Multiple sequence alignment - TraesCS3B01G419600

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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 TraesCS3B01G419600 chr3B 100.000 3158 0 0 1 3158 656067954 656064797 0.000000e+00 5832.0
1 TraesCS3B01G419600 chr3B 88.324 531 59 2 2571 3099 66529744 66530273 4.440000e-178 634.0
2 TraesCS3B01G419600 chr3B 91.928 446 36 0 2575 3020 376341648 376342093 2.670000e-175 625.0
3 TraesCS3B01G419600 chr3B 94.382 89 5 0 1 89 141629621 141629533 1.530000e-28 137.0
4 TraesCS3B01G419600 chr3B 94.186 86 5 0 1 86 817225063 817225148 7.110000e-27 132.0
5 TraesCS3B01G419600 chr3A 92.595 1688 69 15 447 2125 638017129 638015489 0.000000e+00 2374.0
6 TraesCS3B01G419600 chr3A 94.505 273 15 0 2226 2498 638015454 638015182 3.770000e-114 422.0
7 TraesCS3B01G419600 chr3A 94.309 123 3 2 329 449 638017395 638017275 5.380000e-43 185.0
8 TraesCS3B01G419600 chr3A 94.118 85 5 0 1 85 131116220 131116136 2.560000e-26 130.0
9 TraesCS3B01G419600 chr3A 91.566 83 5 2 3077 3158 28235539 28235620 2.570000e-21 113.0
10 TraesCS3B01G419600 chr3A 81.633 98 14 4 2993 3086 346867506 346867603 9.390000e-11 78.7
11 TraesCS3B01G419600 chr3D 92.656 1457 67 26 672 2125 496768871 496767452 0.000000e+00 2061.0
12 TraesCS3B01G419600 chr3D 91.704 446 28 3 2132 2574 496767481 496767042 7.490000e-171 610.0
13 TraesCS3B01G419600 chr3D 92.760 221 14 2 447 666 496769278 496769059 5.080000e-83 318.0
14 TraesCS3B01G419600 chr3D 83.533 334 43 7 118 449 496769747 496769424 5.120000e-78 302.0
15 TraesCS3B01G419600 chr5B 84.345 1137 115 36 953 2058 661525094 661523990 0.000000e+00 1055.0
16 TraesCS3B01G419600 chr5B 85.494 972 99 22 1120 2055 661612158 661613123 0.000000e+00 976.0
17 TraesCS3B01G419600 chr5B 92.018 451 36 0 2575 3025 307959574 307960024 4.440000e-178 634.0
18 TraesCS3B01G419600 chr5B 91.667 96 8 0 1955 2050 661863309 661863404 1.980000e-27 134.0
19 TraesCS3B01G419600 chr5B 94.118 85 5 0 1 85 512388029 512387945 2.560000e-26 130.0
20 TraesCS3B01G419600 chr5A 86.880 968 93 15 1120 2058 653475327 653474365 0.000000e+00 1053.0
21 TraesCS3B01G419600 chr5A 85.813 1015 95 23 1082 2055 653563349 653564355 0.000000e+00 1031.0
22 TraesCS3B01G419600 chr5A 94.737 76 1 3 3083 3158 468628405 468628477 7.160000e-22 115.0
23 TraesCS3B01G419600 chr5A 91.566 83 4 3 3077 3158 38010106 38010026 9.260000e-21 111.0
24 TraesCS3B01G419600 chr5D 84.243 1136 111 35 964 2055 526432276 526433387 0.000000e+00 1044.0
25 TraesCS3B01G419600 chr5D 83.762 1127 126 36 966 2058 526411406 526410303 0.000000e+00 1014.0
26 TraesCS3B01G419600 chr5D 88.915 433 36 4 1619 2039 526422496 526422928 1.000000e-144 523.0
27 TraesCS3B01G419600 chr2B 92.444 450 34 0 2575 3024 311854817 311854368 0.000000e+00 643.0
28 TraesCS3B01G419600 chr2B 92.394 447 34 0 2575 3021 367671664 367671218 3.440000e-179 638.0
29 TraesCS3B01G419600 chr2B 94.118 85 5 0 1 85 220441514 220441598 2.560000e-26 130.0
30 TraesCS3B01G419600 chr1B 92.444 450 33 1 2575 3024 216481900 216481452 2.660000e-180 641.0
31 TraesCS3B01G419600 chr1B 94.595 74 4 0 3085 3158 315199138 315199065 7.160000e-22 115.0
32 TraesCS3B01G419600 chr6B 88.658 529 53 6 2575 3099 360383380 360383905 3.440000e-179 638.0
33 TraesCS3B01G419600 chr6B 86.278 532 68 4 2571 3099 360375598 360376127 9.830000e-160 573.0
34 TraesCS3B01G419600 chr6B 94.118 85 5 0 1 85 555475792 555475876 2.560000e-26 130.0
35 TraesCS3B01G419600 chr7B 90.968 465 42 0 2575 3039 345759227 345758763 7.440000e-176 627.0
36 TraesCS3B01G419600 chr7B 95.349 86 4 0 1 86 739923148 739923233 1.530000e-28 137.0
37 TraesCS3B01G419600 chr7B 94.118 85 5 0 1 85 74385698 74385782 2.560000e-26 130.0
38 TraesCS3B01G419600 chr2D 79.318 909 151 27 1152 2052 376356683 376355804 1.250000e-168 603.0
39 TraesCS3B01G419600 chrUn 86.792 106 14 0 1 106 200936056 200936161 5.530000e-23 119.0
40 TraesCS3B01G419600 chrUn 93.671 79 2 3 3081 3158 77000836 77000912 7.160000e-22 115.0
41 TraesCS3B01G419600 chrUn 94.667 75 2 2 3084 3158 254245327 254245399 7.160000e-22 115.0
42 TraesCS3B01G419600 chr1A 92.683 82 3 1 3077 3158 196784303 196784225 7.160000e-22 115.0
43 TraesCS3B01G419600 chr7A 91.667 84 4 3 3075 3158 541341610 541341690 2.570000e-21 113.0
44 TraesCS3B01G419600 chr7A 81.553 103 7 11 2993 3086 344966094 344965995 1.210000e-09 75.0
45 TraesCS3B01G419600 chr4B 93.590 78 2 1 3081 3158 367197017 367197091 2.570000e-21 113.0
46 TraesCS3B01G419600 chr4A 83.146 89 9 5 2993 3077 339430463 339430377 3.380000e-10 76.8
47 TraesCS3B01G419600 chr4A 78.261 115 19 4 2993 3103 281059949 281059837 5.650000e-08 69.4


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 TraesCS3B01G419600 chr3B 656064797 656067954 3157 True 5832.000000 5832 100.00000 1 3158 1 chr3B.!!$R2 3157
1 TraesCS3B01G419600 chr3B 66529744 66530273 529 False 634.000000 634 88.32400 2571 3099 1 chr3B.!!$F1 528
