Multiple sequence alignment - TraesCS4D01G351700

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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 TraesCS4D01G351700 chr4D 100.000 3397 0 0 1 3397 503449807 503453203 0.000000e+00 6274.0
1 TraesCS4D01G351700 chr4D 92.519 802 39 12 833 1614 503507694 503506894 0.000000e+00 1129.0
2 TraesCS4D01G351700 chr4D 90.065 614 58 2 963 1576 503498437 503499047 0.000000e+00 793.0
3 TraesCS4D01G351700 chr4D 92.632 285 21 0 1709 1993 503499448 503499732 8.770000e-111 411.0
4 TraesCS4D01G351700 chr4D 84.161 423 31 16 2139 2553 503499821 503500215 8.900000e-101 377.0
5 TraesCS4D01G351700 chr4D 92.337 261 20 0 1709 1969 503506842 503506582 4.140000e-99 372.0
6 TraesCS4D01G351700 chr4D 80.208 480 48 34 2144 2613 503506400 503505958 1.970000e-82 316.0
7 TraesCS4D01G351700 chr4D 81.429 140 12 7 2710 2846 503500383 503500511 6.000000e-18 102.0
8 TraesCS4D01G351700 chr4D 90.476 63 5 1 1570 1632 503499350 503499411 7.810000e-12 82.4
9 TraesCS4D01G351700 chr4D 80.357 112 17 5 2652 2761 503505967 503505859 2.810000e-11 80.5
10 TraesCS4D01G351700 chr4D 77.692 130 15 9 2552 2679 503500251 503500368 2.190000e-07 67.6
11 TraesCS4D01G351700 chr5A 87.973 2486 142 68 620 3021 687873182 687875594 0.000000e+00 2789.0
12 TraesCS4D01G351700 chr5A 94.745 647 34 0 990 1636 687937386 687936740 0.000000e+00 1007.0
13 TraesCS4D01G351700 chr5A 86.219 283 20 12 2047 2320 687936235 687935963 4.290000e-74 289.0
14 TraesCS4D01G351700 chr5A 92.073 164 11 1 3049 3212 687876020 687876181 2.640000e-56 230.0
15 TraesCS4D01G351700 chr5A 79.718 355 38 17 2710 3050 687895205 687895539 3.410000e-55 226.0
16 TraesCS4D01G351700 chr5A 87.333 150 13 3 1690 1833 687936731 687936582 2.100000e-37 167.0
17 TraesCS4D01G351700 chr4B 91.871 1390 75 9 620 1994 648914247 648912881 0.000000e+00 1906.0
18 TraesCS4D01G351700 chr4B 91.560 1019 57 10 620 1614 648572177 648573190 0.000000e+00 1378.0
19 TraesCS4D01G351700 chr4B 88.863 844 56 15 812 1635 649223148 649222323 0.000000e+00 1003.0
20 TraesCS4D01G351700 chr4B 91.394 581 48 2 961 1540 648695671 648695092 0.000000e+00 795.0
21 TraesCS4D01G351700 chr4B 88.911 505 23 9 2050 2553 648912875 648912403 2.920000e-165 592.0
22 TraesCS4D01G351700 chr4B 84.000 600 33 20 2620 3212 648912102 648911559 5.020000e-143 518.0
23 TraesCS4D01G351700 chr4B 93.571 280 13 2 1709 1988 649222282 649222008 2.440000e-111 412.0
24 TraesCS4D01G351700 chr4B 86.141 368 33 12 2144 2497 649221812 649221449 6.880000e-102 381.0
25 TraesCS4D01G351700 chr4B 92.278 259 20 0 1711 1969 648573243 648573501 5.360000e-98 368.0
26 TraesCS4D01G351700 chr4B 91.386 267 18 2 1727 1993 648695005 648694744 8.960000e-96 361.0
27 TraesCS4D01G351700 chr4B 84.656 378 23 16 1830 2193 18702062 18702418 9.020000e-91 344.0
28 TraesCS4D01G351700 chr4B 95.031 161 8 0 2144 2304 648573706 648573866 1.560000e-63 254.0
29 TraesCS4D01G351700 chr4B 75.581 430 46 34 2652 3056 648694167 648693772 1.260000e-34 158.0
30 TraesCS4D01G351700 chr4B 76.944 360 32 25 2200 2553 648694610 648694296 1.260000e-34 158.0
31 TraesCS4D01G351700 chr4B 96.970 66 2 0 2563 2628 648912318 648912253 9.960000e-21 111.0
32 TraesCS4D01G351700 chr4B 94.203 69 3 1 3215 3282 648911525 648911457 1.670000e-18 104.0
33 TraesCS4D01G351700 chr4B 81.452 124 14 9 2652 2771 648574068 648574186 3.610000e-15 93.5
34 TraesCS4D01G351700 chr4B 98.077 52 1 0 2710 2761 649179870 649179921 1.300000e-14 91.6
35 TraesCS4D01G351700 chr4B 89.062 64 7 0 1572 1635 648695104 648695041 2.810000e-11 80.5
36 TraesCS4D01G351700 chr2B 88.799 616 63 6 8 620 677342501 677343113 0.000000e+00 750.0
37 TraesCS4D01G351700 chr6D 88.455 615 66 5 8 619 303055651 303056263 0.000000e+00 737.0
38 TraesCS4D01G351700 chr6D 89.744 585 36 15 1743 2325 17447939 17447377 0.000000e+00 726.0
39 TraesCS4D01G351700 chr7D 89.744 585 36 14 1743 2325 569233163 569232601 0.000000e+00 726.0
40 TraesCS4D01G351700 chr7D 87.132 544 63 7 77 619 552273228 552272691 8.060000e-171 610.0
41 TraesCS4D01G351700 chr3D 89.054 539 53 6 82 619 22721558 22722091 0.000000e+00 664.0
42 TraesCS4D01G351700 chr3D 87.409 548 59 10 77 620 280280517 280279976 3.720000e-174 621.0
43 TraesCS4D01G351700 chr1D 88.139 548 56 7 77 619 405389495 405390038 0.000000e+00 643.0
