Multiple sequence alignment - TraesCS7B01G325200

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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 TraesCS7B01G325200 chr7B 100.000 3493 0 0 1 3493 577562585 577559093 0.000000e+00 6451
1 TraesCS7B01G325200 chr7B 93.852 2814 165 6 684 3493 730041548 730044357 0.000000e+00 4231
2 TraesCS7B01G325200 chr7B 89.498 438 39 6 385 820 535843068 535842636 6.590000e-152 547
3 TraesCS7B01G325200 chr7B 93.939 330 17 3 57 384 577555018 577554690 2.420000e-136 496
4 TraesCS7B01G325200 chr7B 94.444 270 13 2 385 654 730041286 730041553 6.980000e-112 414
5 TraesCS7B01G325200 chr1A 94.857 2625 116 10 875 3493 208901578 208898967 0.000000e+00 4082
6 TraesCS7B01G325200 chr1A 86.667 90 10 2 626 715 208901813 208901726 7.980000e-17 99
7 TraesCS7B01G325200 chr1B 94.971 2585 121 6 916 3493 424422864 424425446 0.000000e+00 4045
8 TraesCS7B01G325200 chr3B 95.752 2495 97 5 1001 3493 279659177 279656690 0.000000e+00 4012
9 TraesCS7B01G325200 chr3B 95.631 2495 103 4 1001 3493 245928380 245930870 0.000000e+00 3999
10 TraesCS7B01G325200 chr3B 95.026 2513 123 2 983 3493 68354223 68351711 0.000000e+00 3947
11 TraesCS7B01G325200 chr3B 89.342 319 22 8 385 699 428108643 428108333 1.180000e-104 390
12 TraesCS7B01G325200 chr6A 94.252 2627 142 7 872 3493 55358299 55360921 0.000000e+00 4006
13 TraesCS7B01G325200 chr6A 87.778 90 9 2 626 715 55358057 55358144 1.710000e-18 104
14 TraesCS7B01G325200 chr7D 95.511 2495 109 3 1001 3493 388643332 388640839 0.000000e+00 3984
15 TraesCS7B01G325200 chr7D 95.387 2493 109 4 1003 3493 414100224 414097736 0.000000e+00 3962
16 TraesCS7B01G325200 chr2B 93.694 333 19 2 57 387 143279801 143279469 6.730000e-137 497
17 TraesCS7B01G325200 chr2B 90.991 333 21 8 57 384 448288938 448288610 1.150000e-119 440
18 TraesCS7B01G325200 chr3A 84.387 506 41 19 384 887 353182052 353181583 2.460000e-126 462
19 TraesCS7B01G325200 chr3A 88.889 90 8 2 626 715 630805694 630805607 3.690000e-20 110
20 TraesCS7B01G325200 chr2D 83.953 511 50 17 383 887 601957528 601958012 8.830000e-126 460
21 TraesCS7B01G325200 chr2D 94.466 253 10 4 384 634 15465740 15465490 1.520000e-103 387
22 TraesCS7B01G325200 chr2D 82.222 180 16 9 745 919 15465458 15465290 1.310000e-29 141
23 TraesCS7B01G325200 chr5B 91.212 330 27 2 57 384 708848339 708848010 6.880000e-122 448
24 TraesCS7B01G325200 chr5B 91.212 330 27 2 57 384 708860610 708860281 6.880000e-122 448
25 TraesCS7B01G325200 chr5B 90.991 333 22 6 57 384 160141999 160141670 3.200000e-120 442
26 TraesCS7B01G325200 chr2A 91.265 332 23 6 57 384 520555687 520556016 6.880000e-122 448
27 TraesCS7B01G325200 chr2A 91.265 332 23 6 57 384 520560858 520561187 6.880000e-122 448
28 TraesCS7B01G325200 chr2A 82.122 509 48 23 385 889 333714156 333713687 2.530000e-106 396
29 TraesCS7B01G325200 chr6B 90.909 330 22 8 57 382 141616979 141617304 1.490000e-118 436
30 TraesCS7B01G325200 chr5A 89.625 347 23 7 384 727 547391972 547391636 2.490000e-116 429
31 TraesCS7B01G325200 chr4A 90.029 341 21 7 385 722 30761933 30761603 2.490000e-116 429
32 TraesCS7B01G325200 chr5D 93.227 251 14 3 385 634 128318559 128318311 1.980000e-97 366


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 TraesCS7B01G325200 chr7B 577559093 577562585 3492 True 6451.0 6451 100.000 1 3493 1 chr7B.!!$R3 3492
1 TraesCS7B01G325200 chr7B 730041286 730044357 3071 False 2322.5 4231 94.148 385 3493 2 chr7B.!!$F1 3108
2 TraesCS7B01G325200 chr1A 208898967 208901813 2846 True 2090.5 4082 90.762 626 3493 2 chr1A.!!$R1 2867
3 TraesCS7B01G325200 chr1B 424422864 424425446 2582 False 4045.0 4045 94.971 916 3493 1 chr1B.!!$F1 2577
4 TraesCS7B01G325200 chr3B 279656690 279659177 2487 True 4012.0 4012 95.752 1001 3493 1 chr3B.!!$R2 2492
5 TraesCS7B01G325200 chr3B 245928380 245930870 2490 False 3999.0 3999 95.631 1001 3493 1 chr3B.!!$F1 2492
6 TraesCS7B01G325200 chr3B 68351711 68354223 2512 True 3947.0 3947 95.026 983 3493 1 chr3B.!!$R1 2510
7 TraesCS7B01G325200 chr6A 55358057 55360921 2864 False 2055.0 4006 91.015 626 3493 2 chr6A.!!$F1 2867
8 TraesCS7B01G325200 chr7D 388640839 388643332 2493 True 3984.0 3984 95.511 1001 3493 1 chr7D.!!$R1 2492
9 TraesCS7B01G325200 chr7D 414097736 414100224 2488 True 3962.0 3962 95.387 1003 3493 1 chr7D.!!$R2 2490

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
102 103 0.032813 TAGGACGGAGGTTGTAGGGG 60.033 60.0 0.00 0.00 0.00 4.79 F
219 220 0.107800 GTTTAGGGTTCCGGCTCCTC 60.108 60.0 12.29 4.77 32.46 3.71 F
965 1054 0.112606 TTCTCGTCCAGACCCTCTGT 59.887 55.0 0.00 0.00 42.80 3.41 F
1611 1709 0.470766 TTGGTTGTCGTACTTGCCCT 59.529 50.0 0.00 0.00 0.00 5.19 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1663 1761 0.395311 TCCTTACGGAGCCGAGACAT 60.395 55.0 16.83 0.00 42.83 3.06 R
1906 2007 1.252215 TAGTCGCAATGTGGACGGGA 61.252 55.0 0.00 0.00 38.20 5.14 R
2404 2511 0.032815 TCAAGGATGACGCGACAACA 59.967 50.0 15.93 7.85 0.00 3.33 R
3204 3311 0.036105 CACCACCATGTAGAGCAGCA 60.036 55.0 0.00 0.00 0.00 4.41 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
22 23 5.700402 AGTGCCTACAATATTCTCAGGTT 57.300 39.130 7.86 0.00 0.00 3.50
