Multiple sequence alignment - TraesCS5A01G107100

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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 TraesCS5A01G107100 chr5A 100.000 2288 0 0 1 2288 180346402 180348689 0.000000e+00 4226.0
1 TraesCS5A01G107100 chr5A 91.776 304 24 1 378 680 574021155 574021458 2.720000e-114 422.0
2 TraesCS5A01G107100 chr5A 95.200 125 5 1 205 328 180313196 180313320 1.790000e-46 196.0
3 TraesCS5A01G107100 chr5A 85.938 64 7 2 209 270 479784191 479784254 1.470000e-07 67.6
4 TraesCS5A01G107100 chr7A 97.504 1362 22 2 939 2288 259569221 259567860 0.000000e+00 2316.0
5 TraesCS5A01G107100 chr7A 88.448 277 22 3 678 951 345229992 345229723 2.190000e-85 326.0
6 TraesCS5A01G107100 chr7A 90.196 204 18 1 1 204 139792672 139792873 4.850000e-67 265.0
7 TraesCS5A01G107100 chr7A 94.488 127 6 1 209 334 259569343 259569217 6.450000e-46 195.0
8 TraesCS5A01G107100 chrUn 97.357 1362 21 3 939 2288 94922616 94923974 0.000000e+00 2302.0
9 TraesCS5A01G107100 chrUn 90.196 204 16 1 1 204 102523181 102522982 1.740000e-66 263.0
10 TraesCS5A01G107100 chrUn 93.130 131 8 1 205 334 94922490 94922620 8.340000e-45 191.0
11 TraesCS5A01G107100 chr2D 97.357 1362 19 5 939 2288 190400461 190401817 0.000000e+00 2300.0
12 TraesCS5A01G107100 chr2D 94.656 131 6 1 205 334 190400335 190400465 3.850000e-48 202.0
13 TraesCS5A01G107100 chr3D 96.329 1362 26 4 939 2288 167405095 167406444 0.000000e+00 2217.0
14 TraesCS5A01G107100 chr6D 97.112 1316 26 2 939 2242 7900162 7898847 0.000000e+00 2209.0
15 TraesCS5A01G107100 chr6D 96.182 1362 23 3 939 2288 142858754 142860098 0.000000e+00 2200.0
16 TraesCS5A01G107100 chr6D 94.656 131 6 1 205 334 142858628 142858758 3.850000e-48 202.0
17 TraesCS5A01G107100 chr6D 93.893 131 7 1 205 334 7900288 7900158 1.790000e-46 196.0
18 TraesCS5A01G107100 chr6B 91.850 1043 40 8 939 1970 33378627 33377619 0.000000e+00 1413.0
19 TraesCS5A01G107100 chr6B 95.821 335 5 1 1963 2288 33376405 33376071 1.200000e-147 532.0
20 TraesCS5A01G107100 chr6B 91.496 341 27 2 1632 1970 425603850 425604190 3.440000e-128 468.0
21 TraesCS5A01G107100 chr6B 92.256 297 21 2 382 677 555292003 555292298 9.770000e-114 420.0
22 TraesCS5A01G107100 chr6B 87.702 309 34 2 1324 1632 431504083 431503779 7.770000e-95 357.0
23 TraesCS5A01G107100 chr6B 92.683 123 9 0 2165 2287 425605148 425605270 6.500000e-41 178.0
24 TraesCS5A01G107100 chr6B 90.000 50 4 1 1966 2015 485760318 485760366 1.900000e-06 63.9
25 TraesCS5A01G107100 chr1B 90.672 461 17 3 952 1407 667628663 667629102 7.040000e-165 590.0
26 TraesCS5A01G107100 chr1B 92.157 204 16 0 1 204 619385772 619385569 2.880000e-74 289.0
27 TraesCS5A01G107100 chr1B 91.129 124 11 0 2165 2288 674397638 674397761 3.910000e-38 169.0
28 TraesCS5A01G107100 chr4A 89.813 481 16 7 939 1407 738541313 738540854 9.110000e-164 586.0
29 TraesCS5A01G107100 chr4A 88.889 270 20 3 678 944 419965972 419965710 7.880000e-85 324.0
30 TraesCS5A01G107100 chr2A 81.587 630 90 14 331 943 241962751 241962131 4.390000e-137 497.0
31 TraesCS5A01G107100 chr2A 89.299 271 18 4 678 944 74682220 74681957 1.690000e-86 329.0
32 TraesCS5A01G107100 chr2A 88.930 271 20 4 678 945 46687146 46686883 2.190000e-85 326.0
33 TraesCS5A01G107100 chr2A 94.444 36 2 0 1287 1322 73144784 73144819 3.180000e-04 56.5
34 TraesCS5A01G107100 chr2A 94.444 36 2 0 1287 1322 520316404 520316439 3.180000e-04 56.5
35 TraesCS5A01G107100 chr7B 90.395 354 26 7 1622 1970 446193584 446193234 2.070000e-125 459.0
36 TraesCS5A01G107100 chr7B 87.291 299 33 2 1325 1623 607315709 607316002 1.010000e-88 337.0
37 TraesCS5A01G107100 chr7B 93.284 134 9 0 2155 2288 446192571 446192438 4.990000e-47 198.0
38 TraesCS5A01G107100 chr1A 91.693 313 23 1 368 677 535438989 535439301 4.520000e-117 431.0
39 TraesCS5A01G107100 chr1A 88.278 273 22 2 675 944 99199541 99199806 3.670000e-83 318.0
40 TraesCS5A01G107100 chr1A 92.647 204 15 0 1 204 486960006 486960209 6.180000e-76 294.0
41 TraesCS5A01G107100 chr1D 91.531 307 24 2 373 678 456276762 456276457 2.720000e-114 422.0
42 TraesCS5A01G107100 chr5D 92.517 294 21 1 381 674 209014695 209014987 9.770000e-114 420.0
43 TraesCS5A01G107100 chr5D 90.354 311 28 2 374 683 5561164 5560855 7.610000e-110 407.0
44 TraesCS5A01G107100 chr4B 92.177 294 23 0 381 674 626075423 626075716 1.260000e-112 416.0
45 TraesCS5A01G107100 chr4B 89.139 267 19 3 678 941 410241677 410241418 7.880000e-85 324.0
46 TraesCS5A01G107100 chr3A 91.946 298 23 1 381 677 444288558 444288261 1.260000e-112 416.0
47 TraesCS5A01G107100 chr3A 89.139 267 19 3 678 941 142951392 142951133 7.880000e-85 324.0
48 TraesCS5A01G107100 chr3A 92.893 197 14 0 1 197 89575010 89574814 1.030000e-73 287.0
49 TraesCS5A01G107100 chr3A 89.268 205 19 3 1 204 89576745 89576947 1.050000e-63 254.0
50 TraesCS5A01G107100 chr5B 89.338 272 18 4 678 945 90506823 90506559 4.710000e-87 331.0
51 TraesCS5A01G107100 chr2B 90.090 222 20 1 1 222 45644843 45645062 1.030000e-73 287.0
52 TraesCS5A01G107100 chr2B 95.238 126 6 0 2155 2280 125255265 125255140 1.390000e-47 200.0
