Multiple sequence alignment - TraesCS7A01G046800

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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 TraesCS7A01G046800 chr7A 100.000 3852 0 0 1 3852 21207553 21203702 0.000000e+00 7114.0
1 TraesCS7A01G046800 chr7D 95.403 3111 113 16 746 3852 20728166 20725082 0.000000e+00 4926.0
2 TraesCS7A01G046800 chr7D 91.667 108 9 0 638 745 20729453 20729346 2.400000e-32 150.0
3 TraesCS7A01G046800 chr7D 82.105 95 13 4 1944 2037 96758431 96758522 1.150000e-10 78.7
4 TraesCS7A01G046800 chr4A 90.345 1450 119 9 1946 3389 669391206 669389772 0.000000e+00 1882.0
5 TraesCS7A01G046800 chr4A 95.087 977 44 4 983 1957 669392339 669391365 0.000000e+00 1535.0
6 TraesCS7A01G046800 chr4A 85.471 647 70 15 3 637 591673402 591674036 0.000000e+00 652.0
7 TraesCS7A01G046800 chr4A 85.362 649 71 15 1 637 591292130 591292766 0.000000e+00 651.0
8 TraesCS7A01G046800 chr4A 85.208 649 72 13 1 637 592311269 592310633 0.000000e+00 645.0
9 TraesCS7A01G046800 chr4A 85.185 648 74 15 1 637 592363548 592362912 0.000000e+00 645.0
10 TraesCS7A01G046800 chr4A 83.621 464 72 4 3390 3852 669389733 669389273 2.130000e-117 433.0
11 TraesCS7A01G046800 chr4A 83.369 463 74 3 3391 3852 252716825 252717285 3.560000e-115 425.0
12 TraesCS7A01G046800 chr4A 83.298 467 73 5 3389 3852 413246908 413246444 3.560000e-115 425.0
13 TraesCS7A01G046800 chr4A 83.607 183 12 10 791 970 669392563 669392396 5.150000e-34 156.0
14 TraesCS7A01G046800 chr6D 83.771 838 117 9 1001 1824 458530999 458530167 0.000000e+00 776.0
15 TraesCS7A01G046800 chr6D 83.553 833 122 11 1001 1824 458508808 458507982 0.000000e+00 765.0
16 TraesCS7A01G046800 chr6D 86.529 631 63 13 19 637 384353457 384354077 0.000000e+00 675.0
17 TraesCS7A01G046800 chr6D 82.270 564 68 23 2519 3055 458530054 458529496 3.510000e-125 459.0
18 TraesCS7A01G046800 chr6D 80.273 659 79 35 1 637 242211991 242211362 2.110000e-122 449.0
19 TraesCS7A01G046800 chr6D 80.092 653 75 31 1 637 365585824 365586437 5.910000e-118 435.0
20 TraesCS7A01G046800 chr6D 87.375 301 33 2 3089 3388 353202293 353201997 1.330000e-89 340.0
21 TraesCS7A01G046800 chr6D 74.738 669 99 41 1 637 291391716 291391086 6.430000e-58 235.0
22 TraesCS7A01G046800 chr6D 83.721 86 14 0 1944 2029 344172600 344172515 8.870000e-12 82.4
23 TraesCS7A01G046800 chr6D 94.595 37 2 0 1950 1986 10746667 10746703 1.490000e-04 58.4
24 TraesCS7A01G046800 chr6D 96.970 33 1 0 1950 1982 312190130 312190098 5.380000e-04 56.5
25 TraesCS7A01G046800 chr3D 87.385 650 62 13 1 637 351131045 351130403 0.000000e+00 728.0
26 TraesCS7A01G046800 chr3D 85.714 455 63 2 3390 3843 252848805 252849258 2.690000e-131 479.0
27 TraesCS7A01G046800 chr1D 87.481 647 59 12 1 637 261091559 261092193 0.000000e+00 726.0
