Multiple sequence alignment - TraesCS5B01G553700

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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 TraesCS5B01G553700 chr5B 100.000 3384 0 0 1 3384 703643542 703646925 0.000000e+00 6250.0
1 TraesCS5B01G553700 chr5B 91.977 2256 131 15 884 3117 699556681 699558908 0.000000e+00 3118.0
2 TraesCS5B01G553700 chr5B 95.793 618 23 2 1 618 699439108 699439722 0.000000e+00 994.0
3 TraesCS5B01G553700 chr5B 76.168 1691 301 65 1006 2625 699597111 699598770 0.000000e+00 797.0
4 TraesCS5B01G553700 chr5B 76.533 1598 284 54 1006 2544 703716211 703717776 0.000000e+00 789.0
5 TraesCS5B01G553700 chr5B 76.102 1611 290 58 1006 2550 700006995 700008576 0.000000e+00 754.0
6 TraesCS5B01G553700 chr5B 77.471 435 89 8 1710 2141 699950700 699951128 5.610000e-63 252.0
7 TraesCS5B01G553700 chr5B 90.058 171 11 5 654 820 699556206 699556374 2.040000e-52 217.0
8 TraesCS5B01G553700 chr5B 85.246 183 24 2 992 1174 703529378 703529557 5.770000e-43 185.0
9 TraesCS5B01G553700 chr5B 86.310 168 23 0 1007 1174 699415132 699415299 2.070000e-42 183.0
10 TraesCS5B01G553700 chr5B 73.234 538 109 22 977 1498 699260084 699260602 2.700000e-36 163.0
11 TraesCS5B01G553700 chr5D 90.924 1774 125 13 1081 2847 552352792 552351048 0.000000e+00 2351.0
12 TraesCS5B01G553700 chr5D 76.803 1276 218 52 1310 2533 543536474 543535225 0.000000e+00 645.0
13 TraesCS5B01G553700 chr5D 91.054 313 28 0 2844 3156 509441250 509440938 1.120000e-114 424.0
14 TraesCS5B01G553700 chr5D 90.062 322 29 2 2844 3163 488189487 488189807 6.760000e-112 414.0
15 TraesCS5B01G553700 chr5D 89.297 327 33 2 2838 3163 276551012 276551337 3.140000e-110 409.0
16 TraesCS5B01G553700 chr5D 91.593 226 15 2 3162 3384 552351029 552350805 3.280000e-80 309.0
17 TraesCS5B01G553700 chr5D 76.134 507 87 24 1006 1498 552422771 552422285 5.650000e-58 235.0
18 TraesCS5B01G553700 chr5D 86.310 168 23 0 1007 1174 551119877 551120044 2.070000e-42 183.0
19 TraesCS5B01G553700 chr5D 78.598 271 53 4 1006 1272 552051619 552051350 1.250000e-39 174.0
20 TraesCS5B01G553700 chr5D 88.596 114 11 2 12 124 552389301 552389189 1.640000e-28 137.0
21 TraesCS5B01G553700 chr1B 74.572 1868 336 86 1023 2792 115749021 115750847 0.000000e+00 689.0
22 TraesCS5B01G553700 chr1B 79.592 441 67 20 1705 2129 39517012 39516579 9.180000e-76 294.0
23 TraesCS5B01G553700 chr6D 90.683 322 28 1 2844 3163 116858599 116858278 8.680000e-116 427.0
24 TraesCS5B01G553700 chr6D 90.343 321 28 3 2844 3163 47179135 47178817 5.220000e-113 418.0
25 TraesCS5B01G553700 chr1A 90.683 322 26 3 2844 3163 589613698 589613379 3.120000e-115 425.0
26 TraesCS5B01G553700 chr1A 79.953 429 72 10 1705 2129 24151607 24151189 1.530000e-78 303.0
27 TraesCS5B01G553700 chr1A 95.455 44 0 2 785 828 587864826 587864867 6.060000e-08 69.4
28 TraesCS5B01G553700 chr1D 90.123 324 30 1 2844 3165 194182622 194182945 1.450000e-113 420.0
29 TraesCS5B01G553700 chr3D 89.783 323 30 2 2844 3164 27679647 27679326 8.740000e-111 411.0
30 TraesCS5B01G553700 chr4A 74.903 518 108 16 1006 1506 616238362 616237850 2.040000e-52 217.0
31 TraesCS5B01G553700 chr7B 75.385 390 71 15 1595 1974 1252179 1252553 7.510000e-37 165.0
32 TraesCS5B01G553700 chr5A 95.455 44 0 2 785 828 623328524 623328483 6.060000e-08 69.4


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 TraesCS5B01G553700 chr5B 703643542 703646925 3383 False 6250.0 6250 100.0000 1 3384 1 chr5B.!!$F8 3383
1 TraesCS5B01G553700 chr5B 699556206 699558908 2702 False 1667.5 3118 91.0175 654 3117 2 chr5B.!!$F10 2463
