Multiple sequence alignment - TraesCS1A01G375500

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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 TraesCS1A01G375500 chr1A 100.000 5534 0 0 1 5534 550297300 550302833 0.000000e+00 10220
1 TraesCS1A01G375500 chr1A 97.007 1203 32 4 3098 4297 557915073 557913872 0.000000e+00 2019
2 TraesCS1A01G375500 chr1A 96.093 1203 45 2 3097 4298 321899565 321900766 0.000000e+00 1960
3 TraesCS1A01G375500 chr1A 82.585 1872 197 52 1286 3097 550137418 550135616 0.000000e+00 1531
4 TraesCS1A01G375500 chr1A 84.225 1420 159 27 1705 3097 550217692 550219073 0.000000e+00 1321
5 TraesCS1A01G375500 chr1A 91.829 514 35 3 979 1491 550216958 550217465 0.000000e+00 710
6 TraesCS1A01G375500 chr1A 83.356 727 75 26 1789 2507 550209993 550210681 1.010000e-176 630
7 TraesCS1A01G375500 chr1A 86.949 544 51 10 915 1454 550203602 550204129 1.330000e-165 593
8 TraesCS1A01G375500 chr1A 85.124 484 41 15 4291 4747 550219056 550219535 3.020000e-127 466
9 TraesCS1A01G375500 chr1A 86.945 383 31 14 829 1209 550137788 550137423 3.990000e-111 412
10 TraesCS1A01G375500 chr1A 86.989 269 32 3 1450 1717 550209382 550209648 3.240000e-77 300
11 TraesCS1A01G375500 chr1A 87.004 277 22 8 13 282 550216438 550216707 3.240000e-77 300
12 TraesCS1A01G375500 chr1A 92.647 204 15 0 1480 1683 550217424 550217627 1.510000e-75 294
13 TraesCS1A01G375500 chr1A 87.302 252 25 5 333 580 550216713 550216961 1.170000e-71 281
14 TraesCS1A01G375500 chr1A 77.326 344 62 9 2767 3098 294041543 294041882 7.320000e-44 189
15 TraesCS1A01G375500 chr1A 82.022 178 22 5 115 285 550138186 550138012 5.780000e-30 143
16 TraesCS1A01G375500 chr1A 88.421 95 9 1 4745 4837 550219577 550219671 4.530000e-21 113
17 TraesCS1A01G375500 chr1D 97.436 1638 34 2 1467 3097 457844632 457846268 0.000000e+00 2785
18 TraesCS1A01G375500 chr1D 82.340 1863 199 57 1286 3097 457548198 457546415 0.000000e+00 1498
19 TraesCS1A01G375500 chr1D 83.691 1398 146 52 122 1477 457581662 457583019 0.000000e+00 1243
20 TraesCS1A01G375500 chr1D 98.033 661 11 1 4298 4958 457846260 457846918 0.000000e+00 1147
21 TraesCS1A01G375500 chr1D 85.553 796 78 16 915 1679 457812138 457812927 0.000000e+00 798
22 TraesCS1A01G375500 chr1D 85.030 668 69 16 1789 2455 457583264 457583901 0.000000e+00 651
23 TraesCS1A01G375500 chr1D 82.944 727 79 26 1789 2507 457820592 457821281 1.020000e-171 614
24 TraesCS1A01G375500 chr1D 84.318 440 63 4 2088 2527 208415555 208415122 5.120000e-115 425
25 TraesCS1A01G375500 chr1D 84.475 438 53 11 2100 2524 226944387 226944822 8.570000e-113 418
26 TraesCS1A01G375500 chr1D 83.700 454 58 12 2088 2527 261723913 261724364 1.110000e-111 414
27 TraesCS1A01G375500 chr1D 86.684 383 31 14 829 1209 457548567 457548203 1.860000e-109 407
28 TraesCS1A01G375500 chr1D 83.834 433 62 5 2100 2527 226468423 226468852 6.680000e-109 405
29 TraesCS1A01G375500 chr1D 86.253 371 47 3 2088 2456 226826500 226826868 3.110000e-107 399
30 TraesCS1A01G375500 chr1D 80.174 575 71 22 1576 2122 226467834 226468393 1.870000e-104 390
31 TraesCS1A01G375500 chr1D 82.135 459 59 13 4301 4742 457546420 457545968 6.770000e-99 372
32 TraesCS1A01G375500 chr1D 88.462 286 29 2 915 1199 457811626 457811908 5.310000e-90 342
33 TraesCS1A01G375500 chr1D 81.752 411 51 12 4305 4691 457584459 457584869 6.920000e-84 322
34 TraesCS1A01G375500 chr1D 85.870 276 31 5 1480 1751 457582992 457583263 2.520000e-73 287
35 TraesCS1A01G375500 chr1D 92.453 159 7 1 13 171 457844481 457844634 7.220000e-54 222
36 TraesCS1A01G375500 chr1D 80.471 297 46 7 2813 3098 208413055 208412760 3.360000e-52 217
