Multiple sequence alignment - TraesCS2D01G283900

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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 TraesCS2D01G283900 chr2D 100.000 3690 0 0 1 3690 357975038 357978727 0.000000e+00 6815.0
1 TraesCS2D01G283900 chr2B 88.608 3125 196 75 666 3690 425436890 425439954 0.000000e+00 3651.0
2 TraesCS2D01G283900 chr2A 88.537 1073 50 34 674 1743 478901192 478902194 0.000000e+00 1232.0
3 TraesCS2D01G283900 chr2A 85.835 713 57 20 2077 2786 478902549 478903220 0.000000e+00 717.0
4 TraesCS2D01G283900 chr2A 86.756 521 36 14 3011 3501 478907955 478908472 1.940000e-152 549.0
5 TraesCS2D01G283900 chr2A 90.659 182 10 4 1856 2030 478902241 478902422 6.160000e-58 235.0
6 TraesCS2D01G283900 chr2A 89.610 154 15 1 3538 3690 478908561 478908714 1.050000e-45 195.0
7 TraesCS2D01G283900 chr7A 95.033 604 28 2 1 603 198691786 198691184 0.000000e+00 948.0
8 TraesCS2D01G283900 chr3B 93.355 602 35 3 1 600 2503477 2504075 0.000000e+00 885.0
9 TraesCS2D01G283900 chr3B 92.537 603 39 4 1 600 17366801 17367400 0.000000e+00 859.0
10 TraesCS2D01G283900 chr3B 89.764 127 11 2 473 599 420655445 420655569 1.060000e-35 161.0
11 TraesCS2D01G283900 chr1B 92.727 605 39 4 1 602 572152242 572152844 0.000000e+00 869.0
12 TraesCS2D01G283900 chr5B 92.821 599 41 2 1 597 569540159 569539561 0.000000e+00 867.0
13 TraesCS2D01G283900 chr5B 82.270 141 18 5 3361 3499 706348854 706348719 8.370000e-22 115.0
14 TraesCS2D01G283900 chr1A 92.180 601 45 2 1 600 308577371 308577970 0.000000e+00 848.0
15 TraesCS2D01G283900 chr1A 93.059 461 24 6 1 458 217609553 217610008 0.000000e+00 667.0
16 TraesCS2D01G283900 chr5A 90.349 601 40 2 1 601 54467967 54467385 0.000000e+00 773.0
17 TraesCS2D01G283900 chr1D 85.831 614 50 18 1 599 492128259 492128850 5.240000e-173 617.0
18 TraesCS2D01G283900 chr3A 89.231 130 12 2 471 600 525211555 525211682 1.060000e-35 161.0
19 TraesCS2D01G283900 chr5D 83.846 130 17 3 3372 3499 563967336 563967209 1.800000e-23 121.0
20 TraesCS2D01G283900 chr4A 83.077 130 18 3 3372 3499 608560916 608561043 8.370000e-22 115.0
21 TraesCS2D01G283900 chr4A 95.918 49 2 0 3452 3500 623384977 623385025 3.050000e-11 80.5


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 TraesCS2D01G283900 chr2D 357975038 357978727 3689 False 6815 6815 100.000000 1 3690 1 chr2D.!!$F1 3689
1 TraesCS2D01G283900 chr2B 425436890 425439954 3064 False 3651 3651 88.608000 666 3690 1 chr2B.!!$F1 3024
2 TraesCS2D01G283900 chr2A 478901192 478903220 2028 False 728 1232 88.343667 674 2786 3 chr2A.!!$F1 2112
3 TraesCS2D01G283900 chr2A 478907955 478908714 759 False 372 549 88.183000 3011 3690 2 chr2A.!!$F2 679
4 TraesCS2D01G283900 chr7A 198691184 198691786 602 True 948 948 95.033000 1 603 1 chr7A.!!$R1 602
5 TraesCS2D01G283900 chr3B 2503477 2504075 598 False 885 885 93.355000 1 600 1 chr3B.!!$F1 599
6 TraesCS2D01G283900 chr3B 17366801 17367400 599 False 859 859 92.537000 1 600 1 chr3B.!!$F2 599
7 TraesCS2D01G283900 chr1B 572152242 572152844 602 False 869 869 92.727000 1 602 1 chr1B.!!$F1 601
8 TraesCS2D01G283900 chr5B 569539561 569540159 598 True 867 867 92.821000 1 597 1 chr5B.!!$R1 596
9 TraesCS2D01G283900 chr1A 308577371 308577970 599 False 848 848 92.180000 1 600 1 chr1A.!!$F2 599
10 TraesCS2D01G283900 chr5A 54467385 54467967 582 True 773 773 90.349000 1 601 1 chr5A.!!$R1 600
11 TraesCS2D01G283900 chr1D 492128259 492128850 591 False 617 617 85.831000 1 599 1 chr1D.!!$F1 598

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
247 256 0.031178 GCTTATCCATGGCGGCTTTG 59.969 55.0 11.43 8.03 33.14 2.77 F
636 656 0.104304 CCAACGGAGGATTAGGACGG 59.896 60.0 0.00 0.00 0.00 4.79 F
655 675 0.233848 GAACCCGTACGTGCACTTTG 59.766 55.0 16.19 1.51 0.00 2.77 F
658 678 0.319727 CCCGTACGTGCACTTTGGTA 60.320 55.0 16.19 6.75 0.00 3.25 F
1808 1857 0.324285 CCTGTGCTTCTCTGCTCCTT 59.676 55.0 0.00 0.00 0.00 3.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1932 1997 0.473694 TCTTCAGGTGGGGAAGAGCA 60.474 55.000 0.99 0.0 44.21 4.26 R
2112 2265 1.066502 TGCTAGCCTGCAATGTTACGA 60.067 47.619 13.29 0.0 40.29 3.43 R
2293 2446 1.570813 TTCTCTGTCGTGTGCAACTG 58.429 50.000 0.00 0.0 38.04 3.16 R
2387 2542 2.202570 CTGAGCCTGCATTTGCGC 60.203 61.111 0.00 0.0 45.83 6.09 R
2944 3109 0.542467 ACACCCATCCATTTGCAGCA 60.542 50.000 0.00 0.0 0.00 4.41 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
47 48 8.100791 TGGTGTCTTGTTGAAGCTTTATATACT 58.899 33.333 0.00 0.00 0.00 2.12
86 87 4.840772 CGAATCGAACAGTTGTAGCTTTTG 59.159 41.667 0.00 0.00 0.00 2.44
247 256 0.031178 GCTTATCCATGGCGGCTTTG 59.969 55.000 11.43 8.03 33.14 2.77
