 32.27 4.01
87 88 3.673809 GTCTCGCAACGATTAAAGTCACT 59.326 43.478 0.00 0.00 34.61 3.41
89 90 3.909430 AGTCTCGCAACGATTAAAGTCA 58.091 40.909 0.00 0.00 34.61 3.41
90 91 3.303760 GGAGTCTCGCAACGATTAAAGTC 59.696 47.826 0.00 0.00 34.61 3.01
92 93 3.304559 CAGGAGTCTCGCAACGATTAAAG 59.695 47.826 0.00 0.00 34.61 1.85
93 94 3.057104 TCAGGAGTCTCGCAACGATTAAA 60.057 43.478 0.00 0.00 34.61 1.52
94 95 2.490509 TCAGGAGTCTCGCAACGATTAA 59.509 45.455 0.00 0.00 34.61 1.40
96 97 0.888619 TCAGGAGTCTCGCAACGATT 59.111 50.000 0.00 0.00 34.61 3.34
97 98 0.888619 TTCAGGAGTCTCGCAACGAT 59.111 50.000 0.00 0.00 34.61 3.73
98 99 0.241213 CTTCAGGAGTCTCGCAACGA 59.759 55.000 0.00 0.00 0.00 3.85
99 100 0.734253 CCTTCAGGAGTCTCGCAACG 60.734 60.000 0.00 0.00 37.39 4.10
100 101 0.603569 TCCTTCAGGAGTCTCGCAAC 59.396 55.000 0.00 0.00 39.78 4.17
101 102 3.051617 TCCTTCAGGAGTCTCGCAA 57.948 52.632 0.00 0.00 39.78 4.85
110 111 1.919240 TAACGAGCACTCCTTCAGGA 58.081 50.000 0.00 0.00 43.08 3.86
112 113 3.305398 AGTTAACGAGCACTCCTTCAG 57.695 47.619 0.00 0.00 0.00 3.02
114 115 4.437772 ACTAGTTAACGAGCACTCCTTC 57.562 45.455 14.82 0.00 0.00 3.46
116 117 3.614390 GCAACTAGTTAACGAGCACTCCT 60.614 47.826 14.82 0.00 0.00 3.69
117 118 2.666994 GCAACTAGTTAACGAGCACTCC 59.333 50.000 14.82 0.00 0.00 3.85
118 119 3.576648 AGCAACTAGTTAACGAGCACTC 58.423 45.455 14.82 3.42 0.00 3.51
120 121 4.377124 GGAAAGCAACTAGTTAACGAGCAC 60.377 45.833 14.82 5.58 0.00 4.40
121 122 3.744426 GGAAAGCAACTAGTTAACGAGCA 59.256 43.478 14.82 0.00 0.00 4.26
123 124 4.989168 ACAGGAAAGCAACTAGTTAACGAG 59.011 41.667 13.50 13.50 0.00 4.18
124 125 4.952460 ACAGGAAAGCAACTAGTTAACGA 58.048 39.130 8.04 0.00 0.00 3.85
125 126 5.668558 AACAGGAAAGCAACTAGTTAACG 57.331 39.130 8.04 0.00 0.00 3.18
126 127 7.222031 CCAAAAACAGGAAAGCAACTAGTTAAC 59.778 37.037 8.04 3.72 0.00 2.01
128 129 6.183360 CCCAAAAACAGGAAAGCAACTAGTTA 60.183 38.462 8.04 0.00 0.00 2.24
130 131 4.099419 CCCAAAAACAGGAAAGCAACTAGT 59.901 41.667 0.00 0.00 0.00 2.57
132 133 3.386402 CCCCAAAAACAGGAAAGCAACTA 59.614 43.478 0.00 0.00 0.00 2.24
133 134 2.170397 CCCCAAAAACAGGAAAGCAACT 59.830 45.455 0.00 0.00 0.00 3.16
134 135 2.093181 ACCCCAAAAACAGGAAAGCAAC 60.093 45.455 0.00 0.00 0.00 4.17
135 136 2.169561 GACCCCAAAAACAGGAAAGCAA 59.830 45.455 0.00 0.00 0.00 3.91
136 137 1.760029 GACCCCAAAAACAGGAAAGCA 59.240 47.619 0.00 0.00 0.00 3.91
137 138 1.760029 TGACCCCAAAAACAGGAAAGC 59.240 47.619 0.00 0.00 0.00 3.51
138 139 3.031013 AGTGACCCCAAAAACAGGAAAG 58.969 45.455 0.00 0.00 0.00 2.62
