Multiple sequence alignment - TraesCS3D01G028500

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 TraesCS3D01G028500 chr3D 100.000 4835 0 0 1 4835 10132292 10137126 0.000000e+00 8929.0
1 TraesCS3D01G028500 chr3D 91.228 171 9 6 138 307 8441564 8441399 1.350000e-55 228.0
2 TraesCS3D01G028500 chr3D 95.522 134 6 0 2 135 58425691 58425824 1.050000e-51 215.0
3 TraesCS3D01G028500 chr3B 93.000 4700 254 38 95 4763 14327067 14331722 0.000000e+00 6787.0
4 TraesCS3D01G028500 chr3B 94.815 135 7 0 1 135 778158229 778158095 1.360000e-50 211.0
5 TraesCS3D01G028500 chr3B 91.736 121 8 2 574 693 14333348 14333467 2.990000e-37 167.0
6 TraesCS3D01G028500 chr7D 84.813 777 87 18 4061 4835 2838926 2838179 0.000000e+00 752.0
7 TraesCS3D01G028500 chr7D 89.151 212 16 7 4062 4273 2834238 2834034 1.730000e-64 257.0
8 TraesCS3D01G028500 chr7D 92.353 170 9 3 137 304 514404667 514404500 6.250000e-59 239.0
9 TraesCS3D01G028500 chr7D 95.522 134 6 0 2 135 13363748 13363881 1.050000e-51 215.0
10 TraesCS3D01G028500 chr5B 88.995 209 18 3 4062 4270 371186023 371186226 2.230000e-63 254.0
11 TraesCS3D01G028500 chr1A 92.308 169 9 3 137 304 539541455 539541620 2.250000e-58 237.0
12 TraesCS3D01G028500 chr1A 92.727 165 9 2 137 301 539436768 539436929 8.090000e-58 235.0
13 TraesCS3D01G028500 chr1A 92.308 169 7 5 137 304 539502644 539502807 8.090000e-58 235.0
14 TraesCS3D01G028500 chr1A 91.124 169 11 3 137 304 539499613 539499778 4.870000e-55 226.0
15 TraesCS3D01G028500 chr1A 91.018 167 11 3 137 302 539462192 539462355 6.300000e-54 222.0
16 TraesCS3D01G028500 chr7B 96.269 134 5 0 2 135 284571428 284571561 2.270000e-53 220.0
17 TraesCS3D01G028500 chr4A 95.522 134 6 0 2 135 177783776 177783643 1.050000e-51 215.0
18 TraesCS3D01G028500 chr3A 95.522 134 6 0 2 135 739600367 739600234 1.050000e-51 215.0
19 TraesCS3D01G028500 chr1D 95.522 134 6 0 2 135 363511686 363511553 1.050000e-51 215.0
20 TraesCS3D01G028500 chr6D 95.489 133 6 0 5 137 123786826 123786694 3.790000e-51 213.0
21 TraesCS3D01G028500 chr6D 74.150 147 34 3 1094 1238 24299275 24299131 1.880000e-04 58.4
22 TraesCS3D01G028500 chr6D 74.419 129 31 2 1111 1238 24348677 24348550 2.000000e-03 54.7
23 TraesCS3D01G028500 chr6D 74.242 132 32 2 1108 1238 24390647 24390777 2.000000e-03 54.7
24 TraesCS3D01G028500 chr6D 100.000 28 0 0 1211 1238 24357859 24357832 9.000000e-03 52.8
25 TraesCS3D01G028500 chr6B 94.815 135 7 0 2 136 189607580 189607446 1.360000e-50 211.0
26 TraesCS3D01G028500 chr6B 100.000 29 0 0 1211 1239 39431770 39431798 2.000000e-03 54.7
27 TraesCS3D01G028500 chr6A 74.000 150 39 0 1094 1243 23023218 23023367 1.450000e-05 62.1
28 TraesCS3D01G028500 chr6A 75.000 132 31 2 1108 1238 22826377 22826507 5.230000e-05 60.2


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 TraesCS3D01G028500 chr3D 10132292 10137126 4834 False 8929.0 8929 100.000 1 4835 1 chr3D.!!$F1 4834
1 TraesCS3D01G028500 chr3B 14327067 14333467 6400 False 3477.0 6787 92.368 95 4763 2 chr3B.!!$F1 4668
2 TraesCS3D01G028500 chr7D 2834034 2838926 4892 True 504.5 752 86.982 4061 4835 2 chr7D.!!$R2 774
3 TraesCS3D01G028500 chr1A 539499613 539502807 3194 False 230.5 235 91.716 137 304 2 chr1A.!!$F4 167

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
91 92 0.383737 GTCTATGACGCTCGCTCTCG 60.384 60.0 0.00 0.00 0.00 4.04 F
1234 4148 0.039256 CAACAGAACCGGCCATGTTG 60.039 55.0 23.55 23.55 44.43 3.33 F
1239 4153 0.039527 GAACCGGCCATGTTGTCAAC 60.040 55.0 12.10 8.86 0.00 3.18 F
2141 5061 0.315251 GGAGCACTTCCAAAACTGGC 59.685 55.0 0.00 0.00 46.01 4.85 F
3405 6326 0.185416 TCGAGTCCCTGGACCTATCC 59.815 60.0 12.66 0.00 45.59 2.59 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1268 4188 0.039074 GATATCACCTCCCACTCGCG 60.039 60.0 0.00 0.00 0.00 5.87 R
2750 5671 0.255318 AAGATCTCCCTGCTGGCAAG 59.745 55.0 3.63 4.13 0.00 4.01 R
3226 6147 2.561478 ACCATGTACGGCAACTCTTT 57.439 45.0 0.00 0.00 0.00 2.52 R
3492 6413 0.042581 TCCCTGCTGGTATCTGTCCA 59.957 55.0 9.00 0.00 34.77 4.02 R
4739 7661 0.682209 GCATGTCATCCACAAGGGCT 60.682 55.0 0.00 0.00 38.97 5.19 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
28 29 9.988815 TCATTGATTAATAAAGCTAGTCTCCTC 57.011 33.333 0.00 0.00 0.00 3.71
29 30 9.213799 CATTGATTAATAAAGCTAGTCTCCTCC 57.786 37.037 0.00 0.00 0.00 4.30
30 31 7.914427 TGATTAATAAAGCTAGTCTCCTCCA 57.086 36.000 0.00 0.00 0.00 3.86
31 32 8.497910 TGATTAATAAAGCTAGTCTCCTCCAT 57.502 34.615 0.00 0.00 0.00 3.41
32 33 9.601810 TGATTAATAAAGCTAGTCTCCTCCATA 57.398 33.333 0.00 0.00 0.00 2.74
35 36 9.830186 TTAATAAAGCTAGTCTCCTCCATATCT 57.170 33.333 0.00 0.00 0.00 1.98
37 38 4.316025 AGCTAGTCTCCTCCATATCTCC 57.684 50.000 0.00 0.00 0.00 3.71
39 40 3.011257 GCTAGTCTCCTCCATATCTCCCT 59.989 52.174 0.00 0.00 0.00 4.20
40 41 3.541242 AGTCTCCTCCATATCTCCCTG 57.459 52.381 0.00 0.00 0.00 4.45
41 42 2.794760 AGTCTCCTCCATATCTCCCTGT 59.205 50.000 0.00 0.00 0.00 4.00
42 43 2.896685 GTCTCCTCCATATCTCCCTGTG 59.103 54.545 0.00 0.00 0.00 3.66
43 44 2.520120 TCTCCTCCATATCTCCCTGTGT 59.480 50.000 0.00 0.00 0.00 3.72
45 46 2.247372 TCCTCCATATCTCCCTGTGTCA 59.753 50.000 0.00 0.00 0.00 3.58
46 47 3.116590 TCCTCCATATCTCCCTGTGTCAT 60.117 47.826 0.00 0.00 0.00 3.06
