Multiple sequence alignment - TraesCS7B01G462800

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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 TraesCS7B01G462800 chr7B 100.000 4112 0 0 1 4112 719924605 719920494 0.000000e+00 7594.0
1 TraesCS7B01G462800 chr7B 81.818 308 38 11 3678 3975 719857659 719857360 4.110000e-60 243.0
2 TraesCS7B01G462800 chr7B 95.683 139 6 0 2 140 677722234 677722096 1.490000e-54 224.0
3 TraesCS7B01G462800 chr7B 89.610 154 12 3 1107 1258 332242737 332242888 4.190000e-45 193.0
4 TraesCS7B01G462800 chr7B 92.771 83 6 0 3271 3353 428965927 428965845 2.010000e-23 121.0
5 TraesCS7B01G462800 chr7D 96.058 2765 77 8 1257 3995 622125736 622122978 0.000000e+00 4473.0
6 TraesCS7B01G462800 chr7D 89.829 993 70 10 141 1133 622126696 622125735 0.000000e+00 1245.0
7 TraesCS7B01G462800 chr7D 82.828 297 27 12 3678 3965 622102011 622101730 1.140000e-60 244.0
8 TraesCS7B01G462800 chr7D 82.437 279 40 8 379 652 84247330 84247604 6.870000e-58 235.0
9 TraesCS7B01G462800 chr7D 80.769 286 48 6 373 652 176580894 176580610 2.490000e-52 217.0
10 TraesCS7B01G462800 chr7D 93.197 147 9 1 2 147 29194055 29194201 8.950000e-52 215.0
11 TraesCS7B01G462800 chr7D 96.154 130 4 1 3983 4112 622122935 622122807 1.160000e-50 211.0
12 TraesCS7B01G462800 chr7D 85.326 184 21 5 3678 3861 622082375 622082198 7.020000e-43 185.0
13 TraesCS7B01G462800 chr7D 85.542 83 12 0 3271 3353 83656295 83656213 2.040000e-13 87.9
14 TraesCS7B01G462800 chr7D 84.270 89 11 3 134 221 598253674 598253760 2.630000e-12 84.2
15 TraesCS7B01G462800 chr7A 92.886 2769 143 13 1257 3989 717780395 717777645 0.000000e+00 3973.0
16 TraesCS7B01G462800 chr7A 89.790 999 82 11 141 1133 717781378 717780394 0.000000e+00 1262.0
17 TraesCS7B01G462800 chr7A 91.463 82 7 0 4007 4088 717777307 717777226 3.360000e-21 113.0
18 TraesCS7B01G462800 chr7A 85.321 109 13 2 3254 3361 33885908 33885802 4.350000e-20 110.0
19 TraesCS7B01G462800 chr7A 89.535 86 9 0 3272 3357 572188384 572188299 4.350000e-20 110.0
20 TraesCS7B01G462800 chr7A 86.250 80 7 3 141 219 68753631 68753555 2.630000e-12 84.2
21 TraesCS7B01G462800 chr7A 100.000 32 0 0 3991 4022 717777584 717777553 4.440000e-05 60.2
22 TraesCS7B01G462800 chr1D 81.787 291 44 6 365 649 425526937 425526650 6.870000e-58 235.0
23 TraesCS7B01G462800 chr1D 93.750 144 7 2 2 145 1237515 1237374 8.950000e-52 215.0
24 TraesCS7B01G462800 chr1D 88.608 79 8 1 141 219 494021439 494021362 1.220000e-15 95.3
25 TraesCS7B01G462800 chr1D 86.207 87 11 1 3271 3356 245893701 245893787 4.380000e-15 93.5
26 TraesCS7B01G462800 chr1D 84.337 83 13 0 3271 3353 403516128 403516046 9.470000e-12 82.4
27 TraesCS7B01G462800 chr1D 79.381 97 16 4 3261 3355 37302535 37302441 9.540000e-07 65.8
28 TraesCS7B01G462800 chr1D 80.682 88 13 4 3272 3357 416034107 416034192 9.540000e-07 65.8
29 TraesCS7B01G462800 chr2D 81.690 284 48 4 373 655 407983842 407984122 2.470000e-57 233.0
30 TraesCS7B01G462800 chr2D 95.683 139 6 0 2 140 617670952 617670814 1.490000e-54 224.0
31 TraesCS7B01G462800 chr2D 93.793 145 9 0 2 146 14902823 14902679 6.920000e-53 219.0
32 TraesCS7B01G462800 chr5D 96.403 139 5 0 2 140 428478454 428478316 3.200000e-56 230.0
33 TraesCS7B01G462800 chr5D 90.588 85 6 1 3271 3353 535136176 535136260 1.210000e-20 111.0
34 TraesCS7B01G462800 chr5D 87.500 88 11 0 3271 3358 188826617 188826530 7.270000e-18 102.0
35 TraesCS7B01G462800 chr5D 87.952 83 10 0 3271 3353 556451478 556451396 9.410000e-17 99.0
36 TraesCS7B01G462800 chr5D 89.706 68 3 3 153 219 501424168 501424104 2.630000e-12 84.2
37 TraesCS7B01G462800 chr5B 95.714 140 6 0 2 141 586210634 586210773 4.140000e-55 226.0
38 TraesCS7B01G462800 chr5B 94.048 84 5 0 3273 3356 27817302 27817219 1.200000e-25 128.0
39 TraesCS7B01G462800 chr3D 95.714 140 6 0 2 141 607728133 607727994 4.140000e-55 226.0
40 TraesCS7B01G462800 chr3D 80.866 277 50 3 365 639 607008109 607008384 8.950000e-52 215.0
41 TraesCS7B01G462800 chr3D 86.585 82 11 0 3272 3353 599385816 599385735 1.570000e-14 91.6
42 TraesCS7B01G462800 chr3D 86.420 81 7 3 141 219 583468354 583468432 7.320000e-13 86.1
43 TraesCS7B01G462800 chr1B 95.035 141 7 0 1 141 39707237 39707097 5.350000e-54 222.0
44 TraesCS7B01G462800 chr3B 81.429 280 43 5 365 642 652799907 652799635 1.920000e-53 220.0
45 TraesCS7B01G462800 chr4A 95.455 132 6 0 1130 1261 692357971 692357840 1.160000e-50 211.0
46 TraesCS7B01G462800 chr4A 90.217 92 8 1 3263 3353 590227919 590228010 7.220000e-23 119.0
47 TraesCS7B01G462800 chr4A 86.047 86 7 4 135 219 6350118 6350037 2.040000e-13 87.9
