Multiple sequence alignment - TraesCS3B01G460500

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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 TraesCS3B01G460500 chr3B 100.000 5099 0 0 1 5099 704039256 704044354 0.000000e+00 9417.0
1 TraesCS3B01G460500 chr3B 98.421 1393 22 0 3258 4650 704136007 704137399 0.000000e+00 2451.0
2 TraesCS3B01G460500 chr3B 97.866 937 20 0 888 1824 704134915 704135851 0.000000e+00 1620.0
3 TraesCS3B01G460500 chr3B 96.481 824 29 0 1 824 704131336 704132159 0.000000e+00 1362.0
4 TraesCS3B01G460500 chr3B 97.788 452 10 0 4648 5099 704157677 704158128 0.000000e+00 780.0
5 TraesCS3B01G460500 chr3B 85.067 596 82 3 1884 2479 761930751 761930163 7.300000e-168 601.0
6 TraesCS3B01G460500 chr3B 98.235 170 1 1 3054 3221 704135851 704136020 3.860000e-76 296.0
7 TraesCS3B01G460500 chr3B 91.304 46 2 2 845 888 704133845 704133890 1.530000e-05 62.1
8 TraesCS3B01G460500 chr3A 92.516 1844 133 5 3258 5099 667278879 667280719 0.000000e+00 2636.0
9 TraesCS3B01G460500 chr3A 94.667 975 46 3 3258 4226 667220180 667221154 0.000000e+00 1507.0
10 TraesCS3B01G460500 chr3A 95.391 933 43 0 888 1820 667219083 667220015 0.000000e+00 1485.0
11 TraesCS3B01G460500 chr3A 96.252 507 19 0 1314 1820 667278208 667278714 0.000000e+00 832.0
12 TraesCS3B01G460500 chr3A 93.911 427 26 0 888 1314 667262152 667262578 0.000000e+00 645.0
13 TraesCS3B01G460500 chr3A 80.451 665 90 27 1 636 667217299 667217952 5.980000e-129 472.0
14 TraesCS3B01G460500 chr3A 82.474 97 10 5 2962 3053 556300456 556300550 1.520000e-10 78.7
15 TraesCS3B01G460500 chr3A 87.143 70 3 3 2990 3055 586073412 586073479 1.970000e-09 75.0
16 TraesCS3B01G460500 chr3A 95.238 42 1 1 845 885 667216604 667216645 1.190000e-06 65.8
17 TraesCS3B01G460500 chr3A 92.857 42 2 1 845 885 667259661 667259702 5.510000e-05 60.2
18 TraesCS3B01G460500 chr7B 96.260 1123 34 6 1841 2958 254679447 254678328 0.000000e+00 1834.0
19 TraesCS3B01G460500 chr7B 89.030 711 64 4 1870 2573 586938209 586938912 0.000000e+00 869.0
20 TraesCS3B01G460500 chr7B 95.249 442 11 8 2536 2972 254679966 254679530 0.000000e+00 691.0
21 TraesCS3B01G460500 chr7B 78.541 233 28 19 2741 2957 707406376 707406150 3.200000e-27 134.0
22 TraesCS3B01G460500 chr7B 75.207 363 40 34 2741 3059 707407532 707407176 5.360000e-25 126.0
23 TraesCS3B01G460500 chr7B 91.566 83 7 0 741 823 151405845 151405763 1.160000e-21 115.0
24 TraesCS3B01G460500 chr7B 89.362 94 7 3 732 823 741390393 741390301 1.160000e-21 115.0
25 TraesCS3B01G460500 chr2B 93.099 826 41 13 2152 2967 677629112 677629931 0.000000e+00 1195.0
26 TraesCS3B01G460500 chr2B 89.938 487 47 1 1845 2331 677628766 677629250 1.210000e-175 627.0
27 TraesCS3B01G460500 chr2B 90.476 84 8 0 740 823 785199024 785198941 1.500000e-20 111.0
28 TraesCS3B01G460500 chr2B 90.244 82 6 1 745 824 542899995 542899914 6.980000e-19 106.0
29 TraesCS3B01G460500 chrUn 89.108 863 50 29 2215 3055 347792338 347791498 0.000000e+00 1033.0
30 TraesCS3B01G460500 chrUn 89.108 863 50 29 2215 3055 370646294 370645454 0.000000e+00 1033.0
31 TraesCS3B01G460500 chrUn 100.000 41 0 0 3223 3263 117301695 117301735 5.470000e-10 76.8
32 TraesCS3B01G460500 chrUn 100.000 37 0 0 3223 3259 466962225 466962189 9.160000e-08 69.4
33 TraesCS3B01G460500 chr7A 88.274 614 36 27 2457 3055 7527093 7526501 0.000000e+00 702.0
34 TraesCS3B01G460500 chr7A 88.361 421 41 2 1841 2259 564078631 564078217 2.740000e-137 499.0
