Multiple sequence alignment - TraesCS6A01G013500

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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 TraesCS6A01G013500 chr6A 100.000 4193 0 0 1 4193 6698199 6702391 0.000000e+00 7744.0
1 TraesCS6A01G013500 chr6A 81.017 1554 276 15 1623 3171 5940895 5942434 0.000000e+00 1218.0
2 TraesCS6A01G013500 chr6A 80.711 1576 290 11 1623 3191 5901941 5903509 0.000000e+00 1214.0
3 TraesCS6A01G013500 chr6A 80.257 1555 295 12 1623 3171 5917921 5919469 0.000000e+00 1160.0
4 TraesCS6A01G013500 chr6A 77.389 1371 242 34 506 1837 5939552 5940893 0.000000e+00 752.0
5 TraesCS6A01G013500 chr6A 79.030 639 114 15 1006 1640 5901264 5901886 1.800000e-113 420.0
6 TraesCS6A01G013500 chr6A 80.081 492 72 12 508 984 5900723 5901203 4.010000e-90 342.0
7 TraesCS6A01G013500 chr6A 77.176 517 84 12 506 1002 5916502 5917004 1.920000e-68 270.0
8 TraesCS6A01G013500 chr6D 95.747 3809 109 20 221 3999 7031980 7035765 0.000000e+00 6087.0
9 TraesCS6A01G013500 chr6D 81.206 1559 284 7 1623 3178 6371597 6373149 0.000000e+00 1247.0
10 TraesCS6A01G013500 chr6D 80.779 1566 285 16 1623 3180 6353193 6354750 0.000000e+00 1210.0
11 TraesCS6A01G013500 chr6D 80.554 1553 285 15 1623 3171 6426528 6428067 0.000000e+00 1179.0
12 TraesCS6A01G013500 chr6D 80.359 1558 288 17 1623 3171 6497721 6499269 0.000000e+00 1166.0
13 TraesCS6A01G013500 chr6D 81.890 1016 178 6 2159 3171 6465715 6466727 0.000000e+00 852.0
14 TraesCS6A01G013500 chr6D 80.153 1174 179 20 508 1640 6496290 6497450 0.000000e+00 828.0
15 TraesCS6A01G013500 chr6D 77.899 1371 235 34 506 1837 6425185 6426526 0.000000e+00 791.0
16 TraesCS6A01G013500 chr6D 77.428 1174 196 37 506 1640 6441814 6442957 1.640000e-178 636.0
17 TraesCS6A01G013500 chr6D 80.924 498 69 12 508 990 6351618 6352104 1.840000e-98 370.0
18 TraesCS6A01G013500 chr6D 86.341 205 11 5 1 194 7031791 7031989 1.530000e-49 207.0
19 TraesCS6A01G013500 chr6B 82.200 1118 189 10 2059 3171 11599607 11600719 0.000000e+00 953.0
20 TraesCS6A01G013500 chr6B 78.543 741 114 22 508 1216 11592851 11593578 2.970000e-121 446.0
21 TraesCS6A01G013500 chr6B 80.227 440 56 12 508 928 11792353 11792780 6.810000e-78 302.0
22 TraesCS6A01G013500 chr7D 78.222 225 46 1 630 854 1091466 1091245 1.570000e-29 141.0
23 TraesCS6A01G013500 chr7D 88.060 67 6 2 3858 3924 400942912 400942976 1.250000e-10 78.7
24 TraesCS6A01G013500 chrUn 79.054 148 28 1 707 854 51405312 51405456 9.590000e-17 99.0
25 TraesCS6A01G013500 chr7A 89.706 68 5 2 3860 3925 481567685 481567618 7.470000e-13 86.1
26 TraesCS6A01G013500 chr2B 77.019 161 29 7 3860 4016 543479875 543479719 7.470000e-13 86.1
27 TraesCS6A01G013500 chr2A 86.250 80 9 2 3859 3938 661958218 661958295 7.470000e-13 86.1
28 TraesCS6A01G013500 chr7B 85.714 77 11 0 3864 3940 402798836 402798760 9.660000e-12 82.4
29 TraesCS6A01G013500 chr7B 100.000 28 0 0 79 106 382612439 382612466 8.000000e-03 52.8
30 TraesCS6A01G013500 chr7B 96.875 32 0 1 3676 3707 525832618 525832588 8.000000e-03 52.8
31 TraesCS6A01G013500 chr4D 85.185 81 8 4 3861 3939 71806048 71805970 3.480000e-11 80.5
32 TraesCS6A01G013500 chr4D 83.544 79 13 0 3860 3938 37089111 37089033 1.620000e-09 75.0
33 TraesCS6A01G013500 chr5A 85.333 75 11 0 3861 3935 292865032 292865106 1.250000e-10 78.7


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 TraesCS6A01G013500 chr6A 6698199 6702391 4192 False 7744.000000 7744 100.000000 1 4193 1 chr6A.!!$F1 4192
1 TraesCS6A01G013500 chr6A 5939552 5942434 2882 False 985.000000 1218 79.203000 506 3171 2 chr6A.!!$F4 2665
2 TraesCS6A01G013500 chr6A 5916502 5919469 2967 False 715.000000 1160 78.716500 506 3171 2 chr6A.!!$F3 2665
3 TraesCS6A01G013500 chr6A 5900723 5903509 2786 False 658.666667 1214 79.940667 508 3191 3 chr6A.!!$F2 2683
4 TraesCS6A01G013500 chr6D 7031791 7035765 3974 False 3147.000000 6087 91.044000 1 3999 2 chr6D.!!$F7 3998
5 TraesCS6A01G013500 chr6D 6371597 6373149 1552 False 1247.000000 1247 81.206000 1623 3178 1 chr6D.!!$F1 1555
6 TraesCS6A01G013500 chr6D 6496290 6499269 2979 False 997.000000 1166 80.256000 508 3171 2 chr6D.!!$F6 2663
7 TraesCS6A01G013500 chr6D 6425185 6428067 2882 False 985.000000 1179 79.226500 506 3171 2 chr6D.!!$F5 2665
8 TraesCS6A01G013500 chr6D 6465715 6466727 1012 False 852.000000 852 81.890000 2159 3171 1 chr6D.!!$F3 1012
9 TraesCS6A01G013500 chr6D 6351618 6354750 3132 False 790.000000 1210 80.851500 508 3180 2 chr6D.!!$F4 2672
10 TraesCS6A01G013500 chr6D 6441814 6442957 1143 False 636.000000 636 77.428000 506 1640 1 chr6D.!!$F2 1134
11 TraesCS6A01G013500 chr6B 11599607 11600719 1112 False 953.000000 953 82.200000 2059 3171 1 chr6B.!!$F2 1112
12 TraesCS6A01G013500 chr6B 11592851 11593578 727 False 446.000000 446 78.543000 508 1216 1 chr6B.!!$F1 708

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
194 206 0.034059 CGGCCTCCACAGATACATCC 59.966 60.000 0.00 0.00 0.00 3.51 F
583 598 0.107703 CGGCAACCTGGATCAGCTTA 60.108 55.000 0.00 0.00 0.00 3.09 F
870 904 0.253894 CTCTGTGTGGGCATGATGGA 59.746 55.000 0.00 0.00 0.00 3.41 F
1557 1723 1.205417 AGCAGCAACAATATGGTTGGC 59.795 47.619 21.87 17.41 46.36 4.52 F
2987 3801 1.003118 TGTGAATCAACCGAGAAGGGG 59.997 52.381 0.00 0.00 46.96 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1297 1445 0.109342 GGACCATGCAGGGAGGTATG 59.891 60.000 26.87 0.0 43.89 2.39 R
