Multiple sequence alignment - TraesCS6D01G050100

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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 TraesCS6D01G050100 chr6D 100.000 4277 0 0 1 4277 24233288 24229012 0.000000e+00 7899.0
1 TraesCS6D01G050100 chr6D 87.476 1054 77 19 1887 2910 24262722 24261694 0.000000e+00 1164.0
2 TraesCS6D01G050100 chr6D 90.769 195 12 2 3058 3252 24892876 24893064 5.490000e-64 255.0
3 TraesCS6D01G050100 chr6D 76.744 473 88 16 488 950 305618826 305618366 1.190000e-60 244.0
4 TraesCS6D01G050100 chr6D 86.239 109 12 3 4167 4272 24882542 24882650 9.720000e-22 115.0
5 TraesCS6D01G050100 chr6D 80.576 139 23 4 1297 1432 24263319 24263182 2.100000e-18 104.0
6 TraesCS6D01G050100 chr6D 92.857 70 4 1 2906 2974 24261639 24261570 2.720000e-17 100.0
7 TraesCS6D01G050100 chr6D 89.231 65 3 2 1826 1887 410109209 410109272 1.280000e-10 78.7
8 TraesCS6D01G050100 chr6B 90.723 3126 136 42 942 4028 39199946 39196936 0.000000e+00 4024.0
9 TraesCS6D01G050100 chr6B 86.368 1049 86 21 1885 2901 39339895 39338872 0.000000e+00 1092.0
10 TraesCS6D01G050100 chr6B 94.106 492 25 3 1 491 39201013 39200525 0.000000e+00 745.0
11 TraesCS6D01G050100 chr6B 90.313 351 34 0 489 839 39200331 39199981 1.080000e-125 460.0
12 TraesCS6D01G050100 chr6B 83.565 359 40 7 1104 1459 336900597 336900255 6.900000e-83 318.0
13 TraesCS6D01G050100 chr6B 96.753 154 3 2 4019 4171 39196658 39196506 5.490000e-64 255.0
14 TraesCS6D01G050100 chr6B 75.602 623 70 36 1271 1830 39340501 39339898 2.570000e-57 233.0
15 TraesCS6D01G050100 chr6B 96.429 112 4 0 4166 4277 39196481 39196370 7.300000e-43 185.0
16 TraesCS6D01G050100 chr6B 90.769 65 2 2 1826 1887 661073192 661073255 2.740000e-12 84.2
17 TraesCS6D01G050100 chr6A 92.335 2544 78 27 1654 4171 22696668 22694216 0.000000e+00 3509.0
18 TraesCS6D01G050100 chr6A 88.107 1051 79 15 489 1531 22697727 22696715 0.000000e+00 1206.0
19 TraesCS6D01G050100 chr6A 87.393 1047 78 19 1887 2904 22804477 22803456 0.000000e+00 1153.0
20 TraesCS6D01G050100 chr6A 86.014 429 41 5 64 491 22698331 22697921 3.930000e-120 442.0
21 TraesCS6D01G050100 chr6A 89.840 187 13 2 3078 3264 23332045 23331865 7.150000e-58 235.0
22 TraesCS6D01G050100 chr6A 98.214 112 2 0 4166 4277 22694191 22694080 3.370000e-46 196.0
23 TraesCS6D01G050100 chr6A 88.350 103 11 1 1684 1786 583766018 583765917 5.810000e-24 122.0
24 TraesCS6D01G050100 chr6A 77.340 203 34 6 2908 3101 22803395 22803196 4.520000e-20 110.0
25 TraesCS6D01G050100 chr3A 80.584 1267 148 51 1907 3126 601555418 601556633 0.000000e+00 887.0
26 TraesCS6D01G050100 chr3A 85.644 202 24 2 3128 3329 601556537 601556733 1.560000e-49 207.0
27 TraesCS6D01G050100 chr3A 88.889 81 7 2 3477 3556 601556925 601557004 9.790000e-17 99.0
28 TraesCS6D01G050100 chr3A 81.905 105 11 4 2627 2725 601556196 601556298 9.860000e-12 82.4
29 TraesCS6D01G050100 chr3B 89.402 585 60 2 1910 2493 607385486 607384903 0.000000e+00 736.0
30 TraesCS6D01G050100 chr3B 77.370 654 78 41 2492 3126 607384877 607384275 1.480000e-84 324.0
31 TraesCS6D01G050100 chr3B 86.139 202 23 2 3128 3329 607384371 607384175 3.350000e-51 213.0
32 TraesCS6D01G050100 chr3B 88.462 78 7 2 3480 3556 607383980 607383904 4.550000e-15 93.5
33 TraesCS6D01G050100 chr3B 80.952 105 12 4 2627 2725 607384712 607384610 4.590000e-10 76.8
34 TraesCS6D01G050100 chr5B 84.447 733 91 12 1885 2596 166168017 166167287 0.000000e+00 701.0
35 TraesCS6D01G050100 chr5B 84.311 733 92 12 1885 2596 165776682 165775952 0.000000e+00 695.0
36 TraesCS6D01G050100 chr5B 80.383 418 70 10 544 957 682461927 682461518 1.490000e-79 307.0
37 TraesCS6D01G050100 chr5B 79.187 418 77 9 544 957 422552093 422552504 9.050000e-72 281.0
