Multiple sequence alignment - TraesCS5A01G482200

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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 TraesCS5A01G482200 chr5A 100.000 4835 0 0 1 4835 654077441 654082275 0.000000e+00 8929
1 TraesCS5A01G482200 chr5D 93.288 2667 131 27 1529 4176 526880143 526882780 0.000000e+00 3890
2 TraesCS5A01G482200 chr5D 89.948 955 77 13 237 1184 526878383 526879325 0.000000e+00 1214
3 TraesCS5A01G482200 chr5D 94.767 172 5 2 68 239 526878153 526878320 1.030000e-66 265
4 TraesCS5A01G482200 chr5D 76.471 476 59 29 4384 4835 526883464 526883910 4.900000e-50 209
5 TraesCS5A01G482200 chr5D 81.275 251 21 11 1182 1408 526879532 526879780 3.840000e-41 180
6 TraesCS5A01G482200 chr5B 95.532 2417 101 3 1527 3939 662961057 662963470 0.000000e+00 3858
7 TraesCS5A01G482200 chr5B 88.518 958 97 8 237 1184 662959559 662960513 0.000000e+00 1147
8 TraesCS5A01G482200 chr5B 93.249 237 12 2 1 233 662959261 662959497 3.580000e-91 346
9 TraesCS5A01G482200 chr5B 89.683 126 11 2 1193 1317 662960587 662960711 5.010000e-35 159
10 TraesCS5A01G482200 chr2A 81.481 432 69 9 2274 2698 194130021 194129594 1.290000e-90 344
11 TraesCS5A01G482200 chr2B 81.429 420 67 9 2279 2691 236527275 236526860 2.790000e-87 333
12 TraesCS5A01G482200 chr2D 81.030 427 70 9 2279 2698 179692156 179691734 3.610000e-86 329
13 TraesCS5A01G482200 chr7D 83.529 340 50 4 2316 2652 366451257 366451593 3.630000e-81 313
14 TraesCS5A01G482200 chr1D 80.288 416 79 3 2279 2691 99830557 99830142 1.310000e-80 311
15 TraesCS5A01G482200 chr1A 80.096 417 80 3 2278 2691 95313235 95312819 1.690000e-79 307
16 TraesCS5A01G482200 chrUn 81.074 391 61 11 2316 2698 5436050 5435665 2.830000e-77 300
17 TraesCS5A01G482200 chr4B 87.500 168 9 6 4030 4188 30727279 30727115 2.970000e-42 183


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 TraesCS5A01G482200 chr5A 654077441 654082275 4834 False 8929.0 8929 100.0000 1 4835 1 chr5A.!!$F1 4834
1 TraesCS5A01G482200 chr5D 526878153 526883910 5757 False 1151.6 3890 87.1498 68 4835 5 chr5D.!!$F1 4767
2 TraesCS5A01G482200 chr5B 662959261 662963470 4209 False 1377.5 3858 91.7455 1 3939 4 chr5B.!!$F1 3938

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
918 995 0.249120 AGCGACGATGGGTCAATGAA 59.751 50.000 0.00 0.0 46.42 2.57 F
1060 1137 1.005215 CAAGCTTGGATGGGAAGGAGT 59.995 52.381 19.14 0.0 0.00 3.85 F
1561 2220 1.008538 GGTGTTTGTTGCAGGCTCG 60.009 57.895 0.00 0.0 0.00 5.03 F
3507 4172 0.880278 TCAAGCTGACGTCCAAGCAC 60.880 55.000 24.67 4.9 0.00 4.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2807 3469 0.321653 GGTGTTCCATTGCTCCGACT 60.322 55.000 0.0 0.0 0.00 4.18 R
3384 4049 4.680237 TGCTCGTTCCGCCACCAG 62.680 66.667 0.0 0.0 0.00 4.00 R
3765 4431 0.718343 CTACGACAAGCAAGAGCAGC 59.282 55.000 0.0 0.0 45.49 5.25 R
4376 5248 0.175073 GTACAAGTCTGGGGTAGCGG 59.825 60.000 0.0 0.0 0.00 5.52 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
33 34 2.595463 GTTGCCAGCTCTGTGCCA 60.595 61.111 0.00 0.00 44.23 4.92
57 58 4.944962 TCAACAACATCCATCGACATTC 57.055 40.909 0.00 0.00 0.00 2.67
96 97 7.396339 CCCCTTAAAAACACCTTCTTAAGCTAT 59.604 37.037 0.00 0.00 32.42 2.97
172 173 9.685276 AATAACATGTTGAGACTATGATGGAAA 57.315 29.630 21.42 0.00 0.00 3.13
239 308 7.857404 AAGTAGACACAATATGTAGGGCTAT 57.143 36.000 0.00 0.00 43.56 2.97
282 351 1.279271 CTTAGGAGTCCACCACCCTTG 59.721 57.143 12.86 0.00 30.58 3.61
296 366 1.410050 CCCTTGGCTTGGCAAAAGGT 61.410 55.000 21.68 0.00 40.21 3.50
297 367 0.469494 CCTTGGCTTGGCAAAAGGTT 59.531 50.000 17.35 0.00 38.37 3.50
341 413 2.408050 CAGCAGACCCATCGCTAATAC 58.592 52.381 0.00 0.00 34.39 1.89
342 414 2.036475 CAGCAGACCCATCGCTAATACT 59.964 50.000 0.00 0.00 34.39 2.12
356 428 7.972832 TCGCTAATACTTTTCAAAGGAAGAA 57.027 32.000 4.36 0.00 40.31 2.52
368 440 5.511363 TCAAAGGAAGAACCACCACTTAAA 58.489 37.500 0.00 0.00 42.04 1.52
410 484 6.823286 TTGGGACCATCACTAAGATCATTA 57.177 37.500 0.00 0.00 33.72 1.90
433 507 8.716646 TTAGTGATGTGTTATGTTATCACCTG 57.283 34.615 11.34 0.00 46.51 4.00
438 512 7.826744 TGATGTGTTATGTTATCACCTGCTTAA 59.173 33.333 0.00 0.00 0.00 1.85
439 513 7.609760 TGTGTTATGTTATCACCTGCTTAAG 57.390 36.000 0.00 0.00 0.00 1.85
452 526 4.584325 ACCTGCTTAAGAGTGCAAATTTCA 59.416 37.500 6.67 0.00 38.81 2.69
484 558 7.230849 AGTTATGAAAATTCATGAGTGGCAA 57.769 32.000 16.85 1.09 46.68 4.52
520 594 1.674817 CGACCCGAAAGCCATACAAGT 60.675 52.381 0.00 0.00 0.00 3.16
621 696 7.798801 TCACCTATGTGTGTTTTAATGTAACG 58.201 34.615 0.00 0.00 43.26 3.18
624 699 7.095102 ACCTATGTGTGTTTTAATGTAACGACC 60.095 37.037 0.00 0.00 0.00 4.79
654 729 7.552687 TGTTTAGTATTGGACTAGCAAATGGAG 59.447 37.037 0.00 0.00 41.75 3.86
655 730 4.455606 AGTATTGGACTAGCAAATGGAGC 58.544 43.478 0.00 0.00 36.27 4.70
801 878 4.734398 AAGTTCTTGCACATTTTGGTGA 57.266 36.364 0.00 0.00 41.32 4.02
815 892 8.352201 CACATTTTGGTGAGATAAGAGTCAAAA 58.648 33.333 0.00 0.00 41.32 2.44
816 893 9.082313 ACATTTTGGTGAGATAAGAGTCAAAAT 57.918 29.630 0.00 0.00 41.20 1.82
824 901 6.535150 TGAGATAAGAGTCAAAATTAGCCACG 59.465 38.462 0.00 0.00 0.00 4.94
839 916 3.758425 AGCCACGGGTTAACAAAATACT 58.242 40.909 8.10 0.00 0.00 2.12
840 917 4.909001 AGCCACGGGTTAACAAAATACTA 58.091 39.130 8.10 0.00 0.00 1.82
912 989 0.739561 AGAAGTAGCGACGATGGGTC 59.260 55.000 0.00 0.00 42.48 4.46
918 995 0.249120 AGCGACGATGGGTCAATGAA 59.751 50.000 0.00 0.00 46.42 2.57
