Multiple sequence alignment - TraesCS1D01G310800

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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 TraesCS1D01G310800 chr1D 100.000 4945 0 0 1 4945 406818252 406823196 0.000000e+00 9132.0
1 TraesCS1D01G310800 chr1D 98.240 682 9 3 1 680 256265304 256265984 0.000000e+00 1190.0
2 TraesCS1D01G310800 chr1D 97.131 697 17 3 2120 2814 54563746 54563051 0.000000e+00 1173.0
3 TraesCS1D01G310800 chr1D 91.107 596 49 2 4338 4932 304101059 304100467 0.000000e+00 804.0
4 TraesCS1D01G310800 chr1D 81.279 657 52 32 3285 3923 406664173 406664776 2.700000e-127 466.0
5 TraesCS1D01G310800 chr1D 94.942 257 10 3 3007 3263 158306379 158306632 2.770000e-107 399.0
6 TraesCS1D01G310800 chr1D 91.003 289 15 6 2980 3263 435378451 435378733 3.610000e-101 379.0
7 TraesCS1D01G310800 chr1D 90.074 272 6 6 689 954 256266088 256266344 2.850000e-87 333.0
8 TraesCS1D01G310800 chr1D 96.491 114 4 0 1990 2103 412883160 412883047 6.530000e-44 189.0
9 TraesCS1D01G310800 chr1D 94.872 117 4 1 1987 2103 9148457 9148571 1.090000e-41 182.0
10 TraesCS1D01G310800 chr1D 95.455 66 1 2 889 953 360381640 360381576 2.430000e-18 104.0
11 TraesCS1D01G310800 chr1B 93.107 1088 62 7 3264 4339 547166958 547168044 0.000000e+00 1581.0
12 TraesCS1D01G310800 chr1B 91.449 690 53 6 1307 1994 547166276 547166961 0.000000e+00 942.0
13 TraesCS1D01G310800 chr1B 81.126 657 60 28 3285 3921 546953147 546953759 7.500000e-128 468.0
14 TraesCS1D01G310800 chr1B 80.273 659 66 28 3285 3923 546831498 546832112 5.880000e-119 438.0
15 TraesCS1D01G310800 chr1B 86.364 396 43 6 3537 3923 547028907 547029300 5.920000e-114 422.0
16 TraesCS1D01G310800 chr1B 87.784 352 25 10 961 1310 547165858 547166193 3.590000e-106 396.0
17 TraesCS1D01G310800 chr1B 96.522 115 4 0 1994 2108 122262160 122262046 1.820000e-44 191.0
18 TraesCS1D01G310800 chr1B 95.283 106 3 1 133 238 366491148 366491045 3.060000e-37 167.0
19 TraesCS1D01G310800 chr6D 93.986 981 46 10 2136 3109 132936929 132935955 0.000000e+00 1472.0
20 TraesCS1D01G310800 chr6D 92.316 976 46 18 2136 3109 430202867 430203815 0.000000e+00 1360.0
21 TraesCS1D01G310800 chr6D 91.037 926 58 19 2136 3050 430653301 430654212 0.000000e+00 1227.0
22 TraesCS1D01G310800 chr6D 94.784 671 10 4 34 680 59096323 59095654 0.000000e+00 1022.0
23 TraesCS1D01G310800 chr6D 92.657 463 11 10 241 680 258341362 258341824 0.000000e+00 645.0
24 TraesCS1D01G310800 chr6D 92.657 463 11 10 241 680 258346820 258347282 0.000000e+00 645.0
25 TraesCS1D01G310800 chr6D 92.009 463 14 10 241 680 258359225 258359687 3.250000e-176 628.0
26 TraesCS1D01G310800 chr6D 95.618 251 8 2 3013 3263 19031216 19030969 2.770000e-107 399.0
27 TraesCS1D01G310800 chr6D 96.653 239 3 4 34 270 258358527 258358762 4.640000e-105 392.0
28 TraesCS1D01G310800 chr6D 95.436 241 3 5 34 270 258340662 258340898 1.300000e-100 377.0
29 TraesCS1D01G310800 chr6D 95.436 241 3 5 34 270 258346120 258346356 1.300000e-100 377.0
30 TraesCS1D01G310800 chr6D 91.870 246 7 3 721 954 258360389 258360633 1.030000e-86 331.0
31 TraesCS1D01G310800 chr6D 90.650 246 9 4 721 954 258347826 258348069 1.030000e-81 315.0
32 TraesCS1D01G310800 chr6D 90.650 246 9 4 721 954 258361143 258361386 1.030000e-81 315.0
33 TraesCS1D01G310800 chr6D 89.617 183 4 4 782 953 59095575 59095397 8.330000e-53 219.0
34 TraesCS1D01G310800 chr6D 96.899 129 3 1 553 680 258347604 258347732 1.080000e-51 215.0
35 TraesCS1D01G310800 chr6D 96.899 129 3 1 553 680 258360167 258360295 1.080000e-51 215.0
36 TraesCS1D01G310800 chr6D 95.935 123 5 0 1994 2116 65384868 65384746 3.020000e-47 200.0
37 TraesCS1D01G310800 chr6D 97.297 111 3 0 1993 2103 266018798 266018908 6.530000e-44 189.0
38 TraesCS1D01G310800 chr6D 97.297 111 3 0 1993 2103 313406620 313406730 6.530000e-44 189.0
39 TraesCS1D01G310800 chr6D 97.273 110 3 0 1994 2103 250204658 250204767 2.350000e-43 187.0
40 TraesCS1D01G310800 chr6D 97.273 110 3 0 1994 2103 443163433 443163542 2.350000e-43 187.0
41 TraesCS1D01G310800 chr6D 96.396 111 4 0 1993 2103 25068457 25068567 3.040000e-42 183.0
42 TraesCS1D01G310800 chr6D 97.222 108 3 0 1992 2099 38196698 38196591 3.040000e-42 183.0
43 TraesCS1D01G310800 chr6D 95.614 114 5 0 1990 2103 40660302 40660415 3.040000e-42 183.0
44 TraesCS1D01G310800 chr6D 96.396 111 4 0 1993 2103 45832920 45833030 3.040000e-42 183.0
45 TraesCS1D01G310800 chr6D 96.396 111 4 0 1993 2103 170683534 170683424 3.040000e-42 183.0
46 TraesCS1D01G310800 chr6D 96.429 112 3 1 553 663 258359784 258359895 3.040000e-42 183.0
47 TraesCS1D01G310800 chr6D 95.614 114 4 1 1990 2103 329481821 329481709 1.090000e-41 182.0
48 TraesCS1D01G310800 chr6D 96.364 110 4 0 1994 2103 351864501 351864392 1.090000e-41 182.0
49 TraesCS1D01G310800 chr6D 96.364 110 4 0 1994 2103 438569542 438569433 1.090000e-41 182.0
50 TraesCS1D01G310800 chr6D 89.362 141 13 2 1977 2116 387614521 387614382 5.090000e-40 176.0
51 TraesCS1D01G310800 chr6D 85.000 180 6 3 34 212 258359066 258359225 3.960000e-36 163.0
52 TraesCS1D01G310800 chr6D 83.978 181 7 3 34 212 258341202 258341362 2.380000e-33 154.0
53 TraesCS1D01G310800 chr6D 83.978 181 7 3 34 212 258346660 258346820 2.380000e-33 154.0
54 TraesCS1D01G310800 chr6D 98.276 58 1 0 896 953 382616623 382616680 8.760000e-18 102.0
55 TraesCS1D01G310800 chr6D 94.030 67 3 1 888 953 313020204 313020270 3.150000e-17 100.0
56 TraesCS1D01G310800 chr6D 92.754 69 3 2 887 953 392406839 392406771 1.130000e-16 99.0
57 TraesCS1D01G310800 chr6D 98.182 55 1 0 626 680 258360995 258361049 4.070000e-16 97.1
58 TraesCS1D01G310800 chr6D 93.651 63 2 2 887 947 392414800 392414738 5.270000e-15 93.5
59 TraesCS1D01G310800 chr6D 92.063 63 3 2 887 947 392409093 392409031 2.450000e-13 87.9
