Multiple sequence alignment - TraesCS4A01G101800

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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 TraesCS4A01G101800 chr4A 100.000 6008 0 0 1 6008 114481706 114487713 0.000000e+00 11095
1 TraesCS4A01G101800 chr4D 94.777 2642 112 11 2443 5069 350555959 350553329 0.000000e+00 4091
2 TraesCS4A01G101800 chr4D 89.912 1021 61 24 1456 2449 350557154 350556149 0.000000e+00 1277
3 TraesCS4A01G101800 chr4D 88.953 1041 41 29 458 1450 350558212 350557198 0.000000e+00 1218
4 TraesCS4A01G101800 chr4D 93.857 407 22 2 5238 5641 350552919 350552513 1.430000e-170 610
5 TraesCS4A01G101800 chr4D 88.918 379 19 15 5643 6008 350552454 350552086 4.270000e-121 446
6 TraesCS4A01G101800 chr4D 84.471 425 39 13 11 420 350559330 350558918 1.570000e-105 394
7 TraesCS4A01G101800 chr4B 93.330 2129 100 17 3512 5615 433964462 433962351 0.000000e+00 3107
8 TraesCS4A01G101800 chr4B 91.983 2058 83 21 1456 3468 433966713 433964693 0.000000e+00 2811
9 TraesCS4A01G101800 chr4B 90.387 749 26 19 729 1455 433967477 433966753 0.000000e+00 942
10 TraesCS4A01G101800 chr4B 90.560 339 29 1 82 420 433969583 433969248 4.270000e-121 446
11 TraesCS4A01G101800 chr4B 88.571 385 17 13 5642 6008 433961945 433961570 5.530000e-120 442
12 TraesCS4A01G101800 chr4B 94.382 89 2 1 604 689 433969043 433968955 3.780000e-27 134
13 TraesCS4A01G101800 chr2D 88.496 113 12 1 2721 2832 187460519 187460631 1.050000e-27 135
14 TraesCS4A01G101800 chr2A 88.496 113 12 1 2721 2832 67077931 67078043 1.050000e-27 135
15 TraesCS4A01G101800 chr2B 85.841 113 14 2 2721 2832 104074728 104074839 1.060000e-22 119
16 TraesCS4A01G101800 chr6A 86.239 109 14 1 2721 2828 615432702 615432594 3.800000e-22 117


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 TraesCS4A01G101800 chr4A 114481706 114487713 6007 False 11095.000000 11095 100.0000 1 6008 1 chr4A.!!$F1 6007
1 TraesCS4A01G101800 chr4D 350552086 350559330 7244 True 1339.333333 4091 90.1480 11 6008 6 chr4D.!!$R1 5997
2 TraesCS4A01G101800 chr4B 433961570 433969583 8013 True 1313.666667 3107 91.5355 82 6008 6 chr4B.!!$R1 5926

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
56 59 0.034896 AAGCGTCGTCTTCCCACATT 59.965 50.000 0.00 0.00 0.00 2.71 F
791 2950 0.109039 GACCAGTGAGAACGCTCTCC 60.109 60.000 13.08 5.01 46.67 3.71 F
1488 3725 0.323629 TGGGTTGGTACTGCTACTGC 59.676 55.000 0.00 0.00 40.20 4.40 F
1893 4136 0.453282 CTTCGCTCACATTGTTGGCG 60.453 55.000 20.27 20.27 45.93 5.69 F
2706 5181 0.679960 GCAGGGGGCGTTTCTATGTT 60.680 55.000 0.00 0.00 0.00 2.71 F
3331 5825 1.596954 CGTAGCCATGCGGTTTTATGC 60.597 52.381 0.00 0.00 33.28 3.14 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1861 4104 0.108186 AGCGAAGATCCATTCACGCA 60.108 50.000 0.00 0.00 46.79 5.24 R
2709 5184 0.109342 AACAAGCTGACCCCACAGAG 59.891 55.000 0.00 0.00 39.94 3.35 R
3379 5873 2.224354 CCTCAACCTGCAAAAGCCAATT 60.224 45.455 0.00 0.00 0.00 2.32 R
3628 6309 0.618458 TTCCTGCTTCCGTGGCTATT 59.382 50.000 0.00 0.00 0.00 1.73 R
3714 6396 1.069427 GGCTGTGTTTGGCATTGCA 59.931 52.632 11.39 0.00 32.52 4.08 R
5170 8167 0.589708 GGGTAAACTGGTTCGTGCAC 59.410 55.000 6.82 6.82 0.00 4.57 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
26 27 3.131577 TGATACCTTCGCCGTGTATTTCT 59.868 43.478 0.00 0.00 0.00 2.52
28 29 2.344025 ACCTTCGCCGTGTATTTCTTC 58.656 47.619 0.00 0.00 0.00 2.87
29 30 2.028385 ACCTTCGCCGTGTATTTCTTCT 60.028 45.455 0.00 0.00 0.00 2.85
30 31 2.348666 CCTTCGCCGTGTATTTCTTCTG 59.651 50.000 0.00 0.00 0.00 3.02
31 32 1.355971 TCGCCGTGTATTTCTTCTGC 58.644 50.000 0.00 0.00 0.00 4.26
33 34 1.448985 GCCGTGTATTTCTTCTGCCA 58.551 50.000 0.00 0.00 0.00 4.92
34 35 1.130561 GCCGTGTATTTCTTCTGCCAC 59.869 52.381 0.00 0.00 0.00 5.01
43 46 0.944386 TCTTCTGCCACAAAAGCGTC 59.056 50.000 0.00 0.00 0.00 5.19
46 49 1.082756 CTGCCACAAAAGCGTCGTC 60.083 57.895 0.00 0.00 0.00 4.20
56 59 0.034896 AAGCGTCGTCTTCCCACATT 59.965 50.000 0.00 0.00 0.00 2.71
59 62 1.265905 GCGTCGTCTTCCCACATTTTT 59.734 47.619 0.00 0.00 0.00 1.94