23 24 5.431765 AGTGCCTACAATATTCTCAGGTTG 58.568 41.667 7.86 0.00 0.00 3.77
24 25 4.035675 GTGCCTACAATATTCTCAGGTTGC 59.964 45.833 7.86 0.00 0.00 4.17
25 26 4.199310 GCCTACAATATTCTCAGGTTGCA 58.801 43.478 7.86 0.00 0.00 4.08
26 27 4.823989 GCCTACAATATTCTCAGGTTGCAT 59.176 41.667 0.00 0.00 0.00 3.96
27 28 5.300286 GCCTACAATATTCTCAGGTTGCATT 59.700 40.000 0.00 0.00 0.00 3.56
28 29 6.183360 GCCTACAATATTCTCAGGTTGCATTT 60.183 38.462 0.00 0.00 0.00 2.32
29 30 7.631377 GCCTACAATATTCTCAGGTTGCATTTT 60.631 37.037 0.00 0.00 0.00 1.82
30 31 8.253113 CCTACAATATTCTCAGGTTGCATTTTT 58.747 33.333 0.00 0.00 0.00 1.94
53 54 9.598517 TTTTTCAAATGCTGAATGTTTAGTTCT 57.401 25.926 0.00 0.00 43.64 3.01
54 55 9.598517 TTTTCAAATGCTGAATGTTTAGTTCTT 57.401 25.926 0.00 0.00 43.64 2.52
55 56 8.801715 TTCAAATGCTGAATGTTTAGTTCTTC 57.198 30.769 0.00 0.00 39.20 2.87
56 57 8.169977 TCAAATGCTGAATGTTTAGTTCTTCT 57.830 30.769 0.00 0.00 0.00 2.85
57 58 8.077991 TCAAATGCTGAATGTTTAGTTCTTCTG 58.922 33.333 0.00 0.00 0.00 3.02
58 59 5.947228 TGCTGAATGTTTAGTTCTTCTGG 57.053 39.130 0.00 0.00 0.00 3.86
59 60 5.376625 TGCTGAATGTTTAGTTCTTCTGGT 58.623 37.500 0.00 0.00 0.00 4.00
60 61 6.530120 TGCTGAATGTTTAGTTCTTCTGGTA 58.470 36.000 0.00 0.00 0.00 3.25
61 62 6.650807 TGCTGAATGTTTAGTTCTTCTGGTAG 59.349 38.462 0.00 0.00 0.00 3.18
62 63 6.092807 GCTGAATGTTTAGTTCTTCTGGTAGG 59.907 42.308 0.00 0.00 0.00 3.18
63 64 7.311092 TGAATGTTTAGTTCTTCTGGTAGGA 57.689 36.000 0.00 0.00 0.00 2.94
64 65 7.386851 TGAATGTTTAGTTCTTCTGGTAGGAG 58.613 38.462 0.00 0.00 0.00 3.69
65 66 5.148651 TGTTTAGTTCTTCTGGTAGGAGC 57.851 43.478 0.00 0.00 0.00 4.70
66 67 4.838986 TGTTTAGTTCTTCTGGTAGGAGCT 59.161 41.667 0.00 0.00 0.00 4.09
67 68 6.014647 TGTTTAGTTCTTCTGGTAGGAGCTA 58.985 40.000 0.00 0.00 0.00 3.32
68 69 6.153000 TGTTTAGTTCTTCTGGTAGGAGCTAG 59.847 42.308 0.00 0.00 0.00 3.42
69 70 3.637769 AGTTCTTCTGGTAGGAGCTAGG 58.362 50.000 0.00 0.00 0.00 3.02
70 71 2.696187 GTTCTTCTGGTAGGAGCTAGGG 59.304 54.545 0.00 0.00 0.00 3.53
71 72 1.930914 TCTTCTGGTAGGAGCTAGGGT 59.069 52.381 0.00 0.00 0.00 4.34
72 73 2.315155 TCTTCTGGTAGGAGCTAGGGTT 59.685 50.000 0.00 0.00 0.00 4.11
73 74 2.456073 TCTGGTAGGAGCTAGGGTTC 57.544 55.000 0.00 0.00 0.00 3.62
74 75 1.930914 TCTGGTAGGAGCTAGGGTTCT 59.069 52.381 0.00 0.00 0.00 3.01
75 76 3.128848 TCTGGTAGGAGCTAGGGTTCTA 58.871 50.000 0.00 0.00 0.00 2.10
76 77 3.117587 TCTGGTAGGAGCTAGGGTTCTAC 60.118 52.174 6.64 6.64 0.00 2.59
77 78 2.091444 TGGTAGGAGCTAGGGTTCTACC 60.091 54.545 20.99 20.99 37.60 3.18
78 79 2.228925 GTAGGAGCTAGGGTTCTACCG 58.771 57.143 4.39 0.00 39.83 4.02
79 80 0.106116 AGGAGCTAGGGTTCTACCGG 60.106 60.000 0.00 0.00 39.83 5.28
80 81 1.114119 GGAGCTAGGGTTCTACCGGG 61.114 65.000 6.32 0.00 39.83 5.73
81 82 0.396835 GAGCTAGGGTTCTACCGGGT 60.397 60.000 6.32 4.46 39.83 5.28
82 83 0.396835 AGCTAGGGTTCTACCGGGTC 60.397 60.000 6.32 0.00 39.83 4.46
83 84 0.396835 GCTAGGGTTCTACCGGGTCT 60.397 60.000 6.32 0.00 39.83 3.85
84 85 1.133668 GCTAGGGTTCTACCGGGTCTA 60.134 57.143 6.32 0.00 39.83 2.59
85 86 2.861274 CTAGGGTTCTACCGGGTCTAG 58.139 57.143 6.32 3.35 39.83 2.43
86 87 0.261109 AGGGTTCTACCGGGTCTAGG 59.739 60.000 6.32 0.00 39.83 3.02
87 88 0.259938 GGGTTCTACCGGGTCTAGGA 59.740 60.000 6.32 0.00 39.83 2.94
88 89 1.397672 GGTTCTACCGGGTCTAGGAC 58.602 60.000 6.32 0.63 0.00 3.85
89 90 1.020437 GTTCTACCGGGTCTAGGACG 58.980 60.000 6.32 0.00 32.65 4.79
94 95 2.274760 CGGGTCTAGGACGGAGGT 59.725 66.667 0.00 0.00 32.65 3.85
95 96 1.379576 CGGGTCTAGGACGGAGGTT 60.380 63.158 0.00 0.00 32.65 3.50
96 97 1.664321 CGGGTCTAGGACGGAGGTTG 61.664 65.000 0.00 0.00 32.65 3.77
97 98 0.614134 GGGTCTAGGACGGAGGTTGT 60.614 60.000 0.00 0.00 32.65 3.32
98 99 1.341383 GGGTCTAGGACGGAGGTTGTA 60.341 57.143 0.00 0.00 32.65 2.41
99 100 2.022934 GGTCTAGGACGGAGGTTGTAG 58.977 57.143 0.00 0.00 32.65 2.74
100 101 2.022934 GTCTAGGACGGAGGTTGTAGG 58.977 57.143 0.00 0.00 0.00 3.18
101 102 1.064166 TCTAGGACGGAGGTTGTAGGG 60.064 57.143 0.00 0.00 0.00 3.53
102 103 0.032813 TAGGACGGAGGTTGTAGGGG 60.033 60.000 0.00 0.00 0.00 4.79
103 104 1.305549 GGACGGAGGTTGTAGGGGA 60.306 63.158 0.00 0.00 0.00 4.81
104 105 0.906282 GGACGGAGGTTGTAGGGGAA 60.906 60.000 0.00 0.00 0.00 3.97
105 106 0.535797 GACGGAGGTTGTAGGGGAAG 59.464 60.000 0.00 0.00 0.00 3.46
106 107 0.908180 ACGGAGGTTGTAGGGGAAGG 60.908 60.000 0.00 0.00 0.00 3.46
107 108 0.616679 CGGAGGTTGTAGGGGAAGGA 60.617 60.000 0.00 0.00 0.00 3.36
108 109 1.665137 GGAGGTTGTAGGGGAAGGAA 58.335 55.000 0.00 0.00 0.00 3.36
109 110 1.560146 GGAGGTTGTAGGGGAAGGAAG 59.440 57.143 0.00 0.00 0.00 3.46
110 111 1.560146 GAGGTTGTAGGGGAAGGAAGG 59.440 57.143 0.00 0.00 0.00 3.46
111 112 1.153565 AGGTTGTAGGGGAAGGAAGGA 59.846 52.381 0.00 0.00 0.00 3.36
112 113 1.560146 GGTTGTAGGGGAAGGAAGGAG 59.440 57.143 0.00 0.00 0.00 3.69
113 114 2.267192 GTTGTAGGGGAAGGAAGGAGT 58.733 52.381 0.00 0.00 0.00 3.85
114 115 2.643304 GTTGTAGGGGAAGGAAGGAGTT 59.357 50.000 0.00 0.00 0.00 3.01
115 116 2.266279 TGTAGGGGAAGGAAGGAGTTG 58.734 52.381 0.00 0.00 0.00 3.16
116 117 1.560146 GTAGGGGAAGGAAGGAGTTGG 59.440 57.143 0.00 0.00 0.00 3.77
117 118 0.846870 AGGGGAAGGAAGGAGTTGGG 60.847 60.000 0.00 0.00 0.00 4.12