48 TraesCS7B01G462800 chr2B 96.124 129 5 0 1130 1258 545760386 545760514 1.160000e-50 211.0
49 TraesCS7B01G462800 chr2B 90.850 153 12 2 1132 1283 392896974 392896823 1.940000e-48 204.0
50 TraesCS7B01G462800 chr6B 95.420 131 5 1 1132 1261 207511027 207510897 1.500000e-49 207.0
51 TraesCS7B01G462800 chr6B 94.118 136 8 0 1130 1265 660666016 660665881 1.500000e-49 207.0
52 TraesCS7B01G462800 chr3A 94.776 134 5 1 1132 1263 644809255 644809122 1.500000e-49 207.0
53 TraesCS7B01G462800 chr3A 79.795 292 52 6 365 655 17733652 17733367 5.390000e-49 206.0
54 TraesCS7B01G462800 chr3A 87.342 79 6 4 141 218 719363351 719363276 2.040000e-13 87.9
55 TraesCS7B01G462800 chr2A 91.216 148 10 2 1132 1279 580939393 580939537 9.020000e-47 198.0
56 TraesCS7B01G462800 chrUn 90.000 150 14 1 1132 1281 10314604 10314456 4.190000e-45 193.0
57 TraesCS7B01G462800 chrUn 84.091 88 14 0 3267 3354 96588238 96588325 7.320000e-13 86.1
58 TraesCS7B01G462800 chr1A 87.356 87 11 0 3271 3357 436259735 436259649 2.620000e-17 100.0
59 TraesCS7B01G462800 chr1A 86.747 83 10 1 3272 3353 45583213 45583295 1.570000e-14 91.6
60 TraesCS7B01G462800 chr1A 85.542 83 12 0 3271 3353 498666620 498666538 2.040000e-13 87.9
61 TraesCS7B01G462800 chr1A 84.146 82 13 0 3271 3352 61387957 61387876 3.410000e-11 80.5
62 TraesCS7B01G462800 chr1A 82.418 91 10 6 3271 3358 535030839 535030926 1.590000e-09 75.0
63 TraesCS7B01G462800 chr4B 86.170 94 10 2 3261 3354 22844032 22844122 9.410000e-17 99.0
64 TraesCS7B01G462800 chr6D 80.208 96 15 4 3263 3356 45481861 45481768 7.380000e-08 69.4
65 TraesCS7B01G462800 chr6D 95.122 41 2 0 3313 3353 57176722 57176682 9.540000e-07 65.8
66 TraesCS7B01G462800 chr6D 91.304 46 2 2 3312 3356 437965410 437965454 1.230000e-05 62.1
67 TraesCS7B01G462800 chr6D 90.698 43 2 2 3314 3355 305174034 305174075 5.740000e-04 56.5
68 TraesCS7B01G462800 chr6D 78.125 96 16 5 3263 3355 369072992 369072899 5.740000e-04 56.5


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 TraesCS7B01G462800 chr7B 719920494 719924605 4111 True 7594.000000 7594 100.000000 1 4112 1 chr7B.!!$R4 4111
1 TraesCS7B01G462800 chr7D 622122807 622126696 3889 True 1976.333333 4473 94.013667 141 4112 3 chr7D.!!$R5 3971
2 TraesCS7B01G462800 chr7A 717777226 717781378 4152 True 1352.050000 3973 93.534750 141 4088 4 chr7A.!!$R4 3947

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
57 58 0.104304 GCTCACGAACCGGGACATAT 59.896 55.0 6.32 0.0 32.99 1.78 F
663 668 0.324943 GGCTGTGTCTGCCCTCTAAA 59.675 55.0 6.42 0.0 41.62 1.85 F
1149 1156 0.032813 ATACTCCCTCCGTCCGGAAA 60.033 55.0 5.23 0.0 44.66 3.13 F
1153 1160 0.032813 TCCCTCCGTCCGGAAATACT 60.033 55.0 5.23 0.0 44.66 2.12 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1131 1138 0.032813 ATTTCCGGACGGAGGGAGTA 60.033 55.000 13.64 0.0 46.06 2.59 R
2444 2493 0.671796 CCAAACGAAAACAGACCCCC 59.328 55.000 0.00 0.0 0.00 5.40 R
2680 2729 2.218454 CCCCTGTTACGACCCCACA 61.218 63.158 0.00 0.0 0.00 4.17 R
3580 3637 9.267084 TGCTTTGAACCCAATATCTTTAAAAAC 57.733 29.630 0.00 0.0 31.46 2.43 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
18 19 2.438434 GGGACCAATGCCCACGAG 60.438 66.667 0.00 0.00 45.31 4.18
19 20 2.438434 GGACCAATGCCCACGAGG 60.438 66.667 0.00 0.00 39.47 4.63
47 48 4.410400 CCCCCTGGGCTCACGAAC 62.410 72.222 7.39 0.00 35.35 3.95
48 49 4.410400 CCCCTGGGCTCACGAACC 62.410 72.222 7.39 0.00 0.00 3.62
49 50 4.760047 CCCTGGGCTCACGAACCG 62.760 72.222 0.00 0.00 0.00 4.44
50 51 4.760047 CCTGGGCTCACGAACCGG 62.760 72.222 0.00 0.00 0.00 5.28
51 52 4.760047 CTGGGCTCACGAACCGGG 62.760 72.222 6.32 0.00 0.00 5.73
53 54 4.754667 GGGCTCACGAACCGGGAC 62.755 72.222 6.32 0.00 32.99 4.46
54 55 3.998672 GGCTCACGAACCGGGACA 61.999 66.667 6.32 0.00 32.99 4.02
55 56 2.264794 GCTCACGAACCGGGACAT 59.735 61.111 6.32 0.00 32.99 3.06
56 57 1.514087 GCTCACGAACCGGGACATA 59.486 57.895 6.32 0.00 32.99 2.29
57 58 0.104304 GCTCACGAACCGGGACATAT 59.896 55.000 6.32 0.00 32.99 1.78
58 59 1.472728 GCTCACGAACCGGGACATATT 60.473 52.381 6.32 0.00 32.99 1.28
59 60 2.470821 CTCACGAACCGGGACATATTC 58.529 52.381 6.32 0.00 32.99 1.75
60 61 1.137479 TCACGAACCGGGACATATTCC 59.863 52.381 6.32 0.00 45.00 3.01
77 78 2.683475 CCCCATGGGTCCCTGTTC 59.317 66.667 29.33 0.00 38.25 3.18
78 79 2.237965 CCCCATGGGTCCCTGTTCA 61.238 63.158 29.33 0.00 38.25 3.18
79 80 1.583784 CCCCATGGGTCCCTGTTCAT 61.584 60.000 29.33 0.00 38.25 2.57
80 81 0.396139 CCCATGGGTCCCTGTTCATG 60.396 60.000 23.93 3.78 37.37 3.07
81 82 0.625316 CCATGGGTCCCTGTTCATGA 59.375 55.000 10.00 0.00 39.27 3.07
82 83 1.683011 CCATGGGTCCCTGTTCATGAC 60.683 57.143 10.00 0.00 39.27 3.06