44 TraesCS4D01G351700 chr5B 87.912 546 60 6 77 620 302836004 302836545 3.700000e-179 638.0
45 TraesCS4D01G351700 chr5B 87.500 544 61 7 77 619 530799532 530798995 3.720000e-174 621.0
46 TraesCS4D01G351700 chr5D 87.454 542 63 5 79 619 501431517 501430980 1.340000e-173 619.0
47 TraesCS4D01G351700 chr1B 86.798 356 38 5 901 1255 280756432 280756085 4.110000e-104 388.0
48 TraesCS4D01G351700 chr7A 81.159 207 31 5 1389 1588 30090106 30090311 3.510000e-35 159.0


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 TraesCS4D01G351700 chr4D 503449807 503453203 3396 False 6274.000000 6274 100.000000 1 3397 1 chr4D.!!$F1 3396
1 TraesCS4D01G351700 chr4D 503505859 503507694 1835 True 474.375000 1129 86.355250 833 2761 4 chr4D.!!$R1 1928
2 TraesCS4D01G351700 chr4D 503498437 503500511 2074 False 305.500000 793 86.075833 963 2846 6 chr4D.!!$F2 1883
3 TraesCS4D01G351700 chr5A 687873182 687876181 2999 False 1509.500000 2789 90.023000 620 3212 2 chr5A.!!$F2 2592
4 TraesCS4D01G351700 chr5A 687935963 687937386 1423 True 487.666667 1007 89.432333 990 2320 3 chr5A.!!$R1 1330
5 TraesCS4D01G351700 chr4B 648911457 648914247 2790 True 646.200000 1906 91.191000 620 3282 5 chr4B.!!$R2 2662
6 TraesCS4D01G351700 chr4B 649221449 649223148 1699 True 598.666667 1003 89.525000 812 2497 3 chr4B.!!$R3 1685
7 TraesCS4D01G351700 chr4B 648572177 648574186 2009 False 523.375000 1378 90.080250 620 2771 4 chr4B.!!$F3 2151
8 TraesCS4D01G351700 chr4B 648693772 648695671 1899 True 310.500000 795 84.873400 961 3056 5 chr4B.!!$R1 2095
9 TraesCS4D01G351700 chr2B 677342501 677343113 612 False 750.000000 750 88.799000 8 620 1 chr2B.!!$F1 612
10 TraesCS4D01G351700 chr6D 303055651 303056263 612 False 737.000000 737 88.455000 8 619 1 chr6D.!!$F1 611
11 TraesCS4D01G351700 chr6D 17447377 17447939 562 True 726.000000 726 89.744000 1743 2325 1 chr6D.!!$R1 582
12 TraesCS4D01G351700 chr7D 569232601 569233163 562 True 726.000000 726 89.744000 1743 2325 1 chr7D.!!$R2 582
13 TraesCS4D01G351700 chr7D 552272691 552273228 537 True 610.000000 610 87.132000 77 619 1 chr7D.!!$R1 542
14 TraesCS4D01G351700 chr3D 22721558 22722091 533 False 664.000000 664 89.054000 82 619 1 chr3D.!!$F1 537
15 TraesCS4D01G351700 chr3D 280279976 280280517 541 True 621.000000 621 87.409000 77 620 1 chr3D.!!$R1 543
16 TraesCS4D01G351700 chr1D 405389495 405390038 543 False 643.000000 643 88.139000 77 619 1 chr1D.!!$F1 542
17 TraesCS4D01G351700 chr5B 302836004 302836545 541 False 638.000000 638 87.912000 77 620 1 chr5B.!!$F1 543
18 TraesCS4D01G351700 chr5B 530798995 530799532 537 True 621.000000 621 87.500000 77 619 1 chr5B.!!$R1 542
19 TraesCS4D01G351700 chr5D 501430980 501431517 537 True 619.000000 619 87.454000 79 619 1 chr5D.!!$R1 540

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
51 52 0.106918 TGGGCATTTATCCGGTCACC 60.107 55.0 0.00 0.00 0.00 4.02 F
58 59 0.244450 TTATCCGGTCACCACACGTC 59.756 55.0 0.00 0.00 0.00 4.34 F
765 839 0.467844 TGCCATCAAATCATCGGGGG 60.468 55.0 0.00 0.00 0.00 5.40 F
910 1024 0.615827 TCTCTGGCAAGCTAGCTCCA 60.616 55.0 19.65 20.31 34.17 3.86 F
2326 3033 0.033504 GGCTCGAGTCAACAAGGACA 59.966 55.0 13.26 0.00 40.29 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1425 1539 0.252197 AATGGCCGAGGTAGTTGGTC 59.748 55.000 0.00 0.0 34.33 4.02 R
1777 2245 1.301716 GTTGGCGAGCTTGGAGACA 60.302 57.895 2.37 0.0 39.83 3.41 R
2109 2774 0.026027 CTACGTACGTCAGCGAGGAC 59.974 60.000 26.53 0.0 42.00 3.85 R
2341 3048 0.321919 TGATGTTCCTGTCCAGCAGC 60.322 55.000 0.00 0.0 43.71 5.25 R
3142 4604 2.125202 GAAAACCTTGTGCCCGGTCG 62.125 60.000 0.00 0.0 31.87 4.79 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
21 22 1.320344 TAGCCTGCCACGTAGGACTG 61.320 60.000 7.05 3.66 37.63 3.51
22 23 2.579201 CCTGCCACGTAGGACTGG 59.421 66.667 8.04 8.35 37.63 4.00
23 24 2.579201 CTGCCACGTAGGACTGGG 59.421 66.667 8.04 0.00 41.22 4.45
24 25 3.665675 CTGCCACGTAGGACTGGGC 62.666 68.421 8.04 6.09 44.82 5.36
25 26 3.391382 GCCACGTAGGACTGGGCT 61.391 66.667 8.04 0.00 41.39 5.19
26 27 2.579201 CCACGTAGGACTGGGCTG 59.421 66.667 0.00 0.00 41.22 4.85
27 28 1.982395 CCACGTAGGACTGGGCTGA 60.982 63.158 0.00 0.00 41.22 4.26
28 29 1.330655 CCACGTAGGACTGGGCTGAT 61.331 60.000 0.00 0.00 41.22 2.90
29 30 0.179100 CACGTAGGACTGGGCTGATG 60.179 60.000 0.00 0.00 0.00 3.07
