Multiple sequence alignment - TraesCS3A01G041700

Loading Multiple Alignment...

Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS3A01G041700 chr3A 100.000 3028 0 0 1 3028 22473909 22476936 0.000000e+00 5592.0
1 TraesCS3A01G041700 chr3A 84.534 1222 115 35 1154 2354 22429857 22428689 0.000000e+00 1142.0
2 TraesCS3A01G041700 chr3A 85.530 1085 104 29 1154 2220 22422661 22421612 0.000000e+00 1085.0
3 TraesCS3A01G041700 chr3A 96.970 33 0 1 1577 1608 658864927 658864895 2.000000e-03 54.7
4 TraesCS3A01G041700 chr3D 85.051 2368 175 89 187 2440 14230987 14228685 0.000000e+00 2246.0
5 TraesCS3A01G041700 chr3D 88.369 705 61 9 1125 1826 14278312 14278998 0.000000e+00 828.0
6 TraesCS3A01G041700 chr3D 80.657 548 64 25 1817 2354 14280099 14280614 1.320000e-103 387.0
7 TraesCS3A01G041700 chr3D 87.879 66 8 0 2356 2421 14280820 14280885 9.000000e-11 78.7
8 TraesCS3A01G041700 chr3B 86.812 1926 126 67 612 2465 21004277 21002408 0.000000e+00 2032.0
9 TraesCS3A01G041700 chr3B 88.540 733 60 8 1154 1886 21161541 21162249 0.000000e+00 867.0
10 TraesCS3A01G041700 chr3B 81.226 522 41 30 1872 2354 21162858 21163361 4.770000e-98 368.0
11 TraesCS3A01G041700 chr3B 98.507 67 1 0 2962 3028 21002058 21001992 5.300000e-23 119.0
12 TraesCS3A01G041700 chr3B 98.387 62 1 0 8 69 21005114 21005053 3.190000e-20 110.0
13 TraesCS3A01G041700 chr3B 90.667 75 5 1 466 538 21004437 21004363 6.910000e-17 99.0
14 TraesCS3A01G041700 chr4A 91.667 120 6 3 1394 1513 153776722 153776837 2.420000e-36 163.0
15 TraesCS3A01G041700 chr2D 91.667 120 6 3 1394 1513 499309577 499309462 2.420000e-36 163.0
16 TraesCS3A01G041700 chr6B 92.453 53 3 1 2518 2569 151557491 151557543 1.160000e-09 75.0
17 TraesCS3A01G041700 chr7B 80.220 91 17 1 2505 2594 421805685 421805595 1.950000e-07 67.6


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 TraesCS3A01G041700 chr3A 22473909 22476936 3027 False 5592.000000 5592 100.00000 1 3028 1 chr3A.!!$F1 3027
1 TraesCS3A01G041700 chr3A 22428689 22429857 1168 True 1142.000000 1142 84.53400 1154 2354 1 chr3A.!!$R2 1200
2 TraesCS3A01G041700 chr3A 22421612 22422661 1049 True 1085.000000 1085 85.53000 1154 2220 1 chr3A.!!$R1 1066
3 TraesCS3A01G041700 chr3D 14228685 14230987 2302 True 2246.000000 2246 85.05100 187 2440 1 chr3D.!!$R1 2253
4 TraesCS3A01G041700 chr3D 14278312 14280885 2573 False 431.233333 828 85.63500 1125 2421 3 chr3D.!!$F1 1296
5 TraesCS3A01G041700 chr3B 21161541 21163361 1820 False 617.500000 867 84.88300 1154 2354 2 chr3B.!!$F1 1200
6 TraesCS3A01G041700 chr3B 21001992 21005114 3122 True 590.000000 2032 93.59325 8 3028 4 chr3B.!!$R1 3020

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
429 732 0.321298 CGTTCCGTTCCACCCAGATT 60.321 55.0 0.00 0.0 0.00 2.40 F
1077 1492 0.254747 CTCTCTCTGAGGAGTCGGGT 59.745 60.0 4.59 0.0 40.29 5.28 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1736 2173 1.466529 CCACTGACGACGACTGATCAG 60.467 57.143 21.37 21.37 43.47 2.90 R
2988 5581 0.579156 GCTAGCTTCGGCGAGAAATG 59.421 55.000 10.46 3.34 44.63 2.32 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
69 70 0.893727 ATCCAAGTTCGTGCCAACCC 60.894 55.000 0.00 0.00 0.00 4.11
70 71 1.528309 CCAAGTTCGTGCCAACCCT 60.528 57.895 0.00 0.00 0.00 4.34
71 72 1.106944 CCAAGTTCGTGCCAACCCTT 61.107 55.000 0.00 0.00 0.00 3.95
73 74 1.950909 CAAGTTCGTGCCAACCCTTTA 59.049 47.619 0.00 0.00 0.00 1.85
74 75 2.351706 AGTTCGTGCCAACCCTTTAA 57.648 45.000 0.00 0.00 0.00 1.52
75 76 2.657143 AGTTCGTGCCAACCCTTTAAA 58.343 42.857 0.00 0.00 0.00 1.52
76 77 3.025262 AGTTCGTGCCAACCCTTTAAAA 58.975 40.909 0.00 0.00 0.00 1.52
112 410 1.746615 GGCATGGCATCACGTCTGT 60.747 57.895 15.47 0.00 0.00 3.41
114 412 1.300971 GCATGGCATCACGTCTGTGT 61.301 55.000 0.00 0.00 46.49 3.72
115 413 1.159285 CATGGCATCACGTCTGTGTT 58.841 50.000 0.00 0.00 46.49 3.32
133 431 2.097791 TGTTTGTTTGGTCGCCTTACAC 59.902 45.455 0.00 0.00 0.00 2.90
136 434 1.944024 TGTTTGGTCGCCTTACACTTG 59.056 47.619 0.00 0.00 0.00 3.16
146 444 4.273969 TCGCCTTACACTTGTTTAACCTTG 59.726 41.667 0.00 0.00 0.00 3.61
148 446 5.220892 CGCCTTACACTTGTTTAACCTTGAA 60.221 40.000 0.00 0.00 0.00 2.69
150 448 6.861572 GCCTTACACTTGTTTAACCTTGAATC 59.138 38.462 0.00 0.00 0.00 2.52
151 449 7.469456 GCCTTACACTTGTTTAACCTTGAATCA 60.469 37.037 0.00 0.00 0.00 2.57
153 451 9.796120 CTTACACTTGTTTAACCTTGAATCAAA 57.204 29.630 0.00 0.00 0.00 2.69
155 453 8.702163 ACACTTGTTTAACCTTGAATCAAAAG 57.298 30.769 0.00 0.00 0.00 2.27
156 454 8.527810 ACACTTGTTTAACCTTGAATCAAAAGA 58.472 29.630 6.75 0.00 0.00 2.52
167 465 8.992073 ACCTTGAATCAAAAGATTATGTTTTGC 58.008 29.630 18.78 8.87 42.28 3.68
171 469 8.486383 TGAATCAAAAGATTATGTTTTGCAACG 58.514 29.630 18.78 0.50 42.28 4.10
172 470 7.945033 ATCAAAAGATTATGTTTTGCAACGT 57.055 28.000 18.78 0.00 42.28 3.99
173 471 9.469807 AATCAAAAGATTATGTTTTGCAACGTA 57.530 25.926 18.78 5.17 42.28 3.57