83 84 1.283029 CATGGGTCCCTGTTCATGACT 59.717 52.381 10.00 0.00 39.27 3.41
84 85 0.692476 TGGGTCCCTGTTCATGACTG 59.308 55.000 10.00 0.00 0.00 3.51
85 86 0.984230 GGGTCCCTGTTCATGACTGA 59.016 55.000 0.00 0.00 0.00 3.41
86 87 1.351017 GGGTCCCTGTTCATGACTGAA 59.649 52.381 0.00 0.00 39.07 3.02
93 94 3.927555 TTCATGACTGAACCGGGAC 57.072 52.632 6.32 0.00 36.46 4.46
94 95 1.348064 TTCATGACTGAACCGGGACT 58.652 50.000 6.32 0.00 36.46 3.85
95 96 2.225382 TCATGACTGAACCGGGACTA 57.775 50.000 6.32 0.00 0.00 2.59
96 97 2.531771 TCATGACTGAACCGGGACTAA 58.468 47.619 6.32 0.00 0.00 2.24
97 98 3.104512 TCATGACTGAACCGGGACTAAT 58.895 45.455 6.32 0.00 0.00 1.73
98 99 3.118775 TCATGACTGAACCGGGACTAATG 60.119 47.826 6.32 0.82 0.00 1.90
99 100 1.553248 TGACTGAACCGGGACTAATGG 59.447 52.381 6.32 0.00 0.00 3.16
100 101 0.909623 ACTGAACCGGGACTAATGGG 59.090 55.000 6.32 0.00 0.00 4.00
101 102 0.909623 CTGAACCGGGACTAATGGGT 59.090 55.000 6.32 0.00 0.00 4.51
102 103 1.280998 CTGAACCGGGACTAATGGGTT 59.719 52.381 6.32 0.00 45.02 4.11
103 104 1.003812 TGAACCGGGACTAATGGGTTG 59.996 52.381 6.32 0.00 42.54 3.77
104 105 0.330267 AACCGGGACTAATGGGTTGG 59.670 55.000 6.32 0.00 41.04 3.77
105 106 1.453197 CCGGGACTAATGGGTTGGC 60.453 63.158 0.00 0.00 0.00 4.52
106 107 1.453197 CGGGACTAATGGGTTGGCC 60.453 63.158 0.00 0.00 0.00 5.36
107 108 1.694856 GGGACTAATGGGTTGGCCA 59.305 57.895 0.00 0.00 36.17 5.36
108 109 0.395724 GGGACTAATGGGTTGGCCAG 60.396 60.000 5.11 0.00 36.17 4.85
109 110 0.395724 GGACTAATGGGTTGGCCAGG 60.396 60.000 5.11 0.00 36.17 4.45
110 111 1.000359 ACTAATGGGTTGGCCAGGC 60.000 57.895 5.11 1.26 36.17 4.85
121 122 3.431725 GCCAGGCCCGAACGAAAG 61.432 66.667 0.00 0.00 0.00 2.62
122 123 3.431725 CCAGGCCCGAACGAAAGC 61.432 66.667 0.00 0.00 0.00 3.51
123 124 3.431725 CAGGCCCGAACGAAAGCC 61.432 66.667 0.00 12.37 46.13 4.35
125 126 4.717313 GGCCCGAACGAAAGCCCT 62.717 66.667 0.00 0.00 39.60 5.19
126 127 3.431725 GCCCGAACGAAAGCCCTG 61.432 66.667 0.00 0.00 0.00 4.45
127 128 2.032071 CCCGAACGAAAGCCCTGT 59.968 61.111 0.00 0.00 0.00 4.00
128 129 1.599797 CCCGAACGAAAGCCCTGTT 60.600 57.895 0.00 0.00 0.00 3.16
129 130 1.170290 CCCGAACGAAAGCCCTGTTT 61.170 55.000 0.00 0.00 0.00 2.83
130 131 0.666374 CCGAACGAAAGCCCTGTTTT 59.334 50.000 0.00 0.00 0.00 2.43
131 132 1.334689 CCGAACGAAAGCCCTGTTTTC 60.335 52.381 0.00 0.00 31.18 2.29
132 133 1.602377 CGAACGAAAGCCCTGTTTTCT 59.398 47.619 0.00 0.00 32.09 2.52
133 134 2.803956 CGAACGAAAGCCCTGTTTTCTA 59.196 45.455 0.00 0.00 32.09 2.10
134 135 3.363673 CGAACGAAAGCCCTGTTTTCTAC 60.364 47.826 0.00 0.00 32.09 2.59
135 136 3.487120 ACGAAAGCCCTGTTTTCTACT 57.513 42.857 0.00 0.00 32.09 2.57
136 137 4.612264 ACGAAAGCCCTGTTTTCTACTA 57.388 40.909 0.00 0.00 32.09 1.82
137 138 4.566987 ACGAAAGCCCTGTTTTCTACTAG 58.433 43.478 0.00 0.00 32.09 2.57
138 139 4.040095 ACGAAAGCCCTGTTTTCTACTAGT 59.960 41.667 0.00 0.00 32.09 2.57
139 140 4.389077 CGAAAGCCCTGTTTTCTACTAGTG 59.611 45.833 5.39 0.00 32.09 2.74
144 145 4.385825 CCCTGTTTTCTACTAGTGTGCAA 58.614 43.478 5.39 0.00 0.00 4.08
150 151 5.398176 TTTCTACTAGTGTGCAAACAACG 57.602 39.130 10.29 0.00 0.00 4.10
176 177 2.602933 CCAACTCACGCACACATGAAAG 60.603 50.000 0.00 0.00 0.00 2.62
222 223 8.233190 GTCATATAAGACCAAAGCTATGCATTC 58.767 37.037 3.54 0.00 32.36 2.67
238 239 7.984050 GCTATGCATTCTTATTAGCTAGGATGA 59.016 37.037 3.54 0.00 0.00 2.92
318 319 1.081481 TCCCCTCCAGTGAGTCACTA 58.919 55.000 25.04 10.38 43.43 2.74
362 363 0.532862 AGCTCACGAACCAACCACTG 60.533 55.000 0.00 0.00 0.00 3.66
371 372 1.966762 CCAACCACTGGCCAACATC 59.033 57.895 7.01 0.00 38.76 3.06
432 433 2.826725 CGAGGGTTCAGGTCTAGACTTT 59.173 50.000 21.88 8.55 0.00 2.66
450 451 1.438651 TTACACTGGTGCTCGCATTC 58.561 50.000 0.17 0.00 0.00 2.67
489 490 1.614317 CCTTCTGGTGATGTGGGTTCC 60.614 57.143 0.00 0.00 0.00 3.62
538 539 2.050351 ACGTCTGTGGCGACTTCG 60.050 61.111 0.00 5.07 43.27 3.79
558 559 3.867493 TCGTCAATCTCAAGATGATGTGC 59.133 43.478 0.00 0.00 34.49 4.57
560 561 3.943381 GTCAATCTCAAGATGATGTGCCA 59.057 43.478 0.00 0.00 34.49 4.92
561 562 3.943381 TCAATCTCAAGATGATGTGCCAC 59.057 43.478 0.00 0.00 34.49 5.01
595 596 3.243724 GAGGTGCTCATAAGGATAGGGT 58.756 50.000 0.00 0.00 0.00 4.34
600 601 2.104792 GCTCATAAGGATAGGGTGTGCA 59.895 50.000 0.00 0.00 31.69 4.57
642 647 6.256975 GGTGAGTAAATGTGCGTATGTATGAA 59.743 38.462 0.00 0.00 0.00 2.57
644 649 6.020201 TGAGTAAATGTGCGTATGTATGAACG 60.020 38.462 0.00 0.00 41.92 3.95
645 650 4.530094 AAATGTGCGTATGTATGAACGG 57.470 40.909 0.00 0.00 39.46 4.44
653 658 3.733988 CGTATGTATGAACGGCTGTGTCT 60.734 47.826 0.00 0.00 35.51 3.41
656 661 0.391130 TATGAACGGCTGTGTCTGCC 60.391 55.000 0.00 7.44 43.55 4.85
