Multiple sequence alignment - TraesCS1D01G327400

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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 TraesCS1D01G327400 chr1D 100.000 2439 0 0 1 2439 419601087 419603525 0.000000e+00 4505.0
1 TraesCS1D01G327400 chr1D 92.717 508 34 2 1 505 356706703 356706196 0.000000e+00 730.0
2 TraesCS1D01G327400 chr1D 90.141 71 5 2 508 576 316266742 316266812 9.290000e-15 91.6
3 TraesCS1D01G327400 chr1A 87.255 1530 117 45 765 2249 516454265 516455761 0.000000e+00 1674.0
4 TraesCS1D01G327400 chr1A 85.859 198 26 1 2240 2437 516455909 516456104 2.460000e-50 209.0
5 TraesCS1D01G327400 chr1A 94.059 101 5 1 690 790 516454165 516454264 4.200000e-33 152.0
6 TraesCS1D01G327400 chr1B 88.453 1325 74 38 765 2045 566720721 566722010 0.000000e+00 1526.0
7 TraesCS1D01G327400 chr1B 91.160 181 8 5 614 790 566720544 566720720 3.130000e-59 239.0
8 TraesCS1D01G327400 chr2D 92.731 509 33 3 1 505 400291236 400291744 0.000000e+00 732.0
9 TraesCS1D01G327400 chr2A 92.731 509 33 3 1 505 66516723 66517231 0.000000e+00 732.0
10 TraesCS1D01G327400 chr2A 92.338 509 35 3 1 505 66476379 66476887 0.000000e+00 721.0
11 TraesCS1D01G327400 chr6D 92.731 509 30 6 1 505 335975558 335976063 0.000000e+00 728.0
12 TraesCS1D01G327400 chr6D 92.688 506 34 2 1 503 159272228 159271723 0.000000e+00 726.0
13 TraesCS1D01G327400 chr6D 92.338 509 35 3 1 505 335939192 335939700 0.000000e+00 721.0
14 TraesCS1D01G327400 chr5D 92.353 510 32 6 1 505 386931920 386932427 0.000000e+00 719.0
15 TraesCS1D01G327400 chr5D 92.308 507 35 3 1 503 82299523 82300029 0.000000e+00 717.0
16 TraesCS1D01G327400 chr7D 94.030 67 3 1 507 573 490266012 490265947 1.540000e-17 100.0
17 TraesCS1D01G327400 chr4D 90.541 74 6 1 507 579 489088099 489088026 2.000000e-16 97.1
18 TraesCS1D01G327400 chr6A 91.429 70 5 1 507 575 150961398 150961467 7.180000e-16 95.3
19 TraesCS1D01G327400 chr7B 90.141 71 6 1 507 576 6674199 6674269 9.290000e-15 91.6
20 TraesCS1D01G327400 chr3A 90.000 70 6 1 507 575 9772647 9772716 3.340000e-14 89.8
21 TraesCS1D01G327400 chr3A 89.855 69 7 0 507 575 568453137 568453205 3.340000e-14 89.8
22 TraesCS1D01G327400 chr7A 88.889 72 6 2 507 576 98755740 98755669 1.200000e-13 87.9
23 TraesCS1D01G327400 chr2B 88.889 72 6 2 507 576 89540754 89540683 1.200000e-13 87.9
24 TraesCS1D01G327400 chr3D 91.304 46 4 0 2118 2163 13414513 13414558 2.020000e-06 63.9


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 TraesCS1D01G327400 chr1D 419601087 419603525 2438 False 4505.000000 4505 100.000000 1 2439 1 chr1D.!!$F2 2438
1 TraesCS1D01G327400 chr1D 356706196 356706703 507 True 730.000000 730 92.717000 1 505 1 chr1D.!!$R1 504
2 TraesCS1D01G327400 chr1A 516454165 516456104 1939 False 678.333333 1674 89.057667 690 2437 3 chr1A.!!$F1 1747
3 TraesCS1D01G327400 chr1B 566720544 566722010 1466 False 882.500000 1526 89.806500 614 2045 2 chr1B.!!$F1 1431
4 TraesCS1D01G327400 chr2D 400291236 400291744 508 False 732.000000 732 92.731000 1 505 1 chr2D.!!$F1 504
5 TraesCS1D01G327400 chr2A 66516723 66517231 508 False 732.000000 732 92.731000 1 505 1 chr2A.!!$F2 504
6 TraesCS1D01G327400 chr2A 66476379 66476887 508 False 721.000000 721 92.338000 1 505 1 chr2A.!!$F1 504
7 TraesCS1D01G327400 chr6D 335975558 335976063 505 False 728.000000 728 92.731000 1 505 1 chr6D.!!$F2 504
