Multiple sequence alignment - TraesCS2D01G143100

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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 TraesCS2D01G143100 chr2D 100.000 5522 0 0 1 5522 84759378 84764899 0.000000e+00 10198.0
1 TraesCS2D01G143100 chr2D 90.267 1274 96 7 4252 5522 84921112 84922360 0.000000e+00 1640.0
2 TraesCS2D01G143100 chr2D 80.141 710 81 28 3090 3762 83821267 83820581 5.010000e-130 475.0
3 TraesCS2D01G143100 chr2D 96.124 258 10 0 3882 4139 83820045 83819788 6.610000e-114 422.0
4 TraesCS2D01G143100 chr2D 92.857 126 9 0 1949 2074 83821547 83821422 3.400000e-42 183.0
5 TraesCS2D01G143100 chr2D 100.000 30 0 0 2115 2144 83821421 83821392 7.730000e-04 56.5
6 TraesCS2D01G143100 chr2B 93.206 4622 208 28 918 5522 136619510 136624042 0.000000e+00 6698.0
7 TraesCS2D01G143100 chr2B 78.438 1716 219 74 2115 3758 135691005 135689369 0.000000e+00 979.0
8 TraesCS2D01G143100 chr2B 90.164 366 35 1 3764 4128 135689206 135688841 5.010000e-130 475.0
9 TraesCS2D01G143100 chr2A 97.873 2022 42 1 3502 5522 85598035 85600056 0.000000e+00 3494.0
10 TraesCS2D01G143100 chr2A 89.581 2601 161 36 920 3499 85595476 85597987 0.000000e+00 3201.0
11 TraesCS2D01G143100 chr2A 88.847 798 54 18 1 786 85594566 85595340 0.000000e+00 948.0
12 TraesCS2D01G143100 chr2A 77.714 1732 217 84 2115 3762 84551693 84550047 0.000000e+00 904.0
13 TraesCS2D01G143100 chr2A 92.362 563 40 3 4255 4816 84151811 84151251 0.000000e+00 798.0
14 TraesCS2D01G143100 chr2A 93.229 192 12 1 3949 4139 84549782 84549591 1.170000e-71 281.0
15 TraesCS2D01G143100 chr2A 78.910 422 72 15 1494 1907 84552227 84551815 2.540000e-68 270.0
16 TraesCS2D01G143100 chr2A 91.304 161 11 2 5362 5522 84151255 84151098 3.350000e-52 217.0
17 TraesCS2D01G143100 chr4D 86.554 1770 224 7 3762 5519 450327653 450329420 0.000000e+00 1938.0
18 TraesCS2D01G143100 chr4D 81.849 1774 229 53 1781 3499 450324872 450326607 0.000000e+00 1406.0
19 TraesCS2D01G143100 chr4D 85.636 550 75 3 982 1529 450324124 450324671 4.800000e-160 575.0
20 TraesCS2D01G143100 chr4D 80.723 166 22 9 681 841 450323814 450323974 2.700000e-23 121.0
21 TraesCS2D01G143100 chr4D 94.805 77 3 1 843 918 481110356 481110280 9.720000e-23 119.0
22 TraesCS2D01G143100 chr4D 93.590 78 4 1 843 919 28237818 28237895 1.260000e-21 115.0
23 TraesCS2D01G143100 chr4A 86.400 1772 229 6 3762 5522 16251723 16249953 0.000000e+00 1927.0
24 TraesCS2D01G143100 chr4A 80.652 1995 267 70 1781 3722 16253823 16251895 0.000000e+00 1435.0
25 TraesCS2D01G143100 chr4A 86.679 548 73 0 982 1529 16254569 16254022 4.730000e-170 608.0
26 TraesCS2D01G143100 chr4B 85.924 1769 237 6 3762 5519 563624163 563625930 0.000000e+00 1877.0
27 TraesCS2D01G143100 chr4B 81.611 1800 237 54 1781 3527 563621743 563623501 0.000000e+00 1404.0
28 TraesCS2D01G143100 chr4B 85.064 549 81 1 982 1529 563620994 563621542 4.830000e-155 558.0
29 TraesCS2D01G143100 chr4B 93.750 80 4 1 841 919 91298392 91298313 9.720000e-23 119.0
30 TraesCS2D01G143100 chr4B 92.593 81 5 1 843 922 432817368 432817288 1.260000e-21 115.0
31 TraesCS2D01G143100 chr6B 91.860 86 5 2 836 920 26654557 26654473 9.720000e-23 119.0
32 TraesCS2D01G143100 chr6B 88.764 89 9 1 839 926 503534754 503534842 2.100000e-19 108.0
33 TraesCS2D01G143100 chr5D 93.671 79 4 1 844 921 255685645 255685723 3.490000e-22 117.0
34 TraesCS2D01G143100 chr7D 90.361 83 8 0 843 925 414277608 414277690 5.850000e-20 110.0
35 TraesCS2D01G143100 chr6D 91.358 81 5 2 843 922 6967943 6968022 5.850000e-20 110.0


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 TraesCS2D01G143100 chr2D 84759378 84764899 5521 False 10198.000000 10198 100.000000 1 5522 1 chr2D.!!$F1 5521
1 TraesCS2D01G143100 chr2D 84921112 84922360 1248 False 1640.000000 1640 90.267000 4252 5522 1 chr2D.!!$F2 1270
2 TraesCS2D01G143100 chr2D 83819788 83821547 1759 True 284.125000 475 92.280500 1949 4139 4 chr2D.!!$R1 2190
3 TraesCS2D01G143100 chr2B 136619510 136624042 4532 False 6698.000000 6698 93.206000 918 5522 1 chr2B.!!$F1 4604
4 TraesCS2D01G143100 chr2B 135688841 135691005 2164 True 727.000000 979 84.301000 2115 4128 2 chr2B.!!$R1 2013
5 TraesCS2D01G143100 chr2A 85594566 85600056 5490 False 2547.666667 3494 92.100333 1 5522 3 chr2A.!!$F1 5521
6 TraesCS2D01G143100 chr2A 84151098 84151811 713 True 507.500000 798 91.833000 4255 5522 2 chr2A.!!$R1 1267
