Multiple sequence alignment - TraesCS7D01G102100

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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 TraesCS7D01G102100 chr7D 100.000 3527 0 0 1 3527 61234334 61237860 0.000000e+00 6514.0
1 TraesCS7D01G102100 chr7D 92.060 529 24 7 2647 3160 461236886 461237411 0.000000e+00 728.0
2 TraesCS7D01G102100 chr7A 96.767 2351 66 4 297 2646 65162834 65165175 0.000000e+00 3912.0
3 TraesCS7D01G102100 chr7A 91.698 530 31 5 2644 3160 475770244 475769715 0.000000e+00 723.0
4 TraesCS7D01G102100 chr7A 91.729 399 21 4 2774 3160 475769560 475769162 8.610000e-151 544.0
5 TraesCS7D01G102100 chr7A 82.079 279 40 8 2 277 645317106 645317377 2.740000e-56 230.0
6 TraesCS7D01G102100 chr7A 81.362 279 43 7 2 277 645322515 645322787 5.930000e-53 219.0
7 TraesCS7D01G102100 chr2A 88.882 1682 165 14 967 2646 2731895 2730234 0.000000e+00 2050.0
8 TraesCS7D01G102100 chr2A 85.696 1559 181 27 994 2536 1785289 1783757 0.000000e+00 1605.0
9 TraesCS7D01G102100 chr2A 85.779 1547 182 23 994 2526 1776718 1778240 0.000000e+00 1604.0
10 TraesCS7D01G102100 chr2A 83.992 506 66 10 298 792 2732473 2731972 4.120000e-129 472.0
11 TraesCS7D01G102100 chr4D 85.752 1530 196 12 1016 2529 494877182 494878705 0.000000e+00 1598.0
12 TraesCS7D01G102100 chr4B 85.195 1540 201 12 1007 2525 634981265 634982798 0.000000e+00 1555.0
13 TraesCS7D01G102100 chr4B 84.680 1547 207 14 1007 2529 634460846 634459306 0.000000e+00 1517.0
14 TraesCS7D01G102100 chr5A 84.815 1541 201 17 1007 2529 674576216 674577741 0.000000e+00 1519.0
15 TraesCS7D01G102100 chr5A 91.651 527 30 6 2645 3160 659424591 659424068 0.000000e+00 717.0
16 TraesCS7D01G102100 chr2D 88.648 969 96 2 1139 2107 2944323 2945277 0.000000e+00 1168.0
17 TraesCS7D01G102100 chr2D 93.156 526 22 7 2647 3160 601175895 601175372 0.000000e+00 760.0
18 TraesCS7D01G102100 chr2D 93.510 339 20 2 3189 3527 601175071 601174735 1.460000e-138 503.0
19 TraesCS7D01G102100 chr3B 89.978 908 62 18 2647 3526 452980087 452980993 0.000000e+00 1146.0
20 TraesCS7D01G102100 chr3B 91.651 527 31 5 2646 3160 572848038 572847513 0.000000e+00 717.0
21 TraesCS7D01G102100 chr3B 93.510 339 21 1 3189 3527 572847162 572846825 1.460000e-138 503.0
22 TraesCS7D01G102100 chr5B 89.278 914 65 21 2644 3526 602837398 602838309 0.000000e+00 1114.0
23 TraesCS7D01G102100 chr5B 84.892 278 33 7 2 275 572355236 572354964 4.490000e-69 272.0
24 TraesCS7D01G102100 chr2B 83.077 975 129 24 994 1943 305616 304653 0.000000e+00 854.0
25 TraesCS7D01G102100 chr2B 85.320 688 63 21 2648 3321 685500887 685500224 0.000000e+00 676.0
26 TraesCS7D01G102100 chr2B 84.422 597 83 5 1936 2529 304417 303828 2.360000e-161 579.0
27 TraesCS7D01G102100 chr2B 91.765 340 21 4 3189 3527 667233010 667232677 1.920000e-127 466.0
28 TraesCS7D01G102100 chr4A 91.589 535 30 7 2638 3160 725323640 725323109 0.000000e+00 725.0
29 TraesCS7D01G102100 chr4A 94.118 340 17 2 3189 3527 725322764 725322427 6.750000e-142 514.0
30 TraesCS7D01G102100 chr4A 96.875 32 1 0 1338 1369 5349049 5349080 2.000000e-03 54.7
31 TraesCS7D01G102100 chr3A 91.271 527 35 4 2645 3160 634711196 634710670 0.000000e+00 708.0
32 TraesCS7D01G102100 chr1B 89.209 556 31 15 2999 3526 610895596 610896150 0.000000e+00 667.0
33 TraesCS7D01G102100 chr7B 88.342 549 41 16 2640 3169 656516265 656515721 3.840000e-179 638.0
34 TraesCS7D01G102100 chr7B 91.765 340 20 5 3189 3527 99919109 99919441 1.920000e-127 466.0
35 TraesCS7D01G102100 chr7B 91.765 340 20 5 3189 3527 656515389 656515057 1.920000e-127 466.0
36 TraesCS7D01G102100 chr1A 88.512 531 46 9 2644 3160 517638344 517637815 2.310000e-176 628.0
37 TraesCS7D01G102100 chr6A 87.947 531 49 6 2646 3161 520926114 520926644 2.330000e-171 612.0
38 TraesCS7D01G102100 chr5D 85.385 260 31 6 2 258 465003212 465002957 2.700000e-66 263.0


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 TraesCS7D01G102100 chr7D 61234334 61237860 3526 False 6514.0 6514 100.0000 1 3527 1 chr7D.!!$F1 3526
1 TraesCS7D01G102100 chr7D 461236886 461237411 525 False 728.0 728 92.0600 2647 3160 1 chr7D.!!$F2 513
2 TraesCS7D01G102100 chr7A 65162834 65165175 2341 False 3912.0 3912 96.7670 297 2646 1 chr7A.!!$F1 2349
3 TraesCS7D01G102100 chr7A 475769162 475770244 1082 True 633.5 723 91.7135 2644 3160 2 chr7A.!!$R1 516
4 TraesCS7D01G102100 chr2A 1783757 1785289 1532 True 1605.0 1605 85.6960 994 2536 1 chr2A.!!$R1 1542
5 TraesCS7D01G102100 chr2A 1776718 1778240 1522 False 1604.0 1604 85.7790 994 2526 1 chr2A.!!$F1 1532
6 TraesCS7D01G102100 chr2A 2730234 2732473 2239 True 1261.0 2050 86.4370 298 2646 2 chr2A.!!$R2 2348