28 TraesCS7A01G046800 chr1D 78.268 635 86 29 1 610 443793686 443793079 1.020000e-95 361.0
29 TraesCS7A01G046800 chr1D 83.721 86 13 1 1952 2037 50710584 50710668 3.190000e-11 80.5
30 TraesCS7A01G046800 chr7B 85.714 651 73 14 1 637 517097000 517096356 0.000000e+00 669.0
31 TraesCS7A01G046800 chr7B 82.317 656 82 13 3 643 595793591 595792955 4.380000e-149 538.0
32 TraesCS7A01G046800 chr7B 80.560 643 99 16 7 637 195361594 195360966 4.500000e-129 472.0
33 TraesCS7A01G046800 chr7B 80.460 87 12 4 1944 2030 51069887 51069968 1.160000e-05 62.1
34 TraesCS7A01G046800 chr6A 81.443 776 121 13 3089 3852 92573360 92572596 7.070000e-172 614.0
35 TraesCS7A01G046800 chr6A 77.033 418 74 13 3 410 483904296 483904701 1.800000e-53 220.0
36 TraesCS7A01G046800 chr6A 79.331 329 40 20 328 636 72876468 72876148 5.040000e-49 206.0
37 TraesCS7A01G046800 chr6A 77.215 316 54 16 336 637 578532542 578532853 6.620000e-38 169.0
38 TraesCS7A01G046800 chr6A 76.220 328 65 13 328 647 562700750 562700428 1.110000e-35 161.0
39 TraesCS7A01G046800 chr6A 76.656 317 54 17 328 629 59328372 59328061 1.430000e-34 158.0
40 TraesCS7A01G046800 chr5D 84.154 650 67 18 4 637 69986349 69985720 7.120000e-167 597.0
41 TraesCS7A01G046800 chr5D 83.801 463 74 1 3391 3852 391852410 391851948 4.570000e-119 438.0
42 TraesCS7A01G046800 chr5D 83.153 463 77 1 3391 3852 280744690 280745152 4.600000e-114 422.0
43 TraesCS7A01G046800 chr5D 82.022 445 58 17 210 637 528757926 528758365 3.660000e-95 359.0
44 TraesCS7A01G046800 chr5D 78.605 430 58 15 237 637 284122458 284122034 1.780000e-63 254.0
45 TraesCS7A01G046800 chr5D 84.158 101 14 2 1929 2029 413619775 413619873 3.170000e-16 97.1
46 TraesCS7A01G046800 chr5D 82.292 96 14 3 1935 2029 521497526 521497433 3.190000e-11 80.5
47 TraesCS7A01G046800 chr6B 82.875 654 85 18 1 637 515566020 515566663 2.600000e-156 562.0
48 TraesCS7A01G046800 chr6B 82.389 653 86 19 2 636 523943817 523944458 3.390000e-150 542.0
49 TraesCS7A01G046800 chr6B 82.298 531 75 13 2519 3030 696994571 696994041 3.530000e-120 442.0
50 TraesCS7A01G046800 chr6B 87.417 302 32 3 3089 3388 56420229 56419932 3.690000e-90 342.0
51 TraesCS7A01G046800 chr6B 79.326 445 64 18 222 643 516872126 516871687 1.750000e-73 287.0
52 TraesCS7A01G046800 chr6B 88.235 85 10 0 1945 2029 255535420 255535504 6.810000e-18 102.0
53 TraesCS7A01G046800 chr6B 88.571 70 7 1 1943 2012 403189497 403189565 2.470000e-12 84.2
54 TraesCS7A01G046800 chr4B 83.031 607 69 19 44 637 632334711 632334126 1.590000e-143 520.0
55 TraesCS7A01G046800 chr4B 76.115 628 110 27 35 643 584134371 584133765 3.760000e-75 292.0
56 TraesCS7A01G046800 chr4D 84.658 541 56 14 108 637 69477601 69478125 7.380000e-142 514.0
57 TraesCS7A01G046800 chr4D 82.741 591 68 22 69 637 60157498 60158076 2.670000e-136 496.0
