Multiple sequence alignment - TraesCS5D01G355200

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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 TraesCS5D01G355200 chr5D 100.000 4675 0 0 1 4675 437014195 437018869 0.000000e+00 8634.0
1 TraesCS5D01G355200 chr5D 86.751 551 71 2 1008 1557 553910509 553911058 3.090000e-171 612.0
2 TraesCS5D01G355200 chr5D 81.129 726 113 17 2140 2844 553911785 553912507 1.140000e-155 560.0
3 TraesCS5D01G355200 chr5D 81.495 535 97 2 1001 1534 445486030 445485497 5.550000e-119 438.0
4 TraesCS5D01G355200 chr5D 81.798 456 72 10 2898 3343 553912498 553912952 5.710000e-99 372.0
5 TraesCS5D01G355200 chr5D 84.756 328 44 6 3048 3370 445489966 445489640 1.620000e-84 324.0
6 TraesCS5D01G355200 chr5D 85.036 274 34 5 3522 3794 436983750 436984017 5.960000e-69 272.0
7 TraesCS5D01G355200 chr5D 87.719 114 12 2 2148 2260 445484831 445484719 1.060000e-26 132.0
8 TraesCS5D01G355200 chr5D 72.749 411 78 20 125 527 437037318 437037702 1.780000e-19 108.0
9 TraesCS5D01G355200 chr5D 75.431 232 48 7 1855 2086 553911488 553911710 2.300000e-18 104.0
10 TraesCS5D01G355200 chr5D 78.676 136 22 6 384 516 445380697 445380566 3.000000e-12 84.2
11 TraesCS5D01G355200 chr5A 91.852 4038 251 36 617 4622 552298024 552302015 0.000000e+00 5563.0
12 TraesCS5D01G355200 chr5A 92.463 544 24 4 2 528 552282709 552283252 0.000000e+00 761.0
13 TraesCS5D01G355200 chr5A 74.813 536 81 33 1 505 552305342 552305854 4.770000e-45 193.0
14 TraesCS5D01G355200 chr5A 87.931 58 6 1 458 514 562895850 562895793 3.020000e-07 67.6
15 TraesCS5D01G355200 chr5B 93.492 3411 148 30 620 3997 531204303 531207672 0.000000e+00 5001.0
16 TraesCS5D01G355200 chr5B 85.660 530 25 8 1 527 531203799 531204280 1.160000e-140 510.0
17 TraesCS5D01G355200 chr5B 82.900 538 82 9 1001 1530 543282508 543281973 4.230000e-130 475.0
18 TraesCS5D01G355200 chr5B 88.350 309 36 0 3042 3350 543270182 543269874 5.710000e-99 372.0
19 TraesCS5D01G355200 chr5B 84.024 338 47 7 3039 3370 543297753 543297417 7.550000e-83 318.0
20 TraesCS5D01G355200 chr5B 89.041 219 20 3 4063 4277 531207871 531208089 7.710000e-68 268.0
21 TraesCS5D01G355200 chr5B 74.556 338 63 14 210 541 531212690 531213010 4.910000e-25 126.0
22 TraesCS5D01G355200 chr5B 95.238 42 2 0 473 514 542955923 542955882 3.020000e-07 67.6
23 TraesCS5D01G355200 chr5B 76.596 141 19 11 380 516 542984100 542983970 1.090000e-06 65.8
24 TraesCS5D01G355200 chr2B 82.432 518 85 6 1020 1534 794611699 794611185 9.230000e-122 448.0
25 TraesCS5D01G355200 chr1A 75.254 986 196 31 2729 3694 506278027 506277070 4.320000e-115 425.0
26 TraesCS5D01G355200 chr7A 80.871 528 96 4 1008 1534 7817266 7817789 1.210000e-110 411.0
27 TraesCS5D01G355200 chr4B 84.112 428 57 8 2121 2539 2206400 2206825 2.030000e-108 403.0
28 TraesCS5D01G355200 chr4B 84.112 428 57 8 2121 2539 2235809 2236234 2.030000e-108 403.0
29 TraesCS5D01G355200 chr4B 80.814 516 89 9 1001 1511 2205415 2205925 3.390000e-106 396.0
30 TraesCS5D01G355200 chr4B 80.233 516 92 9 1001 1511 2234824 2235334 3.410000e-101 379.0
31 TraesCS5D01G355200 chr4D 81.132 424 68 11 2927 3341 1689481 1689901 3.490000e-86 329.0
32 TraesCS5D01G355200 chr4D 85.342 307 44 1 3042 3347 1638526 1638832 2.720000e-82 316.0
33 TraesCS5D01G355200 chrUn 91.667 72 6 0 2692 2763 310057553 310057482 2.980000e-17 100.0
34 TraesCS5D01G355200 chr3D 96.774 31 1 0 2615 2645 607234003 607234033 8.000000e-03 52.8


