Multiple sequence alignment - TraesCS6D01G185700

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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 TraesCS6D01G185700 chr6D 100.000 9120 0 0 1 9120 240123352 240114233 0.000000e+00 16842.0
1 TraesCS6D01G185700 chr6D 92.733 1032 28 12 5203 6203 234155384 234154369 0.000000e+00 1447.0
2 TraesCS6D01G185700 chr6D 95.424 896 39 2 109 1002 240130768 240129873 0.000000e+00 1426.0
3 TraesCS6D01G185700 chr6D 94.303 825 23 7 5732 6548 470172952 470173760 0.000000e+00 1242.0
4 TraesCS6D01G185700 chr6D 87.542 891 94 15 1 881 329650697 329651580 0.000000e+00 1014.0
5 TraesCS6D01G185700 chr6D 84.495 1019 125 29 1 1002 164138467 164139469 0.000000e+00 976.0
6 TraesCS6D01G185700 chr6D 92.926 622 33 2 8279 8899 240129726 240129115 0.000000e+00 894.0
7 TraesCS6D01G185700 chr6D 71.307 1645 406 44 6550 8147 353364565 353366190 6.730000e-96 363.0
8 TraesCS6D01G185700 chr6D 93.151 146 9 1 8975 9120 240129113 240128969 7.170000e-51 213.0
9 TraesCS6D01G185700 chr6D 90.972 144 10 2 8151 8291 240129884 240129741 3.360000e-44 191.0
10 TraesCS6D01G185700 chr6D 90.625 64 5 1 9042 9105 310848806 310848868 5.870000e-12 84.2
11 TraesCS6D01G185700 chr6D 89.062 64 6 1 9042 9105 310841240 310841302 2.730000e-10 78.7
12 TraesCS6D01G185700 chr2A 90.154 3301 313 10 1016 4311 699591704 699588411 0.000000e+00 4285.0
13 TraesCS6D01G185700 chr2A 88.608 1580 153 7 6550 8102 699578237 699576658 0.000000e+00 1895.0
14 TraesCS6D01G185700 chr2A 88.344 163 15 4 8611 8773 312388500 312388342 9.350000e-45 193.0
15 TraesCS6D01G185700 chr2A 90.411 146 9 4 4911 5054 24274821 24274679 4.350000e-43 187.0
16 TraesCS6D01G185700 chr2D 85.268 3903 559 15 1024 4915 546423577 546419680 0.000000e+00 4008.0
17 TraesCS6D01G185700 chr2D 90.674 1662 88 22 4916 6553 146807990 146809608 0.000000e+00 2148.0
18 TraesCS6D01G185700 chr2D 88.504 1531 91 40 4914 6409 38534856 38536336 0.000000e+00 1773.0
19 TraesCS6D01G185700 chr2D 91.927 991 48 11 5569 6548 244010681 244009712 0.000000e+00 1358.0
20 TraesCS6D01G185700 chr2D 88.268 895 92 11 1 888 190563739 190564627 0.000000e+00 1059.0
21 TraesCS6D01G185700 chr2D 87.835 896 95 13 1 888 190556726 190557615 0.000000e+00 1038.0
22 TraesCS6D01G185700 chr2D 86.464 953 108 20 1 941 235081868 235082811 0.000000e+00 1026.0
23 TraesCS6D01G185700 chr2D 91.018 167 10 2 4916 5077 98658144 98657978 4.290000e-53 220.0
24 TraesCS6D01G185700 chr5D 84.913 3904 570 18 1024 4915 553918963 553915067 0.000000e+00 3928.0
25 TraesCS6D01G185700 chr5D 90.576 1666 43 20 4916 6520 439484191 439485803 0.000000e+00 2102.0
26 TraesCS6D01G185700 chr5D 91.633 1482 47 23 4916 6362 403997089 403998528 0.000000e+00 1978.0
27 TraesCS6D01G185700 chr5D 94.118 1258 39 10 5311 6548 554904641 554903399 0.000000e+00 1881.0
28 TraesCS6D01G185700 chr5D 91.558 1386 40 18 4916 6251 62890526 62891884 0.000000e+00 1840.0
29 TraesCS6D01G185700 chr5D 92.084 1099 34 15 5092 6174 421885385 421886446 0.000000e+00 1498.0
30 TraesCS6D01G185700 chr5D 91.790 1084 22 11 4916 5946 416728060 416726991 0.000000e+00 1447.0
31 TraesCS6D01G185700 chr5D 82.292 1632 250 26 6550 8148 553915071 553913446 0.000000e+00 1376.0
32 TraesCS6D01G185700 chr5D 84.766 1024 121 30 1 1002 258379548 258380558 0.000000e+00 994.0
33 TraesCS6D01G185700 chr5D 85.963 919 105 21 1 909 12641339 12642243 0.000000e+00 961.0
34 TraesCS6D01G185700 chr5D 87.781 401 10 10 4916 5292 226663058 226663443 5.060000e-117 433.0
35 TraesCS6D01G185700 chr5D 91.071 112 6 4 5247 5356 547292956 547292847 2.050000e-31 148.0
36 TraesCS6D01G185700 chr5D 90.625 64 5 1 9042 9105 16242900 16242838 5.870000e-12 84.2
37 TraesCS6D01G185700 chr5B 84.556 3859 566 21 1071 4915 136424781 136428623 0.000000e+00 3797.0
38 TraesCS6D01G185700 chr5B 82.471 3845 646 16 1079 4915 384578962 384582786 0.000000e+00 3341.0
39 TraesCS6D01G185700 chr5B 82.005 1556 245 20 6621 8147 349093716 349092167 0.000000e+00 1290.0
40 TraesCS6D01G185700 chr5B 84.921 1008 109 28 16 1002 653381425 653382410 0.000000e+00 979.0
41 TraesCS6D01G185700 chr5B 77.500 160 29 7 6550 6705 44473594 44473750 1.260000e-13 89.8
42 TraesCS6D01G185700 chr3B 83.180 3906 630 26 1024 4915 144803686 144807578 0.000000e+00 3548.0
43 TraesCS6D01G185700 chr3B 83.107 3901 628 21 1024 4915 646286907 646283029 0.000000e+00 3524.0
44 TraesCS6D01G185700 chr3B 89.225 1717 179 6 1021 2734 105447668 105449381 0.000000e+00 2141.0
45 TraesCS6D01G185700 chr3B 88.357 1589 159 10 6550 8112 105460235 105461823 0.000000e+00 1886.0
46 TraesCS6D01G185700 chr3B 80.880 1637 267 29 6550 8151 646283033 646281408 0.000000e+00 1247.0
47 TraesCS6D01G185700 chr3B 91.617 167 11 3 4914 5077 764150860 764151026 2.560000e-55 228.0
48 TraesCS6D01G185700 chr4A 82.761 3904 646 23 1025 4915 732071030 732067141 0.000000e+00 3456.0
49 TraesCS6D01G185700 chr4A 78.004 1623 302 29 6550 8140 732067145 732065546 0.000000e+00 968.0
50 TraesCS6D01G185700 chr4A 88.636 264 20 6 8279 8540 247118186 247118441 6.880000e-81 313.0
51 TraesCS6D01G185700 chr4A 83.333 144 23 1 8586 8729 247126290 247126432 2.070000e-26 132.0
52 TraesCS6D01G185700 chr4A 100.000 28 0 0 8498 8525 252129943 252129970 1.700000e-02 52.8
53 TraesCS6D01G185700 chr4A 100.000 28 0 0 8498 8525 418237491 418237464 1.700000e-02 52.8
54 TraesCS6D01G185700 chr1A 86.751 2838 359 14 2083 4913 550227129 550224302 0.000000e+00 3142.0
55 TraesCS6D01G185700 chr1A 82.731 1633 246 21 6550 8147 550224304 550222673 0.000000e+00 1421.0
56 TraesCS6D01G185700 chr1A 87.879 264 23 6 8279 8540 379324102 379324358 1.490000e-77 302.0
57 TraesCS6D01G185700 chr1A 88.194 144 16 1 8586 8729 379324358 379324500 4.380000e-38 171.0
58 TraesCS6D01G185700 chr4D 92.509 1682 49 32 4916 6548 135016003 135014350 0.000000e+00 2337.0
59 TraesCS6D01G185700 chr4D 90.971 1329 46 30 4916 6203 151226823 151225528 0.000000e+00 1722.0