139 140 3.108847 AGTGACCCCAAAAACAGGAAA 57.891 42.857 0.00 0.00 0.00 3.13
141 142 2.243736 AGAAGTGACCCCAAAAACAGGA 59.756 45.455 0.00 0.00 0.00 3.86
142 143 2.666317 AGAAGTGACCCCAAAAACAGG 58.334 47.619 0.00 0.00 0.00 4.00
260 266 3.062466 TCGTCTGCCGAGGTGAGG 61.062 66.667 0.00 0.00 41.60 3.86
272 278 0.742281 GCCATGTGTCATGCTCGTCT 60.742 55.000 4.43 0.00 0.00 4.18
326 356 1.643292 CAACGAGTATGCATGCCCG 59.357 57.895 16.60 16.60 0.00 6.13
332 362 1.447140 GCCGACCAACGAGTATGCA 60.447 57.895 0.00 0.00 45.77 3.96
333 363 2.171725 GGCCGACCAACGAGTATGC 61.172 63.158 0.00 0.00 45.77 3.14
337 367 4.003788 CCAGGCCGACCAACGAGT 62.004 66.667 0.00 0.00 45.77 4.18
338 368 2.162338 TAACCAGGCCGACCAACGAG 62.162 60.000 0.00 0.00 45.77 4.18
345 375 1.092348 GACCATTTAACCAGGCCGAC 58.908 55.000 0.00 0.00 0.00 4.79
349 379 2.507407 TGAGGACCATTTAACCAGGC 57.493 50.000 0.00 0.00 0.00 4.85
354 384 4.336713 GGAAGCTGATGAGGACCATTTAAC 59.663 45.833 0.00 0.00 35.17 2.01
356 386 3.117888 GGGAAGCTGATGAGGACCATTTA 60.118 47.826 0.00 0.00 35.17 1.40
357 387 2.357569 GGGAAGCTGATGAGGACCATTT 60.358 50.000 0.00 0.00 35.17 2.32
358 388 1.213926 GGGAAGCTGATGAGGACCATT 59.786 52.381 0.00 0.00 35.17 3.16
359 389 0.842635 GGGAAGCTGATGAGGACCAT 59.157 55.000 0.00 0.00 38.43 3.55
360 390 1.617018 CGGGAAGCTGATGAGGACCA 61.617 60.000 0.00 0.00 0.00 4.02
361 391 1.144936 CGGGAAGCTGATGAGGACC 59.855 63.158 0.00 0.00 0.00 4.46
362 392 0.103937 CTCGGGAAGCTGATGAGGAC 59.896 60.000 0.00 0.00 0.00 3.85
363 393 2.509512 CTCGGGAAGCTGATGAGGA 58.490 57.895 0.00 0.00 0.00 3.71
364 394 1.445095 CCTCGGGAAGCTGATGAGG 59.555 63.158 9.38 9.38 40.19 3.86
365 395 1.227497 GCCTCGGGAAGCTGATGAG 60.227 63.158 0.00 0.00 0.00 2.90
366 396 2.735772 GGCCTCGGGAAGCTGATGA 61.736 63.158 0.00 0.00 0.00 2.92
367 397 2.203126 GGCCTCGGGAAGCTGATG 60.203 66.667 0.00 0.00 0.00 3.07
368 398 3.854669 CGGCCTCGGGAAGCTGAT 61.855 66.667 0.00 0.00 37.58 2.90
398 428 2.430367 AGGTGGGCCTCGTGAAAC 59.570 61.111 4.53 0.00 42.67 2.78
493 523 2.004583 CTATGTGTGTACACCACCGG 57.995 55.000 22.91 0.00 45.88 5.28
519 549 7.170998 AGTTTGACTACACAGAAATTTAGGTCG 59.829 37.037 0.00 0.00 0.00 4.79
588 618 0.503117 GCGCTCTCCTAATAAACGCG 59.497 55.000 3.53 3.53 41.74 6.01
747 784 4.400251 TCTCCAGCAGCTTATTTTTCATGG 59.600 41.667 0.00 0.00 0.00 3.66
757 796 1.871418 AGACCATCTCCAGCAGCTTA 58.129 50.000 0.00 0.00 0.00 3.09
798 837 1.609072 CCGACTATGCAATCCGAGAGA 59.391 52.381 0.00 0.00 0.00 3.10
801 840 0.946221 GCCCGACTATGCAATCCGAG 60.946 60.000 0.00 0.00 0.00 4.63
