Multiple sequence alignment - TraesCS5B01G491300

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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 TraesCS5B01G491300 chr5B 100.000 2885 0 0 1 2885 659747045 659749929 0.000000e+00 5328.0
1 TraesCS5B01G491300 chr5B 91.158 803 44 14 2108 2885 547398588 547397788 0.000000e+00 1064.0
2 TraesCS5B01G491300 chr5B 86.702 940 87 18 1980 2885 293547004 293547939 0.000000e+00 1009.0
3 TraesCS5B01G491300 chr5B 83.155 374 46 11 1203 1576 659679440 659679796 2.770000e-85 326.0
4 TraesCS5B01G491300 chr5B 76.763 241 42 10 1286 1519 659505982 659505749 3.900000e-24 122.0
5 TraesCS5B01G491300 chr5D 86.734 1583 102 51 436 1984 525387814 525389322 0.000000e+00 1661.0
6 TraesCS5B01G491300 chr5D 86.917 1544 103 48 309 1812 23870198 23871682 0.000000e+00 1640.0
7 TraesCS5B01G491300 chr5D 88.539 445 21 8 1 430 525381343 525381772 1.980000e-141 512.0
8 TraesCS5B01G491300 chr5D 84.960 379 39 10 1204 1576 525317398 525317764 4.540000e-98 368.0
9 TraesCS5B01G491300 chr5D 82.339 436 45 19 1163 1582 525226906 525226487 1.650000e-92 350.0
10 TraesCS5B01G491300 chr5D 81.984 383 48 11 1201 1577 525250355 525250722 3.610000e-79 305.0
11 TraesCS5B01G491300 chr5D 85.085 295 25 9 1 277 23869910 23870203 1.690000e-72 283.0
12 TraesCS5B01G491300 chr5A 87.125 1266 73 33 623 1839 651790618 651791842 0.000000e+00 1352.0
13 TraesCS5B01G491300 chr5A 85.405 555 32 21 1 515 651790036 651790581 5.470000e-147 531.0
14 TraesCS5B01G491300 chr5A 85.027 374 42 7 1204 1576 651755107 651755467 4.540000e-98 368.0
15 TraesCS5B01G491300 chr5A 85.255 373 35 8 1211 1576 651635600 651635959 1.630000e-97 366.0
16 TraesCS5B01G491300 chr5A 83.727 381 40 13 1163 1528 651569680 651569307 9.900000e-90 340.0
17 TraesCS5B01G491300 chr5A 82.532 395 46 13 1192 1576 651588631 651589012 2.770000e-85 326.0
18 TraesCS5B01G491300 chr5A 81.206 431 46 20 1163 1577 651564362 651563951 6.000000e-82 315.0
19 TraesCS5B01G491300 chr5A 80.637 377 55 8 1206 1576 651763475 651763839 2.830000e-70 276.0
20 TraesCS5B01G491300 chr5A 79.592 392 43 18 1166 1533 651555968 651555590 2.220000e-61 246.0
21 TraesCS5B01G491300 chr5A 81.513 238 27 10 1286 1513 651759103 651759333 2.280000e-41 180.0
22 TraesCS5B01G491300 chr5A 97.727 44 1 0 534 577 651790579 651790622 3.080000e-10 76.8
23 TraesCS5B01G491300 chr2B 91.272 928 54 8 1983 2885 110757736 110756811 0.000000e+00 1240.0
24 TraesCS5B01G491300 chr2B 88.511 940 56 17 1981 2885 461254908 461253986 0.000000e+00 1090.0
25 TraesCS5B01G491300 chr2B 88.621 747 68 14 1980 2718 44939990 44939253 0.000000e+00 893.0
26 TraesCS5B01G491300 chr2B 87.805 123 12 2 1983 2102 442534975 442534853 1.080000e-29 141.0
27 TraesCS5B01G491300 chr2B 82.911 158 24 2 1983 2137 202909591 202909434 3.880000e-29 139.0
28 TraesCS5B01G491300 chr2B 78.453 181 34 4 1981 2156 448932616 448932436 2.350000e-21 113.0