37 TraesCS1A01G375500 chr1D 84.052 232 27 5 1011 1242 226467588 226467809 1.210000e-51 215
38 TraesCS1A01G375500 chr1D 78.994 338 49 12 2774 3098 223164437 223164765 1.560000e-50 211
39 TraesCS1A01G375500 chr1D 96.000 125 5 0 3936 4060 12065706 12065582 2.610000e-48 204
40 TraesCS1A01G375500 chr1D 79.461 297 50 4 2812 3098 227375817 227376112 3.380000e-47 200
41 TraesCS1A01G375500 chr1D 94.030 134 5 1 3927 4060 462735674 462735544 3.380000e-47 200
42 TraesCS1A01G375500 chr1D 86.264 182 19 6 4291 4468 457821834 457822013 5.660000e-45 193
43 TraesCS1A01G375500 chr1D 80.451 266 29 10 154 410 457806983 457807234 1.220000e-41 182
44 TraesCS1A01G375500 chr1D 82.123 179 22 7 115 285 457548992 457548816 1.610000e-30 145
45 TraesCS1A01G375500 chr1D 79.327 208 38 5 981 1183 227653051 227653258 2.080000e-29 141
46 TraesCS1A01G375500 chr1D 74.696 411 57 23 2701 3098 227649713 227650089 7.480000e-29 139
47 TraesCS1A01G375500 chr1B 90.514 1634 110 15 1484 3095 627923420 627925030 0.000000e+00 2117
48 TraesCS1A01G375500 chr1B 81.562 1421 164 51 1705 3097 627782272 627783622 0.000000e+00 1083
49 TraesCS1A01G375500 chr1B 82.895 1140 105 38 2016 3097 627157128 627156021 0.000000e+00 942
50 TraesCS1A01G375500 chr1B 85.619 904 92 23 320 1199 627922358 627923247 0.000000e+00 915
51 TraesCS1A01G375500 chr1B 93.677 601 36 2 3098 3698 49344014 49344612 0.000000e+00 898
52 TraesCS1A01G375500 chr1B 82.579 729 80 31 1789 2507 627886504 627887195 2.850000e-167 599
53 TraesCS1A01G375500 chr1B 89.646 396 34 5 1286 1676 627157791 627157398 1.070000e-136 497
54 TraesCS1A01G375500 chr1B 84.545 440 65 3 2088 2527 327343235 327343671 3.060000e-117 433
55 TraesCS1A01G375500 chr1B 88.022 359 24 8 4553 4901 627925309 627925658 1.860000e-109 407
56 TraesCS1A01G375500 chr1B 93.704 270 17 0 4298 4567 627925024 627925293 6.680000e-109 405
57 TraesCS1A01G375500 chr1B 87.749 351 33 5 909 1254 627885354 627885699 8.640000e-108 401
58 TraesCS1A01G375500 chr1B 83.736 455 42 11 1250 1683 627885858 627886301 8.640000e-108 401
59 TraesCS1A01G375500 chr1B 93.388 242 11 4 4059 4298 36275843 36275605 2.450000e-93 353
60 TraesCS1A01G375500 chr1B 87.681 276 29 5 4291 4562 627783605 627783879 3.220000e-82 316
61 TraesCS1A01G375500 chr1B 79.665 418 65 10 4334 4742 627155985 627155579 3.260000e-72 283
62 TraesCS1A01G375500 chr1B 85.507 276 35 5 4291 4562 627887753 627888027 3.260000e-72 283
63 TraesCS1A01G375500 chr1B 84.429 289 34 2 2815 3094 627887481 627887767 1.960000e-69 274
64 TraesCS1A01G375500 chr1B 79.420 345 56 7 2766 3098 322475620 322475961 4.310000e-56 230
65 TraesCS1A01G375500 chr1B 79.070 344 56 10 2767 3098 327229748 327230087 7.220000e-54 222
66 TraesCS1A01G375500 chr1B 86.139 202 13 6 126 321 627922069 627922261 2.610000e-48 204
67 TraesCS1A01G375500 chr1B 80.066 301 33 11 112 399 627884708 627884994 1.220000e-46 198
68 TraesCS1A01G375500 chr1B 86.034 179 12 4 4578 4747 627888088 627888262 4.400000e-41 180
69 TraesCS1A01G375500 chr1B 81.991 211 30 7 1696 1901 627157410 627157203 7.370000e-39 172
70 TraesCS1A01G375500 chr1B 79.279 222 39 6 981 1195 327347918 327348139 1.240000e-31 148
71 TraesCS1A01G375500 chr5A 96.672 1202 37 3 3097 4297 564430633 564429434 0.000000e+00 1995
72 TraesCS1A01G375500 chr3B 92.874 1235 52 2 3098 4297 809150336 809151569 0.000000e+00 1760
73 TraesCS1A01G375500 chr3B 92.994 471 31 2 3098 3567 794286119 794285650 0.000000e+00 686
74 TraesCS1A01G375500 chr3B 95.015 341 16 1 3098 3438 33953823 33954162 8.160000e-148 534
75 TraesCS1A01G375500 chr3B 95.021 241 11 1 4059 4298 617377232 617377472 1.460000e-100 377
