Multiple sequence alignment - TraesCS4D01G182200

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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 TraesCS4D01G182200 chr4D 100.000 4031 0 0 1 4031 318493055 318489025 0.000000e+00 7444.0
1 TraesCS4D01G182200 chr4D 97.101 69 2 0 1869 1937 22644821 22644889 2.550000e-22 117.0
2 TraesCS4D01G182200 chr4D 97.101 69 2 0 1869 1937 123413556 123413624 2.550000e-22 117.0
3 TraesCS4D01G182200 chr4D 97.101 69 2 0 1869 1937 123538578 123538646 2.550000e-22 117.0
4 TraesCS4D01G182200 chr4D 94.444 36 2 0 3656 3691 318489362 318489327 5.630000e-04 56.5
5 TraesCS4D01G182200 chr4D 94.444 36 2 0 3694 3729 318489400 318489365 5.630000e-04 56.5
6 TraesCS4D01G182200 chr4B 97.206 1682 36 7 1713 3389 395733063 395731388 0.000000e+00 2835.0
7 TraesCS4D01G182200 chr4B 96.778 931 10 2 808 1718 395734664 395733734 0.000000e+00 1535.0
8 TraesCS4D01G182200 chr4B 92.530 415 20 7 421 825 395816270 395815857 5.810000e-163 584.0
9 TraesCS4D01G182200 chr4B 93.503 354 23 0 1 354 395816988 395816635 9.920000e-146 527.0
10 TraesCS4D01G182200 chr4B 93.916 263 14 2 3469 3729 395731387 395731125 2.920000e-106 396.0
11 TraesCS4D01G182200 chr4B 94.118 255 8 3 3656 3908 395731160 395730911 8.180000e-102 381.0
12 TraesCS4D01G182200 chr4B 96.098 205 7 1 421 624 395816637 395816433 2.320000e-87 333.0
13 TraesCS4D01G182200 chr4B 93.252 163 11 0 192 354 395816430 395816268 1.450000e-59 241.0
14 TraesCS4D01G182200 chr4B 97.222 36 1 0 3694 3729 395731198 395731163 1.210000e-05 62.1
15 TraesCS4D01G182200 chr4B 94.444 36 2 0 3656 3691 395731121 395731086 5.630000e-04 56.5
16 TraesCS4D01G182200 chr4A 94.541 1209 49 6 528 1720 155811111 155809904 0.000000e+00 1851.0
17 TraesCS4D01G182200 chr4A 96.957 986 26 2 2382 3363 155807951 155806966 0.000000e+00 1652.0
18 TraesCS4D01G182200 chr4A 97.644 679 14 2 1713 2390 155809190 155808513 0.000000e+00 1164.0
19 TraesCS4D01G182200 chr4A 93.018 444 27 3 1 441 155827629 155827187 0.000000e+00 645.0
20 TraesCS4D01G182200 chr4A 92.754 207 14 1 3374 3580 155806929 155806724 8.470000e-77 298.0
21 TraesCS4D01G182200 chr4A 88.636 220 8 7 3690 3908 155806543 155806340 6.690000e-63 252.0
22 TraesCS4D01G182200 chr4A 100.000 28 0 0 3656 3683 155806539 155806512 7.000000e-03 52.8
23 TraesCS4D01G182200 chr6A 83.629 507 42 14 3396 3894 572334264 572333791 4.780000e-119 438.0
24 TraesCS4D01G182200 chr2D 93.600 125 8 0 3907 4031 165543397 165543273 1.910000e-43 187.0
25 TraesCS4D01G182200 chr2D 94.167 120 4 1 1939 2058 591995230 591995114 3.200000e-41 180.0
26 TraesCS4D01G182200 chr7B 82.870 216 28 4 3415 3623 218530909 218531122 6.880000e-43 185.0
27 TraesCS4D01G182200 chr1A 93.548 124 8 0 3908 4031 243798877 243798754 6.880000e-43 185.0
28 TraesCS4D01G182200 chrUn 94.167 120 4 1 1939 2058 341018765 341018649 3.200000e-41 180.0
29 TraesCS4D01G182200 chrUn 94.167 120 4 1 1939 2058 355919991 355919875 3.200000e-41 180.0
30 TraesCS4D01G182200 chrUn 94.167 120 4 1 1939 2058 362350439 362350323 3.200000e-41 180.0
31 TraesCS4D01G182200 chrUn 94.167 120 4 1 1939 2058 454067251 454067135 3.200000e-41 180.0
32 TraesCS4D01G182200 chrUn 97.101 69 2 0 1869 1937 189393203 189393271 2.550000e-22 117.0
33 TraesCS4D01G182200 chr5D 94.167 120 4 1 1939 2058 503255226 503255342 3.200000e-41 180.0
