Multiple sequence alignment - TraesCS6A01G062000

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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 TraesCS6A01G062000 chr6A 100.000 6327 0 0 1 6327 33189506 33183180 0.000000e+00 11684.0
1 TraesCS6A01G062000 chr6A 78.344 471 61 14 3552 4017 46114538 46114104 3.760000e-67 267.0
2 TraesCS6A01G062000 chr6A 78.344 471 61 14 3552 4017 46116319 46115885 3.760000e-67 267.0
3 TraesCS6A01G062000 chr6A 78.803 401 76 6 1091 1485 47685552 47685155 1.750000e-65 261.0
4 TraesCS6A01G062000 chr6A 79.404 403 48 18 3553 3946 47467355 47466979 1.050000e-62 252.0
5 TraesCS6A01G062000 chr6A 80.571 350 42 19 3599 3946 47483398 47483073 4.900000e-61 246.0
6 TraesCS6A01G062000 chr6A 85.088 228 34 0 3552 3779 45756213 45756440 3.810000e-57 233.0
7 TraesCS6A01G062000 chr6A 82.117 274 36 9 3552 3823 33014834 33014572 8.260000e-54 222.0
8 TraesCS6A01G062000 chr6A 90.476 147 14 0 4417 4563 36053028 36052882 1.800000e-45 195.0
9 TraesCS6A01G062000 chr6A 76.230 366 80 6 1909 2269 33016498 33016135 3.010000e-43 187.0
10 TraesCS6A01G062000 chr6A 81.065 169 25 4 4586 4754 34012637 34012798 1.850000e-25 128.0
11 TraesCS6A01G062000 chr6A 71.587 542 115 31 1746 2266 46295803 46295280 1.860000e-20 111.0
12 TraesCS6A01G062000 chr6A 95.238 42 1 1 4111 4152 45979053 45979013 1.470000e-06 65.8
13 TraesCS6A01G062000 chr6B 95.159 2417 89 9 1148 3549 60090977 60088574 0.000000e+00 3790.0
14 TraesCS6A01G062000 chr6B 93.527 1375 55 7 4254 5625 60087583 60086240 0.000000e+00 2015.0
15 TraesCS6A01G062000 chr6B 95.527 626 27 1 3545 4170 60088540 60087916 0.000000e+00 1000.0
16 TraesCS6A01G062000 chr6B 91.011 356 13 10 644 996 60091771 60091432 4.470000e-126 462.0
17 TraesCS6A01G062000 chr6B 82.639 288 34 12 5615 5897 60084770 60084494 2.280000e-59 241.0
18 TraesCS6A01G062000 chr6B 78.481 395 65 13 1076 1460 83200569 83200953 2.280000e-59 241.0
19 TraesCS6A01G062000 chr6B 85.153 229 33 1 3552 3779 79299861 79299633 3.810000e-57 233.0
20 TraesCS6A01G062000 chr6B 90.000 150 15 0 4414 4563 66917583 66917434 1.800000e-45 195.0
21 TraesCS6A01G062000 chr6B 90.000 150 15 0 4414 4563 66942173 66942024 1.800000e-45 195.0
22 TraesCS6A01G062000 chr6B 81.065 169 25 4 4586 4754 62122386 62122547 1.850000e-25 128.0
23 TraesCS6A01G062000 chr6B 71.956 542 113 33 1746 2266 79555154 79554631 8.610000e-24 122.0
24 TraesCS6A01G062000 chr6B 71.771 542 113 34 1746 2266 79437661 79437139 4.010000e-22 117.0
25 TraesCS6A01G062000 chr6B 81.429 140 26 0 1184 1323 59008503 59008364 1.440000e-21 115.0
26 TraesCS6A01G062000 chr6B 71.004 538 122 30 1746 2266 79641479 79640959 1.450000e-16 99.0
27 TraesCS6A01G062000 chr6B 96.491 57 2 0 3066 3122 500227086 500227030 1.880000e-15 95.3
28 TraesCS6A01G062000 chr6B 72.619 336 69 22 1941 2264 61790795 61791119 8.740000e-14 89.8
29 TraesCS6A01G062000 chr6D 95.472 2076 75 11 4262 6327 29228703 29230769 0.000000e+00 3295.0
30 TraesCS6A01G062000 chr6D 95.416 2007 60 13 952 2933 29205014 29207013 0.000000e+00 3168.0
31 TraesCS6A01G062000 chr6D 95.827 1222 37 4 2957 4170 29221631 29222846 0.000000e+00 1962.0
32 TraesCS6A01G062000 chr6D 90.040 743 50 8 154 892 29204281 29205003 0.000000e+00 941.0
33 TraesCS6A01G062000 chr6D 97.059 102 3 0 4166 4267 29223348 29223449 8.430000e-39 172.0
34 TraesCS6A01G062000 chr6D 83.471 121 19 1 4634 4754 28663241 28663122 1.860000e-20 111.0
35 TraesCS6A01G062000 chrUn 81.184 473 61 16 3552 4017 27875217 27875668 7.800000e-94 355.0
36 TraesCS6A01G062000 chrUn 78.214 560 94 23 2420 2965 27579626 27579081 3.660000e-87 333.0
37 TraesCS6A01G062000 chrUn 84.494 316 37 8 3558 3869 27971551 27971244 1.030000e-77 302.0
38 TraesCS6A01G062000 chrUn 77.778 495 90 16 1076 1563 26705191 26704710 2.890000e-73 287.0
39 TraesCS6A01G062000 chrUn 78.883 412 76 8 1076 1484 26698146 26697743 1.050000e-67 268.0
40 TraesCS6A01G062000 chrUn 82.971 276 40 6 1074 1347 26885434 26885704 6.340000e-60 243.0
41 TraesCS6A01G062000 chrUn 75.982 433 93 9 1060 1485 26905241 26905669 4.970000e-51 213.0
42 TraesCS6A01G062000 chrUn 90.000 120 12 0 4416 4535 344892826 344892945 8.490000e-34 156.0
43 TraesCS6A01G062000 chrUn 71.719 541 116 32 1746 2266 112303834 112303311 4.010000e-22 117.0
44 TraesCS6A01G062000 chrUn 81.731 104 12 5 4586 4689 112599071 112599167 5.260000e-11 80.5
45 TraesCS6A01G062000 chrUn 94.872 39 1 1 2179 2216 105552856 105552894 6.850000e-05 60.2
46 TraesCS6A01G062000 chr4A 91.579 95 8 0 4 98 614827794 614827700 1.430000e-26 132.0
47 TraesCS6A01G062000 chr5B 72.525 404 90 13 1878 2264 697029889 697029490 1.860000e-20 111.0
48 TraesCS6A01G062000 chr5A 88.764 89 10 0 4428 4516 336463696 336463608 6.710000e-20 110.0
49 TraesCS6A01G062000 chr5A 94.915 59 2 1 3066 3124 295072688 295072745 2.430000e-14 91.6
50 TraesCS6A01G062000 chr7A 93.846 65 2 2 3066 3129 83784886 83784823 5.220000e-16 97.1
