Multiple sequence alignment - TraesCS6D01G305900

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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 TraesCS6D01G305900 chr6D 100.000 2560 0 0 1 2560 414483457 414480898 0.000000e+00 4728
1 TraesCS6D01G305900 chr6D 83.254 627 52 26 125 710 414541718 414541104 6.270000e-146 527
2 TraesCS6D01G305900 chr6D 79.755 489 60 19 1022 1491 414541007 414540539 4.110000e-83 318
3 TraesCS6D01G305900 chr6D 83.206 131 8 5 508 625 414494366 414494237 9.690000e-20 108
4 TraesCS6D01G305900 chr6B 92.908 1269 54 11 947 2210 624803520 624802283 0.000000e+00 1812
5 TraesCS6D01G305900 chr6B 89.564 527 23 12 327 821 624804078 624803552 7.720000e-180 640
6 TraesCS6D01G305900 chr6B 77.798 554 79 17 1006 1533 624883345 624882810 4.140000e-78 302
7 TraesCS6D01G305900 chr6B 84.064 251 28 9 1245 1491 624826461 624826219 5.510000e-57 231
8 TraesCS6D01G305900 chr6B 86.667 225 10 10 518 729 624883610 624883393 5.510000e-57 231
9 TraesCS6D01G305900 chr6B 87.425 167 6 6 2402 2560 624801984 624801825 7.280000e-41 178
10 TraesCS6D01G305900 chr6A 90.649 1294 56 16 826 2094 559429310 559428057 0.000000e+00 1659
11 TraesCS6D01G305900 chr6A 85.118 551 41 21 190 710 559494211 559493672 2.260000e-145 525
12 TraesCS6D01G305900 chr6A 85.028 541 41 20 200 710 559463638 559463108 4.880000e-142 514
13 TraesCS6D01G305900 chr6A 85.028 541 41 19 200 710 559478867 559478337 4.880000e-142 514
14 TraesCS6D01G305900 chr6A 89.583 336 13 6 508 821 559433440 559433105 8.530000e-110 407
15 TraesCS6D01G305900 chr6A 85.156 384 30 9 353 710 559448462 559448080 4.020000e-98 368
16 TraesCS6D01G305900 chr6A 79.885 522 73 15 1025 1533 559463008 559462506 1.130000e-93 353
17 TraesCS6D01G305900 chr6A 81.405 484 42 20 200 673 559482307 559481862 4.050000e-93 351
18 TraesCS6D01G305900 chr6A 79.044 544 76 19 1006 1533 559447999 559447478 3.160000e-89 339
19 TraesCS6D01G305900 chr6A 78.453 543 81 17 1006 1533 559478256 559477735 3.180000e-84 322
20 TraesCS6D01G305900 chr6A 78.493 544 79 19 1006 1533 559493591 559493070 3.180000e-84 322
21 TraesCS6D01G305900 chr6A 88.672 256 21 3 829 1076 559481675 559481420 3.200000e-79 305
22 TraesCS6D01G305900 chr6A 87.970 266 17 4 826 1076 559450973 559450708 1.490000e-77 300
23 TraesCS6D01G305900 chr6A 86.842 266 20 4 826 1076 559466457 559466192 1.500000e-72 283
24 TraesCS6D01G305900 chr6A 86.561 253 19 9 200 446 559467086 559466843 5.430000e-67 265
25 TraesCS6D01G305900 chr6A 85.897 234 21 7 478 703 559451358 559451129 3.290000e-59 239
26 TraesCS6D01G305900 chr6A 90.526 95 5 2 2120 2210 559427826 559427732 3.460000e-24 122
27 TraesCS6D01G305900 chr6A 83.212 137 12 6 1983 2115 559446912 559446783 5.790000e-22 115
28 TraesCS6D01G305900 chr6A 81.752 137 14 6 1983 2115 559492493 559492364 1.250000e-18 104
29 TraesCS6D01G305900 chr6A 80.851 141 16 6 1983 2119 559477158 559477025 1.620000e-17 100


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 TraesCS6D01G305900 chr6D 414480898 414483457 2559 True 4728.000000 4728 100.000000 1 2560 1 chr6D.!!$R1 2559
1 TraesCS6D01G305900 chr6D 414540539 414541718 1179 True 422.500000 527 81.504500 125 1491 2 chr6D.!!$R3 1366
2 TraesCS6D01G305900 chr6B 624801825 624804078 2253 True 876.666667 1812 89.965667 327 2560 3 chr6B.!!$R2 2233
3 TraesCS6D01G305900 chr6B 624882810 624883610 800 True 266.500000 302 82.232500 518 1533 2 chr6B.!!$R3 1015
4 TraesCS6D01G305900 chr6A 559427732 559433440 5708 True 729.333333 1659 90.252667 508 2210 3 chr6A.!!$R1 1702
5 TraesCS6D01G305900 chr6A 559462506 559467086 4580 True 353.750000 514 84.579000 200 1533 4 chr6A.!!$R3 1333
6 TraesCS6D01G305900 chr6A 559477025 559482307 5282 True 318.400000 514 82.881800 200 2119 5 chr6A.!!$R4 1919
7 TraesCS6D01G305900 chr6A 559492364 559494211 1847 True 317.000000 525 81.787667 190 2115 3 chr6A.!!$R5 1925
8 TraesCS6D01G305900 chr6A 559446783 559451358 4575 True 272.200000 368 84.255800 353 2115 5 chr6A.!!$R2 1762

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
492 3984 0.032952 TCCAGTTGAAAGGTCGACGG 59.967 55.0 9.92 1.57 42.33 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2163 9972 0.320421 GGTTCGGACTGCTGTTGCTA 60.32 55.0 0.0 0.0 40.48 3.49 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 6.598753 GATTGCTTACCACATATGTTACGT 57.401 37.500 5.37 5.49 0.00 3.57
24 25 7.703298 GATTGCTTACCACATATGTTACGTA 57.297 36.000 5.37 4.50 0.00 3.57
25 26 7.709269 ATTGCTTACCACATATGTTACGTAG 57.291 36.000 5.37 1.91 0.00 3.51
27 28 6.267817 TGCTTACCACATATGTTACGTAGTC 58.732 40.000 5.37 4.12 43.93 2.59
28 29 6.127675 TGCTTACCACATATGTTACGTAGTCA 60.128 38.462 5.37 6.26 43.93 3.41
29 30 6.417044 GCTTACCACATATGTTACGTAGTCAG 59.583 42.308 5.37 3.66 43.93 3.51
30 31 7.628769 TTACCACATATGTTACGTAGTCAGA 57.371 36.000 5.37 0.00 43.93 3.27
31 32 6.519679 ACCACATATGTTACGTAGTCAGAA 57.480 37.500 5.37 0.00 43.93 3.02
32 33 6.927416 ACCACATATGTTACGTAGTCAGAAA 58.073 36.000 5.37 0.00 43.93 2.52
