Multiple sequence alignment - TraesCS1A01G225900

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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 TraesCS1A01G225900 chr1A 100.000 6382 0 0 1 6382 396282080 396288461 0.000000e+00 11786.0
1 TraesCS1A01G225900 chr1A 88.225 1155 98 17 3016 4133 396282412 396283565 0.000000e+00 1345.0
2 TraesCS1A01G225900 chr1A 88.225 1155 98 17 333 1486 396285095 396286212 0.000000e+00 1345.0
3 TraesCS1A01G225900 chr1A 83.764 696 73 26 930 1608 396262278 396262950 1.950000e-174 623.0
4 TraesCS1A01G225900 chr1A 85.870 276 28 7 4577 4846 396272500 396272770 3.770000e-72 283.0
5 TraesCS1A01G225900 chr1A 85.621 153 18 4 4727 4875 396284675 396284827 2.380000e-34 158.0
6 TraesCS1A01G225900 chr1A 85.621 153 18 4 2596 2748 396286806 396286954 2.380000e-34 158.0
7 TraesCS1A01G225900 chr1A 95.385 65 2 1 232 295 396282253 396282317 1.130000e-17 102.0
8 TraesCS1A01G225900 chr1A 95.385 65 2 1 174 238 396282311 396282374 1.130000e-17 102.0
9 TraesCS1A01G225900 chr1B 89.139 1731 129 18 2574 4301 427595418 427597092 0.000000e+00 2100.0
10 TraesCS1A01G225900 chr1B 91.503 1530 105 15 2778 4301 427775872 427777382 0.000000e+00 2082.0
11 TraesCS1A01G225900 chr1B 89.158 1282 90 21 3024 4291 427773452 427774698 0.000000e+00 1552.0
12 TraesCS1A01G225900 chr1B 86.144 1530 103 39 235 1719 427773345 427774810 0.000000e+00 1550.0
13 TraesCS1A01G225900 chr1B 87.987 1257 88 14 232 1486 427525099 427526294 0.000000e+00 1426.0
14 TraesCS1A01G225900 chr1B 86.609 1262 125 19 3016 4270 427525200 427526424 0.000000e+00 1354.0
15 TraesCS1A01G225900 chr1B 86.154 1170 106 27 319 1486 427776099 427777214 0.000000e+00 1212.0
16 TraesCS1A01G225900 chr1B 85.714 1169 106 25 319 1486 427595823 427596931 0.000000e+00 1177.0
17 TraesCS1A01G225900 chr1B 87.174 998 79 18 1764 2748 427774938 427775899 0.000000e+00 1088.0
18 TraesCS1A01G225900 chr1B 89.847 847 72 14 930 1768 427543046 427543886 0.000000e+00 1075.0
19 TraesCS1A01G225900 chr1B 84.792 697 75 19 930 1608 427522990 427523673 0.000000e+00 671.0
20 TraesCS1A01G225900 chr1B 86.808 614 60 12 5160 5773 427534213 427534805 0.000000e+00 665.0
21 TraesCS1A01G225900 chr1B 86.146 563 62 12 3583 4133 427543046 427543604 1.530000e-165 593.0
22 TraesCS1A01G225900 chr1B 81.018 727 88 27 3583 4297 427522990 427523678 3.390000e-147 532.0
23 TraesCS1A01G225900 chr1B 84.000 575 57 19 4965 5534 427777841 427778385 2.640000e-143 520.0
24 TraesCS1A01G225900 chr1B 91.257 366 28 2 4578 4941 427527090 427527453 4.440000e-136 496.0
25 TraesCS1A01G225900 chr1B 82.313 588 29 23 1987 2573 427544187 427544700 2.110000e-119 440.0
26 TraesCS1A01G225900 chr1B 92.359 301 16 4 4646 4941 427597307 427597605 7.650000e-114 422.0
27 TraesCS1A01G225900 chr1B 88.703 239 14 4 1764 2000 427543944 427544171 4.870000e-71 279.0
28 TraesCS1A01G225900 chr1B 86.695 233 25 2 5038 5264 427597649 427597881 2.950000e-63 254.0
29 TraesCS1A01G225900 chr1B 84.000 275 33 4 4646 4916 427772396 427772663 2.950000e-63 254.0
30 TraesCS1A01G225900 chr1B 96.026 151 6 0 4790 4940 427777703 427777853 4.940000e-61 246.0
31 TraesCS1A01G225900 chr1B 87.805 205 20 4 5260 5461 427599432 427599634 1.070000e-57 235.0
32 TraesCS1A01G225900 chr1B 94.667 150 8 0 4308 4457 427777444 427777593 3.850000e-57 233.0
33 TraesCS1A01G225900 chr1B 94.815 135 6 1 4446 4580 658317919 658318052 6.480000e-50 209.0
34 TraesCS1A01G225900 chr1B 95.385 130 6 0 4451 4580 669582963 669583092 2.330000e-49 207.0
35 TraesCS1A01G225900 chr1B 85.806 155 16 5 2596 2748 427597387 427597537 6.620000e-35 159.0
36 TraesCS1A01G225900 chr1B 88.028 142 5 5 5022 5158 427527475 427527609 2.380000e-34 158.0
37 TraesCS1A01G225900 chr1B 90.083 121 7 4 410 529 427599460 427599576 1.110000e-32 152.0
38 TraesCS1A01G225900 chr1B 85.816 141 14 5 6229 6368 427628423 427628558 1.850000e-30 145.0
39 TraesCS1A01G225900 chr1B 86.232 138 10 5 107 238 427773270 427773404 2.400000e-29 141.0
40 TraesCS1A01G225900 chr1B 85.926 135 14 4 3077 3210 427599446 427599576 8.630000e-29 139.0
41 TraesCS1A01G225900 chr1B 89.655 87 8 1 2662 2748 427777703 427777788 6.760000e-20 110.0
42 TraesCS1A01G225900 chr1B 96.491 57 2 0 4848 4904 427595623 427595679 1.890000e-15 95.3
43 TraesCS1A01G225900 chr1B 94.915 59 3 0 4344 4402 427527052 427526994 6.810000e-15 93.5
44 TraesCS1A01G225900 chr1B 94.915 59 3 0 4965 5023 427527440 427527498 6.810000e-15 93.5
45 TraesCS1A01G225900 chr1B 100.000 40 0 0 4303 4342 427526504 427526543 2.470000e-09 75.0
46 TraesCS1A01G225900 chr1B 96.970 33 1 0 245 277 427527464 427527496 8.940000e-04 56.5
47 TraesCS1A01G225900 chr1D 93.239 1420 75 10 2889 4301 315642629 315644034 0.000000e+00 2071.0
48 TraesCS1A01G225900 chr1D 87.740 1509 117 26 283 1768 315639614 315641077 0.000000e+00 1700.0
49 TraesCS1A01G225900 chr1D 93.180 1041 48 14 1765 2799 315641136 315642159 0.000000e+00 1507.0
50 TraesCS1A01G225900 chr1D 90.328 1158 91 9 2989 4133 315639646 315640795 0.000000e+00 1498.0
51 TraesCS1A01G225900 chr1D 88.356 1168 96 14 322 1486 315642743 315643873 0.000000e+00 1367.0