51 TraesCS6A01G062000 chr7A 85.897 78 8 3 3066 3141 68881222 68881298 5.260000e-11 80.5
52 TraesCS6A01G062000 chr7A 89.231 65 6 1 5655 5718 80918278 80918342 5.260000e-11 80.5
53 TraesCS6A01G062000 chr7A 89.231 65 6 1 5655 5718 298483118 298483054 5.260000e-11 80.5
54 TraesCS6A01G062000 chr5D 95.000 60 3 0 3066 3125 97834703 97834762 1.880000e-15 95.3
55 TraesCS6A01G062000 chr7B 92.308 65 5 0 3066 3130 462530509 462530445 6.750000e-15 93.5
56 TraesCS6A01G062000 chr1A 95.000 60 2 1 3066 3125 25707909 25707967 6.750000e-15 93.5
57 TraesCS6A01G062000 chr3B 89.231 65 6 1 5655 5718 492110377 492110441 5.260000e-11 80.5


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS6A01G062000 chr6A 33183180 33189506 6326 True 11684.0 11684 100.0000 1 6327 1 chr6A.!!$R1 6326
1 TraesCS6A01G062000 chr6A 46114104 46116319 2215 True 267.0 267 78.3440 3552 4017 2 chr6A.!!$R9 465
2 TraesCS6A01G062000 chr6A 33014572 33016498 1926 True 204.5 222 79.1735 1909 3823 2 chr6A.!!$R8 1914
3 TraesCS6A01G062000 chr6B 60084494 60091771 7277 True 1501.6 3790 91.5726 644 5897 5 chr6B.!!$R9 5253
4 TraesCS6A01G062000 chr6D 29228703 29230769 2066 False 3295.0 3295 95.4720 4262 6327 1 chr6D.!!$F1 2065
5 TraesCS6A01G062000 chr6D 29204281 29207013 2732 False 2054.5 3168 92.7280 154 2933 2 chr6D.!!$F2 2779
6 TraesCS6A01G062000 chr6D 29221631 29223449 1818 False 1067.0 1962 96.4430 2957 4267 2 chr6D.!!$F3 1310
7 TraesCS6A01G062000 chrUn 27579081 27579626 545 True 333.0 333 78.2140 2420 2965 1 chrUn.!!$R3 545

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
115 116 0.044855 AGCTACAATGGTCCTCCCCT 59.955 55.000 0.00 0.00 0.00 4.79 F
862 866 0.106521 TTTTTCAGGGGCTGCAAAGC 59.893 50.000 0.50 0.00 29.67 3.51 F
1694 2011 1.010419 CCGCTTCCAATTGCAAGCAC 61.010 55.000 28.72 5.89 44.53 4.40 F
3120 3616 0.894835 CACCGGGCTGCCTTTTTATT 59.105 50.000 19.68 0.00 0.00 1.40 F
3906 4890 2.057922 CCCACCTAGCCACCTCATATT 58.942 52.381 0.00 0.00 0.00 1.28 F
4149 5135 0.105709 GCTCTTCTCCCTCTAGCCCT 60.106 60.000 0.00 0.00 0.00 5.19 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1731 2048 0.168788 CACAGCGGGTATGTTGCAAG 59.831 55.0 0.0 0.0 0.0 4.01 R
1976 2294 0.609131 CTTCCCAGCACCCACGAATT 60.609 55.0 0.0 0.0 0.0 2.17 R
3416 3921 0.894835 TGAGGCACGAACTAGCATGA 59.105 50.0 0.0 0.0 0.0 3.07 R
3982 4968 0.822121 AAAGGCACGGGGAACAGAAC 60.822 55.0 0.0 0.0 0.0 3.01 R
5199 7270 0.043907 CGCGATGCTGATACAACACG 60.044 55.0 0.0 0.0 0.0 4.49 R
5832 9389 1.843368 AGATTGCCCTGTCATTGGTG 58.157 50.0 0.0 0.0 0.0 4.17 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
22 23 5.017294 TGAAAAACCAGCCTTTAGTTTGG 57.983 39.130 0.00 0.00 34.12 3.28
23 24 4.468153 TGAAAAACCAGCCTTTAGTTTGGT 59.532 37.500 0.00 0.00 45.47 3.67
27 28 3.637769 ACCAGCCTTTAGTTTGGTTTGA 58.362 40.909 0.00 0.00 40.94 2.69
28 29 4.223144 ACCAGCCTTTAGTTTGGTTTGAT 58.777 39.130 0.00 0.00 40.94 2.57
29 30 4.653801 ACCAGCCTTTAGTTTGGTTTGATT 59.346 37.500 0.00 0.00 40.94 2.57
30 31 5.221441 ACCAGCCTTTAGTTTGGTTTGATTC 60.221 40.000 0.00 0.00 40.94 2.52
31 32 5.221422 CCAGCCTTTAGTTTGGTTTGATTCA 60.221 40.000 0.00 0.00 0.00 2.57
32 33 5.691754 CAGCCTTTAGTTTGGTTTGATTCAC 59.308 40.000 0.00 0.00 0.00 3.18
33 34 4.988540 GCCTTTAGTTTGGTTTGATTCACC 59.011 41.667 0.00 0.00 34.52 4.02
34 35 5.538118 CCTTTAGTTTGGTTTGATTCACCC 58.462 41.667 0.00 0.00 32.71 4.61
35 36 5.510690 CCTTTAGTTTGGTTTGATTCACCCC 60.511 44.000 0.00 0.00 32.71 4.95
36 37 2.325484 AGTTTGGTTTGATTCACCCCC 58.675 47.619 0.00 0.00 32.71 5.40
37 38 1.000394 GTTTGGTTTGATTCACCCCCG 60.000 52.381 0.00 0.00 32.71 5.73
38 39 0.540830 TTGGTTTGATTCACCCCCGG 60.541 55.000 0.00 0.00 32.71 5.73
39 40 1.680989 GGTTTGATTCACCCCCGGG 60.681 63.158 15.80 15.80 42.03 5.73
51 52 2.528673 CCCCCGGGGTTTATTGTTAA 57.471 50.000 37.66 0.00 38.25 2.01
52 53 2.380941 CCCCCGGGGTTTATTGTTAAG 58.619 52.381 37.66 14.27 38.25 1.85
53 54 2.291735 CCCCCGGGGTTTATTGTTAAGT 60.292 50.000 37.66 0.00 38.25 2.24
54 55 3.433343 CCCCGGGGTTTATTGTTAAGTT 58.567 45.455 33.25 0.00 0.00 2.66
55 56 3.833650 CCCCGGGGTTTATTGTTAAGTTT 59.166 43.478 33.25 0.00 0.00 2.66
56 57 4.082081 CCCCGGGGTTTATTGTTAAGTTTC 60.082 45.833 33.25 0.00 0.00 2.78
57 58 4.768448 CCCGGGGTTTATTGTTAAGTTTCT 59.232 41.667 14.71 0.00 0.00 2.52
58 59 5.244402 CCCGGGGTTTATTGTTAAGTTTCTT 59.756 40.000 14.71 0.00 0.00 2.52
59 60 6.433716 CCCGGGGTTTATTGTTAAGTTTCTTA 59.566 38.462 14.71 0.00 0.00 2.10
60 61 7.307694 CCGGGGTTTATTGTTAAGTTTCTTAC 58.692 38.462 0.00 0.00 0.00 2.34
61 62 7.017055 CGGGGTTTATTGTTAAGTTTCTTACG 58.983 38.462 0.00 0.00 0.00 3.18
62 63 7.095271 CGGGGTTTATTGTTAAGTTTCTTACGA 60.095 37.037 0.00 0.00 0.00 3.43
63 64 8.567104 GGGGTTTATTGTTAAGTTTCTTACGAA 58.433 33.333 0.00 0.00 0.00 3.85
64 65 9.385902 GGGTTTATTGTTAAGTTTCTTACGAAC 57.614 33.333 0.00 0.00 0.00 3.95
65 66 9.095529 GGTTTATTGTTAAGTTTCTTACGAACG 57.904 33.333 0.00 0.00 32.99 3.95
66 67 9.848172 GTTTATTGTTAAGTTTCTTACGAACGA 57.152 29.630 0.14 0.00 32.99 3.85
