Multiple sequence alignment - TraesCS5D01G373900

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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 TraesCS5D01G373900 chr5D 100.000 4101 0 0 1 4101 447204178 447208278 0.000000e+00 7574.0
1 TraesCS5D01G373900 chr5D 98.303 766 13 0 3336 4101 447214343 447215108 0.000000e+00 1343.0
2 TraesCS5D01G373900 chr5D 97.914 767 15 1 3336 4101 119726287 119727053 0.000000e+00 1327.0
3 TraesCS5D01G373900 chr5D 84.890 953 119 13 1633 2581 230638807 230639738 0.000000e+00 939.0
4 TraesCS5D01G373900 chr5D 84.696 954 119 15 1633 2581 447237551 447238482 0.000000e+00 928.0
5 TraesCS5D01G373900 chr5D 88.866 494 45 6 2643 3128 447238798 447239289 2.110000e-167 599.0
6 TraesCS5D01G373900 chr5D 81.880 585 64 26 836 1393 447236479 447237048 4.830000e-124 455.0
7 TraesCS5D01G373900 chr5D 84.672 274 31 4 2308 2581 442366886 442367148 3.140000e-66 263.0
8 TraesCS5D01G373900 chr5A 93.164 1653 102 8 1686 3333 565404402 565402756 0.000000e+00 2416.0
9 TraesCS5D01G373900 chr5A 83.874 986 107 20 1633 2581 565397765 565396795 0.000000e+00 893.0
10 TraesCS5D01G373900 chr5A 91.039 491 38 6 141 627 565407461 565406973 0.000000e+00 658.0
11 TraesCS5D01G373900 chr5A 93.662 426 17 4 741 1163 565405419 565405001 2.690000e-176 628.0
12 TraesCS5D01G373900 chr5A 91.200 375 29 3 2742 3112 565396332 565395958 1.320000e-139 507.0
13 TraesCS5D01G373900 chr5A 82.828 594 57 23 836 1393 565398865 565398281 1.320000e-134 490.0
14 TraesCS5D01G373900 chr5A 86.799 303 30 8 1163 1462 565404960 565404665 3.060000e-86 329.0
15 TraesCS5D01G373900 chr5A 92.079 101 2 5 3 100 85355254 85355351 1.990000e-28 137.0
16 TraesCS5D01G373900 chr5A 88.750 80 5 2 2643 2720 565396479 565396402 1.210000e-15 95.3
17 TraesCS5D01G373900 chr4D 98.044 767 14 1 3336 4101 319101640 319102406 0.000000e+00 1332.0
18 TraesCS5D01G373900 chr4D 84.307 274 32 4 2308 2581 3464961 3465223 1.460000e-64 257.0
19 TraesCS5D01G373900 chr1D 97.795 771 16 1 3332 4101 54188695 54187925 0.000000e+00 1328.0
20 TraesCS5D01G373900 chr1D 97.668 772 13 2 3334 4101 462189265 462190035 0.000000e+00 1321.0
21 TraesCS5D01G373900 chr6D 97.908 765 15 1 3338 4101 270702324 270701560 0.000000e+00 1323.0
22 TraesCS5D01G373900 chr6D 84.890 953 119 13 1633 2581 15852579 15851648 0.000000e+00 939.0
23 TraesCS5D01G373900 chr6D 92.391 184 14 0 1210 1393 15853253 15853070 3.140000e-66 263.0
24 TraesCS5D01G373900 chr7D 97.784 767 16 1 3336 4101 439602195 439602961 0.000000e+00 1321.0
25 TraesCS5D01G373900 chr2D 97.784 767 16 1 3336 4101 372484185 372483419 0.000000e+00 1321.0
26 TraesCS5D01G373900 chr2D 97.653 767 17 1 3335 4101 401555520 401554755 0.000000e+00 1315.0
27 TraesCS5D01G373900 chr2D 83.529 85 8 6 3128 3209 648576270 648576351 1.580000e-09 75.0
28 TraesCS5D01G373900 chr5B 92.191 922 61 8 1686 2604 545429176 545428263 0.000000e+00 1293.0
29 TraesCS5D01G373900 chr5B 94.041 688 33 6 2652 3333 545428264 545427579 0.000000e+00 1037.0
30 TraesCS5D01G373900 chr5B 86.207 870 103 10 1699 2566 545408285 545407431 0.000000e+00 926.0
31 TraesCS5D01G373900 chr5B 86.478 673 52 20 750 1394 545430288 545429627 0.000000e+00 702.0
32 TraesCS5D01G373900 chr5B 85.127 511 52 10 139 627 545466569 545466061 6.120000e-138 501.0
33 TraesCS5D01G373900 chr5B 82.992 488 38 18 942 1393 545409324 545408846 2.300000e-107 399.0
34 TraesCS5D01G373900 chr5B 85.455 385 51 3 2748 3127 545407015 545406631 2.970000e-106 396.0
35 TraesCS5D01G373900 chr5B 90.580 276 14 4 727 1002 545486070 545485807 5.040000e-94 355.0
36 TraesCS5D01G373900 chr1B 82.225 962 131 22 1623 2574 159410094 159409163 0.000000e+00 793.0
37 TraesCS5D01G373900 chr1B 88.660 97 5 1 3 99 16507994 16507904 3.350000e-21 113.0
38 TraesCS5D01G373900 chr1A 93.137 102 3 4 3 100 548445054 548445155 3.300000e-31 147.0
39 TraesCS5D01G373900 chr1A 90.000 100 5 3 3 99 1800829 1800926 1.550000e-24 124.0
40 TraesCS5D01G373900 chr3A 91.089 101 6 3 3 100 744793499 744793399 2.570000e-27 134.0
41 TraesCS5D01G373900 chr3A 93.750 48 2 1 3128 3175 702010680 702010726 2.050000e-08 71.3
42 TraesCS5D01G373900 chrUn 90.909 99 8 1 3 100 71298344 71298442 9.250000e-27 132.0
43 TraesCS5D01G373900 chr7A 92.391 92 5 2 7 97 2571706 2571616 3.330000e-26 130.0
44 TraesCS5D01G373900 chr7A 86.667 90 6 6 3126 3210 485190697 485190785 1.210000e-15 95.3
45 TraesCS5D01G373900 chr6B 93.103 87 3 3 3 87 25265159 25265244 1.550000e-24 124.0
46 TraesCS5D01G373900 chr6B 93.750 48 1 2 3128 3174 625380790 625380744 2.050000e-08 71.3
47 TraesCS5D01G373900 chr7B 88.776 98 10 1 1 98 517056749 517056845 7.200000e-23 119.0
48 TraesCS5D01G373900 chr7B 87.500 88 4 6 3126 3210 246514703 246514620 1.210000e-15 95.3
49 TraesCS5D01G373900 chr7B 95.349 43 1 1 3128 3170 164586162 164586203 2.650000e-07 67.6
