Multiple sequence alignment - TraesCS2B01G229300

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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 TraesCS2B01G229300 chr2B 100.000 2996 0 0 1 2996 224648253 224651248 0.000000e+00 5533.0
1 TraesCS2B01G229300 chr2B 84.129 649 69 18 92 722 154188836 154188204 5.530000e-167 597.0
2 TraesCS2B01G229300 chr2B 85.254 590 60 16 142 714 504197797 504197218 1.550000e-162 582.0
3 TraesCS2B01G229300 chr2A 94.292 1717 46 15 806 2494 176670530 176672222 0.000000e+00 2580.0
4 TraesCS2B01G229300 chr2A 96.805 313 5 3 2688 2996 176672217 176672528 4.430000e-143 518.0
5 TraesCS2B01G229300 chr2A 94.969 159 3 1 2533 2691 688640986 688640833 8.300000e-61 244.0
6 TraesCS2B01G229300 chr2D 92.210 1733 46 22 787 2494 163020525 163018857 0.000000e+00 2370.0
7 TraesCS2B01G229300 chr2D 82.187 567 85 13 1 559 637136426 637136984 9.720000e-130 473.0
8 TraesCS2B01G229300 chr2D 98.084 261 5 0 2688 2948 163018862 163018602 3.520000e-124 455.0
9 TraesCS2B01G229300 chr2D 97.500 40 0 1 2490 2529 367920028 367919990 1.930000e-07 67.6
10 TraesCS2B01G229300 chr1B 83.616 708 78 26 30 711 334441753 334442448 5.450000e-177 630.0
11 TraesCS2B01G229300 chr1B 77.982 218 21 19 2479 2691 478590820 478590625 8.780000e-21 111.0
12 TraesCS2B01G229300 chr7B 84.980 506 63 10 211 711 202504984 202504487 4.460000e-138 501.0
13 TraesCS2B01G229300 chr7B 94.375 160 3 2 2541 2699 588861701 588861855 1.070000e-59 241.0
14 TraesCS2B01G229300 chr5B 84.351 524 63 11 206 715 670300670 670301188 2.070000e-136 496.0
15 TraesCS2B01G229300 chr5B 81.818 209 32 3 512 715 118505729 118505522 1.430000e-38 171.0
16 TraesCS2B01G229300 chr4B 85.745 463 46 15 206 656 135585747 135585293 3.500000e-129 472.0
17 TraesCS2B01G229300 chr6B 84.956 452 53 11 3 447 476107693 476108136 7.620000e-121 444.0
18 TraesCS2B01G229300 chr6B 80.932 472 57 14 1 467 626881455 626881898 2.860000e-90 342.0
19 TraesCS2B01G229300 chr6B 83.562 219 29 4 503 714 715532993 715533211 6.550000e-47 198.0
20 TraesCS2B01G229300 chr6B 83.486 218 30 3 503 714 715539042 715539259 6.550000e-47 198.0
21 TraesCS2B01G229300 chr6B 100.000 37 0 0 2491 2527 290638552 290638516 5.360000e-08 69.4
22 TraesCS2B01G229300 chr5A 82.600 477 66 13 1 467 589377034 589377503 3.600000e-109 405.0
23 TraesCS2B01G229300 chr5A 80.376 479 64 20 1 467 484627427 484626967 1.330000e-88 337.0
24 TraesCS2B01G229300 chr5A 93.827 162 4 2 2541 2702 687682730 687682575 3.860000e-59 239.0
25 TraesCS2B01G229300 chr5A 87.582 153 16 2 3 155 9215310 9215459 1.100000e-39 174.0
26 TraesCS2B01G229300 chr5A 84.940 166 19 3 1 164 40630705 40630866 2.390000e-36 163.0
27 TraesCS2B01G229300 chrUn 81.369 526 70 18 206 714 250781829 250781315 1.290000e-108 403.0
28 TraesCS2B01G229300 chrUn 81.333 525 71 18 206 714 87813863 87813350 4.650000e-108 401.0
29 TraesCS2B01G229300 chrUn 95.349 43 0 2 2483 2525 87983106 87983146 1.930000e-07 67.6
30 TraesCS2B01G229300 chr3D 82.489 474 65 11 1 466 179463408 179463871 1.670000e-107 399.0
31 TraesCS2B01G229300 chr3D 94.340 159 5 3 2541 2699 490735635 490735481 1.070000e-59 241.0
32 TraesCS2B01G229300 chr3D 94.340 159 4 1 2533 2691 581983598 581983445 3.860000e-59 239.0
33 TraesCS2B01G229300 chr3D 100.000 37 0 0 2491 2527 379823882 379823846 5.360000e-08 69.4
34 TraesCS2B01G229300 chr3D 91.837 49 3 1 2478 2525 520722591 520722639 1.930000e-07 67.6
35 TraesCS2B01G229300 chr7A 95.597 159 5 2 2533 2691 431992891 431992735 1.380000e-63 254.0
36 TraesCS2B01G229300 chr4D 91.573 178 8 5 2531 2707 465124221 465124392 3.860000e-59 239.0
37 TraesCS2B01G229300 chr1D 94.340 159 4 2 2541 2699 331539284 331539437 3.860000e-59 239.0
38 TraesCS2B01G229300 chr7D 93.827 162 3 3 2541 2701 192936039 192936194 1.390000e-58 237.0
39 TraesCS2B01G229300 chr7D 100.000 37 0 0 2491 2527 101559139 101559175 5.360000e-08 69.4
40 TraesCS2B01G229300 chr5D 100.000 38 0 0 2490 2527 111788748 111788711 1.490000e-08 71.3
41 TraesCS2B01G229300 chr4A 78.151 119 21 3 1417 1534 450765153 450765039 1.490000e-08 71.3
42 TraesCS2B01G229300 chr3A 91.304 46 3 1 2478 2522 656108923 656108968 8.970000e-06 62.1


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 TraesCS2B01G229300 chr2B 224648253 224651248 2995 False 5533.0 5533 100.0000 1 2996 1 chr2B.!!$F1 2995
1 TraesCS2B01G229300 chr2B 154188204 154188836 632 True 597.0 597 84.1290 92 722 1 chr2B.!!$R1 630
2 TraesCS2B01G229300 chr2B 504197218 504197797 579 True 582.0 582 85.2540 142 714 1 chr2B.!!$R2 572
3 TraesCS2B01G229300 chr2A 176670530 176672528 1998 False 1549.0 2580 95.5485 806 2996 2 chr2A.!!$F1 2190
4 TraesCS2B01G229300 chr2D 163018602 163020525 1923 True 1412.5 2370 95.1470 787 2948 2 chr2D.!!$R2 2161
5 TraesCS2B01G229300 chr2D 637136426 637136984 558 False 473.0 473 82.1870 1 559 1 chr2D.!!$F1 558
6 TraesCS2B01G229300 chr1B 334441753 334442448 695 False 630.0 630 83.6160 30 711 1 chr1B.!!$F1 681