69 70 7.467557 TTGTTAAGTTTCTTACGAACGATGT 57.532 32.000 0.14 0.00 32.99 3.06
70 71 8.572828 TTGTTAAGTTTCTTACGAACGATGTA 57.427 30.769 0.14 0.00 32.99 2.29
71 72 8.219436 TGTTAAGTTTCTTACGAACGATGTAG 57.781 34.615 0.14 0.00 32.99 2.74
72 73 5.758570 AAGTTTCTTACGAACGATGTAGC 57.241 39.130 0.14 0.00 0.00 3.58
73 74 5.056894 AGTTTCTTACGAACGATGTAGCT 57.943 39.130 0.14 0.00 0.00 3.32
74 75 4.857588 AGTTTCTTACGAACGATGTAGCTG 59.142 41.667 0.00 0.00 0.00 4.24
75 76 4.430137 TTCTTACGAACGATGTAGCTGT 57.570 40.909 0.00 0.00 0.00 4.40
76 77 3.754955 TCTTACGAACGATGTAGCTGTG 58.245 45.455 0.00 0.00 0.00 3.66
77 78 2.554806 TACGAACGATGTAGCTGTGG 57.445 50.000 0.00 0.00 0.00 4.17
78 79 0.601558 ACGAACGATGTAGCTGTGGT 59.398 50.000 0.00 0.00 0.00 4.16
79 80 1.000506 ACGAACGATGTAGCTGTGGTT 59.999 47.619 0.00 0.00 0.00 3.67
80 81 2.066262 CGAACGATGTAGCTGTGGTTT 58.934 47.619 0.00 0.00 0.00 3.27
81 82 2.159841 CGAACGATGTAGCTGTGGTTTG 60.160 50.000 0.00 0.00 0.00 2.93
82 83 2.831685 ACGATGTAGCTGTGGTTTGA 57.168 45.000 0.00 0.00 0.00 2.69
83 84 2.688507 ACGATGTAGCTGTGGTTTGAG 58.311 47.619 0.00 0.00 0.00 3.02
84 85 2.037251 ACGATGTAGCTGTGGTTTGAGT 59.963 45.455 0.00 0.00 0.00 3.41
85 86 3.067106 CGATGTAGCTGTGGTTTGAGTT 58.933 45.455 0.00 0.00 0.00 3.01
86 87 3.498397 CGATGTAGCTGTGGTTTGAGTTT 59.502 43.478 0.00 0.00 0.00 2.66
87 88 4.688879 CGATGTAGCTGTGGTTTGAGTTTA 59.311 41.667 0.00 0.00 0.00 2.01
88 89 5.178623 CGATGTAGCTGTGGTTTGAGTTTAA 59.821 40.000 0.00 0.00 0.00 1.52
89 90 6.128282 CGATGTAGCTGTGGTTTGAGTTTAAT 60.128 38.462 0.00 0.00 0.00 1.40
90 91 7.064134 CGATGTAGCTGTGGTTTGAGTTTAATA 59.936 37.037 0.00 0.00 0.00 0.98
91 92 8.630054 ATGTAGCTGTGGTTTGAGTTTAATAA 57.370 30.769 0.00 0.00 0.00 1.40
92 93 8.453238 TGTAGCTGTGGTTTGAGTTTAATAAA 57.547 30.769 0.00 0.00 0.00 1.40
93 94 8.564574 TGTAGCTGTGGTTTGAGTTTAATAAAG 58.435 33.333 0.00 0.00 0.00 1.85
94 95 6.447162 AGCTGTGGTTTGAGTTTAATAAAGC 58.553 36.000 0.00 0.00 33.68 3.51
95 96 6.265422 AGCTGTGGTTTGAGTTTAATAAAGCT 59.735 34.615 0.00 0.00 34.08 3.74
96 97 7.447238 AGCTGTGGTTTGAGTTTAATAAAGCTA 59.553 33.333 0.00 0.00 34.08 3.32
97 98 7.750903 GCTGTGGTTTGAGTTTAATAAAGCTAG 59.249 37.037 0.00 0.00 34.08 3.42
98 99 7.590279 TGTGGTTTGAGTTTAATAAAGCTAGC 58.410 34.615 6.62 6.62 34.08 3.42
99 100 7.447238 TGTGGTTTGAGTTTAATAAAGCTAGCT 59.553 33.333 12.68 12.68 34.08 3.32
100 101 8.943002 GTGGTTTGAGTTTAATAAAGCTAGCTA 58.057 33.333 19.70 3.08 34.08 3.32
101 102 8.943002 TGGTTTGAGTTTAATAAAGCTAGCTAC 58.057 33.333 19.70 10.63 34.08 3.58
102 103 8.943002 GGTTTGAGTTTAATAAAGCTAGCTACA 58.057 33.333 19.70 9.28 0.00 2.74
106 107 9.109393 TGAGTTTAATAAAGCTAGCTACAATGG 57.891 33.333 19.70 0.00 0.00 3.16
107 108 9.110502 GAGTTTAATAAAGCTAGCTACAATGGT 57.889 33.333 19.70 0.00 0.00 3.55
108 109 9.110502 AGTTTAATAAAGCTAGCTACAATGGTC 57.889 33.333 19.70 6.67 0.00 4.02
109 110 8.343366 GTTTAATAAAGCTAGCTACAATGGTCC 58.657 37.037 19.70 0.00 0.00 4.46
110 111 5.896073 ATAAAGCTAGCTACAATGGTCCT 57.104 39.130 19.70 0.00 0.00 3.85
111 112 3.828875 AAGCTAGCTACAATGGTCCTC 57.171 47.619 19.70 0.00 0.00 3.71
112 113 2.043227 AGCTAGCTACAATGGTCCTCC 58.957 52.381 17.69 0.00 0.00 4.30
113 114 1.070914 GCTAGCTACAATGGTCCTCCC 59.929 57.143 7.70 0.00 0.00 4.30
114 115 1.694696 CTAGCTACAATGGTCCTCCCC 59.305 57.143 0.00 0.00 0.00 4.81
115 116 0.044855 AGCTACAATGGTCCTCCCCT 59.955 55.000 0.00 0.00 0.00 4.79
116 117 1.294068 AGCTACAATGGTCCTCCCCTA 59.706 52.381 0.00 0.00 0.00 3.53
117 118 2.124411 GCTACAATGGTCCTCCCCTAA 58.876 52.381 0.00 0.00 0.00 2.69
118 119 2.508300 GCTACAATGGTCCTCCCCTAAA 59.492 50.000 0.00 0.00 0.00 1.85
119 120 3.053917 GCTACAATGGTCCTCCCCTAAAA 60.054 47.826 0.00 0.00 0.00 1.52
120 121 4.569015 GCTACAATGGTCCTCCCCTAAAAA 60.569 45.833 0.00 0.00 0.00 1.94
140 141 4.736126 AAAAGAAGGTGGGTTTGTCAAG 57.264 40.909 0.00 0.00 0.00 3.02
141 142 1.692411 AGAAGGTGGGTTTGTCAAGC 58.308 50.000 0.00 0.00 0.00 4.01
148 149 3.773117 GGTTTGTCAAGCCATGTCG 57.227 52.632 13.19 0.00 0.00 4.35
149 150 0.951558 GGTTTGTCAAGCCATGTCGT 59.048 50.000 13.19 0.00 0.00 4.34
150 151 1.069227 GGTTTGTCAAGCCATGTCGTC 60.069 52.381 13.19 0.00 0.00 4.20
151 152 1.601903 GTTTGTCAAGCCATGTCGTCA 59.398 47.619 0.00 0.00 0.00 4.35
152 153 1.960417 TTGTCAAGCCATGTCGTCAA 58.040 45.000 0.00 0.00 0.00 3.18
160 161 2.026262 AGCCATGTCGTCAACCCTAAAT 60.026 45.455 0.00 0.00 0.00 1.40
176 177 8.725148 CAACCCTAAATTATGAGCTCATATGTC 58.275 37.037 31.73 0.00 38.49 3.06
182 183 6.864151 ATTATGAGCTCATATGTCTGCCTA 57.136 37.500 31.73 17.00 38.49 3.93
245 246 6.365520 GTCTCCCCAATAACATAGTTTGGAT 58.634 40.000 2.57 0.00 42.02 3.41
247 248 5.373222 TCCCCAATAACATAGTTTGGATCG 58.627 41.667 2.57 0.00 42.02 3.69
248 249 4.023193 CCCCAATAACATAGTTTGGATCGC 60.023 45.833 2.57 0.00 42.02 4.58
273 274 7.309920 CCGCCATACAAACAACTAAACTATTT 58.690 34.615 0.00 0.00 0.00 1.40
334 335 6.820656 CAGTAAAGCCAAGTCTACAATCATCT 59.179 38.462 0.00 0.00 0.00 2.90
