Multiple sequence alignment - TraesCS3A01G138400

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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 TraesCS3A01G138400 chr3A 100.000 5420 0 0 1 5420 115843968 115838549 0.000000e+00 10009.0
1 TraesCS3A01G138400 chr3A 97.486 5092 109 11 336 5420 115615481 115610402 0.000000e+00 8676.0
2 TraesCS3A01G138400 chr3A 97.427 5091 113 11 336 5420 115394018 115388940 0.000000e+00 8660.0
3 TraesCS3A01G138400 chr3A 95.844 3393 117 9 2033 5420 115164580 115161207 0.000000e+00 5463.0
4 TraesCS3A01G138400 chr3A 95.055 1719 76 6 336 2048 115167530 115165815 0.000000e+00 2695.0
5 TraesCS3A01G138400 chr3A 82.034 1770 262 30 2808 4561 116075567 116073838 0.000000e+00 1456.0
6 TraesCS3A01G138400 chr3A 82.374 1407 186 35 1235 2594 116077223 116075832 0.000000e+00 1168.0
7 TraesCS3A01G138400 chr3A 80.610 459 65 16 336 782 116078603 116078157 3.130000e-87 333.0
8 TraesCS3A01G138400 chr3A 84.791 263 34 5 77 336 1646596 1646337 5.390000e-65 259.0
9 TraesCS3A01G138400 chr3B 85.839 2754 255 63 876 3535 148547227 148544515 0.000000e+00 2800.0
10 TraesCS3A01G138400 chr3B 85.839 2754 255 63 876 3535 148583676 148580964 0.000000e+00 2800.0
11 TraesCS3A01G138400 chr3B 85.839 2754 255 63 876 3535 148625013 148622301 0.000000e+00 2800.0
12 TraesCS3A01G138400 chr3B 85.595 2749 262 64 876 3531 148660962 148658255 0.000000e+00 2760.0
13 TraesCS3A01G138400 chr3B 86.064 1184 151 8 3588 4759 148658232 148657051 0.000000e+00 1260.0
14 TraesCS3A01G138400 chr3B 86.912 871 98 9 3902 4759 148543747 148542880 0.000000e+00 963.0
15 TraesCS3A01G138400 chr3B 90.746 389 20 7 488 872 148661380 148661004 6.270000e-139 505.0
16 TraesCS3A01G138400 chr3B 90.464 388 21 7 488 872 148584092 148583718 1.050000e-136 497.0
17 TraesCS3A01G138400 chr3B 90.464 388 21 7 488 872 148625429 148625055 1.050000e-136 497.0
18 TraesCS3A01G138400 chr3B 89.974 389 22 7 488 872 148547644 148547269 2.270000e-133 486.0
19 TraesCS3A01G138400 chr3B 85.200 250 29 7 49 293 768307609 768307363 3.240000e-62 250.0
20 TraesCS3A01G138400 chr3B 91.391 151 12 1 336 485 148685060 148684910 7.120000e-49 206.0
21 TraesCS3A01G138400 chr3D 89.988 1648 135 15 882 2502 98150581 98148937 0.000000e+00 2102.0
22 TraesCS3A01G138400 chr3D 85.025 1222 152 18 3554 4759 98147857 98146651 0.000000e+00 1214.0
23 TraesCS3A01G138400 chr3D 91.324 438 29 6 336 769 98151841 98151409 1.680000e-164 590.0
24 TraesCS3A01G138400 chr3D 96.491 57 2 0 823 879 98150676 98150620 1.610000e-15 95.3
25 TraesCS3A01G138400 chr7A 78.052 811 169 9 3618 4421 76355870 76355062 2.250000e-138 503.0
26 TraesCS3A01G138400 chr7A 78.082 803 167 9 3618 4413 76453543 76452743 2.910000e-137 499.0
27 TraesCS3A01G138400 chr6A 77.792 806 166 10 3626 4421 106737141 106737943 8.160000e-133 484.0
28 TraesCS3A01G138400 chr5B 85.280 428 59 4 4904 5328 507806142 507805716 6.450000e-119 438.0
29 TraesCS3A01G138400 chr5B 84.906 265 32 8 75 336 704157673 704157932 1.500000e-65 261.0
30 TraesCS3A01G138400 chr5B 76.154 260 44 10 1246 1487 546522783 546522524 2.650000e-23 121.0
31 TraesCS3A01G138400 chr6D 85.122 410 55 6 4915 5320 294412511 294412918 1.090000e-111 414.0
32 TraesCS3A01G138400 chr2D 84.500 400 58 3 4924 5320 24220933 24221331 5.090000e-105 392.0
33 TraesCS3A01G138400 chr6B 85.450 378 49 6 4914 5289 688597563 688597190 6.580000e-104 388.0
34 TraesCS3A01G138400 chr4D 84.478 393 54 7 4930 5319 16717373 16716985 1.100000e-101 381.0
35 TraesCS3A01G138400 chr4D 85.317 252 28 6 49 299 58984467 58984710 9.010000e-63 252.0
36 TraesCS3A01G138400 chr5A 83.293 413 57 10 4911 5319 533345397 533345801 2.380000e-98 370.0
37 TraesCS3A01G138400 chr1D 88.192 271 22 8 49 317 366007730 366007992 1.130000e-81 315.0
38 TraesCS3A01G138400 chr5D 88.889 252 23 4 49 299 460398326 460398573 6.820000e-79 305.0
39 TraesCS3A01G138400 chr7B 84.375 288 35 7 49 334 512003274 512002995 1.920000e-69 274.0
40 TraesCS3A01G138400 chr7D 87.149 249 21 7 46 293 35196037 35195799 6.920000e-69 272.0
41 TraesCS3A01G138400 chr1B 83.525 261 37 6 78 336 501358394 501358138 7.020000e-59 239.0


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 TraesCS3A01G138400 chr3A 115838549 115843968 5419 True 10009.000000 10009 100.000000 1 5420 1 chr3A.!!$R4 5419
1 TraesCS3A01G138400 chr3A 115610402 115615481 5079 True 8676.000000 8676 97.486000 336 5420 1 chr3A.!!$R3 5084
2 TraesCS3A01G138400 chr3A 115388940 115394018 5078 True 8660.000000 8660 97.427000 336 5420 1 chr3A.!!$R2 5084
3 TraesCS3A01G138400 chr3A 115161207 115167530 6323 True 4079.000000 5463 95.449500 336 5420 2 chr3A.!!$R5 5084
4 TraesCS3A01G138400 chr3A 116073838 116078603 4765 True 985.666667 1456 81.672667 336 4561 3 chr3A.!!$R6 4225
5 TraesCS3A01G138400 chr3B 148580964 148584092 3128 True 1648.500000 2800 88.151500 488 3535 2 chr3B.!!$R4 3047
6 TraesCS3A01G138400 chr3B 148622301 148625429 3128 True 1648.500000 2800 88.151500 488 3535 2 chr3B.!!$R5 3047