35 TraesCS3B01G460500 chr5B 82.392 744 100 18 1832 2554 599016049 599015316 2.020000e-173 619.0
36 TraesCS3B01G460500 chr5B 88.403 457 53 0 1845 2301 315327169 315327625 7.460000e-153 551.0
37 TraesCS3B01G460500 chr5B 80.597 335 37 18 2741 3055 685162724 685163050 3.070000e-57 233.0
38 TraesCS3B01G460500 chr5B 77.299 348 33 35 2740 3053 695817681 695817346 4.080000e-36 163.0
39 TraesCS3B01G460500 chr5B 100.000 35 0 0 3223 3257 431806691 431806657 1.190000e-06 65.8
40 TraesCS3B01G460500 chr4D 90.068 443 38 1 1867 2309 280788574 280789010 2.060000e-158 569.0
41 TraesCS3B01G460500 chr4D 90.667 75 2 4 2990 3059 137013451 137013377 1.510000e-15 95.3
42 TraesCS3B01G460500 chr7D 87.257 463 49 4 1841 2301 623616257 623615803 2.100000e-143 520.0
43 TraesCS3B01G460500 chr7D 89.412 85 9 0 740 824 613823935 613824019 1.940000e-19 108.0
44 TraesCS3B01G460500 chr7D 83.810 105 8 5 2951 3053 14256945 14256848 1.960000e-14 91.6
45 TraesCS3B01G460500 chr5D 87.613 444 43 7 1821 2259 215143066 215142630 5.890000e-139 505.0
46 TraesCS3B01G460500 chr3D 83.768 345 55 1 2212 2556 100401619 100401962 4.920000e-85 326.0
47 TraesCS3B01G460500 chr3D 90.476 84 8 0 741 824 108242304 108242221 1.500000e-20 111.0
48 TraesCS3B01G460500 chr1A 82.920 363 58 4 2215 2577 424210543 424210185 1.770000e-84 324.0
49 TraesCS3B01G460500 chr1A 83.529 340 54 2 2215 2554 424211595 424211258 2.960000e-82 316.0
50 TraesCS3B01G460500 chr1A 92.593 135 9 1 2838 2971 568652176 568652042 5.210000e-45 193.0
51 TraesCS3B01G460500 chr1A 88.372 86 10 0 739 824 466926504 466926419 2.510000e-18 104.0
52 TraesCS3B01G460500 chr6B 83.235 340 27 19 2741 3053 20800585 20800921 8.360000e-73 285.0
53 TraesCS3B01G460500 chr6B 82.948 346 26 20 2741 3056 20799038 20799380 1.080000e-71 281.0
54 TraesCS3B01G460500 chr6B 83.186 113 9 6 2944 3053 712476072 712475967 1.510000e-15 95.3
55 TraesCS3B01G460500 chr6B 97.674 43 0 1 3223 3264 239602207 239602249 7.080000e-09 73.1
56 TraesCS3B01G460500 chr6B 100.000 38 0 0 3223 3260 576435242 576435279 2.550000e-08 71.3
57 TraesCS3B01G460500 chr5A 87.755 98 12 0 2601 2698 17163448 17163351 1.160000e-21 115.0
58 TraesCS3B01G460500 chr5A 84.466 103 5 6 2952 3053 11122824 11122732 1.960000e-14 91.6
59 TraesCS3B01G460500 chr1B 94.595 74 4 0 2597 2670 520791241 520791314 1.160000e-21 115.0
60 TraesCS3B01G460500 chr6D 88.043 92 10 1 733 824 6440854 6440944 1.940000e-19 108.0
61 TraesCS3B01G460500 chr4A 86.275 102 4 6 2957 3054 603278408 603278313 9.030000e-18 102.0
62 TraesCS3B01G460500 chr4A 100.000 38 0 0 3223 3260 531079283 531079320 2.550000e-08 71.3
63 TraesCS3B01G460500 chr6A 100.000 37 0 0 3223 3259 445264829 445264793 9.160000e-08 69.4
64 TraesCS3B01G460500 chr2A 95.238 42 2 0 3223 3264 572697932 572697891 3.290000e-07 67.6
65 TraesCS3B01G460500 chr4B 100.000 33 0 0 3223 3255 566116895 566116863 1.530000e-05 62.1


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 TraesCS3B01G460500 chr3B 704039256 704044354 5098 False 9417.00 9417 100.00000 1 5099 1 chr3B.!!$F1 5098
1 TraesCS3B01G460500 chr3B 704131336 704137399 6063 False 1158.22 2451 96.46140 1 4650 5 chr3B.!!$F3 4649
2 TraesCS3B01G460500 chr3B 761930163 761930751 588 True 601.00 601 85.06700 1884 2479 1 chr3B.!!$R1 595
3 TraesCS3B01G460500 chr3A 667278208 667280719 2511 False 1734.00 2636 94.38400 1314 5099 2 chr3A.!!$F5 3785
4 TraesCS3B01G460500 chr3A 667216604 667221154 4550 False 882.45 1507 91.43675 1 4226 4 chr3A.!!$F3 4225