47 48 3.260380 CCTCCATATCTCCCTGTGTCATC 59.740 52.174 0.00 0.00 0.00 2.92
49 50 5.328565 CTCCATATCTCCCTGTGTCATCTA 58.671 45.833 0.00 0.00 0.00 1.98
50 51 5.080337 TCCATATCTCCCTGTGTCATCTAC 58.920 45.833 0.00 0.00 0.00 2.59
51 52 5.083122 CCATATCTCCCTGTGTCATCTACT 58.917 45.833 0.00 0.00 0.00 2.57
52 53 5.541868 CCATATCTCCCTGTGTCATCTACTT 59.458 44.000 0.00 0.00 0.00 2.24
53 54 6.042552 CCATATCTCCCTGTGTCATCTACTTT 59.957 42.308 0.00 0.00 0.00 2.66
54 55 5.606348 ATCTCCCTGTGTCATCTACTTTC 57.394 43.478 0.00 0.00 0.00 2.62
55 56 3.444034 TCTCCCTGTGTCATCTACTTTCG 59.556 47.826 0.00 0.00 0.00 3.46
56 57 2.094182 TCCCTGTGTCATCTACTTTCGC 60.094 50.000 0.00 0.00 0.00 4.70
57 58 1.920574 CCTGTGTCATCTACTTTCGCG 59.079 52.381 0.00 0.00 0.00 5.87
58 59 2.596452 CTGTGTCATCTACTTTCGCGT 58.404 47.619 5.77 0.00 0.00 6.01
60 61 2.287970 TGTGTCATCTACTTTCGCGTGT 60.288 45.455 5.77 6.70 0.00 4.49
61 62 2.729882 GTGTCATCTACTTTCGCGTGTT 59.270 45.455 5.77 0.00 0.00 3.32
62 63 2.984471 TGTCATCTACTTTCGCGTGTTC 59.016 45.455 5.77 0.00 0.00 3.18
63 64 2.026507 GTCATCTACTTTCGCGTGTTCG 59.973 50.000 5.77 0.00 40.37 3.95
64 65 2.095617 TCATCTACTTTCGCGTGTTCGA 60.096 45.455 5.77 5.16 39.71 3.71
66 67 1.265095 TCTACTTTCGCGTGTTCGACT 59.735 47.619 5.77 0.00 38.30 4.18
67 68 2.480037 TCTACTTTCGCGTGTTCGACTA 59.520 45.455 5.77 0.00 38.30 2.59
68 69 2.124011 ACTTTCGCGTGTTCGACTAA 57.876 45.000 5.77 0.00 38.30 2.24
70 71 3.054878 ACTTTCGCGTGTTCGACTAATT 58.945 40.909 5.77 0.00 38.30 1.40
71 72 3.120782 ACTTTCGCGTGTTCGACTAATTC 59.879 43.478 5.77 0.00 38.30 2.17
90 91 3.448076 GTCTATGACGCTCGCTCTC 57.552 57.895 0.00 0.00 0.00 3.20
91 92 0.383737 GTCTATGACGCTCGCTCTCG 60.384 60.000 0.00 0.00 0.00 4.04
92 93 1.724234 CTATGACGCTCGCTCTCGC 60.724 63.158 0.00 0.00 35.26 5.03
93 94 2.111932 CTATGACGCTCGCTCTCGCT 62.112 60.000 0.00 0.00 35.26 4.93
99 100 4.482684 CTCGCTCTCGCTCCGCAA 62.483 66.667 0.00 0.00 35.26 4.85
100 101 4.778415 TCGCTCTCGCTCCGCAAC 62.778 66.667 0.00 0.00 35.26 4.17
153 3049 2.302733 ACAAAACGGACTAATACGGGGT 59.697 45.455 0.00 0.00 35.98 4.95
195 3092 1.212935 CCCACCAGTTAGAATCAGGGG 59.787 57.143 0.00 0.00 0.00 4.79
196 3093 1.212935 CCACCAGTTAGAATCAGGGGG 59.787 57.143 0.00 0.00 36.42 5.40
277 3174 1.353022 TCCGTAAAGGCCTGTGGATTT 59.647 47.619 5.69 0.00 40.77 2.17
278 3175 2.167662 CCGTAAAGGCCTGTGGATTTT 58.832 47.619 5.69 0.00 0.00 1.82
283 3180 6.394809 CGTAAAGGCCTGTGGATTTTTATTT 58.605 36.000 5.69 0.00 0.00 1.40
308 3205 1.892474 TGTGTAGCATTTTTGGGCCTC 59.108 47.619 4.53 0.00 0.00 4.70
315 3212 1.241315 ATTTTTGGGCCTCGACACCG 61.241 55.000 4.53 0.00 37.07 4.94
349 3246 1.324005 CGTCCAGGACTTCCCTCTCC 61.324 65.000 17.95 0.00 45.60 3.71
399 3303 2.034879 CGATCACCAGGCACACCAC 61.035 63.158 0.00 0.00 39.06 4.16
459 3363 2.447887 CGCGTACCAGCTGAGCAAG 61.448 63.158 17.39 0.00 34.40 4.01
462 3366 1.071605 CGTACCAGCTGAGCAAGAAC 58.928 55.000 17.39 0.00 0.00 3.01
494 3406 4.030452 GTTGCTCCTGGCGTGCAC 62.030 66.667 6.82 6.82 45.43 4.57
496 3408 4.994471 TGCTCCTGGCGTGCACAG 62.994 66.667 18.64 10.86 45.43 3.66
545 3457 3.913163 AGTGTTCTCTTCTTCCCCATCTT 59.087 43.478 0.00 0.00 0.00 2.40
547 3459 3.009473 TGTTCTCTTCTTCCCCATCTTGG 59.991 47.826 0.00 0.00 37.25 3.61
589 3501 4.467438 GGAATCTTGTCCAACCATTTCCAT 59.533 41.667 0.00 0.00 37.65 3.41
621 3533 0.946528 GTGTTCAGCTGTGTGATGCA 59.053 50.000 14.67 0.00 31.07 3.96
638 3550 1.972223 CAGGTCAGTCCGTCGGTCT 60.972 63.158 11.88 8.37 41.99 3.85
716 3628 5.872617 ACTTCATCGTTAATTCGTCCAATCA 59.127 36.000 0.00 0.00 0.00 2.57
778 3691 1.507140 TCATCGGGGCTAGGTCAATT 58.493 50.000 0.00 0.00 0.00 2.32
803 3716 5.512942 TTCCCCAAGTGATTAAGACATCA 57.487 39.130 0.00 0.00 0.00 3.07
849 3762 5.180868 ACATGACTGAAGACTTTGAATGAGC 59.819 40.000 0.00 0.00 0.00 4.26
908 3821 9.866798 CTGAGTTGCTGAGATTTGCTATATATA 57.133 33.333 0.00 0.00 0.00 0.86
935 3848 4.944048 TGCTGTTCTGCACGTATATACAT 58.056 39.130 13.22 0.00 38.12 2.29
945 3859 8.626526 TCTGCACGTATATACATAACAAGAGAA 58.373 33.333 13.22 0.00 0.00 2.87
958 3872 4.519540 ACAAGAGAAGAGAGAGTGAAGC 57.480 45.455 0.00 0.00 0.00 3.86
1007 3921 2.691409 TCCCTACTGAAAATGGCTCG 57.309 50.000 0.00 0.00 0.00 5.03
1017 3931 1.526575 AAATGGCTCGGCACTGGTTG 61.527 55.000 0.00 0.00 0.00 3.77
1038 3952 0.685097 TAGCCTTGGTCTCGTTGCTT 59.315 50.000 0.00 0.00 0.00 3.91
1078 3992 2.092212 TCCATTTCCTCCCTTGATGCTC 60.092 50.000 0.00 0.00 0.00 4.26
1080 3994 0.984230 TTTCCTCCCTTGATGCTCGT 59.016 50.000 0.00 0.00 0.00 4.18
1091 4005 0.668706 GATGCTCGTGGATCGGATGG 60.669 60.000 3.18 0.00 40.32 3.51
1094 4008 1.662608 CTCGTGGATCGGATGGGAG 59.337 63.158 0.00 0.00 40.32 4.30
1095 4009 2.029666 CGTGGATCGGATGGGAGC 59.970 66.667 0.00 0.00 35.71 4.70
1101 4015 2.650813 GATCGGATGGGAGCTGCGTT 62.651 60.000 0.00 0.00 0.00 4.84
1104 4018 3.869272 GATGGGAGCTGCGTTGCG 61.869 66.667 0.00 0.00 38.13 4.85
1116 4030 2.437359 GTTGCGCATGAGAGGGCT 60.437 61.111 12.75 0.00 46.41 5.19
1134 4048 1.271054 GCTGCACTCCTCTCCTTCAAA 60.271 52.381 0.00 0.00 0.00 2.69
1154 4068 1.371558 GAAGCTTGTCAGACCCCGT 59.628 57.895 2.10 0.00 0.00 5.28
1158 4072 0.951040 GCTTGTCAGACCCCGTGAAG 60.951 60.000 0.00 0.00 0.00 3.02
