Multiple sequence alignment - TraesCS3A01G320800

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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 TraesCS3A01G320800 chr3A 100.000 6053 0 0 1 6053 564339666 564345718 0.000000e+00 11178
1 TraesCS3A01G320800 chr3A 91.753 97 6 1 2794 2888 80090861 80090957 3.810000e-27 134
2 TraesCS3A01G320800 chr3D 94.890 4423 162 37 1082 5474 424661377 424656989 0.000000e+00 6857
3 TraesCS3A01G320800 chr3D 87.500 432 49 4 1 429 424665642 424665213 1.520000e-135 494
4 TraesCS3A01G320800 chr3D 91.692 325 23 2 5729 6053 424656711 424656391 1.200000e-121 448
5 TraesCS3A01G320800 chr3D 91.558 308 22 4 744 1049 424661981 424661676 7.250000e-114 422
6 TraesCS3A01G320800 chr3B 94.796 2210 96 11 3274 5474 554699450 554697251 0.000000e+00 3426
7 TraesCS3A01G320800 chr3B 91.720 2500 128 39 744 3206 554701896 554699439 0.000000e+00 3397
8 TraesCS3A01G320800 chr3B 91.622 752 52 8 1 744 554702534 554701786 0.000000e+00 1029
9 TraesCS3A01G320800 chr3B 91.473 258 18 2 5800 6053 554649743 554649486 9.650000e-93 351
10 TraesCS3A01G320800 chr6D 91.611 2396 120 33 1971 4326 469512065 469509711 0.000000e+00 3236
11 TraesCS3A01G320800 chr6D 92.004 2126 103 24 2229 4326 469492989 469490903 0.000000e+00 2922
12 TraesCS3A01G320800 chr6D 87.914 513 30 10 4311 4794 469489324 469488815 5.260000e-160 575
13 TraesCS3A01G320800 chr6D 87.524 513 32 10 4311 4794 469508134 469507625 1.140000e-156 564
14 TraesCS3A01G320800 chr6D 87.660 470 27 6 5011 5474 457065388 457064944 8.990000e-143 518
15 TraesCS3A01G320800 chr6D 87.926 323 23 6 1305 1611 469512662 469512340 3.450000e-97 366
16 TraesCS3A01G320800 chr6D 90.119 253 25 0 5801 6053 457011844 457011592 4.520000e-86 329
17 TraesCS3A01G320800 chr6D 92.788 208 12 3 4622 4829 457068347 457068143 1.280000e-76 298
18 TraesCS3A01G320800 chr6D 87.665 227 10 7 964 1180 469521764 469521546 1.300000e-61 248
19 TraesCS3A01G320800 chr6D 92.405 158 5 2 1790 1940 469512222 469512065 1.020000e-52 219
20 TraesCS3A01G320800 chr6D 85.222 203 20 7 1176 1369 469512864 469512663 3.700000e-47 200
21 TraesCS3A01G320800 chr6D 92.086 139 10 1 4890 5028 457065604 457065467 1.720000e-45 195
22 TraesCS3A01G320800 chr5D 86.901 626 44 25 4626 5246 547260245 547260837 0.000000e+00 667
23 TraesCS3A01G320800 chr5D 93.839 422 12 6 3483 3903 547259839 547260247 1.850000e-174 623
24 TraesCS3A01G320800 chr5D 91.892 259 20 1 5795 6053 547260909 547261166 1.600000e-95 361
25 TraesCS3A01G320800 chr5D 93.684 95 5 1 2794 2887 134780599 134780505 2.270000e-29 141
26 TraesCS3A01G320800 chrUn 91.029 379 23 5 2302 2669 480365466 480365844 9.060000e-138 501
27 TraesCS3A01G320800 chr7B 91.089 101 5 2 2794 2894 329083561 329083657 3.810000e-27 134
28 TraesCS3A01G320800 chr5B 91.753 97 5 2 2793 2889 17982697 17982604 1.370000e-26 132
29 TraesCS3A01G320800 chr5A 91.667 96 6 1 2794 2887 393476443 393476348 1.370000e-26 132
30 TraesCS3A01G320800 chr2D 90.816 98 9 0 2791 2888 376700830 376700733 1.370000e-26 132
31 TraesCS3A01G320800 chr2A 90.291 103 5 4 2792 2889 746253395 746253497 4.920000e-26 130


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 TraesCS3A01G320800 chr3A 564339666 564345718 6052 False 11178.000000 11178 100.000000 1 6053 1 chr3A.!!$F2 6052
1 TraesCS3A01G320800 chr3D 424656391 424665642 9251 True 2055.250000 6857 91.410000 1 6053 4 chr3D.!!$R1 6052
2 TraesCS3A01G320800 chr3B 554697251 554702534 5283 True 2617.333333 3426 92.712667 1 5474 3 chr3B.!!$R2 5473
3 TraesCS3A01G320800 chr6D 469488815 469492989 4174 True 1748.500000 2922 89.959000 2229 4794 2 chr6D.!!$R4 2565
4 TraesCS3A01G320800 chr6D 469507625 469512864 5239 True 917.000000 3236 88.937600 1176 4794 5 chr6D.!!$R5 3618
5 TraesCS3A01G320800 chr6D 457064944 457068347 3403 True 337.000000 518 90.844667 4622 5474 3 chr6D.!!$R3 852
6 TraesCS3A01G320800 chr5D 547259839 547261166 1327 False 550.333333 667 90.877333 3483 6053 3 chr5D.!!$F1 2570

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
746 3793 0.186630 ACCACGGGCCCTAAAAACTT 59.813 50.000 22.43 0.00 0.00 2.66 F
749 3796 0.251474 ACGGGCCCTAAAAACTTCCC 60.251 55.000 22.43 0.00 0.00 3.97 F
1824 5234 0.400213 TCTGTCGAAACCCCAATGCT 59.600 50.000 0.00 0.00 0.00 3.79 F
1948 5365 1.134818 CCAGTCTACCGCAATGTAGCA 60.135 52.381 0.00 0.00 38.46 3.49 F
1965 5382 1.936436 GCATTTGCTGGCGGATCACA 61.936 55.000 0.00 0.00 38.21 3.58 F
3795 7263 2.524306 CCAGAAAATGGTAACTGGCCA 58.476 47.619 4.71 4.71 44.91 5.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2103 5521 0.035343 GTAGTTTCAGGGAGGGTGCC 60.035 60.000 0.00 0.00 0.00 5.01 R
2381 5832 3.674138 GCTGCATTTATTATCCATGGGCG 60.674 47.826 13.02 2.18 0.00 6.13 R
3422 6890 1.156736 GGAGCAAACGAAAGCTAGCA 58.843 50.000 18.83 0.00 42.04 3.49 R
3795 7263 9.076781 CCAATTTCCAACCTCCAAAATAAATTT 57.923 29.630 0.00 0.00 0.00 1.82 R
4007 7475 4.110036 TCTCATGTATCACAGACAACCG 57.890 45.455 0.00 0.00 0.00 4.44 R
5726 13463 0.034380 GCTGGGGTTTTACTCCCTCC 60.034 60.000 0.00 0.00 38.22 4.30 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