1557 1723 1.404986 CCCATTCTGTTTGGCAGCATG 60.405 52.381 0.00 0.0 44.69 4.06 R
2156 2970 2.168496 GGAGGAAAACCAAGTTAGGCC 58.832 52.381 0.00 0.0 0.00 5.19 R
3160 3974 1.252904 GCCTTGCCATTTCTCCTGCA 61.253 55.000 0.00 0.0 0.00 4.41 R
4030 4860 0.027063 AAAGCGTGTTTTCCGTCGTG 59.973 50.000 0.00 0.0 0.00 4.35 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
45 46 7.821652 TCGTAAATGATCACAATTTTTAGGCA 58.178 30.769 0.00 0.00 0.00 4.75
48 49 9.294030 GTAAATGATCACAATTTTTAGGCAGAG 57.706 33.333 0.00 0.00 0.00 3.35
49 50 7.707624 AATGATCACAATTTTTAGGCAGAGA 57.292 32.000 0.00 0.00 0.00 3.10
51 52 7.707624 TGATCACAATTTTTAGGCAGAGATT 57.292 32.000 0.00 0.00 0.00 2.40
53 54 6.182039 TCACAATTTTTAGGCAGAGATTCG 57.818 37.500 0.00 0.00 0.00 3.34
54 55 5.705441 TCACAATTTTTAGGCAGAGATTCGT 59.295 36.000 0.00 0.00 0.00 3.85
55 56 6.876789 TCACAATTTTTAGGCAGAGATTCGTA 59.123 34.615 0.00 0.00 0.00 3.43
56 57 7.389330 TCACAATTTTTAGGCAGAGATTCGTAA 59.611 33.333 0.00 0.00 0.00 3.18
57 58 8.020819 CACAATTTTTAGGCAGAGATTCGTAAA 58.979 33.333 0.00 0.00 0.00 2.01
58 59 8.739972 ACAATTTTTAGGCAGAGATTCGTAAAT 58.260 29.630 0.00 0.00 0.00 1.40
88 89 9.554395 TTCTCATCTACACTGTTTGATTTTACA 57.446 29.630 0.00 0.00 0.00 2.41
110 111 5.877012 ACACAGAGATTCGTGCAAATCTTAT 59.123 36.000 13.54 5.01 44.16 1.73
190 202 1.755380 ACTAACGGCCTCCACAGATAC 59.245 52.381 0.00 0.00 0.00 2.24
191 203 1.754803 CTAACGGCCTCCACAGATACA 59.245 52.381 0.00 0.00 0.00 2.29
192 204 1.204146 AACGGCCTCCACAGATACAT 58.796 50.000 0.00 0.00 0.00 2.29
193 205 0.753262 ACGGCCTCCACAGATACATC 59.247 55.000 0.00 0.00 0.00 3.06
194 206 0.034059 CGGCCTCCACAGATACATCC 59.966 60.000 0.00 0.00 0.00 3.51
195 207 1.131638 GGCCTCCACAGATACATCCA 58.868 55.000 0.00 0.00 0.00 3.41
196 208 1.701847 GGCCTCCACAGATACATCCAT 59.298 52.381 0.00 0.00 0.00 3.41
197 209 2.289945 GGCCTCCACAGATACATCCATC 60.290 54.545 0.00 0.00 0.00 3.51
198 210 2.636893 GCCTCCACAGATACATCCATCT 59.363 50.000 0.00 0.00 35.60 2.90
199 211 3.306641 GCCTCCACAGATACATCCATCTC 60.307 52.174 0.00 0.00 32.83 2.75
200 212 4.158786 CCTCCACAGATACATCCATCTCT 58.841 47.826 0.00 0.00 32.83 3.10
201 213 4.220382 CCTCCACAGATACATCCATCTCTC 59.780 50.000 0.00 0.00 32.83 3.20
202 214 4.808042 TCCACAGATACATCCATCTCTCA 58.192 43.478 0.00 0.00 32.83 3.27
203 215 5.400870 TCCACAGATACATCCATCTCTCAT 58.599 41.667 0.00 0.00 32.83 2.90
204 216 5.479724 TCCACAGATACATCCATCTCTCATC 59.520 44.000 0.00 0.00 32.83 2.92
205 217 5.481122 CCACAGATACATCCATCTCTCATCT 59.519 44.000 0.00 0.00 32.83 2.90
206 218 6.014413 CCACAGATACATCCATCTCTCATCTT 60.014 42.308 0.00 0.00 32.83 2.40
207 219 7.443477 CACAGATACATCCATCTCTCATCTTT 58.557 38.462 0.00 0.00 32.83 2.52
208 220 7.932491 CACAGATACATCCATCTCTCATCTTTT 59.068 37.037 0.00 0.00 32.83 2.27
209 221 8.492782 ACAGATACATCCATCTCTCATCTTTTT 58.507 33.333 0.00 0.00 32.83 1.94
280 292 0.469917 CTTGACCGGCCCATATGACT 59.530 55.000 0.00 0.00 0.00 3.41
317 329 2.322081 GCCGGCACACACACGTTAT 61.322 57.895 24.80 0.00 0.00 1.89
318 330 1.015085 GCCGGCACACACACGTTATA 61.015 55.000 24.80 0.00 0.00 0.98
330 342 2.093181 ACACGTTATAGCTGCCATGGAA 60.093 45.455 18.40 3.09 0.00 3.53
454 466 6.182634 CCGTTCGTAGCACAAACTAATAATG 58.817 40.000 0.00 0.00 0.00 1.90
485 497 3.306989 CCAGTCTTTGTAGCATCTCACCA 60.307 47.826 0.00 0.00 0.00 4.17
583 598 0.107703 CGGCAACCTGGATCAGCTTA 60.108 55.000 0.00 0.00 0.00 3.09
870 904 0.253894 CTCTGTGTGGGCATGATGGA 59.746 55.000 0.00 0.00 0.00 3.41
991 1025 4.736126 TCAAAGCTGGAATATCTCGACA 57.264 40.909 0.00 0.00 0.00 4.35
1070 1218 8.723942 AGGTTGATGTATCTTGACATTAGTTC 57.276 34.615 0.00 0.00 40.18 3.01
1106 1254 1.978454 ATAGCTGATTGGCCTCTTGC 58.022 50.000 3.32 3.48 40.16 4.01
1131 1279 6.514870 CGGTGAACATGATTCCTTCTTTGAAA 60.515 38.462 0.00 0.00 0.00 2.69
1374 1522 4.671766 CGCCAGCTAAACTTTTATCACCAC 60.672 45.833 0.00 0.00 0.00 4.16
1389 1555 2.507886 TCACCACTCTTTTGGAACTGGA 59.492 45.455 0.00 0.00 39.24 3.86
1557 1723 1.205417 AGCAGCAACAATATGGTTGGC 59.795 47.619 21.87 17.41 46.36 4.52
1974 2788 6.260936 AGAACTTAAGGCACATGGATTTATCG 59.739 38.462 7.53 0.00 0.00 2.92
2156 2970 6.294880 AGAACTTCCTCAGTGTTCTCACGG 62.295 50.000 0.00 0.00 44.65 4.94
2356 3170 7.580688 ACAACTTGTTGTATGGAGATATTCCGA 60.581 37.037 16.35 0.00 40.16 4.55
2400 3214 6.006449 ACACCTTCATCAATTGAGTTTAGCT 58.994 36.000 14.54 0.00 35.27 3.32
2799 3613 3.374988 CGGCAAGCTTATCTGAATTGACA 59.625 43.478 0.00 0.00 0.00 3.58
2820 3634 7.001674 TGACATTTTTAAGCTCCTTGGACTTA 58.998 34.615 0.00 7.26 0.00 2.24
2987 3801 1.003118 TGTGAATCAACCGAGAAGGGG 59.997 52.381 0.00 0.00 46.96 4.79
2989 3803 1.078426 AATCAACCGAGAAGGGGCG 60.078 57.895 0.00 0.00 46.96 6.13
3016 3830 7.327032 GTGTTTATGAGGCAAAGATGTTCTTTC 59.673 37.037 0.00 0.00 42.60 2.62
3160 3974 4.337145 TGTGTTTGTGGTTCTTACTTGGT 58.663 39.130 0.00 0.00 0.00 3.67
3167 3981 2.224523 TGGTTCTTACTTGGTGCAGGAG 60.225 50.000 0.00 0.00 0.00 3.69
3199 4013 3.682858 GGCAAGTACAAGTTGAGCGATAA 59.317 43.478 10.54 0.00 30.18 1.75
3225 4039 4.256110 TGACAATTAGATGGTGCTGTCAG 58.744 43.478 0.00 0.00 38.52 3.51
3231 4045 2.682594 AGATGGTGCTGTCAGCCTATA 58.317 47.619 21.99 6.51 41.51 1.31
3239 4053 5.336055 GGTGCTGTCAGCCTATAGTACATAG 60.336 48.000 21.99 0.84 41.51 2.23
3250 4064 4.761591 ATAGTACATAGTGGGCCCTAGT 57.238 45.455 25.70 15.91 0.00 2.57