2 TraesCS5B01G553700 chr5B 699439108 699439722 614 False 994.0 994 95.7930 1 618 1 chr5B.!!$F3 617
3 TraesCS5B01G553700 chr5B 699597111 699598770 1659 False 797.0 797 76.1680 1006 2625 1 chr5B.!!$F4 1619
4 TraesCS5B01G553700 chr5B 703716211 703717776 1565 False 789.0 789 76.5330 1006 2544 1 chr5B.!!$F9 1538
5 TraesCS5B01G553700 chr5B 700006995 700008576 1581 False 754.0 754 76.1020 1006 2550 1 chr5B.!!$F6 1544
6 TraesCS5B01G553700 chr5D 552350805 552352792 1987 True 1330.0 2351 91.2585 1081 3384 2 chr5D.!!$R6 2303
7 TraesCS5B01G553700 chr5D 543535225 543536474 1249 True 645.0 645 76.8030 1310 2533 1 chr5D.!!$R2 1223
8 TraesCS5B01G553700 chr1B 115749021 115750847 1826 False 689.0 689 74.5720 1023 2792 1 chr1B.!!$F1 1769
9 TraesCS5B01G553700 chr4A 616237850 616238362 512 True 217.0 217 74.9030 1006 1506 1 chr4A.!!$R1 500

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
651 652 0.038166 AGCACGGGTTGATTGACCAT 59.962 50.0 0.0 0.0 41.65 3.55 F
652 653 0.171007 GCACGGGTTGATTGACCATG 59.829 55.0 0.0 0.0 41.65 3.66 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2093 2425 0.038166 TGGACTGGGGAAACTCATGC 59.962 55.000 0.0 0.0 42.56 4.06 R
2391 2764 1.949525 CCTGCCCTTCATATTCAACCG 59.050 52.381 0.0 0.0 0.00 4.44 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
25 26 6.367422 GCATATACTAGAAGACTGCAATGACC 59.633 42.308 0.00 0.00 0.00 4.02
83 84 6.016024 TCAGAGTGATAATTGCAACTGCTTTT 60.016 34.615 0.00 0.00 42.66 2.27
94 95 4.337836 TGCAACTGCTTTTACATTCACAGA 59.662 37.500 2.95 0.00 42.66 3.41
101 102 7.014615 ACTGCTTTTACATTCACAGATTTTCCT 59.985 33.333 0.00 0.00 0.00 3.36
146 147 0.804364 TGAGCACGCATTTTAGCCAG 59.196 50.000 0.00 0.00 0.00 4.85
147 148 0.099436 GAGCACGCATTTTAGCCAGG 59.901 55.000 0.00 0.00 0.00 4.45
178 179 3.390175 TTTTCCCTCACTTTGGTCCAA 57.610 42.857 0.00 0.00 0.00 3.53
192 193 2.092429 TGGTCCAATGGCTGAATACTCC 60.092 50.000 0.00 0.00 0.00 3.85
198 199 4.378774 CAATGGCTGAATACTCCTCTGAG 58.621 47.826 0.00 0.00 44.62 3.35
248 249 3.214328 TCCAGACTTGCTGTTTTCTTCC 58.786 45.455 0.00 0.00 43.33 3.46
264 265 3.822192 CCGCCCACGAGATGACGA 61.822 66.667 0.00 0.00 43.93 4.20
265 266 2.413351 CGCCCACGAGATGACGAT 59.587 61.111 0.00 0.00 43.93 3.73
315 316 7.504924 ACAAATCTGAAATTAACCTCGTGAA 57.495 32.000 0.00 0.00 0.00 3.18
344 345 3.589988 ACTACTACATGTCAAGTGCTGC 58.410 45.455 0.00 0.00 0.00 5.25
351 352 0.758734 TGTCAAGTGCTGCTGGTACT 59.241 50.000 0.00 0.00 42.55 2.73
415 416 2.284190 GTGGAAGAGGTATTGCTCTGC 58.716 52.381 0.00 0.00 0.00 4.26
417 418 2.573462 TGGAAGAGGTATTGCTCTGCTT 59.427 45.455 0.00 0.00 0.00 3.91
418 419 2.941720 GGAAGAGGTATTGCTCTGCTTG 59.058 50.000 0.00 0.00 0.00 4.01
419 420 2.706339 AGAGGTATTGCTCTGCTTGG 57.294 50.000 0.00 0.00 0.00 3.61
548 549 5.954150 ACTTGCCTGTCCATCTTTCATATTT 59.046 36.000 0.00 0.00 0.00 1.40
612 613 9.613428 TTACTAGTCCATATTGTTGGAGATTTG 57.387 33.333 0.00 0.00 46.31 2.32
618 619 7.872483 GTCCATATTGTTGGAGATTTGTTTTGT 59.128 33.333 0.00 0.00 46.31 2.83
619 620 8.428063 TCCATATTGTTGGAGATTTGTTTTGTT 58.572 29.630 0.00 0.00 40.90 2.83
620 621 9.703892 CCATATTGTTGGAGATTTGTTTTGTTA 57.296 29.630 0.00 0.00 39.25 2.41
625 626 8.755696 TGTTGGAGATTTGTTTTGTTATATGC 57.244 30.769 0.00 0.00 0.00 3.14
626 627 8.584157 TGTTGGAGATTTGTTTTGTTATATGCT 58.416 29.630 0.00 0.00 0.00 3.79
627 628 8.863049 GTTGGAGATTTGTTTTGTTATATGCTG 58.137 33.333 0.00 0.00 0.00 4.41
628 629 7.546358 TGGAGATTTGTTTTGTTATATGCTGG 58.454 34.615 0.00 0.00 0.00 4.85
629 630 6.476706 GGAGATTTGTTTTGTTATATGCTGGC 59.523 38.462 0.00 0.00 0.00 4.85
