Multiple sequence alignment - TraesCS7D01G198700

Loading Multiple Alignment...

Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS7D01G198700 chr7D 100.000 5830 0 0 1 5830 155440339 155434510 0.000000e+00 10767.0
1 TraesCS7D01G198700 chr7D 90.761 184 12 3 3967 4148 351657952 351658132 2.100000e-59 241.0
2 TraesCS7D01G198700 chr7D 91.160 181 10 4 3970 4148 488095068 488094892 2.100000e-59 241.0
3 TraesCS7D01G198700 chr7D 91.946 149 9 3 2809 2954 600232660 600232808 7.660000e-49 206.0
4 TraesCS7D01G198700 chr4A 91.695 2059 112 26 3 2033 6125242 6123215 0.000000e+00 2800.0
5 TraesCS7D01G198700 chr4A 96.670 961 31 1 1775 2735 332964481 332965440 0.000000e+00 1596.0
6 TraesCS7D01G198700 chr4A 96.555 958 32 1 1778 2735 704409676 704408720 0.000000e+00 1585.0
7 TraesCS7D01G198700 chr4A 92.063 189 10 2 3974 4161 689215353 689215169 1.610000e-65 261.0
8 TraesCS7D01G198700 chr4A 95.960 99 4 0 3296 3394 619866135 619866233 1.680000e-35 161.0
9 TraesCS7D01G198700 chr5A 91.476 2053 124 18 3 2033 550034861 550036884 0.000000e+00 2774.0
10 TraesCS7D01G198700 chr5A 89.718 1809 112 27 3 1772 75784847 75783074 0.000000e+00 2242.0
11 TraesCS7D01G198700 chr5A 96.868 958 29 1 1775 2732 516903648 516904604 0.000000e+00 1602.0
12 TraesCS7D01G198700 chr5A 90.647 1144 82 16 3 1126 69014019 69012881 0.000000e+00 1496.0
13 TraesCS7D01G198700 chr5A 89.948 1144 89 15 3 1126 12619034 12620171 0.000000e+00 1452.0
14 TraesCS7D01G198700 chr5A 96.154 208 8 0 2748 2955 75781400 75781193 2.010000e-89 340.0
15 TraesCS7D01G198700 chr5A 92.670 191 10 2 3972 4161 219189480 219189667 7.440000e-69 272.0
16 TraesCS7D01G198700 chr4B 90.750 2054 114 21 3 2029 646749842 646747838 0.000000e+00 2671.0
17 TraesCS7D01G198700 chr4B 94.554 404 21 1 4160 4563 626695393 626694991 1.780000e-174 623.0
18 TraesCS7D01G198700 chr4B 96.564 291 10 0 3622 3912 546865831 546865541 3.160000e-132 483.0
19 TraesCS7D01G198700 chr4B 96.809 188 6 0 3622 3809 604267682 604267869 1.220000e-81 315.0
20 TraesCS7D01G198700 chr4B 95.055 182 9 0 2961 3142 218937413 218937594 2.660000e-73 287.0
21 TraesCS7D01G198700 chr4B 92.896 183 9 2 2956 3138 127537832 127538010 4.480000e-66 263.0
22 TraesCS7D01G198700 chr4B 98.276 116 2 0 3279 3394 546865936 546865821 2.750000e-48 204.0
23 TraesCS7D01G198700 chr4B 97.414 116 3 0 3279 3394 604267577 604267692 1.280000e-46 198.0
24 TraesCS7D01G198700 chr4B 96.078 102 4 0 2854 2955 603004683 603004784 3.610000e-37 167.0
25 TraesCS7D01G198700 chr4B 96.809 94 3 0 3091 3184 546866022 546865929 2.170000e-34 158.0
26 TraesCS7D01G198700 chr4B 94.681 94 5 0 3091 3184 604267491 604267584 4.710000e-31 147.0
27 TraesCS7D01G198700 chr2B 90.432 2059 124 23 3 2033 757722454 757724467 0.000000e+00 2643.0
28 TraesCS7D01G198700 chr2B 94.180 1031 35 9 1004 2033 690570951 690571957 0.000000e+00 1548.0
29 TraesCS7D01G198700 chr2B 94.558 588 31 1 3221 3808 174400727 174400141 0.000000e+00 907.0
30 TraesCS7D01G198700 chr2B 95.792 404 13 2 4160 4563 216214375 216214774 0.000000e+00 649.0
31 TraesCS7D01G198700 chr2B 94.118 221 9 1 2961 3181 174400943 174400727 3.370000e-87 333.0
32 TraesCS7D01G198700 chr2B 91.237 194 12 3 3970 4161 654571237 654571047 5.800000e-65 259.0
33 TraesCS7D01G198700 chr2B 96.053 76 3 0 4728 4803 127020345 127020420 2.210000e-24 124.0
34 TraesCS7D01G198700 chr3A 90.821 1645 102 22 161 1772 241729658 241731286 0.000000e+00 2156.0
35 TraesCS7D01G198700 chr3A 92.245 1109 48 15 4728 5830 56503419 56504495 0.000000e+00 1537.0