60 63 2.916111 CGTCGTCTTCCCACATTTTTG 58.084 47.619 0.00 0.00 0.00 2.44
72 75 4.219033 CCACATTTTTGCGAAGTGTACTC 58.781 43.478 6.51 0.00 0.00 2.59
75 78 1.886886 TTTTGCGAAGTGTACTCCCC 58.113 50.000 0.00 0.00 0.00 4.81
76 79 1.053424 TTTGCGAAGTGTACTCCCCT 58.947 50.000 0.00 0.00 0.00 4.79
77 80 0.606604 TTGCGAAGTGTACTCCCCTC 59.393 55.000 0.00 0.00 0.00 4.30
78 81 1.255667 TGCGAAGTGTACTCCCCTCC 61.256 60.000 0.00 0.00 0.00 4.30
79 82 1.957765 GCGAAGTGTACTCCCCTCCC 61.958 65.000 0.00 0.00 0.00 4.30
80 83 0.613853 CGAAGTGTACTCCCCTCCCA 60.614 60.000 0.00 0.00 0.00 4.37
103 106 1.280133 CCCAGCATATCGGATCACCAT 59.720 52.381 0.00 0.00 35.59 3.55
117 127 5.546526 GGATCACCATCCTACAAATCTCTC 58.453 45.833 0.00 0.00 45.06 3.20
120 130 5.272402 TCACCATCCTACAAATCTCTCTGA 58.728 41.667 0.00 0.00 0.00 3.27
188 198 2.158959 GTCCACGCAGTTCGATCCG 61.159 63.158 0.00 0.00 41.61 4.18
266 276 1.080498 AGACCTGACATGGAACCCCTA 59.920 52.381 0.00 0.00 0.00 3.53
271 281 0.179119 GACATGGAACCCCTACGACG 60.179 60.000 0.00 0.00 0.00 5.12
272 282 0.901580 ACATGGAACCCCTACGACGT 60.902 55.000 5.52 5.52 0.00 4.34
278 288 2.505557 CCCCTACGACGTTGACGC 60.506 66.667 10.51 0.00 44.43 5.19
280 290 2.256158 CCTACGACGTTGACGCCA 59.744 61.111 10.51 0.00 44.43 5.69
281 291 1.800315 CCTACGACGTTGACGCCAG 60.800 63.158 10.51 0.00 44.43 4.85
282 292 1.208358 CTACGACGTTGACGCCAGA 59.792 57.895 10.51 0.00 44.43 3.86
294 304 1.219393 CGCCAGAAGGAGGAGGAAC 59.781 63.158 0.00 0.00 36.89 3.62
298 308 1.918957 CCAGAAGGAGGAGGAACCATT 59.081 52.381 0.00 0.00 42.04 3.16
300 310 3.350833 CAGAAGGAGGAGGAACCATTTG 58.649 50.000 0.00 0.00 42.04 2.32
331 341 2.114670 CATCACCGGTGGCCACATC 61.115 63.158 35.78 19.37 0.00 3.06
338 348 1.679977 GGTGGCCACATCTGCATGT 60.680 57.895 35.78 0.00 44.72 3.21
454 483 2.654749 TGGTACTCATGCGACTCTTG 57.345 50.000 0.00 0.00 0.00 3.02
455 484 1.281899 GGTACTCATGCGACTCTTGC 58.718 55.000 0.00 0.00 0.00 4.01
456 485 0.917259 GTACTCATGCGACTCTTGCG 59.083 55.000 0.00 0.00 34.24 4.85
483 1173 1.876156 ACTTGCAGCTCCGAAAGAAAG 59.124 47.619 0.00 0.00 0.00 2.62
486 1176 2.571212 TGCAGCTCCGAAAGAAAGAAA 58.429 42.857 0.00 0.00 0.00 2.52
487 1177 2.290641 TGCAGCTCCGAAAGAAAGAAAC 59.709 45.455 0.00 0.00 0.00 2.78
489 1179 2.226674 CAGCTCCGAAAGAAAGAAACCC 59.773 50.000 0.00 0.00 0.00 4.11
492 1182 3.685272 GCTCCGAAAGAAAGAAACCCTAG 59.315 47.826 0.00 0.00 0.00 3.02
513 1203 4.640364 AGAGAAAGAAACTGCAGGAAGAG 58.360 43.478 19.93 0.00 0.00 2.85
573 1270 3.596066 GAAGCGAGCCAGCCAGTGA 62.596 63.158 0.00 0.00 38.01 3.41
574 1271 3.890936 AAGCGAGCCAGCCAGTGAC 62.891 63.158 0.00 0.00 38.01 3.67
576 1273 2.125753 CGAGCCAGCCAGTGACTC 60.126 66.667 0.00 0.00 0.00 3.36
711 2864 4.546829 TTTAATCACCAAGCGTACTCCT 57.453 40.909 0.00 0.00 0.00 3.69
712 2865 2.674796 AATCACCAAGCGTACTCCTC 57.325 50.000 0.00 0.00 0.00 3.71
713 2866 1.557099 ATCACCAAGCGTACTCCTCA 58.443 50.000 0.00 0.00 0.00 3.86
714 2867 0.888619 TCACCAAGCGTACTCCTCAG 59.111 55.000 0.00 0.00 0.00 3.35
715 2868 0.737715 CACCAAGCGTACTCCTCAGC 60.738 60.000 0.00 0.00 0.00 4.26
716 2869 1.185618 ACCAAGCGTACTCCTCAGCA 61.186 55.000 0.00 0.00 0.00 4.41
717 2870 0.737715 CCAAGCGTACTCCTCAGCAC 60.738 60.000 0.00 0.00 0.00 4.40
777 2936 2.656069 CCACCCACCCGTAGACCAG 61.656 68.421 0.00 0.00 0.00 4.00
791 2950 0.109039 GACCAGTGAGAACGCTCTCC 60.109 60.000 13.08 5.01 46.67 3.71
797 2956 2.756283 AGAACGCTCTCCTCCGGG 60.756 66.667 0.00 0.00 0.00 5.73
798 2957 3.069318 GAACGCTCTCCTCCGGGT 61.069 66.667 0.00 0.00 0.00 5.28
799 2958 3.066233 GAACGCTCTCCTCCGGGTC 62.066 68.421 0.00 0.00 0.00 4.46
834 2994 1.674908 GCAAACGCTCTTTCCTTTCG 58.325 50.000 0.00 0.00 0.00 3.46
881 3048 3.423154 GCCCTCGGTTTCTGTGCG 61.423 66.667 0.00 0.00 0.00 5.34
882 3049 2.742372 CCCTCGGTTTCTGTGCGG 60.742 66.667 0.00 0.00 0.00 5.69
933 3100 1.072505 ATTTTCCCCGTGCACTCGT 59.927 52.632 16.19 0.00 0.00 4.18
1027 3201 1.372683 GTCAACTGGGAGCTGCAGA 59.627 57.895 20.43 0.00 0.00 4.26
1198 3373 3.893763 TGTTTGCACGGGGTTGCG 61.894 61.111 0.00 0.00 46.20 4.85