950 1027 6.012858 TCCATATATAGGGTTGATTCCACACC 60.013 42.308 12.96 0.00 0.00 4.16
951 1028 4.724279 ATATAGGGTTGATTCCACACCC 57.276 45.455 7.46 7.46 40.82 4.61
964 1041 2.359967 ACACCCGAGCTAGCCTTCC 61.360 63.158 12.13 0.00 0.00 3.46
965 1042 2.060980 CACCCGAGCTAGCCTTCCT 61.061 63.158 12.13 0.00 0.00 3.36
977 1054 3.515602 AGCCTTCCTGTCAAGAACAAT 57.484 42.857 0.00 0.00 37.45 2.71
984 1061 5.339008 TCCTGTCAAGAACAATATAGCGT 57.661 39.130 0.00 0.00 37.45 5.07
989 1066 5.028375 GTCAAGAACAATATAGCGTTTGGC 58.972 41.667 0.00 0.00 44.05 4.52
1029 1106 7.227314 TCAATGACATATATCACCAAGAAGCAC 59.773 37.037 0.00 0.00 0.00 4.40
1037 1114 2.299013 TCACCAAGAAGCACGACTATGT 59.701 45.455 0.00 0.00 0.00 2.29
1043 1120 2.738846 AGAAGCACGACTATGTTGCAAG 59.261 45.455 0.00 0.00 0.00 4.01
1052 1129 2.756760 ACTATGTTGCAAGCTTGGATGG 59.243 45.455 27.10 14.28 0.00 3.51
1060 1137 1.005215 CAAGCTTGGATGGGAAGGAGT 59.995 52.381 19.14 0.00 0.00 3.85
1069 1146 4.516195 GGAAGGAGTCGCCCGAGC 62.516 72.222 0.00 0.00 37.37 5.03
1072 1149 3.376935 AAGGAGTCGCCCGAGCATG 62.377 63.158 0.00 0.00 39.83 4.06
1086 1163 2.467826 GCATGAGAAGTCGGCCAGC 61.468 63.158 2.24 0.00 0.00 4.85
1089 1166 2.048127 GAGAAGTCGGCCAGCGTT 60.048 61.111 2.24 0.00 0.00 4.84
1095 1172 4.069232 TCGGCCAGCGTTGAGAGG 62.069 66.667 2.24 0.00 0.00 3.69
1098 1175 2.579201 GCCAGCGTTGAGAGGCTA 59.421 61.111 0.00 0.00 44.63 3.93
1104 1181 1.067495 AGCGTTGAGAGGCTACTTGTC 60.067 52.381 0.00 0.00 44.59 3.18
1107 1184 1.544691 GTTGAGAGGCTACTTGTCCGA 59.455 52.381 0.00 0.00 0.00 4.55
1125 1202 2.683867 CCGAACCACAAAACTTACCACA 59.316 45.455 0.00 0.00 0.00 4.17
1161 1238 5.636965 GCTGTACAGGTAATCATCAGCTATG 59.363 44.000 23.95 0.00 42.00 2.23
1275 1566 2.621070 AGCAGAGTTCCAAGGGAAGTA 58.379 47.619 5.37 0.00 44.44 2.24
1310 1601 9.912634 AAGTAAAACAATTGGATGTGATAGTTG 57.087 29.630 10.83 0.00 32.81 3.16
1369 1766 9.631257 TTGGATGCTGAATCTGATAAGAATTTA 57.369 29.630 0.00 0.00 35.43 1.40
1370 1767 9.060347 TGGATGCTGAATCTGATAAGAATTTAC 57.940 33.333 0.00 0.00 35.43 2.01
1374 1771 7.068341 GCTGAATCTGATAAGAATTTACTGCG 58.932 38.462 4.85 0.00 0.00 5.18
1386 1802 6.779117 AGAATTTACTGCGACAAATGATGAG 58.221 36.000 0.00 0.00 0.00 2.90
1434 2037 6.347644 CGTGTCATGAAATCTAGTGCTCAAAA 60.348 38.462 0.00 0.00 0.00 2.44
1444 2047 8.621532 AATCTAGTGCTCAAAAGTGACATTTA 57.378 30.769 0.00 0.00 0.00 1.40
1450 2053 9.382275 AGTGCTCAAAAGTGACATTTAAAAATT 57.618 25.926 0.00 0.00 0.00 1.82
1462 2071 8.983724 TGACATTTAAAAATTTCGAATTCACCC 58.016 29.630 6.22 0.00 29.81 4.61
1477 2086 5.972107 ATTCACCCTTTCAATTGAGTGAG 57.028 39.130 20.82 14.65 35.81 3.51
1479 2088 4.136796 TCACCCTTTCAATTGAGTGAGTG 58.863 43.478 19.01 18.34 31.10 3.51
1485 2094 3.407424 TCAATTGAGTGAGTGGGAGTG 57.593 47.619 3.38 0.00 0.00 3.51
1486 2095 1.808945 CAATTGAGTGAGTGGGAGTGC 59.191 52.381 0.00 0.00 0.00 4.40
1497 2106 4.891168 TGAGTGGGAGTGCGTATAGAAATA 59.109 41.667 0.00 0.00 0.00 1.40
1539 2198 4.749598 GGAAAATGACAAAGTGGCGAAAAT 59.250 37.500 0.00 0.00 0.00 1.82
1548 2207 2.238521 AGTGGCGAAAATCATGGTGTT 58.761 42.857 0.00 0.00 0.00 3.32
1549 2208 2.627699 AGTGGCGAAAATCATGGTGTTT 59.372 40.909 0.00 0.00 0.00 2.83
1550 2209 2.730928 GTGGCGAAAATCATGGTGTTTG 59.269 45.455 0.00 0.00 0.00 2.93
1561 2220 1.008538 GGTGTTTGTTGCAGGCTCG 60.009 57.895 0.00 0.00 0.00 5.03
1580 2239 2.028476 TCGTGGTCTTTGTTCGGATGAT 60.028 45.455 0.00 0.00 0.00 2.45
1610 2269 2.030893 TGCTGTTCTTCAAATGGCGAAG 60.031 45.455 0.00 0.00 41.05 3.79
1683 2342 4.175337 ACCATGTCCATCGCCGGG 62.175 66.667 2.18 0.00 0.00 5.73
1786 2445 3.708220 GAGGAGTCGCTGCTTCCGG 62.708 68.421 0.00 0.00 30.82 5.14
1815 2474 4.651008 TTCGTCACCACCGCCGAC 62.651 66.667 0.00 0.00 0.00 4.79
2075 2734 1.424638 TCAAGGGCTGACTATAGGGC 58.575 55.000 4.43 5.49 0.00 5.19
2078 2737 1.893315 AGGGCTGACTATAGGGCAAA 58.107 50.000 4.43 0.00 29.31 3.68
2238 2897 1.194772 GTTGTTGAAGTGCTAGTCGGC 59.805 52.381 0.00 0.00 0.00 5.54
2287 2946 2.095461 TCAGTGATCTTCTGGACCTCG 58.905 52.381 14.89 0.00 34.15 4.63
2737 3399 3.114616 CTGGCAAGGACGTCGCTG 61.115 66.667 9.92 10.16 0.00 5.18
2766 3428 2.143122 GACAAGTTTGGCATCTCGACA 58.857 47.619 0.00 0.00 35.83 4.35
2807 3469 1.452145 GCGGCCTTGAACTTGAACCA 61.452 55.000 0.00 0.00 0.00 3.67
2907 3572 2.044555 CGGCTACGAGGACAGGACA 61.045 63.158 0.00 0.00 44.60 4.02
2958 3623 1.362717 CACCGTGACAGAGGACGTT 59.637 57.895 4.06 0.00 33.66 3.99
3210 3875 3.447586 CGTTCACCTCCATCTTTCTCCTA 59.552 47.826 0.00 0.00 0.00 2.94
3305 3970 3.252484 GTCGGCCACGTACATCGC 61.252 66.667 2.24 0.00 44.19 4.58
3375 4040 1.153229 GAGGTGGTCGGGCATAACC 60.153 63.158 0.00 0.00 36.03 2.85
3384 4049 2.516225 GGCATAACCCTGGGCGAC 60.516 66.667 14.08 0.00 0.00 5.19
3507 4172 0.880278 TCAAGCTGACGTCCAAGCAC 60.880 55.000 24.67 4.90 0.00 4.40
3715 4381 1.847506 TGGGTGGTGGTGCATCTCT 60.848 57.895 0.00 0.00 0.00 3.10
3765 4431 2.357517 AGCAAGACGTTGAGCCCG 60.358 61.111 0.00 0.00 35.46 6.13
3833 4499 4.142116 TGTCCTCCATTTGCATATGCTTTG 60.142 41.667 27.13 19.80 42.66 2.77
3838 4504 7.889600 TCCTCCATTTGCATATGCTTTGATATA 59.110 33.333 27.13 2.54 42.66 0.86
3876 4542 7.360017 GCCCACTAGTAAAATTTCAAATGCAAC 60.360 37.037 0.00 0.00 0.00 4.17
3878 4544 9.260002 CCACTAGTAAAATTTCAAATGCAACTT 57.740 29.630 0.00 0.00 0.00 2.66
3919 4585 2.463752 AGTAACTACTTCATCCGCCCA 58.536 47.619 0.00 0.00 31.13 5.36