53 TraesCS5A01G107100 chr7D 89.216 204 22 0 1 204 508829251 508829048 2.920000e-64 255.0
54 TraesCS5A01G107100 chr7D 95.161 62 1 2 1963 2022 634366728 634366667 1.870000e-16 97.1
55 TraesCS5A01G107100 chr3B 88.780 205 23 0 1 205 684259205 684259001 3.770000e-63 252.0


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 TraesCS5A01G107100 chr5A 180346402 180348689 2287 False 4226.0 4226 100.0000 1 2288 1 chr5A.!!$F2 2287
1 TraesCS5A01G107100 chr7A 259567860 259569343 1483 True 1255.5 2316 95.9960 209 2288 2 chr7A.!!$R2 2079
2 TraesCS5A01G107100 chrUn 94922490 94923974 1484 False 1246.5 2302 95.2435 205 2288 2 chrUn.!!$F1 2083
3 TraesCS5A01G107100 chr2D 190400335 190401817 1482 False 1251.0 2300 96.0065 205 2288 2 chr2D.!!$F1 2083
4 TraesCS5A01G107100 chr3D 167405095 167406444 1349 False 2217.0 2217 96.3290 939 2288 1 chr3D.!!$F1 1349
5 TraesCS5A01G107100 chr6D 7898847 7900288 1441 True 1202.5 2209 95.5025 205 2242 2 chr6D.!!$R1 2037
6 TraesCS5A01G107100 chr6D 142858628 142860098 1470 False 1201.0 2200 95.4190 205 2288 2 chr6D.!!$F1 2083
7 TraesCS5A01G107100 chr6B 33376071 33378627 2556 True 972.5 1413 93.8355 939 2288 2 chr6B.!!$R2 1349
8 TraesCS5A01G107100 chr6B 425603850 425605270 1420 False 323.0 468 92.0895 1632 2287 2 chr6B.!!$F3 655
9 TraesCS5A01G107100 chr2A 241962131 241962751 620 True 497.0 497 81.5870 331 943 1 chr2A.!!$R3 612
10 TraesCS5A01G107100 chr7B 446192438 446193584 1146 True 328.5 459 91.8395 1622 2288 2 chr7B.!!$R1 666

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
81 82 0.033504 GAGCCAGGACTGACGTTTCA 59.966 55.0 0.0 0.0 0.0 2.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1855 1899 0.61326 GAAGGCAAAATTCCACCCCC 59.387 55.0 0.0 0.0 0.0 5.4 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
20 21 2.843401 TATGGGCCGCATATAAACGT 57.157 45.000 9.20 0.00 0.00 3.99
21 22 1.234821 ATGGGCCGCATATAAACGTG 58.765 50.000 0.00 0.00 0.00 4.49
22 23 0.816018 TGGGCCGCATATAAACGTGG 60.816 55.000 0.00 0.00 35.82 4.94
23 24 0.816421 GGGCCGCATATAAACGTGGT 60.816 55.000 0.00 0.00 35.14 4.16
24 25 0.584876 GGCCGCATATAAACGTGGTC 59.415 55.000 0.00 0.00 35.14 4.02
25 26 1.578583 GCCGCATATAAACGTGGTCT 58.421 50.000 0.00 0.00 35.14 3.85
26 27 1.937899 GCCGCATATAAACGTGGTCTT 59.062 47.619 0.00 0.00 35.14 3.01
27 28 2.033151 GCCGCATATAAACGTGGTCTTC 60.033 50.000 0.00 0.00 35.14 2.87
28 29 3.191669 CCGCATATAAACGTGGTCTTCA 58.808 45.455 0.00 0.00 0.00 3.02
29 30 3.000925 CCGCATATAAACGTGGTCTTCAC 59.999 47.826 0.00 0.00 42.74 3.18
30 31 3.863424 CGCATATAAACGTGGTCTTCACT 59.137 43.478 0.00 0.00 43.94 3.41
31 32 5.038683 CGCATATAAACGTGGTCTTCACTA 58.961 41.667 0.00 0.00 43.94 2.74
32 33 5.051907 CGCATATAAACGTGGTCTTCACTAC 60.052 44.000 0.00 0.00 43.94 2.73
33 34 5.808540 GCATATAAACGTGGTCTTCACTACA 59.191 40.000 0.00 0.00 43.94 2.74
34 35 6.019801 GCATATAAACGTGGTCTTCACTACAG 60.020 42.308 0.00 0.00 43.94 2.74
35 36 5.717078 ATAAACGTGGTCTTCACTACAGA 57.283 39.130 0.00 0.00 43.94 3.41
36 37 4.395959 AAACGTGGTCTTCACTACAGAA 57.604 40.909 0.00 0.00 43.94 3.02
37 38 4.395959 AACGTGGTCTTCACTACAGAAA 57.604 40.909 0.00 0.00 43.94 2.52
38 39 4.602340 ACGTGGTCTTCACTACAGAAAT 57.398 40.909 0.00 0.00 43.94 2.17
39 40 5.717078 ACGTGGTCTTCACTACAGAAATA 57.283 39.130 0.00 0.00 43.94 1.40
40 41 5.467705 ACGTGGTCTTCACTACAGAAATAC 58.532 41.667 0.00 0.00 43.94 1.89
41 42 4.557690 CGTGGTCTTCACTACAGAAATACG 59.442 45.833 0.00 0.00 43.94 3.06
42 43 5.618418 CGTGGTCTTCACTACAGAAATACGA 60.618 44.000 0.00 0.00 43.94 3.43
43 44 5.800941 GTGGTCTTCACTACAGAAATACGAG 59.199 44.000 0.00 0.00 42.86 4.18
44 45 5.708697 TGGTCTTCACTACAGAAATACGAGA 59.291 40.000 0.00 0.00 0.00 4.04
45 46 6.377429 TGGTCTTCACTACAGAAATACGAGAT 59.623 38.462 0.00 0.00 0.00 2.75
46 47 7.555195 TGGTCTTCACTACAGAAATACGAGATA 59.445 37.037 0.00 0.00 0.00 1.98
47 48 7.856894 GGTCTTCACTACAGAAATACGAGATAC 59.143 40.741 0.00 0.00 0.00 2.24
66 67 1.823828 CGTATGTGACGTGTAGAGCC 58.176 55.000 0.00 0.00 46.86 4.70
67 68 1.131693 CGTATGTGACGTGTAGAGCCA 59.868 52.381 0.00 0.00 46.86 4.75
68 69 2.791503 CGTATGTGACGTGTAGAGCCAG 60.792 54.545 0.00 0.00 46.86 4.85
69 70 0.532573 ATGTGACGTGTAGAGCCAGG 59.467 55.000 0.00 0.00 0.00 4.45
70 71 0.538746 TGTGACGTGTAGAGCCAGGA 60.539 55.000 0.00 0.00 0.00 3.86
71 72 0.109226 GTGACGTGTAGAGCCAGGAC 60.109 60.000 0.00 0.00 0.00 3.85
72 73 0.251209 TGACGTGTAGAGCCAGGACT 60.251 55.000 0.00 0.00 0.00 3.85
73 74 0.171455 GACGTGTAGAGCCAGGACTG 59.829 60.000 0.00 0.00 0.00 3.51
74 75 0.251209 ACGTGTAGAGCCAGGACTGA 60.251 55.000 0.00 0.00 0.00 3.41
75 76 0.171455 CGTGTAGAGCCAGGACTGAC 59.829 60.000 0.00 0.00 0.00 3.51
76 77 0.171455 GTGTAGAGCCAGGACTGACG 59.829 60.000 0.00 0.00 0.00 4.35
77 78 0.251209 TGTAGAGCCAGGACTGACGT 60.251 55.000 0.00 0.00 0.00 4.34
78 79 0.889306 GTAGAGCCAGGACTGACGTT 59.111 55.000 0.00 0.00 0.00 3.99
79 80 1.272769 GTAGAGCCAGGACTGACGTTT 59.727 52.381 0.00 0.00 0.00 3.60
80 81 0.318762 AGAGCCAGGACTGACGTTTC 59.681 55.000 0.00 0.00 0.00 2.78
81 82 0.033504 GAGCCAGGACTGACGTTTCA 59.966 55.000 0.00 0.00 0.00 2.69