1450 3649 0.750546 GCAATCTCAGCAGCCATGGA 60.751 55.000 18.40 0.00 0.00 3.41
1451 3650 1.309950 CAATCTCAGCAGCCATGGAG 58.690 55.000 18.40 8.23 0.00 3.86
1453 3652 0.917533 ATCTCAGCAGCCATGGAGTT 59.082 50.000 18.40 1.42 0.00 3.01
1454 3653 1.571955 TCTCAGCAGCCATGGAGTTA 58.428 50.000 18.40 0.00 0.00 2.24
1485 3722 3.192633 CCATTTTGGGTTGGTACTGCTAC 59.807 47.826 0.00 0.00 32.67 3.58
1486 3723 3.868619 TTTTGGGTTGGTACTGCTACT 57.131 42.857 0.00 0.00 0.00 2.57
1487 3724 2.851263 TTGGGTTGGTACTGCTACTG 57.149 50.000 0.00 0.00 0.00 2.74
1488 3725 0.323629 TGGGTTGGTACTGCTACTGC 59.676 55.000 0.00 0.00 40.20 4.40
1489 3726 0.613777 GGGTTGGTACTGCTACTGCT 59.386 55.000 0.00 0.00 40.48 4.24
1490 3727 1.829222 GGGTTGGTACTGCTACTGCTA 59.171 52.381 0.00 0.00 40.48 3.49
1491 3728 2.159085 GGGTTGGTACTGCTACTGCTAG 60.159 54.545 0.00 0.00 40.48 3.42
1492 3729 2.541556 GTTGGTACTGCTACTGCTAGC 58.458 52.381 8.10 8.10 45.19 3.42
1493 3730 2.145397 TGGTACTGCTACTGCTAGCT 57.855 50.000 17.23 0.00 45.20 3.32
1494 3731 3.292492 TGGTACTGCTACTGCTAGCTA 57.708 47.619 17.23 0.00 45.20 3.32
1495 3732 3.215151 TGGTACTGCTACTGCTAGCTAG 58.785 50.000 16.84 16.84 45.20 3.42
1496 3733 2.554893 GGTACTGCTACTGCTAGCTAGG 59.445 54.545 22.10 9.03 45.20 3.02
1497 3734 2.445682 ACTGCTACTGCTAGCTAGGT 57.554 50.000 22.10 14.31 45.20 3.08
1498 3735 2.028130 ACTGCTACTGCTAGCTAGGTG 58.972 52.381 22.10 9.52 45.20 4.00
1499 3736 2.302260 CTGCTACTGCTAGCTAGGTGA 58.698 52.381 22.10 0.00 45.20 4.02
1500 3737 2.890311 CTGCTACTGCTAGCTAGGTGAT 59.110 50.000 22.10 0.00 45.20 3.06
1567 3808 2.158769 CCAGTTCGGATGATGGATTCCA 60.159 50.000 8.08 8.08 35.36 3.53
1774 4017 7.596494 TCTGGTCAAAAGATGCTAATTTTCTG 58.404 34.615 0.00 0.00 0.00 3.02
1846 4089 3.866651 ACTGGTCATGCAGATTAGTGAC 58.133 45.455 7.23 7.23 40.07 3.67
1850 4093 3.119291 GTCATGCAGATTAGTGACTCGG 58.881 50.000 8.31 0.00 38.29 4.63
1860 4103 1.840737 AGTGACTCGGTGATAGCAGT 58.159 50.000 0.00 0.00 0.00 4.40
1861 4104 2.171840 AGTGACTCGGTGATAGCAGTT 58.828 47.619 0.00 0.00 0.00 3.16
1888 4131 2.768253 TGGATCTTCGCTCACATTGT 57.232 45.000 0.00 0.00 0.00 2.71
1889 4132 3.057969 TGGATCTTCGCTCACATTGTT 57.942 42.857 0.00 0.00 0.00 2.83
1890 4133 2.743664 TGGATCTTCGCTCACATTGTTG 59.256 45.455 0.00 0.00 0.00 3.33
1891 4134 2.096496 GGATCTTCGCTCACATTGTTGG 59.904 50.000 0.00 0.00 0.00 3.77
1892 4135 0.874390 TCTTCGCTCACATTGTTGGC 59.126 50.000 0.00 0.00 0.00 4.52
1893 4136 0.453282 CTTCGCTCACATTGTTGGCG 60.453 55.000 20.27 20.27 45.93 5.69
1894 4137 1.851021 TTCGCTCACATTGTTGGCGG 61.851 55.000 23.58 11.78 44.88 6.13
1895 4138 2.126346 GCTCACATTGTTGGCGGC 60.126 61.111 0.00 0.00 0.00 6.53
2039 4303 6.038382 TCTGATTAGTAGTCATCGGAGTTGTC 59.962 42.308 0.00 0.00 32.14 3.18
2049 4313 1.135199 TCGGAGTTGTCTCGCCATTAC 60.135 52.381 0.00 0.00 41.26 1.89
2056 4320 0.814010 GTCTCGCCATTACCCGCAAT 60.814 55.000 0.00 0.00 0.00 3.56
2061 4325 2.753452 TCGCCATTACCCGCAATAAAAA 59.247 40.909 0.00 0.00 0.00 1.94
2076 4340 5.180680 GCAATAAAAAGAGGAGTTGTACCGT 59.819 40.000 0.00 0.00 0.00 4.83
2123 4391 2.425668 TCGCCGTTGATCTATTCTGTCA 59.574 45.455 0.00 0.00 0.00 3.58
2165 4435 7.055667 TGTGCCCAATATTTGTTTTTGTCTA 57.944 32.000 0.00 0.00 0.00 2.59
2225 4504 5.300752 ACTGATATTTATTGCTGGAGACCG 58.699 41.667 0.00 0.00 0.00 4.79
2233 4512 0.684535 TGCTGGAGACCGTTGATTCA 59.315 50.000 0.00 0.00 0.00 2.57
2253 4532 4.023980 TCAGTATGTGGACAACCCTAGAG 58.976 47.826 0.00 0.00 37.40 2.43
2515 4990 6.153680 AGAGATTTCATCAAAGACCTACGACT 59.846 38.462 0.00 0.00 0.00 4.18
2517 4992 5.462530 TTTCATCAAAGACCTACGACTGA 57.537 39.130 0.00 0.00 0.00 3.41
2553 5028 4.202151 GCACCATTTTCAAGTGAGGAGTTT 60.202 41.667 0.00 0.00 33.21 2.66
2569 5044 7.004086 TGAGGAGTTTTGGTGAAAGATTGTAT 58.996 34.615 0.00 0.00 0.00 2.29
2644 5119 5.648572 GCTAAAATGGACTAGTCGTGTAGT 58.351 41.667 16.56 3.23 35.88 2.73
2706 5181 0.679960 GCAGGGGGCGTTTCTATGTT 60.680 55.000 0.00 0.00 0.00 2.71
2709 5184 2.681344 CAGGGGGCGTTTCTATGTTTAC 59.319 50.000 0.00 0.00 0.00 2.01
3244 5736 5.186021 TCTGAGTTCCTTGTCTATGTCCTTC 59.814 44.000 0.00 0.00 0.00 3.46