5 TraesCS3B01G460500 chr3A 667259661 667262578 2917 False 352.60 645 93.38400 845 1314 2 chr3A.!!$F4 469
6 TraesCS3B01G460500 chr7B 254678328 254679966 1638 True 1262.50 1834 95.75450 1841 2972 2 chr7B.!!$R3 1131
7 TraesCS3B01G460500 chr7B 586938209 586938912 703 False 869.00 869 89.03000 1870 2573 1 chr7B.!!$F1 703
8 TraesCS3B01G460500 chr2B 677628766 677629931 1165 False 911.00 1195 91.51850 1845 2967 2 chr2B.!!$F1 1122
9 TraesCS3B01G460500 chrUn 347791498 347792338 840 True 1033.00 1033 89.10800 2215 3055 1 chrUn.!!$R1 840
10 TraesCS3B01G460500 chrUn 370645454 370646294 840 True 1033.00 1033 89.10800 2215 3055 1 chrUn.!!$R2 840
11 TraesCS3B01G460500 chr7A 7526501 7527093 592 True 702.00 702 88.27400 2457 3055 1 chr7A.!!$R1 598
12 TraesCS3B01G460500 chr5B 599015316 599016049 733 True 619.00 619 82.39200 1832 2554 1 chr5B.!!$R2 722
13 TraesCS3B01G460500 chr1A 424210185 424211595 1410 True 320.00 324 83.22450 2215 2577 2 chr1A.!!$R3 362
14 TraesCS3B01G460500 chr6B 20799038 20800921 1883 False 283.00 285 83.09150 2741 3056 2 chr6B.!!$F3 315

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
848 2514 0.034089 AGAAAATTGGCCTCCCTCCG 60.034 55.0 3.32 0.0 0.00 4.63 F
1121 5253 0.333652 TGATGAGGACCCACGACCTA 59.666 55.0 0.00 0.0 36.57 3.08 F
1433 5565 0.674534 AGAAGTCCGAGTTCGTGCTT 59.325 50.0 9.80 4.5 37.74 3.91 F
1864 5996 0.742635 GAAGAAGAGGCGCCTTGAGG 60.743 60.0 33.34 0.0 38.53 3.86 F
3255 8795 0.763986 ATGCACCAGGTTGCCCTTTT 60.764 50.0 10.46 0.0 42.25 2.27 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1843 5975 0.247736 TCAAGGCGCCTCTTCTTCTC 59.752 55.0 32.93 0.00 0.00 2.87 R
3010 8539 0.458716 GCGCCGCTTCTTCTTCTACT 60.459 55.0 0.00 0.00 0.00 2.57 R
3291 8831 0.601558 GCGCCTCCGAATATGTCCTA 59.398 55.0 0.00 0.00 36.29 2.94 R
3399 8939 0.679505 AGTGCACCTAGAACGCTTCA 59.320 50.0 14.63 0.00 0.00 3.02 R
4943 10490 0.377554 GTCTCGCGATCGAAGAGGAA 59.622 55.0 28.39 15.51 44.98 3.36 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
334 335 6.606234 TCTAACGTTGTTTGTTATGAAGCA 57.394 33.333 11.99 0.00 31.85 3.91
562 563 2.125685 GCTTAATCGCTTACTCCCGTC 58.874 52.381 0.00 0.00 0.00 4.79
578 579 1.033746 CGTCGTCTGGGTAAGGCCTA 61.034 60.000 5.16 0.00 37.43 3.93
582 583 2.841881 TCGTCTGGGTAAGGCCTAATTT 59.158 45.455 5.16 0.00 37.43 1.82
655 656 6.884280 ATATGCCATAAGGTTTTCTGTAGC 57.116 37.500 0.00 0.00 37.19 3.58
660 661 2.943036 AAGGTTTTCTGTAGCGGGAA 57.057 45.000 0.00 0.00 0.00 3.97
666 667 4.272748 GGTTTTCTGTAGCGGGAATATCAC 59.727 45.833 0.00 0.00 0.00 3.06
675 676 5.392767 AGCGGGAATATCACATACTAGTG 57.607 43.478 5.39 0.00 40.85 2.74
700 701 6.600427 GTGATACTAGCCTACCTTCTAGATCC 59.400 46.154 0.00 0.00 36.63 3.36
824 825 1.476891 TGATCAACTAGACCGACTGCC 59.523 52.381 0.00 0.00 0.00 4.85
826 827 1.629043 TCAACTAGACCGACTGCCTT 58.371 50.000 0.00 0.00 0.00 4.35
829 830 2.211250 ACTAGACCGACTGCCTTGTA 57.789 50.000 0.00 0.00 0.00 2.41
830 831 2.093106 ACTAGACCGACTGCCTTGTAG 58.907 52.381 0.00 0.00 0.00 2.74
831 832 2.290768 ACTAGACCGACTGCCTTGTAGA 60.291 50.000 0.00 0.00 0.00 2.59
834 835 2.367567 AGACCGACTGCCTTGTAGAAAA 59.632 45.455 0.00 0.00 0.00 2.29
835 836 3.008049 AGACCGACTGCCTTGTAGAAAAT 59.992 43.478 0.00 0.00 0.00 1.82
836 837 3.751518 ACCGACTGCCTTGTAGAAAATT 58.248 40.909 0.00 0.00 0.00 1.82
838 839 3.119849 CCGACTGCCTTGTAGAAAATTGG 60.120 47.826 0.00 0.00 0.00 3.16
840 841 2.562738 ACTGCCTTGTAGAAAATTGGCC 59.437 45.455 0.00 0.00 39.60 5.36