82 83 0.468226 AGCCAGGACTGACGTTTCAA 59.532 50.000 0.00 0.00 0.00 2.69
83 84 1.072331 AGCCAGGACTGACGTTTCAAT 59.928 47.619 0.00 0.00 0.00 2.57
84 85 1.464997 GCCAGGACTGACGTTTCAATC 59.535 52.381 0.00 0.00 0.00 2.67
85 86 2.872038 GCCAGGACTGACGTTTCAATCT 60.872 50.000 0.00 0.00 28.40 2.40
86 87 2.996621 CCAGGACTGACGTTTCAATCTC 59.003 50.000 0.00 0.00 28.40 2.75
87 88 3.554960 CCAGGACTGACGTTTCAATCTCA 60.555 47.826 0.00 0.00 28.40 3.27
88 89 3.677121 CAGGACTGACGTTTCAATCTCAG 59.323 47.826 0.00 0.00 36.90 3.35
89 90 2.996621 GGACTGACGTTTCAATCTCAGG 59.003 50.000 0.00 0.00 35.43 3.86
90 91 2.996621 GACTGACGTTTCAATCTCAGGG 59.003 50.000 0.00 0.00 35.43 4.45
91 92 2.632996 ACTGACGTTTCAATCTCAGGGA 59.367 45.455 0.00 0.00 35.43 4.20
92 93 2.996621 CTGACGTTTCAATCTCAGGGAC 59.003 50.000 0.00 0.00 0.00 4.46
93 94 2.289444 TGACGTTTCAATCTCAGGGACC 60.289 50.000 0.00 0.00 0.00 4.46
94 95 1.337823 ACGTTTCAATCTCAGGGACCG 60.338 52.381 0.00 0.00 0.00 4.79
95 96 1.337823 CGTTTCAATCTCAGGGACCGT 60.338 52.381 0.00 0.00 0.00 4.83
96 97 2.094390 CGTTTCAATCTCAGGGACCGTA 60.094 50.000 0.00 0.00 0.00 4.02
97 98 3.430374 CGTTTCAATCTCAGGGACCGTAT 60.430 47.826 0.00 0.00 0.00 3.06
98 99 4.514401 GTTTCAATCTCAGGGACCGTATT 58.486 43.478 0.00 0.00 0.00 1.89
99 100 3.819564 TCAATCTCAGGGACCGTATTG 57.180 47.619 2.90 2.90 0.00 1.90
100 101 3.371034 TCAATCTCAGGGACCGTATTGA 58.629 45.455 6.72 6.72 32.51 2.57
101 102 3.967326 TCAATCTCAGGGACCGTATTGAT 59.033 43.478 6.72 0.29 30.59 2.57
102 103 4.039245 TCAATCTCAGGGACCGTATTGATC 59.961 45.833 6.72 0.00 30.59 2.92
103 104 3.026707 TCTCAGGGACCGTATTGATCA 57.973 47.619 0.00 0.00 0.00 2.92
104 105 2.693591 TCTCAGGGACCGTATTGATCAC 59.306 50.000 0.00 0.00 0.00 3.06
105 106 1.407618 TCAGGGACCGTATTGATCACG 59.592 52.381 0.00 0.00 39.10 4.35
106 107 1.136305 CAGGGACCGTATTGATCACGT 59.864 52.381 0.00 0.00 37.71 4.49
107 108 2.359848 CAGGGACCGTATTGATCACGTA 59.640 50.000 0.00 0.00 37.71 3.57
108 109 3.005472 CAGGGACCGTATTGATCACGTAT 59.995 47.826 0.00 0.00 37.71 3.06
109 110 3.640029 AGGGACCGTATTGATCACGTATT 59.360 43.478 0.00 0.00 37.71 1.89
110 111 4.100498 AGGGACCGTATTGATCACGTATTT 59.900 41.667 0.00 0.00 37.71 1.40
111 112 4.812626 GGGACCGTATTGATCACGTATTTT 59.187 41.667 0.00 0.00 37.71 1.82
112 113 5.050567 GGGACCGTATTGATCACGTATTTTC 60.051 44.000 0.00 0.00 37.71 2.29
113 114 5.521010 GGACCGTATTGATCACGTATTTTCA 59.479 40.000 0.00 0.00 37.71 2.69
114 115 6.202188 GGACCGTATTGATCACGTATTTTCAT 59.798 38.462 0.00 0.00 37.71 2.57
115 116 6.943981 ACCGTATTGATCACGTATTTTCATG 58.056 36.000 0.00 0.00 37.71 3.07
116 117 6.537301 ACCGTATTGATCACGTATTTTCATGT 59.463 34.615 0.00 0.00 37.71 3.21
117 118 7.707464 ACCGTATTGATCACGTATTTTCATGTA 59.293 33.333 0.00 0.00 37.71 2.29
118 119 8.002107 CCGTATTGATCACGTATTTTCATGTAC 58.998 37.037 0.00 0.00 37.71 2.90
119 120 8.002107 CGTATTGATCACGTATTTTCATGTACC 58.998 37.037 0.00 0.00 34.74 3.34
120 121 5.959652 TGATCACGTATTTTCATGTACCG 57.040 39.130 0.00 0.00 0.00 4.02
121 122 4.806775 TGATCACGTATTTTCATGTACCGG 59.193 41.667 0.00 0.00 0.00 5.28
122 123 3.523547 TCACGTATTTTCATGTACCGGG 58.476 45.455 6.32 0.00 0.00 5.73
123 124 3.195182 TCACGTATTTTCATGTACCGGGA 59.805 43.478 6.32 0.00 0.00 5.14
124 125 3.307782 CACGTATTTTCATGTACCGGGAC 59.692 47.826 10.93 10.93 0.00 4.46
125 126 2.867975 CGTATTTTCATGTACCGGGACC 59.132 50.000 16.09 0.00 0.00 4.46
126 127 2.032680 ATTTTCATGTACCGGGACCG 57.967 50.000 16.09 5.55 39.44 4.79
127 128 0.686224 TTTTCATGTACCGGGACCGT 59.314 50.000 16.09 0.00 37.81 4.83
128 129 1.554836 TTTCATGTACCGGGACCGTA 58.445 50.000 16.09 0.00 37.81 4.02
129 130 1.779221 TTCATGTACCGGGACCGTAT 58.221 50.000 16.09 0.00 37.81 3.06
130 131 1.779221 TCATGTACCGGGACCGTATT 58.221 50.000 16.09 0.00 37.81 1.89
131 132 1.409790 TCATGTACCGGGACCGTATTG 59.590 52.381 16.09 4.44 37.81 1.90
132 133 1.409790 CATGTACCGGGACCGTATTGA 59.590 52.381 16.09 0.00 37.81 2.57
133 134 1.554836 TGTACCGGGACCGTATTGAA 58.445 50.000 16.09 0.00 37.81 2.69
134 135 1.477700 TGTACCGGGACCGTATTGAAG 59.522 52.381 16.09 0.00 37.81 3.02
135 136 0.461135 TACCGGGACCGTATTGAAGC 59.539 55.000 6.32 0.00 37.81 3.86
136 137 1.219664 CCGGGACCGTATTGAAGCA 59.780 57.895 10.17 0.00 37.81 3.91
137 138 0.391927 CCGGGACCGTATTGAAGCAA 60.392 55.000 10.17 0.00 37.81 3.91
138 139 1.663695 CGGGACCGTATTGAAGCAAT 58.336 50.000 1.86 0.00 37.80 3.56
139 140 2.484065 CCGGGACCGTATTGAAGCAATA 60.484 50.000 10.17 0.00 34.71 1.90
152 153 7.935338 ATTGAAGCAATACACAAGTTTCAAG 57.065 32.000 0.00 0.00 42.69 3.02
153 154 6.691754 TGAAGCAATACACAAGTTTCAAGA 57.308 33.333 0.00 0.00 31.14 3.02
154 155 6.494842 TGAAGCAATACACAAGTTTCAAGAC 58.505 36.000 0.00 0.00 31.14 3.01
155 156 6.318648 TGAAGCAATACACAAGTTTCAAGACT 59.681 34.615 0.00 0.00 31.14 3.24
156 157 6.064846 AGCAATACACAAGTTTCAAGACTG 57.935 37.500 0.00 0.00 0.00 3.51
157 158 5.822519 AGCAATACACAAGTTTCAAGACTGA 59.177 36.000 0.00 0.00 0.00 3.41
158 159 6.318648 AGCAATACACAAGTTTCAAGACTGAA 59.681 34.615 0.00 0.00 39.87 3.02
159 160 7.013655 AGCAATACACAAGTTTCAAGACTGAAT 59.986 33.333 0.00 0.00 41.22 2.57