38 TraesCS6D01G050100 chr5B 87.417 151 17 2 544 692 682421737 682421587 5.690000e-39 172.0
39 TraesCS6D01G050100 chr5B 92.857 56 4 0 1830 1885 427246219 427246164 9.860000e-12 82.4
40 TraesCS6D01G050100 chr5A 84.375 736 87 10 1885 2596 465111016 465111747 0.000000e+00 697.0
41 TraesCS6D01G050100 chr2A 84.375 736 87 11 1885 2596 425813415 425812684 0.000000e+00 697.0
42 TraesCS6D01G050100 chr2A 78.947 437 80 12 527 957 523447093 523447523 1.950000e-73 287.0
43 TraesCS6D01G050100 chr2A 88.136 59 6 1 1830 1888 36408566 36408509 7.670000e-08 69.4
44 TraesCS6D01G050100 chr7A 83.051 472 71 8 489 957 700095877 700096342 1.840000e-113 420.0
45 TraesCS6D01G050100 chr7A 82.857 315 50 4 643 957 700097542 700097232 3.260000e-71 279.0
46 TraesCS6D01G050100 chr4A 89.073 302 29 3 1084 1383 696691175 696691474 5.220000e-99 372.0
47 TraesCS6D01G050100 chr4A 88.079 302 32 3 1084 1383 696647188 696647487 5.260000e-94 355.0
48 TraesCS6D01G050100 chr4A 88.699 292 29 3 1094 1383 696667135 696667424 1.890000e-93 353.0
49 TraesCS6D01G050100 chr4A 91.250 240 14 3 1577 1815 696668127 696668360 1.920000e-83 320.0
50 TraesCS6D01G050100 chr4A 91.250 240 14 3 1577 1815 696692177 696692410 1.920000e-83 320.0
51 TraesCS6D01G050100 chr4A 90.204 245 17 3 1577 1820 696648189 696648427 3.210000e-81 313.0
52 TraesCS6D01G050100 chr4A 82.313 147 12 7 1686 1830 541116020 541115886 9.720000e-22 115.0
53 TraesCS6D01G050100 chr3D 76.723 653 86 37 2492 3126 459468166 459467562 1.930000e-78 303.0
54 TraesCS6D01G050100 chr3D 86.802 197 21 2 3133 3329 459467653 459467462 9.310000e-52 215.0
55 TraesCS6D01G050100 chr3D 89.744 78 6 2 3480 3556 459467191 459467115 9.790000e-17 99.0
56 TraesCS6D01G050100 chr3D 81.905 105 11 4 2627 2725 459468001 459467899 9.860000e-12 82.4
57 TraesCS6D01G050100 chr3D 89.231 65 3 2 1826 1887 501289622 501289685 1.280000e-10 78.7
58 TraesCS6D01G050100 chr4D 75.113 442 90 18 527 957 16508741 16508309 5.650000e-44 189.0
59 TraesCS6D01G050100 chr1B 93.269 104 7 0 1720 1823 179580991 179580888 2.060000e-33 154.0
60 TraesCS6D01G050100 chr5D 94.643 56 3 0 1830 1885 361647900 361647845 2.120000e-13 87.9
61 TraesCS6D01G050100 chr2B 90.769 65 6 0 4208 4272 788835886 788835950 2.120000e-13 87.9
62 TraesCS6D01G050100 chr7B 89.231 65 3 2 1826 1887 537569991 537570054 1.280000e-10 78.7
63 TraesCS6D01G050100 chr7D 97.297 37 1 0 1784 1820 109922144 109922180 3.570000e-06 63.9
64 TraesCS6D01G050100 chr7D 92.500 40 3 0 1784 1823 60105566 60105527 1.660000e-04 58.4


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 TraesCS6D01G050100 chr6D 24229012 24233288 4276 True 7899.00 7899 100.000000 1 4277 1 chr6D.!!$R1 4276
1 TraesCS6D01G050100 chr6D 24261570 24263319 1749 True 456.00 1164 86.969667 1297 2974 3 chr6D.!!$R3 1677
2 TraesCS6D01G050100 chr6B 39196370 39201013 4643 True 1133.80 4024 93.664800 1 4277 5 chr6B.!!$R2 4276
3 TraesCS6D01G050100 chr6B 39338872 39340501 1629 True 662.50 1092 80.985000 1271 2901 2 chr6B.!!$R3 1630
4 TraesCS6D01G050100 chr6A 22694080 22698331 4251 True 1338.25 3509 91.167500 64 4277 4 chr6A.!!$R3 4213
5 TraesCS6D01G050100 chr6A 22803196 22804477 1281 True 631.50 1153 82.366500 1887 3101 2 chr6A.!!$R4 1214
6 TraesCS6D01G050100 chr3A 601555418 601557004 1586 False 318.85 887 84.255500 1907 3556 4 chr3A.!!$F1 1649
7 TraesCS6D01G050100 chr3B 607383904 607385486 1582 True 288.66 736 84.465000 1910 3556 5 chr3B.!!$R1 1646
8 TraesCS6D01G050100 chr5B 166167287 166168017 730 True 701.00 701 84.447000 1885 2596 1 chr5B.!!$R2 711
9 TraesCS6D01G050100 chr5B 165775952 165776682 730 True 695.00 695 84.311000 1885 2596 1 chr5B.!!$R1 711