7 TraesCS2B01G229300 chr5B 670300670 670301188 518 False 496.0 496 84.3510 206 715 1 chr5B.!!$F1 509
8 TraesCS2B01G229300 chrUn 250781315 250781829 514 True 403.0 403 81.3690 206 714 1 chrUn.!!$R2 508
9 TraesCS2B01G229300 chrUn 87813350 87813863 513 True 401.0 401 81.3330 206 714 1 chrUn.!!$R1 508

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
783 846 0.175302 TCCGCGAATAAAAGGCCGTA 59.825 50.0 8.23 0.0 0.0 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2511 2635 0.106167 TCTGTATGGGACGGAGGGAG 60.106 60.0 0.0 0.0 38.61 4.3 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
36 37 4.006989 TCCCATGTTGATAGGTTTTGACG 58.993 43.478 0.00 0.00 0.00 4.35
39 40 5.048364 CCCATGTTGATAGGTTTTGACGAAA 60.048 40.000 0.00 0.00 0.00 3.46
40 41 6.442952 CCATGTTGATAGGTTTTGACGAAAA 58.557 36.000 0.00 0.00 0.00 2.29
41 42 6.920758 CCATGTTGATAGGTTTTGACGAAAAA 59.079 34.615 0.00 0.00 35.35 1.94
89 101 4.144418 CCGAACCGGGAACACAAA 57.856 55.556 6.32 0.00 44.15 2.83
135 147 1.244019 GCCCGTGCCTCTGACAAAAT 61.244 55.000 0.00 0.00 0.00 1.82
190 206 4.500127 CAGAAAACACGGTTTTCCCTTTT 58.500 39.130 25.48 12.98 38.74 2.27
240 256 2.251642 GCAAAACCGTGCCTCTCGT 61.252 57.895 0.00 0.00 38.66 4.18
417 442 2.182842 GCCATGCCTCTCGCGAAAT 61.183 57.895 11.33 0.00 42.08 2.17
453 478 1.322040 CGCAAAAACAAAACCGTGACC 59.678 47.619 0.00 0.00 0.00 4.02
543 576 2.696506 CTAGGGAAGACCGGTGAAAAC 58.303 52.381 14.63 0.00 46.96 2.43
549 582 3.441163 GAAGACCGGTGAAAACCAAAAC 58.559 45.455 14.63 0.00 0.00 2.43
550 583 2.448453 AGACCGGTGAAAACCAAAACA 58.552 42.857 14.63 0.00 0.00 2.83
551 584 3.028130 AGACCGGTGAAAACCAAAACAT 58.972 40.909 14.63 0.00 0.00 2.71
552 585 4.208746 AGACCGGTGAAAACCAAAACATA 58.791 39.130 14.63 0.00 0.00 2.29
638 700 2.019951 CCTAAAGCGCGACACGTGT 61.020 57.895 23.64 23.64 46.11 4.49
652 714 0.317160 ACGTGTCGAATGGCTGAGAA 59.683 50.000 0.00 0.00 0.00 2.87
656 718 1.014044 GTCGAATGGCTGAGAACGCA 61.014 55.000 0.00 0.00 0.00 5.24
711 774 2.284417 GGAGCGCTCGTTAATTAGTTGG 59.716 50.000 29.81 0.00 0.00 3.77
715 778 3.241995 GCGCTCGTTAATTAGTTGGTCTG 60.242 47.826 0.00 0.00 0.00 3.51
716 779 3.241995 CGCTCGTTAATTAGTTGGTCTGC 60.242 47.826 0.00 0.00 0.00 4.26
717 780 3.063588 GCTCGTTAATTAGTTGGTCTGCC 59.936 47.826 0.00 0.00 0.00 4.85
726 789 4.597032 TGGTCTGCCAAAACAGGG 57.403 55.556 0.00 0.00 42.83 4.45
727 790 1.152567 TGGTCTGCCAAAACAGGGG 60.153 57.895 0.00 0.00 42.83 4.79
733 796 3.051617 GCCAAAACAGGGGCTAACT 57.948 52.632 0.00 0.00 46.74 2.24
734 797 1.338107 GCCAAAACAGGGGCTAACTT 58.662 50.000 0.00 0.00 46.74 2.66
735 798 1.000843 GCCAAAACAGGGGCTAACTTG 59.999 52.381 0.00 0.00 46.74 3.16
736 799 1.618343 CCAAAACAGGGGCTAACTTGG 59.382 52.381 0.00 0.00 0.00 3.61
737 800 2.593026 CAAAACAGGGGCTAACTTGGA 58.407 47.619 0.00 0.00 0.00 3.53
738 801 2.287977 AAACAGGGGCTAACTTGGAC 57.712 50.000 0.00 0.00 0.00 4.02
739 802 0.404426 AACAGGGGCTAACTTGGACC 59.596 55.000 0.00 0.00 0.00 4.46
740 803 1.078426 CAGGGGCTAACTTGGACCG 60.078 63.158 0.00 0.00 31.27 4.79
741 804 2.437895 GGGGCTAACTTGGACCGC 60.438 66.667 0.00 0.00 31.27 5.68
742 805 2.818274 GGGCTAACTTGGACCGCG 60.818 66.667 0.00 0.00 0.00 6.46
743 806 2.263540 GGCTAACTTGGACCGCGA 59.736 61.111 8.23 0.00 0.00 5.87
744 807 1.810030 GGCTAACTTGGACCGCGAG 60.810 63.158 8.23 0.00 0.00 5.03
745 808 1.080025 GCTAACTTGGACCGCGAGT 60.080 57.895 8.23 3.14 0.00 4.18
746 809 1.077089 GCTAACTTGGACCGCGAGTC 61.077 60.000 8.23 13.63 45.51 3.36
753 816 4.057428 GACCGCGAGTCAGGCTGT 62.057 66.667 15.27 0.00 45.55 4.40
754 817 4.363990 ACCGCGAGTCAGGCTGTG 62.364 66.667 15.27 4.53 0.00 3.66
755 818 4.363990 CCGCGAGTCAGGCTGTGT 62.364 66.667 15.27 2.42 0.00 3.72
756 819 2.807045 CGCGAGTCAGGCTGTGTC 60.807 66.667 15.27 11.16 0.00 3.67
757 820 2.807045 GCGAGTCAGGCTGTGTCG 60.807 66.667 26.20 26.20 0.00 4.35
758 821 2.645567 CGAGTCAGGCTGTGTCGT 59.354 61.111 23.83 5.20 0.00 4.34
759 822 1.730902 CGAGTCAGGCTGTGTCGTG 60.731 63.158 23.83 6.50 0.00 4.35
760 823 2.024319 GAGTCAGGCTGTGTCGTGC 61.024 63.158 15.27 0.00 0.00 5.34
766 829 3.044305 GCTGTGTCGTGCCAGTCC 61.044 66.667 0.00 0.00 0.00 3.85
767 830 2.734723 CTGTGTCGTGCCAGTCCG 60.735 66.667 0.00 0.00 0.00 4.79
768 831 4.961511 TGTGTCGTGCCAGTCCGC 62.962 66.667 0.00 0.00 0.00 5.54
772 835 4.063967 TCGTGCCAGTCCGCGAAT 62.064 61.111 8.23 0.00 43.76 3.34
773 836 2.202690 CGTGCCAGTCCGCGAATA 60.203 61.111 8.23 0.00 40.91 1.75
774 837 1.807981 CGTGCCAGTCCGCGAATAA 60.808 57.895 8.23 0.00 40.91 1.40
775 838 1.355796 CGTGCCAGTCCGCGAATAAA 61.356 55.000 8.23 0.00 40.91 1.40
776 839 0.800012 GTGCCAGTCCGCGAATAAAA 59.200 50.000 8.23 0.00 0.00 1.52
777 840 1.083489 TGCCAGTCCGCGAATAAAAG 58.917 50.000 8.23 0.00 0.00 2.27
778 841 0.377203 GCCAGTCCGCGAATAAAAGG 59.623 55.000 8.23 0.64 0.00 3.11
779 842 0.377203 CCAGTCCGCGAATAAAAGGC 59.623 55.000 8.23 0.00 0.00 4.35
