Multiple sequence alignment - TraesCS6B01G309200

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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 TraesCS6B01G309200 chr6B 100.000 5356 0 0 1 5356 553411963 553417318 0.000000e+00 9891.0
1 TraesCS6B01G309200 chr6B 88.123 522 49 9 4847 5356 241099433 241099953 4.990000e-170 608.0
2 TraesCS6B01G309200 chr6B 96.000 175 7 0 613 787 553408858 553408684 9.560000e-73 285.0
3 TraesCS6B01G309200 chr6B 80.132 302 54 6 3773 4071 522642661 522642959 2.730000e-53 220.0
4 TraesCS6B01G309200 chr6B 100.000 96 0 0 5733 5828 553417695 553417790 1.670000e-40 178.0
5 TraesCS6B01G309200 chr6B 86.792 159 19 2 2860 3017 522641742 522641899 6.000000e-40 176.0
6 TraesCS6B01G309200 chr6A 93.700 4095 155 50 789 4850 508717257 508713233 0.000000e+00 6037.0
7 TraesCS6B01G309200 chr6A 73.663 729 153 33 3364 4071 486549543 486550253 4.510000e-61 246.0
8 TraesCS6B01G309200 chr6A 77.612 335 65 9 2860 3189 486549036 486549365 1.660000e-45 195.0
9 TraesCS6B01G309200 chr6D 95.638 2820 94 19 1517 4323 368112138 368109335 0.000000e+00 4499.0
10 TraesCS6B01G309200 chr6D 94.371 533 21 2 4316 4848 368108253 368107730 0.000000e+00 809.0
11 TraesCS6B01G309200 chr6D 93.075 491 17 9 789 1269 368112791 368112308 0.000000e+00 702.0
12 TraesCS6B01G309200 chr6D 88.932 515 47 6 4851 5356 462527638 462528151 1.380000e-175 627.0
13 TraesCS6B01G309200 chr6D 88.178 516 49 8 4850 5356 15586600 15587112 6.460000e-169 604.0
14 TraesCS6B01G309200 chr6D 79.667 300 59 2 3773 4071 355137140 355136842 1.270000e-51 215.0
15 TraesCS6B01G309200 chr6D 76.385 343 73 7 2860 3198 355138065 355137727 1.670000e-40 178.0
16 TraesCS6B01G309200 chr4A 94.828 986 42 6 2251 3235 590935891 590934914 0.000000e+00 1530.0
17 TraesCS6B01G309200 chr4A 96.066 788 28 1 1 788 191049880 191050664 0.000000e+00 1280.0
18 TraesCS6B01G309200 chr3A 96.193 788 26 1 1 788 565456327 565455544 0.000000e+00 1286.0
19 TraesCS6B01G309200 chr3A 93.750 96 6 0 5733 5828 725934892 725934797 1.690000e-30 145.0
20 TraesCS6B01G309200 chr1B 95.839 793 28 2 1 792 63178409 63179197 0.000000e+00 1277.0
21 TraesCS6B01G309200 chr1A 95.076 792 33 2 1 789 386436450 386435662 0.000000e+00 1242.0
22 TraesCS6B01G309200 chr1A 81.045 823 98 24 1 788 590521444 590522243 2.320000e-168 603.0
23 TraesCS6B01G309200 chr1A 95.455 176 8 0 613 788 386440410 386440585 1.240000e-71 281.0
24 TraesCS6B01G309200 chr7B 93.139 787 54 0 1 787 642145402 642144616 0.000000e+00 1155.0
25 TraesCS6B01G309200 chr7B 89.474 513 40 10 4851 5350 263400818 263400307 2.290000e-178 636.0
26 TraesCS6B01G309200 chr7B 92.708 96 7 0 5733 5828 510609413 510609508 7.870000e-29 139.0
27 TraesCS6B01G309200 chr7B 91.667 96 8 0 5733 5828 53641758 53641663 3.660000e-27 134.0
28 TraesCS6B01G309200 chr4D 90.097 515 40 7 4852 5356 430826992 430827505 0.000000e+00 658.0
29 TraesCS6B01G309200 chrUn 88.417 518 47 9 4850 5356 30147483 30146968 3.860000e-171 612.0
30 TraesCS6B01G309200 chrUn 92.711 343 25 0 445 787 310232449 310232107 4.060000e-136 496.0
31 TraesCS6B01G309200 chr5B 88.757 507 43 9 4860 5356 671362964 671363466 4.990000e-170 608.0
32 TraesCS6B01G309200 chr5B 92.708 96 7 0 5733 5828 36339295 36339200 7.870000e-29 139.0
33 TraesCS6B01G309200 chr5B 91.667 96 8 0 5733 5828 14538982 14538887 3.660000e-27 134.0
34 TraesCS6B01G309200 chr5B 91.667 96 7 1 5733 5828 551765403 551765497 1.320000e-26 132.0
35 TraesCS6B01G309200 chr3B 88.031 518 49 9 4851 5356 366143524 366144040 8.360000e-168 601.0
36 TraesCS6B01G309200 chr3B 82.759 87 9 4 3102 3185 42126017 42126100 8.100000e-09 73.1