3920 4586 3.039011 AGTAACTACTTCATCCGCCCAT 58.961 45.455 0.00 0.00 31.13 4.00
3941 4607 7.478322 CCCATAATTTGACTCAGATTTGTCTG 58.522 38.462 0.41 0.00 39.00 3.51
3943 4609 5.972107 AATTTGACTCAGATTTGTCTGGG 57.028 39.130 3.85 3.85 43.57 4.45
3953 4619 4.028131 AGATTTGTCTGGGTACGGATGTA 58.972 43.478 0.00 0.00 33.82 2.29
3954 4620 4.654262 AGATTTGTCTGGGTACGGATGTAT 59.346 41.667 0.00 0.00 33.82 2.29
3955 4621 3.812156 TTGTCTGGGTACGGATGTATG 57.188 47.619 0.00 0.00 33.82 2.39
3958 4624 4.279982 TGTCTGGGTACGGATGTATGTAA 58.720 43.478 0.00 0.00 33.82 2.41
3968 4634 8.881743 GGTACGGATGTATGTAAACACATTTTA 58.118 33.333 0.00 0.00 35.55 1.52
3969 4635 9.910511 GTACGGATGTATGTAAACACATTTTAG 57.089 33.333 0.00 0.00 35.55 1.85
3970 4636 8.556213 ACGGATGTATGTAAACACATTTTAGT 57.444 30.769 0.00 0.00 35.55 2.24
3971 4637 8.447833 ACGGATGTATGTAAACACATTTTAGTG 58.552 33.333 0.00 0.00 44.93 2.74
3982 4648 5.269505 CACATTTTAGTGTTGGGTTTGGA 57.730 39.130 0.00 0.00 34.83 3.53
3984 4650 6.987386 CACATTTTAGTGTTGGGTTTGGATA 58.013 36.000 0.00 0.00 34.83 2.59
3985 4651 7.437748 CACATTTTAGTGTTGGGTTTGGATAA 58.562 34.615 0.00 0.00 34.83 1.75
3986 4652 7.928706 CACATTTTAGTGTTGGGTTTGGATAAA 59.071 33.333 0.00 0.00 34.83 1.40
3987 4653 8.655901 ACATTTTAGTGTTGGGTTTGGATAAAT 58.344 29.630 0.00 0.00 0.00 1.40
3988 4654 9.150348 CATTTTAGTGTTGGGTTTGGATAAATC 57.850 33.333 0.00 0.00 0.00 2.17
3989 4655 7.841282 TTTAGTGTTGGGTTTGGATAAATCA 57.159 32.000 0.00 0.00 0.00 2.57
3992 4658 9.707957 TTAGTGTTGGGTTTGGATAAATCATAT 57.292 29.630 0.00 0.00 0.00 1.78
3993 4659 8.237811 AGTGTTGGGTTTGGATAAATCATATC 57.762 34.615 0.00 0.00 0.00 1.63
3994 4660 8.061304 AGTGTTGGGTTTGGATAAATCATATCT 58.939 33.333 0.00 0.00 0.00 1.98
3995 4661 9.349713 GTGTTGGGTTTGGATAAATCATATCTA 57.650 33.333 0.00 0.00 0.00 1.98
3996 4662 9.573166 TGTTGGGTTTGGATAAATCATATCTAG 57.427 33.333 0.00 0.00 0.00 2.43
3997 4663 9.793259 GTTGGGTTTGGATAAATCATATCTAGA 57.207 33.333 0.00 0.00 0.00 2.43
4023 4689 9.793259 AAAATCTAAGACAACTAATTGGACAGA 57.207 29.630 0.00 0.00 40.42 3.41
4024 4690 9.793259 AAATCTAAGACAACTAATTGGACAGAA 57.207 29.630 0.00 0.00 40.42 3.02
4025 4691 9.793259 AATCTAAGACAACTAATTGGACAGAAA 57.207 29.630 0.00 0.00 40.42 2.52
4026 4692 9.965902 ATCTAAGACAACTAATTGGACAGAAAT 57.034 29.630 0.00 0.00 40.42 2.17
4053 4719 5.921004 TTTGAAGTTAATTGCATGTTGGC 57.079 34.783 0.00 0.00 0.00 4.52
4055 4721 4.305769 TGAAGTTAATTGCATGTTGGCAC 58.694 39.130 0.00 0.00 44.86 5.01
4058 4724 2.736192 GTTAATTGCATGTTGGCACCAC 59.264 45.455 0.00 0.00 44.86 4.16
4060 4726 0.757512 ATTGCATGTTGGCACCACAA 59.242 45.000 0.00 0.00 44.86 3.33
4062 4728 0.757512 TGCATGTTGGCACCACAATT 59.242 45.000 0.00 0.00 39.25 2.32
4087 4759 3.636282 AACGAATTGGTACCACTTTGC 57.364 42.857 25.06 11.43 0.00 3.68
4088 4760 1.533731 ACGAATTGGTACCACTTTGCG 59.466 47.619 25.06 21.70 0.00 4.85
4119 4791 4.202441 ACATGTCAATATCAAGTCTGGGC 58.798 43.478 0.00 0.00 0.00 5.36
4120 4792 3.998913 TGTCAATATCAAGTCTGGGCA 57.001 42.857 0.00 0.00 0.00 5.36
4121 4793 3.877559 TGTCAATATCAAGTCTGGGCAG 58.122 45.455 0.00 0.00 0.00 4.85
4122 4794 3.519107 TGTCAATATCAAGTCTGGGCAGA 59.481 43.478 0.00 0.00 34.56 4.26
4142 4814 5.334569 GCAGACCGTAACAAATTGAGCTAAA 60.335 40.000 0.00 0.00 0.00 1.85
4146 4818 5.533528 ACCGTAACAAATTGAGCTAAACCTT 59.466 36.000 0.00 0.00 0.00 3.50
4165 4837 7.604657 AACCTTGTATAAACCCATTTTGACA 57.395 32.000 0.00 0.00 0.00 3.58
4172 4844 4.415881 AAACCCATTTTGACAGGGAAAC 57.584 40.909 3.32 0.00 45.80 2.78
4173 4845 3.328535 ACCCATTTTGACAGGGAAACT 57.671 42.857 3.32 0.00 45.80 2.66
4203 5074 1.272704 GGCCCTTCCTTCCTCATGTTT 60.273 52.381 0.00 0.00 0.00 2.83
4205 5076 2.359900 CCCTTCCTTCCTCATGTTTCG 58.640 52.381 0.00 0.00 0.00 3.46
4207 5078 3.055385 CCCTTCCTTCCTCATGTTTCGTA 60.055 47.826 0.00 0.00 0.00 3.43
4211 5082 4.817517 TCCTTCCTCATGTTTCGTACTTC 58.182 43.478 0.00 0.00 0.00 3.01
4224 5095 2.092861 TCGTACTTCTCCTCCTCCTCAG 60.093 54.545 0.00 0.00 0.00 3.35
4227 5098 2.000048 ACTTCTCCTCCTCCTCAGTCT 59.000 52.381 0.00 0.00 0.00 3.24
4228 5099 2.025321 ACTTCTCCTCCTCCTCAGTCTC 60.025 54.545 0.00 0.00 0.00 3.36
4229 5100 0.544223 TCTCCTCCTCCTCAGTCTCG 59.456 60.000 0.00 0.00 0.00 4.04
4232 5103 0.750182 CCTCCTCCTCAGTCTCGGTC 60.750 65.000 0.00 0.00 0.00 4.79
4241 5112 3.278574 CTCAGTCTCGGTCTCTCATCTT 58.721 50.000 0.00 0.00 0.00 2.40
4242 5113 3.691575 TCAGTCTCGGTCTCTCATCTTT 58.308 45.455 0.00 0.00 0.00 2.52
4252 5123 4.097892 GGTCTCTCATCTTTCTGTCTCTCC 59.902 50.000 0.00 0.00 0.00 3.71
4253 5124 4.097892 GTCTCTCATCTTTCTGTCTCTCCC 59.902 50.000 0.00 0.00 0.00 4.30
4254 5125 3.020274 TCTCATCTTTCTGTCTCTCCCG 58.980 50.000 0.00 0.00 0.00 5.14
4274 5145 1.341383 GGTGCAAGAACCTCCATGGAT 60.341 52.381 16.63 0.00 39.71 3.41
4279 5150 2.679837 CAAGAACCTCCATGGATGAACG 59.320 50.000 22.35 7.46 39.71 3.95
4283 5154 1.224315 CTCCATGGATGAACGCCCA 59.776 57.895 16.63 0.00 36.79 5.36
4292 5163 4.035102 GAACGCCCAAGCTCCCCT 62.035 66.667 0.00 0.00 36.60 4.79
4299 5170 3.785859 CAAGCTCCCCTGCCGCTA 61.786 66.667 0.00 0.00 32.90 4.26
4309 5180 2.202878 TGCCGCTAATCTGGACGC 60.203 61.111 0.00 0.00 0.00 5.19
4311 5182 2.499205 CCGCTAATCTGGACGCCA 59.501 61.111 0.00 0.00 0.00 5.69
4331 5202 0.533308 TCCGTTGTCGAAACCCTTGG 60.533 55.000 0.00 0.00 39.71 3.61
4334 5205 0.822121 GTTGTCGAAACCCTTGGGCT 60.822 55.000 5.46 0.00 0.00 5.19
4339 5210 3.860930 GAAACCCTTGGGCTGCCGA 62.861 63.158 13.40 5.79 0.00 5.54
