Multiple sequence alignment - TraesCS4B01G016700

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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 TraesCS4B01G016700 chr4B 100.000 2288 0 0 1 2288 12015406 12017693 0.000000e+00 4226.0
1 TraesCS4B01G016700 chr4B 85.319 940 70 20 540 1470 11995208 11996088 0.000000e+00 909.0
2 TraesCS4B01G016700 chr4B 90.735 313 28 1 985 1297 12051706 12052017 1.260000e-112 416.0
3 TraesCS4B01G016700 chr4B 91.892 148 9 3 1 147 201148906 201148761 1.070000e-48 204.0
4 TraesCS4B01G016700 chr4B 83.784 111 0 4 1587 1680 649653966 649654075 3.130000e-14 89.8
5 TraesCS4B01G016700 chr4B 100.000 48 0 0 1634 1681 657247727 657247680 3.130000e-14 89.8
6 TraesCS4B01G016700 chr4D 87.107 1241 78 31 267 1470 6698448 6699643 0.000000e+00 1330.0
7 TraesCS4B01G016700 chr4D 91.040 625 36 13 857 1470 6682167 6682782 0.000000e+00 826.0
8 TraesCS4B01G016700 chr4D 87.156 327 32 8 976 1297 6684811 6685132 1.670000e-96 363.0
9 TraesCS4B01G016700 chr4D 89.668 271 13 4 597 863 6681884 6682143 4.710000e-87 331.0
10 TraesCS4B01G016700 chr4D 91.333 150 10 3 1 149 506413869 506413722 3.850000e-48 202.0
11 TraesCS4B01G016700 chr4D 92.857 140 7 3 8 146 455259916 455260053 1.390000e-47 200.0
12 TraesCS4B01G016700 chr4D 88.811 143 12 4 406 546 6681732 6681872 3.020000e-39 172.0
13 TraesCS4B01G016700 chr4D 100.000 48 0 0 1592 1639 20041919 20041872 3.130000e-14 89.8
14 TraesCS4B01G016700 chr4D 100.000 47 0 0 1634 1680 20041860 20041814 1.130000e-13 87.9
15 TraesCS4B01G016700 chr4D 87.671 73 5 1 151 223 6698041 6698109 5.240000e-12 82.4
16 TraesCS4B01G016700 chr4A 86.594 1186 87 30 300 1464 596689289 596688155 0.000000e+00 1243.0
17 TraesCS4B01G016700 chr4A 86.926 1132 70 36 389 1473 596713964 596712864 0.000000e+00 1199.0
18 TraesCS4B01G016700 chr4A 92.308 234 18 0 1052 1285 596683262 596683029 1.310000e-87 333.0
19 TraesCS4B01G016700 chr4A 100.000 48 0 0 1591 1638 738496304 738496257 3.130000e-14 89.8
20 TraesCS4B01G016700 chr4A 100.000 47 0 0 1592 1638 661023914 661023868 1.130000e-13 87.9
21 TraesCS4B01G016700 chr4A 100.000 47 0 0 1634 1680 738496244 738496198 1.130000e-13 87.9
22 TraesCS4B01G016700 chr2B 97.059 612 17 1 1676 2287 583070777 583071387 0.000000e+00 1029.0
23 TraesCS4B01G016700 chr2B 100.000 48 0 0 1591 1638 629169712 629169759 3.130000e-14 89.8
24 TraesCS4B01G016700 chr2B 100.000 47 0 0 1634 1680 45541092 45541138 1.130000e-13 87.9
25 TraesCS4B01G016700 chr3D 97.500 320 8 0 1968 2287 524770442 524770123 4.300000e-152 547.0
26 TraesCS4B01G016700 chr3D 94.040 302 17 1 1678 1979 524770825 524770525 7.450000e-125 457.0
27 TraesCS4B01G016700 chr3D 91.613 155 8 5 1 152 59922693 59922541 2.300000e-50 209.0
28 TraesCS4B01G016700 chr3B 96.250 320 12 0 1968 2287 692125213 692124894 2.010000e-145 525.0
29 TraesCS4B01G016700 chr3B 93.377 302 19 1 1678 1979 692125596 692125296 1.610000e-121 446.0
30 TraesCS4B01G016700 chr3B 93.878 147 7 2 1 146 748423126 748422981 1.060000e-53 220.0
31 TraesCS4B01G016700 chr3B 100.000 48 0 0 1591 1638 32382893 32382940 3.130000e-14 89.8
32 TraesCS4B01G016700 chr3A 94.375 320 18 0 1968 2287 659036393 659036074 2.040000e-135 492.0
33 TraesCS4B01G016700 chr3A 94.702 302 15 1 1678 1979 659036782 659036482 3.440000e-128 468.0
34 TraesCS4B01G016700 chr7B 94.040 151 8 1 1 151 595799435 595799286 6.360000e-56 228.0
35 TraesCS4B01G016700 chr7B 100.000 47 0 0 1634 1680 616816414 616816460 1.130000e-13 87.9
36 TraesCS4B01G016700 chr7B 100.000 47 0 0 1634 1680 616817420 616817374 1.130000e-13 87.9
37 TraesCS4B01G016700 chr5D 93.151 146 7 3 1 146 446817655 446817513 6.400000e-51 211.0
38 TraesCS4B01G016700 chr1B 93.103 145 8 2 1 145 297324932 297324790 6.400000e-51 211.0
39 TraesCS4B01G016700 chr1B 100.000 48 0 0 1591 1638 24113429 24113382 3.130000e-14 89.8
40 TraesCS4B01G016700 chr1B 100.000 47 0 0 1634 1680 67526250 67526296 1.130000e-13 87.9
41 TraesCS4B01G016700 chr5A 90.728 151 7 4 1 146 702982153 702982301 6.450000e-46 195.0
42 TraesCS4B01G016700 chr5B 100.000 48 0 0 1591 1638 438020605 438020652 3.130000e-14 89.8
43 TraesCS4B01G016700 chr5B 100.000 48 0 0 1591 1638 489099086 489099039 3.130000e-14 89.8
44 TraesCS4B01G016700 chr5B 100.000 48 0 0 1591 1638 621506192 621506145 3.130000e-14 89.8
45 TraesCS4B01G016700 chr6B 100.000 47 0 0 1634 1680 43143502 43143548 1.130000e-13 87.9


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 TraesCS4B01G016700 chr4B 12015406 12017693 2287 False 4226.0 4226 100.00000 1 2288 1 chr4B.!!$F2 2287
1 TraesCS4B01G016700 chr4B 11995208 11996088 880 False 909.0 909 85.31900 540 1470 1 chr4B.!!$F1 930
2 TraesCS4B01G016700 chr4D 6698041 6699643 1602 False 706.2 1330 87.38900 151 1470 2 chr4D.!!$F3 1319
3 TraesCS4B01G016700 chr4D 6681732 6685132 3400 False 423.0 826 89.16875 406 1470 4 chr4D.!!$F2 1064
4 TraesCS4B01G016700 chr4A 596688155 596689289 1134 True 1243.0 1243 86.59400 300 1464 1 chr4A.!!$R2 1164
5 TraesCS4B01G016700 chr4A 596712864 596713964 1100 True 1199.0 1199 86.92600 389 1473 1 chr4A.!!$R3 1084
