Multiple sequence alignment - TraesCS2D01G381600

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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 TraesCS2D01G381600 chr2D 100.000 5632 0 0 1 5632 485841348 485846979 0.000000e+00 10401
1 TraesCS2D01G381600 chr2D 94.850 602 26 3 1 601 446961820 446962417 0.000000e+00 935
2 TraesCS2D01G381600 chr2D 91.376 603 34 10 1 602 458151817 458151232 0.000000e+00 809
3 TraesCS2D01G381600 chr2D 91.045 603 47 5 1 601 427318849 427319446 0.000000e+00 808
4 TraesCS2D01G381600 chr2D 90.572 594 49 5 9 600 167007495 167008083 0.000000e+00 780
5 TraesCS2D01G381600 chr2D 93.333 135 9 0 2370 2504 62293423 62293289 3.440000e-47 200
6 TraesCS2D01G381600 chr2B 94.908 3162 122 18 2495 5632 570880004 570883150 0.000000e+00 4911
7 TraesCS2D01G381600 chr2B 95.275 1164 50 4 1212 2371 570878843 570880005 0.000000e+00 1840
8 TraesCS2D01G381600 chr2B 89.207 593 53 5 9 599 230913930 230913347 0.000000e+00 730
9 TraesCS2D01G381600 chr2B 92.857 350 19 4 734 1081 570876772 570877117 2.340000e-138 503
10 TraesCS2D01G381600 chr2B 93.793 145 3 1 691 835 570878259 570878397 4.420000e-51 213
11 TraesCS2D01G381600 chr2B 93.333 135 9 0 2363 2497 199013859 199013725 3.440000e-47 200
12 TraesCS2D01G381600 chr2A 96.404 2864 78 13 2495 5340 631521031 631523887 0.000000e+00 4695
13 TraesCS2D01G381600 chr2A 94.863 1168 52 6 1212 2371 631519865 631521032 0.000000e+00 1818
14 TraesCS2D01G381600 chr2A 93.919 444 15 7 737 1173 631519432 631519870 0.000000e+00 660
15 TraesCS2D01G381600 chr2A 92.857 238 12 2 5395 5632 631524010 631524242 1.940000e-89 340
16 TraesCS2D01G381600 chr6B 92.916 607 38 3 3 608 500644705 500644103 0.000000e+00 878
17 TraesCS2D01G381600 chr6B 92.674 273 19 1 46 318 664894283 664894554 5.290000e-105 392
18 TraesCS2D01G381600 chr1A 86.242 596 77 3 10 604 42599962 42600553 4.760000e-180 641
19 TraesCS2D01G381600 chr7B 92.409 303 16 3 300 601 9324283 9323987 5.220000e-115 425
20 TraesCS2D01G381600 chr7B 92.254 142 11 0 2361 2502 470313018 470313159 9.570000e-48 202
21 TraesCS2D01G381600 chr7A 89.627 241 18 5 363 602 544264723 544264489 3.300000e-77 300
22 TraesCS2D01G381600 chr7A 95.385 130 6 0 2370 2499 593450702 593450831 2.060000e-49 207
23 TraesCS2D01G381600 chr5B 95.420 131 5 1 2367 2496 560436874 560436744 2.060000e-49 207
24 TraesCS2D01G381600 chr7D 94.030 134 8 0 2370 2503 94444620 94444487 2.660000e-48 204
25 TraesCS2D01G381600 chr5A 93.382 136 8 1 2370 2504 492896671 492896806 3.440000e-47 200
26 TraesCS2D01G381600 chr4D 92.754 138 9 1 2370 2506 36413235 36413372 1.240000e-46 198
27 TraesCS2D01G381600 chr3B 93.284 134 9 0 2370 2503 814799612 814799745 1.240000e-46 198


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 TraesCS2D01G381600 chr2D 485841348 485846979 5631 False 10401.00 10401 100.00000 1 5632 1 chr2D.!!$F4 5631
1 TraesCS2D01G381600 chr2D 446961820 446962417 597 False 935.00 935 94.85000 1 601 1 chr2D.!!$F3 600
2 TraesCS2D01G381600 chr2D 458151232 458151817 585 True 809.00 809 91.37600 1 602 1 chr2D.!!$R2 601
3 TraesCS2D01G381600 chr2D 427318849 427319446 597 False 808.00 808 91.04500 1 601 1 chr2D.!!$F2 600
4 TraesCS2D01G381600 chr2D 167007495 167008083 588 False 780.00 780 90.57200 9 600 1 chr2D.!!$F1 591
5 TraesCS2D01G381600 chr2B 570876772 570883150 6378 False 1866.75 4911 94.20825 691 5632 4 chr2B.!!$F1 4941
6 TraesCS2D01G381600 chr2B 230913347 230913930 583 True 730.00 730 89.20700 9 599 1 chr2B.!!$R2 590
7 TraesCS2D01G381600 chr2A 631519432 631524242 4810 False 1878.25 4695 94.51075 737 5632 4 chr2A.!!$F1 4895
8 TraesCS2D01G381600 chr6B 500644103 500644705 602 True 878.00 878 92.91600 3 608 1 chr6B.!!$R1 605
9 TraesCS2D01G381600 chr1A 42599962 42600553 591 False 641.00 641 86.24200 10 604 1 chr1A.!!$F1 594

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
187 188 0.036448 AGCAGCTGTGTGCAGAGATT 59.964 50.000 16.64 0.0 46.60 2.40 F
699 703 0.107654 GCGATTGGTGGCTAGGTCTT 60.108 55.000 0.00 0.0 0.00 3.01 F
706 710 0.107945 GTGGCTAGGTCTTCCTGCTG 60.108 60.000 0.00 0.0 44.81 4.41 F
708 712 0.176910 GGCTAGGTCTTCCTGCTGTC 59.823 60.000 0.00 0.0 44.81 3.51 F
1448 3106 0.179000 ACCGATGTGCCATTCTCTCC 59.821 55.000 0.00 0.0 0.00 3.71 F
2386 4048 0.115745 ACTACTCCCTCCGTCCCAAA 59.884 55.000 0.00 0.0 0.00 3.28 F
3192 4861 0.693430 TCTCAGGCTGCAGATGGGAT 60.693 55.000 20.43 0.0 0.00 3.85 F
3950 5622 2.105649 TCCTTGACCACTGCACATGTTA 59.894 45.455 0.00 0.0 0.00 2.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1974 3635 0.388907 ATCCATTGCTTGCACAACGC 60.389 50.000 0.00 0.0 42.89 4.84 R
2370 4032 1.004394 GAATTTTGGGACGGAGGGAGT 59.996 52.381 0.00 0.0 0.00 3.85 R
2371 4033 1.282157 AGAATTTTGGGACGGAGGGAG 59.718 52.381 0.00 0.0 0.00 4.30 R
2372 4034 1.368374 AGAATTTTGGGACGGAGGGA 58.632 50.000 0.00 0.0 0.00 4.20 R
3099 4768 0.039527 CCAGTGCCGCACCTTTTAAC 60.040 55.000 19.96 0.0 34.49 2.01 R
3391 5063 2.009051 CACAGAGAACACACTGTTGCA 58.991 47.619 0.00 0.0 43.52 4.08 R
4487 6159 0.179145 CGGCGTCTTCGTTACATCCT 60.179 55.000 0.00 0.0 39.49 3.24 R
5545 7298 0.035725 TCAGCTGGCAGATTGTGAGG 60.036 55.000 20.86 0.0 0.00 3.86 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
86 87 4.057428 AGGTGCGAGCTCACGACC 62.057 66.667 15.40 15.20 37.83 4.79
150 151 3.787001 GGGGGCTTCTCCAGGACG 61.787 72.222 0.00 0.00 36.21 4.79