60 TraesCS1D01G310800 chr1A 95.161 930 37 7 1071 1994 502498928 502499855 0.000000e+00 1461.0
61 TraesCS1D01G310800 chr1A 94.110 798 43 3 3264 4057 502499852 502500649 0.000000e+00 1210.0
62 TraesCS1D01G310800 chr1A 92.905 592 37 4 4343 4932 454967826 454967238 0.000000e+00 856.0
63 TraesCS1D01G310800 chr1A 84.848 594 47 21 1991 2565 510383010 510382441 4.320000e-155 558.0
64 TraesCS1D01G310800 chr1A 96.610 118 2 2 1994 2110 219306994 219307110 1.400000e-45 195.0
65 TraesCS1D01G310800 chr7D 89.465 1158 73 22 2120 3263 512189842 512188720 0.000000e+00 1417.0
66 TraesCS1D01G310800 chr7D 89.262 922 63 20 2136 3050 111009787 111010679 0.000000e+00 1122.0
67 TraesCS1D01G310800 chr7D 91.283 608 50 3 4340 4944 425516489 425517096 0.000000e+00 826.0
68 TraesCS1D01G310800 chr7D 90.600 617 44 7 4341 4944 239532534 239533149 0.000000e+00 806.0
69 TraesCS1D01G310800 chr7D 90.828 447 17 9 2668 3109 196550411 196550838 1.190000e-160 577.0
70 TraesCS1D01G310800 chr7D 93.919 296 16 2 2968 3263 633328846 633328553 3.510000e-121 446.0
71 TraesCS1D01G310800 chr7D 95.257 253 10 2 3013 3264 38533916 38533665 2.770000e-107 399.0
72 TraesCS1D01G310800 chr7D 94.942 257 6 3 3013 3264 79707181 79706927 3.590000e-106 396.0
73 TraesCS1D01G310800 chr7D 96.694 121 2 1 1992 2110 25145712 25145832 3.020000e-47 200.0
74 TraesCS1D01G310800 chr4B 88.316 1164 83 27 2136 3263 539375269 539376415 0.000000e+00 1347.0
75 TraesCS1D01G310800 chr4B 80.417 623 97 14 1369 1979 613908821 613908212 7.550000e-123 451.0
76 TraesCS1D01G310800 chr4B 86.908 359 44 3 953 1310 613909326 613908970 2.770000e-107 399.0
77 TraesCS1D01G310800 chr4B 93.496 123 8 0 1994 2116 75838741 75838619 3.040000e-42 183.0
78 TraesCS1D01G310800 chr7B 87.591 959 75 23 2115 3047 716332941 716333881 0.000000e+00 1072.0
79 TraesCS1D01G310800 chr7B 93.496 123 7 1 1994 2116 561755901 561756022 1.090000e-41 182.0
80 TraesCS1D01G310800 chr7B 95.455 66 3 0 888 953 220139286 220139351 6.770000e-19 106.0
81 TraesCS1D01G310800 chr7A 87.757 923 82 20 2136 3044 111253178 111254083 0.000000e+00 1050.0
82 TraesCS1D01G310800 chr4D 91.776 608 47 2 4340 4944 470476311 470475704 0.000000e+00 843.0
83 TraesCS1D01G310800 chr4D 91.625 597 47 3 4339 4932 357838596 357838000 0.000000e+00 822.0
84 TraesCS1D01G310800 chr4D 93.521 463 7 2 241 680 490962201 490961739 0.000000e+00 667.0
85 TraesCS1D01G310800 chr4D 79.968 624 99 16 1369 1979 483176996 483177606 2.110000e-118 436.0
86 TraesCS1D01G310800 chr4D 95.455 264 10 2 3007 3270 169555061 169555322 2.130000e-113 420.0
87 TraesCS1D01G310800 chr4D 96.639 238 5 3 34 270 490962898 490962663 4.640000e-105 392.0
88 TraesCS1D01G310800 chr4D 84.078 358 40 9 953 1295 483176477 483176832 3.690000e-86 329.0
89 TraesCS1D01G310800 chr4D 91.532 248 5 5 721 955 490961614 490961370 1.330000e-85 327.0
90 TraesCS1D01G310800 chr4D 87.151 179 3 2 34 212 490962359 490962201 8.450000e-43 185.0
91 TraesCS1D01G310800 chr4D 91.473 129 10 1 1976 2103 501579164 501579292 5.090000e-40 176.0
92 TraesCS1D01G310800 chr4D 95.082 61 3 0 893 953 170626070 170626130 4.070000e-16 97.1
93 TraesCS1D01G310800 chr4D 92.424 66 1 2 896 958 455586146 455586082 1.900000e-14 91.6
94 TraesCS1D01G310800 chr3A 92.282 596 42 4 4340 4932 620667034 620667628 0.000000e+00 843.0
95 TraesCS1D01G310800 chr3A 89.088 614 20 12 1 590 142969211 142969801 0.000000e+00 719.0
96 TraesCS1D01G310800 chr3A 94.309 123 7 0 1994 2116 208920624 208920746 6.530000e-44 189.0
97 TraesCS1D01G310800 chr3A 97.087 103 2 1 34 136 17711989 17711888 6.580000e-39 172.0
98 TraesCS1D01G310800 chr2A 88.434 709 64 13 2562 3264 242989853 242989157 0.000000e+00 839.0
99 TraesCS1D01G310800 chr2A 82.993 147 15 9 2907 3050 767617739 767617600 1.870000e-24 124.0
100 TraesCS1D01G310800 chr2B 91.104 607 44 8 4339 4944 454001671 454002268 0.000000e+00 813.0
101 TraesCS1D01G310800 chr2B 95.618 251 10 1 3013 3263 167566544 167566295 7.710000e-108 401.0
102 TraesCS1D01G310800 chr2B 93.651 126 6 1 1993 2116 205495328 205495203 2.350000e-43 187.0
103 TraesCS1D01G310800 chr2B 93.636 110 5 2 27 136 520196114 520196221 3.960000e-36 163.0
104 TraesCS1D01G310800 chr2B 91.453 117 8 1 255 371 785202356 785202242 5.120000e-35 159.0
105 TraesCS1D01G310800 chr2B 76.271 295 39 26 675 953 136764210 136764489 1.440000e-25 128.0
106 TraesCS1D01G310800 chr2B 77.959 245 14 17 384 590 136763746 136763988 3.130000e-22 117.0
107 TraesCS1D01G310800 chr2B 97.500 40 1 0 1 40 520194872 520194911 8.880000e-08 69.4
108 TraesCS1D01G310800 chr5D 90.759 606 53 2 4340 4944 352665833 352666436 0.000000e+00 806.0
109 TraesCS1D01G310800 chr5D 94.030 67 4 0 887 953 175944333 175944267 8.760000e-18 102.0
110 TraesCS1D01G310800 chr5D 94.030 67 2 2 888 953 43199912 43199977 3.150000e-17 100.0
111 TraesCS1D01G310800 chr6B 86.242 596 49 17 1994 2565 263410565 263409979 2.530000e-172 616.0
112 TraesCS1D01G310800 chr6B 90.598 234 10 3 721 953 504300341 504300563 2.890000e-77 300.0
113 TraesCS1D01G310800 chr6B 89.744 234 12 5 721 953 504301322 504301544 6.260000e-74 289.0
114 TraesCS1D01G310800 chr6B 95.541 157 7 0 133 289 482068782 482068626 8.220000e-63 252.0
115 TraesCS1D01G310800 chr6B 95.455 154 6 1 133 285 504298557 504298710 1.380000e-60 244.0
116 TraesCS1D01G310800 chr6B 85.652 230 21 4 725 954 482067956 482067739 1.070000e-56 231.0
117 TraesCS1D01G310800 chr6B 94.815 135 4 1 140 274 131673827 131673958 1.800000e-49 207.0
118 TraesCS1D01G310800 chr6B 88.158 152 12 6 804 953 131674582 131674729 5.090000e-40 176.0
119 TraesCS1D01G310800 chr6B 96.117 103 3 1 34 136 131667740 131667841 3.060000e-37 167.0
120 TraesCS1D01G310800 chr6B 95.146 103 4 1 34 136 546989131 546989030 1.420000e-35 161.0
121 TraesCS1D01G310800 chr6B 93.204 103 6 1 34 136 482068919 482068818 3.080000e-32 150.0
