Multiple sequence alignment - TraesCS1D01G130800

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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 TraesCS1D01G130800 chr1D 100.000 9164 0 0 1 9164 145932552 145941715 0.000000e+00 16923.0
1 TraesCS1D01G130800 chr1D 83.770 382 41 10 2173 2534 448221581 448221201 8.810000e-90 342.0
2 TraesCS1D01G130800 chr1D 97.500 80 2 0 8542 8621 145941172 145941093 4.460000e-28 137.0
3 TraesCS1D01G130800 chr1D 89.362 94 3 4 8538 8624 24780840 24780747 2.700000e-20 111.0
4 TraesCS1D01G130800 chr1D 90.000 90 3 2 8539 8622 471286124 471286035 2.700000e-20 111.0
5 TraesCS1D01G130800 chr1D 89.130 92 5 1 8535 8621 104427163 104427254 9.730000e-20 110.0
6 TraesCS1D01G130800 chr1D 80.882 136 23 3 8967 9102 485851044 485851176 4.530000e-18 104.0
7 TraesCS1D01G130800 chr1D 100.000 47 0 0 4732 4778 150863905 150863859 4.560000e-13 87.9
8 TraesCS1D01G130800 chr1D 97.872 47 1 0 4732 4778 150855745 150855699 2.120000e-11 82.4
9 TraesCS1D01G130800 chr1D 84.706 85 8 4 4694 4778 207541210 207541131 7.630000e-11 80.5
10 TraesCS1D01G130800 chr1D 94.231 52 3 0 4727 4778 220657878 220657827 7.630000e-11 80.5
11 TraesCS1D01G130800 chr1D 79.487 117 19 5 4662 4778 205947903 205948014 2.740000e-10 78.7
12 TraesCS1D01G130800 chr1D 95.556 45 2 0 6051 6095 49932200 49932244 1.280000e-08 73.1
13 TraesCS1D01G130800 chr1D 97.619 42 1 0 6054 6095 381307088 381307047 1.280000e-08 73.1
14 TraesCS1D01G130800 chr1D 93.617 47 3 0 6049 6095 120537611 120537657 4.590000e-08 71.3
15 TraesCS1D01G130800 chr1D 100.000 37 0 0 6053 6089 381306991 381307027 1.650000e-07 69.4
16 TraesCS1D01G130800 chr1D 82.353 85 10 5 4694 4778 486502238 486502317 1.650000e-07 69.4
17 TraesCS1D01G130800 chr1A 96.289 3988 92 23 854 4825 143810181 143814128 0.000000e+00 6493.0
18 TraesCS1D01G130800 chr1A 95.316 3992 132 24 854 4825 143748565 143752521 0.000000e+00 6285.0
19 TraesCS1D01G130800 chr1A 96.375 2317 45 8 4818 7132 143814640 143816919 0.000000e+00 3777.0
20 TraesCS1D01G130800 chr1A 98.578 1406 18 1 7140 8545 143817302 143818705 0.000000e+00 2484.0
21 TraesCS1D01G130800 chr1A 97.798 545 8 2 8620 9164 143818702 143819242 0.000000e+00 937.0
22 TraesCS1D01G130800 chr1A 84.281 668 80 16 1645 2294 572220775 572220115 6.040000e-176 628.0
23 TraesCS1D01G130800 chr1A 80.076 793 152 5 1 790 339169222 339168433 1.330000e-162 584.0
24 TraesCS1D01G130800 chr1A 73.115 703 170 18 1 695 584750602 584751293 5.530000e-57 233.0
25 TraesCS1D01G130800 chr1A 88.430 121 11 2 9026 9145 58289714 58289596 9.590000e-30 143.0
26 TraesCS1D01G130800 chr1A 77.542 236 36 16 6853 7082 36276876 36276652 9.660000e-25 126.0
27 TraesCS1D01G130800 chr1A 80.342 117 15 7 4662 4778 67855172 67855280 2.120000e-11 82.4
28 TraesCS1D01G130800 chr1A 87.879 66 6 2 791 856 143781475 143781538 9.870000e-10 76.8
29 TraesCS1D01G130800 chr1A 87.879 66 5 3 791 856 143745914 143745976 3.550000e-09 75.0
30 TraesCS1D01G130800 chr1A 95.652 46 2 0 6050 6095 481924417 481924462 3.550000e-09 75.0
31 TraesCS1D01G130800 chr1A 93.617 47 3 0 4732 4778 187289431 187289385 4.590000e-08 71.3
32 TraesCS1D01G130800 chr1B 98.315 3680 54 4 4868 8545 194789299 194792972 0.000000e+00 6445.0
33 TraesCS1D01G130800 chr1B 97.076 2462 52 8 1929 4388 194785632 194788075 0.000000e+00 4130.0
34 TraesCS1D01G130800 chr1B 97.855 1119 23 1 814 1931 194784367 194785485 0.000000e+00 1932.0
35 TraesCS1D01G130800 chr1B 96.881 545 11 2 8620 9164 194792973 194793511 0.000000e+00 907.0
36 TraesCS1D01G130800 chr1B 97.738 442 6 1 4388 4829 194788863 194789300 0.000000e+00 758.0
37 TraesCS1D01G130800 chr1B 93.750 352 20 2 438 789 194720074 194720423 2.270000e-145 527.0
38 TraesCS1D01G130800 chr1B 87.850 107 6 3 8525 8625 586295722 586295827 1.620000e-22 119.0
39 TraesCS1D01G130800 chr1B 79.508 122 17 8 4657 4778 218247202 218247089 7.630000e-11 80.5
40 TraesCS1D01G130800 chr1B 100.000 28 0 0 804 831 194784323 194784350 1.700000e-02 52.8
41 TraesCS1D01G130800 chr4B 94.028 653 36 2 1 650 459005679 459005027 0.000000e+00 987.0
42 TraesCS1D01G130800 chr4B 82.458 895 107 22 1643 2513 4477174 4478042 0.000000e+00 737.0
43 TraesCS1D01G130800 chr4B 95.455 176 8 0 2914 3089 630084923 630085098 1.950000e-71 281.0
44 TraesCS1D01G130800 chr4B 93.007 143 10 0 648 790 458991261 458991119 9.320000e-50 209.0
45 TraesCS1D01G130800 chr4B 84.615 143 20 2 8979 9120 34729952 34729811 3.450000e-29 141.0
46 TraesCS1D01G130800 chr4B 93.258 89 1 1 8539 8622 264286187 264286275 9.660000e-25 126.0
47 TraesCS1D01G130800 chr4B 93.023 86 6 0 8537 8622 579587833 579587918 9.660000e-25 126.0
48 TraesCS1D01G130800 chr4B 92.135 89 2 1 8539 8622 222672147 222672235 4.490000e-23 121.0
49 TraesCS1D01G130800 chr4B 91.304 92 3 1 8539 8625 367831877 367831786 4.490000e-23 121.0
50 TraesCS1D01G130800 chr4B 79.091 110 21 2 8977 9086 517616255 517616362 3.550000e-09 75.0