50 TraesCS5D01G373900 chr2B 95.349 43 1 1 3128 3170 422982237 422982278 2.650000e-07 67.6


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 TraesCS5D01G373900 chr5D 447204178 447208278 4100 False 7574.000000 7574 100.000000 1 4101 1 chr5D.!!$F4 4100
1 TraesCS5D01G373900 chr5D 447214343 447215108 765 False 1343.000000 1343 98.303000 3336 4101 1 chr5D.!!$F5 765
2 TraesCS5D01G373900 chr5D 119726287 119727053 766 False 1327.000000 1327 97.914000 3336 4101 1 chr5D.!!$F1 765
3 TraesCS5D01G373900 chr5D 230638807 230639738 931 False 939.000000 939 84.890000 1633 2581 1 chr5D.!!$F2 948
4 TraesCS5D01G373900 chr5D 447236479 447239289 2810 False 660.666667 928 85.147333 836 3128 3 chr5D.!!$F6 2292
5 TraesCS5D01G373900 chr5A 565395958 565407461 11503 True 752.037500 2416 88.914500 141 3333 8 chr5A.!!$R1 3192
6 TraesCS5D01G373900 chr4D 319101640 319102406 766 False 1332.000000 1332 98.044000 3336 4101 1 chr4D.!!$F2 765
7 TraesCS5D01G373900 chr1D 54187925 54188695 770 True 1328.000000 1328 97.795000 3332 4101 1 chr1D.!!$R1 769
8 TraesCS5D01G373900 chr1D 462189265 462190035 770 False 1321.000000 1321 97.668000 3334 4101 1 chr1D.!!$F1 767
9 TraesCS5D01G373900 chr6D 270701560 270702324 764 True 1323.000000 1323 97.908000 3338 4101 1 chr6D.!!$R1 763
10 TraesCS5D01G373900 chr6D 15851648 15853253 1605 True 601.000000 939 88.640500 1210 2581 2 chr6D.!!$R2 1371
11 TraesCS5D01G373900 chr7D 439602195 439602961 766 False 1321.000000 1321 97.784000 3336 4101 1 chr7D.!!$F1 765
12 TraesCS5D01G373900 chr2D 372483419 372484185 766 True 1321.000000 1321 97.784000 3336 4101 1 chr2D.!!$R1 765
13 TraesCS5D01G373900 chr2D 401554755 401555520 765 True 1315.000000 1315 97.653000 3335 4101 1 chr2D.!!$R2 766
14 TraesCS5D01G373900 chr5B 545427579 545430288 2709 True 1010.666667 1293 90.903333 750 3333 3 chr5B.!!$R4 2583
15 TraesCS5D01G373900 chr5B 545406631 545409324 2693 True 573.666667 926 84.884667 942 3127 3 chr5B.!!$R3 2185
16 TraesCS5D01G373900 chr5B 545466061 545466569 508 True 501.000000 501 85.127000 139 627 1 chr5B.!!$R1 488
17 TraesCS5D01G373900 chr1B 159409163 159410094 931 True 793.000000 793 82.225000 1623 2574 1 chr1B.!!$R2 951

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
698 2221 0.035725 AAGGCAAACTACCCGCTACC 60.036 55.0 0.0 0.0 0.0 3.18 F
1548 3488 0.031994 ATTTTTGCGGGGATATGCGC 59.968 50.0 0.0 0.0 0.0 6.09 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2345 4385 0.983905 AACCCCCGGCAAAAAGGTTT 60.984 50.0 0.0 0.0 37.55 3.27 R
3226 5565 0.182775 AACCAACAGGCCGTCTCTTT 59.817 50.0 0.0 0.0 0.00 2.52 R

All possible primers

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

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
69 70 8.635765 TGAATTTATTATTCATAGAGGGTGCC 57.364 34.615 0.00 0.00 33.55 5.01
70 71 8.448008 TGAATTTATTATTCATAGAGGGTGCCT 58.552 33.333 0.00 0.00 33.55 4.75
71 72 9.959721 GAATTTATTATTCATAGAGGGTGCCTA 57.040 33.333 0.00 0.00 31.76 3.93
72 73 9.965902 AATTTATTATTCATAGAGGGTGCCTAG 57.034 33.333 0.00 0.00 31.76 3.02
73 74 7.496346 TTATTATTCATAGAGGGTGCCTAGG 57.504 40.000 3.67 3.67 31.76 3.02
74 75 1.424638 TTCATAGAGGGTGCCTAGGC 58.575 55.000 27.71 27.71 42.35 3.93
86 87 3.854669 CTAGGCACCCGGGAGCTG 61.855 72.222 36.82 24.42 32.43 4.24
87 88 4.715130 TAGGCACCCGGGAGCTGT 62.715 66.667 36.82 27.32 32.43 4.40
89 90 2.808761 TAGGCACCCGGGAGCTGTTA 62.809 60.000 36.82 24.60 32.43 2.41
90 91 2.436115 GCACCCGGGAGCTGTTAC 60.436 66.667 32.83 5.42 0.00 2.50
91 92 3.065306 CACCCGGGAGCTGTTACA 58.935 61.111 32.02 0.00 0.00 2.41
92 93 1.375523 CACCCGGGAGCTGTTACAC 60.376 63.158 32.02 0.00 0.00 2.90
93 94 2.267961 CCCGGGAGCTGTTACACC 59.732 66.667 18.48 0.00 0.00 4.16
94 95 2.291043 CCCGGGAGCTGTTACACCT 61.291 63.158 18.48 0.00 0.00 4.00
95 96 1.677552 CCGGGAGCTGTTACACCTT 59.322 57.895 0.00 0.00 0.00 3.50
96 97 0.036306 CCGGGAGCTGTTACACCTTT 59.964 55.000 0.00 0.00 0.00 3.11
97 98 1.439679 CGGGAGCTGTTACACCTTTC 58.560 55.000 0.00 0.00 0.00 2.62
98 99 1.002087 CGGGAGCTGTTACACCTTTCT 59.998 52.381 0.00 0.00 0.00 2.52
99 100 2.427506 GGGAGCTGTTACACCTTTCTG 58.572 52.381 0.00 0.00 0.00 3.02
100 101 1.807142 GGAGCTGTTACACCTTTCTGC 59.193 52.381 0.00 0.00 0.00 4.26
101 102 2.494059 GAGCTGTTACACCTTTCTGCA 58.506 47.619 0.00 0.00 0.00 4.41
102 103 3.077359 GAGCTGTTACACCTTTCTGCAT 58.923 45.455 0.00 0.00 0.00 3.96
103 104 4.253685 GAGCTGTTACACCTTTCTGCATA 58.746 43.478 0.00 0.00 0.00 3.14
104 105 4.256920 AGCTGTTACACCTTTCTGCATAG 58.743 43.478 0.00 0.00 0.00 2.23
105 106 4.020218 AGCTGTTACACCTTTCTGCATAGA 60.020 41.667 0.00 0.00 0.00 1.98
106 107 4.695455 GCTGTTACACCTTTCTGCATAGAA 59.305 41.667 0.00 0.00 41.06 2.10
107 108 5.355350 GCTGTTACACCTTTCTGCATAGAAT 59.645 40.000 0.00 0.00 42.25 2.40
108 109 6.538742 GCTGTTACACCTTTCTGCATAGAATA 59.461 38.462 0.00 0.00 42.25 1.75
109 110 7.227512 GCTGTTACACCTTTCTGCATAGAATAT 59.772 37.037 0.00 0.00 42.25 1.28