122 TraesCS1D01G310800 chr6B 93.902 82 3 2 511 590 131674158 131674239 6.720000e-24 122.0
123 TraesCS1D01G310800 chr6B 98.551 69 1 0 416 484 504298827 504298895 6.720000e-24 122.0
124 TraesCS1D01G310800 chr6B 93.590 78 4 1 511 587 482068339 482068262 1.120000e-21 115.0
125 TraesCS1D01G310800 chr6B 94.595 74 4 0 414 487 482068488 482068415 1.120000e-21 115.0
126 TraesCS1D01G310800 chr6B 100.000 54 0 0 414 467 131668145 131668198 3.150000e-17 100.0
127 TraesCS1D01G310800 chr6B 88.506 87 4 1 675 761 546988291 546988211 3.150000e-17 100.0
128 TraesCS1D01G310800 chr6B 97.872 47 1 0 675 721 504300271 504300317 1.140000e-11 82.4
129 TraesCS1D01G310800 chr6B 97.872 47 1 0 675 721 504301252 504301298 1.140000e-11 82.4
130 TraesCS1D01G310800 chr6B 86.792 53 1 1 750 796 546988208 546988156 2.000000e-03 54.7
131 TraesCS1D01G310800 chr3B 83.527 601 51 28 1994 2565 799539589 799540170 7.340000e-143 518.0
132 TraesCS1D01G310800 chr3B 90.717 237 10 3 721 956 144799767 144799992 6.220000e-79 305.0
133 TraesCS1D01G310800 chr3B 90.598 234 10 3 721 953 677293612 677293390 2.890000e-77 300.0
134 TraesCS1D01G310800 chr3B 87.029 239 16 10 725 953 677295241 677295008 6.350000e-64 255.0
135 TraesCS1D01G310800 chr3B 98.592 71 1 0 414 484 144798242 144798312 5.200000e-25 126.0
136 TraesCS1D01G310800 chr3B 97.872 47 1 0 675 721 144799697 144799743 1.140000e-11 82.4
137 TraesCS1D01G310800 chr3B 97.872 47 1 0 675 721 677293682 677293636 1.140000e-11 82.4
138 TraesCS1D01G310800 chr4A 94.817 328 9 1 1 328 593467780 593468099 5.710000e-139 505.0
139 TraesCS1D01G310800 chr4A 90.805 348 9 2 356 680 593468450 593468797 1.260000e-120 444.0
140 TraesCS1D01G310800 chr4A 90.043 231 5 3 739 952 593468942 593469171 2.910000e-72 283.0
141 TraesCS1D01G310800 chr4A 93.846 130 7 1 1987 2116 200388140 200388012 1.400000e-45 195.0
142 TraesCS1D01G310800 chr4A 93.798 129 3 1 1993 2116 638754696 638754824 6.530000e-44 189.0
143 TraesCS1D01G310800 chr5A 80.578 623 94 16 1369 1979 663372936 663373543 5.840000e-124 455.0
144 TraesCS1D01G310800 chr5A 86.667 360 43 5 953 1310 663372431 663372787 1.290000e-105 394.0
145 TraesCS1D01G310800 chr5A 94.318 88 5 0 249 336 169190901 169190814 8.630000e-28 135.0
146 TraesCS1D01G310800 chr5B 90.598 234 10 5 721 953 597243221 597243443 2.890000e-77 300.0
147 TraesCS1D01G310800 chr5B 95.455 154 6 1 133 285 597241437 597241590 1.380000e-60 244.0
148 TraesCS1D01G310800 chr5B 96.117 103 3 1 34 136 273693314 273693213 3.060000e-37 167.0
149 TraesCS1D01G310800 chr5B 98.592 71 1 0 414 484 597241705 597241775 5.200000e-25 126.0
150 TraesCS1D01G310800 chr5B 97.872 47 1 0 675 721 597243151 597243197 1.140000e-11 82.4
151 TraesCS1D01G310800 chrUn 86.885 244 16 11 721 953 435292433 435292671 4.910000e-65 259.0
152 TraesCS1D01G310800 chrUn 96.364 110 4 0 1994 2103 69033190 69033299 1.090000e-41 182.0
153 TraesCS1D01G310800 chrUn 96.364 110 4 0 1994 2103 70486073 70486182 1.090000e-41 182.0
154 TraesCS1D01G310800 chrUn 96.364 110 4 0 1994 2103 102177977 102178086 1.090000e-41 182.0
155 TraesCS1D01G310800 chrUn 96.364 110 4 0 1994 2103 309242297 309242406 1.090000e-41 182.0
156 TraesCS1D01G310800 chrUn 98.058 103 2 0 1994 2096 98971543 98971645 3.930000e-41 180.0
157 TraesCS1D01G310800 chrUn 98.058 103 2 0 1994 2096 110950261 110950363 3.930000e-41 180.0
158 TraesCS1D01G310800 chrUn 96.296 108 4 0 1989 2096 59151847 59151954 1.410000e-40 178.0
159 TraesCS1D01G310800 chrUn 95.495 111 5 0 1993 2103 114642375 114642265 1.410000e-40 178.0
160 TraesCS1D01G310800 chrUn 95.495 111 5 0 1993 2103 132204125 132204235 1.410000e-40 178.0
161 TraesCS1D01G310800 chrUn 95.455 110 5 0 1994 2103 69182979 69183088 5.090000e-40 176.0
162 TraesCS1D01G310800 chrUn 93.277 119 7 1 1990 2108 322026084 322026201 1.830000e-39 174.0
163 TraesCS1D01G310800 chrUn 97.647 85 2 0 52 136 354393224 354393308 3.990000e-31 147.0
164 TraesCS1D01G310800 chrUn 80.383 209 16 8 439 625 435292011 435292216 8.630000e-28 135.0
165 TraesCS1D01G310800 chrUn 100.000 61 0 0 133 193 354393344 354393404 4.050000e-21 113.0
166 TraesCS1D01G310800 chrUn 98.305 59 1 0 622 680 435292249 435292307 2.430000e-18 104.0
167 TraesCS1D01G310800 chrUn 94.915 59 2 1 901 959 331436969 331436912 1.900000e-14 91.6
168 TraesCS1D01G310800 chrUn 100.000 46 0 0 908 953 91458225 91458180 8.820000e-13 86.1
169 TraesCS1D01G310800 chrUn 97.872 47 1 0 675 721 435292363 435292409 1.140000e-11 82.4
170 TraesCS1D01G310800 chrUn 97.872 47 1 0 908 954 458972827 458972873 1.140000e-11 82.4
171 TraesCS1D01G310800 chrUn 97.826 46 1 0 908 953 29537103 29537148 4.100000e-11 80.5
172 TraesCS1D01G310800 chrUn 94.231 52 2 1 910 960 48816919 48816868 1.480000e-10 78.7
173 TraesCS1D01G310800 chrUn 88.235 68 5 3 887 953 96447686 96447751 1.480000e-10 78.7
174 TraesCS1D01G310800 chr2D 94.400 125 5 2 1993 2116 357442190 357442067 1.820000e-44 191.0
175 TraesCS1D01G310800 chr3D 94.355 124 6 1 1994 2116 607371554 607371431 6.530000e-44 189.0
176 TraesCS1D01G310800 chr3D 92.857 126 8 1 1991 2116 230664135 230664259 1.090000e-41 182.0
177 TraesCS1D01G310800 chr6A 95.690 116 5 0 1994 2109 354692081 354691966 2.350000e-43 187.0
178 TraesCS1D01G310800 chr6A 94.215 121 6 1 1990 2110 477731895 477732014 3.040000e-42 183.0
179 TraesCS1D01G310800 chr6A 93.056 72 3 2 887 956 38946847 38946776 2.430000e-18 104.0


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 TraesCS1D01G310800 chr1D 406818252 406823196 4944 False 9132.000000 9132 100.000000 1 4945 1 chr1D.!!$F4 4944
1 TraesCS1D01G310800 chr1D 54563051 54563746 695 True 1173.000000 1173 97.131000 2120 2814 1 chr1D.!!$R1 694
2 TraesCS1D01G310800 chr1D 304100467 304101059 592 True 804.000000 804 91.107000 4338 4932 1 chr1D.!!$R2 594
