Multiple sequence alignment - TraesCS5D01G051400

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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 TraesCS5D01G051400 chr5D 100.000 4193 0 0 1 4193 49293061 49297253 0.000000e+00 7744.0
1 TraesCS5D01G051400 chr5D 84.689 1352 179 23 1807 3147 454204056 454205390 0.000000e+00 1325.0
2 TraesCS5D01G051400 chr5D 82.833 600 74 12 34 629 513902909 513903483 1.040000e-140 510.0
3 TraesCS5D01G051400 chr5D 83.363 565 69 10 121 671 88524094 88523541 2.250000e-137 499.0
4 TraesCS5D01G051400 chr5A 95.920 2402 82 8 1801 4193 38790667 38793061 0.000000e+00 3879.0
5 TraesCS5D01G051400 chr5A 84.145 1356 188 22 1803 3147 573601879 573603218 0.000000e+00 1288.0
6 TraesCS5D01G051400 chr5A 92.127 851 27 14 672 1482 38789787 38790637 0.000000e+00 1164.0
7 TraesCS5D01G051400 chr5A 83.363 559 61 13 125 669 82314974 82314434 4.870000e-134 488.0
8 TraesCS5D01G051400 chr5A 86.400 250 27 3 28 276 641682126 641682369 2.490000e-67 267.0
9 TraesCS5D01G051400 chr5A 96.774 62 2 0 672 733 38789435 38789496 2.060000e-18 104.0
10 TraesCS5D01G051400 chr5B 92.886 1996 92 25 1643 3633 51969111 51971061 0.000000e+00 2854.0
11 TraesCS5D01G051400 chr5B 90.854 820 32 12 735 1542 51968294 51969082 0.000000e+00 1059.0
12 TraesCS5D01G051400 chr5B 94.118 680 27 5 1 669 51964374 51965051 0.000000e+00 1022.0
13 TraesCS5D01G051400 chr5B 83.363 559 69 9 3645 4193 51971492 51972036 2.910000e-136 496.0
14 TraesCS5D01G051400 chr5B 83.363 559 68 10 125 669 94099786 94099239 1.050000e-135 494.0
15 TraesCS5D01G051400 chr7B 75.709 247 52 7 3923 4166 79074723 79074964 2.650000e-22 117.0
16 TraesCS5D01G051400 chr3D 72.603 292 71 9 3832 4122 579329045 579329328 2.080000e-13 87.9
17 TraesCS5D01G051400 chr7D 80.172 116 20 3 4052 4166 458592164 458592051 2.690000e-12 84.2
18 TraesCS5D01G051400 chr3A 84.706 85 10 3 3826 3908 224379274 224379357 9.660000e-12 82.4
19 TraesCS5D01G051400 chr3B 73.333 180 40 8 3990 4166 561855270 561855444 4.530000e-05 60.2


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 TraesCS5D01G051400 chr5D 49293061 49297253 4192 False 7744.000000 7744 100.000000 1 4193 1 chr5D.!!$F1 4192
1 TraesCS5D01G051400 chr5D 454204056 454205390 1334 False 1325.000000 1325 84.689000 1807 3147 1 chr5D.!!$F2 1340
2 TraesCS5D01G051400 chr5D 513902909 513903483 574 False 510.000000 510 82.833000 34 629 1 chr5D.!!$F3 595
3 TraesCS5D01G051400 chr5D 88523541 88524094 553 True 499.000000 499 83.363000 121 671 1 chr5D.!!$R1 550
4 TraesCS5D01G051400 chr5A 38789435 38793061 3626 False 1715.666667 3879 94.940333 672 4193 3 chr5A.!!$F3 3521
5 TraesCS5D01G051400 chr5A 573601879 573603218 1339 False 1288.000000 1288 84.145000 1803 3147 1 chr5A.!!$F1 1344
6 TraesCS5D01G051400 chr5A 82314434 82314974 540 True 488.000000 488 83.363000 125 669 1 chr5A.!!$R1 544
7 TraesCS5D01G051400 chr5B 51964374 51972036 7662 False 1357.750000 2854 90.305250 1 4193 4 chr5B.!!$F1 4192
8 TraesCS5D01G051400 chr5B 94099239 94099786 547 True 494.000000 494 83.363000 125 669 1 chr5B.!!$R1 544

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
735 4114 0.512952 CTCCTTCCTTGTCGCAAACG 59.487 55.000 0.00 0.00 42.01 3.60 F
840 4229 0.955428 GCCTGATTCCACTCAACGCA 60.955 55.000 0.00 0.00 0.00 5.24 F
1639 5070 1.002773 GGTGATGAACCGTTACACCCT 59.997 52.381 17.08 0.00 43.29 4.34 F
2451 5882 0.106519 GCATGGACTGGGCCAAGTAT 60.107 55.000 14.50 0.18 42.16 2.12 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1619 5050 1.002773 AGGGTGTAACGGTTCATCACC 59.997 52.381 22.75 22.75 45.17 4.02 R
