Multiple sequence alignment - TraesCS5A01G277600

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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 TraesCS5A01G277600 chr5A 100.000 5145 0 0 1 5145 487374928 487380072 0.000000e+00 9502.0
1 TraesCS5A01G277600 chr5A 95.000 740 34 3 3953 4690 337925312 337924574 0.000000e+00 1158.0
2 TraesCS5A01G277600 chr5A 88.602 465 46 5 640 1099 487375119 487375581 4.500000e-155 558.0
3 TraesCS5A01G277600 chr5A 88.578 464 48 3 192 654 487375567 487376026 4.500000e-155 558.0
4 TraesCS5A01G277600 chr5A 77.913 901 140 47 2838 3705 514401578 514402452 1.650000e-139 507.0
5 TraesCS5A01G277600 chr5A 80.000 230 44 2 1973 2200 522352877 522353106 8.860000e-38 169.0
6 TraesCS5A01G277600 chr5D 94.966 1748 81 4 99 1839 385622760 385624507 0.000000e+00 2734.0
7 TraesCS5A01G277600 chr5D 92.431 1440 92 11 2528 3956 385689965 385691398 0.000000e+00 2039.0
8 TraesCS5A01G277600 chr5D 90.387 697 54 7 1831 2525 385665558 385666243 0.000000e+00 904.0
9 TraesCS5A01G277600 chr5D 89.579 451 47 0 204 654 385623315 385623765 1.610000e-159 573.0
10 TraesCS5A01G277600 chr5D 89.056 466 43 6 640 1099 385622853 385623316 5.780000e-159 571.0
11 TraesCS5A01G277600 chr5D 76.769 947 156 45 2838 3751 408478698 408479613 6.030000e-129 472.0
12 TraesCS5A01G277600 chr5D 75.728 206 39 6 1996 2200 238943066 238943261 5.490000e-15 93.5
13 TraesCS5A01G277600 chr5D 86.585 82 6 4 1 78 327503155 327503235 9.180000e-13 86.1
14 TraesCS5A01G277600 chr5B 91.761 1408 88 16 129 1527 462903519 462904907 0.000000e+00 1932.0
15 TraesCS5A01G277600 chr5B 89.381 452 44 2 652 1099 462903593 462904044 2.690000e-157 566.0
16 TraesCS5A01G277600 chr5B 86.422 464 45 6 192 654 462904030 462904476 4.630000e-135 492.0
17 TraesCS5A01G277600 chr5B 76.320 701 116 35 2853 3534 347777691 347778360 3.840000e-86 329.0
18 TraesCS5A01G277600 chr4A 91.631 1183 91 8 3956 5136 495604811 495603635 0.000000e+00 1629.0
19 TraesCS5A01G277600 chr4A 90.535 1215 76 21 3957 5145 25455619 25454418 0.000000e+00 1570.0
20 TraesCS5A01G277600 chr4A 89.984 1218 91 14 3956 5145 553016452 553015238 0.000000e+00 1544.0
21 TraesCS5A01G277600 chr4A 84.337 498 65 12 3467 3956 490354349 490353857 4.660000e-130 475.0
22 TraesCS5A01G277600 chr3D 90.250 1200 77 21 3957 5131 187722435 187723619 0.000000e+00 1531.0
23 TraesCS5A01G277600 chr3D 80.366 1146 165 43 2838 3956 254595697 254596809 0.000000e+00 815.0
24 TraesCS5A01G277600 chr3D 84.369 499 62 10 3462 3956 396611194 396611680 4.660000e-130 475.0
25 TraesCS5A01G277600 chr3D 76.956 703 126 30 2851 3534 309104309 309104994 8.140000e-98 368.0
26 TraesCS5A01G277600 chr3D 78.311 521 70 28 1773 2269 537903724 537904225 3.900000e-76 296.0
27 TraesCS5A01G277600 chr3D 79.803 406 60 13 1772 2156 434165117 434164713 5.070000e-70 276.0
28 TraesCS5A01G277600 chr3D 73.977 684 123 34 1572 2211 551302578 551301906 5.180000e-55 226.0
29 TraesCS5A01G277600 chr3A 88.935 1211 90 24 3956 5145 683636167 683637354 0.000000e+00 1454.0
30 TraesCS5A01G277600 chr3A 88.950 905 89 8 4250 5145 478364130 478363228 0.000000e+00 1107.0
31 TraesCS5A01G277600 chr3A 81.081 481 66 14 1772 2230 572959271 572958794 1.360000e-95 361.0
32 TraesCS5A01G277600 chr3A 78.318 535 96 18 2837 3357 158745393 158744865 1.380000e-85 327.0
33 TraesCS5A01G277600 chr3A 83.529 85 10 4 1 83 718070195 718070277 5.520000e-10 76.8
34 TraesCS5A01G277600 chr1B 88.393 1120 112 15 3956 5068 618948708 618949816 0.000000e+00 1332.0
35 TraesCS5A01G277600 chr1B 77.734 768 123 38 3221 3956 495100485 495101236 1.320000e-115 427.0
36 TraesCS5A01G277600 chr1B 79.853 407 58 14 1816 2200 683222598 683223002 5.070000e-70 276.0
37 TraesCS5A01G277600 chr1B 81.379 290 42 5 1983 2268 662782012 662782293 5.180000e-55 226.0
38 TraesCS5A01G277600 chr1B 86.667 75 9 1 1 74 168350924 168350998 1.190000e-11 82.4
39 TraesCS5A01G277600 chr1B 91.228 57 5 0 1 57 307478927 307478871 1.540000e-10 78.7
40 TraesCS5A01G277600 chr7B 86.866 1203 133 23 3957 5145 344246668 344247859 0.000000e+00 1323.0
41 TraesCS5A01G277600 chr7B 78.295 516 82 20 3210 3705 135873452 135873957 6.470000e-79 305.0
42 TraesCS5A01G277600 chr1A 86.469 1212 138 22 3950 5145 480122320 480121119 0.000000e+00 1306.0
43 TraesCS5A01G277600 chr1A 84.263 502 64 11 3462 3956 491287759 491287266 4.660000e-130 475.0
44 TraesCS5A01G277600 chr1A 78.637 763 120 30 3221 3956 470342568 470343314 2.810000e-127 466.0
45 TraesCS5A01G277600 chr1A 84.615 273 36 5 1973 2241 464909871 464910141 3.050000e-67 267.0
46 TraesCS5A01G277600 chr1A 87.805 82 5 4 1 78 588291894 588291974 1.970000e-14 91.6