2 TraesCS3B01G419600 chr3A 638015182 638017395 2213 True 993.666667 2374 93.80300 329 2498 3 chr3A.!!$R2 2169
3 TraesCS3B01G419600 chr3D 496767042 496769747 2705 True 822.750000 2061 90.16325 118 2574 4 chr3D.!!$R1 2456
4 TraesCS3B01G419600 chr5B 661523990 661525094 1104 True 1055.000000 1055 84.34500 953 2058 1 chr5B.!!$R2 1105
5 TraesCS3B01G419600 chr5B 661612158 661613123 965 False 976.000000 976 85.49400 1120 2055 1 chr5B.!!$F2 935
6 TraesCS3B01G419600 chr5A 653474365 653475327 962 True 1053.000000 1053 86.88000 1120 2058 1 chr5A.!!$R2 938
7 TraesCS3B01G419600 chr5A 653563349 653564355 1006 False 1031.000000 1031 85.81300 1082 2055 1 chr5A.!!$F2 973
8 TraesCS3B01G419600 chr5D 526432276 526433387 1111 False 1044.000000 1044 84.24300 964 2055 1 chr5D.!!$F2 1091
9 TraesCS3B01G419600 chr5D 526410303 526411406 1103 True 1014.000000 1014 83.76200 966 2058 1 chr5D.!!$R1 1092
10 TraesCS3B01G419600 chr6B 360383380 360383905 525 False 638.000000 638 88.65800 2575 3099 1 chr6B.!!$F2 524
11 TraesCS3B01G419600 chr6B 360375598 360376127 529 False 573.000000 573 86.27800 2571 3099 1 chr6B.!!$F1 528
12 TraesCS3B01G419600 chr2D 376355804 376356683 879 True 603.000000 603 79.31800 1152 2052 1 chr2D.!!$R1 900

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
602 759 0.040058 AGAATCCACAGCAATGCCCA 59.960 50.0 0.0 0.0 0.00 5.36 F
1332 1745 0.108472 CAGCAGAGCAACATCCTCGA 60.108 55.0 0.0 0.0 34.56 4.04 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1951 2406 0.540597 GCCTTGCCTTGGACTCCTTT 60.541 55.0 0.00 0.0 0.0 3.11 R
2766 3226 0.035458 CTGTTTCGTGGCCTTCCTCT 59.965 55.0 3.32 0.0 0.0 3.69 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
23 24 5.422214 AAAGGGTCAGATCGTGAAATACT 57.578 39.130 0.00 0.00 36.74 2.12
24 25 5.422214 AAGGGTCAGATCGTGAAATACTT 57.578 39.130 0.00 0.00 36.74 2.24
25 26 5.422214 AGGGTCAGATCGTGAAATACTTT 57.578 39.130 0.00 0.00 36.74 2.66
26 27 5.420409 AGGGTCAGATCGTGAAATACTTTC 58.580 41.667 0.00 0.00 36.74 2.62
27 28 5.046591 AGGGTCAGATCGTGAAATACTTTCA 60.047 40.000 0.00 0.00 46.68 2.69
45 46 9.825972 ATACTTTCATGTCGAATTTACTTTGTG 57.174 29.630 0.00 0.00 32.32 3.33
46 47 7.925993 ACTTTCATGTCGAATTTACTTTGTGA 58.074 30.769 0.00 0.00 32.32 3.58
47 48 7.855904 ACTTTCATGTCGAATTTACTTTGTGAC 59.144 33.333 0.00 0.00 32.32 3.67
48 49 6.852858 TCATGTCGAATTTACTTTGTGACA 57.147 33.333 0.00 0.00 38.98 3.58
49 50 7.252965 TCATGTCGAATTTACTTTGTGACAA 57.747 32.000 0.00 0.00 38.25 3.18
50 51 7.698628 TCATGTCGAATTTACTTTGTGACAAA 58.301 30.769 10.65 10.65 38.25 2.83
51 52 7.855409 TCATGTCGAATTTACTTTGTGACAAAG 59.145 33.333 30.37 30.37 38.25 2.77
52 53 7.079182 TGTCGAATTTACTTTGTGACAAAGT 57.921 32.000 36.41 36.41 42.53 2.66
53 54 7.531716 TGTCGAATTTACTTTGTGACAAAGTT 58.468 30.769 38.44 25.51 40.58 2.66
54 55 8.024285 TGTCGAATTTACTTTGTGACAAAGTTT 58.976 29.630 38.44 29.08 40.58 2.66
55 56 8.311120 GTCGAATTTACTTTGTGACAAAGTTTG 58.689 33.333 38.44 26.65 40.58 2.93
56 57 7.008810 TCGAATTTACTTTGTGACAAAGTTTGC 59.991 33.333 38.44 24.33 40.58 3.68
57 58 7.009174 CGAATTTACTTTGTGACAAAGTTTGCT 59.991 33.333 38.44 24.57 40.58 3.91
58 59 6.942886 TTTACTTTGTGACAAAGTTTGCTG 57.057 33.333 38.44 16.98 40.58 4.41
59 60 4.782019 ACTTTGTGACAAAGTTTGCTGA 57.218 36.364 31.61 0.00 37.18 4.26
60 61 5.132897 ACTTTGTGACAAAGTTTGCTGAA 57.867 34.783 31.61 0.00 37.18 3.02
61 62 5.537188 ACTTTGTGACAAAGTTTGCTGAAA 58.463 33.333 31.61 8.53 37.18 2.69
62 63 5.634859 ACTTTGTGACAAAGTTTGCTGAAAG 59.365 36.000 31.61 17.68 37.18 2.62
63 64 4.108699 TGTGACAAAGTTTGCTGAAAGG 57.891 40.909 15.59 0.00 0.00 3.11
64 65 3.119173 TGTGACAAAGTTTGCTGAAAGGG 60.119 43.478 15.59 0.00 0.00 3.95
65 66 3.096092 TGACAAAGTTTGCTGAAAGGGT 58.904 40.909 15.59 0.00 0.00 4.34
66 67 3.513515 TGACAAAGTTTGCTGAAAGGGTT 59.486 39.130 15.59 0.00 0.00 4.11
67 68 4.707448 TGACAAAGTTTGCTGAAAGGGTTA 59.293 37.500 15.59 0.00 0.00 2.85
68 69 5.186021 TGACAAAGTTTGCTGAAAGGGTTAA 59.814 36.000 15.59 0.00 0.00 2.01
69 70 6.043854 ACAAAGTTTGCTGAAAGGGTTAAA 57.956 33.333 15.59 0.00 0.00 1.52
70 71 6.468543 ACAAAGTTTGCTGAAAGGGTTAAAA 58.531 32.000 15.59 0.00 0.00 1.52
71 72 7.109501 ACAAAGTTTGCTGAAAGGGTTAAAAT 58.890 30.769 15.59 0.00 0.00 1.82
72 73 8.261522 ACAAAGTTTGCTGAAAGGGTTAAAATA 58.738 29.630 15.59 0.00 0.00 1.40
73 74 8.764287 CAAAGTTTGCTGAAAGGGTTAAAATAG 58.236 33.333 1.96 0.00 0.00 1.73
74 75 7.597288 AGTTTGCTGAAAGGGTTAAAATAGT 57.403 32.000 0.00 0.00 0.00 2.12
75 76 7.433680 AGTTTGCTGAAAGGGTTAAAATAGTG 58.566 34.615 0.00 0.00 0.00 2.74
76 77 7.286775 AGTTTGCTGAAAGGGTTAAAATAGTGA 59.713 33.333 0.00 0.00 0.00 3.41
77 78 7.775053 TTGCTGAAAGGGTTAAAATAGTGAT 57.225 32.000 0.00 0.00 0.00 3.06
78 79 7.775053 TGCTGAAAGGGTTAAAATAGTGATT 57.225 32.000 0.00 0.00 0.00 2.57
79 80 8.189119 TGCTGAAAGGGTTAAAATAGTGATTT 57.811 30.769 0.00 0.00 36.82 2.17
80 81 8.646900 TGCTGAAAGGGTTAAAATAGTGATTTT 58.353 29.630 1.65 1.65 45.29 1.82
81 82 8.925700 GCTGAAAGGGTTAAAATAGTGATTTTG 58.074 33.333 6.01 0.00 43.58 2.44