3267 4081 8.573885 GGGCCCTAGTAATAAATGAATGTAAAC 58.426 37.037 17.04 0.00 0.00 2.01
3608 4426 6.715347 AATTCATATGCCAACTACCTTTCC 57.285 37.500 0.00 0.00 0.00 3.13
3622 4440 4.236527 ACCTTTCCAACTCTTCAACACT 57.763 40.909 0.00 0.00 0.00 3.55
3637 4455 7.445121 TCTTCAACACTTCAACAGATATGAGT 58.555 34.615 0.00 0.00 0.00 3.41
3669 4487 8.994170 ACAAAGAGATTAAAGTGCTTCTACTTC 58.006 33.333 0.00 0.00 39.86 3.01
3681 4501 5.740099 GTGCTTCTACTTCGTCATCTCTAAC 59.260 44.000 0.00 0.00 0.00 2.34
3695 4515 9.605955 CGTCATCTCTAACAGATATAAGTGAAG 57.394 37.037 0.00 0.00 40.20 3.02
3727 4551 9.844257 AGAGTAATATAAAGCTTGCAATTCTCT 57.156 29.630 0.00 10.50 0.00 3.10
3749 4573 3.462954 TCCCATGCAATTCTCTCCCAATA 59.537 43.478 0.00 0.00 0.00 1.90
3757 4581 6.891361 TGCAATTCTCTCCCAATATCAAAAGA 59.109 34.615 0.00 0.00 0.00 2.52
3759 4583 8.419442 GCAATTCTCTCCCAATATCAAAAGATT 58.581 33.333 0.00 0.00 0.00 2.40
3814 4639 5.516984 AGAAGGAAATGATGCTCCAAGAAT 58.483 37.500 0.00 0.00 33.83 2.40
3827 4652 8.978874 ATGCTCCAAGAATTACACATATTACA 57.021 30.769 0.00 0.00 0.00 2.41
3829 4654 7.011016 TGCTCCAAGAATTACACATATTACACG 59.989 37.037 0.00 0.00 0.00 4.49
3966 4796 2.382770 ACAGTGTTGTGGCCTCCCA 61.383 57.895 3.32 0.00 39.32 4.37
3977 4807 2.683465 GCCTCCCATGGGCTCTTCA 61.683 63.158 27.41 6.67 45.57 3.02
3979 4809 1.565390 CCTCCCATGGGCTCTTCACA 61.565 60.000 27.41 5.01 34.68 3.58
3982 4812 1.746615 CCATGGGCTCTTCACACCG 60.747 63.158 2.85 0.00 0.00 4.94
3995 4825 2.885644 CACCGTTCGATCTGCCCG 60.886 66.667 0.00 0.00 0.00 6.13
3999 4829 2.582498 GTTCGATCTGCCCGGACG 60.582 66.667 0.73 0.00 0.00 4.79
4000 4830 3.833645 TTCGATCTGCCCGGACGG 61.834 66.667 0.73 3.25 0.00 4.79
4022 4852 3.314331 CACCCAGGCGTGTCTCCT 61.314 66.667 5.57 0.00 0.00 3.69
4023 4853 2.997897 ACCCAGGCGTGTCTCCTC 60.998 66.667 5.57 0.00 0.00 3.71
4024 4854 4.135153 CCCAGGCGTGTCTCCTCG 62.135 72.222 5.57 0.00 0.00 4.63
4025 4855 4.135153 CCAGGCGTGTCTCCTCGG 62.135 72.222 5.57 0.00 0.00 4.63
4026 4856 4.135153 CAGGCGTGTCTCCTCGGG 62.135 72.222 0.00 0.00 0.00 5.14
4027 4857 4.361971 AGGCGTGTCTCCTCGGGA 62.362 66.667 0.00 0.00 0.00 5.14
4028 4858 3.148279 GGCGTGTCTCCTCGGGAT 61.148 66.667 0.00 0.00 0.00 3.85
4029 4859 2.722201 GGCGTGTCTCCTCGGGATT 61.722 63.158 0.00 0.00 0.00 3.01
4030 4860 1.227002 GCGTGTCTCCTCGGGATTC 60.227 63.158 0.00 0.00 0.00 2.52
4031 4861 1.945354 GCGTGTCTCCTCGGGATTCA 61.945 60.000 0.00 0.00 0.00 2.57
4032 4862 0.179134 CGTGTCTCCTCGGGATTCAC 60.179 60.000 12.77 12.77 34.46 3.18
4033 4863 0.179134 GTGTCTCCTCGGGATTCACG 60.179 60.000 0.76 0.76 30.59 4.35
4034 4864 0.323087 TGTCTCCTCGGGATTCACGA 60.323 55.000 11.09 11.09 38.79 4.35
4035 4865 0.100861 GTCTCCTCGGGATTCACGAC 59.899 60.000 6.98 0.00 36.25 4.34
4036 4866 1.064296 CTCCTCGGGATTCACGACG 59.936 63.158 6.98 3.84 36.25 5.12
4037 4867 2.104331 CCTCGGGATTCACGACGG 59.896 66.667 6.98 9.39 36.25 4.79
4038 4868 2.412323 CCTCGGGATTCACGACGGA 61.412 63.158 16.91 0.00 36.25 4.69
4039 4869 1.509463 CTCGGGATTCACGACGGAA 59.491 57.895 6.98 0.25 36.25 4.30
4040 4870 0.108992 CTCGGGATTCACGACGGAAA 60.109 55.000 6.98 0.00 36.25 3.13
4041 4871 0.317799 TCGGGATTCACGACGGAAAA 59.682 50.000 6.98 0.00 35.12 2.29
4042 4872 0.441145 CGGGATTCACGACGGAAAAC 59.559 55.000 0.96 0.11 0.00 2.43
4043 4873 1.515081 GGGATTCACGACGGAAAACA 58.485 50.000 0.00 0.00 0.00 2.83
4044 4874 1.196127 GGGATTCACGACGGAAAACAC 59.804 52.381 0.00 0.00 0.00 3.32
4045 4875 1.136446 GGATTCACGACGGAAAACACG 60.136 52.381 0.00 0.00 37.36 4.49
4046 4876 0.233848 ATTCACGACGGAAAACACGC 59.766 50.000 0.00 0.00 34.00 5.34
4047 4877 0.806884 TTCACGACGGAAAACACGCT 60.807 50.000 0.00 0.00 34.00 5.07
4048 4878 0.806884 TCACGACGGAAAACACGCTT 60.807 50.000 0.00 0.00 34.00 4.68
4049 4879 0.027063 CACGACGGAAAACACGCTTT 59.973 50.000 0.00 0.00 34.00 3.51
4050 4880 0.728542 ACGACGGAAAACACGCTTTT 59.271 45.000 0.00 0.00 34.00 2.27
4051 4881 1.932511 ACGACGGAAAACACGCTTTTA 59.067 42.857 0.00 0.00 34.00 1.52
4052 4882 2.351111 ACGACGGAAAACACGCTTTTAA 59.649 40.909 0.00 0.00 34.00 1.52
4053 4883 2.710460 CGACGGAAAACACGCTTTTAAC 59.290 45.455 0.00 0.00 34.00 2.01
4054 4884 3.682921 GACGGAAAACACGCTTTTAACA 58.317 40.909 0.00 0.00 34.00 2.41
4055 4885 3.687200 ACGGAAAACACGCTTTTAACAG 58.313 40.909 0.00 0.00 34.00 3.16
4056 4886 2.466205 CGGAAAACACGCTTTTAACAGC 59.534 45.455 3.41 3.41 36.33 4.40
4057 4887 2.792674 GGAAAACACGCTTTTAACAGCC 59.207 45.455 8.00 0.00 36.31 4.85
4058 4888 2.502213 AAACACGCTTTTAACAGCCC 57.498 45.000 8.00 0.00 36.31 5.19
4059 4889 1.394618 AACACGCTTTTAACAGCCCA 58.605 45.000 8.00 0.00 36.31 5.36
4060 4890 1.616159 ACACGCTTTTAACAGCCCAT 58.384 45.000 8.00 0.00 36.31 4.00
4061 4891 2.785562 ACACGCTTTTAACAGCCCATA 58.214 42.857 8.00 0.00 36.31 2.74
4062 4892 2.747446 ACACGCTTTTAACAGCCCATAG 59.253 45.455 8.00 0.00 36.31 2.23
4063 4893 1.743394 ACGCTTTTAACAGCCCATAGC 59.257 47.619 8.00 0.00 44.25 2.97
4078 4908 6.597832 GCCCATAGCTCTAATTCTCTAGAA 57.402 41.667 0.00 0.00 38.99 2.10
4079 4909 6.998802 GCCCATAGCTCTAATTCTCTAGAAA 58.001 40.000 0.00 0.00 36.63 2.52
4080 4910 7.096551 GCCCATAGCTCTAATTCTCTAGAAAG 58.903 42.308 0.00 0.00 36.63 2.62
4081 4911 7.096551 CCCATAGCTCTAATTCTCTAGAAAGC 58.903 42.308 0.00 6.16 37.61 3.51
4082 4912 7.039082 CCCATAGCTCTAATTCTCTAGAAAGCT 60.039 40.741 16.65 16.65 37.61 3.74