62 65 9.130312 CCGAATCTAACTTGCTATACATAGTTC 57.870 37.037 0.00 0.00 34.04 3.01
67 70 8.794553 TCTAACTTGCTATACATAGTTCTAGGC 58.205 37.037 0.00 0.00 34.04 3.93
82 85 3.856900 TCTAGGCTGAGGCATACCATTA 58.143 45.455 9.23 0.00 40.87 1.90
84 87 2.412591 AGGCTGAGGCATACCATTAGT 58.587 47.619 9.23 0.00 40.87 2.24
93 96 3.632145 GGCATACCATTAGTCAAACCCTG 59.368 47.826 0.00 0.00 35.26 4.45
159 162 1.141254 TCAAAGTGGGCCGTAAAGTCA 59.859 47.619 0.00 0.00 0.00 3.41
160 163 2.159382 CAAAGTGGGCCGTAAAGTCAT 58.841 47.619 0.00 0.00 0.00 3.06
161 164 2.556622 CAAAGTGGGCCGTAAAGTCATT 59.443 45.455 0.00 0.00 0.00 2.57
162 165 2.579410 AGTGGGCCGTAAAGTCATTT 57.421 45.000 0.00 0.00 0.00 2.32
253 257 1.236616 TGTGGAATGTGCGGCTCAAG 61.237 55.000 8.95 0.00 0.00 3.02
283 287 3.006247 GAGAGGGACATTCAGAAGTTGC 58.994 50.000 0.00 0.00 0.00 4.17
386 391 7.067496 AGAAGATGTGAAGACCTTACTTTGA 57.933 36.000 0.00 0.00 0.00 2.69
415 420 8.502738 AGGCAAGAATTTTAGATTAGATGGGTA 58.497 33.333 0.00 0.00 0.00 3.69
416 421 9.301897 GGCAAGAATTTTAGATTAGATGGGTAT 57.698 33.333 0.00 0.00 0.00 2.73
423 428 9.936329 ATTTTAGATTAGATGGGTATGGTGTTT 57.064 29.630 0.00 0.00 0.00 2.83
460 3500 3.069586 CACATCGGTTAGCCTAAGATGGA 59.930 47.826 14.62 0.00 41.96 3.41
527 3569 8.783093 CCCGATTCTATTTTAAGCATTGTATCA 58.217 33.333 0.00 0.00 0.00 2.15
536 3578 9.868277 ATTTTAAGCATTGTATCATCGGAAAAA 57.132 25.926 0.00 0.00 0.00 1.94
540 3582 7.281040 AGCATTGTATCATCGGAAAAATCAT 57.719 32.000 0.00 0.00 0.00 2.45
587 3629 9.667107 ATGAACGGTCTTTTGAATCTAGAATTA 57.333 29.630 0.33 0.00 0.00 1.40
680 3727 1.268352 ACTGACGAACTCTCAGCACTC 59.732 52.381 0.00 0.00 39.08 3.51
699 3746 2.712087 CTCCTCTAGTCCTACTAGGGCA 59.288 54.545 9.46 0.00 45.72 5.36
700 3747 3.128848 TCCTCTAGTCCTACTAGGGCAA 58.871 50.000 9.46 0.17 45.72 4.52
701 3748 3.138653 TCCTCTAGTCCTACTAGGGCAAG 59.861 52.174 9.46 3.66 45.72 4.01
702 3749 3.138653 CCTCTAGTCCTACTAGGGCAAGA 59.861 52.174 9.46 5.53 45.72 3.02
703 3750 4.386536 CCTCTAGTCCTACTAGGGCAAGAA 60.387 50.000 9.46 0.00 45.72 2.52
704 3751 4.534797 TCTAGTCCTACTAGGGCAAGAAC 58.465 47.826 9.46 0.00 44.17 3.01
705 3752 3.185880 AGTCCTACTAGGGCAAGAACA 57.814 47.619 9.46 0.00 44.17 3.18
706 3753 3.100671 AGTCCTACTAGGGCAAGAACAG 58.899 50.000 9.46 0.00 44.17 3.16
707 3754 3.097614 GTCCTACTAGGGCAAGAACAGA 58.902 50.000 1.44 0.00 40.51 3.41
708 3755 3.514309 GTCCTACTAGGGCAAGAACAGAA 59.486 47.826 1.44 0.00 40.51 3.02
709 3756 3.769844 TCCTACTAGGGCAAGAACAGAAG 59.230 47.826 2.04 0.00 35.59 2.85
710 3757 3.515901 CCTACTAGGGCAAGAACAGAAGT 59.484 47.826 0.00 0.00 0.00 3.01
711 3758 4.020128 CCTACTAGGGCAAGAACAGAAGTT 60.020 45.833 0.00 0.00 41.64 2.66
712 3759 4.439253 ACTAGGGCAAGAACAGAAGTTT 57.561 40.909 0.00 0.00 38.30 2.66
713 3760 4.793201 ACTAGGGCAAGAACAGAAGTTTT 58.207 39.130 0.00 0.00 38.30 2.43
714 3761 4.822350 ACTAGGGCAAGAACAGAAGTTTTC 59.178 41.667 0.00 0.00 38.30 2.29
715 3762 3.903467 AGGGCAAGAACAGAAGTTTTCT 58.097 40.909 0.00 0.00 41.70 2.52
716 3763 3.885901 AGGGCAAGAACAGAAGTTTTCTC 59.114 43.478 0.00 0.00 38.11 2.87
717 3764 3.632145 GGGCAAGAACAGAAGTTTTCTCA 59.368 43.478 0.00 0.00 38.11 3.27
718 3765 4.279420 GGGCAAGAACAGAAGTTTTCTCAT 59.721 41.667 0.00 0.00 38.11 2.90
719 3766 5.218139 GGCAAGAACAGAAGTTTTCTCATG 58.782 41.667 0.00 0.00 38.11 3.07
720 3767 4.678742 GCAAGAACAGAAGTTTTCTCATGC 59.321 41.667 0.00 0.00 38.11 4.06
721 3768 4.739046 AGAACAGAAGTTTTCTCATGCG 57.261 40.909 0.00 0.00 38.11 4.73
722 3769 2.977405 ACAGAAGTTTTCTCATGCGC 57.023 45.000 0.00 0.00 38.11 6.09
723 3770 2.221169 ACAGAAGTTTTCTCATGCGCA 58.779 42.857 14.96 14.96 38.11 6.09
724 3771 2.031682 ACAGAAGTTTTCTCATGCGCAC 60.032 45.455 14.90 0.00 38.11 5.34
725 3772 2.225019 CAGAAGTTTTCTCATGCGCACT 59.775 45.455 14.90 0.00 38.11 4.40
726 3773 2.481952 AGAAGTTTTCTCATGCGCACTC 59.518 45.455 14.90 0.00 34.07 3.51
727 3774 1.882912 AGTTTTCTCATGCGCACTCA 58.117 45.000 14.90 0.00 0.00 3.41
728 3775 1.532868 AGTTTTCTCATGCGCACTCAC 59.467 47.619 14.90 2.67 0.00 3.51
729 3776 0.874390 TTTTCTCATGCGCACTCACC 59.126 50.000 14.90 0.00 0.00 4.02
730 3777 0.250252 TTTCTCATGCGCACTCACCA 60.250 50.000 14.90 0.00 0.00 4.17
731 3778 0.950555 TTCTCATGCGCACTCACCAC 60.951 55.000 14.90 0.00 0.00 4.16
732 3779 2.733671 CTCATGCGCACTCACCACG 61.734 63.158 14.90 0.00 0.00 4.94
733 3780 3.792047 CATGCGCACTCACCACGG 61.792 66.667 14.90 0.00 0.00 4.94
739 3786 3.000819 CACTCACCACGGGCCCTA 61.001 66.667 22.43 0.00 0.00 3.53
740 3787 2.203877 ACTCACCACGGGCCCTAA 60.204 61.111 22.43 0.00 0.00 2.69
741 3788 1.844289 ACTCACCACGGGCCCTAAA 60.844 57.895 22.43 0.00 0.00 1.85
742 3789 1.377229 CTCACCACGGGCCCTAAAA 59.623 57.895 22.43 0.00 0.00 1.52
743 3790 0.250989 CTCACCACGGGCCCTAAAAA 60.251 55.000 22.43 0.00 0.00 1.94
744 3791 0.537828 TCACCACGGGCCCTAAAAAC 60.538 55.000 22.43 0.00 0.00 2.43
745 3792 0.538746 CACCACGGGCCCTAAAAACT 60.539 55.000 22.43 0.00 0.00 2.66
746 3793 0.186630 ACCACGGGCCCTAAAAACTT 59.813 50.000 22.43 0.00 0.00 2.66