82 83 9.423061 CTGAAAGGGTTAAAATAGTGATTTTGG 57.577 33.333 6.01 0.00 43.58 3.28
83 84 7.875554 TGAAAGGGTTAAAATAGTGATTTTGGC 59.124 33.333 6.01 0.17 43.58 4.52
84 85 6.294361 AGGGTTAAAATAGTGATTTTGGCC 57.706 37.500 0.00 0.00 43.58 5.36
85 86 6.022958 AGGGTTAAAATAGTGATTTTGGCCT 58.977 36.000 3.32 0.00 43.58 5.19
86 87 6.154534 AGGGTTAAAATAGTGATTTTGGCCTC 59.845 38.462 3.32 0.00 43.58 4.70
87 88 6.071051 GGGTTAAAATAGTGATTTTGGCCTCA 60.071 38.462 3.32 0.00 43.58 3.86
88 89 7.035612 GGTTAAAATAGTGATTTTGGCCTCAG 58.964 38.462 3.32 0.00 43.58 3.35
89 90 5.665916 AAAATAGTGATTTTGGCCTCAGG 57.334 39.130 3.32 0.00 42.46 3.86
90 91 3.448660 AAATAGTGATTTTGGCCTCAGGC 59.551 43.478 7.37 7.37 38.96 4.85
91 92 5.938004 AAATAGTGATTTTGGCCTCAGGCG 61.938 45.833 10.39 0.00 39.93 5.52
116 117 3.873812 CCGGGCCGCCCTAGATTT 61.874 66.667 26.29 0.00 42.67 2.17
117 118 2.591715 CGGGCCGCCCTAGATTTG 60.592 66.667 26.29 4.81 42.67 2.32
118 119 2.203351 GGGCCGCCCTAGATTTGG 60.203 66.667 22.31 0.00 41.34 3.28
131 132 3.210012 ATTTGGGCTGCCGGTCAGT 62.210 57.895 21.68 3.93 44.66 3.41
144 145 1.005867 GTCAGTCCGGGCGTTTGTA 60.006 57.895 0.00 0.00 0.00 2.41
145 146 1.005867 TCAGTCCGGGCGTTTGTAC 60.006 57.895 0.00 0.00 0.00 2.90
161 162 1.202557 TGTACGCGGTTTGAGAGGTTT 60.203 47.619 12.47 0.00 0.00 3.27
163 164 0.179067 ACGCGGTTTGAGAGGTTTGA 60.179 50.000 12.47 0.00 0.00 2.69
175 179 5.208121 TGAGAGGTTTGATTGGGTCTTTTT 58.792 37.500 0.00 0.00 0.00 1.94
193 197 2.940994 TTTTTGACTGGTGGATCGGA 57.059 45.000 0.00 0.00 0.00 4.55
197 201 3.718210 GACTGGTGGATCGGACGGC 62.718 68.421 0.00 0.00 0.00 5.68
212 216 2.187946 GGCCTGTCCGGACATCTG 59.812 66.667 36.21 26.49 42.15 2.90
213 217 2.359169 GGCCTGTCCGGACATCTGA 61.359 63.158 36.21 14.57 42.15 3.27
214 218 1.142748 GCCTGTCCGGACATCTGAG 59.857 63.158 36.21 23.62 41.01 3.35
215 219 1.323271 GCCTGTCCGGACATCTGAGA 61.323 60.000 36.21 13.02 41.01 3.27
216 220 0.457851 CCTGTCCGGACATCTGAGAC 59.542 60.000 36.21 7.52 41.01 3.36
217 221 0.099613 CTGTCCGGACATCTGAGACG 59.900 60.000 36.21 18.79 41.01 4.18
218 222 1.313091 TGTCCGGACATCTGAGACGG 61.313 60.000 33.23 3.12 45.52 4.79
219 223 1.753078 TCCGGACATCTGAGACGGG 60.753 63.158 0.00 0.00 44.36 5.28
220 224 2.052690 CCGGACATCTGAGACGGGT 61.053 63.158 0.00 0.00 40.79 5.28
221 225 0.750546 CCGGACATCTGAGACGGGTA 60.751 60.000 0.00 0.00 40.79 3.69
222 226 0.381089 CGGACATCTGAGACGGGTAC 59.619 60.000 0.00 0.00 0.00 3.34
231 235 2.753043 GACGGGTACGAGAGGGCA 60.753 66.667 0.00 0.00 44.60 5.36
233 237 3.528370 CGGGTACGAGAGGGCAGG 61.528 72.222 0.00 0.00 44.60 4.85
234 238 3.155167 GGGTACGAGAGGGCAGGG 61.155 72.222 0.00 0.00 0.00 4.45
245 249 1.147153 GGGCAGGGTGTAGATGCTC 59.853 63.158 0.00 0.00 39.88 4.26
248 252 0.175760 GCAGGGTGTAGATGCTCGAA 59.824 55.000 0.00 0.00 37.00 3.71
249 253 1.405526 GCAGGGTGTAGATGCTCGAAA 60.406 52.381 0.00 0.00 37.00 3.46
250 254 2.544685 CAGGGTGTAGATGCTCGAAAG 58.455 52.381 0.00 0.00 0.00 2.62
265 269 3.002791 TCGAAAGCTTAGCTGAATGGTG 58.997 45.455 7.77 0.00 39.62 4.17
270 274 1.718757 CTTAGCTGAATGGTGCGGGC 61.719 60.000 0.00 0.00 0.00 6.13
292 296 3.307242 CGACAACAGCTAAGAGCATAACC 59.693 47.826 0.64 0.00 45.56 2.85
302 306 3.460857 AGAGCATAACCGAGAATGACC 57.539 47.619 0.00 0.00 0.00 4.02
305 309 1.859080 GCATAACCGAGAATGACCGAC 59.141 52.381 0.00 0.00 0.00 4.79
314 318 4.348656 CGAGAATGACCGACGAAGAAATA 58.651 43.478 0.00 0.00 0.00 1.40
340 344 1.788308 CATACGACAAAACCGACGTGT 59.212 47.619 0.00 0.00 37.79 4.49
355 359 3.693654 GACGTGTTTTCGGGCTTAAAAA 58.306 40.909 0.00 0.00 34.94 1.94
356 360 3.697982 ACGTGTTTTCGGGCTTAAAAAG 58.302 40.909 0.00 0.00 34.94 2.27
458 612 1.608025 GCTTCACAGACACGGATGGAA 60.608 52.381 0.00 0.00 0.00 3.53
528 684 6.919662 CAGCATGCAATATTTTAGTCGGAATT 59.080 34.615 21.98 0.00 0.00 2.17
554 710 1.670811 AGGAACACAACTGCTTCAACG 59.329 47.619 0.00 0.00 0.00 4.10
602 759 0.040058 AGAATCCACAGCAATGCCCA 59.960 50.000 0.00 0.00 0.00 5.36
626 783 0.323629 ATGATCGTGGAACCGGTGTT 59.676 50.000 8.52 0.00 37.42 3.32
756 1112 1.527311 GCACCGACAAAACTCTCTGTC 59.473 52.381 0.00 0.00 38.87 3.51
757 1113 2.803492 GCACCGACAAAACTCTCTGTCT 60.803 50.000 1.21 0.00 39.87 3.41
758 1114 2.797156 CACCGACAAAACTCTCTGTCTG 59.203 50.000 1.21 0.00 39.87 3.51
759 1115 2.431057 ACCGACAAAACTCTCTGTCTGT 59.569 45.455 1.21 0.00 39.87 3.41
762 1118 4.112634 CGACAAAACTCTCTGTCTGTTCA 58.887 43.478 1.21 0.00 39.87 3.18
777 1133 0.251209 GTTCAGAACCCCCACTTCCC 60.251 60.000 1.29 0.00 0.00 3.97
928 1287 1.912763 GCCATGGCCAAACAGGGAA 60.913 57.895 27.24 0.00 44.73 3.97
1031 1395 1.444553 CACTCGGCGTCTGGAGTTC 60.445 63.158 6.85 0.00 41.37 3.01
1047 1419 1.279271 AGTTCGGGGAGGAGATTGTTG 59.721 52.381 0.00 0.00 0.00 3.33
1077 1449 3.463505 CGCTTGTGGTGACGCTAG 58.536 61.111 0.00 0.00 44.86 3.42
1332 1745 0.108472 CAGCAGAGCAACATCCTCGA 60.108 55.000 0.00 0.00 34.56 4.04
1401 1814 1.292223 CGTCCAGTTCCACGGATGT 59.708 57.895 0.00 0.00 34.20 3.06
1432 1851 1.640069 CGCGGCTGATCAATGTCTG 59.360 57.895 0.00 0.00 0.00 3.51