30 31 0.614979 ACGTAGGACTGGGCTGATGT 60.615 55.000 0.00 0.00 0.00 3.06
31 32 1.341679 ACGTAGGACTGGGCTGATGTA 60.342 52.381 0.00 0.00 0.00 2.29
32 33 1.964223 CGTAGGACTGGGCTGATGTAT 59.036 52.381 0.00 0.00 0.00 2.29
33 34 2.288457 CGTAGGACTGGGCTGATGTATG 60.288 54.545 0.00 0.00 0.00 2.39
34 35 1.135094 AGGACTGGGCTGATGTATGG 58.865 55.000 0.00 0.00 0.00 2.74
35 36 0.109342 GGACTGGGCTGATGTATGGG 59.891 60.000 0.00 0.00 0.00 4.00
36 37 0.536006 GACTGGGCTGATGTATGGGC 60.536 60.000 0.00 0.00 0.00 5.36
37 38 1.281199 ACTGGGCTGATGTATGGGCA 61.281 55.000 0.00 0.00 0.00 5.36
38 39 0.111832 CTGGGCTGATGTATGGGCAT 59.888 55.000 0.00 0.00 0.00 4.40
39 40 0.557238 TGGGCTGATGTATGGGCATT 59.443 50.000 0.00 0.00 0.00 3.56
40 41 1.063038 TGGGCTGATGTATGGGCATTT 60.063 47.619 0.00 0.00 0.00 2.32
41 42 2.176581 TGGGCTGATGTATGGGCATTTA 59.823 45.455 0.00 0.00 0.00 1.40
42 43 3.181419 TGGGCTGATGTATGGGCATTTAT 60.181 43.478 0.00 0.00 0.00 1.40
43 44 3.445096 GGGCTGATGTATGGGCATTTATC 59.555 47.826 0.00 0.00 0.00 1.75
44 45 3.445096 GGCTGATGTATGGGCATTTATCC 59.555 47.826 0.00 0.00 0.00 2.59
45 46 3.127548 GCTGATGTATGGGCATTTATCCG 59.872 47.826 0.00 0.00 0.00 4.18
46 47 3.684908 TGATGTATGGGCATTTATCCGG 58.315 45.455 0.00 0.00 0.00 5.14
47 48 3.073798 TGATGTATGGGCATTTATCCGGT 59.926 43.478 0.00 0.00 0.00 5.28
48 49 3.134574 TGTATGGGCATTTATCCGGTC 57.865 47.619 0.00 0.00 0.00 4.79
49 50 2.439880 TGTATGGGCATTTATCCGGTCA 59.560 45.455 0.00 0.00 0.00 4.02
50 51 1.981256 ATGGGCATTTATCCGGTCAC 58.019 50.000 0.00 0.00 0.00 3.67
51 52 0.106918 TGGGCATTTATCCGGTCACC 60.107 55.000 0.00 0.00 0.00 4.02
52 53 0.106918 GGGCATTTATCCGGTCACCA 60.107 55.000 0.00 0.00 0.00 4.17
53 54 1.021968 GGCATTTATCCGGTCACCAC 58.978 55.000 0.00 0.00 0.00 4.16
54 55 1.680555 GGCATTTATCCGGTCACCACA 60.681 52.381 0.00 0.00 0.00 4.17
55 56 1.400494 GCATTTATCCGGTCACCACAC 59.600 52.381 0.00 0.00 0.00 3.82
56 57 1.663643 CATTTATCCGGTCACCACACG 59.336 52.381 0.00 0.00 0.00 4.49
57 58 0.680618 TTTATCCGGTCACCACACGT 59.319 50.000 0.00 0.00 0.00 4.49
58 59 0.244450 TTATCCGGTCACCACACGTC 59.756 55.000 0.00 0.00 0.00 4.34
59 60 1.597797 TATCCGGTCACCACACGTCC 61.598 60.000 0.00 0.00 0.00 4.79
61 62 4.274700 CGGTCACCACACGTCCGT 62.275 66.667 0.00 0.00 36.99 4.69
62 63 2.107546 GGTCACCACACGTCCGTT 59.892 61.111 0.00 0.00 0.00 4.44
63 64 1.522130 GGTCACCACACGTCCGTTT 60.522 57.895 0.00 0.00 0.00 3.60
64 65 1.493134 GGTCACCACACGTCCGTTTC 61.493 60.000 0.00 0.00 0.00 2.78
65 66 0.806884 GTCACCACACGTCCGTTTCA 60.807 55.000 0.00 0.00 0.00 2.69
66 67 0.806884 TCACCACACGTCCGTTTCAC 60.807 55.000 0.00 0.00 0.00 3.18
67 68 1.522130 ACCACACGTCCGTTTCACC 60.522 57.895 0.00 0.00 0.00 4.02
68 69 1.521906 CCACACGTCCGTTTCACCA 60.522 57.895 0.00 0.00 0.00 4.17
69 70 0.882927 CCACACGTCCGTTTCACCAT 60.883 55.000 0.00 0.00 0.00 3.55
70 71 1.605968 CCACACGTCCGTTTCACCATA 60.606 52.381 0.00 0.00 0.00 2.74
71 72 2.136728 CACACGTCCGTTTCACCATAA 58.863 47.619 0.00 0.00 0.00 1.90
72 73 2.156891 CACACGTCCGTTTCACCATAAG 59.843 50.000 0.00 0.00 0.00 1.73
73 74 1.730064 CACGTCCGTTTCACCATAAGG 59.270 52.381 0.00 0.00 42.21 2.69
74 75 1.619827 ACGTCCGTTTCACCATAAGGA 59.380 47.619 0.00 0.00 38.69 3.36
75 76 2.268298 CGTCCGTTTCACCATAAGGAG 58.732 52.381 0.00 0.00 38.69 3.69
96 153 3.030652 CTGGTGTGTGGGCGTTTC 58.969 61.111 0.00 0.00 0.00 2.78
122 179 1.732683 GCCCACACGCCAATTTTCG 60.733 57.895 0.00 0.00 0.00 3.46
143 200 2.611800 ATGCAGAGGGGCTGGTGA 60.612 61.111 0.00 0.00 45.03 4.02
154 211 2.617274 GCTGGTGAGTGGGCGTTTC 61.617 63.158 0.00 0.00 0.00 2.78
216 274 1.240256 GGTGTGTGGGCGTTTATCAA 58.760 50.000 0.00 0.00 0.00 2.57
228 286 3.190535 GCGTTTATCAATTCACCCACACT 59.809 43.478 0.00 0.00 0.00 3.55
236 295 1.052124 TTCACCCACACTCCCGTCTT 61.052 55.000 0.00 0.00 0.00 3.01
280 340 0.758310 TGCCATGTGTTTTGCAGGGA 60.758 50.000 0.00 0.00 39.89 4.20
353 416 1.883275 CCCGAGTTGCCATGTGTTTTA 59.117 47.619 0.00 0.00 0.00 1.52
370 433 3.380471 TTTAGCAGGGTACATGGCAAT 57.620 42.857 0.00 0.00 0.00 3.56
386 449 2.599659 GCAATTGCCTTACTGTGCTTC 58.400 47.619 20.06 0.00 34.31 3.86
414 477 2.743636 TGGCAACTCTCTCTTTACCG 57.256 50.000 0.00 0.00 37.61 4.02
475 543 2.405892 GCAACTGCCAAGTGTTAGTG 57.594 50.000 0.00 0.00 36.51 2.74
486 554 0.951558 GTGTTAGTGGGTGGCAACTG 59.048 55.000 0.97 0.00 37.61 3.16