51 TraesCS1D01G130800 chr6D 84.083 911 105 16 1644 2531 17962695 17963588 0.000000e+00 843.0
52 TraesCS1D01G130800 chr6D 73.718 780 197 8 1 776 6378468 6377693 1.930000e-76 298.0
53 TraesCS1D01G130800 chr6D 93.103 174 12 0 2916 3089 426154723 426154550 1.180000e-63 255.0
54 TraesCS1D01G130800 chr6D 93.103 174 12 0 2916 3089 456312076 456312249 1.180000e-63 255.0
55 TraesCS1D01G130800 chr6D 93.750 80 5 0 8542 8621 207267951 207268030 4.490000e-23 121.0
56 TraesCS1D01G130800 chr6D 88.776 98 5 2 8533 8625 139569722 139569818 2.090000e-21 115.0
57 TraesCS1D01G130800 chr6D 89.474 95 4 2 8536 8625 295270486 295270393 2.090000e-21 115.0
58 TraesCS1D01G130800 chr6D 90.698 86 3 1 8542 8622 65395429 65395514 9.730000e-20 110.0
59 TraesCS1D01G130800 chr6D 89.773 88 4 1 8541 8623 103601939 103601852 3.500000e-19 108.0
60 TraesCS1D01G130800 chr6D 78.191 188 25 11 8969 9151 449250834 449251010 1.260000e-18 106.0
61 TraesCS1D01G130800 chr6D 80.000 110 22 0 9007 9116 10754808 10754917 2.120000e-11 82.4
62 TraesCS1D01G130800 chr6D 97.872 47 1 0 4732 4778 214184659 214184705 2.120000e-11 82.4
63 TraesCS1D01G130800 chr6D 97.872 47 1 0 4732 4778 286282889 286282935 2.120000e-11 82.4
64 TraesCS1D01G130800 chr6D 84.706 85 8 5 4694 4778 177102068 177101989 7.630000e-11 80.5
65 TraesCS1D01G130800 chr6D 94.000 50 3 0 4732 4781 183631305 183631256 9.870000e-10 76.8
66 TraesCS1D01G130800 chr6D 83.529 85 9 5 4694 4778 238532795 238532874 3.550000e-09 75.0
67 TraesCS1D01G130800 chr6D 95.238 42 2 0 6054 6095 11363682 11363723 5.940000e-07 67.6
68 TraesCS1D01G130800 chr6D 95.238 42 2 0 6054 6095 264679148 264679107 5.940000e-07 67.6
69 TraesCS1D01G130800 chr6D 93.333 45 3 0 6051 6095 366679060 366679104 5.940000e-07 67.6
70 TraesCS1D01G130800 chr6D 95.238 42 2 0 6054 6095 426495763 426495804 5.940000e-07 67.6
71 TraesCS1D01G130800 chr6D 88.000 50 4 2 6047 6095 128879394 128879346 3.570000e-04 58.4
72 TraesCS1D01G130800 chr6D 100.000 31 0 0 6050 6080 204684785 204684755 3.570000e-04 58.4
73 TraesCS1D01G130800 chr6D 92.308 39 2 1 6940 6978 461707951 461707914 5.000000e-03 54.7
74 TraesCS1D01G130800 chr6D 88.372 43 5 0 6053 6095 369858666 369858624 1.700000e-02 52.8
75 TraesCS1D01G130800 chr5D 83.297 922 107 31 1643 2531 527144903 527145810 0.000000e+00 806.0
76 TraesCS1D01G130800 chr5D 82.449 923 121 21 1644 2530 9390420 9391337 0.000000e+00 769.0
77 TraesCS1D01G130800 chr5D 82.380 857 113 28 1701 2530 390422790 390421945 0.000000e+00 712.0
78 TraesCS1D01G130800 chr5D 80.756 582 82 19 1644 2216 7480458 7481018 2.360000e-115 427.0
79 TraesCS1D01G130800 chr5D 93.750 176 11 0 2914 3089 500160233 500160058 1.960000e-66 265.0
80 TraesCS1D01G130800 chr5D 83.537 164 25 2 8959 9122 255076214 255076375 1.590000e-32 152.0
81 TraesCS1D01G130800 chr5D 92.941 85 6 0 8540 8624 381397405 381397321 3.470000e-24 124.0
82 TraesCS1D01G130800 chr5D 82.292 96 14 3 8994 9088 488862222 488862315 7.630000e-11 80.5
83 TraesCS1D01G130800 chr5D 79.487 117 17 7 4662 4778 219845639 219845748 9.870000e-10 76.8
84 TraesCS1D01G130800 chr5D 97.619 42 1 0 6054 6095 420277225 420277184 1.280000e-08 73.1
85 TraesCS1D01G130800 chr5D 97.619 42 1 0 6054 6095 457676022 457676063 1.280000e-08 73.1
86 TraesCS1D01G130800 chr5D 91.837 49 4 0 6044 6092 297981406 297981358 1.650000e-07 69.4
87 TraesCS1D01G130800 chr5D 77.778 117 19 7 4662 4778 151127677 151127786 2.140000e-06 65.8
88 TraesCS1D01G130800 chr7A 82.398 909 119 22 1652 2521 121933981 121934887 0.000000e+00 754.0
89 TraesCS1D01G130800 chr7A 90.155 193 19 0 2338 2530 287885458 287885266 1.530000e-62 252.0
90 TraesCS1D01G130800 chr7A 75.967 491 103 12 169 650 74597256 74597740 1.190000e-58 239.0
91 TraesCS1D01G130800 chr7A 83.420 193 32 0 8969 9161 77076555 77076747 7.310000e-41 180.0
92 TraesCS1D01G130800 chr7A 82.022 178 28 4 8964 9140 391906514 391906688 2.060000e-31 148.0
93 TraesCS1D01G130800 chr7A 89.796 49 4 1 4857 4904 171441902 171441854 2.760000e-05 62.1
94 TraesCS1D01G130800 chr6A 82.649 853 119 21 1702 2527 2937930 2938780 0.000000e+00 728.0
95 TraesCS1D01G130800 chr6A 95.745 47 2 0 4732 4778 71871958 71871912 9.870000e-10 76.8
96 TraesCS1D01G130800 chr6A 97.674 43 1 0 6053 6095 311856995 311856953 3.550000e-09 75.0
97 TraesCS1D01G130800 chr6A 100.000 33 0 0 6940 6972 608626528 608626496 2.760000e-05 62.1
98 TraesCS1D01G130800 chr7B 81.633 931 122 33 1644 2531 534537362 534536438 0.000000e+00 726.0
99 TraesCS1D01G130800 chr7B 82.483 862 110 32 1705 2530 707611088 707610232 0.000000e+00 717.0
100 TraesCS1D01G130800 chr7B 82.759 174 27 3 8968 9140 297400712 297400541 1.590000e-32 152.0
101 TraesCS1D01G130800 chr7B 80.851 188 36 0 24 211 526389440 526389253 2.060000e-31 148.0
102 TraesCS1D01G130800 chr7B 93.258 89 1 1 8539 8622 402543605 402543693 9.660000e-25 126.0
103 TraesCS1D01G130800 chr7B 91.525 59 3 1 6054 6110 708918114 708918056 7.630000e-11 80.5
