Multiple sequence alignment - TraesCS7B01G059100

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 TraesCS7B01G059100 chr7B 100.000 3686 0 0 1 3686 61629795 61626110 0.000000e+00 6807.0
1 TraesCS7B01G059100 chr7B 89.479 1939 154 22 805 2731 61747323 61745423 0.000000e+00 2405.0
2 TraesCS7B01G059100 chr7B 94.142 239 14 0 2868 3106 721136884 721137122 7.520000e-97 364.0
3 TraesCS7B01G059100 chr7B 93.697 238 15 0 2868 3105 97327488 97327251 1.260000e-94 357.0
4 TraesCS7B01G059100 chr7B 94.043 235 14 0 2868 3102 500786547 500786781 1.260000e-94 357.0
5 TraesCS7B01G059100 chr7B 93.697 238 15 0 2868 3105 682794089 682793852 1.260000e-94 357.0
6 TraesCS7B01G059100 chr7B 92.339 248 18 1 2868 3114 406937166 406937413 5.860000e-93 351.0
7 TraesCS7B01G059100 chr7B 94.767 172 6 1 3106 3274 500786931 500787102 7.850000e-67 265.0
8 TraesCS7B01G059100 chr7B 84.956 113 16 1 1957 2068 425159131 425159243 3.010000e-21 113.0
9 TraesCS7B01G059100 chr7D 94.020 2341 82 27 540 2864 103212412 103210114 0.000000e+00 3494.0
10 TraesCS7B01G059100 chr7D 89.860 1923 140 21 805 2724 103333382 103331512 0.000000e+00 2420.0
11 TraesCS7B01G059100 chr7D 83.630 562 72 12 1 546 540638344 540638901 9.130000e-141 510.0
12 TraesCS7B01G059100 chr7D 87.927 381 33 7 2870 3240 47604013 47603636 1.570000e-118 436.0
13 TraesCS7B01G059100 chr7D 84.071 113 17 1 1957 2068 410522324 410522212 1.400000e-19 108.0
14 TraesCS7B01G059100 chr7A 94.737 2166 72 15 544 2699 107918107 107915974 0.000000e+00 3330.0
15 TraesCS7B01G059100 chr7A 87.379 103 13 0 1957 2059 471551682 471551784 6.470000e-23 119.0
16 TraesCS7B01G059100 chr4A 97.122 417 11 1 3271 3686 657127132 657127548 0.000000e+00 702.0
17 TraesCS7B01G059100 chr4A 97.337 413 10 1 3275 3686 657113684 657114096 0.000000e+00 701.0
18 TraesCS7B01G059100 chr4A 93.089 246 16 1 2870 3114 734230178 734229933 3.500000e-95 359.0
19 TraesCS7B01G059100 chr6D 96.882 417 11 2 3271 3686 63919406 63919821 0.000000e+00 697.0
20 TraesCS7B01G059100 chr6D 84.473 541 70 10 1 528 156441047 156441586 4.220000e-144 521.0
21 TraesCS7B01G059100 chr6D 83.848 551 71 8 1 546 35017258 35017795 3.280000e-140 508.0
22 TraesCS7B01G059100 chr6D 82.060 563 74 13 3 546 437961496 437960942 4.340000e-124 455.0
23 TraesCS7B01G059100 chr6D 80.531 565 81 15 3 545 448634204 448634761 1.230000e-109 407.0
24 TraesCS7B01G059100 chr6D 80.496 564 79 21 3 546 83176689 83177241 1.590000e-108 403.0
25 TraesCS7B01G059100 chr6D 80.243 577 76 21 1 545 57793026 57792456 2.060000e-107 399.0
26 TraesCS7B01G059100 chr6D 84.197 386 54 4 3 382 470277796 470278180 5.820000e-98 368.0
27 TraesCS7B01G059100 chr6D 77.975 563 100 16 3 546 473051375 473050818 7.630000e-87 331.0
28 TraesCS7B01G059100 chr6D 81.075 428 65 13 129 545 430363052 430363474 9.870000e-86 327.0
29 TraesCS7B01G059100 chr6D 91.561 237 18 2 3 238 17390246 17390481 3.550000e-85 326.0
30 TraesCS7B01G059100 chr6D 84.277 318 40 7 72 382 470279941 470280255 5.980000e-78 302.0
31 TraesCS7B01G059100 chr6D 85.644 202 25 4 347 544 186551540 186551741 3.730000e-50 209.0
32 TraesCS7B01G059100 chr6D 76.179 424 78 18 142 545 115577526 115577946 6.240000e-48 202.0
33 TraesCS7B01G059100 chr6D 83.654 208 26 5 342 543 12830198 12830403 4.860000e-44 189.0
34 TraesCS7B01G059100 chr6D 83.333 198 29 3 353 546 417883669 417883472 2.920000e-41 180.0
35 TraesCS7B01G059100 chr6D 80.645 155 26 2 402 552 412021956 412021802 2.330000e-22 117.0
36 TraesCS7B01G059100 chr5B 97.101 414 11 1 3274 3686 92900907 92900494 0.000000e+00 697.0
