Multiple sequence alignment - TraesCS2D01G519300

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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 TraesCS2D01G519300 chr2D 100.000 4090 0 0 1 4090 609235658 609239747 0.000000e+00 7553.0
1 TraesCS2D01G519300 chr2D 74.462 372 85 7 2669 3038 642985319 642985682 7.080000e-33 152.0
2 TraesCS2D01G519300 chr2D 100.000 33 0 0 1945 1977 637677648 637677616 1.230000e-05 62.1
3 TraesCS2D01G519300 chr2B 90.467 3451 192 46 17 3412 743310816 743314184 0.000000e+00 4423.0
4 TraesCS2D01G519300 chr2B 87.467 375 39 7 3717 4090 743314713 743315080 3.780000e-115 425.0
5 TraesCS2D01G519300 chr2B 87.087 333 31 7 3416 3736 743314348 743314680 2.320000e-97 366.0
6 TraesCS2D01G519300 chr2B 97.778 45 1 0 1 45 743310768 743310812 1.220000e-10 78.7
7 TraesCS2D01G519300 chr2B 100.000 33 0 0 1945 1977 795081679 795081647 1.230000e-05 62.1
8 TraesCS2D01G519300 chr2B 100.000 32 0 0 1946 1977 795109523 795109492 4.420000e-05 60.2
9 TraesCS2D01G519300 chr2B 94.595 37 0 2 1941 1977 795554206 795554172 5.710000e-04 56.5
10 TraesCS2D01G519300 chr2A 81.220 1033 150 23 1541 2536 741986534 741985509 0.000000e+00 793.0
11 TraesCS2D01G519300 chr2A 87.273 495 63 0 2612 3106 741985466 741984972 2.130000e-157 566.0
12 TraesCS2D01G519300 chr2A 85.495 455 62 4 993 1444 741987007 741986554 4.790000e-129 472.0
13 TraesCS2D01G519300 chr2A 83.758 314 42 6 3520 3825 687281155 687281467 5.170000e-74 289.0
14 TraesCS2D01G519300 chr2A 100.000 33 0 0 1945 1977 762257335 762257367 1.230000e-05 62.1
15 TraesCS2D01G519300 chr4A 83.758 314 41 7 3520 3825 472089420 472089109 5.170000e-74 289.0
16 TraesCS2D01G519300 chr5A 83.387 313 44 5 3520 3825 592251166 592251477 2.410000e-72 283.0
17 TraesCS2D01G519300 chr7A 83.121 314 43 7 3520 3825 155135478 155135789 1.120000e-70 278.0
18 TraesCS2D01G519300 chr6B 87.821 156 18 1 3 158 265915502 265915348 9.030000e-42 182.0
19 TraesCS2D01G519300 chr6B 87.821 156 18 1 3 158 265967760 265967606 9.030000e-42 182.0
20 TraesCS2D01G519300 chrUn 73.282 393 97 5 2641 3032 31593747 31594132 1.980000e-28 137.0
21 TraesCS2D01G519300 chrUn 100.000 33 0 0 1945 1977 22827535 22827503 1.230000e-05 62.1


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 TraesCS2D01G519300 chr2D 609235658 609239747 4089 False 7553.000000 7553 100.000000 1 4090 1 chr2D.!!$F1 4089
1 TraesCS2D01G519300 chr2B 743310768 743315080 4312 False 1323.175000 4423 90.699750 1 4090 4 chr2B.!!$F1 4089
2 TraesCS2D01G519300 chr2A 741984972 741987007 2035 True 610.333333 793 84.662667 993 3106 3 chr2A.!!$R1 2113

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
984 1063 0.251386 AACCAGAGAGGAGAGCGACA 60.251 55.0 0.00 0.0 41.22 4.35 F
1664 1771 0.039617 TTGGCGCTGATTGAAAACGG 60.040 50.0 7.64 0.0 0.00 4.44 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2731 2891 0.475906 AGACCAGGAGCAAGCAACTT 59.524 50.0 0.0 0.0 0.0 2.66 R
3516 3837 0.742281 AGGTCGCTGTCACATCATGC 60.742 55.0 0.0 0.0 0.0 4.06 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
80 81 3.453070 GAGCGACCTCCCAGCATCC 62.453 68.421 0.00 0.00 31.68 3.51
98 99 1.007271 CGATGCTTCGGGCGAGTAT 60.007 57.895 13.82 0.00 45.43 2.12
177 232 4.077184 GCCCCGTCATGGTCGTCA 62.077 66.667 9.50 0.00 35.15 4.35
186 249 2.927580 ATGGTCGTCAACGCGGTCT 61.928 57.895 12.47 0.00 39.60 3.85
246 309 1.444672 GGTTATTCGACTCCGGGGG 59.555 63.158 6.13 0.00 36.24 5.40
270 333 2.871080 CAATTGACGCGCGCCTTG 60.871 61.111 32.58 22.54 0.00 3.61
297 360 4.054455 CGCCGTGGTTGTTCGACG 62.054 66.667 0.00 0.00 45.33 5.12
357 420 2.037136 GCACCACCTGCAGCACTAG 61.037 63.158 8.66 0.00 46.29 2.57
358 421 2.037136 CACCACCTGCAGCACTAGC 61.037 63.158 8.66 0.00 42.56 3.42
391 454 1.075659 GGCACCCTCCTTTCTTGCT 59.924 57.895 0.00 0.00 33.55 3.91
466 536 2.311542 TCAACCATGGTGGCCTAGAATT 59.688 45.455 20.60 0.00 42.67 2.17
471 541 1.281419 TGGTGGCCTAGAATTTCCGA 58.719 50.000 3.32 0.00 0.00 4.55
479 549 3.181465 GCCTAGAATTTCCGATGGTGAGA 60.181 47.826 0.00 0.00 0.00 3.27
480 550 4.503991 GCCTAGAATTTCCGATGGTGAGAT 60.504 45.833 0.00 0.00 0.00 2.75
481 551 5.233988 CCTAGAATTTCCGATGGTGAGATC 58.766 45.833 0.00 0.00 0.00 2.75
482 552 4.078639 AGAATTTCCGATGGTGAGATCC 57.921 45.455 0.00 0.00 0.00 3.36
483 553 3.455910 AGAATTTCCGATGGTGAGATCCA 59.544 43.478 0.00 0.00 42.01 3.41
485 555 2.916702 TTCCGATGGTGAGATCCATG 57.083 50.000 2.82 0.00 46.72 3.66
486 556 2.086610 TCCGATGGTGAGATCCATGA 57.913 50.000 2.82 0.00 46.72 3.07
487 557 2.613129 TCCGATGGTGAGATCCATGAT 58.387 47.619 2.82 0.00 46.72 2.45
488 558 2.974794 TCCGATGGTGAGATCCATGATT 59.025 45.455 2.82 0.00 46.72 2.57
489 559 3.007290 TCCGATGGTGAGATCCATGATTC 59.993 47.826 2.82 0.00 46.72 2.52
490 560 3.244318 CCGATGGTGAGATCCATGATTCA 60.244 47.826 2.82 0.00 46.72 2.57
