Multiple sequence alignment - TraesCS6A01G335400

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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 TraesCS6A01G335400 chr6A 100.000 5160 0 0 1 5160 567937606 567932447 0.000000e+00 9529
1 TraesCS6A01G335400 chr6A 78.026 537 98 10 4552 5070 617752211 617751677 2.320000e-83 320
2 TraesCS6A01G335400 chr6B 88.449 4043 287 82 1236 5159 638831526 638827545 0.000000e+00 4713
3 TraesCS6A01G335400 chr6B 90.992 1099 63 14 1 1085 638832678 638831602 0.000000e+00 1448
4 TraesCS6A01G335400 chr6B 88.043 92 8 2 1129 1218 638831610 638831520 7.070000e-19 106
5 TraesCS6A01G335400 chr6D 89.304 2599 157 56 1129 3639 423749924 423752489 0.000000e+00 3147
6 TraesCS6A01G335400 chr6D 91.226 946 56 14 3676 4601 423752626 423753564 0.000000e+00 1262
7 TraesCS6A01G335400 chr6D 88.731 1056 69 20 55 1088 423748909 423749936 0.000000e+00 1245
8 TraesCS6A01G335400 chr1A 78.850 539 96 11 4544 5064 536932402 536931864 1.060000e-91 348
9 TraesCS6A01G335400 chr7B 78.748 527 93 10 4552 5059 747359151 747358625 8.280000e-88 335
10 TraesCS6A01G335400 chr7B 78.062 547 100 12 4543 5071 748331626 748331082 1.390000e-85 327
11 TraesCS6A01G335400 chr3A 78.000 550 99 14 4544 5072 558879592 558880140 4.980000e-85 326
12 TraesCS6A01G335400 chr5B 79.289 478 81 11 4595 5059 330558074 330557602 8.340000e-83 318
13 TraesCS6A01G335400 chr2B 78.471 497 86 15 4579 5059 773992781 773993272 6.490000e-79 305
14 TraesCS6A01G335400 chr2B 77.305 282 53 8 4547 4820 621290807 621290529 6.920000e-34 156
15 TraesCS6A01G335400 chr2D 77.264 541 98 17 4544 5064 102278179 102278714 1.410000e-75 294
16 TraesCS6A01G335400 chr2D 84.052 232 34 3 4830 5059 37219743 37219513 2.420000e-53 220
17 TraesCS6A01G335400 chr3D 80.679 383 57 11 4683 5052 93478633 93478255 1.090000e-71 281
18 TraesCS6A01G335400 chr3D 77.978 445 83 9 4629 5059 401170120 401169677 1.100000e-66 265
19 TraesCS6A01G335400 chr1D 77.490 502 91 16 4558 5041 461826339 461826836 1.090000e-71 281
20 TraesCS6A01G335400 chr4D 78.984 433 72 13 4641 5059 58982276 58981849 1.420000e-70 278
21 TraesCS6A01G335400 chr7D 76.894 528 97 18 4544 5051 624811887 624811365 5.090000e-70 276
22 TraesCS6A01G335400 chr4A 80.541 370 57 10 4703 5059 451752959 451753326 2.370000e-68 270
23 TraesCS6A01G335400 chr5D 76.673 493 89 18 4545 5016 551727095 551727582 3.080000e-62 250


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 TraesCS6A01G335400 chr6A 567932447 567937606 5159 True 9529.000000 9529 100.000000 1 5160 1 chr6A.!!$R1 5159
1 TraesCS6A01G335400 chr6A 617751677 617752211 534 True 320.000000 320 78.026000 4552 5070 1 chr6A.!!$R2 518
2 TraesCS6A01G335400 chr6B 638827545 638832678 5133 True 2089.000000 4713 89.161333 1 5159 3 chr6B.!!$R1 5158
3 TraesCS6A01G335400 chr6D 423748909 423753564 4655 False 1884.666667 3147 89.753667 55 4601 3 chr6D.!!$F1 4546
4 TraesCS6A01G335400 chr1A 536931864 536932402 538 True 348.000000 348 78.850000 4544 5064 1 chr1A.!!$R1 520
5 TraesCS6A01G335400 chr7B 747358625 747359151 526 True 335.000000 335 78.748000 4552 5059 1 chr7B.!!$R1 507
6 TraesCS6A01G335400 chr7B 748331082 748331626 544 True 327.000000 327 78.062000 4543 5071 1 chr7B.!!$R2 528
7 TraesCS6A01G335400 chr3A 558879592 558880140 548 False 326.000000 326 78.000000 4544 5072 1 chr3A.!!$F1 528
8 TraesCS6A01G335400 chr2D 102278179 102278714 535 False 294.000000 294 77.264000 4544 5064 1 chr2D.!!$F1 520
9 TraesCS6A01G335400 chr7D 624811365 624811887 522 True 276.000000 276 76.894000 4544 5051 1 chr7D.!!$R1 507

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
554 562 0.035820 TAAACCAGGCCTCGCGAATT 60.036 50.0 11.33 0.0 0.0 2.17 F
1130 1159 0.108945 GCTTGCCTGTGGATTGCTTC 60.109 55.0 0.00 0.0 0.0 3.86 F
1777 1875 0.038599 TCTGAGTGTGTAGGGCCGTA 59.961 55.0 0.00 0.0 0.0 4.02 F
3310 3502 0.689623 AGCAGCTAGACAGGCAAAGT 59.310 50.0 0.00 0.0 0.0 2.66 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1614 1702 0.179100 TCATCAGGAACAGCTAGCGC 60.179 55.0 9.55 0.0 0.0 5.92 R
2251 2359 0.457853 GCGAATCCACTCAGCGTGTA 60.458 55.0 0.00 0.0 42.2 2.90 R