4083 4913 7.814107 CCATAGCTCTAATTCTCTAGAAAGCTG 59.186 40.741 19.69 9.85 37.61 4.24
4084 4914 6.790232 AGCTCTAATTCTCTAGAAAGCTGT 57.210 37.500 13.29 0.00 37.61 4.40
4085 4915 6.805713 AGCTCTAATTCTCTAGAAAGCTGTC 58.194 40.000 13.29 0.00 37.61 3.51
4086 4916 5.983118 GCTCTAATTCTCTAGAAAGCTGTCC 59.017 44.000 0.00 0.00 37.61 4.02
4087 4917 6.137794 TCTAATTCTCTAGAAAGCTGTCCG 57.862 41.667 0.00 0.00 37.61 4.79
4088 4918 4.810191 AATTCTCTAGAAAGCTGTCCGT 57.190 40.909 0.00 0.00 37.61 4.69
4089 4919 3.577649 TTCTCTAGAAAGCTGTCCGTG 57.422 47.619 0.00 0.00 0.00 4.94
4090 4920 2.791655 TCTCTAGAAAGCTGTCCGTGA 58.208 47.619 0.00 0.00 0.00 4.35
4091 4921 2.750166 TCTCTAGAAAGCTGTCCGTGAG 59.250 50.000 0.00 6.21 0.00 3.51
4092 4922 2.490115 CTCTAGAAAGCTGTCCGTGAGT 59.510 50.000 0.00 0.00 0.00 3.41
4093 4923 2.229062 TCTAGAAAGCTGTCCGTGAGTG 59.771 50.000 0.00 0.00 0.00 3.51
4094 4924 0.753262 AGAAAGCTGTCCGTGAGTGT 59.247 50.000 0.00 0.00 0.00 3.55
4095 4925 1.961394 AGAAAGCTGTCCGTGAGTGTA 59.039 47.619 0.00 0.00 0.00 2.90
4096 4926 2.029828 AGAAAGCTGTCCGTGAGTGTAG 60.030 50.000 0.00 0.00 0.00 2.74
4097 4927 0.038159 AAGCTGTCCGTGAGTGTAGC 60.038 55.000 0.00 0.00 0.00 3.58
4098 4928 1.179174 AGCTGTCCGTGAGTGTAGCA 61.179 55.000 0.00 0.00 33.81 3.49
4099 4929 0.108615 GCTGTCCGTGAGTGTAGCAT 60.109 55.000 0.00 0.00 0.00 3.79
4100 4930 1.673033 GCTGTCCGTGAGTGTAGCATT 60.673 52.381 0.00 0.00 0.00 3.56
4101 4931 1.995484 CTGTCCGTGAGTGTAGCATTG 59.005 52.381 0.00 0.00 0.00 2.82
4102 4932 1.343142 TGTCCGTGAGTGTAGCATTGT 59.657 47.619 0.00 0.00 0.00 2.71
4103 4933 2.224185 TGTCCGTGAGTGTAGCATTGTT 60.224 45.455 0.00 0.00 0.00 2.83
4104 4934 2.157668 GTCCGTGAGTGTAGCATTGTTG 59.842 50.000 0.00 0.00 0.00 3.33
4105 4935 2.143122 CCGTGAGTGTAGCATTGTTGT 58.857 47.619 0.00 0.00 0.00 3.32
4106 4936 2.548057 CCGTGAGTGTAGCATTGTTGTT 59.452 45.455 0.00 0.00 0.00 2.83
4107 4937 3.003275 CCGTGAGTGTAGCATTGTTGTTT 59.997 43.478 0.00 0.00 0.00 2.83
4108 4938 4.497340 CCGTGAGTGTAGCATTGTTGTTTT 60.497 41.667 0.00 0.00 0.00 2.43
4109 4939 4.670621 CGTGAGTGTAGCATTGTTGTTTTC 59.329 41.667 0.00 0.00 0.00 2.29
4110 4940 4.670621 GTGAGTGTAGCATTGTTGTTTTCG 59.329 41.667 0.00 0.00 0.00 3.46
4111 4941 3.628017 AGTGTAGCATTGTTGTTTTCGC 58.372 40.909 0.00 0.00 0.00 4.70
4112 4942 3.315191 AGTGTAGCATTGTTGTTTTCGCT 59.685 39.130 0.00 0.00 0.00 4.93
4113 4943 4.041723 GTGTAGCATTGTTGTTTTCGCTT 58.958 39.130 0.00 0.00 0.00 4.68
4114 4944 4.502645 GTGTAGCATTGTTGTTTTCGCTTT 59.497 37.500 0.00 0.00 0.00 3.51
4115 4945 5.005299 GTGTAGCATTGTTGTTTTCGCTTTT 59.995 36.000 0.00 0.00 0.00 2.27
4116 4946 4.777140 AGCATTGTTGTTTTCGCTTTTC 57.223 36.364 0.00 0.00 0.00 2.29
4117 4947 3.555547 AGCATTGTTGTTTTCGCTTTTCC 59.444 39.130 0.00 0.00 0.00 3.13
4118 4948 3.303066 GCATTGTTGTTTTCGCTTTTCCC 60.303 43.478 0.00 0.00 0.00 3.97
4119 4949 2.196295 TGTTGTTTTCGCTTTTCCCG 57.804 45.000 0.00 0.00 0.00 5.14
4120 4950 1.202313 TGTTGTTTTCGCTTTTCCCGG 60.202 47.619 0.00 0.00 0.00 5.73
4121 4951 1.104630 TTGTTTTCGCTTTTCCCGGT 58.895 45.000 0.00 0.00 0.00 5.28
4122 4952 0.664224 TGTTTTCGCTTTTCCCGGTC 59.336 50.000 0.00 0.00 0.00 4.79
4123 4953 0.949397 GTTTTCGCTTTTCCCGGTCT 59.051 50.000 0.00 0.00 0.00 3.85
4124 4954 0.948678 TTTTCGCTTTTCCCGGTCTG 59.051 50.000 0.00 0.00 0.00 3.51
4125 4955 0.887387 TTTCGCTTTTCCCGGTCTGG 60.887 55.000 0.00 0.00 37.55 3.86
4126 4956 2.032071 CGCTTTTCCCGGTCTGGT 59.968 61.111 0.00 0.00 35.15 4.00
4127 4957 2.325082 CGCTTTTCCCGGTCTGGTG 61.325 63.158 0.00 0.00 35.15 4.17
4128 4958 2.626780 GCTTTTCCCGGTCTGGTGC 61.627 63.158 0.00 0.00 35.15 5.01
4129 4959 1.228124 CTTTTCCCGGTCTGGTGCA 60.228 57.895 0.00 0.00 35.15 4.57
4130 4960 0.609131 CTTTTCCCGGTCTGGTGCAT 60.609 55.000 0.00 0.00 35.15 3.96
4131 4961 0.893270 TTTTCCCGGTCTGGTGCATG 60.893 55.000 0.00 0.00 35.15 4.06
4132 4962 2.762969 TTTCCCGGTCTGGTGCATGG 62.763 60.000 0.00 0.00 35.15 3.66
4133 4963 4.033776 CCCGGTCTGGTGCATGGT 62.034 66.667 0.00 0.00 35.15 3.55
4134 4964 2.747460 CCGGTCTGGTGCATGGTG 60.747 66.667 0.00 0.00 0.00 4.17
4135 4965 2.032528 CGGTCTGGTGCATGGTGT 59.967 61.111 0.00 0.00 0.00 4.16
4136 4966 2.327343 CGGTCTGGTGCATGGTGTG 61.327 63.158 0.00 0.00 0.00 3.82
4137 4967 1.228245 GGTCTGGTGCATGGTGTGT 60.228 57.895 0.00 0.00 0.00 3.72
4138 4968 1.518056 GGTCTGGTGCATGGTGTGTG 61.518 60.000 0.00 0.00 0.00 3.82
4139 4969 1.898094 TCTGGTGCATGGTGTGTGC 60.898 57.895 0.00 0.00 42.81 4.57
4140 4970 2.911509 TGGTGCATGGTGTGTGCC 60.912 61.111 0.00 0.00 41.83 5.01
4141 4971 2.598394 GGTGCATGGTGTGTGCCT 60.598 61.111 0.00 0.00 41.83 4.75
4142 4972 2.646719 GTGCATGGTGTGTGCCTG 59.353 61.111 0.00 0.00 41.83 4.85
4143 4973 2.598099 TGCATGGTGTGTGCCTGG 60.598 61.111 0.00 0.00 41.83 4.45
4144 4974 4.060038 GCATGGTGTGTGCCTGGC 62.060 66.667 12.87 12.87 36.61 4.85
4145 4975 2.282674 CATGGTGTGTGCCTGGCT 60.283 61.111 21.03 0.00 0.00 4.75
4146 4976 1.904865 CATGGTGTGTGCCTGGCTT 60.905 57.895 21.03 0.00 0.00 4.35
4147 4977 1.904865 ATGGTGTGTGCCTGGCTTG 60.905 57.895 21.03 0.00 0.00 4.01
4148 4978 3.297620 GGTGTGTGCCTGGCTTGG 61.298 66.667 21.03 0.00 0.00 3.61
4156 4986 3.458163 CCTGGCTTGGCTGGCATG 61.458 66.667 4.22 8.83 41.63 4.06
4157 4987 3.458163 CTGGCTTGGCTGGCATGG 61.458 66.667 16.87 9.20 41.63 3.66
4159 4989 4.764771 GGCTTGGCTGGCATGGGA 62.765 66.667 16.87 0.00 0.00 4.37