6 TraesCS4B01G016700 chr2B 583070777 583071387 610 False 1029.0 1029 97.05900 1676 2287 1 chr2B.!!$F2 611
7 TraesCS4B01G016700 chr3D 524770123 524770825 702 True 502.0 547 95.77000 1678 2287 2 chr3D.!!$R2 609
8 TraesCS4B01G016700 chr3B 692124894 692125596 702 True 485.5 525 94.81350 1678 2287 2 chr3B.!!$R2 609
9 TraesCS4B01G016700 chr3A 659036074 659036782 708 True 480.0 492 94.53850 1678 2287 2 chr3A.!!$R1 609

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
70 71 0.036671 CCCTAAAAACGCTCGTCCCT 60.037 55.0 0.0 0.0 0.0 4.2 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1585 2373 0.107703 TAGTGATTTCGGCCTGCTGG 60.108 55.0 5.03 5.03 0.0 4.85 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
25 26 8.910351 GCATTGGTTAATCTAGATTCTAGGTT 57.090 34.615 21.17 20.21 32.50 3.50
26 27 8.778358 GCATTGGTTAATCTAGATTCTAGGTTG 58.222 37.037 23.65 13.92 32.50 3.77
27 28 9.277783 CATTGGTTAATCTAGATTCTAGGTTGG 57.722 37.037 23.65 3.63 32.50 3.77
28 29 7.989947 TGGTTAATCTAGATTCTAGGTTGGT 57.010 36.000 23.65 5.84 32.50 3.67
29 30 8.019656 TGGTTAATCTAGATTCTAGGTTGGTC 57.980 38.462 23.65 14.97 32.50 4.02
30 31 7.844779 TGGTTAATCTAGATTCTAGGTTGGTCT 59.155 37.037 23.65 5.21 32.50 3.85
31 32 8.706521 GGTTAATCTAGATTCTAGGTTGGTCTT 58.293 37.037 23.65 4.59 32.50 3.01
35 36 6.407202 TCTAGATTCTAGGTTGGTCTTTTGC 58.593 40.000 18.43 0.00 0.00 3.68
36 37 4.003648 AGATTCTAGGTTGGTCTTTTGCG 58.996 43.478 0.00 0.00 0.00 4.85
37 38 3.478857 TTCTAGGTTGGTCTTTTGCGA 57.521 42.857 0.00 0.00 0.00 5.10
38 39 3.695830 TCTAGGTTGGTCTTTTGCGAT 57.304 42.857 0.00 0.00 0.00 4.58
39 40 4.015872 TCTAGGTTGGTCTTTTGCGATT 57.984 40.909 0.00 0.00 0.00 3.34
40 41 4.394729 TCTAGGTTGGTCTTTTGCGATTT 58.605 39.130 0.00 0.00 0.00 2.17
41 42 3.643159 AGGTTGGTCTTTTGCGATTTC 57.357 42.857 0.00 0.00 0.00 2.17
42 43 3.222603 AGGTTGGTCTTTTGCGATTTCT 58.777 40.909 0.00 0.00 0.00 2.52
43 44 3.004734 AGGTTGGTCTTTTGCGATTTCTG 59.995 43.478 0.00 0.00 0.00 3.02
44 45 2.704725 TGGTCTTTTGCGATTTCTGC 57.295 45.000 0.00 0.00 0.00 4.26
45 46 1.069296 TGGTCTTTTGCGATTTCTGCG 60.069 47.619 0.00 0.00 34.24 5.18
46 47 1.196808 GGTCTTTTGCGATTTCTGCGA 59.803 47.619 0.00 0.00 34.24 5.10
47 48 2.234187 GTCTTTTGCGATTTCTGCGAC 58.766 47.619 0.00 0.00 34.24 5.19
48 49 1.136363 TCTTTTGCGATTTCTGCGACG 60.136 47.619 0.00 0.00 34.24 5.12
49 50 0.584396 TTTTGCGATTTCTGCGACGT 59.416 45.000 0.00 0.00 34.24 4.34
50 51 0.584396 TTTGCGATTTCTGCGACGTT 59.416 45.000 0.00 0.00 34.24 3.99
51 52 0.162933 TTGCGATTTCTGCGACGTTC 59.837 50.000 0.00 0.00 34.24 3.95
52 53 1.058903 GCGATTTCTGCGACGTTCC 59.941 57.895 0.00 0.00 0.00 3.62
53 54 1.708027 CGATTTCTGCGACGTTCCC 59.292 57.895 0.00 0.00 0.00 3.97
54 55 0.736325 CGATTTCTGCGACGTTCCCT 60.736 55.000 0.00 0.00 0.00 4.20
55 56 1.468565 CGATTTCTGCGACGTTCCCTA 60.469 52.381 0.00 0.00 0.00 3.53
56 57 2.613691 GATTTCTGCGACGTTCCCTAA 58.386 47.619 0.00 0.00 0.00 2.69
57 58 2.529780 TTTCTGCGACGTTCCCTAAA 57.470 45.000 0.00 0.00 0.00 1.85
58 59 2.529780 TTCTGCGACGTTCCCTAAAA 57.470 45.000 0.00 0.00 0.00 1.52
59 60 2.529780 TCTGCGACGTTCCCTAAAAA 57.470 45.000 0.00 0.00 0.00 1.94
60 61 2.137523 TCTGCGACGTTCCCTAAAAAC 58.862 47.619 0.00 0.00 0.00 2.43
65 66 3.941194 CGTTCCCTAAAAACGCTCG 57.059 52.632 0.00 0.00 42.40 5.03
66 67 1.142474 CGTTCCCTAAAAACGCTCGT 58.858 50.000 0.00 0.00 42.40 4.18
67 68 1.125566 CGTTCCCTAAAAACGCTCGTC 59.874 52.381 0.00 0.00 42.40 4.20
68 69 1.462283 GTTCCCTAAAAACGCTCGTCC 59.538 52.381 0.00 0.00 0.00 4.79
69 70 0.037046 TCCCTAAAAACGCTCGTCCC 60.037 55.000 0.00 0.00 0.00 4.46
70 71 0.036671 CCCTAAAAACGCTCGTCCCT 60.037 55.000 0.00 0.00 0.00 4.20
71 72 1.356938 CCTAAAAACGCTCGTCCCTC 58.643 55.000 0.00 0.00 0.00 4.30
72 73 1.067071 CCTAAAAACGCTCGTCCCTCT 60.067 52.381 0.00 0.00 0.00 3.69
73 74 1.993370 CTAAAAACGCTCGTCCCTCTG 59.007 52.381 0.00 0.00 0.00 3.35
74 75 0.106149 AAAAACGCTCGTCCCTCTGT 59.894 50.000 0.00 0.00 0.00 3.41
75 76 0.963962 AAAACGCTCGTCCCTCTGTA 59.036 50.000 0.00 0.00 0.00 2.74
76 77 0.963962 AAACGCTCGTCCCTCTGTAA 59.036 50.000 0.00 0.00 0.00 2.41
77 78 0.963962 AACGCTCGTCCCTCTGTAAA 59.036 50.000 0.00 0.00 0.00 2.01
78 79 1.183549 ACGCTCGTCCCTCTGTAAAT 58.816 50.000 0.00 0.00 0.00 1.40
79 80 1.549170 ACGCTCGTCCCTCTGTAAATT 59.451 47.619 0.00 0.00 0.00 1.82
80 81 1.927174 CGCTCGTCCCTCTGTAAATTG 59.073 52.381 0.00 0.00 0.00 2.32
81 82 1.666189 GCTCGTCCCTCTGTAAATTGC 59.334 52.381 0.00 0.00 0.00 3.56
82 83 2.935238 GCTCGTCCCTCTGTAAATTGCA 60.935 50.000 0.00 0.00 0.00 4.08
83 84 3.535561 CTCGTCCCTCTGTAAATTGCAT 58.464 45.455 0.00 0.00 0.00 3.96
84 85 3.531538 TCGTCCCTCTGTAAATTGCATC 58.468 45.455 0.00 0.00 0.00 3.91
85 86 3.197766 TCGTCCCTCTGTAAATTGCATCT 59.802 43.478 0.00 0.00 0.00 2.90
86 87 3.941483 CGTCCCTCTGTAAATTGCATCTT 59.059 43.478 0.00 0.00 0.00 2.40
87 88 4.396166 CGTCCCTCTGTAAATTGCATCTTT 59.604 41.667 0.00 0.00 0.00 2.52
88 89 5.106157 CGTCCCTCTGTAAATTGCATCTTTT 60.106 40.000 0.00 0.00 0.00 2.27
89 90 6.570378 CGTCCCTCTGTAAATTGCATCTTTTT 60.570 38.462 0.00 0.00 0.00 1.94
90 91 6.808704 GTCCCTCTGTAAATTGCATCTTTTTC 59.191 38.462 0.00 0.00 0.00 2.29