118 119 1.000771 GGGAAGGAAGGAGTTGGGC 60.001 63.158 0.00 0.00 0.00 5.36
119 120 1.377333 GGAAGGAAGGAGTTGGGCG 60.377 63.158 0.00 0.00 0.00 6.13
120 121 1.375326 GAAGGAAGGAGTTGGGCGT 59.625 57.895 0.00 0.00 0.00 5.68
121 122 0.955919 GAAGGAAGGAGTTGGGCGTG 60.956 60.000 0.00 0.00 0.00 5.34
122 123 2.359975 GGAAGGAGTTGGGCGTGG 60.360 66.667 0.00 0.00 0.00 4.94
123 124 2.747686 GAAGGAGTTGGGCGTGGA 59.252 61.111 0.00 0.00 0.00 4.02
124 125 1.671379 GAAGGAGTTGGGCGTGGAC 60.671 63.158 0.00 0.00 0.00 4.02
125 126 3.530910 AAGGAGTTGGGCGTGGACG 62.531 63.158 0.00 0.00 43.27 4.79
126 127 3.998672 GGAGTTGGGCGTGGACGA 61.999 66.667 2.73 0.00 43.02 4.20
127 128 2.432628 GAGTTGGGCGTGGACGAG 60.433 66.667 2.73 0.00 43.02 4.18
128 129 4.681978 AGTTGGGCGTGGACGAGC 62.682 66.667 2.73 0.00 43.02 5.03
129 130 4.681978 GTTGGGCGTGGACGAGCT 62.682 66.667 2.73 0.00 43.02 4.09
130 131 4.373116 TTGGGCGTGGACGAGCTC 62.373 66.667 2.73 2.73 43.02 4.09
202 203 3.083997 CAGGAGGCGGCTAGGGTT 61.084 66.667 13.24 0.00 0.00 4.11
203 204 2.285442 AGGAGGCGGCTAGGGTTT 60.285 61.111 13.24 0.00 0.00 3.27
204 205 1.002533 AGGAGGCGGCTAGGGTTTA 59.997 57.895 13.24 0.00 0.00 2.01
205 206 1.049289 AGGAGGCGGCTAGGGTTTAG 61.049 60.000 13.24 0.00 0.00 1.85
206 207 1.446366 GAGGCGGCTAGGGTTTAGG 59.554 63.158 13.24 0.00 0.00 2.69
207 208 2.041206 GAGGCGGCTAGGGTTTAGGG 62.041 65.000 13.24 0.00 0.00 3.53
208 209 2.372890 GGCGGCTAGGGTTTAGGGT 61.373 63.158 0.00 0.00 0.00 4.34
209 210 1.605992 GCGGCTAGGGTTTAGGGTT 59.394 57.895 0.00 0.00 0.00 4.11
210 211 0.463295 GCGGCTAGGGTTTAGGGTTC 60.463 60.000 0.00 0.00 0.00 3.62
211 212 0.179702 CGGCTAGGGTTTAGGGTTCC 59.820 60.000 0.00 0.00 0.00 3.62
212 213 0.179702 GGCTAGGGTTTAGGGTTCCG 59.820 60.000 0.00 0.00 0.00 4.30
213 214 0.179702 GCTAGGGTTTAGGGTTCCGG 59.820 60.000 0.00 0.00 0.00 5.14
214 215 0.179702 CTAGGGTTTAGGGTTCCGGC 59.820 60.000 0.00 0.00 0.00 6.13
215 216 0.252835 TAGGGTTTAGGGTTCCGGCT 60.253 55.000 0.00 0.00 0.00 5.52
216 217 1.077930 GGGTTTAGGGTTCCGGCTC 60.078 63.158 0.00 0.00 0.00 4.70
217 218 1.077930 GGTTTAGGGTTCCGGCTCC 60.078 63.158 0.00 0.53 0.00 4.70
218 219 1.559965 GGTTTAGGGTTCCGGCTCCT 61.560 60.000 13.24 13.24 34.85 3.69
219 220 0.107800 GTTTAGGGTTCCGGCTCCTC 60.108 60.000 12.29 4.77 32.46 3.71
220 221 0.252558 TTTAGGGTTCCGGCTCCTCT 60.253 55.000 12.29 10.56 32.46 3.69
221 222 0.686769 TTAGGGTTCCGGCTCCTCTC 60.687 60.000 12.29 0.00 32.46 3.20
222 223 2.905935 TAGGGTTCCGGCTCCTCTCG 62.906 65.000 12.29 0.00 32.46 4.04
223 224 3.839432 GGTTCCGGCTCCTCTCGG 61.839 72.222 0.00 0.00 46.89 4.63
234 235 3.854669 CTCTCGGAGCCGGGCAAT 61.855 66.667 23.09 0.00 40.19 3.56
235 236 2.443203 TCTCGGAGCCGGGCAATA 60.443 61.111 23.09 2.39 40.19 1.90
236 237 2.029666 CTCGGAGCCGGGCAATAG 59.970 66.667 23.09 8.94 40.25 1.73
237 238 2.443203 TCGGAGCCGGGCAATAGA 60.443 61.111 23.09 11.80 40.25 1.98
238 239 2.028125 CTCGGAGCCGGGCAATAGAA 62.028 60.000 23.09 0.15 40.25 2.10
239 240 1.153249 CGGAGCCGGGCAATAGAAA 60.153 57.895 23.09 0.00 35.56 2.52
240 241 0.535102 CGGAGCCGGGCAATAGAAAT 60.535 55.000 23.09 0.00 35.56 2.17
241 242 1.270625 CGGAGCCGGGCAATAGAAATA 60.271 52.381 23.09 0.00 35.56 1.40
242 243 2.427506 GGAGCCGGGCAATAGAAATAG 58.572 52.381 23.09 0.00 0.00 1.73
243 244 2.224548 GGAGCCGGGCAATAGAAATAGT 60.225 50.000 23.09 0.00 0.00 2.12
244 245 3.067833 GAGCCGGGCAATAGAAATAGTC 58.932 50.000 23.09 0.92 0.00 2.59
245 246 2.706190 AGCCGGGCAATAGAAATAGTCT 59.294 45.455 23.09 0.00 40.71 3.24
246 247 3.136626 AGCCGGGCAATAGAAATAGTCTT 59.863 43.478 23.09 0.00 37.84 3.01
247 248 4.347000 AGCCGGGCAATAGAAATAGTCTTA 59.653 41.667 23.09 0.00 37.84 2.10
248 249 5.013183 AGCCGGGCAATAGAAATAGTCTTAT 59.987 40.000 23.09 0.00 37.84 1.73
249 250 5.705905 GCCGGGCAATAGAAATAGTCTTATT 59.294 40.000 15.62 0.00 37.84 1.40
250 251 6.348540 GCCGGGCAATAGAAATAGTCTTATTG 60.349 42.308 15.62 0.00 37.84 1.90
251 252 6.348540 CCGGGCAATAGAAATAGTCTTATTGC 60.349 42.308 16.81 16.81 43.56 3.56
252 253 6.428159 CGGGCAATAGAAATAGTCTTATTGCT 59.572 38.462 20.95 8.40 43.65 3.91
253 254 7.041098 CGGGCAATAGAAATAGTCTTATTGCTT 60.041 37.037 20.95 0.00 43.65 3.91
254 255 9.284968 GGGCAATAGAAATAGTCTTATTGCTTA 57.715 33.333 20.95 0.00 43.65 3.09
261 262 9.189156 AGAAATAGTCTTATTGCTTAATTGCCA 57.811 29.630 0.00 0.00 32.15 4.92
262 263 9.801873 GAAATAGTCTTATTGCTTAATTGCCAA 57.198 29.630 0.00 0.00 30.00 4.52
265 266 9.807649 ATAGTCTTATTGCTTAATTGCCAAAAG 57.192 29.630 0.00 0.00 0.00 2.27
266 267 7.895759 AGTCTTATTGCTTAATTGCCAAAAGA 58.104 30.769 0.00 0.00 0.00 2.52
267 268 8.031277 AGTCTTATTGCTTAATTGCCAAAAGAG 58.969 33.333 0.00 0.00 0.00 2.85
268 269 7.814587 GTCTTATTGCTTAATTGCCAAAAGAGT 59.185 33.333 0.00 0.00 0.00 3.24
269 270 8.028938 TCTTATTGCTTAATTGCCAAAAGAGTC 58.971 33.333 0.00 0.00 0.00 3.36
270 271 5.789643 TTGCTTAATTGCCAAAAGAGTCT 57.210 34.783 0.00 0.00 0.00 3.24
271 272 5.789643 TGCTTAATTGCCAAAAGAGTCTT 57.210 34.783 0.00 0.00 0.00 3.01
272 273 6.892658 TGCTTAATTGCCAAAAGAGTCTTA 57.107 33.333 5.65 0.00 0.00 2.10
273 274 6.677913 TGCTTAATTGCCAAAAGAGTCTTAC 58.322 36.000 5.65 0.00 0.00 2.34
274 275 6.264292 TGCTTAATTGCCAAAAGAGTCTTACA 59.736 34.615 5.65 0.00 0.00 2.41