160 161 7.649306 GCAATACACAAGTTTCAAGACTGAATT 59.351 33.333 0.00 0.00 41.22 2.17
161 162 8.961092 CAATACACAAGTTTCAAGACTGAATTG 58.039 33.333 0.00 0.00 41.22 2.32
162 163 5.894807 ACACAAGTTTCAAGACTGAATTGG 58.105 37.500 6.29 0.53 41.22 3.16
163 164 5.652014 ACACAAGTTTCAAGACTGAATTGGA 59.348 36.000 6.29 0.00 41.22 3.53
164 165 6.322201 ACACAAGTTTCAAGACTGAATTGGAT 59.678 34.615 6.29 0.00 41.22 3.41
165 166 6.639686 CACAAGTTTCAAGACTGAATTGGATG 59.360 38.462 6.29 0.00 41.22 3.51
166 167 6.322201 ACAAGTTTCAAGACTGAATTGGATGT 59.678 34.615 6.29 0.00 41.22 3.06
167 168 6.323203 AGTTTCAAGACTGAATTGGATGTG 57.677 37.500 0.00 0.00 41.22 3.21
168 169 6.064060 AGTTTCAAGACTGAATTGGATGTGA 58.936 36.000 0.00 0.00 41.22 3.58
169 170 5.947228 TTCAAGACTGAATTGGATGTGAC 57.053 39.130 0.00 0.00 36.62 3.67
170 171 4.326826 TCAAGACTGAATTGGATGTGACC 58.673 43.478 0.00 0.00 0.00 4.02
171 172 4.074259 CAAGACTGAATTGGATGTGACCA 58.926 43.478 0.00 0.00 38.24 4.02
172 173 3.947868 AGACTGAATTGGATGTGACCAG 58.052 45.455 0.00 0.00 41.19 4.00
173 174 2.421424 GACTGAATTGGATGTGACCAGC 59.579 50.000 0.00 0.00 41.19 4.85
174 175 2.224843 ACTGAATTGGATGTGACCAGCA 60.225 45.455 0.00 0.00 41.19 4.41
175 176 2.821378 CTGAATTGGATGTGACCAGCAA 59.179 45.455 0.00 0.00 41.19 3.91
176 177 2.821378 TGAATTGGATGTGACCAGCAAG 59.179 45.455 0.00 0.00 41.19 4.01
177 178 2.592102 ATTGGATGTGACCAGCAAGT 57.408 45.000 0.00 0.00 41.19 3.16
178 179 3.719268 ATTGGATGTGACCAGCAAGTA 57.281 42.857 0.00 0.00 41.19 2.24
179 180 2.472695 TGGATGTGACCAGCAAGTAC 57.527 50.000 0.00 0.00 34.77 2.73
180 181 1.337728 TGGATGTGACCAGCAAGTACG 60.338 52.381 0.00 0.00 34.77 3.67
181 182 1.067142 GGATGTGACCAGCAAGTACGA 60.067 52.381 0.00 0.00 0.00 3.43
182 183 2.263077 GATGTGACCAGCAAGTACGAG 58.737 52.381 0.00 0.00 0.00 4.18
183 184 0.317160 TGTGACCAGCAAGTACGAGG 59.683 55.000 0.00 0.00 0.00 4.63
184 185 0.601558 GTGACCAGCAAGTACGAGGA 59.398 55.000 0.00 0.00 0.00 3.71
185 186 0.601558 TGACCAGCAAGTACGAGGAC 59.398 55.000 0.00 0.00 0.00 3.85
186 187 0.889306 GACCAGCAAGTACGAGGACT 59.111 55.000 0.00 0.00 0.00 3.85
187 188 2.089980 GACCAGCAAGTACGAGGACTA 58.910 52.381 0.00 0.00 0.00 2.59
188 189 2.688958 GACCAGCAAGTACGAGGACTAT 59.311 50.000 0.00 0.00 0.00 2.12
189 190 3.881688 GACCAGCAAGTACGAGGACTATA 59.118 47.826 0.00 0.00 0.00 1.31
190 191 3.884091 ACCAGCAAGTACGAGGACTATAG 59.116 47.826 0.00 0.00 0.00 1.31
191 192 4.135306 CCAGCAAGTACGAGGACTATAGA 58.865 47.826 6.78 0.00 0.00 1.98
192 193 4.762765 CCAGCAAGTACGAGGACTATAGAT 59.237 45.833 6.78 0.00 0.00 1.98
193 194 5.335269 CCAGCAAGTACGAGGACTATAGATG 60.335 48.000 6.78 0.00 0.00 2.90
194 195 4.216687 AGCAAGTACGAGGACTATAGATGC 59.783 45.833 6.78 1.85 31.29 3.91
195 196 4.023107 GCAAGTACGAGGACTATAGATGCA 60.023 45.833 6.78 0.00 31.44 3.96
196 197 5.507482 GCAAGTACGAGGACTATAGATGCAA 60.507 44.000 6.78 0.00 31.44 4.08
197 198 6.682746 CAAGTACGAGGACTATAGATGCAAT 58.317 40.000 6.78 0.00 0.00 3.56
198 199 6.902771 AGTACGAGGACTATAGATGCAATT 57.097 37.500 6.78 0.00 0.00 2.32
199 200 7.997773 AGTACGAGGACTATAGATGCAATTA 57.002 36.000 6.78 0.00 0.00 1.40
200 201 8.582657 AGTACGAGGACTATAGATGCAATTAT 57.417 34.615 6.78 0.00 0.00 1.28
201 202 8.679100 AGTACGAGGACTATAGATGCAATTATC 58.321 37.037 6.78 0.00 0.00 1.75
202 203 7.710676 ACGAGGACTATAGATGCAATTATCT 57.289 36.000 6.78 0.00 40.39 1.98
203 204 7.767261 ACGAGGACTATAGATGCAATTATCTC 58.233 38.462 6.78 0.00 38.35 2.75
207 208 6.406400 GGACTATAGATGCAATTATCTCGGCT 60.406 42.308 6.78 0.00 38.35 5.52
286 288 4.827087 CTGCGCCGTGATGAGCCT 62.827 66.667 4.18 0.00 0.00 4.58
329 331 0.037232 CGTTCCCTCAGTCTCCAACC 60.037 60.000 0.00 0.00 0.00 3.77
348 350 2.130272 CCTAAGGCCTCCTTTGGTTC 57.870 55.000 5.23 0.00 46.36 3.62
349 351 1.679032 CCTAAGGCCTCCTTTGGTTCG 60.679 57.143 5.23 0.00 46.36 3.95
350 352 1.278127 CTAAGGCCTCCTTTGGTTCGA 59.722 52.381 5.23 0.00 41.69 3.71
363 365 6.508777 CCTTTGGTTCGAAGGAATTTTGTAA 58.491 36.000 0.00 0.00 45.40 2.41
364 366 6.981559 CCTTTGGTTCGAAGGAATTTTGTAAA 59.018 34.615 0.00 0.00 45.40 2.01
366 368 8.950208 TTTGGTTCGAAGGAATTTTGTAAAAT 57.050 26.923 0.00 0.00 40.15 1.82
386 388 4.936685 ATTTTCATAGGATAGGGCCTCC 57.063 45.455 10.74 6.49 39.50 4.30
403 405 4.141251 GGCCTCCTTTGGTTCATAGGATAA 60.141 45.833 0.00 0.00 39.94 1.75
404 406 5.458215 GGCCTCCTTTGGTTCATAGGATAAT 60.458 44.000 0.00 0.00 39.94 1.28
406 408 7.231467 GCCTCCTTTGGTTCATAGGATAATAA 58.769 38.462 7.38 0.00 39.94 1.40
408 410 9.813826 CCTCCTTTGGTTCATAGGATAATAATT 57.186 33.333 7.38 0.00 39.94 1.40
448 456 3.119291 CGTAGGAAGTGAGATGACATGC 58.881 50.000 0.00 0.00 0.00 4.06
465 473 7.307131 TGACATGCATCTCAATTCCTATAGA 57.693 36.000 1.73 0.00 0.00 1.98
466 474 7.384477 TGACATGCATCTCAATTCCTATAGAG 58.616 38.462 1.73 0.00 0.00 2.43
469 487 8.435187 ACATGCATCTCAATTCCTATAGAGAAA 58.565 33.333 0.00 0.00 40.19 2.52
476 494 8.584157 TCTCAATTCCTATAGAGAAAGAGATGC 58.416 37.037 20.46 0.00 35.41 3.91
483 501 7.290948 TCCTATAGAGAAAGAGATGCCATTTGA 59.709 37.037 0.00 0.00 0.00 2.69
485 503 7.747155 ATAGAGAAAGAGATGCCATTTGATG 57.253 36.000 0.00 0.00 0.00 3.07