491 561 3.995048 CGATGGTGAGATCCATGATTCAG 59.005 47.826 2.82 0.00 46.72 3.02
492 562 4.262335 CGATGGTGAGATCCATGATTCAGA 60.262 45.833 2.82 0.00 46.72 3.27
493 563 4.684484 TGGTGAGATCCATGATTCAGAG 57.316 45.455 0.00 0.00 31.96 3.35
494 564 3.390311 TGGTGAGATCCATGATTCAGAGG 59.610 47.826 0.00 2.33 31.96 3.69
495 565 3.244491 GGTGAGATCCATGATTCAGAGGG 60.244 52.174 0.00 2.66 0.00 4.30
496 566 3.645212 GTGAGATCCATGATTCAGAGGGA 59.355 47.826 0.00 7.33 0.00 4.20
497 567 3.902467 TGAGATCCATGATTCAGAGGGAG 59.098 47.826 0.00 0.00 0.00 4.30
498 568 4.158786 GAGATCCATGATTCAGAGGGAGA 58.841 47.826 0.00 0.00 0.00 3.71
499 569 4.161876 AGATCCATGATTCAGAGGGAGAG 58.838 47.826 0.00 0.00 0.00 3.20
505 575 4.812403 TGATTCAGAGGGAGAGAGAGAT 57.188 45.455 0.00 0.00 0.00 2.75
540 610 1.959226 GAGACGTGCGGCTGGAAAA 60.959 57.895 4.07 0.00 30.74 2.29
552 622 2.417243 GGCTGGAAAATGTTTCATCGGG 60.417 50.000 3.35 0.00 0.00 5.14
571 641 4.518211 TCGGGATAACGAGAAAGAGGATAC 59.482 45.833 0.00 0.00 38.06 2.24
599 669 4.814294 GGCCCTAGTGGACACGCG 62.814 72.222 3.53 3.53 44.36 6.01
600 670 4.065281 GCCCTAGTGGACACGCGT 62.065 66.667 5.58 5.58 35.39 6.01
601 671 2.181021 CCCTAGTGGACACGCGTC 59.819 66.667 9.86 0.00 41.80 5.19
602 672 2.202440 CCTAGTGGACACGCGTCG 60.202 66.667 9.86 8.08 43.61 5.12
603 673 2.874780 CTAGTGGACACGCGTCGC 60.875 66.667 9.86 7.29 43.61 5.19
675 745 1.078528 TTTCCGGGAGAGAGCCAGA 59.921 57.895 0.00 0.00 0.00 3.86
699 769 1.884075 TTGGATCGGTGTCGTGAGGG 61.884 60.000 0.00 0.00 37.69 4.30
710 780 1.067495 GTCGTGAGGGAAAGTGGAGAG 60.067 57.143 0.00 0.00 0.00 3.20
761 831 3.122297 ACGACCGATCACGTAACAAAAA 58.878 40.909 7.60 0.00 40.92 1.94
763 833 3.662454 CGACCGATCACGTAACAAAAACC 60.662 47.826 0.00 0.00 37.88 3.27
764 834 3.204526 ACCGATCACGTAACAAAAACCA 58.795 40.909 0.00 0.00 37.88 3.67
765 835 3.002553 ACCGATCACGTAACAAAAACCAC 59.997 43.478 0.00 0.00 37.88 4.16
837 916 2.277084 GCCGTCTCGTTGAAACCATAT 58.723 47.619 0.00 0.00 0.00 1.78
840 919 4.510340 GCCGTCTCGTTGAAACCATATAAT 59.490 41.667 0.00 0.00 0.00 1.28
842 921 6.346359 GCCGTCTCGTTGAAACCATATAATAC 60.346 42.308 0.00 0.00 0.00 1.89
843 922 6.921857 CCGTCTCGTTGAAACCATATAATACT 59.078 38.462 0.00 0.00 0.00 2.12
844 923 8.077991 CCGTCTCGTTGAAACCATATAATACTA 58.922 37.037 0.00 0.00 0.00 1.82
845 924 8.899776 CGTCTCGTTGAAACCATATAATACTAC 58.100 37.037 0.00 0.00 0.00 2.73
846 925 9.962783 GTCTCGTTGAAACCATATAATACTACT 57.037 33.333 0.00 0.00 0.00 2.57
857 936 9.516546 ACCATATAATACTACTCGATCAAGACA 57.483 33.333 0.00 0.00 0.00 3.41
858 937 9.995957 CCATATAATACTACTCGATCAAGACAG 57.004 37.037 0.00 0.00 0.00 3.51
863 942 0.811915 ACTCGATCAAGACAGGGACG 59.188 55.000 0.00 0.00 0.00 4.79
889 968 3.932089 CCCCTGAACAACAACAACAAAAG 59.068 43.478 0.00 0.00 0.00 2.27
952 1031 2.484594 GGAAAGCCTGCTACCTCATCTC 60.485 54.545 0.00 0.00 0.00 2.75
955 1034 2.406559 AGCCTGCTACCTCATCTCAAT 58.593 47.619 0.00 0.00 0.00 2.57
959 1038 2.038295 CTGCTACCTCATCTCAATCCCC 59.962 54.545 0.00 0.00 0.00 4.81
961 1040 2.694397 CTACCTCATCTCAATCCCCCA 58.306 52.381 0.00 0.00 0.00 4.96
965 1044 3.077391 ACCTCATCTCAATCCCCCAAAAA 59.923 43.478 0.00 0.00 0.00 1.94
984 1063 0.251386 AACCAGAGAGGAGAGCGACA 60.251 55.000 0.00 0.00 41.22 4.35
1148 1227 1.066430 GTGGAGGCGGATACACAAAGA 60.066 52.381 0.00 0.00 33.91 2.52
1167 1246 4.810191 AGAGGAAAGCAGTAAATCGTCT 57.190 40.909 0.00 0.00 33.54 4.18
1177 1256 4.811024 GCAGTAAATCGTCTTGGATGATCA 59.189 41.667 0.00 0.00 37.32 2.92
1188 1267 0.657840 GGATGATCACCGGAAAAGCG 59.342 55.000 9.46 0.00 0.00 4.68
1369 1448 2.895680 CCTCCGAGCTGCTTAGCA 59.104 61.111 6.76 6.76 37.25 3.49
1385 1464 7.107639 TGCTTAGCACTACATACAGATTACA 57.892 36.000 1.39 0.00 31.71 2.41
1392 1471 5.459107 CACTACATACAGATTACAGCGGAAC 59.541 44.000 0.00 0.00 0.00 3.62
1433 1534 0.612174 ACCGAGGCTGCTGAGAGTAA 60.612 55.000 0.00 0.00 0.00 2.24
1439 1540 1.548269 GGCTGCTGAGAGTAAGAGTGT 59.452 52.381 0.00 0.00 0.00 3.55
1449 1550 6.692486 TGAGAGTAAGAGTGTGGAGAATTTC 58.308 40.000 0.00 0.00 0.00 2.17
1450 1551 5.715070 AGAGTAAGAGTGTGGAGAATTTCG 58.285 41.667 0.00 0.00 0.00 3.46
1456 1557 2.305927 AGTGTGGAGAATTTCGACCCAT 59.694 45.455 10.05 0.00 33.96 4.00
1460 1561 5.696724 GTGTGGAGAATTTCGACCCATATAG 59.303 44.000 10.05 0.00 33.96 1.31
1461 1562 4.691216 GTGGAGAATTTCGACCCATATAGC 59.309 45.833 10.05 0.00 0.00 2.97
1467 1568 1.215647 CGACCCATATAGCGAGGGC 59.784 63.158 0.00 0.00 46.88 5.19
1470 1571 1.194781 ACCCATATAGCGAGGGCAGG 61.195 60.000 0.00 0.00 46.88 4.85
1475 1576 0.106167 TATAGCGAGGGCAGGAGTGT 60.106 55.000 0.00 0.00 43.41 3.55
1495 1602 3.068732 TGTTGAGAGTGAGAGTGAGGTTG 59.931 47.826 0.00 0.00 0.00 3.77
1496 1603 3.229697 TGAGAGTGAGAGTGAGGTTGA 57.770 47.619 0.00 0.00 0.00 3.18
1509 1616 0.608640 AGGTTGAGGGTGACGATGAC 59.391 55.000 0.00 0.00 0.00 3.06