630 631 7.174107 AGATTTGTTTTGTTATATGCTGGCT 57.826 32.000 0.00 0.00 0.00 4.75
631 632 7.037438 AGATTTGTTTTGTTATATGCTGGCTG 58.963 34.615 0.00 0.00 0.00 4.85
632 633 5.973899 TTGTTTTGTTATATGCTGGCTGA 57.026 34.783 0.00 0.00 0.00 4.26
633 634 5.565592 TGTTTTGTTATATGCTGGCTGAG 57.434 39.130 0.00 0.00 0.00 3.35
642 643 3.052082 CTGGCTGAGCACGGGTTG 61.052 66.667 6.82 0.00 0.00 3.77
643 644 3.535629 CTGGCTGAGCACGGGTTGA 62.536 63.158 6.82 0.00 0.00 3.18
644 645 2.045926 GGCTGAGCACGGGTTGAT 60.046 61.111 6.82 0.00 0.00 2.57
645 646 1.675641 GGCTGAGCACGGGTTGATT 60.676 57.895 6.82 0.00 0.00 2.57
646 647 1.503542 GCTGAGCACGGGTTGATTG 59.496 57.895 0.00 0.00 0.00 2.67
647 648 0.955428 GCTGAGCACGGGTTGATTGA 60.955 55.000 0.00 0.00 0.00 2.57
648 649 0.798776 CTGAGCACGGGTTGATTGAC 59.201 55.000 0.00 0.00 0.00 3.18
649 650 0.605319 TGAGCACGGGTTGATTGACC 60.605 55.000 0.00 0.00 39.04 4.02
650 651 0.605319 GAGCACGGGTTGATTGACCA 60.605 55.000 0.00 0.00 41.65 4.02
651 652 0.038166 AGCACGGGTTGATTGACCAT 59.962 50.000 0.00 0.00 41.65 3.55
652 653 0.171007 GCACGGGTTGATTGACCATG 59.829 55.000 0.00 0.00 41.65 3.66
667 668 0.752054 CCATGTGGTTGTGCTTGGTT 59.248 50.000 0.00 0.00 0.00 3.67
699 700 6.619874 GCTGTTTTCGGATTTCATCGTTAAGA 60.620 38.462 0.00 0.00 0.00 2.10
705 706 7.843490 TCGGATTTCATCGTTAAGAATTCTT 57.157 32.000 23.53 23.53 39.85 2.52
715 716 7.303634 TCGTTAAGAATTCTTGACTATTGCC 57.696 36.000 29.60 11.22 39.45 4.52
719 720 4.530875 AGAATTCTTGACTATTGCCTGGG 58.469 43.478 0.88 0.00 0.00 4.45
722 723 4.380843 TTCTTGACTATTGCCTGGGAAA 57.619 40.909 4.27 0.00 0.00 3.13
724 725 4.934356 TCTTGACTATTGCCTGGGAAATT 58.066 39.130 4.27 0.00 0.00 1.82
725 726 4.949856 TCTTGACTATTGCCTGGGAAATTC 59.050 41.667 4.27 2.52 0.00 2.17
753 756 5.232463 TGGACTTAAACACGACATAACCTC 58.768 41.667 0.00 0.00 0.00 3.85
755 758 5.476614 GACTTAAACACGACATAACCTCCT 58.523 41.667 0.00 0.00 0.00 3.69
760 763 2.163010 ACACGACATAACCTCCTGTACG 59.837 50.000 0.00 0.00 0.00 3.67
764 767 3.374988 CGACATAACCTCCTGTACGTGTA 59.625 47.826 0.00 0.00 0.00 2.90
782 785 7.823149 ACGTGTACATATAGGTTTCTTGTTC 57.177 36.000 0.00 0.00 0.00 3.18
789 792 7.709947 ACATATAGGTTTCTTGTTCATGCATG 58.290 34.615 21.07 21.07 0.00 4.06
810 814 5.372343 TGTACCGTGTAGGACTAGGATTA 57.628 43.478 0.00 0.00 45.00 1.75
816 820 5.394883 CCGTGTAGGACTAGGATTAGCAAAA 60.395 44.000 0.00 0.00 45.00 2.44
819 823 4.505324 AGGACTAGGATTAGCAAAACCC 57.495 45.455 0.00 0.00 0.00 4.11
822 826 4.120589 GACTAGGATTAGCAAAACCCGAG 58.879 47.826 0.00 0.00 0.00 4.63
823 827 3.518303 ACTAGGATTAGCAAAACCCGAGT 59.482 43.478 0.00 0.00 0.00 4.18
824 828 4.713321 ACTAGGATTAGCAAAACCCGAGTA 59.287 41.667 0.00 0.00 28.26 2.59
825 829 4.138487 AGGATTAGCAAAACCCGAGTAG 57.862 45.455 0.00 0.00 0.00 2.57
827 831 4.713321 AGGATTAGCAAAACCCGAGTAGTA 59.287 41.667 0.00 0.00 0.00 1.82
828 832 4.807834 GGATTAGCAAAACCCGAGTAGTAC 59.192 45.833 0.00 0.00 0.00 2.73
829 833 5.394993 GGATTAGCAAAACCCGAGTAGTACT 60.395 44.000 1.37 1.37 0.00 2.73
830 834 6.183360 GGATTAGCAAAACCCGAGTAGTACTA 60.183 42.308 1.88 0.00 0.00 1.82
831 835 6.780457 TTAGCAAAACCCGAGTAGTACTAT 57.220 37.500 5.75 0.00 0.00 2.12
832 836 7.880160 TTAGCAAAACCCGAGTAGTACTATA 57.120 36.000 5.75 0.00 0.00 1.31
833 837 6.973460 AGCAAAACCCGAGTAGTACTATAT 57.027 37.500 5.75 0.00 0.00 0.86
834 838 9.573166 TTAGCAAAACCCGAGTAGTACTATATA 57.427 33.333 5.75 0.00 0.00 0.86
835 839 8.647256 AGCAAAACCCGAGTAGTACTATATAT 57.353 34.615 5.75 0.00 0.00 0.86
836 840 9.745018 AGCAAAACCCGAGTAGTACTATATATA 57.255 33.333 5.75 0.00 0.00 0.86