76 TraesCS1A01G375500 chr3B 94.421 233 12 1 4067 4298 487555519 487555287 1.900000e-94 357
77 TraesCS1A01G375500 chr3B 80.567 494 66 17 1482 1954 705148047 705148531 2.450000e-93 353
78 TraesCS1A01G375500 chr7A 95.660 576 22 2 4959 5534 2933606 2934178 0.000000e+00 922
79 TraesCS1A01G375500 chr7A 90.753 292 25 2 3636 3927 336000440 336000151 6.720000e-104 388
80 TraesCS1A01G375500 chr5B 92.537 603 42 2 3098 3698 507760507 507761108 0.000000e+00 861
81 TraesCS1A01G375500 chr5B 93.960 298 17 1 3621 3918 526767601 526767897 3.040000e-122 449
82 TraesCS1A01G375500 chr5B 87.156 109 14 0 4956 5064 594754893 594755001 2.090000e-24 124
83 TraesCS1A01G375500 chr2B 95.560 473 19 2 3096 3567 788847385 788846914 0.000000e+00 756
84 TraesCS1A01G375500 chr2B 87.625 501 39 6 5037 5524 784605475 784605965 1.350000e-155 560
85 TraesCS1A01G375500 chr2B 94.137 307 17 1 3621 3927 638416384 638416689 3.020000e-127 466
86 TraesCS1A01G375500 chr2B 93.000 300 20 1 3621 3920 638408253 638408551 2.370000e-118 436
87 TraesCS1A01G375500 chr2B 94.215 242 10 3 4059 4298 788844959 788844720 3.150000e-97 366
88 TraesCS1A01G375500 chr2A 88.795 589 47 6 4959 5534 514195681 514195099 0.000000e+00 704
89 TraesCS1A01G375500 chr2A 93.293 328 22 0 4958 5285 475929946 475930273 8.330000e-133 484
90 TraesCS1A01G375500 chr2A 93.272 327 18 3 4959 5285 718726428 718726106 3.880000e-131 479
91 TraesCS1A01G375500 chr2A 94.796 269 11 1 5266 5534 718725834 718725569 3.080000e-112 416
92 TraesCS1A01G375500 chr2A 94.052 269 13 1 5266 5534 475930545 475930810 6.680000e-109 405
93 TraesCS1A01G375500 chr3D 78.337 974 146 39 1011 1954 532869115 532870053 2.240000e-158 569
94 TraesCS1A01G375500 chr3D 84.722 432 58 4 2100 2526 532870236 532870664 5.120000e-115 425
95 TraesCS1A01G375500 chr3D 95.082 122 6 0 3936 4057 64758806 64758927 5.660000e-45 193
96 TraesCS1A01G375500 chr3D 79.781 183 22 7 731 899 532868893 532869074 9.740000e-23 119
97 TraesCS1A01G375500 chr4A 93.293 328 22 0 4958 5285 609633996 609633669 8.330000e-133 484
98 TraesCS1A01G375500 chr4A 94.052 269 13 1 5266 5534 609633397 609633132 6.680000e-109 405
99 TraesCS1A01G375500 chr4A 90.146 274 25 2 3361 3634 344446778 344447049 6.820000e-94 355
100 TraesCS1A01G375500 chr7D 79.562 685 88 26 1011 1681 90408613 90409259 5.090000e-120 442
101 TraesCS1A01G375500 chr5D 92.366 262 18 2 3666 3927 495358423 495358682 6.770000e-99 372
102 TraesCS1A01G375500 chr3A 82.327 447 62 9 1482 1912 668583194 668583639 6.770000e-99 372
103 TraesCS1A01G375500 chr3A 77.518 556 67 31 1604 2132 668225506 668226030 1.170000e-71 281
104 TraesCS1A01G375500 chr2D 91.870 246 15 3 4056 4298 164280666 164280909 6.870000e-89 339
105 TraesCS1A01G375500 chr2D 88.172 93 11 0 4958 5050 18357379 18357471 1.630000e-20 111
106 TraesCS1A01G375500 chr7B 87.129 202 24 1 1480 1681 41284987 41285186 1.550000e-55 228
107 TraesCS1A01G375500 chr7B 94.776 134 7 0 3927 4060 580167758 580167625 5.620000e-50 209
108 TraesCS1A01G375500 chr6D 95.200 125 6 0 3936 4060 380441798 380441922 1.220000e-46 198


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 TraesCS1A01G375500 chr1A 550297300 550302833 5533 False 10220.000000 10220 100.000000 1 5534 1 chr1A.!!$F4 5533
1 TraesCS1A01G375500 chr1A 557913872 557915073 1201 True 2019.000000 2019 97.007000 3098 4297 1 chr1A.!!$R1 1199
2 TraesCS1A01G375500 chr1A 321899565 321900766 1201 False 1960.000000 1960 96.093000 3097 4298 1 chr1A.!!$F2 1201
3 TraesCS1A01G375500 chr1A 550135616 550138186 2570 True 695.333333 1531 83.850667 115 3097 3 chr1A.!!$R2 2982