1544 1651 3.464720 TGAGGAGATTGAGAGTGAGGT 57.535 47.619 0.00 0.00 0.00 3.85
1547 1654 3.766591 GAGGAGATTGAGAGTGAGGTTGA 59.233 47.826 0.00 0.00 0.00 3.18
1548 1655 3.768757 AGGAGATTGAGAGTGAGGTTGAG 59.231 47.826 0.00 0.00 0.00 3.02
1549 1656 3.766591 GGAGATTGAGAGTGAGGTTGAGA 59.233 47.826 0.00 0.00 0.00 3.27
1550 1657 4.142182 GGAGATTGAGAGTGAGGTTGAGAG 60.142 50.000 0.00 0.00 0.00 3.20
1551 1658 4.415596 AGATTGAGAGTGAGGTTGAGAGT 58.584 43.478 0.00 0.00 0.00 3.24
1552 1659 4.220382 AGATTGAGAGTGAGGTTGAGAGTG 59.780 45.833 0.00 0.00 0.00 3.51
1553 1660 3.229697 TGAGAGTGAGGTTGAGAGTGA 57.770 47.619 0.00 0.00 0.00 3.41
1554 1661 3.772387 TGAGAGTGAGGTTGAGAGTGAT 58.228 45.455 0.00 0.00 0.00 3.06
1555 1662 3.509184 TGAGAGTGAGGTTGAGAGTGATG 59.491 47.826 0.00 0.00 0.00 3.07
1556 1663 3.761218 GAGAGTGAGGTTGAGAGTGATGA 59.239 47.826 0.00 0.00 0.00 2.92
1557 1664 4.352009 AGAGTGAGGTTGAGAGTGATGAT 58.648 43.478 0.00 0.00 0.00 2.45
1558 1665 4.160065 AGAGTGAGGTTGAGAGTGATGATG 59.840 45.833 0.00 0.00 0.00 3.07
1559 1666 4.092279 AGTGAGGTTGAGAGTGATGATGA 58.908 43.478 0.00 0.00 0.00 2.92
1560 1667 4.715792 AGTGAGGTTGAGAGTGATGATGAT 59.284 41.667 0.00 0.00 0.00 2.45
1561 1668 5.189342 AGTGAGGTTGAGAGTGATGATGATT 59.811 40.000 0.00 0.00 0.00 2.57
1562 1669 5.293814 GTGAGGTTGAGAGTGATGATGATTG 59.706 44.000 0.00 0.00 0.00 2.67
1563 1670 5.046087 TGAGGTTGAGAGTGATGATGATTGT 60.046 40.000 0.00 0.00 0.00 2.71
1564 1671 5.813383 AGGTTGAGAGTGATGATGATTGTT 58.187 37.500 0.00 0.00 0.00 2.83
1596 1703 2.035961 CGAGGAGATTCCCAGCGAAATA 59.964 50.000 0.00 0.00 37.19 1.40
1601 1708 3.144506 AGATTCCCAGCGAAATATGCAG 58.855 45.455 0.00 0.00 33.08 4.41
1631 1738 5.163913 CCAAGTACTTGAGATTTTGCTCTCG 60.164 44.000 32.50 10.14 43.84 4.04
1664 1771 0.039617 TTGGCGCTGATTGAAAACGG 60.040 50.000 7.64 0.00 0.00 4.44
1675 1800 6.258727 GCTGATTGAAAACGGAGATGAAGATA 59.741 38.462 0.00 0.00 0.00 1.98
1680 1805 8.792830 TTGAAAACGGAGATGAAGATAAAGAT 57.207 30.769 0.00 0.00 0.00 2.40
1683 1814 8.792830 AAAACGGAGATGAAGATAAAGATGAA 57.207 30.769 0.00 0.00 0.00 2.57
1686 1817 7.961351 ACGGAGATGAAGATAAAGATGAAGAT 58.039 34.615 0.00 0.00 0.00 2.40
1692 1823 9.947433 GATGAAGATAAAGATGAAGATGAGGAT 57.053 33.333 0.00 0.00 0.00 3.24
1719 1850 2.977580 TGAGGATGGGGATGAAGATGAG 59.022 50.000 0.00 0.00 0.00 2.90
1725 1856 3.605879 TGGGGATGAAGATGAGGATGAT 58.394 45.455 0.00 0.00 0.00 2.45
1726 1857 3.329814 TGGGGATGAAGATGAGGATGATG 59.670 47.826 0.00 0.00 0.00 3.07
1729 1860 5.186942 GGGATGAAGATGAGGATGATGATG 58.813 45.833 0.00 0.00 0.00 3.07
1730 1861 5.045797 GGGATGAAGATGAGGATGATGATGA 60.046 44.000 0.00 0.00 0.00 2.92
1731 1862 6.110033 GGATGAAGATGAGGATGATGATGAG 58.890 44.000 0.00 0.00 0.00 2.90
1732 1863 5.485209 TGAAGATGAGGATGATGATGAGG 57.515 43.478 0.00 0.00 0.00 3.86
1733 1864 5.152934 TGAAGATGAGGATGATGATGAGGA 58.847 41.667 0.00 0.00 0.00 3.71
1734 1865 5.246429 TGAAGATGAGGATGATGATGAGGAG 59.754 44.000 0.00 0.00 0.00 3.69
1735 1866 4.098155 AGATGAGGATGATGATGAGGAGG 58.902 47.826 0.00 0.00 0.00 4.30
1736 1867 3.625252 TGAGGATGATGATGAGGAGGA 57.375 47.619 0.00 0.00 0.00 3.71
1737 1868 3.508426 TGAGGATGATGATGAGGAGGAG 58.492 50.000 0.00 0.00 0.00 3.69
1747 1878 3.075283 TGATGAGGAGGAGGAGGATAGAC 59.925 52.174 0.00 0.00 0.00 2.59
1765 1896 2.695666 AGACCCACATTGGAGTATCTCG 59.304 50.000 0.00 0.00 40.96 4.04
1772 1903 5.178797 CACATTGGAGTATCTCGAAAAGGT 58.821 41.667 0.00 0.00 32.48 3.50
2148 2291 7.012704 CGTTGTTGATCTATTCCATCAGGATTT 59.987 37.037 0.00 0.00 45.26 2.17
2238 2393 1.579084 GGACCGCAACCGCAACATTA 61.579 55.000 0.00 0.00 38.40 1.90
2257 2412 6.997655 ACATTATATTCTCTCGATCAAGGCA 58.002 36.000 0.00 0.00 0.00 4.75
2357 2513 1.267121 TTCCTAGTCCACTGGAGTGC 58.733 55.000 14.91 0.00 44.34 4.40
2358 2514 0.409876 TCCTAGTCCACTGGAGTGCT 59.590 55.000 14.91 4.05 44.34 4.40
2370 2530 3.589288 ACTGGAGTGCTTTCCTAGGAAAT 59.411 43.478 32.18 20.24 42.34 2.17
2429 2589 5.163364 GGATTCTTCTCTATGCTTGACTGGA 60.163 44.000 0.00 0.00 0.00 3.86
2495 2655 7.232118 AGTTGAACTCAAAATAAATGAGGGG 57.768 36.000 8.26 0.00 46.81 4.79
2511 2671 0.179054 GGGGGCCGAAGAAGATACAC 60.179 60.000 0.00 0.00 0.00 2.90
2548 2708 2.351738 GCAACCACCTTTATGACAGTGC 60.352 50.000 0.00 0.00 0.00 4.40
2551 2711 4.568072 ACCACCTTTATGACAGTGCATA 57.432 40.909 0.00 0.00 0.00 3.14
2552 2712 5.116084 ACCACCTTTATGACAGTGCATAT 57.884 39.130 0.00 0.00 31.34 1.78
2569 2729 9.333497 CAGTGCATATTATGATTTAAATGTCCG 57.667 33.333 5.17 0.00 0.00 4.79
2580 2740 1.523758 AAATGTCCGTCAACTGAGGC 58.476 50.000 0.00 0.00 0.00 4.70
2597 2757 1.429423 GCCCGCAACTGTTGATAGC 59.571 57.895 23.81 16.80 0.00 2.97
2600 2760 1.331756 CCCGCAACTGTTGATAGCATC 59.668 52.381 23.81 3.60 0.00 3.91
2650 2810 4.622740 GTGTGATGCAGAATTAACCTTTGC 59.377 41.667 0.00 0.00 35.42 3.68
2652 2812 2.346099 TGCAGAATTAACCTTTGCGC 57.654 45.000 0.00 0.00 37.58 6.09