37 TraesCS6B01G309200 chr3B 88.136 59 7 0 3144 3202 42047467 42047409 2.910000e-08 71.3
38 TraesCS6B01G309200 chr1D 87.961 515 51 7 4851 5356 267995449 267995961 1.080000e-166 597.0
39 TraesCS6B01G309200 chr1D 95.604 91 4 0 5738 5828 480529451 480529541 4.710000e-31 147.0
40 TraesCS6B01G309200 chr2A 81.466 464 66 13 338 787 575673791 575674248 4.290000e-96 363.0
41 TraesCS6B01G309200 chr2A 97.619 42 1 0 3144 3185 672945950 672945909 8.100000e-09 73.1
42 TraesCS6B01G309200 chr2D 93.750 176 11 0 613 788 569377045 569377220 1.250000e-66 265.0
43 TraesCS6B01G309200 chr2D 91.667 96 8 0 5733 5828 81002055 81001960 3.660000e-27 134.0
44 TraesCS6B01G309200 chr2D 95.238 42 2 0 3144 3185 528099398 528099357 3.770000e-07 67.6
45 TraesCS6B01G309200 chr4B 93.750 96 6 0 5733 5828 215088321 215088416 1.690000e-30 145.0


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 TraesCS6B01G309200 chr6B 553411963 553417790 5827 False 5034.500000 9891 100.000000 1 5828 2 chr6B.!!$F3 5827
1 TraesCS6B01G309200 chr6B 241099433 241099953 520 False 608.000000 608 88.123000 4847 5356 1 chr6B.!!$F1 509
2 TraesCS6B01G309200 chr6A 508713233 508717257 4024 True 6037.000000 6037 93.700000 789 4850 1 chr6A.!!$R1 4061
3 TraesCS6B01G309200 chr6A 486549036 486550253 1217 False 220.500000 246 75.637500 2860 4071 2 chr6A.!!$F1 1211
4 TraesCS6B01G309200 chr6D 368107730 368112791 5061 True 2003.333333 4499 94.361333 789 4848 3 chr6D.!!$R2 4059
5 TraesCS6B01G309200 chr6D 462527638 462528151 513 False 627.000000 627 88.932000 4851 5356 1 chr6D.!!$F2 505
6 TraesCS6B01G309200 chr6D 15586600 15587112 512 False 604.000000 604 88.178000 4850 5356 1 chr6D.!!$F1 506
7 TraesCS6B01G309200 chr4A 590934914 590935891 977 True 1530.000000 1530 94.828000 2251 3235 1 chr4A.!!$R1 984
8 TraesCS6B01G309200 chr4A 191049880 191050664 784 False 1280.000000 1280 96.066000 1 788 1 chr4A.!!$F1 787
9 TraesCS6B01G309200 chr3A 565455544 565456327 783 True 1286.000000 1286 96.193000 1 788 1 chr3A.!!$R1 787
10 TraesCS6B01G309200 chr1B 63178409 63179197 788 False 1277.000000 1277 95.839000 1 792 1 chr1B.!!$F1 791
11 TraesCS6B01G309200 chr1A 386435662 386436450 788 True 1242.000000 1242 95.076000 1 789 1 chr1A.!!$R1 788
12 TraesCS6B01G309200 chr1A 590521444 590522243 799 False 603.000000 603 81.045000 1 788 1 chr1A.!!$F2 787
13 TraesCS6B01G309200 chr7B 642144616 642145402 786 True 1155.000000 1155 93.139000 1 787 1 chr7B.!!$R3 786
14 TraesCS6B01G309200 chr7B 263400307 263400818 511 True 636.000000 636 89.474000 4851 5350 1 chr7B.!!$R2 499
15 TraesCS6B01G309200 chr4D 430826992 430827505 513 False 658.000000 658 90.097000 4852 5356 1 chr4D.!!$F1 504
16 TraesCS6B01G309200 chrUn 30146968 30147483 515 True 612.000000 612 88.417000 4850 5356 1 chrUn.!!$R1 506
17 TraesCS6B01G309200 chr5B 671362964 671363466 502 False 608.000000 608 88.757000 4860 5356 1 chr5B.!!$F2 496
18 TraesCS6B01G309200 chr3B 366143524 366144040 516 False 601.000000 601 88.031000 4851 5356 1 chr3B.!!$F2 505
19 TraesCS6B01G309200 chr1D 267995449 267995961 512 False 597.000000 597 87.961000 4851 5356 1 chr1D.!!$F1 505

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
997 1045 0.886490 CTCACCTCACAAGCACACCC 60.886 60.000 0.00 0.0 0.00 4.61 F
1007 1055 0.034089 AAGCACACCCATTCCCTAGC 60.034 55.000 0.00 0.0 0.00 3.42 F
1385 1446 0.035317 TCATGCGTGACTGCTTCCTT 59.965 50.000 3.97 0.0 35.36 3.36 F
1551 1633 0.178990 GGGACCCCACAGGATTATGC 60.179 60.000 0.00 0.0 39.89 3.14 F
2202 2316 0.612732 TCAAGGCAATGGCTCCAAGG 60.613 55.000 10.47 0.0 37.50 3.61 F
2208 2322 1.002134 AATGGCTCCAAGGACCGTG 60.002 57.895 0.00 0.0 0.00 4.94 F