3756 4057 0.040067 GCGTTCAAAGTCAGGCCAAG 60.040 55.0 5.01 0.0 0.0 3.61 R
4256 4560 0.107703 CCGAGAACTATGGGCTGCAA 60.108 55.0 0.50 0.0 0.0 4.08 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
35 36 7.174080 TGTTTTCACAATCGATTGAATCAGGTA 59.826 33.333 37.75 17.82 40.14 3.08
73 74 3.126858 TCCGTCATTGCTTTTATGTCAGC 59.873 43.478 0.00 0.00 36.49 4.26
74 75 3.127548 CCGTCATTGCTTTTATGTCAGCT 59.872 43.478 0.00 0.00 36.92 4.24
124 125 6.961359 TCAAAATATCTTCACACCACTACG 57.039 37.500 0.00 0.00 0.00 3.51
195 196 6.901081 ATTCTCGAGGAAACCAAAATTCTT 57.099 33.333 13.56 0.00 37.49 2.52
265 266 3.823281 TCACTGTTTAACCGGTCTTCA 57.177 42.857 8.04 4.51 0.00 3.02
311 316 1.685820 CAAGAACTGGTCCCCTCCC 59.314 63.158 0.00 0.00 0.00 4.30
412 420 2.414161 GCAGTAAAAATCTCCACGCCAC 60.414 50.000 0.00 0.00 0.00 5.01
466 474 7.812669 CAGTTACAAATTCACCCATTACTTTCC 59.187 37.037 0.00 0.00 0.00 3.13
527 535 5.910614 TGGTCATGATAATGTCTGTCTCTG 58.089 41.667 0.00 0.00 0.00 3.35
536 544 2.578786 TGTCTGTCTCTGTCACGGTTA 58.421 47.619 0.00 0.00 0.00 2.85
548 556 1.004200 ACGGTTAAACCAGGCCTCG 60.004 57.895 0.00 0.00 38.47 4.63
554 562 0.035820 TAAACCAGGCCTCGCGAATT 60.036 50.000 11.33 0.00 0.00 2.17
564 572 2.908634 CCTCGCGAATTACAATGATGC 58.091 47.619 11.33 0.00 0.00 3.91
566 574 3.242706 CCTCGCGAATTACAATGATGCAA 60.243 43.478 11.33 0.00 0.00 4.08
605 613 4.969484 AGAACTAGGAAACACATCGGTTT 58.031 39.130 0.00 0.00 43.30 3.27
611 619 1.463444 GAAACACATCGGTTTCCTCCG 59.537 52.381 7.39 0.00 46.88 4.63
619 627 0.251073 CGGTTTCCTCCGTGGGTTAT 59.749 55.000 0.00 0.00 44.77 1.89
707 724 1.202746 GGGAAGCCAAACCATTTGCAA 60.203 47.619 0.00 0.00 39.31 4.08
712 729 4.571372 AGCCAAACCATTTGCAATTTTG 57.429 36.364 0.00 7.99 39.31 2.44
815 834 5.358160 GCAATAAAATAAGAGCTGAGGGTGT 59.642 40.000 0.00 0.00 0.00 4.16
817 836 7.067008 GCAATAAAATAAGAGCTGAGGGTGTTA 59.933 37.037 0.00 0.00 34.18 2.41
863 882 4.102113 CCAAGTGGGCAAAGGGAG 57.898 61.111 0.00 0.00 0.00 4.30
872 891 1.761174 GCAAAGGGAGGGAGTGACA 59.239 57.895 0.00 0.00 0.00 3.58
1027 1055 0.173708 CCCCTCTTCTTCGTCTTCCG 59.826 60.000 0.00 0.00 38.13 4.30
1035 1063 0.522915 CTTCGTCTTCCGCCTACGAC 60.523 60.000 0.00 0.00 44.53 4.34
1080 1109 0.172803 AGGTCTTTCCGATCGTTCCG 59.827 55.000 15.09 0.00 41.99 4.30
1081 1110 1.419107 GGTCTTTCCGATCGTTCCGC 61.419 60.000 15.09 0.00 0.00 5.54
1082 1111 1.153706 TCTTTCCGATCGTTCCGCC 60.154 57.895 15.09 0.00 0.00 6.13
1083 1112 2.125431 TTTCCGATCGTTCCGCCC 60.125 61.111 15.09 0.00 0.00 6.13
1084 1113 3.668980 TTTCCGATCGTTCCGCCCC 62.669 63.158 15.09 0.00 0.00 5.80
1099 1128 2.739132 CCCCCGGTAGCGGTTATC 59.261 66.667 29.86 0.00 0.00 1.75
1100 1129 2.739132 CCCCGGTAGCGGTTATCC 59.261 66.667 29.86 0.00 0.00 2.59
1101 1130 1.835712 CCCCGGTAGCGGTTATCCT 60.836 63.158 29.86 0.00 0.00 3.24
1102 1131 1.405272 CCCCGGTAGCGGTTATCCTT 61.405 60.000 29.86 0.00 0.00 3.36
1103 1132 0.466963 CCCGGTAGCGGTTATCCTTT 59.533 55.000 29.86 0.00 0.00 3.11
1104 1133 1.578583 CCGGTAGCGGTTATCCTTTG 58.421 55.000 24.98 0.00 0.00 2.77
1105 1134 0.935196 CGGTAGCGGTTATCCTTTGC 59.065 55.000 6.39 0.00 0.00 3.68
1106 1135 1.472728 CGGTAGCGGTTATCCTTTGCT 60.473 52.381 6.39 0.00 39.59 3.91
1107 1136 1.940613 GGTAGCGGTTATCCTTTGCTG 59.059 52.381 0.00 0.00 37.12 4.41
1108 1137 1.940613 GTAGCGGTTATCCTTTGCTGG 59.059 52.381 0.00 0.00 37.12 4.85
1109 1138 0.328258 AGCGGTTATCCTTTGCTGGT 59.672 50.000 0.00 0.00 33.99 4.00
1110 1139 1.557832 AGCGGTTATCCTTTGCTGGTA 59.442 47.619 0.00 0.00 33.99 3.25
1111 1140 1.940613 GCGGTTATCCTTTGCTGGTAG 59.059 52.381 0.00 0.00 0.00 3.18
1112 1141 1.940613 CGGTTATCCTTTGCTGGTAGC 59.059 52.381 0.00 0.00 42.82 3.58
1113 1142 2.420129 CGGTTATCCTTTGCTGGTAGCT 60.420 50.000 2.24 0.00 42.97 3.32
1114 1143 3.621558 GGTTATCCTTTGCTGGTAGCTT 58.378 45.455 0.00 0.00 42.97 3.74
1115 1144 3.378427 GGTTATCCTTTGCTGGTAGCTTG 59.622 47.826 0.00 0.00 42.97 4.01
1116 1145 1.467920 ATCCTTTGCTGGTAGCTTGC 58.532 50.000 0.00 0.00 42.97 4.01
1117 1146 0.609131 TCCTTTGCTGGTAGCTTGCC 60.609 55.000 0.00 0.00 42.97 4.52
1118 1147 0.610232 CCTTTGCTGGTAGCTTGCCT 60.610 55.000 0.00 0.00 42.97 4.75
1119 1148 0.524862 CTTTGCTGGTAGCTTGCCTG 59.475 55.000 0.00 0.00 42.97 4.85
