Multiple sequence alignment - TraesCS2D01G544400

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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 TraesCS2D01G544400 chr2D 100.000 4310 0 0 1 4310 621561559 621557250 0.000000e+00 7960.0
1 TraesCS2D01G544400 chr2D 78.067 1076 225 7 2052 3126 318338439 318337374 0.000000e+00 669.0
2 TraesCS2D01G544400 chr2D 75.507 641 139 15 1068 1696 318340222 318339588 9.060000e-77 298.0
3 TraesCS2D01G544400 chr2D 74.443 763 148 32 14 759 8475644 8476376 7.050000e-73 285.0
4 TraesCS2D01G544400 chr2D 100.000 34 0 0 3741 3774 621557727 621557694 3.600000e-06 63.9
5 TraesCS2D01G544400 chr2D 100.000 34 0 0 3833 3866 621557819 621557786 3.600000e-06 63.9
6 TraesCS2D01G544400 chr2B 96.015 1907 50 10 1813 3693 762520063 762518157 0.000000e+00 3077.0
7 TraesCS2D01G544400 chr2B 96.033 1336 38 3 1890 3216 762533358 762532029 0.000000e+00 2159.0
8 TraesCS2D01G544400 chr2B 92.737 895 37 8 881 1758 762520961 762520078 0.000000e+00 1267.0
9 TraesCS2D01G544400 chr2B 92.956 866 30 6 908 1758 762537243 762536394 0.000000e+00 1232.0
10 TraesCS2D01G544400 chr2B 94.023 619 29 6 3696 4310 762517998 762517384 0.000000e+00 931.0
11 TraesCS2D01G544400 chr2B 77.530 1077 229 9 2052 3126 386314627 386313562 1.690000e-178 636.0
12 TraesCS2D01G544400 chr2B 75.663 641 140 14 1067 1696 386316412 386315777 5.410000e-79 305.0
13 TraesCS2D01G544400 chr2B 83.540 322 49 4 220 537 762521284 762520963 9.060000e-77 298.0
14 TraesCS2D01G544400 chr2B 90.291 103 6 2 1813 1911 762536379 762536277 9.730000e-27 132.0
15 TraesCS2D01G544400 chr2B 100.000 34 0 0 3741 3774 762517859 762517826 3.600000e-06 63.9
16 TraesCS2D01G544400 chr5A 85.788 1555 187 21 1859 3383 622782493 622780943 0.000000e+00 1616.0
17 TraesCS2D01G544400 chr5A 90.944 784 50 7 994 1756 622783343 622782560 0.000000e+00 1035.0
18 TraesCS2D01G544400 chr5B 85.536 1521 205 11 1859 3366 617833999 617832481 0.000000e+00 1576.0
19 TraesCS2D01G544400 chr5B 89.734 526 23 5 995 1489 617836290 617835765 1.010000e-180 643.0
20 TraesCS2D01G544400 chr5B 93.981 216 13 0 1481 1696 617834318 617834103 1.160000e-85 327.0
21 TraesCS2D01G544400 chr5D 83.490 1593 197 31 1808 3383 498556253 498554710 0.000000e+00 1424.0
22 TraesCS2D01G544400 chr5D 90.875 789 46 11 994 1758 498557049 498556263 0.000000e+00 1035.0
23 TraesCS2D01G544400 chr5D 75.000 560 101 25 216 759 435992377 435991841 5.610000e-54 222.0
24 TraesCS2D01G544400 chr5D 76.126 444 77 18 338 765 364231465 364231035 5.650000e-49 206.0
25 TraesCS2D01G544400 chr5D 73.333 525 121 16 1184 1696 84787593 84788110 4.430000e-40 176.0
26 TraesCS2D01G544400 chr3A 92.089 493 31 7 3820 4310 53226737 53227223 0.000000e+00 688.0
27 TraesCS2D01G544400 chr3A 97.297 37 1 0 3738 3774 53226747 53226783 3.600000e-06 63.9
28 TraesCS2D01G544400 chr2A 78.102 1064 222 7 2052 3114 413324006 413325059 0.000000e+00 664.0
29 TraesCS2D01G544400 chr2A 75.194 645 142 14 1064 1696 413322131 413322769 5.450000e-74 289.0
30 TraesCS2D01G544400 chr2A 77.925 453 73 17 12 461 83994138 83994566 1.540000e-64 257.0
31 TraesCS2D01G544400 chr3D 82.219 793 115 13 1 774 48792798 48793583 0.000000e+00 660.0
32 TraesCS2D01G544400 chr3D 79.198 798 130 17 1 781 133918972 133919750 4.940000e-144 521.0
33 TraesCS2D01G544400 chr3D 77.597 799 153 21 23 807 550250515 550249729 1.090000e-125 460.0
34 TraesCS2D01G544400 chr3D 75.773 776 140 30 15 780 337246622 337247359 8.870000e-92 348.0
35 TraesCS2D01G544400 chr7A 79.975 794 125 17 3 774 610457512 610456731 4.870000e-154 555.0
36 TraesCS2D01G544400 chr3B 78.320 738 129 16 59 773 825865795 825865066 8.500000e-122 448.0
37 TraesCS2D01G544400 chr3B 92.164 268 19 2 4045 4310 800670350 800670617 1.130000e-100 377.0
38 TraesCS2D01G544400 chr4B 76.020 784 159 23 25 795 419611510 419610743 3.150000e-101 379.0
39 TraesCS2D01G544400 chr4D 75.945 794 133 39 23 800 46196741 46195990 5.300000e-94 355.0
40 TraesCS2D01G544400 chrUn 77.044 636 118 13 155 769 37098987 37099615 1.480000e-89 340.0
41 TraesCS2D01G544400 chrUn 75.733 750 140 26 12 738 86618399 86619129 5.340000e-89 339.0
42 TraesCS2D01G544400 chr6D 77.951 576 104 20 241 804 1426724 1427288 5.340000e-89 339.0
43 TraesCS2D01G544400 chr6D 79.193 322 56 8 353 667 84636522 84636205 3.380000e-51 213.0
44 TraesCS2D01G544400 chr6B 76.149 696 131 30 124 804 685708165 685707490 2.480000e-87 333.0
45 TraesCS2D01G544400 chr6B 86.387 191 23 3 593 781 16516930 16517119 5.650000e-49 206.0
46 TraesCS2D01G544400 chr7D 79.800 401 70 6 1 400 436494662 436495052 9.130000e-72 281.0
47 TraesCS2D01G544400 chr7D 74.449 771 130 48 23 750 136858361 136859107 1.980000e-68 270.0
48 TraesCS2D01G544400 chr4A 73.529 748 151 27 24 752 597056694 597055975 1.550000e-59 241.0
49 TraesCS2D01G544400 chr7B 78.371 356 68 7 12 365 693170413 693170761 5.610000e-54 222.0
