Multiple sequence alignment - TraesCS1A01G367400

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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 TraesCS1A01G367400 chr1A 100.000 3389 0 0 1 3389 545907191 545910579 0.000000e+00 6259.0
1 TraesCS1A01G367400 chr1A 82.172 1335 210 19 1157 2471 545897009 545898335 0.000000e+00 1122.0
2 TraesCS1A01G367400 chr1A 88.009 442 37 5 343 778 545896260 545896691 3.020000e-140 508.0
3 TraesCS1A01G367400 chr1A 91.275 298 24 2 3045 3340 137859673 137859376 4.070000e-109 405.0
4 TraesCS1A01G367400 chr1A 87.967 241 22 3 543 778 516149410 516149172 9.260000e-71 278.0
5 TraesCS1A01G367400 chr1A 86.531 245 29 1 1 245 482816322 482816562 2.000000e-67 267.0
6 TraesCS1A01G367400 chr1A 92.308 130 9 1 995 1124 545896880 545897008 2.080000e-42 183.0
7 TraesCS1A01G367400 chr1D 95.244 2334 75 10 263 2592 451194536 451196837 0.000000e+00 3663.0
8 TraesCS1A01G367400 chr1D 84.229 1674 224 20 816 2471 451244089 451245740 0.000000e+00 1592.0
9 TraesCS1A01G367400 chr1D 84.038 1491 208 17 995 2471 451140962 451142436 0.000000e+00 1408.0
10 TraesCS1A01G367400 chr1D 86.652 442 43 5 343 778 451140263 451140694 3.060000e-130 475.0
11 TraesCS1A01G367400 chr1D 96.364 220 8 0 2583 2802 451213273 451213492 2.490000e-96 363.0
12 TraesCS1A01G367400 chr1D 90.299 134 13 0 19 152 454481475 454481342 3.480000e-40 176.0
13 TraesCS1A01G367400 chr1D 97.297 37 1 0 3346 3382 436338095 436338131 2.820000e-06 63.9
14 TraesCS1A01G367400 chr1B 93.000 1800 104 10 1010 2802 619430629 619432413 0.000000e+00 2606.0
15 TraesCS1A01G367400 chr1B 86.728 2170 207 42 266 2398 619535143 619537268 0.000000e+00 2337.0
16 TraesCS1A01G367400 chr1B 90.895 1296 94 10 911 2196 619544903 619546184 0.000000e+00 1718.0
17 TraesCS1A01G367400 chr1B 83.166 1491 213 23 999 2471 619529576 619531046 0.000000e+00 1328.0
18 TraesCS1A01G367400 chr1B 87.733 375 37 4 343 716 619430168 619430534 2.420000e-116 429.0
19 TraesCS1A01G367400 chr1B 85.082 429 44 10 343 764 619528862 619529277 1.450000e-113 420.0
20 TraesCS1A01G367400 chr1B 94.175 206 12 0 2192 2397 619550240 619550445 7.060000e-82 315.0
21 TraesCS1A01G367400 chr1B 87.755 196 13 6 2438 2627 619537264 619537454 5.690000e-53 219.0
22 TraesCS1A01G367400 chr7D 91.376 487 37 5 2907 3389 208819742 208819257 0.000000e+00 662.0
23 TraesCS1A01G367400 chr7D 89.474 247 26 0 1 247 528890561 528890807 2.540000e-81 313.0
24 TraesCS1A01G367400 chr2B 92.183 371 23 5 3021 3387 326496643 326497011 1.390000e-143 520.0
25 TraesCS1A01G367400 chr2B 90.000 200 16 4 2907 3104 667819012 667818815 4.340000e-64 255.0
26 TraesCS1A01G367400 chr2B 96.154 78 2 1 2812 2888 667819078 667819001 3.550000e-25 126.0
27 TraesCS1A01G367400 chr4B 90.411 365 25 5 2907 3269 391565131 391565487 3.960000e-129 472.0
28 TraesCS1A01G367400 chr4B 92.222 180 12 2 2627 2805 484011304 484011126 1.560000e-63 254.0
29 TraesCS1A01G367400 chr4B 92.000 125 6 1 3263 3387 391565595 391565715 4.500000e-39 172.0
30 TraesCS1A01G367400 chr4B 95.062 81 3 1 2809 2888 391565062 391565142 3.550000e-25 126.0
31 TraesCS1A01G367400 chr7A 92.580 283 20 1 3105 3387 221746405 221746686 4.070000e-109 405.0
32 TraesCS1A01G367400 chr7A 90.865 208 16 3 2907 3111 221747627 221747420 3.330000e-70 276.0
33 TraesCS1A01G367400 chr7A 84.211 247 31 6 1 247 501656226 501656464 2.030000e-57 233.0
34 TraesCS1A01G367400 chr2D 91.525 295 23 2 3045 3337 395592267 395592561 4.070000e-109 405.0
35 TraesCS1A01G367400 chr2D 97.321 112 3 0 2678 2789 476331496 476331385 1.240000e-44 191.0
36 TraesCS1A01G367400 chr2D 94.118 68 4 0 2809 2876 190401250 190401317 1.660000e-18 104.0
37 TraesCS1A01G367400 chr2D 95.918 49 2 0 3341 3389 395593362 395593410 2.800000e-11 80.5
38 TraesCS1A01G367400 chr5A 71.591 1232 302 34 1196 2405 588561035 588562240 3.310000e-75 292.0
39 TraesCS1A01G367400 chr5A 87.705 244 30 0 2 245 645423035 645422792 5.530000e-73 285.0
40 TraesCS1A01G367400 chr5A 88.382 241 21 3 543 778 364529075 364529313 1.990000e-72 283.0
41 TraesCS1A01G367400 chr5A 94.118 68 4 0 2809 2876 180348131 180348198 1.660000e-18 104.0
42 TraesCS1A01G367400 chr6B 88.703 239 20 3 545 778 94140367 94140131 5.530000e-73 285.0
43 TraesCS1A01G367400 chr6B 86.636 217 27 2 1 216 507370414 507370199 4.370000e-59 239.0
44 TraesCS1A01G367400 chr6D 88.382 241 21 3 543 778 318999482 318999244 1.990000e-72 283.0
45 TraesCS1A01G367400 chr6D 86.400 250 32 2 1 249 88871266 88871514 4.310000e-69 272.0
46 TraesCS1A01G367400 chr6D 95.385 65 3 0 2812 2876 7899365 7899301 1.660000e-18 104.0
47 TraesCS1A01G367400 chr6D 94.118 68 4 0 2809 2876 142859531 142859598 1.660000e-18 104.0