275 276 7.145323 GCTTAATTGCCAAAAGAGTCTTACAA 58.855 34.615 5.65 9.04 0.00 2.41
276 277 7.814587 GCTTAATTGCCAAAAGAGTCTTACAAT 59.185 33.333 5.65 10.79 0.00 2.71
277 278 9.696917 CTTAATTGCCAAAAGAGTCTTACAATT 57.303 29.630 24.32 24.32 39.21 2.32
278 279 7.951530 AATTGCCAAAAGAGTCTTACAATTG 57.048 32.000 22.36 16.24 35.72 2.32
279 280 6.463995 TTGCCAAAAGAGTCTTACAATTGT 57.536 33.333 16.68 16.68 0.00 2.71
280 281 6.463995 TGCCAAAAGAGTCTTACAATTGTT 57.536 33.333 17.78 0.00 0.00 2.83
281 282 6.872920 TGCCAAAAGAGTCTTACAATTGTTT 58.127 32.000 17.78 0.00 0.00 2.83
282 283 8.001881 TGCCAAAAGAGTCTTACAATTGTTTA 57.998 30.769 17.78 4.69 0.00 2.01
283 284 8.637986 TGCCAAAAGAGTCTTACAATTGTTTAT 58.362 29.630 17.78 0.00 0.00 1.40
296 297 9.938670 TTACAATTGTTTATATAACCACGATGC 57.061 29.630 17.78 0.00 0.00 3.91
297 298 8.220755 ACAATTGTTTATATAACCACGATGCT 57.779 30.769 4.92 0.00 0.00 3.79
298 299 9.332502 ACAATTGTTTATATAACCACGATGCTA 57.667 29.630 4.92 0.00 0.00 3.49
327 328 6.944234 AATAAGATAACTTGTGGGCTAAGC 57.056 37.500 0.00 0.00 37.53 3.09
328 329 3.621558 AAGATAACTTGTGGGCTAAGCC 58.378 45.455 0.00 0.00 40.53 4.35
340 341 2.928334 GGCTAAGCCCCTAACTAAACC 58.072 52.381 0.00 0.00 44.06 3.27
341 342 2.508716 GGCTAAGCCCCTAACTAAACCT 59.491 50.000 0.00 0.00 44.06 3.50
342 343 3.053842 GGCTAAGCCCCTAACTAAACCTT 60.054 47.826 0.00 0.00 44.06 3.50
343 344 4.197750 GCTAAGCCCCTAACTAAACCTTC 58.802 47.826 0.00 0.00 0.00 3.46
344 345 3.733883 AAGCCCCTAACTAAACCTTCC 57.266 47.619 0.00 0.00 0.00 3.46
345 346 1.921049 AGCCCCTAACTAAACCTTCCC 59.079 52.381 0.00 0.00 0.00 3.97
346 347 1.637035 GCCCCTAACTAAACCTTCCCA 59.363 52.381 0.00 0.00 0.00 4.37
347 348 2.356844 GCCCCTAACTAAACCTTCCCAG 60.357 54.545 0.00 0.00 0.00 4.45
348 349 2.917600 CCCCTAACTAAACCTTCCCAGT 59.082 50.000 0.00 0.00 0.00 4.00
349 350 3.308188 CCCCTAACTAAACCTTCCCAGTG 60.308 52.174 0.00 0.00 0.00 3.66
350 351 3.308188 CCCTAACTAAACCTTCCCAGTGG 60.308 52.174 0.63 0.63 0.00 4.00
351 352 2.971901 AACTAAACCTTCCCAGTGGG 57.028 50.000 23.57 23.57 46.11 4.61
352 353 0.404426 ACTAAACCTTCCCAGTGGGC 59.596 55.000 24.75 0.00 43.94 5.36
353 354 0.323451 CTAAACCTTCCCAGTGGGCC 60.323 60.000 24.75 0.00 43.94 5.80
354 355 0.774491 TAAACCTTCCCAGTGGGCCT 60.774 55.000 24.75 6.08 43.94 5.19
355 356 2.081585 AAACCTTCCCAGTGGGCCTC 62.082 60.000 24.75 0.00 43.94 4.70
356 357 3.732849 CCTTCCCAGTGGGCCTCC 61.733 72.222 24.75 0.00 43.94 4.30
357 358 2.612115 CTTCCCAGTGGGCCTCCT 60.612 66.667 24.75 0.00 43.94 3.69
358 359 2.610859 TTCCCAGTGGGCCTCCTC 60.611 66.667 24.75 0.00 43.94 3.71
359 360 4.741239 TCCCAGTGGGCCTCCTCC 62.741 72.222 24.75 0.00 43.94 4.30
364 365 4.791069 GTGGGCCTCCTCCGGGTA 62.791 72.222 4.53 0.00 0.00 3.69
365 366 3.774336 TGGGCCTCCTCCGGGTAT 61.774 66.667 4.53 0.00 0.00 2.73
366 367 2.405612 TGGGCCTCCTCCGGGTATA 61.406 63.158 4.53 0.00 0.00 1.47
367 368 1.152183 GGGCCTCCTCCGGGTATAA 60.152 63.158 0.84 0.00 0.00 0.98
368 369 1.192803 GGGCCTCCTCCGGGTATAAG 61.193 65.000 0.84 0.00 0.00 1.73
369 370 0.471401 GGCCTCCTCCGGGTATAAGT 60.471 60.000 0.00 0.00 0.00 2.24
370 371 1.421480 GCCTCCTCCGGGTATAAGTT 58.579 55.000 0.00 0.00 0.00 2.66
371 372 2.601905 GCCTCCTCCGGGTATAAGTTA 58.398 52.381 0.00 0.00 0.00 2.24
372 373 2.298446 GCCTCCTCCGGGTATAAGTTAC 59.702 54.545 0.00 0.00 0.00 2.50
373 374 2.896044 CCTCCTCCGGGTATAAGTTACC 59.104 54.545 0.00 0.00 36.88 2.85
441 442 7.733402 TTGTATTTATCCCGTTGTATAAGGC 57.267 36.000 0.00 0.00 0.00 4.35
458 459 2.017049 AGGCGTTTCCTGCATATGTTC 58.983 47.619 4.29 0.00 45.54 3.18
543 544 6.270231 CCTAACATGGTATTAGAGCCTTAGGT 59.730 42.308 0.00 0.00 32.31 3.08
566 567 0.448197 TTTTTCGCACGTGCAACTCA 59.552 45.000 37.03 17.02 42.21 3.41
590 591 0.670706 CTCGATCCAATCTCCGAGCA 59.329 55.000 0.00 0.00 41.31 4.26
594 595 2.374830 ATCCAATCTCCGAGCAGCCG 62.375 60.000 0.00 0.00 0.00 5.52
616 617 0.525882 GTCCTTCTTCTACGAGCGGC 60.526 60.000 0.00 0.00 0.00 6.53
617 618 0.963856 TCCTTCTTCTACGAGCGGCA 60.964 55.000 1.45 0.00 0.00 5.69
670 671 1.807573 CTTCTGCCCTCGAGTTCGC 60.808 63.158 12.31 10.33 39.60 4.70
677 678 4.735132 CTCGAGTTCGCCCGCCAA 62.735 66.667 3.62 0.00 39.60 4.52
761 763 1.519719 GTCCAGCTCGAGCAATCCT 59.480 57.895 36.87 15.35 45.16 3.24
787 874 1.302271 CTCCTGCTGCTGCTTGTCA 60.302 57.895 17.00 0.00 40.48 3.58
793 880 0.886563 GCTGCTGCTTGTCAAGGATT 59.113 50.000 14.40 0.00 36.03 3.01
820 907 2.113774 CTGCTGTTGCCCAGGACA 59.886 61.111 3.03 0.00 41.81 4.02
821 908 2.203337 TGCTGTTGCCCAGGACAC 60.203 61.111 3.03 0.00 41.81 3.67
822 909 2.113986 GCTGTTGCCCAGGACACT 59.886 61.111 3.03 0.00 41.81 3.55
833 920 4.129148 GGACACTGGCCCCATCCC 62.129 72.222 0.00 0.00 0.00 3.85
845 932 0.897863 CCCATCCCGTTTTCCAAGCA 60.898 55.000 0.00 0.00 0.00 3.91
965 1054 0.112606 TTCTCGTCCAGACCCTCTGT 59.887 55.000 0.00 0.00 42.80 3.41
983 1073 0.949397 GTTGGTTCCCTTCCGTTGAC 59.051 55.000 0.00 0.00 0.00 3.18
984 1074 0.547075 TTGGTTCCCTTCCGTTGACA 59.453 50.000 0.00 0.00 0.00 3.58
1187 1284 2.124236 CCCTACTCCGCCGACTCT 60.124 66.667 0.00 0.00 0.00 3.24
1320 1418 2.760650 TCAGACGTATCATGGTGCTCTT 59.239 45.455 0.00 0.00 0.00 2.85
1531 1629 3.010250 TCTTCAGCAGGGTGACTCTACTA 59.990 47.826 0.00 0.00 0.00 1.82