572 642 5.412594 TGTCCAAAAATGACATCTAGCACTC 59.587 40.000 0.00 0.00 37.80 3.51
573 643 5.412594 GTCCAAAAATGACATCTAGCACTCA 59.587 40.000 0.00 0.00 32.91 3.41
765 839 0.467844 TGCCATCAAATCATCGGGGG 60.468 55.000 0.00 0.00 0.00 5.40
796 880 2.609183 ATTAGCTCCGTCCGTCGCAC 62.609 60.000 0.00 0.00 38.35 5.34
815 899 2.033602 GTACTTGGGCTTGGGCGT 59.966 61.111 0.00 0.00 39.81 5.68
910 1024 0.615827 TCTCTGGCAAGCTAGCTCCA 60.616 55.000 19.65 20.31 34.17 3.86
941 1055 3.315470 CCGAGTGTCGATCAGGAAGATAA 59.685 47.826 0.00 0.00 43.74 1.75
1060 1174 4.388499 GCGGGTTCGGCTCCAAGA 62.388 66.667 0.00 0.00 36.79 3.02
1122 1236 1.450134 GCTCACCGCCATCATCACA 60.450 57.895 0.00 0.00 0.00 3.58
1191 1305 2.436646 GGTGCGAGGGTGGTCATG 60.437 66.667 0.00 0.00 0.00 3.07
1293 1407 2.101965 CTCGACCTCAGCTCGCTG 59.898 66.667 12.54 12.54 44.86 5.18
1425 1539 1.874019 CGTGGAGATGACCTTCGCG 60.874 63.158 0.00 0.00 46.51 5.87
1461 1575 2.616510 CCATTTCCTCCTGACGAAGCTT 60.617 50.000 0.00 0.00 0.00 3.74
1627 2072 2.363788 TCTTTCATCGGTCCTTCACG 57.636 50.000 0.00 0.00 0.00 4.35
1637 2082 2.673833 GGTCCTTCACGTAACTCTGTG 58.326 52.381 0.00 0.00 37.44 3.66
1796 2264 1.004440 GTCTCCAAGCTCGCCAACT 60.004 57.895 0.00 0.00 0.00 3.16
1963 2525 0.913451 AGCTGCTCAAGACCATCCCT 60.913 55.000 0.00 0.00 0.00 4.20
1993 2601 4.081420 AGGTGACGATTAATCAACTGCTCT 60.081 41.667 15.57 1.56 42.63 4.09
1994 2602 5.127194 AGGTGACGATTAATCAACTGCTCTA 59.873 40.000 15.57 0.00 42.63 2.43
1995 2603 5.810587 GGTGACGATTAATCAACTGCTCTAA 59.189 40.000 15.57 0.00 30.67 2.10
1996 2604 6.480320 GGTGACGATTAATCAACTGCTCTAAT 59.520 38.462 15.57 0.00 30.67 1.73
1997 2605 7.306866 GGTGACGATTAATCAACTGCTCTAATC 60.307 40.741 15.57 0.00 30.67 1.75
1998 2606 7.436673 GTGACGATTAATCAACTGCTCTAATCT 59.563 37.037 15.57 0.00 30.26 2.40
1999 2607 7.436376 TGACGATTAATCAACTGCTCTAATCTG 59.564 37.037 15.57 0.00 30.26 2.90
2000 2608 6.201806 ACGATTAATCAACTGCTCTAATCTGC 59.798 38.462 15.57 0.00 30.26 4.26
2009 2617 4.987285 ACTGCTCTAATCTGCGTTATCATG 59.013 41.667 0.00 0.00 0.00 3.07
2012 2620 4.747108 GCTCTAATCTGCGTTATCATGTGT 59.253 41.667 0.00 0.00 0.00 3.72
2138 2812 1.351012 CGTACGTAGTGCCCTCTCG 59.649 63.158 7.22 0.00 45.73 4.04
2325 3032 1.009389 CGGCTCGAGTCAACAAGGAC 61.009 60.000 18.62 0.00 38.08 3.85
2326 3033 0.033504 GGCTCGAGTCAACAAGGACA 59.966 55.000 13.26 0.00 40.29 4.02
2327 3034 1.540363 GGCTCGAGTCAACAAGGACAA 60.540 52.381 13.26 0.00 40.29 3.18
2328 3035 1.795286 GCTCGAGTCAACAAGGACAAG 59.205 52.381 15.13 0.00 40.29 3.16
2329 3036 2.803492 GCTCGAGTCAACAAGGACAAGT 60.803 50.000 15.13 0.00 40.29 3.16
2330 3037 3.552273 GCTCGAGTCAACAAGGACAAGTA 60.552 47.826 15.13 0.00 40.29 2.24
2331 3038 3.973657 TCGAGTCAACAAGGACAAGTAC 58.026 45.455 0.00 0.00 40.29 2.73
2332 3039 3.635373 TCGAGTCAACAAGGACAAGTACT 59.365 43.478 0.00 0.00 40.29 2.73
2333 3040 3.982058 CGAGTCAACAAGGACAAGTACTC 59.018 47.826 0.00 0.00 40.29 2.59
2334 3041 4.308265 GAGTCAACAAGGACAAGTACTCC 58.692 47.826 0.00 0.00 40.29 3.85
2335 3042 3.709653 AGTCAACAAGGACAAGTACTCCA 59.290 43.478 0.00 0.00 40.29 3.86
2336 3043 4.163458 AGTCAACAAGGACAAGTACTCCAA 59.837 41.667 0.00 0.00 40.29 3.53
2337 3044 5.063880 GTCAACAAGGACAAGTACTCCAAT 58.936 41.667 0.00 0.00 37.73 3.16
2338 3045 6.042781 AGTCAACAAGGACAAGTACTCCAATA 59.957 38.462 0.00 0.00 40.29 1.90
2339 3046 6.147328 GTCAACAAGGACAAGTACTCCAATAC 59.853 42.308 0.00 0.00 37.73 1.89
2340 3047 4.817517 ACAAGGACAAGTACTCCAATACG 58.182 43.478 0.00 0.00 0.00 3.06
2341 3048 4.181578 CAAGGACAAGTACTCCAATACGG 58.818 47.826 0.00 0.00 0.00 4.02
2342 3049 2.167900 AGGACAAGTACTCCAATACGGC 59.832 50.000 0.00 0.00 33.14 5.68
2343 3050 2.167900 GGACAAGTACTCCAATACGGCT 59.832 50.000 0.00 0.00 33.14 5.52
2344 3051 3.187700 GACAAGTACTCCAATACGGCTG 58.812 50.000 0.00 0.00 33.14 4.85
2346 3053 1.486211 AGTACTCCAATACGGCTGCT 58.514 50.000 0.00 0.00 33.14 4.24
2360 3082 3.942351 CTGCTGGACAGGAACATCA 57.058 52.632 1.01 0.00 43.19 3.07
2410 3149 3.128349 CCGTGTAAACATATTCCTCCCG 58.872 50.000 0.00 0.00 0.00 5.14
2514 3255 4.051237 TGTTTGTCACAGAGTGAAGATCG 58.949 43.478 0.82 0.00 44.49 3.69
2532 3273 2.093106 TCGTCTGTAAGGAAGAGCTCC 58.907 52.381 10.93 0.00 45.81 4.70
2706 3692 4.222886 CACATACAGTATGCTCGTAGCTC 58.777 47.826 18.99 0.00 42.97 4.09