50 TraesCS2D01G544400 chr7B 75.113 442 85 20 348 777 36857365 36857793 2.650000e-42 183.0
51 TraesCS2D01G544400 chr7B 71.591 528 130 16 1182 1696 454620944 454620424 4.520000e-25 126.0
52 TraesCS2D01G544400 chr1D 86.813 91 11 1 697 786 5433140 5433050 2.740000e-17 100.0


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 TraesCS2D01G544400 chr2D 621557250 621561559 4309 True 2695.933333 7960 100.000000 1 4310 3 chr2D.!!$R2 4309
1 TraesCS2D01G544400 chr2D 318337374 318340222 2848 True 483.500000 669 76.787000 1068 3126 2 chr2D.!!$R1 2058
2 TraesCS2D01G544400 chr2D 8475644 8476376 732 False 285.000000 285 74.443000 14 759 1 chr2D.!!$F1 745
3 TraesCS2D01G544400 chr2B 762532029 762537243 5214 True 1174.333333 2159 93.093333 908 3216 3 chr2B.!!$R3 2308
4 TraesCS2D01G544400 chr2B 762517384 762521284 3900 True 1127.380000 3077 93.263000 220 4310 5 chr2B.!!$R2 4090
5 TraesCS2D01G544400 chr2B 386313562 386316412 2850 True 470.500000 636 76.596500 1067 3126 2 chr2B.!!$R1 2059
6 TraesCS2D01G544400 chr5A 622780943 622783343 2400 True 1325.500000 1616 88.366000 994 3383 2 chr5A.!!$R1 2389
7 TraesCS2D01G544400 chr5B 617832481 617836290 3809 True 848.666667 1576 89.750333 995 3366 3 chr5B.!!$R1 2371
8 TraesCS2D01G544400 chr5D 498554710 498557049 2339 True 1229.500000 1424 87.182500 994 3383 2 chr5D.!!$R3 2389
9 TraesCS2D01G544400 chr5D 435991841 435992377 536 True 222.000000 222 75.000000 216 759 1 chr5D.!!$R2 543
10 TraesCS2D01G544400 chr2A 413322131 413325059 2928 False 476.500000 664 76.648000 1064 3114 2 chr2A.!!$F2 2050
11 TraesCS2D01G544400 chr3D 48792798 48793583 785 False 660.000000 660 82.219000 1 774 1 chr3D.!!$F1 773
12 TraesCS2D01G544400 chr3D 133918972 133919750 778 False 521.000000 521 79.198000 1 781 1 chr3D.!!$F2 780
13 TraesCS2D01G544400 chr3D 550249729 550250515 786 True 460.000000 460 77.597000 23 807 1 chr3D.!!$R1 784
14 TraesCS2D01G544400 chr3D 337246622 337247359 737 False 348.000000 348 75.773000 15 780 1 chr3D.!!$F3 765
15 TraesCS2D01G544400 chr7A 610456731 610457512 781 True 555.000000 555 79.975000 3 774 1 chr7A.!!$R1 771
16 TraesCS2D01G544400 chr3B 825865066 825865795 729 True 448.000000 448 78.320000 59 773 1 chr3B.!!$R1 714
17 TraesCS2D01G544400 chr4B 419610743 419611510 767 True 379.000000 379 76.020000 25 795 1 chr4B.!!$R1 770
18 TraesCS2D01G544400 chr4D 46195990 46196741 751 True 355.000000 355 75.945000 23 800 1 chr4D.!!$R1 777
19 TraesCS2D01G544400 chrUn 37098987 37099615 628 False 340.000000 340 77.044000 155 769 1 chrUn.!!$F1 614
20 TraesCS2D01G544400 chrUn 86618399 86619129 730 False 339.000000 339 75.733000 12 738 1 chrUn.!!$F2 726
21 TraesCS2D01G544400 chr6D 1426724 1427288 564 False 339.000000 339 77.951000 241 804 1 chr6D.!!$F1 563
22 TraesCS2D01G544400 chr6B 685707490 685708165 675 True 333.000000 333 76.149000 124 804 1 chr6B.!!$R1 680
23 TraesCS2D01G544400 chr7D 136858361 136859107 746 False 270.000000 270 74.449000 23 750 1 chr7D.!!$F1 727
24 TraesCS2D01G544400 chr4A 597055975 597056694 719 True 241.000000 241 73.529000 24 752 1 chr4A.!!$R1 728

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
859 967 0.036388 CCGGCCGTGGATGCTTATAT 60.036 55.000 26.12 0.0 0.0 0.86 F
896 1004 0.340208 GAAGGAGAAGGGAGAGGGGA 59.660 60.000 0.00 0.0 0.0 4.81 F
897 1005 0.800239 AAGGAGAAGGGAGAGGGGAA 59.200 55.000 0.00 0.0 0.0 3.97 F
997 1105 0.813210 CTTCCCGAGCAGAGCCATTC 60.813 60.000 0.00 0.0 0.0 2.67 F
1026 1134 1.004745 CCTTGGGCCTTGCTCTTTCTA 59.995 52.381 4.53 0.0 0.0 2.10 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1769 3692 1.890489 TGTCGCTACCTTGTAGAAGCA 59.110 47.619 5.48 0.00 34.60 3.91 R
2567 7955 1.896220 ATGAACAACACCTGCGTCAT 58.104 45.000 0.00 0.00 31.36 3.06 R
2893 8281 2.348998 CACAGGAGCACCAGGGTC 59.651 66.667 2.07 0.00 43.35 4.46 R
2976 8364 0.602905 GCGGGAATATGGGGACTTCG 60.603 60.000 0.00 0.00 0.00 3.79 R
3370 8774 2.491675 ACTTTAGTTGGTGCCTAGGC 57.508 50.000 27.71 27.71 42.35 3.93 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
46 47 0.603569 GTCGACTGTGGTGTCATCCT 59.396 55.000 8.70 0.00 36.82 3.24
133 136 2.483491 GACCGACTACGAGATATGTCCC 59.517 54.545 0.00 0.00 42.66 4.46
184 190 3.531207 CAGATCCTCCGGCGCTGA 61.531 66.667 20.25 9.02 0.00 4.26
197 203 1.878069 CGCTGAATCATCGCCGTCA 60.878 57.895 0.00 0.00 0.00 4.35
261 275 2.599677 GGAGTATGAGTCCTACCAGGG 58.400 57.143 2.30 0.00 34.81 4.45
264 278 0.941963 TATGAGTCCTACCAGGGCCT 59.058 55.000 0.00 0.00 42.20 5.19
290 304 2.060980 CGTCCTGGGAAGGAGAGGG 61.061 68.421 0.00 0.00 38.88 4.30
373 408 4.463879 CGGGCTGCCACAGAGGAG 62.464 72.222 22.05 0.00 41.22 3.69
419 454 2.031163 GGCAGCAGAGGAACACGT 59.969 61.111 0.00 0.00 0.00 4.49
481 520 1.196104 CCGGACTACCCACCCAAGAA 61.196 60.000 0.00 0.00 34.14 2.52
494 549 1.557371 CCCAAGAAGGAGAAGGAGGAC 59.443 57.143 0.00 0.00 41.22 3.85
497 552 2.903135 CAAGAAGGAGAAGGAGGACAGT 59.097 50.000 0.00 0.00 0.00 3.55