58 TraesCS7A01G046800 chr4D 87.500 304 33 3 3086 3388 449061158 449061457 2.850000e-91 346.0
59 TraesCS7A01G046800 chr4D 76.855 337 52 20 316 637 307227206 307227531 2.380000e-37 167.0
60 TraesCS7A01G046800 chr4D 80.097 206 27 7 328 521 10646797 10647000 1.440000e-29 141.0
61 TraesCS7A01G046800 chr4D 95.000 40 2 0 53 92 69477562 69477601 3.210000e-06 63.9
62 TraesCS7A01G046800 chr4D 95.000 40 2 0 1942 1981 381141147 381141108 3.210000e-06 63.9
63 TraesCS7A01G046800 chr4D 94.595 37 1 1 1942 1977 427029638 427029602 5.380000e-04 56.5
64 TraesCS7A01G046800 chr4D 94.595 37 1 1 1942 1977 469167298 469167334 5.380000e-04 56.5
65 TraesCS7A01G046800 chr5A 83.656 465 74 2 3390 3852 353608962 353609426 1.640000e-118 436.0
66 TraesCS7A01G046800 chr1A 89.362 329 26 5 33 361 402261155 402260836 4.630000e-109 405.0
67 TraesCS7A01G046800 chr1A 81.266 395 52 15 259 637 373787686 373787298 2.250000e-77 300.0
68 TraesCS7A01G046800 chr1A 80.172 232 24 17 329 546 548400245 548400022 1.850000e-33 154.0
69 TraesCS7A01G046800 chr1A 79.018 224 37 8 419 637 459179267 459179485 1.120000e-30 145.0
70 TraesCS7A01G046800 chr1A 74.044 366 62 23 297 637 586262812 586262455 6.760000e-23 119.0
71 TraesCS7A01G046800 chr1A 80.272 147 22 7 404 547 449515147 449515289 1.890000e-18 104.0
72 TraesCS7A01G046800 chr1A 73.684 342 58 19 320 637 586256324 586255991 1.890000e-18 104.0
73 TraesCS7A01G046800 chr1A 74.888 223 48 8 418 637 514061261 514061044 1.140000e-15 95.3
74 TraesCS7A01G046800 chr1A 82.558 86 14 1 1952 2037 49892408 49892492 1.480000e-09 75.0
75 TraesCS7A01G046800 chr1A 91.111 45 4 0 1946 1990 62614124 62614080 1.160000e-05 62.1
76 TraesCS7A01G046800 chr2D 88.372 301 28 4 3089 3388 495126365 495126071 4.730000e-94 355.0
77 TraesCS7A01G046800 chr2D 79.487 351 56 10 297 637 318560263 318560607 6.430000e-58 235.0
78 TraesCS7A01G046800 chr2D 86.667 90 8 4 1942 2029 51248116 51248203 3.170000e-16 97.1
79 TraesCS7A01G046800 chr3A 88.333 300 27 5 3089 3386 247743215 247743508 1.700000e-93 353.0
80 TraesCS7A01G046800 chr3A 84.375 64 4 5 1924 1982 743110115 743110177 1.490000e-04 58.4
81 TraesCS7A01G046800 chr5B 87.829 304 30 4 3087 3388 318378033 318378331 2.200000e-92 350.0
82 TraesCS7A01G046800 chr5B 87.789 303 29 5 3089 3388 318385206 318385503 7.920000e-92 348.0
83 TraesCS7A01G046800 chr5B 83.908 87 14 0 1943 2029 406932571 406932657 2.470000e-12 84.2
84 TraesCS7A01G046800 chr5B 83.529 85 12 2 1945 2029 384594904 384594822 1.150000e-10 78.7
85 TraesCS7A01G046800 chrUn 77.642 246 34 12 285 519 214471531 214471296 3.120000e-26 130.0
86 TraesCS7A01G046800 chr2B 89.286 84 8 1 1943 2026 136171324 136171406 1.890000e-18 104.0
87 TraesCS7A01G046800 chr2A 85.859 99 9 5 1937 2033 531859072 531858977 2.450000e-17 100.0