663 668 0.324943 GGCTGTGTCTGCCCTCTAAA 59.675 55.000 6.42 0.00 41.62 1.85
668 673 4.379918 GCTGTGTCTGCCCTCTAAATTTTC 60.380 45.833 0.00 0.00 0.00 2.29
786 793 7.043590 CCTCCACGTTTACATCTATAAAACTCG 60.044 40.741 0.00 0.00 32.25 4.18
792 799 3.381949 ACATCTATAAAACTCGAGGCGC 58.618 45.455 18.41 0.00 0.00 6.53
820 827 1.302431 CACGTTCACATGCCTCCCA 60.302 57.895 0.00 0.00 0.00 4.37
936 943 2.816087 CTGACAAACCATCACCTCCTTG 59.184 50.000 0.00 0.00 0.00 3.61
1002 1009 5.793952 CCGCGTAGTACTTATAAGCTGTATG 59.206 44.000 12.54 7.65 0.00 2.39
1128 1135 6.373779 TCGTAGTCTACTTTTGTTCTTACGG 58.626 40.000 8.37 0.00 0.00 4.02
1131 1138 7.965107 CGTAGTCTACTTTTGTTCTTACGGTAT 59.035 37.037 8.37 0.00 0.00 2.73
1134 1141 9.018582 AGTCTACTTTTGTTCTTACGGTATACT 57.981 33.333 2.25 0.00 0.00 2.12
1135 1142 9.283420 GTCTACTTTTGTTCTTACGGTATACTC 57.717 37.037 2.25 0.00 0.00 2.59
1136 1143 8.462016 TCTACTTTTGTTCTTACGGTATACTCC 58.538 37.037 2.25 0.00 0.00 3.85
1137 1144 6.401394 ACTTTTGTTCTTACGGTATACTCCC 58.599 40.000 2.25 0.00 0.00 4.30
1138 1145 6.212187 ACTTTTGTTCTTACGGTATACTCCCT 59.788 38.462 2.25 0.00 0.00 4.20
1139 1146 5.841957 TTGTTCTTACGGTATACTCCCTC 57.158 43.478 2.25 0.00 0.00 4.30
1140 1147 4.210331 TGTTCTTACGGTATACTCCCTCC 58.790 47.826 2.25 0.00 0.00 4.30
1141 1148 3.131709 TCTTACGGTATACTCCCTCCG 57.868 52.381 2.25 0.00 46.98 4.63
1144 1151 2.638744 CGGTATACTCCCTCCGTCC 58.361 63.158 2.25 0.00 38.45 4.79
1145 1152 1.233285 CGGTATACTCCCTCCGTCCG 61.233 65.000 2.25 0.00 38.45 4.79
1146 1153 0.892814 GGTATACTCCCTCCGTCCGG 60.893 65.000 2.25 0.00 0.00 5.14
1147 1154 0.109342 GTATACTCCCTCCGTCCGGA 59.891 60.000 0.00 0.00 42.90 5.14
1148 1155 0.846015 TATACTCCCTCCGTCCGGAA 59.154 55.000 5.23 0.00 44.66 4.30
1149 1156 0.032813 ATACTCCCTCCGTCCGGAAA 60.033 55.000 5.23 0.00 44.66 3.13
1150 1157 0.032813 TACTCCCTCCGTCCGGAAAT 60.033 55.000 5.23 0.00 44.66 2.17
1151 1158 0.032813 ACTCCCTCCGTCCGGAAATA 60.033 55.000 5.23 0.00 44.66 1.40
1152 1159 0.388294 CTCCCTCCGTCCGGAAATAC 59.612 60.000 5.23 0.00 44.66 1.89
1153 1160 0.032813 TCCCTCCGTCCGGAAATACT 60.033 55.000 5.23 0.00 44.66 2.12
1154 1161 0.828677 CCCTCCGTCCGGAAATACTT 59.171 55.000 5.23 0.00 44.66 2.24
1155 1162 1.472728 CCCTCCGTCCGGAAATACTTG 60.473 57.143 5.23 0.00 44.66 3.16
1156 1163 1.206371 CCTCCGTCCGGAAATACTTGT 59.794 52.381 5.23 0.00 44.66 3.16
1157 1164 2.537401 CTCCGTCCGGAAATACTTGTC 58.463 52.381 5.23 0.00 44.66 3.18
1158 1165 2.165845 CTCCGTCCGGAAATACTTGTCT 59.834 50.000 5.23 0.00 44.66 3.41
1159 1166 2.564062 TCCGTCCGGAAATACTTGTCTT 59.436 45.455 5.23 0.00 42.05 3.01
1160 1167 2.928116 CCGTCCGGAAATACTTGTCTTC 59.072 50.000 5.23 0.00 37.50 2.87
1161 1168 3.581755 CGTCCGGAAATACTTGTCTTCA 58.418 45.455 5.23 0.00 0.00 3.02
1162 1169 3.991773 CGTCCGGAAATACTTGTCTTCAA 59.008 43.478 5.23 0.00 0.00 2.69
1163 1170 4.449743 CGTCCGGAAATACTTGTCTTCAAA 59.550 41.667 5.23 0.00 32.87 2.69
1164 1171 5.049954 CGTCCGGAAATACTTGTCTTCAAAA 60.050 40.000 5.23 0.00 32.87 2.44
1165 1172 6.348213 CGTCCGGAAATACTTGTCTTCAAAAT 60.348 38.462 5.23 0.00 32.87 1.82
1166 1173 7.148540 CGTCCGGAAATACTTGTCTTCAAAATA 60.149 37.037 5.23 0.00 32.87 1.40
1167 1174 8.175716 GTCCGGAAATACTTGTCTTCAAAATAG 58.824 37.037 5.23 0.00 32.87 1.73
1168 1175 8.098286 TCCGGAAATACTTGTCTTCAAAATAGA 58.902 33.333 0.00 0.00 32.87 1.98
1169 1176 8.893727 CCGGAAATACTTGTCTTCAAAATAGAT 58.106 33.333 0.00 0.00 32.87 1.98
1177 1184 9.025041 ACTTGTCTTCAAAATAGATAAAAGGGG 57.975 33.333 0.00 0.00 32.87 4.79
1178 1185 9.243105 CTTGTCTTCAAAATAGATAAAAGGGGA 57.757 33.333 0.00 0.00 32.87 4.81
1179 1186 9.768215 TTGTCTTCAAAATAGATAAAAGGGGAT 57.232 29.630 0.00 0.00 0.00 3.85
1180 1187 9.189156 TGTCTTCAAAATAGATAAAAGGGGATG 57.811 33.333 0.00 0.00 0.00 3.51
1181 1188 9.190317 GTCTTCAAAATAGATAAAAGGGGATGT 57.810 33.333 0.00 0.00 0.00 3.06
1190 1197 7.469537 AGATAAAAGGGGATGTATCTAGACG 57.530 40.000 0.00 0.00 32.73 4.18
1191 1198 7.011382 AGATAAAAGGGGATGTATCTAGACGT 58.989 38.462 0.00 0.00 32.73 4.34
1192 1199 8.168725 AGATAAAAGGGGATGTATCTAGACGTA 58.831 37.037 0.00 0.00 32.73 3.57
1193 1200 8.896722 ATAAAAGGGGATGTATCTAGACGTAT 57.103 34.615 0.00 0.00 0.00 3.06
1194 1201 7.613551 AAAAGGGGATGTATCTAGACGTATT 57.386 36.000 0.00 0.00 0.00 1.89
1195 1202 7.613551 AAAGGGGATGTATCTAGACGTATTT 57.386 36.000 0.00 0.00 0.00 1.40
1196 1203 7.613551 AAGGGGATGTATCTAGACGTATTTT 57.386 36.000 0.00 0.00 0.00 1.82
1197 1204 8.716674 AAGGGGATGTATCTAGACGTATTTTA 57.283 34.615 0.00 0.00 0.00 1.52
1198 1205 8.350852 AGGGGATGTATCTAGACGTATTTTAG 57.649 38.462 0.00 0.00 0.00 1.85