187 188 0.036448 AGCAGCTGTGTGCAGAGATT 59.964 50.000 16.64 0.00 46.60 2.40
227 228 1.272490 CTCCTCGGCACTTGTTGTCTA 59.728 52.381 0.00 0.00 0.00 2.59
250 251 2.564947 GGAATCACTGATCCGGCTATCT 59.435 50.000 0.00 0.00 0.00 1.98
269 270 1.829523 TTGGAAGCTTTGGCATGCCC 61.830 55.000 33.44 18.09 41.70 5.36
310 311 3.835978 TCTTGATCTCGGGGTAGACAAAA 59.164 43.478 0.00 0.00 0.00 2.44
452 453 3.476552 TCACTTTTGAAGGACGAGCATT 58.523 40.909 0.00 0.00 0.00 3.56
464 465 3.009723 GACGAGCATTGAATTGGGAAGA 58.990 45.455 0.00 0.00 0.00 2.87
543 547 0.179018 GATTCCCCACGATCCCCTTG 60.179 60.000 0.00 0.00 0.00 3.61
618 622 2.521708 AAAAAGCTGCTGCCGGGT 60.522 55.556 12.44 0.00 40.80 5.28
619 623 2.859981 AAAAAGCTGCTGCCGGGTG 61.860 57.895 12.44 0.00 40.80 4.61
625 629 4.577677 TGCTGCCGGGTGCTCAAA 62.578 61.111 2.18 0.00 42.00 2.69
626 630 3.294493 GCTGCCGGGTGCTCAAAA 61.294 61.111 2.18 0.00 42.00 2.44
627 631 2.855514 GCTGCCGGGTGCTCAAAAA 61.856 57.895 2.18 0.00 42.00 1.94
646 650 2.584492 AAATAAAATCAGCTGCCGCC 57.416 45.000 9.47 0.00 36.60 6.13
647 651 0.381801 AATAAAATCAGCTGCCGCCG 59.618 50.000 9.47 0.00 36.60 6.46
648 652 1.447317 ATAAAATCAGCTGCCGCCGG 61.447 55.000 9.47 0.00 36.60 6.13
649 653 2.529454 TAAAATCAGCTGCCGCCGGA 62.529 55.000 7.68 0.00 36.60 5.14
650 654 4.845580 AATCAGCTGCCGCCGGAG 62.846 66.667 7.68 0.00 36.60 4.63
664 668 3.647771 GGAGGTGGACCGGGCTTT 61.648 66.667 7.57 0.00 42.08 3.51
665 669 2.359975 GAGGTGGACCGGGCTTTG 60.360 66.667 7.57 0.00 42.08 2.77
666 670 4.660938 AGGTGGACCGGGCTTTGC 62.661 66.667 7.57 0.00 42.08 3.68
667 671 4.660938 GGTGGACCGGGCTTTGCT 62.661 66.667 7.57 0.00 0.00 3.91
668 672 2.349755 GTGGACCGGGCTTTGCTA 59.650 61.111 7.57 0.00 0.00 3.49
669 673 1.745489 GTGGACCGGGCTTTGCTAG 60.745 63.158 7.57 0.00 0.00 3.42
670 674 2.124695 GGACCGGGCTTTGCTAGG 60.125 66.667 7.57 0.00 0.00 3.02
678 682 3.567797 CTTTGCTAGGCCGCGCTC 61.568 66.667 18.11 0.00 0.00 5.03
693 697 2.499205 CTCCGCGATTGGTGGCTA 59.501 61.111 8.23 0.00 46.36 3.93
694 698 1.592669 CTCCGCGATTGGTGGCTAG 60.593 63.158 8.23 0.00 46.36 3.42
695 699 2.588877 CCGCGATTGGTGGCTAGG 60.589 66.667 8.23 0.00 39.96 3.02
696 700 2.186903 CGCGATTGGTGGCTAGGT 59.813 61.111 0.00 0.00 0.00 3.08
697 701 1.883084 CGCGATTGGTGGCTAGGTC 60.883 63.158 0.00 0.00 0.00 3.85
698 702 1.522569 GCGATTGGTGGCTAGGTCT 59.477 57.895 0.00 0.00 0.00 3.85
699 703 0.107654 GCGATTGGTGGCTAGGTCTT 60.108 55.000 0.00 0.00 0.00 3.01
700 704 1.941325 CGATTGGTGGCTAGGTCTTC 58.059 55.000 0.00 0.00 0.00 2.87
701 705 1.473434 CGATTGGTGGCTAGGTCTTCC 60.473 57.143 0.00 0.00 0.00 3.46
703 707 0.984230 TTGGTGGCTAGGTCTTCCTG 59.016 55.000 0.00 0.00 44.81 3.86
704 708 1.222113 GGTGGCTAGGTCTTCCTGC 59.778 63.158 0.00 0.00 44.81 4.85
705 709 1.268283 GGTGGCTAGGTCTTCCTGCT 61.268 60.000 0.00 0.00 44.81 4.24
706 710 0.107945 GTGGCTAGGTCTTCCTGCTG 60.108 60.000 0.00 0.00 44.81 4.41
707 711 0.545309 TGGCTAGGTCTTCCTGCTGT 60.545 55.000 0.00 0.00 44.81 4.40
708 712 0.176910 GGCTAGGTCTTCCTGCTGTC 59.823 60.000 0.00 0.00 44.81 3.51
709 713 0.179124 GCTAGGTCTTCCTGCTGTCG 60.179 60.000 0.00 0.00 44.81 4.35
710 714 0.179124 CTAGGTCTTCCTGCTGTCGC 60.179 60.000 0.00 0.00 44.81 5.19
711 715 1.605058 TAGGTCTTCCTGCTGTCGCC 61.605 60.000 0.00 0.00 44.81 5.54
712 716 2.811317 GTCTTCCTGCTGTCGCCG 60.811 66.667 0.00 0.00 34.43 6.46
713 717 4.742201 TCTTCCTGCTGTCGCCGC 62.742 66.667 0.00 0.00 34.43 6.53
718 722 3.869272 CTGCTGTCGCCGCCAATC 61.869 66.667 0.00 0.00 34.43 2.67
721 725 2.499205 CTGTCGCCGCCAATCCTA 59.501 61.111 0.00 0.00 0.00 2.94
722 726 1.069765 CTGTCGCCGCCAATCCTAT 59.930 57.895 0.00 0.00 0.00 2.57
723 727 0.532862 CTGTCGCCGCCAATCCTATT 60.533 55.000 0.00 0.00 0.00 1.73
724 728 0.531974 TGTCGCCGCCAATCCTATTC 60.532 55.000 0.00 0.00 0.00 1.75
725 729 1.070786 TCGCCGCCAATCCTATTCC 59.929 57.895 0.00 0.00 0.00 3.01
726 730 1.071471 CGCCGCCAATCCTATTCCT 59.929 57.895 0.00 0.00 0.00 3.36
727 731 0.320374 CGCCGCCAATCCTATTCCTA 59.680 55.000 0.00 0.00 0.00 2.94
728 732 1.809684 GCCGCCAATCCTATTCCTAC 58.190 55.000 0.00 0.00 0.00 3.18
729 733 1.939838 GCCGCCAATCCTATTCCTACG 60.940 57.143 0.00 0.00 0.00 3.51
730 734 1.429463 CGCCAATCCTATTCCTACGC 58.571 55.000 0.00 0.00 0.00 4.42
731 735 1.270094 CGCCAATCCTATTCCTACGCA 60.270 52.381 0.00 0.00 0.00 5.24
732 736 2.143925 GCCAATCCTATTCCTACGCAC 58.856 52.381 0.00 0.00 0.00 5.34
733 737 2.767505 CCAATCCTATTCCTACGCACC 58.232 52.381 0.00 0.00 0.00 5.01
734 738 2.550208 CCAATCCTATTCCTACGCACCC 60.550 54.545 0.00 0.00 0.00 4.61
735 739 2.368875 CAATCCTATTCCTACGCACCCT 59.631 50.000 0.00 0.00 0.00 4.34
770 783 2.487986 CCAGTTTTCCCACAGAAGCTCT 60.488 50.000 0.00 0.00 35.40 4.09
778 791 4.521062 CAGAAGCTCTCCCCGCCG 62.521 72.222 0.00 0.00 0.00 6.46
893 907 2.768492 CCGCCATTTCCAGAGCTGC 61.768 63.158 0.00 0.00 0.00 5.25
972 986 0.811915 TTCGTCTGGAGAGTGCTAGC 59.188 55.000 8.10 8.10 0.00 3.42
1097 1111 4.509737 GTACGCCACCTCGCCCTC 62.510 72.222 0.00 0.00 0.00 4.30
1114 2314 3.090532 CCCTTCCCTTCTCCCCCG 61.091 72.222 0.00 0.00 0.00 5.73
1115 2315 3.798511 CCTTCCCTTCTCCCCCGC 61.799 72.222 0.00 0.00 0.00 6.13
1153 2806 2.687425 CTGGATCTAGATGCGGATCGAT 59.313 50.000 24.68 8.98 37.68 3.59
1172 2825 4.935205 TCGATGCTACAACTTTGTATGCTT 59.065 37.500 17.09 13.39 42.26 3.91
1173 2826 5.411361 TCGATGCTACAACTTTGTATGCTTT 59.589 36.000 17.09 9.77 42.26 3.51
