Multiple sequence alignment - TraesCS7D01G404300

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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 TraesCS7D01G404300 chr7D 100.000 2313 0 0 929 3241 521761716 521759404 0.000000e+00 4272
1 TraesCS7D01G404300 chr7D 93.023 1677 54 9 978 2614 587754205 587752552 0.000000e+00 2390
2 TraesCS7D01G404300 chr7D 100.000 591 0 0 1 591 521762644 521762054 0.000000e+00 1092
3 TraesCS7D01G404300 chr3D 96.033 1714 37 14 929 2612 357079085 357080797 0.000000e+00 2760
4 TraesCS7D01G404300 chr3D 95.693 1695 38 6 939 2614 101712020 101710342 0.000000e+00 2693
5 TraesCS7D01G404300 chr3D 93.772 1686 61 11 971 2615 114126765 114125083 0.000000e+00 2492
6 TraesCS7D01G404300 chr3D 94.145 427 17 4 171 589 357078428 357078854 0.000000e+00 643
7 TraesCS7D01G404300 chr3D 92.548 416 26 2 168 578 101714244 101713829 2.780000e-165 592
8 TraesCS7D01G404300 chr4A 95.894 1705 45 11 933 2614 690128806 690127104 0.000000e+00 2737
9 TraesCS7D01G404300 chr1D 95.311 1706 54 10 929 2612 399697502 399695801 0.000000e+00 2684
10 TraesCS7D01G404300 chr4D 97.114 1559 34 5 929 2477 19342342 19340785 0.000000e+00 2619
11 TraesCS7D01G404300 chr4D 92.037 427 26 4 171 591 206715842 206716266 7.740000e-166 593
12 TraesCS7D01G404300 chr4D 92.683 205 2 2 2420 2612 489511339 489511136 1.900000e-72 283
13 TraesCS7D01G404300 chr4D 96.622 148 4 1 2467 2614 486563471 486563617 8.980000e-61 244
14 TraesCS7D01G404300 chr7A 96.144 1556 46 6 932 2477 119612902 119611351 0.000000e+00 2529
15 TraesCS7D01G404300 chr7A 84.727 550 50 18 2721 3241 19174033 19173489 1.330000e-143 520
16 TraesCS7D01G404300 chr2B 95.585 1563 48 9 929 2477 175542601 175541046 0.000000e+00 2484
17 TraesCS7D01G404300 chr2B 92.958 426 24 3 171 591 256312163 256311739 1.650000e-172 616
18 TraesCS7D01G404300 chr2B 83.729 547 57 12 2703 3241 283290829 283290307 3.760000e-134 488
19 TraesCS7D01G404300 chr1A 95.527 1565 50 7 929 2474 143746594 143748157 0.000000e+00 2484
20 TraesCS7D01G404300 chr1A 93.458 428 17 5 168 591 143745972 143746392 2.750000e-175 625
21 TraesCS7D01G404300 chr3B 92.993 1684 72 15 971 2612 414797320 414798999 0.000000e+00 2414
22 TraesCS7D01G404300 chr3B 92.732 399 22 4 169 562 728513518 728513122 1.300000e-158 569
23 TraesCS7D01G404300 chr3B 91.216 296 10 5 2332 2614 405405634 405405342 3.920000e-104 388
24 TraesCS7D01G404300 chr3B 89.796 294 12 2 929 1222 728512867 728512592 8.550000e-96 361
25 TraesCS7D01G404300 chr2A 94.214 1521 42 7 931 2443 133964753 133963271 0.000000e+00 2279
26 TraesCS7D01G404300 chr2A 93.473 429 23 4 168 591 133965385 133964957 1.640000e-177 632
27 TraesCS7D01G404300 chr6B 92.958 426 25 2 171 591 118883668 118883243 1.650000e-172 616
28 TraesCS7D01G404300 chr5D 92.290 428 27 4 168 590 553974719 553975145 1.290000e-168 603
29 TraesCS7D01G404300 chr4B 84.162 543 54 18 2704 3239 195448765 195448248 6.240000e-137 497
30 TraesCS7D01G404300 chr6D 92.754 207 2 2 2420 2614 65085525 65085320 1.470000e-73 287
31 TraesCS7D01G404300 chrUn 91.346 208 5 2 2420 2615 359158728 359158934 4.120000e-69 272


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 TraesCS7D01G404300 chr7D 521759404 521762644 3240 True 2682.0 4272 100.0000 1 3241 2 chr7D.!!$R2 3240
1 TraesCS7D01G404300 chr7D 587752552 587754205 1653 True 2390.0 2390 93.0230 978 2614 1 chr7D.!!$R1 1636
2 TraesCS7D01G404300 chr3D 114125083 114126765 1682 True 2492.0 2492 93.7720 971 2615 1 chr3D.!!$R1 1644
3 TraesCS7D01G404300 chr3D 357078428 357080797 2369 False 1701.5 2760 95.0890 171 2612 2 chr3D.!!$F1 2441
4 TraesCS7D01G404300 chr3D 101710342 101714244 3902 True 1642.5 2693 94.1205 168 2614 2 chr3D.!!$R2 2446
5 TraesCS7D01G404300 chr4A 690127104 690128806 1702 True 2737.0 2737 95.8940 933 2614 1 chr4A.!!$R1 1681
6 TraesCS7D01G404300 chr1D 399695801 399697502 1701 True 2684.0 2684 95.3110 929 2612 1 chr1D.!!$R1 1683
7 TraesCS7D01G404300 chr4D 19340785 19342342 1557 True 2619.0 2619 97.1140 929 2477 1 chr4D.!!$R1 1548
8 TraesCS7D01G404300 chr7A 119611351 119612902 1551 True 2529.0 2529 96.1440 932 2477 1 chr7A.!!$R2 1545
9 TraesCS7D01G404300 chr7A 19173489 19174033 544 True 520.0 520 84.7270 2721 3241 1 chr7A.!!$R1 520
10 TraesCS7D01G404300 chr2B 175541046 175542601 1555 True 2484.0 2484 95.5850 929 2477 1 chr2B.!!$R1 1548
11 TraesCS7D01G404300 chr2B 283290307 283290829 522 True 488.0 488 83.7290 2703 3241 1 chr2B.!!$R3 538
12 TraesCS7D01G404300 chr1A 143745972 143748157 2185 False 1554.5 2484 94.4925 168 2474 2 chr1A.!!$F1 2306
13 TraesCS7D01G404300 chr3B 414797320 414798999 1679 False 2414.0 2414 92.9930 971 2612 1 chr3B.!!$F1 1641
14 TraesCS7D01G404300 chr3B 728512592 728513518 926 True 465.0 569 91.2640 169 1222 2 chr3B.!!$R2 1053
15 TraesCS7D01G404300 chr2A 133963271 133965385 2114 True 1455.5 2279 93.8435 168 2443 2 chr2A.!!$R1 2275
16 TraesCS7D01G404300 chr4B 195448248 195448765 517 True 497.0 497 84.1620 2704 3239 1 chr4B.!!$R1 535

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
24 25 0.034960 GGGAGGCCCTTCTTTCAGTC 60.035 60.0 0.00 0.00 41.34 3.51 F