842 843 2.825532 TGCCTTGTAGAAAATTGGCCTC 59.174 45.455 3.32 0.00 39.60 4.70
848 2514 0.034089 AGAAAATTGGCCTCCCTCCG 60.034 55.000 3.32 0.00 0.00 4.63
1121 5253 0.333652 TGATGAGGACCCACGACCTA 59.666 55.000 0.00 0.00 36.57 3.08
1193 5325 1.442148 GAAGGGTATCGGCTTCGCT 59.558 57.895 0.00 0.00 0.00 4.93
1433 5565 0.674534 AGAAGTCCGAGTTCGTGCTT 59.325 50.000 9.80 4.50 37.74 3.91
1493 5625 1.671742 GCTGGACTTCTTCCCGTCA 59.328 57.895 0.00 0.00 45.17 4.35
1788 5920 9.256477 CCTACGCTATTAATGTGATTCAAGTAA 57.744 33.333 0.00 0.00 0.00 2.24
1828 5960 7.518731 CAAGAAAGTAGTCTTGCTCTGATAC 57.481 40.000 2.26 0.00 45.84 2.24
1829 5961 6.215495 AGAAAGTAGTCTTGCTCTGATACC 57.785 41.667 0.00 0.00 34.68 2.73
1830 5962 5.717178 AGAAAGTAGTCTTGCTCTGATACCA 59.283 40.000 0.00 0.00 34.68 3.25
1831 5963 6.211584 AGAAAGTAGTCTTGCTCTGATACCAA 59.788 38.462 0.00 0.00 34.68 3.67
1832 5964 5.590530 AGTAGTCTTGCTCTGATACCAAG 57.409 43.478 6.55 6.55 37.80 3.61
1833 5965 5.265191 AGTAGTCTTGCTCTGATACCAAGA 58.735 41.667 9.88 9.88 41.72 3.02
1834 5966 4.734398 AGTCTTGCTCTGATACCAAGAG 57.266 45.455 12.74 0.00 43.79 2.85
1835 5967 4.093011 AGTCTTGCTCTGATACCAAGAGT 58.907 43.478 12.74 12.95 43.79 3.24
1836 5968 4.530161 AGTCTTGCTCTGATACCAAGAGTT 59.470 41.667 12.74 5.53 43.19 3.01
1837 5969 4.629200 GTCTTGCTCTGATACCAAGAGTTG 59.371 45.833 12.74 0.00 43.79 3.16
1838 5970 2.977914 TGCTCTGATACCAAGAGTTGC 58.022 47.619 2.68 0.00 32.67 4.17
1839 5971 2.302733 TGCTCTGATACCAAGAGTTGCA 59.697 45.455 2.68 0.00 32.67 4.08
1840 5972 3.244526 TGCTCTGATACCAAGAGTTGCAA 60.245 43.478 0.00 0.00 32.67 4.08
1841 5973 3.373439 GCTCTGATACCAAGAGTTGCAAG 59.627 47.826 0.00 0.00 32.67 4.01
1843 5975 3.012518 CTGATACCAAGAGTTGCAAGGG 58.987 50.000 0.00 0.00 0.00 3.95
1849 5981 2.224621 CCAAGAGTTGCAAGGGAGAAGA 60.225 50.000 0.00 0.00 0.00 2.87
1852 5984 2.975489 AGAGTTGCAAGGGAGAAGAAGA 59.025 45.455 0.00 0.00 0.00 2.87
1859 5991 2.363172 GGGAGAAGAAGAGGCGCCT 61.363 63.158 33.48 33.48 0.00 5.52
1860 5992 1.599576 GGAGAAGAAGAGGCGCCTT 59.400 57.895 33.34 17.05 0.00 4.35
1864 5996 0.742635 GAAGAAGAGGCGCCTTGAGG 60.743 60.000 33.34 0.00 38.53 3.86
1865 5997 1.194781 AAGAAGAGGCGCCTTGAGGA 61.195 55.000 33.34 0.00 37.39 3.71
2025 6159 1.874231 GTCTCCATCATCGTCGAGCTA 59.126 52.381 0.00 0.00 0.00 3.32
2260 6489 3.948719 ACCGGTGGCGAACATGGT 61.949 61.111 6.12 0.00 36.29 3.55
2594 7917 3.053917 GGTTAGTGGGTTGGTCATATGGT 60.054 47.826 2.13 0.00 0.00 3.55
2851 8342 4.021544 TGCATTGTGTAATGGGAAAAGGAC 60.022 41.667 0.00 0.00 43.12 3.85
2949 8448 1.202710 TCCTTGGTACATGCGTGTGTT 60.203 47.619 21.92 0.00 39.30 3.32
2968 8467 3.233578 GTTGTGTGTGTGTGTGTTCTTG 58.766 45.455 0.00 0.00 0.00 3.02
2970 8469 2.225255 TGTGTGTGTGTGTGTTCTTGTG 59.775 45.455 0.00 0.00 0.00 3.33
2971 8470 2.225491 GTGTGTGTGTGTGTTCTTGTGT 59.775 45.455 0.00 0.00 0.00 3.72
2972 8471 2.225255 TGTGTGTGTGTGTTCTTGTGTG 59.775 45.455 0.00 0.00 0.00 3.82
2973 8472 2.482336 GTGTGTGTGTGTTCTTGTGTGA 59.518 45.455 0.00 0.00 0.00 3.58
2975 8474 3.000041 GTGTGTGTGTTCTTGTGTGAGA 59.000 45.455 0.00 0.00 0.00 3.27
2976 8475 3.000041 TGTGTGTGTTCTTGTGTGAGAC 59.000 45.455 0.00 0.00 0.00 3.36
2977 8476 3.000041 GTGTGTGTTCTTGTGTGAGACA 59.000 45.455 0.00 0.00 0.00 3.41
2980 8498 4.517075 TGTGTGTTCTTGTGTGAGACAAAA 59.483 37.500 0.00 0.00 44.14 2.44
3001 8530 7.337942 ACAAAAATGAAGAGAAGAGAGTTGTGT 59.662 33.333 0.00 0.00 0.00 3.72
3009 8538 2.540265 AGAGAGTTGTGTGAGGCAAG 57.460 50.000 0.00 0.00 0.00 4.01