176 474 8.751335 CAAAAGATTATGTTTTGCAACGTAGTT 58.249 29.630 13.25 0.00 42.47 2.24
189 487 1.875514 ACGTAGTTTCCGGGAAAAAGC 59.124 47.619 23.05 11.58 37.78 3.51
198 496 1.226018 GGGAAAAAGCGATCGTGCG 60.226 57.895 17.81 0.00 40.67 5.34
212 510 1.996898 TCGTGCGCTCGTCAAATATTT 59.003 42.857 28.33 0.00 0.00 1.40
254 552 9.004717 AGTATATAGTATCGTAGCATAGCATGG 57.995 37.037 0.00 0.00 0.00 3.66
259 557 3.582714 TCGTAGCATAGCATGGATGAG 57.417 47.619 0.00 0.00 0.00 2.90
293 591 0.512952 GCACCGGCTAATTATCGCAG 59.487 55.000 0.00 0.00 36.96 5.18
315 613 2.614057 CCACGATAAAATGGAGCCAGAC 59.386 50.000 0.00 0.00 38.34 3.51
317 615 2.222027 CGATAAAATGGAGCCAGACCC 58.778 52.381 0.00 0.00 0.00 4.46
318 616 2.587522 GATAAAATGGAGCCAGACCCC 58.412 52.381 0.00 0.00 0.00 4.95
325 623 1.606601 GAGCCAGACCCCCAAAACC 60.607 63.158 0.00 0.00 0.00 3.27
335 633 1.560505 CCCCAAAACCAGCTGCTAAT 58.439 50.000 8.66 0.00 0.00 1.73
336 634 1.901833 CCCCAAAACCAGCTGCTAATT 59.098 47.619 8.66 0.00 0.00 1.40
337 635 3.096092 CCCCAAAACCAGCTGCTAATTA 58.904 45.455 8.66 0.00 0.00 1.40
354 652 7.465989 TGCTAATTAAACGAAAACTAATCCGG 58.534 34.615 0.00 0.00 0.00 5.14
389 692 0.944386 CACCACTCACGTTCAAAGGG 59.056 55.000 0.00 0.00 0.00 3.95
407 710 1.666872 GCACGACCCATATACCCGC 60.667 63.158 0.00 0.00 0.00 6.13
408 711 1.005394 CACGACCCATATACCCGCC 60.005 63.158 0.00 0.00 0.00 6.13
412 715 2.926242 CCCATATACCCGCCCCGT 60.926 66.667 0.00 0.00 0.00 5.28
413 716 2.522367 CCCATATACCCGCCCCGTT 61.522 63.158 0.00 0.00 0.00 4.44
429 732 0.321298 CGTTCCGTTCCACCCAGATT 60.321 55.000 0.00 0.00 0.00 2.40
431 734 0.768622 TTCCGTTCCACCCAGATTGT 59.231 50.000 0.00 0.00 0.00 2.71
457 770 8.195436 TCGATAGATAGACCACCTTTTTAGTTG 58.805 37.037 0.00 0.00 42.67 3.16
492 817 6.064060 TCTAATCTGGTGGCAGGAAAATATG 58.936 40.000 0.00 0.00 0.00 1.78
493 818 3.017048 TCTGGTGGCAGGAAAATATGG 57.983 47.619 0.00 0.00 0.00 2.74
542 883 4.803426 GCTCACCTCACGCGGGAG 62.803 72.222 31.35 31.35 34.62 4.30
592 935 3.656045 CGGTGGGTGGCAACGAAC 61.656 66.667 0.00 0.00 42.51 3.95
593 936 3.656045 GGTGGGTGGCAACGAACG 61.656 66.667 0.00 0.00 42.51 3.95
689 1067 3.017442 TCTCGCCCCGAATAGATAGATG 58.983 50.000 0.00 0.00 34.74 2.90
705 1087 2.370349 AGATGGAGTAGGTCAGACACG 58.630 52.381 2.17 0.00 0.00 4.49
725 1109 1.615883 GCACAGTCACAGGAGAGAGAA 59.384 52.381 0.00 0.00 0.00 2.87
726 1110 2.609244 GCACAGTCACAGGAGAGAGAAC 60.609 54.545 0.00 0.00 0.00 3.01
728 1112 1.883275 CAGTCACAGGAGAGAGAACGT 59.117 52.381 0.00 0.00 0.00 3.99
730 1114 1.880675 GTCACAGGAGAGAGAACGTGA 59.119 52.381 0.00 0.00 0.00 4.35
731 1115 2.095466 GTCACAGGAGAGAGAACGTGAG 60.095 54.545 0.00 0.00 34.30 3.51
732 1116 2.155279 CACAGGAGAGAGAACGTGAGA 58.845 52.381 0.00 0.00 0.00 3.27
734 1118 3.192422 CACAGGAGAGAGAACGTGAGAAT 59.808 47.826 0.00 0.00 0.00 2.40
735 1119 3.829601 ACAGGAGAGAGAACGTGAGAATT 59.170 43.478 0.00 0.00 0.00 2.17
736 1120 4.282195 ACAGGAGAGAGAACGTGAGAATTT 59.718 41.667 0.00 0.00 0.00 1.82
737 1121 5.221541 ACAGGAGAGAGAACGTGAGAATTTT 60.222 40.000 0.00 0.00 0.00 1.82
738 1122 5.698545 CAGGAGAGAGAACGTGAGAATTTTT 59.301 40.000 0.00 0.00 0.00 1.94
907 1319 1.535860 GCACGAGTGGTTGTTTTGCAT 60.536 47.619 5.32 0.00 0.00 3.96
910 1322 2.118683 CGAGTGGTTGTTTTGCATGTG 58.881 47.619 0.00 0.00 0.00 3.21
1022 1435 1.607148 GCACCGCTTTTTGTACTCCTT 59.393 47.619 0.00 0.00 0.00 3.36
1067 1482 1.154207 CGTTTCGCGCTCTCTCTGA 60.154 57.895 5.56 0.00 0.00 3.27
1068 1483 1.131037 CGTTTCGCGCTCTCTCTGAG 61.131 60.000 5.56 0.00 45.33 3.35
1069 1484 0.800300 GTTTCGCGCTCTCTCTGAGG 60.800 60.000 5.56 0.00 42.87 3.86
1070 1485 0.960861 TTTCGCGCTCTCTCTGAGGA 60.961 55.000 5.56 0.56 42.87 3.71
1071 1486 1.372838 TTCGCGCTCTCTCTGAGGAG 61.373 60.000 5.56 14.90 42.87 3.69
1073 1488 1.727467 GCGCTCTCTCTGAGGAGTC 59.273 63.158 18.25 12.37 42.87 3.36
1074 1489 2.013807 CGCTCTCTCTGAGGAGTCG 58.986 63.158 18.25 17.32 42.87 4.18
1075 1490 1.436195 CGCTCTCTCTGAGGAGTCGG 61.436 65.000 18.25 9.19 42.87 4.79
1076 1491 1.101049 GCTCTCTCTGAGGAGTCGGG 61.101 65.000 18.25 1.59 42.87 5.14
1077 1492 0.254747 CTCTCTCTGAGGAGTCGGGT 59.745 60.000 4.59 0.00 40.29 5.28
1078 1493 0.699399 TCTCTCTGAGGAGTCGGGTT 59.301 55.000 4.59 0.00 40.29 4.11
1103 1522 3.708734 CGTTCACGTCCGTTGCCC 61.709 66.667 0.00 0.00 34.11 5.36
1104 1523 3.351416 GTTCACGTCCGTTGCCCC 61.351 66.667 0.00 0.00 0.00 5.80
1136 1562 3.618171 CCTCCGAGGGAAACGAAAA 57.382 52.632 6.53 0.00 0.00 2.29
1142 1568 2.737252 CCGAGGGAAACGAAAAGAAGAG 59.263 50.000 0.00 0.00 0.00 2.85
1144 1570 3.808174 CGAGGGAAACGAAAAGAAGAGTT 59.192 43.478 0.00 0.00 0.00 3.01
1178 1612 4.647825 GAGAGCTCCTCCTCGTCA 57.352 61.111 10.93 0.00 36.95 4.35
1179 1613 3.109847 GAGAGCTCCTCCTCGTCAT 57.890 57.895 10.93 0.00 36.95 3.06
1180 1614 0.951558 GAGAGCTCCTCCTCGTCATC 59.048 60.000 10.93 0.00 36.95 2.92
1213 1650 2.235016 CGTATACCGGCGGCAACAG 61.235 63.158 28.71 11.56 0.00 3.16