110 111 9.113838 CTGTTACACCTTTCTGCATAGAATATT 57.886 33.333 0.00 0.00 42.25 1.28
111 112 8.892723 TGTTACACCTTTCTGCATAGAATATTG 58.107 33.333 0.00 0.00 42.25 1.90
112 113 6.382869 ACACCTTTCTGCATAGAATATTGC 57.617 37.500 0.00 0.00 42.25 3.56
113 114 5.300286 ACACCTTTCTGCATAGAATATTGCC 59.700 40.000 0.00 0.00 42.25 4.52
114 115 5.533903 CACCTTTCTGCATAGAATATTGCCT 59.466 40.000 0.00 0.00 42.25 4.75
115 116 5.767168 ACCTTTCTGCATAGAATATTGCCTC 59.233 40.000 0.00 0.00 42.25 4.70
116 117 5.182760 CCTTTCTGCATAGAATATTGCCTCC 59.817 44.000 0.00 0.00 42.25 4.30
117 118 4.980339 TCTGCATAGAATATTGCCTCCA 57.020 40.909 0.00 0.00 38.08 3.86
118 119 5.308976 TCTGCATAGAATATTGCCTCCAA 57.691 39.130 0.00 0.00 38.08 3.53
119 120 5.884322 TCTGCATAGAATATTGCCTCCAAT 58.116 37.500 0.00 0.00 43.74 3.16
120 121 5.708697 TCTGCATAGAATATTGCCTCCAATG 59.291 40.000 0.00 0.00 41.58 2.82
121 122 5.633117 TGCATAGAATATTGCCTCCAATGA 58.367 37.500 0.00 0.00 41.58 2.57
122 123 5.474532 TGCATAGAATATTGCCTCCAATGAC 59.525 40.000 0.00 0.00 41.58 3.06
123 124 5.105997 GCATAGAATATTGCCTCCAATGACC 60.106 44.000 0.00 0.00 41.58 4.02
124 125 3.480470 AGAATATTGCCTCCAATGACCG 58.520 45.455 0.00 0.00 41.58 4.79
125 126 3.117888 AGAATATTGCCTCCAATGACCGT 60.118 43.478 0.00 0.00 41.58 4.83
126 127 2.799126 TATTGCCTCCAATGACCGTT 57.201 45.000 0.00 0.00 41.58 4.44
127 128 1.923356 ATTGCCTCCAATGACCGTTT 58.077 45.000 0.00 0.00 40.09 3.60
128 129 0.958091 TTGCCTCCAATGACCGTTTG 59.042 50.000 0.00 0.00 0.00 2.93
129 130 0.179004 TGCCTCCAATGACCGTTTGT 60.179 50.000 0.00 0.00 0.00 2.83
130 131 0.240945 GCCTCCAATGACCGTTTGTG 59.759 55.000 0.00 0.00 0.00 3.33
131 132 1.604604 CCTCCAATGACCGTTTGTGT 58.395 50.000 0.00 0.00 0.00 3.72
132 133 1.266718 CCTCCAATGACCGTTTGTGTG 59.733 52.381 0.00 0.00 0.00 3.82
133 134 0.665835 TCCAATGACCGTTTGTGTGC 59.334 50.000 0.00 0.00 0.00 4.57
134 135 0.383590 CCAATGACCGTTTGTGTGCA 59.616 50.000 0.00 0.00 0.00 4.57
135 136 1.000385 CCAATGACCGTTTGTGTGCAT 60.000 47.619 0.00 0.00 0.00 3.96
136 137 2.227626 CCAATGACCGTTTGTGTGCATA 59.772 45.455 0.00 0.00 0.00 3.14
137 138 3.119531 CCAATGACCGTTTGTGTGCATAT 60.120 43.478 0.00 0.00 0.00 1.78
146 147 5.404968 CCGTTTGTGTGCATATGAAAATTGT 59.595 36.000 6.97 0.00 0.00 2.71
192 193 1.330521 GCACACAAAGAGCGACTTCAA 59.669 47.619 0.00 0.00 37.93 2.69
194 195 3.548818 GCACACAAAGAGCGACTTCAATT 60.549 43.478 0.00 0.00 37.93 2.32
198 199 3.432252 ACAAAGAGCGACTTCAATTACCG 59.568 43.478 0.00 0.00 37.93 4.02
223 224 8.601476 CGTAAGTGACTTTTACTCAAAGAGTTT 58.399 33.333 1.97 0.00 44.40 2.66
246 247 7.633018 TTATGTAGATTTGGGAGAGGCTATT 57.367 36.000 0.00 0.00 0.00 1.73
327 345 2.091278 TCCTCCTTGTACCCTCATCGAT 60.091 50.000 0.00 0.00 0.00 3.59
328 346 2.036475 CCTCCTTGTACCCTCATCGATG 59.964 54.545 19.61 19.61 0.00 3.84
459 477 1.471676 CCTCATTCTTCGGCGCTAACT 60.472 52.381 7.64 0.00 0.00 2.24
461 479 1.203758 TCATTCTTCGGCGCTAACTGA 59.796 47.619 7.64 0.00 0.00 3.41
472 492 2.222819 GCGCTAACTGATGTACTTGCAC 60.223 50.000 0.00 0.00 0.00 4.57
495 515 1.229464 AGCCCTCTTGCTCACCTCT 60.229 57.895 0.00 0.00 36.75 3.69
574 596 4.806330 TGACGAGTGAATTGAGGTCTTAC 58.194 43.478 0.00 0.00 0.00 2.34
609 631 8.682936 TTTTGTGCCAAATAAAATGGTATGTT 57.317 26.923 1.89 0.00 40.23 2.71
657 680 8.311836 TCTACTTTTAAGTGTACCATGAGAAGG 58.688 37.037 5.41 0.00 40.07 3.46
660 683 6.681729 TTTAAGTGTACCATGAGAAGGAGT 57.318 37.500 0.00 0.00 0.00 3.85
661 684 7.786046 TTTAAGTGTACCATGAGAAGGAGTA 57.214 36.000 0.00 0.00 0.00 2.59
662 685 5.923733 AAGTGTACCATGAGAAGGAGTAG 57.076 43.478 0.00 0.00 0.00 2.57
663 686 5.194473 AGTGTACCATGAGAAGGAGTAGA 57.806 43.478 0.00 0.00 0.00 2.59
667 690 7.181125 AGTGTACCATGAGAAGGAGTAGATTTT 59.819 37.037 0.00 0.00 0.00 1.82
668 691 7.824779 GTGTACCATGAGAAGGAGTAGATTTTT 59.175 37.037 0.00 0.00 0.00 1.94
669 692 7.824289 TGTACCATGAGAAGGAGTAGATTTTTG 59.176 37.037 0.00 0.00 0.00 2.44
691 2214 2.229062 GAGGCAAGAAAGGCAAACTACC 59.771 50.000 0.00 0.00 36.37 3.18
692 2215 1.272490 GGCAAGAAAGGCAAACTACCC 59.728 52.381 0.00 0.00 0.00 3.69
693 2216 1.068541 GCAAGAAAGGCAAACTACCCG 60.069 52.381 0.00 0.00 0.00 5.28
694 2217 1.068541 CAAGAAAGGCAAACTACCCGC 60.069 52.381 0.00 0.00 0.00 6.13
695 2218 0.400594 AGAAAGGCAAACTACCCGCT 59.599 50.000 0.00 0.00 0.00 5.52
696 2219 1.626825 AGAAAGGCAAACTACCCGCTA 59.373 47.619 0.00 0.00 0.00 4.26
697 2220 1.736126 GAAAGGCAAACTACCCGCTAC 59.264 52.381 0.00 0.00 0.00 3.58
698 2221 0.035725 AAGGCAAACTACCCGCTACC 60.036 55.000 0.00 0.00 0.00 3.18
699 2222 1.450848 GGCAAACTACCCGCTACCC 60.451 63.158 0.00 0.00 0.00 3.69
700 2223 1.297364 GCAAACTACCCGCTACCCA 59.703 57.895 0.00 0.00 0.00 4.51
701 2224 1.022982 GCAAACTACCCGCTACCCAC 61.023 60.000 0.00 0.00 0.00 4.61
702 2225 0.611714 CAAACTACCCGCTACCCACT 59.388 55.000 0.00 0.00 0.00 4.00
703 2226 0.900421 AAACTACCCGCTACCCACTC 59.100 55.000 0.00 0.00 0.00 3.51