780 843 0.377203 CAGTCCGCGAATAAAAGGCC 59.623 55.000 8.23 0.00 0.00 5.19
781 844 1.087771 AGTCCGCGAATAAAAGGCCG 61.088 55.000 8.23 0.00 0.00 6.13
782 845 1.078988 TCCGCGAATAAAAGGCCGT 60.079 52.632 8.23 0.00 0.00 5.68
783 846 0.175302 TCCGCGAATAAAAGGCCGTA 59.825 50.000 8.23 0.00 0.00 4.02
784 847 1.202557 TCCGCGAATAAAAGGCCGTAT 60.203 47.619 8.23 0.00 0.00 3.06
785 848 1.070175 CCGCGAATAAAAGGCCGTATG 60.070 52.381 8.23 0.00 0.00 2.39
840 903 1.272760 ACAAACAGTTCCACCAACCCA 60.273 47.619 0.00 0.00 35.28 4.51
866 929 2.714250 ACTTAACCCAATCCACTCACCA 59.286 45.455 0.00 0.00 0.00 4.17
869 932 0.401738 ACCCAATCCACTCACCACAG 59.598 55.000 0.00 0.00 0.00 3.66
941 1005 2.928396 ACTTCCCCCACCACTCGG 60.928 66.667 0.00 0.00 38.77 4.63
1020 1085 1.153745 GACTCAGGAAGACGCGCAT 60.154 57.895 5.73 0.00 0.00 4.73
1079 1144 2.119655 CGGAGTACTACGCAGCCCT 61.120 63.158 15.87 0.00 0.00 5.19
1215 1280 1.873903 GCGCTCGTATTCATGGTCCAT 60.874 52.381 0.00 0.00 0.00 3.41
1350 1415 2.732619 GGCCTTCGTCCCCGATCTT 61.733 63.158 0.00 0.00 43.80 2.40
1539 1604 0.395686 CCATGTGCAGGATCTCCGAT 59.604 55.000 0.00 0.00 42.08 4.18
1994 2059 2.046314 GCCGGCAGCAACTTCCTA 60.046 61.111 24.80 0.00 42.97 2.94
2046 2132 6.675026 CATTCTATTCGGATTGTGCAATGAT 58.325 36.000 1.77 0.00 0.00 2.45
2047 2133 7.573656 GCATTCTATTCGGATTGTGCAATGATA 60.574 37.037 1.77 0.00 0.00 2.15
2050 2136 8.394971 TCTATTCGGATTGTGCAATGATAAAT 57.605 30.769 1.77 0.98 0.00 1.40
2051 2137 8.849168 TCTATTCGGATTGTGCAATGATAAATT 58.151 29.630 1.77 0.00 0.00 1.82
2052 2138 7.703298 ATTCGGATTGTGCAATGATAAATTG 57.297 32.000 1.77 0.00 0.00 2.32
2086 2189 3.156511 TGTGCGATGATTCTGTCTCTC 57.843 47.619 0.00 0.00 0.00 3.20
2087 2190 2.757314 TGTGCGATGATTCTGTCTCTCT 59.243 45.455 0.00 0.00 0.00 3.10
2088 2191 3.181492 TGTGCGATGATTCTGTCTCTCTC 60.181 47.826 0.00 0.00 0.00 3.20
2089 2192 3.066621 GTGCGATGATTCTGTCTCTCTCT 59.933 47.826 0.00 0.00 0.00 3.10
2090 2193 4.274705 GTGCGATGATTCTGTCTCTCTCTA 59.725 45.833 0.00 0.00 0.00 2.43
2091 2194 5.048782 GTGCGATGATTCTGTCTCTCTCTAT 60.049 44.000 0.00 0.00 0.00 1.98
2092 2195 6.148645 GTGCGATGATTCTGTCTCTCTCTATA 59.851 42.308 0.00 0.00 0.00 1.31
2093 2196 6.883756 TGCGATGATTCTGTCTCTCTCTATAT 59.116 38.462 0.00 0.00 0.00 0.86
2145 2248 7.173218 TGTCTTTGGTCAACTTTACATGATCTC 59.827 37.037 0.00 0.00 0.00 2.75
2238 2341 4.527583 CTCTCTGCCGGAGCCAGC 62.528 72.222 5.05 0.00 41.60 4.85
2253 2356 3.392228 AGCGTTGGATCTGCTGGA 58.608 55.556 0.00 0.00 37.62 3.86
2254 2357 1.220206 AGCGTTGGATCTGCTGGAG 59.780 57.895 0.00 0.00 37.62 3.86
2255 2358 2.467826 GCGTTGGATCTGCTGGAGC 61.468 63.158 0.00 0.00 42.50 4.70
2268 2371 4.467084 GGAGCCGGCGTTGGATCA 62.467 66.667 23.20 0.00 46.29 2.92
2315 2439 2.388232 GCAGTACAAGGCGTTCCCG 61.388 63.158 0.00 0.00 39.21 5.14
2334 2458 2.182842 GCCCTGTATCAGCTTGGCG 61.183 63.158 0.00 0.00 29.70 5.69
2497 2621 9.836179 AATATCTGATCATTTCTAGTACTCCCT 57.164 33.333 0.00 0.00 0.00 4.20
2498 2622 7.775053 ATCTGATCATTTCTAGTACTCCCTC 57.225 40.000 0.00 0.00 0.00 4.30
2499 2623 6.071984 TCTGATCATTTCTAGTACTCCCTCC 58.928 44.000 0.00 0.00 0.00 4.30
2500 2624 4.827835 TGATCATTTCTAGTACTCCCTCCG 59.172 45.833 0.00 0.00 0.00 4.63
2501 2625 4.246712 TCATTTCTAGTACTCCCTCCGT 57.753 45.455 0.00 0.00 0.00 4.69
2502 2626 4.607239 TCATTTCTAGTACTCCCTCCGTT 58.393 43.478 0.00 0.00 0.00 4.44
2503 2627 4.643784 TCATTTCTAGTACTCCCTCCGTTC 59.356 45.833 0.00 0.00 0.00 3.95
2504 2628 2.725221 TCTAGTACTCCCTCCGTTCC 57.275 55.000 0.00 0.00 0.00 3.62
2505 2629 2.203584 TCTAGTACTCCCTCCGTTCCT 58.796 52.381 0.00 0.00 0.00 3.36
2506 2630 3.387962 TCTAGTACTCCCTCCGTTCCTA 58.612 50.000 0.00 0.00 0.00 2.94
2507 2631 3.782523 TCTAGTACTCCCTCCGTTCCTAA 59.217 47.826 0.00 0.00 0.00 2.69
2508 2632 3.463048 AGTACTCCCTCCGTTCCTAAA 57.537 47.619 0.00 0.00 0.00 1.85
2509 2633 3.991683 AGTACTCCCTCCGTTCCTAAAT 58.008 45.455 0.00 0.00 0.00 1.40
2510 2634 5.134725 AGTACTCCCTCCGTTCCTAAATA 57.865 43.478 0.00 0.00 0.00 1.40
2511 2635 4.892345 AGTACTCCCTCCGTTCCTAAATAC 59.108 45.833 0.00 0.00 0.00 1.89
2512 2636 3.991683 ACTCCCTCCGTTCCTAAATACT 58.008 45.455 0.00 0.00 0.00 2.12
2513 2637 3.959449 ACTCCCTCCGTTCCTAAATACTC 59.041 47.826 0.00 0.00 0.00 2.59
2514 2638 3.303049 TCCCTCCGTTCCTAAATACTCC 58.697 50.000 0.00 0.00 0.00 3.85
2515 2639 2.367894 CCCTCCGTTCCTAAATACTCCC 59.632 54.545 0.00 0.00 0.00 4.30
2516 2640 3.306613 CCTCCGTTCCTAAATACTCCCT 58.693 50.000 0.00 0.00 0.00 4.20
2517 2641 3.321396 CCTCCGTTCCTAAATACTCCCTC 59.679 52.174 0.00 0.00 0.00 4.30
2518 2642 3.303049 TCCGTTCCTAAATACTCCCTCC 58.697 50.000 0.00 0.00 0.00 4.30
2519 2643 2.035576 CCGTTCCTAAATACTCCCTCCG 59.964 54.545 0.00 0.00 0.00 4.63
2520 2644 2.692041 CGTTCCTAAATACTCCCTCCGT 59.308 50.000 0.00 0.00 0.00 4.69
2521 2645 3.243334 CGTTCCTAAATACTCCCTCCGTC 60.243 52.174 0.00 0.00 0.00 4.79
2522 2646 2.954792 TCCTAAATACTCCCTCCGTCC 58.045 52.381 0.00 0.00 0.00 4.79
2523 2647 1.969208 CCTAAATACTCCCTCCGTCCC 59.031 57.143 0.00 0.00 0.00 4.46