7 TraesCS7D01G102100 chr4D 494877182 494878705 1523 False 1598.0 1598 85.7520 1016 2529 1 chr4D.!!$F1 1513
8 TraesCS7D01G102100 chr4B 634981265 634982798 1533 False 1555.0 1555 85.1950 1007 2525 1 chr4B.!!$F1 1518
9 TraesCS7D01G102100 chr4B 634459306 634460846 1540 True 1517.0 1517 84.6800 1007 2529 1 chr4B.!!$R1 1522
10 TraesCS7D01G102100 chr5A 674576216 674577741 1525 False 1519.0 1519 84.8150 1007 2529 1 chr5A.!!$F1 1522
11 TraesCS7D01G102100 chr5A 659424068 659424591 523 True 717.0 717 91.6510 2645 3160 1 chr5A.!!$R1 515
12 TraesCS7D01G102100 chr2D 2944323 2945277 954 False 1168.0 1168 88.6480 1139 2107 1 chr2D.!!$F1 968
13 TraesCS7D01G102100 chr2D 601174735 601175895 1160 True 631.5 760 93.3330 2647 3527 2 chr2D.!!$R1 880
14 TraesCS7D01G102100 chr3B 452980087 452980993 906 False 1146.0 1146 89.9780 2647 3526 1 chr3B.!!$F1 879
15 TraesCS7D01G102100 chr3B 572846825 572848038 1213 True 610.0 717 92.5805 2646 3527 2 chr3B.!!$R1 881
16 TraesCS7D01G102100 chr5B 602837398 602838309 911 False 1114.0 1114 89.2780 2644 3526 1 chr5B.!!$F1 882
17 TraesCS7D01G102100 chr2B 303828 305616 1788 True 716.5 854 83.7495 994 2529 2 chr2B.!!$R3 1535
18 TraesCS7D01G102100 chr2B 685500224 685500887 663 True 676.0 676 85.3200 2648 3321 1 chr2B.!!$R2 673
19 TraesCS7D01G102100 chr4A 725322427 725323640 1213 True 619.5 725 92.8535 2638 3527 2 chr4A.!!$R1 889
20 TraesCS7D01G102100 chr3A 634710670 634711196 526 True 708.0 708 91.2710 2645 3160 1 chr3A.!!$R1 515
21 TraesCS7D01G102100 chr1B 610895596 610896150 554 False 667.0 667 89.2090 2999 3526 1 chr1B.!!$F1 527
22 TraesCS7D01G102100 chr7B 656515057 656516265 1208 True 552.0 638 90.0535 2640 3527 2 chr7B.!!$R1 887
23 TraesCS7D01G102100 chr1A 517637815 517638344 529 True 628.0 628 88.5120 2644 3160 1 chr1A.!!$R1 516
24 TraesCS7D01G102100 chr6A 520926114 520926644 530 False 612.0 612 87.9470 2646 3161 1 chr6A.!!$F1 515

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
84 85 0.035056 GTGGTTGAGGTGCTATGCCT 60.035 55.0 0.0 0.0 39.42 4.75 F
201 202 0.036732 TCCCATGTCCTGAACACAGC 59.963 55.0 0.0 0.0 41.75 4.40 F
202 203 0.037303 CCCATGTCCTGAACACAGCT 59.963 55.0 0.0 0.0 41.75 4.24 F
275 276 0.107703 CATGAAGCGAACAGGCCCTA 60.108 55.0 0.0 0.0 0.00 3.53 F
277 278 0.398696 TGAAGCGAACAGGCCCTAAA 59.601 50.0 0.0 0.0 0.00 1.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1645 1683 0.390860 GGGATGATGTGTCGGAGGAG 59.609 60.000 0.00 0.00 0.00 3.69 R
2204 2518 1.135094 CATCCTCCCCATGCAGTAGT 58.865 55.000 0.00 0.00 0.00 2.73 R
2290 2604 1.019673 TATGACGGCTCGTACCTCAC 58.980 55.000 0.09 0.00 41.37 3.51 R
2322 2636 2.281208 CTGGGACCGGCGTTGAAA 60.281 61.111 6.01 0.00 0.00 2.69 R
2553 2867 6.306117 TGCGCATACATAATACGTACATGTAC 59.694 38.462 23.53 23.53 37.82 2.90 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
18 19 4.380945 GGTCAATGGGCCCCAGCA 62.381 66.667 22.27 0.00 42.56 4.41
19 20 2.042639 GTCAATGGGCCCCAGCAT 60.043 61.111 22.27 1.99 42.56 3.79
20 21 2.042741 TCAATGGGCCCCAGCATG 60.043 61.111 22.27 11.12 42.56 4.06
21 22 3.857038 CAATGGGCCCCAGCATGC 61.857 66.667 22.27 10.51 42.56 4.06
22 23 4.401876 AATGGGCCCCAGCATGCA 62.402 61.111 22.27 0.00 42.56 3.96
26 27 4.746309 GGCCCCAGCATGCACAGA 62.746 66.667 21.98 0.00 42.56 3.41
27 28 2.441532 GCCCCAGCATGCACAGAT 60.442 61.111 21.98 0.00 39.53 2.90
28 29 2.487532 GCCCCAGCATGCACAGATC 61.488 63.158 21.98 0.07 39.53 2.75
29 30 1.826921 CCCCAGCATGCACAGATCC 60.827 63.158 21.98 0.00 31.97 3.36
30 31 1.077285 CCCAGCATGCACAGATCCA 60.077 57.895 21.98 0.00 31.97 3.41
31 32 0.467474 CCCAGCATGCACAGATCCAT 60.467 55.000 21.98 0.00 31.97 3.41
32 33 0.952280 CCAGCATGCACAGATCCATC 59.048 55.000 21.98 0.00 31.97 3.51
33 34 1.477014 CCAGCATGCACAGATCCATCT 60.477 52.381 21.98 0.00 33.34 2.90
34 35 1.874231 CAGCATGCACAGATCCATCTC 59.126 52.381 21.98 0.00 34.22 2.75
35 36 0.866427 GCATGCACAGATCCATCTCG 59.134 55.000 14.21 0.00 34.22 4.04
36 37 1.809271 GCATGCACAGATCCATCTCGT 60.809 52.381 14.21 0.00 34.22 4.18
37 38 2.558378 CATGCACAGATCCATCTCGTT 58.442 47.619 0.00 0.00 34.22 3.85
38 39 2.299993 TGCACAGATCCATCTCGTTC 57.700 50.000 0.00 0.00 34.22 3.95
39 40 1.827344 TGCACAGATCCATCTCGTTCT 59.173 47.619 0.00 0.00 34.22 3.01
40 41 2.200067 GCACAGATCCATCTCGTTCTG 58.800 52.381 0.00 0.00 41.06 3.02
41 42 2.159184 GCACAGATCCATCTCGTTCTGA 60.159 50.000 5.84 0.00 38.25 3.27
42 43 3.704512 CACAGATCCATCTCGTTCTGAG 58.295 50.000 5.84 0.00 46.72 3.35
43 44 2.100584 ACAGATCCATCTCGTTCTGAGC 59.899 50.000 5.84 0.00 44.86 4.26
44 45 2.361757 CAGATCCATCTCGTTCTGAGCT 59.638 50.000 0.00 0.00 44.86 4.09