88 TraesCS7A01G046800 chr1B 80.682 88 15 2 1943 2029 398148690 398148776 2.480000e-07 67.6


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 TraesCS7A01G046800 chr7A 21203702 21207553 3851 True 7114.00 7114 100.0000 1 3852 1 chr7A.!!$R1 3851
1 TraesCS7A01G046800 chr7D 20725082 20729453 4371 True 2538.00 4926 93.5350 638 3852 2 chr7D.!!$R1 3214
2 TraesCS7A01G046800 chr4A 669389273 669392563 3290 True 1001.50 1882 88.1650 791 3852 4 chr4A.!!$R4 3061
3 TraesCS7A01G046800 chr4A 591673402 591674036 634 False 652.00 652 85.4710 3 637 1 chr4A.!!$F3 634
4 TraesCS7A01G046800 chr4A 591292130 591292766 636 False 651.00 651 85.3620 1 637 1 chr4A.!!$F2 636
5 TraesCS7A01G046800 chr4A 592310633 592311269 636 True 645.00 645 85.2080 1 637 1 chr4A.!!$R2 636
6 TraesCS7A01G046800 chr4A 592362912 592363548 636 True 645.00 645 85.1850 1 637 1 chr4A.!!$R3 636
7 TraesCS7A01G046800 chr6D 458507982 458508808 826 True 765.00 765 83.5530 1001 1824 1 chr6D.!!$R6 823
8 TraesCS7A01G046800 chr6D 384353457 384354077 620 False 675.00 675 86.5290 19 637 1 chr6D.!!$F3 618
9 TraesCS7A01G046800 chr6D 458529496 458530999 1503 True 617.50 776 83.0205 1001 3055 2 chr6D.!!$R7 2054
10 TraesCS7A01G046800 chr6D 242211362 242211991 629 True 449.00 449 80.2730 1 637 1 chr6D.!!$R1 636
11 TraesCS7A01G046800 chr6D 365585824 365586437 613 False 435.00 435 80.0920 1 637 1 chr6D.!!$F2 636
12 TraesCS7A01G046800 chr6D 291391086 291391716 630 True 235.00 235 74.7380 1 637 1 chr6D.!!$R2 636
13 TraesCS7A01G046800 chr3D 351130403 351131045 642 True 728.00 728 87.3850 1 637 1 chr3D.!!$R1 636
14 TraesCS7A01G046800 chr1D 261091559 261092193 634 False 726.00 726 87.4810 1 637 1 chr1D.!!$F2 636
15 TraesCS7A01G046800 chr1D 443793079 443793686 607 True 361.00 361 78.2680 1 610 1 chr1D.!!$R1 609
16 TraesCS7A01G046800 chr7B 517096356 517097000 644 True 669.00 669 85.7140 1 637 1 chr7B.!!$R2 636
17 TraesCS7A01G046800 chr7B 595792955 595793591 636 True 538.00 538 82.3170 3 643 1 chr7B.!!$R3 640
18 TraesCS7A01G046800 chr7B 195360966 195361594 628 True 472.00 472 80.5600 7 637 1 chr7B.!!$R1 630
19 TraesCS7A01G046800 chr6A 92572596 92573360 764 True 614.00 614 81.4430 3089 3852 1 chr6A.!!$R3 763
20 TraesCS7A01G046800 chr5D 69985720 69986349 629 True 597.00 597 84.1540 4 637 1 chr5D.!!$R1 633
21 TraesCS7A01G046800 chr6B 515566020 515566663 643 False 562.00 562 82.8750 1 637 1 chr6B.!!$F3 636
22 TraesCS7A01G046800 chr6B 523943817 523944458 641 False 542.00 542 82.3890 2 636 1 chr6B.!!$F4 634
23 TraesCS7A01G046800 chr6B 696994041 696994571 530 True 442.00 442 82.2980 2519 3030 1 chr6B.!!$R3 511
24 TraesCS7A01G046800 chr4B 632334126 632334711 585 True 520.00 520 83.0310 44 637 1 chr4B.!!$R2 593
25 TraesCS7A01G046800 chr4B 584133765 584134371 606 True 292.00 292 76.1150 35 643 1 chr4B.!!$R1 608