2524 2648 2.674420 CTAAATACTCCCTCCGTCCCA 58.326 52.381 0.00 0.00 0.00 4.37
2525 2649 2.191981 AAATACTCCCTCCGTCCCAT 57.808 50.000 0.00 0.00 0.00 4.00
2526 2650 3.339713 AAATACTCCCTCCGTCCCATA 57.660 47.619 0.00 0.00 0.00 2.74
2527 2651 2.305858 ATACTCCCTCCGTCCCATAC 57.694 55.000 0.00 0.00 0.00 2.39
2528 2652 0.928505 TACTCCCTCCGTCCCATACA 59.071 55.000 0.00 0.00 0.00 2.29
2529 2653 0.397254 ACTCCCTCCGTCCCATACAG 60.397 60.000 0.00 0.00 0.00 2.74
2530 2654 0.106167 CTCCCTCCGTCCCATACAGA 60.106 60.000 0.00 0.00 0.00 3.41
2531 2655 0.561184 TCCCTCCGTCCCATACAGAT 59.439 55.000 0.00 0.00 0.00 2.90
2532 2656 0.681733 CCCTCCGTCCCATACAGATG 59.318 60.000 0.00 0.00 0.00 2.90
2546 2670 6.179906 CATACAGATGGAGGGAGTATTTGT 57.820 41.667 0.00 0.00 0.00 2.83
2547 2671 4.762289 ACAGATGGAGGGAGTATTTGTC 57.238 45.455 0.00 0.00 0.00 3.18
2548 2672 4.366267 ACAGATGGAGGGAGTATTTGTCT 58.634 43.478 0.00 0.00 0.00 3.41
2549 2673 4.785376 ACAGATGGAGGGAGTATTTGTCTT 59.215 41.667 0.00 0.00 0.00 3.01
2550 2674 5.251700 ACAGATGGAGGGAGTATTTGTCTTT 59.748 40.000 0.00 0.00 0.00 2.52
2551 2675 6.183347 CAGATGGAGGGAGTATTTGTCTTTT 58.817 40.000 0.00 0.00 0.00 2.27
2552 2676 6.660949 CAGATGGAGGGAGTATTTGTCTTTTT 59.339 38.462 0.00 0.00 0.00 1.94
2553 2677 7.829211 CAGATGGAGGGAGTATTTGTCTTTTTA 59.171 37.037 0.00 0.00 0.00 1.52
2554 2678 8.049721 AGATGGAGGGAGTATTTGTCTTTTTAG 58.950 37.037 0.00 0.00 0.00 1.85
2555 2679 7.324388 TGGAGGGAGTATTTGTCTTTTTAGA 57.676 36.000 0.00 0.00 0.00 2.10
2556 2680 7.394816 TGGAGGGAGTATTTGTCTTTTTAGAG 58.605 38.462 0.00 0.00 0.00 2.43
2557 2681 7.236847 TGGAGGGAGTATTTGTCTTTTTAGAGA 59.763 37.037 0.00 0.00 0.00 3.10
2558 2682 8.268605 GGAGGGAGTATTTGTCTTTTTAGAGAT 58.731 37.037 0.00 0.00 0.00 2.75
2559 2683 9.674068 GAGGGAGTATTTGTCTTTTTAGAGATT 57.326 33.333 0.00 0.00 0.00 2.40
2569 2693 9.965824 TTGTCTTTTTAGAGATTTCAAATGGAC 57.034 29.630 0.00 0.00 0.00 4.02
2570 2694 9.354673 TGTCTTTTTAGAGATTTCAAATGGACT 57.645 29.630 0.00 0.00 0.00 3.85
2582 2706 4.121906 TGGACTACCACATGCGGA 57.878 55.556 6.80 0.00 41.77 5.54
2583 2707 2.602890 TGGACTACCACATGCGGAT 58.397 52.632 6.80 0.00 41.77 4.18
2584 2708 0.177836 TGGACTACCACATGCGGATG 59.822 55.000 16.07 16.07 41.77 3.51
2585 2709 0.178068 GGACTACCACATGCGGATGT 59.822 55.000 17.64 17.64 44.08 3.06
2586 2710 1.411246 GGACTACCACATGCGGATGTA 59.589 52.381 22.75 6.53 41.12 2.29
2587 2711 2.037251 GGACTACCACATGCGGATGTAT 59.963 50.000 22.75 15.65 41.12 2.29
2588 2712 3.257375 GGACTACCACATGCGGATGTATA 59.743 47.826 22.75 15.93 41.12 1.47
2589 2713 4.486090 GACTACCACATGCGGATGTATAG 58.514 47.826 25.94 25.94 41.12 1.31
2590 2714 3.895656 ACTACCACATGCGGATGTATAGT 59.104 43.478 26.85 26.85 41.12 2.12
2591 2715 5.074804 ACTACCACATGCGGATGTATAGTA 58.925 41.667 29.18 24.09 41.12 1.82
2592 2716 5.715279 ACTACCACATGCGGATGTATAGTAT 59.285 40.000 29.18 15.75 41.12 2.12
2593 2717 6.888088 ACTACCACATGCGGATGTATAGTATA 59.112 38.462 29.18 14.60 41.12 1.47
2594 2718 6.791867 ACCACATGCGGATGTATAGTATAT 57.208 37.500 22.75 0.00 41.12 0.86
2595 2719 7.891498 ACCACATGCGGATGTATAGTATATA 57.109 36.000 22.75 0.00 41.12 0.86
2596 2720 7.941919 ACCACATGCGGATGTATAGTATATAG 58.058 38.462 22.75 6.01 41.12 1.31
2597 2721 7.778382 ACCACATGCGGATGTATAGTATATAGA 59.222 37.037 22.75 0.00 41.12 1.98
2598 2722 8.076781 CCACATGCGGATGTATAGTATATAGAC 58.923 40.741 22.75 0.00 41.12 2.59
2599 2723 8.621286 CACATGCGGATGTATAGTATATAGACA 58.379 37.037 22.75 0.00 41.12 3.41
2600 2724 9.355916 ACATGCGGATGTATAGTATATAGACAT 57.644 33.333 21.92 0.00 41.27 3.06
2633 2757 7.036220 AGTGTAGATTCACTCATTTTACTCCG 58.964 38.462 0.00 0.00 44.07 4.63
2634 2758 6.812160 GTGTAGATTCACTCATTTTACTCCGT 59.188 38.462 0.00 0.00 35.68 4.69
2635 2759 7.972277 GTGTAGATTCACTCATTTTACTCCGTA 59.028 37.037 0.00 0.00 35.68 4.02
2636 2760 8.692710 TGTAGATTCACTCATTTTACTCCGTAT 58.307 33.333 0.00 0.00 0.00 3.06
2637 2761 8.969267 GTAGATTCACTCATTTTACTCCGTATG 58.031 37.037 0.00 0.00 0.00 2.39
2638 2762 7.556844 AGATTCACTCATTTTACTCCGTATGT 58.443 34.615 0.00 0.00 0.00 2.29
2639 2763 8.692710 AGATTCACTCATTTTACTCCGTATGTA 58.307 33.333 0.00 0.00 0.00 2.29
2640 2764 8.873215 ATTCACTCATTTTACTCCGTATGTAG 57.127 34.615 0.00 0.00 0.00 2.74
2641 2765 7.400599 TCACTCATTTTACTCCGTATGTAGT 57.599 36.000 0.00 0.00 0.00 2.73
2642 2766 7.478322 TCACTCATTTTACTCCGTATGTAGTC 58.522 38.462 0.00 0.00 0.00 2.59
2643 2767 7.121611 TCACTCATTTTACTCCGTATGTAGTCA 59.878 37.037 0.00 0.00 0.00 3.41
2644 2768 7.220300 CACTCATTTTACTCCGTATGTAGTCAC 59.780 40.741 0.00 0.00 0.00 3.67
2645 2769 7.122353 ACTCATTTTACTCCGTATGTAGTCACT 59.878 37.037 0.00 0.00 0.00 3.41
2646 2770 7.833786 TCATTTTACTCCGTATGTAGTCACTT 58.166 34.615 0.00 0.00 0.00 3.16
2647 2771 7.758076 TCATTTTACTCCGTATGTAGTCACTTG 59.242 37.037 0.00 0.00 0.00 3.16
2648 2772 6.579666 TTTACTCCGTATGTAGTCACTTGT 57.420 37.500 0.00 0.00 0.00 3.16