7 TraesCS2D01G143100 chr2A 84549591 84552227 2636 True 485.000000 904 83.284333 1494 4139 3 chr2A.!!$R2 2645
8 TraesCS2D01G143100 chr4D 450323814 450329420 5606 False 1010.000000 1938 83.690500 681 5519 4 chr4D.!!$F2 4838
9 TraesCS2D01G143100 chr4A 16249953 16254569 4616 True 1323.333333 1927 84.577000 982 5522 3 chr4A.!!$R1 4540
10 TraesCS2D01G143100 chr4B 563620994 563625930 4936 False 1279.666667 1877 84.199667 982 5519 3 chr4B.!!$F1 4537

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
520 528 0.108186 TGTTCGTGCTGGCTATCTGG 60.108 55.000 0.0 0.0 0.00 3.86 F
613 624 0.473755 TGAGCTTCTTGTTCCTGCCA 59.526 50.000 0.0 0.0 0.00 4.92 F
1629 1766 1.089920 AGGTGCATTCAACTCATCGC 58.910 50.000 0.0 0.0 34.53 4.58 F
2320 2528 1.136695 TGCTTTTGCCCTGTTCAGTTG 59.863 47.619 0.0 0.0 46.87 3.16 F
2855 3105 1.408702 CCTCAGTGCCTAGCTCTCTTC 59.591 57.143 0.0 0.0 29.56 2.87 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2041 2199 1.865865 TTTCCAGAGTGAACAGCGAC 58.134 50.000 0.0 0.0 0.00 5.19 R
2293 2501 2.381911 ACAGGGCAAAAGCAGGATATG 58.618 47.619 0.0 0.0 0.00 1.78 R
2997 3259 0.541764 GCCAACATTCACAGGGGGAA 60.542 55.000 0.0 0.0 0.00 3.97 R
4166 5592 0.462759 AGACCGGCTATCAGCTTTGC 60.463 55.000 0.0 0.0 41.99 3.68 R
4552 5984 0.965439 TGACCTTGCATTTTTCCCCG 59.035 50.000 0.0 0.0 0.00 5.73 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
24 25 1.421646 CACTTCACTTCTCCCCCACTT 59.578 52.381 0.00 0.00 0.00 3.16
25 26 1.421646 ACTTCACTTCTCCCCCACTTG 59.578 52.381 0.00 0.00 0.00 3.16
62 63 3.890936 AACAGAGCAGCTCCCGCAC 62.891 63.158 19.40 0.00 39.10 5.34
63 64 4.079850 CAGAGCAGCTCCCGCACT 62.080 66.667 19.40 0.00 39.10 4.40
64 65 3.317571 AGAGCAGCTCCCGCACTT 61.318 61.111 19.40 0.00 39.10 3.16
65 66 3.123620 GAGCAGCTCCCGCACTTG 61.124 66.667 11.84 0.00 39.10 3.16
68 69 2.265739 CAGCTCCCGCACTTGCTA 59.734 61.111 0.00 0.00 39.10 3.49
69 70 1.812922 CAGCTCCCGCACTTGCTAG 60.813 63.158 0.00 0.00 39.10 3.42
70 71 3.198489 GCTCCCGCACTTGCTAGC 61.198 66.667 8.10 8.10 39.32 3.42
71 72 2.512515 CTCCCGCACTTGCTAGCC 60.513 66.667 13.29 0.00 39.32 3.93
72 73 4.096003 TCCCGCACTTGCTAGCCC 62.096 66.667 13.29 0.00 39.32 5.19
134 135 1.068921 GCTCCGGCTCTCCAGATTC 59.931 63.158 0.00 0.00 35.22 2.52
162 163 4.163268 GCCTCTTCTCCTCAAGGTATCTTT 59.837 45.833 0.00 0.00 36.34 2.52
193 194 2.676471 GCCATTTCGCACCCACCT 60.676 61.111 0.00 0.00 0.00 4.00
211 216 1.382695 TCATCCCGTCTCCCCCTTC 60.383 63.158 0.00 0.00 0.00 3.46
232 237 2.203422 TCCGTGCAGTTTTGGGGG 60.203 61.111 0.00 0.00 0.00 5.40
344 350 3.753797 GCCTTTGTCTGGAAGGTTTCTAG 59.246 47.826 4.95 0.00 44.44 2.43
345 351 4.505039 GCCTTTGTCTGGAAGGTTTCTAGA 60.505 45.833 4.95 1.35 43.80 2.43
349 355 7.308830 CCTTTGTCTGGAAGGTTTCTAGATTTG 60.309 40.741 7.91 1.44 46.77 2.32
369 375 2.222027 GATTAGGCCCAAATCGAGTGG 58.778 52.381 11.54 10.36 35.77 4.00
385 391 1.978580 AGTGGTTTCTTGAGGTCGGAT 59.021 47.619 0.00 0.00 0.00 4.18
387 393 1.697432 TGGTTTCTTGAGGTCGGATGT 59.303 47.619 0.00 0.00 0.00 3.06
393 400 2.897326 TCTTGAGGTCGGATGTGAGAAA 59.103 45.455 0.00 0.00 0.00 2.52
395 402 3.981071 TGAGGTCGGATGTGAGAAATT 57.019 42.857 0.00 0.00 0.00 1.82
402 409 6.884295 AGGTCGGATGTGAGAAATTAAAATCA 59.116 34.615 0.00 0.00 0.00 2.57
423 430 0.395724 ATCAGAATCGGGGTTTGGGC 60.396 55.000 0.00 0.00 0.00 5.36
469 477 1.215382 CGAGCACCCGAATCTGTGA 59.785 57.895 4.34 0.00 34.37 3.58
470 478 1.078759 CGAGCACCCGAATCTGTGAC 61.079 60.000 4.34 0.00 34.37 3.67
474 482 1.372582 CACCCGAATCTGTGACCATG 58.627 55.000 0.00 0.00 34.37 3.66
489 497 4.634443 GTGACCATGTTTAATTACGCTCCT 59.366 41.667 0.00 0.00 0.00 3.69
520 528 0.108186 TGTTCGTGCTGGCTATCTGG 60.108 55.000 0.00 0.00 0.00 3.86
536 545 2.126346 GGCAACGAATGTGCTGGC 60.126 61.111 0.00 0.00 0.00 4.85
542 551 3.836949 CAACGAATGTGCTGGCTTATTT 58.163 40.909 0.00 0.00 0.00 1.40
544 553 2.095853 ACGAATGTGCTGGCTTATTTCG 59.904 45.455 13.86 13.86 0.00 3.46
550 559 0.931005 GCTGGCTTATTTCGTCTCCG 59.069 55.000 0.00 0.00 0.00 4.63
551 560 1.739371 GCTGGCTTATTTCGTCTCCGT 60.739 52.381 0.00 0.00 35.01 4.69
552 561 2.194271 CTGGCTTATTTCGTCTCCGTC 58.806 52.381 0.00 0.00 35.01 4.79
554 563 2.159282 TGGCTTATTTCGTCTCCGTCTC 60.159 50.000 0.00 0.00 35.01 3.36
556 565 3.429135 GGCTTATTTCGTCTCCGTCTCTT 60.429 47.826 0.00 0.00 35.01 2.85
601 612 1.203287 GGTTGGATTTGGCTGAGCTTC 59.797 52.381 3.72 0.00 0.00 3.86
603 614 2.560105 GTTGGATTTGGCTGAGCTTCTT 59.440 45.455 3.72 0.00 0.00 2.52
