Multiple sequence alignment - TraesCS1B01G443500

Loading Multiple Alignment...

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 TraesCS1B01G443500 chr1B 100.000 2618 0 0 1 2618 664760760 664763377 0.000000e+00 4835.0
1 TraesCS1B01G443500 chr1A 95.652 1495 46 13 1140 2618 573206400 573207891 0.000000e+00 2383.0
2 TraesCS1B01G443500 chr1A 92.547 805 38 11 312 1102 573205443 573206239 0.000000e+00 1134.0
3 TraesCS1B01G443500 chr1A 85.079 315 44 2 1 315 403724278 403724589 4.200000e-83 318.0
4 TraesCS1B01G443500 chr1A 84.071 226 26 10 461 682 498534237 498534456 2.640000e-50 209.0
5 TraesCS1B01G443500 chr1D 95.942 1035 28 2 1140 2160 477165961 477166995 0.000000e+00 1666.0
6 TraesCS1B01G443500 chr1D 93.665 805 34 12 312 1102 477164999 477165800 0.000000e+00 1188.0
7 TraesCS1B01G443500 chr1D 87.332 892 95 5 1140 2015 416356194 416355305 0.000000e+00 1005.0
8 TraesCS1B01G443500 chr1D 96.544 463 15 1 2157 2618 477167075 477167537 0.000000e+00 765.0
9 TraesCS1B01G443500 chr1D 84.839 310 43 4 1 309 205116458 205116764 2.530000e-80 309.0
10 TraesCS1B01G443500 chr1D 84.043 282 39 5 36 316 414928851 414928575 1.540000e-67 267.0
11 TraesCS1B01G443500 chr1D 82.594 293 46 4 25 315 324055932 324055643 1.200000e-63 254.0
12 TraesCS1B01G443500 chr1D 96.124 129 5 0 1140 1268 416356826 416356698 7.340000e-51 211.0
13 TraesCS1B01G443500 chr6B 86.073 876 107 5 1140 2001 52682906 52682032 0.000000e+00 928.0
14 TraesCS1B01G443500 chr6B 77.549 873 159 26 1167 2014 21459018 21459878 2.340000e-135 492.0
15 TraesCS1B01G443500 chr6B 86.547 446 47 4 1306 1738 55723726 55723281 1.820000e-131 479.0
16 TraesCS1B01G443500 chr6B 76.228 896 189 20 1140 2016 53062230 53061340 1.100000e-123 453.0
17 TraesCS1B01G443500 chr6B 93.137 306 21 0 2058 2363 55723272 55722967 1.430000e-122 449.0
18 TraesCS1B01G443500 chr6B 80.508 590 106 9 1431 2015 14622155 14621570 6.650000e-121 444.0
19 TraesCS1B01G443500 chr6B 75.146 857 193 11 1169 2008 26512465 26513318 4.090000e-103 385.0
20 TraesCS1B01G443500 chr6B 74.890 912 175 36 1140 2014 16608246 16609140 1.480000e-97 366.0
21 TraesCS1B01G443500 chr6B 78.281 442 88 8 1578 2014 41228412 41227974 7.140000e-71 278.0
22 TraesCS1B01G443500 chr6B 75.456 603 109 23 1422 2014 40657915 40657342 9.300000e-65 257.0
23 TraesCS1B01G443500 chr6B 93.478 138 8 1 2458 2594 55722606 55722469 1.230000e-48 204.0
24 TraesCS1B01G443500 chr6B 89.032 155 17 0 991 1145 52568252 52568098 2.660000e-45 193.0
25 TraesCS1B01G443500 chr6B 88.591 149 17 0 991 1139 16267382 16267530 5.760000e-42 182.0
26 TraesCS1B01G443500 chr6B 84.021 194 22 5 956 1145 15234894 15234706 7.450000e-41 178.0
27 TraesCS1B01G443500 chr6B 88.696 115 8 4 2402 2515 15383670 15383560 4.540000e-28 135.0
28 TraesCS1B01G443500 chr6B 84.524 84 11 1 2273 2356 670600928 670600847 6.010000e-12 82.4
29 TraesCS1B01G443500 chr6B 79.245 106 17 5 214 316 599879367 599879470 4.680000e-08 69.4
30 TraesCS1B01G443500 chr6D 79.953 1282 207 32 1140 2387 8858456 8859721 0.000000e+00 898.0
31 TraesCS1B01G443500 chr6D 79.361 1284 204 39 1140 2390 8480182 8478927 0.000000e+00 846.0
32 TraesCS1B01G443500 chr6D 81.050 876 144 13 1157 2014 34017745 34018616 0.000000e+00 678.0
33 TraesCS1B01G443500 chr6D 77.212 904 167 30 1140 2015 7993985 7993093 2.340000e-135 492.0
34 TraesCS1B01G443500 chr6D 79.167 504 96 9 1516 2014 25018088 25017589 8.970000e-90 340.0
35 TraesCS1B01G443500 chr6D 87.892 223 26 1 2391 2613 8571675 8571454 7.190000e-66 261.0
36 TraesCS1B01G443500 chr6D 87.387 222 23 5 2391 2610 8859885 8860103 1.560000e-62 250.0
37 TraesCS1B01G443500 chr6D 86.937 222 24 5 2391 2610 8478767 8478549 7.240000e-61 244.0
38 TraesCS1B01G443500 chr6D 87.097 217 21 5 2391 2601 34003040 34003255 3.370000e-59 239.0
39 TraesCS1B01G443500 chr6D 89.506 162 14 2 2160 2318 8572041 8571880 4.420000e-48 202.0
40 TraesCS1B01G443500 chr6D 87.333 150 17 2 994 1142 8397158 8397010 1.250000e-38 171.0
41 TraesCS1B01G443500 chr6D 87.248 149 19 0 991 1139 33995138 33995286 1.250000e-38 171.0
42 TraesCS1B01G443500 chr6D 86.452 155 17 3 991 1142 8402428 8402275 1.610000e-37 167.0
43 TraesCS1B01G443500 chr6D 75.094 265 50 13 1157 1410 9057173 9057432 2.750000e-20 110.0
44 TraesCS1B01G443500 chr2B 77.455 896 170 24 1140 2012 709425894 709425008 8.360000e-140 507.0
45 TraesCS1B01G443500 chr2B 90.135 223 19 3 444 666 89506046 89506265 1.190000e-73 287.0
46 TraesCS1B01G443500 chr2B 88.272 162 19 0 75 236 664125383 664125544 7.390000e-46 195.0
47 TraesCS1B01G443500 chr2B 75.562 356 55 24 1963 2307 748707386 748707720 2.100000e-31 147.0
48 TraesCS1B01G443500 chr2B 79.882 169 25 2 2195 2356 373067306 373067140 5.920000e-22 115.0
49 TraesCS1B01G443500 chr6A 77.344 896 174 22 1140 2012 8202048 8201159 1.080000e-138 503.0
50 TraesCS1B01G443500 chrUn 84.375 416 46 8 1804 2207 477783064 477782656 8.790000e-105 390.0
51 TraesCS1B01G443500 chrUn 83.529 85 10 3 2273 2356 65789500 65789419 2.790000e-10 76.8
52 TraesCS1B01G443500 chrUn 100.000 29 0 0 167 195 160367913 160367941 1.000000e-03 54.7
53 TraesCS1B01G443500 chr4D 82.353 306 49 4 7 311 166935884 166936185 7.190000e-66 261.0
54 TraesCS1B01G443500 chr4D 82.578 287 43 6 25 308 166825998 166825716 2.010000e-61 246.0
55 TraesCS1B01G443500 chr5A 83.486 218 33 3 461 678 613583509 613583723 1.590000e-47 200.0