3263 3561 1.068055 GGCGACGAGTCTTACAAGGAA 60.068 52.381 0.00 0.0 0.00 3.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2185 2299 0.613012 GTCCTTGGAGCCATTGCCTT 60.613 55.000 0.00 0.0 38.69 4.35 R
2190 2304 1.002134 CACGGTCCTTGGAGCCATT 60.002 57.895 12.54 0.0 0.00 3.16 R
2230 2344 1.135139 CGTCGACCCATCTTCAGTGAT 59.865 52.381 10.58 0.0 0.00 3.06 R
2725 2852 1.625315 TCACAAGTCCCTGGTCATCAG 59.375 52.381 0.00 0.0 43.00 2.90 R
3830 4137 1.376466 GAAGAACTCCAGCTGCCCA 59.624 57.895 8.66 0.0 0.00 5.36 R
4164 4471 6.591935 CAAGCCCACTTATAGATACCTCAAA 58.408 40.000 0.00 0.0 33.74 2.69 R
5021 6424 0.106149 CGGCGGCTAGGGTTTAGAAT 59.894 55.000 7.61 0.0 0.00 2.40 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
143 152 4.135153 CCCCGTCGTCCTGCTGAG 62.135 72.222 0.00 0.00 0.00 3.35
183 192 1.039233 GTGGTCGTATCCTCCCGGAA 61.039 60.000 0.73 0.00 44.02 4.30
201 213 2.774234 GGAATCCTCCTCCTGACATGAA 59.226 50.000 0.00 0.00 38.88 2.57
243 255 1.282570 CGTGCGCACAACCATTCTT 59.717 52.632 37.03 0.00 0.00 2.52
319 358 2.482333 CGCTCCCGTCCTTCTCGAT 61.482 63.158 0.00 0.00 0.00 3.59
682 724 1.515954 GGAAGGAGCGAACGGATCA 59.484 57.895 0.00 0.00 30.89 2.92
750 792 3.702048 GGCAGGGGTACGCACAGA 61.702 66.667 12.45 0.00 46.88 3.41
798 840 2.759839 TTTTCTTCCCCGGGAAAAGT 57.240 45.000 26.32 0.00 41.54 2.66
840 882 3.445687 CCATGCACGCTGCCACAT 61.446 61.111 7.38 0.00 44.23 3.21
970 1017 1.985460 ATAAATACGCGCCCACCCCA 61.985 55.000 5.73 0.00 0.00 4.96
997 1045 0.886490 CTCACCTCACAAGCACACCC 60.886 60.000 0.00 0.00 0.00 4.61
998 1046 1.152984 CACCTCACAAGCACACCCA 60.153 57.895 0.00 0.00 0.00 4.51
999 1047 0.538057 CACCTCACAAGCACACCCAT 60.538 55.000 0.00 0.00 0.00 4.00
1000 1048 0.185901 ACCTCACAAGCACACCCATT 59.814 50.000 0.00 0.00 0.00 3.16
1001 1049 0.883833 CCTCACAAGCACACCCATTC 59.116 55.000 0.00 0.00 0.00 2.67
1002 1050 0.883833 CTCACAAGCACACCCATTCC 59.116 55.000 0.00 0.00 0.00 3.01
1003 1051 0.539438 TCACAAGCACACCCATTCCC 60.539 55.000 0.00 0.00 0.00 3.97
1004 1052 0.540365 CACAAGCACACCCATTCCCT 60.540 55.000 0.00 0.00 0.00 4.20
1005 1053 1.072266 ACAAGCACACCCATTCCCTA 58.928 50.000 0.00 0.00 0.00 3.53
1006 1054 1.004745 ACAAGCACACCCATTCCCTAG 59.995 52.381 0.00 0.00 0.00 3.02
1007 1055 0.034089 AAGCACACCCATTCCCTAGC 60.034 55.000 0.00 0.00 0.00 3.42
1009 1057 0.464554 GCACACCCATTCCCTAGCTC 60.465 60.000 0.00 0.00 0.00 4.09
1037 1085 2.048127 GTCTCCGTTTGCTCGCCT 60.048 61.111 0.00 0.00 0.00 5.52
1093 1142 2.544698 TACGTGGTGCGGTTTTGCC 61.545 57.895 0.00 0.00 46.52 4.52
1193 1242 1.281656 GCCGTGGTCGTTTCCTTTG 59.718 57.895 0.00 0.00 35.01 2.77
1298 1350 5.857268 AGTATACATATGTGCAGTGCATGA 58.143 37.500 22.87 11.75 41.91 3.07
1299 1351 5.698089 AGTATACATATGTGCAGTGCATGAC 59.302 40.000 22.87 9.29 41.91 3.06
1302 1354 0.248843 TATGTGCAGTGCATGACCGA 59.751 50.000 22.87 1.00 41.91 4.69
1322 1383 1.321474 TGTTGTCTCCTCGTTACCGT 58.679 50.000 0.00 0.00 35.01 4.83
1372 1433 3.906649 GCGACGTCAGCTCATGCG 61.907 66.667 17.16 0.00 45.42 4.73
1375 1436 1.444383 GACGTCAGCTCATGCGTGA 60.444 57.895 11.55 8.64 45.42 4.35
1376 1437 1.678269 GACGTCAGCTCATGCGTGAC 61.678 60.000 11.55 10.33 45.42 3.67
1377 1438 1.445066 CGTCAGCTCATGCGTGACT 60.445 57.895 3.97 4.92 45.42 3.41
1378 1439 1.681025 CGTCAGCTCATGCGTGACTG 61.681 60.000 22.30 22.30 45.42 3.51
1379 1440 1.739196 TCAGCTCATGCGTGACTGC 60.739 57.895 22.98 18.10 45.42 4.40
1380 1441 1.740664 CAGCTCATGCGTGACTGCT 60.741 57.895 15.04 15.04 45.42 4.24
1381 1442 1.004080 AGCTCATGCGTGACTGCTT 60.004 52.632 15.04 2.64 45.42 3.91
1382 1443 1.018226 AGCTCATGCGTGACTGCTTC 61.018 55.000 15.04 0.00 45.42 3.86
1383 1444 1.975363 GCTCATGCGTGACTGCTTCC 61.975 60.000 3.97 0.00 35.36 3.46