45 46 3.030291 AGATCCATCTCGTTCTGAGCTT 58.970 45.455 0.00 0.00 44.86 3.74
46 47 2.662006 TCCATCTCGTTCTGAGCTTG 57.338 50.000 0.00 0.00 44.86 4.01
47 48 2.171003 TCCATCTCGTTCTGAGCTTGA 58.829 47.619 0.00 0.00 44.86 3.02
48 49 2.762887 TCCATCTCGTTCTGAGCTTGAT 59.237 45.455 0.00 0.00 44.86 2.57
49 50 2.864946 CCATCTCGTTCTGAGCTTGATG 59.135 50.000 12.78 12.78 44.86 3.07
50 51 3.519579 CATCTCGTTCTGAGCTTGATGT 58.480 45.455 12.03 0.00 44.86 3.06
51 52 2.951726 TCTCGTTCTGAGCTTGATGTG 58.048 47.619 0.00 0.00 44.86 3.21
52 53 1.998315 CTCGTTCTGAGCTTGATGTGG 59.002 52.381 0.00 0.00 38.03 4.17
53 54 1.081892 CGTTCTGAGCTTGATGTGGG 58.918 55.000 0.00 0.00 0.00 4.61
54 55 1.609061 CGTTCTGAGCTTGATGTGGGT 60.609 52.381 0.00 0.00 0.00 4.51
55 56 2.079925 GTTCTGAGCTTGATGTGGGTC 58.920 52.381 0.00 0.00 0.00 4.46
56 57 0.615331 TCTGAGCTTGATGTGGGTCC 59.385 55.000 0.00 0.00 0.00 4.46
57 58 0.393537 CTGAGCTTGATGTGGGTCCC 60.394 60.000 0.00 0.00 0.00 4.46
58 59 1.133181 TGAGCTTGATGTGGGTCCCA 61.133 55.000 6.47 6.47 0.00 4.37
59 60 0.038166 GAGCTTGATGTGGGTCCCAA 59.962 55.000 13.78 3.53 34.18 4.12
60 61 0.251341 AGCTTGATGTGGGTCCCAAC 60.251 55.000 13.78 7.86 34.18 3.77
61 62 1.586154 GCTTGATGTGGGTCCCAACG 61.586 60.000 13.78 0.00 34.18 4.10
62 63 0.250727 CTTGATGTGGGTCCCAACGT 60.251 55.000 13.78 8.54 34.18 3.99
63 64 0.536233 TTGATGTGGGTCCCAACGTG 60.536 55.000 13.78 0.00 34.18 4.49
64 65 1.072505 GATGTGGGTCCCAACGTGT 59.927 57.895 13.78 0.00 34.18 4.49
65 66 1.228124 ATGTGGGTCCCAACGTGTG 60.228 57.895 13.78 0.00 34.18 3.82
66 67 1.990160 ATGTGGGTCCCAACGTGTGT 61.990 55.000 13.78 0.00 34.18 3.72
67 68 2.184167 GTGGGTCCCAACGTGTGTG 61.184 63.158 13.78 0.00 34.18 3.82
68 69 2.593436 GGGTCCCAACGTGTGTGG 60.593 66.667 1.78 0.00 0.00 4.17
69 70 2.191109 GGTCCCAACGTGTGTGGT 59.809 61.111 4.14 0.00 0.00 4.16
70 71 1.452470 GGTCCCAACGTGTGTGGTT 60.452 57.895 4.14 0.00 0.00 3.67
71 72 1.720694 GGTCCCAACGTGTGTGGTTG 61.721 60.000 4.14 0.00 43.33 3.77
72 73 0.745128 GTCCCAACGTGTGTGGTTGA 60.745 55.000 6.26 0.00 45.85 3.18
73 74 0.462937 TCCCAACGTGTGTGGTTGAG 60.463 55.000 6.26 0.00 45.85 3.02
74 75 1.444119 CCCAACGTGTGTGGTTGAGG 61.444 60.000 6.26 2.84 45.85 3.86
75 76 0.746563 CCAACGTGTGTGGTTGAGGT 60.747 55.000 6.26 0.00 45.85 3.85
76 77 0.376852 CAACGTGTGTGGTTGAGGTG 59.623 55.000 0.00 0.00 45.85 4.00
77 78 1.373590 AACGTGTGTGGTTGAGGTGC 61.374 55.000 0.00 0.00 0.00 5.01
78 79 1.523711 CGTGTGTGGTTGAGGTGCT 60.524 57.895 0.00 0.00 0.00 4.40
79 80 0.249699 CGTGTGTGGTTGAGGTGCTA 60.250 55.000 0.00 0.00 0.00 3.49
80 81 1.608025 CGTGTGTGGTTGAGGTGCTAT 60.608 52.381 0.00 0.00 0.00 2.97
81 82 1.806542 GTGTGTGGTTGAGGTGCTATG 59.193 52.381 0.00 0.00 0.00 2.23
82 83 0.804989 GTGTGGTTGAGGTGCTATGC 59.195 55.000 0.00 0.00 0.00 3.14
83 84 0.322456 TGTGGTTGAGGTGCTATGCC 60.322 55.000 0.00 0.00 0.00 4.40
84 85 0.035056 GTGGTTGAGGTGCTATGCCT 60.035 55.000 0.00 0.00 39.42 4.75
99 100 2.594303 CCTCAGGCCAACGTGCAA 60.594 61.111 5.01 0.00 0.00 4.08
100 101 2.192861 CCTCAGGCCAACGTGCAAA 61.193 57.895 5.01 0.00 0.00 3.68
101 102 1.732917 CTCAGGCCAACGTGCAAAA 59.267 52.632 5.01 0.00 0.00 2.44
102 103 0.102120 CTCAGGCCAACGTGCAAAAA 59.898 50.000 5.01 0.00 0.00 1.94
121 122 2.503895 AAAAGAGCTGGGACTGGATG 57.496 50.000 0.00 0.00 0.00 3.51
122 123 1.366319 AAAGAGCTGGGACTGGATGT 58.634 50.000 0.00 0.00 0.00 3.06
123 124 1.366319 AAGAGCTGGGACTGGATGTT 58.634 50.000 0.00 0.00 0.00 2.71
124 125 1.366319 AGAGCTGGGACTGGATGTTT 58.634 50.000 0.00 0.00 0.00 2.83
125 126 1.004044 AGAGCTGGGACTGGATGTTTG 59.996 52.381 0.00 0.00 0.00 2.93
126 127 0.773644 AGCTGGGACTGGATGTTTGT 59.226 50.000 0.00 0.00 0.00 2.83
127 128 1.145738 AGCTGGGACTGGATGTTTGTT 59.854 47.619 0.00 0.00 0.00 2.83
128 129 1.963515 GCTGGGACTGGATGTTTGTTT 59.036 47.619 0.00 0.00 0.00 2.83
129 130 2.365293 GCTGGGACTGGATGTTTGTTTT 59.635 45.455 0.00 0.00 0.00 2.43
130 131 3.552890 GCTGGGACTGGATGTTTGTTTTC 60.553 47.826 0.00 0.00 0.00 2.29
131 132 3.891366 CTGGGACTGGATGTTTGTTTTCT 59.109 43.478 0.00 0.00 0.00 2.52
132 133 4.285863 TGGGACTGGATGTTTGTTTTCTT 58.714 39.130 0.00 0.00 0.00 2.52
133 134 4.714308 TGGGACTGGATGTTTGTTTTCTTT 59.286 37.500 0.00 0.00 0.00 2.52
134 135 5.163457 TGGGACTGGATGTTTGTTTTCTTTC 60.163 40.000 0.00 0.00 0.00 2.62
135 136 5.289595 GGACTGGATGTTTGTTTTCTTTCC 58.710 41.667 0.00 0.00 0.00 3.13
136 137 5.163457 GGACTGGATGTTTGTTTTCTTTCCA 60.163 40.000 0.00 0.00 0.00 3.53
137 138 6.293004 ACTGGATGTTTGTTTTCTTTCCAA 57.707 33.333 0.00 0.00 0.00 3.53
138 139 6.706295 ACTGGATGTTTGTTTTCTTTCCAAA 58.294 32.000 0.00 0.00 0.00 3.28
139 140 6.818142 ACTGGATGTTTGTTTTCTTTCCAAAG 59.182 34.615 0.00 0.00 37.36 2.77