36 TraesCS7D01G198700 chr3A 95.202 917 38 1 3245 4161 56495077 56495987 0.000000e+00 1445.0
37 TraesCS7D01G198700 chr3A 94.885 567 27 2 2957 3523 570022986 570022422 0.000000e+00 885.0
38 TraesCS7D01G198700 chr3A 92.439 529 34 6 5306 5830 216934263 216934789 0.000000e+00 750.0
39 TraesCS7D01G198700 chr3A 92.439 529 34 5 5306 5830 217009694 217010220 0.000000e+00 750.0
40 TraesCS7D01G198700 chr3A 94.607 445 24 0 4160 4604 56496048 56496492 0.000000e+00 689.0
41 TraesCS7D01G198700 chr3A 93.247 385 26 0 4896 5280 570022394 570022010 8.480000e-158 568.0
42 TraesCS7D01G198700 chr3A 83.859 539 82 3 4745 5280 729876465 729875929 5.210000e-140 508.0
43 TraesCS7D01G198700 chr3A 96.970 66 2 0 2748 2813 241732537 241732602 1.720000e-20 111.0
44 TraesCS7D01G198700 chr3A 97.778 45 1 0 3812 3856 298754717 298754673 1.740000e-10 78.7
45 TraesCS7D01G198700 chr1D 97.217 1150 31 1 3012 4161 9923049 9921901 0.000000e+00 1945.0
46 TraesCS7D01G198700 chr1D 96.567 1165 27 3 3009 4161 10038174 10039337 0.000000e+00 1917.0
47 TraesCS7D01G198700 chr1D 92.799 1111 44 8 4728 5830 10040002 10041084 0.000000e+00 1576.0
48 TraesCS7D01G198700 chr1D 92.711 1029 39 8 4728 5747 9921236 9920235 0.000000e+00 1452.0
49 TraesCS7D01G198700 chr1D 95.076 589 24 3 4160 4744 10039398 10039985 0.000000e+00 922.0
50 TraesCS7D01G198700 chr1D 94.915 590 25 4 4160 4745 9921840 9921252 0.000000e+00 918.0
51 TraesCS7D01G198700 chr1D 91.758 182 10 4 4568 4745 126249957 126249777 1.250000e-61 248.0
52 TraesCS7D01G198700 chr5B 96.000 1150 44 2 3012 4161 453115954 453114807 0.000000e+00 1868.0
53 TraesCS7D01G198700 chr5B 97.182 958 24 3 1778 2735 505281596 505280642 0.000000e+00 1616.0
54 TraesCS7D01G198700 chr5B 92.281 868 38 5 4728 5594 453114168 453113329 0.000000e+00 1205.0
55 TraesCS7D01G198700 chr5B 89.134 589 35 9 4160 4745 453114746 453114184 0.000000e+00 706.0
56 TraesCS7D01G198700 chr5B 94.545 330 14 2 2961 3290 678890461 678890786 1.870000e-139 507.0
57 TraesCS7D01G198700 chr5B 90.602 266 11 4 1589 1854 658639004 658639255 2.010000e-89 340.0
58 TraesCS7D01G198700 chr5B 98.649 74 1 0 3296 3369 613243530 613243603 1.320000e-26 132.0
59 TraesCS7D01G198700 chr4D 95.475 1105 42 5 4728 5830 294032034 294030936 0.000000e+00 1757.0
60 TraesCS7D01G198700 chr4D 96.133 362 8 5 4386 4745 294032407 294032050 2.340000e-163 586.0
61 TraesCS7D01G198700 chr5D 95.204 1105 45 5 4728 5830 123155246 123156344 0.000000e+00 1740.0
62 TraesCS7D01G198700 chr5D 96.226 371 11 3 4380 4748 123154865 123155234 6.460000e-169 604.0
63 TraesCS7D01G198700 chr6A 97.599 958 22 1 1778 2735 47994096 47993140 0.000000e+00 1640.0
64 TraesCS7D01G198700 chr6A 97.642 212 3 2 2741 2952 62450489 62450280 4.290000e-96 363.0
65 TraesCS7D01G198700 chr6A 93.989 183 10 1 2956 3138 571617496 571617315 5.750000e-70 276.0
66 TraesCS7D01G198700 chr6A 91.758 182 10 4 4568 4745 561223016 561222836 1.250000e-61 248.0
67 TraesCS7D01G198700 chr6A 96.970 66 2 0 2748 2813 47992840 47992775 1.720000e-20 111.0
68 TraesCS7D01G198700 chr6A 97.778 45 1 0 3812 3856 579427413 579427457 1.740000e-10 78.7
69 TraesCS7D01G198700 chr3B 97.390 958 24 1 1778 2735 739880920 739879964 0.000000e+00 1629.0
70 TraesCS7D01G198700 chr3B 91.758 182 10 4 4568 4745 779171189 779171369 1.250000e-61 248.0
71 TraesCS7D01G198700 chr3B 96.053 76 3 0 4728 4803 779171385 779171460 2.210000e-24 124.0
72 TraesCS7D01G198700 chr3B 94.737 76 3 1 4728 4803 210824848 210824922 3.690000e-22 117.0