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 TraesCS5D01G355200 chr5D 437014195 437018869 4674 False 8634.000000 8634 100.000000 1 4675 1 chr5D.!!$F2 4674
1 TraesCS5D01G355200 chr5D 553910509 553912952 2443 False 412.000000 612 81.277250 1008 3343 4 chr5D.!!$F4 2335
2 TraesCS5D01G355200 chr5D 445484719 445489966 5247 True 298.000000 438 84.656667 1001 3370 3 chr5D.!!$R2 2369
3 TraesCS5D01G355200 chr5A 552298024 552305854 7830 False 2878.000000 5563 83.332500 1 4622 2 chr5A.!!$F2 4621
4 TraesCS5D01G355200 chr5A 552282709 552283252 543 False 761.000000 761 92.463000 2 528 1 chr5A.!!$F1 526
5 TraesCS5D01G355200 chr5B 531203799 531208089 4290 False 1926.333333 5001 89.397667 1 4277 3 chr5B.!!$F2 4276
6 TraesCS5D01G355200 chr5B 543281973 543282508 535 True 475.000000 475 82.900000 1001 1530 1 chr5B.!!$R4 529
7 TraesCS5D01G355200 chr2B 794611185 794611699 514 True 448.000000 448 82.432000 1020 1534 1 chr2B.!!$R1 514
8 TraesCS5D01G355200 chr1A 506277070 506278027 957 True 425.000000 425 75.254000 2729 3694 1 chr1A.!!$R1 965
9 TraesCS5D01G355200 chr7A 7817266 7817789 523 False 411.000000 411 80.871000 1008 1534 1 chr7A.!!$F1 526
10 TraesCS5D01G355200 chr4B 2205415 2206825 1410 False 399.500000 403 82.463000 1001 2539 2 chr4B.!!$F1 1538
11 TraesCS5D01G355200 chr4B 2234824 2236234 1410 False 391.000000 403 82.172500 1001 2539 2 chr4B.!!$F2 1538

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
567 611 0.032678 ATGCACGCTCCCTAATCGAG 59.967 55.000 0.00 0.0 0.0 4.04 F
640 684 0.176680 GCGATGTGGGACAGAGTCAT 59.823 55.000 0.00 0.0 41.8 3.06 F
1616 4559 0.249031 GCCGATAAGCAACCAATGGC 60.249 55.000 0.00 0.0 0.0 4.40 F
1862 5286 0.543749 GATACAGCTGAGCCCAACCT 59.456 55.000 23.35 0.0 0.0 3.50 F
2172 5617 1.200716 CTGTCATTTGCAGCAATCGGT 59.799 47.619 9.12 0.0 0.0 4.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1598 4541 0.029300 CGCCATTGGTTGCTTATCGG 59.971 55.000 4.26 0.0 0.00 4.18 R
1693 4639 0.473755 TCCTTGCCAGTCTTGCTTGA 59.526 50.000 0.00 0.0 0.00 3.02 R
2754 6217 1.741401 CAGATTTCGCCTCGTGCCA 60.741 57.895 0.00 0.0 36.24 4.92 R
3647 7135 2.024941 AGCTTGTAGGATTTCTTGGGGG 60.025 50.000 0.00 0.0 0.00 5.40 R
4147 7794 2.029380 TCAGTAAGCTCTGCGCAAAGTA 60.029 45.455 13.16 0.0 42.61 2.24 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
42 43 3.391665 GACGGTCAGGCCCATCTGG 62.392 68.421 0.00 0.00 35.58 3.86
69 70 3.190535 CCCAACACCAATTACAGCTACAC 59.809 47.826 0.00 0.00 0.00 2.90
156 171 3.382832 CAGGGCCGGAGTTCTCGT 61.383 66.667 5.05 0.00 0.00 4.18
295 310 3.316573 GAGACTCAAGGTGGCGGGG 62.317 68.421 0.00 0.00 0.00 5.73
381 396 2.507769 CGGGAAACGGCGTACTCC 60.508 66.667 25.20 25.20 39.42 3.85
388 403 3.751246 CGGCGTACTCCGGGTGAA 61.751 66.667 16.56 0.00 45.38 3.18
390 405 2.643232 GGCGTACTCCGGGTGAACT 61.643 63.158 0.00 0.00 36.94 3.01
391 406 1.445582 GCGTACTCCGGGTGAACTG 60.446 63.158 0.00 0.00 36.94 3.16
392 407 1.445582 CGTACTCCGGGTGAACTGC 60.446 63.158 0.00 0.00 0.00 4.40
394 409 3.291101 TACTCCGGGTGAACTGCGC 62.291 63.158 0.00 0.00 0.00 6.09
469 510 2.183046 GGTCGAGGTCAGCAGCTC 59.817 66.667 0.00 0.00 42.82 4.09
515 559 4.074627 TGTGTTTATTCCCGTCTGTTCA 57.925 40.909 0.00 0.00 0.00 3.18
528 572 2.475487 GTCTGTTCAACTGCGTCCTAAC 59.525 50.000 0.00 0.00 0.00 2.34
529 573 2.364324 TCTGTTCAACTGCGTCCTAACT 59.636 45.455 0.00 0.00 0.00 2.24
530 574 3.131396 CTGTTCAACTGCGTCCTAACTT 58.869 45.455 0.00 0.00 0.00 2.66
531 575 2.869801 TGTTCAACTGCGTCCTAACTTG 59.130 45.455 0.00 0.00 0.00 3.16
532 576 1.508632 TCAACTGCGTCCTAACTTGC 58.491 50.000 0.00 0.00 0.00 4.01
