Multiple sequence alignment - TraesCS5D01G202300

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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 TraesCS5D01G202300 chr5D 100.000 4278 0 0 2027 6304 307087251 307091528 0.000000e+00 7901.0
1 TraesCS5D01G202300 chr5D 100.000 1810 0 0 1 1810 307085225 307087034 0.000000e+00 3343.0
2 TraesCS5D01G202300 chr5D 83.346 1279 168 34 4087 5342 300144089 300145345 0.000000e+00 1140.0
3 TraesCS5D01G202300 chr5D 92.473 186 14 0 2287 2472 169955015 169955200 3.750000e-67 267.0
4 TraesCS5D01G202300 chr5D 80.163 368 55 8 4983 5342 300958153 300957796 6.270000e-65 259.0
5 TraesCS5D01G202300 chr5D 86.161 224 29 2 4624 4846 300313613 300313835 2.270000e-59 241.0
6 TraesCS5D01G202300 chr5D 83.404 235 27 3 4623 4846 300958482 300958249 2.300000e-49 207.0
7 TraesCS5D01G202300 chr5D 83.333 204 17 8 5705 5905 307186030 307186219 8.400000e-39 172.0
8 TraesCS5D01G202300 chr5D 83.708 178 26 2 992 1166 300142994 300143171 1.410000e-36 165.0
9 TraesCS5D01G202300 chr5D 82.439 205 18 9 5705 5905 307133967 307134157 5.060000e-36 163.0
10 TraesCS5D01G202300 chr5D 82.439 205 16 10 5705 5905 307353288 307353476 1.820000e-35 161.0
11 TraesCS5D01G202300 chr5D 80.982 163 19 10 2040 2196 125783320 125783164 1.110000e-22 119.0
12 TraesCS5D01G202300 chr5D 95.385 65 3 0 6056 6120 298141179 298141243 3.110000e-18 104.0
13 TraesCS5D01G202300 chr5D 96.226 53 2 0 6056 6108 298465821 298465769 3.130000e-13 87.9
14 TraesCS5D01G202300 chr5B 94.953 3685 116 22 2287 5926 352307956 352311615 0.000000e+00 5710.0
15 TraesCS5D01G202300 chr5B 91.040 1741 97 19 107 1810 352305674 352307392 0.000000e+00 2296.0
16 TraesCS5D01G202300 chr5B 83.607 1281 161 34 4087 5342 343949211 343950467 0.000000e+00 1157.0
17 TraesCS5D01G202300 chr5B 83.351 925 123 24 4438 5341 339980726 339979812 0.000000e+00 826.0
18 TraesCS5D01G202300 chr5B 82.704 821 112 23 4542 5342 340137497 340136687 0.000000e+00 702.0
19 TraesCS5D01G202300 chr5B 82.704 821 112 23 4542 5342 340327570 340326760 0.000000e+00 702.0
20 TraesCS5D01G202300 chr5B 88.854 323 34 2 2605 2926 622970751 622971072 4.580000e-106 396.0
21 TraesCS5D01G202300 chr5B 87.963 324 36 3 2605 2926 633310408 633310086 4.610000e-101 379.0
22 TraesCS5D01G202300 chr5B 95.567 203 7 1 2089 2289 352307698 352307900 2.190000e-84 324.0
23 TraesCS5D01G202300 chr5B 93.333 180 12 0 2293 2472 166829583 166829404 3.750000e-67 267.0
24 TraesCS5D01G202300 chr5B 78.533 368 61 9 4983 5342 344232421 344232778 6.360000e-55 226.0
25 TraesCS5D01G202300 chr5B 93.750 128 8 0 5928 6055 352311701 352311828 6.450000e-45 193.0
26 TraesCS5D01G202300 chr5B 83.146 178 27 2 992 1166 343948116 343948293 6.540000e-35 159.0
27 TraesCS5D01G202300 chr5B 89.256 121 12 1 4438 4557 340154646 340154526 3.940000e-32 150.0
28 TraesCS5D01G202300 chr5B 91.667 108 8 1 2488 2594 622970581 622970688 1.420000e-31 148.0
29 TraesCS5D01G202300 chr5B 88.525 122 12 2 4438 4557 340344734 340344613 5.090000e-31 147.0
30 TraesCS5D01G202300 chr5B 81.325 166 14 8 2040 2196 545015736 545015579 1.110000e-22 119.0
31 TraesCS5D01G202300 chr5A 93.637 3379 137 34 2589 5934 390368954 390365621 0.000000e+00 4977.0
32 TraesCS5D01G202300 chr5A 89.062 1856 121 40 15 1810 390371474 390369641 0.000000e+00 2228.0
33 TraesCS5D01G202300 chr5A 84.050 1279 159 33 4087 5342 397783664 397784920 0.000000e+00 1190.0
34 TraesCS5D01G202300 chr5A 82.639 1296 164 41 4087 5339 415629026 415627749 0.000000e+00 1090.0
35 TraesCS5D01G202300 chr5A 96.091 307 12 0 2287 2593 390369299 390368993 9.430000e-138 501.0
36 TraesCS5D01G202300 chr5A 92.748 262 15 3 2031 2289 390369615 390369355 5.970000e-100 375.0
37 TraesCS5D01G202300 chr5A 87.616 323 38 2 2605 2926 626026908 626026587 2.150000e-99 374.0
38 TraesCS5D01G202300 chr5A 84.022 363 45 6 4983 5335 396418073 396417714 2.820000e-88 337.0
39 TraesCS5D01G202300 chr5A 95.187 187 8 1 6118 6304 390365319 390365134 1.720000e-75 294.0
40 TraesCS5D01G202300 chr5A 93.889 180 11 0 2293 2472 177613958 177613779 8.050000e-69 272.0
41 TraesCS5D01G202300 chr5A 84.358 179 25 2 992 1167 397782586 397782764 8.400000e-39 172.0
42 TraesCS5D01G202300 chr5A 81.183 186 20 8 5725 5905 390240306 390240131 1.100000e-27 135.0
43 TraesCS5D01G202300 chr5A 88.889 108 9 2 2488 2594 626027076 626026971 5.130000e-26 130.0