56 TraesCS1B01G443500 chr4A 86.364 176 24 0 1 176 535877593 535877418 2.660000e-45 193.0
57 TraesCS1B01G443500 chr7B 81.532 222 34 7 462 682 329084842 329085057 2.680000e-40 176.0
58 TraesCS1B01G443500 chr7B 74.834 151 35 3 167 316 46971454 46971306 6.050000e-07 65.8
59 TraesCS1B01G443500 chr3D 87.261 157 15 3 993 1145 33330499 33330344 9.630000e-40 174.0
60 TraesCS1B01G443500 chr3A 76.266 316 71 4 1 315 234117042 234117354 5.800000e-37 165.0
61 TraesCS1B01G443500 chr7D 80.357 224 35 9 462 681 37589752 37589970 7.500000e-36 161.0
62 TraesCS1B01G443500 chr7D 79.911 224 34 11 462 682 436499200 436498985 1.250000e-33 154.0
63 TraesCS1B01G443500 chr7A 78.603 229 37 10 462 681 216831409 216831184 9.770000e-30 141.0
64 TraesCS1B01G443500 chr5B 89.565 115 7 3 2402 2515 556788351 556788241 9.770000e-30 141.0
65 TraesCS1B01G443500 chr5B 71.956 271 64 12 52 316 679307005 679307269 4.680000e-08 69.4
66 TraesCS1B01G443500 chr3B 77.889 199 35 6 118 315 417718631 417718441 5.920000e-22 115.0
67 TraesCS1B01G443500 chr5D 74.170 271 58 11 51 315 212563920 212563656 4.610000e-18 102.0
68 TraesCS1B01G443500 chr5D 82.927 82 12 2 2273 2354 42074858 42074937 3.610000e-09 73.1


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 TraesCS1B01G443500 chr1B 664760760 664763377 2617 False 4835.000000 4835 100.000000 1 2618 1 chr1B.!!$F1 2617
1 TraesCS1B01G443500 chr1A 573205443 573207891 2448 False 1758.500000 2383 94.099500 312 2618 2 chr1A.!!$F3 2306
2 TraesCS1B01G443500 chr1D 477164999 477167537 2538 False 1206.333333 1666 95.383667 312 2618 3 chr1D.!!$F2 2306
3 TraesCS1B01G443500 chr1D 416355305 416356826 1521 True 608.000000 1005 91.728000 1140 2015 2 chr1D.!!$R3 875
4 TraesCS1B01G443500 chr6B 52682032 52682906 874 True 928.000000 928 86.073000 1140 2001 1 chr6B.!!$R7 861
5 TraesCS1B01G443500 chr6B 21459018 21459878 860 False 492.000000 492 77.549000 1167 2014 1 chr6B.!!$F3 847
6 TraesCS1B01G443500 chr6B 53061340 53062230 890 True 453.000000 453 76.228000 1140 2016 1 chr6B.!!$R8 876
7 TraesCS1B01G443500 chr6B 14621570 14622155 585 True 444.000000 444 80.508000 1431 2015 1 chr6B.!!$R1 584
8 TraesCS1B01G443500 chr6B 26512465 26513318 853 False 385.000000 385 75.146000 1169 2008 1 chr6B.!!$F4 839
9 TraesCS1B01G443500 chr6B 55722469 55723726 1257 True 377.333333 479 91.054000 1306 2594 3 chr6B.!!$R10 1288
10 TraesCS1B01G443500 chr6B 16608246 16609140 894 False 366.000000 366 74.890000 1140 2014 1 chr6B.!!$F2 874
11 TraesCS1B01G443500 chr6B 40657342 40657915 573 True 257.000000 257 75.456000 1422 2014 1 chr6B.!!$R4 592
12 TraesCS1B01G443500 chr6D 34017745 34018616 871 False 678.000000 678 81.050000 1157 2014 1 chr6D.!!$F4 857
13 TraesCS1B01G443500 chr6D 8858456 8860103 1647 False 574.000000 898 83.670000 1140 2610 2 chr6D.!!$F5 1470
14 TraesCS1B01G443500 chr6D 8478549 8480182 1633 True 545.000000 846 83.149000 1140 2610 2 chr6D.!!$R5 1470
15 TraesCS1B01G443500 chr6D 7993093 7993985 892 True 492.000000 492 77.212000 1140 2015 1 chr6D.!!$R1 875
16 TraesCS1B01G443500 chr6D 8571454 8572041 587 True 231.500000 261 88.699000 2160 2613 2 chr6D.!!$R6 453
17 TraesCS1B01G443500 chr2B 709425008 709425894 886 True 507.000000 507 77.455000 1140 2012 1 chr2B.!!$R2 872
18 TraesCS1B01G443500 chr6A 8201159 8202048 889 True 503.000000 503 77.344000 1140 2012 1 chr6A.!!$R1 872

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
317 318 0.039527 AAACACGAAATTCTGCCGGC 60.04 50.0 22.73 22.73 0.0 6.13 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1738 2548 0.25589 AATGTATGCCGGTTCCAGCT 59.744 50.0 1.9 0.0 0.0 4.24 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
29 30 4.351054 CCCACACACCAGCCCCTC 62.351 72.222 0.00 0.00 0.00 4.30
30 31 4.351054 CCACACACCAGCCCCTCC 62.351 72.222 0.00 0.00 0.00 4.30
31 32 4.351054 CACACACCAGCCCCTCCC 62.351 72.222 0.00 0.00 0.00 4.30
32 33 4.918360 ACACACCAGCCCCTCCCA 62.918 66.667 0.00 0.00 0.00 4.37
33 34 3.579302 CACACCAGCCCCTCCCAA 61.579 66.667 0.00 0.00 0.00 4.12
34 35 2.535317 ACACCAGCCCCTCCCAAT 60.535 61.111 0.00 0.00 0.00 3.16
35 36 2.276740 CACCAGCCCCTCCCAATC 59.723 66.667 0.00 0.00 0.00 2.67
36 37 2.128226 ACCAGCCCCTCCCAATCT 59.872 61.111 0.00 0.00 0.00 2.40
37 38 1.544917 ACCAGCCCCTCCCAATCTT 60.545 57.895 0.00 0.00 0.00 2.40
38 39 0.253630 ACCAGCCCCTCCCAATCTTA 60.254 55.000 0.00 0.00 0.00 2.10
39 40 1.152649 CCAGCCCCTCCCAATCTTAT 58.847 55.000 0.00 0.00 0.00 1.73
40 41 1.074566 CCAGCCCCTCCCAATCTTATC 59.925 57.143 0.00 0.00 0.00 1.75
41 42 1.074566 CAGCCCCTCCCAATCTTATCC 59.925 57.143 0.00 0.00 0.00 2.59
42 43 1.149101 GCCCCTCCCAATCTTATCCA 58.851 55.000 0.00 0.00 0.00 3.41
43 44 1.202940 GCCCCTCCCAATCTTATCCAC 60.203 57.143 0.00 0.00 0.00 4.02
44 45 1.425448 CCCCTCCCAATCTTATCCACC 59.575 57.143 0.00 0.00 0.00 4.61
45 46 1.425448 CCCTCCCAATCTTATCCACCC 59.575 57.143 0.00 0.00 0.00 4.61
46 47 1.425448 CCTCCCAATCTTATCCACCCC 59.575 57.143 0.00 0.00 0.00 4.95
47 48 2.135189 CTCCCAATCTTATCCACCCCA 58.865 52.381 0.00 0.00 0.00 4.96
48 49 2.107204 CTCCCAATCTTATCCACCCCAG 59.893 54.545 0.00 0.00 0.00 4.45
49 50 1.145738 CCCAATCTTATCCACCCCAGG 59.854 57.143 0.00 0.00 0.00 4.45
50 51 2.135189 CCAATCTTATCCACCCCAGGA 58.865 52.381 0.00 0.00 43.01 3.86
