Multiple sequence alignment - TraesCS7A01G530700

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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 TraesCS7A01G530700 chr7A 100.000 3788 0 0 1 3788 709739760 709735973 0.000000e+00 6996
1 TraesCS7A01G530700 chr7B 95.459 2026 80 8 804 2825 711068606 711066589 0.000000e+00 3221
2 TraesCS7A01G530700 chr7B 85.330 818 103 15 745 1553 710265505 710264696 0.000000e+00 830
3 TraesCS7A01G530700 chr7B 84.963 818 106 15 745 1553 710643021 710642212 0.000000e+00 813
4 TraesCS7A01G530700 chr7B 84.533 653 88 7 1028 1679 709595523 709596163 5.340000e-178 634
5 TraesCS7A01G530700 chr7B 90.845 426 30 7 2863 3281 711066499 711066076 2.550000e-156 562
6 TraesCS7A01G530700 chr7B 92.838 377 25 1 2449 2825 710040134 710039760 2.570000e-151 545
7 TraesCS7A01G530700 chr7B 92.838 377 25 1 2449 2825 710101732 710101358 2.570000e-151 545
8 TraesCS7A01G530700 chr7B 85.932 526 44 12 3277 3785 711065164 711064652 5.570000e-148 534
9 TraesCS7A01G530700 chr7B 89.920 377 34 4 1682 2055 709596748 709597123 2.050000e-132 483
10 TraesCS7A01G530700 chr7B 80.776 593 57 22 2944 3489 710039663 710039081 9.790000e-111 411
11 TraesCS7A01G530700 chr7B 80.471 594 58 22 2944 3489 710101261 710100678 5.890000e-108 401
12 TraesCS7A01G530700 chr7B 87.464 343 35 1 2052 2394 709598637 709598971 4.590000e-104 388
13 TraesCS7A01G530700 chr7B 84.383 397 48 9 3100 3484 710443651 710443257 9.930000e-101 377
14 TraesCS7A01G530700 chr7B 83.375 397 52 9 3100 3484 710398407 710398013 4.650000e-94 355
15 TraesCS7A01G530700 chr7B 82.587 402 44 12 3100 3486 709898348 709897958 7.840000e-87 331
16 TraesCS7A01G530700 chr7B 90.377 239 18 3 2453 2686 709898726 709898488 3.670000e-80 309
17 TraesCS7A01G530700 chr7B 88.716 257 19 7 2449 2698 710444026 710443773 4.750000e-79 305
18 TraesCS7A01G530700 chr7B 87.109 256 33 0 1298 1553 710040382 710040127 1.330000e-74 291
19 TraesCS7A01G530700 chr7B 87.109 256 33 0 1298 1553 710101980 710101725 1.330000e-74 291
20 TraesCS7A01G530700 chr7B 89.381 226 15 2 2457 2682 710398742 710398526 3.730000e-70 276
21 TraesCS7A01G530700 chr7B 96.923 65 1 1 2752 2816 709898467 709898404 1.440000e-19 108
22 TraesCS7A01G530700 chr7B 95.385 65 2 1 2752 2816 710443770 710443707 6.690000e-18 102
23 TraesCS7A01G530700 chr7D 93.731 2026 115 8 804 2825 617023803 617021786 0.000000e+00 3027
24 TraesCS7A01G530700 chr7D 89.022 1002 103 7 908 1906 616567550 616566553 0.000000e+00 1234
25 TraesCS7A01G530700 chr7D 86.589 1029 120 12 819 1839 616777198 616776180 0.000000e+00 1120
26 TraesCS7A01G530700 chr7D 87.000 600 35 13 2958 3518 617021630 617021035 1.480000e-178 636
27 TraesCS7A01G530700 chr7D 88.845 511 46 5 2861 3363 616776166 616775659 5.380000e-173 617
28 TraesCS7A01G530700 chr7D 93.750 288 15 1 374 658 617024165 617023878 2.700000e-116 429
29 TraesCS7A01G530700 chr7D 91.093 247 7 6 120 351 617024483 617024237 1.700000e-83 320
30 TraesCS7A01G530700 chr7D 82.437 279 22 14 3517 3785 617020873 617020612 6.370000e-53 219
31 TraesCS7A01G530700 chr7D 85.294 136 13 5 2142 2277 616442279 616442407 2.370000e-27 134
32 TraesCS7A01G530700 chr7D 91.765 85 5 2 2440 2523 616451992 616452075 2.390000e-22 117
33 TraesCS7A01G530700 chr7D 82.645 121 16 5 3368 3485 616775629 616775511 6.690000e-18 102
34 TraesCS7A01G530700 chr6D 91.860 86 6 1 267 351 468893781 468893866 6.650000e-23 119
35 TraesCS7A01G530700 chr3D 92.405 79 6 0 273 351 20623754 20623676 3.090000e-21 113


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 TraesCS7A01G530700 chr7A 709735973 709739760 3787 True 6996.000000 6996 100.000000 1 3788 1 chr7A.!!$R1 3787
1 TraesCS7A01G530700 chr7B 711064652 711068606 3954 True 1439.000000 3221 90.745333 804 3785 3 chr7B.!!$R8 2981
2 TraesCS7A01G530700 chr7B 710264696 710265505 809 True 830.000000 830 85.330000 745 1553 1 chr7B.!!$R1 808
3 TraesCS7A01G530700 chr7B 710642212 710643021 809 True 813.000000 813 84.963000 745 1553 1 chr7B.!!$R2 808
4 TraesCS7A01G530700 chr7B 709595523 709598971 3448 False 501.666667 634 87.305667 1028 2394 3 chr7B.!!$F1 1366
5 TraesCS7A01G530700 chr7B 710039081 710040382 1301 True 415.666667 545 86.907667 1298 3489 3 chr7B.!!$R4 2191
6 TraesCS7A01G530700 chr7B 710100678 710101980 1302 True 412.333333 545 86.806000 1298 3489 3 chr7B.!!$R5 2191
7 TraesCS7A01G530700 chr7B 710398013 710398742 729 True 315.500000 355 86.378000 2457 3484 2 chr7B.!!$R6 1027
8 TraesCS7A01G530700 chr7B 710443257 710444026 769 True 261.333333 377 89.494667 2449 3484 3 chr7B.!!$R7 1035
9 TraesCS7A01G530700 chr7B 709897958 709898726 768 True 249.333333 331 89.962333 2453 3486 3 chr7B.!!$R3 1033