1498 1935 0.108756 CCCTCTTTTCTCGGGTCGTC 60.109 60.000 0.00 0.00 33.16 4.20
1540 1977 1.301479 GTTCCTGACCTCGCCGTTT 60.301 57.895 0.00 0.00 0.00 3.60
1951 2406 4.722535 AGGAGCAAGAGGGGGCGA 62.723 66.667 0.00 0.00 34.54 5.54
2095 2550 2.235650 TCATCCCTCAGTGCAGAGAAAG 59.764 50.000 4.59 0.00 37.87 2.62
2106 2561 6.263842 TCAGTGCAGAGAAAGAAAACATCAAT 59.736 34.615 0.00 0.00 0.00 2.57
2144 2599 7.763172 TTTTTGACCACAAACATCAATACAC 57.237 32.000 0.00 0.00 44.22 2.90
2145 2600 6.456795 TTTGACCACAAACATCAATACACA 57.543 33.333 0.00 0.00 40.47 3.72
2146 2601 6.647334 TTGACCACAAACATCAATACACAT 57.353 33.333 0.00 0.00 32.73 3.21
2147 2602 6.647334 TGACCACAAACATCAATACACATT 57.353 33.333 0.00 0.00 0.00 2.71
2148 2603 6.676950 TGACCACAAACATCAATACACATTC 58.323 36.000 0.00 0.00 0.00 2.67
2149 2604 6.489700 TGACCACAAACATCAATACACATTCT 59.510 34.615 0.00 0.00 0.00 2.40
2150 2605 7.014134 TGACCACAAACATCAATACACATTCTT 59.986 33.333 0.00 0.00 0.00 2.52
2151 2606 7.725251 ACCACAAACATCAATACACATTCTTT 58.275 30.769 0.00 0.00 0.00 2.52
2152 2607 8.855110 ACCACAAACATCAATACACATTCTTTA 58.145 29.630 0.00 0.00 0.00 1.85
2153 2608 9.859427 CCACAAACATCAATACACATTCTTTAT 57.141 29.630 0.00 0.00 0.00 1.40
2195 2651 0.250124 TTAGGGCATATGGGCGAACG 60.250 55.000 4.56 0.00 44.56 3.95
2196 2652 1.404479 TAGGGCATATGGGCGAACGT 61.404 55.000 4.56 0.00 44.56 3.99
2197 2653 1.822186 GGGCATATGGGCGAACGTT 60.822 57.895 0.00 0.00 44.56 3.99
2198 2654 1.381165 GGGCATATGGGCGAACGTTT 61.381 55.000 0.46 0.00 44.56 3.60
2199 2655 0.454196 GGCATATGGGCGAACGTTTT 59.546 50.000 0.46 0.00 33.57 2.43
2364 2821 9.846248 TTTTGCTTCTTCTTCTATTTAATCAGC 57.154 29.630 0.00 0.00 0.00 4.26
2366 2823 7.041721 TGCTTCTTCTTCTATTTAATCAGCGA 58.958 34.615 0.00 0.00 0.00 4.93
2399 2856 4.746115 TGTACCTCGTGAAACATGTACAAC 59.254 41.667 0.00 0.00 35.74 3.32
2508 2968 7.421530 TTGTCTACTAGCACATTCACTTTTC 57.578 36.000 0.00 0.00 0.00 2.29
2513 2973 5.615289 ACTAGCACATTCACTTTTCAGAGT 58.385 37.500 0.00 0.00 0.00 3.24
2515 2975 4.454678 AGCACATTCACTTTTCAGAGTCA 58.545 39.130 0.00 0.00 0.00 3.41
2517 2977 5.533903 AGCACATTCACTTTTCAGAGTCAAT 59.466 36.000 0.00 0.00 0.00 2.57
2520 2980 8.668353 GCACATTCACTTTTCAGAGTCAATATA 58.332 33.333 0.00 0.00 0.00 0.86
2549 3009 5.308497 TGAATGACTAGAAGGGTGGTTGTAA 59.692 40.000 0.00 0.00 0.00 2.41
2600 3060 0.683973 GAGCATCCCACGATCATCCT 59.316 55.000 0.00 0.00 0.00 3.24
2620 3080 5.386060 TCCTCATGGACGTATCTACATCTT 58.614 41.667 0.00 0.00 37.46 2.40
2621 3081 5.833667 TCCTCATGGACGTATCTACATCTTT 59.166 40.000 0.00 0.00 37.46 2.52
2629 3089 6.132791 ACGTATCTACATCTTTCACGACAT 57.867 37.500 0.00 0.00 0.00 3.06
2632 3092 6.858478 CGTATCTACATCTTTCACGACATCAT 59.142 38.462 0.00 0.00 0.00 2.45
2700 3160 0.252479 ACTCGCTCCTCTCCGAACTA 59.748 55.000 0.00 0.00 32.56 2.24
2766 3226 7.476540 AACACTATGTGTGATCAGGTACTTA 57.523 36.000 0.00 0.00 46.79 2.24
2970 3430 3.322466 CAGCCGACCCAAGTCCCT 61.322 66.667 0.00 0.00 40.12 4.20
2998 3458 4.477975 GCTACAGCGAGCGGACGT 62.478 66.667 1.67 0.00 35.59 4.34
3033 3493 0.037139 CGACCGGTAATTCCACACCA 60.037 55.000 7.34 0.00 34.25 4.17
3036 3496 1.278127 ACCGGTAATTCCACACCAGAG 59.722 52.381 4.49 0.00 34.25 3.35
3037 3497 1.369625 CGGTAATTCCACACCAGAGC 58.630 55.000 0.00 0.00 34.25 4.09
3039 3499 1.004277 GGTAATTCCACACCAGAGCCA 59.996 52.381 0.00 0.00 34.77 4.75
3040 3500 2.554344 GGTAATTCCACACCAGAGCCAA 60.554 50.000 0.00 0.00 34.77 4.52
3041 3501 1.620822 AATTCCACACCAGAGCCAAC 58.379 50.000 0.00 0.00 0.00 3.77
3058 3520 2.202676 CTCTGCGAGACCGAAGCC 60.203 66.667 0.00 0.00 41.26 4.35
3102 3564 3.637273 GGCCACCTCCGGACTGTT 61.637 66.667 0.00 0.00 0.00 3.16
3103 3565 2.358737 GCCACCTCCGGACTGTTG 60.359 66.667 0.00 0.00 0.00 3.33
3104 3566 2.347490 CCACCTCCGGACTGTTGG 59.653 66.667 0.00 1.67 0.00 3.77
3105 3567 2.347490 CACCTCCGGACTGTTGGG 59.653 66.667 0.00 0.76 0.00 4.12
3106 3568 2.928396 ACCTCCGGACTGTTGGGG 60.928 66.667 0.00 0.00 0.00 4.96
3107 3569 2.606519 CCTCCGGACTGTTGGGGA 60.607 66.667 0.00 0.00 0.00 4.81
3108 3570 2.221299 CCTCCGGACTGTTGGGGAA 61.221 63.158 0.00 0.00 0.00 3.97
3109 3571 1.003718 CTCCGGACTGTTGGGGAAC 60.004 63.158 0.00 0.00 0.00 3.62
3110 3572 2.358247 CCGGACTGTTGGGGAACG 60.358 66.667 0.00 0.00 0.00 3.95
3111 3573 2.424302 CGGACTGTTGGGGAACGT 59.576 61.111 0.00 0.00 0.00 3.99
3112 3574 1.667151 CGGACTGTTGGGGAACGTA 59.333 57.895 0.00 0.00 0.00 3.57
3113 3575 0.389426 CGGACTGTTGGGGAACGTAG 60.389 60.000 0.00 0.00 0.00 3.51
3114 3576 0.672711 GGACTGTTGGGGAACGTAGC 60.673 60.000 0.00 0.00 0.00 3.58
3115 3577 0.034337 GACTGTTGGGGAACGTAGCA 59.966 55.000 0.00 0.00 0.00 3.49
3116 3578 0.034896 ACTGTTGGGGAACGTAGCAG 59.965 55.000 0.00 0.00 34.29 4.24
3117 3579 0.320374 CTGTTGGGGAACGTAGCAGA 59.680 55.000 0.00 0.00 31.30 4.26
3118 3580 0.759959 TGTTGGGGAACGTAGCAGAA 59.240 50.000 0.00 0.00 0.00 3.02
3119 3581 1.141254 TGTTGGGGAACGTAGCAGAAA 59.859 47.619 0.00 0.00 0.00 2.52