4160 4990 2.443390 GCTTGGCTGGCATGGGAT 60.443 61.111 16.87 0.00 0.00 3.85
4161 4991 2.792947 GCTTGGCTGGCATGGGATG 61.793 63.158 16.87 0.00 0.00 3.51
4162 4992 2.042741 TTGGCTGGCATGGGATGG 60.043 61.111 4.22 0.00 0.00 3.51
4163 4993 2.577020 CTTGGCTGGCATGGGATGGA 62.577 60.000 4.22 0.00 0.00 3.41
4164 4994 2.165643 TTGGCTGGCATGGGATGGAA 62.166 55.000 4.22 0.00 0.00 3.53
4165 4995 2.129785 GGCTGGCATGGGATGGAAC 61.130 63.158 0.00 0.00 0.00 3.62
4179 5009 2.529780 TGGAACATGTAACGTCGGTT 57.470 45.000 0.00 0.00 40.20 4.44
4180 5010 2.136728 TGGAACATGTAACGTCGGTTG 58.863 47.619 0.00 0.00 36.90 3.77
4181 5011 1.461897 GGAACATGTAACGTCGGTTGG 59.538 52.381 0.00 0.00 36.90 3.77
4182 5012 2.137523 GAACATGTAACGTCGGTTGGT 58.862 47.619 0.00 0.00 36.90 3.67
4183 5013 3.316283 GAACATGTAACGTCGGTTGGTA 58.684 45.455 0.00 0.00 36.90 3.25
4184 5014 3.598019 ACATGTAACGTCGGTTGGTAT 57.402 42.857 0.00 0.00 36.90 2.73
4185 5015 3.255725 ACATGTAACGTCGGTTGGTATG 58.744 45.455 0.00 0.00 36.90 2.39
4186 5016 2.367030 TGTAACGTCGGTTGGTATGG 57.633 50.000 0.00 0.00 36.90 2.74
4187 5017 1.067000 TGTAACGTCGGTTGGTATGGG 60.067 52.381 0.00 0.00 36.90 4.00
4188 5018 0.108233 TAACGTCGGTTGGTATGGGC 60.108 55.000 0.00 0.00 36.90 5.36
4189 5019 1.833787 AACGTCGGTTGGTATGGGCT 61.834 55.000 0.00 0.00 34.37 5.19
4190 5020 1.520787 CGTCGGTTGGTATGGGCTC 60.521 63.158 0.00 0.00 0.00 4.70
4191 5021 1.520787 GTCGGTTGGTATGGGCTCG 60.521 63.158 0.00 0.00 0.00 5.03
4192 5022 1.985662 TCGGTTGGTATGGGCTCGT 60.986 57.895 0.00 0.00 0.00 4.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
23 24 9.241919 TCTCTGCCTAAAAATTGTGATCATTTA 57.758 29.630 0.00 0.00 0.00 1.40
33 34 9.573133 AATTTACGAATCTCTGCCTAAAAATTG 57.427 29.630 0.00 0.00 0.00 2.32
41 42 7.987458 TGAGAATTAATTTACGAATCTCTGCCT 59.013 33.333 1.43 0.00 0.00 4.75
42 43 8.142994 TGAGAATTAATTTACGAATCTCTGCC 57.857 34.615 1.43 0.00 0.00 4.85
75 76 7.351981 CACGAATCTCTGTGTAAAATCAAACA 58.648 34.615 0.00 0.00 0.00 2.83
76 77 6.303259 GCACGAATCTCTGTGTAAAATCAAAC 59.697 38.462 0.00 0.00 38.36 2.93
88 89 5.220739 GCATAAGATTTGCACGAATCTCTGT 60.221 40.000 12.85 2.55 43.66 3.41
110 111 4.499019 GGAACTTTTCCTTGTGAATTCGCA 60.499 41.667 17.57 17.57 46.57 5.10
211 223 5.078949 TGAGAGATGGATTTGCCTCAAAAA 58.921 37.500 0.00 0.00 36.90 1.94
212 224 4.665451 TGAGAGATGGATTTGCCTCAAAA 58.335 39.130 0.00 0.00 36.90 2.44
213 225 4.305539 TGAGAGATGGATTTGCCTCAAA 57.694 40.909 0.00 0.00 37.75 2.69
214 226 4.165565 AGATGAGAGATGGATTTGCCTCAA 59.834 41.667 0.00 0.00 37.63 3.02
215 227 3.715315 AGATGAGAGATGGATTTGCCTCA 59.285 43.478 0.00 0.00 37.63 3.86
216 228 4.354893 AGATGAGAGATGGATTTGCCTC 57.645 45.455 0.00 0.00 37.63 4.70
217 229 5.901413 TTAGATGAGAGATGGATTTGCCT 57.099 39.130 0.00 0.00 37.63 4.75
218 230 6.060788 ACTTTAGATGAGAGATGGATTTGCC 58.939 40.000 0.00 0.00 37.10 4.52
219 231 6.765036 TGACTTTAGATGAGAGATGGATTTGC 59.235 38.462 0.00 0.00 0.00 3.68
220 232 7.042858 CGTGACTTTAGATGAGAGATGGATTTG 60.043 40.741 0.00 0.00 0.00 2.32
221 233 6.983307 CGTGACTTTAGATGAGAGATGGATTT 59.017 38.462 0.00 0.00 0.00 2.17
222 234 6.462207 CCGTGACTTTAGATGAGAGATGGATT 60.462 42.308 0.00 0.00 0.00 3.01
223 235 5.010516 CCGTGACTTTAGATGAGAGATGGAT 59.989 44.000 0.00 0.00 0.00 3.41
224 236 4.339530 CCGTGACTTTAGATGAGAGATGGA 59.660 45.833 0.00 0.00 0.00 3.41
225 237 4.615949 CCGTGACTTTAGATGAGAGATGG 58.384 47.826 0.00 0.00 0.00 3.51
280 292 1.003839 ACGTACGTACCTCGACCCA 60.004 57.895 21.41 0.00 42.86 4.51
284 296 3.177600 GGCACGTACGTACCTCGA 58.822 61.111 26.98 0.00 42.86 4.04
317 329 0.739462 CGTTCGTTCCATGGCAGCTA 60.739 55.000 6.96 0.00 0.00 3.32
318 330 2.034879 CGTTCGTTCCATGGCAGCT 61.035 57.895 6.96 0.00 0.00 4.24
330 342 1.741145 GTTGGGATTTATGCCGTTCGT 59.259 47.619 0.00 0.00 41.80 3.85
475 487 1.065926 TGACAGATGGTGGTGAGATGC 60.066 52.381 0.00 0.00 0.00 3.91
485 497 1.114627 TGCTAGCGATGACAGATGGT 58.885 50.000 10.77 0.00 0.00 3.55
583 598 4.515404 GCGTAGGCGACAAGGAAT 57.485 55.556 0.00 0.00 41.33 3.01
652 667 2.095059 GTCGTTGATGCCTTGCTTGAAT 60.095 45.455 0.00 0.00 0.00 2.57
844 865 1.351076 TGCCCACACAGAGATTGAGA 58.649 50.000 0.00 0.00 0.00 3.27
870 904 2.904434 ACCCAAGAACTCTGGAATACGT 59.096 45.455 0.00 0.00 0.00 3.57
1106 1254 4.455533 TCAAAGAAGGAATCATGTTCACCG 59.544 41.667 9.31 0.00 0.00 4.94
1131 1279 1.550976 CAGTAAGAAAGGCGGAGGTCT 59.449 52.381 0.00 0.00 0.00 3.85
1297 1445 0.109342 GGACCATGCAGGGAGGTATG 59.891 60.000 26.87 0.00 43.89 2.39
1374 1522 4.734695 GCTGTGTTTCCAGTTCCAAAAGAG 60.735 45.833 0.00 0.00 34.84 2.85
1389 1555 2.378038 ACTGTCATTGTGGCTGTGTTT 58.622 42.857 0.00 0.00 32.89 2.83
1557 1723 1.404986 CCCATTCTGTTTGGCAGCATG 60.405 52.381 0.00 0.00 44.69 4.06
1974 2788 5.679601 AGAGGTCCTGAGAAAGAATTATGC 58.320 41.667 0.00 0.00 0.00 3.14
2156 2970 2.168496 GGAGGAAAACCAAGTTAGGCC 58.832 52.381 0.00 0.00 0.00 5.19
2356 3170 5.882557 GGTGTTGAAGATTGGTGATAGTCAT 59.117 40.000 0.00 0.00 0.00 3.06
2518 3332 5.649782 ACATGCCAAACTCCTCTAAATTG 57.350 39.130 0.00 0.00 0.00 2.32
2706 3520 2.620251 TCATAGCCCCAATCTTCGTG 57.380 50.000 0.00 0.00 0.00 4.35
2799 3613 8.829373 ATGATAAGTCCAAGGAGCTTAAAAAT 57.171 30.769 12.11 6.64 0.00 1.82
2987 3801 1.810151 TCTTTGCCTCATAAACACCGC 59.190 47.619 0.00 0.00 0.00 5.68
2989 3803 5.183904 AGAACATCTTTGCCTCATAAACACC 59.816 40.000 0.00 0.00 0.00 4.16