93 94 0.035056 CCCTGGGAGTGAATCACCAC 60.035 60.0 7.01 3.55 34.49 4.16 F
145 146 0.178953 AAGAAGCCACCTGGTGCAAT 60.179 50.0 21.47 8.64 37.57 3.56 F
1677 3206 0.037139 GCATTGTTGGGCATTGCTCA 60.037 50.0 7.23 7.23 45.70 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1303 2805 3.023119 TCCTCAATGCGTTGCCAATAAT 58.977 40.909 14.04 0.0 35.26 1.28 R
1652 3181 3.139850 CAATGCCCAACAATGCTTGAAA 58.860 40.909 3.37 0.0 0.00 2.69 R
1917 3450 6.183360 GCAAGTTTCACCTCTTTCTTTCTCTT 60.183 38.462 0.00 0.0 0.00 2.85 R
2938 4512 0.036732 ATGCACCGAACATGTCACCT 59.963 50.000 0.00 0.0 0.00 4.00 R

All possible primers

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

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 4.439901 GGAGGGGGAGGCCCTTCT 62.440 72.222 0.00 0.87 44.66 2.85
18 19 2.286502 GAGGGGGAGGCCCTTCTT 60.287 66.667 0.00 0.00 44.66 2.52
19 20 1.931180 GAGGGGGAGGCCCTTCTTT 60.931 63.158 0.00 0.00 44.66 2.52
20 21 1.927569 GAGGGGGAGGCCCTTCTTTC 61.928 65.000 0.00 0.00 44.66 2.62
21 22 2.238701 GGGGGAGGCCCTTCTTTCA 61.239 63.158 0.00 0.00 44.66 2.69
22 23 1.304617 GGGGAGGCCCTTCTTTCAG 59.695 63.158 0.00 0.00 44.66 3.02
23 24 1.501654 GGGGAGGCCCTTCTTTCAGT 61.502 60.000 0.00 0.00 44.66 3.41
24 25 0.034960 GGGAGGCCCTTCTTTCAGTC 60.035 60.000 0.00 0.00 41.34 3.51
25 26 0.693049 GGAGGCCCTTCTTTCAGTCA 59.307 55.000 0.00 0.00 0.00 3.41
26 27 1.073923 GGAGGCCCTTCTTTCAGTCAA 59.926 52.381 0.00 0.00 0.00 3.18
27 28 2.489073 GGAGGCCCTTCTTTCAGTCAAA 60.489 50.000 0.00 0.00 0.00 2.69
28 29 3.222603 GAGGCCCTTCTTTCAGTCAAAA 58.777 45.455 0.00 0.00 0.00 2.44
29 30 3.636764 GAGGCCCTTCTTTCAGTCAAAAA 59.363 43.478 0.00 0.00 0.00 1.94
61 62 9.877178 AATCTCTCTGACTTAAATTTCATACGT 57.123 29.630 0.00 0.00 0.00 3.57
62 63 8.912787 TCTCTCTGACTTAAATTTCATACGTC 57.087 34.615 0.00 0.00 0.00 4.34
63 64 7.696872 TCTCTCTGACTTAAATTTCATACGTCG 59.303 37.037 0.00 0.00 0.00 5.12
64 65 7.532571 TCTCTGACTTAAATTTCATACGTCGA 58.467 34.615 0.00 0.00 0.00 4.20
65 66 7.696872 TCTCTGACTTAAATTTCATACGTCGAG 59.303 37.037 0.00 3.57 31.57 4.04
66 67 6.750501 TCTGACTTAAATTTCATACGTCGAGG 59.249 38.462 3.03 3.03 0.00 4.63
67 68 6.392354 TGACTTAAATTTCATACGTCGAGGT 58.608 36.000 15.89 15.89 0.00 3.85
68 69 6.869913 TGACTTAAATTTCATACGTCGAGGTT 59.130 34.615 16.86 1.76 0.00 3.50
69 70 7.057149 ACTTAAATTTCATACGTCGAGGTTG 57.943 36.000 16.86 13.62 0.00 3.77
70 71 4.336532 AAATTTCATACGTCGAGGTTGC 57.663 40.909 16.86 0.00 0.00 4.17
71 72 2.442212 TTTCATACGTCGAGGTTGCA 57.558 45.000 16.86 0.00 0.00 4.08
72 73 1.990799 TTCATACGTCGAGGTTGCAG 58.009 50.000 16.86 4.56 0.00 4.41
73 74 0.885879 TCATACGTCGAGGTTGCAGT 59.114 50.000 16.86 0.00 0.00 4.40
74 75 1.135489 TCATACGTCGAGGTTGCAGTC 60.135 52.381 16.86 0.00 0.00 3.51
75 76 0.172803 ATACGTCGAGGTTGCAGTCC 59.827 55.000 16.86 2.31 0.00 3.85
76 77 1.870055 TACGTCGAGGTTGCAGTCCC 61.870 60.000 16.86 0.00 0.00 4.46
77 78 2.932234 CGTCGAGGTTGCAGTCCCT 61.932 63.158 6.42 4.14 0.00 4.20
78 79 1.374758 GTCGAGGTTGCAGTCCCTG 60.375 63.158 6.40 0.79 34.12 4.45
79 80 2.046892 CGAGGTTGCAGTCCCTGG 60.047 66.667 6.40 2.21 31.21 4.45
80 81 2.352805 GAGGTTGCAGTCCCTGGG 59.647 66.667 6.33 6.33 31.21 4.45
81 82 2.121963 AGGTTGCAGTCCCTGGGA 60.122 61.111 12.53 12.53 31.21 4.37
82 83 2.190488 GAGGTTGCAGTCCCTGGGAG 62.190 65.000 17.73 6.65 29.39 4.30
83 84 2.529744 GGTTGCAGTCCCTGGGAGT 61.530 63.158 17.73 17.68 35.46 3.85
89 90 3.815717 AGTCCCTGGGAGTGAATCA 57.184 52.632 22.35 0.00 33.56 2.57
90 91 1.280457 AGTCCCTGGGAGTGAATCAC 58.720 55.000 22.35 5.02 33.56 3.06
91 92 0.253327 GTCCCTGGGAGTGAATCACC 59.747 60.000 17.73 0.00 34.49 4.02
92 93 0.178876 TCCCTGGGAGTGAATCACCA 60.179 55.000 12.53 0.05 34.49 4.17
93 94 0.035056 CCCTGGGAGTGAATCACCAC 60.035 60.000 7.01 3.55 34.49 4.16
94 95 0.692476 CCTGGGAGTGAATCACCACA 59.308 55.000 10.12 8.07 39.42 4.17
95 96 1.283029 CCTGGGAGTGAATCACCACAT 59.717 52.381 10.12 0.00 39.42 3.21
96 97 2.636830 CTGGGAGTGAATCACCACATC 58.363 52.381 10.12 0.71 39.42 3.06
97 98 2.238144 CTGGGAGTGAATCACCACATCT 59.762 50.000 10.12 0.00 39.42 2.90
98 99 2.237143 TGGGAGTGAATCACCACATCTC 59.763 50.000 10.12 1.49 39.42 2.75
99 100 2.237143 GGGAGTGAATCACCACATCTCA 59.763 50.000 10.12 0.00 39.42 3.27
100 101 3.529533 GGAGTGAATCACCACATCTCAG 58.470 50.000 10.12 0.00 39.42 3.35
101 102 3.196469 GGAGTGAATCACCACATCTCAGA 59.804 47.826 10.12 0.00 39.42 3.27
102 103 4.141756 GGAGTGAATCACCACATCTCAGAT 60.142 45.833 10.12 0.00 39.42 2.90
103 104 5.069648 GGAGTGAATCACCACATCTCAGATA 59.930 44.000 10.12 0.00 39.42 1.98
104 105 5.911752 AGTGAATCACCACATCTCAGATAC 58.088 41.667 10.12 0.00 39.42 2.24
105 106 5.660417 AGTGAATCACCACATCTCAGATACT 59.340 40.000 10.12 0.00 39.42 2.12
106 107 5.982516 GTGAATCACCACATCTCAGATACTC 59.017 44.000 1.10 0.00 37.04 2.59
107 108 5.896106 TGAATCACCACATCTCAGATACTCT 59.104 40.000 0.00 0.00 0.00 3.24
108 109 6.382282 TGAATCACCACATCTCAGATACTCTT 59.618 38.462 0.00 0.00 0.00 2.85
109 110 5.843673 TCACCACATCTCAGATACTCTTC 57.156 43.478 0.00 0.00 0.00 2.87
110 111 5.514169 TCACCACATCTCAGATACTCTTCT 58.486 41.667 0.00 0.00 0.00 2.85
111 112 5.954752 TCACCACATCTCAGATACTCTTCTT 59.045 40.000 0.00 0.00 0.00 2.52