10 TraesCS6D01G050100 chr5A 465111016 465111747 731 False 697.00 697 84.375000 1885 2596 1 chr5A.!!$F1 711
11 TraesCS6D01G050100 chr2A 425812684 425813415 731 True 697.00 697 84.375000 1885 2596 1 chr2A.!!$R2 711
12 TraesCS6D01G050100 chr4A 696691175 696692410 1235 False 346.00 372 90.161500 1084 1815 2 chr4A.!!$F3 731
13 TraesCS6D01G050100 chr4A 696667135 696668360 1225 False 336.50 353 89.974500 1094 1815 2 chr4A.!!$F2 721
14 TraesCS6D01G050100 chr4A 696647188 696648427 1239 False 334.00 355 89.141500 1084 1820 2 chr4A.!!$F1 736

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
663 865 0.035056 CGAGCATTGGGGGAAACTCT 60.035 55.0 0.00 0.0 0.00 3.24 F
1535 2335 0.036732 AGCATGTGTACACAGTGGGG 59.963 55.0 30.65 18.6 45.48 4.96 F
1540 2340 0.251165 GTGTACACAGTGGGGGCATT 60.251 55.0 21.14 0.0 0.00 3.56 F
2703 3686 0.039764 ACCTAAAAAGAGGGGCAGGC 59.960 55.0 0.00 0.0 41.36 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1558 2358 0.037790 TTGCCAAGTAAAATGCCCGC 60.038 50.0 0.0 0.0 0.0 6.13 R
2697 3680 0.398318 ATATCCTTTCGAGGCCTGCC 59.602 55.0 12.0 0.0 0.0 4.85 R
2965 4018 0.671796 GCTGGGTTGGGTTGTACAAC 59.328 55.0 27.2 27.2 45.6 3.32 R
4074 5534 0.178992 TGGTTCTTGGTTGCTCTGGG 60.179 55.0 0.0 0.0 0.0 4.45 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
88 89 1.603236 CTCTGCTCGAGCTTCAGGGT 61.603 60.000 35.27 0.00 42.66 4.34
225 230 1.616327 CACCACCATCCCCTCCAGA 60.616 63.158 0.00 0.00 0.00 3.86
278 283 1.154225 CATTTCCTGCGTTCACGGC 60.154 57.895 0.81 0.00 40.23 5.68
332 338 2.041366 GAGATGCGCTCTTTTCGGCC 62.041 60.000 9.73 0.00 40.61 6.13
351 357 0.962356 CCGTTGGCTCATTTGGCTCT 60.962 55.000 0.00 0.00 0.00 4.09
422 428 3.640000 CGTTCATCCCGGCGCATC 61.640 66.667 10.83 0.00 0.00 3.91
528 730 1.341531 ACCTCCTCTTCGACAGTGTTG 59.658 52.381 3.89 3.89 0.00 3.33
530 732 0.318699 TCCTCTTCGACAGTGTTGCG 60.319 55.000 5.55 1.65 0.00 4.85
532 734 1.670087 CCTCTTCGACAGTGTTGCGAT 60.670 52.381 7.77 0.00 34.52 4.58
573 775 4.757149 GGCTAAACCCTACATCTTATGCTG 59.243 45.833 0.00 0.00 0.00 4.41
579 781 1.797046 CTACATCTTATGCTGGCAGCG 59.203 52.381 32.12 19.10 46.26 5.18
613 815 1.343465 GTGTCGTCCCCTTCTTGAAGA 59.657 52.381 11.53 0.00 0.00 2.87
663 865 0.035056 CGAGCATTGGGGGAAACTCT 60.035 55.000 0.00 0.00 0.00 3.24
719 921 6.017192 TGTCTAGGTGTCACTATTCTCCTTT 58.983 40.000 2.35 0.00 0.00 3.11
780 982 1.574702 GGCTTCGGAGTTTTGGTCGG 61.575 60.000 0.00 0.00 0.00 4.79
791 993 1.600023 TTTGGTCGGCTAGTTGTTGG 58.400 50.000 0.00 0.00 0.00 3.77
813 1015 1.425066 TGGATTGCTTCTCCAGTTGGT 59.575 47.619 0.00 0.00 37.87 3.67
851 1053 0.110238 CGTTGTTTGGGTCGAGCATG 60.110 55.000 17.59 0.00 0.00 4.06
862 1064 3.376540 GGTCGAGCATGTTATGTCTCTC 58.623 50.000 10.30 0.00 33.90 3.20
871 1073 2.097629 TGTTATGTCTCTCCGCTTCGAG 59.902 50.000 0.00 0.00 0.00 4.04
886 1088 0.108662 TCGAGCATCATGTTCACGCT 60.109 50.000 2.10 0.00 35.14 5.07
887 1089 0.723414 CGAGCATCATGTTCACGCTT 59.277 50.000 2.10 0.00 31.86 4.68
891 1093 3.599343 AGCATCATGTTCACGCTTCTTA 58.401 40.909 0.00 0.00 0.00 2.10
892 1094 4.194640 AGCATCATGTTCACGCTTCTTAT 58.805 39.130 0.00 0.00 0.00 1.73
893 1095 4.637534 AGCATCATGTTCACGCTTCTTATT 59.362 37.500 0.00 0.00 0.00 1.40
921 1124 7.361971 CCATGTCATGTGTTTTACAAGCTCATA 60.362 37.037 11.84 0.00 43.77 2.15
926 1129 9.098355 TCATGTGTTTTACAAGCTCATATACTC 57.902 33.333 0.00 0.00 43.77 2.59
937 1140 9.757227 ACAAGCTCATATACTCATTCTAACTTC 57.243 33.333 0.00 0.00 0.00 3.01
951 1154 8.820933 TCATTCTAACTTCTTCTATCAAATGCG 58.179 33.333 0.00 0.00 0.00 4.73
959 1162 7.281774 ACTTCTTCTATCAAATGCGATGATTGT 59.718 33.333 4.33 0.00 38.44 2.71
1169 1379 4.514577 ACGCATCTTCCGCCGGAG 62.515 66.667 5.05 0.00 31.21 4.63