60 TraesCS6D01G185700 chr4D 87.661 1086 39 25 4916 5930 411195136 411196197 0.000000e+00 1175.0
61 TraesCS6D01G185700 chr4D 91.018 334 30 0 8671 9004 232465757 232465424 1.400000e-122 451.0
62 TraesCS6D01G185700 chr4D 91.018 334 30 0 8671 9004 232474310 232473977 1.400000e-122 451.0
63 TraesCS6D01G185700 chr4D 91.473 258 21 1 8747 9004 238851320 238851576 4.050000e-93 353.0
64 TraesCS6D01G185700 chr4D 91.085 258 22 1 8747 9004 238857013 238857269 1.880000e-91 348.0
65 TraesCS6D01G185700 chr4D 91.960 199 15 1 8740 8938 250687939 250688136 2.510000e-70 278.0
66 TraesCS6D01G185700 chr4D 89.950 199 19 1 8740 8938 250650163 250650360 1.180000e-63 255.0
67 TraesCS6D01G185700 chr4D 89.950 199 19 1 8740 8938 250680413 250680610 1.180000e-63 255.0
68 TraesCS6D01G185700 chr4D 90.625 64 5 1 9042 9105 154052394 154052456 5.870000e-12 84.2
69 TraesCS6D01G185700 chr4D 89.062 64 6 1 9042 9105 173784801 173784863 2.730000e-10 78.7
70 TraesCS6D01G185700 chr7D 85.695 2167 302 7 2752 4915 538852489 538850328 0.000000e+00 2278.0
71 TraesCS6D01G185700 chr7D 91.696 1698 44 19 4916 6549 150112075 150113739 0.000000e+00 2265.0
72 TraesCS6D01G185700 chr7D 94.831 1122 26 11 5410 6520 99722266 99723366 0.000000e+00 1722.0
73 TraesCS6D01G185700 chr7D 87.778 900 92 14 1 888 460840189 460839296 0.000000e+00 1037.0
74 TraesCS6D01G185700 chr7D 89.011 728 31 9 4916 5619 79708054 79707352 0.000000e+00 856.0
75 TraesCS6D01G185700 chr7D 91.232 422 13 3 5005 5402 559835936 559835515 3.720000e-153 553.0
76 TraesCS6D01G185700 chr7D 90.939 309 24 3 8696 9004 145131889 145131585 6.590000e-111 412.0
77 TraesCS6D01G185700 chr7D 89.634 164 13 3 4916 5077 117177799 117177960 1.200000e-48 206.0
78 TraesCS6D01G185700 chr7D 92.188 64 4 1 9042 9105 185626090 185626152 1.260000e-13 89.8
79 TraesCS6D01G185700 chr1D 91.793 1645 54 22 4916 6520 127025894 127027497 0.000000e+00 2215.0
80 TraesCS6D01G185700 chr1D 84.800 1625 218 13 6550 8147 84706909 84705287 0.000000e+00 1605.0
81 TraesCS6D01G185700 chr1D 90.625 64 5 1 9042 9105 134363056 134363118 5.870000e-12 84.2
82 TraesCS6D01G185700 chr1D 90.625 64 5 1 9042 9105 134383714 134383776 5.870000e-12 84.2
83 TraesCS6D01G185700 chrUn 92.729 1334 43 18 5247 6548 104913642 104914953 0.000000e+00 1877.0
84 TraesCS6D01G185700 chrUn 93.548 186 12 0 8654 8839 12913092 12912907 2.510000e-70 278.0
85 TraesCS6D01G185700 chr3D 91.492 1387 27 18 4916 6247 190949798 190948448 0.000000e+00 1823.0
86 TraesCS6D01G185700 chr3D 84.828 1628 211 18 6550 8147 556255953 556257574 0.000000e+00 1605.0
87 TraesCS6D01G185700 chr3D 90.640 1218 57 19 4916 6094 25656193 25654994 0.000000e+00 1565.0
88 TraesCS6D01G185700 chr3D 91.927 1090 33 11 4916 5953 586774822 586773736 0.000000e+00 1474.0
89 TraesCS6D01G185700 chr3D 92.961 966 39 17 5247 6200 230665293 230666241 0.000000e+00 1380.0
90 TraesCS6D01G185700 chr3D 87.869 948 97 14 1 941 134038399 134039335 0.000000e+00 1098.0
91 TraesCS6D01G185700 chr3D 91.003 289 26 0 8716 9004 472581777 472581489 3.090000e-104 390.0
92 TraesCS6D01G185700 chr3D 91.473 258 19 2 8747 9004 210081796 210082050 1.460000e-92 351.0
93 TraesCS6D01G185700 chr7A 82.496 1971 320 19 1021 2978 563838914 563836956 0.000000e+00 1705.0
94 TraesCS6D01G185700 chr7A 86.090 532 64 6 7629 8150 159420282 159420813 1.720000e-156 564.0
95 TraesCS6D01G185700 chr7A 90.208 337 23 2 7821 8147 637996047 637995711 1.820000e-116 431.0
96 TraesCS6D01G185700 chr1B 83.058 1635 239 22 6550 8148 633621622 633623254 0.000000e+00 1450.0
97 TraesCS6D01G185700 chr1B 79.558 1629 271 27 6550 8146 368205250 368203652 0.000000e+00 1107.0
98 TraesCS6D01G185700 chr2B 81.265 1628 273 18 6550 8148 87533853 87532229 0.000000e+00 1288.0
99 TraesCS6D01G185700 chr2B 81.903 431 60 8 6550 6963 584807281 584807710 1.880000e-91 348.0
100 TraesCS6D01G185700 chr2B 91.716 169 9 2 4914 5077 68761650 68761482 7.120000e-56 230.0
101 TraesCS6D01G185700 chr3A 90.323 775 69 4 8279 9053 583365840 583365072 0.000000e+00 1011.0
102 TraesCS6D01G185700 chr3A 90.194 775 69 4 8279 9053 583315799 583315032 0.000000e+00 1003.0
103 TraesCS6D01G185700 chr3A 86.489 903 91 16 8175 9053 248729877 248728982 0.000000e+00 963.0
104 TraesCS6D01G185700 chr3A 84.692 908 84 15 8171 9053 248721785 248720908 0.000000e+00 856.0
105 TraesCS6D01G185700 chr3A 97.872 47 0 1 8237 8282 150340515 150340561 7.590000e-11 80.5
106 TraesCS6D01G185700 chr6A 85.261 977 122 21 1 963 227400153 227401121 0.000000e+00 987.0
107 TraesCS6D01G185700 chr6B 84.184 999 127 26 17 1002 108854993 108854013 0.000000e+00 941.0
108 TraesCS6D01G185700 chr6B 93.293 164 9 1 4914 5077 352190254 352190415 3.290000e-59 241.0
109 TraesCS6D01G185700 chr6B 96.000 50 1 1 8234 8282 424779086 424779135 7.590000e-11 80.5
110 TraesCS6D01G185700 chr7B 87.646 769 76 11 7390 8148 540809584 540808825 0.000000e+00 876.0
111 TraesCS6D01G185700 chr5A 89.754 244 23 1 8812 9053 301718617 301718374 2.470000e-80 311.0
112 TraesCS6D01G185700 chr5A 90.303 165 9 4 4914 5077 696673754 696673596 9.280000e-50 209.0
113 TraesCS6D01G185700 chr5A 88.485 165 15 2 4914 5077 318433957 318433796 7.220000e-46 196.0
114 TraesCS6D01G185700 chr5A 87.879 165 18 2 4914 5077 549003359 549003522 9.350000e-45 193.0
115 TraesCS6D01G185700 chr5A 95.775 71 2 1 9051 9120 97337500 97337570 7.480000e-21 113.0
116 TraesCS6D01G185700 chr5A 92.958 71 4 1 9051 9120 97362964 97363034 1.620000e-17 102.0
117 TraesCS6D01G185700 chr4B 90.909 66 4 2 9038 9103 281142199 281142262 4.540000e-13 87.9
118 TraesCS6D01G185700 chr4B 87.324 71 7 2 9035 9105 266198209 266198277 7.590000e-11 80.5
119 TraesCS6D01G185700 chr4B 74.843 159 35 5 6550 6705 567180347 567180191 5.910000e-07 67.6


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 TraesCS6D01G185700 chr6D 240114233 240123352 9119 True 16842.0 16842 100.00000 1 9120 1 chr6D.!!$R2 9119