73 TraesCS7D01G198700 chr7A 97.077 958 27 1 1778 2735 621160335 621159379 0.000000e+00 1613.0
74 TraesCS7D01G198700 chr7A 92.780 928 34 11 1107 2033 692989669 692988774 0.000000e+00 1312.0
75 TraesCS7D01G198700 chr7A 90.176 967 77 11 3 961 692990899 692989943 0.000000e+00 1243.0
76 TraesCS7D01G198700 chr7A 92.989 542 33 2 1232 1772 346317075 346316538 0.000000e+00 785.0
77 TraesCS7D01G198700 chr7A 94.554 404 18 2 4160 4563 298784435 298784834 6.420000e-174 621.0
78 TraesCS7D01G198700 chr7A 95.146 206 9 1 2748 2953 49523262 49523466 2.030000e-84 324.0
79 TraesCS7D01G198700 chr7A 96.791 187 5 1 2956 3142 160398604 160398419 1.580000e-80 311.0
80 TraesCS7D01G198700 chr7A 95.082 183 8 1 2956 3138 115554215 115554396 2.660000e-73 287.0
81 TraesCS7D01G198700 chr7A 94.536 183 9 1 2956 3138 732693299 732693118 1.240000e-71 281.0
82 TraesCS7D01G198700 chr7A 90.541 148 13 1 2809 2955 700209474 700209327 1.660000e-45 195.0
83 TraesCS7D01G198700 chr7A 97.196 107 3 0 3858 3964 618430943 618431049 1.290000e-41 182.0
84 TraesCS7D01G198700 chr7A 96.923 65 2 0 2748 2812 621159079 621159015 6.180000e-20 110.0
85 TraesCS7D01G198700 chr7A 97.872 47 1 0 3810 3856 95111380 95111334 1.350000e-11 82.4
86 TraesCS7D01G198700 chr1B 96.868 958 30 0 1778 2735 650784563 650783606 0.000000e+00 1604.0
87 TraesCS7D01G198700 chr1B 95.545 404 16 2 4160 4563 196084868 196085269 0.000000e+00 645.0
88 TraesCS7D01G198700 chr1B 97.436 78 1 1 3887 3964 76953772 76953848 1.320000e-26 132.0
89 TraesCS7D01G198700 chr1B 97.297 74 2 0 3296 3369 522942066 522941993 6.130000e-25 126.0
90 TraesCS7D01G198700 chr1B 96.923 65 2 0 2748 2812 650783306 650783242 6.180000e-20 110.0
91 TraesCS7D01G198700 chr6B 96.555 958 30 2 1778 2735 14049194 14048240 0.000000e+00 1583.0
92 TraesCS7D01G198700 chr6B 94.802 404 20 1 4160 4563 65424628 65424226 3.830000e-176 628.0
93 TraesCS7D01G198700 chr6B 93.636 330 17 2 2961 3290 446282630 446282955 1.890000e-134 490.0
94 TraesCS7D01G198700 chr6B 95.722 187 7 1 2956 3142 16906225 16906040 3.410000e-77 300.0
95 TraesCS7D01G198700 chr6B 98.718 78 1 0 3887 3964 505326497 505326574 7.880000e-29 139.0
96 TraesCS7D01G198700 chr6B 96.923 65 2 0 2748 2812 14047940 14047876 6.180000e-20 110.0
97 TraesCS7D01G198700 chr1A 89.773 1144 88 16 3 1126 310698670 310699804 0.000000e+00 1437.0
98 TraesCS7D01G198700 chr1A 96.923 65 2 0 2748 2812 139356342 139356406 6.180000e-20 110.0
99 TraesCS7D01G198700 chr2D 94.890 861 30 8 2956 3808 121004804 121003950 0.000000e+00 1334.0
100 TraesCS7D01G198700 chr2D 94.845 776 36 3 5057 5830 72857768 72856995 0.000000e+00 1208.0
101 TraesCS7D01G198700 chr2D 95.580 362 13 3 4386 4745 72858410 72858050 1.410000e-160 577.0
102 TraesCS7D01G198700 chr2D 97.436 78 2 0 3887 3964 233137716 233137639 3.670000e-27 134.0
103 TraesCS7D01G198700 chr2D 95.833 48 2 0 3568 3615 121004324 121004277 1.740000e-10 78.7
104 TraesCS7D01G198700 chr2A 91.088 965 76 5 3 959 137273109 137272147 0.000000e+00 1297.0
105 TraesCS7D01G198700 chr2A 94.494 672 36 1 3137 3808 125209713 125209043 0.000000e+00 1035.0
106 TraesCS7D01G198700 chr2A 93.169 527 33 2 5306 5830 315963551 315964076 0.000000e+00 771.0
107 TraesCS7D01G198700 chr2A 96.791 187 5 1 2956 3142 317993971 317994156 1.580000e-80 311.0
108 TraesCS7D01G198700 chr2A 97.253 182 5 0 2961 3142 259613948 259614129 5.670000e-80 309.0
109 TraesCS7D01G198700 chr2A 95.833 48 2 0 3568 3615 125209417 125209370 1.740000e-10 78.7