112 113 6.096141 TCACCACATCTCAGATACTCTTCTTC 59.904 42.308 0.00 0.00 0.00 2.87
113 114 5.954752 ACCACATCTCAGATACTCTTCTTCA 59.045 40.000 0.00 0.00 0.00 3.02
114 115 6.127479 ACCACATCTCAGATACTCTTCTTCAC 60.127 42.308 0.00 0.00 0.00 3.18
115 116 5.970612 CACATCTCAGATACTCTTCTTCACG 59.029 44.000 0.00 0.00 0.00 4.35
116 117 5.883115 ACATCTCAGATACTCTTCTTCACGA 59.117 40.000 0.00 0.00 0.00 4.35
117 118 6.375736 ACATCTCAGATACTCTTCTTCACGAA 59.624 38.462 0.00 0.00 0.00 3.85
118 119 7.068103 ACATCTCAGATACTCTTCTTCACGAAT 59.932 37.037 0.00 0.00 0.00 3.34
119 120 6.790282 TCTCAGATACTCTTCTTCACGAATG 58.210 40.000 0.00 0.00 0.00 2.67
120 121 6.375736 TCTCAGATACTCTTCTTCACGAATGT 59.624 38.462 0.00 0.00 0.00 2.71
121 122 6.556212 TCAGATACTCTTCTTCACGAATGTC 58.444 40.000 0.00 0.00 0.00 3.06
122 123 5.453909 CAGATACTCTTCTTCACGAATGTCG 59.546 44.000 0.00 0.00 46.93 4.35
123 124 3.917329 ACTCTTCTTCACGAATGTCGA 57.083 42.857 4.40 0.00 43.74 4.20
124 125 3.566523 ACTCTTCTTCACGAATGTCGAC 58.433 45.455 9.11 9.11 43.74 4.20
125 126 2.917971 CTCTTCTTCACGAATGTCGACC 59.082 50.000 14.12 0.00 43.74 4.79
126 127 2.295070 TCTTCTTCACGAATGTCGACCA 59.705 45.455 14.12 1.26 43.74 4.02
127 128 2.804697 TCTTCACGAATGTCGACCAA 57.195 45.000 14.12 0.00 43.74 3.67
128 129 2.672714 TCTTCACGAATGTCGACCAAG 58.327 47.619 14.12 4.52 43.74 3.61
129 130 2.295070 TCTTCACGAATGTCGACCAAGA 59.705 45.455 14.12 6.24 43.74 3.02
130 131 2.804697 TCACGAATGTCGACCAAGAA 57.195 45.000 14.12 0.00 43.74 2.52
131 132 2.672714 TCACGAATGTCGACCAAGAAG 58.327 47.619 14.12 2.31 43.74 2.85
132 133 1.126846 CACGAATGTCGACCAAGAAGC 59.873 52.381 14.12 0.00 43.74 3.86
133 134 0.721718 CGAATGTCGACCAAGAAGCC 59.278 55.000 14.12 0.00 43.74 4.35
134 135 1.808411 GAATGTCGACCAAGAAGCCA 58.192 50.000 14.12 0.00 0.00 4.75
135 136 1.464997 GAATGTCGACCAAGAAGCCAC 59.535 52.381 14.12 0.00 0.00 5.01
136 137 0.321653 ATGTCGACCAAGAAGCCACC 60.322 55.000 14.12 0.00 0.00 4.61
137 138 1.371558 GTCGACCAAGAAGCCACCT 59.628 57.895 3.51 0.00 0.00 4.00
138 139 0.951040 GTCGACCAAGAAGCCACCTG 60.951 60.000 3.51 0.00 0.00 4.00
139 140 1.672356 CGACCAAGAAGCCACCTGG 60.672 63.158 0.00 0.00 38.53 4.45
140 141 1.456287 GACCAAGAAGCCACCTGGT 59.544 57.895 0.00 0.00 37.57 4.00
141 142 0.890996 GACCAAGAAGCCACCTGGTG 60.891 60.000 20.01 20.01 37.57 4.17
142 143 2.270986 CCAAGAAGCCACCTGGTGC 61.271 63.158 21.47 15.94 37.57 5.01
143 144 1.529010 CAAGAAGCCACCTGGTGCA 60.529 57.895 21.47 0.00 37.57 4.57
144 145 1.108727 CAAGAAGCCACCTGGTGCAA 61.109 55.000 21.47 0.00 37.57 4.08
145 146 0.178953 AAGAAGCCACCTGGTGCAAT 60.179 50.000 21.47 8.64 37.57 3.56
146 147 0.896940 AGAAGCCACCTGGTGCAATG 60.897 55.000 21.47 8.79 37.57 2.82
147 148 1.880819 GAAGCCACCTGGTGCAATGG 61.881 60.000 21.47 8.61 37.57 3.16
148 149 2.283101 GCCACCTGGTGCAATGGA 60.283 61.111 21.47 0.00 37.57 3.41
149 150 1.683365 GCCACCTGGTGCAATGGAT 60.683 57.895 21.47 0.00 37.57 3.41
150 151 1.952102 GCCACCTGGTGCAATGGATG 61.952 60.000 21.47 6.22 37.57 3.51
161 162 1.830279 CAATGGATGCAGGTCACACT 58.170 50.000 0.00 0.00 0.00 3.55
162 163 2.989909 CAATGGATGCAGGTCACACTA 58.010 47.619 0.00 0.00 0.00 2.74
163 164 2.679837 CAATGGATGCAGGTCACACTAC 59.320 50.000 0.00 0.00 0.00 2.73
164 165 1.644509 TGGATGCAGGTCACACTACT 58.355 50.000 0.00 0.00 0.00 2.57
165 166 1.977854 TGGATGCAGGTCACACTACTT 59.022 47.619 0.00 0.00 0.00 2.24
166 167 2.371841 TGGATGCAGGTCACACTACTTT 59.628 45.455 0.00 0.00 0.00 2.66
177 178 6.663953 AGGTCACACTACTTTCTTAGAGCATA 59.336 38.462 0.00 0.00 0.00 3.14
221 222 4.280929 GGTCAAACCCTCAAAATAACTGCT 59.719 41.667 0.00 0.00 30.04 4.24
1303 2805 2.935505 CCGATCAAACCGGGAAACA 58.064 52.632 6.32 0.00 43.05 2.83
1549 3078 9.638239 CATGCTTTATTTACTTGTTGGTTATGT 57.362 29.630 0.00 0.00 0.00 2.29
1677 3206 0.037139 GCATTGTTGGGCATTGCTCA 60.037 50.000 7.23 7.23 45.70 4.26
1917 3450 6.061022 TGGAGACAAAGCTTATTATCACCA 57.939 37.500 0.00 6.80 37.44 4.17
2309 3848 5.845391 ATGTGATGATGATCATTTGCACA 57.155 34.783 26.36 26.36 40.76 4.57
2519 4090 0.401356 TTTGAGGGCACTGATCTGCA 59.599 50.000 0.00 0.00 39.08 4.41
2520 4091 0.321919 TTGAGGGCACTGATCTGCAC 60.322 55.000 0.00 5.25 41.28 4.57
2615 4187 4.987912 GGCTCTGTTAGACATGCTCTTATC 59.012 45.833 0.00 0.00 31.12 1.75
2616 4188 4.987912 GCTCTGTTAGACATGCTCTTATCC 59.012 45.833 0.00 0.00 0.00 2.59
2617 4189 5.452496 GCTCTGTTAGACATGCTCTTATCCA 60.452 44.000 0.00 0.00 0.00 3.41
2618 4190 5.907207 TCTGTTAGACATGCTCTTATCCAC 58.093 41.667 0.00 0.00 0.00 4.02
2619 4191 5.658634 TCTGTTAGACATGCTCTTATCCACT 59.341 40.000 0.00 0.00 0.00 4.00
2620 4192 5.907207 TGTTAGACATGCTCTTATCCACTC 58.093 41.667 0.00 0.00 0.00 3.51
2621 4193 5.422012 TGTTAGACATGCTCTTATCCACTCA 59.578 40.000 0.00 0.00 0.00 3.41
2622 4194 4.399004 AGACATGCTCTTATCCACTCAC 57.601 45.455 0.00 0.00 0.00 3.51
2623 4195 3.133721 AGACATGCTCTTATCCACTCACC 59.866 47.826 0.00 0.00 0.00 4.02
2624 4196 2.159043 ACATGCTCTTATCCACTCACCG 60.159 50.000 0.00 0.00 0.00 4.94
2625 4197 1.557099 TGCTCTTATCCACTCACCGT 58.443 50.000 0.00 0.00 0.00 4.83
2626 4198 1.899814 TGCTCTTATCCACTCACCGTT 59.100 47.619 0.00 0.00 0.00 4.44