34 TraesCS4D01G182200 chr3D 92.742 124 9 0 3908 4031 575838228 575838105 3.200000e-41 180.0
35 TraesCS4D01G182200 chr3D 94.167 120 4 1 1939 2058 589250614 589250730 3.200000e-41 180.0
36 TraesCS4D01G182200 chr6D 97.101 69 2 0 1869 1937 83976015 83975947 2.550000e-22 117.0
37 TraesCS4D01G182200 chr1D 97.101 69 2 0 1869 1937 141320936 141320868 2.550000e-22 117.0
38 TraesCS4D01G182200 chr1D 97.101 69 2 0 1869 1937 185770119 185770187 2.550000e-22 117.0
39 TraesCS4D01G182200 chr3A 80.833 120 23 0 3911 4030 641335776 641335657 1.190000e-15 95.3


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 TraesCS4D01G182200 chr4D 318489025 318493055 4030 True 2519.00 7444 96.296000 1 4031 3 chr4D.!!$R1 4030
1 TraesCS4D01G182200 chr4B 395730911 395734664 3753 True 877.60 2835 95.614000 808 3908 6 chr4B.!!$R1 3100
2 TraesCS4D01G182200 chr4B 395815857 395816988 1131 True 421.25 584 93.845750 1 825 4 chr4B.!!$R2 824
3 TraesCS4D01G182200 chr4A 155806340 155811111 4771 True 878.30 1851 95.088667 528 3908 6 chr4A.!!$R2 3380

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
411 412 0.106569 CTTGCAGCCCATATCACCCA 60.107 55.000 0.00 0.0 0.00 4.51 F
1442 1846 0.466189 GGGGCAATCGATGGATGTGT 60.466 55.000 3.24 0.0 31.83 3.72 F
2248 4052 1.294780 GGGAGTGGTCAGCTCACAG 59.705 63.158 6.78 0.0 36.46 3.66 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2059 3863 0.171903 CTTCAAGAAAGCGCCCATGG 59.828 55.0 2.29 4.14 0.00 3.66 R
2796 5170 1.767759 ACATGCTTGGGAATAGGTGC 58.232 50.0 4.44 0.00 0.00 5.01 R
3921 6501 0.039035 AGTTGAGAGTCGGGAGAGCT 59.961 55.0 0.00 0.00 41.26 4.09 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
37 38 1.351017 TCCCTTCTTTGGTCGCTTCAT 59.649 47.619 0.00 0.00 0.00 2.57
40 41 3.568538 CCTTCTTTGGTCGCTTCATTTG 58.431 45.455 0.00 0.00 0.00 2.32
52 53 2.029606 GCTTCATTTGCTATTTTGCGGC 59.970 45.455 0.00 0.00 35.36 6.53
81 82 6.230472 TGCCACATCCATATTAGTGATGTAC 58.770 40.000 4.24 1.79 45.37 2.90
90 91 7.785028 TCCATATTAGTGATGTACAAGTCCTCT 59.215 37.037 0.00 0.00 0.00 3.69
105 106 1.285023 CTCTGCCAGTGCTTTGTGC 59.715 57.895 0.00 0.00 43.25 4.57
110 111 0.386838 GCCAGTGCTTTGTGCTTCTT 59.613 50.000 0.00 0.00 43.37 2.52
116 117 2.975851 GTGCTTTGTGCTTCTTTGATCG 59.024 45.455 0.00 0.00 43.37 3.69
130 131 2.634982 TGATCGCCAATGTTTCAAGC 57.365 45.000 0.00 0.00 0.00 4.01
155 156 7.272731 GCGTAGTAGCATTGTCGATATGATTAA 59.727 37.037 12.94 0.00 37.05 1.40
229 230 1.967779 GCTATGACTCCTCTTCCTCCC 59.032 57.143 0.00 0.00 0.00 4.30
238 239 3.391382 CTTCCTCCCGCCCGAAGT 61.391 66.667 0.00 0.00 0.00 3.01
240 241 2.294132 CTTCCTCCCGCCCGAAGTAC 62.294 65.000 0.00 0.00 0.00 2.73
265 266 4.201705 GCCACATCAACATTTATTTTGGCG 60.202 41.667 0.00 0.00 37.82 5.69
279 280 4.530857 GGCGTGTCCATCCCTCGG 62.531 72.222 0.00 0.00 34.01 4.63
320 321 6.703607 CGGTTTATGCAGAACTCTAATCTCAT 59.296 38.462 13.47 0.00 0.00 2.90
339 340 4.384940 TCATCCACGAAGTTGTTGATGAA 58.615 39.130 11.28 0.00 43.78 2.57
354 355 3.137533 TGATGAATGAGTGTGTCGCAAA 58.862 40.909 0.00 0.00 0.00 3.68
356 357 1.260297 TGAATGAGTGTGTCGCAAACG 59.740 47.619 0.00 0.00 42.01 3.60
357 358 0.586319 AATGAGTGTGTCGCAAACGG 59.414 50.000 0.00 0.00 40.63 4.44
358 359 0.249699 ATGAGTGTGTCGCAAACGGA 60.250 50.000 0.00 0.00 40.63 4.69
359 360 0.874175 TGAGTGTGTCGCAAACGGAG 60.874 55.000 0.00 0.00 40.63 4.63