1235 1445 3.855853 GCCCTCCCTCTTCCTCGC 61.856 72.222 0.00 0.00 0.00 5.03
1237 1447 2.364317 CCTCCCTCTTCCTCGCCA 60.364 66.667 0.00 0.00 0.00 5.69
1267 1477 2.363795 CCACCGCCCTCCTAGACA 60.364 66.667 0.00 0.00 0.00 3.41
1268 1478 1.762460 CCACCGCCCTCCTAGACAT 60.762 63.158 0.00 0.00 0.00 3.06
1279 1489 0.540830 CCTAGACATCCCCTCCTCGG 60.541 65.000 0.00 0.00 0.00 4.63
1404 2075 1.216444 CTGCCGCTTGAGCTACTGA 59.784 57.895 1.07 0.00 39.32 3.41
1429 2128 1.232621 TGCTGCTGCTTGTGCTACTG 61.233 55.000 17.00 0.00 40.48 2.74
1430 2129 1.500844 CTGCTGCTTGTGCTACTGC 59.499 57.895 0.00 0.00 40.48 4.40
1434 2133 1.077123 CTGCTTGTGCTACTGCTCTG 58.923 55.000 0.00 0.00 40.48 3.35
1438 2137 2.487934 CTTGTGCTACTGCTCTGTTGT 58.512 47.619 0.00 0.00 40.48 3.32
1439 2138 1.869774 TGTGCTACTGCTCTGTTGTG 58.130 50.000 0.00 0.00 40.48 3.33
1440 2139 0.514691 GTGCTACTGCTCTGTTGTGC 59.485 55.000 0.00 0.00 40.48 4.57
1441 2140 0.603707 TGCTACTGCTCTGTTGTGCC 60.604 55.000 0.00 0.00 40.48 5.01
1442 2141 0.603707 GCTACTGCTCTGTTGTGCCA 60.604 55.000 0.00 0.00 36.03 4.92
1443 2142 1.947678 GCTACTGCTCTGTTGTGCCAT 60.948 52.381 0.00 0.00 36.03 4.40
1444 2143 1.736126 CTACTGCTCTGTTGTGCCATG 59.264 52.381 0.00 0.00 32.27 3.66
1445 2144 0.892358 ACTGCTCTGTTGTGCCATGG 60.892 55.000 7.63 7.63 32.27 3.66
1446 2145 0.607217 CTGCTCTGTTGTGCCATGGA 60.607 55.000 18.40 0.00 32.27 3.41
1447 2146 0.038599 TGCTCTGTTGTGCCATGGAT 59.961 50.000 18.40 0.00 32.27 3.41
1448 2147 0.454600 GCTCTGTTGTGCCATGGATG 59.545 55.000 18.40 0.00 0.00 3.51
1458 2157 3.196040 CCATGGATGGGTGGTTCTG 57.804 57.895 5.56 0.00 44.31 3.02
1460 2159 0.323633 CATGGATGGGTGGTTCTGCA 60.324 55.000 0.00 0.00 0.00 4.41
1535 2335 0.036732 AGCATGTGTACACAGTGGGG 59.963 55.000 30.65 18.60 45.48 4.96
1536 2336 0.960364 GCATGTGTACACAGTGGGGG 60.960 60.000 30.65 17.09 45.48 5.40
1537 2337 0.960364 CATGTGTACACAGTGGGGGC 60.960 60.000 30.65 1.15 45.48 5.80
1538 2338 1.422977 ATGTGTACACAGTGGGGGCA 61.423 55.000 30.65 7.13 45.48 5.36
1539 2339 1.378762 GTGTACACAGTGGGGGCAT 59.621 57.895 21.14 0.00 0.00 4.40
1540 2340 0.251165 GTGTACACAGTGGGGGCATT 60.251 55.000 21.14 0.00 0.00 3.56
1541 2341 0.480690 TGTACACAGTGGGGGCATTT 59.519 50.000 5.31 0.00 0.00 2.32
1542 2342 1.133325 TGTACACAGTGGGGGCATTTT 60.133 47.619 5.31 0.00 0.00 1.82
1543 2343 1.967779 GTACACAGTGGGGGCATTTTT 59.032 47.619 5.31 0.00 0.00 1.94
1544 2344 1.047801 ACACAGTGGGGGCATTTTTC 58.952 50.000 5.31 0.00 0.00 2.29
1545 2345 0.321346 CACAGTGGGGGCATTTTTCC 59.679 55.000 0.00 0.00 0.00 3.13
1546 2346 0.835971 ACAGTGGGGGCATTTTTCCC 60.836 55.000 0.00 0.00 43.15 3.97
1555 2355 3.648739 GGGCATTTTTCCCCCTAATACA 58.351 45.455 0.00 0.00 37.81 2.29
1556 2356 3.386726 GGGCATTTTTCCCCCTAATACAC 59.613 47.826 0.00 0.00 37.81 2.90
1557 2357 4.027437 GGCATTTTTCCCCCTAATACACA 58.973 43.478 0.00 0.00 0.00 3.72
1558 2358 4.099419 GGCATTTTTCCCCCTAATACACAG 59.901 45.833 0.00 0.00 0.00 3.66
1559 2359 4.441495 GCATTTTTCCCCCTAATACACAGC 60.441 45.833 0.00 0.00 0.00 4.40
1560 2360 2.702592 TTTCCCCCTAATACACAGCG 57.297 50.000 0.00 0.00 0.00 5.18
1561 2361 0.834612 TTCCCCCTAATACACAGCGG 59.165 55.000 0.00 0.00 0.00 5.52
1562 2362 1.052124 TCCCCCTAATACACAGCGGG 61.052 60.000 0.00 0.00 33.07 6.13
1595 2441 5.263599 TGGCAACTGATATTTGTGGAGATT 58.736 37.500 0.00 0.00 37.61 2.40
1636 2482 8.893727 GTTGTTTGTAGATAGTGCTTAATGGAT 58.106 33.333 0.00 0.00 0.00 3.41
1768 2674 6.126594 TGGTTAATATCCCAAGTGTTCCCTAG 60.127 42.308 0.00 0.00 0.00 3.02
1786 2692 5.538053 TCCCTAGATGAAAGTAGAGATGCAG 59.462 44.000 0.00 0.00 0.00 4.41
1893 2801 2.224305 ACAGAGGGAGTACAAGTGTTGC 60.224 50.000 0.00 0.00 0.00 4.17
1963 2871 4.875544 TGTAGCTGTGAAAGTGTTTGAC 57.124 40.909 0.00 0.00 0.00 3.18