704 2227 0.974525 AACTACCCGCTACCCACTCC 60.975 60.000 0.00 0.00 0.00 3.85
705 2228 1.076192 CTACCCGCTACCCACTCCT 60.076 63.158 0.00 0.00 0.00 3.69
706 2229 0.686769 CTACCCGCTACCCACTCCTT 60.687 60.000 0.00 0.00 0.00 3.36
707 2230 0.252375 TACCCGCTACCCACTCCTTT 60.252 55.000 0.00 0.00 0.00 3.11
708 2231 1.078426 CCCGCTACCCACTCCTTTG 60.078 63.158 0.00 0.00 0.00 2.77
709 2232 1.745489 CCGCTACCCACTCCTTTGC 60.745 63.158 0.00 0.00 0.00 3.68
710 2233 1.296715 CGCTACCCACTCCTTTGCT 59.703 57.895 0.00 0.00 0.00 3.91
711 2234 0.535335 CGCTACCCACTCCTTTGCTA 59.465 55.000 0.00 0.00 0.00 3.49
712 2235 1.066430 CGCTACCCACTCCTTTGCTAA 60.066 52.381 0.00 0.00 0.00 3.09
713 2236 2.614481 CGCTACCCACTCCTTTGCTAAA 60.614 50.000 0.00 0.00 0.00 1.85
714 2237 3.418047 GCTACCCACTCCTTTGCTAAAA 58.582 45.455 0.00 0.00 0.00 1.52
715 2238 3.440522 GCTACCCACTCCTTTGCTAAAAG 59.559 47.826 0.00 0.00 42.17 2.27
716 2239 2.239400 ACCCACTCCTTTGCTAAAAGC 58.761 47.619 0.00 0.00 41.33 3.51
769 2292 1.462238 ACTCCACTCCACTGGCCTT 60.462 57.895 3.32 0.00 0.00 4.35
777 2300 1.153549 CCACTGGCCTTAGCTCGTC 60.154 63.158 3.32 0.00 39.73 4.20
780 2303 0.900647 ACTGGCCTTAGCTCGTCTGT 60.901 55.000 3.32 0.00 39.73 3.41
781 2304 0.179124 CTGGCCTTAGCTCGTCTGTC 60.179 60.000 3.32 0.00 39.73 3.51
782 2305 0.612174 TGGCCTTAGCTCGTCTGTCT 60.612 55.000 3.32 0.00 39.73 3.41
832 2355 7.489757 TCGTTTGTTTTTCAAGAAAATTCCGAT 59.510 29.630 8.62 0.00 39.69 4.18
850 2373 1.911293 ATGTACGCTGCGTGCCAAAG 61.911 55.000 35.11 1.35 41.42 2.77
985 2527 2.259818 CTCCTCGCGTGCTTCTGT 59.740 61.111 5.77 0.00 0.00 3.41
993 2535 2.846918 GTGCTTCTGTGCGACGAC 59.153 61.111 0.00 0.00 35.36 4.34
1026 2576 4.856607 GCGGCGTCCTTCCTCTCG 62.857 72.222 9.37 0.00 0.00 4.04
1177 2772 4.093408 CCACAGGTATCATTTTCTCGTGTG 59.907 45.833 0.00 0.00 41.42 3.82
1182 2777 0.400213 TCATTTTCTCGTGTGCCCCT 59.600 50.000 0.00 0.00 0.00 4.79
1183 2778 0.804989 CATTTTCTCGTGTGCCCCTC 59.195 55.000 0.00 0.00 0.00 4.30
1184 2779 0.693049 ATTTTCTCGTGTGCCCCTCT 59.307 50.000 0.00 0.00 0.00 3.69
1185 2780 0.034896 TTTTCTCGTGTGCCCCTCTC 59.965 55.000 0.00 0.00 0.00 3.20
1186 2781 2.154798 TTTCTCGTGTGCCCCTCTCG 62.155 60.000 0.00 0.00 0.00 4.04
1208 2803 1.000607 GTCCTGTGTCGTGTTGAGCTA 60.001 52.381 0.00 0.00 0.00 3.32
1264 2863 2.125106 GTGGGATCGGCAGTGGTC 60.125 66.667 0.00 0.00 0.00 4.02
1276 2875 2.663852 GTGGTCGGTGGTGAACGG 60.664 66.667 0.00 0.00 0.00 4.44
1361 2960 2.776913 GGAGGCCTTCGACGAGGAG 61.777 68.421 6.77 0.00 39.25 3.69
1413 3327 4.708726 ATGCCATGCTCTTACTGTTTTC 57.291 40.909 0.00 0.00 0.00 2.29
1418 3332 5.403466 GCCATGCTCTTACTGTTTTCTTTTG 59.597 40.000 0.00 0.00 0.00 2.44
1421 3335 6.524101 TGCTCTTACTGTTTTCTTTTGGTT 57.476 33.333 0.00 0.00 0.00 3.67
1422 3336 6.930731 TGCTCTTACTGTTTTCTTTTGGTTT 58.069 32.000 0.00 0.00 0.00 3.27
1424 3338 8.188139 TGCTCTTACTGTTTTCTTTTGGTTTAG 58.812 33.333 0.00 0.00 0.00 1.85
1425 3339 7.167635 GCTCTTACTGTTTTCTTTTGGTTTAGC 59.832 37.037 0.00 0.00 0.00 3.09
1436 3350 1.967494 GGTTTAGCCGGCGGTTTGA 60.967 57.895 28.82 11.16 0.00 2.69
1440 3354 1.022451 TTAGCCGGCGGTTTGATCAC 61.022 55.000 28.82 7.88 0.00 3.06
1462 3376 8.177119 TCACACTAATTTAGTTTCCAGCAAAT 57.823 30.769 6.34 0.00 36.76 2.32
1471 3385 5.859205 AGTTTCCAGCAAATTCTTCTGTT 57.141 34.783 0.00 0.00 0.00 3.16
1476 3390 4.279169 TCCAGCAAATTCTTCTGTTTCCAG 59.721 41.667 0.00 0.00 40.25 3.86
1477 3391 3.985925 CAGCAAATTCTTCTGTTTCCAGC 59.014 43.478 0.00 0.00 38.66 4.85
1479 3393 4.099881 AGCAAATTCTTCTGTTTCCAGCAA 59.900 37.500 0.00 0.00 38.66 3.91
1480 3394 4.810491 GCAAATTCTTCTGTTTCCAGCAAA 59.190 37.500 0.00 0.00 38.66 3.68
1484 3424 4.589216 TCTTCTGTTTCCAGCAAATTGG 57.411 40.909 0.00 0.00 38.66 3.16
1496 3436 4.322198 CCAGCAAATTGGTCAAGCAATACT 60.322 41.667 7.77 4.16 33.38 2.12
1497 3437 4.624024 CAGCAAATTGGTCAAGCAATACTG 59.376 41.667 7.77 11.22 0.00 2.74
1509 3449 1.734465 GCAATACTGCCCGATCTATGC 59.266 52.381 0.00 0.00 43.26 3.14
1510 3450 2.871637 GCAATACTGCCCGATCTATGCA 60.872 50.000 0.00 0.00 43.26 3.96
1511 3451 2.738846 CAATACTGCCCGATCTATGCAC 59.261 50.000 0.00 0.00 0.00 4.57
1512 3452 1.704641 TACTGCCCGATCTATGCACT 58.295 50.000 0.00 0.00 0.00 4.40
1513 3453 1.704641 ACTGCCCGATCTATGCACTA 58.295 50.000 0.00 0.00 0.00 2.74
1514 3454 1.615883 ACTGCCCGATCTATGCACTAG 59.384 52.381 0.00 0.00 0.00 2.57
1515 3455 0.318441 TGCCCGATCTATGCACTAGC 59.682 55.000 0.00 0.00 42.57 3.42
1539 3479 8.450180 AGCAGATTTTTATTTTATTTTTGCGGG 58.550 29.630 0.00 0.00 0.00 6.13
1540 3480 7.696035 GCAGATTTTTATTTTATTTTTGCGGGG 59.304 33.333 0.00 0.00 0.00 5.73
1541 3481 8.940952 CAGATTTTTATTTTATTTTTGCGGGGA 58.059 29.630 0.00 0.00 0.00 4.81
1542 3482 9.679661 AGATTTTTATTTTATTTTTGCGGGGAT 57.320 25.926 0.00 0.00 0.00 3.85
1546 3486 7.954788 TTATTTTATTTTTGCGGGGATATGC 57.045 32.000 0.00 0.00 0.00 3.14