1384 1445 0.390866 CTCATGCGTGACTGCTTCCT 60.391 55.000 3.97 0.00 35.36 3.36
1385 1446 0.035317 TCATGCGTGACTGCTTCCTT 59.965 50.000 3.97 0.00 35.36 3.36
1386 1447 0.877071 CATGCGTGACTGCTTCCTTT 59.123 50.000 0.00 0.00 35.36 3.11
1387 1448 1.135859 CATGCGTGACTGCTTCCTTTC 60.136 52.381 0.00 0.00 35.36 2.62
1388 1449 1.221466 TGCGTGACTGCTTCCTTTCG 61.221 55.000 1.69 0.00 35.36 3.46
1389 1450 1.222115 GCGTGACTGCTTCCTTTCGT 61.222 55.000 0.00 0.00 0.00 3.85
1390 1451 0.784778 CGTGACTGCTTCCTTTCGTC 59.215 55.000 0.00 0.00 0.00 4.20
1391 1452 1.603172 CGTGACTGCTTCCTTTCGTCT 60.603 52.381 0.00 0.00 0.00 4.18
1392 1453 2.062519 GTGACTGCTTCCTTTCGTCTC 58.937 52.381 0.00 0.00 0.00 3.36
1393 1454 1.335964 TGACTGCTTCCTTTCGTCTCG 60.336 52.381 0.00 0.00 0.00 4.04
1394 1455 0.959553 ACTGCTTCCTTTCGTCTCGA 59.040 50.000 0.00 0.00 0.00 4.04
1395 1456 1.546476 ACTGCTTCCTTTCGTCTCGAT 59.454 47.619 0.00 0.00 35.23 3.59
1396 1457 2.189342 CTGCTTCCTTTCGTCTCGATC 58.811 52.381 0.00 0.00 35.23 3.69
1397 1458 1.819288 TGCTTCCTTTCGTCTCGATCT 59.181 47.619 0.00 0.00 35.23 2.75
1398 1459 2.231478 TGCTTCCTTTCGTCTCGATCTT 59.769 45.455 0.00 0.00 35.23 2.40
1401 1462 3.489180 TCCTTTCGTCTCGATCTTGAC 57.511 47.619 5.27 5.27 35.23 3.18
1434 1516 2.762535 TTCTCCGATGGACTGGTTTC 57.237 50.000 0.00 0.00 0.00 2.78
1483 1565 6.538742 TGTGCAAAAGCATATAGGAGTAACTC 59.461 38.462 0.00 0.00 0.00 3.01
1486 1568 8.651389 TGCAAAAGCATATAGGAGTAACTCTAT 58.349 33.333 0.00 0.00 0.00 1.98
1497 1579 4.498345 GGAGTAACTCTATTCACCGCTCTG 60.498 50.000 0.00 0.00 0.00 3.35
1551 1633 0.178990 GGGACCCCACAGGATTATGC 60.179 60.000 0.00 0.00 39.89 3.14
1552 1634 0.846693 GGACCCCACAGGATTATGCT 59.153 55.000 0.00 0.00 39.89 3.79
1553 1635 2.054799 GGACCCCACAGGATTATGCTA 58.945 52.381 0.00 0.00 39.89 3.49
1554 1636 2.644798 GGACCCCACAGGATTATGCTAT 59.355 50.000 0.00 0.00 39.89 2.97
1555 1637 3.844211 GGACCCCACAGGATTATGCTATA 59.156 47.826 0.00 0.00 39.89 1.31
1556 1638 4.475016 GGACCCCACAGGATTATGCTATAT 59.525 45.833 0.00 0.00 39.89 0.86
1557 1639 5.665812 GGACCCCACAGGATTATGCTATATA 59.334 44.000 0.00 0.00 39.89 0.86
1558 1640 6.408206 GGACCCCACAGGATTATGCTATATAC 60.408 46.154 0.00 0.00 39.89 1.47
1559 1641 5.428783 ACCCCACAGGATTATGCTATATACC 59.571 44.000 0.00 0.00 39.89 2.73
1560 1642 5.428457 CCCCACAGGATTATGCTATATACCA 59.572 44.000 0.00 0.00 38.24 3.25
1561 1643 6.101734 CCCCACAGGATTATGCTATATACCAT 59.898 42.308 0.00 0.00 38.24 3.55
1562 1644 7.220030 CCCACAGGATTATGCTATATACCATC 58.780 42.308 0.00 0.00 33.47 3.51
1636 1735 6.696441 AGAGAAAGAAGTACCGGTAGTATG 57.304 41.667 22.18 0.00 32.28 2.39
1649 1748 1.855360 GTAGTATGCACGCTTCTGAGC 59.145 52.381 0.00 0.00 45.65 4.26
1734 1842 5.734720 ACAAACTGATCATGTTAGGTCGAT 58.265 37.500 0.00 0.00 0.00 3.59
1753 1861 9.583765 AGGTCGATATAGTGTCTTTTTCTTAAC 57.416 33.333 0.00 0.00 0.00 2.01
1791 1900 3.055385 GGAGTATACTTTGGCAGTGGTCA 60.055 47.826 6.88 0.00 35.97 4.02
1805 1914 2.376518 AGTGGTCACATGGTTTCATCCT 59.623 45.455 0.00 0.00 0.00 3.24
1875 1984 2.673368 GCCTCACACAAAGAAGTATCGG 59.327 50.000 0.00 0.00 0.00 4.18
1995 2105 4.159857 GCACGCCAACATTTCGTATAAAA 58.840 39.130 0.00 0.00 34.81 1.52
2045 2155 1.154205 CCGCAGCCAACCGATTAGAG 61.154 60.000 0.00 0.00 0.00 2.43
2060 2170 7.428020 ACCGATTAGAGCGTATGTAAAATACA 58.572 34.615 0.00 0.00 43.80 2.29
2068 2178 9.431887 AGAGCGTATGTAAAATACAGAAAAAGA 57.568 29.630 0.00 0.00 42.77 2.52
2109 2223 8.432805 TGGTTAGGAATCTCAAGGATTATCTTC 58.567 37.037 0.00 0.00 43.90 2.87
2185 2299 2.100197 AGAGAATTCACCGGACGATCA 58.900 47.619 9.46 0.00 0.00 2.92
2190 2304 1.822114 TTCACCGGACGATCAAGGCA 61.822 55.000 9.46 0.00 0.00 4.75
