Multiple sequence alignment - TraesCS7D01G135000

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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 TraesCS7D01G135000 chr7D 100.000 4082 0 0 1 4082 86298714 86294633 0.000000e+00 7539.0
1 TraesCS7D01G135000 chr7D 87.890 2246 230 33 128 2357 86768801 86766582 0.000000e+00 2603.0
2 TraesCS7D01G135000 chr7D 87.401 2262 217 31 132 2357 87212742 87210513 0.000000e+00 2536.0
3 TraesCS7D01G135000 chr7D 87.261 2245 232 35 132 2357 86927571 86925362 0.000000e+00 2512.0
4 TraesCS7D01G135000 chr7D 87.152 1938 204 34 435 2357 86924515 86922608 0.000000e+00 2158.0
5 TraesCS7D01G135000 chr7D 85.901 1993 224 28 378 2357 86800993 86799045 0.000000e+00 2071.0
6 TraesCS7D01G135000 chr7D 88.525 1037 90 13 2360 3370 86799005 86797972 0.000000e+00 1229.0
7 TraesCS7D01G135000 chr7D 92.123 876 56 3 2360 3234 87210473 87209610 0.000000e+00 1223.0
8 TraesCS7D01G135000 chr7D 89.627 617 55 4 3470 4082 86797971 86797360 0.000000e+00 776.0
9 TraesCS7D01G135000 chr7D 88.853 619 58 5 3470 4082 86921528 86920915 0.000000e+00 750.0
10 TraesCS7D01G135000 chr7D 88.799 616 52 5 3470 4082 87209428 87208827 0.000000e+00 739.0
11 TraesCS7D01G135000 chr7D 89.483 542 48 4 3470 4007 86765503 86764967 0.000000e+00 676.0
12 TraesCS7D01G135000 chr7B 87.867 2283 220 24 86 2357 35513591 35511355 0.000000e+00 2628.0
13 TraesCS7D01G135000 chr7B 86.781 2156 238 29 211 2345 35313792 35311663 0.000000e+00 2359.0
14 TraesCS7D01G135000 chr7B 84.339 2254 274 49 118 2346 35257617 35255418 0.000000e+00 2134.0
15 TraesCS7D01G135000 chr7B 89.027 1048 76 20 2360 3370 35311603 35310558 0.000000e+00 1262.0
16 TraesCS7D01G135000 chr7B 93.560 823 52 1 2363 3185 35511312 35510491 0.000000e+00 1225.0
17 TraesCS7D01G135000 chr7B 91.354 613 48 4 3470 4082 35310557 35309950 0.000000e+00 833.0
18 TraesCS7D01G135000 chr7B 88.493 617 60 6 3470 4082 35510228 35509619 0.000000e+00 736.0
19 TraesCS7D01G135000 chr7B 92.784 97 4 3 3366 3462 514630109 514630016 1.980000e-28 137.0
20 TraesCS7D01G135000 chr7A 87.446 2302 241 30 74 2357 88014701 88012430 0.000000e+00 2606.0
21 TraesCS7D01G135000 chr7A 87.193 2241 244 23 134 2357 88127924 88125710 0.000000e+00 2508.0
22 TraesCS7D01G135000 chr7A 87.026 2243 239 21 132 2357 88323970 88321763 0.000000e+00 2483.0
23 TraesCS7D01G135000 chr7A 86.749 2264 226 31 132 2357 88442172 88439945 0.000000e+00 2451.0
24 TraesCS7D01G135000 chr7A 85.791 2245 254 31 132 2357 88178675 88176477 0.000000e+00 2318.0
25 TraesCS7D01G135000 chr7A 86.972 1658 185 18 708 2357 87456919 87455285 0.000000e+00 1836.0
26 TraesCS7D01G135000 chr7A 89.207 1047 68 20 2360 3370 88012390 88011353 0.000000e+00 1266.0
27 TraesCS7D01G135000 chr7A 88.528 1046 76 20 2360 3370 88176437 88175401 0.000000e+00 1227.0
28 TraesCS7D01G135000 chr7A 88.443 1047 76 20 2360 3370 88125670 88124633 0.000000e+00 1221.0
29 TraesCS7D01G135000 chr7A 91.448 877 63 2 2360 3235 87455245 87454380 0.000000e+00 1194.0
30 TraesCS7D01G135000 chr7A 91.448 877 58 5 2360 3235 88439905 88439045 0.000000e+00 1188.0
31 TraesCS7D01G135000 chr7A 86.893 885 73 26 2527 3370 88320596 88319714 0.000000e+00 952.0
32 TraesCS7D01G135000 chr7A 89.034 611 56 5 3477 4081 87454177 87453572 0.000000e+00 747.0
33 TraesCS7D01G135000 chr7A 88.581 613 56 10 3470 4082 88124632 88124034 0.000000e+00 732.0
34 TraesCS7D01G135000 chr7A 88.581 613 56 9 3470 4082 88175400 88174802 0.000000e+00 732.0
35 TraesCS7D01G135000 chr7A 88.254 613 58 9 3470 4082 88011352 88010754 0.000000e+00 721.0
36 TraesCS7D01G135000 chr7A 87.987 616 57 7 3470 4082 88438864 88438263 0.000000e+00 712.0
37 TraesCS7D01G135000 chr7A 87.439 613 47 17 74 677 87457509 87456918 0.000000e+00 678.0
38 TraesCS7D01G135000 chr7A 88.307 573 50 6 3470 4039 88319713 88319155 0.000000e+00 671.0
39 TraesCS7D01G135000 chr7A 93.204 103 7 0 3268 3370 87454284 87454182 7.070000e-33 152.0
40 TraesCS7D01G135000 chr7A 95.122 41 1 1 74 114 88324009 88323970 3.410000e-06 63.9
41 TraesCS7D01G135000 chr3B 96.629 89 3 0 3376 3464 798547418 798547506 9.140000e-32 148.0
42 TraesCS7D01G135000 chr3B 90.826 109 4 6 3362 3468 259911557 259911453 1.530000e-29 141.0
43 TraesCS7D01G135000 chr5A 91.837 98 8 0 3375 3472 64382191 64382094 1.980000e-28 137.0
44 TraesCS7D01G135000 chr1D 91.176 102 7 2 3361 3461 473932915 473933015 1.980000e-28 137.0
45 TraesCS7D01G135000 chr4D 89.286 112 7 5 3357 3468 62006707 62006813 7.120000e-28 135.0
46 TraesCS7D01G135000 chr3D 95.294 85 4 0 3377 3461 172830824 172830740 7.120000e-28 135.0
47 TraesCS7D01G135000 chr1B 91.176 102 5 4 3366 3466 74411511 74411609 7.120000e-28 135.0
48 TraesCS7D01G135000 chr6D 87.931 116 11 2 3357 3472 149721768 149721656 2.560000e-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 TraesCS7D01G135000 chr7D 86294633 86298714 4081 True 7539.000000 7539 100.000000 1 4082 1 chr7D.!!$R1 4081
1 TraesCS7D01G135000 chr7D 86920915 86927571 6656 True 1806.666667 2512 87.755333 132 4082 3 chr7D.!!$R4 3950
2 TraesCS7D01G135000 chr7D 86764967 86768801 3834 True 1639.500000 2603 88.686500 128 4007 2 chr7D.!!$R2 3879
3 TraesCS7D01G135000 chr7D 87208827 87212742 3915 True 1499.333333 2536 89.441000 132 4082 3 chr7D.!!$R5 3950