613 624 0.473755 TGAGCTTCTTGTTCCTGCCA 59.526 50.000 0.00 0.00 0.00 4.92
622 633 5.692115 TCTTGTTCCTGCCAGTGATTATA 57.308 39.130 0.00 0.00 0.00 0.98
624 635 7.373617 TCTTGTTCCTGCCAGTGATTATATA 57.626 36.000 0.00 0.00 0.00 0.86
625 636 7.977818 TCTTGTTCCTGCCAGTGATTATATAT 58.022 34.615 0.00 0.00 0.00 0.86
627 638 8.995027 TTGTTCCTGCCAGTGATTATATATTT 57.005 30.769 0.00 0.00 0.00 1.40
628 639 8.995027 TGTTCCTGCCAGTGATTATATATTTT 57.005 30.769 0.00 0.00 0.00 1.82
629 640 9.066892 TGTTCCTGCCAGTGATTATATATTTTC 57.933 33.333 0.00 0.00 0.00 2.29
631 642 8.853077 TCCTGCCAGTGATTATATATTTTCTG 57.147 34.615 0.00 0.00 0.00 3.02
633 644 9.288576 CCTGCCAGTGATTATATATTTTCTGAA 57.711 33.333 0.00 0.00 0.00 3.02
653 664 4.992319 TGAAGGAAAATGCATGCTCTTTTG 59.008 37.500 25.86 0.00 0.00 2.44
655 666 3.325716 AGGAAAATGCATGCTCTTTTGGT 59.674 39.130 25.86 15.08 0.00 3.67
656 667 4.527816 AGGAAAATGCATGCTCTTTTGGTA 59.472 37.500 25.86 4.02 0.00 3.25
657 668 5.188359 AGGAAAATGCATGCTCTTTTGGTAT 59.812 36.000 25.86 10.21 0.00 2.73
658 669 5.292589 GGAAAATGCATGCTCTTTTGGTATG 59.707 40.000 25.86 0.00 0.00 2.39
661 672 3.515330 GCATGCTCTTTTGGTATGCTT 57.485 42.857 11.37 0.00 44.96 3.91
662 673 3.184541 GCATGCTCTTTTGGTATGCTTG 58.815 45.455 11.37 0.00 44.96 4.01
663 674 3.184541 CATGCTCTTTTGGTATGCTTGC 58.815 45.455 0.00 0.00 0.00 4.01
664 675 2.517959 TGCTCTTTTGGTATGCTTGCT 58.482 42.857 0.00 0.00 0.00 3.91
665 676 2.229543 TGCTCTTTTGGTATGCTTGCTG 59.770 45.455 0.00 0.00 0.00 4.41
672 683 1.140375 GTATGCTTGCTGGCTTGCC 59.860 57.895 4.43 4.43 0.00 4.52
699 710 8.910944 GCGGACTATATTAGTGGGATTAGAATA 58.089 37.037 0.00 0.00 39.59 1.75
754 766 6.486253 TGAAATCGTTCATCTTTCCTTGAG 57.514 37.500 0.00 0.00 38.88 3.02
755 767 4.954092 AATCGTTCATCTTTCCTTGAGC 57.046 40.909 0.00 0.00 0.00 4.26
767 779 7.206981 TCTTTCCTTGAGCTTACAGATTTTG 57.793 36.000 0.00 0.00 0.00 2.44
786 836 5.455056 TTTGTGTTGTGTTTGTTACCAGT 57.545 34.783 0.00 0.00 0.00 4.00
837 887 3.025322 TCTGTTGGGTCATGGTGTTTT 57.975 42.857 0.00 0.00 0.00 2.43
841 891 3.708631 TGTTGGGTCATGGTGTTTTCATT 59.291 39.130 0.00 0.00 0.00 2.57
842 892 4.202202 TGTTGGGTCATGGTGTTTTCATTC 60.202 41.667 0.00 0.00 0.00 2.67
843 893 2.556189 TGGGTCATGGTGTTTTCATTCG 59.444 45.455 0.00 0.00 0.00 3.34
844 894 2.556622 GGGTCATGGTGTTTTCATTCGT 59.443 45.455 0.00 0.00 0.00 3.85
845 895 3.365969 GGGTCATGGTGTTTTCATTCGTC 60.366 47.826 0.00 0.00 0.00 4.20
848 898 2.350057 TGGTGTTTTCATTCGTCCCA 57.650 45.000 0.00 0.00 0.00 4.37
849 899 2.656002 TGGTGTTTTCATTCGTCCCAA 58.344 42.857 0.00 0.00 0.00 4.12
850 900 3.024547 TGGTGTTTTCATTCGTCCCAAA 58.975 40.909 0.00 0.00 0.00 3.28
851 901 3.447586 TGGTGTTTTCATTCGTCCCAAAA 59.552 39.130 0.00 0.00 0.00 2.44
852 902 4.100189 TGGTGTTTTCATTCGTCCCAAAAT 59.900 37.500 0.00 0.00 0.00 1.82
853 903 5.302059 TGGTGTTTTCATTCGTCCCAAAATA 59.698 36.000 0.00 0.00 0.00 1.40
855 905 6.364976 GGTGTTTTCATTCGTCCCAAAATAAG 59.635 38.462 0.00 0.00 0.00 1.73
856 906 6.921307 GTGTTTTCATTCGTCCCAAAATAAGT 59.079 34.615 0.00 0.00 0.00 2.24
859 909 5.873179 TCATTCGTCCCAAAATAAGTGAC 57.127 39.130 0.00 0.00 0.00 3.67
860 910 5.556915 TCATTCGTCCCAAAATAAGTGACT 58.443 37.500 0.00 0.00 0.00 3.41
861 911 5.642063 TCATTCGTCCCAAAATAAGTGACTC 59.358 40.000 0.00 0.00 0.00 3.36
863 913 4.963373 TCGTCCCAAAATAAGTGACTCAA 58.037 39.130 0.00 0.00 0.00 3.02
864 914 4.753107 TCGTCCCAAAATAAGTGACTCAAC 59.247 41.667 0.00 0.00 0.00 3.18
865 915 4.755123 CGTCCCAAAATAAGTGACTCAACT 59.245 41.667 0.00 0.00 0.00 3.16
866 916 5.238650 CGTCCCAAAATAAGTGACTCAACTT 59.761 40.000 0.00 0.00 42.89 2.66
867 917 6.238648 CGTCCCAAAATAAGTGACTCAACTTT 60.239 38.462 0.00 0.00 40.77 2.66
868 918 7.041644 CGTCCCAAAATAAGTGACTCAACTTTA 60.042 37.037 0.00 0.00 40.77 1.85
869 919 8.793592 GTCCCAAAATAAGTGACTCAACTTTAT 58.206 33.333 0.00 0.00 40.77 1.40
872 922 9.755064 CCAAAATAAGTGACTCAACTTTATACG 57.245 33.333 0.00 0.00 40.77 3.06
875 925 9.924650 AAATAAGTGACTCAACTTTATACGACT 57.075 29.630 0.00 0.00 40.77 4.18
876 926 9.924650 AATAAGTGACTCAACTTTATACGACTT 57.075 29.630 0.00 0.00 40.77 3.01
879 929 8.967552 AGTGACTCAACTTTATACGACTTTAG 57.032 34.615 0.00 0.00 0.00 1.85
881 931 7.327761 GTGACTCAACTTTATACGACTTTAGCA 59.672 37.037 0.00 0.00 0.00 3.49
882 932 7.327761 TGACTCAACTTTATACGACTTTAGCAC 59.672 37.037 0.00 0.00 0.00 4.40
883 933 7.149973 ACTCAACTTTATACGACTTTAGCACA 58.850 34.615 0.00 0.00 0.00 4.57
