Multiple sequence alignment - TraesCS4D01G223600

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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 TraesCS4D01G223600 chr4D 100.000 5629 0 0 1 5629 380448371 380453999 0.000000e+00 10395.0
1 TraesCS4D01G223600 chr4D 96.296 54 1 1 5482 5534 327379916 327379863 2.790000e-13 87.9
2 TraesCS4D01G223600 chr4B 89.070 5572 310 151 30 5466 467902063 467907470 0.000000e+00 6639.0
3 TraesCS4D01G223600 chr4B 90.600 3149 163 69 1 3118 467902046 467905092 0.000000e+00 4052.0
4 TraesCS4D01G223600 chr4B 91.026 78 5 2 5543 5619 476352672 476352748 2.770000e-18 104.0
5 TraesCS4D01G223600 chr4B 98.148 54 0 1 5482 5534 406678157 406678104 6.000000e-15 93.5
6 TraesCS4D01G223600 chr4A 93.779 3199 122 33 1743 4884 83357362 83354184 0.000000e+00 4734.0
7 TraesCS4D01G223600 chr4A 88.189 1524 89 45 1 1479 83359263 83357786 0.000000e+00 1733.0
8 TraesCS4D01G223600 chr4A 88.076 369 26 11 5144 5506 83353880 83353524 6.740000e-114 422.0
9 TraesCS4D01G223600 chr4A 93.590 234 13 2 1490 1721 83357738 83357505 1.160000e-91 348.0
10 TraesCS4D01G223600 chr4A 98.148 54 0 1 5482 5534 143701111 143701164 6.000000e-15 93.5
11 TraesCS4D01G223600 chr6D 91.026 78 6 1 5543 5619 131608735 131608812 2.770000e-18 104.0
12 TraesCS4D01G223600 chr7D 89.873 79 6 2 5543 5619 428711374 428711452 3.590000e-17 100.0
13 TraesCS4D01G223600 chr7D 88.462 78 8 1 5543 5619 439473087 439473010 6.000000e-15 93.5
14 TraesCS4D01G223600 chr6B 89.610 77 6 2 5543 5617 228975197 228975273 4.640000e-16 97.1
15 TraesCS4D01G223600 chr1D 89.610 77 6 2 5543 5617 343883228 343883152 4.640000e-16 97.1
16 TraesCS4D01G223600 chr2D 89.474 76 7 1 5545 5619 23479848 23479773 1.670000e-15 95.3
17 TraesCS4D01G223600 chr2D 88.608 79 6 2 5543 5619 216331326 216331249 6.000000e-15 93.5
18 TraesCS4D01G223600 chr3A 88.462 78 8 1 5543 5619 551412074 551411997 6.000000e-15 93.5
19 TraesCS4D01G223600 chr2B 96.154 52 2 0 5483 5534 389368710 389368659 1.000000e-12 86.1
20 TraesCS4D01G223600 chr5D 94.340 53 3 0 5482 5534 281011458 281011406 1.300000e-11 82.4
21 TraesCS4D01G223600 chr5D 94.231 52 3 0 5483 5534 340530861 340530912 4.670000e-11 80.5
22 TraesCS4D01G223600 chr1B 94.340 53 3 0 5482 5534 338419148 338419096 1.300000e-11 82.4
23 TraesCS4D01G223600 chr7B 95.918 49 2 0 5486 5534 354632346 354632298 4.670000e-11 80.5


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS4D01G223600 chr4D 380448371 380453999 5628 False 10395.00 10395 100.0000 1 5629 1 chr4D.!!$F1 5628
1 TraesCS4D01G223600 chr4B 467902046 467907470 5424 False 5345.50 6639 89.8350 1 5466 2 chr4B.!!$F2 5465
2 TraesCS4D01G223600 chr4A 83353524 83359263 5739 True 1809.25 4734 90.9085 1 5506 4 chr4A.!!$R1 5505

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
689 729 0.249398 CGGGGTGGTTAGAGTCCAAG 59.751 60.0 0.00 0.0 36.68 3.61 F
1121 1194 0.168128 CGGTTTGGAAACTGATCCGC 59.832 55.0 5.29 0.0 45.87 5.54 F
2485 2729 0.110688 CCAGCGATGTTGTTGTCGTG 60.111 55.0 0.00 0.0 39.87 4.35 F
2603 2847 0.178767 TCCTCAGGTGCGAATCATGG 59.821 55.0 0.00 0.0 0.00 3.66 F
3794 4078 0.898320 AGCGCTGAAGTACCATCTGT 59.102 50.0 10.39 0.0 0.00 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1896 2137 0.605589 AGCCGAAAACCAGCCTACAC 60.606 55.000 0.0 0.0 0.00 2.90 R
2657 2901 0.663153 GCATTAACATCGCCAGGGTC 59.337 55.000 0.0 0.0 0.00 4.46 R
4335 4637 0.109532 TCATCGGGTTTTGCTGTGGA 59.890 50.000 0.0 0.0 0.00 4.02 R
4410 4712 2.191908 TGGCACAACGGCTTCAGT 59.808 55.556 0.0 0.0 41.89 3.41 R
5177 5622 0.033601 TCAAAGTGGTGGTGTTGGCT 60.034 50.000 0.0 0.0 0.00 4.75 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
70 78 0.682209 GGGCTCACCTGCATGTCATT 60.682 55.000 0.00 0.00 35.85 2.57
86 94 1.079127 ATTTCGACGGAGCCTGTGG 60.079 57.895 0.00 0.00 0.00 4.17
101 114 1.001048 CTGTGGTGTGTTGCTTGGATG 60.001 52.381 0.00 0.00 0.00 3.51
102 115 1.032014 GTGGTGTGTTGCTTGGATGT 58.968 50.000 0.00 0.00 0.00 3.06
104 117 1.408340 TGGTGTGTTGCTTGGATGTTG 59.592 47.619 0.00 0.00 0.00 3.33
105 118 1.269726 GGTGTGTTGCTTGGATGTTGG 60.270 52.381 0.00 0.00 0.00 3.77
106 119 1.680735 GTGTGTTGCTTGGATGTTGGA 59.319 47.619 0.00 0.00 0.00 3.53
107 120 2.297033 GTGTGTTGCTTGGATGTTGGAT 59.703 45.455 0.00 0.00 0.00 3.41
108 121 2.557924 TGTGTTGCTTGGATGTTGGATC 59.442 45.455 0.00 0.00 0.00 3.36
109 122 2.094545 GTGTTGCTTGGATGTTGGATCC 60.095 50.000 4.20 4.20 38.66 3.36
110 123 2.225091 TGTTGCTTGGATGTTGGATCCT 60.225 45.455 14.23 0.00 38.95 3.24