1766 2207 4.736896 GTCAGTGGACGGGCGGAC 62.737 72.222 0.00 0.00 33.68 4.79
1936 4114 7.715265 TGATGTAGAGAGAACAAAAAGTCAC 57.285 36.000 0.00 0.00 0.00 3.67
1937 4115 7.272244 TGATGTAGAGAGAACAAAAAGTCACA 58.728 34.615 0.00 0.00 0.00 3.58
1948 4126 6.927933 ACAAAAAGTCACACGAAGAAAAAG 57.072 33.333 0.00 0.00 0.00 2.27
1951 4129 7.812669 ACAAAAAGTCACACGAAGAAAAAGAAT 59.187 29.630 0.00 0.00 0.00 2.40
1952 4130 7.971004 AAAAGTCACACGAAGAAAAAGAATC 57.029 32.000 0.00 0.00 0.00 2.52
1956 4149 6.422400 AGTCACACGAAGAAAAAGAATCTCTC 59.578 38.462 0.00 0.00 0.00 3.20
2072 4310 9.905171 TTTTATTTTGGCCAAGAAAAATTATGC 57.095 25.926 19.48 0.00 37.25 3.14
2075 4313 7.665561 TTTTGGCCAAGAAAAATTATGCTAC 57.334 32.000 19.48 0.00 0.00 3.58
2077 4315 7.710676 TTGGCCAAGAAAAATTATGCTACTA 57.289 32.000 16.05 0.00 0.00 1.82
2078 4316 7.095695 TGGCCAAGAAAAATTATGCTACTAC 57.904 36.000 0.61 0.00 0.00 2.73
2186 4431 3.582780 GTTGGACGTTGACCTAACCTAG 58.417 50.000 0.00 0.00 35.84 3.02
2297 4554 3.191581 TCAGAAGCTTCTAGTGTTCCTCG 59.808 47.826 28.02 12.10 35.34 4.63
2298 4555 2.494073 AGAAGCTTCTAGTGTTCCTCGG 59.506 50.000 27.47 0.00 35.34 4.63
2312 4569 5.759763 GTGTTCCTCGGGTTTCTTTACTTTA 59.240 40.000 0.00 0.00 0.00 1.85
2354 4616 5.351465 TGACAATTCTCCAGCGTTTATTCTC 59.649 40.000 0.00 0.00 0.00 2.87
2373 4839 1.346395 TCGGATGGGGTGGATAATTCG 59.654 52.381 0.00 0.00 0.00 3.34
2407 4873 5.472137 GGTTGACCTGTAAAACAAGAGCATA 59.528 40.000 0.00 0.00 0.00 3.14
2434 4934 6.129194 GCCAAGATACGTTGTGTTTTGATTTC 60.129 38.462 0.00 0.00 0.00 2.17
2435 4935 6.086241 CCAAGATACGTTGTGTTTTGATTTCG 59.914 38.462 0.00 0.00 0.00 3.46
2440 4940 6.312645 ACGTTGTGTTTTGATTTCGAAAAG 57.687 33.333 15.66 0.00 31.57 2.27
2441 4941 5.287513 ACGTTGTGTTTTGATTTCGAAAAGG 59.712 36.000 15.66 2.63 31.57 3.11
2443 4943 6.034044 CGTTGTGTTTTGATTTCGAAAAGGAA 59.966 34.615 15.66 6.86 31.57 3.36
2514 5024 7.706281 AGAATCTGCAACATTACTATCTTCG 57.294 36.000 0.00 0.00 0.00 3.79
2515 5025 7.268586 AGAATCTGCAACATTACTATCTTCGT 58.731 34.615 0.00 0.00 0.00 3.85
2516 5026 7.436673 AGAATCTGCAACATTACTATCTTCGTC 59.563 37.037 0.00 0.00 0.00 4.20
2517 5027 5.348986 TCTGCAACATTACTATCTTCGTCC 58.651 41.667 0.00 0.00 0.00 4.79
2518 5028 5.127194 TCTGCAACATTACTATCTTCGTCCT 59.873 40.000 0.00 0.00 0.00 3.85
2519 5029 5.109210 TGCAACATTACTATCTTCGTCCTG 58.891 41.667 0.00 0.00 0.00 3.86
2520 5030 4.508124 GCAACATTACTATCTTCGTCCTGG 59.492 45.833 0.00 0.00 0.00 4.45
2521 5031 5.661458 CAACATTACTATCTTCGTCCTGGT 58.339 41.667 0.00 0.00 0.00 4.00
2522 5032 5.934402 ACATTACTATCTTCGTCCTGGTT 57.066 39.130 0.00 0.00 0.00 3.67
2523 5033 6.295719 ACATTACTATCTTCGTCCTGGTTT 57.704 37.500 0.00 0.00 0.00 3.27
2524 5034 7.414222 ACATTACTATCTTCGTCCTGGTTTA 57.586 36.000 0.00 0.00 0.00 2.01
2525 5035 8.019656 ACATTACTATCTTCGTCCTGGTTTAT 57.980 34.615 0.00 0.00 0.00 1.40
2526 5036 8.483758 ACATTACTATCTTCGTCCTGGTTTATT 58.516 33.333 0.00 0.00 0.00 1.40
2527 5037 9.976511 CATTACTATCTTCGTCCTGGTTTATTA 57.023 33.333 0.00 0.00 0.00 0.98
2529 5039 6.514063 ACTATCTTCGTCCTGGTTTATTAGC 58.486 40.000 0.00 0.00 0.00 3.09
2530 5040 4.133013 TCTTCGTCCTGGTTTATTAGCC 57.867 45.455 0.00 0.00 0.00 3.93
2531 5041 2.994186 TCGTCCTGGTTTATTAGCCC 57.006 50.000 0.00 0.00 0.00 5.19
2532 5042 2.474112 TCGTCCTGGTTTATTAGCCCT 58.526 47.619 0.00 0.00 0.00 5.19
2533 5043 2.433239 TCGTCCTGGTTTATTAGCCCTC 59.567 50.000 0.00 0.00 0.00 4.30
2534 5044 2.434702 CGTCCTGGTTTATTAGCCCTCT 59.565 50.000 0.00 0.00 0.00 3.69
2535 5045 3.118371 CGTCCTGGTTTATTAGCCCTCTT 60.118 47.826 0.00 0.00 0.00 2.85
2536 5046 4.100498 CGTCCTGGTTTATTAGCCCTCTTA 59.900 45.833 0.00 0.00 0.00 2.10
2537 5047 5.395990 CGTCCTGGTTTATTAGCCCTCTTAA 60.396 44.000 0.00 0.00 0.00 1.85
2538 5048 6.602278 GTCCTGGTTTATTAGCCCTCTTAAT 58.398 40.000 0.00 0.00 0.00 1.40
2539 5049 7.472381 CGTCCTGGTTTATTAGCCCTCTTAATA 60.472 40.741 0.00 0.00 0.00 0.98
2540 5050 8.383947 GTCCTGGTTTATTAGCCCTCTTAATAT 58.616 37.037 0.00 0.00 0.00 1.28
2541 5051 8.955794 TCCTGGTTTATTAGCCCTCTTAATATT 58.044 33.333 0.00 0.00 0.00 1.28
2542 5052 9.588096 CCTGGTTTATTAGCCCTCTTAATATTT 57.412 33.333 0.00 0.00 0.00 1.40
2550 5060 8.871629 TTAGCCCTCTTAATATTTTGTGTCAA 57.128 30.769 0.00 0.00 0.00 3.18
2551 5061 7.775053 AGCCCTCTTAATATTTTGTGTCAAA 57.225 32.000 0.00 0.00 0.00 2.69
2552 5062 8.366359 AGCCCTCTTAATATTTTGTGTCAAAT 57.634 30.769 0.00 0.00 0.00 2.32
2553 5063 8.815912 AGCCCTCTTAATATTTTGTGTCAAATT 58.184 29.630 0.00 0.00 0.00 1.82
2554 5064 9.435688 GCCCTCTTAATATTTTGTGTCAAATTT 57.564 29.630 0.00 0.00 0.00 1.82
2678 5188 7.528481 TGACGTGCGTTAATATTTTATCAGT 57.472 32.000 0.00 0.00 0.00 3.41
2679 5189 7.966111 TGACGTGCGTTAATATTTTATCAGTT 58.034 30.769 0.00 0.00 0.00 3.16
2680 5190 9.085250 TGACGTGCGTTAATATTTTATCAGTTA 57.915 29.630 0.00 0.00 0.00 2.24
2681 5191 9.904647 GACGTGCGTTAATATTTTATCAGTTAA 57.095 29.630 0.00 0.00 0.00 2.01
2730 5240 8.915871 AAATACGAAAATGACCAATGAATCAG 57.084 30.769 0.00 0.00 0.00 2.90