110 TraesCS7D01G198700 chr7B 96.287 404 14 1 4160 4563 683092825 683092423 0.000000e+00 662.0
111 TraesCS7D01G198700 chr7B 95.960 99 4 0 2855 2953 559712513 559712415 1.680000e-35 161.0
112 TraesCS7D01G198700 chr3D 83.514 552 67 16 4746 5280 600126618 600126074 1.460000e-135 494.0
113 TraesCS7D01G198700 chr3D 97.872 47 1 0 3810 3856 498705988 498706034 1.350000e-11 82.4
114 TraesCS7D01G198700 chr6D 97.468 79 2 0 3887 3965 283302674 283302596 1.020000e-27 135.0


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 TraesCS7D01G198700 chr7D 155434510 155440339 5829 True 10767.000000 10767 100.000000 1 5830 1 chr7D.!!$R1 5829
1 TraesCS7D01G198700 chr4A 6123215 6125242 2027 True 2800.000000 2800 91.695000 3 2033 1 chr4A.!!$R1 2030
2 TraesCS7D01G198700 chr4A 332964481 332965440 959 False 1596.000000 1596 96.670000 1775 2735 1 chr4A.!!$F1 960
3 TraesCS7D01G198700 chr4A 704408720 704409676 956 True 1585.000000 1585 96.555000 1778 2735 1 chr4A.!!$R3 957
4 TraesCS7D01G198700 chr5A 550034861 550036884 2023 False 2774.000000 2774 91.476000 3 2033 1 chr5A.!!$F4 2030
5 TraesCS7D01G198700 chr5A 516903648 516904604 956 False 1602.000000 1602 96.868000 1775 2732 1 chr5A.!!$F3 957
6 TraesCS7D01G198700 chr5A 69012881 69014019 1138 True 1496.000000 1496 90.647000 3 1126 1 chr5A.!!$R1 1123
7 TraesCS7D01G198700 chr5A 12619034 12620171 1137 False 1452.000000 1452 89.948000 3 1126 1 chr5A.!!$F1 1123
8 TraesCS7D01G198700 chr5A 75781193 75784847 3654 True 1291.000000 2242 92.936000 3 2955 2 chr5A.!!$R2 2952
9 TraesCS7D01G198700 chr4B 646747838 646749842 2004 True 2671.000000 2671 90.750000 3 2029 1 chr4B.!!$R2 2026
10 TraesCS7D01G198700 chr2B 757722454 757724467 2013 False 2643.000000 2643 90.432000 3 2033 1 chr2B.!!$F4 2030
11 TraesCS7D01G198700 chr2B 690570951 690571957 1006 False 1548.000000 1548 94.180000 1004 2033 1 chr2B.!!$F3 1029
12 TraesCS7D01G198700 chr2B 174400141 174400943 802 True 620.000000 907 94.338000 2961 3808 2 chr2B.!!$R2 847
13 TraesCS7D01G198700 chr3A 56503419 56504495 1076 False 1537.000000 1537 92.245000 4728 5830 1 chr3A.!!$F1 1102
14 TraesCS7D01G198700 chr3A 241729658 241732602 2944 False 1133.500000 2156 93.895500 161 2813 2 chr3A.!!$F5 2652
15 TraesCS7D01G198700 chr3A 56495077 56496492 1415 False 1067.000000 1445 94.904500 3245 4604 2 chr3A.!!$F4 1359
16 TraesCS7D01G198700 chr3A 216934263 216934789 526 False 750.000000 750 92.439000 5306 5830 1 chr3A.!!$F2 524
17 TraesCS7D01G198700 chr3A 217009694 217010220 526 False 750.000000 750 92.439000 5306 5830 1 chr3A.!!$F3 524
18 TraesCS7D01G198700 chr3A 570022010 570022986 976 True 726.500000 885 94.066000 2957 5280 2 chr3A.!!$R3 2323
19 TraesCS7D01G198700 chr3A 729875929 729876465 536 True 508.000000 508 83.859000 4745 5280 1 chr3A.!!$R2 535
20 TraesCS7D01G198700 chr1D 10038174 10041084 2910 False 1471.666667 1917 94.814000 3009 5830 3 chr1D.!!$F1 2821
21 TraesCS7D01G198700 chr1D 9920235 9923049 2814 True 1438.333333 1945 94.947667 3012 5747 3 chr1D.!!$R2 2735
22 TraesCS7D01G198700 chr5B 505280642 505281596 954 True 1616.000000 1616 97.182000 1778 2735 1 chr5B.!!$R1 957
23 TraesCS7D01G198700 chr5B 453113329 453115954 2625 True 1259.666667 1868 92.471667 3012 5594 3 chr5B.!!$R2 2582
24 TraesCS7D01G198700 chr4D 294030936 294032407 1471 True 1171.500000 1757 95.804000 4386 5830 2 chr4D.!!$R1 1444
25 TraesCS7D01G198700 chr5D 123154865 123156344 1479 False 1172.000000 1740 95.715000 4380 5830 2 chr5D.!!$F1 1450