2054 2972 2.103941 CTCCTCCAGGATGTTTCTAGCC 59.896 54.545 0.00 0.00 44.46 3.93
2314 3232 3.643792 GGAGACAAGTACTATGCAGGGAT 59.356 47.826 0.00 0.00 0.00 3.85
2327 3245 2.500098 TGCAGGGATAGTTGTCAGGTAC 59.500 50.000 0.00 0.00 0.00 3.34
2369 3289 3.260884 ACACCGTTGTCTATGAAGATGGT 59.739 43.478 0.00 0.00 33.30 3.55
2688 3671 5.130975 AGTGCATCAGGTGATATTCAACCTA 59.869 40.000 5.62 0.00 33.71 3.08
2692 3675 7.395772 TGCATCAGGTGATATTCAACCTAAAAA 59.604 33.333 5.62 0.00 33.71 1.94
2693 3676 7.917505 GCATCAGGTGATATTCAACCTAAAAAG 59.082 37.037 5.62 0.00 33.71 2.27
2695 3678 8.792830 TCAGGTGATATTCAACCTAAAAAGAG 57.207 34.615 5.62 0.00 33.71 2.85
2696 3679 7.829211 TCAGGTGATATTCAACCTAAAAAGAGG 59.171 37.037 5.62 0.00 42.89 3.69
2697 3680 7.067494 CAGGTGATATTCAACCTAAAAAGAGGG 59.933 40.741 5.62 0.00 41.36 4.30
2698 3681 6.321435 GGTGATATTCAACCTAAAAAGAGGGG 59.679 42.308 0.00 0.00 41.36 4.79
2699 3682 5.891551 TGATATTCAACCTAAAAAGAGGGGC 59.108 40.000 0.00 0.00 41.36 5.80
2700 3683 3.603965 TTCAACCTAAAAAGAGGGGCA 57.396 42.857 0.00 0.00 41.36 5.36
2701 3684 3.154827 TCAACCTAAAAAGAGGGGCAG 57.845 47.619 0.00 0.00 41.36 4.85
2702 3685 2.171003 CAACCTAAAAAGAGGGGCAGG 58.829 52.381 0.00 0.00 41.36 4.85
2703 3686 0.039764 ACCTAAAAAGAGGGGCAGGC 59.960 55.000 0.00 0.00 41.36 4.85
2704 3687 0.684479 CCTAAAAAGAGGGGCAGGCC 60.684 60.000 3.77 3.77 32.39 5.19
2705 3688 0.332972 CTAAAAAGAGGGGCAGGCCT 59.667 55.000 13.81 0.00 36.10 5.19
2706 3689 0.331616 TAAAAAGAGGGGCAGGCCTC 59.668 55.000 13.81 7.89 36.66 4.70
2707 3690 2.771328 AAAAAGAGGGGCAGGCCTCG 62.771 60.000 13.81 0.00 42.67 4.63
2708 3691 4.722535 AAGAGGGGCAGGCCTCGA 62.723 66.667 13.81 0.00 42.67 4.04
2709 3692 4.722535 AGAGGGGCAGGCCTCGAA 62.723 66.667 13.81 0.00 42.67 3.71
2710 3693 3.717294 GAGGGGCAGGCCTCGAAA 61.717 66.667 13.81 0.00 42.67 3.46
2711 3694 3.689002 GAGGGGCAGGCCTCGAAAG 62.689 68.421 13.81 0.00 42.67 2.62
2712 3695 4.803908 GGGGCAGGCCTCGAAAGG 62.804 72.222 13.81 0.00 46.44 3.11
2713 3696 3.717294 GGGCAGGCCTCGAAAGGA 61.717 66.667 0.00 0.00 46.67 3.36
2714 3697 2.592308 GGCAGGCCTCGAAAGGAT 59.408 61.111 0.00 0.00 46.67 3.24
2715 3698 1.696097 GGGCAGGCCTCGAAAGGATA 61.696 60.000 0.00 0.00 46.67 2.59
2716 3699 0.398318 GGCAGGCCTCGAAAGGATAT 59.602 55.000 0.00 0.00 46.67 1.63
2720 3703 3.330267 CAGGCCTCGAAAGGATATAAGC 58.670 50.000 0.00 0.00 46.67 3.09
2793 3785 6.126038 ACCTGGAGAGAAGAGTATTGATAGGA 60.126 42.308 0.00 0.00 0.00 2.94
2807 3799 8.928448 AGTATTGATAGGAGCAAATTAGAGACA 58.072 33.333 0.00 0.00 0.00 3.41
2965 4018 2.035674 CGACGCTAGCTTTCAATGTACG 60.036 50.000 13.93 4.13 0.00 3.67
3108 4173 3.778954 AGGAGTTCTCCTTGTGGAAAG 57.221 47.619 14.85 0.00 42.66 2.62
3217 4283 2.755103 CCTTGTGGAAATGGAACCTAGC 59.245 50.000 0.00 0.00 34.57 3.42
3401 4478 3.123621 GCGAATTTATCTCACCTATGCGG 59.876 47.826 0.00 0.00 39.35 5.69
3482 4570 6.581919 CGAATCTACAAGAGATGTATCAGCAG 59.418 42.308 0.00 0.00 44.68 4.24
3504 4639 1.743252 CCTTGCTTCCTGAGACGGC 60.743 63.158 0.00 0.00 0.00 5.68
3689 4826 3.885297 AGGAAAACAGAACACCATGACAG 59.115 43.478 0.00 0.00 0.00 3.51
3768 4908 4.856664 AGATGATACGATACAACGGTGAC 58.143 43.478 7.88 0.00 37.61 3.67
3852 4992 4.522297 GTTCAGAGAAGAACACACACAC 57.478 45.455 0.00 0.00 45.53 3.82
3955 5104 1.489481 TCAGGTGAGATAGTGGCTGG 58.511 55.000 0.00 0.00 0.00 4.85
4060 5520 7.661536 TTAGTACTTTCTATGTCCAGAGCAT 57.338 36.000 0.00 0.00 0.00 3.79
4061 5521 8.762481 TTAGTACTTTCTATGTCCAGAGCATA 57.238 34.615 0.00 0.00 0.00 3.14
4062 5522 7.847711 AGTACTTTCTATGTCCAGAGCATAT 57.152 36.000 0.00 0.00 0.00 1.78
4063 5523 7.891561 AGTACTTTCTATGTCCAGAGCATATC 58.108 38.462 0.00 0.00 0.00 1.63