51 52 2.158608 CCAATCTTATCCACCCCAGGAC 60.159 54.545 0.00 0.00 41.30 3.85
52 53 1.821088 ATCTTATCCACCCCAGGACC 58.179 55.000 0.00 0.00 41.30 4.46
53 54 0.327191 TCTTATCCACCCCAGGACCC 60.327 60.000 0.00 0.00 41.30 4.46
54 55 0.327576 CTTATCCACCCCAGGACCCT 60.328 60.000 0.00 0.00 41.30 4.34
55 56 1.028638 TTATCCACCCCAGGACCCTA 58.971 55.000 0.00 0.00 41.30 3.53
56 57 0.266753 TATCCACCCCAGGACCCTAC 59.733 60.000 0.00 0.00 41.30 3.18
57 58 2.562973 ATCCACCCCAGGACCCTACC 62.563 65.000 0.00 0.00 41.30 3.18
58 59 3.081409 CACCCCAGGACCCTACCG 61.081 72.222 0.00 0.00 34.73 4.02
62 63 3.470888 CCAGGACCCTACCGCCAG 61.471 72.222 0.00 0.00 34.73 4.85
63 64 3.470888 CAGGACCCTACCGCCAGG 61.471 72.222 0.00 0.00 45.13 4.45
76 77 2.762459 CCAGGGCCCGTAGCAGTA 60.762 66.667 18.44 0.00 46.50 2.74
77 78 2.797278 CCAGGGCCCGTAGCAGTAG 61.797 68.421 18.44 0.00 46.50 2.57
78 79 2.444140 AGGGCCCGTAGCAGTAGG 60.444 66.667 18.44 0.00 46.50 3.18
79 80 2.762875 GGGCCCGTAGCAGTAGGT 60.763 66.667 5.69 0.00 46.50 3.08
80 81 2.499685 GGCCCGTAGCAGTAGGTG 59.500 66.667 0.00 0.00 46.50 4.00
81 82 2.356780 GGCCCGTAGCAGTAGGTGT 61.357 63.158 0.00 0.00 46.50 4.16
82 83 1.595357 GCCCGTAGCAGTAGGTGTT 59.405 57.895 0.00 0.00 42.97 3.32
83 84 0.819582 GCCCGTAGCAGTAGGTGTTA 59.180 55.000 0.00 0.00 42.97 2.41
84 85 1.202382 GCCCGTAGCAGTAGGTGTTAG 60.202 57.143 0.00 0.00 42.97 2.34
85 86 2.097825 CCCGTAGCAGTAGGTGTTAGT 58.902 52.381 0.00 0.00 0.00 2.24
86 87 3.282021 CCCGTAGCAGTAGGTGTTAGTA 58.718 50.000 0.00 0.00 0.00 1.82
87 88 3.314635 CCCGTAGCAGTAGGTGTTAGTAG 59.685 52.174 0.00 0.00 0.00 2.57
88 89 3.243002 CCGTAGCAGTAGGTGTTAGTAGC 60.243 52.174 0.00 0.00 0.00 3.58
89 90 3.243002 CGTAGCAGTAGGTGTTAGTAGCC 60.243 52.174 0.00 0.00 0.00 3.93
90 91 3.103080 AGCAGTAGGTGTTAGTAGCCT 57.897 47.619 0.00 0.00 36.47 4.58
91 92 4.246712 AGCAGTAGGTGTTAGTAGCCTA 57.753 45.455 0.00 0.00 34.07 3.93
94 95 3.978718 GTAGGTGTTAGTAGCCTACCG 57.021 52.381 8.37 0.00 45.38 4.02
95 96 1.109609 AGGTGTTAGTAGCCTACCGC 58.890 55.000 0.00 0.00 36.55 5.68
96 97 0.103755 GGTGTTAGTAGCCTACCGCC 59.896 60.000 0.00 0.00 38.78 6.13
97 98 0.819582 GTGTTAGTAGCCTACCGCCA 59.180 55.000 0.00 0.00 38.78 5.69
98 99 1.108776 TGTTAGTAGCCTACCGCCAG 58.891 55.000 0.00 0.00 38.78 4.85
99 100 0.388294 GTTAGTAGCCTACCGCCAGG 59.612 60.000 0.00 0.00 45.13 4.45
100 101 0.757935 TTAGTAGCCTACCGCCAGGG 60.758 60.000 0.00 0.00 43.47 4.45
112 113 3.000819 CCAGGGTCTGTGGCGGTA 61.001 66.667 0.00 0.00 0.00 4.02
113 114 2.579201 CAGGGTCTGTGGCGGTAG 59.421 66.667 0.00 0.00 0.00 3.18
114 115 2.683933 AGGGTCTGTGGCGGTAGG 60.684 66.667 0.00 0.00 0.00 3.18
115 116 3.782443 GGGTCTGTGGCGGTAGGG 61.782 72.222 0.00 0.00 0.00 3.53
116 117 3.001406 GGTCTGTGGCGGTAGGGT 61.001 66.667 0.00 0.00 0.00 4.34
117 118 2.577593 GTCTGTGGCGGTAGGGTC 59.422 66.667 0.00 0.00 0.00 4.46
118 119 2.682494 TCTGTGGCGGTAGGGTCC 60.682 66.667 0.00 0.00 0.00 4.46
119 120 2.683933 CTGTGGCGGTAGGGTCCT 60.684 66.667 0.00 0.00 0.00 3.85
120 121 2.203877 TGTGGCGGTAGGGTCCTT 60.204 61.111 0.00 0.00 0.00 3.36
121 122 1.838073 CTGTGGCGGTAGGGTCCTTT 61.838 60.000 0.00 0.00 0.00 3.11
122 123 1.377612 GTGGCGGTAGGGTCCTTTT 59.622 57.895 0.00 0.00 0.00 2.27
123 124 0.675837 GTGGCGGTAGGGTCCTTTTC 60.676 60.000 0.00 0.00 0.00 2.29
124 125 1.077930 GGCGGTAGGGTCCTTTTCC 60.078 63.158 0.00 0.00 0.00 3.13
125 126 1.681076 GCGGTAGGGTCCTTTTCCA 59.319 57.895 0.00 0.00 0.00 3.53
126 127 0.675837 GCGGTAGGGTCCTTTTCCAC 60.676 60.000 0.00 0.00 0.00 4.02
127 128 0.390735 CGGTAGGGTCCTTTTCCACG 60.391 60.000 0.00 0.00 0.00 4.94
128 129 0.689055 GGTAGGGTCCTTTTCCACGT 59.311 55.000 0.00 0.00 0.00 4.49
129 130 1.338484 GGTAGGGTCCTTTTCCACGTC 60.338 57.143 0.00 0.00 0.00 4.34
130 131 1.345415 GTAGGGTCCTTTTCCACGTCA 59.655 52.381 0.00 0.00 0.00 4.35
131 132 0.841289 AGGGTCCTTTTCCACGTCAA 59.159 50.000 0.00 0.00 0.00 3.18
132 133 0.949397 GGGTCCTTTTCCACGTCAAC 59.051 55.000 0.00 0.00 0.00 3.18
133 134 1.476291 GGGTCCTTTTCCACGTCAACT 60.476 52.381 0.00 0.00 0.00 3.16
134 135 1.602377 GGTCCTTTTCCACGTCAACTG 59.398 52.381 0.00 0.00 0.00 3.16
135 136 2.285977 GTCCTTTTCCACGTCAACTGT 58.714 47.619 0.00 0.00 0.00 3.55
136 137 3.460103 GTCCTTTTCCACGTCAACTGTA 58.540 45.455 0.00 0.00 0.00 2.74
137 138 3.493503 GTCCTTTTCCACGTCAACTGTAG 59.506 47.826 0.00 0.00 0.00 2.74
138 139 3.133362 TCCTTTTCCACGTCAACTGTAGT 59.867 43.478 0.00 0.00 0.00 2.73
139 140 3.875134 CCTTTTCCACGTCAACTGTAGTT 59.125 43.478 0.00 0.00 39.12 2.24
149 150 2.561478 AACTGTAGTTGATGGCCGTT 57.439 45.000 0.00 0.00 36.80 4.44
150 151 3.688694 AACTGTAGTTGATGGCCGTTA 57.311 42.857 0.00 0.00 36.80 3.18
151 152 3.247006 ACTGTAGTTGATGGCCGTTAG 57.753 47.619 0.00 0.00 0.00 2.34
152 153 2.093658 ACTGTAGTTGATGGCCGTTAGG 60.094 50.000 0.00 0.00 41.62 2.69
162 163 3.269347 CCGTTAGGCGCAATCCCG 61.269 66.667 10.83 4.09 39.71 5.14
163 164 2.510691 CGTTAGGCGCAATCCCGT 60.511 61.111 10.83 0.00 0.00 5.28
164 165 2.522638 CGTTAGGCGCAATCCCGTC 61.523 63.158 10.83 0.00 0.00 4.79
165 166 1.448893 GTTAGGCGCAATCCCGTCA 60.449 57.895 10.83 0.00 34.80 4.35
166 167 1.448893 TTAGGCGCAATCCCGTCAC 60.449 57.895 10.83 0.00 34.80 3.67
167 168 2.862674 TTAGGCGCAATCCCGTCACC 62.863 60.000 10.83 0.00 34.80 4.02
168 169 4.778143 GGCGCAATCCCGTCACCT 62.778 66.667 10.83 0.00 32.16 4.00
169 170 2.185867 GCGCAATCCCGTCACCTA 59.814 61.111 0.30 0.00 0.00 3.08