533 577 1.070134 TCAACTGCGTCCTAACTTGCT 59.930 47.619 0.00 0.00 0.00 3.91
534 578 1.195448 CAACTGCGTCCTAACTTGCTG 59.805 52.381 0.00 0.00 0.00 4.41
537 581 0.037326 TGCGTCCTAACTTGCTGGAG 60.037 55.000 0.00 0.00 0.00 3.86
540 584 2.735762 GCGTCCTAACTTGCTGGAGTAG 60.736 54.545 0.00 0.00 0.00 2.57
541 585 2.159226 CGTCCTAACTTGCTGGAGTAGG 60.159 54.545 0.00 0.00 0.00 3.18
544 588 4.098196 GTCCTAACTTGCTGGAGTAGGTAG 59.902 50.000 0.00 0.00 0.00 3.18
547 591 3.383698 ACTTGCTGGAGTAGGTAGCTA 57.616 47.619 0.00 0.00 38.25 3.32
549 593 4.290942 ACTTGCTGGAGTAGGTAGCTAAT 58.709 43.478 2.58 1.68 38.25 1.73
550 594 4.100189 ACTTGCTGGAGTAGGTAGCTAATG 59.900 45.833 6.65 0.00 38.25 1.90
551 595 2.365617 TGCTGGAGTAGGTAGCTAATGC 59.634 50.000 13.12 13.12 38.25 3.56
553 597 3.800604 GCTGGAGTAGGTAGCTAATGCAC 60.801 52.174 17.80 11.86 42.74 4.57
556 600 2.032620 AGTAGGTAGCTAATGCACGCT 58.967 47.619 2.58 11.17 42.74 5.07
558 602 0.105039 AGGTAGCTAATGCACGCTCC 59.895 55.000 9.91 10.88 42.74 4.70
559 603 0.880718 GGTAGCTAATGCACGCTCCC 60.881 60.000 9.91 5.46 42.74 4.30
560 604 0.105039 GTAGCTAATGCACGCTCCCT 59.895 55.000 9.91 0.00 42.74 4.20
561 605 1.340248 GTAGCTAATGCACGCTCCCTA 59.660 52.381 9.91 0.00 42.74 3.53
562 606 0.830648 AGCTAATGCACGCTCCCTAA 59.169 50.000 0.00 0.00 42.74 2.69
563 607 1.417890 AGCTAATGCACGCTCCCTAAT 59.582 47.619 0.00 0.00 42.74 1.73
564 608 1.801178 GCTAATGCACGCTCCCTAATC 59.199 52.381 0.00 0.00 39.41 1.75
566 610 0.464036 AATGCACGCTCCCTAATCGA 59.536 50.000 0.00 0.00 0.00 3.59
567 611 0.032678 ATGCACGCTCCCTAATCGAG 59.967 55.000 0.00 0.00 0.00 4.04
575 619 3.641437 CTCCCTAATCGAGCTCAAGAG 57.359 52.381 15.40 4.81 0.00 2.85
588 632 2.344950 CTCAAGAGCCATGTCACTCAC 58.655 52.381 9.50 0.00 35.28 3.51
598 642 1.159713 TGTCACTCACGCTTGCTTGG 61.160 55.000 0.00 0.00 0.00 3.61
601 645 2.979676 CTCACGCTTGCTTGGCCA 60.980 61.111 0.00 0.00 0.00 5.36
603 647 2.126228 CACGCTTGCTTGGCCATG 60.126 61.111 6.09 11.02 0.00 3.66
604 648 4.060038 ACGCTTGCTTGGCCATGC 62.060 61.111 31.32 31.32 33.86 4.06
614 658 2.676471 GGCCATGCCCTGTTTCGT 60.676 61.111 0.00 0.00 44.06 3.85
616 660 1.080569 GCCATGCCCTGTTTCGTTG 60.081 57.895 0.00 0.00 0.00 4.10
617 661 1.080569 CCATGCCCTGTTTCGTTGC 60.081 57.895 0.00 0.00 0.00 4.17
629 673 1.840630 TTCGTTGCACTGCGATGTGG 61.841 55.000 9.86 0.00 38.31 4.17
640 684 0.176680 GCGATGTGGGACAGAGTCAT 59.823 55.000 0.00 0.00 41.80 3.06
655 699 6.410540 ACAGAGTCATAAAGAAATGGGTCTC 58.589 40.000 0.00 0.00 0.00 3.36
657 701 6.760770 CAGAGTCATAAAGAAATGGGTCTCTC 59.239 42.308 0.00 0.00 32.84 3.20
661 705 6.881602 GTCATAAAGAAATGGGTCTCTCAAGT 59.118 38.462 0.00 0.00 0.00 3.16
662 706 6.881065 TCATAAAGAAATGGGTCTCTCAAGTG 59.119 38.462 0.00 0.00 0.00 3.16
663 707 3.064900 AGAAATGGGTCTCTCAAGTGC 57.935 47.619 0.00 0.00 0.00 4.40
667 711 0.394192 TGGGTCTCTCAAGTGCTGTG 59.606 55.000 0.00 0.00 0.00 3.66
670 720 1.586422 GTCTCTCAAGTGCTGTGCAA 58.414 50.000 0.00 0.00 41.47 4.08
674 724 1.202794 TCTCAAGTGCTGTGCAATCCA 60.203 47.619 0.00 0.00 41.47 3.41
682 732 0.893270 CTGTGCAATCCAAACCCGGA 60.893 55.000 0.73 0.00 40.07 5.14
704 754 2.540973 GCGTGGTGGAAAGTGAAAAGAC 60.541 50.000 0.00 0.00 0.00 3.01
711 761 3.134081 TGGAAAGTGAAAAGACGAGAGGT 59.866 43.478 0.00 0.00 0.00 3.85
723 773 9.152595 GAAAAGACGAGAGGTAATCAAGTAAAT 57.847 33.333 0.00 0.00 0.00 1.40
731 783 8.331931 AGAGGTAATCAAGTAAATATGGGTCA 57.668 34.615 0.00 0.00 0.00 4.02
772 824 3.173953 AGATAGAGAGGAGGGCATCAG 57.826 52.381 0.08 0.00 0.00 2.90
774 826 2.373335 TAGAGAGGAGGGCATCAGTC 57.627 55.000 0.08 0.00 0.00 3.51