341 350 3.845259 GGTATGGACCTGCGCGGA 61.845 66.667 20.25 3.19 43.16 5.54
375 391 1.107114 GCGGTGAGATCTGAAGGAGA 58.893 55.000 0.00 0.00 34.25 3.71
378 394 3.617531 GCGGTGAGATCTGAAGGAGAAAA 60.618 47.826 0.00 0.00 33.12 2.29
384 400 5.782331 TGAGATCTGAAGGAGAAAAAGGAGA 59.218 40.000 0.00 0.00 33.12 3.71
505 525 0.839946 GAAGATAAGGCAGGGGCAGA 59.160 55.000 0.00 0.00 43.71 4.26
603 623 4.142966 CCGCTTAGAAACGTTTCCCTAAAG 60.143 45.833 31.87 27.35 37.92 1.85
604 624 4.142966 CGCTTAGAAACGTTTCCCTAAAGG 60.143 45.833 31.87 19.53 37.92 3.11
605 625 4.758674 GCTTAGAAACGTTTCCCTAAAGGT 59.241 41.667 31.87 16.62 43.59 3.50
606 626 5.334646 GCTTAGAAACGTTTCCCTAAAGGTG 60.335 44.000 31.87 16.02 41.53 4.00
607 627 4.160642 AGAAACGTTTCCCTAAAGGTGT 57.839 40.909 31.87 11.16 41.53 4.16
608 628 4.529897 AGAAACGTTTCCCTAAAGGTGTT 58.470 39.130 31.87 10.68 41.53 3.32
609 629 4.951715 AGAAACGTTTCCCTAAAGGTGTTT 59.048 37.500 31.87 10.49 41.53 2.83
610 630 5.419788 AGAAACGTTTCCCTAAAGGTGTTTT 59.580 36.000 31.87 10.09 41.53 2.43
611 631 4.642445 ACGTTTCCCTAAAGGTGTTTTG 57.358 40.909 0.00 0.00 41.01 2.44
612 632 4.018490 ACGTTTCCCTAAAGGTGTTTTGT 58.982 39.130 0.00 0.00 41.01 2.83
613 633 4.096833 ACGTTTCCCTAAAGGTGTTTTGTC 59.903 41.667 0.00 0.00 41.01 3.18
614 634 4.096682 CGTTTCCCTAAAGGTGTTTTGTCA 59.903 41.667 0.00 0.00 36.75 3.58
615 635 5.345702 GTTTCCCTAAAGGTGTTTTGTCAC 58.654 41.667 0.00 0.00 36.75 3.67
616 636 4.513406 TCCCTAAAGGTGTTTTGTCACT 57.487 40.909 0.00 0.00 38.28 3.41
617 637 4.457466 TCCCTAAAGGTGTTTTGTCACTC 58.543 43.478 0.00 0.00 38.28 3.51
618 638 3.568430 CCCTAAAGGTGTTTTGTCACTCC 59.432 47.826 0.00 0.00 38.28 3.85
619 639 4.204012 CCTAAAGGTGTTTTGTCACTCCA 58.796 43.478 0.00 0.00 38.28 3.86
620 640 4.642885 CCTAAAGGTGTTTTGTCACTCCAA 59.357 41.667 0.00 0.00 38.28 3.53
621 641 4.450082 AAAGGTGTTTTGTCACTCCAAC 57.550 40.909 0.00 0.00 38.28 3.77
622 642 2.014128 AGGTGTTTTGTCACTCCAACG 58.986 47.619 0.00 0.00 38.28 4.10
623 643 1.064952 GGTGTTTTGTCACTCCAACGG 59.935 52.381 0.00 0.00 38.28 4.44
624 644 2.011222 GTGTTTTGTCACTCCAACGGA 58.989 47.619 0.00 0.00 35.68 4.69
634 654 2.892784 CTCCAACGGAGGATTAGGAC 57.107 55.000 1.84 0.00 45.43 3.85
635 655 1.067212 CTCCAACGGAGGATTAGGACG 59.933 57.143 1.84 0.00 45.43 4.79
636 656 0.104304 CCAACGGAGGATTAGGACGG 59.896 60.000 0.00 0.00 0.00 4.79
637 657 1.108776 CAACGGAGGATTAGGACGGA 58.891 55.000 0.00 0.00 0.00 4.69
638 658 1.479323 CAACGGAGGATTAGGACGGAA 59.521 52.381 0.00 0.00 0.00 4.30
639 659 1.109609 ACGGAGGATTAGGACGGAAC 58.890 55.000 0.00 0.00 0.00 3.62
640 660 0.388294 CGGAGGATTAGGACGGAACC 59.612 60.000 0.00 0.00 0.00 3.62
641 661 0.757512 GGAGGATTAGGACGGAACCC 59.242 60.000 0.00 0.00 0.00 4.11
651 671 3.107661 CGGAACCCGTACGTGCAC 61.108 66.667 15.21 6.82 42.73 4.57
652 672 2.341176 GGAACCCGTACGTGCACT 59.659 61.111 16.19 4.64 0.00 4.40
653 673 1.301165 GGAACCCGTACGTGCACTT 60.301 57.895 16.19 8.40 0.00 3.16
654 674 0.881600 GGAACCCGTACGTGCACTTT 60.882 55.000 16.19 4.04 0.00 2.66
655 675 0.233848 GAACCCGTACGTGCACTTTG 59.766 55.000 16.19 1.51 0.00 2.77
656 676 1.161563 AACCCGTACGTGCACTTTGG 61.162 55.000 16.19 10.93 0.00 3.28
657 677 1.595929 CCCGTACGTGCACTTTGGT 60.596 57.895 16.19 7.82 0.00 3.67
658 678 0.319727 CCCGTACGTGCACTTTGGTA 60.320 55.000 16.19 6.75 0.00 3.25
659 679 1.500108 CCGTACGTGCACTTTGGTAA 58.500 50.000 16.19 0.00 0.00 2.85
660 680 1.865970 CCGTACGTGCACTTTGGTAAA 59.134 47.619 16.19 0.00 0.00 2.01
661 681 2.096614 CCGTACGTGCACTTTGGTAAAG 60.097 50.000 16.19 7.20 44.10 1.85
662 682 2.796031 CGTACGTGCACTTTGGTAAAGA 59.204 45.455 16.19 0.00 41.02 2.52
663 683 3.245754 CGTACGTGCACTTTGGTAAAGAA 59.754 43.478 16.19 0.00 41.02 2.52
664 684 4.260294 CGTACGTGCACTTTGGTAAAGAAA 60.260 41.667 16.19 0.00 41.02 2.52
669 689 6.077838 CGTGCACTTTGGTAAAGAAATACTC 58.922 40.000 16.19 0.00 41.02 2.59
670 690 6.379386 GTGCACTTTGGTAAAGAAATACTCC 58.621 40.000 10.32 0.00 41.02 3.85
779 799 1.694150 TGCAGGTTGTGTCTAGAAGCT 59.306 47.619 0.00 0.00 38.30 3.74
780 800 2.289072 TGCAGGTTGTGTCTAGAAGCTC 60.289 50.000 0.00 0.00 35.96 4.09
781 801 2.289072 GCAGGTTGTGTCTAGAAGCTCA 60.289 50.000 0.00 0.00 35.96 4.26
782 802 3.321497 CAGGTTGTGTCTAGAAGCTCAC 58.679 50.000 0.00 0.00 35.96 3.51
783 803 2.965831 AGGTTGTGTCTAGAAGCTCACA 59.034 45.455 9.24 9.24 33.17 3.58
784 804 3.006323 AGGTTGTGTCTAGAAGCTCACAG 59.994 47.826 12.17 0.00 40.90 3.66
849 869 1.479420 CCATACGCGACGTGTCATGG 61.479 60.000 18.67 21.67 41.39 3.66
861 881 1.451028 GTCATGGCAGCCTGAGACC 60.451 63.158 14.15 0.00 0.00 3.85