7 TraesCS3A01G138400 chr3B 148657051 148661380 4329 True 1508.333333 2760 87.468333 488 4759 3 chr3B.!!$R6 4271
8 TraesCS3A01G138400 chr3B 148542880 148547644 4764 True 1416.333333 2800 87.575000 488 4759 3 chr3B.!!$R3 4271
9 TraesCS3A01G138400 chr3D 98146651 98151841 5190 True 1000.325000 2102 90.707000 336 4759 4 chr3D.!!$R1 4423
10 TraesCS3A01G138400 chr7A 76355062 76355870 808 True 503.000000 503 78.052000 3618 4421 1 chr7A.!!$R1 803
11 TraesCS3A01G138400 chr7A 76452743 76453543 800 True 499.000000 499 78.082000 3618 4413 1 chr7A.!!$R2 795
12 TraesCS3A01G138400 chr6A 106737141 106737943 802 False 484.000000 484 77.792000 3626 4421 1 chr6A.!!$F1 795

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
106 107 0.032615 AGGGACAGAGTGAGCTAGGG 60.033 60.000 0.00 0.0 0.00 3.53 F
288 289 0.108019 GGTCCAGTTGGGTCGAGTTT 59.892 55.000 0.00 0.0 38.11 2.66 F
313 314 0.249120 TGACCCATCACTAACTGGCG 59.751 55.000 0.00 0.0 0.00 5.69 F
314 315 0.462047 GACCCATCACTAACTGGCGG 60.462 60.000 0.00 0.0 0.00 6.13 F
334 335 1.026718 CCGGTCCAGGCATTTGAGAC 61.027 60.000 0.00 0.0 0.00 3.36 F
431 435 1.044611 TTGGGCCTGGTTTTACTTGC 58.955 50.000 4.53 0.0 0.00 4.01 F
486 498 1.199615 CAGGAACCCCTTCTCTCTCC 58.800 60.000 0.00 0.0 42.02 3.71 F
3490 6220 1.416772 GGCATACTCAAGGTACTCCCC 59.583 57.143 0.00 0.0 38.49 4.81 F
3641 6373 3.965379 TTTGACAGCCCGACATAACTA 57.035 42.857 0.00 0.0 0.00 2.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1285 2554 0.176449 CGGTGACAGCAGATGGATCA 59.824 55.000 5.35 0.0 0.00 2.92 R
1333 2602 0.466124 CTAGCCAGTACCTCCCAAGC 59.534 60.000 0.00 0.0 0.00 4.01 R
2053 4625 1.815421 CGCTGAAATCCCGAGGTGG 60.815 63.158 0.00 0.0 37.55 4.61 R
2758 5404 3.611113 CCTATACGATTATGTTTCGGCGG 59.389 47.826 7.21 0.0 40.83 6.13 R
3277 6004 0.532862 CCTATTCCAGGCAACGCGAT 60.533 55.000 15.93 0.0 46.39 4.58 R
3322 6052 9.739276 ACATTCACAGATTAGTTATTGGAGAAA 57.261 29.630 0.00 0.0 0.00 2.52 R
3641 6373 2.046892 GATGCTGACACCTGGCGT 60.047 61.111 0.00 0.0 0.00 5.68 R
4296 7473 4.379243 CCGCCTTGCACTCTCCGT 62.379 66.667 0.00 0.0 0.00 4.69 R
4807 8004 4.558226 TGCCTCTTCTATGTCATGTGTT 57.442 40.909 0.00 0.0 0.00 3.32 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 3.403936 GGTGGATGGGATCGGAAAG 57.596 57.895 0.00 0.00 0.00 2.62
19 20 0.179018 GGTGGATGGGATCGGAAAGG 60.179 60.000 0.00 0.00 0.00 3.11
20 21 0.179018 GTGGATGGGATCGGAAAGGG 60.179 60.000 0.00 0.00 0.00 3.95
21 22 0.327095 TGGATGGGATCGGAAAGGGA 60.327 55.000 0.00 0.00 0.00 4.20
22 23 0.398318 GGATGGGATCGGAAAGGGAG 59.602 60.000 0.00 0.00 0.00 4.30
23 24 1.424638 GATGGGATCGGAAAGGGAGA 58.575 55.000 0.00 0.00 0.00 3.71
24 25 1.346068 GATGGGATCGGAAAGGGAGAG 59.654 57.143 0.00 0.00 0.00 3.20
25 26 0.691078 TGGGATCGGAAAGGGAGAGG 60.691 60.000 0.00 0.00 0.00 3.69
26 27 1.411651 GGGATCGGAAAGGGAGAGGG 61.412 65.000 0.00 0.00 0.00 4.30
27 28 0.398664 GGATCGGAAAGGGAGAGGGA 60.399 60.000 0.00 0.00 0.00 4.20
28 29 1.044611 GATCGGAAAGGGAGAGGGAG 58.955 60.000 0.00 0.00 0.00 4.30
29 30 0.637195 ATCGGAAAGGGAGAGGGAGA 59.363 55.000 0.00 0.00 0.00 3.71
30 31 0.033011 TCGGAAAGGGAGAGGGAGAG 60.033 60.000 0.00 0.00 0.00 3.20
31 32 1.045911 CGGAAAGGGAGAGGGAGAGG 61.046 65.000 0.00 0.00 0.00 3.69
32 33 0.340208 GGAAAGGGAGAGGGAGAGGA 59.660 60.000 0.00 0.00 0.00 3.71
33 34 1.691163 GGAAAGGGAGAGGGAGAGGAG 60.691 61.905 0.00 0.00 0.00 3.69
34 35 1.007842 GAAAGGGAGAGGGAGAGGAGT 59.992 57.143 0.00 0.00 0.00 3.85
35 36 0.338120 AAGGGAGAGGGAGAGGAGTG 59.662 60.000 0.00 0.00 0.00 3.51
36 37 1.075600 GGGAGAGGGAGAGGAGTGG 60.076 68.421 0.00 0.00 0.00 4.00
37 38 1.585651 GGGAGAGGGAGAGGAGTGGA 61.586 65.000 0.00 0.00 0.00 4.02
38 39 0.396556 GGAGAGGGAGAGGAGTGGAC 60.397 65.000 0.00 0.00 0.00 4.02
39 40 0.750182 GAGAGGGAGAGGAGTGGACG 60.750 65.000 0.00 0.00 0.00 4.79
40 41 1.755008 GAGGGAGAGGAGTGGACGG 60.755 68.421 0.00 0.00 0.00 4.79
41 42 2.212794 GAGGGAGAGGAGTGGACGGA 62.213 65.000 0.00 0.00 0.00 4.69
42 43 1.755008 GGGAGAGGAGTGGACGGAG 60.755 68.421 0.00 0.00 0.00 4.63
43 44 2.419739 GGAGAGGAGTGGACGGAGC 61.420 68.421 0.00 0.00 0.00 4.70
44 45 1.679305 GAGAGGAGTGGACGGAGCA 60.679 63.158 0.00 0.00 0.00 4.26
45 46 1.228894 AGAGGAGTGGACGGAGCAA 60.229 57.895 0.00 0.00 0.00 3.91
46 47 1.216710 GAGGAGTGGACGGAGCAAG 59.783 63.158 0.00 0.00 0.00 4.01
47 48 1.228894 AGGAGTGGACGGAGCAAGA 60.229 57.895 0.00 0.00 0.00 3.02
48 49 1.216710 GGAGTGGACGGAGCAAGAG 59.783 63.158 0.00 0.00 0.00 2.85
49 50 1.251527 GGAGTGGACGGAGCAAGAGA 61.252 60.000 0.00 0.00 0.00 3.10
50 51 0.172352 GAGTGGACGGAGCAAGAGAG 59.828 60.000 0.00 0.00 0.00 3.20
51 52 0.251386 AGTGGACGGAGCAAGAGAGA 60.251 55.000 0.00 0.00 0.00 3.10
52 53 0.172352 GTGGACGGAGCAAGAGAGAG 59.828 60.000 0.00 0.00 0.00 3.20
53 54 0.967887 TGGACGGAGCAAGAGAGAGG 60.968 60.000 0.00 0.00 0.00 3.69
54 55 1.671901 GGACGGAGCAAGAGAGAGGG 61.672 65.000 0.00 0.00 0.00 4.30
55 56 0.681564 GACGGAGCAAGAGAGAGGGA 60.682 60.000 0.00 0.00 0.00 4.20