747 3794 0.885879 CCACGGGCCCTAAAAACTTC 59.114 55.000 22.43 0.00 0.00 3.01
748 3795 0.885879 CACGGGCCCTAAAAACTTCC 59.114 55.000 22.43 0.00 0.00 3.46
749 3796 0.251474 ACGGGCCCTAAAAACTTCCC 60.251 55.000 22.43 0.00 0.00 3.97
750 3797 0.968901 CGGGCCCTAAAAACTTCCCC 60.969 60.000 22.43 0.00 0.00 4.81
751 3798 0.412244 GGGCCCTAAAAACTTCCCCT 59.588 55.000 17.04 0.00 0.00 4.79
752 3799 1.203262 GGGCCCTAAAAACTTCCCCTT 60.203 52.381 17.04 0.00 0.00 3.95
753 3800 2.616524 GGCCCTAAAAACTTCCCCTTT 58.383 47.619 0.00 0.00 0.00 3.11
754 3801 3.502672 GGGCCCTAAAAACTTCCCCTTTA 60.503 47.826 17.04 0.00 0.00 1.85
755 3802 4.161876 GGCCCTAAAAACTTCCCCTTTAA 58.838 43.478 0.00 0.00 0.00 1.52
756 3803 4.222145 GGCCCTAAAAACTTCCCCTTTAAG 59.778 45.833 0.00 0.00 0.00 1.85
757 3804 5.081728 GCCCTAAAAACTTCCCCTTTAAGA 58.918 41.667 0.00 0.00 0.00 2.10
758 3805 5.541101 GCCCTAAAAACTTCCCCTTTAAGAA 59.459 40.000 0.00 0.00 0.00 2.52
759 3806 6.042322 GCCCTAAAAACTTCCCCTTTAAGAAA 59.958 38.462 0.00 0.00 0.00 2.52
760 3807 7.419287 GCCCTAAAAACTTCCCCTTTAAGAAAA 60.419 37.037 0.00 0.00 0.00 2.29
761 3808 8.487848 CCCTAAAAACTTCCCCTTTAAGAAAAA 58.512 33.333 0.00 0.00 0.00 1.94
762 3809 9.321562 CCTAAAAACTTCCCCTTTAAGAAAAAC 57.678 33.333 0.00 0.00 0.00 2.43
763 3810 9.321562 CTAAAAACTTCCCCTTTAAGAAAAACC 57.678 33.333 0.00 0.00 0.00 3.27
764 3811 7.504926 AAAACTTCCCCTTTAAGAAAAACCT 57.495 32.000 0.00 0.00 0.00 3.50
765 3812 6.726490 AACTTCCCCTTTAAGAAAAACCTC 57.274 37.500 0.00 0.00 0.00 3.85
766 3813 5.773091 ACTTCCCCTTTAAGAAAAACCTCA 58.227 37.500 0.00 0.00 0.00 3.86
767 3814 6.382087 ACTTCCCCTTTAAGAAAAACCTCAT 58.618 36.000 0.00 0.00 0.00 2.90
768 3815 7.532199 ACTTCCCCTTTAAGAAAAACCTCATA 58.468 34.615 0.00 0.00 0.00 2.15
769 3816 8.008332 ACTTCCCCTTTAAGAAAAACCTCATAA 58.992 33.333 0.00 0.00 0.00 1.90
770 3817 8.785184 TTCCCCTTTAAGAAAAACCTCATAAA 57.215 30.769 0.00 0.00 0.00 1.40
771 3818 8.785184 TCCCCTTTAAGAAAAACCTCATAAAA 57.215 30.769 0.00 0.00 0.00 1.52
772 3819 8.644216 TCCCCTTTAAGAAAAACCTCATAAAAC 58.356 33.333 0.00 0.00 0.00 2.43
773 3820 7.876068 CCCCTTTAAGAAAAACCTCATAAAACC 59.124 37.037 0.00 0.00 0.00 3.27
774 3821 8.425703 CCCTTTAAGAAAAACCTCATAAAACCA 58.574 33.333 0.00 0.00 0.00 3.67
775 3822 9.825109 CCTTTAAGAAAAACCTCATAAAACCAA 57.175 29.630 0.00 0.00 0.00 3.67
777 3824 8.859517 TTAAGAAAAACCTCATAAAACCAACG 57.140 30.769 0.00 0.00 0.00 4.10
778 3825 6.702716 AGAAAAACCTCATAAAACCAACGA 57.297 33.333 0.00 0.00 0.00 3.85
779 3826 7.102847 AGAAAAACCTCATAAAACCAACGAA 57.897 32.000 0.00 0.00 0.00 3.85
780 3827 7.200455 AGAAAAACCTCATAAAACCAACGAAG 58.800 34.615 0.00 0.00 0.00 3.79
782 3829 5.684550 AACCTCATAAAACCAACGAAGTC 57.315 39.130 0.00 0.00 45.00 3.01
783 3830 4.969484 ACCTCATAAAACCAACGAAGTCT 58.031 39.130 0.00 0.00 45.00 3.24
784 3831 4.995487 ACCTCATAAAACCAACGAAGTCTC 59.005 41.667 0.00 0.00 45.00 3.36
785 3832 4.994852 CCTCATAAAACCAACGAAGTCTCA 59.005 41.667 0.00 0.00 45.00 3.27
786 3833 5.468746 CCTCATAAAACCAACGAAGTCTCAA 59.531 40.000 0.00 0.00 45.00 3.02
787 3834 6.295039 TCATAAAACCAACGAAGTCTCAAC 57.705 37.500 0.00 0.00 45.00 3.18
788 3835 5.818336 TCATAAAACCAACGAAGTCTCAACA 59.182 36.000 0.00 0.00 45.00 3.33
789 3836 6.485313 TCATAAAACCAACGAAGTCTCAACAT 59.515 34.615 0.00 0.00 45.00 2.71
790 3837 5.576447 AAAACCAACGAAGTCTCAACATT 57.424 34.783 0.00 0.00 45.00 2.71
791 3838 5.576447 AAACCAACGAAGTCTCAACATTT 57.424 34.783 0.00 0.00 45.00 2.32
792 3839 4.813296 ACCAACGAAGTCTCAACATTTC 57.187 40.909 0.00 0.00 45.00 2.17
793 3840 4.451900 ACCAACGAAGTCTCAACATTTCT 58.548 39.130 0.00 0.00 45.00 2.52
794 3841 4.511826 ACCAACGAAGTCTCAACATTTCTC 59.488 41.667 0.00 0.00 45.00 2.87
795 3842 4.752101 CCAACGAAGTCTCAACATTTCTCT 59.248 41.667 0.00 0.00 45.00 3.10
796 3843 5.926542 CCAACGAAGTCTCAACATTTCTCTA 59.073 40.000 0.00 0.00 45.00 2.43
797 3844 6.423905 CCAACGAAGTCTCAACATTTCTCTAA 59.576 38.462 0.00 0.00 45.00 2.10
798 3845 7.118390 CCAACGAAGTCTCAACATTTCTCTAAT 59.882 37.037 0.00 0.00 45.00 1.73
799 3846 7.820044 ACGAAGTCTCAACATTTCTCTAATC 57.180 36.000 0.00 0.00 29.74 1.75
800 3847 6.814146 ACGAAGTCTCAACATTTCTCTAATCC 59.186 38.462 0.00 0.00 29.74 3.01
801 3848 7.038659 CGAAGTCTCAACATTTCTCTAATCCT 58.961 38.462 0.00 0.00 0.00 3.24
802 3849 8.191446 CGAAGTCTCAACATTTCTCTAATCCTA 58.809 37.037 0.00 0.00 0.00 2.94
825 3872 8.049721 CCTATTAGGACAAGAACAGAAATCCTT 58.950 37.037 3.41 0.00 37.67 3.36
834 3881 1.131126 ACAGAAATCCTTTCATGCGCG 59.869 47.619 0.00 0.00 42.10 6.86
1098 4412 3.197116 CCCACCACTCGTATAACTTCCTT 59.803 47.826 0.00 0.00 0.00 3.36
1105 4419 6.127535 CCACTCGTATAACTTCCTTGGTTCTA 60.128 42.308 0.00 0.00 0.00 2.10
1143 4457 1.563111 TCGCGAATCCGTTTGGTATC 58.437 50.000 6.20 0.00 38.24 2.24
1225 4541 2.427453 TCCTTCCGAGTACTCATTGCTC 59.573 50.000 22.37 0.00 0.00 4.26
1366 4759 4.351874 TGTTGTGGTAGGAAAGAAGAGG 57.648 45.455 0.00 0.00 0.00 3.69
1419 4816 4.093743 TGTAGTGCAGAAGATTGGGACTA 58.906 43.478 0.00 0.00 34.88 2.59
1420 4817 4.530553 TGTAGTGCAGAAGATTGGGACTAA 59.469 41.667 0.00 0.00 37.24 2.24