1174 2827 5.509272 CGATGCTACAACTTTGTATGCTTTG 59.491 40.000 17.09 13.21 42.26 2.77
1175 2828 6.573664 ATGCTACAACTTTGTATGCTTTGA 57.426 33.333 17.09 5.31 42.26 2.69
1176 2829 5.757886 TGCTACAACTTTGTATGCTTTGAC 58.242 37.500 17.09 0.00 42.26 3.18
1177 2830 5.530915 TGCTACAACTTTGTATGCTTTGACT 59.469 36.000 17.09 0.00 42.26 3.41
1178 2831 6.708502 TGCTACAACTTTGTATGCTTTGACTA 59.291 34.615 17.09 2.13 42.26 2.59
1179 2832 7.095229 TGCTACAACTTTGTATGCTTTGACTAG 60.095 37.037 17.09 0.00 42.26 2.57
1180 2833 7.117812 GCTACAACTTTGTATGCTTTGACTAGA 59.882 37.037 0.00 0.00 42.26 2.43
1181 2834 7.426929 ACAACTTTGTATGCTTTGACTAGAG 57.573 36.000 0.00 0.00 40.16 2.43
1182 2835 6.073003 ACAACTTTGTATGCTTTGACTAGAGC 60.073 38.462 0.00 0.00 40.16 4.09
1183 2836 5.799213 ACTTTGTATGCTTTGACTAGAGCT 58.201 37.500 0.00 0.00 39.60 4.09
1184 2837 6.936279 ACTTTGTATGCTTTGACTAGAGCTA 58.064 36.000 0.00 0.00 39.60 3.32
1185 2838 7.560368 ACTTTGTATGCTTTGACTAGAGCTAT 58.440 34.615 0.00 0.00 39.60 2.97
1186 2839 8.696374 ACTTTGTATGCTTTGACTAGAGCTATA 58.304 33.333 0.00 0.00 39.60 1.31
1187 2840 9.534565 CTTTGTATGCTTTGACTAGAGCTATAA 57.465 33.333 0.00 0.00 39.60 0.98
1188 2841 9.534565 TTTGTATGCTTTGACTAGAGCTATAAG 57.465 33.333 0.00 0.00 39.60 1.73
1189 2842 7.148641 TGTATGCTTTGACTAGAGCTATAAGC 58.851 38.462 5.96 5.96 42.84 3.09
1190 2843 4.950050 TGCTTTGACTAGAGCTATAAGCC 58.050 43.478 9.63 0.00 43.77 4.35
1191 2844 4.202264 TGCTTTGACTAGAGCTATAAGCCC 60.202 45.833 9.63 0.00 43.77 5.19
1192 2845 4.551388 CTTTGACTAGAGCTATAAGCCCG 58.449 47.826 0.00 0.00 43.77 6.13
1193 2846 3.225177 TGACTAGAGCTATAAGCCCGT 57.775 47.619 0.00 0.00 43.77 5.28
1194 2847 4.362470 TGACTAGAGCTATAAGCCCGTA 57.638 45.455 0.00 0.00 43.77 4.02
1195 2848 4.325119 TGACTAGAGCTATAAGCCCGTAG 58.675 47.826 0.00 0.00 43.77 3.51
1196 2849 4.041321 TGACTAGAGCTATAAGCCCGTAGA 59.959 45.833 0.00 0.00 43.77 2.59
1197 2850 4.983053 ACTAGAGCTATAAGCCCGTAGAA 58.017 43.478 0.00 0.00 43.77 2.10
1198 2851 5.383476 ACTAGAGCTATAAGCCCGTAGAAA 58.617 41.667 0.00 0.00 43.77 2.52
1199 2852 4.587584 AGAGCTATAAGCCCGTAGAAAC 57.412 45.455 0.00 0.00 43.77 2.78
1200 2853 3.004524 AGAGCTATAAGCCCGTAGAAACG 59.995 47.826 0.00 0.00 43.77 3.60
1201 2854 2.692041 AGCTATAAGCCCGTAGAAACGT 59.308 45.455 0.00 0.00 43.77 3.99
1202 2855 3.490419 AGCTATAAGCCCGTAGAAACGTG 60.490 47.826 0.00 0.00 43.77 4.49
1203 2856 5.941794 AGCTATAAGCCCGTAGAAACGTGT 61.942 45.833 0.00 0.00 43.77 4.49
1204 2857 7.669070 AGCTATAAGCCCGTAGAAACGTGTC 62.669 48.000 0.00 0.00 43.77 3.67
1209 2862 3.879912 CGTAGAAACGTGTCACCCT 57.120 52.632 8.78 0.00 44.21 4.34
1210 2863 2.995466 CGTAGAAACGTGTCACCCTA 57.005 50.000 8.78 0.00 44.21 3.53
1211 2864 3.287312 CGTAGAAACGTGTCACCCTAA 57.713 47.619 8.78 0.00 44.21 2.69
1212 2865 3.841643 CGTAGAAACGTGTCACCCTAAT 58.158 45.455 8.78 0.00 44.21 1.73
1213 2866 3.611113 CGTAGAAACGTGTCACCCTAATG 59.389 47.826 8.78 0.00 44.21 1.90
1214 2867 2.423577 AGAAACGTGTCACCCTAATGC 58.576 47.619 8.78 0.00 0.00 3.56
1215 2868 2.038557 AGAAACGTGTCACCCTAATGCT 59.961 45.455 8.78 0.00 0.00 3.79
1231 2884 2.333225 CTTCTCGCGAGGATCCCG 59.667 66.667 33.98 11.69 0.00 5.14
1239 2893 1.665161 CGCGAGGATCCCGTACAATAC 60.665 57.143 19.53 4.92 0.00 1.89
1253 2907 5.496330 GTACAATACGAGCACCGATAATG 57.504 43.478 5.53 2.38 41.76 1.90
1307 2962 1.002502 GTCCGGGTAAAGCTTGGCT 60.003 57.895 0.00 0.00 42.56 4.75
1326 2981 3.181500 GGCTTCCATGATTTGTAACGACC 60.181 47.826 0.00 0.00 0.00 4.79
1336 2991 1.441738 TGTAACGACCGACGATCTCA 58.558 50.000 0.00 0.00 45.77 3.27
1343 3001 3.367025 ACGACCGACGATCTCAATTTTTC 59.633 43.478 0.00 0.00 45.77 2.29
1344 3002 3.366724 CGACCGACGATCTCAATTTTTCA 59.633 43.478 0.00 0.00 45.77 2.69
1448 3106 0.179000 ACCGATGTGCCATTCTCTCC 59.821 55.000 0.00 0.00 0.00 3.71
1454 3112 1.911357 TGTGCCATTCTCTCCACTCAT 59.089 47.619 0.00 0.00 0.00 2.90
1647 3305 5.277779 CGAAACCACTTGCAGATTTAAGACA 60.278 40.000 0.00 0.00 0.00 3.41
1666 3324 3.159472 ACATGCTTCTCAAATTGAGGCA 58.841 40.909 22.47 22.47 44.39 4.75
1733 3391 1.739562 CTGCAGCTCGGGACTCAAC 60.740 63.158 0.00 0.00 0.00 3.18
1822 3480 7.016268 AGGTTTCTTCTAGTTGTGAGACCATAA 59.984 37.037 13.99 0.00 36.52 1.90
1856 3517 7.495135 TGATTTGGAAAATTCTTCTTTTGGC 57.505 32.000 0.00 0.00 0.00 4.52
1899 3560 4.019860 TCAAGGAACTCCAGAATCAGGAAG 60.020 45.833 0.00 0.00 38.49 3.46
1910 3571 4.934602 CAGAATCAGGAAGGACAAGTTCTC 59.065 45.833 0.00 0.00 0.00 2.87
1930 3591 3.030291 TCACAACCTGGTTGCTTCAAAT 58.970 40.909 33.52 14.06 46.20 2.32
1961 3622 1.030488 CCAAGCATCTGGACCTGCAG 61.030 60.000 6.78 6.78 40.88 4.41
1974 3635 3.367703 GGACCTGCAGATGAAAATGTTGG 60.368 47.826 17.39 0.00 0.00 3.77
1977 3638 1.612950 TGCAGATGAAAATGTTGGCGT 59.387 42.857 0.00 0.00 0.00 5.68
2179 3841 8.816640 ATAACTGTTTCTACAAGCAAATTTGG 57.183 30.769 19.47 5.90 32.92 3.28
2190 3852 5.125356 CAAGCAAATTTGGTTTTCCCTCTT 58.875 37.500 28.19 12.89 45.64 2.85
2303 3965 6.311735 AGTACTTTGAAAAGAGGGCCAAATA 58.688 36.000 6.18 0.00 39.31 1.40
2369 4031 7.122055 CCTCAGATCAGAGTGAAAGTAAGTACT 59.878 40.741 13.47 0.00 34.30 2.73
2370 4032 9.168451 CTCAGATCAGAGTGAAAGTAAGTACTA 57.832 37.037 6.95 0.00 34.99 1.82
2371 4033 8.948145 TCAGATCAGAGTGAAAGTAAGTACTAC 58.052 37.037 0.00 0.00 34.99 2.73
2372 4034 8.952278 CAGATCAGAGTGAAAGTAAGTACTACT 58.048 37.037 0.00 0.00 43.06 2.57