3 TraesCS1D01G310800 chr1D 256265304 256266344 1040 False 761.500000 1190 94.157000 1 954 2 chr1D.!!$F6 953
4 TraesCS1D01G310800 chr1D 406664173 406664776 603 False 466.000000 466 81.279000 3285 3923 1 chr1D.!!$F3 638
5 TraesCS1D01G310800 chr1B 547165858 547168044 2186 False 973.000000 1581 90.780000 961 4339 3 chr1B.!!$F4 3378
6 TraesCS1D01G310800 chr1B 546953147 546953759 612 False 468.000000 468 81.126000 3285 3921 1 chr1B.!!$F2 636
7 TraesCS1D01G310800 chr1B 546831498 546832112 614 False 438.000000 438 80.273000 3285 3923 1 chr1B.!!$F1 638
8 TraesCS1D01G310800 chr6D 132935955 132936929 974 True 1472.000000 1472 93.986000 2136 3109 1 chr6D.!!$R4 973
9 TraesCS1D01G310800 chr6D 430202867 430203815 948 False 1360.000000 1360 92.316000 2136 3109 1 chr6D.!!$F9 973
10 TraesCS1D01G310800 chr6D 430653301 430654212 911 False 1227.000000 1227 91.037000 2136 3050 1 chr6D.!!$F10 914
11 TraesCS1D01G310800 chr6D 59095397 59096323 926 True 620.500000 1022 92.200500 34 953 2 chr6D.!!$R11 919
12 TraesCS1D01G310800 chr6D 258340662 258341824 1162 False 392.000000 645 90.690333 34 680 3 chr6D.!!$F12 646
13 TraesCS1D01G310800 chr6D 258346120 258348069 1949 False 341.200000 645 91.924000 34 954 5 chr6D.!!$F13 920
14 TraesCS1D01G310800 chr6D 258358527 258361386 2859 False 290.512500 628 93.461500 34 954 8 chr6D.!!$F14 920
15 TraesCS1D01G310800 chr1A 502498928 502500649 1721 False 1335.500000 1461 94.635500 1071 4057 2 chr1A.!!$F2 2986
16 TraesCS1D01G310800 chr1A 454967238 454967826 588 True 856.000000 856 92.905000 4343 4932 1 chr1A.!!$R1 589
17 TraesCS1D01G310800 chr1A 510382441 510383010 569 True 558.000000 558 84.848000 1991 2565 1 chr1A.!!$R2 574
18 TraesCS1D01G310800 chr7D 512188720 512189842 1122 True 1417.000000 1417 89.465000 2120 3263 1 chr7D.!!$R3 1143
19 TraesCS1D01G310800 chr7D 111009787 111010679 892 False 1122.000000 1122 89.262000 2136 3050 1 chr7D.!!$F2 914
20 TraesCS1D01G310800 chr7D 425516489 425517096 607 False 826.000000 826 91.283000 4340 4944 1 chr7D.!!$F5 604
21 TraesCS1D01G310800 chr7D 239532534 239533149 615 False 806.000000 806 90.600000 4341 4944 1 chr7D.!!$F4 603
22 TraesCS1D01G310800 chr4B 539375269 539376415 1146 False 1347.000000 1347 88.316000 2136 3263 1 chr4B.!!$F1 1127
23 TraesCS1D01G310800 chr4B 613908212 613909326 1114 True 425.000000 451 83.662500 953 1979 2 chr4B.!!$R2 1026
24 TraesCS1D01G310800 chr7B 716332941 716333881 940 False 1072.000000 1072 87.591000 2115 3047 1 chr7B.!!$F3 932
25 TraesCS1D01G310800 chr7A 111253178 111254083 905 False 1050.000000 1050 87.757000 2136 3044 1 chr7A.!!$F1 908
26 TraesCS1D01G310800 chr4D 470475704 470476311 607 True 843.000000 843 91.776000 4340 4944 1 chr4D.!!$R3 604
27 TraesCS1D01G310800 chr4D 357838000 357838596 596 True 822.000000 822 91.625000 4339 4932 1 chr4D.!!$R1 593
28 TraesCS1D01G310800 chr4D 490961370 490962898 1528 True 392.750000 667 92.210750 34 955 4 chr4D.!!$R4 921
29 TraesCS1D01G310800 chr4D 483176477 483177606 1129 False 382.500000 436 82.023000 953 1979 2 chr4D.!!$F4 1026
30 TraesCS1D01G310800 chr3A 620667034 620667628 594 False 843.000000 843 92.282000 4340 4932 1 chr3A.!!$F3 592
31 TraesCS1D01G310800 chr3A 142969211 142969801 590 False 719.000000 719 89.088000 1 590 1 chr3A.!!$F1 589
32 TraesCS1D01G310800 chr2A 242989157 242989853 696 True 839.000000 839 88.434000 2562 3264 1 chr2A.!!$R1 702
33 TraesCS1D01G310800 chr2B 454001671 454002268 597 False 813.000000 813 91.104000 4339 4944 1 chr2B.!!$F1 605
34 TraesCS1D01G310800 chr5D 352665833 352666436 603 False 806.000000 806 90.759000 4340 4944 1 chr5D.!!$F2 604
35 TraesCS1D01G310800 chr6B 263409979 263410565 586 True 616.000000 616 86.242000 1994 2565 1 chr6B.!!$R1 571
36 TraesCS1D01G310800 chr3B 799539589 799540170 581 False 518.000000 518 83.527000 1994 2565 1 chr3B.!!$F1 571
37 TraesCS1D01G310800 chr3B 677293390 677295241 1851 True 212.466667 300 91.833000 675 953 3 chr3B.!!$R1 278
38 TraesCS1D01G310800 chr4A 593467780 593469171 1391 False 410.666667 505 91.888333 1 952 3 chr4A.!!$F2 951
39 TraesCS1D01G310800 chr5A 663372431 663373543 1112 False 424.500000 455 83.622500 953 1979 2 chr5A.!!$F1 1026

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
547 1368 0.037877 TCGGAGAGGAAGAAGACGGT 59.962 55.000 0.00 0.00 0.00 4.83 F
573 1394 0.174389 GCTCAGGAGATGACGCAGAA 59.826 55.000 0.00 0.00 34.28 3.02 F
632 1453 0.304705 CACAGCTCGCGTTTCTGTTT 59.695 50.000 21.16 5.53 38.85 2.83 F
635 1456 0.307760 AGCTCGCGTTTCTGTTTTGG 59.692 50.000 5.77 0.00 0.00 3.28 F
669 1490 0.525668 GTGTGGATGGAGCTCGTACG 60.526 60.000 9.53 9.53 0.00 3.67 F
1035 3964 1.262683 GATGTTAAGCAGCGGCAGATC 59.737 52.381 12.44 0.16 44.61 2.75 F
2071 5185 1.771565 TGGTGCGCTACTAGTACCAT 58.228 50.000 9.73 0.00 46.69 3.55 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1621 4729 1.271871 TGTTCCTGTGCACCAATAGGG 60.272 52.381 15.69 7.02 44.81 3.53 R
1949 5063 3.159472 TCACCGGCGATAACCATATAGT 58.841 45.455 9.30 0.00 0.00 2.12 R
2141 5301 3.709653 AGATTAAGCCATAGTGACCCGAA 59.290 43.478 0.00 0.00 0.00 4.30 R
2789 5994 1.407618 GTGGACCGCCTTTTCAGTTTT 59.592 47.619 0.00 0.00 34.31 2.43 R
2880 6101 2.943033 GGTGCGCCATTACTAGTTGAAT 59.057 45.455 12.58 0.00 34.09 2.57 R
3215 6496 0.253044 ATGGACACTAATGGCGCACT 59.747 50.000 10.83 0.00 32.81 4.40 R
4006 7309 0.462789 GCCAAATTCAGCCATCCTGG 59.537 55.000 0.00 0.00 42.05 4.45 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 1.423584 TGTCTGTCTCCACATGGTGT 58.576 50.000 0.00 0.00 36.34 4.16
302 800 7.120923 AGGACTTTAGCAATATCCTTTACGA 57.879 36.000 0.00 0.00 36.33 3.43
510 1331 4.609018 CCTAGGGCGTGATGGGCG 62.609 72.222 0.00 0.00 0.00 6.13
511 1332 3.536917 CTAGGGCGTGATGGGCGA 61.537 66.667 0.00 0.00 0.00 5.54