802 854 1.737793 CAAACACGGGAGGAATGTAGC 59.262 52.381 0.00 0.00 0.00 3.58
803 855 0.981183 AACACGGGAGGAATGTAGCA 59.019 50.000 0.00 0.00 0.00 3.49
854 906 3.808726 GGCACATCAACATCAAAAAGCAA 59.191 39.130 0.00 0.00 0.00 3.91
900 952 5.208890 TGGTAAGCTCTAGCCTTGATTAGA 58.791 41.667 0.00 0.00 43.38 2.10
902 954 4.953940 AAGCTCTAGCCTTGATTAGAGG 57.046 45.455 9.75 0.00 41.95 3.69
912 964 6.909076 AGCCTTGATTAGAGGATGATTTTCT 58.091 36.000 0.00 0.00 36.33 2.52
1374 4311 0.812811 CTGCCATCACCCAGATCACG 60.813 60.000 0.00 0.00 33.72 4.35
1582 4525 4.515191 GCCCGTATGCATTATTTCAGAAGA 59.485 41.667 3.54 0.00 0.00 2.87
1583 4526 5.182001 GCCCGTATGCATTATTTCAGAAGAT 59.818 40.000 3.54 0.00 0.00 2.40
1584 4527 6.605849 CCCGTATGCATTATTTCAGAAGATG 58.394 40.000 3.54 0.00 0.00 2.90
1596 4539 4.548451 TCAGAAGATGACACAGATGCTT 57.452 40.909 0.00 0.00 31.12 3.91
1598 4541 3.008330 AGAAGATGACACAGATGCTTGC 58.992 45.455 0.00 0.00 0.00 4.01
1615 4558 1.102154 TGCCGATAAGCAACCAATGG 58.898 50.000 0.00 0.00 40.56 3.16
1616 4559 0.249031 GCCGATAAGCAACCAATGGC 60.249 55.000 0.00 0.00 0.00 4.40
1622 4565 1.679977 AGCAACCAATGGCGATGCT 60.680 52.632 18.26 18.26 42.19 3.79
1623 4566 1.517694 GCAACCAATGGCGATGCTG 60.518 57.895 15.26 0.00 34.29 4.41
1627 4570 2.411701 CAATGGCGATGCTGCAGG 59.588 61.111 17.12 3.68 36.28 4.85
1628 4571 3.524606 AATGGCGATGCTGCAGGC 61.525 61.111 17.12 17.17 42.22 4.85
1692 4638 3.616956 TCTGCTCTCCGTTTGATGATT 57.383 42.857 0.00 0.00 0.00 2.57
1693 4639 3.942829 TCTGCTCTCCGTTTGATGATTT 58.057 40.909 0.00 0.00 0.00 2.17
1703 4649 4.618489 CCGTTTGATGATTTCAAGCAAGAC 59.382 41.667 3.67 0.00 44.90 3.01
1818 5086 4.460382 ACAATTGACCTTGAGCATAACCAG 59.540 41.667 13.59 0.00 0.00 4.00
1830 5098 3.584848 AGCATAACCAGACTCCTCAAGTT 59.415 43.478 0.00 0.00 38.74 2.66
1862 5286 0.543749 GATACAGCTGAGCCCAACCT 59.456 55.000 23.35 0.00 0.00 3.50
1916 5340 3.907894 AAAGCGCAGAATCCGTAAAAA 57.092 38.095 11.47 0.00 0.00 1.94
2046 5470 2.494471 TGAATCATTGCAAGAAGGGCTG 59.506 45.455 4.94 0.00 0.00 4.85
2048 5472 2.877097 TCATTGCAAGAAGGGCTGTA 57.123 45.000 4.94 0.00 0.00 2.74
2055 5479 2.093235 GCAAGAAGGGCTGTATGAGACT 60.093 50.000 0.00 0.00 0.00 3.24
2104 5546 2.653726 TGGCACACATCACAGAAGTTT 58.346 42.857 0.00 0.00 0.00 2.66
2117 5562 5.125257 TCACAGAAGTTTCACTGATGCAAAA 59.875 36.000 0.00 0.00 37.54 2.44
2166 5611 2.268762 TGTACCTGTCATTTGCAGCA 57.731 45.000 0.00 0.00 32.93 4.41
2172 5617 1.200716 CTGTCATTTGCAGCAATCGGT 59.799 47.619 9.12 0.00 0.00 4.69
2550 6013 1.774254 CACAGGGGCCAATGGACTATA 59.226 52.381 4.56 0.00 0.00 1.31
2638 6101 1.227793 TGGCACATCGCAACAGACA 60.228 52.632 0.00 0.00 45.17 3.41
2754 6217 3.393609 TCAATCCTGAGATGCTATTGCCT 59.606 43.478 0.00 0.00 38.71 4.75
3425 6907 8.752187 ACATTTCCATCTTAGTTGCATATTTGT 58.248 29.630 0.00 0.00 0.00 2.83
3459 6941 6.074142 GGAAGCTTTTGTTGTTCATTGTGATC 60.074 38.462 0.00 0.00 0.00 2.92
3647 7135 0.249238 CTGGCGCATCTACCTCTCAC 60.249 60.000 10.83 0.00 0.00 3.51
3715 7203 3.859961 CCGTATCGATTATGCATGGAGAC 59.140 47.826 10.16 7.84 30.57 3.36
3862 7370 1.802553 TACCCTCTTATCCCCACAGC 58.197 55.000 0.00 0.00 0.00 4.40
3881 7389 5.922544 CACAGCGATCATGTCTGTAATATGA 59.077 40.000 10.53 0.00 38.85 2.15
3927 7435 5.769662 AGCATGTTTGTAAGAGTGGATTTGA 59.230 36.000 0.00 0.00 0.00 2.69
3943 7451 7.067859 AGTGGATTTGATGTGATAGTCATTTGG 59.932 37.037 0.00 0.00 0.00 3.28
4043 7610 5.300034 TCAATATCCATGATTGTGCAACTCC 59.700 40.000 0.00 0.00 38.04 3.85