2832 3840 2.042686 GCTGGTGCAAGGTGATGATA 57.957 50.000 0.00 0.00 39.41 2.15
2833 3841 1.672881 GCTGGTGCAAGGTGATGATAC 59.327 52.381 0.00 0.00 39.41 2.24
2837 3845 3.774766 TGGTGCAAGGTGATGATACTACT 59.225 43.478 0.00 0.00 0.00 2.57
2838 3846 4.959839 TGGTGCAAGGTGATGATACTACTA 59.040 41.667 0.00 0.00 0.00 1.82
2888 3909 2.247637 CGCTGTATTGTCTCGTTCGAA 58.752 47.619 0.00 0.00 0.00 3.71
2901 3922 1.531264 CGTTCGAATGGACTCGTCGAT 60.531 52.381 9.62 0.00 39.84 3.59
2909 3930 4.175489 ACTCGTCGATCGGCCGTG 62.175 66.667 27.15 18.56 40.32 4.94
2945 3975 1.335142 GCCTGTCGAGACGTATCATCC 60.335 57.143 11.25 0.00 0.00 3.51
2949 3979 0.942252 TCGAGACGTATCATCCACGG 59.058 55.000 11.25 0.00 43.59 4.94
3036 4498 3.691342 GGCCGTTTTCCCTTGGGC 61.691 66.667 0.00 0.00 43.01 5.36
3063 4525 1.871126 GCTTCCTTGAACAGGGCTGC 61.871 60.000 0.00 0.00 44.12 5.25
3103 4565 4.897509 TTCTTCTGTGACATGAGATGGT 57.102 40.909 0.00 0.00 33.60 3.55
3174 4636 4.703093 ACAAGGTTTTCCGTTTCTTTCTGA 59.297 37.500 0.00 0.00 46.35 3.27
3175 4637 4.895224 AGGTTTTCCGTTTCTTTCTGAC 57.105 40.909 0.00 0.00 46.35 3.51
3249 4742 1.806461 GAGTGAGGGCTCGTGTCACA 61.806 60.000 7.16 0.00 42.59 3.58
3282 4776 5.183904 CCTTTTATTCGGGGATTCCATCATC 59.816 44.000 4.80 0.00 34.36 2.92
3283 4777 4.991789 TTATTCGGGGATTCCATCATCA 57.008 40.909 4.80 0.00 34.36 3.07
3284 4778 2.638480 TTCGGGGATTCCATCATCAC 57.362 50.000 4.80 0.00 34.36 3.06
3285 4779 1.806496 TCGGGGATTCCATCATCACT 58.194 50.000 4.80 0.00 34.36 3.41
3286 4780 2.970987 TCGGGGATTCCATCATCACTA 58.029 47.619 4.80 0.00 34.36 2.74
3287 4781 3.520696 TCGGGGATTCCATCATCACTAT 58.479 45.455 4.80 0.00 34.36 2.12
3288 4782 3.909995 TCGGGGATTCCATCATCACTATT 59.090 43.478 4.80 0.00 34.36 1.73
3289 4783 4.350816 TCGGGGATTCCATCATCACTATTT 59.649 41.667 4.80 0.00 34.36 1.40
3290 4784 5.546110 TCGGGGATTCCATCATCACTATTTA 59.454 40.000 4.80 0.00 34.36 1.40
3291 4785 6.215431 TCGGGGATTCCATCATCACTATTTAT 59.785 38.462 4.80 0.00 34.36 1.40
3292 4786 6.540189 CGGGGATTCCATCATCACTATTTATC 59.460 42.308 4.80 0.00 34.36 1.75
3293 4787 6.830838 GGGGATTCCATCATCACTATTTATCC 59.169 42.308 4.80 0.00 35.00 2.59
3294 4788 7.405292 GGGATTCCATCATCACTATTTATCCA 58.595 38.462 4.80 0.00 31.62 3.41
3295 4789 8.057623 GGGATTCCATCATCACTATTTATCCAT 58.942 37.037 4.80 0.00 31.62 3.41
3321 4815 8.336801 AGAACTACAAGGATAACAAATTGGAC 57.663 34.615 0.00 0.00 0.00 4.02
3322 4816 7.393515 AGAACTACAAGGATAACAAATTGGACC 59.606 37.037 0.00 0.00 0.00 4.46
3323 4817 5.646360 ACTACAAGGATAACAAATTGGACCG 59.354 40.000 0.00 0.00 0.00 4.79
3324 4818 4.658063 ACAAGGATAACAAATTGGACCGA 58.342 39.130 0.00 0.00 0.00 4.69
3325 4819 4.700213 ACAAGGATAACAAATTGGACCGAG 59.300 41.667 0.00 0.00 0.00 4.63
3326 4820 3.886123 AGGATAACAAATTGGACCGAGG 58.114 45.455 0.00 0.00 0.00 4.63
3327 4821 3.265995 AGGATAACAAATTGGACCGAGGT 59.734 43.478 0.00 0.00 0.00 3.85
3328 4822 4.014406 GGATAACAAATTGGACCGAGGTT 58.986 43.478 0.00 0.00 0.00 3.50
3329 4823 4.461431 GGATAACAAATTGGACCGAGGTTT 59.539 41.667 0.00 0.00 0.00 3.27
3330 4824 5.648960 GGATAACAAATTGGACCGAGGTTTA 59.351 40.000 0.00 0.00 0.00 2.01
3331 4825 6.151480 GGATAACAAATTGGACCGAGGTTTAA 59.849 38.462 0.00 0.00 0.00 1.52
3332 4826 7.147966 GGATAACAAATTGGACCGAGGTTTAAT 60.148 37.037 0.00 0.00 0.00 1.40
3333 4827 6.413783 AACAAATTGGACCGAGGTTTAATT 57.586 33.333 0.00 4.34 0.00 1.40
3334 4828 6.413783 ACAAATTGGACCGAGGTTTAATTT 57.586 33.333 17.14 17.14 35.93 1.82
3335 4829 6.822442 ACAAATTGGACCGAGGTTTAATTTT 58.178 32.000 18.87 12.30 34.68 1.82
3336 4830 7.276658 ACAAATTGGACCGAGGTTTAATTTTT 58.723 30.769 18.87 13.97 34.68 1.94
3376 4870 3.705051 TGGACCTCCAATAGTCTAACGT 58.295 45.455 0.00 0.00 44.35 3.99
3377 4871 4.858850 TGGACCTCCAATAGTCTAACGTA 58.141 43.478 0.00 0.00 44.35 3.57
3378 4872 5.452255 TGGACCTCCAATAGTCTAACGTAT 58.548 41.667 0.00 0.00 44.35 3.06
3379 4873 5.301045 TGGACCTCCAATAGTCTAACGTATG 59.699 44.000 0.00 0.00 44.35 2.39
3380 4874 5.301298 GGACCTCCAATAGTCTAACGTATGT 59.699 44.000 0.00 0.00 35.64 2.29
3381 4875 6.145338 ACCTCCAATAGTCTAACGTATGTG 57.855 41.667 0.00 0.00 0.00 3.21
3382 4876 4.982916 CCTCCAATAGTCTAACGTATGTGC 59.017 45.833 0.00 0.00 0.00 4.57
3383 4877 4.603985 TCCAATAGTCTAACGTATGTGCG 58.396 43.478 0.00 0.00 37.94 5.34
3392 4886 2.380084 ACGTATGTGCGTTCAGGATT 57.620 45.000 0.00 0.00 43.04 3.01