855 914 2.148916 ATATGCGTGTACCATCGTGG 57.851 50.000 2.92 2.92 45.02 4.94
858 917 1.375013 GCGTGTACCATCGTGGGTT 60.375 57.895 6.10 0.00 43.37 4.11
859 918 0.952010 GCGTGTACCATCGTGGGTTT 60.952 55.000 6.10 0.00 43.37 3.27
865 924 1.604604 ACCATCGTGGGTTTGTGAAG 58.395 50.000 8.57 0.00 43.37 3.02
867 926 2.105134 ACCATCGTGGGTTTGTGAAGTA 59.895 45.455 8.57 0.00 43.37 2.24
868 927 3.142951 CCATCGTGGGTTTGTGAAGTAA 58.857 45.455 0.00 0.00 32.67 2.24
872 931 6.094881 CCATCGTGGGTTTGTGAAGTAATAAT 59.905 38.462 0.00 0.00 32.67 1.28
873 932 7.281324 CCATCGTGGGTTTGTGAAGTAATAATA 59.719 37.037 0.00 0.00 32.67 0.98
874 933 8.670135 CATCGTGGGTTTGTGAAGTAATAATAA 58.330 33.333 0.00 0.00 0.00 1.40
875 934 8.795842 TCGTGGGTTTGTGAAGTAATAATAAT 57.204 30.769 0.00 0.00 0.00 1.28
876 935 9.887629 TCGTGGGTTTGTGAAGTAATAATAATA 57.112 29.630 0.00 0.00 0.00 0.98
936 1182 0.675837 TCAATCAGCAGGTGCAGCTC 60.676 55.000 17.16 11.10 45.16 4.09
941 1187 3.191539 GCAGGTGCAGCTCGCTAC 61.192 66.667 23.89 7.94 43.06 3.58
988 1251 2.034179 CCAAAACCAAAACCCTCGTCTC 59.966 50.000 0.00 0.00 0.00 3.36
1017 1280 0.608308 CCATGATGCTGCCCGATGAT 60.608 55.000 0.00 0.00 0.00 2.45
1020 1283 0.471191 TGATGCTGCCCGATGATCTT 59.529 50.000 0.00 0.00 0.00 2.40
1409 1708 1.436600 CTGACGAAGATGCAAGCACT 58.563 50.000 0.00 0.00 0.00 4.40
1548 1871 9.269108 CATGGTGCTCATTGTGTTATACACCTC 62.269 44.444 9.93 0.00 45.18 3.85
1598 1921 3.790437 CGAGCCCCAGACATGCCT 61.790 66.667 0.00 0.00 0.00 4.75
1721 2050 6.036083 CACATAACAGGATTTCTGAAGTACGG 59.964 42.308 0.00 0.00 46.18 4.02
1793 2125 6.150140 GGATCTCTCATTATTGGTGCCAATAC 59.850 42.308 19.83 8.03 45.23 1.89
2093 2425 2.947852 TGTTTGGTGTTTGTTTCCGTG 58.052 42.857 0.00 0.00 0.00 4.94
2288 2660 8.611757 GCAAACTTTCAAATGTTCACCTAATTT 58.388 29.630 0.00 0.00 0.00 1.82
2294 2667 7.887996 TCAAATGTTCACCTAATTTGCAATC 57.112 32.000 0.00 0.00 39.85 2.67
2432 2808 3.084039 GAGGCCATTGTCATCAAACAGA 58.916 45.455 5.01 0.00 37.11 3.41
2473 2857 3.624861 GCGAGATGGTCTTGTGATGAATT 59.375 43.478 0.00 0.00 30.44 2.17
2647 3054 6.255453 TGCTCTGTTGTTTAATTTGCTTGAAC 59.745 34.615 0.00 0.00 34.72 3.18
2655 3063 2.719426 ATTTGCTTGAACTGCAGCTC 57.281 45.000 15.27 12.53 41.71 4.09
2717 3130 0.534203 TGTCGTCCAAGCTTTGACCC 60.534 55.000 21.38 14.08 0.00 4.46
2731 3152 6.116126 AGCTTTGACCCAACTCTATATTCAC 58.884 40.000 0.00 0.00 0.00 3.18
2737 3158 4.656112 ACCCAACTCTATATTCACCTCCAG 59.344 45.833 0.00 0.00 0.00 3.86
2771 3192 1.271543 TGTTGAGCAGATGTTCAGGGG 60.272 52.381 0.00 0.00 36.65 4.79
2893 3314 0.179056 CGGTGTTCACTGGGAGTGTT 60.179 55.000 3.75 0.00 46.03 3.32
2895 3316 1.141053 GGTGTTCACTGGGAGTGTTCT 59.859 52.381 3.75 0.00 46.03 3.01
2900 3321 2.526432 TCACTGGGAGTGTTCTAGACC 58.474 52.381 3.75 0.00 46.03 3.85
2901 3322 2.158370 TCACTGGGAGTGTTCTAGACCA 60.158 50.000 3.75 0.00 46.03 4.02
2916 3337 0.112412 GACCAGTGTGGGACCCAATT 59.888 55.000 16.98 0.08 43.37 2.32
2917 3338 0.560688 ACCAGTGTGGGACCCAATTT 59.439 50.000 16.98 0.00 43.37 1.82
2925 3346 4.881850 GTGTGGGACCCAATTTAGATAGTG 59.118 45.833 16.98 0.00 34.18 2.74
2930 3351 4.141482 GGACCCAATTTAGATAGTGGCTCA 60.141 45.833 0.00 0.00 0.00 4.26
2931 3352 5.437060 GACCCAATTTAGATAGTGGCTCAA 58.563 41.667 0.00 0.00 0.00 3.02
2975 3396 0.613260 AGGCTTTGGTGCGATGTCTA 59.387 50.000 0.00 0.00 0.00 2.59
2980 3401 3.126858 GCTTTGGTGCGATGTCTATTTGA 59.873 43.478 0.00 0.00 0.00 2.69
2989 3410 5.874810 TGCGATGTCTATTTGATATTAGGCC 59.125 40.000 0.00 0.00 0.00 5.19
3034 3455 5.023452 TCAAGGAGATAGGAGTAGCAACAA 58.977 41.667 0.00 0.00 0.00 2.83