2666 2826 0.521291 TTGCGCAGTTTGATACAGCC 59.479 50.000 11.31 0.00 36.00 4.85
2731 2891 2.289569 GGCCTTTCAAATGTGGATGCAA 60.290 45.455 0.00 0.00 0.00 4.08
2768 2928 3.065925 GGTCTGCTGCAACAAGGAATATC 59.934 47.826 3.02 0.00 0.00 1.63
2847 3007 7.054124 TGTAGGATCAAATGGTTACCTTCATC 58.946 38.462 2.07 0.00 0.00 2.92
2867 3027 4.066646 TCTGTCGAGAAATGTTGTTCCA 57.933 40.909 0.00 0.00 0.00 3.53
3125 3285 9.162764 GTGTATTGATCCAACTATTTGTGTACT 57.837 33.333 0.00 0.00 0.00 2.73
3143 3303 8.818622 TGTGTACTGACTATAATAGGACTTGT 57.181 34.615 0.00 0.00 0.00 3.16
3158 3318 5.003804 AGGACTTGTTATGCTAGTGGTTTG 58.996 41.667 0.00 0.00 33.49 2.93
3173 3333 7.653311 GCTAGTGGTTTGTCAAAATCAAATTCT 59.347 33.333 0.00 0.00 38.12 2.40
3175 3335 6.258507 AGTGGTTTGTCAAAATCAAATTCTGC 59.741 34.615 0.00 0.00 38.12 4.26
3178 3338 6.419413 GGTTTGTCAAAATCAAATTCTGCGTA 59.581 34.615 0.00 0.00 37.18 4.42
3188 3348 6.603237 TCAAATTCTGCGTATATCAACCTG 57.397 37.500 0.00 0.00 0.00 4.00
3191 3351 3.819564 TCTGCGTATATCAACCTGCTT 57.180 42.857 0.00 0.00 0.00 3.91
3213 3373 3.607422 CACTCGAGTGTTTGATTTGCA 57.393 42.857 32.77 0.00 40.96 4.08
3218 3378 3.249799 TCGAGTGTTTGATTTGCATCGTT 59.750 39.130 0.00 0.00 31.08 3.85
3219 3379 4.449405 TCGAGTGTTTGATTTGCATCGTTA 59.551 37.500 0.00 0.00 31.08 3.18
3267 3427 8.908903 TCTTTTACCAACTTTCATTTAGCTTCA 58.091 29.630 0.00 0.00 0.00 3.02
3276 3436 7.163441 ACTTTCATTTAGCTTCATTTGGCAAT 58.837 30.769 0.00 0.00 0.00 3.56
3278 3438 9.321562 CTTTCATTTAGCTTCATTTGGCAATAT 57.678 29.630 0.00 0.00 0.00 1.28
3280 3440 9.669887 TTCATTTAGCTTCATTTGGCAATATTT 57.330 25.926 0.00 0.00 0.00 1.40
3314 3475 7.063456 GCTGTATGTATATTTGTGTGTTAGCG 58.937 38.462 0.00 0.00 0.00 4.26
3329 3490 5.410439 TGTGTTAGCGGGATTAAAACTCTTC 59.590 40.000 0.00 0.00 0.00 2.87
3351 3512 0.102663 GAGTGGTTACGGCTAGAGGC 59.897 60.000 0.00 0.00 40.90 4.70
3352 3513 0.613853 AGTGGTTACGGCTAGAGGCA 60.614 55.000 3.81 0.00 44.01 4.75
3381 3542 1.331214 AGGCCTTGTTTGGATGTGTG 58.669 50.000 0.00 0.00 0.00 3.82
3397 3558 3.197265 TGTGTGTCACTGTGTCATCAAG 58.803 45.455 10.70 0.00 35.11 3.02
3414 3575 3.451526 TCAAGCAATCGATCACTGCTAG 58.548 45.455 20.34 4.21 45.50 3.42
3440 3761 1.648504 GCCCATGCAAATTCTGAAGC 58.351 50.000 0.00 0.00 37.47 3.86
3455 3776 3.111098 CTGAAGCTGTTTGTGTGAAAGC 58.889 45.455 0.00 0.00 0.00 3.51
3494 3815 6.073276 CCACTGTTCTATTCGATTCACAACAA 60.073 38.462 0.00 0.00 0.00 2.83
3502 3823 5.682943 TTCGATTCACAACAAAACTAGGG 57.317 39.130 0.00 0.00 0.00 3.53
3532 3853 1.521580 TTTGCATGATGTGACAGCGA 58.478 45.000 0.00 0.00 0.00 4.93
3535 3856 0.742281 GCATGATGTGACAGCGACCT 60.742 55.000 0.00 0.00 0.00 3.85
3551 3872 3.735208 GCGACCTGATCTTTCGATGAGAA 60.735 47.826 13.23 0.00 33.30 2.87
3561 3882 5.611374 TCTTTCGATGAGAATGGGGATAAC 58.389 41.667 0.00 0.00 38.86 1.89
3568 3889 5.723672 TGAGAATGGGGATAACTATCGAC 57.276 43.478 0.00 0.00 33.52 4.20
3589 3910 5.853282 CGACTTGGTGAATTTTGATCTTGAC 59.147 40.000 0.00 0.00 0.00 3.18
3590 3911 5.762045 ACTTGGTGAATTTTGATCTTGACG 58.238 37.500 0.00 0.00 0.00 4.35
3604 3925 0.963962 TTGACGATCCGGCTATACCC 59.036 55.000 0.00 0.00 35.04 3.69
3622 3943 0.692476 CCCCCGATGATATGCCTTGA 59.308 55.000 0.00 0.00 0.00 3.02
3636 3957 3.950397 TGCCTTGACAATCGATAAACCT 58.050 40.909 0.00 0.00 0.00 3.50
3637 3958 4.331968 TGCCTTGACAATCGATAAACCTT 58.668 39.130 0.00 0.00 0.00 3.50
3639 3960 5.095490 GCCTTGACAATCGATAAACCTTTG 58.905 41.667 0.00 0.00 0.00 2.77
3646 3971 8.664798 TGACAATCGATAAACCTTTGATAGTTG 58.335 33.333 0.00 0.00 0.00 3.16
3662 3987 6.057533 TGATAGTTGTTGATCTTGCCATAGG 58.942 40.000 0.00 0.00 0.00 2.57
3678 4003 5.434352 CCATAGGCATGATCAACTTGAAG 57.566 43.478 0.00 0.00 33.67 3.02
3681 4006 6.459298 CCATAGGCATGATCAACTTGAAGAAC 60.459 42.308 0.00 0.00 33.67 3.01
3683 4008 3.436704 GGCATGATCAACTTGAAGAACGA 59.563 43.478 0.00 0.00 0.00 3.85
3711 4036 3.631250 AGTTCCTGCAAGAAACCAAAGA 58.369 40.909 0.00 0.00 34.07 2.52
3713 4038 4.112634 GTTCCTGCAAGAAACCAAAGAAC 58.887 43.478 0.00 0.00 34.07 3.01
3714 4039 3.631250 TCCTGCAAGAAACCAAAGAACT 58.369 40.909 0.00 0.00 34.07 3.01
3719 4104 4.036734 TGCAAGAAACCAAAGAACTAGCAG 59.963 41.667 0.00 0.00 0.00 4.24
3793 4178 3.828875 AGATGAAAGAGTTCGGATCCC 57.171 47.619 6.06 0.00 36.46 3.85
3803 4188 1.065418 GTTCGGATCCCACTGTGGATT 60.065 52.381 27.94 14.28 45.25 3.01
3811 4196 4.715534 TCCCACTGTGGATTTAACAAGA 57.284 40.909 27.94 10.19 40.96 3.02
3834 4219 2.486191 GGCAGTCCTACATCAAGATGGG 60.486 54.545 14.04 6.95 42.91 4.00
3840 4225 2.213499 CTACATCAAGATGGGAACGGC 58.787 52.381 14.04 0.00 42.91 5.68
3843 4228 0.462047 ATCAAGATGGGAACGGCGAC 60.462 55.000 16.62 7.14 0.00 5.19
3867 4252 1.006220 CCTTCGGGTTTTGCTTGGC 60.006 57.895 0.00 0.00 0.00 4.52
3877 4262 2.091640 TTTGCTTGGCCATCCTCCCA 62.092 55.000 6.09 0.00 0.00 4.37