3016 3830 2.224867 ACCCAGATCCAAGTCCAAAGTG 60.225 50.000 0.00 0.00 0.00 3.16
3160 3974 1.252904 GCCTTGCCATTTCTCCTGCA 61.253 55.000 0.00 0.00 0.00 4.41
3167 3981 3.005791 ACTTGTACTTGCCTTGCCATTTC 59.994 43.478 0.00 0.00 0.00 2.17
3199 4013 5.503927 ACAGCACCATCTAATTGTCATCTT 58.496 37.500 0.00 0.00 0.00 2.40
3225 4039 2.500504 GGGCCCACTATGTACTATAGGC 59.499 54.545 19.95 9.31 38.45 3.93
3231 4045 4.547886 TTACTAGGGCCCACTATGTACT 57.452 45.455 27.56 1.16 0.00 2.73
3239 4053 6.068670 ACATTCATTTATTACTAGGGCCCAC 58.931 40.000 27.56 0.00 0.00 4.61
3350 4164 8.740906 TGTTGACTTTTGATTTAGTACAAACCA 58.259 29.630 0.00 0.00 36.06 3.67
3392 4206 5.664908 ACTCACCAAGGATACATTCTCATCT 59.335 40.000 0.00 0.00 41.41 2.90
3393 4207 5.757320 CACTCACCAAGGATACATTCTCATC 59.243 44.000 0.00 0.00 41.41 2.92
3394 4208 5.397221 CCACTCACCAAGGATACATTCTCAT 60.397 44.000 0.00 0.00 41.41 2.90
3395 4209 4.080919 CCACTCACCAAGGATACATTCTCA 60.081 45.833 0.00 0.00 41.41 3.27
3396 4210 4.162320 TCCACTCACCAAGGATACATTCTC 59.838 45.833 0.00 0.00 41.41 2.87
3397 4211 4.104086 TCCACTCACCAAGGATACATTCT 58.896 43.478 0.00 0.00 41.41 2.40
3398 4212 4.446371 CTCCACTCACCAAGGATACATTC 58.554 47.826 0.00 0.00 41.41 2.67
3399 4213 3.370953 GCTCCACTCACCAAGGATACATT 60.371 47.826 0.00 0.00 41.41 2.71
3400 4214 2.171448 GCTCCACTCACCAAGGATACAT 59.829 50.000 0.00 0.00 41.41 2.29
3401 4215 1.555075 GCTCCACTCACCAAGGATACA 59.445 52.381 0.00 0.00 41.41 2.29
3402 4216 1.555075 TGCTCCACTCACCAAGGATAC 59.445 52.381 0.00 0.00 0.00 2.24
3410 4224 1.555075 TGATAGGTTGCTCCACTCACC 59.445 52.381 1.79 0.00 39.02 4.02
3437 4251 9.504708 TTGGCAATTGATTTTAGACAATTTGAT 57.495 25.926 10.34 0.00 42.35 2.57
3583 4401 7.836685 TGGAAAGGTAGTTGGCATATGAATTAA 59.163 33.333 6.97 0.00 0.00 1.40
3608 4426 5.801350 TCTGTTGAAGTGTTGAAGAGTTG 57.199 39.130 0.00 0.00 0.00 3.16
3622 4440 8.675705 TTTGTTCTTCACTCATATCTGTTGAA 57.324 30.769 0.00 0.00 0.00 2.69
3637 4455 7.807977 AGCACTTTAATCTCTTTGTTCTTCA 57.192 32.000 0.00 0.00 0.00 3.02
3669 4487 9.605955 CTTCACTTATATCTGTTAGAGATGACG 57.394 37.037 1.87 0.00 41.86 4.35
3714 4538 1.202382 GCATGGGAGAGAATTGCAAGC 60.202 52.381 4.94 0.00 33.58 4.01
3718 4542 3.383825 AGAATTGCATGGGAGAGAATTGC 59.616 43.478 0.00 0.00 0.00 3.56
3719 4543 4.888239 AGAGAATTGCATGGGAGAGAATTG 59.112 41.667 0.00 0.00 0.00 2.32
3721 4545 4.446023 GGAGAGAATTGCATGGGAGAGAAT 60.446 45.833 0.00 0.00 0.00 2.40
3722 4546 3.118112 GGAGAGAATTGCATGGGAGAGAA 60.118 47.826 0.00 0.00 0.00 2.87
3723 4547 2.437281 GGAGAGAATTGCATGGGAGAGA 59.563 50.000 0.00 0.00 0.00 3.10
3724 4548 2.486907 GGGAGAGAATTGCATGGGAGAG 60.487 54.545 0.00 0.00 0.00 3.20
3725 4549 1.492176 GGGAGAGAATTGCATGGGAGA 59.508 52.381 0.00 0.00 0.00 3.71
3726 4550 1.213678 TGGGAGAGAATTGCATGGGAG 59.786 52.381 0.00 0.00 0.00 4.30
3727 4551 1.297968 TGGGAGAGAATTGCATGGGA 58.702 50.000 0.00 0.00 0.00 4.37
3728 4552 2.148446 TTGGGAGAGAATTGCATGGG 57.852 50.000 0.00 0.00 0.00 4.00
3783 4607 8.274322 TGGAGCATCATTTCCTTCTTCTATTTA 58.726 33.333 0.00 0.00 36.25 1.40
3787 4611 5.698741 TGGAGCATCATTTCCTTCTTCTA 57.301 39.130 0.00 0.00 36.25 2.10
3789 4613 4.946157 TCTTGGAGCATCATTTCCTTCTTC 59.054 41.667 0.00 0.00 36.25 2.87
3792 4617 5.848833 ATTCTTGGAGCATCATTTCCTTC 57.151 39.130 0.00 0.00 36.25 3.46
3795 4620 6.127647 TGTGTAATTCTTGGAGCATCATTTCC 60.128 38.462 0.00 0.00 36.25 3.13
3951 4781 1.978617 CCATGGGAGGCCACAACAC 60.979 63.158 5.01 0.00 0.00 3.32
3954 4784 4.380945 GCCCATGGGAGGCCACAA 62.381 66.667 36.00 0.00 45.16 3.33
3966 4796 0.321653 GAACGGTGTGAAGAGCCCAT 60.322 55.000 0.00 0.00 0.00 4.00
3975 4805 1.080093 GGCAGATCGAACGGTGTGA 60.080 57.895 8.70 0.00 0.00 3.58
3977 4807 2.264794 GGGCAGATCGAACGGTGT 59.735 61.111 0.00 0.00 0.00 4.16
3979 4809 4.143333 CCGGGCAGATCGAACGGT 62.143 66.667 11.36 0.00 39.70 4.83
3982 4812 2.582498 CGTCCGGGCAGATCGAAC 60.582 66.667 6.96 0.00 0.00 3.95
4005 4835 3.302347 GAGGAGACACGCCTGGGTG 62.302 68.421 12.21 12.21 43.54 4.61
4006 4836 2.997897 GAGGAGACACGCCTGGGT 60.998 66.667 0.00 0.00 32.83 4.51
4007 4837 4.135153 CGAGGAGACACGCCTGGG 62.135 72.222 0.00 0.00 37.67 4.45
4008 4838 4.135153 CCGAGGAGACACGCCTGG 62.135 72.222 0.00 0.00 43.43 4.45
4009 4839 4.135153 CCCGAGGAGACACGCCTG 62.135 72.222 0.00 0.00 43.43 4.85
4010 4840 3.663815 ATCCCGAGGAGACACGCCT 62.664 63.158 0.00 0.00 43.43 5.52
4011 4841 2.630592 GAATCCCGAGGAGACACGCC 62.631 65.000 0.00 0.00 43.43 5.68
4012 4842 1.227002 GAATCCCGAGGAGACACGC 60.227 63.158 0.00 0.00 43.43 5.34
4013 4843 0.179134 GTGAATCCCGAGGAGACACG 60.179 60.000 12.50 0.00 44.43 4.49
4014 4844 0.179134 CGTGAATCCCGAGGAGACAC 60.179 60.000 15.35 15.35 37.87 3.67
4015 4845 0.323087 TCGTGAATCCCGAGGAGACA 60.323 55.000 0.00 0.00 34.05 3.41
4016 4846 0.100861 GTCGTGAATCCCGAGGAGAC 59.899 60.000 0.00 0.00 34.05 3.36
4017 4847 1.374343 CGTCGTGAATCCCGAGGAGA 61.374 60.000 1.83 0.00 41.33 3.71
4018 4848 1.064296 CGTCGTGAATCCCGAGGAG 59.936 63.158 1.83 0.00 41.33 3.69
4019 4849 2.412323 CCGTCGTGAATCCCGAGGA 61.412 63.158 9.20 0.00 41.33 3.71
4020 4850 1.940883 TTCCGTCGTGAATCCCGAGG 61.941 60.000 1.07 1.07 39.26 4.63
4021 4851 0.108992 TTTCCGTCGTGAATCCCGAG 60.109 55.000 0.00 0.00 34.56 4.63
4022 4852 0.317799 TTTTCCGTCGTGAATCCCGA 59.682 50.000 0.00 0.00 0.00 5.14
4023 4853 0.441145 GTTTTCCGTCGTGAATCCCG 59.559 55.000 0.00 0.00 0.00 5.14