2373 4035 9.169592 AGATCAGAGTGAAAGTAAGTACTACTC 57.830 37.037 10.46 10.46 40.14 2.59
2374 4036 7.684937 TCAGAGTGAAAGTAAGTACTACTCC 57.315 40.000 13.58 6.86 40.14 3.85
2375 4037 6.658391 TCAGAGTGAAAGTAAGTACTACTCCC 59.342 42.308 13.58 6.61 40.14 4.30
2376 4038 6.660094 CAGAGTGAAAGTAAGTACTACTCCCT 59.340 42.308 13.58 2.42 40.14 4.20
2377 4039 6.885918 AGAGTGAAAGTAAGTACTACTCCCTC 59.114 42.308 13.58 9.14 40.14 4.30
2378 4040 5.951148 AGTGAAAGTAAGTACTACTCCCTCC 59.049 44.000 0.00 0.00 40.14 4.30
2379 4041 4.946157 TGAAAGTAAGTACTACTCCCTCCG 59.054 45.833 0.00 0.00 40.14 4.63
2380 4042 4.582973 AAGTAAGTACTACTCCCTCCGT 57.417 45.455 0.00 0.00 40.14 4.69
2381 4043 4.149511 AGTAAGTACTACTCCCTCCGTC 57.850 50.000 0.00 0.00 35.90 4.79
2382 4044 2.433662 AAGTACTACTCCCTCCGTCC 57.566 55.000 0.00 0.00 0.00 4.79
2383 4045 0.550432 AGTACTACTCCCTCCGTCCC 59.450 60.000 0.00 0.00 0.00 4.46
2384 4046 0.257039 GTACTACTCCCTCCGTCCCA 59.743 60.000 0.00 0.00 0.00 4.37
2385 4047 1.002069 TACTACTCCCTCCGTCCCAA 58.998 55.000 0.00 0.00 0.00 4.12
2386 4048 0.115745 ACTACTCCCTCCGTCCCAAA 59.884 55.000 0.00 0.00 0.00 3.28
2387 4049 1.272807 CTACTCCCTCCGTCCCAAAA 58.727 55.000 0.00 0.00 0.00 2.44
2388 4050 1.838077 CTACTCCCTCCGTCCCAAAAT 59.162 52.381 0.00 0.00 0.00 1.82
2389 4051 1.073098 ACTCCCTCCGTCCCAAAATT 58.927 50.000 0.00 0.00 0.00 1.82
2390 4052 1.004394 ACTCCCTCCGTCCCAAAATTC 59.996 52.381 0.00 0.00 0.00 2.17
2391 4053 1.282157 CTCCCTCCGTCCCAAAATTCT 59.718 52.381 0.00 0.00 0.00 2.40
2392 4054 1.708551 TCCCTCCGTCCCAAAATTCTT 59.291 47.619 0.00 0.00 0.00 2.52
2393 4055 1.818674 CCCTCCGTCCCAAAATTCTTG 59.181 52.381 0.00 0.00 0.00 3.02
2394 4056 2.514803 CCTCCGTCCCAAAATTCTTGT 58.485 47.619 0.00 0.00 0.00 3.16
2395 4057 2.488153 CCTCCGTCCCAAAATTCTTGTC 59.512 50.000 0.00 0.00 0.00 3.18
2396 4058 3.412386 CTCCGTCCCAAAATTCTTGTCT 58.588 45.455 0.00 0.00 0.00 3.41
2397 4059 3.821033 CTCCGTCCCAAAATTCTTGTCTT 59.179 43.478 0.00 0.00 0.00 3.01
2398 4060 4.975631 TCCGTCCCAAAATTCTTGTCTTA 58.024 39.130 0.00 0.00 0.00 2.10
2399 4061 5.001232 TCCGTCCCAAAATTCTTGTCTTAG 58.999 41.667 0.00 0.00 0.00 2.18
2400 4062 5.001232 CCGTCCCAAAATTCTTGTCTTAGA 58.999 41.667 0.00 0.00 0.00 2.10
2401 4063 5.648092 CCGTCCCAAAATTCTTGTCTTAGAT 59.352 40.000 0.00 0.00 0.00 1.98
2402 4064 6.151144 CCGTCCCAAAATTCTTGTCTTAGATT 59.849 38.462 0.00 0.00 0.00 2.40
2403 4065 7.309194 CCGTCCCAAAATTCTTGTCTTAGATTT 60.309 37.037 0.00 0.00 0.00 2.17
2404 4066 7.538678 CGTCCCAAAATTCTTGTCTTAGATTTG 59.461 37.037 0.00 0.00 29.84 2.32
2405 4067 8.360390 GTCCCAAAATTCTTGTCTTAGATTTGT 58.640 33.333 0.00 0.00 28.79 2.83
2406 4068 8.576442 TCCCAAAATTCTTGTCTTAGATTTGTC 58.424 33.333 0.00 0.00 28.79 3.18
2407 4069 8.579863 CCCAAAATTCTTGTCTTAGATTTGTCT 58.420 33.333 0.00 0.00 28.79 3.41
2429 4091 8.947115 TGTCTAGATATGGATGTATCTAACACG 58.053 37.037 0.00 0.00 41.00 4.49
2430 4092 9.163899 GTCTAGATATGGATGTATCTAACACGA 57.836 37.037 0.00 0.00 41.00 4.35
2431 4093 9.734984 TCTAGATATGGATGTATCTAACACGAA 57.265 33.333 0.00 0.00 41.00 3.85
2436 4098 9.778741 ATATGGATGTATCTAACACGAAAATGT 57.221 29.630 0.00 0.00 42.09 2.71
2438 4100 9.607988 ATGGATGTATCTAACACGAAAATGTAA 57.392 29.630 0.00 0.00 42.09 2.41
2439 4101 8.875803 TGGATGTATCTAACACGAAAATGTAAC 58.124 33.333 0.00 0.00 42.09 2.50
2440 4102 9.095065 GGATGTATCTAACACGAAAATGTAACT 57.905 33.333 0.00 0.00 42.09 2.24
2450 4112 9.871238 AACACGAAAATGTAACTAGATACATCT 57.129 29.630 21.77 14.07 43.83 2.90
2451 4113 9.302345 ACACGAAAATGTAACTAGATACATCTG 57.698 33.333 21.77 15.03 43.83 2.90
2452 4114 9.302345 CACGAAAATGTAACTAGATACATCTGT 57.698 33.333 21.77 15.51 43.83 3.41
2483 4145 9.933723 AGACAAATCTAAATCAAGAATTTTGGG 57.066 29.630 0.00 0.00 38.53 4.12
2484 4146 9.927668 GACAAATCTAAATCAAGAATTTTGGGA 57.072 29.630 0.00 0.00 38.53 4.37
2487 4149 9.895138 AAATCTAAATCAAGAATTTTGGGATGG 57.105 29.630 0.00 0.00 38.53 3.51
2488 4150 8.843308 ATCTAAATCAAGAATTTTGGGATGGA 57.157 30.769 0.00 0.00 38.53 3.41
2489 4151 8.297470 TCTAAATCAAGAATTTTGGGATGGAG 57.703 34.615 0.00 0.00 38.53 3.86
2490 4152 5.945144 AATCAAGAATTTTGGGATGGAGG 57.055 39.130 0.00 0.00 0.00 4.30
2491 4153 3.711863 TCAAGAATTTTGGGATGGAGGG 58.288 45.455 2.07 0.00 0.00 4.30
2492 4154 3.336391 TCAAGAATTTTGGGATGGAGGGA 59.664 43.478 2.07 0.00 0.00 4.20
2493 4155 3.677156 AGAATTTTGGGATGGAGGGAG 57.323 47.619 0.00 0.00 0.00 4.30
2969 4631 7.532682 TTTGTTTGTCTTATGGCTTTTGTTC 57.467 32.000 0.00 0.00 0.00 3.18
3040 4709 7.337938 TGAAGCATACTTTGAAGGTGATATGA 58.662 34.615 0.00 0.00 35.82 2.15
3099 4768 4.335416 AGATGAAGTGTGGTATTTGTGGG 58.665 43.478 0.00 0.00 0.00 4.61
3192 4861 0.693430 TCTCAGGCTGCAGATGGGAT 60.693 55.000 20.43 0.00 0.00 3.85
3211 4880 3.471680 GATGAAGTAAGTCCTGCATCCC 58.528 50.000 0.00 0.00 40.37 3.85
3365 5037 2.200067 CTGCCATGTGAGAGATCGAAC 58.800 52.381 0.00 0.00 0.00 3.95
3391 5063 4.729918 CAAGAAGGCCGCCCAGCT 62.730 66.667 5.55 0.00 0.00 4.24
3410 5082 2.283298 CTGCAACAGTGTGTTCTCTGT 58.717 47.619 0.00 0.00 46.12 3.41
3468 5140 5.672503 CATCTGTCTCTTGATGGACTTCAT 58.327 41.667 0.00 0.00 37.13 2.57
3505 5177 4.563580 GCCAGACCATCTTCTGAAACAGTA 60.564 45.833 1.60 0.00 45.19 2.74
3950 5622 2.105649 TCCTTGACCACTGCACATGTTA 59.894 45.455 0.00 0.00 0.00 2.41
3964 5636 6.898041 TGCACATGTTAAGACACAATAGTTC 58.102 36.000 0.00 0.00 38.91 3.01
3986 5658 3.363970 CGCTTACATGTGGTCACTTTGTC 60.364 47.826 9.11 1.70 33.07 3.18