1120 1149 0.178992 TTTGCTGGTAGCTTGCCTGT 60.179 50.000 12.89 0.00 42.97 4.00
1121 1150 0.890542 TTGCTGGTAGCTTGCCTGTG 60.891 55.000 12.89 4.37 42.97 3.66
1122 1151 2.042831 GCTGGTAGCTTGCCTGTGG 61.043 63.158 12.89 0.00 38.45 4.17
1123 1152 1.679311 CTGGTAGCTTGCCTGTGGA 59.321 57.895 0.00 0.00 0.00 4.02
1124 1153 0.254178 CTGGTAGCTTGCCTGTGGAT 59.746 55.000 0.00 0.00 0.00 3.41
1125 1154 0.698238 TGGTAGCTTGCCTGTGGATT 59.302 50.000 0.00 0.00 0.00 3.01
1126 1155 1.098050 GGTAGCTTGCCTGTGGATTG 58.902 55.000 0.00 0.00 0.00 2.67
1127 1156 0.453390 GTAGCTTGCCTGTGGATTGC 59.547 55.000 0.00 0.00 0.00 3.56
1128 1157 0.329261 TAGCTTGCCTGTGGATTGCT 59.671 50.000 0.00 0.00 0.00 3.91
1129 1158 0.541296 AGCTTGCCTGTGGATTGCTT 60.541 50.000 0.00 0.00 0.00 3.91
1130 1159 0.108945 GCTTGCCTGTGGATTGCTTC 60.109 55.000 0.00 0.00 0.00 3.86
1131 1160 1.542492 CTTGCCTGTGGATTGCTTCT 58.458 50.000 0.00 0.00 0.00 2.85
1132 1161 1.471684 CTTGCCTGTGGATTGCTTCTC 59.528 52.381 0.00 0.00 0.00 2.87
1136 1165 0.392193 CTGTGGATTGCTTCTCGCCT 60.392 55.000 0.00 0.00 38.05 5.52
1157 1187 1.333931 CCTGCGTCGTCTTGCTAGATA 59.666 52.381 0.05 0.00 31.86 1.98
1158 1188 2.030717 CCTGCGTCGTCTTGCTAGATAT 60.031 50.000 0.05 0.00 31.86 1.63
1186 1218 4.150804 GTGGTCAGAACGTGAATCTTTCTC 59.849 45.833 0.00 0.00 36.74 2.87
1246 1280 2.288948 TGGATTTGGTTTGCATGTCAGC 60.289 45.455 0.00 0.00 0.00 4.26
1273 1307 1.830279 CATGGATGCAGTTGACTGGT 58.170 50.000 12.65 0.00 43.94 4.00
1295 1329 2.151502 TGAGGATCTCCCACTCTCAC 57.848 55.000 0.00 0.00 37.41 3.51
1320 1393 5.928264 ACAGTTGCTCTTTTAATTTGATGGC 59.072 36.000 0.00 0.00 0.00 4.40
1330 1403 6.516739 TTTAATTTGATGGCGTGTGGATTA 57.483 33.333 0.00 0.00 0.00 1.75
1334 1407 1.238439 GATGGCGTGTGGATTATGGG 58.762 55.000 0.00 0.00 0.00 4.00
1371 1444 2.951642 TGGGAGCTGTTCTTGACTTTTG 59.048 45.455 0.00 0.00 0.00 2.44
1440 1513 5.565592 TGCCATCATCGCCATTAATTATC 57.434 39.130 0.00 0.00 0.00 1.75
1442 1515 4.496341 GCCATCATCGCCATTAATTATCGG 60.496 45.833 0.00 0.00 0.00 4.18
1466 1540 1.775385 CCGGCAAATAATTGACCCCT 58.225 50.000 0.00 0.00 41.90 4.79
1470 1544 2.539476 GCAAATAATTGACCCCTTGCG 58.461 47.619 0.00 0.00 38.94 4.85
1515 1603 0.596082 CAGTTAACAACCTTGCCCCG 59.404 55.000 8.61 0.00 0.00 5.73
1556 1644 7.591426 GCTAGTTCCTCTGTTTGTGTTAATTTG 59.409 37.037 0.00 0.00 0.00 2.32
1564 1652 5.491982 TGTTTGTGTTAATTTGGCCTTGTT 58.508 33.333 3.32 0.00 0.00 2.83
1582 1670 7.122204 GGCCTTGTTATTTCACTAACCATAGTT 59.878 37.037 0.00 0.00 40.44 2.24
1611 1699 7.793927 AGTATAGCTTCCTACAAGAAATTGC 57.206 36.000 0.00 0.00 0.00 3.56
1612 1700 7.338710 AGTATAGCTTCCTACAAGAAATTGCA 58.661 34.615 0.00 0.00 0.00 4.08
1613 1701 7.995488 AGTATAGCTTCCTACAAGAAATTGCAT 59.005 33.333 0.00 0.00 0.00 3.96
1614 1702 5.320549 AGCTTCCTACAAGAAATTGCATG 57.679 39.130 0.00 0.00 0.00 4.06
1615 1703 3.861689 GCTTCCTACAAGAAATTGCATGC 59.138 43.478 11.82 11.82 0.00 4.06
1651 1739 1.973515 TGACACTTGGTGAGAGCTGAT 59.026 47.619 0.00 0.00 36.96 2.90
1720 1810 7.912250 CAGTTGGTTAGCATCAGAAATATCAAC 59.088 37.037 0.00 0.00 0.00 3.18
1762 1860 7.582667 TGATAACTCGATTTATCTGGTCTGA 57.417 36.000 26.37 9.87 38.69 3.27
1763 1861 7.652727 TGATAACTCGATTTATCTGGTCTGAG 58.347 38.462 26.37 0.00 38.69 3.35
1772 1870 1.924731 TCTGGTCTGAGTGTGTAGGG 58.075 55.000 0.00 0.00 0.00 3.53
1773 1871 0.247736 CTGGTCTGAGTGTGTAGGGC 59.752 60.000 0.00 0.00 0.00 5.19
1775 1873 1.215647 GTCTGAGTGTGTAGGGCCG 59.784 63.158 0.00 0.00 0.00 6.13
1777 1875 0.038599 TCTGAGTGTGTAGGGCCGTA 59.961 55.000 0.00 0.00 0.00 4.02
1956 2054 2.514458 CCACCCAATGGTAAGCTCTT 57.486 50.000 0.00 0.00 45.57 2.85
1987 2091 6.092955 ACTGAACTTCGTTTAGGATACACA 57.907 37.500 4.01 0.00 34.17 3.72
1988 2092 6.518493 ACTGAACTTCGTTTAGGATACACAA 58.482 36.000 4.01 0.00 34.17 3.33
2143 2247 4.821805 CGGGCTATGGTATGTCTTTCAAAT 59.178 41.667 0.00 0.00 0.00 2.32
2179 2284 4.492570 CGCTATCAAATTGTCAACTCCGAC 60.493 45.833 0.00 0.00 36.40 4.79
2206 2311 8.930846 ATATTTTAATTCATCACTGAGGGAGG 57.069 34.615 0.00 0.00 31.68 4.30
2391 2499 2.901839 AGTAGAGACGGCCTGGTTTAAA 59.098 45.455 0.00 0.00 0.00 1.52
2397 2505 3.817084 AGACGGCCTGGTTTAAACTTAAC 59.183 43.478 17.50 5.98 0.00 2.01