1536 1634 3.702045 AGCAGGGTGACTCTACTATTGAC 59.298 47.826 0.00 0.00 0.00 3.18
1611 1709 0.470766 TTGGTTGTCGTACTTGCCCT 59.529 50.000 0.00 0.00 0.00 5.19
1663 1761 1.081094 TCATCGCGTCTACGAGTTCA 58.919 50.000 5.77 0.00 46.69 3.18
1721 1819 1.453015 AGTTGTTTGCTCGTGGCCA 60.453 52.632 0.00 0.00 40.92 5.36
1781 1879 1.204941 GGAGACTCGCTTACATGGTGT 59.795 52.381 0.00 0.00 0.00 4.16
1789 1887 2.606795 CGCTTACATGGTGTTGGTTTGG 60.607 50.000 0.00 0.00 0.00 3.28
1906 2007 3.073735 CTGGAGGCTCAGGTCGCT 61.074 66.667 17.69 0.00 0.00 4.93
1956 2058 5.651612 ATGATGGTCATATTGAGTCCCAA 57.348 39.130 0.00 0.00 34.88 4.12
2035 2137 5.770162 TCATCATCTACCTCGATAGCTTCAA 59.230 40.000 0.00 0.00 0.00 2.69
2161 2265 1.556911 CTGAGCAACCACCCTCTACAT 59.443 52.381 0.00 0.00 0.00 2.29
2162 2266 1.555075 TGAGCAACCACCCTCTACATC 59.445 52.381 0.00 0.00 0.00 3.06
2177 2281 2.160721 ACATCGTCAGGTACATCCCT 57.839 50.000 0.00 0.00 36.75 4.20
2327 2434 3.198853 AGAGGCAATCTTACCACTCCTTC 59.801 47.826 0.00 0.00 32.99 3.46
2328 2435 3.185455 AGGCAATCTTACCACTCCTTCT 58.815 45.455 0.00 0.00 0.00 2.85
2329 2436 3.589288 AGGCAATCTTACCACTCCTTCTT 59.411 43.478 0.00 0.00 0.00 2.52
2335 2442 8.204836 GCAATCTTACCACTCCTTCTTATTCTA 58.795 37.037 0.00 0.00 0.00 2.10
2404 2511 4.973168 TGCTGGTCAACTTACTGATTCTT 58.027 39.130 0.00 0.00 0.00 2.52
2450 2557 1.974236 CTCTTGTTCTGTCCAGGACCT 59.026 52.381 17.59 0.00 36.06 3.85
2478 2585 2.121963 ACTCTGGTTGGGGCTGGA 60.122 61.111 0.00 0.00 0.00 3.86
2539 2646 1.406887 GGCTTCATGTTCCTTCCGCTA 60.407 52.381 0.00 0.00 0.00 4.26
2571 2678 0.035458 CCAGTTCCTCCGCTTCAGTT 59.965 55.000 0.00 0.00 0.00 3.16
2626 2733 2.724977 TCGACTTGGTCATCTGTGTC 57.275 50.000 0.00 0.00 32.09 3.67
2632 2739 3.181465 ACTTGGTCATCTGTGTCGTTCTT 60.181 43.478 0.00 0.00 0.00 2.52
2671 2778 0.997363 TCGAGGTCTTCTGGGGTCTA 59.003 55.000 0.00 0.00 0.00 2.59
2674 2781 2.321719 GAGGTCTTCTGGGGTCTATCC 58.678 57.143 0.00 0.00 0.00 2.59
2785 2892 6.270815 CGTCCTTTCGATTTAGTCCATTCTA 58.729 40.000 0.00 0.00 0.00 2.10
2800 2907 2.922740 TTCTAATGTATGGGGTCCGC 57.077 50.000 0.00 0.00 0.00 5.54
2991 3098 0.601558 TTGACTCCGCTGGTGAGTAC 59.398 55.000 0.00 0.00 42.94 2.73
3091 3198 1.598130 GGTGTGGCTGAGCGAAAGT 60.598 57.895 0.00 0.00 0.00 2.66
3131 3238 1.402968 GGCTCGTGCATTGATGATTGT 59.597 47.619 12.07 0.00 41.91 2.71
3186 3293 2.158652 CGTCTCCACCTCCACCTATCTA 60.159 54.545 0.00 0.00 0.00 1.98
3203 3310 8.153550 CACCTATCTAATCAATCTACAGCCTTT 58.846 37.037 0.00 0.00 0.00 3.11
3204 3311 8.718656 ACCTATCTAATCAATCTACAGCCTTTT 58.281 33.333 0.00 0.00 0.00 2.27
3281 3388 0.110238 TCGATGCTTCGCTTGTTTGC 60.110 50.000 16.54 0.00 45.10 3.68
3317 3424 3.171828 TTCTTGCCCCTCGCGAACA 62.172 57.895 11.33 3.24 42.08 3.18
3403 3510 4.262463 GCTATCGTTGTTGGGATCCTATCA 60.262 45.833 12.58 8.34 0.00 2.15
3453 3560 3.320826 TGACTTTTGATGAGTCTCGTCCA 59.679 43.478 17.65 5.74 43.07 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 4.035675 GCAACCTGAGAATATTGTAGGCAC 59.964 45.833 0.00 0.00 31.69 5.01
2 3 4.199310 GCAACCTGAGAATATTGTAGGCA 58.801 43.478 0.00 0.00 31.69 4.75
3 4 4.199310 TGCAACCTGAGAATATTGTAGGC 58.801 43.478 0.00 0.00 31.69 3.93
4 5 6.949352 AATGCAACCTGAGAATATTGTAGG 57.051 37.500 0.00 0.22 34.70 3.18
31 32 8.077991 CAGAAGAACTAAACATTCAGCATTTGA 58.922 33.333 0.00 0.00 0.00 2.69
32 33 7.327761 CCAGAAGAACTAAACATTCAGCATTTG 59.672 37.037 0.00 0.00 0.00 2.32
33 34 7.014615 ACCAGAAGAACTAAACATTCAGCATTT 59.985 33.333 0.00 0.00 0.00 2.32
34 35 6.491403 ACCAGAAGAACTAAACATTCAGCATT 59.509 34.615 0.00 0.00 0.00 3.56
35 36 6.006449 ACCAGAAGAACTAAACATTCAGCAT 58.994 36.000 0.00 0.00 0.00 3.79
36 37 5.376625 ACCAGAAGAACTAAACATTCAGCA 58.623 37.500 0.00 0.00 0.00 4.41
37 38 5.948992 ACCAGAAGAACTAAACATTCAGC 57.051 39.130 0.00 0.00 0.00 4.26
38 39 7.386851 TCCTACCAGAAGAACTAAACATTCAG 58.613 38.462 0.00 0.00 0.00 3.02
39 40 7.311092 TCCTACCAGAAGAACTAAACATTCA 57.689 36.000 0.00 0.00 0.00 2.57
40 41 6.314152 GCTCCTACCAGAAGAACTAAACATTC 59.686 42.308 0.00 0.00 0.00 2.67
41 42 6.013293 AGCTCCTACCAGAAGAACTAAACATT 60.013 38.462 0.00 0.00 0.00 2.71
42 43 5.485708 AGCTCCTACCAGAAGAACTAAACAT 59.514 40.000 0.00 0.00 0.00 2.71
43 44 4.838986 AGCTCCTACCAGAAGAACTAAACA 59.161 41.667 0.00 0.00 0.00 2.83
44 45 5.408880 AGCTCCTACCAGAAGAACTAAAC 57.591 43.478 0.00 0.00 0.00 2.01
45 46 5.657302 CCTAGCTCCTACCAGAAGAACTAAA 59.343 44.000 0.00 0.00 0.00 1.85
46 47 5.202004 CCTAGCTCCTACCAGAAGAACTAA 58.798 45.833 0.00 0.00 0.00 2.24
47 48 4.386536 CCCTAGCTCCTACCAGAAGAACTA 60.387 50.000 0.00 0.00 0.00 2.24
48 49 3.628769 CCCTAGCTCCTACCAGAAGAACT 60.629 52.174 0.00 0.00 0.00 3.01
49 50 2.696187 CCCTAGCTCCTACCAGAAGAAC 59.304 54.545 0.00 0.00 0.00 3.01
50 51 2.315155 ACCCTAGCTCCTACCAGAAGAA 59.685 50.000 0.00 0.00 0.00 2.52
51 52 1.930914 ACCCTAGCTCCTACCAGAAGA 59.069 52.381 0.00 0.00 0.00 2.87
52 53 2.463047 ACCCTAGCTCCTACCAGAAG 57.537 55.000 0.00 0.00 0.00 2.85
53 54 2.315155 AGAACCCTAGCTCCTACCAGAA 59.685 50.000 0.00 0.00 0.00 3.02
54 55 1.930914 AGAACCCTAGCTCCTACCAGA 59.069 52.381 0.00 0.00 0.00 3.86
55 56 2.463047 AGAACCCTAGCTCCTACCAG 57.537 55.000 0.00 0.00 0.00 4.00
56 57 2.091444 GGTAGAACCCTAGCTCCTACCA 60.091 54.545 16.95 0.00 45.25 3.25