486 504 4.338682 AGAGAAAGAGATGCCATTTGATGC 59.661 41.667 0.00 0.00 0.00 3.91
499 517 5.477984 GCCATTTGATGCATAGGATAGGAAA 59.522 40.000 0.00 0.00 0.00 3.13
527 545 9.793259 TTTCCATTGAGTCTAGACTAATGTTTT 57.207 29.630 29.22 12.63 42.66 2.43
550 569 5.726980 TTTCCTCCAAAATGTGAAGGATG 57.273 39.130 0.00 0.00 0.00 3.51
552 571 3.333381 TCCTCCAAAATGTGAAGGATGGA 59.667 43.478 0.00 0.00 35.74 3.41
553 572 4.017222 TCCTCCAAAATGTGAAGGATGGAT 60.017 41.667 0.00 0.00 36.45 3.41
554 573 4.713321 CCTCCAAAATGTGAAGGATGGATT 59.287 41.667 0.00 0.00 36.45 3.01
602 621 6.682537 TCCATTCCTATAAATCAAAGGGCTT 58.317 36.000 0.00 0.00 0.00 4.35
603 622 6.777580 TCCATTCCTATAAATCAAAGGGCTTC 59.222 38.462 0.00 0.00 0.00 3.86
611 630 5.830799 AAATCAAAGGGCTTCAAAGGAAT 57.169 34.783 0.00 0.00 31.34 3.01
612 631 5.830799 AATCAAAGGGCTTCAAAGGAATT 57.169 34.783 0.00 0.00 31.34 2.17
613 632 5.830799 ATCAAAGGGCTTCAAAGGAATTT 57.169 34.783 0.00 0.00 31.34 1.82
614 633 5.628797 TCAAAGGGCTTCAAAGGAATTTT 57.371 34.783 0.00 0.00 31.34 1.82
663 683 9.574516 AGAGTTCCTACAAAATTCATACAAACT 57.425 29.630 0.00 0.00 0.00 2.66
684 704 9.449719 CAAACTAAAGAAGGCCTAAGATTTCTA 57.550 33.333 5.16 0.00 30.19 2.10
719 739 4.821805 CCTTCAGAGCTCTTTGGTTTGTAA 59.178 41.667 15.27 0.00 31.30 2.41
720 740 5.474876 CCTTCAGAGCTCTTTGGTTTGTAAT 59.525 40.000 15.27 0.00 31.30 1.89
764 787 7.482169 GGAATTTTTCCTATCCTTCAACCTT 57.518 36.000 0.00 0.00 46.57 3.50
801 824 9.959721 AGGAAAATAAACATTAGCTTAGACTCA 57.040 29.630 0.00 0.00 0.00 3.41
839 862 4.346730 TGATGTGAATCAAAGGGCATCTT 58.653 39.130 10.68 0.00 37.28 2.40
840 863 4.773674 TGATGTGAATCAAAGGGCATCTTT 59.226 37.500 10.68 0.00 45.85 2.52
841 864 5.246656 TGATGTGAATCAAAGGGCATCTTTT 59.753 36.000 10.68 0.00 42.62 2.27
842 865 5.549742 TGTGAATCAAAGGGCATCTTTTT 57.450 34.783 2.11 0.00 42.62 1.94
933 956 7.889589 GGTTTTCCAATCTTATGAACCAAAG 57.110 36.000 0.00 0.00 40.31 2.77
934 957 7.666623 GGTTTTCCAATCTTATGAACCAAAGA 58.333 34.615 0.00 0.00 40.31 2.52
935 958 8.147704 GGTTTTCCAATCTTATGAACCAAAGAA 58.852 33.333 0.00 0.00 40.31 2.52
936 959 9.196552 GTTTTCCAATCTTATGAACCAAAGAAG 57.803 33.333 0.00 0.00 35.47 2.85
937 960 7.466746 TTCCAATCTTATGAACCAAAGAAGG 57.533 36.000 0.00 0.00 35.47 3.46
1075 1113 3.465403 CTCTGGTGGCGGAGGAGG 61.465 72.222 0.00 0.00 0.00 4.30
1076 1114 3.965026 CTCTGGTGGCGGAGGAGGA 62.965 68.421 0.00 0.00 0.00 3.71
1077 1115 3.465403 CTGGTGGCGGAGGAGGAG 61.465 72.222 0.00 0.00 0.00 3.69
1145 1183 1.531840 CCCTCGTCATCCCGGATCT 60.532 63.158 0.73 0.00 0.00 2.75
1701 1742 8.530269 TTCTTCCAAGACGAATTAGTAACTTC 57.470 34.615 0.00 0.00 34.13 3.01
2138 3431 1.111277 GGTGAGGCCAACAAAACTGT 58.889 50.000 5.01 0.00 37.17 3.55
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.006940 CACGTTTATATGCGGCCCATAT 58.993 45.455 22.52 22.52 46.32 1.78
1 2 2.418692 CACGTTTATATGCGGCCCATA 58.581 47.619 14.08 14.08 40.52 2.74
2 3 1.234821 CACGTTTATATGCGGCCCAT 58.765 50.000 10.96 10.96 37.97 4.00
3 4 0.816018 CCACGTTTATATGCGGCCCA 60.816 55.000 0.00 0.00 0.00 5.36
4 5 0.816421 ACCACGTTTATATGCGGCCC 60.816 55.000 0.00 0.00 0.00 5.80
5 6 0.584876 GACCACGTTTATATGCGGCC 59.415 55.000 0.00 0.00 0.00 6.13
6 7 1.578583 AGACCACGTTTATATGCGGC 58.421 50.000 0.00 0.00 0.00 6.53
7 8 3.000925 GTGAAGACCACGTTTATATGCGG 59.999 47.826 0.00 0.00 35.86 5.69
8 9 4.178156 GTGAAGACCACGTTTATATGCG 57.822 45.455 0.00 0.00 35.86 4.73
19 20 5.706916 TCGTATTTCTGTAGTGAAGACCAC 58.293 41.667 0.00 0.00 46.03 4.16
20 21 5.708697 TCTCGTATTTCTGTAGTGAAGACCA 59.291 40.000 0.00 0.00 0.00 4.02
21 22 6.192234 TCTCGTATTTCTGTAGTGAAGACC 57.808 41.667 0.00 0.00 0.00 3.85
22 23 7.583401 CGTATCTCGTATTTCTGTAGTGAAGAC 59.417 40.741 0.00 0.00 34.52 3.01
23 24 7.628235 CGTATCTCGTATTTCTGTAGTGAAGA 58.372 38.462 0.00 0.00 34.52 2.87
24 25 7.824100 CGTATCTCGTATTTCTGTAGTGAAG 57.176 40.000 0.00 0.00 34.52 3.02
48 49 2.479730 CCTGGCTCTACACGTCACATAC 60.480 54.545 0.00 0.00 0.00 2.39
49 50 1.749063 CCTGGCTCTACACGTCACATA 59.251 52.381 0.00 0.00 0.00 2.29
50 51 0.532573 CCTGGCTCTACACGTCACAT 59.467 55.000 0.00 0.00 0.00 3.21
51 52 0.538746 TCCTGGCTCTACACGTCACA 60.539 55.000 0.00 0.00 0.00 3.58
52 53 0.109226 GTCCTGGCTCTACACGTCAC 60.109 60.000 0.00 0.00 0.00 3.67
53 54 0.251209 AGTCCTGGCTCTACACGTCA 60.251 55.000 0.00 0.00 0.00 4.35
54 55 0.171455 CAGTCCTGGCTCTACACGTC 59.829 60.000 0.00 0.00 0.00 4.34
55 56 0.251209 TCAGTCCTGGCTCTACACGT 60.251 55.000 0.00 0.00 0.00 4.49
56 57 0.171455 GTCAGTCCTGGCTCTACACG 59.829 60.000 0.00 0.00 31.34 4.49
57 58 0.171455 CGTCAGTCCTGGCTCTACAC 59.829 60.000 0.00 0.00 31.96 2.90
58 59 0.251209 ACGTCAGTCCTGGCTCTACA 60.251 55.000 0.00 0.00 31.96 2.74
59 60 0.889306 AACGTCAGTCCTGGCTCTAC 59.111 55.000 0.00 0.00 31.96 2.59
60 61 1.544691 GAAACGTCAGTCCTGGCTCTA 59.455 52.381 0.00 0.00 31.96 2.43
61 62 0.318762 GAAACGTCAGTCCTGGCTCT 59.681 55.000 0.00 0.00 31.96 4.09
62 63 0.033504 TGAAACGTCAGTCCTGGCTC 59.966 55.000 0.00 0.00 31.96 4.70
63 64 0.468226 TTGAAACGTCAGTCCTGGCT 59.532 50.000 0.00 0.00 34.49 4.75
