Multiple sequence alignment - TraesCS5B01G102500

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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 TraesCS5B01G102500 chr5B 100.000 5652 0 0 1 5652 136409543 136415194 0.000000e+00 10438.0
1 TraesCS5B01G102500 chr5B 99.778 451 1 0 486 936 136409580 136410030 0.000000e+00 828.0
2 TraesCS5B01G102500 chr5B 99.778 451 1 0 38 488 136410028 136410478 0.000000e+00 828.0
3 TraesCS5B01G102500 chr5B 88.172 186 14 5 4076 4261 98836024 98836201 1.230000e-51 215.0
4 TraesCS5B01G102500 chr5B 93.939 99 3 2 914 1011 123755665 123755761 4.560000e-31 147.0
5 TraesCS5B01G102500 chr5B 100.000 28 0 0 876 903 553925904 553925877 1.000000e-02 52.8
6 TraesCS5B01G102500 chr5B 100.000 28 0 0 428 455 553925904 553925877 1.000000e-02 52.8
7 TraesCS5B01G102500 chr5A 95.628 2173 68 13 1469 3618 136394226 136396394 0.000000e+00 3461.0
8 TraesCS5B01G102500 chr5A 90.414 1450 62 29 3682 5114 136396393 136397782 0.000000e+00 1836.0
9 TraesCS5B01G102500 chr5A 95.552 607 22 4 907 1512 136393624 136394226 0.000000e+00 966.0
10 TraesCS5B01G102500 chr5A 100.000 28 0 0 876 903 321667508 321667481 1.000000e-02 52.8
11 TraesCS5B01G102500 chr5A 100.000 28 0 0 428 455 321667508 321667481 1.000000e-02 52.8
12 TraesCS5B01G102500 chr5D 96.473 1616 42 5 2004 3618 123457915 123459516 0.000000e+00 2654.0
13 TraesCS5B01G102500 chr5D 93.148 1401 61 16 3682 5076 123459515 123460886 0.000000e+00 2023.0
14 TraesCS5B01G102500 chr5D 89.260 1108 71 19 907 2007 123451819 123452885 0.000000e+00 1343.0
15 TraesCS5B01G102500 chr5D 83.794 253 35 6 1 249 522298746 522298996 9.470000e-58 235.0
16 TraesCS5B01G102500 chr5D 75.541 462 109 4 5113 5572 484013818 484013359 2.050000e-54 224.0
17 TraesCS5B01G102500 chr5D 82.407 216 32 6 486 697 522298783 522298996 3.480000e-42 183.0
18 TraesCS5B01G102500 chr5D 94.505 91 5 0 907 997 113386824 113386914 2.120000e-29 141.0
19 TraesCS5B01G102500 chr5D 92.857 70 5 0 3614 3683 441356339 441356408 1.000000e-17 102.0
20 TraesCS5B01G102500 chr5D 76.056 213 32 13 2 208 445627799 445627600 6.030000e-15 93.5
21 TraesCS5B01G102500 chr5D 87.500 72 6 3 588 656 445627671 445627600 4.690000e-11 80.5
22 TraesCS5B01G102500 chr5D 100.000 28 0 0 876 903 26301569 26301542 1.000000e-02 52.8
23 TraesCS5B01G102500 chr5D 100.000 28 0 0 428 455 26301569 26301542 1.000000e-02 52.8
24 TraesCS5B01G102500 chr2B 98.889 540 6 0 5113 5652 8558719 8559258 0.000000e+00 965.0
25 TraesCS5B01G102500 chr2B 91.781 73 4 2 3613 3683 27088460 27088388 3.600000e-17 100.0
26 TraesCS5B01G102500 chr2B 100.000 29 0 0 876 904 584118610 584118582 3.000000e-03 54.7
27 TraesCS5B01G102500 chr2B 100.000 29 0 0 428 456 584118610 584118582 3.000000e-03 54.7
28 TraesCS5B01G102500 chr2B 100.000 29 0 0 876 904 731605731 731605703 3.000000e-03 54.7
29 TraesCS5B01G102500 chr2B 100.000 29 0 0 428 456 731605731 731605703 3.000000e-03 54.7
30 TraesCS5B01G102500 chr2B 100.000 28 0 0 428 455 743698056 743698083 1.000000e-02 52.8
31 TraesCS5B01G102500 chr2B 100.000 28 0 0 876 903 743698056 743698083 1.000000e-02 52.8
32 TraesCS5B01G102500 chr4B 97.632 549 13 0 5104 5652 412772392 412772940 0.000000e+00 942.0
33 TraesCS5B01G102500 chr4B 90.909 176 15 1 4072 4246 28618454 28618629 9.470000e-58 235.0
34 TraesCS5B01G102500 chr4B 96.512 86 3 0 912 997 625077146 625077231 5.900000e-30 143.0
35 TraesCS5B01G102500 chr4B 91.837 49 4 0 5240 5288 393410160 393410112 1.020000e-07 69.4
36 TraesCS5B01G102500 chr4B 81.176 85 16 0 5204 5288 399757986 399758070 1.020000e-07 69.4
37 TraesCS5B01G102500 chr7B 98.148 540 9 1 5113 5652 64177673 64177135 0.000000e+00 941.0
38 TraesCS5B01G102500 chr7B 88.104 538 63 1 5113 5649 242995919 242996456 6.180000e-179 638.0
39 TraesCS5B01G102500 chr7B 88.542 192 11 9 4062 4252 12186442 12186623 7.370000e-54 222.0
40 TraesCS5B01G102500 chr7B 84.649 228 30 5 1 225 607333533 607333758 7.370000e-54 222.0
41 TraesCS5B01G102500 chr7B 84.817 191 24 5 486 673 607333570 607333758 2.690000e-43 187.0
42 TraesCS5B01G102500 chr6B 97.778 540 12 0 5113 5652 478892521 478891982 0.000000e+00 931.0
43 TraesCS5B01G102500 chr6B 93.137 102 3 4 907 1005 720559365 720559465 4.560000e-31 147.0
44 TraesCS5B01G102500 chr4A 97.593 540 13 0 5113 5652 132053848 132053309 0.000000e+00 926.0
45 TraesCS5B01G102500 chr4A 84.962 532 79 1 5113 5643 83309785 83309254 6.440000e-149 538.0
46 TraesCS5B01G102500 chr4A 90.964 166 15 0 4079 4244 139530241 139530076 2.050000e-54 224.0
47 TraesCS5B01G102500 chr4A 89.655 174 18 0 4075 4248 27645888 27645715 7.370000e-54 222.0
48 TraesCS5B01G102500 chr4A 92.857 84 6 0 1312 1395 64156949 64157032 7.690000e-24 122.0
49 TraesCS5B01G102500 chr2D 95.926 540 18 2 5113 5652 53240733 53241268 0.000000e+00 872.0
50 TraesCS5B01G102500 chr2D 92.958 71 3 1 3617 3685 267707165 267707095 1.000000e-17 102.0
51 TraesCS5B01G102500 chr2D 90.541 74 5 2 3610 3683 70029040 70029111 4.660000e-16 97.1
52 TraesCS5B01G102500 chr3D 90.000 540 54 0 5113 5652 7506430 7505891 0.000000e+00 699.0
53 TraesCS5B01G102500 chr3D 89.714 175 10 7 4076 4250 449740443 449740277 3.430000e-52 217.0
54 TraesCS5B01G102500 chr3D 89.266 177 14 2 4075 4251 546470222 546470393 3.430000e-52 217.0
