Multiple sequence alignment - TraesCS3D01G320900

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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 TraesCS3D01G320900 chr3D 100.000 2216 0 0 1 2216 433762774 433764989 0.000000e+00 4093.0
1 TraesCS3D01G320900 chr3D 90.244 533 29 12 1 519 152814872 152815395 0.000000e+00 675.0
2 TraesCS3D01G320900 chr3D 84.493 503 55 18 40 522 12766778 12766279 1.990000e-130 475.0
3 TraesCS3D01G320900 chr3D 84.646 254 38 1 1785 2037 121797471 121797218 3.650000e-63 252.0
4 TraesCS3D01G320900 chr3D 84.646 254 38 1 1785 2037 121875868 121875615 3.650000e-63 252.0
5 TraesCS3D01G320900 chr3D 79.018 224 20 14 552 773 152815387 152815585 6.420000e-26 128.0
6 TraesCS3D01G320900 chr3D 76.000 225 45 5 991 1215 433816741 433816956 8.370000e-20 108.0
7 TraesCS3D01G320900 chr3D 91.667 60 3 2 378 435 152815291 152815350 5.070000e-12 82.4
8 TraesCS3D01G320900 chr3A 89.645 705 51 8 781 1478 572345777 572346466 0.000000e+00 878.0
9 TraesCS3D01G320900 chr3A 85.160 748 85 20 1479 2216 572346927 572347658 0.000000e+00 743.0
10 TraesCS3D01G320900 chr3A 81.556 347 58 5 1690 2032 741622222 741621878 4.660000e-72 281.0
11 TraesCS3D01G320900 chr3B 91.254 606 27 9 781 1378 566995019 566995606 0.000000e+00 802.0
12 TraesCS3D01G320900 chr6D 83.396 795 44 34 1 777 24270352 24269628 0.000000e+00 656.0
13 TraesCS3D01G320900 chr6D 89.055 402 33 9 1 398 41201932 41202326 2.560000e-134 488.0
14 TraesCS3D01G320900 chr6D 83.289 377 51 7 1667 2031 388207166 388207542 9.800000e-89 337.0
15 TraesCS3D01G320900 chr6D 89.189 148 12 3 627 773 85543719 85543863 4.860000e-42 182.0
16 TraesCS3D01G320900 chr2A 91.076 437 36 3 1 435 767748631 767748196 2.450000e-164 588.0
17 TraesCS3D01G320900 chr2A 79.088 373 57 13 1669 2034 686814021 686814379 1.020000e-58 237.0
18 TraesCS3D01G320900 chr2A 85.185 135 14 5 2085 2216 733620775 733620906 1.380000e-27 134.0
19 TraesCS3D01G320900 chr5D 92.000 400 30 2 1 398 542361196 542361595 5.340000e-156 560.0
20 TraesCS3D01G320900 chr5D 88.337 403 35 11 1 398 8175528 8175923 7.160000e-130 473.0
21 TraesCS3D01G320900 chr5D 84.848 132 16 3 2085 2215 200488393 200488521 1.790000e-26 130.0
22 TraesCS3D01G320900 chr7D 87.191 445 45 7 2 435 545354316 545353873 1.530000e-136 496.0
23 TraesCS3D01G320900 chr7D 92.800 125 6 3 651 773 545353757 545353634 6.290000e-41 178.0
24 TraesCS3D01G320900 chr7D 85.714 133 14 4 2086 2215 102546328 102546458 3.840000e-28 135.0
25 TraesCS3D01G320900 chr4A 84.007 544 57 20 243 773 41995146 41994620 1.530000e-136 496.0
26 TraesCS3D01G320900 chr4A 86.058 416 41 15 1 406 666435975 666435567 4.370000e-117 431.0
27 TraesCS3D01G320900 chr2B 83.144 528 66 18 5 519 667768747 667769264 5.580000e-126 460.0
28 TraesCS3D01G320900 chr2B 79.167 360 71 4 1679 2034 692626956 692627315 1.700000e-61 246.0
29 TraesCS3D01G320900 chr2B 83.491 212 31 4 1666 1873 635345743 635345954 6.240000e-46 195.0
30 TraesCS3D01G320900 chr2D 82.081 346 57 5 1690 2033 10736092 10735750 7.740000e-75 291.0
31 TraesCS3D01G320900 chr2D 80.347 346 48 10 1670 2008 544568160 544568492 6.110000e-61 244.0
32 TraesCS3D01G320900 chr2D 84.328 134 18 2 2085 2216 306316089 306315957 6.420000e-26 128.0
33 TraesCS3D01G320900 chr1D 81.921 354 55 5 1663 2011 381063594 381063245 7.740000e-75 291.0
34 TraesCS3D01G320900 chr1D 89.076 119 11 2 654 771 446793403 446793520 1.770000e-31 147.0
35 TraesCS3D01G320900 chrUn 80.000 335 58 6 1699 2032 280234135 280233809 2.840000e-59 239.0