140 141 6.706295 TGGATGTTTGTTTTCTTTCCAAAGT 58.294 32.000 0.00 0.00 37.31 2.66
141 142 7.841956 TGGATGTTTGTTTTCTTTCCAAAGTA 58.158 30.769 0.00 0.00 37.31 2.24
142 143 7.762159 TGGATGTTTGTTTTCTTTCCAAAGTAC 59.238 33.333 0.00 0.00 37.31 2.73
143 144 7.762159 GGATGTTTGTTTTCTTTCCAAAGTACA 59.238 33.333 0.00 1.11 37.31 2.90
144 145 8.702163 ATGTTTGTTTTCTTTCCAAAGTACAG 57.298 30.769 0.00 0.00 37.31 2.74
145 146 7.093992 TGTTTGTTTTCTTTCCAAAGTACAGG 58.906 34.615 0.00 0.00 37.31 4.00
146 147 5.257082 TGTTTTCTTTCCAAAGTACAGGC 57.743 39.130 0.00 0.00 37.31 4.85
147 148 4.098807 TGTTTTCTTTCCAAAGTACAGGCC 59.901 41.667 0.00 0.00 37.31 5.19
148 149 3.876309 TTCTTTCCAAAGTACAGGCCT 57.124 42.857 0.00 0.00 37.31 5.19
149 150 4.986054 TTCTTTCCAAAGTACAGGCCTA 57.014 40.909 3.98 0.00 37.31 3.93
150 151 4.553330 TCTTTCCAAAGTACAGGCCTAG 57.447 45.455 3.98 2.19 37.31 3.02
151 152 3.263425 TCTTTCCAAAGTACAGGCCTAGG 59.737 47.826 3.98 3.67 37.31 3.02
152 153 2.634639 TCCAAAGTACAGGCCTAGGA 57.365 50.000 14.75 1.40 0.00 2.94
153 154 2.910544 TCCAAAGTACAGGCCTAGGAA 58.089 47.619 14.75 0.00 0.00 3.36
154 155 3.253220 TCCAAAGTACAGGCCTAGGAAA 58.747 45.455 14.75 0.00 0.00 3.13
155 156 3.008704 TCCAAAGTACAGGCCTAGGAAAC 59.991 47.826 14.75 1.17 0.00 2.78
157 158 4.224370 CCAAAGTACAGGCCTAGGAAACTA 59.776 45.833 14.75 0.00 43.67 2.24
158 159 5.104485 CCAAAGTACAGGCCTAGGAAACTAT 60.104 44.000 14.75 0.00 43.39 2.12
159 160 5.873146 AAGTACAGGCCTAGGAAACTATC 57.127 43.478 14.75 0.00 43.39 2.08
180 181 5.097742 TCCAAAAGATAGGAAAGCATCGA 57.902 39.130 0.00 0.00 0.00 3.59
181 182 5.684704 TCCAAAAGATAGGAAAGCATCGAT 58.315 37.500 0.00 0.00 0.00 3.59
182 183 6.122277 TCCAAAAGATAGGAAAGCATCGATT 58.878 36.000 0.00 0.00 0.00 3.34
183 184 6.260936 TCCAAAAGATAGGAAAGCATCGATTC 59.739 38.462 0.00 0.00 0.00 2.52
184 185 6.433766 CAAAAGATAGGAAAGCATCGATTCC 58.566 40.000 7.33 7.33 44.45 3.01
185 186 4.278975 AGATAGGAAAGCATCGATTCCC 57.721 45.455 11.12 1.94 45.08 3.97
186 187 3.648067 AGATAGGAAAGCATCGATTCCCA 59.352 43.478 11.12 0.00 45.08 4.37
187 188 4.288105 AGATAGGAAAGCATCGATTCCCAT 59.712 41.667 11.12 4.34 45.08 4.00
188 189 2.579873 AGGAAAGCATCGATTCCCATG 58.420 47.619 11.12 0.00 45.08 3.66
189 190 2.092212 AGGAAAGCATCGATTCCCATGT 60.092 45.455 11.12 0.00 45.08 3.21
190 191 2.291741 GGAAAGCATCGATTCCCATGTC 59.708 50.000 4.45 0.00 39.36 3.06
191 192 1.972872 AAGCATCGATTCCCATGTCC 58.027 50.000 0.00 0.00 0.00 4.02
192 193 1.135094 AGCATCGATTCCCATGTCCT 58.865 50.000 0.00 0.00 0.00 3.85
193 194 1.202734 AGCATCGATTCCCATGTCCTG 60.203 52.381 0.00 0.00 0.00 3.86
194 195 1.202687 GCATCGATTCCCATGTCCTGA 60.203 52.381 0.00 0.00 0.00 3.86
195 196 2.746142 GCATCGATTCCCATGTCCTGAA 60.746 50.000 0.00 0.00 0.00 3.02
196 197 2.691409 TCGATTCCCATGTCCTGAAC 57.309 50.000 0.00 0.00 0.00 3.18
197 198 1.905894 TCGATTCCCATGTCCTGAACA 59.094 47.619 0.00 0.00 43.51 3.18
198 199 2.009774 CGATTCCCATGTCCTGAACAC 58.990 52.381 0.00 0.00 41.75 3.32
199 200 2.615240 CGATTCCCATGTCCTGAACACA 60.615 50.000 0.00 0.00 41.75 3.72
200 201 2.566833 TTCCCATGTCCTGAACACAG 57.433 50.000 0.00 0.00 41.75 3.66
201 202 0.036732 TCCCATGTCCTGAACACAGC 59.963 55.000 0.00 0.00 41.75 4.40
202 203 0.037303 CCCATGTCCTGAACACAGCT 59.963 55.000 0.00 0.00 41.75 4.24
203 204 1.278985 CCCATGTCCTGAACACAGCTA 59.721 52.381 0.00 0.00 41.75 3.32
204 205 2.350522 CCATGTCCTGAACACAGCTAC 58.649 52.381 0.00 0.00 41.75 3.58
205 206 2.289631 CCATGTCCTGAACACAGCTACA 60.290 50.000 0.00 0.00 41.75 2.74
206 207 2.820059 TGTCCTGAACACAGCTACAG 57.180 50.000 0.00 0.00 31.20 2.74
207 208 2.039418 TGTCCTGAACACAGCTACAGT 58.961 47.619 0.00 0.00 31.20 3.55
208 209 2.224042 TGTCCTGAACACAGCTACAGTG 60.224 50.000 1.32 1.32 42.56 3.66
209 210 2.035961 GTCCTGAACACAGCTACAGTGA 59.964 50.000 9.47 2.07 40.16 3.41
210 211 2.698274 TCCTGAACACAGCTACAGTGAA 59.302 45.455 9.47 0.00 40.16 3.18
211 212 3.133901 TCCTGAACACAGCTACAGTGAAA 59.866 43.478 9.47 0.00 40.16 2.69
212 213 3.876914 CCTGAACACAGCTACAGTGAAAA 59.123 43.478 9.47 0.00 40.16 2.29
213 214 4.335315 CCTGAACACAGCTACAGTGAAAAA 59.665 41.667 9.47 0.00 40.16 1.94
245 246 6.502136 GAAATGATTCCTTCGAAGTTTCCT 57.498 37.500 23.03 7.60 29.94 3.36
246 247 6.901081 AAATGATTCCTTCGAAGTTTCCTT 57.099 33.333 23.03 12.39 0.00 3.36
247 248 6.502136 AATGATTCCTTCGAAGTTTCCTTC 57.498 37.500 23.03 11.33 43.09 3.46
256 257 3.284323 GAAGTTTCCTTCGCTTTTCCC 57.716 47.619 0.00 0.00 37.92 3.97
257 258 2.358322 AGTTTCCTTCGCTTTTCCCA 57.642 45.000 0.00 0.00 0.00 4.37
258 259 2.876581 AGTTTCCTTCGCTTTTCCCAT 58.123 42.857 0.00 0.00 0.00 4.00
259 260 2.558359 AGTTTCCTTCGCTTTTCCCATG 59.442 45.455 0.00 0.00 0.00 3.66