55 TraesCS5B01G102500 chr3D 79.341 334 42 14 1 313 608410128 608409801 5.740000e-50 209.0
56 TraesCS5B01G102500 chr3D 80.000 295 35 11 487 762 608410089 608409800 4.470000e-46 196.0
57 TraesCS5B01G102500 chr3D 93.814 97 3 3 907 1002 90781615 90781709 5.900000e-30 143.0
58 TraesCS5B01G102500 chr3D 93.478 92 3 3 910 1000 90783791 90783880 3.550000e-27 134.0
59 TraesCS5B01G102500 chr3D 91.667 84 7 0 1312 1395 548211355 548211438 3.580000e-22 117.0
60 TraesCS5B01G102500 chr3D 89.157 83 9 0 1312 1394 548233500 548233582 2.790000e-18 104.0
61 TraesCS5B01G102500 chr1A 89.013 537 57 2 5113 5649 299265250 299265784 0.000000e+00 664.0
62 TraesCS5B01G102500 chr1A 89.307 505 53 1 5146 5649 494750014 494750518 2.870000e-177 632.0
63 TraesCS5B01G102500 chr1A 82.083 240 38 5 1 236 315488768 315488530 3.450000e-47 200.0
64 TraesCS5B01G102500 chr1A 81.773 203 32 5 486 684 315488731 315488530 1.260000e-36 165.0
65 TraesCS5B01G102500 chr1A 98.837 86 1 0 915 1000 119739096 119739011 2.730000e-33 154.0
66 TraesCS5B01G102500 chr1D 88.827 537 60 0 5113 5649 104296665 104297201 0.000000e+00 660.0
67 TraesCS5B01G102500 chr1D 94.681 94 5 0 907 1000 112632856 112632763 4.560000e-31 147.0
68 TraesCS5B01G102500 chr1D 93.333 75 3 2 3611 3683 464799720 464799794 5.990000e-20 110.0
69 TraesCS5B01G102500 chr1D 100.000 28 0 0 428 455 477783831 477783858 1.000000e-02 52.8
70 TraesCS5B01G102500 chr1D 100.000 28 0 0 876 903 477783831 477783858 1.000000e-02 52.8
71 TraesCS5B01G102500 chr7D 87.081 209 25 2 1 208 203456574 203456781 9.470000e-58 235.0
72 TraesCS5B01G102500 chr7D 97.753 89 1 1 907 995 583409436 583409523 9.810000e-33 152.0
73 TraesCS5B01G102500 chr7D 94.949 99 2 3 906 1004 583594816 583594911 9.810000e-33 152.0
74 TraesCS5B01G102500 chr7D 96.667 90 3 0 914 1003 634682036 634682125 3.530000e-32 150.0
75 TraesCS5B01G102500 chr7D 92.958 71 5 0 3613 3683 236822610 236822680 2.790000e-18 104.0
76 TraesCS5B01G102500 chr7D 92.754 69 3 1 3617 3683 46702731 46702663 1.300000e-16 99.0
77 TraesCS5B01G102500 chr6A 85.217 230 30 4 1 227 564685936 564686164 3.400000e-57 233.0
78 TraesCS5B01G102500 chr6A 96.774 93 1 2 908 1000 146548601 146548511 2.730000e-33 154.0
79 TraesCS5B01G102500 chr6A 94.898 98 4 1 903 1000 615434023 615433927 9.810000e-33 152.0
80 TraesCS5B01G102500 chr6A 94.382 89 3 2 907 994 446750167 446750080 9.880000e-28 135.0
81 TraesCS5B01G102500 chr1B 76.026 463 103 7 5114 5572 555338817 555339275 3.400000e-57 233.0
82 TraesCS5B01G102500 chr1B 76.119 335 78 2 5239 5572 146306038 146305705 2.090000e-39 174.0
83 TraesCS5B01G102500 chr1B 95.789 95 4 0 907 1001 172256312 172256218 2.730000e-33 154.0
84 TraesCS5B01G102500 chr1B 91.667 84 7 0 1312 1395 253067547 253067464 3.580000e-22 117.0
85 TraesCS5B01G102500 chr3A 89.714 175 13 2 4075 4249 683240590 683240759 9.530000e-53 219.0
86 TraesCS5B01G102500 chr3A 100.000 28 0 0 181 208 235821664 235821691 1.000000e-02 52.8
87 TraesCS5B01G102500 chr3A 100.000 28 0 0 629 656 235821664 235821691 1.000000e-02 52.8
88 TraesCS5B01G102500 chr7A 88.525 183 16 4 4068 4249 214303343 214303165 3.430000e-52 217.0
89 TraesCS5B01G102500 chr7A 95.699 93 2 2 907 999 731255736 731255826 1.270000e-31 148.0
90 TraesCS5B01G102500 chr7A 91.892 74 3 2 3611 3684 127675730 127675660 3.600000e-17 100.0
91 TraesCS5B01G102500 chr4D 75.949 395 93 2 5226 5619 325063255 325063648 9.600000e-48 202.0
92 TraesCS5B01G102500 chr4D 96.471 85 2 1 916 1000 92221662 92221579 7.640000e-29 139.0
93 TraesCS5B01G102500 chr4D 98.684 76 1 0 922 997 216545598 216545673 9.880000e-28 135.0
94 TraesCS5B01G102500 chr4D 95.455 66 2 1 914 979 92222369 92222305 2.790000e-18 104.0
95 TraesCS5B01G102500 chr4D 100.000 28 0 0 876 903 323929593 323929566 1.000000e-02 52.8
96 TraesCS5B01G102500 chr4D 100.000 28 0 0 428 455 323929593 323929566 1.000000e-02 52.8
97 TraesCS5B01G102500 chr6D 94.118 102 4 2 903 1004 470603316 470603217 2.730000e-33 154.0
98 TraesCS5B01G102500 chr6D 94.318 88 4 1 907 994 310124451 310124365 3.550000e-27 134.0
99 TraesCS5B01G102500 chr6D 90.667 75 6 1 3610 3683 472540222 472540296 1.300000e-16 99.0


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 TraesCS5B01G102500 chr5B 136409543 136415194 5651 False 10438.000000 10438 100.000000 1 5652 1 chr5B.!!$F3 5651
1 TraesCS5B01G102500 chr5B 136409580 136410478 898 False 828.000000 828 99.778000 38 936 2 chr5B.!!$F4 898
2 TraesCS5B01G102500 chr5A 136393624 136397782 4158 False 2087.666667 3461 93.864667 907 5114 3 chr5A.!!$F1 4207
3 TraesCS5B01G102500 chr5D 123457915 123460886 2971 False 2338.500000 2654 94.810500 2004 5076 2 chr5D.!!$F4 3072
4 TraesCS5B01G102500 chr5D 123451819 123452885 1066 False 1343.000000 1343 89.260000 907 2007 1 chr5D.!!$F2 1100
5 TraesCS5B01G102500 chr2B 8558719 8559258 539 False 965.000000 965 98.889000 5113 5652 1 chr2B.!!$F1 539
6 TraesCS5B01G102500 chr4B 412772392 412772940 548 False 942.000000 942 97.632000 5104 5652 1 chr4B.!!$F3 548
7 TraesCS5B01G102500 chr7B 64177135 64177673 538 True 941.000000 941 98.148000 5113 5652 1 chr7B.!!$R1 539
8 TraesCS5B01G102500 chr7B 242995919 242996456 537 False 638.000000 638 88.104000 5113 5649 1 chr7B.!!$F2 536