4 TraesCS1A01G375500 chr1A 550203602 550204129 527 False 593.000000 593 86.949000 915 1454 1 chr1A.!!$F3 539
5 TraesCS1A01G375500 chr1A 550216438 550219671 3233 False 497.857143 1321 88.078857 13 4837 7 chr1A.!!$F6 4824
6 TraesCS1A01G375500 chr1A 550209382 550210681 1299 False 465.000000 630 85.172500 1450 2507 2 chr1A.!!$F5 1057
7 TraesCS1A01G375500 chr1D 457844481 457846918 2437 False 1384.666667 2785 95.974000 13 4958 3 chr1D.!!$F12 4945
8 TraesCS1A01G375500 chr1D 457581662 457584869 3207 False 625.750000 1243 84.085750 122 4691 4 chr1D.!!$F9 4569
9 TraesCS1A01G375500 chr1D 457545968 457548992 3024 True 605.500000 1498 83.320500 115 4742 4 chr1D.!!$R4 4627
10 TraesCS1A01G375500 chr1D 457811626 457812927 1301 False 570.000000 798 87.007500 915 1679 2 chr1D.!!$F10 764
11 TraesCS1A01G375500 chr1D 457820592 457822013 1421 False 403.500000 614 84.604000 1789 4468 2 chr1D.!!$F11 2679
12 TraesCS1A01G375500 chr1D 226467588 226468852 1264 False 336.666667 405 82.686667 1011 2527 3 chr1D.!!$F7 1516
13 TraesCS1A01G375500 chr1D 208412760 208415555 2795 True 321.000000 425 82.394500 2088 3098 2 chr1D.!!$R3 1010
14 TraesCS1A01G375500 chr1B 49344014 49344612 598 False 898.000000 898 93.677000 3098 3698 1 chr1B.!!$F1 600
15 TraesCS1A01G375500 chr1B 627922069 627925658 3589 False 809.600000 2117 88.799600 126 4901 5 chr1B.!!$F8 4775
16 TraesCS1A01G375500 chr1B 627782272 627783879 1607 False 699.500000 1083 84.621500 1705 4562 2 chr1B.!!$F6 2857
17 TraesCS1A01G375500 chr1B 627155579 627157791 2212 True 473.500000 942 83.549250 1286 4742 4 chr1B.!!$R2 3456
18 TraesCS1A01G375500 chr1B 627884708 627888262 3554 False 333.714286 599 84.300000 112 4747 7 chr1B.!!$F7 4635
19 TraesCS1A01G375500 chr5A 564429434 564430633 1199 True 1995.000000 1995 96.672000 3097 4297 1 chr5A.!!$R1 1200
20 TraesCS1A01G375500 chr3B 809150336 809151569 1233 False 1760.000000 1760 92.874000 3098 4297 1 chr3B.!!$F4 1199
21 TraesCS1A01G375500 chr7A 2933606 2934178 572 False 922.000000 922 95.660000 4959 5534 1 chr7A.!!$F1 575
22 TraesCS1A01G375500 chr5B 507760507 507761108 601 False 861.000000 861 92.537000 3098 3698 1 chr5B.!!$F1 600
23 TraesCS1A01G375500 chr2B 788844720 788847385 2665 True 561.000000 756 94.887500 3096 4298 2 chr2B.!!$R1 1202
24 TraesCS1A01G375500 chr2A 514195099 514195681 582 True 704.000000 704 88.795000 4959 5534 1 chr2A.!!$R1 575
25 TraesCS1A01G375500 chr2A 718725569 718726428 859 True 447.500000 479 94.034000 4959 5534 2 chr2A.!!$R2 575
26 TraesCS1A01G375500 chr2A 475929946 475930810 864 False 444.500000 484 93.672500 4958 5534 2 chr2A.!!$F1 576
27 TraesCS1A01G375500 chr3D 532868893 532870664 1771 False 371.000000 569 80.946667 731 2526 3 chr3D.!!$F2 1795
28 TraesCS1A01G375500 chr4A 609633132 609633996 864 True 444.500000 484 93.672500 4958 5534 2 chr4A.!!$R1 576
29 TraesCS1A01G375500 chr7D 90408613 90409259 646 False 442.000000 442 79.562000 1011 1681 1 chr7D.!!$F1 670
30 TraesCS1A01G375500 chr3A 668225506 668226030 524 False 281.000000 281 77.518000 1604 2132 1 chr3A.!!$F1 528

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
434 587 0.385390 AGCACCCTTTTGCAGAAACG 59.615 50.0 0.00 0.0 45.62 3.60 F
1460 2433 0.250727 GGTGCCTGCAAGTAACTCCA 60.251 55.0 0.00 0.0 0.00 3.86 F
2430 3991 0.033366 AATTTGAAGTTGGCGGGCAC 59.967 50.0 2.73 0.0 0.00 5.01 F
3585 7253 2.500098 CACGAGGATAAGAAAGGGACCA 59.500 50.0 0.00 0.0 0.00 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2411 3972 0.033366 GTGCCCGCCAACTTCAAATT 59.967 50.000 0.00 0.00 0.00 1.82 R