904 925 2.804856 GAGCGTCTCTCTCCTGGC 59.195 66.667 0.00 0.00 38.78 4.85
921 942 2.167861 GCCTCATTCTCACGGTCGC 61.168 63.158 0.00 0.00 0.00 5.19
926 947 2.283529 ATTCTCACGGTCGCCACCT 61.284 57.895 0.00 0.00 41.17 4.00
927 948 0.968901 ATTCTCACGGTCGCCACCTA 60.969 55.000 0.00 0.00 41.17 3.08
928 949 0.968901 TTCTCACGGTCGCCACCTAT 60.969 55.000 0.00 0.00 41.17 2.57
929 950 1.065928 CTCACGGTCGCCACCTATC 59.934 63.158 0.00 0.00 41.17 2.08
930 951 2.278596 CACGGTCGCCACCTATCG 60.279 66.667 0.00 0.00 41.17 2.92
931 952 4.203076 ACGGTCGCCACCTATCGC 62.203 66.667 0.00 0.00 41.17 4.58
932 953 4.201679 CGGTCGCCACCTATCGCA 62.202 66.667 0.00 0.00 41.17 5.10
934 955 2.494918 GTCGCCACCTATCGCAGT 59.505 61.111 0.00 0.00 0.00 4.40
935 956 1.153628 GTCGCCACCTATCGCAGTT 60.154 57.895 0.00 0.00 0.00 3.16
951 974 1.654137 GTTTGCAACACAGCCGTCG 60.654 57.895 0.00 0.00 0.00 5.12
955 978 2.661537 CAACACAGCCGTCGAGCA 60.662 61.111 8.15 0.00 34.23 4.26
956 979 2.108157 AACACAGCCGTCGAGCAA 59.892 55.556 8.15 0.00 34.23 3.91
969 992 1.303317 GAGCAAAGCCCCGAGGAAA 60.303 57.895 0.00 0.00 33.47 3.13
971 994 2.343426 GCAAAGCCCCGAGGAAAGG 61.343 63.158 0.00 0.00 33.47 3.11
981 1005 1.628846 CCGAGGAAAGGAGGAAGGAAA 59.371 52.381 0.00 0.00 0.00 3.13
1210 1238 3.636231 CGGGGAAGGTGGTGCTCA 61.636 66.667 0.00 0.00 0.00 4.26
1267 1295 5.124617 CGGATAATGGAGATTCTCGATCAGA 59.875 44.000 11.08 2.08 37.22 3.27
1281 1309 5.362717 TCTCGATCAGAGTTGCCCTTATTTA 59.637 40.000 12.27 0.00 46.86 1.40
1284 1312 6.049149 CGATCAGAGTTGCCCTTATTTAAGA 58.951 40.000 0.00 0.00 35.33 2.10
1319 1351 8.311395 TGATCAGATATGTATATTCCTGGGTC 57.689 38.462 0.00 0.00 0.00 4.46
1323 1355 2.482414 TGTATATTCCTGGGTCCCGT 57.518 50.000 2.65 0.00 0.00 5.28
1341 1373 2.290641 CCGTTTAACTTGACTTGCTGCT 59.709 45.455 0.00 0.00 0.00 4.24
1346 1378 1.027357 ACTTGACTTGCTGCTTGTGG 58.973 50.000 0.00 0.00 0.00 4.17
1553 1585 1.084289 GCTTTGGCCGGTGTAAGTAG 58.916 55.000 1.90 0.00 0.00 2.57
1558 1594 1.294138 GCCGGTGTAAGTAGCCACA 59.706 57.895 1.90 0.00 33.19 4.17
1574 1610 0.380733 CACATGCTGTGCTATGCCTG 59.619 55.000 0.00 0.00 41.89 4.85
1585 1621 1.271271 GCTATGCCTGCCTTGATAGCT 60.271 52.381 10.34 0.00 40.03 3.32
1590 1626 1.881498 GCCTGCCTTGATAGCTCATCC 60.881 57.143 0.00 0.00 32.09 3.51
1602 1638 7.491161 TGATAGCTCATCCATCGTGTACACG 62.491 48.000 36.46 36.46 43.31 4.49
1616 1657 3.068560 TGTACACGTATGTTTTGAGCCC 58.931 45.455 0.00 0.00 40.48 5.19
1673 1714 1.686355 TCTTGTGAACAATGCCGGTT 58.314 45.000 1.90 0.00 35.02 4.44
1714 1755 4.148825 GAGGTGCCCGATGTCGCT 62.149 66.667 0.00 0.00 38.18 4.93
1727 1768 1.098869 TGTCGCTGGTTTCAAGCAAA 58.901 45.000 0.00 0.00 35.79 3.68
1743 1784 2.070783 GCAAATCTTGGTACCGTTCGA 58.929 47.619 7.57 1.04 0.00 3.71
1758 1807 2.479730 CGTTCGATCTCTACCCACCTTG 60.480 54.545 0.00 0.00 0.00 3.61
1763 1812 4.401519 TCGATCTCTACCCACCTTGTTTAG 59.598 45.833 0.00 0.00 0.00 1.85
1764 1813 4.401519 CGATCTCTACCCACCTTGTTTAGA 59.598 45.833 0.00 0.00 0.00 2.10
1765 1814 5.662456 GATCTCTACCCACCTTGTTTAGAC 58.338 45.833 0.00 0.00 0.00 2.59
1766 1815 4.748701 TCTCTACCCACCTTGTTTAGACT 58.251 43.478 0.00 0.00 0.00 3.24
1767 1816 4.771054 TCTCTACCCACCTTGTTTAGACTC 59.229 45.833 0.00 0.00 0.00 3.36
1768 1817 4.748701 TCTACCCACCTTGTTTAGACTCT 58.251 43.478 0.00 0.00 0.00 3.24
1769 1818 5.152934 TCTACCCACCTTGTTTAGACTCTT 58.847 41.667 0.00 0.00 0.00 2.85
1770 1819 4.353383 ACCCACCTTGTTTAGACTCTTC 57.647 45.455 0.00 0.00 0.00 2.87
1771 1820 3.714798 ACCCACCTTGTTTAGACTCTTCA 59.285 43.478 0.00 0.00 0.00 3.02
1772 1821 4.351111 ACCCACCTTGTTTAGACTCTTCAT 59.649 41.667 0.00 0.00 0.00 2.57
1773 1822 5.546499 ACCCACCTTGTTTAGACTCTTCATA 59.454 40.000 0.00 0.00 0.00 2.15
1774 1823 6.043938 ACCCACCTTGTTTAGACTCTTCATAA 59.956 38.462 0.00 0.00 0.00 1.90
1775 1824 7.112779 CCCACCTTGTTTAGACTCTTCATAAT 58.887 38.462 0.00 0.00 0.00 1.28
1776 1825 8.265055 CCCACCTTGTTTAGACTCTTCATAATA 58.735 37.037 0.00 0.00 0.00 0.98
1777 1826 9.838339 CCACCTTGTTTAGACTCTTCATAATAT 57.162 33.333 0.00 0.00 0.00 1.28
1790 1839 8.763601 ACTCTTCATAATATAGCCCTATGTTCC 58.236 37.037 1.29 0.00 31.01 3.62
1808 1857 0.324285 CCTGTGCTTCTCTGCTCCTT 59.676 55.000 0.00 0.00 0.00 3.36
1809 1858 1.675415 CCTGTGCTTCTCTGCTCCTTC 60.675 57.143 0.00 0.00 0.00 3.46
1810 1859 1.275856 CTGTGCTTCTCTGCTCCTTCT 59.724 52.381 0.00 0.00 0.00 2.85
1811 1860 1.696336 TGTGCTTCTCTGCTCCTTCTT 59.304 47.619 0.00 0.00 0.00 2.52
1812 1861 2.075338 GTGCTTCTCTGCTCCTTCTTG 58.925 52.381 0.00 0.00 0.00 3.02
1813 1862 1.085893 GCTTCTCTGCTCCTTCTTGC 58.914 55.000 0.00 0.00 0.00 4.01
1814 1863 1.338960 GCTTCTCTGCTCCTTCTTGCT 60.339 52.381 0.00 0.00 0.00 3.91