33 34 7.553334 ACCACATATGTTACGTAGTCAGAAAT 58.447 34.615 5.37 0.00 43.93 2.17
34 35 8.038944 ACCACATATGTTACGTAGTCAGAAATT 58.961 33.333 5.37 0.00 43.93 1.82
35 36 8.540492 CCACATATGTTACGTAGTCAGAAATTC 58.460 37.037 5.37 0.00 43.93 2.17
36 37 8.540492 CACATATGTTACGTAGTCAGAAATTCC 58.460 37.037 5.37 0.00 43.93 3.01
37 38 8.475639 ACATATGTTACGTAGTCAGAAATTCCT 58.524 33.333 1.41 0.00 43.93 3.36
38 39 8.969267 CATATGTTACGTAGTCAGAAATTCCTC 58.031 37.037 0.00 0.00 43.93 3.71
39 40 6.335471 TGTTACGTAGTCAGAAATTCCTCA 57.665 37.500 0.00 0.00 43.93 3.86
40 41 6.387465 TGTTACGTAGTCAGAAATTCCTCAG 58.613 40.000 0.00 0.00 43.93 3.35
41 42 6.015688 TGTTACGTAGTCAGAAATTCCTCAGT 60.016 38.462 0.00 0.00 43.93 3.41
42 43 5.470047 ACGTAGTCAGAAATTCCTCAGTT 57.530 39.130 0.00 0.00 29.74 3.16
43 44 5.471257 ACGTAGTCAGAAATTCCTCAGTTC 58.529 41.667 0.00 0.00 29.74 3.01
44 45 5.010719 ACGTAGTCAGAAATTCCTCAGTTCA 59.989 40.000 0.00 0.00 29.74 3.18
45 46 5.574830 CGTAGTCAGAAATTCCTCAGTTCAG 59.425 44.000 0.00 0.00 0.00 3.02
46 47 5.559148 AGTCAGAAATTCCTCAGTTCAGT 57.441 39.130 0.00 0.00 0.00 3.41
47 48 6.672266 AGTCAGAAATTCCTCAGTTCAGTA 57.328 37.500 0.00 0.00 0.00 2.74
48 49 6.459923 AGTCAGAAATTCCTCAGTTCAGTAC 58.540 40.000 0.00 0.00 0.00 2.73
49 50 6.268847 AGTCAGAAATTCCTCAGTTCAGTACT 59.731 38.462 0.00 0.00 37.68 2.73
50 51 7.451877 AGTCAGAAATTCCTCAGTTCAGTACTA 59.548 37.037 0.00 0.00 34.56 1.82
51 52 7.542824 GTCAGAAATTCCTCAGTTCAGTACTAC 59.457 40.741 0.00 0.00 34.56 2.73
52 53 7.451877 TCAGAAATTCCTCAGTTCAGTACTACT 59.548 37.037 0.00 0.00 34.56 2.57
53 54 8.740906 CAGAAATTCCTCAGTTCAGTACTACTA 58.259 37.037 0.00 0.00 34.56 1.82
54 55 8.741841 AGAAATTCCTCAGTTCAGTACTACTAC 58.258 37.037 0.00 0.00 34.56 2.73
55 56 8.653036 AAATTCCTCAGTTCAGTACTACTACT 57.347 34.615 0.00 0.00 34.56 2.57
68 69 6.807789 AGTACTACTACTGAGCTTAATTGGC 58.192 40.000 0.00 0.00 31.46 4.52
69 70 5.677319 ACTACTACTGAGCTTAATTGGCA 57.323 39.130 7.73 0.00 0.00 4.92
70 71 6.049955 ACTACTACTGAGCTTAATTGGCAA 57.950 37.500 0.68 0.68 0.00 4.52
71 72 5.875359 ACTACTACTGAGCTTAATTGGCAAC 59.125 40.000 0.00 0.00 0.00 4.17
72 73 3.684788 ACTACTGAGCTTAATTGGCAACG 59.315 43.478 0.00 0.00 42.51 4.10
73 74 2.504367 ACTGAGCTTAATTGGCAACGT 58.496 42.857 0.00 0.00 42.51 3.99
74 75 2.884639 ACTGAGCTTAATTGGCAACGTT 59.115 40.909 0.00 0.00 42.51 3.99
75 76 3.317993 ACTGAGCTTAATTGGCAACGTTT 59.682 39.130 0.00 0.00 42.51 3.60
76 77 4.202111 ACTGAGCTTAATTGGCAACGTTTT 60.202 37.500 0.00 0.00 42.51 2.43
77 78 4.295051 TGAGCTTAATTGGCAACGTTTTC 58.705 39.130 0.00 0.00 42.51 2.29
78 79 4.202060 TGAGCTTAATTGGCAACGTTTTCA 60.202 37.500 0.00 0.00 42.51 2.69
79 80 4.688021 AGCTTAATTGGCAACGTTTTCAA 58.312 34.783 0.00 13.31 42.51 2.69
80 81 5.112686 AGCTTAATTGGCAACGTTTTCAAA 58.887 33.333 14.47 3.92 42.51 2.69
81 82 5.757808 AGCTTAATTGGCAACGTTTTCAAAT 59.242 32.000 14.47 10.28 42.51 2.32
82 83 6.926272 AGCTTAATTGGCAACGTTTTCAAATA 59.074 30.769 14.47 9.49 42.51 1.40
83 84 7.602265 AGCTTAATTGGCAACGTTTTCAAATAT 59.398 29.630 14.47 8.54 42.51 1.28
84 85 8.227119 GCTTAATTGGCAACGTTTTCAAATATT 58.773 29.630 14.47 8.94 42.51 1.28
87 88 7.721286 ATTGGCAACGTTTTCAAATATTTCA 57.279 28.000 14.47 0.00 42.51 2.69
88 89 7.721286 TTGGCAACGTTTTCAAATATTTCAT 57.279 28.000 0.00 0.00 42.51 2.57
89 90 7.114882 TGGCAACGTTTTCAAATATTTCATG 57.885 32.000 0.00 0.00 42.51 3.07
90 91 6.703607 TGGCAACGTTTTCAAATATTTCATGT 59.296 30.769 0.00 0.00 42.51 3.21
91 92 7.225538 TGGCAACGTTTTCAAATATTTCATGTT 59.774 29.630 0.00 0.00 42.51 2.71
92 93 7.530190 GGCAACGTTTTCAAATATTTCATGTTG 59.470 33.333 17.42 17.42 35.99 3.33
93 94 7.530190 GCAACGTTTTCAAATATTTCATGTTGG 59.470 33.333 20.20 4.33 34.12 3.77
94 95 7.650834 ACGTTTTCAAATATTTCATGTTGGG 57.349 32.000 0.00 0.00 0.00 4.12
95 96 6.648725 ACGTTTTCAAATATTTCATGTTGGGG 59.351 34.615 0.00 0.00 0.00 4.96
96 97 6.402011 CGTTTTCAAATATTTCATGTTGGGGC 60.402 38.462 0.00 0.00 0.00 5.80
97 98 4.383850 TCAAATATTTCATGTTGGGGCG 57.616 40.909 0.00 0.00 0.00 6.13
98 99 2.865551 CAAATATTTCATGTTGGGGCGC 59.134 45.455 0.00 0.00 0.00 6.53
99 100 1.774110 ATATTTCATGTTGGGGCGCA 58.226 45.000 10.83 0.00 0.00 6.09
100 101 1.550327 TATTTCATGTTGGGGCGCAA 58.450 45.000 13.46 13.46 0.00 4.85
101 102 0.903942 ATTTCATGTTGGGGCGCAAT 59.096 45.000 20.31 2.15 0.00 3.56
102 103 0.683973 TTTCATGTTGGGGCGCAATT 59.316 45.000 20.31 8.43 0.00 2.32
103 104 0.246086 TTCATGTTGGGGCGCAATTC 59.754 50.000 20.31 8.97 0.00 2.17
104 105 0.897401 TCATGTTGGGGCGCAATTCA 60.897 50.000 20.31 14.38 0.00 2.57
105 106 0.458889 CATGTTGGGGCGCAATTCAG 60.459 55.000 20.31 7.33 0.00 3.02
106 107 2.125952 GTTGGGGCGCAATTCAGC 60.126 61.111 20.31 3.19 0.00 4.26
107 108 2.283101 TTGGGGCGCAATTCAGCT 60.283 55.556 13.46 0.00 0.00 4.24
108 109 2.342650 TTGGGGCGCAATTCAGCTC 61.343 57.895 13.46 0.00 0.00 4.09
109 110 2.751436 GGGGCGCAATTCAGCTCA 60.751 61.111 10.83 0.00 35.08 4.26
110 111 2.342650 GGGGCGCAATTCAGCTCAA 61.343 57.895 10.83 0.00 35.08 3.02
111 112 1.153958 GGGCGCAATTCAGCTCAAC 60.154 57.895 10.83 0.00 33.25 3.18