1995 5426 1.593296 GGTCGAGGCGGTTGTAGTCT 61.593 60.000 0.00 0.00 0.00 3.24 R
3099 6530 1.227943 GAGCACCTTGGCAGTGTCA 60.228 57.895 8.44 0.00 37.56 3.58 R
4001 7867 0.919981 CGCTGTCGATGAAGAGAAGC 59.080 55.000 0.00 0.00 38.10 3.86 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
41 42 7.386848 GGTAGCAACTAACTGAACAATCAACTA 59.613 37.037 0.00 0.00 34.49 2.24
149 150 8.559536 GTTTTGAATCTGTGTCTAACTGAATCA 58.440 33.333 0.63 0.63 41.95 2.57
171 172 6.980593 TCATTGTGTATTTTCCCTTTGTCTG 58.019 36.000 0.00 0.00 0.00 3.51
200 208 5.560722 TTCAGGTGGTTTACAAGATCTGA 57.439 39.130 0.00 0.00 0.00 3.27
323 334 5.846203 AGTTATTCTTGCATGCTTTGTTGT 58.154 33.333 20.33 1.76 0.00 3.32
340 352 1.671054 GTGGCGCTCCAGCTTGTTA 60.671 57.895 7.64 0.00 44.48 2.41
475 487 2.274437 CTGACCATTGGATCAGACACG 58.726 52.381 21.28 4.33 44.32 4.49
526 538 9.468532 GTAGATTCTCAAAGCTCAAAATGTTTT 57.531 29.630 0.00 0.00 32.32 2.43
560 573 8.514330 TTTCAAGTTCTCAAGGCTAAAACTAA 57.486 30.769 0.00 0.00 30.37 2.24
607 623 4.276678 TGAAATTCAGAACTTGACAGGCTG 59.723 41.667 14.16 14.16 34.94 4.85
631 647 1.473080 GGCATCAGAGCTGAAGGACTC 60.473 57.143 4.06 0.00 43.58 3.36
635 659 0.536260 CAGAGCTGAAGGACTCCCAG 59.464 60.000 0.00 0.00 33.18 4.45
726 4105 1.889170 GGCCTTTCAACTCCTTCCTTG 59.111 52.381 0.00 0.00 0.00 3.61
733 4112 1.946768 CAACTCCTTCCTTGTCGCAAA 59.053 47.619 0.00 0.00 0.00 3.68
735 4114 0.512952 CTCCTTCCTTGTCGCAAACG 59.487 55.000 0.00 0.00 42.01 3.60
787 4169 3.245315 GCCGCGTACGTACTGCAG 61.245 66.667 28.60 22.72 37.70 4.41
788 4170 3.245315 CCGCGTACGTACTGCAGC 61.245 66.667 28.60 21.32 37.70 5.25
789 4171 2.503158 CGCGTACGTACTGCAGCA 60.503 61.111 28.60 0.00 33.53 4.41
802 4184 3.023949 GCAGCATCTCCGGTGAGGT 62.024 63.158 18.31 10.11 41.99 3.85
835 4224 0.976641 AACTCGCCTGATTCCACTCA 59.023 50.000 0.00 0.00 0.00 3.41
840 4229 0.955428 GCCTGATTCCACTCAACGCA 60.955 55.000 0.00 0.00 0.00 5.24
1404 4811 1.459455 CCATCGAGATCCCAGTCGCT 61.459 60.000 0.00 0.00 36.11 4.93
1427 4844 5.910614 TGGTGAATCACATGTCTGATCTAG 58.089 41.667 15.86 0.00 35.86 2.43
1444 4865 4.223556 TCTAGGGCTAGATCGTATCCTG 57.776 50.000 0.00 2.95 37.28 3.86
1487 4908 3.782656 ATGCATGCATGGATGAGTAGA 57.217 42.857 31.74 8.29 37.46 2.59
1489 4910 3.888583 TGCATGCATGGATGAGTAGAAA 58.111 40.909 29.10 3.76 0.00 2.52
1490 4911 3.628942 TGCATGCATGGATGAGTAGAAAC 59.371 43.478 29.10 10.29 0.00 2.78
1535 4966 9.461312 AATCACCTTAACTTACATGCAAATCTA 57.539 29.630 0.00 0.00 0.00 1.98
1542 4973 7.759489 AACTTACATGCAAATCTAAGGTTCA 57.241 32.000 0.00 0.00 0.00 3.18
1543 4974 7.759489 ACTTACATGCAAATCTAAGGTTCAA 57.241 32.000 0.00 0.00 0.00 2.69
1544 4975 7.593825 ACTTACATGCAAATCTAAGGTTCAAC 58.406 34.615 0.00 0.00 0.00 3.18
1545 4976 5.391312 ACATGCAAATCTAAGGTTCAACC 57.609 39.130 0.00 0.00 38.99 3.77
1561 4992 7.089770 GGTTCAACCTAGATCTTCATTTTCC 57.910 40.000 0.00 0.00 34.73 3.13
1562 4993 6.183360 GGTTCAACCTAGATCTTCATTTTCCG 60.183 42.308 0.00 0.00 34.73 4.30
1564 4995 5.874810 TCAACCTAGATCTTCATTTTCCGTG 59.125 40.000 0.00 0.00 0.00 4.94
1568 4999 5.297776 CCTAGATCTTCATTTTCCGTGCAAT 59.702 40.000 0.00 0.00 0.00 3.56
1569 5000 5.240713 AGATCTTCATTTTCCGTGCAATC 57.759 39.130 0.00 0.00 0.00 2.67
1572 5003 6.599244 AGATCTTCATTTTCCGTGCAATCTTA 59.401 34.615 0.00 0.00 0.00 2.10
1574 5005 7.857734 TCTTCATTTTCCGTGCAATCTTATA 57.142 32.000 0.00 0.00 0.00 0.98
1575 5006 7.693952 TCTTCATTTTCCGTGCAATCTTATAC 58.306 34.615 0.00 0.00 0.00 1.47
1576 5007 7.552687 TCTTCATTTTCCGTGCAATCTTATACT 59.447 33.333 0.00 0.00 0.00 2.12
1577 5008 7.015226 TCATTTTCCGTGCAATCTTATACTG 57.985 36.000 0.00 0.00 0.00 2.74