36 TraesCS3D01G320900 chrUn 85.606 132 16 3 2086 2215 311939762 311939892 3.840000e-28 135.0
37 TraesCS3D01G320900 chr7B 86.893 206 24 3 573 776 389984080 389983876 6.160000e-56 228.0
38 TraesCS3D01G320900 chr4B 83.251 203 25 8 573 768 616612012 616611812 6.290000e-41 178.0
39 TraesCS3D01G320900 chr1A 92.063 126 6 3 651 773 489357845 489357721 8.130000e-40 174.0
40 TraesCS3D01G320900 chr5B 88.000 125 14 1 2086 2209 16680797 16680673 1.770000e-31 147.0
41 TraesCS3D01G320900 chr5B 86.400 125 16 1 2086 2209 16700740 16700616 3.840000e-28 135.0
42 TraesCS3D01G320900 chr5A 89.286 112 10 2 2102 2213 38537269 38537378 2.970000e-29 139.0


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 TraesCS3D01G320900 chr3D 433762774 433764989 2215 False 4093.000000 4093 100.000000 1 2216 1 chr3D.!!$F1 2215
1 TraesCS3D01G320900 chr3D 152814872 152815585 713 False 295.133333 675 86.976333 1 773 3 chr3D.!!$F3 772
2 TraesCS3D01G320900 chr3A 572345777 572347658 1881 False 810.500000 878 87.402500 781 2216 2 chr3A.!!$F1 1435
3 TraesCS3D01G320900 chr3B 566995019 566995606 587 False 802.000000 802 91.254000 781 1378 1 chr3B.!!$F1 597
4 TraesCS3D01G320900 chr6D 24269628 24270352 724 True 656.000000 656 83.396000 1 777 1 chr6D.!!$R1 776
5 TraesCS3D01G320900 chr7D 545353634 545354316 682 True 337.000000 496 89.995500 2 773 2 chr7D.!!$R1 771
6 TraesCS3D01G320900 chr4A 41994620 41995146 526 True 496.000000 496 84.007000 243 773 1 chr4A.!!$R1 530
7 TraesCS3D01G320900 chr2B 667768747 667769264 517 False 460.000000 460 83.144000 5 519 1 chr2B.!!$F2 514

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
530 606 0.095935 CGTACGTACACCTCGACAGG 59.904 60.0 24.5 1.32 46.87 4.0 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1824 2402 0.037326 GGCTGTCATCGACAAGGTCA 60.037 55.0 0.0 0.0 42.26 4.02 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
45 46 3.195698 GGCGGTGATGCGGAAGAC 61.196 66.667 0.00 0.00 35.06 3.01
103 104 2.490217 CGGATGAGCTCGTCGGTT 59.510 61.111 27.04 2.71 32.78 4.44
192 193 2.060567 ATGGATGCCACCGAGATGGG 62.061 60.000 0.00 0.00 44.64 4.00
196 197 1.561769 ATGCCACCGAGATGGGAACA 61.562 55.000 0.00 0.00 44.11 3.18
506 582 0.757561 TCCTTGACCACGACTGGACA 60.758 55.000 0.00 0.00 40.55 4.02
508 584 1.270839 CCTTGACCACGACTGGACATT 60.271 52.381 0.00 0.00 41.17 2.71
517 593 2.342910 GACTGGACATTGTCGTACGT 57.657 50.000 16.05 0.00 32.65 3.57
518 594 3.476295 GACTGGACATTGTCGTACGTA 57.524 47.619 16.05 2.87 32.65 3.57
519 595 3.166657 GACTGGACATTGTCGTACGTAC 58.833 50.000 15.90 15.90 32.65 3.67
520 596 2.553602 ACTGGACATTGTCGTACGTACA 59.446 45.455 24.50 14.80 32.65 2.90
521 597 2.912967 CTGGACATTGTCGTACGTACAC 59.087 50.000 24.50 19.91 32.65 2.90
522 598 2.253603 GGACATTGTCGTACGTACACC 58.746 52.381 24.50 14.35 32.65 4.16
523 599 2.095059 GGACATTGTCGTACGTACACCT 60.095 50.000 24.50 9.61 32.65 4.00
524 600 3.166657 GACATTGTCGTACGTACACCTC 58.833 50.000 24.50 11.78 0.00 3.85
525 601 2.171567 CATTGTCGTACGTACACCTCG 58.828 52.381 24.50 11.02 0.00 4.63
526 602 1.507562 TTGTCGTACGTACACCTCGA 58.492 50.000 24.50 13.18 0.00 4.04
527 603 0.790207 TGTCGTACGTACACCTCGAC 59.210 55.000 24.50 22.97 46.89 4.20
528 604 0.790207 GTCGTACGTACACCTCGACA 59.210 55.000 24.50 0.00 46.28 4.35
529 605 1.070821 TCGTACGTACACCTCGACAG 58.929 55.000 24.50 5.90 0.00 3.51
530 606 0.095935 CGTACGTACACCTCGACAGG 59.904 60.000 24.50 1.32 46.87 4.00
542 618 2.732658 GACAGGTCGGGTCGTGTT 59.267 61.111 0.00 0.00 36.72 3.32
543 619 1.068585 GACAGGTCGGGTCGTGTTT 59.931 57.895 0.00 0.00 36.72 2.83