4064 5524 6.737720 ACTTTCTATGTCCAGAGCATATCA 57.262 37.500 0.00 0.00 0.00 2.15
4065 5525 7.129457 ACTTTCTATGTCCAGAGCATATCAA 57.871 36.000 0.00 0.00 0.00 2.57
4066 5526 7.568349 ACTTTCTATGTCCAGAGCATATCAAA 58.432 34.615 0.00 0.00 0.00 2.69
4067 5527 8.216423 ACTTTCTATGTCCAGAGCATATCAAAT 58.784 33.333 0.00 0.00 0.00 2.32
4068 5528 8.985315 TTTCTATGTCCAGAGCATATCAAATT 57.015 30.769 0.00 0.00 0.00 1.82
4129 5589 9.793252 GTTCTAGCACAATATGAAAAACATCAT 57.207 29.630 0.00 0.00 42.52 2.45
4184 5675 1.469917 CAGCAACAACTTCGCAACAG 58.530 50.000 0.00 0.00 0.00 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
332 338 0.962356 AGAGCCAAATGAGCCAACGG 60.962 55.000 0.00 0.00 0.00 4.44
342 348 1.844687 GAGGAGCCAAAGAGCCAAAT 58.155 50.000 0.00 0.00 0.00 2.32
351 357 3.296709 GAGACGCCGAGGAGCCAAA 62.297 63.158 0.00 0.00 0.00 3.28
408 414 1.530655 TAGAGATGCGCCGGGATGA 60.531 57.895 4.18 0.00 0.00 2.92
417 423 0.317436 GCCAGAGACGTAGAGATGCG 60.317 60.000 0.00 0.00 0.00 4.73
421 427 2.467962 CGTGCCAGAGACGTAGAGA 58.532 57.895 0.00 0.00 32.06 3.10
451 457 0.912486 AAAGGAGATGGAAGGGGACG 59.088 55.000 0.00 0.00 0.00 4.79
528 730 1.227060 GCCAATTCCAAGCCATCGC 60.227 57.895 0.00 0.00 0.00 4.58
682 884 3.883489 CACCTAGACACCATCGTCATCTA 59.117 47.826 0.00 0.00 38.43 1.98
719 921 3.625764 GCAACCAAGATAACGCCTTCATA 59.374 43.478 0.00 0.00 0.00 2.15
731 933 3.127533 GCCGCGAGCAACCAAGAT 61.128 61.111 8.23 0.00 42.97 2.40
780 982 2.558359 AGCAATCCAACCAACAACTAGC 59.442 45.455 0.00 0.00 0.00 3.42
791 993 2.229784 CCAACTGGAGAAGCAATCCAAC 59.770 50.000 6.10 0.00 46.04 3.77
813 1015 2.223876 ACGAAGAACACGGCTAAACTCA 60.224 45.455 0.00 0.00 34.93 3.41
851 1053 2.722071 CTCGAAGCGGAGAGACATAAC 58.278 52.381 0.06 0.00 36.65 1.89
862 1064 0.302890 GAACATGATGCTCGAAGCGG 59.697 55.000 0.00 0.00 46.26 5.52
871 1073 2.907910 AAGAAGCGTGAACATGATGC 57.092 45.000 0.00 0.00 0.00 3.91
886 1088 9.906660 GTAAAACACATGACATGGAAATAAGAA 57.093 29.630 19.39 0.00 33.60 2.52
887 1089 9.072375 TGTAAAACACATGACATGGAAATAAGA 57.928 29.630 19.39 0.00 30.04 2.10
891 1093 6.646240 GCTTGTAAAACACATGACATGGAAAT 59.354 34.615 19.39 4.64 36.90 2.17
892 1094 5.982516 GCTTGTAAAACACATGACATGGAAA 59.017 36.000 19.39 1.94 36.90 3.13
893 1095 5.301551 AGCTTGTAAAACACATGACATGGAA 59.698 36.000 19.39 0.00 36.90 3.53
926 1129 8.820933 TCGCATTTGATAGAAGAAGTTAGAATG 58.179 33.333 0.00 0.00 0.00 2.67
937 1140 6.722301 ACACAATCATCGCATTTGATAGAAG 58.278 36.000 0.00 0.00 33.52 2.85
944 1147 4.207635 GCCAATACACAATCATCGCATTTG 59.792 41.667 0.00 0.00 0.00 2.32
951 1154 8.627487 TTATTTTTCGCCAATACACAATCATC 57.373 30.769 0.00 0.00 0.00 2.92
959 1162 7.541091 TGCGTTTATTTATTTTTCGCCAATACA 59.459 29.630 0.00 0.00 41.15 2.29
1127 1337 3.081409 GGAGTAAGCGAGGGGGCA 61.081 66.667 0.00 0.00 34.64 5.36
1267 1477 3.470888 CGTTGCCGAGGAGGGGAT 61.471 66.667 0.00 0.00 41.48 3.85
1268 1478 4.689549 TCGTTGCCGAGGAGGGGA 62.690 66.667 0.00 0.00 38.40 4.81
1279 1489 2.750888 GGCAGATTCGGGTCGTTGC 61.751 63.158 0.00 0.00 0.00 4.17
1404 2075 0.031585 CACAAGCAGCAGCACAACAT 59.968 50.000 3.17 0.00 45.49 2.71
1438 2137 1.000233 GAACCACCCATCCATGGCA 60.000 57.895 6.96 0.00 46.70 4.92
1439 2138 1.039233 CAGAACCACCCATCCATGGC 61.039 60.000 6.96 0.00 46.70 4.40
1441 2140 0.323633 TGCAGAACCACCCATCCATG 60.324 55.000 0.00 0.00 0.00 3.66
1442 2141 0.323725 GTGCAGAACCACCCATCCAT 60.324 55.000 0.00 0.00 0.00 3.41
1443 2142 1.074775 GTGCAGAACCACCCATCCA 59.925 57.895 0.00 0.00 0.00 3.41
1444 2143 0.251341 AAGTGCAGAACCACCCATCC 60.251 55.000 0.00 0.00 36.38 3.51
1445 2144 0.883833 CAAGTGCAGAACCACCCATC 59.116 55.000 0.00 0.00 36.38 3.51
1446 2145 0.185901 ACAAGTGCAGAACCACCCAT 59.814 50.000 0.00 0.00 36.38 4.00