1578 5009 5.811399 TTTTCCGTGCAATCTTATACTGG 57.189 39.130 0.00 0.00 0.00 4.00
1579 5010 4.746535 TTCCGTGCAATCTTATACTGGA 57.253 40.909 0.00 0.00 0.00 3.86
1580 5011 4.955811 TCCGTGCAATCTTATACTGGAT 57.044 40.909 0.00 0.00 0.00 3.41
1581 5012 5.290493 TCCGTGCAATCTTATACTGGATT 57.710 39.130 0.00 0.00 33.09 3.01
1582 5013 6.413783 TCCGTGCAATCTTATACTGGATTA 57.586 37.500 0.00 0.00 31.86 1.75
1584 5015 6.041637 TCCGTGCAATCTTATACTGGATTAGT 59.958 38.462 0.00 0.00 43.56 2.24
1586 5017 6.146184 CGTGCAATCTTATACTGGATTAGTGG 59.854 42.308 0.00 0.00 40.65 4.00
1587 5018 5.997746 TGCAATCTTATACTGGATTAGTGGC 59.002 40.000 0.00 0.00 40.65 5.01
1588 5019 5.120830 GCAATCTTATACTGGATTAGTGGCG 59.879 44.000 0.00 0.00 40.65 5.69
1589 5020 6.455647 CAATCTTATACTGGATTAGTGGCGA 58.544 40.000 0.00 0.00 40.65 5.54
1590 5021 6.859112 ATCTTATACTGGATTAGTGGCGAT 57.141 37.500 0.00 0.00 40.65 4.58
1591 5022 6.025749 TCTTATACTGGATTAGTGGCGATG 57.974 41.667 0.00 0.00 40.65 3.84
1592 5023 5.773176 TCTTATACTGGATTAGTGGCGATGA 59.227 40.000 0.00 0.00 40.65 2.92
1593 5024 4.955811 ATACTGGATTAGTGGCGATGAA 57.044 40.909 0.00 0.00 40.65 2.57
1594 5025 2.906354 ACTGGATTAGTGGCGATGAAC 58.094 47.619 0.00 0.00 38.49 3.18
1595 5026 2.213499 CTGGATTAGTGGCGATGAACC 58.787 52.381 0.00 0.00 0.00 3.62
1596 5027 1.557371 TGGATTAGTGGCGATGAACCA 59.443 47.619 0.00 0.00 33.84 3.67
1597 5028 2.172505 TGGATTAGTGGCGATGAACCAT 59.827 45.455 0.00 0.00 39.95 3.55
1598 5029 3.214328 GGATTAGTGGCGATGAACCATT 58.786 45.455 0.00 0.00 39.95 3.16
1599 5030 3.632145 GGATTAGTGGCGATGAACCATTT 59.368 43.478 0.00 0.00 39.95 2.32
1600 5031 4.097892 GGATTAGTGGCGATGAACCATTTT 59.902 41.667 0.00 0.00 39.95 1.82
1601 5032 5.394115 GGATTAGTGGCGATGAACCATTTTT 60.394 40.000 0.00 0.00 39.95 1.94
1620 5051 4.653806 TTTTGTTGTTGCGAAAAAGTGG 57.346 36.364 0.00 0.00 0.00 4.00
1621 5052 3.305398 TTGTTGTTGCGAAAAAGTGGT 57.695 38.095 0.00 0.00 0.00 4.16
1622 5053 2.600731 TGTTGTTGCGAAAAAGTGGTG 58.399 42.857 0.00 0.00 0.00 4.17
1623 5054 2.229062 TGTTGTTGCGAAAAAGTGGTGA 59.771 40.909 0.00 0.00 0.00 4.02
1624 5055 3.119316 TGTTGTTGCGAAAAAGTGGTGAT 60.119 39.130 0.00 0.00 0.00 3.06
1625 5056 3.077229 TGTTGCGAAAAAGTGGTGATG 57.923 42.857 0.00 0.00 0.00 3.07
1626 5057 2.685388 TGTTGCGAAAAAGTGGTGATGA 59.315 40.909 0.00 0.00 0.00 2.92
1627 5058 3.129462 TGTTGCGAAAAAGTGGTGATGAA 59.871 39.130 0.00 0.00 0.00 2.57
1628 5059 3.347958 TGCGAAAAAGTGGTGATGAAC 57.652 42.857 0.00 0.00 0.00 3.18
1638 5069 1.445871 GGTGATGAACCGTTACACCC 58.554 55.000 17.08 6.22 43.29 4.61
1639 5070 1.002773 GGTGATGAACCGTTACACCCT 59.997 52.381 17.08 0.00 43.29 4.34
1640 5071 2.344025 GTGATGAACCGTTACACCCTC 58.656 52.381 0.00 0.00 0.00 4.30
1641 5072 1.972075 TGATGAACCGTTACACCCTCA 59.028 47.619 0.00 0.00 0.00 3.86
1642 5073 2.569853 TGATGAACCGTTACACCCTCAT 59.430 45.455 0.00 0.00 0.00 2.90
1643 5074 3.008594 TGATGAACCGTTACACCCTCATT 59.991 43.478 0.00 0.00 0.00 2.57
1644 5075 2.773487 TGAACCGTTACACCCTCATTG 58.227 47.619 0.00 0.00 0.00 2.82
1645 5076 2.105134 TGAACCGTTACACCCTCATTGT 59.895 45.455 0.00 0.00 0.00 2.71
1646 5077 2.943036 ACCGTTACACCCTCATTGTT 57.057 45.000 0.00 0.00 0.00 2.83
1647 5078 3.217681 ACCGTTACACCCTCATTGTTT 57.782 42.857 0.00 0.00 0.00 2.83
1648 5079 3.143728 ACCGTTACACCCTCATTGTTTC 58.856 45.455 0.00 0.00 0.00 2.78
1649 5080 3.142951 CCGTTACACCCTCATTGTTTCA 58.857 45.455 0.00 0.00 0.00 2.69
1650 5081 3.188460 CCGTTACACCCTCATTGTTTCAG 59.812 47.826 0.00 0.00 0.00 3.02
1651 5082 3.364964 CGTTACACCCTCATTGTTTCAGC 60.365 47.826 0.00 0.00 0.00 4.26
1652 5083 2.363306 ACACCCTCATTGTTTCAGCA 57.637 45.000 0.00 0.00 0.00 4.41