47 TraesCS5A01G277600 chr6B 80.340 1119 167 46 2858 3956 663558923 663557838 0.000000e+00 798.0
48 TraesCS5A01G277600 chr6B 83.978 181 28 1 1574 1754 547765756 547765577 6.850000e-39 172.0
49 TraesCS5A01G277600 chr6D 80.455 747 119 19 3225 3956 166756500 166757234 3.500000e-151 545.0
50 TraesCS5A01G277600 chr6D 75.944 715 123 34 2838 3537 309708034 309707354 6.430000e-84 322.0
51 TraesCS5A01G277600 chr6D 74.446 767 124 38 3221 3950 127079742 127079011 1.100000e-66 265.0
52 TraesCS5A01G277600 chr6D 92.537 67 4 1 2838 2904 198208654 198208719 1.530000e-15 95.3
53 TraesCS5A01G277600 chr6D 86.420 81 10 1 2953 3032 355889225 355889305 2.550000e-13 87.9
54 TraesCS5A01G277600 chr6D 89.552 67 7 0 2838 2904 392958794 392958728 9.180000e-13 86.1
55 TraesCS5A01G277600 chr6D 87.500 72 9 0 2840 2911 58323311 58323382 3.300000e-12 84.2
56 TraesCS5A01G277600 chr6D 94.118 51 3 0 1 51 275895318 275895268 1.540000e-10 78.7
57 TraesCS5A01G277600 chr6D 78.462 130 19 7 3214 3337 435221397 435221523 5.520000e-10 76.8
58 TraesCS5A01G277600 chr1D 79.381 776 116 24 3210 3954 31678178 31678940 1.650000e-139 507.0
59 TraesCS5A01G277600 chr1D 79.079 760 118 31 3221 3956 371196288 371197030 7.750000e-133 484.0
60 TraesCS5A01G277600 chr1D 77.007 461 86 17 2838 3284 182633755 182633301 3.980000e-61 246.0
61 TraesCS5A01G277600 chr1D 74.910 558 114 20 2838 3379 111354138 111353591 1.110000e-56 231.0
62 TraesCS5A01G277600 chr1D 75.143 523 100 23 2838 3337 111389261 111388746 8.670000e-53 219.0
63 TraesCS5A01G277600 chr1D 75.893 448 79 21 2853 3285 238095850 238095417 8.740000e-48 202.0
64 TraesCS5A01G277600 chr1D 83.495 206 23 4 2068 2271 365792419 365792615 1.140000e-41 182.0
65 TraesCS5A01G277600 chr1D 82.249 169 25 4 2075 2241 347393145 347393310 1.930000e-29 141.0
66 TraesCS5A01G277600 chr1D 77.778 234 35 10 2838 3065 363119455 363119233 1.500000e-25 128.0
67 TraesCS5A01G277600 chr1D 84.545 110 16 1 3209 3317 176791343 176791234 1.960000e-19 108.0
68 TraesCS5A01G277600 chr1D 75.701 214 39 11 2838 3042 351370795 351370586 1.530000e-15 95.3
69 TraesCS5A01G277600 chr1D 92.982 57 4 0 1 57 2430671 2430615 3.300000e-12 84.2
70 TraesCS5A01G277600 chr1D 86.486 74 10 0 2838 2911 304345395 304345322 1.190000e-11 82.4
71 TraesCS5A01G277600 chr1D 85.366 82 7 4 1 78 62783309 62783389 4.270000e-11 80.5
72 TraesCS5A01G277600 chr1D 82.418 91 15 1 2838 2928 298322342 298322431 1.540000e-10 78.7
73 TraesCS5A01G277600 chr1D 79.091 110 22 1 3145 3253 234916123 234916232 1.990000e-09 75.0
74 TraesCS5A01G277600 chr1D 87.302 63 8 0 2838 2900 288863992 288864054 7.150000e-09 73.1
75 TraesCS5A01G277600 chr1D 90.909 55 3 2 2836 2888 368648422 368648368 7.150000e-09 73.1
76 TraesCS5A01G277600 chr1D 90.385 52 5 0 2853 2904 20584296 20584245 9.240000e-08 69.4
77 TraesCS5A01G277600 chr1D 88.679 53 6 0 1 53 353656408 353656356 1.200000e-06 65.8
78 TraesCS5A01G277600 chr4D 78.846 780 105 31 1537 2269 394863200 394862434 6.030000e-129 472.0
79 TraesCS5A01G277600 chr4D 83.929 504 64 14 3462 3956 80842557 80842062 2.810000e-127 466.0
80 TraesCS5A01G277600 chr4D 78.809 722 116 31 2838 3537 85256246 85255540 7.860000e-123 451.0
81 TraesCS5A01G277600 chr4D 76.845 691 117 32 2840 3505 40961394 40962066 2.950000e-92 350.0
82 TraesCS5A01G277600 chr4D 75.697 502 78 23 1791 2269 96146859 96147339 1.450000e-50 211.0
83 TraesCS5A01G277600 chr4D 75.540 417 84 16 2851 3253 189235640 189236052 6.800000e-44 189.0
84 TraesCS5A01G277600 chr4D 81.517 211 29 8 2838 3042 308817542 308817748 1.150000e-36 165.0
85 TraesCS5A01G277600 chr4D 80.233 172 29 3 2918 3084 296983442 296983613 1.950000e-24 124.0
86 TraesCS5A01G277600 chr4D 74.517 259 46 18 2837 3082 332011950 332011699 1.530000e-15 95.3
87 TraesCS5A01G277600 chr4D 94.340 53 3 0 1 53 491564562 491564510 1.190000e-11 82.4
88 TraesCS5A01G277600 chr4D 91.228 57 5 0 1 57 381405954 381405898 1.540000e-10 78.7
89 TraesCS5A01G277600 chr4D 93.333 45 3 0 9 53 431315738 431315694 3.320000e-07 67.6
90 TraesCS5A01G277600 chr7D 83.800 500 69 10 3462 3956 140333931 140333439 1.010000e-126 464.0
91 TraesCS5A01G277600 chr7D 76.800 375 67 14 1793 2154 548945402 548945035 5.260000e-45 193.0
92 TraesCS5A01G277600 chr7D 92.453 53 4 0 1 53 20732485 20732537 5.520000e-10 76.8
93 TraesCS5A01G277600 chr2A 80.515 621 88 26 3210 3815 622145891 622146493 3.650000e-121 446.0
94 TraesCS5A01G277600 chr2D 77.595 790 114 47 2838 3601 399341010 399340258 2.220000e-113 420.0
95 TraesCS5A01G277600 chr2D 77.820 523 86 22 2838 3338 367820680 367820166 3.900000e-76 296.0