3267 5759 6.680810 TCAATTCTGAAATGTAGGTGCAAAG 58.319 36.000 5.44 0.00 0.00 2.77
3331 5825 1.596954 CGTAGCCATGCGGTTTTATGC 60.597 52.381 0.00 0.00 33.28 3.14
3342 5836 3.547601 CGGTTTTATGCTTTCGTTCGTT 58.452 40.909 0.00 0.00 0.00 3.85
3347 5841 6.797995 GGTTTTATGCTTTCGTTCGTTAATGA 59.202 34.615 0.00 0.00 0.00 2.57
3350 5844 7.769719 TTATGCTTTCGTTCGTTAATGAAAC 57.230 32.000 11.66 5.95 42.79 2.78
3482 5976 3.589951 AATCTTGCCTGCTGGATGTAT 57.410 42.857 14.77 0.00 34.57 2.29
3483 5977 4.712051 AATCTTGCCTGCTGGATGTATA 57.288 40.909 14.77 0.00 34.57 1.47
3490 5984 3.813443 CCTGCTGGATGTATAAAGCACT 58.187 45.455 2.92 0.00 40.59 4.40
3498 5992 7.095439 GCTGGATGTATAAAGCACTTACTCATC 60.095 40.741 11.79 11.79 35.00 2.92
3524 6205 4.362677 TCCCTCTGCCTTATACAAGTCTT 58.637 43.478 0.00 0.00 0.00 3.01
3576 6257 8.026396 AGTAGTGGGTTCTTTAGTTCAGTTTA 57.974 34.615 0.00 0.00 0.00 2.01
3628 6309 2.936919 TTATACTCTACCGCGGGAGA 57.063 50.000 37.00 37.00 34.11 3.71
3638 6319 2.280186 GCGGGAGAATAGCCACGG 60.280 66.667 0.00 0.00 0.00 4.94
3697 6378 9.692325 AATAGATAGAAGCTCATTGGAAAAACT 57.308 29.630 0.00 0.00 0.00 2.66
3700 6381 3.575687 AGAAGCTCATTGGAAAAACTGGG 59.424 43.478 0.00 0.00 0.00 4.45
3714 6396 6.352137 GGAAAAACTGGGCTTCATTATCCAAT 60.352 38.462 0.00 0.00 0.00 3.16
3779 6461 6.131972 TGTTTCTTTCCCTGATTGAGAGAT 57.868 37.500 0.00 0.00 0.00 2.75
3788 6470 5.889853 TCCCTGATTGAGAGATTGATTTTGG 59.110 40.000 0.00 0.00 0.00 3.28
3800 6482 4.935352 TTGATTTTGGTGAACCTCTTGG 57.065 40.909 0.37 0.00 36.82 3.61
3843 6525 2.164422 CTCTCCGTAAGACTCATGTGCA 59.836 50.000 0.00 0.00 43.02 4.57
3919 6601 4.606961 TCGTTCTTTTCATGCCTTCAAAC 58.393 39.130 0.00 0.00 0.00 2.93
3925 6607 6.275335 TCTTTTCATGCCTTCAAACAAGAAG 58.725 36.000 0.00 0.00 43.60 2.85
3933 6615 5.301551 TGCCTTCAAACAAGAAGCTCAAATA 59.698 36.000 0.00 0.00 42.84 1.40
3991 6673 9.626045 GTCATTTCCCACTTGTTCTTATTTTAG 57.374 33.333 0.00 0.00 0.00 1.85
4026 6709 8.690680 TTTTATTTCGTGCTACTGTTTTGTTT 57.309 26.923 0.00 0.00 0.00 2.83
4079 6762 5.888161 GGGAATGGTGTTCATACTTTCATCT 59.112 40.000 0.00 0.00 34.44 2.90
4091 6774 8.996651 TCATACTTTCATCTACACATCTCCTA 57.003 34.615 0.00 0.00 0.00 2.94
4213 6896 6.326064 TGATTTCCTTCATTTGTTTCTTCCCA 59.674 34.615 0.00 0.00 0.00 4.37
4223 6906 5.923733 TTGTTTCTTCCCACTTGCTTTAA 57.076 34.783 0.00 0.00 0.00 1.52
4227 6910 6.267471 TGTTTCTTCCCACTTGCTTTAATCAT 59.733 34.615 0.00 0.00 0.00 2.45
4338 7021 9.606631 AACTATGACTCCATCTTCATTTAGAAC 57.393 33.333 0.00 0.00 34.28 3.01
4343 7026 7.038017 TGACTCCATCTTCATTTAGAACTTCCT 60.038 37.037 0.00 0.00 31.61 3.36
4403 7086 7.221452 GGTTTCATCATATTCATTGCTGTTGTC 59.779 37.037 0.00 0.00 0.00 3.18
4497 7180 8.052621 AGACCCCCTGTGCTTATATTATTTTA 57.947 34.615 0.00 0.00 0.00 1.52
4568 7251 8.812329 TGTAAATGTGTTCTTATGTTTGTTTGC 58.188 29.630 0.00 0.00 0.00 3.68
4587 7275 3.090790 TGCATGCACAGGTGTTATGAAT 58.909 40.909 18.46 0.00 32.77 2.57
4890 7578 7.285172 TGTTTCCATGATATTGTATGAAGGTGG 59.715 37.037 0.00 0.00 0.00 4.61
4947 7635 5.576563 TTGATACTCTTTGTTTCAGGGGA 57.423 39.130 0.00 0.00 37.77 4.81
5164 8161 7.168972 GCTATTCATGTTCTGCAGAGTACTTAG 59.831 40.741 17.43 13.31 0.00 2.18
5170 8167 6.390721 TGTTCTGCAGAGTACTTAGCTTTAG 58.609 40.000 17.43 9.72 0.00 1.85
5175 8172 4.327627 GCAGAGTACTTAGCTTTAGTGCAC 59.672 45.833 9.40 9.40 31.59 4.57
5205 8202 7.093771 CCAGTTTACCCAAAGCTATTGAGAATT 60.094 37.037 9.37 0.00 0.00 2.17
5210 8207 7.573968 ACCCAAAGCTATTGAGAATTGATAC 57.426 36.000 9.37 0.00 0.00 2.24
5224 8221 5.652452 AGAATTGATACGCCTTTTAGCCTTT 59.348 36.000 0.00 0.00 0.00 3.11
5226 8223 7.502561 AGAATTGATACGCCTTTTAGCCTTTAT 59.497 33.333 0.00 0.00 0.00 1.40
5227 8224 7.582667 ATTGATACGCCTTTTAGCCTTTATT 57.417 32.000 0.00 0.00 0.00 1.40
5228 8225 8.685838 ATTGATACGCCTTTTAGCCTTTATTA 57.314 30.769 0.00 0.00 0.00 0.98
5432 8440 1.071314 TCCATGGGGGACAGGTTGTT 61.071 55.000 13.02 0.00 42.15 2.83
5434 8442 0.611896 CATGGGGGACAGGTTGTTCC 60.612 60.000 0.00 0.00 45.60 3.62