111 124 3.010027 TGTTGCTTGGATGTTGGATCCTA 59.990 43.478 14.23 1.56 38.95 2.94
112 125 4.210331 GTTGCTTGGATGTTGGATCCTAT 58.790 43.478 14.23 4.87 38.95 2.57
113 126 3.824133 TGCTTGGATGTTGGATCCTATG 58.176 45.455 14.23 0.00 38.95 2.23
114 127 2.555757 GCTTGGATGTTGGATCCTATGC 59.444 50.000 14.23 10.51 38.95 3.14
115 128 3.824133 CTTGGATGTTGGATCCTATGCA 58.176 45.455 14.23 12.89 38.95 3.96
116 129 3.949586 TGGATGTTGGATCCTATGCAA 57.050 42.857 14.23 0.00 38.31 4.08
117 130 3.824133 TGGATGTTGGATCCTATGCAAG 58.176 45.455 14.23 0.00 41.35 4.01
135 148 3.730061 GCAAGGCTCACTCGATGAAATTG 60.730 47.826 0.00 0.00 36.69 2.32
136 149 3.616956 AGGCTCACTCGATGAAATTGA 57.383 42.857 0.00 0.00 36.69 2.57
137 150 4.148128 AGGCTCACTCGATGAAATTGAT 57.852 40.909 0.00 0.00 35.83 2.57
140 153 5.032863 GGCTCACTCGATGAAATTGATTTG 58.967 41.667 0.00 0.00 35.83 2.32
141 154 4.498323 GCTCACTCGATGAAATTGATTTGC 59.502 41.667 0.00 0.00 35.83 3.68
143 156 6.258230 TCACTCGATGAAATTGATTTGCTT 57.742 33.333 0.00 0.00 35.83 3.91
146 159 5.346822 ACTCGATGAAATTGATTTGCTTTGC 59.653 36.000 0.00 0.00 35.83 3.68
147 160 5.472148 TCGATGAAATTGATTTGCTTTGCT 58.528 33.333 0.00 0.00 29.84 3.91
148 161 5.927689 TCGATGAAATTGATTTGCTTTGCTT 59.072 32.000 0.00 0.00 29.84 3.91
149 162 6.424509 TCGATGAAATTGATTTGCTTTGCTTT 59.575 30.769 0.00 0.00 29.84 3.51
150 163 7.598118 TCGATGAAATTGATTTGCTTTGCTTTA 59.402 29.630 0.00 0.00 29.84 1.85
151 164 8.385111 CGATGAAATTGATTTGCTTTGCTTTAT 58.615 29.630 0.00 0.00 0.00 1.40
152 165 9.485591 GATGAAATTGATTTGCTTTGCTTTATG 57.514 29.630 0.00 0.00 0.00 1.90
154 167 7.444792 TGAAATTGATTTGCTTTGCTTTATGGT 59.555 29.630 0.00 0.00 0.00 3.55
155 168 8.845413 AAATTGATTTGCTTTGCTTTATGGTA 57.155 26.923 0.00 0.00 0.00 3.25
156 169 7.832503 ATTGATTTGCTTTGCTTTATGGTAC 57.167 32.000 0.00 0.00 0.00 3.34
196 219 5.069648 TCGAGAGCCTCATCTGAATAATTGT 59.930 40.000 0.00 0.00 0.00 2.71
255 278 4.537945 TCCATGCTACTACTAAGTCCCT 57.462 45.455 0.00 0.00 37.15 4.20
259 282 5.221342 CCATGCTACTACTAAGTCCCTGAAG 60.221 48.000 0.00 0.00 37.15 3.02
336 369 5.957220 GCAAACCAAAACGACATTTTCTTTC 59.043 36.000 0.00 0.00 38.50 2.62
377 411 7.532209 GCTTTTCTTGATTTCGACAGAGTTTAG 59.468 37.037 0.00 0.00 0.00 1.85
471 505 5.831702 ACGGTAGCATATACTATACCAGC 57.168 43.478 8.87 0.00 38.04 4.85
474 508 6.039493 ACGGTAGCATATACTATACCAGCATC 59.961 42.308 8.87 0.00 38.04 3.91
516 556 5.163513 CAGCGTTGAAAATTCCTGCTTATT 58.836 37.500 0.00 0.00 0.00 1.40
517 557 6.072175 ACAGCGTTGAAAATTCCTGCTTATTA 60.072 34.615 6.16 0.00 0.00 0.98
518 558 6.470235 CAGCGTTGAAAATTCCTGCTTATTAG 59.530 38.462 0.00 0.00 0.00 1.73
519 559 6.151144 AGCGTTGAAAATTCCTGCTTATTAGT 59.849 34.615 0.00 0.00 0.00 2.24
520 560 6.806739 GCGTTGAAAATTCCTGCTTATTAGTT 59.193 34.615 0.00 0.00 0.00 2.24
521 561 7.328493 GCGTTGAAAATTCCTGCTTATTAGTTT 59.672 33.333 0.00 0.00 0.00 2.66
561 601 7.889589 AAGAAAATAAAAGAAATCCCGCTTG 57.110 32.000 0.00 0.00 0.00 4.01
565 605 1.595093 AAAGAAATCCCGCTTGCCCG 61.595 55.000 0.00 0.00 0.00 6.13
644 684 8.803397 ATAGACCTGGTAAAATAAGGAAACAC 57.197 34.615 0.00 0.00 34.97 3.32
689 729 0.249398 CGGGGTGGTTAGAGTCCAAG 59.751 60.000 0.00 0.00 36.68 3.61
690 730 1.652947 GGGGTGGTTAGAGTCCAAGA 58.347 55.000 0.00 0.00 36.68 3.02
691 731 1.555533 GGGGTGGTTAGAGTCCAAGAG 59.444 57.143 0.00 0.00 36.68 2.85
692 732 1.555533 GGGTGGTTAGAGTCCAAGAGG 59.444 57.143 0.00 0.00 36.68 3.69
693 733 1.066071 GGTGGTTAGAGTCCAAGAGGC 60.066 57.143 0.00 0.00 36.68 4.70
694 734 0.895530 TGGTTAGAGTCCAAGAGGCG 59.104 55.000 0.00 0.00 33.74 5.52
695 735 1.183549 GGTTAGAGTCCAAGAGGCGA 58.816 55.000 0.00 0.00 33.74 5.54
696 736 1.135053 GGTTAGAGTCCAAGAGGCGAC 60.135 57.143 0.00 0.00 33.74 5.19
697 737 0.809385 TTAGAGTCCAAGAGGCGACG 59.191 55.000 0.00 0.00 34.10 5.12
698 738 1.654954 TAGAGTCCAAGAGGCGACGC 61.655 60.000 12.43 12.43 34.10 5.19
763 825 4.109675 CCCTCCCCGCATTCCGTT 62.110 66.667 0.00 0.00 34.38 4.44
1015 1082 1.152881 AAGATGATGGGCGGCTTCC 60.153 57.895 9.56 0.00 0.00 3.46
1102 1171 4.452114 GGTCCTGCCAAATTTGTCATTTTC 59.548 41.667 16.73 2.29 37.17 2.29
1105 1174 4.057432 CTGCCAAATTTGTCATTTTCGGT 58.943 39.130 16.73 0.00 0.00 4.69
1121 1194 0.168128 CGGTTTGGAAACTGATCCGC 59.832 55.000 5.29 0.00 45.87 5.54
1191 1271 4.973055 TCGGTTGGTGCCCGTTCG 62.973 66.667 0.00 0.00 45.63 3.95
1202 1282 4.148825 CCGTTCGGAGGGCTCAGG 62.149 72.222 5.19 0.00 0.00 3.86
1210 1290 1.075050 CGGAGGGCTCAGGGTACTATA 59.925 57.143 0.00 0.00 0.00 1.31
1213 1293 4.168883 GGAGGGCTCAGGGTACTATATTT 58.831 47.826 0.00 0.00 0.00 1.40