512 1333 2.842462 TAGGGCGTGATGGGCGAT 60.842 61.111 0.00 0.00 0.00 4.58
515 1336 1.741770 GGGCGTGATGGGCGATATC 60.742 63.158 0.00 0.00 0.00 1.63
516 1337 1.741770 GGCGTGATGGGCGATATCC 60.742 63.158 0.00 0.00 0.00 2.59
517 1338 2.094659 GCGTGATGGGCGATATCCG 61.095 63.158 0.00 0.00 42.21 4.18
518 1339 1.289066 CGTGATGGGCGATATCCGT 59.711 57.895 0.00 0.00 41.15 4.69
525 1346 2.235546 GGCGATATCCGTCCTTTGC 58.764 57.895 0.00 0.00 41.15 3.68
526 1347 1.228657 GGCGATATCCGTCCTTTGCC 61.229 60.000 0.00 0.00 41.15 4.52
527 1348 1.557443 GCGATATCCGTCCTTTGCCG 61.557 60.000 0.00 0.00 41.15 5.69
528 1349 0.249322 CGATATCCGTCCTTTGCCGT 60.249 55.000 0.00 0.00 0.00 5.68
529 1350 1.499049 GATATCCGTCCTTTGCCGTC 58.501 55.000 0.00 0.00 0.00 4.79
530 1351 0.249322 ATATCCGTCCTTTGCCGTCG 60.249 55.000 0.00 0.00 0.00 5.12
532 1353 4.367023 CCGTCCTTTGCCGTCGGA 62.367 66.667 17.49 0.00 43.22 4.55
533 1354 2.809601 CGTCCTTTGCCGTCGGAG 60.810 66.667 17.49 3.12 0.00 4.63
534 1355 2.654877 GTCCTTTGCCGTCGGAGA 59.345 61.111 17.49 0.00 0.00 3.71
535 1356 1.446272 GTCCTTTGCCGTCGGAGAG 60.446 63.158 17.49 8.66 36.95 3.20
536 1357 2.125512 CCTTTGCCGTCGGAGAGG 60.126 66.667 17.49 14.05 42.73 3.69
537 1358 2.646175 CCTTTGCCGTCGGAGAGGA 61.646 63.158 17.49 0.00 46.48 3.71
538 1359 1.292223 CTTTGCCGTCGGAGAGGAA 59.708 57.895 17.49 0.42 46.48 3.36
540 1361 1.183030 TTTGCCGTCGGAGAGGAAGA 61.183 55.000 17.49 0.00 46.48 2.87
541 1362 1.183030 TTGCCGTCGGAGAGGAAGAA 61.183 55.000 17.49 0.00 46.48 2.52
542 1363 1.139947 GCCGTCGGAGAGGAAGAAG 59.860 63.158 17.49 0.00 46.48 2.85
543 1364 1.313812 GCCGTCGGAGAGGAAGAAGA 61.314 60.000 17.49 0.00 46.48 2.87
544 1365 0.452585 CCGTCGGAGAGGAAGAAGAC 59.547 60.000 4.91 0.00 46.48 3.01
545 1366 0.097325 CGTCGGAGAGGAAGAAGACG 59.903 60.000 1.51 1.51 46.48 4.18
547 1368 0.037877 TCGGAGAGGAAGAAGACGGT 59.962 55.000 0.00 0.00 0.00 4.83
548 1369 1.280133 TCGGAGAGGAAGAAGACGGTA 59.720 52.381 0.00 0.00 0.00 4.02
550 1371 2.025898 GGAGAGGAAGAAGACGGTAGG 58.974 57.143 0.00 0.00 0.00 3.18
554 1375 1.141234 GAAGAAGACGGTAGGCGGG 59.859 63.158 0.00 0.00 0.00 6.13
555 1376 2.902759 GAAGAAGACGGTAGGCGGGC 62.903 65.000 0.00 0.00 0.00 6.13
556 1377 3.459063 GAAGACGGTAGGCGGGCT 61.459 66.667 9.68 9.68 34.49 5.19
557 1378 3.427598 GAAGACGGTAGGCGGGCTC 62.428 68.421 7.59 0.00 31.55 4.70
559 1380 4.208686 GACGGTAGGCGGGCTCAG 62.209 72.222 7.59 3.27 0.00 3.35
562 1383 3.541713 GGTAGGCGGGCTCAGGAG 61.542 72.222 7.59 0.00 0.00 3.69
564 1385 1.834822 GTAGGCGGGCTCAGGAGAT 60.835 63.158 7.59 0.00 0.00 2.75
565 1386 1.834378 TAGGCGGGCTCAGGAGATG 60.834 63.158 7.59 0.00 0.00 2.90
566 1387 2.298335 TAGGCGGGCTCAGGAGATGA 62.298 60.000 7.59 0.00 36.21 2.92
567 1388 2.107953 GCGGGCTCAGGAGATGAC 59.892 66.667 0.00 0.00 33.22 3.06
569 1390 2.107953 GGGCTCAGGAGATGACGC 59.892 66.667 0.00 0.00 33.22 5.19
572 1393 1.670949 GGCTCAGGAGATGACGCAGA 61.671 60.000 0.00 0.00 35.20 4.26
573 1394 0.174389 GCTCAGGAGATGACGCAGAA 59.826 55.000 0.00 0.00 34.28 3.02
576 1397 1.618343 TCAGGAGATGACGCAGAAACA 59.382 47.619 0.00 0.00 31.12 2.83
577 1398 1.998315 CAGGAGATGACGCAGAAACAG 59.002 52.381 0.00 0.00 0.00 3.16
578 1399 0.723981 GGAGATGACGCAGAAACAGC 59.276 55.000 0.00 0.00 0.00 4.40
580 1401 1.016130 AGATGACGCAGAAACAGCCG 61.016 55.000 0.00 0.00 0.00 5.52
581 1402 1.291877 GATGACGCAGAAACAGCCGT 61.292 55.000 0.00 0.00 0.00 5.68
585 1406 2.558313 GCAGAAACAGCCGTGAGC 59.442 61.111 0.00 0.00 44.25 4.26
614 1435 3.714001 CAGAGGCTGCAGCTCCCA 61.714 66.667 35.82 0.00 41.70 4.37
615 1436 3.715097 AGAGGCTGCAGCTCCCAC 61.715 66.667 35.82 20.17 41.70 4.61
616 1437 4.025858 GAGGCTGCAGCTCCCACA 62.026 66.667 35.82 0.00 41.70 4.17
617 1438 3.972971 GAGGCTGCAGCTCCCACAG 62.973 68.421 35.82 0.00 41.70 3.66
626 1447 2.357517 CTCCCACAGCTCGCGTTT 60.358 61.111 5.77 0.00 0.00 3.60
627 1448 2.357034 TCCCACAGCTCGCGTTTC 60.357 61.111 5.77 0.00 0.00 2.78
628 1449 2.357517 CCCACAGCTCGCGTTTCT 60.358 61.111 5.77 0.00 0.00 2.52
629 1450 2.671177 CCCACAGCTCGCGTTTCTG 61.671 63.158 18.13 18.13 0.00 3.02
630 1451 1.956170 CCACAGCTCGCGTTTCTGT 60.956 57.895 19.14 19.14 41.29 3.41
631 1452 1.498865 CCACAGCTCGCGTTTCTGTT 61.499 55.000 21.16 9.58 38.85 3.16
632 1453 0.304705 CACAGCTCGCGTTTCTGTTT 59.695 50.000 21.16 5.53 38.85 2.83
634 1455 1.268032 ACAGCTCGCGTTTCTGTTTTG 60.268 47.619 19.14 5.42 37.78 2.44
635 1456 0.307760 AGCTCGCGTTTCTGTTTTGG 59.692 50.000 5.77 0.00 0.00 3.28
637 1458 0.991770 CTCGCGTTTCTGTTTTGGCG 60.992 55.000 5.77 0.00 44.47 5.69
638 1459 2.008697 CGCGTTTCTGTTTTGGCGG 61.009 57.895 0.00 0.00 39.94 6.13
639 1460 2.300066 GCGTTTCTGTTTTGGCGGC 61.300 57.895 0.00 0.00 0.00 6.53
641 1462 1.065109 GTTTCTGTTTTGGCGGCGT 59.935 52.632 9.37 0.00 0.00 5.68
642 1463 1.064946 TTTCTGTTTTGGCGGCGTG 59.935 52.632 9.37 0.00 0.00 5.34
657 1478 3.411351 GTGCGTTCGCGTGTGGAT 61.411 61.111 5.77 0.00 43.62 3.41
659 1480 4.147322 GCGTTCGCGTGTGGATGG 62.147 66.667 5.77 0.00 43.62 3.51
663 1484 2.942796 TTCGCGTGTGGATGGAGCT 61.943 57.895 5.77 0.00 0.00 4.09
664 1485 2.835701 TTCGCGTGTGGATGGAGCTC 62.836 60.000 4.71 4.71 0.00 4.09
666 1487 2.573869 CGTGTGGATGGAGCTCGT 59.426 61.111 7.83 0.00 0.00 4.18
667 1488 1.807226 CGTGTGGATGGAGCTCGTA 59.193 57.895 7.83 0.00 0.00 3.43
669 1490 0.525668 GTGTGGATGGAGCTCGTACG 60.526 60.000 9.53 9.53 0.00 3.67
671 1492 2.027751 GGATGGAGCTCGTACGCC 59.972 66.667 11.24 6.54 0.00 5.68
672 1493 2.782222 GGATGGAGCTCGTACGCCA 61.782 63.158 11.24 12.63 44.02 5.69
674 1495 2.685387 GATGGAGCTCGTACGCCAGG 62.685 65.000 11.24 1.82 43.10 4.45
675 1496 3.138798 GGAGCTCGTACGCCAGGA 61.139 66.667 11.24 0.00 0.00 3.86
676 1497 2.707849 GGAGCTCGTACGCCAGGAA 61.708 63.158 11.24 0.00 0.00 3.36
678 1499 1.654954 GAGCTCGTACGCCAGGAAGA 61.655 60.000 11.24 0.00 0.00 2.87