544 620 0.531311 GACAGGTCGGGTCGTGTTTT 60.531 55.000 0.00 0.00 36.72 2.43
545 621 0.107557 ACAGGTCGGGTCGTGTTTTT 60.108 50.000 0.00 0.00 33.55 1.94
623 720 3.066190 TCGCCGTACAGGACCTGG 61.066 66.667 25.34 8.83 45.00 4.45
625 722 3.702048 GCCGTACAGGACCTGGCA 61.702 66.667 25.34 10.09 45.06 4.92
645 742 2.550101 GGGTATAGCCTCGTCGCGT 61.550 63.158 13.90 0.00 37.43 6.01
732 831 0.686769 AAGGGGTACGGAGCGATCTT 60.687 55.000 0.00 0.00 0.00 2.40
760 860 5.389725 CGTTGTTGTATTTAGGGGTTGTACG 60.390 44.000 0.00 0.00 0.00 3.67
773 873 2.479275 GGTTGTACGGAAGAAGAAGTGC 59.521 50.000 0.00 0.00 0.00 4.40
777 877 4.806330 TGTACGGAAGAAGAAGTGCTTAG 58.194 43.478 0.00 0.00 36.83 2.18
778 878 2.689646 ACGGAAGAAGAAGTGCTTAGC 58.310 47.619 0.00 0.00 36.83 3.09
779 879 2.003301 CGGAAGAAGAAGTGCTTAGCC 58.997 52.381 0.29 0.00 36.83 3.93
839 939 1.135721 GGACCCATGACGTGTAGTACC 59.864 57.143 0.00 0.00 0.00 3.34
923 1023 2.747460 CCCACACCCACAGCATCG 60.747 66.667 0.00 0.00 0.00 3.84
937 1037 1.519455 CATCGGAGTTGGAGGCGAC 60.519 63.158 0.00 0.00 0.00 5.19
955 1060 0.530288 ACAGCAACCACACACCAAAC 59.470 50.000 0.00 0.00 0.00 2.93
989 1094 1.915228 GCTGGCCTGGATACCTTGA 59.085 57.895 12.06 0.00 0.00 3.02
1046 1154 1.077357 TCCTCCTCGTCCTGCTCTC 60.077 63.158 0.00 0.00 0.00 3.20
1061 1169 2.125350 CTCCTTGGCGAGCCTCAC 60.125 66.667 15.75 0.00 36.94 3.51
1286 1401 2.101917 GCAGCCCAGCATATGTGATTTT 59.898 45.455 4.29 0.00 0.00 1.82
1305 1420 0.179062 TTGTGGTGTGCAATTTGGGC 60.179 50.000 0.00 0.00 0.00 5.36
1306 1421 1.047596 TGTGGTGTGCAATTTGGGCT 61.048 50.000 0.00 0.00 0.00 5.19
1307 1422 0.106521 GTGGTGTGCAATTTGGGCTT 59.893 50.000 0.00 0.00 0.00 4.35
1308 1423 0.835941 TGGTGTGCAATTTGGGCTTT 59.164 45.000 0.00 0.00 0.00 3.51
1309 1424 1.228533 GGTGTGCAATTTGGGCTTTG 58.771 50.000 0.00 0.00 0.00 2.77
1310 1425 1.228533 GTGTGCAATTTGGGCTTTGG 58.771 50.000 0.00 0.00 0.00 3.28
1311 1426 0.108207 TGTGCAATTTGGGCTTTGGG 59.892 50.000 0.00 0.00 0.00 4.12
1312 1427 0.606130 GTGCAATTTGGGCTTTGGGG 60.606 55.000 0.00 0.00 0.00 4.96
1313 1428 1.059006 TGCAATTTGGGCTTTGGGGT 61.059 50.000 0.00 0.00 0.00 4.95
1314 1429 0.606130 GCAATTTGGGCTTTGGGGTG 60.606 55.000 0.00 0.00 0.00 4.61
1315 1430 1.055040 CAATTTGGGCTTTGGGGTGA 58.945 50.000 0.00 0.00 0.00 4.02
1316 1431 1.419387 CAATTTGGGCTTTGGGGTGAA 59.581 47.619 0.00 0.00 0.00 3.18
1317 1432 1.351076 ATTTGGGCTTTGGGGTGAAG 58.649 50.000 0.00 0.00 0.00 3.02
1318 1433 0.263172 TTTGGGCTTTGGGGTGAAGA 59.737 50.000 0.00 0.00 0.00 2.87
1319 1434 0.469144 TTGGGCTTTGGGGTGAAGAC 60.469 55.000 0.00 0.00 0.00 3.01
1326 1441 3.406764 CTTTGGGGTGAAGACTCAAGAG 58.593 50.000 0.00 0.00 31.88 2.85
1369 1484 2.723530 TCCTCTCCCTTGACTCCTTT 57.276 50.000 0.00 0.00 0.00 3.11
1382 1497 1.101331 CTCCTTTGGATGGCAGCTTC 58.899 55.000 1.50 0.00 0.00 3.86
1393 1508 0.528924 GGCAGCTTCATGTGATTGCA 59.471 50.000 13.78 0.00 31.91 4.08
1407 1522 3.798337 GTGATTGCAGTGTGTTTTTCCAG 59.202 43.478 0.00 0.00 0.00 3.86
1414 1529 4.869861 GCAGTGTGTTTTTCCAGTTCAAAT 59.130 37.500 0.00 0.00 0.00 2.32
1418 1533 7.759433 CAGTGTGTTTTTCCAGTTCAAATTACT 59.241 33.333 0.00 0.00 0.00 2.24
1420 1535 9.016623 GTGTGTTTTTCCAGTTCAAATTACTAC 57.983 33.333 0.00 0.00 0.00 2.73
1422 1537 9.797556 GTGTTTTTCCAGTTCAAATTACTACTT 57.202 29.630 0.00 0.00 0.00 2.24
1459 1574 8.978539 TGATATACACATCGTCTTCAAAATAGC 58.021 33.333 0.00 0.00 0.00 2.97
1469 1584 5.621228 CGTCTTCAAAATAGCACTTTGTCAC 59.379 40.000 5.44 1.91 35.65 3.67
1484 2059 4.902443 TTGTCACTAATTTCCGTGCAAA 57.098 36.364 0.00 0.00 30.31 3.68
1521 2096 5.945784 TGCAAAGGTAATTTAGATGCAGAGT 59.054 36.000 0.00 0.00 0.00 3.24