1214 1294 4.597940 GGAGGGCTCAGGGTACTATATTTT 59.402 45.833 0.00 0.00 0.00 1.82
1215 1295 5.513267 GGAGGGCTCAGGGTACTATATTTTG 60.513 48.000 0.00 0.00 0.00 2.44
1218 1298 5.531287 GGGCTCAGGGTACTATATTTTGTTG 59.469 44.000 0.00 0.00 0.00 3.33
1219 1299 5.008712 GGCTCAGGGTACTATATTTTGTTGC 59.991 44.000 0.00 0.00 0.00 4.17
1223 1303 9.391006 CTCAGGGTACTATATTTTGTTGCTTTA 57.609 33.333 0.00 0.00 0.00 1.85
1322 1402 4.493545 CCGGACGCATTCACAAGTTTATAC 60.494 45.833 0.00 0.00 0.00 1.47
1323 1403 4.574759 GGACGCATTCACAAGTTTATACG 58.425 43.478 0.00 0.00 0.00 3.06
1326 1406 6.183360 GGACGCATTCACAAGTTTATACGTAA 60.183 38.462 0.00 0.00 0.00 3.18
1372 1452 1.378646 TCGAGGTCGAGGAGCATGT 60.379 57.895 0.00 0.00 44.22 3.21
1423 1503 5.163854 CGGTCAAATGTTCTCTTCGCTTATT 60.164 40.000 0.00 0.00 0.00 1.40
1424 1504 6.251549 GGTCAAATGTTCTCTTCGCTTATTC 58.748 40.000 0.00 0.00 0.00 1.75
1427 1507 8.656849 GTCAAATGTTCTCTTCGCTTATTCTTA 58.343 33.333 0.00 0.00 0.00 2.10
1428 1508 9.383519 TCAAATGTTCTCTTCGCTTATTCTTAT 57.616 29.630 0.00 0.00 0.00 1.73
1431 1511 9.817809 AATGTTCTCTTCGCTTATTCTTATACA 57.182 29.630 0.00 0.00 0.00 2.29
1432 1512 8.858003 TGTTCTCTTCGCTTATTCTTATACAG 57.142 34.615 0.00 0.00 0.00 2.74
1481 1561 8.853077 ATTCTTGTCTGATAGTCAATTTCACA 57.147 30.769 0.00 0.00 0.00 3.58
1482 1562 7.658179 TCTTGTCTGATAGTCAATTTCACAC 57.342 36.000 0.00 0.00 0.00 3.82
1483 1563 6.366061 TCTTGTCTGATAGTCAATTTCACACG 59.634 38.462 0.00 0.00 0.00 4.49
1484 1564 5.538118 TGTCTGATAGTCAATTTCACACGT 58.462 37.500 0.00 0.00 0.00 4.49
1487 1567 5.408299 TCTGATAGTCAATTTCACACGTTGG 59.592 40.000 0.00 0.00 0.00 3.77
1538 1655 4.096382 GTCAAACTCACTTTTCAGGCTTGA 59.904 41.667 0.00 0.00 0.00 3.02
1540 1657 6.017109 GTCAAACTCACTTTTCAGGCTTGATA 60.017 38.462 0.00 0.00 32.27 2.15
1589 1707 1.737838 TGCATCCACCGACATCTTTC 58.262 50.000 0.00 0.00 0.00 2.62
1635 1753 3.924073 GCCTTGTTTGTTCGTGTTCTTTT 59.076 39.130 0.00 0.00 0.00 2.27
1647 1765 1.134848 TGTTCTTTTGTGCAAGTGCCC 60.135 47.619 0.00 0.00 41.18 5.36
1654 1773 1.112315 TGTGCAAGTGCCCCGAAAAT 61.112 50.000 0.00 0.00 41.18 1.82
1661 1781 1.353022 AGTGCCCCGAAAATTAGTCCA 59.647 47.619 0.00 0.00 0.00 4.02
1663 1783 2.357952 GTGCCCCGAAAATTAGTCCATC 59.642 50.000 0.00 0.00 0.00 3.51
1680 1800 1.115467 ATCGAAGGATGCCGAGAAGT 58.885 50.000 0.00 0.00 38.25 3.01
1708 1828 2.231964 TCAGTGCATCTTCAAAATGGCC 59.768 45.455 0.00 0.00 0.00 5.36
1844 2085 7.817478 CAGGGATATTATGTTTATAGCGTGTGA 59.183 37.037 0.00 0.00 0.00 3.58
1895 2136 7.281774 TGTTTTGGTGTTTGATGCACAATTTAT 59.718 29.630 0.00 0.00 38.36 1.40
1896 2137 6.782298 TTGGTGTTTGATGCACAATTTATG 57.218 33.333 0.00 0.00 38.36 1.90
2051 2295 5.165961 AGAAGTTCACAGCATTAGCCTAA 57.834 39.130 5.50 0.00 43.56 2.69
2062 2306 6.717084 ACAGCATTAGCCTAAGGGAATAATTC 59.283 38.462 0.00 0.00 43.56 2.17
2063 2307 6.716628 CAGCATTAGCCTAAGGGAATAATTCA 59.283 38.462 0.00 0.00 43.56 2.57
2187 2431 4.959596 TGCATTCTTTCATCAGCTCTTC 57.040 40.909 0.00 0.00 0.00 2.87
2188 2432 4.329392 TGCATTCTTTCATCAGCTCTTCA 58.671 39.130 0.00 0.00 0.00 3.02
2293 2537 2.727429 ACCCCAGGACAAAGGTACTA 57.273 50.000 0.00 0.00 35.42 1.82
2355 2599 9.665719 TCTGCACATTGAAGTATTTAACTGATA 57.334 29.630 0.00 0.00 38.88 2.15
2485 2729 0.110688 CCAGCGATGTTGTTGTCGTG 60.111 55.000 0.00 0.00 39.87 4.35
2603 2847 0.178767 TCCTCAGGTGCGAATCATGG 59.821 55.000 0.00 0.00 0.00 3.66
2619 2863 6.368791 CGAATCATGGGTACTGTATTATGGTG 59.631 42.308 0.00 0.00 0.00 4.17
2657 2901 9.590451 AGCTATTGAACCAATTGATGTATTTTG 57.410 29.630 7.12 0.00 35.54 2.44
2725 2969 3.403968 AGGCCTTTCTCGTTTTCTCTTC 58.596 45.455 0.00 0.00 0.00 2.87
2859 3103 3.763671 GTGTTTGGCACCCCTGAG 58.236 61.111 0.00 0.00 42.10 3.35
2878 3122 5.757320 CCTGAGATGTATTGCAGTTTAGGAG 59.243 44.000 0.00 0.00 0.00 3.69
3103 3348 4.270808 TGAATGCATACTGAACTACGCATG 59.729 41.667 0.00 0.00 39.84 4.06
3118 3363 3.956233 ACGCATGTGCATTTGACATATC 58.044 40.909 6.08 0.00 42.21 1.63
3584 3864 9.806203 TTCATTTGGAACTGCAATAGAAATATG 57.194 29.630 0.00 0.00 0.00 1.78
3637 3920 7.642669 ACAAATATATGTTCTCTGGCATTTCG 58.357 34.615 0.00 0.00 0.00 3.46
3770 4054 9.706691 ATATACTGTAATATGAAACGGAACCTG 57.293 33.333 0.00 0.00 0.00 4.00
3794 4078 0.898320 AGCGCTGAAGTACCATCTGT 59.102 50.000 10.39 0.00 0.00 3.41
3812 4096 6.763610 CCATCTGTAGTTAAACCTCAATCCTC 59.236 42.308 0.00 0.00 0.00 3.71
3951 4236 3.694072 TCTATGGCCGAAGATTGGTTTTG 59.306 43.478 0.00 0.00 0.00 2.44
3974 4259 7.169158 TGAATAAACTTGGGCTGATTTTAGG 57.831 36.000 0.00 0.00 0.00 2.69