26 TraesCS7D01G198700 chr6A 47992775 47994096 1321 True 875.500000 1640 97.284500 1778 2813 2 chr6A.!!$R4 1035
27 TraesCS7D01G198700 chr3B 739879964 739880920 956 True 1629.000000 1629 97.390000 1778 2735 1 chr3B.!!$R1 957
28 TraesCS7D01G198700 chr7A 692988774 692990899 2125 True 1277.500000 1312 91.478000 3 2033 2 chr7A.!!$R7 2030
29 TraesCS7D01G198700 chr7A 621159015 621160335 1320 True 861.500000 1613 97.000000 1778 2812 2 chr7A.!!$R6 1034
30 TraesCS7D01G198700 chr7A 346316538 346317075 537 True 785.000000 785 92.989000 1232 1772 1 chr7A.!!$R3 540
31 TraesCS7D01G198700 chr1B 650783242 650784563 1321 True 857.000000 1604 96.895500 1778 2812 2 chr1B.!!$R2 1034
32 TraesCS7D01G198700 chr6B 14047876 14049194 1318 True 846.500000 1583 96.739000 1778 2812 2 chr6B.!!$R3 1034
33 TraesCS7D01G198700 chr1A 310698670 310699804 1134 False 1437.000000 1437 89.773000 3 1126 1 chr1A.!!$F2 1123
34 TraesCS7D01G198700 chr2D 72856995 72858410 1415 True 892.500000 1208 95.212500 4386 5830 2 chr2D.!!$R2 1444
35 TraesCS7D01G198700 chr2D 121003950 121004804 854 True 706.350000 1334 95.361500 2956 3808 2 chr2D.!!$R3 852
36 TraesCS7D01G198700 chr2A 137272147 137273109 962 True 1297.000000 1297 91.088000 3 959 1 chr2A.!!$R1 956
37 TraesCS7D01G198700 chr2A 315963551 315964076 525 False 771.000000 771 93.169000 5306 5830 1 chr2A.!!$F2 524
38 TraesCS7D01G198700 chr2A 125209043 125209713 670 True 556.850000 1035 95.163500 3137 3808 2 chr2A.!!$R2 671
39 TraesCS7D01G198700 chr3D 600126074 600126618 544 True 494.000000 494 83.514000 4746 5280 1 chr3D.!!$R1 534

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
978 993 0.324830 CCTCTCGAACCCCTCTCCTT 60.325 60.000 0.00 0.0 0.00 3.36 F
979 994 1.562783 CTCTCGAACCCCTCTCCTTT 58.437 55.000 0.00 0.0 0.00 3.11 F
1898 2496 1.614413 AGTCTTCCAAGGTCTGTCGTC 59.386 52.381 0.00 0.0 0.00 4.20 F
2956 3845 0.745845 GCTCATGTGTGCTCCGGATT 60.746 55.000 3.57 0.0 0.00 3.01 F
4258 5230 0.771755 TATCCCTCGCTCTAGCTCCA 59.228 55.000 0.00 0.0 39.32 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1898 2496 0.317160 TGTGAACACTAGCAGGACGG 59.683 55.000 6.51 0.0 0.00 4.79 R
2838 3727 1.863454 GGCAACGTAGATCATCAGCAG 59.137 52.381 0.00 0.0 0.00 4.24 R
3372 4269 1.457346 CTGGAGTAAAGGCCAAGCAG 58.543 55.000 5.01 0.0 32.95 4.24 R
4616 5593 0.378257 GCAGCACCATGTTACCATCG 59.622 55.000 0.00 0.0 0.00 3.84 R
5152 6180 1.313772 TGCAACACATTTACCGCAGT 58.686 45.000 0.00 0.0 0.00 4.40 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
22 23 3.853355 AACATTGTTTGCCATCCCAAA 57.147 38.095 0.00 0.00 32.66 3.28
92 98 5.892686 TGTGGCCATAAGATTGATCATTTGA 59.107 36.000 9.72 0.00 0.00 2.69
109 115 6.160684 TCATTTGACTTGAAAGCCATGAATG 58.839 36.000 0.00 0.00 0.00 2.67
131 137 8.510243 AATGTTCACACATGATAGCTCATTTA 57.490 30.769 0.00 0.00 43.34 1.40
218 224 7.355017 GTCACATATAATGACACAATGCGAAT 58.645 34.615 13.14 0.00 44.87 3.34
237 243 8.370493 TGCGAATGTTTTCCAAATTTTTGATA 57.630 26.923 4.63 0.00 40.55 2.15
290 297 1.950472 GTTCAAAACGTCGAGCATGG 58.050 50.000 0.00 0.00 0.00 3.66
318 325 7.562135 GTTCCTACCTAGTGGTTGAATATTGA 58.438 38.462 0.00 0.00 46.05 2.57
319 326 7.361457 TCCTACCTAGTGGTTGAATATTGAG 57.639 40.000 0.00 0.00 46.05 3.02
433 442 2.295909 TCAAATTTGACCCGCTTTCAGG 59.704 45.455 16.91 0.00 31.01 3.86
522 531 8.298729 TGGTCAATTGTACATTAAATATGGCA 57.701 30.769 5.13 0.00 0.00 4.92
800 815 9.409312 CAAAATAGCTGACATGATTTTAACACA 57.591 29.630 0.00 0.00 31.86 3.72