4 TraesCS7D01G135000 chr7D 86797360 86800993 3633 True 1358.666667 2071 88.017667 378 4082 3 chr7D.!!$R3 3704
5 TraesCS7D01G135000 chr7B 35255418 35257617 2199 True 2134.000000 2134 84.339000 118 2346 1 chr7B.!!$R1 2228
6 TraesCS7D01G135000 chr7B 35509619 35513591 3972 True 1529.666667 2628 89.973333 86 4082 3 chr7B.!!$R4 3996
7 TraesCS7D01G135000 chr7B 35309950 35313792 3842 True 1484.666667 2359 89.054000 211 4082 3 chr7B.!!$R3 3871
8 TraesCS7D01G135000 chr7A 88010754 88014701 3947 True 1531.000000 2606 88.302333 74 4082 3 chr7A.!!$R2 4008
9 TraesCS7D01G135000 chr7A 88124034 88127924 3890 True 1487.000000 2508 88.072333 134 4082 3 chr7A.!!$R3 3948
10 TraesCS7D01G135000 chr7A 88438263 88442172 3909 True 1450.333333 2451 88.728000 132 4082 3 chr7A.!!$R6 3950
11 TraesCS7D01G135000 chr7A 88174802 88178675 3873 True 1425.666667 2318 87.633333 132 4082 3 chr7A.!!$R4 3950
12 TraesCS7D01G135000 chr7A 88319155 88324009 4854 True 1042.475000 2483 89.337000 74 4039 4 chr7A.!!$R5 3965
13 TraesCS7D01G135000 chr7A 87453572 87457509 3937 True 921.400000 1836 89.619400 74 4081 5 chr7A.!!$R1 4007

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
931 3734 0.259065 TACTCCGCACTCTCCATCCT 59.741 55.0 0.00 0.0 0.0 3.24 F
1318 4130 0.112606 CTATGAGCTACCGGGGGAGA 59.887 60.0 6.32 0.0 0.0 3.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2790 6669 1.003116 GCTGCCAATAGCTCATTGTCG 60.003 52.381 0.00 0.0 42.22 4.35 R
3187 7070 0.254462 TGCCGGCCATAATGTCTTGA 59.746 50.000 26.77 0.0 0.00 3.02 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
28 29 7.740519 AAATCTATATTCGTTTTGCAACAGC 57.259 32.000 0.00 0.00 32.54 4.40
29 30 6.683974 ATCTATATTCGTTTTGCAACAGCT 57.316 33.333 0.00 0.00 32.54 4.24
30 31 7.786178 ATCTATATTCGTTTTGCAACAGCTA 57.214 32.000 0.00 0.00 32.54 3.32
31 32 7.786178 TCTATATTCGTTTTGCAACAGCTAT 57.214 32.000 0.00 0.00 32.54 2.97
32 33 7.630026 TCTATATTCGTTTTGCAACAGCTATG 58.370 34.615 0.00 0.00 32.54 2.23
33 34 3.980646 TTCGTTTTGCAACAGCTATGT 57.019 38.095 0.00 0.00 43.15 2.29
34 35 3.266541 TCGTTTTGCAACAGCTATGTG 57.733 42.857 0.00 0.00 40.39 3.21
35 36 2.616376 TCGTTTTGCAACAGCTATGTGT 59.384 40.909 0.00 0.00 40.39 3.72
36 37 3.810386 TCGTTTTGCAACAGCTATGTGTA 59.190 39.130 0.00 0.00 40.39 2.90
37 38 4.454161 TCGTTTTGCAACAGCTATGTGTAT 59.546 37.500 0.00 0.00 40.39 2.29
38 39 5.049060 TCGTTTTGCAACAGCTATGTGTATT 60.049 36.000 0.00 0.00 40.39 1.89
39 40 5.283717 CGTTTTGCAACAGCTATGTGTATTC 59.716 40.000 0.00 0.00 40.39 1.75
40 41 5.956068 TTTGCAACAGCTATGTGTATTCA 57.044 34.783 0.00 0.00 40.39 2.57
41 42 6.513806 TTTGCAACAGCTATGTGTATTCAT 57.486 33.333 0.00 0.00 40.39 2.57
42 43 5.488645 TGCAACAGCTATGTGTATTCATG 57.511 39.130 0.00 0.00 40.39 3.07
43 44 4.201940 TGCAACAGCTATGTGTATTCATGC 60.202 41.667 0.00 0.00 40.39 4.06
44 45 4.201940 GCAACAGCTATGTGTATTCATGCA 60.202 41.667 0.00 0.00 40.39 3.96
45 46 5.268544 CAACAGCTATGTGTATTCATGCAC 58.731 41.667 0.00 1.35 40.39 4.57
46 47 4.774124 ACAGCTATGTGTATTCATGCACT 58.226 39.130 9.12 0.00 42.76 4.40
47 48 5.917462 ACAGCTATGTGTATTCATGCACTA 58.083 37.500 9.12 0.00 42.76 2.74
48 49 5.987953 ACAGCTATGTGTATTCATGCACTAG 59.012 40.000 9.12 8.85 42.76 2.57
49 50 5.987953 CAGCTATGTGTATTCATGCACTAGT 59.012 40.000 9.12 0.00 42.76 2.57
50 51 5.987953 AGCTATGTGTATTCATGCACTAGTG 59.012 40.000 18.93 18.93 42.76 2.74
51 52 5.755375 GCTATGTGTATTCATGCACTAGTGT 59.245 40.000 23.44 5.73 42.76 3.55
52 53 6.074088 GCTATGTGTATTCATGCACTAGTGTC 60.074 42.308 23.44 15.87 42.76 3.67
53 54 5.405935 TGTGTATTCATGCACTAGTGTCT 57.594 39.130 23.44 8.94 42.76 3.41
54 55 5.410924 TGTGTATTCATGCACTAGTGTCTC 58.589 41.667 23.44 8.27 42.76 3.36
55 56 5.047377 TGTGTATTCATGCACTAGTGTCTCA 60.047 40.000 23.44 13.66 42.76 3.27
56 57 5.869344 GTGTATTCATGCACTAGTGTCTCAA 59.131 40.000 23.44 12.19 39.79 3.02
57 58 6.368791 GTGTATTCATGCACTAGTGTCTCAAA 59.631 38.462 23.44 12.21 39.79 2.69
58 59 6.934083 TGTATTCATGCACTAGTGTCTCAAAA 59.066 34.615 23.44 11.97 0.00 2.44
59 60 6.882610 ATTCATGCACTAGTGTCTCAAAAA 57.117 33.333 23.44 11.67 0.00 1.94
60 61 5.929697 TCATGCACTAGTGTCTCAAAAAG 57.070 39.130 23.44 6.33 0.00 2.27
61 62 4.214119 TCATGCACTAGTGTCTCAAAAAGC 59.786 41.667 23.44 6.17 0.00 3.51
62 63 3.540617 TGCACTAGTGTCTCAAAAAGCA 58.459 40.909 23.44 8.77 0.00 3.91
63 64 3.312421 TGCACTAGTGTCTCAAAAAGCAC 59.688 43.478 23.44 3.32 34.31 4.40
64 65 3.312421 GCACTAGTGTCTCAAAAAGCACA 59.688 43.478 23.44 0.00 35.65 4.57
65 66 4.023707 GCACTAGTGTCTCAAAAAGCACAT 60.024 41.667 23.44 0.00 35.65 3.21
66 67 5.506317 GCACTAGTGTCTCAAAAAGCACATT 60.506 40.000 23.44 0.00 35.65 2.71
67 68 5.911280 CACTAGTGTCTCAAAAAGCACATTG 59.089 40.000 15.06 0.00 35.65 2.82
68 69 5.822519 ACTAGTGTCTCAAAAAGCACATTGA 59.177 36.000 0.00 0.00 35.65 2.57
69 70 5.779529 AGTGTCTCAAAAAGCACATTGAT 57.220 34.783 0.00 0.00 35.20 2.57
70 71 6.152932 AGTGTCTCAAAAAGCACATTGATT 57.847 33.333 0.00 0.00 35.20 2.57
71 72 7.275888 AGTGTCTCAAAAAGCACATTGATTA 57.724 32.000 0.00 0.00 35.20 1.75
72 73 7.715657 AGTGTCTCAAAAAGCACATTGATTAA 58.284 30.769 0.00 0.00 35.20 1.40
152 153 5.610132 AGAGAGAGAGAGAGAGAGATGGAAT 59.390 44.000 0.00 0.00 0.00 3.01
185 186 8.519526 GTGTCAAATTTATTGACTTCATGGGTA 58.480 33.333 18.77 0.00 46.53 3.69
249 254 6.480763 TGTAGGTATGTCACAATTGATTGGT 58.519 36.000 13.59 0.00 41.96 3.67