1171 1234 1.152139 GGGGAGATCTGGGGAGGAG 60.152 68.421 0.00 0.00 0.00 3.69
1338 1421 5.096215 CCGTCAGGGAAAAATCGAGAGAAA 61.096 45.833 0.00 0.00 40.99 2.52
1340 1423 2.094182 CCGTCAGGGAAAAATCGAGAGA 60.094 50.000 0.00 0.00 41.75 3.10
1341 1424 2.271800 CCGTCAGGGAAAAATCGAGAG 58.728 52.381 0.00 0.00 38.47 3.20
1342 1425 1.674817 GCCGTCAGGGAAAAATCGAGA 60.675 52.381 0.00 0.00 38.47 4.04
1724 1833 6.708054 AGTGAGAAGAGTGGTACAAAATGAAG 59.292 38.462 0.00 0.00 44.16 3.02
1737 1846 4.843220 AATTTTGGCAGTGAGAAGAGTG 57.157 40.909 0.00 0.00 0.00 3.51
1751 1860 2.240279 TCACGGGTGGGTTAATTTTGG 58.760 47.619 0.00 0.00 0.00 3.28
1768 1878 1.532007 TCAACCGTTTGGCGTTATCAC 59.468 47.619 0.00 0.00 39.70 3.06
1778 1888 3.374058 AGTGTTCTCTGTTCAACCGTTTG 59.626 43.478 0.00 0.00 0.00 2.93
1781 1891 2.167693 TCAGTGTTCTCTGTTCAACCGT 59.832 45.455 0.00 0.00 36.85 4.83
1783 1893 3.798202 AGTCAGTGTTCTCTGTTCAACC 58.202 45.455 0.00 0.00 36.85 3.77
1829 1939 3.851105 GCTGTGTCAAATCAGTGCAGTTC 60.851 47.826 0.00 0.00 34.57 3.01
1830 1940 2.033801 GCTGTGTCAAATCAGTGCAGTT 59.966 45.455 0.00 0.00 34.57 3.16
1832 1942 1.605232 TGCTGTGTCAAATCAGTGCAG 59.395 47.619 0.00 0.00 34.57 4.41
1834 1944 1.068748 CCTGCTGTGTCAAATCAGTGC 60.069 52.381 0.00 0.00 34.57 4.40
1835 1945 2.224606 ACCTGCTGTGTCAAATCAGTG 58.775 47.619 0.00 0.00 34.57 3.66
1836 1946 2.620115 CAACCTGCTGTGTCAAATCAGT 59.380 45.455 0.00 0.00 34.57 3.41
1837 1947 2.880268 TCAACCTGCTGTGTCAAATCAG 59.120 45.455 0.00 0.00 35.12 2.90
1838 1948 2.929641 TCAACCTGCTGTGTCAAATCA 58.070 42.857 0.00 0.00 0.00 2.57
1840 1950 4.655963 ACTATCAACCTGCTGTGTCAAAT 58.344 39.130 0.00 0.00 0.00 2.32
1841 1951 4.085357 ACTATCAACCTGCTGTGTCAAA 57.915 40.909 0.00 0.00 0.00 2.69
1842 1952 3.769739 ACTATCAACCTGCTGTGTCAA 57.230 42.857 0.00 0.00 0.00 3.18
2041 2151 2.880890 AGTTGCATCACAGTTGTTCTCC 59.119 45.455 0.00 0.00 0.00 3.71
2057 2167 1.300388 CCCAAAGCAGTGCAGTTGC 60.300 57.895 19.20 13.80 41.83 4.17
2058 2168 0.031178 GTCCCAAAGCAGTGCAGTTG 59.969 55.000 19.20 19.35 0.00 3.16
2163 2277 5.640357 ACGTTCGGCAATTAGAATTAGAACA 59.360 36.000 19.04 0.00 36.89 3.18
2181 2295 1.648504 GGGATCCTGGTTTACGTTCG 58.351 55.000 12.58 0.00 0.00 3.95
2398 2512 3.831911 TGCACAAAAGGGGGAAATTCTAG 59.168 43.478 0.00 0.00 0.00 2.43
2401 2515 3.244526 ACATGCACAAAAGGGGGAAATTC 60.245 43.478 0.00 0.00 0.00 2.17
2402 2516 2.710471 ACATGCACAAAAGGGGGAAATT 59.290 40.909 0.00 0.00 0.00 1.82
2411 2525 1.068055 GCCAGAGGACATGCACAAAAG 60.068 52.381 0.00 0.00 0.00 2.27