1567 4973 2.521224 GGGTCGCTCTATCGGGGT 60.521 66.667 0.00 0.00 0.00 4.95
1603 5009 3.359654 CCAGTTTAGCGTTCAACAACAC 58.640 45.455 0.00 0.00 32.14 3.32
1638 5044 5.221641 TGCAGAGTATTGAACCACTTGTACT 60.222 40.000 0.00 0.00 0.00 2.73
1750 5156 8.796475 AGTAGTGACTTTAAAACTATACACGGA 58.204 33.333 0.00 0.00 28.61 4.69
1751 5157 9.410556 GTAGTGACTTTAAAACTATACACGGAA 57.589 33.333 0.00 0.00 33.18 4.30
1752 5158 8.530269 AGTGACTTTAAAACTATACACGGAAG 57.470 34.615 0.00 0.00 33.18 3.46
1809 5219 7.151999 TGAATTTACGTGCCATTAATTCTGT 57.848 32.000 0.00 0.00 36.60 3.41
1824 5234 0.400213 TCTGTCGAAACCCCAATGCT 59.600 50.000 0.00 0.00 0.00 3.79
1873 5286 8.345565 CAGTGGCCTGAAATTAAACATCTATAC 58.654 37.037 3.32 0.00 41.50 1.47
1874 5287 7.226720 AGTGGCCTGAAATTAAACATCTATACG 59.773 37.037 3.32 0.00 0.00 3.06
1948 5365 1.134818 CCAGTCTACCGCAATGTAGCA 60.135 52.381 0.00 0.00 38.46 3.49
1949 5366 2.483714 CCAGTCTACCGCAATGTAGCAT 60.484 50.000 0.00 0.00 38.46 3.79
1965 5382 1.936436 GCATTTGCTGGCGGATCACA 61.936 55.000 0.00 0.00 38.21 3.58
2022 5439 2.988010 TGCCCGATCCATATAGATGC 57.012 50.000 0.00 0.00 0.00 3.91
2054 5472 7.177184 TGCTTAGATACCCATGCATATTCATT 58.823 34.615 0.00 0.00 0.00 2.57
2085 5503 5.181811 TCATGCATTTTCGAACTCTGACAAT 59.818 36.000 0.00 0.00 0.00 2.71
2212 5640 7.360113 ACCCTTTGTTGAACATATTCAGTTT 57.640 32.000 0.00 0.00 45.54 2.66
2214 5642 8.264347 ACCCTTTGTTGAACATATTCAGTTTTT 58.736 29.630 0.00 0.00 45.54 1.94
2255 5683 4.994220 TTAAAGCACGTCAGCGATAAAA 57.006 36.364 0.00 0.00 42.00 1.52
2291 5719 8.260270 TCAATCAGAACATATTCAGTTGTCAG 57.740 34.615 0.00 0.00 37.29 3.51
2381 5832 3.119173 AGAGAGCACTGTTATCTCACTGC 60.119 47.826 16.94 0.00 41.58 4.40
2437 5892 8.721478 GCTGAAATGAGTATAAAGTTGTCTTGA 58.279 33.333 0.00 0.00 33.79 3.02
2823 6285 6.362820 CCTCCGTAAAGAAATATAAGAGCGTC 59.637 42.308 0.00 0.00 0.00 5.19
2913 6375 8.410673 TTGTTAAATTGCATACAAGGAACCTA 57.589 30.769 0.00 0.00 39.69 3.08
2960 6422 6.320164 TGCAGTTCTGGTGTACATTAACTTTT 59.680 34.615 0.00 0.00 34.67 2.27
3044 6507 5.890419 AGATGATGAAGGAAGTCCATTTTCC 59.110 40.000 0.00 0.00 43.59 3.13
3333 6797 3.861840 TGTCACATTAGGCTGCTTAGTC 58.138 45.455 0.00 0.00 0.00 2.59
3534 7002 9.803507 ACATATCATGAATTCCTGACAATATGT 57.196 29.630 20.95 20.95 0.00 2.29
3795 7263 2.524306 CCAGAAAATGGTAACTGGCCA 58.476 47.619 4.71 4.71 44.91 5.36
4101 7569 4.342092 CCACCTGAAATTTCTCCTGTGTTT 59.658 41.667 18.64 0.00 0.00 2.83
4247 7715 8.709386 AGTTTTAGCTTGTCACATACTATCAG 57.291 34.615 0.00 0.00 0.00 2.90
4277 7745 3.450457 TGATCTTTTGTGTTGCCCAAGTT 59.550 39.130 0.00 0.00 0.00 2.66
4361 9423 6.094048 ACATGAGTTGCATATGGTTGAAGTAC 59.906 38.462 4.56 0.00 34.82 2.73
4368 9430 4.260375 GCATATGGTTGAAGTACAGAAGCG 60.260 45.833 4.56 0.00 0.00 4.68
4419 9481 1.542915 GCATGTCACATATGGGGATGC 59.457 52.381 20.35 20.35 0.00 3.91
4421 9483 2.643995 TGTCACATATGGGGATGCTG 57.356 50.000 4.82 0.00 0.00 4.41
4446 9508 3.666883 TTTGTTGTGCGTGAGTAACTG 57.333 42.857 0.00 0.00 0.00 3.16
4450 9513 0.249699 TGTGCGTGAGTAACTGTGGG 60.250 55.000 0.00 0.00 0.00 4.61
4458 9521 3.773119 GTGAGTAACTGTGGGGATCCTTA 59.227 47.826 12.58 0.00 0.00 2.69
4467 9530 3.075283 TGTGGGGATCCTTATGTTGTTGT 59.925 43.478 12.58 0.00 0.00 3.32
4797 9888 4.826274 AGCAGCACTAATCCTGTCTTTA 57.174 40.909 0.00 0.00 0.00 1.85
4832 9923 5.698741 TCAGTCATGATTCTGTATGGGTT 57.301 39.130 11.82 0.00 33.89 4.11
4843 9934 4.359105 TCTGTATGGGTTTACTACAGCCT 58.641 43.478 4.48 0.00 41.25 4.58
4858 9951 7.010339 ACTACAGCCTGTTCTCTTTTTCTAT 57.990 36.000 1.02 0.00 0.00 1.98
4866 9962 6.480320 CCTGTTCTCTTTTTCTATCCCATACG 59.520 42.308 0.00 0.00 0.00 3.06
4869 9965 8.195436 TGTTCTCTTTTTCTATCCCATACGTAG 58.805 37.037 0.08 0.00 0.00 3.51
4884 9980 9.887629 TCCCATACGTAGTTTTCACAAATATTA 57.112 29.630 0.08 0.00 37.78 0.98
4886 9982 9.925268 CCATACGTAGTTTTCACAAATATTACC 57.075 33.333 0.08 0.00 37.78 2.85
4936 12506 5.734720 TCTTTCTGGAAGTTGCTAATCGAT 58.265 37.500 0.00 0.00 36.70 3.59
5065 12732 0.171007 CAAGTAAGGCGCAACCATGG 59.829 55.000 11.19 11.19 43.14 3.66
5090 12758 7.001073 GTCAGAAAGGAAAGGGCTATTATCAT 58.999 38.462 0.00 0.00 0.00 2.45
5112 12780 2.114616 CCTAGACTCATGTGCCCTTCT 58.885 52.381 0.00 0.00 0.00 2.85
5113 12781 2.102252 CCTAGACTCATGTGCCCTTCTC 59.898 54.545 0.00 0.00 0.00 2.87
5202 12870 0.518636 CAGCGACCTGACATTGTTGG 59.481 55.000 7.85 7.85 41.77 3.77
5363 13037 1.008079 GTGTGAGCCAGTTTGCTGC 60.008 57.895 0.00 0.00 42.95 5.25
5379 13053 1.489481 CTGCCCACTGGATGTCTCTA 58.511 55.000 0.00 0.00 0.00 2.43
5406 13081 4.275443 CCATTCCTTCAGCATTCTTCTAGC 59.725 45.833 0.00 0.00 0.00 3.42
5453 13130 2.028876 ACCCCAAAACAAAAGAGACGG 58.971 47.619 0.00 0.00 0.00 4.79
5457 13134 4.546570 CCCAAAACAAAAGAGACGGAATC 58.453 43.478 0.00 0.00 0.00 2.52
5490 13211 3.518634 TCCAAAATTTATGCGAAGGCC 57.481 42.857 0.00 0.00 38.85 5.19
5496 13217 2.708216 TTTATGCGAAGGCCAGATCA 57.292 45.000 5.01 0.00 38.85 2.92
5497 13218 1.953559 TTATGCGAAGGCCAGATCAC 58.046 50.000 5.01 0.00 38.85 3.06
5508 13229 1.470285 GCCAGATCACGTTAGCGGTTA 60.470 52.381 3.45 0.00 43.45 2.85