2202 2316 0.612732 TCAAGGCAATGGCTCCAAGG 60.613 55.000 10.47 0.00 37.50 3.61
2208 2322 1.002134 AATGGCTCCAAGGACCGTG 60.002 57.895 0.00 0.00 0.00 4.94
2249 2363 2.544685 CATCACTGAAGATGGGTCGAC 58.455 52.381 7.13 7.13 41.29 4.20
2297 2411 2.242043 AGCAAACACTGGGAAATGGAG 58.758 47.619 0.00 0.00 0.00 3.86
2463 2577 2.074547 ACTATGCGCTTGTAACGTGT 57.925 45.000 9.73 0.00 0.00 4.49
2697 2811 7.813852 AATCGATCGTAATACAGGCTTATTC 57.186 36.000 15.94 0.43 0.00 1.75
2699 2813 7.677454 TCGATCGTAATACAGGCTTATTCTA 57.323 36.000 15.94 0.00 0.00 2.10
2725 2852 6.808008 TTGGATTGTTCTGATCTGAACTTC 57.192 37.500 32.51 28.05 44.63 3.01
3263 3561 1.068055 GGCGACGAGTCTTACAAGGAA 60.068 52.381 0.00 0.00 0.00 3.36
3359 3657 2.194868 TGCGAGCCGGAGAGGATA 59.805 61.111 5.05 0.00 39.82 2.59
3512 3810 1.149101 AAGGGACCACCATGAACACT 58.851 50.000 0.00 0.00 43.89 3.55
3770 4074 3.073735 CAGCCGAGCTCCCTGAGT 61.074 66.667 19.28 0.00 36.40 3.41
3830 4137 1.614903 TCGGAGGTGTTCATGTACGTT 59.385 47.619 0.00 0.00 0.00 3.99
4040 4347 1.183549 GGTTCTACTTCCTCCTCGCA 58.816 55.000 0.00 0.00 0.00 5.10
4164 4471 3.181441 TGTTTAGGGCCTTTTTCGTACCT 60.181 43.478 13.45 0.00 0.00 3.08
4314 4621 3.006537 TCCTAGTTTCAACTCCAAGACCG 59.993 47.826 0.00 0.00 40.37 4.79
4364 5760 3.559811 CCAAGAGTCATGGTCCATGTCAA 60.560 47.826 27.50 9.44 41.98 3.18
4424 5820 3.316868 TCAAAAGGAAGCAAGTTTACCGG 59.683 43.478 0.00 0.00 0.00 5.28
4427 5823 1.633945 AGGAAGCAAGTTTACCGGGAT 59.366 47.619 6.32 0.00 0.00 3.85
4433 5829 5.048846 AGCAAGTTTACCGGGATTATGAT 57.951 39.130 6.32 0.00 0.00 2.45
4441 5837 4.451629 ACCGGGATTATGATGACGATAC 57.548 45.455 6.32 0.00 0.00 2.24
4487 5883 1.550976 GGTGATCAGTTCGGACTTCCT 59.449 52.381 0.00 0.00 32.54 3.36
4489 5885 1.550524 TGATCAGTTCGGACTTCCTGG 59.449 52.381 0.00 0.00 32.54 4.45
4516 5912 0.233848 CAACACTACGCAAACCGGAC 59.766 55.000 9.46 0.00 42.52 4.79
4548 5944 3.197790 CCGGATGAGGCTGTTGCG 61.198 66.667 0.00 0.00 40.82 4.85
4710 6106 8.575649 TGATGTAGAGTGATGAACTACAAGTA 57.424 34.615 0.00 0.00 45.69 2.24
4712 6108 9.672086 GATGTAGAGTGATGAACTACAAGTATC 57.328 37.037 0.00 0.00 45.69 2.24
4730 6126 5.675538 AGTATCTGTTTATGGTGCTTCCTC 58.324 41.667 0.80 0.00 37.07 3.71
4731 6127 2.972625 TCTGTTTATGGTGCTTCCTCG 58.027 47.619 0.80 0.00 37.07 4.63
4732 6128 2.009774 CTGTTTATGGTGCTTCCTCGG 58.990 52.381 0.80 0.00 37.07 4.63
4833 6229 9.271828 AGAAATCACAAAGAACAAAACAAAACT 57.728 25.926 0.00 0.00 0.00 2.66
4914 6313 5.009610 GGATTTGTTCTGCCTTGTCTTGTAA 59.990 40.000 0.00 0.00 0.00 2.41
4937 6336 9.817809 GTAATTCAAGTAGATCATTGTACTCCA 57.182 33.333 0.00 0.00 31.09 3.86
4938 6337 8.954950 AATTCAAGTAGATCATTGTACTCCAG 57.045 34.615 0.00 0.00 31.09 3.86
4992 6395 4.218417 CGAACAATTCAACCAATCCCTCTT 59.782 41.667 0.00 0.00 0.00 2.85
5021 6424 3.992943 AACATGGTATCAGTTTCCGGA 57.007 42.857 0.00 0.00 0.00 5.14
5195 6603 0.325272 GCTCCGGGGTTTTCTCTCTT 59.675 55.000 1.62 0.00 0.00 2.85
5198 6606 0.690762 CCGGGGTTTTCTCTCTTCCA 59.309 55.000 0.00 0.00 0.00 3.53
5229 6637 2.222886 TGATCGGCGGTTTCTTTTTGA 58.777 42.857 7.21 0.00 0.00 2.69
5257 6671 3.914966 CGATCTAATCTTATTGCGTCGCT 59.085 43.478 19.50 0.87 0.00 4.93
5329 6743 1.869690 GGCTTCTTCACCGACAAGC 59.130 57.895 0.00 0.00 40.52 4.01
5331 6745 0.603975 GCTTCTTCACCGACAAGCCT 60.604 55.000 0.00 0.00 36.11 4.58
5794 7208 3.134127 GTCATGTGGCGGCCCTTC 61.134 66.667 17.97 7.75 0.00 3.46
5795 7209 3.645660 TCATGTGGCGGCCCTTCA 61.646 61.111 17.97 13.35 0.00 3.02
5796 7210 3.443045 CATGTGGCGGCCCTTCAC 61.443 66.667 17.97 8.49 0.00 3.18
5797 7211 4.740822 ATGTGGCGGCCCTTCACC 62.741 66.667 17.97 0.00 0.00 4.02
5804 7218 3.712907 GGCCCTTCACCGCCACTA 61.713 66.667 0.00 0.00 45.01 2.74