1 TraesCS6D01G185700 chr6D 234154369 234155384 1015 True 1447.0 1447 92.73300 5203 6203 1 chr6D.!!$R1 1000
2 TraesCS6D01G185700 chr6D 470172952 470173760 808 False 1242.0 1242 94.30300 5732 6548 1 chr6D.!!$F6 816
3 TraesCS6D01G185700 chr6D 329650697 329651580 883 False 1014.0 1014 87.54200 1 881 1 chr6D.!!$F4 880
4 TraesCS6D01G185700 chr6D 164138467 164139469 1002 False 976.0 976 84.49500 1 1002 1 chr6D.!!$F1 1001
5 TraesCS6D01G185700 chr6D 240128969 240130768 1799 True 681.0 1426 93.11825 109 9120 4 chr6D.!!$R3 9011
6 TraesCS6D01G185700 chr6D 353364565 353366190 1625 False 363.0 363 71.30700 6550 8147 1 chr6D.!!$F5 1597
7 TraesCS6D01G185700 chr2A 699588411 699591704 3293 True 4285.0 4285 90.15400 1016 4311 1 chr2A.!!$R4 3295
8 TraesCS6D01G185700 chr2A 699576658 699578237 1579 True 1895.0 1895 88.60800 6550 8102 1 chr2A.!!$R3 1552
9 TraesCS6D01G185700 chr2D 546419680 546423577 3897 True 4008.0 4008 85.26800 1024 4915 1 chr2D.!!$R3 3891
10 TraesCS6D01G185700 chr2D 146807990 146809608 1618 False 2148.0 2148 90.67400 4916 6553 1 chr2D.!!$F2 1637
11 TraesCS6D01G185700 chr2D 38534856 38536336 1480 False 1773.0 1773 88.50400 4914 6409 1 chr2D.!!$F1 1495
12 TraesCS6D01G185700 chr2D 244009712 244010681 969 True 1358.0 1358 91.92700 5569 6548 1 chr2D.!!$R2 979
13 TraesCS6D01G185700 chr2D 190563739 190564627 888 False 1059.0 1059 88.26800 1 888 1 chr2D.!!$F4 887
14 TraesCS6D01G185700 chr2D 190556726 190557615 889 False 1038.0 1038 87.83500 1 888 1 chr2D.!!$F3 887
15 TraesCS6D01G185700 chr2D 235081868 235082811 943 False 1026.0 1026 86.46400 1 941 1 chr2D.!!$F5 940
16 TraesCS6D01G185700 chr5D 553913446 553918963 5517 True 2652.0 3928 83.60250 1024 8148 2 chr5D.!!$R5 7124
17 TraesCS6D01G185700 chr5D 439484191 439485803 1612 False 2102.0 2102 90.57600 4916 6520 1 chr5D.!!$F7 1604
18 TraesCS6D01G185700 chr5D 403997089 403998528 1439 False 1978.0 1978 91.63300 4916 6362 1 chr5D.!!$F5 1446
19 TraesCS6D01G185700 chr5D 554903399 554904641 1242 True 1881.0 1881 94.11800 5311 6548 1 chr5D.!!$R4 1237
20 TraesCS6D01G185700 chr5D 62890526 62891884 1358 False 1840.0 1840 91.55800 4916 6251 1 chr5D.!!$F2 1335
21 TraesCS6D01G185700 chr5D 421885385 421886446 1061 False 1498.0 1498 92.08400 5092 6174 1 chr5D.!!$F6 1082
22 TraesCS6D01G185700 chr5D 416726991 416728060 1069 True 1447.0 1447 91.79000 4916 5946 1 chr5D.!!$R2 1030
23 TraesCS6D01G185700 chr5D 258379548 258380558 1010 False 994.0 994 84.76600 1 1002 1 chr5D.!!$F4 1001
24 TraesCS6D01G185700 chr5D 12641339 12642243 904 False 961.0 961 85.96300 1 909 1 chr5D.!!$F1 908
25 TraesCS6D01G185700 chr5B 136424781 136428623 3842 False 3797.0 3797 84.55600 1071 4915 1 chr5B.!!$F2 3844
26 TraesCS6D01G185700 chr5B 384578962 384582786 3824 False 3341.0 3341 82.47100 1079 4915 1 chr5B.!!$F3 3836
27 TraesCS6D01G185700 chr5B 349092167 349093716 1549 True 1290.0 1290 82.00500 6621 8147 1 chr5B.!!$R1 1526
28 TraesCS6D01G185700 chr5B 653381425 653382410 985 False 979.0 979 84.92100 16 1002 1 chr5B.!!$F4 986
29 TraesCS6D01G185700 chr3B 144803686 144807578 3892 False 3548.0 3548 83.18000 1024 4915 1 chr3B.!!$F3 3891
30 TraesCS6D01G185700 chr3B 646281408 646286907 5499 True 2385.5 3524 81.99350 1024 8151 2 chr3B.!!$R1 7127
31 TraesCS6D01G185700 chr3B 105447668 105449381 1713 False 2141.0 2141 89.22500 1021 2734 1 chr3B.!!$F1 1713
32 TraesCS6D01G185700 chr3B 105460235 105461823 1588 False 1886.0 1886 88.35700 6550 8112 1 chr3B.!!$F2 1562
33 TraesCS6D01G185700 chr4A 732065546 732071030 5484 True 2212.0 3456 80.38250 1025 8140 2 chr4A.!!$R2 7115
34 TraesCS6D01G185700 chr1A 550222673 550227129 4456 True 2281.5 3142 84.74100 2083 8147 2 chr1A.!!$R1 6064
35 TraesCS6D01G185700 chr4D 135014350 135016003 1653 True 2337.0 2337 92.50900 4916 6548 1 chr4D.!!$R1 1632
36 TraesCS6D01G185700 chr4D 151225528 151226823 1295 True 1722.0 1722 90.97100 4916 6203 1 chr4D.!!$R2 1287
37 TraesCS6D01G185700 chr4D 411195136 411196197 1061 False 1175.0 1175 87.66100 4916 5930 1 chr4D.!!$F8 1014
38 TraesCS6D01G185700 chr7D 538850328 538852489 2161 True 2278.0 2278 85.69500 2752 4915 1 chr7D.!!$R4 2163
39 TraesCS6D01G185700 chr7D 150112075 150113739 1664 False 2265.0 2265 91.69600 4916 6549 1 chr7D.!!$F3 1633
40 TraesCS6D01G185700 chr7D 99722266 99723366 1100 False 1722.0 1722 94.83100 5410 6520 1 chr7D.!!$F1 1110
41 TraesCS6D01G185700 chr7D 460839296 460840189 893 True 1037.0 1037 87.77800 1 888 1 chr7D.!!$R3 887
42 TraesCS6D01G185700 chr7D 79707352 79708054 702 True 856.0 856 89.01100 4916 5619 1 chr7D.!!$R1 703
43 TraesCS6D01G185700 chr1D 127025894 127027497 1603 False 2215.0 2215 91.79300 4916 6520 1 chr1D.!!$F1 1604
44 TraesCS6D01G185700 chr1D 84705287 84706909 1622 True 1605.0 1605 84.80000 6550 8147 1 chr1D.!!$R1 1597
45 TraesCS6D01G185700 chrUn 104913642 104914953 1311 False 1877.0 1877 92.72900 5247 6548 1 chrUn.!!$F1 1301
46 TraesCS6D01G185700 chr3D 190948448 190949798 1350 True 1823.0 1823 91.49200 4916 6247 1 chr3D.!!$R2 1331
47 TraesCS6D01G185700 chr3D 556255953 556257574 1621 False 1605.0 1605 84.82800 6550 8147 1 chr3D.!!$F4 1597
48 TraesCS6D01G185700 chr3D 25654994 25656193 1199 True 1565.0 1565 90.64000 4916 6094 1 chr3D.!!$R1 1178
49 TraesCS6D01G185700 chr3D 586773736 586774822 1086 True 1474.0 1474 91.92700 4916 5953 1 chr3D.!!$R4 1037
50 TraesCS6D01G185700 chr3D 230665293 230666241 948 False 1380.0 1380 92.96100 5247 6200 1 chr3D.!!$F3 953
51 TraesCS6D01G185700 chr3D 134038399 134039335 936 False 1098.0 1098 87.86900 1 941 1 chr3D.!!$F1 940
52 TraesCS6D01G185700 chr7A 563836956 563838914 1958 True 1705.0 1705 82.49600 1021 2978 1 chr7A.!!$R1 1957
53 TraesCS6D01G185700 chr7A 159420282 159420813 531 False 564.0 564 86.09000 7629 8150 1 chr7A.!!$F1 521
54 TraesCS6D01G185700 chr1B 633621622 633623254 1632 False 1450.0 1450 83.05800 6550 8148 1 chr1B.!!$F1 1598