29 TraesCS5B01G491300 chr6B 90.789 912 65 15 1983 2882 47870062 47870966 0.000000e+00 1201.0
30 TraesCS5B01G491300 chr6B 91.421 746 54 8 1980 2718 701907194 701906452 0.000000e+00 1014.0
31 TraesCS5B01G491300 chr6B 92.599 608 39 4 2114 2718 474180337 474180941 0.000000e+00 869.0
32 TraesCS5B01G491300 chr6B 92.053 302 16 5 2585 2885 638945023 638944729 4.450000e-113 418.0
33 TraesCS5B01G491300 chr6B 84.375 128 17 2 1163 1290 528288843 528288967 3.900000e-24 122.0
34 TraesCS5B01G491300 chr4B 93.505 739 41 4 1984 2718 116349647 116348912 0.000000e+00 1092.0
35 TraesCS5B01G491300 chr4B 94.243 608 30 4 2114 2718 562343878 562344483 0.000000e+00 924.0
36 TraesCS5B01G491300 chr4B 86.667 60 8 0 1455 1514 434714203 434714262 1.860000e-07 67.6
37 TraesCS5B01G491300 chr7B 88.627 932 59 14 1983 2884 74102888 74103802 0.000000e+00 1090.0
38 TraesCS5B01G491300 chr7B 94.983 299 14 1 2588 2885 553327678 553327380 4.350000e-128 468.0
39 TraesCS5B01G491300 chr7B 89.632 299 21 7 2588 2885 24070824 24070535 3.510000e-99 372.0
40 TraesCS5B01G491300 chr3B 91.622 752 49 12 1974 2718 739875543 739876287 0.000000e+00 1027.0
41 TraesCS5B01G491300 chrUn 80.672 238 35 10 1286 1516 67240926 67241159 1.060000e-39 174.0
42 TraesCS5B01G491300 chr2D 83.832 167 23 3 1981 2144 525939863 525939698 3.850000e-34 156.0
43 TraesCS5B01G491300 chr2D 83.333 168 24 3 1979 2144 556363972 556363807 4.980000e-33 152.0
44 TraesCS5B01G491300 chr7D 83.333 162 22 3 1980 2139 426175358 426175200 8.330000e-31 145.0


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 TraesCS5B01G491300 chr5B 659747045 659749929 2884 False 5328.000000 5328 100.000000 1 2885 1 chr5B.!!$F3 2884
1 TraesCS5B01G491300 chr5B 547397788 547398588 800 True 1064.000000 1064 91.158000 2108 2885 1 chr5B.!!$R1 777
2 TraesCS5B01G491300 chr5B 293547004 293547939 935 False 1009.000000 1009 86.702000 1980 2885 1 chr5B.!!$F1 905
3 TraesCS5B01G491300 chr5D 525387814 525389322 1508 False 1661.000000 1661 86.734000 436 1984 1 chr5D.!!$F4 1548
4 TraesCS5B01G491300 chr5D 23869910 23871682 1772 False 961.500000 1640 86.001000 1 1812 2 chr5D.!!$F5 1811
5 TraesCS5B01G491300 chr5A 651790036 651791842 1806 False 653.266667 1352 90.085667 1 1839 3 chr5A.!!$F5 1838
6 TraesCS5B01G491300 chr5A 651755107 651759333 4226 False 274.000000 368 83.270000 1204 1576 2 chr5A.!!$F4 372
7 TraesCS5B01G491300 chr2B 110756811 110757736 925 True 1240.000000 1240 91.272000 1983 2885 1 chr2B.!!$R2 902
8 TraesCS5B01G491300 chr2B 461253986 461254908 922 True 1090.000000 1090 88.511000 1981 2885 1 chr2B.!!$R6 904
9 TraesCS5B01G491300 chr2B 44939253 44939990 737 True 893.000000 893 88.621000 1980 2718 1 chr2B.!!$R1 738
10 TraesCS5B01G491300 chr6B 47870062 47870966 904 False 1201.000000 1201 90.789000 1983 2882 1 chr6B.!!$F1 899