553 626 1.858091 CTCGATCCATACTGCGCTTT 58.142 50.000 9.73 0.00 0.00 3.51
554 627 2.205074 CTCGATCCATACTGCGCTTTT 58.795 47.619 9.73 0.00 0.00 2.27
556 629 3.787785 TCGATCCATACTGCGCTTTTAA 58.212 40.909 9.73 0.00 0.00 1.52
648 738 9.429359 CATGTAGGTAAAACATGCCAAATTTTA 57.571 29.630 3.51 0.00 45.43 1.52
769 877 5.677319 TTGAGATTCCGGTTATGAGAAGT 57.323 39.130 0.00 0.00 0.00 3.01
782 890 7.095229 CGGTTATGAGAAGTGAAATTTGAGACA 60.095 37.037 0.00 0.00 0.00 3.41
790 898 5.491070 AGTGAAATTTGAGACATGATCGGA 58.509 37.500 0.00 0.00 0.00 4.55
823 931 0.592637 TGCGTCTGTGCATTTGAAGG 59.407 50.000 0.00 0.00 40.62 3.46
824 932 0.593128 GCGTCTGTGCATTTGAAGGT 59.407 50.000 0.00 0.00 34.15 3.50
825 933 1.400242 GCGTCTGTGCATTTGAAGGTC 60.400 52.381 0.00 0.00 34.15 3.85
826 934 1.197721 CGTCTGTGCATTTGAAGGTCC 59.802 52.381 0.00 0.00 0.00 4.46
827 935 2.229792 GTCTGTGCATTTGAAGGTCCA 58.770 47.619 0.00 0.00 0.00 4.02
828 936 2.227388 GTCTGTGCATTTGAAGGTCCAG 59.773 50.000 0.00 0.00 0.00 3.86
829 937 2.106338 TCTGTGCATTTGAAGGTCCAGA 59.894 45.455 0.00 0.00 0.00 3.86
830 938 3.087031 CTGTGCATTTGAAGGTCCAGAT 58.913 45.455 0.00 0.00 0.00 2.90
831 939 3.499338 TGTGCATTTGAAGGTCCAGATT 58.501 40.909 0.00 0.00 0.00 2.40
832 940 3.896888 TGTGCATTTGAAGGTCCAGATTT 59.103 39.130 0.00 0.00 0.00 2.17
833 941 4.240096 GTGCATTTGAAGGTCCAGATTTG 58.760 43.478 0.00 0.00 0.00 2.32
834 942 4.022068 GTGCATTTGAAGGTCCAGATTTGA 60.022 41.667 0.00 0.00 0.00 2.69
835 943 4.022068 TGCATTTGAAGGTCCAGATTTGAC 60.022 41.667 0.00 0.00 0.00 3.18
836 944 4.022068 GCATTTGAAGGTCCAGATTTGACA 60.022 41.667 0.00 0.00 34.36 3.58
837 945 5.509501 GCATTTGAAGGTCCAGATTTGACAA 60.510 40.000 0.00 0.00 34.36 3.18
838 946 5.772825 TTTGAAGGTCCAGATTTGACAAG 57.227 39.130 0.00 0.00 34.36 3.16
839 947 4.437682 TGAAGGTCCAGATTTGACAAGT 57.562 40.909 0.00 0.00 34.36 3.16
840 948 4.389374 TGAAGGTCCAGATTTGACAAGTC 58.611 43.478 2.59 2.59 34.36 3.01
841 949 3.425162 AGGTCCAGATTTGACAAGTCC 57.575 47.619 7.05 0.00 34.36 3.85
842 950 2.076863 GGTCCAGATTTGACAAGTCCG 58.923 52.381 7.05 0.00 34.36 4.79
843 951 2.076863 GTCCAGATTTGACAAGTCCGG 58.923 52.381 6.62 6.62 32.91 5.14
844 952 0.804989 CCAGATTTGACAAGTCCGGC 59.195 55.000 7.05 0.00 0.00 6.13
845 953 0.804989 CAGATTTGACAAGTCCGGCC 59.195 55.000 7.05 0.00 0.00 6.13
846 954 0.673644 AGATTTGACAAGTCCGGCCG 60.674 55.000 21.04 21.04 0.00 6.13
847 955 0.953960 GATTTGACAAGTCCGGCCGT 60.954 55.000 26.12 3.22 0.00 5.68
848 956 1.234615 ATTTGACAAGTCCGGCCGTG 61.235 55.000 26.12 18.26 0.00 4.94
849 957 3.818121 TTGACAAGTCCGGCCGTGG 62.818 63.158 26.12 10.11 0.00 4.94
850 958 3.998672 GACAAGTCCGGCCGTGGA 61.999 66.667 26.12 12.73 35.04 4.02
851 959 3.310860 GACAAGTCCGGCCGTGGAT 62.311 63.158 26.12 4.46 40.91 3.41
852 960 2.819595 CAAGTCCGGCCGTGGATG 60.820 66.667 26.12 13.86 40.91 3.51
853 961 4.778143 AAGTCCGGCCGTGGATGC 62.778 66.667 26.12 7.05 40.91 3.91
855 963 4.778143 GTCCGGCCGTGGATGCTT 62.778 66.667 26.12 0.00 40.91 3.91
856 964 3.078196 TCCGGCCGTGGATGCTTA 61.078 61.111 26.12 0.00 31.53 3.09
857 965 2.111043 CCGGCCGTGGATGCTTAT 59.889 61.111 26.12 0.00 0.00 1.73
858 966 1.116536 TCCGGCCGTGGATGCTTATA 61.117 55.000 26.12 0.00 31.53 0.98
859 967 0.036388 CCGGCCGTGGATGCTTATAT 60.036 55.000 26.12 0.00 0.00 0.86
860 968 1.078709 CGGCCGTGGATGCTTATATG 58.921 55.000 19.50 0.00 0.00 1.78
861 969 1.337728 CGGCCGTGGATGCTTATATGA 60.338 52.381 19.50 0.00 0.00 2.15
862 970 2.778299 GGCCGTGGATGCTTATATGAA 58.222 47.619 0.00 0.00 0.00 2.57
863 971 3.146066 GGCCGTGGATGCTTATATGAAA 58.854 45.455 0.00 0.00 0.00 2.69
864 972 3.568007 GGCCGTGGATGCTTATATGAAAA 59.432 43.478 0.00 0.00 0.00 2.29
865 973 4.320494 GGCCGTGGATGCTTATATGAAAAG 60.320 45.833 0.00 0.00 0.00 2.27
866 974 4.320494 GCCGTGGATGCTTATATGAAAAGG 60.320 45.833 0.00 0.00 0.00 3.11
867 975 4.216257 CCGTGGATGCTTATATGAAAAGGG 59.784 45.833 0.00 0.00 0.00 3.95
868 976 5.063204 CGTGGATGCTTATATGAAAAGGGA 58.937 41.667 0.00 0.00 0.00 4.20
869 977 5.530915 CGTGGATGCTTATATGAAAAGGGAA 59.469 40.000 0.00 0.00 0.00 3.97
870 978 6.293626 CGTGGATGCTTATATGAAAAGGGAAG 60.294 42.308 0.00 0.00 0.00 3.46
871 979 6.015940 GTGGATGCTTATATGAAAAGGGAAGG 60.016 42.308 0.00 0.00 0.00 3.46
872 980 6.126215 TGGATGCTTATATGAAAAGGGAAGGA 60.126 38.462 0.00 0.00 0.00 3.36
873 981 6.777580 GGATGCTTATATGAAAAGGGAAGGAA 59.222 38.462 0.00 0.00 0.00 3.36
874 982 7.287696 GGATGCTTATATGAAAAGGGAAGGAAA 59.712 37.037 0.00 0.00 0.00 3.13
875 983 7.645058 TGCTTATATGAAAAGGGAAGGAAAG 57.355 36.000 0.00 0.00 0.00 2.62
876 984 7.410174 TGCTTATATGAAAAGGGAAGGAAAGA 58.590 34.615 0.00 0.00 0.00 2.52
877 985 7.557719 TGCTTATATGAAAAGGGAAGGAAAGAG 59.442 37.037 0.00 0.00 0.00 2.85
878 986 7.775561 GCTTATATGAAAAGGGAAGGAAAGAGA 59.224 37.037 0.00 0.00 0.00 3.10
879 987 9.686683 CTTATATGAAAAGGGAAGGAAAGAGAA 57.313 33.333 0.00 0.00 0.00 2.87