55 TraesCS6D01G185700 chr1B 368203652 368205250 1598 True 1107.0 1107 79.55800 6550 8146 1 chr1B.!!$R1 1596
56 TraesCS6D01G185700 chr2B 87532229 87533853 1624 True 1288.0 1288 81.26500 6550 8148 1 chr2B.!!$R2 1598
57 TraesCS6D01G185700 chr3A 583365072 583365840 768 True 1011.0 1011 90.32300 8279 9053 1 chr3A.!!$R4 774
58 TraesCS6D01G185700 chr3A 583315032 583315799 767 True 1003.0 1003 90.19400 8279 9053 1 chr3A.!!$R3 774
59 TraesCS6D01G185700 chr3A 248728982 248729877 895 True 963.0 963 86.48900 8175 9053 1 chr3A.!!$R2 878
60 TraesCS6D01G185700 chr3A 248720908 248721785 877 True 856.0 856 84.69200 8171 9053 1 chr3A.!!$R1 882
61 TraesCS6D01G185700 chr6A 227400153 227401121 968 False 987.0 987 85.26100 1 963 1 chr6A.!!$F1 962
62 TraesCS6D01G185700 chr6B 108854013 108854993 980 True 941.0 941 84.18400 17 1002 1 chr6B.!!$R1 985
63 TraesCS6D01G185700 chr7B 540808825 540809584 759 True 876.0 876 87.64600 7390 8148 1 chr7B.!!$R1 758

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
87 89 0.931662 AAACAGACGTCGTCGAACGG 60.932 55.000 19.11 10.30 46.72 4.44 F
1006 1048 0.251474 AGCAGGGCGACGGGTATATA 60.251 55.000 0.00 0.00 0.00 0.86 F
2216 2290 0.037790 GCTCGAGTCAAGTGCCTCTT 60.038 55.000 15.13 0.00 36.75 2.85 F
3022 3099 0.178967 TTGCATTCCCTGGAGCAACA 60.179 50.000 8.34 0.00 41.55 3.33 F
4366 4451 0.107165 GGCCTTTCGTGCCTCCTTAT 60.107 55.000 0.00 0.00 45.70 1.73 F
4891 4976 0.712380 ATTCTGGTGGGGGAGCAAAT 59.288 50.000 0.00 0.00 0.00 2.32 F
5579 5812 1.203052 TGTTACTAGTGGCGCACCTAC 59.797 52.381 10.83 2.11 34.49 3.18 F
6685 7029 0.323178 CCCAGAGGCTTTGAGTGCAT 60.323 55.000 6.61 0.00 0.00 3.96 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1058 1102 0.665835 GATCTCCATGTCGAGCGAGT 59.334 55.000 0.00 0.00 0.00 4.18 R
2126 2187 0.947244 CTGCTCCACGCTTTCTGTTT 59.053 50.000 0.00 0.00 40.11 2.83 R
3580 3660 0.248661 CCGATGTGTACAGCTCCTCG 60.249 60.000 0.00 0.00 0.00 4.63 R
4728 4813 0.105760 TGTTTGCAATCCACCCCTGT 60.106 50.000 0.00 0.00 0.00 4.00 R
6032 6328 1.553248 TGGTGCGCCATTAGTAGTTCT 59.447 47.619 16.89 0.00 40.46 3.01 R
6575 6918 0.837272 CCTCCCATTCCTTTCGGCTA 59.163 55.000 0.00 0.00 0.00 3.93 R
7309 7674 0.033796 AGGGAATGCCACCATGAGTG 60.034 55.000 0.00 0.35 46.83 3.51 R
8403 8844 0.031994 CGTTTTCCCCTGCACCTTTG 59.968 55.000 0.00 0.00 0.00 2.77 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
29 31 1.678101 GGTTATGGTCATCTTGCCTGC 59.322 52.381 0.00 0.00 0.00 4.85
59 61 5.752650 TCTAGGAAGAAGAACGAGTCCATA 58.247 41.667 0.00 0.00 0.00 2.74
60 62 4.993029 AGGAAGAAGAACGAGTCCATAG 57.007 45.455 0.00 0.00 0.00 2.23
72 74 3.368427 CGAGTCCATAGAGAAGGCAAACA 60.368 47.826 0.00 0.00 0.00 2.83
78 80 2.156343 AGAGAAGGCAAACAGACGTC 57.844 50.000 7.70 7.70 33.43 4.34
87 89 0.931662 AAACAGACGTCGTCGAACGG 60.932 55.000 19.11 10.30 46.72 4.44
374 399 3.011821 TGTTATTAACCATGGCAAGGGGA 59.988 43.478 13.04 0.00 0.00 4.81
438 464 3.372514 GCCGGAACAACAAACAACAATTT 59.627 39.130 5.05 0.00 0.00 1.82
759 789 7.509141 TTAAATATGATGCACGGTTCATGAT 57.491 32.000 10.18 0.00 34.52 2.45
810 841 5.998454 ATCTGTAAATATGCAGTGCACTC 57.002 39.130 22.44 12.59 43.04 3.51
881 923 1.683365 GGCCCAACATGCACAGGAT 60.683 57.895 0.00 0.00 0.00 3.24
1003 1045 3.849951 CAGCAGGGCGACGGGTAT 61.850 66.667 0.00 0.00 0.00 2.73
1005 1047 1.533273 AGCAGGGCGACGGGTATAT 60.533 57.895 0.00 0.00 0.00 0.86
1006 1048 0.251474 AGCAGGGCGACGGGTATATA 60.251 55.000 0.00 0.00 0.00 0.86
1007 1049 0.604578 GCAGGGCGACGGGTATATAA 59.395 55.000 0.00 0.00 0.00 0.98
1008 1050 1.403780 GCAGGGCGACGGGTATATAAG 60.404 57.143 0.00 0.00 0.00 1.73
1009 1051 0.893447 AGGGCGACGGGTATATAAGC 59.107 55.000 0.00 0.00 0.00 3.09
1010 1052 0.604578 GGGCGACGGGTATATAAGCA 59.395 55.000 0.00 0.00 0.00 3.91
1011 1053 1.001181 GGGCGACGGGTATATAAGCAA 59.999 52.381 0.00 0.00 0.00 3.91
1012 1054 2.548493 GGGCGACGGGTATATAAGCAAA 60.548 50.000 0.00 0.00 0.00 3.68
1013 1055 3.332034 GGCGACGGGTATATAAGCAAAT 58.668 45.455 0.00 0.00 0.00 2.32
1014 1056 3.749609 GGCGACGGGTATATAAGCAAATT 59.250 43.478 0.00 0.00 0.00 1.82
1015 1057 4.378046 GGCGACGGGTATATAAGCAAATTG 60.378 45.833 0.00 0.00 0.00 2.32
1016 1058 4.212636 GCGACGGGTATATAAGCAAATTGT 59.787 41.667 0.00 0.00 0.00 2.71
1017 1059 5.675970 CGACGGGTATATAAGCAAATTGTG 58.324 41.667 0.00 0.00 0.00 3.33
1018 1060 5.235616 CGACGGGTATATAAGCAAATTGTGT 59.764 40.000 0.00 0.00 0.00 3.72
1019 1061 6.563381 CGACGGGTATATAAGCAAATTGTGTC 60.563 42.308 0.00 0.00 0.00 3.67
1031 1073 3.922171 AATTGTGTCTGATCCCCTCTC 57.078 47.619 0.00 0.00 0.00 3.20
1032 1074 2.325661 TTGTGTCTGATCCCCTCTCA 57.674 50.000 0.00 0.00 0.00 3.27
1049 1091 5.821097 CCTCTCATTAGGGTTTTTCTTCCT 58.179 41.667 0.00 0.00 32.55 3.36
1052 1096 4.930696 TCATTAGGGTTTTTCTTCCTCCC 58.069 43.478 0.00 0.00 38.50 4.30
1058 1102 2.684192 TTTTTCTTCCTCCCGCGGCA 62.684 55.000 22.85 2.88 0.00 5.69
1108 1155 2.989639 CTTCCCTGCCACCGATCA 59.010 61.111 0.00 0.00 0.00 2.92
1222 1273 1.079127 CGATGGAGGGCTCAACGTT 60.079 57.895 0.00 0.00 0.00 3.99
1243 1294 1.205657 GCGTCTAAATCGGCGATGAA 58.794 50.000 24.73 13.39 0.00 2.57
1305 1356 5.908590 AGGATGATCTGGTGGATATAGTCA 58.091 41.667 0.00 0.00 34.33 3.41
1322 1373 8.866823 ATATAGTCATGGAGGATGGTGATATT 57.133 34.615 0.00 0.00 32.26 1.28
1374 1425 1.372872 CGTGTGCACATCGACAGGA 60.373 57.895 24.69 0.00 31.10 3.86
1410 1461 1.611491 GGTTTTTCCGCAACATGAGGA 59.389 47.619 0.00 0.00 44.66 3.71
1443 1495 2.191128 AGCGCAAGAGGTCAAATTCT 57.809 45.000 11.47 0.00 43.02 2.40
1453 1505 2.443255 AGGTCAAATTCTGTCCACTGGT 59.557 45.455 0.00 0.00 35.83 4.00
1502 1554 4.514577 CTCGGCGATTGGGAGCGT 62.515 66.667 11.27 0.00 36.94 5.07
1542 1594 2.034066 CCTTCAAGGGCAAGGCGA 59.966 61.111 0.00 0.00 34.21 5.54
1643 1695 1.878088 GACCTCCCGGAACTGTTTTTC 59.122 52.381 0.73 0.00 0.00 2.29
1772 1824 1.374758 AAAGCCTCTCAGGAACGCG 60.375 57.895 3.53 3.53 37.67 6.01
1834 1886 2.497675 TCAAGTATGAGAGACTGCCCAC 59.502 50.000 0.00 0.00 0.00 4.61