1160 4074 1.691195 TTGTCAGACCCCGTGAAGCA 61.691 55.000 0.00 0.00 0.00 3.91
1161 4075 1.374758 GTCAGACCCCGTGAAGCAG 60.375 63.158 0.00 0.00 0.00 4.24
1183 4097 1.452110 TTCATCGTGGCATGGTGAAG 58.548 50.000 27.15 0.38 0.00 3.02
1188 4102 0.179156 CGTGGCATGGTGAAGATTGC 60.179 55.000 0.00 0.00 0.00 3.56
1199 4113 0.322816 GAAGATTGCTGCACCTGGGA 60.323 55.000 0.00 0.00 0.00 4.37
1234 4148 0.039256 CAACAGAACCGGCCATGTTG 60.039 55.000 23.55 23.55 44.43 3.33
1239 4153 0.039527 GAACCGGCCATGTTGTCAAC 60.040 55.000 12.10 8.86 0.00 3.18
1252 4166 2.614057 GTTGTCAACCTCAACCTCAGTG 59.386 50.000 4.21 0.00 39.13 3.66
1258 4172 2.031012 TCAACCTCAGTGGCTGCG 59.969 61.111 0.00 0.00 40.22 5.18
1263 4177 2.503061 CTCAGTGGCTGCGGCTAT 59.497 61.111 18.85 0.11 38.73 2.97
1284 4204 4.148825 GCGCGAGTGGGAGGTGAT 62.149 66.667 12.10 0.00 0.00 3.06
1303 4223 3.135348 TGATATCAGCCCCTCTTTGACTG 59.865 47.826 0.00 0.00 0.00 3.51
1308 4228 0.328258 GCCCCTCTTTGACTGCCTTA 59.672 55.000 0.00 0.00 0.00 2.69
1311 4231 2.427506 CCCTCTTTGACTGCCTTACAC 58.572 52.381 0.00 0.00 0.00 2.90
1319 4239 2.171659 TGACTGCCTTACACCACTTGAA 59.828 45.455 0.00 0.00 0.00 2.69
1340 4260 6.230472 TGAAGTATTTAGACTTGAGCTGCAA 58.770 36.000 1.02 0.00 39.79 4.08
1356 4276 0.385390 GCAACAACTTCAGTGGGGTG 59.615 55.000 0.00 0.00 0.00 4.61
1369 4289 3.305181 GGGGTGCAGATCCCAAAAT 57.695 52.632 12.64 0.00 43.19 1.82
1370 4290 1.571955 GGGGTGCAGATCCCAAAATT 58.428 50.000 12.64 0.00 43.19 1.82
1371 4291 1.908619 GGGGTGCAGATCCCAAAATTT 59.091 47.619 12.64 0.00 43.19 1.82
1372 4292 2.355007 GGGGTGCAGATCCCAAAATTTG 60.355 50.000 12.64 0.00 43.19 2.32
1376 4296 3.187022 GTGCAGATCCCAAAATTTGTTGC 59.813 43.478 4.92 7.08 0.00 4.17
1411 4331 6.474630 AGTCTTCAGCATCTTGATCTTTCTT 58.525 36.000 0.00 0.00 0.00 2.52
1412 4332 6.941436 AGTCTTCAGCATCTTGATCTTTCTTT 59.059 34.615 0.00 0.00 0.00 2.52
1431 4351 1.042003 TTGCAAGCTTTGTGGGCAGA 61.042 50.000 8.24 0.00 35.68 4.26
1465 4385 5.296283 CAGCTTGGTAATCTCTCCAATCTTG 59.704 44.000 0.00 0.00 41.89 3.02
1506 4426 5.582665 GGACAATCCTTTGTACTCAGATGAC 59.417 44.000 0.00 0.00 46.01 3.06
1569 4489 6.430308 TCGATATGAGCTCGGTTAATCTTAGT 59.570 38.462 9.64 0.00 36.78 2.24
1573 4493 6.710597 TGAGCTCGGTTAATCTTAGTACAT 57.289 37.500 9.64 0.00 0.00 2.29
1574 4494 6.736123 TGAGCTCGGTTAATCTTAGTACATC 58.264 40.000 9.64 0.00 0.00 3.06
1624 4544 6.721704 AGCTTCCTTCATTGAAAGTTCTTT 57.278 33.333 0.01 0.00 0.00 2.52
1715 4635 4.689345 GGTGTTGGATATCAGCGGTAATAC 59.311 45.833 4.83 0.00 0.00 1.89
1727 4647 1.940613 CGGTAATACCTTTCAGGCTGC 59.059 52.381 10.34 0.00 39.63 5.25
1796 4716 3.266510 TCTCTCCCAATGTGATTTCCG 57.733 47.619 0.00 0.00 0.00 4.30
1800 4720 1.352687 TCCCAATGTGATTTCCGTGGA 59.647 47.619 0.00 0.00 0.00 4.02
1803 4723 3.016031 CCAATGTGATTTCCGTGGATCA 58.984 45.455 0.00 0.00 0.00 2.92
1959 4879 3.580458 CCACAGGGGATATAGGAGAACTG 59.420 52.174 0.00 0.00 40.01 3.16
2002 4922 1.301401 TGGGACAAGCTGTACGTGC 60.301 57.895 0.00 0.00 29.95 5.34
2070 4990 8.098912 TGGTTTAGACCTCTAACTAATTTGACC 58.901 37.037 3.79 0.00 46.66 4.02
2141 5061 0.315251 GGAGCACTTCCAAAACTGGC 59.685 55.000 0.00 0.00 46.01 4.85
2145 5065 4.261801 GAGCACTTCCAAAACTGGCTATA 58.738 43.478 0.00 0.00 0.00 1.31
2148 5068 4.142600 GCACTTCCAAAACTGGCTATACTG 60.143 45.833 0.00 0.00 0.00 2.74
2289 5210 3.561313 GGGTTCCTTCATTCAGGCTACAA 60.561 47.826 0.00 0.00 33.35 2.41
2332 5253 1.076777 ATTGGACCCGCATTCCCAG 60.077 57.895 0.00 0.00 31.33 4.45
2490 5411 1.004044 ACACTCCCAGCATCCTTTGAG 59.996 52.381 0.00 0.00 0.00 3.02
2497 5418 2.419159 CCAGCATCCTTTGAGACGATGA 60.419 50.000 0.00 0.00 36.33 2.92
2503 5424 3.067106 TCCTTTGAGACGATGAAAGCAC 58.933 45.455 0.00 0.00 0.00 4.40
2504 5425 2.159787 CCTTTGAGACGATGAAAGCACG 60.160 50.000 0.00 0.00 0.00 5.34
2507 5428 1.204704 TGAGACGATGAAAGCACGGAT 59.795 47.619 0.00 0.00 0.00 4.18
2521 5442 3.131396 GCACGGATAATGGACCTAAGTG 58.869 50.000 0.00 0.00 0.00 3.16
2522 5443 3.131396 CACGGATAATGGACCTAAGTGC 58.869 50.000 0.00 0.00 34.33 4.40
2539 5460 8.204836 ACCTAAGTGCTAATAGATTTACTGGTG 58.795 37.037 0.00 0.00 0.00 4.17
2617 5538 1.994463 GGGACACTGCCCTCAGATT 59.006 57.895 0.00 0.00 45.12 2.40
2618 5539 0.393537 GGGACACTGCCCTCAGATTG 60.394 60.000 0.00 0.00 45.12 2.67
2664 5585 7.594758 GTGCTTGCTCTTTACAACAATTCAATA 59.405 33.333 0.00 0.00 0.00 1.90
2750 5671 1.187087 CTGACAGGAGAGGTACCCAC 58.813 60.000 8.74 3.19 0.00 4.61
2783 5704 1.002134 ATCTTGGGGGCTTCACACG 60.002 57.895 0.00 0.00 0.00 4.49
2889 5810 8.791327 TTCTTGATCTTGCATACAATCAGTTA 57.209 30.769 0.00 0.00 34.61 2.24
3033 5954 0.608856 TGGACCTCGCATGCAACAAT 60.609 50.000 19.57 0.00 0.00 2.71
3100 6021 6.525578 TCGCTCGGATTAATGGATATAGTT 57.474 37.500 0.00 0.00 0.00 2.24
3152 6073 0.608582 AGCTTTCTTCAGGCAGCCAG 60.609 55.000 15.80 5.66 32.25 4.85
3156 6077 1.352083 TTCTTCAGGCAGCCAGTACT 58.648 50.000 15.80 0.00 0.00 2.73
3174 6095 2.767505 ACTGCTAGGGTCAAACTTTCG 58.232 47.619 0.00 0.00 0.00 3.46
3216 6137 5.544650 GTGCTTACTAAGGGACAACAACTA 58.455 41.667 0.00 0.00 0.00 2.24
3226 6147 4.165372 AGGGACAACAACTAGAGTTTTCCA 59.835 41.667 25.11 0.00 44.00 3.53
3237 6158 2.618709 AGAGTTTTCCAAAGAGTTGCCG 59.381 45.455 0.00 0.00 33.01 5.69