3896 4281 1.741770 CCGGCGAGAGAAACCCAAG 60.742 63.158 9.30 0.00 0.00 3.61
3899 4284 1.003233 GCGAGAGAAACCCAAGCCT 60.003 57.895 0.00 0.00 0.00 4.58
3906 4291 2.366153 GAAACCCAAGCCTGTCCCCA 62.366 60.000 0.00 0.00 0.00 4.96
3909 4294 2.276740 CCAAGCCTGTCCCCATCC 59.723 66.667 0.00 0.00 0.00 3.51
3912 4297 3.908712 AAGCCTGTCCCCATCCCCA 62.909 63.158 0.00 0.00 0.00 4.96
3915 4300 2.018447 CCTGTCCCCATCCCCAAAT 58.982 57.895 0.00 0.00 0.00 2.32
3918 4303 0.630673 TGTCCCCATCCCCAAATCTG 59.369 55.000 0.00 0.00 0.00 2.90
3983 4368 0.465642 GGAACCCATCCCGATGAACC 60.466 60.000 6.25 1.18 43.00 3.62
3984 4369 0.254747 GAACCCATCCCGATGAACCA 59.745 55.000 6.25 0.00 41.20 3.67
3986 4371 1.814429 ACCCATCCCGATGAACCATA 58.186 50.000 6.25 0.00 41.20 2.74
3988 4373 2.512056 ACCCATCCCGATGAACCATAAA 59.488 45.455 6.25 0.00 41.20 1.40
3991 4376 4.202111 CCCATCCCGATGAACCATAAAAAC 60.202 45.833 6.25 0.00 41.20 2.43
3994 4379 5.379732 TCCCGATGAACCATAAAAACAAC 57.620 39.130 0.00 0.00 0.00 3.32
3995 4380 4.827835 TCCCGATGAACCATAAAAACAACA 59.172 37.500 0.00 0.00 0.00 3.33
3996 4381 5.048364 TCCCGATGAACCATAAAAACAACAG 60.048 40.000 0.00 0.00 0.00 3.16
3997 4382 4.621034 CCGATGAACCATAAAAACAACAGC 59.379 41.667 0.00 0.00 0.00 4.40
4011 4396 1.001181 CAACAGCAACATTTGGGAGGG 59.999 52.381 0.00 0.00 0.00 4.30
4032 4417 4.473922 GGGGACACTAGGAGGTAAGAAATT 59.526 45.833 0.00 0.00 0.00 1.82
4037 4422 5.309806 ACACTAGGAGGTAAGAAATTGGTGT 59.690 40.000 0.00 0.00 0.00 4.16
4042 4427 4.394729 GAGGTAAGAAATTGGTGTGTGGA 58.605 43.478 0.00 0.00 0.00 4.02
4050 4435 7.219484 AGAAATTGGTGTGTGGATTTTAGAG 57.781 36.000 0.00 0.00 0.00 2.43
4060 4445 5.303333 GTGTGGATTTTAGAGTTTTTGGGGA 59.697 40.000 0.00 0.00 0.00 4.81
4073 4458 0.106569 TTGGGGATGAGCATGCGATT 60.107 50.000 13.01 0.00 0.00 3.34
4078 4463 2.481952 GGGATGAGCATGCGATTTAGAC 59.518 50.000 13.01 0.00 0.00 2.59
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
61 62 3.781770 GATGCTGGGAGGTCGCTCG 62.782 68.421 0.00 0.00 0.00 5.03
62 63 2.107953 GATGCTGGGAGGTCGCTC 59.892 66.667 0.00 0.00 0.00 5.03
63 64 3.474570 GGATGCTGGGAGGTCGCT 61.475 66.667 0.00 0.00 0.00 4.93
64 65 4.899239 CGGATGCTGGGAGGTCGC 62.899 72.222 0.00 0.00 0.00 5.19
65 66 2.502492 ATCGGATGCTGGGAGGTCG 61.502 63.158 0.00 0.00 0.00 4.79
66 67 1.070445 CATCGGATGCTGGGAGGTC 59.930 63.158 4.84 0.00 0.00 3.85
67 68 3.234349 CATCGGATGCTGGGAGGT 58.766 61.111 4.84 0.00 0.00 3.85
177 232 0.807667 GATGATGCTGAGACCGCGTT 60.808 55.000 4.92 0.00 0.00 4.84
186 249 4.159901 TGGCCGCGATGATGCTGA 62.160 61.111 8.23 0.00 0.00 4.26
254 317 3.027170 CTCAAGGCGCGCGTCAATT 62.027 57.895 37.48 20.70 0.00 2.32
297 360 2.662091 AAAAAGCGTGCTGTGACGGC 62.662 55.000 9.96 9.96 39.81 5.68
357 420 2.279517 CCGGTGCCGTGAGATAGC 60.280 66.667 9.90 0.00 37.81 2.97
358 421 2.279517 GCCGGTGCCGTGAGATAG 60.280 66.667 1.90 0.00 37.81 2.08
359 422 3.071837 TGCCGGTGCCGTGAGATA 61.072 61.111 1.90 0.00 37.81 1.98
360 423 4.760047 GTGCCGGTGCCGTGAGAT 62.760 66.667 1.90 0.00 37.81 2.75
391 454 2.029518 CTGGACGTGTGAGCTGCA 59.970 61.111 1.02 0.00 0.00 4.41
466 536 2.397597 TCATGGATCTCACCATCGGAA 58.602 47.619 0.00 0.00 46.24 4.30
479 549 4.140734 TCTCTCTCCCTCTGAATCATGGAT 60.141 45.833 4.38 0.00 0.00 3.41
480 550 3.206185 TCTCTCTCCCTCTGAATCATGGA 59.794 47.826 4.38 1.13 0.00 3.41
481 551 3.574749 TCTCTCTCCCTCTGAATCATGG 58.425 50.000 0.00 0.00 0.00 3.66
482 552 4.472496 TCTCTCTCTCCCTCTGAATCATG 58.528 47.826 0.00 0.00 0.00 3.07
483 553 4.812403 TCTCTCTCTCCCTCTGAATCAT 57.188 45.455 0.00 0.00 0.00 2.45
484 554 4.167697 TCATCTCTCTCTCCCTCTGAATCA 59.832 45.833 0.00 0.00 0.00 2.57
485 555 4.728772 TCATCTCTCTCTCCCTCTGAATC 58.271 47.826 0.00 0.00 0.00 2.52
486 556 4.416513 TCTCATCTCTCTCTCCCTCTGAAT 59.583 45.833 0.00 0.00 0.00 2.57
487 557 3.785325 TCTCATCTCTCTCTCCCTCTGAA 59.215 47.826 0.00 0.00 0.00 3.02
488 558 3.392730 TCTCATCTCTCTCTCCCTCTGA 58.607 50.000 0.00 0.00 0.00 3.27
489 559 3.862877 TCTCATCTCTCTCTCCCTCTG 57.137 52.381 0.00 0.00 0.00 3.35
490 560 3.139025 CCTTCTCATCTCTCTCTCCCTCT 59.861 52.174 0.00 0.00 0.00 3.69
491 561 3.490348 CCTTCTCATCTCTCTCTCCCTC 58.510 54.545 0.00 0.00 0.00 4.30
492 562 2.177669 CCCTTCTCATCTCTCTCTCCCT 59.822 54.545 0.00 0.00 0.00 4.20
493 563 2.597455 CCCTTCTCATCTCTCTCTCCC 58.403 57.143 0.00 0.00 0.00 4.30
494 564 1.963515 GCCCTTCTCATCTCTCTCTCC 59.036 57.143 0.00 0.00 0.00 3.71
495 565 1.608590 CGCCCTTCTCATCTCTCTCTC 59.391 57.143 0.00 0.00 0.00 3.20
496 566 1.691196 CGCCCTTCTCATCTCTCTCT 58.309 55.000 0.00 0.00 0.00 3.10
497 567 0.673437 CCGCCCTTCTCATCTCTCTC 59.327 60.000 0.00 0.00 0.00 3.20
498 568 0.758685 CCCGCCCTTCTCATCTCTCT 60.759 60.000 0.00 0.00 0.00 3.10
499 569 1.745264 CCCGCCCTTCTCATCTCTC 59.255 63.158 0.00 0.00 0.00 3.20
505 575 4.697756 CAACGCCCGCCCTTCTCA 62.698 66.667 0.00 0.00 0.00 3.27