4370 4672 4.378874 CCCGATGAGAAGACAAAGAAAAGC 60.379 45.833 0.00 0.00 0.00 3.51
4410 4712 2.607442 TAGTGCCTGCTCCAGCCA 60.607 61.111 0.00 0.00 41.18 4.75
4515 4817 3.825160 GACGTTGCTGTGGAGGGCA 62.825 63.158 0.00 0.00 36.62 5.36
4598 4900 3.205536 GCCAAGCTAAGGAGGCGC 61.206 66.667 9.21 0.00 37.41 6.53
4780 5086 3.135895 TCACCCGTTCCTTTCTTCTTTCT 59.864 43.478 0.00 0.00 0.00 2.52
4836 5142 5.298989 AGTTGTAAATATCACCGGGCATA 57.701 39.130 6.32 1.08 0.00 3.14
4867 5173 0.810648 ATTGTTGGCATGTGCTACGG 59.189 50.000 4.84 0.00 41.70 4.02
4940 5307 3.254657 AGTGTCTGTCTAGAGTCTGCAAC 59.745 47.826 1.86 0.00 32.48 4.17
4972 5339 6.545508 TGCATAATCGACATTCTTCTTGTTG 58.454 36.000 0.00 0.00 0.00 3.33
4974 5341 6.545508 CATAATCGACATTCTTCTTGTTGCA 58.454 36.000 0.00 0.00 0.00 4.08
4978 5345 8.437360 AATCGACATTCTTCTTGTTGCATATA 57.563 30.769 0.00 0.00 0.00 0.86
4980 5347 7.264947 TCGACATTCTTCTTGTTGCATATAGA 58.735 34.615 0.00 0.00 0.00 1.98
5009 5423 5.768164 GGACTTCTTGTTGGAAAAGGATGTA 59.232 40.000 0.00 0.00 0.00 2.29
5011 5425 5.241728 ACTTCTTGTTGGAAAAGGATGTAGC 59.758 40.000 0.00 0.00 0.00 3.58
5022 5436 3.819564 AGGATGTAGCGCATGTTCTTA 57.180 42.857 11.47 0.00 38.06 2.10
5026 5440 4.025647 GGATGTAGCGCATGTTCTTAGAAC 60.026 45.833 17.34 17.34 38.06 3.01
5027 5441 4.188247 TGTAGCGCATGTTCTTAGAACT 57.812 40.909 23.27 8.57 0.00 3.01
5028 5442 4.566004 TGTAGCGCATGTTCTTAGAACTT 58.434 39.130 23.27 15.65 0.00 2.66
5032 5446 5.479306 AGCGCATGTTCTTAGAACTTCTTA 58.521 37.500 23.27 5.70 0.00 2.10
5048 5462 8.548877 AGAACTTCTTATTGGAAATGGCTACTA 58.451 33.333 0.00 0.00 0.00 1.82
5060 5474 8.065007 TGGAAATGGCTACTAAAAAGGGATATT 58.935 33.333 0.00 0.00 0.00 1.28
5177 5622 7.771826 AGCACCAGAAGTAAAGTTTAGTGTTAA 59.228 33.333 3.71 0.00 0.00 2.01
5194 5639 2.429250 GTTAAGCCAACACCACCACTTT 59.571 45.455 0.00 0.00 37.09 2.66
5195 5640 0.823460 AAGCCAACACCACCACTTTG 59.177 50.000 0.00 0.00 0.00 2.77
5196 5641 0.033601 AGCCAACACCACCACTTTGA 60.034 50.000 0.00 0.00 0.00 2.69
5197 5642 0.385390 GCCAACACCACCACTTTGAG 59.615 55.000 0.00 0.00 0.00 3.02
5198 5643 1.032014 CCAACACCACCACTTTGAGG 58.968 55.000 0.00 0.00 0.00 3.86
5199 5644 1.409521 CCAACACCACCACTTTGAGGA 60.410 52.381 0.00 0.00 0.00 3.71
5200 5645 2.374184 CAACACCACCACTTTGAGGAA 58.626 47.619 0.00 0.00 0.00 3.36
5209 5654 4.821805 CACCACTTTGAGGAAGAAGCTTTA 59.178 41.667 0.00 0.00 38.77 1.85
5239 5684 0.966920 AGACGAACAATGGAGTCCGT 59.033 50.000 4.30 0.00 34.41 4.69
5252 5697 2.531206 GAGTCCGTCTGTATGCTTCAC 58.469 52.381 0.00 0.00 0.00 3.18
5253 5698 1.893137 AGTCCGTCTGTATGCTTCACA 59.107 47.619 0.00 0.00 0.00 3.58
5254 5699 2.299013 AGTCCGTCTGTATGCTTCACAA 59.701 45.455 0.00 0.00 0.00 3.33
5255 5700 3.055819 AGTCCGTCTGTATGCTTCACAAT 60.056 43.478 0.00 0.00 0.00 2.71
5256 5701 3.062639 GTCCGTCTGTATGCTTCACAATG 59.937 47.826 0.00 0.00 0.00 2.82
5257 5702 2.223112 CCGTCTGTATGCTTCACAATGC 60.223 50.000 0.00 0.00 0.00 3.56
5258 5703 2.674852 CGTCTGTATGCTTCACAATGCT 59.325 45.455 0.00 0.00 0.00 3.79
5466 5930 5.108385 AGTTCCATTGATGTTTCACGAAC 57.892 39.130 0.00 0.00 35.17 3.95
5478 5945 4.281435 TGTTTCACGAACAGGACCATACTA 59.719 41.667 0.00 0.00 43.13 1.82
5499 5966 6.116126 ACTAATGGAAGAGGATTTGTAGCAC 58.884 40.000 0.00 0.00 0.00 4.40
5523 5990 1.729586 GTGCTCCACCCCCTATATGA 58.270 55.000 0.00 0.00 0.00 2.15
5524 5991 2.054799 GTGCTCCACCCCCTATATGAA 58.945 52.381 0.00 0.00 0.00 2.57
5525 5992 2.054799 TGCTCCACCCCCTATATGAAC 58.945 52.381 0.00 0.00 0.00 3.18
5526 5993 2.054799 GCTCCACCCCCTATATGAACA 58.945 52.381 0.00 0.00 0.00 3.18
5527 5994 2.644798 GCTCCACCCCCTATATGAACAT 59.355 50.000 0.00 0.00 0.00 2.71
5528 5995 3.074538 GCTCCACCCCCTATATGAACATT 59.925 47.826 0.00 0.00 0.00 2.71
5529 5996 4.288626 GCTCCACCCCCTATATGAACATTA 59.711 45.833 0.00 0.00 0.00 1.90
5530 5997 5.222048 GCTCCACCCCCTATATGAACATTAA 60.222 44.000 0.00 0.00 0.00 1.40
5531 5998 6.448369 TCCACCCCCTATATGAACATTAAG 57.552 41.667 0.00 0.00 0.00 1.85
5532 5999 5.914716 TCCACCCCCTATATGAACATTAAGT 59.085 40.000 0.00 0.00 0.00 2.24
5533 6000 6.391649 TCCACCCCCTATATGAACATTAAGTT 59.608 38.462 0.00 0.00 44.93 2.66
5534 6001 7.066781 CCACCCCCTATATGAACATTAAGTTT 58.933 38.462 0.00 0.00 41.51 2.66
5535 6002 7.563556 CCACCCCCTATATGAACATTAAGTTTT 59.436 37.037 0.00 0.00 41.51 2.43
5536 6003 8.630037 CACCCCCTATATGAACATTAAGTTTTC 58.370 37.037 0.00 0.00 41.51 2.29
5537 6004 7.783119 ACCCCCTATATGAACATTAAGTTTTCC 59.217 37.037 0.00 0.00 41.51 3.13
5538 6005 7.232737 CCCCCTATATGAACATTAAGTTTTCCC 59.767 40.741 0.00 0.00 41.51 3.97