260 261 2.556622 GTTTCCTTCGCTTTTCCCATGA 59.443 45.455 0.00 0.00 0.00 3.07
261 262 2.577606 TCCTTCGCTTTTCCCATGAA 57.422 45.000 0.00 0.00 0.00 2.57
262 263 2.436417 TCCTTCGCTTTTCCCATGAAG 58.564 47.619 0.00 0.00 36.63 3.02
263 264 1.135286 CCTTCGCTTTTCCCATGAAGC 60.135 52.381 6.76 6.76 43.62 3.86
267 268 1.982612 GCTTTTCCCATGAAGCGAAC 58.017 50.000 0.00 0.00 38.89 3.95
268 269 1.269448 GCTTTTCCCATGAAGCGAACA 59.731 47.619 0.00 0.00 38.89 3.18
269 270 2.669391 GCTTTTCCCATGAAGCGAACAG 60.669 50.000 0.00 0.00 38.89 3.16
270 271 1.533625 TTTCCCATGAAGCGAACAGG 58.466 50.000 0.00 0.00 0.00 4.00
271 272 0.960364 TTCCCATGAAGCGAACAGGC 60.960 55.000 0.00 0.00 0.00 4.85
272 273 2.409870 CCCATGAAGCGAACAGGCC 61.410 63.158 0.00 0.00 0.00 5.19
273 274 2.409870 CCATGAAGCGAACAGGCCC 61.410 63.158 0.00 0.00 0.00 5.80
274 275 1.377725 CATGAAGCGAACAGGCCCT 60.378 57.895 0.00 0.00 0.00 5.19
275 276 0.107703 CATGAAGCGAACAGGCCCTA 60.108 55.000 0.00 0.00 0.00 3.53
276 277 0.618458 ATGAAGCGAACAGGCCCTAA 59.382 50.000 0.00 0.00 0.00 2.69
277 278 0.398696 TGAAGCGAACAGGCCCTAAA 59.601 50.000 0.00 0.00 0.00 1.85
278 279 1.202830 TGAAGCGAACAGGCCCTAAAA 60.203 47.619 0.00 0.00 0.00 1.52
279 280 1.199327 GAAGCGAACAGGCCCTAAAAC 59.801 52.381 0.00 0.00 0.00 2.43
280 281 0.400594 AGCGAACAGGCCCTAAAACT 59.599 50.000 0.00 0.00 0.00 2.66
281 282 1.202891 AGCGAACAGGCCCTAAAACTT 60.203 47.619 0.00 0.00 0.00 2.66
282 283 1.611977 GCGAACAGGCCCTAAAACTTT 59.388 47.619 0.00 0.00 0.00 2.66
283 284 2.035449 GCGAACAGGCCCTAAAACTTTT 59.965 45.455 0.00 0.00 0.00 2.27
284 285 3.491964 GCGAACAGGCCCTAAAACTTTTT 60.492 43.478 0.00 0.00 0.00 1.94
317 318 7.482654 AAAAGAAAGGCTAAAACTTTGATGC 57.517 32.000 0.00 0.00 38.21 3.91
325 326 6.437162 AGGCTAAAACTTTGATGCCAGATTTA 59.563 34.615 13.95 0.00 42.46 1.40
401 402 7.369803 TGAAAATTTTAGTTTGCAAGCACAA 57.630 28.000 16.04 6.19 0.00 3.33
430 431 8.135529 ACTTTCTAACAACAAATAAACTGAGGC 58.864 33.333 0.00 0.00 0.00 4.70
492 493 4.502645 GTGTACACAAGTTGCCATGAAAAC 59.497 41.667 21.14 0.00 0.00 2.43
652 654 6.347483 GGTTCTTGGAATTTCTCACTACGAAC 60.347 42.308 0.00 0.00 0.00 3.95
668 670 6.145534 CACTACGAACTAAGTTTGCAAGATGA 59.854 38.462 0.00 0.00 30.59 2.92
893 905 1.149987 TTGTTGAATACACCGCCGAC 58.850 50.000 0.00 0.00 36.21 4.79
960 972 2.930040 AGTTGAATACACGAGCAATCCG 59.070 45.455 0.00 0.00 0.00 4.18
1425 1454 2.746277 CCCCGTTTCCGCTCCTTG 60.746 66.667 0.00 0.00 0.00 3.61
2204 2518 5.410746 CCGGCGACAAGATACTTATCTACTA 59.589 44.000 9.30 0.00 41.96 1.82
2322 2636 2.632377 CCGTCATACAAGTTCATGGCT 58.368 47.619 0.00 0.00 0.00 4.75
2412 2726 2.548178 CATGCTGTGGAACTTCGCT 58.452 52.632 0.00 0.00 38.04 4.93
2481 2795 2.270352 TTCACATGAAGAACGGGCTT 57.730 45.000 0.00 0.00 0.00 4.35
2551 2865 5.402398 TCGCATATAGCAGACATGTACATC 58.598 41.667 5.07 0.00 46.13 3.06
2552 2866 5.048083 TCGCATATAGCAGACATGTACATCA 60.048 40.000 5.07 0.00 46.13 3.07
2553 2867 5.287992 CGCATATAGCAGACATGTACATCAG 59.712 44.000 5.07 0.00 46.13 2.90
2579 2893 5.867174 ACATGTACGTATTATGTATGCGCAT 59.133 36.000 28.23 28.23 44.90 4.73
2814 3130 1.335145 GCCGGGATAACCAGCTACTA 58.665 55.000 2.18 0.00 40.22 1.82
2838 3154 2.350738 CACAAGAATTTGGGCCGGT 58.649 52.632 1.90 0.00 38.66 5.28
2856 3172 2.875933 CGGTCCACTACAACACAACAAT 59.124 45.455 0.00 0.00 0.00 2.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 3.857038 GCATGCTGGGGCCCATTG 61.857 66.667 28.95 23.60 37.74 2.82
5 6 4.401876 TGCATGCTGGGGCCCATT 62.402 61.111 28.95 11.64 37.74 3.16
10 11 2.441532 ATCTGTGCATGCTGGGGC 60.442 61.111 20.33 4.69 39.26 5.80
11 12 1.826921 GGATCTGTGCATGCTGGGG 60.827 63.158 20.33 6.71 0.00 4.96
12 13 0.467474 ATGGATCTGTGCATGCTGGG 60.467 55.000 20.33 8.52 34.84 4.45
13 14 0.952280 GATGGATCTGTGCATGCTGG 59.048 55.000 20.33 8.89 36.44 4.85
14 15 1.874231 GAGATGGATCTGTGCATGCTG 59.126 52.381 20.33 9.28 36.44 4.41
15 16 1.540580 CGAGATGGATCTGTGCATGCT 60.541 52.381 20.33 0.00 36.44 3.79
16 17 0.866427 CGAGATGGATCTGTGCATGC 59.134 55.000 11.82 11.82 36.44 4.06
17 18 2.235845 ACGAGATGGATCTGTGCATG 57.764 50.000 0.00 0.00 36.44 4.06
18 19 2.433604 AGAACGAGATGGATCTGTGCAT 59.566 45.455 0.00 0.00 39.30 3.96
19 20 1.827344 AGAACGAGATGGATCTGTGCA 59.173 47.619 0.00 0.00 37.25 4.57
20 21 2.159184 TCAGAACGAGATGGATCTGTGC 60.159 50.000 0.00 0.00 40.11 4.57
21 22 3.704512 CTCAGAACGAGATGGATCTGTG 58.295 50.000 0.00 0.00 45.45 3.66
22 23 2.100584 GCTCAGAACGAGATGGATCTGT 59.899 50.000 0.00 0.00 45.45 3.41
23 24 2.361757 AGCTCAGAACGAGATGGATCTG 59.638 50.000 0.00 0.00 45.45 2.90
24 25 2.665165 AGCTCAGAACGAGATGGATCT 58.335 47.619 0.00 0.00 45.45 2.75