56 57 0.682855 ACGGAGCAAGAGAGAGGGAG 60.683 60.000 0.00 0.00 0.00 4.30
57 58 0.395036 CGGAGCAAGAGAGAGGGAGA 60.395 60.000 0.00 0.00 0.00 3.71
58 59 1.402787 GGAGCAAGAGAGAGGGAGAG 58.597 60.000 0.00 0.00 0.00 3.20
59 60 1.402787 GAGCAAGAGAGAGGGAGAGG 58.597 60.000 0.00 0.00 0.00 3.69
60 61 1.006813 AGCAAGAGAGAGGGAGAGGA 58.993 55.000 0.00 0.00 0.00 3.71
61 62 1.063717 AGCAAGAGAGAGGGAGAGGAG 60.064 57.143 0.00 0.00 0.00 3.69
62 63 1.341976 GCAAGAGAGAGGGAGAGGAGT 60.342 57.143 0.00 0.00 0.00 3.85
63 64 2.378038 CAAGAGAGAGGGAGAGGAGTG 58.622 57.143 0.00 0.00 0.00 3.51
64 65 0.926293 AGAGAGAGGGAGAGGAGTGG 59.074 60.000 0.00 0.00 0.00 4.00
65 66 0.923358 GAGAGAGGGAGAGGAGTGGA 59.077 60.000 0.00 0.00 0.00 4.02
66 67 0.629058 AGAGAGGGAGAGGAGTGGAC 59.371 60.000 0.00 0.00 0.00 4.02
67 68 0.750182 GAGAGGGAGAGGAGTGGACG 60.750 65.000 0.00 0.00 0.00 4.79
68 69 1.755008 GAGGGAGAGGAGTGGACGG 60.755 68.421 0.00 0.00 0.00 4.79
69 70 2.212794 GAGGGAGAGGAGTGGACGGA 62.213 65.000 0.00 0.00 0.00 4.69
70 71 1.755008 GGGAGAGGAGTGGACGGAG 60.755 68.421 0.00 0.00 0.00 4.63
71 72 2.419739 GGAGAGGAGTGGACGGAGC 61.420 68.421 0.00 0.00 0.00 4.70
72 73 1.679305 GAGAGGAGTGGACGGAGCA 60.679 63.158 0.00 0.00 0.00 4.26
73 74 1.228894 AGAGGAGTGGACGGAGCAA 60.229 57.895 0.00 0.00 0.00 3.91
74 75 1.216710 GAGGAGTGGACGGAGCAAG 59.783 63.158 0.00 0.00 0.00 4.01
75 76 1.228894 AGGAGTGGACGGAGCAAGA 60.229 57.895 0.00 0.00 0.00 3.02
76 77 1.216710 GGAGTGGACGGAGCAAGAG 59.783 63.158 0.00 0.00 0.00 2.85
77 78 1.251527 GGAGTGGACGGAGCAAGAGA 61.252 60.000 0.00 0.00 0.00 3.10
78 79 0.172352 GAGTGGACGGAGCAAGAGAG 59.828 60.000 0.00 0.00 0.00 3.20
79 80 0.251386 AGTGGACGGAGCAAGAGAGA 60.251 55.000 0.00 0.00 0.00 3.10
80 81 0.172352 GTGGACGGAGCAAGAGAGAG 59.828 60.000 0.00 0.00 0.00 3.20
81 82 0.038310 TGGACGGAGCAAGAGAGAGA 59.962 55.000 0.00 0.00 0.00 3.10
82 83 0.738389 GGACGGAGCAAGAGAGAGAG 59.262 60.000 0.00 0.00 0.00 3.20
83 84 1.680555 GGACGGAGCAAGAGAGAGAGA 60.681 57.143 0.00 0.00 0.00 3.10
84 85 1.670811 GACGGAGCAAGAGAGAGAGAG 59.329 57.143 0.00 0.00 0.00 3.20
85 86 1.280710 ACGGAGCAAGAGAGAGAGAGA 59.719 52.381 0.00 0.00 0.00 3.10
86 87 1.942657 CGGAGCAAGAGAGAGAGAGAG 59.057 57.143 0.00 0.00 0.00 3.20
87 88 2.419990 CGGAGCAAGAGAGAGAGAGAGA 60.420 54.545 0.00 0.00 0.00 3.10
88 89 3.209410 GGAGCAAGAGAGAGAGAGAGAG 58.791 54.545 0.00 0.00 0.00 3.20
89 90 3.209410 GAGCAAGAGAGAGAGAGAGAGG 58.791 54.545 0.00 0.00 0.00 3.69
90 91 2.092212 AGCAAGAGAGAGAGAGAGAGGG 60.092 54.545 0.00 0.00 0.00 4.30
91 92 2.092429 GCAAGAGAGAGAGAGAGAGGGA 60.092 54.545 0.00 0.00 0.00 4.20
92 93 3.545703 CAAGAGAGAGAGAGAGAGGGAC 58.454 54.545 0.00 0.00 0.00 4.46
93 94 2.845659 AGAGAGAGAGAGAGAGGGACA 58.154 52.381 0.00 0.00 0.00 4.02
94 95 2.774234 AGAGAGAGAGAGAGAGGGACAG 59.226 54.545 0.00 0.00 0.00 3.51
95 96 2.771943 GAGAGAGAGAGAGAGGGACAGA 59.228 54.545 0.00 0.00 0.00 3.41
96 97 2.774234 AGAGAGAGAGAGAGGGACAGAG 59.226 54.545 0.00 0.00 0.00 3.35
97 98 2.505819 GAGAGAGAGAGAGGGACAGAGT 59.494 54.545 0.00 0.00 0.00 3.24
98 99 2.239654 AGAGAGAGAGAGGGACAGAGTG 59.760 54.545 0.00 0.00 0.00 3.51
99 100 2.238646 GAGAGAGAGAGGGACAGAGTGA 59.761 54.545 0.00 0.00 0.00 3.41
100 101 2.239654 AGAGAGAGAGGGACAGAGTGAG 59.760 54.545 0.00 0.00 0.00 3.51
101 102 1.102978 GAGAGAGGGACAGAGTGAGC 58.897 60.000 0.00 0.00 0.00 4.26
102 103 0.704076 AGAGAGGGACAGAGTGAGCT 59.296 55.000 0.00 0.00 0.00 4.09
103 104 1.919654 AGAGAGGGACAGAGTGAGCTA 59.080 52.381 0.00 0.00 0.00 3.32
104 105 2.092429 AGAGAGGGACAGAGTGAGCTAG 60.092 54.545 0.00 0.00 0.00 3.42
105 106 1.064017 AGAGGGACAGAGTGAGCTAGG 60.064 57.143 0.00 0.00 0.00 3.02
106 107 0.032615 AGGGACAGAGTGAGCTAGGG 60.033 60.000 0.00 0.00 0.00 3.53
107 108 0.324830 GGGACAGAGTGAGCTAGGGT 60.325 60.000 0.00 0.00 0.00 4.34
108 109 1.562783 GGACAGAGTGAGCTAGGGTT 58.437 55.000 0.00 0.00 0.00 4.11
109 110 1.903183 GGACAGAGTGAGCTAGGGTTT 59.097 52.381 0.00 0.00 0.00 3.27
110 111 2.354203 GGACAGAGTGAGCTAGGGTTTG 60.354 54.545 0.00 0.00 0.00 2.93
111 112 2.563179 GACAGAGTGAGCTAGGGTTTGA 59.437 50.000 0.00 0.00 0.00 2.69
112 113 2.564947 ACAGAGTGAGCTAGGGTTTGAG 59.435 50.000 0.00 0.00 0.00 3.02
113 114 1.552792 AGAGTGAGCTAGGGTTTGAGC 59.447 52.381 0.00 0.00 39.08 4.26
117 118 1.219393 AGCTAGGGTTTGAGCTCGC 59.781 57.895 9.64 3.45 46.08 5.03
118 119 1.815840 GCTAGGGTTTGAGCTCGCC 60.816 63.158 9.64 10.96 35.73 5.54
119 120 1.519455 CTAGGGTTTGAGCTCGCCG 60.519 63.158 9.64 0.00 0.00 6.46
120 121 3.659089 TAGGGTTTGAGCTCGCCGC 62.659 63.158 9.64 7.57 39.57 6.53
150 151 2.907917 TTTTTGTGGGGTCGGCGG 60.908 61.111 7.21 0.00 0.00 6.13
151 152 3.717924 TTTTTGTGGGGTCGGCGGT 62.718 57.895 7.21 0.00 0.00 5.68
152 153 4.939368 TTTGTGGGGTCGGCGGTG 62.939 66.667 7.21 0.00 0.00 4.94
167 168 4.394712 GTGGGTCGGGCCTGTCAG 62.395 72.222 12.43 0.00 37.43 3.51
208 209 4.699522 GGCCGCCCCATATCCGTC 62.700 72.222 0.00 0.00 0.00 4.79
209 210 4.699522 GCCGCCCCATATCCGTCC 62.700 72.222 0.00 0.00 0.00 4.79