44 TraesCS5D01G202300 chr5A 84.444 90 8 5 6184 6268 400570755 400570843 4.050000e-12 84.2
45 TraesCS5D01G202300 chr3D 82.029 1252 167 28 4134 5348 482007231 482006001 0.000000e+00 1013.0
46 TraesCS5D01G202300 chr1D 80.949 1286 193 27 4102 5354 18804379 18803113 0.000000e+00 970.0
47 TraesCS5D01G202300 chr2A 91.471 340 23 2 2589 2928 393114345 393114678 4.450000e-126 462.0
48 TraesCS5D01G202300 chr2A 83.486 327 48 5 2919 3241 761956734 761956410 3.690000e-77 300.0
49 TraesCS5D01G202300 chr2A 83.540 322 48 4 2924 3241 762494936 762495256 4.780000e-76 296.0
50 TraesCS5D01G202300 chr2A 77.099 131 19 8 42 162 11747475 11747346 1.470000e-06 65.8
51 TraesCS5D01G202300 chr3A 89.274 317 32 2 2608 2923 38273396 38273081 4.580000e-106 396.0
52 TraesCS5D01G202300 chr3A 82.209 326 50 7 2926 3244 150062235 150062559 2.240000e-69 274.0
53 TraesCS5D01G202300 chr3A 92.793 111 7 1 2485 2594 38273573 38273463 6.540000e-35 159.0
54 TraesCS5D01G202300 chr7B 88.199 322 35 3 2605 2924 612313427 612313107 1.280000e-101 381.0
55 TraesCS5D01G202300 chr7B 92.391 92 6 1 2504 2594 612313582 612313491 5.130000e-26 130.0
56 TraesCS5D01G202300 chr7B 90.000 60 2 3 107 164 175990455 175990512 2.440000e-09 75.0
57 TraesCS5D01G202300 chr7B 88.679 53 6 0 46 98 728061526 728061474 1.470000e-06 65.8
58 TraesCS5D01G202300 chr3B 88.125 320 34 3 2605 2920 490891036 490890717 1.660000e-100 377.0
59 TraesCS5D01G202300 chr3B 84.062 320 46 4 2926 3241 800988641 800988959 2.860000e-78 303.0
60 TraesCS5D01G202300 chr3B 100.000 32 0 0 3356 3387 823908138 823908107 6.830000e-05 60.2
61 TraesCS5D01G202300 chr4B 84.227 317 45 4 2929 3241 603528744 603528429 2.860000e-78 303.0
62 TraesCS5D01G202300 chr4B 77.848 158 24 8 2040 2197 630382880 630382734 3.130000e-13 87.9
63 TraesCS5D01G202300 chr4B 77.848 158 24 8 2040 2197 630385915 630385769 3.130000e-13 87.9
64 TraesCS5D01G202300 chr4D 83.699 319 47 4 2927 3241 12500747 12501064 4.780000e-76 296.0
65 TraesCS5D01G202300 chr4D 92.857 112 8 0 3245 3356 83279777 83279888 5.060000e-36 163.0
66 TraesCS5D01G202300 chr7A 83.438 320 48 4 2926 3241 185633073 185633391 6.180000e-75 292.0
67 TraesCS5D01G202300 chr7A 81.548 168 14 7 2040 2196 563818392 563818553 8.580000e-24 122.0
68 TraesCS5D01G202300 chr7A 84.810 79 7 4 2111 2187 252711828 252711753 2.440000e-09 75.0
69 TraesCS5D01G202300 chr1B 83.281 317 48 4 2929 3241 560012340 560012025 2.880000e-73 287.0
70 TraesCS5D01G202300 chr1B 88.679 53 6 0 46 98 688996256 688996204 1.470000e-06 65.8
71 TraesCS5D01G202300 chr1A 82.500 320 51 4 2926 3241 585523272 585523590 6.230000e-70 276.0
72 TraesCS5D01G202300 chr1A 76.642 137 20 10 2059 2186 117959403 117959536 1.470000e-06 65.8
73 TraesCS5D01G202300 chr6D 87.037 108 13 1 2488 2594 287018207 287018314 3.090000e-23 121.0
74 TraesCS5D01G202300 chr6D 88.525 61 5 2 107 166 260045837 260045896 8.770000e-09 73.1
75 TraesCS5D01G202300 chr6B 87.037 108 13 1 2488 2594 447885648 447885755 3.090000e-23 121.0
76 TraesCS5D01G202300 chr6A 87.619 105 12 1 2491 2594 438588227 438588123 3.090000e-23 121.0
77 TraesCS5D01G202300 chr7D 79.012 162 23 8 2040 2196 183725369 183725524 4.020000e-17 100.0
78 TraesCS5D01G202300 chr7D 89.855 69 4 3 107 173 118874974 118874907 1.130000e-12 86.1
79 TraesCS5D01G202300 chr2D 94.340 53 3 0 112 164 17466155 17466207 1.460000e-11 82.4
80 TraesCS5D01G202300 chrUn 89.655 58 6 0 107 164 293009256 293009313 2.440000e-09 75.0
81 TraesCS5D01G202300 chrUn 89.655 58 6 0 107 164 356646227 356646170 2.440000e-09 75.0
82 TraesCS5D01G202300 chrUn 89.655 58 6 0 107 164 357269266 357269323 2.440000e-09 75.0
83 TraesCS5D01G202300 chr2B 80.000 90 14 4 2098 2186 25430281 25430195 5.280000e-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 TraesCS5D01G202300 chr5D 307085225 307091528 6303 False 5622.00 7901 100.0000 1 6304 2 chr5D.!!$F8 6303
1 TraesCS5D01G202300 chr5D 300142994 300145345 2351 False 652.50 1140 83.5270 992 5342 2 chr5D.!!$F7 4350
2 TraesCS5D01G202300 chr5D 300957796 300958482 686 True 233.00 259 81.7835 4623 5342 2 chr5D.!!$R3 719
3 TraesCS5D01G202300 chr5B 352305674 352311828 6154 False 2130.75 5710 93.8275 107 6055 4 chr5B.!!$F3 5948
4 TraesCS5D01G202300 chr5B 339979812 339980726 914 True 826.00 826 83.3510 4438 5341 1 chr5B.!!$R2 903
5 TraesCS5D01G202300 chr5B 340136687 340137497 810 True 702.00 702 82.7040 4542 5342 1 chr5B.!!$R3 800