4069 5741 5.538433 CCTGAATTTACTTTGGTTTCCCTCA 59.462 40.000 0.00 0.00 0.00 3.86
4279 5951 8.948853 TCGTTGAGAAAATTAGCAAAATGTAG 57.051 30.769 0.00 0.00 0.00 2.74
4307 5979 5.426689 AATCTGAACAGGCTATTGAGTGA 57.573 39.130 1.93 0.00 0.00 3.41
4308 5980 4.193826 TCTGAACAGGCTATTGAGTGAC 57.806 45.455 1.93 0.00 0.00 3.67
4351 6023 3.891366 CCAAGTCTGTTTTCAGGGTTGAT 59.109 43.478 10.02 0.00 46.94 2.57
4400 6072 4.458295 ACATTCAAGGTTGAGCTTGATGAG 59.542 41.667 21.90 17.06 39.04 2.90
4487 6159 5.415077 TGTTTACAACAAGGAAGTTCCGAAA 59.585 36.000 16.31 6.72 37.86 3.46
4511 6183 3.621520 AACGAAGACGCCGTTGAC 58.378 55.556 0.00 0.00 46.77 3.18
4577 6249 0.320073 CATTTGGCTGCAGGGTTGTG 60.320 55.000 17.12 0.00 0.00 3.33
4794 6466 8.934023 AAGAAAATCTTATGTTTCACCTACCA 57.066 30.769 0.00 0.00 34.42 3.25
4886 6558 4.082125 AGGTTTGCTCTAAAAGACCCATG 58.918 43.478 0.00 0.00 0.00 3.66
4921 6594 8.683615 GGATTTAACCTGGAAATTTCGTTCTAT 58.316 33.333 11.95 7.64 0.00 1.98
4922 6595 9.503427 GATTTAACCTGGAAATTTCGTTCTATG 57.497 33.333 11.95 0.00 0.00 2.23
4934 6607 1.839424 GTTCTATGCCTTTGGGTGCT 58.161 50.000 0.00 0.00 34.45 4.40
4938 6615 1.747355 CTATGCCTTTGGGTGCTCAAG 59.253 52.381 0.00 0.00 34.45 3.02
4940 6617 0.538057 TGCCTTTGGGTGCTCAAGAG 60.538 55.000 0.00 0.00 34.45 2.85
4957 6634 6.127786 GCTCAAGAGTTTCTGAATTTGGCTAT 60.128 38.462 0.00 0.00 0.00 2.97
4960 6637 4.095483 AGAGTTTCTGAATTTGGCTATGCG 59.905 41.667 0.00 0.00 0.00 4.73
4962 6639 2.418368 TCTGAATTTGGCTATGCGGT 57.582 45.000 0.00 0.00 0.00 5.68
4970 6647 1.882912 TGGCTATGCGGTTGATCATC 58.117 50.000 0.00 0.00 0.00 2.92
5059 6736 1.915769 GGAGGCTGAGGTCACTGGT 60.916 63.158 0.00 0.00 0.00 4.00
5061 6738 0.398318 GAGGCTGAGGTCACTGGTTT 59.602 55.000 0.00 0.00 0.00 3.27
5062 6739 0.109342 AGGCTGAGGTCACTGGTTTG 59.891 55.000 0.00 0.00 0.00 2.93
5063 6740 0.890996 GGCTGAGGTCACTGGTTTGG 60.891 60.000 0.00 0.00 0.00 3.28
5064 6741 0.890996 GCTGAGGTCACTGGTTTGGG 60.891 60.000 0.00 0.00 0.00 4.12
5065 6742 0.474184 CTGAGGTCACTGGTTTGGGT 59.526 55.000 0.00 0.00 0.00 4.51
5067 6744 0.182775 GAGGTCACTGGTTTGGGTGT 59.817 55.000 0.00 0.00 35.26 4.16
5068 6745 0.182775 AGGTCACTGGTTTGGGTGTC 59.817 55.000 0.00 0.00 35.26 3.67
5183 6860 1.821759 TTGGTGTGGTGTTGCCTCG 60.822 57.895 0.00 0.00 38.35 4.63
5190 6867 2.639286 GTGTTGCCTCGTGCCAAG 59.361 61.111 0.00 0.00 40.16 3.61
5199 6876 0.249868 CTCGTGCCAAGACAACTCCA 60.250 55.000 0.00 0.00 0.00 3.86
5275 6952 4.104183 GGATCCCCGGCGGTGAAA 62.104 66.667 26.32 7.24 0.00 2.69
5292 6969 2.890311 TGAAACCATGGCGTTCTTCAAT 59.110 40.909 22.75 0.00 0.00 2.57
5334 7011 2.611971 CGAAATCCTGACGAGGTTCCAA 60.612 50.000 0.00 0.00 40.76 3.53
5341 7026 0.534203 GACGAGGTTCCAAAGGTGCA 60.534 55.000 0.00 0.00 0.00 4.57
5358 7043 3.428589 GGTGCAAGCTCATCTTTCCAATC 60.429 47.826 0.00 0.00 31.27 2.67
5361 7046 3.012518 CAAGCTCATCTTTCCAATCCGT 58.987 45.455 0.00 0.00 31.27 4.69
5406 7159 3.057033 GTCTTTTGCTCATGCTTGGATGT 60.057 43.478 0.00 0.00 40.48 3.06
5485 7238 2.864343 GCGATACCATGTACAGGTGAAC 59.136 50.000 20.68 13.09 40.26 3.18
5545 7298 0.878416 TATTTGTTGTCAGCGGTGCC 59.122 50.000 10.38 0.00 0.00 5.01
5550 7303 3.825160 TTGTCAGCGGTGCCCTCAC 62.825 63.158 10.38 2.88 42.40 3.51
5572 7325 1.114627 TCTGCCAGCTGATCGTATGT 58.885 50.000 17.39 0.00 0.00 2.29
5574 7327 2.893489 TCTGCCAGCTGATCGTATGTAT 59.107 45.455 17.39 0.00 0.00 2.29
5575 7328 2.991866 CTGCCAGCTGATCGTATGTATG 59.008 50.000 17.39 0.00 0.00 2.39
5587 7340 2.632377 GTATGTATGTGTGTGCAGGCT 58.368 47.619 0.00 0.00 0.00 4.58
5620 7373 0.109412 CCGAGAACGTGTACCTGTCC 60.109 60.000 0.00 0.00 37.88 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
150 151 0.032540 CTGCAGCACCTTTTTCACCC 59.967 55.000 0.00 0.00 0.00 4.61
187 188 1.691196 CCCAGAAAAGTTCCACTGCA 58.309 50.000 0.00 0.00 0.00 4.41
227 228 1.144057 GCCGGATCAGTGATTCCGT 59.856 57.895 27.41 3.60 43.50 4.69
250 251 1.672898 GGCATGCCAAAGCTTCCAA 59.327 52.632 32.08 0.00 40.80 3.53
269 270 0.035458 AGCAAGTGAAAGTCCCTCCG 59.965 55.000 0.00 0.00 0.00 4.63
310 311 2.304092 AGAATCGCATGCAATCACCAT 58.696 42.857 19.57 0.00 0.00 3.55
485 486 6.210078 CGGCCAGAATCTAAAGAACTAGTAG 58.790 44.000 2.24 0.00 0.00 2.57
486 487 5.451520 GCGGCCAGAATCTAAAGAACTAGTA 60.452 44.000 2.24 0.00 0.00 1.82
487 488 4.680975 GCGGCCAGAATCTAAAGAACTAGT 60.681 45.833 2.24 0.00 0.00 2.57
543 547 4.694037 AGTTGCGAGGTTTACAGGAATAAC 59.306 41.667 0.00 0.00 0.00 1.89
625 629 3.261580 GGCGGCAGCTGATTTTATTTTT 58.738 40.909 20.43 0.00 44.37 1.94
626 630 2.892374 GGCGGCAGCTGATTTTATTTT 58.108 42.857 20.43 0.00 44.37 1.82
627 631 2.584492 GGCGGCAGCTGATTTTATTT 57.416 45.000 20.43 0.00 44.37 1.40
647 651 3.647771 AAAGCCCGGTCCACCTCC 61.648 66.667 0.00 0.00 0.00 4.30
648 652 2.359975 CAAAGCCCGGTCCACCTC 60.360 66.667 0.00 0.00 0.00 3.85
649 653 4.660938 GCAAAGCCCGGTCCACCT 62.661 66.667 0.00 0.00 0.00 4.00
650 654 3.262448 TAGCAAAGCCCGGTCCACC 62.262 63.158 0.00 0.00 0.00 4.61
651 655 1.745489 CTAGCAAAGCCCGGTCCAC 60.745 63.158 0.00 0.00 0.00 4.02
652 656 2.668632 CTAGCAAAGCCCGGTCCA 59.331 61.111 0.00 0.00 0.00 4.02
653 657 2.124695 CCTAGCAAAGCCCGGTCC 60.125 66.667 0.00 0.00 0.00 4.46
654 658 2.824489 GCCTAGCAAAGCCCGGTC 60.824 66.667 0.00 0.00 0.00 4.79
655 659 4.426313 GGCCTAGCAAAGCCCGGT 62.426 66.667 0.00 0.00 43.76 5.28
661 665 3.567797 GAGCGCGGCCTAGCAAAG 61.568 66.667 19.29 0.00 36.85 2.77