210 211 2.923035 CCGCCCCATATCCGTCCT 60.923 66.667 0.00 0.00 0.00 3.85
211 212 1.608336 CCGCCCCATATCCGTCCTA 60.608 63.158 0.00 0.00 0.00 2.94
212 213 0.976073 CCGCCCCATATCCGTCCTAT 60.976 60.000 0.00 0.00 0.00 2.57
213 214 1.687054 CCGCCCCATATCCGTCCTATA 60.687 57.143 0.00 0.00 0.00 1.31
214 215 2.317040 CGCCCCATATCCGTCCTATAT 58.683 52.381 0.00 0.00 0.00 0.86
215 216 2.698797 CGCCCCATATCCGTCCTATATT 59.301 50.000 0.00 0.00 0.00 1.28
216 217 3.134081 CGCCCCATATCCGTCCTATATTT 59.866 47.826 0.00 0.00 0.00 1.40
217 218 4.451900 GCCCCATATCCGTCCTATATTTG 58.548 47.826 0.00 0.00 0.00 2.32
218 219 4.686122 GCCCCATATCCGTCCTATATTTGG 60.686 50.000 0.00 0.00 0.00 3.28
219 220 4.141482 CCCCATATCCGTCCTATATTTGGG 60.141 50.000 0.00 0.00 39.96 4.12
220 221 4.451900 CCATATCCGTCCTATATTTGGGC 58.548 47.826 0.00 0.00 0.00 5.36
227 228 4.772886 GTCCTATATTTGGGCGGGATAT 57.227 45.455 0.00 0.00 0.00 1.63
228 229 4.451900 GTCCTATATTTGGGCGGGATATG 58.548 47.826 0.00 0.00 0.00 1.78
229 230 4.163458 GTCCTATATTTGGGCGGGATATGA 59.837 45.833 0.00 0.00 0.00 2.15
230 231 4.408921 TCCTATATTTGGGCGGGATATGAG 59.591 45.833 0.00 0.00 0.00 2.90
231 232 3.652057 ATATTTGGGCGGGATATGAGG 57.348 47.619 0.00 0.00 0.00 3.86
232 233 0.405585 ATTTGGGCGGGATATGAGGG 59.594 55.000 0.00 0.00 0.00 4.30
233 234 1.715019 TTTGGGCGGGATATGAGGGG 61.715 60.000 0.00 0.00 0.00 4.79
234 235 2.529389 GGGCGGGATATGAGGGGT 60.529 66.667 0.00 0.00 0.00 4.95
235 236 2.750350 GGCGGGATATGAGGGGTG 59.250 66.667 0.00 0.00 0.00 4.61
236 237 2.032681 GCGGGATATGAGGGGTGC 59.967 66.667 0.00 0.00 0.00 5.01
237 238 2.750350 CGGGATATGAGGGGTGCC 59.250 66.667 0.00 0.00 0.00 5.01
238 239 2.750350 GGGATATGAGGGGTGCCG 59.250 66.667 0.00 0.00 0.00 5.69
239 240 2.750350 GGATATGAGGGGTGCCGG 59.250 66.667 0.00 0.00 0.00 6.13
240 241 2.147387 GGATATGAGGGGTGCCGGT 61.147 63.158 1.90 0.00 0.00 5.28
241 242 1.371558 GATATGAGGGGTGCCGGTC 59.628 63.158 1.90 0.00 0.00 4.79
242 243 1.383943 ATATGAGGGGTGCCGGTCA 60.384 57.895 1.90 0.00 0.00 4.02
243 244 1.410850 ATATGAGGGGTGCCGGTCAG 61.411 60.000 1.90 0.00 0.00 3.51
267 268 2.549282 CGTTGTCCGCGGTTTGAG 59.451 61.111 27.15 11.56 0.00 3.02
268 269 1.952133 CGTTGTCCGCGGTTTGAGA 60.952 57.895 27.15 0.06 0.00 3.27
269 270 1.860078 GTTGTCCGCGGTTTGAGAG 59.140 57.895 27.15 0.00 0.00 3.20
270 271 1.301401 TTGTCCGCGGTTTGAGAGG 60.301 57.895 27.15 0.00 0.00 3.69
271 272 2.035237 TTGTCCGCGGTTTGAGAGGT 62.035 55.000 27.15 0.00 0.00 3.85
272 273 1.737008 GTCCGCGGTTTGAGAGGTC 60.737 63.158 27.15 0.48 0.00 3.85
273 274 2.434359 CCGCGGTTTGAGAGGTCC 60.434 66.667 19.50 0.00 0.00 4.46
274 275 2.342279 CGCGGTTTGAGAGGTCCA 59.658 61.111 0.00 0.00 0.00 4.02
275 276 1.738099 CGCGGTTTGAGAGGTCCAG 60.738 63.158 0.00 0.00 0.00 3.86
276 277 1.371558 GCGGTTTGAGAGGTCCAGT 59.628 57.895 0.00 0.00 0.00 4.00
277 278 0.250338 GCGGTTTGAGAGGTCCAGTT 60.250 55.000 0.00 0.00 0.00 3.16
278 279 1.512926 CGGTTTGAGAGGTCCAGTTG 58.487 55.000 0.00 0.00 0.00 3.16
279 280 1.878102 CGGTTTGAGAGGTCCAGTTGG 60.878 57.143 0.00 0.00 0.00 3.77
280 281 1.545651 GGTTTGAGAGGTCCAGTTGGG 60.546 57.143 0.00 0.00 35.41 4.12
281 282 1.143073 GTTTGAGAGGTCCAGTTGGGT 59.857 52.381 0.00 0.00 38.11 4.51
282 283 1.056660 TTGAGAGGTCCAGTTGGGTC 58.943 55.000 0.00 0.00 38.11 4.46
283 284 1.185618 TGAGAGGTCCAGTTGGGTCG 61.186 60.000 0.00 0.00 38.11 4.79
284 285 0.898789 GAGAGGTCCAGTTGGGTCGA 60.899 60.000 0.00 0.00 38.11 4.20
285 286 0.900647 AGAGGTCCAGTTGGGTCGAG 60.901 60.000 0.00 0.00 38.11 4.04
286 287 1.152312 AGGTCCAGTTGGGTCGAGT 60.152 57.895 0.00 0.00 38.11 4.18
287 288 0.763223 AGGTCCAGTTGGGTCGAGTT 60.763 55.000 0.00 0.00 38.11 3.01
288 289 0.108019 GGTCCAGTTGGGTCGAGTTT 59.892 55.000 0.00 0.00 38.11 2.66
289 290 1.476291 GGTCCAGTTGGGTCGAGTTTT 60.476 52.381 0.00 0.00 38.11 2.43
290 291 2.294979 GTCCAGTTGGGTCGAGTTTTT 58.705 47.619 0.00 0.00 38.11 1.94
312 313 2.489938 TTGACCCATCACTAACTGGC 57.510 50.000 0.00 0.00 33.38 4.85
313 314 0.249120 TGACCCATCACTAACTGGCG 59.751 55.000 0.00 0.00 0.00 5.69
314 315 0.462047 GACCCATCACTAACTGGCGG 60.462 60.000 0.00 0.00 0.00 6.13
315 316 1.819632 CCCATCACTAACTGGCGGC 60.820 63.158 0.00 0.00 0.00 6.53
316 317 1.819632 CCATCACTAACTGGCGGCC 60.820 63.158 13.32 13.32 0.00 6.13
317 318 2.173669 CATCACTAACTGGCGGCCG 61.174 63.158 24.05 24.05 0.00 6.13
318 319 3.385749 ATCACTAACTGGCGGCCGG 62.386 63.158 29.38 26.03 35.68 6.13
319 320 4.388499 CACTAACTGGCGGCCGGT 62.388 66.667 27.54 27.54 46.37 5.28
320 321 4.078516 ACTAACTGGCGGCCGGTC 62.079 66.667 32.27 11.26 43.15 4.79
321 322 4.832608 CTAACTGGCGGCCGGTCC 62.833 72.222 32.27 21.23 43.15 4.46
332 333 3.909662 CCGGTCCAGGCATTTGAG 58.090 61.111 0.00 0.00 0.00 3.02
333 334 1.299648 CCGGTCCAGGCATTTGAGA 59.700 57.895 0.00 0.00 0.00 3.27
334 335 1.026718 CCGGTCCAGGCATTTGAGAC 61.027 60.000 0.00 0.00 0.00 3.36
418 422 1.989706 TCTGTGTAGGTTTTTGGGCC 58.010 50.000 0.00 0.00 0.00 5.80