540 610 4.665833 TCTCGTTATCCCGATGAAACAT 57.334 40.909 0.00 0.00 36.08 2.71
552 622 3.907194 CGCGTATCCTCTTTCTCGTTATC 59.093 47.826 0.00 0.00 0.00 1.75
561 631 4.515404 GCACCGCGTATCCTCTTT 57.485 55.556 4.92 0.00 0.00 2.52
604 674 3.204827 ATCAACCTCCATGCGCGC 61.205 61.111 27.26 27.26 0.00 6.86
605 675 2.711311 CATCAACCTCCATGCGCG 59.289 61.111 0.00 0.00 0.00 6.86
606 676 2.410469 GCATCAACCTCCATGCGC 59.590 61.111 0.00 0.00 36.33 6.09
608 678 0.179156 CAACGCATCAACCTCCATGC 60.179 55.000 0.00 0.00 41.79 4.06
609 679 0.452987 CCAACGCATCAACCTCCATG 59.547 55.000 0.00 0.00 0.00 3.66
617 687 1.270571 TGTAGACAGCCAACGCATCAA 60.271 47.619 0.00 0.00 37.52 2.57
675 745 2.028476 TCACGACACCGATCCAATCTTT 60.028 45.455 0.00 0.00 39.50 2.52
699 769 0.037232 CCACGTCCCTCTCCACTTTC 60.037 60.000 0.00 0.00 0.00 2.62
761 831 1.338294 TGTTATGCGATCGGTTGTGGT 60.338 47.619 18.30 0.00 0.00 4.16
763 833 1.999735 ACTGTTATGCGATCGGTTGTG 59.000 47.619 18.30 0.00 0.00 3.33
764 834 2.380084 ACTGTTATGCGATCGGTTGT 57.620 45.000 18.30 0.00 0.00 3.32
765 835 2.538449 GGTACTGTTATGCGATCGGTTG 59.462 50.000 18.30 0.00 0.00 3.77
837 916 6.485984 GTCCCTGTCTTGATCGAGTAGTATTA 59.514 42.308 9.87 0.00 0.00 0.98
840 919 4.197750 GTCCCTGTCTTGATCGAGTAGTA 58.802 47.826 9.87 0.00 0.00 1.82
842 921 2.032302 CGTCCCTGTCTTGATCGAGTAG 59.968 54.545 9.87 9.32 0.00 2.57
843 922 2.014857 CGTCCCTGTCTTGATCGAGTA 58.985 52.381 9.87 0.35 0.00 2.59
844 923 0.811915 CGTCCCTGTCTTGATCGAGT 59.188 55.000 9.87 0.00 0.00 4.18
845 924 0.101399 CCGTCCCTGTCTTGATCGAG 59.899 60.000 3.24 3.24 0.00 4.04
846 925 0.611062 ACCGTCCCTGTCTTGATCGA 60.611 55.000 0.00 0.00 0.00 3.59
870 949 8.647143 ATTATCCTTTTGTTGTTGTTGTTCAG 57.353 30.769 0.00 0.00 0.00 3.02
884 963 2.096909 CGCCGCGTAGATTATCCTTTTG 60.097 50.000 4.92 0.00 0.00 2.44
889 968 2.092882 GCCGCCGCGTAGATTATCC 61.093 63.158 12.58 0.00 0.00 2.59
927 1006 2.399356 GGTAGCAGGCTTTCCACGC 61.399 63.158 0.00 0.00 34.36 5.34
932 1011 2.169352 TGAGATGAGGTAGCAGGCTTTC 59.831 50.000 0.00 0.00 0.00 2.62
933 1012 2.191400 TGAGATGAGGTAGCAGGCTTT 58.809 47.619 0.00 0.00 0.00 3.51
965 1044 0.251386 TGTCGCTCTCCTCTCTGGTT 60.251 55.000 0.00 0.00 37.07 3.67
1082 1161 3.345808 GCACGTCTTTGCGCTCCA 61.346 61.111 9.73 0.00 34.88 3.86
1148 1227 4.003648 CCAAGACGATTTACTGCTTTCCT 58.996 43.478 0.00 0.00 0.00 3.36
1167 1246 2.091541 GCTTTTCCGGTGATCATCCAA 58.908 47.619 0.00 0.00 0.00 3.53
1369 1448 5.360144 AGTTCCGCTGTAATCTGTATGTAGT 59.640 40.000 0.00 0.00 0.00 2.73
1385 1464 0.175989 GAAATCCTCCGAGTTCCGCT 59.824 55.000 0.00 0.00 37.17 5.52
1392 1471 4.946478 ATCTTGGTAGAAATCCTCCGAG 57.054 45.455 0.00 0.00 33.20 4.63
1433 1534 2.028020 GGGTCGAAATTCTCCACACTCT 60.028 50.000 0.00 0.00 0.00 3.24
1439 1540 4.560716 CGCTATATGGGTCGAAATTCTCCA 60.561 45.833 0.00 4.78 0.00 3.86
1449 1550 1.215647 GCCCTCGCTATATGGGTCG 59.784 63.158 0.00 0.00 42.77 4.79
1450 1551 0.247736 CTGCCCTCGCTATATGGGTC 59.752 60.000 0.00 0.00 42.77 4.46
1456 1557 0.106167 ACACTCCTGCCCTCGCTATA 60.106 55.000 0.00 0.00 35.36 1.31
1460 1561 2.743928 CAACACTCCTGCCCTCGC 60.744 66.667 0.00 0.00 0.00 5.03
1461 1562 1.079543 CTCAACACTCCTGCCCTCG 60.080 63.158 0.00 0.00 0.00 4.63
1467 1568 2.890311 ACTCTCACTCTCAACACTCCTG 59.110 50.000 0.00 0.00 0.00 3.86
1470 1571 3.057596 CCTCACTCTCACTCTCAACACTC 60.058 52.174 0.00 0.00 0.00 3.51
1475 1576 3.566351 TCAACCTCACTCTCACTCTCAA 58.434 45.455 0.00 0.00 0.00 3.02
1495 1602 0.108615 CCACAGTCATCGTCACCCTC 60.109 60.000 0.00 0.00 0.00 4.30
1496 1603 0.832135 ACCACAGTCATCGTCACCCT 60.832 55.000 0.00 0.00 0.00 4.34
1509 1616 1.478105 TCCTCATCGTCATCACCACAG 59.522 52.381 0.00 0.00 0.00 3.66
1544 1651 9.052759 CATCATAACAATCATCATCACTCTCAA 57.947 33.333 0.00 0.00 0.00 3.02
1547 1654 9.220767 CATCATCATAACAATCATCATCACTCT 57.779 33.333 0.00 0.00 0.00 3.24
1548 1655 9.216117 TCATCATCATAACAATCATCATCACTC 57.784 33.333 0.00 0.00 0.00 3.51
1549 1656 9.000486 GTCATCATCATAACAATCATCATCACT 58.000 33.333 0.00 0.00 0.00 3.41
1550 1657 7.955864 CGTCATCATCATAACAATCATCATCAC 59.044 37.037 0.00 0.00 0.00 3.06
1551 1658 7.874016 TCGTCATCATCATAACAATCATCATCA 59.126 33.333 0.00 0.00 0.00 3.07
1552 1659 8.248117 TCGTCATCATCATAACAATCATCATC 57.752 34.615 0.00 0.00 0.00 2.92
1553 1660 7.333672 CCTCGTCATCATCATAACAATCATCAT 59.666 37.037 0.00 0.00 0.00 2.45
1554 1661 6.647895 CCTCGTCATCATCATAACAATCATCA 59.352 38.462 0.00 0.00 0.00 3.07
1555 1662 6.870439 TCCTCGTCATCATCATAACAATCATC 59.130 38.462 0.00 0.00 0.00 2.92
1556 1663 6.762333 TCCTCGTCATCATCATAACAATCAT 58.238 36.000 0.00 0.00 0.00 2.45
1557 1664 6.040842 TCTCCTCGTCATCATCATAACAATCA 59.959 38.462 0.00 0.00 0.00 2.57
1558 1665 6.450545 TCTCCTCGTCATCATCATAACAATC 58.549 40.000 0.00 0.00 0.00 2.67
1559 1666 6.410942 TCTCCTCGTCATCATCATAACAAT 57.589 37.500 0.00 0.00 0.00 2.71