8 TraesCS1D01G327400 chr6D 159271723 159272228 505 True 726.000000 726 92.688000 1 503 1 chr6D.!!$R1 502
9 TraesCS1D01G327400 chr6D 335939192 335939700 508 False 721.000000 721 92.338000 1 505 1 chr6D.!!$F1 504
10 TraesCS1D01G327400 chr5D 386931920 386932427 507 False 719.000000 719 92.353000 1 505 1 chr5D.!!$F2 504
11 TraesCS1D01G327400 chr5D 82299523 82300029 506 False 717.000000 717 92.308000 1 503 1 chr5D.!!$F1 502

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
591 598 0.106519 AAAAGCATCTCCCCGGATGG 60.107 55.0 0.73 0.0 42.21 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2274 2535 0.035056 AAGGGAGCGAAATGGGACTG 60.035 55.0 0.0 0.0 0.0 3.51 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
113 114 2.519377 TCACCCAGTTACGTTGTGAG 57.481 50.000 0.00 0.00 32.56 3.51
144 145 0.178068 CACAGGGTATTCCTCCGGTG 59.822 60.000 0.00 0.00 46.12 4.94
165 166 0.467384 CCGGGAGTTGCATGATCTCT 59.533 55.000 0.00 0.00 0.00 3.10
169 170 1.674962 GGAGTTGCATGATCTCTTGGC 59.325 52.381 0.00 0.00 0.00 4.52
174 175 3.076079 TGCATGATCTCTTGGCTGAAA 57.924 42.857 0.00 0.00 0.00 2.69
319 322 7.633789 ACAACTCATGTCTATGGTTAGGAAAT 58.366 34.615 0.00 0.00 37.96 2.17
360 364 3.896888 ACGAGCTAGTCTAGTAGAGGCTA 59.103 47.826 17.02 8.89 38.80 3.93
362 366 4.927425 CGAGCTAGTCTAGTAGAGGCTAAG 59.073 50.000 17.02 12.47 41.91 2.18
378 383 6.789959 AGAGGCTAAGTAGGGACATGATATTT 59.210 38.462 0.00 0.00 0.00 1.40
423 430 6.894339 AAGTTTCCGGTCAATACAATTCTT 57.106 33.333 0.00 0.00 0.00 2.52
428 435 4.704540 TCCGGTCAATACAATTCTTGCATT 59.295 37.500 0.00 0.00 0.00 3.56
505 512 3.467803 CCTCTAGGGCTTATTTCCAACG 58.532 50.000 0.00 0.00 0.00 4.10
506 513 3.467803 CTCTAGGGCTTATTTCCAACGG 58.532 50.000 0.00 0.00 0.00 4.44
507 514 2.841881 TCTAGGGCTTATTTCCAACGGT 59.158 45.455 0.00 0.00 0.00 4.83
508 515 1.834188 AGGGCTTATTTCCAACGGTG 58.166 50.000 0.00 0.00 0.00 4.94
509 516 0.172578 GGGCTTATTTCCAACGGTGC 59.827 55.000 0.00 0.00 0.00 5.01
510 517 0.885196 GGCTTATTTCCAACGGTGCA 59.115 50.000 0.00 0.00 0.00 4.57
511 518 1.476488 GGCTTATTTCCAACGGTGCAT 59.524 47.619 0.00 0.00 0.00 3.96
512 519 2.094234 GGCTTATTTCCAACGGTGCATT 60.094 45.455 0.00 0.00 0.00 3.56
513 520 3.179048 GCTTATTTCCAACGGTGCATTC 58.821 45.455 0.00 0.00 0.00 2.67
514 521 3.366883 GCTTATTTCCAACGGTGCATTCA 60.367 43.478 0.00 0.00 0.00 2.57
515 522 4.677779 GCTTATTTCCAACGGTGCATTCAT 60.678 41.667 0.00 0.00 0.00 2.57
516 523 5.449862 GCTTATTTCCAACGGTGCATTCATA 60.450 40.000 0.00 0.00 0.00 2.15
517 524 4.637483 ATTTCCAACGGTGCATTCATAG 57.363 40.909 0.00 0.00 0.00 2.23
518 525 2.036958 TCCAACGGTGCATTCATAGG 57.963 50.000 0.00 0.00 0.00 2.57
519 526 1.024271 CCAACGGTGCATTCATAGGG 58.976 55.000 0.00 0.00 0.00 3.53
520 527 1.408127 CCAACGGTGCATTCATAGGGA 60.408 52.381 0.00 0.00 0.00 4.20
521 528 2.575532 CAACGGTGCATTCATAGGGAT 58.424 47.619 0.00 0.00 0.00 3.85
522 529 2.260844 ACGGTGCATTCATAGGGATG 57.739 50.000 0.00 0.00 0.00 3.51
523 530 1.768275 ACGGTGCATTCATAGGGATGA 59.232 47.619 0.00 0.00 40.45 2.92
524 531 2.224378 ACGGTGCATTCATAGGGATGAG 60.224 50.000 0.00 0.00 43.03 2.90
525 532 2.224378 CGGTGCATTCATAGGGATGAGT 60.224 50.000 0.00 0.00 43.03 3.41
527 534 3.434167 GGTGCATTCATAGGGATGAGTGT 60.434 47.826 0.00 0.00 46.40 3.55
528 535 4.202357 GGTGCATTCATAGGGATGAGTGTA 60.202 45.833 0.00 5.11 46.40 2.90
529 536 5.513788 GGTGCATTCATAGGGATGAGTGTAT 60.514 44.000 0.00 0.00 46.40 2.29