335 336 7.010923 CAGTAAAGCCAAGTCTACAATCATCTC 59.989 40.741 0.00 0.00 0.00 2.75
336 337 5.690464 AAGCCAAGTCTACAATCATCTCT 57.310 39.130 0.00 0.00 0.00 3.10
337 338 5.021033 AGCCAAGTCTACAATCATCTCTG 57.979 43.478 0.00 0.00 0.00 3.35
338 339 3.559242 GCCAAGTCTACAATCATCTCTGC 59.441 47.826 0.00 0.00 0.00 4.26
339 340 4.763073 CCAAGTCTACAATCATCTCTGCA 58.237 43.478 0.00 0.00 0.00 4.41
340 341 4.569966 CCAAGTCTACAATCATCTCTGCAC 59.430 45.833 0.00 0.00 0.00 4.57
421 422 1.488812 TCCCATCGACCCTTATTGGTG 59.511 52.381 0.00 0.00 39.24 4.17
458 459 4.004982 TCGTGCTTGTTATTAACCTTCCC 58.995 43.478 4.17 0.00 0.00 3.97
459 460 4.007659 CGTGCTTGTTATTAACCTTCCCT 58.992 43.478 4.17 0.00 0.00 4.20
480 481 6.399639 CCTATTTTTAGGGTTTGTGTGTGT 57.600 37.500 0.00 0.00 33.60 3.72
481 482 6.212955 CCTATTTTTAGGGTTTGTGTGTGTG 58.787 40.000 0.00 0.00 33.60 3.82
495 496 4.162812 GTGTGTGTGTCGAAAACAAATGT 58.837 39.130 3.90 0.00 40.31 2.71
559 560 9.322776 CATAAAATCAACTTCGAACTCTCAAAG 57.677 33.333 0.00 0.00 0.00 2.77
561 562 4.665833 TCAACTTCGAACTCTCAAAGGA 57.334 40.909 0.00 0.00 0.00 3.36
591 592 8.767478 AAAATCTAAAACCAAATCTGCATCTG 57.233 30.769 0.00 0.00 0.00 2.90
668 669 3.894427 TCTTGGGCTATGCAAAGAACAAA 59.106 39.130 0.00 0.00 32.55 2.83
669 670 4.527816 TCTTGGGCTATGCAAAGAACAAAT 59.472 37.500 0.00 0.00 32.55 2.32
705 706 9.736023 CAAAAATTGGACCTACTATTTGCTATC 57.264 33.333 0.00 0.00 0.00 2.08
719 723 3.198409 TGCTATCATGGATCCACACAC 57.802 47.619 18.99 5.48 0.00 3.82
862 866 0.106521 TTTTTCAGGGGCTGCAAAGC 59.893 50.000 0.50 0.00 29.67 3.51
950 957 1.965754 GCCCAGCATCTCTTCCGTCT 61.966 60.000 0.00 0.00 0.00 4.18
965 972 4.388499 TCTCTTTCACGGGGCGCC 62.388 66.667 21.18 21.18 0.00 6.53
1367 1684 2.050714 GCGACGACGACTGGTTCA 60.051 61.111 12.29 0.00 42.66 3.18
1370 1687 1.733399 GACGACGACTGGTTCAGGC 60.733 63.158 0.00 0.00 35.89 4.85
1471 1788 1.237285 ACAAGCACTGGATTGCCGTC 61.237 55.000 0.00 0.00 44.08 4.79
1578 1895 4.592426 GGTAAGCACCACCGAGAC 57.408 61.111 0.00 0.00 45.04 3.36
1694 2011 1.010419 CCGCTTCCAATTGCAAGCAC 61.010 55.000 28.72 5.89 44.53 4.40
1731 2048 4.963276 TTGAATGTCCGACCATGATTTC 57.037 40.909 0.00 0.00 0.00 2.17
1737 2054 2.487762 GTCCGACCATGATTTCTTGCAA 59.512 45.455 0.00 0.00 0.00 4.08
1744 2061 4.160252 ACCATGATTTCTTGCAACATACCC 59.840 41.667 0.00 0.00 0.00 3.69
1976 2294 5.587043 ACGAAGGTCATTTGTGACTGTTTTA 59.413 36.000 8.30 0.00 38.74 1.52
1977 2295 6.094325 ACGAAGGTCATTTGTGACTGTTTTAA 59.906 34.615 8.30 0.00 38.74 1.52
1988 2306 3.003897 TGACTGTTTTAATTCGTGGGTGC 59.996 43.478 0.00 0.00 0.00 5.01
2037 2355 4.400567 GCTATTTCTGCTGGATTCAAAGGT 59.599 41.667 0.00 0.00 0.00 3.50
2224 2545 6.151144 CAGGTAATAGCTTGCTTTACAACCTT 59.849 38.462 19.07 5.27 33.68 3.50
2336 2672 5.618056 TCTCTTTTGATGCTTGATGACAC 57.382 39.130 0.00 0.00 0.00 3.67
2338 2674 3.507233 TCTTTTGATGCTTGATGACACCC 59.493 43.478 0.00 0.00 0.00 4.61
2346 2682 3.008923 TGCTTGATGACACCCTCAACATA 59.991 43.478 0.00 0.00 32.12 2.29
2434 2894 9.710818 TTATGATCTGTAAAGTAGTACTCCCTT 57.289 33.333 2.58 0.00 0.00 3.95
2479 2943 1.079317 AAACACCAACCGTTTTGCGC 61.079 50.000 0.00 0.00 39.71 6.09
2480 2944 2.656973 CACCAACCGTTTTGCGCC 60.657 61.111 4.18 0.00 39.71 6.53
2510 2974 5.664457 AGGGTATCGGAAAGGTTATTAGTGT 59.336 40.000 0.00 0.00 0.00 3.55
2631 3097 2.483877 CCTGCACATGTGTCACGTAATT 59.516 45.455 26.01 0.00 0.00 1.40
2845 3337 2.238144 CAGGTGGTGGATTCACTGATCT 59.762 50.000 3.62 0.00 43.17 2.75
2846 3338 3.452264 CAGGTGGTGGATTCACTGATCTA 59.548 47.826 3.62 0.00 43.17 1.98
2847 3339 3.452627 AGGTGGTGGATTCACTGATCTAC 59.547 47.826 3.62 0.00 43.17 2.59
3118 3614 2.272447 GCACCGGGCTGCCTTTTTA 61.272 57.895 19.68 0.00 40.25 1.52
3119 3615 1.604147 GCACCGGGCTGCCTTTTTAT 61.604 55.000 19.68 0.00 40.25 1.40
3120 3616 0.894835 CACCGGGCTGCCTTTTTATT 59.105 50.000 19.68 0.00 0.00 1.40
3230 3726 2.406130 CACACATTTGGGTGCATGTTC 58.594 47.619 0.00 0.00 43.10 3.18
3240 3736 2.607038 GGGTGCATGTTCGAGGAAAAAC 60.607 50.000 0.00 0.00 0.00 2.43
3352 3857 4.394920 GCTGTACATGCCTTTGCTACTAAA 59.605 41.667 0.00 0.00 38.71 1.85
3380 3885 2.687935 AGGTTGTTCGCTTGTGACAATT 59.312 40.909 0.00 0.00 0.00 2.32
3416 3921 4.054724 TGTTCTGAAACCAGCATTAGCGT 61.055 43.478 0.00 0.00 39.21 5.07
3664 4643 2.369860 GGTGGACATGATGGAGCTGATA 59.630 50.000 0.00 0.00 0.00 2.15
3684 4663 6.114767 TGATATCTTGCACAGCACATAAGAA 58.885 36.000 3.98 0.00 38.71 2.52
3699 4679 6.458342 GCACATAAGAAGATTTTCCGGTTAGG 60.458 42.308 0.00 0.00 42.97 2.69
3906 4890 2.057922 CCCACCTAGCCACCTCATATT 58.942 52.381 0.00 0.00 0.00 1.28
3942 4926 6.567959 CCAGGCTAAATCTTGAATCTTTTCC 58.432 40.000 0.00 0.00 0.00 3.13
3982 4968 1.141449 CTTCCTCAGCAGCTCTCCG 59.859 63.158 0.00 0.00 0.00 4.63
4022 5008 6.039829 CCTTTAAATTGCTGATCTTCTACCCC 59.960 42.308 0.00 0.00 0.00 4.95
4057 5043 2.106566 TGCTCTTTTGTTTGCCCTCAA 58.893 42.857 0.00 0.00 0.00 3.02
4149 5135 0.105709 GCTCTTCTCCCTCTAGCCCT 60.106 60.000 0.00 0.00 0.00 5.19