1547 3487 3.634568 TTATTTTTGCGGGGATATGCG 57.365 42.857 0.00 0.00 0.00 4.73
1548 3488 0.031994 ATTTTTGCGGGGATATGCGC 59.968 50.000 0.00 0.00 0.00 6.09
1549 3489 1.034838 TTTTTGCGGGGATATGCGCT 61.035 50.000 9.73 0.00 0.00 5.92
1552 3493 2.434359 GCGGGGATATGCGCTACC 60.434 66.667 9.73 6.57 0.00 3.18
1562 3503 4.865365 GGATATGCGCTACCAGTAGATTTC 59.135 45.833 9.73 0.00 35.21 2.17
1608 3550 5.017294 TCTCACAAAATTGGTTTCCAACC 57.983 39.130 3.23 0.00 46.95 3.77
1622 3564 6.588348 GTTTCCAACCTTTTTGTCATCAAG 57.412 37.500 0.00 0.00 34.88 3.02
1661 3687 0.401738 ACCTGGGATGTGAACTGTGG 59.598 55.000 0.00 0.00 0.00 4.17
1671 3697 2.026729 TGTGAACTGTGGTGTCCTTTCA 60.027 45.455 0.00 0.00 0.00 2.69
1675 3705 4.709397 TGAACTGTGGTGTCCTTTCATTTT 59.291 37.500 0.00 0.00 0.00 1.82
1676 3706 5.186797 TGAACTGTGGTGTCCTTTCATTTTT 59.813 36.000 0.00 0.00 0.00 1.94
1706 3736 8.692710 ACGTATATGTTTCAGAGTTAATCTCCA 58.307 33.333 0.00 0.00 43.71 3.86
1707 3737 8.969267 CGTATATGTTTCAGAGTTAATCTCCAC 58.031 37.037 0.00 0.00 43.71 4.02
1728 3758 8.421249 TCCACAAGATCAATTTTATTTGACCT 57.579 30.769 0.00 0.00 38.37 3.85
1753 3783 4.125912 GCTGATTGCAGTTATAAGAGCG 57.874 45.455 0.00 0.00 44.17 5.03
1903 3935 2.034221 GGGAAGCCAAGTCGCCTT 59.966 61.111 0.00 0.00 0.00 4.35
1907 3939 0.884704 GAAGCCAAGTCGCCTTGTGA 60.885 55.000 5.37 0.00 45.49 3.58
1915 3947 2.767505 AGTCGCCTTGTGAGGTTTAAG 58.232 47.619 0.00 0.00 45.44 1.85
1947 3979 6.877611 ATACCTTGTGGTGTTCTTTAACAG 57.122 37.500 0.00 0.00 46.06 3.16
2012 4046 9.605275 AAAATGTTTTCTCGATCAGATCATCTA 57.395 29.630 11.12 0.00 0.00 1.98
2020 4054 6.597280 TCTCGATCAGATCATCTATGGTACTG 59.403 42.308 11.12 0.00 0.00 2.74
2022 4056 6.597280 TCGATCAGATCATCTATGGTACTGAG 59.403 42.308 11.12 0.00 36.25 3.35
2023 4057 6.374053 CGATCAGATCATCTATGGTACTGAGT 59.626 42.308 11.12 0.00 36.25 3.41
2104 4142 3.423539 TGCTCAAGGTTACAAGCTCAT 57.576 42.857 0.00 0.00 35.34 2.90
2213 4252 0.325933 AAGGCTATGTGCACTGCTGA 59.674 50.000 19.41 0.00 45.15 4.26
2327 4367 2.485814 GCTTCAGACCAAAGTAAGCAGG 59.514 50.000 0.00 0.00 41.65 4.85
2345 4385 5.376625 AGCAGGACACTGTATTTTCTGAAA 58.623 37.500 0.00 0.00 46.62 2.69
2382 4423 9.917129 CCGGGGGTTTATGTATTAAAAATTATC 57.083 33.333 0.00 0.00 31.69 1.75
2409 4450 6.911308 ACCAGGTTGCTTAATATTCACCTAT 58.089 36.000 0.00 0.00 0.00 2.57
2555 4597 1.922880 GCGACCGTTGCAAGGTAAAAC 60.923 52.381 17.23 6.45 43.01 2.43
2723 5038 1.265635 TGCACTAAACATTCACACCGC 59.734 47.619 0.00 0.00 0.00 5.68
2737 5056 7.282224 ACATTCACACCGCACAATATAAATAGT 59.718 33.333 0.00 0.00 0.00 2.12
2738 5057 7.618502 TTCACACCGCACAATATAAATAGTT 57.381 32.000 0.00 0.00 0.00 2.24
2740 5059 6.819146 TCACACCGCACAATATAAATAGTTGA 59.181 34.615 0.00 0.00 0.00 3.18
2822 5148 1.737793 GAATACTTGGCACCGAACCAG 59.262 52.381 0.00 0.00 38.73 4.00
3005 5343 3.314635 GCAATATCTGGTCTGCAAGGAAG 59.685 47.826 0.00 0.00 34.87 3.46
3082 5420 4.720649 TCTTCAGACATACCCTTCTTCG 57.279 45.455 0.00 0.00 0.00 3.79
3200 5539 3.815809 AGTTGAGACATTTTTGGGACGA 58.184 40.909 0.00 0.00 0.00 4.20
3201 5540 3.815401 AGTTGAGACATTTTTGGGACGAG 59.185 43.478 0.00 0.00 0.00 4.18
3226 5565 6.207810 GGGGAGTATGTTTTATGTGTGTTTCA 59.792 38.462 0.00 0.00 0.00 2.69
3235 5574 5.666969 TTATGTGTGTTTCAAAGAGACGG 57.333 39.130 0.00 0.00 0.00 4.79
3325 5664 4.842139 ATAAAATCTTGACGAGCGTGAC 57.158 40.909 0.00 0.00 0.00 3.67
3381 7665 8.809159 TTCAAAATTTTCTACGCATCATCAAA 57.191 26.923 0.00 0.00 0.00 2.69
3517 7988 2.672961 TTCAGATCGCGGTTGATTCT 57.327 45.000 6.13 0.00 0.00 2.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
43 44 9.077885 GGCACCCTCTATGAATAATAAATTCAA 57.922 33.333 4.67 0.00 40.84 2.69
44 45 8.448008 AGGCACCCTCTATGAATAATAAATTCA 58.552 33.333 3.13 3.13 41.59 2.57
45 46 8.870075 AGGCACCCTCTATGAATAATAAATTC 57.130 34.615 0.00 0.00 0.00 2.17
46 47 9.965902 CTAGGCACCCTCTATGAATAATAAATT 57.034 33.333 0.00 0.00 34.61 1.82
47 48 8.552296 CCTAGGCACCCTCTATGAATAATAAAT 58.448 37.037 0.00 0.00 34.61 1.40
48 49 7.528881 GCCTAGGCACCCTCTATGAATAATAAA 60.529 40.741 29.33 0.00 41.49 1.40
49 50 6.070194 GCCTAGGCACCCTCTATGAATAATAA 60.070 42.308 29.33 0.00 41.49 1.40
50 51 5.425539 GCCTAGGCACCCTCTATGAATAATA 59.574 44.000 29.33 0.00 41.49 0.98
51 52 4.226168 GCCTAGGCACCCTCTATGAATAAT 59.774 45.833 29.33 0.00 41.49 1.28
52 53 3.583086 GCCTAGGCACCCTCTATGAATAA 59.417 47.826 29.33 0.00 41.49 1.40
53 54 3.173965 GCCTAGGCACCCTCTATGAATA 58.826 50.000 29.33 0.00 41.49 1.75
54 55 1.981495 GCCTAGGCACCCTCTATGAAT 59.019 52.381 29.33 0.00 41.49 2.57
55 56 1.424638 GCCTAGGCACCCTCTATGAA 58.575 55.000 29.33 0.00 41.49 2.57
56 57 3.149436 GCCTAGGCACCCTCTATGA 57.851 57.895 29.33 0.00 41.49 2.15
69 70 3.854669 CAGCTCCCGGGTGCCTAG 61.855 72.222 37.33 25.70 36.61 3.02
70 71 2.808761 TAACAGCTCCCGGGTGCCTA 62.809 60.000 37.33 25.05 46.30 3.93
72 73 3.712907 TAACAGCTCCCGGGTGCC 61.713 66.667 37.33 22.60 46.30 5.01