3241 6875 0.323178 GTCCGTCCCCACTAGTCAGA 60.323 60.000 0.00 0.00 0.00 3.27 R
3595 7263 1.298014 CCCACTGGTGAGCTCCTTC 59.702 63.158 12.15 1.59 0.00 3.46 R
5211 10644 0.182061 AATCGCAGCCCATGACTGAT 59.818 50.000 17.02 2.97 37.32 2.90 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
55 56 4.336153 TGCACTGTGGCAATATGAATAGTG 59.664 41.667 10.21 0.00 41.65 2.74
293 334 4.082463 GCGATTCACACCAATCCCTTTTAA 60.082 41.667 0.00 0.00 30.03 1.52
294 335 5.640732 CGATTCACACCAATCCCTTTTAAG 58.359 41.667 0.00 0.00 30.03 1.85
295 336 5.183140 CGATTCACACCAATCCCTTTTAAGT 59.817 40.000 0.00 0.00 30.03 2.24
296 337 6.373216 CGATTCACACCAATCCCTTTTAAGTA 59.627 38.462 0.00 0.00 30.03 2.24
297 338 7.414098 CGATTCACACCAATCCCTTTTAAGTAG 60.414 40.741 0.00 0.00 30.03 2.57
298 339 5.566469 TCACACCAATCCCTTTTAAGTAGG 58.434 41.667 0.00 0.00 0.00 3.18
330 470 8.322906 TGTCAGGTTAAAAATATGAGACTGTG 57.677 34.615 0.00 0.00 0.00 3.66
402 554 2.786027 CGACAAGATGACTGCATACTCG 59.214 50.000 0.00 0.00 34.11 4.18
434 587 0.385390 AGCACCCTTTTGCAGAAACG 59.615 50.000 0.00 0.00 45.62 3.60
443 596 2.177394 TTGCAGAAACGCCATCAGTA 57.823 45.000 0.00 0.00 0.00 2.74
444 597 2.177394 TGCAGAAACGCCATCAGTAA 57.823 45.000 0.00 0.00 0.00 2.24
469 632 3.149196 ACAGTGTTGGTCCTAATGCTTG 58.851 45.455 0.00 0.00 0.00 4.01
472 635 3.569701 AGTGTTGGTCCTAATGCTTGTTG 59.430 43.478 0.00 0.00 0.00 3.33
473 636 3.317993 GTGTTGGTCCTAATGCTTGTTGT 59.682 43.478 0.00 0.00 0.00 3.32
474 637 4.517453 GTGTTGGTCCTAATGCTTGTTGTA 59.483 41.667 0.00 0.00 0.00 2.41
478 641 5.428253 TGGTCCTAATGCTTGTTGTAGATC 58.572 41.667 0.00 0.00 0.00 2.75
566 732 4.569564 CCTTAACATTCCGCTGTTAGGTAC 59.430 45.833 5.40 0.00 41.32 3.34
602 768 3.990469 CCGCGAATAAACTCAGATAGCAT 59.010 43.478 8.23 0.00 0.00 3.79
611 788 2.224719 ACTCAGATAGCATCCCAATGGC 60.225 50.000 0.00 0.00 33.19 4.40
614 791 1.160137 GATAGCATCCCAATGGCGAC 58.840 55.000 0.00 0.00 33.19 5.19
666 862 3.327757 ACCTTATCACTCTTGCCACTGAA 59.672 43.478 0.00 0.00 0.00 3.02
694 893 6.419771 GCGCTTAGTTCTCGCTATTTATTTT 58.580 36.000 0.00 0.00 44.79 1.82
728 927 4.391405 AAGTGGCCTCTTCAAAACAAAG 57.609 40.909 14.34 0.00 0.00 2.77
733 932 5.817296 GTGGCCTCTTCAAAACAAAGAAAAT 59.183 36.000 3.32 0.00 32.60 1.82
757 957 6.352016 AGAAGAAGAGAAGAGTGCATGTTA 57.648 37.500 0.00 0.00 0.00 2.41
778 978 3.495434 TGTCGTTTGTACCCCAGATTT 57.505 42.857 0.00 0.00 0.00 2.17
781 987 3.187842 GTCGTTTGTACCCCAGATTTGTC 59.812 47.826 0.00 0.00 0.00 3.18
795 1001 6.018751 CCCAGATTTGTCACATGATAACTACG 60.019 42.308 0.00 0.00 0.00 3.51
846 1059 8.143193 ACAAATCACTGTATGCAAGATTTTCAA 58.857 29.630 16.13 0.00 37.34 2.69
874 1087 9.299963 CATATAACATGAACATAGAGAGCTAGC 57.700 37.037 6.62 6.62 0.00 3.42
890 1103 2.158900 GCTAGCTATTCTGCACCCTTCA 60.159 50.000 7.70 0.00 34.99 3.02
930 1146 7.756272 TGAATATTGCAACTTGTTTATCTGCTG 59.244 33.333 0.00 0.00 34.10 4.41
1149 1879 3.523564 ACTGCTCTGGGTACAATTGGTAT 59.476 43.478 10.83 0.00 33.76 2.73
1162 1897 3.811722 ATTGGTATGCATCATAACGCG 57.188 42.857 0.19 3.53 36.88 6.01
1170 1905 2.744741 TGCATCATAACGCGAAAGGAAA 59.255 40.909 15.93 0.00 0.00 3.13
1340 2258 1.541147 CTCGCACACCCATGAAAACAT 59.459 47.619 0.00 0.00 0.00 2.71
1460 2433 0.250727 GGTGCCTGCAAGTAACTCCA 60.251 55.000 0.00 0.00 0.00 3.86
1461 2434 1.604604 GTGCCTGCAAGTAACTCCAA 58.395 50.000 0.00 0.00 0.00 3.53
1462 2435 1.953686 GTGCCTGCAAGTAACTCCAAA 59.046 47.619 0.00 0.00 0.00 3.28
1463 2436 2.030805 GTGCCTGCAAGTAACTCCAAAG 60.031 50.000 0.00 0.00 0.00 2.77
1464 2437 1.068264 GCCTGCAAGTAACTCCAAAGC 60.068 52.381 0.00 0.00 0.00 3.51
1465 2438 2.229792 CCTGCAAGTAACTCCAAAGCA 58.770 47.619 0.00 0.00 0.00 3.91