880 988 9.686683 TTATATGAAAAGGGAAGGAAAGAGAAG 57.313 33.333 0.00 0.00 0.00 2.85
881 989 4.729868 TGAAAAGGGAAGGAAAGAGAAGG 58.270 43.478 0.00 0.00 0.00 3.46
882 990 4.415512 TGAAAAGGGAAGGAAAGAGAAGGA 59.584 41.667 0.00 0.00 0.00 3.36
883 991 4.649267 AAAGGGAAGGAAAGAGAAGGAG 57.351 45.455 0.00 0.00 0.00 3.69
884 992 3.569135 AGGGAAGGAAAGAGAAGGAGA 57.431 47.619 0.00 0.00 0.00 3.71
885 993 3.875571 AGGGAAGGAAAGAGAAGGAGAA 58.124 45.455 0.00 0.00 0.00 2.87
886 994 3.843619 AGGGAAGGAAAGAGAAGGAGAAG 59.156 47.826 0.00 0.00 0.00 2.85
887 995 3.054728 GGGAAGGAAAGAGAAGGAGAAGG 60.055 52.174 0.00 0.00 0.00 3.46
888 996 3.054728 GGAAGGAAAGAGAAGGAGAAGGG 60.055 52.174 0.00 0.00 0.00 3.95
889 997 3.569135 AGGAAAGAGAAGGAGAAGGGA 57.431 47.619 0.00 0.00 0.00 4.20
890 998 3.449918 AGGAAAGAGAAGGAGAAGGGAG 58.550 50.000 0.00 0.00 0.00 4.30
891 999 3.078305 AGGAAAGAGAAGGAGAAGGGAGA 59.922 47.826 0.00 0.00 0.00 3.71
892 1000 3.450817 GGAAAGAGAAGGAGAAGGGAGAG 59.549 52.174 0.00 0.00 0.00 3.20
893 1001 2.846665 AGAGAAGGAGAAGGGAGAGG 57.153 55.000 0.00 0.00 0.00 3.69
894 1002 1.290732 AGAGAAGGAGAAGGGAGAGGG 59.709 57.143 0.00 0.00 0.00 4.30
895 1003 0.341609 AGAAGGAGAAGGGAGAGGGG 59.658 60.000 0.00 0.00 0.00 4.79
896 1004 0.340208 GAAGGAGAAGGGAGAGGGGA 59.660 60.000 0.00 0.00 0.00 4.81
897 1005 0.800239 AAGGAGAAGGGAGAGGGGAA 59.200 55.000 0.00 0.00 0.00 3.97
898 1006 0.800239 AGGAGAAGGGAGAGGGGAAA 59.200 55.000 0.00 0.00 0.00 3.13
899 1007 1.208706 GGAGAAGGGAGAGGGGAAAG 58.791 60.000 0.00 0.00 0.00 2.62
900 1008 1.556002 GGAGAAGGGAGAGGGGAAAGT 60.556 57.143 0.00 0.00 0.00 2.66
901 1009 2.292984 GGAGAAGGGAGAGGGGAAAGTA 60.293 54.545 0.00 0.00 0.00 2.24
902 1010 3.451890 GAGAAGGGAGAGGGGAAAGTAA 58.548 50.000 0.00 0.00 0.00 2.24
903 1011 3.452990 GAGAAGGGAGAGGGGAAAGTAAG 59.547 52.174 0.00 0.00 0.00 2.34
904 1012 1.585895 AGGGAGAGGGGAAAGTAAGC 58.414 55.000 0.00 0.00 0.00 3.09
905 1013 1.081343 AGGGAGAGGGGAAAGTAAGCT 59.919 52.381 0.00 0.00 0.00 3.74
906 1014 1.210722 GGGAGAGGGGAAAGTAAGCTG 59.789 57.143 0.00 0.00 0.00 4.24
951 1059 4.021104 TGAGTCAACTGAACTCGGATGAAT 60.021 41.667 0.53 0.00 36.10 2.57
953 1061 3.304559 GTCAACTGAACTCGGATGAATCG 59.695 47.826 0.53 0.00 36.10 3.34
964 1072 1.593006 GGATGAATCGCGATCGTGTTT 59.407 47.619 23.92 23.78 36.96 2.83
976 1084 4.326278 GCGATCGTGTTTAAACTGATCTGA 59.674 41.667 29.97 17.33 38.34 3.27
977 1085 5.499334 GCGATCGTGTTTAAACTGATCTGAG 60.499 44.000 29.97 22.57 38.34 3.35
997 1105 0.813210 CTTCCCGAGCAGAGCCATTC 60.813 60.000 0.00 0.00 0.00 2.67
1026 1134 1.004745 CCTTGGGCCTTGCTCTTTCTA 59.995 52.381 4.53 0.00 0.00 2.10
1349 1475 3.726517 GCGCGTTGACCAGCATGT 61.727 61.111 8.43 0.00 0.00 3.21
1548 3157 3.068691 CGCGAGGAGGAGTGGGAA 61.069 66.667 0.00 0.00 0.00 3.97
1575 3184 4.570663 GCGGAGGCGAGCACGTAT 62.571 66.667 5.23 0.00 41.98 3.06
1657 3266 2.158959 GTCTTCGACGGCGTCATGG 61.159 63.158 35.62 24.05 38.98 3.66
1711 3322 1.180029 GGTAGCGACCTGGTGAACTA 58.820 55.000 2.82 0.00 43.16 2.24
1758 3681 8.463930 TGTGATCTGAAAGTTTTATTTCCAGT 57.536 30.769 0.00 0.00 38.21 4.00
1759 3682 9.567776 TGTGATCTGAAAGTTTTATTTCCAGTA 57.432 29.630 0.00 0.00 38.21 2.74
1760 3683 9.827411 GTGATCTGAAAGTTTTATTTCCAGTAC 57.173 33.333 0.00 0.00 38.21 2.73
1761 3684 9.793259 TGATCTGAAAGTTTTATTTCCAGTACT 57.207 29.630 0.00 0.00 38.21 2.73
1775 3698 7.817418 TTTCCAGTACTAATTTTGTGCTTCT 57.183 32.000 0.00 0.00 0.00 2.85
1777 3700 7.900782 TCCAGTACTAATTTTGTGCTTCTAC 57.099 36.000 0.00 0.00 0.00 2.59
1779 3702 7.934665 TCCAGTACTAATTTTGTGCTTCTACAA 59.065 33.333 0.00 0.00 38.69 2.41
1780 3703 8.230486 CCAGTACTAATTTTGTGCTTCTACAAG 58.770 37.037 0.00 0.00 41.18 3.16
1781 3704 8.230486 CAGTACTAATTTTGTGCTTCTACAAGG 58.770 37.037 0.00 0.00 41.18 3.61
1782 3705 7.937394 AGTACTAATTTTGTGCTTCTACAAGGT 59.063 33.333 0.00 0.00 41.18 3.50
1786 3709 2.363788 TGTGCTTCTACAAGGTAGCG 57.636 50.000 0.00 0.00 36.43 4.26
1787 3710 1.890489 TGTGCTTCTACAAGGTAGCGA 59.110 47.619 0.00 0.00 36.43 4.93
1788 3711 2.260481 GTGCTTCTACAAGGTAGCGAC 58.740 52.381 0.00 0.00 36.43 5.19
1789 3712 1.890489 TGCTTCTACAAGGTAGCGACA 59.110 47.619 0.00 0.00 36.43 4.35
1797 3720 3.933155 CAAGGTAGCGACATTGTGATC 57.067 47.619 15.03 0.00 41.39 2.92
1798 3721 3.525537 CAAGGTAGCGACATTGTGATCT 58.474 45.455 15.03 0.00 41.39 2.75
1799 3722 4.682787 CAAGGTAGCGACATTGTGATCTA 58.317 43.478 15.03 0.00 41.39 1.98
1800 3723 5.109210 CAAGGTAGCGACATTGTGATCTAA 58.891 41.667 15.03 0.00 41.39 2.10
1802 3725 5.918608 AGGTAGCGACATTGTGATCTAATT 58.081 37.500 0.00 0.00 0.00 1.40
1803 3726 6.349300 AGGTAGCGACATTGTGATCTAATTT 58.651 36.000 0.00 0.00 0.00 1.82
1805 3728 6.907212 GGTAGCGACATTGTGATCTAATTTTG 59.093 38.462 0.00 0.00 0.00 2.44
1806 3729 6.500684 AGCGACATTGTGATCTAATTTTGT 57.499 33.333 0.00 0.00 0.00 2.83
1840 3842 9.482627 GTCTGAAATCCTAGTTTATGATGTAGG 57.517 37.037 0.00 0.00 34.42 3.18