361 362 0.386476 AGTGTGTCGCAAACGGAGTA 59.614 50.000 0.00 0.00 45.00 2.59
362 363 1.000506 AGTGTGTCGCAAACGGAGTAT 59.999 47.619 0.00 0.00 45.00 2.12
363 364 1.126113 GTGTGTCGCAAACGGAGTATG 59.874 52.381 0.00 0.00 45.00 2.39
364 365 0.719465 GTGTCGCAAACGGAGTATGG 59.281 55.000 0.00 0.00 45.00 2.74
365 366 0.604073 TGTCGCAAACGGAGTATGGA 59.396 50.000 0.00 0.00 45.00 3.41
366 367 1.001068 TGTCGCAAACGGAGTATGGAA 59.999 47.619 0.00 0.00 45.00 3.53
367 368 1.659098 GTCGCAAACGGAGTATGGAAG 59.341 52.381 0.00 0.00 45.00 3.46
368 369 1.546923 TCGCAAACGGAGTATGGAAGA 59.453 47.619 0.00 0.00 45.00 2.87
369 370 2.167693 TCGCAAACGGAGTATGGAAGAT 59.832 45.455 0.00 0.00 45.00 2.40
370 371 2.285220 CGCAAACGGAGTATGGAAGATG 59.715 50.000 0.00 0.00 45.00 2.90
371 372 3.270877 GCAAACGGAGTATGGAAGATGT 58.729 45.455 0.00 0.00 45.00 3.06
372 373 3.309954 GCAAACGGAGTATGGAAGATGTC 59.690 47.826 0.00 0.00 45.00 3.06
373 374 3.821421 AACGGAGTATGGAAGATGTCC 57.179 47.619 0.00 0.00 45.00 4.02
374 375 3.033659 ACGGAGTATGGAAGATGTCCT 57.966 47.619 0.00 0.00 44.26 3.85
375 376 3.375699 ACGGAGTATGGAAGATGTCCTT 58.624 45.455 0.00 0.00 44.26 3.36
376 377 3.133003 ACGGAGTATGGAAGATGTCCTTG 59.867 47.826 0.00 0.00 44.26 3.61
377 378 5.362068 ACGGAGTATGGAAGATGTCCTTGT 61.362 45.833 0.00 0.00 44.26 3.16
378 379 7.360920 ACGGAGTATGGAAGATGTCCTTGTG 62.361 48.000 0.00 0.00 44.26 3.33
385 386 4.200092 GGAAGATGTCCTTGTGGATTACC 58.800 47.826 0.00 0.00 45.29 2.85
386 387 4.080299 GGAAGATGTCCTTGTGGATTACCT 60.080 45.833 0.00 0.00 45.29 3.08
387 388 5.501156 GAAGATGTCCTTGTGGATTACCTT 58.499 41.667 0.00 0.00 45.29 3.50
388 389 5.104259 AGATGTCCTTGTGGATTACCTTC 57.896 43.478 0.00 0.00 45.29 3.46
389 390 3.713826 TGTCCTTGTGGATTACCTTCC 57.286 47.619 0.00 0.00 45.29 3.46
390 391 2.983192 TGTCCTTGTGGATTACCTTCCA 59.017 45.455 0.00 0.00 45.29 3.53
398 399 3.889815 TGGATTACCTTCCATCTTGCAG 58.110 45.455 0.00 0.00 40.90 4.41
399 400 2.620585 GGATTACCTTCCATCTTGCAGC 59.379 50.000 0.00 0.00 35.72 5.25
400 401 2.128771 TTACCTTCCATCTTGCAGCC 57.871 50.000 0.00 0.00 0.00 4.85
401 402 0.255890 TACCTTCCATCTTGCAGCCC 59.744 55.000 0.00 0.00 0.00 5.19
402 403 1.000521 CCTTCCATCTTGCAGCCCA 60.001 57.895 0.00 0.00 0.00 5.36
403 404 0.396695 CCTTCCATCTTGCAGCCCAT 60.397 55.000 0.00 0.00 0.00 4.00
404 405 1.133699 CCTTCCATCTTGCAGCCCATA 60.134 52.381 0.00 0.00 0.00 2.74
405 406 2.490351 CCTTCCATCTTGCAGCCCATAT 60.490 50.000 0.00 0.00 0.00 1.78
406 407 2.574006 TCCATCTTGCAGCCCATATC 57.426 50.000 0.00 0.00 0.00 1.63
407 408 1.776063 TCCATCTTGCAGCCCATATCA 59.224 47.619 0.00 0.00 0.00 2.15
408 409 1.884579 CCATCTTGCAGCCCATATCAC 59.115 52.381 0.00 0.00 0.00 3.06
409 410 1.884579 CATCTTGCAGCCCATATCACC 59.115 52.381 0.00 0.00 0.00 4.02
410 411 0.183492 TCTTGCAGCCCATATCACCC 59.817 55.000 0.00 0.00 0.00 4.61
411 412 0.106569 CTTGCAGCCCATATCACCCA 60.107 55.000 0.00 0.00 0.00 4.51
412 413 0.557238 TTGCAGCCCATATCACCCAT 59.443 50.000 0.00 0.00 0.00 4.00
413 414 1.443852 TGCAGCCCATATCACCCATA 58.556 50.000 0.00 0.00 0.00 2.74
414 415 1.994794 TGCAGCCCATATCACCCATAT 59.005 47.619 0.00 0.00 0.00 1.78
415 416 2.291089 TGCAGCCCATATCACCCATATG 60.291 50.000 0.00 0.00 43.01 1.78
462 463 4.143543 TCCTGTTGCATTGTCTCATTCAA 58.856 39.130 0.00 0.00 0.00 2.69
466 467 2.184385 GCATTGTCTCATTCAAGGCG 57.816 50.000 0.00 0.00 41.31 5.52