3249 6170 3.332034 AGAGTTGCCGTACATGGTAAAC 58.668 45.455 0.00 0.00 35.29 2.01
3255 6176 3.437395 TGCCGTACATGGTAAACATTGAC 59.563 43.478 0.00 0.00 37.84 3.18
3258 6179 5.421277 CCGTACATGGTAAACATTGACCTA 58.579 41.667 0.00 0.00 37.84 3.08
3261 6182 6.759356 CGTACATGGTAAACATTGACCTATCA 59.241 38.462 0.00 0.00 37.84 2.15
3269 6190 5.981088 AACATTGACCTATCATGCAACAA 57.019 34.783 0.00 0.00 33.85 2.83
3271 6192 6.140303 ACATTGACCTATCATGCAACAATC 57.860 37.500 0.00 0.00 33.85 2.67
3276 6197 5.108187 ACCTATCATGCAACAATCTGACT 57.892 39.130 0.00 0.00 0.00 3.41
3288 6209 1.813102 ATCTGACTGGAGGAATCCCC 58.187 55.000 0.00 0.00 0.00 4.81
3291 6212 0.252513 TGACTGGAGGAATCCCCGAA 60.253 55.000 0.00 0.00 40.87 4.30
3292 6213 0.466124 GACTGGAGGAATCCCCGAAG 59.534 60.000 0.00 0.00 40.87 3.79
3341 6262 6.469782 AAGCTTGAACTTTTCTTGGAATCA 57.530 33.333 0.00 0.00 0.00 2.57
3347 6268 7.206981 TGAACTTTTCTTGGAATCATCTGAC 57.793 36.000 0.00 0.00 0.00 3.51
3360 6281 2.121948 CATCTGACTGGGAGGATTCCA 58.878 52.381 5.29 0.00 46.31 3.53
3372 6293 5.636977 TGGGAGGATTCCAAAGAATATTGGG 60.637 44.000 5.29 0.00 44.63 4.12
3380 6301 7.124147 GATTCCAAAGAATATTGGGAACCTCAA 59.876 37.037 0.00 0.00 46.69 3.02
3405 6326 0.185416 TCGAGTCCCTGGACCTATCC 59.815 60.000 12.66 0.00 45.59 2.59
3415 6336 1.968493 TGGACCTATCCCATAACGAGC 59.032 52.381 0.00 0.00 45.59 5.03
3479 6400 2.289382 TGAGCCGCTTCAACTTGTCATA 60.289 45.455 0.00 0.00 0.00 2.15
3517 6438 1.419387 AGATACCAGCAGGGAATCAGC 59.581 52.381 13.06 0.00 41.15 4.26
3524 6445 2.119655 CAGGGAATCAGCTGCAGGC 61.120 63.158 17.12 7.98 42.19 4.85
3600 6521 3.959535 CTCTTGAAGAGTTGCTCTCCT 57.040 47.619 13.93 0.00 40.28 3.69
3604 6525 5.728471 TCTTGAAGAGTTGCTCTCCTAATG 58.272 41.667 0.00 0.00 40.28 1.90
3624 6545 3.707316 TGCAACAATAATTACCCCAGCT 58.293 40.909 0.00 0.00 0.00 4.24
3626 6547 4.642885 TGCAACAATAATTACCCCAGCTAC 59.357 41.667 0.00 0.00 0.00 3.58
3637 6558 0.399454 CCCAGCTACAGATGATGGGG 59.601 60.000 8.99 0.00 45.78 4.96
3651 6572 2.243490 TGGGGATCATCACCATGGG 58.757 57.895 18.09 5.22 46.95 4.00
3654 6575 4.681901 TGGGGATCATCACCATGGGGTA 62.682 54.545 15.27 0.60 46.95 3.69
3672 6593 1.955080 GTAGGGACGTCCATCTACCTG 59.045 57.143 34.40 0.00 38.24 4.00
3681 6602 2.042464 TCCATCTACCTGAGCATGGTC 58.958 52.381 18.01 18.01 38.88 4.02
3732 6653 5.504665 GGTCTTCTGTGTCATGTTGTTCAAG 60.505 44.000 0.00 0.00 0.00 3.02
3765 6686 2.467566 ACGCCTATTTCCGTTTCACT 57.532 45.000 0.00 0.00 33.26 3.41
3792 6713 1.437625 TGTACCACATGATGTGCGTG 58.562 50.000 19.69 9.17 46.51 5.34
3797 6718 1.605232 CCACATGATGTGCGTGCATAT 59.395 47.619 19.69 3.61 46.51 1.78
3802 6723 5.916320 CACATGATGTGCGTGCATATAATTT 59.084 36.000 13.15 0.00 41.89 1.82
3821 6742 0.555769 TTTGCCTGGAACCTCCTTGT 59.444 50.000 0.00 0.00 37.46 3.16
3838 6759 5.316158 CCTTGTGAGGAAGGGATGATTAT 57.684 43.478 0.00 0.00 46.74 1.28
3872 6793 5.011125 CAGTGAAGGGAGGATATACAACGAT 59.989 44.000 0.00 0.00 0.00 3.73
3935 6856 7.603784 TCAGTACTTCGAGTGTGTATGTAACTA 59.396 37.037 0.00 0.00 0.00 2.24
3961 6882 1.484653 CTCCATTCATACGGGTGGTGA 59.515 52.381 0.00 0.00 33.47 4.02
3996 6917 9.023967 GGTATACTTTTGTGTAACTATGTACCG 57.976 37.037 2.25 0.00 38.04 4.02
4032 6953 5.332355 GCTACATAAATAAGGTCTGTTCGCG 60.332 44.000 0.00 0.00 0.00 5.87
4034 6955 0.719465 AAATAAGGTCTGTTCGCGCG 59.281 50.000 26.76 26.76 0.00 6.86
4054 6975 4.445718 CGCGCTCATGAATAAATACTGAGT 59.554 41.667 5.56 0.00 36.55 3.41
4105 7026 4.080582 TGGATGTAAACCGACCTGATGATT 60.081 41.667 0.00 0.00 0.00 2.57
4173 7094 8.689251 TCACTTGAGTCTATTCGTTTTCTATG 57.311 34.615 0.00 0.00 0.00 2.23
4186 7107 5.984926 TCGTTTTCTATGTTCTTGTAACCGT 59.015 36.000 0.00 0.00 0.00 4.83
4254 7175 0.108520 TACGTTTCCACCCATCGCTC 60.109 55.000 0.00 0.00 0.00 5.03
4255 7176 1.079127 CGTTTCCACCCATCGCTCT 60.079 57.895 0.00 0.00 0.00 4.09
4278 7199 6.262944 TCTCCTACGAGCGTTTAAATGGTATA 59.737 38.462 11.92 7.32 35.94 1.47
4279 7200 6.804677 TCCTACGAGCGTTTAAATGGTATAA 58.195 36.000 11.92 0.66 0.00 0.98
4285 7206 8.355169 ACGAGCGTTTAAATGGTATAATAGAGA 58.645 33.333 11.92 0.00 0.00 3.10
4296 7217 6.378745 TGGTATAATAGAGACTGTTAGCCCA 58.621 40.000 0.00 0.00 0.00 5.36
4319 7240 1.646447 TGGCTCCTTCTTCCTCCTCTA 59.354 52.381 0.00 0.00 0.00 2.43
4324 7245 4.653801 GCTCCTTCTTCCTCCTCTATTTCT 59.346 45.833 0.00 0.00 0.00 2.52
4339 7261 5.618236 TCTATTTCTGCATCCTCAATCAGG 58.382 41.667 0.00 0.00 45.15 3.86
4358 7280 2.342179 GGAAGTCTCCGAAAAGCTCAG 58.658 52.381 0.00 0.00 30.03 3.35
4362 7284 2.894126 AGTCTCCGAAAAGCTCAGAAGA 59.106 45.455 0.00 0.00 0.00 2.87
4363 7285 2.990514 GTCTCCGAAAAGCTCAGAAGAC 59.009 50.000 0.00 0.00 0.00 3.01
4446 7368 2.810439 ATCTAGATGGCTCGCTTCAC 57.190 50.000 3.89 0.00 0.00 3.18
4497 7419 0.551131 ATGGGGGAAGTCAGGAAGCT 60.551 55.000 0.00 0.00 0.00 3.74
4505 7427 2.008242 AGTCAGGAAGCTGTCACTCT 57.992 50.000 0.00 0.00 0.00 3.24
4559 7481 4.628963 ACAAGTTCTGGGGTACGTATTT 57.371 40.909 0.00 0.00 0.00 1.40
4597 7519 0.667792 GTGTTGACTCAGGTCGCCTC 60.668 60.000 0.00 0.00 44.83 4.70
4598 7520 0.827925 TGTTGACTCAGGTCGCCTCT 60.828 55.000 0.00 0.00 44.83 3.69
4599 7521 0.318762 GTTGACTCAGGTCGCCTCTT 59.681 55.000 0.00 0.00 44.83 2.85
4600 7522 0.318441 TTGACTCAGGTCGCCTCTTG 59.682 55.000 0.00 0.00 44.83 3.02