1842 3844 9.703892 CTGAAATCCTAGTTTATGATGTAGGAG 57.296 37.037 3.51 0.00 43.38 3.69
1969 7346 9.507329 TTTTCATAGCTCATAGTTTCAAGTTCT 57.493 29.630 0.00 0.00 0.00 3.01
1994 7373 4.581824 ACCATAATGAGCATCCAACATCAC 59.418 41.667 0.00 0.00 0.00 3.06
2003 7382 1.838112 TCCAACATCACCAGCATTCC 58.162 50.000 0.00 0.00 0.00 3.01
2040 7422 7.294720 TCCATCCTATACCACATTCACCTAATT 59.705 37.037 0.00 0.00 0.00 1.40
2334 7717 4.097892 GCGTGGTTATGGGATCATTTCTTT 59.902 41.667 0.00 0.00 34.96 2.52
2567 7955 3.979347 ACCCGGAATCTCTACTACTCCTA 59.021 47.826 0.73 0.00 0.00 2.94
2893 8281 1.081376 ACTTCGTCGAGCTTCGTGG 60.081 57.895 0.00 0.00 41.35 4.94
2976 8364 3.391382 CCGAGACCTGACCACCCC 61.391 72.222 0.00 0.00 0.00 4.95
3370 8774 8.420374 TCTTTCTTTTACACTGTAACAGAGTG 57.580 34.615 14.54 11.04 45.39 3.51
3414 8818 9.783256 GTATCTACGGTTTTGCTAATTTTCATT 57.217 29.630 0.00 0.00 0.00 2.57
3466 8870 2.642139 TGTGTCCGTTCGATCCTTAC 57.358 50.000 0.00 0.00 0.00 2.34
3478 8882 0.102481 ATCCTTACGCAGCGATTCGT 59.898 50.000 24.65 2.96 42.09 3.85
3479 8883 0.524816 TCCTTACGCAGCGATTCGTC 60.525 55.000 24.65 0.28 39.79 4.20
3507 8911 5.440234 TCGCTTGGTTATTTGTTTTAGCA 57.560 34.783 0.00 0.00 0.00 3.49
3547 8952 0.746923 GGCTCCCATTAACCCGTGTC 60.747 60.000 0.00 0.00 0.00 3.67
3561 8966 1.282875 GTGTCGCTGCCTGTTTTCC 59.717 57.895 0.00 0.00 0.00 3.13
3565 8970 0.467290 TCGCTGCCTGTTTTCCCTTT 60.467 50.000 0.00 0.00 0.00 3.11
3570 8975 3.862264 GCTGCCTGTTTTCCCTTTGATTC 60.862 47.826 0.00 0.00 0.00 2.52
3662 9067 0.547471 TTGAGAGCATGGACAGGGGA 60.547 55.000 0.00 0.00 0.00 4.81
3693 9098 2.543430 GCGATTTCCATTCTGAGCTCTC 59.457 50.000 16.19 0.00 0.00 3.20
3694 9099 3.790091 CGATTTCCATTCTGAGCTCTCA 58.210 45.455 16.19 0.00 38.06 3.27
3705 9266 1.270518 TGAGCTCTCAGTTGCTGTTCC 60.271 52.381 16.19 0.00 39.91 3.62
3722 9283 3.999663 TGTTCCTGTTTTTGCCTTGTTTG 59.000 39.130 0.00 0.00 0.00 2.93
3723 9284 3.971245 TCCTGTTTTTGCCTTGTTTGT 57.029 38.095 0.00 0.00 0.00 2.83
3725 9286 3.999663 TCCTGTTTTTGCCTTGTTTGTTG 59.000 39.130 0.00 0.00 0.00 3.33
3726 9287 3.426025 CCTGTTTTTGCCTTGTTTGTTGC 60.426 43.478 0.00 0.00 0.00 4.17
3727 9288 3.406764 TGTTTTTGCCTTGTTTGTTGCT 58.593 36.364 0.00 0.00 0.00 3.91
3728 9289 3.188048 TGTTTTTGCCTTGTTTGTTGCTG 59.812 39.130 0.00 0.00 0.00 4.41
3785 9349 7.230108 TCAATCTGCTTCTTGACTCTGAAAATT 59.770 33.333 0.00 0.00 0.00 1.82
3807 9371 0.734889 CTTCTTGCCCGCCAATACAG 59.265 55.000 0.00 0.00 31.91 2.74
3819 9383 4.236935 CGCCAATACAGATTTTTGCAGTT 58.763 39.130 0.00 0.00 0.00 3.16
3820 9384 5.398169 CGCCAATACAGATTTTTGCAGTTA 58.602 37.500 0.00 0.00 0.00 2.24
3821 9385 6.035843 CGCCAATACAGATTTTTGCAGTTAT 58.964 36.000 0.00 0.00 0.00 1.89
3823 9387 7.035004 GCCAATACAGATTTTTGCAGTTATGA 58.965 34.615 0.00 0.00 0.00 2.15
3870 9434 8.097038 TGTCTTATCAATCTGCTTCTTGTTACT 58.903 33.333 0.00 0.00 0.00 2.24
3941 9505 5.335976 GCAGCAGAATTTACTTGGTTTAGCT 60.336 40.000 0.00 0.00 0.00 3.32
3949 9513 8.685838 AATTTACTTGGTTTAGCTGAGTGTAA 57.314 30.769 0.00 0.00 0.00 2.41
3979 9543 8.796475 TGGGTGTACTAGTACTGTTACTTTTAG 58.204 37.037 28.56 0.00 39.43 1.85
4058 9622 8.561738 TTTCTTTTCTGTTTCTGTAGAAGTGT 57.438 30.769 0.00 0.00 34.68 3.55
4099 9663 5.502079 TCCTGTTTCAACAACCTTTACTCA 58.498 37.500 0.00 0.00 38.66 3.41
4105 9669 8.617809 TGTTTCAACAACCTTTACTCACTATTC 58.382 33.333 0.00 0.00 35.67 1.75
4109 9673 5.246307 ACAACCTTTACTCACTATTCTGGC 58.754 41.667 0.00 0.00 0.00 4.85
4112 9676 6.067217 ACCTTTACTCACTATTCTGGCAAT 57.933 37.500 0.00 0.00 0.00 3.56
4113 9677 5.882557 ACCTTTACTCACTATTCTGGCAATG 59.117 40.000 0.00 0.00 0.00 2.82
4255 9819 0.471591 ATTTGCAAGGCCCCTTCACA 60.472 50.000 0.00 0.00 33.42 3.58
4289 9853 5.865085 AGACTATGGTTGCAAGAACTGTAA 58.135 37.500 0.00 0.00 0.00 2.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 1.092348 CGGATCTGTACTGGTCGTCA 58.908 55.000 6.90 0.00 0.00 4.35
46 47 5.192927 CCATTGCCTCCTTCAAACTACATA 58.807 41.667 0.00 0.00 0.00 2.29
184 190 0.319040 CCGAGATGACGGCGATGATT 60.319 55.000 16.62 0.00 46.20 2.57
193 199 0.528684 GGAAGGCTTCCGAGATGACG 60.529 60.000 29.19 0.00 40.59 4.35
204 210 2.291865 GGAAAGGGAGATTGGAAGGCTT 60.292 50.000 0.00 0.00 0.00 4.35
276 290 0.980231 CCTCACCCTCTCCTTCCCAG 60.980 65.000 0.00 0.00 0.00 4.45
290 304 3.053849 GAGCCTCGACGACCCTCAC 62.054 68.421 12.66 0.00 0.00 3.51
391 426 0.673644 TCTGCTGCCGCTTCTTTACC 60.674 55.000 0.70 0.00 36.97 2.85
476 515 2.903135 ACTGTCCTCCTTCTCCTTCTTG 59.097 50.000 0.00 0.00 0.00 3.02
481 520 1.888826 CGTCACTGTCCTCCTTCTCCT 60.889 57.143 0.00 0.00 0.00 3.69
494 549 0.389391 AGTTGTCTGACCCGTCACTG 59.611 55.000 5.17 0.00 35.46 3.66
497 552 0.757561 TGGAGTTGTCTGACCCGTCA 60.758 55.000 5.17 0.00 38.06 4.35
572 645 2.434359 GGCTTCCTTGTCGTCCCG 60.434 66.667 0.00 0.00 0.00 5.14
573 646 2.434359 CGGCTTCCTTGTCGTCCC 60.434 66.667 0.00 0.00 0.00 4.46
648 738 3.110705 AGGACATTGCCATCAGACTACT 58.889 45.455 0.00 0.00 0.00 2.57