3393 4887 3.513680 ACGTATGTGCGTTCAGGATTA 57.486 42.857 0.00 0.00 43.04 1.75
3394 4888 3.184541 ACGTATGTGCGTTCAGGATTAC 58.815 45.455 0.00 0.00 43.04 1.89
3395 4889 3.183754 CGTATGTGCGTTCAGGATTACA 58.816 45.455 0.00 0.00 0.00 2.41
3396 4890 3.802139 CGTATGTGCGTTCAGGATTACAT 59.198 43.478 0.00 0.00 33.74 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.248289 GTCCTACGTGGCAGGCTAAA 59.752 55.000 7.17 0.00 35.26 1.85
2 3 1.000019 AGTCCTACGTGGCAGGCTA 60.000 57.895 7.17 0.00 35.26 3.93
3 4 2.283966 AGTCCTACGTGGCAGGCT 60.284 61.111 7.17 0.00 35.26 4.58
4 5 2.125512 CAGTCCTACGTGGCAGGC 60.126 66.667 7.17 0.00 35.26 4.85
5 6 2.579201 CCAGTCCTACGTGGCAGG 59.421 66.667 5.50 5.50 35.26 4.85
6 7 2.579201 CCCAGTCCTACGTGGCAG 59.421 66.667 0.00 0.00 35.26 4.85
21 22 1.708341 AAATGCCCATACATCAGCCC 58.292 50.000 0.00 0.00 0.00 5.19
22 23 3.445096 GGATAAATGCCCATACATCAGCC 59.555 47.826 5.11 0.00 0.00 4.85
23 24 3.127548 CGGATAAATGCCCATACATCAGC 59.872 47.826 0.00 0.00 0.00 4.26
24 25 3.691118 CCGGATAAATGCCCATACATCAG 59.309 47.826 0.00 2.08 0.00 2.90
25 26 3.073798 ACCGGATAAATGCCCATACATCA 59.926 43.478 9.46 0.00 0.00 3.07
26 27 3.686016 ACCGGATAAATGCCCATACATC 58.314 45.455 9.46 0.00 0.00 3.06
27 28 3.073798 TGACCGGATAAATGCCCATACAT 59.926 43.478 9.46 0.00 0.00 2.29
28 29 2.439880 TGACCGGATAAATGCCCATACA 59.560 45.455 9.46 0.00 0.00 2.29
29 30 2.812011 GTGACCGGATAAATGCCCATAC 59.188 50.000 9.46 0.00 0.00 2.39
30 31 2.224670 GGTGACCGGATAAATGCCCATA 60.225 50.000 9.46 0.00 0.00 2.74
31 32 1.478654 GGTGACCGGATAAATGCCCAT 60.479 52.381 9.46 0.00 0.00 4.00
32 33 0.106918 GGTGACCGGATAAATGCCCA 60.107 55.000 9.46 0.00 0.00 5.36
33 34 0.106918 TGGTGACCGGATAAATGCCC 60.107 55.000 9.46 0.00 0.00 5.36
34 35 1.021968 GTGGTGACCGGATAAATGCC 58.978 55.000 9.46 0.45 0.00 4.40
35 36 1.400494 GTGTGGTGACCGGATAAATGC 59.600 52.381 9.46 0.00 0.00 3.56
36 37 1.663643 CGTGTGGTGACCGGATAAATG 59.336 52.381 9.46 0.00 0.00 2.32
37 38 1.276989 ACGTGTGGTGACCGGATAAAT 59.723 47.619 9.46 0.00 0.00 1.40
38 39 0.680618 ACGTGTGGTGACCGGATAAA 59.319 50.000 9.46 0.00 0.00 1.40
39 40 0.244450 GACGTGTGGTGACCGGATAA 59.756 55.000 9.46 0.00 0.00 1.75
40 41 1.597797 GGACGTGTGGTGACCGGATA 61.598 60.000 9.46 0.00 0.00 2.59
41 42 2.654877 GACGTGTGGTGACCGGAT 59.345 61.111 9.46 0.00 0.00 4.18
42 43 3.608662 GGACGTGTGGTGACCGGA 61.609 66.667 9.46 0.00 0.00 5.14
45 46 1.493134 GAAACGGACGTGTGGTGACC 61.493 60.000 0.00 0.00 0.00 4.02
46 47 0.806884 TGAAACGGACGTGTGGTGAC 60.807 55.000 0.00 0.00 0.00 3.67
47 48 0.806884 GTGAAACGGACGTGTGGTGA 60.807 55.000 0.00 0.00 0.00 4.02
48 49 1.639534 GTGAAACGGACGTGTGGTG 59.360 57.895 0.00 0.00 0.00 4.17
49 50 1.522130 GGTGAAACGGACGTGTGGT 60.522 57.895 0.00 0.00 38.12 4.16
50 51 0.882927 ATGGTGAAACGGACGTGTGG 60.883 55.000 0.00 0.00 38.12 4.17
51 52 1.785768 TATGGTGAAACGGACGTGTG 58.214 50.000 0.00 0.00 38.12 3.82
52 53 2.409975 CTTATGGTGAAACGGACGTGT 58.590 47.619 0.00 0.00 38.12 4.49
53 54 1.730064 CCTTATGGTGAAACGGACGTG 59.270 52.381 0.00 0.00 38.12 4.49
54 55 1.619827 TCCTTATGGTGAAACGGACGT 59.380 47.619 0.00 0.00 38.12 4.34
55 56 2.268298 CTCCTTATGGTGAAACGGACG 58.732 52.381 0.00 0.00 38.12 4.79
56 57 2.629051 CCTCCTTATGGTGAAACGGAC 58.371 52.381 0.00 0.00 38.12 4.79
57 58 1.557832 CCCTCCTTATGGTGAAACGGA 59.442 52.381 0.00 0.00 38.12 4.69
58 59 1.408266 CCCCTCCTTATGGTGAAACGG 60.408 57.143 0.00 0.00 38.12 4.44
59 60 2.017113 GCCCCTCCTTATGGTGAAACG 61.017 57.143 0.00 0.00 38.12 3.60
60 61 1.285078 AGCCCCTCCTTATGGTGAAAC 59.715 52.381 0.00 0.00 34.23 2.78
61 62 1.284785 CAGCCCCTCCTTATGGTGAAA 59.715 52.381 0.00 0.00 34.23 2.69
62 63 0.918983 CAGCCCCTCCTTATGGTGAA 59.081 55.000 0.00 0.00 34.23 3.18
63 64 0.988145 CCAGCCCCTCCTTATGGTGA 60.988 60.000 0.00 0.00 34.23 4.02
64 65 1.281925 ACCAGCCCCTCCTTATGGTG 61.282 60.000 0.00 0.00 42.56 4.17
65 66 1.084842 ACCAGCCCCTCCTTATGGT 59.915 57.895 0.00 0.00 39.42 3.55
66 67 1.281925 ACACCAGCCCCTCCTTATGG 61.282 60.000 0.00 0.00 37.07 2.74
67 68 0.107017 CACACCAGCCCCTCCTTATG 60.107 60.000 0.00 0.00 0.00 1.90
68 69 0.550147 ACACACCAGCCCCTCCTTAT 60.550 55.000 0.00 0.00 0.00 1.73
69 70 1.151899 ACACACCAGCCCCTCCTTA 60.152 57.895 0.00 0.00 0.00 2.69
70 71 2.450502 ACACACCAGCCCCTCCTT 60.451 61.111 0.00 0.00 0.00 3.36
71 72 3.252284 CACACACCAGCCCCTCCT 61.252 66.667 0.00 0.00 0.00 3.69