4601 7523 0.539669 TGACTCAGGTCGCCTCTTGA 60.540 55.000 0.00 0.00 44.83 3.02
4602 7524 0.109039 GACTCAGGTCGCCTCTTGAC 60.109 60.000 0.00 0.00 35.60 3.18
4606 7528 2.182030 GGTCGCCTCTTGACCGAG 59.818 66.667 0.00 0.00 45.82 4.63
4612 7534 3.534721 CCTCTTGACCGAGGGAAAC 57.465 57.895 0.00 0.00 45.53 2.78
4665 7587 1.373497 CAGTCTCGTGCTCACACCC 60.373 63.158 0.69 0.00 44.40 4.61
4739 7661 7.766278 GCTACAGATAGTTTCTCCAAGATGAAA 59.234 37.037 0.00 0.00 29.93 2.69
4770 7692 1.092348 TGACATGCATCTTCAGCAGC 58.908 50.000 0.00 0.00 46.36 5.25
4778 7816 2.159544 GCATCTTCAGCAGCAGAAAGAC 60.160 50.000 1.45 0.00 0.00 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 9.988815 GAGGAGACTAGCTTTATTAATCAATGA 57.011 33.333 0.00 0.00 44.43 2.57
3 4 9.213799 GGAGGAGACTAGCTTTATTAATCAATG 57.786 37.037 0.00 0.00 44.43 2.82
4 5 8.938883 TGGAGGAGACTAGCTTTATTAATCAAT 58.061 33.333 0.00 0.00 44.43 2.57
5 6 8.319057 TGGAGGAGACTAGCTTTATTAATCAA 57.681 34.615 0.00 0.00 44.43 2.57
6 7 7.914427 TGGAGGAGACTAGCTTTATTAATCA 57.086 36.000 0.00 0.00 44.43 2.57
9 10 9.830186 AGATATGGAGGAGACTAGCTTTATTAA 57.170 33.333 0.00 0.00 44.43 1.40
12 13 6.895204 GGAGATATGGAGGAGACTAGCTTTAT 59.105 42.308 0.00 0.00 44.43 1.40
13 14 6.249951 GGAGATATGGAGGAGACTAGCTTTA 58.750 44.000 0.00 0.00 44.43 1.85
14 15 5.083821 GGAGATATGGAGGAGACTAGCTTT 58.916 45.833 0.00 0.00 44.43 3.51
15 16 4.510205 GGGAGATATGGAGGAGACTAGCTT 60.510 50.000 0.00 0.00 44.43 3.74
16 17 3.011257 GGGAGATATGGAGGAGACTAGCT 59.989 52.174 0.00 0.00 44.43 3.32
17 18 3.011257 AGGGAGATATGGAGGAGACTAGC 59.989 52.174 0.00 0.00 44.43 3.42
18 19 4.044065 ACAGGGAGATATGGAGGAGACTAG 59.956 50.000 0.00 0.00 44.43 2.57
21 22 2.896685 CACAGGGAGATATGGAGGAGAC 59.103 54.545 0.00 0.00 0.00 3.36
22 23 2.520120 ACACAGGGAGATATGGAGGAGA 59.480 50.000 0.00 0.00 0.00 3.71
23 24 2.896685 GACACAGGGAGATATGGAGGAG 59.103 54.545 0.00 0.00 0.00 3.69
24 25 2.247372 TGACACAGGGAGATATGGAGGA 59.753 50.000 0.00 0.00 0.00 3.71
25 26 2.682594 TGACACAGGGAGATATGGAGG 58.317 52.381 0.00 0.00 0.00 4.30
26 27 4.158786 AGATGACACAGGGAGATATGGAG 58.841 47.826 0.00 0.00 0.00 3.86
28 29 5.083122 AGTAGATGACACAGGGAGATATGG 58.917 45.833 0.00 0.00 0.00 2.74
29 30 6.662865 AAGTAGATGACACAGGGAGATATG 57.337 41.667 0.00 0.00 0.00 1.78
30 31 6.015856 CGAAAGTAGATGACACAGGGAGATAT 60.016 42.308 0.00 0.00 0.00 1.63
31 32 5.299531 CGAAAGTAGATGACACAGGGAGATA 59.700 44.000 0.00 0.00 0.00 1.98
32 33 4.098654 CGAAAGTAGATGACACAGGGAGAT 59.901 45.833 0.00 0.00 0.00 2.75
33 34 3.444034 CGAAAGTAGATGACACAGGGAGA 59.556 47.826 0.00 0.00 0.00 3.71
35 36 2.094182 GCGAAAGTAGATGACACAGGGA 60.094 50.000 0.00 0.00 0.00 4.20
37 38 1.920574 CGCGAAAGTAGATGACACAGG 59.079 52.381 0.00 0.00 0.00 4.00
39 40 2.287970 ACACGCGAAAGTAGATGACACA 60.288 45.455 15.93 0.00 0.00 3.72
40 41 2.325761 ACACGCGAAAGTAGATGACAC 58.674 47.619 15.93 0.00 0.00 3.67
41 42 2.717580 ACACGCGAAAGTAGATGACA 57.282 45.000 15.93 0.00 0.00 3.58
42 43 2.026507 CGAACACGCGAAAGTAGATGAC 59.973 50.000 15.93 0.00 0.00 3.06
43 44 2.095617 TCGAACACGCGAAAGTAGATGA 60.096 45.455 15.93 2.24 37.35 2.92
45 46 2.095364 AGTCGAACACGCGAAAGTAGAT 60.095 45.455 15.93 0.00 42.55 1.98
46 47 1.265095 AGTCGAACACGCGAAAGTAGA 59.735 47.619 15.93 8.85 42.55 2.59
47 48 1.682982 AGTCGAACACGCGAAAGTAG 58.317 50.000 15.93 6.64 42.55 2.57
49 50 2.124011 TTAGTCGAACACGCGAAAGT 57.876 45.000 15.93 5.29 42.55 2.66
50 51 3.646303 GAATTAGTCGAACACGCGAAAG 58.354 45.455 15.93 4.52 42.55 2.62
51 52 3.693300 GAATTAGTCGAACACGCGAAA 57.307 42.857 15.93 0.00 42.55 3.46
72 73 0.383737 CGAGAGCGAGCGTCATAGAC 60.384 60.000 0.00 0.00 40.82 2.59
74 75 4.505972 CGAGAGCGAGCGTCATAG 57.494 61.111 0.00 0.00 40.82 2.23
97 98 2.572284 GAGTCCGGTCCGAGGTTG 59.428 66.667 14.39 0.00 0.00 3.77
118 119 2.065906 TTTTGTTCCGCAACTCCGCC 62.066 55.000 0.00 0.00 36.72 6.13
120 121 0.656205 CGTTTTGTTCCGCAACTCCG 60.656 55.000 0.00 0.00 36.72 4.63
121 122 0.317519 CCGTTTTGTTCCGCAACTCC 60.318 55.000 0.00 0.00 36.72 3.85
122 123 0.658897 TCCGTTTTGTTCCGCAACTC 59.341 50.000 0.00 0.00 36.72 3.01
123 124 0.379316 GTCCGTTTTGTTCCGCAACT 59.621 50.000 0.00 0.00 36.72 3.16
126 127 1.950828 TTAGTCCGTTTTGTTCCGCA 58.049 45.000 0.00 0.00 0.00 5.69
127 128 3.482436 CGTATTAGTCCGTTTTGTTCCGC 60.482 47.826 0.00 0.00 0.00 5.54
131 132 3.244526 ACCCCGTATTAGTCCGTTTTGTT 60.245 43.478 0.00 0.00 0.00 2.83
132 133 2.302733 ACCCCGTATTAGTCCGTTTTGT 59.697 45.455 0.00 0.00 0.00 2.83
133 134 2.976589 ACCCCGTATTAGTCCGTTTTG 58.023 47.619 0.00 0.00 0.00 2.44
134 135 3.701205 AACCCCGTATTAGTCCGTTTT 57.299 42.857 0.00 0.00 0.00 2.43
153 3049 2.562876 GGCGCCAAACCCCGTAAAA 61.563 57.895 24.80 0.00 0.00 1.52
195 3092 2.194868 CCTGATTAACCGGGCCCC 59.805 66.667 18.66 0.00 0.00 5.80
196 3093 1.148498 CTCCTGATTAACCGGGCCC 59.852 63.158 13.57 13.57 32.56 5.80
209 3106 3.435169 GGGCTAATTAACCTTCCCTCCTG 60.435 52.174 4.93 0.00 0.00 3.86
277 3174 7.168302 CCAAAAATGCTACACACACGAAATAAA 59.832 33.333 0.00 0.00 0.00 1.40
278 3175 6.638873 CCAAAAATGCTACACACACGAAATAA 59.361 34.615 0.00 0.00 0.00 1.40
283 3180 2.292016 CCCAAAAATGCTACACACACGA 59.708 45.455 0.00 0.00 0.00 4.35
308 3205 2.660552 GTGTGGGTCACGGTGTCG 60.661 66.667 8.17 0.00 37.14 4.35