96 TraesCS5A01G277600 chr2D 74.593 492 89 25 2838 3316 367826415 367825947 3.160000e-42 183.0
97 TraesCS5A01G277600 chr2D 76.431 297 53 15 2835 3120 187883604 187883314 1.490000e-30 145.0
98 TraesCS5A01G277600 chr2D 96.078 51 2 0 1 51 198705161 198705111 3.300000e-12 84.2
99 TraesCS5A01G277600 chr2D 92.157 51 4 0 3 53 210904748 210904698 7.150000e-09 73.1
100 TraesCS5A01G277600 chr3B 78.032 742 108 22 1543 2237 708387442 708386709 2.870000e-112 416.0
101 TraesCS5A01G277600 chr3B 80.800 250 42 5 1996 2241 801140989 801141236 1.890000e-44 191.0
102 TraesCS5A01G277600 chr4B 76.244 884 148 51 2851 3705 415029284 415028434 3.710000e-111 412.0
103 TraesCS5A01G277600 chr4B 76.751 714 128 29 2838 3530 169814026 169813330 1.050000e-96 364.0
104 TraesCS5A01G277600 chr4B 77.886 511 86 17 2838 3327 127007339 127006835 5.040000e-75 292.0
105 TraesCS5A01G277600 chr4B 77.732 485 84 19 2838 3305 127090689 127090212 5.070000e-70 276.0
106 TraesCS5A01G277600 chr4B 77.494 431 77 14 2838 3251 487706427 487706854 1.850000e-59 241.0
107 TraesCS5A01G277600 chr4B 75.087 574 107 26 2838 3387 67600210 67600771 8.610000e-58 235.0
108 TraesCS5A01G277600 chr4B 82.061 262 39 6 2853 3108 436859854 436860113 3.120000e-52 217.0
109 TraesCS5A01G277600 chr4B 75.356 491 85 20 1772 2241 136163681 136164156 2.430000e-48 204.0
110 TraesCS5A01G277600 chr4B 84.146 82 9 4 1 79 27247510 27247430 5.520000e-10 76.8
111 TraesCS5A01G277600 chr6A 76.803 513 102 13 3038 3537 446505164 446504656 6.560000e-69 272.0
112 TraesCS5A01G277600 chr6A 94.828 58 3 0 1 58 594569771 594569828 1.970000e-14 91.6
113 TraesCS5A01G277600 chrUn 80.793 328 43 17 3387 3705 294211274 294211590 6.660000e-59 239.0
114 TraesCS5A01G277600 chrUn 80.793 328 43 17 3387 3705 294237763 294238079 6.660000e-59 239.0
115 TraesCS5A01G277600 chrUn 80.793 328 43 17 3387 3705 320032443 320032127 6.660000e-59 239.0
116 TraesCS5A01G277600 chrUn 74.708 257 46 17 2838 3082 121881026 121881275 4.240000e-16 97.1
117 TraesCS5A01G277600 chrUn 75.916 191 37 9 2935 3120 76350210 76350396 7.100000e-14 89.8
118 TraesCS5A01G277600 chrUn 73.828 256 50 13 2838 3082 217166865 217166616 9.180000e-13 86.1
119 TraesCS5A01G277600 chrUn 73.828 256 50 13 2838 3082 230128919 230128670 9.180000e-13 86.1
120 TraesCS5A01G277600 chrUn 73.930 257 48 18 2838 3082 294734592 294734841 9.180000e-13 86.1
121 TraesCS5A01G277600 chrUn 86.364 66 9 0 2838 2903 56822571 56822636 7.150000e-09 73.1
122 TraesCS5A01G277600 chrUn 89.474 57 6 0 1 57 415726587 415726643 7.150000e-09 73.1
123 TraesCS5A01G277600 chrUn 93.478 46 3 0 2838 2883 21818014 21818059 9.240000e-08 69.4
124 TraesCS5A01G277600 chrUn 88.679 53 6 0 2838 2890 10923522 10923470 1.200000e-06 65.8
125 TraesCS5A01G277600 chr7A 87.500 72 7 2 9 79 17093366 17093436 1.190000e-11 82.4
126 TraesCS5A01G277600 chr7A 85.366 82 7 4 1 78 52410778 52410858 4.270000e-11 80.5
127 TraesCS5A01G277600 chr7A 85.000 80 8 4 1 77 37655134 37655056 1.540000e-10 78.7


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 TraesCS5A01G277600 chr5A 487374928 487380072 5144 False 9502.000000 9502 100.000000 1 5145 1 chr5A.!!$F1 5144
1 TraesCS5A01G277600 chr5A 337924574 337925312 738 True 1158.000000 1158 95.000000 3953 4690 1 chr5A.!!$R1 737
2 TraesCS5A01G277600 chr5A 487375119 487376026 907 False 558.000000 558 88.590000 192 1099 2 chr5A.!!$F4 907
3 TraesCS5A01G277600 chr5A 514401578 514402452 874 False 507.000000 507 77.913000 2838 3705 1 chr5A.!!$F2 867
4 TraesCS5A01G277600 chr5D 385689965 385691398 1433 False 2039.000000 2039 92.431000 2528 3956 1 chr5D.!!$F4 1428
5 TraesCS5A01G277600 chr5D 385622760 385624507 1747 False 1292.666667 2734 91.200333 99 1839 3 chr5D.!!$F6 1740
6 TraesCS5A01G277600 chr5D 385665558 385666243 685 False 904.000000 904 90.387000 1831 2525 1 chr5D.!!$F3 694
7 TraesCS5A01G277600 chr5D 408478698 408479613 915 False 472.000000 472 76.769000 2838 3751 1 chr5D.!!$F5 913
8 TraesCS5A01G277600 chr5B 462903519 462904907 1388 False 996.666667 1932 89.188000 129 1527 3 chr5B.!!$F2 1398
9 TraesCS5A01G277600 chr5B 347777691 347778360 669 False 329.000000 329 76.320000 2853 3534 1 chr5B.!!$F1 681
10 TraesCS5A01G277600 chr4A 495603635 495604811 1176 True 1629.000000 1629 91.631000 3956 5136 1 chr4A.!!$R3 1180
11 TraesCS5A01G277600 chr4A 25454418 25455619 1201 True 1570.000000 1570 90.535000 3957 5145 1 chr4A.!!$R1 1188
12 TraesCS5A01G277600 chr4A 553015238 553016452 1214 True 1544.000000 1544 89.984000 3956 5145 1 chr4A.!!$R4 1189
13 TraesCS5A01G277600 chr3D 187722435 187723619 1184 False 1531.000000 1531 90.250000 3957 5131 1 chr3D.!!$F1 1174