170 171 2.171725 GCGCAATCCCGTCACCTAC 61.172 63.158 0.30 0.00 0.00 3.18
171 172 1.520787 CGCAATCCCGTCACCTACC 60.521 63.158 0.00 0.00 0.00 3.18
172 173 1.520787 GCAATCCCGTCACCTACCG 60.521 63.158 0.00 0.00 0.00 4.02
173 174 1.520787 CAATCCCGTCACCTACCGC 60.521 63.158 0.00 0.00 0.00 5.68
174 175 2.728435 AATCCCGTCACCTACCGCC 61.728 63.158 0.00 0.00 0.00 6.13
175 176 3.968837 ATCCCGTCACCTACCGCCA 62.969 63.158 0.00 0.00 0.00 5.69
176 177 4.143333 CCCGTCACCTACCGCCAG 62.143 72.222 0.00 0.00 0.00 4.85
177 178 4.143333 CCGTCACCTACCGCCAGG 62.143 72.222 0.00 0.00 45.13 4.45
178 179 4.143333 CGTCACCTACCGCCAGGG 62.143 72.222 5.62 0.00 43.47 4.45
179 180 2.682494 GTCACCTACCGCCAGGGA 60.682 66.667 5.62 0.00 43.47 4.20
180 181 2.682494 TCACCTACCGCCAGGGAC 60.682 66.667 5.62 0.00 43.47 4.46
181 182 3.782443 CACCTACCGCCAGGGACC 61.782 72.222 5.62 0.00 43.47 4.46
215 216 3.408853 GGGGGCTACCACCTGGAC 61.409 72.222 0.00 0.00 42.91 4.02
216 217 3.408853 GGGGCTACCACCTGGACC 61.409 72.222 0.00 0.00 39.85 4.46
217 218 3.408853 GGGCTACCACCTGGACCC 61.409 72.222 0.00 2.44 38.47 4.46
218 219 3.408853 GGCTACCACCTGGACCCC 61.409 72.222 0.00 0.00 38.94 4.95
219 220 2.285442 GCTACCACCTGGACCCCT 60.285 66.667 0.00 0.00 38.94 4.79
220 221 1.002533 GCTACCACCTGGACCCCTA 59.997 63.158 0.00 0.00 38.94 3.53
221 222 1.049289 GCTACCACCTGGACCCCTAG 61.049 65.000 0.00 0.00 38.94 3.02
222 223 1.002533 TACCACCTGGACCCCTAGC 59.997 63.158 0.00 0.00 38.94 3.42
223 224 2.866523 TACCACCTGGACCCCTAGCG 62.867 65.000 0.00 0.00 38.94 4.26
224 225 3.470888 CACCTGGACCCCTAGCGG 61.471 72.222 0.00 0.00 0.00 5.52
225 226 4.007323 ACCTGGACCCCTAGCGGT 62.007 66.667 0.00 0.00 39.49 5.68
226 227 2.281091 CCTGGACCCCTAGCGGTA 59.719 66.667 0.00 0.00 35.79 4.02
227 228 1.833049 CCTGGACCCCTAGCGGTAG 60.833 68.421 14.73 14.73 35.79 3.18
228 229 1.833049 CTGGACCCCTAGCGGTAGG 60.833 68.421 29.84 29.84 45.25 3.18
229 230 3.232483 GGACCCCTAGCGGTAGGC 61.232 72.222 31.08 19.14 44.39 3.93
230 231 2.443390 GACCCCTAGCGGTAGGCA 60.443 66.667 31.08 0.00 44.39 4.75
231 232 2.039951 ACCCCTAGCGGTAGGCAA 59.960 61.111 31.08 0.00 44.39 4.52
232 233 1.614226 ACCCCTAGCGGTAGGCAAA 60.614 57.895 31.08 0.00 44.39 3.68
233 234 1.202769 ACCCCTAGCGGTAGGCAAAA 61.203 55.000 31.08 0.00 44.39 2.44
234 235 0.463833 CCCCTAGCGGTAGGCAAAAG 60.464 60.000 31.08 18.49 44.39 2.27
235 236 0.463833 CCCTAGCGGTAGGCAAAAGG 60.464 60.000 31.08 15.17 44.39 3.11
236 237 3.129729 CCCTAGCGGTAGGCAAAAGGT 62.130 57.143 31.08 0.00 44.39 3.50
237 238 4.590280 CCCTAGCGGTAGGCAAAAGGTT 62.590 54.545 31.08 0.00 44.39 3.50
239 240 2.636299 GCGGTAGGCAAAAGGTTCA 58.364 52.632 0.00 0.00 42.87 3.18
240 241 1.173913 GCGGTAGGCAAAAGGTTCAT 58.826 50.000 0.00 0.00 42.87 2.57
241 242 2.361789 GCGGTAGGCAAAAGGTTCATA 58.638 47.619 0.00 0.00 42.87 2.15
242 243 2.949644 GCGGTAGGCAAAAGGTTCATAT 59.050 45.455 0.00 0.00 42.87 1.78
243 244 3.243068 GCGGTAGGCAAAAGGTTCATATG 60.243 47.826 0.00 0.00 42.87 1.78
244 245 3.243068 CGGTAGGCAAAAGGTTCATATGC 60.243 47.826 0.00 0.00 36.31 3.14
250 251 5.473796 GCAAAAGGTTCATATGCCAATTG 57.526 39.130 0.00 0.00 0.00 2.32
251 252 4.937015 GCAAAAGGTTCATATGCCAATTGT 59.063 37.500 4.43 0.00 0.00 2.71
252 253 5.412286 GCAAAAGGTTCATATGCCAATTGTT 59.588 36.000 4.43 0.00 0.00 2.83
253 254 6.072563 GCAAAAGGTTCATATGCCAATTGTTT 60.073 34.615 4.43 0.00 0.00 2.83
254 255 7.521910 GCAAAAGGTTCATATGCCAATTGTTTT 60.522 33.333 4.43 0.00 0.00 2.43
255 256 8.351461 CAAAAGGTTCATATGCCAATTGTTTTT 58.649 29.630 4.43 0.00 0.00 1.94
256 257 7.437793 AAGGTTCATATGCCAATTGTTTTTG 57.562 32.000 4.43 0.00 0.00 2.44
257 258 5.412286 AGGTTCATATGCCAATTGTTTTTGC 59.588 36.000 4.43 0.57 0.00 3.68
258 259 5.180868 GGTTCATATGCCAATTGTTTTTGCA 59.819 36.000 8.46 8.46 0.00 4.08
259 260 6.293845 GGTTCATATGCCAATTGTTTTTGCAA 60.294 34.615 9.83 0.00 0.00 4.08
260 261 6.872628 TCATATGCCAATTGTTTTTGCAAA 57.127 29.167 8.05 8.05 31.63 3.68
261 262 7.268199 TCATATGCCAATTGTTTTTGCAAAA 57.732 28.000 20.46 20.46 31.63 2.44
262 263 7.361127 TCATATGCCAATTGTTTTTGCAAAAG 58.639 30.769 22.78 11.80 31.63 2.27
263 264 4.367386 TGCCAATTGTTTTTGCAAAAGG 57.633 36.364 22.78 19.62 32.81 3.11
264 265 3.129988 TGCCAATTGTTTTTGCAAAAGGG 59.870 39.130 22.78 18.01 31.36 3.95
265 266 3.490590 GCCAATTGTTTTTGCAAAAGGGG 60.491 43.478 22.78 18.29 31.36 4.79
266 267 3.490590 CCAATTGTTTTTGCAAAAGGGGC 60.491 43.478 22.78 15.07 31.63 5.80
267 268 1.756430 TTGTTTTTGCAAAAGGGGCC 58.244 45.000 22.78 11.29 0.00 5.80
268 269 0.620556 TGTTTTTGCAAAAGGGGCCA 59.379 45.000 22.78 13.36 0.00 5.36
269 270 1.308047 GTTTTTGCAAAAGGGGCCAG 58.692 50.000 22.78 0.00 0.00 4.85
270 271 1.134250 GTTTTTGCAAAAGGGGCCAGA 60.134 47.619 22.78 4.75 0.00 3.86
271 272 1.433121 TTTTGCAAAAGGGGCCAGAT 58.567 45.000 20.46 0.00 0.00 2.90
272 273 0.975887 TTTGCAAAAGGGGCCAGATC 59.024 50.000 10.02 0.00 0.00 2.75
273 274 0.904394 TTGCAAAAGGGGCCAGATCC 60.904 55.000 4.39 0.00 0.00 3.36
274 275 2.060383 GCAAAAGGGGCCAGATCCC 61.060 63.158 4.39 0.00 45.80 3.85
282 283 1.605753 GGGCCAGATCCCGAAATAAC 58.394 55.000 4.39 0.00 36.38 1.89
283 284 1.133915 GGGCCAGATCCCGAAATAACA 60.134 52.381 4.39 0.00 36.38 2.41
284 285 1.947456 GGCCAGATCCCGAAATAACAC 59.053 52.381 0.00 0.00 0.00 3.32
285 286 1.947456 GCCAGATCCCGAAATAACACC 59.053 52.381 0.00 0.00 0.00 4.16