2406 2530 7.488150 GCCTGGTTTAAACTTAACATAATCTGC 59.512 37.037 17.50 2.07 0.00 4.26
2454 2596 1.382695 TCTCCCCCGGTGATTCCTC 60.383 63.158 0.00 0.00 0.00 3.71
2476 2618 6.640499 CCTCGCAAAAATCATCTTAACACAAA 59.360 34.615 0.00 0.00 0.00 2.83
2640 2805 6.477253 TGGTTATGAGCAATTACAGTGGTTA 58.523 36.000 0.00 0.00 0.00 2.85
2642 2807 6.038271 GGTTATGAGCAATTACAGTGGTTAGG 59.962 42.308 0.00 0.00 0.00 2.69
2658 2840 2.890945 GTTAGGAAAATGTGCTGGTGGT 59.109 45.455 0.00 0.00 0.00 4.16
2660 2842 2.397597 AGGAAAATGTGCTGGTGGTTT 58.602 42.857 0.00 0.00 0.00 3.27
2676 2858 7.123355 TGGTGGTTTTGATTCTTGAATTCTT 57.877 32.000 7.05 0.00 0.00 2.52
2726 2908 5.164051 CGTGATGAGAATATCGTGTTATGGC 60.164 44.000 0.00 0.00 0.00 4.40
2737 2921 9.905713 AATATCGTGTTATGGCCTATATCATTT 57.094 29.630 3.32 0.00 0.00 2.32
2764 2949 7.465353 TTGCATGAACCAGATTTCATTTCTA 57.535 32.000 0.00 0.00 42.45 2.10
2813 2998 2.266055 CCAGTCCTCCGTTGCCTC 59.734 66.667 0.00 0.00 0.00 4.70
2814 2999 2.266055 CAGTCCTCCGTTGCCTCC 59.734 66.667 0.00 0.00 0.00 4.30
2843 3028 8.780846 TGTTCTTCCTTATGCGTTAAAGAATA 57.219 30.769 0.00 0.00 35.78 1.75
2850 3035 9.990360 TCCTTATGCGTTAAAGAATATCATGTA 57.010 29.630 0.00 0.00 0.00 2.29
2896 3081 1.882623 GCTTTGTAAAGGCTCTGTGCT 59.117 47.619 6.50 0.00 46.52 4.40
2913 3098 6.188407 TCTGTGCTTCTAGTTATGTAGAGGT 58.812 40.000 0.00 0.00 30.59 3.85
2984 3170 1.635487 TGGTAATTGCTCTGGAAGGCT 59.365 47.619 0.00 0.00 32.37 4.58
3000 3186 2.924105 GCTGGTTGGTGCTTCCTGC 61.924 63.158 0.00 0.00 43.25 4.85
3033 3219 8.651588 CCTTGCTTTCGTAATCACATATCTATC 58.348 37.037 0.00 0.00 0.00 2.08
3034 3220 9.196552 CTTGCTTTCGTAATCACATATCTATCA 57.803 33.333 0.00 0.00 0.00 2.15
3035 3221 9.541143 TTGCTTTCGTAATCACATATCTATCAA 57.459 29.630 0.00 0.00 0.00 2.57
3085 3271 2.821366 CCCTGAGACGCATGTGGC 60.821 66.667 11.65 7.81 39.90 5.01
3138 3328 1.896465 GTAAGTGACCTGTCCTGCTCT 59.104 52.381 0.00 0.00 0.00 4.09
3220 3411 4.401519 TGTACAGCCTGAGACCAATAGTAC 59.598 45.833 0.00 0.00 0.00 2.73
3244 3435 4.062293 TGTGCAGTGTTACCTTGTCATAC 58.938 43.478 0.00 0.00 0.00 2.39
3310 3502 0.689623 AGCAGCTAGACAGGCAAAGT 59.310 50.000 0.00 0.00 0.00 2.66
3482 3677 0.953960 AGTTCCATTGCCCGTCGAAC 60.954 55.000 0.00 0.00 34.40 3.95
3603 3798 5.245075 TCACCAAAAACAGAAAGGTTCTTGT 59.755 36.000 0.00 0.00 38.11 3.16
3651 3910 8.773645 GCCATTGTTAATTAATATTTCTTGCCC 58.226 33.333 0.31 0.00 0.00 5.36
3700 4000 5.754782 AGTGCCTATGGTTATGTGAAATGA 58.245 37.500 0.00 0.00 0.00 2.57
3756 4057 2.793933 TGTATCGCTACTCGTTTCTGC 58.206 47.619 0.00 0.00 39.67 4.26
3808 4109 2.772691 GCCCTACCTCCACGAGTCG 61.773 68.421 11.85 11.85 0.00 4.18
3943 4247 2.461110 CGCGAATTCCCTGGGTTCG 61.461 63.158 25.83 25.83 45.35 3.95
4126 4430 0.616111 ACCATCTCAGCTTCTCCGGT 60.616 55.000 0.00 0.00 0.00 5.28
4129 4433 1.411977 CATCTCAGCTTCTCCGGTCAT 59.588 52.381 0.00 0.00 0.00 3.06
4132 4436 2.303022 TCTCAGCTTCTCCGGTCATTTT 59.697 45.455 0.00 0.00 0.00 1.82
4141 4445 0.893270 CCGGTCATTTTGGCCAGTCA 60.893 55.000 5.11 0.00 43.88 3.41
4259 4563 3.461946 GTGTATCTCACAGTGCTTTGC 57.538 47.619 0.00 0.00 45.51 3.68
4381 4700 1.728971 CATCTTGTGTTCTGCTCGACC 59.271 52.381 0.00 0.00 0.00 4.79
4410 4729 2.553602 GTGTGCTCACATGTGAATTCCA 59.446 45.455 27.63 18.62 43.97 3.53
4418 4737 5.904941 TCACATGTGAATTCCATAAATGCC 58.095 37.500 26.02 0.00 36.53 4.40
4496 4815 3.602513 CTTCACGCAGCTGCCTCCT 62.603 63.158 32.07 9.99 37.91 3.69
4528 4847 1.155390 TTGGTCCACCTCGTCTCCT 59.845 57.895 0.00 0.00 36.82 3.69
4541 4873 1.760613 CGTCTCCTTTAGGGCCATGTA 59.239 52.381 6.18 0.00 35.41 2.29
4593 4930 8.300286 TGTTTTAGATGTTTCAGTTGTGTTTGA 58.700 29.630 0.00 0.00 0.00 2.69
4616 4953 3.634397 TTGTATCTTGCCCAGGAAGAG 57.366 47.619 4.85 0.00 33.01 2.85
4621 4958 3.121929 TCTTGCCCAGGAAGAGTAGAT 57.878 47.619 0.00 0.00 0.00 1.98
4624 4961 1.273838 TGCCCAGGAAGAGTAGATGGT 60.274 52.381 0.00 0.00 0.00 3.55
4626 4963 2.752030 CCCAGGAAGAGTAGATGGTGA 58.248 52.381 0.00 0.00 0.00 4.02
4643 4980 3.078837 GGTGACGGCTCCTTAAAAATGA 58.921 45.455 0.95 0.00 0.00 2.57
4717 5058 0.673985 TGAGTGTGGAGGTTGTCTCG 59.326 55.000 0.00 0.00 43.34 4.04
4752 5093 5.354234 TCTTTAGTGGATTTGCTCGGATTTC 59.646 40.000 0.00 0.00 0.00 2.17