1653 5084 2.233271 ACACCCTCATTGTTTCAGCAG 58.767 47.619 0.00 0.00 0.00 4.24
1654 5085 1.542915 CACCCTCATTGTTTCAGCAGG 59.457 52.381 0.00 0.00 0.00 4.85
1655 5086 1.425066 ACCCTCATTGTTTCAGCAGGA 59.575 47.619 0.00 0.00 0.00 3.86
1656 5087 2.089980 CCCTCATTGTTTCAGCAGGAG 58.910 52.381 0.00 0.00 0.00 3.69
1657 5088 2.290514 CCCTCATTGTTTCAGCAGGAGA 60.291 50.000 0.00 0.00 0.00 3.71
1658 5089 3.008330 CCTCATTGTTTCAGCAGGAGAG 58.992 50.000 0.00 0.00 0.00 3.20
1659 5090 3.307269 CCTCATTGTTTCAGCAGGAGAGA 60.307 47.826 0.00 0.00 0.00 3.10
1660 5091 4.321718 CTCATTGTTTCAGCAGGAGAGAA 58.678 43.478 0.00 0.00 0.00 2.87
1663 5094 5.771666 TCATTGTTTCAGCAGGAGAGAAATT 59.228 36.000 0.00 0.00 34.23 1.82
1666 5097 5.132502 TGTTTCAGCAGGAGAGAAATTTGA 58.867 37.500 0.00 0.00 34.23 2.69
1674 5105 5.335504 GCAGGAGAGAAATTTGAGGAAGTTG 60.336 44.000 0.00 0.00 0.00 3.16
1689 5120 4.881850 AGGAAGTTGGTTACAAGTCTGTTG 59.118 41.667 0.00 0.00 39.28 3.33
1692 5123 3.377172 AGTTGGTTACAAGTCTGTTGTGC 59.623 43.478 0.61 0.00 35.34 4.57
1713 5144 5.927030 TGCTCAACACATTTTTAGATCGTC 58.073 37.500 0.00 0.00 0.00 4.20
1715 5146 5.790495 GCTCAACACATTTTTAGATCGTCAC 59.210 40.000 0.00 0.00 0.00 3.67
1716 5147 6.347725 GCTCAACACATTTTTAGATCGTCACT 60.348 38.462 0.00 0.00 0.00 3.41
1717 5148 6.887368 TCAACACATTTTTAGATCGTCACTG 58.113 36.000 0.00 0.00 0.00 3.66
1718 5149 6.481976 TCAACACATTTTTAGATCGTCACTGT 59.518 34.615 0.00 0.00 0.00 3.55
1719 5150 6.467723 ACACATTTTTAGATCGTCACTGTC 57.532 37.500 0.00 0.00 0.00 3.51
1720 5151 5.118664 ACACATTTTTAGATCGTCACTGTCG 59.881 40.000 0.00 0.00 0.00 4.35
1721 5152 5.118664 CACATTTTTAGATCGTCACTGTCGT 59.881 40.000 0.00 0.00 0.00 4.34
1722 5153 5.694910 ACATTTTTAGATCGTCACTGTCGTT 59.305 36.000 0.00 0.00 0.00 3.85
1723 5154 6.864685 ACATTTTTAGATCGTCACTGTCGTTA 59.135 34.615 0.00 0.00 0.00 3.18
1724 5155 7.383029 ACATTTTTAGATCGTCACTGTCGTTAA 59.617 33.333 0.00 0.00 0.00 2.01
1725 5156 7.878477 TTTTTAGATCGTCACTGTCGTTAAT 57.122 32.000 0.00 0.00 0.00 1.40
1726 5157 7.878477 TTTTAGATCGTCACTGTCGTTAATT 57.122 32.000 0.00 0.00 0.00 1.40
1727 5158 7.878477 TTTAGATCGTCACTGTCGTTAATTT 57.122 32.000 0.00 0.00 0.00 1.82
1730 5161 6.818416 AGATCGTCACTGTCGTTAATTTTTC 58.182 36.000 0.00 0.00 0.00 2.29
1739 5170 8.953990 CACTGTCGTTAATTTTTCCAGTTAAAG 58.046 33.333 0.00 0.00 29.78 1.85
1750 5181 8.508883 TTTTTCCAGTTAAAGTTAGTGTAGCA 57.491 30.769 0.00 0.00 0.00 3.49
1754 5185 9.781633 TTCCAGTTAAAGTTAGTGTAGCATTAA 57.218 29.630 0.00 0.00 0.00 1.40
1762 5193 9.569122 AAAGTTAGTGTAGCATTAAAAGAAGGA 57.431 29.630 0.00 0.00 0.00 3.36
1772 5203 8.763049 AGCATTAAAAGAAGGATTTTTACTGC 57.237 30.769 17.59 17.59 46.20 4.40
1773 5204 7.666377 GCATTAAAAGAAGGATTTTTACTGCG 58.334 34.615 13.30 0.00 41.92 5.18
1774 5205 7.328493 GCATTAAAAGAAGGATTTTTACTGCGT 59.672 33.333 13.30 0.00 41.92 5.24
1775 5206 9.834628 CATTAAAAGAAGGATTTTTACTGCGTA 57.165 29.630 0.00 0.00 34.35 4.42
1796 5227 6.410845 CGTATATTAATCGCATGGTATGTGC 58.589 40.000 0.00 0.00 40.47 4.57
2451 5882 0.106519 GCATGGACTGGGCCAAGTAT 60.107 55.000 14.50 0.18 42.16 2.12
2758 6189 4.323477 CCTCCGGCGAAACCACCA 62.323 66.667 9.30 0.00 39.03 4.17
3099 6530 2.844839 GGCCTCCACGCCTCCTAT 60.845 66.667 0.00 0.00 46.10 2.57
3233 6664 5.502153 AGATTAGTGATCTGTACGTCCAC 57.498 43.478 0.00 0.00 43.52 4.02
3294 6730 8.919661 GCTACTAGTAGTGTCGTTTTATTTGTT 58.080 33.333 26.76 0.00 35.65 2.83
3431 6868 6.636447 TGATCTGCGTAACATTTTGTTTTCAG 59.364 34.615 0.00 4.61 41.45 3.02
3479 6916 7.847096 TGCTATATAACTTGACCAAGACTTGA 58.153 34.615 16.99 0.00 40.79 3.02
3490 6927 8.690203 TTGACCAAGACTTGATTAAATCTCAA 57.310 30.769 16.99 6.98 0.00 3.02