2420 2534 5.184892 AGTAAATTTCAGCCAGAGGACAT 57.815 39.130 0.00 0.00 0.00 3.06
2422 2536 5.966742 AAAGTAAATTTCAGCCAGAGGAC 57.033 39.130 0.00 0.00 0.00 3.85
2491 2613 9.304731 TCATTTGTCTTTCTGTTTTCTTCATTG 57.695 29.630 0.00 0.00 0.00 2.82
2604 2726 6.706055 ATAATTCTTATGCACATCGTACCG 57.294 37.500 0.00 0.00 0.00 4.02
2612 2734 9.219603 GCTATCAAGGTATAATTCTTATGCACA 57.780 33.333 0.00 0.00 30.88 4.57
2626 2748 8.023021 TGTAGTCTTTCATGCTATCAAGGTAT 57.977 34.615 0.00 0.00 0.00 2.73
3212 3341 3.920231 AGCTGCTTCCACTCATGAATA 57.080 42.857 0.00 0.00 0.00 1.75
3307 3436 3.563390 GTCCCTTGATTAGAGCTCAATGC 59.437 47.826 17.77 3.08 43.29 3.56
3446 3575 3.317993 ACCAAAGCACAAAAGAACGCTAT 59.682 39.130 0.00 0.00 33.45 2.97
3681 3810 7.603024 ACTGACTTTAGGCACAGAGTTATTAAC 59.397 37.037 0.00 0.00 34.88 2.01
3708 3837 4.743493 ACATTCACACACCAAGTTTCAAC 58.257 39.130 0.00 0.00 0.00 3.18
3738 3867 7.895429 TCAGGGATAAAATGAGGTCAGATTTTT 59.105 33.333 0.00 0.00 34.42 1.94
3885 4021 4.785346 ATGTGGCAGAATAGAATCCACT 57.215 40.909 10.53 0.00 45.43 4.00
4179 4322 8.736244 ACCAATTACCTGTTTATGTTGATGTAC 58.264 33.333 0.00 0.00 0.00 2.90
4307 4452 1.485210 GGCCCATAGGTACCCTCTGAT 60.485 57.143 8.74 0.00 34.61 2.90
4473 7614 6.729690 TTCTGATCAACCAAGAAAACCAAT 57.270 33.333 0.00 0.00 0.00 3.16
4798 9989 8.760103 TTGTTTTAGTACAAAGACCCAAAAAC 57.240 30.769 0.00 0.00 35.22 2.43
4817 10008 4.259933 AGTAGGAACCCTGGTTTGTTTT 57.740 40.909 2.55 0.00 38.60 2.43
4818 10009 3.965470 AGTAGGAACCCTGGTTTGTTT 57.035 42.857 2.55 0.00 38.60 2.83
5319 10645 5.104485 AGGTCAGGTTGTTCTTCTACACTTT 60.104 40.000 0.00 0.00 0.00 2.66
5360 10686 2.596346 TGGCAGTGTCCATGAAAACAT 58.404 42.857 0.00 0.00 0.00 2.71
5409 10737 0.962356 ATGGCAGCAAAGAAGACCGG 60.962 55.000 0.00 0.00 0.00 5.28
5411 10739 0.529378 CCATGGCAGCAAAGAAGACC 59.471 55.000 0.00 0.00 0.00 3.85
5412 10740 1.200948 GTCCATGGCAGCAAAGAAGAC 59.799 52.381 6.96 0.00 0.00 3.01
5440 10768 5.534278 TGTTCACTAGTTTGCATGGAATTCA 59.466 36.000 7.93 0.00 0.00 2.57
5479 10944 5.481105 CAAGATTTACAATGCCCACAACAT 58.519 37.500 0.00 0.00 0.00 2.71
5481 10946 3.679502 GCAAGATTTACAATGCCCACAAC 59.320 43.478 0.00 0.00 32.73 3.32
5488 10953 7.306167 CCAATATTCGTGCAAGATTTACAATGC 60.306 37.037 2.36 0.00 39.22 3.56
5509 10975 1.206132 ACGAACGCTGTGGATCCAATA 59.794 47.619 18.20 7.95 0.00 1.90
5541 11007 3.131709 AGGCGGATTTATGGTGAGATG 57.868 47.619 0.00 0.00 0.00 2.90
5576 11045 0.321298 CGGACAAACGGAGGGTTCAT 60.321 55.000 0.00 0.00 38.08 2.57
5581 11050 1.080025 GTCTCGGACAAACGGAGGG 60.080 63.158 0.00 0.00 43.26 4.30