104 TraesCS1D01G130800 chr5A 82.562 843 121 16 1701 2526 546884040 546884873 0.000000e+00 719.0
105 TraesCS1D01G130800 chr5A 80.942 934 125 31 1643 2528 10843945 10844873 0.000000e+00 689.0
106 TraesCS1D01G130800 chr5A 84.615 195 28 2 8968 9161 445134153 445133960 9.390000e-45 193.0
107 TraesCS1D01G130800 chr5A 81.461 178 24 8 8956 9132 382337552 382337383 4.460000e-28 137.0
108 TraesCS1D01G130800 chr5A 77.419 186 32 7 8966 9145 652650648 652650467 1.630000e-17 102.0
109 TraesCS1D01G130800 chr5A 97.826 46 1 0 6044 6089 401142938 401142983 7.630000e-11 80.5
110 TraesCS1D01G130800 chr5A 95.745 47 2 0 4732 4778 210769778 210769732 9.870000e-10 76.8
111 TraesCS1D01G130800 chr5A 97.619 42 1 0 6054 6095 533944283 533944242 1.280000e-08 73.1
112 TraesCS1D01G130800 chr5A 74.658 146 33 4 264 407 22490648 22490505 2.760000e-05 62.1
113 TraesCS1D01G130800 chr2D 80.786 942 136 23 1627 2527 589507565 589508502 0.000000e+00 695.0
114 TraesCS1D01G130800 chr2D 77.032 775 168 10 6 775 8459652 8458883 3.930000e-118 436.0
115 TraesCS1D01G130800 chr2D 83.237 173 17 7 8973 9142 274849607 274849770 2.060000e-31 148.0
116 TraesCS1D01G130800 chr2D 79.508 122 18 7 4657 4778 360173940 360174054 7.630000e-11 80.5
117 TraesCS1D01G130800 chr5B 85.520 663 70 19 1643 2294 641249175 641248528 0.000000e+00 669.0
118 TraesCS1D01G130800 chr5B 82.828 198 25 8 8964 9158 328374002 328373811 1.580000e-37 169.0
119 TraesCS1D01G130800 chr5B 98.750 80 1 0 8542 8621 63941590 63941669 9.590000e-30 143.0
120 TraesCS1D01G130800 chr5B 95.402 87 4 0 8539 8625 63941672 63941586 1.240000e-28 139.0
121 TraesCS1D01G130800 chr5B 84.404 109 16 1 9051 9159 271946304 271946197 1.260000e-18 106.0
122 TraesCS1D01G130800 chr6B 76.535 635 147 2 15 649 675206589 675207221 6.810000e-91 346.0
123 TraesCS1D01G130800 chr6B 93.878 49 3 0 6047 6095 310357675 310357723 3.550000e-09 75.0
124 TraesCS1D01G130800 chr4A 76.258 636 149 2 15 649 674442605 674443239 4.100000e-88 337.0
125 TraesCS1D01G130800 chr4A 84.553 123 19 0 6845 6967 3353955 3353833 1.250000e-23 122.0
126 TraesCS1D01G130800 chr4A 79.508 122 17 7 4657 4778 400233304 400233191 7.630000e-11 80.5
127 TraesCS1D01G130800 chr3B 76.190 588 139 1 15 602 546911582 546912168 8.940000e-80 309.0
128 TraesCS1D01G130800 chr3B 93.605 172 11 0 2916 3087 480377202 480377031 3.280000e-64 257.0
129 TraesCS1D01G130800 chr3B 95.349 86 3 1 8538 8622 825250113 825250028 1.610000e-27 135.0
130 TraesCS1D01G130800 chr3D 90.206 194 16 3 2896 3089 369414440 369414250 5.490000e-62 250.0
131 TraesCS1D01G130800 chr3D 94.118 85 5 0 8538 8622 558557512 558557428 7.470000e-26 130.0
132 TraesCS1D01G130800 chr3D 94.048 84 5 0 8539 8622 558557426 558557509 2.690000e-25 128.0
133 TraesCS1D01G130800 chr3D 93.902 82 4 1 8542 8623 457400787 457400867 1.250000e-23 122.0
134 TraesCS1D01G130800 chr3D 92.045 88 4 3 8539 8624 457400869 457400783 4.490000e-23 121.0
135 TraesCS1D01G130800 chr3D 95.745 47 2 0 4732 4778 202579340 202579294 9.870000e-10 76.8
136 TraesCS1D01G130800 chr3D 83.721 86 8 6 4694 4778 433343250 433343330 9.870000e-10 76.8
137 TraesCS1D01G130800 chr3D 93.878 49 3 0 6047 6095 119116781 119116829 3.550000e-09 75.0
138 TraesCS1D01G130800 chr3D 95.556 45 2 0 6051 6095 157099354 157099398 1.280000e-08 73.1
139 TraesCS1D01G130800 chr3D 95.556 45 2 0 6051 6095 173623493 173623537 1.280000e-08 73.1
140 TraesCS1D01G130800 chr2A 78.886 341 70 2 22 362 122053300 122052962 7.160000e-56 230.0
141 TraesCS1D01G130800 chr2A 79.677 310 50 11 6803 7112 4179973 4179677 2.590000e-50 211.0
142 TraesCS1D01G130800 chr2A 94.253 87 4 1 8535 8621 549890381 549890466 2.080000e-26 132.0
143 TraesCS1D01G130800 chr4D 85.135 148 21 1 9015 9162 138704991 138704845 5.730000e-32 150.0
144 TraesCS1D01G130800 chr4D 90.110 91 4 1 8537 8622 23884420 23884330 7.520000e-21 113.0
145 TraesCS1D01G130800 chr4D 81.538 130 18 5 9002 9129 291740983 291740858 1.630000e-17 102.0
146 TraesCS1D01G130800 chr4D 83.178 107 14 4 5355 5459 471347206 471347310 2.720000e-15 95.3
147 TraesCS1D01G130800 chr4D 97.619 42 1 0 6054 6095 303839388 303839429 1.280000e-08 73.1
148 TraesCS1D01G130800 chr4D 97.619 42 1 0 6054 6095 322662508 322662549 1.280000e-08 73.1
149 TraesCS1D01G130800 chr4D 97.619 42 1 0 6054 6095 362116506 362116465 1.280000e-08 73.1
150 TraesCS1D01G130800 chr4D 97.561 41 1 0 6054 6094 320044258 320044218 4.590000e-08 71.3
151 TraesCS1D01G130800 chr7D 97.561 82 1 1 8542 8623 439239120 439239040 1.240000e-28 139.0
152 TraesCS1D01G130800 chr7D 97.531 81 1 1 8542 8622 439239042 439239121 4.460000e-28 137.0
153 TraesCS1D01G130800 chr7D 81.379 145 13 5 1640 1770 551503905 551503761 1.260000e-18 106.0
154 TraesCS1D01G130800 chr7D 95.652 46 2 0 6050 6095 497023237 497023282 3.550000e-09 75.0
155 TraesCS1D01G130800 chrUn 88.462 104 8 1 8524 8623 338590851 338590748 1.250000e-23 122.0
156 TraesCS1D01G130800 chrUn 90.909 88 3 3 8540 8622 119047629 119047542 7.520000e-21 113.0