286 287 2.682563 GCCAGATCCCGAAATAACACCA 60.683 50.000 0.00 0.00 0.00 4.17
287 288 2.943033 CCAGATCCCGAAATAACACCAC 59.057 50.000 0.00 0.00 0.00 4.16
288 289 3.605634 CAGATCCCGAAATAACACCACA 58.394 45.455 0.00 0.00 0.00 4.17
289 290 4.006989 CAGATCCCGAAATAACACCACAA 58.993 43.478 0.00 0.00 0.00 3.33
290 291 4.457603 CAGATCCCGAAATAACACCACAAA 59.542 41.667 0.00 0.00 0.00 2.83
291 292 5.048364 CAGATCCCGAAATAACACCACAAAA 60.048 40.000 0.00 0.00 0.00 2.44
292 293 4.839668 TCCCGAAATAACACCACAAAAG 57.160 40.909 0.00 0.00 0.00 2.27
293 294 3.570550 TCCCGAAATAACACCACAAAAGG 59.429 43.478 0.00 0.00 0.00 3.11
294 295 3.305744 CCCGAAATAACACCACAAAAGGG 60.306 47.826 0.00 0.00 0.00 3.95
295 296 3.319689 CCGAAATAACACCACAAAAGGGT 59.680 43.478 0.00 0.00 39.88 4.34
296 297 4.542735 CGAAATAACACCACAAAAGGGTC 58.457 43.478 0.00 0.00 36.19 4.46
297 298 4.036971 CGAAATAACACCACAAAAGGGTCA 59.963 41.667 0.00 0.00 36.19 4.02
298 299 5.450688 CGAAATAACACCACAAAAGGGTCAA 60.451 40.000 0.00 0.00 36.19 3.18
299 300 5.941555 AATAACACCACAAAAGGGTCAAA 57.058 34.783 0.00 0.00 36.19 2.69
300 301 5.941555 ATAACACCACAAAAGGGTCAAAA 57.058 34.783 0.00 0.00 36.19 2.44
301 302 3.603158 ACACCACAAAAGGGTCAAAAC 57.397 42.857 0.00 0.00 36.19 2.43
302 303 2.900546 ACACCACAAAAGGGTCAAAACA 59.099 40.909 0.00 0.00 36.19 2.83
303 304 3.258228 CACCACAAAAGGGTCAAAACAC 58.742 45.455 0.00 0.00 36.19 3.32
304 305 2.094442 ACCACAAAAGGGTCAAAACACG 60.094 45.455 0.00 0.00 31.49 4.49
305 306 2.164624 CCACAAAAGGGTCAAAACACGA 59.835 45.455 0.00 0.00 32.44 4.35
306 307 3.367498 CCACAAAAGGGTCAAAACACGAA 60.367 43.478 0.00 0.00 32.44 3.85
307 308 4.238514 CACAAAAGGGTCAAAACACGAAA 58.761 39.130 0.00 0.00 32.44 3.46
308 309 4.867608 CACAAAAGGGTCAAAACACGAAAT 59.132 37.500 0.00 0.00 32.44 2.17
309 310 5.350091 CACAAAAGGGTCAAAACACGAAATT 59.650 36.000 0.00 0.00 32.44 1.82
310 311 5.579119 ACAAAAGGGTCAAAACACGAAATTC 59.421 36.000 0.00 0.00 32.44 2.17
311 312 5.592104 AAAGGGTCAAAACACGAAATTCT 57.408 34.783 0.00 0.00 32.44 2.40
312 313 4.568152 AGGGTCAAAACACGAAATTCTG 57.432 40.909 0.00 0.00 32.44 3.02
313 314 3.049912 GGGTCAAAACACGAAATTCTGC 58.950 45.455 0.00 0.00 0.00 4.26
314 315 3.049912 GGTCAAAACACGAAATTCTGCC 58.950 45.455 0.00 0.00 0.00 4.85
315 316 2.719046 GTCAAAACACGAAATTCTGCCG 59.281 45.455 0.00 0.00 0.00 5.69
316 317 2.050691 CAAAACACGAAATTCTGCCGG 58.949 47.619 0.00 0.00 0.00 6.13
317 318 0.039527 AAACACGAAATTCTGCCGGC 60.040 50.000 22.73 22.73 0.00 6.13
318 319 0.889186 AACACGAAATTCTGCCGGCT 60.889 50.000 29.70 5.42 0.00 5.52
319 320 0.889186 ACACGAAATTCTGCCGGCTT 60.889 50.000 29.70 13.49 0.00 4.35
338 339 0.991146 TGGGCTCTGCATGGTTCTAA 59.009 50.000 0.00 0.00 0.00 2.10
355 356 4.492494 TCTAATTGATGAGCTTCAGCCA 57.508 40.909 0.00 0.00 43.38 4.75
356 357 4.449131 TCTAATTGATGAGCTTCAGCCAG 58.551 43.478 0.00 0.00 43.38 4.85
389 390 0.609131 GCTGGCTTTTCTAGGTGGCA 60.609 55.000 0.00 0.00 0.00 4.92
427 428 1.066858 CAGGGACATAGTTGCACGAGT 60.067 52.381 0.00 0.00 0.00 4.18
437 438 4.008933 GCACGAGTGGCTCAGGGT 62.009 66.667 5.32 0.00 0.00 4.34
443 444 1.939769 GAGTGGCTCAGGGTCGAGTC 61.940 65.000 0.00 0.00 38.16 3.36
470 471 3.659786 CGTGATGTTTTGTACTCCCTCA 58.340 45.455 0.00 0.00 0.00 3.86
1335 2128 0.619255 TGCCCCTCTTCGGTTCCATA 60.619 55.000 0.00 0.00 0.00 2.74
1366 2163 3.491652 GAGTTCTCAAGCGCGGCC 61.492 66.667 8.83 0.00 0.00 6.13
1738 2548 4.686695 CCTCATCTCCGAGGTGGA 57.313 61.111 8.84 0.00 46.48 4.02
1787 2597 1.674441 CCGGTATTGCTCTCGTACAGA 59.326 52.381 0.00 0.00 0.00 3.41
1932 2747 2.779430 ACATATGCCCTCACATGGAAGA 59.221 45.455 1.58 0.00 31.57 2.87
2055 2875 2.380064 ACTGCACCCCAAAGATTTCA 57.620 45.000 0.00 0.00 0.00 2.69
2072 2892 0.764890 TCACTTGGGCAGTAAGCTGT 59.235 50.000 0.00 0.00 44.32 4.40
2119 2943 4.870991 GCCTAACTAGATGTTGGTTGTCTC 59.129 45.833 0.00 0.00 39.55 3.36
2150 2976 3.758554 GTCTATGACATGCTGGTTTGGTT 59.241 43.478 0.00 0.00 32.09 3.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 4.351054 GAGGGGCTGGTGTGTGGG 62.351 72.222 0.00 0.00 0.00 4.61
13 14 4.351054 GGAGGGGCTGGTGTGTGG 62.351 72.222 0.00 0.00 0.00 4.17
14 15 4.351054 GGGAGGGGCTGGTGTGTG 62.351 72.222 0.00 0.00 0.00 3.82
15 16 4.918360 TGGGAGGGGCTGGTGTGT 62.918 66.667 0.00 0.00 0.00 3.72
16 17 2.843912 GATTGGGAGGGGCTGGTGTG 62.844 65.000 0.00 0.00 0.00 3.82
17 18 2.535317 ATTGGGAGGGGCTGGTGT 60.535 61.111 0.00 0.00 0.00 4.16
18 19 1.867595 AAGATTGGGAGGGGCTGGTG 61.868 60.000 0.00 0.00 0.00 4.17
19 20 0.253630 TAAGATTGGGAGGGGCTGGT 60.254 55.000 0.00 0.00 0.00 4.00
20 21 1.074566 GATAAGATTGGGAGGGGCTGG 59.925 57.143 0.00 0.00 0.00 4.85
21 22 1.074566 GGATAAGATTGGGAGGGGCTG 59.925 57.143 0.00 0.00 0.00 4.85
22 23 1.346465 TGGATAAGATTGGGAGGGGCT 60.346 52.381 0.00 0.00 0.00 5.19
23 24 1.149101 TGGATAAGATTGGGAGGGGC 58.851 55.000 0.00 0.00 0.00 5.80
24 25 1.425448 GGTGGATAAGATTGGGAGGGG 59.575 57.143 0.00 0.00 0.00 4.79
25 26 1.425448 GGGTGGATAAGATTGGGAGGG 59.575 57.143 0.00 0.00 0.00 4.30
26 27 1.425448 GGGGTGGATAAGATTGGGAGG 59.575 57.143 0.00 0.00 0.00 4.30
27 28 2.107204 CTGGGGTGGATAAGATTGGGAG 59.893 54.545 0.00 0.00 0.00 4.30
28 29 2.135189 CTGGGGTGGATAAGATTGGGA 58.865 52.381 0.00 0.00 0.00 4.37
29 30 1.145738 CCTGGGGTGGATAAGATTGGG 59.854 57.143 0.00 0.00 0.00 4.12
30 31 2.135189 TCCTGGGGTGGATAAGATTGG 58.865 52.381 0.00 0.00 0.00 3.16