769 877 5.244755 TGTCCGATCATGTCTCAAATTTCA 58.755 37.500 0.00 0.00 0.00 2.69
782 890 0.999406 CGCGAAAACTGTCCGATCAT 59.001 50.000 0.00 0.00 0.00 2.45
807 915 2.227388 CTGGACCTTCAAATGCACAGAC 59.773 50.000 0.00 0.00 0.00 3.51
808 916 2.106338 TCTGGACCTTCAAATGCACAGA 59.894 45.455 0.00 0.00 0.00 3.41
809 917 2.507484 TCTGGACCTTCAAATGCACAG 58.493 47.619 0.00 0.00 0.00 3.66
810 918 2.655090 TCTGGACCTTCAAATGCACA 57.345 45.000 0.00 0.00 0.00 4.57
811 919 4.022068 TCAAATCTGGACCTTCAAATGCAC 60.022 41.667 0.00 0.00 0.00 4.57
812 920 4.022068 GTCAAATCTGGACCTTCAAATGCA 60.022 41.667 0.00 0.00 0.00 3.96
813 921 4.022068 TGTCAAATCTGGACCTTCAAATGC 60.022 41.667 0.00 0.00 34.36 3.56
814 922 5.710513 TGTCAAATCTGGACCTTCAAATG 57.289 39.130 0.00 0.00 34.36 2.32
815 923 5.835280 ACTTGTCAAATCTGGACCTTCAAAT 59.165 36.000 0.00 0.00 34.36 2.32
816 924 5.200483 ACTTGTCAAATCTGGACCTTCAAA 58.800 37.500 0.00 0.00 34.36 2.69
817 925 4.792068 ACTTGTCAAATCTGGACCTTCAA 58.208 39.130 0.00 0.00 34.36 2.69
818 926 4.389374 GACTTGTCAAATCTGGACCTTCA 58.611 43.478 0.00 0.00 34.36 3.02
819 927 3.753797 GGACTTGTCAAATCTGGACCTTC 59.246 47.826 3.08 0.00 34.36 3.46
820 928 3.756117 GGACTTGTCAAATCTGGACCTT 58.244 45.455 3.08 0.00 34.36 3.50
821 929 2.289694 CGGACTTGTCAAATCTGGACCT 60.290 50.000 3.08 0.00 34.36 3.85
822 930 2.076863 CGGACTTGTCAAATCTGGACC 58.923 52.381 3.08 0.00 34.36 4.46
823 931 2.076863 CCGGACTTGTCAAATCTGGAC 58.923 52.381 15.52 0.00 40.81 4.02
824 932 1.610624 GCCGGACTTGTCAAATCTGGA 60.611 52.381 23.13 0.00 40.81 3.86
825 933 0.804989 GCCGGACTTGTCAAATCTGG 59.195 55.000 16.14 16.14 41.21 3.86
826 934 0.804989 GGCCGGACTTGTCAAATCTG 59.195 55.000 5.05 0.00 0.00 2.90
827 935 0.673644 CGGCCGGACTTGTCAAATCT 60.674 55.000 20.10 0.00 0.00 2.40
828 936 0.953960 ACGGCCGGACTTGTCAAATC 60.954 55.000 31.76 0.00 0.00 2.17
829 937 1.072505 ACGGCCGGACTTGTCAAAT 59.927 52.632 31.76 0.00 0.00 2.32
830 938 1.890041 CACGGCCGGACTTGTCAAA 60.890 57.895 31.76 0.00 0.00 2.69
831 939 2.280524 CACGGCCGGACTTGTCAA 60.281 61.111 31.76 0.00 0.00 3.18
832 940 4.308458 CCACGGCCGGACTTGTCA 62.308 66.667 31.76 0.00 0.00 3.58
833 941 3.310860 ATCCACGGCCGGACTTGTC 62.311 63.158 31.76 0.00 38.07 3.18
834 942 3.319198 ATCCACGGCCGGACTTGT 61.319 61.111 31.76 3.35 38.07 3.16
835 943 2.819595 CATCCACGGCCGGACTTG 60.820 66.667 31.76 18.49 38.07 3.16
836 944 4.778143 GCATCCACGGCCGGACTT 62.778 66.667 31.76 4.77 38.07 3.01
838 946 2.660258 ATAAGCATCCACGGCCGGAC 62.660 60.000 31.76 0.00 38.07 4.79
839 947 1.116536 TATAAGCATCCACGGCCGGA 61.117 55.000 31.76 18.87 40.07 5.14
840 948 0.036388 ATATAAGCATCCACGGCCGG 60.036 55.000 31.76 18.27 0.00 6.13
841 949 1.078709 CATATAAGCATCCACGGCCG 58.921 55.000 26.86 26.86 0.00 6.13
842 950 2.472695 TCATATAAGCATCCACGGCC 57.527 50.000 0.00 0.00 0.00 6.13
843 951 4.320494 CCTTTTCATATAAGCATCCACGGC 60.320 45.833 0.00 0.00 0.00 5.68
844 952 4.216257 CCCTTTTCATATAAGCATCCACGG 59.784 45.833 0.00 0.00 0.00 4.94
845 953 5.063204 TCCCTTTTCATATAAGCATCCACG 58.937 41.667 0.00 0.00 0.00 4.94
846 954 6.015940 CCTTCCCTTTTCATATAAGCATCCAC 60.016 42.308 0.00 0.00 0.00 4.02
847 955 6.070656 CCTTCCCTTTTCATATAAGCATCCA 58.929 40.000 0.00 0.00 0.00 3.41
848 956 6.306987 TCCTTCCCTTTTCATATAAGCATCC 58.693 40.000 0.00 0.00 0.00 3.51
849 957 7.823745 TTCCTTCCCTTTTCATATAAGCATC 57.176 36.000 0.00 0.00 0.00 3.91
850 958 8.061304 TCTTTCCTTCCCTTTTCATATAAGCAT 58.939 33.333 0.00 0.00 0.00 3.79
851 959 7.410174 TCTTTCCTTCCCTTTTCATATAAGCA 58.590 34.615 0.00 0.00 0.00 3.91
852 960 7.775561 TCTCTTTCCTTCCCTTTTCATATAAGC 59.224 37.037 0.00 0.00 0.00 3.09
853 961 9.686683 TTCTCTTTCCTTCCCTTTTCATATAAG 57.313 33.333 0.00 0.00 0.00 1.73
854 962 9.686683 CTTCTCTTTCCTTCCCTTTTCATATAA 57.313 33.333 0.00 0.00 0.00 0.98
855 963 8.275040 CCTTCTCTTTCCTTCCCTTTTCATATA 58.725 37.037 0.00 0.00 0.00 0.86
856 964 7.036571 TCCTTCTCTTTCCTTCCCTTTTCATAT 60.037 37.037 0.00 0.00 0.00 1.78
857 965 6.274672 TCCTTCTCTTTCCTTCCCTTTTCATA 59.725 38.462 0.00 0.00 0.00 2.15
858 966 5.075067 TCCTTCTCTTTCCTTCCCTTTTCAT 59.925 40.000 0.00 0.00 0.00 2.57
859 967 4.415512 TCCTTCTCTTTCCTTCCCTTTTCA 59.584 41.667 0.00 0.00 0.00 2.69
860 968 4.986783 TCCTTCTCTTTCCTTCCCTTTTC 58.013 43.478 0.00 0.00 0.00 2.29
861 969 4.665483 TCTCCTTCTCTTTCCTTCCCTTTT 59.335 41.667 0.00 0.00 0.00 2.27
862 970 4.243643 TCTCCTTCTCTTTCCTTCCCTTT 58.756 43.478 0.00 0.00 0.00 3.11
863 971 3.875571 TCTCCTTCTCTTTCCTTCCCTT 58.124 45.455 0.00 0.00 0.00 3.95
864 972 3.569135 TCTCCTTCTCTTTCCTTCCCT 57.431 47.619 0.00 0.00 0.00 4.20
865 973 3.054728 CCTTCTCCTTCTCTTTCCTTCCC 60.055 52.174 0.00 0.00 0.00 3.97
866 974 3.054728 CCCTTCTCCTTCTCTTTCCTTCC 60.055 52.174 0.00 0.00 0.00 3.46
867 975 3.841255 TCCCTTCTCCTTCTCTTTCCTTC 59.159 47.826 0.00 0.00 0.00 3.46
868 976 3.843619 CTCCCTTCTCCTTCTCTTTCCTT 59.156 47.826 0.00 0.00 0.00 3.36
869 977 3.078305 TCTCCCTTCTCCTTCTCTTTCCT 59.922 47.826 0.00 0.00 0.00 3.36