516 517 2.031157 GGTTGGTGCACATGTGTTCTAC 60.031 50.000 26.01 19.47 0.00 2.59
526 527 4.553815 CACATGTGTTCTACTAAGTCGTCG 59.446 45.833 18.03 0.00 0.00 5.12
550 551 2.147150 GAGAGAGCCCAAACACTTCAC 58.853 52.381 0.00 0.00 0.00 3.18
688 1055 3.207669 GCCAGCCTCCATGCGAAG 61.208 66.667 0.00 0.00 36.02 3.79
703 1070 5.407995 CCATGCGAAGATAGAGAGGATTTTC 59.592 44.000 0.00 0.00 0.00 2.29
791 1168 5.956642 AGAGAGAAATGGACTCGAAGTTAC 58.043 41.667 0.00 0.00 39.12 2.50
917 1301 2.165167 CTCCTACACTAACCCACACGA 58.835 52.381 0.00 0.00 0.00 4.35
986 1390 2.943033 GAGAGAGAGAGTCCGAAGAAGG 59.057 54.545 0.00 0.00 0.00 3.46
1359 1763 0.742505 CGTGCCTCTACGATTACCCA 59.257 55.000 0.00 0.00 46.46 4.51
1442 1846 0.466189 GGGGCAATCGATGGATGTGT 60.466 55.000 3.24 0.00 31.83 3.72
1544 1948 3.679389 TGCTCCTTGAGAAAATGTCCTC 58.321 45.455 0.00 0.00 0.00 3.71
1773 3576 8.226448 CAGCGAAAATAAGACATCTAATGATCC 58.774 37.037 0.00 0.00 0.00 3.36
1891 3695 5.106277 ACGAGAACAAGACGACAGATCAATA 60.106 40.000 0.00 0.00 0.00 1.90
1921 3725 7.041780 CCAATTTCTACAATATCTCGGGTGAAG 60.042 40.741 0.00 0.00 0.00 3.02
1936 3740 3.128068 GGGTGAAGACGTGAAAAAGTGTT 59.872 43.478 0.00 0.00 0.00 3.32
1937 3741 4.333372 GGGTGAAGACGTGAAAAAGTGTTA 59.667 41.667 0.00 0.00 0.00 2.41
2248 4052 1.294780 GGGAGTGGTCAGCTCACAG 59.705 63.158 6.78 0.00 36.46 3.66
2420 4794 7.658982 CAGTCTGTCACCATATATGCTTAATGT 59.341 37.037 7.24 0.00 0.00 2.71
2796 5170 1.590238 GCGAGGTGATTGAAGATGACG 59.410 52.381 0.00 0.00 0.00 4.35
3145 5523 9.995003 AAGATCAAATGCTGGTTTGTTTTATAA 57.005 25.926 0.00 0.00 39.50 0.98
3146 5524 9.423061 AGATCAAATGCTGGTTTGTTTTATAAC 57.577 29.630 0.00 0.00 39.50 1.89
3184 5562 3.685139 TCTAGAACCCTGCACTTCTTG 57.315 47.619 0.00 1.96 0.00 3.02
3215 5593 1.933853 GCCTAGTGATTACCTGCAACG 59.066 52.381 0.00 0.00 0.00 4.10
3317 5695 4.553330 TCTTTCCCTCTACCACATTCAC 57.447 45.455 0.00 0.00 0.00 3.18
3318 5696 4.168101 TCTTTCCCTCTACCACATTCACT 58.832 43.478 0.00 0.00 0.00 3.41
3394 5798 6.537660 AGGTAATTCTGAAACTACATTACGGC 59.462 38.462 12.37 0.00 0.00 5.68
3417 5821 0.958382 TTGCAACGGGATACACTGGC 60.958 55.000 0.00 0.00 39.74 4.85
3418 5822 1.376683 GCAACGGGATACACTGGCA 60.377 57.895 0.00 0.00 39.74 4.92
3434 5838 2.288666 TGGCAGCGAAATTGGACTATC 58.711 47.619 0.00 0.00 0.00 2.08
3448 5852 3.194116 TGGACTATCGTGTGGTAGAAACC 59.806 47.826 0.00 0.00 46.98 3.27
3616 6155 7.224297 TCTCCCTGTATGGCTATAACAAAATC 58.776 38.462 0.00 0.00 0.00 2.17
3735 6314 7.693969 ATCTCCAACTTTTCTATTCAAGGTG 57.306 36.000 0.00 0.00 37.45 4.00
3758 6337 4.385825 CAACCAGTACAGTACACACCATT 58.614 43.478 13.37 0.00 0.00 3.16
3882 6462 9.367444 ACTTAAAAAGTTATTCGATCTCGATGT 57.633 29.630 2.75 0.00 43.13 3.06
3912 6492 7.541916 AGTGGTAAGAATTATACCTAGAGCC 57.458 40.000 16.74 0.00 42.73 4.70
3913 6493 7.306781 AGTGGTAAGAATTATACCTAGAGCCT 58.693 38.462 16.74 5.12 42.73 4.58
3914 6494 7.233757 AGTGGTAAGAATTATACCTAGAGCCTG 59.766 40.741 16.74 0.00 42.73 4.85
3915 6495 7.015389 GTGGTAAGAATTATACCTAGAGCCTGT 59.985 40.741 16.74 0.00 42.73 4.00
3916 6496 7.567622 TGGTAAGAATTATACCTAGAGCCTGTT 59.432 37.037 16.74 0.00 42.73 3.16
3917 6497 8.089597 GGTAAGAATTATACCTAGAGCCTGTTC 58.910 40.741 11.10 0.00 39.79 3.18
3918 6498 6.334102 AGAATTATACCTAGAGCCTGTTCG 57.666 41.667 0.00 0.00 0.00 3.95
3919 6499 5.244178 AGAATTATACCTAGAGCCTGTTCGG 59.756 44.000 0.00 0.00 0.00 4.30