884 934 7.654520 ACTCAACTTTATACGACTTTAGCACAA 59.345 33.333 0.00 0.00 0.00 3.33
887 937 7.958053 ACTTTATACGACTTTAGCACAAACT 57.042 32.000 0.00 0.00 0.00 2.66
888 938 8.374327 ACTTTATACGACTTTAGCACAAACTT 57.626 30.769 0.00 0.00 0.00 2.66
889 939 8.280497 ACTTTATACGACTTTAGCACAAACTTG 58.720 33.333 0.00 0.00 0.00 3.16
890 940 7.949903 TTATACGACTTTAGCACAAACTTGA 57.050 32.000 0.00 0.00 0.00 3.02
891 941 4.795970 ACGACTTTAGCACAAACTTGAG 57.204 40.909 0.00 0.00 0.00 3.02
892 942 4.189231 ACGACTTTAGCACAAACTTGAGT 58.811 39.130 0.00 0.00 0.00 3.41
893 943 4.270325 ACGACTTTAGCACAAACTTGAGTC 59.730 41.667 0.00 0.00 31.90 3.36
894 944 4.270084 CGACTTTAGCACAAACTTGAGTCA 59.730 41.667 0.00 0.00 33.45 3.41
895 945 5.485662 ACTTTAGCACAAACTTGAGTCAC 57.514 39.130 0.00 0.00 0.00 3.67
896 946 5.186198 ACTTTAGCACAAACTTGAGTCACT 58.814 37.500 0.00 0.00 0.00 3.41
897 947 5.648092 ACTTTAGCACAAACTTGAGTCACTT 59.352 36.000 0.00 0.00 0.00 3.16
898 948 6.821665 ACTTTAGCACAAACTTGAGTCACTTA 59.178 34.615 0.00 0.00 0.00 2.24
899 949 7.499232 ACTTTAGCACAAACTTGAGTCACTTAT 59.501 33.333 0.00 0.00 0.00 1.73
900 950 7.801716 TTAGCACAAACTTGAGTCACTTATT 57.198 32.000 0.00 0.00 0.00 1.40
901 951 6.699575 AGCACAAACTTGAGTCACTTATTT 57.300 33.333 0.00 0.00 0.00 1.40
902 952 7.100458 AGCACAAACTTGAGTCACTTATTTT 57.900 32.000 0.00 0.00 0.00 1.82
903 953 6.974622 AGCACAAACTTGAGTCACTTATTTTG 59.025 34.615 0.00 0.00 0.00 2.44
904 954 6.198966 GCACAAACTTGAGTCACTTATTTTGG 59.801 38.462 9.57 2.86 0.00 3.28
905 955 6.697019 CACAAACTTGAGTCACTTATTTTGGG 59.303 38.462 9.57 3.67 0.00 4.12
906 956 6.605594 ACAAACTTGAGTCACTTATTTTGGGA 59.394 34.615 9.57 0.00 0.00 4.37
907 957 6.635030 AACTTGAGTCACTTATTTTGGGAC 57.365 37.500 0.00 0.00 0.00 4.46
908 958 4.755123 ACTTGAGTCACTTATTTTGGGACG 59.245 41.667 0.00 0.00 33.84 4.79
909 959 3.670625 TGAGTCACTTATTTTGGGACGG 58.329 45.455 0.00 0.00 33.84 4.79
910 960 3.325425 TGAGTCACTTATTTTGGGACGGA 59.675 43.478 0.00 0.00 33.84 4.69
911 961 3.933332 GAGTCACTTATTTTGGGACGGAG 59.067 47.826 0.00 0.00 33.84 4.63
912 962 3.007635 GTCACTTATTTTGGGACGGAGG 58.992 50.000 0.00 0.00 0.00 4.30
913 963 2.026636 TCACTTATTTTGGGACGGAGGG 60.027 50.000 0.00 0.00 0.00 4.30
914 964 2.026636 CACTTATTTTGGGACGGAGGGA 60.027 50.000 0.00 0.00 0.00 4.20
915 965 2.238898 ACTTATTTTGGGACGGAGGGAG 59.761 50.000 0.00 0.00 0.00 4.30
916 966 1.961133 TATTTTGGGACGGAGGGAGT 58.039 50.000 0.00 0.00 0.00 3.85
965 1015 6.033831 CACAAACGATATTTTCAATGCACTCC 59.966 38.462 0.00 0.00 0.00 3.85
1246 1383 3.736996 AAGTTGCCCTGTGCCAGCA 62.737 57.895 0.00 0.00 40.16 4.41
1603 1740 2.092429 GGAAAGGACAGCATGGGTATCA 60.092 50.000 0.00 0.00 43.62 2.15
1629 1766 1.089920 AGGTGCATTCAACTCATCGC 58.910 50.000 0.00 0.00 34.53 4.58
1671 1808 5.070180 TCAATGCATCTTGTTTCCCTCAAAA 59.930 36.000 0.00 0.00 0.00 2.44
1672 1809 5.750352 ATGCATCTTGTTTCCCTCAAAAT 57.250 34.783 0.00 0.00 0.00 1.82
1676 1813 7.999679 TGCATCTTGTTTCCCTCAAAATATAG 58.000 34.615 0.00 0.00 0.00 1.31
1749 1905 3.213506 TCCCATGATCGCAACAAATAGG 58.786 45.455 0.00 0.00 0.00 2.57
1754 1910 5.065859 CCATGATCGCAACAAATAGGTTACA 59.934 40.000 0.00 0.00 0.00 2.41
1839 1996 6.203723 GCCTCATTACTTAGTTAAGCCTCATG 59.796 42.308 0.00 0.00 36.79 3.07
1852 2009 5.990120 AAGCCTCATGAACTGCTTAAAAT 57.010 34.783 19.58 2.27 41.93 1.82
1854 2011 5.958955 AGCCTCATGAACTGCTTAAAATTC 58.041 37.500 7.94 0.00 0.00 2.17
1862 2019 6.888430 TGAACTGCTTAAAATTCTCGAGTTC 58.112 36.000 13.13 5.44 38.90 3.01
1865 2022 5.465724 ACTGCTTAAAATTCTCGAGTTCGTT 59.534 36.000 13.13 5.94 40.80 3.85
1891 2048 9.237187 TGAAACTTATGCCAACATGATAAGTTA 57.763 29.630 20.92 10.41 45.59 2.24
1932 2089 7.711846 AGTTATTACTGACTAGCTGACATCTG 58.288 38.462 0.00 0.00 31.99 2.90
1961 2118 4.743057 AGCCCAAGGAAATTGCTTTATC 57.257 40.909 0.00 0.00 37.60 1.75
2020 2178 4.880120 ACAAGCAAGGACATGATGACATAG 59.120 41.667 0.00 0.00 35.09 2.23
2041 2199 3.935203 AGACATTTACAATGAGGTCTGCG 59.065 43.478 3.47 0.00 34.57 5.18
2068 2226 6.183360 CGCTGTTCACTCTGGAAATGATAATT 60.183 38.462 0.00 0.00 0.00 1.40
2234 2423 2.938253 TGCGCTTGAAGCAACTCG 59.062 55.556 18.22 1.14 42.58 4.18
2242 2431 3.120060 GCTTGAAGCAACTCGATGATGTT 60.120 43.478 13.09 0.00 41.89 2.71
2315 2523 1.260544 ATCCTGCTTTTGCCCTGTTC 58.739 50.000 0.00 0.00 46.87 3.18
2320 2528 1.136695 TGCTTTTGCCCTGTTCAGTTG 59.863 47.619 0.00 0.00 46.87 3.16
2330 2538 3.420893 CCTGTTCAGTTGCAGGGAAATA 58.579 45.455 2.86 0.00 46.27 1.40