52 TraesCS1A01G225900 chr1D 87.485 807 54 16 2125 2921 315638212 315638981 0.000000e+00 887.0
53 TraesCS1A01G225900 chr1D 81.599 1163 110 48 5026 6130 315645159 315646275 0.000000e+00 867.0
54 TraesCS1A01G225900 chr1D 83.780 709 76 23 930 1620 315616743 315617430 2.510000e-178 636.0
55 TraesCS1A01G225900 chr1D 94.382 356 13 4 4578 4932 315644566 315644915 2.020000e-149 540.0
56 TraesCS1A01G225900 chr1D 81.077 724 82 27 3583 4297 315616743 315617420 1.580000e-145 527.0
57 TraesCS1A01G225900 chr1D 90.423 355 23 9 1764 2111 315636980 315637330 2.100000e-124 457.0
58 TraesCS1A01G225900 chr1D 80.626 511 72 17 5229 5728 315642766 315643260 2.810000e-98 370.0
59 TraesCS1A01G225900 chr1D 84.593 344 36 11 323 655 315618709 315619046 6.170000e-85 326.0
60 TraesCS1A01G225900 chr1D 85.489 317 31 8 4626 4934 315618201 315618510 3.710000e-82 316.0
61 TraesCS1A01G225900 chr1D 78.287 502 69 21 3028 3527 315645372 315645835 2.910000e-73 287.0
62 TraesCS1A01G225900 chr1D 96.154 130 5 0 4453 4582 116238381 116238510 5.010000e-51 213.0
63 TraesCS1A01G225900 chr1D 90.850 153 11 3 6229 6379 315646306 315646457 1.080000e-47 202.0
64 TraesCS1A01G225900 chr1D 75.878 427 59 27 347 771 315645374 315645758 1.830000e-40 178.0
65 TraesCS1A01G225900 chr1D 86.792 106 11 2 4726 4828 315638681 315638786 1.450000e-21 115.0
66 TraesCS1A01G225900 chr1D 82.609 138 15 8 2596 2733 315644716 315644844 5.230000e-21 113.0
67 TraesCS1A01G225900 chr1D 98.276 58 1 0 2793 2850 315642572 315642629 1.130000e-17 102.0
68 TraesCS1A01G225900 chr1D 94.828 58 3 0 4400 4457 315644513 315644570 2.450000e-14 91.6
69 TraesCS1A01G225900 chr1D 97.674 43 1 0 2916 2958 315639605 315639647 2.470000e-09 75.0
70 TraesCS1A01G225900 chr1D 100.000 28 0 0 4303 4330 315644093 315644120 1.200000e-02 52.8
71 TraesCS1A01G225900 chr2D 96.923 130 4 0 4453 4582 592468109 592467980 1.080000e-52 219.0
72 TraesCS1A01G225900 chr4A 96.212 132 5 0 4448 4579 675518142 675518273 3.870000e-52 217.0
73 TraesCS1A01G225900 chr4A 78.199 211 32 11 5 208 62309838 62309635 8.690000e-24 122.0
74 TraesCS1A01G225900 chr4B 94.853 136 6 1 4445 4580 660689362 660689496 1.800000e-50 211.0
75 TraesCS1A01G225900 chr4B 93.056 144 9 1 4452 4595 658652040 658651898 6.480000e-50 209.0
76 TraesCS1A01G225900 chr7B 92.361 144 9 2 4445 4587 227053793 227053651 3.020000e-48 204.0
77 TraesCS1A01G225900 chr7B 90.066 151 12 3 4433 4581 141907215 141907364 6.530000e-45 193.0
78 TraesCS1A01G225900 chr7B 93.939 99 6 0 946 1044 645090222 645090320 3.990000e-32 150.0
79 TraesCS1A01G225900 chr7B 93.939 99 6 0 3599 3697 645090222 645090320 3.990000e-32 150.0
80 TraesCS1A01G225900 chr7B 84.828 145 19 2 5 149 640272372 640272231 6.670000e-30 143.0
81 TraesCS1A01G225900 chr6B 85.517 145 18 2 5 149 659509465 659509324 1.430000e-31 148.0
82 TraesCS1A01G225900 chr3B 85.135 148 19 2 2 149 811506177 811506321 1.430000e-31 148.0
83 TraesCS1A01G225900 chr7D 81.250 192 24 9 3 187 117879061 117879247 1.850000e-30 145.0
84 TraesCS1A01G225900 chr5A 84.211 152 20 3 2 152 299294987 299294839 1.850000e-30 145.0
85 TraesCS1A01G225900 chr5A 84.828 145 19 2 5 149 633031549 633031690 6.670000e-30 143.0
86 TraesCS1A01G225900 chr2B 80.412 194 26 10 3 189 788519000 788519188 3.100000e-28 137.0
87 TraesCS1A01G225900 chr2B 81.006 179 25 7 1 176 483513366 483513538 4.010000e-27 134.0


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 TraesCS1A01G225900 chr1A 396282080 396288461 6381 False 11786.000000 11786 100.000000 1 6382 1 chr1A.!!$F3 6381
1 TraesCS1A01G225900 chr1A 396262278 396262950 672 False 623.000000 623 83.764000 930 1608 1 chr1A.!!$F1 678
2 TraesCS1A01G225900 chr1A 396282253 396286954 4701 False 535.000000 1345 89.743667 174 4875 6 chr1A.!!$F4 4701
3 TraesCS1A01G225900 chr1B 427772396 427778385 5989 False 817.090909 2082 88.610273 107 5534 11 chr1B.!!$F8 5427
4 TraesCS1A01G225900 chr1B 427534213 427534805 592 False 665.000000 665 86.808000 5160 5773 1 chr1B.!!$F1 613
5 TraesCS1A01G225900 chr1B 427543046 427544700 1654 False 596.750000 1075 86.752250 930 4133 4 chr1B.!!$F6 3203
6 TraesCS1A01G225900 chr1B 427522990 427527609 4619 False 540.222222 1426 90.175111 232 5158 9 chr1B.!!$F5 4926
7 TraesCS1A01G225900 chr1B 427595418 427599634 4216 False 525.922222 2100 88.890889 319 5461 9 chr1B.!!$F7 5142
8 TraesCS1A01G225900 chr1D 315636980 315646457 9477 False 656.863158 2071 89.081684 283 6379 19 chr1D.!!$F3 6096
9 TraesCS1A01G225900 chr1D 315616743 315619046 2303 False 451.250000 636 83.734750 323 4934 4 chr1D.!!$F2 4611

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
118 887 0.105401 TCATCGGGGTAGGGTATGCA 60.105 55.000 0.00 0.00 0.00 3.96 F
154 923 3.701205 AAGGATGAGTGTATGTGCACA 57.299 42.857 24.08 24.08 41.52 4.57 F
4942 9962 1.003580 ACACATGCAGTTAGGTCTGGG 59.996 52.381 0.00 0.00 36.12 4.45 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
4906 9924 7.923344 ACTGCATGTGTCTATTCTATCTACAAC 59.077 37.037 0.00 0.0 0.00 3.32 R
4961 9981 0.586802 GAACAGACCGAACTGCAACC 59.413 55.000 8.33 0.0 41.06 3.77 R
6002 12841 0.375106 GCTTAGCACCAGTTGATCGC 59.625 55.000 0.00 0.0 0.00 4.58 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