1447 2146 0.751277 CACAAGTGCAGAACCACCCA 60.751 55.000 0.00 0.00 36.38 4.51
1448 2147 2.032981 CACAAGTGCAGAACCACCC 58.967 57.895 0.00 0.00 36.38 4.61
1460 2159 0.604780 CCACTAGCAGCAGCACAAGT 60.605 55.000 3.17 0.77 45.49 3.16
1535 2335 4.027437 TGTGTATTAGGGGGAAAAATGCC 58.973 43.478 0.00 0.00 0.00 4.40
1536 2336 4.441495 GCTGTGTATTAGGGGGAAAAATGC 60.441 45.833 0.00 0.00 0.00 3.56
1537 2337 4.202010 CGCTGTGTATTAGGGGGAAAAATG 60.202 45.833 0.00 0.00 0.00 2.32
1538 2338 3.951680 CGCTGTGTATTAGGGGGAAAAAT 59.048 43.478 0.00 0.00 0.00 1.82
1539 2339 3.349022 CGCTGTGTATTAGGGGGAAAAA 58.651 45.455 0.00 0.00 0.00 1.94
1540 2340 2.356330 CCGCTGTGTATTAGGGGGAAAA 60.356 50.000 0.00 0.00 42.68 2.29
1541 2341 1.210967 CCGCTGTGTATTAGGGGGAAA 59.789 52.381 0.00 0.00 42.68 3.13
1542 2342 0.834612 CCGCTGTGTATTAGGGGGAA 59.165 55.000 0.00 0.00 42.68 3.97
1543 2343 2.523440 CCGCTGTGTATTAGGGGGA 58.477 57.895 0.00 0.00 42.68 4.81
1545 2345 1.227853 GCCCGCTGTGTATTAGGGG 60.228 63.158 0.70 0.00 45.11 4.79
1546 2346 0.108585 ATGCCCGCTGTGTATTAGGG 59.891 55.000 0.00 0.00 44.72 3.53
1547 2347 1.967319 AATGCCCGCTGTGTATTAGG 58.033 50.000 0.00 0.00 0.00 2.69
1548 2348 4.574828 AGTAAAATGCCCGCTGTGTATTAG 59.425 41.667 0.00 0.00 0.00 1.73
1549 2349 4.519213 AGTAAAATGCCCGCTGTGTATTA 58.481 39.130 0.00 0.00 0.00 0.98
1550 2350 3.352648 AGTAAAATGCCCGCTGTGTATT 58.647 40.909 0.00 0.00 0.00 1.89
1551 2351 2.999331 AGTAAAATGCCCGCTGTGTAT 58.001 42.857 0.00 0.00 0.00 2.29
1552 2352 2.483014 AGTAAAATGCCCGCTGTGTA 57.517 45.000 0.00 0.00 0.00 2.90
1553 2353 1.269448 CAAGTAAAATGCCCGCTGTGT 59.731 47.619 0.00 0.00 0.00 3.72
1554 2354 1.402720 CCAAGTAAAATGCCCGCTGTG 60.403 52.381 0.00 0.00 0.00 3.66
1555 2355 0.887933 CCAAGTAAAATGCCCGCTGT 59.112 50.000 0.00 0.00 0.00 4.40
1556 2356 0.458370 GCCAAGTAAAATGCCCGCTG 60.458 55.000 0.00 0.00 0.00 5.18
1557 2357 0.897863 TGCCAAGTAAAATGCCCGCT 60.898 50.000 0.00 0.00 0.00 5.52
1558 2358 0.037790 TTGCCAAGTAAAATGCCCGC 60.038 50.000 0.00 0.00 0.00 6.13
1559 2359 1.272212 AGTTGCCAAGTAAAATGCCCG 59.728 47.619 0.00 0.00 0.00 6.13
1560 2360 2.298729 TCAGTTGCCAAGTAAAATGCCC 59.701 45.455 0.00 0.00 0.00 5.36
1561 2361 3.658757 TCAGTTGCCAAGTAAAATGCC 57.341 42.857 0.00 0.00 0.00 4.40
1562 2362 7.331687 ACAAATATCAGTTGCCAAGTAAAATGC 59.668 33.333 0.00 0.00 0.00 3.56
1595 2441 1.391577 ACAACAGAGCAATGCACACA 58.608 45.000 8.35 0.00 0.00 3.72
1768 2674 6.753180 TGATACCTGCATCTCTACTTTCATC 58.247 40.000 0.00 0.00 0.00 2.92
1893 2801 7.585573 GCATGTCGAAAAATAAGAGATAGCAAG 59.414 37.037 0.00 0.00 0.00 4.01
1963 2871 5.766222 ACTCAAAGAACAAGCAAGCATAAG 58.234 37.500 0.00 0.00 0.00 1.73
2054 2972 3.379372 ACTGCATCGATTCCTTGGATTTG 59.621 43.478 0.00 0.00 0.00 2.32
2239 3157 3.242969 CCATTCACCAAAGCGATGATCAG 60.243 47.826 0.09 0.00 0.00 2.90
2327 3245 3.562141 TGTACCAATTGTTTCCACTGTCG 59.438 43.478 4.43 0.00 0.00 4.35
2369 3289 2.568956 CCACTCAAGATCTTCCTGGTCA 59.431 50.000 4.57 0.00 0.00 4.02
2688 3671 1.077445 GAGGCCTGCCCCTCTTTTT 59.923 57.895 12.00 0.00 46.39 1.94
2693 3676 3.689002 CTTTCGAGGCCTGCCCCTC 62.689 68.421 12.00 0.00 46.42 4.30
2695 3678 4.803908 CCTTTCGAGGCCTGCCCC 62.804 72.222 12.00 0.00 36.58 5.80
2696 3679 1.696097 TATCCTTTCGAGGCCTGCCC 61.696 60.000 12.00 0.00 36.58 5.36
2697 3680 0.398318 ATATCCTTTCGAGGCCTGCC 59.602 55.000 12.00 0.00 0.00 4.85
2698 3681 3.330267 CTTATATCCTTTCGAGGCCTGC 58.670 50.000 12.00 0.00 0.00 4.85
2699 3682 3.244215 TGCTTATATCCTTTCGAGGCCTG 60.244 47.826 12.00 2.19 0.00 4.85
2700 3683 2.972713 TGCTTATATCCTTTCGAGGCCT 59.027 45.455 3.86 3.86 0.00 5.19
2701 3684 3.067833 GTGCTTATATCCTTTCGAGGCC 58.932 50.000 0.00 0.00 0.00 5.19
2702 3685 3.728845 TGTGCTTATATCCTTTCGAGGC 58.271 45.455 0.00 0.00 0.00 4.70