11 TraesCS5B01G491300 chr6B 701906452 701907194 742 True 1014.000000 1014 91.421000 1980 2718 1 chr6B.!!$R2 738
12 TraesCS5B01G491300 chr6B 474180337 474180941 604 False 869.000000 869 92.599000 2114 2718 1 chr6B.!!$F2 604
13 TraesCS5B01G491300 chr4B 116348912 116349647 735 True 1092.000000 1092 93.505000 1984 2718 1 chr4B.!!$R1 734
14 TraesCS5B01G491300 chr4B 562343878 562344483 605 False 924.000000 924 94.243000 2114 2718 1 chr4B.!!$F2 604
15 TraesCS5B01G491300 chr7B 74102888 74103802 914 False 1090.000000 1090 88.627000 1983 2884 1 chr7B.!!$F1 901
16 TraesCS5B01G491300 chr3B 739875543 739876287 744 False 1027.000000 1027 91.622000 1974 2718 1 chr3B.!!$F1 744

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
442 492 0.250166 ACCGACCGACCAGAAAAAGG 60.250 55.0 0.0 0.0 0.0 3.11 F
1071 1171 0.179070 GCTTCTCCTCACCCGAATCC 60.179 60.0 0.0 0.0 0.0 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1282 1412 0.539438 TTGCACATGAACTCCCCACC 60.539 55.0 0.00 0.0 0.00 4.61 R
2110 2429 1.128147 GTATTCTTGCGCGTTGCTGC 61.128 55.0 8.43 0.0 46.63 5.25 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
49 56 1.578206 GCTTCTCGGCAAGTTGGGTC 61.578 60.000 4.75 0.00 0.00 4.46
66 73 2.872925 CGGAATCGACGACGCGTT 60.873 61.111 15.53 0.00 41.37 4.84
67 74 2.430942 CGGAATCGACGACGCGTTT 61.431 57.895 15.53 2.88 41.37 3.60
71 81 2.531610 GGAATCGACGACGCGTTTTTAG 60.532 50.000 15.53 4.69 41.37 1.85
90 100 0.947180 GCACGTAAACCGAGGCAGAA 60.947 55.000 0.00 0.00 40.70 3.02
114 124 2.354109 TCTGAACTGACGACAGATGC 57.646 50.000 21.50 10.00 46.03 3.91
115 125 1.613437 TCTGAACTGACGACAGATGCA 59.387 47.619 21.50 13.56 46.03 3.96
160 173 6.183360 GGCAACGAATTTCTTACTAGTACCAC 60.183 42.308 0.91 0.00 0.00 4.16
177 191 7.817418 AGTACCACACATGTCTTTGTTTTAT 57.183 32.000 0.00 0.00 0.00 1.40
205 227 6.240549 AGTACCATACCTGATCCTCAAAAG 57.759 41.667 0.00 0.00 0.00 2.27
219 255 7.333423 TGATCCTCAAAAGAAAAGTACCATACG 59.667 37.037 0.00 0.00 0.00 3.06
263 299 3.688330 ACACGAAACACGCTCGCG 61.688 61.111 10.06 10.06 46.94 5.87
309 345 5.041951 TGGATGTTTACAAGAATGAACGC 57.958 39.130 0.00 0.00 0.00 4.84
311 347 4.851558 GGATGTTTACAAGAATGAACGCAC 59.148 41.667 0.00 0.00 0.00 5.34
330 378 3.670359 GCACAATGTATTTTGAGCGAGCA 60.670 43.478 0.00 0.00 34.39 4.26
352 400 2.340328 GGCGCACGGGGAAAATTCT 61.340 57.895 10.83 0.00 0.00 2.40
389 437 3.570212 AAGCCCACGACCAAGCCT 61.570 61.111 0.00 0.00 0.00 4.58
390 438 3.553095 AAGCCCACGACCAAGCCTC 62.553 63.158 0.00 0.00 0.00 4.70
430 480 2.815211 TAGACGACCGACCGACCG 60.815 66.667 3.56 0.00 0.00 4.79
432 482 4.451652 GACGACCGACCGACCGAC 62.452 72.222 9.46 1.85 0.00 4.79
435 485 4.112341 GACCGACCGACCGACCAG 62.112 72.222 0.00 0.00 0.00 4.00
437 487 3.367743 CCGACCGACCGACCAGAA 61.368 66.667 0.00 0.00 0.00 3.02
438 488 2.646719 CGACCGACCGACCAGAAA 59.353 61.111 0.00 0.00 0.00 2.52
440 490 0.598158 CGACCGACCGACCAGAAAAA 60.598 55.000 0.00 0.00 0.00 1.94