2649 2773 6.579666 TTACTCCGTATGTAGTCACTTGTT 57.420 37.500 0.00 0.00 0.00 2.83
2650 2774 4.806330 ACTCCGTATGTAGTCACTTGTTG 58.194 43.478 0.00 0.00 0.00 3.33
2651 2775 4.521639 ACTCCGTATGTAGTCACTTGTTGA 59.478 41.667 0.00 0.00 0.00 3.18
2652 2776 5.010314 ACTCCGTATGTAGTCACTTGTTGAA 59.990 40.000 0.00 0.00 35.39 2.69
2653 2777 5.845103 TCCGTATGTAGTCACTTGTTGAAA 58.155 37.500 0.00 0.00 35.39 2.69
2654 2778 6.460781 TCCGTATGTAGTCACTTGTTGAAAT 58.539 36.000 0.00 0.00 35.39 2.17
2655 2779 6.588756 TCCGTATGTAGTCACTTGTTGAAATC 59.411 38.462 0.00 0.00 35.39 2.17
2656 2780 6.590292 CCGTATGTAGTCACTTGTTGAAATCT 59.410 38.462 0.00 0.00 35.39 2.40
2657 2781 7.201444 CCGTATGTAGTCACTTGTTGAAATCTC 60.201 40.741 0.00 0.00 35.39 2.75
2658 2782 7.542477 CGTATGTAGTCACTTGTTGAAATCTCT 59.458 37.037 0.00 0.00 35.39 3.10
2659 2783 9.856488 GTATGTAGTCACTTGTTGAAATCTCTA 57.144 33.333 0.00 0.00 35.39 2.43
2660 2784 8.994429 ATGTAGTCACTTGTTGAAATCTCTAG 57.006 34.615 0.00 0.00 35.39 2.43
2661 2785 8.178313 TGTAGTCACTTGTTGAAATCTCTAGA 57.822 34.615 0.00 0.00 35.39 2.43
2662 2786 8.638873 TGTAGTCACTTGTTGAAATCTCTAGAA 58.361 33.333 0.00 0.00 35.39 2.10
2663 2787 9.477484 GTAGTCACTTGTTGAAATCTCTAGAAA 57.523 33.333 0.00 0.00 35.39 2.52
2664 2788 8.600449 AGTCACTTGTTGAAATCTCTAGAAAG 57.400 34.615 0.00 0.00 35.39 2.62
2665 2789 8.424918 AGTCACTTGTTGAAATCTCTAGAAAGA 58.575 33.333 0.00 0.00 35.39 2.52
2666 2790 8.491950 GTCACTTGTTGAAATCTCTAGAAAGAC 58.508 37.037 0.00 0.00 35.39 3.01
2667 2791 8.204160 TCACTTGTTGAAATCTCTAGAAAGACA 58.796 33.333 0.00 0.00 0.00 3.41
2668 2792 8.830580 CACTTGTTGAAATCTCTAGAAAGACAA 58.169 33.333 0.00 0.00 0.00 3.18
2669 2793 9.396022 ACTTGTTGAAATCTCTAGAAAGACAAA 57.604 29.630 0.00 0.00 0.00 2.83
2685 2809 9.413734 AGAAAGACAAATATTTAGGAATGGAGG 57.586 33.333 0.00 0.00 0.00 4.30
2686 2810 8.539117 AAAGACAAATATTTAGGAATGGAGGG 57.461 34.615 0.00 0.00 0.00 4.30
2687 2811 7.465900 AGACAAATATTTAGGAATGGAGGGA 57.534 36.000 0.00 0.00 0.00 4.20
2688 2812 7.521669 AGACAAATATTTAGGAATGGAGGGAG 58.478 38.462 0.00 0.00 0.00 4.30
2723 2847 7.356089 TCATGGGAGTGTAATATTAAGTCGT 57.644 36.000 0.00 0.00 0.00 4.34
2885 3009 2.968574 GCAGATGGTAGAGGAGATTGGA 59.031 50.000 0.00 0.00 0.00 3.53
2900 3024 9.566432 GAGGAGATTGGACATTCATAACTATTT 57.434 33.333 0.00 0.00 0.00 1.40
2931 3055 1.675641 GGCCTTGGTAGTGCCTGTG 60.676 63.158 0.00 0.00 42.01 3.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
167 181 2.028876 AGGGAAAACCGTGTTTTCTGG 58.971 47.619 26.73 0.00 46.96 3.86
168 182 3.793797 AAGGGAAAACCGTGTTTTCTG 57.206 42.857 26.73 0.00 46.96 3.02
179 193 3.067601 TGCCTCTTTCGAAAAGGGAAAAC 59.932 43.478 26.39 16.54 33.37 2.43
190 206 2.125147 CGGGCATGCCTCTTTCGA 60.125 61.111 34.70 0.00 36.10 3.71
314 332 3.626680 CTTCCGCGAGAGGCACGAA 62.627 63.158 8.23 0.00 43.84 3.85
315 333 4.116328 CTTCCGCGAGAGGCACGA 62.116 66.667 8.23 0.00 43.84 4.35
402 427 0.108186 TGTGATTTCGCGAGAGGCAT 60.108 50.000 9.59 0.00 43.84 4.40
561 606 4.483311 TGTGTTTTCGGCTTTTTAAACGT 58.517 34.783 0.00 0.00 34.16 3.99
622 684 3.529504 GACACGTGTCGCGCTTTA 58.470 55.556 31.03 0.00 46.11 1.85
638 700 0.108186 ATGCGTTCTCAGCCATTCGA 60.108 50.000 0.00 0.00 0.00 3.71
677 739 2.185608 GCTCCTTCGACAGCCTCC 59.814 66.667 0.00 0.00 0.00 4.30
716 779 1.618343 CCAAGTTAGCCCCTGTTTTGG 59.382 52.381 0.00 0.00 0.00 3.28
717 780 2.296190 GTCCAAGTTAGCCCCTGTTTTG 59.704 50.000 0.00 0.00 0.00 2.44
720 783 0.404426 GGTCCAAGTTAGCCCCTGTT 59.596 55.000 0.00 0.00 0.00 3.16
721 784 1.838073 CGGTCCAAGTTAGCCCCTGT 61.838 60.000 0.00 0.00 0.00 4.00
722 785 1.078426 CGGTCCAAGTTAGCCCCTG 60.078 63.158 0.00 0.00 0.00 4.45
723 786 2.967946 GCGGTCCAAGTTAGCCCCT 61.968 63.158 0.00 0.00 0.00 4.79
724 787 2.437895 GCGGTCCAAGTTAGCCCC 60.438 66.667 0.00 0.00 0.00 5.80
725 788 2.818274 CGCGGTCCAAGTTAGCCC 60.818 66.667 0.00 0.00 0.00 5.19
726 789 1.810030 CTCGCGGTCCAAGTTAGCC 60.810 63.158 6.13 0.00 0.00 3.93
727 790 1.077089 GACTCGCGGTCCAAGTTAGC 61.077 60.000 6.13 0.00 38.93 3.09
728 791 0.242825 TGACTCGCGGTCCAAGTTAG 59.757 55.000 20.21 4.93 43.89 2.34
729 792 0.242825 CTGACTCGCGGTCCAAGTTA 59.757 55.000 20.21 7.12 43.89 2.24
730 793 1.006102 CTGACTCGCGGTCCAAGTT 60.006 57.895 20.21 0.00 43.89 2.66
731 794 2.651361 CTGACTCGCGGTCCAAGT 59.349 61.111 20.21 10.66 43.89 3.16
732 795 2.125912 CCTGACTCGCGGTCCAAG 60.126 66.667 20.21 13.60 43.89 3.61
733 796 4.373116 GCCTGACTCGCGGTCCAA 62.373 66.667 20.21 6.47 43.89 3.53
735 798 4.803426 CAGCCTGACTCGCGGTCC 62.803 72.222 20.21 8.95 43.89 4.46
736 799 4.057428 ACAGCCTGACTCGCGGTC 62.057 66.667 17.43 17.43 44.70 4.79
737 800 4.363990 CACAGCCTGACTCGCGGT 62.364 66.667 6.13 2.39 34.88 5.68
738 801 4.363990 ACACAGCCTGACTCGCGG 62.364 66.667 6.13 0.00 0.00 6.46
739 802 2.807045 GACACAGCCTGACTCGCG 60.807 66.667 0.00 0.00 0.00 5.87
740 803 2.807045 CGACACAGCCTGACTCGC 60.807 66.667 0.00 0.00 0.00 5.03
741 804 1.730902 CACGACACAGCCTGACTCG 60.731 63.158 0.00 6.48 0.00 4.18