2627 4199 2.094182 TGCTCTTATCCACTCACCGTTC 60.094 50.000 0.00 0.00 0.00 3.95
2628 4200 2.166664 GCTCTTATCCACTCACCGTTCT 59.833 50.000 0.00 0.00 0.00 3.01
2629 4201 3.735514 GCTCTTATCCACTCACCGTTCTC 60.736 52.174 0.00 0.00 0.00 2.87
2630 4202 2.758979 TCTTATCCACTCACCGTTCTCC 59.241 50.000 0.00 0.00 0.00 3.71
2631 4203 2.225382 TATCCACTCACCGTTCTCCA 57.775 50.000 0.00 0.00 0.00 3.86
2632 4204 1.348064 ATCCACTCACCGTTCTCCAA 58.652 50.000 0.00 0.00 0.00 3.53
2633 4205 0.391597 TCCACTCACCGTTCTCCAAC 59.608 55.000 0.00 0.00 0.00 3.77
2634 4206 0.393077 CCACTCACCGTTCTCCAACT 59.607 55.000 0.00 0.00 0.00 3.16
2635 4207 1.605712 CCACTCACCGTTCTCCAACTC 60.606 57.143 0.00 0.00 0.00 3.01
2636 4208 1.068588 CACTCACCGTTCTCCAACTCA 59.931 52.381 0.00 0.00 0.00 3.41
2637 4209 1.760613 ACTCACCGTTCTCCAACTCAA 59.239 47.619 0.00 0.00 0.00 3.02
2638 4210 2.135933 CTCACCGTTCTCCAACTCAAC 58.864 52.381 0.00 0.00 0.00 3.18
2639 4211 1.483004 TCACCGTTCTCCAACTCAACA 59.517 47.619 0.00 0.00 0.00 3.33
2640 4212 2.104111 TCACCGTTCTCCAACTCAACAT 59.896 45.455 0.00 0.00 0.00 2.71
2641 4213 2.224079 CACCGTTCTCCAACTCAACATG 59.776 50.000 0.00 0.00 0.00 3.21
2642 4214 2.158813 ACCGTTCTCCAACTCAACATGT 60.159 45.455 0.00 0.00 0.00 3.21
2643 4215 2.224079 CCGTTCTCCAACTCAACATGTG 59.776 50.000 0.00 0.00 0.00 3.21
2644 4216 2.349817 CGTTCTCCAACTCAACATGTGC 60.350 50.000 0.00 0.00 0.00 4.57
2645 4217 2.880890 GTTCTCCAACTCAACATGTGCT 59.119 45.455 0.00 0.00 0.00 4.40
2646 4218 3.213206 TCTCCAACTCAACATGTGCTT 57.787 42.857 0.00 0.00 0.00 3.91
2647 4219 3.141398 TCTCCAACTCAACATGTGCTTC 58.859 45.455 0.00 0.00 0.00 3.86
2648 4220 2.227388 CTCCAACTCAACATGTGCTTCC 59.773 50.000 0.00 0.00 0.00 3.46
2649 4221 1.270550 CCAACTCAACATGTGCTTCCC 59.729 52.381 0.00 0.00 0.00 3.97
2650 4222 2.233271 CAACTCAACATGTGCTTCCCT 58.767 47.619 0.00 0.00 0.00 4.20
2651 4223 1.901591 ACTCAACATGTGCTTCCCTG 58.098 50.000 0.00 0.00 0.00 4.45
2652 4224 1.171308 CTCAACATGTGCTTCCCTGG 58.829 55.000 0.00 0.00 0.00 4.45
2653 4225 0.770499 TCAACATGTGCTTCCCTGGA 59.230 50.000 0.00 0.00 0.00 3.86
2654 4226 0.883833 CAACATGTGCTTCCCTGGAC 59.116 55.000 0.00 0.00 0.00 4.02
2655 4227 0.478072 AACATGTGCTTCCCTGGACA 59.522 50.000 0.00 0.00 42.15 4.02
2657 4229 1.340405 ACATGTGCTTCCCTGGACATC 60.340 52.381 0.00 0.00 45.00 3.06
2658 4230 0.257039 ATGTGCTTCCCTGGACATCC 59.743 55.000 0.00 0.00 43.76 3.51
2659 4231 1.133181 TGTGCTTCCCTGGACATCCA 61.133 55.000 0.00 0.00 45.30 3.41
2669 4241 1.131638 TGGACATCCAGCTGGTATCC 58.868 55.000 31.58 30.73 42.01 2.59
2670 4242 1.344393 TGGACATCCAGCTGGTATCCT 60.344 52.381 33.28 17.55 42.01 3.24
2671 4243 1.346068 GGACATCCAGCTGGTATCCTC 59.654 57.143 31.58 18.40 36.34 3.71
2672 4244 2.042464 GACATCCAGCTGGTATCCTCA 58.958 52.381 31.58 11.74 36.34 3.86
2673 4245 2.435805 GACATCCAGCTGGTATCCTCAA 59.564 50.000 31.58 10.93 36.34 3.02
2674 4246 2.437281 ACATCCAGCTGGTATCCTCAAG 59.563 50.000 31.58 10.64 36.34 3.02
2675 4247 2.254152 TCCAGCTGGTATCCTCAAGT 57.746 50.000 31.58 0.00 36.34 3.16
2676 4248 2.551270 TCCAGCTGGTATCCTCAAGTT 58.449 47.619 31.58 0.00 36.34 2.66
2677 4249 2.912956 TCCAGCTGGTATCCTCAAGTTT 59.087 45.455 31.58 0.00 36.34 2.66
2678 4250 3.330701 TCCAGCTGGTATCCTCAAGTTTT 59.669 43.478 31.58 0.00 36.34 2.43
2679 4251 4.082125 CCAGCTGGTATCCTCAAGTTTTT 58.918 43.478 25.53 0.00 0.00 1.94
2680 4252 5.013704 TCCAGCTGGTATCCTCAAGTTTTTA 59.986 40.000 31.58 3.54 36.34 1.52
2681 4253 5.123979 CCAGCTGGTATCCTCAAGTTTTTAC 59.876 44.000 25.53 0.00 0.00 2.01
2682 4254 5.705441 CAGCTGGTATCCTCAAGTTTTTACA 59.295 40.000 5.57 0.00 0.00 2.41
2683 4255 6.375455 CAGCTGGTATCCTCAAGTTTTTACAT 59.625 38.462 5.57 0.00 0.00 2.29
2684 4256 7.552687 CAGCTGGTATCCTCAAGTTTTTACATA 59.447 37.037 5.57 0.00 0.00 2.29
2685 4257 8.275040 AGCTGGTATCCTCAAGTTTTTACATAT 58.725 33.333 0.00 0.00 0.00 1.78
2686 4258 8.560374 GCTGGTATCCTCAAGTTTTTACATATC 58.440 37.037 0.00 0.00 0.00 1.63
2687 4259 9.838339 CTGGTATCCTCAAGTTTTTACATATCT 57.162 33.333 0.00 0.00 0.00 1.98
2688 4260 9.613428 TGGTATCCTCAAGTTTTTACATATCTG 57.387 33.333 0.00 0.00 0.00 2.90
2689 4261 9.832445 GGTATCCTCAAGTTTTTACATATCTGA 57.168 33.333 0.00 0.00 0.00 3.27
2700 4272 9.140286 GTTTTTACATATCTGAAAAAGAAGGGC 57.860 33.333 0.00 0.00 38.79 5.19
2701 4273 7.404671 TTTACATATCTGAAAAAGAAGGGCC 57.595 36.000 0.00 0.00 38.79 5.80
2702 4274 4.934356 ACATATCTGAAAAAGAAGGGCCA 58.066 39.130 6.18 0.00 38.79 5.36
2703 4275 5.522641 ACATATCTGAAAAAGAAGGGCCAT 58.477 37.500 6.18 0.00 38.79 4.40
2704 4276 5.960202 ACATATCTGAAAAAGAAGGGCCATT 59.040 36.000 0.07 0.07 38.79 3.16
2705 4277 6.441604 ACATATCTGAAAAAGAAGGGCCATTT 59.558 34.615 3.12 0.00 38.79 2.32
2706 4278 5.830799 ATCTGAAAAAGAAGGGCCATTTT 57.169 34.783 3.12 7.31 38.79 1.82
2707 4279 5.628797 TCTGAAAAAGAAGGGCCATTTTT 57.371 34.783 20.10 20.10 38.47 1.94
2753 4325 2.368221 GCAGAGCTCTAGGATTGGACAT 59.632 50.000 17.75 0.00 0.00 3.06
2766 4339 6.484288 AGGATTGGACATATTCAGACAACAA 58.516 36.000 0.00 0.00 0.00 2.83
2772 4346 6.939730 TGGACATATTCAGACAACAAAAGCTA 59.060 34.615 0.00 0.00 0.00 3.32
2777 4351 9.003112 CATATTCAGACAACAAAAGCTAATTCG 57.997 33.333 0.00 0.00 0.00 3.34