14 TraesCS5A01G277600 chr3D 254595697 254596809 1112 False 815.000000 815 80.366000 2838 3956 1 chr3D.!!$F2 1118
15 TraesCS5A01G277600 chr3D 309104309 309104994 685 False 368.000000 368 76.956000 2851 3534 1 chr3D.!!$F3 683
16 TraesCS5A01G277600 chr3D 537903724 537904225 501 False 296.000000 296 78.311000 1773 2269 1 chr3D.!!$F5 496
17 TraesCS5A01G277600 chr3D 551301906 551302578 672 True 226.000000 226 73.977000 1572 2211 1 chr3D.!!$R2 639
18 TraesCS5A01G277600 chr3A 683636167 683637354 1187 False 1454.000000 1454 88.935000 3956 5145 1 chr3A.!!$F1 1189
19 TraesCS5A01G277600 chr3A 478363228 478364130 902 True 1107.000000 1107 88.950000 4250 5145 1 chr3A.!!$R2 895
20 TraesCS5A01G277600 chr3A 158744865 158745393 528 True 327.000000 327 78.318000 2837 3357 1 chr3A.!!$R1 520
21 TraesCS5A01G277600 chr1B 618948708 618949816 1108 False 1332.000000 1332 88.393000 3956 5068 1 chr1B.!!$F3 1112
22 TraesCS5A01G277600 chr1B 495100485 495101236 751 False 427.000000 427 77.734000 3221 3956 1 chr1B.!!$F2 735
23 TraesCS5A01G277600 chr7B 344246668 344247859 1191 False 1323.000000 1323 86.866000 3957 5145 1 chr7B.!!$F2 1188
24 TraesCS5A01G277600 chr7B 135873452 135873957 505 False 305.000000 305 78.295000 3210 3705 1 chr7B.!!$F1 495
25 TraesCS5A01G277600 chr1A 480121119 480122320 1201 True 1306.000000 1306 86.469000 3950 5145 1 chr1A.!!$R1 1195
26 TraesCS5A01G277600 chr1A 470342568 470343314 746 False 466.000000 466 78.637000 3221 3956 1 chr1A.!!$F2 735
27 TraesCS5A01G277600 chr6B 663557838 663558923 1085 True 798.000000 798 80.340000 2858 3956 1 chr6B.!!$R2 1098
28 TraesCS5A01G277600 chr6D 166756500 166757234 734 False 545.000000 545 80.455000 3225 3956 1 chr6D.!!$F2 731
29 TraesCS5A01G277600 chr6D 309707354 309708034 680 True 322.000000 322 75.944000 2838 3537 1 chr6D.!!$R3 699
30 TraesCS5A01G277600 chr6D 127079011 127079742 731 True 265.000000 265 74.446000 3221 3950 1 chr6D.!!$R1 729
31 TraesCS5A01G277600 chr1D 31678178 31678940 762 False 507.000000 507 79.381000 3210 3954 1 chr1D.!!$F1 744
32 TraesCS5A01G277600 chr1D 371196288 371197030 742 False 484.000000 484 79.079000 3221 3956 1 chr1D.!!$F8 735
33 TraesCS5A01G277600 chr1D 111353591 111354138 547 True 231.000000 231 74.910000 2838 3379 1 chr1D.!!$R3 541
34 TraesCS5A01G277600 chr1D 111388746 111389261 515 True 219.000000 219 75.143000 2838 3337 1 chr1D.!!$R4 499
35 TraesCS5A01G277600 chr4D 394862434 394863200 766 True 472.000000 472 78.846000 1537 2269 1 chr4D.!!$R5 732
36 TraesCS5A01G277600 chr4D 85255540 85256246 706 True 451.000000 451 78.809000 2838 3537 1 chr4D.!!$R2 699
37 TraesCS5A01G277600 chr4D 40961394 40962066 672 False 350.000000 350 76.845000 2840 3505 1 chr4D.!!$F1 665
38 TraesCS5A01G277600 chr2A 622145891 622146493 602 False 446.000000 446 80.515000 3210 3815 1 chr2A.!!$F1 605
39 TraesCS5A01G277600 chr2D 399340258 399341010 752 True 420.000000 420 77.595000 2838 3601 1 chr2D.!!$R6 763
40 TraesCS5A01G277600 chr2D 367820166 367820680 514 True 296.000000 296 77.820000 2838 3338 1 chr2D.!!$R4 500
41 TraesCS5A01G277600 chr3B 708386709 708387442 733 True 416.000000 416 78.032000 1543 2237 1 chr3B.!!$R1 694
42 TraesCS5A01G277600 chr4B 415028434 415029284 850 True 412.000000 412 76.244000 2851 3705 1 chr4B.!!$R5 854
43 TraesCS5A01G277600 chr4B 169813330 169814026 696 True 364.000000 364 76.751000 2838 3530 1 chr4B.!!$R4 692
44 TraesCS5A01G277600 chr4B 127006835 127007339 504 True 292.000000 292 77.886000 2838 3327 1 chr4B.!!$R2 489
45 TraesCS5A01G277600 chr4B 67600210 67600771 561 False 235.000000 235 75.087000 2838 3387 1 chr4B.!!$F1 549
46 TraesCS5A01G277600 chr6A 446504656 446505164 508 True 272.000000 272 76.803000 3038 3537 1 chr6A.!!$R1 499

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
59 60 0.605589 GCTTGGCCCAACTCGTAAGT 60.606 55.000 0.0 0.0 37.32 2.24 F
1278 1284 1.140816 GAGTGGTGTCGTCTCTTTGC 58.859 55.000 0.0 0.0 0.00 3.68 F
1781 1821 0.399233 CCCTCCTTACCCTCCTCCTG 60.399 65.000 0.0 0.0 0.00 3.86 F
2291 2358 1.074775 TTGGGTAGCTGGCAAGTGG 59.925 57.895 0.0 0.0 0.00 4.00 F
2829 2899 0.674581 TCGCCAATGCAGACCAAGAG 60.675 55.000 0.0 0.0 37.32 2.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1714 1726 0.837272 TCCCCTTCTAATTCGGCCTG 59.163 55.000 0.00 0.0 0.00 4.85 R
2465 2532 0.040058 AGGGCAACTCCAATGCATGA 59.960 50.000 0.00 0.0 45.60 3.07 R
2714 2784 0.319986 TCGAAGTATGTGCGCAACCA 60.320 50.000 14.00 7.6 0.00 3.67 R
3103 3199 1.888436 TAGGCGCACCCTTGTCTCAG 61.888 60.000 10.83 0.0 43.06 3.35 R