64 65 1.464997 GATTGAAACGTCAGTCCTGGC 59.535 52.381 0.00 0.00 35.10 4.85
65 66 2.996621 GAGATTGAAACGTCAGTCCTGG 59.003 50.000 0.00 0.00 40.48 4.45
66 67 3.653344 TGAGATTGAAACGTCAGTCCTG 58.347 45.455 0.00 0.00 40.48 3.86
67 68 3.306364 CCTGAGATTGAAACGTCAGTCCT 60.306 47.826 0.00 0.00 40.48 3.85
68 69 2.996621 CCTGAGATTGAAACGTCAGTCC 59.003 50.000 0.00 0.00 40.48 3.85
69 70 2.996621 CCCTGAGATTGAAACGTCAGTC 59.003 50.000 0.00 0.00 40.03 3.51
70 71 2.632996 TCCCTGAGATTGAAACGTCAGT 59.367 45.455 0.00 0.00 35.62 3.41
71 72 2.996621 GTCCCTGAGATTGAAACGTCAG 59.003 50.000 0.00 0.00 36.89 3.51
72 73 2.289444 GGTCCCTGAGATTGAAACGTCA 60.289 50.000 0.00 0.00 0.00 4.35
73 74 2.347731 GGTCCCTGAGATTGAAACGTC 58.652 52.381 0.00 0.00 0.00 4.34
74 75 1.337823 CGGTCCCTGAGATTGAAACGT 60.338 52.381 0.00 0.00 0.00 3.99
75 76 1.337823 ACGGTCCCTGAGATTGAAACG 60.338 52.381 0.00 0.00 0.00 3.60
76 77 2.474410 ACGGTCCCTGAGATTGAAAC 57.526 50.000 0.00 0.00 0.00 2.78
77 78 4.224147 TCAATACGGTCCCTGAGATTGAAA 59.776 41.667 0.00 0.00 32.03 2.69
78 79 3.772572 TCAATACGGTCCCTGAGATTGAA 59.227 43.478 0.00 0.00 32.03 2.69
79 80 3.371034 TCAATACGGTCCCTGAGATTGA 58.629 45.455 0.00 0.00 32.41 2.57
80 81 3.819564 TCAATACGGTCCCTGAGATTG 57.180 47.619 0.00 0.00 0.00 2.67
81 82 3.967326 TGATCAATACGGTCCCTGAGATT 59.033 43.478 0.00 0.00 0.00 2.40
82 83 3.322254 GTGATCAATACGGTCCCTGAGAT 59.678 47.826 0.00 0.00 0.00 2.75
83 84 2.693591 GTGATCAATACGGTCCCTGAGA 59.306 50.000 0.00 0.00 0.00 3.27
84 85 2.543861 CGTGATCAATACGGTCCCTGAG 60.544 54.545 0.00 0.00 37.86 3.35
85 86 1.407618 CGTGATCAATACGGTCCCTGA 59.592 52.381 0.00 0.00 37.86 3.86
86 87 1.136305 ACGTGATCAATACGGTCCCTG 59.864 52.381 0.00 0.00 45.24 4.45
87 88 1.481871 ACGTGATCAATACGGTCCCT 58.518 50.000 0.00 0.00 45.24 4.20
88 89 3.655276 ATACGTGATCAATACGGTCCC 57.345 47.619 0.00 0.00 45.24 4.46
89 90 5.521010 TGAAAATACGTGATCAATACGGTCC 59.479 40.000 0.00 0.00 45.24 4.46
90 91 6.578020 TGAAAATACGTGATCAATACGGTC 57.422 37.500 0.00 0.00 45.24 4.79
91 92 6.537301 ACATGAAAATACGTGATCAATACGGT 59.463 34.615 0.00 0.00 45.24 4.83
92 93 6.943981 ACATGAAAATACGTGATCAATACGG 58.056 36.000 0.00 0.00 45.24 4.02
93 94 8.002107 GGTACATGAAAATACGTGATCAATACG 58.998 37.037 0.00 0.00 46.31 3.06
94 95 8.002107 CGGTACATGAAAATACGTGATCAATAC 58.998 37.037 0.00 5.02 0.00 1.89
95 96 7.170151 CCGGTACATGAAAATACGTGATCAATA 59.830 37.037 0.00 0.00 0.00 1.90
96 97 6.018262 CCGGTACATGAAAATACGTGATCAAT 60.018 38.462 0.00 0.00 0.00 2.57
97 98 5.292345 CCGGTACATGAAAATACGTGATCAA 59.708 40.000 0.00 0.00 0.00 2.57
98 99 4.806775 CCGGTACATGAAAATACGTGATCA 59.193 41.667 0.00 0.00 0.00 2.92
99 100 4.210537 CCCGGTACATGAAAATACGTGATC 59.789 45.833 0.00 0.00 0.00 2.92
100 101 4.124238 CCCGGTACATGAAAATACGTGAT 58.876 43.478 0.00 0.00 0.00 3.06
101 102 3.195182 TCCCGGTACATGAAAATACGTGA 59.805 43.478 0.00 0.00 0.00 4.35
102 103 3.307782 GTCCCGGTACATGAAAATACGTG 59.692 47.826 0.00 0.00 0.00 4.49
103 104 3.524541 GTCCCGGTACATGAAAATACGT 58.475 45.455 0.00 0.00 0.00 3.57
104 105 2.867975 GGTCCCGGTACATGAAAATACG 59.132 50.000 0.00 0.00 0.00 3.06
105 106 2.867975 CGGTCCCGGTACATGAAAATAC 59.132 50.000 0.00 0.00 35.56 1.89
106 107 2.500910 ACGGTCCCGGTACATGAAAATA 59.499 45.455 10.91 0.00 44.69 1.40
107 108 1.279846 ACGGTCCCGGTACATGAAAAT 59.720 47.619 10.91 0.00 44.69 1.82
108 109 0.686224 ACGGTCCCGGTACATGAAAA 59.314 50.000 10.91 0.00 44.69 2.29
109 110 1.554836 TACGGTCCCGGTACATGAAA 58.445 50.000 10.91 0.00 44.69 2.69
110 111 1.779221 ATACGGTCCCGGTACATGAA 58.221 50.000 10.91 0.00 44.69 2.57
111 112 1.409790 CAATACGGTCCCGGTACATGA 59.590 52.381 10.91 0.00 44.69 3.07
112 113 1.409790 TCAATACGGTCCCGGTACATG 59.590 52.381 10.91 0.00 44.69 3.21
113 114 1.779221 TCAATACGGTCCCGGTACAT 58.221 50.000 10.91 0.00 44.69 2.29
114 115 1.477700 CTTCAATACGGTCCCGGTACA 59.522 52.381 10.91 0.00 44.69 2.90
115 116 1.803998 GCTTCAATACGGTCCCGGTAC 60.804 57.143 10.91 0.00 44.69 3.34
116 117 0.461135 GCTTCAATACGGTCCCGGTA 59.539 55.000 10.91 1.00 44.69 4.02
117 118 1.219935 GCTTCAATACGGTCCCGGT 59.780 57.895 10.91 0.00 44.69 5.28
118 119 0.391927 TTGCTTCAATACGGTCCCGG 60.392 55.000 10.91 0.00 44.69 5.73
119 120 1.663695 ATTGCTTCAATACGGTCCCG 58.336 50.000 3.76 3.76 46.03 5.14
127 128 8.845227 TCTTGAAACTTGTGTATTGCTTCAATA 58.155 29.630 0.00 0.00 35.54 1.90
128 129 7.649306 GTCTTGAAACTTGTGTATTGCTTCAAT 59.351 33.333 0.00 0.00 37.80 2.57
129 130 6.972328 GTCTTGAAACTTGTGTATTGCTTCAA 59.028 34.615 0.00 0.00 31.34 2.69
130 131 6.318648 AGTCTTGAAACTTGTGTATTGCTTCA 59.681 34.615 0.00 0.00 0.00 3.02
131 132 6.634436 CAGTCTTGAAACTTGTGTATTGCTTC 59.366 38.462 0.00 0.00 0.00 3.86
132 133 6.318648 TCAGTCTTGAAACTTGTGTATTGCTT 59.681 34.615 0.00 0.00 0.00 3.91
133 134 5.822519 TCAGTCTTGAAACTTGTGTATTGCT 59.177 36.000 0.00 0.00 0.00 3.91
134 135 6.060028 TCAGTCTTGAAACTTGTGTATTGC 57.940 37.500 0.00 0.00 0.00 3.56
135 136 8.961092 CAATTCAGTCTTGAAACTTGTGTATTG 58.039 33.333 0.00 0.00 45.82 1.90
136 137 8.137437 CCAATTCAGTCTTGAAACTTGTGTATT 58.863 33.333 0.00 0.00 45.82 1.89
137 138 7.502226 TCCAATTCAGTCTTGAAACTTGTGTAT 59.498 33.333 0.00 0.00 45.82 2.29