1537 2112 6.599356 TGCAGAGTCTAGTGTTATAAACCA 57.401 37.500 0.00 0.00 0.00 3.67
1554 2129 5.841957 AAACCAGCTATTTTAGATGCAGG 57.158 39.130 0.00 0.00 40.69 4.85
1555 2130 3.825328 ACCAGCTATTTTAGATGCAGGG 58.175 45.455 0.00 0.00 40.69 4.45
1558 2133 3.501445 CAGCTATTTTAGATGCAGGGAGC 59.499 47.826 0.00 0.00 45.96 4.70
1567 2142 2.436109 GCAGGGAGCAGGGTCAAA 59.564 61.111 0.56 0.00 44.79 2.69
1568 2143 1.973812 GCAGGGAGCAGGGTCAAAC 60.974 63.158 0.56 0.00 44.79 2.93
1569 2144 1.455849 CAGGGAGCAGGGTCAAACA 59.544 57.895 0.56 0.00 0.00 2.83
1570 2145 0.178992 CAGGGAGCAGGGTCAAACAA 60.179 55.000 0.56 0.00 0.00 2.83
1608 2183 5.050972 GCATAATTCGAAAAGGACTCCTACG 60.051 44.000 0.00 5.58 31.13 3.51
1616 2191 7.775120 TCGAAAAGGACTCCTACGTTTTATAT 58.225 34.615 14.58 0.00 36.14 0.86
1619 2194 8.943909 AAAAGGACTCCTACGTTTTATATCAG 57.056 34.615 0.00 0.00 34.91 2.90
1623 2198 6.086785 ACTCCTACGTTTTATATCAGAGGC 57.913 41.667 0.00 0.00 0.00 4.70
1632 2207 7.822822 ACGTTTTATATCAGAGGCAGTAGTTTT 59.177 33.333 0.00 0.00 0.00 2.43
1633 2208 8.328864 CGTTTTATATCAGAGGCAGTAGTTTTC 58.671 37.037 0.00 0.00 0.00 2.29
1634 2209 9.162764 GTTTTATATCAGAGGCAGTAGTTTTCA 57.837 33.333 0.00 0.00 0.00 2.69
1635 2210 9.905713 TTTTATATCAGAGGCAGTAGTTTTCAT 57.094 29.630 0.00 0.00 0.00 2.57
1640 2215 6.970484 TCAGAGGCAGTAGTTTTCATTTTTC 58.030 36.000 0.00 0.00 0.00 2.29
1645 2220 5.751509 GGCAGTAGTTTTCATTTTTCCGTTT 59.248 36.000 0.00 0.00 0.00 3.60
1650 2225 5.972935 AGTTTTCATTTTTCCGTTTGAGGT 58.027 33.333 0.00 0.00 0.00 3.85
1657 2235 6.596497 TCATTTTTCCGTTTGAGGTATAGGAC 59.404 38.462 0.00 0.00 0.00 3.85
1663 2241 4.980434 CCGTTTGAGGTATAGGACGTAATG 59.020 45.833 0.00 0.00 0.00 1.90
1664 2242 4.980434 CGTTTGAGGTATAGGACGTAATGG 59.020 45.833 0.00 0.00 0.00 3.16
1669 2247 6.949715 TGAGGTATAGGACGTAATGGTTTTT 58.050 36.000 0.00 0.00 0.00 1.94
1737 2315 5.659440 ACAAAGCACCCCAAACATAATAG 57.341 39.130 0.00 0.00 0.00 1.73
1739 2317 5.777732 ACAAAGCACCCCAAACATAATAGAA 59.222 36.000 0.00 0.00 0.00 2.10
1763 2341 7.553881 AATTACATCGAGGTTAATGGACAAG 57.446 36.000 8.51 0.00 0.00 3.16
1776 2354 1.421485 GACAAGCGAGCGACCATTG 59.579 57.895 0.00 0.00 0.00 2.82
1798 2376 3.767230 CGACAGAACGCGCCACAG 61.767 66.667 5.73 0.00 0.00 3.66
1799 2377 2.661866 GACAGAACGCGCCACAGT 60.662 61.111 5.73 0.08 0.00 3.55
1810 2388 3.625897 CCACAGTCGTGCCTCCCA 61.626 66.667 0.00 0.00 42.17 4.37
1811 2389 2.665000 CACAGTCGTGCCTCCCAT 59.335 61.111 0.00 0.00 36.06 4.00
1812 2390 1.613317 CCACAGTCGTGCCTCCCATA 61.613 60.000 0.00 0.00 42.17 2.74
1814 2392 0.902984 ACAGTCGTGCCTCCCATACA 60.903 55.000 0.00 0.00 0.00 2.29
1815 2393 0.179100 CAGTCGTGCCTCCCATACAG 60.179 60.000 0.00 0.00 0.00 2.74
1816 2394 0.324368 AGTCGTGCCTCCCATACAGA 60.324 55.000 0.00 0.00 0.00 3.41
1817 2395 0.103208 GTCGTGCCTCCCATACAGAG 59.897 60.000 0.00 0.00 0.00 3.35
1818 2396 1.227380 CGTGCCTCCCATACAGAGC 60.227 63.158 0.00 0.00 0.00 4.09
1820 2398 2.423446 GCCTCCCATACAGAGCCG 59.577 66.667 0.00 0.00 0.00 5.52
1821 2399 3.142393 CCTCCCATACAGAGCCGG 58.858 66.667 0.00 0.00 0.00 6.13
1822 2400 2.423446 CTCCCATACAGAGCCGGC 59.577 66.667 21.89 21.89 0.00 6.13
1824 2402 1.762522 CTCCCATACAGAGCCGGCAT 61.763 60.000 31.54 14.70 0.00 4.40
1827 2406 0.882042 CCATACAGAGCCGGCATGAC 60.882 60.000 31.28 18.79 0.00 3.06
1841 2420 1.662629 GCATGACCTTGTCGATGACAG 59.337 52.381 0.00 0.00 43.69 3.51
1844 2423 0.037326 GACCTTGTCGATGACAGCCA 60.037 55.000 0.00 0.00 43.69 4.75
1845 2424 0.036952 ACCTTGTCGATGACAGCCAG 60.037 55.000 0.00 0.00 43.69 4.85