4756 5097 1.330829 GGATTTGCTCGGATTTCGTCC 59.669 52.381 0.00 0.00 44.10 4.79
4839 5192 1.067693 CGACAGTGATGCGCTTGTTA 58.932 50.000 9.73 0.00 0.00 2.41
4881 5235 7.794810 CGATGACTTTTCGACTGTCTACTATAG 59.205 40.741 6.21 0.00 38.88 1.31
4931 5286 3.945434 GATGATGGCAGCGCACCG 61.945 66.667 11.47 0.00 0.00 4.94
4977 5333 2.098770 GTCGCTAGGTGGTCTACGAATT 59.901 50.000 0.00 0.00 35.22 2.17
5093 5452 3.728076 ATGTATGTGCCGACGAGTAAT 57.272 42.857 0.00 0.00 0.00 1.89
5126 5485 2.691526 CTGCAAGCAATGATGGGTACAT 59.308 45.455 0.00 0.00 40.85 2.29
5140 5499 5.593679 TGGGTACATTGACTAGTTCTAGC 57.406 43.478 0.00 1.78 0.00 3.42
5148 5507 7.540299 ACATTGACTAGTTCTAGCTTGTAGTC 58.460 38.462 13.73 13.73 39.96 2.59
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 6.573664 ACCTGATTCAATCGATTGTGAAAA 57.426 33.333 31.49 21.19 37.31 2.29
15 16 7.250445 TCATTACCTGATTCAATCGATTGTG 57.750 36.000 31.49 20.26 38.84 3.33
19 20 9.730705 ACATTATCATTACCTGATTCAATCGAT 57.269 29.630 0.00 0.00 42.07 3.59
20 21 9.559732 AACATTATCATTACCTGATTCAATCGA 57.440 29.630 0.00 0.00 42.07 3.59
24 25 9.066892 GGCTAACATTATCATTACCTGATTCAA 57.933 33.333 0.00 0.00 42.07 2.69
26 27 8.854614 AGGCTAACATTATCATTACCTGATTC 57.145 34.615 0.00 0.00 42.07 2.52
27 28 7.885399 GGAGGCTAACATTATCATTACCTGATT 59.115 37.037 0.00 0.00 42.07 2.57
28 29 7.398024 GGAGGCTAACATTATCATTACCTGAT 58.602 38.462 0.00 0.00 46.49 2.90
29 30 6.518369 CGGAGGCTAACATTATCATTACCTGA 60.518 42.308 0.00 0.00 38.53 3.86
30 31 5.639506 CGGAGGCTAACATTATCATTACCTG 59.360 44.000 0.00 0.00 0.00 4.00
31 32 5.307196 ACGGAGGCTAACATTATCATTACCT 59.693 40.000 0.00 0.00 0.00 3.08
35 36 5.290493 TGACGGAGGCTAACATTATCATT 57.710 39.130 0.00 0.00 0.00 2.57
73 74 9.628983 GTTTAGTGTACTTTTTGTTTACGAGAG 57.371 33.333 0.00 0.00 0.00 3.20
74 75 9.149225 TGTTTAGTGTACTTTTTGTTTACGAGA 57.851 29.630 0.00 0.00 0.00 4.04
124 125 2.791004 GCAAGTTGATGCAAGTGACAAC 59.209 45.455 7.16 3.34 45.70 3.32
311 316 6.566141 CCCAATGGTTTTATAGTTTAACCCG 58.434 40.000 0.00 0.00 40.44 5.28
389 396 2.488153 GGCGTGGAGATTTTTACTGCTT 59.512 45.455 0.00 0.00 0.00 3.91
400 407 1.134401 CAACATAGGTGGCGTGGAGAT 60.134 52.381 0.00 0.00 0.00 2.75
412 420 5.423015 AGTTGATGCTAGTGACAACATAGG 58.577 41.667 20.70 0.00 43.06 2.57
466 474 1.522668 TGATGTTGGTTTGCTCGAGG 58.477 50.000 15.58 0.00 0.00 4.63
498 506 9.093458 AGACAGACATTATCATGACCATGTATA 57.907 33.333 17.63 4.62 39.72 1.47
527 535 0.250597 AGGCCTGGTTTAACCGTGAC 60.251 55.000 3.11 5.07 42.58 3.67
536 544 0.035820 TAATTCGCGAGGCCTGGTTT 60.036 50.000 12.00 4.82 0.00 3.27
548 556 7.029925 CATATGTTGCATCATTGTAATTCGC 57.970 36.000 15.16 0.00 29.89 4.70
564 572 9.416794 CTAGTTCTAGGTTATGAGCATATGTTG 57.583 37.037 4.29 0.00 0.00 3.33
566 574 7.950684 TCCTAGTTCTAGGTTATGAGCATATGT 59.049 37.037 20.92 0.00 38.38 2.29
574 582 7.786046 TGTGTTTCCTAGTTCTAGGTTATGA 57.214 36.000 20.92 3.63 38.38 2.15
605 613 6.041979 GGTTTTATAGTATAACCCACGGAGGA 59.958 42.308 1.92 0.00 41.22 3.71
611 619 6.994496 GGGAGTGGTTTTATAGTATAACCCAC 59.006 42.308 26.30 26.30 38.51 4.61
619 627 5.664457 GGAGAAGGGGAGTGGTTTTATAGTA 59.336 44.000 0.00 0.00 0.00 1.82
633 641 2.961536 TTGTATGGAGGAGAAGGGGA 57.038 50.000 0.00 0.00 0.00 4.81
658 666 2.683211 ATTCCAAGTTTGAGCTGGGT 57.317 45.000 0.00 0.00 31.44 4.51
661 669 3.739300 CAGCAAATTCCAAGTTTGAGCTG 59.261 43.478 0.00 0.00 38.51 4.24
662 670 3.385755 ACAGCAAATTCCAAGTTTGAGCT 59.614 39.130 3.03 0.00 38.51 4.09
663 671 3.492011 CACAGCAAATTCCAAGTTTGAGC 59.508 43.478 3.03 0.00 38.51 4.26
707 724 6.351286 GGGAGAGAACATTGGCAATACAAAAT 60.351 38.462 13.23 0.00 33.48 1.82
712 729 3.378427 GTGGGAGAGAACATTGGCAATAC 59.622 47.826 13.23 7.66 0.00 1.89
815 834 6.495526 CCCCTTTTATCCTTTGTTCCAAGTAA 59.504 38.462 0.00 0.00 0.00 2.24
817 836 4.838423 CCCCTTTTATCCTTTGTTCCAAGT 59.162 41.667 0.00 0.00 0.00 3.16
847 866 1.607467 CCCTCCCTTTGCCCACTTG 60.607 63.158 0.00 0.00 0.00 3.16
849 868 2.121506 TCCCTCCCTTTGCCCACT 60.122 61.111 0.00 0.00 0.00 4.00
850 869 2.356667 CTCCCTCCCTTTGCCCAC 59.643 66.667 0.00 0.00 0.00 4.61
851 870 2.121506 ACTCCCTCCCTTTGCCCA 60.122 61.111 0.00 0.00 0.00 5.36
852 871 2.231380 TCACTCCCTCCCTTTGCCC 61.231 63.158 0.00 0.00 0.00 5.36