963 978 2.520549 ACCAACCCTAGCTCTATCCTCT 59.479 50.000 0.00 0.00 0.00 3.69
964 979 3.161866 CCAACCCTAGCTCTATCCTCTC 58.838 54.545 0.00 0.00 0.00 3.20
966 981 2.340731 ACCCTAGCTCTATCCTCTCGA 58.659 52.381 0.00 0.00 0.00 4.04
967 982 2.712087 ACCCTAGCTCTATCCTCTCGAA 59.288 50.000 0.00 0.00 0.00 3.71
968 983 3.078837 CCCTAGCTCTATCCTCTCGAAC 58.921 54.545 0.00 0.00 0.00 3.95
969 984 3.078837 CCTAGCTCTATCCTCTCGAACC 58.921 54.545 0.00 0.00 0.00 3.62
970 985 1.989706 AGCTCTATCCTCTCGAACCC 58.010 55.000 0.00 0.00 0.00 4.11
971 986 0.963225 GCTCTATCCTCTCGAACCCC 59.037 60.000 0.00 0.00 0.00 4.95
973 988 2.510613 CTCTATCCTCTCGAACCCCTC 58.489 57.143 0.00 0.00 0.00 4.30
978 993 0.324830 CCTCTCGAACCCCTCTCCTT 60.325 60.000 0.00 0.00 0.00 3.36
979 994 1.562783 CTCTCGAACCCCTCTCCTTT 58.437 55.000 0.00 0.00 0.00 3.11
1336 1510 2.031163 ACGCTTGTGGAGGCAGAC 59.969 61.111 0.00 0.00 0.00 3.51
1898 2496 1.614413 AGTCTTCCAAGGTCTGTCGTC 59.386 52.381 0.00 0.00 0.00 4.20
1930 2528 3.118038 AGTGTTCACAGCCTTCCAAGTTA 60.118 43.478 5.74 0.00 0.00 2.24
1940 2538 2.042433 CCTTCCAAGTTAATGGGGGTCA 59.958 50.000 0.00 0.00 41.05 4.02
2117 2717 2.611518 GACTATCGCAGTTGCTTCTGT 58.388 47.619 2.29 0.00 37.72 3.41
2353 2953 2.822707 AGCGGTAGAAGAGGGAGTTA 57.177 50.000 0.00 0.00 0.00 2.24
2548 3149 9.678260 AATGTGATATATAGATTCTTCCCTTGC 57.322 33.333 0.00 0.00 0.00 4.01
2818 3707 9.783256 GTATTGTTTTGTAATGGATTAGTGACC 57.217 33.333 0.00 0.00 0.00 4.02
2819 3708 6.489127 TGTTTTGTAATGGATTAGTGACCG 57.511 37.500 0.00 0.00 0.00 4.79
2838 3727 4.840271 ACCGGCCTAAATGCTTATATACC 58.160 43.478 0.00 0.00 0.00 2.73
2841 3730 4.332819 CGGCCTAAATGCTTATATACCTGC 59.667 45.833 0.00 0.00 0.00 4.85
2853 3742 6.915300 GCTTATATACCTGCTGATGATCTACG 59.085 42.308 0.00 0.00 0.00 3.51
2912 3801 4.062991 CGAGCATGTACTATTTAACCCCC 58.937 47.826 0.00 0.00 0.00 5.40
2955 3844 1.153289 GCTCATGTGTGCTCCGGAT 60.153 57.895 3.57 0.00 0.00 4.18
2956 3845 0.745845 GCTCATGTGTGCTCCGGATT 60.746 55.000 3.57 0.00 0.00 3.01
2957 3846 1.473257 GCTCATGTGTGCTCCGGATTA 60.473 52.381 3.57 0.00 0.00 1.75
2958 3847 2.905075 CTCATGTGTGCTCCGGATTAA 58.095 47.619 3.57 0.00 0.00 1.40
2959 3848 2.868583 CTCATGTGTGCTCCGGATTAAG 59.131 50.000 3.57 0.00 0.00 1.85
3061 3950 8.725405 TTATTGTGTCTGTTTGACTTGAGTTA 57.275 30.769 0.00 0.00 45.54 2.24
3372 4269 6.404708 AGACATGCATATCATCATACTGGAC 58.595 40.000 7.88 0.00 31.79 4.02
3414 4311 4.932200 GCATGTGCTAGGATATACAAGACC 59.068 45.833 0.00 0.00 38.21 3.85
3545 4443 9.794719 AGGTTGATAAGGGCTTAAATAAGTATC 57.205 33.333 2.42 3.00 35.75 2.24
3750 4660 6.385176 TCTTTTCATCCTCACATGATACCTCT 59.615 38.462 0.00 0.00 32.69 3.69
3810 4720 6.320672 AGAACATCAAGTGAATCATTGGGATC 59.679 38.462 0.00 0.00 34.28 3.36
3912 4822 9.404348 CTGCTATTGTCATATCTACTACTTGTG 57.596 37.037 0.00 0.00 0.00 3.33
3983 4893 1.772182 ACGCTGAGATATAACGCTGC 58.228 50.000 5.74 5.74 0.00 5.25
3992 4902 3.569701 AGATATAACGCTGCCAATTTGGG 59.430 43.478 17.03 2.63 38.19 4.12
4082 4992 9.308318 GATCTTAGGATGTTAAAGACTTCTGTC 57.692 37.037 0.00 0.00 36.56 3.51
4178 5150 6.476378 ACTGCTAGTGTTACAAATCCTTCAT 58.524 36.000 0.00 0.00 0.00 2.57
4180 5152 5.647658 TGCTAGTGTTACAAATCCTTCATGG 59.352 40.000 0.00 0.00 37.10 3.66
4224 5196 0.944311 CACAAGACGACCAAGGTCCG 60.944 60.000 13.35 10.74 41.76 4.79
4258 5230 0.771755 TATCCCTCGCTCTAGCTCCA 59.228 55.000 0.00 0.00 39.32 3.86
4730 5740 2.040178 CCCACCTAGTTTATCGGCTCT 58.960 52.381 0.00 0.00 0.00 4.09
4776 5789 1.001641 AAGACTCATGGTGCTGGCC 60.002 57.895 0.00 0.00 0.00 5.36