25 26 3.122297 CAAGCTCAGAACGAGATGGATC 58.878 50.000 0.00 0.00 45.45 3.36
26 27 2.762887 TCAAGCTCAGAACGAGATGGAT 59.237 45.455 0.00 0.00 45.45 3.41
27 28 2.171003 TCAAGCTCAGAACGAGATGGA 58.829 47.619 0.00 0.00 45.45 3.41
28 29 2.662006 TCAAGCTCAGAACGAGATGG 57.338 50.000 0.00 0.00 45.45 3.51
29 30 3.306434 CACATCAAGCTCAGAACGAGATG 59.694 47.826 0.00 0.00 45.45 2.90
30 31 3.519579 CACATCAAGCTCAGAACGAGAT 58.480 45.455 0.00 0.00 45.45 2.75
31 32 2.353109 CCACATCAAGCTCAGAACGAGA 60.353 50.000 0.00 0.00 45.45 4.04
32 33 1.998315 CCACATCAAGCTCAGAACGAG 59.002 52.381 0.00 0.00 45.37 4.18
33 34 1.338105 CCCACATCAAGCTCAGAACGA 60.338 52.381 0.00 0.00 0.00 3.85
34 35 1.081892 CCCACATCAAGCTCAGAACG 58.918 55.000 0.00 0.00 0.00 3.95
35 36 2.079925 GACCCACATCAAGCTCAGAAC 58.920 52.381 0.00 0.00 0.00 3.01
36 37 1.003580 GGACCCACATCAAGCTCAGAA 59.996 52.381 0.00 0.00 0.00 3.02
37 38 0.615331 GGACCCACATCAAGCTCAGA 59.385 55.000 0.00 0.00 0.00 3.27
38 39 0.393537 GGGACCCACATCAAGCTCAG 60.394 60.000 5.33 0.00 0.00 3.35
39 40 1.133181 TGGGACCCACATCAAGCTCA 61.133 55.000 9.95 0.00 0.00 4.26
40 41 0.038166 TTGGGACCCACATCAAGCTC 59.962 55.000 14.59 0.00 30.78 4.09
41 42 0.251341 GTTGGGACCCACATCAAGCT 60.251 55.000 14.59 0.00 30.78 3.74
42 43 1.586154 CGTTGGGACCCACATCAAGC 61.586 60.000 14.59 0.00 30.78 4.01
43 44 0.250727 ACGTTGGGACCCACATCAAG 60.251 55.000 14.59 3.24 30.78 3.02
44 45 0.536233 CACGTTGGGACCCACATCAA 60.536 55.000 14.59 0.00 30.78 2.57
45 46 1.072332 CACGTTGGGACCCACATCA 59.928 57.895 14.59 0.00 30.78 3.07
46 47 1.072505 ACACGTTGGGACCCACATC 59.927 57.895 14.59 6.09 30.78 3.06
47 48 1.228124 CACACGTTGGGACCCACAT 60.228 57.895 14.59 0.00 30.78 3.21
48 49 2.190843 CACACGTTGGGACCCACA 59.809 61.111 14.59 1.55 30.78 4.17
49 50 2.184167 CACACACGTTGGGACCCAC 61.184 63.158 14.59 7.89 30.78 4.61
50 51 2.190843 CACACACGTTGGGACCCA 59.809 61.111 9.95 9.95 0.00 4.51
51 52 2.593436 CCACACACGTTGGGACCC 60.593 66.667 2.45 2.45 0.00 4.46
52 53 1.452470 AACCACACACGTTGGGACC 60.452 57.895 9.49 0.00 0.00 4.46
53 54 0.745128 TCAACCACACACGTTGGGAC 60.745 55.000 9.49 0.00 40.80 4.46
54 55 0.462937 CTCAACCACACACGTTGGGA 60.463 55.000 9.49 0.00 43.16 4.37
55 56 1.444119 CCTCAACCACACACGTTGGG 61.444 60.000 9.49 1.78 40.70 4.12
56 57 0.746563 ACCTCAACCACACACGTTGG 60.747 55.000 3.15 3.15 40.80 3.77
57 58 0.376852 CACCTCAACCACACACGTTG 59.623 55.000 0.00 0.00 41.61 4.10
58 59 1.373590 GCACCTCAACCACACACGTT 61.374 55.000 0.00 0.00 0.00 3.99
59 60 1.817941 GCACCTCAACCACACACGT 60.818 57.895 0.00 0.00 0.00 4.49
60 61 0.249699 TAGCACCTCAACCACACACG 60.250 55.000 0.00 0.00 0.00 4.49
61 62 1.806542 CATAGCACCTCAACCACACAC 59.193 52.381 0.00 0.00 0.00 3.82
62 63 1.881925 GCATAGCACCTCAACCACACA 60.882 52.381 0.00 0.00 0.00 3.72
63 64 0.804989 GCATAGCACCTCAACCACAC 59.195 55.000 0.00 0.00 0.00 3.82
64 65 0.322456 GGCATAGCACCTCAACCACA 60.322 55.000 0.00 0.00 0.00 4.17
65 66 0.035056 AGGCATAGCACCTCAACCAC 60.035 55.000 0.00 0.00 28.76 4.16
66 67 2.386864 AGGCATAGCACCTCAACCA 58.613 52.632 0.00 0.00 28.76 3.67
82 83 1.733402 TTTTGCACGTTGGCCTGAGG 61.733 55.000 3.32 0.00 0.00 3.86
83 84 0.102120 TTTTTGCACGTTGGCCTGAG 59.898 50.000 3.32 0.00 0.00 3.35
84 85 2.193532 TTTTTGCACGTTGGCCTGA 58.806 47.368 3.32 0.00 0.00 3.86
85 86 4.823276 TTTTTGCACGTTGGCCTG 57.177 50.000 3.32 0.00 0.00 4.85
101 102 2.108952 ACATCCAGTCCCAGCTCTTTTT 59.891 45.455 0.00 0.00 0.00 1.94
102 103 1.707427 ACATCCAGTCCCAGCTCTTTT 59.293 47.619 0.00 0.00 0.00 2.27
103 104 1.366319 ACATCCAGTCCCAGCTCTTT 58.634 50.000 0.00 0.00 0.00 2.52
104 105 1.366319 AACATCCAGTCCCAGCTCTT 58.634 50.000 0.00 0.00 0.00 2.85
105 106 1.004044 CAAACATCCAGTCCCAGCTCT 59.996 52.381 0.00 0.00 0.00 4.09
106 107 1.271597 ACAAACATCCAGTCCCAGCTC 60.272 52.381 0.00 0.00 0.00 4.09
107 108 0.773644 ACAAACATCCAGTCCCAGCT 59.226 50.000 0.00 0.00 0.00 4.24
108 109 1.620822 AACAAACATCCAGTCCCAGC 58.379 50.000 0.00 0.00 0.00 4.85
109 110 3.891366 AGAAAACAAACATCCAGTCCCAG 59.109 43.478 0.00 0.00 0.00 4.45
110 111 3.909732 AGAAAACAAACATCCAGTCCCA 58.090 40.909 0.00 0.00 0.00 4.37
111 112 4.937201 AAGAAAACAAACATCCAGTCCC 57.063 40.909 0.00 0.00 0.00 4.46
112 113 5.163457 TGGAAAGAAAACAAACATCCAGTCC 60.163 40.000 0.00 0.00 32.10 3.85
113 114 5.901552 TGGAAAGAAAACAAACATCCAGTC 58.098 37.500 0.00 0.00 32.10 3.51
114 115 5.930837 TGGAAAGAAAACAAACATCCAGT 57.069 34.783 0.00 0.00 32.10 4.00
115 116 6.818142 ACTTTGGAAAGAAAACAAACATCCAG 59.182 34.615 6.13 0.00 39.31 3.86
116 117 6.706295 ACTTTGGAAAGAAAACAAACATCCA 58.294 32.000 6.13 0.00 39.31 3.41
117 118 7.762159 TGTACTTTGGAAAGAAAACAAACATCC 59.238 33.333 6.13 0.00 39.31 3.51