37 TraesCS7B01G059100 chr5B 81.905 105 19 0 1961 2065 372081463 372081359 5.070000e-14 89.8
38 TraesCS7B01G059100 chr4B 97.101 414 11 1 3274 3686 486313868 486314281 0.000000e+00 697.0
39 TraesCS7B01G059100 chr4B 97.101 414 11 1 3274 3686 591505082 591504669 0.000000e+00 697.0
40 TraesCS7B01G059100 chr1D 94.966 437 18 4 3251 3686 60124382 60123949 0.000000e+00 682.0
41 TraesCS7B01G059100 chr1D 94.570 442 18 6 3247 3686 192168368 192167931 0.000000e+00 678.0
42 TraesCS7B01G059100 chr1D 85.689 566 58 15 1 546 403231945 403232507 3.190000e-160 575.0
43 TraesCS7B01G059100 chr1D 84.794 559 70 8 1 545 418099468 418100025 6.960000e-152 547.0
44 TraesCS7B01G059100 chr1D 83.803 568 69 12 1 545 462270729 462270162 5.460000e-143 518.0
45 TraesCS7B01G059100 chr1D 84.647 482 59 12 83 551 408538002 408537523 2.000000e-127 466.0
46 TraesCS7B01G059100 chr5D 86.964 560 57 6 1 545 507868304 507868862 1.880000e-172 616.0
47 TraesCS7B01G059100 chr5D 86.762 559 60 5 1 545 507873863 507874421 8.750000e-171 610.0
48 TraesCS7B01G059100 chr5D 85.586 555 70 7 1 545 404765458 404764904 1.150000e-159 573.0
49 TraesCS7B01G059100 chr5D 85.152 559 66 11 1 545 28039630 28039075 1.160000e-154 556.0
50 TraesCS7B01G059100 chr5D 82.857 105 18 0 1961 2065 320873688 320873584 1.090000e-15 95.3
51 TraesCS7B01G059100 chr4D 86.559 558 60 8 1 545 432418423 432417868 5.270000e-168 601.0
52 TraesCS7B01G059100 chr4D 82.353 561 74 14 1 545 324470849 324470298 7.210000e-127 464.0
53 TraesCS7B01G059100 chr4D 82.290 559 69 20 3 549 30280513 30279973 1.210000e-124 457.0
54 TraesCS7B01G059100 chr4D 81.900 558 82 12 3 545 487404814 487405367 1.560000e-123 453.0
55 TraesCS7B01G059100 chr4D 81.720 558 85 14 3 545 133735651 133736206 2.020000e-122 449.0
56 TraesCS7B01G059100 chr4D 79.964 559 88 16 3 545 461766824 461767374 1.240000e-104 390.0
57 TraesCS7B01G059100 chr4D 87.143 140 15 2 409 546 386493889 386494027 4.930000e-34 156.0
58 TraesCS7B01G059100 chr3B 85.099 557 65 12 1 545 644319797 644319247 1.500000e-153 553.0
59 TraesCS7B01G059100 chr6B 84.629 579 61 16 1 562 655887068 655887635 5.380000e-153 551.0
60 TraesCS7B01G059100 chr6B 92.742 248 17 1 2868 3114 49801583 49801830 1.260000e-94 357.0
61 TraesCS7B01G059100 chr3A 85.118 551 68 10 1 539 468735653 468736201 5.380000e-153 551.0
62 TraesCS7B01G059100 chr5A 83.811 593 74 17 3106 3686 214890136 214890718 9.000000e-151 544.0
63 TraesCS7B01G059100 chr5A 94.767 172 6 1 3106 3274 631477974 631477803 7.850000e-67 265.0
64 TraesCS7B01G059100 chr5A 84.848 99 15 0 1961 2059 413429637 413429735 2.340000e-17 100.0
65 TraesCS7B01G059100 chr1B 84.810 553 66 10 1 546 442963108 442962567 1.160000e-149 540.0
66 TraesCS7B01G059100 chr1B 83.957 561 70 12 1 546 444039047 444039602 1.520000e-143 520.0
67 TraesCS7B01G059100 chr1B 94.767 172 6 1 3106 3274 53923658 53923829 7.850000e-67 265.0
68 TraesCS7B01G059100 chr3D 84.420 552 72 11 1 543 593914563 593914017 7.010000e-147 531.0
69 TraesCS7B01G059100 chr2A 87.589 419 44 5 2864 3274 751744319 751743901 2.570000e-131 479.0
70 TraesCS7B01G059100 chr2A 89.542 153 14 2 1946 2097 100627766 100627615 3.760000e-45 193.0
71 TraesCS7B01G059100 chrUn 93.605 172 8 1 3106 3274 395969980 395969809 1.700000e-63 254.0
72 TraesCS7B01G059100 chrUn 93.605 172 8 1 3106 3274 438964171 438964342 1.700000e-63 254.0
73 TraesCS7B01G059100 chrUn 74.614 583 105 19 3 546 84334582 84335160 2.230000e-52 217.0
74 TraesCS7B01G059100 chrUn 74.614 583 105 19 3 546 265277194 265276616 2.230000e-52 217.0