157 TraesCS1D01G130800 chrUn 89.888 89 4 4 8538 8621 119047539 119047627 9.730000e-20 110.0
158 TraesCS1D01G130800 chrUn 89.773 88 4 1 8542 8624 23900937 23900850 3.500000e-19 108.0
159 TraesCS1D01G130800 chrUn 90.588 85 3 1 8542 8621 23900853 23900937 3.500000e-19 108.0
160 TraesCS1D01G130800 chrUn 88.889 90 4 2 8542 8625 92738992 92738903 1.260000e-18 106.0
161 TraesCS1D01G130800 chrUn 89.655 87 4 4 8541 8622 297037505 297037419 1.260000e-18 106.0
162 TraesCS1D01G130800 chrUn 89.655 87 4 4 8541 8622 301355110 301355024 1.260000e-18 106.0
163 TraesCS1D01G130800 chrUn 89.412 85 4 1 8542 8621 17148599 17148683 1.630000e-17 102.0
164 TraesCS1D01G130800 chrUn 80.909 110 21 0 9007 9116 35380766 35380875 4.560000e-13 87.9
165 TraesCS1D01G130800 chrUn 95.745 47 2 0 4732 4778 11088292 11088338 9.870000e-10 76.8
166 TraesCS1D01G130800 chrUn 95.745 47 2 0 4732 4778 11096203 11096249 9.870000e-10 76.8
167 TraesCS1D01G130800 chrUn 95.745 47 2 0 4732 4778 25640663 25640709 9.870000e-10 76.8
168 TraesCS1D01G130800 chrUn 95.745 47 2 0 4732 4778 47215953 47215999 9.870000e-10 76.8
169 TraesCS1D01G130800 chrUn 95.745 47 2 0 4732 4778 92246750 92246704 9.870000e-10 76.8
170 TraesCS1D01G130800 chrUn 95.745 47 2 0 4732 4778 92254945 92254899 9.870000e-10 76.8
171 TraesCS1D01G130800 chrUn 94.000 50 3 0 4732 4781 150889271 150889222 9.870000e-10 76.8
172 TraesCS1D01G130800 chrUn 95.745 47 2 0 4732 4778 476602185 476602139 9.870000e-10 76.8
173 TraesCS1D01G130800 chrUn 94.000 50 2 1 6047 6095 65440850 65440899 3.550000e-09 75.0
174 TraesCS1D01G130800 chrUn 80.000 95 19 0 9021 9115 162960282 162960376 4.590000e-08 71.3
175 TraesCS1D01G130800 chrUn 79.208 101 21 0 9015 9115 162999816 162999916 4.590000e-08 71.3
176 TraesCS1D01G130800 chrUn 79.208 101 21 0 9015 9115 163046684 163046784 4.590000e-08 71.3
177 TraesCS1D01G130800 chrUn 79.208 101 21 0 9015 9115 278292069 278292169 4.590000e-08 71.3
178 TraesCS1D01G130800 chrUn 79.208 101 21 0 9015 9115 378473672 378473772 4.590000e-08 71.3
179 TraesCS1D01G130800 chrUn 87.719 57 7 0 9059 9115 163000004 163000060 5.940000e-07 67.6
180 TraesCS1D01G130800 chrUn 87.719 57 7 0 9059 9115 378473860 378473916 5.940000e-07 67.6
181 TraesCS1D01G130800 chrUn 100.000 35 0 0 3604 3638 30085034 30085068 2.140000e-06 65.8
182 TraesCS1D01G130800 chrUn 97.143 35 1 0 6054 6088 399231008 399231042 9.940000e-05 60.2
183 TraesCS1D01G130800 chrUn 100.000 29 0 0 6050 6078 296736922 296736950 5.000000e-03 54.7
184 TraesCS1D01G130800 chrUn 100.000 29 0 0 6050 6078 307808478 307808450 5.000000e-03 54.7
185 TraesCS1D01G130800 chrUn 96.875 32 1 0 6049 6080 422881446 422881477 5.000000e-03 54.7
186 TraesCS1D01G130800 chrUn 100.000 28 0 0 6053 6080 27746564 27746591 1.700000e-02 52.8
187 TraesCS1D01G130800 chrUn 100.000 28 0 0 6053 6080 34213230 34213257 1.700000e-02 52.8
188 TraesCS1D01G130800 chrUn 100.000 28 0 0 6053 6080 194666111 194666138 1.700000e-02 52.8
189 TraesCS1D01G130800 chrUn 100.000 28 0 0 6053 6080 215727710 215727683 1.700000e-02 52.8
190 TraesCS1D01G130800 chrUn 88.636 44 3 2 6053 6095 347805191 347805149 1.700000e-02 52.8
191 TraesCS1D01G130800 chr3A 77.457 173 33 6 6846 7014 472366796 472366626 2.110000e-16 99.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS1D01G130800 chr1D 145932552 145941715 9163 False 16923.00 16923 100.0000 1 9164 1 chr1D.!!$F4 9163
1 TraesCS1D01G130800 chr1A 143810181 143819242 9061 False 3422.75 6493 97.2600 854 9164 4 chr1A.!!$F6 8310
2 TraesCS1D01G130800 chr1A 143745914 143752521 6607 False 3180.00 6285 91.5975 791 4825 2 chr1A.!!$F5 4034
3 TraesCS1D01G130800 chr1A 572220115 572220775 660 True 628.00 628 84.2810 1645 2294 1 chr1A.!!$R5 649
4 TraesCS1D01G130800 chr1A 339168433 339169222 789 True 584.00 584 80.0760 1 790 1 chr1A.!!$R4 789
5 TraesCS1D01G130800 chr1A 584750602 584751293 691 False 233.00 233 73.1150 1 695 1 chr1A.!!$F4 694
6 TraesCS1D01G130800 chr1B 194784323 194793511 9188 False 2370.80 6445 97.9775 804 9164 6 chr1B.!!$F3 8360
7 TraesCS1D01G130800 chr4B 459005027 459005679 652 True 987.00 987 94.0280 1 650 1 chr4B.!!$R4 649
8 TraesCS1D01G130800 chr4B 4477174 4478042 868 False 737.00 737 82.4580 1643 2513 1 chr4B.!!$F1 870
9 TraesCS1D01G130800 chr6D 17962695 17963588 893 False 843.00 843 84.0830 1644 2531 1 chr6D.!!$F3 887
10 TraesCS1D01G130800 chr6D 6377693 6378468 775 True 298.00 298 73.7180 1 776 1 chr6D.!!$R1 775
11 TraesCS1D01G130800 chr5D 527144903 527145810 907 False 806.00 806 83.2970 1643 2531 1 chr5D.!!$F8 888
12 TraesCS1D01G130800 chr5D 9390420 9391337 917 False 769.00 769 82.4490 1644 2530 1 chr5D.!!$F2 886
13 TraesCS1D01G130800 chr5D 390421945 390422790 845 True 712.00 712 82.3800 1701 2530 1 chr5D.!!$R3 829
14 TraesCS1D01G130800 chr5D 7480458 7481018 560 False 427.00 427 80.7560 1644 2216 1 chr5D.!!$F1 572
15 TraesCS1D01G130800 chr7A 121933981 121934887 906 False 754.00 754 82.3980 1652 2521 1 chr7A.!!$F3 869