3036 3457 4.353777 AGGAGATAGGAGTAGCAACAACA 58.646 43.478 0.00 0.00 0.00 3.33
3039 3460 5.525378 GGAGATAGGAGTAGCAACAACATTG 59.475 44.000 0.00 0.00 0.00 2.82
3051 3472 1.001181 ACAACATTGCCAAGATGGTGC 59.999 47.619 2.28 0.00 44.19 5.01
3121 3542 7.671495 TTAATAATATGACTGCATGCATCGT 57.329 32.000 22.97 21.61 35.94 3.73
3122 3543 5.791367 ATAATATGACTGCATGCATCGTC 57.209 39.130 25.45 25.45 35.94 4.20
3123 3544 1.869774 TATGACTGCATGCATCGTCC 58.130 50.000 27.70 15.64 35.94 4.79
3124 3545 0.107557 ATGACTGCATGCATCGTCCA 60.108 50.000 27.70 19.32 32.31 4.02
3125 3546 0.741927 TGACTGCATGCATCGTCCAG 60.742 55.000 27.70 15.95 0.00 3.86
3126 3547 0.460811 GACTGCATGCATCGTCCAGA 60.461 55.000 22.97 0.00 0.00 3.86
3127 3548 0.179702 ACTGCATGCATCGTCCAGAT 59.820 50.000 22.97 0.00 41.01 2.90
3137 3558 0.665298 TCGTCCAGATGCAGAGATCG 59.335 55.000 0.00 0.00 0.00 3.69
3138 3559 0.318529 CGTCCAGATGCAGAGATCGG 60.319 60.000 0.00 0.00 0.00 4.18
3139 3560 0.033228 GTCCAGATGCAGAGATCGGG 59.967 60.000 0.00 0.00 38.63 5.14
3140 3561 1.117749 TCCAGATGCAGAGATCGGGG 61.118 60.000 4.66 0.00 38.03 5.73
3141 3562 1.301558 CAGATGCAGAGATCGGGGC 60.302 63.158 0.00 0.00 0.00 5.80
3142 3563 1.459158 AGATGCAGAGATCGGGGCT 60.459 57.895 0.00 0.00 0.00 5.19
3143 3564 0.178950 AGATGCAGAGATCGGGGCTA 60.179 55.000 0.00 0.00 0.00 3.93
3144 3565 0.037790 GATGCAGAGATCGGGGCTAC 60.038 60.000 0.00 0.00 0.00 3.58
3145 3566 0.760567 ATGCAGAGATCGGGGCTACA 60.761 55.000 0.00 0.00 0.00 2.74
3146 3567 0.760567 TGCAGAGATCGGGGCTACAT 60.761 55.000 6.99 0.00 0.00 2.29
3147 3568 0.037790 GCAGAGATCGGGGCTACATC 60.038 60.000 0.00 0.00 0.00 3.06
3148 3569 0.605589 CAGAGATCGGGGCTACATCC 59.394 60.000 0.00 0.00 0.00 3.51
3149 3570 0.485099 AGAGATCGGGGCTACATCCT 59.515 55.000 0.00 0.00 0.00 3.24
3150 3571 0.892063 GAGATCGGGGCTACATCCTC 59.108 60.000 0.00 0.00 0.00 3.71
3151 3572 0.543174 AGATCGGGGCTACATCCTCC 60.543 60.000 0.00 0.00 0.00 4.30
3152 3573 0.543174 GATCGGGGCTACATCCTCCT 60.543 60.000 0.00 0.00 0.00 3.69
3153 3574 0.104934 ATCGGGGCTACATCCTCCTT 60.105 55.000 0.00 0.00 0.00 3.36
3154 3575 0.326238 TCGGGGCTACATCCTCCTTT 60.326 55.000 0.00 0.00 0.00 3.11
3155 3576 0.546598 CGGGGCTACATCCTCCTTTT 59.453 55.000 0.00 0.00 0.00 2.27
3156 3577 1.766496 CGGGGCTACATCCTCCTTTTA 59.234 52.381 0.00 0.00 0.00 1.52
3157 3578 2.171870 CGGGGCTACATCCTCCTTTTAA 59.828 50.000 0.00 0.00 0.00 1.52
3158 3579 3.371166 CGGGGCTACATCCTCCTTTTAAA 60.371 47.826 0.00 0.00 0.00 1.52
3159 3580 4.606210 GGGGCTACATCCTCCTTTTAAAA 58.394 43.478 0.00 0.00 0.00 1.52
3160 3581 5.020795 GGGGCTACATCCTCCTTTTAAAAA 58.979 41.667 1.66 0.00 0.00 1.94
3191 3612 3.105187 TGCCTTGCATCCATAGCAG 57.895 52.632 0.00 0.00 43.75 4.24
3268 3692 7.956315 AGCTCAATTATAATCCACTAGGTAGGA 59.044 37.037 0.00 3.69 38.50 2.94
3276 3700 5.878406 ATCCACTAGGTAGGAATTCACAG 57.122 43.478 7.93 0.00 37.48 3.66
3279 3703 2.772515 ACTAGGTAGGAATTCACAGCCC 59.227 50.000 7.93 0.00 0.00 5.19
3280 3704 0.541863 AGGTAGGAATTCACAGCCCG 59.458 55.000 7.93 0.00 0.00 6.13
3298 3722 1.546961 CGGGGAGAGACTACTTGTGT 58.453 55.000 0.00 0.00 0.00 3.72
3299 3723 1.893801 CGGGGAGAGACTACTTGTGTT 59.106 52.381 0.00 0.00 0.00 3.32
3316 3740 6.655848 ACTTGTGTTTCACTGTTAAGTTGGTA 59.344 34.615 1.72 0.00 32.98 3.25
3322 3746 5.217978 TCACTGTTAAGTTGGTATTCGGT 57.782 39.130 0.00 0.00 32.98 4.69
3335 3759 6.392625 TGGTATTCGGTTTGTCATTTTTCA 57.607 33.333 0.00 0.00 0.00 2.69
3338 3762 6.581166 GGTATTCGGTTTGTCATTTTTCACTC 59.419 38.462 0.00 0.00 0.00 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
23 24 3.764434 ACATCTTCGTCTCACTACATGGT 59.236 43.478 0.00 0.00 0.00 3.55