6 TraesCS5D01G202300 chr5B 340326760 340327570 810 True 702.00 702 82.7040 4542 5342 1 chr5B.!!$R5 800
7 TraesCS5D01G202300 chr5B 343948116 343950467 2351 False 658.00 1157 83.3765 992 5342 2 chr5B.!!$F2 4350
8 TraesCS5D01G202300 chr5A 390365134 390371474 6340 True 1675.00 4977 93.3450 15 6304 5 chr5A.!!$R5 6289
9 TraesCS5D01G202300 chr5A 415627749 415629026 1277 True 1090.00 1090 82.6390 4087 5339 1 chr5A.!!$R4 1252
10 TraesCS5D01G202300 chr5A 397782586 397784920 2334 False 681.00 1190 84.2040 992 5342 2 chr5A.!!$F2 4350
11 TraesCS5D01G202300 chr3D 482006001 482007231 1230 True 1013.00 1013 82.0290 4134 5348 1 chr3D.!!$R1 1214
12 TraesCS5D01G202300 chr1D 18803113 18804379 1266 True 970.00 970 80.9490 4102 5354 1 chr1D.!!$R1 1252

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
104 105 0.108898 CTCGGAGGTGCTCTTGAGTG 60.109 60.000 0.00 0.0 32.56 3.51 F
849 887 0.249120 CACCCACACCGAATCTAGCA 59.751 55.000 0.00 0.0 0.00 3.49 F
876 915 0.318784 GGCTTCGTGTTGACTCGTCT 60.319 55.000 5.64 0.0 34.81 4.18 F
2156 2290 0.679505 ACACCGACAGCACACATAGT 59.320 50.000 0.00 0.0 0.00 2.12 F
2899 3137 1.202651 GCACCTTGCCGATATGGTACT 60.203 52.381 0.00 0.0 41.21 2.73 F
3115 3363 0.392461 GGCGTAGTCAAAGGGCATCA 60.392 55.000 0.00 0.0 0.00 3.07 F
3133 3381 1.071699 TCACCTAGCAGACCAAACCAC 59.928 52.381 0.00 0.0 0.00 4.16 F
3427 3701 1.478510 AGATACACCAAGGAGCACTCG 59.521 52.381 0.00 0.0 0.00 4.18 F
3849 4385 1.742831 GATTGCGCCAATCCACTGTTA 59.257 47.619 16.79 0.0 42.90 2.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2100 2232 0.043940 ATCTCTTCTCCCCTGTGCCT 59.956 55.000 0.00 0.00 0.00 4.75 R
2507 2702 1.209128 GACCATATCGGCAGTTCACG 58.791 55.000 0.00 0.00 39.03 4.35 R
2809 3047 6.183360 CGGTAACCCATATATCGGTAGGTTAG 60.183 46.154 2.10 0.00 39.76 2.34 R
3115 3363 0.034896 CGTGGTTTGGTCTGCTAGGT 59.965 55.000 0.00 0.00 0.00 3.08 R
3913 4456 1.214175 TCAGTTCCCCACTCTTTGCAA 59.786 47.619 0.00 0.00 30.92 4.08 R
4020 4563 1.242076 GTGATTGCACCACTCTTGCT 58.758 50.000 10.30 0.00 40.86 3.91 R
4027 4570 1.577328 CCCAGTCGTGATTGCACCAC 61.577 60.000 8.05 8.05 42.09 4.16 R
4884 5463 3.557054 CCAGAGCAACCTACAAGCTGTAA 60.557 47.826 0.00 0.00 39.02 2.41 R
5742 6349 0.986992 GTTGCAAAAGCAGCGCATAG 59.013 50.000 11.47 0.00 35.19 2.23 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
23 24 1.616865 TCATTGGGACGAGACGTTCTT 59.383 47.619 2.71 0.00 41.37 2.52
26 27 0.748450 TGGGACGAGACGTTCTTGTT 59.252 50.000 8.64 0.00 41.04 2.83
33 34 2.978489 CGAGACGTTCTTGTTGACTACC 59.022 50.000 0.00 0.00 0.00 3.18
36 37 2.475487 GACGTTCTTGTTGACTACCAGC 59.525 50.000 0.00 0.00 0.00 4.85
39 40 2.169832 TCTTGTTGACTACCAGCTGC 57.830 50.000 8.66 0.00 0.00 5.25
44 45 2.370519 TGTTGACTACCAGCTGCCTTTA 59.629 45.455 8.66 0.00 0.00 1.85
49 50 2.840651 ACTACCAGCTGCCTTTAGTGAT 59.159 45.455 8.66 0.00 0.00 3.06
51 52 2.716217 ACCAGCTGCCTTTAGTGATTC 58.284 47.619 8.66 0.00 0.00 2.52
53 54 1.667724 CAGCTGCCTTTAGTGATTCCG 59.332 52.381 0.00 0.00 0.00 4.30
59 60 4.331968 TGCCTTTAGTGATTCCGTCAATT 58.668 39.130 0.00 0.00 38.90 2.32
81 82 4.639135 TCAAGATGATATATCGGCTCGG 57.361 45.455 8.19 4.70 0.00 4.63
88 89 1.723220 TATATCGGCTCGGTCTCTCG 58.277 55.000 0.00 0.00 0.00 4.04
92 93 3.213402 GGCTCGGTCTCTCGGAGG 61.213 72.222 4.96 0.00 41.72 4.30
98 99 1.379309 GGTCTCTCGGAGGTGCTCT 60.379 63.158 4.96 0.00 0.00 4.09
103 104 0.251386 TCTCGGAGGTGCTCTTGAGT 60.251 55.000 4.96 0.00 35.81 3.41
104 105 0.108898 CTCGGAGGTGCTCTTGAGTG 60.109 60.000 0.00 0.00 32.56 3.51
105 106 0.827925 TCGGAGGTGCTCTTGAGTGT 60.828 55.000 0.00 0.00 0.00 3.55
111 124 4.037446 GGAGGTGCTCTTGAGTGTATAGAG 59.963 50.000 0.00 0.00 38.71 2.43
137 150 7.080353 TGAGTGTATGCGCGTATATATAAGT 57.920 36.000 19.79 9.15 0.00 2.24
138 151 6.964934 TGAGTGTATGCGCGTATATATAAGTG 59.035 38.462 19.79 13.05 0.00 3.16
140 153 7.310664 AGTGTATGCGCGTATATATAAGTGTT 58.689 34.615 19.79 9.97 0.00 3.32
141 154 7.811236 AGTGTATGCGCGTATATATAAGTGTTT 59.189 33.333 19.79 9.70 0.00 2.83
148 161 6.520790 CGCGTATATATAAGTGTTTGCGTCTA 59.479 38.462 10.11 0.00 37.34 2.59
252 269 3.157932 TCTTTTTGGCCACGAAAACAG 57.842 42.857 3.88 0.00 35.54 3.16
255 272 0.741915 TTTGGCCACGAAAACAGTCC 59.258 50.000 3.88 0.00 0.00 3.85
256 273 0.394488 TTGGCCACGAAAACAGTCCA 60.394 50.000 3.88 0.00 0.00 4.02