3010 8539 2.042464 AGAGAGTTGTGTGAGGCAAGA 58.958 47.619 0.00 0.00 0.00 3.02
3232 8772 8.980143 TTTTTATAAATTGTACAAGCAGGAGC 57.020 30.769 14.65 0.00 42.56 4.70
3247 8787 3.558674 GAGCTACATGCACCAGGTT 57.441 52.632 0.00 0.00 45.94 3.50
3248 8788 1.089920 GAGCTACATGCACCAGGTTG 58.910 55.000 0.00 0.00 45.94 3.77
3249 8789 0.962356 AGCTACATGCACCAGGTTGC 60.962 55.000 8.03 8.03 44.17 4.17
3250 8790 1.937546 GCTACATGCACCAGGTTGCC 61.938 60.000 10.46 0.00 39.88 4.52
3251 8791 1.304052 TACATGCACCAGGTTGCCC 60.304 57.895 10.46 0.00 42.25 5.36
3252 8792 1.788518 TACATGCACCAGGTTGCCCT 61.789 55.000 10.46 0.00 42.25 5.19
3253 8793 1.909781 CATGCACCAGGTTGCCCTT 60.910 57.895 10.46 0.00 42.25 3.95
3254 8794 1.152269 ATGCACCAGGTTGCCCTTT 60.152 52.632 10.46 0.00 42.25 3.11
3255 8795 0.763986 ATGCACCAGGTTGCCCTTTT 60.764 50.000 10.46 0.00 42.25 2.27
3256 8796 0.980231 TGCACCAGGTTGCCCTTTTT 60.980 50.000 10.46 0.00 42.25 1.94
3399 8939 2.623416 GCAAAGGCACAACTAGAGGTTT 59.377 45.455 0.00 0.00 40.72 3.27
3538 9078 2.115911 CCCGTGAGTCGAGAGAGGG 61.116 68.421 0.00 0.00 43.49 4.30
4116 9662 5.593909 TGATTGTGTGAATTCTCTTGGTGTT 59.406 36.000 7.05 0.00 0.00 3.32
4328 9874 6.322201 GGGTGATATTTGGTGACATCAAATCT 59.678 38.462 26.09 18.39 41.97 2.40
4386 9933 1.038130 CGGGTCACTACCTCCTCCTG 61.038 65.000 0.00 0.00 45.95 3.86
4665 10212 4.581409 CCAATTCAGCATGTCCATATCACA 59.419 41.667 0.00 0.00 37.40 3.58
4691 10238 5.363562 TCTCTCATGCCATTCAACTATGT 57.636 39.130 0.00 0.00 0.00 2.29
4719 10266 0.399833 TGTATGCCCACACTCAAGCA 59.600 50.000 0.00 0.00 40.00 3.91
4724 10271 0.961019 GCCCACACTCAAGCAATCAA 59.039 50.000 0.00 0.00 0.00 2.57
4739 10286 4.721776 AGCAATCAAGAACCCTAGATGGTA 59.278 41.667 0.00 0.00 37.76 3.25
4742 10289 6.465035 GCAATCAAGAACCCTAGATGGTAGAT 60.465 42.308 0.00 0.00 37.76 1.98
4749 10296 2.029828 CCCTAGATGGTAGATGCGTCAC 60.030 54.545 8.99 4.46 0.00 3.67
4750 10297 2.029828 CCTAGATGGTAGATGCGTCACC 60.030 54.545 8.99 13.53 0.00 4.02
4753 10300 0.465705 ATGGTAGATGCGTCACCCTG 59.534 55.000 18.85 0.00 0.00 4.45
4761 10308 1.215647 GCGTCACCCTGTCGATCTT 59.784 57.895 0.00 0.00 30.84 2.40
4764 10311 1.743958 CGTCACCCTGTCGATCTTACT 59.256 52.381 0.00 0.00 30.84 2.24
4767 10314 2.492088 TCACCCTGTCGATCTTACTGTG 59.508 50.000 0.00 0.00 0.00 3.66
4788 10335 2.604614 GGACGAACACATTCAACCTTGC 60.605 50.000 0.00 0.00 34.14 4.01
4790 10337 1.335872 CGAACACATTCAACCTTGCCC 60.336 52.381 0.00 0.00 34.14 5.36
4796 10343 1.005924 CATTCAACCTTGCCCCTACCT 59.994 52.381 0.00 0.00 0.00 3.08
4861 10408 0.902531 TGGAAGACCGGGCTTCTTAG 59.097 55.000 41.40 0.00 42.96 2.18
4869 10416 1.955080 CCGGGCTTCTTAGTCGACTAT 59.045 52.381 25.17 4.18 0.00 2.12
4870 10417 2.287668 CCGGGCTTCTTAGTCGACTATG 60.288 54.545 25.17 25.16 0.00 2.23
4872 10419 2.694109 GGGCTTCTTAGTCGACTATGGT 59.306 50.000 28.36 8.74 0.00 3.55
4876 10423 5.921408 GGCTTCTTAGTCGACTATGGTTATG 59.079 44.000 28.36 16.99 0.00 1.90
4902 10449 9.634021 GAAAGTCCTGATTAAAGAAAGGGATAT 57.366 33.333 0.00 0.00 0.00 1.63
4905 10452 8.214364 AGTCCTGATTAAAGAAAGGGATATGTC 58.786 37.037 0.00 0.00 0.00 3.06
4926 10473 0.251077 CCCTAGCAAGGCATCCCATC 60.251 60.000 0.00 0.00 42.14 3.51
4940 10487 0.548510 CCCATCTCTTTCACCCCTCC 59.451 60.000 0.00 0.00 0.00 4.30
4943 10490 2.310052 CCATCTCTTTCACCCCTCCTTT 59.690 50.000 0.00 0.00 0.00 3.11
4944 10491 3.245407 CCATCTCTTTCACCCCTCCTTTT 60.245 47.826 0.00 0.00 0.00 2.27
4945 10492 3.790089 TCTCTTTCACCCCTCCTTTTC 57.210 47.619 0.00 0.00 0.00 2.29