9 TraesCS5B01G102500 chr6B 478891982 478892521 539 True 931.000000 931 97.778000 5113 5652 1 chr6B.!!$R1 539
10 TraesCS5B01G102500 chr4A 132053309 132053848 539 True 926.000000 926 97.593000 5113 5652 1 chr4A.!!$R3 539
11 TraesCS5B01G102500 chr4A 83309254 83309785 531 True 538.000000 538 84.962000 5113 5643 1 chr4A.!!$R2 530
12 TraesCS5B01G102500 chr2D 53240733 53241268 535 False 872.000000 872 95.926000 5113 5652 1 chr2D.!!$F1 539
13 TraesCS5B01G102500 chr3D 7505891 7506430 539 True 699.000000 699 90.000000 5113 5652 1 chr3D.!!$R1 539
14 TraesCS5B01G102500 chr1A 299265250 299265784 534 False 664.000000 664 89.013000 5113 5649 1 chr1A.!!$F1 536
15 TraesCS5B01G102500 chr1A 494750014 494750518 504 False 632.000000 632 89.307000 5146 5649 1 chr1A.!!$F2 503
16 TraesCS5B01G102500 chr1D 104296665 104297201 536 False 660.000000 660 88.827000 5113 5649 1 chr1D.!!$F1 536

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
24 25 0.103208 CTCCGTCACCACCATCTAGC 59.897 60.000 0.00 0.0 0.00 3.42 F
26 27 0.179100 CCGTCACCACCATCTAGCAG 60.179 60.000 0.00 0.0 0.00 4.24 F
1758 1818 0.516877 TCGAGATGCGCCTTTTTGTG 59.483 50.000 4.18 0.0 40.61 3.33 F
2413 2475 1.344763 GTCAAGTAGCACCTGGACTGT 59.655 52.381 0.00 0.0 33.37 3.55 F
4062 4146 0.406750 TGAGGAACTGAGGACCCGTA 59.593 55.000 0.00 0.0 41.55 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1693 1752 0.252193 AGACAGAGGCCTGCTCTCTT 60.252 55.000 12.00 0.0 44.16 2.85 R
1845 1906 1.351017 CCAGTTCCACCACACATACCT 59.649 52.381 0.00 0.0 0.00 3.08 R
3398 3480 2.520904 GCGATGCAGCTCGACCTTC 61.521 63.158 13.68 0.0 41.12 3.46 R
4345 4429 2.608090 GCCGGCTTTCATAAGTACACTC 59.392 50.000 22.15 0.0 33.74 3.51 R
5108 5233 0.917333 AATTCCCTCCGCCCCAGTTA 60.917 55.000 0.00 0.0 0.00 2.24 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
17 18 2.494918 CGATCCTCCGTCACCACC 59.505 66.667 0.00 0.00 0.00 4.61
18 19 2.348104 CGATCCTCCGTCACCACCA 61.348 63.158 0.00 0.00 0.00 4.17
19 20 1.676678 CGATCCTCCGTCACCACCAT 61.677 60.000 0.00 0.00 0.00 3.55
20 21 0.105039 GATCCTCCGTCACCACCATC 59.895 60.000 0.00 0.00 0.00 3.51
21 22 0.325671 ATCCTCCGTCACCACCATCT 60.326 55.000 0.00 0.00 0.00 2.90
22 23 0.333652 TCCTCCGTCACCACCATCTA 59.666 55.000 0.00 0.00 0.00 1.98
23 24 0.747255 CCTCCGTCACCACCATCTAG 59.253 60.000 0.00 0.00 0.00 2.43
24 25 0.103208 CTCCGTCACCACCATCTAGC 59.897 60.000 0.00 0.00 0.00 3.42
25 26 0.613572 TCCGTCACCACCATCTAGCA 60.614 55.000 0.00 0.00 0.00 3.49
26 27 0.179100 CCGTCACCACCATCTAGCAG 60.179 60.000 0.00 0.00 0.00 4.24
27 28 0.817654 CGTCACCACCATCTAGCAGA 59.182 55.000 0.00 0.00 0.00 4.26
28 29 1.469940 CGTCACCACCATCTAGCAGAC 60.470 57.143 0.00 0.00 0.00 3.51
29 30 1.827969 GTCACCACCATCTAGCAGACT 59.172 52.381 0.00 0.00 0.00 3.24
30 31 2.234908 GTCACCACCATCTAGCAGACTT 59.765 50.000 0.00 0.00 0.00 3.01
31 32 2.497675 TCACCACCATCTAGCAGACTTC 59.502 50.000 0.00 0.00 0.00 3.01
32 33 1.478510 ACCACCATCTAGCAGACTTCG 59.521 52.381 0.00 0.00 0.00 3.79
33 34 1.478510 CCACCATCTAGCAGACTTCGT 59.521 52.381 0.00 0.00 0.00 3.85
34 35 2.534298 CACCATCTAGCAGACTTCGTG 58.466 52.381 0.00 0.00 0.00 4.35
35 36 1.478510 ACCATCTAGCAGACTTCGTGG 59.521 52.381 0.00 0.00 0.00 4.94
36 37 1.565305 CATCTAGCAGACTTCGTGGC 58.435 55.000 0.00 0.00 0.00 5.01
886 887 4.477302 AACGTTCTTGTATTTTGGGACG 57.523 40.909 0.00 0.00 0.00 4.79
887 888 2.809696 ACGTTCTTGTATTTTGGGACGG 59.190 45.455 0.00 0.00 0.00 4.79
888 889 3.068560 CGTTCTTGTATTTTGGGACGGA 58.931 45.455 0.00 0.00 0.00 4.69
889 890 3.124636 CGTTCTTGTATTTTGGGACGGAG 59.875 47.826 0.00 0.00 0.00 4.63
890 891 3.343941 TCTTGTATTTTGGGACGGAGG 57.656 47.619 0.00 0.00 0.00 4.30
891 892 2.026636 TCTTGTATTTTGGGACGGAGGG 60.027 50.000 0.00 0.00 0.00 4.30
892 893 1.659022 TGTATTTTGGGACGGAGGGA 58.341 50.000 0.00 0.00 0.00 4.20
893 894 1.557832 TGTATTTTGGGACGGAGGGAG 59.442 52.381 0.00 0.00 0.00 4.30
894 895 1.558294 GTATTTTGGGACGGAGGGAGT 59.442 52.381 0.00 0.00 0.00 3.85
895 896 1.961133 ATTTTGGGACGGAGGGAGTA 58.039 50.000 0.00 0.00 0.00 2.59
896 897 1.961133 TTTTGGGACGGAGGGAGTAT 58.039 50.000 0.00 0.00 0.00 2.12
897 898 2.852714 TTTGGGACGGAGGGAGTATA 57.147 50.000 0.00 0.00 0.00 1.47
898 899 2.852714 TTGGGACGGAGGGAGTATAA 57.147 50.000 0.00 0.00 0.00 0.98
899 900 3.339713 TTGGGACGGAGGGAGTATAAT 57.660 47.619 0.00 0.00 0.00 1.28
900 901 4.474303 TTGGGACGGAGGGAGTATAATA 57.526 45.455 0.00 0.00 0.00 0.98
901 902 3.771216 TGGGACGGAGGGAGTATAATAC 58.229 50.000 0.00 0.00 0.00 1.89
902 903 3.140707 TGGGACGGAGGGAGTATAATACA 59.859 47.826 0.00 0.00 0.00 2.29
903 904 4.202749 TGGGACGGAGGGAGTATAATACAT 60.203 45.833 0.00 0.00 0.00 2.29
904 905 4.159879 GGGACGGAGGGAGTATAATACATG 59.840 50.000 0.00 0.00 0.00 3.21
905 906 4.771054 GGACGGAGGGAGTATAATACATGT 59.229 45.833 2.69 2.69 0.00 3.21
906 907 5.948162 GGACGGAGGGAGTATAATACATGTA 59.052 44.000 8.27 8.27 0.00 2.29
907 908 6.435277 GGACGGAGGGAGTATAATACATGTAA 59.565 42.308 10.14 0.00 0.00 2.41
908 909 7.039504 GGACGGAGGGAGTATAATACATGTAAA 60.040 40.741 10.14 1.53 0.00 2.01
909 910 7.893658 ACGGAGGGAGTATAATACATGTAAAG 58.106 38.462 10.14 0.00 0.00 1.85
910 911 7.727186 ACGGAGGGAGTATAATACATGTAAAGA 59.273 37.037 10.14 0.00 0.00 2.52
911 912 8.582437 CGGAGGGAGTATAATACATGTAAAGAA 58.418 37.037 10.14 0.00 0.00 2.52
912 913 9.930693 GGAGGGAGTATAATACATGTAAAGAAG 57.069 37.037 10.14 0.00 0.00 2.85