4347 5218 4.554036 GGGCTGCCGACCAGATCC 62.554 72.222 13.40 4.37 44.64 3.36
4352 5223 3.458163 GCCGACCAGATCCGGTGA 61.458 66.667 5.02 0.00 46.84 4.02
4376 5248 1.227973 GGCCGGATCTGTCCATTCC 60.228 63.158 5.05 0.00 45.37 3.01
4378 5250 1.069765 CCGGATCTGTCCATTCCCG 59.930 63.158 0.00 0.00 45.37 5.14
4381 5253 1.048601 GGATCTGTCCATTCCCGCTA 58.951 55.000 0.00 0.00 44.42 4.26
4385 5257 2.325393 CTGTCCATTCCCGCTACCCC 62.325 65.000 0.00 0.00 0.00 4.95
4386 5258 2.041430 TCCATTCCCGCTACCCCA 59.959 61.111 0.00 0.00 0.00 4.96
4387 5259 2.070039 TCCATTCCCGCTACCCCAG 61.070 63.158 0.00 0.00 0.00 4.45
4388 5260 2.070039 CCATTCCCGCTACCCCAGA 61.070 63.158 0.00 0.00 0.00 3.86
4391 5263 0.620700 ATTCCCGCTACCCCAGACTT 60.621 55.000 0.00 0.00 0.00 3.01
4403 5554 2.567169 CCCCAGACTTGTACTGACATGA 59.433 50.000 0.00 0.00 37.54 3.07
4405 5556 4.248859 CCCAGACTTGTACTGACATGAAG 58.751 47.826 0.00 0.00 37.54 3.02
4442 5601 4.838986 TGGTACCAATTCTCTATCCTAGCC 59.161 45.833 13.60 0.00 0.00 3.93
4444 5603 4.220861 ACCAATTCTCTATCCTAGCCCT 57.779 45.455 0.00 0.00 0.00 5.19
4452 5611 7.979786 TTCTCTATCCTAGCCCTAATTATGG 57.020 40.000 2.57 2.57 0.00 2.74
4459 5618 5.308759 TCCTAGCCCTAATTATGGTACCAAC 59.691 44.000 20.76 0.25 0.00 3.77
4460 5619 5.072600 CCTAGCCCTAATTATGGTACCAACA 59.927 44.000 20.76 8.91 0.00 3.33
4522 5681 5.178996 GCGATGAGCTGATAATTCTTCATGT 59.821 40.000 0.00 0.00 44.04 3.21
4546 5705 0.670546 GCTTTCTGCGCCTGTGTCTA 60.671 55.000 4.18 0.00 0.00 2.59
4551 5710 0.387202 CTGCGCCTGTGTCTAGCTAT 59.613 55.000 4.18 0.00 0.00 2.97
4552 5711 0.824109 TGCGCCTGTGTCTAGCTATT 59.176 50.000 4.18 0.00 0.00 1.73
4564 5723 5.011125 GTGTCTAGCTATTAGCCAGGATCAA 59.989 44.000 12.05 0.00 43.77 2.57
4567 5726 2.700897 AGCTATTAGCCAGGATCAACGT 59.299 45.455 12.05 0.00 43.77 3.99
4568 5727 3.060602 GCTATTAGCCAGGATCAACGTC 58.939 50.000 4.21 0.00 34.48 4.34
4569 5728 3.492656 GCTATTAGCCAGGATCAACGTCA 60.493 47.826 4.21 0.00 34.48 4.35
4571 5730 3.627395 TTAGCCAGGATCAACGTCAAT 57.373 42.857 0.00 0.00 0.00 2.57
4572 5731 1.742761 AGCCAGGATCAACGTCAATG 58.257 50.000 0.00 0.00 0.00 2.82
4573 5732 0.099436 GCCAGGATCAACGTCAATGC 59.901 55.000 0.00 0.00 0.00 3.56
4574 5733 1.742761 CCAGGATCAACGTCAATGCT 58.257 50.000 0.00 0.00 0.00 3.79
4575 5734 2.905075 CCAGGATCAACGTCAATGCTA 58.095 47.619 4.24 0.00 0.00 3.49
4576 5735 3.470709 CCAGGATCAACGTCAATGCTAT 58.529 45.455 4.24 0.00 0.00 2.97
4577 5736 4.631131 CCAGGATCAACGTCAATGCTATA 58.369 43.478 4.24 0.00 0.00 1.31
4578 5737 5.240891 CCAGGATCAACGTCAATGCTATAT 58.759 41.667 4.24 0.00 0.00 0.86
4579 5738 5.349817 CCAGGATCAACGTCAATGCTATATC 59.650 44.000 4.24 0.00 0.00 1.63
4580 5739 6.162079 CAGGATCAACGTCAATGCTATATCT 58.838 40.000 4.24 0.00 0.00 1.98
4581 5740 7.315890 CAGGATCAACGTCAATGCTATATCTA 58.684 38.462 4.24 0.00 0.00 1.98
4582 5741 7.814587 CAGGATCAACGTCAATGCTATATCTAA 59.185 37.037 4.24 0.00 0.00 2.10
4583 5742 7.815068 AGGATCAACGTCAATGCTATATCTAAC 59.185 37.037 2.86 0.00 0.00 2.34
4584 5743 7.815068 GGATCAACGTCAATGCTATATCTAACT 59.185 37.037 0.00 0.00 0.00 2.24
4585 5744 8.749841 ATCAACGTCAATGCTATATCTAACTC 57.250 34.615 0.00 0.00 0.00 3.01
4586 5745 7.712797 TCAACGTCAATGCTATATCTAACTCA 58.287 34.615 0.00 0.00 0.00 3.41
4587 5746 8.360390 TCAACGTCAATGCTATATCTAACTCAT 58.640 33.333 0.00 0.00 0.00 2.90
4588 5747 8.982685 CAACGTCAATGCTATATCTAACTCATT 58.017 33.333 0.00 0.00 0.00 2.57
4589 5748 8.526218 ACGTCAATGCTATATCTAACTCATTG 57.474 34.615 0.00 0.00 40.99 2.82
4590 5749 7.116948 ACGTCAATGCTATATCTAACTCATTGC 59.883 37.037 7.62 3.71 40.04 3.56
4591 5750 7.116805 CGTCAATGCTATATCTAACTCATTGCA 59.883 37.037 7.62 0.00 40.04 4.08
4592 5751 8.777413 GTCAATGCTATATCTAACTCATTGCAA 58.223 33.333 0.00 0.00 40.04 4.08
4593 5752 8.996271 TCAATGCTATATCTAACTCATTGCAAG 58.004 33.333 4.94 0.00 40.04 4.01
4594 5753 8.781196 CAATGCTATATCTAACTCATTGCAAGT 58.219 33.333 4.94 0.00 35.86 3.16
4597 5756 7.074502 GCTATATCTAACTCATTGCAAGTTGC 58.925 38.462 21.17 21.17 45.29 4.17
4618 5777 8.646004 AGTTGCACATCATACTCATCTATAGTT 58.354 33.333 0.00 0.00 0.00 2.24
4624 5783 2.423926 ACTCATCTATAGTTGCGCCG 57.576 50.000 4.18 0.00 0.00 6.46
4625 5784 1.063806 CTCATCTATAGTTGCGCCGC 58.936 55.000 4.18 0.00 0.00 6.53
4660 5819 6.605119 CCTAACATTGGGTGATATTTCTCCT 58.395 40.000 4.57 0.00 36.08 3.69
4662 5821 7.229506 CCTAACATTGGGTGATATTTCTCCTTC 59.770 40.741 4.57 0.00 36.08 3.46
4664 5823 3.838244 TGGGTGATATTTCTCCTTCGG 57.162 47.619 4.57 0.00 36.08 4.30
4668 5827 3.802685 GGTGATATTTCTCCTTCGGTTCG 59.197 47.826 0.00 0.00 33.55 3.95
4669 5828 4.430908 GTGATATTTCTCCTTCGGTTCGT 58.569 43.478 0.00 0.00 0.00 3.85
4671 5830 5.686397 GTGATATTTCTCCTTCGGTTCGTAG 59.314 44.000 0.00 0.00 0.00 3.51
4674 5833 1.093159 TCTCCTTCGGTTCGTAGCTC 58.907 55.000 0.00 0.00 0.00 4.09
4675 5834 0.100861 CTCCTTCGGTTCGTAGCTCC 59.899 60.000 0.00 0.00 0.00 4.70
4677 5836 1.226603 CTTCGGTTCGTAGCTCCGG 60.227 63.158 10.55 0.00 41.75 5.14
4680 5840 1.804326 CGGTTCGTAGCTCCGGTTG 60.804 63.158 0.00 0.00 39.04 3.77
4683 5843 1.505425 GTTCGTAGCTCCGGTTGTTT 58.495 50.000 0.00 0.00 0.00 2.83
4706 5866 6.459670 TCCTGTGGTTTTCTTTAGGTTTTC 57.540 37.500 0.00 0.00 0.00 2.29
4708 5868 6.320418 TCCTGTGGTTTTCTTTAGGTTTTCTC 59.680 38.462 0.00 0.00 0.00 2.87
4709 5869 6.459670 TGTGGTTTTCTTTAGGTTTTCTCC 57.540 37.500 0.00 0.00 0.00 3.71
4710 5870 5.952947 TGTGGTTTTCTTTAGGTTTTCTCCA 59.047 36.000 0.00 0.00 0.00 3.86