138 139 6.826231 TCCAATTCAGTCTTGAAACTTGTGTA 59.174 34.615 0.00 0.00 45.82 2.90
139 140 5.652014 TCCAATTCAGTCTTGAAACTTGTGT 59.348 36.000 0.00 0.00 45.82 3.72
140 141 6.135290 TCCAATTCAGTCTTGAAACTTGTG 57.865 37.500 0.00 0.00 45.82 3.33
141 142 6.322201 ACATCCAATTCAGTCTTGAAACTTGT 59.678 34.615 0.00 0.00 45.82 3.16
142 143 6.639686 CACATCCAATTCAGTCTTGAAACTTG 59.360 38.462 0.00 0.00 45.82 3.16
143 144 6.547141 TCACATCCAATTCAGTCTTGAAACTT 59.453 34.615 0.00 0.00 45.82 2.66
144 145 6.016777 GTCACATCCAATTCAGTCTTGAAACT 60.017 38.462 0.00 0.00 45.82 2.66
145 146 6.145535 GTCACATCCAATTCAGTCTTGAAAC 58.854 40.000 0.00 0.00 45.82 2.78
146 147 5.241506 GGTCACATCCAATTCAGTCTTGAAA 59.758 40.000 0.00 0.00 45.82 2.69
147 148 4.761739 GGTCACATCCAATTCAGTCTTGAA 59.238 41.667 0.00 0.00 46.67 2.69
148 149 4.202451 TGGTCACATCCAATTCAGTCTTGA 60.202 41.667 0.00 0.00 34.24 3.02
149 150 4.074259 TGGTCACATCCAATTCAGTCTTG 58.926 43.478 0.00 0.00 34.24 3.02
150 151 4.330250 CTGGTCACATCCAATTCAGTCTT 58.670 43.478 0.00 0.00 37.01 3.01
151 152 3.871463 GCTGGTCACATCCAATTCAGTCT 60.871 47.826 0.00 0.00 37.01 3.24
152 153 2.421424 GCTGGTCACATCCAATTCAGTC 59.579 50.000 0.00 0.00 37.01 3.51
153 154 2.224843 TGCTGGTCACATCCAATTCAGT 60.225 45.455 0.00 0.00 37.01 3.41
154 155 2.439409 TGCTGGTCACATCCAATTCAG 58.561 47.619 0.00 0.00 37.01 3.02
155 156 2.583024 TGCTGGTCACATCCAATTCA 57.417 45.000 0.00 0.00 37.01 2.57
156 157 2.821969 ACTTGCTGGTCACATCCAATTC 59.178 45.455 0.00 0.00 37.01 2.17
157 158 2.880443 ACTTGCTGGTCACATCCAATT 58.120 42.857 0.00 0.00 37.01 2.32
158 159 2.592102 ACTTGCTGGTCACATCCAAT 57.408 45.000 0.00 0.00 37.01 3.16
159 160 2.778299 GTACTTGCTGGTCACATCCAA 58.222 47.619 0.00 0.00 37.01 3.53
160 161 1.337728 CGTACTTGCTGGTCACATCCA 60.338 52.381 0.00 0.00 36.00 3.41
161 162 1.067142 TCGTACTTGCTGGTCACATCC 60.067 52.381 0.00 0.00 0.00 3.51
162 163 2.263077 CTCGTACTTGCTGGTCACATC 58.737 52.381 0.00 0.00 0.00 3.06
163 164 1.066858 CCTCGTACTTGCTGGTCACAT 60.067 52.381 0.00 0.00 0.00 3.21
164 165 0.317160 CCTCGTACTTGCTGGTCACA 59.683 55.000 0.00 0.00 0.00 3.58
165 166 0.601558 TCCTCGTACTTGCTGGTCAC 59.398 55.000 0.00 0.00 0.00 3.67
166 167 0.601558 GTCCTCGTACTTGCTGGTCA 59.398 55.000 0.00 0.00 0.00 4.02
167 168 0.889306 AGTCCTCGTACTTGCTGGTC 59.111 55.000 0.00 0.00 0.00 4.02
168 169 2.211250 TAGTCCTCGTACTTGCTGGT 57.789 50.000 0.00 0.00 0.00 4.00
169 170 4.135306 TCTATAGTCCTCGTACTTGCTGG 58.865 47.826 0.00 0.00 0.00 4.85
170 171 5.694816 CATCTATAGTCCTCGTACTTGCTG 58.305 45.833 0.00 0.00 0.00 4.41
171 172 4.216687 GCATCTATAGTCCTCGTACTTGCT 59.783 45.833 0.00 0.00 29.59 3.91
172 173 4.023107 TGCATCTATAGTCCTCGTACTTGC 60.023 45.833 0.00 0.00 31.75 4.01
173 174 5.690997 TGCATCTATAGTCCTCGTACTTG 57.309 43.478 0.00 0.00 0.00 3.16
174 175 6.902771 ATTGCATCTATAGTCCTCGTACTT 57.097 37.500 0.00 0.00 0.00 2.24
175 176 6.902771 AATTGCATCTATAGTCCTCGTACT 57.097 37.500 0.00 0.00 0.00 2.73
176 177 8.679100 AGATAATTGCATCTATAGTCCTCGTAC 58.321 37.037 0.00 0.00 33.41 3.67
177 178 8.809468 AGATAATTGCATCTATAGTCCTCGTA 57.191 34.615 0.00 0.00 33.41 3.43
178 179 7.414651 CGAGATAATTGCATCTATAGTCCTCGT 60.415 40.741 0.00 0.00 35.37 4.18
179 180 6.909895 CGAGATAATTGCATCTATAGTCCTCG 59.090 42.308 0.00 0.00 35.37 4.63
180 181 7.199766 CCGAGATAATTGCATCTATAGTCCTC 58.800 42.308 0.00 0.00 35.37 3.71
181 182 6.406400 GCCGAGATAATTGCATCTATAGTCCT 60.406 42.308 0.00 0.00 35.37 3.85
182 183 5.751028 GCCGAGATAATTGCATCTATAGTCC 59.249 44.000 0.00 0.00 35.37 3.85
183 184 6.568869 AGCCGAGATAATTGCATCTATAGTC 58.431 40.000 0.00 0.00 35.37 2.59
184 185 6.537453 AGCCGAGATAATTGCATCTATAGT 57.463 37.500 0.00 0.00 35.37 2.12
185 186 8.932945 TTTAGCCGAGATAATTGCATCTATAG 57.067 34.615 0.00 0.00 35.37 1.31
186 187 9.719355 TTTTTAGCCGAGATAATTGCATCTATA 57.281 29.630 0.00 0.00 35.37 1.31
187 188 8.621532 TTTTTAGCCGAGATAATTGCATCTAT 57.378 30.769 0.00 0.00 35.37 1.98
189 190 6.942532 TTTTTAGCCGAGATAATTGCATCT 57.057 33.333 0.00 0.00 37.99 2.90
253 255 1.632589 GCAGTGGTTTTTCCCCTCAT 58.367 50.000 0.00 0.00 34.77 2.90
329 331 1.679032 CGAACCAAAGGAGGCCTTAGG 60.679 57.143 6.77 7.55 43.92 2.69
357 359 8.700973 GGCCCTATCCTATGAAAATTTTACAAA 58.299 33.333 2.75 0.00 0.00 2.83
363 365 5.376861 AGGAGGCCCTATCCTATGAAAATTT 59.623 40.000 10.28 0.00 45.58 1.82
364 366 4.922613 AGGAGGCCCTATCCTATGAAAATT 59.077 41.667 10.28 0.00 45.58 1.82
366 368 3.954662 AGGAGGCCCTATCCTATGAAAA 58.045 45.455 10.28 0.00 45.58 2.29
379 381 1.410224 CCTATGAACCAAAGGAGGCCC 60.410 57.143 0.00 0.00 31.64 5.80
419 427 6.814146 GTCATCTCACTTCCTACGATTTTTCT 59.186 38.462 0.00 0.00 0.00 2.52
420 428 6.590292 TGTCATCTCACTTCCTACGATTTTTC 59.410 38.462 0.00 0.00 0.00 2.29
421 429 6.464222 TGTCATCTCACTTCCTACGATTTTT 58.536 36.000 0.00 0.00 0.00 1.94
422 430 6.037786 TGTCATCTCACTTCCTACGATTTT 57.962 37.500 0.00 0.00 0.00 1.82
423 431 5.661056 TGTCATCTCACTTCCTACGATTT 57.339 39.130 0.00 0.00 0.00 2.17
424 432 5.595885 CATGTCATCTCACTTCCTACGATT 58.404 41.667 0.00 0.00 0.00 3.34
425 433 4.500545 GCATGTCATCTCACTTCCTACGAT 60.501 45.833 0.00 0.00 0.00 3.73