4024 4854 1.196127 GTGTTTTCCGTCGTGAATCCC 59.804 52.381 0.00 0.00 0.00 3.85
4025 4855 1.136446 CGTGTTTTCCGTCGTGAATCC 60.136 52.381 0.00 0.00 0.00 3.01
4026 4856 1.720547 GCGTGTTTTCCGTCGTGAATC 60.721 52.381 0.00 0.00 0.00 2.52
4027 4857 0.233848 GCGTGTTTTCCGTCGTGAAT 59.766 50.000 0.00 0.00 0.00 2.57
4028 4858 0.806884 AGCGTGTTTTCCGTCGTGAA 60.807 50.000 0.00 0.00 0.00 3.18
4029 4859 0.806884 AAGCGTGTTTTCCGTCGTGA 60.807 50.000 0.00 0.00 0.00 4.35
4030 4860 0.027063 AAAGCGTGTTTTCCGTCGTG 59.973 50.000 0.00 0.00 0.00 4.35
4031 4861 0.728542 AAAAGCGTGTTTTCCGTCGT 59.271 45.000 0.00 0.00 0.00 4.34
4032 4862 2.649140 TAAAAGCGTGTTTTCCGTCG 57.351 45.000 1.50 0.00 0.00 5.12
4033 4863 3.682921 TGTTAAAAGCGTGTTTTCCGTC 58.317 40.909 1.50 0.00 0.00 4.79
4034 4864 3.687200 CTGTTAAAAGCGTGTTTTCCGT 58.313 40.909 1.50 0.00 0.00 4.69
4035 4865 2.466205 GCTGTTAAAAGCGTGTTTTCCG 59.534 45.455 0.86 0.00 32.56 4.30
4036 4866 2.792674 GGCTGTTAAAAGCGTGTTTTCC 59.207 45.455 11.53 0.00 44.52 3.13
4037 4867 2.792674 GGGCTGTTAAAAGCGTGTTTTC 59.207 45.455 11.53 0.00 44.52 2.29
4038 4868 2.166664 TGGGCTGTTAAAAGCGTGTTTT 59.833 40.909 11.53 3.60 44.52 2.43
4039 4869 1.751924 TGGGCTGTTAAAAGCGTGTTT 59.248 42.857 11.53 0.00 44.52 2.83
4040 4870 1.394618 TGGGCTGTTAAAAGCGTGTT 58.605 45.000 11.53 0.00 44.52 3.32
4041 4871 1.616159 ATGGGCTGTTAAAAGCGTGT 58.384 45.000 11.53 0.00 44.52 4.49
4042 4872 2.477863 GCTATGGGCTGTTAAAAGCGTG 60.478 50.000 11.53 1.42 44.52 5.34
4043 4873 1.743394 GCTATGGGCTGTTAAAAGCGT 59.257 47.619 11.53 3.17 44.52 5.07
4044 4874 2.475200 GCTATGGGCTGTTAAAAGCG 57.525 50.000 11.53 0.00 44.52 4.68
4053 4883 7.256119 TTTCTAGAGAATTAGAGCTATGGGCTG 60.256 40.741 0.00 0.00 41.80 4.85
4054 4884 6.784969 TTTCTAGAGAATTAGAGCTATGGGCT 59.215 38.462 0.00 0.00 43.26 5.19
4055 4885 6.597832 TTCTAGAGAATTAGAGCTATGGGC 57.402 41.667 0.00 0.00 42.19 5.36
4056 4886 7.039082 AGCTTTCTAGAGAATTAGAGCTATGGG 60.039 40.741 12.41 0.00 40.61 4.00
4057 4887 7.814107 CAGCTTTCTAGAGAATTAGAGCTATGG 59.186 40.741 13.29 2.27 40.51 2.74
4058 4888 8.359642 ACAGCTTTCTAGAGAATTAGAGCTATG 58.640 37.037 13.29 7.97 40.51 2.23
4059 4889 8.477419 ACAGCTTTCTAGAGAATTAGAGCTAT 57.523 34.615 13.29 3.19 40.51 2.97
4060 4890 7.013846 GGACAGCTTTCTAGAGAATTAGAGCTA 59.986 40.741 13.29 0.00 40.51 3.32
4061 4891 6.183360 GGACAGCTTTCTAGAGAATTAGAGCT 60.183 42.308 9.43 9.43 42.14 4.09
4062 4892 5.983118 GGACAGCTTTCTAGAGAATTAGAGC 59.017 44.000 0.00 5.81 35.51 4.09
4063 4893 6.183360 ACGGACAGCTTTCTAGAGAATTAGAG 60.183 42.308 0.00 0.00 33.54 2.43
4064 4894 5.652891 ACGGACAGCTTTCTAGAGAATTAGA 59.347 40.000 0.00 0.00 33.54 2.10
4065 4895 5.746245 CACGGACAGCTTTCTAGAGAATTAG 59.254 44.000 0.00 0.00 33.54 1.73
4066 4896 5.417894 TCACGGACAGCTTTCTAGAGAATTA 59.582 40.000 0.00 0.00 33.54 1.40
4067 4897 4.220821 TCACGGACAGCTTTCTAGAGAATT 59.779 41.667 0.00 0.00 33.54 2.17
4068 4898 3.764434 TCACGGACAGCTTTCTAGAGAAT 59.236 43.478 0.00 0.00 33.54 2.40
4069 4899 3.154710 TCACGGACAGCTTTCTAGAGAA 58.845 45.455 0.00 0.00 0.00 2.87
4070 4900 2.750166 CTCACGGACAGCTTTCTAGAGA 59.250 50.000 0.00 0.00 0.00 3.10
4071 4901 2.490115 ACTCACGGACAGCTTTCTAGAG 59.510 50.000 12.15 12.15 0.00 2.43
4072 4902 2.229062 CACTCACGGACAGCTTTCTAGA 59.771 50.000 0.00 0.00 0.00 2.43
4073 4903 2.029828 ACACTCACGGACAGCTTTCTAG 60.030 50.000 0.00 0.00 0.00 2.43
4074 4904 1.961394 ACACTCACGGACAGCTTTCTA 59.039 47.619 0.00 0.00 0.00 2.10
4075 4905 0.753262 ACACTCACGGACAGCTTTCT 59.247 50.000 0.00 0.00 0.00 2.52
4076 4906 2.329379 CTACACTCACGGACAGCTTTC 58.671 52.381 0.00 0.00 0.00 2.62
4077 4907 1.605712 GCTACACTCACGGACAGCTTT 60.606 52.381 0.00 0.00 0.00 3.51
4078 4908 0.038159 GCTACACTCACGGACAGCTT 60.038 55.000 0.00 0.00 0.00 3.74
4079 4909 1.179174 TGCTACACTCACGGACAGCT 61.179 55.000 0.00 0.00 0.00 4.24
4080 4910 0.108615 ATGCTACACTCACGGACAGC 60.109 55.000 0.00 0.00 0.00 4.40
4081 4911 1.995484 CAATGCTACACTCACGGACAG 59.005 52.381 0.00 0.00 0.00 3.51
4082 4912 1.343142 ACAATGCTACACTCACGGACA 59.657 47.619 0.00 0.00 0.00 4.02
4083 4913 2.080286 ACAATGCTACACTCACGGAC 57.920 50.000 0.00 0.00 0.00 4.79
4084 4914 2.224185 ACAACAATGCTACACTCACGGA 60.224 45.455 0.00 0.00 0.00 4.69
4085 4915 2.143122 ACAACAATGCTACACTCACGG 58.857 47.619 0.00 0.00 0.00 4.94
4086 4916 3.878086 AACAACAATGCTACACTCACG 57.122 42.857 0.00 0.00 0.00 4.35
4087 4917 4.670621 CGAAAACAACAATGCTACACTCAC 59.329 41.667 0.00 0.00 0.00 3.51
4088 4918 4.788201 GCGAAAACAACAATGCTACACTCA 60.788 41.667 0.00 0.00 0.00 3.41
4089 4919 3.664025 GCGAAAACAACAATGCTACACTC 59.336 43.478 0.00 0.00 0.00 3.51
4090 4920 3.315191 AGCGAAAACAACAATGCTACACT 59.685 39.130 0.00 0.00 0.00 3.55
4091 4921 3.628017 AGCGAAAACAACAATGCTACAC 58.372 40.909 0.00 0.00 0.00 2.90
4092 4922 3.980646 AGCGAAAACAACAATGCTACA 57.019 38.095 0.00 0.00 0.00 2.74
4093 4923 5.332280 GGAAAAGCGAAAACAACAATGCTAC 60.332 40.000 0.00 0.00 31.41 3.58
4094 4924 4.742659 GGAAAAGCGAAAACAACAATGCTA 59.257 37.500 0.00 0.00 31.41 3.49
4095 4925 3.555547 GGAAAAGCGAAAACAACAATGCT 59.444 39.130 0.00 0.00 0.00 3.79
4096 4926 3.303066 GGGAAAAGCGAAAACAACAATGC 60.303 43.478 0.00 0.00 0.00 3.56
4097 4927 3.060607 CGGGAAAAGCGAAAACAACAATG 60.061 43.478 0.00 0.00 0.00 2.82
4098 4928 3.120041 CGGGAAAAGCGAAAACAACAAT 58.880 40.909 0.00 0.00 0.00 2.71