4469 4723 1.513158 CCGATGAGAGGAGCGTTGT 59.487 57.895 0.00 0.0 0.00 3.32 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
30 31 3.338250 CTGGGGCAACTGGGGCTA 61.338 66.667 0.00 0.00 0.00 3.93
31 32 2.616893 TGGGGCAACTGGGGCTAT 60.617 61.111 0.00 0.00 0.00 2.97
32 33 1.308304 TGGGGCAACTGGGGCTATA 60.308 57.895 0.00 0.00 0.00 1.31
33 34 1.352622 TGGGGCAACTGGGGCTATAG 61.353 60.000 0.00 0.00 0.00 1.31
34 35 1.228276 GGGCAACTGGGGCTATAGC 60.228 63.158 16.78 16.78 41.14 2.97
56 57 2.349755 GGCTTGGCCCAACTCGTA 59.650 61.111 0.00 0.00 44.06 3.43
57 58 1.302993 GGCTTGGCCCAACTCGTAA 60.303 57.895 0.00 0.00 44.06 3.18
58 59 1.305930 GGCTTGGCCCAACTCGTAAG 61.306 60.000 0.00 0.00 44.06 2.34
59 60 0.605589 GCTTGGCCCAACTCGTAAGT 60.606 55.000 0.00 0.00 37.32 2.24
60 61 1.338389 GCTTGGCCCAACTCGTAAGTA 60.338 52.381 0.00 0.00 33.48 2.24
61 62 2.872842 GCTTGGCCCAACTCGTAAGTAA 60.873 50.000 0.00 0.00 33.48 2.24
62 63 3.404899 CTTGGCCCAACTCGTAAGTAAA 58.595 45.455 0.00 0.00 33.48 2.01
63 64 3.706600 TGGCCCAACTCGTAAGTAAAT 57.293 42.857 0.00 0.00 33.48 1.40
64 65 3.340034 TGGCCCAACTCGTAAGTAAATG 58.660 45.455 0.00 0.00 33.48 2.32
65 66 2.096980 GGCCCAACTCGTAAGTAAATGC 59.903 50.000 0.00 0.00 33.48 3.56
66 67 2.096980 GCCCAACTCGTAAGTAAATGCC 59.903 50.000 0.00 0.00 33.48 4.40
67 68 3.340034 CCCAACTCGTAAGTAAATGCCA 58.660 45.455 0.00 0.00 33.48 4.92
68 69 3.374058 CCCAACTCGTAAGTAAATGCCAG 59.626 47.826 0.00 0.00 33.48 4.85
69 70 4.000988 CCAACTCGTAAGTAAATGCCAGT 58.999 43.478 0.00 0.00 33.48 4.00
70 71 5.172934 CCAACTCGTAAGTAAATGCCAGTA 58.827 41.667 0.00 0.00 33.48 2.74
71 72 5.291128 CCAACTCGTAAGTAAATGCCAGTAG 59.709 44.000 0.00 0.00 33.48 2.57
72 73 5.909621 ACTCGTAAGTAAATGCCAGTAGA 57.090 39.130 0.00 0.00 32.59 2.59
73 74 6.276832 ACTCGTAAGTAAATGCCAGTAGAA 57.723 37.500 0.00 0.00 32.59 2.10
74 75 6.875076 ACTCGTAAGTAAATGCCAGTAGAAT 58.125 36.000 0.00 0.00 32.59 2.40
75 76 7.328737 ACTCGTAAGTAAATGCCAGTAGAATT 58.671 34.615 0.00 0.00 32.59 2.17
76 77 7.822822 ACTCGTAAGTAAATGCCAGTAGAATTT 59.177 33.333 0.00 0.00 32.59 1.82
77 78 8.556213 TCGTAAGTAAATGCCAGTAGAATTTT 57.444 30.769 0.00 0.00 39.48 1.82
78 79 9.005777 TCGTAAGTAAATGCCAGTAGAATTTTT 57.994 29.630 0.00 0.00 39.48 1.94
121 122 5.324409 TGAGTTATTTGGGTTGCATCTTCT 58.676 37.500 0.00 0.00 0.00 2.85
1121 1127 6.074648 AGGGAGTTTATGTTTTTCCATCACA 58.925 36.000 0.00 0.00 0.00 3.58
1278 1284 1.140816 GAGTGGTGTCGTCTCTTTGC 58.859 55.000 0.00 0.00 0.00 3.68
1307 1313 4.630069 CGAAAGGGTACTGTGATAAAGGTG 59.370 45.833 0.00 0.00 0.00 4.00
1386 1392 1.278985 ACCACCGAATTCTGCTCATCA 59.721 47.619 3.52 0.00 0.00 3.07
1526 1537 8.832521 TCAATGGAACGGTACAATAATATGTTC 58.167 33.333 0.00 0.00 34.75 3.18
1607 1618 3.124128 GGTTCCGGAGACATACGAAAAAC 59.876 47.826 3.34 0.00 33.12 2.43
1714 1726 3.056754 ATCGGCTTTGGTAGGCCCC 62.057 63.158 0.00 0.00 46.31 5.80
1781 1821 0.399233 CCCTCCTTACCCTCCTCCTG 60.399 65.000 0.00 0.00 0.00 3.86
1803 1843 7.132016 TCCTGCTCCTACTTATATATATGGGGA 59.868 40.741 5.44 15.28 0.00 4.81
1878 1921 2.158755 CCATGCTCTCCCGGTCTAATTT 60.159 50.000 0.00 0.00 0.00 1.82
1885 1929 3.387050 TCTCCCGGTCTAATTTCCTAAGC 59.613 47.826 0.00 0.00 0.00 3.09
1907 1951 5.304614 AGCGTTTAGGCTCCTAATTAGATGA 59.695 40.000 14.28 2.90 39.61 2.92
1994 2058 7.593644 GCAATTTTCGCTTAGTTTTCTTCCTAA 59.406 33.333 0.00 0.00 0.00 2.69
2082 2147 8.833231 TTGACTCTTATCTCGAAGAACAATTT 57.167 30.769 0.00 0.00 35.06 1.82
2117 2182 3.610911 GTGTAACCTAGCTGCAGGAATT 58.389 45.455 17.12 10.46 39.18 2.17
2204 2271 5.945144 GGTCCTTACCACCATCTTTAGTA 57.055 43.478 0.00 0.00 45.98 1.82
2220 2287 7.718334 TCTTTAGTATTCCTGAGTGTGATCA 57.282 36.000 0.00 0.00 0.00 2.92
2234 2301 5.779806 GTGTGATCACGTAGCATAGTTTT 57.220 39.130 20.54 0.00 34.79 2.43
2235 2302 6.165659 GTGTGATCACGTAGCATAGTTTTT 57.834 37.500 20.54 0.00 34.79 1.94
2269 2336 1.406341 GCATAGCACGTTCCCCTACAA 60.406 52.381 0.00 0.00 0.00 2.41
2273 2340 2.185387 AGCACGTTCCCCTACAATAGT 58.815 47.619 0.00 0.00 0.00 2.12
2291 2358 1.074775 TTGGGTAGCTGGCAAGTGG 59.925 57.895 0.00 0.00 0.00 4.00
2302 2369 4.388499 CAAGTGGGGTCGGGTCGG 62.388 72.222 0.00 0.00 0.00 4.79
2336 2403 3.004734 GCTATATGTGTGGATGCAAACCC 59.995 47.826 4.92 3.89 0.00 4.11
2348 2415 2.317040 TGCAAACCCGACCCAAATTTA 58.683 42.857 0.00 0.00 0.00 1.40
2363 2430 5.043248 CCAAATTTAGGATGGATTTGCGTC 58.957 41.667 0.00 0.00 38.69 5.19
2397 2464 7.225538 ACTTTAGACAGACACTGAATGAGTTTG 59.774 37.037 5.76 0.00 35.18 2.93
2402 2469 2.802816 GACACTGAATGAGTTTGCGTCT 59.197 45.455 0.00 0.00 29.75 4.18
2403 2470 3.987868 GACACTGAATGAGTTTGCGTCTA 59.012 43.478 0.00 0.00 29.75 2.59
2422 2489 1.315257 ATGCGTTGGGCTGTCATTCC 61.315 55.000 0.00 0.00 44.05 3.01