441 491 1.145803 GACCGACCGACCAGAAAAAG 58.854 55.000 0.00 0.00 0.00 2.27
442 492 0.250166 ACCGACCGACCAGAAAAAGG 60.250 55.000 0.00 0.00 0.00 3.11
443 493 0.250166 CCGACCGACCAGAAAAAGGT 60.250 55.000 0.00 0.00 43.46 3.50
518 592 0.806102 CGATGCCCATTCTCGTTCGT 60.806 55.000 0.00 0.00 0.00 3.85
520 594 0.462047 ATGCCCATTCTCGTTCGTCC 60.462 55.000 0.00 0.00 0.00 4.79
524 598 2.165301 CATTCTCGTTCGTCCGGCC 61.165 63.158 0.00 0.00 0.00 6.13
525 599 3.695022 ATTCTCGTTCGTCCGGCCG 62.695 63.158 21.04 21.04 0.00 6.13
582 657 2.648143 ATACGTTTCCCCGGTGCGA 61.648 57.895 0.00 0.00 0.00 5.10
782 872 3.181469 ACGTACGTAGGCATCAATCCAAT 60.181 43.478 21.41 0.00 0.00 3.16
784 874 3.558931 ACGTAGGCATCAATCCAATCA 57.441 42.857 0.00 0.00 0.00 2.57
785 875 3.884895 ACGTAGGCATCAATCCAATCAA 58.115 40.909 0.00 0.00 0.00 2.57
786 876 4.269183 ACGTAGGCATCAATCCAATCAAA 58.731 39.130 0.00 0.00 0.00 2.69
787 877 4.336433 ACGTAGGCATCAATCCAATCAAAG 59.664 41.667 0.00 0.00 0.00 2.77
789 879 2.100252 AGGCATCAATCCAATCAAAGCG 59.900 45.455 0.00 0.00 0.00 4.68
792 882 1.164411 TCAATCCAATCAAAGCGCGT 58.836 45.000 8.43 0.00 0.00 6.01
795 888 1.376609 ATCCAATCAAAGCGCGTCCC 61.377 55.000 8.43 0.00 0.00 4.46
807 900 4.373116 CGTCCCGGTGAGTGGTGG 62.373 72.222 0.00 0.00 0.00 4.61
822 915 1.075659 GTGGGCAAGGAAGGAAGCT 59.924 57.895 0.00 0.00 0.00 3.74
823 916 0.962855 GTGGGCAAGGAAGGAAGCTC 60.963 60.000 0.00 0.00 0.00 4.09
828 921 0.391793 CAAGGAAGGAAGCTCGGGAC 60.392 60.000 0.00 0.00 0.00 4.46
972 1072 3.327404 TCTTTCCCGTCCAGGCCC 61.327 66.667 0.00 0.00 39.21 5.80
1051 1151 1.973812 GGAACAGCCAGCCACCTTC 60.974 63.158 0.00 0.00 36.34 3.46
1052 1152 2.281761 AACAGCCAGCCACCTTCG 60.282 61.111 0.00 0.00 0.00 3.79
1054 1154 4.711949 CAGCCAGCCACCTTCGCT 62.712 66.667 0.00 0.00 36.91 4.93
1055 1155 3.958860 AGCCAGCCACCTTCGCTT 61.959 61.111 0.00 0.00 33.17 4.68
1056 1156 3.435186 GCCAGCCACCTTCGCTTC 61.435 66.667 0.00 0.00 33.17 3.86
1057 1157 2.348998 CCAGCCACCTTCGCTTCT 59.651 61.111 0.00 0.00 33.17 2.85
1058 1158 1.743252 CCAGCCACCTTCGCTTCTC 60.743 63.158 0.00 0.00 33.17 2.87
1059 1159 1.743252 CAGCCACCTTCGCTTCTCC 60.743 63.158 0.00 0.00 33.17 3.71
1060 1160 1.915769 AGCCACCTTCGCTTCTCCT 60.916 57.895 0.00 0.00 30.57 3.69
1061 1161 1.448717 GCCACCTTCGCTTCTCCTC 60.449 63.158 0.00 0.00 0.00 3.71
1062 1162 1.975327 CCACCTTCGCTTCTCCTCA 59.025 57.895 0.00 0.00 0.00 3.86
1063 1163 0.390472 CCACCTTCGCTTCTCCTCAC 60.390 60.000 0.00 0.00 0.00 3.51
1064 1164 0.390472 CACCTTCGCTTCTCCTCACC 60.390 60.000 0.00 0.00 0.00 4.02
1065 1165 1.219393 CCTTCGCTTCTCCTCACCC 59.781 63.158 0.00 0.00 0.00 4.61
1066 1166 1.153745 CTTCGCTTCTCCTCACCCG 60.154 63.158 0.00 0.00 0.00 5.28
1067 1167 1.595993 CTTCGCTTCTCCTCACCCGA 61.596 60.000 0.00 0.00 0.00 5.14
1068 1168 1.183030 TTCGCTTCTCCTCACCCGAA 61.183 55.000 0.00 0.00 33.05 4.30
1069 1169 0.970937 TCGCTTCTCCTCACCCGAAT 60.971 55.000 0.00 0.00 0.00 3.34