4841 5864 6.264292 TGTTGTTGTATGGGGATATATGCAAC 59.736 38.462 6.56 9.13 44.69 4.17
4863 5888 4.019321 ACAGCTATGTAACATGTGGGTTCT 60.019 41.667 0.00 0.00 38.09 3.01
4876 5901 1.705186 TGGGTTCTAAGCCTGCTCTTT 59.295 47.619 11.89 0.00 46.54 2.52
5152 6180 7.828717 TGACTGGATGCTTTAAAATATGAGTCA 59.171 33.333 0.00 0.00 34.16 3.41
5178 6206 4.606961 CGGTAAATGTGTTGCAAAGTCTT 58.393 39.130 0.00 0.00 0.00 3.01
5217 6246 4.212425 CACATGCATTTGTTTGTCATGCTT 59.788 37.500 4.61 0.00 38.88 3.91
5222 6251 4.965158 GCATTTGTTTGTCATGCTTTGTTG 59.035 37.500 0.00 0.00 35.55 3.33
5311 6340 7.654022 ATTTTTCCTGGTAACTCTGTCAAAA 57.346 32.000 0.00 0.00 37.61 2.44
5323 6352 4.141482 ACTCTGTCAAAAACTTAGAGCCCA 60.141 41.667 0.00 0.00 38.70 5.36
5352 6381 3.730215 TGCTCAACCCCTAAATTGCTA 57.270 42.857 0.00 0.00 0.00 3.49
5451 6486 5.106157 GCATGGTACTAGCTGAATTTGTGTT 60.106 40.000 0.00 0.00 0.00 3.32
5523 6561 6.866770 GGTATTTTGGCTCCAGTTTTTCTAAC 59.133 38.462 0.00 0.00 0.00 2.34
5633 6671 2.267324 GTCCTGACAGGAGCAGGC 59.733 66.667 24.95 8.84 46.90 4.85
5700 6743 9.171701 GAACATAGCTCGTAACTATCTTGTTAG 57.828 37.037 0.00 0.00 33.67 2.34
5785 6828 3.087370 TGTAGAGCTTCTGGTAGAGCA 57.913 47.619 0.00 0.00 0.00 4.26
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.951775 TGGGATGGCAAACAATGTTAC 57.048 42.857 0.00 0.00 0.00 2.50
92 98 4.341806 TGTGAACATTCATGGCTTTCAAGT 59.658 37.500 0.00 0.00 39.73 3.16
109 115 8.146479 TCATAAATGAGCTATCATGTGTGAAC 57.854 34.615 5.64 0.00 44.07 3.18
281 288 2.055633 TAGGAACGGCCATGCTCGA 61.056 57.895 2.24 0.00 40.02 4.04
284 291 0.689745 TAGGTAGGAACGGCCATGCT 60.690 55.000 2.24 3.87 40.02 3.79
433 442 2.223377 AGACAAATTTTCGCCGACTCAC 59.777 45.455 0.00 0.00 0.00 3.51
650 660 8.600449 TTGGAATAAAAACAATGTTGCCTAAG 57.400 30.769 0.00 0.00 0.00 2.18
835 850 9.150348 CCAATCATAATGCAGTATGACGTTATA 57.850 33.333 32.40 13.99 41.97 0.98
963 978 2.025636 AAGAAAGGAGAGGGGTTCGA 57.974 50.000 0.00 0.00 0.00 3.71
964 979 2.303311 AGAAAGAAAGGAGAGGGGTTCG 59.697 50.000 0.00 0.00 0.00 3.95
966 981 4.447908 GGAAAGAAAGAAAGGAGAGGGGTT 60.448 45.833 0.00 0.00 0.00 4.11
967 982 3.074687 GGAAAGAAAGAAAGGAGAGGGGT 59.925 47.826 0.00 0.00 0.00 4.95
968 983 3.562393 GGGAAAGAAAGAAAGGAGAGGGG 60.562 52.174 0.00 0.00 0.00 4.79
969 984 3.074538 TGGGAAAGAAAGAAAGGAGAGGG 59.925 47.826 0.00 0.00 0.00 4.30
970 985 4.075682 GTGGGAAAGAAAGAAAGGAGAGG 58.924 47.826 0.00 0.00 0.00 3.69
971 986 4.075682 GGTGGGAAAGAAAGAAAGGAGAG 58.924 47.826 0.00 0.00 0.00 3.20
973 988 2.814336 CGGTGGGAAAGAAAGAAAGGAG 59.186 50.000 0.00 0.00 0.00 3.69
978 993 2.578786 GGTTCGGTGGGAAAGAAAGAA 58.421 47.619 0.00 0.00 36.14 2.52
979 994 1.541670 CGGTTCGGTGGGAAAGAAAGA 60.542 52.381 0.00 0.00 36.14 2.52
1898 2496 0.317160 TGTGAACACTAGCAGGACGG 59.683 55.000 6.51 0.00 0.00 4.79
1930 2528 3.044894 ACAAACAAACATGACCCCCATT 58.955 40.909 0.00 0.00 31.94 3.16
1940 2538 8.145767 AGAATCATCACATGAACAAACAAACAT 58.854 29.630 0.00 0.00 43.50 2.71
2117 2717 2.739849 TTCCTGATGCCCGCGAAACA 62.740 55.000 8.23 2.21 0.00 2.83
2548 3149 6.507023 ACAGTTTCTGGCAATCAGTTAAAAG 58.493 36.000 1.90 0.00 43.76 2.27
2742 3344 6.128661 GCAAACATGATTGGCAGCAATATATG 60.129 38.462 16.42 0.00 0.00 1.78
2745 3347 4.124238 GCAAACATGATTGGCAGCAATAT 58.876 39.130 16.42 0.00 0.00 1.28
2746 3348 3.196039 AGCAAACATGATTGGCAGCAATA 59.804 39.130 16.42 0.00 0.00 1.90
2814 3703 4.634012 ATATAAGCATTTAGGCCGGTCA 57.366 40.909 9.71 0.00 0.00 4.02
2818 3707 4.332819 GCAGGTATATAAGCATTTAGGCCG 59.667 45.833 0.00 0.00 0.00 6.13