288 305 6.872608 ACAAAAGCGTGCATTTTACAATAAC 58.127 32.000 0.00 0.00 0.00 1.89
290 307 7.170658 ACAAAAGCGTGCATTTTACAATAACAT 59.829 29.630 0.00 0.00 0.00 2.71
292 309 8.749841 AAAGCGTGCATTTTACAATAACATAA 57.250 26.923 0.00 0.00 0.00 1.90
328 351 5.793817 TCAATCAATCTACATATGGACGGG 58.206 41.667 7.80 0.00 0.00 5.28
352 375 3.715628 AAGTGACAGATTTGGTTGCAC 57.284 42.857 0.00 0.00 0.00 4.57
390 414 5.728637 ACAGAACCCTGGATTTGAATTTC 57.271 39.130 0.00 0.00 44.60 2.17
410 434 1.522806 TGACACGGGCACACAGAAC 60.523 57.895 0.00 0.00 0.00 3.01
433 457 1.450134 CCATGTGCCAGCGCTCTAA 60.450 57.895 7.13 0.00 35.36 2.10
460 484 6.824305 TTCAATTCCCAAGAAAAGCTCTAG 57.176 37.500 0.00 0.00 35.09 2.43
504 528 3.228243 AAATCCAGCCAGCCAGCCA 62.228 57.895 0.00 0.00 0.00 4.75
692 719 1.010046 AGATCTCATCTCCCCACCCAA 59.990 52.381 0.00 0.00 33.42 4.12
700 727 3.517497 CCCCACCCAACCCAACCT 61.517 66.667 0.00 0.00 0.00 3.50
762 800 4.162690 GCATCCGCTCCCGTTCCT 62.163 66.667 0.00 0.00 34.30 3.36
788 826 0.675522 AATCCGTTACCACCAAGGCG 60.676 55.000 0.00 0.00 43.14 5.52
789 827 2.530958 ATCCGTTACCACCAAGGCGG 62.531 60.000 0.00 0.00 43.14 6.13
799 837 2.618045 CCACCAAGGCGGAAGATTTAGT 60.618 50.000 0.00 0.00 38.63 2.24
801 839 3.621715 CACCAAGGCGGAAGATTTAGTAC 59.378 47.826 0.00 0.00 38.63 2.73
802 840 3.518303 ACCAAGGCGGAAGATTTAGTACT 59.482 43.478 0.00 0.00 38.63 2.73
803 841 4.120589 CCAAGGCGGAAGATTTAGTACTC 58.879 47.826 0.00 0.00 36.56 2.59
804 842 4.120589 CAAGGCGGAAGATTTAGTACTCC 58.879 47.826 0.00 0.00 0.00 3.85
805 843 3.644335 AGGCGGAAGATTTAGTACTCCT 58.356 45.455 0.00 0.00 0.00 3.69
806 844 3.637694 AGGCGGAAGATTTAGTACTCCTC 59.362 47.826 0.00 0.00 0.00 3.71
807 845 3.243805 GGCGGAAGATTTAGTACTCCTCC 60.244 52.174 0.00 0.00 0.00 4.30
808 846 3.637694 GCGGAAGATTTAGTACTCCTCCT 59.362 47.826 0.00 0.00 0.00 3.69
809 847 4.261698 GCGGAAGATTTAGTACTCCTCCTC 60.262 50.000 0.00 0.00 0.00 3.71
810 848 4.023878 CGGAAGATTTAGTACTCCTCCTCG 60.024 50.000 0.00 0.00 0.00 4.63
811 849 4.888823 GGAAGATTTAGTACTCCTCCTCGT 59.111 45.833 0.00 0.00 0.00 4.18
812 850 5.008911 GGAAGATTTAGTACTCCTCCTCGTC 59.991 48.000 0.00 0.00 0.00 4.20
813 851 5.376756 AGATTTAGTACTCCTCCTCGTCT 57.623 43.478 0.00 0.00 0.00 4.18
817 855 5.690464 TTAGTACTCCTCCTCGTCTACTT 57.310 43.478 0.00 0.00 0.00 2.24
836 874 1.673665 CTTGCTCAGCTCCACCCAC 60.674 63.158 0.00 0.00 0.00 4.61
840 878 3.596066 CTCAGCTCCACCCACACCG 62.596 68.421 0.00 0.00 0.00 4.94
846 884 1.191535 CTCCACCCACACCGAATCTA 58.808 55.000 0.00 0.00 0.00 1.98
847 885 1.137086 CTCCACCCACACCGAATCTAG 59.863 57.143 0.00 0.00 0.00 2.43
848 886 0.462047 CCACCCACACCGAATCTAGC 60.462 60.000 0.00 0.00 0.00 3.42
849 887 0.249120 CACCCACACCGAATCTAGCA 59.751 55.000 0.00 0.00 0.00 3.49
857 896 2.710971 CGAATCTAGCATCGCGGCG 61.711 63.158 17.70 17.70 39.27 6.46
876 915 0.318784 GGCTTCGTGTTGACTCGTCT 60.319 55.000 5.64 0.00 34.81 4.18
993 1032 3.309121 GGTTCTTGGATTTGGATCTCCCA 60.309 47.826 0.00 0.00 44.93 4.37
1035 1074 3.619233 GAGCTCTTCACGAGATCCTAC 57.381 52.381 6.43 0.00 46.84 3.18
1281 1342 5.006386 CCCTTGAGTTTCTTGCTTCAGTAT 58.994 41.667 0.00 0.00 0.00 2.12
1282 1343 5.474876 CCCTTGAGTTTCTTGCTTCAGTATT 59.525 40.000 0.00 0.00 0.00 1.89
1284 1345 5.362556 TGAGTTTCTTGCTTCAGTATTGC 57.637 39.130 0.00 0.00 0.00 3.56
1285 1346 5.065914 TGAGTTTCTTGCTTCAGTATTGCT 58.934 37.500 0.00 0.00 0.00 3.91
1286 1347 6.230472 TGAGTTTCTTGCTTCAGTATTGCTA 58.770 36.000 0.00 0.00 0.00 3.49
1287 1348 6.369890 TGAGTTTCTTGCTTCAGTATTGCTAG 59.630 38.462 0.00 0.00 0.00 3.42
1289 1350 6.148480 AGTTTCTTGCTTCAGTATTGCTAGTG 59.852 38.462 0.00 0.00 32.91 2.74
1293 1356 5.343307 TGCTTCAGTATTGCTAGTGATGA 57.657 39.130 7.50 0.00 37.20 2.92
1506 1603 2.548057 TGGTCATCGTGACTGCTTTTTC 59.452 45.455 14.77 1.19 46.19 2.29
1537 1634 8.850452 GTTGCCTTCTCTTTAACAAAATAATCG 58.150 33.333 0.00 0.00 0.00 3.34
1551 1648 6.468956 ACAAAATAATCGAATCATTGACACGC 59.531 34.615 8.72 0.00 0.00 5.34
1553 1650 3.933155 AATCGAATCATTGACACGCTC 57.067 42.857 8.72 0.00 0.00 5.03
1700 1797 7.047271 TGTTGTGCTATATTGCTAGTGAATCA 58.953 34.615 10.48 0.00 0.00 2.57
1710 1807 3.129871 GCTAGTGAATCAGATGTGAGGC 58.870 50.000 0.00 0.00 35.66 4.70
1784 1889 8.845413 TGGAAGCTTAACATTTGCAAAATATT 57.155 26.923 17.19 12.71 0.00 1.28
1789 1894 9.248291 AGCTTAACATTTGCAAAATATTATCCG 57.752 29.630 17.19 7.81 0.00 4.18
2051 2156 3.106827 CCCACCTTAATTCATTTGCCCT 58.893 45.455 0.00 0.00 0.00 5.19