1544 2599 8.504815 CCATATGTTGCTCTTTCTCTTATGATG 58.495 37.037 1.24 0.00 0.00 3.07
1586 2641 1.960763 TCACACGGTGCATGCAGAC 60.961 57.895 23.41 16.31 32.98 3.51
1756 2954 2.292569 AGTGCATCACAAGTTTGAGCTG 59.707 45.455 0.00 0.00 36.74 4.24
1834 3223 6.265422 CCTTTTCCCATTAACAAGTCACTTCT 59.735 38.462 0.00 0.00 0.00 2.85
1836 3225 7.654022 TTTCCCATTAACAAGTCACTTCTTT 57.346 32.000 0.00 0.00 0.00 2.52
1932 3357 7.444792 ACCGTTATAGTCTTCCAGAGTACATAG 59.555 40.741 0.00 0.00 33.34 2.23
2006 3436 8.862325 TTTCATCTCTCCTTAAATGCTTAACA 57.138 30.769 0.00 0.00 0.00 2.41
2125 3626 6.555812 ACTTTTAACTAAACACAGCTAGCC 57.444 37.500 12.13 0.00 0.00 3.93
2411 3972 4.342951 TCAGAACTTTGTCCGTTCTCCTAA 59.657 41.667 2.70 0.00 45.81 2.69
2430 3991 0.033366 AATTTGAAGTTGGCGGGCAC 59.967 50.000 2.73 0.00 0.00 5.01
2636 4336 5.222027 TGTTGTCCCTTCAGATATTCCAACA 60.222 40.000 0.00 0.00 37.79 3.33
2874 6491 7.312154 CACATTCTTCAAATACATTTTCCCGA 58.688 34.615 0.00 0.00 0.00 5.14
2879 6496 6.311935 TCTTCAAATACATTTTCCCGAGTACG 59.688 38.462 0.00 0.00 39.43 3.67
3092 6726 9.629878 CTAGAACTACAAGTTAAGATCTCCCTA 57.370 37.037 0.00 0.00 38.80 3.53
3093 6727 8.528044 AGAACTACAAGTTAAGATCTCCCTAG 57.472 38.462 0.00 0.00 38.80 3.02
3094 6728 6.718522 ACTACAAGTTAAGATCTCCCTAGC 57.281 41.667 0.00 0.00 0.00 3.42
3241 6875 6.647481 GTGATTTAGCCCGTTTAACCATTTTT 59.353 34.615 0.00 0.00 0.00 1.94
3255 6889 3.655777 ACCATTTTTCTGACTAGTGGGGA 59.344 43.478 0.00 0.00 0.00 4.81
3388 7029 3.591254 GAAGAAGCAGGACGGCGGT 62.591 63.158 13.24 0.00 39.27 5.68
3585 7253 2.500098 CACGAGGATAAGAAAGGGACCA 59.500 50.000 0.00 0.00 0.00 4.02
4298 9584 2.627699 TGGTTTCTTGCAATTCACTCCC 59.372 45.455 0.00 0.00 0.00 4.30
4299 9585 2.029020 GGTTTCTTGCAATTCACTCCCC 60.029 50.000 0.00 0.00 0.00 4.81
4300 9586 2.893489 GTTTCTTGCAATTCACTCCCCT 59.107 45.455 0.00 0.00 0.00 4.79
4318 9605 3.069729 CCCCTAGCAACTATAGTGTGGTC 59.930 52.174 17.29 3.66 0.00 4.02
4389 9683 3.646534 TGAGGTGATGGCAGATCTCTTA 58.353 45.455 10.10 0.00 0.00 2.10
4454 9748 3.519510 CCACTCAAGGAACTCCAGGATAA 59.480 47.826 0.00 0.00 38.49 1.75
4484 9778 9.451002 CAGAGGGTATCTTATAGAATCGAAGTA 57.549 37.037 0.00 0.00 35.47 2.24
4719 10103 5.364778 TGCAAGTACTTCAATGTGTGTACT 58.635 37.500 4.77 0.00 44.87 2.73
4848 10280 2.417379 CCACAGGAATCTTCGTCATCGT 60.417 50.000 0.00 0.00 38.33 3.73
4849 10281 2.600420 CACAGGAATCTTCGTCATCGTG 59.400 50.000 0.00 0.00 38.33 4.35
4850 10282 2.231478 ACAGGAATCTTCGTCATCGTGT 59.769 45.455 0.00 0.00 36.43 4.49
5052 10484 5.014018 ACCTGATAAACAATGGGGCAAAATT 59.986 36.000 0.00 0.00 0.00 1.82
5075 10507 0.391793 TATGCATCGTCGTTTGCCCA 60.392 50.000 0.19 5.44 38.08 5.36
5077 10509 2.032634 GCATCGTCGTTTGCCCAGA 61.033 57.895 10.50 0.00 32.66 3.86
5093 10525 3.489398 GCCCAGACAGAAGTGTACGATAG 60.489 52.174 0.00 0.00 36.88 2.08
5102 10534 8.008513 ACAGAAGTGTACGATAGGTGATAAAT 57.991 34.615 0.00 0.00 43.77 1.40
5109 10541 9.701098 GTGTACGATAGGTGATAAATAAATGGA 57.299 33.333 0.00 0.00 43.77 3.41
5145 10578 4.979943 TTTGAGCAGAACACAACAATGA 57.020 36.364 0.00 0.00 0.00 2.57
5211 10644 2.451693 GCAGTCGGCGTAATGTTCA 58.548 52.632 6.85 0.00 0.00 3.18
5464 11201 7.673180 TCGTCTTTCTCCTGATTAGGTAAAAA 58.327 34.615 3.04 2.74 44.88 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 2.921754 GACAGTTGATATATACGGCGGC 59.078 50.000 13.24 0.00 0.00 6.53
2 3 4.436242 AGACAGTTGATATATACGGCGG 57.564 45.455 13.24 0.00 0.00 6.13
3 4 5.220381 ACAAGACAGTTGATATATACGGCG 58.780 41.667 4.80 4.80 0.00 6.46
5 6 7.883217 AGGTACAAGACAGTTGATATATACGG 58.117 38.462 0.00 0.00 0.00 4.02