676 680 1.592669 CTAGCCACCAATCGCGGAG 60.593 63.158 6.13 0.00 0.00 4.63
677 681 2.499205 CTAGCCACCAATCGCGGA 59.501 61.111 6.13 0.00 0.00 5.54
678 682 2.588877 CCTAGCCACCAATCGCGG 60.589 66.667 6.13 0.00 0.00 6.46
679 683 1.883084 GACCTAGCCACCAATCGCG 60.883 63.158 0.00 0.00 0.00 5.87
680 684 0.107654 AAGACCTAGCCACCAATCGC 60.108 55.000 0.00 0.00 0.00 4.58
681 685 1.473434 GGAAGACCTAGCCACCAATCG 60.473 57.143 0.00 0.00 0.00 3.34
682 686 1.840635 AGGAAGACCTAGCCACCAATC 59.159 52.381 0.00 0.00 45.83 2.67
683 687 1.561542 CAGGAAGACCTAGCCACCAAT 59.438 52.381 0.00 0.00 45.94 3.16
684 688 0.984230 CAGGAAGACCTAGCCACCAA 59.016 55.000 0.00 0.00 45.94 3.67
685 689 1.553690 GCAGGAAGACCTAGCCACCA 61.554 60.000 0.00 0.00 45.94 4.17
686 690 1.222113 GCAGGAAGACCTAGCCACC 59.778 63.158 0.00 0.00 45.94 4.61
687 691 0.107945 CAGCAGGAAGACCTAGCCAC 60.108 60.000 0.00 0.00 45.94 5.01
688 692 0.545309 ACAGCAGGAAGACCTAGCCA 60.545 55.000 0.00 0.00 45.94 4.75
689 693 0.176910 GACAGCAGGAAGACCTAGCC 59.823 60.000 0.00 0.00 45.94 3.93
690 694 0.179124 CGACAGCAGGAAGACCTAGC 60.179 60.000 0.00 0.00 45.94 3.42
691 695 0.179124 GCGACAGCAGGAAGACCTAG 60.179 60.000 0.00 0.00 45.94 3.02
692 696 1.605058 GGCGACAGCAGGAAGACCTA 61.605 60.000 0.00 0.00 45.94 3.08
703 707 2.996168 ATAGGATTGGCGGCGACAGC 62.996 60.000 17.88 12.67 44.18 4.40
704 708 0.532862 AATAGGATTGGCGGCGACAG 60.533 55.000 17.88 0.00 0.00 3.51
705 709 0.531974 GAATAGGATTGGCGGCGACA 60.532 55.000 13.60 13.60 0.00 4.35
706 710 1.228657 GGAATAGGATTGGCGGCGAC 61.229 60.000 12.98 9.31 0.00 5.19
707 711 1.070786 GGAATAGGATTGGCGGCGA 59.929 57.895 12.98 0.00 0.00 5.54
708 712 0.320374 TAGGAATAGGATTGGCGGCG 59.680 55.000 0.51 0.51 0.00 6.46
709 713 1.809684 GTAGGAATAGGATTGGCGGC 58.190 55.000 0.00 0.00 0.00 6.53
710 714 1.939838 GCGTAGGAATAGGATTGGCGG 60.940 57.143 0.00 0.00 0.00 6.13
711 715 1.270094 TGCGTAGGAATAGGATTGGCG 60.270 52.381 0.00 0.00 0.00 5.69
712 716 2.143925 GTGCGTAGGAATAGGATTGGC 58.856 52.381 0.00 0.00 0.00 4.52
713 717 2.550208 GGGTGCGTAGGAATAGGATTGG 60.550 54.545 0.00 0.00 0.00 3.16
714 718 2.368875 AGGGTGCGTAGGAATAGGATTG 59.631 50.000 0.00 0.00 0.00 2.67
715 719 2.690840 AGGGTGCGTAGGAATAGGATT 58.309 47.619 0.00 0.00 0.00 3.01
716 720 2.400467 AGGGTGCGTAGGAATAGGAT 57.600 50.000 0.00 0.00 0.00 3.24
717 721 2.037144 GAAGGGTGCGTAGGAATAGGA 58.963 52.381 0.00 0.00 0.00 2.94
718 722 1.070289 GGAAGGGTGCGTAGGAATAGG 59.930 57.143 0.00 0.00 0.00 2.57
719 723 2.040178 AGGAAGGGTGCGTAGGAATAG 58.960 52.381 0.00 0.00 0.00 1.73
720 724 2.170012 AGGAAGGGTGCGTAGGAATA 57.830 50.000 0.00 0.00 0.00 1.75
721 725 1.209747 GAAGGAAGGGTGCGTAGGAAT 59.790 52.381 0.00 0.00 0.00 3.01
722 726 0.611714 GAAGGAAGGGTGCGTAGGAA 59.388 55.000 0.00 0.00 0.00 3.36
723 727 0.543410 TGAAGGAAGGGTGCGTAGGA 60.543 55.000 0.00 0.00 0.00 2.94
724 728 0.323629 TTGAAGGAAGGGTGCGTAGG 59.676 55.000 0.00 0.00 0.00 3.18
725 729 2.076863 CTTTGAAGGAAGGGTGCGTAG 58.923 52.381 0.00 0.00 0.00 3.51
726 730 1.880646 GCTTTGAAGGAAGGGTGCGTA 60.881 52.381 0.00 0.00 0.00 4.42
727 731 1.172812 GCTTTGAAGGAAGGGTGCGT 61.173 55.000 0.00 0.00 0.00 5.24
728 732 1.172180 TGCTTTGAAGGAAGGGTGCG 61.172 55.000 0.00 0.00 0.00 5.34
729 733 0.600057 CTGCTTTGAAGGAAGGGTGC 59.400 55.000 0.00 0.00 0.00 5.01
730 734 0.600057 GCTGCTTTGAAGGAAGGGTG 59.400 55.000 0.00 0.00 0.00 4.61
731 735 0.540597 GGCTGCTTTGAAGGAAGGGT 60.541 55.000 0.00 0.00 0.00 4.34
732 736 0.540365 TGGCTGCTTTGAAGGAAGGG 60.540 55.000 0.00 0.00 0.00 3.95
733 737 0.886563 CTGGCTGCTTTGAAGGAAGG 59.113 55.000 0.00 0.00 0.00 3.46
734 738 1.613836 ACTGGCTGCTTTGAAGGAAG 58.386 50.000 0.00 0.00 0.00 3.46
735 739 2.071778 AACTGGCTGCTTTGAAGGAA 57.928 45.000 0.00 0.00 0.00 3.36
778 791 4.910956 GAAATTTTCGGGCAGGGC 57.089 55.556 0.00 0.00 0.00 5.19
1093 1107 1.694525 GGGAGAAGGGAAGGGAGGG 60.695 68.421 0.00 0.00 0.00 4.30
1094 1108 1.694525 GGGGAGAAGGGAAGGGAGG 60.695 68.421 0.00 0.00 0.00 4.30
1095 1109 1.694525 GGGGGAGAAGGGAAGGGAG 60.695 68.421 0.00 0.00 0.00 4.30
1096 1110 2.459710 GGGGGAGAAGGGAAGGGA 59.540 66.667 0.00 0.00 0.00 4.20
1097 1111 3.090532 CGGGGGAGAAGGGAAGGG 61.091 72.222 0.00 0.00 0.00 3.95
1114 2314 0.466124 AGAGAACTAAGATGCGGGGC 59.534 55.000 0.00 0.00 0.00 5.80
1115 2315 1.202580 CCAGAGAACTAAGATGCGGGG 60.203 57.143 0.00 0.00 0.00 5.73
1119 2319 6.892658 TCTAGATCCAGAGAACTAAGATGC 57.107 41.667 0.00 0.00 28.05 3.91
1121 2321 6.150976 CGCATCTAGATCCAGAGAACTAAGAT 59.849 42.308 1.03 0.00 28.05 2.40
1123 2323 5.335583 CCGCATCTAGATCCAGAGAACTAAG 60.336 48.000 1.03 0.00 28.05 2.18
1124 2324 4.520874 CCGCATCTAGATCCAGAGAACTAA 59.479 45.833 1.03 0.00 28.05 2.24
1126 2326 2.890311 CCGCATCTAGATCCAGAGAACT 59.110 50.000 1.03 0.00 0.00 3.01
1153 2806 5.530915 AGTCAAAGCATACAAAGTTGTAGCA 59.469 36.000 18.93 0.00 45.80 3.49
1172 2825 3.563223 ACGGGCTTATAGCTCTAGTCAA 58.437 45.455 0.00 0.00 40.30 3.18
1173 2826 3.225177 ACGGGCTTATAGCTCTAGTCA 57.775 47.619 0.00 0.00 40.30 3.41
1174 2827 4.577875 TCTACGGGCTTATAGCTCTAGTC 58.422 47.826 0.00 0.00 40.30 2.59
1175 2828 4.637387 TCTACGGGCTTATAGCTCTAGT 57.363 45.455 0.00 0.00 40.30 2.57
1176 2829 5.617308 CGTTTCTACGGGCTTATAGCTCTAG 60.617 48.000 0.00 0.00 40.30 2.43
1177 2830 4.214971 CGTTTCTACGGGCTTATAGCTCTA 59.785 45.833 0.00 0.00 40.30 2.43
1178 2831 3.004524 CGTTTCTACGGGCTTATAGCTCT 59.995 47.826 0.00 0.00 40.30 4.09