2100 2232 2.409064 TAGGGTCCAAGTGAACAGGA 57.591 50.000 0.00 0.00 29.57 3.86
2156 2290 0.679505 ACACCGACAGCACACATAGT 59.320 50.000 0.00 0.00 0.00 2.12
2227 2361 2.224066 CGCTAGGAATCGACAGGGAATT 60.224 50.000 0.00 0.00 0.00 2.17
2289 2426 2.951642 TGAAGAACCAGAGCACTTTTGG 59.048 45.455 0.00 1.79 37.98 3.28
2342 2537 8.024145 CCTTATATAGGCTAGGGAATTACAGG 57.976 42.308 0.00 0.00 37.17 4.00
2410 2605 6.070309 GGGAAACAGAGATAGGCATAGATCAT 60.070 42.308 0.00 0.00 0.00 2.45
2455 2650 7.071071 CCCTCCAATCTTCTCTCTTATCTTCTT 59.929 40.741 0.00 0.00 0.00 2.52
2507 2702 3.869065 TCACTGTTCCAAATATCGGTCC 58.131 45.455 0.00 0.00 0.00 4.46
2564 2759 2.698797 GACCCTTCCCGATATGAGAACA 59.301 50.000 0.00 0.00 0.00 3.18
2613 2851 1.439353 AATCATTGGCCTGCTACGCG 61.439 55.000 3.53 3.53 0.00 6.01
2669 2907 2.851263 TTTCGGTGTGCAGGTCTATT 57.149 45.000 0.00 0.00 0.00 1.73
2717 2955 3.953612 TCAGAACATCAAGGCAACACTTT 59.046 39.130 0.00 0.00 41.41 2.66
2809 3047 9.627123 CCTAGGATATATAGATATGGCTCTAGC 57.373 40.741 1.05 0.00 41.14 3.42
2835 3073 3.382546 CCTACCGATATATGGGTTACCGG 59.617 52.174 22.66 13.69 39.69 5.28
2899 3137 1.202651 GCACCTTGCCGATATGGTACT 60.203 52.381 0.00 0.00 41.21 2.73
2924 3162 5.421056 AGTTACCGATATCTTGAACACTGGA 59.579 40.000 0.34 0.00 0.00 3.86
2941 3179 6.640518 ACACTGGATGTAATCTAACGACATT 58.359 36.000 0.00 0.00 44.71 2.71
3073 3321 3.231736 ACGTGAGGCCAAGACGGT 61.232 61.111 20.92 7.86 37.42 4.83
3115 3363 0.392461 GGCGTAGTCAAAGGGCATCA 60.392 55.000 0.00 0.00 0.00 3.07
3133 3381 1.071699 TCACCTAGCAGACCAAACCAC 59.928 52.381 0.00 0.00 0.00 4.16
3319 3584 3.802675 GCAGGGTCGACTTGTTAAGAGTT 60.803 47.826 16.46 0.00 0.00 3.01
3427 3701 1.478510 AGATACACCAAGGAGCACTCG 59.521 52.381 0.00 0.00 0.00 4.18
3444 3718 2.181021 GAGACCGGCCACACTACG 59.819 66.667 0.00 0.00 0.00 3.51
3555 3829 8.824159 GCAGTATTGCTCTTGAATCTATCTTA 57.176 34.615 2.45 0.00 46.95 2.10
3571 3845 6.875076 TCTATCTTAACTGAGGTTTACTGCC 58.125 40.000 0.00 0.00 36.92 4.85
3756 4196 4.764823 TCAGTGGATCCATTTGTGGTTTAC 59.235 41.667 19.62 0.00 0.00 2.01
3783 4313 2.288948 GCTGATGCAATGGTGGTTCAAA 60.289 45.455 0.00 0.00 39.41 2.69
3849 4385 1.742831 GATTGCGCCAATCCACTGTTA 59.257 47.619 16.79 0.00 42.90 2.41
3892 4428 7.823745 ATGTTGACATGAAAAGTAAGTCCTT 57.176 32.000 0.00 0.00 34.83 3.36
3923 4466 8.723942 ACTCTAAATTATCGATTGCAAAGAGT 57.276 30.769 18.84 18.84 33.79 3.24
4362 4905 5.067023 GGCCTGATCAAAAGATGAAGTAAGG 59.933 44.000 0.00 0.00 42.54 2.69
4884 5463 5.359576 TGAGAAGCACAAGGTAAACATTTGT 59.640 36.000 0.00 0.00 35.56 2.83
5375 5981 2.365293 CAGGATGATACGTCCATCACCA 59.635 50.000 23.60 0.00 41.52 4.17
5397 6003 5.163364 CCATAGGCACTGATTTCACTAGACT 60.163 44.000 0.00 0.00 41.52 3.24
5449 6055 2.890945 ACAATTTGCAGGAGTTGGTACC 59.109 45.455 4.43 4.43 0.00 3.34
5591 6197 3.576648 TGACGTCGTTGTGTAATATGCA 58.423 40.909 11.62 0.00 0.00 3.96
5635 6242 5.833406 TGGTGTATCTTGCATTGTAATGG 57.167 39.130 6.72 0.00 36.90 3.16
5676 6283 7.041721 AGTTCCAAAGAAACTTTCAACATTCC 58.958 34.615 4.34 0.00 32.58 3.01
5678 6285 6.572519 TCCAAAGAAACTTTCAACATTCCTG 58.427 36.000 4.34 0.00 0.00 3.86
5793 6403 6.499106 AAACCCATCCCCAATAATTTGATC 57.501 37.500 0.00 0.00 34.60 2.92
5799 6409 8.713036 CCCATCCCCAATAATTTGATCTTTTTA 58.287 33.333 0.00 0.00 34.60 1.52
5958 6659 3.708403 TGCATGACTGGTCTCATTTCT 57.292 42.857 0.00 0.00 0.00 2.52
5973 6674 4.803452 TCATTTCTTCCCAAACTTCACCT 58.197 39.130 0.00 0.00 0.00 4.00
5987 6688 5.326200 ACTTCACCTAGGTTTCTGTATCG 57.674 43.478 13.15 0.00 0.00 2.92
6041 6742 3.455910 TGGTATTGCTGACAGATTAGGCT 59.544 43.478 6.65 0.00 0.00 4.58
6051 6752 4.098914 ACAGATTAGGCTGTTGGTTTCA 57.901 40.909 0.00 0.00 46.42 2.69
6055 6756 3.806949 TTAGGCTGTTGGTTTCATCCT 57.193 42.857 0.00 0.00 35.86 3.24
6056 6757 2.683211 AGGCTGTTGGTTTCATCCTT 57.317 45.000 0.00 0.00 28.62 3.36
6057 6758 3.806949 AGGCTGTTGGTTTCATCCTTA 57.193 42.857 0.00 0.00 28.62 2.69
6058 6759 3.690460 AGGCTGTTGGTTTCATCCTTAG 58.310 45.455 0.00 0.00 28.62 2.18
6059 6760 2.755103 GGCTGTTGGTTTCATCCTTAGG 59.245 50.000 0.00 0.00 0.00 2.69
6060 6761 2.164422 GCTGTTGGTTTCATCCTTAGGC 59.836 50.000 0.00 0.00 0.00 3.93
6061 6762 3.420893 CTGTTGGTTTCATCCTTAGGCA 58.579 45.455 0.00 0.00 0.00 4.75
6062 6763 3.420893 TGTTGGTTTCATCCTTAGGCAG 58.579 45.455 0.00 0.00 0.00 4.85
6063 6764 3.181434 TGTTGGTTTCATCCTTAGGCAGT 60.181 43.478 0.00 0.00 0.00 4.40