2786 4360 8.038944 ACAACAAAAGCTAATTCGGTCTATCTA 58.961 33.333 0.00 0.00 0.00 1.98
2787 4361 9.046296 CAACAAAAGCTAATTCGGTCTATCTAT 57.954 33.333 0.00 0.00 0.00 1.98
2793 4367 8.184304 AGCTAATTCGGTCTATCTATGACTTT 57.816 34.615 0.00 0.00 35.04 2.66
2845 4419 4.334552 TGGCTTCAACTGCTAATTCATGA 58.665 39.130 0.00 0.00 0.00 3.07
2866 4440 2.649816 AGCCATCTTGTTACCTTCCCTT 59.350 45.455 0.00 0.00 0.00 3.95
2869 4443 3.420893 CATCTTGTTACCTTCCCTTGCA 58.579 45.455 0.00 0.00 0.00 4.08
2875 4449 0.400213 TACCTTCCCTTGCAGTGTGG 59.600 55.000 0.00 0.00 0.00 4.17
2893 4467 0.250513 GGGTCACCTCGAAAGCAGAT 59.749 55.000 0.00 0.00 0.00 2.90
2902 4476 2.447250 TCGAAAGCAGATAACGTAGCG 58.553 47.619 0.00 0.00 0.00 4.26
2906 4480 1.676746 AGCAGATAACGTAGCGAGGA 58.323 50.000 0.00 0.00 0.00 3.71
2914 4488 2.961526 ACGTAGCGAGGACATCATTT 57.038 45.000 0.00 0.00 0.00 2.32
2918 4492 4.278669 ACGTAGCGAGGACATCATTTAGAT 59.721 41.667 0.00 0.00 37.48 1.98
2919 4493 4.854291 CGTAGCGAGGACATCATTTAGATC 59.146 45.833 0.00 0.00 33.72 2.75
2920 4494 4.944619 AGCGAGGACATCATTTAGATCA 57.055 40.909 0.00 0.00 33.72 2.92
2921 4495 4.626042 AGCGAGGACATCATTTAGATCAC 58.374 43.478 0.00 0.00 33.72 3.06
2922 4496 4.343526 AGCGAGGACATCATTTAGATCACT 59.656 41.667 0.00 0.00 33.72 3.41
2923 4497 4.447054 GCGAGGACATCATTTAGATCACTG 59.553 45.833 0.00 0.00 33.72 3.66
2924 4498 5.737349 GCGAGGACATCATTTAGATCACTGA 60.737 44.000 0.00 0.00 33.72 3.41
2925 4499 6.453943 CGAGGACATCATTTAGATCACTGAT 58.546 40.000 0.00 0.00 33.72 2.90
2926 4500 6.365518 CGAGGACATCATTTAGATCACTGATG 59.634 42.308 17.86 17.86 46.60 3.07
2927 4501 7.370905 AGGACATCATTTAGATCACTGATGA 57.629 36.000 22.69 14.54 44.93 2.92
2928 4502 7.443477 AGGACATCATTTAGATCACTGATGAG 58.557 38.462 22.69 11.47 44.93 2.90
2929 4503 6.649973 GGACATCATTTAGATCACTGATGAGG 59.350 42.308 22.69 16.56 44.93 3.86
2930 4504 5.996513 ACATCATTTAGATCACTGATGAGGC 59.003 40.000 22.69 0.00 44.93 4.70
2931 4505 4.965814 TCATTTAGATCACTGATGAGGCC 58.034 43.478 0.00 0.00 38.57 5.19
2932 4506 4.409901 TCATTTAGATCACTGATGAGGCCA 59.590 41.667 5.01 0.00 38.57 5.36
2933 4507 5.072736 TCATTTAGATCACTGATGAGGCCAT 59.927 40.000 5.01 0.00 38.57 4.40
2934 4508 6.270695 TCATTTAGATCACTGATGAGGCCATA 59.729 38.462 5.01 0.00 38.57 2.74
2935 4509 5.735285 TTAGATCACTGATGAGGCCATAG 57.265 43.478 5.01 0.00 38.57 2.23
2936 4510 3.585360 AGATCACTGATGAGGCCATAGT 58.415 45.455 5.01 0.00 38.57 2.12
2937 4511 4.745351 AGATCACTGATGAGGCCATAGTA 58.255 43.478 5.01 0.00 38.57 1.82
2938 4512 5.150715 AGATCACTGATGAGGCCATAGTAA 58.849 41.667 5.01 0.00 38.57 2.24
2939 4513 4.944619 TCACTGATGAGGCCATAGTAAG 57.055 45.455 5.01 0.00 32.09 2.34
2940 4514 3.643320 TCACTGATGAGGCCATAGTAAGG 59.357 47.826 5.01 0.00 32.09 2.69
2941 4515 3.389329 CACTGATGAGGCCATAGTAAGGT 59.611 47.826 5.01 0.00 32.09 3.50
2945 4534 2.827755 TGAGGCCATAGTAAGGTGACA 58.172 47.619 5.01 0.00 0.00 3.58
2959 4548 1.401409 GGTGACATGTTCGGTGCATTG 60.401 52.381 0.00 0.00 0.00 2.82
2979 4568 2.223947 TGTTCTTCAGTGCGTCTGCTAA 60.224 45.455 4.18 0.00 43.32 3.09
3007 4630 2.027192 GCAGTCCACCTCCAACTGAATA 60.027 50.000 5.95 0.00 42.37 1.75
3012 4635 5.251700 AGTCCACCTCCAACTGAATATTTCT 59.748 40.000 0.00 0.00 0.00 2.52
3014 4637 5.488919 TCCACCTCCAACTGAATATTTCTCT 59.511 40.000 0.00 0.00 0.00 3.10
3022 4645 8.154203 TCCAACTGAATATTTCTCTTGTACACA 58.846 33.333 0.00 0.00 0.00 3.72
3024 4647 8.993121 CAACTGAATATTTCTCTTGTACACAGT 58.007 33.333 0.00 0.00 35.68 3.55
3027 4650 9.208022 CTGAATATTTCTCTTGTACACAGTTGA 57.792 33.333 0.00 0.00 0.00 3.18
3044 4669 0.250252 TGAAAGTGCATGCAGTCCGA 60.250 50.000 27.60 11.75 0.00 4.55
3057 4682 3.601685 TCCGACGAGTGCAGCACA 61.602 61.111 27.35 1.48 36.74 4.57
3109 4734 0.674895 GCAACTCCTTGCGGACTGAT 60.675 55.000 0.00 0.00 43.42 2.90
3206 4831 9.017669 CAGCATCTGAATTTAATTTAGCAACTC 57.982 33.333 4.81 0.00 32.44 3.01
3208 4833 7.436376 GCATCTGAATTTAATTTAGCAACTCCC 59.564 37.037 4.81 0.00 0.00 4.30
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 2.216782 CTGAAAGAAGGGCCTCCCCC 62.217 65.000 6.46 0.00 46.05 5.40
4 5 1.304617 CTGAAAGAAGGGCCTCCCC 59.695 63.158 6.46 0.00 45.43 4.81
5 6 0.034960 GACTGAAAGAAGGGCCTCCC 60.035 60.000 6.46 1.38 40.42 4.30
6 7 0.693049 TGACTGAAAGAAGGGCCTCC 59.307 55.000 6.46 0.00 37.43 4.30
7 8 2.568623 TTGACTGAAAGAAGGGCCTC 57.431 50.000 6.46 0.00 37.43 4.70
8 9 3.312736 TTTTGACTGAAAGAAGGGCCT 57.687 42.857 0.00 0.00 37.43 5.19
35 36 9.877178 ACGTATGAAATTTAAGTCAGAGAGATT 57.123 29.630 0.00 0.00 0.00 2.40
36 37 9.522804 GACGTATGAAATTTAAGTCAGAGAGAT 57.477 33.333 0.00 0.00 31.16 2.75
37 38 7.696872 CGACGTATGAAATTTAAGTCAGAGAGA 59.303 37.037 0.00 0.00 31.16 3.10
38 39 7.696872 TCGACGTATGAAATTTAAGTCAGAGAG 59.303 37.037 0.00 0.00 31.16 3.20
39 40 7.532571 TCGACGTATGAAATTTAAGTCAGAGA 58.467 34.615 0.00 0.00 31.16 3.10
40 41 7.043986 CCTCGACGTATGAAATTTAAGTCAGAG 60.044 40.741 13.56 13.56 33.82 3.35
41 42 6.750501 CCTCGACGTATGAAATTTAAGTCAGA 59.249 38.462 0.00 0.00 31.16 3.27
42 43 6.530534 ACCTCGACGTATGAAATTTAAGTCAG 59.469 38.462 0.00 0.00 31.16 3.51
43 44 6.392354 ACCTCGACGTATGAAATTTAAGTCA 58.608 36.000 0.00 0.00 31.16 3.41