1179 2832 3.306818 CGTTTCTACGGGCTTATAGCTC 58.693 50.000 0.00 0.00 43.94 4.09
1180 2833 3.366440 CGTTTCTACGGGCTTATAGCT 57.634 47.619 0.00 0.00 43.94 3.32
1192 2845 3.370061 GCATTAGGGTGACACGTTTCTAC 59.630 47.826 3.00 0.16 0.00 2.59
1193 2846 3.259876 AGCATTAGGGTGACACGTTTCTA 59.740 43.478 3.00 0.00 0.00 2.10
1194 2847 2.038557 AGCATTAGGGTGACACGTTTCT 59.961 45.455 3.00 0.00 0.00 2.52
1195 2848 2.423577 AGCATTAGGGTGACACGTTTC 58.576 47.619 0.00 0.00 0.00 2.78
1196 2849 2.561478 AGCATTAGGGTGACACGTTT 57.439 45.000 0.00 0.00 0.00 3.60
1197 2850 2.038557 AGAAGCATTAGGGTGACACGTT 59.961 45.455 0.00 0.00 0.00 3.99
1198 2851 1.623811 AGAAGCATTAGGGTGACACGT 59.376 47.619 0.00 0.00 0.00 4.49
1199 2852 2.271800 GAGAAGCATTAGGGTGACACG 58.728 52.381 0.00 0.00 0.00 4.49
1200 2853 2.271800 CGAGAAGCATTAGGGTGACAC 58.728 52.381 0.00 0.00 0.00 3.67
1201 2854 2.672961 CGAGAAGCATTAGGGTGACA 57.327 50.000 0.00 0.00 0.00 3.58
1213 2866 2.028337 GGGATCCTCGCGAGAAGC 59.972 66.667 36.59 21.57 41.32 3.86
1231 2884 4.143389 GCATTATCGGTGCTCGTATTGTAC 60.143 45.833 0.00 0.00 39.45 2.90
1270 2925 4.336280 GGACCCAAATCTAGCAAAGTTCT 58.664 43.478 0.00 0.00 0.00 3.01
1272 2927 3.081804 CGGACCCAAATCTAGCAAAGTT 58.918 45.455 0.00 0.00 0.00 2.66
1307 2962 3.680937 GTCGGTCGTTACAAATCATGGAA 59.319 43.478 0.00 0.00 0.00 3.53
1311 2966 3.220507 TCGTCGGTCGTTACAAATCAT 57.779 42.857 0.00 0.00 40.80 2.45
1448 3106 1.854743 CGTCACAAGGCGATATGAGTG 59.145 52.381 0.00 0.00 0.00 3.51
1454 3112 3.857052 AGAAATTCGTCACAAGGCGATA 58.143 40.909 0.00 0.00 36.97 2.92
1647 3305 4.382685 CCAATGCCTCAATTTGAGAAGCAT 60.383 41.667 25.15 25.15 46.74 3.79
1666 3324 3.245016 TGCTCCTCTGAATGTTCACCAAT 60.245 43.478 0.00 0.00 32.90 3.16
1856 3517 2.485814 GAGAAGTAGCCTTTGCAACTGG 59.514 50.000 12.06 12.06 41.13 4.00
1873 3534 4.019860 CCTGATTCTGGAGTTCCTTGAGAA 60.020 45.833 3.58 1.32 36.82 2.87
1899 3560 2.222027 CCAGGTTGTGAGAACTTGTCC 58.778 52.381 4.03 0.00 0.00 4.02
1910 3571 2.957491 TTTGAAGCAACCAGGTTGTG 57.043 45.000 29.46 10.40 44.40 3.33
1930 3591 2.025981 AGATGCTTGGTTACATGGCAGA 60.026 45.455 0.00 0.00 38.44 4.26
1961 3622 2.155539 GCACAACGCCAACATTTTCATC 59.844 45.455 0.00 0.00 32.94 2.92
1974 3635 0.388907 ATCCATTGCTTGCACAACGC 60.389 50.000 0.00 0.00 42.89 4.84
1977 3638 1.546923 CAGGATCCATTGCTTGCACAA 59.453 47.619 15.82 0.00 0.00 3.33
2179 3841 4.202253 ACCAGATGCAAAAAGAGGGAAAAC 60.202 41.667 0.00 0.00 0.00 2.43
2220 3882 3.437049 CCGGTTTCAGGAGTGAGATTTTC 59.563 47.826 0.00 0.00 32.98 2.29
2303 3965 7.500892 CAGTCCTCTAGTACTGTCATCTGTTAT 59.499 40.741 5.39 0.00 38.62 1.89
2369 4031 1.961133 ATTTTGGGACGGAGGGAGTA 58.039 50.000 0.00 0.00 0.00 2.59
2370 4032 1.004394 GAATTTTGGGACGGAGGGAGT 59.996 52.381 0.00 0.00 0.00 3.85
2371 4033 1.282157 AGAATTTTGGGACGGAGGGAG 59.718 52.381 0.00 0.00 0.00 4.30
2372 4034 1.368374 AGAATTTTGGGACGGAGGGA 58.632 50.000 0.00 0.00 0.00 4.20
2373 4035 1.818674 CAAGAATTTTGGGACGGAGGG 59.181 52.381 0.00 0.00 0.00 4.30
2374 4036 2.488153 GACAAGAATTTTGGGACGGAGG 59.512 50.000 0.00 0.00 0.00 4.30
2375 4037 3.412386 AGACAAGAATTTTGGGACGGAG 58.588 45.455 0.00 0.00 0.00 4.63
2376 4038 3.502123 AGACAAGAATTTTGGGACGGA 57.498 42.857 0.00 0.00 0.00 4.69
2377 4039 5.001232 TCTAAGACAAGAATTTTGGGACGG 58.999 41.667 0.00 0.00 0.00 4.79
2378 4040 6.743575 ATCTAAGACAAGAATTTTGGGACG 57.256 37.500 5.68 0.00 0.00 4.79
2379 4041 8.360390 ACAAATCTAAGACAAGAATTTTGGGAC 58.640 33.333 0.00 0.00 33.04 4.46
2380 4042 8.477419 ACAAATCTAAGACAAGAATTTTGGGA 57.523 30.769 0.00 0.00 33.04 4.37
2381 4043 8.579863 AGACAAATCTAAGACAAGAATTTTGGG 58.420 33.333 0.00 0.00 33.04 4.12
2403 4065 8.947115 CGTGTTAGATACATCCATATCTAGACA 58.053 37.037 0.00 7.61 42.43 3.41
2404 4066 9.163899 TCGTGTTAGATACATCCATATCTAGAC 57.836 37.037 0.00 5.83 42.43 2.59
2405 4067 9.734984 TTCGTGTTAGATACATCCATATCTAGA 57.265 33.333 0.00 0.00 42.43 2.43
2410 4072 9.778741 ACATTTTCGTGTTAGATACATCCATAT 57.221 29.630 0.00 0.00 39.39 1.78
2412 4074 9.607988 TTACATTTTCGTGTTAGATACATCCAT 57.392 29.630 0.00 0.00 39.39 3.41
2413 4075 8.875803 GTTACATTTTCGTGTTAGATACATCCA 58.124 33.333 0.00 0.00 39.39 3.41
2414 4076 9.095065 AGTTACATTTTCGTGTTAGATACATCC 57.905 33.333 0.00 0.00 39.39 3.51
2424 4086 9.871238 AGATGTATCTAGTTACATTTTCGTGTT 57.129 29.630 21.77 3.61 41.67 3.32
2425 4087 9.302345 CAGATGTATCTAGTTACATTTTCGTGT 57.698 33.333 21.77 4.20 41.67 4.49
2426 4088 9.302345 ACAGATGTATCTAGTTACATTTTCGTG 57.698 33.333 21.77 16.75 41.67 4.35
2457 4119 9.933723 CCCAAAATTCTTGATTTAGATTTGTCT 57.066 29.630 0.00 0.00 36.96 3.41
2458 4120 9.927668 TCCCAAAATTCTTGATTTAGATTTGTC 57.072 29.630 0.00 0.00 36.96 3.18
2461 4123 9.895138 CCATCCCAAAATTCTTGATTTAGATTT 57.105 29.630 3.00 0.00 36.96 2.17
2462 4124 9.270707 TCCATCCCAAAATTCTTGATTTAGATT 57.729 29.630 3.00 0.00 36.96 2.40
2463 4125 8.843308 TCCATCCCAAAATTCTTGATTTAGAT 57.157 30.769 3.00 0.00 36.96 1.98
2464 4126 7.342799 CCTCCATCCCAAAATTCTTGATTTAGA 59.657 37.037 3.00 0.00 36.96 2.10
2465 4127 7.418254 CCCTCCATCCCAAAATTCTTGATTTAG 60.418 40.741 3.00 0.00 36.96 1.85
2466 4128 6.383726 CCCTCCATCCCAAAATTCTTGATTTA 59.616 38.462 3.00 0.00 36.96 1.40
2467 4129 5.190330 CCCTCCATCCCAAAATTCTTGATTT 59.810 40.000 3.00 0.00 39.63 2.17
2468 4130 4.718276 CCCTCCATCCCAAAATTCTTGATT 59.282 41.667 3.00 0.00 0.00 2.57