10 TraesCS7A01G530700 chr7D 616566553 616567550 997 True 1234.000000 1234 89.022000 908 1906 1 chr7D.!!$R1 998
11 TraesCS7A01G530700 chr7D 617020612 617024483 3871 True 926.200000 3027 89.602200 120 3785 5 chr7D.!!$R3 3665
12 TraesCS7A01G530700 chr7D 616775511 616777198 1687 True 613.000000 1120 86.026333 819 3485 3 chr7D.!!$R2 2666

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
142 143 0.107017 AAGTTGATCTGGGCCATCCG 60.107 55.0 6.72 0.0 38.76 4.18 F
759 827 0.178992 CTGCCTGAAACCTTGGACCA 60.179 55.0 0.00 0.0 0.00 4.02 F
1347 1472 0.468226 TCACCTTCTCAACTGCCGTT 59.532 50.0 0.00 0.0 0.00 4.44 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2100 2226 0.034767 CCAGCTCAAATGCCTCCTCA 60.035 55.000 0.0 0.0 0.0 3.86 R
2178 2304 1.221840 CCTATGTGTCCGGCAAGCT 59.778 57.895 0.0 0.0 0.0 3.74 R
3274 4608 0.995024 AGCACCAGGGATAGCAAACT 59.005 50.000 0.0 0.0 0.0 2.66 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
20 21 3.191078 CTATGCTCTTGTTCCTCCCTG 57.809 52.381 0.00 0.00 0.00 4.45
21 22 1.366319 ATGCTCTTGTTCCTCCCTGT 58.634 50.000 0.00 0.00 0.00 4.00
22 23 0.687354 TGCTCTTGTTCCTCCCTGTC 59.313 55.000 0.00 0.00 0.00 3.51
23 24 0.980423 GCTCTTGTTCCTCCCTGTCT 59.020 55.000 0.00 0.00 0.00 3.41
24 25 2.180276 GCTCTTGTTCCTCCCTGTCTA 58.820 52.381 0.00 0.00 0.00 2.59
25 26 2.167487 GCTCTTGTTCCTCCCTGTCTAG 59.833 54.545 0.00 0.00 0.00 2.43
26 27 3.702792 CTCTTGTTCCTCCCTGTCTAGA 58.297 50.000 0.00 0.00 0.00 2.43
27 28 3.432378 TCTTGTTCCTCCCTGTCTAGAC 58.568 50.000 16.32 16.32 0.00 2.59
28 29 3.076182 TCTTGTTCCTCCCTGTCTAGACT 59.924 47.826 23.01 0.00 0.00 3.24
29 30 2.808919 TGTTCCTCCCTGTCTAGACTG 58.191 52.381 23.01 21.33 0.00 3.51
30 31 2.104170 GTTCCTCCCTGTCTAGACTGG 58.896 57.143 31.81 31.81 46.26 4.00
41 42 4.923415 TGTCTAGACTGGACAGATTCTCA 58.077 43.478 23.01 0.00 38.57 3.27
42 43 5.325239 TGTCTAGACTGGACAGATTCTCAA 58.675 41.667 23.01 0.00 38.57 3.02
43 44 5.775195 TGTCTAGACTGGACAGATTCTCAAA 59.225 40.000 23.01 0.00 38.57 2.69
44 45 6.267699 TGTCTAGACTGGACAGATTCTCAAAA 59.732 38.462 23.01 0.00 38.57 2.44
45 46 7.155328 GTCTAGACTGGACAGATTCTCAAAAA 58.845 38.462 15.91 0.00 34.23 1.94
46 47 7.330700 GTCTAGACTGGACAGATTCTCAAAAAG 59.669 40.741 15.91 0.00 34.23 2.27
47 48 5.312079 AGACTGGACAGATTCTCAAAAAGG 58.688 41.667 6.29 0.00 0.00 3.11
48 49 5.072329 AGACTGGACAGATTCTCAAAAAGGA 59.928 40.000 6.29 0.00 0.00 3.36
49 50 5.885465 ACTGGACAGATTCTCAAAAAGGAT 58.115 37.500 6.29 0.00 0.00 3.24
50 51 7.020827 ACTGGACAGATTCTCAAAAAGGATA 57.979 36.000 6.29 0.00 0.00 2.59
51 52 7.461749 ACTGGACAGATTCTCAAAAAGGATAA 58.538 34.615 6.29 0.00 0.00 1.75
52 53 7.944554 ACTGGACAGATTCTCAAAAAGGATAAA 59.055 33.333 6.29 0.00 0.00 1.40
53 54 8.704849 TGGACAGATTCTCAAAAAGGATAAAA 57.295 30.769 0.00 0.00 0.00 1.52
54 55 9.142014 TGGACAGATTCTCAAAAAGGATAAAAA 57.858 29.630 0.00 0.00 0.00 1.94
79 80 7.741554 AAATCTAGACTGGACAATTCCTAGT 57.258 36.000 0.00 0.00 43.31 2.57
80 81 7.741554 AATCTAGACTGGACAATTCCTAGTT 57.258 36.000 0.00 0.00 43.31 2.24
81 82 8.840200 AATCTAGACTGGACAATTCCTAGTTA 57.160 34.615 0.00 0.00 43.31 2.24
82 83 7.642082 TCTAGACTGGACAATTCCTAGTTAC 57.358 40.000 0.00 0.00 43.31 2.50
83 84 5.678955 AGACTGGACAATTCCTAGTTACC 57.321 43.478 0.00 0.00 43.31 2.85
84 85 5.342866 AGACTGGACAATTCCTAGTTACCT 58.657 41.667 0.00 0.00 43.31 3.08
85 86 5.422650 AGACTGGACAATTCCTAGTTACCTC 59.577 44.000 0.00 0.00 43.31 3.85
86 87 4.470304 ACTGGACAATTCCTAGTTACCTCC 59.530 45.833 0.00 0.00 43.31 4.30
87 88 4.431378 TGGACAATTCCTAGTTACCTCCA 58.569 43.478 0.00 0.00 43.31 3.86
88 89 4.847512 TGGACAATTCCTAGTTACCTCCAA 59.152 41.667 0.00 0.00 43.31 3.53
89 90 5.183969 GGACAATTCCTAGTTACCTCCAAC 58.816 45.833 0.00 0.00 39.13 3.77
90 91 5.280317 GGACAATTCCTAGTTACCTCCAACA 60.280 44.000 0.00 0.00 39.13 3.33
91 92 6.388619 ACAATTCCTAGTTACCTCCAACAT 57.611 37.500 0.00 0.00 0.00 2.71
92 93 7.365295 GGACAATTCCTAGTTACCTCCAACATA 60.365 40.741 0.00 0.00 39.13 2.29
93 94 7.924541 ACAATTCCTAGTTACCTCCAACATAA 58.075 34.615 0.00 0.00 0.00 1.90
94 95 8.387813 ACAATTCCTAGTTACCTCCAACATAAA 58.612 33.333 0.00 0.00 0.00 1.40
95 96 9.408648 CAATTCCTAGTTACCTCCAACATAAAT 57.591 33.333 0.00 0.00 0.00 1.40
98 99 9.895138 TTCCTAGTTACCTCCAACATAAATAAC 57.105 33.333 0.00 0.00 0.00 1.89
99 100 9.049050 TCCTAGTTACCTCCAACATAAATAACA 57.951 33.333 0.00 0.00 0.00 2.41
100 101 9.326413 CCTAGTTACCTCCAACATAAATAACAG 57.674 37.037 0.00 0.00 0.00 3.16
103 104 9.802039 AGTTACCTCCAACATAAATAACAGAAA 57.198 29.630 0.00 0.00 0.00 2.52
118 119 8.409358 AATAACAGAAAATTAAGCTCCACTGT 57.591 30.769 0.00 0.00 38.67 3.55
142 143 0.107017 AAGTTGATCTGGGCCATCCG 60.107 55.000 6.72 0.00 38.76 4.18