26 TraesCS7A01G046800 chr4D 60157498 60158076 578 False 496.00 496 82.7410 69 637 1 chr4D.!!$F2 568
27 TraesCS7A01G046800 chr4D 69477562 69478125 563 False 288.95 514 89.8290 53 637 2 chr4D.!!$F6 584

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
811 2101 0.036732 TTCAGCAGACAGGCGGAATT 59.963 50.0 0.00 0.0 41.81 2.17 F
1680 3016 0.250901 GGGCCTATCCGCACATCAAT 60.251 55.0 0.84 0.0 34.94 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2355 3879 1.237954 TGGCGGCTTTATCGTGCAAA 61.238 50.0 11.43 0.0 0.0 3.68 R
3678 5275 0.096976 GTTGACATGTTCCGGCATCG 59.903 55.0 0.00 0.0 0.0 3.84 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
21 22 4.631740 TGAGCCTCCACCGACCCA 62.632 66.667 0.00 0.00 0.00 4.51
98 104 3.053896 TCGTTCAGAGAGCGGCGA 61.054 61.111 12.98 0.00 36.93 5.54
184 225 4.093743 GGGAGAGAGGAAAAGAGAGTTCT 58.906 47.826 0.00 0.00 34.29 3.01
257 310 4.681978 GTTCACCGGCGAGGCAGT 62.682 66.667 9.30 0.00 46.52 4.40
548 652 1.897133 GGCCCTAACCGGTGAAAATTT 59.103 47.619 8.52 0.00 0.00 1.82
551 655 2.232696 CCCTAACCGGTGAAAATTTGGG 59.767 50.000 8.52 7.43 32.07 4.12
552 656 2.353307 CCTAACCGGTGAAAATTTGGGC 60.353 50.000 8.52 0.00 0.00 5.36
555 659 1.295101 CGGTGAAAATTTGGGCCCC 59.705 57.895 22.27 1.27 0.00 5.80
556 660 1.191489 CGGTGAAAATTTGGGCCCCT 61.191 55.000 22.27 0.00 0.00 4.79
619 729 0.827507 GGCTTTGAGGGCCTGTTGAA 60.828 55.000 12.95 0.00 45.57 2.69
676 787 3.129813 CACATCCATTCACAAGTCCATGG 59.870 47.826 4.97 4.97 38.04 3.66
679 790 2.094675 CCATTCACAAGTCCATGGGTC 58.905 52.381 13.02 5.81 33.70 4.46
681 792 0.762418 TTCACAAGTCCATGGGTCGT 59.238 50.000 13.02 1.35 0.00 4.34
698 809 3.797256 GGTCGTATTTTGATCACGAGGAG 59.203 47.826 5.69 0.00 44.53 3.69
709 820 0.891373 CACGAGGAGTCCATGTGTCT 59.109 55.000 20.16 0.00 0.00 3.41
723 834 4.949238 CCATGTGTCTACATCCATCCAAAA 59.051 41.667 0.00 0.00 45.53 2.44
724 835 5.163622 CCATGTGTCTACATCCATCCAAAAC 60.164 44.000 0.00 0.00 45.53 2.43
748 2038 0.318762 TGCCTGTGTGCACATACGTA 59.681 50.000 24.69 10.97 41.01 3.57
763 2053 6.633683 CACATACGTATTCGCTTTTACGATT 58.366 36.000 5.03 0.00 42.83 3.34
764 2054 7.565610 GCACATACGTATTCGCTTTTACGATTA 60.566 37.037 15.52 0.00 42.83 1.75
769 2059 5.999361 CGTATTCGCTTTTACGATTATTCCG 59.001 40.000 0.00 0.00 42.83 4.30
784 2074 7.094334 ACGATTATTCCGCTATGAGATGTCTTA 60.094 37.037 0.00 0.00 0.00 2.10
803 2093 6.090129 GTCTTAGTTACTCTTCAGCAGACAG 58.910 44.000 0.00 0.00 0.00 3.51
811 2101 0.036732 TTCAGCAGACAGGCGGAATT 59.963 50.000 0.00 0.00 41.81 2.17
812 2102 0.901827 TCAGCAGACAGGCGGAATTA 59.098 50.000 0.00 0.00 35.07 1.40
814 2104 1.667724 CAGCAGACAGGCGGAATTAAG 59.332 52.381 0.00 0.00 39.27 1.85
815 2105 1.017387 GCAGACAGGCGGAATTAAGG 58.983 55.000 0.00 0.00 0.00 2.69
817 2107 0.546598 AGACAGGCGGAATTAAGGGG 59.453 55.000 0.00 0.00 0.00 4.79