91 92 6.721208 TCCCTCTGTAAATTGCATCTTTTTCT 59.279 34.615 0.00 0.00 0.00 2.52
92 93 7.031975 CCCTCTGTAAATTGCATCTTTTTCTC 58.968 38.462 0.00 0.00 0.00 2.87
93 94 7.031975 CCTCTGTAAATTGCATCTTTTTCTCC 58.968 38.462 0.00 0.00 0.00 3.71
94 95 7.309377 CCTCTGTAAATTGCATCTTTTTCTCCA 60.309 37.037 0.00 0.00 0.00 3.86
95 96 8.125978 TCTGTAAATTGCATCTTTTTCTCCAT 57.874 30.769 0.00 0.00 0.00 3.41
96 97 8.246180 TCTGTAAATTGCATCTTTTTCTCCATC 58.754 33.333 0.00 0.00 0.00 3.51
97 98 8.125978 TGTAAATTGCATCTTTTTCTCCATCT 57.874 30.769 0.00 0.00 0.00 2.90
98 99 8.246180 TGTAAATTGCATCTTTTTCTCCATCTC 58.754 33.333 0.00 0.00 0.00 2.75
99 100 7.477945 AAATTGCATCTTTTTCTCCATCTCT 57.522 32.000 0.00 0.00 0.00 3.10
100 101 7.477945 AATTGCATCTTTTTCTCCATCTCTT 57.522 32.000 0.00 0.00 0.00 2.85
101 102 6.506500 TTGCATCTTTTTCTCCATCTCTTC 57.493 37.500 0.00 0.00 0.00 2.87
102 103 5.813383 TGCATCTTTTTCTCCATCTCTTCT 58.187 37.500 0.00 0.00 0.00 2.85
103 104 6.950842 TGCATCTTTTTCTCCATCTCTTCTA 58.049 36.000 0.00 0.00 0.00 2.10
104 105 7.571919 TGCATCTTTTTCTCCATCTCTTCTAT 58.428 34.615 0.00 0.00 0.00 1.98
105 106 8.708378 TGCATCTTTTTCTCCATCTCTTCTATA 58.292 33.333 0.00 0.00 0.00 1.31
106 107 9.553064 GCATCTTTTTCTCCATCTCTTCTATAA 57.447 33.333 0.00 0.00 0.00 0.98
116 117 8.738645 TCCATCTCTTCTATAAAGAAAAAGGC 57.261 34.615 0.00 0.00 41.19 4.35
117 118 8.328758 TCCATCTCTTCTATAAAGAAAAAGGCA 58.671 33.333 0.00 0.00 41.19 4.75
118 119 8.619546 CCATCTCTTCTATAAAGAAAAAGGCAG 58.380 37.037 0.00 0.00 41.19 4.85
119 120 9.171877 CATCTCTTCTATAAAGAAAAAGGCAGT 57.828 33.333 0.00 0.00 41.19 4.40
120 121 8.553459 TCTCTTCTATAAAGAAAAAGGCAGTG 57.447 34.615 0.00 0.00 41.19 3.66
121 122 7.119846 TCTCTTCTATAAAGAAAAAGGCAGTGC 59.880 37.037 6.55 6.55 41.19 4.40
122 123 6.942576 TCTTCTATAAAGAAAAAGGCAGTGCT 59.057 34.615 16.11 0.00 41.19 4.40
123 124 6.743575 TCTATAAAGAAAAAGGCAGTGCTC 57.256 37.500 16.11 3.97 0.00 4.26
124 125 4.790765 ATAAAGAAAAAGGCAGTGCTCC 57.209 40.909 16.11 0.00 0.00 4.70
125 126 2.371658 AAGAAAAAGGCAGTGCTCCT 57.628 45.000 16.11 0.92 34.90 3.69
126 127 1.613836 AGAAAAAGGCAGTGCTCCTG 58.386 50.000 16.11 0.20 44.53 3.86
133 134 2.743928 CAGTGCTCCTGCCGGTTC 60.744 66.667 1.90 0.00 38.71 3.62
134 135 4.021925 AGTGCTCCTGCCGGTTCC 62.022 66.667 1.90 0.00 38.71 3.62
135 136 4.021925 GTGCTCCTGCCGGTTCCT 62.022 66.667 1.90 0.00 38.71 3.36
136 137 3.706373 TGCTCCTGCCGGTTCCTC 61.706 66.667 1.90 0.00 38.71 3.71
137 138 3.706373 GCTCCTGCCGGTTCCTCA 61.706 66.667 1.90 0.00 0.00 3.86
138 139 3.068881 CTCCTGCCGGTTCCTCAA 58.931 61.111 1.90 0.00 0.00 3.02
139 140 1.374947 CTCCTGCCGGTTCCTCAAA 59.625 57.895 1.90 0.00 0.00 2.69
140 141 0.250727 CTCCTGCCGGTTCCTCAAAA 60.251 55.000 1.90 0.00 0.00 2.44
141 142 0.183971 TCCTGCCGGTTCCTCAAAAA 59.816 50.000 1.90 0.00 0.00 1.94
182 183 3.444742 CCATTCAGAAGTTGCTTGCCATA 59.555 43.478 0.00 0.00 0.00 2.74
183 184 4.098960 CCATTCAGAAGTTGCTTGCCATAT 59.901 41.667 0.00 0.00 0.00 1.78
184 185 5.300034 CCATTCAGAAGTTGCTTGCCATATA 59.700 40.000 0.00 0.00 0.00 0.86
185 186 6.015688 CCATTCAGAAGTTGCTTGCCATATAT 60.016 38.462 0.00 0.00 0.00 0.86
186 187 7.175467 CCATTCAGAAGTTGCTTGCCATATATA 59.825 37.037 0.00 0.00 0.00 0.86
187 188 8.737175 CATTCAGAAGTTGCTTGCCATATATAT 58.263 33.333 0.00 0.00 0.00 0.86
214 215 0.620556 ATGGTGGGAGCACTGGTAAG 59.379 55.000 0.00 0.00 0.00 2.34
223 224 1.878775 CACTGGTAAGCTGGCTTGC 59.121 57.895 16.87 15.14 37.47 4.01
226 227 3.815396 GGTAAGCTGGCTTGCCGC 61.815 66.667 22.35 16.42 45.86 6.53
227 228 2.747855 GTAAGCTGGCTTGCCGCT 60.748 61.111 19.48 19.48 39.13 5.52
228 229 2.747460 TAAGCTGGCTTGCCGCTG 60.747 61.111 23.47 11.51 39.13 5.18
232 233 3.200593 CTGGCTTGCCGCTGCTAG 61.201 66.667 7.18 7.18 42.33 3.42
233 234 3.965539 CTGGCTTGCCGCTGCTAGT 62.966 63.158 12.51 0.00 41.61 2.57
234 235 3.503363 GGCTTGCCGCTGCTAGTG 61.503 66.667 12.51 0.00 41.61 2.74
235 236 2.743928 GCTTGCCGCTGCTAGTGT 60.744 61.111 12.51 0.00 41.61 3.55
237 238 2.047274 TTGCCGCTGCTAGTGTCC 60.047 61.111 0.70 0.00 38.71 4.02
238 239 3.605749 TTGCCGCTGCTAGTGTCCC 62.606 63.158 0.70 0.00 38.71 4.46
241 242 2.507102 CGCTGCTAGTGTCCCGTG 60.507 66.667 0.00 0.00 0.00 4.94
252 510 2.441348 TCCCGTGATGCGCTCCTA 60.441 61.111 9.73 0.00 39.71 2.94
261 519 3.062774 GTGATGCGCTCCTAAGACTTTTC 59.937 47.826 9.73 0.00 0.00 2.29
263 521 1.000145 GCGCTCCTAAGACTTTTCCG 59.000 55.000 0.00 0.00 0.00 4.30
264 522 1.403780 GCGCTCCTAAGACTTTTCCGA 60.404 52.381 0.00 0.00 0.00 4.55
281 577 2.031508 TCCGAGCGTGATTTTTGGTTTC 60.032 45.455 0.00 0.00 0.00 2.78
285 581 1.269361 GCGTGATTTTTGGTTTCCGGT 60.269 47.619 0.00 0.00 0.00 5.28
387 686 6.793492 ATGTTTCTCTCTCTAGTGTTTTGC 57.207 37.500 0.00 0.00 0.00 3.68
610 922 2.242196 GGGGATCAGAGTTGGATTTCCA 59.758 50.000 0.00 0.00 45.94 3.53
708 1024 1.906824 GGACCTCTCCACACGACCA 60.907 63.158 0.00 0.00 36.42 4.02
847 1167 1.641577 GTAGGATGAAGCACACGTCC 58.358 55.000 0.00 0.00 42.00 4.79
848 1168 2.366469 AGGATGAAGCACACGTCCT 58.634 52.632 11.14 11.14 45.49 3.85
849 1169 2.460330 GGATGAAGCACACGTCCTG 58.540 57.895 0.00 0.00 39.52 3.86