331 337 4.153117 GCCTATAGATGGAATTTCGTGCAG 59.847 45.833 0.00 0.00 0.00 4.41
423 442 9.265901 CATATATGTAGCCTAGTTATTCATGGC 57.734 37.037 4.43 0.00 43.52 4.40
482 510 7.436080 GCAATAAAACTCCATTGATACATGTGG 59.564 37.037 9.11 0.00 34.69 4.17
487 515 3.281158 TCCATTGATACATGTGGCACTG 58.719 45.455 19.83 15.98 0.00 3.66
522 552 0.994247 TGGAGATCCTGTGTGCCATT 59.006 50.000 0.00 0.00 36.82 3.16
538 568 4.275936 GTGCCATTTATATTTGAGAGCGGT 59.724 41.667 0.00 0.00 0.00 5.68
597 634 2.802792 ATGTCATGCATGCACGCC 59.197 55.556 25.37 4.76 36.26 5.68
627 664 6.128227 GCGTGTTCTATCTATCTAGACCGAAT 60.128 42.308 0.00 0.00 34.72 3.34
632 669 9.615295 GTTCTATCTATCTAGACCGAATTTGAC 57.385 37.037 0.00 0.00 34.72 3.18
633 670 8.919777 TCTATCTATCTAGACCGAATTTGACA 57.080 34.615 0.00 0.00 34.72 3.58
647 684 6.072728 CCGAATTTGACAAACACTCAATAGGA 60.073 38.462 1.94 0.00 0.00 2.94
677 714 7.132863 GTGTGTTGTTTCTACCAATCTTCTTC 58.867 38.462 0.00 0.00 0.00 2.87
767 810 5.679906 CACAATGTCGAGGTCAACTTAAAG 58.320 41.667 0.00 0.00 0.00 1.85
770 813 6.987992 ACAATGTCGAGGTCAACTTAAAGTAA 59.012 34.615 0.00 0.00 0.00 2.24
792 836 1.452833 GGCATGTTCCTCAGAGGGC 60.453 63.158 17.10 11.09 35.59 5.19
846 894 1.249407 TTTGTATGGACCGGCAAACC 58.751 50.000 0.00 0.25 0.00 3.27
853 901 1.004862 TGGACCGGCAAACCATCAATA 59.995 47.619 0.00 0.00 34.57 1.90
918 3717 8.189460 GGGCTATAAATACACTATCTTACTCCG 58.811 40.741 0.00 0.00 0.00 4.63
931 3734 0.259065 TACTCCGCACTCTCCATCCT 59.741 55.000 0.00 0.00 0.00 3.24
932 3735 1.326213 ACTCCGCACTCTCCATCCTG 61.326 60.000 0.00 0.00 0.00 3.86
936 3739 0.820226 CGCACTCTCCATCCTGAAGA 59.180 55.000 0.00 0.00 0.00 2.87
1006 3812 7.232534 GTCCAACTATCTAGTCTCTCATGGATT 59.767 40.741 8.64 0.00 37.77 3.01
1016 3822 7.615039 AGTCTCTCATGGATTCAATAGTCAT 57.385 36.000 0.00 0.00 0.00 3.06
1036 3842 1.341156 CCAGGGGTGGACCTCATCTC 61.341 65.000 0.00 0.00 39.62 2.75
1065 3871 0.745845 AGGCACGATCACTCATTGCC 60.746 55.000 2.59 2.59 44.95 4.52
1093 3899 6.456795 TCAACACCAACAAAATCATGTACA 57.543 33.333 0.00 0.00 32.02 2.90
1097 3906 4.148000 CACCAACAAAATCATGTACAACGC 59.852 41.667 0.00 0.00 32.02 4.84
1158 3967 1.634973 TCTCTCCATGCATTGTTCCCA 59.365 47.619 0.00 0.00 0.00 4.37
1164 3973 3.581770 TCCATGCATTGTTCCCATCAAAA 59.418 39.130 0.00 0.00 0.00 2.44
1171 3980 3.399440 TGTTCCCATCAAAAACCATGC 57.601 42.857 0.00 0.00 0.00 4.06
1186 3995 8.465999 CAAAAACCATGCAACAGGTAATAGATA 58.534 33.333 8.98 0.00 37.07 1.98
1213 4022 2.945008 GTTGATCTCGCCATGGAAATGA 59.055 45.455 18.40 7.77 0.00 2.57
1270 4079 0.965439 TGGTAGCCCACAAAACATGC 59.035 50.000 0.00 0.00 35.17 4.06
1318 4130 0.112606 CTATGAGCTACCGGGGGAGA 59.887 60.000 6.32 0.00 0.00 3.71
1345 4160 1.659098 GTGCTAGCAACATACACGGTC 59.341 52.381 21.29 0.00 0.00 4.79
1393 4208 2.614734 GGAAACTTTGGGGTACGAGAGG 60.615 54.545 0.00 0.00 0.00 3.69
1394 4209 2.019807 AACTTTGGGGTACGAGAGGA 57.980 50.000 0.00 0.00 0.00 3.71
1395 4210 1.558233 ACTTTGGGGTACGAGAGGAG 58.442 55.000 0.00 0.00 0.00 3.69
1584 4409 5.454613 GGATTTTTGGACCAACAAGGAACAT 60.455 40.000 6.36 0.00 41.22 2.71
1599 4424 3.314541 GAACATAGGTTCGTCCACAGT 57.685 47.619 4.27 0.00 43.54 3.55
1634 4460 9.677567 TCTTCTTTGTCATGTACTTTTAATTGC 57.322 29.630 0.00 0.00 0.00 3.56
1716 4543 9.685276 AAGATTGGTAGATTACATTTGTGATGA 57.315 29.630 0.00 0.00 0.00 2.92
1717 4544 9.857656 AGATTGGTAGATTACATTTGTGATGAT 57.142 29.630 0.00 0.00 0.00 2.45
1727 4554 9.830294 ATTACATTTGTGATGATATATTGCACG 57.170 29.630 0.00 0.00 32.39 5.34
1762 4590 4.889409 ACACATGGACACTGTCAATTTCTT 59.111 37.500 11.34 0.00 33.68 2.52
1778 4606 6.041409 TCAATTTCTTTTTACAGCATGGGTGA 59.959 34.615 2.05 0.00 43.62 4.02
1823 4651 2.565391 TGCAAGAGGACGAGGATACAAA 59.435 45.455 0.00 0.00 41.41 2.83
1857 4703 2.890311 TGGATTTCCATTTCGTTGTGCT 59.110 40.909 0.00 0.00 42.01 4.40
1904 4750 2.031768 GGAGGCTCGGATGATGGC 59.968 66.667 8.69 0.00 0.00 4.40
1924 4770 2.880890 GCAGACAAGAACAAGATGGTGT 59.119 45.455 0.00 0.00 0.00 4.16
2015 4861 3.978687 AGGAACACAAGTTAGTCGACAG 58.021 45.455 19.50 2.65 38.30 3.51
2028 4874 4.857509 AGTCGACAGCTATATTCTTCCC 57.142 45.455 19.50 0.00 0.00 3.97
2121 4973 9.930158 AATTTTATGAGGCAGGTAGGTTAAATA 57.070 29.630 0.00 0.00 0.00 1.40
2128 4980 6.136155 AGGCAGGTAGGTTAAATATGCAATT 58.864 36.000 0.00 0.00 33.94 2.32
2327 5195 7.696992 AAATTCCAATATGGTACGTCTTGTT 57.303 32.000 0.00 0.00 39.03 2.83
2358 5235 9.906660 TCAAACAAATCAATAACCTGTAATGTC 57.093 29.630 0.00 0.00 0.00 3.06
2459 5373 9.550406 CATTCTATCCAGTACCCGTAAATAAAA 57.450 33.333 0.00 0.00 0.00 1.52
2494 5408 3.371591 GTGTTGTTGTAGTGGTTCGAACA 59.628 43.478 28.24 12.75 0.00 3.18
2567 6446 4.499183 ACTCCACGATTCATCTTTCAGTC 58.501 43.478 0.00 0.00 0.00 3.51
2580 6459 8.231692 TCATCTTTCAGTCAACAATTTAACCA 57.768 30.769 0.00 0.00 0.00 3.67
2584 6463 8.527810 TCTTTCAGTCAACAATTTAACCAAACT 58.472 29.630 0.00 0.00 0.00 2.66
2613 6492 3.595173 TGAACATTATGTCCACAGGTCG 58.405 45.455 0.00 0.00 0.00 4.79
2619 6498 2.457366 ATGTCCACAGGTCGTTTCTC 57.543 50.000 0.00 0.00 0.00 2.87
2632 6511 2.569853 TCGTTTCTCTATGGGCTGGAAA 59.430 45.455 0.00 0.00 0.00 3.13
2736 6615 8.868916 GCACAAAAGTTTTTCAAGAGAATACAA 58.131 29.630 0.00 0.00 32.89 2.41
2790 6669 2.408271 TCAATGATGTGAGGCTCCAC 57.592 50.000 12.86 10.72 37.55 4.02
2817 6696 4.637483 TGAGCTATTGGCAGCAAATAAC 57.363 40.909 3.71 0.00 44.35 1.89