5805 7219 2.590092 GCCCTTCACCGCCACTAT 59.410 61.111 0.00 0.00 0.00 2.12
5806 7220 1.077716 GCCCTTCACCGCCACTATT 60.078 57.895 0.00 0.00 0.00 1.73
5807 7221 1.095807 GCCCTTCACCGCCACTATTC 61.096 60.000 0.00 0.00 0.00 1.75
5808 7222 0.810031 CCCTTCACCGCCACTATTCG 60.810 60.000 0.00 0.00 0.00 3.34
5809 7223 1.429148 CCTTCACCGCCACTATTCGC 61.429 60.000 0.00 0.00 0.00 4.70
5811 7225 3.925238 CACCGCCACTATTCGCGC 61.925 66.667 0.00 0.00 46.88 6.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
143 152 1.337635 CGCCATGATAGGAGAAGGAGC 60.338 57.143 0.00 0.00 0.00 4.70
183 192 1.767681 GCTTCATGTCAGGAGGAGGAT 59.232 52.381 0.19 0.00 0.00 3.24
319 358 2.221169 CAGTTTGAAGCTGCAGTACCA 58.779 47.619 16.64 7.73 0.00 3.25
536 575 7.679638 GCCTTTTCAATCAGATACGCATACTTT 60.680 37.037 0.00 0.00 0.00 2.66
682 724 3.886329 GACCGTCGCCGTTCGTTCT 62.886 63.158 4.29 0.00 39.67 3.01
798 840 2.030185 GTGACAGCTGGTTTCTCGACTA 60.030 50.000 19.93 0.00 0.00 2.59
997 1045 2.105649 GGGAAGAAGGAGCTAGGGAATG 59.894 54.545 0.00 0.00 0.00 2.67
998 1046 2.413601 GGGAAGAAGGAGCTAGGGAAT 58.586 52.381 0.00 0.00 0.00 3.01
999 1047 1.625508 GGGGAAGAAGGAGCTAGGGAA 60.626 57.143 0.00 0.00 0.00 3.97
1000 1048 0.031010 GGGGAAGAAGGAGCTAGGGA 60.031 60.000 0.00 0.00 0.00 4.20
1001 1049 1.403687 CGGGGAAGAAGGAGCTAGGG 61.404 65.000 0.00 0.00 0.00 3.53
1002 1050 0.688087 ACGGGGAAGAAGGAGCTAGG 60.688 60.000 0.00 0.00 0.00 3.02
1003 1051 0.747852 GACGGGGAAGAAGGAGCTAG 59.252 60.000 0.00 0.00 0.00 3.42
1004 1052 0.335361 AGACGGGGAAGAAGGAGCTA 59.665 55.000 0.00 0.00 0.00 3.32
1005 1053 0.973496 GAGACGGGGAAGAAGGAGCT 60.973 60.000 0.00 0.00 0.00 4.09
1006 1054 1.518302 GAGACGGGGAAGAAGGAGC 59.482 63.158 0.00 0.00 0.00 4.70
1007 1055 2.203806 GGAGACGGGGAAGAAGGAG 58.796 63.158 0.00 0.00 0.00 3.69
1037 1085 3.474486 TTGCTTGCTCTCACCGGCA 62.474 57.895 0.00 0.00 36.62 5.69
1067 1116 4.712425 GCACCACGTACGGCGAGT 62.712 66.667 21.06 7.84 44.77 4.18
1093 1142 1.561542 AGGCCTCCAGACATTTACAGG 59.438 52.381 0.00 0.00 0.00 4.00
1122 1171 2.661566 GACGACACCTCGACGACGA 61.662 63.158 9.98 9.98 43.06 4.20
1193 1242 3.173240 GGACGACGAGCGCTTCAC 61.173 66.667 13.26 4.90 46.04 3.18
1226 1275 1.374252 CGGTACAGGAACGCAGCTT 60.374 57.895 0.00 0.00 0.00 3.74
1284 1336 0.393402 ATCGGTCATGCACTGCACAT 60.393 50.000 5.67 0.00 43.04 3.21
1298 1350 0.966920 AACGAGGAGACAACATCGGT 59.033 50.000 0.00 0.00 45.96 4.69
1299 1351 2.527100 GTAACGAGGAGACAACATCGG 58.473 52.381 0.00 0.00 45.96 4.18
1359 1420 1.445066 AGTCACGCATGAGCTGACG 60.445 57.895 18.64 6.57 45.36 4.35
1372 1433 2.062519 GAGACGAAAGGAAGCAGTCAC 58.937 52.381 0.00 0.00 34.56 3.67
1375 1436 0.959553 TCGAGACGAAAGGAAGCAGT 59.040 50.000 0.00 0.00 31.06 4.40
1376 1437 2.159310 AGATCGAGACGAAAGGAAGCAG 60.159 50.000 0.00 0.00 39.99 4.24
1377 1438 1.819288 AGATCGAGACGAAAGGAAGCA 59.181 47.619 0.00 0.00 39.99 3.91
1378 1439 2.570442 AGATCGAGACGAAAGGAAGC 57.430 50.000 0.00 0.00 39.99 3.86
1379 1440 3.854809 GTCAAGATCGAGACGAAAGGAAG 59.145 47.826 5.10 0.00 39.99 3.46
1380 1441 3.367087 GGTCAAGATCGAGACGAAAGGAA 60.367 47.826 12.43 0.00 39.99 3.36
1381 1442 2.163815 GGTCAAGATCGAGACGAAAGGA 59.836 50.000 12.43 0.00 39.99 3.36
1382 1443 2.164624 AGGTCAAGATCGAGACGAAAGG 59.835 50.000 12.43 0.00 39.99 3.11
1383 1444 3.495670 AGGTCAAGATCGAGACGAAAG 57.504 47.619 12.43 0.00 39.99 2.62
1384 1445 3.254903 TGAAGGTCAAGATCGAGACGAAA 59.745 43.478 12.43 0.00 39.99 3.46
1385 1446 2.817844 TGAAGGTCAAGATCGAGACGAA 59.182 45.455 12.43 0.00 39.99 3.85
1386 1447 2.433436 TGAAGGTCAAGATCGAGACGA 58.567 47.619 12.43 0.00 41.13 4.20
1387 1448 2.921634 TGAAGGTCAAGATCGAGACG 57.078 50.000 12.43 0.00 35.63 4.18