48 TraesCS1A01G367400 chr5B 88.655 238 20 3 546 778 673112319 673112084 1.990000e-72 283.0
49 TraesCS1A01G367400 chr5B 95.312 64 3 0 2812 2875 405976595 405976532 5.980000e-18 102.0
50 TraesCS1A01G367400 chr3B 92.778 180 11 2 2627 2805 457424946 457424768 3.350000e-65 259.0
51 TraesCS1A01G367400 chr7B 92.222 180 13 1 2627 2805 39921156 39920977 1.560000e-63 254.0
52 TraesCS1A01G367400 chr7B 91.620 179 14 1 2627 2805 417038530 417038353 2.610000e-61 246.0
53 TraesCS1A01G367400 chr7B 87.151 179 17 5 2627 2805 473410647 473410475 7.420000e-47 198.0
54 TraesCS1A01G367400 chr7B 96.875 64 2 0 2812 2875 446193470 446193407 1.290000e-19 108.0
55 TraesCS1A01G367400 chr3D 93.252 163 10 1 2635 2796 96007152 96007314 4.370000e-59 239.0
56 TraesCS1A01G367400 chr3D 94.118 68 4 0 2809 2876 167405889 167405956 1.660000e-18 104.0
57 TraesCS1A01G367400 chr6A 85.938 192 27 0 2 193 77021283 77021474 4.430000e-49 206.0
58 TraesCS1A01G367400 chr2A 77.054 353 64 14 2057 2399 582840998 582841343 1.610000e-43 187.0
59 TraesCS1A01G367400 chr5D 97.297 37 1 0 3346 3382 25045922 25045886 2.820000e-06 63.9
60 TraesCS1A01G367400 chr5D 97.297 37 1 0 3346 3382 276296014 276295978 2.820000e-06 63.9
61 TraesCS1A01G367400 chr4D 97.297 37 1 0 3346 3382 492818911 492818875 2.820000e-06 63.9


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 TraesCS1A01G367400 chr1A 545907191 545910579 3388 False 6259.000000 6259 100.000000 1 3389 1 chr1A.!!$F2 3388
1 TraesCS1A01G367400 chr1A 545896260 545898335 2075 False 604.333333 1122 87.496333 343 2471 3 chr1A.!!$F3 2128
2 TraesCS1A01G367400 chr1D 451194536 451196837 2301 False 3663.000000 3663 95.244000 263 2592 1 chr1D.!!$F2 2329
3 TraesCS1A01G367400 chr1D 451244089 451245740 1651 False 1592.000000 1592 84.229000 816 2471 1 chr1D.!!$F4 1655
4 TraesCS1A01G367400 chr1D 451140263 451142436 2173 False 941.500000 1408 85.345000 343 2471 2 chr1D.!!$F5 2128
5 TraesCS1A01G367400 chr1B 619544903 619546184 1281 False 1718.000000 1718 90.895000 911 2196 1 chr1B.!!$F1 1285
6 TraesCS1A01G367400 chr1B 619430168 619432413 2245 False 1517.500000 2606 90.366500 343 2802 2 chr1B.!!$F3 2459
7 TraesCS1A01G367400 chr1B 619535143 619537454 2311 False 1278.000000 2337 87.241500 266 2627 2 chr1B.!!$F5 2361
8 TraesCS1A01G367400 chr1B 619528862 619531046 2184 False 874.000000 1328 84.124000 343 2471 2 chr1B.!!$F4 2128
9 TraesCS1A01G367400 chr4B 391565062 391565715 653 False 256.666667 472 92.491000 2809 3387 3 chr4B.!!$F1 578
10 TraesCS1A01G367400 chr2D 395592267 395593410 1143 False 242.750000 405 93.721500 3045 3389 2 chr2D.!!$F2 344
11 TraesCS1A01G367400 chr5A 588561035 588562240 1205 False 292.000000 292 71.591000 1196 2405 1 chr5A.!!$F3 1209

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
86 87 0.032130 CGGAGCTCAGGCGCTAAATA 59.968 55.0 17.19 0.0 41.08 1.40 F
1045 1212 0.033504 GTCAGAACTCCCGCAAGACA 59.966 55.0 0.00 0.0 43.02 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1553 1729 0.458370 CATGACAGCGACGATGTCCA 60.458 55.0 35.21 25.42 46.70 4.02 R
2925 3121 0.248565 AGCTTGAAGCAGAGCGATGA 59.751 50.0 20.45 0.00 45.56 2.92 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
41 42 3.284449 GGCGCACGGGACACTTTT 61.284 61.111 10.83 0.00 0.00 2.27
42 43 2.251371 GCGCACGGGACACTTTTC 59.749 61.111 0.30 0.00 0.00 2.29
43 44 2.539338 GCGCACGGGACACTTTTCA 61.539 57.895 0.30 0.00 0.00 2.69
44 45 1.278637 CGCACGGGACACTTTTCAC 59.721 57.895 0.00 0.00 0.00 3.18
48 49 1.278637 CGGGACACTTTTCACGTGC 59.721 57.895 11.67 0.00 37.64 5.34
49 50 1.278637 GGGACACTTTTCACGTGCG 59.721 57.895 11.67 1.50 35.84 5.34
50 51 1.433837 GGGACACTTTTCACGTGCGT 61.434 55.000 11.67 2.18 35.84 5.24
51 52 0.315869 GGACACTTTTCACGTGCGTG 60.316 55.000 17.44 17.44 46.64 5.34
61 62 2.886859 ACGTGCGTGAGAAGTTCAG 58.113 52.632 5.50 0.00 36.21 3.02
62 63 1.215655 ACGTGCGTGAGAAGTTCAGC 61.216 55.000 5.50 5.76 36.21 4.26
63 64 1.488957 GTGCGTGAGAAGTTCAGCG 59.511 57.895 5.50 7.42 36.21 5.18
64 65 2.310233 TGCGTGAGAAGTTCAGCGC 61.310 57.895 22.71 22.71 46.67 5.92
65 66 2.765785 CGTGAGAAGTTCAGCGCG 59.234 61.111 14.37 14.37 36.21 6.86
66 67 2.472049 GTGAGAAGTTCAGCGCGC 59.528 61.111 26.66 26.66 36.21 6.86
67 68 2.738521 TGAGAAGTTCAGCGCGCC 60.739 61.111 30.33 12.88 0.00 6.53
68 69 3.843240 GAGAAGTTCAGCGCGCCG 61.843 66.667 30.33 19.82 0.00 6.46
83 84 3.838271 CCGGAGCTCAGGCGCTAA 61.838 66.667 20.34 0.00 41.08 3.09
84 85 2.184322 CGGAGCTCAGGCGCTAAA 59.816 61.111 17.19 0.00 41.08 1.85
85 86 1.227380 CGGAGCTCAGGCGCTAAAT 60.227 57.895 17.19 0.00 41.08 1.40
86 87 0.032130 CGGAGCTCAGGCGCTAAATA 59.968 55.000 17.19 0.00 41.08 1.40