1177 1178 3.077359 CGAGCTCAAATCTTGTTTCCCT 58.923 45.455 15.40 0.00 0.00 4.20
1180 1181 2.162408 GCTCAAATCTTGTTTCCCTCCG 59.838 50.000 0.00 0.00 0.00 4.63
1181 1182 3.412386 CTCAAATCTTGTTTCCCTCCGT 58.588 45.455 0.00 0.00 0.00 4.69
1213 1214 0.666577 CGCTTCGTCTCCCTCGTTTT 60.667 55.000 0.00 0.00 0.00 2.43
1446 1447 9.581289 CAGTATTATATATTGGGTTGGGTTTGA 57.419 33.333 0.00 0.00 0.00 2.69
1487 1488 1.933853 GTACCATGTTCTAGCCTTGCG 59.066 52.381 0.00 0.00 0.00 4.85
1541 1599 4.134563 AGTTTTACTTGCGTCCATCAGTT 58.865 39.130 0.00 0.00 0.00 3.16
1552 1611 4.651994 CGTCCATCAGTTCTAAACATTGC 58.348 43.478 0.00 0.00 0.00 3.56
1604 1663 2.258013 CGCCACCGCCTCTTCAAAA 61.258 57.895 0.00 0.00 0.00 2.44
1673 1732 3.936772 AAATGCCGGGTGATGCCGT 62.937 57.895 2.18 0.00 38.44 5.68
1693 1752 1.368641 GTGCTCGCCACATAACATCA 58.631 50.000 1.81 0.00 44.06 3.07
1700 1759 2.286294 CGCCACATAACATCAAGAGAGC 59.714 50.000 0.00 0.00 0.00 4.09
1705 1764 2.698855 TAACATCAAGAGAGCAGGCC 57.301 50.000 0.00 0.00 0.00 5.19
1758 1818 0.516877 TCGAGATGCGCCTTTTTGTG 59.483 50.000 4.18 0.00 40.61 3.33
1793 1853 8.283291 CCTTGTAAACTCTTCTATTGTGTCAAC 58.717 37.037 0.00 0.00 0.00 3.18
1845 1906 6.459670 AGCACATCTGATTTGCAATGAATA 57.540 33.333 25.52 0.00 38.81 1.75
1847 1908 5.690409 GCACATCTGATTTGCAATGAATAGG 59.310 40.000 20.62 0.00 36.22 2.57
1938 1999 3.864243 ACCGTGTCAGTAAAACAACAGA 58.136 40.909 0.00 0.00 0.00 3.41
2048 2110 3.445096 GCTGTGCTTTGGGAATATCTGTT 59.555 43.478 0.00 0.00 0.00 3.16
2055 2117 5.506982 GCTTTGGGAATATCTGTTCTCATGC 60.507 44.000 0.00 0.00 38.33 4.06
2377 2439 3.005684 GCATGGTCCAGATTTGTTGTGAA 59.994 43.478 0.00 0.00 0.00 3.18
2410 2472 2.543777 TTGTCAAGTAGCACCTGGAC 57.456 50.000 0.00 3.78 36.17 4.02
2413 2475 1.344763 GTCAAGTAGCACCTGGACTGT 59.655 52.381 0.00 0.00 33.37 3.55
2537 2617 9.720769 AAGAAACCCTTTATATATGTACCATCG 57.279 33.333 0.00 0.00 0.00 3.84
2833 2914 2.439409 TGCAAACATGTCTGCAGCTAT 58.561 42.857 22.66 2.51 43.44 2.97
2934 3015 3.619929 CCGATGGAGGTTTTAAAGGTACG 59.380 47.826 0.00 0.00 0.00 3.67
2939 3020 5.733676 TGGAGGTTTTAAAGGTACGGTATC 58.266 41.667 0.00 0.00 0.00 2.24
3034 3115 4.387256 GTCACAGATGAGTACAAGCAGAAC 59.613 45.833 0.00 0.00 34.75 3.01
3175 3256 3.003394 TGATGAGGCCAAACAGGTATG 57.997 47.619 5.01 0.00 40.61 2.39
3249 3331 3.679389 ACTAATTGAGCCACCACTGAAG 58.321 45.455 0.00 0.00 0.00 3.02
3398 3480 2.821969 AGCTATTTTTCTGTGTGGCTGG 59.178 45.455 0.00 0.00 0.00 4.85
3622 3704 9.027202 TGGAAAACTTTGGTAAATAATACTCCC 57.973 33.333 0.00 0.00 0.00 4.30
3623 3705 9.251440 GGAAAACTTTGGTAAATAATACTCCCT 57.749 33.333 0.00 0.00 0.00 4.20
3625 3707 9.816787 AAAACTTTGGTAAATAATACTCCCTCA 57.183 29.630 0.00 0.00 0.00 3.86
3626 3708 9.462606 AAACTTTGGTAAATAATACTCCCTCAG 57.537 33.333 0.00 0.00 0.00 3.35
3627 3709 8.159229 ACTTTGGTAAATAATACTCCCTCAGT 57.841 34.615 0.00 0.00 39.41 3.41
3628 3710 8.265764 ACTTTGGTAAATAATACTCCCTCAGTC 58.734 37.037 0.00 0.00 36.43 3.51
3629 3711 6.742559 TGGTAAATAATACTCCCTCAGTCC 57.257 41.667 0.00 0.00 36.43 3.85
3630 3712 5.605488 TGGTAAATAATACTCCCTCAGTCCC 59.395 44.000 0.00 0.00 36.43 4.46
3631 3713 5.605488 GGTAAATAATACTCCCTCAGTCCCA 59.395 44.000 0.00 0.00 36.43 4.37
3632 3714 6.272558 GGTAAATAATACTCCCTCAGTCCCAT 59.727 42.308 0.00 0.00 36.43 4.00
3633 3715 7.456902 GGTAAATAATACTCCCTCAGTCCCATA 59.543 40.741 0.00 0.00 36.43 2.74
3634 3716 7.947782 AAATAATACTCCCTCAGTCCCATAA 57.052 36.000 0.00 0.00 36.43 1.90
3635 3717 8.525729 AAATAATACTCCCTCAGTCCCATAAT 57.474 34.615 0.00 0.00 36.43 1.28
3636 3718 9.629649 AAATAATACTCCCTCAGTCCCATAATA 57.370 33.333 0.00 0.00 36.43 0.98
3637 3719 9.805204 AATAATACTCCCTCAGTCCCATAATAT 57.195 33.333 0.00 0.00 36.43 1.28
3640 3722 8.846423 ATACTCCCTCAGTCCCATAATATAAG 57.154 38.462 0.00 0.00 36.43 1.73
3641 3723 6.875469 ACTCCCTCAGTCCCATAATATAAGA 58.125 40.000 0.00 0.00 0.00 2.10
3642 3724 6.957020 ACTCCCTCAGTCCCATAATATAAGAG 59.043 42.308 0.00 0.00 0.00 2.85
3643 3725 5.721960 TCCCTCAGTCCCATAATATAAGAGC 59.278 44.000 0.00 0.00 0.00 4.09
3644 3726 5.394663 CCCTCAGTCCCATAATATAAGAGCG 60.395 48.000 0.00 0.00 0.00 5.03
3645 3727 5.186021 CCTCAGTCCCATAATATAAGAGCGT 59.814 44.000 0.00 0.00 0.00 5.07
3646 3728 6.295349 CCTCAGTCCCATAATATAAGAGCGTT 60.295 42.308 0.00 0.00 0.00 4.84
3647 3729 7.062749 TCAGTCCCATAATATAAGAGCGTTT 57.937 36.000 0.00 0.00 0.00 3.60
3648 3730 7.506114 TCAGTCCCATAATATAAGAGCGTTTT 58.494 34.615 0.00 0.00 0.00 2.43
3649 3731 7.990886 TCAGTCCCATAATATAAGAGCGTTTTT 59.009 33.333 0.00 0.00 0.00 1.94
3650 3732 8.070171 CAGTCCCATAATATAAGAGCGTTTTTG 58.930 37.037 0.00 0.00 0.00 2.44
3651 3733 7.990886 AGTCCCATAATATAAGAGCGTTTTTGA 59.009 33.333 0.00 0.00 0.00 2.69
3652 3734 8.068380 GTCCCATAATATAAGAGCGTTTTTGAC 58.932 37.037 0.00 0.00 0.00 3.18
3653 3735 7.771361 TCCCATAATATAAGAGCGTTTTTGACA 59.229 33.333 0.00 0.00 0.00 3.58
3654 3736 7.855904 CCCATAATATAAGAGCGTTTTTGACAC 59.144 37.037 0.00 0.00 0.00 3.67
3655 3737 8.612619 CCATAATATAAGAGCGTTTTTGACACT 58.387 33.333 0.00 0.00 0.00 3.55
3659 3741 9.988350 AATATAAGAGCGTTTTTGACACTATTG 57.012 29.630 0.00 0.00 0.00 1.90
3660 3742 5.751243 AAGAGCGTTTTTGACACTATTGT 57.249 34.783 0.00 0.00 39.32 2.71
3661 3743 6.854496 AAGAGCGTTTTTGACACTATTGTA 57.146 33.333 0.00 0.00 35.47 2.41