19 20 0.615331 TGCATTCAGTGGGAGGAGAC 59.385 55.000 0.00 0.00 0.00 3.36
38 39 3.411415 ACGTTCCCGTCGACTATAAAG 57.589 47.619 14.70 9.08 46.28 1.85
39 40 3.009723 ACGTTCCCGTCGACTATAAAGA 58.990 45.455 14.70 0.00 46.28 2.52
50 51 5.280911 GTCGACTATAAAGACGTATGCGATG 59.719 44.000 11.07 0.00 40.91 3.84
51 52 5.178067 TCGACTATAAAGACGTATGCGATGA 59.822 40.000 11.07 0.00 40.91 2.92
53 54 6.315091 ACTATAAAGACGTATGCGATGACT 57.685 37.500 11.07 0.90 42.00 3.41
54 55 6.736123 ACTATAAAGACGTATGCGATGACTT 58.264 36.000 11.07 6.99 42.00 3.01
65 66 2.293677 CGATGACTTCGTCAATCCCA 57.706 50.000 0.36 0.00 45.96 4.37
67 68 2.604914 CGATGACTTCGTCAATCCCAAG 59.395 50.000 0.36 0.00 45.96 3.61
69 70 3.981071 TGACTTCGTCAATCCCAAGAT 57.019 42.857 0.00 0.00 39.78 2.40
72 73 4.080919 TGACTTCGTCAATCCCAAGATGAT 60.081 41.667 0.00 0.00 39.78 2.45
73 74 4.194640 ACTTCGTCAATCCCAAGATGATG 58.805 43.478 0.00 0.00 31.29 3.07
75 76 3.534554 TCGTCAATCCCAAGATGATGTG 58.465 45.455 0.00 0.00 31.29 3.21
78 79 3.066342 GTCAATCCCAAGATGATGTGCTG 59.934 47.826 0.00 0.00 31.29 4.41
79 80 2.359981 ATCCCAAGATGATGTGCTGG 57.640 50.000 0.00 0.00 0.00 4.85
80 81 0.394762 TCCCAAGATGATGTGCTGGC 60.395 55.000 0.00 0.00 0.00 4.85
81 82 0.395311 CCCAAGATGATGTGCTGGCT 60.395 55.000 0.00 0.00 0.00 4.75
84 85 1.671328 CAAGATGATGTGCTGGCTCAG 59.329 52.381 3.83 0.00 34.12 3.35
86 87 1.134461 AGATGATGTGCTGGCTCAGTC 60.134 52.381 3.83 2.71 33.43 3.51
90 91 0.982704 ATGTGCTGGCTCAGTCTCTT 59.017 50.000 3.83 0.00 33.43 2.85
92 93 1.547820 TGTGCTGGCTCAGTCTCTTAG 59.452 52.381 4.45 0.00 33.43 2.18
93 94 1.821753 GTGCTGGCTCAGTCTCTTAGA 59.178 52.381 4.45 0.00 33.43 2.10
94 95 2.098614 TGCTGGCTCAGTCTCTTAGAG 58.901 52.381 2.23 2.23 33.43 2.43
95 96 1.408702 GCTGGCTCAGTCTCTTAGAGG 59.591 57.143 9.58 0.00 33.43 3.69
98 99 1.136110 GGCTCAGTCTCTTAGAGGTGC 59.864 57.143 9.58 6.03 0.00 5.01
99 100 2.099405 GCTCAGTCTCTTAGAGGTGCT 58.901 52.381 9.58 3.11 0.00 4.40
101 102 3.351740 CTCAGTCTCTTAGAGGTGCTCA 58.648 50.000 9.58 0.00 32.06 4.26
102 103 3.953612 CTCAGTCTCTTAGAGGTGCTCAT 59.046 47.826 9.58 0.00 32.06 2.90
103 104 3.951037 TCAGTCTCTTAGAGGTGCTCATC 59.049 47.826 9.58 0.00 32.06 2.92
105 106 2.034053 GTCTCTTAGAGGTGCTCATCGG 59.966 54.545 9.58 0.00 32.06 4.18
106 107 1.339610 CTCTTAGAGGTGCTCATCGGG 59.660 57.143 0.41 0.00 32.06 5.14
109 110 0.554305 TAGAGGTGCTCATCGGGGTA 59.446 55.000 0.00 0.00 32.06 3.69
118 887 0.105401 TCATCGGGGTAGGGTATGCA 60.105 55.000 0.00 0.00 0.00 3.96
152 921 9.034800 TCATATATAAGGATGAGTGTATGTGCA 57.965 33.333 0.00 0.00 0.00 4.57
154 923 3.701205 AAGGATGAGTGTATGTGCACA 57.299 42.857 24.08 24.08 41.52 4.57
159 929 5.598417 AGGATGAGTGTATGTGCACAGTATA 59.402 40.000 25.84 10.17 41.52 1.47
4906 9924 5.205056 AGGAAACATGTAGAGAGGTAGGAG 58.795 45.833 0.00 0.00 0.00 3.69
4934 9954 9.131791 TGTAGATAGAATAGACACATGCAGTTA 57.868 33.333 0.00 0.00 0.00 2.24
4940 9960 3.325293 AGACACATGCAGTTAGGTCTG 57.675 47.619 8.05 0.00 31.85 3.51
4941 9961 2.027745 AGACACATGCAGTTAGGTCTGG 60.028 50.000 8.05 0.00 31.85 3.86
4942 9962 1.003580 ACACATGCAGTTAGGTCTGGG 59.996 52.381 0.00 0.00 36.12 4.45
4943 9963 1.003580 CACATGCAGTTAGGTCTGGGT 59.996 52.381 0.00 0.00 36.12 4.51
4944 9964 1.705186 ACATGCAGTTAGGTCTGGGTT 59.295 47.619 0.00 0.00 36.12 4.11
4945 9965 2.108250 ACATGCAGTTAGGTCTGGGTTT 59.892 45.455 0.00 0.00 36.12 3.27
4946 9966 3.157087 CATGCAGTTAGGTCTGGGTTTT 58.843 45.455 0.00 0.00 36.12 2.43
4947 9967 3.306472 TGCAGTTAGGTCTGGGTTTTT 57.694 42.857 0.00 0.00 36.12 1.94
4975 9995 3.723348 GCGGGTTGCAGTTCGGTC 61.723 66.667 6.75 0.00 45.45 4.79
4976 9996 2.030562 CGGGTTGCAGTTCGGTCT 59.969 61.111 0.00 0.00 0.00 3.85
4983 10003 2.254546 TGCAGTTCGGTCTGTTCAAT 57.745 45.000 8.89 0.00 37.70 2.57
4985 10005 2.290367 TGCAGTTCGGTCTGTTCAATTG 59.710 45.455 0.00 0.00 37.70 2.32
4987 10007 3.364366 GCAGTTCGGTCTGTTCAATTGAG 60.364 47.826 8.41 0.00 37.70 3.02
4994 10185 4.151335 CGGTCTGTTCAATTGAGAGAGTTG 59.849 45.833 15.91 8.10 0.00 3.16
5019 10210 6.746364 GCTGAAATAATGACAAGAAGCAAGAG 59.254 38.462 0.00 0.00 0.00 2.85
5150 10378 5.634859 ACGCAATAAAATGCTTCCTTTTCTG 59.365 36.000 0.00 0.00 44.21 3.02
5161 10389 7.492352 TGCTTCCTTTTCTGAAAACTACTAC 57.508 36.000 11.33 1.86 0.00 2.73
5206 10440 8.768957 TTCAAAATTGAACTGTCAAAACATCA 57.231 26.923 4.52 0.00 46.66 3.07
5271 12059 5.239525 CAGTGATGGTAATAAGGCCTTAAGC 59.760 44.000 28.50 21.65 42.60 3.09
5282 12076 1.135373 GGCCTTAAGCGAAAGAAAGCC 60.135 52.381 0.00 0.00 45.17 4.35
5414 12213 4.383948 GCTTGCATTAGTTTCTTTGAGCAC 59.616 41.667 0.00 0.00 0.00 4.40
5415 12214 5.512753 TTGCATTAGTTTCTTTGAGCACA 57.487 34.783 0.00 0.00 0.00 4.57
5489 12291 2.381911 ACGAAGGGGAGCGTTAAGATA 58.618 47.619 0.00 0.00 37.48 1.98
5494 12304 1.798813 GGGGAGCGTTAAGATAATGCG 59.201 52.381 8.26 0.00 37.26 4.73
5510 12320 3.850923 CGTACCACGCATCGTTGT 58.149 55.556 1.93 1.93 38.32 3.32
5541 12351 4.419522 AAGCACCAATGACATCGTAAAC 57.580 40.909 0.00 0.00 0.00 2.01
5551 12361 0.875728 CATCGTAAACGCCCCAAACA 59.124 50.000 0.00 0.00 39.60 2.83
5556 12366 2.420722 CGTAAACGCCCCAAACATACAT 59.579 45.455 0.00 0.00 0.00 2.29