1560 1667 5.852282 TCTCCTCGTCATCATCATAACAA 57.148 39.130 0.00 0.00 0.00 2.83
1561 1668 6.410942 AATCTCCTCGTCATCATCATAACA 57.589 37.500 0.00 0.00 0.00 2.41
1562 1669 5.866633 GGAATCTCCTCGTCATCATCATAAC 59.133 44.000 0.00 0.00 32.53 1.89
1563 1670 5.047021 GGGAATCTCCTCGTCATCATCATAA 60.047 44.000 0.00 0.00 36.57 1.90
1564 1671 4.464244 GGGAATCTCCTCGTCATCATCATA 59.536 45.833 0.00 0.00 36.57 2.15
1596 1703 3.324846 TCAAGTACTTGGTGAGACTGCAT 59.675 43.478 30.35 0.00 40.78 3.96
1631 1738 2.484264 AGCGCCAACTTGTTCTCATAAC 59.516 45.455 2.29 0.00 0.00 1.89
1664 1771 9.426837 CCTCATCTTCATCTTTATCTTCATCTC 57.573 37.037 0.00 0.00 0.00 2.75
1675 1800 6.329460 TCATCCTCATCCTCATCTTCATCTTT 59.671 38.462 0.00 0.00 0.00 2.52
1680 1805 3.902467 CCTCATCCTCATCCTCATCTTCA 59.098 47.826 0.00 0.00 0.00 3.02
1683 1814 3.919304 TCCTCATCCTCATCCTCATCT 57.081 47.619 0.00 0.00 0.00 2.90
1686 1817 2.617658 CCATCCTCATCCTCATCCTCA 58.382 52.381 0.00 0.00 0.00 3.86
1692 1823 1.223858 TCATCCCCATCCTCATCCTCA 59.776 52.381 0.00 0.00 0.00 3.86
1719 1850 2.833338 CTCCTCCTCCTCATCATCATCC 59.167 54.545 0.00 0.00 0.00 3.51
1725 1856 3.075283 GTCTATCCTCCTCCTCCTCATCA 59.925 52.174 0.00 0.00 0.00 3.07
1726 1857 3.563479 GGTCTATCCTCCTCCTCCTCATC 60.563 56.522 0.00 0.00 0.00 2.92
1729 1860 1.076513 GGGTCTATCCTCCTCCTCCTC 59.923 61.905 0.00 0.00 36.25 3.71
1730 1861 1.163408 GGGTCTATCCTCCTCCTCCT 58.837 60.000 0.00 0.00 36.25 3.69
1731 1862 0.861155 TGGGTCTATCCTCCTCCTCC 59.139 60.000 0.00 0.00 36.25 4.30
1732 1863 1.218196 TGTGGGTCTATCCTCCTCCTC 59.782 57.143 0.00 0.00 36.25 3.71
1733 1864 1.319947 TGTGGGTCTATCCTCCTCCT 58.680 55.000 0.00 0.00 36.25 3.69
1734 1865 2.370189 CAATGTGGGTCTATCCTCCTCC 59.630 54.545 0.00 0.00 36.25 4.30
1735 1866 2.370189 CCAATGTGGGTCTATCCTCCTC 59.630 54.545 0.00 0.00 32.67 3.71
1736 1867 2.022035 TCCAATGTGGGTCTATCCTCCT 60.022 50.000 0.00 0.00 38.32 3.69
1737 1868 2.370189 CTCCAATGTGGGTCTATCCTCC 59.630 54.545 0.00 0.00 38.32 4.30
1747 1878 3.819564 TTCGAGATACTCCAATGTGGG 57.180 47.619 0.00 0.00 38.32 4.61
1765 1896 5.877012 TCTGTTCATCAGCTATCACCTTTTC 59.123 40.000 0.00 0.00 43.32 2.29
1772 1903 7.360353 CGAAACTTTTCTGTTCATCAGCTATCA 60.360 37.037 0.00 0.00 43.32 2.15
1788 1919 5.733109 GTCATATTCTTCGCCGAAACTTTTC 59.267 40.000 0.00 0.00 0.00 2.29
1789 1920 5.411669 AGTCATATTCTTCGCCGAAACTTTT 59.588 36.000 0.00 0.00 0.00 2.27
1907 2038 9.294030 GGAAGCAAACAGATGATACAAATTTAG 57.706 33.333 0.00 0.00 0.00 1.85
2091 2234 0.477202 ATAGCAGCAGGGGATGGGAT 60.477 55.000 0.00 0.00 0.00 3.85
2295 2450 6.453092 AGAAAAATGAGGAGCAAACTGAATG 58.547 36.000 0.00 0.00 0.00 2.67
2357 2513 7.104043 TGATTGCAATGATTTCCTAGGAAAG 57.896 36.000 34.12 23.68 45.66 2.62
2358 2514 7.396907 TCTTGATTGCAATGATTTCCTAGGAAA 59.603 33.333 33.59 33.59 39.56 3.13
2495 2655 2.614057 CAATGGTGTATCTTCTTCGGCC 59.386 50.000 0.00 0.00 0.00 6.13
2511 2671 3.256383 TGGTTGCAAGAACTGATCAATGG 59.744 43.478 0.00 0.00 0.00 3.16
2551 2711 9.173021 TCAGTTGACGGACATTTAAATCATAAT 57.827 29.630 0.00 0.00 0.00 1.28
2552 2712 8.554835 TCAGTTGACGGACATTTAAATCATAA 57.445 30.769 0.00 0.00 0.00 1.90
2569 2729 2.281484 TTGCGGGCCTCAGTTGAC 60.281 61.111 0.84 0.00 0.00 3.18
2574 2734 2.281761 AACAGTTGCGGGCCTCAG 60.282 61.111 0.84 0.00 0.00 3.35
2580 2740 1.331756 GATGCTATCAACAGTTGCGGG 59.668 52.381 8.58 2.16 0.00 6.13
2597 2757 5.106791 GCCACGGATGAATATTGAAGAGATG 60.107 44.000 0.00 0.00 0.00 2.90
2600 2760 4.212847 CAGCCACGGATGAATATTGAAGAG 59.787 45.833 0.00 0.00 32.62 2.85
2652 2812 2.002586 CTGGACGGCTGTATCAAACTG 58.997 52.381 0.00 0.00 0.00 3.16
2666 2826 2.034066 ACAATGGTGGCCTGGACG 59.966 61.111 3.32 0.00 0.00 4.79
2731 2891 0.475906 AGACCAGGAGCAAGCAACTT 59.524 50.000 0.00 0.00 0.00 2.66
2847 3007 3.809832 ACTGGAACAACATTTCTCGACAG 59.190 43.478 0.00 0.00 38.70 3.51
2867 3027 3.709653 TCAGTGTTCCTTGTAACTCCACT 59.290 43.478 0.00 0.00 0.00 4.00
3098 3258 9.162764 GTACACAAATAGTTGGATCAATACACT 57.837 33.333 7.93 0.00 39.22 3.55
3136 3296 4.760204 ACAAACCACTAGCATAACAAGTCC 59.240 41.667 0.00 0.00 0.00 3.85
3143 3303 7.517614 TGATTTTGACAAACCACTAGCATAA 57.482 32.000 0.00 0.00 0.00 1.90
3158 3318 9.502145 TTGATATACGCAGAATTTGATTTTGAC 57.498 29.630 0.00 0.00 0.00 3.18
3173 3333 1.939934 GCAAGCAGGTTGATATACGCA 59.060 47.619 16.74 0.00 38.60 5.24
3175 3335 3.198068 AGTGCAAGCAGGTTGATATACG 58.802 45.455 16.74 0.00 38.60 3.06
3178 3338 2.093500 TCGAGTGCAAGCAGGTTGATAT 60.093 45.455 16.74 0.03 38.60 1.63
3205 3365 9.764363 AACTAGATAGAATAACGATGCAAATCA 57.236 29.630 0.00 0.00 0.00 2.57
3234 3394 9.599866 AAATGAAAGTTGGTAAAAGAAAGGAAG 57.400 29.630 0.00 0.00 0.00 3.46
3247 3407 6.930722 CCAAATGAAGCTAAATGAAAGTTGGT 59.069 34.615 0.00 0.00 0.00 3.67
3249 3409 6.424509 TGCCAAATGAAGCTAAATGAAAGTTG 59.575 34.615 0.00 0.00 0.00 3.16
3329 3490 1.331138 CTCTAGCCGTAACCACTCTCG 59.669 57.143 0.00 0.00 0.00 4.04