4175 5677 2.044832 GACTGGCAGCTTAGCATGCG 62.045 60.000 15.89 0.00 43.49 4.73
4180 5682 0.579156 GCAGCTTAGCATGCGACTAC 59.421 55.000 13.01 2.25 35.28 2.73
4296 6263 6.436847 TCTTCAATTTTGGCCACTATTGATGA 59.563 34.615 30.29 30.29 38.12 2.92
4359 6326 4.406648 TTGATTCTATCACTGATGCCGT 57.593 40.909 1.42 0.00 39.39 5.68
4361 6328 4.769688 TGATTCTATCACTGATGCCGTTT 58.230 39.130 1.42 0.00 33.59 3.60
4362 6329 5.185454 TGATTCTATCACTGATGCCGTTTT 58.815 37.500 1.42 0.00 33.59 2.43
4473 6440 2.176546 CGTGCAAATCCAGTGGCG 59.823 61.111 3.51 0.00 0.00 5.69
4505 6472 0.250467 ACTCATATGCATGTCCGGCC 60.250 55.000 10.16 0.00 33.57 6.13
4519 6486 1.102978 CCGGCCGGATTCAATCTTTT 58.897 50.000 41.82 0.00 37.50 2.27
4582 6549 4.271661 TCTGAATGTATTGCTTGATGGCA 58.728 39.130 0.00 0.00 40.74 4.92
4596 6563 6.094048 TGCTTGATGGCATAGAGAGTAAAAAC 59.906 38.462 0.00 0.00 37.29 2.43
4698 6665 8.649841 TGCAAGAATTTGATGAAAATCGATTTC 58.350 29.630 22.93 16.09 40.98 2.17
4763 6730 5.606348 AGAGTTAGAAACCTGCTATCCTG 57.394 43.478 0.00 0.00 0.00 3.86
4765 6732 3.118223 AGTTAGAAACCTGCTATCCTGCC 60.118 47.826 0.00 0.00 0.00 4.85
4786 6753 2.408050 CCATGAGCCTCTACGCATAAC 58.592 52.381 0.00 0.00 0.00 1.89
4811 6778 7.651704 ACAGTGTTGCCAAAAACTTACAATATC 59.348 33.333 0.00 0.00 30.95 1.63
4817 6784 7.090173 TGCCAAAAACTTACAATATCAGAAGC 58.910 34.615 0.00 0.00 0.00 3.86
4920 6987 2.949451 ACTCTGGAGCTTATGACACG 57.051 50.000 0.00 0.00 0.00 4.49
4988 7055 6.659242 ACTCCCAATAACTTTTCCTGTATGTG 59.341 38.462 0.00 0.00 0.00 3.21
5089 7160 4.883006 GGTCTGTCGAGTATAGTTCCTTCT 59.117 45.833 0.00 0.00 0.00 2.85
5199 7270 2.163412 TGCATGCGTTTGATTACCTTCC 59.837 45.455 14.09 0.00 0.00 3.46
5226 7297 0.179048 ATCAGCATCGCGGGATTTCA 60.179 50.000 12.94 0.00 0.00 2.69
5328 7400 7.067372 TGACTAATGAATGTTGAATCCCATCAC 59.933 37.037 0.00 0.00 0.00 3.06
5348 7420 1.905215 CTGTGACCTGGAGATGGAAGT 59.095 52.381 0.00 0.00 0.00 3.01
5418 7490 1.203013 GGGAAGGCTTGGGTAAGTTGT 60.203 52.381 3.46 0.00 36.27 3.32
5419 7491 2.594131 GGAAGGCTTGGGTAAGTTGTT 58.406 47.619 3.46 0.00 36.27 2.83
5455 7529 3.054875 TGTCTCTTTGCACTGATAGGCAT 60.055 43.478 0.00 0.00 40.17 4.40
5492 7566 1.880027 ACAAACTTCTGCATCCGTTCC 59.120 47.619 0.00 0.00 0.00 3.62
5702 9258 3.576078 TTGTGAGTTGGTGAGGTGAAT 57.424 42.857 0.00 0.00 0.00 2.57
5721 9278 7.781693 AGGTGAATGATTTATGAGTTGGCTAAT 59.218 33.333 0.00 0.00 0.00 1.73
5832 9389 9.886132 TTCTGAAGAACTATTAATTCCTGGTAC 57.114 33.333 0.00 0.00 0.00 3.34
5935 9500 6.592994 GCACAGCTCAGATAATTAGCATGATA 59.407 38.462 3.17 0.00 38.75 2.15
5982 9547 5.776208 GGGACAAGGAAAATTAAAGGGTACA 59.224 40.000 0.00 0.00 0.00 2.90
5998 9563 3.527533 GGTACACAAGTGAACACTGACA 58.472 45.455 7.28 0.00 41.58 3.58
6045 9610 2.995283 TGAGAGGTCATGCCATCTTTG 58.005 47.619 8.58 0.00 40.61 2.77
6110 9675 6.016360 TGGTCTGAGTTTTGATAACAATGTGG 60.016 38.462 0.00 0.00 35.85 4.17
6112 9677 5.048083 TCTGAGTTTTGATAACAATGTGGCC 60.048 40.000 0.00 0.00 35.85 5.36
6160 9725 4.074970 AGGAGACATTGCCAGTTGTTTAG 58.925 43.478 0.00 0.00 0.00 1.85
6170 9735 5.175859 TGCCAGTTGTTTAGTATGCTAGTC 58.824 41.667 0.00 0.00 0.00 2.59
6302 9977 1.115467 CCTCTACCCAGCTCGTTGAT 58.885 55.000 0.00 0.00 0.00 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 5.018539 ACCAAACTAAAGGCTGGTTTTTC 57.981 39.130 9.67 0.00 39.14 2.29
6 7 3.637769 TCAAACCAAACTAAAGGCTGGT 58.362 40.909 0.00 0.67 44.12 4.00
7 8 4.871933 ATCAAACCAAACTAAAGGCTGG 57.128 40.909 0.00 0.00 34.95 4.85
8 9 5.691754 GTGAATCAAACCAAACTAAAGGCTG 59.308 40.000 0.00 0.00 0.00 4.85
9 10 5.221441 GGTGAATCAAACCAAACTAAAGGCT 60.221 40.000 0.00 0.00 37.65 4.58
10 11 4.988540 GGTGAATCAAACCAAACTAAAGGC 59.011 41.667 0.00 0.00 37.65 4.35
11 12 5.510690 GGGGTGAATCAAACCAAACTAAAGG 60.511 44.000 7.41 0.00 39.65 3.11
12 13 5.510690 GGGGGTGAATCAAACCAAACTAAAG 60.511 44.000 7.41 0.00 39.65 1.85
13 14 4.345547 GGGGGTGAATCAAACCAAACTAAA 59.654 41.667 7.41 0.00 39.65 1.85
14 15 3.898741 GGGGGTGAATCAAACCAAACTAA 59.101 43.478 7.41 0.00 39.65 2.24
15 16 3.502356 GGGGGTGAATCAAACCAAACTA 58.498 45.455 7.41 0.00 39.65 2.24
16 17 2.325484 GGGGGTGAATCAAACCAAACT 58.675 47.619 7.41 0.00 39.65 2.66
17 18 1.000394 CGGGGGTGAATCAAACCAAAC 60.000 52.381 7.41 0.00 39.65 2.93
18 19 1.333177 CGGGGGTGAATCAAACCAAA 58.667 50.000 7.41 0.00 39.65 3.28
19 20 0.540830 CCGGGGGTGAATCAAACCAA 60.541 55.000 0.00 0.00 39.65 3.67
20 21 1.075836 CCGGGGGTGAATCAAACCA 59.924 57.895 0.00 0.00 39.65 3.67
21 22 1.680989 CCCGGGGGTGAATCAAACC 60.681 63.158 14.71 0.00 36.94 3.27
22 23 1.680989 CCCCGGGGGTGAATCAAAC 60.681 63.158 34.01 0.00 38.25 2.93
23 24 2.767352 CCCCGGGGGTGAATCAAA 59.233 61.111 34.01 0.00 38.25 2.69
33 34 3.090210 ACTTAACAATAAACCCCGGGG 57.910 47.619 39.18 39.18 42.03 5.73
34 35 4.768448 AGAAACTTAACAATAAACCCCGGG 59.232 41.667 15.80 15.80 0.00 5.73
35 36 5.970317 AGAAACTTAACAATAAACCCCGG 57.030 39.130 0.00 0.00 0.00 5.73
36 37 7.017055 CGTAAGAAACTTAACAATAAACCCCG 58.983 38.462 0.00 0.00 43.02 5.73