1850 1902 4.996434 ACCTGGTGCGCTGTCTGC 62.996 66.667 9.73 0.00 38.57 4.26
1866 1918 0.459899 CTGCGGTATGCTAGGTCACA 59.540 55.000 0.00 0.00 46.63 3.58
1985 2037 2.668632 GAGAATGCACCGGGTGGA 59.331 61.111 27.41 25.77 38.41 4.02
2037 2095 1.227853 GGTCGTGGAGCAAACCAGT 60.228 57.895 0.00 0.00 40.85 4.00
2126 2187 0.253160 ACATGGTAGGGGCTGAAGGA 60.253 55.000 0.00 0.00 0.00 3.36
2216 2290 0.037790 GCTCGAGTCAAGTGCCTCTT 60.038 55.000 15.13 0.00 36.75 2.85
2248 2324 1.749638 CGGCGGTACCTCAGAGTCT 60.750 63.158 10.90 0.00 35.61 3.24
2252 2328 2.367486 GCGGTACCTCAGAGTCTAACT 58.633 52.381 10.90 0.00 0.00 2.24
2278 2354 1.797025 CAGGAACCAAAGAGGACGAC 58.203 55.000 0.00 0.00 41.22 4.34
2310 2386 3.243501 GCTGATGTTTGAGCAAGGAAACA 60.244 43.478 0.00 0.00 44.07 2.83
2345 2421 0.961019 GCAACAACCCTTCTGATGCA 59.039 50.000 0.00 0.00 40.98 3.96
2442 2518 1.429148 CCCGCGATAGTTTGTGAGCC 61.429 60.000 8.23 0.00 39.35 4.70
2510 2586 4.985538 TGAAACACAAATAGAGGGCTCTT 58.014 39.130 0.00 0.00 40.93 2.85
2560 2636 7.770801 AGGTTTCAATAAAAGTTTTGCTGTC 57.229 32.000 11.18 4.28 0.00 3.51
2592 2668 3.181464 GGAAGGAGTGGAGGCTTATGTAC 60.181 52.174 0.00 0.00 0.00 2.90
2610 2686 9.573133 CTTATGTACCTTTTGGAATGATGAAAC 57.427 33.333 0.00 0.00 44.07 2.78
2689 2765 7.275183 CAATGGTTGATATCAGGACAAGAGTA 58.725 38.462 5.39 0.00 0.00 2.59
2745 2822 1.917872 TACAAAACCTGGGACATGCC 58.082 50.000 0.00 0.00 38.20 4.40
2860 2937 0.463620 GGAGTCAGGCTCAGATGGAC 59.536 60.000 3.96 0.00 45.88 4.02
2909 2986 6.376018 GTGTGGTCTCTCAGATATAGGATACC 59.624 46.154 0.00 0.00 37.17 2.73
3022 3099 0.178967 TTGCATTCCCTGGAGCAACA 60.179 50.000 8.34 0.00 41.55 3.33
3038 3115 2.935201 GCAACATTGGAGCACAAAACAA 59.065 40.909 0.00 0.00 43.46 2.83
3067 3144 2.104967 TCCGATCACGTACCCATCTTT 58.895 47.619 0.00 0.00 37.88 2.52
3129 3206 9.736023 GCCAAGATCATTTAAATACGAAATCTT 57.264 29.630 0.00 7.86 0.00 2.40
3222 3299 4.219288 CCAAGAGCTAAAGGACAAAATGCT 59.781 41.667 0.00 0.00 0.00 3.79
3312 3389 0.453793 CTGAGGAGACAGCTACACGG 59.546 60.000 0.00 0.00 0.00 4.94
3316 3393 1.592223 GAGACAGCTACACGGGCTT 59.408 57.895 0.00 0.00 38.03 4.35
3435 3512 0.392193 AGAGCAAGATTGGAGTGGCG 60.392 55.000 0.00 0.00 0.00 5.69
3466 3543 7.527568 TGGGGACAAAAATACGTATTTCTTT 57.472 32.000 28.64 19.33 37.44 2.52
3472 3549 9.113876 GACAAAAATACGTATTTCTTTCACCTG 57.886 33.333 28.64 18.01 35.00 4.00
3689 3771 7.382898 TGAATCACTTAATGCGCCATATACTA 58.617 34.615 4.18 0.00 0.00 1.82
3755 3837 0.772124 ACCCGGCCCAGATGGATATT 60.772 55.000 0.00 0.00 37.39 1.28
3757 3839 0.391661 CCGGCCCAGATGGATATTCG 60.392 60.000 0.00 0.00 37.39 3.34
3758 3840 0.608130 CGGCCCAGATGGATATTCGA 59.392 55.000 0.00 0.00 37.39 3.71
3861 3944 2.671351 CGGCCGCGAGTATAAATGAGAT 60.671 50.000 14.67 0.00 0.00 2.75
3871 3954 7.169982 GCGAGTATAAATGAGATTGTGCTAGTT 59.830 37.037 0.00 0.00 0.00 2.24
3962 4047 5.551760 ACAAGATCGCTTCAAAGGTAATG 57.448 39.130 0.00 0.00 30.14 1.90
3973 4058 0.323087 AAGGTAATGTCCAACCGCCC 60.323 55.000 0.00 0.00 40.88 6.13
3993 4078 2.028385 CCAAAGCTAGTGTTACCCGACT 60.028 50.000 0.00 0.00 0.00 4.18
4083 4168 9.524106 CTTATGAATGCTTGCATTTTATGAAGA 57.476 29.630 19.90 3.53 0.00 2.87
4190 4275 4.079787 AGAGCCATAATGCTTAAGTTGGGA 60.080 41.667 4.02 0.00 42.95 4.37
4205 4290 2.303022 GTTGGGATTCACAGAGAGGTGA 59.697 50.000 0.00 0.00 45.54 4.02
4257 4342 5.295292 ACAGTGAAGTTCTCTGTCATGTTTG 59.705 40.000 27.05 8.52 44.91 2.93
4366 4451 0.107165 GGCCTTTCGTGCCTCCTTAT 60.107 55.000 0.00 0.00 45.70 1.73
4379 4464 4.968719 TGCCTCCTTATATCCAGAAGTGAA 59.031 41.667 0.00 0.00 0.00 3.18
4407 4492 4.764823 CCAATCTAAGTGGTTTGCAGGTAA 59.235 41.667 0.00 0.00 0.00 2.85
4446 4531 6.719370 ACCAGTGAATCACCTTTTATTTGCTA 59.281 34.615 10.12 0.00 34.49 3.49
4511 4596 4.993705 TGAGGTAAACCAGGTTCTGAAT 57.006 40.909 4.93 0.00 38.89 2.57
4512 4597 6.636454 ATGAGGTAAACCAGGTTCTGAATA 57.364 37.500 4.93 0.00 38.89 1.75
4515 4600 7.466804 TGAGGTAAACCAGGTTCTGAATATTT 58.533 34.615 4.93 0.00 38.89 1.40
4531 4616 9.547753 TCTGAATATTTTATTGTCAGGCTACTC 57.452 33.333 0.00 0.00 37.03 2.59
4541 4626 1.073216 CAGGCTACTCGTCAACGCAG 61.073 60.000 0.00 0.00 39.60 5.18
4545 4630 1.387084 GCTACTCGTCAACGCAGAAAG 59.613 52.381 0.00 0.00 39.60 2.62
4630 4715 0.948678 GCTGCTTAACGTCCCAAACA 59.051 50.000 0.00 0.00 0.00 2.83
4666 4751 4.102524 AGAAATATGTGGGAATGCCGTCTA 59.897 41.667 0.00 0.00 33.83 2.59
4673 4758 4.141597 TGTGGGAATGCCGTCTAATATTGA 60.142 41.667 0.00 0.00 33.83 2.57
4728 4813 1.547372 GACCGGCTGTGGAGTAAAGTA 59.453 52.381 0.00 0.00 0.00 2.24
4752 4837 2.224499 GGGGTGGATTGCAAACACAATT 60.224 45.455 27.93 3.37 40.31 2.32
4786 4871 5.533528 GGTAAAGAAGTCCTTGTTAAAGCCA 59.466 40.000 0.00 0.00 34.79 4.75
4790 4875 6.374417 AGAAGTCCTTGTTAAAGCCATAGA 57.626 37.500 0.00 0.00 31.51 1.98
4794 4879 6.904626 AGTCCTTGTTAAAGCCATAGATCAT 58.095 36.000 0.00 0.00 31.51 2.45
4833 4918 1.174712 TGTCTTGCTTCAAGCTGCCC 61.175 55.000 11.57 0.00 42.97 5.36
4891 4976 0.712380 ATTCTGGTGGGGGAGCAAAT 59.288 50.000 0.00 0.00 0.00 2.32
4910 4995 2.300956 TAGGGCAAATGCAAACCTCA 57.699 45.000 7.80 0.00 44.36 3.86
4911 4996 1.648116 AGGGCAAATGCAAACCTCAT 58.352 45.000 7.80 0.00 44.36 2.90
4912 4997 1.980036 AGGGCAAATGCAAACCTCATT 59.020 42.857 7.80 0.00 44.36 2.57
5125 5229 5.424757 AGAAGTGCGCCATTAGTAACAATA 58.575 37.500 4.18 0.00 0.00 1.90
5579 5812 1.203052 TGTTACTAGTGGCGCACCTAC 59.797 52.381 10.83 2.11 34.49 3.18
5612 5845 5.342259 GCGCCACTAGTAAGTTTGAAAATTG 59.658 40.000 0.00 0.00 31.97 2.32
5729 6006 7.299586 CGGTTAAATTCGGATGTAACTTTTCA 58.700 34.615 15.08 0.00 36.56 2.69
6030 6326 5.581085 GGTGTGCCATTAGTAGTTCAACTAG 59.419 44.000 0.00 0.00 32.48 2.57
6031 6327 6.164176 GTGTGCCATTAGTAGTTCAACTAGT 58.836 40.000 9.89 9.89 37.97 2.57
6032 6328 7.318141 GTGTGCCATTAGTAGTTCAACTAGTA 58.682 38.462 7.90 7.90 35.97 1.82
6033 6329 7.488471 GTGTGCCATTAGTAGTTCAACTAGTAG 59.512 40.741 11.25 3.34 37.74 2.57