3351 3512 4.559153 CAAACAAGGCCTTAATCCACTTG 58.441 43.478 20.00 5.62 43.01 3.16
3352 3513 3.578282 CCAAACAAGGCCTTAATCCACTT 59.422 43.478 20.00 1.02 0.00 3.16
3381 3542 3.424039 CGATTGCTTGATGACACAGTGAC 60.424 47.826 7.81 0.92 0.00 3.67
3397 3558 1.506493 CCCTAGCAGTGATCGATTGC 58.494 55.000 11.75 11.75 38.09 3.56
3423 3744 3.587797 ACAGCTTCAGAATTTGCATGG 57.412 42.857 0.00 0.00 0.00 3.66
3455 3776 3.441496 ACAGTGGCACTTTGTGAAATG 57.559 42.857 19.43 6.80 35.23 2.32
3464 3785 3.678056 TCGAATAGAACAGTGGCACTT 57.322 42.857 19.43 4.03 0.00 3.16
3516 3837 0.742281 AGGTCGCTGTCACATCATGC 60.742 55.000 0.00 0.00 0.00 4.06
3518 3839 0.897621 TCAGGTCGCTGTCACATCAT 59.102 50.000 0.00 0.00 0.00 2.45
3551 3872 4.040461 CACCAAGTCGATAGTTATCCCCAT 59.960 45.833 0.00 0.00 37.40 4.00
3561 3882 7.545362 AGATCAAAATTCACCAAGTCGATAG 57.455 36.000 0.00 0.00 0.00 2.08
3568 3889 6.000891 TCGTCAAGATCAAAATTCACCAAG 57.999 37.500 0.00 0.00 0.00 3.61
3589 3910 3.295800 GGGGGTATAGCCGGATCG 58.704 66.667 14.66 0.00 38.44 3.69
3604 3925 1.072173 TGTCAAGGCATATCATCGGGG 59.928 52.381 0.00 0.00 0.00 5.73
3607 3928 3.989817 TCGATTGTCAAGGCATATCATCG 59.010 43.478 1.28 1.28 0.00 3.84
3608 3929 7.601073 TTATCGATTGTCAAGGCATATCATC 57.399 36.000 1.71 0.00 0.00 2.92
3622 3943 8.561738 ACAACTATCAAAGGTTTATCGATTGT 57.438 30.769 1.71 0.00 0.00 2.71
3636 3957 6.839124 ATGGCAAGATCAACAACTATCAAA 57.161 33.333 0.00 0.00 0.00 2.69
3637 3958 6.543465 CCTATGGCAAGATCAACAACTATCAA 59.457 38.462 0.00 0.00 0.00 2.57
3639 3960 6.551385 CCTATGGCAAGATCAACAACTATC 57.449 41.667 0.00 0.00 0.00 2.08
3662 3987 4.436584 CCTCGTTCTTCAAGTTGATCATGC 60.437 45.833 6.36 0.00 0.00 4.06
3673 3998 3.875134 GGAACTTGAACCTCGTTCTTCAA 59.125 43.478 6.13 0.00 42.39 2.69
3675 4000 3.495001 CAGGAACTTGAACCTCGTTCTTC 59.505 47.826 6.13 2.31 39.17 2.87
3678 4003 1.531578 GCAGGAACTTGAACCTCGTTC 59.468 52.381 0.00 0.00 38.97 3.95
3681 4006 1.532868 CTTGCAGGAACTTGAACCTCG 59.467 52.381 0.00 0.00 34.60 4.63
3683 4008 3.297134 TTCTTGCAGGAACTTGAACCT 57.703 42.857 7.24 0.00 34.60 3.50
3740 4125 8.186163 TGCTCAGTTTATTATCTGCAATTTCAG 58.814 33.333 0.00 0.00 35.46 3.02
3750 4135 8.621532 TCTTTTGTGTGCTCAGTTTATTATCT 57.378 30.769 0.00 0.00 0.00 1.98
3793 4178 3.364964 GCCGTCTTGTTAAATCCACAGTG 60.365 47.826 0.00 0.00 0.00 3.66
3803 4188 2.629137 TGTAGGACTGCCGTCTTGTTAA 59.371 45.455 8.25 0.00 40.10 2.01
3811 4196 1.557099 TCTTGATGTAGGACTGCCGT 58.443 50.000 0.00 0.00 39.96 5.68
3834 4219 3.278592 AAGGGTCTCGTCGCCGTTC 62.279 63.158 0.00 0.00 35.01 3.95
3850 4235 1.006220 GGCCAAGCAAAACCCGAAG 60.006 57.895 0.00 0.00 0.00 3.79
3853 4238 1.079888 GATGGCCAAGCAAAACCCG 60.080 57.895 10.96 0.00 0.00 5.28
3863 4248 3.727258 CGGTGGGAGGATGGCCAA 61.727 66.667 10.96 0.00 36.29 4.52
3877 4262 2.450479 CTTGGGTTTCTCTCGCCGGT 62.450 60.000 1.90 0.00 0.00 5.28
3881 4266 1.003233 AGGCTTGGGTTTCTCTCGC 60.003 57.895 0.00 0.00 0.00 5.03
3906 4291 2.114670 CGCGCACAGATTTGGGGAT 61.115 57.895 8.75 0.00 0.00 3.85
3909 4294 3.814268 CCCGCGCACAGATTTGGG 61.814 66.667 8.75 2.73 0.00 4.12
3912 4297 2.746277 GTCCCCGCGCACAGATTT 60.746 61.111 8.75 0.00 0.00 2.17
3918 4303 2.841160 AAAAACTGTCCCCGCGCAC 61.841 57.895 8.75 0.00 0.00 5.34
3937 4322 1.839148 TACGGAAAACCGGATGGGCA 61.839 55.000 9.46 0.00 40.62 5.36
3964 4349 0.465642 GGTTCATCGGGATGGGTTCC 60.466 60.000 8.68 3.58 44.62 3.62
3975 4360 5.218885 TGCTGTTGTTTTTATGGTTCATCG 58.781 37.500 0.00 0.00 0.00 3.84
3976 4361 6.478344 TGTTGCTGTTGTTTTTATGGTTCATC 59.522 34.615 0.00 0.00 0.00 2.92
3983 4368 6.259608 TCCCAAATGTTGCTGTTGTTTTTATG 59.740 34.615 0.00 0.00 0.00 1.90
3984 4369 6.352516 TCCCAAATGTTGCTGTTGTTTTTAT 58.647 32.000 0.00 0.00 0.00 1.40
3986 4371 4.583871 TCCCAAATGTTGCTGTTGTTTTT 58.416 34.783 0.00 0.00 0.00 1.94
3988 4373 3.432046 CCTCCCAAATGTTGCTGTTGTTT 60.432 43.478 0.00 0.00 0.00 2.83
3991 4376 1.001181 CCCTCCCAAATGTTGCTGTTG 59.999 52.381 0.00 0.00 0.00 3.33
3994 4379 0.251742 TCCCCTCCCAAATGTTGCTG 60.252 55.000 0.00 0.00 0.00 4.41
3995 4380 0.251787 GTCCCCTCCCAAATGTTGCT 60.252 55.000 0.00 0.00 0.00 3.91
3996 4381 0.541764 TGTCCCCTCCCAAATGTTGC 60.542 55.000 0.00 0.00 0.00 4.17
3997 4382 1.203050 AGTGTCCCCTCCCAAATGTTG 60.203 52.381 0.00 0.00 0.00 3.33
4011 4396 5.045797 ACCAATTTCTTACCTCCTAGTGTCC 60.046 44.000 0.00 0.00 0.00 4.02
4032 4417 6.406400 CCAAAAACTCTAAAATCCACACACCA 60.406 38.462 0.00 0.00 0.00 4.17
4037 4422 5.459505 TCCCCAAAAACTCTAAAATCCACA 58.540 37.500 0.00 0.00 0.00 4.17
4042 4427 5.779771 TGCTCATCCCCAAAAACTCTAAAAT 59.220 36.000 0.00 0.00 0.00 1.82
4050 4435 1.736696 CGCATGCTCATCCCCAAAAAC 60.737 52.381 17.13 0.00 0.00 2.43
4060 4445 3.055591 CTCGTCTAAATCGCATGCTCAT 58.944 45.455 17.13 4.55 0.00 2.90


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

AutoCloner maintained by Alex Coulton.