16 TraesCS1D01G130800 chr6A 2937930 2938780 850 False 728.00 728 82.6490 1702 2527 1 chr6A.!!$F1 825
17 TraesCS1D01G130800 chr7B 534536438 534537362 924 True 726.00 726 81.6330 1644 2531 1 chr7B.!!$R3 887
18 TraesCS1D01G130800 chr7B 707610232 707611088 856 True 717.00 717 82.4830 1705 2530 1 chr7B.!!$R4 825
19 TraesCS1D01G130800 chr5A 546884040 546884873 833 False 719.00 719 82.5620 1701 2526 1 chr5A.!!$F3 825
20 TraesCS1D01G130800 chr5A 10843945 10844873 928 False 689.00 689 80.9420 1643 2528 1 chr5A.!!$F1 885
21 TraesCS1D01G130800 chr2D 589507565 589508502 937 False 695.00 695 80.7860 1627 2527 1 chr2D.!!$F3 900
22 TraesCS1D01G130800 chr2D 8458883 8459652 769 True 436.00 436 77.0320 6 775 1 chr2D.!!$R1 769
23 TraesCS1D01G130800 chr5B 641248528 641249175 647 True 669.00 669 85.5200 1643 2294 1 chr5B.!!$R4 651
24 TraesCS1D01G130800 chr6B 675206589 675207221 632 False 346.00 346 76.5350 15 649 1 chr6B.!!$F2 634
25 TraesCS1D01G130800 chr4A 674442605 674443239 634 False 337.00 337 76.2580 15 649 1 chr4A.!!$F1 634
26 TraesCS1D01G130800 chr3B 546911582 546912168 586 False 309.00 309 76.1900 15 602 1 chr3B.!!$F1 587

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
685 692 1.547820 TGTCCTGAAGCAGCAGAGTAG 59.452 52.381 7.34 0.00 38.14 2.57 F
1146 3791 0.756903 GCCATACGTACATCACCCCT 59.243 55.000 0.00 0.00 0.00 4.79 F
1546 4191 4.941609 GCTTTGCGAGGATCCTCA 57.058 55.556 35.32 19.31 42.86 3.86 F
2343 5216 1.207089 TGACCAGGCTGACTAATTCGG 59.793 52.381 17.94 0.00 0.00 4.30 F
3174 6050 1.372004 CACGACGGCCTTACAACGA 60.372 57.895 0.00 0.00 0.00 3.85 F
3244 6120 0.603569 TTCAGTTGCCTCGAGGACTC 59.396 55.000 35.69 21.43 37.39 3.36 F
4949 9136 1.810031 CGGCATAACCACGGACATGAT 60.810 52.381 0.00 0.00 39.03 2.45 F
5192 9379 0.106894 GAACCCAAGCCTATCTCCCG 59.893 60.000 0.00 0.00 0.00 5.14 F
5417 9604 2.116238 GGTCAGGTCCTAATAGTGGCA 58.884 52.381 0.00 0.00 0.00 4.92 F
7269 11836 2.542020 TCTGCAACGGATGTGAGAAA 57.458 45.000 0.00 0.00 0.00 2.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1546 4191 0.539051 CTGGGGTCATTCGAGAGCTT 59.461 55.000 4.18 0.00 36.33 3.74 R
2192 5036 5.639082 GGCCAACGATTTTTCAAATCAATCT 59.361 36.000 0.00 0.00 0.00 2.40 R
3237 6113 0.322636 TCACAGTCCCTCGAGTCCTC 60.323 60.000 12.31 0.00 0.00 3.71 R
3238 6114 0.333312 ATCACAGTCCCTCGAGTCCT 59.667 55.000 12.31 0.63 0.00 3.85 R
4527 8195 0.796312 TTCGTTTCCGCTGATGCTTC 59.204 50.000 0.00 0.00 36.97 3.86 R
5174 9361 1.984288 GCGGGAGATAGGCTTGGGTT 61.984 60.000 0.00 0.00 0.00 4.11 R
6553 10742 3.603532 CTGTGGTCTACTGATGTGCAAT 58.396 45.455 0.00 0.00 0.00 3.56 R
7090 11281 8.302515 ACAGCCTCTTTGATTCAAATGATTAT 57.697 30.769 12.04 0.00 32.70 1.28 R
7321 11888 3.063997 GCCAACATGAGATGGAAAGTACG 59.936 47.826 17.24 0.00 39.92 3.67 R
8605 13172 0.115745 AAAGTACTCCCTCCGTCCCA 59.884 55.000 0.00 0.00 0.00 4.37 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
57 58 6.052360 TGCATCCCTTTTTAAAAGTTTGGAC 58.948 36.000 15.19 6.01 0.00 4.02
99 100 2.912956 ACACAAAGGATGAGCCCTTCTA 59.087 45.455 0.00 0.00 45.30 2.10
145 147 4.446371 CAGAGGGGTAGTATTTTGCTCTG 58.554 47.826 0.00 0.00 0.00 3.35
223 225 4.328169 GCCAACATTGCAAGATTAAAGCTC 59.672 41.667 4.94 0.00 0.00 4.09
234 236 7.553760 TGCAAGATTAAAGCTCTGAATATCACA 59.446 33.333 0.00 0.00 0.00 3.58
260 262 3.060611 CCCATTCCTCCCCATACCTTTA 58.939 50.000 0.00 0.00 0.00 1.85
342 344 7.054124 CCCCACCAATAATGCGATATAGTATT 58.946 38.462 4.70 4.70 0.00 1.89
407 411 1.618837 TCGCATAGGTAGGAATGGCTC 59.381 52.381 0.00 0.00 0.00 4.70
519 524 5.476254 TCATATGTTTGAAGCAATCCACACA 59.524 36.000 1.90 0.00 0.00 3.72
590 597 9.676861 AAGATTCAGTCATAATGTCAAGAATCA 57.323 29.630 16.40 0.00 41.35 2.57
616 623 2.304180 CACTTCCACCTTCTCATCCACT 59.696 50.000 0.00 0.00 0.00 4.00
661 668 4.899352 AGAGGATTTGACAGCACTAACT 57.101 40.909 0.00 0.00 0.00 2.24
663 670 5.971763 AGAGGATTTGACAGCACTAACTAG 58.028 41.667 0.00 0.00 0.00 2.57
685 692 1.547820 TGTCCTGAAGCAGCAGAGTAG 59.452 52.381 7.34 0.00 38.14 2.57
691 698 2.827921 TGAAGCAGCAGAGTAGTCATCA 59.172 45.455 0.00 0.00 0.00 3.07
703 710 7.201866 GCAGAGTAGTCATCAAGAATCCTCTTA 60.202 40.741 0.00 0.00 40.05 2.10
707 714 9.261035 AGTAGTCATCAAGAATCCTCTTAAGAA 57.739 33.333 6.63 0.00 40.05 2.52
710 717 7.992033 AGTCATCAAGAATCCTCTTAAGAATGG 59.008 37.037 6.63 5.55 40.05 3.16
718 725 7.718753 AGAATCCTCTTAAGAATGGTAGCATTG 59.281 37.037 24.07 9.85 0.00 2.82
784 791 8.753497 ATAATAAGTGAGAAATGAAAGGGGAC 57.247 34.615 0.00 0.00 0.00 4.46
787 794 3.009584 AGTGAGAAATGAAAGGGGACTCC 59.990 47.826 0.00 0.00 42.68 3.85
1146 3791 0.756903 GCCATACGTACATCACCCCT 59.243 55.000 0.00 0.00 0.00 4.79
1546 4191 4.941609 GCTTTGCGAGGATCCTCA 57.058 55.556 35.32 19.31 42.86 3.86
2192 5036 2.438254 CATAGGCCGGTTGCTGCA 60.438 61.111 1.90 0.00 40.92 4.41
2246 5092 9.331282 TCAAATCGTAAACCAAATCCAAAATTT 57.669 25.926 0.00 0.00 0.00 1.82
2342 5215 2.544685 CTGACCAGGCTGACTAATTCG 58.455 52.381 17.94 0.00 0.00 3.34