530 537 5.410746 GTGCATTCATAGGGATGAGTGTATG 59.589 44.000 0.00 3.63 46.40 2.39
531 538 4.394300 GCATTCATAGGGATGAGTGTATGC 59.606 45.833 0.00 8.64 46.40 3.14
532 539 5.554070 CATTCATAGGGATGAGTGTATGCA 58.446 41.667 0.00 0.00 43.03 3.96
533 540 4.607293 TCATAGGGATGAGTGTATGCAC 57.393 45.455 5.71 5.71 45.57 4.57
545 552 3.670203 GTGTATGCACGTGTAAATGAGC 58.330 45.455 18.38 0.00 35.75 4.26
546 553 2.347150 TGTATGCACGTGTAAATGAGCG 59.653 45.455 18.38 0.00 0.00 5.03
547 554 1.438651 ATGCACGTGTAAATGAGCGT 58.561 45.000 18.38 0.00 38.14 5.07
548 555 1.222300 TGCACGTGTAAATGAGCGTT 58.778 45.000 18.38 0.00 35.25 4.84
549 556 1.600013 TGCACGTGTAAATGAGCGTTT 59.400 42.857 18.38 0.00 35.25 3.60
550 557 1.969256 GCACGTGTAAATGAGCGTTTG 59.031 47.619 18.38 0.00 35.25 2.93
551 558 1.969256 CACGTGTAAATGAGCGTTTGC 59.031 47.619 7.58 0.00 43.24 3.68
562 569 2.810486 GCGTTTGCGTCTGTACTCT 58.190 52.632 0.00 0.00 40.81 3.24
563 570 0.435008 GCGTTTGCGTCTGTACTCTG 59.565 55.000 0.00 0.00 40.81 3.35
564 571 1.767289 CGTTTGCGTCTGTACTCTGT 58.233 50.000 0.00 0.00 0.00 3.41
565 572 2.124903 CGTTTGCGTCTGTACTCTGTT 58.875 47.619 0.00 0.00 0.00 3.16
566 573 3.302555 CGTTTGCGTCTGTACTCTGTTA 58.697 45.455 0.00 0.00 0.00 2.41
567 574 3.732219 CGTTTGCGTCTGTACTCTGTTAA 59.268 43.478 0.00 0.00 0.00 2.01
568 575 4.207635 CGTTTGCGTCTGTACTCTGTTAAA 59.792 41.667 0.00 0.00 0.00 1.52
569 576 5.276489 CGTTTGCGTCTGTACTCTGTTAAAA 60.276 40.000 0.00 0.00 0.00 1.52
570 577 6.480285 GTTTGCGTCTGTACTCTGTTAAAAA 58.520 36.000 0.00 0.00 0.00 1.94
590 597 1.767759 AAAAAGCATCTCCCCGGATG 58.232 50.000 0.73 0.00 44.08 3.51
591 598 0.106519 AAAAGCATCTCCCCGGATGG 60.107 55.000 0.73 0.00 42.21 3.51
602 609 4.802051 CGGATGGGCCACCTGGTG 62.802 72.222 20.01 20.01 37.76 4.17
603 610 3.661648 GGATGGGCCACCTGGTGT 61.662 66.667 24.32 6.34 37.76 4.16
604 611 2.044946 GATGGGCCACCTGGTGTC 60.045 66.667 24.32 12.96 37.76 3.67
605 612 3.645268 GATGGGCCACCTGGTGTCC 62.645 68.421 24.32 21.52 37.76 4.02
608 615 4.660938 GGCCACCTGGTGTCCCAC 62.661 72.222 24.32 8.88 35.17 4.61
609 616 3.884774 GCCACCTGGTGTCCCACA 61.885 66.667 24.32 0.00 35.17 4.17
665 672 2.307098 CTGGGCCCCTAGATCCTATTTG 59.693 54.545 22.27 0.00 0.00 2.32
666 673 2.349445 GGGCCCCTAGATCCTATTTGT 58.651 52.381 12.23 0.00 0.00 2.83
669 677 3.262151 GGCCCCTAGATCCTATTTGTCTC 59.738 52.174 0.00 0.00 0.00 3.36
895 932 6.348786 CCACCATAAGAGAGTGACATTTGTTG 60.349 42.308 0.00 0.00 33.21 3.33
896 933 5.707298 ACCATAAGAGAGTGACATTTGTTGG 59.293 40.000 0.00 0.00 0.00 3.77
901 945 6.773976 AGAGAGTGACATTTGTTGGAAAAA 57.226 33.333 0.00 0.00 0.00 1.94
968 1019 4.562082 CCGAACGGGTGCTAATAATATCA 58.438 43.478 5.25 0.00 0.00 2.15
969 1020 4.387862 CCGAACGGGTGCTAATAATATCAC 59.612 45.833 5.25 0.00 0.00 3.06
975 1026 5.551233 GGGTGCTAATAATATCACTGCAGA 58.449 41.667 23.35 0.00 30.63 4.26
976 1027 5.409826 GGGTGCTAATAATATCACTGCAGAC 59.590 44.000 23.35 1.99 30.63 3.51
977 1028 6.226787 GGTGCTAATAATATCACTGCAGACT 58.773 40.000 23.35 6.70 30.63 3.24
978 1029 6.146837 GGTGCTAATAATATCACTGCAGACTG 59.853 42.308 23.35 9.62 30.63 3.51
979 1030 5.698089 TGCTAATAATATCACTGCAGACTGC 59.302 40.000 23.35 20.86 45.29 4.40
1035 1086 0.753479 CCGCCCTCTGCTCTCTTCTA 60.753 60.000 0.00 0.00 38.05 2.10
1115 1166 5.907079 AGCCTCCAAATCCCATTTATTTCAT 59.093 36.000 0.00 0.00 0.00 2.57
1117 1168 7.056006 GCCTCCAAATCCCATTTATTTCATTT 58.944 34.615 0.00 0.00 0.00 2.32