1199 1206 7.949006 AGGGGATGTATCTAGACGTATTTTAGT 59.051 37.037 0.00 0.00 0.00 2.24
1200 1207 8.583296 GGGGATGTATCTAGACGTATTTTAGTT 58.417 37.037 0.00 0.00 0.00 2.24
1201 1208 9.623350 GGGATGTATCTAGACGTATTTTAGTTC 57.377 37.037 0.00 0.00 0.00 3.01
1234 1241 9.472361 CATCTCATTTTATCCATTTTGATGACC 57.528 33.333 0.00 0.00 32.05 4.02
1235 1242 8.592529 TCTCATTTTATCCATTTTGATGACCA 57.407 30.769 0.00 0.00 0.00 4.02
1236 1243 8.689061 TCTCATTTTATCCATTTTGATGACCAG 58.311 33.333 0.00 0.00 0.00 4.00
1237 1244 8.365060 TCATTTTATCCATTTTGATGACCAGT 57.635 30.769 0.00 0.00 0.00 4.00
1238 1245 9.473007 TCATTTTATCCATTTTGATGACCAGTA 57.527 29.630 0.00 0.00 0.00 2.74
1244 1251 6.851609 TCCATTTTGATGACCAGTATTTTCG 58.148 36.000 0.00 0.00 0.00 3.46
1245 1252 6.432783 TCCATTTTGATGACCAGTATTTTCGT 59.567 34.615 0.00 0.00 0.00 3.85
1246 1253 7.608376 TCCATTTTGATGACCAGTATTTTCGTA 59.392 33.333 0.00 0.00 0.00 3.43
1247 1254 7.696453 CCATTTTGATGACCAGTATTTTCGTAC 59.304 37.037 0.00 0.00 0.00 3.67
1248 1255 6.397831 TTTGATGACCAGTATTTTCGTACG 57.602 37.500 9.53 9.53 0.00 3.67
1249 1256 4.426416 TGATGACCAGTATTTTCGTACGG 58.574 43.478 16.52 0.00 0.00 4.02
1250 1257 4.158209 TGATGACCAGTATTTTCGTACGGA 59.842 41.667 16.52 2.84 0.00 4.69
1251 1258 4.100707 TGACCAGTATTTTCGTACGGAG 57.899 45.455 16.52 0.00 0.00 4.63
1252 1259 3.119388 TGACCAGTATTTTCGTACGGAGG 60.119 47.826 16.52 5.53 0.00 4.30
1253 1260 2.167075 ACCAGTATTTTCGTACGGAGGG 59.833 50.000 16.52 8.46 0.00 4.30
1254 1261 2.428171 CCAGTATTTTCGTACGGAGGGA 59.572 50.000 16.52 0.00 0.00 4.20
1255 1262 3.490419 CCAGTATTTTCGTACGGAGGGAG 60.490 52.174 16.52 0.00 0.00 4.30
1364 1371 3.057174 TCCGACATGTTTTATGGGTTTGC 60.057 43.478 0.00 0.00 0.00 3.68
1441 1451 2.814336 ACGCCTTTGAAGAATGGAGTTC 59.186 45.455 0.00 0.00 36.42 3.01
1521 1544 7.071069 AGATCATTTCCAGAGCACATATACA 57.929 36.000 0.00 0.00 0.00 2.29
1544 1567 8.771920 ACAATTTCTGATGATGTTTCTACGTA 57.228 30.769 0.00 0.00 0.00 3.57
1632 1656 9.790344 CCCATCTCAAATGAGTAATTTATCTCT 57.210 33.333 10.06 0.00 42.60 3.10
1680 1704 9.602568 TTCTAATTGACACGCCTTAATATTACA 57.397 29.630 0.00 0.00 0.00 2.41
1732 1756 2.956132 TGTTTGCCAAATCCTCTTCCA 58.044 42.857 0.00 0.00 0.00 3.53
1785 1810 2.556287 CGCGAGGCAAAGTTGGAC 59.444 61.111 0.00 0.00 0.00 4.02
1788 1813 2.250939 CGAGGCAAAGTTGGACGCA 61.251 57.895 0.00 0.00 0.00 5.24
1933 1958 6.206042 ACAGTTCCTAGAATATCCCTTGACT 58.794 40.000 0.00 0.00 0.00 3.41
1959 1984 2.415893 GCTTGATTTACCATGCGTGCTT 60.416 45.455 0.00 0.00 0.00 3.91
1969 1994 2.486918 CATGCGTGCTTGAGGATGATA 58.513 47.619 1.79 0.00 38.26 2.15
2007 2032 2.125673 CCACAGGAAGGTACGCGG 60.126 66.667 12.47 0.00 0.00 6.46
2066 2091 1.134965 ACGCTTGATGTCTACTCCTGC 60.135 52.381 0.00 0.00 0.00 4.85
2134 2159 2.512692 TGCTGGCCATATTGAACTGT 57.487 45.000 5.51 0.00 0.00 3.55
2247 2272 3.134442 ACTTTGATCAAGCAAGGGCAAAA 59.866 39.130 8.41 0.00 44.61 2.44
2249 2274 1.344114 TGATCAAGCAAGGGCAAAACC 59.656 47.619 0.00 0.00 44.61 3.27
2444 2493 2.350772 GGATCTTTGCACTGACAAACGG 60.351 50.000 0.00 0.00 34.68 4.44
2680 2729 6.945435 TCAAACTATGTTATTGGTCCACACAT 59.055 34.615 12.91 12.91 32.80 3.21
3360 3409 4.154942 GGGACGGAGGGAGTATATAACAA 58.845 47.826 0.00 0.00 0.00 2.83
3363 3412 5.148651 ACGGAGGGAGTATATAACAATGC 57.851 43.478 0.00 0.00 0.00 3.56
3580 3637 8.342634 GGTTGCACCATAGTACAAATGTATTAG 58.657 37.037 0.00 0.00 38.42 1.73
3729 3786 0.814010 AGCTTGTTTCCACGCGTTCT 60.814 50.000 10.22 0.00 40.55 3.01
3731 3788 1.398071 GCTTGTTTCCACGCGTTCTAC 60.398 52.381 10.22 6.30 0.00 2.59
3807 3864 5.610235 AAATCGGCAATGTTTCATTTTGG 57.390 34.783 0.00 0.00 0.00 3.28
3965 4022 1.593006 ACAACGTGAGAAGCAACGAAG 59.407 47.619 1.80 0.00 0.00 3.79
4040 4417 2.885135 TGCTGGATCTGGTTTCACAT 57.115 45.000 0.00 0.00 0.00 3.21
4103 4480 4.176271 GCTTGATTATTGGGTTTGTGCTC 58.824 43.478 0.00 0.00 0.00 4.26
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 2.438434 CTCGTGGGCATTGGTCCC 60.438 66.667 0.00 0.00 44.17 4.46
2 3 2.438434 CCTCGTGGGCATTGGTCC 60.438 66.667 0.00 0.00 40.08 4.46
31 32 4.410400 GGTTCGTGAGCCCAGGGG 62.410 72.222 7.91 3.48 38.57 4.79
32 33 4.760047 CGGTTCGTGAGCCCAGGG 62.760 72.222 0.00 0.00 0.00 4.45
33 34 4.760047 CCGGTTCGTGAGCCCAGG 62.760 72.222 0.00 0.00 0.00 4.45
34 35 4.760047 CCCGGTTCGTGAGCCCAG 62.760 72.222 0.00 0.00 0.00 4.45
36 37 4.754667 GTCCCGGTTCGTGAGCCC 62.755 72.222 0.00 0.00 0.00 5.19
37 38 1.952102 TATGTCCCGGTTCGTGAGCC 61.952 60.000 0.00 0.00 0.00 4.70
38 39 0.104304 ATATGTCCCGGTTCGTGAGC 59.896 55.000 0.00 0.00 0.00 4.26
39 40 2.470821 GAATATGTCCCGGTTCGTGAG 58.529 52.381 0.00 0.00 0.00 3.51
40 41 1.137479 GGAATATGTCCCGGTTCGTGA 59.863 52.381 0.00 0.00 41.10 4.35