5607 11076 2.910360 CTCCATGGATGCCCACGA 59.090 61.111 16.63 0.00 46.98 4.35
5625 11094 1.066573 CCAAGTAGCCTGTGGTCTGAG 60.067 57.143 0.00 0.00 0.00 3.35
5626 11095 0.976641 CCAAGTAGCCTGTGGTCTGA 59.023 55.000 0.00 0.00 0.00 3.27
5628 11097 1.270907 CTCCAAGTAGCCTGTGGTCT 58.729 55.000 0.00 0.00 33.88 3.85
5632 11101 0.539051 CCTCCTCCAAGTAGCCTGTG 59.461 60.000 0.00 0.00 0.00 3.66
5654 11123 4.558226 ATTCTTCCCTTTCATTTTGGCC 57.442 40.909 0.00 0.00 0.00 5.36
5666 11135 5.297799 AGTCAGGGGTTAATATTCTTCCCT 58.702 41.667 13.60 13.60 44.89 4.20
5667 11136 5.648330 AGTCAGGGGTTAATATTCTTCCC 57.352 43.478 11.72 11.72 37.59 3.97
5680 11149 0.115349 AGTGTCTGCTAGTCAGGGGT 59.885 55.000 12.35 0.00 43.06 4.95
5716 11187 3.316308 AGTCAATTGAAGTGTCAGTTGCC 59.684 43.478 10.35 0.00 46.03 4.52
5727 11198 4.074259 TCCATGTGGTCAGTCAATTGAAG 58.926 43.478 10.35 6.27 36.34 3.02
5751 11222 3.979911 AGATTGCCAACCACATAATCCA 58.020 40.909 0.00 0.00 0.00 3.41
5752 11223 4.402155 TGAAGATTGCCAACCACATAATCC 59.598 41.667 0.00 0.00 0.00 3.01
5753 11224 5.581126 TGAAGATTGCCAACCACATAATC 57.419 39.130 0.00 0.00 0.00 1.75
5754 11225 5.999205 TTGAAGATTGCCAACCACATAAT 57.001 34.783 0.00 0.00 0.00 1.28
5755 11226 5.798125 TTTGAAGATTGCCAACCACATAA 57.202 34.783 0.00 0.00 0.00 1.90
5783 11254 3.123621 CGCAAGGTCAAGTGTGAAGATAC 59.876 47.826 0.00 0.00 34.87 2.24
5788 11259 0.746204 TGCGCAAGGTCAAGTGTGAA 60.746 50.000 8.16 0.00 34.22 3.18
5790 11261 1.009675 GTGCGCAAGGTCAAGTGTG 60.010 57.895 14.00 0.00 38.28 3.82
5824 11296 1.001641 AAGGATGGCAGGAGCACAC 60.002 57.895 0.00 0.00 44.61 3.82
5825 11297 1.001764 CAAGGATGGCAGGAGCACA 60.002 57.895 0.00 0.00 44.61 4.57
5850 11322 8.618677 ACTGATGTGCATTGATAAATTCTACAG 58.381 33.333 0.00 0.00 0.00 2.74
5911 11409 3.367498 GCCGTGATCTGAACTGTACTTCT 60.367 47.826 0.00 0.00 0.00 2.85
5912 11410 2.924290 GCCGTGATCTGAACTGTACTTC 59.076 50.000 0.00 0.00 0.00 3.01
5914 11412 1.893137 TGCCGTGATCTGAACTGTACT 59.107 47.619 0.00 0.00 0.00 2.73
5919 11417 1.078848 GCCTGCCGTGATCTGAACT 60.079 57.895 0.00 0.00 0.00 3.01
5924 11422 1.145598 CATCTGCCTGCCGTGATCT 59.854 57.895 0.00 0.00 0.00 2.75
5931 11429 1.890979 CGATCACCATCTGCCTGCC 60.891 63.158 0.00 0.00 0.00 4.85
5936 11434 2.463620 TTGCGCGATCACCATCTGC 61.464 57.895 12.10 0.00 0.00 4.26
5997 11497 4.332543 TGATATGTTCAACAATCCTGACGC 59.667 41.667 0.00 0.00 0.00 5.19
6000 11500 6.183360 GCACATGATATGTTCAACAATCCTGA 60.183 38.462 16.96 1.94 42.70 3.86
6007 11507 9.729281 AGATATATGCACATGATATGTTCAACA 57.271 29.630 0.00 0.00 42.70 3.33