6064 6765 3.806949 TGGTTTCATCCTTAGGCAGTT 57.193 42.857 0.00 0.00 0.00 3.16
6065 6766 3.420893 TGGTTTCATCCTTAGGCAGTTG 58.579 45.455 0.00 0.00 0.00 3.16
6066 6767 2.755103 GGTTTCATCCTTAGGCAGTTGG 59.245 50.000 0.00 0.00 0.00 3.77
6067 6768 3.421844 GTTTCATCCTTAGGCAGTTGGT 58.578 45.455 0.00 0.00 0.00 3.67
6068 6769 3.806949 TTCATCCTTAGGCAGTTGGTT 57.193 42.857 0.00 0.00 0.00 3.67
6076 6777 0.251787 AGGCAGTTGGTTTCATCCCC 60.252 55.000 0.00 0.00 0.00 4.81
6083 6784 1.202099 TGGTTTCATCCCCCGTAGCA 61.202 55.000 0.00 0.00 0.00 3.49
6084 6785 0.746923 GGTTTCATCCCCCGTAGCAC 60.747 60.000 0.00 0.00 0.00 4.40
6104 6805 6.241207 GCACAAAGCTAGAATGTTAACTGA 57.759 37.500 7.22 0.00 41.15 3.41
6129 6879 4.036852 AGTTTGTGCTCTTGAGGTTTTAGC 59.963 41.667 0.00 0.00 0.00 3.09
6140 6890 7.257722 TCTTGAGGTTTTAGCAAAAGACAAAG 58.742 34.615 0.00 0.00 0.00 2.77
6158 6908 0.896226 AGGTAGAGTTGAGGCCGTTC 59.104 55.000 0.00 0.00 0.00 3.95
6238 6988 3.136763 CAGGCACCTGCTATTGTCTATG 58.863 50.000 3.23 0.00 41.70 2.23
6243 6993 3.806521 CACCTGCTATTGTCTATGTCTGC 59.193 47.826 0.00 0.00 0.00 4.26
6258 7008 9.868277 GTCTATGTCTGCAGCTTAATAATATCT 57.132 33.333 9.47 0.00 0.00 1.98
6259 7009 9.866798 TCTATGTCTGCAGCTTAATAATATCTG 57.133 33.333 9.47 0.00 0.00 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.446161 AGAACGTCTCGTCCCAATGAATA 59.554 43.478 0.00 0.00 39.99 1.75
1 2 2.233922 AGAACGTCTCGTCCCAATGAAT 59.766 45.455 0.00 0.00 39.99 2.57
2 3 1.616865 AGAACGTCTCGTCCCAATGAA 59.383 47.619 0.00 0.00 39.99 2.57
3 4 1.254026 AGAACGTCTCGTCCCAATGA 58.746 50.000 0.00 0.00 39.99 2.57
6 7 0.748450 ACAAGAACGTCTCGTCCCAA 59.252 50.000 0.00 0.00 39.99 4.12
7 8 0.748450 AACAAGAACGTCTCGTCCCA 59.252 50.000 0.00 0.00 39.99 4.37
8 9 1.137513 CAACAAGAACGTCTCGTCCC 58.862 55.000 0.00 0.00 39.99 4.46
9 10 1.785430 GTCAACAAGAACGTCTCGTCC 59.215 52.381 0.00 0.00 39.99 4.79
10 11 2.728922 AGTCAACAAGAACGTCTCGTC 58.271 47.619 0.00 0.00 39.99 4.20
11 12 2.865343 AGTCAACAAGAACGTCTCGT 57.135 45.000 0.00 0.00 43.97 4.18
12 13 2.978489 GGTAGTCAACAAGAACGTCTCG 59.022 50.000 0.00 0.00 0.00 4.04
13 14 3.973657 TGGTAGTCAACAAGAACGTCTC 58.026 45.455 0.00 0.00 0.00 3.36
23 24 0.764890 AAGGCAGCTGGTAGTCAACA 59.235 50.000 17.12 0.00 0.00 3.33
26 27 2.028112 CACTAAAGGCAGCTGGTAGTCA 60.028 50.000 17.12 0.00 0.00 3.41
33 34 1.667724 CGGAATCACTAAAGGCAGCTG 59.332 52.381 10.11 10.11 0.00 4.24
36 37 2.972625 TGACGGAATCACTAAAGGCAG 58.027 47.619 0.00 0.00 29.99 4.85
39 40 6.494893 TGAAATTGACGGAATCACTAAAGG 57.505 37.500 0.00 0.00 36.92 3.11
44 45 5.939883 TCATCTTGAAATTGACGGAATCACT 59.060 36.000 0.00 0.00 36.92 3.41
49 50 8.925700 CGATATATCATCTTGAAATTGACGGAA 58.074 33.333 13.11 0.00 0.00 4.30
51 52 7.674937 GCCGATATATCATCTTGAAATTGACGG 60.675 40.741 13.11 0.00 33.88 4.79
53 54 8.261492 AGCCGATATATCATCTTGAAATTGAC 57.739 34.615 13.11 0.00 0.00 3.18
59 60 4.462834 ACCGAGCCGATATATCATCTTGAA 59.537 41.667 13.11 0.00 0.00 2.69
81 82 0.172352 CAAGAGCACCTCCGAGAGAC 59.828 60.000 0.00 0.00 0.00 3.36
88 89 3.954904 TCTATACACTCAAGAGCACCTCC 59.045 47.826 0.00 0.00 0.00 4.30
92 93 6.039270 ACTCATCTCTATACACTCAAGAGCAC 59.961 42.308 0.00 0.00 37.31 4.40
98 99 7.520614 CGCATACACTCATCTCTATACACTCAA 60.521 40.741 0.00 0.00 0.00 3.02
103 104 4.378459 CGCGCATACACTCATCTCTATACA 60.378 45.833 8.75 0.00 0.00 2.29
104 105 4.092120 CGCGCATACACTCATCTCTATAC 58.908 47.826 8.75 0.00 0.00 1.47
105 106 3.751698 ACGCGCATACACTCATCTCTATA 59.248 43.478 5.73 0.00 0.00 1.31
111 124 7.856398 ACTTATATATACGCGCATACACTCATC 59.144 37.037 5.73 0.00 0.00 2.92
137 150 7.479897 TTTTAACACAGTATAGACGCAAACA 57.520 32.000 0.00 0.00 0.00 2.83
215 231 7.651808 CCAAAAAGAAAGAAAGCTCACTCATA 58.348 34.615 0.00 0.00 0.00 2.15
252 269 2.290641 ACGCTTTTGTCAACTCATGGAC 59.709 45.455 0.00 0.00 34.63 4.02
255 272 2.046313 GCACGCTTTTGTCAACTCATG 58.954 47.619 0.00 0.00 0.00 3.07
256 273 1.675483 TGCACGCTTTTGTCAACTCAT 59.325 42.857 0.00 0.00 0.00 2.90
299 316 7.490725 GTCCATATGTAGATTGATTGATCTCGG 59.509 40.741 1.24 0.00 37.54 4.63
315 338 1.758280 ACTTTCGCCCGTCCATATGTA 59.242 47.619 1.24 0.00 0.00 2.29
328 351 3.300009 CAACCAAATCTGTCACTTTCGC 58.700 45.455 0.00 0.00 0.00 4.70
352 375 4.433805 GGTTCTGTAAGCACGTCGTATTTG 60.434 45.833 0.00 0.00 27.73 2.32
390 414 3.337889 CTGTGTGCCCGTGTCACG 61.338 66.667 18.54 18.54 42.11 4.35