1118 1169 7.227314 GCCTCCAAATCCCATTTATTTCATTTC 59.773 37.037 0.00 0.00 0.00 2.17
1119 1170 8.266473 CCTCCAAATCCCATTTATTTCATTTCA 58.734 33.333 0.00 0.00 0.00 2.69
1176 1235 8.983702 TGGTTCATTTCAATATGATGAGATCA 57.016 30.769 0.00 0.00 44.55 2.92
1481 1545 2.031944 CGTCTCGATATTCGCTTCTCCA 60.032 50.000 0.00 0.00 40.21 3.86
1492 1560 5.871396 TTCGCTTCTCCAGTAGGAATTAT 57.129 39.130 0.00 0.00 45.19 1.28
1524 1592 9.624373 AGACATTTCTCATAGATATTTGCTTGT 57.376 29.630 0.00 0.00 0.00 3.16
1525 1593 9.875675 GACATTTCTCATAGATATTTGCTTGTC 57.124 33.333 0.00 0.00 0.00 3.18
1526 1594 8.844244 ACATTTCTCATAGATATTTGCTTGTCC 58.156 33.333 0.00 0.00 0.00 4.02
1527 1595 9.064706 CATTTCTCATAGATATTTGCTTGTCCT 57.935 33.333 0.00 0.00 0.00 3.85
1528 1596 8.668510 TTTCTCATAGATATTTGCTTGTCCTC 57.331 34.615 0.00 0.00 0.00 3.71
1529 1597 7.365497 TCTCATAGATATTTGCTTGTCCTCA 57.635 36.000 0.00 0.00 0.00 3.86
1530 1598 7.971201 TCTCATAGATATTTGCTTGTCCTCAT 58.029 34.615 0.00 0.00 0.00 2.90
1531 1599 8.093307 TCTCATAGATATTTGCTTGTCCTCATC 58.907 37.037 0.00 0.00 0.00 2.92
1537 1605 3.325293 TTGCTTGTCCTCATCTCTCAC 57.675 47.619 0.00 0.00 0.00 3.51
1550 1618 6.093219 CCTCATCTCTCACAAACCAATTACAG 59.907 42.308 0.00 0.00 0.00 2.74
1561 1629 6.928492 ACAAACCAATTACAGCCAGTTTATTG 59.072 34.615 0.00 0.00 33.93 1.90
1577 1645 0.747283 ATTGAGGTAGCAGCAGCAGC 60.747 55.000 3.17 0.46 45.49 5.25
1582 1678 1.437772 GGTAGCAGCAGCAGCAGATG 61.438 60.000 12.92 0.00 45.49 2.90
1596 1695 4.097135 GCAGCAGATGTAGTTAGTCTCAGA 59.903 45.833 0.00 0.00 0.00 3.27
1601 1700 6.511416 CAGATGTAGTTAGTCTCAGATTGGG 58.489 44.000 0.00 0.00 0.00 4.12
1837 1936 4.507756 CGGATGTCGTTATGTCACATCATT 59.492 41.667 12.13 0.00 45.61 2.57
1842 1943 9.210426 GATGTCGTTATGTCACATCATTAAAAC 57.790 33.333 0.00 0.00 43.98 2.43
2025 2128 8.291740 ACGTGTAAAATATAAACCCTCAAACAC 58.708 33.333 0.00 0.00 0.00 3.32
2029 2132 9.401873 GTAAAATATAAACCCTCAAACACACAC 57.598 33.333 0.00 0.00 0.00 3.82
2048 2151 7.094205 ACACACACTTCTGGAATCCAAAATATC 60.094 37.037 2.61 0.00 30.80 1.63
2049 2152 6.094048 ACACACTTCTGGAATCCAAAATATCG 59.906 38.462 2.61 0.00 30.80 2.92
2051 2154 5.822519 CACTTCTGGAATCCAAAATATCGGA 59.177 40.000 2.61 0.00 30.80 4.55
2123 2227 2.190578 GCATCTACAGCCGGGCTT 59.809 61.111 21.26 13.44 36.40 4.35
2124 2228 1.889573 GCATCTACAGCCGGGCTTC 60.890 63.158 21.26 0.00 36.40 3.86
2130 2234 0.618458 TACAGCCGGGCTTCTCAAAT 59.382 50.000 21.26 1.57 36.40 2.32
2134 2238 1.379044 CCGGGCTTCTCAAATGCCT 60.379 57.895 0.00 0.00 45.45 4.75
2144 2248 5.767168 GCTTCTCAAATGCCTCCTATATGTT 59.233 40.000 0.00 0.00 0.00 2.71
2146 2250 7.572523 TTCTCAAATGCCTCCTATATGTTTG 57.427 36.000 0.00 0.00 0.00 2.93
2152 2256 2.367567 GCCTCCTATATGTTTGGACGGA 59.632 50.000 0.00 0.00 0.00 4.69
2157 2261 0.463116 ATATGTTTGGACGGACGGCC 60.463 55.000 10.23 10.23 45.60 6.13
2158 2262 2.524951 TATGTTTGGACGGACGGCCC 62.525 60.000 14.95 6.31 44.50 5.80
2190 2294 3.305064 CCGGTCACAAAAATGTAACCCAG 60.305 47.826 0.00 0.00 0.00 4.45
2191 2295 3.649073 GGTCACAAAAATGTAACCCAGC 58.351 45.455 0.00 0.00 0.00 4.85
2194 2298 3.320541 TCACAAAAATGTAACCCAGCCAG 59.679 43.478 0.00 0.00 0.00 4.85
2198 2302 2.789409 AATGTAACCCAGCCAGACTC 57.211 50.000 0.00 0.00 0.00 3.36
2206 2310 0.689623 CCAGCCAGACTCCTCAAACT 59.310 55.000 0.00 0.00 0.00 2.66
2210 2314 0.689623 CCAGACTCCTCAAACTGGCT 59.310 55.000 0.00 0.00 42.30 4.75