5539 6006 7.782644 CCCCTATATGAACATTAAGTTTTCCCA 59.217 37.037 0.00 0.00 41.51 4.37
5540 6007 9.196139 CCCTATATGAACATTAAGTTTTCCCAA 57.804 33.333 0.00 0.00 41.51 4.12
5550 6017 9.927668 ACATTAAGTTTTCCCAAATGATAAGTG 57.072 29.630 0.00 0.00 32.99 3.16
5551 6018 8.872845 CATTAAGTTTTCCCAAATGATAAGTGC 58.127 33.333 0.00 0.00 30.77 4.40
5552 6019 5.405935 AGTTTTCCCAAATGATAAGTGCC 57.594 39.130 0.00 0.00 0.00 5.01
5553 6020 4.837860 AGTTTTCCCAAATGATAAGTGCCA 59.162 37.500 0.00 0.00 0.00 4.92
5554 6021 4.799564 TTTCCCAAATGATAAGTGCCAC 57.200 40.909 0.00 0.00 0.00 5.01
5555 6022 3.448093 TCCCAAATGATAAGTGCCACA 57.552 42.857 0.00 0.00 0.00 4.17
5556 6023 3.088532 TCCCAAATGATAAGTGCCACAC 58.911 45.455 0.00 0.00 34.10 3.82
5557 6024 2.159393 CCCAAATGATAAGTGCCACACG 60.159 50.000 0.00 0.00 39.64 4.49
5558 6025 2.487762 CCAAATGATAAGTGCCACACGT 59.512 45.455 0.00 0.00 39.64 4.49
5559 6026 3.491356 CAAATGATAAGTGCCACACGTG 58.509 45.455 15.48 15.48 39.64 4.49
5560 6027 2.472695 ATGATAAGTGCCACACGTGT 57.527 45.000 17.22 17.22 39.64 4.49
5561 6028 1.507562 TGATAAGTGCCACACGTGTG 58.492 50.000 36.13 36.13 45.23 3.82
5579 6046 4.745549 GCACGAAGCAATTCCGAC 57.254 55.556 0.00 0.00 44.79 4.79
5580 6047 1.225745 GCACGAAGCAATTCCGACG 60.226 57.895 0.00 0.00 44.79 5.12
5581 6048 1.897398 GCACGAAGCAATTCCGACGT 61.897 55.000 0.00 0.00 44.79 4.34
5582 6049 0.179250 CACGAAGCAATTCCGACGTG 60.179 55.000 0.00 0.00 43.10 4.49
5583 6050 0.319211 ACGAAGCAATTCCGACGTGA 60.319 50.000 0.00 0.00 32.93 4.35
5584 6051 0.093026 CGAAGCAATTCCGACGTGAC 59.907 55.000 0.00 0.00 0.00 3.67
5585 6052 1.429463 GAAGCAATTCCGACGTGACT 58.571 50.000 0.00 0.00 0.00 3.41
5586 6053 1.798813 GAAGCAATTCCGACGTGACTT 59.201 47.619 0.00 0.00 0.00 3.01
5587 6054 1.878953 AGCAATTCCGACGTGACTTT 58.121 45.000 0.00 0.00 0.00 2.66
5588 6055 2.218603 AGCAATTCCGACGTGACTTTT 58.781 42.857 0.00 0.00 0.00 2.27
5589 6056 2.616842 AGCAATTCCGACGTGACTTTTT 59.383 40.909 0.00 0.00 0.00 1.94
5614 6081 9.456147 TTTATGGCAAGTTTAGTTATTAGAGCA 57.544 29.630 0.00 0.00 0.00 4.26
5615 6082 9.627123 TTATGGCAAGTTTAGTTATTAGAGCAT 57.373 29.630 0.00 0.00 0.00 3.79
5616 6083 7.320443 TGGCAAGTTTAGTTATTAGAGCATG 57.680 36.000 0.00 0.00 0.00 4.06
5617 6084 6.318648 TGGCAAGTTTAGTTATTAGAGCATGG 59.681 38.462 0.00 0.00 0.00 3.66
5618 6085 6.202226 GCAAGTTTAGTTATTAGAGCATGGC 58.798 40.000 0.00 0.00 0.00 4.40
5619 6086 6.038714 GCAAGTTTAGTTATTAGAGCATGGCT 59.961 38.462 0.00 0.00 43.88 4.75
5620 6087 7.415653 GCAAGTTTAGTTATTAGAGCATGGCTT 60.416 37.037 0.00 0.00 39.88 4.35
5621 6088 8.462016 CAAGTTTAGTTATTAGAGCATGGCTTT 58.538 33.333 0.00 0.00 39.88 3.51
5622 6089 9.681062 AAGTTTAGTTATTAGAGCATGGCTTTA 57.319 29.630 0.00 0.00 39.88 1.85
5623 6090 9.681062 AGTTTAGTTATTAGAGCATGGCTTTAA 57.319 29.630 4.05 4.05 39.88 1.52
5628 6095 9.807649 AGTTATTAGAGCATGGCTTTAAAATTG 57.192 29.630 5.48 0.00 38.41 2.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
31 32 1.555075 CATGTAGGTGTAGGTGCAGGT 59.445 52.381 0.00 0.00 0.00 4.00
32 33 1.134401 CCATGTAGGTGTAGGTGCAGG 60.134 57.143 0.00 0.00 0.00 4.85
33 34 1.134401 CCCATGTAGGTGTAGGTGCAG 60.134 57.143 0.00 0.00 34.66 4.41
34 35 0.908910 CCCATGTAGGTGTAGGTGCA 59.091 55.000 0.00 0.00 34.66 4.57
35 36 0.463833 GCCCATGTAGGTGTAGGTGC 60.464 60.000 0.00 0.00 34.66 5.01
36 37 1.139058 GAGCCCATGTAGGTGTAGGTG 59.861 57.143 0.00 0.00 34.66 4.00
37 38 1.273609 TGAGCCCATGTAGGTGTAGGT 60.274 52.381 0.00 0.00 34.66 3.08
38 39 1.139058 GTGAGCCCATGTAGGTGTAGG 59.861 57.143 0.00 0.00 34.66 3.18
39 40 1.139058 GGTGAGCCCATGTAGGTGTAG 59.861 57.143 0.00 0.00 34.66 2.74
40 41 1.200519 GGTGAGCCCATGTAGGTGTA 58.799 55.000 0.00 0.00 34.66 2.90
41 42 0.547712 AGGTGAGCCCATGTAGGTGT 60.548 55.000 0.00 0.00 34.66 4.16
42 43 0.107508 CAGGTGAGCCCATGTAGGTG 60.108 60.000 0.00 0.00 34.66 4.00
43 44 1.915078 GCAGGTGAGCCCATGTAGGT 61.915 60.000 0.00 0.00 34.66 3.08
70 78 2.915659 ACCACAGGCTCCGTCGAA 60.916 61.111 0.00 0.00 0.00 3.71
86 94 1.680735 TCCAACATCCAAGCAACACAC 59.319 47.619 0.00 0.00 0.00 3.82
108 121 6.768596 TTCATCGAGTGAGCCTTGCATAGG 62.769 50.000 9.75 9.75 38.70 2.57
109 122 2.133553 CATCGAGTGAGCCTTGCATAG 58.866 52.381 0.00 0.00 0.00 2.23
110 123 1.756538 TCATCGAGTGAGCCTTGCATA 59.243 47.619 0.00 0.00 31.80 3.14
111 124 0.538584 TCATCGAGTGAGCCTTGCAT 59.461 50.000 0.00 0.00 31.80 3.96
112 125 0.321346 TTCATCGAGTGAGCCTTGCA 59.679 50.000 0.00 0.00 38.29 4.08
113 126 1.442769 TTTCATCGAGTGAGCCTTGC 58.557 50.000 0.00 0.00 38.29 4.01
114 127 3.686241 TCAATTTCATCGAGTGAGCCTTG 59.314 43.478 0.00 1.76 38.29 3.61