41 42 1.578583 GGAATATGTCCCGGTTCGTG 58.421 55.000 0.00 0.00 41.10 4.35
61 62 0.396139 CATGAACAGGGACCCATGGG 60.396 60.000 30.23 30.23 42.03 4.00
62 63 0.625316 TCATGAACAGGGACCCATGG 59.375 55.000 14.60 4.14 37.55 3.66
63 64 1.283029 AGTCATGAACAGGGACCCATG 59.717 52.381 14.60 10.69 38.12 3.66
64 65 1.283029 CAGTCATGAACAGGGACCCAT 59.717 52.381 14.60 0.00 31.99 4.00
65 66 0.692476 CAGTCATGAACAGGGACCCA 59.308 55.000 14.60 0.00 31.99 4.51
66 67 0.984230 TCAGTCATGAACAGGGACCC 59.016 55.000 0.59 0.59 30.61 4.46
67 68 2.859165 TTCAGTCATGAACAGGGACC 57.141 50.000 0.00 0.00 40.54 4.46
75 76 1.348064 AGTCCCGGTTCAGTCATGAA 58.652 50.000 0.00 0.00 43.20 2.57
76 77 2.225382 TAGTCCCGGTTCAGTCATGA 57.775 50.000 0.00 0.00 0.00 3.07
77 78 3.198068 CATTAGTCCCGGTTCAGTCATG 58.802 50.000 0.00 0.00 0.00 3.07
78 79 2.170607 CCATTAGTCCCGGTTCAGTCAT 59.829 50.000 0.00 0.00 0.00 3.06
79 80 1.553248 CCATTAGTCCCGGTTCAGTCA 59.447 52.381 0.00 0.00 0.00 3.41
80 81 1.134491 CCCATTAGTCCCGGTTCAGTC 60.134 57.143 0.00 0.00 0.00 3.51
81 82 0.909623 CCCATTAGTCCCGGTTCAGT 59.090 55.000 0.00 0.00 0.00 3.41
82 83 0.909623 ACCCATTAGTCCCGGTTCAG 59.090 55.000 0.00 0.00 0.00 3.02
83 84 1.003812 CAACCCATTAGTCCCGGTTCA 59.996 52.381 0.00 0.00 36.45 3.18
84 85 1.680860 CCAACCCATTAGTCCCGGTTC 60.681 57.143 0.00 0.00 36.45 3.62
85 86 0.330267 CCAACCCATTAGTCCCGGTT 59.670 55.000 0.00 0.00 39.18 4.44
86 87 1.996086 CCAACCCATTAGTCCCGGT 59.004 57.895 0.00 0.00 0.00 5.28
87 88 1.453197 GCCAACCCATTAGTCCCGG 60.453 63.158 0.00 0.00 0.00 5.73
88 89 1.453197 GGCCAACCCATTAGTCCCG 60.453 63.158 0.00 0.00 0.00 5.14
89 90 0.395724 CTGGCCAACCCATTAGTCCC 60.396 60.000 7.01 0.00 44.33 4.46
90 91 0.395724 CCTGGCCAACCCATTAGTCC 60.396 60.000 7.01 0.00 44.33 3.85
91 92 1.037579 GCCTGGCCAACCCATTAGTC 61.038 60.000 7.01 0.00 44.33 2.59
92 93 1.000359 GCCTGGCCAACCCATTAGT 60.000 57.895 7.01 0.00 44.33 2.24
93 94 3.939564 GCCTGGCCAACCCATTAG 58.060 61.111 7.01 0.00 44.33 1.73
104 105 3.431725 CTTTCGTTCGGGCCTGGC 61.432 66.667 12.87 11.05 0.00 4.85
105 106 3.431725 GCTTTCGTTCGGGCCTGG 61.432 66.667 12.87 0.00 0.00 4.45
106 107 3.431725 GGCTTTCGTTCGGGCCTG 61.432 66.667 4.71 4.71 41.20 4.85
107 108 4.717313 GGGCTTTCGTTCGGGCCT 62.717 66.667 0.84 0.00 43.62 5.19
108 109 4.717313 AGGGCTTTCGTTCGGGCC 62.717 66.667 0.00 0.00 44.57 5.80
109 110 3.431725 CAGGGCTTTCGTTCGGGC 61.432 66.667 0.00 0.00 0.00 6.13
110 111 1.170290 AAACAGGGCTTTCGTTCGGG 61.170 55.000 0.00 0.00 0.00 5.14
111 112 0.666374 AAAACAGGGCTTTCGTTCGG 59.334 50.000 0.00 0.00 0.00 4.30
112 113 1.602377 AGAAAACAGGGCTTTCGTTCG 59.398 47.619 0.00 0.00 37.76 3.95
113 114 3.813724 AGTAGAAAACAGGGCTTTCGTTC 59.186 43.478 0.00 0.00 37.76 3.95
114 115 3.816994 AGTAGAAAACAGGGCTTTCGTT 58.183 40.909 0.00 0.00 37.76 3.85
115 116 3.487120 AGTAGAAAACAGGGCTTTCGT 57.513 42.857 0.00 0.00 37.76 3.85
116 117 4.389077 CACTAGTAGAAAACAGGGCTTTCG 59.611 45.833 3.59 0.00 37.76 3.46
117 118 5.179555 CACACTAGTAGAAAACAGGGCTTTC 59.820 44.000 3.59 0.00 33.75 2.62
118 119 5.063880 CACACTAGTAGAAAACAGGGCTTT 58.936 41.667 3.59 0.00 0.00 3.51
119 120 4.642429 CACACTAGTAGAAAACAGGGCTT 58.358 43.478 3.59 0.00 0.00 4.35
120 121 3.557264 GCACACTAGTAGAAAACAGGGCT 60.557 47.826 3.59 0.00 0.00 5.19
121 122 2.742589 GCACACTAGTAGAAAACAGGGC 59.257 50.000 3.59 0.00 0.00 5.19
122 123 4.002906 TGCACACTAGTAGAAAACAGGG 57.997 45.455 3.59 0.00 0.00 4.45
123 124 5.295787 TGTTTGCACACTAGTAGAAAACAGG 59.704 40.000 21.36 0.82 32.86 4.00
124 125 6.358118 TGTTTGCACACTAGTAGAAAACAG 57.642 37.500 21.36 1.43 32.86 3.16
125 126 6.548171 GTTGTTTGCACACTAGTAGAAAACA 58.452 36.000 21.36 21.36 34.46 2.83
126 127 5.675444 CGTTGTTTGCACACTAGTAGAAAAC 59.325 40.000 17.98 17.98 30.32 2.43
127 128 5.352016 ACGTTGTTTGCACACTAGTAGAAAA 59.648 36.000 3.59 0.00 30.32 2.29
128 129 4.871557 ACGTTGTTTGCACACTAGTAGAAA 59.128 37.500 3.59 0.00 30.32 2.52
129 130 4.435425 ACGTTGTTTGCACACTAGTAGAA 58.565 39.130 3.59 0.00 30.32 2.10
130 131 4.049546 ACGTTGTTTGCACACTAGTAGA 57.950 40.909 3.59 0.00 30.32 2.59
131 132 4.741185 TGTACGTTGTTTGCACACTAGTAG 59.259 41.667 4.37 0.00 30.32 2.57
132 133 4.503734 GTGTACGTTGTTTGCACACTAGTA 59.496 41.667 4.37 3.59 37.20 1.82
133 134 3.307782 GTGTACGTTGTTTGCACACTAGT 59.692 43.478 4.37 4.49 37.20 2.57
134 135 3.302870 GGTGTACGTTGTTTGCACACTAG 60.303 47.826 13.48 0.00 39.50 2.57
135 136 2.608546 GGTGTACGTTGTTTGCACACTA 59.391 45.455 13.48 0.00 39.50 2.74
136 137 1.399089 GGTGTACGTTGTTTGCACACT 59.601 47.619 13.48 0.00 39.50 3.55
137 138 1.130749 TGGTGTACGTTGTTTGCACAC 59.869 47.619 6.91 6.91 38.97 3.82