1815 1864 2.620242 CTTCTCTGCTCCTTCTTGCTC 58.380 52.381 0.00 0.00 0.00 4.26
1816 1865 0.901124 TCTCTGCTCCTTCTTGCTCC 59.099 55.000 0.00 0.00 0.00 4.70
1817 1866 0.903942 CTCTGCTCCTTCTTGCTCCT 59.096 55.000 0.00 0.00 0.00 3.69
1824 1873 3.128415 GCTCCTTCTTGCTCCTCAATTTC 59.872 47.826 0.00 0.00 33.57 2.17
1826 1875 4.330250 TCCTTCTTGCTCCTCAATTTCTG 58.670 43.478 0.00 0.00 33.57 3.02
1873 1931 6.964876 ATTCCATCATCTCCCTTCATGATA 57.035 37.500 0.00 0.00 37.60 2.15
1883 1941 7.862274 TCTCCCTTCATGATACTGATATGTT 57.138 36.000 0.00 0.00 0.00 2.71
1884 1942 7.674120 TCTCCCTTCATGATACTGATATGTTG 58.326 38.462 0.00 0.00 0.00 3.33
1885 1943 6.772605 TCCCTTCATGATACTGATATGTTGG 58.227 40.000 0.00 0.00 0.00 3.77
1886 1944 5.413833 CCCTTCATGATACTGATATGTTGGC 59.586 44.000 0.00 0.00 0.00 4.52
1890 1955 4.864704 TGATACTGATATGTTGGCGCTA 57.135 40.909 7.64 0.00 0.00 4.26
1896 1961 2.368548 TGATATGTTGGCGCTACAGGAT 59.631 45.455 18.01 14.13 0.00 3.24
1932 1997 2.672996 GTGCATCCAACCCACGCT 60.673 61.111 0.00 0.00 0.00 5.07
2047 2113 8.333235 ACAATGTACTAATACAAATCCCTCCAA 58.667 33.333 0.00 0.00 44.47 3.53
2052 2118 9.841295 GTACTAATACAAATCCCTCCAACATTA 57.159 33.333 0.00 0.00 0.00 1.90
2078 2231 6.321435 CAGTTCCTTTTCCCTTTCTAGTTTGT 59.679 38.462 0.00 0.00 0.00 2.83
2089 2242 6.461509 CCCTTTCTAGTTTGTGCATTTTGAGT 60.462 38.462 0.00 0.00 0.00 3.41
2162 2315 2.676822 TGAGCTTCGCCGAGACCT 60.677 61.111 0.00 0.00 0.00 3.85
2288 2441 0.809385 GGTCGATCAAGACACGAGGA 59.191 55.000 0.00 0.00 42.62 3.71
2293 2446 2.854777 CGATCAAGACACGAGGAATGTC 59.145 50.000 0.00 0.00 45.70 3.06
2299 2452 1.461127 GACACGAGGAATGTCAGTTGC 59.539 52.381 0.00 0.00 44.87 4.17
2300 2453 1.202639 ACACGAGGAATGTCAGTTGCA 60.203 47.619 0.00 0.00 0.00 4.08
2301 2454 1.195448 CACGAGGAATGTCAGTTGCAC 59.805 52.381 0.00 0.00 0.00 4.57
2302 2455 1.202639 ACGAGGAATGTCAGTTGCACA 60.203 47.619 0.00 0.00 0.00 4.57
2304 2457 1.195448 GAGGAATGTCAGTTGCACACG 59.805 52.381 0.00 0.00 0.00 4.49
2305 2458 1.202639 AGGAATGTCAGTTGCACACGA 60.203 47.619 0.00 0.00 0.00 4.35
2306 2459 1.069906 GGAATGTCAGTTGCACACGAC 60.070 52.381 0.00 0.00 32.65 4.34
2308 2461 1.220529 ATGTCAGTTGCACACGACAG 58.779 50.000 14.46 0.00 40.14 3.51
2319 2474 2.663602 GCACACGACAGAGAATACACAG 59.336 50.000 0.00 0.00 0.00 3.66
2349 2504 3.462483 TTCTGTAGAAGTTGTCGCCAA 57.538 42.857 0.00 0.00 0.00 4.52
2382 2537 3.520290 ACCATGCTCATGCTTGATTTG 57.480 42.857 2.33 1.97 44.17 2.32
2383 2538 2.201732 CCATGCTCATGCTTGATTTGC 58.798 47.619 2.33 4.26 44.17 3.68
2384 2539 2.418060 CCATGCTCATGCTTGATTTGCA 60.418 45.455 14.62 14.62 44.17 4.08
2386 2541 3.159353 TGCTCATGCTTGATTTGCATC 57.841 42.857 9.94 0.00 46.80 3.91
2387 2542 2.117137 GCTCATGCTTGATTTGCATCG 58.883 47.619 2.33 0.00 46.80 3.84
2388 2543 2.117137 CTCATGCTTGATTTGCATCGC 58.883 47.619 2.33 0.00 46.80 4.58
2408 2563 1.246056 GCAAATGCAGGCTCAGGTGA 61.246 55.000 0.00 0.00 41.59 4.02
2416 2571 4.292784 GCTCAGGTGAGGCTGTTC 57.707 61.111 9.03 0.00 42.29 3.18
2461 2616 2.353607 GAGGCTATCGTGGACGCG 60.354 66.667 3.53 3.53 39.60 6.01
2527 2682 2.948720 GCTGTTCCTCTGGCGGTCT 61.949 63.158 0.00 0.00 0.00 3.85
2681 2836 0.796312 GCACACGTCGGACATCAAAT 59.204 50.000 9.10 0.00 0.00 2.32
2758 2915 3.914426 AAGATAGAATGGCGAGGTGTT 57.086 42.857 0.00 0.00 0.00 3.32
2759 2916 6.665992 ATAAGATAGAATGGCGAGGTGTTA 57.334 37.500 0.00 0.00 0.00 2.41
2760 2917 4.592485 AGATAGAATGGCGAGGTGTTAG 57.408 45.455 0.00 0.00 0.00 2.34
2763 2920 2.973945 AGAATGGCGAGGTGTTAGTTC 58.026 47.619 0.00 0.00 0.00 3.01
2764 2921 2.567615 AGAATGGCGAGGTGTTAGTTCT 59.432 45.455 0.00 0.00 0.00 3.01
2806 2963 8.617761 TGGTTTGTGTAAATTTAAGTTTCGTC 57.382 30.769 0.00 0.00 0.00 4.20
2807 2964 7.428761 TGGTTTGTGTAAATTTAAGTTTCGTCG 59.571 33.333 0.00 0.00 0.00 5.12
2808 2965 7.639461 GGTTTGTGTAAATTTAAGTTTCGTCGA 59.361 33.333 0.00 0.00 0.00 4.20
2866 3023 8.970859 AAACTCTCTTCTTTTGAATCTCTCAA 57.029 30.769 0.00 0.00 42.48 3.02
2879 3044 7.630242 TGAATCTCTCAACAACAAGAAAACT 57.370 32.000 0.00 0.00 0.00 2.66
2882 3047 5.496556 TCTCTCAACAACAAGAAAACTCCA 58.503 37.500 0.00 0.00 0.00 3.86
2912 3077 2.881352 GAAGTTCTCGCGCTCCGG 60.881 66.667 5.56 0.00 37.59 5.14
2913 3078 4.436998 AAGTTCTCGCGCTCCGGG 62.437 66.667 5.56 0.00 41.10 5.73
2915 3080 4.736896 GTTCTCGCGCTCCGGGTT 62.737 66.667 5.56 0.00 40.60 4.11
2916 3081 3.998672 TTCTCGCGCTCCGGGTTT 61.999 61.111 5.56 0.00 40.60 3.27
2917 3082 2.638354 TTCTCGCGCTCCGGGTTTA 61.638 57.895 5.56 0.00 40.60 2.01
2918 3083 2.552585 TTCTCGCGCTCCGGGTTTAG 62.553 60.000 5.56 0.00 40.60 1.85
2919 3084 3.060020 CTCGCGCTCCGGGTTTAGA 62.060 63.158 5.56 0.00 40.60 2.10