44 45 6.882458 ACCTCGACGTATGAAATTTAAGTC 57.118 37.500 0.00 0.00 0.00 3.01
45 46 6.401796 GCAACCTCGACGTATGAAATTTAAGT 60.402 38.462 0.00 0.00 0.00 2.24
46 47 5.957796 GCAACCTCGACGTATGAAATTTAAG 59.042 40.000 0.00 0.00 0.00 1.85
47 48 5.408909 TGCAACCTCGACGTATGAAATTTAA 59.591 36.000 0.00 0.00 0.00 1.52
48 49 4.930405 TGCAACCTCGACGTATGAAATTTA 59.070 37.500 0.00 0.00 0.00 1.40
49 50 3.749088 TGCAACCTCGACGTATGAAATTT 59.251 39.130 0.00 0.00 0.00 1.82
50 51 3.331150 TGCAACCTCGACGTATGAAATT 58.669 40.909 0.00 0.00 0.00 1.82
51 52 2.930040 CTGCAACCTCGACGTATGAAAT 59.070 45.455 0.00 0.00 0.00 2.17
52 53 2.288579 ACTGCAACCTCGACGTATGAAA 60.289 45.455 0.00 0.00 0.00 2.69
53 54 1.271379 ACTGCAACCTCGACGTATGAA 59.729 47.619 0.00 0.00 0.00 2.57
54 55 0.885879 ACTGCAACCTCGACGTATGA 59.114 50.000 0.00 0.00 0.00 2.15
55 56 1.269166 GACTGCAACCTCGACGTATG 58.731 55.000 0.00 0.00 0.00 2.39
56 57 0.172803 GGACTGCAACCTCGACGTAT 59.827 55.000 0.00 0.00 0.00 3.06
57 58 1.582968 GGACTGCAACCTCGACGTA 59.417 57.895 0.00 0.00 0.00 3.57
58 59 2.338984 GGACTGCAACCTCGACGT 59.661 61.111 0.00 0.00 0.00 4.34
59 60 2.432628 GGGACTGCAACCTCGACG 60.433 66.667 9.06 0.00 0.00 5.12
60 61 3.060866 AGGGACTGCAACCTCGAC 58.939 61.111 9.06 0.00 37.18 4.20
70 71 4.325729 GGTGATTCACTCCCAGGGACTG 62.326 59.091 16.02 6.43 44.76 3.51
71 72 1.280457 GTGATTCACTCCCAGGGACT 58.720 55.000 3.01 0.00 43.88 3.85
72 73 0.253327 GGTGATTCACTCCCAGGGAC 59.747 60.000 16.02 0.00 34.40 4.46
73 74 0.178876 TGGTGATTCACTCCCAGGGA 60.179 55.000 16.02 8.35 34.40 4.20
74 75 0.035056 GTGGTGATTCACTCCCAGGG 60.035 60.000 16.02 0.00 34.40 4.45
75 76 0.692476 TGTGGTGATTCACTCCCAGG 59.308 55.000 16.02 0.00 38.40 4.45
76 77 2.238144 AGATGTGGTGATTCACTCCCAG 59.762 50.000 16.02 0.00 38.40 4.45
77 78 2.237143 GAGATGTGGTGATTCACTCCCA 59.763 50.000 16.02 10.46 38.40 4.37
78 79 2.237143 TGAGATGTGGTGATTCACTCCC 59.763 50.000 16.02 0.98 38.40 4.30
79 80 3.196469 TCTGAGATGTGGTGATTCACTCC 59.804 47.826 16.02 7.80 38.40 3.85
80 81 4.462508 TCTGAGATGTGGTGATTCACTC 57.537 45.455 16.02 10.27 38.40 3.51
81 82 5.660417 AGTATCTGAGATGTGGTGATTCACT 59.340 40.000 16.02 0.00 38.40 3.41
82 83 5.911752 AGTATCTGAGATGTGGTGATTCAC 58.088 41.667 4.96 8.34 38.09 3.18
83 84 6.154203 GAGTATCTGAGATGTGGTGATTCA 57.846 41.667 4.96 0.00 0.00 2.57
96 97 8.403230 CGACATTCGTGAAGAAGAGTATCTGAG 61.403 44.444 0.00 0.00 42.92 3.35
97 98 6.675728 CGACATTCGTGAAGAAGAGTATCTGA 60.676 42.308 0.00 0.00 42.92 3.27
98 99 5.453909 CGACATTCGTGAAGAAGAGTATCTG 59.546 44.000 0.00 0.00 42.92 2.90
99 100 5.354513 TCGACATTCGTGAAGAAGAGTATCT 59.645 40.000 0.00 0.00 44.89 1.98
100 101 5.452944 GTCGACATTCGTGAAGAAGAGTATC 59.547 44.000 11.55 0.00 42.92 2.24
101 102 5.333513 GTCGACATTCGTGAAGAAGAGTAT 58.666 41.667 11.55 0.00 42.92 2.12
102 103 4.379186 GGTCGACATTCGTGAAGAAGAGTA 60.379 45.833 18.91 0.00 42.92 2.59
103 104 3.566523 GTCGACATTCGTGAAGAAGAGT 58.433 45.455 11.55 0.00 42.92 3.24
104 105 2.917971 GGTCGACATTCGTGAAGAAGAG 59.082 50.000 18.91 0.00 42.92 2.85
105 106 2.295070 TGGTCGACATTCGTGAAGAAGA 59.705 45.455 18.91 0.00 42.92 2.87
106 107 2.672714 TGGTCGACATTCGTGAAGAAG 58.327 47.619 18.91 0.00 42.92 2.85
107 108 2.804697 TGGTCGACATTCGTGAAGAA 57.195 45.000 18.91 0.00 41.35 2.52
108 109 2.295070 TCTTGGTCGACATTCGTGAAGA 59.705 45.455 18.91 9.16 41.35 2.87
109 110 2.672714 TCTTGGTCGACATTCGTGAAG 58.327 47.619 18.91 7.12 41.35 3.02
110 111 2.804697 TCTTGGTCGACATTCGTGAA 57.195 45.000 18.91 0.00 41.35 3.18
111 112 2.672714 CTTCTTGGTCGACATTCGTGA 58.327 47.619 18.91 3.55 41.35 4.35
112 113 1.126846 GCTTCTTGGTCGACATTCGTG 59.873 52.381 18.91 4.27 41.35 4.35
113 114 1.429463 GCTTCTTGGTCGACATTCGT 58.571 50.000 18.91 0.00 41.35 3.85
114 115 0.721718 GGCTTCTTGGTCGACATTCG 59.278 55.000 18.91 2.47 42.10 3.34
115 116 1.464997 GTGGCTTCTTGGTCGACATTC 59.535 52.381 18.91 0.00 0.00 2.67
116 117 1.523758 GTGGCTTCTTGGTCGACATT 58.476 50.000 18.91 0.00 0.00 2.71
117 118 0.321653 GGTGGCTTCTTGGTCGACAT 60.322 55.000 18.91 0.00 0.00 3.06
118 119 1.070786 GGTGGCTTCTTGGTCGACA 59.929 57.895 18.91 0.27 0.00 4.35
119 120 0.951040 CAGGTGGCTTCTTGGTCGAC 60.951 60.000 7.13 7.13 0.00 4.20
120 121 1.371183 CAGGTGGCTTCTTGGTCGA 59.629 57.895 0.00 0.00 0.00 4.20
121 122 1.672356 CCAGGTGGCTTCTTGGTCG 60.672 63.158 4.00 0.00 31.24 4.79
122 123 0.890996 CACCAGGTGGCTTCTTGGTC 60.891 60.000 12.40 0.00 44.12 4.02
123 124 1.151450 CACCAGGTGGCTTCTTGGT 59.849 57.895 12.40 10.13 46.28 3.67
124 125 2.270986 GCACCAGGTGGCTTCTTGG 61.271 63.158 21.77 9.08 39.90 3.61
125 126 1.108727 TTGCACCAGGTGGCTTCTTG 61.109 55.000 21.77 0.00 39.32 3.02
126 127 0.178953 ATTGCACCAGGTGGCTTCTT 60.179 50.000 21.77 0.00 39.32 2.52
127 128 0.896940 CATTGCACCAGGTGGCTTCT 60.897 55.000 21.77 0.78 39.32 2.85
128 129 1.588082 CATTGCACCAGGTGGCTTC 59.412 57.895 21.77 4.84 39.32 3.86
129 130 1.909781 CCATTGCACCAGGTGGCTT 60.910 57.895 21.77 3.50 39.32 4.35
130 131 2.159101 ATCCATTGCACCAGGTGGCT 62.159 55.000 21.77 0.00 39.32 4.75
131 132 1.683365 ATCCATTGCACCAGGTGGC 60.683 57.895 21.77 13.63 39.32 5.01
132 133 2.195389 CATCCATTGCACCAGGTGG 58.805 57.895 21.77 4.07 42.17 4.61
142 143 1.830279 AGTGTGACCTGCATCCATTG 58.170 50.000 0.00 0.00 0.00 2.82