5516 13237 3.674753 TCACGTTAGCGGTTAGTAAAAGC 59.325 43.478 3.45 3.41 43.45 3.51
5529 13250 2.092323 GTAAAAGCGCTTCCAAGGGAT 58.908 47.619 25.24 1.21 41.06 3.85
5532 13253 2.439156 GCGCTTCCAAGGGATGCT 60.439 61.111 17.60 0.00 46.46 3.79
5536 13257 0.839946 GCTTCCAAGGGATGCTAGGA 59.160 55.000 13.97 0.00 45.59 2.94
5543 13264 4.726825 TCCAAGGGATGCTAGGAAATACTT 59.273 41.667 0.00 0.00 0.00 2.24
5544 13265 5.193728 TCCAAGGGATGCTAGGAAATACTTT 59.806 40.000 0.00 0.00 0.00 2.66
5545 13266 5.532779 CCAAGGGATGCTAGGAAATACTTTC 59.467 44.000 0.00 0.00 38.94 2.62
5546 13267 6.360618 CAAGGGATGCTAGGAAATACTTTCT 58.639 40.000 0.00 0.00 39.59 2.52
5547 13268 6.582929 AGGGATGCTAGGAAATACTTTCTT 57.417 37.500 0.00 0.00 39.59 2.52
5548 13269 6.974795 AGGGATGCTAGGAAATACTTTCTTT 58.025 36.000 0.00 0.00 39.59 2.52
5573 13294 6.998968 AAAAACTTTGCATGGATTGTTTCA 57.001 29.167 14.79 0.00 0.00 2.69
5574 13295 6.998968 AAAACTTTGCATGGATTGTTTCAA 57.001 29.167 14.79 0.00 0.00 2.69
5575 13296 5.989551 AACTTTGCATGGATTGTTTCAAC 57.010 34.783 0.00 0.00 0.00 3.18
5576 13297 5.280654 ACTTTGCATGGATTGTTTCAACT 57.719 34.783 0.00 0.00 0.00 3.16
5577 13298 5.291971 ACTTTGCATGGATTGTTTCAACTC 58.708 37.500 0.00 0.00 0.00 3.01
5578 13299 4.933505 TTGCATGGATTGTTTCAACTCA 57.066 36.364 0.00 0.00 0.00 3.41
5579 13300 4.933505 TGCATGGATTGTTTCAACTCAA 57.066 36.364 0.00 0.00 0.00 3.02
5580 13301 4.619973 TGCATGGATTGTTTCAACTCAAC 58.380 39.130 0.00 0.00 0.00 3.18
5581 13302 4.341806 TGCATGGATTGTTTCAACTCAACT 59.658 37.500 0.00 0.00 0.00 3.16
5582 13303 5.163426 TGCATGGATTGTTTCAACTCAACTT 60.163 36.000 0.00 0.00 0.00 2.66
5583 13304 5.403466 GCATGGATTGTTTCAACTCAACTTC 59.597 40.000 0.00 0.00 0.00 3.01
5584 13305 5.514274 TGGATTGTTTCAACTCAACTTCC 57.486 39.130 0.00 0.00 32.26 3.46
5585 13306 5.200483 TGGATTGTTTCAACTCAACTTCCT 58.800 37.500 0.00 0.00 32.58 3.36
5586 13307 5.067674 TGGATTGTTTCAACTCAACTTCCTG 59.932 40.000 0.00 0.00 32.58 3.86
5587 13308 5.299279 GGATTGTTTCAACTCAACTTCCTGA 59.701 40.000 0.00 0.00 30.52 3.86
5588 13309 6.183360 GGATTGTTTCAACTCAACTTCCTGAA 60.183 38.462 0.00 0.00 30.52 3.02
5589 13310 5.818136 TGTTTCAACTCAACTTCCTGAAG 57.182 39.130 5.37 5.37 43.79 3.02
5606 13327 9.678941 CTTCCTGAAGTTTAACAAAGTTTATCC 57.321 33.333 0.00 0.00 34.32 2.59
5607 13328 8.754991 TCCTGAAGTTTAACAAAGTTTATCCA 57.245 30.769 0.00 0.00 34.32 3.41
5608 13329 9.191479 TCCTGAAGTTTAACAAAGTTTATCCAA 57.809 29.630 0.00 0.00 34.32 3.53
5609 13330 9.810545 CCTGAAGTTTAACAAAGTTTATCCAAA 57.189 29.630 0.00 0.00 34.32 3.28
5643 13364 7.526608 ACATTCACAATAACAAATCTGTACCG 58.473 34.615 0.00 0.00 33.45 4.02
5649 13370 8.879759 CACAATAACAAATCTGTACCGTTAGAT 58.120 33.333 0.00 0.00 33.45 1.98
5659 13380 8.645814 ATCTGTACCGTTAGATACATAATGGA 57.354 34.615 10.85 0.00 42.24 3.41
5720 13457 6.821665 TCAAACCCTATAAATTCGACTTGAGG 59.178 38.462 0.00 0.00 0.00 3.86
5725 13462 6.458342 CCCTATAAATTCGACTTGAGGCAAAC 60.458 42.308 6.07 0.00 0.00 2.93
5726 13463 2.969443 AATTCGACTTGAGGCAAACG 57.031 45.000 0.00 0.00 0.00 3.60
5727 13464 1.156736 ATTCGACTTGAGGCAAACGG 58.843 50.000 0.00 0.00 0.00 4.44
5731 13492 0.955919 GACTTGAGGCAAACGGAGGG 60.956 60.000 0.00 0.00 0.00 4.30
5739 13500 1.538512 GGCAAACGGAGGGAGTAAAAC 59.461 52.381 0.00 0.00 0.00 2.43
5795 13589 7.549134 TCAGCAACTACACCATATTCAAAGTAG 59.451 37.037 0.00 0.00 36.08 2.57
5796 13590 7.334421 CAGCAACTACACCATATTCAAAGTAGT 59.666 37.037 0.00 0.00 42.64 2.73
5797 13591 8.537016 AGCAACTACACCATATTCAAAGTAGTA 58.463 33.333 0.00 0.00 40.68 1.82
5798 13592 9.326413 GCAACTACACCATATTCAAAGTAGTAT 57.674 33.333 0.00 0.00 40.68 2.12
5898 13692 1.658686 GGTCAGCGATCTCACCTCGT 61.659 60.000 0.00 0.00 38.37 4.18
5899 13693 0.248296 GTCAGCGATCTCACCTCGTC 60.248 60.000 0.00 0.00 38.37 4.20
6023 13817 1.383799 CCAATGCCAGTCCTTCCCA 59.616 57.895 0.00 0.00 0.00 4.37
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
62 65 3.580458 ACTAATGGTATGCCTCAGCCTAG 59.420 47.826 0.16 0.00 38.69 3.02
67 70 4.576463 GGTTTGACTAATGGTATGCCTCAG 59.424 45.833 0.16 0.00 35.27 3.35
82 85 2.158608 CCAAGGTCTTCAGGGTTTGACT 60.159 50.000 0.00 0.00 34.94 3.41
84 87 1.850345 ACCAAGGTCTTCAGGGTTTGA 59.150 47.619 0.00 0.00 0.00 2.69
93 96 5.048713 CACAAAGAACCATACCAAGGTCTTC 60.049 44.000 0.00 0.00 38.76 2.87
162 165 8.263640 TCTTTGATCCCAAGTTCAAATGAAAAA 58.736 29.630 0.00 0.00 39.67 1.94
253 257 1.333177 ATGTCCCTCTCGATGGCTAC 58.667 55.000 0.00 0.00 0.00 3.58
415 420 3.069443 ACGCTTCATTTCCAAAACACCAT 59.931 39.130 0.00 0.00 0.00 3.55
416 421 2.428890 ACGCTTCATTTCCAAAACACCA 59.571 40.909 0.00 0.00 0.00 4.17
423 428 2.159430 CGATGTGACGCTTCATTTCCAA 59.841 45.455 0.00 0.00 33.11 3.53
477 3517 7.551617 GGGGACTCGAAATCAGACTTTAAATAA 59.448 37.037 0.00 0.00 0.00 1.40
491 3531 4.957684 AATAGAATCGGGGACTCGAAAT 57.042 40.909 0.00 0.00 42.69 2.17
616 3662 4.767928 GGAGAAGTGAAGAGAGGTTACAGA 59.232 45.833 0.00 0.00 0.00 3.41
655 3701 4.686554 GTGCTGAGAGTTCGTCAGTTTTAT 59.313 41.667 2.30 0.00 43.00 1.40
699 3746 4.555511 GCGCATGAGAAAACTTCTGTTCTT 60.556 41.667 0.30 0.00 40.87 2.52