87 88 1.337260 CGGAGCTCAGGCGCTAAATAT 60.337 52.381 17.19 0.00 41.08 1.28
88 89 2.094700 CGGAGCTCAGGCGCTAAATATA 60.095 50.000 17.19 0.00 41.08 0.86
89 90 3.254892 GGAGCTCAGGCGCTAAATATAC 58.745 50.000 17.19 0.00 41.08 1.47
90 91 2.917971 GAGCTCAGGCGCTAAATATACG 59.082 50.000 9.40 0.00 41.08 3.06
91 92 1.993370 GCTCAGGCGCTAAATATACGG 59.007 52.381 7.64 0.00 0.00 4.02
92 93 2.609737 GCTCAGGCGCTAAATATACGGT 60.610 50.000 7.64 0.00 0.00 4.83
93 94 3.650139 CTCAGGCGCTAAATATACGGTT 58.350 45.455 7.64 0.00 0.00 4.44
94 95 4.056050 CTCAGGCGCTAAATATACGGTTT 58.944 43.478 7.64 0.00 0.00 3.27
95 96 3.805422 TCAGGCGCTAAATATACGGTTTG 59.195 43.478 7.64 0.00 0.00 2.93
96 97 2.546789 AGGCGCTAAATATACGGTTTGC 59.453 45.455 7.64 0.00 0.00 3.68
97 98 2.556806 GCGCTAAATATACGGTTTGCG 58.443 47.619 0.00 13.35 38.20 4.85
98 99 2.219216 GCGCTAAATATACGGTTTGCGA 59.781 45.455 18.60 0.00 37.81 5.10
99 100 3.120786 GCGCTAAATATACGGTTTGCGAT 60.121 43.478 18.60 0.00 37.81 4.58
100 101 4.625135 CGCTAAATATACGGTTTGCGATC 58.375 43.478 12.74 0.00 37.81 3.69
101 102 4.433805 CGCTAAATATACGGTTTGCGATCC 60.434 45.833 12.74 0.00 37.81 3.36
102 103 4.449743 GCTAAATATACGGTTTGCGATCCA 59.550 41.667 1.94 0.00 0.00 3.41
103 104 5.049954 GCTAAATATACGGTTTGCGATCCAA 60.050 40.000 1.94 0.00 0.00 3.53
104 105 6.348213 GCTAAATATACGGTTTGCGATCCAAT 60.348 38.462 1.94 0.00 32.49 3.16
105 106 6.385649 AAATATACGGTTTGCGATCCAATT 57.614 33.333 1.94 0.00 32.49 2.32
106 107 3.963383 ATACGGTTTGCGATCCAATTC 57.037 42.857 1.94 0.00 32.49 2.17
107 108 0.808755 ACGGTTTGCGATCCAATTCC 59.191 50.000 1.94 4.12 32.49 3.01
108 109 0.248054 CGGTTTGCGATCCAATTCCG 60.248 55.000 17.27 17.27 41.29 4.30
109 110 0.808755 GGTTTGCGATCCAATTCCGT 59.191 50.000 0.00 0.00 32.49 4.69
110 111 1.202143 GGTTTGCGATCCAATTCCGTC 60.202 52.381 0.00 0.00 32.49 4.79
111 112 1.091537 TTTGCGATCCAATTCCGTCC 58.908 50.000 0.00 0.00 32.49 4.79
112 113 1.087202 TTGCGATCCAATTCCGTCCG 61.087 55.000 0.00 0.00 0.00 4.79
113 114 2.244651 GCGATCCAATTCCGTCCGG 61.245 63.158 0.00 0.00 0.00 5.14
114 115 2.244651 CGATCCAATTCCGTCCGGC 61.245 63.158 0.00 0.00 34.68 6.13
115 116 2.203015 ATCCAATTCCGTCCGGCG 60.203 61.111 10.75 10.75 40.95 6.46
125 126 4.143363 GTCCGGCGCGCTAAACAC 62.143 66.667 32.29 16.27 0.00 3.32
126 127 4.367023 TCCGGCGCGCTAAACACT 62.367 61.111 32.29 0.00 0.00 3.55
127 128 3.419759 CCGGCGCGCTAAACACTT 61.420 61.111 32.29 0.00 0.00 3.16
128 129 2.554272 CGGCGCGCTAAACACTTT 59.446 55.556 32.29 0.00 0.00 2.66
129 130 1.082366 CGGCGCGCTAAACACTTTT 60.082 52.632 32.29 0.00 0.00 2.27
130 131 0.659123 CGGCGCGCTAAACACTTTTT 60.659 50.000 32.29 0.00 0.00 1.94
131 132 1.398705 CGGCGCGCTAAACACTTTTTA 60.399 47.619 32.29 0.00 0.00 1.52
132 133 1.974000 GGCGCGCTAAACACTTTTTAC 59.026 47.619 32.29 4.57 0.00 2.01
133 134 2.602694 GGCGCGCTAAACACTTTTTACA 60.603 45.455 32.29 0.00 0.00 2.41
134 135 2.650297 GCGCGCTAAACACTTTTTACAG 59.350 45.455 26.67 0.00 0.00 2.74
135 136 3.223157 CGCGCTAAACACTTTTTACAGG 58.777 45.455 5.56 0.00 0.00 4.00
136 137 3.059461 CGCGCTAAACACTTTTTACAGGA 60.059 43.478 5.56 0.00 0.00 3.86
137 138 4.378046 CGCGCTAAACACTTTTTACAGGAT 60.378 41.667 5.56 0.00 0.00 3.24
138 139 4.851558 GCGCTAAACACTTTTTACAGGATG 59.148 41.667 0.00 0.00 46.00 3.51
139 140 4.851558 CGCTAAACACTTTTTACAGGATGC 59.148 41.667 0.00 0.00 42.53 3.91
140 141 5.334879 CGCTAAACACTTTTTACAGGATGCT 60.335 40.000 0.00 0.00 42.53 3.79
141 142 6.447162 GCTAAACACTTTTTACAGGATGCTT 58.553 36.000 0.00 0.00 42.53 3.91
142 143 6.923508 GCTAAACACTTTTTACAGGATGCTTT 59.076 34.615 0.00 0.00 42.53 3.51
143 144 8.079809 GCTAAACACTTTTTACAGGATGCTTTA 58.920 33.333 0.00 0.00 42.53 1.85
153 154 7.652300 TTACAGGATGCTTTATTATGTAGCG 57.348 36.000 0.00 0.00 42.53 4.26
154 155 4.452455 ACAGGATGCTTTATTATGTAGCGC 59.548 41.667 0.00 0.00 42.53 5.92
155 156 4.452114 CAGGATGCTTTATTATGTAGCGCA 59.548 41.667 11.47 0.00 37.73 6.09
156 157 4.452455 AGGATGCTTTATTATGTAGCGCAC 59.548 41.667 11.47 6.60 37.73 5.34
157 158 3.852471 TGCTTTATTATGTAGCGCACG 57.148 42.857 11.47 0.00 37.73 5.34
158 159 2.033236 TGCTTTATTATGTAGCGCACGC 60.033 45.455 11.47 6.99 37.73 5.34
168 169 3.240203 GCGCACGCTGAAGTGTTA 58.760 55.556 7.96 0.00 43.61 2.41
169 170 1.787847 GCGCACGCTGAAGTGTTAT 59.212 52.632 7.96 0.00 43.61 1.89
170 171 0.165944 GCGCACGCTGAAGTGTTATT 59.834 50.000 7.96 0.00 43.61 1.40
171 172 1.399727 GCGCACGCTGAAGTGTTATTT 60.400 47.619 7.96 0.00 43.61 1.40
172 173 2.916111 CGCACGCTGAAGTGTTATTTT 58.084 42.857 0.00 0.00 43.61 1.82
173 174 2.902484 CGCACGCTGAAGTGTTATTTTC 59.098 45.455 0.00 0.00 43.61 2.29
174 175 3.605922 CGCACGCTGAAGTGTTATTTTCA 60.606 43.478 0.00 0.00 43.61 2.69