112 113 1.512734 GGCGCAATTCAGCTCAACG 60.513 57.895 10.83 0.00 0.00 4.10
113 114 1.207593 GCGCAATTCAGCTCAACGT 59.792 52.632 0.30 0.00 0.00 3.99
114 115 0.385974 GCGCAATTCAGCTCAACGTT 60.386 50.000 0.30 0.00 0.00 3.99
115 116 1.925946 GCGCAATTCAGCTCAACGTTT 60.926 47.619 0.30 0.00 0.00 3.60
116 117 2.384382 CGCAATTCAGCTCAACGTTTT 58.616 42.857 0.00 0.00 0.00 2.43
117 118 2.401720 CGCAATTCAGCTCAACGTTTTC 59.598 45.455 0.00 0.00 0.00 2.29
118 119 3.371168 GCAATTCAGCTCAACGTTTTCA 58.629 40.909 0.00 0.00 0.00 2.69
119 120 3.983344 GCAATTCAGCTCAACGTTTTCAT 59.017 39.130 0.00 0.00 0.00 2.57
120 121 5.153513 GCAATTCAGCTCAACGTTTTCATA 58.846 37.500 0.00 0.00 0.00 2.15
121 122 5.801947 GCAATTCAGCTCAACGTTTTCATAT 59.198 36.000 0.00 0.00 0.00 1.78
122 123 6.966632 GCAATTCAGCTCAACGTTTTCATATA 59.033 34.615 0.00 0.00 0.00 0.86
123 124 7.484641 GCAATTCAGCTCAACGTTTTCATATAA 59.515 33.333 0.00 0.00 0.00 0.98
129 130 8.285394 CAGCTCAACGTTTTCATATAATATGCT 58.715 33.333 0.00 0.00 0.00 3.79
160 161 1.271871 GGTGGTCATGGAATCACACCA 60.272 52.381 6.76 6.37 45.72 4.17
176 177 2.293170 CACCACACACACCAACATGTA 58.707 47.619 0.00 0.00 0.00 2.29
184 185 4.391830 CACACACCAACATGTAGTACCATC 59.608 45.833 0.00 0.00 0.00 3.51
185 186 3.938963 CACACCAACATGTAGTACCATCC 59.061 47.826 0.00 0.00 0.00 3.51
186 187 3.194861 CACCAACATGTAGTACCATCCG 58.805 50.000 0.00 0.00 0.00 4.18
187 188 2.169769 ACCAACATGTAGTACCATCCGG 59.830 50.000 0.00 0.00 38.77 5.14
198 208 0.326618 ACCATCCGGTCCTCCTGAAT 60.327 55.000 0.00 0.00 44.71 2.57
203 213 2.108168 TCCGGTCCTCCTGAATAGTTG 58.892 52.381 0.00 0.00 0.00 3.16
236 246 7.351981 GTTTGCATTGGTTTGGTTAATTTCTC 58.648 34.615 0.00 0.00 0.00 2.87
254 264 1.142262 CTCCCGGGGGTAATTAAGGTG 59.858 57.143 23.50 0.00 36.47 4.00
281 291 1.063006 GATGGCGACGTACGTGCTA 59.937 57.895 28.16 24.89 44.60 3.49
302 312 2.603110 ACAATTCCATCGTTCATCGTCG 59.397 45.455 0.00 0.00 40.80 5.12
303 313 2.579207 ATTCCATCGTTCATCGTCGT 57.421 45.000 0.00 0.00 40.80 4.34
304 314 1.904144 TTCCATCGTTCATCGTCGTC 58.096 50.000 0.00 0.00 40.80 4.20
306 316 1.191944 CCATCGTTCATCGTCGTCAG 58.808 55.000 0.00 0.00 40.80 3.51
323 333 5.452623 GTCGTCAGCTTTTTCTTCTTTTCAC 59.547 40.000 0.00 0.00 0.00 3.18
324 334 4.434588 CGTCAGCTTTTTCTTCTTTTCACG 59.565 41.667 0.00 0.00 0.00 4.35
465 3945 1.202110 GCTACACTGCACATCACATGC 60.202 52.381 0.00 0.00 43.68 4.06
492 3984 0.032952 TCCAGTTGAAAGGTCGACGG 59.967 55.000 9.92 1.57 42.33 4.79
761 4309 2.579738 GACCGGAGAAGGTGAGCC 59.420 66.667 9.46 0.00 46.09 4.70
768 4316 3.787001 GAAGGTGAGCCCCTCCCG 61.787 72.222 0.00 0.00 32.13 5.14
818 4366 3.185594 CACGGCAGTCAATCGTTTCTTTA 59.814 43.478 0.00 0.00 34.73 1.85
821 4369 4.092821 CGGCAGTCAATCGTTTCTTTATCA 59.907 41.667 0.00 0.00 0.00 2.15
822 4370 5.220662 CGGCAGTCAATCGTTTCTTTATCAT 60.221 40.000 0.00 0.00 0.00 2.45
824 4372 6.037610 GGCAGTCAATCGTTTCTTTATCATCT 59.962 38.462 0.00 0.00 0.00 2.90
841 8179 0.107312 TCTCGCCGGAACTAGCTAGT 60.107 55.000 20.95 20.95 38.39 2.57
872 8210 3.623060 GTGCTTTATCATCTCGCTGGAAA 59.377 43.478 0.00 0.00 0.00 3.13
886 8224 6.002062 TCGCTGGAAAATTTCTTCTTCTTC 57.998 37.500 5.65 0.00 0.00 2.87
901 8245 3.389983 TCTTCTTCTTCCTTCCGGTTGAA 59.610 43.478 0.00 2.01 0.00 2.69
952 8296 1.004200 CGGGGAGTTAAACAGGCGT 60.004 57.895 0.00 0.00 0.00 5.68
982 8330 1.872952 CCTGCGTTGTTGTTGATCTCA 59.127 47.619 0.00 0.00 0.00 3.27
1102 8471 3.760035 CCCAGTACGCACTCGGCT 61.760 66.667 0.00 0.00 41.67 5.52
1123 8501 1.229177 TACCACCTCTGCAGCCAGA 60.229 57.895 9.47 0.00 45.54 3.86
1164 8560 2.102084 CTCTGCTGTTAGGCTAGATGCA 59.898 50.000 13.75 13.75 45.15 3.96
1166 8562 2.806818 CTGCTGTTAGGCTAGATGCATG 59.193 50.000 2.46 0.00 45.15 4.06
1180 8576 0.901827 TGCATGCTAGACTTTCCGGA 59.098 50.000 20.33 0.00 0.00 5.14
1553 8962 0.680061 ACTTTCTCCGTGGAGGTGAC 59.320 55.000 15.67 0.00 41.74 3.67
1554 8963 0.679505 CTTTCTCCGTGGAGGTGACA 59.320 55.000 15.67 0.00 41.74 3.58
1555 8964 1.070134 CTTTCTCCGTGGAGGTGACAA 59.930 52.381 15.67 0.00 41.74 3.18
1556 8965 0.391597 TTCTCCGTGGAGGTGACAAC 59.608 55.000 15.67 0.00 41.74 3.32
1557 8966 0.469331 TCTCCGTGGAGGTGACAACT 60.469 55.000 15.67 0.00 42.20 3.16
1558 8967 0.319900 CTCCGTGGAGGTGACAACTG 60.320 60.000 8.09 0.00 41.99 3.16
1559 8968 0.757561 TCCGTGGAGGTGACAACTGA 60.758 55.000 0.00 0.00 41.99 3.41
1616 9080 9.890352 GGGTAGTTCTAAGTGATAATAAGTACG 57.110 37.037 0.00 0.00 0.00 3.67
1724 9196 6.416415 TGTGGTGTTAATTATATTGGACCGT 58.584 36.000 0.00 0.00 0.00 4.83
1840 9344 6.803807 GCATGTTGTTTAGGAAGAGATGTTTC 59.196 38.462 0.00 0.00 0.00 2.78
1841 9345 7.522073 GCATGTTGTTTAGGAAGAGATGTTTCA 60.522 37.037 0.00 0.00 0.00 2.69
1842 9346 7.496529 TGTTGTTTAGGAAGAGATGTTTCAG 57.503 36.000 0.00 0.00 0.00 3.02
1846 9350 8.327941 TGTTTAGGAAGAGATGTTTCAGATTG 57.672 34.615 0.00 0.00 0.00 2.67
1849 9353 8.954950 TTAGGAAGAGATGTTTCAGATTGATC 57.045 34.615 0.00 0.00 0.00 2.92
1850 9354 6.955364 AGGAAGAGATGTTTCAGATTGATCA 58.045 36.000 0.00 0.00 0.00 2.92
1851 9355 7.400439 AGGAAGAGATGTTTCAGATTGATCAA 58.600 34.615 11.26 11.26 0.00 2.57