3120 3582 2.224670 TGTTGGGGAACGTAGCAGAAAT 60.225 45.455 0.00 0.00 0.00 2.17
3121 3583 2.817844 GTTGGGGAACGTAGCAGAAATT 59.182 45.455 0.00 0.00 0.00 1.82
3122 3584 2.706890 TGGGGAACGTAGCAGAAATTC 58.293 47.619 0.00 0.00 0.00 2.17
3123 3585 2.039216 TGGGGAACGTAGCAGAAATTCA 59.961 45.455 0.00 0.00 0.00 2.57
3124 3586 3.078837 GGGGAACGTAGCAGAAATTCAA 58.921 45.455 0.00 0.00 0.00 2.69
3125 3587 3.504520 GGGGAACGTAGCAGAAATTCAAA 59.495 43.478 0.00 0.00 0.00 2.69
3126 3588 4.022676 GGGGAACGTAGCAGAAATTCAAAA 60.023 41.667 0.00 0.00 0.00 2.44
3127 3589 5.336451 GGGGAACGTAGCAGAAATTCAAAAT 60.336 40.000 0.00 0.00 0.00 1.82
3128 3590 6.156519 GGGAACGTAGCAGAAATTCAAAATT 58.843 36.000 0.00 0.00 0.00 1.82
3129 3591 6.645003 GGGAACGTAGCAGAAATTCAAAATTT 59.355 34.615 0.00 0.00 0.00 1.82
3130 3592 7.170828 GGGAACGTAGCAGAAATTCAAAATTTT 59.829 33.333 0.00 0.00 0.00 1.82
3131 3593 8.214472 GGAACGTAGCAGAAATTCAAAATTTTC 58.786 33.333 0.00 0.00 33.08 2.29
3132 3594 7.637709 ACGTAGCAGAAATTCAAAATTTTCC 57.362 32.000 0.00 0.00 33.30 3.13
3133 3595 7.433680 ACGTAGCAGAAATTCAAAATTTTCCT 58.566 30.769 0.00 0.86 33.30 3.36
3134 3596 8.573035 ACGTAGCAGAAATTCAAAATTTTCCTA 58.427 29.630 0.00 0.00 33.30 2.94
3135 3597 8.850452 CGTAGCAGAAATTCAAAATTTTCCTAC 58.150 33.333 0.00 13.60 33.30 3.18
3136 3598 7.873739 AGCAGAAATTCAAAATTTTCCTACG 57.126 32.000 0.00 0.00 33.30 3.51
3137 3599 7.433680 AGCAGAAATTCAAAATTTTCCTACGT 58.566 30.769 0.00 0.00 33.30 3.57
3138 3600 7.382218 AGCAGAAATTCAAAATTTTCCTACGTG 59.618 33.333 0.00 0.00 33.30 4.49
3139 3601 7.169140 GCAGAAATTCAAAATTTTCCTACGTGT 59.831 33.333 0.00 0.00 33.30 4.49
3140 3602 8.690840 CAGAAATTCAAAATTTTCCTACGTGTC 58.309 33.333 0.00 0.00 33.30 3.67
3141 3603 8.410141 AGAAATTCAAAATTTTCCTACGTGTCA 58.590 29.630 0.00 0.00 33.30 3.58
3142 3604 7.924103 AATTCAAAATTTTCCTACGTGTCAC 57.076 32.000 0.00 0.00 0.00 3.67
3143 3605 5.427036 TCAAAATTTTCCTACGTGTCACC 57.573 39.130 0.00 0.00 0.00 4.02
3144 3606 4.882427 TCAAAATTTTCCTACGTGTCACCA 59.118 37.500 0.00 0.00 0.00 4.17
3145 3607 5.357314 TCAAAATTTTCCTACGTGTCACCAA 59.643 36.000 0.00 0.00 0.00 3.67
3146 3608 5.432885 AAATTTTCCTACGTGTCACCAAG 57.567 39.130 0.00 0.00 0.00 3.61
3147 3609 3.823281 TTTTCCTACGTGTCACCAAGA 57.177 42.857 0.00 0.00 0.00 3.02
3148 3610 4.345859 TTTTCCTACGTGTCACCAAGAT 57.654 40.909 0.00 0.00 0.00 2.40
3149 3611 3.587797 TTCCTACGTGTCACCAAGATC 57.412 47.619 0.00 0.00 0.00 2.75
3150 3612 2.803956 TCCTACGTGTCACCAAGATCT 58.196 47.619 0.00 0.00 0.00 2.75
3151 3613 3.959293 TCCTACGTGTCACCAAGATCTA 58.041 45.455 0.00 0.00 0.00 1.98
3152 3614 4.533815 TCCTACGTGTCACCAAGATCTAT 58.466 43.478 0.00 0.00 0.00 1.98
3153 3615 4.579340 TCCTACGTGTCACCAAGATCTATC 59.421 45.833 0.00 0.00 0.00 2.08
3154 3616 4.580995 CCTACGTGTCACCAAGATCTATCT 59.419 45.833 0.00 0.00 39.22 1.98
3155 3617 5.763698 CCTACGTGTCACCAAGATCTATCTA 59.236 44.000 0.00 0.00 35.76 1.98
3156 3618 6.431543 CCTACGTGTCACCAAGATCTATCTAT 59.568 42.308 0.00 0.00 35.76 1.98
3157 3619 6.078202 ACGTGTCACCAAGATCTATCTATG 57.922 41.667 0.00 0.00 35.76 2.23
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 5.805728 AGTATTTCACGATCTGACCCTTTT 58.194 37.500 0.00 0.00 0.00 2.27
1 2 5.422214 AGTATTTCACGATCTGACCCTTT 57.578 39.130 0.00 0.00 0.00 3.11
2 3 5.422214 AAGTATTTCACGATCTGACCCTT 57.578 39.130 0.00 0.00 0.00 3.95
3 4 5.422214 AAAGTATTTCACGATCTGACCCT 57.578 39.130 0.00 0.00 27.08 4.34
19 20 9.825972 CACAAAGTAAATTCGACATGAAAGTAT 57.174 29.630 0.00 0.00 40.71 2.12
20 21 9.047371 TCACAAAGTAAATTCGACATGAAAGTA 57.953 29.630 0.00 0.00 40.71 2.24
21 22 7.855904 GTCACAAAGTAAATTCGACATGAAAGT 59.144 33.333 0.00 0.00 40.71 2.66
22 23 7.855409 TGTCACAAAGTAAATTCGACATGAAAG 59.145 33.333 0.00 0.00 40.71 2.62
23 24 7.698628 TGTCACAAAGTAAATTCGACATGAAA 58.301 30.769 0.00 0.00 40.71 2.69
24 25 7.252965 TGTCACAAAGTAAATTCGACATGAA 57.747 32.000 0.00 0.00 41.81 2.57
25 26 6.852858 TGTCACAAAGTAAATTCGACATGA 57.147 33.333 0.00 0.00 0.00 3.07
26 27 7.643764 ACTTTGTCACAAAGTAAATTCGACATG 59.356 33.333 30.56 4.67 38.58 3.21
27 28 7.703328 ACTTTGTCACAAAGTAAATTCGACAT 58.297 30.769 30.56 5.09 38.58 3.06
28 29 7.079182 ACTTTGTCACAAAGTAAATTCGACA 57.921 32.000 30.56 4.80 38.58 4.35
29 30 7.964545 AACTTTGTCACAAAGTAAATTCGAC 57.035 32.000 31.47 3.23 39.36 4.20
30 31 7.008810 GCAAACTTTGTCACAAAGTAAATTCGA 59.991 33.333 31.47 0.00 39.36 3.71
31 32 7.009174 AGCAAACTTTGTCACAAAGTAAATTCG 59.991 33.333 31.47 18.23 39.36 3.34
32 33 8.110002 CAGCAAACTTTGTCACAAAGTAAATTC 58.890 33.333 31.47 19.49 39.36 2.17
33 34 7.816995 TCAGCAAACTTTGTCACAAAGTAAATT 59.183 29.630 31.47 21.03 39.36 1.82
34 35 7.319646 TCAGCAAACTTTGTCACAAAGTAAAT 58.680 30.769 31.47 19.64 39.36 1.40
35 36 6.682746 TCAGCAAACTTTGTCACAAAGTAAA 58.317 32.000 31.47 13.61 39.36 2.01
36 37 6.260870 TCAGCAAACTTTGTCACAAAGTAA 57.739 33.333 31.47 13.30 39.36 2.24
37 38 5.888691 TCAGCAAACTTTGTCACAAAGTA 57.111 34.783 31.47 15.37 39.36 2.24
38 39 4.782019 TCAGCAAACTTTGTCACAAAGT 57.218 36.364 27.17 27.17 41.82 2.66