4711 5871 6.096282 TGTGGTTTTCTTTAGGTTTTCTCCAG 59.904 38.462 0.00 0.00 0.00 3.86
4713 5873 5.831525 GGTTTTCTTTAGGTTTTCTCCAGGA 59.168 40.000 0.00 0.00 0.00 3.86
4715 5875 6.954487 TTTCTTTAGGTTTTCTCCAGGAAC 57.046 37.500 0.00 0.00 33.13 3.62
4717 5877 7.383156 TTCTTTAGGTTTTCTCCAGGAACTA 57.617 36.000 0.00 0.00 36.02 2.24
4718 5878 7.383156 TCTTTAGGTTTTCTCCAGGAACTAA 57.617 36.000 0.00 0.00 36.02 2.24
4776 5950 9.903682 TTCAATTGATCATTTGTTTCTTCTCTC 57.096 29.630 22.99 0.00 0.00 3.20
4787 5961 4.881850 TGTTTCTTCTCTCGCCTTTCTTTT 59.118 37.500 0.00 0.00 0.00 2.27
4789 5963 5.674933 TTCTTCTCTCGCCTTTCTTTTTC 57.325 39.130 0.00 0.00 0.00 2.29
4792 5966 5.823045 TCTTCTCTCGCCTTTCTTTTTCTTT 59.177 36.000 0.00 0.00 0.00 2.52
4793 5967 5.674933 TCTCTCGCCTTTCTTTTTCTTTC 57.325 39.130 0.00 0.00 0.00 2.62
4794 5968 5.123227 TCTCTCGCCTTTCTTTTTCTTTCA 58.877 37.500 0.00 0.00 0.00 2.69
4795 5969 5.007724 TCTCTCGCCTTTCTTTTTCTTTCAC 59.992 40.000 0.00 0.00 0.00 3.18
4796 5970 4.036380 TCTCGCCTTTCTTTTTCTTTCACC 59.964 41.667 0.00 0.00 0.00 4.02
4798 5972 4.044426 CGCCTTTCTTTTTCTTTCACCAG 58.956 43.478 0.00 0.00 0.00 4.00
4799 5973 4.202010 CGCCTTTCTTTTTCTTTCACCAGA 60.202 41.667 0.00 0.00 0.00 3.86
4800 5974 5.660460 GCCTTTCTTTTTCTTTCACCAGAA 58.340 37.500 0.00 0.00 0.00 3.02
4801 5975 6.283694 GCCTTTCTTTTTCTTTCACCAGAAT 58.716 36.000 0.00 0.00 32.69 2.40
4803 5977 7.042456 GCCTTTCTTTTTCTTTCACCAGAATTC 60.042 37.037 0.00 0.00 32.69 2.17
4804 5978 8.200120 CCTTTCTTTTTCTTTCACCAGAATTCT 58.800 33.333 0.88 0.88 32.69 2.40
4805 5979 8.931385 TTTCTTTTTCTTTCACCAGAATTCTG 57.069 30.769 25.75 25.75 43.40 3.02
4806 5980 7.645058 TCTTTTTCTTTCACCAGAATTCTGT 57.355 32.000 29.03 16.95 42.27 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 2.295349 CAGAGCTGGCAACACTGAAATT 59.705 45.455 9.35 0.00 46.17 1.82
15 16 3.418685 TGGCACAGAGCTGGCAACA 62.419 57.895 0.00 0.00 43.29 3.33
16 17 2.595463 TGGCACAGAGCTGGCAAC 60.595 61.111 0.00 0.00 43.29 4.17
33 34 3.738982 TGTCGATGGATGTTGTTGAACT 58.261 40.909 0.00 0.00 32.79 3.01
57 58 5.975693 TTTTAAGGGGTATGTGCTTTCTG 57.024 39.130 0.00 0.00 0.00 3.02
96 97 2.952978 GACGAGGAGAAGGAGAAGCATA 59.047 50.000 0.00 0.00 0.00 3.14
199 204 7.830201 TGTGTCTACTTTGTTTCTCCCTTTTAA 59.170 33.333 0.00 0.00 0.00 1.52
202 207 5.751586 TGTGTCTACTTTGTTTCTCCCTTT 58.248 37.500 0.00 0.00 0.00 3.11
239 308 2.028476 GGGTACGTGCATGCCATCTATA 60.028 50.000 16.68 0.00 0.00 1.31
244 313 2.513666 CGGGTACGTGCATGCCAT 60.514 61.111 16.68 2.70 34.81 4.40
282 351 0.249868 GGTCAACCTTTTGCCAAGCC 60.250 55.000 0.00 0.00 32.29 4.35
306 378 1.004044 CTGCTGGAAACTGATCCCACT 59.996 52.381 0.00 0.00 38.82 4.00
315 387 0.036010 CGATGGGTCTGCTGGAAACT 60.036 55.000 0.00 0.00 0.00 2.66
341 413 4.402474 AGTGGTGGTTCTTCCTTTGAAAAG 59.598 41.667 0.00 0.00 37.07 2.27
342 414 4.349365 AGTGGTGGTTCTTCCTTTGAAAA 58.651 39.130 0.00 0.00 37.07 2.29
356 428 7.286775 ACTTATGACACAATTTTAAGTGGTGGT 59.713 33.333 0.25 0.00 39.99 4.16
389 463 6.426646 ACTAATGATCTTAGTGATGGTCCC 57.573 41.667 13.46 0.00 35.14 4.46
410 484 5.586243 GCAGGTGATAACATAACACATCACT 59.414 40.000 11.94 0.00 44.28 3.41
433 507 8.970691 TTTAGATGAAATTTGCACTCTTAAGC 57.029 30.769 0.00 0.00 0.00 3.09
476 550 2.162408 GCCTAACATTCACTTGCCACTC 59.838 50.000 0.00 0.00 0.00 3.51
484 558 1.207329 GGTCGAGGCCTAACATTCACT 59.793 52.381 4.42 0.00 0.00 3.41
520 594 2.043752 TCCTACGGCGACCCATCA 60.044 61.111 16.62 0.00 0.00 3.07
621 696 6.315642 GCTAGTCCAATACTAAACAAAGGGTC 59.684 42.308 0.00 0.00 40.21 4.46
624 699 7.681939 TTGCTAGTCCAATACTAAACAAAGG 57.318 36.000 0.00 0.00 40.21 3.11
654 729 2.132740 TTGCTGATTTGTTTCCACGC 57.867 45.000 0.00 0.00 0.00 5.34
655 730 3.426191 CACATTGCTGATTTGTTTCCACG 59.574 43.478 0.00 0.00 0.00 4.94
757 834 2.029970 ACACACGCTTAGTTTGTTCACG 59.970 45.455 0.00 0.00 40.54 4.35
801 878 5.817816 CCGTGGCTAATTTTGACTCTTATCT 59.182 40.000 0.00 0.00 0.00 1.98
815 892 5.947566 AGTATTTTGTTAACCCGTGGCTAAT 59.052 36.000 2.48 0.00 0.00 1.73
816 893 5.315348 AGTATTTTGTTAACCCGTGGCTAA 58.685 37.500 2.48 0.00 0.00 3.09
818 895 3.758425 AGTATTTTGTTAACCCGTGGCT 58.242 40.909 2.48 0.00 0.00 4.75
840 917 8.867097 TCCGTACTTATCCTAGCTTATTCATTT 58.133 33.333 0.00 0.00 0.00 2.32
881 958 5.062308 CGTCGCTACTTCTTTTCTGCTTTAT 59.938 40.000 0.00 0.00 0.00 1.40
886 963 2.325761 TCGTCGCTACTTCTTTTCTGC 58.674 47.619 0.00 0.00 0.00 4.26
912 989 8.331740 ACCCTATATATGGAGGACATTTCATTG 58.668 37.037 10.72 0.00 41.03 2.82
918 995 8.468547 AATCAACCCTATATATGGAGGACATT 57.531 34.615 10.72 0.40 41.03 2.71
950 1027 1.323271 TGACAGGAAGGCTAGCTCGG 61.323 60.000 15.72 3.94 0.00 4.63
951 1028 0.532573 TTGACAGGAAGGCTAGCTCG 59.467 55.000 15.72 0.00 0.00 5.03
964 1041 6.250819 CCAAACGCTATATTGTTCTTGACAG 58.749 40.000 0.00 0.00 39.94 3.51
965 1042 5.391523 GCCAAACGCTATATTGTTCTTGACA 60.392 40.000 0.00 0.00 36.19 3.58
977 1054 0.107410 CCCACTGGCCAAACGCTATA 60.107 55.000 7.01 0.00 37.74 1.31
984 1061 1.607178 CATGCTCCCACTGGCCAAA 60.607 57.895 7.01 0.00 0.00 3.28
989 1066 1.100510 CATTGACATGCTCCCACTGG 58.899 55.000 0.00 0.00 0.00 4.00
1029 1106 2.076100 TCCAAGCTTGCAACATAGTCG 58.924 47.619 21.43 3.37 0.00 4.18
1037 1114 1.259609 CTTCCCATCCAAGCTTGCAA 58.740 50.000 21.43 11.38 0.00 4.08
1043 1120 0.462759 CGACTCCTTCCCATCCAAGC 60.463 60.000 0.00 0.00 0.00 4.01
1052 1129 4.516195 GCTCGGGCGACTCCTTCC 62.516 72.222 0.00 0.00 34.39 3.46