145 146 1.561769 TTGATCTGGGCCATCCGTGT 61.562 55.000 6.72 0.00 38.76 4.49
185 186 1.620413 CGGCCGTTCGTTACCTGAAC 61.620 60.000 19.50 0.00 41.75 3.18
192 193 4.707791 GTTACCTGAACGGGGGTG 57.292 61.111 4.64 0.00 37.07 4.61
193 194 2.060370 GTTACCTGAACGGGGGTGA 58.940 57.895 4.64 0.00 37.07 4.02
373 412 4.171103 GGTAGCGGGCCACGGATT 62.171 66.667 4.39 0.00 44.51 3.01
375 414 3.078196 TAGCGGGCCACGGATTGA 61.078 61.111 4.39 0.00 44.51 2.57
484 549 3.124636 CACCTTGGTAACTCGATTTTCCG 59.875 47.826 6.67 0.00 37.61 4.30
485 550 3.007182 ACCTTGGTAACTCGATTTTCCGA 59.993 43.478 6.67 4.29 37.03 4.55
490 555 6.211587 TGGTAACTCGATTTTCCGATTCTA 57.788 37.500 6.67 0.00 37.96 2.10
499 564 6.765989 TCGATTTTCCGATTCTATTTCCATGT 59.234 34.615 0.00 0.00 33.14 3.21
508 573 7.429633 CGATTCTATTTCCATGTCTGTCTAGT 58.570 38.462 0.00 0.00 0.00 2.57
529 594 3.592898 TCGTGCATATCAACTCAGTGT 57.407 42.857 0.00 0.00 0.00 3.55
630 698 2.872858 GGATAGTGGGCTTTCGAATGTC 59.127 50.000 12.12 9.74 0.00 3.06
631 699 2.004583 TAGTGGGCTTTCGAATGTCG 57.995 50.000 12.12 0.00 42.10 4.35
646 714 1.025812 TGTCGGGAAAACAAATGCGT 58.974 45.000 0.00 0.00 0.00 5.24
658 726 4.410492 ACAAATGCGTCTTCAACTGATC 57.590 40.909 0.00 0.00 0.00 2.92
659 727 3.814842 ACAAATGCGTCTTCAACTGATCA 59.185 39.130 0.00 0.00 0.00 2.92
660 728 4.083643 ACAAATGCGTCTTCAACTGATCAG 60.084 41.667 21.37 21.37 0.00 2.90
661 729 2.084610 TGCGTCTTCAACTGATCAGG 57.915 50.000 26.08 9.99 0.00 3.86
662 730 1.618343 TGCGTCTTCAACTGATCAGGA 59.382 47.619 26.08 12.22 0.00 3.86
663 731 2.234661 TGCGTCTTCAACTGATCAGGAT 59.765 45.455 26.08 12.21 0.00 3.24
664 732 2.863137 GCGTCTTCAACTGATCAGGATC 59.137 50.000 26.08 8.50 38.29 3.36
665 733 3.452474 CGTCTTCAACTGATCAGGATCC 58.548 50.000 26.08 2.48 37.02 3.36
666 734 3.131933 CGTCTTCAACTGATCAGGATCCT 59.868 47.826 26.08 9.02 37.02 3.24
667 735 4.382470 CGTCTTCAACTGATCAGGATCCTT 60.382 45.833 26.08 8.59 37.02 3.36
668 736 5.163509 CGTCTTCAACTGATCAGGATCCTTA 60.164 44.000 26.08 4.35 37.02 2.69
669 737 6.628175 CGTCTTCAACTGATCAGGATCCTTAA 60.628 42.308 26.08 3.42 37.02 1.85
670 738 7.278875 GTCTTCAACTGATCAGGATCCTTAAT 58.721 38.462 26.08 8.94 37.02 1.40
671 739 7.440856 GTCTTCAACTGATCAGGATCCTTAATC 59.559 40.741 26.08 17.85 37.02 1.75
672 740 6.813293 TCAACTGATCAGGATCCTTAATCA 57.187 37.500 26.08 25.11 37.02 2.57
673 741 7.384524 TCAACTGATCAGGATCCTTAATCAT 57.615 36.000 26.19 15.87 37.02 2.45
674 742 7.222161 TCAACTGATCAGGATCCTTAATCATG 58.778 38.462 26.19 22.92 45.46 3.07
675 743 6.760440 ACTGATCAGGATCCTTAATCATGT 57.240 37.500 26.19 22.70 44.62 3.21
676 744 7.146715 ACTGATCAGGATCCTTAATCATGTT 57.853 36.000 26.19 16.11 44.62 2.71
677 745 8.267620 ACTGATCAGGATCCTTAATCATGTTA 57.732 34.615 26.19 11.44 44.62 2.41
678 746 8.373981 ACTGATCAGGATCCTTAATCATGTTAG 58.626 37.037 26.19 19.46 44.62 2.34
679 747 8.267620 TGATCAGGATCCTTAATCATGTTAGT 57.732 34.615 23.86 0.00 44.62 2.24
680 748 8.152898 TGATCAGGATCCTTAATCATGTTAGTG 58.847 37.037 23.86 6.93 44.62 2.74
681 749 6.830912 TCAGGATCCTTAATCATGTTAGTGG 58.169 40.000 13.00 0.00 44.62 4.00
682 750 6.386927 TCAGGATCCTTAATCATGTTAGTGGT 59.613 38.462 13.00 0.00 44.62 4.16
683 751 6.708054 CAGGATCCTTAATCATGTTAGTGGTC 59.292 42.308 13.00 0.00 40.49 4.02
684 752 6.386927 AGGATCCTTAATCATGTTAGTGGTCA 59.613 38.462 9.02 0.00 35.96 4.02
685 753 7.072961 AGGATCCTTAATCATGTTAGTGGTCAT 59.927 37.037 9.02 0.00 35.96 3.06
686 754 7.721399 GGATCCTTAATCATGTTAGTGGTCATT 59.279 37.037 3.84 0.00 35.96 2.57
687 755 9.125026 GATCCTTAATCATGTTAGTGGTCATTT 57.875 33.333 0.00 0.00 34.26 2.32
689 757 9.613428 TCCTTAATCATGTTAGTGGTCATTTAG 57.387 33.333 0.00 0.00 0.00 1.85
690 758 9.613428 CCTTAATCATGTTAGTGGTCATTTAGA 57.387 33.333 0.00 0.00 0.00 2.10
694 762 9.520515 AATCATGTTAGTGGTCATTTAGAAAGT 57.479 29.630 0.00 0.00 0.00 2.66
695 763 8.918202 TCATGTTAGTGGTCATTTAGAAAGTT 57.082 30.769 0.00 0.00 0.00 2.66
696 764 9.349713 TCATGTTAGTGGTCATTTAGAAAGTTT 57.650 29.630 0.00 0.00 0.00 2.66
697 765 9.612620 CATGTTAGTGGTCATTTAGAAAGTTTC 57.387 33.333 7.57 7.57 0.00 2.78
698 766 8.740123 TGTTAGTGGTCATTTAGAAAGTTTCA 57.260 30.769 17.65 1.42 0.00 2.69
699 767 9.349713 TGTTAGTGGTCATTTAGAAAGTTTCAT 57.650 29.630 17.65 5.73 0.00 2.57
716 784 9.830975 AAAGTTTCATTTTTATAGGTTTGCAGT 57.169 25.926 0.00 0.00 0.00 4.40
717 785 9.830975 AAGTTTCATTTTTATAGGTTTGCAGTT 57.169 25.926 0.00 0.00 0.00 3.16
718 786 9.260002 AGTTTCATTTTTATAGGTTTGCAGTTG 57.740 29.630 0.00 0.00 0.00 3.16
719 787 7.650834 TTCATTTTTATAGGTTTGCAGTTGC 57.349 32.000 0.00 0.00 42.50 4.17
732 800 3.736530 GCAGTTGCACTCTGATGTAAG 57.263 47.619 18.56 0.00 41.59 2.34