1852 9356 8.053963 AGGAAGAGATGTTTCAGATTGATCAAT 58.946 33.333 20.85 20.85 0.00 2.57
2084 9682 5.859648 GCAGATAGAAACGGCTAGTAGAATC 59.140 44.000 0.00 0.00 0.00 2.52
2197 10006 1.336517 CGAACCTCGAAGCTACACCAA 60.337 52.381 0.00 0.00 43.74 3.67
2199 10008 3.335579 GAACCTCGAAGCTACACCAATT 58.664 45.455 0.00 0.00 0.00 2.32
2210 10019 6.715347 AGCTACACCAATTATTTTGATCCC 57.285 37.500 0.00 0.00 0.00 3.85
2211 10020 5.299279 AGCTACACCAATTATTTTGATCCCG 59.701 40.000 0.00 0.00 0.00 5.14
2212 10021 5.067283 GCTACACCAATTATTTTGATCCCGT 59.933 40.000 0.00 0.00 0.00 5.28
2214 10023 5.013547 ACACCAATTATTTTGATCCCGTGA 58.986 37.500 0.00 0.00 0.00 4.35
2215 10024 5.105917 ACACCAATTATTTTGATCCCGTGAC 60.106 40.000 0.00 0.00 0.00 3.67
2217 10026 4.400884 CCAATTATTTTGATCCCGTGACCA 59.599 41.667 0.00 0.00 0.00 4.02
2218 10027 5.068987 CCAATTATTTTGATCCCGTGACCAT 59.931 40.000 0.00 0.00 0.00 3.55
2219 10028 5.772825 ATTATTTTGATCCCGTGACCATG 57.227 39.130 0.00 0.00 0.00 3.66
2220 10029 2.577606 TTTTGATCCCGTGACCATGT 57.422 45.000 0.00 0.00 0.00 3.21
2221 10030 1.819928 TTTGATCCCGTGACCATGTG 58.180 50.000 0.00 0.00 0.00 3.21
2223 10032 0.980423 TGATCCCGTGACCATGTGAA 59.020 50.000 0.00 0.00 0.00 3.18
2224 10033 1.349357 TGATCCCGTGACCATGTGAAA 59.651 47.619 0.00 0.00 0.00 2.69
2225 10034 2.224646 TGATCCCGTGACCATGTGAAAA 60.225 45.455 0.00 0.00 0.00 2.29
2226 10035 2.350057 TCCCGTGACCATGTGAAAAA 57.650 45.000 0.00 0.00 0.00 1.94
2245 10054 2.640346 AAAACGTGTGACAAACCACC 57.360 45.000 0.00 0.00 36.26 4.61
2246 10055 1.535833 AAACGTGTGACAAACCACCA 58.464 45.000 0.00 0.00 36.26 4.17
2247 10056 1.757682 AACGTGTGACAAACCACCAT 58.242 45.000 0.00 0.00 36.26 3.55
2248 10057 1.021202 ACGTGTGACAAACCACCATG 58.979 50.000 0.00 0.00 36.26 3.66
2249 10058 1.021202 CGTGTGACAAACCACCATGT 58.979 50.000 0.00 0.00 36.26 3.21
2250 10059 1.002900 CGTGTGACAAACCACCATGTC 60.003 52.381 0.00 0.00 44.84 3.06
2257 10066 5.004922 GACAAACCACCATGTCAAAAAGA 57.995 39.130 1.30 0.00 44.19 2.52
2258 10067 5.413309 ACAAACCACCATGTCAAAAAGAA 57.587 34.783 0.00 0.00 0.00 2.52
2259 10068 5.418676 ACAAACCACCATGTCAAAAAGAAG 58.581 37.500 0.00 0.00 0.00 2.85
2274 10083 6.589523 TCAAAAAGAAGTGTGACAAACCAATG 59.410 34.615 0.00 0.00 0.00 2.82
2275 10084 5.659440 AAAGAAGTGTGACAAACCAATGT 57.341 34.783 0.00 0.00 35.90 2.71
2286 10095 6.582295 GTGACAAACCAATGTAATGCAAGTAG 59.418 38.462 0.00 0.00 32.57 2.57
2288 10097 6.913170 ACAAACCAATGTAATGCAAGTAGAG 58.087 36.000 0.00 0.00 0.00 2.43
2291 10100 7.759489 AACCAATGTAATGCAAGTAGAGAAA 57.241 32.000 0.00 0.00 0.00 2.52
2296 10105 9.294030 CAATGTAATGCAAGTAGAGAAATTTCC 57.706 33.333 14.61 6.57 0.00 3.13
2297 10106 7.391148 TGTAATGCAAGTAGAGAAATTTCCC 57.609 36.000 14.61 2.73 0.00 3.97
2298 10107 6.945435 TGTAATGCAAGTAGAGAAATTTCCCA 59.055 34.615 14.61 0.00 0.00 4.37
2299 10108 6.916360 AATGCAAGTAGAGAAATTTCCCAA 57.084 33.333 14.61 0.00 0.00 4.12
2300 10109 7.486407 AATGCAAGTAGAGAAATTTCCCAAT 57.514 32.000 14.61 0.00 0.00 3.16
2301 10110 6.515272 TGCAAGTAGAGAAATTTCCCAATC 57.485 37.500 14.61 5.87 0.00 2.67
2302 10111 5.418840 TGCAAGTAGAGAAATTTCCCAATCC 59.581 40.000 14.61 0.00 0.00 3.01
2343 10319 7.804614 GTTGAATTGGCAACGTTTTCATATA 57.195 32.000 13.10 0.00 38.79 0.86
2345 10321 8.868916 GTTGAATTGGCAACGTTTTCATATATT 58.131 29.630 13.10 5.00 38.79 1.28
2346 10322 8.994429 TGAATTGGCAACGTTTTCATATATTT 57.006 26.923 0.00 0.00 42.51 1.40
2356 10332 8.012957 ACGTTTTCATATATTTATTTGGGGCA 57.987 30.769 0.00 0.00 0.00 5.36
2374 10350 1.402456 GCACAATTCAGCTCAGCAAGG 60.402 52.381 0.00 0.00 0.00 3.61
2386 10362 3.372730 GCAAGGCATGCGTTCCCA 61.373 61.111 22.06 0.00 46.87 4.37
2387 10363 2.879907 CAAGGCATGCGTTCCCAG 59.120 61.111 22.06 8.11 0.00 4.45
2388 10364 1.675310 CAAGGCATGCGTTCCCAGA 60.675 57.895 22.06 0.00 0.00 3.86
2389 10365 1.675641 AAGGCATGCGTTCCCAGAC 60.676 57.895 19.45 0.00 0.00 3.51
2390 10366 2.045926 GGCATGCGTTCCCAGACT 60.046 61.111 12.44 0.00 0.00 3.24
2391 10367 2.109126 GGCATGCGTTCCCAGACTC 61.109 63.158 12.44 0.00 0.00 3.36
2392 10368 2.109126 GCATGCGTTCCCAGACTCC 61.109 63.158 0.00 0.00 0.00 3.85
2393 10369 1.296392 CATGCGTTCCCAGACTCCA 59.704 57.895 0.00 0.00 0.00 3.86
2394 10370 0.742281 CATGCGTTCCCAGACTCCAG 60.742 60.000 0.00 0.00 0.00 3.86
2395 10371 1.194781 ATGCGTTCCCAGACTCCAGT 61.195 55.000 0.00 0.00 0.00 4.00
2396 10372 0.541063 TGCGTTCCCAGACTCCAGTA 60.541 55.000 0.00 0.00 0.00 2.74
2397 10373 0.824759 GCGTTCCCAGACTCCAGTAT 59.175 55.000 0.00 0.00 0.00 2.12
2398 10374 1.471676 GCGTTCCCAGACTCCAGTATG 60.472 57.143 0.00 0.00 37.04 2.39
2399 10375 2.100197 CGTTCCCAGACTCCAGTATGA 58.900 52.381 2.83 0.00 39.44 2.15
2400 10376 2.496070 CGTTCCCAGACTCCAGTATGAA 59.504 50.000 2.83 0.00 39.44 2.57
2401 10377 3.676324 CGTTCCCAGACTCCAGTATGAAC 60.676 52.174 2.83 0.40 39.44 3.18
2438 10414 3.434940 ACCAAGCCGGACTCTTTATTT 57.565 42.857 5.05 0.00 38.63 1.40
2442 10418 4.335594 CCAAGCCGGACTCTTTATTTAAGG 59.664 45.833 5.05 0.00 36.56 2.69
2447 10423 7.344134 AGCCGGACTCTTTATTTAAGGTTTAT 58.656 34.615 5.05 0.00 34.46 1.40