31 32 2.158608 GGTCCTGGGGTGGATAAGATTG 60.159 54.545 0.00 0.00 38.52 2.67
32 33 2.136026 GGTCCTGGGGTGGATAAGATT 58.864 52.381 0.00 0.00 38.52 2.40
33 34 1.699257 GGGTCCTGGGGTGGATAAGAT 60.699 57.143 0.00 0.00 38.52 2.40
34 35 0.327191 GGGTCCTGGGGTGGATAAGA 60.327 60.000 0.00 0.00 38.52 2.10
35 36 0.327576 AGGGTCCTGGGGTGGATAAG 60.328 60.000 0.00 0.00 38.52 1.73
36 37 1.028638 TAGGGTCCTGGGGTGGATAA 58.971 55.000 0.00 0.00 38.52 1.75
37 38 0.266753 GTAGGGTCCTGGGGTGGATA 59.733 60.000 0.00 0.00 38.52 2.59
38 39 1.004361 GTAGGGTCCTGGGGTGGAT 59.996 63.158 0.00 0.00 38.52 3.41
39 40 2.453054 GTAGGGTCCTGGGGTGGA 59.547 66.667 0.00 0.00 0.00 4.02
40 41 2.691252 GGTAGGGTCCTGGGGTGG 60.691 72.222 0.00 0.00 0.00 4.61
41 42 3.081409 CGGTAGGGTCCTGGGGTG 61.081 72.222 0.00 0.00 0.00 4.61
45 46 3.470888 CTGGCGGTAGGGTCCTGG 61.471 72.222 0.00 0.00 0.00 4.45
46 47 3.470888 CCTGGCGGTAGGGTCCTG 61.471 72.222 0.00 0.00 34.06 3.86
59 60 2.762459 TACTGCTACGGGCCCTGG 60.762 66.667 22.43 7.85 40.92 4.45
60 61 2.797278 CCTACTGCTACGGGCCCTG 61.797 68.421 22.43 16.23 40.92 4.45
61 62 2.444140 CCTACTGCTACGGGCCCT 60.444 66.667 22.43 9.76 40.92 5.19
62 63 2.762875 ACCTACTGCTACGGGCCC 60.763 66.667 13.57 13.57 40.92 5.80
63 64 1.896122 AACACCTACTGCTACGGGCC 61.896 60.000 0.00 0.00 40.92 5.80
64 65 0.819582 TAACACCTACTGCTACGGGC 59.180 55.000 0.00 0.00 42.22 6.13
65 66 2.097825 ACTAACACCTACTGCTACGGG 58.902 52.381 0.00 0.00 0.00 5.28
66 67 3.243002 GCTACTAACACCTACTGCTACGG 60.243 52.174 0.00 0.00 0.00 4.02
67 68 3.243002 GGCTACTAACACCTACTGCTACG 60.243 52.174 0.00 0.00 0.00 3.51
68 69 3.952967 AGGCTACTAACACCTACTGCTAC 59.047 47.826 0.00 0.00 29.98 3.58
69 70 4.246712 AGGCTACTAACACCTACTGCTA 57.753 45.455 0.00 0.00 29.98 3.49
70 71 3.103080 AGGCTACTAACACCTACTGCT 57.897 47.619 0.00 0.00 29.98 4.24
75 76 2.301346 GCGGTAGGCTACTAACACCTA 58.699 52.381 23.01 0.00 36.67 3.08
76 77 1.109609 GCGGTAGGCTACTAACACCT 58.890 55.000 23.01 0.00 36.67 4.00
77 78 0.103755 GGCGGTAGGCTACTAACACC 59.896 60.000 23.01 13.58 42.94 4.16
78 79 0.819582 TGGCGGTAGGCTACTAACAC 59.180 55.000 23.01 10.54 44.18 3.32
79 80 1.108776 CTGGCGGTAGGCTACTAACA 58.891 55.000 23.01 16.94 44.18 2.41
80 81 0.388294 CCTGGCGGTAGGCTACTAAC 59.612 60.000 23.01 13.67 44.18 2.34
81 82 0.757935 CCCTGGCGGTAGGCTACTAA 60.758 60.000 23.01 6.76 44.18 2.24
82 83 1.152610 CCCTGGCGGTAGGCTACTA 60.153 63.158 23.01 7.73 44.18 1.82
83 84 2.444140 CCCTGGCGGTAGGCTACT 60.444 66.667 23.01 0.00 44.18 2.57
84 85 2.762875 ACCCTGGCGGTAGGCTAC 60.763 66.667 16.40 16.40 45.97 3.58
95 96 3.000819 TACCGCCACAGACCCTGG 61.001 66.667 0.00 0.00 35.51 4.45
96 97 2.579201 CTACCGCCACAGACCCTG 59.421 66.667 0.00 0.00 37.52 4.45
97 98 2.683933 CCTACCGCCACAGACCCT 60.684 66.667 0.00 0.00 0.00 4.34
98 99 3.782443 CCCTACCGCCACAGACCC 61.782 72.222 0.00 0.00 0.00 4.46
99 100 3.001406 ACCCTACCGCCACAGACC 61.001 66.667 0.00 0.00 0.00 3.85
100 101 2.577593 GACCCTACCGCCACAGAC 59.422 66.667 0.00 0.00 0.00 3.51
101 102 2.682494 GGACCCTACCGCCACAGA 60.682 66.667 0.00 0.00 0.00 3.41
102 103 1.838073 AAAGGACCCTACCGCCACAG 61.838 60.000 0.00 0.00 34.73 3.66
103 104 1.420532 AAAAGGACCCTACCGCCACA 61.421 55.000 0.00 0.00 34.73 4.17
104 105 0.675837 GAAAAGGACCCTACCGCCAC 60.676 60.000 0.00 0.00 34.73 5.01
105 106 1.681076 GAAAAGGACCCTACCGCCA 59.319 57.895 0.00 0.00 34.73 5.69
106 107 1.077930 GGAAAAGGACCCTACCGCC 60.078 63.158 0.00 0.00 34.73 6.13
107 108 0.675837 GTGGAAAAGGACCCTACCGC 60.676 60.000 0.00 0.00 34.73 5.68
108 109 0.390735 CGTGGAAAAGGACCCTACCG 60.391 60.000 0.00 0.00 34.73 4.02
109 110 0.689055 ACGTGGAAAAGGACCCTACC 59.311 55.000 0.00 0.00 0.00 3.18
110 111 1.345415 TGACGTGGAAAAGGACCCTAC 59.655 52.381 0.00 0.00 0.00 3.18
111 112 1.719529 TGACGTGGAAAAGGACCCTA 58.280 50.000 0.00 0.00 0.00 3.53
112 113 0.841289 TTGACGTGGAAAAGGACCCT 59.159 50.000 0.00 0.00 0.00 4.34
113 114 0.949397 GTTGACGTGGAAAAGGACCC 59.051 55.000 0.00 0.00 0.00 4.46
114 115 1.602377 CAGTTGACGTGGAAAAGGACC 59.398 52.381 0.00 0.00 0.00 4.46
115 116 2.285977 ACAGTTGACGTGGAAAAGGAC 58.714 47.619 0.00 0.00 0.00 3.85
116 117 2.702592 ACAGTTGACGTGGAAAAGGA 57.297 45.000 0.00 0.00 0.00 3.36
117 118 3.463944 ACTACAGTTGACGTGGAAAAGG 58.536 45.455 0.00 0.00 0.00 3.11
130 131 2.561478 AACGGCCATCAACTACAGTT 57.439 45.000 2.24 0.00 39.12 3.16
131 132 2.093658 CCTAACGGCCATCAACTACAGT 60.094 50.000 2.24 0.00 0.00 3.55
132 133 2.550978 CCTAACGGCCATCAACTACAG 58.449 52.381 2.24 0.00 0.00 2.74
133 134 2.684001 CCTAACGGCCATCAACTACA 57.316 50.000 2.24 0.00 0.00 2.74
145 146 3.269347 CGGGATTGCGCCTAACGG 61.269 66.667 4.18 0.00 43.93 4.44
147 148 1.448893 TGACGGGATTGCGCCTAAC 60.449 57.895 4.18 0.00 0.00 2.34
148 149 1.448893 GTGACGGGATTGCGCCTAA 60.449 57.895 4.18 0.00 0.00 2.69
149 150 2.185867 GTGACGGGATTGCGCCTA 59.814 61.111 4.18 0.00 0.00 3.93
150 151 4.778143 GGTGACGGGATTGCGCCT 62.778 66.667 4.18 0.00 0.00 5.52
151 152 3.379865 TAGGTGACGGGATTGCGCC 62.380 63.158 4.18 0.00 0.00 6.53
152 153 2.171725 GTAGGTGACGGGATTGCGC 61.172 63.158 0.00 0.00 0.00 6.09
153 154 1.520787 GGTAGGTGACGGGATTGCG 60.521 63.158 0.00 0.00 0.00 4.85
154 155 1.520787 CGGTAGGTGACGGGATTGC 60.521 63.158 0.00 0.00 0.00 3.56
155 156 1.520787 GCGGTAGGTGACGGGATTG 60.521 63.158 0.00 0.00 0.00 2.67
156 157 2.728435 GGCGGTAGGTGACGGGATT 61.728 63.158 0.00 0.00 0.00 3.01