1851 2430 1.996191 GTCGATGACAGCCAGAAAGTC 59.004 52.381 0.00 0.00 32.09 3.01
1858 2437 0.514691 CAGCCAGAAAGTCTTCGTGC 59.485 55.000 0.00 0.00 36.61 5.34
1859 2438 0.106708 AGCCAGAAAGTCTTCGTGCA 59.893 50.000 0.00 0.00 36.18 4.57
1860 2439 0.235926 GCCAGAAAGTCTTCGTGCAC 59.764 55.000 6.82 6.82 36.61 4.57
1861 2440 0.508641 CCAGAAAGTCTTCGTGCACG 59.491 55.000 32.76 32.76 36.61 5.34
1862 2441 0.111089 CAGAAAGTCTTCGTGCACGC 60.111 55.000 33.63 19.65 39.60 5.34
1874 2453 2.107141 GCACGCGCCTCTAAGGAT 59.893 61.111 5.73 0.00 37.67 3.24
1913 2492 3.798202 AGACGTGGCTATTGAATCCTTC 58.202 45.455 0.00 0.00 0.00 3.46
1926 2505 6.915544 TTGAATCCTTCAATCGATCTGAAG 57.084 37.500 26.51 26.51 44.21 3.02
1979 2558 3.490399 CACGACGAGAAACTCTAACCTC 58.510 50.000 0.00 0.00 0.00 3.85
1982 2561 2.923605 CGAGAAACTCTAACCTCGCT 57.076 50.000 0.00 0.00 41.31 4.93
1984 2563 2.095161 CGAGAAACTCTAACCTCGCTGT 60.095 50.000 0.00 0.00 41.31 4.40
1997 2576 2.973899 GCTGTTCCGAGGAGCTGA 59.026 61.111 14.92 0.00 0.00 4.26
1999 2578 1.967535 CTGTTCCGAGGAGCTGACA 59.032 57.895 7.47 1.45 0.00 3.58
2016 2595 0.683504 ACAGGAATCTACGCCGGAGT 60.684 55.000 17.10 17.10 0.00 3.85
2039 2618 1.135141 CGTTTAACCCGTCCCGACATA 60.135 52.381 0.00 0.00 0.00 2.29
2049 2628 4.491676 CCGTCCCGACATATAATAGTTGG 58.508 47.826 0.00 0.00 38.74 3.77
2121 2702 3.770666 ACACACAGACGCTCATACATAC 58.229 45.455 0.00 0.00 0.00 2.39
2122 2703 3.192633 ACACACAGACGCTCATACATACA 59.807 43.478 0.00 0.00 0.00 2.29
2135 2716 6.199154 GCTCATACATACACACATACACTCAC 59.801 42.308 0.00 0.00 0.00 3.51
2141 2722 3.450904 ACACACATACACTCACCCCTAT 58.549 45.455 0.00 0.00 0.00 2.57
2142 2723 4.616553 ACACACATACACTCACCCCTATA 58.383 43.478 0.00 0.00 0.00 1.31
2150 2731 1.903860 ACTCACCCCTATAAACGCACA 59.096 47.619 0.00 0.00 0.00 4.57
2153 2734 1.735571 CACCCCTATAAACGCACACAC 59.264 52.381 0.00 0.00 0.00 3.82
2154 2735 1.003851 CCCCTATAAACGCACACACG 58.996 55.000 0.00 0.00 39.50 4.49
2166 2747 0.037326 CACACACGCACATCCTACCT 60.037 55.000 0.00 0.00 0.00 3.08
2167 2748 1.203758 CACACACGCACATCCTACCTA 59.796 52.381 0.00 0.00 0.00 3.08
2171 2752 5.048294 CACACACGCACATCCTACCTATATA 60.048 44.000 0.00 0.00 0.00 0.86
2179 2760 6.295916 GCACATCCTACCTATATAAGCACCTT 60.296 42.308 0.00 0.00 0.00 3.50
2192 2773 0.885196 GCACCTTCGAGAGACTGAGT 59.115 55.000 0.00 0.00 41.84 3.41
2204 2785 1.135915 AGACTGAGTCGGCACATCATC 59.864 52.381 6.99 0.00 37.67 2.92
2209 2790 1.929836 GAGTCGGCACATCATCTTGAC 59.070 52.381 0.00 0.00 0.00 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
69 70 2.351276 GGCTCGGGTTGATGGTGT 59.649 61.111 0.00 0.00 0.00 4.16
192 193 1.728426 CTCCACCGACGACGTGTTC 60.728 63.158 4.58 0.00 37.88 3.18
196 197 2.592574 TCACTCCACCGACGACGT 60.593 61.111 0.00 0.00 37.88 4.34
341 343 3.357079 GCCCCGATGCGCCATTAG 61.357 66.667 4.18 0.00 0.00 1.73
489 565 1.800586 CAATGTCCAGTCGTGGTCAAG 59.199 52.381 0.00 0.00 43.89 3.02
506 582 2.076100 TCGAGGTGTACGTACGACAAT 58.924 47.619 24.41 13.04 0.00 2.71
508 584 3.209266 TCGAGGTGTACGTACGACA 57.791 52.632 24.41 18.10 0.00 4.35
525 601 0.531311 AAAACACGACCCGACCTGTC 60.531 55.000 0.00 0.00 0.00 3.51
526 602 0.107557 AAAAACACGACCCGACCTGT 60.108 50.000 0.00 0.00 0.00 4.00
527 603 2.697819 AAAAACACGACCCGACCTG 58.302 52.632 0.00 0.00 0.00 4.00
543 619 3.928375 GCCGTCTACGTATGAAGGAAAAA 59.072 43.478 21.72 0.00 35.57 1.94
544 620 3.514645 GCCGTCTACGTATGAAGGAAAA 58.485 45.455 21.72 0.00 35.57 2.29
545 621 2.159198 GGCCGTCTACGTATGAAGGAAA 60.159 50.000 21.72 0.00 35.57 3.13