3662 3744 7.435068 AAGAGCGTTTTTGACACTATTGTAT 57.565 32.000 0.00 0.00 35.47 2.29
3663 3745 8.542497 AAGAGCGTTTTTGACACTATTGTATA 57.458 30.769 0.00 0.00 35.47 1.47
3664 3746 8.718102 AGAGCGTTTTTGACACTATTGTATAT 57.282 30.769 0.00 0.00 35.47 0.86
3665 3747 9.162764 AGAGCGTTTTTGACACTATTGTATATT 57.837 29.630 0.00 0.00 35.47 1.28
3673 3755 9.483916 TTTGACACTATTGTATATTATGGGACG 57.516 33.333 0.00 0.00 35.47 4.79
3674 3756 7.608153 TGACACTATTGTATATTATGGGACGG 58.392 38.462 0.00 0.00 35.47 4.79
3675 3757 7.452189 TGACACTATTGTATATTATGGGACGGA 59.548 37.037 0.00 0.00 35.47 4.69
3676 3758 7.837863 ACACTATTGTATATTATGGGACGGAG 58.162 38.462 0.00 0.00 32.60 4.63
3677 3759 7.093465 ACACTATTGTATATTATGGGACGGAGG 60.093 40.741 0.00 0.00 32.60 4.30
3678 3760 5.693769 ATTGTATATTATGGGACGGAGGG 57.306 43.478 0.00 0.00 0.00 4.30
3679 3761 4.407329 TGTATATTATGGGACGGAGGGA 57.593 45.455 0.00 0.00 0.00 4.20
3680 3762 4.350245 TGTATATTATGGGACGGAGGGAG 58.650 47.826 0.00 0.00 0.00 4.30
3681 3763 3.562108 ATATTATGGGACGGAGGGAGT 57.438 47.619 0.00 0.00 0.00 3.85
3682 3764 4.687262 ATATTATGGGACGGAGGGAGTA 57.313 45.455 0.00 0.00 0.00 2.59
3695 3777 7.418254 GGACGGAGGGAGTATTAAATTTAGTCA 60.418 40.741 0.00 0.00 0.00 3.41
3854 3937 7.138054 AGAAAGTTATCCCCACCAACTATAG 57.862 40.000 0.00 0.00 32.35 1.31
3878 3961 6.012508 AGGAGGATTCACATTTTCTAGAACCA 60.013 38.462 4.18 0.00 0.00 3.67
3885 3968 3.440173 ACATTTTCTAGAACCACATGCCG 59.560 43.478 4.18 0.00 0.00 5.69
3887 3970 3.965379 TTTCTAGAACCACATGCCGTA 57.035 42.857 4.18 0.00 0.00 4.02
3928 4012 8.303876 TGGGAATTAAGTGTAAGAAAAATGCTC 58.696 33.333 0.00 0.00 0.00 4.26
3957 4041 3.969287 TTGGAGGTCACAGATCTCAAG 57.031 47.619 9.29 0.00 41.21 3.02
4058 4142 0.545548 AGGGTGAGGAACTGAGGACC 60.546 60.000 0.00 0.00 41.55 4.46
4059 4143 1.554583 GGGTGAGGAACTGAGGACCC 61.555 65.000 0.00 0.00 41.55 4.46
4060 4144 1.592223 GTGAGGAACTGAGGACCCG 59.408 63.158 0.00 0.00 41.55 5.28
4061 4145 1.155390 TGAGGAACTGAGGACCCGT 59.845 57.895 0.00 0.00 41.55 5.28
4062 4146 0.406750 TGAGGAACTGAGGACCCGTA 59.593 55.000 0.00 0.00 41.55 4.02
4175 4259 9.409918 TCTACACTCTAAAGCATGTCTATAACT 57.590 33.333 0.00 0.00 0.00 2.24
4176 4260 9.672086 CTACACTCTAAAGCATGTCTATAACTC 57.328 37.037 0.00 0.00 0.00 3.01
4177 4261 8.299990 ACACTCTAAAGCATGTCTATAACTCT 57.700 34.615 0.00 0.00 0.00 3.24
4178 4262 9.409918 ACACTCTAAAGCATGTCTATAACTCTA 57.590 33.333 0.00 0.00 0.00 2.43
4321 4405 6.889301 TCATTTGCAACTCTTGAGAGAAAT 57.111 33.333 14.61 7.17 44.74 2.17
4322 4406 7.281040 TCATTTGCAACTCTTGAGAGAAATT 57.719 32.000 14.61 0.00 44.74 1.82
4323 4407 7.719483 TCATTTGCAACTCTTGAGAGAAATTT 58.281 30.769 14.61 0.00 44.74 1.82
4324 4408 8.199449 TCATTTGCAACTCTTGAGAGAAATTTT 58.801 29.630 14.61 0.00 44.74 1.82
4362 4446 7.190920 ACTTTGTGAGTGTACTTATGAAAGC 57.809 36.000 0.00 0.00 37.17 3.51
4517 4602 7.926555 CGGATTAGTTTCTATTTGAGCCTCTTA 59.073 37.037 0.00 0.00 0.00 2.10
4670 4755 3.185246 AGTACCGCATGAGATTGAAGG 57.815 47.619 0.00 0.00 0.00 3.46
4677 4762 5.829924 ACCGCATGAGATTGAAGGAAAATAT 59.170 36.000 0.00 0.00 0.00 1.28
4712 4797 6.341316 TGTATTTGTCTAGTTGGAGAGCATC 58.659 40.000 0.00 0.00 0.00 3.91
4753 4854 5.988310 TCAGCATTTCTTTCCACATTCAT 57.012 34.783 0.00 0.00 0.00 2.57
4754 4855 5.957798 TCAGCATTTCTTTCCACATTCATC 58.042 37.500 0.00 0.00 0.00 2.92
4755 4856 5.477637 TCAGCATTTCTTTCCACATTCATCA 59.522 36.000 0.00 0.00 0.00 3.07
4756 4857 6.153851 TCAGCATTTCTTTCCACATTCATCAT 59.846 34.615 0.00 0.00 0.00 2.45
4757 4858 6.255670 CAGCATTTCTTTCCACATTCATCATG 59.744 38.462 0.00 0.00 39.07 3.07
4758 4859 6.153851 AGCATTTCTTTCCACATTCATCATGA 59.846 34.615 0.00 0.00 36.24 3.07
4759 4860 6.255020 GCATTTCTTTCCACATTCATCATGAC 59.745 38.462 0.00 0.00 36.24 3.06
4760 4861 6.897706 TTTCTTTCCACATTCATCATGACA 57.102 33.333 0.00 0.00 36.24 3.58
4761 4862 6.897706 TTCTTTCCACATTCATCATGACAA 57.102 33.333 0.00 0.00 36.24 3.18
4762 4863 6.897706 TCTTTCCACATTCATCATGACAAA 57.102 33.333 0.00 0.00 36.24 2.83
4763 4864 6.916440 TCTTTCCACATTCATCATGACAAAG 58.084 36.000 0.00 0.00 36.24 2.77
4764 4865 5.648178 TTCCACATTCATCATGACAAAGG 57.352 39.130 0.00 0.00 36.24 3.11
4765 4866 4.920999 TCCACATTCATCATGACAAAGGA 58.079 39.130 0.00 1.49 36.24 3.36
4766 4867 5.323581 TCCACATTCATCATGACAAAGGAA 58.676 37.500 0.00 0.00 36.24 3.36
4767 4868 5.774184 TCCACATTCATCATGACAAAGGAAA 59.226 36.000 0.00 0.00 36.24 3.13
4768 4869 6.267242 TCCACATTCATCATGACAAAGGAAAA 59.733 34.615 0.00 0.00 36.24 2.29
4769 4870 7.038870 TCCACATTCATCATGACAAAGGAAAAT 60.039 33.333 0.00 0.00 36.24 1.82
4770 4871 7.604927 CCACATTCATCATGACAAAGGAAAATT 59.395 33.333 0.00 0.00 36.24 1.82
4771 4872 8.653338 CACATTCATCATGACAAAGGAAAATTC 58.347 33.333 0.00 0.00 36.24 2.17
4772 4873 8.369424 ACATTCATCATGACAAAGGAAAATTCA 58.631 29.630 0.00 0.00 36.24 2.57
4778 4879 6.720748 TCATGACAAAGGAAAATTCATGAGGA 59.279 34.615 8.19 0.00 44.76 3.71
4805 4906 9.424319 TCTGTCAGAATTGTAGTACTGATTTTC 57.576 33.333 5.39 4.22 40.61 2.29
4863 4975 5.047092 TGGTTAGCCTGTACTACTTGTTACC 60.047 44.000 0.00 0.00 35.27 2.85
4909 5023 4.402793 ACAGTAGCGAGGACAGAATAATGT 59.597 41.667 0.00 0.00 35.68 2.71
4910 5024 5.105310 ACAGTAGCGAGGACAGAATAATGTT 60.105 40.000 0.00 0.00 32.25 2.71
4911 5025 6.096423 ACAGTAGCGAGGACAGAATAATGTTA 59.904 38.462 0.00 0.00 32.25 2.41