115 128 3.942829 TCAATTTCATCGAGTGAGCCTT 58.057 40.909 0.00 0.00 38.29 4.35
116 129 3.616956 TCAATTTCATCGAGTGAGCCT 57.383 42.857 0.00 0.00 38.29 4.58
117 130 4.889832 AATCAATTTCATCGAGTGAGCC 57.110 40.909 0.00 0.00 38.29 4.70
118 131 4.498323 GCAAATCAATTTCATCGAGTGAGC 59.502 41.667 0.00 0.00 38.29 4.26
135 148 7.201548 CCAATGTACCATAAAGCAAAGCAAATC 60.202 37.037 0.00 0.00 0.00 2.17
136 149 6.594937 CCAATGTACCATAAAGCAAAGCAAAT 59.405 34.615 0.00 0.00 0.00 2.32
137 150 5.931146 CCAATGTACCATAAAGCAAAGCAAA 59.069 36.000 0.00 0.00 0.00 3.68
140 153 5.072040 ACCAATGTACCATAAAGCAAAGC 57.928 39.130 0.00 0.00 0.00 3.51
154 167 2.227626 TCGAAACGACGGTACCAATGTA 59.772 45.455 13.54 0.00 0.00 2.29
155 168 1.000385 TCGAAACGACGGTACCAATGT 60.000 47.619 13.54 1.00 0.00 2.71
156 169 1.652124 CTCGAAACGACGGTACCAATG 59.348 52.381 13.54 2.55 0.00 2.82
157 170 1.541147 TCTCGAAACGACGGTACCAAT 59.459 47.619 13.54 0.00 0.00 3.16
158 171 0.950836 TCTCGAAACGACGGTACCAA 59.049 50.000 13.54 0.00 0.00 3.67
160 173 0.796113 GCTCTCGAAACGACGGTACC 60.796 60.000 0.16 0.16 0.00 3.34
196 219 5.598417 TGATTCTCTCCGGTAATCATTCTCA 59.402 40.000 15.38 3.05 35.32 3.27
277 304 6.091169 GGTGATAATTCGGTCGTTTTACTTCA 59.909 38.462 0.00 0.00 0.00 3.02
350 383 5.059833 ACTCTGTCGAAATCAAGAAAAGCT 58.940 37.500 0.00 0.00 0.00 3.74
351 384 5.349824 ACTCTGTCGAAATCAAGAAAAGC 57.650 39.130 0.00 0.00 0.00 3.51
430 464 3.389983 CCGTACTTCATTCCCCTTATCCA 59.610 47.826 0.00 0.00 0.00 3.41
544 584 1.822371 GGGCAAGCGGGATTTCTTTTA 59.178 47.619 0.00 0.00 0.00 1.52
558 598 4.521062 CTCGCTCCCTCGGGCAAG 62.521 72.222 0.00 0.00 34.68 4.01
565 605 3.151022 CCCCTGTCTCGCTCCCTC 61.151 72.222 0.00 0.00 0.00 4.30
763 825 0.759812 TATACCCGGAATGCGGTGGA 60.760 55.000 13.07 0.27 33.36 4.02
793 855 0.106894 GGAAGTTATCCCTCCTGCGG 59.893 60.000 0.00 0.00 43.00 5.69
809 871 1.690633 CCTGCCTGCCTCTAGGGAA 60.691 63.158 0.00 0.00 37.75 3.97
871 934 4.404098 GGAAGGCGGCCGGAGAAA 62.404 66.667 29.38 0.00 0.00 2.52
889 952 0.326618 GGGTGAGGAGGGATCTGGAA 60.327 60.000 0.00 0.00 0.00 3.53
1102 1171 0.168128 GCGGATCAGTTTCCAAACCG 59.832 55.000 0.00 0.00 39.71 4.44
1105 1174 1.582610 GCCGCGGATCAGTTTCCAAA 61.583 55.000 33.48 0.00 35.34 3.28
1138 1211 8.424274 TTTGAAGAAAAATCAGAAGAAAAGCC 57.576 30.769 0.00 0.00 0.00 4.35
1191 1271 2.994957 TATAGTACCCTGAGCCCTCC 57.005 55.000 0.00 0.00 0.00 4.30
1331 1411 6.645003 CGAGGCAATAAACATGTAGTAGCATA 59.355 38.462 0.00 0.00 0.00 3.14
1332 1412 5.466728 CGAGGCAATAAACATGTAGTAGCAT 59.533 40.000 0.00 0.00 0.00 3.79
1333 1413 4.808895 CGAGGCAATAAACATGTAGTAGCA 59.191 41.667 0.00 0.00 0.00 3.49
1334 1414 5.047847 TCGAGGCAATAAACATGTAGTAGC 58.952 41.667 0.00 0.00 0.00 3.58
1335 1415 5.692204 CCTCGAGGCAATAAACATGTAGTAG 59.308 44.000 20.67 0.00 0.00 2.57
1336 1416 5.128171 ACCTCGAGGCAATAAACATGTAGTA 59.872 40.000 31.56 0.00 39.32 1.82
1337 1417 4.081087 ACCTCGAGGCAATAAACATGTAGT 60.081 41.667 31.56 2.53 39.32 2.73
1372 1452 8.095937 TGTGCAATGCATTGAAAAATTTATCA 57.904 26.923 37.36 20.65 41.91 2.15
1479 1559 7.650104 CAGATAACCAAATTAAAACCAACGTGT 59.350 33.333 0.00 0.00 0.00 4.49
1480 1560 7.358848 GCAGATAACCAAATTAAAACCAACGTG 60.359 37.037 0.00 0.00 0.00 4.49
1481 1561 6.643360 GCAGATAACCAAATTAAAACCAACGT 59.357 34.615 0.00 0.00 0.00 3.99
1482 1562 6.090223 GGCAGATAACCAAATTAAAACCAACG 59.910 38.462 0.00 0.00 0.00 4.10
1483 1563 6.931840 TGGCAGATAACCAAATTAAAACCAAC 59.068 34.615 0.00 0.00 33.12 3.77
1484 1564 7.067496 TGGCAGATAACCAAATTAAAACCAA 57.933 32.000 0.00 0.00 33.12 3.67
1487 1567 7.870445 TGAACTGGCAGATAACCAAATTAAAAC 59.130 33.333 23.66 0.00 36.56 2.43
1538 1655 8.028938 GGTTACATTTGTGAGCTTGTTTCATAT 58.971 33.333 0.00 0.00 0.00 1.78
1540 1657 6.183360 TGGTTACATTTGTGAGCTTGTTTCAT 60.183 34.615 6.29 0.00 33.85 2.57
1573 1691 2.430694 TCGATGAAAGATGTCGGTGGAT 59.569 45.455 0.00 0.00 36.14 3.41
1589 1707 4.468765 AATATGGAGGCAGATCTCGATG 57.531 45.455 0.00 0.00 34.73 3.84
1616 1734 4.149046 GCACAAAAGAACACGAACAAACAA 59.851 37.500 0.00 0.00 0.00 2.83
1647 1765 4.439057 TCCTTCGATGGACTAATTTTCGG 58.561 43.478 15.68 0.00 0.00 4.30
1654 1773 1.068588 CGGCATCCTTCGATGGACTAA 59.931 52.381 21.28 0.55 45.25 2.24
1661 1781 1.115467 ACTTCTCGGCATCCTTCGAT 58.885 50.000 0.00 0.00 34.77 3.59
1663 1783 1.281899 GAACTTCTCGGCATCCTTCG 58.718 55.000 0.00 0.00 0.00 3.79
1680 1800 7.171848 CCATTTTGAAGATGCACTGAATTTGAA 59.828 33.333 0.00 0.00 0.00 2.69
1782 2023 6.053005 AGTTCTTTTCCACGTGATTTGACTA 58.947 36.000 19.30 0.00 0.00 2.59