1060 1137 2.284798 GACTTCTCATGCTCGGGCGA 62.285 60.000 1.14 0.00 42.25 5.54
1069 1146 2.169789 CGCTGGCCGACTTCTCATG 61.170 63.158 0.00 0.00 40.02 3.07
1072 1149 2.048127 AACGCTGGCCGACTTCTC 60.048 61.111 0.00 0.00 41.02 2.87
1086 1163 1.732732 CGGACAAGTAGCCTCTCAACG 60.733 57.143 0.00 0.00 0.00 4.10
1089 1166 1.544691 GTTCGGACAAGTAGCCTCTCA 59.455 52.381 0.00 0.00 0.00 3.27
1095 1172 1.873698 TTGTGGTTCGGACAAGTAGC 58.126 50.000 0.00 0.00 0.00 3.58
1098 1175 2.718563 AGTTTTGTGGTTCGGACAAGT 58.281 42.857 0.00 0.00 34.85 3.16
1104 1181 2.683867 TGTGGTAAGTTTTGTGGTTCGG 59.316 45.455 0.00 0.00 0.00 4.30
1107 1184 5.125900 GGTAACTGTGGTAAGTTTTGTGGTT 59.874 40.000 0.00 0.00 40.77 3.67
1125 1202 3.583086 ACCTGTACAGCTTGATGGTAACT 59.417 43.478 17.86 0.00 37.61 2.24
1189 1270 7.710676 ACTAGTTGAACTACTCATGAGTCAT 57.289 36.000 31.09 17.74 42.54 3.06
1220 1510 6.452244 ACAAATTTTAACTCTGCGCATTTC 57.548 33.333 12.24 0.00 0.00 2.17
1306 1597 9.665719 AACAAGAAAATAATTGGTCAAACAACT 57.334 25.926 0.00 0.00 32.39 3.16
1328 1713 7.946207 TCAGCATCCAATTGTAAAGTAAACAA 58.054 30.769 4.43 0.00 40.85 2.83
1343 1734 8.529424 AAATTCTTATCAGATTCAGCATCCAA 57.471 30.769 0.00 0.00 31.20 3.53
1345 1736 9.282569 AGTAAATTCTTATCAGATTCAGCATCC 57.717 33.333 0.00 0.00 31.20 3.51
1369 1766 3.668447 AGAACTCATCATTTGTCGCAGT 58.332 40.909 0.00 0.00 0.00 4.40
1370 1767 4.675190 AAGAACTCATCATTTGTCGCAG 57.325 40.909 0.00 0.00 0.00 5.18
1444 2047 8.675705 ATTGAAAGGGTGAATTCGAAATTTTT 57.324 26.923 0.00 0.00 0.00 1.94
1450 2053 5.534654 ACTCAATTGAAAGGGTGAATTCGAA 59.465 36.000 9.88 0.00 0.00 3.71
1456 2059 4.580167 CACTCACTCAATTGAAAGGGTGAA 59.420 41.667 24.94 12.45 33.67 3.18
1458 2061 3.254166 CCACTCACTCAATTGAAAGGGTG 59.746 47.826 23.35 23.35 32.43 4.61
1459 2062 3.490348 CCACTCACTCAATTGAAAGGGT 58.510 45.455 9.88 7.97 0.00 4.34
1462 2071 4.214971 CACTCCCACTCACTCAATTGAAAG 59.785 45.833 9.88 9.64 0.00 2.62
1466 2075 1.808945 GCACTCCCACTCACTCAATTG 59.191 52.381 0.00 0.00 0.00 2.32
1477 2086 7.376615 AGTAATATTTCTATACGCACTCCCAC 58.623 38.462 0.00 0.00 0.00 4.61
1479 2088 7.828712 AGAGTAATATTTCTATACGCACTCCC 58.171 38.462 0.00 0.00 32.25 4.30
1506 2130 9.703892 CCACTTTGTCATTTTCCACATAATTTA 57.296 29.630 0.00 0.00 0.00 1.40
1539 2198 0.388659 GCCTGCAACAAACACCATGA 59.611 50.000 0.00 0.00 0.00 3.07
1548 2207 1.891919 GACCACGAGCCTGCAACAA 60.892 57.895 0.00 0.00 0.00 2.83
1549 2208 2.280797 GACCACGAGCCTGCAACA 60.281 61.111 0.00 0.00 0.00 3.33
1550 2209 1.166531 AAAGACCACGAGCCTGCAAC 61.167 55.000 0.00 0.00 0.00 4.17
1561 2220 3.334691 TGATCATCCGAACAAAGACCAC 58.665 45.455 0.00 0.00 0.00 4.16
1580 2239 3.385193 TGAAGAACAGCACGAAGATGA 57.615 42.857 5.02 0.00 0.00 2.92
1683 2342 3.394836 AGGGCGAACCAGAGCTCC 61.395 66.667 10.93 0.00 43.89 4.70
1786 2445 2.853159 TGACGAACACATCCATGGC 58.147 52.632 6.96 0.00 0.00 4.40
1950 2609 2.512515 CTAGCGAACCAGGCAGCC 60.513 66.667 1.84 1.84 0.00 4.85
1965 2624 0.830444 AGAACGGCACCCACAGTCTA 60.830 55.000 0.00 0.00 0.00 2.59
2206 2865 1.737838 TCAACAACTCCGGCATGATC 58.262 50.000 0.00 0.00 0.00 2.92
2256 2915 2.945398 GATCACTGACGCCGAGCTCC 62.945 65.000 8.47 0.00 0.00 4.70
2316 2975 1.449601 CTCCCGGCACATGTACACC 60.450 63.158 0.00 0.00 0.00 4.16
2565 3224 2.329614 GCGGTTGTGGTTGGCGTAT 61.330 57.895 0.00 0.00 0.00 3.06
2736 3398 1.311859 CAAACTTGTCAGCCTCTGCA 58.688 50.000 0.00 0.00 41.13 4.41
2737 3399 0.595095 CCAAACTTGTCAGCCTCTGC 59.405 55.000 0.00 0.00 37.95 4.26
2807 3469 0.321653 GGTGTTCCATTGCTCCGACT 60.322 55.000 0.00 0.00 0.00 4.18
3384 4049 4.680237 TGCTCGTTCCGCCACCAG 62.680 66.667 0.00 0.00 0.00 4.00
3525 4190 1.990563 CTGTCTTTTACTACACCGCCG 59.009 52.381 0.00 0.00 0.00 6.46
3642 4308 1.900545 CTTTCCTCCACCGTCCCTCC 61.901 65.000 0.00 0.00 0.00 4.30
3715 4381 2.204029 ACCAAGGGCGAAGGGGTA 60.204 61.111 0.00 0.00 0.00 3.69
3765 4431 0.718343 CTACGACAAGCAAGAGCAGC 59.282 55.000 0.00 0.00 45.49 5.25
3777 4443 5.239963 TGATAGAACTGTGAACACTACGACA 59.760 40.000 6.51 0.00 0.00 4.35
3833 4499 5.631119 AGTGGGCCAAATAACAGGTATATC 58.369 41.667 8.40 0.00 0.00 1.63
3838 4504 2.647802 ACTAGTGGGCCAAATAACAGGT 59.352 45.455 8.40 0.00 0.00 4.00
3909 4575 3.118075 TGAGTCAAATTATGGGCGGATGA 60.118 43.478 0.00 0.00 0.00 2.92
3911 4577 3.136443 TCTGAGTCAAATTATGGGCGGAT 59.864 43.478 0.00 0.00 0.00 4.18
3941 4607 4.757594 TGTGTTTACATACATCCGTACCC 58.242 43.478 0.00 0.00 0.00 3.69
3943 4609 9.910511 CTAAAATGTGTTTACATACATCCGTAC 57.089 33.333 0.00 0.00 46.54 3.67
3968 4634 8.061304 AGATATGATTTATCCAAACCCAACACT 58.939 33.333 0.00 0.00 0.00 3.55
3969 4635 8.237811 AGATATGATTTATCCAAACCCAACAC 57.762 34.615 0.00 0.00 0.00 3.32
3970 4636 9.573166 CTAGATATGATTTATCCAAACCCAACA 57.427 33.333 0.00 0.00 0.00 3.33
3971 4637 9.793259 TCTAGATATGATTTATCCAAACCCAAC 57.207 33.333 0.00 0.00 0.00 3.77
3995 4661 9.793259 TGTCCAATTAGTTGTCTTAGATTTTCT 57.207 29.630 0.00 0.00 33.36 2.52
3997 4663 9.793259 TCTGTCCAATTAGTTGTCTTAGATTTT 57.207 29.630 0.00 0.00 33.36 1.82
4027 4693 8.667463 GCCAACATGCAATTAACTTCAAATATT 58.333 29.630 0.00 0.00 0.00 1.28
4029 4695 7.117523 GTGCCAACATGCAATTAACTTCAAATA 59.882 33.333 0.00 0.00 44.11 1.40
4030 4696 5.996513 TGCCAACATGCAATTAACTTCAAAT 59.003 32.000 0.00 0.00 38.56 2.32
4032 4698 4.749099 GTGCCAACATGCAATTAACTTCAA 59.251 37.500 0.00 0.00 44.11 2.69
4042 4708 0.757512 ATTGTGGTGCCAACATGCAA 59.242 45.000 0.00 0.00 44.11 4.08