3920 6500 2.750141 ATACCTAGAGCCTGTTCGGA 57.250 50.000 0.00 0.00 33.16 4.55
3921 6501 2.519771 TACCTAGAGCCTGTTCGGAA 57.480 50.000 0.00 0.00 33.16 4.30
3922 6502 1.187087 ACCTAGAGCCTGTTCGGAAG 58.813 55.000 0.00 0.00 33.16 3.46
3923 6503 0.179097 CCTAGAGCCTGTTCGGAAGC 60.179 60.000 0.00 0.00 33.16 3.86
3924 6504 0.820871 CTAGAGCCTGTTCGGAAGCT 59.179 55.000 2.97 2.97 38.56 3.74
3925 6505 4.193653 GAGCCTGTTCGGAAGCTC 57.806 61.111 12.75 12.75 44.36 4.09
3926 6506 1.594310 GAGCCTGTTCGGAAGCTCT 59.406 57.895 18.09 3.25 46.50 4.09
3927 6507 0.459411 GAGCCTGTTCGGAAGCTCTC 60.459 60.000 18.09 7.85 46.50 3.20
3928 6508 1.448717 GCCTGTTCGGAAGCTCTCC 60.449 63.158 0.00 0.00 41.40 3.71
3929 6509 1.219393 CCTGTTCGGAAGCTCTCCC 59.781 63.158 8.72 0.55 41.87 4.30
3930 6510 1.153745 CTGTTCGGAAGCTCTCCCG 60.154 63.158 13.88 13.88 46.57 5.14
3935 6515 4.347865 GGAAGCTCTCCCGACTCT 57.652 61.111 0.00 0.00 38.44 3.24
3936 6516 2.112029 GGAAGCTCTCCCGACTCTC 58.888 63.158 0.00 0.00 38.44 3.20
3937 6517 0.681564 GGAAGCTCTCCCGACTCTCA 60.682 60.000 0.00 0.00 38.44 3.27
3938 6518 1.178276 GAAGCTCTCCCGACTCTCAA 58.822 55.000 0.00 0.00 0.00 3.02
3939 6519 0.892063 AAGCTCTCCCGACTCTCAAC 59.108 55.000 0.00 0.00 0.00 3.18
3940 6520 0.039035 AGCTCTCCCGACTCTCAACT 59.961 55.000 0.00 0.00 0.00 3.16
3941 6521 0.454196 GCTCTCCCGACTCTCAACTC 59.546 60.000 0.00 0.00 0.00 3.01
3942 6522 1.953311 GCTCTCCCGACTCTCAACTCT 60.953 57.143 0.00 0.00 0.00 3.24
3943 6523 1.742831 CTCTCCCGACTCTCAACTCTG 59.257 57.143 0.00 0.00 0.00 3.35
3944 6524 0.172352 CTCCCGACTCTCAACTCTGC 59.828 60.000 0.00 0.00 0.00 4.26
3945 6525 0.251386 TCCCGACTCTCAACTCTGCT 60.251 55.000 0.00 0.00 0.00 4.24
3946 6526 0.172352 CCCGACTCTCAACTCTGCTC 59.828 60.000 0.00 0.00 0.00 4.26
3947 6527 0.172352 CCGACTCTCAACTCTGCTCC 59.828 60.000 0.00 0.00 0.00 4.70
3948 6528 0.179176 CGACTCTCAACTCTGCTCCG 60.179 60.000 0.00 0.00 0.00 4.63
3949 6529 0.457681 GACTCTCAACTCTGCTCCGC 60.458 60.000 0.00 0.00 0.00 5.54
3950 6530 1.515952 CTCTCAACTCTGCTCCGCG 60.516 63.158 0.00 0.00 0.00 6.46
3951 6531 2.206515 CTCTCAACTCTGCTCCGCGT 62.207 60.000 4.92 0.00 0.00 6.01
3952 6532 2.049156 TCAACTCTGCTCCGCGTG 60.049 61.111 4.92 0.00 0.00 5.34
3953 6533 2.049156 CAACTCTGCTCCGCGTGA 60.049 61.111 4.92 0.59 0.00 4.35
3954 6534 2.091112 CAACTCTGCTCCGCGTGAG 61.091 63.158 17.10 17.10 44.47 3.51
3955 6535 3.288308 AACTCTGCTCCGCGTGAGG 62.288 63.158 21.05 10.36 41.73 3.86
3956 6536 3.443925 CTCTGCTCCGCGTGAGGA 61.444 66.667 21.05 18.36 41.73 3.71
3962 6542 3.443925 TCCGCGTGAGGAGCTGAG 61.444 66.667 4.92 0.00 34.92 3.35
3963 6543 3.753434 CCGCGTGAGGAGCTGAGT 61.753 66.667 4.92 0.00 0.00 3.41
3964 6544 2.259818 CGCGTGAGGAGCTGAGTT 59.740 61.111 0.00 0.00 0.00 3.01
3965 6545 2.091112 CGCGTGAGGAGCTGAGTTG 61.091 63.158 0.00 0.00 0.00 3.16
3966 6546 1.739562 GCGTGAGGAGCTGAGTTGG 60.740 63.158 0.00 0.00 0.00 3.77
3967 6547 1.967535 CGTGAGGAGCTGAGTTGGA 59.032 57.895 0.00 0.00 0.00 3.53
3968 6548 0.108898 CGTGAGGAGCTGAGTTGGAG 60.109 60.000 0.00 0.00 0.00 3.86
3969 6549 0.390998 GTGAGGAGCTGAGTTGGAGC 60.391 60.000 0.00 0.00 36.65 4.70
3970 6550 1.220477 GAGGAGCTGAGTTGGAGCC 59.780 63.158 0.00 0.00 37.12 4.70
3971 6551 2.125350 GGAGCTGAGTTGGAGCCG 60.125 66.667 0.00 0.00 37.12 5.52