723 3520 3.307906 TCCTCGTTCGTGGGTGGG 61.308 66.667 12.24 0.00 0.00 4.61
1008 3937 3.788227 TTATCCAGTATCATGGCCACC 57.212 47.619 8.16 0.00 40.41 4.61
1020 3949 2.670148 GGCCACCGAGGAGGATGTT 61.670 63.158 9.83 0.00 45.00 2.71
1035 3964 1.262683 GATGTTAAGCAGCGGCAGATC 59.737 52.381 12.44 0.16 44.61 2.75
1167 4096 7.807977 ACTTTTCCGTTCTATATACCTCGTA 57.192 36.000 0.00 0.00 0.00 3.43
1297 4242 4.034279 GCTTTGCTGATCTCTTGATCTCAC 59.966 45.833 7.42 0.00 46.84 3.51
1415 4510 7.254227 ACTGCAAAATAACGTTGAGAAACTA 57.746 32.000 11.99 0.00 0.00 2.24
1428 4524 7.017645 CGTTGAGAAACTAGAATGATGTTTGG 58.982 38.462 0.00 0.00 34.55 3.28
1568 4676 6.920569 TTTGACTTGACTGTTTCTAAGACC 57.079 37.500 0.00 0.00 0.00 3.85
1612 4720 9.202273 CTAGTATGCCTTTTCAGCTATCTTAAG 57.798 37.037 0.00 0.00 0.00 1.85
1817 4930 4.508551 TCATGGCTCAGGTAATCACATT 57.491 40.909 0.00 0.00 0.00 2.71
2071 5185 1.771565 TGGTGCGCTACTAGTACCAT 58.228 50.000 9.73 0.00 46.69 3.55
2116 5263 3.493699 GGTGCGCCATTAGTATCTGGTAA 60.494 47.826 12.58 0.00 34.86 2.85
2117 5264 4.315803 GTGCGCCATTAGTATCTGGTAAT 58.684 43.478 4.18 0.00 34.86 1.89
2344 5530 6.681729 ACCTTGTTGATGTCTAGGACTTTA 57.318 37.500 0.00 0.00 33.15 1.85
3128 6409 2.581208 TACTAATGGCGCACCGTGGG 62.581 60.000 10.83 11.12 39.70 4.61
3155 6436 2.687425 TGCGCCATTAGTATTTGCACAT 59.313 40.909 4.18 0.00 0.00 3.21
3191 6472 4.513442 ACACATGGTGCGTCATTAGTATT 58.487 39.130 0.00 0.00 36.98 1.89
3215 6496 2.427753 TGGCGCACCACATGTACA 59.572 55.556 10.83 0.00 42.67 2.90
3237 6518 2.878406 GTGCGCCATTAGTGTCCATATT 59.122 45.455 4.18 0.00 0.00 1.28
3238 6519 2.877786 TGCGCCATTAGTGTCCATATTG 59.122 45.455 4.18 0.00 0.00 1.90
3239 6520 2.226437 GCGCCATTAGTGTCCATATTGG 59.774 50.000 0.00 0.00 39.43 3.16
3247 6528 6.935240 TTAGTGTCCATATTGGCTATAGCT 57.065 37.500 23.53 7.42 41.70 3.32
3248 6529 5.157940 AGTGTCCATATTGGCTATAGCTG 57.842 43.478 23.53 13.43 41.70 4.24
3253 6534 6.833416 TGTCCATATTGGCTATAGCTGTTTTT 59.167 34.615 23.53 6.55 41.70 1.94
3254 6535 7.141363 GTCCATATTGGCTATAGCTGTTTTTG 58.859 38.462 23.53 13.80 41.70 2.44
3264 6545 7.711339 GGCTATAGCTGTTTTTGTAGTAGTGAT 59.289 37.037 23.53 0.00 41.70 3.06
3265 6546 8.543774 GCTATAGCTGTTTTTGTAGTAGTGATG 58.456 37.037 17.75 0.00 38.21 3.07
3266 6547 9.803315 CTATAGCTGTTTTTGTAGTAGTGATGA 57.197 33.333 0.00 0.00 0.00 2.92
3522 6814 8.900983 AAGAAGCTAATCAATAACTGAGGATC 57.099 34.615 0.00 0.00 37.52 3.36
3655 6952 9.146984 CTGCAACAGAAAATGATACAATTGAAT 57.853 29.630 13.59 0.00 32.44 2.57
3746 7043 5.048846 AGGTAGTTCAAAACCTGACACAT 57.951 39.130 0.00 0.00 44.53 3.21
3813 7112 3.429410 GGCTTACCAAAAGCATAGGCAAG 60.429 47.826 11.47 0.00 44.71 4.01
3852 7155 0.250513 GGCTCTGAACCTTGTCCGAT 59.749 55.000 0.00 0.00 0.00 4.18
3875 7178 1.229529 TCCCCTGACTCCAAGGGAC 60.230 63.158 10.17 0.00 45.81 4.46
3933 7236 2.642171 AACTAGGAGATGGTGGTGGA 57.358 50.000 0.00 0.00 0.00 4.02
3962 7265 3.132824 AGTGATGTTCATGTCCTGCGATA 59.867 43.478 0.00 0.00 0.00 2.92
3995 7298 7.308782 AGTACTAATTTGCAGTGTTAGCATC 57.691 36.000 0.00 5.96 42.33 3.91
4030 7333 0.538118 ATGGCTGAATTTGGCGCATT 59.462 45.000 10.83 0.00 0.00 3.56
4065 7368 2.562738 TCTCACATCCTTGAAGCTTCGA 59.437 45.455 21.11 18.41 0.00 3.71
4070 7373 2.631418 TCCTTGAAGCTTCGACTACG 57.369 50.000 21.11 7.72 41.26 3.51
4146 7449 0.996583 GGAGGTTGTGGGGTATTGGA 59.003 55.000 0.00 0.00 0.00 3.53
4156 7459 5.081032 TGTGGGGTATTGGAAGTTTAAAGG 58.919 41.667 0.00 0.00 0.00 3.11
4164 7467 4.986054 TGGAAGTTTAAAGGACAGCCTA 57.014 40.909 0.00 0.00 46.28 3.93
4167 7470 4.936411 GGAAGTTTAAAGGACAGCCTACTC 59.064 45.833 0.00 0.00 46.28 2.59
4170 7473 6.189036 AGTTTAAAGGACAGCCTACTCTTT 57.811 37.500 0.00 0.00 46.28 2.52
4188 7491 5.842874 ACTCTTTAAGTGTAGGGGTAGTTGT 59.157 40.000 0.00 0.00 36.65 3.32
4205 7508 1.975660 TGTTTACTTCCCAGGTGTGC 58.024 50.000 0.00 0.00 0.00 4.57
4220 7523 2.223340 GGTGTGCTGTTGAACTGACAAG 60.223 50.000 6.38 0.00 0.00 3.16
4235 7538 1.277739 CAAGCATGTATCGCCGCTG 59.722 57.895 0.00 0.00 34.26 5.18
4241 7544 0.668706 ATGTATCGCCGCTGCTGATC 60.669 55.000 9.79 0.00 34.31 2.92
4250 7553 1.202568 CCGCTGCTGATCCTCATGTAA 60.203 52.381 0.00 0.00 0.00 2.41
4267 7570 3.815809 TGTAACAGAACTTTGTCCCCAG 58.184 45.455 0.00 0.00 0.00 4.45
4275 7578 3.806949 ACTTTGTCCCCAGAATAAGCA 57.193 42.857 0.00 0.00 0.00 3.91
4281 7584 1.017387 CCCCAGAATAAGCAACTCGC 58.983 55.000 0.00 0.00 42.91 5.03
4299 7602 3.921677 TCGCACGACTTCTTATTTCCTT 58.078 40.909 0.00 0.00 0.00 3.36
4306 7609 7.584987 CACGACTTCTTATTTCCTTTGACATT 58.415 34.615 0.00 0.00 0.00 2.71
4317 7620 7.496529 TTTCCTTTGACATTCACTCTAACAG 57.503 36.000 0.00 0.00 0.00 3.16
4347 7650 6.032956 TGTATGGTTCTCTGTTGATACGTT 57.967 37.500 0.00 0.00 0.00 3.99
4464 7768 8.865244 TTTGGGACTAACCTATAAACCTAGAT 57.135 34.615 0.00 0.00 38.98 1.98
4549 7856 6.434340 GGAGTCCAATTGACCTGAAACTTTAT 59.566 38.462 7.12 0.00 45.68 1.40
4590 7897 1.183676 AGAAGCCCACGAAGTACCGT 61.184 55.000 0.00 0.00 41.61 4.83
4753 8072 4.020378 GAGTTTCGCCGCCGCAAA 62.020 61.111 0.00 0.00 34.03 3.68
4789 8108 3.292492 AAAACCAATCGGGACCCTATC 57.708 47.619 9.41 0.00 41.15 2.08
4828 8147 1.679139 GGAAATCATCACCGATGGCA 58.321 50.000 4.24 0.00 40.15 4.92
4944 8269 7.067372 TCTCTCTCTCTCTCATGTTCTTGATTC 59.933 40.741 0.00 0.00 0.00 2.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
30 31 9.973661 TCCTTTATATTCCAGATGTCTTTTTCA 57.026 29.630 0.00 0.00 0.00 2.69
59 61 5.385198 ACTTTCATTTAAGCTCACCTCCAA 58.615 37.500 0.00 0.00 0.00 3.53
212 218 9.793259 AGGTTCATTTTAGTAAGAAGAACATGA 57.207 29.630 17.92 0.00 36.52 3.07
302 800 5.258051 TCCGTAAAGAATATTGCCCTGTTT 58.742 37.500 0.00 0.00 0.00 2.83
517 1338 1.446272 CTCTCCGACGGCAAAGGAC 60.446 63.158 9.66 0.00 0.00 3.85
518 1339 2.646175 CCTCTCCGACGGCAAAGGA 61.646 63.158 18.79 7.77 0.00 3.36
520 1341 0.737715 CTTCCTCTCCGACGGCAAAG 60.738 60.000 9.66 1.26 0.00 2.77