2957 6836 7.257016 CCCCTCCATATATAATCAACAAGTGGA 60.257 40.741 0.00 0.00 0.00 4.02
3019 6898 1.220749 GCAGCTGTTATGGACGGGA 59.779 57.895 16.64 0.00 35.05 5.14
3145 7028 1.227102 GCCAGGCATGTGTCCCATA 59.773 57.895 6.55 0.00 30.71 2.74
3158 7041 6.687081 TGTGTCCCATAAATAAACGGATTC 57.313 37.500 0.00 0.00 0.00 2.52
3177 7060 3.914426 TCTCCTCCTAAAGATGGCAAC 57.086 47.619 0.00 0.00 0.00 4.17
3178 7061 8.548625 GGATTCTCCTCCTAAAGATGGCAACA 62.549 46.154 0.00 0.00 42.67 3.33
3221 7104 3.181480 GGCCGGCATGTGTGTTTAATAAT 60.181 43.478 30.85 0.00 0.00 1.28
3222 7105 3.796178 GCCGGCATGTGTGTTTAATAATG 59.204 43.478 24.80 0.00 0.00 1.90
3225 7134 5.514914 CCGGCATGTGTGTTTAATAATGAAC 59.485 40.000 0.00 0.00 0.00 3.18
3325 7306 5.239744 TGTTGTTGTATTACCATGCGAAAGT 59.760 36.000 0.00 0.00 0.00 2.66
3332 7313 7.266400 TGTATTACCATGCGAAAGTGTACATA 58.734 34.615 0.00 0.00 0.00 2.29
3370 7352 5.368230 TGGCCCTGACTGTTGTATCATAATA 59.632 40.000 0.00 0.00 0.00 0.98
3371 7353 6.044287 TGGCCCTGACTGTTGTATCATAATAT 59.956 38.462 0.00 0.00 0.00 1.28
3372 7354 7.236640 TGGCCCTGACTGTTGTATCATAATATA 59.763 37.037 0.00 0.00 0.00 0.86
3373 7355 8.267894 GGCCCTGACTGTTGTATCATAATATAT 58.732 37.037 0.00 0.00 0.00 0.86
3374 7356 9.319143 GCCCTGACTGTTGTATCATAATATATC 57.681 37.037 0.00 0.00 0.00 1.63
3389 7371 9.647918 TCATAATATATCATACTCCCTCTGTCC 57.352 37.037 0.00 0.00 0.00 4.02
3390 7372 8.865090 CATAATATATCATACTCCCTCTGTCCC 58.135 40.741 0.00 0.00 0.00 4.46
3391 7373 2.002505 ATCATACTCCCTCTGTCCCG 57.997 55.000 0.00 0.00 0.00 5.14
3392 7374 0.629596 TCATACTCCCTCTGTCCCGT 59.370 55.000 0.00 0.00 0.00 5.28
3393 7375 1.848388 TCATACTCCCTCTGTCCCGTA 59.152 52.381 0.00 0.00 0.00 4.02
3394 7376 2.242965 TCATACTCCCTCTGTCCCGTAA 59.757 50.000 0.00 0.00 0.00 3.18
3395 7377 3.117246 TCATACTCCCTCTGTCCCGTAAT 60.117 47.826 0.00 0.00 0.00 1.89
3396 7378 4.105217 TCATACTCCCTCTGTCCCGTAATA 59.895 45.833 0.00 0.00 0.00 0.98
3397 7379 3.614568 ACTCCCTCTGTCCCGTAATAT 57.385 47.619 0.00 0.00 0.00 1.28
3398 7380 4.736611 ACTCCCTCTGTCCCGTAATATA 57.263 45.455 0.00 0.00 0.00 0.86
3399 7381 5.070823 ACTCCCTCTGTCCCGTAATATAA 57.929 43.478 0.00 0.00 0.00 0.98
3400 7382 5.078256 ACTCCCTCTGTCCCGTAATATAAG 58.922 45.833 0.00 0.00 0.00 1.73
3401 7383 5.163012 ACTCCCTCTGTCCCGTAATATAAGA 60.163 44.000 0.00 0.00 0.00 2.10
3402 7384 5.322754 TCCCTCTGTCCCGTAATATAAGAG 58.677 45.833 0.00 0.00 0.00 2.85
3403 7385 4.082136 CCCTCTGTCCCGTAATATAAGAGC 60.082 50.000 0.00 0.00 0.00 4.09
3404 7386 4.379603 CCTCTGTCCCGTAATATAAGAGCG 60.380 50.000 0.00 0.00 0.00 5.03
3405 7387 4.139786 TCTGTCCCGTAATATAAGAGCGT 58.860 43.478 0.00 0.00 0.00 5.07
3406 7388 4.581824 TCTGTCCCGTAATATAAGAGCGTT 59.418 41.667 0.00 0.00 0.00 4.84
3407 7389 5.068198 TCTGTCCCGTAATATAAGAGCGTTT 59.932 40.000 0.00 0.00 0.00 3.60
3408 7390 5.663456 TGTCCCGTAATATAAGAGCGTTTT 58.337 37.500 0.00 0.00 0.00 2.43
3409 7391 6.108015 TGTCCCGTAATATAAGAGCGTTTTT 58.892 36.000 0.00 0.00 0.00 1.94
3410 7392 7.264221 TGTCCCGTAATATAAGAGCGTTTTTA 58.736 34.615 0.00 0.00 0.00 1.52
3411 7393 7.927629 TGTCCCGTAATATAAGAGCGTTTTTAT 59.072 33.333 0.91 0.91 0.00 1.40
3412 7394 8.430828 GTCCCGTAATATAAGAGCGTTTTTATC 58.569 37.037 0.00 0.00 0.00 1.75
3413 7395 8.143193 TCCCGTAATATAAGAGCGTTTTTATCA 58.857 33.333 0.00 0.00 0.00 2.15
3414 7396 8.219105 CCCGTAATATAAGAGCGTTTTTATCAC 58.781 37.037 0.00 0.00 0.00 3.06
3415 7397 8.975439 CCGTAATATAAGAGCGTTTTTATCACT 58.025 33.333 0.00 0.00 0.00 3.41
3422 7404 7.813852 AAGAGCGTTTTTATCACTACACTAG 57.186 36.000 0.00 0.00 0.00 2.57
3423 7405 6.921914 AGAGCGTTTTTATCACTACACTAGT 58.078 36.000 0.00 0.00 40.28 2.57
3436 7418 6.579491 ACTACACTAGTGTCAAAAACGTTC 57.421 37.500 31.11 0.00 43.74 3.95
3437 7419 6.335777 ACTACACTAGTGTCAAAAACGTTCT 58.664 36.000 31.11 5.44 43.74 3.01
3438 7420 6.815142 ACTACACTAGTGTCAAAAACGTTCTT 59.185 34.615 31.11 4.99 43.74 2.52
3439 7421 7.975616 ACTACACTAGTGTCAAAAACGTTCTTA 59.024 33.333 31.11 8.36 43.74 2.10
3440 7422 7.781548 ACACTAGTGTCAAAAACGTTCTTAT 57.218 32.000 22.95 0.00 40.24 1.73
3441 7423 8.876275 ACACTAGTGTCAAAAACGTTCTTATA 57.124 30.769 22.95 0.00 40.24 0.98
3442 7424 9.485206 ACACTAGTGTCAAAAACGTTCTTATAT 57.515 29.630 22.95 0.00 40.24 0.86
3448 7430 9.498307 GTGTCAAAAACGTTCTTATATTATGGG 57.502 33.333 0.00 0.00 0.00 4.00
3449 7431 9.451002 TGTCAAAAACGTTCTTATATTATGGGA 57.549 29.630 0.00 0.00 0.00 4.37
3450 7432 9.712359 GTCAAAAACGTTCTTATATTATGGGAC 57.288 33.333 0.00 0.00 0.00 4.46
3464 7446 1.866015 TGGGACAGAGGGAGTACATG 58.134 55.000 0.00 0.00 0.00 3.21
3465 7447 1.361197 TGGGACAGAGGGAGTACATGA 59.639 52.381 0.00 0.00 0.00 3.07
3466 7448 2.023015 TGGGACAGAGGGAGTACATGAT 60.023 50.000 0.00 0.00 0.00 2.45
3467 7449 3.041946 GGGACAGAGGGAGTACATGATT 58.958 50.000 0.00 0.00 0.00 2.57
3468 7450 3.181461 GGGACAGAGGGAGTACATGATTG 60.181 52.174 0.00 0.00 0.00 2.67
3481 7463 7.445402 GGAGTACATGATTGTTGCCTACATTAT 59.555 37.037 0.00 0.00 36.44 1.28
3520 7502 5.511888 CCCATGAAAAAGCACAGGAATCTTT 60.512 40.000 0.00 0.00 0.00 2.52
3584 7566 8.729805 TTCAGTTGCCAAATTACTTGAAAATT 57.270 26.923 0.00 0.00 37.17 1.82
3665 7649 4.261994 GCATGTTGGCTCTTCCTGTTTTTA 60.262 41.667 0.00 0.00 35.26 1.52
3675 7659 6.248569 TCTTCCTGTTTTTAGTCCAAGAGT 57.751 37.500 0.00 0.00 0.00 3.24
3679 7663 4.072839 CTGTTTTTAGTCCAAGAGTCCCC 58.927 47.826 0.00 0.00 0.00 4.81