2462 2691 8.029522 TCTATTACTCGCAATATCTGGATTGAC 58.970 37.037 0.40 0.00 38.83 3.18
2468 2697 5.589855 TCGCAATATCTGGATTGACAAATGT 59.410 36.000 0.00 0.00 38.83 2.71
2470 2699 7.445096 TCGCAATATCTGGATTGACAAATGTAT 59.555 33.333 0.00 0.00 38.83 2.29
2527 2768 1.468985 ACAGAGTCGTGATGAGGAGG 58.531 55.000 0.00 0.00 0.00 4.30
2537 2778 4.065088 CGTGATGAGGAGGAAGAAACAAA 58.935 43.478 0.00 0.00 0.00 2.83
2564 2805 4.290722 AGGAGAAGGTGAAGATGTCCAAAT 59.709 41.667 0.00 0.00 0.00 2.32
2565 2806 5.488919 AGGAGAAGGTGAAGATGTCCAAATA 59.511 40.000 0.00 0.00 0.00 1.40
2572 2813 7.184862 AGGTGAAGATGTCCAAATAAAAGGAT 58.815 34.615 0.00 0.00 36.11 3.24
2573 2814 7.123247 AGGTGAAGATGTCCAAATAAAAGGATG 59.877 37.037 0.00 0.00 36.11 3.51
2588 2829 2.719739 AGGATGCATGGAGAACAACAG 58.280 47.619 2.46 0.00 0.00 3.16
2597 2838 6.127083 TGCATGGAGAACAACAGTATATCTGA 60.127 38.462 8.56 0.00 46.27 3.27
2788 3036 9.525409 CTAATTGCAATTATCTTCTTCCCTTTG 57.475 33.333 27.56 10.57 31.03 2.77
2802 3051 9.678941 CTTCTTCCCTTTGTTTGTTTCTTATAC 57.321 33.333 0.00 0.00 0.00 1.47
2851 3101 2.534042 TTACCTCAGTGCCTAGCTCT 57.466 50.000 0.00 0.00 32.36 4.09
2855 3105 1.408702 CCTCAGTGCCTAGCTCTCTTC 59.591 57.143 0.00 0.00 29.56 2.87
2872 3123 6.195983 GCTCTCTTCATAATTGTTTTCATGCG 59.804 38.462 0.00 0.00 0.00 4.73
3015 3277 2.236489 ATTCCCCCTGTGAATGTTGG 57.764 50.000 0.00 0.00 31.42 3.77
3069 3337 9.352784 TGTGACTATTTTGCATTTAATTACTGC 57.647 29.630 10.82 10.82 36.45 4.40
3079 3347 7.891561 TGCATTTAATTACTGCAAGGTTTAGT 58.108 30.769 15.94 0.00 42.53 2.24
3117 3386 5.984725 TCTTACTGGTTGTCTTGAAACAGA 58.015 37.500 5.35 0.00 42.39 3.41
3156 3425 5.371115 TCCAATCATTTTTCGTTCTCACC 57.629 39.130 0.00 0.00 0.00 4.02
3215 3492 9.131791 ACTGTTTTGTATTCCTTTACACATTCT 57.868 29.630 0.00 0.00 31.98 2.40
3550 4202 4.247267 ACACAACTTCATTTGGCATCAG 57.753 40.909 0.00 0.00 0.00 2.90
3622 4274 8.991783 ATTAGTTCTGGATGTCATCATTCATT 57.008 30.769 14.72 0.00 38.69 2.57
3654 4306 8.095792 TCTTCACCGGTTTATTTGTCATTAGTA 58.904 33.333 2.97 0.00 0.00 1.82
4166 5592 4.950475 TCCACTGTATGACTTCTACTCCTG 59.050 45.833 0.00 0.00 0.00 3.86
4409 5839 4.530553 TGCACTTGGAAGTATAAGGACTCA 59.469 41.667 0.00 0.00 37.08 3.41
4446 5876 4.451900 TCTCAGGAACCTTGTTTCAGAAC 58.548 43.478 0.00 0.00 36.29 3.01
4552 5984 3.059352 ACTAAGCAAGGTGGACATGTC 57.941 47.619 17.91 17.91 0.00 3.06
4797 6233 1.509548 CCTGAGGGGTTTGGTGGGAT 61.510 60.000 0.00 0.00 0.00 3.85
5224 6663 4.052229 CTCCCTCGTCGGTGCGTT 62.052 66.667 0.00 0.00 0.00 4.84
5449 6888 3.861276 TGATGATTTTGAGCTTGCCAG 57.139 42.857 0.00 0.00 0.00 4.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 1.056660 GTGGGGGAGAAGTGAAGTGA 58.943 55.000 0.00 0.00 0.00 3.41
18 19 1.954362 CTCCTCGAGGCTCAAGTGGG 61.954 65.000 27.39 8.37 34.44 4.61
40 41 0.739112 CGGGAGCTGCTCTGTTCTTC 60.739 60.000 27.09 10.05 0.00 2.87
62 63 4.512914 GGGGCTGGGGCTAGCAAG 62.513 72.222 18.24 11.70 45.46 4.01
85 86 2.292803 GATTTCTCGAGTCGCCTGC 58.707 57.895 13.13 0.00 0.00 4.85
134 135 1.481772 CTTGAGGAGAAGAGGCAGAGG 59.518 57.143 0.00 0.00 0.00 3.69
162 163 3.753272 CGAAATGGCAGGAAGAAGAAGAA 59.247 43.478 0.00 0.00 0.00 2.52
193 194 1.382695 GAAGGGGGAGACGGGATGA 60.383 63.158 0.00 0.00 0.00 2.92
232 237 0.105224 CGGTCCAAAAACCCCCAAAC 59.895 55.000 0.00 0.00 35.79 2.93
291 297 3.181417 TGATCCTACCCCGAATGAGAGAT 60.181 47.826 0.00 0.00 0.00 2.75
345 351 4.339247 CACTCGATTTGGGCCTAATCAAAT 59.661 41.667 30.73 17.35 43.64 2.32
349 355 2.222027 CCACTCGATTTGGGCCTAATC 58.778 52.381 24.99 24.99 0.00 1.75
369 375 2.996621 CTCACATCCGACCTCAAGAAAC 59.003 50.000 0.00 0.00 0.00 2.78
387 393 9.992910 CGATTCTGATGTGATTTTAATTTCTCA 57.007 29.630 0.00 0.00 0.00 3.27
393 400 6.129179 ACCCCGATTCTGATGTGATTTTAAT 58.871 36.000 0.00 0.00 0.00 1.40
395 402 5.110814 ACCCCGATTCTGATGTGATTTTA 57.889 39.130 0.00 0.00 0.00 1.52
402 409 1.340991 CCCAAACCCCGATTCTGATGT 60.341 52.381 0.00 0.00 0.00 3.06
411 418 4.966787 GTGCTGCCCAAACCCCGA 62.967 66.667 0.00 0.00 0.00 5.14
423 430 3.578456 CGGCAAACCTAGGTGCTG 58.422 61.111 17.14 16.73 40.70 4.41
459 467 6.899771 CGTAATTAAACATGGTCACAGATTCG 59.100 38.462 0.00 0.00 0.00 3.34
460 468 6.687105 GCGTAATTAAACATGGTCACAGATTC 59.313 38.462 0.00 0.00 0.00 2.52
469 477 4.394920 CACAGGAGCGTAATTAAACATGGT 59.605 41.667 0.00 0.00 0.00 3.55
470 478 4.730613 GCACAGGAGCGTAATTAAACATGG 60.731 45.833 0.00 0.00 0.00 3.66