870 978 3.445987 TCTCCCTTCTCCTTCTCTTTCC 58.554 50.000 0.00 0.00 0.00 3.13
871 979 3.450817 CCTCTCCCTTCTCCTTCTCTTTC 59.549 52.174 0.00 0.00 0.00 2.62
872 980 3.449918 CCTCTCCCTTCTCCTTCTCTTT 58.550 50.000 0.00 0.00 0.00 2.52
873 981 2.292851 CCCTCTCCCTTCTCCTTCTCTT 60.293 54.545 0.00 0.00 0.00 2.85
874 982 1.290732 CCCTCTCCCTTCTCCTTCTCT 59.709 57.143 0.00 0.00 0.00 3.10
875 983 1.691163 CCCCTCTCCCTTCTCCTTCTC 60.691 61.905 0.00 0.00 0.00 2.87
876 984 0.341609 CCCCTCTCCCTTCTCCTTCT 59.658 60.000 0.00 0.00 0.00 2.85
877 985 0.340208 TCCCCTCTCCCTTCTCCTTC 59.660 60.000 0.00 0.00 0.00 3.46
878 986 0.800239 TTCCCCTCTCCCTTCTCCTT 59.200 55.000 0.00 0.00 0.00 3.36
879 987 0.800239 TTTCCCCTCTCCCTTCTCCT 59.200 55.000 0.00 0.00 0.00 3.69
880 988 1.208706 CTTTCCCCTCTCCCTTCTCC 58.791 60.000 0.00 0.00 0.00 3.71
881 989 1.959710 ACTTTCCCCTCTCCCTTCTC 58.040 55.000 0.00 0.00 0.00 2.87
882 990 3.455849 CTTACTTTCCCCTCTCCCTTCT 58.544 50.000 0.00 0.00 0.00 2.85
883 991 2.092861 GCTTACTTTCCCCTCTCCCTTC 60.093 54.545 0.00 0.00 0.00 3.46
884 992 1.916874 GCTTACTTTCCCCTCTCCCTT 59.083 52.381 0.00 0.00 0.00 3.95
885 993 1.081343 AGCTTACTTTCCCCTCTCCCT 59.919 52.381 0.00 0.00 0.00 4.20
886 994 1.210722 CAGCTTACTTTCCCCTCTCCC 59.789 57.143 0.00 0.00 0.00 4.30
887 995 1.909986 ACAGCTTACTTTCCCCTCTCC 59.090 52.381 0.00 0.00 0.00 3.71
888 996 2.303311 ACACAGCTTACTTTCCCCTCTC 59.697 50.000 0.00 0.00 0.00 3.20
889 997 2.339769 ACACAGCTTACTTTCCCCTCT 58.660 47.619 0.00 0.00 0.00 3.69
890 998 2.814336 CAACACAGCTTACTTTCCCCTC 59.186 50.000 0.00 0.00 0.00 4.30
891 999 2.863809 CAACACAGCTTACTTTCCCCT 58.136 47.619 0.00 0.00 0.00 4.79
892 1000 1.269723 GCAACACAGCTTACTTTCCCC 59.730 52.381 0.00 0.00 0.00 4.81
893 1001 1.069227 CGCAACACAGCTTACTTTCCC 60.069 52.381 0.00 0.00 0.00 3.97
894 1002 1.602377 ACGCAACACAGCTTACTTTCC 59.398 47.619 0.00 0.00 0.00 3.13
895 1003 2.031683 ACACGCAACACAGCTTACTTTC 59.968 45.455 0.00 0.00 0.00 2.62
896 1004 2.014128 ACACGCAACACAGCTTACTTT 58.986 42.857 0.00 0.00 0.00 2.66
897 1005 1.663695 ACACGCAACACAGCTTACTT 58.336 45.000 0.00 0.00 0.00 2.24
898 1006 2.519377 TACACGCAACACAGCTTACT 57.481 45.000 0.00 0.00 0.00 2.24
899 1007 2.093783 GGATACACGCAACACAGCTTAC 59.906 50.000 0.00 0.00 0.00 2.34
900 1008 2.343101 GGATACACGCAACACAGCTTA 58.657 47.619 0.00 0.00 0.00 3.09
901 1009 1.156736 GGATACACGCAACACAGCTT 58.843 50.000 0.00 0.00 0.00 3.74
902 1010 1.014044 CGGATACACGCAACACAGCT 61.014 55.000 0.00 0.00 0.00 4.24
903 1011 1.011968 TCGGATACACGCAACACAGC 61.012 55.000 0.00 0.00 0.00 4.40
904 1012 0.713883 GTCGGATACACGCAACACAG 59.286 55.000 0.00 0.00 0.00 3.66
905 1013 0.668096 GGTCGGATACACGCAACACA 60.668 55.000 0.00 0.00 0.00 3.72
906 1014 1.356527 GGGTCGGATACACGCAACAC 61.357 60.000 0.00 0.00 33.14 3.32
951 1059 2.663808 TCAGTTTAAACACGATCGCGA 58.336 42.857 20.06 13.09 41.64 5.87
953 1061 4.326278 TCAGATCAGTTTAAACACGATCGC 59.674 41.667 27.61 16.36 41.31 4.58
964 1072 3.096852 TCGGGAAGCTCAGATCAGTTTA 58.903 45.455 0.00 0.00 0.00 2.01
1091 1208 2.604174 GCGTGGTCTGGTTTGGTCG 61.604 63.158 0.00 0.00 0.00 4.79
1345 1471 4.530857 GGGGAGCGGGTCGACATG 62.531 72.222 18.91 9.93 0.00 3.21
1575 3184 3.051479 CACATGTGGCGCTGCTCA 61.051 61.111 18.51 0.00 0.00 4.26
1711 3322 7.228507 TCACAATGTCAGCACAAAATTAGTAGT 59.771 33.333 0.00 0.00 35.64 2.73
1758 3681 9.431887 CTACCTTGTAGAAGCACAAAATTAGTA 57.568 33.333 0.00 0.00 37.93 1.82
1759 3682 7.094762 GCTACCTTGTAGAAGCACAAAATTAGT 60.095 37.037 5.48 0.00 37.93 2.24
1760 3683 7.244192 GCTACCTTGTAGAAGCACAAAATTAG 58.756 38.462 5.48 0.00 37.93 1.73
1761 3684 6.128391 CGCTACCTTGTAGAAGCACAAAATTA 60.128 38.462 5.48 0.00 37.93 1.40
1762 3685 5.334879 CGCTACCTTGTAGAAGCACAAAATT 60.335 40.000 5.48 0.00 37.93 1.82
1763 3686 4.154195 CGCTACCTTGTAGAAGCACAAAAT 59.846 41.667 5.48 0.00 37.93 1.82
1764 3687 3.496884 CGCTACCTTGTAGAAGCACAAAA 59.503 43.478 5.48 0.00 37.93 2.44
1766 3689 2.297880 TCGCTACCTTGTAGAAGCACAA 59.702 45.455 5.48 0.00 36.94 3.33
1768 3691 2.260481 GTCGCTACCTTGTAGAAGCAC 58.740 52.381 5.48 0.00 34.60 4.40
1769 3692 1.890489 TGTCGCTACCTTGTAGAAGCA 59.110 47.619 5.48 0.00 34.60 3.91
1771 3694 4.327357 CACAATGTCGCTACCTTGTAGAAG 59.673 45.833 10.84 0.00 40.96 2.85
1772 3695 4.021807 TCACAATGTCGCTACCTTGTAGAA 60.022 41.667 10.84 0.00 40.96 2.10
1775 3698 3.945981 TCACAATGTCGCTACCTTGTA 57.054 42.857 10.84 0.24 40.96 2.41
1777 3700 3.525537 AGATCACAATGTCGCTACCTTG 58.474 45.455 5.09 5.09 37.29 3.61
1779 3702 5.537300 ATTAGATCACAATGTCGCTACCT 57.463 39.130 0.00 0.00 0.00 3.08
1780 3703 6.604735 AAATTAGATCACAATGTCGCTACC 57.395 37.500 0.00 0.00 0.00 3.18
1781 3704 7.426456 CACAAAATTAGATCACAATGTCGCTAC 59.574 37.037 0.00 0.00 0.00 3.58
1782 3705 7.463544 CACAAAATTAGATCACAATGTCGCTA 58.536 34.615 0.00 0.00 0.00 4.26
1786 3709 6.467047 CGAGCACAAAATTAGATCACAATGTC 59.533 38.462 0.00 0.00 0.00 3.06