138 139 1.450025 TGGTGTACGTTGTTTGCACA 58.550 45.000 0.00 0.00 0.00 4.57
139 140 2.159490 AGTTGGTGTACGTTGTTTGCAC 60.159 45.455 0.00 0.00 0.00 4.57
144 145 1.928503 CGTGAGTTGGTGTACGTTGTT 59.071 47.619 0.00 0.00 0.00 2.83
150 151 0.580104 GTGTGCGTGAGTTGGTGTAC 59.420 55.000 0.00 0.00 0.00 2.90
176 177 3.507786 ACTTTGCTTTTGTCGGTGTTTC 58.492 40.909 0.00 0.00 0.00 2.78
298 299 0.191064 AGTGACTCACTGGAGGGGAA 59.809 55.000 11.07 0.00 43.63 3.97
343 344 0.532862 CAGTGGTTGGTTCGTGAGCT 60.533 55.000 0.00 0.00 0.00 4.09
371 372 0.179034 GCTCCTAGCCATCCAACCAG 60.179 60.000 0.00 0.00 34.48 4.00
432 433 0.608130 AGAATGCGAGCACCAGTGTA 59.392 50.000 0.00 0.00 0.00 2.90
489 490 2.572284 GGAACGTCTCCTCCCACG 59.428 66.667 8.87 0.00 41.61 4.94
507 508 3.501062 CACAGACGTCTACCTAGTCAACA 59.499 47.826 19.57 0.00 37.36 3.33
538 539 3.943381 TGGCACATCATCTTGAGATTGAC 59.057 43.478 0.90 0.00 31.21 3.18
558 559 1.034838 CCTCCGAGAGACTGAGGTGG 61.035 65.000 0.00 0.00 42.50 4.61
600 601 2.159156 TCACCTCTATAAACGCACGCAT 60.159 45.455 0.00 0.00 0.00 4.73
616 621 4.202245 ACATACGCACATTTACTCACCT 57.798 40.909 0.00 0.00 0.00 4.00
645 650 2.409948 ATTTAGAGGGCAGACACAGC 57.590 50.000 0.00 0.00 0.00 4.40
688 693 8.415192 TCTTGTTATATATGTGAACGTGGTTC 57.585 34.615 0.00 1.65 42.26 3.62
761 766 7.699391 TCGAGTTTTATAGATGTAAACGTGGAG 59.301 37.037 0.00 0.00 36.98 3.86
786 793 4.373116 TGTTCGGGTCTGCGCCTC 62.373 66.667 4.18 0.00 0.00 4.70
792 799 0.528901 TGTGAACGTGTTCGGGTCTG 60.529 55.000 8.11 0.00 42.28 3.51
820 827 8.765488 AAGGATTCAAATTTTTGGATTTTGGT 57.235 26.923 3.38 0.00 36.53 3.67
849 856 7.765307 ACAAAATGGCAAGTCTTGATACTATG 58.235 34.615 16.99 9.79 0.00 2.23
936 943 3.628646 ATTGACTGGTGGAGGCCGC 62.629 63.158 0.00 0.00 0.00 6.53
1128 1135 0.109342 TCCGGACGGAGGGAGTATAC 59.891 60.000 9.76 0.00 39.76 1.47
1131 1138 0.032813 ATTTCCGGACGGAGGGAGTA 60.033 55.000 13.64 0.00 46.06 2.59
1132 1139 0.032813 TATTTCCGGACGGAGGGAGT 60.033 55.000 13.64 0.00 46.06 3.85
1133 1140 0.388294 GTATTTCCGGACGGAGGGAG 59.612 60.000 13.64 0.00 46.06 4.30
1134 1141 0.032813 AGTATTTCCGGACGGAGGGA 60.033 55.000 13.64 4.95 46.06 4.20
1135 1142 0.828677 AAGTATTTCCGGACGGAGGG 59.171 55.000 13.64 0.00 46.06 4.30
1136 1143 1.206371 ACAAGTATTTCCGGACGGAGG 59.794 52.381 13.64 0.00 46.06 4.30
1137 1144 2.165845 AGACAAGTATTTCCGGACGGAG 59.834 50.000 13.64 3.15 46.06 4.63
1138 1145 2.173519 AGACAAGTATTTCCGGACGGA 58.826 47.619 1.83 9.76 43.52 4.69
1139 1146 2.667473 AGACAAGTATTTCCGGACGG 57.333 50.000 1.83 3.96 0.00 4.79
1140 1147 3.581755 TGAAGACAAGTATTTCCGGACG 58.418 45.455 1.83 0.00 0.00 4.79
1141 1148 5.934935 TTTGAAGACAAGTATTTCCGGAC 57.065 39.130 1.83 0.00 37.32 4.79
1142 1149 8.098286 TCTATTTTGAAGACAAGTATTTCCGGA 58.902 33.333 0.00 0.00 37.32 5.14
1143 1150 8.263940 TCTATTTTGAAGACAAGTATTTCCGG 57.736 34.615 0.00 0.00 37.32 5.14
1151 1158 9.025041 CCCCTTTTATCTATTTTGAAGACAAGT 57.975 33.333 0.00 0.00 37.32 3.16
1152 1159 9.243105 TCCCCTTTTATCTATTTTGAAGACAAG 57.757 33.333 0.00 0.00 37.32 3.16
1153 1160 9.768215 ATCCCCTTTTATCTATTTTGAAGACAA 57.232 29.630 0.00 0.00 0.00 3.18
1154 1161 9.189156 CATCCCCTTTTATCTATTTTGAAGACA 57.811 33.333 0.00 0.00 0.00 3.41
1155 1162 9.190317 ACATCCCCTTTTATCTATTTTGAAGAC 57.810 33.333 0.00 0.00 0.00 3.01
1164 1171 9.191479 CGTCTAGATACATCCCCTTTTATCTAT 57.809 37.037 0.00 0.00 34.52 1.98
1165 1172 8.168725 ACGTCTAGATACATCCCCTTTTATCTA 58.831 37.037 0.00 0.00 34.04 1.98
1166 1173 7.011382 ACGTCTAGATACATCCCCTTTTATCT 58.989 38.462 0.00 0.00 35.79 1.98
1167 1174 7.229581 ACGTCTAGATACATCCCCTTTTATC 57.770 40.000 0.00 0.00 0.00 1.75
1168 1175 8.896722 ATACGTCTAGATACATCCCCTTTTAT 57.103 34.615 0.00 0.00 0.00 1.40
1169 1176 8.716674 AATACGTCTAGATACATCCCCTTTTA 57.283 34.615 0.00 0.00 0.00 1.52
1170 1177 7.613551 AATACGTCTAGATACATCCCCTTTT 57.386 36.000 0.00 0.00 0.00 2.27
1171 1178 7.613551 AAATACGTCTAGATACATCCCCTTT 57.386 36.000 0.00 0.00 0.00 3.11
1172 1179 7.613551 AAAATACGTCTAGATACATCCCCTT 57.386 36.000 0.00 0.00 0.00 3.95
1173 1180 7.949006 ACTAAAATACGTCTAGATACATCCCCT 59.051 37.037 0.00 0.00 0.00 4.79
1174 1181 8.120140 ACTAAAATACGTCTAGATACATCCCC 57.880 38.462 0.00 0.00 0.00 4.81
1175 1182 9.623350 GAACTAAAATACGTCTAGATACATCCC 57.377 37.037 0.00 0.00 0.00 3.85
1208 1215 9.472361 GGTCATCAAAATGGATAAAATGAGATG 57.528 33.333 0.00 0.00 33.42 2.90
1209 1216 9.204337 TGGTCATCAAAATGGATAAAATGAGAT 57.796 29.630 0.00 0.00 33.42 2.75
1210 1217 8.592529 TGGTCATCAAAATGGATAAAATGAGA 57.407 30.769 0.00 0.00 33.42 3.27
1211 1218 8.472413 ACTGGTCATCAAAATGGATAAAATGAG 58.528 33.333 0.00 0.00 33.42 2.90
1212 1219 8.365060 ACTGGTCATCAAAATGGATAAAATGA 57.635 30.769 0.00 0.00 33.42 2.57