75 TraesCS7B01G059100 chrUn 79.452 219 40 5 337 551 343514324 343514107 2.290000e-32 150.0
76 TraesCS7B01G059100 chrUn 79.452 219 40 5 337 551 388871684 388871467 2.290000e-32 150.0
77 TraesCS7B01G059100 chrUn 77.670 206 35 8 347 545 29820079 29819878 8.360000e-22 115.0
78 TraesCS7B01G059100 chrUn 90.741 54 5 0 3 56 131945642 131945589 5.110000e-09 73.1
79 TraesCS7B01G059100 chr1A 93.605 172 8 1 3106 3274 242696347 242696176 1.700000e-63 254.0
80 TraesCS7B01G059100 chr2D 80.695 259 38 11 1841 2097 100432361 100432609 1.350000e-44 191.0
81 TraesCS7B01G059100 chr2B 79.443 287 41 13 1812 2095 152504411 152504682 1.750000e-43 187.0


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 TraesCS7B01G059100 chr7B 61626110 61629795 3685 True 6807 6807 100.000 1 3686 1 chr7B.!!$R1 3685
1 TraesCS7B01G059100 chr7B 61745423 61747323 1900 True 2405 2405 89.479 805 2731 1 chr7B.!!$R2 1926
2 TraesCS7B01G059100 chr7B 500786547 500787102 555 False 311 357 94.405 2868 3274 2 chr7B.!!$F4 406
3 TraesCS7B01G059100 chr7D 103210114 103212412 2298 True 3494 3494 94.020 540 2864 1 chr7D.!!$R2 2324
4 TraesCS7B01G059100 chr7D 103331512 103333382 1870 True 2420 2420 89.860 805 2724 1 chr7D.!!$R3 1919
5 TraesCS7B01G059100 chr7D 540638344 540638901 557 False 510 510 83.630 1 546 1 chr7D.!!$F1 545
6 TraesCS7B01G059100 chr7A 107915974 107918107 2133 True 3330 3330 94.737 544 2699 1 chr7A.!!$R1 2155
7 TraesCS7B01G059100 chr6D 156441047 156441586 539 False 521 521 84.473 1 528 1 chr6D.!!$F7 527
8 TraesCS7B01G059100 chr6D 35017258 35017795 537 False 508 508 83.848 1 546 1 chr6D.!!$F3 545
9 TraesCS7B01G059100 chr6D 437960942 437961496 554 True 455 455 82.060 3 546 1 chr6D.!!$R4 543
10 TraesCS7B01G059100 chr6D 448634204 448634761 557 False 407 407 80.531 3 545 1 chr6D.!!$F10 542
11 TraesCS7B01G059100 chr6D 83176689 83177241 552 False 403 403 80.496 3 546 1 chr6D.!!$F5 543
12 TraesCS7B01G059100 chr6D 57792456 57793026 570 True 399 399 80.243 1 545 1 chr6D.!!$R1 544
13 TraesCS7B01G059100 chr6D 470277796 470280255 2459 False 335 368 84.237 3 382 2 chr6D.!!$F11 379
14 TraesCS7B01G059100 chr6D 473050818 473051375 557 True 331 331 77.975 3 546 1 chr6D.!!$R5 543
15 TraesCS7B01G059100 chr1D 403231945 403232507 562 False 575 575 85.689 1 546 1 chr1D.!!$F1 545
16 TraesCS7B01G059100 chr1D 418099468 418100025 557 False 547 547 84.794 1 545 1 chr1D.!!$F2 544
17 TraesCS7B01G059100 chr1D 462270162 462270729 567 True 518 518 83.803 1 545 1 chr1D.!!$R4 544
18 TraesCS7B01G059100 chr5D 507868304 507868862 558 False 616 616 86.964 1 545 1 chr5D.!!$F1 544
19 TraesCS7B01G059100 chr5D 507873863 507874421 558 False 610 610 86.762 1 545 1 chr5D.!!$F2 544
20 TraesCS7B01G059100 chr5D 404764904 404765458 554 True 573 573 85.586 1 545 1 chr5D.!!$R3 544
21 TraesCS7B01G059100 chr5D 28039075 28039630 555 True 556 556 85.152 1 545 1 chr5D.!!$R1 544
22 TraesCS7B01G059100 chr4D 432417868 432418423 555 True 601 601 86.559 1 545 1 chr4D.!!$R3 544
23 TraesCS7B01G059100 chr4D 324470298 324470849 551 True 464 464 82.353 1 545 1 chr4D.!!$R2 544
24 TraesCS7B01G059100 chr4D 30279973 30280513 540 True 457 457 82.290 3 549 1 chr4D.!!$R1 546
25 TraesCS7B01G059100 chr4D 487404814 487405367 553 False 453 453 81.900 3 545 1 chr4D.!!$F4 542
26 TraesCS7B01G059100 chr4D 133735651 133736206 555 False 449 449 81.720 3 545 1 chr4D.!!$F1 542
27 TraesCS7B01G059100 chr4D 461766824 461767374 550 False 390 390 79.964 3 545 1 chr4D.!!$F3 542
28 TraesCS7B01G059100 chr3B 644319247 644319797 550 True 553 553 85.099 1 545 1 chr3B.!!$R1 544