6008 11508 9.983804 CAGATATATGCACATGATATGTTCAAC 57.016 33.333 0.00 0.00 42.70 3.18
6009 11509 9.729281 ACAGATATATGCACATGATATGTTCAA 57.271 29.630 0.00 0.00 42.70 2.69
6010 11510 9.729281 AACAGATATATGCACATGATATGTTCA 57.271 29.630 0.00 0.00 42.70 3.18
6013 11513 9.828039 CCTAACAGATATATGCACATGATATGT 57.172 33.333 0.00 0.00 46.22 2.29
6039 11539 0.903236 GGGGCCGGTAGGAGATTATC 59.097 60.000 1.90 0.00 41.02 1.75
6041 11541 1.532316 CGGGGCCGGTAGGAGATTA 60.532 63.158 1.90 0.00 41.02 1.75
6042 11542 2.842936 CGGGGCCGGTAGGAGATT 60.843 66.667 1.90 0.00 41.02 2.40
6054 11554 0.107165 ATGAAAACTAGAGGCGGGGC 60.107 55.000 0.00 0.00 0.00 5.80
6055 11555 1.065418 ACATGAAAACTAGAGGCGGGG 60.065 52.381 0.00 0.00 0.00 5.73
6056 11556 2.403252 ACATGAAAACTAGAGGCGGG 57.597 50.000 0.00 0.00 0.00 6.13
6057 11557 6.085555 TCTATACATGAAAACTAGAGGCGG 57.914 41.667 0.00 0.00 0.00 6.13
6059 11559 7.816995 CCTCATCTATACATGAAAACTAGAGGC 59.183 40.741 0.00 0.00 32.24 4.70
6060 11560 7.816995 GCCTCATCTATACATGAAAACTAGAGG 59.183 40.741 0.00 9.57 39.40 3.69
6061 11561 8.584157 AGCCTCATCTATACATGAAAACTAGAG 58.416 37.037 0.00 0.00 32.24 2.43
6064 11564 8.250143 TCAGCCTCATCTATACATGAAAACTA 57.750 34.615 0.00 0.00 32.24 2.24
6066 11566 6.426328 CCTCAGCCTCATCTATACATGAAAAC 59.574 42.308 0.00 0.00 32.24 2.43
6067 11567 6.464892 CCCTCAGCCTCATCTATACATGAAAA 60.465 42.308 0.00 0.00 32.24 2.29
6068 11568 5.012458 CCCTCAGCCTCATCTATACATGAAA 59.988 44.000 0.00 0.00 32.24 2.69
6069 11569 4.529769 CCCTCAGCCTCATCTATACATGAA 59.470 45.833 0.00 0.00 32.24 2.57
6071 11571 3.369261 GCCCTCAGCCTCATCTATACATG 60.369 52.174 0.00 0.00 34.35 3.21
6072 11572 2.836981 GCCCTCAGCCTCATCTATACAT 59.163 50.000 0.00 0.00 34.35 2.29
6073 11573 2.158249 AGCCCTCAGCCTCATCTATACA 60.158 50.000 0.00 0.00 45.47 2.29
6074 11574 2.233431 CAGCCCTCAGCCTCATCTATAC 59.767 54.545 0.00 0.00 45.47 1.47
6075 11575 2.533916 CAGCCCTCAGCCTCATCTATA 58.466 52.381 0.00 0.00 45.47 1.31
6076 11576 1.350071 CAGCCCTCAGCCTCATCTAT 58.650 55.000 0.00 0.00 45.47 1.98
6077 11577 1.406065 GCAGCCCTCAGCCTCATCTA 61.406 60.000 0.00 0.00 45.47 1.98
6079 11579 2.203181 GCAGCCCTCAGCCTCATC 60.203 66.667 0.00 0.00 45.47 2.92
6090 11590 2.437085 ATAAAGTACAAGGGCAGCCC 57.563 50.000 24.90 24.90 45.90 5.19
6092 11592 5.176958 CACGTATATAAAGTACAAGGGCAGC 59.823 44.000 0.00 0.00 0.00 5.25
6093 11593 5.176958 GCACGTATATAAAGTACAAGGGCAG 59.823 44.000 0.00 0.00 0.00 4.85


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

AutoCloner maintained by Alex Coulton.