700 3747 3.058639 GCGCATGAGAAAACTTCTGTTCT 60.059 43.478 0.30 0.00 40.87 3.01
701 3748 3.229552 GCGCATGAGAAAACTTCTGTTC 58.770 45.455 0.30 0.00 40.87 3.18
702 3749 2.618241 TGCGCATGAGAAAACTTCTGTT 59.382 40.909 5.66 0.00 40.87 3.16
703 3750 2.031682 GTGCGCATGAGAAAACTTCTGT 60.032 45.455 15.91 0.00 40.87 3.41
704 3751 2.225019 AGTGCGCATGAGAAAACTTCTG 59.775 45.455 15.91 0.00 40.87 3.02
705 3752 2.481952 GAGTGCGCATGAGAAAACTTCT 59.518 45.455 15.91 0.00 44.21 2.85
706 3753 2.224079 TGAGTGCGCATGAGAAAACTTC 59.776 45.455 15.91 0.00 0.00 3.01
707 3754 2.031682 GTGAGTGCGCATGAGAAAACTT 60.032 45.455 15.91 0.00 0.00 2.66
708 3755 1.532868 GTGAGTGCGCATGAGAAAACT 59.467 47.619 15.91 2.15 0.00 2.66
709 3756 1.400242 GGTGAGTGCGCATGAGAAAAC 60.400 52.381 15.91 5.58 0.00 2.43
710 3757 0.874390 GGTGAGTGCGCATGAGAAAA 59.126 50.000 15.91 0.00 0.00 2.29
711 3758 0.250252 TGGTGAGTGCGCATGAGAAA 60.250 50.000 15.91 0.00 0.00 2.52
712 3759 0.950555 GTGGTGAGTGCGCATGAGAA 60.951 55.000 15.91 0.00 0.00 2.87
713 3760 1.374631 GTGGTGAGTGCGCATGAGA 60.375 57.895 15.91 0.00 0.00 3.27
714 3761 2.733671 CGTGGTGAGTGCGCATGAG 61.734 63.158 15.91 0.00 0.00 2.90
715 3762 2.738139 CGTGGTGAGTGCGCATGA 60.738 61.111 15.91 0.00 0.00 3.07
716 3763 3.792047 CCGTGGTGAGTGCGCATG 61.792 66.667 15.91 0.00 0.00 4.06
722 3769 2.119484 TTTAGGGCCCGTGGTGAGTG 62.119 60.000 18.44 0.00 0.00 3.51
723 3770 1.420532 TTTTAGGGCCCGTGGTGAGT 61.421 55.000 18.44 0.00 0.00 3.41
724 3771 0.250989 TTTTTAGGGCCCGTGGTGAG 60.251 55.000 18.44 0.00 0.00 3.51
725 3772 0.537828 GTTTTTAGGGCCCGTGGTGA 60.538 55.000 18.44 0.00 0.00 4.02
726 3773 0.538746 AGTTTTTAGGGCCCGTGGTG 60.539 55.000 18.44 0.00 0.00 4.17
727 3774 0.186630 AAGTTTTTAGGGCCCGTGGT 59.813 50.000 18.44 0.00 0.00 4.16
728 3775 0.885879 GAAGTTTTTAGGGCCCGTGG 59.114 55.000 18.44 0.00 0.00 4.94
729 3776 0.885879 GGAAGTTTTTAGGGCCCGTG 59.114 55.000 18.44 0.00 0.00 4.94
730 3777 0.251474 GGGAAGTTTTTAGGGCCCGT 60.251 55.000 18.44 7.64 0.00 5.28
731 3778 0.968901 GGGGAAGTTTTTAGGGCCCG 60.969 60.000 18.44 0.00 36.41 6.13
732 3779 0.412244 AGGGGAAGTTTTTAGGGCCC 59.588 55.000 16.46 16.46 34.79 5.80
733 3780 2.320681 AAGGGGAAGTTTTTAGGGCC 57.679 50.000 0.00 0.00 0.00 5.80
734 3781 5.081728 TCTTAAAGGGGAAGTTTTTAGGGC 58.918 41.667 0.00 0.00 0.00 5.19
735 3782 7.606135 TTTCTTAAAGGGGAAGTTTTTAGGG 57.394 36.000 0.00 0.00 0.00 3.53
736 3783 9.321562 GTTTTTCTTAAAGGGGAAGTTTTTAGG 57.678 33.333 0.00 0.00 0.00 2.69
737 3784 9.321562 GGTTTTTCTTAAAGGGGAAGTTTTTAG 57.678 33.333 0.00 0.00 0.00 1.85
738 3785 9.049050 AGGTTTTTCTTAAAGGGGAAGTTTTTA 57.951 29.630 0.00 0.00 0.00 1.52
739 3786 7.924541 AGGTTTTTCTTAAAGGGGAAGTTTTT 58.075 30.769 0.00 0.00 0.00 1.94
740 3787 7.181305 TGAGGTTTTTCTTAAAGGGGAAGTTTT 59.819 33.333 0.00 0.00 0.00 2.43
741 3788 6.670464 TGAGGTTTTTCTTAAAGGGGAAGTTT 59.330 34.615 0.00 0.00 0.00 2.66
742 3789 6.199376 TGAGGTTTTTCTTAAAGGGGAAGTT 58.801 36.000 0.00 0.00 0.00 2.66
743 3790 5.773091 TGAGGTTTTTCTTAAAGGGGAAGT 58.227 37.500 0.00 0.00 0.00 3.01
744 3791 6.918067 ATGAGGTTTTTCTTAAAGGGGAAG 57.082 37.500 0.00 0.00 0.00 3.46
745 3792 8.785184 TTTATGAGGTTTTTCTTAAAGGGGAA 57.215 30.769 0.00 0.00 0.00 3.97
746 3793 8.644216 GTTTTATGAGGTTTTTCTTAAAGGGGA 58.356 33.333 0.00 0.00 32.05 4.81
747 3794 7.876068 GGTTTTATGAGGTTTTTCTTAAAGGGG 59.124 37.037 0.00 0.00 32.05 4.79
748 3795 8.425703 TGGTTTTATGAGGTTTTTCTTAAAGGG 58.574 33.333 0.00 0.00 32.05 3.95
749 3796 9.825109 TTGGTTTTATGAGGTTTTTCTTAAAGG 57.175 29.630 0.00 0.00 32.05 3.11
751 3798 9.303537 CGTTGGTTTTATGAGGTTTTTCTTAAA 57.696 29.630 0.00 0.00 0.00 1.52
752 3799 8.684520 TCGTTGGTTTTATGAGGTTTTTCTTAA 58.315 29.630 0.00 0.00 0.00 1.85
753 3800 8.223177 TCGTTGGTTTTATGAGGTTTTTCTTA 57.777 30.769 0.00 0.00 0.00 2.10
754 3801 7.102847 TCGTTGGTTTTATGAGGTTTTTCTT 57.897 32.000 0.00 0.00 0.00 2.52
755 3802 6.702716 TCGTTGGTTTTATGAGGTTTTTCT 57.297 33.333 0.00 0.00 0.00 2.52
756 3803 6.976349 ACTTCGTTGGTTTTATGAGGTTTTTC 59.024 34.615 0.00 0.00 0.00 2.29
757 3804 6.869695 ACTTCGTTGGTTTTATGAGGTTTTT 58.130 32.000 0.00 0.00 0.00 1.94
758 3805 6.320418 AGACTTCGTTGGTTTTATGAGGTTTT 59.680 34.615 0.00 0.00 0.00 2.43
759 3806 5.826208 AGACTTCGTTGGTTTTATGAGGTTT 59.174 36.000 0.00 0.00 0.00 3.27
760 3807 5.374071 AGACTTCGTTGGTTTTATGAGGTT 58.626 37.500 0.00 0.00 0.00 3.50
761 3808 4.969484 AGACTTCGTTGGTTTTATGAGGT 58.031 39.130 0.00 0.00 0.00 3.85
762 3809 4.994852 TGAGACTTCGTTGGTTTTATGAGG 59.005 41.667 0.00 0.00 0.00 3.86
763 3810 6.018262 TGTTGAGACTTCGTTGGTTTTATGAG 60.018 38.462 0.00 0.00 0.00 2.90
764 3811 5.818336 TGTTGAGACTTCGTTGGTTTTATGA 59.182 36.000 0.00 0.00 0.00 2.15
765 3812 6.055231 TGTTGAGACTTCGTTGGTTTTATG 57.945 37.500 0.00 0.00 0.00 1.90
766 3813 6.877611 ATGTTGAGACTTCGTTGGTTTTAT 57.122 33.333 0.00 0.00 0.00 1.40
767 3814 6.687081 AATGTTGAGACTTCGTTGGTTTTA 57.313 33.333 0.00 0.00 0.00 1.52
768 3815 5.576447 AATGTTGAGACTTCGTTGGTTTT 57.424 34.783 0.00 0.00 0.00 2.43
769 3816 5.357032 AGAAATGTTGAGACTTCGTTGGTTT 59.643 36.000 0.00 0.00 0.00 3.27