850 1170 1.639298 GGATGAAGCACACGTCCTGC 61.639 60.000 6.63 6.63 39.52 4.85
852 1172 0.671781 ATGAAGCACACGTCCTGCTC 60.672 55.000 15.85 10.77 44.45 4.26
853 1173 2.029844 GAAGCACACGTCCTGCTCC 61.030 63.158 15.85 1.75 44.45 4.70
854 1174 2.441822 GAAGCACACGTCCTGCTCCT 62.442 60.000 15.85 3.66 44.45 3.69
855 1175 2.721971 AAGCACACGTCCTGCTCCTG 62.722 60.000 15.85 0.00 44.45 3.86
856 1176 2.740055 CACACGTCCTGCTCCTGC 60.740 66.667 0.00 0.00 40.20 4.85
857 1177 2.919856 ACACGTCCTGCTCCTGCT 60.920 61.111 0.00 0.00 40.48 4.24
858 1178 1.606601 ACACGTCCTGCTCCTGCTA 60.607 57.895 0.00 0.00 40.48 3.49
907 1269 0.829602 TCGGCCTCATCATCTCTCCC 60.830 60.000 0.00 0.00 0.00 4.30
937 1305 2.126228 TAGAAACCACCGCTCGCG 60.126 61.111 0.00 0.00 39.44 5.87
981 1356 3.432588 CGGTCGAGCGGTCTGACT 61.433 66.667 28.25 0.00 33.21 3.41
987 1374 0.039074 CGAGCGGTCTGACTTGTTCT 60.039 55.000 13.48 0.00 0.00 3.01
994 1389 4.378459 GCGGTCTGACTTGTTCTTTATTGG 60.378 45.833 7.85 0.00 0.00 3.16
1320 1727 4.500837 GTCACTAGAGCATGTGTGAATACG 59.499 45.833 0.00 0.00 40.47 3.06
1346 1753 1.694150 AGCAGTGCCAGTGTAGAAGAA 59.306 47.619 12.58 0.00 0.00 2.52
1353 1760 7.872993 GCAGTGCCAGTGTAGAAGAATATATAA 59.127 37.037 2.85 0.00 0.00 0.98
1459 1871 0.036732 TTGATGTGCTCACTCCACCC 59.963 55.000 1.47 0.00 32.17 4.61
1485 1914 5.113975 CACAAGAACGATTTCAATTGTGTCG 59.886 40.000 20.06 20.06 40.12 4.35
1486 1915 4.404507 AGAACGATTTCAATTGTGTCGG 57.595 40.909 23.11 9.57 36.68 4.79
1493 1922 2.060326 TCAATTGTGTCGGACGAGAC 57.940 50.000 14.12 14.12 41.30 3.36
1500 1929 2.804697 TGTCGGACGAGACATTGAAA 57.195 45.000 3.34 0.00 45.18 2.69
1501 1930 2.400399 TGTCGGACGAGACATTGAAAC 58.600 47.619 3.34 0.00 45.18 2.78
1502 1931 1.725164 GTCGGACGAGACATTGAAACC 59.275 52.381 0.00 0.00 40.65 3.27
1515 1944 3.444703 TTGAAACCACAACCCAAATCG 57.555 42.857 0.00 0.00 0.00 3.34
1516 1945 1.683917 TGAAACCACAACCCAAATCGG 59.316 47.619 0.00 0.00 0.00 4.18
1517 1946 0.391228 AAACCACAACCCAAATCGGC 59.609 50.000 0.00 0.00 0.00 5.54
1518 1947 1.801309 AACCACAACCCAAATCGGCG 61.801 55.000 0.00 0.00 0.00 6.46
1519 1948 1.969064 CCACAACCCAAATCGGCGA 60.969 57.895 13.87 13.87 0.00 5.54
1521 1950 1.374560 CACAACCCAAATCGGCGATA 58.625 50.000 24.28 0.00 0.00 2.92
1522 1951 1.946768 CACAACCCAAATCGGCGATAT 59.053 47.619 24.28 10.62 0.00 1.63
1524 1953 1.535462 CAACCCAAATCGGCGATATCC 59.465 52.381 24.28 0.00 0.00 2.59
1525 1954 0.762418 ACCCAAATCGGCGATATCCA 59.238 50.000 24.28 0.00 0.00 3.41
1526 1955 1.351017 ACCCAAATCGGCGATATCCAT 59.649 47.619 24.28 3.66 0.00 3.41
1527 1956 2.569853 ACCCAAATCGGCGATATCCATA 59.430 45.455 24.28 0.00 0.00 2.74
1528 1957 2.936498 CCCAAATCGGCGATATCCATAC 59.064 50.000 24.28 0.00 0.00 2.39
1554 2342 5.368523 TCCATAGAAGGGTATGTTTAGTGGG 59.631 44.000 0.00 0.00 0.00 4.61
1558 2346 4.225267 AGAAGGGTATGTTTAGTGGGACTG 59.775 45.833 0.00 0.00 0.00 3.51
1559 2347 2.844348 AGGGTATGTTTAGTGGGACTGG 59.156 50.000 0.00 0.00 0.00 4.00
1560 2348 2.092592 GGGTATGTTTAGTGGGACTGGG 60.093 54.545 0.00 0.00 0.00 4.45
1562 2350 3.370209 GGTATGTTTAGTGGGACTGGGAC 60.370 52.174 0.00 0.00 0.00 4.46
1563 2351 2.112279 TGTTTAGTGGGACTGGGACT 57.888 50.000 0.00 0.00 0.00 3.85
1568 2356 1.906824 GTGGGACTGGGACTGACGA 60.907 63.158 0.00 0.00 0.00 4.20
1570 2358 0.970937 TGGGACTGGGACTGACGATC 60.971 60.000 0.00 0.00 0.00 3.69
1571 2359 0.684805 GGGACTGGGACTGACGATCT 60.685 60.000 0.00 0.00 0.00 2.75
1579 2367 1.532007 GGACTGACGATCTACTAGCGG 59.468 57.143 0.00 0.00 42.62 5.52
1585 2373 0.800012 CGATCTACTAGCGGAGGAGC 59.200 60.000 0.00 0.00 35.83 4.70
1586 2374 1.170442 GATCTACTAGCGGAGGAGCC 58.830 60.000 0.00 0.00 35.83 4.70
1587 2375 0.478942 ATCTACTAGCGGAGGAGCCA 59.521 55.000 0.00 0.00 35.83 4.75
1590 2378 2.567664 TACTAGCGGAGGAGCCAGCA 62.568 60.000 0.00 0.00 38.23 4.41
1591 2379 3.149338 CTAGCGGAGGAGCCAGCAG 62.149 68.421 0.00 0.00 38.23 4.24
1602 2390 3.190878 CCAGCAGGCCGAAATCAC 58.809 61.111 0.00 0.00 0.00 3.06
1603 2391 1.377725 CCAGCAGGCCGAAATCACT 60.378 57.895 0.00 0.00 0.00 3.41
1605 2393 1.475751 CCAGCAGGCCGAAATCACTAT 60.476 52.381 0.00 0.00 0.00 2.12
1606 2394 2.292267 CAGCAGGCCGAAATCACTATT 58.708 47.619 0.00 0.00 0.00 1.73
1608 2396 2.171448 AGCAGGCCGAAATCACTATTCT 59.829 45.455 0.00 0.00 0.00 2.40
1609 2397 2.289002 GCAGGCCGAAATCACTATTCTG 59.711 50.000 0.00 0.00 0.00 3.02
1610 2398 3.797039 CAGGCCGAAATCACTATTCTGA 58.203 45.455 0.00 0.00 0.00 3.27
1611 2399 3.557595 CAGGCCGAAATCACTATTCTGAC 59.442 47.826 0.00 0.00 0.00 3.51
1612 2400 2.872858 GGCCGAAATCACTATTCTGACC 59.127 50.000 0.00 0.00 0.00 4.02
1613 2401 3.432326 GGCCGAAATCACTATTCTGACCT 60.432 47.826 0.00 0.00 0.00 3.85
1614 2402 4.192317 GCCGAAATCACTATTCTGACCTT 58.808 43.478 0.00 0.00 0.00 3.50
1616 2404 5.123979 GCCGAAATCACTATTCTGACCTTTT 59.876 40.000 0.00 0.00 0.00 2.27
1617 2405 6.675728 GCCGAAATCACTATTCTGACCTTTTC 60.676 42.308 0.00 0.00 0.00 2.29
1618 2406 6.371548 CCGAAATCACTATTCTGACCTTTTCA 59.628 38.462 0.00 0.00 0.00 2.69
1644 2432 7.109006 CAATCTTTGCCACAAAGTATTTCAC 57.891 36.000 17.10 0.00 35.03 3.18
1646 2434 4.576873 TCTTTGCCACAAAGTATTTCACGA 59.423 37.500 17.10 0.00 35.03 4.35