6 7 8.784994 AGAGGTACAAGACAGTTGATATATACG 58.215 37.037 0.00 0.00 0.00 3.06
8 9 8.577296 GCAGAGGTACAAGACAGTTGATATATA 58.423 37.037 0.00 0.00 0.00 0.86
10 11 6.379988 TGCAGAGGTACAAGACAGTTGATATA 59.620 38.462 0.00 0.00 0.00 0.86
11 12 5.187772 TGCAGAGGTACAAGACAGTTGATAT 59.812 40.000 0.00 0.00 0.00 1.63
18 19 2.036475 ACAGTGCAGAGGTACAAGACAG 59.964 50.000 0.00 0.00 31.27 3.51
293 334 7.549147 TTTTAACCTGACATGTACTCCTACT 57.451 36.000 0.00 0.00 0.00 2.57
294 335 8.788325 ATTTTTAACCTGACATGTACTCCTAC 57.212 34.615 0.00 0.00 0.00 3.18
296 337 9.396022 CATATTTTTAACCTGACATGTACTCCT 57.604 33.333 0.00 0.00 0.00 3.69
297 338 9.391006 TCATATTTTTAACCTGACATGTACTCC 57.609 33.333 0.00 0.00 0.00 3.85
321 461 6.995686 TCAGTTTAAATAAAGCCACAGTCTCA 59.004 34.615 0.00 0.00 0.00 3.27
330 470 5.332707 CGCTTCCTCAGTTTAAATAAAGCC 58.667 41.667 0.00 0.00 35.60 4.35
343 483 1.712977 GATGGCAAGCGCTTCCTCAG 61.713 60.000 27.51 16.82 38.60 3.35
402 554 0.318955 GGGTGCTGCATTCAACACAC 60.319 55.000 5.27 0.00 40.18 3.82
434 587 5.183140 ACCAACACTGTAATTTACTGATGGC 59.817 40.000 21.98 0.00 35.33 4.40
443 596 6.010219 AGCATTAGGACCAACACTGTAATTT 58.990 36.000 0.00 0.00 0.00 1.82
444 597 5.570320 AGCATTAGGACCAACACTGTAATT 58.430 37.500 0.00 0.00 0.00 1.40
472 635 4.399618 TCTCTACTGCTGGTTGTGATCTAC 59.600 45.833 0.00 0.00 0.00 2.59
473 636 4.399618 GTCTCTACTGCTGGTTGTGATCTA 59.600 45.833 0.00 0.00 0.00 1.98
474 637 3.194542 GTCTCTACTGCTGGTTGTGATCT 59.805 47.826 0.00 0.00 0.00 2.75
478 641 4.727507 ATAGTCTCTACTGCTGGTTGTG 57.272 45.455 0.00 0.00 36.36 3.33
566 732 0.735471 TCGCGGAGAGATCTCACTTG 59.265 55.000 24.39 15.03 44.60 3.16
602 768 3.366476 CGTTTAAATTGTCGCCATTGGGA 60.366 43.478 4.53 0.00 35.59 4.37
611 788 1.200484 CCACCCCCGTTTAAATTGTCG 59.800 52.381 0.00 0.00 0.00 4.35
614 791 1.273886 CACCCACCCCCGTTTAAATTG 59.726 52.381 0.00 0.00 0.00 2.32
615 792 1.634960 CACCCACCCCCGTTTAAATT 58.365 50.000 0.00 0.00 0.00 1.82
625 802 2.203582 GTTGAACCCACCCACCCC 60.204 66.667 0.00 0.00 0.00 4.95
648 844 4.382040 GCTAGTTCAGTGGCAAGAGTGATA 60.382 45.833 0.00 0.00 0.00 2.15
650 846 2.289072 GCTAGTTCAGTGGCAAGAGTGA 60.289 50.000 0.00 0.00 0.00 3.41
666 862 3.626154 GCGAGAACTAAGCGCTAGT 57.374 52.632 12.05 12.05 46.53 2.57
705 904 4.385358 TTGTTTTGAAGAGGCCACTTTC 57.615 40.909 17.05 11.36 0.00 2.62
728 927 7.897575 TGCACTCTTCTCTTCTTCTATTTTC 57.102 36.000 0.00 0.00 0.00 2.29
733 932 5.991933 ACATGCACTCTTCTCTTCTTCTA 57.008 39.130 0.00 0.00 0.00 2.10
740 939 4.081972 ACGACATAACATGCACTCTTCTCT 60.082 41.667 0.00 0.00 0.00 3.10
741 940 4.177026 ACGACATAACATGCACTCTTCTC 58.823 43.478 0.00 0.00 0.00 2.87
742 941 4.193826 ACGACATAACATGCACTCTTCT 57.806 40.909 0.00 0.00 0.00 2.85
746 946 4.404507 ACAAACGACATAACATGCACTC 57.595 40.909 0.00 0.00 0.00 3.51
757 957 3.713826 AATCTGGGGTACAAACGACAT 57.286 42.857 0.00 0.00 0.00 3.06
856 1069 7.577426 GCAGAATAGCTAGCTCTCTATGTTCAT 60.577 40.741 23.26 1.52 0.00 2.57
869 1082 2.158900 TGAAGGGTGCAGAATAGCTAGC 60.159 50.000 6.62 6.62 34.99 3.42
873 1086 4.725790 AAATTGAAGGGTGCAGAATAGC 57.274 40.909 0.00 0.00 0.00 2.97
874 1087 5.394553 GGGAAAATTGAAGGGTGCAGAATAG 60.395 44.000 0.00 0.00 0.00 1.73
890 1103 5.191323 TGCAATATTCACCATGGGGAAAATT 59.809 36.000 32.49 19.11 38.05 1.82
992 1721 9.749490 CTGAAATTTGACAATGCATAAATCAAC 57.251 29.630 15.89 8.39 0.00 3.18
1149 1879 2.017138 TCCTTTCGCGTTATGATGCA 57.983 45.000 5.77 0.00 37.67 3.96
1340 2258 4.471025 TCCTATCAAGCTTCATTGTCTGGA 59.529 41.667 0.00 0.00 0.00 3.86
1454 2427 4.685924 CATCTTGTTTGTGCTTTGGAGTT 58.314 39.130 0.00 0.00 0.00 3.01
1463 2436 3.047796 CACTTGAGCATCTTGTTTGTGC 58.952 45.455 0.00 0.00 39.10 4.57