157 158 3.152400 GGCGGTAGGTGACGGGAT 61.152 66.667 0.00 0.00 0.00 3.85
158 159 4.682334 TGGCGGTAGGTGACGGGA 62.682 66.667 0.00 0.00 0.00 5.14
159 160 4.143333 CTGGCGGTAGGTGACGGG 62.143 72.222 0.00 0.00 0.00 5.28
160 161 4.143333 CCTGGCGGTAGGTGACGG 62.143 72.222 0.00 0.00 32.99 4.79
161 162 4.143333 CCCTGGCGGTAGGTGACG 62.143 72.222 0.00 0.00 36.02 4.35
162 163 2.682494 TCCCTGGCGGTAGGTGAC 60.682 66.667 0.00 0.00 36.02 3.67
163 164 2.682494 GTCCCTGGCGGTAGGTGA 60.682 66.667 0.00 0.00 36.02 4.02
164 165 3.782443 GGTCCCTGGCGGTAGGTG 61.782 72.222 0.00 0.00 36.02 4.00
198 199 3.408853 GTCCAGGTGGTAGCCCCC 61.409 72.222 0.00 0.00 36.34 5.40
199 200 3.408853 GGTCCAGGTGGTAGCCCC 61.409 72.222 0.00 0.00 36.34 5.80
200 201 3.408853 GGGTCCAGGTGGTAGCCC 61.409 72.222 9.24 9.24 36.33 5.19
201 202 2.540842 TAGGGGTCCAGGTGGTAGCC 62.541 65.000 0.00 2.50 36.34 3.93
202 203 1.002533 TAGGGGTCCAGGTGGTAGC 59.997 63.158 0.00 0.00 36.34 3.58
203 204 1.049289 GCTAGGGGTCCAGGTGGTAG 61.049 65.000 0.00 0.00 36.34 3.18
204 205 1.002533 GCTAGGGGTCCAGGTGGTA 59.997 63.158 0.00 0.00 36.34 3.25
205 206 2.285442 GCTAGGGGTCCAGGTGGT 60.285 66.667 0.00 0.00 36.34 4.16
206 207 3.470888 CGCTAGGGGTCCAGGTGG 61.471 72.222 0.00 0.00 0.00 4.61
207 208 2.866523 TACCGCTAGGGGTCCAGGTG 62.867 65.000 32.72 4.38 43.47 4.00
208 209 2.584873 CTACCGCTAGGGGTCCAGGT 62.585 65.000 32.72 11.84 43.47 4.00
209 210 1.833049 CTACCGCTAGGGGTCCAGG 60.833 68.421 32.72 17.83 43.47 4.45
210 211 1.833049 CCTACCGCTAGGGGTCCAG 60.833 68.421 32.72 24.44 43.47 3.86
211 212 2.281091 CCTACCGCTAGGGGTCCA 59.719 66.667 32.72 17.02 43.47 4.02
212 213 3.232483 GCCTACCGCTAGGGGTCC 61.232 72.222 32.72 18.93 40.26 4.46
213 214 1.619807 TTTGCCTACCGCTAGGGGTC 61.620 60.000 32.72 19.86 40.26 4.46
214 215 1.202769 TTTTGCCTACCGCTAGGGGT 61.203 55.000 31.62 31.62 40.26 4.95
215 216 0.463833 CTTTTGCCTACCGCTAGGGG 60.464 60.000 23.57 23.57 40.26 4.79
216 217 0.463833 CCTTTTGCCTACCGCTAGGG 60.464 60.000 5.94 0.00 40.26 3.53
217 218 0.252197 ACCTTTTGCCTACCGCTAGG 59.748 55.000 0.00 0.00 42.60 3.02
218 219 2.007608 GAACCTTTTGCCTACCGCTAG 58.992 52.381 0.00 0.00 38.78 3.42
219 220 1.348366 TGAACCTTTTGCCTACCGCTA 59.652 47.619 0.00 0.00 38.78 4.26
220 221 0.109723 TGAACCTTTTGCCTACCGCT 59.890 50.000 0.00 0.00 38.78 5.52
221 222 1.173913 ATGAACCTTTTGCCTACCGC 58.826 50.000 0.00 0.00 38.31 5.68
222 223 3.243068 GCATATGAACCTTTTGCCTACCG 60.243 47.826 6.97 0.00 0.00 4.02
223 224 4.307443 GCATATGAACCTTTTGCCTACC 57.693 45.455 6.97 0.00 0.00 3.18
228 229 4.937015 ACAATTGGCATATGAACCTTTTGC 59.063 37.500 10.83 0.00 0.00 3.68
229 230 7.437793 AAACAATTGGCATATGAACCTTTTG 57.562 32.000 10.83 9.36 0.00 2.44
230 231 8.351461 CAAAAACAATTGGCATATGAACCTTTT 58.649 29.630 10.83 0.25 0.00 2.27
231 232 7.521910 GCAAAAACAATTGGCATATGAACCTTT 60.522 33.333 10.83 0.00 0.00 3.11
232 233 6.072563 GCAAAAACAATTGGCATATGAACCTT 60.073 34.615 10.83 0.00 0.00 3.50
233 234 5.412286 GCAAAAACAATTGGCATATGAACCT 59.588 36.000 10.83 0.00 0.00 3.50
234 235 5.180868 TGCAAAAACAATTGGCATATGAACC 59.819 36.000 10.83 0.00 0.00 3.62
235 236 6.238610 TGCAAAAACAATTGGCATATGAAC 57.761 33.333 10.83 0.00 0.00 3.18
236 237 6.872628 TTGCAAAAACAATTGGCATATGAA 57.127 29.167 10.83 0.00 32.00 2.57
237 238 6.872628 TTTGCAAAAACAATTGGCATATGA 57.127 29.167 10.02 0.00 32.00 2.15
238 239 6.583050 CCTTTTGCAAAAACAATTGGCATATG 59.417 34.615 23.92 8.26 32.00 1.78
239 240 6.294620 CCCTTTTGCAAAAACAATTGGCATAT 60.295 34.615 23.92 0.00 32.00 1.78
240 241 5.009410 CCCTTTTGCAAAAACAATTGGCATA 59.991 36.000 23.92 1.81 32.00 3.14
241 242 4.202131 CCCTTTTGCAAAAACAATTGGCAT 60.202 37.500 23.92 0.00 32.00 4.40
242 243 3.129988 CCCTTTTGCAAAAACAATTGGCA 59.870 39.130 23.92 6.31 0.00 4.92
243 244 3.490590 CCCCTTTTGCAAAAACAATTGGC 60.491 43.478 23.92 3.51 0.00 4.52
244 245 3.490590 GCCCCTTTTGCAAAAACAATTGG 60.491 43.478 23.92 19.16 0.00 3.16
245 246 3.490590 GGCCCCTTTTGCAAAAACAATTG 60.491 43.478 23.92 11.94 0.00 2.32
246 247 2.692557 GGCCCCTTTTGCAAAAACAATT 59.307 40.909 23.92 0.00 0.00 2.32
247 248 2.305928 GGCCCCTTTTGCAAAAACAAT 58.694 42.857 23.92 0.00 0.00 2.71
248 249 1.004745 TGGCCCCTTTTGCAAAAACAA 59.995 42.857 23.92 6.50 0.00 2.83
249 250 0.620556 TGGCCCCTTTTGCAAAAACA 59.379 45.000 23.92 14.89 0.00 2.83
250 251 1.134250 TCTGGCCCCTTTTGCAAAAAC 60.134 47.619 23.92 13.85 0.00 2.43
251 252 1.207791 TCTGGCCCCTTTTGCAAAAA 58.792 45.000 23.92 8.59 0.00 1.94
252 253 1.347378 GATCTGGCCCCTTTTGCAAAA 59.653 47.619 22.61 22.61 0.00 2.44
253 254 0.975887 GATCTGGCCCCTTTTGCAAA 59.024 50.000 8.05 8.05 0.00 3.68
254 255 0.904394 GGATCTGGCCCCTTTTGCAA 60.904 55.000 0.00 0.00 0.00 4.08
255 256 1.305213 GGATCTGGCCCCTTTTGCA 60.305 57.895 0.00 0.00 0.00 4.08
256 257 2.060383 GGGATCTGGCCCCTTTTGC 61.060 63.158 0.00 0.00 42.62 3.68
257 258 1.754234 CGGGATCTGGCCCCTTTTG 60.754 63.158 0.00 0.00 45.84 2.44
258 259 1.506028 TTCGGGATCTGGCCCCTTTT 61.506 55.000 0.00 0.00 45.84 2.27
259 260 1.506028 TTTCGGGATCTGGCCCCTTT 61.506 55.000 0.00 0.00 45.84 3.11
260 261 1.289244 ATTTCGGGATCTGGCCCCTT 61.289 55.000 0.00 0.00 45.84 3.95
261 262 0.401395 TATTTCGGGATCTGGCCCCT 60.401 55.000 0.00 0.00 45.84 4.79
262 263 0.476771 TTATTTCGGGATCTGGCCCC 59.523 55.000 0.00 0.00 45.84 5.80
263 264 1.133915 TGTTATTTCGGGATCTGGCCC 60.134 52.381 0.00 0.00 45.10 5.80