420 424 1.613437 CTGTGTAGGTTTTTGGGCCTG 59.387 52.381 4.53 0.00 36.38 4.85
431 435 1.044611 TTGGGCCTGGTTTTACTTGC 58.955 50.000 4.53 0.00 0.00 4.01
478 482 2.702270 AGAAATTGCAGGAACCCCTT 57.298 45.000 0.00 0.00 42.02 3.95
486 498 1.199615 CAGGAACCCCTTCTCTCTCC 58.800 60.000 0.00 0.00 42.02 3.71
590 603 9.323985 CTTCAATGGGTCAAATTTTTGTTTCTA 57.676 29.630 3.18 0.00 39.18 2.10
591 604 9.844257 TTCAATGGGTCAAATTTTTGTTTCTAT 57.156 25.926 3.18 0.00 39.18 1.98
721 739 4.503991 GCTTCCTATAAGGACCATGGTCTG 60.504 50.000 37.26 21.73 45.78 3.51
723 741 2.289072 CCTATAAGGACCATGGTCTGCG 60.289 54.545 37.26 21.56 44.04 5.18
802 1516 2.037847 GGTTCTTGCAGCCCCCAT 59.962 61.111 0.00 0.00 0.00 4.00
808 1522 3.465218 TTGCAGCCCCCATGGTTGT 62.465 57.895 11.73 0.00 46.46 3.32
880 2090 3.553511 CGACCTCATGTCATTAAGTCTGC 59.446 47.826 0.00 0.00 44.71 4.26
929 2139 4.752661 GACATGGTCGTCTAGTCCTATC 57.247 50.000 0.00 0.00 32.92 2.08
993 2205 7.703058 TCTTTTGAACTGTTCTTTCTTCCTT 57.297 32.000 20.18 0.00 0.00 3.36
998 2210 4.779993 ACTGTTCTTTCTTCCTTCACCT 57.220 40.909 0.00 0.00 0.00 4.00
1043 2260 7.958025 CCTATGCTATATATACATACACGCGAG 59.042 40.741 15.93 7.88 0.00 5.03
1077 2294 5.163302 ACATAACACTCTTCTCGAGATCG 57.837 43.478 17.44 10.79 42.62 3.69
1110 2327 2.871633 GAGGATAGCTTTCTCTTGCTGC 59.128 50.000 4.10 0.00 40.08 5.25
1178 2423 8.880750 GTCGAGCAAAGTAAGTTATAATTCCTT 58.119 33.333 0.00 0.00 0.00 3.36
1216 2482 9.361315 GACTTTAACTTTGGCTTGTTCTAAAAA 57.639 29.630 0.00 0.00 0.00 1.94
1242 2511 2.094494 TCTGACCTCTCTTCGCATGTTC 60.094 50.000 0.00 0.00 0.00 3.18
1285 2554 3.270433 ACATGGGGGAGAAGAAACATGAT 59.730 43.478 0.00 0.00 39.08 2.45
1333 2602 3.132289 ACCATGACATACTAACCTCCGTG 59.868 47.826 0.00 0.00 0.00 4.94
1840 3154 4.641989 CCCAAGTCAGACATTAGAAATGGG 59.358 45.833 2.66 3.79 36.30 4.00
2758 5404 3.183775 ACGTCAAGTGTCAAATTAGCGTC 59.816 43.478 0.00 0.00 0.00 5.19
3318 6048 6.994221 AGGGTCGATCGTCATATATTTTCTT 58.006 36.000 15.94 0.00 0.00 2.52
3319 6049 7.442656 AGGGTCGATCGTCATATATTTTCTTT 58.557 34.615 15.94 0.00 0.00 2.52
3320 6050 7.931948 AGGGTCGATCGTCATATATTTTCTTTT 59.068 33.333 15.94 0.00 0.00 2.27
3321 6051 8.221766 GGGTCGATCGTCATATATTTTCTTTTC 58.778 37.037 15.94 0.00 0.00 2.29
3322 6052 8.979574 GGTCGATCGTCATATATTTTCTTTTCT 58.020 33.333 15.94 0.00 0.00 2.52
3490 6220 1.416772 GGCATACTCAAGGTACTCCCC 59.583 57.143 0.00 0.00 38.49 4.81
3641 6373 3.965379 TTTGACAGCCCGACATAACTA 57.035 42.857 0.00 0.00 0.00 2.24
4296 7473 6.403866 TTTAGGGTGTCGTTTACTACAAGA 57.596 37.500 0.00 0.00 0.00 3.02
4807 8004 8.231837 GGCACGACTTTGTAACAGAAAATTATA 58.768 33.333 0.00 0.00 0.00 0.98
4921 8118 1.027792 TATTTTCCGGAAGCGGCCAC 61.028 55.000 17.97 0.00 0.00 5.01
4963 8160 2.041081 AGCCAAGGCATTAACAGTACCA 59.959 45.455 14.40 0.00 44.88 3.25
5341 8540 2.340721 ATTTTCCCTGGAATTGCCCA 57.659 45.000 0.00 0.00 33.79 5.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.179018 CCTTTCCGATCCCATCCACC 60.179 60.000 0.00 0.00 0.00 4.61
1 2 0.179018 CCCTTTCCGATCCCATCCAC 60.179 60.000 0.00 0.00 0.00 4.02
2 3 0.327095 TCCCTTTCCGATCCCATCCA 60.327 55.000 0.00 0.00 0.00 3.41
3 4 0.398318 CTCCCTTTCCGATCCCATCC 59.602 60.000 0.00 0.00 0.00 3.51
4 5 1.346068 CTCTCCCTTTCCGATCCCATC 59.654 57.143 0.00 0.00 0.00 3.51
5 6 1.428869 CTCTCCCTTTCCGATCCCAT 58.571 55.000 0.00 0.00 0.00 4.00
6 7 0.691078 CCTCTCCCTTTCCGATCCCA 60.691 60.000 0.00 0.00 0.00 4.37
7 8 1.411651 CCCTCTCCCTTTCCGATCCC 61.412 65.000 0.00 0.00 0.00 3.85
8 9 0.398664 TCCCTCTCCCTTTCCGATCC 60.399 60.000 0.00 0.00 0.00 3.36
9 10 1.044611 CTCCCTCTCCCTTTCCGATC 58.955 60.000 0.00 0.00 0.00 3.69
10 11 0.637195 TCTCCCTCTCCCTTTCCGAT 59.363 55.000 0.00 0.00 0.00 4.18
11 12 0.033011 CTCTCCCTCTCCCTTTCCGA 60.033 60.000 0.00 0.00 0.00 4.55
12 13 1.045911 CCTCTCCCTCTCCCTTTCCG 61.046 65.000 0.00 0.00 0.00 4.30
13 14 0.340208 TCCTCTCCCTCTCCCTTTCC 59.660 60.000 0.00 0.00 0.00 3.13
14 15 1.007842 ACTCCTCTCCCTCTCCCTTTC 59.992 57.143 0.00 0.00 0.00 2.62
15 16 1.097722 ACTCCTCTCCCTCTCCCTTT 58.902 55.000 0.00 0.00 0.00 3.11
16 17 0.338120 CACTCCTCTCCCTCTCCCTT 59.662 60.000 0.00 0.00 0.00 3.95
17 18 1.589399 CCACTCCTCTCCCTCTCCCT 61.589 65.000 0.00 0.00 0.00 4.20
18 19 1.075600 CCACTCCTCTCCCTCTCCC 60.076 68.421 0.00 0.00 0.00 4.30
19 20 0.396556 GTCCACTCCTCTCCCTCTCC 60.397 65.000 0.00 0.00 0.00 3.71
20 21 0.750182 CGTCCACTCCTCTCCCTCTC 60.750 65.000 0.00 0.00 0.00 3.20
21 22 1.304952 CGTCCACTCCTCTCCCTCT 59.695 63.158 0.00 0.00 0.00 3.69
22 23 1.755008 CCGTCCACTCCTCTCCCTC 60.755 68.421 0.00 0.00 0.00 4.30
23 24 2.218115 CTCCGTCCACTCCTCTCCCT 62.218 65.000 0.00 0.00 0.00 4.20
24 25 1.755008 CTCCGTCCACTCCTCTCCC 60.755 68.421 0.00 0.00 0.00 4.30
25 26 2.419739 GCTCCGTCCACTCCTCTCC 61.420 68.421 0.00 0.00 0.00 3.71
26 27 1.251527 TTGCTCCGTCCACTCCTCTC 61.252 60.000 0.00 0.00 0.00 3.20
27 28 1.228894 TTGCTCCGTCCACTCCTCT 60.229 57.895 0.00 0.00 0.00 3.69
28 29 1.216710 CTTGCTCCGTCCACTCCTC 59.783 63.158 0.00 0.00 0.00 3.71