1388 1449 5.062809 GTGAAATGAAGGTCAAGATCGAGAC 59.937 44.000 10.89 10.89 0.00 3.36
1389 1450 5.171476 GTGAAATGAAGGTCAAGATCGAGA 58.829 41.667 0.00 0.00 0.00 4.04
1390 1451 4.331168 GGTGAAATGAAGGTCAAGATCGAG 59.669 45.833 0.00 0.00 0.00 4.04
1391 1452 4.253685 GGTGAAATGAAGGTCAAGATCGA 58.746 43.478 0.00 0.00 0.00 3.59
1392 1453 4.002982 TGGTGAAATGAAGGTCAAGATCG 58.997 43.478 0.00 0.00 0.00 3.69
1393 1454 6.376581 AGAATGGTGAAATGAAGGTCAAGATC 59.623 38.462 0.00 0.00 0.00 2.75
1394 1455 6.251471 AGAATGGTGAAATGAAGGTCAAGAT 58.749 36.000 0.00 0.00 0.00 2.40
1395 1456 5.634118 AGAATGGTGAAATGAAGGTCAAGA 58.366 37.500 0.00 0.00 0.00 3.02
1396 1457 5.105997 GGAGAATGGTGAAATGAAGGTCAAG 60.106 44.000 0.00 0.00 0.00 3.02
1397 1458 4.766891 GGAGAATGGTGAAATGAAGGTCAA 59.233 41.667 0.00 0.00 0.00 3.18
1398 1459 4.335416 GGAGAATGGTGAAATGAAGGTCA 58.665 43.478 0.00 0.00 0.00 4.02
1401 1462 3.609853 TCGGAGAATGGTGAAATGAAGG 58.390 45.455 0.00 0.00 0.00 3.46
1478 1560 4.948004 TCTTCAGAGCGGTGAATAGAGTTA 59.052 41.667 0.00 0.00 35.88 2.24
1483 1565 3.243367 CCTCTCTTCAGAGCGGTGAATAG 60.243 52.174 4.86 7.06 44.61 1.73
1486 1568 0.891373 CCTCTCTTCAGAGCGGTGAA 59.109 55.000 4.86 4.05 44.61 3.18
1497 1579 2.301583 GCATAGGATCCCACCTCTCTTC 59.698 54.545 8.55 0.00 41.00 2.87
1539 1621 7.220030 GGGATGGTATATAGCATAATCCTGTG 58.780 42.308 23.76 0.00 43.71 3.66
1551 1633 9.716556 AGACTACATTTAGGGGATGGTATATAG 57.283 37.037 0.00 0.00 0.00 1.31
1553 1635 8.826765 CAAGACTACATTTAGGGGATGGTATAT 58.173 37.037 0.00 0.00 0.00 0.86
1554 1636 7.236847 CCAAGACTACATTTAGGGGATGGTATA 59.763 40.741 0.00 0.00 0.00 1.47
1555 1637 6.044404 CCAAGACTACATTTAGGGGATGGTAT 59.956 42.308 0.00 0.00 0.00 2.73
1556 1638 5.368523 CCAAGACTACATTTAGGGGATGGTA 59.631 44.000 0.00 0.00 0.00 3.25
1557 1639 4.166144 CCAAGACTACATTTAGGGGATGGT 59.834 45.833 0.00 0.00 0.00 3.55
1558 1640 4.412199 TCCAAGACTACATTTAGGGGATGG 59.588 45.833 0.00 0.00 0.00 3.51
1559 1641 5.630415 TCCAAGACTACATTTAGGGGATG 57.370 43.478 0.00 0.00 0.00 3.51
1560 1642 5.073691 CCATCCAAGACTACATTTAGGGGAT 59.926 44.000 0.00 0.00 31.52 3.85
1561 1643 4.412199 CCATCCAAGACTACATTTAGGGGA 59.588 45.833 0.00 0.00 0.00 4.81
1562 1644 4.412199 TCCATCCAAGACTACATTTAGGGG 59.588 45.833 0.00 0.00 0.00 4.79
1614 1713 5.163581 TGCATACTACCGGTACTTCTTTCTC 60.164 44.000 11.16 0.00 32.72 2.87
1615 1714 4.708421 TGCATACTACCGGTACTTCTTTCT 59.292 41.667 11.16 0.00 32.72 2.52
1616 1715 4.802563 GTGCATACTACCGGTACTTCTTTC 59.197 45.833 11.16 0.00 32.72 2.62
1617 1716 4.676196 CGTGCATACTACCGGTACTTCTTT 60.676 45.833 11.16 0.00 32.72 2.52
1618 1717 3.181493 CGTGCATACTACCGGTACTTCTT 60.181 47.826 11.16 0.00 32.72 2.52
1619 1718 2.357009 CGTGCATACTACCGGTACTTCT 59.643 50.000 11.16 0.00 32.72 2.85
1620 1719 2.724349 CGTGCATACTACCGGTACTTC 58.276 52.381 11.16 0.00 32.72 3.01
1628 1727 2.464865 CTCAGAAGCGTGCATACTACC 58.535 52.381 0.00 0.00 0.00 3.18
1649 1748 1.568606 CATGCACTGTCTGATCTCCG 58.431 55.000 0.00 0.00 0.00 4.63
1768 1876 2.910319 ACCACTGCCAAAGTATACTCCA 59.090 45.455 5.70 1.14 36.83 3.86
1791 1900 4.665451 TCATGTCAAGGATGAAACCATGT 58.335 39.130 0.00 0.00 38.12 3.21
1805 1914 1.272212 TGCGAGTACAGCTCATGTCAA 59.728 47.619 13.27 0.00 44.33 3.18
1875 1984 4.379174 TCCTGCAGGAAGTTTCGC 57.621 55.556 33.41 0.00 42.18 4.70
1939 2049 6.038603 ACATTTTCAGCGTGCAATCATACTAT 59.961 34.615 0.00 0.00 0.00 2.12
2074 2184 9.144298 CCTTGAGATTCCTAACCAATACTAGTA 57.856 37.037 4.77 4.77 0.00 1.82
2075 2185 7.844779 TCCTTGAGATTCCTAACCAATACTAGT 59.155 37.037 0.00 0.00 0.00 2.57
2076 2186 8.251383 TCCTTGAGATTCCTAACCAATACTAG 57.749 38.462 0.00 0.00 0.00 2.57