315 3212 1.885850 GACGTGGTGTGTGGGTCAC 60.886 63.158 0.00 0.00 46.31 3.67
349 3246 2.359848 TGGACGTATGGGTGACGATAAG 59.640 50.000 1.71 0.00 42.98 1.73
459 3363 2.809601 ATCACGTCGCTGGCGTTC 60.810 61.111 14.55 8.46 40.90 3.95
462 3366 3.112075 AACATCACGTCGCTGGCG 61.112 61.111 8.80 8.80 41.35 5.69
516 3428 3.119424 GGAAGAAGAGAACACTACTCCCG 60.119 52.174 0.00 0.00 35.27 5.14
520 3432 3.858135 TGGGGAAGAAGAGAACACTACT 58.142 45.455 0.00 0.00 0.00 2.57
521 3433 4.468153 AGATGGGGAAGAAGAGAACACTAC 59.532 45.833 0.00 0.00 0.00 2.73
522 3434 4.689062 AGATGGGGAAGAAGAGAACACTA 58.311 43.478 0.00 0.00 0.00 2.74
545 3457 4.532521 TCCTTTGGAAACTTCAAAAACCCA 59.467 37.500 0.00 0.00 34.26 4.51
547 3459 7.047891 AGATTCCTTTGGAAACTTCAAAAACC 58.952 34.615 2.98 0.00 45.41 3.27
561 3473 3.230134 TGGTTGGACAAGATTCCTTTGG 58.770 45.455 0.00 0.00 36.51 3.28
610 3522 1.436600 GACTGACCTGCATCACACAG 58.563 55.000 0.00 0.00 34.82 3.66
621 3533 1.674980 GAGACCGACGGACTGACCT 60.675 63.158 23.36 8.24 36.31 3.85
638 3550 4.096382 GGACAGAAAACTGCAACTGAAAGA 59.904 41.667 0.00 0.00 37.43 2.52
661 3573 2.424601 AGATGCACCAATTGACGGATTG 59.575 45.455 7.12 0.00 36.89 2.67
754 3667 0.784495 ACCTAGCCCCGATGATCCTA 59.216 55.000 0.00 0.00 0.00 2.94
778 3691 6.780031 TGATGTCTTAATCACTTGGGGAAAAA 59.220 34.615 0.00 0.00 31.58 1.94
782 3695 4.536090 ACTGATGTCTTAATCACTTGGGGA 59.464 41.667 0.00 0.00 33.08 4.81
849 3762 2.031508 GGTTGTGACACGTTTGGTATGG 60.032 50.000 0.22 0.00 0.00 2.74
935 3848 5.536538 TGCTTCACTCTCTCTTCTCTTGTTA 59.463 40.000 0.00 0.00 0.00 2.41
969 3883 5.086621 AGGGATTTCAGTATGCCTTGTTTT 58.913 37.500 0.00 0.00 43.02 2.43
971 3885 4.322057 AGGGATTTCAGTATGCCTTGTT 57.678 40.909 0.00 0.00 43.02 2.83
972 3886 4.475016 AGTAGGGATTTCAGTATGCCTTGT 59.525 41.667 1.96 0.00 43.02 3.16
973 3887 4.818546 CAGTAGGGATTTCAGTATGCCTTG 59.181 45.833 1.96 0.00 43.02 3.61
974 3888 4.721776 TCAGTAGGGATTTCAGTATGCCTT 59.278 41.667 1.96 0.00 43.02 4.35
975 3889 4.298626 TCAGTAGGGATTTCAGTATGCCT 58.701 43.478 0.00 0.00 46.63 4.75
976 3890 4.689612 TCAGTAGGGATTTCAGTATGCC 57.310 45.455 0.00 0.00 36.35 4.40
977 3891 7.420800 CATTTTCAGTAGGGATTTCAGTATGC 58.579 38.462 0.00 0.00 34.76 3.14
1017 3931 1.362406 GCAACGAGACCAAGGCTAGC 61.362 60.000 6.04 6.04 0.00 3.42
1026 3940 1.016653 GGAGCAGAAGCAACGAGACC 61.017 60.000 0.00 0.00 45.49 3.85
1050 3964 2.131023 AGGGAGGAAATGGATGGAGTC 58.869 52.381 0.00 0.00 0.00 3.36
1056 3970 2.517127 AGCATCAAGGGAGGAAATGGAT 59.483 45.455 0.00 0.00 0.00 3.41
1078 3992 2.029666 GCTCCCATCCGATCCACG 59.970 66.667 0.00 0.00 42.18 4.94
1080 3994 2.811514 GCAGCTCCCATCCGATCCA 61.812 63.158 0.00 0.00 0.00 3.41
1104 4018 1.818785 GAGTGCAGCCCTCTCATGC 60.819 63.158 0.00 0.00 40.40 4.06
1116 4030 2.847327 CTTTGAAGGAGAGGAGTGCA 57.153 50.000 0.00 0.00 0.00 4.57
1134 4048 1.831652 CGGGGTCTGACAAGCTTCCT 61.832 60.000 10.38 0.00 0.00 3.36
1136 4050 0.951040 CACGGGGTCTGACAAGCTTC 60.951 60.000 10.38 0.00 0.00 3.86
1154 4068 1.159285 CCACGATGAAAGCTGCTTCA 58.841 50.000 16.28 14.87 39.56 3.02
1158 4072 0.524816 CATGCCACGATGAAAGCTGC 60.525 55.000 0.00 0.00 0.00 5.25
1160 4074 0.322816 ACCATGCCACGATGAAAGCT 60.323 50.000 0.00 0.00 0.00 3.74
1161 4075 0.179156 CACCATGCCACGATGAAAGC 60.179 55.000 0.00 0.00 0.00 3.51
1183 4097 1.318158 CCTTCCCAGGTGCAGCAATC 61.318 60.000 19.63 0.00 35.06 2.67
1188 4102 0.607489 CAACTCCTTCCCAGGTGCAG 60.607 60.000 0.00 0.00 41.69 4.41
1199 4113 1.109323 GTTGCTGCACCCAACTCCTT 61.109 55.000 14.97 0.00 39.47 3.36
1234 4148 1.884235 CCACTGAGGTTGAGGTTGAC 58.116 55.000 0.00 0.00 0.00 3.18
1252 4166 3.643978 CGCTTCATAGCCGCAGCC 61.644 66.667 0.00 0.00 44.86 4.85
1258 4172 2.240500 CCACTCGCGCTTCATAGCC 61.241 63.158 5.56 0.00 44.86 3.93
1261 4175 1.437573 CTCCCACTCGCGCTTCATA 59.562 57.895 5.56 0.00 0.00 2.15
1263 4177 4.069232 CCTCCCACTCGCGCTTCA 62.069 66.667 5.56 0.00 0.00 3.02
1268 4188 0.039074 GATATCACCTCCCACTCGCG 60.039 60.000 0.00 0.00 0.00 5.87
1284 4204 1.210478 GCAGTCAAAGAGGGGCTGATA 59.790 52.381 0.00 0.00 0.00 2.15
1303 4223 5.959618 AAATACTTCAAGTGGTGTAAGGC 57.040 39.130 0.00 0.00 0.00 4.35
1308 4228 7.506114 TCAAGTCTAAATACTTCAAGTGGTGT 58.494 34.615 0.00 0.00 37.61 4.16
1311 4231 6.876257 AGCTCAAGTCTAAATACTTCAAGTGG 59.124 38.462 0.00 0.00 37.61 4.00
1319 4239 5.551233 TGTTGCAGCTCAAGTCTAAATACT 58.449 37.500 1.17 0.00 34.91 2.12
1340 4260 0.466189 CTGCACCCCACTGAAGTTGT 60.466 55.000 0.00 0.00 0.00 3.32
1356 4276 3.667360 AGCAACAAATTTTGGGATCTGC 58.333 40.909 13.42 12.15 34.12 4.26
1365 4285 9.875691 AGACTTTTAAGAGAAGCAACAAATTTT 57.124 25.926 0.00 0.00 0.00 1.82
1366 4286 9.875691 AAGACTTTTAAGAGAAGCAACAAATTT 57.124 25.926 0.00 0.00 0.00 1.82
1369 4289 8.050778 TGAAGACTTTTAAGAGAAGCAACAAA 57.949 30.769 0.00 0.00 0.00 2.83
1370 4290 7.624360 TGAAGACTTTTAAGAGAAGCAACAA 57.376 32.000 0.00 0.00 0.00 2.83
1371 4291 6.238484 GCTGAAGACTTTTAAGAGAAGCAACA 60.238 38.462 0.00 0.00 0.00 3.33
1372 4292 6.139435 GCTGAAGACTTTTAAGAGAAGCAAC 58.861 40.000 0.00 0.00 0.00 4.17
1376 4296 7.903995 AGATGCTGAAGACTTTTAAGAGAAG 57.096 36.000 0.00 0.00 0.00 2.85
1411 4331 0.179078 CTGCCCACAAAGCTTGCAAA 60.179 50.000 0.00 0.00 0.00 3.68