433 457 7.512130 AGAGCTTTTCTTGGGAATTGAAATTT 58.488 30.769 0.00 0.00 29.61 1.82
460 484 2.971261 GTCGCCAAAACTCGTCAAAATC 59.029 45.455 0.00 0.00 0.00 2.17
504 528 1.676529 CGATCGAGGGCATATCGGTAT 59.323 52.381 10.26 0.00 40.54 2.73
692 719 1.432023 CCACTGGGGTTAGGTTGGGT 61.432 60.000 0.00 0.00 0.00 4.51
762 800 1.406341 GGTGGTAACGGATTGCTGCTA 60.406 52.381 0.00 0.00 42.51 3.49
788 826 4.888823 ACGAGGAGGAGTACTAAATCTTCC 59.111 45.833 0.00 0.00 40.93 3.46
789 827 5.824097 AGACGAGGAGGAGTACTAAATCTTC 59.176 44.000 0.00 0.00 0.00 2.87
799 837 4.515361 CAAGAAGTAGACGAGGAGGAGTA 58.485 47.826 0.00 0.00 0.00 2.59
801 839 2.098443 GCAAGAAGTAGACGAGGAGGAG 59.902 54.545 0.00 0.00 0.00 3.69
802 840 2.093106 GCAAGAAGTAGACGAGGAGGA 58.907 52.381 0.00 0.00 0.00 3.71
803 841 2.096248 AGCAAGAAGTAGACGAGGAGG 58.904 52.381 0.00 0.00 0.00 4.30
804 842 2.750166 TGAGCAAGAAGTAGACGAGGAG 59.250 50.000 0.00 0.00 0.00 3.69
805 843 2.750166 CTGAGCAAGAAGTAGACGAGGA 59.250 50.000 0.00 0.00 0.00 3.71
806 844 2.733858 GCTGAGCAAGAAGTAGACGAGG 60.734 54.545 0.00 0.00 0.00 4.63
807 845 2.163412 AGCTGAGCAAGAAGTAGACGAG 59.837 50.000 7.39 0.00 0.00 4.18
808 846 2.162608 GAGCTGAGCAAGAAGTAGACGA 59.837 50.000 7.39 0.00 0.00 4.20
809 847 2.525055 GAGCTGAGCAAGAAGTAGACG 58.475 52.381 7.39 0.00 0.00 4.18
810 848 2.232452 TGGAGCTGAGCAAGAAGTAGAC 59.768 50.000 7.39 0.00 0.00 2.59
811 849 2.232452 GTGGAGCTGAGCAAGAAGTAGA 59.768 50.000 7.39 0.00 0.00 2.59
812 850 2.615869 GTGGAGCTGAGCAAGAAGTAG 58.384 52.381 7.39 0.00 0.00 2.57
813 851 1.276421 GGTGGAGCTGAGCAAGAAGTA 59.724 52.381 7.39 0.00 0.00 2.24
817 855 1.842920 TGGGTGGAGCTGAGCAAGA 60.843 57.895 7.39 0.00 0.00 3.02
836 874 1.278172 CCGCGATGCTAGATTCGGTG 61.278 60.000 8.23 4.70 35.93 4.94
840 878 2.375766 CCGCCGCGATGCTAGATTC 61.376 63.158 15.93 0.00 0.00 2.52
857 896 0.318784 AGACGAGTCAACACGAAGCC 60.319 55.000 6.97 0.00 34.17 4.35
876 915 4.779733 GAGCCGGGGAGGAGGACA 62.780 72.222 2.18 0.00 45.00 4.02
1101 1143 0.909610 AGAAGGCGACAAGGATGGGA 60.910 55.000 0.00 0.00 0.00 4.37
1225 1286 2.160417 CCAGCAACTAACTGCAGCTTAC 59.840 50.000 15.27 0.00 45.18 2.34
1281 1342 6.936335 TGAGAAAACTGATTCATCACTAGCAA 59.064 34.615 0.00 0.00 32.50 3.91
1282 1343 6.466812 TGAGAAAACTGATTCATCACTAGCA 58.533 36.000 0.00 0.00 32.50 3.49
1537 1634 5.557893 GCATCTAAGAGCGTGTCAATGATTC 60.558 44.000 0.00 0.00 0.00 2.52
1544 1641 0.894835 TGGCATCTAAGAGCGTGTCA 59.105 50.000 0.00 0.00 0.00 3.58
1551 1648 4.156739 GGGAAAACAAGTGGCATCTAAGAG 59.843 45.833 0.00 0.00 0.00 2.85
1553 1650 4.082125 AGGGAAAACAAGTGGCATCTAAG 58.918 43.478 0.00 0.00 0.00 2.18
1700 1797 1.524002 CATGTCCCGCCTCACATCT 59.476 57.895 0.00 0.00 30.48 2.90
1710 1807 2.365617 ACTTGGATAGTAGCATGTCCCG 59.634 50.000 0.00 0.00 34.56 5.14
2026 2131 4.020662 GGCAAATGAATTAAGGTGGGAACA 60.021 41.667 0.00 0.00 38.70 3.18
2027 2132 4.503910 GGCAAATGAATTAAGGTGGGAAC 58.496 43.478 0.00 0.00 0.00 3.62
2028 2133 3.517500 GGGCAAATGAATTAAGGTGGGAA 59.482 43.478 0.00 0.00 0.00 3.97
2029 2134 3.103742 GGGCAAATGAATTAAGGTGGGA 58.896 45.455 0.00 0.00 0.00 4.37
2100 2232 0.043940 ATCTCTTCTCCCCTGTGCCT 59.956 55.000 0.00 0.00 0.00 4.75
2156 2290 5.103855 TGTTTTCCCTCTTTGTTCTCCCTTA 60.104 40.000 0.00 0.00 0.00 2.69
2213 2347 3.009033 TCCACTTCAATTCCCTGTCGATT 59.991 43.478 0.00 0.00 0.00 3.34
2227 2361 6.778821 TGATTTCTTGGTTCTATCCACTTCA 58.221 36.000 0.00 0.00 37.20 3.02
2289 2426 1.611519 CCTGAGAGAGGGGTATCGAC 58.388 60.000 0.00 0.00 38.36 4.20
2342 2537 7.602644 CCTTTCCTTTACTTTCAAATTAAGCCC 59.397 37.037 0.00 0.00 0.00 5.19
2410 2605 2.672098 GGCTAGGATGAGAGGAAGACA 58.328 52.381 0.00 0.00 0.00 3.41
2455 2650 2.522185 GGTGTGTCAGGTACTAGTGGA 58.478 52.381 5.39 0.00 36.02 4.02
2507 2702 1.209128 GACCATATCGGCAGTTCACG 58.791 55.000 0.00 0.00 39.03 4.35
2809 3047 6.183360 CGGTAACCCATATATCGGTAGGTTAG 60.183 46.154 2.10 0.00 39.76 2.34
2835 3073 7.044052 GCGAATCTGCCATTTAACTGAATTTAC 60.044 37.037 0.00 0.00 0.00 2.01
2899 3137 6.604396 TCCAGTGTTCAAGATATCGGTAACTA 59.396 38.462 14.21 3.65 0.00 2.24
2924 3162 4.776349 TGGCCAATGTCGTTAGATTACAT 58.224 39.130 0.61 0.00 35.40 2.29
2941 3179 3.952508 TTTGCTCTCGGCTGGCCA 61.953 61.111 4.71 4.71 42.39 5.36
3115 3363 0.034896 CGTGGTTTGGTCTGCTAGGT 59.965 55.000 0.00 0.00 0.00 3.08
3197 3461 1.639722 ATTTAACCCCCAACACAGGC 58.360 50.000 0.00 0.00 0.00 4.85
3211 3475 5.691815 CCTCGCGTAACCTTTTGAATTTAA 58.308 37.500 5.77 0.00 0.00 1.52