5557 12367 3.119779 CGTAAACGCCCCAAACATACATT 60.120 43.478 0.00 0.00 0.00 2.71
5559 12369 4.712122 AAACGCCCCAAACATACATTAG 57.288 40.909 0.00 0.00 0.00 1.73
5699 12509 8.431593 CAAGGATAAAATTTCGAAATCGCAAAA 58.568 29.630 22.93 7.19 39.60 2.44
5737 12547 6.007703 TCGGAAATTTACATTGGAGTTCCTT 58.992 36.000 0.39 0.00 36.82 3.36
5750 12560 5.053249 TGGAGTTCCTTGTGCAAATATGCT 61.053 41.667 2.22 0.00 44.35 3.79
5783 12593 7.931407 TCTCTGTTCTGTCTTGCAAATTACTAA 59.069 33.333 0.00 0.00 0.00 2.24
5787 12597 9.502091 TGTTCTGTCTTGCAAATTACTAATAGT 57.498 29.630 0.00 0.00 0.00 2.12
5797 12607 9.290988 TGCAAATTACTAATAGTTGTTTCAGGA 57.709 29.630 0.00 0.00 0.00 3.86
5798 12608 9.774742 GCAAATTACTAATAGTTGTTTCAGGAG 57.225 33.333 0.00 0.00 0.00 3.69
5803 12613 9.924650 TTACTAATAGTTGTTTCAGGAGAGTTC 57.075 33.333 0.00 0.00 0.00 3.01
5804 12614 7.387643 ACTAATAGTTGTTTCAGGAGAGTTCC 58.612 38.462 0.00 0.00 44.39 3.62
5805 12615 3.493767 AGTTGTTTCAGGAGAGTTCCC 57.506 47.619 0.00 0.00 45.24 3.97
5806 12616 2.106684 AGTTGTTTCAGGAGAGTTCCCC 59.893 50.000 0.00 0.00 45.24 4.81
5807 12617 1.814429 TGTTTCAGGAGAGTTCCCCA 58.186 50.000 0.00 0.00 45.24 4.96
5815 12642 1.213926 GGAGAGTTCCCCATGCTGATT 59.786 52.381 0.00 0.00 37.53 2.57
5848 12675 0.807496 GCAAGATGCACCCTGACTTC 59.193 55.000 0.00 0.00 44.26 3.01
5850 12678 1.067295 AAGATGCACCCTGACTTCCA 58.933 50.000 0.00 0.00 0.00 3.53
5854 12682 0.764369 TGCACCCTGACTTCCAGAGT 60.764 55.000 0.00 0.00 45.78 3.24
5860 12688 2.451490 CCTGACTTCCAGAGTAGAGCA 58.549 52.381 0.00 0.00 45.78 4.26
5863 12691 0.814457 ACTTCCAGAGTAGAGCAGCG 59.186 55.000 0.00 0.00 36.65 5.18
5871 12699 4.435436 TAGAGCAGCGCCACCGTG 62.435 66.667 2.29 0.00 36.67 4.94
5881 12709 4.308458 CCACCGTGGCCGTCTCAA 62.308 66.667 4.16 0.00 0.00 3.02
5884 12712 3.691342 CCGTGGCCGTCTCAAGGA 61.691 66.667 0.00 0.00 36.15 3.36
5885 12713 2.125912 CGTGGCCGTCTCAAGGAG 60.126 66.667 0.00 0.00 0.00 3.69
5886 12714 2.266055 GTGGCCGTCTCAAGGAGG 59.734 66.667 0.00 0.00 0.00 4.30
5889 12717 4.821589 GCCGTCTCAAGGAGGCCG 62.822 72.222 0.00 0.00 43.54 6.13
5890 12718 4.821589 CCGTCTCAAGGAGGCCGC 62.822 72.222 0.00 0.00 29.32 6.53
5891 12719 4.821589 CGTCTCAAGGAGGCCGCC 62.822 72.222 19.43 19.43 29.32 6.13
5893 12721 2.927856 TCTCAAGGAGGCCGCCAA 60.928 61.111 28.68 11.54 0.00 4.52
5907 12735 3.663176 CCAAGTGCGGTGTGGCTG 61.663 66.667 0.00 0.00 0.00 4.85
5981 12820 0.392461 ATCGGTGCGCTTGTGGTAAT 60.392 50.000 9.73 0.00 0.00 1.89
5982 12821 0.246910 TCGGTGCGCTTGTGGTAATA 59.753 50.000 9.73 0.00 0.00 0.98
5983 12822 1.134640 TCGGTGCGCTTGTGGTAATAT 60.135 47.619 9.73 0.00 0.00 1.28
5984 12823 1.668751 CGGTGCGCTTGTGGTAATATT 59.331 47.619 9.73 0.00 0.00 1.28
5985 12824 2.538737 CGGTGCGCTTGTGGTAATATTG 60.539 50.000 9.73 0.00 0.00 1.90
5986 12825 2.680841 GGTGCGCTTGTGGTAATATTGA 59.319 45.455 9.73 0.00 0.00 2.57
5987 12826 3.242739 GGTGCGCTTGTGGTAATATTGAG 60.243 47.826 9.73 0.00 0.00 3.02
5988 12827 3.621268 GTGCGCTTGTGGTAATATTGAGA 59.379 43.478 9.73 0.00 0.00 3.27
5989 12828 3.621268 TGCGCTTGTGGTAATATTGAGAC 59.379 43.478 9.73 0.00 0.00 3.36
5990 12829 3.002348 GCGCTTGTGGTAATATTGAGACC 59.998 47.826 0.00 0.00 0.00 3.85
6018 12857 1.725641 CAAGCGATCAACTGGTGCTA 58.274 50.000 0.00 0.00 34.19 3.49
6037 12877 2.665649 AAGCATGCATGATTGTGGTG 57.334 45.000 28.15 1.20 34.75 4.17
6046 12886 1.478631 TGATTGTGGTGTGGTTTGCA 58.521 45.000 0.00 0.00 0.00 4.08
6047 12887 1.135915 TGATTGTGGTGTGGTTTGCAC 59.864 47.619 0.00 0.00 36.22 4.57
6048 12888 0.102120 ATTGTGGTGTGGTTTGCACG 59.898 50.000 0.00 0.00 37.70 5.34
6049 12889 2.278531 GTGGTGTGGTTTGCACGC 60.279 61.111 0.00 0.00 37.70 5.34
6050 12890 2.751837 TGGTGTGGTTTGCACGCA 60.752 55.556 0.00 0.00 37.70 5.24
6051 12891 2.278531 GGTGTGGTTTGCACGCAC 60.279 61.111 10.20 10.20 45.84 5.34
6052 12892 2.487428 GTGTGGTTTGCACGCACA 59.513 55.556 12.98 5.03 45.86 4.57
6053 12893 1.065600 GTGTGGTTTGCACGCACAT 59.934 52.632 12.98 0.00 45.86 3.21
6054 12894 1.065436 TGTGGTTTGCACGCACATG 59.935 52.632 0.00 0.00 32.39 3.21
6055 12895 1.065600 GTGGTTTGCACGCACATGT 59.934 52.632 0.00 0.00 0.00 3.21
6056 12896 1.065436 TGGTTTGCACGCACATGTG 59.935 52.632 21.83 21.83 42.81 3.21
6070 12918 4.556501 CGCACATGTGTTCTTGTAATGGTT 60.557 41.667 26.01 0.00 32.05 3.67
6078 12926 8.684386 TGTGTTCTTGTAATGGTTCATCTTAA 57.316 30.769 0.00 0.00 0.00 1.85
6093 12941 9.660180 GGTTCATCTTAAGTGAAAATAGAGAGT 57.340 33.333 16.80 0.00 37.34 3.24
6098 12946 8.896722 TCTTAAGTGAAAATAGAGAGTAGGGT 57.103 34.615 1.63 0.00 0.00 4.34
6099 12947 8.968969 TCTTAAGTGAAAATAGAGAGTAGGGTC 58.031 37.037 1.63 0.00 0.00 4.46
6100 12948 5.838531 AGTGAAAATAGAGAGTAGGGTCG 57.161 43.478 0.00 0.00 0.00 4.79
6101 12949 4.645588 AGTGAAAATAGAGAGTAGGGTCGG 59.354 45.833 0.00 0.00 0.00 4.79
6102 12950 4.401837 GTGAAAATAGAGAGTAGGGTCGGT 59.598 45.833 0.00 0.00 0.00 4.69
6103 12951 5.591877 GTGAAAATAGAGAGTAGGGTCGGTA 59.408 44.000 0.00 0.00 0.00 4.02
6104 12952 5.591877 TGAAAATAGAGAGTAGGGTCGGTAC 59.408 44.000 0.00 0.00 0.00 3.34
6119 12970 2.943843 GGTACGACAACAAGAGCAAC 57.056 50.000 0.00 0.00 0.00 4.17
6130 12981 3.808728 ACAAGAGCAACTCAGCACTAAA 58.191 40.909 0.00 0.00 34.29 1.85