4946 10493 2.375509 TCTCTTTCACCCCTCCTTTTCC 59.624 50.000 0.00 0.00 0.00 3.13
4956 10503 2.482142 CCCTCCTTTTCCTCTTCGATCG 60.482 54.545 9.36 9.36 0.00 3.69
4958 10505 0.924090 CCTTTTCCTCTTCGATCGCG 59.076 55.000 11.09 0.00 39.35 5.87
4975 10522 3.771160 GAGACCGACGCCACCCAT 61.771 66.667 0.00 0.00 0.00 4.00
5000 10547 6.085555 ACCGAGCGAAGATTCTCAAATATA 57.914 37.500 0.00 0.00 0.00 0.86
5038 10586 1.536676 CTCAAGGTGTGGTTGGGGT 59.463 57.895 0.00 0.00 0.00 4.95
5053 10601 0.327191 GGGGTGAGGTATGGGGAGAA 60.327 60.000 0.00 0.00 0.00 2.87
5055 10603 2.136026 GGGTGAGGTATGGGGAGAAAT 58.864 52.381 0.00 0.00 0.00 2.17
5062 10610 7.310734 GGTGAGGTATGGGGAGAAATAATAGAG 60.311 44.444 0.00 0.00 0.00 2.43
5074 10622 7.676468 GGAGAAATAATAGAGAGATGGGGTAGT 59.324 40.741 0.00 0.00 0.00 2.73
5080 10628 2.043227 GAGAGATGGGGTAGTGGAAGG 58.957 57.143 0.00 0.00 0.00 3.46
5095 10643 2.022035 TGGAAGGGAGGTGGATATGTCT 60.022 50.000 0.00 0.00 0.00 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
15 16 0.253113 CCCCAAAATCCCCAACCCAT 60.253 55.000 0.00 0.00 0.00 4.00
222 223 7.495135 AAATTATTTGGTTTCCACTTGCTTG 57.505 32.000 0.00 0.00 30.78 4.01
262 263 4.406326 TGATCATTGCACCAATAGCCAAAT 59.594 37.500 0.00 0.00 32.35 2.32
334 335 9.418045 CATTCATTTTTACCCGTAATCAAAAGT 57.582 29.630 0.00 0.00 0.00 2.66
562 563 3.277142 AAATTAGGCCTTACCCAGACG 57.723 47.619 12.58 0.00 40.58 4.18
587 588 9.049050 TGGTCTAACTAATGGTCAAGGTAAATA 57.951 33.333 0.00 0.00 0.00 1.40
647 648 4.955811 ATGTGATATTCCCGCTACAGAA 57.044 40.909 0.00 0.00 0.00 3.02
675 676 6.600427 GGATCTAGAAGGTAGGCTAGTATCAC 59.400 46.154 0.00 0.00 36.39 3.06
700 701 2.649331 AACGACAATGAGGTCCTACG 57.351 50.000 0.00 0.00 34.24 3.51
749 750 2.285083 GGCGCACTACATTGTGGAATA 58.715 47.619 10.83 0.00 38.31 1.75
753 754 2.749865 CGGGCGCACTACATTGTGG 61.750 63.158 8.62 0.00 38.31 4.17
807 808 1.272490 CAAGGCAGTCGGTCTAGTTGA 59.728 52.381 0.00 0.00 0.00 3.18
812 813 2.502142 TCTACAAGGCAGTCGGTCTA 57.498 50.000 0.00 0.00 0.00 2.59
824 825 3.696548 GAGGGAGGCCAATTTTCTACAAG 59.303 47.826 5.01 0.00 0.00 3.16
826 827 2.025321 GGAGGGAGGCCAATTTTCTACA 60.025 50.000 5.01 0.00 0.00 2.74
829 830 0.034089 CGGAGGGAGGCCAATTTTCT 60.034 55.000 5.01 0.00 0.00 2.52
830 831 0.323451 ACGGAGGGAGGCCAATTTTC 60.323 55.000 5.01 0.00 0.00 2.29
831 832 0.114364 AACGGAGGGAGGCCAATTTT 59.886 50.000 5.01 0.00 0.00 1.82
834 835 1.208165 AGAAACGGAGGGAGGCCAAT 61.208 55.000 5.01 0.00 0.00 3.16
835 836 0.545787 TAGAAACGGAGGGAGGCCAA 60.546 55.000 5.01 0.00 0.00 4.52
836 837 0.326238 ATAGAAACGGAGGGAGGCCA 60.326 55.000 5.01 0.00 0.00 5.36
838 839 2.613223 GCATATAGAAACGGAGGGAGGC 60.613 54.545 0.00 0.00 0.00 4.70
840 841 4.608948 AAGCATATAGAAACGGAGGGAG 57.391 45.455 0.00 0.00 0.00 4.30
842 843 5.723672 TCTAAGCATATAGAAACGGAGGG 57.276 43.478 0.00 0.00 0.00 4.30
879 2545 4.945246 CCGTAGGCTGTGAGTATGTTAAT 58.055 43.478 0.00 0.00 46.14 1.40
880 2546 4.380841 CCGTAGGCTGTGAGTATGTTAA 57.619 45.455 0.00 0.00 46.14 2.01
882 2548 2.961526 CCGTAGGCTGTGAGTATGTT 57.038 50.000 0.00 0.00 46.14 2.71
908 5040 4.761739 AGCTGCTTCTTGTGTAATTTGCTA 59.238 37.500 0.00 0.00 0.00 3.49
1094 5226 1.267574 GGGTCCTCATCACCAGCTCA 61.268 60.000 0.00 0.00 35.35 4.26
1300 5432 2.735772 GCAATGGAGCGGAGGAGGA 61.736 63.158 0.00 0.00 0.00 3.71
1433 5565 0.108992 CGCTTACTTGGTCGTAGGCA 60.109 55.000 6.02 0.00 41.06 4.75
1820 5952 3.937706 CCTTGCAACTCTTGGTATCAGAG 59.062 47.826 0.00 0.00 35.92 3.35
1823 5955 2.642311 TCCCTTGCAACTCTTGGTATCA 59.358 45.455 0.00 0.00 0.00 2.15