2465 2532 6.128580 GCGGACAAAATAAGACAAAATGCATT 60.129 34.615 5.99 5.99 0.00 3.56
2500 2567 2.090999 TGCCCTAAGGGTCTTTTGGTTT 60.091 45.455 0.00 0.00 46.51 3.27
2512 2579 2.847282 TGGTTTTCCATGGCCCGA 59.153 55.556 6.96 0.00 46.22 5.14
2514 2581 2.696759 GGTTTTCCATGGCCCGACG 61.697 63.158 6.96 0.00 40.31 5.12
2520 2587 4.386951 CATGGCCCGACGTGGTGA 62.387 66.667 0.00 0.00 35.15 4.02
2521 2588 3.399181 ATGGCCCGACGTGGTGAT 61.399 61.111 0.00 0.00 35.15 3.06
2522 2589 3.680620 ATGGCCCGACGTGGTGATG 62.681 63.158 0.00 0.00 35.15 3.07
2523 2590 4.077184 GGCCCGACGTGGTGATGA 62.077 66.667 0.00 0.00 35.15 2.92
2524 2591 2.813908 GCCCGACGTGGTGATGAC 60.814 66.667 0.00 0.00 35.15 3.06
2525 2592 2.970639 CCCGACGTGGTGATGACT 59.029 61.111 0.00 0.00 35.15 3.41
2526 2593 1.940883 GCCCGACGTGGTGATGACTA 61.941 60.000 0.00 0.00 35.15 2.59
2547 2614 6.884832 ACTACGATGAATAAGGTCCATTCAA 58.115 36.000 8.32 0.00 43.58 2.69
2555 2622 8.200024 TGAATAAGGTCCATTCAAATTTTCCA 57.800 30.769 2.80 0.00 38.98 3.53
2579 2646 7.226441 CACCAATATGGAGGATCTCATTGTTA 58.774 38.462 2.85 0.00 40.96 2.41
2581 2648 8.451245 ACCAATATGGAGGATCTCATTGTTATT 58.549 33.333 2.85 0.00 40.96 1.40
2621 2690 4.227527 CGGAAGGGCCTAAGGGAATATATT 59.772 45.833 6.41 0.00 33.58 1.28
2631 2700 7.011482 GCCTAAGGGAATATATTAAGCATCACG 59.989 40.741 0.00 0.00 33.58 4.35
2655 2724 7.033791 CGTGTCCTTATAAACACACTCATACT 58.966 38.462 16.74 0.00 44.75 2.12
2668 2737 9.520204 AACACACTCATACTGAAAGAAAAATTG 57.480 29.630 0.00 0.00 37.43 2.32
2714 2784 6.290605 CAAAGTTTTTCTTCCCACATCCATT 58.709 36.000 0.00 0.00 35.02 3.16
2774 2844 0.935898 TCGACGGCGCAAACTTTTTA 59.064 45.000 5.31 0.00 37.46 1.52
2780 2850 2.346832 CGGCGCAAACTTTTTAAAACCG 60.347 45.455 10.83 4.20 0.00 4.44
2782 2852 3.060807 GGCGCAAACTTTTTAAAACCGAG 60.061 43.478 10.83 0.00 0.00 4.63
2805 2875 2.093500 AGCATGTAGAAGCAATGGTCGA 60.093 45.455 0.00 0.00 0.00 4.20
2813 2883 0.737715 AGCAATGGTCGAGAAGTCGC 60.738 55.000 0.00 0.00 46.39 5.19
2829 2899 0.674581 TCGCCAATGCAGACCAAGAG 60.675 55.000 0.00 0.00 37.32 2.85
2916 2986 7.601130 TCAATTATATATGGCGTTGGTGTACTC 59.399 37.037 0.00 0.00 0.00 2.59
3102 3198 2.424842 AATTTGTGCTCGAGGGCCCA 62.425 55.000 27.56 1.18 0.00 5.36
3103 3199 3.842925 TTTGTGCTCGAGGGCCCAC 62.843 63.158 27.56 18.56 0.00 4.61
3243 3367 4.796038 AATTTCAGCCCAATCAGAGTTG 57.204 40.909 0.00 0.00 0.00 3.16
3371 3513 2.420827 GGGCTAAGGAAGAAGAAGGAGC 60.421 54.545 0.00 0.00 0.00 4.70
3375 3521 2.037385 AGGAAGAAGAAGGAGCAGGT 57.963 50.000 0.00 0.00 0.00 4.00
3402 3561 2.657237 CCTCTTCTCGGTGGCGTT 59.343 61.111 0.00 0.00 0.00 4.84
3469 3631 6.719301 AGTTCTTCTTCATTCTCATGGTGAT 58.281 36.000 0.00 0.00 0.00 3.06
3470 3632 6.598457 AGTTCTTCTTCATTCTCATGGTGATG 59.402 38.462 0.00 0.00 0.00 3.07
3634 3828 7.348274 TCTCCCTCTATCTATTTTTGTGGTGAT 59.652 37.037 0.00 0.00 0.00 3.06
3651 3846 5.048434 GTGGTGATTTTAGCTTGCTCTTTCT 60.048 40.000 0.00 0.00 0.00 2.52
3762 3962 5.190330 TGGGGGTACTCTAGGTGAAATAAAC 59.810 44.000 0.00 0.00 0.00 2.01
3894 4106 4.913335 TTCTACCTACGCGATTTCATCT 57.087 40.909 15.93 0.00 0.00 2.90
3906 4118 4.092968 GCGATTTCATCTTACTTTGTCCGT 59.907 41.667 0.00 0.00 0.00 4.69
3920 4132 6.679843 ACTTTGTCCGTTAGAAACAAAAACA 58.320 32.000 0.00 0.00 41.04 2.83
3924 4136 6.853720 TGTCCGTTAGAAACAAAAACATTGA 58.146 32.000 0.00 0.00 0.00 2.57
3969 4181 7.547697 TGAGGGATTATTGATACGTCCATTA 57.452 36.000 0.00 0.00 33.40 1.90
4131 4344 7.067494 GCTGGAAAAGGAGCAAATATTAGAGAA 59.933 37.037 0.00 0.00 35.15 2.87
4222 4435 0.741221 CGCAAGAAGTACCAGAGGGC 60.741 60.000 0.00 0.00 43.02 5.19
4430 4682 1.678970 GCTGTTCTGCCGGGGAAAT 60.679 57.895 2.18 0.00 0.00 2.17
4469 4723 4.576053 GGAAATCATCACCATCGTCATCAA 59.424 41.667 0.00 0.00 0.00 2.57
4495 4749 3.237741 CTCTCATCGGGAGGGGCC 61.238 72.222 0.00 0.00 44.19 5.80
4671 4928 6.100134 TGGTGGAAGATCATATGTTCAGATCA 59.900 38.462 14.67 6.01 40.39 2.92
4842 5103 4.631377 CGTCCTGCTTGATTGTTCTTGATA 59.369 41.667 0.00 0.00 0.00 2.15
4926 5196 6.426587 AGCCTATGGTATGATTGTTGTTCTT 58.573 36.000 0.00 0.00 0.00 2.52
4927 5197 6.319658 AGCCTATGGTATGATTGTTGTTCTTG 59.680 38.462 0.00 0.00 0.00 3.02
4971 5247 4.703575 CGGTTTATATAGACATCGGAGGGA 59.296 45.833 5.83 0.00 0.00 4.20
5091 5369 6.018425 CGGGATGAAGTCTTCAATCTTGTATG 60.018 42.308 18.93 0.15 43.95 2.39
5092 5370 6.238593 GGGATGAAGTCTTCAATCTTGTATGC 60.239 42.308 18.93 5.57 43.95 3.14
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
13 14 1.352622 TATAGCCCCAGTTGCCCCAG 61.353 60.000 0.00 0.00 0.00 4.45
14 15 1.308304 TATAGCCCCAGTTGCCCCA 60.308 57.895 0.00 0.00 0.00 4.96