2703 3686 5.541845 TGATGTGCTTATATCCTTTCGAGG 58.458 41.667 0.00 0.00 0.00 4.63
2704 3687 5.636965 CCTGATGTGCTTATATCCTTTCGAG 59.363 44.000 0.00 0.00 0.00 4.04
2705 3688 5.070446 ACCTGATGTGCTTATATCCTTTCGA 59.930 40.000 0.00 0.00 0.00 3.71
2706 3689 5.178252 CACCTGATGTGCTTATATCCTTTCG 59.822 44.000 0.00 0.00 38.34 3.46
2707 3690 6.291377 TCACCTGATGTGCTTATATCCTTTC 58.709 40.000 0.00 0.00 45.03 2.62
2708 3691 6.252599 TCACCTGATGTGCTTATATCCTTT 57.747 37.500 0.00 0.00 45.03 3.11
2709 3692 5.894298 TCACCTGATGTGCTTATATCCTT 57.106 39.130 0.00 0.00 45.03 3.36
2710 3693 7.746243 ATATCACCTGATGTGCTTATATCCT 57.254 36.000 0.00 0.00 45.03 3.24
2711 3694 8.043113 TGAATATCACCTGATGTGCTTATATCC 58.957 37.037 0.00 0.00 45.03 2.59
2712 3695 9.440773 TTGAATATCACCTGATGTGCTTATATC 57.559 33.333 0.00 0.00 45.03 1.63
2713 3696 9.224267 GTTGAATATCACCTGATGTGCTTATAT 57.776 33.333 0.00 0.00 45.03 0.86
2714 3697 7.661437 GGTTGAATATCACCTGATGTGCTTATA 59.339 37.037 0.00 0.00 45.03 0.98
2715 3698 6.488006 GGTTGAATATCACCTGATGTGCTTAT 59.512 38.462 0.00 0.00 45.03 1.73
2716 3699 5.822519 GGTTGAATATCACCTGATGTGCTTA 59.177 40.000 0.00 0.00 45.03 3.09
2720 3703 7.864108 TTTAGGTTGAATATCACCTGATGTG 57.136 36.000 10.25 0.00 46.88 3.21
2793 3785 3.620966 GCCCTGACTGTCTCTAATTTGCT 60.621 47.826 9.51 0.00 0.00 3.91
2807 3799 3.117888 TCTTCAGTTTTTCTGCCCTGACT 60.118 43.478 0.00 0.00 43.32 3.41
2965 4018 0.671796 GCTGGGTTGGGTTGTACAAC 59.328 55.000 27.20 27.20 45.60 3.32
3108 4173 6.008331 AGAAATTAACCACAACTAGGTTCCC 58.992 40.000 0.18 0.00 45.98 3.97
3187 4253 3.891366 CCATTTCCACAAGGAGAAGTTGT 59.109 43.478 0.00 0.00 46.74 3.32
3217 4283 1.800805 ATTCAGCCAGACGAACACAG 58.199 50.000 0.00 0.00 0.00 3.66
3401 4478 4.592485 TCTCTGAACTCACAAGAACTCC 57.408 45.455 0.00 0.00 0.00 3.85
3482 4570 2.482142 CCGTCTCAGGAAGCAAGGTATC 60.482 54.545 0.00 0.00 0.00 2.24
3606 4741 1.524008 TTCAGAGAAGAGGTGCGCGA 61.524 55.000 12.10 0.00 0.00 5.87
3728 4868 7.846644 ATCATCTTCTTAAGAGCAACTCAAG 57.153 36.000 5.12 0.00 41.61 3.02
3768 4908 8.703604 TCCTGAAGTTTAATTCTATCAGTTCG 57.296 34.615 0.00 0.00 34.03 3.95
3802 4942 4.041691 TCAGCCAAGCTCCTTAAGTAGTTT 59.958 41.667 0.97 0.00 36.40 2.66
3803 4943 3.583086 TCAGCCAAGCTCCTTAAGTAGTT 59.417 43.478 0.97 0.00 36.40 2.24
3807 4947 1.699634 TGTCAGCCAAGCTCCTTAAGT 59.300 47.619 0.97 0.00 36.40 2.24
3808 4948 2.479566 TGTCAGCCAAGCTCCTTAAG 57.520 50.000 0.00 0.00 36.40 1.85
3809 4949 2.040278 ACATGTCAGCCAAGCTCCTTAA 59.960 45.455 0.00 0.00 36.40 1.85
3811 4951 0.403271 ACATGTCAGCCAAGCTCCTT 59.597 50.000 0.00 0.00 36.40 3.36
3812 4952 0.322277 CACATGTCAGCCAAGCTCCT 60.322 55.000 0.00 0.00 36.40 3.69
3883 5032 2.426381 ACTAGGAATCTCCGGTTCGAAC 59.574 50.000 20.14 20.14 42.75 3.95
3955 5104 7.441458 GGGTATCTCATAGTACAAATTGACCAC 59.559 40.741 0.00 0.00 0.00 4.16
4073 5533 1.527433 GGTTCTTGGTTGCTCTGGGC 61.527 60.000 0.00 0.00 42.22 5.36
4074 5534 0.178992 TGGTTCTTGGTTGCTCTGGG 60.179 55.000 0.00 0.00 0.00 4.45
4075 5535 0.954452 GTGGTTCTTGGTTGCTCTGG 59.046 55.000 0.00 0.00 0.00 3.86
4076 5536 0.954452 GGTGGTTCTTGGTTGCTCTG 59.046 55.000 0.00 0.00 0.00 3.35
4077 5537 0.550914 TGGTGGTTCTTGGTTGCTCT 59.449 50.000 0.00 0.00 0.00 4.09
4078 5538 0.954452 CTGGTGGTTCTTGGTTGCTC 59.046 55.000 0.00 0.00 0.00 4.26
4079 5539 0.258774 ACTGGTGGTTCTTGGTTGCT 59.741 50.000 0.00 0.00 0.00 3.91
4080 5540 0.385390 CACTGGTGGTTCTTGGTTGC 59.615 55.000 0.00 0.00 0.00 4.17
4081 5541 0.385390 GCACTGGTGGTTCTTGGTTG 59.615 55.000 2.84 0.00 0.00 3.77
4082 5542 0.258774 AGCACTGGTGGTTCTTGGTT 59.741 50.000 0.00 0.00 38.24 3.67


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

AutoCloner maintained by Alex Coulton.