1070 1170 0.528684 CGCTTCTCCTCACCCGAATC 60.529 60.000 0.00 0.00 0.00 2.52
1071 1171 0.179070 GCTTCTCCTCACCCGAATCC 60.179 60.000 0.00 0.00 0.00 3.01
1072 1172 1.195115 CTTCTCCTCACCCGAATCCA 58.805 55.000 0.00 0.00 0.00 3.41
1073 1173 0.902531 TTCTCCTCACCCGAATCCAC 59.097 55.000 0.00 0.00 0.00 4.02
1074 1174 0.976073 TCTCCTCACCCGAATCCACC 60.976 60.000 0.00 0.00 0.00 4.61
1075 1175 1.972660 CTCCTCACCCGAATCCACCC 61.973 65.000 0.00 0.00 0.00 4.61
1076 1176 2.590092 CTCACCCGAATCCACCCC 59.410 66.667 0.00 0.00 0.00 4.95
1077 1177 1.995626 CTCACCCGAATCCACCCCT 60.996 63.158 0.00 0.00 0.00 4.79
1078 1178 1.972660 CTCACCCGAATCCACCCCTC 61.973 65.000 0.00 0.00 0.00 4.30
1079 1179 2.691252 ACCCGAATCCACCCCTCC 60.691 66.667 0.00 0.00 0.00 4.30
1110 1225 3.682292 ATTTCCCGGCCGCAGTCTC 62.682 63.158 22.85 0.00 0.00 3.36
1132 1256 1.335506 CCGGTTGGTTTTGGTTGATCG 60.336 52.381 0.00 0.00 0.00 3.69
1185 1309 1.803519 GACGAAGCACCAGAGAGCG 60.804 63.158 0.00 0.00 34.39 5.03
1612 1761 8.404765 GGCTAACTTTAGTTCTACTAGTACAGG 58.595 40.741 0.00 0.00 39.31 4.00
1659 1821 4.326205 CGCGACTGATTTGATAGTTGTTG 58.674 43.478 0.00 0.00 32.13 3.33
1677 1856 0.526211 TGCACACTCGTAGCTAGGTG 59.474 55.000 12.88 12.74 35.99 4.00
1748 1933 6.925165 GTGACTTGTTCATTCATTCATTGGTT 59.075 34.615 0.00 0.00 36.32 3.67
1826 2131 0.626916 TCCCATTTTAACGGGGAGGG 59.373 55.000 4.27 0.00 45.83 4.30
1827 2132 0.626916 CCCATTTTAACGGGGAGGGA 59.373 55.000 0.00 0.00 45.08 4.20
1828 2133 1.409661 CCCATTTTAACGGGGAGGGAG 60.410 57.143 0.00 0.00 45.08 4.30
1829 2134 1.409661 CCATTTTAACGGGGAGGGAGG 60.410 57.143 0.00 0.00 0.00 4.30
1830 2135 1.562475 CATTTTAACGGGGAGGGAGGA 59.438 52.381 0.00 0.00 0.00 3.71
1831 2136 0.986527 TTTTAACGGGGAGGGAGGAC 59.013 55.000 0.00 0.00 0.00 3.85
1832 2137 0.178897 TTTAACGGGGAGGGAGGACA 60.179 55.000 0.00 0.00 0.00 4.02
1833 2138 0.178897 TTAACGGGGAGGGAGGACAA 60.179 55.000 0.00 0.00 0.00 3.18
1834 2139 0.616679 TAACGGGGAGGGAGGACAAG 60.617 60.000 0.00 0.00 0.00 3.16
1835 2140 2.284699 CGGGGAGGGAGGACAAGT 60.285 66.667 0.00 0.00 0.00 3.16
1836 2141 1.001248 CGGGGAGGGAGGACAAGTA 59.999 63.158 0.00 0.00 0.00 2.24
1837 2142 0.398664 CGGGGAGGGAGGACAAGTAT 60.399 60.000 0.00 0.00 0.00 2.12
1838 2143 1.132500 GGGGAGGGAGGACAAGTATG 58.868 60.000 0.00 0.00 0.00 2.39
1839 2144 1.344087 GGGGAGGGAGGACAAGTATGA 60.344 57.143 0.00 0.00 0.00 2.15
1840 2145 2.695585 GGGAGGGAGGACAAGTATGAT 58.304 52.381 0.00 0.00 0.00 2.45
1841 2146 2.370189 GGGAGGGAGGACAAGTATGATG 59.630 54.545 0.00 0.00 0.00 3.07
1842 2147 3.309296 GGAGGGAGGACAAGTATGATGA 58.691 50.000 0.00 0.00 0.00 2.92
1843 2148 3.070302 GGAGGGAGGACAAGTATGATGAC 59.930 52.174 0.00 0.00 0.00 3.06
1844 2149 3.964031 GAGGGAGGACAAGTATGATGACT 59.036 47.826 0.00 0.00 0.00 3.41
1845 2150 4.366267 AGGGAGGACAAGTATGATGACTT 58.634 43.478 0.00 0.00 40.35 3.01
1846 2151 4.785376 AGGGAGGACAAGTATGATGACTTT 59.215 41.667 0.00 0.00 37.57 2.66