56 57 2.852413 CCACAGCTACATCGTTCGTAAG 59.148 50.000 0.00 0.00 0.00 2.34
57 58 2.229543 ACCACAGCTACATCGTTCGTAA 59.770 45.455 0.00 0.00 0.00 3.18
58 59 1.814394 ACCACAGCTACATCGTTCGTA 59.186 47.619 0.00 0.00 0.00 3.43
59 60 0.601558 ACCACAGCTACATCGTTCGT 59.398 50.000 0.00 0.00 0.00 3.85
60 61 1.710013 AACCACAGCTACATCGTTCG 58.290 50.000 0.00 0.00 0.00 3.95
61 62 3.064207 TCAAACCACAGCTACATCGTTC 58.936 45.455 0.00 0.00 0.00 3.95
62 63 3.067106 CTCAAACCACAGCTACATCGTT 58.933 45.455 0.00 0.00 0.00 3.85
63 64 2.037251 ACTCAAACCACAGCTACATCGT 59.963 45.455 0.00 0.00 0.00 3.73
64 65 2.688507 ACTCAAACCACAGCTACATCG 58.311 47.619 0.00 0.00 0.00 3.84
65 66 6.554334 TTAAACTCAAACCACAGCTACATC 57.446 37.500 0.00 0.00 0.00 3.06
66 67 8.630054 TTATTAAACTCAAACCACAGCTACAT 57.370 30.769 0.00 0.00 0.00 2.29
67 68 8.453238 TTTATTAAACTCAAACCACAGCTACA 57.547 30.769 0.00 0.00 0.00 2.74
68 69 7.537649 GCTTTATTAAACTCAAACCACAGCTAC 59.462 37.037 0.00 0.00 0.00 3.58
69 70 7.447238 AGCTTTATTAAACTCAAACCACAGCTA 59.553 33.333 0.00 0.00 0.00 3.32
70 71 6.265422 AGCTTTATTAAACTCAAACCACAGCT 59.735 34.615 0.00 0.00 0.00 4.24
71 72 6.447162 AGCTTTATTAAACTCAAACCACAGC 58.553 36.000 0.00 0.00 0.00 4.40
72 73 7.750903 GCTAGCTTTATTAAACTCAAACCACAG 59.249 37.037 7.70 0.00 0.00 3.66
73 74 7.447238 AGCTAGCTTTATTAAACTCAAACCACA 59.553 33.333 12.68 0.00 0.00 4.17
74 75 7.817641 AGCTAGCTTTATTAAACTCAAACCAC 58.182 34.615 12.68 0.00 0.00 4.16
75 76 7.996098 AGCTAGCTTTATTAAACTCAAACCA 57.004 32.000 12.68 0.00 0.00 3.67
76 77 8.943002 TGTAGCTAGCTTTATTAAACTCAAACC 58.057 33.333 24.88 0.00 0.00 3.27
80 81 9.109393 CCATTGTAGCTAGCTTTATTAAACTCA 57.891 33.333 24.88 4.68 0.00 3.41
81 82 9.110502 ACCATTGTAGCTAGCTTTATTAAACTC 57.889 33.333 24.88 2.09 0.00 3.01
82 83 9.110502 GACCATTGTAGCTAGCTTTATTAAACT 57.889 33.333 24.88 0.00 0.00 2.66
83 84 8.343366 GGACCATTGTAGCTAGCTTTATTAAAC 58.657 37.037 24.88 13.49 0.00 2.01
84 85 8.272173 AGGACCATTGTAGCTAGCTTTATTAAA 58.728 33.333 24.88 8.97 0.00 1.52
85 86 7.802117 AGGACCATTGTAGCTAGCTTTATTAA 58.198 34.615 24.88 11.34 0.00 1.40
86 87 7.374975 AGGACCATTGTAGCTAGCTTTATTA 57.625 36.000 24.88 0.15 0.00 0.98
87 88 6.253946 AGGACCATTGTAGCTAGCTTTATT 57.746 37.500 24.88 6.06 0.00 1.40
88 89 5.221742 GGAGGACCATTGTAGCTAGCTTTAT 60.222 44.000 24.88 11.07 35.97 1.40
89 90 4.101119 GGAGGACCATTGTAGCTAGCTTTA 59.899 45.833 24.88 9.64 35.97 1.85
90 91 3.118223 GGAGGACCATTGTAGCTAGCTTT 60.118 47.826 24.88 1.27 35.97 3.51
91 92 2.436173 GGAGGACCATTGTAGCTAGCTT 59.564 50.000 24.88 1.74 35.97 3.74
92 93 2.043227 GGAGGACCATTGTAGCTAGCT 58.957 52.381 23.12 23.12 35.97 3.32
93 94 1.070914 GGGAGGACCATTGTAGCTAGC 59.929 57.143 6.62 6.62 39.85 3.42
94 95 1.694696 GGGGAGGACCATTGTAGCTAG 59.305 57.143 0.00 0.00 42.91 3.42
95 96 1.294068 AGGGGAGGACCATTGTAGCTA 59.706 52.381 0.00 0.00 42.91 3.32
96 97 0.044855 AGGGGAGGACCATTGTAGCT 59.955 55.000 0.00 0.00 42.91 3.32
97 98 1.802553 TAGGGGAGGACCATTGTAGC 58.197 55.000 0.00 0.00 42.91 3.58
98 99 4.855298 TTTTAGGGGAGGACCATTGTAG 57.145 45.455 0.00 0.00 42.91 2.74
118 119 4.622933 GCTTGACAAACCCACCTTCTTTTT 60.623 41.667 0.00 0.00 0.00 1.94
119 120 3.118775 GCTTGACAAACCCACCTTCTTTT 60.119 43.478 0.00 0.00 0.00 2.27
120 121 2.430694 GCTTGACAAACCCACCTTCTTT 59.569 45.455 0.00 0.00 0.00 2.52
121 122 2.031870 GCTTGACAAACCCACCTTCTT 58.968 47.619 0.00 0.00 0.00 2.52
122 123 1.692411 GCTTGACAAACCCACCTTCT 58.308 50.000 0.00 0.00 0.00 2.85
123 124 0.673985 GGCTTGACAAACCCACCTTC 59.326 55.000 0.00 0.00 0.00 3.46
124 125 0.032615 TGGCTTGACAAACCCACCTT 60.033 50.000 5.17 0.00 0.00 3.50
125 126 0.188342 ATGGCTTGACAAACCCACCT 59.812 50.000 5.17 0.00 0.00 4.00
126 127 0.318120 CATGGCTTGACAAACCCACC 59.682 55.000 5.17 0.00 0.00 4.61
127 128 1.000274 GACATGGCTTGACAAACCCAC 60.000 52.381 7.45 0.00 0.00 4.61
128 129 1.327303 GACATGGCTTGACAAACCCA 58.673 50.000 7.45 7.33 0.00 4.51
129 130 0.240945 CGACATGGCTTGACAAACCC 59.759 55.000 7.45 1.81 0.00 4.11
130 131 0.951558 ACGACATGGCTTGACAAACC 59.048 50.000 7.45 0.33 0.00 3.27
131 132 1.601903 TGACGACATGGCTTGACAAAC 59.398 47.619 7.45 0.00 0.00 2.93
132 133 1.960417 TGACGACATGGCTTGACAAA 58.040 45.000 7.45 0.00 0.00 2.83
133 134 1.601903 GTTGACGACATGGCTTGACAA 59.398 47.619 7.45 5.47 0.00 3.18
134 135 1.225855 GTTGACGACATGGCTTGACA 58.774 50.000 7.45 0.00 0.00 3.58
135 136 0.517316 GGTTGACGACATGGCTTGAC 59.483 55.000 7.45 0.00 0.00 3.18
136 137 0.605319 GGGTTGACGACATGGCTTGA 60.605 55.000 7.45 0.00 0.00 3.02
137 138 0.606401 AGGGTTGACGACATGGCTTG 60.606 55.000 0.00 0.00 0.00 4.01
138 139 0.981183 TAGGGTTGACGACATGGCTT 59.019 50.000 0.00 0.00 0.00 4.35
139 140 0.981183 TTAGGGTTGACGACATGGCT 59.019 50.000 0.00 0.00 0.00 4.75
140 141 1.816074 TTTAGGGTTGACGACATGGC 58.184 50.000 0.00 0.00 0.00 4.40
141 142 5.820423 TCATAATTTAGGGTTGACGACATGG 59.180 40.000 0.00 0.00 0.00 3.66
142 143 6.511767 GCTCATAATTTAGGGTTGACGACATG 60.512 42.308 0.00 0.00 0.00 3.21
143 144 5.527582 GCTCATAATTTAGGGTTGACGACAT 59.472 40.000 0.00 0.00 0.00 3.06