2469 4131 4.016292 TCCCTCCATCCCAAAATTCTTGAT 60.016 41.667 3.00 0.00 0.00 2.57
2470 4132 3.336391 TCCCTCCATCCCAAAATTCTTGA 59.664 43.478 3.00 0.00 0.00 3.02
2471 4133 3.703052 CTCCCTCCATCCCAAAATTCTTG 59.297 47.826 0.00 0.00 0.00 3.02
2472 4134 3.337909 ACTCCCTCCATCCCAAAATTCTT 59.662 43.478 0.00 0.00 0.00 2.52
2473 4135 2.929043 ACTCCCTCCATCCCAAAATTCT 59.071 45.455 0.00 0.00 0.00 2.40
2474 4136 3.388552 ACTCCCTCCATCCCAAAATTC 57.611 47.619 0.00 0.00 0.00 2.17
2475 4137 5.487861 AATACTCCCTCCATCCCAAAATT 57.512 39.130 0.00 0.00 0.00 1.82
2476 4138 5.487861 AAATACTCCCTCCATCCCAAAAT 57.512 39.130 0.00 0.00 0.00 1.82
2477 4139 4.965283 AAATACTCCCTCCATCCCAAAA 57.035 40.909 0.00 0.00 0.00 2.44
2478 4140 5.043762 ACTAAATACTCCCTCCATCCCAAA 58.956 41.667 0.00 0.00 0.00 3.28
2479 4141 4.641868 ACTAAATACTCCCTCCATCCCAA 58.358 43.478 0.00 0.00 0.00 4.12
2480 4142 4.295905 ACTAAATACTCCCTCCATCCCA 57.704 45.455 0.00 0.00 0.00 4.37
2481 4143 5.369993 AGAAACTAAATACTCCCTCCATCCC 59.630 44.000 0.00 0.00 0.00 3.85
2482 4144 6.502074 AGAAACTAAATACTCCCTCCATCC 57.498 41.667 0.00 0.00 0.00 3.51
2483 4145 8.706521 AGTTAGAAACTAAATACTCCCTCCATC 58.293 37.037 0.00 0.00 40.69 3.51
2484 4146 8.625467 AGTTAGAAACTAAATACTCCCTCCAT 57.375 34.615 0.00 0.00 40.69 3.41
2485 4147 9.198475 CTAGTTAGAAACTAAATACTCCCTCCA 57.802 37.037 1.55 0.00 42.99 3.86
2486 4148 9.199645 ACTAGTTAGAAACTAAATACTCCCTCC 57.800 37.037 0.00 0.00 42.99 4.30
2969 4631 9.517609 GTAAGTAATCACAACACAGATACTAGG 57.482 37.037 0.00 0.00 0.00 3.02
3016 4685 7.792374 TCATATCACCTTCAAAGTATGCTTC 57.208 36.000 0.00 0.00 33.01 3.86
3040 4709 7.175119 GGCTAACTCAGACTCCAACTTTTTAAT 59.825 37.037 0.00 0.00 0.00 1.40
3099 4768 0.039527 CCAGTGCCGCACCTTTTAAC 60.040 55.000 19.96 0.00 34.49 2.01
3192 4861 2.551270 AGGGATGCAGGACTTACTTCA 58.449 47.619 0.00 0.00 0.00 3.02
3391 5063 2.009051 CACAGAGAACACACTGTTGCA 58.991 47.619 0.00 0.00 43.52 4.08
3410 5082 7.465173 CAAAATGCAGCAATAAATAACATGCA 58.535 30.769 0.00 0.00 45.22 3.96
3468 5140 3.157087 GGTCTGGCAAATTGAGGAAAGA 58.843 45.455 0.00 0.00 0.00 2.52
3538 5210 5.388654 AGTGAGGTCCAAAGTTCATTCATT 58.611 37.500 0.00 0.00 0.00 2.57
3950 5622 5.932303 ACATGTAAGCGAACTATTGTGTCTT 59.068 36.000 0.00 0.00 0.00 3.01
3964 5636 2.548057 ACAAAGTGACCACATGTAAGCG 59.452 45.455 0.00 0.00 33.73 4.68
4069 5741 2.688477 TCCTTCCAAAAAGGGTGCAAT 58.312 42.857 4.10 0.00 37.99 3.56
4279 5951 8.897752 ACTCAATAGCCTGTTCAGATTTTATTC 58.102 33.333 1.00 0.00 0.00 1.75
4307 5979 4.327680 GTGCCTACAGAAAGAAAGATGGT 58.672 43.478 0.00 0.00 0.00 3.55
4308 5980 3.691609 GGTGCCTACAGAAAGAAAGATGG 59.308 47.826 0.00 0.00 0.00 3.51
4351 6023 3.782523 AGGATGGCCAATGAAGTAGAAGA 59.217 43.478 10.96 0.00 36.29 2.87
4487 6159 0.179145 CGGCGTCTTCGTTACATCCT 60.179 55.000 0.00 0.00 39.49 3.24
4511 6183 3.955650 TCCCTCTTACTGAAAACCTCG 57.044 47.619 0.00 0.00 0.00 4.63
4577 6249 2.733956 TCCAAAACCCATGTATGAGGC 58.266 47.619 0.00 0.00 0.00 4.70
4886 6558 2.176045 CAGGTTAAATCCACCCAACCC 58.824 52.381 0.00 0.00 41.14 4.11
4921 6594 0.538057 CTCTTGAGCACCCAAAGGCA 60.538 55.000 0.00 0.00 36.11 4.75
4922 6595 0.538287 ACTCTTGAGCACCCAAAGGC 60.538 55.000 0.00 0.00 36.11 4.35
4934 6607 6.349611 GCATAGCCAAATTCAGAAACTCTTGA 60.350 38.462 0.00 0.00 0.00 3.02
4938 6615 4.346129 CGCATAGCCAAATTCAGAAACTC 58.654 43.478 0.00 0.00 0.00 3.01
4940 6617 3.119495 ACCGCATAGCCAAATTCAGAAAC 60.119 43.478 0.00 0.00 0.00 2.78
4957 6634 1.026182 GCACTGGATGATCAACCGCA 61.026 55.000 16.43 0.02 0.00 5.69
4960 6637 3.726607 CTCTAGCACTGGATGATCAACC 58.273 50.000 14.87 14.87 0.00 3.77
4962 6639 3.465742 GCTCTAGCACTGGATGATCAA 57.534 47.619 0.00 0.00 41.59 2.57
5059 6736 2.441750 AGAAGCAACCTAGACACCCAAA 59.558 45.455 0.00 0.00 0.00 3.28
5061 6738 1.347707 CAGAAGCAACCTAGACACCCA 59.652 52.381 0.00 0.00 0.00 4.51
5062 6739 1.623811 TCAGAAGCAACCTAGACACCC 59.376 52.381 0.00 0.00 0.00 4.61
5063 6740 3.330267 CTTCAGAAGCAACCTAGACACC 58.670 50.000 0.00 0.00 0.00 4.16
5183 6860 1.604278 GTTCTGGAGTTGTCTTGGCAC 59.396 52.381 0.00 0.00 0.00 5.01
5190 6867 2.036089 ACGAAGAGGTTCTGGAGTTGTC 59.964 50.000 0.00 0.00 0.00 3.18
5199 6876 2.486727 GGTGGGAAAACGAAGAGGTTCT 60.487 50.000 0.00 0.00 0.00 3.01
5271 6948 1.974265 TGAAGAACGCCATGGTTTCA 58.026 45.000 22.84 16.97 0.00 2.69
5272 6949 3.244976 CATTGAAGAACGCCATGGTTTC 58.755 45.455 14.67 15.80 0.00 2.78
5275 6952 1.176527 CCATTGAAGAACGCCATGGT 58.823 50.000 14.67 0.00 0.00 3.55
5334 7011 2.165998 GGAAAGATGAGCTTGCACCTT 58.834 47.619 0.00 0.00 36.80 3.50
5341 7026 3.356529 ACGGATTGGAAAGATGAGCTT 57.643 42.857 0.00 0.00 38.88 3.74
5358 7043 3.001330 GCTTCAGTCGGAATGAAATACGG 59.999 47.826 19.77 10.28 36.30 4.02
5361 7046 5.084818 TCTGCTTCAGTCGGAATGAAATA 57.915 39.130 19.77 11.59 36.30 1.40
5485 7238 6.987404 AGTGACTGATTCAAGATGAGATCATG 59.013 38.462 0.00 0.00 34.36 3.07
5525 7278 1.401018 GGCACCGCTGACAACAAATAC 60.401 52.381 0.00 0.00 0.00 1.89
5545 7298 0.035725 TCAGCTGGCAGATTGTGAGG 60.036 55.000 20.86 0.00 0.00 3.86
5550 7303 2.229675 TACGATCAGCTGGCAGATTG 57.770 50.000 20.86 15.44 31.92 2.67
5572 7325 0.673333 CCGAAGCCTGCACACACATA 60.673 55.000 0.00 0.00 0.00 2.29
5574 7327 2.591429 CCGAAGCCTGCACACACA 60.591 61.111 0.00 0.00 0.00 3.72
5575 7328 4.030452 GCCGAAGCCTGCACACAC 62.030 66.667 0.00 0.00 0.00 3.82


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

AutoCloner maintained by Alex Coulton.