6034 6330 7.395206 TGTGCCATTAGTAGTTCAACTAGTAGA 59.605 37.037 11.25 5.02 37.74 2.59
6035 6331 8.248945 GTGCCATTAGTAGTTCAACTAGTAGAA 58.751 37.037 11.25 1.95 37.74 2.10
6036 6332 8.248945 TGCCATTAGTAGTTCAACTAGTAGAAC 58.751 37.037 11.25 0.00 43.33 3.01
6138 6452 2.395988 AATGGCGCACCTGTGAGTGA 62.396 55.000 10.83 0.00 40.34 3.41
6225 6540 3.037686 TAATGGCGCACCGTCCCAT 62.038 57.895 10.83 0.00 40.94 4.00
6531 6874 7.624549 CCATTAGTGTCCATATTGGCTATAGT 58.375 38.462 0.84 0.00 37.47 2.12
6575 6918 4.327680 GGTCTCTTGGCAAACTATGACTT 58.672 43.478 0.00 0.00 38.19 3.01
6577 6920 5.582665 GGTCTCTTGGCAAACTATGACTTAG 59.417 44.000 0.00 0.00 38.19 2.18
6685 7029 0.323178 CCCAGAGGCTTTGAGTGCAT 60.323 55.000 6.61 0.00 0.00 3.96
6891 7254 1.889530 GCAGCCGAGTACAGAACCCT 61.890 60.000 0.00 0.00 0.00 4.34
6907 7270 3.491766 ACCCTCCATCTTTGGTCTCTA 57.508 47.619 0.00 0.00 44.06 2.43
6985 7348 0.379669 GCCAATGGATGCTCGAGTTG 59.620 55.000 15.13 9.11 0.00 3.16
7004 7367 3.214694 TGTTTTGGGGATCCCTCTCTA 57.785 47.619 30.08 8.14 45.70 2.43
7074 7437 2.543848 GTCGTTCACTGTGAAATCAGCA 59.456 45.455 23.55 0.00 38.22 4.41
7128 7491 0.482446 AAGCATGGTTGGAGGGAACA 59.518 50.000 9.83 0.00 0.00 3.18
7131 7494 1.767759 CATGGTTGGAGGGAACATCC 58.232 55.000 0.00 0.00 37.35 3.51
7206 7571 2.360475 GTCCCAGCCAAGGTGAGC 60.360 66.667 0.00 0.00 32.22 4.26
7212 7577 1.614051 CCAGCCAAGGTGAGCATGTTA 60.614 52.381 0.00 0.00 32.22 2.41
7337 7702 2.224523 GGTGGCATTCCCTCATCGAATA 60.225 50.000 0.00 0.00 0.00 1.75
7353 7718 2.545526 CGAATATGCCGCTTCAAGATGT 59.454 45.455 0.00 0.00 0.00 3.06
7439 7806 7.184800 CCAAACAATGGCTTTTTACCTTAAC 57.815 36.000 0.00 0.00 43.80 2.01
7441 7808 7.443879 CCAAACAATGGCTTTTTACCTTAACAT 59.556 33.333 0.00 0.00 43.80 2.71
7447 7814 8.838649 ATGGCTTTTTACCTTAACATAATCCT 57.161 30.769 0.00 0.00 0.00 3.24
7485 7852 1.664965 AGTGCTCGCGGTGACTTTC 60.665 57.895 6.13 0.00 0.00 2.62
7499 7866 1.970640 GACTTTCTGGGCCATTTGGTT 59.029 47.619 6.72 0.00 37.57 3.67
7659 8033 2.356741 GGTGCCTAATGCTAGACCCAAA 60.357 50.000 0.00 0.00 42.00 3.28
7679 8058 2.555633 CCCCTCCAATGGGCTATGA 58.444 57.895 0.00 0.00 45.78 2.15
7684 8063 3.969312 CCCTCCAATGGGCTATGAAAAAT 59.031 43.478 0.00 0.00 40.84 1.82
7719 8098 1.215647 GGTCAGATTCGAGCGTGGT 59.784 57.895 0.00 0.00 0.00 4.16
7756 8135 0.038166 TTGCAGGGATGACCAAGGAC 59.962 55.000 0.00 0.00 43.89 3.85
7828 8207 0.035152 TCTGGAGGCGATTGCATGTT 60.035 50.000 7.38 0.00 45.35 2.71
7840 8219 0.322456 TGCATGTTGGGAGGCACTAC 60.322 55.000 0.00 0.00 41.55 2.73
7866 8245 4.021229 TGGCAGAAGATCTCAATTTGCAT 58.979 39.130 9.78 0.00 0.00 3.96
7981 8389 9.944376 AAATCTCACAGCTACTATTAAGTTTGA 57.056 29.630 0.00 0.00 37.15 2.69
8160 8571 2.360726 AAAAAGTAGGGCGGCGGG 60.361 61.111 9.78 0.00 0.00 6.13
8161 8572 3.200329 AAAAAGTAGGGCGGCGGGT 62.200 57.895 9.78 0.00 0.00 5.28
8162 8573 2.702040 AAAAAGTAGGGCGGCGGGTT 62.702 55.000 9.78 0.00 0.00 4.11
8163 8574 1.840224 AAAAGTAGGGCGGCGGGTTA 61.840 55.000 9.78 0.00 0.00 2.85
8164 8575 2.248086 AAAGTAGGGCGGCGGGTTAG 62.248 60.000 9.78 0.00 0.00 2.34
8165 8576 3.464494 GTAGGGCGGCGGGTTAGT 61.464 66.667 9.78 0.00 0.00 2.24
8223 8636 1.080705 GGCGTCGTGTACTGAAGCT 60.081 57.895 19.49 0.00 40.13 3.74
8225 8638 1.945776 GCGTCGTGTACTGAAGCTGC 61.946 60.000 15.36 0.00 37.76 5.25
8403 8844 1.408702 GAGAGGGAGATGTGAGACAGC 59.591 57.143 0.00 0.00 34.13 4.40
8404 8845 1.189752 GAGGGAGATGTGAGACAGCA 58.810 55.000 0.00 0.00 36.88 4.41
8429 8871 1.073199 CAGGGGAAAACGCAGGAGT 59.927 57.895 0.00 0.00 33.80 3.85
8454 8896 2.202932 GTGCATCTCACCGGCGAT 60.203 61.111 9.30 0.00 39.79 4.58
8609 9051 2.081212 CGACCTTCGTGACAGCGAC 61.081 63.158 0.00 0.00 40.85 5.19
8648 9090 1.302511 GGGCTTGGAGCTCGAAACA 60.303 57.895 12.50 0.00 41.99 2.83
8649 9091 0.889186 GGGCTTGGAGCTCGAAACAA 60.889 55.000 12.50 7.68 41.99 2.83
8652 9094 1.333619 GCTTGGAGCTCGAAACAACAA 59.666 47.619 12.50 5.96 38.45 2.83
8658 9100 1.082104 CTCGAAACAACAAGCGCCC 60.082 57.895 2.29 0.00 0.00 6.13
8660 9102 1.082104 CGAAACAACAAGCGCCCTC 60.082 57.895 2.29 0.00 0.00 4.30
8792 9234 0.527817 CAGAGATGCGACGGGGTTAC 60.528 60.000 0.00 0.00 0.00 2.50
8916 9358 1.076632 AGGGAGCGTACAGGAGGAG 60.077 63.158 0.00 0.00 0.00 3.69
8941 9383 2.388310 GAAGAAACTCCTCTTCGGGG 57.612 55.000 0.00 0.00 41.35 5.73
8986 9428 1.269998 GGATAGTGTGCGCTAGGTAGG 59.730 57.143 9.73 0.00 0.00 3.18
9022 9464 0.106519 GTGTGATTGGGGATGAGGGG 60.107 60.000 0.00 0.00 0.00 4.79
9027 9469 0.777678 ATTGGGGATGAGGGGGATCC 60.778 60.000 1.92 1.92 39.04 3.36
9107 9549 4.351054 CAGGGGAGGCGCTGGTTT 62.351 66.667 7.64 0.00 0.00 3.27
9111 9553 2.626780 GGGAGGCGCTGGTTTGTTC 61.627 63.158 7.64 0.00 0.00 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
29 31 4.402793 TCGTTCTTCTTCCTAGAGGGATTG 59.597 45.833 0.00 0.00 44.66 2.67
59 61 1.603172 CGACGTCTGTTTGCCTTCTCT 60.603 52.381 14.70 0.00 0.00 3.10
60 62 0.784778 CGACGTCTGTTTGCCTTCTC 59.215 55.000 14.70 0.00 0.00 2.87
72 74 1.423056 GATCCGTTCGACGACGTCT 59.577 57.895 24.36 4.90 46.05 4.18
78 80 0.109458 TTGTGAGGATCCGTTCGACG 60.109 55.000 5.98 0.00 42.11 5.12
87 89 0.865769 ACGTTGCGTTTGTGAGGATC 59.134 50.000 0.00 0.00 36.35 3.36
438 464 0.038890 TGCACATGGGGATTTTCCGA 59.961 50.000 0.00 0.00 37.43 4.55
569 595 7.614124 AACCGTAGCTCCGAATTAAATAAAA 57.386 32.000 0.00 0.00 0.00 1.52
881 923 2.615465 CCCAGATCCAGTGCCCCAA 61.615 63.158 0.00 0.00 0.00 4.12
1002 1044 6.491403 GGGGATCAGACACAATTTGCTTATAT 59.509 38.462 0.00 0.00 0.00 0.86
1003 1045 5.827797 GGGGATCAGACACAATTTGCTTATA 59.172 40.000 0.00 0.00 0.00 0.98
1005 1047 4.016444 GGGGATCAGACACAATTTGCTTA 58.984 43.478 0.00 0.00 0.00 3.09
1006 1048 2.827921 GGGGATCAGACACAATTTGCTT 59.172 45.455 0.00 0.00 0.00 3.91
1007 1049 2.042162 AGGGGATCAGACACAATTTGCT 59.958 45.455 0.00 0.00 0.00 3.91
1008 1050 2.424956 GAGGGGATCAGACACAATTTGC 59.575 50.000 0.00 0.00 0.00 3.68
1009 1051 3.944015 GAGAGGGGATCAGACACAATTTG 59.056 47.826 0.00 0.00 0.00 2.32