4073 7718 9.679661 TGATTTACCAGATTACAGCTGAATAAA 57.320 29.630 23.35 11.98 35.39 1.40
4076 7721 4.876107 ACCAGATTACAGCTGAATAAACCG 59.124 41.667 23.35 0.87 35.39 4.44
4147 7794 4.365723 CTTCATTTCTTTGTTGCAGCTGT 58.634 39.130 16.64 0.00 0.00 4.40
4305 7955 3.433598 GCCTATCACTATCAGGTTTGGCA 60.434 47.826 0.00 0.00 36.91 4.92
4393 8043 9.244292 TGATGAGTTCTATTGTACTTGACTACT 57.756 33.333 0.00 0.00 0.00 2.57
4400 8050 8.874744 TCTATTGTACTTGACTACTTGTACCT 57.125 34.615 0.00 0.00 35.68 3.08
4415 8065 3.861840 TGTACCTGAGCTAGCAACAATC 58.138 45.455 18.83 5.69 0.00 2.67
4476 8126 8.738106 GCTACAGTTATATATTACTTCCTCCGT 58.262 37.037 1.61 0.00 0.00 4.69
4492 8142 1.493134 CCGTCCGGGTTTATTAGCGC 61.493 60.000 0.00 0.00 0.00 5.92
4494 8144 1.215244 GTCCGGGTTTATTAGCGCTC 58.785 55.000 16.34 0.00 0.00 5.03
4496 8146 1.068127 TCCGGGTTTATTAGCGCTCTC 59.932 52.381 16.34 0.00 0.00 3.20
4497 8147 1.202486 CCGGGTTTATTAGCGCTCTCA 60.202 52.381 16.34 0.00 0.00 3.27
4499 8149 3.305813 CCGGGTTTATTAGCGCTCTCATA 60.306 47.826 16.34 6.48 0.00 2.15
4500 8150 4.495422 CGGGTTTATTAGCGCTCTCATAT 58.505 43.478 16.34 3.57 0.00 1.78
4501 8151 4.929808 CGGGTTTATTAGCGCTCTCATATT 59.070 41.667 16.34 0.00 0.00 1.28
4502 8152 5.408604 CGGGTTTATTAGCGCTCTCATATTT 59.591 40.000 16.34 0.00 0.00 1.40
4503 8153 6.588756 CGGGTTTATTAGCGCTCTCATATTTA 59.411 38.462 16.34 0.00 0.00 1.40
4504 8154 7.201444 CGGGTTTATTAGCGCTCTCATATTTAG 60.201 40.741 16.34 0.00 0.00 1.85
4505 8155 7.064728 GGGTTTATTAGCGCTCTCATATTTAGG 59.935 40.741 16.34 0.00 0.00 2.69
4506 8156 7.064728 GGTTTATTAGCGCTCTCATATTTAGGG 59.935 40.741 16.34 0.00 0.00 3.53
4574 8240 6.581171 ATTGTGGAAATCCTCTTTGAAGAC 57.419 37.500 0.44 0.00 36.82 3.01
4585 8251 4.095483 CCTCTTTGAAGACAAATCCGATGG 59.905 45.833 0.00 0.00 43.64 3.51
4596 8262 7.741785 AGACAAATCCGATGGTATATTTGGTA 58.258 34.615 10.38 0.00 41.46 3.25
4651 8317 6.708885 TCCTAATGGAGCATTTGATAGGAT 57.291 37.500 0.00 0.00 37.46 3.24
4654 8320 5.464030 AATGGAGCATTTGATAGGATTGC 57.536 39.130 0.00 0.00 28.76 3.56
4655 8321 2.880268 TGGAGCATTTGATAGGATTGCG 59.120 45.455 0.00 0.00 38.32 4.85
4656 8322 2.880890 GGAGCATTTGATAGGATTGCGT 59.119 45.455 0.00 0.00 38.32 5.24
4657 8323 3.316308 GGAGCATTTGATAGGATTGCGTT 59.684 43.478 0.00 0.00 38.32 4.84
4658 8324 4.531332 GAGCATTTGATAGGATTGCGTTC 58.469 43.478 0.00 0.00 38.32 3.95
4660 8326 4.036027 AGCATTTGATAGGATTGCGTTCAG 59.964 41.667 0.00 0.00 38.32 3.02
4661 8327 4.790766 GCATTTGATAGGATTGCGTTCAGG 60.791 45.833 0.00 0.00 0.00 3.86
4662 8328 3.627395 TTGATAGGATTGCGTTCAGGT 57.373 42.857 0.00 0.00 0.00 4.00
4663 8329 3.627395 TGATAGGATTGCGTTCAGGTT 57.373 42.857 0.00 0.00 0.00 3.50
4664 8330 3.950397 TGATAGGATTGCGTTCAGGTTT 58.050 40.909 0.00 0.00 0.00 3.27
4665 8331 4.331968 TGATAGGATTGCGTTCAGGTTTT 58.668 39.130 0.00 0.00 0.00 2.43
4666 8332 4.764823 TGATAGGATTGCGTTCAGGTTTTT 59.235 37.500 0.00 0.00 0.00 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
25 26 3.402681 CCAGATGGGCCTGACCGT 61.403 66.667 4.53 0.00 40.62 4.83
42 43 1.979693 TAATTGGTGTTGGGCCGGC 60.980 57.895 21.18 21.18 0.00 6.13
142 157 3.745803 ACGACGAGAACTCCGGCC 61.746 66.667 0.00 0.00 0.00 6.13
373 388 1.445582 CAGTTCACCCGGAGTACGC 60.446 63.158 0.73 0.00 42.52 4.42
374 389 1.445582 GCAGTTCACCCGGAGTACG 60.446 63.158 0.73 0.00 43.80 3.67
375 390 1.445582 CGCAGTTCACCCGGAGTAC 60.446 63.158 0.73 0.00 0.00 2.73
376 391 2.967397 CGCAGTTCACCCGGAGTA 59.033 61.111 0.73 0.00 0.00 2.59
402 417 2.509336 GAGTGGACGCCGGTCATG 60.509 66.667 1.90 0.00 45.28 3.07