1895 2136 0.887387 GCCGAAAACCAGCCTACACA 60.887 55.000 0.00 0.00 0.00 3.72
1896 2137 0.605589 AGCCGAAAACCAGCCTACAC 60.606 55.000 0.00 0.00 0.00 2.90
2072 2316 8.697507 AAAATCCTAGAGACAAGAAACACAAT 57.302 30.769 0.00 0.00 0.00 2.71
2075 2319 8.834749 ACTAAAATCCTAGAGACAAGAAACAC 57.165 34.615 0.00 0.00 0.00 3.32
2086 2330 7.442666 GTCATAAGGGCAACTAAAATCCTAGAG 59.557 40.741 0.00 0.00 0.00 2.43
2187 2431 4.543590 ACTGATGTTAGGGACTTGTCTG 57.456 45.455 0.61 0.00 41.75 3.51
2188 2432 5.568620 AAACTGATGTTAGGGACTTGTCT 57.431 39.130 0.61 0.00 41.75 3.41
2293 2537 3.837355 AGAAGTTGCAAGGGACAAATCT 58.163 40.909 0.00 0.00 0.00 2.40
2328 2572 8.389779 TCAGTTAAATACTTCAATGTGCAGAA 57.610 30.769 0.00 0.00 33.85 3.02
2343 2587 9.734620 GCAATGAAAGCACATATCAGTTAAATA 57.265 29.630 0.00 0.00 0.00 1.40
2355 2599 0.899720 CCCCTGCAATGAAAGCACAT 59.100 50.000 0.00 0.00 37.02 3.21
2485 2729 1.740025 GCAGCAACCTTCTGGACATAC 59.260 52.381 0.00 0.00 37.04 2.39
2603 2847 6.113411 ACTGAAAGCACCATAATACAGTACC 58.887 40.000 0.00 0.00 37.60 3.34
2657 2901 0.663153 GCATTAACATCGCCAGGGTC 59.337 55.000 0.00 0.00 0.00 4.46
2819 3063 6.596888 CACTTGAGCCATCGGATTATTATCAT 59.403 38.462 0.00 0.00 32.09 2.45
2859 3103 4.878397 AGTGCTCCTAAACTGCAATACATC 59.122 41.667 0.00 0.00 38.50 3.06
2878 3122 7.849804 TCCAAAAGAGACTCATATTAAGTGC 57.150 36.000 5.02 0.00 0.00 4.40
3103 3348 5.296283 AGAAGAGCTGATATGTCAAATGCAC 59.704 40.000 0.00 0.00 33.05 4.57
3584 3864 4.127171 TGAGTGACAGACTTTTTACAGCC 58.873 43.478 0.00 0.00 33.83 4.85
3637 3920 5.428253 TCTTTGTTACAGGGCATATGAGAC 58.572 41.667 6.97 0.00 0.00 3.36
3696 3980 2.032965 TCAGGGTGTTTGGCTACCTA 57.967 50.000 0.00 0.00 37.15 3.08
3770 4054 2.649331 TGGTACTTCAGCGCTTACTC 57.351 50.000 7.50 3.02 0.00 2.59
3951 4236 7.170393 ACCTAAAATCAGCCCAAGTTTATTC 57.830 36.000 0.00 0.00 0.00 1.75
4335 4637 0.109532 TCATCGGGTTTTGCTGTGGA 59.890 50.000 0.00 0.00 0.00 4.02
4410 4712 2.191908 TGGCACAACGGCTTCAGT 59.808 55.556 0.00 0.00 41.89 3.41
4836 5142 7.308770 GCACATGCCAACAATCTGTATATACAT 60.309 37.037 15.81 0.00 33.32 2.29
4867 5173 2.447244 AGCTAGATGCATTCGTAGGC 57.553 50.000 0.00 0.43 45.94 3.93
4940 5307 1.269569 TGTCGATTATGCAGTAGCCGG 60.270 52.381 0.00 0.00 41.13 6.13
4972 5339 8.778358 CCAACAAGAAGTCCTAATTCTATATGC 58.222 37.037 0.00 0.00 35.98 3.14
4978 5345 7.231519 CCTTTTCCAACAAGAAGTCCTAATTCT 59.768 37.037 0.00 0.00 38.65 2.40
4980 5347 7.066781 TCCTTTTCCAACAAGAAGTCCTAATT 58.933 34.615 0.00 0.00 0.00 1.40
4986 5400 5.774498 ACATCCTTTTCCAACAAGAAGTC 57.226 39.130 0.00 0.00 0.00 3.01
5009 5423 3.931578 AGAAGTTCTAAGAACATGCGCT 58.068 40.909 9.73 0.00 0.00 5.92
5011 5425 7.064609 TCCAATAAGAAGTTCTAAGAACATGCG 59.935 37.037 5.65 0.00 0.00 4.73
5022 5436 7.406104 AGTAGCCATTTCCAATAAGAAGTTCT 58.594 34.615 0.00 0.00 0.00 3.01
5028 5442 8.966868 CCTTTTTAGTAGCCATTTCCAATAAGA 58.033 33.333 0.00 0.00 0.00 2.10
5032 5446 6.260663 TCCCTTTTTAGTAGCCATTTCCAAT 58.739 36.000 0.00 0.00 0.00 3.16
5053 5467 7.881775 ACCTATTTTCTTGACACAATATCCC 57.118 36.000 0.00 0.00 0.00 3.85
5060 5474 4.947388 GGGCATACCTATTTTCTTGACACA 59.053 41.667 0.00 0.00 35.85 3.72
5115 5560 5.008613 TGCTTTTGTCATGGTTGTTCTCTAC 59.991 40.000 0.00 0.00 0.00 2.59
5177 5622 0.033601 TCAAAGTGGTGGTGTTGGCT 60.034 50.000 0.00 0.00 0.00 4.75
5185 5630 1.882623 GCTTCTTCCTCAAAGTGGTGG 59.117 52.381 0.00 0.00 36.31 4.61
5188 5633 4.083057 GCTAAAGCTTCTTCCTCAAAGTGG 60.083 45.833 0.00 0.00 35.80 4.00
5194 5639 1.676014 GCCGCTAAAGCTTCTTCCTCA 60.676 52.381 0.00 0.00 39.32 3.86
5195 5640 1.010580 GCCGCTAAAGCTTCTTCCTC 58.989 55.000 0.00 0.00 39.32 3.71
5196 5641 0.324943 TGCCGCTAAAGCTTCTTCCT 59.675 50.000 0.00 0.00 39.32 3.36
5197 5642 1.131315 CTTGCCGCTAAAGCTTCTTCC 59.869 52.381 0.00 0.00 39.32 3.46
5198 5643 1.466529 GCTTGCCGCTAAAGCTTCTTC 60.467 52.381 0.00 0.00 45.31 2.87
5199 5644 0.523519 GCTTGCCGCTAAAGCTTCTT 59.476 50.000 0.00 0.00 45.31 2.52
5200 5645 1.639298 CGCTTGCCGCTAAAGCTTCT 61.639 55.000 12.21 0.00 46.33 2.85
5209 5654 4.357947 TTCGTCTCGCTTGCCGCT 62.358 61.111 0.00 0.00 36.73 5.52
5239 5684 3.941573 TGAGCATTGTGAAGCATACAGA 58.058 40.909 0.00 0.00 0.00 3.41
5256 5701 0.110509 CACACGTGTCAGCATTGAGC 60.111 55.000 20.49 0.00 46.19 4.26
5257 5702 1.070376 CACACACGTGTCAGCATTGAG 60.070 52.381 20.49 6.78 42.83 3.02
5258 5703 0.936600 CACACACGTGTCAGCATTGA 59.063 50.000 20.49 0.00 42.83 2.57
5299 5753 0.701147 CTCTCCCCTTCCCTGCTTTT 59.299 55.000 0.00 0.00 0.00 2.27
5307 5761 0.912486 TGCTAAAGCTCTCCCCTTCC 59.088 55.000 3.26 0.00 42.66 3.46