5455 8463 7.014134 TGTTCCAAATGTATACATAGGGCAATG 59.986 37.037 25.50 14.29 35.10 2.82
5505 8513 2.649531 TTGGATAGGGGCGGTTATTG 57.350 50.000 0.00 0.00 0.00 1.90
5509 8517 2.039879 GGATAGGGGCGGTTATTGATGT 59.960 50.000 0.00 0.00 0.00 3.06
5608 8627 3.364460 TGGTATTCATGGACCAACTGG 57.636 47.619 11.28 0.00 42.81 4.00
5669 9081 7.271223 GTGAAAATAGTTTTGACGTGATGATGG 59.729 37.037 0.00 0.00 31.94 3.51
5670 9082 4.882671 ATAGTTTTGACGTGATGATGGC 57.117 40.909 0.00 0.00 0.00 4.40
5671 9083 1.812571 AGTTTTGACGTGATGATGGCC 59.187 47.619 0.00 0.00 0.00 5.36
5672 9084 1.135402 GTTTTGACGTGATGATGGCCC 60.135 52.381 0.00 0.00 0.00 5.80
5674 9086 1.846712 TTGACGTGATGATGGCCCCA 61.847 55.000 0.00 0.00 0.00 4.96
5675 9087 1.524621 GACGTGATGATGGCCCCAG 60.525 63.158 0.00 0.00 0.00 4.45
5682 9094 3.415087 GATGGCCCCAGCAGGACT 61.415 66.667 0.00 0.00 42.56 3.85
5722 9144 2.432146 TCTGATCTCTTTGATGGACGGG 59.568 50.000 0.00 0.00 35.14 5.28
5768 9190 1.079405 GTTCATTGCCCGGTCTCGA 60.079 57.895 0.00 0.00 39.00 4.04
5775 9197 2.494918 CCCGGTCTCGATGTGGTC 59.505 66.667 0.00 0.00 39.00 4.02
5776 9198 2.052690 CCCGGTCTCGATGTGGTCT 61.053 63.158 0.00 0.00 39.00 3.85
5777 9199 1.139734 CCGGTCTCGATGTGGTCTG 59.860 63.158 0.00 0.00 39.00 3.51
5778 9200 1.595993 CCGGTCTCGATGTGGTCTGT 61.596 60.000 0.00 0.00 39.00 3.41
5786 9211 0.603065 GATGTGGTCTGTTTTGCCCC 59.397 55.000 0.00 0.00 0.00 5.80
5904 9331 1.006805 CGCGCCCATCCTCTTCTAG 60.007 63.158 0.00 0.00 0.00 2.43
5967 9394 0.804364 GGCGAAATGATGACTGTGCA 59.196 50.000 0.00 0.00 0.00 4.57
5973 9410 4.319984 CGAAATGATGACTGTGCATATGGG 60.320 45.833 4.56 0.00 0.00 4.00
5974 9411 1.971481 TGATGACTGTGCATATGGGC 58.029 50.000 4.56 0.00 0.00 5.36
5981 9418 2.025981 ACTGTGCATATGGGCAGAAAGA 60.026 45.455 4.56 0.00 45.96 2.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.108804 CACGGCGAAGGTATCACAGT 60.109 55.000 16.62 0.00 0.00 3.55
1 2 0.108804 ACACGGCGAAGGTATCACAG 60.109 55.000 16.62 0.00 0.00 3.66
2 3 1.175654 TACACGGCGAAGGTATCACA 58.824 50.000 16.62 0.00 0.00 3.58
3 4 2.503920 ATACACGGCGAAGGTATCAC 57.496 50.000 16.62 0.00 0.00 3.06
4 5 3.131577 AGAAATACACGGCGAAGGTATCA 59.868 43.478 16.62 0.00 0.00 2.15
5 6 3.714391 AGAAATACACGGCGAAGGTATC 58.286 45.455 16.62 8.49 0.00 2.24
6 7 3.814005 AGAAATACACGGCGAAGGTAT 57.186 42.857 16.62 15.12 0.00 2.73
7 8 3.194116 AGAAGAAATACACGGCGAAGGTA 59.806 43.478 16.62 13.40 0.00 3.08
8 9 2.028385 AGAAGAAATACACGGCGAAGGT 60.028 45.455 16.62 11.43 0.00 3.50
9 10 2.348666 CAGAAGAAATACACGGCGAAGG 59.651 50.000 16.62 5.02 0.00 3.46
14 15 1.130561 GTGGCAGAAGAAATACACGGC 59.869 52.381 0.00 0.00 0.00 5.68
26 27 1.092921 ACGACGCTTTTGTGGCAGAA 61.093 50.000 0.00 0.00 37.98 3.02
28 29 1.082756 GACGACGCTTTTGTGGCAG 60.083 57.895 0.00 0.00 37.98 4.85
29 30 1.092921 AAGACGACGCTTTTGTGGCA 61.093 50.000 0.00 0.00 37.98 4.92
30 31 0.384353 GAAGACGACGCTTTTGTGGC 60.384 55.000 0.00 0.00 33.83 5.01
31 32 0.234884 GGAAGACGACGCTTTTGTGG 59.765 55.000 0.00 0.00 0.00 4.17
33 34 0.179067 TGGGAAGACGACGCTTTTGT 60.179 50.000 0.00 0.00 0.00 2.83
34 35 0.234884 GTGGGAAGACGACGCTTTTG 59.765 55.000 0.00 0.00 0.00 2.44
43 46 1.265635 TCGCAAAAATGTGGGAAGACG 59.734 47.619 0.00 0.00 37.51 4.18
56 59 1.418637 AGGGGAGTACACTTCGCAAAA 59.581 47.619 7.40 0.00 36.92 2.44
59 62 1.255667 GGAGGGGAGTACACTTCGCA 61.256 60.000 7.40 0.00 36.92 5.10
60 63 1.516423 GGAGGGGAGTACACTTCGC 59.484 63.158 0.00 0.00 34.86 4.70
72 75 2.914734 TATGCTGGGAGTGGGAGGGG 62.915 65.000 0.00 0.00 0.00 4.79
75 78 0.319728 CGATATGCTGGGAGTGGGAG 59.680 60.000 0.00 0.00 0.00 4.30
76 79 1.121407 CCGATATGCTGGGAGTGGGA 61.121 60.000 0.00 0.00 0.00 4.37
77 80 1.121407 TCCGATATGCTGGGAGTGGG 61.121 60.000 0.00 0.00 0.00 4.61
78 81 0.979665 ATCCGATATGCTGGGAGTGG 59.020 55.000 0.00 0.00 34.92 4.00
79 82 1.620323 TGATCCGATATGCTGGGAGTG 59.380 52.381 0.00 0.00 34.92 3.51
80 83 1.620819 GTGATCCGATATGCTGGGAGT 59.379 52.381 0.00 0.00 34.92 3.85
117 127 8.400184 TCCTCTGCATCCATAAATAATTTCAG 57.600 34.615 0.00 0.00 0.00 3.02
120 130 8.443176 TCTCTCCTCTGCATCCATAAATAATTT 58.557 33.333 0.00 0.00 0.00 1.82