29 TraesCS7B01G059100 chr6B 655887068 655887635 567 False 551 551 84.629 1 562 1 chr6B.!!$F2 561
30 TraesCS7B01G059100 chr3A 468735653 468736201 548 False 551 551 85.118 1 539 1 chr3A.!!$F1 538
31 TraesCS7B01G059100 chr5A 214890136 214890718 582 False 544 544 83.811 3106 3686 1 chr5A.!!$F1 580
32 TraesCS7B01G059100 chr1B 442962567 442963108 541 True 540 540 84.810 1 546 1 chr1B.!!$R1 545
33 TraesCS7B01G059100 chr1B 444039047 444039602 555 False 520 520 83.957 1 546 1 chr1B.!!$F2 545
34 TraesCS7B01G059100 chr3D 593914017 593914563 546 True 531 531 84.420 1 543 1 chr3D.!!$R1 542
35 TraesCS7B01G059100 chrUn 84334582 84335160 578 False 217 217 74.614 3 546 1 chrUn.!!$F1 543
36 TraesCS7B01G059100 chrUn 265276616 265277194 578 True 217 217 74.614 3 546 1 chrUn.!!$R3 543

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
695 1271 0.102120 CCTGCAAGAACGTTGCCAAA 59.898 50.0 5.00 0.0 44.32 3.28 F
795 1371 0.107897 ATCGGCGACAACCATGCTAA 60.108 50.0 13.76 0.0 0.00 3.09 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1756 2340 0.996762 TTGGTCTTGGTGGGGAGGTT 60.997 55.0 0.00 0.0 0.00 3.50 R
2747 4124 0.685097 TACAAGCCCACTGGTGACTC 59.315 55.0 1.93 0.0 30.57 3.36 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
70 72 3.140141 CCGTGCCGCATTTGGGAT 61.140 61.111 0.00 0.00 0.00 3.85
311 396 4.380781 TGAATTCGCCGGCGGTGA 62.381 61.111 44.95 36.06 40.77 4.02
366 468 2.125753 GGAGCTCGAGTGTGCAGG 60.126 66.667 15.13 0.00 37.07 4.85
546 1118 1.377536 GGCTGTTGGAGATGCTCTTC 58.622 55.000 0.00 0.00 0.00 2.87
695 1271 0.102120 CCTGCAAGAACGTTGCCAAA 59.898 50.000 5.00 0.00 44.32 3.28
713 1289 3.118454 CGGCGCCAATTCGTCACT 61.118 61.111 28.98 0.00 32.97 3.41
795 1371 0.107897 ATCGGCGACAACCATGCTAA 60.108 50.000 13.76 0.00 0.00 3.09
803 1379 3.545703 GACAACCATGCTAACTGCCTAT 58.454 45.455 0.00 0.00 42.00 2.57
933 1517 5.872617 ACAATCATCAGCAAATCAACCATTG 59.127 36.000 0.00 0.00 0.00 2.82
943 1527 5.691815 CAAATCAACCATTGCAAATCAACC 58.308 37.500 1.71 0.00 37.53 3.77
944 1528 4.620589 ATCAACCATTGCAAATCAACCA 57.379 36.364 1.71 0.00 37.53 3.67
945 1529 4.620589 TCAACCATTGCAAATCAACCAT 57.379 36.364 1.71 0.00 37.53 3.55
946 1530 4.970711 TCAACCATTGCAAATCAACCATT 58.029 34.783 1.71 0.00 37.53 3.16
947 1531 5.374921 TCAACCATTGCAAATCAACCATTT 58.625 33.333 1.71 0.00 37.53 2.32
948 1532 5.826737 TCAACCATTGCAAATCAACCATTTT 59.173 32.000 1.71 0.00 37.53 1.82
974 1558 0.529337 CTGAGCTGCACCGATCGATT 60.529 55.000 18.66 0.00 0.00 3.34
988 1572 2.404789 GATTGTCGCACGCCATGG 59.595 61.111 7.63 7.63 0.00 3.66
989 1573 2.359850 ATTGTCGCACGCCATGGT 60.360 55.556 14.67 0.00 0.00 3.55
990 1574 2.582202 GATTGTCGCACGCCATGGTG 62.582 60.000 23.88 23.88 40.89 4.17
1740 2324 0.882927 CCACCATGAACAACGTCCGT 60.883 55.000 0.00 0.00 0.00 4.69
1782 2373 1.227823 CACCAAGACCAACCTGCGA 60.228 57.895 0.00 0.00 0.00 5.10
2079 2842 1.011595 AGAAGCTCAGGGAGGAGGTA 58.988 55.000 0.00 0.00 44.32 3.08
2158 2921 0.521291 GCTGGTAATGCGCTCAACAA 59.479 50.000 9.73 0.00 0.00 2.83
2159 2922 1.466360 GCTGGTAATGCGCTCAACAAG 60.466 52.381 9.73 7.76 0.00 3.16
2211 3014 0.179059 ATGCACACTCCACAACGACA 60.179 50.000 0.00 0.00 0.00 4.35
2301 3584 0.389025 ACGGCGCTGTGATCATGATA 59.611 50.000 23.67 0.00 0.00 2.15
2313 3596 2.364972 TCATGATAGCGAGGGAGACA 57.635 50.000 0.00 0.00 0.00 3.41
2325 3608 2.737376 GAGACAACGGCGGACACC 60.737 66.667 13.24 0.00 0.00 4.16
2351 3634 2.202932 CGGCGTGAAGATCCCCAG 60.203 66.667 0.00 0.00 0.00 4.45
2677 4050 2.856186 TGCTCAAGCTCCTGGATCAGG 61.856 57.143 7.59 7.59 44.99 3.86