72 73 4.351054 CCACACACCAGCCCCTCC 62.351 72.222 0.00 0.00 0.00 4.30
73 74 4.351054 CCCACACACCAGCCCCTC 62.351 72.222 0.00 0.00 0.00 4.30
216 274 3.900888 ACGGGAGTGTGGGTGAAT 58.099 55.556 0.00 0.00 44.82 2.57
228 286 0.898789 GTGTGGGAGAGAAGACGGGA 60.899 60.000 0.00 0.00 0.00 5.14
236 295 1.142870 CAACTTTGGGTGTGGGAGAGA 59.857 52.381 0.00 0.00 0.00 3.10
328 390 1.468520 CACATGGCAACTCGGGTAAAG 59.531 52.381 0.00 0.00 37.61 1.85
353 416 1.477553 CAATTGCCATGTACCCTGCT 58.522 50.000 0.00 0.00 0.00 4.24
386 449 3.132646 AGAGAGAGTTGCCATCTGCTTAG 59.867 47.826 0.00 0.00 42.00 2.18
465 533 1.214424 AGTTGCCACCCACTAACACTT 59.786 47.619 0.00 0.00 0.00 3.16
475 543 1.328279 AACTTTAGCAGTTGCCACCC 58.672 50.000 0.00 0.00 44.70 4.61
572 642 0.524862 GCAGTTGCCATCTCAGGTTG 59.475 55.000 0.00 0.00 34.31 3.77
573 643 0.111061 TGCAGTTGCCATCTCAGGTT 59.889 50.000 1.06 0.00 41.18 3.50
765 839 6.074249 CGGACGGAGCTAATTTAATTCTTCTC 60.074 42.308 0.00 0.18 0.00 2.87
796 880 2.750237 GCCCAAGCCCAAGTACGG 60.750 66.667 0.00 0.00 0.00 4.02
924 1038 4.421058 CACGTTTATCTTCCTGATCGACA 58.579 43.478 0.00 0.00 36.65 4.35
984 1098 1.227089 CATCTTCGGCCTCCACTCG 60.227 63.158 0.00 0.00 0.00 4.18
1293 1407 3.644399 GAAGTCACGGACGGAGGCC 62.644 68.421 0.00 0.00 37.67 5.19
1398 1512 3.148279 ATCTCCACGCCGTCCTCC 61.148 66.667 0.00 0.00 0.00 4.30
1425 1539 0.252197 AATGGCCGAGGTAGTTGGTC 59.748 55.000 0.00 0.00 34.33 4.02
1461 1575 3.157252 GCCATCCTCCCGAGCAGA 61.157 66.667 0.00 0.00 0.00 4.26
1518 1633 2.029073 ACGCTGGAGGACACGTTG 59.971 61.111 0.00 0.00 34.70 4.10
1542 1657 2.342279 CAGTCGCCGGAGAACCAA 59.658 61.111 10.32 0.00 35.59 3.67
1627 2072 1.344763 ACTGTCAGCCCACAGAGTTAC 59.655 52.381 17.44 0.00 45.92 2.50
1637 2082 2.820037 GGCGCTTACTGTCAGCCC 60.820 66.667 7.64 6.99 41.81 5.19
1746 2214 3.807538 TCGCGTCGTAGGGTCTGC 61.808 66.667 5.77 0.00 0.00 4.26
1767 2235 2.579684 CTTGGAGACAGCGTAGGCCC 62.580 65.000 0.00 0.00 44.54 5.80
1777 2245 1.301716 GTTGGCGAGCTTGGAGACA 60.302 57.895 2.37 0.00 39.83 3.41
1796 2264 2.195567 GCTCCTTGGTGTGCAGCAA 61.196 57.895 14.78 14.78 45.29 3.91
1963 2525 3.767131 TGATTAATCGTCACCTGACCTGA 59.233 43.478 10.80 0.00 41.86 3.86
1993 2601 6.801575 TGTCTACACATGATAACGCAGATTA 58.198 36.000 0.00 0.00 0.00 1.75
1994 2602 5.660460 TGTCTACACATGATAACGCAGATT 58.340 37.500 0.00 0.00 0.00 2.40
1995 2603 5.262588 TGTCTACACATGATAACGCAGAT 57.737 39.130 0.00 0.00 0.00 2.90
1996 2604 4.712122 TGTCTACACATGATAACGCAGA 57.288 40.909 0.00 0.00 0.00 4.26
2109 2774 0.026027 CTACGTACGTCAGCGAGGAC 59.974 60.000 26.53 0.00 42.00 3.85
2114 2779 1.866496 GGCACTACGTACGTCAGCG 60.866 63.158 26.53 14.79 44.93 5.18
2206 2880 2.995574 AGTCGGCCAAGTAGCGGT 60.996 61.111 2.24 0.00 34.87 5.68
2325 3032 1.933853 GCAGCCGTATTGGAGTACTTG 59.066 52.381 0.00 0.00 42.00 3.16
2326 3033 1.831736 AGCAGCCGTATTGGAGTACTT 59.168 47.619 0.00 0.00 42.00 2.24
2327 3034 1.137086 CAGCAGCCGTATTGGAGTACT 59.863 52.381 0.00 0.00 42.00 2.73
2328 3035 1.571919 CAGCAGCCGTATTGGAGTAC 58.428 55.000 0.00 0.00 42.00 2.73
2329 3036 0.464036 CCAGCAGCCGTATTGGAGTA 59.536 55.000 0.00 0.00 42.00 2.59
2330 3037 1.221840 CCAGCAGCCGTATTGGAGT 59.778 57.895 0.00 0.00 42.00 3.85
2331 3038 0.811616 GTCCAGCAGCCGTATTGGAG 60.812 60.000 0.51 0.00 40.20 3.86
2332 3039 1.220749 GTCCAGCAGCCGTATTGGA 59.779 57.895 0.00 0.00 42.00 3.53
2333 3040 1.078497 TGTCCAGCAGCCGTATTGG 60.078 57.895 0.00 0.00 42.50 3.16
2334 3041 1.091771 CCTGTCCAGCAGCCGTATTG 61.092 60.000 0.00 0.00 43.71 1.90
2335 3042 1.221840 CCTGTCCAGCAGCCGTATT 59.778 57.895 0.00 0.00 43.71 1.89
2336 3043 1.264749 TTCCTGTCCAGCAGCCGTAT 61.265 55.000 0.00 0.00 43.71 3.06
2337 3044 1.911269 TTCCTGTCCAGCAGCCGTA 60.911 57.895 0.00 0.00 43.71 4.02
2338 3045 3.241530 TTCCTGTCCAGCAGCCGT 61.242 61.111 0.00 0.00 43.71 5.68
2339 3046 2.743928 GTTCCTGTCCAGCAGCCG 60.744 66.667 0.00 0.00 43.71 5.52
2340 3047 1.001641 ATGTTCCTGTCCAGCAGCC 60.002 57.895 0.00 0.00 43.71 4.85
2341 3048 0.321919 TGATGTTCCTGTCCAGCAGC 60.322 55.000 0.00 0.00 43.71 5.25
2342 3049 1.277273 TCTGATGTTCCTGTCCAGCAG 59.723 52.381 0.00 0.00 44.33 4.24
2343 3050 1.277273 CTCTGATGTTCCTGTCCAGCA 59.723 52.381 0.00 0.00 0.00 4.41
2344 3051 2.011046 GCTCTGATGTTCCTGTCCAGC 61.011 57.143 0.00 0.00 0.00 4.85