2219 2323 5.009811 ACTCCTCAAACTGGCTATATACGTC 59.990 44.000 0.00 0.00 0.00 4.34
2220 2324 5.138276 TCCTCAAACTGGCTATATACGTCT 58.862 41.667 0.00 0.00 0.00 4.18
2229 2333 3.005472 GGCTATATACGTCTGGCTGACAA 59.995 47.826 21.99 11.24 45.60 3.18
2252 2513 3.139077 CACCCTCATATTTAAGCCGGAC 58.861 50.000 5.05 0.00 0.00 4.79
2271 2532 2.235761 GGCAACCCCCAACCCTAGA 61.236 63.158 0.00 0.00 0.00 2.43
2272 2533 1.001269 GCAACCCCCAACCCTAGAC 60.001 63.158 0.00 0.00 0.00 2.59
2274 2535 0.037734 CAACCCCCAACCCTAGACAC 59.962 60.000 0.00 0.00 0.00 3.67
2286 2547 2.418746 CCCTAGACACAGTCCCATTTCG 60.419 54.545 0.00 0.00 32.18 3.46
2295 2556 1.095600 GTCCCATTTCGCTCCCTTTC 58.904 55.000 0.00 0.00 0.00 2.62
2296 2557 0.991920 TCCCATTTCGCTCCCTTTCT 59.008 50.000 0.00 0.00 0.00 2.52
2297 2558 2.093128 GTCCCATTTCGCTCCCTTTCTA 60.093 50.000 0.00 0.00 0.00 2.10
2354 2615 2.284331 TTGTAGCTCTGGCCCGGA 60.284 61.111 0.73 0.00 39.73 5.14
2362 2623 4.918201 CTGGCCCGGAAGCGGATC 62.918 72.222 0.73 0.00 0.00 3.36
2372 2633 1.134521 GGAAGCGGATCACCATGTACA 60.135 52.381 0.00 0.00 35.59 2.90
2373 2634 2.485479 GGAAGCGGATCACCATGTACAT 60.485 50.000 1.41 1.41 35.59 2.29
2374 2635 2.245159 AGCGGATCACCATGTACATG 57.755 50.000 26.02 26.02 38.51 3.21
2395 2656 2.487428 CTCACTCCAGAGCGTCGG 59.513 66.667 0.00 0.00 0.00 4.79
2399 2660 2.811317 CTCCAGAGCGTCGGTTGC 60.811 66.667 0.00 0.00 0.00 4.17
2401 2662 2.434884 CCAGAGCGTCGGTTGCAT 60.435 61.111 0.00 0.00 33.85 3.96
2411 2672 1.751924 GTCGGTTGCATCTCCTAGAGT 59.248 52.381 0.00 0.00 0.00 3.24
2417 2678 4.219725 GGTTGCATCTCCTAGAGTAGATCC 59.780 50.000 0.00 0.00 29.93 3.36
2424 2685 0.112606 CTAGAGTAGATCCGGGCCCA 59.887 60.000 24.92 2.47 0.00 5.36
2425 2686 0.112606 TAGAGTAGATCCGGGCCCAG 59.887 60.000 24.92 11.71 0.00 4.45
2438 2699 3.625897 CCCAGTGTGCCACTCGGA 61.626 66.667 11.72 0.00 43.72 4.55
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
113 114 2.200373 ACCCTGTGTGCTATCAAACC 57.800 50.000 0.00 0.00 29.08 3.27
144 145 0.179000 AGATCATGCAACTCCCGGAC 59.821 55.000 0.73 0.00 0.00 4.79
165 166 8.347004 TGTCAAATACATATTCTTTCAGCCAA 57.653 30.769 0.00 0.00 31.43 4.52
319 322 5.351465 GCTCGTTGATCAAAGATGGTTAAGA 59.649 40.000 21.83 0.00 0.00 2.10
494 501 5.067153 CCTATGAATGCACCGTTGGAAATAA 59.933 40.000 0.00 0.00 0.00 1.40
505 512 3.144506 CACTCATCCCTATGAATGCACC 58.855 50.000 0.00 0.00 41.57 5.01
506 513 3.813443 ACACTCATCCCTATGAATGCAC 58.187 45.455 0.00 0.00 41.91 4.57
507 514 5.554070 CATACACTCATCCCTATGAATGCA 58.446 41.667 0.00 0.00 41.91 3.96
508 515 4.394300 GCATACACTCATCCCTATGAATGC 59.606 45.833 6.88 6.88 41.91 3.56
509 516 5.410746 GTGCATACACTCATCCCTATGAATG 59.589 44.000 0.00 0.00 43.41 2.67
510 517 5.555017 GTGCATACACTCATCCCTATGAAT 58.445 41.667 0.00 0.00 41.57 2.57
511 518 4.501400 CGTGCATACACTCATCCCTATGAA 60.501 45.833 0.00 0.00 45.10 2.57
512 519 3.005791 CGTGCATACACTCATCCCTATGA 59.994 47.826 0.00 0.00 45.10 2.15
513 520 3.243873 ACGTGCATACACTCATCCCTATG 60.244 47.826 0.00 0.00 45.10 2.23
514 521 2.965831 ACGTGCATACACTCATCCCTAT 59.034 45.455 0.00 0.00 45.10 2.57
515 522 2.100749 CACGTGCATACACTCATCCCTA 59.899 50.000 0.82 0.00 45.10 3.53
516 523 1.134699 CACGTGCATACACTCATCCCT 60.135 52.381 0.82 0.00 45.10 4.20
517 524 1.290203 CACGTGCATACACTCATCCC 58.710 55.000 0.82 0.00 45.10 3.85
518 525 2.010145 ACACGTGCATACACTCATCC 57.990 50.000 17.22 0.00 45.10 3.51