2709 4082 2.338500 CCTCTTTGAACGACTACTGCC 58.662 52.381 0.00 0.00 0.00 4.85
2716 4089 4.627611 TGAACGACTACTGCCATAGTAC 57.372 45.455 0.00 0.00 40.89 2.73
2742 4119 8.853345 CAAGTACAAAATACATGAGTGATTTGC 58.147 33.333 0.00 0.00 37.77 3.68
2753 4130 2.863658 GTGATTTGCTCACGAGTCAC 57.136 50.000 0.00 0.00 44.58 3.67
2755 4132 1.069978 TGATTTGCTCACGAGTCACCA 59.930 47.619 0.00 0.00 0.00 4.17
2756 4133 1.728971 GATTTGCTCACGAGTCACCAG 59.271 52.381 0.00 0.00 0.00 4.00
2757 4134 0.464036 TTTGCTCACGAGTCACCAGT 59.536 50.000 0.00 0.00 0.00 4.00
2758 4135 0.249447 TTGCTCACGAGTCACCAGTG 60.249 55.000 0.00 0.00 37.24 3.66
2759 4136 1.373497 GCTCACGAGTCACCAGTGG 60.373 63.158 7.91 7.91 36.60 4.00
2760 4137 1.290324 CTCACGAGTCACCAGTGGG 59.710 63.158 15.21 2.47 41.29 4.61
2761 4138 2.357517 CACGAGTCACCAGTGGGC 60.358 66.667 15.21 3.23 37.90 5.36
2762 4139 2.524394 ACGAGTCACCAGTGGGCT 60.524 61.111 15.21 8.50 37.90 5.19
2763 4140 2.140792 ACGAGTCACCAGTGGGCTT 61.141 57.895 15.21 0.00 37.90 4.35
2764 4141 1.669115 CGAGTCACCAGTGGGCTTG 60.669 63.158 15.21 8.62 37.90 4.01
2769 4146 1.279271 GTCACCAGTGGGCTTGTATCT 59.721 52.381 15.21 0.00 37.90 1.98
2795 4172 2.426738 TGGTTTTGTTTCTGAGCTGTGG 59.573 45.455 0.00 0.00 0.00 4.17
2811 4188 1.204704 TGTGGGCTCGTATCTTCACTG 59.795 52.381 0.00 0.00 0.00 3.66
2812 4189 1.476891 GTGGGCTCGTATCTTCACTGA 59.523 52.381 0.00 0.00 0.00 3.41
2823 4200 7.281098 TCGTATCTTCACTGAGTATACCTCTT 58.719 38.462 0.00 0.00 41.11 2.85
2824 4201 7.441760 TCGTATCTTCACTGAGTATACCTCTTC 59.558 40.741 0.00 0.00 41.11 2.87
2840 4217 3.439476 CCTCTTCCATTTGTGAGCAGAAG 59.561 47.826 0.00 0.00 33.61 2.85
2841 4218 3.415212 TCTTCCATTTGTGAGCAGAAGG 58.585 45.455 0.00 0.00 33.25 3.46
2842 4219 2.957402 TCCATTTGTGAGCAGAAGGT 57.043 45.000 0.00 0.00 0.00 3.50
2843 4220 3.228188 TCCATTTGTGAGCAGAAGGTT 57.772 42.857 0.00 0.00 0.00 3.50
2864 4241 9.582648 AAGGTTGTGAGGTGTTTTTATAAGTAT 57.417 29.630 0.00 0.00 0.00 2.12
2865 4242 9.010029 AGGTTGTGAGGTGTTTTTATAAGTATG 57.990 33.333 0.00 0.00 0.00 2.39
2866 4243 9.005777 GGTTGTGAGGTGTTTTTATAAGTATGA 57.994 33.333 0.00 0.00 0.00 2.15
2934 4311 6.792473 TCAGATTTAATCTCTAAGGGCCCATA 59.208 38.462 27.56 16.81 37.58 2.74
2969 4346 2.702748 AGGTGGTGGGAAGTTTAGTCT 58.297 47.619 0.00 0.00 0.00 3.24
2983 4360 4.772624 AGTTTAGTCTCACCATGCTAGTGA 59.227 41.667 3.68 3.68 41.84 3.41
2986 4363 4.623932 AGTCTCACCATGCTAGTGAAAA 57.376 40.909 5.05 0.00 43.36 2.29
2987 4364 4.973168 AGTCTCACCATGCTAGTGAAAAA 58.027 39.130 5.05 0.00 43.36 1.94
3077 4454 3.522731 CACTCCTCCTCCTCCGCG 61.523 72.222 0.00 0.00 0.00 6.46
3249 4774 2.623915 CGACTCCGTCCCGTTCACT 61.624 63.158 0.00 0.00 0.00 3.41
3254 4779 2.660552 CGTCCCGTTCACTGCGTT 60.661 61.111 0.00 0.00 0.00 4.84
3375 4905 6.879993 TGCTAGAATTGTATTAACCGGAAACA 59.120 34.615 9.46 1.34 0.00 2.83
3405 4935 8.565896 ACATGTGTGAATACATAGACAAACAT 57.434 30.769 0.00 0.00 40.42 2.71
3412 4942 9.366216 GTGAATACATAGACAAACATAGTGTCA 57.634 33.333 7.26 0.00 46.44 3.58
3422 4952 6.936279 ACAAACATAGTGTCACTAGTATGCT 58.064 36.000 17.43 2.14 37.44 3.79
3442 4972 3.854809 GCTTCTACTTGACTAGCTCGTTG 59.145 47.826 0.00 0.00 0.00 4.10
3458 4988 5.122396 AGCTCGTTGAATCAAAGATGGTTAC 59.878 40.000 11.68 0.00 32.24 2.50
3472 5002 4.652421 AGATGGTTACGTTTCCTAGCCATA 59.348 41.667 3.91 0.00 35.85 2.74
3479 5009 3.704566 ACGTTTCCTAGCCATAGACATGA 59.295 43.478 0.00 0.00 33.67 3.07
3500 5030 4.457603 TGAGTTGTCATTTGATTAACGGGG 59.542 41.667 0.00 0.00 32.73 5.73
3503 5033 4.022413 TGTCATTTGATTAACGGGGTCA 57.978 40.909 0.00 0.00 0.00 4.02