4099 4929 2.531206 CGGGAAAAGCGAAAACAACAA 58.469 42.857 0.00 0.00 0.00 2.83
4100 4930 1.202313 CCGGGAAAAGCGAAAACAACA 60.202 47.619 0.00 0.00 0.00 3.33
4101 4931 1.202325 ACCGGGAAAAGCGAAAACAAC 60.202 47.619 6.32 0.00 0.00 3.32
4102 4932 1.065851 GACCGGGAAAAGCGAAAACAA 59.934 47.619 6.32 0.00 0.00 2.83
4103 4933 0.664224 GACCGGGAAAAGCGAAAACA 59.336 50.000 6.32 0.00 0.00 2.83
4104 4934 0.949397 AGACCGGGAAAAGCGAAAAC 59.051 50.000 6.32 0.00 0.00 2.43
4105 4935 0.948678 CAGACCGGGAAAAGCGAAAA 59.051 50.000 6.32 0.00 0.00 2.29
4106 4936 0.887387 CCAGACCGGGAAAAGCGAAA 60.887 55.000 6.32 0.00 0.00 3.46
4107 4937 1.302192 CCAGACCGGGAAAAGCGAA 60.302 57.895 6.32 0.00 0.00 4.70
4108 4938 2.345991 CCAGACCGGGAAAAGCGA 59.654 61.111 6.32 0.00 0.00 4.93
4109 4939 2.032071 ACCAGACCGGGAAAAGCG 59.968 61.111 6.32 0.00 40.22 4.68
4110 4940 2.626780 GCACCAGACCGGGAAAAGC 61.627 63.158 6.32 0.00 40.22 3.51
4111 4941 0.609131 ATGCACCAGACCGGGAAAAG 60.609 55.000 6.32 0.00 40.22 2.27
4112 4942 0.893270 CATGCACCAGACCGGGAAAA 60.893 55.000 6.32 0.00 40.22 2.29
4113 4943 1.303236 CATGCACCAGACCGGGAAA 60.303 57.895 6.32 0.00 40.22 3.13
4114 4944 2.350895 CATGCACCAGACCGGGAA 59.649 61.111 6.32 0.00 40.22 3.97
4115 4945 3.716195 CCATGCACCAGACCGGGA 61.716 66.667 6.32 0.00 40.22 5.14
4116 4946 4.033776 ACCATGCACCAGACCGGG 62.034 66.667 6.32 0.00 40.22 5.73
4117 4947 2.747460 CACCATGCACCAGACCGG 60.747 66.667 0.00 0.00 42.50 5.28
4118 4948 2.032528 ACACCATGCACCAGACCG 59.967 61.111 0.00 0.00 0.00 4.79
4119 4949 1.228245 ACACACCATGCACCAGACC 60.228 57.895 0.00 0.00 0.00 3.85
4120 4950 1.951510 CACACACCATGCACCAGAC 59.048 57.895 0.00 0.00 0.00 3.51
4121 4951 1.898094 GCACACACCATGCACCAGA 60.898 57.895 0.00 0.00 42.88 3.86
4122 4952 2.646719 GCACACACCATGCACCAG 59.353 61.111 0.00 0.00 42.88 4.00
4123 4953 2.911509 GGCACACACCATGCACCA 60.912 61.111 0.00 0.00 45.27 4.17
4124 4954 2.598394 AGGCACACACCATGCACC 60.598 61.111 0.00 0.00 45.27 5.01
4125 4955 2.646719 CAGGCACACACCATGCAC 59.353 61.111 0.00 0.00 45.27 4.57
4126 4956 2.598099 CCAGGCACACACCATGCA 60.598 61.111 0.00 0.00 45.27 3.96
4127 4957 4.060038 GCCAGGCACACACCATGC 62.060 66.667 6.55 0.00 42.62 4.06
4128 4958 1.904865 AAGCCAGGCACACACCATG 60.905 57.895 15.80 0.00 0.00 3.66
4129 4959 1.904865 CAAGCCAGGCACACACCAT 60.905 57.895 15.80 0.00 0.00 3.55
4130 4960 2.519063 CAAGCCAGGCACACACCA 60.519 61.111 15.80 0.00 0.00 4.17
4131 4961 3.297620 CCAAGCCAGGCACACACC 61.298 66.667 15.80 0.00 0.00 4.16
4139 4969 3.458163 CATGCCAGCCAAGCCAGG 61.458 66.667 0.00 0.00 0.00 4.45
4140 4970 3.458163 CCATGCCAGCCAAGCCAG 61.458 66.667 0.00 0.00 0.00 4.85
4142 4972 4.764771 TCCCATGCCAGCCAAGCC 62.765 66.667 0.00 0.00 0.00 4.35
4143 4973 2.443390 ATCCCATGCCAGCCAAGC 60.443 61.111 0.00 0.00 0.00 4.01
4144 4974 2.131709 CCATCCCATGCCAGCCAAG 61.132 63.158 0.00 0.00 0.00 3.61
4145 4975 2.042741 CCATCCCATGCCAGCCAA 60.043 61.111 0.00 0.00 0.00 4.52
4146 4976 2.624454 TTCCATCCCATGCCAGCCA 61.624 57.895 0.00 0.00 0.00 4.75
4147 4977 2.129785 GTTCCATCCCATGCCAGCC 61.130 63.158 0.00 0.00 0.00 4.85
4148 4978 0.757935 ATGTTCCATCCCATGCCAGC 60.758 55.000 0.00 0.00 0.00 4.85
4149 4979 1.037493 CATGTTCCATCCCATGCCAG 58.963 55.000 0.00 0.00 32.80 4.85
4150 4980 0.335705 ACATGTTCCATCCCATGCCA 59.664 50.000 0.00 0.00 41.69 4.92
4151 4981 2.362077 GTTACATGTTCCATCCCATGCC 59.638 50.000 2.30 0.00 41.69 4.40
4152 4982 2.033299 CGTTACATGTTCCATCCCATGC 59.967 50.000 2.30 0.00 41.69 4.06
4153 4983 3.278574 ACGTTACATGTTCCATCCCATG 58.721 45.455 2.30 0.00 43.21 3.66
4154 4984 3.541632 GACGTTACATGTTCCATCCCAT 58.458 45.455 2.30 0.00 0.00 4.00
4155 4985 2.675603 CGACGTTACATGTTCCATCCCA 60.676 50.000 2.30 0.00 0.00 4.37
4156 4986 1.931172 CGACGTTACATGTTCCATCCC 59.069 52.381 2.30 0.00 0.00 3.85
4157 4987 1.931172 CCGACGTTACATGTTCCATCC 59.069 52.381 2.30 0.00 0.00 3.51
4158 4988 2.613691 ACCGACGTTACATGTTCCATC 58.386 47.619 2.30 0.00 0.00 3.51
4159 4989 2.739913 CAACCGACGTTACATGTTCCAT 59.260 45.455 2.30 0.00 0.00 3.41
4160 4990 2.136728 CAACCGACGTTACATGTTCCA 58.863 47.619 2.30 0.00 0.00 3.53
4161 4991 1.461897 CCAACCGACGTTACATGTTCC 59.538 52.381 2.30 0.00 0.00 3.62
4162 4992 2.137523 ACCAACCGACGTTACATGTTC 58.862 47.619 2.30 0.00 0.00 3.18
4163 4993 2.243602 ACCAACCGACGTTACATGTT 57.756 45.000 2.30 0.00 0.00 2.71
4164 4994 3.255725 CATACCAACCGACGTTACATGT 58.744 45.455 2.69 2.69 0.00 3.21
4165 4995 2.605818 CCATACCAACCGACGTTACATG 59.394 50.000 0.00 0.00 0.00 3.21
4166 4996 2.419021 CCCATACCAACCGACGTTACAT 60.419 50.000 0.00 0.00 0.00 2.29
4167 4997 1.067000 CCCATACCAACCGACGTTACA 60.067 52.381 0.00 0.00 0.00 2.41
4168 4998 1.643880 CCCATACCAACCGACGTTAC 58.356 55.000 0.00 0.00 0.00 2.50
4169 4999 0.108233 GCCCATACCAACCGACGTTA 60.108 55.000 0.00 0.00 0.00 3.18
4170 5000 1.376295 GCCCATACCAACCGACGTT 60.376 57.895 0.00 0.00 0.00 3.99
4171 5001 2.234913 GAGCCCATACCAACCGACGT 62.235 60.000 0.00 0.00 0.00 4.34
4172 5002 1.520787 GAGCCCATACCAACCGACG 60.521 63.158 0.00 0.00 0.00 5.12
4173 5003 1.520787 CGAGCCCATACCAACCGAC 60.521 63.158 0.00 0.00 0.00 4.79
4174 5004 1.985662 ACGAGCCCATACCAACCGA 60.986 57.895 0.00 0.00 0.00 4.69
4175 5005 2.582436 ACGAGCCCATACCAACCG 59.418 61.111 0.00 0.00 0.00 4.44


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

AutoCloner maintained by Alex Coulton.