2185 2299 0.613012 GTCCTTGGAGCCATTGCCTT 60.613 55.000 0.00 0.00 38.69 4.35
2190 2304 1.002134 CACGGTCCTTGGAGCCATT 60.002 57.895 12.54 0.00 0.00 3.16
2202 2316 1.745489 GCACTTGGGATCCACGGTC 60.745 63.158 15.23 0.00 30.78 4.79
2208 2322 2.900528 CGATACGCACTTGGGATCC 58.099 57.895 1.92 1.92 0.00 3.36
2230 2344 1.135139 CGTCGACCCATCTTCAGTGAT 59.865 52.381 10.58 0.00 0.00 3.06
2249 2363 1.446272 GAGTTTCCTCGCCTGTCCG 60.446 63.158 0.00 0.00 0.00 4.79
2266 2380 2.097954 CAGTGTTTGCTTTGACTGCTGA 59.902 45.455 0.00 0.00 30.14 4.26
2297 2411 2.289569 CCTAGCAGCAGGATGGAAGATC 60.290 54.545 5.22 0.00 38.00 2.75
2725 2852 1.625315 TCACAAGTCCCTGGTCATCAG 59.375 52.381 0.00 0.00 43.00 2.90
3359 3657 2.529389 AGCCTCCACGGGTCCTTT 60.529 61.111 0.00 0.00 40.09 3.11
3512 3810 3.818586 GTGGAACGACCCGATGTTA 57.181 52.632 0.00 0.00 38.00 2.41
3707 4011 4.988716 TCCACCTCCACGACGCCT 62.989 66.667 0.00 0.00 0.00 5.52
3830 4137 1.376466 GAAGAACTCCAGCTGCCCA 59.624 57.895 8.66 0.00 0.00 5.36
4164 4471 6.591935 CAAGCCCACTTATAGATACCTCAAA 58.408 40.000 0.00 0.00 33.74 2.69
4314 4621 8.038492 ACATTTCTTCAAGCATAAGAACTCTC 57.962 34.615 7.42 0.00 41.43 3.20
4364 5760 1.001378 GTGCGTGTCAGGAAATTTGCT 60.001 47.619 6.36 6.36 0.00 3.91
4424 5820 5.237815 TGCTTGGTATCGTCATCATAATCC 58.762 41.667 0.00 0.00 0.00 3.01
4427 5823 7.416817 CAAATTGCTTGGTATCGTCATCATAA 58.583 34.615 0.00 0.00 0.00 1.90
4487 5883 1.635844 CGTAGTGTTGATTAGCGCCA 58.364 50.000 2.29 0.00 0.00 5.69
4489 5885 0.996462 TGCGTAGTGTTGATTAGCGC 59.004 50.000 0.00 0.00 43.07 5.92
4548 5944 9.683069 ATGAAAAGAACACAATCTTGATGTAAC 57.317 29.630 0.00 0.00 39.54 2.50
4710 6106 3.535561 CGAGGAAGCACCATAAACAGAT 58.464 45.455 2.96 0.00 42.04 2.90
4712 6108 2.009774 CCGAGGAAGCACCATAAACAG 58.990 52.381 2.96 0.00 42.04 3.16
4720 6116 1.079057 GAGGAACCGAGGAAGCACC 60.079 63.158 0.00 0.00 39.35 5.01
4730 6126 1.949525 CAAATAGCATGGGAGGAACCG 59.050 52.381 0.00 0.00 40.11 4.44
4731 6127 3.297134 TCAAATAGCATGGGAGGAACC 57.703 47.619 0.00 0.00 38.08 3.62
4732 6128 3.005155 GCATCAAATAGCATGGGAGGAAC 59.995 47.826 0.00 0.00 0.00 3.62
4833 6229 5.092554 TCAACAAGTGTTACCTGTCTTGA 57.907 39.130 10.09 0.00 39.39 3.02
4871 6268 9.432982 ACAAATCCTAGTCTATCTCATCTTTCT 57.567 33.333 0.00 0.00 0.00 2.52
4914 6313 8.083828 ACTGGAGTACAATGATCTACTTGAAT 57.916 34.615 0.00 0.00 0.00 2.57
4961 6361 8.024285 GGATTGGTTGAATTGTTCGTTGTATTA 58.976 33.333 0.00 0.00 0.00 0.98
4992 6395 6.636454 AACTGATACCATGTTAGAAGGGAA 57.364 37.500 0.00 0.00 0.00 3.97
5021 6424 0.106149 CGGCGGCTAGGGTTTAGAAT 59.894 55.000 7.61 0.00 0.00 2.40
5195 6603 0.459899 CGATCAAGATGACCGGTGGA 59.540 55.000 14.63 0.00 0.00 4.02
5198 6606 1.144057 GCCGATCAAGATGACCGGT 59.856 57.895 6.92 6.92 41.95 5.28
5229 6637 7.359264 CGACGCAATAAGATTAGATCGGAAAAT 60.359 37.037 0.00 0.00 0.00 1.82
5777 7191 3.134127 GAAGGGCCGCCACATGAC 61.134 66.667 12.58 0.00 0.00 3.06
5778 7192 3.645660 TGAAGGGCCGCCACATGA 61.646 61.111 12.58 0.00 0.00 3.07
5779 7193 3.443045 GTGAAGGGCCGCCACATG 61.443 66.667 21.06 0.00 0.00 3.21
5780 7194 4.740822 GGTGAAGGGCCGCCACAT 62.741 66.667 25.07 0.00 36.73 3.21
5788 7202 1.077716 AATAGTGGCGGTGAAGGGC 60.078 57.895 0.00 0.00 0.00 5.19
5789 7203 0.810031 CGAATAGTGGCGGTGAAGGG 60.810 60.000 0.00 0.00 0.00 3.95
5790 7204 1.429148 GCGAATAGTGGCGGTGAAGG 61.429 60.000 0.00 0.00 0.00 3.46
5791 7205 1.752501 CGCGAATAGTGGCGGTGAAG 61.753 60.000 11.87 0.00 46.89 3.02
5792 7206 1.807981 CGCGAATAGTGGCGGTGAA 60.808 57.895 11.87 0.00 46.89 3.18
5793 7207 2.202690 CGCGAATAGTGGCGGTGA 60.203 61.111 11.87 0.00 46.89 4.02


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

AutoCloner maintained by Alex Coulton.