1412 4332 1.042003 TCTGCCCACAAAGCTTGCAA 61.042 50.000 0.00 0.00 0.00 4.08
1465 4385 4.436242 TGTCCGAGACACTGAGAAATAC 57.564 45.455 3.02 0.00 37.67 1.89
1506 4426 4.036027 GTGAGATGTGATAACCATGCAAGG 59.964 45.833 6.39 6.39 0.00 3.61
1569 4489 1.632920 TGCACCCAATCCACTGATGTA 59.367 47.619 0.00 0.00 0.00 2.29
1573 4493 0.966875 GCATGCACCCAATCCACTGA 60.967 55.000 14.21 0.00 0.00 3.41
1574 4494 1.252215 TGCATGCACCCAATCCACTG 61.252 55.000 18.46 0.00 0.00 3.66
1624 4544 4.344968 TCTGAGATCACTGTCTTCCAAACA 59.655 41.667 0.00 0.00 0.00 2.83
1803 4723 7.286316 GTCATACTTCCCATTTCATCAGGAATT 59.714 37.037 0.00 0.00 37.74 2.17
1959 4879 2.336667 CATTTTGGCAACCGTTCCATC 58.663 47.619 0.00 0.00 31.54 3.51
1993 4913 1.920574 CGAGAAATCCAGCACGTACAG 59.079 52.381 0.00 0.00 0.00 2.74
2002 4922 3.138304 TGTTGTTGTCCGAGAAATCCAG 58.862 45.455 0.00 0.00 0.00 3.86
2145 5065 8.263640 ACTAGTTGATTAGAATGAAGATGCAGT 58.736 33.333 0.00 0.00 0.00 4.40
2148 5068 8.341173 CCAACTAGTTGATTAGAATGAAGATGC 58.659 37.037 32.50 0.00 42.93 3.91
2289 5210 3.060866 GACTTCAGGTCGGCCACT 58.939 61.111 9.71 0.00 37.19 4.00
2332 5253 0.737219 GATTGACACCTGAGCCATGC 59.263 55.000 0.00 0.00 0.00 4.06
2362 5283 4.210120 GGACGCATTAGAGATGTCAATGAC 59.790 45.833 6.41 6.41 32.54 3.06
2419 5340 5.523188 CCAAGAGAGTAGCATTTGAAGCTAG 59.477 44.000 0.00 0.00 44.54 3.42
2490 5411 3.059597 CCATTATCCGTGCTTTCATCGTC 60.060 47.826 0.00 0.00 0.00 4.20
2497 5418 4.080526 ACTTAGGTCCATTATCCGTGCTTT 60.081 41.667 0.00 0.00 0.00 3.51
2503 5424 3.753294 AGCACTTAGGTCCATTATCCG 57.247 47.619 0.00 0.00 0.00 4.18
2504 5425 8.135382 TCTATTAGCACTTAGGTCCATTATCC 57.865 38.462 0.00 0.00 0.00 2.59
2521 5442 5.467063 GGACTGCACCAGTAAATCTATTAGC 59.533 44.000 0.00 0.00 45.44 3.09
2522 5443 5.992217 GGGACTGCACCAGTAAATCTATTAG 59.008 44.000 0.00 0.00 45.44 1.73
2539 5460 2.437413 CCTAGGAAACTTTGGGACTGC 58.563 52.381 1.05 0.00 43.67 4.40
2617 5538 1.307517 ATAACTCCCGGGCTTCCCA 60.308 57.895 18.49 0.00 45.83 4.37
2618 5539 1.054978 AGATAACTCCCGGGCTTCCC 61.055 60.000 18.49 2.81 41.09 3.97
2627 5548 2.093235 AGAGCAAGCACAGATAACTCCC 60.093 50.000 0.00 0.00 0.00 4.30
2664 5585 4.508551 TGAAGATGGTATGTTGCCAGAT 57.491 40.909 0.00 0.00 39.65 2.90
2712 5633 5.604231 TGTCAGCATATTTCCTGATAGGTCT 59.396 40.000 0.00 0.00 39.95 3.85
2716 5637 6.014755 TCTCCTGTCAGCATATTTCCTGATAG 60.015 42.308 11.51 11.51 43.05 2.08
2750 5671 0.255318 AAGATCTCCCTGCTGGCAAG 59.745 55.000 3.63 4.13 0.00 4.01
2832 5753 7.830099 ATCTTTTGACCTTTGAAGAACTGAT 57.170 32.000 0.00 0.00 32.47 2.90
2908 5829 6.215636 AGGGATGTCATGTTTTCTACTAACCT 59.784 38.462 0.00 0.00 0.00 3.50
3033 5954 6.447084 AGGATTCAGGTATACCTCCAGAAAAA 59.553 38.462 22.09 7.96 46.65 1.94
3100 6021 7.862274 AATCTGATAGTCCATCCAGTGAATA 57.138 36.000 0.00 0.00 32.09 1.75
3152 6073 3.678548 CGAAAGTTTGACCCTAGCAGTAC 59.321 47.826 0.00 0.00 0.00 2.73
3156 6077 2.922740 ACGAAAGTTTGACCCTAGCA 57.077 45.000 0.00 0.00 46.40 3.49
3174 6095 3.676540 CACGGACAAAGTTGTTGTGTAC 58.323 45.455 16.33 0.00 42.43 2.90
3216 6137 2.618709 CGGCAACTCTTTGGAAAACTCT 59.381 45.455 0.00 0.00 32.81 3.24
3226 6147 2.561478 ACCATGTACGGCAACTCTTT 57.439 45.000 0.00 0.00 0.00 2.52
3237 6158 8.559536 CATGATAGGTCAATGTTTACCATGTAC 58.440 37.037 0.00 0.00 38.01 2.90
3249 6170 6.038936 TCAGATTGTTGCATGATAGGTCAATG 59.961 38.462 0.00 0.00 38.01 2.82
3255 6176 4.275196 CCAGTCAGATTGTTGCATGATAGG 59.725 45.833 0.00 0.00 0.00 2.57
3258 6179 3.945921 CTCCAGTCAGATTGTTGCATGAT 59.054 43.478 0.00 0.00 0.00 2.45
3261 6182 2.306805 TCCTCCAGTCAGATTGTTGCAT 59.693 45.455 0.00 0.00 0.00 3.96
3269 6190 1.813102 GGGGATTCCTCCAGTCAGAT 58.187 55.000 2.01 0.00 44.08 2.90
3271 6192 0.687757 TCGGGGATTCCTCCAGTCAG 60.688 60.000 2.01 0.00 44.08 3.51
3276 6197 4.066614 CCTTCGGGGATTCCTCCA 57.933 61.111 2.01 0.00 44.08 3.86
3288 6209 3.742433 ATCAGAGCACTAATCCCTTCG 57.258 47.619 0.00 0.00 0.00 3.79
3291 6212 2.776536 AGCAATCAGAGCACTAATCCCT 59.223 45.455 0.00 0.00 0.00 4.20
3292 6213 3.205784 AGCAATCAGAGCACTAATCCC 57.794 47.619 0.00 0.00 0.00 3.85
3294 6215 5.808042 TCAAAGCAATCAGAGCACTAATC 57.192 39.130 0.00 0.00 0.00 1.75
3295 6216 6.579666 TTTCAAAGCAATCAGAGCACTAAT 57.420 33.333 0.00 0.00 0.00 1.73
3341 6262 2.575921 TGGAATCCTCCCAGTCAGAT 57.424 50.000 0.00 0.00 41.64 2.90
3347 6268 6.645790 CAATATTCTTTGGAATCCTCCCAG 57.354 41.667 0.00 0.00 41.64 4.45
3360 6281 5.779771 TGCTTTGAGGTTCCCAATATTCTTT 59.220 36.000 0.00 0.00 0.00 2.52
3372 6293 2.062519 GACTCGAGTGCTTTGAGGTTC 58.937 52.381 25.58 0.00 41.04 3.62
3380 6301 1.228894 TCCAGGGACTCGAGTGCTT 60.229 57.895 32.03 24.81 34.60 3.91
3381 6302 1.979693 GTCCAGGGACTCGAGTGCT 60.980 63.158 32.03 17.83 41.57 4.40
3405 6326 1.751351 TCTCCAGACAGCTCGTTATGG 59.249 52.381 11.73 11.73 36.53 2.74
3415 6336 3.988976 TGAAGGGATTTCTCCAGACAG 57.011 47.619 0.00 0.00 44.08 3.51
3479 6400 6.841229 TGGTATCTGTCCAGAGAGATTGTTAT 59.159 38.462 12.04 0.00 41.12 1.89
3492 6413 0.042581 TCCCTGCTGGTATCTGTCCA 59.957 55.000 9.00 0.00 34.77 4.02
3506 6427 2.119655 GCCTGCAGCTGATTCCCTG 61.120 63.158 20.43 2.97 38.99 4.45
3517 6438 3.260483 GTCATCGAGCGCCTGCAG 61.260 66.667 6.78 6.78 46.23 4.41
3536 6457 6.942532 TGTTTCCAATATAACTGGATGCTC 57.057 37.500 7.55 1.85 42.56 4.26