742 805 2.024319 GCACGACACAGCCTGACTC 61.024 63.158 0.00 0.00 0.00 3.36
743 806 2.029666 GCACGACACAGCCTGACT 59.970 61.111 0.00 0.00 0.00 3.41
749 812 3.044305 GGACTGGCACGACACAGC 61.044 66.667 0.00 0.00 38.25 4.40
750 813 2.734723 CGGACTGGCACGACACAG 60.735 66.667 0.00 0.00 40.48 3.66
751 814 4.961511 GCGGACTGGCACGACACA 62.962 66.667 0.00 0.00 0.00 3.72
754 817 2.877360 TATTCGCGGACTGGCACGAC 62.877 60.000 6.13 0.00 33.69 4.34
755 818 2.215465 TTATTCGCGGACTGGCACGA 62.215 55.000 6.13 0.00 0.00 4.35
756 819 1.355796 TTTATTCGCGGACTGGCACG 61.356 55.000 6.13 0.00 0.00 5.34
757 820 0.800012 TTTTATTCGCGGACTGGCAC 59.200 50.000 6.13 0.00 0.00 5.01
758 821 1.083489 CTTTTATTCGCGGACTGGCA 58.917 50.000 6.13 0.00 0.00 4.92
759 822 0.377203 CCTTTTATTCGCGGACTGGC 59.623 55.000 6.13 0.00 0.00 4.85
760 823 0.377203 GCCTTTTATTCGCGGACTGG 59.623 55.000 6.13 1.04 0.00 4.00
761 824 0.377203 GGCCTTTTATTCGCGGACTG 59.623 55.000 6.13 0.00 0.00 3.51
762 825 1.087771 CGGCCTTTTATTCGCGGACT 61.088 55.000 6.13 0.00 0.00 3.85
763 826 1.350665 CGGCCTTTTATTCGCGGAC 59.649 57.895 6.13 0.00 0.00 4.79
764 827 0.175302 TACGGCCTTTTATTCGCGGA 59.825 50.000 6.13 0.00 0.00 5.54
765 828 1.070175 CATACGGCCTTTTATTCGCGG 60.070 52.381 6.13 0.00 0.00 6.46
766 829 1.070175 CCATACGGCCTTTTATTCGCG 60.070 52.381 0.00 0.00 0.00 5.87
767 830 2.215196 TCCATACGGCCTTTTATTCGC 58.785 47.619 0.00 0.00 0.00 4.70
768 831 4.315803 AGATCCATACGGCCTTTTATTCG 58.684 43.478 0.00 0.00 0.00 3.34
769 832 7.739498 TTAAGATCCATACGGCCTTTTATTC 57.261 36.000 0.00 0.00 0.00 1.75
770 833 8.528044 TTTTAAGATCCATACGGCCTTTTATT 57.472 30.769 0.00 0.00 0.00 1.40
771 834 7.255486 GCTTTTAAGATCCATACGGCCTTTTAT 60.255 37.037 0.00 0.00 0.00 1.40
772 835 6.038936 GCTTTTAAGATCCATACGGCCTTTTA 59.961 38.462 0.00 0.00 0.00 1.52
773 836 5.163550 GCTTTTAAGATCCATACGGCCTTTT 60.164 40.000 0.00 0.00 0.00 2.27
774 837 4.338400 GCTTTTAAGATCCATACGGCCTTT 59.662 41.667 0.00 0.00 0.00 3.11
775 838 3.883489 GCTTTTAAGATCCATACGGCCTT 59.117 43.478 0.00 0.00 0.00 4.35
776 839 3.118038 TGCTTTTAAGATCCATACGGCCT 60.118 43.478 0.00 0.00 0.00 5.19
777 840 3.003378 GTGCTTTTAAGATCCATACGGCC 59.997 47.826 0.00 0.00 0.00 6.13
778 841 3.303132 CGTGCTTTTAAGATCCATACGGC 60.303 47.826 0.00 0.00 0.00 5.68
779 842 3.247648 CCGTGCTTTTAAGATCCATACGG 59.752 47.826 0.00 0.00 41.83 4.02
780 843 3.303132 GCCGTGCTTTTAAGATCCATACG 60.303 47.826 0.00 0.00 0.00 3.06
781 844 3.003378 GGCCGTGCTTTTAAGATCCATAC 59.997 47.826 0.00 0.00 0.00 2.39
782 845 3.211045 GGCCGTGCTTTTAAGATCCATA 58.789 45.455 0.00 0.00 0.00 2.74
783 846 2.024414 GGCCGTGCTTTTAAGATCCAT 58.976 47.619 0.00 0.00 0.00 3.41
784 847 1.459450 GGCCGTGCTTTTAAGATCCA 58.541 50.000 0.00 0.00 0.00 3.41
785 848 0.738975 GGGCCGTGCTTTTAAGATCC 59.261 55.000 0.00 0.00 0.00 3.36
840 903 4.105697 TGAGTGGATTGGGTTAAGTTTCCT 59.894 41.667 0.00 0.00 0.00 3.36
990 1055 1.077828 TCCTGAGTCATGGTGAGAGGT 59.922 52.381 0.00 0.00 0.00 3.85
1020 1085 2.664851 CAGAAGTTCACGGGCGCA 60.665 61.111 10.83 0.00 0.00 6.09
1055 1120 2.117156 GCGTAGTACTCCGCCTCCA 61.117 63.158 20.91 0.00 43.96 3.86
1098 1163 1.153823 CGGCGTGGTGAAGTAGGAG 60.154 63.158 0.00 0.00 0.00 3.69
1203 1268 1.202806 CCGTAGCCATGGACCATGAAT 60.203 52.381 32.16 22.10 43.81 2.57
1215 1280 0.246910 TAATGTCGTTGCCGTAGCCA 59.753 50.000 0.00 0.00 38.69 4.75
1858 1923 4.647564 ACATCTTGATGGTCTTGTCCTT 57.352 40.909 14.18 0.00 0.00 3.36
2108 2211 6.491403 AGTTGACCAAAGACAGCTTATCAAAT 59.509 34.615 0.00 0.00 34.82 2.32
2112 2215 5.948992 AAGTTGACCAAAGACAGCTTATC 57.051 39.130 0.00 0.00 37.42 1.75
2113 2216 6.770785 TGTAAAGTTGACCAAAGACAGCTTAT 59.229 34.615 0.00 0.00 38.00 1.73
2114 2217 6.116806 TGTAAAGTTGACCAAAGACAGCTTA 58.883 36.000 0.00 0.00 38.00 3.09
2115 2218 4.947388 TGTAAAGTTGACCAAAGACAGCTT 59.053 37.500 0.00 0.00 39.92 3.74
2116 2219 4.523083 TGTAAAGTTGACCAAAGACAGCT 58.477 39.130 0.00 0.00 31.18 4.24
2117 2220 4.893424 TGTAAAGTTGACCAAAGACAGC 57.107 40.909 0.00 0.00 0.00 4.40
2118 2221 6.618287 TCATGTAAAGTTGACCAAAGACAG 57.382 37.500 0.00 0.00 0.00 3.51
2127 2230 7.919091 TGTATACCGAGATCATGTAAAGTTGAC 59.081 37.037 0.00 0.00 0.00 3.18
2145 2248 5.064707 CAGGAGACAACCATTTTGTATACCG 59.935 44.000 0.00 0.00 31.96 4.02
2238 2341 1.817099 GGCTCCAGCAGATCCAACG 60.817 63.158 0.03 0.00 44.36 4.10
2239 2342 1.817099 CGGCTCCAGCAGATCCAAC 60.817 63.158 0.03 0.00 44.36 3.77
2240 2343 2.586245 CGGCTCCAGCAGATCCAA 59.414 61.111 0.03 0.00 44.36 3.53
2241 2344 3.473647 CCGGCTCCAGCAGATCCA 61.474 66.667 0.03 0.00 44.36 3.41
2242 2345 4.925861 GCCGGCTCCAGCAGATCC 62.926 72.222 22.15 0.00 44.36 3.36
2249 2352 4.473520 ATCCAACGCCGGCTCCAG 62.474 66.667 26.68 11.62 0.00 3.86
2250 2353 4.467084 GATCCAACGCCGGCTCCA 62.467 66.667 26.68 3.66 0.00 3.86
2251 2354 4.467084 TGATCCAACGCCGGCTCC 62.467 66.667 26.68 5.77 0.00 4.70
2252 2355 2.892425 CTGATCCAACGCCGGCTC 60.892 66.667 26.68 14.74 0.00 4.70