1647 2435 5.240623 TCTTTGCCACAAAGTATTTCACGAT 59.759 36.000 17.10 0.00 35.03 3.73
1648 2436 4.678509 TGCCACAAAGTATTTCACGATC 57.321 40.909 0.00 0.00 35.03 3.69
1649 2437 4.323417 TGCCACAAAGTATTTCACGATCT 58.677 39.130 0.00 0.00 35.03 2.75
1650 2438 4.154015 TGCCACAAAGTATTTCACGATCTG 59.846 41.667 0.00 0.00 35.03 2.90
1651 2439 4.391830 GCCACAAAGTATTTCACGATCTGA 59.608 41.667 0.00 0.00 35.03 3.27
1653 2441 5.163854 CCACAAAGTATTTCACGATCTGACC 60.164 44.000 0.00 0.00 35.03 4.02
1654 2442 4.935808 ACAAAGTATTTCACGATCTGACCC 59.064 41.667 0.00 0.00 35.03 4.46
1655 2443 5.178797 CAAAGTATTTCACGATCTGACCCT 58.821 41.667 0.00 0.00 35.03 4.34
1658 2446 5.805728 AGTATTTCACGATCTGACCCTTTT 58.194 37.500 0.00 0.00 0.00 2.27
1659 2447 6.942976 AGTATTTCACGATCTGACCCTTTTA 58.057 36.000 0.00 0.00 0.00 1.52
1660 2448 7.042335 AGTATTTCACGATCTGACCCTTTTAG 58.958 38.462 0.00 0.00 0.00 1.85
1661 2449 3.247006 TCACGATCTGACCCTTTTAGC 57.753 47.619 0.00 0.00 0.00 3.09
1662 2450 2.565391 TCACGATCTGACCCTTTTAGCA 59.435 45.455 0.00 0.00 0.00 3.49
1663 2451 3.007506 TCACGATCTGACCCTTTTAGCAA 59.992 43.478 0.00 0.00 0.00 3.91
1664 2452 3.125316 CACGATCTGACCCTTTTAGCAAC 59.875 47.826 0.00 0.00 0.00 4.17
1666 2454 1.519408 TCTGACCCTTTTAGCAACGC 58.481 50.000 0.00 0.00 0.00 4.84
1667 2455 0.521735 CTGACCCTTTTAGCAACGCC 59.478 55.000 0.00 0.00 0.00 5.68
1668 2456 0.179015 TGACCCTTTTAGCAACGCCA 60.179 50.000 0.00 0.00 0.00 5.69
1669 2457 0.240145 GACCCTTTTAGCAACGCCAC 59.760 55.000 0.00 0.00 0.00 5.01
1670 2458 0.466555 ACCCTTTTAGCAACGCCACA 60.467 50.000 0.00 0.00 0.00 4.17
1671 2459 0.240945 CCCTTTTAGCAACGCCACAG 59.759 55.000 0.00 0.00 0.00 3.66
1672 2460 0.387239 CCTTTTAGCAACGCCACAGC 60.387 55.000 0.00 0.00 0.00 4.40
1673 2461 0.387239 CTTTTAGCAACGCCACAGCC 60.387 55.000 0.00 0.00 34.57 4.85
1674 2462 1.801309 TTTTAGCAACGCCACAGCCC 61.801 55.000 0.00 0.00 34.57 5.19
1921 3823 3.307906 CGGGTGGAAGGTGGACGA 61.308 66.667 0.00 0.00 0.00 4.20
2045 4162 0.320771 CTGCTTGGCGTGTAAGGTCT 60.321 55.000 0.00 0.00 0.00 3.85
2065 4182 4.748798 AGGTCCTCCCCCTGCCAG 62.749 72.222 0.00 0.00 0.00 4.85
2287 4404 1.138069 TCGTTCTCTTTGAGCACACCA 59.862 47.619 0.00 0.00 0.00 4.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 8.778358 CAACCTAGAATCTAGATTAACCAATGC 58.222 37.037 17.94 3.44 0.00 3.56
1 2 9.277783 CCAACCTAGAATCTAGATTAACCAATG 57.722 37.037 17.94 12.62 0.00 2.82
2 3 9.004231 ACCAACCTAGAATCTAGATTAACCAAT 57.996 33.333 17.94 1.72 0.00 3.16
5 6 8.252624 AGACCAACCTAGAATCTAGATTAACC 57.747 38.462 17.94 6.27 0.00 2.85
9 10 7.554476 GCAAAAGACCAACCTAGAATCTAGATT 59.446 37.037 17.96 17.96 0.00 2.40
10 11 7.051000 GCAAAAGACCAACCTAGAATCTAGAT 58.949 38.462 18.25 0.00 0.00 1.98
11 12 6.407202 GCAAAAGACCAACCTAGAATCTAGA 58.593 40.000 18.25 0.00 0.00 2.43
12 13 5.292101 CGCAAAAGACCAACCTAGAATCTAG 59.708 44.000 10.25 10.25 0.00 2.43
13 14 5.046878 TCGCAAAAGACCAACCTAGAATCTA 60.047 40.000 0.00 0.00 0.00 1.98
14 15 4.003648 CGCAAAAGACCAACCTAGAATCT 58.996 43.478 0.00 0.00 0.00 2.40
15 16 4.000988 TCGCAAAAGACCAACCTAGAATC 58.999 43.478 0.00 0.00 0.00 2.52
16 17 4.015872 TCGCAAAAGACCAACCTAGAAT 57.984 40.909 0.00 0.00 0.00 2.40
17 18 3.478857 TCGCAAAAGACCAACCTAGAA 57.521 42.857 0.00 0.00 0.00 2.10
18 19 3.695830 ATCGCAAAAGACCAACCTAGA 57.304 42.857 0.00 0.00 0.00 2.43
19 20 4.455877 AGAAATCGCAAAAGACCAACCTAG 59.544 41.667 0.00 0.00 0.00 3.02
20 21 4.215399 CAGAAATCGCAAAAGACCAACCTA 59.785 41.667 0.00 0.00 0.00 3.08
21 22 3.004734 CAGAAATCGCAAAAGACCAACCT 59.995 43.478 0.00 0.00 0.00 3.50
22 23 3.308530 CAGAAATCGCAAAAGACCAACC 58.691 45.455 0.00 0.00 0.00 3.77
23 24 2.726241 GCAGAAATCGCAAAAGACCAAC 59.274 45.455 0.00 0.00 0.00 3.77
24 25 2.604373 CGCAGAAATCGCAAAAGACCAA 60.604 45.455 0.00 0.00 0.00 3.67
25 26 1.069296 CGCAGAAATCGCAAAAGACCA 60.069 47.619 0.00 0.00 0.00 4.02
26 27 1.196808 TCGCAGAAATCGCAAAAGACC 59.803 47.619 0.00 0.00 0.00 3.85
27 28 2.234187 GTCGCAGAAATCGCAAAAGAC 58.766 47.619 0.00 0.00 39.69 3.01
28 29 1.136363 CGTCGCAGAAATCGCAAAAGA 60.136 47.619 0.00 0.00 39.69 2.52
29 30 1.241744 CGTCGCAGAAATCGCAAAAG 58.758 50.000 0.00 0.00 39.69 2.27
30 31 0.584396 ACGTCGCAGAAATCGCAAAA 59.416 45.000 0.00 0.00 39.69 2.44
31 32 0.584396 AACGTCGCAGAAATCGCAAA 59.416 45.000 0.00 0.00 39.69 3.68
32 33 0.162933 GAACGTCGCAGAAATCGCAA 59.837 50.000 0.00 0.00 39.69 4.85
33 34 1.623081 GGAACGTCGCAGAAATCGCA 61.623 55.000 0.00 0.00 39.69 5.10
34 35 1.058903 GGAACGTCGCAGAAATCGC 59.941 57.895 0.00 0.00 39.69 4.58
35 36 0.736325 AGGGAACGTCGCAGAAATCG 60.736 55.000 0.00 0.00 39.69 3.34
36 37 2.288961 TAGGGAACGTCGCAGAAATC 57.711 50.000 0.00 0.00 39.69 2.17
37 38 2.754946 TTAGGGAACGTCGCAGAAAT 57.245 45.000 0.00 0.00 39.69 2.17
38 39 2.529780 TTTAGGGAACGTCGCAGAAA 57.470 45.000 0.00 0.00 39.69 2.52
39 40 2.529780 TTTTAGGGAACGTCGCAGAA 57.470 45.000 0.00 0.00 39.69 3.02
40 41 2.137523 GTTTTTAGGGAACGTCGCAGA 58.862 47.619 0.00 0.00 0.00 4.26
41 42 1.136446 CGTTTTTAGGGAACGTCGCAG 60.136 52.381 0.00 0.00 43.44 5.18
42 43 0.860533 CGTTTTTAGGGAACGTCGCA 59.139 50.000 0.00 0.00 43.44 5.10
43 44 3.644692 CGTTTTTAGGGAACGTCGC 57.355 52.632 0.00 0.00 43.44 5.19