118 119 8.696410 TGTACTTTGGAAAGAAAACAAACATC 57.304 30.769 6.13 0.00 39.31 3.06
119 120 7.763985 CCTGTACTTTGGAAAGAAAACAAACAT 59.236 33.333 6.13 0.00 39.31 2.71
120 121 7.093992 CCTGTACTTTGGAAAGAAAACAAACA 58.906 34.615 6.13 0.00 39.31 2.83
121 122 6.035650 GCCTGTACTTTGGAAAGAAAACAAAC 59.964 38.462 6.13 0.53 39.31 2.93
122 123 6.103330 GCCTGTACTTTGGAAAGAAAACAAA 58.897 36.000 6.13 0.00 39.31 2.83
123 124 5.394773 GGCCTGTACTTTGGAAAGAAAACAA 60.395 40.000 6.13 0.00 39.31 2.83
124 125 4.098807 GGCCTGTACTTTGGAAAGAAAACA 59.901 41.667 6.13 6.40 39.31 2.83
125 126 4.341235 AGGCCTGTACTTTGGAAAGAAAAC 59.659 41.667 3.11 2.61 39.31 2.43
126 127 4.542697 AGGCCTGTACTTTGGAAAGAAAA 58.457 39.130 3.11 0.00 39.31 2.29
127 128 4.178956 AGGCCTGTACTTTGGAAAGAAA 57.821 40.909 3.11 0.00 39.31 2.52
128 129 3.876309 AGGCCTGTACTTTGGAAAGAA 57.124 42.857 3.11 0.00 39.31 2.52
129 130 3.263425 CCTAGGCCTGTACTTTGGAAAGA 59.737 47.826 17.99 0.00 39.31 2.52
130 131 3.263425 TCCTAGGCCTGTACTTTGGAAAG 59.737 47.826 17.99 0.00 41.73 2.62
131 132 3.253220 TCCTAGGCCTGTACTTTGGAAA 58.747 45.455 17.99 0.00 0.00 3.13
132 133 2.910544 TCCTAGGCCTGTACTTTGGAA 58.089 47.619 17.99 0.00 0.00 3.53
133 134 2.634639 TCCTAGGCCTGTACTTTGGA 57.365 50.000 17.99 8.39 0.00 3.53
134 135 3.009143 AGTTTCCTAGGCCTGTACTTTGG 59.991 47.826 17.99 6.08 0.00 3.28
135 136 4.287766 AGTTTCCTAGGCCTGTACTTTG 57.712 45.455 17.99 0.00 0.00 2.77
136 137 5.130643 GGATAGTTTCCTAGGCCTGTACTTT 59.869 44.000 17.99 6.39 41.78 2.66
137 138 4.654724 GGATAGTTTCCTAGGCCTGTACTT 59.345 45.833 17.99 0.00 41.78 2.24
138 139 4.224762 GGATAGTTTCCTAGGCCTGTACT 58.775 47.826 17.99 13.14 41.78 2.73
139 140 3.965347 TGGATAGTTTCCTAGGCCTGTAC 59.035 47.826 17.99 5.98 45.68 2.90
140 141 4.274794 TGGATAGTTTCCTAGGCCTGTA 57.725 45.455 17.99 0.00 45.68 2.74
141 142 3.130734 TGGATAGTTTCCTAGGCCTGT 57.869 47.619 17.99 0.00 45.68 4.00
142 143 4.503714 TTTGGATAGTTTCCTAGGCCTG 57.496 45.455 17.99 5.26 45.68 4.85
143 144 4.788617 TCTTTTGGATAGTTTCCTAGGCCT 59.211 41.667 11.78 11.78 45.68 5.19
144 145 5.112129 TCTTTTGGATAGTTTCCTAGGCC 57.888 43.478 2.96 0.00 45.68 5.19
145 146 7.971183 CTATCTTTTGGATAGTTTCCTAGGC 57.029 40.000 2.96 0.00 45.31 3.93
156 157 6.826668 TCGATGCTTTCCTATCTTTTGGATA 58.173 36.000 0.00 0.00 35.98 2.59
157 158 5.684704 TCGATGCTTTCCTATCTTTTGGAT 58.315 37.500 0.00 0.00 38.38 3.41
158 159 5.097742 TCGATGCTTTCCTATCTTTTGGA 57.902 39.130 0.00 0.00 0.00 3.53
159 160 6.382869 AATCGATGCTTTCCTATCTTTTGG 57.617 37.500 0.00 0.00 0.00 3.28
160 161 6.433766 GGAATCGATGCTTTCCTATCTTTTG 58.566 40.000 2.72 0.00 38.68 2.44
161 162 5.532779 GGGAATCGATGCTTTCCTATCTTTT 59.467 40.000 13.73 0.00 41.02 2.27
162 163 5.066593 GGGAATCGATGCTTTCCTATCTTT 58.933 41.667 13.73 0.00 41.02 2.52
163 164 4.103153 TGGGAATCGATGCTTTCCTATCTT 59.897 41.667 13.73 0.00 41.02 2.40
164 165 3.648067 TGGGAATCGATGCTTTCCTATCT 59.352 43.478 13.73 0.00 41.02 1.98
165 166 4.008074 TGGGAATCGATGCTTTCCTATC 57.992 45.455 13.73 0.00 41.02 2.08
166 167 4.202503 ACATGGGAATCGATGCTTTCCTAT 60.203 41.667 13.73 10.97 42.08 2.57
167 168 3.136443 ACATGGGAATCGATGCTTTCCTA 59.864 43.478 13.73 9.27 41.02 2.94
168 169 2.092212 ACATGGGAATCGATGCTTTCCT 60.092 45.455 13.73 0.00 41.02 3.36
169 170 2.291741 GACATGGGAATCGATGCTTTCC 59.708 50.000 2.72 5.13 40.60 3.13
170 171 2.291741 GGACATGGGAATCGATGCTTTC 59.708 50.000 2.72 0.00 33.18 2.62
171 172 2.092212 AGGACATGGGAATCGATGCTTT 60.092 45.455 2.72 0.00 33.18 3.51
172 173 1.492176 AGGACATGGGAATCGATGCTT 59.508 47.619 2.72 0.00 33.18 3.91
173 174 1.135094 AGGACATGGGAATCGATGCT 58.865 50.000 2.72 0.00 33.18 3.79
174 175 1.202687 TCAGGACATGGGAATCGATGC 60.203 52.381 0.00 0.00 33.18 3.91
175 176 2.874701 GTTCAGGACATGGGAATCGATG 59.125 50.000 0.00 0.00 35.58 3.84
176 177 2.505407 TGTTCAGGACATGGGAATCGAT 59.495 45.455 0.00 0.00 32.00 3.59
177 178 1.905894 TGTTCAGGACATGGGAATCGA 59.094 47.619 0.00 0.00 32.00 3.59
178 179 2.009774 GTGTTCAGGACATGGGAATCG 58.990 52.381 0.00 0.00 41.10 3.34
179 180 3.012518 CTGTGTTCAGGACATGGGAATC 58.987 50.000 0.00 0.00 41.10 2.52
180 181 2.881403 GCTGTGTTCAGGACATGGGAAT 60.881 50.000 0.00 0.00 41.10 3.01
181 182 1.545428 GCTGTGTTCAGGACATGGGAA 60.545 52.381 0.00 0.00 41.10 3.97
182 183 0.036732 GCTGTGTTCAGGACATGGGA 59.963 55.000 0.00 0.00 41.10 4.37
183 184 0.037303 AGCTGTGTTCAGGACATGGG 59.963 55.000 0.00 0.00 41.10 4.00
184 185 2.289631 TGTAGCTGTGTTCAGGACATGG 60.290 50.000 0.00 0.00 41.10 3.66
185 186 2.998670 CTGTAGCTGTGTTCAGGACATG 59.001 50.000 0.00 0.00 41.10 3.21
186 187 2.634940 ACTGTAGCTGTGTTCAGGACAT 59.365 45.455 0.00 0.00 41.10 3.06
187 188 2.039418 ACTGTAGCTGTGTTCAGGACA 58.961 47.619 0.00 0.00 41.57 4.02