57 58 2.596346 GGTAGAACCCTAGCTCCTACC 58.404 57.143 0.00 0.00 41.49 3.18
58 59 2.228925 CGGTAGAACCCTAGCTCCTAC 58.771 57.143 0.00 0.00 40.31 3.18
59 60 1.144503 CCGGTAGAACCCTAGCTCCTA 59.855 57.143 0.00 0.00 40.31 2.94
60 61 0.106116 CCGGTAGAACCCTAGCTCCT 60.106 60.000 0.00 0.00 40.31 3.69
61 62 1.114119 CCCGGTAGAACCCTAGCTCC 61.114 65.000 0.00 0.00 40.31 4.70
62 63 0.396835 ACCCGGTAGAACCCTAGCTC 60.397 60.000 0.00 0.00 40.31 4.09
63 64 0.396835 GACCCGGTAGAACCCTAGCT 60.397 60.000 0.00 0.00 40.31 3.32
64 65 0.396835 AGACCCGGTAGAACCCTAGC 60.397 60.000 0.00 0.00 39.38 3.42
65 66 2.488710 CCTAGACCCGGTAGAACCCTAG 60.489 59.091 0.00 0.00 33.75 3.02
66 67 1.496429 CCTAGACCCGGTAGAACCCTA 59.504 57.143 0.00 0.00 33.75 3.53
67 68 0.261109 CCTAGACCCGGTAGAACCCT 59.739 60.000 0.00 0.00 33.75 4.34
68 69 0.259938 TCCTAGACCCGGTAGAACCC 59.740 60.000 0.00 0.00 33.75 4.11
69 70 1.397672 GTCCTAGACCCGGTAGAACC 58.602 60.000 0.00 0.00 34.05 3.62
70 71 1.020437 CGTCCTAGACCCGGTAGAAC 58.980 60.000 0.00 0.00 0.00 3.01
71 72 0.107017 CCGTCCTAGACCCGGTAGAA 60.107 60.000 0.00 0.00 37.00 2.10
72 73 0.982852 TCCGTCCTAGACCCGGTAGA 60.983 60.000 0.00 0.00 42.30 2.59
73 74 0.534652 CTCCGTCCTAGACCCGGTAG 60.535 65.000 0.00 0.00 42.30 3.18
74 75 1.528824 CTCCGTCCTAGACCCGGTA 59.471 63.158 0.00 0.00 42.30 4.02
75 76 2.274760 CTCCGTCCTAGACCCGGT 59.725 66.667 0.00 0.00 42.30 5.28
76 77 2.518825 CCTCCGTCCTAGACCCGG 60.519 72.222 0.00 0.00 43.03 5.73
77 78 1.379576 AACCTCCGTCCTAGACCCG 60.380 63.158 0.00 0.00 0.00 5.28
78 79 0.614134 ACAACCTCCGTCCTAGACCC 60.614 60.000 0.00 0.00 0.00 4.46
79 80 2.022934 CTACAACCTCCGTCCTAGACC 58.977 57.143 0.00 0.00 0.00 3.85
80 81 2.022934 CCTACAACCTCCGTCCTAGAC 58.977 57.143 0.00 0.00 0.00 2.59
81 82 1.064166 CCCTACAACCTCCGTCCTAGA 60.064 57.143 0.00 0.00 0.00 2.43
82 83 1.400737 CCCTACAACCTCCGTCCTAG 58.599 60.000 0.00 0.00 0.00 3.02
83 84 0.032813 CCCCTACAACCTCCGTCCTA 60.033 60.000 0.00 0.00 0.00 2.94
84 85 1.305887 CCCCTACAACCTCCGTCCT 60.306 63.158 0.00 0.00 0.00 3.85
85 86 0.906282 TTCCCCTACAACCTCCGTCC 60.906 60.000 0.00 0.00 0.00 4.79
86 87 0.535797 CTTCCCCTACAACCTCCGTC 59.464 60.000 0.00 0.00 0.00 4.79
87 88 0.908180 CCTTCCCCTACAACCTCCGT 60.908 60.000 0.00 0.00 0.00 4.69
88 89 0.616679 TCCTTCCCCTACAACCTCCG 60.617 60.000 0.00 0.00 0.00 4.63
89 90 1.560146 CTTCCTTCCCCTACAACCTCC 59.440 57.143 0.00 0.00 0.00 4.30
90 91 1.560146 CCTTCCTTCCCCTACAACCTC 59.440 57.143 0.00 0.00 0.00 3.85
91 92 1.153565 TCCTTCCTTCCCCTACAACCT 59.846 52.381 0.00 0.00 0.00 3.50
92 93 1.560146 CTCCTTCCTTCCCCTACAACC 59.440 57.143 0.00 0.00 0.00 3.77
93 94 2.267192 ACTCCTTCCTTCCCCTACAAC 58.733 52.381 0.00 0.00 0.00 3.32
94 95 2.642807 CAACTCCTTCCTTCCCCTACAA 59.357 50.000 0.00 0.00 0.00 2.41
95 96 2.266279 CAACTCCTTCCTTCCCCTACA 58.734 52.381 0.00 0.00 0.00 2.74
96 97 1.560146 CCAACTCCTTCCTTCCCCTAC 59.440 57.143 0.00 0.00 0.00 3.18
97 98 1.557188 CCCAACTCCTTCCTTCCCCTA 60.557 57.143 0.00 0.00 0.00 3.53
98 99 0.846870 CCCAACTCCTTCCTTCCCCT 60.847 60.000 0.00 0.00 0.00 4.79
99 100 1.691823 CCCAACTCCTTCCTTCCCC 59.308 63.158 0.00 0.00 0.00 4.81
100 101 1.000771 GCCCAACTCCTTCCTTCCC 60.001 63.158 0.00 0.00 0.00 3.97
101 102 1.377333 CGCCCAACTCCTTCCTTCC 60.377 63.158 0.00 0.00 0.00 3.46
102 103 0.955919 CACGCCCAACTCCTTCCTTC 60.956 60.000 0.00 0.00 0.00 3.46
103 104 1.073199 CACGCCCAACTCCTTCCTT 59.927 57.895 0.00 0.00 0.00 3.36
104 105 2.750350 CACGCCCAACTCCTTCCT 59.250 61.111 0.00 0.00 0.00 3.36
105 106 2.359975 CCACGCCCAACTCCTTCC 60.360 66.667 0.00 0.00 0.00 3.46
106 107 1.671379 GTCCACGCCCAACTCCTTC 60.671 63.158 0.00 0.00 0.00 3.46
107 108 2.430367 GTCCACGCCCAACTCCTT 59.570 61.111 0.00 0.00 0.00 3.36
108 109 4.003788 CGTCCACGCCCAACTCCT 62.004 66.667 0.00 0.00 0.00 3.69
109 110 3.934391 CTCGTCCACGCCCAACTCC 62.934 68.421 0.00 0.00 39.60 3.85
110 111 2.432628 CTCGTCCACGCCCAACTC 60.433 66.667 0.00 0.00 39.60 3.01
111 112 4.681978 GCTCGTCCACGCCCAACT 62.682 66.667 0.00 0.00 39.60 3.16
112 113 4.681978 AGCTCGTCCACGCCCAAC 62.682 66.667 0.00 0.00 39.60 3.77
113 114 4.373116 GAGCTCGTCCACGCCCAA 62.373 66.667 0.00 0.00 39.60 4.12
185 186 1.335132 TAAACCCTAGCCGCCTCCTG 61.335 60.000 0.00 0.00 0.00 3.86
186 187 1.002533 TAAACCCTAGCCGCCTCCT 59.997 57.895 0.00 0.00 0.00 3.69
187 188 1.446366 CTAAACCCTAGCCGCCTCC 59.554 63.158 0.00 0.00 0.00 4.30
188 189 1.446366 CCTAAACCCTAGCCGCCTC 59.554 63.158 0.00 0.00 0.00 4.70
189 190 2.070650 CCCTAAACCCTAGCCGCCT 61.071 63.158 0.00 0.00 0.00 5.52
190 191 1.918467 AACCCTAAACCCTAGCCGCC 61.918 60.000 0.00 0.00 0.00 6.13
191 192 0.463295 GAACCCTAAACCCTAGCCGC 60.463 60.000 0.00 0.00 0.00 6.53
192 193 0.179702 GGAACCCTAAACCCTAGCCG 59.820 60.000 0.00 0.00 0.00 5.52
193 194 0.179702 CGGAACCCTAAACCCTAGCC 59.820 60.000 0.00 0.00 0.00 3.93
194 195 0.179702 CCGGAACCCTAAACCCTAGC 59.820 60.000 0.00 0.00 0.00 3.42
195 196 0.179702 GCCGGAACCCTAAACCCTAG 59.820 60.000 5.05 0.00 0.00 3.02
196 197 0.252835 AGCCGGAACCCTAAACCCTA 60.253 55.000 5.05 0.00 0.00 3.53
197 198 1.540617 AGCCGGAACCCTAAACCCT 60.541 57.895 5.05 0.00 0.00 4.34
198 199 1.077930 GAGCCGGAACCCTAAACCC 60.078 63.158 5.05 0.00 0.00 4.11