164 174 1.289109 CGAACTGCGTGGACGGAAAT 61.289 55.000 0.71 0.00 39.68 2.17
188 198 0.727398 GTCTTGTCAGCGTAATGGCC 59.273 55.000 0.00 0.00 0.00 5.36
271 281 0.390472 CTCCTCCTTCTGGCGTCAAC 60.390 60.000 0.00 0.00 0.00 3.18
272 282 1.544825 CCTCCTCCTTCTGGCGTCAA 61.545 60.000 0.00 0.00 0.00 3.18
278 288 1.589414 ATGGTTCCTCCTCCTTCTGG 58.411 55.000 0.00 0.00 37.07 3.86
280 290 3.260205 TCAAATGGTTCCTCCTCCTTCT 58.740 45.455 0.00 0.00 37.07 2.85
281 291 3.721087 TCAAATGGTTCCTCCTCCTTC 57.279 47.619 0.00 0.00 37.07 3.46
282 292 4.044571 TGATTCAAATGGTTCCTCCTCCTT 59.955 41.667 0.00 0.00 37.07 3.36
294 304 4.395854 TGATGAACGGAGTGATTCAAATGG 59.604 41.667 0.00 0.00 45.00 3.16
298 308 3.334691 GGTGATGAACGGAGTGATTCAA 58.665 45.455 0.00 0.00 45.00 2.69
300 310 1.927174 CGGTGATGAACGGAGTGATTC 59.073 52.381 0.00 0.00 45.00 2.52
338 348 2.664851 CAGAACCGGCGAGCAACA 60.665 61.111 9.30 0.00 0.00 3.33
368 384 3.288092 AGCCCCGAAGAAATGTAAATCC 58.712 45.455 0.00 0.00 0.00 3.01
454 483 0.440371 GAGCTGCAAGTGTAGAACGC 59.560 55.000 1.02 0.00 35.30 4.84
455 484 1.071605 GGAGCTGCAAGTGTAGAACG 58.928 55.000 0.00 0.00 35.30 3.95
456 485 1.071605 CGGAGCTGCAAGTGTAGAAC 58.928 55.000 5.91 0.00 35.30 3.01
483 1173 5.063880 TGCAGTTTCTTTCTCTAGGGTTTC 58.936 41.667 0.00 0.00 0.00 2.78
486 1176 3.008485 CCTGCAGTTTCTTTCTCTAGGGT 59.992 47.826 13.81 0.00 0.00 4.34
487 1177 3.261897 TCCTGCAGTTTCTTTCTCTAGGG 59.738 47.826 13.81 0.00 0.00 3.53
489 1179 5.788450 TCTTCCTGCAGTTTCTTTCTCTAG 58.212 41.667 13.81 0.00 0.00 2.43
492 1182 4.450757 GTCTCTTCCTGCAGTTTCTTTCTC 59.549 45.833 13.81 0.00 0.00 2.87
588 1289 2.515947 GAAGTGCGCGAGAGACGACT 62.516 60.000 12.10 0.00 45.77 4.18
700 2853 0.528470 GAGTGCTGAGGAGTACGCTT 59.472 55.000 0.00 0.00 39.64 4.68
712 2865 2.019948 TGCTAATCTGCTGAGTGCTG 57.980 50.000 3.62 0.00 43.37 4.41
713 2866 2.289882 TGTTGCTAATCTGCTGAGTGCT 60.290 45.455 3.62 0.00 43.37 4.40
714 2867 2.079158 TGTTGCTAATCTGCTGAGTGC 58.921 47.619 3.62 6.23 43.25 4.40
715 2868 4.959596 ATTGTTGCTAATCTGCTGAGTG 57.040 40.909 3.62 0.00 0.00 3.51
716 2869 7.478322 CAATAATTGTTGCTAATCTGCTGAGT 58.522 34.615 1.72 0.00 0.00 3.41
717 2870 7.909777 CAATAATTGTTGCTAATCTGCTGAG 57.090 36.000 1.72 0.00 0.00 3.35
731 2884 3.627577 CGTCTAGCCCAGCAATAATTGTT 59.372 43.478 0.00 0.00 0.00 2.83
802 2961 4.615834 TTTGCGCGTTCGTTGGGC 62.616 61.111 8.43 6.44 44.67 5.36
846 3007 2.294078 CCTGGACCTGGACCTGGAC 61.294 68.421 28.41 16.79 45.37 4.02
933 3100 2.800523 GAAAGGGGGAAGGGGAGGGA 62.801 65.000 0.00 0.00 0.00 4.20
969 3140 3.842923 CAGATCTGCCGTCGCCCT 61.843 66.667 10.38 0.00 0.00 5.19
1198 3373 3.056328 GAACTCCCCGCCACTTGC 61.056 66.667 0.00 0.00 0.00 4.01
1377 3565 1.818674 AGTGGCCGCATTAGAAAAAGG 59.181 47.619 20.59 0.00 0.00 3.11
1393 3586 0.438830 GCTTAAAGCGTCGTCAGTGG 59.561 55.000 0.00 0.00 0.00 4.00
1485 3722 4.054671 GTGCTAAATCACCTAGCTAGCAG 58.945 47.826 18.83 11.93 44.06 4.24
1486 3723 3.706594 AGTGCTAAATCACCTAGCTAGCA 59.293 43.478 18.83 6.58 41.96 3.49
1487 3724 4.329462 AGTGCTAAATCACCTAGCTAGC 57.671 45.455 15.74 6.62 41.96 3.42
1488 3725 6.341316 TCAAAGTGCTAAATCACCTAGCTAG 58.659 40.000 14.20 14.20 41.96 3.42
1489 3726 6.294361 TCAAAGTGCTAAATCACCTAGCTA 57.706 37.500 0.00 0.00 41.96 3.32
1490 3727 5.165961 TCAAAGTGCTAAATCACCTAGCT 57.834 39.130 0.00 0.00 41.96 3.32
1491 3728 5.674820 GCTTCAAAGTGCTAAATCACCTAGC 60.675 44.000 0.00 0.00 41.83 3.42
1492 3729 5.412594 TGCTTCAAAGTGCTAAATCACCTAG 59.587 40.000 0.00 0.00 37.68 3.02
1493 3730 5.312895 TGCTTCAAAGTGCTAAATCACCTA 58.687 37.500 0.00 0.00 37.68 3.08
1494 3731 4.144297 TGCTTCAAAGTGCTAAATCACCT 58.856 39.130 0.00 0.00 37.68 4.00
1495 3732 4.503741 TGCTTCAAAGTGCTAAATCACC 57.496 40.909 0.00 0.00 37.68 4.02
1496 3733 6.476706 ACTTTTGCTTCAAAGTGCTAAATCAC 59.523 34.615 8.03 0.00 34.72 3.06
1497 3734 6.572519 ACTTTTGCTTCAAAGTGCTAAATCA 58.427 32.000 8.03 0.00 34.72 2.57
1498 3735 7.148902 GCTACTTTTGCTTCAAAGTGCTAAATC 60.149 37.037 15.41 0.00 34.72 2.17
1499 3736 6.642540 GCTACTTTTGCTTCAAAGTGCTAAAT 59.357 34.615 15.41 0.00 34.72 1.40