1847 2152 5.251700 AGGGAGGACAAGTATGATGACTTTT 59.748 40.000 0.00 0.00 37.57 2.27
1848 2153 5.355350 GGGAGGACAAGTATGATGACTTTTG 59.645 44.000 0.00 0.00 37.57 2.44
1849 2154 5.940470 GGAGGACAAGTATGATGACTTTTGT 59.060 40.000 0.00 0.00 37.57 2.83
1850 2155 6.431234 GGAGGACAAGTATGATGACTTTTGTT 59.569 38.462 0.00 0.00 37.57 2.83
1851 2156 7.040409 GGAGGACAAGTATGATGACTTTTGTTT 60.040 37.037 0.00 0.00 37.57 2.83
1852 2157 8.918202 AGGACAAGTATGATGACTTTTGTTTA 57.082 30.769 0.00 0.00 37.57 2.01
1853 2158 9.520515 AGGACAAGTATGATGACTTTTGTTTAT 57.479 29.630 0.00 0.00 37.57 1.40
1883 2189 9.840427 CATCGTCCAATATAGTTCTTTTTGTTT 57.160 29.630 0.00 0.00 0.00 2.83
1931 2239 6.071463 CGTTTTTAGTATCTTGTGTGCTGAC 58.929 40.000 0.00 0.00 0.00 3.51
1934 2242 2.693069 AGTATCTTGTGTGCTGACTGC 58.307 47.619 0.00 0.00 43.25 4.40
1961 2269 1.406180 ACTGTTGTAAAACCGTTGCCC 59.594 47.619 0.00 0.00 0.00 5.36
2102 2413 4.818835 GCTAAACTGCAGCGCGCC 62.819 66.667 30.33 14.69 41.33 6.53
2314 2816 8.462811 TGCAAACTAAAGTTCAAGACACAAATA 58.537 29.630 0.00 0.00 37.25 1.40
2362 2864 1.835494 TCGTCCTCATCTTCCGAAGT 58.165 50.000 8.01 0.00 0.00 3.01
2512 3481 5.151184 TCGAAAGACATTCCACCCATGGT 62.151 47.826 11.73 0.00 40.71 3.55
2519 3491 3.009115 CCACCCATGGTCGGAGGT 61.009 66.667 11.73 0.00 41.64 3.85
2722 4103 2.597217 CACCGCCACCCATTGTGT 60.597 61.111 0.00 0.00 43.85 3.72
2736 4117 2.408271 TTGTGTGGATCATGGCTCTC 57.592 50.000 0.00 0.00 0.00 3.20
2864 5726 4.100084 CGCTCCTCCATGCCCACA 62.100 66.667 0.00 0.00 0.00 4.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
49 56 1.937196 AAAACGCGTCGTCGATTCCG 61.937 55.000 14.44 4.47 39.99 4.30
66 73 1.799994 GCCTCGGTTTACGTGCTAAAA 59.200 47.619 0.00 0.00 44.69 1.52
67 74 1.270199 TGCCTCGGTTTACGTGCTAAA 60.270 47.619 0.00 0.00 44.69 1.85
71 81 0.947180 TTCTGCCTCGGTTTACGTGC 60.947 55.000 0.00 0.00 44.69 5.34
90 100 4.790765 TCTGTCGTCAGTTCAGATGATT 57.209 40.909 9.48 0.00 41.91 2.57
114 124 2.659757 CCATTGACGTACGTACACACTG 59.340 50.000 22.87 22.74 0.00 3.66
115 125 2.352030 CCCATTGACGTACGTACACACT 60.352 50.000 22.87 14.63 0.00 3.55
205 227 5.636121 TGACATGACACGTATGGTACTTTTC 59.364 40.000 0.00 0.00 0.00 2.29
219 255 7.273381 GCATGTAATTAAGGTTTGACATGACAC 59.727 37.037 15.08 0.00 44.37 3.67
282 318 6.817765 TCATTCTTGTAAACATCCAGGAAC 57.182 37.500 0.00 0.00 30.76 3.62
309 345 3.848019 GTGCTCGCTCAAAATACATTGTG 59.152 43.478 0.00 0.00 0.00 3.33
311 347 3.093574 CGTGCTCGCTCAAAATACATTG 58.906 45.455 0.00 0.00 0.00 2.82
352 400 4.260456 GCTTGTTTACTTGTACGTCTTGCA 60.260 41.667 0.00 0.00 0.00 4.08
360 408 3.059393 GTCGTGGGCTTGTTTACTTGTAC 60.059 47.826 0.00 0.00 0.00 2.90
430 480 2.467566 TCGGCTACCTTTTTCTGGTC 57.532 50.000 0.00 0.00 38.88 4.02
432 482 3.343617 TGATTCGGCTACCTTTTTCTGG 58.656 45.455 0.00 0.00 0.00 3.86
433 483 3.375299 CCTGATTCGGCTACCTTTTTCTG 59.625 47.826 0.00 0.00 0.00 3.02