143 144 2.573462 AGTAGTGTGACCTGCATCCATT 59.427 45.455 0.00 0.00 0.00 3.16
144 145 2.191400 AGTAGTGTGACCTGCATCCAT 58.809 47.619 0.00 0.00 0.00 3.41
145 146 1.644509 AGTAGTGTGACCTGCATCCA 58.355 50.000 0.00 0.00 0.00 3.41
146 147 2.770164 AAGTAGTGTGACCTGCATCC 57.230 50.000 0.00 0.00 0.00 3.51
147 148 3.931578 AGAAAGTAGTGTGACCTGCATC 58.068 45.455 0.00 0.00 0.00 3.91
148 149 4.357918 AAGAAAGTAGTGTGACCTGCAT 57.642 40.909 0.00 0.00 0.00 3.96
149 150 3.838244 AAGAAAGTAGTGTGACCTGCA 57.162 42.857 0.00 0.00 0.00 4.41
150 151 5.135508 TCTAAGAAAGTAGTGTGACCTGC 57.864 43.478 0.00 0.00 0.00 4.85
151 152 5.164954 GCTCTAAGAAAGTAGTGTGACCTG 58.835 45.833 0.00 0.00 0.00 4.00
152 153 4.833380 TGCTCTAAGAAAGTAGTGTGACCT 59.167 41.667 0.00 0.00 0.00 3.85
153 154 5.135508 TGCTCTAAGAAAGTAGTGTGACC 57.864 43.478 0.00 0.00 0.00 4.02
154 155 8.410141 AGATATGCTCTAAGAAAGTAGTGTGAC 58.590 37.037 0.00 0.00 30.26 3.67
155 156 8.526667 AGATATGCTCTAAGAAAGTAGTGTGA 57.473 34.615 0.00 0.00 30.26 3.58
162 163 8.141268 GCTCTGTTAGATATGCTCTAAGAAAGT 58.859 37.037 0.00 0.00 45.07 2.66
163 164 7.598493 GGCTCTGTTAGATATGCTCTAAGAAAG 59.402 40.741 0.00 0.00 45.07 2.62
164 165 7.437748 GGCTCTGTTAGATATGCTCTAAGAAA 58.562 38.462 0.00 0.00 45.07 2.52
165 166 6.015010 GGGCTCTGTTAGATATGCTCTAAGAA 60.015 42.308 0.00 0.00 45.07 2.52
166 167 5.478679 GGGCTCTGTTAGATATGCTCTAAGA 59.521 44.000 0.00 0.00 45.07 2.10
177 178 3.054802 CCAGTTTGAGGGCTCTGTTAGAT 60.055 47.826 0.00 0.00 0.00 1.98
259 260 3.537337 TGAGGGTTTAGGGATTTGAGGA 58.463 45.455 0.00 0.00 0.00 3.71
300 303 0.034896 GGTTGGCCTCGAACTTGAGA 59.965 55.000 3.32 0.00 38.28 3.27
359 362 2.288666 GCACAGAGTTGACCAAGTGAA 58.711 47.619 0.00 0.00 0.00 3.18
960 2439 3.372730 GTTGGCGGCATTGGAGCA 61.373 61.111 14.32 0.00 35.83 4.26
1303 2805 3.023119 TCCTCAATGCGTTGCCAATAAT 58.977 40.909 14.04 0.00 35.26 1.28
1549 3078 6.873076 GGAAGCATATCAAAATCACAACCAAA 59.127 34.615 0.00 0.00 0.00 3.28
1652 3181 3.139850 CAATGCCCAACAATGCTTGAAA 58.860 40.909 3.37 0.00 0.00 2.69
1677 3206 7.658575 CCTCAATTTCCATTTGTCAAGATGTTT 59.341 33.333 6.86 0.00 0.00 2.83
1917 3450 6.183360 GCAAGTTTCACCTCTTTCTTTCTCTT 60.183 38.462 0.00 0.00 0.00 2.85
2309 3848 7.643569 TGGACATCATAGCAAAACATACAAT 57.356 32.000 0.00 0.00 0.00 2.71
2519 4090 1.800229 AAGGCCGAAAATCCCTGGGT 61.800 55.000 13.56 0.00 0.00 4.51
2520 4091 1.000359 AAGGCCGAAAATCCCTGGG 60.000 57.895 6.33 6.33 0.00 4.45
2615 4187 0.393077 AGTTGGAGAACGGTGAGTGG 59.607 55.000 0.00 0.00 37.15 4.00
2616 4188 1.068588 TGAGTTGGAGAACGGTGAGTG 59.931 52.381 0.00 0.00 37.15 3.51
2617 4189 1.410004 TGAGTTGGAGAACGGTGAGT 58.590 50.000 0.00 0.00 37.15 3.41
2618 4190 2.135933 GTTGAGTTGGAGAACGGTGAG 58.864 52.381 0.00 0.00 37.15 3.51
2619 4191 1.483004 TGTTGAGTTGGAGAACGGTGA 59.517 47.619 0.00 0.00 37.15 4.02
2620 4192 1.948104 TGTTGAGTTGGAGAACGGTG 58.052 50.000 0.00 0.00 37.15 4.94
2621 4193 2.158813 ACATGTTGAGTTGGAGAACGGT 60.159 45.455 0.00 0.00 37.15 4.83
2622 4194 2.224079 CACATGTTGAGTTGGAGAACGG 59.776 50.000 0.00 0.00 37.15 4.44
2623 4195 2.349817 GCACATGTTGAGTTGGAGAACG 60.350 50.000 0.00 0.00 37.15 3.95
2624 4196 2.880890 AGCACATGTTGAGTTGGAGAAC 59.119 45.455 0.00 0.00 0.00 3.01
2625 4197 3.213206 AGCACATGTTGAGTTGGAGAA 57.787 42.857 0.00 0.00 0.00 2.87
2626 4198 2.936919 AGCACATGTTGAGTTGGAGA 57.063 45.000 0.00 0.00 0.00 3.71
2627 4199 2.227388 GGAAGCACATGTTGAGTTGGAG 59.773 50.000 0.00 0.00 0.00 3.86
2628 4200 2.229792 GGAAGCACATGTTGAGTTGGA 58.770 47.619 0.00 0.00 0.00 3.53
2629 4201 1.270550 GGGAAGCACATGTTGAGTTGG 59.729 52.381 0.00 0.00 0.00 3.77
2630 4202 2.030540 CAGGGAAGCACATGTTGAGTTG 60.031 50.000 0.00 0.00 0.00 3.16
2631 4203 2.233271 CAGGGAAGCACATGTTGAGTT 58.767 47.619 0.00 0.00 0.00 3.01
2632 4204 1.546323 CCAGGGAAGCACATGTTGAGT 60.546 52.381 0.00 0.00 0.00 3.41
2633 4205 1.171308 CCAGGGAAGCACATGTTGAG 58.829 55.000 0.00 0.00 0.00 3.02
2634 4206 0.770499 TCCAGGGAAGCACATGTTGA 59.230 50.000 0.00 0.00 0.00 3.18
2635 4207 0.883833 GTCCAGGGAAGCACATGTTG 59.116 55.000 0.00 0.00 0.00 3.33
2636 4208 0.478072 TGTCCAGGGAAGCACATGTT 59.522 50.000 0.00 0.00 0.00 2.71
2637 4209 0.700564 ATGTCCAGGGAAGCACATGT 59.299 50.000 0.00 0.00 0.00 3.21
2638 4210 1.386533 GATGTCCAGGGAAGCACATG 58.613 55.000 0.00 0.00 29.43 3.21
2639 4211 0.257039 GGATGTCCAGGGAAGCACAT 59.743 55.000 0.00 0.00 35.64 3.21
2640 4212 1.133181 TGGATGTCCAGGGAAGCACA 61.133 55.000 0.00 0.00 42.01 4.57
2641 4213 1.685224 TGGATGTCCAGGGAAGCAC 59.315 57.895 0.00 0.00 42.01 4.40
2642 4214 4.248908 TGGATGTCCAGGGAAGCA 57.751 55.556 0.00 0.00 42.01 3.91
2650 4222 1.131638 GGATACCAGCTGGATGTCCA 58.868 55.000 39.19 15.81 45.30 4.02
2651 4223 1.346068 GAGGATACCAGCTGGATGTCC 59.654 57.143 39.19 34.08 38.94 4.02
2652 4224 2.042464 TGAGGATACCAGCTGGATGTC 58.958 52.381 39.19 28.21 38.94 3.06
2653 4225 2.180946 TGAGGATACCAGCTGGATGT 57.819 50.000 39.19 22.73 38.94 3.06
2654 4226 2.437281 ACTTGAGGATACCAGCTGGATG 59.563 50.000 39.19 18.11 38.94 3.51
2655 4227 2.769209 ACTTGAGGATACCAGCTGGAT 58.231 47.619 39.19 25.77 38.94 3.41
2656 4228 2.254152 ACTTGAGGATACCAGCTGGA 57.746 50.000 39.19 22.26 38.94 3.86