2343 5216 1.207089 TGACCAGGCTGACTAATTCGG 59.793 52.381 17.94 0.00 0.00 4.30
2735 5611 7.760437 TGATCTGCGAATTGATTTTCAATGTA 58.240 30.769 3.65 0.00 45.57 2.29
3174 6050 1.372004 CACGACGGCCTTACAACGA 60.372 57.895 0.00 0.00 0.00 3.85
3236 6112 8.349983 TGTTTTCTTAATAGTTTCAGTTGCCTC 58.650 33.333 0.00 0.00 0.00 4.70
3237 6113 6.721571 TTCTTAATAGTTTCAGTTGCCTCG 57.278 37.500 0.00 0.00 0.00 4.63
3238 6114 6.032956 TCTTAATAGTTTCAGTTGCCTCGA 57.967 37.500 0.00 0.00 0.00 4.04
3239 6115 6.100004 TCTTAATAGTTTCAGTTGCCTCGAG 58.900 40.000 5.13 5.13 0.00 4.04
3240 6116 2.743636 TAGTTTCAGTTGCCTCGAGG 57.256 50.000 27.83 27.83 38.53 4.63
3241 6117 1.048601 AGTTTCAGTTGCCTCGAGGA 58.951 50.000 35.69 17.11 37.39 3.71
3242 6118 1.149148 GTTTCAGTTGCCTCGAGGAC 58.851 55.000 35.69 24.09 37.39 3.85
3243 6119 1.048601 TTTCAGTTGCCTCGAGGACT 58.951 50.000 35.69 25.96 37.39 3.85
3244 6120 0.603569 TTCAGTTGCCTCGAGGACTC 59.396 55.000 35.69 21.43 37.39 3.36
3643 6521 2.224719 CCTCCACCATGATGGGATTCTC 60.225 54.545 17.04 0.00 43.37 2.87
3747 6626 3.921119 TGCTTGACTTGTATTGGCTTG 57.079 42.857 0.00 0.00 0.00 4.01
3748 6627 2.557924 TGCTTGACTTGTATTGGCTTGG 59.442 45.455 0.00 0.00 0.00 3.61
3749 6628 2.672195 GCTTGACTTGTATTGGCTTGGC 60.672 50.000 0.00 0.00 0.00 4.52
3750 6629 2.584835 TGACTTGTATTGGCTTGGCT 57.415 45.000 0.00 0.00 0.00 4.75
3751 6630 2.875296 TGACTTGTATTGGCTTGGCTT 58.125 42.857 0.00 0.00 0.00 4.35
4120 7000 2.554893 GTGAGCTCCTAATAGTCTCGGG 59.445 54.545 12.15 0.00 0.00 5.14
4451 8119 6.149474 ACACAACTCTACCATTGAAAGCATAC 59.851 38.462 0.00 0.00 0.00 2.39
4527 8195 4.082787 GGTTTCATGACCCAACAGTACATG 60.083 45.833 10.18 0.00 39.40 3.21
4949 9136 1.810031 CGGCATAACCACGGACATGAT 60.810 52.381 0.00 0.00 39.03 2.45
5192 9379 0.106894 GAACCCAAGCCTATCTCCCG 59.893 60.000 0.00 0.00 0.00 5.14
5220 9407 9.686683 AATATAGTTTTATCCACTTGACAAGCT 57.313 29.630 15.24 3.61 0.00 3.74
5417 9604 2.116238 GGTCAGGTCCTAATAGTGGCA 58.884 52.381 0.00 0.00 0.00 4.92
6455 10644 4.030216 TGATTCAGTAGTAGCCATGACCA 58.970 43.478 0.00 0.00 0.00 4.02
6589 10778 3.809905 ACCACAGGACTGAGTTTTCTTC 58.190 45.455 6.29 0.00 0.00 2.87
6990 11181 6.311723 ACGGAAACTTAGTGCAAATAATTCG 58.688 36.000 0.00 0.00 0.00 3.34
7148 11714 3.429543 TGAAAAGCTGATTTGAAATGCGC 59.570 39.130 0.00 0.00 0.00 6.09
7269 11836 2.542020 TCTGCAACGGATGTGAGAAA 57.458 45.000 0.00 0.00 0.00 2.52
7321 11888 3.788333 ATGCAAGTGTGATATTGGTGC 57.212 42.857 0.00 0.00 0.00 5.01
7409 11976 0.597637 CCCGCGACAGATGTATGGTC 60.598 60.000 8.23 0.00 0.00 4.02
7767 12334 1.064017 GGTGGCCATATCCAGGAAACA 60.064 52.381 9.72 0.00 36.67 2.83
8108 12675 0.251354 ACAGATTCTGATGCAGCGGT 59.749 50.000 20.33 0.00 35.18 5.68
8139 12706 0.044092 TAGATGGAACCTCTGGGCCA 59.956 55.000 5.85 5.85 36.14 5.36
8235 12802 7.959733 TGCGACAGTTAATGTAATTTAGACAG 58.040 34.615 0.00 0.00 44.17 3.51
8523 13090 3.119743 TGAACAGCAATGCTATTGTGCTC 60.120 43.478 7.70 0.00 45.32 4.26
8545 13112 7.773690 TGCTCCTTTGGTTCCTATTTTATACTC 59.226 37.037 0.00 0.00 0.00 2.59
8546 13113 7.228906 GCTCCTTTGGTTCCTATTTTATACTCC 59.771 40.741 0.00 0.00 0.00 3.85
8547 13114 7.580007 TCCTTTGGTTCCTATTTTATACTCCC 58.420 38.462 0.00 0.00 0.00 4.30
8548 13115 7.407918 TCCTTTGGTTCCTATTTTATACTCCCT 59.592 37.037 0.00 0.00 0.00 4.20
8549 13116 7.720074 CCTTTGGTTCCTATTTTATACTCCCTC 59.280 40.741 0.00 0.00 0.00 4.30
8550 13117 6.758806 TGGTTCCTATTTTATACTCCCTCC 57.241 41.667 0.00 0.00 0.00 4.30
8551 13118 6.214278 TGGTTCCTATTTTATACTCCCTCCA 58.786 40.000 0.00 0.00 0.00 3.86
8552 13119 6.855061 TGGTTCCTATTTTATACTCCCTCCAT 59.145 38.462 0.00 0.00 0.00 3.41
8553 13120 7.017254 TGGTTCCTATTTTATACTCCCTCCATC 59.983 40.741 0.00 0.00 0.00 3.51
8554 13121 7.395617 GTTCCTATTTTATACTCCCTCCATCC 58.604 42.308 0.00 0.00 0.00 3.51
8555 13122 6.030082 TCCTATTTTATACTCCCTCCATCCC 58.970 44.000 0.00 0.00 0.00 3.85
8556 13123 5.790618 CCTATTTTATACTCCCTCCATCCCA 59.209 44.000 0.00 0.00 0.00 4.37
8557 13124 6.448387 CCTATTTTATACTCCCTCCATCCCAT 59.552 42.308 0.00 0.00 0.00 4.00
8558 13125 7.627697 CCTATTTTATACTCCCTCCATCCCATA 59.372 40.741 0.00 0.00 0.00 2.74
8559 13126 7.905144 ATTTTATACTCCCTCCATCCCATAA 57.095 36.000 0.00 0.00 0.00 1.90
8560 13127 7.905144 TTTTATACTCCCTCCATCCCATAAT 57.095 36.000 0.00 0.00 0.00 1.28
8561 13128 6.891306 TTATACTCCCTCCATCCCATAATG 57.109 41.667 0.00 0.00 0.00 1.90
8562 13129 3.080660 ACTCCCTCCATCCCATAATGT 57.919 47.619 0.00 0.00 0.00 2.71
8563 13130 4.228237 ACTCCCTCCATCCCATAATGTA 57.772 45.455 0.00 0.00 0.00 2.29
8564 13131 4.577096 ACTCCCTCCATCCCATAATGTAA 58.423 43.478 0.00 0.00 0.00 2.41
8565 13132 4.599241 ACTCCCTCCATCCCATAATGTAAG 59.401 45.833 0.00 0.00 0.00 2.34
8566 13133 4.838403 TCCCTCCATCCCATAATGTAAGA 58.162 43.478 0.00 0.00 0.00 2.10
8567 13134 4.597507 TCCCTCCATCCCATAATGTAAGAC 59.402 45.833 0.00 0.00 0.00 3.01
8568 13135 4.563580 CCCTCCATCCCATAATGTAAGACG 60.564 50.000 0.00 0.00 0.00 4.18