733 801 3.329386 GCAGTTGCACTCTGATGTAAGA 58.671 45.455 18.56 0.00 41.59 2.10
735 803 4.814147 CAGTTGCACTCTGATGTAAGAGA 58.186 43.478 11.34 0.00 45.59 3.10
736 804 4.863689 CAGTTGCACTCTGATGTAAGAGAG 59.136 45.833 11.34 0.00 45.59 3.20
737 805 4.769488 AGTTGCACTCTGATGTAAGAGAGA 59.231 41.667 8.16 0.00 45.59 3.10
738 806 4.979943 TGCACTCTGATGTAAGAGAGAG 57.020 45.455 8.16 0.00 45.59 3.20
739 807 3.698539 TGCACTCTGATGTAAGAGAGAGG 59.301 47.826 8.16 0.00 45.59 3.69
740 808 3.490761 GCACTCTGATGTAAGAGAGAGGC 60.491 52.174 8.16 0.00 45.59 4.70
741 809 3.953612 CACTCTGATGTAAGAGAGAGGCT 59.046 47.826 8.16 0.00 45.59 4.58
742 810 3.953612 ACTCTGATGTAAGAGAGAGGCTG 59.046 47.826 8.16 0.00 45.59 4.85
743 811 2.692557 TCTGATGTAAGAGAGAGGCTGC 59.307 50.000 0.00 0.00 0.00 5.25
759 827 0.178992 CTGCCTGAAACCTTGGACCA 60.179 55.000 0.00 0.00 0.00 4.02
768 836 4.534500 TGAAACCTTGGACCATCTTAGCTA 59.466 41.667 0.00 0.00 0.00 3.32
787 855 6.566197 AGCTAGCATTATAGGTGATTTTGC 57.434 37.500 18.83 0.00 32.42 3.68
952 1071 3.123273 AGGTATTAGTGGTGGGCTGATT 58.877 45.455 0.00 0.00 0.00 2.57
971 1090 1.938585 TCTCTGGGAGAATGGAACGT 58.061 50.000 0.00 0.00 35.59 3.99
975 1094 4.122776 CTCTGGGAGAATGGAACGTAATG 58.877 47.826 0.00 0.00 0.00 1.90
1269 1394 4.753662 TCTAGCACCGGCCGACCT 62.754 66.667 30.73 20.97 42.56 3.85
1338 1463 1.339055 CCGAATGCCTTCACCTTCTCA 60.339 52.381 2.57 0.00 0.00 3.27
1347 1472 0.468226 TCACCTTCTCAACTGCCGTT 59.532 50.000 0.00 0.00 0.00 4.44
1614 1739 2.031683 ACTTTTTGCCGAGTTCAGAACG 59.968 45.455 7.68 0.00 36.23 3.95
1713 1839 1.180456 TTGGCAAGTCTGTGCATGGG 61.180 55.000 0.00 0.00 46.81 4.00
1758 1884 1.882623 TGCAATGGCGTGATTGTTGTA 59.117 42.857 9.40 0.00 45.35 2.41
1760 1886 2.731968 GCAATGGCGTGATTGTTGTAGG 60.732 50.000 9.40 0.00 35.98 3.18
1812 1938 7.066766 GGATTCTACGAGTACTCAAGAAAGGTA 59.933 40.741 28.12 17.52 35.92 3.08
1934 2060 2.819019 AGATGATCGATCGAGATGTGCT 59.181 45.455 23.84 12.17 36.04 4.40
2064 2190 3.252627 ATGCGCCAGCCACTACACA 62.253 57.895 4.18 0.00 44.33 3.72
2337 2463 2.495669 TGCTGTATGGTCGAACATGAGA 59.504 45.455 26.11 2.85 32.39 3.27
2358 2484 2.186076 CGACGAGGCATACAGAAAGAC 58.814 52.381 0.00 0.00 0.00 3.01
2385 2511 3.696051 GGTGCAGCTGGATTGAGATAAAA 59.304 43.478 17.12 0.00 0.00 1.52
2394 2520 6.073548 GCTGGATTGAGATAAAAGACATACCG 60.074 42.308 0.00 0.00 0.00 4.02
2618 2833 1.069513 GGGGTTTGGTTTGCTGGTTAC 59.930 52.381 0.00 0.00 0.00 2.50
2667 2882 0.035630 AGAACCTGAGGATGTGCTGC 60.036 55.000 4.99 0.00 0.00 5.25
2712 2933 5.276461 TCATAAGTGACATTATGGAGCGT 57.724 39.130 11.88 0.00 41.49 5.07
2801 3022 3.152341 ACTGGTGATTCAAGGCTGAAAG 58.848 45.455 0.00 0.00 44.64 2.62
2825 3046 5.576384 GCAAAGTGATTGTCAACTTTGTGAA 59.424 36.000 21.38 0.00 41.69 3.18
2826 3047 6.256321 GCAAAGTGATTGTCAACTTTGTGAAT 59.744 34.615 21.38 0.00 41.69 2.57
2827 3048 7.201548 GCAAAGTGATTGTCAACTTTGTGAATT 60.202 33.333 21.38 0.00 41.69 2.17
2828 3049 7.760131 AAGTGATTGTCAACTTTGTGAATTG 57.240 32.000 0.00 0.00 0.00 2.32
2829 3050 6.866480 AGTGATTGTCAACTTTGTGAATTGT 58.134 32.000 0.00 0.00 0.00 2.71
2830 3051 6.753279 AGTGATTGTCAACTTTGTGAATTGTG 59.247 34.615 0.00 0.00 0.00 3.33
2831 3052 6.751425 GTGATTGTCAACTTTGTGAATTGTGA 59.249 34.615 0.00 0.00 0.00 3.58
2832 3053 7.436080 GTGATTGTCAACTTTGTGAATTGTGAT 59.564 33.333 0.00 0.00 0.00 3.06
2833 3054 8.628280 TGATTGTCAACTTTGTGAATTGTGATA 58.372 29.630 0.00 0.00 0.00 2.15
2834 3055 8.801715 ATTGTCAACTTTGTGAATTGTGATAC 57.198 30.769 0.00 0.00 0.00 2.24
2835 3056 7.326968 TGTCAACTTTGTGAATTGTGATACA 57.673 32.000 0.00 0.00 0.00 2.29
2836 3057 7.416817 TGTCAACTTTGTGAATTGTGATACAG 58.583 34.615 0.00 0.00 0.00 2.74
2837 3058 7.281999 TGTCAACTTTGTGAATTGTGATACAGA 59.718 33.333 0.00 0.00 0.00 3.41
2838 3059 7.800380 GTCAACTTTGTGAATTGTGATACAGAG 59.200 37.037 0.00 0.00 33.13 3.35
2850 3074 5.441500 TGTGATACAGAGGGAAAACAACAA 58.558 37.500 0.00 0.00 0.00 2.83
2851 3075 5.888724 TGTGATACAGAGGGAAAACAACAAA 59.111 36.000 0.00 0.00 0.00 2.83
2859 3083 6.698766 CAGAGGGAAAACAACAAATCTTTGAG 59.301 38.462 9.53 4.47 40.55 3.02
2910 3195 2.383298 AAATGTTCGAGTGCACAACG 57.617 45.000 21.04 22.56 0.00 4.10
2970 3856 6.600822 AGATTTTGTTGACCATAGTCTCCATG 59.399 38.462 0.00 0.00 43.91 3.66
2976 3862 2.990195 ACCATAGTCTCCATGGGCATA 58.010 47.619 13.02 0.57 46.14 3.14
3003 3889 7.198390 ACTTATCACATTTGCACAATATGAGC 58.802 34.615 8.04 0.00 34.50 4.26
3005 3891 3.130869 TCACATTTGCACAATATGAGCCC 59.869 43.478 10.47 0.00 32.90 5.19
3012 3898 3.181455 TGCACAATATGAGCCCGACTTAT 60.181 43.478 0.00 0.00 32.90 1.73
3159 4426 3.517100 ACAGTGTCCAGCATGAGTATCTT 59.483 43.478 0.00 0.00 39.69 2.40
3268 4602 5.946377 AGGAACTTACATGCCTTTTTCTAGG 59.054 40.000 0.00 0.00 34.32 3.02