3513 5043 2.710096 AACGGGGTCACATCATTAGG 57.290 50.000 0.00 0.00 0.00 2.69
3531 5061 7.799081 TCATTAGGAGAATGATGTGATTGACT 58.201 34.615 0.00 0.00 32.21 3.41
3532 5062 8.270030 TCATTAGGAGAATGATGTGATTGACTT 58.730 33.333 0.00 0.00 32.21 3.01
3540 5070 4.665451 TGATGTGATTGACTTGACCCATT 58.335 39.130 0.00 0.00 0.00 3.16
3541 5071 4.701651 TGATGTGATTGACTTGACCCATTC 59.298 41.667 0.00 0.00 0.00 2.67
3542 5072 3.420893 TGTGATTGACTTGACCCATTCC 58.579 45.455 0.00 0.00 0.00 3.01
3549 5079 1.628846 ACTTGACCCATTCCGTTAGCT 59.371 47.619 0.00 0.00 0.00 3.32
3555 5085 1.940613 CCCATTCCGTTAGCTTAGCAC 59.059 52.381 7.07 0.00 0.00 4.40
3557 5087 2.351726 CCATTCCGTTAGCTTAGCACAC 59.648 50.000 7.07 1.09 0.00 3.82
3558 5088 1.705256 TTCCGTTAGCTTAGCACACG 58.295 50.000 17.58 17.58 36.47 4.49
3559 5089 0.883153 TCCGTTAGCTTAGCACACGA 59.117 50.000 23.57 11.12 38.10 4.35
3560 5090 1.475280 TCCGTTAGCTTAGCACACGAT 59.525 47.619 23.57 0.00 38.10 3.73
3561 5091 1.852895 CCGTTAGCTTAGCACACGATC 59.147 52.381 23.57 1.02 38.10 3.69
3562 5092 1.513178 CGTTAGCTTAGCACACGATCG 59.487 52.381 19.12 14.88 38.10 3.69
3563 5093 2.527100 GTTAGCTTAGCACACGATCGT 58.473 47.619 16.60 16.60 0.00 3.73
3566 5096 3.226346 AGCTTAGCACACGATCGTTTA 57.774 42.857 20.14 6.25 0.00 2.01
3567 5097 3.179830 AGCTTAGCACACGATCGTTTAG 58.820 45.455 20.14 10.44 0.00 1.85
3569 5101 4.100529 GCTTAGCACACGATCGTTTAGTA 58.899 43.478 20.14 5.55 0.00 1.82
3571 5103 5.331607 GCTTAGCACACGATCGTTTAGTATG 60.332 44.000 20.14 8.10 0.00 2.39
3575 5107 4.325204 GCACACGATCGTTTAGTATGTTGA 59.675 41.667 20.14 0.00 0.00 3.18
3577 5109 6.402816 CACACGATCGTTTAGTATGTTGATG 58.597 40.000 20.14 4.49 0.00 3.07
3578 5110 6.034577 CACACGATCGTTTAGTATGTTGATGT 59.965 38.462 20.14 5.18 0.00 3.06
3580 5112 6.894517 CACGATCGTTTAGTATGTTGATGTTG 59.105 38.462 20.14 0.00 0.00 3.33
3591 5123 7.310664 AGTATGTTGATGTTGCTTTCTTCATG 58.689 34.615 0.00 0.00 0.00 3.07
3611 5143 9.212641 CTTCATGACTTATACATGTTCCTATGG 57.787 37.037 2.30 0.00 43.56 2.74
3632 5164 4.006319 GGCTATGAGATTATGCAACTCCC 58.994 47.826 0.00 0.00 0.00 4.30
3634 5166 3.845781 ATGAGATTATGCAACTCCCGT 57.154 42.857 0.00 0.00 0.00 5.28
3635 5167 3.627395 TGAGATTATGCAACTCCCGTT 57.373 42.857 0.00 0.00 0.00 4.44
3660 5193 2.610727 GGAGGAACACTCTGTGTGCTAC 60.611 54.545 9.58 0.00 46.79 3.58
3666 5199 1.526887 CACTCTGTGTGCTACCAAACG 59.473 52.381 0.00 0.00 40.06 3.60
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
248 326 0.546747 CCCTCACCCCTTCCTACACA 60.547 60.000 0.00 0.00 0.00 3.72
416 871 0.577269 CATAAGTAGTTCAGCGCGCC 59.423 55.000 30.33 12.88 0.00 6.53
546 1118 4.623814 TCCATGCAGGAAAGCTCG 57.376 55.556 0.00 0.00 45.65 5.03
695 1271 2.495366 TAGTGACGAATTGGCGCCGT 62.495 55.000 23.90 15.71 39.41 5.68
713 1289 2.779755 AGATCATGGTGCGGTGTTTA 57.220 45.000 0.00 0.00 0.00 2.01
933 1517 4.992951 AGCTCTTGAAAATGGTTGATTTGC 59.007 37.500 0.00 0.00 34.30 3.68
935 1519 6.409524 TCAGCTCTTGAAAATGGTTGATTT 57.590 33.333 0.00 0.00 35.65 2.17
936 1520 5.566230 GCTCAGCTCTTGAAAATGGTTGATT 60.566 40.000 0.00 0.00 34.81 2.57
937 1521 4.082354 GCTCAGCTCTTGAAAATGGTTGAT 60.082 41.667 0.00 0.00 34.81 2.57
938 1522 3.254166 GCTCAGCTCTTGAAAATGGTTGA 59.746 43.478 0.00 0.00 34.81 3.18
939 1523 3.255149 AGCTCAGCTCTTGAAAATGGTTG 59.745 43.478 0.00 0.00 30.62 3.77
940 1524 3.255149 CAGCTCAGCTCTTGAAAATGGTT 59.745 43.478 0.00 0.00 36.40 3.67
941 1525 2.818432 CAGCTCAGCTCTTGAAAATGGT 59.182 45.455 0.00 0.00 36.40 3.55
942 1526 2.415625 GCAGCTCAGCTCTTGAAAATGG 60.416 50.000 0.00 0.00 36.40 3.16