2467 10443 8.287503 GGTTTATTTTCTCACGTTACAGATGTT 58.712 33.333 0.00 0.00 0.00 2.71
2493 10472 3.819564 ATAATAGACAAGCCGACTGCA 57.180 42.857 0.00 0.00 44.83 4.41
2498 10477 2.202388 CAAGCCGACTGCATTGCG 60.202 61.111 3.84 1.69 44.83 4.85
2505 10484 0.508641 CGACTGCATTGCGCCTATAC 59.491 55.000 4.18 0.00 41.33 1.47
2507 10486 1.939934 GACTGCATTGCGCCTATACAA 59.060 47.619 4.18 0.00 41.33 2.41
2508 10487 1.670811 ACTGCATTGCGCCTATACAAC 59.329 47.619 4.18 0.00 41.33 3.32
2510 10489 1.670295 TGCATTGCGCCTATACAACAG 59.330 47.619 4.18 0.00 41.33 3.16
2511 10490 1.002468 GCATTGCGCCTATACAACAGG 60.002 52.381 4.18 0.00 36.16 4.00
2512 10491 2.560504 CATTGCGCCTATACAACAGGA 58.439 47.619 4.18 0.00 34.91 3.86
2513 10492 3.141398 CATTGCGCCTATACAACAGGAT 58.859 45.455 4.18 0.00 34.91 3.24
2514 10493 2.526304 TGCGCCTATACAACAGGATC 57.474 50.000 4.18 0.00 34.91 3.36
2515 10494 1.760029 TGCGCCTATACAACAGGATCA 59.240 47.619 4.18 0.00 34.91 2.92
2535 10519 1.134401 ACCACTATGCACATTCCGAGG 60.134 52.381 0.00 0.00 0.00 4.63
2536 10520 0.940126 CACTATGCACATTCCGAGGC 59.060 55.000 0.00 0.00 0.00 4.70
2537 10521 0.179045 ACTATGCACATTCCGAGGCC 60.179 55.000 0.00 0.00 0.00 5.19
2538 10522 1.224069 CTATGCACATTCCGAGGCCG 61.224 60.000 0.00 0.00 0.00 6.13
2539 10523 1.681486 TATGCACATTCCGAGGCCGA 61.681 55.000 0.00 0.00 38.22 5.54
2540 10524 2.892425 GCACATTCCGAGGCCGAG 60.892 66.667 0.00 0.00 38.22 4.63
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 7.270047 ACTACGTAACATATGTGGTAAGCAAT 58.730 34.615 9.63 0.00 37.58 3.56
3 4 6.127675 TGACTACGTAACATATGTGGTAAGCA 60.128 38.462 9.63 9.69 39.15 3.91
4 5 6.267817 TGACTACGTAACATATGTGGTAAGC 58.732 40.000 9.63 7.62 39.15 3.09
5 6 7.700505 TCTGACTACGTAACATATGTGGTAAG 58.299 38.462 9.63 4.17 39.15 2.34
6 7 7.628769 TCTGACTACGTAACATATGTGGTAA 57.371 36.000 9.63 0.00 39.15 2.85
7 8 7.628769 TTCTGACTACGTAACATATGTGGTA 57.371 36.000 9.63 11.02 39.15 3.25
8 9 6.519679 TTCTGACTACGTAACATATGTGGT 57.480 37.500 9.63 10.46 41.31 4.16
9 10 8.420374 AATTTCTGACTACGTAACATATGTGG 57.580 34.615 9.63 4.76 33.02 4.17
10 11 8.540492 GGAATTTCTGACTACGTAACATATGTG 58.460 37.037 9.63 0.00 0.00 3.21
11 12 8.475639 AGGAATTTCTGACTACGTAACATATGT 58.524 33.333 1.41 1.41 0.00 2.29
12 13 8.873215 AGGAATTTCTGACTACGTAACATATG 57.127 34.615 0.00 0.00 0.00 1.78
13 14 8.692710 TGAGGAATTTCTGACTACGTAACATAT 58.307 33.333 0.00 0.00 0.00 1.78
14 15 8.058667 TGAGGAATTTCTGACTACGTAACATA 57.941 34.615 0.00 0.00 0.00 2.29
15 16 6.931838 TGAGGAATTTCTGACTACGTAACAT 58.068 36.000 0.00 0.00 0.00 2.71
16 17 6.015688 ACTGAGGAATTTCTGACTACGTAACA 60.016 38.462 0.00 0.00 0.00 2.41
17 18 6.388278 ACTGAGGAATTTCTGACTACGTAAC 58.612 40.000 0.00 0.00 0.00 2.50
18 19 6.585695 ACTGAGGAATTTCTGACTACGTAA 57.414 37.500 0.00 0.00 0.00 3.18
19 20 6.208007 TGAACTGAGGAATTTCTGACTACGTA 59.792 38.462 0.00 0.00 0.00 3.57
20 21 5.010719 TGAACTGAGGAATTTCTGACTACGT 59.989 40.000 0.00 0.00 0.00 3.57
21 22 5.470368 TGAACTGAGGAATTTCTGACTACG 58.530 41.667 0.00 0.00 0.00 3.51
22 23 6.459923 ACTGAACTGAGGAATTTCTGACTAC 58.540 40.000 0.00 0.00 0.00 2.73
23 24 6.672266 ACTGAACTGAGGAATTTCTGACTA 57.328 37.500 0.00 0.00 0.00 2.59
24 25 5.559148 ACTGAACTGAGGAATTTCTGACT 57.441 39.130 0.00 0.00 0.00 3.41
25 26 6.459923 AGTACTGAACTGAGGAATTTCTGAC 58.540 40.000 0.00 0.00 36.93 3.51
26 27 6.672266 AGTACTGAACTGAGGAATTTCTGA 57.328 37.500 0.00 0.00 36.93 3.27
27 28 7.607250 AGTAGTACTGAACTGAGGAATTTCTG 58.393 38.462 5.39 0.00 39.39 3.02
28 29 7.784470 AGTAGTACTGAACTGAGGAATTTCT 57.216 36.000 5.39 0.00 39.39 2.52
29 30 8.741841 AGTAGTAGTACTGAACTGAGGAATTTC 58.258 37.037 13.29 0.00 38.14 2.17
30 31 8.653036 AGTAGTAGTACTGAACTGAGGAATTT 57.347 34.615 13.29 0.00 38.14 1.82
44 45 6.380274 TGCCAATTAAGCTCAGTAGTAGTACT 59.620 38.462 8.14 8.14 40.38 2.73
45 46 6.570692 TGCCAATTAAGCTCAGTAGTAGTAC 58.429 40.000 0.00 0.00 0.00 2.73
46 47 6.785337 TGCCAATTAAGCTCAGTAGTAGTA 57.215 37.500 0.00 0.00 0.00 1.82
47 48 5.677319 TGCCAATTAAGCTCAGTAGTAGT 57.323 39.130 0.00 0.00 0.00 2.73
48 49 5.005779 CGTTGCCAATTAAGCTCAGTAGTAG 59.994 44.000 0.00 0.00 0.00 2.57
49 50 4.868171 CGTTGCCAATTAAGCTCAGTAGTA 59.132 41.667 0.00 0.00 0.00 1.82
50 51 3.684788 CGTTGCCAATTAAGCTCAGTAGT 59.315 43.478 0.00 0.00 0.00 2.73
51 52 3.684788 ACGTTGCCAATTAAGCTCAGTAG 59.315 43.478 0.00 0.00 0.00 2.57
52 53 3.670625 ACGTTGCCAATTAAGCTCAGTA 58.329 40.909 0.00 0.00 0.00 2.74
53 54 2.504367 ACGTTGCCAATTAAGCTCAGT 58.496 42.857 0.00 0.00 0.00 3.41
54 55 3.559238 AACGTTGCCAATTAAGCTCAG 57.441 42.857 0.00 0.00 0.00 3.35
55 56 4.202060 TGAAAACGTTGCCAATTAAGCTCA 60.202 37.500 0.00 0.00 0.00 4.26
56 57 4.295051 TGAAAACGTTGCCAATTAAGCTC 58.705 39.130 0.00 0.00 0.00 4.09
57 58 4.314740 TGAAAACGTTGCCAATTAAGCT 57.685 36.364 0.00 0.00 0.00 3.74
58 59 5.396750 TTTGAAAACGTTGCCAATTAAGC 57.603 34.783 0.00 0.00 0.00 3.09
61 62 9.261180 TGAAATATTTGAAAACGTTGCCAATTA 57.739 25.926 5.17 10.08 0.00 1.40
62 63 8.147642 TGAAATATTTGAAAACGTTGCCAATT 57.852 26.923 5.17 8.29 0.00 2.32
63 64 7.721286 TGAAATATTTGAAAACGTTGCCAAT 57.279 28.000 5.17 3.93 0.00 3.16