494 538 4.074627 TGAACAGACGGGAATAAACACA 57.925 40.909 0.00 0.00 0.00 3.72
528 572 4.626042 CATTAGCTACCTACTCCAGCAAG 58.374 47.826 0.00 0.00 37.78 4.01
529 573 3.181465 GCATTAGCTACCTACTCCAGCAA 60.181 47.826 0.00 0.00 37.78 3.91
530 574 2.365617 GCATTAGCTACCTACTCCAGCA 59.634 50.000 0.00 0.00 37.78 4.41
531 575 2.365617 TGCATTAGCTACCTACTCCAGC 59.634 50.000 0.00 0.00 42.74 4.85
532 576 3.551046 CGTGCATTAGCTACCTACTCCAG 60.551 52.174 0.00 0.00 42.74 3.86
533 577 2.361119 CGTGCATTAGCTACCTACTCCA 59.639 50.000 0.00 0.00 42.74 3.86
534 578 2.862921 GCGTGCATTAGCTACCTACTCC 60.863 54.545 0.00 0.00 42.74 3.85
537 581 2.395654 GAGCGTGCATTAGCTACCTAC 58.604 52.381 13.05 0.00 44.69 3.18
540 584 2.606275 GGAGCGTGCATTAGCTACC 58.394 57.895 13.05 12.02 44.69 3.18
541 585 0.105039 AGGGAGCGTGCATTAGCTAC 59.895 55.000 13.56 13.56 44.69 3.58
544 588 1.801178 GATTAGGGAGCGTGCATTAGC 59.199 52.381 0.00 0.00 42.57 3.09
547 591 0.464036 TCGATTAGGGAGCGTGCATT 59.536 50.000 0.00 0.00 38.54 3.56
549 593 1.437573 CTCGATTAGGGAGCGTGCA 59.562 57.895 0.00 0.00 38.54 4.57
550 594 1.951631 GCTCGATTAGGGAGCGTGC 60.952 63.158 0.00 0.00 46.38 5.34
551 595 4.327885 GCTCGATTAGGGAGCGTG 57.672 61.111 0.00 0.00 46.38 5.34
556 600 1.683917 GCTCTTGAGCTCGATTAGGGA 59.316 52.381 14.65 0.00 0.00 4.20
558 602 1.410517 TGGCTCTTGAGCTCGATTAGG 59.589 52.381 20.12 0.00 34.73 2.69
559 603 2.879002 TGGCTCTTGAGCTCGATTAG 57.121 50.000 20.12 8.95 34.73 1.73
560 604 2.432146 ACATGGCTCTTGAGCTCGATTA 59.568 45.455 20.12 0.00 34.73 1.75
561 605 1.209019 ACATGGCTCTTGAGCTCGATT 59.791 47.619 20.12 1.55 34.73 3.34
562 606 0.829333 ACATGGCTCTTGAGCTCGAT 59.171 50.000 20.12 8.90 34.73 3.59
563 607 0.174389 GACATGGCTCTTGAGCTCGA 59.826 55.000 20.12 6.32 34.73 4.04
564 608 0.108472 TGACATGGCTCTTGAGCTCG 60.108 55.000 20.12 12.06 34.73 5.03
566 610 0.982704 AGTGACATGGCTCTTGAGCT 59.017 50.000 20.12 2.47 34.73 4.09
567 611 1.338484 TGAGTGACATGGCTCTTGAGC 60.338 52.381 13.69 13.69 33.22 4.26
568 612 2.344950 GTGAGTGACATGGCTCTTGAG 58.655 52.381 4.29 0.00 33.22 3.02
569 613 1.337167 CGTGAGTGACATGGCTCTTGA 60.337 52.381 4.29 0.00 33.22 3.02
570 614 1.073964 CGTGAGTGACATGGCTCTTG 58.926 55.000 4.29 0.00 33.22 3.02
571 615 0.671781 GCGTGAGTGACATGGCTCTT 60.672 55.000 4.29 0.00 36.16 2.85
572 616 1.079543 GCGTGAGTGACATGGCTCT 60.080 57.895 1.91 1.91 36.16 4.09
573 617 0.671781 AAGCGTGAGTGACATGGCTC 60.672 55.000 0.00 0.00 39.15 4.70
574 618 0.952497 CAAGCGTGAGTGACATGGCT 60.952 55.000 0.00 0.00 40.82 4.75
575 619 1.499056 CAAGCGTGAGTGACATGGC 59.501 57.895 0.00 0.00 36.16 4.40
576 620 0.952497 AGCAAGCGTGAGTGACATGG 60.952 55.000 2.99 0.00 36.16 3.66
577 621 0.870393 AAGCAAGCGTGAGTGACATG 59.130 50.000 2.99 0.00 38.43 3.21
578 622 0.870393 CAAGCAAGCGTGAGTGACAT 59.130 50.000 2.99 0.00 0.00 3.06
579 623 1.159713 CCAAGCAAGCGTGAGTGACA 61.160 55.000 9.53 0.00 0.00 3.58
581 625 2.253758 GCCAAGCAAGCGTGAGTGA 61.254 57.895 9.53 0.00 0.00 3.41
583 627 2.980233 GGCCAAGCAAGCGTGAGT 60.980 61.111 9.53 0.00 0.00 3.41
584 628 2.338015 ATGGCCAAGCAAGCGTGAG 61.338 57.895 10.96 1.53 0.00 3.51
598 642 1.080569 CAACGAAACAGGGCATGGC 60.081 57.895 11.56 11.56 0.00 4.40
601 645 0.823356 AGTGCAACGAAACAGGGCAT 60.823 50.000 0.00 0.00 45.86 4.40
603 647 1.008538 CAGTGCAACGAAACAGGGC 60.009 57.895 0.00 0.00 45.86 5.19
604 648 1.008538 GCAGTGCAACGAAACAGGG 60.009 57.895 11.09 0.00 45.86 4.45
605 649 1.369209 CGCAGTGCAACGAAACAGG 60.369 57.895 16.83 0.00 45.86 4.00
606 650 0.235665 ATCGCAGTGCAACGAAACAG 59.764 50.000 16.83 0.00 45.86 3.16