175 176 4.286910 GCACGCTGAAGTGTTATTTTCAA 58.713 39.130 0.00 0.00 43.61 2.69
176 177 4.146443 GCACGCTGAAGTGTTATTTTCAAC 59.854 41.667 0.00 0.00 43.61 3.18
177 178 5.510671 CACGCTGAAGTGTTATTTTCAACT 58.489 37.500 0.00 0.00 36.50 3.16
178 179 5.621228 CACGCTGAAGTGTTATTTTCAACTC 59.379 40.000 0.00 0.00 36.50 3.01
179 180 5.147162 CGCTGAAGTGTTATTTTCAACTCC 58.853 41.667 0.00 0.00 33.30 3.85
180 181 5.147162 GCTGAAGTGTTATTTTCAACTCCG 58.853 41.667 0.00 0.00 33.30 4.63
181 182 5.103290 TGAAGTGTTATTTTCAACTCCGC 57.897 39.130 0.00 0.00 30.84 5.54
182 183 3.806316 AGTGTTATTTTCAACTCCGCG 57.194 42.857 0.00 0.00 0.00 6.46
183 184 2.095919 AGTGTTATTTTCAACTCCGCGC 60.096 45.455 0.00 0.00 0.00 6.86
184 185 1.136197 TGTTATTTTCAACTCCGCGCG 60.136 47.619 25.67 25.67 0.00 6.86
185 186 0.179210 TTATTTTCAACTCCGCGCGC 60.179 50.000 27.36 23.91 0.00 6.86
186 187 2.286349 TATTTTCAACTCCGCGCGCG 62.286 55.000 43.73 43.73 39.44 6.86
189 190 4.703799 TCAACTCCGCGCGCGTTA 62.704 61.111 45.51 33.45 37.81 3.18
190 191 3.769358 CAACTCCGCGCGCGTTAA 61.769 61.111 45.51 31.01 37.81 2.01
191 192 3.037249 AACTCCGCGCGCGTTAAA 61.037 55.556 45.51 28.65 37.81 1.52
192 193 3.285776 AACTCCGCGCGCGTTAAAC 62.286 57.895 45.51 13.26 37.81 2.01
193 194 3.475774 CTCCGCGCGCGTTAAACT 61.476 61.111 45.51 0.00 37.81 2.66
194 195 3.007070 CTCCGCGCGCGTTAAACTT 62.007 57.895 45.51 0.00 37.81 2.66
195 196 2.863347 CCGCGCGCGTTAAACTTG 60.863 61.111 45.51 27.46 37.81 3.16
196 197 3.511582 CGCGCGCGTTAAACTTGC 61.512 61.111 42.49 10.01 34.35 4.01
206 207 5.304211 GCGTTAAACTTGCGAATTTTTGA 57.696 34.783 0.00 0.00 0.00 2.69
207 208 5.354692 GCGTTAAACTTGCGAATTTTTGAG 58.645 37.500 0.00 0.00 0.00 3.02
208 209 5.354692 CGTTAAACTTGCGAATTTTTGAGC 58.645 37.500 0.00 0.00 0.00 4.26
209 210 5.052040 CGTTAAACTTGCGAATTTTTGAGCA 60.052 36.000 0.00 0.00 37.89 4.26
210 211 4.777140 AAACTTGCGAATTTTTGAGCAC 57.223 36.364 0.00 0.00 39.51 4.40
211 212 2.384382 ACTTGCGAATTTTTGAGCACG 58.616 42.857 0.00 0.00 39.51 5.34
212 213 1.715519 CTTGCGAATTTTTGAGCACGG 59.284 47.619 0.00 0.00 39.51 4.94
213 214 0.662970 TGCGAATTTTTGAGCACGGC 60.663 50.000 0.00 0.00 34.39 5.68
214 215 1.664643 GCGAATTTTTGAGCACGGCG 61.665 55.000 4.80 4.80 0.00 6.46
215 216 1.664643 CGAATTTTTGAGCACGGCGC 61.665 55.000 6.90 0.00 42.91 6.53
226 227 0.110644 GCACGGCGCTAATATTGAGC 60.111 55.000 6.90 2.93 37.77 4.26
237 238 6.683090 GCTAATATTGAGCGTCTGTTAGAG 57.317 41.667 0.00 0.00 0.00 2.43
238 239 6.439599 GCTAATATTGAGCGTCTGTTAGAGA 58.560 40.000 0.00 0.00 0.00 3.10
239 240 7.087639 GCTAATATTGAGCGTCTGTTAGAGAT 58.912 38.462 0.00 0.00 31.63 2.75
240 241 8.237949 GCTAATATTGAGCGTCTGTTAGAGATA 58.762 37.037 0.00 0.00 31.63 1.98
241 242 9.549509 CTAATATTGAGCGTCTGTTAGAGATAC 57.450 37.037 0.00 0.00 31.63 2.24
242 243 7.753309 ATATTGAGCGTCTGTTAGAGATACT 57.247 36.000 0.00 0.00 31.63 2.12
243 244 5.487153 TTGAGCGTCTGTTAGAGATACTC 57.513 43.478 5.18 5.18 36.62 2.59
244 245 4.771903 TGAGCGTCTGTTAGAGATACTCT 58.228 43.478 11.01 6.53 43.83 3.24
245 246 5.915175 TGAGCGTCTGTTAGAGATACTCTA 58.085 41.667 11.01 4.64 41.50 2.43
246 247 6.346896 TGAGCGTCTGTTAGAGATACTCTAA 58.653 40.000 14.63 14.63 46.70 2.10
258 259 7.652524 AGAGATACTCTAAAGCTTCACATGA 57.347 36.000 0.00 0.00 39.28 3.07
259 260 7.488322 AGAGATACTCTAAAGCTTCACATGAC 58.512 38.462 0.00 0.00 39.28 3.06
260 261 7.123397 AGAGATACTCTAAAGCTTCACATGACA 59.877 37.037 0.00 0.00 39.28 3.58
261 262 7.790027 AGATACTCTAAAGCTTCACATGACAT 58.210 34.615 0.00 0.00 0.00 3.06
272 273 7.112122 AGCTTCACATGACATAACTTTGGATA 58.888 34.615 0.00 0.00 0.00 2.59
329 330 1.066071 GGAGTTGCCCTACTCAGTTCC 60.066 57.143 11.00 0.00 45.07 3.62
333 334 1.742308 TGCCCTACTCAGTTCCCTTT 58.258 50.000 0.00 0.00 0.00 3.11
334 335 2.062636 TGCCCTACTCAGTTCCCTTTT 58.937 47.619 0.00 0.00 0.00 2.27
336 337 2.039879 GCCCTACTCAGTTCCCTTTTGA 59.960 50.000 0.00 0.00 0.00 2.69
340 341 1.141053 ACTCAGTTCCCTTTTGAGCGT 59.859 47.619 0.94 0.00 41.52 5.07
341 342 2.222027 CTCAGTTCCCTTTTGAGCGTT 58.778 47.619 0.00 0.00 32.78 4.84
522 524 1.227853 GTGGTGGACTGGTGGTGAC 60.228 63.158 0.00 0.00 0.00 3.67
541 543 2.282251 TCCTCCGTGAGCGAGTGT 60.282 61.111 0.00 0.00 41.33 3.55
742 748 2.070039 CCGGTATCTCCTTGGGGCA 61.070 63.158 0.00 0.00 0.00 5.36
865 1026 2.247267 GTGTTCGTTCGCGTTGGG 59.753 61.111 5.77 0.00 42.11 4.12
915 1077 7.226720 GTCAAATTCGGAAGCAATCTATCCTTA 59.773 37.037 0.00 0.00 0.00 2.69
960 1126 2.967397 CCCCGACTACACGCTTGA 59.033 61.111 0.00 0.00 0.00 3.02
961 1127 1.445582 CCCCGACTACACGCTTGAC 60.446 63.158 0.00 0.00 0.00 3.18
962 1128 1.287815 CCCGACTACACGCTTGACA 59.712 57.895 0.00 0.00 0.00 3.58
963 1129 1.007336 CCCGACTACACGCTTGACAC 61.007 60.000 0.00 0.00 0.00 3.67