519 526 5.290885 TCATTTACACGTGCATACACTCATC 59.709 40.000 17.22 0.00 45.10 2.92
520 527 5.175127 TCATTTACACGTGCATACACTCAT 58.825 37.500 17.22 0.00 45.10 2.90
521 528 4.561105 TCATTTACACGTGCATACACTCA 58.439 39.130 17.22 0.00 45.10 3.41
522 529 4.492570 GCTCATTTACACGTGCATACACTC 60.493 45.833 17.22 0.00 45.10 3.51
523 530 3.370978 GCTCATTTACACGTGCATACACT 59.629 43.478 17.22 0.00 45.10 3.55
524 531 3.670203 GCTCATTTACACGTGCATACAC 58.330 45.455 17.22 0.00 43.76 2.90
525 532 2.347150 CGCTCATTTACACGTGCATACA 59.653 45.455 17.22 0.00 0.00 2.29
526 533 2.347452 ACGCTCATTTACACGTGCATAC 59.653 45.455 17.22 0.00 37.37 2.39
527 534 2.612604 ACGCTCATTTACACGTGCATA 58.387 42.857 17.22 0.00 37.37 3.14
528 535 1.438651 ACGCTCATTTACACGTGCAT 58.561 45.000 17.22 2.19 37.37 3.96
529 536 1.222300 AACGCTCATTTACACGTGCA 58.778 45.000 17.22 0.00 39.00 4.57
530 537 1.969256 CAAACGCTCATTTACACGTGC 59.031 47.619 17.22 0.00 39.00 5.34
531 538 1.969256 GCAAACGCTCATTTACACGTG 59.031 47.619 15.48 15.48 39.00 4.49
532 539 1.397945 CGCAAACGCTCATTTACACGT 60.398 47.619 0.00 0.00 41.16 4.49
533 540 1.238281 CGCAAACGCTCATTTACACG 58.762 50.000 0.00 0.00 0.00 4.49
534 541 2.096417 AGACGCAAACGCTCATTTACAC 60.096 45.455 0.00 0.00 45.53 2.90
535 542 2.096466 CAGACGCAAACGCTCATTTACA 60.096 45.455 0.00 0.00 45.53 2.41
536 543 2.096417 ACAGACGCAAACGCTCATTTAC 60.096 45.455 0.00 0.00 45.53 2.01
537 544 2.139917 ACAGACGCAAACGCTCATTTA 58.860 42.857 0.00 0.00 45.53 1.40
538 545 0.944386 ACAGACGCAAACGCTCATTT 59.056 45.000 0.00 0.00 45.53 2.32
539 546 1.459592 GTACAGACGCAAACGCTCATT 59.540 47.619 0.00 0.00 45.53 2.57
540 547 1.068474 GTACAGACGCAAACGCTCAT 58.932 50.000 0.00 0.00 45.53 2.90
541 548 0.031585 AGTACAGACGCAAACGCTCA 59.968 50.000 0.00 0.00 45.53 4.26
542 549 0.708918 GAGTACAGACGCAAACGCTC 59.291 55.000 0.00 0.00 45.53 5.03
543 550 0.314302 AGAGTACAGACGCAAACGCT 59.686 50.000 0.00 0.00 45.53 5.07
544 551 0.435008 CAGAGTACAGACGCAAACGC 59.565 55.000 0.00 0.00 45.53 4.84
546 553 5.646467 TTTAACAGAGTACAGACGCAAAC 57.354 39.130 0.00 0.00 0.00 2.93
547 554 6.665474 TTTTTAACAGAGTACAGACGCAAA 57.335 33.333 0.00 0.00 0.00 3.68
571 578 1.686115 CCATCCGGGGAGATGCTTTTT 60.686 52.381 0.00 0.00 41.98 1.94
572 579 0.106519 CCATCCGGGGAGATGCTTTT 60.107 55.000 0.00 0.00 41.98 2.27
573 580 1.533711 CCATCCGGGGAGATGCTTT 59.466 57.895 0.00 0.00 41.98 3.51
574 581 3.244616 CCATCCGGGGAGATGCTT 58.755 61.111 0.00 0.00 41.98 3.91
585 592 4.802051 CACCAGGTGGCCCATCCG 62.802 72.222 12.40 0.00 39.32 4.18
586 593 3.645268 GACACCAGGTGGCCCATCC 62.645 68.421 24.13 0.00 35.14 3.51
587 594 2.044946 GACACCAGGTGGCCCATC 60.045 66.667 24.13 7.94 35.14 3.51
601 608 3.723772 CCATGTTCAGTGTGGGACA 57.276 52.632 0.00 0.00 0.00 4.02
605 612 0.540365 AAGGCCCATGTTCAGTGTGG 60.540 55.000 0.00 0.00 0.00 4.17
606 613 0.599558 CAAGGCCCATGTTCAGTGTG 59.400 55.000 0.00 0.00 0.00 3.82
607 614 1.181098 GCAAGGCCCATGTTCAGTGT 61.181 55.000 0.00 0.00 0.00 3.55
608 615 1.588082 GCAAGGCCCATGTTCAGTG 59.412 57.895 0.00 0.00 0.00 3.66
609 616 1.607467 GGCAAGGCCCATGTTCAGT 60.607 57.895 0.00 0.00 44.06 3.41
610 617 3.291611 GGCAAGGCCCATGTTCAG 58.708 61.111 0.00 0.00 44.06 3.02
901 945 8.598041 AGTAGGATGTCACTCTCTTATGTTTTT 58.402 33.333 0.00 0.00 0.00 1.94
905 949 9.427821 AATAAGTAGGATGTCACTCTCTTATGT 57.572 33.333 0.00 0.00 31.76 2.29