73 74 2.436115 GTAACAGCTCCCGGGTGC 60.436 66.667 35.10 35.10 46.30 5.01
75 76 2.590114 GGTGTAACAGCTCCCGGGT 61.590 63.158 22.86 1.40 39.98 5.28
76 77 1.838073 AAGGTGTAACAGCTCCCGGG 61.838 60.000 16.85 16.85 41.59 5.73
77 78 0.036306 AAAGGTGTAACAGCTCCCGG 59.964 55.000 0.00 0.00 41.59 5.73
78 79 1.002087 AGAAAGGTGTAACAGCTCCCG 59.998 52.381 0.00 0.00 41.59 5.14
79 80 2.427506 CAGAAAGGTGTAACAGCTCCC 58.572 52.381 0.00 0.00 41.59 4.30
80 81 1.807142 GCAGAAAGGTGTAACAGCTCC 59.193 52.381 0.00 0.00 41.59 4.70
81 82 2.494059 TGCAGAAAGGTGTAACAGCTC 58.506 47.619 0.00 0.00 41.59 4.09
82 83 2.638480 TGCAGAAAGGTGTAACAGCT 57.362 45.000 0.00 0.00 44.48 4.24
83 84 4.253685 TCTATGCAGAAAGGTGTAACAGC 58.746 43.478 0.00 0.00 39.98 4.40
84 85 6.992063 ATTCTATGCAGAAAGGTGTAACAG 57.008 37.500 0.00 0.00 43.89 3.16
85 86 8.892723 CAATATTCTATGCAGAAAGGTGTAACA 58.107 33.333 0.00 0.00 43.89 2.41
86 87 7.857885 GCAATATTCTATGCAGAAAGGTGTAAC 59.142 37.037 0.00 0.00 43.89 2.50
87 88 7.013274 GGCAATATTCTATGCAGAAAGGTGTAA 59.987 37.037 0.00 0.00 43.89 2.41
88 89 6.486657 GGCAATATTCTATGCAGAAAGGTGTA 59.513 38.462 0.00 0.00 43.89 2.90
89 90 5.300286 GGCAATATTCTATGCAGAAAGGTGT 59.700 40.000 0.00 0.00 43.89 4.16
90 91 5.533903 AGGCAATATTCTATGCAGAAAGGTG 59.466 40.000 0.00 0.00 43.89 4.00
91 92 5.699143 AGGCAATATTCTATGCAGAAAGGT 58.301 37.500 0.00 0.00 43.89 3.50
92 93 5.182760 GGAGGCAATATTCTATGCAGAAAGG 59.817 44.000 0.00 0.00 43.89 3.11
93 94 5.766670 TGGAGGCAATATTCTATGCAGAAAG 59.233 40.000 0.00 0.00 43.89 2.62
94 95 5.693961 TGGAGGCAATATTCTATGCAGAAA 58.306 37.500 0.00 0.00 43.89 2.52
95 96 5.308976 TGGAGGCAATATTCTATGCAGAA 57.691 39.130 0.00 0.00 44.77 3.02
96 97 4.980339 TGGAGGCAATATTCTATGCAGA 57.020 40.909 0.00 0.00 44.32 4.26
97 98 5.708697 TCATTGGAGGCAATATTCTATGCAG 59.291 40.000 0.00 0.00 44.32 4.41
98 99 5.474532 GTCATTGGAGGCAATATTCTATGCA 59.525 40.000 0.00 0.00 44.32 3.96
99 100 5.105997 GGTCATTGGAGGCAATATTCTATGC 60.106 44.000 0.00 0.00 41.82 3.14
100 101 5.122869 CGGTCATTGGAGGCAATATTCTATG 59.877 44.000 0.00 0.00 0.00 2.23
101 102 5.221925 ACGGTCATTGGAGGCAATATTCTAT 60.222 40.000 0.00 0.00 0.00 1.98
102 103 4.102524 ACGGTCATTGGAGGCAATATTCTA 59.897 41.667 0.00 0.00 0.00 2.10
103 104 3.117888 ACGGTCATTGGAGGCAATATTCT 60.118 43.478 0.00 0.00 0.00 2.40
104 105 3.214328 ACGGTCATTGGAGGCAATATTC 58.786 45.455 0.00 0.00 0.00 1.75
105 106 3.297134 ACGGTCATTGGAGGCAATATT 57.703 42.857 0.00 0.00 0.00 1.28
106 107 3.297134 AACGGTCATTGGAGGCAATAT 57.703 42.857 0.00 0.00 0.00 1.28
107 108 2.752354 CAAACGGTCATTGGAGGCAATA 59.248 45.455 0.00 0.00 0.00 1.90
108 109 1.545582 CAAACGGTCATTGGAGGCAAT 59.454 47.619 0.00 0.00 0.00 3.56
109 110 0.958091 CAAACGGTCATTGGAGGCAA 59.042 50.000 0.00 0.00 0.00 4.52
110 111 0.179004 ACAAACGGTCATTGGAGGCA 60.179 50.000 0.00 0.00 32.02 4.75
111 112 0.240945 CACAAACGGTCATTGGAGGC 59.759 55.000 0.00 0.00 32.02 4.70
112 113 1.266718 CACACAAACGGTCATTGGAGG 59.733 52.381 0.00 0.00 32.02 4.30
113 114 1.334960 GCACACAAACGGTCATTGGAG 60.335 52.381 0.00 0.00 32.02 3.86
114 115 0.665835 GCACACAAACGGTCATTGGA 59.334 50.000 0.00 0.00 32.02 3.53
115 116 0.383590 TGCACACAAACGGTCATTGG 59.616 50.000 0.00 0.00 32.02 3.16
116 117 2.420628 ATGCACACAAACGGTCATTG 57.579 45.000 0.00 0.00 0.00 2.82
117 118 3.755905 TCATATGCACACAAACGGTCATT 59.244 39.130 0.00 0.00 0.00 2.57
118 119 3.342719 TCATATGCACACAAACGGTCAT 58.657 40.909 0.00 0.00 0.00 3.06
119 120 2.772287 TCATATGCACACAAACGGTCA 58.228 42.857 0.00 0.00 0.00 4.02
120 121 3.822594 TTCATATGCACACAAACGGTC 57.177 42.857 0.00 0.00 0.00 4.79
121 122 4.576216 TTTTCATATGCACACAAACGGT 57.424 36.364 0.00 0.00 0.00 4.83
122 123 5.404968 ACAATTTTCATATGCACACAAACGG 59.595 36.000 0.00 0.00 0.00 4.44
123 124 6.450845 ACAATTTTCATATGCACACAAACG 57.549 33.333 0.00 0.00 0.00 3.60
124 125 8.519492 ACTACAATTTTCATATGCACACAAAC 57.481 30.769 0.00 0.00 0.00 2.93
125 126 9.539825 AAACTACAATTTTCATATGCACACAAA 57.460 25.926 0.00 0.00 0.00 2.83
126 127 9.190858 GAAACTACAATTTTCATATGCACACAA 57.809 29.630 0.00 0.00 33.82 3.33
127 128 8.575589 AGAAACTACAATTTTCATATGCACACA 58.424 29.630 0.00 0.00 35.72 3.72
128 129 8.853345 CAGAAACTACAATTTTCATATGCACAC 58.147 33.333 0.00 0.00 35.72 3.82
129 130 8.791675 TCAGAAACTACAATTTTCATATGCACA 58.208 29.630 0.00 0.00 35.72 4.57
130 131 9.282247 CTCAGAAACTACAATTTTCATATGCAC 57.718 33.333 0.00 0.00 35.72 4.57
131 132 9.013229 ACTCAGAAACTACAATTTTCATATGCA 57.987 29.630 0.00 0.00 35.72 3.96
132 133 9.846248 AACTCAGAAACTACAATTTTCATATGC 57.154 29.630 0.00 0.00 35.72 3.14
137 138 9.734620 CAATCAACTCAGAAACTACAATTTTCA 57.265 29.630 0.00 0.00 35.72 2.69
180 181 4.082354 ACTTACGGTAATTGAAGTCGCTCT 60.082 41.667 0.29 0.00 0.00 4.09
192 193 8.891671 TTTGAGTAAAAGTCACTTACGGTAAT 57.108 30.769 0.29 0.00 34.96 1.89
194 195 7.715657 TCTTTGAGTAAAAGTCACTTACGGTA 58.284 34.615 0.00 0.00 44.83 4.02