435 485 3.344515 ACCTGATTCGGCTACCTTTTTC 58.655 45.455 0.00 0.00 0.00 2.29
437 487 4.514401 CTTACCTGATTCGGCTACCTTTT 58.486 43.478 0.00 0.00 0.00 2.27
438 488 3.118371 CCTTACCTGATTCGGCTACCTTT 60.118 47.826 0.00 0.00 0.00 3.11
440 490 2.040178 CCTTACCTGATTCGGCTACCT 58.960 52.381 0.00 0.00 0.00 3.08
441 491 1.761198 ACCTTACCTGATTCGGCTACC 59.239 52.381 0.00 0.00 0.00 3.18
442 492 3.195661 CAACCTTACCTGATTCGGCTAC 58.804 50.000 0.00 0.00 0.00 3.58
443 493 2.169769 CCAACCTTACCTGATTCGGCTA 59.830 50.000 0.00 0.00 0.00 3.93
595 670 2.608970 GATGGTGGTGACGGGATGGG 62.609 65.000 0.00 0.00 0.00 4.00
596 671 1.153168 GATGGTGGTGACGGGATGG 60.153 63.158 0.00 0.00 0.00 3.51
597 672 0.462581 CAGATGGTGGTGACGGGATG 60.463 60.000 0.00 0.00 0.00 3.51
598 673 1.626356 CCAGATGGTGGTGACGGGAT 61.626 60.000 0.00 0.00 42.17 3.85
599 674 2.290287 CCAGATGGTGGTGACGGGA 61.290 63.158 0.00 0.00 42.17 5.14
600 675 2.268920 CCAGATGGTGGTGACGGG 59.731 66.667 0.00 0.00 42.17 5.28
757 838 0.799152 TTGATGCCTACGTACGTGCG 60.799 55.000 30.25 24.57 37.94 5.34
772 853 1.745087 ACGCGCTTTGATTGGATTGAT 59.255 42.857 5.73 0.00 0.00 2.57
795 888 2.669569 CTTGCCCACCACTCACCG 60.670 66.667 0.00 0.00 0.00 4.94
807 900 1.746991 CCGAGCTTCCTTCCTTGCC 60.747 63.158 0.00 0.00 0.00 4.52
913 1009 4.641645 CAGCCAGGCGGTTGGTCA 62.642 66.667 5.55 0.00 39.73 4.02
972 1072 3.306166 GGTGCGTGCGGCTTTATATATAG 59.694 47.826 0.00 0.00 44.05 1.31
1051 1151 0.528684 GATTCGGGTGAGGAGAAGCG 60.529 60.000 0.00 0.00 0.00 4.68
1052 1152 0.179070 GGATTCGGGTGAGGAGAAGC 60.179 60.000 0.00 0.00 0.00 3.86
1053 1153 1.134670 GTGGATTCGGGTGAGGAGAAG 60.135 57.143 0.00 0.00 0.00 2.85
1054 1154 0.902531 GTGGATTCGGGTGAGGAGAA 59.097 55.000 0.00 0.00 0.00 2.87
1055 1155 0.976073 GGTGGATTCGGGTGAGGAGA 60.976 60.000 0.00 0.00 0.00 3.71
1056 1156 1.522569 GGTGGATTCGGGTGAGGAG 59.477 63.158 0.00 0.00 0.00 3.69
1057 1157 1.993391 GGGTGGATTCGGGTGAGGA 60.993 63.158 0.00 0.00 0.00 3.71
1058 1158 2.590092 GGGTGGATTCGGGTGAGG 59.410 66.667 0.00 0.00 0.00 3.86
1059 1159 1.972660 GAGGGGTGGATTCGGGTGAG 61.973 65.000 0.00 0.00 0.00 3.51
1060 1160 1.993391 GAGGGGTGGATTCGGGTGA 60.993 63.158 0.00 0.00 0.00 4.02
1061 1161 2.590092 GAGGGGTGGATTCGGGTG 59.410 66.667 0.00 0.00 0.00 4.61
1062 1162 2.691252 GGAGGGGTGGATTCGGGT 60.691 66.667 0.00 0.00 0.00 5.28
1063 1163 3.489513 GGGAGGGGTGGATTCGGG 61.490 72.222 0.00 0.00 0.00 5.14
1064 1164 3.861797 CGGGAGGGGTGGATTCGG 61.862 72.222 0.00 0.00 0.00 4.30
1065 1165 4.547367 GCGGGAGGGGTGGATTCG 62.547 72.222 0.00 0.00 0.00 3.34
1066 1166 4.191015 GGCGGGAGGGGTGGATTC 62.191 72.222 0.00 0.00 0.00 2.52
1074 1174 3.974757 GTACGATCGGCGGGAGGG 61.975 72.222 20.98 0.00 46.49 4.30
1075 1175 2.083835 AATGTACGATCGGCGGGAGG 62.084 60.000 20.98 0.00 46.49 4.30
1076 1176 0.249322 AAATGTACGATCGGCGGGAG 60.249 55.000 20.98 0.42 46.49 4.30