3538 6459 6.925165 CCAATGTTTCCAATATAACTGGATGC 59.075 38.462 7.55 5.25 42.56 3.91
3555 6476 3.247162 AGGCCCACATAAACCAATGTTT 58.753 40.909 0.00 0.00 46.22 2.83
3594 6515 7.040409 GGGGTAATTATTGTTGCATTAGGAGAG 60.040 40.741 0.00 0.00 0.00 3.20
3600 6521 5.896678 AGCTGGGGTAATTATTGTTGCATTA 59.103 36.000 0.00 0.00 0.00 1.90
3604 6525 4.642885 TGTAGCTGGGGTAATTATTGTTGC 59.357 41.667 0.00 0.00 0.00 4.17
3611 6532 5.013079 CCATCATCTGTAGCTGGGGTAATTA 59.987 44.000 0.00 0.00 0.00 1.40
3614 6535 2.705658 CCATCATCTGTAGCTGGGGTAA 59.294 50.000 0.00 0.00 0.00 2.85
3646 6567 1.054406 ATGGACGTCCCTACCCCATG 61.054 60.000 31.19 0.00 35.44 3.66
3651 6572 1.133544 AGGTAGATGGACGTCCCTACC 60.134 57.143 37.91 37.91 44.53 3.18
3654 6575 0.629596 TCAGGTAGATGGACGTCCCT 59.370 55.000 31.19 22.52 35.38 4.20
3656 6577 0.386113 GCTCAGGTAGATGGACGTCC 59.614 60.000 28.17 28.17 0.00 4.79
3672 6593 0.109597 CAAAGCCAACGACCATGCTC 60.110 55.000 0.00 0.00 32.62 4.26
3681 6602 1.082104 GCCGAAGACAAAGCCAACG 60.082 57.895 0.00 0.00 0.00 4.10
3732 6653 5.652994 AATAGGCGTATCTCCATCTCTTC 57.347 43.478 0.00 0.00 0.00 2.87
3792 6713 5.917462 AGGTTCCAGGCAAAAATTATATGC 58.083 37.500 2.36 2.36 39.33 3.14
3797 6718 4.126520 AGGAGGTTCCAGGCAAAAATTA 57.873 40.909 0.00 0.00 39.61 1.40
3802 6723 0.555769 ACAAGGAGGTTCCAGGCAAA 59.444 50.000 0.00 0.00 39.61 3.68
3835 6756 9.053472 TCCTCCCTTCACTGTATCTAAAAATAA 57.947 33.333 0.00 0.00 0.00 1.40
3838 6759 6.945636 TCCTCCCTTCACTGTATCTAAAAA 57.054 37.500 0.00 0.00 0.00 1.94
3848 6769 4.341235 TCGTTGTATATCCTCCCTTCACTG 59.659 45.833 0.00 0.00 0.00 3.66
3849 6770 4.543689 TCGTTGTATATCCTCCCTTCACT 58.456 43.478 0.00 0.00 0.00 3.41
3858 6779 7.577807 GCATAGGAGAACATCGTTGTATATCCT 60.578 40.741 21.39 21.39 41.45 3.24
3859 6780 6.531948 GCATAGGAGAACATCGTTGTATATCC 59.468 42.308 13.09 13.09 34.06 2.59
3872 6793 0.543277 CCCAGCTGCATAGGAGAACA 59.457 55.000 8.66 0.00 0.00 3.18
3935 6856 2.373169 ACCCGTATGAATGGAGATGCAT 59.627 45.455 0.00 0.00 33.01 3.96
4032 6953 5.914085 ACTCAGTATTTATTCATGAGCGC 57.086 39.130 0.00 0.00 40.82 5.92
4034 6955 8.279103 GCTACAACTCAGTATTTATTCATGAGC 58.721 37.037 0.00 0.00 40.82 4.26
4054 6975 9.151471 GACTGATTTGTATTCTAACAGCTACAA 57.849 33.333 0.00 0.00 33.51 2.41
4105 7026 2.688958 CAAACCACCACCGAACCTTTAA 59.311 45.455 0.00 0.00 0.00 1.52
4173 7094 5.623673 CAGCAATTACAACGGTTACAAGAAC 59.376 40.000 0.00 0.00 0.00 3.01
4186 7107 7.535139 GTGTTTATAAGGAGCAGCAATTACAA 58.465 34.615 0.00 0.00 0.00 2.41
4254 7175 3.518590 ACCATTTAAACGCTCGTAGGAG 58.481 45.455 8.10 8.10 43.46 3.69
4255 7176 3.598019 ACCATTTAAACGCTCGTAGGA 57.402 42.857 0.00 0.00 0.00 2.94
4278 7199 6.365970 CCATATGGGCTAACAGTCTCTATT 57.634 41.667 14.52 0.00 0.00 1.73
4296 7217 3.116395 AGAGGAGGAAGAAGGAGCCATAT 60.116 47.826 0.00 0.00 0.00 1.78
4319 7240 4.515028 TCCTGATTGAGGATGCAGAAAT 57.485 40.909 0.00 0.00 46.96 2.17
4339 7261 3.305398 TCTGAGCTTTTCGGAGACTTC 57.695 47.619 0.00 0.00 36.26 3.01
4347 7269 5.049818 ACAATTCTGTCTTCTGAGCTTTTCG 60.050 40.000 0.00 0.00 0.00 3.46
4362 7284 2.254546 TCCGCAAGACACAATTCTGT 57.745 45.000 0.00 0.00 43.02 3.41
4363 7285 3.558505 CTTTCCGCAAGACACAATTCTG 58.441 45.455 0.00 0.00 43.02 3.02
4417 7339 5.504173 GCGAGCCATCTAGATAACCAAAAAC 60.504 44.000 4.54 0.00 0.00 2.43
4420 7342 3.388024 AGCGAGCCATCTAGATAACCAAA 59.612 43.478 4.54 0.00 0.00 3.28
4421 7343 2.965831 AGCGAGCCATCTAGATAACCAA 59.034 45.455 4.54 0.00 0.00 3.67
4446 7368 1.993370 GTGATGGTTTTCTCCGTCTCG 59.007 52.381 6.52 0.00 42.26 4.04
4448 7370 1.697432 TGGTGATGGTTTTCTCCGTCT 59.303 47.619 6.52 0.00 42.26 4.18
4497 7419 1.626356 GGGCATGGGCTAGAGTGACA 61.626 60.000 0.00 0.00 40.87 3.58
4559 7481 4.175962 ACACTTCCTTGGAGAGGGAATTA 58.824 43.478 7.68 0.00 46.31 1.40
4597 7519 4.716003 GGGTTTCCCTCGGTCAAG 57.284 61.111 0.00 0.00 41.34 3.02
4606 7528 2.583441 GCTGCCCAAAGGGTTTCCC 61.583 63.158 3.68 0.00 46.51 3.97
4607 7529 2.583441 GGCTGCCCAAAGGGTTTCC 61.583 63.158 7.66 0.00 46.51 3.13
4608 7530 2.583441 GGGCTGCCCAAAGGGTTTC 61.583 63.158 32.46 0.14 46.51 2.78
4609 7531 2.526624 GGGCTGCCCAAAGGGTTT 60.527 61.111 32.46 0.00 46.51 3.27
4665 7587 4.008330 GACATGGCCATCCTGATATTGAG 58.992 47.826 17.61 2.13 0.00 3.02
4700 7622 7.461182 ACTATCTGTAGCAGACATATTCTCC 57.539 40.000 0.53 0.00 43.63 3.71
4702 7624 9.142014 AGAAACTATCTGTAGCAGACATATTCT 57.858 33.333 0.53 7.00 43.63 2.40
4716 7638 6.597280 GCTTTCATCTTGGAGAAACTATCTGT 59.403 38.462 0.00 0.00 38.96 3.41
4722 7644 3.075134 AGGGCTTTCATCTTGGAGAAACT 59.925 43.478 0.00 0.00 31.11 2.66
4723 7645 3.425659 AGGGCTTTCATCTTGGAGAAAC 58.574 45.455 0.00 0.00 31.11 2.78
4739 7661 0.682209 GCATGTCATCCACAAGGGCT 60.682 55.000 0.00 0.00 38.97 5.19
4764 7686 5.353400 TCATCATAAAGTCTTTCTGCTGCTG 59.647 40.000 0.00 0.00 0.00 4.41
4765 7687 5.353678 GTCATCATAAAGTCTTTCTGCTGCT 59.646 40.000 0.00 0.00 0.00 4.24
4769 7691 5.220491 GGTCGTCATCATAAAGTCTTTCTGC 60.220 44.000 0.00 0.00 0.00 4.26
4770 7692 6.035435 CAGGTCGTCATCATAAAGTCTTTCTG 59.965 42.308 0.00 2.68 0.00 3.02
4778 7816 7.545362 AAGAAATCAGGTCGTCATCATAAAG 57.455 36.000 0.00 0.00 0.00 1.85


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

AutoCloner maintained by Alex Coulton.