853 872 1.002011 GTCACTCCCTCCCTTTGCC 60.002 63.158 0.00 0.00 0.00 4.52
854 873 0.606673 GTGTCACTCCCTCCCTTTGC 60.607 60.000 0.00 0.00 0.00 3.68
855 874 0.320771 CGTGTCACTCCCTCCCTTTG 60.321 60.000 0.65 0.00 0.00 2.77
856 875 1.481056 CCGTGTCACTCCCTCCCTTT 61.481 60.000 0.65 0.00 0.00 3.11
857 876 1.913762 CCGTGTCACTCCCTCCCTT 60.914 63.158 0.65 0.00 0.00 3.95
858 877 2.283966 CCGTGTCACTCCCTCCCT 60.284 66.667 0.65 0.00 0.00 4.20
859 878 2.603776 ACCGTGTCACTCCCTCCC 60.604 66.667 0.65 0.00 0.00 4.30
860 879 2.971452 GACCGTGTCACTCCCTCC 59.029 66.667 0.65 0.00 32.09 4.30
861 880 1.924320 CTCGACCGTGTCACTCCCTC 61.924 65.000 0.65 0.00 32.09 4.30
862 881 1.972223 CTCGACCGTGTCACTCCCT 60.972 63.158 0.65 0.00 32.09 4.20
863 882 2.567049 CTCGACCGTGTCACTCCC 59.433 66.667 0.65 0.00 32.09 4.30
1035 1063 2.325661 AGATGGGAAAACCTTTGGGG 57.674 50.000 0.00 0.00 41.11 4.96
1086 1115 0.935196 GCAAAGGATAACCGCTACCG 59.065 55.000 0.00 0.00 41.83 4.02
1087 1116 1.940613 CAGCAAAGGATAACCGCTACC 59.059 52.381 0.00 0.00 41.83 3.18
1088 1117 1.940613 CCAGCAAAGGATAACCGCTAC 59.059 52.381 0.00 0.00 41.83 3.58
1089 1118 1.557832 ACCAGCAAAGGATAACCGCTA 59.442 47.619 0.00 0.00 41.83 4.26
1090 1119 0.328258 ACCAGCAAAGGATAACCGCT 59.672 50.000 0.00 0.00 41.83 5.52
1091 1120 1.940613 CTACCAGCAAAGGATAACCGC 59.059 52.381 0.00 0.00 41.83 5.68
1092 1121 1.940613 GCTACCAGCAAAGGATAACCG 59.059 52.381 0.00 0.00 41.89 4.44
1093 1122 3.283259 AGCTACCAGCAAAGGATAACC 57.717 47.619 0.38 0.00 45.56 2.85
1094 1123 3.181496 GCAAGCTACCAGCAAAGGATAAC 60.181 47.826 0.38 0.00 45.56 1.89
1095 1124 3.016736 GCAAGCTACCAGCAAAGGATAA 58.983 45.455 0.38 0.00 45.56 1.75
1096 1125 2.643551 GCAAGCTACCAGCAAAGGATA 58.356 47.619 0.38 0.00 45.56 2.59
1097 1126 1.467920 GCAAGCTACCAGCAAAGGAT 58.532 50.000 0.38 0.00 45.56 3.24
1098 1127 0.609131 GGCAAGCTACCAGCAAAGGA 60.609 55.000 0.38 0.00 45.56 3.36
1099 1128 0.610232 AGGCAAGCTACCAGCAAAGG 60.610 55.000 8.33 0.00 45.56 3.11
1100 1129 0.524862 CAGGCAAGCTACCAGCAAAG 59.475 55.000 8.33 0.00 45.56 2.77
1101 1130 0.178992 ACAGGCAAGCTACCAGCAAA 60.179 50.000 8.33 0.00 45.56 3.68
1102 1131 0.890542 CACAGGCAAGCTACCAGCAA 60.891 55.000 8.33 0.00 45.56 3.91
1103 1132 1.302752 CACAGGCAAGCTACCAGCA 60.303 57.895 8.33 0.00 45.56 4.41
1104 1133 2.042831 CCACAGGCAAGCTACCAGC 61.043 63.158 8.33 0.56 42.84 4.85
1105 1134 0.254178 ATCCACAGGCAAGCTACCAG 59.746 55.000 8.33 2.82 0.00 4.00
1106 1135 0.698238 AATCCACAGGCAAGCTACCA 59.302 50.000 8.33 0.00 0.00 3.25
1107 1136 1.098050 CAATCCACAGGCAAGCTACC 58.902 55.000 0.00 0.00 0.00 3.18
1108 1137 0.453390 GCAATCCACAGGCAAGCTAC 59.547 55.000 0.00 0.00 0.00 3.58
1109 1138 0.329261 AGCAATCCACAGGCAAGCTA 59.671 50.000 0.00 0.00 0.00 3.32
1110 1139 0.541296 AAGCAATCCACAGGCAAGCT 60.541 50.000 0.00 0.00 0.00 3.74
1111 1140 0.108945 GAAGCAATCCACAGGCAAGC 60.109 55.000 0.00 0.00 0.00 4.01
1112 1141 1.471684 GAGAAGCAATCCACAGGCAAG 59.528 52.381 0.00 0.00 0.00 4.01
1113 1142 1.538047 GAGAAGCAATCCACAGGCAA 58.462 50.000 0.00 0.00 0.00 4.52
1114 1143 0.674581 CGAGAAGCAATCCACAGGCA 60.675 55.000 0.00 0.00 0.00 4.75
1115 1144 2.093216 CGAGAAGCAATCCACAGGC 58.907 57.895 0.00 0.00 0.00 4.85
1136 1165 0.958876 TCTAGCAAGACGACGCAGGA 60.959 55.000 0.00 0.00 0.00 3.86
1148 1178 5.972935 TCTGACCACGAAAATATCTAGCAA 58.027 37.500 0.00 0.00 0.00 3.91
1157 1187 2.828877 TCACGTTCTGACCACGAAAAT 58.171 42.857 8.71 0.00 40.20 1.82
1158 1188 2.296831 TCACGTTCTGACCACGAAAA 57.703 45.000 8.71 0.00 40.20 2.29
1186 1218 2.672996 CCAGCCAAGAACCACGGG 60.673 66.667 0.00 0.00 0.00 5.28
1273 1307 2.313041 TGAGAGTGGGAGATCCTCAAGA 59.687 50.000 0.00 0.00 36.20 3.02
1295 1329 6.128742 GCCATCAAATTAAAAGAGCAACTGTG 60.129 38.462 0.00 0.00 0.00 3.66
1320 1393 2.221169 CACCATCCCATAATCCACACG 58.779 52.381 0.00 0.00 0.00 4.49
1330 1403 0.398948 GCCCAAATCCACCATCCCAT 60.399 55.000 0.00 0.00 0.00 4.00
1334 1407 1.044790 CCCAGCCCAAATCCACCATC 61.045 60.000 0.00 0.00 0.00 3.51
1371 1444 2.045131 CAAGGAGCTGCTCAAGGCC 61.045 63.158 28.95 13.61 40.92 5.19
1442 1515 2.267426 GTCAATTATTTGCCGGCCAAC 58.733 47.619 26.77 1.66 31.97 3.77