8569 13136 4.040461 CCTCCATCCCATAATGTAAGACGT 59.960 45.833 0.00 0.00 0.00 4.34
8570 13137 5.454755 CCTCCATCCCATAATGTAAGACGTT 60.455 44.000 0.00 0.00 0.00 3.99
8571 13138 5.996644 TCCATCCCATAATGTAAGACGTTT 58.003 37.500 0.00 0.00 0.00 3.60
8572 13139 6.419791 TCCATCCCATAATGTAAGACGTTTT 58.580 36.000 0.00 0.00 0.00 2.43
8573 13140 6.887545 TCCATCCCATAATGTAAGACGTTTTT 59.112 34.615 0.00 0.00 0.00 1.94
8613 13180 3.720949 CGTCTTACATTATGGGACGGA 57.279 47.619 20.50 2.30 43.69 4.69
8614 13181 3.639538 CGTCTTACATTATGGGACGGAG 58.360 50.000 20.50 2.74 43.69 4.63
8615 13182 3.552273 CGTCTTACATTATGGGACGGAGG 60.552 52.174 20.50 5.87 43.69 4.30
8616 13183 2.969950 TCTTACATTATGGGACGGAGGG 59.030 50.000 0.00 0.00 0.00 4.30
8617 13184 2.779429 TACATTATGGGACGGAGGGA 57.221 50.000 0.00 0.00 0.00 4.20
8618 13185 1.424638 ACATTATGGGACGGAGGGAG 58.575 55.000 0.00 0.00 0.00 4.30
8619 13186 1.344087 ACATTATGGGACGGAGGGAGT 60.344 52.381 0.00 0.00 0.00 3.85
8620 13187 2.090943 ACATTATGGGACGGAGGGAGTA 60.091 50.000 0.00 0.00 0.00 2.59
8621 13188 2.077687 TTATGGGACGGAGGGAGTAC 57.922 55.000 0.00 0.00 0.00 2.73
8835 13402 2.435437 TGTTGCTGCAGATATGAGGCTA 59.565 45.455 20.43 0.00 0.00 3.93
8939 13506 2.158769 TCACCAGTTGCAAGTGATCTGT 60.159 45.455 31.39 19.14 35.67 3.41
8963 13530 6.120507 AGAAAGACATTGCTAACTCCTCTT 57.879 37.500 0.00 0.00 0.00 2.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
99 100 5.648092 GGTGACCTGCTAAATTGTGAACTAT 59.352 40.000 0.00 0.00 0.00 2.12
145 147 3.879892 ACTCTCTTTGTGCCAAAGTTCTC 59.120 43.478 20.22 0.00 0.00 2.87
223 225 5.361857 AGGAATGGGCTTTTGTGATATTCAG 59.638 40.000 0.00 0.00 0.00 3.02
234 236 0.718408 ATGGGGAGGAATGGGCTTTT 59.282 50.000 0.00 0.00 0.00 2.27
260 262 3.480470 CTTGGTGGAAGATGTGTGTTCT 58.520 45.455 0.00 0.00 32.82 3.01
342 344 7.012327 CGAAGAAAATATGCAAGGGAATCACTA 59.988 37.037 0.00 0.00 0.00 2.74
381 385 2.097110 TCCTACCTATGCGATGGGTT 57.903 50.000 8.92 0.00 41.93 4.11
519 524 4.410099 ACCATCAATGATTGGTGTTGACT 58.590 39.130 16.46 0.00 40.17 3.41
590 597 0.398318 GAGAAGGTGGAAGTGTGCCT 59.602 55.000 0.00 0.00 0.00 4.75
680 687 8.908903 TCTTAAGAGGATTCTTGATGACTACTC 58.091 37.037 0.00 0.00 43.41 2.59
685 692 7.772757 ACCATTCTTAAGAGGATTCTTGATGAC 59.227 37.037 15.75 0.00 43.41 3.06
691 698 7.200434 TGCTACCATTCTTAAGAGGATTCTT 57.800 36.000 15.75 0.00 45.45 2.52
703 710 1.753073 GCTGCCAATGCTACCATTCTT 59.247 47.619 0.00 0.00 39.60 2.52
707 714 1.133575 AGATGCTGCCAATGCTACCAT 60.134 47.619 0.00 0.00 38.71 3.55
781 788 2.093658 TGCTCTCAAAATACGGGAGTCC 60.094 50.000 0.00 0.00 45.66 3.85
784 791 1.936547 GCTGCTCTCAAAATACGGGAG 59.063 52.381 0.00 0.00 0.00 4.30
787 794 5.741388 AATAAGCTGCTCTCAAAATACGG 57.259 39.130 1.00 0.00 0.00 4.02
831 838 1.686325 CGGCTAGCTTTAGGGCCAGA 61.686 60.000 15.72 0.00 44.27 3.86
910 3544 7.164803 GCAGATAAAACTAGCCCAGATTAGAT 58.835 38.462 0.00 0.00 0.00 1.98
1068 3713 0.587242 CGATGCCAATCTTGTTCGCG 60.587 55.000 0.00 0.00 0.00 5.87
1146 3791 2.852075 AGGAAACCGTGGCCTGGA 60.852 61.111 19.87 0.00 0.00 3.86
1336 3981 0.323087 ACAAGCGGTTTCCCCCATAC 60.323 55.000 0.00 0.00 0.00 2.39
1546 4191 0.539051 CTGGGGTCATTCGAGAGCTT 59.461 55.000 4.18 0.00 36.33 3.74
2192 5036 5.639082 GGCCAACGATTTTTCAAATCAATCT 59.361 36.000 0.00 0.00 0.00 2.40
2342 5215 5.875359 ACGATTAACTGAGGTCTTCAATTCC 59.125 40.000 0.00 0.00 34.81 3.01
2343 5216 6.590292 TCACGATTAACTGAGGTCTTCAATTC 59.410 38.462 0.00 0.00 34.81 2.17
3028 5904 9.865321 AACTACTTTTCATGATGAATCAAATGG 57.135 29.630 8.90 0.00 40.69 3.16
3152 6028 3.116531 GTAAGGCCGTCGTGCACC 61.117 66.667 12.15 0.00 0.00 5.01
3174 6050 0.877213 GTCGGTGTACAGCCACGTTT 60.877 55.000 18.90 0.00 36.16 3.60
3237 6113 0.322636 TCACAGTCCCTCGAGTCCTC 60.323 60.000 12.31 0.00 0.00 3.71
3238 6114 0.333312 ATCACAGTCCCTCGAGTCCT 59.667 55.000 12.31 0.63 0.00 3.85
3239 6115 0.741915 GATCACAGTCCCTCGAGTCC 59.258 60.000 12.31 0.00 0.00 3.85
3240 6116 1.757682 AGATCACAGTCCCTCGAGTC 58.242 55.000 12.31 1.58 0.00 3.36
3241 6117 2.240160 ACTAGATCACAGTCCCTCGAGT 59.760 50.000 12.31 0.00 0.00 4.18
3242 6118 2.875933 GACTAGATCACAGTCCCTCGAG 59.124 54.545 5.13 5.13 37.11 4.04
3243 6119 2.506231 AGACTAGATCACAGTCCCTCGA 59.494 50.000 18.74 0.00 42.85 4.04
3244 6120 2.925724 AGACTAGATCACAGTCCCTCG 58.074 52.381 18.74 0.00 42.85 4.63
3747 6626 3.633525 TGATATTCACATGAAGCCAAGCC 59.366 43.478 0.00 0.00 37.48 4.35
3748 6627 4.906065 TGATATTCACATGAAGCCAAGC 57.094 40.909 0.00 0.00 37.48 4.01
3749 6628 7.318141 ACTTTTGATATTCACATGAAGCCAAG 58.682 34.615 0.00 0.53 37.48 3.61
3750 6629 7.230849 ACTTTTGATATTCACATGAAGCCAA 57.769 32.000 0.00 2.19 37.48 4.52
3751 6630 6.839124 ACTTTTGATATTCACATGAAGCCA 57.161 33.333 0.00 0.00 37.48 4.75
3844 6723 4.153117 GCATGTATACAATCTAGCACTGCC 59.847 45.833 10.14 0.00 0.00 4.85
3938 6818 4.120946 GGGTTATGGGCCCATGTAATAA 57.879 45.455 42.19 27.34 45.40 1.40
3939 6819 3.818295 GGGTTATGGGCCCATGTAATA 57.182 47.619 42.19 23.15 45.40 0.98
3940 6820 2.694616 GGGTTATGGGCCCATGTAAT 57.305 50.000 42.19 23.22 45.40 1.89