4912 5026 6.418226 CAGTAGCGAGGACAGAATAATGTTAC 59.582 42.308 0.00 0.00 32.25 2.50
4913 5027 5.599999 AGCGAGGACAGAATAATGTTACT 57.400 39.130 0.00 0.00 32.25 2.24
4914 5028 5.593010 AGCGAGGACAGAATAATGTTACTC 58.407 41.667 0.00 0.00 35.68 2.59
4915 5029 5.361285 AGCGAGGACAGAATAATGTTACTCT 59.639 40.000 0.00 0.00 36.31 3.24
4916 5030 5.688176 GCGAGGACAGAATAATGTTACTCTC 59.312 44.000 0.00 0.00 36.31 3.20
4917 5031 6.210078 CGAGGACAGAATAATGTTACTCTCC 58.790 44.000 9.35 0.00 36.31 3.71
4918 5032 6.183360 CGAGGACAGAATAATGTTACTCTCCA 60.183 42.308 0.00 0.00 36.31 3.86
4919 5033 7.470702 CGAGGACAGAATAATGTTACTCTCCAT 60.471 40.741 0.00 0.00 36.31 3.41
4938 5063 9.224267 CTCTCCATTTCTAATTTTCAGTCTGAA 57.776 33.333 11.36 11.36 34.03 3.02
5108 5233 4.101585 TCAGCTCCACCATCTCGAAAATAT 59.898 41.667 0.00 0.00 0.00 1.28
5134 5259 1.749258 GCGGAGGGAATTGGTGACC 60.749 63.158 0.00 0.00 0.00 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.676678 ATGGTGGTGACGGAGGATCG 61.677 60.000 0.00 0.00 34.37 3.69
1 2 0.105039 GATGGTGGTGACGGAGGATC 59.895 60.000 0.00 0.00 0.00 3.36
3 4 0.333652 TAGATGGTGGTGACGGAGGA 59.666 55.000 0.00 0.00 0.00 3.71
4 5 0.747255 CTAGATGGTGGTGACGGAGG 59.253 60.000 0.00 0.00 0.00 4.30
5 6 0.103208 GCTAGATGGTGGTGACGGAG 59.897 60.000 0.00 0.00 0.00 4.63
6 7 0.613572 TGCTAGATGGTGGTGACGGA 60.614 55.000 0.00 0.00 0.00 4.69
7 8 0.179100 CTGCTAGATGGTGGTGACGG 60.179 60.000 0.00 0.00 0.00 4.79
8 9 0.817654 TCTGCTAGATGGTGGTGACG 59.182 55.000 0.00 0.00 0.00 4.35
9 10 1.827969 AGTCTGCTAGATGGTGGTGAC 59.172 52.381 0.00 0.00 0.00 3.67
10 11 2.238084 AGTCTGCTAGATGGTGGTGA 57.762 50.000 0.00 0.00 0.00 4.02
11 12 2.736719 CGAAGTCTGCTAGATGGTGGTG 60.737 54.545 0.00 0.00 0.00 4.17
12 13 1.478510 CGAAGTCTGCTAGATGGTGGT 59.521 52.381 0.00 0.00 0.00 4.16
13 14 1.478510 ACGAAGTCTGCTAGATGGTGG 59.521 52.381 0.00 0.00 29.74 4.61
14 15 2.534298 CACGAAGTCTGCTAGATGGTG 58.466 52.381 0.00 0.00 41.61 4.17
15 16 1.478510 CCACGAAGTCTGCTAGATGGT 59.521 52.381 0.00 0.00 41.61 3.55
16 17 1.804372 GCCACGAAGTCTGCTAGATGG 60.804 57.143 0.00 0.00 41.61 3.51
17 18 1.565305 GCCACGAAGTCTGCTAGATG 58.435 55.000 0.00 0.00 41.61 2.90
18 19 0.101399 CGCCACGAAGTCTGCTAGAT 59.899 55.000 0.00 0.00 41.61 1.98
19 20 0.958876 TCGCCACGAAGTCTGCTAGA 60.959 55.000 0.00 0.00 41.61 2.43
20 21 0.109272 TTCGCCACGAAGTCTGCTAG 60.109 55.000 0.00 0.00 41.61 3.42
21 22 0.388134 GTTCGCCACGAAGTCTGCTA 60.388 55.000 2.15 0.00 46.54 3.49
22 23 1.664965 GTTCGCCACGAAGTCTGCT 60.665 57.895 2.15 0.00 46.54 4.24
23 24 1.954146 TGTTCGCCACGAAGTCTGC 60.954 57.895 2.15 0.00 46.54 4.26
24 25 0.874175 TGTGTTCGCCACGAAGTCTG 60.874 55.000 2.15 0.00 46.54 3.51
25 26 0.179094 TTGTGTTCGCCACGAAGTCT 60.179 50.000 2.15 0.00 46.54 3.24
26 27 0.865769 ATTGTGTTCGCCACGAAGTC 59.134 50.000 2.15 0.58 46.54 3.01
27 28 0.586319 CATTGTGTTCGCCACGAAGT 59.414 50.000 2.15 0.00 46.54 3.01
28 29 0.110238 CCATTGTGTTCGCCACGAAG 60.110 55.000 2.15 0.00 46.54 3.79
32 33 1.371635 GTGCCATTGTGTTCGCCAC 60.372 57.895 0.00 0.00 44.78 5.01
33 34 1.106351 AAGTGCCATTGTGTTCGCCA 61.106 50.000 0.00 0.00 0.00 5.69
34 35 0.031994 AAAGTGCCATTGTGTTCGCC 59.968 50.000 0.00 0.00 0.00 5.54
35 36 1.851658 AAAAGTGCCATTGTGTTCGC 58.148 45.000 0.00 0.00 0.00 4.70
864 865 4.261280 CCGTCCCAAAATACAAGAACGTTT 60.261 41.667 0.46 0.00 0.00 3.60
865 866 3.251487 CCGTCCCAAAATACAAGAACGTT 59.749 43.478 0.00 0.00 0.00 3.99
866 867 2.809696 CCGTCCCAAAATACAAGAACGT 59.190 45.455 0.00 0.00 0.00 3.99
867 868 3.068560 TCCGTCCCAAAATACAAGAACG 58.931 45.455 0.00 0.00 0.00 3.95
868 869 3.439129 CCTCCGTCCCAAAATACAAGAAC 59.561 47.826 0.00 0.00 0.00 3.01
869 870 3.560453 CCCTCCGTCCCAAAATACAAGAA 60.560 47.826 0.00 0.00 0.00 2.52
870 871 2.026636 CCCTCCGTCCCAAAATACAAGA 60.027 50.000 0.00 0.00 0.00 3.02
871 872 2.026636 TCCCTCCGTCCCAAAATACAAG 60.027 50.000 0.00 0.00 0.00 3.16
872 873 1.986631 TCCCTCCGTCCCAAAATACAA 59.013 47.619 0.00 0.00 0.00 2.41
873 874 1.557832 CTCCCTCCGTCCCAAAATACA 59.442 52.381 0.00 0.00 0.00 2.29
874 875 1.558294 ACTCCCTCCGTCCCAAAATAC 59.442 52.381 0.00 0.00 0.00 1.89
875 876 1.961133 ACTCCCTCCGTCCCAAAATA 58.039 50.000 0.00 0.00 0.00 1.40
876 877 1.961133 TACTCCCTCCGTCCCAAAAT 58.039 50.000 0.00 0.00 0.00 1.82
877 878 1.961133 ATACTCCCTCCGTCCCAAAA 58.039 50.000 0.00 0.00 0.00 2.44
878 879 2.852714 TATACTCCCTCCGTCCCAAA 57.147 50.000 0.00 0.00 0.00 3.28
879 880 2.852714 TTATACTCCCTCCGTCCCAA 57.147 50.000 0.00 0.00 0.00 4.12
880 881 3.140707 TGTATTATACTCCCTCCGTCCCA 59.859 47.826 3.92 0.00 0.00 4.37
881 882 3.771216 TGTATTATACTCCCTCCGTCCC 58.229 50.000 3.92 0.00 0.00 4.46
882 883 4.771054 ACATGTATTATACTCCCTCCGTCC 59.229 45.833 0.00 0.00 0.00 4.79
883 884 5.979288 ACATGTATTATACTCCCTCCGTC 57.021 43.478 0.00 0.00 0.00 4.79
884 885 7.727186 TCTTTACATGTATTATACTCCCTCCGT 59.273 37.037 6.36 0.00 0.00 4.69
885 886 8.118976 TCTTTACATGTATTATACTCCCTCCG 57.881 38.462 6.36 0.00 0.00 4.63
886 887 9.930693 CTTCTTTACATGTATTATACTCCCTCC 57.069 37.037 6.36 0.00 0.00 4.30
1032 1033 2.076100 GATTGTGCAATCGGTCTGTGA 58.924 47.619 8.86 0.00 37.97 3.58
1177 1178 0.528466 GCGATCAAGCAGATGACGGA 60.528 55.000 0.00 0.00 37.00 4.69
1180 1181 1.257415 CGAAGCGATCAAGCAGATGAC 59.743 52.381 0.00 0.00 37.00 3.06