3972 6552 2.817396 GAGCTGAGTTGGAGCCGC 60.817 66.667 0.00 0.00 37.12 6.53
3973 6553 3.308014 GAGCTGAGTTGGAGCCGCT 62.308 63.158 0.00 0.00 37.12 5.52
3974 6554 2.817396 GCTGAGTTGGAGCCGCTC 60.817 66.667 12.27 12.27 0.00 5.03
4019 6599 3.571119 CTTCGGGAGCTGCAGTTG 58.429 61.111 16.64 0.00 0.00 3.16
4020 6600 2.032528 TTCGGGAGCTGCAGTTGG 59.967 61.111 16.64 0.99 0.00 3.77
4021 6601 3.551496 TTCGGGAGCTGCAGTTGGG 62.551 63.158 16.64 0.61 0.00 4.12
4023 6603 3.650950 GGGAGCTGCAGTTGGGGA 61.651 66.667 16.64 0.00 0.00 4.81
4024 6604 2.045536 GGAGCTGCAGTTGGGGAG 60.046 66.667 16.64 0.00 0.00 4.30
4028 6608 4.020617 CTGCAGTTGGGGAGCGGA 62.021 66.667 5.25 0.00 36.79 5.54
4029 6609 3.965539 CTGCAGTTGGGGAGCGGAG 62.966 68.421 5.25 0.00 36.79 4.63
4030 6610 4.785453 GCAGTTGGGGAGCGGAGG 62.785 72.222 0.00 0.00 0.00 4.30
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 0.250295 CGACCAAAGAAGGGAGTGCA 60.250 55.000 0.00 0.00 0.00 4.57
13 14 1.578206 GCGACCAAAGAAGGGAGTGC 61.578 60.000 0.00 0.00 0.00 4.40
15 16 0.765510 AAGCGACCAAAGAAGGGAGT 59.234 50.000 0.00 0.00 0.00 3.85
37 38 1.214062 CGGGCCGCAAAATAGCAAA 59.786 52.632 15.42 0.00 0.00 3.68
40 41 1.008538 CATCGGGCCGCAAAATAGC 60.009 57.895 23.83 0.00 0.00 2.97
52 53 2.205022 AATATGGATGTGGCATCGGG 57.795 50.000 0.00 0.00 0.00 5.14
66 67 7.383572 GCAGAGGACTTGTACATCACTAATATG 59.616 40.741 0.00 0.00 0.00 1.78
81 82 0.250640 AAGCACTGGCAGAGGACTTG 60.251 55.000 23.66 8.92 44.61 3.16
105 106 4.797471 TGAAACATTGGCGATCAAAGAAG 58.203 39.130 0.00 0.00 39.05 2.85
110 111 2.945278 GCTTGAAACATTGGCGATCAA 58.055 42.857 0.00 0.00 40.01 2.57
116 117 2.989422 ACTACGCTTGAAACATTGGC 57.011 45.000 0.00 0.00 0.00 4.52
130 131 8.669394 TTAATCATATCGACAATGCTACTACG 57.331 34.615 4.98 0.00 0.00 3.51
155 156 1.740285 GGGCGTCGGTAGTGATGAT 59.260 57.895 0.00 0.00 0.00 2.45
159 160 2.283388 AAGGGGCGTCGGTAGTGA 60.283 61.111 0.00 0.00 0.00 3.41
229 230 2.813908 GTGGCAGTACTTCGGGCG 60.814 66.667 0.00 0.00 39.38 6.13
238 239 7.095910 CCAAAATAAATGTTGATGTGGCAGTA 58.904 34.615 0.00 0.00 0.00 2.74
240 241 5.163834 GCCAAAATAAATGTTGATGTGGCAG 60.164 40.000 5.99 0.00 46.54 4.85
279 280 2.499827 CCGAGGCACTAGCTACCCC 61.500 68.421 0.00 0.00 41.55 4.95
287 288 1.828595 TCTGCATAAACCGAGGCACTA 59.171 47.619 0.00 0.00 41.55 2.74
320 321 4.384940 TCATTCATCAACAACTTCGTGGA 58.615 39.130 0.00 0.00 0.00 4.02
339 340 0.249699 TCCGTTTGCGACACACTCAT 60.250 50.000 0.00 0.00 41.33 2.90
378 379 2.620585 GCTGCAAGATGGAAGGTAATCC 59.379 50.000 0.00 0.00 36.49 3.01
379 380 2.620585 GGCTGCAAGATGGAAGGTAATC 59.379 50.000 0.50 0.00 34.07 1.75
380 381 2.659428 GGCTGCAAGATGGAAGGTAAT 58.341 47.619 0.50 0.00 34.07 1.89
381 382 1.340991 GGGCTGCAAGATGGAAGGTAA 60.341 52.381 0.50 0.00 34.07 2.85
382 383 0.255890 GGGCTGCAAGATGGAAGGTA 59.744 55.000 0.50 0.00 34.07 3.08
383 384 1.000396 GGGCTGCAAGATGGAAGGT 60.000 57.895 0.50 0.00 34.07 3.50
384 385 0.396695 ATGGGCTGCAAGATGGAAGG 60.397 55.000 0.50 0.00 34.07 3.46
385 386 2.353357 TATGGGCTGCAAGATGGAAG 57.647 50.000 0.50 0.00 34.07 3.46
386 387 2.175284 TGATATGGGCTGCAAGATGGAA 59.825 45.455 0.50 0.00 34.07 3.53
387 388 1.776063 TGATATGGGCTGCAAGATGGA 59.224 47.619 0.50 0.00 34.07 3.41
388 389 1.884579 GTGATATGGGCTGCAAGATGG 59.115 52.381 0.50 0.00 34.07 3.51
389 390 1.884579 GGTGATATGGGCTGCAAGATG 59.115 52.381 0.50 0.00 34.07 2.90