223 224 7.633018 AAATAGCCTCTCCCAAATCTACATA 57.367 36.000 0.00 0.00 0.00 2.29
459 477 2.416747 GCTGACTGTGCAAGTACATCA 58.583 47.619 0.00 0.00 40.07 3.07
461 479 1.611673 GGGCTGACTGTGCAAGTACAT 60.612 52.381 0.00 0.00 40.07 2.29
472 492 0.673022 GTGAGCAAGAGGGCTGACTG 60.673 60.000 0.00 0.00 45.99 3.51
565 585 9.516314 GCACAAAATAAATATTGGTAAGACCTC 57.484 33.333 0.00 0.00 39.58 3.85
654 677 4.657814 TGCCTCCAAAAATCTACTCCTT 57.342 40.909 0.00 0.00 0.00 3.36
655 678 4.289672 TCTTGCCTCCAAAAATCTACTCCT 59.710 41.667 0.00 0.00 0.00 3.69
657 680 6.349694 CCTTTCTTGCCTCCAAAAATCTACTC 60.350 42.308 0.00 0.00 0.00 2.59
660 683 4.220602 GCCTTTCTTGCCTCCAAAAATCTA 59.779 41.667 0.00 0.00 0.00 1.98
661 684 3.007290 GCCTTTCTTGCCTCCAAAAATCT 59.993 43.478 0.00 0.00 0.00 2.40
662 685 3.244181 TGCCTTTCTTGCCTCCAAAAATC 60.244 43.478 0.00 0.00 0.00 2.17
663 686 2.705127 TGCCTTTCTTGCCTCCAAAAAT 59.295 40.909 0.00 0.00 0.00 1.82
667 690 1.412343 GTTTGCCTTTCTTGCCTCCAA 59.588 47.619 0.00 0.00 0.00 3.53
668 691 1.039856 GTTTGCCTTTCTTGCCTCCA 58.960 50.000 0.00 0.00 0.00 3.86
669 692 1.332195 AGTTTGCCTTTCTTGCCTCC 58.668 50.000 0.00 0.00 0.00 4.30
691 2214 1.745489 GCAAAGGAGTGGGTAGCGG 60.745 63.158 0.00 0.00 0.00 5.52
692 2215 0.535335 TAGCAAAGGAGTGGGTAGCG 59.465 55.000 0.00 0.00 0.00 4.26
693 2216 2.781681 TTAGCAAAGGAGTGGGTAGC 57.218 50.000 0.00 0.00 0.00 3.58
694 2217 3.440522 GCTTTTAGCAAAGGAGTGGGTAG 59.559 47.826 0.00 0.00 41.89 3.18
695 2218 3.418047 GCTTTTAGCAAAGGAGTGGGTA 58.582 45.455 0.00 0.00 41.89 3.69
696 2219 2.239400 GCTTTTAGCAAAGGAGTGGGT 58.761 47.619 0.00 0.00 41.89 4.51
731 2254 1.497286 TGGAGTGGGTAGCCAGTTTTT 59.503 47.619 21.92 2.41 0.00 1.94
732 2255 1.145571 TGGAGTGGGTAGCCAGTTTT 58.854 50.000 21.92 4.91 0.00 2.43
733 2256 0.400594 GTGGAGTGGGTAGCCAGTTT 59.599 55.000 21.92 7.47 31.18 2.66
734 2257 0.473886 AGTGGAGTGGGTAGCCAGTT 60.474 55.000 21.92 10.07 31.45 3.16
735 2258 0.905337 GAGTGGAGTGGGTAGCCAGT 60.905 60.000 21.23 21.23 38.03 4.00
736 2259 1.617947 GGAGTGGAGTGGGTAGCCAG 61.618 65.000 15.48 0.00 31.18 4.85
737 2260 1.612442 GGAGTGGAGTGGGTAGCCA 60.612 63.158 10.27 10.27 0.00 4.75
738 2261 1.612442 TGGAGTGGAGTGGGTAGCC 60.612 63.158 3.29 3.29 0.00 3.93
739 2262 0.905337 AGTGGAGTGGAGTGGGTAGC 60.905 60.000 0.00 0.00 0.00 3.58
769 2292 1.064685 TCATCCCAGACAGACGAGCTA 60.065 52.381 0.00 0.00 0.00 3.32
777 2300 3.988976 TTCCTTTCTCATCCCAGACAG 57.011 47.619 0.00 0.00 0.00 3.51
780 2303 2.355108 CGCTTTCCTTTCTCATCCCAGA 60.355 50.000 0.00 0.00 0.00 3.86
781 2304 2.012673 CGCTTTCCTTTCTCATCCCAG 58.987 52.381 0.00 0.00 0.00 4.45
782 2305 1.340017 CCGCTTTCCTTTCTCATCCCA 60.340 52.381 0.00 0.00 0.00 4.37
985 2527 2.104132 CATGGATCGGTCGTCGCA 59.896 61.111 0.00 0.00 39.05 5.10
993 2535 1.301244 CGCCTTCTCCATGGATCGG 60.301 63.158 16.63 16.26 0.00 4.18
1158 2711 3.270877 GGCACACGAGAAAATGATACCT 58.729 45.455 0.00 0.00 0.00 3.08
1163 2716 0.400213 AGGGGCACACGAGAAAATGA 59.600 50.000 0.00 0.00 0.00 2.57
1182 2777 1.099295 ACACGACACAGGACACGAGA 61.099 55.000 0.00 0.00 0.00 4.04
1183 2778 0.248907 AACACGACACAGGACACGAG 60.249 55.000 0.00 0.00 0.00 4.18
1184 2779 0.526739 CAACACGACACAGGACACGA 60.527 55.000 0.00 0.00 0.00 4.35
1185 2780 0.526739 TCAACACGACACAGGACACG 60.527 55.000 0.00 0.00 0.00 4.49
1186 2781 1.209128 CTCAACACGACACAGGACAC 58.791 55.000 0.00 0.00 0.00 3.67
1208 2803 2.031616 CCGCCGCCATCAGATCAT 59.968 61.111 0.00 0.00 0.00 2.45
1264 2863 3.353836 CCTTGCCGTTCACCACCG 61.354 66.667 0.00 0.00 0.00 4.94
1322 2921 2.741092 GGCAACTCCACCTCGACA 59.259 61.111 0.00 0.00 34.01 4.35
1345 2944 2.035940 ACTCCTCGTCGAAGGCCT 59.964 61.111 0.00 0.00 36.29 5.19
1375 2974 1.961394 GCATACCCATGTAGGAGTCGA 59.039 52.381 0.00 0.00 41.22 4.20
1413 3327 1.211709 CCGCCGGCTAAACCAAAAG 59.788 57.895 26.68 4.04 39.03 2.27
1418 3332 1.310216 ATCAAACCGCCGGCTAAACC 61.310 55.000 26.68 0.00 0.00 3.27
1421 3335 1.022451 GTGATCAAACCGCCGGCTAA 61.022 55.000 26.68 3.16 0.00 3.09
1422 3336 1.448893 GTGATCAAACCGCCGGCTA 60.449 57.895 26.68 2.73 0.00 3.93
1424 3338 3.053291 TGTGATCAAACCGCCGGC 61.053 61.111 19.07 19.07 0.00 6.13
1425 3339 0.390603 TAGTGTGATCAAACCGCCGG 60.391 55.000 12.62 0.00 0.00 6.13
1436 3350 7.759489 TTGCTGGAAACTAAATTAGTGTGAT 57.241 32.000 6.41 0.00 39.39 3.06
1440 3354 9.696917 AAGAATTTGCTGGAAACTAAATTAGTG 57.303 29.630 6.41 0.00 39.39 2.74
1471 3385 2.037901 TGCTTGACCAATTTGCTGGAA 58.962 42.857 0.00 0.00 38.96 3.53
1476 3390 3.368843 GCAGTATTGCTTGACCAATTTGC 59.631 43.478 2.45 0.00 46.95 3.68
1496 3436 0.318441 GCTAGTGCATAGATCGGGCA 59.682 55.000 5.11 5.11 39.41 5.36
1497 3437 0.318441 TGCTAGTGCATAGATCGGGC 59.682 55.000 0.00 0.16 45.31 6.13
1513 3453 8.450180 CCCGCAAAAATAAAATAAAAATCTGCT 58.550 29.630 0.00 0.00 0.00 4.24
1514 3454 7.696035 CCCCGCAAAAATAAAATAAAAATCTGC 59.304 33.333 0.00 0.00 0.00 4.26
1515 3455 8.940952 TCCCCGCAAAAATAAAATAAAAATCTG 58.059 29.630 0.00 0.00 0.00 2.90