955 1003 5.698089 GCAGTCTGCAGTGATATTATTAGCA 59.302 40.000 20.16 0.00 44.26 3.49
975 1026 1.683917 GGACAGATCGGTAGATGCAGT 59.316 52.381 0.00 0.00 37.19 4.40
976 1027 1.335415 CGGACAGATCGGTAGATGCAG 60.335 57.143 0.00 0.00 37.19 4.41
977 1028 0.668535 CGGACAGATCGGTAGATGCA 59.331 55.000 0.00 0.00 37.19 3.96
978 1029 0.952280 TCGGACAGATCGGTAGATGC 59.048 55.000 0.00 0.00 37.19 3.91
979 1030 3.479505 GATCGGACAGATCGGTAGATG 57.520 52.381 16.84 0.00 45.35 2.90
1028 1079 5.063204 AGATGATCACGAGGAGTAGAAGAG 58.937 45.833 0.00 0.00 0.00 2.85
1029 1080 5.042463 AGATGATCACGAGGAGTAGAAGA 57.958 43.478 0.00 0.00 0.00 2.87
1035 1086 4.640789 GTGTAAGATGATCACGAGGAGT 57.359 45.455 0.00 0.00 0.00 3.85
1115 1166 6.788598 ATGGCCATATGTAACACAATGAAA 57.211 33.333 19.18 0.00 0.00 2.69
1117 1168 6.183360 GGAAATGGCCATATGTAACACAATGA 60.183 38.462 21.15 0.00 0.00 2.57
1118 1169 5.984926 GGAAATGGCCATATGTAACACAATG 59.015 40.000 21.15 0.00 0.00 2.82
1119 1170 5.898972 AGGAAATGGCCATATGTAACACAAT 59.101 36.000 21.15 0.00 0.00 2.71
1122 1173 5.133221 AGAGGAAATGGCCATATGTAACAC 58.867 41.667 21.15 6.32 0.00 3.32
1123 1174 5.387113 AGAGGAAATGGCCATATGTAACA 57.613 39.130 21.15 0.00 0.00 2.41
1124 1175 6.016777 CAGAAGAGGAAATGGCCATATGTAAC 60.017 42.308 21.15 9.44 0.00 2.50
1176 1235 3.009473 AGGTGACTTGCATAACCTCACAT 59.991 43.478 4.73 0.00 38.73 3.21
1184 1243 5.045942 TCCAATCAGTAGGTGACTTGCATAA 60.046 40.000 0.00 0.00 43.67 1.90
1481 1545 9.440761 AGAAATGTCTAGTGGATAATTCCTACT 57.559 33.333 0.00 3.10 36.13 2.57
1510 1578 7.288621 TGAGAGATGAGGACAAGCAAATATCTA 59.711 37.037 0.00 0.00 0.00 1.98
1511 1579 6.099413 TGAGAGATGAGGACAAGCAAATATCT 59.901 38.462 0.00 0.00 0.00 1.98
1512 1580 6.202570 GTGAGAGATGAGGACAAGCAAATATC 59.797 42.308 0.00 0.00 0.00 1.63
1513 1581 6.054295 GTGAGAGATGAGGACAAGCAAATAT 58.946 40.000 0.00 0.00 0.00 1.28
1514 1582 5.046376 TGTGAGAGATGAGGACAAGCAAATA 60.046 40.000 0.00 0.00 0.00 1.40
1517 1585 2.634453 TGTGAGAGATGAGGACAAGCAA 59.366 45.455 0.00 0.00 0.00 3.91
1518 1586 2.250924 TGTGAGAGATGAGGACAAGCA 58.749 47.619 0.00 0.00 0.00 3.91
1519 1587 3.325293 TTGTGAGAGATGAGGACAAGC 57.675 47.619 0.00 0.00 0.00 4.01
1520 1588 3.999663 GGTTTGTGAGAGATGAGGACAAG 59.000 47.826 0.00 0.00 0.00 3.16
1522 1590 2.972021 TGGTTTGTGAGAGATGAGGACA 59.028 45.455 0.00 0.00 0.00 4.02
1523 1591 3.685139 TGGTTTGTGAGAGATGAGGAC 57.315 47.619 0.00 0.00 0.00 3.85
1524 1592 4.916041 ATTGGTTTGTGAGAGATGAGGA 57.084 40.909 0.00 0.00 0.00 3.71
1525 1593 5.939883 TGTAATTGGTTTGTGAGAGATGAGG 59.060 40.000 0.00 0.00 0.00 3.86
1526 1594 6.402983 GCTGTAATTGGTTTGTGAGAGATGAG 60.403 42.308 0.00 0.00 0.00 2.90
1527 1595 5.412594 GCTGTAATTGGTTTGTGAGAGATGA 59.587 40.000 0.00 0.00 0.00 2.92
1528 1596 5.392380 GGCTGTAATTGGTTTGTGAGAGATG 60.392 44.000 0.00 0.00 0.00 2.90
1529 1597 4.702131 GGCTGTAATTGGTTTGTGAGAGAT 59.298 41.667 0.00 0.00 0.00 2.75
1530 1598 4.072131 GGCTGTAATTGGTTTGTGAGAGA 58.928 43.478 0.00 0.00 0.00 3.10
1531 1599 3.820467 TGGCTGTAATTGGTTTGTGAGAG 59.180 43.478 0.00 0.00 0.00 3.20
1537 1605 7.151308 TCAATAAACTGGCTGTAATTGGTTTG 58.849 34.615 21.52 10.66 35.04 2.93
1550 1618 2.356069 GCTGCTACCTCAATAAACTGGC 59.644 50.000 0.00 0.00 0.00 4.85
1561 1629 1.814586 CTGCTGCTGCTGCTACCTC 60.815 63.158 27.67 3.30 40.48 3.85
1577 1645 6.462207 CCCCAATCTGAGACTAACTACATCTG 60.462 46.154 0.00 0.00 0.00 2.90