29 30 1.228894 TCTTGCTCCGTCCACTCCT 60.229 57.895 0.00 0.00 0.00 3.69
30 31 1.216710 CTCTTGCTCCGTCCACTCC 59.783 63.158 0.00 0.00 0.00 3.85
31 32 0.172352 CTCTCTTGCTCCGTCCACTC 59.828 60.000 0.00 0.00 0.00 3.51
32 33 0.251386 TCTCTCTTGCTCCGTCCACT 60.251 55.000 0.00 0.00 0.00 4.00
33 34 0.172352 CTCTCTCTTGCTCCGTCCAC 59.828 60.000 0.00 0.00 0.00 4.02
34 35 0.967887 CCTCTCTCTTGCTCCGTCCA 60.968 60.000 0.00 0.00 0.00 4.02
35 36 1.671901 CCCTCTCTCTTGCTCCGTCC 61.672 65.000 0.00 0.00 0.00 4.79
36 37 0.681564 TCCCTCTCTCTTGCTCCGTC 60.682 60.000 0.00 0.00 0.00 4.79
37 38 0.682855 CTCCCTCTCTCTTGCTCCGT 60.683 60.000 0.00 0.00 0.00 4.69
38 39 0.395036 TCTCCCTCTCTCTTGCTCCG 60.395 60.000 0.00 0.00 0.00 4.63
39 40 1.402787 CTCTCCCTCTCTCTTGCTCC 58.597 60.000 0.00 0.00 0.00 4.70
40 41 1.064017 TCCTCTCCCTCTCTCTTGCTC 60.064 57.143 0.00 0.00 0.00 4.26
41 42 1.006813 TCCTCTCCCTCTCTCTTGCT 58.993 55.000 0.00 0.00 0.00 3.91
42 43 1.341976 ACTCCTCTCCCTCTCTCTTGC 60.342 57.143 0.00 0.00 0.00 4.01
43 44 2.378038 CACTCCTCTCCCTCTCTCTTG 58.622 57.143 0.00 0.00 0.00 3.02
44 45 1.287739 CCACTCCTCTCCCTCTCTCTT 59.712 57.143 0.00 0.00 0.00 2.85
45 46 0.926293 CCACTCCTCTCCCTCTCTCT 59.074 60.000 0.00 0.00 0.00 3.10
46 47 0.923358 TCCACTCCTCTCCCTCTCTC 59.077 60.000 0.00 0.00 0.00 3.20
47 48 0.629058 GTCCACTCCTCTCCCTCTCT 59.371 60.000 0.00 0.00 0.00 3.10
48 49 0.750182 CGTCCACTCCTCTCCCTCTC 60.750 65.000 0.00 0.00 0.00 3.20
49 50 1.304952 CGTCCACTCCTCTCCCTCT 59.695 63.158 0.00 0.00 0.00 3.69
50 51 1.755008 CCGTCCACTCCTCTCCCTC 60.755 68.421 0.00 0.00 0.00 4.30
51 52 2.218115 CTCCGTCCACTCCTCTCCCT 62.218 65.000 0.00 0.00 0.00 4.20
52 53 1.755008 CTCCGTCCACTCCTCTCCC 60.755 68.421 0.00 0.00 0.00 4.30
53 54 2.419739 GCTCCGTCCACTCCTCTCC 61.420 68.421 0.00 0.00 0.00 3.71
54 55 1.251527 TTGCTCCGTCCACTCCTCTC 61.252 60.000 0.00 0.00 0.00 3.20
55 56 1.228894 TTGCTCCGTCCACTCCTCT 60.229 57.895 0.00 0.00 0.00 3.69
56 57 1.216710 CTTGCTCCGTCCACTCCTC 59.783 63.158 0.00 0.00 0.00 3.71
57 58 1.228894 TCTTGCTCCGTCCACTCCT 60.229 57.895 0.00 0.00 0.00 3.69
58 59 1.216710 CTCTTGCTCCGTCCACTCC 59.783 63.158 0.00 0.00 0.00 3.85
59 60 0.172352 CTCTCTTGCTCCGTCCACTC 59.828 60.000 0.00 0.00 0.00 3.51
60 61 0.251386 TCTCTCTTGCTCCGTCCACT 60.251 55.000 0.00 0.00 0.00 4.00
61 62 0.172352 CTCTCTCTTGCTCCGTCCAC 59.828 60.000 0.00 0.00 0.00 4.02
62 63 0.038310 TCTCTCTCTTGCTCCGTCCA 59.962 55.000 0.00 0.00 0.00 4.02
63 64 0.738389 CTCTCTCTCTTGCTCCGTCC 59.262 60.000 0.00 0.00 0.00 4.79
64 65 1.670811 CTCTCTCTCTCTTGCTCCGTC 59.329 57.143 0.00 0.00 0.00 4.79
65 66 1.280710 TCTCTCTCTCTCTTGCTCCGT 59.719 52.381 0.00 0.00 0.00 4.69
66 67 1.942657 CTCTCTCTCTCTCTTGCTCCG 59.057 57.143 0.00 0.00 0.00 4.63
67 68 3.209410 CTCTCTCTCTCTCTCTTGCTCC 58.791 54.545 0.00 0.00 0.00 4.70
68 69 3.209410 CCTCTCTCTCTCTCTCTTGCTC 58.791 54.545 0.00 0.00 0.00 4.26
69 70 2.092212 CCCTCTCTCTCTCTCTCTTGCT 60.092 54.545 0.00 0.00 0.00 3.91
70 71 2.092429 TCCCTCTCTCTCTCTCTCTTGC 60.092 54.545 0.00 0.00 0.00 4.01
71 72 3.054434 TGTCCCTCTCTCTCTCTCTCTTG 60.054 52.174 0.00 0.00 0.00 3.02
72 73 3.189606 TGTCCCTCTCTCTCTCTCTCTT 58.810 50.000 0.00 0.00 0.00 2.85
73 74 2.774234 CTGTCCCTCTCTCTCTCTCTCT 59.226 54.545 0.00 0.00 0.00 3.10
74 75 2.771943 TCTGTCCCTCTCTCTCTCTCTC 59.228 54.545 0.00 0.00 0.00 3.20
75 76 2.774234 CTCTGTCCCTCTCTCTCTCTCT 59.226 54.545 0.00 0.00 0.00 3.10
76 77 2.505819 ACTCTGTCCCTCTCTCTCTCTC 59.494 54.545 0.00 0.00 0.00 3.20
77 78 2.239654 CACTCTGTCCCTCTCTCTCTCT 59.760 54.545 0.00 0.00 0.00 3.10
78 79 2.238646 TCACTCTGTCCCTCTCTCTCTC 59.761 54.545 0.00 0.00 0.00 3.20
79 80 2.239654 CTCACTCTGTCCCTCTCTCTCT 59.760 54.545 0.00 0.00 0.00 3.10
80 81 2.643551 CTCACTCTGTCCCTCTCTCTC 58.356 57.143 0.00 0.00 0.00 3.20
81 82 1.340991 GCTCACTCTGTCCCTCTCTCT 60.341 57.143 0.00 0.00 0.00 3.10
82 83 1.102978 GCTCACTCTGTCCCTCTCTC 58.897 60.000 0.00 0.00 0.00 3.20
83 84 0.704076 AGCTCACTCTGTCCCTCTCT 59.296 55.000 0.00 0.00 0.00 3.10
84 85 2.297701 CTAGCTCACTCTGTCCCTCTC 58.702 57.143 0.00 0.00 0.00 3.20
85 86 1.064017 CCTAGCTCACTCTGTCCCTCT 60.064 57.143 0.00 0.00 0.00 3.69
86 87 1.398692 CCTAGCTCACTCTGTCCCTC 58.601 60.000 0.00 0.00 0.00 4.30
87 88 0.032615 CCCTAGCTCACTCTGTCCCT 60.033 60.000 0.00 0.00 0.00 4.20
88 89 0.324830 ACCCTAGCTCACTCTGTCCC 60.325 60.000 0.00 0.00 0.00 4.46
89 90 1.562783 AACCCTAGCTCACTCTGTCC 58.437 55.000 0.00 0.00 0.00 4.02
90 91 2.563179 TCAAACCCTAGCTCACTCTGTC 59.437 50.000 0.00 0.00 0.00 3.51
91 92 2.564947 CTCAAACCCTAGCTCACTCTGT 59.435 50.000 0.00 0.00 0.00 3.41
92 93 2.676463 GCTCAAACCCTAGCTCACTCTG 60.676 54.545 0.00 0.00 35.80 3.35
93 94 1.552792 GCTCAAACCCTAGCTCACTCT 59.447 52.381 0.00 0.00 35.80 3.24
94 95 1.552792 AGCTCAAACCCTAGCTCACTC 59.447 52.381 0.00 0.00 45.92 3.51
95 96 1.650528 AGCTCAAACCCTAGCTCACT 58.349 50.000 0.00 0.00 45.92 3.41
100 101 1.815840 GGCGAGCTCAAACCCTAGC 60.816 63.158 15.40 5.97 39.08 3.42
101 102 1.519455 CGGCGAGCTCAAACCCTAG 60.519 63.158 15.40 0.00 0.00 3.02