1452 1525 4.882842 AAACGCAAGGGGTCAATTATTT 57.117 36.364 0.00 0.00 46.39 1.40
1466 1540 5.178067 GCTACCTCTAGTAAACAAAACGCAA 59.822 40.000 0.00 0.00 0.00 4.85
1470 1544 7.958053 TTCTGCTACCTCTAGTAAACAAAAC 57.042 36.000 0.00 0.00 0.00 2.43
1556 1644 5.914898 ATGGTTAGTGAAATAACAAGGCC 57.085 39.130 0.00 0.00 37.38 5.19
1589 1677 7.255242 GCATGCAATTTCTTGTAGGAAGCTATA 60.255 37.037 14.21 0.00 31.50 1.31
1590 1678 6.460676 GCATGCAATTTCTTGTAGGAAGCTAT 60.461 38.462 14.21 0.00 31.50 2.97
1594 1682 4.100529 CGCATGCAATTTCTTGTAGGAAG 58.899 43.478 19.57 0.00 31.50 3.46
1597 1685 2.159338 AGCGCATGCAATTTCTTGTAGG 60.159 45.455 19.57 0.00 46.23 3.18
1601 1689 1.850441 GCTAGCGCATGCAATTTCTTG 59.150 47.619 19.57 7.99 46.23 3.02
1604 1692 1.202222 ACAGCTAGCGCATGCAATTTC 60.202 47.619 19.57 3.29 46.23 2.17
1608 1696 1.647545 GGAACAGCTAGCGCATGCAA 61.648 55.000 19.57 0.99 46.23 4.08
1610 1698 1.817099 AGGAACAGCTAGCGCATGC 60.817 57.895 11.47 13.80 43.24 4.06
1611 1699 0.460811 TCAGGAACAGCTAGCGCATG 60.461 55.000 11.47 4.89 39.10 4.06
1612 1700 0.467384 ATCAGGAACAGCTAGCGCAT 59.533 50.000 11.47 0.00 39.10 4.73
1613 1701 0.460811 CATCAGGAACAGCTAGCGCA 60.461 55.000 11.47 0.00 39.10 6.09
1614 1702 0.179100 TCATCAGGAACAGCTAGCGC 60.179 55.000 9.55 0.00 0.00 5.92
1615 1703 1.134995 TGTCATCAGGAACAGCTAGCG 60.135 52.381 9.55 7.05 0.00 4.26
1651 1739 5.764686 ACAATGCTGTCTGTTCATGTCTTTA 59.235 36.000 0.00 0.00 0.00 1.85
1733 1831 6.986817 ACCAGATAAATCGAGTTATCAACCAG 59.013 38.462 34.27 23.28 41.19 4.00
1762 1860 0.606604 CAGTTACGGCCCTACACACT 59.393 55.000 0.00 0.00 0.00 3.55
1763 1861 0.319405 ACAGTTACGGCCCTACACAC 59.681 55.000 0.00 0.00 0.00 3.82
1772 1870 4.165779 CCAAATGAATCAACAGTTACGGC 58.834 43.478 0.00 0.00 0.00 5.68
1773 1871 5.371115 ACCAAATGAATCAACAGTTACGG 57.629 39.130 0.00 0.00 0.00 4.02
1777 1875 9.696917 GAAAGATAACCAAATGAATCAACAGTT 57.303 29.630 0.00 0.00 0.00 3.16
1801 1899 5.007626 GGACGCTGTATTATTGCAGAATGAA 59.992 40.000 6.87 0.00 39.69 2.57
1802 1900 4.511454 GGACGCTGTATTATTGCAGAATGA 59.489 41.667 6.87 0.00 39.69 2.57
1917 2015 2.488153 GGCCATAGTCAGTGTTTTGACC 59.512 50.000 0.00 0.00 46.81 4.02
2006 2110 2.228822 CACACCCCGGAATCAAAGAAAG 59.771 50.000 0.73 0.00 0.00 2.62
2007 2111 2.235016 CACACCCCGGAATCAAAGAAA 58.765 47.619 0.73 0.00 0.00 2.52
2152 2256 3.501828 AGTTGACAATTTGATAGCGTGCA 59.498 39.130 2.79 0.00 0.00 4.57
2232 2340 7.759886 AGCGTGTATTCAGATTATTATATGCGT 59.240 33.333 0.00 0.00 0.00 5.24
2251 2359 0.457853 GCGAATCCACTCAGCGTGTA 60.458 55.000 0.00 0.00 42.20 2.90
2266 2374 6.128282 GGACTGTTGAAAGAATGATAAGCGAA 60.128 38.462 0.00 0.00 0.00 4.70
2269 2377 6.500684 TGGACTGTTGAAAGAATGATAAGC 57.499 37.500 0.00 0.00 0.00 3.09
2363 2471 2.737252 CAGGCCGTCTCTACTTGAAAAC 59.263 50.000 0.00 0.00 0.00 2.43
2369 2477 1.349067 AAACCAGGCCGTCTCTACTT 58.651 50.000 0.00 0.00 0.00 2.24
2406 2530 6.295916 GGTCCCCACCTCTTATGTTATATGAG 60.296 46.154 0.00 0.00 40.00 2.90
2411 2535 3.743132 TGGTCCCCACCTCTTATGTTAT 58.257 45.455 0.00 0.00 44.17 1.89
2434 2576 1.689582 GGAATCACCGGGGGAGAGT 60.690 63.158 2.42 0.00 0.00 3.24
2454 2596 7.159437 TGTTTGTGTTAAGATGATTTTTGCG 57.841 32.000 0.00 0.00 0.00 4.85
2506 2670 5.649782 AAAACCTGCCATTAGAGTTCATG 57.350 39.130 0.00 0.00 0.00 3.07
2507 2671 7.961326 AATAAAACCTGCCATTAGAGTTCAT 57.039 32.000 0.00 0.00 0.00 2.57
2606 2770 6.780457 ATTGCTCATAACCATAAAACAGCT 57.220 33.333 0.00 0.00 0.00 4.24
2640 2805 2.086610 AACCACCAGCACATTTTCCT 57.913 45.000 0.00 0.00 0.00 3.36
2642 2807 3.791245 TCAAAACCACCAGCACATTTTC 58.209 40.909 0.00 0.00 0.00 2.29
2676 2858 9.998106 GGCCTACTAGAAAATAGTGATCAATAA 57.002 33.333 7.01 0.00 0.00 1.40
2726 2908 7.490840 TGGTTCATGCAAACAAATGATATAGG 58.509 34.615 3.80 0.00 33.01 2.57
2737 2921 4.933505 TGAAATCTGGTTCATGCAAACA 57.066 36.364 3.80 0.00 32.56 2.83
2764 2949 4.820775 ACTAGTGGGTATGTGGATGAGAT 58.179 43.478 0.00 0.00 0.00 2.75
2813 2998 1.017387 GCATAAGGAAGAACAGCCGG 58.983 55.000 0.00 0.00 0.00 6.13
2814 2999 0.652592 CGCATAAGGAAGAACAGCCG 59.347 55.000 0.00 0.00 0.00 5.52
2843 3028 8.746530 AGTTCAAGCAAATCAGAAATACATGAT 58.253 29.630 0.00 0.00 37.77 2.45
2850 3035 5.471456 ACGAGAGTTCAAGCAAATCAGAAAT 59.529 36.000 0.00 0.00 46.40 2.17