3680 7664 3.072211 GTTTTTAGTCCAAGAGTCCCCG 58.928 50.000 0.00 0.00 0.00 5.73
3685 7669 0.248565 GTCCAAGAGTCCCCGGTAAC 59.751 60.000 0.00 0.00 0.00 2.50
3724 7709 4.996344 TGCTATGTTGTGGCAATGTAATG 58.004 39.130 0.00 0.00 41.76 1.90
3725 7710 3.798337 GCTATGTTGTGGCAATGTAATGC 59.202 43.478 0.00 0.00 45.67 3.56
3801 7796 9.816354 AAAATTAAGGATTTCATATTTCACCGG 57.184 29.630 0.00 0.00 36.96 5.28
3812 7807 6.588204 TCATATTTCACCGGCACTATAGTTT 58.412 36.000 0.00 0.00 0.00 2.66
3817 7812 0.657840 CCGGCACTATAGTTTGCAGC 59.342 55.000 15.08 9.85 40.75 5.25
3824 7819 4.436584 GCACTATAGTTTGCAGCTTGTCAG 60.437 45.833 1.56 0.00 38.68 3.51
3826 7821 5.180117 CACTATAGTTTGCAGCTTGTCAGTT 59.820 40.000 1.56 0.00 0.00 3.16
3857 7852 7.379529 GTCAAACAGACAAACCAATCAGTTATG 59.620 37.037 0.00 0.00 46.77 1.90
3888 7883 5.835113 ACCCTCACCATCATTTTAAATCG 57.165 39.130 0.00 0.00 0.00 3.34
3902 7897 4.944962 TTAAATCGCAACACTCTCCATG 57.055 40.909 0.00 0.00 0.00 3.66
3915 7910 9.740239 CAACACTCTCCATGATATTAAATTTGG 57.260 33.333 0.00 0.00 0.00 3.28
3954 7949 0.179097 GAAGAGATCAGGGGCACGAC 60.179 60.000 0.00 0.00 0.00 4.34
3964 7959 1.654023 GGGGCACGACTGGCATTTAC 61.654 60.000 2.03 0.00 44.99 2.01
4013 8011 2.924302 TCTAGAGACCTAGGTTGGGACA 59.076 50.000 17.53 0.00 42.06 4.02
4052 8050 8.707938 TTATATATGAAATGGCAGAGATGTCG 57.292 34.615 0.00 0.00 0.00 4.35
4057 8055 4.701651 TGAAATGGCAGAGATGTCGAAAAT 59.298 37.500 0.00 0.00 0.00 1.82
4064 8062 6.429692 TGGCAGAGATGTCGAAAATAAGAAAA 59.570 34.615 0.00 0.00 0.00 2.29
4068 8066 9.643652 CAGAGATGTCGAAAATAAGAAAATAGC 57.356 33.333 0.00 0.00 0.00 2.97
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 8.647226 GCTGTTGCAAAACGAATATAGATTTTT 58.353 29.630 0.00 0.00 39.41 1.94
3 4 8.028938 AGCTGTTGCAAAACGAATATAGATTTT 58.971 29.630 0.00 0.00 42.74 1.82
4 5 7.538575 AGCTGTTGCAAAACGAATATAGATTT 58.461 30.769 0.00 0.00 42.74 2.17
5 6 7.088589 AGCTGTTGCAAAACGAATATAGATT 57.911 32.000 0.00 0.00 42.74 2.40
6 7 6.683974 AGCTGTTGCAAAACGAATATAGAT 57.316 33.333 0.00 0.00 42.74 1.98
7 8 7.279981 ACATAGCTGTTGCAAAACGAATATAGA 59.720 33.333 0.00 0.00 42.74 1.98
8 9 7.374228 CACATAGCTGTTGCAAAACGAATATAG 59.626 37.037 0.00 0.00 42.74 1.31
9 10 7.148323 ACACATAGCTGTTGCAAAACGAATATA 60.148 33.333 0.00 0.00 42.74 0.86
10 11 6.029607 CACATAGCTGTTGCAAAACGAATAT 58.970 36.000 0.00 0.00 42.74 1.28
11 12 5.049060 ACACATAGCTGTTGCAAAACGAATA 60.049 36.000 0.00 0.00 42.74 1.75
12 13 4.229096 CACATAGCTGTTGCAAAACGAAT 58.771 39.130 0.00 0.00 42.74 3.34
13 14 3.066064 ACACATAGCTGTTGCAAAACGAA 59.934 39.130 0.00 0.00 42.74 3.85
14 15 2.616376 ACACATAGCTGTTGCAAAACGA 59.384 40.909 0.00 0.00 42.74 3.85
15 16 2.998772 ACACATAGCTGTTGCAAAACG 58.001 42.857 0.00 0.00 42.74 3.60
16 17 6.148948 TGAATACACATAGCTGTTGCAAAAC 58.851 36.000 0.00 0.00 42.74 2.43
17 18 6.324561 TGAATACACATAGCTGTTGCAAAA 57.675 33.333 0.00 0.00 42.74 2.44
18 19 5.956068 TGAATACACATAGCTGTTGCAAA 57.044 34.783 0.00 0.00 42.74 3.68
19 20 5.676837 GCATGAATACACATAGCTGTTGCAA 60.677 40.000 0.00 0.00 42.74 4.08
20 21 4.201940 GCATGAATACACATAGCTGTTGCA 60.202 41.667 0.00 0.00 42.74 4.08
21 22 4.201940 TGCATGAATACACATAGCTGTTGC 60.202 41.667 0.00 0.00 40.05 4.17
22 23 5.065602 AGTGCATGAATACACATAGCTGTTG 59.934 40.000 0.00 0.00 39.30 3.33
23 24 5.188434 AGTGCATGAATACACATAGCTGTT 58.812 37.500 0.00 0.00 39.30 3.16
24 25 4.774124 AGTGCATGAATACACATAGCTGT 58.226 39.130 0.00 0.00 39.30 4.40
25 26 5.987953 ACTAGTGCATGAATACACATAGCTG 59.012 40.000 0.00 0.00 39.30 4.24
26 27 5.987953 CACTAGTGCATGAATACACATAGCT 59.012 40.000 10.54 0.00 39.30 3.32
27 28 5.755375 ACACTAGTGCATGAATACACATAGC 59.245 40.000 22.90 0.00 39.30 2.97
28 29 7.205992 AGACACTAGTGCATGAATACACATAG 58.794 38.462 22.90 2.32 39.30 2.23
29 30 7.112452 AGACACTAGTGCATGAATACACATA 57.888 36.000 22.90 0.00 39.30 2.29
30 31 5.982356 AGACACTAGTGCATGAATACACAT 58.018 37.500 22.90 0.00 39.30 3.21
31 32 5.047377 TGAGACACTAGTGCATGAATACACA 60.047 40.000 22.90 6.14 39.30 3.72
32 33 5.410924 TGAGACACTAGTGCATGAATACAC 58.589 41.667 22.90 0.00 37.05 2.90
33 34 5.659440 TGAGACACTAGTGCATGAATACA 57.341 39.130 22.90 8.91 0.00 2.29
34 35 6.968131 TTTGAGACACTAGTGCATGAATAC 57.032 37.500 22.90 6.61 0.00 1.89
35 36 7.361201 GCTTTTTGAGACACTAGTGCATGAATA 60.361 37.037 22.90 4.71 0.00 1.75
36 37 6.569226 GCTTTTTGAGACACTAGTGCATGAAT 60.569 38.462 22.90 1.55 0.00 2.57
37 38 5.277974 GCTTTTTGAGACACTAGTGCATGAA 60.278 40.000 22.90 9.08 0.00 2.57
38 39 4.214119 GCTTTTTGAGACACTAGTGCATGA 59.786 41.667 22.90 2.77 0.00 3.07
39 40 4.023792 TGCTTTTTGAGACACTAGTGCATG 60.024 41.667 22.90 0.00 0.00 4.06
40 41 4.023707 GTGCTTTTTGAGACACTAGTGCAT 60.024 41.667 22.90 11.44 32.87 3.96
41 42 3.312421 GTGCTTTTTGAGACACTAGTGCA 59.688 43.478 22.90 10.06 32.87 4.57
42 43 3.312421 TGTGCTTTTTGAGACACTAGTGC 59.688 43.478 22.90 14.96 35.09 4.40
43 44 5.679734 ATGTGCTTTTTGAGACACTAGTG 57.320 39.130 21.44 21.44 35.09 2.74
44 45 5.822519 TCAATGTGCTTTTTGAGACACTAGT 59.177 36.000 0.00 0.00 35.09 2.57
45 46 6.304356 TCAATGTGCTTTTTGAGACACTAG 57.696 37.500 0.00 0.00 35.09 2.57
46 47 6.882610 ATCAATGTGCTTTTTGAGACACTA 57.117 33.333 0.00 0.00 35.47 2.74
47 48 5.779529 ATCAATGTGCTTTTTGAGACACT 57.220 34.783 0.00 0.00 35.47 3.55
48 49 7.928908 TTAATCAATGTGCTTTTTGAGACAC 57.071 32.000 0.00 0.00 35.47 3.67