25 26 5.402398 TGAACATCTTCGTCTCACTACATG 58.598 41.667 0.00 0.00 0.00 3.21
130 131 0.525761 TTCCTGGCTAAAATGCGTGC 59.474 50.000 0.00 0.00 0.00 5.34
146 147 5.070685 AGTGAGGGAAAATTGTACAGTTCC 58.929 41.667 19.45 19.45 39.08 3.62
147 148 6.635030 AAGTGAGGGAAAATTGTACAGTTC 57.365 37.500 3.87 5.88 0.00 3.01
178 179 3.896888 CTCTCAGAGGAGTATTCAGCCAT 59.103 47.826 0.00 0.00 42.05 4.40
192 193 2.943690 CCATTTGCACCATCTCTCAGAG 59.056 50.000 0.00 0.00 0.00 3.35
198 199 3.018856 TCATCACCATTTGCACCATCTC 58.981 45.455 0.00 0.00 0.00 2.75
248 249 0.241213 ATATCGTCATCTCGTGGGCG 59.759 55.000 0.00 0.00 39.92 6.13
264 265 4.041321 TCAGCTAGCATTCAGAAGCCATAT 59.959 41.667 18.83 0.00 35.54 1.78
265 266 3.389002 TCAGCTAGCATTCAGAAGCCATA 59.611 43.478 18.83 0.00 35.54 2.74
315 316 7.495934 GCACTTGACATGTAGTAGTATTTCCAT 59.504 37.037 0.00 0.00 0.00 3.41
415 416 4.274459 GTGAATTAGCTATCAGGCACCAAG 59.726 45.833 0.00 0.00 34.17 3.61
417 418 3.433598 GGTGAATTAGCTATCAGGCACCA 60.434 47.826 18.81 0.00 42.96 4.17
418 419 3.142174 GGTGAATTAGCTATCAGGCACC 58.858 50.000 12.78 12.78 37.91 5.01
419 420 4.078639 AGGTGAATTAGCTATCAGGCAC 57.921 45.455 0.00 0.00 34.81 5.01
501 502 5.123820 GTCATGTAAATCCAAGCTAGTTGCA 59.876 40.000 0.00 0.00 45.94 4.08
503 504 6.992063 AGTCATGTAAATCCAAGCTAGTTG 57.008 37.500 0.00 0.00 35.71 3.16
583 584 8.783660 TCTCCAACAATATGGACTAGTAAGAT 57.216 34.615 0.00 0.00 44.52 2.40
602 603 8.034215 CCAGCATATAACAAAACAAATCTCCAA 58.966 33.333 0.00 0.00 0.00 3.53
625 626 2.809861 ATCAACCCGTGCTCAGCCAG 62.810 60.000 0.00 0.00 0.00 4.85
626 627 2.410322 AATCAACCCGTGCTCAGCCA 62.410 55.000 0.00 0.00 0.00 4.75
627 628 1.675641 AATCAACCCGTGCTCAGCC 60.676 57.895 0.00 0.00 0.00 4.85
628 629 0.955428 TCAATCAACCCGTGCTCAGC 60.955 55.000 0.00 0.00 0.00 4.26
629 630 0.798776 GTCAATCAACCCGTGCTCAG 59.201 55.000 0.00 0.00 0.00 3.35
630 631 0.605319 GGTCAATCAACCCGTGCTCA 60.605 55.000 0.00 0.00 32.82 4.26
631 632 0.605319 TGGTCAATCAACCCGTGCTC 60.605 55.000 0.00 0.00 38.65 4.26
632 633 0.038166 ATGGTCAATCAACCCGTGCT 59.962 50.000 0.00 0.00 38.65 4.40
633 634 0.171007 CATGGTCAATCAACCCGTGC 59.829 55.000 0.00 0.00 38.65 5.34
634 635 1.199789 CACATGGTCAATCAACCCGTG 59.800 52.381 0.00 0.00 38.65 4.94
635 636 1.533625 CACATGGTCAATCAACCCGT 58.466 50.000 0.00 0.00 38.65 5.28
636 637 0.810648 CCACATGGTCAATCAACCCG 59.189 55.000 0.00 0.00 38.65 5.28
648 649 0.752054 AACCAAGCACAACCACATGG 59.248 50.000 0.00 0.00 42.17 3.66
649 650 2.203401 CAAACCAAGCACAACCACATG 58.797 47.619 0.00 0.00 0.00 3.21
650 651 1.830477 ACAAACCAAGCACAACCACAT 59.170 42.857 0.00 0.00 0.00 3.21
651 652 1.067283 CACAAACCAAGCACAACCACA 60.067 47.619 0.00 0.00 0.00 4.17
652 653 1.203523 TCACAAACCAAGCACAACCAC 59.796 47.619 0.00 0.00 0.00 4.16
667 668 4.037327 TGAAATCCGAAAACAGCATCACAA 59.963 37.500 0.00 0.00 0.00 3.33
699 700 4.591321 TCCCAGGCAATAGTCAAGAATT 57.409 40.909 0.00 0.00 0.00 2.17
705 706 4.591321 AGAATTTCCCAGGCAATAGTCA 57.409 40.909 0.00 0.00 0.00 3.41
715 716 6.648879 TTAAGTCCAACAAGAATTTCCCAG 57.351 37.500 0.00 0.00 0.00 4.45
719 720 7.165318 GTCGTGTTTAAGTCCAACAAGAATTTC 59.835 37.037 3.50 0.00 42.02 2.17
722 723 5.587043 TGTCGTGTTTAAGTCCAACAAGAAT 59.413 36.000 3.50 0.00 42.02 2.40
724 725 4.505808 TGTCGTGTTTAAGTCCAACAAGA 58.494 39.130 0.00 0.00 39.40 3.02
725 726 4.868450 TGTCGTGTTTAAGTCCAACAAG 57.132 40.909 0.00 0.00 35.91 3.16
760 763 8.122952 GCATGAACAAGAAACCTATATGTACAC 58.877 37.037 0.00 0.00 0.00 2.90
764 767 7.340232 ACATGCATGAACAAGAAACCTATATGT 59.660 33.333 32.75 1.75 0.00 2.29