15 16 1.456287 CTATAGCCCCAGTTGCCCC 59.544 63.158 0.00 0.00 0.00 5.80
16 17 1.228276 GCTATAGCCCCAGTTGCCC 60.228 63.158 14.13 0.00 34.31 5.36
17 18 4.483090 GCTATAGCCCCAGTTGCC 57.517 61.111 14.13 0.00 34.31 4.52
39 40 3.926657 ACTTACGAGTTGGGCCAAGCC 62.927 57.143 21.62 13.28 39.77 4.35
40 41 0.605589 ACTTACGAGTTGGGCCAAGC 60.606 55.000 21.62 13.98 29.87 4.01
41 42 2.754946 TACTTACGAGTTGGGCCAAG 57.245 50.000 21.62 11.06 37.33 3.61
42 43 3.488778 TTTACTTACGAGTTGGGCCAA 57.511 42.857 16.66 16.66 37.33 4.52
43 44 3.340034 CATTTACTTACGAGTTGGGCCA 58.660 45.455 0.00 0.00 37.33 5.36
44 45 2.096980 GCATTTACTTACGAGTTGGGCC 59.903 50.000 0.00 0.00 37.33 5.80
45 46 2.096980 GGCATTTACTTACGAGTTGGGC 59.903 50.000 0.00 0.00 37.33 5.36
46 47 3.340034 TGGCATTTACTTACGAGTTGGG 58.660 45.455 0.00 0.00 37.33 4.12
47 48 4.000988 ACTGGCATTTACTTACGAGTTGG 58.999 43.478 0.00 0.00 37.33 3.77
48 49 6.097356 TCTACTGGCATTTACTTACGAGTTG 58.903 40.000 0.00 0.00 37.33 3.16
49 50 6.276832 TCTACTGGCATTTACTTACGAGTT 57.723 37.500 0.00 0.00 37.33 3.01
50 51 5.909621 TCTACTGGCATTTACTTACGAGT 57.090 39.130 0.00 0.00 39.97 4.18
51 52 7.772332 AATTCTACTGGCATTTACTTACGAG 57.228 36.000 0.00 0.00 0.00 4.18
52 53 8.556213 AAAATTCTACTGGCATTTACTTACGA 57.444 30.769 0.00 0.00 0.00 3.43
77 78 7.054124 ACTCAAGTTACTGTGAGGATGAAAAA 58.946 34.615 20.16 0.00 44.61 1.94
78 79 6.591935 ACTCAAGTTACTGTGAGGATGAAAA 58.408 36.000 20.16 0.00 44.61 2.29
79 80 6.174720 ACTCAAGTTACTGTGAGGATGAAA 57.825 37.500 20.16 0.00 44.61 2.69
80 81 5.808366 ACTCAAGTTACTGTGAGGATGAA 57.192 39.130 20.16 0.00 44.61 2.57
81 82 5.808366 AACTCAAGTTACTGTGAGGATGA 57.192 39.130 20.16 5.41 44.61 2.92
82 83 8.446273 CAAATAACTCAAGTTACTGTGAGGATG 58.554 37.037 20.16 11.86 44.61 3.51
83 84 7.607991 CCAAATAACTCAAGTTACTGTGAGGAT 59.392 37.037 20.16 13.67 44.61 3.24
84 85 6.934645 CCAAATAACTCAAGTTACTGTGAGGA 59.065 38.462 20.16 12.57 44.61 3.71
85 86 6.149474 CCCAAATAACTCAAGTTACTGTGAGG 59.851 42.308 20.16 8.45 44.61 3.86
86 87 6.710744 ACCCAAATAACTCAAGTTACTGTGAG 59.289 38.462 16.89 16.89 45.59 3.51
87 88 6.597562 ACCCAAATAACTCAAGTTACTGTGA 58.402 36.000 4.80 0.00 42.55 3.58
88 89 6.877611 ACCCAAATAACTCAAGTTACTGTG 57.122 37.500 4.80 4.22 42.55 3.66
89 90 6.238925 GCAACCCAAATAACTCAAGTTACTGT 60.239 38.462 4.80 0.00 42.55 3.55
90 91 6.149633 GCAACCCAAATAACTCAAGTTACTG 58.850 40.000 4.80 5.98 42.55 2.74
91 92 5.830991 TGCAACCCAAATAACTCAAGTTACT 59.169 36.000 4.80 0.00 42.55 2.24
92 93 6.079424 TGCAACCCAAATAACTCAAGTTAC 57.921 37.500 4.80 0.00 42.55 2.50
93 94 6.719370 AGATGCAACCCAAATAACTCAAGTTA 59.281 34.615 5.15 5.15 43.71 2.24
94 95 5.539955 AGATGCAACCCAAATAACTCAAGTT 59.460 36.000 0.00 0.46 41.73 2.66
95 96 5.079643 AGATGCAACCCAAATAACTCAAGT 58.920 37.500 0.00 0.00 0.00 3.16
96 97 5.649782 AGATGCAACCCAAATAACTCAAG 57.350 39.130 0.00 0.00 0.00 3.02
97 98 5.774690 AGAAGATGCAACCCAAATAACTCAA 59.225 36.000 0.00 0.00 0.00 3.02
121 122 2.430332 CCAAAAGACAAGAGCCCACAAA 59.570 45.455 0.00 0.00 0.00 2.83
1227 1233 4.080413 TGACCCAATTATCACATGAGAGCA 60.080 41.667 0.00 0.00 0.00 4.26
1278 1284 4.713824 TCACAGTACCCTTTCGTATCAG 57.286 45.455 0.00 0.00 0.00 2.90
1307 1313 1.788308 GCAATTCACACACACACATGC 59.212 47.619 0.00 0.00 0.00 4.06
1343 1349 2.110967 CCTCTGCAGAATGGTGGCG 61.111 63.158 18.85 3.00 35.86 5.69
1500 1511 8.740123 AACATATTATTGTACCGTTCCATTGA 57.260 30.769 0.00 0.00 0.00 2.57
1509 1520 6.522054 ACCCTGAGAACATATTATTGTACCG 58.478 40.000 0.00 0.00 0.00 4.02
1526 1537 1.134670 GGACTTTCCGATGACCCTGAG 60.135 57.143 0.00 0.00 0.00 3.35
1622 1633 4.254492 GGTCCTTCGCACTTTTCTTCTAT 58.746 43.478 0.00 0.00 0.00 1.98
1714 1726 0.837272 TCCCCTTCTAATTCGGCCTG 59.163 55.000 0.00 0.00 0.00 4.85
1781 1821 7.672239 CCTCTCCCCATATATATAAGTAGGAGC 59.328 44.444 18.07 0.00 38.59 4.70
1885 1929 6.982852 TCTCATCTAATTAGGAGCCTAAACG 58.017 40.000 12.62 5.16 41.21 3.60
1943 1987 5.509163 GGCGCTACTCATCTAATTTGGAGTA 60.509 44.000 7.64 0.00 40.76 2.59
1949 1993 2.135933 GCGGCGCTACTCATCTAATTT 58.864 47.619 26.86 0.00 0.00 1.82
1979 2042 6.980397 AGTTCGACGTTTAGGAAGAAAACTAA 59.020 34.615 0.00 0.00 35.20 2.24
1994 2058 2.049433 CCGGCAGAGTTCGACGTT 60.049 61.111 0.00 0.00 0.00 3.99
2082 2147 1.122632 TTACACCTCCCAGCCACGAA 61.123 55.000 0.00 0.00 0.00 3.85
2200 2265 4.948004 ACGTGATCACACTCAGGAATACTA 59.052 41.667 24.93 0.00 43.99 1.82
2204 2271 3.429547 GCTACGTGATCACACTCAGGAAT 60.430 47.826 24.93 2.02 43.99 3.01
2269 2336 1.916181 ACTTGCCAGCTACCCAACTAT 59.084 47.619 0.00 0.00 0.00 2.12
2273 2340 1.074775 CCACTTGCCAGCTACCCAA 59.925 57.895 0.00 0.00 0.00 4.12
2281 2348 4.722700 CCCGACCCCACTTGCCAG 62.723 72.222 0.00 0.00 0.00 4.85