2731 5241 5.314923 ACGAAAATGACCAATGAATCAGG 57.685 39.130 0.00 0.00 0.00 3.86
2732 5242 5.009631 ACGAAAATGACCAATGAATCAGGA 58.990 37.500 0.00 0.00 0.00 3.86
2733 5243 5.106157 ACGAAAATGACCAATGAATCAGGAC 60.106 40.000 0.00 0.00 0.00 3.85
2734 5244 4.970662 AAATGACCAATGAATCAGGACG 57.029 40.909 0.00 0.00 0.00 4.79
2735 5245 3.912496 ATGACCAATGAATCAGGACGA 57.088 42.857 0.00 0.00 0.00 4.20
2736 5246 3.694043 TGACCAATGAATCAGGACGAA 57.306 42.857 0.00 0.00 0.00 3.85
2737 5247 3.599343 TGACCAATGAATCAGGACGAAG 58.401 45.455 0.00 0.00 0.00 3.79
2738 5248 2.939103 GACCAATGAATCAGGACGAAGG 59.061 50.000 0.00 0.00 0.00 3.46
2739 5249 2.305927 ACCAATGAATCAGGACGAAGGT 59.694 45.455 0.00 0.00 0.00 3.50
2740 5250 3.517901 ACCAATGAATCAGGACGAAGGTA 59.482 43.478 0.00 0.00 0.00 3.08
2741 5251 4.122776 CCAATGAATCAGGACGAAGGTAG 58.877 47.826 0.00 0.00 0.00 3.18
2745 5255 4.597004 TGAATCAGGACGAAGGTAGTAGT 58.403 43.478 0.00 0.00 0.00 2.73
2749 5259 4.147321 TCAGGACGAAGGTAGTAGTTGTT 58.853 43.478 0.00 0.00 0.00 2.83
2751 5261 5.069516 TCAGGACGAAGGTAGTAGTTGTTTT 59.930 40.000 0.00 0.00 0.00 2.43
2756 5266 4.375706 CGAAGGTAGTAGTTGTTTTCGTGC 60.376 45.833 0.00 0.00 33.38 5.34
2760 5270 2.561569 AGTAGTTGTTTTCGTGCAGCT 58.438 42.857 0.00 0.00 0.00 4.24
2762 5272 3.741344 AGTAGTTGTTTTCGTGCAGCTAG 59.259 43.478 0.00 0.00 31.01 3.42
2776 5286 3.819537 GCAGCTAGCAAAAGAGAAACTG 58.180 45.455 18.83 2.54 44.79 3.16
2777 5287 3.365767 GCAGCTAGCAAAAGAGAAACTGG 60.366 47.826 18.83 0.00 44.79 4.00
2786 5374 6.015180 AGCAAAAGAGAAACTGGCATTTCATA 60.015 34.615 18.17 0.00 40.43 2.15
2788 5376 7.332678 GCAAAAGAGAAACTGGCATTTCATAAT 59.667 33.333 18.17 4.44 40.43 1.28
2797 5385 9.768662 AAACTGGCATTTCATAATATTTGGATC 57.231 29.630 0.00 0.00 0.00 3.36
2808 5396 2.787473 ATTTGGATCTGCCGTCTTCA 57.213 45.000 0.00 0.00 40.66 3.02
2809 5397 2.787473 TTTGGATCTGCCGTCTTCAT 57.213 45.000 0.00 0.00 40.66 2.57
2813 5401 4.214986 TGGATCTGCCGTCTTCATAAAA 57.785 40.909 0.00 0.00 40.66 1.52
2814 5402 4.191544 TGGATCTGCCGTCTTCATAAAAG 58.808 43.478 0.00 0.00 40.66 2.27
2815 5403 4.081142 TGGATCTGCCGTCTTCATAAAAGA 60.081 41.667 0.00 0.00 40.66 2.52
2816 5404 4.876107 GGATCTGCCGTCTTCATAAAAGAA 59.124 41.667 0.00 0.00 0.00 2.52
2817 5405 5.220681 GGATCTGCCGTCTTCATAAAAGAAC 60.221 44.000 0.00 0.00 0.00 3.01
2818 5406 3.678072 TCTGCCGTCTTCATAAAAGAACG 59.322 43.478 0.00 0.00 0.00 3.95
2819 5407 3.655486 TGCCGTCTTCATAAAAGAACGA 58.345 40.909 0.00 0.00 0.00 3.85
2820 5408 4.059511 TGCCGTCTTCATAAAAGAACGAA 58.940 39.130 0.00 0.00 0.00 3.85
2821 5409 4.512198 TGCCGTCTTCATAAAAGAACGAAA 59.488 37.500 0.00 0.00 0.00 3.46
2822 5410 5.007823 TGCCGTCTTCATAAAAGAACGAAAA 59.992 36.000 0.00 0.00 0.00 2.29
2839 5427 5.204833 ACGAAAACACATCGATTTTGTCAG 58.795 37.500 9.37 5.21 42.76 3.51
2870 5458 2.031157 GTGGAAACATGTCGGGTCAAAG 60.031 50.000 0.00 0.00 46.14 2.77
2885 5473 2.365617 GTCAAAGTGTCTGGACTCTGGA 59.634 50.000 6.15 5.20 35.58 3.86
2893 5481 1.043816 CTGGACTCTGGACACACACT 58.956 55.000 0.00 0.00 0.00 3.55
2895 5483 1.333177 GGACTCTGGACACACACTCT 58.667 55.000 0.00 0.00 0.00 3.24
2903 5491 1.816224 GGACACACACTCTCTCTCTCC 59.184 57.143 0.00 0.00 0.00 3.71
2907 5495 1.707989 ACACACTCTCTCTCTCCCTCA 59.292 52.381 0.00 0.00 0.00 3.86
2908 5496 2.290896 ACACACTCTCTCTCTCCCTCAG 60.291 54.545 0.00 0.00 0.00 3.35
2911 5504 3.269381 ACACTCTCTCTCTCCCTCAGAAT 59.731 47.826 0.00 0.00 0.00 2.40
2918 5511 8.472007 TCTCTCTCTCCCTCAGAATAAATTAC 57.528 38.462 0.00 0.00 0.00 1.89
2921 5514 7.288852 TCTCTCTCCCTCAGAATAAATTACAGG 59.711 40.741 0.00 0.00 0.00 4.00
2925 5518 5.191722 TCCCTCAGAATAAATTACAGGCACT 59.808 40.000 0.00 0.00 43.88 4.40
2941 5534 5.200368 AGGCACTGTTGGTTGATTTTTAG 57.800 39.130 0.00 0.00 37.18 1.85
2942 5535 4.649218 AGGCACTGTTGGTTGATTTTTAGT 59.351 37.500 0.00 0.00 37.18 2.24
2943 5536 4.744631 GGCACTGTTGGTTGATTTTTAGTG 59.255 41.667 0.00 0.00 37.82 2.74
2944 5537 5.888412 CACTGTTGGTTGATTTTTAGTGC 57.112 39.130 0.00 0.00 0.00 4.40
2945 5538 5.591099 CACTGTTGGTTGATTTTTAGTGCT 58.409 37.500 0.00 0.00 0.00 4.40
2946 5539 6.042143 CACTGTTGGTTGATTTTTAGTGCTT 58.958 36.000 0.00 0.00 0.00 3.91
2947 5540 6.534793 CACTGTTGGTTGATTTTTAGTGCTTT 59.465 34.615 0.00 0.00 0.00 3.51
2948 5541 7.064490 CACTGTTGGTTGATTTTTAGTGCTTTT 59.936 33.333 0.00 0.00 0.00 2.27
2949 5542 7.064490 ACTGTTGGTTGATTTTTAGTGCTTTTG 59.936 33.333 0.00 0.00 0.00 2.44
2950 5543 7.099764 TGTTGGTTGATTTTTAGTGCTTTTGA 58.900 30.769 0.00 0.00 0.00 2.69
2951 5544 7.604164 TGTTGGTTGATTTTTAGTGCTTTTGAA 59.396 29.630 0.00 0.00 0.00 2.69
2952 5545 8.447053 GTTGGTTGATTTTTAGTGCTTTTGAAA 58.553 29.630 0.00 0.00 0.00 2.69
2953 5546 8.729805 TGGTTGATTTTTAGTGCTTTTGAAAT 57.270 26.923 0.00 0.00 0.00 2.17
2954 5547 9.823647 TGGTTGATTTTTAGTGCTTTTGAAATA 57.176 25.926 0.00 0.00 0.00 1.40
2988 5581 4.555511 GCCAGACAAGAAATTATGGATCGC 60.556 45.833 0.00 0.00 0.00 4.58