1218 1225 8.620416 CGAAAATACTGGTCATCAAAATGGATA 58.380 33.333 0.00 0.00 33.42 2.59
1219 1226 7.122650 ACGAAAATACTGGTCATCAAAATGGAT 59.877 33.333 0.00 0.00 33.42 3.41
1220 1227 6.432783 ACGAAAATACTGGTCATCAAAATGGA 59.567 34.615 0.00 0.00 33.42 3.41
1221 1228 6.620678 ACGAAAATACTGGTCATCAAAATGG 58.379 36.000 0.00 0.00 33.42 3.16
1222 1229 7.425309 CGTACGAAAATACTGGTCATCAAAATG 59.575 37.037 10.44 0.00 0.00 2.32
1223 1230 7.413657 CCGTACGAAAATACTGGTCATCAAAAT 60.414 37.037 18.76 0.00 0.00 1.82
1224 1231 6.128499 CCGTACGAAAATACTGGTCATCAAAA 60.128 38.462 18.76 0.00 0.00 2.44
1225 1232 5.349270 CCGTACGAAAATACTGGTCATCAAA 59.651 40.000 18.76 0.00 0.00 2.69
1226 1233 4.865925 CCGTACGAAAATACTGGTCATCAA 59.134 41.667 18.76 0.00 0.00 2.57
1227 1234 4.158209 TCCGTACGAAAATACTGGTCATCA 59.842 41.667 18.76 0.00 0.00 3.07
1228 1235 4.675510 TCCGTACGAAAATACTGGTCATC 58.324 43.478 18.76 0.00 0.00 2.92
1229 1236 4.441079 CCTCCGTACGAAAATACTGGTCAT 60.441 45.833 18.76 0.00 0.00 3.06
1230 1237 3.119388 CCTCCGTACGAAAATACTGGTCA 60.119 47.826 18.76 0.00 0.00 4.02
1231 1238 3.442100 CCTCCGTACGAAAATACTGGTC 58.558 50.000 18.76 0.00 0.00 4.02
1232 1239 2.167075 CCCTCCGTACGAAAATACTGGT 59.833 50.000 18.76 0.00 0.00 4.00
1233 1240 2.428171 TCCCTCCGTACGAAAATACTGG 59.572 50.000 18.76 5.60 0.00 4.00
1234 1241 3.129988 ACTCCCTCCGTACGAAAATACTG 59.870 47.826 18.76 0.00 0.00 2.74
1235 1242 3.359950 ACTCCCTCCGTACGAAAATACT 58.640 45.455 18.76 0.00 0.00 2.12
1236 1243 3.790152 ACTCCCTCCGTACGAAAATAC 57.210 47.619 18.76 0.00 0.00 1.89
1237 1244 6.545666 TGTATTACTCCCTCCGTACGAAAATA 59.454 38.462 18.76 5.82 0.00 1.40
1238 1245 5.360714 TGTATTACTCCCTCCGTACGAAAAT 59.639 40.000 18.76 6.70 0.00 1.82
1239 1246 4.704540 TGTATTACTCCCTCCGTACGAAAA 59.295 41.667 18.76 0.48 0.00 2.29
1240 1247 4.269183 TGTATTACTCCCTCCGTACGAAA 58.731 43.478 18.76 3.28 0.00 3.46
1241 1248 3.884895 TGTATTACTCCCTCCGTACGAA 58.115 45.455 18.76 0.00 0.00 3.85
1242 1249 3.558931 TGTATTACTCCCTCCGTACGA 57.441 47.619 18.76 1.79 0.00 3.43
1243 1250 3.567164 ACATGTATTACTCCCTCCGTACG 59.433 47.826 8.69 8.69 0.00 3.67
1244 1251 4.581824 TGACATGTATTACTCCCTCCGTAC 59.418 45.833 0.00 0.00 0.00 3.67
1245 1252 4.795469 TGACATGTATTACTCCCTCCGTA 58.205 43.478 0.00 0.00 0.00 4.02
1246 1253 3.638860 TGACATGTATTACTCCCTCCGT 58.361 45.455 0.00 0.00 0.00 4.69
1247 1254 4.665833 TTGACATGTATTACTCCCTCCG 57.334 45.455 0.00 0.00 0.00 4.63
1248 1255 5.992217 GTGATTGACATGTATTACTCCCTCC 59.008 44.000 0.00 0.00 0.00 4.30
1249 1256 6.582636 TGTGATTGACATGTATTACTCCCTC 58.417 40.000 0.00 0.00 0.00 4.30
1250 1257 6.560003 TGTGATTGACATGTATTACTCCCT 57.440 37.500 0.00 0.00 0.00 4.20
1323 1330 3.368427 CGGAATCTGATGGCATACGGTAT 60.368 47.826 0.00 0.00 0.00 2.73
1364 1371 9.880157 TGAGATGACACATGATATAATACATGG 57.120 33.333 0.00 10.78 45.31 3.66
1466 1477 6.077838 GTCCATTTGTAGCGTTAAAGAACAG 58.922 40.000 0.00 0.00 35.06 3.16
1471 1482 5.607119 AGTGTCCATTTGTAGCGTTAAAG 57.393 39.130 0.00 0.00 0.00 1.85
1550 1573 9.295825 ACATACAAACACCTTCAATTCTCAATA 57.704 29.630 0.00 0.00 0.00 1.90
1551 1574 8.084073 CACATACAAACACCTTCAATTCTCAAT 58.916 33.333 0.00 0.00 0.00 2.57
1574 1598 2.942804 TCTCCAAGAACCAAATGCACA 58.057 42.857 0.00 0.00 0.00 4.57
1646 1670 4.438744 GGCGTGTCAATTAGAATGGAAAGG 60.439 45.833 0.00 0.00 0.00 3.11
1732 1756 1.069765 CATTCCGGCTAGGCGATGT 59.930 57.895 37.12 19.87 40.77 3.06
1788 1813 4.555709 TGCTGGTTGCCGTCCGTT 62.556 61.111 0.00 0.00 42.00 4.44
1933 1958 1.135141 GCATGGTAAATCAAGCGGCAA 60.135 47.619 1.45 0.00 0.00 4.52
1959 1984 1.895798 GGCCACGAGATATCATCCTCA 59.104 52.381 5.32 0.00 0.00 3.86
2007 2032 0.807667 CCAGAGGCATGAGCGTACAC 60.808 60.000 0.00 0.00 43.41 2.90
2134 2159 5.522097 CAGTGACAGTTGTGTACACATTGTA 59.478 40.000 30.70 21.32 41.52 2.41
2148 2173 3.882131 AAGTGGCACAGTGACAGTT 57.118 47.368 22.15 22.15 43.85 3.16
2349 2398 3.054875 ACCTTAATAGTTTCCACCCGTCC 60.055 47.826 0.00 0.00 0.00 4.79
2444 2493 0.671796 CCAAACGAAAACAGACCCCC 59.328 55.000 0.00 0.00 0.00 5.40
2513 2562 8.833493 TCATCATATTAGTTGTCTGAATTGCAG 58.167 33.333 0.00 0.00 46.31 4.41
2680 2729 2.218454 CCCCTGTTACGACCCCACA 61.218 63.158 0.00 0.00 0.00 4.17
3580 3637 9.267084 TGCTTTGAACCCAATATCTTTAAAAAC 57.733 29.630 0.00 0.00 31.46 2.43
3729 3786 4.892934 ACAGGCCAATCAAACAAGAAAGTA 59.107 37.500 5.01 0.00 0.00 2.24
3731 3788 4.202141 TGACAGGCCAATCAAACAAGAAAG 60.202 41.667 5.01 0.00 0.00 2.62
3965 4022 1.299316 TACGCATTACTACGCCGCC 60.299 57.895 0.00 0.00 0.00 6.13


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

AutoCloner maintained by Alex Coulton.