4047 4713 0.397675 TCCCAATTGTGGTGCCAACA 60.398 50.000 4.43 0.00 44.30 3.33
4053 4719 3.658757 ATTCGTTTCCCAATTGTGGTG 57.341 42.857 4.43 0.00 44.30 4.17
4055 4721 3.244044 ACCAATTCGTTTCCCAATTGTGG 60.244 43.478 4.43 5.70 45.53 4.17
4058 4724 4.021894 TGGTACCAATTCGTTTCCCAATTG 60.022 41.667 13.60 0.00 38.98 2.32
4060 4726 3.508402 GTGGTACCAATTCGTTTCCCAAT 59.492 43.478 18.31 0.00 0.00 3.16
4062 4728 2.106857 AGTGGTACCAATTCGTTTCCCA 59.893 45.455 18.31 0.00 0.00 4.37
4064 4730 4.542735 CAAAGTGGTACCAATTCGTTTCC 58.457 43.478 26.51 6.65 32.85 3.13
4071 4743 4.394439 AAAACGCAAAGTGGTACCAATT 57.606 36.364 21.50 21.50 35.67 2.32
4094 4766 6.318648 GCCCAGACTTGATATTGACATGTAAA 59.681 38.462 0.00 0.00 0.00 2.01
4095 4767 5.822519 GCCCAGACTTGATATTGACATGTAA 59.177 40.000 0.00 0.00 0.00 2.41
4097 4769 4.202441 GCCCAGACTTGATATTGACATGT 58.798 43.478 0.00 0.00 0.00 3.21
4098 4770 4.201657 TGCCCAGACTTGATATTGACATG 58.798 43.478 0.00 0.00 0.00 3.21
4099 4771 4.164796 TCTGCCCAGACTTGATATTGACAT 59.835 41.667 0.00 0.00 31.41 3.06
4100 4772 3.519107 TCTGCCCAGACTTGATATTGACA 59.481 43.478 0.00 0.00 31.41 3.58
4113 4785 0.759959 TTTGTTACGGTCTGCCCAGA 59.240 50.000 0.00 0.00 34.56 3.86
4114 4786 1.821216 ATTTGTTACGGTCTGCCCAG 58.179 50.000 0.00 0.00 0.00 4.45
4115 4787 1.883275 CAATTTGTTACGGTCTGCCCA 59.117 47.619 0.00 0.00 0.00 5.36
4117 4789 2.414161 GCTCAATTTGTTACGGTCTGCC 60.414 50.000 0.00 0.00 0.00 4.85
4119 4791 5.856126 TTAGCTCAATTTGTTACGGTCTG 57.144 39.130 0.00 0.00 0.00 3.51
4120 4792 5.180680 GGTTTAGCTCAATTTGTTACGGTCT 59.819 40.000 0.00 0.00 0.00 3.85
4121 4793 5.180680 AGGTTTAGCTCAATTTGTTACGGTC 59.819 40.000 0.00 0.00 0.00 4.79
4122 4794 5.067954 AGGTTTAGCTCAATTTGTTACGGT 58.932 37.500 0.00 0.00 0.00 4.83
4123 4795 5.622770 AGGTTTAGCTCAATTTGTTACGG 57.377 39.130 0.00 0.00 0.00 4.02
4124 4796 6.435428 ACAAGGTTTAGCTCAATTTGTTACG 58.565 36.000 0.00 0.00 0.00 3.18
4128 4800 9.908152 GTTTATACAAGGTTTAGCTCAATTTGT 57.092 29.630 14.14 14.14 0.00 2.83
4129 4801 9.353999 GGTTTATACAAGGTTTAGCTCAATTTG 57.646 33.333 0.00 0.00 0.00 2.32
4142 4814 6.210584 CCTGTCAAAATGGGTTTATACAAGGT 59.789 38.462 0.00 0.00 0.00 3.50
4146 4818 5.893500 TCCCTGTCAAAATGGGTTTATACA 58.106 37.500 0.00 0.00 41.58 2.29
4165 4837 0.995024 CCCTGGTCATCAGTTTCCCT 59.005 55.000 0.00 0.00 41.83 4.20
4168 4840 0.681243 GGGCCCTGGTCATCAGTTTC 60.681 60.000 17.04 0.00 41.83 2.78
4172 4844 1.225704 GAAGGGCCCTGGTCATCAG 59.774 63.158 29.50 0.00 43.00 2.90
4173 4845 2.308722 GGAAGGGCCCTGGTCATCA 61.309 63.158 29.50 0.00 0.00 3.07
4174 4846 1.575447 AAGGAAGGGCCCTGGTCATC 61.575 60.000 29.50 19.18 36.49 2.92
4175 4847 1.544917 AAGGAAGGGCCCTGGTCAT 60.545 57.895 29.50 16.03 36.49 3.06
4176 4848 2.121506 AAGGAAGGGCCCTGGTCA 60.122 61.111 29.50 0.00 36.49 4.02
4177 4849 2.677848 GAAGGAAGGGCCCTGGTC 59.322 66.667 29.50 20.88 36.49 4.02
4178 4850 2.941583 GGAAGGAAGGGCCCTGGT 60.942 66.667 29.50 11.49 36.49 4.00
4181 4853 1.085605 ATGAGGAAGGAAGGGCCCT 59.914 57.895 22.28 22.28 38.42 5.19
4184 4856 2.095461 GAAACATGAGGAAGGAAGGGC 58.905 52.381 0.00 0.00 0.00 5.19
4187 4859 4.822026 AGTACGAAACATGAGGAAGGAAG 58.178 43.478 0.00 0.00 0.00 3.46
4188 4860 4.884668 AGTACGAAACATGAGGAAGGAA 57.115 40.909 0.00 0.00 0.00 3.36
4203 5074 1.914108 TGAGGAGGAGGAGAAGTACGA 59.086 52.381 0.00 0.00 0.00 3.43
4205 5076 3.053917 AGACTGAGGAGGAGGAGAAGTAC 60.054 52.174 0.00 0.00 0.00 2.73
4207 5078 2.000048 AGACTGAGGAGGAGGAGAAGT 59.000 52.381 0.00 0.00 0.00 3.01
4211 5082 0.465460 CCGAGACTGAGGAGGAGGAG 60.465 65.000 0.00 0.00 0.00 3.69
4224 5095 3.442273 ACAGAAAGATGAGAGACCGAGAC 59.558 47.826 0.00 0.00 0.00 3.36
4227 5098 3.691575 AGACAGAAAGATGAGAGACCGA 58.308 45.455 0.00 0.00 0.00 4.69
4228 5099 3.694072 AGAGACAGAAAGATGAGAGACCG 59.306 47.826 0.00 0.00 0.00 4.79
4229 5100 4.097892 GGAGAGACAGAAAGATGAGAGACC 59.902 50.000 0.00 0.00 0.00 3.85
4232 5103 3.066621 CGGGAGAGACAGAAAGATGAGAG 59.933 52.174 0.00 0.00 0.00 3.20
4241 5112 1.118965 TTGCACCGGGAGAGACAGAA 61.119 55.000 6.32 0.00 0.00 3.02
4242 5113 1.533033 TTGCACCGGGAGAGACAGA 60.533 57.895 6.32 0.00 0.00 3.41
4252 5123 1.002134 ATGGAGGTTCTTGCACCGG 60.002 57.895 0.00 0.00 42.33 5.28
4253 5124 1.308069 CCATGGAGGTTCTTGCACCG 61.308 60.000 5.56 0.00 42.33 4.94
4254 5125 0.038166 TCCATGGAGGTTCTTGCACC 59.962 55.000 11.44 0.00 39.02 5.01
4274 5145 4.344865 GGGGAGCTTGGGCGTTCA 62.345 66.667 0.00 0.00 44.37 3.18
4283 5154 2.330924 GATTAGCGGCAGGGGAGCTT 62.331 60.000 1.45 0.00 41.88 3.74
4292 5163 2.202878 GCGTCCAGATTAGCGGCA 60.203 61.111 1.45 0.00 0.00 5.69
4295 5166 0.946221 GGATGGCGTCCAGATTAGCG 60.946 60.000 20.92 0.00 46.96 4.26
4309 5180 0.321298 AGGGTTTCGACAACGGATGG 60.321 55.000 0.00 0.00 40.21 3.51
4311 5182 1.519408 CAAGGGTTTCGACAACGGAT 58.481 50.000 0.00 0.00 40.21 4.18
4316 5187 0.821711 CAGCCCAAGGGTTTCGACAA 60.822 55.000 7.05 0.00 37.65 3.18
4317 5188 1.228124 CAGCCCAAGGGTTTCGACA 60.228 57.895 7.05 0.00 37.65 4.35
4318 5189 2.626780 GCAGCCCAAGGGTTTCGAC 61.627 63.158 7.05 0.00 37.65 4.20
4319 5190 2.282180 GCAGCCCAAGGGTTTCGA 60.282 61.111 7.05 0.00 37.65 3.71
4322 5193 3.897122 TCGGCAGCCCAAGGGTTT 61.897 61.111 5.63 0.00 37.65 3.27
4331 5202 4.899239 CGGATCTGGTCGGCAGCC 62.899 72.222 0.00 0.00 0.00 4.85
4362 5234 1.048601 TAGCGGGAATGGACAGATCC 58.951 55.000 0.00 0.00 46.48 3.36
4363 5235 1.270358 GGTAGCGGGAATGGACAGATC 60.270 57.143 0.00 0.00 0.00 2.75