546 622 1.406539 GGCCGTCTACGTATGAAGGAA 59.593 52.381 21.72 0.00 35.57 3.36
547 623 1.027357 GGCCGTCTACGTATGAAGGA 58.973 55.000 21.72 4.73 35.57 3.36
548 624 0.031721 GGGCCGTCTACGTATGAAGG 59.968 60.000 16.67 16.67 37.74 3.46
549 625 0.317603 CGGGCCGTCTACGTATGAAG 60.318 60.000 19.97 0.00 37.74 3.02
550 626 0.747644 TCGGGCCGTCTACGTATGAA 60.748 55.000 27.32 0.00 37.74 2.57
551 627 1.153188 TCGGGCCGTCTACGTATGA 60.153 57.895 27.32 0.00 37.74 2.15
552 628 1.009222 GTCGGGCCGTCTACGTATG 60.009 63.158 27.32 0.00 37.74 2.39
553 629 1.451927 TGTCGGGCCGTCTACGTAT 60.452 57.895 27.32 0.00 37.74 3.06
554 630 2.046411 TGTCGGGCCGTCTACGTA 60.046 61.111 27.32 0.36 37.74 3.57
555 631 3.741476 GTGTCGGGCCGTCTACGT 61.741 66.667 27.32 0.00 37.74 3.57
556 632 4.824166 CGTGTCGGGCCGTCTACG 62.824 72.222 27.32 27.04 39.44 3.51
557 633 2.398554 TACGTGTCGGGCCGTCTAC 61.399 63.158 27.32 20.50 38.43 2.59
623 720 1.007618 GACGAGGCTATACCCGTGC 60.008 63.158 2.73 0.00 42.88 5.34
625 722 2.550101 GCGACGAGGCTATACCCGT 61.550 63.158 0.00 0.00 44.69 5.28
732 831 3.263937 ACCCCTAAATACAACAACGGCTA 59.736 43.478 0.00 0.00 0.00 3.93
760 860 3.059352 TGGCTAAGCACTTCTTCTTCC 57.941 47.619 0.00 0.00 36.25 3.46
803 903 0.035630 GTCCACAGCCAAGAGAGCAT 60.036 55.000 0.00 0.00 0.00 3.79
807 907 3.483587 GGGTCCACAGCCAAGAGA 58.516 61.111 0.00 0.00 40.30 3.10
839 939 2.926200 CGGCAAGATCTGTTGACTAGTG 59.074 50.000 0.00 0.00 32.74 2.74
923 1023 2.435059 GCTGTCGCCTCCAACTCC 60.435 66.667 0.00 0.00 0.00 3.85
937 1037 0.179113 GGTTTGGTGTGTGGTTGCTG 60.179 55.000 0.00 0.00 0.00 4.41
955 1060 3.503363 GCGCAGGCAGCTTGTAGG 61.503 66.667 0.30 0.00 42.61 3.18
989 1094 6.052405 AGAAGCTTCTCATCTTGTGATCTT 57.948 37.500 23.49 0.00 35.97 2.40
1061 1169 1.443872 CTTCCTTCCGTGACGTCCG 60.444 63.158 14.12 15.50 0.00 4.79
1232 1340 0.108186 CACAGAATCGCTAGGTGCCA 60.108 55.000 0.00 0.00 38.78 4.92
1233 1341 0.175760 TCACAGAATCGCTAGGTGCC 59.824 55.000 0.00 0.00 38.78 5.01
1286 1401 0.179062 GCCCAAATTGCACACCACAA 60.179 50.000 0.00 0.00 0.00 3.33
1305 1420 3.406764 CTCTTGAGTCTTCACCCCAAAG 58.593 50.000 0.00 0.00 31.71 2.77
1306 1421 2.106511 CCTCTTGAGTCTTCACCCCAAA 59.893 50.000 0.00 0.00 31.71 3.28
1307 1422 1.699634 CCTCTTGAGTCTTCACCCCAA 59.300 52.381 0.00 0.00 31.71 4.12
1308 1423 1.352083 CCTCTTGAGTCTTCACCCCA 58.648 55.000 0.00 0.00 31.71 4.96
1309 1424 0.035915 GCCTCTTGAGTCTTCACCCC 60.036 60.000 0.00 0.00 31.71 4.95
1310 1425 0.687354 TGCCTCTTGAGTCTTCACCC 59.313 55.000 0.00 0.00 31.71 4.61
1311 1426 2.354259 CATGCCTCTTGAGTCTTCACC 58.646 52.381 0.00 0.00 31.71 4.02
1312 1427 2.027745 TCCATGCCTCTTGAGTCTTCAC 60.028 50.000 0.00 0.00 31.71 3.18
1313 1428 2.235650 CTCCATGCCTCTTGAGTCTTCA 59.764 50.000 0.00 0.00 0.00 3.02
1314 1429 2.235898 ACTCCATGCCTCTTGAGTCTTC 59.764 50.000 0.00 0.00 32.85 2.87
1315 1430 2.264455 ACTCCATGCCTCTTGAGTCTT 58.736 47.619 0.00 0.00 32.85 3.01
1316 1431 1.949799 ACTCCATGCCTCTTGAGTCT 58.050 50.000 0.00 0.00 32.85 3.24
1317 1432 2.354259 CAACTCCATGCCTCTTGAGTC 58.646 52.381 1.26 0.00 37.09 3.36
1318 1433 1.004044 CCAACTCCATGCCTCTTGAGT 59.996 52.381 0.00 0.00 39.66 3.41
1319 1434 1.280133 TCCAACTCCATGCCTCTTGAG 59.720 52.381 0.00 0.00 0.00 3.02
1326 1441 4.646492 AGAAAATGTATCCAACTCCATGCC 59.354 41.667 0.00 0.00 0.00 4.40
1369 1484 0.328926 TCACATGAAGCTGCCATCCA 59.671 50.000 0.00 0.00 0.00 3.41
1382 1497 4.209703 GGAAAAACACACTGCAATCACATG 59.790 41.667 0.00 0.00 0.00 3.21
1393 1508 7.836842 AGTAATTTGAACTGGAAAAACACACT 58.163 30.769 0.00 0.00 0.00 3.55
1433 1548 8.978539 GCTATTTTGAAGACGATGTGTATATCA 58.021 33.333 0.00 0.00 0.00 2.15