264 265 1.947456 GTGTTATTTCGGGATCTGGCC 59.053 52.381 0.00 0.00 0.00 5.36
265 266 1.947456 GGTGTTATTTCGGGATCTGGC 59.053 52.381 0.00 0.00 0.00 4.85
266 267 2.943033 GTGGTGTTATTTCGGGATCTGG 59.057 50.000 0.00 0.00 0.00 3.86
267 268 3.605634 TGTGGTGTTATTTCGGGATCTG 58.394 45.455 0.00 0.00 0.00 2.90
268 269 3.992943 TGTGGTGTTATTTCGGGATCT 57.007 42.857 0.00 0.00 0.00 2.75
269 270 5.379732 TTTTGTGGTGTTATTTCGGGATC 57.620 39.130 0.00 0.00 0.00 3.36
270 271 4.219725 CCTTTTGTGGTGTTATTTCGGGAT 59.780 41.667 0.00 0.00 0.00 3.85
271 272 3.570550 CCTTTTGTGGTGTTATTTCGGGA 59.429 43.478 0.00 0.00 0.00 5.14
272 273 3.305744 CCCTTTTGTGGTGTTATTTCGGG 60.306 47.826 0.00 0.00 0.00 5.14
273 274 3.319689 ACCCTTTTGTGGTGTTATTTCGG 59.680 43.478 0.00 0.00 33.94 4.30
274 275 4.036971 TGACCCTTTTGTGGTGTTATTTCG 59.963 41.667 0.00 0.00 35.85 3.46
275 276 5.523438 TGACCCTTTTGTGGTGTTATTTC 57.477 39.130 0.00 0.00 35.85 2.17
276 277 5.941555 TTGACCCTTTTGTGGTGTTATTT 57.058 34.783 0.00 0.00 35.85 1.40
277 278 5.941555 TTTGACCCTTTTGTGGTGTTATT 57.058 34.783 0.00 0.00 35.85 1.40
278 279 5.187967 TGTTTTGACCCTTTTGTGGTGTTAT 59.812 36.000 0.00 0.00 35.85 1.89
279 280 4.527038 TGTTTTGACCCTTTTGTGGTGTTA 59.473 37.500 0.00 0.00 35.85 2.41
280 281 3.325135 TGTTTTGACCCTTTTGTGGTGTT 59.675 39.130 0.00 0.00 35.85 3.32
281 282 2.900546 TGTTTTGACCCTTTTGTGGTGT 59.099 40.909 0.00 0.00 35.85 4.16
282 283 3.258228 GTGTTTTGACCCTTTTGTGGTG 58.742 45.455 0.00 0.00 35.85 4.17
283 284 2.094442 CGTGTTTTGACCCTTTTGTGGT 60.094 45.455 0.00 0.00 39.32 4.16
284 285 2.164624 TCGTGTTTTGACCCTTTTGTGG 59.835 45.455 0.00 0.00 0.00 4.17
285 286 3.495670 TCGTGTTTTGACCCTTTTGTG 57.504 42.857 0.00 0.00 0.00 3.33
286 287 4.522722 TTTCGTGTTTTGACCCTTTTGT 57.477 36.364 0.00 0.00 0.00 2.83
287 288 5.810074 AGAATTTCGTGTTTTGACCCTTTTG 59.190 36.000 0.00 0.00 0.00 2.44
288 289 5.810074 CAGAATTTCGTGTTTTGACCCTTTT 59.190 36.000 0.00 0.00 0.00 2.27
289 290 5.348164 CAGAATTTCGTGTTTTGACCCTTT 58.652 37.500 0.00 0.00 0.00 3.11
290 291 4.736464 GCAGAATTTCGTGTTTTGACCCTT 60.736 41.667 0.00 0.00 0.00 3.95
291 292 3.243401 GCAGAATTTCGTGTTTTGACCCT 60.243 43.478 0.00 0.00 0.00 4.34
292 293 3.049912 GCAGAATTTCGTGTTTTGACCC 58.950 45.455 0.00 0.00 0.00 4.46
293 294 3.049912 GGCAGAATTTCGTGTTTTGACC 58.950 45.455 0.00 0.00 0.00 4.02
294 295 2.719046 CGGCAGAATTTCGTGTTTTGAC 59.281 45.455 0.00 0.00 0.00 3.18
295 296 2.287308 CCGGCAGAATTTCGTGTTTTGA 60.287 45.455 0.00 0.00 0.00 2.69
296 297 2.050691 CCGGCAGAATTTCGTGTTTTG 58.949 47.619 0.00 0.00 0.00 2.44
297 298 1.601914 GCCGGCAGAATTTCGTGTTTT 60.602 47.619 24.80 0.00 0.00 2.43
298 299 0.039527 GCCGGCAGAATTTCGTGTTT 60.040 50.000 24.80 0.00 0.00 2.83
299 300 0.889186 AGCCGGCAGAATTTCGTGTT 60.889 50.000 31.54 0.00 0.00 3.32
300 301 0.889186 AAGCCGGCAGAATTTCGTGT 60.889 50.000 31.54 0.00 0.00 4.49
301 302 0.454957 CAAGCCGGCAGAATTTCGTG 60.455 55.000 31.54 7.88 0.00 4.35
302 303 1.586154 CCAAGCCGGCAGAATTTCGT 61.586 55.000 31.54 0.00 0.00 3.85
303 304 1.137404 CCAAGCCGGCAGAATTTCG 59.863 57.895 31.54 1.79 0.00 3.46
304 305 1.512694 CCCAAGCCGGCAGAATTTC 59.487 57.895 31.54 0.00 0.00 2.17
305 306 3.698765 CCCAAGCCGGCAGAATTT 58.301 55.556 31.54 11.17 0.00 1.82
313 314 4.809496 ATGCAGAGCCCAAGCCGG 62.809 66.667 0.00 0.00 41.25 6.13
314 315 3.515286 CATGCAGAGCCCAAGCCG 61.515 66.667 0.00 0.00 41.25 5.52
315 316 3.145551 CCATGCAGAGCCCAAGCC 61.146 66.667 0.00 0.00 41.25 4.35
316 317 1.941999 GAACCATGCAGAGCCCAAGC 61.942 60.000 0.00 0.00 40.32 4.01
317 318 0.323178 AGAACCATGCAGAGCCCAAG 60.323 55.000 0.00 0.00 0.00 3.61
318 319 0.991146 TAGAACCATGCAGAGCCCAA 59.009 50.000 0.00 0.00 0.00 4.12
319 320 0.991146 TTAGAACCATGCAGAGCCCA 59.009 50.000 0.00 0.00 0.00 5.36
338 339 1.390565 GCTGGCTGAAGCTCATCAAT 58.609 50.000 1.74 0.00 40.20 2.57
355 356 3.157252 AGCCCCGTCATCATCGCT 61.157 61.111 0.00 0.00 0.00 4.93
356 357 2.969238 CAGCCCCGTCATCATCGC 60.969 66.667 0.00 0.00 0.00 4.58
389 390 2.614779 CTGTTGTCATCGTCAGCTCAT 58.385 47.619 0.00 0.00 0.00 2.90
427 428 2.680352 GGACTCGACCCTGAGCCA 60.680 66.667 0.00 0.00 39.68 4.75
437 438 3.122971 ATCACGCGACGGACTCGA 61.123 61.111 15.93 0.00 46.14 4.04
443 444 0.785378 TACAAAACATCACGCGACGG 59.215 50.000 15.93 1.17 0.00 4.79
470 471 6.435277 TCTTATACGTGGAGTACAAGGAAACT 59.565 38.462 0.00 0.00 39.61 2.66
705 706 2.211250 TTGGTAGTACTCGCTCTGGT 57.789 50.000 0.00 0.00 0.00 4.00
1101 1121 2.783288 GCTAGGGTTCGGGGAGACG 61.783 68.421 0.00 0.00 0.00 4.18
1102 1122 0.976590 AAGCTAGGGTTCGGGGAGAC 60.977 60.000 0.00 0.00 0.00 3.36
1103 1123 0.686769 GAAGCTAGGGTTCGGGGAGA 60.687 60.000 0.00 0.00 30.55 3.71
1104 1124 1.823976 GAAGCTAGGGTTCGGGGAG 59.176 63.158 0.00 0.00 30.55 4.30
1105 1125 4.045469 GAAGCTAGGGTTCGGGGA 57.955 61.111 0.00 0.00 30.55 4.81
1335 2128 2.036089 GAGAACTCGAAGGGTGTTGTCT 59.964 50.000 4.89 0.00 38.59 3.41
1366 2163 7.708051 TCAAGATCAGACGAGATAAGGTAAAG 58.292 38.462 0.00 0.00 0.00 1.85
1738 2548 0.255890 AATGTATGCCGGTTCCAGCT 59.744 50.000 1.90 0.00 0.00 4.24
2072 2892 6.664515 CACGAATACTGAAACAAAAGGCTAA 58.335 36.000 0.00 0.00 0.00 3.09
2208 3117 3.710165 TCTCTGCTGAATGATGAGATGGT 59.290 43.478 0.00 0.00 0.00 3.55
2429 3651 6.308766 GCAAGCAACCAACAAACTATATCAAG 59.691 38.462 0.00 0.00 0.00 3.02


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

AutoCloner maintained by Alex Coulton.