199 200 1.077930 GGAGCCGGAACCCTAAACC 60.078 63.158 5.05 0.00 0.00 3.27
200 201 0.107800 GAGGAGCCGGAACCCTAAAC 60.108 60.000 5.05 0.00 0.00 2.01
201 202 0.252558 AGAGGAGCCGGAACCCTAAA 60.253 55.000 5.05 0.00 0.00 1.85
202 203 0.686769 GAGAGGAGCCGGAACCCTAA 60.687 60.000 5.05 0.00 0.00 2.69
203 204 1.076192 GAGAGGAGCCGGAACCCTA 60.076 63.158 5.05 0.00 0.00 3.53
204 205 2.364448 GAGAGGAGCCGGAACCCT 60.364 66.667 5.05 7.67 0.00 4.34
205 206 3.839432 CGAGAGGAGCCGGAACCC 61.839 72.222 5.05 1.57 0.00 4.11
217 218 2.427540 CTATTGCCCGGCTCCGAGAG 62.428 65.000 11.61 0.00 42.83 3.20
218 219 2.443203 TATTGCCCGGCTCCGAGA 60.443 61.111 11.61 0.00 42.83 4.04
219 220 2.028125 TTCTATTGCCCGGCTCCGAG 62.028 60.000 11.61 0.00 42.83 4.63
220 221 1.618876 TTTCTATTGCCCGGCTCCGA 61.619 55.000 11.61 0.00 42.83 4.55
221 222 0.535102 ATTTCTATTGCCCGGCTCCG 60.535 55.000 11.61 0.48 39.44 4.63
222 223 2.224548 ACTATTTCTATTGCCCGGCTCC 60.225 50.000 11.61 0.00 0.00 4.70
223 224 3.067833 GACTATTTCTATTGCCCGGCTC 58.932 50.000 11.61 0.00 0.00 4.70
224 225 2.706190 AGACTATTTCTATTGCCCGGCT 59.294 45.455 11.61 0.00 30.17 5.52
225 226 3.127425 AGACTATTTCTATTGCCCGGC 57.873 47.619 1.04 1.04 30.17 6.13
226 227 6.348540 GCAATAAGACTATTTCTATTGCCCGG 60.349 42.308 14.12 0.00 40.71 5.73
227 228 6.428159 AGCAATAAGACTATTTCTATTGCCCG 59.572 38.462 18.67 0.00 43.54 6.13
228 229 7.751768 AGCAATAAGACTATTTCTATTGCCC 57.248 36.000 18.67 1.54 43.54 5.36
235 236 9.189156 TGGCAATTAAGCAATAAGACTATTTCT 57.811 29.630 0.00 0.00 33.67 2.52
236 237 9.801873 TTGGCAATTAAGCAATAAGACTATTTC 57.198 29.630 0.00 0.00 35.83 2.17
239 240 9.807649 CTTTTGGCAATTAAGCAATAAGACTAT 57.192 29.630 0.00 0.00 35.83 2.12
240 241 9.019656 TCTTTTGGCAATTAAGCAATAAGACTA 57.980 29.630 0.00 0.00 35.83 2.59
241 242 7.895759 TCTTTTGGCAATTAAGCAATAAGACT 58.104 30.769 0.00 0.00 35.83 3.24
242 243 7.814587 ACTCTTTTGGCAATTAAGCAATAAGAC 59.185 33.333 0.00 0.00 35.83 3.01
243 244 7.895759 ACTCTTTTGGCAATTAAGCAATAAGA 58.104 30.769 0.00 2.96 35.83 2.10
244 245 8.031277 AGACTCTTTTGGCAATTAAGCAATAAG 58.969 33.333 0.00 0.00 35.83 1.73
245 246 7.895759 AGACTCTTTTGGCAATTAAGCAATAA 58.104 30.769 0.00 0.00 35.83 1.40
246 247 7.466746 AGACTCTTTTGGCAATTAAGCAATA 57.533 32.000 0.00 0.00 35.83 1.90
247 248 6.350629 AGACTCTTTTGGCAATTAAGCAAT 57.649 33.333 0.00 0.00 35.83 3.56
248 249 5.789643 AGACTCTTTTGGCAATTAAGCAA 57.210 34.783 0.00 0.00 35.83 3.91
249 250 5.789643 AAGACTCTTTTGGCAATTAAGCA 57.210 34.783 0.00 0.00 35.83 3.91
250 251 6.677913 TGTAAGACTCTTTTGGCAATTAAGC 58.322 36.000 0.00 0.00 0.00 3.09
251 252 9.696917 AATTGTAAGACTCTTTTGGCAATTAAG 57.303 29.630 0.00 2.74 34.73 1.85
252 253 9.474920 CAATTGTAAGACTCTTTTGGCAATTAA 57.525 29.630 0.00 0.00 34.73 1.40
253 254 8.637986 ACAATTGTAAGACTCTTTTGGCAATTA 58.362 29.630 9.97 0.00 34.73 1.40
254 255 7.500141 ACAATTGTAAGACTCTTTTGGCAATT 58.500 30.769 9.97 6.94 36.23 2.32
255 256 7.054491 ACAATTGTAAGACTCTTTTGGCAAT 57.946 32.000 9.97 1.80 0.00 3.56
256 257 6.463995 ACAATTGTAAGACTCTTTTGGCAA 57.536 33.333 9.97 0.00 0.00 4.52
257 258 6.463995 AACAATTGTAAGACTCTTTTGGCA 57.536 33.333 12.39 0.00 0.00 4.92
270 271 9.938670 GCATCGTGGTTATATAAACAATTGTAA 57.061 29.630 14.75 3.64 34.20 2.41
271 272 9.332502 AGCATCGTGGTTATATAAACAATTGTA 57.667 29.630 14.75 0.00 34.20 2.41
272 273 8.220755 AGCATCGTGGTTATATAAACAATTGT 57.779 30.769 14.75 4.92 34.20 2.71
301 302 8.251026 GCTTAGCCCACAAGTTATCTTATTTTT 58.749 33.333 0.00 0.00 32.07 1.94
302 303 7.147897 GGCTTAGCCCACAAGTTATCTTATTTT 60.148 37.037 13.12 0.00 44.06 1.82
303 304 6.321435 GGCTTAGCCCACAAGTTATCTTATTT 59.679 38.462 13.12 0.00 44.06 1.40
304 305 5.828328 GGCTTAGCCCACAAGTTATCTTATT 59.172 40.000 13.12 0.00 44.06 1.40
305 306 5.377478 GGCTTAGCCCACAAGTTATCTTAT 58.623 41.667 13.12 0.00 44.06 1.73
306 307 4.777463 GGCTTAGCCCACAAGTTATCTTA 58.223 43.478 13.12 0.00 44.06 2.10
307 308 3.621558 GGCTTAGCCCACAAGTTATCTT 58.378 45.455 13.12 0.00 44.06 2.40
308 309 3.283259 GGCTTAGCCCACAAGTTATCT 57.717 47.619 13.12 0.00 44.06 1.98
321 322 3.928005 AGGTTTAGTTAGGGGCTTAGC 57.072 47.619 0.00 0.00 0.00 3.09
322 323 4.384978 GGGAAGGTTTAGTTAGGGGCTTAG 60.385 50.000 0.00 0.00 0.00 2.18
323 324 3.524789 GGGAAGGTTTAGTTAGGGGCTTA 59.475 47.826 0.00 0.00 0.00 3.09
324 325 2.310945 GGGAAGGTTTAGTTAGGGGCTT 59.689 50.000 0.00 0.00 0.00 4.35
325 326 1.921049 GGGAAGGTTTAGTTAGGGGCT 59.079 52.381 0.00 0.00 0.00 5.19
326 327 1.637035 TGGGAAGGTTTAGTTAGGGGC 59.363 52.381 0.00 0.00 0.00 5.80
327 328 2.917600 ACTGGGAAGGTTTAGTTAGGGG 59.082 50.000 0.00 0.00 0.00 4.79
328 329 3.308188 CCACTGGGAAGGTTTAGTTAGGG 60.308 52.174 0.00 0.00 35.59 3.53
329 330 3.951663 CCACTGGGAAGGTTTAGTTAGG 58.048 50.000 0.00 0.00 35.59 2.69
361 362 6.183360 ACAGTTATGACGGGGTAACTTATACC 60.183 42.308 6.05 0.00 38.67 2.73
362 363 6.809869 ACAGTTATGACGGGGTAACTTATAC 58.190 40.000 6.05 0.00 38.67 1.47
363 364 7.422465 AACAGTTATGACGGGGTAACTTATA 57.578 36.000 6.05 0.00 38.67 0.98
364 365 5.945144 ACAGTTATGACGGGGTAACTTAT 57.055 39.130 6.05 0.00 38.67 1.73
365 366 5.743636 AACAGTTATGACGGGGTAACTTA 57.256 39.130 6.05 0.00 38.67 2.24
366 367 4.628963 AACAGTTATGACGGGGTAACTT 57.371 40.909 6.05 0.00 38.67 2.66