3274 4608 5.499004 ACATGCCTTTTTCTAGGTCTGTA 57.501 39.130 0.00 0.00 37.63 2.74
3281 4615 5.998363 CCTTTTTCTAGGTCTGTAGTTTGCT 59.002 40.000 0.00 0.00 0.00 3.91
3295 5607 2.576191 AGTTTGCTATCCCTGGTGCTAA 59.424 45.455 0.00 0.00 0.00 3.09
3325 5732 3.421919 TGGTCATGCTCTGTTGAATCA 57.578 42.857 0.00 0.00 0.00 2.57
3545 6439 7.663081 ACCGTATATCATTTGAGCATGAAGATT 59.337 33.333 0.00 0.00 36.74 2.40
3552 6446 7.832769 TCATTTGAGCATGAAGATTCATTCAA 58.167 30.769 14.39 14.39 45.13 2.69
3568 6469 6.564709 TCATTCAAATGAACAAGGAGTCTG 57.435 37.500 2.97 0.00 42.11 3.51
3570 6471 6.429078 TCATTCAAATGAACAAGGAGTCTGAG 59.571 38.462 2.97 0.00 42.11 3.35
3573 6474 0.687354 TGAACAAGGAGTCTGAGCCC 59.313 55.000 0.00 0.00 0.00 5.19
3586 6487 1.228245 GAGCCCTGTGCCTTGTGAA 60.228 57.895 0.00 0.00 42.71 3.18
3593 6494 2.163010 CCTGTGCCTTGTGAATGATGTC 59.837 50.000 0.00 0.00 0.00 3.06
3594 6495 2.815503 CTGTGCCTTGTGAATGATGTCA 59.184 45.455 0.00 0.00 0.00 3.58
3595 6496 3.423749 TGTGCCTTGTGAATGATGTCAT 58.576 40.909 0.00 0.00 38.41 3.06
3596 6497 4.587891 TGTGCCTTGTGAATGATGTCATA 58.412 39.130 0.00 0.00 35.10 2.15
3597 6498 5.195185 TGTGCCTTGTGAATGATGTCATAT 58.805 37.500 0.00 0.00 35.10 1.78
3598 6499 5.653330 TGTGCCTTGTGAATGATGTCATATT 59.347 36.000 0.00 0.00 35.10 1.28
3599 6500 5.975344 GTGCCTTGTGAATGATGTCATATTG 59.025 40.000 0.00 0.00 35.10 1.90
3600 6501 5.653330 TGCCTTGTGAATGATGTCATATTGT 59.347 36.000 0.00 0.00 35.10 2.71
3691 6592 6.825721 GTCCAACTAATCCTGATGTCTCATTT 59.174 38.462 0.00 0.00 0.00 2.32
3706 6607 9.683069 GATGTCTCATTTTGTGATTAGTTGTTT 57.317 29.630 0.00 0.00 35.97 2.83
3707 6608 9.683069 ATGTCTCATTTTGTGATTAGTTGTTTC 57.317 29.630 0.00 0.00 35.97 2.78
3718 6619 7.065324 TGTGATTAGTTGTTTCGATGGGAATAC 59.935 37.037 0.00 0.00 33.85 1.89
3748 6652 7.633193 TTTTTCCTTGAGCTTAGTTACACAA 57.367 32.000 0.00 0.00 0.00 3.33
3750 6654 7.817418 TTTCCTTGAGCTTAGTTACACAATT 57.183 32.000 0.00 0.00 0.00 2.32
3751 6655 7.817418 TTCCTTGAGCTTAGTTACACAATTT 57.183 32.000 0.00 0.00 0.00 1.82
3752 6656 7.202016 TCCTTGAGCTTAGTTACACAATTTG 57.798 36.000 0.00 0.00 0.00 2.32
3755 6659 6.573664 TGAGCTTAGTTACACAATTTGCAT 57.426 33.333 0.00 0.00 0.00 3.96
3756 6660 6.380995 TGAGCTTAGTTACACAATTTGCATG 58.619 36.000 0.00 0.00 0.00 4.06
3757 6661 6.206438 TGAGCTTAGTTACACAATTTGCATGA 59.794 34.615 0.00 0.00 0.00 3.07
3758 6662 6.980593 AGCTTAGTTACACAATTTGCATGAA 58.019 32.000 0.00 0.00 0.00 2.57
3759 6663 6.863126 AGCTTAGTTACACAATTTGCATGAAC 59.137 34.615 0.00 0.00 0.00 3.18
3768 6672 7.604549 ACACAATTTGCATGAACATAATCTCA 58.395 30.769 0.00 0.00 0.00 3.27
3772 6676 9.308318 CAATTTGCATGAACATAATCTCAATCA 57.692 29.630 0.00 0.00 0.00 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.503356 ACAGGGAGGAACAAGAGCATAG 59.497 50.000 0.00 0.00 0.00 2.23
2 3 1.280421 GACAGGGAGGAACAAGAGCAT 59.720 52.381 0.00 0.00 0.00 3.79
3 4 0.687354 GACAGGGAGGAACAAGAGCA 59.313 55.000 0.00 0.00 0.00 4.26
4 5 0.980423 AGACAGGGAGGAACAAGAGC 59.020 55.000 0.00 0.00 0.00 4.09
5 6 3.445805 GTCTAGACAGGGAGGAACAAGAG 59.554 52.174 18.20 0.00 0.00 2.85
6 7 3.076182 AGTCTAGACAGGGAGGAACAAGA 59.924 47.826 24.44 0.00 0.00 3.02
7 8 3.194542 CAGTCTAGACAGGGAGGAACAAG 59.805 52.174 24.44 0.00 0.00 3.16
8 9 3.165875 CAGTCTAGACAGGGAGGAACAA 58.834 50.000 24.44 0.00 0.00 2.83
9 10 2.557676 CCAGTCTAGACAGGGAGGAACA 60.558 54.545 23.27 0.00 34.70 3.18
10 11 2.104170 CCAGTCTAGACAGGGAGGAAC 58.896 57.143 23.27 0.00 34.70 3.62
11 12 2.000803 TCCAGTCTAGACAGGGAGGAA 58.999 52.381 28.35 10.78 38.38 3.36
12 13 1.285373 GTCCAGTCTAGACAGGGAGGA 59.715 57.143 28.35 20.38 38.38 3.71
13 14 1.006043 TGTCCAGTCTAGACAGGGAGG 59.994 57.143 28.35 18.78 39.29 4.30
14 15 2.516227 TGTCCAGTCTAGACAGGGAG 57.484 55.000 28.35 11.60 39.29 4.30
19 20 4.923415 TGAGAATCTGTCCAGTCTAGACA 58.077 43.478 24.44 3.64 41.84 3.41
20 21 5.906113 TTGAGAATCTGTCCAGTCTAGAC 57.094 43.478 15.41 15.41 34.92 2.59
21 22 6.918067 TTTTGAGAATCTGTCCAGTCTAGA 57.082 37.500 0.00 0.00 34.92 2.43
22 23 6.593382 CCTTTTTGAGAATCTGTCCAGTCTAG 59.407 42.308 0.00 0.00 34.92 2.43
23 24 6.270000 TCCTTTTTGAGAATCTGTCCAGTCTA 59.730 38.462 0.00 0.00 34.92 2.59
24 25 5.072329 TCCTTTTTGAGAATCTGTCCAGTCT 59.928 40.000 0.00 0.00 34.92 3.24
25 26 5.308825 TCCTTTTTGAGAATCTGTCCAGTC 58.691 41.667 0.00 0.00 34.92 3.51
26 27 5.310409 TCCTTTTTGAGAATCTGTCCAGT 57.690 39.130 0.00 0.00 34.92 4.00
27 28 7.928307 TTATCCTTTTTGAGAATCTGTCCAG 57.072 36.000 0.00 0.00 34.92 3.86
28 29 8.704849 TTTTATCCTTTTTGAGAATCTGTCCA 57.295 30.769 0.00 0.00 34.92 4.02
92 93 8.860088 ACAGTGGAGCTTAATTTTCTGTTATTT 58.140 29.630 0.00 0.00 32.15 1.40
93 94 8.409358 ACAGTGGAGCTTAATTTTCTGTTATT 57.591 30.769 0.00 0.00 32.15 1.40