964 1130 0.318360 CCGACTACACGCTTGACACA 60.318 55.000 0.00 0.00 0.00 3.72
1045 1212 0.033504 GTCAGAACTCCCGCAAGACA 59.966 55.000 0.00 0.00 43.02 3.41
1164 1331 2.084546 GCTAAACCCGCTGACTTCAAT 58.915 47.619 0.00 0.00 0.00 2.57
1169 1336 1.017387 CCCGCTGACTTCAATAAGGC 58.983 55.000 0.00 0.00 41.59 4.35
1275 1448 3.825160 TTCGGCTTCACGGCAGCTT 62.825 57.895 0.00 0.00 37.43 3.74
1310 1486 1.068748 GTCAGACGGCTCGTTCTACAA 60.069 52.381 0.00 0.00 41.37 2.41
1478 1654 0.671781 GGCATCACTGTGTCGCTTCT 60.672 55.000 18.52 0.00 0.00 2.85
1831 2017 1.817941 AGTGTGTGGCGCGAAGTTT 60.818 52.632 12.10 0.00 0.00 2.66
1935 2124 2.477176 CGAGGACTCTGAGGAGCGG 61.477 68.421 9.85 0.00 42.98 5.52
2012 2204 5.698741 ACATGGTTAGATGATGAGGTTCA 57.301 39.130 0.00 0.00 0.00 3.18
2126 2318 9.413048 GCCTCAATATAGTATCAACTTCACTAC 57.587 37.037 0.00 0.00 37.15 2.73
2223 2415 5.464030 AAGCACTTTTCATCAGCAGATTT 57.536 34.783 0.00 0.00 30.20 2.17
2580 2775 4.745125 CAGATCAATTTCCATGCTTCATGC 59.255 41.667 0.00 0.00 40.20 4.06
2644 2839 6.149474 AGTTCTAATGAAATATACATGCCGCC 59.851 38.462 0.00 0.00 33.52 6.13
2651 2846 0.250295 TATACATGCCGCCCAGAAGC 60.250 55.000 0.00 0.00 0.00 3.86
2656 2851 1.987807 ATGCCGCCCAGAAGCTATGT 61.988 55.000 0.00 0.00 0.00 2.29
2658 2853 0.035458 GCCGCCCAGAAGCTATGTAT 59.965 55.000 0.00 0.00 0.00 2.29
2660 2855 1.609061 CCGCCCAGAAGCTATGTATGG 60.609 57.143 0.00 0.00 0.00 2.74
2752 2947 9.934190 ATGAAAAATAAACATTTGCACTTGTTC 57.066 25.926 12.48 1.80 35.09 3.18
2802 2997 6.183360 GCTCCTTCTCTTTCTGTTGATTGATC 60.183 42.308 0.00 0.00 0.00 2.92
2803 2998 6.772605 TCCTTCTCTTTCTGTTGATTGATCA 58.227 36.000 0.00 0.00 34.44 2.92
2804 2999 7.400439 TCCTTCTCTTTCTGTTGATTGATCAT 58.600 34.615 0.00 0.00 36.56 2.45
2805 3000 8.542926 TCCTTCTCTTTCTGTTGATTGATCATA 58.457 33.333 0.00 0.00 36.56 2.15
2806 3001 9.339850 CCTTCTCTTTCTGTTGATTGATCATAT 57.660 33.333 0.00 0.00 36.56 1.78
2810 3005 9.932699 CTCTTTCTGTTGATTGATCATATGAAC 57.067 33.333 9.99 7.84 36.56 3.18
2820 3015 8.909923 TGATTGATCATATGAACAAAAGAGCAT 58.090 29.630 26.19 12.33 39.64 3.79
2891 3087 7.867445 CTGTTTTTGACTTACAGTGTTGTTT 57.133 32.000 0.00 0.00 38.76 2.83
2892 3088 8.293114 CTGTTTTTGACTTACAGTGTTGTTTT 57.707 30.769 0.00 0.00 38.76 2.43
2893 3089 8.649973 TGTTTTTGACTTACAGTGTTGTTTTT 57.350 26.923 0.00 0.00 38.76 1.94
2925 3121 5.400066 AAAACTTACAGTGTTGTTTGGCT 57.600 34.783 20.33 8.61 38.76 4.75
2929 3125 4.275936 ACTTACAGTGTTGTTTGGCTCATC 59.724 41.667 0.00 0.00 38.76 2.92
2952 3148 1.966354 TCTGCTTCAAGCTCTCACTGA 59.034 47.619 11.57 0.00 42.97 3.41
2953 3149 2.566279 TCTGCTTCAAGCTCTCACTGAT 59.434 45.455 11.57 0.00 42.97 2.90
2955 3151 2.008329 GCTTCAAGCTCTCACTGATGG 58.992 52.381 0.71 0.00 38.45 3.51
2997 3193 1.658994 GACGTGTCCAAACCAACAGA 58.341 50.000 0.00 0.00 0.00 3.41
3015 3211 3.661944 CAGAGTTGTGAATGAGCTCTGT 58.338 45.455 16.19 1.89 44.64 3.41
3091 3288 2.358267 GCTAGGTAGCGTGTCACTGTAT 59.642 50.000 0.65 0.00 39.82 2.29
3115 3313 4.141711 TGTGTATGTCTATTCCTTCTGCCC 60.142 45.833 0.00 0.00 0.00 5.36
3131 3329 3.132289 TCTGCCCTTTTCCTATCTGTACG 59.868 47.826 0.00 0.00 0.00 3.67
3156 3354 3.042887 GGAGAAAAATGCACACGTGTTC 58.957 45.455 20.79 15.89 0.00 3.18
3184 3382 5.177326 TGCATTTGACAATTCCATTTAGGC 58.823 37.500 0.00 0.00 37.29 3.93
3277 3589 7.119846 GTGATGTCCATGAATACTATTAAGGCC 59.880 40.741 0.00 0.00 0.00 5.19
3337 3649 6.017605 GGAGAATAAGGCATACATGTTGTCAG 60.018 42.308 2.30 0.00 0.00 3.51
3340 3652 3.988976 AGGCATACATGTTGTCAGAGT 57.011 42.857 2.30 0.00 0.00 3.24
3341 3653 3.603532 AGGCATACATGTTGTCAGAGTG 58.396 45.455 2.30 0.00 0.00 3.51
3342 3654 3.008375 AGGCATACATGTTGTCAGAGTGT 59.992 43.478 2.30 0.00 0.00 3.55
3343 3655 3.372206 GGCATACATGTTGTCAGAGTGTC 59.628 47.826 2.30 0.00 0.00 3.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
24 25 3.249973 GAAAAGTGTCCCGTGCGCC 62.250 63.158 4.18 0.00 0.00 6.53
25 26 2.251371 GAAAAGTGTCCCGTGCGC 59.749 61.111 0.00 0.00 0.00 6.09
26 27 1.278637 GTGAAAAGTGTCCCGTGCG 59.721 57.895 0.00 0.00 0.00 5.34
27 28 1.278637 CGTGAAAAGTGTCCCGTGC 59.721 57.895 0.00 0.00 0.00 5.34
28 29 0.303493 CACGTGAAAAGTGTCCCGTG 59.697 55.000 10.90 0.00 41.55 4.94
29 30 2.685364 CACGTGAAAAGTGTCCCGT 58.315 52.632 10.90 0.00 41.55 5.28
42 43 0.504384 CTGAACTTCTCACGCACGTG 59.496 55.000 16.73 16.73 46.64 4.49
43 44 1.215655 GCTGAACTTCTCACGCACGT 61.216 55.000 0.00 0.00 31.98 4.49
44 45 1.488957 GCTGAACTTCTCACGCACG 59.511 57.895 0.00 0.00 31.98 5.34
45 46 1.488957 CGCTGAACTTCTCACGCAC 59.511 57.895 0.00 0.00 31.98 5.34
46 47 2.310233 GCGCTGAACTTCTCACGCA 61.310 57.895 0.00 0.00 45.63 5.24
47 48 2.472049 GCGCTGAACTTCTCACGC 59.528 61.111 0.00 7.54 42.76 5.34