2346 3053 1.351076 TGCTCTGATGTTCCTGTCCA 58.649 50.000 0.00 0.00 0.00 4.02
2360 3082 2.563179 ACACAAAGTAGTCGGATGCTCT 59.437 45.455 0.00 0.00 0.00 4.09
2410 3149 2.463876 GCTTGAAGCAGAACAAACCAC 58.536 47.619 13.09 0.00 41.89 4.16
2514 3255 2.093106 TCGGAGCTCTTCCTTACAGAC 58.907 52.381 14.64 0.00 44.41 3.51
2532 3273 2.662006 ACACATGGATCTCACAGTCG 57.338 50.000 0.00 0.00 0.00 4.18
2706 3692 3.249091 CTTCTCTGACATGAACAGACCG 58.751 50.000 17.99 12.29 39.10 4.79
2765 3766 2.280119 AAGTTGCACAGCGAGCGA 60.280 55.556 0.00 0.00 33.85 4.93
2771 3772 4.363999 ACGATAGATAGAAGTTGCACAGC 58.636 43.478 0.00 0.00 41.38 4.40
2772 3773 7.589395 AGATACGATAGATAGAAGTTGCACAG 58.411 38.462 0.00 0.00 41.38 3.66
2773 3774 7.445707 AGAGATACGATAGATAGAAGTTGCACA 59.554 37.037 0.00 0.00 41.38 4.57
2774 3775 7.812648 AGAGATACGATAGATAGAAGTTGCAC 58.187 38.462 0.00 0.00 41.38 4.57
2775 3776 7.987750 AGAGATACGATAGATAGAAGTTGCA 57.012 36.000 0.00 0.00 41.38 4.08
2827 3835 2.356695 TGCACGCACGTAGTAGTATCAT 59.643 45.455 0.00 0.00 41.61 2.45
2832 3840 0.457853 CCATGCACGCACGTAGTAGT 60.458 55.000 0.00 0.00 41.61 2.73
2833 3841 1.145759 CCCATGCACGCACGTAGTAG 61.146 60.000 0.00 0.00 41.61 2.57
2873 3890 4.669318 GAGTCCATTCGAACGAGACAATA 58.331 43.478 20.06 0.00 0.00 1.90
2888 3909 2.722487 GCCGATCGACGAGTCCAT 59.278 61.111 18.66 0.00 45.77 3.41
2933 3963 1.740285 GGCCGTGGATGATACGTCT 59.260 57.895 0.00 0.00 39.76 4.18
2945 3975 2.023181 CGCAATCATTCGGCCGTG 59.977 61.111 27.15 17.74 0.00 4.94
2949 3979 4.612536 CCGGCGCAATCATTCGGC 62.613 66.667 10.83 5.94 45.92 5.54
3063 4525 0.036875 AAGAAAGCGACCCTCCAAGG 59.963 55.000 0.00 0.00 34.30 3.61
3103 4565 2.171003 TCATCGAGAGACAGGAAGCAA 58.829 47.619 0.00 0.00 46.97 3.91
3142 4604 2.125202 GAAAACCTTGTGCCCGGTCG 62.125 60.000 0.00 0.00 31.87 4.79
3189 4651 6.108247 CACCCATTTACGGTGGAAAGTTCC 62.108 50.000 2.93 2.93 45.94 3.62
3212 4674 6.274157 TCACTCTGATAGAAGAGGAACAAC 57.726 41.667 6.21 0.00 46.73 3.32
3213 4675 5.420421 CCTCACTCTGATAGAAGAGGAACAA 59.580 44.000 16.19 0.00 46.73 2.83
3295 4789 9.444600 GTCCAATTTGTTATCCTTGTAGTTCTA 57.555 33.333 0.00 0.00 0.00 2.10
3296 4790 7.393515 GGTCCAATTTGTTATCCTTGTAGTTCT 59.606 37.037 0.00 0.00 0.00 3.01
3297 4791 7.535997 GGTCCAATTTGTTATCCTTGTAGTTC 58.464 38.462 0.00 0.00 0.00 3.01
3298 4792 6.150474 CGGTCCAATTTGTTATCCTTGTAGTT 59.850 38.462 0.00 0.00 0.00 2.24
3299 4793 5.646360 CGGTCCAATTTGTTATCCTTGTAGT 59.354 40.000 0.00 0.00 0.00 2.73
3300 4794 5.878116 TCGGTCCAATTTGTTATCCTTGTAG 59.122 40.000 0.00 0.00 0.00 2.74
3301 4795 5.806818 TCGGTCCAATTTGTTATCCTTGTA 58.193 37.500 0.00 0.00 0.00 2.41
3302 4796 4.658063 TCGGTCCAATTTGTTATCCTTGT 58.342 39.130 0.00 0.00 0.00 3.16
3303 4797 4.096382 CCTCGGTCCAATTTGTTATCCTTG 59.904 45.833 0.00 0.00 0.00 3.61
3304 4798 4.263771 ACCTCGGTCCAATTTGTTATCCTT 60.264 41.667 0.00 0.00 0.00 3.36
3305 4799 3.265995 ACCTCGGTCCAATTTGTTATCCT 59.734 43.478 0.00 0.00 0.00 3.24
3306 4800 3.617284 ACCTCGGTCCAATTTGTTATCC 58.383 45.455 0.00 0.00 0.00 2.59
3307 4801 5.638596 AAACCTCGGTCCAATTTGTTATC 57.361 39.130 0.00 0.00 0.00 1.75
3308 4802 7.712204 ATTAAACCTCGGTCCAATTTGTTAT 57.288 32.000 0.00 0.00 0.00 1.89
3309 4803 7.527568 AATTAAACCTCGGTCCAATTTGTTA 57.472 32.000 0.00 0.00 0.00 2.41
3310 4804 6.413783 AATTAAACCTCGGTCCAATTTGTT 57.586 33.333 0.00 0.00 0.00 2.83
3311 4805 6.413783 AAATTAAACCTCGGTCCAATTTGT 57.586 33.333 14.68 0.07 33.80 2.83
3312 4806 7.722795 AAAAATTAAACCTCGGTCCAATTTG 57.277 32.000 15.53 0.00 34.54 2.32
3355 4849 3.705051 ACGTTAGACTATTGGAGGTCCA 58.295 45.455 0.00 0.00 45.94 4.02
3356 4850 5.301298 ACATACGTTAGACTATTGGAGGTCC 59.699 44.000 0.00 0.00 33.39 4.46
3357 4851 6.207213 CACATACGTTAGACTATTGGAGGTC 58.793 44.000 0.00 0.00 0.00 3.85
3358 4852 5.451520 GCACATACGTTAGACTATTGGAGGT 60.452 44.000 0.00 0.00 0.00 3.85
3359 4853 4.982916 GCACATACGTTAGACTATTGGAGG 59.017 45.833 0.00 0.00 0.00 4.30
3360 4854 4.675565 CGCACATACGTTAGACTATTGGAG 59.324 45.833 0.00 0.00 0.00 3.86
3361 4855 4.096833 ACGCACATACGTTAGACTATTGGA 59.903 41.667 0.00 0.00 45.75 3.53
3362 4856 4.357142 ACGCACATACGTTAGACTATTGG 58.643 43.478 0.00 0.00 45.75 3.16
3374 4868 3.183754 TGTAATCCTGAACGCACATACG 58.816 45.455 0.00 0.00 39.50 3.06


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

AutoCloner maintained by Alex Coulton.