474 482 4.616181 ATGCACAGGAGCGTAATTAAAC 57.384 40.909 0.00 0.00 37.31 2.01
489 497 1.197492 GCACGAACATCAGAATGCACA 59.803 47.619 0.00 0.00 36.26 4.57
520 528 0.521291 TAAGCCAGCACATTCGTTGC 59.479 50.000 0.00 0.00 0.00 4.17
525 533 3.375299 AGACGAAATAAGCCAGCACATTC 59.625 43.478 0.00 0.00 0.00 2.67
544 553 1.887198 TCAGGAACAAGAGACGGAGAC 59.113 52.381 0.00 0.00 0.00 3.36
550 559 2.551071 CCCAACCTCAGGAACAAGAGAC 60.551 54.545 0.00 0.00 35.27 3.36
551 560 1.699634 CCCAACCTCAGGAACAAGAGA 59.300 52.381 0.00 0.00 35.27 3.10
552 561 1.699634 TCCCAACCTCAGGAACAAGAG 59.300 52.381 0.00 0.00 33.51 2.85
554 563 2.656947 TTCCCAACCTCAGGAACAAG 57.343 50.000 0.00 0.00 37.23 3.16
556 565 2.490718 CCAATTCCCAACCTCAGGAACA 60.491 50.000 0.00 0.00 44.70 3.18
601 612 8.627208 AATATATAATCACTGGCAGGAACAAG 57.373 34.615 20.34 1.44 0.00 3.16
603 614 8.995027 AAAATATATAATCACTGGCAGGAACA 57.005 30.769 20.34 6.00 0.00 3.18
627 638 4.084287 AGAGCATGCATTTTCCTTCAGAA 58.916 39.130 21.98 0.00 0.00 3.02
628 639 3.693807 AGAGCATGCATTTTCCTTCAGA 58.306 40.909 21.98 0.00 0.00 3.27
629 640 4.451629 AAGAGCATGCATTTTCCTTCAG 57.548 40.909 21.98 0.00 0.00 3.02
631 642 4.390909 CCAAAAGAGCATGCATTTTCCTTC 59.609 41.667 23.17 10.12 0.00 3.46
633 644 3.325716 ACCAAAAGAGCATGCATTTTCCT 59.674 39.130 23.17 12.82 0.00 3.36
634 645 3.667360 ACCAAAAGAGCATGCATTTTCC 58.333 40.909 23.17 6.44 0.00 3.13
653 664 1.140375 GCAAGCCAGCAAGCATACC 59.860 57.895 0.55 0.00 34.23 2.73
655 666 2.409055 CGGCAAGCCAGCAAGCATA 61.409 57.895 12.19 0.00 35.83 3.14
656 667 3.755628 CGGCAAGCCAGCAAGCAT 61.756 61.111 12.19 0.00 35.83 3.79
663 674 2.363711 TATAGTCCGCGGCAAGCCAG 62.364 60.000 23.51 4.29 44.76 4.85
664 675 1.754380 ATATAGTCCGCGGCAAGCCA 61.754 55.000 23.51 0.00 44.76 4.75
665 676 0.602905 AATATAGTCCGCGGCAAGCC 60.603 55.000 23.51 5.33 44.76 4.35
672 683 4.451629 AATCCCACTAATATAGTCCGCG 57.548 45.455 0.00 0.00 36.76 6.46
699 710 3.706600 ATGCCAGCATTCCATGTTTTT 57.293 38.095 0.00 0.00 31.82 1.94
700 711 3.706600 AATGCCAGCATTCCATGTTTT 57.293 38.095 12.02 0.00 42.32 2.43
713 724 7.276218 ACGATTTCATCACAAAATAAATGCCAG 59.724 33.333 0.00 0.00 0.00 4.85
754 766 6.310224 ACAAACACAACACAAAATCTGTAAGC 59.690 34.615 0.00 0.00 36.10 3.09
755 767 7.810766 ACAAACACAACACAAAATCTGTAAG 57.189 32.000 0.00 0.00 36.10 2.34
786 836 6.379703 ACATTTAATTGTGGGCATAACTAGCA 59.620 34.615 2.28 0.00 0.00 3.49
837 887 5.556915 AGTCACTTATTTTGGGACGAATGA 58.443 37.500 0.00 0.00 33.84 2.57
841 891 4.610605 TGAGTCACTTATTTTGGGACGA 57.389 40.909 0.00 0.00 33.84 4.20
842 892 4.755123 AGTTGAGTCACTTATTTTGGGACG 59.245 41.667 0.00 0.00 33.84 4.79
843 893 6.635030 AAGTTGAGTCACTTATTTTGGGAC 57.365 37.500 0.00 0.00 35.10 4.46
844 894 8.934023 ATAAAGTTGAGTCACTTATTTTGGGA 57.066 30.769 0.00 0.00 35.87 4.37
849 899 9.924650 AGTCGTATAAAGTTGAGTCACTTATTT 57.075 29.630 0.00 0.00 35.87 1.40
850 900 9.924650 AAGTCGTATAAAGTTGAGTCACTTATT 57.075 29.630 0.00 0.00 35.87 1.40
851 901 9.924650 AAAGTCGTATAAAGTTGAGTCACTTAT 57.075 29.630 0.00 0.00 35.87 1.73
853 903 9.408069 CTAAAGTCGTATAAAGTTGAGTCACTT 57.592 33.333 0.00 0.00 38.74 3.16
855 905 7.327761 TGCTAAAGTCGTATAAAGTTGAGTCAC 59.672 37.037 0.00 0.00 0.00 3.67
856 906 7.327761 GTGCTAAAGTCGTATAAAGTTGAGTCA 59.672 37.037 0.00 0.00 0.00 3.41
859 909 7.576750 TGTGCTAAAGTCGTATAAAGTTGAG 57.423 36.000 0.00 0.00 0.00 3.02
860 910 7.949903 TTGTGCTAAAGTCGTATAAAGTTGA 57.050 32.000 0.00 0.00 0.00 3.18
861 911 8.280497 AGTTTGTGCTAAAGTCGTATAAAGTTG 58.720 33.333 0.00 0.00 0.00 3.16
863 913 7.958053 AGTTTGTGCTAAAGTCGTATAAAGT 57.042 32.000 0.00 0.00 0.00 2.66
864 914 8.492748 TCAAGTTTGTGCTAAAGTCGTATAAAG 58.507 33.333 0.00 0.00 0.00 1.85
865 915 8.367943 TCAAGTTTGTGCTAAAGTCGTATAAA 57.632 30.769 0.00 0.00 0.00 1.40
866 916 7.654520 ACTCAAGTTTGTGCTAAAGTCGTATAA 59.345 33.333 0.00 0.00 0.00 0.98
867 917 7.149973 ACTCAAGTTTGTGCTAAAGTCGTATA 58.850 34.615 0.00 0.00 0.00 1.47
868 918 5.989777 ACTCAAGTTTGTGCTAAAGTCGTAT 59.010 36.000 0.00 0.00 0.00 3.06
869 919 5.353938 ACTCAAGTTTGTGCTAAAGTCGTA 58.646 37.500 0.00 0.00 0.00 3.43
871 921 4.270084 TGACTCAAGTTTGTGCTAAAGTCG 59.730 41.667 0.00 0.00 35.06 4.18
872 922 5.294552 AGTGACTCAAGTTTGTGCTAAAGTC 59.705 40.000 0.00 0.00 33.95 3.01
873 923 5.186198 AGTGACTCAAGTTTGTGCTAAAGT 58.814 37.500 0.00 0.00 0.00 2.66
874 924 5.741388 AGTGACTCAAGTTTGTGCTAAAG 57.259 39.130 0.00 0.00 0.00 1.85