94 95 9.515226 TTACAGTGGAGCTTAATTTTCTGTTAT 57.485 29.630 0.00 0.00 36.52 1.89
95 96 8.780249 GTTACAGTGGAGCTTAATTTTCTGTTA 58.220 33.333 0.00 0.00 36.52 2.41
96 97 7.502561 AGTTACAGTGGAGCTTAATTTTCTGTT 59.497 33.333 0.00 0.00 36.52 3.16
97 98 6.998673 AGTTACAGTGGAGCTTAATTTTCTGT 59.001 34.615 0.00 0.00 38.26 3.41
98 99 7.440523 AGTTACAGTGGAGCTTAATTTTCTG 57.559 36.000 0.00 0.00 0.00 3.02
99 100 9.220767 CTTAGTTACAGTGGAGCTTAATTTTCT 57.779 33.333 0.00 0.00 0.00 2.52
100 101 9.000486 ACTTAGTTACAGTGGAGCTTAATTTTC 58.000 33.333 0.00 0.00 0.00 2.29
101 102 8.919777 ACTTAGTTACAGTGGAGCTTAATTTT 57.080 30.769 0.00 0.00 0.00 1.82
102 103 8.784043 CAACTTAGTTACAGTGGAGCTTAATTT 58.216 33.333 0.00 0.00 0.00 1.82
103 104 8.154856 TCAACTTAGTTACAGTGGAGCTTAATT 58.845 33.333 0.00 0.00 0.00 1.40
104 105 7.676947 TCAACTTAGTTACAGTGGAGCTTAAT 58.323 34.615 0.00 0.00 0.00 1.40
105 106 7.058023 TCAACTTAGTTACAGTGGAGCTTAA 57.942 36.000 0.00 0.00 0.00 1.85
106 107 6.659745 TCAACTTAGTTACAGTGGAGCTTA 57.340 37.500 0.00 0.00 0.00 3.09
107 108 5.546621 TCAACTTAGTTACAGTGGAGCTT 57.453 39.130 0.00 0.00 0.00 3.74
108 109 5.482175 AGATCAACTTAGTTACAGTGGAGCT 59.518 40.000 0.00 0.00 36.33 4.09
109 110 5.578727 CAGATCAACTTAGTTACAGTGGAGC 59.421 44.000 0.00 0.00 31.67 4.70
110 111 6.102663 CCAGATCAACTTAGTTACAGTGGAG 58.897 44.000 0.00 0.00 27.23 3.86
111 112 5.046591 CCCAGATCAACTTAGTTACAGTGGA 60.047 44.000 13.83 1.43 0.00 4.02
112 113 5.178797 CCCAGATCAACTTAGTTACAGTGG 58.821 45.833 0.00 3.36 0.00 4.00
113 114 4.631813 GCCCAGATCAACTTAGTTACAGTG 59.368 45.833 0.00 0.00 0.00 3.66
114 115 4.323562 GGCCCAGATCAACTTAGTTACAGT 60.324 45.833 0.00 0.00 0.00 3.55
115 116 4.192317 GGCCCAGATCAACTTAGTTACAG 58.808 47.826 0.00 0.00 0.00 2.74
116 117 3.585289 TGGCCCAGATCAACTTAGTTACA 59.415 43.478 0.00 0.00 0.00 2.41
117 118 4.216411 TGGCCCAGATCAACTTAGTTAC 57.784 45.455 0.00 0.00 0.00 2.50
118 119 4.141482 GGATGGCCCAGATCAACTTAGTTA 60.141 45.833 0.00 0.00 34.14 2.24
142 143 5.178438 GTGATTGAACAAGGAGAAGAGACAC 59.822 44.000 0.00 0.00 0.00 3.67
145 146 4.560128 CGTGATTGAACAAGGAGAAGAGA 58.440 43.478 0.00 0.00 0.00 3.10
185 186 4.430765 CTTCGGTCGTCACCCCCG 62.431 72.222 0.00 0.00 40.01 5.73
191 192 0.040692 CTGTCGTTCTTCGGTCGTCA 60.041 55.000 0.00 0.00 40.32 4.35
192 193 0.040603 ACTGTCGTTCTTCGGTCGTC 60.041 55.000 0.00 0.00 40.32 4.20
193 194 1.196354 CTACTGTCGTTCTTCGGTCGT 59.804 52.381 0.00 0.00 40.32 4.34
281 291 3.787001 CGCCTCCCCTTGGGACTC 61.787 72.222 7.38 0.00 46.17 3.36
358 397 3.078196 TCAATCCGTGGCCCGCTA 61.078 61.111 0.00 0.00 34.38 4.26
369 408 0.741221 GAGTGGACACGCCTCAATCC 60.741 60.000 0.00 0.00 37.63 3.01
372 411 2.741092 GGAGTGGACACGCCTCAA 59.259 61.111 16.52 0.00 46.05 3.02
377 416 1.745489 GGATTGGGAGTGGACACGC 60.745 63.158 0.00 0.00 36.20 5.34
380 419 2.966732 GCCGGATTGGGAGTGGACA 61.967 63.158 5.05 0.00 38.63 4.02
419 484 1.678728 GCTCCGTGGACAATCAATCCA 60.679 52.381 0.00 0.00 44.20 3.41
461 526 4.320870 GGAAAATCGAGTTACCAAGGTGA 58.679 43.478 0.00 0.00 0.00 4.02
463 528 3.007182 TCGGAAAATCGAGTTACCAAGGT 59.993 43.478 0.00 0.00 34.82 3.50
484 549 9.255304 GAACTAGACAGACATGGAAATAGAATC 57.745 37.037 0.00 0.00 0.00 2.52
485 550 7.923344 CGAACTAGACAGACATGGAAATAGAAT 59.077 37.037 0.00 0.00 0.00 2.40
490 555 5.171476 CACGAACTAGACAGACATGGAAAT 58.829 41.667 0.00 0.00 0.00 2.17
499 564 5.125578 AGTTGATATGCACGAACTAGACAGA 59.874 40.000 0.00 0.00 0.00 3.41
508 573 3.925379 ACACTGAGTTGATATGCACGAA 58.075 40.909 0.00 0.00 0.00 3.85
529 594 1.596752 AAGTCGCGGCAACACATGA 60.597 52.632 15.58 0.00 0.00 3.07
630 698 2.287308 TGAAGACGCATTTGTTTTCCCG 60.287 45.455 0.00 0.00 33.35 5.14
631 699 3.363341 TGAAGACGCATTTGTTTTCCC 57.637 42.857 0.00 0.00 33.35 3.97
646 714 6.874278 TTAAGGATCCTGATCAGTTGAAGA 57.126 37.500 17.02 11.08 39.54 2.87
658 726 6.595682 ACCACTAACATGATTAAGGATCCTG 58.404 40.000 17.02 3.98 36.71 3.86
659 727 6.386927 TGACCACTAACATGATTAAGGATCCT 59.613 38.462 9.02 9.02 33.60 3.24
660 728 6.591935 TGACCACTAACATGATTAAGGATCC 58.408 40.000 2.48 2.48 33.60 3.36
661 729 8.682936 AATGACCACTAACATGATTAAGGATC 57.317 34.615 0.00 0.00 35.21 3.36
663 731 9.613428 CTAAATGACCACTAACATGATTAAGGA 57.387 33.333 0.00 0.00 0.00 3.36
664 732 9.613428 TCTAAATGACCACTAACATGATTAAGG 57.387 33.333 0.00 0.00 0.00 2.69
668 736 9.520515 ACTTTCTAAATGACCACTAACATGATT 57.479 29.630 0.00 0.00 0.00 2.57
669 737 9.520515 AACTTTCTAAATGACCACTAACATGAT 57.479 29.630 0.00 0.00 0.00 2.45
670 738 8.918202 AACTTTCTAAATGACCACTAACATGA 57.082 30.769 0.00 0.00 0.00 3.07
671 739 9.612620 GAAACTTTCTAAATGACCACTAACATG 57.387 33.333 0.00 0.00 0.00 3.21