2851 3036 4.816385 ACGAGAGTTCAAGCAAATCAGAAA 59.184 37.500 0.00 0.00 46.40 2.52
2862 3047 2.213499 ACAAAGCCACGAGAGTTCAAG 58.787 47.619 0.00 0.00 46.40 3.02
2863 3048 2.325583 ACAAAGCCACGAGAGTTCAA 57.674 45.000 0.00 0.00 46.40 2.69
2896 3081 6.363065 ACATCCGACCTCTACATAACTAGAA 58.637 40.000 0.00 0.00 0.00 2.10
2913 3098 1.411246 GCTGGTACCACATACATCCGA 59.589 52.381 11.60 0.00 35.23 4.55
3000 3186 4.215399 TGATTACGAAAGCAAGGTTTGGAG 59.785 41.667 12.51 2.87 0.00 3.86
3085 3271 4.650754 ATAACTAGTGCCTAACAGGACG 57.349 45.455 0.00 0.00 37.67 4.79
3220 3411 2.942376 TGACAAGGTAACACTGCACAAG 59.058 45.455 0.00 0.00 41.41 3.16
3244 3435 0.174845 TGAAGGCATCTTCCGTACCG 59.825 55.000 4.01 0.00 46.61 4.02
3392 3585 3.582647 TCCATGTACAACTGGTCAGTCAT 59.417 43.478 13.88 1.27 41.58 3.06
3439 3634 2.825836 GTTGCAGATGCCCCTCCG 60.826 66.667 1.72 0.00 41.18 4.63
3482 3677 2.030262 GGGCTCATCCGCTGCTAG 59.970 66.667 0.00 0.00 34.94 3.42
3603 3798 4.732355 GCAAAGTAAACAAAGGACAAGCGA 60.732 41.667 0.00 0.00 0.00 4.93
3651 3910 4.433615 TGAGCTTCTTATAAGTTGCGAGG 58.566 43.478 12.19 0.00 33.31 4.63
3756 4057 0.040067 GCGTTCAAAGTCAGGCCAAG 60.040 55.000 5.01 0.00 0.00 3.61
3901 4205 2.263540 GCAATGGCCTTGGTGCAG 59.736 61.111 3.32 0.00 36.97 4.41
3943 4247 1.113517 TGCCTAGCCGTAGATGGGTC 61.114 60.000 0.00 0.00 40.88 4.46
3993 4297 1.596934 GAGGACATCGCCTTGGACA 59.403 57.895 0.00 0.00 38.73 4.02
4126 4430 0.597568 CGCTTGACTGGCCAAAATGA 59.402 50.000 7.01 0.00 0.00 2.57
4129 4433 1.452145 GGTCGCTTGACTGGCCAAAA 61.452 55.000 7.01 0.39 42.47 2.44
4132 4436 4.680237 CGGTCGCTTGACTGGCCA 62.680 66.667 4.71 4.71 43.90 5.36
4141 4445 4.320494 CCTTATTACGTATACCGGTCGCTT 60.320 45.833 12.40 0.00 42.24 4.68
4249 4553 0.454600 CTATGGGCTGCAAAGCACTG 59.545 55.000 0.50 0.00 39.34 3.66
4253 4557 1.403323 GAGAACTATGGGCTGCAAAGC 59.597 52.381 0.50 0.00 0.00 3.51
4256 4560 0.107703 CCGAGAACTATGGGCTGCAA 60.108 55.000 0.50 0.00 0.00 4.08
4257 4561 1.522092 CCGAGAACTATGGGCTGCA 59.478 57.895 0.50 0.00 0.00 4.41
4258 4562 1.889573 GCCGAGAACTATGGGCTGC 60.890 63.158 0.00 0.00 42.29 5.25
4259 4563 4.445699 GCCGAGAACTATGGGCTG 57.554 61.111 0.00 0.00 42.29 4.85
4345 4664 0.931005 GATGAGTTCCGCGACCAATC 59.069 55.000 8.23 0.00 0.00 2.67
4418 4737 8.577939 CAACTGCTGAAATTTTATGATTACACG 58.422 33.333 0.00 0.00 0.00 4.49
4509 4828 1.186267 AGGAGACGAGGTGGACCAAC 61.186 60.000 0.00 0.00 38.89 3.77
4554 4886 0.594110 TAAAACAAAGCCCTTCCGCG 59.406 50.000 0.00 0.00 0.00 6.46
4593 4930 3.330701 TCTTCCTGGGCAAGATACAAACT 59.669 43.478 0.00 0.00 0.00 2.66
4616 4953 0.824759 AAGGAGCCGTCACCATCTAC 59.175 55.000 0.00 0.00 0.00 2.59
4621 4958 2.642154 TTTTTAAGGAGCCGTCACCA 57.358 45.000 0.00 0.00 0.00 4.17
4624 4961 5.975693 ATTTCATTTTTAAGGAGCCGTCA 57.024 34.783 0.00 0.00 0.00 4.35
4626 4963 7.892609 ACTTTATTTCATTTTTAAGGAGCCGT 58.107 30.769 0.00 0.00 0.00 5.68
4643 4980 4.383880 GGCTAGACGGGGAGAACTTTATTT 60.384 45.833 0.00 0.00 0.00 1.40
4697 5035 1.273606 CGAGACAACCTCCACACTCAT 59.726 52.381 0.00 0.00 38.71 2.90
4717 5058 2.838202 TCCACTAAAGACAGATCCACCC 59.162 50.000 0.00 0.00 0.00 4.61
4752 5093 5.977725 ACATAAACGTAGATGATCAAGGACG 59.022 40.000 19.21 19.21 36.42 4.79
4756 5097 9.478019 GAAAACACATAAACGTAGATGATCAAG 57.522 33.333 14.66 0.00 0.00 3.02
4835 5188 5.936187 TCGTGTTAAGACCCCATATAACA 57.064 39.130 0.00 0.00 36.27 2.41
4839 5192 4.654262 AGTCATCGTGTTAAGACCCCATAT 59.346 41.667 0.00 0.00 0.00 1.78
4881 5235 0.741915 TGGAACCGGACAAAACTTGC 59.258 50.000 9.46 0.00 0.00 4.01
4931 5286 3.436700 ACAAACACTAAAGCAAGCCAC 57.563 42.857 0.00 0.00 0.00 5.01
4937 5293 3.732219 CGACGACTACAAACACTAAAGCA 59.268 43.478 0.00 0.00 0.00 3.91
5078 5437 2.159156 AGCAATATTACTCGTCGGCACA 60.159 45.455 0.00 0.00 0.00 4.57
5081 5440 1.192534 GCAGCAATATTACTCGTCGGC 59.807 52.381 0.00 0.00 0.00 5.54
5083 5442 3.602491 GCTTGCAGCAATATTACTCGTCG 60.602 47.826 8.67 0.00 41.89 5.12
5113 5472 7.200434 AGAACTAGTCAATGTACCCATCATT 57.800 36.000 0.00 0.00 36.16 2.57
5126 5485 8.102047 ACTAGACTACAAGCTAGAACTAGTCAA 58.898 37.037 14.51 0.00 37.05 3.18


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

AutoCloner maintained by Alex Coulton.