1787 3710 6.072508 ACGAGCACAAAATTAGATCACAATGT 60.073 34.615 0.00 0.00 0.00 2.71
1788 3711 6.317088 ACGAGCACAAAATTAGATCACAATG 58.683 36.000 0.00 0.00 0.00 2.82
1789 3712 6.500684 ACGAGCACAAAATTAGATCACAAT 57.499 33.333 0.00 0.00 0.00 2.71
1792 3715 5.689819 ACAACGAGCACAAAATTAGATCAC 58.310 37.500 0.00 0.00 0.00 3.06
1796 3719 5.053811 TCAGACAACGAGCACAAAATTAGA 58.946 37.500 0.00 0.00 0.00 2.10
1797 3720 5.342806 TCAGACAACGAGCACAAAATTAG 57.657 39.130 0.00 0.00 0.00 1.73
1798 3721 5.743026 TTCAGACAACGAGCACAAAATTA 57.257 34.783 0.00 0.00 0.00 1.40
1799 3722 4.630894 TTCAGACAACGAGCACAAAATT 57.369 36.364 0.00 0.00 0.00 1.82
1800 3723 4.630894 TTTCAGACAACGAGCACAAAAT 57.369 36.364 0.00 0.00 0.00 1.82
1802 3725 3.003275 GGATTTCAGACAACGAGCACAAA 59.997 43.478 0.00 0.00 0.00 2.83
1803 3726 2.548057 GGATTTCAGACAACGAGCACAA 59.452 45.455 0.00 0.00 0.00 3.33
1805 3728 2.417719 AGGATTTCAGACAACGAGCAC 58.582 47.619 0.00 0.00 0.00 4.40
1806 3729 2.839486 AGGATTTCAGACAACGAGCA 57.161 45.000 0.00 0.00 0.00 4.26
1838 3840 7.523380 CGATCCCGTATGAAATTAAGTACTCCT 60.523 40.741 0.00 0.00 0.00 3.69
1839 3841 6.585322 CGATCCCGTATGAAATTAAGTACTCC 59.415 42.308 0.00 0.00 0.00 3.85
1840 3842 7.564044 CGATCCCGTATGAAATTAAGTACTC 57.436 40.000 0.00 0.00 0.00 2.59
1969 7346 6.262944 GTGATGTTGGATGCTCATTATGGTTA 59.737 38.462 0.00 0.00 0.00 2.85
1994 7373 5.547465 TGGAATACTTATACGGAATGCTGG 58.453 41.667 0.00 0.00 0.00 4.85
2003 7382 8.963725 TGTGGTATAGGATGGAATACTTATACG 58.036 37.037 0.00 0.00 27.86 3.06
2040 7422 8.132604 ACGAAAAACAGTTCAAAGTTCAAAAA 57.867 26.923 0.00 0.00 0.00 1.94
2567 7955 1.896220 ATGAACAACACCTGCGTCAT 58.104 45.000 0.00 0.00 31.36 3.06
2893 8281 2.348998 CACAGGAGCACCAGGGTC 59.651 66.667 2.07 0.00 43.35 4.46
2976 8364 0.602905 GCGGGAATATGGGGACTTCG 60.603 60.000 0.00 0.00 0.00 3.79
3370 8774 2.491675 ACTTTAGTTGGTGCCTAGGC 57.508 50.000 27.71 27.71 42.35 3.93
3381 8785 9.662947 ATTAGCAAAACCGTAGATACTTTAGTT 57.337 29.630 0.00 0.00 0.00 2.24
3388 8792 9.783256 AATGAAAATTAGCAAAACCGTAGATAC 57.217 29.630 0.00 0.00 0.00 2.24
3466 8870 3.902063 CACGGACGAATCGCTGCG 61.902 66.667 17.25 17.25 0.00 5.18
3478 8882 0.036765 AATAACCAAGCGAGCACGGA 60.037 50.000 5.52 0.00 40.15 4.69
3479 8883 0.802494 AAATAACCAAGCGAGCACGG 59.198 50.000 5.52 0.00 40.15 4.94
3507 8911 2.283298 CATAAACACATGAGCGAGCCT 58.717 47.619 0.00 0.00 0.00 4.58
3547 8952 0.318955 CAAAGGGAAAACAGGCAGCG 60.319 55.000 0.00 0.00 0.00 5.18
3561 8966 6.874288 ACAGAGAAGTTTCAGAATCAAAGG 57.126 37.500 0.00 0.00 0.00 3.11
3565 8970 4.449068 GCGAACAGAGAAGTTTCAGAATCA 59.551 41.667 0.00 0.00 0.00 2.57
3570 8975 3.428198 CAGAGCGAACAGAGAAGTTTCAG 59.572 47.826 0.00 0.00 0.00 3.02
3693 9098 2.604462 GCAAAAACAGGAACAGCAACTG 59.396 45.455 0.00 0.00 38.19 3.16
3694 9099 2.418609 GGCAAAAACAGGAACAGCAACT 60.419 45.455 0.00 0.00 0.00 3.16
3698 9259 2.204237 CAAGGCAAAAACAGGAACAGC 58.796 47.619 0.00 0.00 0.00 4.40
3705 9266 3.436359 AGCAACAAACAAGGCAAAAACAG 59.564 39.130 0.00 0.00 0.00 3.16
3722 9283 9.155975 TCAGAGAAATAGAATTAGAACAGCAAC 57.844 33.333 0.00 0.00 0.00 4.17
3723 9284 9.725019 TTCAGAGAAATAGAATTAGAACAGCAA 57.275 29.630 0.00 0.00 0.00 3.91
3725 9286 9.377312 AGTTCAGAGAAATAGAATTAGAACAGC 57.623 33.333 0.00 0.00 36.29 4.40
3761 9323 7.521871 AATTTTCAGAGTCAAGAAGCAGATT 57.478 32.000 0.00 0.00 0.00 2.40
3764 9326 5.401674 GCAAATTTTCAGAGTCAAGAAGCAG 59.598 40.000 0.00 0.00 0.00 4.24
3807 9371 7.542025 ACAGGAGAATCATAACTGCAAAAATC 58.458 34.615 0.00 0.00 36.25 2.17
3819 9383 7.487822 AGTTCAGAGAAACAGGAGAATCATA 57.512 36.000 0.00 0.00 36.25 2.15
3820 9384 6.371595 AGTTCAGAGAAACAGGAGAATCAT 57.628 37.500 0.00 0.00 36.25 2.45
3821 9385 5.815233 AGTTCAGAGAAACAGGAGAATCA 57.185 39.130 0.00 0.00 36.25 2.57
3823 9387 5.934781 ACAAGTTCAGAGAAACAGGAGAAT 58.065 37.500 0.00 0.00 0.00 2.40
3906 9470 9.956720 AAGTAAATTCTGCTGCAATAATCATAC 57.043 29.630 3.02 12.31 0.00 2.39
3915 9479 4.935352 AACCAAGTAAATTCTGCTGCAA 57.065 36.364 3.02 0.00 0.00 4.08
3941 9505 5.599656 ACTAGTACACCCAAGTTTACACTCA 59.400 40.000 0.00 0.00 32.56 3.41
3949 9513 6.779539 AGTAACAGTACTAGTACACCCAAGTT 59.220 38.462 29.87 23.11 38.87 2.66
4034 9598 9.661563 TTACACTTCTACAGAAACAGAAAAGAA 57.338 29.630 0.00 0.00 33.07 2.52
4037 9601 9.314321 CTCTTACACTTCTACAGAAACAGAAAA 57.686 33.333 0.00 0.00 33.07 2.29
4058 9622 7.496346 AACAGGAACATTGGTAGATCTCTTA 57.504 36.000 0.00 0.00 0.00 2.10
4099 9663 5.324409 TGGAGAAAACATTGCCAGAATAGT 58.676 37.500 0.00 0.00 0.00 2.12
4105 9669 3.991773 CACATTGGAGAAAACATTGCCAG 59.008 43.478 0.00 0.00 0.00 4.85
4109 9673 5.199024 TCACCACATTGGAGAAAACATTG 57.801 39.130 0.00 0.00 40.96 2.82
4235 9799 0.247460 GTGAAGGGGCCTTGCAAATC 59.753 55.000 0.00 0.00 36.26 2.17
4255 9819 6.112734 TGCAACCATAGTCTTCAAATATCGT 58.887 36.000 0.00 0.00 0.00 3.73


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

AutoCloner maintained by Alex Coulton.