3499 6936 9.890352 GACTTGATTAAATCTCAATCAATAGCC 57.110 33.333 10.07 0.00 46.11 3.93
3501 6938 9.674824 CTTGATTAAATCTCAATCAATAGCCAC 57.325 33.333 10.07 0.00 46.11 5.01
3502 6939 8.750515 TGATTAAATCTCAATCAATAGCCACA 57.249 30.769 0.00 0.00 38.98 4.17
3503 6940 9.187996 TGATTAAATCTCAATCAATAGCCACAA 57.812 29.630 0.00 0.00 38.98 3.33
3505 6942 5.841957 AATCTCAATCAATAGCCACAACC 57.158 39.130 0.00 0.00 0.00 3.77
3506 6943 4.574674 TCTCAATCAATAGCCACAACCT 57.425 40.909 0.00 0.00 0.00 3.50
3721 7581 1.152694 TTAGGGCCATGGAGCATGC 60.153 57.895 18.40 10.51 40.20 4.06
3730 7590 0.400975 ATGGAGCATGCTGGATCTCC 59.599 55.000 28.27 19.37 44.04 3.71
3796 7657 0.333312 TGTTGGGGTTTGTGTCCTGT 59.667 50.000 0.00 0.00 0.00 4.00
3807 7668 3.319198 GTCCTGTCCGGGAAGGCA 61.319 66.667 16.25 3.63 40.77 4.75
3813 7674 1.072505 GTCCGGGAAGGCAAGACAA 59.927 57.895 0.00 0.00 40.77 3.18
3823 7684 0.663153 GGCAAGACAACGACAGCTTT 59.337 50.000 0.00 0.00 0.00 3.51
3827 7688 3.120854 GCAAGACAACGACAGCTTTCTAG 60.121 47.826 0.00 0.00 0.00 2.43
3966 7832 5.277442 GGATCTAGTCTTCGTTCTTCTACGG 60.277 48.000 0.00 0.00 41.67 4.02
3969 7835 3.410508 AGTCTTCGTTCTTCTACGGTCT 58.589 45.455 0.00 0.00 41.67 3.85
3984 7850 4.395959 ACGGTCTTGTGTCTTCAAGTTA 57.604 40.909 6.38 0.00 43.44 2.24
3992 7858 7.377131 GTCTTGTGTCTTCAAGTTAAATGCTTC 59.623 37.037 6.38 0.00 43.44 3.86
4001 7867 5.584649 TCAAGTTAAATGCTTCCGACCTATG 59.415 40.000 0.00 0.00 0.00 2.23
4002 7868 3.877508 AGTTAAATGCTTCCGACCTATGC 59.122 43.478 0.00 0.00 0.00 3.14
4013 7879 3.319405 TCCGACCTATGCTTCTCTTCATC 59.681 47.826 0.00 0.00 0.00 2.92
4117 7983 2.033602 TGACTCCGGCGACAGAGA 59.966 61.111 8.93 0.89 34.13 3.10
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
41 42 7.117667 CAGTTTTTCTACCAAAAACAAAGCTGT 59.882 33.333 19.58 0.00 46.78 4.40
149 150 6.777580 AGTCAGACAAAGGGAAAATACACAAT 59.222 34.615 2.66 0.00 0.00 2.71
171 172 7.739498 TCTTGTAAACCACCTGAAATTAGTC 57.261 36.000 0.00 0.00 0.00 2.59
200 208 3.053619 AGTCACCTTTTTGTCTTCTGGGT 60.054 43.478 0.00 0.00 0.00 4.51
258 269 8.255905 CAGAAGCAATGGAGGAAGAATTAAATT 58.744 33.333 0.00 0.00 0.00 1.82
276 287 0.867746 GCATCGACACACAGAAGCAA 59.132 50.000 0.00 0.00 32.14 3.91
340 352 2.530701 CAGGAACTCCACTACTCCAGT 58.469 52.381 0.00 0.00 34.60 4.00
475 487 1.413077 CCACTCTTACCCCGAGGATTC 59.587 57.143 0.00 0.00 36.73 2.52
560 573 3.012518 GCTCTGCAACATAATCACAGGT 58.987 45.455 0.00 0.00 0.00 4.00
584 600 4.276678 CAGCCTGTCAAGTTCTGAATTTCA 59.723 41.667 0.00 0.00 35.22 2.69
607 623 1.077930 TTCAGCTCTGATGCCCTGC 60.078 57.895 0.00 0.00 39.64 4.85
631 647 1.471119 AGCTGCAAATCATGTCTGGG 58.529 50.000 1.02 0.00 0.00 4.45
635 659 9.403110 CCTTTATATTTAGCTGCAAATCATGTC 57.597 33.333 1.02 0.00 30.84 3.06
703 727 1.912371 GAAGGAGTTGAAAGGCCGCG 61.912 60.000 0.00 0.00 0.00 6.46
787 4169 0.321653 AACAACCTCACCGGAGATGC 60.322 55.000 9.46 0.00 44.26 3.91
788 4170 1.001974 TCAACAACCTCACCGGAGATG 59.998 52.381 9.46 5.34 44.26 2.90
789 4171 1.002087 GTCAACAACCTCACCGGAGAT 59.998 52.381 9.46 0.00 44.26 2.75
802 4184 1.593933 GCGAGTTGGTTACGTCAACAA 59.406 47.619 17.68 8.60 44.84 2.83
835 4224 1.639534 CGGTGAGTTCGTTTGCGTT 59.360 52.632 0.00 0.00 39.49 4.84
840 4229 1.609841 GGGAATCCGGTGAGTTCGTTT 60.610 52.381 0.00 0.00 0.00 3.60
1284 4691 2.610859 TCCTTGGCCTCCTGTCCC 60.611 66.667 3.32 0.00 0.00 4.46
1404 4811 4.831674 AGATCAGACATGTGATTCACCA 57.168 40.909 14.05 3.23 37.29 4.17
1413 4830 4.461450 TCTAGCCCTAGATCAGACATGT 57.539 45.455 0.00 0.00 37.28 3.21
1427 4844 0.171455 CGCAGGATACGATCTAGCCC 59.829 60.000 0.00 0.00 46.39 5.19