39 40 5.062558 CCTTTCAGCAAACTTTGTCACAAAG 59.937 40.000 25.84 25.84 0.00 2.77
40 41 4.928615 CCTTTCAGCAAACTTTGTCACAAA 59.071 37.500 2.24 2.24 0.00 2.83
41 42 4.493547 CCTTTCAGCAAACTTTGTCACAA 58.506 39.130 3.48 0.00 0.00 3.33
42 43 3.119173 CCCTTTCAGCAAACTTTGTCACA 60.119 43.478 3.48 0.00 0.00 3.58
43 44 3.119137 ACCCTTTCAGCAAACTTTGTCAC 60.119 43.478 3.48 0.00 0.00 3.67
44 45 3.096092 ACCCTTTCAGCAAACTTTGTCA 58.904 40.909 3.48 0.00 0.00 3.58
45 46 3.801114 ACCCTTTCAGCAAACTTTGTC 57.199 42.857 3.48 0.00 0.00 3.18
46 47 5.669164 TTAACCCTTTCAGCAAACTTTGT 57.331 34.783 3.48 0.00 0.00 2.83
47 48 6.976636 TTTTAACCCTTTCAGCAAACTTTG 57.023 33.333 0.00 0.00 0.00 2.77
48 49 8.482943 ACTATTTTAACCCTTTCAGCAAACTTT 58.517 29.630 0.00 0.00 0.00 2.66
49 50 7.926018 CACTATTTTAACCCTTTCAGCAAACTT 59.074 33.333 0.00 0.00 0.00 2.66
50 51 7.286775 TCACTATTTTAACCCTTTCAGCAAACT 59.713 33.333 0.00 0.00 0.00 2.66
51 52 7.430441 TCACTATTTTAACCCTTTCAGCAAAC 58.570 34.615 0.00 0.00 0.00 2.93
52 53 7.589958 TCACTATTTTAACCCTTTCAGCAAA 57.410 32.000 0.00 0.00 0.00 3.68
53 54 7.775053 ATCACTATTTTAACCCTTTCAGCAA 57.225 32.000 0.00 0.00 0.00 3.91
54 55 7.775053 AATCACTATTTTAACCCTTTCAGCA 57.225 32.000 0.00 0.00 0.00 4.41
55 56 8.925700 CAAAATCACTATTTTAACCCTTTCAGC 58.074 33.333 0.00 0.00 42.18 4.26
56 57 9.423061 CCAAAATCACTATTTTAACCCTTTCAG 57.577 33.333 0.00 0.00 42.18 3.02
57 58 7.875554 GCCAAAATCACTATTTTAACCCTTTCA 59.124 33.333 0.00 0.00 42.18 2.69
58 59 7.333423 GGCCAAAATCACTATTTTAACCCTTTC 59.667 37.037 0.00 0.00 42.18 2.62
59 60 7.017155 AGGCCAAAATCACTATTTTAACCCTTT 59.983 33.333 5.01 0.00 42.18 3.11
60 61 6.500400 AGGCCAAAATCACTATTTTAACCCTT 59.500 34.615 5.01 0.00 42.18 3.95
61 62 6.022958 AGGCCAAAATCACTATTTTAACCCT 58.977 36.000 5.01 0.00 42.18 4.34
62 63 6.071051 TGAGGCCAAAATCACTATTTTAACCC 60.071 38.462 5.01 0.00 42.18 4.11
63 64 6.930731 TGAGGCCAAAATCACTATTTTAACC 58.069 36.000 5.01 0.00 42.18 2.85
64 65 7.035612 CCTGAGGCCAAAATCACTATTTTAAC 58.964 38.462 5.01 0.00 42.18 2.01
65 66 6.350949 GCCTGAGGCCAAAATCACTATTTTAA 60.351 38.462 13.77 0.00 41.68 1.52
66 67 5.127031 GCCTGAGGCCAAAATCACTATTTTA 59.873 40.000 13.77 0.00 41.68 1.52
67 68 4.081476 GCCTGAGGCCAAAATCACTATTTT 60.081 41.667 13.77 0.00 44.06 1.82
68 69 3.448660 GCCTGAGGCCAAAATCACTATTT 59.551 43.478 13.77 0.00 44.06 1.40
69 70 3.026694 GCCTGAGGCCAAAATCACTATT 58.973 45.455 13.77 0.00 44.06 1.73
70 71 2.659428 GCCTGAGGCCAAAATCACTAT 58.341 47.619 13.77 0.00 44.06 2.12
71 72 2.128771 GCCTGAGGCCAAAATCACTA 57.871 50.000 13.77 0.00 44.06 2.74
72 73 2.967270 GCCTGAGGCCAAAATCACT 58.033 52.632 13.77 0.00 44.06 3.41
101 102 2.203351 CCAAATCTAGGGCGGCCC 60.203 66.667 31.03 31.03 45.90 5.80
102 103 2.203351 CCCAAATCTAGGGCGGCC 60.203 66.667 22.67 22.67 39.96 6.13
108 109 1.526917 CCGGCAGCCCAAATCTAGG 60.527 63.158 5.63 0.00 0.00 3.02
109 110 0.815615 GACCGGCAGCCCAAATCTAG 60.816 60.000 5.63 0.00 0.00 2.43
110 111 1.223487 GACCGGCAGCCCAAATCTA 59.777 57.895 5.63 0.00 0.00 1.98
111 112 2.044946 GACCGGCAGCCCAAATCT 60.045 61.111 5.63 0.00 0.00 2.40
112 113 2.361104 TGACCGGCAGCCCAAATC 60.361 61.111 5.63 0.00 0.00 2.17
113 114 2.361610 CTGACCGGCAGCCCAAAT 60.362 61.111 5.63 0.00 37.90 2.32
138 139 1.193874 CCTCTCAAACCGCGTACAAAC 59.806 52.381 4.92 0.00 0.00 2.93
144 145 0.179067 TCAAACCTCTCAAACCGCGT 60.179 50.000 4.92 0.00 0.00 6.01
145 146 1.156736 ATCAAACCTCTCAAACCGCG 58.843 50.000 0.00 0.00 0.00 6.46
147 148 2.228822 CCCAATCAAACCTCTCAAACCG 59.771 50.000 0.00 0.00 0.00 4.44
175 179 1.606994 CGTCCGATCCACCAGTCAAAA 60.607 52.381 0.00 0.00 0.00 2.44
197 201 0.457851 GTCTCAGATGTCCGGACAGG 59.542 60.000 37.98 28.97 45.48 4.00
206 210 1.065636 TCTCGTACCCGTCTCAGATGT 60.066 52.381 0.00 0.00 35.01 3.06
208 212 1.475392 CCTCTCGTACCCGTCTCAGAT 60.475 57.143 0.00 0.00 35.01 2.90
210 214 1.096386 CCCTCTCGTACCCGTCTCAG 61.096 65.000 0.00 0.00 35.01 3.35
212 216 2.479750 GCCCTCTCGTACCCGTCTC 61.480 68.421 0.00 0.00 35.01 3.36
213 217 2.439883 GCCCTCTCGTACCCGTCT 60.440 66.667 0.00 0.00 35.01 4.18
214 218 2.753043 TGCCCTCTCGTACCCGTC 60.753 66.667 0.00 0.00 35.01 4.79
215 219 2.754658 CTGCCCTCTCGTACCCGT 60.755 66.667 0.00 0.00 35.01 5.28
216 220 3.528370 CCTGCCCTCTCGTACCCG 61.528 72.222 0.00 0.00 0.00 5.28
217 221 3.155167 CCCTGCCCTCTCGTACCC 61.155 72.222 0.00 0.00 0.00 3.69
218 222 2.363925 ACCCTGCCCTCTCGTACC 60.364 66.667 0.00 0.00 0.00 3.34
219 223 0.682209 TACACCCTGCCCTCTCGTAC 60.682 60.000 0.00 0.00 0.00 3.67
220 224 0.395311 CTACACCCTGCCCTCTCGTA 60.395 60.000 0.00 0.00 0.00 3.43
221 225 1.682684 CTACACCCTGCCCTCTCGT 60.683 63.158 0.00 0.00 0.00 4.18
222 226 0.757188 ATCTACACCCTGCCCTCTCG 60.757 60.000 0.00 0.00 0.00 4.04
231 235 1.134670 GCTTTCGAGCATCTACACCCT 60.135 52.381 0.00 0.00 34.41 4.34
233 237 2.301577 AGCTTTCGAGCATCTACACC 57.698 50.000 0.88 0.00 37.25 4.16
234 238 3.244111 GCTAAGCTTTCGAGCATCTACAC 59.756 47.826 13.64 0.00 36.20 2.90