2255 2358 3.197790 CAGCTGATCCAACGCCGG 61.198 66.667 8.42 0.00 0.00 6.13
2256 2359 3.197790 CCAGCTGATCCAACGCCG 61.198 66.667 17.39 0.00 0.00 6.46
2257 2360 2.825836 CCCAGCTGATCCAACGCC 60.826 66.667 17.39 0.00 0.00 5.68
2258 2361 2.825836 CCCCAGCTGATCCAACGC 60.826 66.667 17.39 0.00 0.00 4.84
2315 2439 1.825622 GCCAAGCTGATACAGGGCC 60.826 63.158 0.00 0.00 32.69 5.80
2334 2458 2.550180 GGCTGGAGATAAAATTCGCTCC 59.450 50.000 0.00 0.00 45.59 4.70
2490 2614 5.134725 AGTATTTAGGAACGGAGGGAGTA 57.865 43.478 0.00 0.00 0.00 2.59
2491 2615 3.959449 GAGTATTTAGGAACGGAGGGAGT 59.041 47.826 0.00 0.00 0.00 3.85
2492 2616 3.321396 GGAGTATTTAGGAACGGAGGGAG 59.679 52.174 0.00 0.00 0.00 4.30
2493 2617 3.303049 GGAGTATTTAGGAACGGAGGGA 58.697 50.000 0.00 0.00 0.00 4.20
2494 2618 2.367894 GGGAGTATTTAGGAACGGAGGG 59.632 54.545 0.00 0.00 0.00 4.30
2495 2619 3.306613 AGGGAGTATTTAGGAACGGAGG 58.693 50.000 0.00 0.00 0.00 4.30
2496 2620 3.321396 GGAGGGAGTATTTAGGAACGGAG 59.679 52.174 0.00 0.00 0.00 4.63
2497 2621 3.303049 GGAGGGAGTATTTAGGAACGGA 58.697 50.000 0.00 0.00 0.00 4.69
2498 2622 2.035576 CGGAGGGAGTATTTAGGAACGG 59.964 54.545 0.00 0.00 0.00 4.44
2499 2623 2.692041 ACGGAGGGAGTATTTAGGAACG 59.308 50.000 0.00 0.00 0.00 3.95
2500 2624 3.069300 GGACGGAGGGAGTATTTAGGAAC 59.931 52.174 0.00 0.00 0.00 3.62
2501 2625 3.303049 GGACGGAGGGAGTATTTAGGAA 58.697 50.000 0.00 0.00 0.00 3.36
2502 2626 2.425392 GGGACGGAGGGAGTATTTAGGA 60.425 54.545 0.00 0.00 0.00 2.94
2503 2627 1.969208 GGGACGGAGGGAGTATTTAGG 59.031 57.143 0.00 0.00 0.00 2.69
2504 2628 2.674420 TGGGACGGAGGGAGTATTTAG 58.326 52.381 0.00 0.00 0.00 1.85
2505 2629 2.852714 TGGGACGGAGGGAGTATTTA 57.147 50.000 0.00 0.00 0.00 1.40
2506 2630 2.191981 ATGGGACGGAGGGAGTATTT 57.808 50.000 0.00 0.00 0.00 1.40
2507 2631 2.090943 TGTATGGGACGGAGGGAGTATT 60.091 50.000 0.00 0.00 0.00 1.89
2508 2632 1.502039 TGTATGGGACGGAGGGAGTAT 59.498 52.381 0.00 0.00 0.00 2.12
2509 2633 0.928505 TGTATGGGACGGAGGGAGTA 59.071 55.000 0.00 0.00 0.00 2.59
2510 2634 0.397254 CTGTATGGGACGGAGGGAGT 60.397 60.000 0.00 0.00 36.40 3.85
2511 2635 0.106167 TCTGTATGGGACGGAGGGAG 60.106 60.000 0.00 0.00 38.61 4.30
2512 2636 0.561184 ATCTGTATGGGACGGAGGGA 59.439 55.000 0.00 0.00 46.80 4.20
2513 2637 0.681733 CATCTGTATGGGACGGAGGG 59.318 60.000 0.00 0.00 46.80 4.30
2514 2638 0.681733 CCATCTGTATGGGACGGAGG 59.318 60.000 0.00 0.00 46.80 4.30
2523 2647 6.042552 AGACAAATACTCCCTCCATCTGTATG 59.957 42.308 0.00 0.00 0.00 2.39
2524 2648 6.146760 AGACAAATACTCCCTCCATCTGTAT 58.853 40.000 0.00 0.00 0.00 2.29
2525 2649 5.529289 AGACAAATACTCCCTCCATCTGTA 58.471 41.667 0.00 0.00 0.00 2.74
2526 2650 4.366267 AGACAAATACTCCCTCCATCTGT 58.634 43.478 0.00 0.00 0.00 3.41
2527 2651 5.365021 AAGACAAATACTCCCTCCATCTG 57.635 43.478 0.00 0.00 0.00 2.90
2528 2652 6.394345 AAAAGACAAATACTCCCTCCATCT 57.606 37.500 0.00 0.00 0.00 2.90
2529 2653 8.047310 TCTAAAAAGACAAATACTCCCTCCATC 58.953 37.037 0.00 0.00 0.00 3.51
2530 2654 7.928873 TCTAAAAAGACAAATACTCCCTCCAT 58.071 34.615 0.00 0.00 0.00 3.41
2531 2655 7.236847 TCTCTAAAAAGACAAATACTCCCTCCA 59.763 37.037 0.00 0.00 0.00 3.86
2532 2656 7.621796 TCTCTAAAAAGACAAATACTCCCTCC 58.378 38.462 0.00 0.00 0.00 4.30
2533 2657 9.674068 AATCTCTAAAAAGACAAATACTCCCTC 57.326 33.333 0.00 0.00 0.00 4.30
2543 2667 9.965824 GTCCATTTGAAATCTCTAAAAAGACAA 57.034 29.630 0.00 0.00 0.00 3.18
2544 2668 9.354673 AGTCCATTTGAAATCTCTAAAAAGACA 57.645 29.630 0.00 0.00 0.00 3.41
2548 2672 9.581289 TGGTAGTCCATTTGAAATCTCTAAAAA 57.419 29.630 0.00 0.00 39.03 1.94
2549 2673 9.010029 GTGGTAGTCCATTTGAAATCTCTAAAA 57.990 33.333 0.00 0.00 46.20 1.52
2550 2674 8.160765 TGTGGTAGTCCATTTGAAATCTCTAAA 58.839 33.333 0.00 0.00 46.20 1.85
2551 2675 7.685481 TGTGGTAGTCCATTTGAAATCTCTAA 58.315 34.615 0.00 0.00 46.20 2.10
2552 2676 7.252612 TGTGGTAGTCCATTTGAAATCTCTA 57.747 36.000 0.00 0.00 46.20 2.43
2553 2677 6.126863 TGTGGTAGTCCATTTGAAATCTCT 57.873 37.500 0.00 0.00 46.20 3.10
2554 2678 6.678900 GCATGTGGTAGTCCATTTGAAATCTC 60.679 42.308 0.00 0.00 46.20 2.75
2555 2679 5.126061 GCATGTGGTAGTCCATTTGAAATCT 59.874 40.000 0.00 0.00 46.20 2.40
2556 2680 5.343249 GCATGTGGTAGTCCATTTGAAATC 58.657 41.667 0.00 0.00 46.20 2.17
2557 2681 4.142403 CGCATGTGGTAGTCCATTTGAAAT 60.142 41.667 0.00 0.00 46.20 2.17
2558 2682 3.190327 CGCATGTGGTAGTCCATTTGAAA 59.810 43.478 0.00 0.00 46.20 2.69
2559 2683 2.746904 CGCATGTGGTAGTCCATTTGAA 59.253 45.455 0.00 0.00 46.20 2.69
2560 2684 2.355197 CGCATGTGGTAGTCCATTTGA 58.645 47.619 0.00 0.00 46.20 2.69
2561 2685 1.401552 CCGCATGTGGTAGTCCATTTG 59.598 52.381 17.59 0.00 46.20 2.32
2562 2686 1.280710 TCCGCATGTGGTAGTCCATTT 59.719 47.619 24.28 0.00 46.20 2.32
2563 2687 0.908910 TCCGCATGTGGTAGTCCATT 59.091 50.000 24.28 0.00 46.20 3.16
2564 2688 1.131638 ATCCGCATGTGGTAGTCCAT 58.868 50.000 24.28 7.12 46.20 3.41
2565 2689 0.177836 CATCCGCATGTGGTAGTCCA 59.822 55.000 24.28 4.84 42.05 4.02