875 925 7.801716 ATAAGTGACTCAAGTTTGTGCTAAA 57.198 32.000 0.00 0.00 0.00 1.85
876 926 7.801716 AATAAGTGACTCAAGTTTGTGCTAA 57.198 32.000 0.00 0.00 0.00 3.09
878 928 6.699575 AAATAAGTGACTCAAGTTTGTGCT 57.300 33.333 0.00 0.00 0.00 4.40
879 929 6.198966 CCAAAATAAGTGACTCAAGTTTGTGC 59.801 38.462 15.07 0.00 0.00 4.57
881 931 6.605594 TCCCAAAATAAGTGACTCAAGTTTGT 59.394 34.615 15.07 0.00 0.00 2.83
882 932 6.918022 GTCCCAAAATAAGTGACTCAAGTTTG 59.082 38.462 11.50 11.50 0.00 2.93
883 933 6.238648 CGTCCCAAAATAAGTGACTCAAGTTT 60.239 38.462 0.00 0.00 0.00 2.66
884 934 5.238650 CGTCCCAAAATAAGTGACTCAAGTT 59.761 40.000 0.00 0.00 0.00 2.66
887 937 4.069304 CCGTCCCAAAATAAGTGACTCAA 58.931 43.478 0.00 0.00 0.00 3.02
888 938 3.325425 TCCGTCCCAAAATAAGTGACTCA 59.675 43.478 0.00 0.00 0.00 3.41
889 939 3.933332 CTCCGTCCCAAAATAAGTGACTC 59.067 47.826 0.00 0.00 0.00 3.36
890 940 3.307480 CCTCCGTCCCAAAATAAGTGACT 60.307 47.826 0.00 0.00 0.00 3.41
891 941 3.007635 CCTCCGTCCCAAAATAAGTGAC 58.992 50.000 0.00 0.00 0.00 3.67
892 942 2.026636 CCCTCCGTCCCAAAATAAGTGA 60.027 50.000 0.00 0.00 0.00 3.41
893 943 2.026636 TCCCTCCGTCCCAAAATAAGTG 60.027 50.000 0.00 0.00 0.00 3.16
894 944 2.238898 CTCCCTCCGTCCCAAAATAAGT 59.761 50.000 0.00 0.00 0.00 2.24
895 945 2.238898 ACTCCCTCCGTCCCAAAATAAG 59.761 50.000 0.00 0.00 0.00 1.73
896 946 2.271777 ACTCCCTCCGTCCCAAAATAA 58.728 47.619 0.00 0.00 0.00 1.40
897 947 1.961133 ACTCCCTCCGTCCCAAAATA 58.039 50.000 0.00 0.00 0.00 1.40
898 948 1.961133 TACTCCCTCCGTCCCAAAAT 58.039 50.000 0.00 0.00 0.00 1.82
899 949 1.557832 CATACTCCCTCCGTCCCAAAA 59.442 52.381 0.00 0.00 0.00 2.44
900 950 1.200519 CATACTCCCTCCGTCCCAAA 58.799 55.000 0.00 0.00 0.00 3.28
901 951 0.042131 ACATACTCCCTCCGTCCCAA 59.958 55.000 0.00 0.00 0.00 4.12
902 952 0.928505 TACATACTCCCTCCGTCCCA 59.071 55.000 0.00 0.00 0.00 4.37
903 953 1.326328 GTACATACTCCCTCCGTCCC 58.674 60.000 0.00 0.00 0.00 4.46
904 954 2.062971 TGTACATACTCCCTCCGTCC 57.937 55.000 0.00 0.00 0.00 4.79
905 955 2.288273 GCATGTACATACTCCCTCCGTC 60.288 54.545 8.32 0.00 0.00 4.79
906 956 1.687123 GCATGTACATACTCCCTCCGT 59.313 52.381 8.32 0.00 0.00 4.69
907 957 1.686587 TGCATGTACATACTCCCTCCG 59.313 52.381 8.32 0.00 0.00 4.63
908 958 3.495100 CCTTGCATGTACATACTCCCTCC 60.495 52.174 8.32 0.00 0.00 4.30
909 959 3.495100 CCCTTGCATGTACATACTCCCTC 60.495 52.174 8.32 0.00 0.00 4.30
910 960 2.439507 CCCTTGCATGTACATACTCCCT 59.560 50.000 8.32 0.00 0.00 4.20
911 961 2.172717 ACCCTTGCATGTACATACTCCC 59.827 50.000 8.32 0.00 0.00 4.30
912 962 3.118408 TCACCCTTGCATGTACATACTCC 60.118 47.826 8.32 0.00 0.00 3.85
913 963 4.137116 TCACCCTTGCATGTACATACTC 57.863 45.455 8.32 1.70 0.00 2.59
914 964 4.568072 TTCACCCTTGCATGTACATACT 57.432 40.909 8.32 0.00 0.00 2.12
915 965 4.700213 ACTTTCACCCTTGCATGTACATAC 59.300 41.667 8.32 3.18 0.00 2.39
916 966 4.917385 ACTTTCACCCTTGCATGTACATA 58.083 39.130 8.32 0.00 0.00 2.29
1246 1383 3.362399 CTGATGTCTCCAGCGCCGT 62.362 63.158 2.29 0.00 0.00 5.68
1391 1528 8.680001 CATCATCAGAATCAAGTAAAATGACCA 58.320 33.333 0.00 0.00 0.00 4.02
1603 1740 3.890756 TGAGTTGAATGCACCTCATTGTT 59.109 39.130 0.00 0.00 44.95 2.83
1644 1781 5.070180 TGAGGGAAACAAGATGCATTGAAAA 59.930 36.000 0.00 0.00 34.20 2.29
1749 1905 8.236586 TCACTGCTTTGTTAATGATCATGTAAC 58.763 33.333 21.47 21.47 0.00 2.50
1754 1910 5.163723 CCGTCACTGCTTTGTTAATGATCAT 60.164 40.000 1.18 1.18 0.00 2.45
1839 1996 6.010074 CGAACTCGAGAATTTTAAGCAGTTC 58.990 40.000 21.68 7.32 43.02 3.01
1852 2009 5.107607 GCATAAGTTTCAACGAACTCGAGAA 60.108 40.000 21.68 6.86 38.86 2.87
1854 2011 4.434330 GGCATAAGTTTCAACGAACTCGAG 60.434 45.833 11.84 11.84 38.86 4.04
1862 2019 4.793071 TCATGTTGGCATAAGTTTCAACG 58.207 39.130 0.00 0.00 41.45 4.10
1865 2022 7.701539 ACTTATCATGTTGGCATAAGTTTCA 57.298 32.000 9.74 0.00 39.33 2.69
1908 2065 7.433719 CACAGATGTCAGCTAGTCAGTAATAAC 59.566 40.741 0.00 0.00 0.00 1.89
1926 2083 2.363306 TGGGCTTGAAACACAGATGT 57.637 45.000 0.00 0.00 42.46 3.06
1932 2089 3.751479 ATTTCCTTGGGCTTGAAACAC 57.249 42.857 0.00 0.00 31.41 3.32
1961 2118 4.316645 CTCTGAAGTATCATGGCCATCAG 58.683 47.826 17.61 18.98 34.37 2.90
2020 2178 3.684788 ACGCAGACCTCATTGTAAATGTC 59.315 43.478 0.26 0.00 0.00 3.06
2041 2199 1.865865 TTTCCAGAGTGAACAGCGAC 58.134 50.000 0.00 0.00 0.00 5.19
2101 2260 8.928270 ATTACCAGTAGTTCTCTAATTGAACG 57.072 34.615 0.00 0.00 45.84 3.95
2177 2340 3.879892 GGCCAAGGACTTCTGATGTTATC 59.120 47.826 0.00 0.00 0.00 1.75