1444 4865 2.930682 GAGTCAATGGAAGTAGGAACGC 59.069 50.000 0.00 0.00 0.00 4.84
1482 4903 6.711277 TCAATGCATGGAGTTAGTTTCTACT 58.289 36.000 0.00 0.00 38.44 2.57
1483 4904 6.985188 TCAATGCATGGAGTTAGTTTCTAC 57.015 37.500 0.00 0.00 0.00 2.59
1485 4906 8.579850 TTAATCAATGCATGGAGTTAGTTTCT 57.420 30.769 9.71 0.00 0.00 2.52
1486 4907 9.455847 GATTAATCAATGCATGGAGTTAGTTTC 57.544 33.333 9.71 0.00 0.00 2.78
1487 4908 8.970020 TGATTAATCAATGCATGGAGTTAGTTT 58.030 29.630 15.82 0.00 33.08 2.66
1489 4910 7.013655 GGTGATTAATCAATGCATGGAGTTAGT 59.986 37.037 19.55 5.40 38.75 2.24
1490 4911 7.230108 AGGTGATTAATCAATGCATGGAGTTAG 59.770 37.037 19.55 0.00 38.75 2.34
1542 4973 4.636206 GCACGGAAAATGAAGATCTAGGTT 59.364 41.667 0.00 0.00 0.00 3.50
1543 4974 4.192317 GCACGGAAAATGAAGATCTAGGT 58.808 43.478 0.00 0.00 0.00 3.08
1544 4975 4.191544 TGCACGGAAAATGAAGATCTAGG 58.808 43.478 0.00 0.00 0.00 3.02
1545 4976 5.801350 TTGCACGGAAAATGAAGATCTAG 57.199 39.130 0.00 0.00 0.00 2.43
1547 4978 4.946157 AGATTGCACGGAAAATGAAGATCT 59.054 37.500 0.00 0.00 0.00 2.75
1548 4979 5.240713 AGATTGCACGGAAAATGAAGATC 57.759 39.130 0.00 0.00 0.00 2.75
1550 4981 6.757897 ATAAGATTGCACGGAAAATGAAGA 57.242 33.333 0.00 0.00 0.00 2.87
1551 4982 7.641411 CAGTATAAGATTGCACGGAAAATGAAG 59.359 37.037 0.00 0.00 0.00 3.02
1553 4984 6.038161 CCAGTATAAGATTGCACGGAAAATGA 59.962 38.462 0.00 0.00 0.00 2.57
1554 4985 6.038161 TCCAGTATAAGATTGCACGGAAAATG 59.962 38.462 0.00 0.00 0.00 2.32
1557 4988 5.092554 TCCAGTATAAGATTGCACGGAAA 57.907 39.130 0.00 0.00 0.00 3.13
1558 4989 4.746535 TCCAGTATAAGATTGCACGGAA 57.253 40.909 0.00 0.00 0.00 4.30
1560 4991 6.146184 CACTAATCCAGTATAAGATTGCACGG 59.854 42.308 0.00 0.00 34.98 4.94
1561 4992 6.146184 CCACTAATCCAGTATAAGATTGCACG 59.854 42.308 0.00 0.00 34.98 5.34
1562 4993 6.073003 GCCACTAATCCAGTATAAGATTGCAC 60.073 42.308 0.00 0.00 34.98 4.57
1564 4995 5.120830 CGCCACTAATCCAGTATAAGATTGC 59.879 44.000 0.00 0.00 34.98 3.56
1568 4999 5.773176 TCATCGCCACTAATCCAGTATAAGA 59.227 40.000 0.00 0.00 34.98 2.10
1569 5000 6.025749 TCATCGCCACTAATCCAGTATAAG 57.974 41.667 0.00 0.00 34.98 1.73
1572 5003 4.503296 GGTTCATCGCCACTAATCCAGTAT 60.503 45.833 0.00 0.00 34.98 2.12
1574 5005 2.420129 GGTTCATCGCCACTAATCCAGT 60.420 50.000 0.00 0.00 38.32 4.00
1575 5006 2.213499 GGTTCATCGCCACTAATCCAG 58.787 52.381 0.00 0.00 0.00 3.86
1576 5007 1.557371 TGGTTCATCGCCACTAATCCA 59.443 47.619 0.00 0.00 0.00 3.41
1577 5008 2.325583 TGGTTCATCGCCACTAATCC 57.674 50.000 0.00 0.00 0.00 3.01
1578 5009 4.900635 AAATGGTTCATCGCCACTAATC 57.099 40.909 0.00 0.00 39.03 1.75
1579 5010 5.659440 AAAAATGGTTCATCGCCACTAAT 57.341 34.783 0.00 0.00 39.03 1.73
1598 5029 4.511826 ACCACTTTTTCGCAACAACAAAAA 59.488 33.333 0.00 0.00 0.00 1.94
1599 5030 4.058817 ACCACTTTTTCGCAACAACAAAA 58.941 34.783 0.00 0.00 0.00 2.44
1600 5031 3.430218 CACCACTTTTTCGCAACAACAAA 59.570 39.130 0.00 0.00 0.00 2.83
1601 5032 2.989840 CACCACTTTTTCGCAACAACAA 59.010 40.909 0.00 0.00 0.00 2.83
1602 5033 2.229062 TCACCACTTTTTCGCAACAACA 59.771 40.909 0.00 0.00 0.00 3.33
1603 5034 2.869897 TCACCACTTTTTCGCAACAAC 58.130 42.857 0.00 0.00 0.00 3.32
1604 5035 3.129462 TCATCACCACTTTTTCGCAACAA 59.871 39.130 0.00 0.00 0.00 2.83
1605 5036 2.685388 TCATCACCACTTTTTCGCAACA 59.315 40.909 0.00 0.00 0.00 3.33
1606 5037 3.347958 TCATCACCACTTTTTCGCAAC 57.652 42.857 0.00 0.00 0.00 4.17
1607 5038 3.490078 GGTTCATCACCACTTTTTCGCAA 60.490 43.478 0.00 0.00 46.42 4.85
1608 5039 2.034053 GGTTCATCACCACTTTTTCGCA 59.966 45.455 0.00 0.00 46.42 5.10
1609 5040 2.661594 GGTTCATCACCACTTTTTCGC 58.338 47.619 0.00 0.00 46.42 4.70
1619 5050 1.002773 AGGGTGTAACGGTTCATCACC 59.997 52.381 22.75 22.75 45.17 4.02