64 65 7.225538 ACATGAAATATTTGAAAACGTTGCCAA 59.774 29.630 5.17 6.54 0.00 4.52
65 66 6.703607 ACATGAAATATTTGAAAACGTTGCCA 59.296 30.769 5.17 0.00 0.00 4.92
66 67 7.116061 ACATGAAATATTTGAAAACGTTGCC 57.884 32.000 5.17 0.00 0.00 4.52
67 68 7.530190 CCAACATGAAATATTTGAAAACGTTGC 59.470 33.333 5.17 0.00 0.00 4.17
68 69 8.008844 CCCAACATGAAATATTTGAAAACGTTG 58.991 33.333 5.17 9.68 0.00 4.10
69 70 7.172361 CCCCAACATGAAATATTTGAAAACGTT 59.828 33.333 5.17 0.00 0.00 3.99
70 71 6.648725 CCCCAACATGAAATATTTGAAAACGT 59.351 34.615 5.17 0.00 0.00 3.99
71 72 6.402011 GCCCCAACATGAAATATTTGAAAACG 60.402 38.462 5.17 0.00 0.00 3.60
72 73 6.402011 CGCCCCAACATGAAATATTTGAAAAC 60.402 38.462 5.17 0.00 0.00 2.43
73 74 5.641209 CGCCCCAACATGAAATATTTGAAAA 59.359 36.000 5.17 0.00 0.00 2.29
74 75 5.174395 CGCCCCAACATGAAATATTTGAAA 58.826 37.500 5.17 0.00 0.00 2.69
75 76 4.753233 CGCCCCAACATGAAATATTTGAA 58.247 39.130 5.17 0.00 0.00 2.69
76 77 3.430098 GCGCCCCAACATGAAATATTTGA 60.430 43.478 5.17 0.00 0.00 2.69
77 78 2.865551 GCGCCCCAACATGAAATATTTG 59.134 45.455 5.17 0.00 0.00 2.32
78 79 2.499289 TGCGCCCCAACATGAAATATTT 59.501 40.909 4.18 0.00 0.00 1.40
79 80 2.106566 TGCGCCCCAACATGAAATATT 58.893 42.857 4.18 0.00 0.00 1.28
80 81 1.774110 TGCGCCCCAACATGAAATAT 58.226 45.000 4.18 0.00 0.00 1.28
81 82 1.550327 TTGCGCCCCAACATGAAATA 58.450 45.000 4.18 0.00 0.00 1.40
82 83 0.903942 ATTGCGCCCCAACATGAAAT 59.096 45.000 4.18 0.00 35.99 2.17
83 84 0.683973 AATTGCGCCCCAACATGAAA 59.316 45.000 4.18 0.00 35.99 2.69
84 85 0.246086 GAATTGCGCCCCAACATGAA 59.754 50.000 4.18 0.00 35.99 2.57
85 86 0.897401 TGAATTGCGCCCCAACATGA 60.897 50.000 4.18 0.00 35.99 3.07
86 87 0.458889 CTGAATTGCGCCCCAACATG 60.459 55.000 4.18 0.00 35.99 3.21
87 88 1.892338 CTGAATTGCGCCCCAACAT 59.108 52.632 4.18 0.00 35.99 2.71
88 89 2.929903 GCTGAATTGCGCCCCAACA 61.930 57.895 4.18 0.00 35.99 3.33
89 90 2.125952 GCTGAATTGCGCCCCAAC 60.126 61.111 4.18 0.00 35.99 3.77
90 91 2.283101 AGCTGAATTGCGCCCCAA 60.283 55.556 4.18 0.00 38.13 4.12
91 92 2.751436 GAGCTGAATTGCGCCCCA 60.751 61.111 4.18 0.00 38.13 4.96
92 93 2.342650 TTGAGCTGAATTGCGCCCC 61.343 57.895 4.18 0.00 38.13 5.80
93 94 1.153958 GTTGAGCTGAATTGCGCCC 60.154 57.895 4.18 0.00 38.13 6.13
94 95 1.512734 CGTTGAGCTGAATTGCGCC 60.513 57.895 4.18 0.00 38.13 6.53
95 96 0.385974 AACGTTGAGCTGAATTGCGC 60.386 50.000 0.00 0.00 38.13 6.09
96 97 2.036556 AAACGTTGAGCTGAATTGCG 57.963 45.000 0.00 0.00 38.13 4.85
97 98 3.371168 TGAAAACGTTGAGCTGAATTGC 58.629 40.909 0.00 0.00 0.00 3.56
98 99 8.894409 TTATATGAAAACGTTGAGCTGAATTG 57.106 30.769 0.00 0.00 0.00 2.32
102 103 8.282592 GCATATTATATGAAAACGTTGAGCTGA 58.717 33.333 15.63 0.00 0.00 4.26
103 104 8.285394 AGCATATTATATGAAAACGTTGAGCTG 58.715 33.333 15.63 0.00 0.00 4.24
104 105 8.285394 CAGCATATTATATGAAAACGTTGAGCT 58.715 33.333 15.63 0.00 0.00 4.09
105 106 7.059945 GCAGCATATTATATGAAAACGTTGAGC 59.940 37.037 15.63 0.00 0.00 4.26
106 107 8.069574 TGCAGCATATTATATGAAAACGTTGAG 58.930 33.333 15.63 0.00 0.00 3.02
107 108 7.924940 TGCAGCATATTATATGAAAACGTTGA 58.075 30.769 15.63 0.00 0.00 3.18
108 109 7.149080 GCTGCAGCATATTATATGAAAACGTTG 60.149 37.037 33.36 0.00 41.59 4.10
109 110 6.857964 GCTGCAGCATATTATATGAAAACGTT 59.142 34.615 33.36 0.00 41.59 3.99
110 111 6.373779 GCTGCAGCATATTATATGAAAACGT 58.626 36.000 33.36 0.00 41.59 3.99
111 112 6.843676 GCTGCAGCATATTATATGAAAACG 57.156 37.500 33.36 2.57 41.59 3.60
141 142 1.812571 GTGGTGTGATTCCATGACCAC 59.187 52.381 13.08 13.08 44.36 4.16
142 143 1.423161 TGTGGTGTGATTCCATGACCA 59.577 47.619 0.00 0.00 36.13 4.02
143 144 1.812571 GTGTGGTGTGATTCCATGACC 59.187 52.381 0.00 0.00 37.30 4.02
144 145 2.226437 GTGTGTGGTGTGATTCCATGAC 59.774 50.000 0.00 0.00 37.30 3.06
153 154 0.036875 TGTTGGTGTGTGTGGTGTGA 59.963 50.000 0.00 0.00 0.00 3.58
160 161 3.134985 TGGTACTACATGTTGGTGTGTGT 59.865 43.478 2.30 0.00 33.62 3.72
184 185 2.101582 CTCAACTATTCAGGAGGACCGG 59.898 54.545 0.00 0.00 41.83 5.28
185 186 2.761208 ACTCAACTATTCAGGAGGACCG 59.239 50.000 0.00 0.00 41.83 4.79
186 187 6.209788 CCTATACTCAACTATTCAGGAGGACC 59.790 46.154 0.00 0.00 0.00 4.46
187 188 6.778559 ACCTATACTCAACTATTCAGGAGGAC 59.221 42.308 0.00 0.00 0.00 3.85
198 208 6.717289 ACCAATGCAAACCTATACTCAACTA 58.283 36.000 0.00 0.00 0.00 2.24
203 213 5.185056 ACCAAACCAATGCAAACCTATACTC 59.815 40.000 0.00 0.00 0.00 2.59
236 246 1.142262 CTCACCTTAATTACCCCCGGG 59.858 57.143 15.80 15.80 42.03 5.73
254 264 0.587285 ACGTCGCCATCGTCTATCTC 59.413 55.000 0.00 0.00 36.85 2.75
281 291 2.603110 CGACGATGAACGATGGAATTGT 59.397 45.455 0.00 0.00 44.73 2.71
302 312 4.205181 GCGTGAAAAGAAGAAAAAGCTGAC 59.795 41.667 0.00 0.00 0.00 3.51
303 313 4.351192 GCGTGAAAAGAAGAAAAAGCTGA 58.649 39.130 0.00 0.00 0.00 4.26
304 314 3.178423 CGCGTGAAAAGAAGAAAAAGCTG 59.822 43.478 0.00 0.00 0.00 4.24
306 316 2.097877 GCGCGTGAAAAGAAGAAAAAGC 60.098 45.455 8.43 0.00 0.00 3.51
323 333 2.187599 CTCCAAACTCCAAAGGCGCG 62.188 60.000 0.00 0.00 0.00 6.86
324 334 1.172812 ACTCCAAACTCCAAAGGCGC 61.173 55.000 0.00 0.00 0.00 6.53