6132 12983 4.823989 ACAAGAGCAACTCAGCACTAAAAT 59.176 37.500 0.00 0.00 34.29 1.82
6133 12984 5.300286 ACAAGAGCAACTCAGCACTAAAATT 59.700 36.000 0.00 0.00 34.29 1.82
6134 12985 5.368256 AGAGCAACTCAGCACTAAAATTG 57.632 39.130 0.00 0.00 33.62 2.32
6135 12986 4.217118 AGAGCAACTCAGCACTAAAATTGG 59.783 41.667 0.00 0.00 33.62 3.16
6136 12987 2.989166 GCAACTCAGCACTAAAATTGGC 59.011 45.455 0.00 0.00 0.00 4.52
6137 12988 3.236816 CAACTCAGCACTAAAATTGGCG 58.763 45.455 0.00 0.00 0.00 5.69
6138 12989 1.200020 ACTCAGCACTAAAATTGGCGC 59.800 47.619 0.00 0.00 0.00 6.53
6139 12990 1.199789 CTCAGCACTAAAATTGGCGCA 59.800 47.619 10.83 0.00 0.00 6.09
6140 12991 1.068610 TCAGCACTAAAATTGGCGCAC 60.069 47.619 10.83 0.00 0.00 5.34
6141 12992 0.243636 AGCACTAAAATTGGCGCACC 59.756 50.000 10.83 0.00 0.00 5.01
6142 12993 0.735978 GCACTAAAATTGGCGCACCC 60.736 55.000 10.83 0.00 33.59 4.61
6143 12994 0.108851 CACTAAAATTGGCGCACCCC 60.109 55.000 10.83 0.00 33.59 4.95
6144 12995 0.251608 ACTAAAATTGGCGCACCCCT 60.252 50.000 10.83 0.00 33.59 4.79
6145 12996 0.173255 CTAAAATTGGCGCACCCCTG 59.827 55.000 10.83 0.00 33.59 4.45
6146 12997 1.254284 TAAAATTGGCGCACCCCTGG 61.254 55.000 10.83 0.00 33.59 4.45
6147 12998 3.826265 AAATTGGCGCACCCCTGGT 62.826 57.895 10.83 0.00 35.62 4.00
6157 13008 3.821306 ACCCCTGGTGAACTTCAAC 57.179 52.632 0.00 0.00 32.98 3.18
6158 13009 0.923358 ACCCCTGGTGAACTTCAACA 59.077 50.000 9.21 9.21 42.67 3.33
6159 13010 1.499007 ACCCCTGGTGAACTTCAACAT 59.501 47.619 9.99 0.00 44.04 2.71
6160 13011 1.888512 CCCCTGGTGAACTTCAACATG 59.111 52.381 9.99 7.46 44.04 3.21
6161 13012 2.488891 CCCCTGGTGAACTTCAACATGA 60.489 50.000 9.99 0.00 44.04 3.07
6162 13013 3.221771 CCCTGGTGAACTTCAACATGAA 58.778 45.455 9.99 0.00 44.04 2.57
6163 13014 3.004734 CCCTGGTGAACTTCAACATGAAC 59.995 47.826 9.99 0.00 44.04 3.18
6164 13015 3.885297 CCTGGTGAACTTCAACATGAACT 59.115 43.478 9.99 0.00 44.04 3.01
6175 13026 6.322201 ACTTCAACATGAACTGGAAACTTGAT 59.678 34.615 0.00 0.00 32.21 2.57
6179 13030 4.217118 ACATGAACTGGAAACTTGATGAGC 59.783 41.667 0.00 0.00 0.00 4.26
6180 13031 3.149196 TGAACTGGAAACTTGATGAGCC 58.851 45.455 0.00 0.00 0.00 4.70
6181 13032 2.957402 ACTGGAAACTTGATGAGCCA 57.043 45.000 0.00 0.00 0.00 4.75
6182 13033 3.446442 ACTGGAAACTTGATGAGCCAT 57.554 42.857 0.00 0.00 0.00 4.40
6183 13034 3.087031 ACTGGAAACTTGATGAGCCATG 58.913 45.455 0.00 0.00 0.00 3.66
6184 13035 3.087031 CTGGAAACTTGATGAGCCATGT 58.913 45.455 0.00 0.00 0.00 3.21
6185 13036 2.821378 TGGAAACTTGATGAGCCATGTG 59.179 45.455 0.00 0.00 0.00 3.21
6186 13037 2.416431 GGAAACTTGATGAGCCATGTGC 60.416 50.000 0.00 0.00 41.71 4.57
6187 13038 1.913778 AACTTGATGAGCCATGTGCA 58.086 45.000 8.58 0.00 44.83 4.57
6188 13039 2.139323 ACTTGATGAGCCATGTGCAT 57.861 45.000 8.58 1.14 44.83 3.96
6189 13040 2.453521 ACTTGATGAGCCATGTGCATT 58.546 42.857 8.58 0.00 44.83 3.56
6191 13042 2.951457 TGATGAGCCATGTGCATTTG 57.049 45.000 8.58 0.00 44.83 2.32
6192 13043 1.478916 TGATGAGCCATGTGCATTTGG 59.521 47.619 12.31 12.31 44.83 3.28
6193 13044 1.479323 GATGAGCCATGTGCATTTGGT 59.521 47.619 16.54 6.31 44.83 3.67
6194 13045 1.340088 TGAGCCATGTGCATTTGGTT 58.660 45.000 16.54 12.06 44.83 3.67
6195 13046 1.001068 TGAGCCATGTGCATTTGGTTG 59.999 47.619 16.54 0.00 44.83 3.77
6196 13047 1.273048 GAGCCATGTGCATTTGGTTGA 59.727 47.619 16.54 0.00 44.83 3.18
6197 13048 1.693062 AGCCATGTGCATTTGGTTGAA 59.307 42.857 16.54 0.00 44.83 2.69
6198 13049 2.104451 AGCCATGTGCATTTGGTTGAAA 59.896 40.909 16.54 0.00 44.83 2.69
6199 13050 3.075884 GCCATGTGCATTTGGTTGAAAT 58.924 40.909 16.54 0.00 40.77 2.17
6222 13073 9.846248 AAATGTGAATCTTAAATCTTACAGTGC 57.154 29.630 0.00 0.00 0.00 4.40
6223 13074 8.798859 ATGTGAATCTTAAATCTTACAGTGCT 57.201 30.769 0.00 0.00 0.00 4.40
6224 13075 9.890629 ATGTGAATCTTAAATCTTACAGTGCTA 57.109 29.630 0.00 0.00 0.00 3.49
6225 13076 9.719355 TGTGAATCTTAAATCTTACAGTGCTAA 57.281 29.630 0.00 0.00 0.00 3.09
6278 13130 0.314935 AATCAACCACTTGCTTGCCG 59.685 50.000 0.00 0.00 0.00 5.69
6286 13138 0.314935 ACTTGCTTGCCGTGGATTTG 59.685 50.000 0.00 0.00 0.00 2.32
6297 13149 1.605710 CGTGGATTTGATCATCTGGGC 59.394 52.381 0.00 0.00 0.00 5.36
6340 13192 1.202417 ACCTCATCGGTCAGCATAACG 60.202 52.381 0.00 0.00 44.93 3.18
6349 13201 0.175760 TCAGCATAACGGGAGCTCAC 59.824 55.000 17.19 11.90 36.26 3.51
6352 13204 0.811616 GCATAACGGGAGCTCACAGG 60.812 60.000 17.92 2.63 0.00 4.00
6355 13207 1.568504 TAACGGGAGCTCACAGGAAT 58.431 50.000 17.92 0.00 0.00 3.01
6357 13209 1.794714 ACGGGAGCTCACAGGAATAT 58.205 50.000 17.92 0.00 0.00 1.28
6358 13210 1.414181 ACGGGAGCTCACAGGAATATG 59.586 52.381 17.92 0.00 0.00 1.78
6359 13211 1.875576 CGGGAGCTCACAGGAATATGC 60.876 57.143 17.92 0.00 0.00 3.14
6360 13212 1.544314 GGGAGCTCACAGGAATATGCC 60.544 57.143 17.19 0.00 0.00 4.40
6361 13213 1.141657 GGAGCTCACAGGAATATGCCA 59.858 52.381 17.19 0.00 0.00 4.92
6362 13214 2.492012 GAGCTCACAGGAATATGCCAG 58.508 52.381 9.40 0.00 0.00 4.85
6363 13215 1.842562 AGCTCACAGGAATATGCCAGT 59.157 47.619 1.47 0.00 0.00 4.00
6364 13216 1.945394 GCTCACAGGAATATGCCAGTG 59.055 52.381 17.44 17.44 44.20 3.66
6365 13217 2.681976 GCTCACAGGAATATGCCAGTGT 60.682 50.000 21.47 6.95 43.54 3.55