4451 8119 9.755804 TGCTCTCTTATGAGACTTTGTTATATG 57.244 33.333 4.26 0.00 43.73 1.78
4527 8195 0.796312 TTCGTTTCCGCTGATGCTTC 59.204 50.000 0.00 0.00 36.97 3.86
5174 9361 1.984288 GCGGGAGATAGGCTTGGGTT 61.984 60.000 0.00 0.00 0.00 4.11
5192 9379 9.722056 CTTGTCAAGTGGATAAAACTATATTGC 57.278 33.333 4.27 0.00 0.00 3.56
5220 9407 4.568072 AACATGGTAGGATTGTAGCACA 57.432 40.909 0.00 0.00 33.39 4.57
5417 9604 3.330701 ACATGGTGGGTTGTCTCACTTAT 59.669 43.478 0.00 0.00 34.57 1.73
6553 10742 3.603532 CTGTGGTCTACTGATGTGCAAT 58.396 45.455 0.00 0.00 0.00 3.56
6969 11160 9.274065 CCTTACGAATTATTTGCACTAAGTTTC 57.726 33.333 0.00 0.00 0.00 2.78
7090 11281 8.302515 ACAGCCTCTTTGATTCAAATGATTAT 57.697 30.769 12.04 0.00 32.70 1.28
7240 11806 4.462483 ACATCCGTTGCAGAAACCATTTAT 59.538 37.500 0.00 0.00 35.13 1.40
7269 11836 9.869757 AACTGCTTTTAGTGTTTTAACATTCTT 57.130 25.926 0.00 0.00 41.59 2.52
7321 11888 3.063997 GCCAACATGAGATGGAAAGTACG 59.936 47.826 17.24 0.00 39.92 3.67
7409 11976 5.289675 GGAAAGATGAAGACTACATGACACG 59.710 44.000 0.00 0.00 0.00 4.49
7589 12156 4.261031 GGTGTGCACTCGTTATTTTCAAGT 60.261 41.667 19.41 0.00 0.00 3.16
7767 12334 5.772825 TTTCAACAAGCATAGCAAAGAGT 57.227 34.783 0.00 0.00 0.00 3.24
8139 12706 4.946157 CAGGAATCTACAGCAATTGGAGTT 59.054 41.667 7.72 0.00 38.98 3.01
8523 13090 7.583625 AGGGAGTATAAAATAGGAACCAAAGG 58.416 38.462 0.00 0.00 0.00 3.11
8545 13112 4.563580 CGTCTTACATTATGGGATGGAGGG 60.564 50.000 0.00 0.00 0.00 4.30
8546 13113 4.040461 ACGTCTTACATTATGGGATGGAGG 59.960 45.833 0.00 0.00 0.00 4.30
8547 13114 5.215252 ACGTCTTACATTATGGGATGGAG 57.785 43.478 0.00 0.00 0.00 3.86
8548 13115 5.623956 AACGTCTTACATTATGGGATGGA 57.376 39.130 0.00 0.00 0.00 3.41
8549 13116 6.693315 AAAACGTCTTACATTATGGGATGG 57.307 37.500 0.00 0.00 0.00 3.51
8588 13155 5.122711 CCGTCCCATAATGTAAGACGTTTTT 59.877 40.000 9.63 0.00 46.62 1.94
8589 13156 4.632688 CCGTCCCATAATGTAAGACGTTTT 59.367 41.667 9.63 0.00 46.62 2.43
8590 13157 4.081531 TCCGTCCCATAATGTAAGACGTTT 60.082 41.667 9.63 0.00 46.62 3.60
8591 13158 3.448301 TCCGTCCCATAATGTAAGACGTT 59.552 43.478 9.63 0.00 46.62 3.99
8592 13159 3.025978 TCCGTCCCATAATGTAAGACGT 58.974 45.455 9.63 0.00 46.62 4.34
8594 13161 3.244112 CCCTCCGTCCCATAATGTAAGAC 60.244 52.174 0.00 0.00 0.00 3.01
8595 13162 2.969950 CCCTCCGTCCCATAATGTAAGA 59.030 50.000 0.00 0.00 0.00 2.10
8596 13163 2.969950 TCCCTCCGTCCCATAATGTAAG 59.030 50.000 0.00 0.00 0.00 2.34
8597 13164 2.969950 CTCCCTCCGTCCCATAATGTAA 59.030 50.000 0.00 0.00 0.00 2.41
8598 13165 2.090943 ACTCCCTCCGTCCCATAATGTA 60.091 50.000 0.00 0.00 0.00 2.29
8599 13166 1.344087 ACTCCCTCCGTCCCATAATGT 60.344 52.381 0.00 0.00 0.00 2.71
8600 13167 1.424638 ACTCCCTCCGTCCCATAATG 58.575 55.000 0.00 0.00 0.00 1.90
8601 13168 2.179424 AGTACTCCCTCCGTCCCATAAT 59.821 50.000 0.00 0.00 0.00 1.28
8602 13169 1.572415 AGTACTCCCTCCGTCCCATAA 59.428 52.381 0.00 0.00 0.00 1.90
8603 13170 1.229131 AGTACTCCCTCCGTCCCATA 58.771 55.000 0.00 0.00 0.00 2.74
8604 13171 0.338814 AAGTACTCCCTCCGTCCCAT 59.661 55.000 0.00 0.00 0.00 4.00
8605 13172 0.115745 AAAGTACTCCCTCCGTCCCA 59.884 55.000 0.00 0.00 0.00 4.37
8606 13173 0.822811 GAAAGTACTCCCTCCGTCCC 59.177 60.000 0.00 0.00 0.00 4.46
8607 13174 0.822811 GGAAAGTACTCCCTCCGTCC 59.177 60.000 0.00 0.00 0.00 4.79
8608 13175 1.849977 AGGAAAGTACTCCCTCCGTC 58.150 55.000 10.16 0.00 35.95 4.79
8609 13176 1.900486 CAAGGAAAGTACTCCCTCCGT 59.100 52.381 14.88 8.64 35.95 4.69
8610 13177 1.207329 CCAAGGAAAGTACTCCCTCCG 59.793 57.143 14.88 10.32 35.95 4.63
8611 13178 2.502130 CTCCAAGGAAAGTACTCCCTCC 59.498 54.545 14.88 12.20 35.95 4.30
8612 13179 2.093394 GCTCCAAGGAAAGTACTCCCTC 60.093 54.545 14.88 4.58 35.95 4.30
8613 13180 1.909986 GCTCCAAGGAAAGTACTCCCT 59.090 52.381 10.16 10.16 35.95 4.20
8614 13181 1.628846 TGCTCCAAGGAAAGTACTCCC 59.371 52.381 0.00 0.50 35.95 4.30
8615 13182 3.418684 TTGCTCCAAGGAAAGTACTCC 57.581 47.619 0.00 0.00 35.51 3.85
8616 13183 5.299531 AGTTTTTGCTCCAAGGAAAGTACTC 59.700 40.000 0.00 0.00 36.88 2.59
8617 13184 5.067805 CAGTTTTTGCTCCAAGGAAAGTACT 59.932 40.000 0.00 0.00 36.88 2.73
8618 13185 5.163550 ACAGTTTTTGCTCCAAGGAAAGTAC 60.164 40.000 0.00 0.00 36.88 2.73
8619 13186 4.953579 ACAGTTTTTGCTCCAAGGAAAGTA 59.046 37.500 0.00 0.00 36.88 2.24
8620 13187 3.769300 ACAGTTTTTGCTCCAAGGAAAGT 59.231 39.130 0.00 0.00 36.88 2.66
8621 13188 4.391405 ACAGTTTTTGCTCCAAGGAAAG 57.609 40.909 0.00 0.00 36.88 2.62
8669 13236 9.534565 CGTTAGATGGATCAAAGATTAAGAAGA 57.465 33.333 0.00 0.00 0.00 2.87
8670 13237 8.279103 GCGTTAGATGGATCAAAGATTAAGAAG 58.721 37.037 0.00 0.00 0.00 2.85
8835 13402 5.655532 AGGCTTTCTACAAATCATCAAGCAT 59.344 36.000 0.00 0.00 37.49 3.79
8939 13506 6.859112 AGAGGAGTTAGCAATGTCTTTCTA 57.141 37.500 0.00 0.00 0.00 2.10
8963 13530 7.010160 AGACCTTCAAATAATTTGGAACAGGA 58.990 34.615 0.00 0.00 42.39 3.86


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

AutoCloner maintained by Alex Coulton.