367 368 5.018809 TCTAACAGTTATGACGGGGTAACT 58.981 41.667 0.00 3.66 40.71 2.24
368 369 5.105595 ACTCTAACAGTTATGACGGGGTAAC 60.106 44.000 0.00 0.00 26.56 2.50
369 370 5.018809 ACTCTAACAGTTATGACGGGGTAA 58.981 41.667 0.00 0.00 26.56 2.85
370 371 4.603131 ACTCTAACAGTTATGACGGGGTA 58.397 43.478 0.00 0.00 26.56 3.69
371 372 3.438183 ACTCTAACAGTTATGACGGGGT 58.562 45.455 0.00 0.00 26.56 4.95
372 373 4.467198 AACTCTAACAGTTATGACGGGG 57.533 45.455 0.00 0.00 44.13 5.73
415 416 8.623030 GCCTTATACAACGGGATAAATACAAAA 58.377 33.333 0.00 0.00 0.00 2.44
441 442 2.746904 TGTGGAACATATGCAGGAAACG 59.253 45.455 1.58 0.00 45.67 3.60
458 459 8.135529 CCGATATATATACATGTACAGGTGTGG 58.864 40.741 22.69 8.15 0.00 4.17
492 493 3.624777 AGCAACTTGTATTCCCATGAGG 58.375 45.455 0.00 0.00 0.00 3.86
551 552 3.243128 CATGAGTTGCACGTGCGA 58.757 55.556 33.22 30.05 45.83 5.10
566 567 1.271934 CGGAGATTGGATCGAGAGCAT 59.728 52.381 0.00 0.00 0.00 3.79
572 573 0.670706 CTGCTCGGAGATTGGATCGA 59.329 55.000 9.69 0.00 33.89 3.59
590 591 1.681327 TAGAAGAAGGACGGCGGCT 60.681 57.895 14.66 0.00 0.00 5.52
594 595 0.525882 GCTCGTAGAAGAAGGACGGC 60.526 60.000 0.00 0.00 37.20 5.68
616 617 1.334556 CTCGATGAGGAGAGAGCAGTG 59.665 57.143 0.00 0.00 36.65 3.66
617 618 1.679139 CTCGATGAGGAGAGAGCAGT 58.321 55.000 0.00 0.00 36.65 4.40
677 678 4.148825 GGATCGGGCAGCACGAGT 62.149 66.667 26.43 13.55 44.24 4.18
740 741 1.078848 ATTGCTCGAGCTGGACCAC 60.079 57.895 35.27 7.21 42.66 4.16
761 763 1.683707 AGCAGCAGGAGATCGGACA 60.684 57.895 0.00 0.00 0.00 4.02
787 874 0.886563 GCAGCAGCTGTTCAATCCTT 59.113 50.000 23.60 0.00 37.91 3.36
820 907 2.781431 GAAAACGGGATGGGGCCAGT 62.781 60.000 4.39 0.00 37.99 4.00
821 908 2.037208 AAAACGGGATGGGGCCAG 59.963 61.111 4.39 0.00 0.00 4.85
822 909 2.036572 GAAAACGGGATGGGGCCA 59.963 61.111 4.39 0.00 0.00 5.36
824 911 1.604147 CTTGGAAAACGGGATGGGGC 61.604 60.000 0.00 0.00 0.00 5.80
833 920 0.110644 GCGACTCTGCTTGGAAAACG 60.111 55.000 0.00 0.00 0.00 3.60
1113 1210 1.515521 CGCCAGAAAGAACACCCCAC 61.516 60.000 0.00 0.00 0.00 4.61
1320 1418 1.493022 AGCCACTGGGTGTAAACAGAA 59.507 47.619 0.00 0.00 38.09 3.02
1531 1629 4.081972 ACTCTGTGCATAGAAGTCGTCAAT 60.082 41.667 14.54 0.00 0.00 2.57
1536 1634 3.856521 CAGAACTCTGTGCATAGAAGTCG 59.143 47.826 14.54 5.34 39.09 4.18
1663 1761 0.395311 TCCTTACGGAGCCGAGACAT 60.395 55.000 16.83 0.00 42.83 3.06
1721 1819 2.636893 AGCGCCTCCATGAGAGAAATAT 59.363 45.455 2.29 0.00 46.50 1.28
1775 1873 1.703411 CTCCACCAAACCAACACCAT 58.297 50.000 0.00 0.00 0.00 3.55
1781 1879 3.524346 GGAACCTCCACCAAACCAA 57.476 52.632 0.00 0.00 36.28 3.67
1846 1947 2.826738 ACTCGAGCGAGAGAGGGC 60.827 66.667 24.81 0.00 44.53 5.19
1850 1951 2.109739 GGAGCACTCGAGCGAGAGA 61.110 63.158 24.81 0.00 44.53 3.10
1906 2007 1.252215 TAGTCGCAATGTGGACGGGA 61.252 55.000 0.00 0.00 38.20 5.14
1956 2058 3.326747 GTGTTTCCTCTTCGTGTAGCAT 58.673 45.455 0.00 0.00 0.00 3.79
2035 2137 1.985473 TGCTCAGTCAAAGCAATGGT 58.015 45.000 0.00 0.00 46.29 3.55
2161 2265 2.594131 CCATAGGGATGTACCTGACGA 58.406 52.381 0.00 0.00 42.02 4.20
2177 2281 2.026262 GCTCCAGAGTCCAAAACCCATA 60.026 50.000 0.00 0.00 0.00 2.74
2327 2434 8.504815 CATGAGCAACATCAGGAATAGAATAAG 58.495 37.037 0.00 0.00 37.07 1.73
2328 2435 7.994911 ACATGAGCAACATCAGGAATAGAATAA 59.005 33.333 0.00 0.00 37.07 1.40
2329 2436 7.512130 ACATGAGCAACATCAGGAATAGAATA 58.488 34.615 0.00 0.00 37.07 1.75
2335 2442 3.698040 GGAACATGAGCAACATCAGGAAT 59.302 43.478 0.00 0.00 37.07 3.01
2404 2511 0.032815 TCAAGGATGACGCGACAACA 59.967 50.000 15.93 7.85 0.00 3.33
2425 2532 3.648067 TCCTGGACAGAACAAGAGTCAAT 59.352 43.478 0.00 0.00 34.04 2.57
2450 2557 2.661537 CCAGAGTGTGCGTGCGAA 60.662 61.111 0.00 0.00 0.00 4.70
2478 2585 2.227089 GAGAATCACGGTGGCGAGGT 62.227 60.000 8.50 0.00 33.17 3.85
2539 2646 0.249398 GAACTGGCGATAGTGGTGGT 59.751 55.000 0.00 0.00 39.35 4.16
2571 2678 0.834687 AGGAACCAGTAACGGAGGCA 60.835 55.000 0.00 0.00 0.00 4.75
2626 2733 3.800506 ACTAAAGACGACAACCAAGAACG 59.199 43.478 0.00 0.00 0.00 3.95
2632 2739 3.374745 GACGAACTAAAGACGACAACCA 58.625 45.455 0.00 0.00 0.00 3.67
2671 2778 5.147032 CTCTAAAGAGACATCTCCTGGGAT 58.853 45.833 5.25 0.00 44.74 3.85
2674 2781 4.709397 ACACTCTAAAGAGACATCTCCTGG 59.291 45.833 13.84 0.00 44.74 4.45
2785 2892 1.705997 GGAGGCGGACCCCATACATT 61.706 60.000 2.29 0.00 36.11 2.71
2856 2963 5.796350 AATAAAGCCATGTGTAACGAGAC 57.204 39.130 0.00 0.00 42.39 3.36
3091 3198 3.243101 GCCGTCTCAAGAAGATGACGATA 60.243 47.826 14.59 0.00 43.87 2.92
3131 3238 3.077556 GAGGCGGGAGAGAGGCAA 61.078 66.667 0.00 0.00 35.18 4.52
3203 3310 0.692476 ACCACCATGTAGAGCAGCAA 59.308 50.000 0.00 0.00 0.00 3.91
3204 3311 0.036105 CACCACCATGTAGAGCAGCA 60.036 55.000 0.00 0.00 0.00 4.41
3216 3323 0.534203 GCTCGAAAGGAACACCACCA 60.534 55.000 0.00 0.00 0.00 4.17
3281 3388 5.400485 GCAAGAAGAACATAGCAAACACAAG 59.600 40.000 0.00 0.00 0.00 3.16
3317 3424 0.532862 CTGAGCGGTCAGTTTGGTGT 60.533 55.000 31.45 0.00 44.72 4.16
3403 3510 0.587285 GAGATACGCATCCGACGACT 59.413 55.000 0.00 0.00 38.29 4.18
3453 3560 1.141053 GAAGATGGGCGTGGGTAGAAT 59.859 52.381 0.00 0.00 0.00 2.40


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

AutoCloner maintained by Alex Coulton.