6366 13218 3.432186 GCTCACAGGAATATGCCAGTGTA 60.432 47.826 21.47 10.08 43.54 2.90
6368 13220 3.118408 TCACAGGAATATGCCAGTGTACC 60.118 47.826 21.47 0.00 43.54 3.34
6369 13221 2.843730 ACAGGAATATGCCAGTGTACCA 59.156 45.455 1.47 0.00 0.00 3.25
6379 13231 3.244735 TGCCAGTGTACCACAATACATGT 60.245 43.478 2.69 2.69 45.34 3.21
6380 13232 3.756434 GCCAGTGTACCACAATACATGTT 59.244 43.478 2.30 0.00 41.46 2.71
6381 13233 4.938832 GCCAGTGTACCACAATACATGTTA 59.061 41.667 2.30 0.00 41.46 2.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 0.460987 CGTCTCCTCCCACTGAATGC 60.461 60.000 0.00 0.00 0.00 3.56
3 4 1.550976 GAACGTCTCCTCCCACTGAAT 59.449 52.381 0.00 0.00 0.00 2.57
6 7 1.592223 GGAACGTCTCCTCCCACTG 59.408 63.158 8.87 0.00 41.61 3.66
26 27 4.766007 TCGCATACGTCTTTATAGTCGAC 58.234 43.478 7.70 7.70 41.18 4.20
27 28 5.178067 TCATCGCATACGTCTTTATAGTCGA 59.822 40.000 6.81 0.00 41.18 4.20
28 29 5.280911 GTCATCGCATACGTCTTTATAGTCG 59.719 44.000 0.00 0.00 41.18 4.18
29 30 6.372185 AGTCATCGCATACGTCTTTATAGTC 58.628 40.000 0.00 0.00 41.18 2.59
34 35 4.033019 CGAAGTCATCGCATACGTCTTTA 58.967 43.478 0.00 0.00 45.89 1.85
53 54 3.940852 CACATCATCTTGGGATTGACGAA 59.059 43.478 0.00 0.00 0.00 3.85
54 55 3.534554 CACATCATCTTGGGATTGACGA 58.465 45.455 0.00 0.00 0.00 4.20
56 57 3.066342 CAGCACATCATCTTGGGATTGAC 59.934 47.826 0.00 0.00 0.00 3.18
57 58 3.284617 CAGCACATCATCTTGGGATTGA 58.715 45.455 0.00 0.00 0.00 2.57
59 60 2.662866 CCAGCACATCATCTTGGGATT 58.337 47.619 0.00 0.00 0.00 3.01
62 63 0.395311 AGCCAGCACATCATCTTGGG 60.395 55.000 0.00 0.00 0.00 4.12
63 64 1.022735 GAGCCAGCACATCATCTTGG 58.977 55.000 0.00 0.00 0.00 3.61
64 65 1.671328 CTGAGCCAGCACATCATCTTG 59.329 52.381 0.00 0.00 0.00 3.02
65 66 1.281287 ACTGAGCCAGCACATCATCTT 59.719 47.619 2.50 0.00 34.37 2.40
67 68 1.134461 AGACTGAGCCAGCACATCATC 60.134 52.381 2.50 0.00 34.37 2.92
69 70 0.248565 GAGACTGAGCCAGCACATCA 59.751 55.000 2.50 0.00 34.37 3.07
72 73 1.547820 CTAAGAGACTGAGCCAGCACA 59.452 52.381 2.50 0.00 34.37 4.57
73 74 1.821753 TCTAAGAGACTGAGCCAGCAC 59.178 52.381 2.50 0.00 34.37 4.40
75 76 1.408702 CCTCTAAGAGACTGAGCCAGC 59.591 57.143 0.00 0.00 34.37 4.85
78 79 1.136110 GCACCTCTAAGAGACTGAGCC 59.864 57.143 0.00 0.00 0.00 4.70
79 80 2.099098 GAGCACCTCTAAGAGACTGAGC 59.901 54.545 0.00 0.00 0.00 4.26
80 81 3.351740 TGAGCACCTCTAAGAGACTGAG 58.648 50.000 0.00 0.00 0.00 3.35
81 82 3.441500 TGAGCACCTCTAAGAGACTGA 57.558 47.619 0.00 0.00 0.00 3.41
84 85 2.034053 CCGATGAGCACCTCTAAGAGAC 59.966 54.545 0.00 0.00 0.00 3.36
86 87 1.339610 CCCGATGAGCACCTCTAAGAG 59.660 57.143 0.00 0.00 0.00 2.85
90 91 0.554305 TACCCCGATGAGCACCTCTA 59.446 55.000 0.00 0.00 0.00 2.43
92 93 1.742768 CTACCCCGATGAGCACCTC 59.257 63.158 0.00 0.00 0.00 3.85
93 94 1.762460 CCTACCCCGATGAGCACCT 60.762 63.158 0.00 0.00 0.00 4.00
94 95 2.808206 CCCTACCCCGATGAGCACC 61.808 68.421 0.00 0.00 0.00 5.01
95 96 0.757935 TACCCTACCCCGATGAGCAC 60.758 60.000 0.00 0.00 0.00 4.40
98 99 0.608640 GCATACCCTACCCCGATGAG 59.391 60.000 0.00 0.00 0.00 2.90
99 100 0.105401 TGCATACCCTACCCCGATGA 60.105 55.000 0.00 0.00 0.00 2.92
101 102 0.984230 CATGCATACCCTACCCCGAT 59.016 55.000 0.00 0.00 0.00 4.18
102 103 0.399376 ACATGCATACCCTACCCCGA 60.399 55.000 0.00 0.00 0.00 5.14
103 104 0.250295 CACATGCATACCCTACCCCG 60.250 60.000 0.00 0.00 0.00 5.73
105 106 1.211949 ACACACATGCATACCCTACCC 59.788 52.381 0.00 0.00 0.00 3.69
106 107 2.710096 ACACACATGCATACCCTACC 57.290 50.000 0.00 0.00 0.00 3.18
109 110 2.877097 TGAACACACATGCATACCCT 57.123 45.000 0.00 0.00 0.00 4.34
118 887 9.716531 CACTCATCCTTATATATGAACACACAT 57.283 33.333 0.00 0.00 31.97 3.21
152 921 5.463392 CACAGAACGCATATGCTTATACTGT 59.537 40.000 24.56 23.49 39.32 3.55
154 923 5.601662 ACACAGAACGCATATGCTTATACT 58.398 37.500 24.56 12.85 39.32 2.12
159 929 3.073678 TGAACACAGAACGCATATGCTT 58.926 40.909 24.56 13.70 39.32 3.91
4906 9924 7.923344 ACTGCATGTGTCTATTCTATCTACAAC 59.077 37.037 0.00 0.00 0.00 3.32
4958 9978 3.723348 GACCGAACTGCAACCCGC 61.723 66.667 0.00 0.00 42.89 6.13
4959 9979 2.030562 AGACCGAACTGCAACCCG 59.969 61.111 0.00 0.00 0.00 5.28
4960 9980 0.818040 AACAGACCGAACTGCAACCC 60.818 55.000 8.33 0.00 41.06 4.11
4961 9981 0.586802 GAACAGACCGAACTGCAACC 59.413 55.000 8.33 0.00 41.06 3.77
4962 9982 1.295792 TGAACAGACCGAACTGCAAC 58.704 50.000 8.33 2.72 41.06 4.17
4963 9983 2.031258 TTGAACAGACCGAACTGCAA 57.969 45.000 8.33 4.16 41.06 4.08
4964 9984 2.254546 ATTGAACAGACCGAACTGCA 57.745 45.000 8.33 0.00 41.06 4.41
4965 9985 2.548057 TCAATTGAACAGACCGAACTGC 59.452 45.455 5.45 0.00 41.06 4.40
4966 9986 4.058124 TCTCAATTGAACAGACCGAACTG 58.942 43.478 9.88 7.15 42.78 3.16
4967 9987 4.039245 TCTCTCAATTGAACAGACCGAACT 59.961 41.667 9.88 0.00 0.00 3.01
4968 9988 4.307432 TCTCTCAATTGAACAGACCGAAC 58.693 43.478 9.88 0.00 0.00 3.95
4969 9989 4.039245 ACTCTCTCAATTGAACAGACCGAA 59.961 41.667 9.88 0.00 0.00 4.30
4970 9990 3.574396 ACTCTCTCAATTGAACAGACCGA 59.426 43.478 9.88 0.54 0.00 4.69
4971 9991 3.919216 ACTCTCTCAATTGAACAGACCG 58.081 45.455 9.88 5.86 0.00 4.79
4972 9992 4.083590 GCAACTCTCTCAATTGAACAGACC 60.084 45.833 9.88 0.00 0.00 3.85