465 3945 2.559668 ACCTTTCAACTGGATGTGCATG 59.440 45.455 0.00 0.00 0.00 4.06
469 3960 2.480419 GTCGACCTTTCAACTGGATGTG 59.520 50.000 3.51 0.00 0.00 3.21
818 4366 0.315568 GCTAGTTCCGGCGAGATGAT 59.684 55.000 9.30 0.00 0.00 2.45
821 4369 1.240256 CTAGCTAGTTCCGGCGAGAT 58.760 55.000 9.30 0.00 34.04 2.75
822 4370 0.107312 ACTAGCTAGTTCCGGCGAGA 60.107 55.000 20.95 0.12 35.66 4.04
824 4372 0.454600 CAACTAGCTAGTTCCGGCGA 59.545 55.000 31.68 0.00 44.19 5.54
872 8210 6.809630 CGGAAGGAAGAAGAAGAAGAAATT 57.190 37.500 0.00 0.00 0.00 1.82
901 8245 5.041940 GGAACGATCGACACTAGCTTAATT 58.958 41.667 24.34 0.00 0.00 1.40
952 8296 8.646203 ATCAACAACAACGCAGGTTAGTTGATA 61.646 37.037 23.64 12.51 46.44 2.15
1051 8420 2.796651 GTAGGCGACGACGGTGAT 59.203 61.111 9.67 0.00 40.15 3.06
1102 8471 2.665000 GCTGCAGAGGTGGTAGCA 59.335 61.111 20.43 0.00 42.58 3.49
1123 8501 3.956848 GAGTAGACGGGTTAGGTTGGTAT 59.043 47.826 0.00 0.00 0.00 2.73
1164 8560 1.471119 TCGTCCGGAAAGTCTAGCAT 58.529 50.000 5.23 0.00 0.00 3.79
1166 8562 1.404391 TGATCGTCCGGAAAGTCTAGC 59.596 52.381 5.23 0.00 0.00 3.42
1382 8778 1.679305 GGTGACCTCGAGCTGGAGA 60.679 63.158 25.62 4.43 36.08 3.71
1455 8851 1.497161 CCGAAGAGGTATCCTGGGTT 58.503 55.000 0.00 0.00 31.76 4.11
1486 8882 0.955919 GAAGCAGAAGGTGAACCCGG 60.956 60.000 0.00 0.00 38.74 5.73
1553 8962 3.126514 GCATGATCCTCACTTGTCAGTTG 59.873 47.826 0.00 0.00 0.00 3.16
1554 8963 3.341823 GCATGATCCTCACTTGTCAGTT 58.658 45.455 0.00 0.00 0.00 3.16
1555 8964 2.355513 GGCATGATCCTCACTTGTCAGT 60.356 50.000 0.00 0.00 0.00 3.41
1556 8965 2.286872 GGCATGATCCTCACTTGTCAG 58.713 52.381 0.00 0.00 0.00 3.51
1557 8966 1.065199 GGGCATGATCCTCACTTGTCA 60.065 52.381 0.00 0.00 0.00 3.58
1558 8967 1.065199 TGGGCATGATCCTCACTTGTC 60.065 52.381 0.00 0.00 0.00 3.18
1559 8968 0.994247 TGGGCATGATCCTCACTTGT 59.006 50.000 0.00 0.00 0.00 3.16
1576 9032 1.480954 ACTACCCGCAGTACTTCATGG 59.519 52.381 0.00 0.00 0.00 3.66
1616 9080 7.218145 ACGAAATCGATTCACACATAAGTAC 57.782 36.000 11.83 0.00 43.02 2.73
1617 9081 8.186163 ACTACGAAATCGATTCACACATAAGTA 58.814 33.333 11.83 2.79 43.02 2.24
1618 9082 7.033791 ACTACGAAATCGATTCACACATAAGT 58.966 34.615 11.83 4.90 43.02 2.24
1619 9083 7.451281 ACTACGAAATCGATTCACACATAAG 57.549 36.000 11.83 4.32 43.02 1.73
1620 9084 8.964150 CATACTACGAAATCGATTCACACATAA 58.036 33.333 11.83 0.00 43.02 1.90
1827 9313 7.621428 TTGATCAATCTGAAACATCTCTTCC 57.379 36.000 3.38 0.00 0.00 3.46
1862 9366 9.539194 ACTGACATGTATATCCATCTATCTGAA 57.461 33.333 0.00 0.00 0.00 3.02
1863 9367 9.539194 AACTGACATGTATATCCATCTATCTGA 57.461 33.333 0.00 0.00 0.00 3.27
1883 9387 9.593134 ACTGATCAATCTGAAACTATAACTGAC 57.407 33.333 0.00 0.00 0.00 3.51
1897 9470 8.331730 TGGAATGCATATAACTGATCAATCTG 57.668 34.615 0.00 0.00 0.00 2.90
2084 9682 2.416296 CCATGTAGTGTGCTTGCATTGG 60.416 50.000 0.00 0.00 0.00 3.16
2163 9972 0.320421 GGTTCGGACTGCTGTTGCTA 60.320 55.000 0.00 0.00 40.48 3.49
2197 10006 5.067674 CACATGGTCACGGGATCAAAATAAT 59.932 40.000 3.85 0.00 37.77 1.28
2199 10008 3.944650 CACATGGTCACGGGATCAAAATA 59.055 43.478 3.85 0.00 37.77 1.40
2225 10034 2.296471 TGGTGGTTTGTCACACGTTTTT 59.704 40.909 0.00 0.00 39.27 1.94
2226 10035 1.887198 TGGTGGTTTGTCACACGTTTT 59.113 42.857 0.00 0.00 39.27 2.43
2227 10036 1.535833 TGGTGGTTTGTCACACGTTT 58.464 45.000 0.00 0.00 39.27 3.60
2228 10037 1.403679 CATGGTGGTTTGTCACACGTT 59.596 47.619 0.00 0.00 39.27 3.99
2229 10038 1.021202 CATGGTGGTTTGTCACACGT 58.979 50.000 0.00 0.00 39.27 4.49
2230 10039 1.002900 GACATGGTGGTTTGTCACACG 60.003 52.381 0.00 0.00 41.48 4.49
2231 10040 2.020720 TGACATGGTGGTTTGTCACAC 58.979 47.619 0.00 0.00 45.35 3.82
2232 10041 2.426842 TGACATGGTGGTTTGTCACA 57.573 45.000 0.00 0.00 45.35 3.58
2235 10044 5.004922 TCTTTTTGACATGGTGGTTTGTC 57.995 39.130 0.00 0.00 42.05 3.18
2236 10045 5.046663 ACTTCTTTTTGACATGGTGGTTTGT 60.047 36.000 0.00 0.00 0.00 2.83
2237 10046 5.291614 CACTTCTTTTTGACATGGTGGTTTG 59.708 40.000 0.00 0.00 0.00 2.93
2238 10047 5.046663 ACACTTCTTTTTGACATGGTGGTTT 60.047 36.000 0.00 0.00 0.00 3.27
2239 10048 4.466015 ACACTTCTTTTTGACATGGTGGTT 59.534 37.500 0.00 0.00 0.00 3.67
2240 10049 4.023291 ACACTTCTTTTTGACATGGTGGT 58.977 39.130 0.00 0.00 0.00 4.16
2241 10050 4.097741 TCACACTTCTTTTTGACATGGTGG 59.902 41.667 0.00 0.00 0.00 4.61
2242 10051 5.036737 GTCACACTTCTTTTTGACATGGTG 58.963 41.667 0.00 0.00 38.60 4.17
2243 10052 4.704540 TGTCACACTTCTTTTTGACATGGT 59.295 37.500 0.00 0.00 42.61 3.55
2244 10053 5.247507 TGTCACACTTCTTTTTGACATGG 57.752 39.130 0.00 0.00 42.61 3.66
2245 10054 6.034898 GGTTTGTCACACTTCTTTTTGACATG 59.965 38.462 4.23 0.00 45.81 3.21
2246 10055 6.099341 GGTTTGTCACACTTCTTTTTGACAT 58.901 36.000 4.23 0.00 45.81 3.06
2247 10056 5.010112 TGGTTTGTCACACTTCTTTTTGACA 59.990 36.000 0.00 0.00 45.08 3.58
2248 10057 5.465935 TGGTTTGTCACACTTCTTTTTGAC 58.534 37.500 0.00 0.00 39.09 3.18
2249 10058 5.713792 TGGTTTGTCACACTTCTTTTTGA 57.286 34.783 0.00 0.00 0.00 2.69
2250 10059 6.368516 ACATTGGTTTGTCACACTTCTTTTTG 59.631 34.615 0.00 0.00 0.00 2.44