48 49 2.765785 CGCGCTGAACTTCTCACG 59.234 61.111 5.56 0.00 34.04 4.35
49 50 2.472049 GCGCGCTGAACTTCTCAC 59.528 61.111 26.67 0.00 0.00 3.51
50 51 2.738521 GGCGCGCTGAACTTCTCA 60.739 61.111 32.29 0.00 0.00 3.27
51 52 3.843240 CGGCGCGCTGAACTTCTC 61.843 66.667 35.90 11.37 0.00 2.87
66 67 2.650813 ATTTAGCGCCTGAGCTCCGG 62.651 60.000 19.19 19.19 45.67 5.14
67 68 0.032130 TATTTAGCGCCTGAGCTCCG 59.968 55.000 12.15 8.94 45.67 4.63
68 69 2.464157 ATATTTAGCGCCTGAGCTCC 57.536 50.000 12.15 0.00 45.67 4.70
69 70 2.917971 CGTATATTTAGCGCCTGAGCTC 59.082 50.000 6.82 6.82 45.67 4.09
71 72 1.993370 CCGTATATTTAGCGCCTGAGC 59.007 52.381 2.29 0.00 37.41 4.26
72 73 3.299340 ACCGTATATTTAGCGCCTGAG 57.701 47.619 2.29 0.00 0.00 3.35
73 74 3.738830 AACCGTATATTTAGCGCCTGA 57.261 42.857 2.29 0.00 0.00 3.86
74 75 3.606153 GCAAACCGTATATTTAGCGCCTG 60.606 47.826 2.29 0.00 0.00 4.85
75 76 2.546789 GCAAACCGTATATTTAGCGCCT 59.453 45.455 2.29 0.00 0.00 5.52
76 77 2.660900 CGCAAACCGTATATTTAGCGCC 60.661 50.000 2.29 0.00 33.36 6.53
77 78 2.219216 TCGCAAACCGTATATTTAGCGC 59.781 45.455 0.00 0.00 36.94 5.92
78 79 4.433805 GGATCGCAAACCGTATATTTAGCG 60.434 45.833 0.00 0.00 37.63 4.26
79 80 4.449743 TGGATCGCAAACCGTATATTTAGC 59.550 41.667 0.00 0.00 38.35 3.09
80 81 6.533819 TTGGATCGCAAACCGTATATTTAG 57.466 37.500 0.00 0.00 38.35 1.85
81 82 7.308109 GGAATTGGATCGCAAACCGTATATTTA 60.308 37.037 1.49 0.00 38.35 1.40
82 83 6.385649 AATTGGATCGCAAACCGTATATTT 57.614 33.333 1.49 0.00 38.35 1.40
83 84 5.048991 GGAATTGGATCGCAAACCGTATATT 60.049 40.000 1.49 0.00 38.35 1.28
84 85 4.454504 GGAATTGGATCGCAAACCGTATAT 59.545 41.667 1.49 0.00 38.35 0.86
85 86 3.810941 GGAATTGGATCGCAAACCGTATA 59.189 43.478 1.49 0.00 38.35 1.47
86 87 2.616842 GGAATTGGATCGCAAACCGTAT 59.383 45.455 1.49 0.00 38.35 3.06
87 88 2.011222 GGAATTGGATCGCAAACCGTA 58.989 47.619 1.49 0.00 38.35 4.02
88 89 0.808755 GGAATTGGATCGCAAACCGT 59.191 50.000 1.49 0.00 38.35 4.83
89 90 0.248054 CGGAATTGGATCGCAAACCG 60.248 55.000 19.70 19.70 38.61 4.44
90 91 0.808755 ACGGAATTGGATCGCAAACC 59.191 50.000 1.49 6.93 0.00 3.27
91 92 1.202143 GGACGGAATTGGATCGCAAAC 60.202 52.381 1.49 0.55 0.00 2.93
92 93 1.091537 GGACGGAATTGGATCGCAAA 58.908 50.000 1.49 0.00 0.00 3.68
93 94 1.087202 CGGACGGAATTGGATCGCAA 61.087 55.000 0.02 0.02 0.00 4.85
94 95 1.520564 CGGACGGAATTGGATCGCA 60.521 57.895 0.00 0.00 0.00 5.10
95 96 2.244651 CCGGACGGAATTGGATCGC 61.245 63.158 4.40 0.00 37.50 4.58
96 97 2.244651 GCCGGACGGAATTGGATCG 61.245 63.158 15.99 0.00 37.50 3.69
97 98 2.244651 CGCCGGACGGAATTGGATC 61.245 63.158 15.99 0.00 38.44 3.36
98 99 2.203015 CGCCGGACGGAATTGGAT 60.203 61.111 15.99 0.00 38.44 3.41
108 109 4.143363 GTGTTTAGCGCGCCGGAC 62.143 66.667 30.33 22.93 0.00 4.79
109 110 3.869473 AAGTGTTTAGCGCGCCGGA 62.869 57.895 30.33 11.20 0.00 5.14
110 111 2.452366 AAAAGTGTTTAGCGCGCCGG 62.452 55.000 30.33 0.00 0.00 6.13
111 112 0.659123 AAAAAGTGTTTAGCGCGCCG 60.659 50.000 30.33 0.00 0.00 6.46
112 113 1.974000 GTAAAAAGTGTTTAGCGCGCC 59.026 47.619 30.33 13.41 0.00 6.53
113 114 2.641912 TGTAAAAAGTGTTTAGCGCGC 58.358 42.857 26.66 26.66 0.00 6.86
114 115 3.059461 TCCTGTAAAAAGTGTTTAGCGCG 60.059 43.478 0.00 0.00 0.00 6.86
115 116 4.477302 TCCTGTAAAAAGTGTTTAGCGC 57.523 40.909 0.00 0.00 0.00 5.92
116 117 4.851558 GCATCCTGTAAAAAGTGTTTAGCG 59.148 41.667 0.00 0.00 0.00 4.26
117 118 6.013842 AGCATCCTGTAAAAAGTGTTTAGC 57.986 37.500 0.00 0.00 0.00 3.09
127 128 8.556194 CGCTACATAATAAAGCATCCTGTAAAA 58.444 33.333 0.00 0.00 35.98 1.52
128 129 7.307751 GCGCTACATAATAAAGCATCCTGTAAA 60.308 37.037 0.00 0.00 35.98 2.01
129 130 6.147164 GCGCTACATAATAAAGCATCCTGTAA 59.853 38.462 0.00 0.00 35.98 2.41
130 131 5.637810 GCGCTACATAATAAAGCATCCTGTA 59.362 40.000 0.00 0.00 35.98 2.74
131 132 4.452455 GCGCTACATAATAAAGCATCCTGT 59.548 41.667 0.00 0.00 35.98 4.00
132 133 4.452114 TGCGCTACATAATAAAGCATCCTG 59.548 41.667 9.73 0.00 35.98 3.86
133 134 4.452455 GTGCGCTACATAATAAAGCATCCT 59.548 41.667 9.73 0.00 35.98 3.24
134 135 4.666655 CGTGCGCTACATAATAAAGCATCC 60.667 45.833 9.73 0.00 35.98 3.51
135 136 4.386230 CGTGCGCTACATAATAAAGCATC 58.614 43.478 9.73 0.00 35.98 3.91
136 137 3.363970 GCGTGCGCTACATAATAAAGCAT 60.364 43.478 9.73 0.00 35.98 3.79
137 138 2.033236 GCGTGCGCTACATAATAAAGCA 60.033 45.455 9.73 0.00 35.98 3.91
138 139 2.560896 GCGTGCGCTACATAATAAAGC 58.439 47.619 9.73 0.00 38.26 3.51
151 152 0.165944 AATAACACTTCAGCGTGCGC 59.834 50.000 8.67 8.67 38.45 6.09
152 153 2.594529 AAATAACACTTCAGCGTGCG 57.405 45.000 0.00 0.00 38.45 5.34
153 154 3.884169 TGAAAATAACACTTCAGCGTGC 58.116 40.909 0.00 0.00 38.45 5.34