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.887387 ATTTGGGACGGACAACCACG 60.887 55.000 0.00 0.00 33.20 4.94
1 2 2.188062 TATTTGGGACGGACAACCAC 57.812 50.000 0.00 0.00 33.20 4.16
2 3 2.953284 TTATTTGGGACGGACAACCA 57.047 45.000 0.00 0.00 35.59 3.67
3 4 2.490509 CCTTTATTTGGGACGGACAACC 59.509 50.000 0.00 0.00 0.00 3.77
4 5 3.057806 CACCTTTATTTGGGACGGACAAC 60.058 47.826 0.00 0.00 0.00 3.32
5 6 3.150767 CACCTTTATTTGGGACGGACAA 58.849 45.455 0.00 0.00 0.00 3.18
6 7 2.553466 CCACCTTTATTTGGGACGGACA 60.553 50.000 0.00 0.00 0.00 4.02
33 34 1.078143 ATGGGAGAAAGAGCGCCAC 60.078 57.895 2.29 0.00 0.00 5.01
78 79 2.270352 TGCCATCAGGACGAACTTTT 57.730 45.000 0.00 0.00 36.89 2.27
79 80 2.086869 CATGCCATCAGGACGAACTTT 58.913 47.619 0.00 0.00 36.89 2.66
80 81 1.679944 CCATGCCATCAGGACGAACTT 60.680 52.381 0.00 0.00 36.89 2.66
81 82 0.107508 CCATGCCATCAGGACGAACT 60.108 55.000 0.00 0.00 36.89 3.01
83 84 1.451927 GCCATGCCATCAGGACGAA 60.452 57.895 0.00 0.00 36.89 3.85
84 85 1.986632 ATGCCATGCCATCAGGACGA 61.987 55.000 0.00 0.00 36.89 4.20
86 87 0.466739 TGATGCCATGCCATCAGGAC 60.467 55.000 15.02 0.00 44.79 3.85
90 388 1.077572 ACGTGATGCCATGCCATCA 60.078 52.632 15.02 15.02 46.78 3.07
93 391 1.746239 CAGACGTGATGCCATGCCA 60.746 57.895 0.00 0.00 32.58 4.92
112 410 2.097791 GTGTAAGGCGACCAAACAAACA 59.902 45.455 0.00 0.00 0.00 2.83
113 411 2.356695 AGTGTAAGGCGACCAAACAAAC 59.643 45.455 0.00 0.00 0.00 2.93
114 412 2.645802 AGTGTAAGGCGACCAAACAAA 58.354 42.857 0.00 0.00 0.00 2.83
115 413 2.335316 AGTGTAAGGCGACCAAACAA 57.665 45.000 0.00 0.00 0.00 2.83
146 444 8.487176 ACGTTGCAAAACATAATCTTTTGATTC 58.513 29.630 0.00 0.00 45.26 2.52
148 446 7.945033 ACGTTGCAAAACATAATCTTTTGAT 57.055 28.000 0.00 0.00 39.85 2.57
150 448 8.280909 ACTACGTTGCAAAACATAATCTTTTG 57.719 30.769 0.00 0.00 40.25 2.44
151 449 8.865590 AACTACGTTGCAAAACATAATCTTTT 57.134 26.923 0.00 0.00 0.00 2.27
153 451 7.593644 GGAAACTACGTTGCAAAACATAATCTT 59.406 33.333 0.00 0.00 0.00 2.40
154 452 7.081976 GGAAACTACGTTGCAAAACATAATCT 58.918 34.615 0.00 0.00 0.00 2.40
155 453 6.032042 CGGAAACTACGTTGCAAAACATAATC 59.968 38.462 0.00 0.00 0.00 1.75
156 454 5.854338 CGGAAACTACGTTGCAAAACATAAT 59.146 36.000 0.00 0.00 0.00 1.28
159 457 3.549221 CCGGAAACTACGTTGCAAAACAT 60.549 43.478 0.00 0.00 0.00 2.71
161 459 2.377880 CCGGAAACTACGTTGCAAAAC 58.622 47.619 0.00 0.00 0.00 2.43
164 462 0.106335 TCCCGGAAACTACGTTGCAA 59.894 50.000 0.73 0.00 0.00 4.08
165 463 0.106335 TTCCCGGAAACTACGTTGCA 59.894 50.000 0.73 0.00 0.00 4.08
166 464 1.228533 TTTCCCGGAAACTACGTTGC 58.771 50.000 8.63 0.00 0.00 4.17
167 465 3.850740 GCTTTTTCCCGGAAACTACGTTG 60.851 47.826 12.37 0.00 30.83 4.10
169 467 1.875514 GCTTTTTCCCGGAAACTACGT 59.124 47.619 12.37 0.00 30.83 3.57
170 468 1.136169 CGCTTTTTCCCGGAAACTACG 60.136 52.381 12.37 11.69 30.83 3.51
171 469 2.145536 TCGCTTTTTCCCGGAAACTAC 58.854 47.619 12.37 3.96 30.83 2.73
172 470 2.547299 TCGCTTTTTCCCGGAAACTA 57.453 45.000 12.37 3.24 30.83 2.24
173 471 1.810755 GATCGCTTTTTCCCGGAAACT 59.189 47.619 12.37 0.00 30.83 2.66
176 474 0.320946 ACGATCGCTTTTTCCCGGAA 60.321 50.000 16.60 0.00 0.00 4.30
179 477 1.226018 GCACGATCGCTTTTTCCCG 60.226 57.895 16.60 0.00 0.00 5.14
181 479 4.342964 CGCACGATCGCTTTTTCC 57.657 55.556 16.60 0.00 0.00 3.13
198 496 8.736751 TTTTTGGAGTAAAATATTTGACGAGC 57.263 30.769 9.61 4.46 38.03 5.03
238 536 3.678252 GCTCATCCATGCTATGCTACGAT 60.678 47.826 0.00 0.00 0.00 3.73
251 549 6.830324 TGCTTGACTTTTATTAGCTCATCCAT 59.170 34.615 0.00 0.00 33.15 3.41
254 552 6.490534 GGTGCTTGACTTTTATTAGCTCATC 58.509 40.000 0.00 0.00 33.15 2.92
259 557 3.730963 GCCGGTGCTTGACTTTTATTAGC 60.731 47.826 1.90 0.00 33.53 3.09
293 591 1.334869 CTGGCTCCATTTTATCGTGGC 59.665 52.381 0.00 0.00 35.43 5.01
297 595 2.222027 GGGTCTGGCTCCATTTTATCG 58.778 52.381 0.00 0.00 0.00 2.92
306 604 1.606601 GTTTTGGGGGTCTGGCTCC 60.607 63.158 0.00 0.00 36.85 4.70
315 613 0.541764 TTAGCAGCTGGTTTTGGGGG 60.542 55.000 25.47 0.00 0.00 5.40
317 615 4.799564 TTAATTAGCAGCTGGTTTTGGG 57.200 40.909 25.47 0.00 0.00 4.12
318 616 4.621034 CGTTTAATTAGCAGCTGGTTTTGG 59.379 41.667 25.47 6.45 0.00 3.28
325 623 8.895932 ATTAGTTTTCGTTTAATTAGCAGCTG 57.104 30.769 10.11 10.11 0.00 4.24
335 633 3.439825 GGCCCGGATTAGTTTTCGTTTAA 59.560 43.478 0.73 0.00 0.00 1.52
336 634 3.009026 GGCCCGGATTAGTTTTCGTTTA 58.991 45.455 0.73 0.00 0.00 2.01
337 635 1.814394 GGCCCGGATTAGTTTTCGTTT 59.186 47.619 0.73 0.00 0.00 3.60
389 692 1.666872 GCGGGTATATGGGTCGTGC 60.667 63.158 0.00 0.00 0.00 5.34
412 715 0.768622 ACAATCTGGGTGGAACGGAA 59.231 50.000 0.00 0.00 38.12 4.30
413 716 0.323629 GACAATCTGGGTGGAACGGA 59.676 55.000 0.00 0.00 38.12 4.69
420 723 5.336055 GGTCTATCTATCGACAATCTGGGTG 60.336 48.000 0.00 0.00 31.88 4.61
429 732 6.540438 AAAAAGGTGGTCTATCTATCGACA 57.460 37.500 0.00 0.00 31.88 4.35
431 734 7.893124 ACTAAAAAGGTGGTCTATCTATCGA 57.107 36.000 0.00 0.00 0.00 3.59