2293 2501 2.381911 ACAGGGCAAAAGCAGGATATG 58.618 47.619 0.00 0.00 0.00 1.78
2315 2523 7.775120 ACTAAAATCATATTTCCCTGCAACTG 58.225 34.615 0.00 0.00 0.00 3.16
2320 2528 9.468532 GATGAAACTAAAATCATATTTCCCTGC 57.531 33.333 0.00 0.00 36.45 4.85
2356 2567 9.733556 TTTGAAACTGAGTAGGCATATTTTCTA 57.266 29.630 0.00 0.00 0.00 2.10
2421 2650 7.644551 GCGAGTAATAGACAATATTATCTCCCG 59.355 40.741 0.00 0.00 0.00 5.14
2437 2666 7.814587 TGTCAATCCAGATATTGCGAGTAATAG 59.185 37.037 0.00 0.00 36.89 1.73
2443 2672 5.739752 TTTGTCAATCCAGATATTGCGAG 57.260 39.130 0.00 0.00 36.89 5.03
2488 2717 7.229306 ACTCTGTTGAAATGCAAGATAGTGAAA 59.771 33.333 0.00 0.00 36.35 2.69
2527 2768 5.009110 CACCTTCTCCTTCCTTTGTTTCTTC 59.991 44.000 0.00 0.00 0.00 2.87
2537 2778 3.517500 GACATCTTCACCTTCTCCTTCCT 59.482 47.826 0.00 0.00 0.00 3.36
2564 2805 5.076182 TGTTGTTCTCCATGCATCCTTTTA 58.924 37.500 0.00 0.00 0.00 1.52
2565 2806 3.896888 TGTTGTTCTCCATGCATCCTTTT 59.103 39.130 0.00 0.00 0.00 2.27
2572 2813 6.051074 CAGATATACTGTTGTTCTCCATGCA 58.949 40.000 0.00 0.00 41.30 3.96
2573 2814 6.283694 TCAGATATACTGTTGTTCTCCATGC 58.716 40.000 0.00 0.00 45.86 4.06
2764 3005 7.910584 ACAAAGGGAAGAAGATAATTGCAATT 58.089 30.769 26.72 26.72 0.00 2.32
2774 3015 7.423844 AAGAAACAAACAAAGGGAAGAAGAT 57.576 32.000 0.00 0.00 0.00 2.40
2802 3051 6.541278 TCATGAAATGCTGAGATCTAACTTGG 59.459 38.462 0.00 0.00 46.21 3.61
2817 3066 5.533903 ACTGAGGTAATCCATCATGAAATGC 59.466 40.000 0.00 0.00 39.34 3.56
2851 3101 5.101628 GCCGCATGAAAACAATTATGAAGA 58.898 37.500 0.00 0.00 0.00 2.87
2855 3105 4.175516 ACTGCCGCATGAAAACAATTATG 58.824 39.130 0.00 0.00 0.00 1.90
2872 3123 4.439289 GCTGAGAACCATTTCATTACTGCC 60.439 45.833 0.00 0.00 33.72 4.85
2981 3243 8.808092 CACAGGGGGAATATTGTTTTTAACTTA 58.192 33.333 0.00 0.00 0.00 2.24
2984 3246 7.234661 TCACAGGGGGAATATTGTTTTTAAC 57.765 36.000 0.00 0.00 0.00 2.01
2992 3254 4.099881 CCAACATTCACAGGGGGAATATTG 59.900 45.833 5.47 5.47 38.34 1.90
2994 3256 3.914771 CCAACATTCACAGGGGGAATAT 58.085 45.455 0.00 0.00 33.40 1.28
2995 3257 2.622977 GCCAACATTCACAGGGGGAATA 60.623 50.000 0.00 0.00 33.40 1.75
2996 3258 1.896755 GCCAACATTCACAGGGGGAAT 60.897 52.381 0.00 0.00 35.43 3.01
2997 3259 0.541764 GCCAACATTCACAGGGGGAA 60.542 55.000 0.00 0.00 0.00 3.97
2998 3260 1.076549 GCCAACATTCACAGGGGGA 59.923 57.895 0.00 0.00 0.00 4.81
2999 3261 0.542702 AAGCCAACATTCACAGGGGG 60.543 55.000 0.00 0.00 0.00 5.40
3000 3262 0.890683 GAAGCCAACATTCACAGGGG 59.109 55.000 0.00 0.00 0.00 4.79
3001 3263 0.890683 GGAAGCCAACATTCACAGGG 59.109 55.000 0.00 0.00 0.00 4.45
3002 3264 0.890683 GGGAAGCCAACATTCACAGG 59.109 55.000 0.00 0.00 30.15 4.00
3003 3265 0.890683 GGGGAAGCCAACATTCACAG 59.109 55.000 0.00 0.00 31.40 3.66
3015 3277 1.613836 CTCAGGCATTATGGGGAAGC 58.386 55.000 0.00 0.00 0.00 3.86
3061 3329 5.830991 TCCAACACTAAACCTTGCAGTAATT 59.169 36.000 0.00 0.00 0.00 1.40
3069 3337 2.948979 TGTGCTCCAACACTAAACCTTG 59.051 45.455 0.00 0.00 41.30 3.61
3079 3347 2.299013 AGTAAGATCGTGTGCTCCAACA 59.701 45.455 0.00 0.00 0.00 3.33
3141 3410 6.834168 AATATGTGGGTGAGAACGAAAAAT 57.166 33.333 0.00 0.00 0.00 1.82
3156 3425 6.487668 TGATGGTAGAGCATCAAAATATGTGG 59.512 38.462 19.29 0.00 37.82 4.17
3550 4202 7.916450 AGAAGACGCTATAACTAGTTGATGTTC 59.084 37.037 18.56 10.21 0.00 3.18
3622 4274 8.630917 TGACAAATAAACCGGTGAAGAAAATTA 58.369 29.630 8.52 0.00 0.00 1.40
3669 4652 4.850680 TGGGTGCTCGTATAGGAATTTTT 58.149 39.130 0.00 0.00 0.00 1.94
3673 4656 3.006967 GTCATGGGTGCTCGTATAGGAAT 59.993 47.826 0.00 0.00 0.00 3.01
3826 5250 8.361169 AGAATATCTCCTGAAGGATTAGTAGC 57.639 38.462 0.00 0.00 44.46 3.58
3979 5405 1.073763 AGAACCTGGTGCATGTGCTAA 59.926 47.619 7.75 0.00 42.66 3.09
4166 5592 0.462759 AGACCGGCTATCAGCTTTGC 60.463 55.000 0.00 0.00 41.99 3.68
4409 5839 3.840666 TCCTGAGAGCACCACTTTTCTAT 59.159 43.478 0.00 0.00 0.00 1.98
4446 5876 3.077359 GTTGAAGACCTCCTTGACATGG 58.923 50.000 0.00 0.80 34.68 3.66
4552 5984 0.965439 TGACCTTGCATTTTTCCCCG 59.035 50.000 0.00 0.00 0.00 5.73
4797 6233 3.743899 GCACTTTTGCTGAATTTCCCCAA 60.744 43.478 0.00 0.00 46.17 4.12
5102 6541 1.351017 TGGTCTGGAGTTGATTCACCC 59.649 52.381 0.00 0.00 0.00 4.61
5224 6663 1.301322 TCCAGAATGACAACGCGCA 60.301 52.632 5.73 0.00 39.69 6.09
5449 6888 1.140816 GCTCTCTGAAACGTCCACAC 58.859 55.000 0.00 0.00 0.00 3.82


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

AutoCloner maintained by Alex Coulton.