2920 3085 2.125832 CGCGCTCCGGGTTTAGAA 60.126 61.111 5.56 0.00 35.14 2.10
2982 3147 4.101942 GTGTGCATTCGAAACTGAAACAA 58.898 39.130 0.00 0.00 0.00 2.83
2986 3151 3.182372 GCATTCGAAACTGAAACAAAGCC 59.818 43.478 0.00 0.00 0.00 4.35
2999 3167 3.429372 AAAGCCCCTCGCACACCAA 62.429 57.895 0.00 0.00 41.38 3.67
3039 3217 1.666189 GAGCATACAACGGGCTTCTTC 59.334 52.381 0.00 0.00 38.15 2.87
3062 3240 1.716050 CAATATCGACGATGCTCACGG 59.284 52.381 20.42 0.00 34.93 4.94
3064 3242 0.028902 TATCGACGATGCTCACGGTG 59.971 55.000 20.42 0.56 34.93 4.94
3070 3248 0.031314 CGATGCTCACGGTGATAGCT 59.969 55.000 19.16 8.32 37.16 3.32
3261 3465 4.026293 CATATATGCAACGTTTGTGCCA 57.974 40.909 8.16 0.00 0.00 4.92
3262 3466 4.609947 CATATATGCAACGTTTGTGCCAT 58.390 39.130 8.16 4.63 0.00 4.40
3263 3467 2.344504 TATGCAACGTTTGTGCCATG 57.655 45.000 8.16 0.00 0.00 3.66
3265 3469 1.067250 GCAACGTTTGTGCCATGGT 59.933 52.632 14.67 0.00 0.00 3.55
3266 3470 0.312416 GCAACGTTTGTGCCATGGTA 59.688 50.000 14.67 5.86 0.00 3.25
3267 3471 1.665735 GCAACGTTTGTGCCATGGTAG 60.666 52.381 14.67 0.00 0.00 3.18
3268 3472 1.068610 CAACGTTTGTGCCATGGTAGG 60.069 52.381 14.67 2.81 0.00 3.18
3270 3474 1.312371 CGTTTGTGCCATGGTAGGGG 61.312 60.000 14.67 0.00 0.00 4.79
3271 3475 0.039035 GTTTGTGCCATGGTAGGGGA 59.961 55.000 14.67 0.00 0.00 4.81
3272 3476 1.006813 TTTGTGCCATGGTAGGGGAT 58.993 50.000 14.67 0.00 0.00 3.85
3273 3477 1.900254 TTGTGCCATGGTAGGGGATA 58.100 50.000 14.67 0.00 0.00 2.59
3288 3503 2.825532 GGGGATACACACACTGCAAAAT 59.174 45.455 0.00 0.00 42.67 1.82
3289 3504 3.119495 GGGGATACACACACTGCAAAATC 60.119 47.826 0.00 0.00 42.67 2.17
3290 3505 3.119495 GGGATACACACACTGCAAAATCC 60.119 47.826 0.00 0.00 39.74 3.01
3332 3547 2.191375 CGATGCTGATGGGCAGGT 59.809 61.111 0.00 0.00 45.75 4.00
3407 3622 1.745141 CGCCCTACTACGTCTACAGGT 60.745 57.143 0.00 0.00 0.00 4.00
3444 3659 2.939261 GCTCCGTCTTCCCCGACAA 61.939 63.158 0.00 0.00 33.54 3.18
3507 3722 2.530177 CATAGGCGAGGTATGCATACG 58.470 52.381 26.38 18.18 30.74 3.06
3514 3729 3.364023 GCGAGGTATGCATACGTTACATC 59.636 47.826 27.59 15.33 34.11 3.06
3516 3731 4.381863 CGAGGTATGCATACGTTACATCAC 59.618 45.833 27.59 14.93 34.11 3.06
3536 3754 1.066303 CAGCATACGTCTCTCCAGGAC 59.934 57.143 0.00 0.00 0.00 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
47 48 3.125146 CGATTCGAAAGATTCAACCAGCA 59.875 43.478 0.00 0.00 39.73 4.41
86 87 0.383949 ATGTTGCAACCGACAACCAC 59.616 50.000 26.14 0.00 45.42 4.16
341 350 4.875713 CGCCGGCTAGCCCCAATT 62.876 66.667 28.09 0.00 0.00 2.32
375 391 1.603739 GGCCACGCCTCTCCTTTTT 60.604 57.895 0.00 0.00 46.69 1.94
584 604 5.683681 ACACCTTTAGGGAAACGTTTCTAA 58.316 37.500 33.23 23.72 40.27 2.10
603 623 1.064952 CCGTTGGAGTGACAAAACACC 59.935 52.381 0.00 0.00 41.12 4.16
604 624 2.011222 TCCGTTGGAGTGACAAAACAC 58.989 47.619 0.00 0.00 40.60 3.32
605 625 2.285083 CTCCGTTGGAGTGACAAAACA 58.715 47.619 4.65 0.00 44.25 2.83
616 636 1.108776 CGTCCTAATCCTCCGTTGGA 58.891 55.000 0.00 0.00 40.82 3.53
617 637 0.104304 CCGTCCTAATCCTCCGTTGG 59.896 60.000 0.00 0.00 0.00 3.77
618 638 1.108776 TCCGTCCTAATCCTCCGTTG 58.891 55.000 0.00 0.00 0.00 4.10
619 639 1.479730 GTTCCGTCCTAATCCTCCGTT 59.520 52.381 0.00 0.00 0.00 4.44
620 640 1.109609 GTTCCGTCCTAATCCTCCGT 58.890 55.000 0.00 0.00 0.00 4.69
621 641 0.388294 GGTTCCGTCCTAATCCTCCG 59.612 60.000 0.00 0.00 0.00 4.63
622 642 0.757512 GGGTTCCGTCCTAATCCTCC 59.242 60.000 0.00 0.00 0.00 4.30
623 643 0.388294 CGGGTTCCGTCCTAATCCTC 59.612 60.000 0.00 0.00 42.73 3.71
624 644 2.512973 CGGGTTCCGTCCTAATCCT 58.487 57.895 0.00 0.00 42.73 3.24
635 655 0.881600 AAAGTGCACGTACGGGTTCC 60.882 55.000 20.35 7.23 0.00 3.62
636 656 0.233848 CAAAGTGCACGTACGGGTTC 59.766 55.000 20.35 12.29 0.00 3.62
637 657 1.161563 CCAAAGTGCACGTACGGGTT 61.162 55.000 20.35 2.27 0.00 4.11
638 658 1.595929 CCAAAGTGCACGTACGGGT 60.596 57.895 20.35 0.00 0.00 5.28
639 659 0.319727 TACCAAAGTGCACGTACGGG 60.320 55.000 21.06 18.06 0.00 5.28
640 660 1.500108 TTACCAAAGTGCACGTACGG 58.500 50.000 21.06 14.65 0.00 4.02
641 661 2.796031 TCTTTACCAAAGTGCACGTACG 59.204 45.455 15.01 15.01 39.52 3.67
642 662 4.799419 TTCTTTACCAAAGTGCACGTAC 57.201 40.909 12.01 0.00 39.52 3.67
643 663 6.707161 AGTATTTCTTTACCAAAGTGCACGTA 59.293 34.615 12.01 4.66 39.52 3.57
644 664 4.911514 ATTTCTTTACCAAAGTGCACGT 57.088 36.364 12.01 5.01 39.52 4.49
645 665 5.997385 AGTATTTCTTTACCAAAGTGCACG 58.003 37.500 12.01 0.00 39.52 5.34
646 666 6.206829 AGGAGTATTTCTTTACCAAAGTGCAC 59.793 38.462 9.40 9.40 39.52 4.57
647 667 6.206634 CAGGAGTATTTCTTTACCAAAGTGCA 59.793 38.462 0.00 0.00 39.52 4.57