1500 3737 5.977129 GCTACTTTTGCTTCAAAGTGCTAAA 59.023 36.000 15.41 0.00 34.72 1.85
1567 3808 2.146342 GGCGCTATCACATTGTGCTAT 58.854 47.619 12.04 4.25 40.49 2.97
1611 3854 3.045601 ACTCCATGTGACGAAGAAAGG 57.954 47.619 0.00 0.00 0.00 3.11
1619 3862 3.297830 TGTGAACTACTCCATGTGACG 57.702 47.619 0.00 0.00 0.00 4.35
1669 3912 2.550208 GCCTTGGATACCCCTGTTATCG 60.550 54.545 0.00 0.00 35.38 2.92
1774 4017 1.808945 CCAAGACAGCACACATTCTCC 59.191 52.381 0.00 0.00 0.00 3.71
1846 4089 0.458543 ACGCAACTGCTATCACCGAG 60.459 55.000 0.00 0.00 39.32 4.63
1850 4093 2.223112 CCATTCACGCAACTGCTATCAC 60.223 50.000 0.00 0.00 39.32 3.06
1860 4103 0.726827 GCGAAGATCCATTCACGCAA 59.273 50.000 0.00 0.00 45.13 4.85
1861 4104 0.108186 AGCGAAGATCCATTCACGCA 60.108 50.000 0.00 0.00 46.79 5.24
1895 4138 1.154093 CTTCACATGCTGCGCCAAG 60.154 57.895 4.18 0.00 0.00 3.61
1934 4177 3.499737 CCTTTAGCTGCACCCGCG 61.500 66.667 0.00 0.00 42.97 6.46
1937 4180 0.251165 TTGTCCCTTTAGCTGCACCC 60.251 55.000 1.02 0.00 0.00 4.61
2039 4303 1.588674 TTATTGCGGGTAATGGCGAG 58.411 50.000 0.00 0.00 0.00 5.03
2049 4313 3.506067 ACAACTCCTCTTTTTATTGCGGG 59.494 43.478 0.00 0.00 0.00 6.13
2056 4320 5.534207 TGACGGTACAACTCCTCTTTTTA 57.466 39.130 0.00 0.00 0.00 1.52
2061 4325 3.446516 GGTAATGACGGTACAACTCCTCT 59.553 47.826 0.00 0.00 0.00 3.69
2076 4340 1.757118 CTCCTCTCTTGCGGGTAATGA 59.243 52.381 0.00 0.00 0.00 2.57
2123 4391 6.883217 TGGGCACAACAAATTATGCAATAAAT 59.117 30.769 0.00 0.00 42.96 1.40
2141 4409 5.923204 AGACAAAAACAAATATTGGGCACA 58.077 33.333 0.00 0.00 34.12 4.57
2165 4435 9.671279 AAGTTTTGAACATGGAAGAAAAAGAAT 57.329 25.926 0.00 0.00 0.00 2.40
2174 4444 6.317789 TCAGCTAAGTTTTGAACATGGAAG 57.682 37.500 0.00 0.00 0.00 3.46
2192 4471 8.834465 CAGCAATAAATATCAGTTAGTTCAGCT 58.166 33.333 0.00 0.00 0.00 4.24
2225 4504 4.156008 GGGTTGTCCACATACTGAATCAAC 59.844 45.833 0.00 0.00 34.95 3.18
2233 4512 3.375699 CCTCTAGGGTTGTCCACATACT 58.624 50.000 0.00 0.00 38.24 2.12
2317 4596 8.870075 AAATTAAAGGACAGAGCTTGATAAGT 57.130 30.769 0.00 0.00 0.00 2.24
2324 4603 9.836864 AAATTTGAAAATTAAAGGACAGAGCTT 57.163 25.926 1.61 0.00 37.62 3.74
2515 4990 1.342975 TGGTGCTAGTGGAGGCTATCA 60.343 52.381 0.00 0.00 0.00 2.15
2517 4992 2.109229 ATGGTGCTAGTGGAGGCTAT 57.891 50.000 0.00 0.00 0.00 2.97
2644 5119 5.250543 TGCCTGCTATATAGGAGCCATTAAA 59.749 40.000 22.31 0.00 40.04 1.52
2706 5181 1.347707 CAAGCTGACCCCACAGAGTAA 59.652 52.381 0.00 0.00 39.94 2.24
2709 5184 0.109342 AACAAGCTGACCCCACAGAG 59.891 55.000 0.00 0.00 39.94 3.35
2860 5348 2.608261 GCAGTTGTCTCTCTAGTTGCGT 60.608 50.000 0.00 0.00 0.00 5.24
3072 5560 9.984190 GTAGTATCGAGGAAAAGAGGAAATAAT 57.016 33.333 0.00 0.00 0.00 1.28
3198 5686 8.730680 TCAGAAGATGCCTTTTAAATGTTCTAC 58.269 33.333 0.00 0.00 33.55 2.59
3244 5736 6.680810 TCTTTGCACCTACATTTCAGAATTG 58.319 36.000 3.87 3.87 0.00 2.32
3331 5825 6.415702 TGTGAGTTTCATTAACGAACGAAAG 58.584 36.000 0.14 0.00 41.78 2.62
3342 5836 9.851686 ATTATTATCAGCCTGTGAGTTTCATTA 57.148 29.630 0.00 0.00 39.07 1.90
3379 5873 2.224354 CCTCAACCTGCAAAAGCCAATT 60.224 45.455 0.00 0.00 0.00 2.32
3482 5976 3.454812 GGAGGGGATGAGTAAGTGCTTTA 59.545 47.826 0.00 0.00 0.00 1.85
3483 5977 2.239907 GGAGGGGATGAGTAAGTGCTTT 59.760 50.000 0.00 0.00 0.00 3.51
3490 5984 1.692762 GCAGAGGGAGGGGATGAGTAA 60.693 57.143 0.00 0.00 0.00 2.24
3498 5992 1.353091 GTATAAGGCAGAGGGAGGGG 58.647 60.000 0.00 0.00 0.00 4.79
3547 6228 6.891388 TGAACTAAAGAACCCACTACTTTCA 58.109 36.000 0.00 0.00 35.79 2.69
3556 6237 5.058490 CCGTAAACTGAACTAAAGAACCCA 58.942 41.667 0.00 0.00 0.00 4.51
3628 6309 0.618458 TTCCTGCTTCCGTGGCTATT 59.382 50.000 0.00 0.00 0.00 1.73
3638 6319 4.237724 GCTAACCAATGTTTTCCTGCTTC 58.762 43.478 0.00 0.00 35.87 3.86
3697 6378 3.029483 TGCATTGGATAATGAAGCCCA 57.971 42.857 4.33 0.00 45.21 5.36
3700 6381 3.744426 GGCATTGCATTGGATAATGAAGC 59.256 43.478 11.39 2.31 45.21 3.86
3714 6396 1.069427 GGCTGTGTTTGGCATTGCA 59.931 52.632 11.39 0.00 32.52 4.08
3779 6461 4.340950 GTCCAAGAGGTTCACCAAAATCAA 59.659 41.667 0.00 0.00 38.89 2.57