821 2111 1.076265 GGCGGAATTAAGGGGCCTT 60.076 57.895 0.84 0.00 40.59 4.35
893 2185 1.680338 AAGAACAGGACAGCCAACAC 58.320 50.000 0.00 0.00 36.29 3.32
918 2210 5.269991 TGCTATATGTATAGGTCAGTCCCC 58.730 45.833 8.66 0.00 36.90 4.81
919 2211 4.650131 GCTATATGTATAGGTCAGTCCCCC 59.350 50.000 8.66 0.00 36.90 5.40
920 2212 2.011122 ATGTATAGGTCAGTCCCCCG 57.989 55.000 0.00 0.00 36.75 5.73
921 2213 0.928505 TGTATAGGTCAGTCCCCCGA 59.071 55.000 0.00 0.00 36.75 5.14
922 2214 1.326328 GTATAGGTCAGTCCCCCGAC 58.674 60.000 0.00 0.00 39.50 4.79
965 2257 1.153369 ACGAGCACAACACAGCACT 60.153 52.632 0.00 0.00 0.00 4.40
970 2262 1.097547 GCACAACACAGCACTGAGGT 61.098 55.000 4.31 0.00 0.00 3.85
971 2263 0.940126 CACAACACAGCACTGAGGTC 59.060 55.000 4.31 0.00 0.00 3.85
972 2264 0.833287 ACAACACAGCACTGAGGTCT 59.167 50.000 4.31 0.00 0.00 3.85
973 2265 2.039418 ACAACACAGCACTGAGGTCTA 58.961 47.619 4.31 0.00 0.00 2.59
975 2267 2.802816 CAACACAGCACTGAGGTCTAAC 59.197 50.000 4.31 0.00 0.00 2.34
976 2268 1.344763 ACACAGCACTGAGGTCTAACC 59.655 52.381 4.31 0.00 38.99 2.85
981 2317 2.089980 GCACTGAGGTCTAACCGTCTA 58.910 52.381 0.00 0.00 44.90 2.59
993 2329 7.016858 AGGTCTAACCGTCTAAGAGAGAGATAT 59.983 40.741 0.00 0.00 44.90 1.63
1194 2530 4.862092 CTGATCGCCGCGCTGTCT 62.862 66.667 8.21 0.00 0.00 3.41
1680 3016 0.250901 GGGCCTATCCGCACATCAAT 60.251 55.000 0.84 0.00 34.94 2.57
1692 3028 3.021269 CACATCAATTGCACTGTGCTT 57.979 42.857 30.43 16.66 45.31 3.91
1854 3202 7.665559 TCCCACATGCTCATATATTAGGTTTTC 59.334 37.037 0.00 0.00 0.00 2.29
2064 3584 9.773328 CATATTGTACTTATTTGGTGTTGTGAG 57.227 33.333 0.00 0.00 0.00 3.51
2077 3597 5.293324 TGGTGTTGTGAGCGTTGATATATTC 59.707 40.000 0.00 0.00 0.00 1.75
2350 3874 2.835764 AGGCAACATGGAATCTTGCAAT 59.164 40.909 16.85 5.16 41.77 3.56
2355 3879 3.705051 ACATGGAATCTTGCAATGACCT 58.295 40.909 0.00 0.00 30.51 3.85
2785 4320 2.012673 AGCGACATCTTCATGAAAGCC 58.987 47.619 9.88 0.00 34.76 4.35
3189 4738 8.996271 TGCTATAACTGCTATGATCTTGAAATG 58.004 33.333 0.00 0.00 0.00 2.32
3214 4763 5.765677 TGTGATTCGGTGGAAAACTCATAAA 59.234 36.000 0.00 0.00 35.40 1.40
3366 4924 7.956420 AACAACATTGAGAGTATGACGTTAA 57.044 32.000 0.00 0.00 0.00 2.01
3393 4989 7.913423 AGAACGATCATATTGAATTGTGTCAG 58.087 34.615 0.00 0.00 0.00 3.51
3412 5008 9.147732 TGTGTCAGAAGTCTATTGATATACCAT 57.852 33.333 0.00 0.00 0.00 3.55
3515 5112 4.163458 TCAAACGTCAGCTATAACACGA 57.837 40.909 7.94 0.00 36.14 4.35
3591 5188 3.326006 AGCTCAAGAGTGTGATTTCCTCA 59.674 43.478 0.00 0.00 0.00 3.86
3623 5220 4.172020 GGAGAGATATTCTTAGGGCCCTT 58.828 47.826 34.04 14.96 35.87 3.95
3647 5244 1.003580 GTGTGATGACACCCACCATCT 59.996 52.381 3.79 0.00 45.96 2.90
3678 5275 4.038883 AGACACAGGTGACTAGGTAACAAC 59.961 45.833 6.40 0.00 40.21 3.32
3786 5383 0.471211 GGATACATCTCACCCCGGGA 60.471 60.000 26.32 0.00 0.00 5.14