1439 1554 4.997395 AGTGCTATTTTGAAGACGATGTGT 59.003 37.500 0.00 0.00 0.00 3.72
1440 1555 5.536554 AGTGCTATTTTGAAGACGATGTG 57.463 39.130 0.00 0.00 0.00 3.21
1459 1574 4.219033 GCACGGAAATTAGTGACAAAGTG 58.781 43.478 11.34 0.00 40.56 3.16
1469 1584 4.173036 ACCATGTTTGCACGGAAATTAG 57.827 40.909 0.00 0.00 31.40 1.73
1484 2059 2.173519 CCTTTGCATGAGGAACCATGT 58.826 47.619 10.38 0.00 44.25 3.21
1491 2066 6.039717 GCATCTAAATTACCTTTGCATGAGGA 59.960 38.462 20.17 2.78 37.72 3.71
1533 2108 4.079787 TCCCTGCATCTAAAATAGCTGGTT 60.080 41.667 0.00 0.00 42.42 3.67
1537 2112 3.749226 GCTCCCTGCATCTAAAATAGCT 58.251 45.455 0.00 0.00 42.31 3.32
1554 2129 3.181466 ACATTTTTGTTTGACCCTGCTCC 60.181 43.478 0.00 0.00 0.00 4.70
1555 2130 4.058721 ACATTTTTGTTTGACCCTGCTC 57.941 40.909 0.00 0.00 0.00 4.26
1567 2142 9.086336 CGAATTATGCTATCCAAACATTTTTGT 57.914 29.630 3.78 0.00 40.61 2.83
1568 2143 9.299963 TCGAATTATGCTATCCAAACATTTTTG 57.700 29.630 0.00 0.00 41.71 2.44
1569 2144 9.868277 TTCGAATTATGCTATCCAAACATTTTT 57.132 25.926 0.00 0.00 0.00 1.94
1570 2145 9.868277 TTTCGAATTATGCTATCCAAACATTTT 57.132 25.926 0.00 0.00 0.00 1.82
1591 2166 4.326504 AAAACGTAGGAGTCCTTTTCGA 57.673 40.909 26.28 6.35 34.61 3.71
1608 2183 9.162764 TGAAAACTACTGCCTCTGATATAAAAC 57.837 33.333 0.00 0.00 0.00 2.43
1616 2191 6.016276 GGAAAAATGAAAACTACTGCCTCTGA 60.016 38.462 0.00 0.00 0.00 3.27
1619 2194 5.154222 CGGAAAAATGAAAACTACTGCCTC 58.846 41.667 0.00 0.00 0.00 4.70
1623 2198 7.167468 CCTCAAACGGAAAAATGAAAACTACTG 59.833 37.037 0.00 0.00 0.00 2.74
1632 2207 6.596497 GTCCTATACCTCAAACGGAAAAATGA 59.404 38.462 0.00 0.00 0.00 2.57
1633 2208 6.456449 CGTCCTATACCTCAAACGGAAAAATG 60.456 42.308 0.00 0.00 0.00 2.32
1634 2209 5.583457 CGTCCTATACCTCAAACGGAAAAAT 59.417 40.000 0.00 0.00 0.00 1.82
1635 2210 4.931002 CGTCCTATACCTCAAACGGAAAAA 59.069 41.667 0.00 0.00 0.00 1.94
1640 2215 4.637483 TTACGTCCTATACCTCAAACGG 57.363 45.455 0.00 0.00 34.63 4.44
1645 2220 6.549433 AAAACCATTACGTCCTATACCTCA 57.451 37.500 0.00 0.00 0.00 3.86
1708 2286 1.600023 TGGGGTGCTTTGTACTTTCG 58.400 50.000 0.00 0.00 0.00 3.46
1709 2287 3.131400 TGTTTGGGGTGCTTTGTACTTTC 59.869 43.478 0.00 0.00 0.00 2.62
1720 2298 7.777095 TGTAATTTCTATTATGTTTGGGGTGC 58.223 34.615 0.00 0.00 0.00 5.01
1737 2315 7.548196 TGTCCATTAACCTCGATGTAATTTC 57.452 36.000 0.00 0.00 0.00 2.17
1739 2317 6.038271 GCTTGTCCATTAACCTCGATGTAATT 59.962 38.462 0.00 0.00 0.00 1.40
1753 2331 0.459585 GGTCGCTCGCTTGTCCATTA 60.460 55.000 0.00 0.00 0.00 1.90
1783 2361 2.661866 GACTGTGGCGCGTTCTGT 60.662 61.111 8.43 8.63 0.00 3.41
1797 2375 0.324368 TCTGTATGGGAGGCACGACT 60.324 55.000 0.00 0.00 0.00 4.18
1798 2376 0.103208 CTCTGTATGGGAGGCACGAC 59.897 60.000 0.00 0.00 0.00 4.34
1799 2377 1.676678 GCTCTGTATGGGAGGCACGA 61.677 60.000 0.00 0.00 0.00 4.35
1806 2384 1.766059 ATGCCGGCTCTGTATGGGA 60.766 57.895 29.70 2.45 0.00 4.37
1808 2386 0.882042 GTCATGCCGGCTCTGTATGG 60.882 60.000 29.70 7.87 0.00 2.74
1809 2387 0.882042 GGTCATGCCGGCTCTGTATG 60.882 60.000 29.70 21.81 0.00 2.39
1810 2388 1.050988 AGGTCATGCCGGCTCTGTAT 61.051 55.000 29.70 9.53 43.70 2.29
1811 2389 1.264749 AAGGTCATGCCGGCTCTGTA 61.265 55.000 29.70 7.00 43.70 2.74
1812 2390 2.596851 AAGGTCATGCCGGCTCTGT 61.597 57.895 29.70 8.26 43.70 3.41
1814 2392 2.270205 CAAGGTCATGCCGGCTCT 59.730 61.111 29.70 12.59 43.70 4.09
1815 2393 2.045926 ACAAGGTCATGCCGGCTC 60.046 61.111 29.70 14.81 43.70 4.70
1816 2394 2.045926 GACAAGGTCATGCCGGCT 60.046 61.111 29.70 10.60 43.70 5.52