5473 5940 7.934120 GTGCTACAAATCCTCTTCCATTAGTAT 59.066 37.037 0.00 0.00 0.00 2.12
5478 5945 4.273318 GGTGCTACAAATCCTCTTCCATT 58.727 43.478 0.00 0.00 0.00 3.16
5487 5954 1.029947 CACCCCGGTGCTACAAATCC 61.030 60.000 0.00 0.00 39.39 3.01
5506 5973 2.054799 TGTTCATATAGGGGGTGGAGC 58.945 52.381 0.00 0.00 0.00 4.70
5507 5974 6.044404 ACTTAATGTTCATATAGGGGGTGGAG 59.956 42.308 0.00 0.00 0.00 3.86
5508 5975 5.914716 ACTTAATGTTCATATAGGGGGTGGA 59.085 40.000 0.00 0.00 0.00 4.02
5509 5976 6.200878 ACTTAATGTTCATATAGGGGGTGG 57.799 41.667 0.00 0.00 0.00 4.61
5510 5977 8.533569 AAAACTTAATGTTCATATAGGGGGTG 57.466 34.615 0.00 0.00 38.03 4.61
5511 5978 7.783119 GGAAAACTTAATGTTCATATAGGGGGT 59.217 37.037 0.00 0.00 38.03 4.95
5512 5979 7.232737 GGGAAAACTTAATGTTCATATAGGGGG 59.767 40.741 0.00 0.00 38.03 5.40
5513 5980 7.782644 TGGGAAAACTTAATGTTCATATAGGGG 59.217 37.037 0.00 0.00 38.03 4.79
5514 5981 8.760980 TGGGAAAACTTAATGTTCATATAGGG 57.239 34.615 0.00 0.00 38.03 3.53
5524 5991 9.927668 CACTTATCATTTGGGAAAACTTAATGT 57.072 29.630 0.00 0.00 0.00 2.71
5525 5992 8.872845 GCACTTATCATTTGGGAAAACTTAATG 58.127 33.333 0.00 0.00 0.00 1.90
5526 5993 8.040727 GGCACTTATCATTTGGGAAAACTTAAT 58.959 33.333 0.00 0.00 0.00 1.40
5527 5994 7.015682 TGGCACTTATCATTTGGGAAAACTTAA 59.984 33.333 0.00 0.00 0.00 1.85
5528 5995 6.495181 TGGCACTTATCATTTGGGAAAACTTA 59.505 34.615 0.00 0.00 0.00 2.24
5529 5996 5.306678 TGGCACTTATCATTTGGGAAAACTT 59.693 36.000 0.00 0.00 0.00 2.66
5530 5997 4.837860 TGGCACTTATCATTTGGGAAAACT 59.162 37.500 0.00 0.00 0.00 2.66
5531 5998 4.929211 GTGGCACTTATCATTTGGGAAAAC 59.071 41.667 11.13 0.00 0.00 2.43
5532 5999 4.590647 TGTGGCACTTATCATTTGGGAAAA 59.409 37.500 19.83 0.00 0.00 2.29
5533 6000 4.021544 GTGTGGCACTTATCATTTGGGAAA 60.022 41.667 19.83 0.00 0.00 3.13
5534 6001 3.509575 GTGTGGCACTTATCATTTGGGAA 59.490 43.478 19.83 0.00 0.00 3.97
5535 6002 3.088532 GTGTGGCACTTATCATTTGGGA 58.911 45.455 19.83 0.00 0.00 4.37
5536 6003 2.159393 CGTGTGGCACTTATCATTTGGG 60.159 50.000 19.83 0.00 31.34 4.12
5537 6004 2.487762 ACGTGTGGCACTTATCATTTGG 59.512 45.455 19.83 0.00 31.34 3.28
5538 6005 3.058293 ACACGTGTGGCACTTATCATTTG 60.058 43.478 22.71 7.02 34.19 2.32
5539 6006 3.058293 CACACGTGTGGCACTTATCATTT 60.058 43.478 35.65 0.00 42.10 2.32
5540 6007 2.483877 CACACGTGTGGCACTTATCATT 59.516 45.455 35.65 0.00 42.10 2.57
5541 6008 2.076100 CACACGTGTGGCACTTATCAT 58.924 47.619 35.65 0.33 42.10 2.45
5542 6009 1.507562 CACACGTGTGGCACTTATCA 58.492 50.000 35.65 0.00 42.10 2.15
5557 6024 0.387239 GGAATTGCTTCGTGCCACAC 60.387 55.000 0.00 0.00 42.00 3.82
5558 6025 1.851021 CGGAATTGCTTCGTGCCACA 61.851 55.000 0.00 0.00 42.00 4.17
5559 6026 1.154225 CGGAATTGCTTCGTGCCAC 60.154 57.895 0.00 0.00 42.00 5.01
5560 6027 1.302112 TCGGAATTGCTTCGTGCCA 60.302 52.632 0.00 0.00 42.00 4.92
5561 6028 1.134694 GTCGGAATTGCTTCGTGCC 59.865 57.895 0.00 0.00 42.00 5.01
5562 6029 1.225745 CGTCGGAATTGCTTCGTGC 60.226 57.895 0.00 0.00 43.25 5.34
5563 6030 0.179250 CACGTCGGAATTGCTTCGTG 60.179 55.000 21.10 21.10 41.40 4.35
5564 6031 0.319211 TCACGTCGGAATTGCTTCGT 60.319 50.000 9.54 9.54 31.75 3.85
5565 6032 0.093026 GTCACGTCGGAATTGCTTCG 59.907 55.000 0.00 8.49 31.75 3.79
5566 6033 1.429463 AGTCACGTCGGAATTGCTTC 58.571 50.000 0.00 0.00 0.00 3.86
5567 6034 1.878953 AAGTCACGTCGGAATTGCTT 58.121 45.000 0.00 0.00 0.00 3.91
5568 6035 1.878953 AAAGTCACGTCGGAATTGCT 58.121 45.000 0.00 0.00 0.00 3.91
5569 6036 2.681152 AAAAGTCACGTCGGAATTGC 57.319 45.000 0.00 0.00 0.00 3.56
5588 6055 9.456147 TGCTCTAATAACTAAACTTGCCATAAA 57.544 29.630 0.00 0.00 0.00 1.40
5589 6056 9.627123 ATGCTCTAATAACTAAACTTGCCATAA 57.373 29.630 0.00 0.00 0.00 1.90
5590 6057 9.056005 CATGCTCTAATAACTAAACTTGCCATA 57.944 33.333 0.00 0.00 0.00 2.74
5591 6058 7.013655 CCATGCTCTAATAACTAAACTTGCCAT 59.986 37.037 0.00 0.00 0.00 4.40
5592 6059 6.318648 CCATGCTCTAATAACTAAACTTGCCA 59.681 38.462 0.00 0.00 0.00 4.92
5593 6060 6.729187 CCATGCTCTAATAACTAAACTTGCC 58.271 40.000 0.00 0.00 0.00 4.52
5594 6061 6.038714 AGCCATGCTCTAATAACTAAACTTGC 59.961 38.462 0.00 0.00 30.62 4.01
5595 6062 7.559590 AGCCATGCTCTAATAACTAAACTTG 57.440 36.000 0.00 0.00 30.62 3.16
5596 6063 8.581253 AAAGCCATGCTCTAATAACTAAACTT 57.419 30.769 0.00 0.00 38.25 2.66
5597 6064 9.681062 TTAAAGCCATGCTCTAATAACTAAACT 57.319 29.630 0.00 0.00 38.25 2.66
5602 6069 9.807649 CAATTTTAAAGCCATGCTCTAATAACT 57.192 29.630 0.00 0.00 38.25 2.24


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

AutoCloner maintained by Alex Coulton.