672 740 9.349713 TGAAACTTTCTAAATGACCACTAACAT 57.650 29.630 3.22 0.00 0.00 2.71
673 741 8.740123 TGAAACTTTCTAAATGACCACTAACA 57.260 30.769 3.22 0.00 0.00 2.41
690 758 9.830975 ACTGCAAACCTATAAAAATGAAACTTT 57.169 25.926 0.00 0.00 0.00 2.66
691 759 9.830975 AACTGCAAACCTATAAAAATGAAACTT 57.169 25.926 0.00 0.00 0.00 2.66
692 760 9.260002 CAACTGCAAACCTATAAAAATGAAACT 57.740 29.630 0.00 0.00 0.00 2.66
693 761 8.009409 GCAACTGCAAACCTATAAAAATGAAAC 58.991 33.333 0.00 0.00 41.59 2.78
694 762 8.082334 GCAACTGCAAACCTATAAAAATGAAA 57.918 30.769 0.00 0.00 41.59 2.69
695 763 7.650834 GCAACTGCAAACCTATAAAAATGAA 57.349 32.000 0.00 0.00 41.59 2.57
715 783 5.065704 TCTCTCTTACATCAGAGTGCAAC 57.934 43.478 0.00 0.00 41.18 4.17
716 784 4.159321 CCTCTCTCTTACATCAGAGTGCAA 59.841 45.833 0.00 0.00 41.18 4.08
717 785 3.698539 CCTCTCTCTTACATCAGAGTGCA 59.301 47.826 0.00 0.00 41.18 4.57
718 786 3.490761 GCCTCTCTCTTACATCAGAGTGC 60.491 52.174 0.00 0.00 41.18 4.40
719 787 3.953612 AGCCTCTCTCTTACATCAGAGTG 59.046 47.826 0.00 0.00 41.18 3.51
720 788 3.953612 CAGCCTCTCTCTTACATCAGAGT 59.046 47.826 0.00 0.00 41.18 3.24
721 789 3.243501 GCAGCCTCTCTCTTACATCAGAG 60.244 52.174 0.00 0.00 41.69 3.35
722 790 2.692557 GCAGCCTCTCTCTTACATCAGA 59.307 50.000 0.00 0.00 0.00 3.27
723 791 2.224018 GGCAGCCTCTCTCTTACATCAG 60.224 54.545 3.29 0.00 0.00 2.90
724 792 1.759445 GGCAGCCTCTCTCTTACATCA 59.241 52.381 3.29 0.00 0.00 3.07
725 793 2.038659 AGGCAGCCTCTCTCTTACATC 58.961 52.381 8.70 0.00 0.00 3.06
726 794 1.761784 CAGGCAGCCTCTCTCTTACAT 59.238 52.381 12.53 0.00 0.00 2.29
727 795 1.189752 CAGGCAGCCTCTCTCTTACA 58.810 55.000 12.53 0.00 0.00 2.41
728 796 1.479709 TCAGGCAGCCTCTCTCTTAC 58.520 55.000 12.53 0.00 0.00 2.34
729 797 2.234908 GTTTCAGGCAGCCTCTCTCTTA 59.765 50.000 12.53 0.00 0.00 2.10
730 798 1.003003 GTTTCAGGCAGCCTCTCTCTT 59.997 52.381 12.53 0.00 0.00 2.85
731 799 0.612744 GTTTCAGGCAGCCTCTCTCT 59.387 55.000 12.53 0.00 0.00 3.10
732 800 0.392327 GGTTTCAGGCAGCCTCTCTC 60.392 60.000 12.53 2.72 0.00 3.20
733 801 0.839853 AGGTTTCAGGCAGCCTCTCT 60.840 55.000 12.53 1.73 0.00 3.10
734 802 0.037447 AAGGTTTCAGGCAGCCTCTC 59.963 55.000 12.53 1.95 0.00 3.20
735 803 0.251077 CAAGGTTTCAGGCAGCCTCT 60.251 55.000 12.53 1.60 0.00 3.69
736 804 1.246737 CCAAGGTTTCAGGCAGCCTC 61.247 60.000 12.53 0.00 0.00 4.70
737 805 1.228675 CCAAGGTTTCAGGCAGCCT 60.229 57.895 8.70 8.70 0.00 4.58
738 806 1.228552 TCCAAGGTTTCAGGCAGCC 60.229 57.895 1.84 1.84 0.00 4.85
739 807 1.527433 GGTCCAAGGTTTCAGGCAGC 61.527 60.000 0.00 0.00 0.00 5.25
740 808 0.178992 TGGTCCAAGGTTTCAGGCAG 60.179 55.000 0.00 0.00 0.00 4.85
741 809 0.482446 ATGGTCCAAGGTTTCAGGCA 59.518 50.000 0.00 0.00 0.00 4.75
742 810 1.177401 GATGGTCCAAGGTTTCAGGC 58.823 55.000 0.00 0.00 0.00 4.85
743 811 2.887151 AGATGGTCCAAGGTTTCAGG 57.113 50.000 0.00 0.00 0.00 3.86
768 836 8.416329 CCTTTAAGCAAAATCACCTATAATGCT 58.584 33.333 0.00 0.00 39.84 3.79
787 855 7.996098 TTTGAGAACCAGATTACCCTTTAAG 57.004 36.000 0.00 0.00 0.00 1.85
863 977 0.754587 TGCCTGCAATTCCACACACA 60.755 50.000 0.00 0.00 0.00 3.72
865 979 0.178995 TCTGCCTGCAATTCCACACA 60.179 50.000 0.00 0.00 0.00 3.72
867 981 1.250328 CTTCTGCCTGCAATTCCACA 58.750 50.000 0.00 0.00 0.00 4.17
868 982 1.251251 ACTTCTGCCTGCAATTCCAC 58.749 50.000 0.00 0.00 0.00 4.02
869 983 2.715046 CTACTTCTGCCTGCAATTCCA 58.285 47.619 0.00 0.00 0.00 3.53
870 984 1.403323 GCTACTTCTGCCTGCAATTCC 59.597 52.381 0.00 0.00 0.00 3.01
871 985 2.086869 TGCTACTTCTGCCTGCAATTC 58.913 47.619 0.00 0.00 0.00 2.17
872 986 2.089980 CTGCTACTTCTGCCTGCAATT 58.910 47.619 0.00 0.00 33.07 2.32
927 1046 1.416772 GCCCACCACTAATACCTCCTC 59.583 57.143 0.00 0.00 0.00 3.71
952 1071 1.938585 ACGTTCCATTCTCCCAGAGA 58.061 50.000 0.00 0.00 36.86 3.10
1131 1250 1.402968 GCGATGATGTGGTTGCAAGAT 59.597 47.619 0.00 0.00 0.00 2.40
1269 1394 1.302511 GAGGGAAACAGCAAGGCGA 60.303 57.895 0.00 0.00 0.00 5.54
1275 1400 1.841556 ACGGAGGAGGGAAACAGCA 60.842 57.895 0.00 0.00 0.00 4.41
1338 1463 3.411351 CACGCGCTAACGGCAGTT 61.411 61.111 5.73 7.54 43.95 3.16
1501 1626 1.149174 CCGGAGCAGCCATACCAAT 59.851 57.895 0.00 0.00 35.94 3.16
1502 1627 2.589540 CCGGAGCAGCCATACCAA 59.410 61.111 0.00 0.00 35.94 3.67
1614 1739 1.394572 GGCGCCATGAAATTGCTTTTC 59.605 47.619 24.80 5.94 43.42 2.29
1677 1803 3.429372 AACTCCAAGCCGCCCAACA 62.429 57.895 0.00 0.00 0.00 3.33
1758 1884 2.290323 GGAGTACATGTCAACCAAGCCT 60.290 50.000 0.00 0.00 0.00 4.58
1760 1886 2.778299 TGGAGTACATGTCAACCAAGC 58.222 47.619 0.00 0.00 0.00 4.01
2064 2190 1.638388 CGAGCATGTCAACCGCACAT 61.638 55.000 0.00 0.00 34.67 3.21
2100 2226 0.034767 CCAGCTCAAATGCCTCCTCA 60.035 55.000 0.00 0.00 0.00 3.86