2657 4229 3.356529 AAACTTGAGGATACCAGCTGG 57.643 47.619 31.60 31.60 42.17 4.85
2658 4230 5.705441 TGTAAAAACTTGAGGATACCAGCTG 59.295 40.000 6.78 6.78 37.17 4.24
2659 4231 5.876357 TGTAAAAACTTGAGGATACCAGCT 58.124 37.500 0.00 0.00 37.17 4.24
2660 4232 6.759497 ATGTAAAAACTTGAGGATACCAGC 57.241 37.500 0.00 0.00 37.17 4.85
2661 4233 9.838339 AGATATGTAAAAACTTGAGGATACCAG 57.162 33.333 0.00 0.00 37.17 4.00
2662 4234 9.613428 CAGATATGTAAAAACTTGAGGATACCA 57.387 33.333 0.00 0.00 37.17 3.25
2663 4235 9.832445 TCAGATATGTAAAAACTTGAGGATACC 57.168 33.333 0.00 0.00 37.17 2.73
2674 4246 9.140286 GCCCTTCTTTTTCAGATATGTAAAAAC 57.860 33.333 6.37 0.00 31.00 2.43
2675 4247 8.311109 GGCCCTTCTTTTTCAGATATGTAAAAA 58.689 33.333 6.37 7.80 32.72 1.94
2676 4248 7.453126 TGGCCCTTCTTTTTCAGATATGTAAAA 59.547 33.333 0.00 5.02 0.00 1.52
2677 4249 6.951198 TGGCCCTTCTTTTTCAGATATGTAAA 59.049 34.615 0.00 0.00 0.00 2.01
2678 4250 6.489603 TGGCCCTTCTTTTTCAGATATGTAA 58.510 36.000 0.00 0.00 0.00 2.41
2679 4251 6.073447 TGGCCCTTCTTTTTCAGATATGTA 57.927 37.500 0.00 0.00 0.00 2.29
2680 4252 4.934356 TGGCCCTTCTTTTTCAGATATGT 58.066 39.130 0.00 0.00 0.00 2.29
2681 4253 6.475596 AATGGCCCTTCTTTTTCAGATATG 57.524 37.500 0.00 0.00 0.00 1.78
2682 4254 7.500629 AAAATGGCCCTTCTTTTTCAGATAT 57.499 32.000 0.00 0.00 0.00 1.63
2683 4255 6.933514 AAAATGGCCCTTCTTTTTCAGATA 57.066 33.333 0.00 0.00 0.00 1.98
2684 4256 5.830799 AAAATGGCCCTTCTTTTTCAGAT 57.169 34.783 0.00 0.00 0.00 2.90
2685 4257 5.628797 AAAAATGGCCCTTCTTTTTCAGA 57.371 34.783 0.00 0.00 28.63 3.27
2753 4325 7.174253 ACCGAATTAGCTTTTGTTGTCTGAATA 59.826 33.333 0.00 0.00 0.00 1.75
2766 4339 8.184304 AGTCATAGATAGACCGAATTAGCTTT 57.816 34.615 0.00 0.00 36.68 3.51
2772 4346 5.921408 GCGAAAGTCATAGATAGACCGAATT 59.079 40.000 0.00 0.00 36.68 2.17
2777 4351 4.585955 TGGCGAAAGTCATAGATAGACC 57.414 45.455 0.00 0.00 43.37 3.85
2845 4419 2.279173 AGGGAAGGTAACAAGATGGCT 58.721 47.619 0.00 0.00 41.41 4.75
2875 4449 2.930682 GTTATCTGCTTTCGAGGTGACC 59.069 50.000 0.00 0.00 0.00 4.02
2893 4467 4.380841 AAATGATGTCCTCGCTACGTTA 57.619 40.909 0.00 0.00 0.00 3.18
2902 4476 7.440198 TCATCAGTGATCTAAATGATGTCCTC 58.560 38.462 17.76 0.00 45.87 3.71
2906 4480 5.996513 GCCTCATCAGTGATCTAAATGATGT 59.003 40.000 17.76 0.00 45.87 3.06
2914 4488 4.745351 ACTATGGCCTCATCAGTGATCTA 58.255 43.478 3.32 0.00 34.96 1.98
2918 4492 3.643320 CCTTACTATGGCCTCATCAGTGA 59.357 47.826 3.32 0.00 34.96 3.41
2919 4493 3.389329 ACCTTACTATGGCCTCATCAGTG 59.611 47.826 3.32 0.00 34.96 3.66
2920 4494 3.389329 CACCTTACTATGGCCTCATCAGT 59.611 47.826 3.32 2.40 34.96 3.41
2921 4495 3.643320 TCACCTTACTATGGCCTCATCAG 59.357 47.826 3.32 0.00 34.96 2.90
2922 4496 3.388024 GTCACCTTACTATGGCCTCATCA 59.612 47.826 3.32 0.00 34.96 3.07
2923 4497 3.388024 TGTCACCTTACTATGGCCTCATC 59.612 47.826 3.32 0.00 34.96 2.92
2924 4498 3.384168 TGTCACCTTACTATGGCCTCAT 58.616 45.455 3.32 0.00 37.40 2.90
2925 4499 2.827755 TGTCACCTTACTATGGCCTCA 58.172 47.619 3.32 0.00 0.00 3.86
2926 4500 3.134804 ACATGTCACCTTACTATGGCCTC 59.865 47.826 3.32 0.00 0.00 4.70
2927 4501 3.115390 ACATGTCACCTTACTATGGCCT 58.885 45.455 3.32 0.00 0.00 5.19
2928 4502 3.560636 ACATGTCACCTTACTATGGCC 57.439 47.619 0.00 0.00 0.00 5.36
2929 4503 3.555956 CGAACATGTCACCTTACTATGGC 59.444 47.826 0.00 0.00 0.00 4.40
2930 4504 4.119862 CCGAACATGTCACCTTACTATGG 58.880 47.826 0.00 0.00 0.00 2.74
2931 4505 4.566759 CACCGAACATGTCACCTTACTATG 59.433 45.833 0.00 0.00 0.00 2.23
2932 4506 4.755411 CACCGAACATGTCACCTTACTAT 58.245 43.478 0.00 0.00 0.00 2.12
2933 4507 3.615592 GCACCGAACATGTCACCTTACTA 60.616 47.826 0.00 0.00 0.00 1.82
2934 4508 2.870435 GCACCGAACATGTCACCTTACT 60.870 50.000 0.00 0.00 0.00 2.24
2935 4509 1.463444 GCACCGAACATGTCACCTTAC 59.537 52.381 0.00 0.00 0.00 2.34
2936 4510 1.070914 TGCACCGAACATGTCACCTTA 59.929 47.619 0.00 0.00 0.00 2.69
2937 4511 0.179032 TGCACCGAACATGTCACCTT 60.179 50.000 0.00 0.00 0.00 3.50
2938 4512 0.036732 ATGCACCGAACATGTCACCT 59.963 50.000 0.00 0.00 0.00 4.00
2939 4513 0.881118 AATGCACCGAACATGTCACC 59.119 50.000 0.00 0.00 0.00 4.02
2940 4514 1.266718 ACAATGCACCGAACATGTCAC 59.733 47.619 0.00 0.00 0.00 3.67
2941 4515 1.603456 ACAATGCACCGAACATGTCA 58.397 45.000 0.00 0.00 0.00 3.58
2945 4534 2.884012 TGAAGAACAATGCACCGAACAT 59.116 40.909 0.00 0.00 0.00 2.71
3007 4630 7.679638 GCACTTTCAACTGTGTACAAGAGAAAT 60.680 37.037 0.00 3.52 36.63 2.17
3012 4635 4.257731 TGCACTTTCAACTGTGTACAAGA 58.742 39.130 0.00 0.00 36.63 3.02
3014 4637 4.733230 GCATGCACTTTCAACTGTGTACAA 60.733 41.667 14.21 0.00 36.63 2.41
3022 4645 1.610522 GGACTGCATGCACTTTCAACT 59.389 47.619 18.46 0.00 0.00 3.16
3024 4647 0.592637 CGGACTGCATGCACTTTCAA 59.407 50.000 18.46 0.00 0.00 2.69
3027 4650 1.568612 CGTCGGACTGCATGCACTTT 61.569 55.000 18.46 3.52 0.00 2.66
3044 4669 0.671781 GAAGGATGTGCTGCACTCGT 60.672 55.000 30.43 22.28 35.11 4.18
3057 4682 1.280421 GTGTGGAAGAGGCTGAAGGAT 59.720 52.381 0.00 0.00 0.00 3.24
3125 4750 2.670479 CGCGATTGCTAGAGATCACAT 58.330 47.619 0.00 0.00 39.65 3.21


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

AutoCloner maintained by Alex Coulton.