49 50 8.523523 CATTAATCAATGTGCTTTTTGAGACA 57.476 30.769 0.00 0.00 37.37 3.41
113 114 4.063689 CTCTCTCTCTCTCTCTCTCATGC 58.936 52.174 0.00 0.00 0.00 4.06
114 115 5.303845 TCTCTCTCTCTCTCTCTCTCTCATG 59.696 48.000 0.00 0.00 0.00 3.07
115 116 5.462240 TCTCTCTCTCTCTCTCTCTCTCAT 58.538 45.833 0.00 0.00 0.00 2.90
116 117 4.871822 TCTCTCTCTCTCTCTCTCTCTCA 58.128 47.826 0.00 0.00 0.00 3.27
230 234 5.895636 TGGACCAATCAATTGTGACATAC 57.104 39.130 5.13 0.00 36.31 2.39
331 337 2.290896 TGACCATTCTTCCCACATCCAC 60.291 50.000 0.00 0.00 0.00 4.02
455 483 7.166307 CACATGTATCAATGGAGTTTTATTGCG 59.834 37.037 0.00 0.00 34.96 4.85
482 510 3.994853 GGGTTTGGCTGCCAGTGC 61.995 66.667 22.17 14.91 33.81 4.40
487 515 2.573340 CATTCGGGTTTGGCTGCC 59.427 61.111 12.87 12.87 0.00 4.85
497 525 0.833287 ACACAGGATCTCCATTCGGG 59.167 55.000 0.00 0.00 38.89 5.14
522 552 4.202223 GGTCTCCACCGCTCTCAAATATAA 60.202 45.833 0.00 0.00 31.06 0.98
538 568 2.338809 AGACTCAAACCATGGTCTCCA 58.661 47.619 20.07 1.55 35.79 3.86
595 632 2.231215 AGATAGAACACGCATCTGGC 57.769 50.000 0.00 0.00 39.90 4.85
597 634 7.240674 GTCTAGATAGATAGAACACGCATCTG 58.759 42.308 0.00 0.00 33.66 2.90
627 664 5.008613 GCAGTCCTATTGAGTGTTTGTCAAA 59.991 40.000 0.00 0.00 44.82 2.69
632 669 3.067106 ACGCAGTCCTATTGAGTGTTTG 58.933 45.455 0.00 0.00 44.82 2.93
633 670 3.067106 CACGCAGTCCTATTGAGTGTTT 58.933 45.455 1.71 0.00 44.82 2.83
677 714 1.792949 GCAGACCTCCAAATATACGCG 59.207 52.381 3.53 3.53 0.00 6.01
741 784 0.107643 TTGACCTCGACATTGTGCCA 59.892 50.000 0.00 0.00 0.00 4.92
767 810 4.096984 CCTCTGAGGAACATGCCAAATTAC 59.903 45.833 19.13 0.00 37.67 1.89
770 813 2.622452 CCCTCTGAGGAACATGCCAAAT 60.622 50.000 25.18 0.00 37.67 2.32
868 3667 3.120321 TGTGTGCAGTCCTATTTTCGT 57.880 42.857 0.00 0.00 0.00 3.85
874 3673 1.556911 CCCTCTTGTGTGCAGTCCTAT 59.443 52.381 0.00 0.00 0.00 2.57
982 3788 7.232330 TGAATCCATGAGAGACTAGATAGTTGG 59.768 40.741 0.00 0.00 36.50 3.77
991 3797 8.718158 ATGACTATTGAATCCATGAGAGACTA 57.282 34.615 0.00 0.00 0.00 2.59
1006 3812 2.126882 CCACCCCTGGATGACTATTGA 58.873 52.381 0.00 0.00 40.55 2.57
1016 3822 1.306997 GATGAGGTCCACCCCTGGA 60.307 63.158 0.00 0.00 45.11 3.86
1036 3842 0.671251 GATCGTGCCTCCTCTACCTG 59.329 60.000 0.00 0.00 0.00 4.00
1065 3871 2.957491 TTTTGTTGGTGTTGAGCCTG 57.043 45.000 0.00 0.00 0.00 4.85
1093 3899 2.884012 TGTTCTTGTCATCATTGGCGTT 59.116 40.909 0.00 0.00 0.00 4.84
1097 3906 5.159209 GCTTCTTGTTCTTGTCATCATTGG 58.841 41.667 0.00 0.00 0.00 3.16
1158 3967 5.543507 TTACCTGTTGCATGGTTTTTGAT 57.456 34.783 11.02 0.00 37.74 2.57
1164 3973 8.766994 AAATATCTATTACCTGTTGCATGGTT 57.233 30.769 11.02 0.00 37.74 3.67
1186 3995 4.717877 TCCATGGCGAGATCAACATAAAT 58.282 39.130 6.96 0.00 0.00 1.40
1213 4022 3.654806 CCCTCCCTCAACTGGATCATATT 59.345 47.826 0.00 0.00 0.00 1.28
1284 4093 4.471386 AGCTCATAGTTACCATTGACAGGT 59.529 41.667 0.00 0.00 43.14 4.00
1318 4130 4.396166 GTGTATGTTGCTAGCACCATTCTT 59.604 41.667 29.55 11.71 31.60 2.52
1371 4186 1.001181 TCTCGTACCCCAAAGTTTCCG 59.999 52.381 0.00 0.00 0.00 4.30
1373 4188 2.301009 TCCTCTCGTACCCCAAAGTTTC 59.699 50.000 0.00 0.00 0.00 2.78
1393 4208 0.036388 TCCACGATTGTTGCCTCCTC 60.036 55.000 0.00 0.00 0.00 3.71
1394 4209 0.321653 GTCCACGATTGTTGCCTCCT 60.322 55.000 0.00 0.00 0.00 3.69
1395 4210 0.605319 TGTCCACGATTGTTGCCTCC 60.605 55.000 0.00 0.00 0.00 4.30
1562 4387 5.628797 ATGTTCCTTGTTGGTCCAAAAAT 57.371 34.783 7.71 0.00 37.07 1.82
1584 4409 4.877378 ATACAAACTGTGGACGAACCTA 57.123 40.909 0.00 0.00 39.86 3.08
1690 4517 9.685276 TCATCACAAATGTAATCTACCAATCTT 57.315 29.630 0.00 0.00 0.00 2.40
1701 4528 9.830294 CGTGCAATATATCATCACAAATGTAAT 57.170 29.630 0.00 0.00 0.00 1.89
1705 4532 9.106286 GTAACGTGCAATATATCATCACAAATG 57.894 33.333 0.00 0.00 0.00 2.32
1706 4533 9.056005 AGTAACGTGCAATATATCATCACAAAT 57.944 29.630 0.00 2.25 0.00 2.32
1717 4544 9.583765 TGTGTACATTTAGTAACGTGCAATATA 57.416 29.630 0.00 0.00 33.72 0.86
1724 4551 6.366604 TGTCCATGTGTACATTTAGTAACGTG 59.633 38.462 0.00 0.00 33.61 4.49
1727 4554 7.386848 ACAGTGTCCATGTGTACATTTAGTAAC 59.613 37.037 0.00 0.00 33.61 2.50
1762 4590 2.890311 CAAGGTCACCCATGCTGTAAAA 59.110 45.455 0.00 0.00 0.00 1.52
1778 4606 5.826208 ACCTCGAAGTTTTCATTAACAAGGT 59.174 36.000 0.00 0.00 30.72 3.50
1797 4625 1.153939 CTCGTCCTCTTGCACCTCG 60.154 63.158 0.00 0.00 0.00 4.63
1843 4671 1.466167 CTCCAGAGCACAACGAAATGG 59.534 52.381 0.00 0.00 0.00 3.16
1857 4703 4.278310 TCGTGATTCTTGTATCCTCCAGA 58.722 43.478 0.00 0.00 0.00 3.86
1904 4750 4.336433 ACAACACCATCTTGTTCTTGTCTG 59.664 41.667 0.00 0.00 37.62 3.51
1991 4837 4.823442 TGTCGACTAACTTGTGTTCCTCTA 59.177 41.667 17.92 0.00 37.59 2.43
2015 4861 6.998802 ACTACATGACAGGGAAGAATATAGC 58.001 40.000 0.00 0.00 0.00 2.97
2085 4931 6.480981 CCTGCCTCATAAAATTAATTTGCAGG 59.519 38.462 31.98 31.98 44.98 4.85
2232 5084 9.823647 TCACATAAATTTGTTAAGCCAGAAAAA 57.176 25.926 0.00 0.00 0.00 1.94
2233 5085 9.995003 ATCACATAAATTTGTTAAGCCAGAAAA 57.005 25.926 0.00 0.00 0.00 2.29
2234 5086 9.995003 AATCACATAAATTTGTTAAGCCAGAAA 57.005 25.926 0.00 0.00 0.00 2.52
2235 5087 9.995003 AAATCACATAAATTTGTTAAGCCAGAA 57.005 25.926 0.00 0.00 0.00 3.02
2236 5088 9.421806 CAAATCACATAAATTTGTTAAGCCAGA 57.578 29.630 0.00 0.00 38.64 3.86
2290 5158 9.439500 CCATATTGGAATTTAATGGCCTATTTG 57.561 33.333 3.32 0.00 40.96 2.32