522 1343 1.183030 TTCTTCCTCTCCGACGGCAA 61.183 55.000 9.66 0.00 0.00 4.52
523 1344 1.595993 CTTCTTCCTCTCCGACGGCA 61.596 60.000 9.66 0.00 0.00 5.69
525 1346 0.452585 GTCTTCTTCCTCTCCGACGG 59.547 60.000 7.84 7.84 0.00 4.79
526 1347 0.097325 CGTCTTCTTCCTCTCCGACG 59.903 60.000 0.00 0.00 38.31 5.12
527 1348 0.452585 CCGTCTTCTTCCTCTCCGAC 59.547 60.000 0.00 0.00 0.00 4.79
528 1349 0.037877 ACCGTCTTCTTCCTCTCCGA 59.962 55.000 0.00 0.00 0.00 4.55
529 1350 1.671845 CTACCGTCTTCTTCCTCTCCG 59.328 57.143 0.00 0.00 0.00 4.63
530 1351 2.025898 CCTACCGTCTTCTTCCTCTCC 58.974 57.143 0.00 0.00 0.00 3.71
532 1353 1.476477 GCCTACCGTCTTCTTCCTCT 58.524 55.000 0.00 0.00 0.00 3.69
533 1354 0.100861 CGCCTACCGTCTTCTTCCTC 59.899 60.000 0.00 0.00 0.00 3.71
534 1355 1.321074 CCGCCTACCGTCTTCTTCCT 61.321 60.000 0.00 0.00 34.38 3.36
535 1356 1.141234 CCGCCTACCGTCTTCTTCC 59.859 63.158 0.00 0.00 34.38 3.46
536 1357 1.141234 CCCGCCTACCGTCTTCTTC 59.859 63.158 0.00 0.00 34.38 2.87
537 1358 3.015312 GCCCGCCTACCGTCTTCTT 62.015 63.158 0.00 0.00 34.38 2.52
538 1359 3.459063 GCCCGCCTACCGTCTTCT 61.459 66.667 0.00 0.00 34.38 2.85
540 1361 3.459063 GAGCCCGCCTACCGTCTT 61.459 66.667 0.00 0.00 34.38 3.01
541 1362 4.753662 TGAGCCCGCCTACCGTCT 62.754 66.667 0.00 0.00 34.38 4.18
542 1363 4.208686 CTGAGCCCGCCTACCGTC 62.209 72.222 0.00 0.00 34.38 4.79
545 1366 3.541713 CTCCTGAGCCCGCCTACC 61.542 72.222 0.00 0.00 0.00 3.18
547 1368 1.834378 CATCTCCTGAGCCCGCCTA 60.834 63.158 0.00 0.00 0.00 3.93
548 1369 3.160047 CATCTCCTGAGCCCGCCT 61.160 66.667 0.00 0.00 0.00 5.52
550 1371 2.107953 GTCATCTCCTGAGCCCGC 59.892 66.667 0.00 0.00 33.51 6.13
554 1375 0.174389 TTCTGCGTCATCTCCTGAGC 59.826 55.000 0.00 0.00 33.51 4.26
555 1376 2.266554 GTTTCTGCGTCATCTCCTGAG 58.733 52.381 0.00 0.00 33.51 3.35
556 1377 1.618343 TGTTTCTGCGTCATCTCCTGA 59.382 47.619 0.00 0.00 0.00 3.86
557 1378 1.998315 CTGTTTCTGCGTCATCTCCTG 59.002 52.381 0.00 0.00 0.00 3.86
559 1380 0.723981 GCTGTTTCTGCGTCATCTCC 59.276 55.000 0.00 0.00 0.00 3.71
560 1381 0.723981 GGCTGTTTCTGCGTCATCTC 59.276 55.000 0.00 0.00 0.00 2.75
561 1382 1.016130 CGGCTGTTTCTGCGTCATCT 61.016 55.000 0.00 0.00 0.00 2.90
562 1383 1.291877 ACGGCTGTTTCTGCGTCATC 61.292 55.000 0.00 0.00 0.00 2.92
564 1385 2.108157 ACGGCTGTTTCTGCGTCA 59.892 55.556 0.00 0.00 0.00 4.35
565 1386 1.891060 CTCACGGCTGTTTCTGCGTC 61.891 60.000 0.00 0.00 0.00 5.19
566 1387 1.956170 CTCACGGCTGTTTCTGCGT 60.956 57.895 0.00 0.00 0.00 5.24
567 1388 2.856032 CTCACGGCTGTTTCTGCG 59.144 61.111 0.00 0.00 0.00 5.18
569 1390 1.621301 CTCGCTCACGGCTGTTTCTG 61.621 60.000 0.00 0.00 40.63 3.02
572 1393 2.357517 CCTCGCTCACGGCTGTTT 60.358 61.111 0.00 0.00 40.63 2.83
578 1399 4.193334 TGATCGCCTCGCTCACGG 62.193 66.667 0.00 0.00 40.63 4.94
580 1401 2.959071 GCTGATCGCCTCGCTCAC 60.959 66.667 0.00 0.00 29.19 3.51
581 1402 3.421687 CTGCTGATCGCCTCGCTCA 62.422 63.158 7.00 0.00 38.05 4.26
585 1406 2.027314 CCTCTGCTGATCGCCTCG 59.973 66.667 7.00 0.00 38.05 4.63
586 1407 2.280052 GCCTCTGCTGATCGCCTC 60.280 66.667 7.00 0.00 38.05 4.70
600 1421 4.031129 CTGTGGGAGCTGCAGCCT 62.031 66.667 34.39 21.60 43.38 4.58
609 1430 2.357517 AAACGCGAGCTGTGGGAG 60.358 61.111 15.93 0.00 0.00 4.30
610 1431 2.357034 GAAACGCGAGCTGTGGGA 60.357 61.111 15.93 0.00 0.00 4.37
611 1432 2.357517 AGAAACGCGAGCTGTGGG 60.358 61.111 15.93 0.00 0.00 4.61
612 1433 1.498865 AACAGAAACGCGAGCTGTGG 61.499 55.000 24.95 8.24 41.65 4.17
614 1435 1.014352 AAAACAGAAACGCGAGCTGT 58.986 45.000 15.93 19.36 44.15 4.40
615 1436 1.388888 CAAAACAGAAACGCGAGCTG 58.611 50.000 15.93 18.68 35.81 4.24
616 1437 0.307760 CCAAAACAGAAACGCGAGCT 59.692 50.000 15.93 3.30 0.00 4.09
617 1438 1.268778 GCCAAAACAGAAACGCGAGC 61.269 55.000 15.93 0.41 0.00 5.03
618 1439 0.991770 CGCCAAAACAGAAACGCGAG 60.992 55.000 15.93 0.00 42.03 5.03
619 1440 1.010574 CGCCAAAACAGAAACGCGA 60.011 52.632 15.93 0.00 42.03 5.87
621 1442 2.300066 GCCGCCAAAACAGAAACGC 61.300 57.895 0.00 0.00 0.00 4.84
622 1443 2.008697 CGCCGCCAAAACAGAAACG 61.009 57.895 0.00 0.00 0.00 3.60
623 1444 1.065109 ACGCCGCCAAAACAGAAAC 59.935 52.632 0.00 0.00 0.00 2.78
624 1445 1.064946 CACGCCGCCAAAACAGAAA 59.935 52.632 0.00 0.00 0.00 2.52
625 1446 2.718731 CACGCCGCCAAAACAGAA 59.281 55.556 0.00 0.00 0.00 3.02
626 1447 3.959975 GCACGCCGCCAAAACAGA 61.960 61.111 0.00 0.00 32.94 3.41
629 1450 4.916273 AACGCACGCCGCCAAAAC 62.916 61.111 0.00 0.00 41.76 2.43
630 1451 4.615834 GAACGCACGCCGCCAAAA 62.616 61.111 0.00 0.00 41.76 2.44
641 1462 3.410516 CATCCACACGCGAACGCA 61.411 61.111 15.93 0.00 45.53 5.24
642 1463 4.147322 CCATCCACACGCGAACGC 62.147 66.667 15.93 9.20 45.53 4.84
645 1466 2.434185 GCTCCATCCACACGCGAA 60.434 61.111 15.93 0.00 0.00 4.70
646 1467 3.356639 GAGCTCCATCCACACGCGA 62.357 63.158 15.93 0.00 0.00 5.87
647 1468 2.887568 GAGCTCCATCCACACGCG 60.888 66.667 3.53 3.53 0.00 6.01
648 1469 2.279502 TACGAGCTCCATCCACACGC 62.280 60.000 8.47 0.00 0.00 5.34
649 1470 0.525668 GTACGAGCTCCATCCACACG 60.526 60.000 8.47 0.00 0.00 4.49
650 1471 0.525668 CGTACGAGCTCCATCCACAC 60.526 60.000 10.44 0.00 0.00 3.82
654 1475 2.027751 GGCGTACGAGCTCCATCC 59.972 66.667 21.65 3.77 37.29 3.51
655 1476 1.299468 CTGGCGTACGAGCTCCATC 60.299 63.158 21.65 0.00 37.29 3.51
656 1477 2.786495 CCTGGCGTACGAGCTCCAT 61.786 63.158 21.65 0.00 37.29 3.41
657 1478 3.449227 CCTGGCGTACGAGCTCCA 61.449 66.667 21.65 15.49 37.29 3.86
659 1480 1.226717 CTTCCTGGCGTACGAGCTC 60.227 63.158 21.65 2.73 37.29 4.09
663 1484 0.963962 AACTTCTTCCTGGCGTACGA 59.036 50.000 21.65 0.00 0.00 3.43
664 1485 1.459592 CAAACTTCTTCCTGGCGTACG 59.540 52.381 11.84 11.84 0.00 3.67
666 1487 3.695830 ATCAAACTTCTTCCTGGCGTA 57.304 42.857 0.00 0.00 0.00 4.42
667 1488 2.568623 ATCAAACTTCTTCCTGGCGT 57.431 45.000 0.00 0.00 0.00 5.68