1464 2437 4.036027 AGTCACTTGAGCATCTTGTTTGTG 59.964 41.667 0.00 0.00 34.92 3.33
1465 2438 4.202441 AGTCACTTGAGCATCTTGTTTGT 58.798 39.130 0.00 0.00 34.92 2.83
1544 2599 0.681243 GCTCCAAACATCCCTGGGAC 60.681 60.000 19.82 0.00 32.98 4.46
1586 2641 9.132521 GAATGGTTGAATATTGACAACTCAAAG 57.867 33.333 15.67 0.00 43.68 2.77
1721 2835 9.838975 CTTGTGATGCACTAAGACTATATAGAG 57.161 37.037 16.79 5.77 35.11 2.43
1793 3180 5.245075 GGGAAAAGGAATTGACCATGTTACA 59.755 40.000 0.00 0.00 0.00 2.41
1809 3196 6.265422 AGAAGTGACTTGTTAATGGGAAAAGG 59.735 38.462 0.90 0.00 0.00 3.11
1850 3239 2.346803 TGCAGTCAACGGATAAGCTTC 58.653 47.619 0.00 0.00 0.00 3.86
2006 3436 8.664669 AAAACATATAATCAACTTTCACCCCT 57.335 30.769 0.00 0.00 0.00 4.79
2098 3547 8.771766 GCTAGCTGTGTTTAGTTAAAAGTTAGT 58.228 33.333 7.70 0.00 0.00 2.24
2109 3558 3.139077 GTTGTGGCTAGCTGTGTTTAGT 58.861 45.455 15.72 0.00 0.00 2.24
2125 3626 3.120199 CCATTCTGGAAAGCGTAGTTGTG 60.120 47.826 0.00 0.00 40.96 3.33
2411 3972 0.033366 GTGCCCGCCAACTTCAAATT 59.967 50.000 0.00 0.00 0.00 1.82
2636 4336 7.947332 TGCTTAGAGATCATACTAAGATGTCCT 59.053 37.037 24.74 0.00 44.55 3.85
3094 6728 4.741676 GTGGTTTCTTGCAATTCACTCTTG 59.258 41.667 0.00 0.00 0.00 3.02
3241 6875 0.323178 GTCCGTCCCCACTAGTCAGA 60.323 60.000 0.00 0.00 0.00 3.27
3255 6889 4.202264 CCAAATCAGCTCCTTATAGTCCGT 60.202 45.833 0.00 0.00 0.00 4.69
3459 7100 4.143333 CAGTTCCGCCGGATCCGT 62.143 66.667 31.22 9.45 37.81 4.69
3481 7122 3.610791 CTCTCAGTTCGTCGCGCCA 62.611 63.158 0.00 0.00 0.00 5.69
3595 7263 1.298014 CCCACTGGTGAGCTCCTTC 59.702 63.158 12.15 1.59 0.00 3.46
3663 7373 2.045829 TCGAGCGAGCAGAGGACT 60.046 61.111 0.00 0.00 0.00 3.85
3922 9171 2.525629 TGCTCCGTGAAGACCCCA 60.526 61.111 0.00 0.00 0.00 4.96
4298 9584 4.402793 ACAGACCACACTATAGTTGCTAGG 59.597 45.833 1.56 3.74 0.00 3.02
4299 9585 5.125578 TCACAGACCACACTATAGTTGCTAG 59.874 44.000 1.56 0.00 0.00 3.42
4300 9586 5.014202 TCACAGACCACACTATAGTTGCTA 58.986 41.667 1.56 0.00 0.00 3.49
4318 9605 5.048294 GGGGGTTACAAACAGTATTTCACAG 60.048 44.000 0.00 0.00 31.53 3.66
4389 9683 2.303022 CCCTTCTGGATGTGTACACACT 59.697 50.000 30.11 18.73 45.05 3.55
4454 9748 6.887545 CGATTCTATAAGATACCCTCTGGACT 59.112 42.308 0.00 0.00 33.29 3.85
4484 9778 1.347707 TGAAATCTGCCTTGAGGACGT 59.652 47.619 0.06 0.00 37.39 4.34
4719 10103 3.181476 ACATGATCGACGGAACATCATCA 60.181 43.478 0.00 2.01 33.86 3.07
4848 10280 6.099341 CCTTGCGAGCATACATATGTATACA 58.901 40.000 24.50 8.27 39.06 2.29
4849 10281 5.520288 CCCTTGCGAGCATACATATGTATAC 59.480 44.000 24.50 19.94 39.06 1.47
4850 10282 5.660460 CCCTTGCGAGCATACATATGTATA 58.340 41.667 24.50 8.53 39.06 1.47
5011 10443 1.731969 GTGTGTACGCTGTCCCGTC 60.732 63.158 8.10 0.00 42.20 4.79
5052 10484 2.413502 GGCAAACGACGATGCATAACAA 60.414 45.455 24.02 0.00 44.32 2.83
5075 10507 4.586884 TCACCTATCGTACACTTCTGTCT 58.413 43.478 0.00 0.00 0.00 3.41
5077 10509 7.400599 TTTATCACCTATCGTACACTTCTGT 57.599 36.000 0.00 0.00 0.00 3.41
5145 10578 3.678056 TGACAACGCTTGATAGGAACT 57.322 42.857 5.01 0.00 46.37 3.01
5153 10586 0.323302 TAGCCCATGACAACGCTTGA 59.677 50.000 0.00 0.00 32.76 3.02
5211 10644 0.182061 AATCGCAGCCCATGACTGAT 59.818 50.000 17.02 2.97 37.32 2.90
5262 10707 3.537206 GAGCAGCCGAAGTGGTGGT 62.537 63.158 0.00 0.00 41.21 4.16
5301 11038 4.404185 AGTCCAGCCTATTTTTCCCTTT 57.596 40.909 0.00 0.00 0.00 3.11
5302 11039 5.449553 CATAGTCCAGCCTATTTTTCCCTT 58.550 41.667 0.00 0.00 0.00 3.95
5303 11040 4.141158 CCATAGTCCAGCCTATTTTTCCCT 60.141 45.833 0.00 0.00 0.00 4.20


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

AutoCloner maintained by Alex Coulton.