390 391 1.202976 GGGTGATATGGGCTGCAAGAT 60.203 52.381 0.50 0.00 34.07 2.40
391 392 0.183492 GGGTGATATGGGCTGCAAGA 59.817 55.000 0.50 0.00 34.07 3.02
392 393 0.106569 TGGGTGATATGGGCTGCAAG 60.107 55.000 0.50 0.00 0.00 4.01
393 394 0.557238 ATGGGTGATATGGGCTGCAA 59.443 50.000 0.50 0.00 0.00 4.08
394 395 1.443852 TATGGGTGATATGGGCTGCA 58.556 50.000 0.50 0.00 0.00 4.41
395 396 2.372264 CATATGGGTGATATGGGCTGC 58.628 52.381 0.00 0.00 40.24 5.25
408 409 5.997746 ACTCGAATGATTGTAACCATATGGG 59.002 40.000 25.55 8.07 44.81 4.00
409 410 8.777865 ATACTCGAATGATTGTAACCATATGG 57.222 34.615 20.68 20.68 42.17 2.74
413 414 9.996554 TGATTATACTCGAATGATTGTAACCAT 57.003 29.630 0.00 0.00 0.00 3.55
414 415 9.996554 ATGATTATACTCGAATGATTGTAACCA 57.003 29.630 0.00 0.00 0.00 3.67
418 419 9.860898 CAGGATGATTATACTCGAATGATTGTA 57.139 33.333 0.00 0.00 39.69 2.41
419 420 8.370940 ACAGGATGATTATACTCGAATGATTGT 58.629 33.333 0.00 0.00 39.69 2.71
420 421 8.768957 ACAGGATGATTATACTCGAATGATTG 57.231 34.615 0.00 0.00 39.69 2.67
421 422 9.212641 CAACAGGATGATTATACTCGAATGATT 57.787 33.333 0.00 0.00 39.69 2.57
422 423 7.332926 GCAACAGGATGATTATACTCGAATGAT 59.667 37.037 0.00 0.00 39.69 2.45
423 424 6.646653 GCAACAGGATGATTATACTCGAATGA 59.353 38.462 0.00 0.00 39.69 2.57
424 425 6.424812 TGCAACAGGATGATTATACTCGAATG 59.575 38.462 0.00 0.00 39.69 2.67
425 426 6.524734 TGCAACAGGATGATTATACTCGAAT 58.475 36.000 0.00 0.00 39.69 3.34
426 427 5.912892 TGCAACAGGATGATTATACTCGAA 58.087 37.500 0.00 0.00 39.69 3.71
427 428 5.529581 TGCAACAGGATGATTATACTCGA 57.470 39.130 0.00 0.00 39.69 4.04
428 429 6.203530 ACAATGCAACAGGATGATTATACTCG 59.796 38.462 0.00 0.00 39.69 4.18
516 517 2.476519 GCTCTCTCCAACGACGACTTAG 60.477 54.545 0.00 0.00 0.00 2.18
526 527 1.202818 AGTGTTTGGGCTCTCTCCAAC 60.203 52.381 0.00 0.00 43.20 3.77
550 551 2.538333 GCTACTCAATTGCAGCATGTCG 60.538 50.000 16.78 0.00 39.31 4.35
791 1168 2.293677 TGTTGGAGATGAACCGATCG 57.706 50.000 8.51 8.51 0.00 3.69
1359 1763 1.392131 GGGGCAAAGGAAGGGGAAT 59.608 57.895 0.00 0.00 0.00 3.01
1442 1846 1.497286 AGGCAAACAAACTACTCCCCA 59.503 47.619 0.00 0.00 0.00 4.96
1544 1948 1.547820 TGCACTAGGTGAAGAGCAGAG 59.452 52.381 1.57 0.00 38.02 3.35
1773 3576 3.139077 ACTTTAAGTTGAGGTGCTTCCG 58.861 45.455 0.00 0.00 41.99 4.30
1819 3622 8.010105 ACAATTATTCCCCAATTAGGAGCATAA 58.990 33.333 0.00 0.00 41.22 1.90
1891 3695 6.936900 CCCGAGATATTGTAGAAATTGGTCAT 59.063 38.462 0.00 0.00 0.00 3.06
2059 3863 0.171903 CTTCAAGAAAGCGCCCATGG 59.828 55.000 2.29 4.14 0.00 3.66
2103 3907 3.819564 ATTGTAATCAGCCGAGCTACA 57.180 42.857 0.00 0.00 36.40 2.74
2796 5170 1.767759 ACATGCTTGGGAATAGGTGC 58.232 50.000 4.44 0.00 0.00 5.01
3184 5562 5.294552 GGTAATCACTAGGCAATGACACTTC 59.705 44.000 0.00 0.00 0.00 3.01
3448 5852 2.541346 CGTTGATGCTGCTATGGTAGTG 59.459 50.000 0.00 0.00 0.00 2.74
3449 5853 2.168521 ACGTTGATGCTGCTATGGTAGT 59.831 45.455 0.00 0.00 0.00 2.73
3453 5857 2.409715 CGATACGTTGATGCTGCTATGG 59.590 50.000 0.00 0.00 0.00 2.74
3586 5990 7.224297 TGTTATAGCCATACAGGGAGATTTTC 58.776 38.462 0.00 0.00 38.09 2.29
3591 5996 6.569127 TTTTGTTATAGCCATACAGGGAGA 57.431 37.500 0.00 0.00 38.09 3.71
3735 6314 2.140717 GGTGTGTACTGTACTGGTTGC 58.859 52.381 17.98 3.99 0.00 4.17
3746 6325 9.815306 AGTATATAGAGATCAATGGTGTGTACT 57.185 33.333 0.00 0.00 0.00 2.73