782 785 2.159099 AGTCCTACACGGTACATGCATG 60.159 50.000 25.09 25.09 0.00 4.06
789 792 4.215185 GCTAATCCTAGTCCTACACGGTAC 59.785 50.000 0.00 0.00 0.00 3.34
810 814 6.973460 ATATAGTACTACTCGGGTTTTGCT 57.027 37.500 4.31 0.00 0.00 3.91
816 820 9.650539 CGCATATATATATAGTACTACTCGGGT 57.349 37.037 4.31 0.00 0.00 5.28
845 904 2.105134 ACTTCACAAACCCACGATGGTA 59.895 45.455 1.17 0.00 37.76 3.25
847 906 1.604604 ACTTCACAAACCCACGATGG 58.395 50.000 0.00 0.00 37.25 3.51
848 907 6.489127 TTATTACTTCACAAACCCACGATG 57.511 37.500 0.00 0.00 0.00 3.84
849 908 8.795842 TTATTATTACTTCACAAACCCACGAT 57.204 30.769 0.00 0.00 0.00 3.73
909 1155 3.691118 GCACCTGCTGATTGATTCAACTA 59.309 43.478 0.15 0.00 38.21 2.24
910 1156 2.490903 GCACCTGCTGATTGATTCAACT 59.509 45.455 0.15 0.00 38.21 3.16
936 1182 3.610495 TGTGATTGATACGTACGTAGCG 58.390 45.455 31.25 13.51 39.57 4.26
941 1187 4.036567 TCCCTTGTGATTGATACGTACG 57.963 45.455 15.01 15.01 0.00 3.67
988 1251 2.114670 GCATCATGGTCGGTGGTGG 61.115 63.158 0.00 0.00 0.00 4.61
1140 1403 0.681243 GGGGAGCACCATGAAACTCC 60.681 60.000 15.61 15.61 46.61 3.85
1409 1708 2.951642 CTGGTTCTGCTTTGTCCTTTGA 59.048 45.455 0.00 0.00 0.00 2.69
1548 1871 1.135916 GTCTCCGACGAGAACACAGAG 60.136 57.143 0.00 0.00 46.74 3.35
1591 1914 3.087031 CAAGATCAAGACCAAGGCATGT 58.913 45.455 0.00 0.00 0.00 3.21
1598 1921 3.002791 GCATCGTCAAGATCAAGACCAA 58.997 45.455 10.74 2.26 37.52 3.67
1721 2050 3.058639 CGATAAGCAATTAGAGCCCAAGC 60.059 47.826 0.00 0.00 40.32 4.01
1793 2125 1.271934 CGTCCTCCATAGCCATGAGAG 59.728 57.143 0.00 0.00 33.67 3.20
2093 2425 0.038166 TGGACTGGGGAAACTCATGC 59.962 55.000 0.00 0.00 42.56 4.06
2175 2512 9.906660 TCTATATTTTGTTTGTTTGGCTAACTG 57.093 29.630 12.76 0.00 37.64 3.16
2210 2555 9.399403 GAACATCAAGTAAAATTTTCAGTCTCC 57.601 33.333 6.72 0.00 0.00 3.71
2386 2759 3.942748 GCCCTTCATATTCAACCGTACAA 59.057 43.478 0.00 0.00 0.00 2.41
2391 2764 1.949525 CCTGCCCTTCATATTCAACCG 59.050 52.381 0.00 0.00 0.00 4.44
2432 2808 4.279145 TCGCCTCCTAGTAGTCATCTTTT 58.721 43.478 0.00 0.00 0.00 2.27
2473 2857 9.430399 ACCAAACCAGCTACTAGATACTTTATA 57.570 33.333 0.00 0.00 0.00 0.98
2561 2949 6.387192 AATATAATCCGATCCATTCACCCA 57.613 37.500 0.00 0.00 0.00 4.51
2647 3054 6.862608 CACTAAGATATTGTCTAGAGCTGCAG 59.137 42.308 10.11 10.11 35.67 4.41
2687 3099 4.083271 AGCTTGGACGACAAATTTTAGAGC 60.083 41.667 0.00 0.00 38.91 4.09
2700 3112 0.181587 TTGGGTCAAAGCTTGGACGA 59.818 50.000 24.45 12.95 34.87 4.20
2702 3114 1.609072 GAGTTGGGTCAAAGCTTGGAC 59.391 52.381 23.65 23.65 0.00 4.02
2717 3130 6.989169 CCTTTCTGGAGGTGAATATAGAGTTG 59.011 42.308 0.00 0.00 38.35 3.16
2731 3152 1.985895 AGTTGTACCCCTTTCTGGAGG 59.014 52.381 0.00 0.00 38.35 4.30
2737 3158 2.552743 GCTCAACAGTTGTACCCCTTTC 59.447 50.000 13.14 0.00 0.00 2.62
2764 3185 4.153411 GCTAGCTCTAGTAATCCCCTGAA 58.847 47.826 7.70 0.00 35.65 3.02
2766 3187 2.490115 CGCTAGCTCTAGTAATCCCCTG 59.510 54.545 13.93 0.00 35.65 4.45
2771 3192 5.811100 ACAAAAACCGCTAGCTCTAGTAATC 59.189 40.000 13.93 0.00 35.65 1.75
2814 3235 9.474313 TGGTATTATGGAAAAGTTAATTGAGCT 57.526 29.630 0.00 0.00 0.00 4.09
2870 3291 1.227823 TCCCAGTGAACACCGCAAG 60.228 57.895 1.11 0.00 0.00 4.01
2871 3292 1.227823 CTCCCAGTGAACACCGCAA 60.228 57.895 1.11 0.00 0.00 4.85
2893 3314 0.252103 GGGTCCCACACTGGTCTAGA 60.252 60.000 1.78 0.00 35.17 2.43
2895 3316 0.104882 TTGGGTCCCACACTGGTCTA 60.105 55.000 11.24 0.00 35.17 2.59
2900 3321 3.433306 TCTAAATTGGGTCCCACACTG 57.567 47.619 11.24 0.28 30.78 3.66
2901 3322 4.788617 ACTATCTAAATTGGGTCCCACACT 59.211 41.667 11.24 0.00 30.78 3.55