943 1527 2.228103 TGCAGCTCAGCTCTTGAAAATG 59.772 45.455 0.00 0.00 36.40 2.32
944 1528 2.228343 GTGCAGCTCAGCTCTTGAAAAT 59.772 45.455 0.00 0.00 36.40 1.82
945 1529 1.605710 GTGCAGCTCAGCTCTTGAAAA 59.394 47.619 0.00 0.00 36.40 2.29
946 1530 1.233019 GTGCAGCTCAGCTCTTGAAA 58.767 50.000 0.00 0.00 36.40 2.69
947 1531 0.604780 GGTGCAGCTCAGCTCTTGAA 60.605 55.000 9.07 0.00 36.40 2.69
948 1532 1.004080 GGTGCAGCTCAGCTCTTGA 60.004 57.895 9.07 0.00 36.40 3.02
988 1572 2.590007 CGCCATAGCCAGAGCCAC 60.590 66.667 0.00 0.00 41.25 5.01
989 1573 4.552365 GCGCCATAGCCAGAGCCA 62.552 66.667 0.00 0.00 41.25 4.75
1239 1823 1.369091 CCTTGTACTGCGGCATCACC 61.369 60.000 1.75 0.00 0.00 4.02
1605 2189 2.031516 CAGCTCCACGAACTGCTGG 61.032 63.158 13.98 0.08 46.24 4.85
1756 2340 0.996762 TTGGTCTTGGTGGGGAGGTT 60.997 55.000 0.00 0.00 0.00 3.50
2158 2921 1.811778 TGATGGGATAGGCTTGAGCT 58.188 50.000 0.00 0.00 41.70 4.09
2159 2922 2.875094 ATGATGGGATAGGCTTGAGC 57.125 50.000 0.00 0.00 41.14 4.26
2161 2924 3.975982 TCAGAATGATGGGATAGGCTTGA 59.024 43.478 0.00 0.00 42.56 3.02
2301 3584 4.070552 GCCGTTGTCTCCCTCGCT 62.071 66.667 0.00 0.00 0.00 4.93
2328 3611 3.701604 GATCTTCACGCCGCCGAGT 62.702 63.158 0.00 0.00 38.29 4.18
2351 3634 2.036862 GGTATCATGGTAGTCGTTCCCC 59.963 54.545 0.00 0.00 0.00 4.81
2355 3638 3.005472 CCATCGGTATCATGGTAGTCGTT 59.995 47.826 8.08 0.00 36.74 3.85
2361 3644 1.623163 TCGCCATCGGTATCATGGTA 58.377 50.000 2.41 0.00 42.68 3.25
2415 3698 2.985847 GGCTTGAACTTGCCGGCT 60.986 61.111 29.70 6.86 39.71 5.52
2422 3705 2.032071 CCGGTCCGGCTTGAACTT 59.968 61.111 19.48 0.00 41.17 2.66
2561 3934 3.124921 CGAACCGGCGCAGGATTT 61.125 61.111 33.66 17.91 34.73 2.17
2562 3935 4.077184 TCGAACCGGCGCAGGATT 62.077 61.111 33.66 21.80 34.73 3.01
2683 4056 1.618837 AGTCGTTCAAAGAGGCAGCTA 59.381 47.619 0.00 0.00 0.00 3.32
2716 4089 8.853345 GCAAATCACTCATGTATTTTGTACTTG 58.147 33.333 0.00 0.00 33.48 3.16
2742 4119 1.290324 CCCACTGGTGACTCGTGAG 59.710 63.158 1.93 0.00 35.42 3.51
2747 4124 0.685097 TACAAGCCCACTGGTGACTC 59.315 55.000 1.93 0.00 30.57 3.36
2751 4128 2.496899 AAGATACAAGCCCACTGGTG 57.503 50.000 0.00 0.00 30.57 4.17
2752 4129 3.525800 AAAAGATACAAGCCCACTGGT 57.474 42.857 0.00 0.00 33.41 4.00
2774 4151 2.426738 CCACAGCTCAGAAACAAAACCA 59.573 45.455 0.00 0.00 0.00 3.67
2776 4153 2.799562 GCCCACAGCTCAGAAACAAAAC 60.800 50.000 0.00 0.00 38.99 2.43
2780 4157 4.481195 GCCCACAGCTCAGAAACA 57.519 55.556 0.00 0.00 38.99 2.83
2795 4172 4.839668 ATACTCAGTGAAGATACGAGCC 57.160 45.455 0.00 0.00 0.00 4.70
2811 4188 5.755861 GCTCACAAATGGAAGAGGTATACTC 59.244 44.000 2.25 0.00 46.98 2.59
2812 4189 5.189736 TGCTCACAAATGGAAGAGGTATACT 59.810 40.000 2.25 0.00 0.00 2.12
2823 4200 2.886523 CAACCTTCTGCTCACAAATGGA 59.113 45.455 0.00 0.00 0.00 3.41
2824 4201 2.624838 ACAACCTTCTGCTCACAAATGG 59.375 45.455 0.00 0.00 0.00 3.16
2840 4217 9.005777 TCATACTTATAAAAACACCTCACAACC 57.994 33.333 0.00 0.00 0.00 3.77
2864 4241 5.163663 GCCCGTCTCATATTTCAACAATTCA 60.164 40.000 0.00 0.00 0.00 2.57
2865 4242 5.273944 GCCCGTCTCATATTTCAACAATTC 58.726 41.667 0.00 0.00 0.00 2.17
2866 4243 4.097892 GGCCCGTCTCATATTTCAACAATT 59.902 41.667 0.00 0.00 0.00 2.32
2904 4281 9.574516 GGCCCTTAGAGATTAAATCTGAAATTA 57.425 33.333 0.00 0.00 40.38 1.40
2934 4311 1.064463 CCACCTTGTCATGCCACCTAT 60.064 52.381 0.00 0.00 0.00 2.57
2986 4363 6.045106 TCCCTTATAAACCACTCCAACTCTTT 59.955 38.462 0.00 0.00 0.00 2.52
2987 4364 5.550403 TCCCTTATAAACCACTCCAACTCTT 59.450 40.000 0.00 0.00 0.00 2.85
3045 4422 3.491652 GTGCGCGAGGGCTTCTTC 61.492 66.667 12.10 0.00 36.88 2.87