608 652 0.041312 ACATCGCAGTGCAACGAAAC 60.041 50.000 16.83 0.00 45.86 2.78
609 653 0.041400 CACATCGCAGTGCAACGAAA 60.041 50.000 16.83 0.00 45.86 3.46
610 654 1.569003 CACATCGCAGTGCAACGAA 59.431 52.632 16.83 0.00 45.86 3.85
611 655 2.316867 CCACATCGCAGTGCAACGA 61.317 57.895 16.83 9.77 45.86 3.85
612 656 2.174107 CCACATCGCAGTGCAACG 59.826 61.111 16.83 4.46 45.86 4.10
614 658 1.965930 GTCCCACATCGCAGTGCAA 60.966 57.895 16.83 0.00 38.18 4.08
616 660 2.358615 TGTCCCACATCGCAGTGC 60.359 61.111 4.58 4.58 38.18 4.40
617 661 0.738762 CTCTGTCCCACATCGCAGTG 60.739 60.000 0.71 0.71 39.21 3.66
629 673 5.501156 ACCCATTTCTTTATGACTCTGTCC 58.499 41.667 0.00 0.00 0.00 4.02
640 684 5.003804 GCACTTGAGAGACCCATTTCTTTA 58.996 41.667 0.00 0.00 0.00 1.85
655 699 1.241165 TGGATTGCACAGCACTTGAG 58.759 50.000 0.00 0.00 38.71 3.02
657 701 2.129607 GTTTGGATTGCACAGCACTTG 58.870 47.619 0.00 0.00 38.71 3.16
661 705 1.804396 CGGGTTTGGATTGCACAGCA 61.804 55.000 0.00 0.00 36.47 4.41
662 706 1.080569 CGGGTTTGGATTGCACAGC 60.081 57.895 0.00 0.00 0.00 4.40
663 707 0.893270 TCCGGGTTTGGATTGCACAG 60.893 55.000 0.00 0.00 31.53 3.66
667 711 2.885113 GCTCCGGGTTTGGATTGC 59.115 61.111 0.00 0.00 37.41 3.56
670 720 2.046314 CACGCTCCGGGTTTGGAT 60.046 61.111 0.00 0.00 37.41 3.41
674 724 4.636435 CCACCACGCTCCGGGTTT 62.636 66.667 0.00 0.00 34.45 3.27
682 732 1.676006 CTTTTCACTTTCCACCACGCT 59.324 47.619 0.00 0.00 0.00 5.07
704 754 7.442656 ACCCATATTTACTTGATTACCTCTCG 58.557 38.462 0.00 0.00 0.00 4.04
711 761 9.793259 GGAATCTGACCCATATTTACTTGATTA 57.207 33.333 0.00 0.00 0.00 1.75
723 773 7.292356 TGCTTTTCTATAGGAATCTGACCCATA 59.708 37.037 0.00 0.00 33.53 2.74
743 795 5.504853 CCCTCCTCTCTATCTTTTGCTTTT 58.495 41.667 0.00 0.00 0.00 2.27
802 854 6.305693 GCTGGAGGCAATTAATTAGTACTG 57.694 41.667 5.39 0.00 41.35 2.74
854 906 1.476833 GGAATGGGGTGCGATGTATGT 60.477 52.381 0.00 0.00 0.00 2.29
900 952 3.011032 AGGTGAGGCAAGAAAATCATCCT 59.989 43.478 0.00 0.00 0.00 3.24
902 954 3.760684 ACAGGTGAGGCAAGAAAATCATC 59.239 43.478 0.00 0.00 0.00 2.92
912 964 2.829384 GGGGTCACAGGTGAGGCAA 61.829 63.158 1.66 0.00 40.75 4.52
1374 4311 2.292267 CAGAACACATAGATGGCCACC 58.708 52.381 8.16 0.00 0.00 4.61
1513 4456 2.586245 CTCGGATGAGCTGGCCAA 59.414 61.111 7.01 0.00 34.96 4.52
1572 4515 5.498393 AGCATCTGTGTCATCTTCTGAAAT 58.502 37.500 0.00 0.00 35.07 2.17
1576 4519 3.181509 GCAAGCATCTGTGTCATCTTCTG 60.182 47.826 0.00 0.00 0.00 3.02
1582 4525 0.036105 TCGGCAAGCATCTGTGTCAT 60.036 50.000 0.00 0.00 0.00 3.06
1583 4526 0.036105 ATCGGCAAGCATCTGTGTCA 60.036 50.000 0.00 0.00 0.00 3.58
1584 4527 1.939974 TATCGGCAAGCATCTGTGTC 58.060 50.000 0.00 0.00 0.00 3.67
1596 4539 1.102154 CCATTGGTTGCTTATCGGCA 58.898 50.000 0.00 0.00 40.74 5.69
1598 4541 0.029300 CGCCATTGGTTGCTTATCGG 59.971 55.000 4.26 0.00 0.00 4.18
1622 4565 1.861542 AATAAACTTGCGCGCCTGCA 61.862 50.000 30.77 6.71 44.61 4.41
1623 4566 1.154035 AATAAACTTGCGCGCCTGC 60.154 52.632 30.77 0.29 37.91 4.85
1627 4570 1.895051 ACATCAATAAACTTGCGCGC 58.105 45.000 27.26 27.26 0.00 6.86
1628 4571 2.026742 GCAACATCAATAAACTTGCGCG 59.973 45.455 0.00 0.00 0.00 6.86
1631 4574 5.120674 GGAAAGGCAACATCAATAAACTTGC 59.879 40.000 0.00 0.00 37.16 4.01
1632 4575 6.222389 TGGAAAGGCAACATCAATAAACTTG 58.778 36.000 0.00 0.00 41.41 3.16
1633 4576 6.267471 TCTGGAAAGGCAACATCAATAAACTT 59.733 34.615 0.00 0.00 41.41 2.66
1636 4579 5.774690 ACTCTGGAAAGGCAACATCAATAAA 59.225 36.000 0.00 0.00 41.41 1.40
1637 4580 5.183713 CACTCTGGAAAGGCAACATCAATAA 59.816 40.000 0.00 0.00 41.41 1.40