1620 5051 2.289195 TGAGGGTGTAACGGTTCATCAC 60.289 50.000 0.00 6.00 38.12 3.06
1621 5052 1.972075 TGAGGGTGTAACGGTTCATCA 59.028 47.619 0.00 0.00 38.12 3.07
1622 5053 2.754946 TGAGGGTGTAACGGTTCATC 57.245 50.000 0.00 0.00 38.12 2.92
1623 5054 3.244770 ACAATGAGGGTGTAACGGTTCAT 60.245 43.478 0.00 0.00 38.12 2.57
1624 5055 2.105134 ACAATGAGGGTGTAACGGTTCA 59.895 45.455 0.00 0.00 38.12 3.18
1625 5056 2.774687 ACAATGAGGGTGTAACGGTTC 58.225 47.619 0.00 0.00 38.12 3.62
1626 5057 2.943036 ACAATGAGGGTGTAACGGTT 57.057 45.000 0.00 0.00 38.12 4.44
1627 5058 2.943036 AACAATGAGGGTGTAACGGT 57.057 45.000 0.00 0.00 38.12 4.83
1628 5059 3.142951 TGAAACAATGAGGGTGTAACGG 58.857 45.455 0.00 0.00 38.12 4.44
1629 5060 3.364964 GCTGAAACAATGAGGGTGTAACG 60.365 47.826 0.00 0.00 38.12 3.18
1630 5061 3.568007 TGCTGAAACAATGAGGGTGTAAC 59.432 43.478 0.00 0.00 0.00 2.50
1631 5062 3.820467 CTGCTGAAACAATGAGGGTGTAA 59.180 43.478 0.00 0.00 0.00 2.41
1632 5063 3.411446 CTGCTGAAACAATGAGGGTGTA 58.589 45.455 0.00 0.00 0.00 2.90
1633 5064 2.233271 CTGCTGAAACAATGAGGGTGT 58.767 47.619 0.00 0.00 0.00 4.16
1634 5065 1.542915 CCTGCTGAAACAATGAGGGTG 59.457 52.381 0.00 0.00 0.00 4.61
1635 5066 1.425066 TCCTGCTGAAACAATGAGGGT 59.575 47.619 0.00 0.00 0.00 4.34
1636 5067 2.089980 CTCCTGCTGAAACAATGAGGG 58.910 52.381 0.00 0.00 0.00 4.30
1637 5068 3.008330 CTCTCCTGCTGAAACAATGAGG 58.992 50.000 0.00 0.00 0.00 3.86
1638 5069 3.935315 TCTCTCCTGCTGAAACAATGAG 58.065 45.455 0.00 0.00 0.00 2.90
1639 5070 4.356405 TTCTCTCCTGCTGAAACAATGA 57.644 40.909 0.00 0.00 0.00 2.57
1640 5071 5.640189 ATTTCTCTCCTGCTGAAACAATG 57.360 39.130 0.00 0.00 33.36 2.82
1641 5072 6.266103 TCAAATTTCTCTCCTGCTGAAACAAT 59.734 34.615 0.00 0.00 33.36 2.71
1642 5073 5.593909 TCAAATTTCTCTCCTGCTGAAACAA 59.406 36.000 0.00 0.00 33.36 2.83
1643 5074 5.132502 TCAAATTTCTCTCCTGCTGAAACA 58.867 37.500 0.00 0.00 33.36 2.83
1644 5075 5.335504 CCTCAAATTTCTCTCCTGCTGAAAC 60.336 44.000 0.00 0.00 33.36 2.78
1645 5076 4.763793 CCTCAAATTTCTCTCCTGCTGAAA 59.236 41.667 0.00 0.00 34.75 2.69
1646 5077 4.042062 TCCTCAAATTTCTCTCCTGCTGAA 59.958 41.667 0.00 0.00 0.00 3.02
1647 5078 3.584406 TCCTCAAATTTCTCTCCTGCTGA 59.416 43.478 0.00 0.00 0.00 4.26
1648 5079 3.947868 TCCTCAAATTTCTCTCCTGCTG 58.052 45.455 0.00 0.00 0.00 4.41
1649 5080 4.042684 ACTTCCTCAAATTTCTCTCCTGCT 59.957 41.667 0.00 0.00 0.00 4.24
1650 5081 4.331108 ACTTCCTCAAATTTCTCTCCTGC 58.669 43.478 0.00 0.00 0.00 4.85
1651 5082 5.182760 CCAACTTCCTCAAATTTCTCTCCTG 59.817 44.000 0.00 0.00 0.00 3.86
1652 5083 5.163045 ACCAACTTCCTCAAATTTCTCTCCT 60.163 40.000 0.00 0.00 0.00 3.69
1653 5084 5.073428 ACCAACTTCCTCAAATTTCTCTCC 58.927 41.667 0.00 0.00 0.00 3.71
1654 5085 6.641169 AACCAACTTCCTCAAATTTCTCTC 57.359 37.500 0.00 0.00 0.00 3.20
1655 5086 7.060421 TGTAACCAACTTCCTCAAATTTCTCT 58.940 34.615 0.00 0.00 0.00 3.10
1656 5087 7.272037 TGTAACCAACTTCCTCAAATTTCTC 57.728 36.000 0.00 0.00 0.00 2.87
1657 5088 7.342026 ACTTGTAACCAACTTCCTCAAATTTCT 59.658 33.333 0.00 0.00 0.00 2.52
1658 5089 7.489160 ACTTGTAACCAACTTCCTCAAATTTC 58.511 34.615 0.00 0.00 0.00 2.17
1659 5090 7.342026 AGACTTGTAACCAACTTCCTCAAATTT 59.658 33.333 0.00 0.00 0.00 1.82
1660 5091 6.833933 AGACTTGTAACCAACTTCCTCAAATT 59.166 34.615 0.00 0.00 0.00 1.82
1663 5094 5.123227 CAGACTTGTAACCAACTTCCTCAA 58.877 41.667 0.00 0.00 0.00 3.02
1666 5097 4.772886 ACAGACTTGTAACCAACTTCCT 57.227 40.909 0.00 0.00 35.25 3.36
1674 5105 3.202906 TGAGCACAACAGACTTGTAACC 58.797 45.455 0.00 0.00 36.23 2.85
1692 5123 7.011773 CAGTGACGATCTAAAAATGTGTTGAG 58.988 38.462 0.00 0.00 0.00 3.02