1010 1052 3.588842 TGAGAGGGGATCAGACACAATTT 59.411 43.478 0.00 0.00 0.00 1.82
1011 1053 3.184628 TGAGAGGGGATCAGACACAATT 58.815 45.455 0.00 0.00 0.00 2.32
1012 1054 2.837947 TGAGAGGGGATCAGACACAAT 58.162 47.619 0.00 0.00 0.00 2.71
1013 1055 2.325661 TGAGAGGGGATCAGACACAA 57.674 50.000 0.00 0.00 0.00 3.33
1014 1056 2.557555 ATGAGAGGGGATCAGACACA 57.442 50.000 0.00 0.00 0.00 3.72
1015 1057 3.323403 CCTAATGAGAGGGGATCAGACAC 59.677 52.174 0.00 0.00 32.39 3.67
1016 1058 3.581101 CCTAATGAGAGGGGATCAGACA 58.419 50.000 0.00 0.00 32.39 3.41
1031 1073 3.694566 CGGGAGGAAGAAAAACCCTAATG 59.305 47.826 0.00 0.00 38.51 1.90
1032 1074 3.876550 GCGGGAGGAAGAAAAACCCTAAT 60.877 47.826 0.00 0.00 38.51 1.73
1044 1086 4.821589 GAGTGCCGCGGGAGGAAG 62.822 72.222 29.38 0.00 0.00 3.46
1058 1102 0.665835 GATCTCCATGTCGAGCGAGT 59.334 55.000 0.00 0.00 0.00 4.18
1122 1170 1.900981 CAACCACGATGCCAACCCA 60.901 57.895 0.00 0.00 0.00 4.51
1123 1171 1.602323 TCAACCACGATGCCAACCC 60.602 57.895 0.00 0.00 0.00 4.11
1126 1174 0.888736 CCTGTCAACCACGATGCCAA 60.889 55.000 0.00 0.00 0.00 4.52
1222 1273 0.874175 CATCGCCGATTTAGACGCCA 60.874 55.000 0.00 0.00 0.00 5.69
1243 1294 2.086094 TCATCATTGCTTGCATGTCGT 58.914 42.857 1.14 0.00 0.00 4.34
1251 1302 3.119245 CCCAACTCCTTCATCATTGCTTG 60.119 47.826 0.00 0.00 0.00 4.01
1305 1356 2.573462 CCGGAATATCACCATCCTCCAT 59.427 50.000 0.00 0.00 0.00 3.41
1322 1373 3.452786 CGAGCAGCTTCCTCCGGA 61.453 66.667 2.93 2.93 0.00 5.14
1374 1425 8.403236 GCGGAAAAACCAATACTGACTATATTT 58.597 33.333 0.00 0.00 38.90 1.40
1453 1505 5.685520 TTGCAGTGTGTATAGGTTATCCA 57.314 39.130 0.00 0.00 35.89 3.41
1469 1521 1.446907 CGAGGCAAGAGAATTGCAGT 58.553 50.000 13.94 1.17 46.58 4.40
1502 1554 2.424667 CCATGGCCCATCTTCCATTACA 60.425 50.000 0.00 0.00 40.88 2.41
1542 1594 4.686972 CCATCATATGGCTCGATAACGAT 58.313 43.478 2.13 0.00 44.70 3.73
1572 1624 7.072177 TGTTCAAACTAATCGATGATGGTTC 57.928 36.000 0.00 0.00 0.00 3.62
1573 1625 7.447374 TTGTTCAAACTAATCGATGATGGTT 57.553 32.000 0.00 0.00 0.00 3.67
1643 1695 2.031097 GCAAGGGATTTGATCAGGGGG 61.031 57.143 0.00 0.00 39.21 5.40
1680 1732 4.752101 GGATTTGGGTTCATCGTAGATGAG 59.248 45.833 11.82 0.00 45.12 2.90
1688 1740 1.064758 TCCTGGGATTTGGGTTCATCG 60.065 52.381 0.00 0.00 0.00 3.84
1690 1742 2.003072 AGTCCTGGGATTTGGGTTCAT 58.997 47.619 0.00 0.00 0.00 2.57
1734 1786 3.847671 TGTGACATCCACCTTTACACA 57.152 42.857 0.00 0.00 45.09 3.72
1772 1824 4.000988 TCTTCTTAATCACCAGCGAAACC 58.999 43.478 0.00 0.00 0.00 3.27
1850 1902 2.890808 ACATGTGACCTAGCATACCG 57.109 50.000 0.00 0.00 0.00 4.02
1866 1918 7.658525 TTCCATTGCCACATTCTTTATACAT 57.341 32.000 0.00 0.00 0.00 2.29
2037 2095 3.872603 ACGCTGACTTGCACCCCA 61.873 61.111 0.00 0.00 0.00 4.96
2126 2187 0.947244 CTGCTCCACGCTTTCTGTTT 59.053 50.000 0.00 0.00 40.11 2.83
2170 2231 2.238942 TGTAGCATATTCTGGCACCG 57.761 50.000 0.00 0.00 0.00 4.94
2228 2304 4.554363 CTCTGAGGTACCGCCGCG 62.554 72.222 13.56 5.59 43.70 6.46
2252 2328 5.037179 TCCTCTTTGGTTCCTGCTTGGAA 62.037 47.826 7.51 7.51 44.81 3.53
2345 2421 1.838073 CTAGGGAGCCCACCAAACGT 61.838 60.000 8.53 0.00 38.92 3.99
2459 2535 1.913419 TGCGATAGAGGGGGAAAGTTT 59.087 47.619 0.00 0.00 39.76 2.66
2465 2541 2.567169 CAATACATGCGATAGAGGGGGA 59.433 50.000 0.00 0.00 39.76 4.81
2510 2586 3.634448 GTGCCTGCTAGATTCTCTACTCA 59.366 47.826 0.00 0.00 0.00 3.41
2560 2636 1.202582 CCACTCCTTCCACGACTACTG 59.797 57.143 0.00 0.00 0.00 2.74
2592 2668 5.993441 AGCTTTGTTTCATCATTCCAAAAGG 59.007 36.000 0.00 0.00 0.00 3.11
2610 2686 3.420839 AACCGACAACTTCAAGCTTTG 57.579 42.857 0.00 0.00 0.00 2.77
2689 2765 1.816572 GCCTCCCCGTACACAAAAGTT 60.817 52.381 0.00 0.00 0.00 2.66
2745 2822 1.358046 GTTCCGACGATACCCCTCG 59.642 63.158 0.00 0.00 44.14 4.63
2860 2937 3.459232 TCCAGAGCATCACGGAATAAG 57.541 47.619 0.00 0.00 36.21 1.73
2909 2986 2.134630 AAAGTCCAGCTGCTCCCAGG 62.135 60.000 8.66 0.00 39.54 4.45
2992 3069 0.947244 GGAATGCAATAGACCAGGCG 59.053 55.000 0.00 0.00 0.00 5.52
3022 3099 2.431782 AGCTGTTGTTTTGTGCTCCAAT 59.568 40.909 0.00 0.00 31.81 3.16
3038 3115 1.103803 ACGTGATCGGATGTAGCTGT 58.896 50.000 0.00 0.00 41.85 4.40
3067 3144 4.377943 GCATGCAAATCACTGTAACGTACA 60.378 41.667 14.21 0.00 37.13 2.90
3097 3174 6.183360 CGTATTTAAATGATCTTGGCCCACTT 60.183 38.462 11.05 0.00 0.00 3.16
3154 3231 4.314440 GCGGTCTCCACCACAGCA 62.314 66.667 0.00 0.00 44.02 4.41
3176 3253 1.308128 AGGATGCCCCAGTGGATGA 60.308 57.895 11.95 0.00 37.41 2.92
3310 3387 0.249489 CTAGGGAATCACGAAGCCCG 60.249 60.000 0.00 0.00 45.40 6.13
3312 3389 1.120530 TCCTAGGGAATCACGAAGCC 58.879 55.000 9.46 0.00 0.00 4.35
3316 3393 3.891977 CTGATCTTCCTAGGGAATCACGA 59.108 47.826 9.46 0.00 41.23 4.35
3435 3512 2.837532 ATTTTTGTCCCCATGTGTGC 57.162 45.000 0.00 0.00 0.00 4.57
3466 3543 3.523972 TCCTTCTACTAGCTCTCAGGTGA 59.476 47.826 0.00 0.00 0.00 4.02
3472 3549 5.043737 TCCTTCTCCTTCTACTAGCTCTC 57.956 47.826 0.00 0.00 0.00 3.20
3577 3657 2.096980 CGATGTGTACAGCTCCTCGTAA 59.903 50.000 0.00 0.00 0.00 3.18
3580 3660 0.248661 CCGATGTGTACAGCTCCTCG 60.249 60.000 0.00 0.00 0.00 4.63
3820 3903 0.752658 TCTCCGTACCCTCGACGATA 59.247 55.000 0.00 0.00 42.98 2.92
3861 3944 4.324254 CCTTGGGGATTAGAACTAGCACAA 60.324 45.833 0.00 0.00 33.58 3.33
3973 4058 3.314541 AGTCGGGTAACACTAGCTTTG 57.685 47.619 0.00 0.00 39.74 2.77
3993 4078 4.256920 GCTGACTGCTCCTCAGAAATAAA 58.743 43.478 9.29 0.00 45.72 1.40
4024 4109 1.103803 GTCGGTGATCAGTCTGCCTA 58.896 55.000 0.00 0.00 0.00 3.93
4083 4168 4.517285 TGATGCTTCTTCGCCTTATTTCT 58.483 39.130 0.88 0.00 0.00 2.52
4190 4275 3.643320 TGTCAACTCACCTCTCTGTGAAT 59.357 43.478 0.00 0.00 44.19 2.57
4205 4290 7.332926 GTCACAAGATTCATCACTATGTCAACT 59.667 37.037 0.00 0.00 34.50 3.16
4366 4451 7.384524 AGATTGGATGATTCACTTCTGGATA 57.615 36.000 0.00 0.00 0.00 2.59
4379 4464 5.263599 TGCAAACCACTTAGATTGGATGAT 58.736 37.500 0.00 0.00 37.58 2.45
4407 4492 1.625818 CACTGGTGGAGCTAAGGAAGT 59.374 52.381 0.00 0.00 0.00 3.01