4973 9993 4.754114 AGCAACTCTCTCAATTGAACAGAC 59.246 41.667 9.88 2.74 0.00 3.51
4974 9994 4.753610 CAGCAACTCTCTCAATTGAACAGA 59.246 41.667 9.88 12.15 0.00 3.41
4975 9995 4.753610 TCAGCAACTCTCTCAATTGAACAG 59.246 41.667 9.88 8.49 0.00 3.16
4976 9996 4.707105 TCAGCAACTCTCTCAATTGAACA 58.293 39.130 9.88 0.00 0.00 3.18
4983 10003 6.936335 TGTCATTATTTCAGCAACTCTCTCAA 59.064 34.615 0.00 0.00 0.00 3.02
4985 10005 6.974932 TGTCATTATTTCAGCAACTCTCTC 57.025 37.500 0.00 0.00 0.00 3.20
4987 10007 7.369803 TCTTGTCATTATTTCAGCAACTCTC 57.630 36.000 0.00 0.00 0.00 3.20
4994 10185 6.615088 TCTTGCTTCTTGTCATTATTTCAGC 58.385 36.000 0.00 0.00 0.00 4.26
5224 10458 7.880195 ACTGCTTATTCTCAATGAAACTACACT 59.120 33.333 0.00 0.00 38.29 3.55
5233 10467 5.748402 ACCATCACTGCTTATTCTCAATGA 58.252 37.500 0.00 0.00 0.00 2.57
5271 12059 1.403249 CCTTGCCATGGCTTTCTTTCG 60.403 52.381 35.53 14.78 42.51 3.46
5300 12095 2.680577 CCAGAAATGTGCCTTCTTTGC 58.319 47.619 0.00 0.00 30.58 3.68
5379 12175 6.927294 ACTAATGCAAGCAAGACCTAATAC 57.073 37.500 0.00 0.00 0.00 1.89
5414 12213 5.273170 TCAACTCGCAAAAAGAAAGACATG 58.727 37.500 0.00 0.00 0.00 3.21
5415 12214 5.499139 TCAACTCGCAAAAAGAAAGACAT 57.501 34.783 0.00 0.00 0.00 3.06
5470 12269 3.447918 TTATCTTAACGCTCCCCTTCG 57.552 47.619 0.00 0.00 0.00 3.79
5494 12304 2.673976 AAAACAACGATGCGTGGTAC 57.326 45.000 0.00 0.00 43.70 3.34
5510 12320 6.707440 TGTCATTGGTGCTTTCTTCTAAAA 57.293 33.333 0.00 0.00 0.00 1.52
5541 12351 4.712122 AAACTAATGTATGTTTGGGGCG 57.288 40.909 0.00 0.00 35.40 6.13
5559 12369 8.837389 GTGGGTCCTTATGATTTCTGTATAAAC 58.163 37.037 0.00 0.00 0.00 2.01
5630 12440 6.693315 ATGAACTTCCGTTTTCAAAGAAGA 57.307 33.333 5.67 0.00 38.38 2.87
5631 12441 7.305418 CGAAATGAACTTCCGTTTTCAAAGAAG 60.305 37.037 0.00 0.00 41.20 2.85
5750 12560 5.046376 TGCAAGACAGAACAGAGATATCCAA 60.046 40.000 0.00 0.00 0.00 3.53
5757 12567 6.291377 AGTAATTTGCAAGACAGAACAGAGA 58.709 36.000 0.00 0.00 0.00 3.10
5783 12593 4.019231 GGGGAACTCTCCTGAAACAACTAT 60.019 45.833 0.00 0.00 42.05 2.12
5787 12597 2.131854 TGGGGAACTCTCCTGAAACAA 58.868 47.619 0.00 0.00 42.05 2.83
5797 12607 3.463048 AAAATCAGCATGGGGAACTCT 57.537 42.857 0.00 0.00 36.16 3.24
5848 12675 2.105930 GGCGCTGCTCTACTCTGG 59.894 66.667 7.64 0.00 0.00 3.86
5850 12678 2.716017 GGTGGCGCTGCTCTACTCT 61.716 63.158 7.64 0.00 0.00 3.24
5854 12682 4.435436 CACGGTGGCGCTGCTCTA 62.435 66.667 7.64 0.00 0.00 2.43
5871 12699 4.475135 GGCCTCCTTGAGACGGCC 62.475 72.222 11.87 11.87 45.63 6.13
5873 12701 4.821589 GCGGCCTCCTTGAGACGG 62.822 72.222 0.00 0.00 33.18 4.79
5875 12703 3.254024 TTGGCGGCCTCCTTGAGAC 62.254 63.158 21.46 0.00 0.00 3.36
5876 12704 2.927856 TTGGCGGCCTCCTTGAGA 60.928 61.111 21.46 0.00 0.00 3.27
5877 12705 2.437359 CTTGGCGGCCTCCTTGAG 60.437 66.667 21.46 4.71 0.00 3.02
5878 12706 3.249189 ACTTGGCGGCCTCCTTGA 61.249 61.111 21.46 0.00 0.00 3.02
5879 12707 3.058160 CACTTGGCGGCCTCCTTG 61.058 66.667 21.46 8.13 0.00 3.61
5890 12718 3.663176 CAGCCACACCGCACTTGG 61.663 66.667 0.00 0.00 0.00 3.61
5891 12719 3.663176 CCAGCCACACCGCACTTG 61.663 66.667 0.00 0.00 0.00 3.16
5946 12779 1.211743 CGATCGCTTGCATCTTAGCA 58.788 50.000 0.26 0.00 43.99 3.49
5947 12780 0.510359 CCGATCGCTTGCATCTTAGC 59.490 55.000 10.32 0.00 0.00 3.09
5950 12783 1.709147 GCACCGATCGCTTGCATCTT 61.709 55.000 26.20 0.00 36.22 2.40
5951 12784 2.176273 GCACCGATCGCTTGCATCT 61.176 57.895 26.20 0.00 36.22 2.90
5952 12785 2.325857 GCACCGATCGCTTGCATC 59.674 61.111 26.20 5.53 36.22 3.91
5981 12820 2.802792 CGCCGGTCGGTCTCAATA 59.197 61.111 11.25 0.00 37.65 1.90
5982 12821 4.814294 GCGCCGGTCGGTCTCAAT 62.814 66.667 17.73 0.00 38.94 2.57
6002 12841 0.375106 GCTTAGCACCAGTTGATCGC 59.625 55.000 0.00 0.00 0.00 4.58
6008 12847 1.475280 CATGCATGCTTAGCACCAGTT 59.525 47.619 20.33 0.00 45.95 3.16
6011 12850 2.061509 ATCATGCATGCTTAGCACCA 57.938 45.000 22.25 10.50 45.95 4.17
6018 12857 1.897133 ACACCACAATCATGCATGCTT 59.103 42.857 22.25 15.99 0.00 3.91
6037 12877 1.065600 ACATGTGCGTGCAAACCAC 59.934 52.632 0.00 0.00 41.15 4.16
6046 12886 3.058293 CCATTACAAGAACACATGTGCGT 60.058 43.478 25.68 13.99 0.00 5.24
6047 12887 3.058293 ACCATTACAAGAACACATGTGCG 60.058 43.478 25.68 11.36 0.00 5.34
6048 12888 4.503741 ACCATTACAAGAACACATGTGC 57.496 40.909 25.68 10.49 0.00 4.57
6049 12889 6.070897 TGAACCATTACAAGAACACATGTG 57.929 37.500 24.25 24.25 0.00 3.21
6050 12890 6.716628 AGATGAACCATTACAAGAACACATGT 59.283 34.615 0.00 0.00 0.00 3.21
6051 12891 7.149569 AGATGAACCATTACAAGAACACATG 57.850 36.000 0.00 0.00 0.00 3.21
6052 12892 7.765695 AAGATGAACCATTACAAGAACACAT 57.234 32.000 0.00 0.00 0.00 3.21
6053 12893 8.684386 TTAAGATGAACCATTACAAGAACACA 57.316 30.769 0.00 0.00 0.00 3.72
6054 12894 8.784043 ACTTAAGATGAACCATTACAAGAACAC 58.216 33.333 10.09 0.00 0.00 3.32
6055 12895 8.783093 CACTTAAGATGAACCATTACAAGAACA 58.217 33.333 10.09 0.00 0.00 3.18
6056 12896 8.999431 TCACTTAAGATGAACCATTACAAGAAC 58.001 33.333 10.09 0.00 0.00 3.01
6078 12926 4.645588 CCGACCCTACTCTCTATTTTCACT 59.354 45.833 0.00 0.00 0.00 3.41
6088 12936 3.768633 TCGTACCGACCCTACTCTC 57.231 57.895 0.00 0.00 0.00 3.20
6098 12946 0.669619 TGCTCTTGTTGTCGTACCGA 59.330 50.000 0.00 0.00 0.00 4.69