3319 3584 0.824109 CGAGTCATTCTGGGGTAGCA 59.176 55.000 0.00 0.00 0.00 3.49
3427 3701 2.181021 CGTAGTGTGGCCGGTCTC 59.819 66.667 7.97 3.76 0.00 3.36
3555 3829 3.826729 GGAAATGGCAGTAAACCTCAGTT 59.173 43.478 0.00 0.00 38.03 3.16
3559 3833 3.017442 GAGGGAAATGGCAGTAAACCTC 58.983 50.000 13.94 13.94 36.81 3.85
3571 3845 7.391833 AGTTTGAGCTTAGTTAAGAGGGAAATG 59.608 37.037 3.15 0.00 35.33 2.32
3833 4369 2.561569 ACTATAACAGTGGATTGGCGC 58.438 47.619 0.00 0.00 35.62 6.53
3849 4385 5.909621 ACATGAGTTACCACACGTACTAT 57.090 39.130 0.00 0.00 0.00 2.12
3913 4456 1.214175 TCAGTTCCCCACTCTTTGCAA 59.786 47.619 0.00 0.00 30.92 4.08
3923 4466 2.647299 TCTGGCTTATTTCAGTTCCCCA 59.353 45.455 0.00 0.00 33.13 4.96
4020 4563 1.242076 GTGATTGCACCACTCTTGCT 58.758 50.000 10.30 0.00 40.86 3.91
4027 4570 1.577328 CCCAGTCGTGATTGCACCAC 61.577 60.000 8.05 8.05 42.09 4.16
4362 4905 4.384940 AGAGCTTGTTCTTGTTTCTCTCC 58.615 43.478 0.00 0.00 0.00 3.71
4426 4979 7.062957 TCAGTCTGGGAGAAAGAAAAGAAAAT 58.937 34.615 0.00 0.00 0.00 1.82
4884 5463 3.557054 CCAGAGCAACCTACAAGCTGTAA 60.557 47.826 0.00 0.00 39.02 2.41
5375 5981 5.163364 CCAGTCTAGTGAAATCAGTGCCTAT 60.163 44.000 0.98 0.00 0.00 2.57
5397 6003 4.384940 TGTTTGACACGAAGATTGATCCA 58.615 39.130 0.00 0.00 0.00 3.41
5635 6242 8.047310 TCTTTGGAACTTCTTATCCAGATTACC 58.953 37.037 0.00 0.00 45.94 2.85
5696 6303 1.144503 AGCTGGAGATGCTTATTGGGG 59.855 52.381 0.00 0.00 37.52 4.96
5742 6349 0.986992 GTTGCAAAAGCAGCGCATAG 59.013 50.000 11.47 0.00 35.19 2.23
5747 6355 1.925847 TCAAAAGTTGCAAAAGCAGCG 59.074 42.857 0.00 0.00 33.85 5.18
5764 6373 8.270744 CAAATTATTGGGGATGGGTTTATTCAA 58.729 33.333 0.00 0.00 32.69 2.69
5765 6374 7.625280 TCAAATTATTGGGGATGGGTTTATTCA 59.375 33.333 0.00 0.00 37.15 2.57
5793 6403 7.748241 GCAAGTGCAGAGAGAAGTATTAAAAAG 59.252 37.037 0.00 0.00 41.59 2.27
5911 6524 5.482878 ACAAGGCTCATGGAGATTCAAATTT 59.517 36.000 0.00 0.00 0.00 1.82
5958 6659 4.167307 AGAAACCTAGGTGAAGTTTGGGAA 59.833 41.667 17.14 0.00 34.00 3.97
5973 6674 3.028850 CAGTCCCCGATACAGAAACCTA 58.971 50.000 0.00 0.00 0.00 3.08
5987 6688 0.961753 CAAGGCAGTTTTCAGTCCCC 59.038 55.000 0.00 0.00 0.00 4.81
6021 6722 4.446371 ACAGCCTAATCTGTCAGCAATAC 58.554 43.478 0.00 0.00 43.28 1.89
6041 6742 3.181434 ACTGCCTAAGGATGAAACCAACA 60.181 43.478 0.00 0.00 0.00 3.33
6051 6752 3.806949 TGAAACCAACTGCCTAAGGAT 57.193 42.857 0.00 0.00 0.00 3.24
6055 6756 2.556559 GGGGATGAAACCAACTGCCTAA 60.557 50.000 0.00 0.00 0.00 2.69
6056 6757 1.005450 GGGGATGAAACCAACTGCCTA 59.995 52.381 0.00 0.00 0.00 3.93
6057 6758 0.251787 GGGGATGAAACCAACTGCCT 60.252 55.000 0.00 0.00 0.00 4.75
6058 6759 1.257750 GGGGGATGAAACCAACTGCC 61.258 60.000 0.00 0.00 0.00 4.85
6059 6760 1.595093 CGGGGGATGAAACCAACTGC 61.595 60.000 0.00 0.00 0.00 4.40
6060 6761 0.251165 ACGGGGGATGAAACCAACTG 60.251 55.000 0.00 0.00 0.00 3.16
6061 6762 1.280998 CTACGGGGGATGAAACCAACT 59.719 52.381 0.00 0.00 0.00 3.16
6062 6763 1.746470 CTACGGGGGATGAAACCAAC 58.254 55.000 0.00 0.00 0.00 3.77
6063 6764 0.034863 GCTACGGGGGATGAAACCAA 60.035 55.000 0.00 0.00 0.00 3.67
6064 6765 1.202099 TGCTACGGGGGATGAAACCA 61.202 55.000 0.00 0.00 0.00 3.67
6065 6766 0.746923 GTGCTACGGGGGATGAAACC 60.747 60.000 0.00 0.00 0.00 3.27
6066 6767 0.035820 TGTGCTACGGGGGATGAAAC 60.036 55.000 0.00 0.00 0.00 2.78
6067 6768 0.693622 TTGTGCTACGGGGGATGAAA 59.306 50.000 0.00 0.00 0.00 2.69
6068 6769 0.693622 TTTGTGCTACGGGGGATGAA 59.306 50.000 0.00 0.00 0.00 2.57
6083 6784 8.451908 ACTTTCAGTTAACATTCTAGCTTTGT 57.548 30.769 8.61 0.00 0.00 2.83
6084 6785 9.736023 AAACTTTCAGTTAACATTCTAGCTTTG 57.264 29.630 8.61 0.00 37.47 2.77
6091 6792 7.067494 AGAGCACAAACTTTCAGTTAACATTCT 59.933 33.333 8.61 0.00 37.47 2.40
6104 6805 5.405935 AAAACCTCAAGAGCACAAACTTT 57.594 34.783 0.00 0.00 0.00 2.66
6108 6809 3.951037 TGCTAAAACCTCAAGAGCACAAA 59.049 39.130 0.00 0.00 38.20 2.83
6109 6810 3.550820 TGCTAAAACCTCAAGAGCACAA 58.449 40.909 0.00 0.00 38.20 3.33
6129 6879 5.278022 GCCTCAACTCTACCTTTGTCTTTTG 60.278 44.000 0.00 0.00 0.00 2.44
6140 6890 0.108281 GGAACGGCCTCAACTCTACC 60.108 60.000 0.00 0.00 0.00 3.18
6158 6908 4.298332 CAAACGAAACTGGAAAGGAATGG 58.702 43.478 0.00 0.00 0.00 3.16
6258 7008 8.902540 AAGAAACTCAGACATGTAACATTACA 57.097 30.769 0.00 6.92 46.55 2.41


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

AutoCloner maintained by Alex Coulton.