154 155 5.510671 AGTTGAAAATAACACTTCAGCGTG 58.489 37.500 0.00 0.00 37.71 5.34
155 156 5.277828 GGAGTTGAAAATAACACTTCAGCGT 60.278 40.000 0.00 0.00 37.71 5.07
156 157 5.147162 GGAGTTGAAAATAACACTTCAGCG 58.853 41.667 0.00 0.00 37.71 5.18
157 158 5.147162 CGGAGTTGAAAATAACACTTCAGC 58.853 41.667 0.00 0.00 33.30 4.26
158 159 5.147162 GCGGAGTTGAAAATAACACTTCAG 58.853 41.667 0.00 0.00 33.30 3.02
159 160 4.319190 CGCGGAGTTGAAAATAACACTTCA 60.319 41.667 0.00 0.00 33.02 3.02
160 161 4.148891 CGCGGAGTTGAAAATAACACTTC 58.851 43.478 0.00 0.00 33.02 3.01
161 162 3.608474 GCGCGGAGTTGAAAATAACACTT 60.608 43.478 8.83 0.00 33.02 3.16
162 163 2.095919 GCGCGGAGTTGAAAATAACACT 60.096 45.455 8.83 0.00 33.02 3.55
163 164 2.239201 GCGCGGAGTTGAAAATAACAC 58.761 47.619 8.83 0.00 33.02 3.32
164 165 1.136197 CGCGCGGAGTTGAAAATAACA 60.136 47.619 24.84 0.00 33.02 2.41
165 166 1.520368 CGCGCGGAGTTGAAAATAAC 58.480 50.000 24.84 0.00 0.00 1.89
166 167 0.179210 GCGCGCGGAGTTGAAAATAA 60.179 50.000 33.06 0.00 0.00 1.40
167 168 1.422269 GCGCGCGGAGTTGAAAATA 59.578 52.632 33.06 0.00 0.00 1.40
168 169 2.175811 GCGCGCGGAGTTGAAAAT 59.824 55.556 33.06 0.00 0.00 1.82
169 170 4.362946 CGCGCGCGGAGTTGAAAA 62.363 61.111 43.28 0.00 35.56 2.29
180 181 3.511582 CGCAAGTTTAACGCGCGC 61.512 61.111 32.58 23.91 42.79 6.86
184 185 5.304211 TCAAAAATTCGCAAGTTTAACGC 57.696 34.783 0.00 0.00 39.48 4.84
185 186 5.052040 TGCTCAAAAATTCGCAAGTTTAACG 60.052 36.000 0.00 0.00 39.48 3.18
186 187 6.120157 GTGCTCAAAAATTCGCAAGTTTAAC 58.880 36.000 0.00 0.00 33.74 2.01
187 188 5.052040 CGTGCTCAAAAATTCGCAAGTTTAA 60.052 36.000 0.00 0.00 33.74 1.52
188 189 4.439449 CGTGCTCAAAAATTCGCAAGTTTA 59.561 37.500 0.00 0.00 33.74 2.01
189 190 3.242712 CGTGCTCAAAAATTCGCAAGTTT 59.757 39.130 0.00 0.00 33.74 2.66
190 191 2.788786 CGTGCTCAAAAATTCGCAAGTT 59.211 40.909 0.00 0.00 33.74 2.66
191 192 2.384382 CGTGCTCAAAAATTCGCAAGT 58.616 42.857 0.00 0.00 33.74 3.16
192 193 1.715519 CCGTGCTCAAAAATTCGCAAG 59.284 47.619 0.00 0.00 33.74 4.01
193 194 1.764851 CCGTGCTCAAAAATTCGCAA 58.235 45.000 0.00 0.00 33.74 4.85
194 195 0.662970 GCCGTGCTCAAAAATTCGCA 60.663 50.000 0.00 0.00 0.00 5.10
195 196 1.664643 CGCCGTGCTCAAAAATTCGC 61.665 55.000 0.00 0.00 0.00 4.70
196 197 1.664643 GCGCCGTGCTCAAAAATTCG 61.665 55.000 0.00 0.00 41.73 3.34
197 198 2.061977 GCGCCGTGCTCAAAAATTC 58.938 52.632 0.00 0.00 41.73 2.17
198 199 4.243383 GCGCCGTGCTCAAAAATT 57.757 50.000 0.00 0.00 41.73 1.82
207 208 0.110644 GCTCAATATTAGCGCCGTGC 60.111 55.000 2.29 0.00 46.98 5.34
214 215 6.439599 TCTCTAACAGACGCTCAATATTAGC 58.560 40.000 6.77 6.77 36.60 3.09
215 216 9.549509 GTATCTCTAACAGACGCTCAATATTAG 57.450 37.037 0.00 0.00 32.26 1.73
216 217 9.286170 AGTATCTCTAACAGACGCTCAATATTA 57.714 33.333 0.00 0.00 32.26 0.98
217 218 8.172352 AGTATCTCTAACAGACGCTCAATATT 57.828 34.615 0.00 0.00 32.26 1.28
218 219 7.753309 AGTATCTCTAACAGACGCTCAATAT 57.247 36.000 0.00 0.00 32.26 1.28
219 220 7.192148 GAGTATCTCTAACAGACGCTCAATA 57.808 40.000 0.00 0.00 36.20 1.90
220 221 6.067263 GAGTATCTCTAACAGACGCTCAAT 57.933 41.667 0.00 0.00 36.20 2.57
221 222 5.487153 GAGTATCTCTAACAGACGCTCAA 57.513 43.478 0.00 0.00 36.20 3.02
237 238 9.534565 TTATGTCATGTGAAGCTTTAGAGTATC 57.465 33.333 0.00 0.00 0.00 2.24
238 239 9.319143 GTTATGTCATGTGAAGCTTTAGAGTAT 57.681 33.333 0.00 0.00 0.00 2.12
239 240 8.531982 AGTTATGTCATGTGAAGCTTTAGAGTA 58.468 33.333 0.00 0.00 0.00 2.59
240 241 7.390027 AGTTATGTCATGTGAAGCTTTAGAGT 58.610 34.615 0.00 0.00 0.00 3.24
241 242 7.840342 AGTTATGTCATGTGAAGCTTTAGAG 57.160 36.000 0.00 0.00 0.00 2.43
242 243 8.506437 CAAAGTTATGTCATGTGAAGCTTTAGA 58.494 33.333 0.00 0.00 0.00 2.10
243 244 7.752239 CCAAAGTTATGTCATGTGAAGCTTTAG 59.248 37.037 0.00 0.00 0.00 1.85
244 245 7.446931 TCCAAAGTTATGTCATGTGAAGCTTTA 59.553 33.333 0.00 0.00 0.00 1.85
245 246 6.265196 TCCAAAGTTATGTCATGTGAAGCTTT 59.735 34.615 0.00 0.00 0.00 3.51
246 247 5.769662 TCCAAAGTTATGTCATGTGAAGCTT 59.230 36.000 0.00 0.00 0.00 3.74
247 248 5.316167 TCCAAAGTTATGTCATGTGAAGCT 58.684 37.500 0.00 0.00 0.00 3.74
248 249 5.627499 TCCAAAGTTATGTCATGTGAAGC 57.373 39.130 0.00 0.00 0.00 3.86
251 252 9.460019 TCATTTATCCAAAGTTATGTCATGTGA 57.540 29.630 0.00 0.00 0.00 3.58
340 341 3.283684 CTTGGCCACCGCGTTCAA 61.284 61.111 3.88 1.16 35.02 2.69
434 435 2.372040 CTTCCACGTCGTTCCCCACA 62.372 60.000 0.00 0.00 0.00 4.17
742 748 2.444421 CAGGACGAGTACTACCACCTT 58.556 52.381 13.32 0.00 0.00 3.50
915 1077 5.980116 CGCGAGTACTACCCTACGTATATAT 59.020 44.000 0.00 0.00 0.00 0.86
960 1126 1.209990 TCGGGTAGGTTTGTGTTGTGT 59.790 47.619 0.00 0.00 0.00 3.72
961 1127 1.956297 TCGGGTAGGTTTGTGTTGTG 58.044 50.000 0.00 0.00 0.00 3.33
962 1128 2.551504 GGATCGGGTAGGTTTGTGTTGT 60.552 50.000 0.00 0.00 0.00 3.32