3749 6328 9.373450 AGAAGTATATAGAGATCAATGGTGTGT 57.627 33.333 0.00 0.00 0.00 3.72
3750 6329 9.636879 CAGAAGTATATAGAGATCAATGGTGTG 57.363 37.037 0.00 0.00 0.00 3.82
3848 6427 8.674263 TCGAATAACTTTTTAAGTGGGTGTAA 57.326 30.769 0.00 0.00 41.91 2.41
3908 6488 4.193653 GAGCTTCCGAACAGGCTC 57.806 61.111 5.40 5.40 43.07 4.70
3909 6489 1.594310 GAGAGCTTCCGAACAGGCT 59.406 57.895 0.00 0.00 40.77 4.58
3910 6490 1.448717 GGAGAGCTTCCGAACAGGC 60.449 63.158 0.00 0.00 40.77 4.85
3911 6491 4.921834 GGAGAGCTTCCGAACAGG 57.078 61.111 0.00 0.00 42.97 4.00
3918 6498 0.681564 TGAGAGTCGGGAGAGCTTCC 60.682 60.000 6.43 6.43 46.00 3.46
3919 6499 1.135228 GTTGAGAGTCGGGAGAGCTTC 60.135 57.143 0.00 0.00 41.26 3.86
3920 6500 0.892063 GTTGAGAGTCGGGAGAGCTT 59.108 55.000 0.00 0.00 41.26 3.74
3921 6501 0.039035 AGTTGAGAGTCGGGAGAGCT 59.961 55.000 0.00 0.00 41.26 4.09
3922 6502 0.454196 GAGTTGAGAGTCGGGAGAGC 59.546 60.000 0.00 0.00 41.26 4.09
3923 6503 1.742831 CAGAGTTGAGAGTCGGGAGAG 59.257 57.143 0.00 0.00 41.26 3.20
3924 6504 1.827681 CAGAGTTGAGAGTCGGGAGA 58.172 55.000 0.00 0.00 0.00 3.71
3925 6505 0.172352 GCAGAGTTGAGAGTCGGGAG 59.828 60.000 0.00 0.00 0.00 4.30
3926 6506 0.251386 AGCAGAGTTGAGAGTCGGGA 60.251 55.000 0.00 0.00 0.00 5.14
3927 6507 0.172352 GAGCAGAGTTGAGAGTCGGG 59.828 60.000 0.00 0.00 0.00 5.14
3928 6508 0.172352 GGAGCAGAGTTGAGAGTCGG 59.828 60.000 0.00 0.00 0.00 4.79
3929 6509 0.179176 CGGAGCAGAGTTGAGAGTCG 60.179 60.000 0.00 0.00 0.00 4.18
3930 6510 3.712020 CGGAGCAGAGTTGAGAGTC 57.288 57.895 0.00 0.00 0.00 3.36
3945 6525 3.443925 CTCAGCTCCTCACGCGGA 61.444 66.667 12.47 3.82 0.00 5.54
3946 6526 3.288308 AACTCAGCTCCTCACGCGG 62.288 63.158 12.47 0.00 0.00 6.46
3947 6527 2.091112 CAACTCAGCTCCTCACGCG 61.091 63.158 3.53 3.53 0.00 6.01
3948 6528 1.739562 CCAACTCAGCTCCTCACGC 60.740 63.158 0.00 0.00 0.00 5.34
3949 6529 0.108898 CTCCAACTCAGCTCCTCACG 60.109 60.000 0.00 0.00 0.00 4.35
3950 6530 0.390998 GCTCCAACTCAGCTCCTCAC 60.391 60.000 0.00 0.00 33.75 3.51
3951 6531 1.548357 GGCTCCAACTCAGCTCCTCA 61.548 60.000 0.00 0.00 37.05 3.86
3952 6532 1.220477 GGCTCCAACTCAGCTCCTC 59.780 63.158 0.00 0.00 37.05 3.71
3953 6533 2.654079 CGGCTCCAACTCAGCTCCT 61.654 63.158 0.00 0.00 37.05 3.69
3954 6534 2.125350 CGGCTCCAACTCAGCTCC 60.125 66.667 0.00 0.00 37.05 4.70
3955 6535 2.817396 GCGGCTCCAACTCAGCTC 60.817 66.667 0.00 0.00 37.05 4.09
3956 6536 3.308014 GAGCGGCTCCAACTCAGCT 62.308 63.158 19.20 0.00 37.05 4.24
3957 6537 2.817396 GAGCGGCTCCAACTCAGC 60.817 66.667 19.20 0.00 36.02 4.26
4002 6582 2.037136 CCAACTGCAGCTCCCGAAG 61.037 63.158 15.27 0.00 0.00 3.79
4003 6583 2.032528 CCAACTGCAGCTCCCGAA 59.967 61.111 15.27 0.00 0.00 4.30
4004 6584 4.020617 CCCAACTGCAGCTCCCGA 62.021 66.667 15.27 0.00 0.00 5.14
4006 6586 3.635268 CTCCCCAACTGCAGCTCCC 62.635 68.421 15.27 0.00 0.00 4.30
4007 6587 2.045536 CTCCCCAACTGCAGCTCC 60.046 66.667 15.27 0.00 0.00 4.70
4008 6588 2.749441 GCTCCCCAACTGCAGCTC 60.749 66.667 15.27 0.00 0.00 4.09
4009 6589 4.711949 CGCTCCCCAACTGCAGCT 62.712 66.667 15.27 0.00 0.00 4.24
4011 6591 3.965539 CTCCGCTCCCCAACTGCAG 62.966 68.421 13.48 13.48 0.00 4.41
4012 6592 4.020617 CTCCGCTCCCCAACTGCA 62.021 66.667 0.00 0.00 0.00 4.41
4013 6593 4.785453 CCTCCGCTCCCCAACTGC 62.785 72.222 0.00 0.00 0.00 4.40


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

AutoCloner maintained by Alex Coulton.