2819 3708 5.355350 CAGCAGGTATATAAGCATTTAGGCC 59.645 44.000 0.00 0.00 0.00 5.19
2838 3727 1.863454 GGCAACGTAGATCATCAGCAG 59.137 52.381 0.00 0.00 0.00 4.24
2841 3730 2.286294 GCAAGGCAACGTAGATCATCAG 59.714 50.000 0.00 0.00 46.39 2.90
2853 3742 3.119029 ACATCCATTACATGCAAGGCAAC 60.119 43.478 0.00 0.00 43.62 4.17
2912 3801 1.992667 TGTTTGCGTGATTAGCTCTCG 59.007 47.619 0.00 0.00 42.33 4.04
2955 3844 5.258051 ACAGAACAACACCAGGAAACTTAA 58.742 37.500 0.00 0.00 40.21 1.85
2956 3845 4.850680 ACAGAACAACACCAGGAAACTTA 58.149 39.130 0.00 0.00 40.21 2.24
2957 3846 3.697166 ACAGAACAACACCAGGAAACTT 58.303 40.909 0.00 0.00 40.21 2.66
2958 3847 3.366052 ACAGAACAACACCAGGAAACT 57.634 42.857 0.00 0.00 46.44 2.66
2959 3848 3.428862 CCAACAGAACAACACCAGGAAAC 60.429 47.826 0.00 0.00 0.00 2.78
3061 3950 3.007614 ACAAGCGACCCTAACTGTACAAT 59.992 43.478 0.00 0.00 0.00 2.71
3372 4269 1.457346 CTGGAGTAAAGGCCAAGCAG 58.543 55.000 5.01 0.00 32.95 4.24
3517 4415 8.521170 ACTTATTTAAGCCCTTATCAACCTTC 57.479 34.615 0.00 0.00 36.79 3.46
3800 4710 3.765381 TGCAAGAAACAGATCCCAATGA 58.235 40.909 0.00 0.00 0.00 2.57
3810 4720 6.744537 GCTTCACAAGTATATGCAAGAAACAG 59.255 38.462 0.00 0.00 0.00 3.16
3856 4766 3.327757 TCAAAGTGCTCCTGTTACCAGAT 59.672 43.478 0.00 0.00 41.50 2.90
3983 4893 3.189285 CTGCGCTATTTTCCCAAATTGG 58.811 45.455 9.73 4.74 34.29 3.16
3992 4902 5.163854 TGCTTCTTAAGACTGCGCTATTTTC 60.164 40.000 9.73 0.00 0.00 2.29
4082 4992 7.993101 ACACATGGTTCAAGAAGAATGATATG 58.007 34.615 0.00 0.00 38.76 1.78
4178 5150 3.455910 AGCAGGAGTATTCAATAGCACCA 59.544 43.478 0.00 0.00 0.00 4.17
4180 5152 3.249559 GCAGCAGGAGTATTCAATAGCAC 59.750 47.826 0.00 0.00 0.00 4.40
4224 5196 0.600782 GGATAGCAGCAGAGCAGAGC 60.601 60.000 0.00 0.00 36.85 4.09
4258 5230 3.435105 TTTTCTTGTGCAGCAACGAAT 57.565 38.095 0.00 0.00 32.90 3.34
4616 5593 0.378257 GCAGCACCATGTTACCATCG 59.622 55.000 0.00 0.00 0.00 3.84
4722 5699 3.589988 CAACTACAAGTCAAGAGCCGAT 58.410 45.455 0.00 0.00 0.00 4.18
4723 5700 2.288825 CCAACTACAAGTCAAGAGCCGA 60.289 50.000 0.00 0.00 0.00 5.54
4724 5701 2.069273 CCAACTACAAGTCAAGAGCCG 58.931 52.381 0.00 0.00 0.00 5.52
4730 5740 4.020839 GCTACCTACCCAACTACAAGTCAA 60.021 45.833 0.00 0.00 0.00 3.18
4776 5789 4.630894 TGCATATAAACTTTTGCTCCCG 57.369 40.909 0.00 0.00 36.10 5.14
4841 5864 4.517285 AGAACCCACATGTTACATAGCTG 58.483 43.478 0.00 0.00 0.00 4.24
5048 6076 8.893219 TCAGATATACAGAAACCATGCTTAAG 57.107 34.615 0.00 0.00 0.00 1.85
5152 6180 1.313772 TGCAACACATTTACCGCAGT 58.686 45.000 0.00 0.00 0.00 4.40
5178 6206 4.582240 TGCATGTGTTTCTGAAACCACATA 59.418 37.500 29.25 20.93 39.15 2.29
5217 6246 5.473504 GGAGCTTTATCTTGAGGAACAACAA 59.526 40.000 0.00 0.00 34.56 2.83
5222 6251 5.707764 ACAAAGGAGCTTTATCTTGAGGAAC 59.292 40.000 0.00 0.00 31.96 3.62
5311 6340 4.265073 CAAAGCTACATGGGCTCTAAGTT 58.735 43.478 14.25 4.13 39.30 2.66
5323 6352 1.355720 AGGGGTTGAGCAAAGCTACAT 59.644 47.619 0.00 0.00 39.88 2.29
5352 6381 4.389890 TTGAGCAATTTGAAACAGCAGT 57.610 36.364 0.00 0.00 0.00 4.40
5523 6561 7.119553 AGCTTTAAAAAGATCAGCAGAGAAGAG 59.880 37.037 6.64 0.00 38.28 2.85
5633 6671 2.675767 TAGCGATCGTAAACTAGGCG 57.324 50.000 17.81 0.00 0.00 5.52
5700 6743 3.435671 GGTTACAAGCTCCACATGTGTAC 59.564 47.826 23.79 12.68 0.00 2.90
5754 6797 7.324178 ACCAGAAGCTCTACAAGTGTAATAAG 58.676 38.462 0.00 0.00 0.00 1.73
5785 6828 8.148351 ACACGTAATAAGCTCCAACATATACAT 58.852 33.333 0.00 0.00 0.00 2.29


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

AutoCloner maintained by Alex Coulton.