1516 3456 9.679661 ATCCCCGCAAAAATAAAATAAAAATCT 57.320 25.926 0.00 0.00 0.00 2.40
1520 3460 8.831550 GCATATCCCCGCAAAAATAAAATAAAA 58.168 29.630 0.00 0.00 0.00 1.52
1521 3461 7.169982 CGCATATCCCCGCAAAAATAAAATAAA 59.830 33.333 0.00 0.00 0.00 1.40
1522 3462 6.642950 CGCATATCCCCGCAAAAATAAAATAA 59.357 34.615 0.00 0.00 0.00 1.40
1523 3463 6.153067 CGCATATCCCCGCAAAAATAAAATA 58.847 36.000 0.00 0.00 0.00 1.40
1524 3464 4.987912 CGCATATCCCCGCAAAAATAAAAT 59.012 37.500 0.00 0.00 0.00 1.82
1525 3465 4.363999 CGCATATCCCCGCAAAAATAAAA 58.636 39.130 0.00 0.00 0.00 1.52
1526 3466 3.971150 CGCATATCCCCGCAAAAATAAA 58.029 40.909 0.00 0.00 0.00 1.40
1527 3467 3.634568 CGCATATCCCCGCAAAAATAA 57.365 42.857 0.00 0.00 0.00 1.40
1536 3476 1.079819 CTGGTAGCGCATATCCCCG 60.080 63.158 11.47 0.00 0.00 5.73
1537 3477 1.204941 CTACTGGTAGCGCATATCCCC 59.795 57.143 11.47 0.00 0.00 4.81
1538 3478 2.168496 TCTACTGGTAGCGCATATCCC 58.832 52.381 11.47 1.64 33.32 3.85
1539 3479 4.457834 AATCTACTGGTAGCGCATATCC 57.542 45.455 11.47 6.70 33.32 2.59
1540 3480 5.470368 TGAAATCTACTGGTAGCGCATATC 58.530 41.667 11.47 0.00 33.32 1.63
1541 3481 5.468540 TGAAATCTACTGGTAGCGCATAT 57.531 39.130 11.47 0.00 33.32 1.78
1542 3482 4.929819 TGAAATCTACTGGTAGCGCATA 57.070 40.909 11.47 0.00 33.32 3.14
1543 3483 3.819564 TGAAATCTACTGGTAGCGCAT 57.180 42.857 11.47 0.00 33.32 4.73
1544 3484 3.132111 TGATGAAATCTACTGGTAGCGCA 59.868 43.478 11.47 0.00 45.81 6.09
1545 3485 3.717707 TGATGAAATCTACTGGTAGCGC 58.282 45.455 0.00 0.00 45.81 5.92
1546 3486 6.313905 ACTTTTGATGAAATCTACTGGTAGCG 59.686 38.462 3.13 0.00 45.81 4.26
1547 3487 7.617041 ACTTTTGATGAAATCTACTGGTAGC 57.383 36.000 3.13 0.00 45.81 3.58
1608 3550 4.911610 CCGCAGTTACTTGATGACAAAAAG 59.088 41.667 0.00 0.23 35.49 2.27
1614 3556 6.534079 ACTTATAACCGCAGTTACTTGATGAC 59.466 38.462 0.00 0.00 41.19 3.06
1617 3559 5.293569 GCACTTATAACCGCAGTTACTTGAT 59.706 40.000 0.00 0.00 41.19 2.57
1620 3562 4.390909 GTGCACTTATAACCGCAGTTACTT 59.609 41.667 10.32 0.00 41.19 2.24
1622 3564 3.063045 GGTGCACTTATAACCGCAGTTAC 59.937 47.826 17.98 0.00 41.19 2.50
1680 3710 8.692710 TGGAGATTAACTCTGAAACATATACGT 58.307 33.333 0.00 0.00 44.37 3.57
1681 3711 8.969267 GTGGAGATTAACTCTGAAACATATACG 58.031 37.037 0.00 0.00 44.37 3.06
1682 3712 9.817809 TGTGGAGATTAACTCTGAAACATATAC 57.182 33.333 0.00 0.00 44.37 1.47
1684 3714 9.388506 CTTGTGGAGATTAACTCTGAAACATAT 57.611 33.333 0.00 0.00 44.37 1.78
1753 3783 2.045926 AGCGTGTCCATTCCAGGC 60.046 61.111 0.00 0.00 42.42 4.85
1877 3909 1.913419 ACTTGGCTTCCCGAAATAGGA 59.087 47.619 0.00 0.00 0.00 2.94
1903 3935 5.836024 ATACACCTTCCTTAAACCTCACA 57.164 39.130 0.00 0.00 0.00 3.58
1961 3993 7.397221 TCTGAACAAATAGACAGACATCCAAT 58.603 34.615 0.00 0.00 35.01 3.16
2002 4036 6.714356 TCTCACTCAGTACCATAGATGATCTG 59.286 42.308 4.96 0.00 0.00 2.90
2012 4046 4.774726 ACAGACATTCTCACTCAGTACCAT 59.225 41.667 0.00 0.00 0.00 3.55
2020 4054 7.897575 AACATAGAAACAGACATTCTCACTC 57.102 36.000 0.00 0.00 38.13 3.51
2022 4056 9.173939 CAAAAACATAGAAACAGACATTCTCAC 57.826 33.333 0.00 0.00 38.13 3.51
2023 4057 8.352201 CCAAAAACATAGAAACAGACATTCTCA 58.648 33.333 0.00 0.00 38.13 3.27
2078 4116 4.223923 AGCTTGTAACCTTGAGCATACTCT 59.776 41.667 0.00 0.00 43.85 3.24
2327 4367 8.926715 AAAGGTTTTTCAGAAAATACAGTGTC 57.073 30.769 9.19 0.00 37.12 3.67
2345 4385 0.983905 AACCCCCGGCAAAAAGGTTT 60.984 50.000 0.00 0.00 37.55 3.27
2382 4423 6.772716 AGGTGAATATTAAGCAACCTGGTATG 59.227 38.462 0.00 2.17 0.00 2.39
2409 4450 7.164230 ACCATGTTTGTAAGAACACAAAAGA 57.836 32.000 3.19 0.00 46.81 2.52
2416 4457 5.590530 AGCAAACCATGTTTGTAAGAACA 57.409 34.783 17.95 0.00 43.08 3.18
2555 4597 6.038603 TCAACCACAGAAACAGATCTTGAAAG 59.961 38.462 0.00 0.00 0.00 2.62
2737 5056 9.809096 CAGAGAAACTAAGCATAGAGTATTCAA 57.191 33.333 2.38 0.00 33.15 2.69
2738 5057 8.972127 ACAGAGAAACTAAGCATAGAGTATTCA 58.028 33.333 2.38 0.00 33.15 2.57
2822 5148 3.242543 CGGAATGTCAGCATAGTTTCTGC 60.243 47.826 0.00 0.00 39.97 4.26
3005 5343 1.459450 TTTCCCTTTGCTGATACCGC 58.541 50.000 0.00 0.00 0.00 5.68
3082 5420 0.390472 CTCAGGCTGGAACTTCGTCC 60.390 60.000 15.73 0.00 38.27 4.79
3200 5539 5.514500 ACACACATAAAACATACTCCCCT 57.486 39.130 0.00 0.00 0.00 4.79
3201 5540 6.207810 TGAAACACACATAAAACATACTCCCC 59.792 38.462 0.00 0.00 0.00 4.81
3226 5565 0.182775 AACCAACAGGCCGTCTCTTT 59.817 50.000 0.00 0.00 0.00 2.52
3235 5574 1.866601 GCACAAATTCAACCAACAGGC 59.133 47.619 0.00 0.00 0.00 4.85
3325 5664 1.472480 GTTCCCCAACAATCATGACGG 59.528 52.381 0.00 0.00 32.14 4.79
3381 7665 9.717942 GTTGCTAGATTACTCCATAGATTGATT 57.282 33.333 0.00 0.00 0.00 2.57
3517 7988 4.839121 ACCGTTCTTTGGTGCTTATATCA 58.161 39.130 0.00 0.00 38.60 2.15
3814 8353 2.784654 CCCCTTGGGGTGGAAACCA 61.785 63.158 16.51 0.00 42.41 3.67


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

AutoCloner maintained by Alex Coulton.