1077 1177 0.249155 GAAATGTACGATCGGCGGGA 60.249 55.000 20.98 0.00 46.49 5.14
1078 1178 1.219522 GGAAATGTACGATCGGCGGG 61.220 60.000 20.98 0.00 46.49 6.13
1079 1179 1.219522 GGGAAATGTACGATCGGCGG 61.220 60.000 20.98 0.00 46.49 6.13
1088 1203 2.437002 TGCGGCCGGGAAATGTAC 60.437 61.111 29.38 7.00 0.00 2.90
1120 1244 3.663995 TCGACTACCGATCAACCAAAA 57.336 42.857 0.00 0.00 43.23 2.44
1132 1256 1.683917 AGCTGTGATGGATCGACTACC 59.316 52.381 0.00 0.00 0.00 3.18
1159 1283 2.109126 GGTGCTTCGTCATGGAGGC 61.109 63.158 0.00 0.00 39.28 4.70
1280 1410 1.377202 CACATGAACTCCCCACCGG 60.377 63.158 0.00 0.00 0.00 5.28
1281 1411 2.040544 GCACATGAACTCCCCACCG 61.041 63.158 0.00 0.00 0.00 4.94
1282 1412 0.539438 TTGCACATGAACTCCCCACC 60.539 55.000 0.00 0.00 0.00 4.61
1612 1761 2.763448 ACTACAGAGCCAGATCAGAACC 59.237 50.000 0.00 0.00 0.00 3.62
1659 1821 0.802607 GCACCTAGCTACGAGTGTGC 60.803 60.000 12.85 11.76 41.75 4.57
1677 1856 3.374988 TGAATGAATGAACCACGATCAGC 59.625 43.478 0.00 0.00 0.00 4.26
1769 2067 4.739046 AAAGAGACGAGCAAATCAGTTG 57.261 40.909 0.00 0.00 40.50 3.16
1826 2131 7.440523 AACAAAAGTCATCATACTTGTCCTC 57.559 36.000 0.00 0.00 39.62 3.71
1827 2132 7.823745 AAACAAAAGTCATCATACTTGTCCT 57.176 32.000 0.00 0.00 39.62 3.85
1857 2162 9.840427 AAACAAAAAGAACTATATTGGACGATG 57.160 29.630 0.00 0.00 0.00 3.84
1883 2189 9.280174 ACGGTAATAAAGTGAAAAGAAGAATGA 57.720 29.630 0.00 0.00 0.00 2.57
1902 2208 7.389607 AGCACACAAGATACTAAAAACGGTAAT 59.610 33.333 0.00 0.00 0.00 1.89
1905 2211 5.049680 CAGCACACAAGATACTAAAAACGGT 60.050 40.000 0.00 0.00 0.00 4.83
1906 2212 5.178623 TCAGCACACAAGATACTAAAAACGG 59.821 40.000 0.00 0.00 0.00 4.44
1907 2213 6.071463 GTCAGCACACAAGATACTAAAAACG 58.929 40.000 0.00 0.00 0.00 3.60
1908 2214 7.072030 CAGTCAGCACACAAGATACTAAAAAC 58.928 38.462 0.00 0.00 0.00 2.43
1931 2239 1.155889 TTACAACAGTGGCATCGCAG 58.844 50.000 0.00 0.00 0.00 5.18
1934 2242 2.664424 CGGTTTTACAACAGTGGCATCG 60.664 50.000 0.00 0.00 34.15 3.84
1961 2269 3.770263 AAGTGCATTCGACATTGATGG 57.230 42.857 0.00 0.00 0.00 3.51
2035 2345 3.342627 CAAACCGGTCGAAGCGCA 61.343 61.111 8.04 0.00 37.85 6.09
2075 2385 1.809619 CAGTTTAGCGCGGCTGCTA 60.810 57.895 17.03 17.99 45.14 3.49
2110 2429 1.128147 GTATTCTTGCGCGTTGCTGC 61.128 55.000 8.43 0.00 46.63 5.25
2314 2816 7.391833 ACGAGAAAGAGGATTGCTATTTCTTTT 59.608 33.333 23.10 13.53 39.61 2.27
2322 2824 4.438880 CGAAGACGAGAAAGAGGATTGCTA 60.439 45.833 0.00 0.00 42.66 3.49
2324 2826 2.600867 CGAAGACGAGAAAGAGGATTGC 59.399 50.000 0.00 0.00 42.66 3.56
2362 2864 1.317431 TTCGGAGGCGGAAGAATCGA 61.317 55.000 0.00 0.00 0.00 3.59
2722 4103 2.577563 TCCAAAAGAGAGCCATGATCCA 59.422 45.455 0.00 0.00 0.00 3.41
2736 4117 5.334414 CCGTGAAGAAGTCTTGATCCAAAAG 60.334 44.000 0.00 0.00 36.11 2.27
2864 5726 1.213926 GTGGCATTGGAGGAGAGGAAT 59.786 52.381 0.00 0.00 0.00 3.01


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

AutoCloner maintained by Alex Coulton.