2327 5195 7.961351 ACAGGTTATTGATTTGTTTGATTGGA 58.039 30.769 0.00 0.00 0.00 3.53
2459 5373 9.624697 CACTACAACAACACATGCTTATTATTT 57.375 29.630 0.00 0.00 0.00 1.40
2462 5376 6.712998 ACCACTACAACAACACATGCTTATTA 59.287 34.615 0.00 0.00 0.00 0.98
2494 5408 7.759489 TTGAAGCAAAGTACCTATTTGACAT 57.241 32.000 9.56 0.00 39.50 3.06
2548 6427 4.452114 TGTTGACTGAAAGATGAATCGTGG 59.548 41.667 0.00 0.00 37.43 4.94
2580 6459 9.739276 TGGACATAATGTTCAAGAGAATAGTTT 57.261 29.630 0.00 0.00 31.81 2.66
2584 6463 7.770433 CCTGTGGACATAATGTTCAAGAGAATA 59.230 37.037 0.00 0.00 37.66 1.75
2590 6469 4.093408 CGACCTGTGGACATAATGTTCAAG 59.907 45.833 0.00 0.00 37.66 3.02
2613 6492 4.786425 AGATTTCCAGCCCATAGAGAAAC 58.214 43.478 0.00 0.00 29.89 2.78
2619 6498 4.583871 GACCATAGATTTCCAGCCCATAG 58.416 47.826 0.00 0.00 0.00 2.23
2781 6660 1.086634 GCTCATTGTCGTGGAGCCTC 61.087 60.000 0.00 0.00 46.35 4.70
2790 6669 1.003116 GCTGCCAATAGCTCATTGTCG 60.003 52.381 0.00 0.00 42.22 4.35
2817 6696 3.190738 TTGCCGGGGGACAGAACTG 62.191 63.158 2.18 0.00 0.00 3.16
2934 6813 9.948964 TGATCCACTTGTTGATTATATATGGAG 57.051 33.333 0.00 0.00 37.15 3.86
2957 6836 0.330604 ACTCCACATTGGCTGCTGAT 59.669 50.000 0.00 0.00 37.47 2.90
3019 6898 4.978099 CCATCAGGCACATAGTTTCCTAT 58.022 43.478 0.00 0.00 34.07 2.57
3052 6934 7.043565 ACATTGCCAAGATAAAAATAAGCTGG 58.956 34.615 0.00 0.00 0.00 4.85
3158 7041 3.634397 TGTTGCCATCTTTAGGAGGAG 57.366 47.619 0.00 0.00 0.00 3.69
3177 7060 6.147581 GCCATAATGTCTTGAGCATGTTATG 58.852 40.000 0.00 0.00 0.00 1.90
3178 7061 5.242393 GGCCATAATGTCTTGAGCATGTTAT 59.758 40.000 0.00 0.00 0.00 1.89
3179 7062 4.580167 GGCCATAATGTCTTGAGCATGTTA 59.420 41.667 0.00 0.00 0.00 2.41
3180 7063 3.382546 GGCCATAATGTCTTGAGCATGTT 59.617 43.478 0.00 0.00 0.00 2.71
3181 7064 2.954318 GGCCATAATGTCTTGAGCATGT 59.046 45.455 0.00 0.00 0.00 3.21
3182 7065 2.031420 CGGCCATAATGTCTTGAGCATG 60.031 50.000 2.24 0.00 0.00 4.06
3183 7066 2.224606 CGGCCATAATGTCTTGAGCAT 58.775 47.619 2.24 0.00 0.00 3.79
3184 7067 1.667236 CGGCCATAATGTCTTGAGCA 58.333 50.000 2.24 0.00 0.00 4.26
3185 7068 0.947244 CCGGCCATAATGTCTTGAGC 59.053 55.000 2.24 0.00 0.00 4.26
3186 7069 0.947244 GCCGGCCATAATGTCTTGAG 59.053 55.000 18.11 0.00 0.00 3.02
3187 7070 0.254462 TGCCGGCCATAATGTCTTGA 59.746 50.000 26.77 0.00 0.00 3.02
3221 7104 8.786826 ACTATCGAAGGTGAAATATTTGTTCA 57.213 30.769 5.17 0.00 32.62 3.18
3222 7105 9.099454 AGACTATCGAAGGTGAAATATTTGTTC 57.901 33.333 5.17 2.88 0.00 3.18
3225 7134 8.648557 TGAGACTATCGAAGGTGAAATATTTG 57.351 34.615 5.17 0.00 0.00 2.32
3262 7219 7.827236 ACGAAATAAGGGAGATGACAAACAATA 59.173 33.333 0.00 0.00 0.00 1.90
3263 7220 6.659242 ACGAAATAAGGGAGATGACAAACAAT 59.341 34.615 0.00 0.00 0.00 2.71
3318 7296 6.403333 TTGAGACAATATGTACACTTTCGC 57.597 37.500 0.00 0.00 0.00 4.70
3325 7306 5.751509 GCCACGTATTGAGACAATATGTACA 59.248 40.000 21.08 0.00 32.69 2.90
3332 7313 1.559682 AGGGCCACGTATTGAGACAAT 59.440 47.619 6.18 0.00 0.00 2.71
3370 7352 3.076182 ACGGGACAGAGGGAGTATGATAT 59.924 47.826 0.00 0.00 0.00 1.63
3371 7353 2.445905 ACGGGACAGAGGGAGTATGATA 59.554 50.000 0.00 0.00 0.00 2.15
3372 7354 1.218196 ACGGGACAGAGGGAGTATGAT 59.782 52.381 0.00 0.00 0.00 2.45
3373 7355 0.629596 ACGGGACAGAGGGAGTATGA 59.370 55.000 0.00 0.00 0.00 2.15
3374 7356 2.359981 TACGGGACAGAGGGAGTATG 57.640 55.000 0.00 0.00 0.00 2.39
3375 7357 3.614568 ATTACGGGACAGAGGGAGTAT 57.385 47.619 0.00 0.00 0.00 2.12
3376 7358 4.736611 ATATTACGGGACAGAGGGAGTA 57.263 45.455 0.00 0.00 0.00 2.59
3377 7359 3.614568 ATATTACGGGACAGAGGGAGT 57.385 47.619 0.00 0.00 0.00 3.85
3378 7360 5.322754 TCTTATATTACGGGACAGAGGGAG 58.677 45.833 0.00 0.00 0.00 4.30
3379 7361 5.322754 CTCTTATATTACGGGACAGAGGGA 58.677 45.833 0.00 0.00 0.00 4.20
3380 7362 4.082136 GCTCTTATATTACGGGACAGAGGG 60.082 50.000 0.00 0.00 0.00 4.30
3381 7363 4.379603 CGCTCTTATATTACGGGACAGAGG 60.380 50.000 0.00 0.00 0.00 3.69
3382 7364 4.215827 ACGCTCTTATATTACGGGACAGAG 59.784 45.833 0.00 0.00 0.00 3.35
3383 7365 4.139786 ACGCTCTTATATTACGGGACAGA 58.860 43.478 0.00 0.00 0.00 3.41
3384 7366 4.500603 ACGCTCTTATATTACGGGACAG 57.499 45.455 0.00 0.00 0.00 3.51
3385 7367 4.924305 AACGCTCTTATATTACGGGACA 57.076 40.909 0.00 0.00 0.00 4.02
3386 7368 6.594284 AAAAACGCTCTTATATTACGGGAC 57.406 37.500 0.00 0.00 0.00 4.46
3387 7369 8.143193 TGATAAAAACGCTCTTATATTACGGGA 58.857 33.333 0.00 0.00 0.00 5.14
3388 7370 8.219105 GTGATAAAAACGCTCTTATATTACGGG 58.781 37.037 0.00 0.00 0.00 5.28
3389 7371 8.975439 AGTGATAAAAACGCTCTTATATTACGG 58.025 33.333 0.00 0.00 0.00 4.02
3396 7378 9.517609 CTAGTGTAGTGATAAAAACGCTCTTAT 57.482 33.333 0.00 0.00 34.68 1.73
3397 7379 8.517878 ACTAGTGTAGTGATAAAAACGCTCTTA 58.482 33.333 0.00 0.00 37.69 2.10
3398 7380 7.376615 ACTAGTGTAGTGATAAAAACGCTCTT 58.623 34.615 0.00 0.00 37.69 2.85
3399 7381 6.921914 ACTAGTGTAGTGATAAAAACGCTCT 58.078 36.000 0.00 0.00 37.69 4.09
3413 7395 6.335777 AGAACGTTTTTGACACTAGTGTAGT 58.664 36.000 27.98 15.35 45.05 2.73
3414 7396 6.823678 AGAACGTTTTTGACACTAGTGTAG 57.176 37.500 27.98 14.79 45.05 2.74
3415 7397 8.876275 ATAAGAACGTTTTTGACACTAGTGTA 57.124 30.769 27.98 11.50 45.05 2.90
3422 7404 9.498307 CCCATAATATAAGAACGTTTTTGACAC 57.502 33.333 13.87 0.00 0.00 3.67
3423 7405 9.451002 TCCCATAATATAAGAACGTTTTTGACA 57.549 29.630 13.87 0.01 0.00 3.58
3424 7406 9.712359 GTCCCATAATATAAGAACGTTTTTGAC 57.288 33.333 13.87 5.89 0.00 3.18