1181 1182 1.134995 ACGAAGCGATCAAGCAGATGA 60.135 47.619 0.00 0.00 37.00 2.92
1446 1447 3.525199 ACTAGCAAATCTGTTCTCCCCAT 59.475 43.478 0.00 0.00 0.00 4.00
1487 1488 4.101741 AGCCCTGAACTATGACAGATTACC 59.898 45.833 0.00 0.00 36.38 2.85
1541 1599 3.701205 TCTCAGCCAGCAATGTTTAGA 57.299 42.857 0.00 0.00 0.00 2.10
1604 1663 1.283321 GGCCTTGGTCATCTCCTTTCT 59.717 52.381 0.00 0.00 0.00 2.52
1673 1732 1.338579 TGATGTTATGTGGCGAGCACA 60.339 47.619 0.00 0.00 36.95 4.57
1693 1752 0.252193 AGACAGAGGCCTGCTCTCTT 60.252 55.000 12.00 0.00 44.16 2.85
1758 1818 4.554960 AGAGTTTACAAGGTCTTAGGGC 57.445 45.455 0.00 0.00 0.00 5.19
1793 1853 5.046910 TGGAAAGAGCTGCTAATTTTTCG 57.953 39.130 0.15 0.00 0.00 3.46
1845 1906 1.351017 CCAGTTCCACCACACATACCT 59.649 52.381 0.00 0.00 0.00 3.08
1847 1908 2.851263 TCCAGTTCCACCACACATAC 57.149 50.000 0.00 0.00 0.00 2.39
2048 2110 6.616237 ACATATAGACCATCATGCATGAGA 57.384 37.500 31.36 12.85 40.64 3.27
2079 2141 7.475015 CATTCCATTCAAATACACGTCTCATT 58.525 34.615 0.00 0.00 0.00 2.57
2217 2279 3.548818 GCTCATTTGTCGCACTCTGTTTT 60.549 43.478 0.00 0.00 0.00 2.43
2225 2287 2.422276 AAAAGGCTCATTTGTCGCAC 57.578 45.000 0.00 0.00 0.00 5.34
2340 2402 2.280628 CCATGCGACCTCCTTAGTTTC 58.719 52.381 0.00 0.00 0.00 2.78
2377 2439 7.552687 TGCTACTTGACAAATATCTCCGAAAAT 59.447 33.333 0.00 0.00 0.00 1.82
2438 2518 8.376203 CAGCGTTATCATTTAGCAGTATATCAC 58.624 37.037 0.00 0.00 0.00 3.06
2833 2914 4.142730 GCAAAGTTTGTTGAACCAAATGCA 60.143 37.500 16.70 0.00 37.59 3.96
3034 3115 5.363868 TCCCTCATCACTCCAATTGTACTAG 59.636 44.000 4.43 0.00 0.00 2.57
3200 3282 3.820689 TGCGACAATTTCATTCCTTTCG 58.179 40.909 0.00 0.00 0.00 3.46
3398 3480 2.520904 GCGATGCAGCTCGACCTTC 61.521 63.158 13.68 0.00 41.12 3.46
3618 3700 6.127196 GCTCTTATATTATGGGACTGAGGGAG 60.127 46.154 0.00 0.00 0.00 4.30
3619 3701 5.721960 GCTCTTATATTATGGGACTGAGGGA 59.278 44.000 0.00 0.00 0.00 4.20
3620 3702 5.394663 CGCTCTTATATTATGGGACTGAGGG 60.395 48.000 0.00 0.00 0.00 4.30
3621 3703 5.186021 ACGCTCTTATATTATGGGACTGAGG 59.814 44.000 0.00 0.00 0.00 3.86
3622 3704 6.274157 ACGCTCTTATATTATGGGACTGAG 57.726 41.667 0.00 0.00 0.00 3.35
3623 3705 6.665992 AACGCTCTTATATTATGGGACTGA 57.334 37.500 0.00 0.00 0.00 3.41
3624 3706 7.730364 AAAACGCTCTTATATTATGGGACTG 57.270 36.000 0.00 0.00 0.00 3.51
3625 3707 7.990886 TCAAAAACGCTCTTATATTATGGGACT 59.009 33.333 0.00 0.00 0.00 3.85
3626 3708 8.068380 GTCAAAAACGCTCTTATATTATGGGAC 58.932 37.037 0.00 0.00 0.00 4.46
3627 3709 7.771361 TGTCAAAAACGCTCTTATATTATGGGA 59.229 33.333 0.00 0.00 0.00 4.37
3628 3710 7.855904 GTGTCAAAAACGCTCTTATATTATGGG 59.144 37.037 0.00 0.00 35.42 4.00
3629 3711 8.612619 AGTGTCAAAAACGCTCTTATATTATGG 58.387 33.333 0.00 0.00 45.69 2.74
3633 3715 9.988350 CAATAGTGTCAAAAACGCTCTTATATT 57.012 29.630 0.00 0.00 45.69 1.28
3634 3716 9.162764 ACAATAGTGTCAAAAACGCTCTTATAT 57.837 29.630 0.00 0.00 45.69 0.86
3635 3717 8.542497 ACAATAGTGTCAAAAACGCTCTTATA 57.458 30.769 0.00 0.00 45.69 0.98
3636 3718 7.435068 ACAATAGTGTCAAAAACGCTCTTAT 57.565 32.000 0.00 0.00 45.69 1.73
3637 3719 6.854496 ACAATAGTGTCAAAAACGCTCTTA 57.146 33.333 0.00 0.00 45.69 2.10
3638 3720 5.751243 ACAATAGTGTCAAAAACGCTCTT 57.249 34.783 0.00 0.00 45.69 2.85
3639 3721 8.718102 ATATACAATAGTGTCAAAAACGCTCT 57.282 30.769 0.00 0.00 45.69 4.09
3647 3729 9.483916 CGTCCCATAATATACAATAGTGTCAAA 57.516 33.333 0.00 0.00 39.30 2.69
3648 3730 8.092068 CCGTCCCATAATATACAATAGTGTCAA 58.908 37.037 0.00 0.00 39.30 3.18
3649 3731 7.452189 TCCGTCCCATAATATACAATAGTGTCA 59.548 37.037 0.00 0.00 39.30 3.58
3650 3732 7.833786 TCCGTCCCATAATATACAATAGTGTC 58.166 38.462 0.00 0.00 39.30 3.67
3651 3733 7.093465 CCTCCGTCCCATAATATACAATAGTGT 60.093 40.741 0.00 0.00 42.09 3.55
3652 3734 7.265673 CCTCCGTCCCATAATATACAATAGTG 58.734 42.308 0.00 0.00 0.00 2.74
3653 3735 6.383147 CCCTCCGTCCCATAATATACAATAGT 59.617 42.308 0.00 0.00 0.00 2.12
3654 3736 6.610020 TCCCTCCGTCCCATAATATACAATAG 59.390 42.308 0.00 0.00 0.00 1.73
3655 3737 6.504849 TCCCTCCGTCCCATAATATACAATA 58.495 40.000 0.00 0.00 0.00 1.90
3656 3738 5.347124 TCCCTCCGTCCCATAATATACAAT 58.653 41.667 0.00 0.00 0.00 2.71
3657 3739 4.754311 TCCCTCCGTCCCATAATATACAA 58.246 43.478 0.00 0.00 0.00 2.41
3658 3740 4.202749 ACTCCCTCCGTCCCATAATATACA 60.203 45.833 0.00 0.00 0.00 2.29
3659 3741 4.351127 ACTCCCTCCGTCCCATAATATAC 58.649 47.826 0.00 0.00 0.00 1.47
3660 3742 4.687262 ACTCCCTCCGTCCCATAATATA 57.313 45.455 0.00 0.00 0.00 0.86
3661 3743 3.562108 ACTCCCTCCGTCCCATAATAT 57.438 47.619 0.00 0.00 0.00 1.28
3662 3744 4.687262 ATACTCCCTCCGTCCCATAATA 57.313 45.455 0.00 0.00 0.00 0.98
3663 3745 3.562108 ATACTCCCTCCGTCCCATAAT 57.438 47.619 0.00 0.00 0.00 1.28
3664 3746 3.339713 AATACTCCCTCCGTCCCATAA 57.660 47.619 0.00 0.00 0.00 1.90
3665 3747 4.474303 TTAATACTCCCTCCGTCCCATA 57.526 45.455 0.00 0.00 0.00 2.74
3666 3748 3.339713 TTAATACTCCCTCCGTCCCAT 57.660 47.619 0.00 0.00 0.00 4.00
3667 3749 2.852714 TTAATACTCCCTCCGTCCCA 57.147 50.000 0.00 0.00 0.00 4.37
3668 3750 4.701651 AATTTAATACTCCCTCCGTCCC 57.298 45.455 0.00 0.00 0.00 4.46
3669 3751 6.824553 ACTAAATTTAATACTCCCTCCGTCC 58.175 40.000 0.00 0.00 0.00 4.79
3670 3752 7.437565 GTGACTAAATTTAATACTCCCTCCGTC 59.562 40.741 0.00 0.14 0.00 4.79
3671 3753 7.125356 AGTGACTAAATTTAATACTCCCTCCGT 59.875 37.037 0.00 0.00 0.00 4.69