3797 5394 1.877443 CACCCCGGGATTTATAAAGCG 59.123 52.381 26.32 2.06 0.00 4.68
3845 5442 1.021968 AACCAAAGGTTCACTCGCAC 58.978 50.000 0.00 0.00 43.05 5.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
85 91 1.927608 CTTCAGTCGCCGCTCTCTGA 61.928 60.000 5.37 5.37 35.54 3.27
98 104 1.452108 GGCGGCTAATGGCTTCAGT 60.452 57.895 0.00 0.00 41.46 3.41
199 246 2.598099 TCTCCCCGTGCACGTACA 60.598 61.111 34.81 18.08 37.74 2.90
200 247 2.181021 CTCTCCCCGTGCACGTAC 59.819 66.667 34.81 0.00 37.74 3.67
201 248 2.034532 TCTCTCCCCGTGCACGTA 59.965 61.111 34.81 20.01 37.74 3.57
202 249 3.374402 CTCTCTCCCCGTGCACGT 61.374 66.667 34.81 0.00 37.74 4.49
459 547 3.352338 GAGGACGCCGGTCAATCGT 62.352 63.158 1.90 2.89 45.28 3.73
548 652 4.631740 TCGTGTCTCAGGGGCCCA 62.632 66.667 27.72 3.26 0.00 5.36
551 655 2.219325 CTCAGTCGTGTCTCAGGGGC 62.219 65.000 0.00 0.00 0.00 5.80
552 656 0.896019 ACTCAGTCGTGTCTCAGGGG 60.896 60.000 0.00 0.00 0.00 4.79
578 684 0.308376 TTTTTAACGCCCACGCTCAC 59.692 50.000 0.00 0.00 45.53 3.51
647 758 2.503331 TGTGAATGGATGTGGACACAC 58.497 47.619 7.37 2.33 45.05 3.82
676 787 3.777478 TCCTCGTGATCAAAATACGACC 58.223 45.455 0.00 0.00 41.33 4.79
679 790 3.797256 GGACTCCTCGTGATCAAAATACG 59.203 47.826 0.00 0.00 39.04 3.06
681 792 5.104941 ACATGGACTCCTCGTGATCAAAATA 60.105 40.000 0.00 0.00 0.00 1.40
698 809 3.134623 TGGATGGATGTAGACACATGGAC 59.865 47.826 0.00 0.00 45.58 4.02
709 820 3.505680 GCACAGTGTTTTGGATGGATGTA 59.494 43.478 1.61 0.00 0.00 2.29
748 2038 4.510340 AGCGGAATAATCGTAAAAGCGAAT 59.490 37.500 0.00 0.00 44.38 3.34
763 2053 7.526142 AACTAAGACATCTCATAGCGGAATA 57.474 36.000 0.00 0.00 0.00 1.75
764 2054 6.412362 AACTAAGACATCTCATAGCGGAAT 57.588 37.500 0.00 0.00 0.00 3.01
769 2059 8.625651 TGAAGAGTAACTAAGACATCTCATAGC 58.374 37.037 0.00 0.00 0.00 2.97
784 2074 2.028567 GCCTGTCTGCTGAAGAGTAACT 60.029 50.000 0.00 0.00 34.84 2.24
803 2093 1.076265 AAGGCCCCTTAATTCCGCC 60.076 57.895 0.00 0.00 40.03 6.13
817 2107 1.545136 GTAGAGCGTATAGGGGAAGGC 59.455 57.143 0.00 0.00 0.00 4.35
821 2111 1.453633 AGGGTAGAGCGTATAGGGGA 58.546 55.000 0.00 0.00 0.00 4.81
825 2115 3.946558 GGGACATAGGGTAGAGCGTATAG 59.053 52.174 0.00 0.00 0.00 1.31
826 2116 3.590630 AGGGACATAGGGTAGAGCGTATA 59.409 47.826 0.00 0.00 0.00 1.47
827 2117 2.379226 AGGGACATAGGGTAGAGCGTAT 59.621 50.000 0.00 0.00 0.00 3.06
828 2118 1.779092 AGGGACATAGGGTAGAGCGTA 59.221 52.381 0.00 0.00 0.00 4.42
829 2119 0.556747 AGGGACATAGGGTAGAGCGT 59.443 55.000 0.00 0.00 0.00 5.07
831 2121 4.048970 TGATAGGGACATAGGGTAGAGC 57.951 50.000 0.00 0.00 0.00 4.09
876 2168 1.267806 CATGTGTTGGCTGTCCTGTTC 59.732 52.381 0.00 0.00 0.00 3.18
878 2170 1.174712 GCATGTGTTGGCTGTCCTGT 61.175 55.000 0.00 0.00 0.00 4.00
893 2185 6.183360 GGGGACTGACCTATACATATAGCATG 60.183 46.154 0.99 0.00 38.98 4.06