2566 2690 0.178068 ACATCCGCATGTGGTAGTCC 59.822 55.000 24.28 0.00 42.05 3.85
2567 2691 2.882927 TACATCCGCATGTGGTAGTC 57.117 50.000 24.28 0.00 43.54 2.59
2568 2692 3.895656 ACTATACATCCGCATGTGGTAGT 59.104 43.478 24.28 23.12 43.54 2.73
2569 2693 4.521130 ACTATACATCCGCATGTGGTAG 57.479 45.455 24.28 18.98 43.54 3.18
2570 2694 7.891498 ATATACTATACATCCGCATGTGGTA 57.109 36.000 24.28 10.63 43.54 3.25
2571 2695 6.791867 ATATACTATACATCCGCATGTGGT 57.208 37.500 24.28 8.62 43.54 4.16
2572 2696 8.076781 GTCTATATACTATACATCCGCATGTGG 58.923 40.741 19.75 19.75 43.54 4.17
2573 2697 8.621286 TGTCTATATACTATACATCCGCATGTG 58.379 37.037 1.14 0.00 43.54 3.21
2574 2698 8.747538 TGTCTATATACTATACATCCGCATGT 57.252 34.615 0.00 0.00 45.73 3.21
2609 2733 6.812160 ACGGAGTAAAATGAGTGAATCTACAC 59.188 38.462 0.00 0.00 41.94 2.90
2610 2734 6.931838 ACGGAGTAAAATGAGTGAATCTACA 58.068 36.000 0.00 0.00 41.94 2.74
2626 2750 7.255555 TTCAACAAGTGACTACATACGGAGTAA 60.256 37.037 0.00 0.00 41.03 2.24
2627 2751 6.207221 TTCAACAAGTGACTACATACGGAGTA 59.793 38.462 0.00 0.00 41.66 2.59
2628 2752 5.010314 TTCAACAAGTGACTACATACGGAGT 59.990 40.000 0.00 0.00 39.84 3.85
2629 2753 5.055642 TCAACAAGTGACTACATACGGAG 57.944 43.478 0.00 0.00 0.00 4.63
2630 2754 5.456548 TTCAACAAGTGACTACATACGGA 57.543 39.130 0.00 0.00 35.39 4.69
2631 2755 6.590292 AGATTTCAACAAGTGACTACATACGG 59.410 38.462 0.00 0.00 35.39 4.02
2632 2756 7.542477 AGAGATTTCAACAAGTGACTACATACG 59.458 37.037 0.00 0.00 35.39 3.06
2633 2757 8.764524 AGAGATTTCAACAAGTGACTACATAC 57.235 34.615 0.00 0.00 35.39 2.39
2635 2759 8.807118 TCTAGAGATTTCAACAAGTGACTACAT 58.193 33.333 0.00 0.00 35.39 2.29
2636 2760 8.178313 TCTAGAGATTTCAACAAGTGACTACA 57.822 34.615 0.00 0.00 35.39 2.74
2637 2761 9.477484 TTTCTAGAGATTTCAACAAGTGACTAC 57.523 33.333 0.00 0.00 35.39 2.73
2638 2762 9.698309 CTTTCTAGAGATTTCAACAAGTGACTA 57.302 33.333 0.00 0.00 35.39 2.59
2639 2763 8.424918 TCTTTCTAGAGATTTCAACAAGTGACT 58.575 33.333 0.00 0.00 35.39 3.41
2640 2764 8.491950 GTCTTTCTAGAGATTTCAACAAGTGAC 58.508 37.037 0.00 0.00 35.39 3.67
2641 2765 8.204160 TGTCTTTCTAGAGATTTCAACAAGTGA 58.796 33.333 0.00 0.00 0.00 3.41
2642 2766 8.370493 TGTCTTTCTAGAGATTTCAACAAGTG 57.630 34.615 0.00 0.00 0.00 3.16
2643 2767 8.964476 TTGTCTTTCTAGAGATTTCAACAAGT 57.036 30.769 0.00 0.00 0.00 3.16
2659 2783 9.413734 CCTCCATTCCTAAATATTTGTCTTTCT 57.586 33.333 11.05 0.00 0.00 2.52
2660 2784 8.633561 CCCTCCATTCCTAAATATTTGTCTTTC 58.366 37.037 11.05 0.00 0.00 2.62
2661 2785 8.343787 TCCCTCCATTCCTAAATATTTGTCTTT 58.656 33.333 11.05 0.00 0.00 2.52
2662 2786 7.882755 TCCCTCCATTCCTAAATATTTGTCTT 58.117 34.615 11.05 0.00 0.00 3.01
2663 2787 7.129504 ACTCCCTCCATTCCTAAATATTTGTCT 59.870 37.037 11.05 0.00 0.00 3.41
2664 2788 7.290813 ACTCCCTCCATTCCTAAATATTTGTC 58.709 38.462 11.05 0.00 0.00 3.18
2665 2789 7.226059 ACTCCCTCCATTCCTAAATATTTGT 57.774 36.000 11.05 0.00 0.00 2.83
2666 2790 8.440771 AGTACTCCCTCCATTCCTAAATATTTG 58.559 37.037 11.05 1.40 0.00 2.32
2667 2791 8.582891 AGTACTCCCTCCATTCCTAAATATTT 57.417 34.615 5.89 5.89 0.00 1.40
2668 2792 9.860393 ATAGTACTCCCTCCATTCCTAAATATT 57.140 33.333 0.00 0.00 0.00 1.28
2669 2793 9.495382 GATAGTACTCCCTCCATTCCTAAATAT 57.505 37.037 0.00 0.00 0.00 1.28
2670 2794 8.689054 AGATAGTACTCCCTCCATTCCTAAATA 58.311 37.037 0.00 0.00 0.00 1.40
2671 2795 7.549141 AGATAGTACTCCCTCCATTCCTAAAT 58.451 38.462 0.00 0.00 0.00 1.40
2672 2796 6.935036 AGATAGTACTCCCTCCATTCCTAAA 58.065 40.000 0.00 0.00 0.00 1.85
2673 2797 6.547396 AGATAGTACTCCCTCCATTCCTAA 57.453 41.667 0.00 0.00 0.00 2.69
2674 2798 7.848821 ATAGATAGTACTCCCTCCATTCCTA 57.151 40.000 0.00 0.00 0.00 2.94
2675 2799 6.744802 ATAGATAGTACTCCCTCCATTCCT 57.255 41.667 0.00 0.00 0.00 3.36
2676 2800 6.954684 TGAATAGATAGTACTCCCTCCATTCC 59.045 42.308 0.00 0.00 0.00 3.01
2677 2801 8.474025 CATGAATAGATAGTACTCCCTCCATTC 58.526 40.741 0.00 6.47 0.00 2.67
2678 2802 7.401493 CCATGAATAGATAGTACTCCCTCCATT 59.599 40.741 0.00 0.00 0.00 3.16
2679 2803 6.900186 CCATGAATAGATAGTACTCCCTCCAT 59.100 42.308 0.00 0.87 0.00 3.41
2680 2804 6.256819 CCATGAATAGATAGTACTCCCTCCA 58.743 44.000 0.00 0.00 0.00 3.86
2681 2805 5.659079 CCCATGAATAGATAGTACTCCCTCC 59.341 48.000 0.00 0.00 0.00 4.30
2682 2806 6.494952 TCCCATGAATAGATAGTACTCCCTC 58.505 44.000 0.00 0.00 0.00 4.30
2683 2807 6.047359 ACTCCCATGAATAGATAGTACTCCCT 59.953 42.308 0.00 0.00 0.00 4.20
2684 2808 6.153680 CACTCCCATGAATAGATAGTACTCCC 59.846 46.154 0.00 0.00 0.00 4.30
2685 2809 6.722129 ACACTCCCATGAATAGATAGTACTCC 59.278 42.308 0.00 0.00 0.00 3.85
2686 2810 7.768807 ACACTCCCATGAATAGATAGTACTC 57.231 40.000 0.00 0.00 0.00 2.59
2687 2811 9.830186 ATTACACTCCCATGAATAGATAGTACT 57.170 33.333 0.00 0.00 0.00 2.73
2723 2847 7.616313 ACAATTTTCAGTTTTTGGGTAAGTCA 58.384 30.769 0.00 0.00 0.00 3.41
2900 3024 2.375174 ACCAAGGCCACTCAAGTAATGA 59.625 45.455 5.01 0.00 36.38 2.57


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

AutoCloner maintained by Alex Coulton.