3249 4774 2.280524 CTCCCGTCAACCAACGCA 60.281 61.111 0.00 0.00 41.26 5.24
3254 4779 2.583441 CCTGCTCTCCCGTCAACCA 61.583 63.158 0.00 0.00 0.00 3.67
3378 4908 9.665719 TGTTTGTCTATGTATTCACACATGTAT 57.334 29.630 0.00 0.00 39.46 2.29
3382 4912 9.890629 ACTATGTTTGTCTATGTATTCACACAT 57.109 29.630 0.00 0.00 41.88 3.21
3405 4935 7.827729 TCAAGTAGAAGCATACTAGTGACACTA 59.172 37.037 14.53 14.53 34.90 2.74
3412 4942 7.057894 AGCTAGTCAAGTAGAAGCATACTAGT 58.942 38.462 0.00 0.00 38.02 2.57
3422 4952 5.700722 TTCAACGAGCTAGTCAAGTAGAA 57.299 39.130 0.00 0.00 0.00 2.10
3442 4972 6.496338 AGGAAACGTAACCATCTTTGATTC 57.504 37.500 12.35 0.00 0.00 2.52
3458 4988 4.202161 ACTCATGTCTATGGCTAGGAAACG 60.202 45.833 0.00 0.00 34.97 3.60
3479 5009 4.403734 ACCCCGTTAATCAAATGACAACT 58.596 39.130 7.65 0.00 0.00 3.16
3493 5023 3.376636 TCCTAATGATGTGACCCCGTTA 58.623 45.455 0.00 0.00 0.00 3.18
3513 5043 5.065731 GGGTCAAGTCAATCACATCATTCTC 59.934 44.000 0.00 0.00 0.00 2.87
3527 5057 2.614481 GCTAACGGAATGGGTCAAGTCA 60.614 50.000 0.00 0.00 0.00 3.41
3531 5061 2.871096 AAGCTAACGGAATGGGTCAA 57.129 45.000 0.00 0.00 0.00 3.18
3532 5062 2.419574 GCTAAGCTAACGGAATGGGTCA 60.420 50.000 0.00 0.00 0.00 4.02
3540 5070 0.883153 TCGTGTGCTAAGCTAACGGA 59.117 50.000 9.65 0.00 38.12 4.69
3541 5071 1.852895 GATCGTGTGCTAAGCTAACGG 59.147 52.381 9.65 0.00 38.12 4.44
3542 5072 1.513178 CGATCGTGTGCTAAGCTAACG 59.487 52.381 7.03 0.00 38.60 3.18
3549 5079 5.643664 ACATACTAAACGATCGTGTGCTAA 58.356 37.500 23.51 6.72 0.00 3.09
3555 5085 6.569228 ACATCAACATACTAAACGATCGTG 57.431 37.500 23.51 12.16 0.00 4.35
3557 5087 5.896432 GCAACATCAACATACTAAACGATCG 59.104 40.000 14.88 14.88 0.00 3.69
3558 5088 7.005062 AGCAACATCAACATACTAAACGATC 57.995 36.000 0.00 0.00 0.00 3.69
3559 5089 6.985188 AGCAACATCAACATACTAAACGAT 57.015 33.333 0.00 0.00 0.00 3.73
3560 5090 6.795098 AAGCAACATCAACATACTAAACGA 57.205 33.333 0.00 0.00 0.00 3.85
3561 5091 7.298122 AGAAAGCAACATCAACATACTAAACG 58.702 34.615 0.00 0.00 0.00 3.60
3562 5092 9.118236 GAAGAAAGCAACATCAACATACTAAAC 57.882 33.333 0.00 0.00 0.00 2.01
3563 5093 8.845227 TGAAGAAAGCAACATCAACATACTAAA 58.155 29.630 0.00 0.00 0.00 1.85
3566 5096 6.882610 TGAAGAAAGCAACATCAACATACT 57.117 33.333 0.00 0.00 0.00 2.12
3567 5097 7.272084 GTCATGAAGAAAGCAACATCAACATAC 59.728 37.037 0.00 0.00 0.00 2.39
3569 5101 6.015688 AGTCATGAAGAAAGCAACATCAACAT 60.016 34.615 0.00 0.00 0.00 2.71
3571 5103 5.766222 AGTCATGAAGAAAGCAACATCAAC 58.234 37.500 0.00 0.00 0.00 3.18
3575 5107 8.565896 TGTATAAGTCATGAAGAAAGCAACAT 57.434 30.769 0.00 0.00 0.00 2.71
3577 5109 8.454106 ACATGTATAAGTCATGAAGAAAGCAAC 58.546 33.333 11.92 0.00 43.47 4.17
3578 5110 8.565896 ACATGTATAAGTCATGAAGAAAGCAA 57.434 30.769 11.92 0.00 43.47 3.91
3580 5112 8.125448 GGAACATGTATAAGTCATGAAGAAAGC 58.875 37.037 0.00 0.00 43.47 3.51
3591 5123 8.531982 TCATAGCCATAGGAACATGTATAAGTC 58.468 37.037 0.00 0.00 0.00 3.01
3608 5140 5.251764 GGAGTTGCATAATCTCATAGCCAT 58.748 41.667 0.00 0.00 0.00 4.40
3611 5143 3.681897 CGGGAGTTGCATAATCTCATAGC 59.318 47.826 0.00 0.00 0.00 2.97
3632 5164 2.288030 ACAGAGTGTTCCTCCGTAAACG 60.288 50.000 0.00 0.00 41.47 3.60
3634 5166 2.696707 ACACAGAGTGTTCCTCCGTAAA 59.303 45.455 0.00 0.00 45.08 2.01
3635 5167 2.035449 CACACAGAGTGTTCCTCCGTAA 59.965 50.000 0.00 0.00 45.08 3.18
3649 5182 1.137282 TGACGTTTGGTAGCACACAGA 59.863 47.619 11.43 0.00 0.00 3.41
3650 5183 1.260561 GTGACGTTTGGTAGCACACAG 59.739 52.381 11.43 6.73 0.00 3.66


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

AutoCloner maintained by Alex Coulton.