4410 4495 2.024176 TTCACTGGTGGAGCTAAGGA 57.976 50.000 0.70 0.00 0.00 3.36
4414 4499 1.555075 GGTGATTCACTGGTGGAGCTA 59.445 52.381 16.02 0.00 34.40 3.32
4446 4531 4.226427 TGAAGAACAGCAGGCTATCATT 57.774 40.909 0.00 0.00 0.00 2.57
4511 4596 6.869695 TGACGAGTAGCCTGACAATAAAATA 58.130 36.000 0.00 0.00 0.00 1.40
4512 4597 5.730550 TGACGAGTAGCCTGACAATAAAAT 58.269 37.500 0.00 0.00 0.00 1.82
4515 4600 4.491676 GTTGACGAGTAGCCTGACAATAA 58.508 43.478 0.00 0.00 0.00 1.40
4531 4616 2.026990 CGAAAACTTTCTGCGTTGACG 58.973 47.619 0.00 0.00 37.44 4.35
4541 4626 9.670719 AGAAGATTGAAGATTTCGAAAACTTTC 57.329 29.630 27.49 21.82 32.15 2.62
4545 4630 9.111702 CTGAAGAAGATTGAAGATTTCGAAAAC 57.888 33.333 15.66 12.58 0.00 2.43
4630 4715 8.328758 TCCCACATATTTCTCATTTAGTGTCTT 58.671 33.333 0.00 0.00 0.00 3.01
4651 4736 4.385825 TCAATATTAGACGGCATTCCCAC 58.614 43.478 0.00 0.00 0.00 4.61
4666 4751 7.015584 GGCCCCATTCTTTGAGTTATCAATATT 59.984 37.037 0.00 0.00 44.75 1.28
4673 4758 4.264352 TGAAGGCCCCATTCTTTGAGTTAT 60.264 41.667 0.00 0.00 0.00 1.89
4728 4813 0.105760 TGTTTGCAATCCACCCCTGT 60.106 50.000 0.00 0.00 0.00 4.00
4752 4837 3.078837 GACTTCTTTACCCGCCATTGAA 58.921 45.455 0.00 0.00 0.00 2.69
4786 4871 3.572632 AACTGGCACTGCATGATCTAT 57.427 42.857 2.82 0.00 0.00 1.98
4891 4976 2.300956 TGAGGTTTGCATTTGCCCTA 57.699 45.000 0.00 0.00 41.18 3.53
4910 4995 3.624959 GCCACTAGTAGGCCTTTTCCAAT 60.625 47.826 12.58 0.00 46.50 3.16
4911 4996 2.290705 GCCACTAGTAGGCCTTTTCCAA 60.291 50.000 12.58 0.00 46.50 3.53
4912 4997 1.280998 GCCACTAGTAGGCCTTTTCCA 59.719 52.381 12.58 0.00 46.50 3.53
5579 5812 4.690719 TAGTGGCGCACCGGTTGG 62.691 66.667 2.97 0.00 39.70 3.77
6010 6306 7.949690 TCTACTAGTTGAACTACTAATGGCA 57.050 36.000 0.00 0.00 30.63 4.92
6030 6326 3.121544 GGTGCGCCATTAGTAGTTCTAC 58.878 50.000 12.58 2.14 34.09 2.59
6031 6327 2.761767 TGGTGCGCCATTAGTAGTTCTA 59.238 45.455 16.89 0.00 40.46 2.10
6032 6328 1.553248 TGGTGCGCCATTAGTAGTTCT 59.447 47.619 16.89 0.00 40.46 3.01
6033 6329 2.018542 TGGTGCGCCATTAGTAGTTC 57.981 50.000 16.89 0.00 40.46 3.01
6102 6413 6.870965 TGCGCCATTAGTAATTTTGTTTCAAT 59.129 30.769 4.18 0.00 0.00 2.57
6106 6417 4.926832 GGTGCGCCATTAGTAATTTTGTTT 59.073 37.500 12.58 0.00 34.09 2.83
6138 6452 3.873910 AGTTGAACTACTAATGGCGCAT 58.126 40.909 10.83 0.00 0.00 4.73
6531 6874 7.558444 AGACCCAATTCACTACTACAAAAACAA 59.442 33.333 0.00 0.00 0.00 2.83
6575 6918 0.837272 CCTCCCATTCCTTTCGGCTA 59.163 55.000 0.00 0.00 0.00 3.93
6577 6920 2.121538 GCCTCCCATTCCTTTCGGC 61.122 63.158 0.00 0.00 0.00 5.54
6592 6935 7.010771 ACTCAAAATCTTTAAAACCTAGGCCT 58.989 34.615 11.78 11.78 0.00 5.19
6685 7029 5.414454 AGACGTATATGCTTTTCAAAAGCCA 59.586 36.000 28.14 18.04 42.36 4.75
6907 7270 4.754618 TGCAGACGTGTGATCAATTAGTTT 59.245 37.500 18.07 0.00 0.00 2.66
7004 7367 6.239008 CCAAAAATCAGGGATATTGCGTGTAT 60.239 38.462 0.00 0.00 0.00 2.29
7128 7491 0.909610 TTGAACTGGAGGAGCCGGAT 60.910 55.000 5.05 0.00 46.81 4.18
7131 7494 1.089920 CATTTGAACTGGAGGAGCCG 58.910 55.000 0.00 0.00 40.66 5.52
7206 7571 2.226437 GGATAGGCGCCACAATAACATG 59.774 50.000 31.54 0.00 0.00 3.21
7212 7577 1.102978 GTTTGGATAGGCGCCACAAT 58.897 50.000 31.54 19.02 34.56 2.71
7309 7674 0.033796 AGGGAATGCCACCATGAGTG 60.034 55.000 0.00 0.35 46.83 3.51
7318 7683 3.678289 CATATTCGATGAGGGAATGCCA 58.322 45.455 0.00 0.00 35.78 4.92
7337 7702 1.210478 AGGTACATCTTGAAGCGGCAT 59.790 47.619 1.45 0.00 0.00 4.40
7353 7718 1.833630 CTGTCATTGAGAGCCCAGGTA 59.166 52.381 0.00 0.00 0.00 3.08
7387 7752 5.488919 AGGGTTCAGAGACTTCCATCATTTA 59.511 40.000 0.00 0.00 0.00 1.40
7439 7806 5.885230 TTTCTGCTGTGACAAGGATTATG 57.115 39.130 0.00 0.00 0.00 1.90
7441 7808 6.003326 TGAATTTCTGCTGTGACAAGGATTA 58.997 36.000 0.00 0.00 0.00 1.75
7447 7814 3.947196 ACTGTGAATTTCTGCTGTGACAA 59.053 39.130 0.00 0.00 0.00 3.18
7499 7866 0.320858 TATTGCCTTTCGTCGTGCCA 60.321 50.000 0.00 0.00 0.00 4.92
7679 8058 3.056304 CCGGCGTCAACATGAAATTTTT 58.944 40.909 6.01 0.00 0.00 1.94
7684 8063 1.969064 CCCCGGCGTCAACATGAAA 60.969 57.895 6.01 0.00 0.00 2.69
7719 8098 0.322456 AAATAGCCGCTGCAGAACCA 60.322 50.000 20.43 0.00 41.13 3.67
7756 8135 4.260170 AGTGCAGAGCTTCCAAGATAAAG 58.740 43.478 0.00 0.00 0.00 1.85
7828 8207 1.998530 CCAATGGTAGTGCCTCCCA 59.001 57.895 0.00 0.00 38.35 4.37
7840 8219 5.348986 CAAATTGAGATCTTCTGCCAATGG 58.651 41.667 7.21 0.00 0.00 3.16
7866 8245 2.666317 TCCGAGGCTATGATGAACTGA 58.334 47.619 0.00 0.00 0.00 3.41
7963 8362 8.660373 CCTCAAACTCAAACTTAATAGTAGCTG 58.340 37.037 0.00 0.00 33.17 4.24
8159 8570 4.424566 TCGCCCGCGTCACTAACC 62.425 66.667 4.92 0.00 40.74 2.85
8160 8571 2.879462 CTCGCCCGCGTCACTAAC 60.879 66.667 4.92 0.00 40.74 2.34
8161 8572 4.789075 GCTCGCCCGCGTCACTAA 62.789 66.667 4.92 0.00 40.74 2.24
8403 8844 0.031994 CGTTTTCCCCTGCACCTTTG 59.968 55.000 0.00 0.00 0.00 2.77
8404 8845 1.744320 GCGTTTTCCCCTGCACCTTT 61.744 55.000 0.00 0.00 0.00 3.11
8429 8871 4.019312 TGAGATGCACTGCCGCCA 62.019 61.111 0.00 0.00 0.00 5.69
8438 8880 0.249447 CTTATCGCCGGTGAGATGCA 60.249 55.000 24.04 2.92 32.85 3.96
8609 9051 3.621892 GACGTCAAGTCCCCGTCCG 62.622 68.421 11.55 0.00 43.77 4.79
8658 9100 2.757508 TCCAGCAGGAGCCTCGAG 60.758 66.667 5.13 5.13 43.56 4.04
8725 9167 2.593725 CCCATGCGCCTCCATCTG 60.594 66.667 4.18 0.00 0.00 2.90
8763 9205 1.903294 GCATCTCTGTCCAGGAGCA 59.097 57.895 0.00 0.00 0.00 4.26
8895 9337 0.183014 CCTCCTGTACGCTCCCTCTA 59.817 60.000 0.00 0.00 0.00 2.43
8916 9358 3.595173 GAAGAGGAGTTTCTTCTGGAGC 58.405 50.000 8.17 0.00 46.12 4.70
8924 9366 1.554583 GCCCCCGAAGAGGAGTTTCT 61.555 60.000 0.00 0.00 45.00 2.52
8941 9383 2.589159 GGAAATCCTCCTCGCGCC 60.589 66.667 0.00 0.00 41.61 6.53
8970 9412 2.722201 GCCCTACCTAGCGCACACT 61.722 63.158 11.47 0.00 0.00 3.55
8986 9428 3.237741 CTCGATCCCCCTCCTGCC 61.238 72.222 0.00 0.00 0.00 4.85


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

AutoCloner maintained by Alex Coulton.