102 103 2.577059 CGGCGAGCTCAAACCCTA 59.423 61.111 15.40 0.00 0.00 3.53
133 134 2.907917 CCGCCGACCCCACAAAAA 60.908 61.111 0.00 0.00 0.00 1.94
134 135 4.192453 ACCGCCGACCCCACAAAA 62.192 61.111 0.00 0.00 0.00 2.44
135 136 4.939368 CACCGCCGACCCCACAAA 62.939 66.667 0.00 0.00 0.00 2.83
150 151 4.394712 CTGACAGGCCCGACCCAC 62.395 72.222 0.00 0.00 40.58 4.61
187 188 4.394712 GATATGGGGCGGCCCGAG 62.395 72.222 38.64 0.00 46.66 4.63
191 192 4.699522 GACGGATATGGGGCGGCC 62.700 72.222 22.00 22.00 0.00 6.13
192 193 4.699522 GGACGGATATGGGGCGGC 62.700 72.222 0.00 0.00 0.00 6.53
193 194 0.976073 ATAGGACGGATATGGGGCGG 60.976 60.000 0.00 0.00 0.00 6.13
194 195 1.771565 TATAGGACGGATATGGGGCG 58.228 55.000 0.00 0.00 0.00 6.13
195 196 4.451900 CAAATATAGGACGGATATGGGGC 58.548 47.826 0.00 0.00 0.00 5.80
196 197 4.141482 CCCAAATATAGGACGGATATGGGG 60.141 50.000 0.00 0.00 32.55 4.96
197 198 4.686122 GCCCAAATATAGGACGGATATGGG 60.686 50.000 0.00 0.00 30.60 4.00
198 199 4.451900 GCCCAAATATAGGACGGATATGG 58.548 47.826 0.00 0.00 0.00 2.74
199 200 4.119862 CGCCCAAATATAGGACGGATATG 58.880 47.826 0.00 0.00 0.00 1.78
200 201 3.134081 CCGCCCAAATATAGGACGGATAT 59.866 47.826 14.27 0.00 42.05 1.63
201 202 2.498481 CCGCCCAAATATAGGACGGATA 59.502 50.000 14.27 0.00 42.05 2.59
202 203 1.278127 CCGCCCAAATATAGGACGGAT 59.722 52.381 14.27 0.00 42.05 4.18
203 204 0.682852 CCGCCCAAATATAGGACGGA 59.317 55.000 14.27 0.00 42.05 4.69
204 205 0.321298 CCCGCCCAAATATAGGACGG 60.321 60.000 12.96 12.96 40.37 4.79
205 206 0.682852 TCCCGCCCAAATATAGGACG 59.317 55.000 0.00 0.00 0.00 4.79
206 207 4.163458 TCATATCCCGCCCAAATATAGGAC 59.837 45.833 0.00 0.00 0.00 3.85
207 208 4.367166 TCATATCCCGCCCAAATATAGGA 58.633 43.478 0.00 0.00 0.00 2.94
208 209 4.444876 CCTCATATCCCGCCCAAATATAGG 60.445 50.000 0.00 0.00 0.00 2.57
209 210 4.444876 CCCTCATATCCCGCCCAAATATAG 60.445 50.000 0.00 0.00 0.00 1.31
210 211 3.458118 CCCTCATATCCCGCCCAAATATA 59.542 47.826 0.00 0.00 0.00 0.86
211 212 2.242196 CCCTCATATCCCGCCCAAATAT 59.758 50.000 0.00 0.00 0.00 1.28
212 213 1.633432 CCCTCATATCCCGCCCAAATA 59.367 52.381 0.00 0.00 0.00 1.40
213 214 0.405585 CCCTCATATCCCGCCCAAAT 59.594 55.000 0.00 0.00 0.00 2.32
214 215 1.715019 CCCCTCATATCCCGCCCAAA 61.715 60.000 0.00 0.00 0.00 3.28
215 216 2.153401 CCCCTCATATCCCGCCCAA 61.153 63.158 0.00 0.00 0.00 4.12
216 217 2.529136 CCCCTCATATCCCGCCCA 60.529 66.667 0.00 0.00 0.00 5.36
217 218 2.529389 ACCCCTCATATCCCGCCC 60.529 66.667 0.00 0.00 0.00 6.13
218 219 2.750350 CACCCCTCATATCCCGCC 59.250 66.667 0.00 0.00 0.00 6.13
219 220 2.032681 GCACCCCTCATATCCCGC 59.967 66.667 0.00 0.00 0.00 6.13
220 221 2.750350 GGCACCCCTCATATCCCG 59.250 66.667 0.00 0.00 0.00 5.14
221 222 2.750350 CGGCACCCCTCATATCCC 59.250 66.667 0.00 0.00 0.00 3.85
222 223 2.113243 GACCGGCACCCCTCATATCC 62.113 65.000 0.00 0.00 0.00 2.59
223 224 1.371558 GACCGGCACCCCTCATATC 59.628 63.158 0.00 0.00 0.00 1.63
224 225 1.383943 TGACCGGCACCCCTCATAT 60.384 57.895 0.00 0.00 0.00 1.78
225 226 2.039787 TGACCGGCACCCCTCATA 59.960 61.111 0.00 0.00 0.00 2.15
226 227 3.402681 CTGACCGGCACCCCTCAT 61.403 66.667 0.00 0.00 0.00 2.90
251 252 1.566018 CCTCTCAAACCGCGGACAAC 61.566 60.000 35.90 0.00 0.00 3.32
252 253 1.301401 CCTCTCAAACCGCGGACAA 60.301 57.895 35.90 13.10 0.00 3.18
253 254 2.342279 CCTCTCAAACCGCGGACA 59.658 61.111 35.90 11.12 0.00 4.02
254 255 1.737008 GACCTCTCAAACCGCGGAC 60.737 63.158 35.90 5.60 0.00 4.79
255 256 2.654877 GACCTCTCAAACCGCGGA 59.345 61.111 35.90 8.44 0.00 5.54
256 257 2.434359 GGACCTCTCAAACCGCGG 60.434 66.667 26.86 26.86 0.00 6.46
257 258 1.738099 CTGGACCTCTCAAACCGCG 60.738 63.158 0.00 0.00 0.00 6.46
258 259 0.250338 AACTGGACCTCTCAAACCGC 60.250 55.000 0.00 0.00 0.00 5.68
259 260 1.512926 CAACTGGACCTCTCAAACCG 58.487 55.000 0.00 0.00 0.00 4.44
260 261 1.545651 CCCAACTGGACCTCTCAAACC 60.546 57.143 0.00 0.00 37.39 3.27
261 262 1.143073 ACCCAACTGGACCTCTCAAAC 59.857 52.381 0.00 0.00 37.39 2.93
262 263 1.420138 GACCCAACTGGACCTCTCAAA 59.580 52.381 0.00 0.00 37.39 2.69
263 264 1.056660 GACCCAACTGGACCTCTCAA 58.943 55.000 0.00 0.00 37.39 3.02
264 265 1.185618 CGACCCAACTGGACCTCTCA 61.186 60.000 0.00 0.00 37.39 3.27
265 266 0.898789 TCGACCCAACTGGACCTCTC 60.899 60.000 0.00 0.00 37.39 3.20
266 267 0.900647 CTCGACCCAACTGGACCTCT 60.901 60.000 0.00 0.00 37.39 3.69
267 268 1.186267 ACTCGACCCAACTGGACCTC 61.186 60.000 0.00 0.00 37.39 3.85
268 269 0.763223 AACTCGACCCAACTGGACCT 60.763 55.000 0.00 0.00 37.39 3.85
269 270 0.108019 AAACTCGACCCAACTGGACC 59.892 55.000 0.00 0.00 37.39 4.46
270 271 1.963172 AAAACTCGACCCAACTGGAC 58.037 50.000 0.00 0.00 37.39 4.02
271 272 2.721425 AAAAACTCGACCCAACTGGA 57.279 45.000 0.00 0.00 37.39 3.86
290 291 3.572255 GCCAGTTAGTGATGGGTCAAAAA 59.428 43.478 0.00 0.00 37.05 1.94
291 292 3.153919 GCCAGTTAGTGATGGGTCAAAA 58.846 45.455 0.00 0.00 37.05 2.44
292 293 2.790433 GCCAGTTAGTGATGGGTCAAA 58.210 47.619 0.00 0.00 37.05 2.69