445 758 5.622346 TTTTCCATGCCAACTAAAAAGGT 57.378 34.783 0.00 0.00 0.00 3.50
457 770 4.038402 CCACCAGATTAGATTTTCCATGCC 59.962 45.833 0.00 0.00 0.00 4.40
492 817 3.509740 GACGGCTACTAAACTTGACTCC 58.490 50.000 0.00 0.00 0.00 3.85
493 818 3.169733 CGACGGCTACTAAACTTGACTC 58.830 50.000 0.00 0.00 0.00 3.36
540 881 4.688966 GATGGATCGGGCGGCCTC 62.689 72.222 27.04 17.44 0.00 4.70
544 885 2.046892 GATGGATGGATCGGGCGG 60.047 66.667 0.00 0.00 0.00 6.13
546 887 2.046892 CGGATGGATGGATCGGGC 60.047 66.667 0.00 0.00 0.00 6.13
547 888 1.293498 GACGGATGGATGGATCGGG 59.707 63.158 0.00 0.00 0.00 5.14
548 889 1.293498 GGACGGATGGATGGATCGG 59.707 63.158 0.00 0.00 0.00 4.18
549 890 0.037882 CTGGACGGATGGATGGATCG 60.038 60.000 0.00 0.00 0.00 3.69
550 891 0.321122 GCTGGACGGATGGATGGATC 60.321 60.000 0.00 0.00 0.00 3.36
551 892 1.757306 GCTGGACGGATGGATGGAT 59.243 57.895 0.00 0.00 0.00 3.41
590 933 1.712350 CGAGATTTGTCGTCGTTCGTT 59.288 47.619 0.00 0.00 40.80 3.85
591 934 1.324718 CGAGATTTGTCGTCGTTCGT 58.675 50.000 0.00 0.00 40.80 3.85
592 935 0.022106 GCGAGATTTGTCGTCGTTCG 59.978 55.000 0.00 0.00 42.17 3.95
593 936 0.365859 GGCGAGATTTGTCGTCGTTC 59.634 55.000 0.00 0.00 42.17 3.95
644 1022 1.886730 ATCTGGAAGGAGGACCGGGA 61.887 60.000 6.32 0.00 41.83 5.14
689 1067 0.109226 GTGCGTGTCTGACCTACTCC 60.109 60.000 5.17 0.00 0.00 3.85
705 1087 1.252175 TCTCTCTCCTGTGACTGTGC 58.748 55.000 0.00 0.00 0.00 4.57
1059 1474 0.699399 AACCCGACTCCTCAGAGAGA 59.301 55.000 0.00 0.00 43.39 3.10
1061 1476 1.678123 CGTAACCCGACTCCTCAGAGA 60.678 57.143 0.00 0.00 43.66 3.10
1062 1477 0.733729 CGTAACCCGACTCCTCAGAG 59.266 60.000 0.00 0.00 46.36 3.35
1063 1478 0.037303 ACGTAACCCGACTCCTCAGA 59.963 55.000 0.00 0.00 40.70 3.27
1064 1479 0.886563 AACGTAACCCGACTCCTCAG 59.113 55.000 0.00 0.00 40.70 3.35
1067 1482 0.600057 GTGAACGTAACCCGACTCCT 59.400 55.000 0.00 0.00 40.70 3.69
1068 1483 0.730494 CGTGAACGTAACCCGACTCC 60.730 60.000 0.00 0.00 40.70 3.85
1069 1484 2.716988 CGTGAACGTAACCCGACTC 58.283 57.895 0.00 0.00 40.70 3.36
1070 1485 4.950744 CGTGAACGTAACCCGACT 57.049 55.556 0.00 0.00 40.70 4.18
1122 1541 3.391049 ACTCTTCTTTTCGTTTCCCTCG 58.609 45.455 0.00 0.00 0.00 4.63
1123 1542 5.749620 GAAACTCTTCTTTTCGTTTCCCTC 58.250 41.667 0.00 0.00 39.32 4.30
1142 1568 2.044946 ATGGCCGGCAGAGGAAAC 60.045 61.111 30.85 8.62 0.00 2.78
1144 1570 4.113815 CCATGGCCGGCAGAGGAA 62.114 66.667 30.85 6.18 0.00 3.36
1178 1612 0.894141 ACGAGCTCAGCAACAGAGAT 59.106 50.000 15.40 0.00 35.09 2.75
1179 1613 1.534729 TACGAGCTCAGCAACAGAGA 58.465 50.000 15.40 0.00 35.09 3.10
1180 1614 2.575694 ATACGAGCTCAGCAACAGAG 57.424 50.000 15.40 0.00 36.21 3.35
1259 1696 3.854669 ATCCTCTTGGCGGCCTCG 61.855 66.667 21.46 11.03 39.81 4.63
1361 1798 1.884926 GGCGCAAATCTCCTCCTCG 60.885 63.158 10.83 0.00 0.00 4.63
1528 1965 2.657102 GAAGCCCCAGATCTGCTCCG 62.657 65.000 17.76 3.45 33.36 4.63
1736 2173 1.466529 CCACTGACGACGACTGATCAG 60.467 57.143 21.37 21.37 43.47 2.90
1761 2198 1.668151 GGCTAATCCATCCGTCCGC 60.668 63.158 0.00 0.00 34.01 5.54
1766 2207 5.582689 AAAAGAAAAGGCTAATCCATCCG 57.417 39.130 0.00 0.00 37.29 4.18
1836 3391 8.103305 TCCTTCTTGCATCTAGAAACTTTACAT 58.897 33.333 0.00 0.00 31.67 2.29
1880 4058 3.130633 GCAACACATTTTCCAGGTTTCC 58.869 45.455 0.00 0.00 0.00 3.13
1936 4114 6.363626 TCTTCGAGAGATTCTTTTTCTTCGTG 59.636 38.462 0.00 0.00 41.60 4.35
1937 4115 6.448006 TCTTCGAGAGATTCTTTTTCTTCGT 58.552 36.000 0.00 0.00 41.60 3.85
1948 4126 6.414408 TGAAGCAATTTCTTCGAGAGATTC 57.586 37.500 12.28 0.00 44.01 2.52
1951 4129 5.482006 TGATGAAGCAATTTCTTCGAGAGA 58.518 37.500 12.28 0.00 44.01 3.10
1952 4130 5.791367 TGATGAAGCAATTTCTTCGAGAG 57.209 39.130 12.28 0.00 44.01 3.20
2036 4274 8.865090 TCTTGGCCAAAATAAAAGATACTTTCA 58.135 29.630 20.91 0.00 0.00 2.69
2037 4275 9.705290 TTCTTGGCCAAAATAAAAGATACTTTC 57.295 29.630 20.91 0.00 0.00 2.62
2069 4307 9.920133 CACTCATTCACATTATAGTAGTAGCAT 57.080 33.333 0.00 0.00 0.00 3.79
2070 4308 8.914011 ACACTCATTCACATTATAGTAGTAGCA 58.086 33.333 0.00 0.00 0.00 3.49
2075 4313 9.600646 CTCGTACACTCATTCACATTATAGTAG 57.399 37.037 0.00 0.00 0.00 2.57
2077 4315 7.997482 ACTCGTACACTCATTCACATTATAGT 58.003 34.615 0.00 0.00 0.00 2.12
2078 4316 8.129211 TGACTCGTACACTCATTCACATTATAG 58.871 37.037 0.00 0.00 0.00 1.31
2186 4431 7.602644 TCTCACTATTTAGGTTTGTCATGTCAC 59.397 37.037 0.00 0.00 0.00 3.67
2218 4475 9.979578 TCACATATGCTTTTATGTTTTCAAACT 57.020 25.926 1.58 0.00 40.07 2.66
2228 4485 7.168637 GGCAGTTGAATCACATATGCTTTTATG 59.831 37.037 1.58 0.00 39.05 1.90
2354 4616 1.610624 CCGAATTATCCACCCCATCCG 60.611 57.143 0.00 0.00 0.00 4.18
2407 4873 4.277174 TCAAAACACAACGTATCTTGGCAT 59.723 37.500 0.00 0.00 0.00 4.40
2473 4983 7.889589 CAGATTCTCTGTACACAAATGTGTA 57.110 36.000 19.58 19.58 46.38 2.90
2478 4988 5.764686 TGTTGCAGATTCTCTGTACACAAAT 59.235 36.000 6.06 0.00 45.94 2.32
2480 4990 4.702831 TGTTGCAGATTCTCTGTACACAA 58.297 39.130 6.06 0.00 45.94 3.33