1692 4638 1.133823 TCCTTGCCAGTCTTGCTTGAA 60.134 47.619 0.00 0.00 0.00 2.69
1693 4639 0.473755 TCCTTGCCAGTCTTGCTTGA 59.526 50.000 0.00 0.00 0.00 3.02
1703 4649 1.131126 CAAGCGTAATGTCCTTGCCAG 59.869 52.381 0.00 0.00 30.83 4.85
1830 5098 3.129462 CAGCTGTATCGTCTTCTCCTTGA 59.871 47.826 5.25 0.00 0.00 3.02
1862 5286 1.128809 TACCCGGGCTTCAGGAACAA 61.129 55.000 24.08 0.00 0.00 2.83
1916 5340 0.610687 GGCCTCAGCGCCTAATATCT 59.389 55.000 2.29 0.00 46.10 1.98
2055 5479 5.650266 TGCTTTTGTGTAGAGAAGACCAAAA 59.350 36.000 0.00 0.00 31.80 2.44
2117 5562 8.514330 TGCTTCCCGTATGTTATTAGAAATTT 57.486 30.769 0.00 0.00 0.00 1.82
2119 5564 7.773690 AGTTGCTTCCCGTATGTTATTAGAAAT 59.226 33.333 0.00 0.00 0.00 2.17
2128 5573 4.216411 ACATAGTTGCTTCCCGTATGTT 57.784 40.909 0.00 0.00 31.70 2.71
2638 6101 3.194062 CACCGTTTTGGAAAAAGCACAT 58.806 40.909 0.00 0.00 42.00 3.21
2754 6217 1.741401 CAGATTTCGCCTCGTGCCA 60.741 57.895 0.00 0.00 36.24 4.92
3425 6907 2.657143 ACAAAAGCTTCCACGGGTAAA 58.343 42.857 0.00 0.00 0.00 2.01
3459 6941 5.741982 GCAAAACTACACTGGTAAACAACAG 59.258 40.000 0.00 0.00 40.48 3.16
3647 7135 2.024941 AGCTTGTAGGATTTCTTGGGGG 60.025 50.000 0.00 0.00 0.00 5.40
3694 7182 4.485163 TGTCTCCATGCATAATCGATACG 58.515 43.478 0.00 0.00 0.00 3.06
3715 7203 9.122613 CATACGAGTAATACAGACATGAGATTG 57.877 37.037 0.00 0.00 0.00 2.67
3862 7370 7.201504 GGAGCATTCATATTACAGACATGATCG 60.202 40.741 0.00 0.00 0.00 3.69
3881 7389 3.759581 ACAGAGTTCAACATGGAGCATT 58.240 40.909 0.00 0.00 0.00 3.56
3943 7451 2.695359 TCAACAGGGTAAGCGATTGTC 58.305 47.619 0.00 0.00 0.00 3.18
4043 7610 5.295292 CAGCTGTAATCTGGTAAATCACAGG 59.705 44.000 5.25 0.00 35.47 4.00
4073 7718 9.315363 AGAGATATGATTATTTCCTTACTCGGT 57.685 33.333 0.00 0.00 0.00 4.69
4076 7721 9.935241 TGCAGAGATATGATTATTTCCTTACTC 57.065 33.333 0.00 0.00 0.00 2.59
4147 7794 2.029380 TCAGTAAGCTCTGCGCAAAGTA 60.029 45.455 13.16 0.00 42.61 2.24
4238 7888 2.668457 AGAGTAACAAAAGCGCGAGATG 59.332 45.455 12.10 5.05 0.00 2.90
4305 7955 1.000506 CAACAAGAGCTGCTGCCAATT 59.999 47.619 7.01 1.94 40.80 2.32
4379 8029 6.516194 GCTCAGGTACAAGTAGTCAAGTACAA 60.516 42.308 0.00 0.00 38.78 2.41
4393 8043 3.762407 TTGTTGCTAGCTCAGGTACAA 57.238 42.857 17.23 12.64 0.00 2.41
4400 8050 5.005740 ACATTTCAGATTGTTGCTAGCTCA 58.994 37.500 17.23 12.28 0.00 4.26
4476 8126 1.068127 GAGAGCGCTAATAAACCCGGA 59.932 52.381 11.50 0.00 0.00 5.14
4574 8240 8.612619 GCTATACCAAATATACCATCGGATTTG 58.387 37.037 0.00 0.00 38.46 2.32
4629 8295 6.349944 GCAATCCTATCAAATGCTCCATTAGG 60.350 42.308 0.00 0.00 32.43 2.69
4630 8296 6.618811 GCAATCCTATCAAATGCTCCATTAG 58.381 40.000 0.00 0.00 32.43 1.73
4631 8297 5.181811 CGCAATCCTATCAAATGCTCCATTA 59.818 40.000 0.00 0.00 32.43 1.90
4635 8301 2.880890 ACGCAATCCTATCAAATGCTCC 59.119 45.455 0.00 0.00 34.93 4.70
4636 8302 4.035558 TGAACGCAATCCTATCAAATGCTC 59.964 41.667 0.00 0.00 34.93 4.26
4637 8303 3.947196 TGAACGCAATCCTATCAAATGCT 59.053 39.130 0.00 0.00 34.93 3.79
4638 8304 4.285292 CTGAACGCAATCCTATCAAATGC 58.715 43.478 0.00 0.00 0.00 3.56
4640 8306 4.526970 ACCTGAACGCAATCCTATCAAAT 58.473 39.130 0.00 0.00 0.00 2.32
4641 8307 3.950397 ACCTGAACGCAATCCTATCAAA 58.050 40.909 0.00 0.00 0.00 2.69
4642 8308 3.627395 ACCTGAACGCAATCCTATCAA 57.373 42.857 0.00 0.00 0.00 2.57
4643 8309 3.627395 AACCTGAACGCAATCCTATCA 57.373 42.857 0.00 0.00 0.00 2.15
4644 8310 4.965119 AAAACCTGAACGCAATCCTATC 57.035 40.909 0.00 0.00 0.00 2.08


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

AutoCloner maintained by Alex Coulton.