648 668 6.612306 CAGGAGTATTTCTTTACCAAAGTGC 58.388 40.000 0.00 0.00 39.52 4.40
649 669 6.206634 TGCAGGAGTATTTCTTTACCAAAGTG 59.793 38.462 0.00 0.00 39.52 3.16
650 670 6.303839 TGCAGGAGTATTTCTTTACCAAAGT 58.696 36.000 0.00 0.00 39.52 2.66
651 671 6.817765 TGCAGGAGTATTTCTTTACCAAAG 57.182 37.500 0.00 0.00 39.88 2.77
652 672 7.001674 TCTTGCAGGAGTATTTCTTTACCAAA 58.998 34.615 0.00 0.00 0.00 3.28
653 673 6.539173 TCTTGCAGGAGTATTTCTTTACCAA 58.461 36.000 0.00 0.00 0.00 3.67
654 674 6.121776 TCTTGCAGGAGTATTTCTTTACCA 57.878 37.500 0.00 0.00 0.00 3.25
655 675 7.040686 TGTTTCTTGCAGGAGTATTTCTTTACC 60.041 37.037 0.00 0.00 0.00 2.85
656 676 7.871853 TGTTTCTTGCAGGAGTATTTCTTTAC 58.128 34.615 0.00 0.00 0.00 2.01
657 677 8.635765 ATGTTTCTTGCAGGAGTATTTCTTTA 57.364 30.769 0.00 0.00 0.00 1.85
658 678 6.959639 TGTTTCTTGCAGGAGTATTTCTTT 57.040 33.333 0.00 0.00 0.00 2.52
659 679 8.814038 ATATGTTTCTTGCAGGAGTATTTCTT 57.186 30.769 0.00 0.00 0.00 2.52
660 680 8.049117 TGATATGTTTCTTGCAGGAGTATTTCT 58.951 33.333 0.00 0.00 0.00 2.52
661 681 8.213518 TGATATGTTTCTTGCAGGAGTATTTC 57.786 34.615 0.00 1.64 0.00 2.17
662 682 8.627403 CATGATATGTTTCTTGCAGGAGTATTT 58.373 33.333 0.00 0.00 0.00 1.40
663 683 7.994911 TCATGATATGTTTCTTGCAGGAGTATT 59.005 33.333 0.00 0.00 0.00 1.89
664 684 7.512130 TCATGATATGTTTCTTGCAGGAGTAT 58.488 34.615 0.00 0.00 0.00 2.12
669 689 5.768662 AGGATCATGATATGTTTCTTGCAGG 59.231 40.000 8.54 0.00 0.00 4.85
670 690 6.879276 AGGATCATGATATGTTTCTTGCAG 57.121 37.500 8.54 0.00 0.00 4.41
701 721 3.818210 TCAAGATTGGTGCATGTACGTTT 59.182 39.130 7.89 0.00 0.00 3.60
779 799 1.889170 CAGAGCTACCTGTGACTGTGA 59.111 52.381 0.00 0.00 34.44 3.58
780 800 1.671261 GCAGAGCTACCTGTGACTGTG 60.671 57.143 4.51 0.00 34.44 3.66
781 801 0.605589 GCAGAGCTACCTGTGACTGT 59.394 55.000 4.51 0.00 34.44 3.55
782 802 0.894141 AGCAGAGCTACCTGTGACTG 59.106 55.000 4.51 0.00 36.99 3.51
783 803 1.181786 GAGCAGAGCTACCTGTGACT 58.818 55.000 4.51 0.00 39.88 3.41
784 804 0.174617 GGAGCAGAGCTACCTGTGAC 59.825 60.000 4.51 0.00 39.88 3.67
904 925 1.519455 GGCGACCGTGAGAATGAGG 60.519 63.158 0.00 0.00 0.00 3.86
934 955 1.771073 CTCGACGGCTGTGTTGCAAA 61.771 55.000 0.80 0.00 34.04 3.68
935 956 2.202946 TCGACGGCTGTGTTGCAA 60.203 55.556 0.80 0.00 34.04 4.08
951 974 1.303317 TTTCCTCGGGGCTTTGCTC 60.303 57.895 0.00 0.00 0.00 4.26
955 978 1.685820 CTCCTTTCCTCGGGGCTTT 59.314 57.895 0.00 0.00 0.00 3.51
956 979 2.301738 CCTCCTTTCCTCGGGGCTT 61.302 63.158 0.00 0.00 0.00 4.35
969 992 1.439143 ACCTCCTCTTTCCTTCCTCCT 59.561 52.381 0.00 0.00 0.00 3.69
971 994 1.478916 CGACCTCCTCTTTCCTTCCTC 59.521 57.143 0.00 0.00 0.00 3.71
1210 1238 4.241555 GGAGGATGCGCCCGTGAT 62.242 66.667 4.18 0.00 37.37 3.06
1267 1295 6.002082 ACGACTTTCTTAAATAAGGGCAACT 58.998 36.000 0.00 0.00 34.14 3.16
1281 1309 7.099764 ACATATCTGATCAACACGACTTTCTT 58.900 34.615 0.00 0.00 0.00 2.52
1319 1351 2.604614 GCAGCAAGTCAAGTTAAACGGG 60.605 50.000 0.00 0.00 0.00 5.28
1323 1355 4.439974 CCACAAGCAGCAAGTCAAGTTAAA 60.440 41.667 0.00 0.00 0.00 1.52
1433 1465 3.411418 GAGATCGGTCGCCTTCGCA 62.411 63.158 0.00 0.00 35.26 5.10
1558 1594 1.826921 GGCAGGCATAGCACAGCAT 60.827 57.895 0.00 0.00 0.00 3.79
1563 1599 2.149578 CTATCAAGGCAGGCATAGCAC 58.850 52.381 0.00 0.00 0.00 4.40
1565 1601 1.163554 GCTATCAAGGCAGGCATAGC 58.836 55.000 8.51 8.51 37.61 2.97
1566 1602 2.038164 TGAGCTATCAAGGCAGGCATAG 59.962 50.000 0.00 0.00 30.61 2.23
1567 1603 2.049372 TGAGCTATCAAGGCAGGCATA 58.951 47.619 0.00 0.00 30.61 3.14
1568 1604 0.841961 TGAGCTATCAAGGCAGGCAT 59.158 50.000 0.00 0.00 30.61 4.40
1574 1610 2.289320 ACGATGGATGAGCTATCAAGGC 60.289 50.000 0.00 0.00 39.39 4.35
1602 1638 4.332828 AGTTACAGGGGCTCAAAACATAC 58.667 43.478 0.00 0.00 0.00 2.39
1606 1642 2.296190 CCAAGTTACAGGGGCTCAAAAC 59.704 50.000 0.00 0.00 0.00 2.43
1607 1643 2.593026 CCAAGTTACAGGGGCTCAAAA 58.407 47.619 0.00 0.00 0.00 2.44
1608 1644 1.203001 CCCAAGTTACAGGGGCTCAAA 60.203 52.381 5.17 0.00 41.58 2.69
1614 1655 2.961424 CTTGCCCAAGTTACAGGGG 58.039 57.895 13.44 10.33 45.58 4.79
1639 1680 4.338012 TCACAAGATGATCCACTGCAATT 58.662 39.130 0.00 0.00 29.99 2.32
1673 1714 3.215568 CCAGCACACGTTGGCCAA 61.216 61.111 16.05 16.05 36.63 4.52
1727 1768 3.288964 AGAGATCGAACGGTACCAAGAT 58.711 45.455 13.54 10.11 0.00 2.40
1737 1778 1.390565 AGGTGGGTAGAGATCGAACG 58.609 55.000 0.00 0.00 0.00 3.95
1743 1784 5.342866 AGTCTAAACAAGGTGGGTAGAGAT 58.657 41.667 0.00 0.00 0.00 2.75
1763 1812 9.810545 GAACATAGGGCTATATTATGAAGAGTC 57.189 37.037 0.00 0.00 0.00 3.36
1764 1813 8.763601 GGAACATAGGGCTATATTATGAAGAGT 58.236 37.037 0.00 0.00 0.00 3.24