188 189 2.035961 TCACTGTAGCTGTGTTCAGGAC 59.964 50.000 0.00 0.00 41.57 3.85
189 190 2.316108 TCACTGTAGCTGTGTTCAGGA 58.684 47.619 0.00 0.00 41.57 3.86
190 191 2.820059 TCACTGTAGCTGTGTTCAGG 57.180 50.000 0.00 0.00 41.57 3.86
191 192 5.484173 TTTTTCACTGTAGCTGTGTTCAG 57.516 39.130 0.00 0.00 43.87 3.02
221 222 5.416013 AGGAAACTTCGAAGGAATCATTTCC 59.584 40.000 30.04 30.04 45.54 3.13
222 223 6.502136 AGGAAACTTCGAAGGAATCATTTC 57.498 37.500 27.86 23.35 37.44 2.17
237 238 8.400409 CTTCATGGGAAAAGCGAAGGAAACTT 62.400 42.308 0.00 0.00 42.88 2.66
238 239 7.007314 CTTCATGGGAAAAGCGAAGGAAACT 62.007 44.000 0.00 0.00 35.38 2.66
239 240 2.556622 TCATGGGAAAAGCGAAGGAAAC 59.443 45.455 0.00 0.00 0.00 2.78
240 241 2.870175 TCATGGGAAAAGCGAAGGAAA 58.130 42.857 0.00 0.00 0.00 3.13
241 242 2.577606 TCATGGGAAAAGCGAAGGAA 57.422 45.000 0.00 0.00 0.00 3.36
242 243 2.436417 CTTCATGGGAAAAGCGAAGGA 58.564 47.619 0.00 0.00 31.35 3.36
243 244 1.135286 GCTTCATGGGAAAAGCGAAGG 60.135 52.381 1.55 0.00 38.60 3.46
244 245 2.268730 GCTTCATGGGAAAAGCGAAG 57.731 50.000 1.55 0.00 38.60 3.79
248 249 1.269448 TGTTCGCTTCATGGGAAAAGC 59.731 47.619 6.76 6.76 46.73 3.51
249 250 2.095059 CCTGTTCGCTTCATGGGAAAAG 60.095 50.000 1.48 1.48 46.73 2.27
250 251 1.885887 CCTGTTCGCTTCATGGGAAAA 59.114 47.619 0.00 0.00 46.73 2.29
251 252 1.533625 CCTGTTCGCTTCATGGGAAA 58.466 50.000 0.00 0.00 46.73 3.13
252 253 0.960364 GCCTGTTCGCTTCATGGGAA 60.960 55.000 0.00 0.00 43.87 3.97
253 254 1.377202 GCCTGTTCGCTTCATGGGA 60.377 57.895 0.00 0.00 35.75 4.37
254 255 2.409870 GGCCTGTTCGCTTCATGGG 61.410 63.158 0.00 0.00 0.00 4.00
255 256 2.409870 GGGCCTGTTCGCTTCATGG 61.410 63.158 0.84 0.00 0.00 3.66
256 257 0.107703 TAGGGCCTGTTCGCTTCATG 60.108 55.000 18.53 0.00 0.00 3.07
257 258 0.618458 TTAGGGCCTGTTCGCTTCAT 59.382 50.000 18.53 0.00 0.00 2.57
258 259 0.398696 TTTAGGGCCTGTTCGCTTCA 59.601 50.000 18.53 0.00 0.00 3.02
259 260 1.199327 GTTTTAGGGCCTGTTCGCTTC 59.801 52.381 18.53 0.00 0.00 3.86
260 261 1.202891 AGTTTTAGGGCCTGTTCGCTT 60.203 47.619 18.53 0.00 0.00 4.68
261 262 0.400594 AGTTTTAGGGCCTGTTCGCT 59.599 50.000 18.53 4.96 0.00 4.93
262 263 1.244816 AAGTTTTAGGGCCTGTTCGC 58.755 50.000 18.53 2.46 0.00 4.70
263 264 4.316205 AAAAAGTTTTAGGGCCTGTTCG 57.684 40.909 18.53 0.00 0.00 3.95
292 293 7.012327 GGCATCAAAGTTTTAGCCTTTCTTTTT 59.988 33.333 13.00 0.00 39.02 1.94
293 294 6.483307 GGCATCAAAGTTTTAGCCTTTCTTTT 59.517 34.615 13.00 0.00 39.02 2.27
294 295 5.991606 GGCATCAAAGTTTTAGCCTTTCTTT 59.008 36.000 13.00 0.00 39.02 2.52
295 296 5.070313 TGGCATCAAAGTTTTAGCCTTTCTT 59.930 36.000 18.36 0.00 42.46 2.52
317 318 7.944061 TCAATTTGCCATGTCTATAAATCTGG 58.056 34.615 0.00 0.00 0.00 3.86
325 326 7.550196 GGAAAACATTCAATTTGCCATGTCTAT 59.450 33.333 12.01 4.90 35.10 1.98
426 427 0.659957 GAGCATGACAAATCCGCCTC 59.340 55.000 0.00 0.00 0.00 4.70
430 431 3.376234 AGTTGATGAGCATGACAAATCCG 59.624 43.478 0.00 0.00 0.00 4.18
492 493 7.655236 TTTTAGGCATGACAAAATGAATGTG 57.345 32.000 0.00 0.00 0.00 3.21
520 522 2.838202 ACCCAGATATCCAGTGAACGTT 59.162 45.455 0.00 0.00 0.00 3.99
652 654 8.578308 TTCAAATTGTCATCTTGCAAACTTAG 57.422 30.769 0.00 0.00 0.00 2.18
668 670 8.702163 AAAAGTTGATTTCGACTTCAAATTGT 57.298 26.923 17.69 12.30 46.83 2.71
906 918 9.464714 CGAGTACTTATATCACATGCTTAAGTT 57.535 33.333 4.02 0.00 35.40 2.66
931 943 5.458779 TGCTCGTGTATTCAACTATTCATCG 59.541 40.000 0.00 0.00 0.00 3.84
960 972 1.181098 ATGCAGTGCACCTTGGGAAC 61.181 55.000 22.44 0.00 43.04 3.62
1645 1683 0.390860 GGGATGATGTGTCGGAGGAG 59.609 60.000 0.00 0.00 0.00 3.69
2204 2518 1.135094 CATCCTCCCCATGCAGTAGT 58.865 55.000 0.00 0.00 0.00 2.73
2290 2604 1.019673 TATGACGGCTCGTACCTCAC 58.980 55.000 0.09 0.00 41.37 3.51
2322 2636 2.281208 CTGGGACCGGCGTTGAAA 60.281 61.111 6.01 0.00 0.00 2.69
2551 2865 7.461026 GCGCATACATAATACGTACATGTACTG 60.461 40.741 28.53 23.58 37.82 2.74
2552 2866 6.525628 GCGCATACATAATACGTACATGTACT 59.474 38.462 28.53 19.29 37.82 2.73
2553 2867 6.306117 TGCGCATACATAATACGTACATGTAC 59.694 38.462 23.53 23.53 37.82 2.90
2760 3076 3.252554 TCCCAGTTTGCCAAATAGGTT 57.747 42.857 9.19 0.00 40.61 3.50
2814 3130 1.067635 GCCCAAATTCTTGTGCGTGAT 60.068 47.619 0.00 0.00 0.00 3.06
2838 3154 6.483974 ACGAATTATTGTTGTGTTGTAGTGGA 59.516 34.615 0.00 0.00 0.00 4.02
2856 3172 8.738554 CGAACATTTTTGAAACTTCACGAATTA 58.261 29.630 0.00 0.00 36.83 1.40
3270 3965 7.969314 TGCACTTTAAATTTTTGTTCAGGTTC 58.031 30.769 0.00 0.00 0.00 3.62
3385 4080 9.994432 GAATTTGTGGTATTTTCTAGATGTCAG 57.006 33.333 0.00 0.00 0.00 3.51


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

AutoCloner maintained by Alex Coulton.