3672 3754 7.498443 AGTGACTAAATTTAATACTCCCTCCG 58.502 38.462 0.00 0.00 0.00 4.63
3695 3777 5.348164 GTGCAATTTGGTTCTGTGTTAAGT 58.652 37.500 0.00 0.00 0.00 2.24
3854 3937 6.094186 GTGGTTCTAGAAAATGTGAATCCTCC 59.906 42.308 6.78 0.00 0.00 4.30
3878 3961 7.602644 CCAACATAAACTATAGATACGGCATGT 59.397 37.037 6.78 3.49 0.00 3.21
3928 4012 7.052873 AGATCTGTGACCTCCAAATAAATGAG 58.947 38.462 0.00 0.00 0.00 2.90
3957 4041 9.074443 GTATAAGATACATTAGCGGCTTAAGAC 57.926 37.037 8.26 1.20 0.00 3.01
4058 4142 9.813446 GGAGGGAGTATATATGTTATTTTACGG 57.187 37.037 0.00 0.00 0.00 4.02
4059 4143 9.512435 CGGAGGGAGTATATATGTTATTTTACG 57.488 37.037 0.00 0.00 0.00 3.18
4062 4146 9.939802 GAACGGAGGGAGTATATATGTTATTTT 57.060 33.333 0.00 0.00 0.00 1.82
4131 4215 7.615403 AGTGTAGATTCACTCATTTTGCTCTA 58.385 34.615 0.00 0.00 44.07 2.43
4173 4257 8.546322 TGGACTACATACGGATGTATATAGAGT 58.454 37.037 20.64 15.35 45.42 3.24
4174 4258 8.959705 TGGACTACATACGGATGTATATAGAG 57.040 38.462 20.64 12.20 45.42 2.43
4179 4263 9.689501 TCAATATGGACTACATACGGATGTATA 57.310 33.333 20.64 11.30 45.42 1.47
4180 4264 8.589701 TCAATATGGACTACATACGGATGTAT 57.410 34.615 20.64 9.39 45.42 2.29
4258 4342 8.980610 CATGATCAAAACTTGTTGAATAAAGCA 58.019 29.630 0.00 0.00 40.76 3.91
4343 4427 3.617263 CCGGCTTTCATAAGTACACTCAC 59.383 47.826 0.00 0.00 33.74 3.51
4344 4428 3.857052 CCGGCTTTCATAAGTACACTCA 58.143 45.455 0.00 0.00 33.74 3.41
4345 4429 2.608090 GCCGGCTTTCATAAGTACACTC 59.392 50.000 22.15 0.00 33.74 3.51
4349 4433 3.007635 AGTTGCCGGCTTTCATAAGTAC 58.992 45.455 29.70 9.40 33.74 2.73
4361 4445 3.267483 TGATCTTTAACTAGTTGCCGGC 58.733 45.455 22.73 22.73 0.00 6.13
4362 4446 4.504858 ACTGATCTTTAACTAGTTGCCGG 58.495 43.478 18.56 0.00 0.00 6.13
4400 4484 5.574188 ACTAGAGCTTTGGATTGATGGTTT 58.426 37.500 0.00 0.00 0.00 3.27
4406 4490 6.127451 TGACGATAACTAGAGCTTTGGATTGA 60.127 38.462 0.00 0.00 0.00 2.57
4517 4602 6.260936 CAGAGTTTGTTAGGAAATCACAGTGT 59.739 38.462 0.00 0.00 0.00 3.55
4687 4772 5.724328 TGCTCTCCAACTAGACAAATACAG 58.276 41.667 0.00 0.00 0.00 2.74
4688 4773 5.738619 TGCTCTCCAACTAGACAAATACA 57.261 39.130 0.00 0.00 0.00 2.29
4689 4774 6.578023 AGATGCTCTCCAACTAGACAAATAC 58.422 40.000 0.00 0.00 0.00 1.89
4690 4775 6.798427 AGATGCTCTCCAACTAGACAAATA 57.202 37.500 0.00 0.00 0.00 1.40
4712 4797 7.615582 TGCTGATAAATGAGTGGAGTAAAAG 57.384 36.000 0.00 0.00 0.00 2.27
4754 4855 6.927416 TCCTCATGAATTTTCCTTTGTCATG 58.073 36.000 0.00 5.75 44.46 3.07
4755 4856 7.618512 AGATCCTCATGAATTTTCCTTTGTCAT 59.381 33.333 0.00 0.00 0.00 3.06
4756 4857 6.950041 AGATCCTCATGAATTTTCCTTTGTCA 59.050 34.615 0.00 0.00 0.00 3.58
4757 4858 7.094032 ACAGATCCTCATGAATTTTCCTTTGTC 60.094 37.037 0.00 0.00 0.00 3.18
4758 4859 6.723052 ACAGATCCTCATGAATTTTCCTTTGT 59.277 34.615 0.00 0.00 0.00 2.83
4759 4860 7.094075 TGACAGATCCTCATGAATTTTCCTTTG 60.094 37.037 0.00 0.00 0.00 2.77
4760 4861 6.950041 TGACAGATCCTCATGAATTTTCCTTT 59.050 34.615 0.00 0.00 0.00 3.11
4761 4862 6.487828 TGACAGATCCTCATGAATTTTCCTT 58.512 36.000 0.00 0.00 0.00 3.36
4762 4863 6.069789 TCTGACAGATCCTCATGAATTTTCCT 60.070 38.462 0.00 0.00 0.00 3.36
4763 4864 6.118170 TCTGACAGATCCTCATGAATTTTCC 58.882 40.000 0.00 0.00 0.00 3.13
4764 4865 7.621428 TTCTGACAGATCCTCATGAATTTTC 57.379 36.000 5.87 0.00 0.00 2.29
4765 4866 8.467598 CAATTCTGACAGATCCTCATGAATTTT 58.532 33.333 5.87 0.00 30.94 1.82
4766 4867 7.614583 ACAATTCTGACAGATCCTCATGAATTT 59.385 33.333 5.87 10.60 30.94 1.82
4767 4868 7.117397 ACAATTCTGACAGATCCTCATGAATT 58.883 34.615 5.87 14.59 32.11 2.17
4768 4869 6.660800 ACAATTCTGACAGATCCTCATGAAT 58.339 36.000 5.87 0.00 0.00 2.57
4769 4870 6.058553 ACAATTCTGACAGATCCTCATGAA 57.941 37.500 5.87 0.00 0.00 2.57
4770 4871 5.688814 ACAATTCTGACAGATCCTCATGA 57.311 39.130 5.87 0.00 0.00 3.07
4771 4872 6.580788 ACTACAATTCTGACAGATCCTCATG 58.419 40.000 5.87 2.66 0.00 3.07
4772 4873 6.805016 ACTACAATTCTGACAGATCCTCAT 57.195 37.500 5.87 0.00 0.00 2.90
4778 4879 9.950496 AAAATCAGTACTACAATTCTGACAGAT 57.050 29.630 5.87 0.00 39.27 2.90
4836 4937 5.488341 ACAAGTAGTACAGGCTAACCATTG 58.512 41.667 2.52 0.00 39.06 2.82
4863 4975 5.290643 GTGACCTGAAGAGAAAATCTGATCG 59.709 44.000 0.00 0.00 38.67 3.69
4910 5024 9.658799 CAGACTGAAAATTAGAAATGGAGAGTA 57.341 33.333 0.00 0.00 0.00 2.59
4911 5025 8.378565 TCAGACTGAAAATTAGAAATGGAGAGT 58.621 33.333 1.64 0.00 0.00 3.24
4912 5026 8.783833 TCAGACTGAAAATTAGAAATGGAGAG 57.216 34.615 1.64 0.00 0.00 3.20
4913 5027 9.003658 GTTCAGACTGAAAATTAGAAATGGAGA 57.996 33.333 19.32 0.00 38.22 3.71
4914 5028 9.007901 AGTTCAGACTGAAAATTAGAAATGGAG 57.992 33.333 19.32 0.00 38.22 3.86
4915 5029 8.924511 AGTTCAGACTGAAAATTAGAAATGGA 57.075 30.769 19.32 0.00 38.22 3.41
4916 5030 9.617975 GAAGTTCAGACTGAAAATTAGAAATGG 57.382 33.333 19.32 0.00 38.22 3.16
4919 5033 9.173021 TGTGAAGTTCAGACTGAAAATTAGAAA 57.827 29.630 19.32 1.77 38.22 2.52
4924 5049 6.260936 ACGATGTGAAGTTCAGACTGAAAATT 59.739 34.615 19.32 16.21 38.22 1.82
4938 5063 8.283291 GTCTGAAGAAAATAAACGATGTGAAGT 58.717 33.333 0.00 0.00 0.00 3.01
5108 5233 0.917333 AATTCCCTCCGCCCCAGTTA 60.917 55.000 0.00 0.00 0.00 2.24
5134 5259 5.808366 TGGATTAGGCTAATAGGTCTGTG 57.192 43.478 19.27 0.00 0.00 3.66


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

AutoCloner maintained by Alex Coulton.