4367 5239 2.372074 GGGGTAGCGGGAATGGACA 61.372 63.158 0.00 0.00 0.00 4.02
4369 5241 2.041430 TGGGGTAGCGGGAATGGA 59.959 61.111 0.00 0.00 0.00 3.41
4376 5248 0.175073 GTACAAGTCTGGGGTAGCGG 59.825 60.000 0.00 0.00 0.00 5.52
4378 5250 2.094130 GTCAGTACAAGTCTGGGGTAGC 60.094 54.545 0.00 0.00 34.15 3.58
4381 5253 2.097110 TGTCAGTACAAGTCTGGGGT 57.903 50.000 0.00 0.00 34.15 4.95
4385 5257 7.482654 TTTTCTTCATGTCAGTACAAGTCTG 57.517 36.000 0.00 0.00 39.58 3.51
4421 5572 5.088026 AGGGCTAGGATAGAGAATTGGTAC 58.912 45.833 0.00 0.00 42.77 3.34
4425 5576 9.829507 CATAATTAGGGCTAGGATAGAGAATTG 57.170 37.037 0.00 0.00 42.77 2.32
4431 5582 7.130775 GGTACCATAATTAGGGCTAGGATAGA 58.869 42.308 15.97 0.00 42.77 1.98
4435 5594 5.095903 TGGTACCATAATTAGGGCTAGGA 57.904 43.478 15.97 0.00 0.00 2.94
4442 5601 6.707440 TTGCATGTTGGTACCATAATTAGG 57.293 37.500 17.17 3.74 0.00 2.69
4497 5656 4.696455 TGAAGAATTATCAGCTCATCGCA 58.304 39.130 0.00 0.00 42.61 5.10
4498 5657 5.178996 ACATGAAGAATTATCAGCTCATCGC 59.821 40.000 0.00 0.00 39.57 4.58
4508 5667 6.483640 AGAAAGCCCGTACATGAAGAATTATC 59.516 38.462 0.00 0.00 0.00 1.75
4546 5705 2.700897 ACGTTGATCCTGGCTAATAGCT 59.299 45.455 12.41 0.00 41.99 3.32
4551 5710 3.270027 CATTGACGTTGATCCTGGCTAA 58.730 45.455 0.00 0.00 0.00 3.09
4552 5711 2.905075 CATTGACGTTGATCCTGGCTA 58.095 47.619 0.00 0.00 0.00 3.93
4564 5723 7.116948 GCAATGAGTTAGATATAGCATTGACGT 59.883 37.037 15.17 0.00 42.99 4.34
4567 5726 8.907222 TTGCAATGAGTTAGATATAGCATTGA 57.093 30.769 15.17 1.23 42.99 2.57
4568 5727 8.781196 ACTTGCAATGAGTTAGATATAGCATTG 58.219 33.333 0.00 0.00 43.12 2.82
4569 5728 8.915057 ACTTGCAATGAGTTAGATATAGCATT 57.085 30.769 0.00 0.00 0.00 3.56
4571 5730 7.254898 GCAACTTGCAATGAGTTAGATATAGCA 60.255 37.037 8.97 0.00 44.26 3.49
4572 5731 7.074502 GCAACTTGCAATGAGTTAGATATAGC 58.925 38.462 8.97 0.00 44.26 2.97
4589 5748 4.334759 AGATGAGTATGATGTGCAACTTGC 59.665 41.667 6.82 6.82 45.29 4.01
4590 5749 7.725818 ATAGATGAGTATGATGTGCAACTTG 57.274 36.000 0.00 0.00 38.04 3.16
4591 5750 8.646004 ACTATAGATGAGTATGATGTGCAACTT 58.354 33.333 6.78 0.00 38.04 2.66
4592 5751 8.187913 ACTATAGATGAGTATGATGTGCAACT 57.812 34.615 6.78 0.00 38.04 3.16
4593 5752 8.706936 CAACTATAGATGAGTATGATGTGCAAC 58.293 37.037 6.78 0.00 37.35 4.17
4594 5753 7.386025 GCAACTATAGATGAGTATGATGTGCAA 59.614 37.037 13.76 0.00 0.00 4.08
4597 5756 6.034363 GCGCAACTATAGATGAGTATGATGTG 59.966 42.308 13.76 0.00 0.00 3.21
4600 5759 5.655488 GGCGCAACTATAGATGAGTATGAT 58.345 41.667 10.83 0.00 0.00 2.45
4603 5762 3.673594 GCGGCGCAACTATAGATGAGTAT 60.674 47.826 29.21 0.00 0.00 2.12
4624 5783 0.886490 ATGTTAGGCTAGCCATGCGC 60.886 55.000 34.70 19.17 38.92 6.09
4625 5784 1.265095 CAATGTTAGGCTAGCCATGCG 59.735 52.381 34.70 12.67 38.92 4.73
4633 5792 7.149202 AGAAATATCACCCAATGTTAGGCTA 57.851 36.000 0.00 0.00 0.00 3.93
4634 5793 6.018433 AGAAATATCACCCAATGTTAGGCT 57.982 37.500 0.00 0.00 0.00 4.58
4636 5795 6.605119 AGGAGAAATATCACCCAATGTTAGG 58.395 40.000 0.00 0.00 37.03 2.69
4662 5821 1.804326 CAACCGGAGCTACGAACCG 60.804 63.158 22.92 12.33 45.24 4.44
4664 5823 1.458445 GAAACAACCGGAGCTACGAAC 59.542 52.381 22.92 0.00 35.47 3.95
4668 5827 1.270678 ACAGGAAACAACCGGAGCTAC 60.271 52.381 9.46 0.00 34.73 3.58
4669 5828 1.053424 ACAGGAAACAACCGGAGCTA 58.947 50.000 9.46 0.00 34.73 3.32
4671 5830 1.515521 CCACAGGAAACAACCGGAGC 61.516 60.000 9.46 0.00 34.73 4.70
4674 5833 1.107945 AAACCACAGGAAACAACCGG 58.892 50.000 0.00 0.00 34.73 5.28
4675 5834 2.425668 AGAAAACCACAGGAAACAACCG 59.574 45.455 0.00 0.00 34.73 4.44
4677 5836 6.040247 CCTAAAGAAAACCACAGGAAACAAC 58.960 40.000 0.00 0.00 0.00 3.32
4680 5840 5.847111 ACCTAAAGAAAACCACAGGAAAC 57.153 39.130 0.00 0.00 0.00 2.78
4683 5843 6.192044 AGAAAACCTAAAGAAAACCACAGGA 58.808 36.000 0.00 0.00 0.00 3.86
4706 5866 8.507249 CAAAACAGATAAACTTAGTTCCTGGAG 58.493 37.037 18.76 5.13 0.00 3.86
4708 5868 8.166422 ACAAAACAGATAAACTTAGTTCCTGG 57.834 34.615 18.76 0.00 0.00 4.45
4709 5869 9.450807 CAACAAAACAGATAAACTTAGTTCCTG 57.549 33.333 15.40 15.40 0.00 3.86
4710 5870 9.185680 ACAACAAAACAGATAAACTTAGTTCCT 57.814 29.630 0.00 0.00 0.00 3.36
4711 5871 9.797556 AACAACAAAACAGATAAACTTAGTTCC 57.202 29.630 0.00 0.00 0.00 3.62
4751 5912 8.232513 CGAGAGAAGAAACAAATGATCAATTGA 58.767 33.333 26.44 11.26 0.00 2.57
4752 5913 7.008086 GCGAGAGAAGAAACAAATGATCAATTG 59.992 37.037 19.71 19.71 0.00 2.32
4753 5914 7.025963 GCGAGAGAAGAAACAAATGATCAATT 58.974 34.615 0.00 0.00 0.00 2.32
4754 5915 6.404074 GGCGAGAGAAGAAACAAATGATCAAT 60.404 38.462 0.00 0.00 0.00 2.57
4755 5916 5.106555 GGCGAGAGAAGAAACAAATGATCAA 60.107 40.000 0.00 0.00 0.00 2.57
4757 5918 4.633565 AGGCGAGAGAAGAAACAAATGATC 59.366 41.667 0.00 0.00 0.00 2.92
4758 5919 4.583871 AGGCGAGAGAAGAAACAAATGAT 58.416 39.130 0.00 0.00 0.00 2.45
4762 5936 4.451900 AGAAAGGCGAGAGAAGAAACAAA 58.548 39.130 0.00 0.00 0.00 2.83
4768 5942 4.962155 AGAAAAAGAAAGGCGAGAGAAGA 58.038 39.130 0.00 0.00 0.00 2.87
4770 5944 5.588648 TGAAAGAAAAAGAAAGGCGAGAGAA 59.411 36.000 0.00 0.00 0.00 2.87
4772 5946 5.208503 GTGAAAGAAAAAGAAAGGCGAGAG 58.791 41.667 0.00 0.00 0.00 3.20
4775 5949 3.697045 TGGTGAAAGAAAAAGAAAGGCGA 59.303 39.130 0.00 0.00 0.00 5.54
4776 5950 4.040445 TGGTGAAAGAAAAAGAAAGGCG 57.960 40.909 0.00 0.00 0.00 5.52


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

AutoCloner maintained by Alex Coulton.