245 249 2.476854 GCACCATTCAGCTAAGCTTTCG 60.477 50.000 3.20 0.00 36.40 3.46
248 252 1.089920 CGCACCATTCAGCTAAGCTT 58.910 50.000 3.48 3.48 36.40 3.74
249 253 0.745845 CCGCACCATTCAGCTAAGCT 60.746 55.000 0.00 0.00 40.77 3.74
250 254 1.718757 CCCGCACCATTCAGCTAAGC 61.719 60.000 0.00 0.00 0.00 3.09
251 255 1.718757 GCCCGCACCATTCAGCTAAG 61.719 60.000 0.00 0.00 0.00 2.18
265 269 2.740714 CTTAGCTGTTGTCGCCCGC 61.741 63.158 0.00 0.00 0.00 6.13
270 274 3.307242 GGTTATGCTCTTAGCTGTTGTCG 59.693 47.826 0.00 0.00 42.97 4.35
292 296 2.257974 TTCTTCGTCGGTCATTCTCG 57.742 50.000 0.00 0.00 0.00 4.04
302 306 5.684184 TCGTATGTTCCATATTTCTTCGTCG 59.316 40.000 0.00 0.00 0.00 5.12
305 309 6.822073 TGTCGTATGTTCCATATTTCTTCG 57.178 37.500 0.00 0.00 0.00 3.79
314 318 3.434299 GTCGGTTTTGTCGTATGTTCCAT 59.566 43.478 0.00 0.00 0.00 3.41
324 328 2.162371 AAAACACGTCGGTTTTGTCG 57.838 45.000 17.90 0.00 46.19 4.35
340 344 5.855740 TTCTTCCTTTTTAAGCCCGAAAA 57.144 34.783 0.00 0.00 0.00 2.29
355 359 4.065789 GTTTCTCCGTGACAATTCTTCCT 58.934 43.478 0.00 0.00 0.00 3.36
356 360 3.120649 CGTTTCTCCGTGACAATTCTTCC 60.121 47.826 0.00 0.00 0.00 3.46
458 612 1.595382 GCACGAGACACCTGCAAGT 60.595 57.895 0.00 0.00 32.37 3.16
602 759 1.815421 GGTTCCACGATCATGCGCT 60.815 57.895 9.73 0.00 33.86 5.92
607 764 0.323629 AACACCGGTTCCACGATCAT 59.676 50.000 2.97 0.00 35.47 2.45
608 765 0.107081 AAACACCGGTTCCACGATCA 59.893 50.000 2.97 0.00 35.82 2.92
641 798 1.528129 TCGGTGTGTTTGCATGCATA 58.472 45.000 23.37 14.80 0.00 3.14
642 799 0.889994 ATCGGTGTGTTTGCATGCAT 59.110 45.000 23.37 0.00 0.00 3.96
643 800 0.240678 GATCGGTGTGTTTGCATGCA 59.759 50.000 18.46 18.46 0.00 3.96
673 1024 4.696172 GTACGCACACGCACGCAC 62.696 66.667 0.00 0.00 45.53 5.34
677 1028 3.759828 GGACGTACGCACACGCAC 61.760 66.667 16.72 2.53 45.77 5.34
681 1032 3.161405 CGACGGACGTACGCACAC 61.161 66.667 22.56 8.61 37.37 3.82
727 1078 3.535629 TTGTCGGTGCCAGCCTCTG 62.536 63.158 0.00 0.00 0.00 3.35
728 1079 2.337879 TTTTGTCGGTGCCAGCCTCT 62.338 55.000 0.00 0.00 0.00 3.69
756 1112 1.545651 GGAAGTGGGGGTTCTGAACAG 60.546 57.143 21.01 0.00 0.00 3.16
757 1113 0.476771 GGAAGTGGGGGTTCTGAACA 59.523 55.000 21.01 0.00 0.00 3.18
758 1114 0.251209 GGGAAGTGGGGGTTCTGAAC 60.251 60.000 12.05 12.05 0.00 3.18
759 1115 1.774894 CGGGAAGTGGGGGTTCTGAA 61.775 60.000 0.00 0.00 0.00 3.02
762 1118 2.933834 CCGGGAAGTGGGGGTTCT 60.934 66.667 0.00 0.00 0.00 3.01
928 1287 0.671781 GCTGATGCCTTGTCGTGTCT 60.672 55.000 0.00 0.00 0.00 3.41
1031 1395 0.107654 GTCCAACAATCTCCTCCCCG 60.108 60.000 0.00 0.00 0.00 5.73
1061 1433 0.108804 TAGCTAGCGTCACCACAAGC 60.109 55.000 9.55 0.00 0.00 4.01
1062 1434 1.202582 AGTAGCTAGCGTCACCACAAG 59.797 52.381 9.55 0.00 0.00 3.16
1063 1435 1.201647 GAGTAGCTAGCGTCACCACAA 59.798 52.381 9.55 0.00 0.00 3.33
1064 1436 0.809385 GAGTAGCTAGCGTCACCACA 59.191 55.000 9.55 0.00 0.00 4.17
1065 1437 0.100861 GGAGTAGCTAGCGTCACCAC 59.899 60.000 9.55 6.31 0.00 4.16
1066 1438 1.374343 CGGAGTAGCTAGCGTCACCA 61.374 60.000 20.72 0.54 0.00 4.17
1067 1439 1.355916 CGGAGTAGCTAGCGTCACC 59.644 63.158 9.55 12.84 0.00 4.02
1068 1440 1.355916 CCGGAGTAGCTAGCGTCAC 59.644 63.158 9.55 8.96 0.00 3.67
1069 1441 2.478890 GCCGGAGTAGCTAGCGTCA 61.479 63.158 5.05 0.00 0.00 4.35
1070 1442 1.726533 AAGCCGGAGTAGCTAGCGTC 61.727 60.000 5.05 7.62 40.49 5.19
1071 1443 1.753463 AAGCCGGAGTAGCTAGCGT 60.753 57.895 5.05 0.00 40.49 5.07
1072 1444 1.299468 CAAGCCGGAGTAGCTAGCG 60.299 63.158 5.05 0.00 40.49 4.26
1073 1445 0.528684 CACAAGCCGGAGTAGCTAGC 60.529 60.000 5.05 6.62 40.49 3.42
1074 1446 0.103208 CCACAAGCCGGAGTAGCTAG 59.897 60.000 5.05 0.00 40.49 3.42
1075 1447 0.613853 ACCACAAGCCGGAGTAGCTA 60.614 55.000 5.05 0.00 40.49 3.32
1076 1448 0.613853 TACCACAAGCCGGAGTAGCT 60.614 55.000 5.05 0.00 44.19 3.32
1077 1449 0.459759 GTACCACAAGCCGGAGTAGC 60.460 60.000 5.05 0.00 0.00 3.58
1078 1450 0.179145 CGTACCACAAGCCGGAGTAG 60.179 60.000 5.05 0.00 0.00 2.57
1297 1701 3.677284 CTGGGTCTGCAGCAGCGAT 62.677 63.158 18.43 0.00 46.23 4.58
1319 1732 1.513158 CGGAGTCGAGGATGTTGCT 59.487 57.895 0.00 0.00 39.00 3.91
1432 1851 4.959596 GAGATGAGCTCGCCGGGC 62.960 72.222 9.54 9.54 33.17 6.13
1586 2029 1.103803 TCCAAATCCGACGGAGAGAG 58.896 55.000 22.99 11.17 34.05 3.20
1951 2406 0.540597 GCCTTGCCTTGGACTCCTTT 60.541 55.000 0.00 0.00 0.00 3.11
2121 2576 6.867550 TGTGTATTGATGTTTGTGGTCAAAA 58.132 32.000 0.00 0.00 43.78 2.44
2122 2577 6.456795 TGTGTATTGATGTTTGTGGTCAAA 57.543 33.333 0.00 0.00 40.64 2.69
2123 2578 6.647334 ATGTGTATTGATGTTTGTGGTCAA 57.353 33.333 0.00 0.00 36.42 3.18
2124 2579 6.489700 AGAATGTGTATTGATGTTTGTGGTCA 59.510 34.615 0.00 0.00 0.00 4.02
2125 2580 6.913170 AGAATGTGTATTGATGTTTGTGGTC 58.087 36.000 0.00 0.00 0.00 4.02
2126 2581 6.899393 AGAATGTGTATTGATGTTTGTGGT 57.101 33.333 0.00 0.00 0.00 4.16
2127 2582 9.859427 ATAAAGAATGTGTATTGATGTTTGTGG 57.141 29.630 0.00 0.00 0.00 4.17
2217 2673 1.757682 AGAGCAAAAACGGTTGTCCA 58.242 45.000 0.00 0.00 0.00 4.02