48 49 1.462283 GGACGAGCGTTTTTAGGGAAC 59.538 52.381 0.00 0.00 0.00 3.62
49 50 1.608801 GGGACGAGCGTTTTTAGGGAA 60.609 52.381 0.00 0.00 0.00 3.97
50 51 0.037046 GGGACGAGCGTTTTTAGGGA 60.037 55.000 0.00 0.00 0.00 4.20
51 52 0.036671 AGGGACGAGCGTTTTTAGGG 60.037 55.000 0.00 0.00 0.00 3.53
52 53 1.067071 AGAGGGACGAGCGTTTTTAGG 60.067 52.381 0.00 0.00 0.00 2.69
53 54 1.993370 CAGAGGGACGAGCGTTTTTAG 59.007 52.381 0.00 0.00 0.00 1.85
54 55 1.342174 ACAGAGGGACGAGCGTTTTTA 59.658 47.619 0.00 0.00 0.00 1.52
55 56 0.106149 ACAGAGGGACGAGCGTTTTT 59.894 50.000 0.00 0.00 0.00 1.94
56 57 0.963962 TACAGAGGGACGAGCGTTTT 59.036 50.000 0.00 0.00 0.00 2.43
57 58 0.963962 TTACAGAGGGACGAGCGTTT 59.036 50.000 0.00 0.00 0.00 3.60
58 59 0.963962 TTTACAGAGGGACGAGCGTT 59.036 50.000 0.00 0.00 0.00 4.84
59 60 1.183549 ATTTACAGAGGGACGAGCGT 58.816 50.000 0.00 0.00 0.00 5.07
60 61 1.927174 CAATTTACAGAGGGACGAGCG 59.073 52.381 0.00 0.00 0.00 5.03
61 62 1.666189 GCAATTTACAGAGGGACGAGC 59.334 52.381 0.00 0.00 0.00 5.03
62 63 2.972625 TGCAATTTACAGAGGGACGAG 58.027 47.619 0.00 0.00 0.00 4.18
63 64 3.197766 AGATGCAATTTACAGAGGGACGA 59.802 43.478 0.00 0.00 0.00 4.20
64 65 3.535561 AGATGCAATTTACAGAGGGACG 58.464 45.455 0.00 0.00 0.00 4.79
65 66 5.904362 AAAGATGCAATTTACAGAGGGAC 57.096 39.130 0.00 0.00 0.00 4.46
66 67 6.721208 AGAAAAAGATGCAATTTACAGAGGGA 59.279 34.615 0.00 0.00 0.00 4.20
67 68 6.928520 AGAAAAAGATGCAATTTACAGAGGG 58.071 36.000 0.00 0.00 0.00 4.30
68 69 7.031975 GGAGAAAAAGATGCAATTTACAGAGG 58.968 38.462 0.00 0.00 0.00 3.69
69 70 7.596494 TGGAGAAAAAGATGCAATTTACAGAG 58.404 34.615 0.00 0.00 0.00 3.35
70 71 7.523293 TGGAGAAAAAGATGCAATTTACAGA 57.477 32.000 0.00 0.00 0.00 3.41
71 72 8.248945 AGATGGAGAAAAAGATGCAATTTACAG 58.751 33.333 0.00 0.00 0.00 2.74
72 73 8.125978 AGATGGAGAAAAAGATGCAATTTACA 57.874 30.769 0.00 0.00 0.00 2.41
73 74 8.465201 AGAGATGGAGAAAAAGATGCAATTTAC 58.535 33.333 0.00 0.00 0.00 2.01
74 75 8.585471 AGAGATGGAGAAAAAGATGCAATTTA 57.415 30.769 0.00 0.00 0.00 1.40
75 76 7.477945 AGAGATGGAGAAAAAGATGCAATTT 57.522 32.000 0.00 0.00 0.00 1.82
76 77 7.396623 AGAAGAGATGGAGAAAAAGATGCAATT 59.603 33.333 0.00 0.00 0.00 2.32
77 78 6.890814 AGAAGAGATGGAGAAAAAGATGCAAT 59.109 34.615 0.00 0.00 0.00 3.56
78 79 6.243900 AGAAGAGATGGAGAAAAAGATGCAA 58.756 36.000 0.00 0.00 0.00 4.08
79 80 5.813383 AGAAGAGATGGAGAAAAAGATGCA 58.187 37.500 0.00 0.00 0.00 3.96
80 81 9.553064 TTATAGAAGAGATGGAGAAAAAGATGC 57.447 33.333 0.00 0.00 0.00 3.91
90 91 8.835439 GCCTTTTTCTTTATAGAAGAGATGGAG 58.165 37.037 8.80 0.00 41.25 3.86
91 92 8.328758 TGCCTTTTTCTTTATAGAAGAGATGGA 58.671 33.333 8.80 0.00 41.25 3.41
92 93 8.511604 TGCCTTTTTCTTTATAGAAGAGATGG 57.488 34.615 8.80 6.71 41.25 3.51
93 94 9.171877 ACTGCCTTTTTCTTTATAGAAGAGATG 57.828 33.333 8.80 3.84 41.25 2.90
94 95 9.171877 CACTGCCTTTTTCTTTATAGAAGAGAT 57.828 33.333 8.80 0.00 41.25 2.75
95 96 7.119846 GCACTGCCTTTTTCTTTATAGAAGAGA 59.880 37.037 8.80 0.00 41.25 3.10
96 97 7.120432 AGCACTGCCTTTTTCTTTATAGAAGAG 59.880 37.037 0.00 0.20 41.25 2.85
97 98 6.942576 AGCACTGCCTTTTTCTTTATAGAAGA 59.057 34.615 0.00 0.00 41.25 2.87
98 99 7.150783 AGCACTGCCTTTTTCTTTATAGAAG 57.849 36.000 0.00 0.00 41.25 2.85
99 100 6.151144 GGAGCACTGCCTTTTTCTTTATAGAA 59.849 38.462 0.00 0.00 38.61 2.10
100 101 5.648092 GGAGCACTGCCTTTTTCTTTATAGA 59.352 40.000 0.00 0.00 0.00 1.98
101 102 5.649831 AGGAGCACTGCCTTTTTCTTTATAG 59.350 40.000 0.00 0.00 29.44 1.31
102 103 5.415701 CAGGAGCACTGCCTTTTTCTTTATA 59.584 40.000 0.00 0.00 40.97 0.98
103 104 4.219288 CAGGAGCACTGCCTTTTTCTTTAT 59.781 41.667 0.00 0.00 40.97 1.40
104 105 3.569701 CAGGAGCACTGCCTTTTTCTTTA 59.430 43.478 0.00 0.00 40.97 1.85
105 106 2.363359 CAGGAGCACTGCCTTTTTCTTT 59.637 45.455 0.00 0.00 40.97 2.52
106 107 1.959282 CAGGAGCACTGCCTTTTTCTT 59.041 47.619 0.00 0.00 40.97 2.52
107 108 1.613836 CAGGAGCACTGCCTTTTTCT 58.386 50.000 0.00 0.00 40.97 2.52
117 118 4.021925 GGAACCGGCAGGAGCACT 62.022 66.667 10.86 0.00 44.61 4.40
118 119 3.959991 GAGGAACCGGCAGGAGCAC 62.960 68.421 10.86 0.00 44.61 4.40
119 120 3.706373 GAGGAACCGGCAGGAGCA 61.706 66.667 10.86 0.00 44.61 4.26
120 121 2.748058 TTTGAGGAACCGGCAGGAGC 62.748 60.000 10.86 0.05 41.02 4.70
121 122 0.250727 TTTTGAGGAACCGGCAGGAG 60.251 55.000 10.86 0.00 41.02 3.69
122 123 0.183971 TTTTTGAGGAACCGGCAGGA 59.816 50.000 10.86 0.00 41.02 3.86
123 124 2.727103 TTTTTGAGGAACCGGCAGG 58.273 52.632 0.00 0.00 45.13 4.85
147 148 7.588497 ACTTCTGAATGGAAGCTAAGTTTTT 57.412 32.000 4.42 0.00 44.51 1.94
148 149 7.428826 CAACTTCTGAATGGAAGCTAAGTTTT 58.571 34.615 3.34 0.00 44.51 2.43
149 150 6.515696 GCAACTTCTGAATGGAAGCTAAGTTT 60.516 38.462 3.34 0.00 44.51 2.66
150 151 5.048434 GCAACTTCTGAATGGAAGCTAAGTT 60.048 40.000 4.42 0.69 44.51 2.66
151 152 4.457257 GCAACTTCTGAATGGAAGCTAAGT 59.543 41.667 4.42 0.00 44.51 2.24
152 153 4.699257 AGCAACTTCTGAATGGAAGCTAAG 59.301 41.667 4.42 0.00 44.51 2.18
182 183 8.515351 AGTGCTCCCACCATAGAGTATATATAT 58.485 37.037 0.00 0.00 43.09 0.86
183 184 7.780271 CAGTGCTCCCACCATAGAGTATATATA 59.220 40.741 0.00 0.00 43.09 0.86