144 145 4.873827 GCTCATAATTTAGGGTTGACGACA 59.126 41.667 0.00 0.00 0.00 4.35
145 146 5.116882 AGCTCATAATTTAGGGTTGACGAC 58.883 41.667 0.00 0.00 0.00 4.34
146 147 5.105106 TGAGCTCATAATTTAGGGTTGACGA 60.105 40.000 13.74 0.00 0.00 4.20
147 148 5.116180 TGAGCTCATAATTTAGGGTTGACG 58.884 41.667 13.74 0.00 0.00 4.35
148 149 8.725148 CATATGAGCTCATAATTTAGGGTTGAC 58.275 37.037 33.98 0.00 41.60 3.18
149 150 8.439971 ACATATGAGCTCATAATTTAGGGTTGA 58.560 33.333 33.98 13.90 41.60 3.18
150 151 8.627208 ACATATGAGCTCATAATTTAGGGTTG 57.373 34.615 33.98 25.83 41.60 3.77
151 152 8.664079 AGACATATGAGCTCATAATTTAGGGTT 58.336 33.333 33.98 15.83 41.60 4.11
152 153 8.099537 CAGACATATGAGCTCATAATTTAGGGT 58.900 37.037 33.98 22.80 41.60 4.34
160 161 5.047021 GGTAGGCAGACATATGAGCTCATAA 60.047 44.000 33.98 20.43 41.60 1.90
176 177 1.066143 ACATTTGTCCTCGGTAGGCAG 60.066 52.381 0.00 0.00 43.31 4.85
182 183 2.536761 TTCGAACATTTGTCCTCGGT 57.463 45.000 0.00 0.00 31.37 4.69
189 190 6.429692 TGTGAAGGTGATATTCGAACATTTGT 59.570 34.615 0.00 0.00 0.00 2.83
192 193 6.094048 CCTTGTGAAGGTGATATTCGAACATT 59.906 38.462 0.00 0.00 43.95 2.71
193 194 5.586243 CCTTGTGAAGGTGATATTCGAACAT 59.414 40.000 0.00 0.00 43.95 2.71
198 199 7.669980 GACCATCCTTGTGAAGGTGATATTCG 61.670 46.154 2.34 0.00 44.91 3.34
229 230 3.250040 GCGGCGATCCAAACTATGTTATT 59.750 43.478 12.98 0.00 0.00 1.40
234 235 0.813610 TGGCGGCGATCCAAACTATG 60.814 55.000 12.98 0.00 0.00 2.23
245 246 0.604243 AGTTGTTTGTATGGCGGCGA 60.604 50.000 12.98 0.00 0.00 5.54
247 248 3.057806 AGTTTAGTTGTTTGTATGGCGGC 60.058 43.478 0.00 0.00 0.00 6.53
248 249 4.759516 AGTTTAGTTGTTTGTATGGCGG 57.240 40.909 0.00 0.00 0.00 6.13
302 303 4.884247 AGACTTGGCTTTACTGTGTAGTC 58.116 43.478 0.00 0.00 38.36 2.59
334 335 4.580167 ACATTAAGCTCAACTTTGTGCAGA 59.420 37.500 16.10 3.17 46.77 4.26
335 336 4.863491 ACATTAAGCTCAACTTTGTGCAG 58.137 39.130 16.10 5.35 46.77 4.41
336 337 4.916983 ACATTAAGCTCAACTTTGTGCA 57.083 36.364 16.10 0.00 46.77 4.57
337 338 5.748152 TCAAACATTAAGCTCAACTTTGTGC 59.252 36.000 7.74 7.74 45.25 4.57
338 339 7.515684 GCTTCAAACATTAAGCTCAACTTTGTG 60.516 37.037 0.00 0.00 43.77 3.33
339 340 6.476706 GCTTCAAACATTAAGCTCAACTTTGT 59.523 34.615 0.00 0.00 43.77 2.83
340 341 6.870517 GCTTCAAACATTAAGCTCAACTTTG 58.129 36.000 0.00 0.00 43.77 2.77
365 366 1.680735 GAGTGTGGGCAATTCACAACA 59.319 47.619 0.41 0.00 45.24 3.33
421 422 6.656003 ACAAGCACGAGTTTTAATAGTGAAC 58.344 36.000 0.00 0.00 35.03 3.18
458 459 6.801575 ACACACACACAAACCCTAAAAATAG 58.198 36.000 0.00 0.00 0.00 1.73
459 460 6.458478 CGACACACACACAAACCCTAAAAATA 60.458 38.462 0.00 0.00 0.00 1.40
470 471 3.898517 TGTTTTCGACACACACACAAA 57.101 38.095 0.00 0.00 32.00 2.83
480 481 9.881529 GTACCTATTTTACATTTGTTTTCGACA 57.118 29.630 0.00 0.00 36.19 4.35
495 496 9.824216 AGTCTATGGAGCATAGTACCTATTTTA 57.176 33.333 0.00 0.00 42.92 1.52
566 567 7.332678 GCAGATGCAGATTTGGTTTTAGATTTT 59.667 33.333 0.00 0.00 41.59 1.82
645 646 3.495331 TGTTCTTTGCATAGCCCAAGAA 58.505 40.909 5.15 5.15 35.73 2.52
647 648 3.940209 TTGTTCTTTGCATAGCCCAAG 57.060 42.857 0.00 0.00 0.00 3.61
657 658 8.755696 TTTGTCCACATATATTTGTTCTTTGC 57.244 30.769 0.00 0.00 0.00 3.68
668 669 9.131791 GTAGGTCCAATTTTTGTCCACATATAT 57.868 33.333 0.00 0.00 0.00 0.86
669 670 8.333235 AGTAGGTCCAATTTTTGTCCACATATA 58.667 33.333 0.00 0.00 0.00 0.86
806 810 3.294038 TTCCAAAAGAAACCCGGTGTA 57.706 42.857 0.00 0.00 0.00 2.90
807 811 2.146920 TTCCAAAAGAAACCCGGTGT 57.853 45.000 0.00 0.00 0.00 4.16
854 858 3.006110 TGAAGAAATTCCAGGCTTTGCAG 59.994 43.478 0.00 0.00 0.00 4.41
855 859 2.964464 TGAAGAAATTCCAGGCTTTGCA 59.036 40.909 0.00 0.00 0.00 4.08
856 860 3.665745 TGAAGAAATTCCAGGCTTTGC 57.334 42.857 0.00 0.00 0.00 3.68
857 861 5.786311 TGATTGAAGAAATTCCAGGCTTTG 58.214 37.500 0.00 0.00 0.00 2.77
858 862 6.423776 TTGATTGAAGAAATTCCAGGCTTT 57.576 33.333 0.00 0.00 0.00 3.51
859 863 6.423776 TTTGATTGAAGAAATTCCAGGCTT 57.576 33.333 0.00 0.00 0.00 4.35
860 864 6.268387 TCTTTTGATTGAAGAAATTCCAGGCT 59.732 34.615 0.00 0.00 30.60 4.58
861 865 6.458210 TCTTTTGATTGAAGAAATTCCAGGC 58.542 36.000 0.00 0.00 30.60 4.85
862 866 8.891671 TTTCTTTTGATTGAAGAAATTCCAGG 57.108 30.769 7.68 0.00 44.06 4.45
902 906 0.306533 GGCCACGGTATAACAATGCG 59.693 55.000 0.00 0.00 0.00 4.73
909 913 1.134037 GGACAATGGGCCACGGTATAA 60.134 52.381 9.28 0.00 0.00 0.98
965 972 4.036498 GGATCTGATGCACTGAAATGAAGG 59.964 45.833 4.12 0.00 0.00 3.46
1370 1687 1.750399 CATGACGGCTTCCAAGGGG 60.750 63.158 0.00 0.00 0.00 4.79
1485 1802 2.048127 GGCTGTCCGAGTCACACC 60.048 66.667 0.00 0.00 0.00 4.16
1578 1895 3.057969 TGGCTCTTGTATGGTCTTGTG 57.942 47.619 0.00 0.00 0.00 3.33
1666 1983 0.463833 ATTGGAAGCGGGATTCGGAC 60.464 55.000 0.00 0.00 39.69 4.79
1694 2011 1.021202 TCAAACGGTGGCAAGTCTTG 58.979 50.000 8.31 8.31 0.00 3.02
1731 2048 0.168788 CACAGCGGGTATGTTGCAAG 59.831 55.000 0.00 0.00 0.00 4.01
1737 2054 2.268920 CCAGCACAGCGGGTATGT 59.731 61.111 0.00 0.00 39.00 2.29