1765 1814 8.986991 AGGAACATAGGGCTATATTATGAAGAG 58.013 37.037 0.00 0.00 0.00 2.85
1766 1815 8.762645 CAGGAACATAGGGCTATATTATGAAGA 58.237 37.037 0.00 0.00 0.00 2.87
1767 1816 8.543774 ACAGGAACATAGGGCTATATTATGAAG 58.456 37.037 0.00 0.00 0.00 3.02
1768 1817 8.321353 CACAGGAACATAGGGCTATATTATGAA 58.679 37.037 0.00 0.00 0.00 2.57
1769 1818 7.581464 GCACAGGAACATAGGGCTATATTATGA 60.581 40.741 0.00 0.00 0.00 2.15
1770 1819 6.540189 GCACAGGAACATAGGGCTATATTATG 59.460 42.308 0.00 0.00 0.00 1.90
1771 1820 6.445139 AGCACAGGAACATAGGGCTATATTAT 59.555 38.462 0.00 0.00 0.00 1.28
1772 1821 5.785423 AGCACAGGAACATAGGGCTATATTA 59.215 40.000 0.00 0.00 0.00 0.98
1773 1822 4.599241 AGCACAGGAACATAGGGCTATATT 59.401 41.667 0.00 0.00 0.00 1.28
1774 1823 4.171234 AGCACAGGAACATAGGGCTATAT 58.829 43.478 0.00 0.00 0.00 0.86
1775 1824 3.587498 AGCACAGGAACATAGGGCTATA 58.413 45.455 0.00 0.00 0.00 1.31
1776 1825 2.412591 AGCACAGGAACATAGGGCTAT 58.587 47.619 0.00 0.00 0.00 2.97
1777 1826 1.879575 AGCACAGGAACATAGGGCTA 58.120 50.000 0.00 0.00 0.00 3.93
1778 1827 0.995024 AAGCACAGGAACATAGGGCT 59.005 50.000 0.00 0.00 0.00 5.19
1779 1828 1.065126 AGAAGCACAGGAACATAGGGC 60.065 52.381 0.00 0.00 0.00 5.19
1784 1833 1.350351 AGCAGAGAAGCACAGGAACAT 59.650 47.619 0.00 0.00 36.85 2.71
1790 1839 1.275856 AGAAGGAGCAGAGAAGCACAG 59.724 52.381 0.00 0.00 36.85 3.66
1808 1857 4.157289 GCATTCAGAAATTGAGGAGCAAGA 59.843 41.667 0.00 0.00 40.42 3.02
1809 1858 4.082408 TGCATTCAGAAATTGAGGAGCAAG 60.082 41.667 0.00 0.00 40.42 4.01
1810 1859 3.827876 TGCATTCAGAAATTGAGGAGCAA 59.172 39.130 0.00 0.00 41.53 3.91
1811 1860 3.423749 TGCATTCAGAAATTGAGGAGCA 58.576 40.909 0.00 0.00 37.07 4.26
1812 1861 4.445452 TTGCATTCAGAAATTGAGGAGC 57.555 40.909 0.00 0.00 37.07 4.70
1813 1862 6.864342 AGAATTGCATTCAGAAATTGAGGAG 58.136 36.000 10.26 0.00 41.71 3.69
1814 1863 6.845758 AGAATTGCATTCAGAAATTGAGGA 57.154 33.333 10.26 0.00 41.71 3.71
1815 1864 7.541162 TGTAGAATTGCATTCAGAAATTGAGG 58.459 34.615 10.26 0.00 41.71 3.86
1845 1894 8.893560 TCATGAAGGGAGATGATGGAATTATAA 58.106 33.333 0.00 0.00 0.00 0.98
1848 1897 6.768641 TCATGAAGGGAGATGATGGAATTA 57.231 37.500 0.00 0.00 0.00 1.40
1850 1899 5.862422 ATCATGAAGGGAGATGATGGAAT 57.138 39.130 0.00 0.00 37.80 3.01
1851 1900 5.848369 AGTATCATGAAGGGAGATGATGGAA 59.152 40.000 0.00 0.00 39.23 3.53
1852 1901 5.247792 CAGTATCATGAAGGGAGATGATGGA 59.752 44.000 0.00 0.00 39.23 3.41
1853 1902 5.247792 TCAGTATCATGAAGGGAGATGATGG 59.752 44.000 0.00 0.00 39.23 3.51
1854 1903 6.356186 TCAGTATCATGAAGGGAGATGATG 57.644 41.667 0.00 0.00 39.23 3.07
1864 1922 5.390251 GCGCCAACATATCAGTATCATGAAG 60.390 44.000 0.00 0.00 31.76 3.02
1873 1931 2.483714 CCTGTAGCGCCAACATATCAGT 60.484 50.000 13.00 0.00 0.00 3.41
1883 1941 0.541392 ATTCACATCCTGTAGCGCCA 59.459 50.000 2.29 0.00 0.00 5.69
1884 1942 1.668419 AATTCACATCCTGTAGCGCC 58.332 50.000 2.29 0.00 0.00 6.53
1885 1943 3.764885 AAAATTCACATCCTGTAGCGC 57.235 42.857 0.00 0.00 0.00 5.92
1886 1944 4.414852 CCAAAAATTCACATCCTGTAGCG 58.585 43.478 0.00 0.00 0.00 4.26
1890 1955 3.586429 ACCCCAAAAATTCACATCCTGT 58.414 40.909 0.00 0.00 0.00 4.00
1896 1961 2.623889 CACCGTACCCCAAAAATTCACA 59.376 45.455 0.00 0.00 0.00 3.58
1902 1967 1.249407 GATGCACCGTACCCCAAAAA 58.751 50.000 0.00 0.00 0.00 1.94
1905 1970 1.780107 TTGGATGCACCGTACCCCAA 61.780 55.000 0.00 0.00 42.61 4.12
1911 1976 1.003112 GTGGGTTGGATGCACCGTA 60.003 57.895 0.00 0.00 42.61 4.02
1932 1997 0.473694 TCTTCAGGTGGGGAAGAGCA 60.474 55.000 0.99 0.00 44.21 4.26
1998 2063 1.138568 AGCTCATCCTAGGCATTGCT 58.861 50.000 2.96 8.53 0.00 3.91
2047 2113 6.373759 AGAAAGGGAAAAGGAACTGTAATGT 58.626 36.000 0.00 0.00 40.86 2.71
2052 2118 5.648330 ACTAGAAAGGGAAAAGGAACTGT 57.352 39.130 0.00 0.00 40.86 3.55
2078 2231 4.091365 CGTATCAGTCGAACTCAAAATGCA 59.909 41.667 0.00 0.00 0.00 3.96
2089 2242 2.251869 CGGAACACGTATCAGTCGAA 57.748 50.000 0.00 0.00 37.93 3.71
2110 2263 2.418628 GCTAGCCTGCAATGTTACGAAA 59.581 45.455 2.29 0.00 0.00 3.46
2112 2265 1.066502 TGCTAGCCTGCAATGTTACGA 60.067 47.619 13.29 0.00 40.29 3.43
2162 2315 4.838152 GCCGAGCTCCATCCGCAA 62.838 66.667 8.47 0.00 0.00 4.85
2288 2441 1.599071 CTGTCGTGTGCAACTGACATT 59.401 47.619 14.29 0.00 46.29 2.71
2293 2446 1.570813 TTCTCTGTCGTGTGCAACTG 58.429 50.000 0.00 0.00 38.04 3.16
2299 2452 3.902150 ACTGTGTATTCTCTGTCGTGTG 58.098 45.455 0.00 0.00 0.00 3.82
2300 2453 4.037565 TCAACTGTGTATTCTCTGTCGTGT 59.962 41.667 0.00 0.00 0.00 4.49
2301 2454 4.546570 TCAACTGTGTATTCTCTGTCGTG 58.453 43.478 0.00 0.00 0.00 4.35
2302 2455 4.848562 TCAACTGTGTATTCTCTGTCGT 57.151 40.909 0.00 0.00 0.00 4.34
2304 2457 7.658179 TCAAATCAACTGTGTATTCTCTGTC 57.342 36.000 0.00 0.00 0.00 3.51