2224 2680 3.806316 ATGTACGAAGAGCAAAAACGG 57.194 42.857 0.00 0.00 0.00 4.44
2341 2798 7.010552 GTCGCTGATTAAATAGAAGAAGAAGCA 59.989 37.037 0.00 0.00 0.00 3.91
2342 2799 7.223777 AGTCGCTGATTAAATAGAAGAAGAAGC 59.776 37.037 0.00 0.00 0.00 3.86
2343 2800 8.538856 CAGTCGCTGATTAAATAGAAGAAGAAG 58.461 37.037 1.18 0.00 32.44 2.85
2346 2803 6.980978 TCCAGTCGCTGATTAAATAGAAGAAG 59.019 38.462 8.20 0.00 32.44 2.85
2364 2821 4.042398 CACGAGGTACAAATATCCAGTCG 58.958 47.826 0.00 0.00 0.00 4.18
2366 2823 5.670792 TTCACGAGGTACAAATATCCAGT 57.329 39.130 0.00 0.00 0.00 4.00
2399 2856 2.159572 CCGATAAGCAGTGGAAAAACGG 60.160 50.000 0.00 0.00 0.00 4.44
2517 2977 9.090103 CCACCCTTCTAGTCATTCAACTATATA 57.910 37.037 0.00 0.00 31.55 0.86
2520 2980 5.726793 ACCACCCTTCTAGTCATTCAACTAT 59.273 40.000 0.00 0.00 31.55 2.12
2539 2999 2.580966 TTTTGCCGTTTACAACCACC 57.419 45.000 0.00 0.00 0.00 4.61
2600 3060 6.504398 GTGAAAGATGTAGATACGTCCATGA 58.496 40.000 8.29 0.00 41.91 3.07
2620 3080 3.133141 TGGTCCAAATGATGTCGTGAA 57.867 42.857 0.00 0.00 0.00 3.18
2621 3081 2.849294 TGGTCCAAATGATGTCGTGA 57.151 45.000 0.00 0.00 0.00 4.35
2629 3089 3.507233 GCTCTTGTCATTGGTCCAAATGA 59.493 43.478 8.75 10.05 42.78 2.57
2632 3092 3.149196 GAGCTCTTGTCATTGGTCCAAA 58.851 45.455 8.75 0.00 0.00 3.28
2668 3128 4.254492 AGGAGCGAGTTCACCTTATTTTC 58.746 43.478 0.00 0.00 0.00 2.29
2671 3131 3.100671 AGAGGAGCGAGTTCACCTTATT 58.899 45.455 0.00 0.00 32.53 1.40
2700 3160 4.955811 TGTCTCATGTGTAGAAAGTGGT 57.044 40.909 0.00 0.00 0.00 4.16
2766 3226 0.035458 CTGTTTCGTGGCCTTCCTCT 59.965 55.000 3.32 0.00 0.00 3.69
2881 3341 4.776322 CAGGCGCCGGATGTCCAA 62.776 66.667 23.19 0.00 35.14 3.53
2970 3430 1.439228 GCTGTAGCTCTCATCGGCA 59.561 57.895 0.00 0.00 38.21 5.69
3021 3481 2.375174 AGTTGGCTCTGGTGTGGAATTA 59.625 45.455 0.00 0.00 0.00 1.40
3024 3484 0.108585 GAGTTGGCTCTGGTGTGGAA 59.891 55.000 0.00 0.00 38.66 3.53
3044 3504 4.373116 GGTGGCTTCGGTCTCGCA 62.373 66.667 0.00 0.00 36.13 5.10
3099 3561 0.759959 TTCTGCTACGTTCCCCAACA 59.240 50.000 0.00 0.00 32.14 3.33
3100 3562 1.886886 TTTCTGCTACGTTCCCCAAC 58.113 50.000 0.00 0.00 0.00 3.77
3101 3563 2.871096 ATTTCTGCTACGTTCCCCAA 57.129 45.000 0.00 0.00 0.00 4.12
3102 3564 2.039216 TGAATTTCTGCTACGTTCCCCA 59.961 45.455 0.00 0.00 0.00 4.96
3103 3565 2.706890 TGAATTTCTGCTACGTTCCCC 58.293 47.619 0.00 0.00 0.00 4.81
3104 3566 4.759516 TTTGAATTTCTGCTACGTTCCC 57.240 40.909 0.00 0.00 0.00 3.97
3105 3567 7.637709 AAATTTTGAATTTCTGCTACGTTCC 57.362 32.000 0.00 0.00 0.00 3.62
3106 3568 8.214472 GGAAAATTTTGAATTTCTGCTACGTTC 58.786 33.333 8.47 0.00 36.15 3.95
3107 3569 7.926018 AGGAAAATTTTGAATTTCTGCTACGTT 59.074 29.630 8.47 0.00 36.15 3.99
3108 3570 7.433680 AGGAAAATTTTGAATTTCTGCTACGT 58.566 30.769 8.47 0.00 36.15 3.57
3109 3571 7.873739 AGGAAAATTTTGAATTTCTGCTACG 57.126 32.000 8.47 0.00 36.15 3.51
3110 3572 8.850452 CGTAGGAAAATTTTGAATTTCTGCTAC 58.150 33.333 8.47 6.07 36.15 3.58
3111 3573 8.573035 ACGTAGGAAAATTTTGAATTTCTGCTA 58.427 29.630 8.47 0.00 36.15 3.49
3112 3574 7.382218 CACGTAGGAAAATTTTGAATTTCTGCT 59.618 33.333 8.47 0.00 36.15 4.24
3113 3575 7.169140 ACACGTAGGAAAATTTTGAATTTCTGC 59.831 33.333 8.47 0.00 36.15 4.26
3114 3576 8.574196 ACACGTAGGAAAATTTTGAATTTCTG 57.426 30.769 8.47 0.00 36.15 3.02
3115 3577 8.410141 TGACACGTAGGAAAATTTTGAATTTCT 58.590 29.630 8.47 0.00 36.15 2.52
3116 3578 8.476925 GTGACACGTAGGAAAATTTTGAATTTC 58.523 33.333 8.47 0.00 35.33 2.17
3117 3579 7.436970 GGTGACACGTAGGAAAATTTTGAATTT 59.563 33.333 8.47 0.00 0.00 1.82
3118 3580 6.921307 GGTGACACGTAGGAAAATTTTGAATT 59.079 34.615 8.47 0.00 0.00 2.17
3119 3581 6.039941 TGGTGACACGTAGGAAAATTTTGAAT 59.960 34.615 8.47 0.00 33.40 2.57
3120 3582 5.357314 TGGTGACACGTAGGAAAATTTTGAA 59.643 36.000 8.47 0.00 33.40 2.69
3121 3583 4.882427 TGGTGACACGTAGGAAAATTTTGA 59.118 37.500 8.47 0.00 33.40 2.69
3122 3584 5.176407 TGGTGACACGTAGGAAAATTTTG 57.824 39.130 8.47 0.00 33.40 2.44
3123 3585 5.591067 TCTTGGTGACACGTAGGAAAATTTT 59.409 36.000 2.28 2.28 42.67 1.82
3124 3586 5.127491 TCTTGGTGACACGTAGGAAAATTT 58.873 37.500 0.00 0.00 42.67 1.82
3125 3587 4.710324 TCTTGGTGACACGTAGGAAAATT 58.290 39.130 0.00 0.00 42.67 1.82
3126 3588 4.345859 TCTTGGTGACACGTAGGAAAAT 57.654 40.909 0.00 0.00 42.67 1.82
3127 3589 3.823281 TCTTGGTGACACGTAGGAAAA 57.177 42.857 0.00 0.00 42.67 2.29
3128 3590 3.576982 AGATCTTGGTGACACGTAGGAAA 59.423 43.478 0.00 0.00 42.67 3.13
3129 3591 3.162666 AGATCTTGGTGACACGTAGGAA 58.837 45.455 0.00 0.00 42.67 3.36
3130 3592 2.803956 AGATCTTGGTGACACGTAGGA 58.196 47.619 0.00 0.00 42.67 2.94
3131 3593 4.580995 AGATAGATCTTGGTGACACGTAGG 59.419 45.833 0.00 0.00 42.67 3.18
3132 3594 5.759506 AGATAGATCTTGGTGACACGTAG 57.240 43.478 0.00 0.00 42.67 3.51
3133 3595 7.203255 CATAGATAGATCTTGGTGACACGTA 57.797 40.000 0.00 0.00 42.67 3.57
3134 3596 6.078202 CATAGATAGATCTTGGTGACACGT 57.922 41.667 0.00 0.00 42.67 4.49


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

AutoCloner maintained by Alex Coulton.