184 185 6.609212 CAGTGCTCCCACCATAGAGTATATAT 59.391 42.308 0.00 0.00 43.09 0.86
185 186 5.952347 CAGTGCTCCCACCATAGAGTATATA 59.048 44.000 0.00 0.00 43.09 0.86
186 187 4.774726 CAGTGCTCCCACCATAGAGTATAT 59.225 45.833 0.00 0.00 43.09 0.86
187 188 4.152647 CAGTGCTCCCACCATAGAGTATA 58.847 47.826 0.00 0.00 43.09 1.47
193 194 1.496060 TACCAGTGCTCCCACCATAG 58.504 55.000 0.00 0.00 43.09 2.23
223 224 3.760035 ACGGGACACTAGCAGCGG 61.760 66.667 0.00 0.00 0.00 5.52
224 225 2.284798 ATCACGGGACACTAGCAGCG 62.285 60.000 0.00 0.00 0.00 5.18
225 226 0.807667 CATCACGGGACACTAGCAGC 60.808 60.000 0.00 0.00 0.00 5.25
226 227 0.807667 GCATCACGGGACACTAGCAG 60.808 60.000 0.00 0.00 0.00 4.24
227 228 1.218047 GCATCACGGGACACTAGCA 59.782 57.895 0.00 0.00 0.00 3.49
228 229 1.878522 CGCATCACGGGACACTAGC 60.879 63.158 0.00 0.00 38.44 3.42
229 230 1.878522 GCGCATCACGGGACACTAG 60.879 63.158 0.30 0.00 43.93 2.57
230 231 2.183300 GCGCATCACGGGACACTA 59.817 61.111 0.30 0.00 43.93 2.74
232 233 3.188786 GAGCGCATCACGGGACAC 61.189 66.667 11.47 0.00 43.93 3.67
233 234 4.451150 GGAGCGCATCACGGGACA 62.451 66.667 11.47 0.00 43.93 4.02
234 235 2.292794 TTAGGAGCGCATCACGGGAC 62.293 60.000 11.47 0.00 43.93 4.46
235 236 2.016393 CTTAGGAGCGCATCACGGGA 62.016 60.000 11.47 0.00 43.93 5.14
237 238 0.872021 GTCTTAGGAGCGCATCACGG 60.872 60.000 11.47 0.00 43.93 4.94
239 240 2.301577 AAGTCTTAGGAGCGCATCAC 57.698 50.000 11.47 0.00 0.00 3.06
241 242 2.609916 GGAAAAGTCTTAGGAGCGCATC 59.390 50.000 11.47 4.01 0.00 3.91
252 510 2.457366 ATCACGCTCGGAAAAGTCTT 57.543 45.000 0.00 0.00 0.00 3.01
261 519 2.315901 GAAACCAAAAATCACGCTCGG 58.684 47.619 0.00 0.00 0.00 4.63
263 521 2.315901 CGGAAACCAAAAATCACGCTC 58.684 47.619 0.00 0.00 0.00 5.03
264 522 1.000717 CCGGAAACCAAAAATCACGCT 60.001 47.619 0.00 0.00 0.00 5.07
356 655 7.558444 ACACTAGAGAGAGAAACATACCTTAGG 59.442 40.741 0.00 0.00 0.00 2.69
359 658 7.784470 AACACTAGAGAGAGAAACATACCTT 57.216 36.000 0.00 0.00 0.00 3.50
362 661 7.385205 TGCAAAACACTAGAGAGAGAAACATAC 59.615 37.037 0.00 0.00 0.00 2.39
561 868 5.944013 TCATCTCTTCTTCTACGAACAGTG 58.056 41.667 0.00 0.00 0.00 3.66
694 1009 2.258591 CGGTGGTCGTGTGGAGAG 59.741 66.667 0.00 0.00 0.00 3.20
708 1024 4.954118 TGACCTGTGGGGAGCGGT 62.954 66.667 0.00 0.00 38.76 5.68
773 1093 3.550431 CCATGGCCCGACCTCGAT 61.550 66.667 0.00 0.00 43.02 3.59
847 1167 1.410882 GGGAAGTAGTAGCAGGAGCAG 59.589 57.143 0.00 0.00 45.49 4.24
848 1168 1.486211 GGGAAGTAGTAGCAGGAGCA 58.514 55.000 0.00 0.00 45.49 4.26
849 1169 0.386113 CGGGAAGTAGTAGCAGGAGC 59.614 60.000 0.00 0.00 42.56 4.70
850 1170 1.033574 CCGGGAAGTAGTAGCAGGAG 58.966 60.000 0.00 0.00 0.00 3.69
851 1171 1.041447 GCCGGGAAGTAGTAGCAGGA 61.041 60.000 2.18 0.00 0.00 3.86
852 1172 1.442148 GCCGGGAAGTAGTAGCAGG 59.558 63.158 2.18 0.00 0.00 4.85
853 1173 1.442148 GGCCGGGAAGTAGTAGCAG 59.558 63.158 2.18 0.00 0.00 4.24
854 1174 2.420568 CGGCCGGGAAGTAGTAGCA 61.421 63.158 20.10 0.00 0.00 3.49
855 1175 1.103398 TACGGCCGGGAAGTAGTAGC 61.103 60.000 31.76 0.00 0.00 3.58
856 1176 1.613836 ATACGGCCGGGAAGTAGTAG 58.386 55.000 31.76 0.00 0.00 2.57
857 1177 2.949177 TATACGGCCGGGAAGTAGTA 57.051 50.000 31.76 10.44 0.00 1.82
858 1178 2.071778 TTATACGGCCGGGAAGTAGT 57.928 50.000 31.76 8.14 0.00 2.73
907 1269 1.002624 TTTCTAGGGTTGGCGCTGG 60.003 57.895 7.64 0.00 38.42 4.85
920 1282 2.126228 CGCGAGCGGTGGTTTCTA 60.126 61.111 9.90 0.00 35.56 2.10
937 1305 2.596851 TTGGAGACCTGGAGCTGCC 61.597 63.158 1.53 0.00 37.10 4.85
966 1341 0.318784 AACAAGTCAGACCGCTCGAC 60.319 55.000 0.00 0.00 0.00 4.20
971 1346 4.378459 CCAATAAAGAACAAGTCAGACCGC 60.378 45.833 0.00 0.00 0.00 5.68
981 1356 3.192422 CCATGGCGACCAATAAAGAACAA 59.808 43.478 0.00 0.00 36.95 2.83
1005 1400 2.035442 GCCGTTCTTCTGCCTCCAC 61.035 63.158 0.00 0.00 0.00 4.02
1012 1407 3.181967 CTCGCCGCCGTTCTTCTG 61.182 66.667 0.00 0.00 35.54 3.02
1301 1700 5.117745 GCATACGTATTCACACATGCTCTAG 59.882 44.000 5.03 0.00 37.99 2.43
1320 1727 0.957395 ACACTGGCACTGCTGCATAC 60.957 55.000 1.31 0.00 46.28 2.39
1383 1793 8.279800 CGTGTATTCATGTACAAAAGAACTGAA 58.720 33.333 0.00 3.85 36.42 3.02
1444 1856 4.314440 GCGGGTGGAGTGAGCACA 62.314 66.667 3.19 0.00 0.00 4.57
1459 1871 3.974401 ACAATTGAAATCGTTCTTGTGCG 59.026 39.130 13.59 0.00 33.31 5.34
1485 1914 2.489971 TGTGGTTTCAATGTCTCGTCC 58.510 47.619 0.00 0.00 0.00 4.79
1486 1915 3.303791 GGTTGTGGTTTCAATGTCTCGTC 60.304 47.826 0.00 0.00 0.00 4.20
1493 1922 3.740321 CGATTTGGGTTGTGGTTTCAATG 59.260 43.478 0.00 0.00 0.00 2.82
1494 1923 3.244044 CCGATTTGGGTTGTGGTTTCAAT 60.244 43.478 0.00 0.00 0.00 2.57
1495 1924 2.101582 CCGATTTGGGTTGTGGTTTCAA 59.898 45.455 0.00 0.00 0.00 2.69
1496 1925 1.683917 CCGATTTGGGTTGTGGTTTCA 59.316 47.619 0.00 0.00 0.00 2.69
1497 1926 1.604438 GCCGATTTGGGTTGTGGTTTC 60.604 52.381 0.00 0.00 38.63 2.78
1498 1927 0.391228 GCCGATTTGGGTTGTGGTTT 59.609 50.000 0.00 0.00 38.63 3.27
1499 1928 1.801309 CGCCGATTTGGGTTGTGGTT 61.801 55.000 0.00 0.00 38.63 3.67
1500 1929 2.265182 CGCCGATTTGGGTTGTGGT 61.265 57.895 0.00 0.00 38.63 4.16
1501 1930 1.312371 ATCGCCGATTTGGGTTGTGG 61.312 55.000 0.00 0.00 38.63 4.17