770 3817 4.881850 AGAAATGTTGAGACTTCGTTGGTT 59.118 37.500 0.00 0.00 0.00 3.67
771 3818 4.451900 AGAAATGTTGAGACTTCGTTGGT 58.548 39.130 0.00 0.00 0.00 3.67
772 3819 4.752101 AGAGAAATGTTGAGACTTCGTTGG 59.248 41.667 0.00 0.00 0.00 3.77
773 3820 5.914085 AGAGAAATGTTGAGACTTCGTTG 57.086 39.130 0.00 0.00 0.00 4.10
774 3821 7.332182 GGATTAGAGAAATGTTGAGACTTCGTT 59.668 37.037 0.00 0.00 0.00 3.85
775 3822 6.814146 GGATTAGAGAAATGTTGAGACTTCGT 59.186 38.462 0.00 0.00 0.00 3.85
776 3823 7.038659 AGGATTAGAGAAATGTTGAGACTTCG 58.961 38.462 0.00 0.00 0.00 3.79
798 3845 7.403231 AGGATTTCTGTTCTTGTCCTAATAGGA 59.597 37.037 4.61 4.61 43.43 2.94
799 3846 7.569240 AGGATTTCTGTTCTTGTCCTAATAGG 58.431 38.462 0.00 0.00 34.48 2.57
800 3847 9.454859 AAAGGATTTCTGTTCTTGTCCTAATAG 57.545 33.333 0.00 0.00 35.14 1.73
820 3867 1.078497 TGACCGCGCATGAAAGGAT 60.078 52.632 8.75 0.00 0.00 3.24
825 3872 3.047280 GTGGTGACCGCGCATGAA 61.047 61.111 8.75 0.00 0.00 2.57
834 3881 3.782443 CTAGGGCCCGTGGTGACC 61.782 72.222 18.44 0.00 0.00 4.02
914 3962 3.930012 GGGAGCCGAGATTCCCCG 61.930 72.222 0.00 0.00 46.15 5.73
1042 4090 1.326213 ATGAGGAGCGTGGAGAGTGG 61.326 60.000 0.00 0.00 0.00 4.00
1079 4127 3.836562 ACCAAGGAAGTTATACGAGTGGT 59.163 43.478 0.00 0.00 32.06 4.16
1098 4412 4.634012 ACAATAGCCAACACTAGAACCA 57.366 40.909 0.00 0.00 0.00 3.67
1105 4419 2.478894 CGAACGAACAATAGCCAACACT 59.521 45.455 0.00 0.00 0.00 3.55
1143 4457 4.044484 CTCGCCGCCCTATCTCCG 62.044 72.222 0.00 0.00 0.00 4.63
1341 4734 3.217681 TCTTTCCTACCACAACAACCC 57.782 47.619 0.00 0.00 0.00 4.11
1419 4816 2.306847 AGAAACCCACGCAATTGACTT 58.693 42.857 10.34 0.00 0.00 3.01
1420 4817 1.981256 AGAAACCCACGCAATTGACT 58.019 45.000 10.34 0.00 0.00 3.41
1508 4909 1.962321 TATGCCGCTTACCGCCAAGA 61.962 55.000 0.00 0.00 35.03 3.02
1567 4973 4.081185 TGGCTCGCTGCGGAATCA 62.081 61.111 23.03 12.44 44.05 2.57
1603 5009 3.784701 ATACTCTGCAACCTGTACTCG 57.215 47.619 0.00 0.00 0.00 4.18
1638 5044 7.394016 TGACAGAATACCAGATTAAGAAGCAA 58.606 34.615 0.00 0.00 0.00 3.91
1741 5147 8.870116 TCAGGTATACTACTACTTCCGTGTATA 58.130 37.037 2.25 0.00 0.00 1.47
1745 5151 6.485984 ACATCAGGTATACTACTACTTCCGTG 59.514 42.308 2.25 0.00 0.00 4.94
1746 5152 6.599445 ACATCAGGTATACTACTACTTCCGT 58.401 40.000 2.25 0.00 0.00 4.69
1809 5219 9.005777 GTAATAAATATAGCATTGGGGTTTCGA 57.994 33.333 0.00 0.00 0.00 3.71
1948 5365 1.027357 GATGTGATCCGCCAGCAAAT 58.973 50.000 0.00 0.00 0.00 2.32
1949 5366 0.322366 TGATGTGATCCGCCAGCAAA 60.322 50.000 0.00 0.00 0.00 3.68
1965 5382 3.464828 AGGGAAGTGGTAATGAGGTGAT 58.535 45.455 0.00 0.00 0.00 3.06
2022 5439 2.627945 TGGGTATCTAAGCAGCAAACG 58.372 47.619 0.00 0.00 0.00 3.60
2054 5472 7.538334 CAGAGTTCGAAAATGCATGAATACAAA 59.462 33.333 0.00 0.00 0.00 2.83
2071 5489 6.801539 AATTAAAGCATTGTCAGAGTTCGA 57.198 33.333 0.00 0.00 0.00 3.71
2103 5521 0.035343 GTAGTTTCAGGGAGGGTGCC 60.035 60.000 0.00 0.00 0.00 5.01
2272 5700 8.902540 TTACAACTGACAACTGAATATGTTCT 57.097 30.769 3.72 0.00 35.33 3.01
2291 5719 9.316859 GCATAAAAGCATTTGTGAAATTACAAC 57.683 29.630 14.28 0.00 39.02 3.32
2335 5786 7.456902 TCTTACCTAGTAGTGTCCAAATTCCTT 59.543 37.037 0.00 0.00 0.00 3.36
2381 5832 3.674138 GCTGCATTTATTATCCATGGGCG 60.674 47.826 13.02 2.18 0.00 6.13
2437 5892 3.886505 TCCTTAAGTGAATTTGGCAACGT 59.113 39.130 0.00 0.00 42.51 3.99
2526 5986 8.957466 GGCTATTACCAAAAGTAAGATGAAAGT 58.043 33.333 0.00 0.00 44.07 2.66
3333 6797 4.409247 AGGCCTCAGGTTTACTTAGGTATG 59.591 45.833 0.00 0.00 41.75 2.39
3422 6890 1.156736 GGAGCAAACGAAAGCTAGCA 58.843 50.000 18.83 0.00 42.04 3.49
3542 7010 9.921637 GATGGAAATGGTCATTTTGTAAAACTA 57.078 29.630 9.88 0.00 40.77 2.24
3795 7263 9.076781 CCAATTTCCAACCTCCAAAATAAATTT 57.923 29.630 0.00 0.00 0.00 1.82
4007 7475 4.110036 TCTCATGTATCACAGACAACCG 57.890 45.455 0.00 0.00 0.00 4.44
4068 7536 1.067295 TTTCAGGTGGTCTGGCATCT 58.933 50.000 0.00 0.00 43.53 2.90
4277 7745 3.572642 TGATAATGGGCTACTTCTCCGA 58.427 45.455 0.00 0.00 0.00 4.55
4361 9423 0.169672 CTGGTTGAATGGCGCTTCTG 59.830 55.000 7.64 0.00 0.00 3.02
4419 9481 3.038017 CTCACGCACAACAAAATCACAG 58.962 45.455 0.00 0.00 0.00 3.66
4421 9483 3.065019 ACTCACGCACAACAAAATCAC 57.935 42.857 0.00 0.00 0.00 3.06
4446 9508 3.697166 ACAACAACATAAGGATCCCCAC 58.303 45.455 8.55 0.00 33.88 4.61
4450 9513 4.380867 CCTGCAACAACAACATAAGGATCC 60.381 45.833 2.48 2.48 0.00 3.36
4458 9521 5.509501 CCATAAAGTCCTGCAACAACAACAT 60.510 40.000 0.00 0.00 0.00 2.71
4467 9530 0.704076 AGGGCCATAAAGTCCTGCAA 59.296 50.000 6.18 0.00 0.00 4.08
4689 9780 6.183810 ACTCTCTCCAATGATGAATATGCA 57.816 37.500 0.00 0.00 0.00 3.96
4832 9923 6.827727 AGAAAAAGAGAACAGGCTGTAGTAA 58.172 36.000 22.37 0.00 0.00 2.24
4843 9934 6.942976 ACGTATGGGATAGAAAAAGAGAACA 58.057 36.000 0.00 0.00 0.00 3.18
4858 9951 8.795842 AATATTTGTGAAAACTACGTATGGGA 57.204 30.769 0.00 0.00 0.00 4.37
5065 12732 6.357367 TGATAATAGCCCTTTCCTTTCTGAC 58.643 40.000 0.00 0.00 0.00 3.51
5090 12758 0.339859 AGGGCACATGAGTCTAGGGA 59.660 55.000 0.00 0.00 0.00 4.20
5112 12780 1.295792 GTGTTGTTTCCGCACTCTGA 58.704 50.000 0.00 0.00 0.00 3.27