1701 5132 7.878477 ATTAACGACAGTGACGATCTAAAAA 57.122 32.000 21.35 1.37 34.70 1.94
1703 5134 7.878477 AAATTAACGACAGTGACGATCTAAA 57.122 32.000 21.35 8.00 34.70 1.85
1705 5136 7.062605 GGAAAAATTAACGACAGTGACGATCTA 59.937 37.037 21.35 6.99 34.70 1.98
1706 5137 6.128634 GGAAAAATTAACGACAGTGACGATCT 60.129 38.462 21.35 7.89 34.70 2.75
1707 5138 6.013689 GGAAAAATTAACGACAGTGACGATC 58.986 40.000 21.35 6.25 34.70 3.69
1708 5139 5.467399 TGGAAAAATTAACGACAGTGACGAT 59.533 36.000 21.35 12.23 34.70 3.73
1709 5140 4.809958 TGGAAAAATTAACGACAGTGACGA 59.190 37.500 21.35 0.00 34.70 4.20
1710 5141 5.085636 TGGAAAAATTAACGACAGTGACG 57.914 39.130 13.38 13.38 0.00 4.35
1711 5142 6.056428 ACTGGAAAAATTAACGACAGTGAC 57.944 37.500 0.00 0.00 36.46 3.67
1713 5144 8.844441 TTTAACTGGAAAAATTAACGACAGTG 57.156 30.769 0.00 0.00 37.71 3.66
1715 5146 9.511144 AACTTTAACTGGAAAAATTAACGACAG 57.489 29.630 0.00 0.00 0.00 3.51
1723 5154 9.961265 GCTACACTAACTTTAACTGGAAAAATT 57.039 29.630 0.00 0.00 0.00 1.82
1724 5155 9.127277 TGCTACACTAACTTTAACTGGAAAAAT 57.873 29.630 0.00 0.00 0.00 1.82
1725 5156 8.508883 TGCTACACTAACTTTAACTGGAAAAA 57.491 30.769 0.00 0.00 0.00 1.94
1726 5157 8.685838 ATGCTACACTAACTTTAACTGGAAAA 57.314 30.769 0.00 0.00 0.00 2.29
1727 5158 8.685838 AATGCTACACTAACTTTAACTGGAAA 57.314 30.769 0.00 0.00 0.00 3.13
1772 5203 6.410845 GCACATACCATGCGATTAATATACG 58.589 40.000 0.00 0.00 32.45 3.06
1995 5426 1.593296 GGTCGAGGCGGTTGTAGTCT 61.593 60.000 0.00 0.00 0.00 3.24
2217 5648 3.491652 GCGAAGAAGAGCACCGCC 61.492 66.667 0.00 0.00 39.97 6.13
2724 6155 2.103736 GCGTAGTAGCGGTGGACC 59.896 66.667 0.00 0.00 0.00 4.46
2758 6189 2.255881 GCTTGTTACGGTTGGCGGT 61.256 57.895 0.00 0.00 0.00 5.68
2892 6323 3.109547 TGCAGGTAAAGCGTCGCG 61.110 61.111 12.30 0.00 33.85 5.87
2979 6410 6.062749 CAGGAAGATGTTGATGAAGATGGAT 58.937 40.000 0.00 0.00 0.00 3.41
3099 6530 1.227943 GAGCACCTTGGCAGTGTCA 60.228 57.895 8.44 0.00 37.56 3.58
3214 6645 7.400599 AAATAGTGGACGTACAGATCACTAA 57.599 36.000 0.00 4.60 39.78 2.24
3406 6843 6.499172 TGAAAACAAAATGTTACGCAGATCA 58.501 32.000 0.00 0.00 40.14 2.92
3451 6888 7.796054 AGTCTTGGTCAAGTTATATAGCATGT 58.204 34.615 10.10 0.00 39.38 3.21
3479 6916 8.416329 GGTTGTGGCTATTGATTGAGATTTAAT 58.584 33.333 0.00 0.00 0.00 1.40
3675 7534 2.169832 AATATGAGGCGGATTGACGG 57.830 50.000 0.00 0.00 0.00 4.79
3715 7574 2.110627 GCGGAGATCCAGCATGCT 59.889 61.111 16.30 16.30 36.21 3.79
3721 7581 2.203126 GGCAAGGCGGAGATCCAG 60.203 66.667 0.00 0.00 35.14 3.86
3796 7657 1.072505 GTTGTCTTGCCTTCCCGGA 59.927 57.895 0.73 0.00 33.16 5.14
3807 7668 4.038162 ACTCTAGAAAGCTGTCGTTGTCTT 59.962 41.667 0.00 0.00 0.00 3.01
3813 7674 2.891580 TCCAACTCTAGAAAGCTGTCGT 59.108 45.455 0.00 0.00 0.00 4.34
3823 7684 6.099845 GGGGAGAACATTATTCCAACTCTAGA 59.900 42.308 0.00 0.00 32.50 2.43
3827 7688 3.877508 CGGGGAGAACATTATTCCAACTC 59.122 47.826 0.00 0.00 32.50 3.01
3870 7731 1.509787 CCTGACGATGCAAAACGCG 60.510 57.895 3.53 3.53 46.97 6.01
3966 7832 6.729187 AGCATTTAACTTGAAGACACAAGAC 58.271 36.000 14.00 0.00 46.85 3.01
3969 7835 6.503524 GGAAGCATTTAACTTGAAGACACAA 58.496 36.000 0.00 0.00 0.00 3.33
3984 7850 2.717639 AGCATAGGTCGGAAGCATTT 57.282 45.000 0.00 0.00 0.00 2.32
3992 7858 3.648009 GATGAAGAGAAGCATAGGTCGG 58.352 50.000 0.00 0.00 0.00 4.79
4001 7867 0.919981 CGCTGTCGATGAAGAGAAGC 59.080 55.000 0.00 0.00 38.10 3.86
4002 7868 0.919981 GCGCTGTCGATGAAGAGAAG 59.080 55.000 0.00 0.00 38.10 2.85
4117 7983 4.664677 GCGCCGGTATCATCGCCT 62.665 66.667 10.31 0.00 41.53 5.52


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

AutoCloner maintained by Alex Coulton.