1502 1931 1.374560 TATCGCCGATTTGGGTTGTG 58.625 50.000 4.31 0.00 38.63 3.33
1515 1944 5.854010 TCTATGGAAGTATGGATATCGCC 57.146 43.478 0.00 0.00 0.00 5.54
1516 1945 6.276847 CCTTCTATGGAAGTATGGATATCGC 58.723 44.000 16.64 0.00 45.36 4.58
1517 1946 6.381420 ACCCTTCTATGGAAGTATGGATATCG 59.619 42.308 16.64 0.00 45.36 2.92
1518 1947 7.741554 ACCCTTCTATGGAAGTATGGATATC 57.258 40.000 16.64 0.00 45.36 1.63
1519 1948 9.218525 CATACCCTTCTATGGAAGTATGGATAT 57.781 37.037 16.64 8.90 45.36 1.63
1521 1950 7.025620 ACATACCCTTCTATGGAAGTATGGAT 58.974 38.462 23.34 11.57 45.36 3.41
1522 1951 6.390504 ACATACCCTTCTATGGAAGTATGGA 58.609 40.000 23.34 10.22 45.36 3.41
1524 1953 9.712305 CTAAACATACCCTTCTATGGAAGTATG 57.288 37.037 20.40 20.40 45.36 2.39
1525 1954 9.448587 ACTAAACATACCCTTCTATGGAAGTAT 57.551 33.333 16.64 7.75 45.36 2.12
1526 1955 8.701895 CACTAAACATACCCTTCTATGGAAGTA 58.298 37.037 16.64 5.84 45.36 2.24
1527 1956 7.365652 CCACTAAACATACCCTTCTATGGAAGT 60.366 40.741 16.64 3.81 45.36 3.01
1528 1957 6.992715 CCACTAAACATACCCTTCTATGGAAG 59.007 42.308 11.68 11.68 46.12 3.46
1544 2332 1.697432 CAGTCCCAGTCCCACTAAACA 59.303 52.381 0.00 0.00 0.00 2.83
1546 2334 1.975680 GTCAGTCCCAGTCCCACTAAA 59.024 52.381 0.00 0.00 0.00 1.85
1550 2338 1.258445 ATCGTCAGTCCCAGTCCCAC 61.258 60.000 0.00 0.00 0.00 4.61
1554 2342 2.645802 AGTAGATCGTCAGTCCCAGTC 58.354 52.381 0.00 0.00 0.00 3.51
1558 2346 1.532007 CGCTAGTAGATCGTCAGTCCC 59.468 57.143 0.00 0.00 0.00 4.46
1559 2347 1.532007 CCGCTAGTAGATCGTCAGTCC 59.468 57.143 0.00 0.00 0.00 3.85
1560 2348 2.477375 CTCCGCTAGTAGATCGTCAGTC 59.523 54.545 0.00 0.00 0.00 3.51
1562 2350 1.801771 CCTCCGCTAGTAGATCGTCAG 59.198 57.143 0.00 0.00 0.00 3.51
1563 2351 1.415289 TCCTCCGCTAGTAGATCGTCA 59.585 52.381 0.00 0.00 0.00 4.35
1568 2356 0.478942 TGGCTCCTCCGCTAGTAGAT 59.521 55.000 0.00 0.00 37.80 1.98
1570 2358 1.801309 GCTGGCTCCTCCGCTAGTAG 61.801 65.000 0.00 0.00 40.23 2.57
1571 2359 1.828660 GCTGGCTCCTCCGCTAGTA 60.829 63.158 0.00 0.00 40.23 1.82
1585 2373 0.107703 TAGTGATTTCGGCCTGCTGG 60.108 55.000 5.03 5.03 0.00 4.85
1586 2374 1.959042 ATAGTGATTTCGGCCTGCTG 58.041 50.000 0.00 0.00 0.00 4.41
1587 2375 2.171448 AGAATAGTGATTTCGGCCTGCT 59.829 45.455 0.00 0.00 0.00 4.24
1590 2378 3.432326 GGTCAGAATAGTGATTTCGGCCT 60.432 47.826 0.00 0.00 0.00 5.19
1591 2379 2.872858 GGTCAGAATAGTGATTTCGGCC 59.127 50.000 0.00 0.00 0.00 6.13
1592 2380 3.798202 AGGTCAGAATAGTGATTTCGGC 58.202 45.455 0.00 0.00 0.00 5.54
1593 2381 6.371548 TGAAAAGGTCAGAATAGTGATTTCGG 59.628 38.462 0.00 0.00 30.52 4.30
1594 2382 7.364522 TGAAAAGGTCAGAATAGTGATTTCG 57.635 36.000 0.00 0.00 30.52 3.46
1620 2408 6.129115 CGTGAAATACTTTGTGGCAAAGATTG 60.129 38.462 23.23 3.54 0.00 2.67
1621 2409 5.920273 CGTGAAATACTTTGTGGCAAAGATT 59.080 36.000 23.23 15.96 0.00 2.40
1622 2410 5.240623 TCGTGAAATACTTTGTGGCAAAGAT 59.759 36.000 23.23 12.18 0.00 2.40
1623 2411 4.576873 TCGTGAAATACTTTGTGGCAAAGA 59.423 37.500 23.23 10.79 0.00 2.52
1624 2412 4.854399 TCGTGAAATACTTTGTGGCAAAG 58.146 39.130 17.04 17.04 0.00 2.77
1625 2413 4.902443 TCGTGAAATACTTTGTGGCAAA 57.098 36.364 0.00 0.00 0.00 3.68
1626 2414 4.759693 AGATCGTGAAATACTTTGTGGCAA 59.240 37.500 0.00 0.00 0.00 4.52
1627 2415 4.154015 CAGATCGTGAAATACTTTGTGGCA 59.846 41.667 0.00 0.00 0.00 4.92
1629 2417 5.163854 GGTCAGATCGTGAAATACTTTGTGG 60.164 44.000 0.00 0.00 36.74 4.17
1630 2418 5.163854 GGGTCAGATCGTGAAATACTTTGTG 60.164 44.000 0.00 0.00 36.74 3.33
1632 2420 5.178797 AGGGTCAGATCGTGAAATACTTTG 58.821 41.667 0.00 0.00 36.74 2.77
1633 2421 5.422214 AGGGTCAGATCGTGAAATACTTT 57.578 39.130 0.00 0.00 36.74 2.66
1634 2422 5.422214 AAGGGTCAGATCGTGAAATACTT 57.578 39.130 0.00 0.00 36.74 2.24
1635 2423 5.422214 AAAGGGTCAGATCGTGAAATACT 57.578 39.130 0.00 0.00 36.74 2.12
1637 2425 5.815740 GCTAAAAGGGTCAGATCGTGAAATA 59.184 40.000 0.00 0.00 36.74 1.40
1638 2426 4.636206 GCTAAAAGGGTCAGATCGTGAAAT 59.364 41.667 0.00 0.00 36.74 2.17
1639 2427 4.000988 GCTAAAAGGGTCAGATCGTGAAA 58.999 43.478 0.00 0.00 36.74 2.69
1641 2429 2.565391 TGCTAAAAGGGTCAGATCGTGA 59.435 45.455 0.00 0.00 0.00 4.35
1642 2430 2.972625 TGCTAAAAGGGTCAGATCGTG 58.027 47.619 0.00 0.00 0.00 4.35
1643 2431 3.335579 GTTGCTAAAAGGGTCAGATCGT 58.664 45.455 0.00 0.00 0.00 3.73
1644 2432 2.348666 CGTTGCTAAAAGGGTCAGATCG 59.651 50.000 0.00 0.00 0.00 3.69
1646 2434 2.084546 GCGTTGCTAAAAGGGTCAGAT 58.915 47.619 0.00 0.00 0.00 2.90
1647 2435 1.519408 GCGTTGCTAAAAGGGTCAGA 58.481 50.000 0.00 0.00 0.00 3.27
1648 2436 0.521735 GGCGTTGCTAAAAGGGTCAG 59.478 55.000 0.00 0.00 0.00 3.51
1649 2437 0.179015 TGGCGTTGCTAAAAGGGTCA 60.179 50.000 0.00 0.00 0.00 4.02
1650 2438 0.240145 GTGGCGTTGCTAAAAGGGTC 59.760 55.000 0.00 0.00 0.00 4.46
1651 2439 0.466555 TGTGGCGTTGCTAAAAGGGT 60.467 50.000 0.00 0.00 0.00 4.34
1653 2441 0.387239 GCTGTGGCGTTGCTAAAAGG 60.387 55.000 0.00 0.00 0.00 3.11
1654 2442 0.387239 GGCTGTGGCGTTGCTAAAAG 60.387 55.000 0.00 0.00 39.81 2.27
1655 2443 1.657556 GGCTGTGGCGTTGCTAAAA 59.342 52.632 0.00 0.00 39.81 1.52


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

AutoCloner maintained by Alex Coulton.