1824 5956 3.055094 TCTCCCTTGCAACTCTTGGTATC 60.055 47.826 0.00 0.00 0.00 2.24
1825 5957 2.912956 TCTCCCTTGCAACTCTTGGTAT 59.087 45.455 0.00 0.00 0.00 2.73
1826 5958 2.334977 TCTCCCTTGCAACTCTTGGTA 58.665 47.619 0.00 0.00 0.00 3.25
1827 5959 1.140312 TCTCCCTTGCAACTCTTGGT 58.860 50.000 0.00 0.00 0.00 3.67
1828 5960 2.157738 CTTCTCCCTTGCAACTCTTGG 58.842 52.381 0.00 0.00 0.00 3.61
1829 5961 3.131709 TCTTCTCCCTTGCAACTCTTG 57.868 47.619 0.00 0.00 0.00 3.02
1830 5962 3.392616 TCTTCTTCTCCCTTGCAACTCTT 59.607 43.478 0.00 0.00 0.00 2.85
1831 5963 2.975489 TCTTCTTCTCCCTTGCAACTCT 59.025 45.455 0.00 0.00 0.00 3.24
1832 5964 3.333804 CTCTTCTTCTCCCTTGCAACTC 58.666 50.000 0.00 0.00 0.00 3.01
1833 5965 2.039613 CCTCTTCTTCTCCCTTGCAACT 59.960 50.000 0.00 0.00 0.00 3.16
1834 5966 2.431454 CCTCTTCTTCTCCCTTGCAAC 58.569 52.381 0.00 0.00 0.00 4.17
1835 5967 1.271597 GCCTCTTCTTCTCCCTTGCAA 60.272 52.381 0.00 0.00 0.00 4.08
1836 5968 0.326264 GCCTCTTCTTCTCCCTTGCA 59.674 55.000 0.00 0.00 0.00 4.08
1837 5969 0.742635 CGCCTCTTCTTCTCCCTTGC 60.743 60.000 0.00 0.00 0.00 4.01
1838 5970 0.742635 GCGCCTCTTCTTCTCCCTTG 60.743 60.000 0.00 0.00 0.00 3.61
1839 5971 1.599576 GCGCCTCTTCTTCTCCCTT 59.400 57.895 0.00 0.00 0.00 3.95
1840 5972 2.363172 GGCGCCTCTTCTTCTCCCT 61.363 63.158 22.15 0.00 0.00 4.20
1841 5973 1.904990 AAGGCGCCTCTTCTTCTCCC 61.905 60.000 32.93 0.00 0.00 4.30
1843 5975 0.247736 TCAAGGCGCCTCTTCTTCTC 59.752 55.000 32.93 0.00 0.00 2.87
1849 5981 1.610673 TCTCCTCAAGGCGCCTCTT 60.611 57.895 32.93 13.32 34.44 2.85
1852 5984 3.080121 CCTCTCCTCAAGGCGCCT 61.080 66.667 27.08 27.08 34.44 5.52
2025 6159 0.805614 CTCTCCATCACTCGTGACGT 59.194 55.000 4.40 0.00 43.11 4.34
2204 6433 4.164796 TGACTCACCTCCATATTCATTGCT 59.835 41.667 0.00 0.00 0.00 3.91
2260 6489 4.680237 CTTGCCGGTGACTCGCCA 62.680 66.667 1.90 0.00 32.88 5.69
2594 7917 1.360931 CCGACTCAATGCATGCACGA 61.361 55.000 25.37 20.91 0.00 4.35
2870 8363 0.981183 ACGGTGGCTACATCCTTTCA 59.019 50.000 1.52 0.00 0.00 2.69
2949 8448 2.225255 CACAAGAACACACACACACACA 59.775 45.455 0.00 0.00 0.00 3.72
2968 8467 7.225538 TCTCTTCTCTTCATTTTTGTCTCACAC 59.774 37.037 0.00 0.00 0.00 3.82
2970 8469 7.440856 ACTCTCTTCTCTTCATTTTTGTCTCAC 59.559 37.037 0.00 0.00 0.00 3.51
2971 8470 7.504403 ACTCTCTTCTCTTCATTTTTGTCTCA 58.496 34.615 0.00 0.00 0.00 3.27
2972 8471 7.961325 ACTCTCTTCTCTTCATTTTTGTCTC 57.039 36.000 0.00 0.00 0.00 3.36
2973 8472 7.772757 ACAACTCTCTTCTCTTCATTTTTGTCT 59.227 33.333 0.00 0.00 0.00 3.41
2975 8474 7.337942 ACACAACTCTCTTCTCTTCATTTTTGT 59.662 33.333 0.00 0.00 0.00 2.83
2976 8475 7.642978 CACACAACTCTCTTCTCTTCATTTTTG 59.357 37.037 0.00 0.00 0.00 2.44
2977 8476 7.554118 TCACACAACTCTCTTCTCTTCATTTTT 59.446 33.333 0.00 0.00 0.00 1.94
2980 8498 6.166984 TCACACAACTCTCTTCTCTTCATT 57.833 37.500 0.00 0.00 0.00 2.57
3001 8530 4.322349 GCTTCTTCTTCTACTCTTGCCTCA 60.322 45.833 0.00 0.00 0.00 3.86
3009 8538 1.551145 CGCCGCTTCTTCTTCTACTC 58.449 55.000 0.00 0.00 0.00 2.59
3010 8539 0.458716 GCGCCGCTTCTTCTTCTACT 60.459 55.000 0.00 0.00 0.00 2.57
3229 8769 1.089920 CAACCTGGTGCATGTAGCTC 58.910 55.000 14.15 0.00 45.94 4.09
3230 8770 0.962356 GCAACCTGGTGCATGTAGCT 60.962 55.000 14.15 0.00 44.29 3.32
3231 8771 1.508088 GCAACCTGGTGCATGTAGC 59.492 57.895 6.00 6.00 44.29 3.58
3232 8772 2.183409 GGCAACCTGGTGCATGTAG 58.817 57.895 18.44 0.00 46.81 2.74
3233 8773 4.413928 GGCAACCTGGTGCATGTA 57.586 55.556 18.44 0.00 46.81 2.29