963 1129 2.081462 GGATCGGGTAGGTTTGTGTTG 58.919 52.381 0.00 0.00 0.00 3.33
964 1130 1.700739 TGGATCGGGTAGGTTTGTGTT 59.299 47.619 0.00 0.00 0.00 3.32
1045 1212 4.004314 CGGTCGATGATGAGGTCTAGTAT 58.996 47.826 0.00 0.00 0.00 2.12
1255 1428 2.690778 GCTGCCGTGAAGCCGAAAT 61.691 57.895 0.00 0.00 34.45 2.17
1275 1448 2.237143 GTCTGACATGACAATCCAGGGA 59.763 50.000 0.00 0.00 36.97 4.20
1478 1654 2.349590 CAATGACAGCATCCAACTCGA 58.650 47.619 0.00 0.00 32.35 4.04
1553 1729 0.458370 CATGACAGCGACGATGTCCA 60.458 55.000 35.21 25.42 46.70 4.02
1831 2017 5.935206 TGTTGCTGGAATCAAAGTTATCGTA 59.065 36.000 0.00 0.00 0.00 3.43
1923 2112 1.743321 CTAAGGCCCGCTCCTCAGAG 61.743 65.000 0.00 0.00 43.57 3.35
1935 2124 2.981859 TCCGAAGTTCATCTAAGGCC 57.018 50.000 3.32 0.00 0.00 5.19
2012 2204 5.829924 GTGATGATATCCTTGGGTTCATGTT 59.170 40.000 0.00 0.00 0.00 2.71
2126 2318 1.621814 TCTCGTAAACCTCCACCTTGG 59.378 52.381 0.00 0.00 39.43 3.61
2223 2415 6.258230 CAAGTATGAATGGACTTGCAGAAA 57.742 37.500 2.13 0.00 44.30 2.52
2494 2686 3.282745 GACGCCTTGTCGCCTCTCA 62.283 63.158 0.00 0.00 37.96 3.27
2580 2775 8.955061 ATCGTTTGAGAAATGTATCAACTTTG 57.045 30.769 0.00 0.00 34.76 2.77
2644 2839 6.949352 ATTTTGTCCATACATAGCTTCTGG 57.051 37.500 0.00 0.00 34.97 3.86
2658 2853 9.964303 GTTACATATATGCATCAATTTTGTCCA 57.036 29.630 12.79 0.00 0.00 4.02
2726 2921 9.934190 GAACAAGTGCAAATGTTTATTTTTCAT 57.066 25.926 16.77 0.00 39.73 2.57
2727 2922 9.160496 AGAACAAGTGCAAATGTTTATTTTTCA 57.840 25.926 16.77 0.00 39.73 2.69
2729 2924 9.986833 GAAGAACAAGTGCAAATGTTTATTTTT 57.013 25.926 16.77 8.85 39.73 1.94
2730 2925 9.160496 TGAAGAACAAGTGCAAATGTTTATTTT 57.840 25.926 16.77 10.64 39.73 1.82
2734 2929 6.862209 ACTGAAGAACAAGTGCAAATGTTTA 58.138 32.000 16.77 6.44 39.73 2.01
2752 2947 7.584987 CAATCTAACAACCCAACTAACTGAAG 58.415 38.462 0.00 0.00 0.00 3.02
2802 2997 6.741109 TGCCATATGCTCTTTTGTTCATATG 58.259 36.000 11.88 11.88 43.87 1.78
2803 2998 6.964807 TGCCATATGCTCTTTTGTTCATAT 57.035 33.333 0.00 0.00 42.00 1.78
2804 2999 6.772360 TTGCCATATGCTCTTTTGTTCATA 57.228 33.333 0.00 0.00 42.00 2.15
2805 3000 5.664294 TTGCCATATGCTCTTTTGTTCAT 57.336 34.783 0.00 0.00 42.00 2.57
2806 3001 5.465532 TTTGCCATATGCTCTTTTGTTCA 57.534 34.783 0.00 0.00 42.00 3.18
2807 3002 6.973229 ATTTTGCCATATGCTCTTTTGTTC 57.027 33.333 0.00 0.00 42.00 3.18
2810 3005 7.010183 CAGAGAATTTTGCCATATGCTCTTTTG 59.990 37.037 0.00 0.00 42.00 2.44
2820 3015 4.099881 GGGATTGCAGAGAATTTTGCCATA 59.900 41.667 7.71 0.00 39.54 2.74
2907 3103 4.611355 CGATGAGCCAAACAACACTGTAAG 60.611 45.833 0.00 0.00 42.29 2.34
2908 3104 3.249799 CGATGAGCCAAACAACACTGTAA 59.750 43.478 0.00 0.00 33.45 2.41
2909 3105 2.805671 CGATGAGCCAAACAACACTGTA 59.194 45.455 0.00 0.00 33.45 2.74
2910 3106 1.603802 CGATGAGCCAAACAACACTGT 59.396 47.619 0.00 0.00 37.39 3.55
2911 3107 1.664016 GCGATGAGCCAAACAACACTG 60.664 52.381 0.00 0.00 40.81 3.66
2912 3108 0.593128 GCGATGAGCCAAACAACACT 59.407 50.000 0.00 0.00 40.81 3.55
2913 3109 3.092081 GCGATGAGCCAAACAACAC 57.908 52.632 0.00 0.00 40.81 3.32
2923 3119 3.241836 GCTTGAAGCAGAGCGATGAGC 62.242 57.143 13.09 0.00 43.58 4.26
2925 3121 0.248565 AGCTTGAAGCAGAGCGATGA 59.751 50.000 20.45 0.00 45.56 2.92
2929 3125 0.389556 TGAGAGCTTGAAGCAGAGCG 60.390 55.000 20.45 0.00 45.56 5.03
2980 3176 1.663695 ACTCTGTTGGTTTGGACACG 58.336 50.000 0.00 0.00 0.00 4.49
2996 3192 5.776519 CTAACAGAGCTCATTCACAACTC 57.223 43.478 17.77 0.00 0.00 3.01
3036 3232 4.159506 AGCTGAGACAGTCTAGAAATGGTC 59.840 45.833 2.00 8.18 33.43 4.02
3049 3245 1.134491 TCATGGCATGAGCTGAGACAG 60.134 52.381 25.63 0.00 41.70 3.51
3073 3270 2.561419 ACAATACAGTGACACGCTACCT 59.439 45.455 0.00 0.00 0.00 3.08
3091 3288 5.428253 GGCAGAAGGAATAGACATACACAA 58.572 41.667 0.00 0.00 0.00 3.33
3115 3313 6.395629 TCTCCAAACGTACAGATAGGAAAAG 58.604 40.000 0.00 0.00 0.00 2.27
3131 3329 3.242712 CACGTGTGCATTTTTCTCCAAAC 59.757 43.478 7.58 0.00 0.00 2.93
3156 3354 7.429636 AAATGGAATTGTCAAATGCAGAAAG 57.570 32.000 1.22 0.00 36.10 2.62
3184 3382 4.627900 ACAAAACAAAGCCAGGTTTTTACG 59.372 37.500 0.00 0.00 42.73 3.18
3277 3589 4.758688 AGGAAAAGGCAAAGTTCAACAAG 58.241 39.130 0.00 0.00 0.00 3.16
3337 3649 1.374758 CACCTGGGAAGCGACACTC 60.375 63.158 0.00 0.00 0.00 3.51
3340 3652 3.059982 CTCACCTGGGAAGCGACA 58.940 61.111 0.00 0.00 0.00 4.35
3341 3653 2.435059 GCTCACCTGGGAAGCGAC 60.435 66.667 6.79 0.00 0.00 5.19
3342 3654 2.604686 AGCTCACCTGGGAAGCGA 60.605 61.111 14.45 0.00 0.00 4.93
3343 3655 2.435586 CAGCTCACCTGGGAAGCG 60.436 66.667 14.45 7.94 37.93 4.68


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

AutoCloner maintained by Alex Coulton.