1744 2061 3.925630 ATCCCCAACCAGCACAGCG 62.926 63.158 0.00 0.00 0.00 5.18
1976 2294 0.609131 CTTCCCAGCACCCACGAATT 60.609 55.000 0.00 0.00 0.00 2.17
1977 2295 1.002134 CTTCCCAGCACCCACGAAT 60.002 57.895 0.00 0.00 0.00 3.34
1988 2306 5.010922 TGTCCATTTCAATTGTTCTTCCCAG 59.989 40.000 5.13 0.00 0.00 4.45
2022 2340 2.639347 TCTCTCACCTTTGAATCCAGCA 59.361 45.455 0.00 0.00 0.00 4.41
2037 2355 6.101881 TCCTACTATCATTGGAGACTCTCTCA 59.898 42.308 6.02 0.27 45.12 3.27
2298 2634 7.726216 TCAAAAGAGAAGTGTCATGAGACTAA 58.274 34.615 24.38 1.52 45.20 2.24
2336 2672 3.304257 GCTTCATCGCAATATGTTGAGGG 60.304 47.826 6.35 0.00 37.53 4.30
2338 2674 4.808077 AGCTTCATCGCAATATGTTGAG 57.192 40.909 6.35 2.73 37.53 3.02
2346 2682 0.870393 CCGCATAGCTTCATCGCAAT 59.130 50.000 0.00 0.00 0.00 3.56
2434 2894 5.947663 TCCACACCTTCCTTTCAAATAAGA 58.052 37.500 0.00 0.00 0.00 2.10
2479 2943 3.279434 CCTTTCCGATACCCTTCTTTGG 58.721 50.000 0.00 0.00 0.00 3.28
2480 2944 3.951663 ACCTTTCCGATACCCTTCTTTG 58.048 45.455 0.00 0.00 0.00 2.77
2510 2974 4.148838 CAGGGTTAGTTTTGTCCATCCAA 58.851 43.478 0.00 0.00 0.00 3.53
2845 3337 7.386851 ACAGAAATGAAGCTTAGCAGTAAGTA 58.613 34.615 7.07 0.00 38.38 2.24
2846 3338 6.234177 ACAGAAATGAAGCTTAGCAGTAAGT 58.766 36.000 7.07 0.00 38.38 2.24
2847 3339 6.734104 ACAGAAATGAAGCTTAGCAGTAAG 57.266 37.500 7.07 0.00 39.04 2.34
3137 3633 7.168135 GGCTGAAACTCAATAAAACAGAAACAG 59.832 37.037 0.00 0.00 0.00 3.16
3230 3726 5.414454 TCTTGGTATCCATTGTTTTTCCTCG 59.586 40.000 0.00 0.00 31.53 4.63
3300 3798 9.662545 CATTATTTCGCATACATCAATACACAA 57.337 29.630 0.00 0.00 0.00 3.33
3352 3857 1.670811 CAAGCGAACAACCTGACTTGT 59.329 47.619 0.00 0.00 35.83 3.16
3380 3885 1.333308 CAGAACAACACAATGTCGGCA 59.667 47.619 0.00 0.00 31.81 5.69
3416 3921 0.894835 TGAGGCACGAACTAGCATGA 59.105 50.000 0.00 0.00 0.00 3.07
3664 4643 4.582869 TCTTCTTATGTGCTGTGCAAGAT 58.417 39.130 0.00 0.00 41.47 2.40
3684 4663 4.772886 AGCATACCTAACCGGAAAATCT 57.227 40.909 9.46 0.00 36.31 2.40
3699 4679 6.280643 TCAACCAGTACATCACATAGCATAC 58.719 40.000 0.00 0.00 0.00 2.39
3906 4890 3.295585 TTAGCCTGGCATCAAAGCATA 57.704 42.857 22.65 0.00 35.83 3.14
3942 4926 2.044551 GAGAAAGCAGGGCCTGGG 60.045 66.667 33.43 11.33 31.21 4.45
3982 4968 0.822121 AAAGGCACGGGGAACAGAAC 60.822 55.000 0.00 0.00 0.00 3.01
4022 5008 4.734398 AAGAGCACATTCAGTAGAGAGG 57.266 45.455 0.00 0.00 0.00 3.69
4057 5043 1.287146 AGCAAGGAGGCTGAATGGAAT 59.713 47.619 0.00 0.00 43.89 3.01
4175 5677 4.833390 ACAGGTTTGCTGGATAAGTAGTC 58.167 43.478 0.00 0.00 0.00 2.59
4180 5682 5.679638 GCCAATTACAGGTTTGCTGGATAAG 60.680 44.000 0.00 0.00 0.00 1.73
4296 6263 8.366359 AGTCCTGCCAAAATTGAAGTATTAAT 57.634 30.769 0.00 0.00 0.00 1.40
4505 6472 6.032775 CGATTCACACAAAAAGATTGAATCCG 59.967 38.462 14.07 7.92 45.09 4.18
4519 6486 5.006165 GGCAAATTTTGAACGATTCACACAA 59.994 36.000 13.26 0.00 39.87 3.33
4596 6563 6.375174 TCCTTCAGTCCAACATGATTGTTATG 59.625 38.462 0.00 0.00 44.24 1.90
4698 6665 2.065899 AGGGCTAGCTAGTCACTGAG 57.934 55.000 25.93 0.00 0.00 3.35
4763 6730 2.423446 CGTAGAGGCTCATGGGGC 59.577 66.667 18.26 12.08 0.00 5.80
4765 6732 0.969149 TATGCGTAGAGGCTCATGGG 59.031 55.000 18.26 3.94 0.00 4.00
4811 6778 2.072298 GTAGCACACCTTCAGCTTCTG 58.928 52.381 0.00 0.00 39.68 3.02
4920 6987 3.981211 ACTCAAACCATCACAATTGTGC 58.019 40.909 29.84 0.00 45.25 4.57
5089 7160 5.529581 TTTCCATGTCGAGCATACAGATA 57.470 39.130 0.00 0.00 35.74 1.98
5199 7270 0.043907 CGCGATGCTGATACAACACG 60.044 55.000 0.00 0.00 0.00 4.49
5226 7297 3.127895 ACACACGCACAAAGTACAACATT 59.872 39.130 0.00 0.00 0.00 2.71
5328 7400 1.905215 ACTTCCATCTCCAGGTCACAG 59.095 52.381 0.00 0.00 0.00 3.66
5348 7420 2.359848 GCATTCCAGCATACATGAGCAA 59.640 45.455 0.00 0.00 0.00 3.91
5434 7508 2.977914 TGCCTATCAGTGCAAAGAGAC 58.022 47.619 0.00 0.00 33.87 3.36
5455 7529 8.686334 AGAAGTTTGTAAATCTCAAAGCAAAGA 58.314 29.630 0.00 0.00 35.83 2.52
5471 7545 3.071479 GGAACGGATGCAGAAGTTTGTA 58.929 45.455 0.00 0.00 0.00 2.41
5702 9258 8.347004 TCAAACATTAGCCAACTCATAAATCA 57.653 30.769 0.00 0.00 0.00 2.57
5832 9389 1.843368 AGATTGCCCTGTCATTGGTG 58.157 50.000 0.00 0.00 0.00 4.17
5897 9462 5.353400 TCTGAGCTGTGCTTCAATTCTATTG 59.647 40.000 0.00 0.00 39.88 1.90
5901 9466 3.413846 TCTGAGCTGTGCTTCAATTCT 57.586 42.857 0.00 0.00 39.88 2.40
5913 9478 8.774890 AACTATCATGCTAATTATCTGAGCTG 57.225 34.615 0.00 0.00 37.12 4.24
5935 9500 5.236478 CCGAGACACACAAAGTATCAAAACT 59.764 40.000 0.00 0.00 0.00 2.66
5944 9509 3.680842 GTCCCGAGACACACAAAGT 57.319 52.632 0.00 0.00 42.99 2.66
5970 9535 6.262273 CAGTGTTCACTTGTGTACCCTTTAAT 59.738 38.462 2.47 0.00 0.00 1.40
5982 9547 7.224297 ACCTATAATTGTCAGTGTTCACTTGT 58.776 34.615 2.47 0.00 0.00 3.16
6110 9675 1.882912 TTCTGTGACACATGACAGGC 58.117 50.000 9.11 0.00 40.11 4.85
6112 9677 5.490139 AAACTTTCTGTGACACATGACAG 57.510 39.130 9.11 12.64 40.89 3.51


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

AutoCloner maintained by Alex Coulton.