1817 2395 3.499737 CGACAAGGTCATGCCGGC 61.500 66.667 22.73 22.73 43.70 6.13
1818 2396 1.153369 ATCGACAAGGTCATGCCGG 60.153 57.895 0.00 0.00 43.70 6.13
1820 2398 1.009829 GTCATCGACAAGGTCATGCC 58.990 55.000 0.00 0.00 32.09 4.40
1821 2399 1.662629 CTGTCATCGACAAGGTCATGC 59.337 52.381 0.00 0.00 42.26 4.06
1822 2400 1.662629 GCTGTCATCGACAAGGTCATG 59.337 52.381 0.00 0.00 42.26 3.07
1824 2402 0.037326 GGCTGTCATCGACAAGGTCA 60.037 55.000 0.00 0.00 42.26 4.02
1827 2406 0.247460 TCTGGCTGTCATCGACAAGG 59.753 55.000 0.00 0.00 42.26 3.61
1837 2416 1.795286 CACGAAGACTTTCTGGCTGTC 59.205 52.381 0.00 0.00 31.76 3.51
1841 2420 0.235926 GTGCACGAAGACTTTCTGGC 59.764 55.000 0.00 0.00 33.35 4.85
1844 2423 1.548973 CGCGTGCACGAAGACTTTCT 61.549 55.000 41.19 0.00 43.02 2.52
1845 2424 1.154836 CGCGTGCACGAAGACTTTC 60.155 57.895 41.19 20.02 43.02 2.62
1851 2430 3.964221 TAGAGGCGCGTGCACGAAG 62.964 63.158 41.19 31.78 45.35 3.79
1858 2437 0.596083 CTGATCCTTAGAGGCGCGTG 60.596 60.000 7.63 0.00 34.61 5.34
1859 2438 1.736586 CTGATCCTTAGAGGCGCGT 59.263 57.895 8.43 0.27 34.61 6.01
1860 2439 1.663074 GCTGATCCTTAGAGGCGCG 60.663 63.158 0.00 0.00 34.61 6.86
1861 2440 1.663074 CGCTGATCCTTAGAGGCGC 60.663 63.158 0.00 0.00 34.61 6.53
1862 2441 0.103208 AACGCTGATCCTTAGAGGCG 59.897 55.000 0.00 0.00 41.73 5.52
1866 2445 0.744874 CCCGAACGCTGATCCTTAGA 59.255 55.000 0.00 0.00 0.00 2.10
1890 2469 4.323553 AGGATTCAATAGCCACGTCTAC 57.676 45.455 0.00 0.00 0.00 2.59
1913 2492 4.328440 GTGTCAGGTTCTTCAGATCGATTG 59.672 45.833 0.00 0.15 0.00 2.67
1918 2497 3.685139 TGGTGTCAGGTTCTTCAGATC 57.315 47.619 0.00 0.00 0.00 2.75
1926 2505 2.607038 GGCGAAATTTGGTGTCAGGTTC 60.607 50.000 0.00 0.00 0.00 3.62
1979 2558 2.507992 CAGCTCCTCGGAACAGCG 60.508 66.667 0.00 0.00 0.00 5.18
1982 2561 1.536073 CCTGTCAGCTCCTCGGAACA 61.536 60.000 0.00 0.00 0.00 3.18
1984 2563 0.541998 TTCCTGTCAGCTCCTCGGAA 60.542 55.000 0.00 0.00 0.00 4.30
1997 2576 0.683504 ACTCCGGCGTAGATTCCTGT 60.684 55.000 6.46 0.00 0.00 4.00
1999 2578 0.745468 GAACTCCGGCGTAGATTCCT 59.255 55.000 6.46 0.00 0.00 3.36
2086 2665 7.225145 AGCGTCTGTGTGTATACTGTTTAAAAA 59.775 33.333 4.17 0.00 0.00 1.94
2091 2670 4.235360 GAGCGTCTGTGTGTATACTGTTT 58.765 43.478 4.17 0.00 0.00 2.83
2101 2682 3.547868 GTGTATGTATGAGCGTCTGTGTG 59.452 47.826 0.00 0.00 0.00 3.82
2104 2685 3.192633 TGTGTGTATGTATGAGCGTCTGT 59.807 43.478 0.00 0.00 0.00 3.41
2109 2690 5.281727 AGTGTATGTGTGTATGTATGAGCG 58.718 41.667 0.00 0.00 0.00 5.03
2121 2702 5.607939 TTATAGGGGTGAGTGTATGTGTG 57.392 43.478 0.00 0.00 0.00 3.82
2122 2703 5.394883 CGTTTATAGGGGTGAGTGTATGTGT 60.395 44.000 0.00 0.00 0.00 3.72
2135 2716 1.003851 CGTGTGTGCGTTTATAGGGG 58.996 55.000 0.00 0.00 0.00 4.79
2141 2722 0.233590 GATGTGCGTGTGTGCGTTTA 59.766 50.000 0.00 0.00 37.81 2.01
2142 2723 1.010125 GATGTGCGTGTGTGCGTTT 60.010 52.632 0.00 0.00 37.81 3.60
2150 2731 5.336531 GCTTATATAGGTAGGATGTGCGTGT 60.337 44.000 0.00 0.00 0.00 4.49
2153 2734 5.103000 GTGCTTATATAGGTAGGATGTGCG 58.897 45.833 0.00 0.00 0.00 5.34
2154 2735 5.187967 AGGTGCTTATATAGGTAGGATGTGC 59.812 44.000 0.00 0.00 0.00 4.57
2166 2747 6.296803 TCAGTCTCTCGAAGGTGCTTATATA 58.703 40.000 0.00 0.00 0.00 0.86
2167 2748 5.133941 TCAGTCTCTCGAAGGTGCTTATAT 58.866 41.667 0.00 0.00 0.00 0.86
2171 2752 1.543802 CTCAGTCTCTCGAAGGTGCTT 59.456 52.381 0.00 0.00 0.00 3.91
2179 2760 1.003718 TGCCGACTCAGTCTCTCGA 60.004 57.895 2.61 0.00 0.00 4.04
2192 2773 2.679336 CAATGTCAAGATGATGTGCCGA 59.321 45.455 0.00 0.00 0.00 5.54


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

AutoCloner maintained by Alex Coulton.