2484 4994 8.879342 ATAGTAATGTTGCAGATTCTCTGTAC 57.121 34.615 6.06 5.60 45.94 2.90
2497 5007 4.508124 CCAGGACGAAGATAGTAATGTTGC 59.492 45.833 0.00 0.00 0.00 4.17
2501 5011 8.888579 AATAAACCAGGACGAAGATAGTAATG 57.111 34.615 0.00 0.00 0.00 1.90
2504 5014 7.255730 GGCTAATAAACCAGGACGAAGATAGTA 60.256 40.741 0.00 0.00 0.00 1.82
2505 5015 6.462628 GGCTAATAAACCAGGACGAAGATAGT 60.463 42.308 0.00 0.00 0.00 2.12
2506 5016 5.927115 GGCTAATAAACCAGGACGAAGATAG 59.073 44.000 0.00 0.00 0.00 2.08
2507 5017 5.221581 GGGCTAATAAACCAGGACGAAGATA 60.222 44.000 0.00 0.00 0.00 1.98
2508 5018 4.444449 GGGCTAATAAACCAGGACGAAGAT 60.444 45.833 0.00 0.00 0.00 2.40
2509 5019 3.118519 GGGCTAATAAACCAGGACGAAGA 60.119 47.826 0.00 0.00 0.00 2.87
2510 5020 3.118371 AGGGCTAATAAACCAGGACGAAG 60.118 47.826 0.00 0.00 0.00 3.79
2511 5021 2.841881 AGGGCTAATAAACCAGGACGAA 59.158 45.455 0.00 0.00 0.00 3.85
2512 5022 2.433239 GAGGGCTAATAAACCAGGACGA 59.567 50.000 0.00 0.00 0.00 4.20
2513 5023 2.434702 AGAGGGCTAATAAACCAGGACG 59.565 50.000 0.00 0.00 0.00 4.79
2514 5024 4.505324 AAGAGGGCTAATAAACCAGGAC 57.495 45.455 0.00 0.00 0.00 3.85
2515 5025 6.841781 ATTAAGAGGGCTAATAAACCAGGA 57.158 37.500 0.00 0.00 0.00 3.86
2516 5026 9.588096 AAATATTAAGAGGGCTAATAAACCAGG 57.412 33.333 0.00 0.00 0.00 4.45
2524 5034 9.474313 TTGACACAAAATATTAAGAGGGCTAAT 57.526 29.630 0.00 0.00 0.00 1.73
2525 5035 8.871629 TTGACACAAAATATTAAGAGGGCTAA 57.128 30.769 0.00 0.00 0.00 3.09
2526 5036 8.871629 TTTGACACAAAATATTAAGAGGGCTA 57.128 30.769 0.00 0.00 0.00 3.93
2527 5037 7.775053 TTTGACACAAAATATTAAGAGGGCT 57.225 32.000 0.00 0.00 0.00 5.19
2528 5038 9.435688 AAATTTGACACAAAATATTAAGAGGGC 57.564 29.630 0.00 0.00 0.00 5.19
2652 5162 9.251792 ACTGATAAAATATTAACGCACGTCATA 57.748 29.630 0.00 0.00 0.00 2.15
2653 5163 8.138365 ACTGATAAAATATTAACGCACGTCAT 57.862 30.769 0.00 0.00 0.00 3.06
2654 5164 7.528481 ACTGATAAAATATTAACGCACGTCA 57.472 32.000 0.00 0.00 0.00 4.35
2655 5165 9.904647 TTAACTGATAAAATATTAACGCACGTC 57.095 29.630 0.00 0.00 0.00 4.34
2704 5214 9.357652 CTGATTCATTGGTCATTTTCGTATTTT 57.642 29.630 0.00 0.00 0.00 1.82
2705 5215 7.975616 CCTGATTCATTGGTCATTTTCGTATTT 59.024 33.333 0.00 0.00 0.00 1.40
2706 5216 7.339212 TCCTGATTCATTGGTCATTTTCGTATT 59.661 33.333 0.00 0.00 0.00 1.89
2707 5217 6.828273 TCCTGATTCATTGGTCATTTTCGTAT 59.172 34.615 0.00 0.00 0.00 3.06
2708 5218 6.093495 GTCCTGATTCATTGGTCATTTTCGTA 59.907 38.462 0.00 0.00 0.00 3.43
2709 5219 5.009631 TCCTGATTCATTGGTCATTTTCGT 58.990 37.500 0.00 0.00 0.00 3.85
2710 5220 5.335127 GTCCTGATTCATTGGTCATTTTCG 58.665 41.667 0.00 0.00 0.00 3.46
2711 5221 5.123820 TCGTCCTGATTCATTGGTCATTTTC 59.876 40.000 0.00 0.00 0.00 2.29
2712 5222 5.009631 TCGTCCTGATTCATTGGTCATTTT 58.990 37.500 0.00 0.00 0.00 1.82
2713 5223 4.588899 TCGTCCTGATTCATTGGTCATTT 58.411 39.130 0.00 0.00 0.00 2.32
2714 5224 4.220693 TCGTCCTGATTCATTGGTCATT 57.779 40.909 0.00 0.00 0.00 2.57
2715 5225 3.912496 TCGTCCTGATTCATTGGTCAT 57.088 42.857 0.00 0.00 0.00 3.06
2716 5226 3.599343 CTTCGTCCTGATTCATTGGTCA 58.401 45.455 0.00 0.00 0.00 4.02
2717 5227 2.939103 CCTTCGTCCTGATTCATTGGTC 59.061 50.000 0.00 0.00 0.00 4.02
2718 5228 2.305927 ACCTTCGTCCTGATTCATTGGT 59.694 45.455 0.00 0.00 0.00 3.67
2719 5229 2.991250 ACCTTCGTCCTGATTCATTGG 58.009 47.619 0.00 0.00 0.00 3.16
2720 5230 4.759782 ACTACCTTCGTCCTGATTCATTG 58.240 43.478 0.00 0.00 0.00 2.82
2721 5231 5.657302 ACTACTACCTTCGTCCTGATTCATT 59.343 40.000 0.00 0.00 0.00 2.57
2722 5232 5.202004 ACTACTACCTTCGTCCTGATTCAT 58.798 41.667 0.00 0.00 0.00 2.57
2723 5233 4.597004 ACTACTACCTTCGTCCTGATTCA 58.403 43.478 0.00 0.00 0.00 2.57
2724 5234 5.105837 ACAACTACTACCTTCGTCCTGATTC 60.106 44.000 0.00 0.00 0.00 2.52
2725 5235 4.771054 ACAACTACTACCTTCGTCCTGATT 59.229 41.667 0.00 0.00 0.00 2.57
2726 5236 4.342359 ACAACTACTACCTTCGTCCTGAT 58.658 43.478 0.00 0.00 0.00 2.90
2727 5237 3.759581 ACAACTACTACCTTCGTCCTGA 58.240 45.455 0.00 0.00 0.00 3.86
2728 5238 4.516365 AACAACTACTACCTTCGTCCTG 57.484 45.455 0.00 0.00 0.00 3.86
2729 5239 5.536260 GAAAACAACTACTACCTTCGTCCT 58.464 41.667 0.00 0.00 0.00 3.85
2730 5240 4.383948 CGAAAACAACTACTACCTTCGTCC 59.616 45.833 0.00 0.00 31.90 4.79
2731 5241 4.978580 ACGAAAACAACTACTACCTTCGTC 59.021 41.667 1.44 0.00 42.49 4.20
2732 5242 4.741676 CACGAAAACAACTACTACCTTCGT 59.258 41.667 1.44 1.44 45.77 3.85
2733 5243 4.375706 GCACGAAAACAACTACTACCTTCG 60.376 45.833 0.00 0.00 39.88 3.79
2734 5244 4.508861 TGCACGAAAACAACTACTACCTTC 59.491 41.667 0.00 0.00 0.00 3.46
2735 5245 4.444536 TGCACGAAAACAACTACTACCTT 58.555 39.130 0.00 0.00 0.00 3.50
2736 5246 4.056050 CTGCACGAAAACAACTACTACCT 58.944 43.478 0.00 0.00 0.00 3.08
2737 5247 3.363673 GCTGCACGAAAACAACTACTACC 60.364 47.826 0.00 0.00 0.00 3.18
2738 5248 3.493503 AGCTGCACGAAAACAACTACTAC 59.506 43.478 1.02 0.00 0.00 2.73
2739 5249 3.724374 AGCTGCACGAAAACAACTACTA 58.276 40.909 1.02 0.00 0.00 1.82