6099 12947 1.191647 GTTGCTCTTGTTGTCGTACCG 59.808 52.381 0.00 0.00 0.00 4.02
6100 12948 2.475487 GAGTTGCTCTTGTTGTCGTACC 59.525 50.000 0.00 0.00 0.00 3.34
6101 12949 3.120792 TGAGTTGCTCTTGTTGTCGTAC 58.879 45.455 0.00 0.00 0.00 3.67
6102 12950 3.381045 CTGAGTTGCTCTTGTTGTCGTA 58.619 45.455 0.00 0.00 0.00 3.43
6103 12951 2.205074 CTGAGTTGCTCTTGTTGTCGT 58.795 47.619 0.00 0.00 0.00 4.34
6104 12952 1.070309 GCTGAGTTGCTCTTGTTGTCG 60.070 52.381 0.00 0.00 0.00 4.35
6105 12953 1.942657 TGCTGAGTTGCTCTTGTTGTC 59.057 47.619 0.00 0.00 0.00 3.18
6109 12960 3.475566 TTAGTGCTGAGTTGCTCTTGT 57.524 42.857 0.00 0.00 37.80 3.16
6119 12970 1.199789 TGCGCCAATTTTAGTGCTGAG 59.800 47.619 4.18 0.00 40.18 3.35
6130 12981 4.299796 ACCAGGGGTGCGCCAATT 62.300 61.111 19.98 0.00 32.98 2.32
6139 12990 0.923358 TGTTGAAGTTCACCAGGGGT 59.077 50.000 4.68 0.00 35.62 4.95
6140 12991 1.888512 CATGTTGAAGTTCACCAGGGG 59.111 52.381 9.13 0.00 0.00 4.79
6141 12992 2.862541 TCATGTTGAAGTTCACCAGGG 58.137 47.619 14.00 6.83 0.00 4.45
6142 12993 3.885297 AGTTCATGTTGAAGTTCACCAGG 59.115 43.478 8.59 8.59 36.70 4.45
6143 12994 4.261322 CCAGTTCATGTTGAAGTTCACCAG 60.261 45.833 9.13 2.20 37.91 4.00
6144 12995 3.631686 CCAGTTCATGTTGAAGTTCACCA 59.368 43.478 4.68 5.12 37.91 4.17
6145 12996 3.882888 TCCAGTTCATGTTGAAGTTCACC 59.117 43.478 4.68 0.00 37.91 4.02
6146 12997 5.499139 TTCCAGTTCATGTTGAAGTTCAC 57.501 39.130 4.68 1.95 37.91 3.18
6147 12998 5.652014 AGTTTCCAGTTCATGTTGAAGTTCA 59.348 36.000 0.08 0.08 37.91 3.18
6148 12999 6.136541 AGTTTCCAGTTCATGTTGAAGTTC 57.863 37.500 0.00 0.00 37.91 3.01
6149 13000 6.152661 TCAAGTTTCCAGTTCATGTTGAAGTT 59.847 34.615 0.00 0.00 37.91 2.66
6150 13001 5.652014 TCAAGTTTCCAGTTCATGTTGAAGT 59.348 36.000 0.00 0.00 40.42 3.01
6151 13002 6.135290 TCAAGTTTCCAGTTCATGTTGAAG 57.865 37.500 0.00 0.00 37.00 3.02
6152 13003 6.320926 TCATCAAGTTTCCAGTTCATGTTGAA 59.679 34.615 0.00 0.00 33.32 2.69
6153 13004 5.827267 TCATCAAGTTTCCAGTTCATGTTGA 59.173 36.000 0.00 0.00 0.00 3.18
6154 13005 6.075762 TCATCAAGTTTCCAGTTCATGTTG 57.924 37.500 0.00 0.00 0.00 3.33
6155 13006 5.278660 GCTCATCAAGTTTCCAGTTCATGTT 60.279 40.000 0.00 0.00 0.00 2.71
6156 13007 4.217118 GCTCATCAAGTTTCCAGTTCATGT 59.783 41.667 0.00 0.00 0.00 3.21
6157 13008 4.380233 GGCTCATCAAGTTTCCAGTTCATG 60.380 45.833 0.00 0.00 0.00 3.07
6158 13009 3.760684 GGCTCATCAAGTTTCCAGTTCAT 59.239 43.478 0.00 0.00 0.00 2.57
6159 13010 3.149196 GGCTCATCAAGTTTCCAGTTCA 58.851 45.455 0.00 0.00 0.00 3.18
6160 13011 3.149196 TGGCTCATCAAGTTTCCAGTTC 58.851 45.455 0.00 0.00 0.00 3.01
6161 13012 3.228188 TGGCTCATCAAGTTTCCAGTT 57.772 42.857 0.00 0.00 0.00 3.16
6162 13013 2.957402 TGGCTCATCAAGTTTCCAGT 57.043 45.000 0.00 0.00 0.00 4.00
6163 13014 3.087031 ACATGGCTCATCAAGTTTCCAG 58.913 45.455 0.00 0.00 0.00 3.86
6164 13015 2.821378 CACATGGCTCATCAAGTTTCCA 59.179 45.455 0.00 0.00 0.00 3.53
6175 13026 1.001068 CAACCAAATGCACATGGCTCA 59.999 47.619 17.35 0.00 45.15 4.26
6179 13030 4.671880 CATTTCAACCAAATGCACATGG 57.328 40.909 16.14 16.14 43.87 3.66
6196 13047 9.846248 GCACTGTAAGATTTAAGATTCACATTT 57.154 29.630 0.00 0.00 37.43 2.32
6197 13048 9.236006 AGCACTGTAAGATTTAAGATTCACATT 57.764 29.630 0.00 0.00 37.43 2.71
6198 13049 8.798859 AGCACTGTAAGATTTAAGATTCACAT 57.201 30.769 0.00 0.00 37.43 3.21
6199 13050 9.719355 TTAGCACTGTAAGATTTAAGATTCACA 57.281 29.630 0.00 0.00 37.43 3.58
6207 13058 9.953565 ACACCTATTTAGCACTGTAAGATTTAA 57.046 29.630 0.00 0.00 37.43 1.52
6208 13059 9.378551 CACACCTATTTAGCACTGTAAGATTTA 57.621 33.333 0.00 0.00 37.43 1.40
6209 13060 8.100791 TCACACCTATTTAGCACTGTAAGATTT 58.899 33.333 0.00 0.00 37.43 2.17
6210 13061 7.620880 TCACACCTATTTAGCACTGTAAGATT 58.379 34.615 0.00 0.00 37.43 2.40
6211 13062 7.182817 TCACACCTATTTAGCACTGTAAGAT 57.817 36.000 0.00 0.00 37.43 2.40
6212 13063 6.599356 TCACACCTATTTAGCACTGTAAGA 57.401 37.500 0.00 0.00 37.43 2.10
6213 13064 7.268586 AGATCACACCTATTTAGCACTGTAAG 58.731 38.462 0.00 0.00 42.29 2.34
6214 13065 7.182817 AGATCACACCTATTTAGCACTGTAA 57.817 36.000 0.00 0.00 0.00 2.41
6215 13066 6.791867 AGATCACACCTATTTAGCACTGTA 57.208 37.500 0.00 0.00 0.00 2.74
6216 13067 5.683876 AGATCACACCTATTTAGCACTGT 57.316 39.130 0.00 0.00 0.00 3.55
6217 13068 6.810911 AGTAGATCACACCTATTTAGCACTG 58.189 40.000 0.00 0.00 0.00 3.66
6218 13069 7.780745 AGTAGTAGATCACACCTATTTAGCACT 59.219 37.037 0.00 0.00 0.00 4.40
6219 13070 7.942990 AGTAGTAGATCACACCTATTTAGCAC 58.057 38.462 0.00 0.00 0.00 4.40
6220 13071 9.809395 ATAGTAGTAGATCACACCTATTTAGCA 57.191 33.333 0.00 0.00 0.00 3.49
6268 13120 0.597568 TCAAATCCACGGCAAGCAAG 59.402 50.000 0.00 0.00 0.00 4.01
6278 13130 1.959282 GGCCCAGATGATCAAATCCAC 59.041 52.381 0.00 0.00 0.00 4.02
6286 13138 1.340405 ACAACAGTGGCCCAGATGATC 60.340 52.381 0.00 0.00 0.00 2.92
6297 13149 6.420604 GGTTCAAAACATGATAACAACAGTGG 59.579 38.462 0.00 0.00 38.03 4.00
6340 13192 1.544314 GGCATATTCCTGTGAGCTCCC 60.544 57.143 12.15 0.00 0.00 4.30
6349 13201 3.558931 TGGTACACTGGCATATTCCTG 57.441 47.619 0.00 0.00 0.00 3.86


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

AutoCloner maintained by Alex Coulton.