2305 2458 8.627208 AATCAAATCAACTGTGTATTCTCTGT 57.373 30.769 0.00 0.00 0.00 3.41
2306 2459 8.944029 AGAATCAAATCAACTGTGTATTCTCTG 58.056 33.333 0.00 0.00 28.85 3.35
2308 2461 8.725148 ACAGAATCAAATCAACTGTGTATTCTC 58.275 33.333 0.00 0.00 39.76 2.87
2319 2474 7.742089 CGACAACTTCTACAGAATCAAATCAAC 59.258 37.037 0.00 0.00 33.01 3.18
2349 2504 6.682113 GCATGAGCATGGTTTGATTCTGTAAT 60.682 38.462 12.00 0.00 41.58 1.89
2383 2538 2.952783 GCCTGCATTTGCGCGATG 60.953 61.111 12.10 16.58 45.83 3.84
2384 2539 3.117175 GAGCCTGCATTTGCGCGAT 62.117 57.895 12.10 0.00 45.83 4.58
2385 2540 3.803082 GAGCCTGCATTTGCGCGA 61.803 61.111 12.10 0.00 45.83 5.87
2386 2541 4.105733 TGAGCCTGCATTTGCGCG 62.106 61.111 0.00 0.00 45.83 6.86
2387 2542 2.202570 CTGAGCCTGCATTTGCGC 60.203 61.111 0.00 0.00 45.83 6.09
2388 2543 2.338015 ACCTGAGCCTGCATTTGCG 61.338 57.895 0.00 0.00 45.83 4.85
2394 2549 4.025858 GCCTCACCTGAGCCTGCA 62.026 66.667 0.00 0.00 40.75 4.41
2408 2563 3.953775 CACCACCGGGAACAGCCT 61.954 66.667 6.32 0.00 38.05 4.58
2449 2604 2.795973 CAGACCGCGTCCACGATA 59.204 61.111 4.92 0.00 43.02 2.92
2508 2663 3.959991 GACCGCCAGAGGAACAGCC 62.960 68.421 0.00 0.00 34.73 4.85
2668 2823 2.403252 ACTCCCATTTGATGTCCGAC 57.597 50.000 0.00 0.00 0.00 4.79
2681 2836 2.430248 TCACGTAGCATCTACTCCCA 57.570 50.000 0.00 0.00 0.00 4.37
2758 2915 6.322456 CCATCCATCACTCTTCACTAGAACTA 59.678 42.308 0.00 0.00 30.91 2.24
2759 2916 5.128499 CCATCCATCACTCTTCACTAGAACT 59.872 44.000 0.00 0.00 30.91 3.01
2760 2917 5.105146 ACCATCCATCACTCTTCACTAGAAC 60.105 44.000 0.00 0.00 30.91 3.01
2763 2920 5.350504 AACCATCCATCACTCTTCACTAG 57.649 43.478 0.00 0.00 0.00 2.57
2764 2921 5.013079 ACAAACCATCCATCACTCTTCACTA 59.987 40.000 0.00 0.00 0.00 2.74
2806 2963 9.409949 GAAACAAAATCATACTTAGTTCGATCG 57.590 33.333 9.36 9.36 0.00 3.69
2839 2996 9.401058 TGAGAGATTCAAAAGAAGAGAGTTTTT 57.599 29.630 0.00 0.00 31.34 1.94
2866 3023 7.610865 TCAAAAGAATGGAGTTTTCTTGTTGT 58.389 30.769 0.00 0.00 41.38 3.32
2882 3047 5.617751 CGCGAGAACTTCCATTCAAAAGAAT 60.618 40.000 0.00 0.00 0.00 2.40
2900 3065 3.060020 CTAAACCCGGAGCGCGAGA 62.060 63.158 12.10 0.00 0.00 4.04
2919 3084 9.956720 CACTGTGAACAAATCTTCTTTCTAATT 57.043 29.630 0.32 0.00 0.00 1.40
2920 3085 8.078596 GCACTGTGAACAAATCTTCTTTCTAAT 58.921 33.333 12.86 0.00 0.00 1.73
2944 3109 0.542467 ACACCCATCCATTTGCAGCA 60.542 50.000 0.00 0.00 0.00 4.41
2982 3147 2.920076 TTTTGGTGTGCGAGGGGCTT 62.920 55.000 0.00 0.00 44.05 4.35
3039 3217 2.983136 GTGAGCATCGTCGATATTGGAG 59.017 50.000 7.56 0.00 38.61 3.86
3062 3240 0.580578 CGCATGCACAGAGCTATCAC 59.419 55.000 19.57 0.00 45.94 3.06
3064 3242 1.839598 GCCGCATGCACAGAGCTATC 61.840 60.000 19.57 0.00 45.94 2.08
3261 3465 2.771943 CAGTGTGTGTATCCCCTACCAT 59.228 50.000 0.00 0.00 0.00 3.55
3262 3466 2.184533 CAGTGTGTGTATCCCCTACCA 58.815 52.381 0.00 0.00 0.00 3.25
3263 3467 1.134491 GCAGTGTGTGTATCCCCTACC 60.134 57.143 0.00 0.00 0.00 3.18
3265 3469 1.945580 TGCAGTGTGTGTATCCCCTA 58.054 50.000 0.00 0.00 0.00 3.53
3266 3470 1.064003 TTGCAGTGTGTGTATCCCCT 58.936 50.000 0.00 0.00 0.00 4.79
3267 3471 1.904287 TTTGCAGTGTGTGTATCCCC 58.096 50.000 0.00 0.00 0.00 4.81
3268 3472 3.119495 GGATTTTGCAGTGTGTGTATCCC 60.119 47.826 0.00 0.00 0.00 3.85
3270 3474 4.475944 GTGGATTTTGCAGTGTGTGTATC 58.524 43.478 0.00 0.00 0.00 2.24
3271 3475 3.255642 GGTGGATTTTGCAGTGTGTGTAT 59.744 43.478 0.00 0.00 0.00 2.29
3272 3476 2.621055 GGTGGATTTTGCAGTGTGTGTA 59.379 45.455 0.00 0.00 0.00 2.90
3273 3477 1.408702 GGTGGATTTTGCAGTGTGTGT 59.591 47.619 0.00 0.00 0.00 3.72
3288 3503 2.525629 TCCTTGCCGACAGGTGGA 60.526 61.111 0.00 0.00 40.50 4.02
3289 3504 2.358737 GTCCTTGCCGACAGGTGG 60.359 66.667 0.00 0.00 40.50 4.61
3290 3505 2.738521 CGTCCTTGCCGACAGGTG 60.739 66.667 0.00 0.00 40.50 4.00
3367 3582 1.153389 GAGGAAGAGCAGGAGCAGC 60.153 63.158 0.00 0.00 45.49 5.25
3374 3589 4.168291 GGGCGGGAGGAAGAGCAG 62.168 72.222 0.00 0.00 0.00 4.24
3407 3622 2.646175 CGAGGAAGGAGGCGGTGAA 61.646 63.158 0.00 0.00 0.00 3.18
3507 3722 4.673441 AGAGACGTATGCTGTGATGTAAC 58.327 43.478 0.00 0.00 0.00 2.50
3514 3729 1.202348 CCTGGAGAGACGTATGCTGTG 60.202 57.143 0.00 0.00 0.00 3.66
3516 3731 1.066303 GTCCTGGAGAGACGTATGCTG 59.934 57.143 0.00 0.00 0.00 4.41
3536 3754 5.235186 CCGTATAGAAAAGGTGAAGCATCTG 59.765 44.000 0.00 0.00 0.00 2.90
3568 3835 7.254795 GCTACACACACAAACAAGAAACTAGAT 60.255 37.037 0.00 0.00 0.00 1.98
3569 3836 6.036735 GCTACACACACAAACAAGAAACTAGA 59.963 38.462 0.00 0.00 0.00 2.43


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

AutoCloner maintained by Alex Coulton.