669 1490 4.751600 CCAAAAATCAAACTTCTTCCTGGC 59.248 41.667 0.00 0.00 0.00 4.85
671 1492 5.687285 CGACCAAAAATCAAACTTCTTCCTG 59.313 40.000 0.00 0.00 0.00 3.86
672 1493 5.592688 TCGACCAAAAATCAAACTTCTTCCT 59.407 36.000 0.00 0.00 0.00 3.36
674 1495 6.363357 CCATCGACCAAAAATCAAACTTCTTC 59.637 38.462 0.00 0.00 0.00 2.87
675 1496 6.040391 TCCATCGACCAAAAATCAAACTTCTT 59.960 34.615 0.00 0.00 0.00 2.52
676 1497 5.534654 TCCATCGACCAAAAATCAAACTTCT 59.465 36.000 0.00 0.00 0.00 2.85
678 1499 5.528870 GTCCATCGACCAAAAATCAAACTT 58.471 37.500 0.00 0.00 32.40 2.66
704 3476 2.732016 CACCCACGAACGAGGACA 59.268 61.111 11.77 0.00 0.00 4.02
737 3534 0.320421 ACGAACGACAAGTCCATGGG 60.320 55.000 13.02 0.00 0.00 4.00
803 3719 0.028770 CTCAGCGTCCGCAAACAAAA 59.971 50.000 14.70 0.00 44.88 2.44
804 3720 1.092921 ACTCAGCGTCCGCAAACAAA 61.093 50.000 14.70 0.00 44.88 2.83
815 3731 2.032030 CGAAAAATCACCAACTCAGCGT 60.032 45.455 0.00 0.00 0.00 5.07
981 3910 7.776969 GTGGCCATGATACTGGATAATATGATT 59.223 37.037 9.72 0.00 38.69 2.57
994 3923 0.398522 TCCTCGGTGGCCATGATACT 60.399 55.000 9.72 0.00 35.26 2.12
1008 3937 1.576356 GCTGCTTAACATCCTCCTCG 58.424 55.000 0.00 0.00 0.00 4.63
1020 3949 1.083806 CAACGATCTGCCGCTGCTTA 61.084 55.000 0.70 0.00 38.71 3.09
1035 3964 0.934496 TTCTTGCACGGTCTTCAACG 59.066 50.000 0.00 0.00 0.00 4.10
1167 4096 4.660168 AGAAGGTCAAGCAACTGATCATT 58.340 39.130 0.00 0.00 0.00 2.57
1297 4242 1.156736 CGAACACAGTTAGGCTTGGG 58.843 55.000 0.00 0.00 0.00 4.12
1568 4676 9.846248 GCATACTAGGGCAAAAATATTATCAAG 57.154 33.333 0.00 0.00 0.00 3.02
1588 4696 7.569240 ACTTAAGATAGCTGAAAAGGCATACT 58.431 34.615 10.09 0.00 0.00 2.12
1612 4720 4.461081 TGTGCACCAATAGGGAATGTAAAC 59.539 41.667 15.69 0.00 41.15 2.01
1621 4729 1.271871 TGTTCCTGTGCACCAATAGGG 60.272 52.381 15.69 7.02 44.81 3.53
1889 5003 7.283329 ACTGTTTCTCCAAAGTTGTCTTCTAT 58.717 34.615 0.00 0.00 32.90 1.98
1898 5012 7.121315 GGCATATAGAACTGTTTCTCCAAAGTT 59.879 37.037 0.00 0.00 41.48 2.66
1949 5063 3.159472 TCACCGGCGATAACCATATAGT 58.841 45.455 9.30 0.00 0.00 2.12
2141 5301 3.709653 AGATTAAGCCATAGTGACCCGAA 59.290 43.478 0.00 0.00 0.00 4.30
2789 5994 1.407618 GTGGACCGCCTTTTCAGTTTT 59.592 47.619 0.00 0.00 34.31 2.43
2880 6101 2.943033 GGTGCGCCATTACTAGTTGAAT 59.057 45.455 12.58 0.00 34.09 2.57
2973 6206 2.203001 CACCACTCACACGGTGCA 60.203 61.111 8.30 0.00 45.77 4.57
3155 6436 1.067985 CATGTGTTGGTGCGCCATTAA 60.068 47.619 21.95 1.53 45.56 1.40
3181 6462 6.425721 GGTGCGCCATTACTAAATACTAATGA 59.574 38.462 12.58 0.00 33.76 2.57
3213 6494 0.673644 GGACACTAATGGCGCACTGT 60.674 55.000 10.83 0.00 32.81 3.55
3214 6495 0.673333 TGGACACTAATGGCGCACTG 60.673 55.000 10.83 0.00 32.81 3.66
3215 6496 0.253044 ATGGACACTAATGGCGCACT 59.747 50.000 10.83 0.00 32.81 4.40
3237 6518 6.816640 CACTACTACAAAAACAGCTATAGCCA 59.183 38.462 21.17 0.00 43.38 4.75
3238 6519 7.039882 TCACTACTACAAAAACAGCTATAGCC 58.960 38.462 21.17 3.64 43.38 3.93
3239 6520 8.543774 CATCACTACTACAAAAACAGCTATAGC 58.456 37.037 17.33 17.33 42.49 2.97
3253 6534 9.836864 AAAAGCATGAATATCATCACTACTACA 57.163 29.630 0.00 0.00 34.28 2.74
3295 6576 7.921786 ATGTGCTAAGAAGTGCAAGTAATAA 57.078 32.000 0.00 0.00 41.10 1.40
3522 6814 1.141858 GGGATCAGCTAGAAACCTGGG 59.858 57.143 0.00 0.00 0.00 4.45
3709 7006 7.229951 TGAACTACCTACCCTAGAATCCTAA 57.770 40.000 0.00 0.00 0.00 2.69
3711 7008 5.745988 TGAACTACCTACCCTAGAATCCT 57.254 43.478 0.00 0.00 0.00 3.24
3746 7043 4.262377 CCCACAATGACCTGCACAATTTAA 60.262 41.667 0.00 0.00 0.00 1.52
3813 7112 3.311596 GCCATAATGTGAACGTTAGTCCC 59.688 47.826 0.00 0.00 31.61 4.46
3933 7236 4.067896 GGACATGAACATCACTTGACAGT 58.932 43.478 0.00 0.00 0.00 3.55
3962 7265 9.667107 ACACTGCAAATTAGTACTATATGTTGT 57.333 29.630 2.79 6.06 0.00 3.32
3995 7298 2.307980 AGCCATCCTGGTCATCCATATG 59.692 50.000 0.00 0.00 43.43 1.78
4006 7309 0.462789 GCCAAATTCAGCCATCCTGG 59.537 55.000 0.00 0.00 42.05 4.45
4030 7333 5.958380 AGGATGTGAGATGTAGACCAAAGTA 59.042 40.000 0.00 0.00 0.00 2.24
4128 7431 2.041216 ACTTCCAATACCCCACAACCTC 59.959 50.000 0.00 0.00 0.00 3.85
4146 7449 5.827326 AGAGTAGGCTGTCCTTTAAACTT 57.173 39.130 0.00 0.00 40.66 2.66
4156 7459 5.652518 CCTACACTTAAAGAGTAGGCTGTC 58.347 45.833 15.62 0.00 46.98 3.51
4164 7467 5.842874 ACAACTACCCCTACACTTAAAGAGT 59.157 40.000 0.00 0.00 39.89 3.24
4167 7470 8.152898 AGTAAACAACTACCCCTACACTTAAAG 58.847 37.037 0.00 0.00 36.36 1.85
4170 7473 7.256296 GGAAGTAAACAACTACCCCTACACTTA 60.256 40.741 0.00 0.00 37.50 2.24
4188 7491 1.493022 ACAGCACACCTGGGAAGTAAA 59.507 47.619 0.00 0.00 46.14 2.01
4205 7508 3.976793 ACATGCTTGTCAGTTCAACAG 57.023 42.857 0.00 0.00 0.00 3.16
4241 7544 4.455877 GGGACAAAGTTCTGTTACATGAGG 59.544 45.833 0.00 0.00 0.00 3.86
4250 7553 3.884037 ATTCTGGGGACAAAGTTCTGT 57.116 42.857 0.00 0.00 42.06 3.41
4267 7570 1.993370 AGTCGTGCGAGTTGCTTATTC 59.007 47.619 3.50 0.00 46.63 1.75
4275 7578 3.678548 GGAAATAAGAAGTCGTGCGAGTT 59.321 43.478 13.60 13.60 40.14 3.01
4281 7584 6.539649 TGTCAAAGGAAATAAGAAGTCGTG 57.460 37.500 0.00 0.00 0.00 4.35
4299 7602 6.611613 AGGATCTGTTAGAGTGAATGTCAA 57.388 37.500 0.00 0.00 0.00 3.18
4317 7620 5.127845 TCAACAGAGAACCATACAGAGGATC 59.872 44.000 0.00 0.00 0.00 3.36
4455 7759 1.561542 CTGGCACTGGGATCTAGGTTT 59.438 52.381 0.00 0.00 0.00 3.27
4464 7768 1.859302 AACAAAAACTGGCACTGGGA 58.141 45.000 0.00 0.00 0.00 4.37
4549 7856 6.234920 TCTTTTGGTCCATAAAGAATCGTCA 58.765 36.000 18.88 3.83 37.42 4.35
4590 7897 1.689575 GGGACTCCTCTGGTGCATCTA 60.690 57.143 0.00 0.00 0.00 1.98
4753 8072 2.583143 GTTTTTGGTGGCTACAGAGGT 58.417 47.619 1.52 0.00 0.00 3.85
4823 8142 3.409570 CCGAGATGATGAAGATTGCCAT 58.590 45.455 0.00 0.00 0.00 4.40
4828 8147 1.069823 AGCGCCGAGATGATGAAGATT 59.930 47.619 2.29 0.00 0.00 2.40


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

AutoCloner maintained by Alex Coulton.