3291 8831 0.601558 GCGCCTCCGAATATGTCCTA 59.398 55.000 0.00 0.00 36.29 2.94
3399 8939 0.679505 AGTGCACCTAGAACGCTTCA 59.320 50.000 14.63 0.00 0.00 3.02
3538 9078 4.398988 TGTGATAACCCATGATTTCACAGC 59.601 41.667 12.02 0.00 38.71 4.40
3831 9371 3.743521 TCCCAAAAGTCTCAGACATGTG 58.256 45.455 7.77 0.00 34.60 3.21
4229 9775 5.464057 TGACACACAATGTTTAGACCTAACG 59.536 40.000 0.00 0.00 43.56 3.18
4386 9933 2.169352 TGAGAATGGGCTGAGTTAGAGC 59.831 50.000 0.00 0.00 35.57 4.09
4552 10099 5.790495 GCTTAGAGTTACGAGTTGCATTTTG 59.210 40.000 0.00 0.00 0.00 2.44
4665 10212 4.597004 AGTTGAATGGCATGAGAGAATGT 58.403 39.130 0.00 0.00 0.00 2.71
4691 10238 1.702401 TGTGGGCATACAAAGACCTGA 59.298 47.619 0.00 0.00 34.31 3.86
4719 10266 6.465035 GCATCTACCATCTAGGGTTCTTGATT 60.465 42.308 0.00 0.00 43.89 2.57
4724 10271 2.894126 CGCATCTACCATCTAGGGTTCT 59.106 50.000 0.00 0.00 43.89 3.01
4739 10286 1.323271 ATCGACAGGGTGACGCATCT 61.323 55.000 1.61 0.00 35.65 2.90
4742 10289 1.532604 AAGATCGACAGGGTGACGCA 61.533 55.000 1.61 0.00 35.65 5.24
4749 10296 2.100197 TCCACAGTAAGATCGACAGGG 58.900 52.381 0.00 0.00 0.00 4.45
4750 10297 2.478031 CGTCCACAGTAAGATCGACAGG 60.478 54.545 0.00 3.20 0.00 4.00
4753 10300 3.169733 GTTCGTCCACAGTAAGATCGAC 58.830 50.000 0.00 0.00 0.00 4.20
4767 10314 2.604614 GCAAGGTTGAATGTGTTCGTCC 60.605 50.000 0.00 0.00 37.15 4.79
4788 10335 1.338769 CGTTGGAGTTTGAGGTAGGGG 60.339 57.143 0.00 0.00 0.00 4.79
4790 10337 2.685100 GACGTTGGAGTTTGAGGTAGG 58.315 52.381 0.00 0.00 0.00 3.18
4796 10343 2.876052 CGTCGACGTTGGAGTTTGA 58.124 52.632 29.08 0.00 34.11 2.69
4861 10408 5.749109 CAGGACTTTCATAACCATAGTCGAC 59.251 44.000 7.70 7.70 36.86 4.20
4869 10416 9.581289 TTTCTTTAATCAGGACTTTCATAACCA 57.419 29.630 0.00 0.00 0.00 3.67
4872 10419 9.243105 CCCTTTCTTTAATCAGGACTTTCATAA 57.757 33.333 0.00 0.00 0.00 1.90
4876 10423 7.946381 ATCCCTTTCTTTAATCAGGACTTTC 57.054 36.000 0.00 0.00 0.00 2.62
4926 10473 2.376855 AGGAAAAGGAGGGGTGAAAGAG 59.623 50.000 0.00 0.00 0.00 2.85
4940 10487 1.849219 CTCGCGATCGAAGAGGAAAAG 59.151 52.381 21.57 0.62 44.98 2.27
4943 10490 0.377554 GTCTCGCGATCGAAGAGGAA 59.622 55.000 28.39 15.51 44.98 3.36
4944 10491 1.437772 GGTCTCGCGATCGAAGAGGA 61.438 60.000 28.39 18.07 44.98 3.71
4945 10492 1.009449 GGTCTCGCGATCGAAGAGG 60.009 63.158 28.39 16.68 44.98 3.69
4946 10493 1.368255 CGGTCTCGCGATCGAAGAG 60.368 63.158 25.43 25.43 46.52 2.85
4958 10505 3.771160 ATGGGTGGCGTCGGTCTC 61.771 66.667 0.00 0.00 0.00 3.36
4965 10512 4.082523 CTCGGTCATGGGTGGCGT 62.083 66.667 0.00 0.00 0.00 5.68
4970 10517 1.330655 ATCTTCGCTCGGTCATGGGT 61.331 55.000 0.00 0.00 0.00 4.51
4974 10521 1.751351 TGAGAATCTTCGCTCGGTCAT 59.249 47.619 0.00 0.00 34.92 3.06
4975 10522 1.173913 TGAGAATCTTCGCTCGGTCA 58.826 50.000 0.00 0.00 34.92 4.02
5000 10547 3.115390 AGGTGTCCCTGTGCATTAGTAT 58.885 45.455 0.00 0.00 40.58 2.12
5031 10578 0.917333 TCCCCATACCTCACCCCAAC 60.917 60.000 0.00 0.00 0.00 3.77
5032 10579 0.623324 CTCCCCATACCTCACCCCAA 60.623 60.000 0.00 0.00 0.00 4.12
5038 10586 7.544650 TCTCTATTATTTCTCCCCATACCTCA 58.455 38.462 0.00 0.00 0.00 3.86
5053 10601 6.875469 TCCACTACCCCATCTCTCTATTATT 58.125 40.000 0.00 0.00 0.00 1.40
5055 10603 5.942977 TCCACTACCCCATCTCTCTATTA 57.057 43.478 0.00 0.00 0.00 0.98
5062 10610 1.132500 CCCTTCCACTACCCCATCTC 58.868 60.000 0.00 0.00 0.00 2.75
5074 10622 2.022035 AGACATATCCACCTCCCTTCCA 60.022 50.000 0.00 0.00 0.00 3.53


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

AutoCloner maintained by Alex Coulton.