918 2210 4.468510 TGTGCTAATTATATAGGGGGTCGG 59.531 45.833 0.00 0.00 0.00 4.79
919 2211 5.670792 TGTGCTAATTATATAGGGGGTCG 57.329 43.478 0.00 0.00 0.00 4.79
920 2212 6.879458 CACTTGTGCTAATTATATAGGGGGTC 59.121 42.308 0.00 0.00 0.00 4.46
921 2213 6.747186 GCACTTGTGCTAATTATATAGGGGGT 60.747 42.308 17.36 0.00 0.00 4.95
922 2214 5.648092 GCACTTGTGCTAATTATATAGGGGG 59.352 44.000 17.36 0.00 0.00 5.40
965 2257 4.224594 TCTCTCTTAGACGGTTAGACCTCA 59.775 45.833 0.00 0.00 35.66 3.86
970 2262 8.028354 CGTATATCTCTCTCTTAGACGGTTAGA 58.972 40.741 0.00 0.00 29.56 2.10
971 2263 8.028354 TCGTATATCTCTCTCTTAGACGGTTAG 58.972 40.741 0.00 0.00 32.93 2.34
972 2264 7.890515 TCGTATATCTCTCTCTTAGACGGTTA 58.109 38.462 0.00 0.00 32.93 2.85
973 2265 6.757237 TCGTATATCTCTCTCTTAGACGGTT 58.243 40.000 0.00 0.00 32.93 4.44
975 2267 7.036829 TGATCGTATATCTCTCTCTTAGACGG 58.963 42.308 0.00 0.00 32.93 4.79
976 2268 8.539674 CATGATCGTATATCTCTCTCTTAGACG 58.460 40.741 0.00 0.00 33.25 4.18
981 2317 5.948758 TGCCATGATCGTATATCTCTCTCTT 59.051 40.000 0.00 0.00 0.00 2.85
993 2329 1.067669 GTCTGAGCTGCCATGATCGTA 59.932 52.381 0.00 0.00 0.00 3.43
1194 2530 2.530151 AGCTTGGACTGGGGCAGA 60.530 61.111 0.00 0.00 35.18 4.26
1202 2538 0.318762 GAGGAACGACAGCTTGGACT 59.681 55.000 0.00 0.00 0.00 3.85
1420 2756 2.033194 GCCCGTCAAAGTCCTTCCG 61.033 63.158 0.00 0.00 0.00 4.30
1978 3496 9.010366 GGCTTTTTCGATCACTATTTTAATGAC 57.990 33.333 0.00 0.00 0.00 3.06
2001 3519 7.785506 ACTCCTTCTGTACACTAATATAAGGCT 59.214 37.037 0.00 0.00 33.75 4.58
2161 3685 4.986659 TCAAACTCGACCAAGTTAACTAGC 59.013 41.667 8.92 0.00 38.52 3.42
2350 3874 1.810151 GGCTTTATCGTGCAAAGGTCA 59.190 47.619 0.00 0.00 34.28 4.02
2355 3879 1.237954 TGGCGGCTTTATCGTGCAAA 61.238 50.000 11.43 0.00 0.00 3.68
2543 4070 2.871637 GCAGAACAGACTACCATGCACA 60.872 50.000 0.00 0.00 32.58 4.57
2785 4320 7.406553 TGAAAATCTTATATTCGCTGAAACCG 58.593 34.615 0.00 0.00 0.00 4.44
3050 4599 5.851177 GGCAATTGTACATTGTATCGTATGC 59.149 40.000 7.40 7.64 0.00 3.14
3189 4738 2.875933 TGAGTTTTCCACCGAATCACAC 59.124 45.455 0.00 0.00 0.00 3.82
3214 4763 0.884704 GTCCTTCCACACATGCACGT 60.885 55.000 0.00 0.00 0.00 4.49
3366 4924 8.729756 TGACACAATTCAATATGATCGTTCTTT 58.270 29.630 0.00 0.00 0.00 2.52
3412 5008 9.565213 GAAACTAAAGCATACGTTAACTCTCTA 57.435 33.333 3.71 0.00 0.00 2.43
3647 5244 2.238646 AGTCACCTGTGTCTGACCAAAA 59.761 45.455 5.17 0.00 38.04 2.44
3678 5275 0.096976 GTTGACATGTTCCGGCATCG 59.903 55.000 0.00 0.00 0.00 3.84
3767 5364 0.471211 TCCCGGGGTGAGATGTATCC 60.471 60.000 23.50 0.00 0.00 2.59
3786 5383 5.539582 TTGCTTCACGACGCTTTATAAAT 57.460 34.783 0.00 0.00 0.00 1.40
3797 5394 2.096013 GCTATTCCCTTTGCTTCACGAC 59.904 50.000 0.00 0.00 0.00 4.34


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

AutoCloner maintained by Alex Coulton.