2251 10060 6.463360 ACATTGGTTTGTCACACTTCTTTTT 58.537 32.000 0.00 0.00 0.00 1.94
2252 10061 6.036577 ACATTGGTTTGTCACACTTCTTTT 57.963 33.333 0.00 0.00 0.00 2.27
2253 10062 5.659440 ACATTGGTTTGTCACACTTCTTT 57.341 34.783 0.00 0.00 0.00 2.52
2254 10063 6.767524 TTACATTGGTTTGTCACACTTCTT 57.232 33.333 0.00 0.00 0.00 2.52
2255 10064 6.735694 GCATTACATTGGTTTGTCACACTTCT 60.736 38.462 0.00 0.00 0.00 2.85
2256 10065 5.402270 GCATTACATTGGTTTGTCACACTTC 59.598 40.000 0.00 0.00 0.00 3.01
2257 10066 5.163468 TGCATTACATTGGTTTGTCACACTT 60.163 36.000 0.00 0.00 0.00 3.16
2258 10067 4.340666 TGCATTACATTGGTTTGTCACACT 59.659 37.500 0.00 0.00 0.00 3.55
2259 10068 4.615949 TGCATTACATTGGTTTGTCACAC 58.384 39.130 0.00 0.00 0.00 3.82
2274 10083 7.391148 TGGGAAATTTCTCTACTTGCATTAC 57.609 36.000 18.69 0.00 0.00 1.89
2275 10084 8.593945 ATTGGGAAATTTCTCTACTTGCATTA 57.406 30.769 18.69 0.00 0.00 1.90
2286 10095 6.939622 ACTGAATTGGATTGGGAAATTTCTC 58.060 36.000 17.42 14.56 0.00 2.87
2288 10097 7.840931 AGTACTGAATTGGATTGGGAAATTTC 58.159 34.615 9.83 9.83 0.00 2.17
2291 10100 7.643123 AGTAGTACTGAATTGGATTGGGAAAT 58.357 34.615 5.39 0.00 0.00 2.17
2317 10126 4.109050 TGAAAACGTTGCCAATTCAACTC 58.891 39.130 0.00 1.20 42.98 3.01
2320 10296 8.994429 AATATATGAAAACGTTGCCAATTCAA 57.006 26.923 14.39 6.69 34.09 2.69
2340 10316 7.289782 AGCTGAATTGTGCCCCAAATAAATATA 59.710 33.333 0.00 0.00 36.44 0.86
2343 10319 4.225717 AGCTGAATTGTGCCCCAAATAAAT 59.774 37.500 0.00 0.00 36.44 1.40
2345 10321 3.172339 AGCTGAATTGTGCCCCAAATAA 58.828 40.909 0.00 0.00 36.44 1.40
2346 10322 2.760092 GAGCTGAATTGTGCCCCAAATA 59.240 45.455 0.00 0.00 36.44 1.40
2347 10323 1.551883 GAGCTGAATTGTGCCCCAAAT 59.448 47.619 0.00 0.00 36.44 2.32
2356 10332 0.886563 GCCTTGCTGAGCTGAATTGT 59.113 50.000 5.83 0.00 0.00 2.71
2374 10350 2.109126 GGAGTCTGGGAACGCATGC 61.109 63.158 7.91 7.91 0.00 4.06
2379 10355 2.100197 TCATACTGGAGTCTGGGAACG 58.900 52.381 0.00 0.00 0.00 3.95
2384 10360 3.511540 TGACTGTTCATACTGGAGTCTGG 59.488 47.826 0.00 0.00 35.18 3.86
2385 10361 4.219507 ACTGACTGTTCATACTGGAGTCTG 59.780 45.833 0.00 0.00 38.12 3.51
2386 10362 4.411927 ACTGACTGTTCATACTGGAGTCT 58.588 43.478 0.00 0.00 35.18 3.24
2387 10363 4.218635 TGACTGACTGTTCATACTGGAGTC 59.781 45.833 0.00 0.00 37.35 3.36
2388 10364 4.021894 GTGACTGACTGTTCATACTGGAGT 60.022 45.833 0.00 0.00 0.00 3.85
2389 10365 4.219507 AGTGACTGACTGTTCATACTGGAG 59.780 45.833 0.00 0.00 31.75 3.86
2390 10366 4.152647 AGTGACTGACTGTTCATACTGGA 58.847 43.478 0.00 0.00 31.75 3.86
2391 10367 4.021981 TGAGTGACTGACTGTTCATACTGG 60.022 45.833 0.00 0.00 33.83 4.00
2392 10368 5.048434 TCTGAGTGACTGACTGTTCATACTG 60.048 44.000 0.00 0.00 33.83 2.74
2393 10369 5.073428 TCTGAGTGACTGACTGTTCATACT 58.927 41.667 0.00 0.00 33.83 2.12
2394 10370 5.378292 TCTGAGTGACTGACTGTTCATAC 57.622 43.478 0.00 0.00 33.83 2.39
2395 10371 6.216569 GTTTCTGAGTGACTGACTGTTCATA 58.783 40.000 0.00 0.00 33.83 2.15
2396 10372 4.944619 TTCTGAGTGACTGACTGTTCAT 57.055 40.909 0.00 0.00 33.83 2.57
2397 10373 4.433615 GTTTCTGAGTGACTGACTGTTCA 58.566 43.478 0.00 0.00 33.83 3.18
2398 10374 3.804873 GGTTTCTGAGTGACTGACTGTTC 59.195 47.826 0.00 0.00 33.83 3.18
2399 10375 3.197766 TGGTTTCTGAGTGACTGACTGTT 59.802 43.478 0.00 0.00 33.83 3.16
2400 10376 2.766263 TGGTTTCTGAGTGACTGACTGT 59.234 45.455 0.00 0.00 33.83 3.55
2401 10377 3.459232 TGGTTTCTGAGTGACTGACTG 57.541 47.619 0.00 0.00 33.83 3.51
2438 10414 9.715121 ATCTGTAACGTGAGAAAATAAACCTTA 57.285 29.630 0.00 0.00 0.00 2.69
2467 10443 7.392393 TGCAGTCGGCTTGTCTATTATAGTATA 59.608 37.037 0.00 0.00 45.15 1.47
2468 10444 6.208797 TGCAGTCGGCTTGTCTATTATAGTAT 59.791 38.462 0.00 0.00 45.15 2.12
2493 10472 3.181455 TGATCCTGTTGTATAGGCGCAAT 60.181 43.478 10.83 4.48 35.23 3.56
2498 10477 3.134804 AGTGGTGATCCTGTTGTATAGGC 59.865 47.826 0.00 0.00 35.23 3.93
2505 10484 2.679837 GTGCATAGTGGTGATCCTGTTG 59.320 50.000 0.00 0.00 34.23 3.33
2507 10486 1.908619 TGTGCATAGTGGTGATCCTGT 59.091 47.619 0.00 0.00 34.23 4.00
2508 10487 2.696989 TGTGCATAGTGGTGATCCTG 57.303 50.000 0.00 0.00 34.23 3.86
2510 10489 2.880890 GGAATGTGCATAGTGGTGATCC 59.119 50.000 0.00 0.00 0.00 3.36
2511 10490 2.545526 CGGAATGTGCATAGTGGTGATC 59.454 50.000 0.00 0.00 0.00 2.92
2512 10491 2.170397 TCGGAATGTGCATAGTGGTGAT 59.830 45.455 0.00 0.00 0.00 3.06
2513 10492 1.552792 TCGGAATGTGCATAGTGGTGA 59.447 47.619 0.00 0.00 0.00 4.02
2514 10493 1.935873 CTCGGAATGTGCATAGTGGTG 59.064 52.381 0.00 0.00 0.00 4.17
2515 10494 1.134401 CCTCGGAATGTGCATAGTGGT 60.134 52.381 0.00 0.00 0.00 4.16
2536 10520 1.993391 TAGGGTTCCAAGGGCTCGG 60.993 63.158 0.00 0.00 0.00 4.63
2537 10521 1.221021 GTAGGGTTCCAAGGGCTCG 59.779 63.158 0.00 0.00 0.00 5.03
2538 10522 1.221021 CGTAGGGTTCCAAGGGCTC 59.779 63.158 0.00 0.00 0.00 4.70
2539 10523 1.538135 ACGTAGGGTTCCAAGGGCT 60.538 57.895 0.00 0.00 0.00 5.19
2540 10524 1.078637 GACGTAGGGTTCCAAGGGC 60.079 63.158 0.00 0.00 0.00 5.19


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

AutoCloner maintained by Alex Coulton.