293 294 1.338674 CGCCAGTTAGTGATGGGTCAA 60.339 52.381 0.00 0.00 37.05 3.18
294 295 0.249120 CGCCAGTTAGTGATGGGTCA 59.751 55.000 0.00 0.00 37.05 4.02
295 296 0.462047 CCGCCAGTTAGTGATGGGTC 60.462 60.000 0.00 0.00 37.05 4.46
296 297 1.602237 CCGCCAGTTAGTGATGGGT 59.398 57.895 0.00 0.00 37.05 4.51
297 298 1.819632 GCCGCCAGTTAGTGATGGG 60.820 63.158 0.00 0.00 37.05 4.00
298 299 1.819632 GGCCGCCAGTTAGTGATGG 60.820 63.158 3.91 0.00 39.73 3.51
299 300 2.173669 CGGCCGCCAGTTAGTGATG 61.174 63.158 14.67 0.00 0.00 3.07
300 301 2.186903 CGGCCGCCAGTTAGTGAT 59.813 61.111 14.67 0.00 0.00 3.06
301 302 4.077184 CCGGCCGCCAGTTAGTGA 62.077 66.667 22.85 0.00 0.00 3.41
302 303 4.388499 ACCGGCCGCCAGTTAGTG 62.388 66.667 22.85 4.97 0.00 2.74
303 304 4.078516 GACCGGCCGCCAGTTAGT 62.079 66.667 22.85 10.64 0.00 2.24
304 305 4.832608 GGACCGGCCGCCAGTTAG 62.833 72.222 22.85 6.71 0.00 2.34
315 316 1.026718 GTCTCAAATGCCTGGACCGG 61.027 60.000 0.00 0.00 0.00 5.28
316 317 1.361668 CGTCTCAAATGCCTGGACCG 61.362 60.000 0.00 0.00 0.00 4.79
317 318 0.321653 ACGTCTCAAATGCCTGGACC 60.322 55.000 0.00 0.00 0.00 4.46
318 319 1.523758 AACGTCTCAAATGCCTGGAC 58.476 50.000 0.00 0.00 0.00 4.02
319 320 2.270352 AAACGTCTCAAATGCCTGGA 57.730 45.000 0.00 0.00 0.00 3.86
320 321 3.369546 AAAAACGTCTCAAATGCCTGG 57.630 42.857 0.00 0.00 0.00 4.45
321 322 9.950680 ATTATATAAAAACGTCTCAAATGCCTG 57.049 29.630 0.00 0.00 0.00 4.85
323 324 9.394477 GGATTATATAAAAACGTCTCAAATGCC 57.606 33.333 0.00 0.00 0.00 4.40
327 328 9.806203 TCGAGGATTATATAAAAACGTCTCAAA 57.194 29.630 0.00 0.00 0.00 2.69
328 329 9.459640 CTCGAGGATTATATAAAAACGTCTCAA 57.540 33.333 3.91 0.00 0.00 3.02
329 330 7.594015 GCTCGAGGATTATATAAAAACGTCTCA 59.406 37.037 15.58 0.00 0.00 3.27
330 331 7.808856 AGCTCGAGGATTATATAAAAACGTCTC 59.191 37.037 15.58 1.08 0.00 3.36
331 332 7.659186 AGCTCGAGGATTATATAAAAACGTCT 58.341 34.615 15.58 0.00 0.00 4.18
332 333 7.062022 GGAGCTCGAGGATTATATAAAAACGTC 59.938 40.741 15.58 5.19 0.00 4.34
333 334 6.867293 GGAGCTCGAGGATTATATAAAAACGT 59.133 38.462 15.58 0.00 0.00 3.99
334 335 6.033619 CGGAGCTCGAGGATTATATAAAAACG 59.966 42.308 15.58 4.28 42.43 3.60
418 422 4.359706 GTCCAGTTTGCAAGTAAAACCAG 58.640 43.478 0.00 0.00 38.10 4.00
420 424 3.131400 TGGTCCAGTTTGCAAGTAAAACC 59.869 43.478 12.76 12.76 38.10 3.27
509 522 9.095065 GGTTCGTTTCTCTAATAGCTAAATTCA 57.905 33.333 0.00 0.00 0.00 2.57
590 603 6.377146 AGTTGATAAAGGTGACGGCAATTTAT 59.623 34.615 18.10 18.10 33.91 1.40
591 604 5.708230 AGTTGATAAAGGTGACGGCAATTTA 59.292 36.000 11.24 11.24 0.00 1.40
707 725 2.045926 GCGCAGACCATGGTCCTT 60.046 61.111 36.09 19.90 45.59 3.36
721 739 0.992802 CGTACCTGAGAAAGAAGCGC 59.007 55.000 0.00 0.00 0.00 5.92
723 741 3.027974 ACACGTACCTGAGAAAGAAGC 57.972 47.619 0.00 0.00 0.00 3.86
802 1516 9.220767 GTGGGCATAAAATTATAAAAACAACCA 57.779 29.630 0.00 0.00 0.00 3.67
880 2090 7.504924 TCTACCACCATTAAACAACTTGAAG 57.495 36.000 0.00 0.00 0.00 3.02
929 2139 1.415374 ACACGTGATCGAGGAAAACG 58.585 50.000 25.01 0.00 40.62 3.60
991 2203 2.437281 AGGTGCTATCCATGAGGTGAAG 59.563 50.000 0.00 0.00 35.89 3.02
993 2205 1.764723 CAGGTGCTATCCATGAGGTGA 59.235 52.381 0.00 0.00 35.89 4.02
1043 2260 6.524101 AGAGTGTTATGTTCTTCTCTCCTC 57.476 41.667 0.00 0.00 0.00 3.71
1077 2294 2.564947 AGCTATCCTCGAATCCATGTCC 59.435 50.000 0.00 0.00 0.00 4.02
1110 2327 0.734253 GTGTGACCAGTAGCAGAGCG 60.734 60.000 0.00 0.00 0.00 5.03
1216 2482 4.008074 TGCGAAGAGAGGTCAGAATTTT 57.992 40.909 0.00 0.00 0.00 1.82
1218 2484 3.055530 ACATGCGAAGAGAGGTCAGAATT 60.056 43.478 0.00 0.00 0.00 2.17
1219 2485 2.499289 ACATGCGAAGAGAGGTCAGAAT 59.501 45.455 0.00 0.00 0.00 2.40
1222 2488 2.266554 GAACATGCGAAGAGAGGTCAG 58.733 52.381 0.00 0.00 0.00 3.51
1242 2511 7.170489 CCATGTACACTATGTAGAGCTGAAATG 59.830 40.741 0.00 0.00 32.84 2.32
1285 2554 0.176449 CGGTGACAGCAGATGGATCA 59.824 55.000 5.35 0.00 0.00 2.92
1333 2602 0.466124 CTAGCCAGTACCTCCCAAGC 59.534 60.000 0.00 0.00 0.00 4.01
1976 3298 4.610007 CGCCGATGATCTTTCTATTGCAAG 60.610 45.833 4.94 0.00 0.00 4.01
2053 4625 1.815421 CGCTGAAATCCCGAGGTGG 60.815 63.158 0.00 0.00 37.55 4.61
2758 5404 3.611113 CCTATACGATTATGTTTCGGCGG 59.389 47.826 7.21 0.00 40.83 6.13
3277 6004 0.532862 CCTATTCCAGGCAACGCGAT 60.533 55.000 15.93 0.00 46.39 4.58
3322 6052 9.739276 ACATTCACAGATTAGTTATTGGAGAAA 57.261 29.630 0.00 0.00 0.00 2.52
3641 6373 2.046892 GATGCTGACACCTGGCGT 60.047 61.111 0.00 0.00 0.00 5.68
3969 7146 1.411977 CTGGCTCTGTCTGGGTCTATG 59.588 57.143 0.00 0.00 0.00 2.23
3970 7147 1.007721 ACTGGCTCTGTCTGGGTCTAT 59.992 52.381 0.00 0.00 0.00 1.98
4296 7473 4.379243 CCGCCTTGCACTCTCCGT 62.379 66.667 0.00 0.00 0.00 4.69
4807 8004 4.558226 TGCCTCTTCTATGTCATGTGTT 57.442 40.909 0.00 0.00 0.00 3.32
4862 8059 4.922206 TGGTCATGTCTAAATGCCTTTCT 58.078 39.130 0.00 0.00 0.00 2.52
5341 8540 6.682861 GCATGAGTTGGTTCCAAACTACTTTT 60.683 38.462 5.81 0.00 0.00 2.27


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

AutoCloner maintained by Alex Coulton.