2916 3337 4.473196 TGTCCCATTTGAGCCACTATCTAA 59.527 41.667 0.00 0.00 0.00 2.10
2917 3338 4.037222 TGTCCCATTTGAGCCACTATCTA 58.963 43.478 0.00 0.00 0.00 1.98
2925 3346 2.046285 CGGGTGTCCCATTTGAGCC 61.046 63.158 5.64 0.00 45.83 4.70
2930 3351 0.406361 TAAAGGCGGGTGTCCCATTT 59.594 50.000 5.64 5.53 45.83 2.32
2931 3352 0.034477 CTAAAGGCGGGTGTCCCATT 60.034 55.000 5.64 0.00 45.83 3.16
2944 3365 4.142381 GCACCAAAGCCTAACATCTAAAGG 60.142 45.833 0.00 0.00 0.00 3.11
2975 3396 4.657814 ATGTCCGGGCCTAATATCAAAT 57.342 40.909 2.12 0.00 0.00 2.32
2980 3401 1.278127 CCGAATGTCCGGGCCTAATAT 59.722 52.381 2.12 0.00 45.43 1.28
3017 3438 4.878397 GCAATGTTGTTGCTACTCCTATCT 59.122 41.667 5.57 0.00 41.87 1.98
3034 3455 0.251922 AGGCACCATCTTGGCAATGT 60.252 50.000 0.00 0.00 42.67 2.71
3036 3457 1.188863 GAAGGCACCATCTTGGCAAT 58.811 50.000 0.00 0.00 42.67 3.56
3039 3460 1.318158 CCTGAAGGCACCATCTTGGC 61.318 60.000 0.00 0.00 42.67 4.52
3109 3530 0.586802 CATCTGGACGATGCATGCAG 59.413 55.000 26.69 15.79 42.75 4.41
3117 3538 1.269174 CGATCTCTGCATCTGGACGAT 59.731 52.381 0.00 0.00 0.00 3.73
3118 3539 0.665298 CGATCTCTGCATCTGGACGA 59.335 55.000 0.00 0.00 0.00 4.20
3119 3540 0.318529 CCGATCTCTGCATCTGGACG 60.319 60.000 0.00 0.00 0.00 4.79
3120 3541 0.033228 CCCGATCTCTGCATCTGGAC 59.967 60.000 0.00 0.00 30.52 4.02
3121 3542 1.117749 CCCCGATCTCTGCATCTGGA 61.118 60.000 0.00 0.00 30.52 3.86
3122 3543 1.370437 CCCCGATCTCTGCATCTGG 59.630 63.158 0.00 0.00 0.00 3.86
3123 3544 1.301558 GCCCCGATCTCTGCATCTG 60.302 63.158 0.00 0.00 0.00 2.90
3124 3545 0.178950 TAGCCCCGATCTCTGCATCT 60.179 55.000 0.00 0.00 0.00 2.90
3125 3546 0.037790 GTAGCCCCGATCTCTGCATC 60.038 60.000 0.00 0.00 0.00 3.91
3126 3547 0.760567 TGTAGCCCCGATCTCTGCAT 60.761 55.000 0.00 0.00 0.00 3.96
3127 3548 0.760567 ATGTAGCCCCGATCTCTGCA 60.761 55.000 0.00 0.00 0.00 4.41
3128 3549 0.037790 GATGTAGCCCCGATCTCTGC 60.038 60.000 0.00 0.00 0.00 4.26
3129 3550 0.605589 GGATGTAGCCCCGATCTCTG 59.394 60.000 0.00 0.00 0.00 3.35
3130 3551 0.485099 AGGATGTAGCCCCGATCTCT 59.515 55.000 0.00 0.00 0.00 3.10
3131 3552 0.892063 GAGGATGTAGCCCCGATCTC 59.108 60.000 0.00 0.00 0.00 2.75
3132 3553 0.543174 GGAGGATGTAGCCCCGATCT 60.543 60.000 0.00 0.00 0.00 2.75
3133 3554 0.543174 AGGAGGATGTAGCCCCGATC 60.543 60.000 0.00 0.00 0.00 3.69
3134 3555 0.104934 AAGGAGGATGTAGCCCCGAT 60.105 55.000 0.00 0.00 0.00 4.18
3135 3556 0.326238 AAAGGAGGATGTAGCCCCGA 60.326 55.000 0.00 0.00 0.00 5.14
3136 3557 0.546598 AAAAGGAGGATGTAGCCCCG 59.453 55.000 0.00 0.00 0.00 5.73
3137 3558 3.945640 TTAAAAGGAGGATGTAGCCCC 57.054 47.619 0.00 0.00 0.00 5.80
3191 3612 3.081804 CCCCAAACTGACAAGGACATAC 58.918 50.000 0.00 0.00 0.00 2.39
3234 3658 9.998106 AGTGGATTATAATTGAGCTATAACGTT 57.002 29.630 5.88 5.88 0.00 3.99
3243 3667 8.135382 TCCTACCTAGTGGATTATAATTGAGC 57.865 38.462 0.00 0.00 37.04 4.26
3265 3689 2.677228 CCCGGGCTGTGAATTCCT 59.323 61.111 8.08 0.00 0.00 3.36
3268 3692 1.915078 CTCTCCCCGGGCTGTGAATT 61.915 60.000 17.73 0.00 0.00 2.17
3276 3700 1.381463 AAGTAGTCTCTCCCCGGGC 60.381 63.158 17.73 0.00 0.00 6.13
3279 3703 1.546961 ACACAAGTAGTCTCTCCCCG 58.453 55.000 0.00 0.00 0.00 5.73
3280 3704 3.323979 TGAAACACAAGTAGTCTCTCCCC 59.676 47.826 0.00 0.00 0.00 4.81
3298 3722 6.056884 ACCGAATACCAACTTAACAGTGAAA 58.943 36.000 0.00 0.00 31.60 2.69
3299 3723 5.613329 ACCGAATACCAACTTAACAGTGAA 58.387 37.500 0.00 0.00 31.60 3.18
3316 3740 6.391227 AGAGTGAAAAATGACAAACCGAAT 57.609 33.333 0.00 0.00 0.00 3.34


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

AutoCloner maintained by Alex Coulton.