3425 7407 9.451002 TGTCCCATAATATAAGAACGTTTTTGA 57.549 29.630 13.87 2.81 0.00 2.69
3426 7408 9.716507 CTGTCCCATAATATAAGAACGTTTTTG 57.283 33.333 13.87 0.00 0.00 2.44
3427 7409 9.675464 TCTGTCCCATAATATAAGAACGTTTTT 57.325 29.630 9.22 9.22 0.00 1.94
3428 7410 9.326413 CTCTGTCCCATAATATAAGAACGTTTT 57.674 33.333 0.46 0.00 0.00 2.43
3429 7411 7.931948 CCTCTGTCCCATAATATAAGAACGTTT 59.068 37.037 0.46 0.00 0.00 3.60
3430 7412 7.442656 CCTCTGTCCCATAATATAAGAACGTT 58.557 38.462 0.00 0.00 0.00 3.99
3431 7413 6.014499 CCCTCTGTCCCATAATATAAGAACGT 60.014 42.308 0.00 0.00 0.00 3.99
3432 7414 6.210784 TCCCTCTGTCCCATAATATAAGAACG 59.789 42.308 0.00 0.00 0.00 3.95
3433 7415 7.235812 ACTCCCTCTGTCCCATAATATAAGAAC 59.764 40.741 0.00 0.00 0.00 3.01
3434 7416 7.313731 ACTCCCTCTGTCCCATAATATAAGAA 58.686 38.462 0.00 0.00 0.00 2.52
3435 7417 6.875469 ACTCCCTCTGTCCCATAATATAAGA 58.125 40.000 0.00 0.00 0.00 2.10
3436 7418 7.674348 TGTACTCCCTCTGTCCCATAATATAAG 59.326 40.741 0.00 0.00 0.00 1.73
3437 7419 7.541074 TGTACTCCCTCTGTCCCATAATATAA 58.459 38.462 0.00 0.00 0.00 0.98
3438 7420 7.111136 TGTACTCCCTCTGTCCCATAATATA 57.889 40.000 0.00 0.00 0.00 0.86
3439 7421 5.977533 TGTACTCCCTCTGTCCCATAATAT 58.022 41.667 0.00 0.00 0.00 1.28
3440 7422 5.412617 TGTACTCCCTCTGTCCCATAATA 57.587 43.478 0.00 0.00 0.00 0.98
3441 7423 4.280789 TGTACTCCCTCTGTCCCATAAT 57.719 45.455 0.00 0.00 0.00 1.28
3442 7424 3.769189 TGTACTCCCTCTGTCCCATAA 57.231 47.619 0.00 0.00 0.00 1.90
3443 7425 3.206639 TCATGTACTCCCTCTGTCCCATA 59.793 47.826 0.00 0.00 0.00 2.74
3444 7426 2.023015 TCATGTACTCCCTCTGTCCCAT 60.023 50.000 0.00 0.00 0.00 4.00
3445 7427 1.361197 TCATGTACTCCCTCTGTCCCA 59.639 52.381 0.00 0.00 0.00 4.37
3446 7428 2.160721 TCATGTACTCCCTCTGTCCC 57.839 55.000 0.00 0.00 0.00 4.46
3447 7429 3.452627 ACAATCATGTACTCCCTCTGTCC 59.547 47.826 0.00 0.00 38.24 4.02
3448 7430 4.744795 ACAATCATGTACTCCCTCTGTC 57.255 45.455 0.00 0.00 38.24 3.51
3449 7431 4.836825 CAACAATCATGTACTCCCTCTGT 58.163 43.478 0.00 0.00 39.40 3.41
3450 7432 3.624861 GCAACAATCATGTACTCCCTCTG 59.375 47.826 0.00 0.00 39.40 3.35
3451 7433 3.370953 GGCAACAATCATGTACTCCCTCT 60.371 47.826 0.00 0.00 39.40 3.69
3452 7434 2.945668 GGCAACAATCATGTACTCCCTC 59.054 50.000 0.00 0.00 39.40 4.30
3453 7435 2.578021 AGGCAACAATCATGTACTCCCT 59.422 45.455 0.00 0.00 39.40 4.20
3454 7436 3.004752 AGGCAACAATCATGTACTCCC 57.995 47.619 0.00 0.00 39.40 4.30
3455 7437 4.513442 TGTAGGCAACAATCATGTACTCC 58.487 43.478 0.00 0.00 39.40 3.85
3456 7438 6.683974 AATGTAGGCAACAATCATGTACTC 57.316 37.500 0.00 0.00 42.70 2.59
3457 7439 7.992608 TCATAATGTAGGCAACAATCATGTACT 59.007 33.333 0.00 0.00 42.70 2.73
3458 7440 8.153479 TCATAATGTAGGCAACAATCATGTAC 57.847 34.615 0.00 0.00 42.70 2.90
3459 7441 8.210265 TCTCATAATGTAGGCAACAATCATGTA 58.790 33.333 0.00 0.00 42.70 2.29
3460 7442 7.056006 TCTCATAATGTAGGCAACAATCATGT 58.944 34.615 0.00 0.00 42.70 3.21
3461 7443 7.500720 TCTCATAATGTAGGCAACAATCATG 57.499 36.000 0.00 0.00 42.70 3.07
3462 7444 8.573885 CAATCTCATAATGTAGGCAACAATCAT 58.426 33.333 0.00 0.00 42.70 2.45
3463 7445 7.469043 GCAATCTCATAATGTAGGCAACAATCA 60.469 37.037 0.00 0.00 42.70 2.57
3464 7446 6.860023 GCAATCTCATAATGTAGGCAACAATC 59.140 38.462 0.00 0.00 42.70 2.67
3465 7447 6.321945 TGCAATCTCATAATGTAGGCAACAAT 59.678 34.615 0.00 0.00 42.70 2.71
3466 7448 5.651576 TGCAATCTCATAATGTAGGCAACAA 59.348 36.000 0.00 0.00 42.70 2.83
3467 7449 5.192176 TGCAATCTCATAATGTAGGCAACA 58.808 37.500 0.00 0.00 43.86 3.33
3468 7450 5.756195 TGCAATCTCATAATGTAGGCAAC 57.244 39.130 0.00 0.00 0.00 4.17
3481 7463 2.025131 TCATGGGGTCATTGCAATCTCA 60.025 45.455 9.53 5.22 0.00 3.27
3556 7538 6.647334 TCAAGTAATTTGGCAACTGAATCA 57.353 33.333 0.00 0.00 37.39 2.57
3584 7566 7.940137 GGATCTGACTATCAAGTAGAAGGTCTA 59.060 40.741 0.00 0.00 35.56 2.59
3665 7649 0.115745 TTACCGGGGACTCTTGGACT 59.884 55.000 6.32 0.00 0.00 3.85
3675 7659 4.141665 CCACACAATATTAGTTACCGGGGA 60.142 45.833 6.32 0.00 0.00 4.81
3679 7663 6.539324 CAACACCACACAATATTAGTTACCG 58.461 40.000 0.00 0.00 0.00 4.02
3680 7664 6.150474 AGCAACACCACACAATATTAGTTACC 59.850 38.462 0.00 0.00 0.00 2.85
3685 7669 7.320443 ACATAGCAACACCACACAATATTAG 57.680 36.000 0.00 0.00 0.00 1.73
3801 7796 3.436704 TGACAAGCTGCAAACTATAGTGC 59.563 43.478 6.06 7.27 41.29 4.40
3812 7807 0.535780 CTCCCAACTGACAAGCTGCA 60.536 55.000 1.02 0.00 0.00 4.41
3817 7812 3.278574 TGTTTGACTCCCAACTGACAAG 58.721 45.455 0.00 0.00 33.85 3.16
3824 7819 3.181490 GGTTTGTCTGTTTGACTCCCAAC 60.181 47.826 0.00 0.00 45.54 3.77
3826 7821 2.025793 TGGTTTGTCTGTTTGACTCCCA 60.026 45.455 0.00 0.00 45.54 4.37
3841 7836 9.191995 GTAAGGTTTTCATAACTGATTGGTTTG 57.808 33.333 0.00 0.00 0.00 2.93
3857 7852 4.028993 TGATGGTGAGGGTAAGGTTTTC 57.971 45.455 0.00 0.00 0.00 2.29
3888 7883 9.241317 CAAATTTAATATCATGGAGAGTGTTGC 57.759 33.333 0.00 0.00 0.00 4.17
3915 7910 5.128499 TCTTCATTCTCCATTCTCAGAGACC 59.872 44.000 0.00 0.00 38.83 3.85
3954 7949 6.757897 TGAAAATACCTCAGTAAATGCCAG 57.242 37.500 0.00 0.00 30.59 4.85
3964 7959 7.596749 AGAACGTAACATGAAAATACCTCAG 57.403 36.000 0.00 0.00 0.00 3.35
4050 8048 9.988350 GTTCATCTGCTATTTTCTTATTTTCGA 57.012 29.630 0.00 0.00 0.00 3.71


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

AutoCloner maintained by Alex Coulton.