5113 12781 0.307760 GGTGTTGTTTCCGCACTCTG 59.692 55.000 0.00 0.00 33.96 3.35
5202 12870 5.120830 CCACTCTATCAAAGTACAACACTGC 59.879 44.000 0.00 0.00 37.63 4.40
5248 12922 0.677731 AGAATACCGACGACCCGACA 60.678 55.000 0.00 0.00 0.00 4.35
5363 13037 1.405821 GACGTAGAGACATCCAGTGGG 59.594 57.143 9.92 0.00 0.00 4.61
5379 13053 2.026822 AGAATGCTGAAGGAATGGACGT 60.027 45.455 0.00 0.00 0.00 4.34
5387 13062 2.739932 GCGCTAGAAGAATGCTGAAGGA 60.740 50.000 0.00 0.00 0.00 3.36
5406 13081 1.663161 GCCTTTCTTTTTCTCGGTGCG 60.663 52.381 0.00 0.00 0.00 5.34
5460 13137 9.434420 TTCGCATAAATTTTGGATTCTCAAATT 57.566 25.926 0.00 2.44 36.63 1.82
5464 13141 6.563422 CCTTCGCATAAATTTTGGATTCTCA 58.437 36.000 0.00 0.00 0.00 3.27
5474 13151 3.953612 TGATCTGGCCTTCGCATAAATTT 59.046 39.130 3.32 0.00 36.38 1.82
5475 13152 3.316308 GTGATCTGGCCTTCGCATAAATT 59.684 43.478 3.32 0.00 36.38 1.82
5476 13153 2.880890 GTGATCTGGCCTTCGCATAAAT 59.119 45.455 3.32 0.00 36.38 1.40
5477 13154 2.288666 GTGATCTGGCCTTCGCATAAA 58.711 47.619 3.32 0.00 36.38 1.40
5490 13211 3.146618 ACTAACCGCTAACGTGATCTG 57.853 47.619 0.00 0.00 37.70 2.90
5496 13217 2.663119 CGCTTTTACTAACCGCTAACGT 59.337 45.455 0.00 0.00 37.70 3.99
5497 13218 2.533561 GCGCTTTTACTAACCGCTAACG 60.534 50.000 0.00 0.00 41.28 3.18
5508 13229 1.073284 TCCCTTGGAAGCGCTTTTACT 59.927 47.619 25.84 0.00 0.00 2.24
5521 13242 4.713792 AGTATTTCCTAGCATCCCTTGG 57.286 45.455 0.00 0.00 37.74 3.61
5552 13273 6.114767 AGTTGAAACAATCCATGCAAAGTTT 58.885 32.000 0.00 0.00 32.48 2.66
5553 13274 5.673514 AGTTGAAACAATCCATGCAAAGTT 58.326 33.333 0.00 0.00 0.00 2.66
5554 13275 5.163426 TGAGTTGAAACAATCCATGCAAAGT 60.163 36.000 0.00 0.00 0.00 2.66
5555 13276 5.291178 TGAGTTGAAACAATCCATGCAAAG 58.709 37.500 0.00 0.00 0.00 2.77
5556 13277 5.273674 TGAGTTGAAACAATCCATGCAAA 57.726 34.783 0.00 0.00 0.00 3.68
5557 13278 4.933505 TGAGTTGAAACAATCCATGCAA 57.066 36.364 0.00 0.00 0.00 4.08
5558 13279 4.341806 AGTTGAGTTGAAACAATCCATGCA 59.658 37.500 0.00 0.00 0.00 3.96
5559 13280 4.874970 AGTTGAGTTGAAACAATCCATGC 58.125 39.130 0.00 0.00 0.00 4.06
5560 13281 5.922544 GGAAGTTGAGTTGAAACAATCCATG 59.077 40.000 0.00 0.00 36.53 3.66
5561 13282 5.835280 AGGAAGTTGAGTTGAAACAATCCAT 59.165 36.000 11.35 0.00 37.84 3.41
5562 13283 5.067674 CAGGAAGTTGAGTTGAAACAATCCA 59.932 40.000 11.35 0.00 37.84 3.41
5563 13284 5.299279 TCAGGAAGTTGAGTTGAAACAATCC 59.701 40.000 0.00 0.00 36.66 3.01
5564 13285 6.377327 TCAGGAAGTTGAGTTGAAACAATC 57.623 37.500 0.00 0.00 0.00 2.67
5565 13286 6.773976 TTCAGGAAGTTGAGTTGAAACAAT 57.226 33.333 0.00 0.00 0.00 2.71
5566 13287 6.194796 CTTCAGGAAGTTGAGTTGAAACAA 57.805 37.500 0.83 0.00 33.87 2.83
5567 13288 5.818136 CTTCAGGAAGTTGAGTTGAAACA 57.182 39.130 0.83 0.00 33.87 2.83
5580 13301 9.678941 GGATAAACTTTGTTAAACTTCAGGAAG 57.321 33.333 7.47 7.47 43.79 3.46
5581 13302 9.191479 TGGATAAACTTTGTTAAACTTCAGGAA 57.809 29.630 0.00 0.00 0.00 3.36
5582 13303 8.754991 TGGATAAACTTTGTTAAACTTCAGGA 57.245 30.769 0.00 0.00 0.00 3.86
5583 13304 9.810545 TTTGGATAAACTTTGTTAAACTTCAGG 57.189 29.630 0.00 0.00 0.00 3.86
5689 13410 9.408648 AGTCGAATTTATAGGGTTTGATCAAAT 57.591 29.630 23.05 10.68 32.36 2.32
5693 13414 8.433421 TCAAGTCGAATTTATAGGGTTTGATC 57.567 34.615 0.00 0.00 0.00 2.92
5696 13417 6.458342 GCCTCAAGTCGAATTTATAGGGTTTG 60.458 42.308 16.01 0.00 0.00 2.93
5697 13418 5.589050 GCCTCAAGTCGAATTTATAGGGTTT 59.411 40.000 16.01 0.00 0.00 3.27
5700 13437 4.703897 TGCCTCAAGTCGAATTTATAGGG 58.296 43.478 16.01 7.33 0.00 3.53
5702 13439 6.185399 CGTTTGCCTCAAGTCGAATTTATAG 58.815 40.000 0.00 0.00 0.00 1.31
5711 13448 1.291877 CCTCCGTTTGCCTCAAGTCG 61.292 60.000 0.00 0.00 0.00 4.18
5720 13457 1.538512 GGTTTTACTCCCTCCGTTTGC 59.461 52.381 0.00 0.00 0.00 3.68
5725 13462 0.252197 CTGGGGTTTTACTCCCTCCG 59.748 60.000 0.00 0.00 38.22 4.63
5726 13463 0.034380 GCTGGGGTTTTACTCCCTCC 60.034 60.000 0.00 0.00 38.22 4.30
5727 13464 0.034380 GGCTGGGGTTTTACTCCCTC 60.034 60.000 0.00 0.00 38.22 4.30
5731 13492 4.617253 AAAAATGGCTGGGGTTTTACTC 57.383 40.909 0.00 0.00 0.00 2.59
5739 13500 4.469657 TGTAGCTATAAAAATGGCTGGGG 58.530 43.478 6.50 0.00 38.82 4.96
5741 13502 5.523369 GCTTGTAGCTATAAAAATGGCTGG 58.477 41.667 4.38 0.00 38.82 4.85
5795 13589 4.992951 ACGTCCAGTGGAAAGTGTTAATAC 59.007 41.667 15.09 0.00 31.38 1.89
5796 13590 5.011329 AGACGTCCAGTGGAAAGTGTTAATA 59.989 40.000 22.00 0.00 31.38 0.98
5797 13591 4.062991 GACGTCCAGTGGAAAGTGTTAAT 58.937 43.478 22.00 1.22 31.38 1.40
5798 13592 3.133362 AGACGTCCAGTGGAAAGTGTTAA 59.867 43.478 22.00 0.00 31.38 2.01
5805 13599 5.011738 AGAGAATAAAGACGTCCAGTGGAAA 59.988 40.000 15.09 0.00 31.38 3.13
5806 13600 4.527038 AGAGAATAAAGACGTCCAGTGGAA 59.473 41.667 15.09 0.00 31.38 3.53
5811 13605 3.128938 ACGGAGAGAATAAAGACGTCCAG 59.871 47.826 13.01 0.00 0.00 3.86
5920 13714 3.270027 CCGAATTACAACAGGCATCAGA 58.730 45.455 0.00 0.00 0.00 3.27
5957 13751 2.383527 CGCCGTCTTCAAGCAGACC 61.384 63.158 0.00 0.00 40.26 3.85


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

AutoCloner maintained by Alex Coulton.