2145 2271 2.184830 CCACAGCATGAGGGCATCG 61.185 63.158 0.00 0.00 43.66 3.84
2178 2304 1.221840 CCTATGTGTCCGGCAAGCT 59.778 57.895 0.00 0.00 0.00 3.74
2337 2463 1.816835 TCTTTCTGTATGCCTCGTCGT 59.183 47.619 0.00 0.00 0.00 4.34
2358 2484 3.292481 AATCCAGCTGCACCCAGGG 62.292 63.158 8.66 2.85 39.54 4.45
2385 2511 3.062639 CGTAGAACACGTACGGTATGTCT 59.937 47.826 21.06 15.47 45.82 3.41
2667 2882 3.071459 GAACGCGTCATGGCAGTCG 62.071 63.158 14.44 0.00 0.00 4.18
2712 2933 3.390967 TCAGATCCCTCACAACAAACTCA 59.609 43.478 0.00 0.00 0.00 3.41
2801 3022 5.101628 TCACAAAGTTGACAATCACTTTGC 58.898 37.500 22.49 0.00 42.42 3.68
2825 3046 6.068010 TGTTGTTTTCCCTCTGTATCACAAT 58.932 36.000 0.00 0.00 0.00 2.71
2826 3047 5.441500 TGTTGTTTTCCCTCTGTATCACAA 58.558 37.500 0.00 0.00 0.00 3.33
2827 3048 5.042463 TGTTGTTTTCCCTCTGTATCACA 57.958 39.130 0.00 0.00 0.00 3.58
2828 3049 6.385649 TTTGTTGTTTTCCCTCTGTATCAC 57.614 37.500 0.00 0.00 0.00 3.06
2829 3050 7.004086 AGATTTGTTGTTTTCCCTCTGTATCA 58.996 34.615 0.00 0.00 0.00 2.15
2830 3051 7.454260 AGATTTGTTGTTTTCCCTCTGTATC 57.546 36.000 0.00 0.00 0.00 2.24
2831 3052 7.839680 AAGATTTGTTGTTTTCCCTCTGTAT 57.160 32.000 0.00 0.00 0.00 2.29
2832 3053 7.340743 TCAAAGATTTGTTGTTTTCCCTCTGTA 59.659 33.333 5.29 0.00 39.18 2.74
2833 3054 6.154363 TCAAAGATTTGTTGTTTTCCCTCTGT 59.846 34.615 5.29 0.00 39.18 3.41
2834 3055 6.572519 TCAAAGATTTGTTGTTTTCCCTCTG 58.427 36.000 5.29 0.00 39.18 3.35
2835 3056 6.381133 ACTCAAAGATTTGTTGTTTTCCCTCT 59.619 34.615 5.29 0.00 39.18 3.69
2836 3057 6.573434 ACTCAAAGATTTGTTGTTTTCCCTC 58.427 36.000 5.29 0.00 39.18 4.30
2837 3058 6.544928 ACTCAAAGATTTGTTGTTTTCCCT 57.455 33.333 5.29 0.00 39.18 4.20
2838 3059 8.887036 AATACTCAAAGATTTGTTGTTTTCCC 57.113 30.769 5.29 0.00 39.18 3.97
2850 3074 8.697507 ACTTTCTTGTGGAATACTCAAAGATT 57.302 30.769 0.00 0.00 33.53 2.40
2851 3075 7.939039 TGACTTTCTTGTGGAATACTCAAAGAT 59.061 33.333 0.00 0.00 33.53 2.40
2859 3083 6.262273 TGTCCTTTGACTTTCTTGTGGAATAC 59.738 38.462 0.00 0.00 42.28 1.89
2910 3195 5.711976 TCCCTTTGGAAGAATGTCAAGATTC 59.288 40.000 0.00 0.00 37.86 2.52
2970 3856 4.580167 TGCAAATGTGATAAGTCTATGCCC 59.420 41.667 0.00 0.00 0.00 5.36
2976 3862 8.510243 TCATATTGTGCAAATGTGATAAGTCT 57.490 30.769 13.16 0.00 0.00 3.24
3003 3889 5.835113 ATGATTTGTTGGAATAAGTCGGG 57.165 39.130 0.00 0.00 0.00 5.14
3005 3891 8.741101 TTCAAATGATTTGTTGGAATAAGTCG 57.259 30.769 16.62 0.00 41.36 4.18
3208 4476 9.669353 CATGAATAATTTAAAGAGATTGTCCCG 57.331 33.333 0.00 0.00 0.00 5.14
3268 4602 3.197983 ACCAGGGATAGCAAACTACAGAC 59.802 47.826 0.00 0.00 0.00 3.51
3274 4608 0.995024 AGCACCAGGGATAGCAAACT 59.005 50.000 0.00 0.00 0.00 2.66
3295 5607 3.755378 CAGAGCATGACCAAAAAGCTACT 59.245 43.478 0.00 0.00 35.36 2.57
3301 5613 4.998671 TTCAACAGAGCATGACCAAAAA 57.001 36.364 0.00 0.00 0.00 1.94
3420 6150 9.043079 TCGTCACAAATAAACAGTAAATACACA 57.957 29.630 0.00 0.00 0.00 3.72
3504 6235 8.584063 TGATATACGGTATATTTAGCACCTCA 57.416 34.615 18.92 9.30 31.74 3.86
3520 6414 7.606858 ATCTTCATGCTCAAATGATATACGG 57.393 36.000 0.00 0.00 36.48 4.02
3545 6439 6.298361 TCAGACTCCTTGTTCATTTGAATGA 58.702 36.000 2.39 2.39 43.28 2.57
3552 6446 2.290577 GGGCTCAGACTCCTTGTTCATT 60.291 50.000 0.00 0.00 0.00 2.57
3557 6451 0.472734 ACAGGGCTCAGACTCCTTGT 60.473 55.000 0.00 0.00 37.77 3.16
3558 6452 0.036577 CACAGGGCTCAGACTCCTTG 60.037 60.000 0.00 0.00 35.78 3.61
3570 6471 0.895100 TCATTCACAAGGCACAGGGC 60.895 55.000 0.00 0.00 43.74 5.19
3573 6474 2.815503 TGACATCATTCACAAGGCACAG 59.184 45.455 0.00 0.00 0.00 3.66
3586 6487 8.283699 TGAACAATGTGACAATATGACATCAT 57.716 30.769 0.00 0.00 40.22 2.45
3593 6494 5.679792 CGCTGATGAACAATGTGACAATATG 59.320 40.000 0.00 0.00 0.00 1.78
3594 6495 5.585844 TCGCTGATGAACAATGTGACAATAT 59.414 36.000 0.00 0.00 0.00 1.28
3595 6496 4.934602 TCGCTGATGAACAATGTGACAATA 59.065 37.500 0.00 0.00 0.00 1.90
3596 6497 3.752747 TCGCTGATGAACAATGTGACAAT 59.247 39.130 0.00 0.00 0.00 2.71
3597 6498 3.137533 TCGCTGATGAACAATGTGACAA 58.862 40.909 0.00 0.00 0.00 3.18
3598 6499 2.765122 TCGCTGATGAACAATGTGACA 58.235 42.857 0.00 0.00 0.00 3.58
3599 6500 3.482786 GTTCGCTGATGAACAATGTGAC 58.517 45.455 7.93 0.00 45.92 3.67
3600 6501 3.811722 GTTCGCTGATGAACAATGTGA 57.188 42.857 7.93 0.00 45.92 3.58
3665 6566 5.026121 TGAGACATCAGGATTAGTTGGACT 58.974 41.667 0.00 0.00 0.00 3.85
3691 6592 5.309638 TCCCATCGAAACAACTAATCACAA 58.690 37.500 0.00 0.00 0.00 3.33
3740 6644 9.357652 AGATTATGTTCATGCAAATTGTGTAAC 57.642 29.630 0.00 0.00 37.35 2.50
3748 6652 9.878667 TTTGATTGAGATTATGTTCATGCAAAT 57.121 25.926 0.00 0.00 29.61 2.32


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

AutoCloner maintained by Alex Coulton.