2308 2375 3.552890 GCATCCACACATATAGCAGACGA 60.553 47.826 0.00 0.00 0.00 4.20
2319 2386 0.251121 TCGGGTTTGCATCCACACAT 60.251 50.000 10.02 0.00 0.00 3.21
2320 2387 1.149401 TCGGGTTTGCATCCACACA 59.851 52.632 10.02 0.00 0.00 3.72
2336 2403 5.591099 CAAATCCATCCTAAATTTGGGTCG 58.409 41.667 18.99 11.57 36.95 4.79
2363 2430 3.489785 GTGTCTGTCTAAAGTTCGTGTGG 59.510 47.826 0.00 0.00 0.00 4.17
2397 2464 2.511600 AGCCCAACGCATAGACGC 60.512 61.111 0.00 0.00 41.38 5.19
2402 2469 1.378531 GAATGACAGCCCAACGCATA 58.621 50.000 0.00 0.00 41.38 3.14
2403 2470 1.315257 GGAATGACAGCCCAACGCAT 61.315 55.000 0.00 0.00 41.38 4.73
2465 2532 0.040058 AGGGCAACTCCAATGCATGA 59.960 50.000 0.00 0.00 45.60 3.07
2500 2567 4.402528 CCACGTCGGGCCATGGAA 62.403 66.667 18.40 0.00 33.80 3.53
2510 2577 0.445043 TCGTAGTCATCACCACGTCG 59.555 55.000 0.00 0.00 35.91 5.12
2512 2579 2.089201 TCATCGTAGTCATCACCACGT 58.911 47.619 0.00 0.00 35.91 4.49
2514 2581 5.692204 CCTTATTCATCGTAGTCATCACCAC 59.308 44.000 0.00 0.00 0.00 4.16
2518 2585 5.596772 TGGACCTTATTCATCGTAGTCATCA 59.403 40.000 0.00 0.00 0.00 3.07
2519 2586 6.085555 TGGACCTTATTCATCGTAGTCATC 57.914 41.667 0.00 0.00 0.00 2.92
2520 2587 6.672266 ATGGACCTTATTCATCGTAGTCAT 57.328 37.500 0.00 0.00 0.00 3.06
2521 2588 6.097696 TGAATGGACCTTATTCATCGTAGTCA 59.902 38.462 3.65 0.00 39.05 3.41
2522 2589 6.513180 TGAATGGACCTTATTCATCGTAGTC 58.487 40.000 3.65 0.00 39.05 2.59
2523 2590 6.479972 TGAATGGACCTTATTCATCGTAGT 57.520 37.500 3.65 0.00 39.05 2.73
2524 2591 7.786178 TTTGAATGGACCTTATTCATCGTAG 57.214 36.000 7.80 0.00 42.31 3.51
2525 2592 8.746052 AATTTGAATGGACCTTATTCATCGTA 57.254 30.769 7.80 0.00 42.31 3.43
2526 2593 7.645058 AATTTGAATGGACCTTATTCATCGT 57.355 32.000 7.80 0.00 42.31 3.73
2555 2622 5.919348 ACAATGAGATCCTCCATATTGGT 57.081 39.130 0.00 0.00 39.03 3.67
2600 2669 6.829298 GCTTAATATATTCCCTTAGGCCCTTC 59.171 42.308 0.00 0.00 0.00 3.46
2621 2690 6.311935 GTGTTTATAAGGACACGTGATGCTTA 59.688 38.462 25.01 23.90 37.08 3.09
2631 2700 8.033038 TCAGTATGAGTGTGTTTATAAGGACAC 58.967 37.037 16.05 16.05 42.56 3.67
2662 2731 7.391275 CACCTCCAAGGATTTAAATGCAATTTT 59.609 33.333 20.17 4.57 40.02 1.82
2668 2737 3.430790 GGCACCTCCAAGGATTTAAATGC 60.431 47.826 11.44 11.44 37.67 3.56
2714 2784 0.319986 TCGAAGTATGTGCGCAACCA 60.320 50.000 14.00 7.60 0.00 3.67
2758 2828 2.604011 GGTTTTAAAAAGTTTGCGCCGT 59.396 40.909 4.18 0.00 0.00 5.68
2774 2844 3.600388 CTTCTACATGCTCCTCGGTTTT 58.400 45.455 0.00 0.00 0.00 2.43
2780 2850 2.877168 CCATTGCTTCTACATGCTCCTC 59.123 50.000 0.00 0.00 0.00 3.71
2782 2852 2.615912 GACCATTGCTTCTACATGCTCC 59.384 50.000 0.00 0.00 0.00 4.70
2805 2875 0.674895 GGTCTGCATTGGCGACTTCT 60.675 55.000 3.40 0.00 45.35 2.85
2813 2883 2.354259 GAGTCTCTTGGTCTGCATTGG 58.646 52.381 0.00 0.00 0.00 3.16
2829 2899 2.612672 TCACAGACGTATCATCGGAGTC 59.387 50.000 0.00 0.00 34.94 3.36
2947 3022 0.597637 ACTGAAACTGTCACTCGGCG 60.598 55.000 0.00 0.00 31.13 6.46
3102 3198 2.031163 GCGCACCCTTGTCTCAGT 59.969 61.111 0.30 0.00 0.00 3.41
3103 3199 1.888436 TAGGCGCACCCTTGTCTCAG 61.888 60.000 10.83 0.00 43.06 3.35
3138 3258 2.907179 GCTACCCACAAGCCACCCT 61.907 63.158 0.00 0.00 33.73 4.34
3243 3367 6.315393 TGTTTCTTTTATAGTTGGAGATCCGC 59.685 38.462 0.00 0.00 39.43 5.54
3383 3540 3.068691 CGCCACCGAGAAGAGGGA 61.069 66.667 0.00 0.00 36.29 4.20
3402 3561 4.329545 GTTCCCGGCAGTGCTCCA 62.330 66.667 16.11 0.00 0.00 3.86
3603 3796 9.790344 CACAAAAATAGATAGAGGGAGATGAAT 57.210 33.333 0.00 0.00 0.00 2.57
3634 3828 8.451908 AAGAAACTAGAAAGAGCAAGCTAAAA 57.548 30.769 0.00 0.00 0.00 1.52
3894 4106 8.295288 TGTTTTTGTTTCTAACGGACAAAGTAA 58.705 29.630 0.00 0.00 42.25 2.24
3920 4132 6.152932 AGTGCAACAAAGAATCACTTCAAT 57.847 33.333 0.00 0.00 41.43 2.57
3924 4136 5.964758 TCAAAGTGCAACAAAGAATCACTT 58.035 33.333 0.00 0.00 46.27 3.16
4131 4344 5.749462 ACTTTTGGAGCTATGCAGAATAGT 58.251 37.500 0.00 0.00 40.52 2.12
4345 4596 1.584380 CGGAGTCTCGTCCCGAAAGT 61.584 60.000 0.00 0.00 45.58 2.66
4469 4723 1.513158 CCGATGAGAGGAGCGTTGT 59.487 57.895 0.00 0.00 0.00 3.32
4494 4748 4.337555 GTGAAGATGTTGATGGAGATTGGG 59.662 45.833 0.00 0.00 0.00 4.12
4495 4749 4.337555 GGTGAAGATGTTGATGGAGATTGG 59.662 45.833 0.00 0.00 0.00 3.16
4603 4860 8.812972 TCAACTACAAGGAGTAATCAACACTAT 58.187 33.333 0.00 0.00 30.92 2.12
4971 5247 2.093106 CGACTCTGTGTAACCCTAGCT 58.907 52.381 0.00 0.00 34.36 3.32
5091 5369 1.471676 CCGGACTGTTGGACTATGAGC 60.472 57.143 0.00 0.00 0.00 4.26
5092 5370 1.471676 GCCGGACTGTTGGACTATGAG 60.472 57.143 5.05 0.00 0.00 2.90


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

AutoCloner maintained by Alex Coulton.