1582 1678 6.098409 TCAATCCCCAATCTGAGACTAACTAC 59.902 42.308 0.00 0.00 0.00 2.73
1632 1731 3.150767 CGTAGTAGCCATCTAGGAAGCT 58.849 50.000 6.56 6.56 41.22 3.74
1873 1974 4.211125 TGAGGGAAAACAATAAGCACACA 58.789 39.130 0.00 0.00 0.00 3.72
1874 1975 4.846779 TGAGGGAAAACAATAAGCACAC 57.153 40.909 0.00 0.00 0.00 3.82
1928 2029 8.146412 AGAAAGTCCATCAGATTTTTCTTTTGG 58.854 33.333 0.00 0.00 37.70 3.28
2010 2113 5.299279 CAGAAGTGTGTGTTTGAGGGTTTAT 59.701 40.000 0.00 0.00 0.00 1.40
2025 2128 6.458751 CCGATATTTTGGATTCCAGAAGTGTG 60.459 42.308 13.49 4.97 31.20 3.82
2029 2132 6.058183 ACTCCGATATTTTGGATTCCAGAAG 58.942 40.000 13.49 1.96 34.73 2.85
2051 2154 2.090494 ACAGGGGCATGAGTATAGGACT 60.090 50.000 0.00 0.00 42.90 3.85
2055 2158 5.745312 TTATCACAGGGGCATGAGTATAG 57.255 43.478 0.00 0.00 0.00 1.31
2090 2194 4.844349 AGATGCTCTAACTTTTGGGCTA 57.156 40.909 0.00 0.00 0.00 3.93
2092 2196 4.261801 TGTAGATGCTCTAACTTTTGGGC 58.738 43.478 0.00 0.00 29.58 5.36
2093 2197 4.333926 GCTGTAGATGCTCTAACTTTTGGG 59.666 45.833 0.00 0.00 29.58 4.12
2097 2201 3.430929 CCGGCTGTAGATGCTCTAACTTT 60.431 47.826 0.00 0.00 29.58 2.66
2123 2227 6.064060 CCAAACATATAGGAGGCATTTGAGA 58.936 40.000 0.00 0.00 0.00 3.27
2124 2228 6.016777 GTCCAAACATATAGGAGGCATTTGAG 60.017 42.308 0.00 0.00 30.78 3.02
2130 2234 2.104111 CCGTCCAAACATATAGGAGGCA 59.896 50.000 0.00 0.00 36.31 4.75
2134 2238 2.363038 CCGTCCGTCCAAACATATAGGA 59.637 50.000 0.00 0.00 0.00 2.94
2170 2274 3.554129 GGCTGGGTTACATTTTTGTGACC 60.554 47.826 10.63 10.63 44.67 4.02
2184 2288 0.768221 TTGAGGAGTCTGGCTGGGTT 60.768 55.000 0.00 0.00 0.00 4.11
2190 2294 3.239861 CCAGTTTGAGGAGTCTGGC 57.760 57.895 0.00 0.00 40.43 4.85
2191 2295 0.689623 AGCCAGTTTGAGGAGTCTGG 59.310 55.000 5.79 5.79 46.96 3.86
2194 2298 5.009811 ACGTATATAGCCAGTTTGAGGAGTC 59.990 44.000 0.00 0.00 0.00 3.36
2198 2302 5.223382 CAGACGTATATAGCCAGTTTGAGG 58.777 45.833 0.00 0.00 0.00 3.86
2206 2310 2.557056 GTCAGCCAGACGTATATAGCCA 59.443 50.000 0.00 0.00 37.53 4.75
2229 2333 2.487265 CCGGCTTAAATATGAGGGTGCT 60.487 50.000 0.00 0.00 0.00 4.40
2252 2513 3.638592 CTAGGGTTGGGGGTTGCCG 62.639 68.421 0.00 0.00 0.00 5.69
2256 2517 0.402272 TGTGTCTAGGGTTGGGGGTT 60.402 55.000 0.00 0.00 0.00 4.11
2263 2524 2.344093 ATGGGACTGTGTCTAGGGTT 57.656 50.000 0.00 0.00 32.47 4.11
2265 2526 2.418746 CGAAATGGGACTGTGTCTAGGG 60.419 54.545 0.00 0.00 32.47 3.53
2267 2528 2.093973 AGCGAAATGGGACTGTGTCTAG 60.094 50.000 0.00 0.00 32.47 2.43
2271 2532 0.321653 GGAGCGAAATGGGACTGTGT 60.322 55.000 0.00 0.00 0.00 3.72
2272 2533 1.026718 GGGAGCGAAATGGGACTGTG 61.027 60.000 0.00 0.00 0.00 3.66
2274 2535 0.035056 AAGGGAGCGAAATGGGACTG 60.035 55.000 0.00 0.00 0.00 3.51
2286 2547 2.203084 GGCGGCTAGAAAGGGAGC 60.203 66.667 0.00 0.00 38.00 4.70
2295 2556 4.778143 GTGGTGGGTGGCGGCTAG 62.778 72.222 11.43 0.00 0.00 3.42
2354 2615 2.564771 CATGTACATGGTGATCCGCTT 58.435 47.619 25.41 0.00 35.24 4.68
2392 2653 2.145397 ACTCTAGGAGATGCAACCGA 57.855 50.000 0.00 0.00 33.32 4.69
2395 2656 4.083003 CGGATCTACTCTAGGAGATGCAAC 60.083 50.000 19.93 3.11 39.71 4.17
2399 2660 3.616219 CCCGGATCTACTCTAGGAGATG 58.384 54.545 9.50 0.00 32.47 2.90
2401 2662 1.351683 GCCCGGATCTACTCTAGGAGA 59.648 57.143 0.73 0.00 33.32 3.71
2411 2672 2.063979 CACACTGGGCCCGGATCTA 61.064 63.158 38.16 7.46 0.00 1.98


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

AutoCloner maintained by Alex Coulton.