3788 6470 7.393515 AGTTATTTATTGGTCCAAGAGGTTCAC 59.606 37.037 10.72 2.00 35.89 3.18
3843 6525 7.757242 AGAACCTAGGGAATTTGATAAGACT 57.243 36.000 14.81 0.00 0.00 3.24
3890 6572 8.735315 TGAAGGCATGAAAAGAACGATAAATTA 58.265 29.630 0.00 0.00 0.00 1.40
3899 6581 6.042143 TCTTGTTTGAAGGCATGAAAAGAAC 58.958 36.000 0.00 0.00 0.00 3.01
3925 6607 9.713740 CAGAGAATTCAAAGTATGTATTTGAGC 57.286 33.333 8.44 0.00 44.86 4.26
3961 6643 4.482990 AGAACAAGTGGGAAATGACCAAT 58.517 39.130 0.00 0.00 40.24 3.16
3991 6673 8.071967 AGTAGCACGAAATAAAAACCAAAGTAC 58.928 33.333 0.00 0.00 0.00 2.73
4009 6692 5.554324 GCAATTGAAACAAAACAGTAGCACG 60.554 40.000 10.34 0.00 0.00 5.34
4026 6709 3.438216 TGAACCCAGATCTGCAATTGA 57.562 42.857 17.76 2.30 0.00 2.57
4079 6762 7.492524 CAATTCTTGTAGCTAGGAGATGTGTA 58.507 38.462 0.00 0.00 0.00 2.90
4091 6774 1.089920 CAGCCGCAATTCTTGTAGCT 58.910 50.000 0.00 0.00 40.26 3.32
4183 6866 8.010733 AGAAACAAATGAAGGAAATCAACAGA 57.989 30.769 0.00 0.00 32.06 3.41
4314 6997 9.829507 AAGTTCTAAATGAAGATGGAGTCATAG 57.170 33.333 0.00 0.00 33.31 2.23
4335 7018 1.163554 CAGGCTGCAGAAGGAAGTTC 58.836 55.000 20.43 0.00 35.08 3.01
4338 7021 3.588336 GCAGGCTGCAGAAGGAAG 58.412 61.111 33.33 1.14 44.26 3.46
4497 7180 2.970987 ACCCTGGGTGCAAAATAAACT 58.029 42.857 19.82 0.00 32.98 2.66
4558 7241 1.206610 ACCTGTGCATGCAAACAAACA 59.793 42.857 24.58 14.02 0.00 2.83
4568 7251 4.577693 AGCTATTCATAACACCTGTGCATG 59.422 41.667 0.00 2.13 0.00 4.06
4587 7275 8.313292 TCCTTACCGTAAACTGAAAATAAGCTA 58.687 33.333 0.00 0.00 0.00 3.32
4890 7578 7.964604 ATACAAAAGTTCTTAGTGTCAGGAC 57.035 36.000 5.48 0.00 0.00 3.85
4947 7635 9.798994 GCACAGAGAAAAATAAATGAGATGAAT 57.201 29.630 0.00 0.00 0.00 2.57
5016 7706 4.156556 TGGAATATTGCAACAGAGAACTGC 59.843 41.667 7.25 0.00 46.95 4.40
5128 8123 8.635328 TGCAGAACATGAATAGCAATATGATTT 58.365 29.630 0.00 0.00 0.00 2.17
5137 8132 4.212143 ACTCTGCAGAACATGAATAGCA 57.788 40.909 18.85 3.58 0.00 3.49
5140 8135 6.980978 GCTAAGTACTCTGCAGAACATGAATA 59.019 38.462 18.85 4.76 0.00 1.75
5164 8161 1.226746 ACTGGTTCGTGCACTAAAGC 58.773 50.000 16.19 17.67 0.00 3.51
5170 8167 0.589708 GGGTAAACTGGTTCGTGCAC 59.410 55.000 6.82 6.82 0.00 4.57
5175 8172 2.227194 AGCTTTGGGTAAACTGGTTCG 58.773 47.619 0.00 0.00 0.00 3.95
5205 8202 6.708949 CCTAATAAAGGCTAAAAGGCGTATCA 59.291 38.462 0.00 0.00 46.58 2.15
5226 8223 8.579850 AGAATGAGAAACAACATATTGCCTAA 57.420 30.769 0.00 0.00 39.66 2.69
5227 8224 8.579850 AAGAATGAGAAACAACATATTGCCTA 57.420 30.769 0.00 0.00 39.66 3.93
5228 8225 7.395489 AGAAGAATGAGAAACAACATATTGCCT 59.605 33.333 0.00 0.00 39.66 4.75
5230 8227 8.976986 AAGAAGAATGAGAAACAACATATTGC 57.023 30.769 0.00 0.00 39.66 3.56
5308 8316 1.000396 GGAGGTGCAAGCCCTGAAT 60.000 57.895 0.00 0.00 32.25 2.57
5432 8440 6.846988 TCATTGCCCTATGTATACATTTGGA 58.153 36.000 25.96 14.56 37.76 3.53
5434 8442 7.750229 ACTCATTGCCCTATGTATACATTTG 57.250 36.000 22.90 15.43 37.76 2.32
5439 8447 7.752695 GCATAAACTCATTGCCCTATGTATAC 58.247 38.462 0.00 0.00 0.00 1.47
5505 8513 4.425577 AAACGCAAGGAAGAATCACATC 57.574 40.909 0.00 0.00 46.39 3.06
5509 8517 5.428253 AGCTATAAACGCAAGGAAGAATCA 58.572 37.500 0.00 0.00 46.39 2.57
5659 9071 2.903855 GCTGGGGCCATCATCACG 60.904 66.667 4.39 0.00 0.00 4.35
5671 9083 3.292481 ATGCCCAAGTCCTGCTGGG 62.292 63.158 10.07 5.91 44.20 4.45
5672 9084 2.050350 CATGCCCAAGTCCTGCTGG 61.050 63.158 2.58 2.58 0.00 4.85
5674 9086 1.303888 CACATGCCCAAGTCCTGCT 60.304 57.895 0.00 0.00 0.00 4.24
5675 9087 2.998279 GCACATGCCCAAGTCCTGC 61.998 63.158 0.00 0.00 34.31 4.85
5722 9144 1.448540 CGATGGACACTGGCCAGTC 60.449 63.158 35.79 24.64 40.20 3.51
5768 9190 0.188342 AGGGGCAAAACAGACCACAT 59.812 50.000 0.00 0.00 38.98 3.21
5967 9394 1.071385 CGCTCCTCTTTCTGCCCATAT 59.929 52.381 0.00 0.00 0.00 1.78
5973 9410 2.164026 CGAGCGCTCCTCTTTCTGC 61.164 63.158 30.66 3.44 38.49 4.26
5974 9411 2.164026 GCGAGCGCTCCTCTTTCTG 61.164 63.158 30.66 15.35 38.49 3.02


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

AutoCloner maintained by Alex Coulton.