2740 5250 2.561569 AGCTGCACGAAAACAACTACT 58.438 42.857 1.02 0.00 0.00 2.57
2741 5251 3.664537 GCTAGCTGCACGAAAACAACTAC 60.665 47.826 7.70 0.00 42.31 2.73
2756 5266 3.365767 GCCAGTTTCTCTTTTGCTAGCTG 60.366 47.826 17.23 0.59 0.00 4.24
2760 5270 5.301551 TGAAATGCCAGTTTCTCTTTTGCTA 59.698 36.000 7.53 0.00 38.58 3.49
2762 5272 4.370917 TGAAATGCCAGTTTCTCTTTTGC 58.629 39.130 7.53 0.00 38.58 3.68
2770 5280 9.768662 ATCCAAATATTATGAAATGCCAGTTTC 57.231 29.630 0.00 0.00 38.32 2.78
2774 5284 7.544566 GCAGATCCAAATATTATGAAATGCCAG 59.455 37.037 11.77 0.00 0.00 4.85
2775 5285 7.380536 GCAGATCCAAATATTATGAAATGCCA 58.619 34.615 11.77 0.00 0.00 4.92
2776 5286 6.815142 GGCAGATCCAAATATTATGAAATGCC 59.185 38.462 19.26 19.26 36.15 4.40
2777 5287 6.529125 CGGCAGATCCAAATATTATGAAATGC 59.471 38.462 13.21 13.21 34.01 3.56
2786 5374 4.780815 TGAAGACGGCAGATCCAAATATT 58.219 39.130 0.00 0.00 34.01 1.28
2788 5376 3.904800 TGAAGACGGCAGATCCAAATA 57.095 42.857 0.00 0.00 34.01 1.40
2797 5385 3.678072 TCGTTCTTTTATGAAGACGGCAG 59.322 43.478 0.00 0.00 0.00 4.85
2808 5396 9.458374 AAAATCGATGTGTTTTCGTTCTTTTAT 57.542 25.926 0.00 0.00 37.82 1.40
2809 5397 8.738554 CAAAATCGATGTGTTTTCGTTCTTTTA 58.261 29.630 0.00 0.00 37.82 1.52
2813 5401 5.816919 ACAAAATCGATGTGTTTTCGTTCT 58.183 33.333 0.00 0.00 37.82 3.01
2814 5402 5.679355 TGACAAAATCGATGTGTTTTCGTTC 59.321 36.000 14.33 3.40 37.82 3.95
2815 5403 5.574082 TGACAAAATCGATGTGTTTTCGTT 58.426 33.333 14.33 0.00 37.82 3.85
2816 5404 5.163302 TGACAAAATCGATGTGTTTTCGT 57.837 34.783 14.33 6.60 37.82 3.85
2817 5405 4.612614 CCTGACAAAATCGATGTGTTTTCG 59.387 41.667 14.33 4.11 37.94 3.46
2818 5406 5.757886 TCCTGACAAAATCGATGTGTTTTC 58.242 37.500 14.33 6.30 0.00 2.29
2819 5407 5.766150 TCCTGACAAAATCGATGTGTTTT 57.234 34.783 14.33 3.01 0.00 2.43
2820 5408 5.766150 TTCCTGACAAAATCGATGTGTTT 57.234 34.783 14.33 2.58 0.00 2.83
2821 5409 5.299279 AGTTTCCTGACAAAATCGATGTGTT 59.701 36.000 14.33 0.76 0.00 3.32
2822 5410 4.821805 AGTTTCCTGACAAAATCGATGTGT 59.178 37.500 13.33 13.33 0.00 3.72
2839 5427 3.139077 ACATGTTTCCACGAGAGTTTCC 58.861 45.455 0.00 0.00 46.40 3.13
2863 5451 2.548920 CCAGAGTCCAGACACTTTGACC 60.549 54.545 0.00 0.00 31.50 4.02
2885 5473 1.427368 AGGGAGAGAGAGAGTGTGTGT 59.573 52.381 0.00 0.00 0.00 3.72
2893 5481 8.061920 TGTAATTTATTCTGAGGGAGAGAGAGA 58.938 37.037 0.00 0.00 30.18 3.10
2895 5483 7.288852 CCTGTAATTTATTCTGAGGGAGAGAGA 59.711 40.741 0.00 0.00 30.18 3.10
2903 5491 5.882557 ACAGTGCCTGTAATTTATTCTGAGG 59.117 40.000 6.10 0.00 43.46 3.86
2907 5495 6.010219 ACCAACAGTGCCTGTAATTTATTCT 58.990 36.000 8.07 0.00 44.62 2.40
2908 5496 6.267496 ACCAACAGTGCCTGTAATTTATTC 57.733 37.500 8.07 0.00 44.62 1.75
2911 5504 5.133941 TCAACCAACAGTGCCTGTAATTTA 58.866 37.500 8.07 0.00 44.62 1.40
2918 5511 3.457610 AAAATCAACCAACAGTGCCTG 57.542 42.857 0.00 1.16 37.52 4.85
2921 5514 5.888412 CACTAAAAATCAACCAACAGTGC 57.112 39.130 0.00 0.00 0.00 4.40
2925 5518 7.099764 TCAAAAGCACTAAAAATCAACCAACA 58.900 30.769 0.00 0.00 0.00 3.33
2940 5533 7.761249 GCTGTCCAAATATATTTCAAAAGCACT 59.239 33.333 18.45 0.00 0.00 4.40
2941 5534 7.010460 GGCTGTCCAAATATATTTCAAAAGCAC 59.990 37.037 21.88 13.48 0.00 4.40
2942 5535 7.041107 GGCTGTCCAAATATATTTCAAAAGCA 58.959 34.615 21.88 11.02 0.00 3.91
2943 5536 7.041107 TGGCTGTCCAAATATATTTCAAAAGC 58.959 34.615 16.56 16.56 39.99 3.51
2944 5537 8.469200 TCTGGCTGTCCAAATATATTTCAAAAG 58.531 33.333 7.76 5.24 42.91 2.27
2945 5538 8.250332 GTCTGGCTGTCCAAATATATTTCAAAA 58.750 33.333 7.76 0.00 42.91 2.44
2946 5539 7.395772 TGTCTGGCTGTCCAAATATATTTCAAA 59.604 33.333 7.76 0.00 42.91 2.69
2947 5540 6.889177 TGTCTGGCTGTCCAAATATATTTCAA 59.111 34.615 7.76 0.00 42.91 2.69
2948 5541 6.422333 TGTCTGGCTGTCCAAATATATTTCA 58.578 36.000 7.76 3.27 42.91 2.69
2949 5542 6.942532 TGTCTGGCTGTCCAAATATATTTC 57.057 37.500 7.76 0.00 42.91 2.17
2950 5543 7.118723 TCTTGTCTGGCTGTCCAAATATATTT 58.881 34.615 4.81 4.81 42.91 1.40
2951 5544 6.662755 TCTTGTCTGGCTGTCCAAATATATT 58.337 36.000 0.00 0.00 42.91 1.28
2952 5545 6.252599 TCTTGTCTGGCTGTCCAAATATAT 57.747 37.500 0.00 0.00 42.91 0.86
2953 5546 5.692115 TCTTGTCTGGCTGTCCAAATATA 57.308 39.130 0.00 0.00 42.91 0.86
2954 5547 4.574674 TCTTGTCTGGCTGTCCAAATAT 57.425 40.909 0.00 0.00 42.91 1.28
2955 5548 4.365514 TTCTTGTCTGGCTGTCCAAATA 57.634 40.909 0.00 0.00 42.91 1.40
2956 5549 2.957402 TCTTGTCTGGCTGTCCAAAT 57.043 45.000 0.00 0.00 42.91 2.32
2957 5550 2.727123 TTCTTGTCTGGCTGTCCAAA 57.273 45.000 0.00 0.00 42.91 3.28
2958 5551 2.727123 TTTCTTGTCTGGCTGTCCAA 57.273 45.000 0.00 0.00 42.91 3.53
2959 5552 2.957402 ATTTCTTGTCTGGCTGTCCA 57.043 45.000 0.00 0.00 40.85 4.02
2960 5553 4.096984 CCATAATTTCTTGTCTGGCTGTCC 59.903 45.833 0.00 0.00 0.00 4.02
2988 5581 0.579156 GCTAGCTTCGGCGAGAAATG 59.421 55.000 10.46 3.34 44.63 2.32


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

AutoCloner maintained by Alex Coulton.