426 434 3.181486 GCATGTCATCTCACTTCCTACGA 60.181 47.826 0.00 0.00 0.00 3.43
427 435 3.119291 GCATGTCATCTCACTTCCTACG 58.881 50.000 0.00 0.00 0.00 3.51
456 464 7.623999 AATGGCATCTCTTTCTCTATAGGAA 57.376 36.000 0.00 0.00 0.00 3.36
463 471 4.338682 GCATCAAATGGCATCTCTTTCTCT 59.661 41.667 0.00 0.00 0.00 3.10
464 472 4.097437 TGCATCAAATGGCATCTCTTTCTC 59.903 41.667 0.00 0.00 34.58 2.87
465 473 4.021229 TGCATCAAATGGCATCTCTTTCT 58.979 39.130 0.00 0.00 34.58 2.52
466 474 4.380841 TGCATCAAATGGCATCTCTTTC 57.619 40.909 0.00 0.00 34.58 2.62
476 494 7.713734 ATTTCCTATCCTATGCATCAAATGG 57.286 36.000 0.19 0.08 0.00 3.16
493 511 8.826765 AGTCTAGACTCAATGGAAAATTTCCTA 58.173 33.333 23.52 11.80 43.58 2.94
499 517 9.965902 AACATTAGTCTAGACTCAATGGAAAAT 57.034 29.630 31.66 22.25 42.54 1.82
533 551 4.711355 GGAATCCATCCTTCACATTTTGGA 59.289 41.667 0.00 0.00 45.56 3.53
534 552 5.014808 GGAATCCATCCTTCACATTTTGG 57.985 43.478 0.00 0.00 45.56 3.28
575 594 7.791282 AGCCCTTTGATTTATAGGAATGGATTT 59.209 33.333 0.00 0.00 0.00 2.17
589 608 5.830799 ATTCCTTTGAAGCCCTTTGATTT 57.169 34.783 0.00 0.00 33.05 2.17
592 611 5.628797 AAAATTCCTTTGAAGCCCTTTGA 57.371 34.783 0.00 0.00 33.05 2.69
647 667 8.925700 GGCCTTCTTTAGTTTGTATGAATTTTG 58.074 33.333 0.00 0.00 0.00 2.44
648 668 8.870116 AGGCCTTCTTTAGTTTGTATGAATTTT 58.130 29.630 0.00 0.00 0.00 1.82
655 675 9.755122 AAATCTTAGGCCTTCTTTAGTTTGTAT 57.245 29.630 12.58 0.00 0.00 2.29
657 677 7.945109 AGAAATCTTAGGCCTTCTTTAGTTTGT 59.055 33.333 12.58 0.00 0.00 2.83
663 683 9.670442 TCCTATAGAAATCTTAGGCCTTCTTTA 57.330 33.333 12.58 5.24 33.85 1.85
700 720 9.346725 GATTTTATTACAAACCAAAGAGCTCTG 57.653 33.333 19.06 7.57 0.00 3.35
746 769 5.576563 TGTGAAGGTTGAAGGATAGGAAA 57.423 39.130 0.00 0.00 0.00 3.13
757 780 7.831691 TTTTCCTATGAAATGTGAAGGTTGA 57.168 32.000 0.00 0.00 40.08 3.18
814 837 5.768662 AGATGCCCTTTGATTCACATCATAG 59.231 40.000 13.54 1.71 39.28 2.23
892 915 8.950007 TGGAAAACCATAAGAATAGGAAAGTT 57.050 30.769 0.00 0.00 0.00 2.66
893 916 8.950007 TTGGAAAACCATAAGAATAGGAAAGT 57.050 30.769 0.00 0.00 0.00 2.66
903 926 8.966868 GGTTCATAAGATTGGAAAACCATAAGA 58.033 33.333 0.00 0.00 35.78 2.10
904 927 8.748412 TGGTTCATAAGATTGGAAAACCATAAG 58.252 33.333 0.00 0.00 39.64 1.73
905 928 8.657387 TGGTTCATAAGATTGGAAAACCATAA 57.343 30.769 0.00 0.00 39.64 1.90
906 929 8.657387 TTGGTTCATAAGATTGGAAAACCATA 57.343 30.769 5.03 0.00 42.88 2.74
907 930 7.552050 TTGGTTCATAAGATTGGAAAACCAT 57.448 32.000 5.03 0.00 42.88 3.55
908 931 6.985653 TTGGTTCATAAGATTGGAAAACCA 57.014 33.333 0.00 0.00 42.00 3.67
909 932 7.666623 TCTTTGGTTCATAAGATTGGAAAACC 58.333 34.615 0.00 0.00 36.16 3.27
910 933 9.196552 CTTCTTTGGTTCATAAGATTGGAAAAC 57.803 33.333 0.00 0.00 31.00 2.43
911 934 8.367156 CCTTCTTTGGTTCATAAGATTGGAAAA 58.633 33.333 0.00 0.00 31.59 2.29
912 935 7.525360 GCCTTCTTTGGTTCATAAGATTGGAAA 60.525 37.037 0.00 0.00 31.59 3.13
913 936 6.071391 GCCTTCTTTGGTTCATAAGATTGGAA 60.071 38.462 0.00 0.00 31.59 3.53
914 937 5.418840 GCCTTCTTTGGTTCATAAGATTGGA 59.581 40.000 0.00 0.00 31.59 3.53
915 938 5.394553 GGCCTTCTTTGGTTCATAAGATTGG 60.395 44.000 0.00 0.00 31.00 3.16
916 939 5.420104 AGGCCTTCTTTGGTTCATAAGATTG 59.580 40.000 0.00 0.00 31.00 2.67
917 940 5.583932 AGGCCTTCTTTGGTTCATAAGATT 58.416 37.500 0.00 0.00 31.00 2.40
918 941 5.198602 AGGCCTTCTTTGGTTCATAAGAT 57.801 39.130 0.00 0.00 31.00 2.40
919 942 4.657814 AGGCCTTCTTTGGTTCATAAGA 57.342 40.909 0.00 0.00 0.00 2.10
920 943 6.834168 TTTAGGCCTTCTTTGGTTCATAAG 57.166 37.500 12.58 0.00 0.00 1.73
921 944 7.182060 AGATTTAGGCCTTCTTTGGTTCATAA 58.818 34.615 12.58 0.00 0.00 1.90
922 945 6.731467 AGATTTAGGCCTTCTTTGGTTCATA 58.269 36.000 12.58 0.00 0.00 2.15
923 946 5.583932 AGATTTAGGCCTTCTTTGGTTCAT 58.416 37.500 12.58 0.00 0.00 2.57
924 947 4.998051 AGATTTAGGCCTTCTTTGGTTCA 58.002 39.130 12.58 0.00 0.00 3.18
925 948 5.984695 AAGATTTAGGCCTTCTTTGGTTC 57.015 39.130 12.58 0.00 0.00 3.62
926 949 6.239600 GGAAAAGATTTAGGCCTTCTTTGGTT 60.240 38.462 24.91 13.80 39.12 3.67
927 950 5.246203 GGAAAAGATTTAGGCCTTCTTTGGT 59.754 40.000 24.91 14.38 39.12 3.67
928 951 5.337571 GGGAAAAGATTTAGGCCTTCTTTGG 60.338 44.000 24.91 0.00 39.12 3.28
929 952 5.337571 GGGGAAAAGATTTAGGCCTTCTTTG 60.338 44.000 24.91 0.00 39.12 2.77
930 953 4.777896 GGGGAAAAGATTTAGGCCTTCTTT 59.222 41.667 20.60 20.60 40.47 2.52
931 954 4.353777 GGGGAAAAGATTTAGGCCTTCTT 58.646 43.478 12.58 12.03 0.00 2.52
932 955 3.309921 GGGGGAAAAGATTTAGGCCTTCT 60.310 47.826 12.58 4.72 0.00 2.85
933 956 3.031736 GGGGGAAAAGATTTAGGCCTTC 58.968 50.000 12.58 1.59 0.00 3.46
934 957 2.660038 AGGGGGAAAAGATTTAGGCCTT 59.340 45.455 12.58 0.00 0.00 4.35
935 958 2.297997 AGGGGGAAAAGATTTAGGCCT 58.702 47.619 11.78 11.78 0.00 5.19
936 959 2.848678 AGGGGGAAAAGATTTAGGCC 57.151 50.000 0.00 0.00 0.00 5.19
937 960 4.207955 CTGTAGGGGGAAAAGATTTAGGC 58.792 47.826 0.00 0.00 0.00 3.93
1855 1899 0.613260 GAAGGCAAAATTCCACCCCC 59.387 55.000 0.00 0.00 0.00 5.40


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

AutoCloner maintained by Alex Coulton.