Multiple sequence alignment - TraesCS7D01G525200

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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 TraesCS7D01G525200 chr7D 100.000 3021 0 0 1 3021 621157546 621160566 0.000000e+00 5579.0
1 TraesCS7D01G525200 chr7D 86.450 1476 140 30 1571 3021 621203452 621204892 0.000000e+00 1563.0
2 TraesCS7D01G525200 chr7D 96.587 586 18 2 2403 2987 621212699 621213283 0.000000e+00 970.0
3 TraesCS7D01G525200 chr7D 90.879 307 27 1 1058 1363 621202798 621203104 7.790000e-111 411.0
4 TraesCS7D01G525200 chr7D 96.078 102 4 0 986 1087 621212523 621212624 1.860000e-37 167.0
5 TraesCS7D01G525200 chr7D 91.667 96 5 3 680 773 629564254 629564160 2.440000e-26 130.0
6 TraesCS7D01G525200 chr7D 89.109 101 10 1 680 779 605155725 605155825 1.140000e-24 124.0
7 TraesCS7D01G525200 chr7D 98.387 62 1 0 1353 1414 621158847 621158908 3.180000e-20 110.0
8 TraesCS7D01G525200 chr7A 89.263 1099 89 15 1627 2706 715925503 715924415 0.000000e+00 1349.0
9 TraesCS7D01G525200 chr7A 85.351 1140 116 24 1354 2451 715785362 715784232 0.000000e+00 1133.0
10 TraesCS7D01G525200 chr7A 96.534 577 18 2 2440 3015 715781411 715780836 0.000000e+00 953.0
11 TraesCS7D01G525200 chr7A 85.259 502 48 16 431 911 715786375 715785879 7.520000e-136 494.0
12 TraesCS7D01G525200 chr7A 86.475 451 31 15 915 1363 715785724 715785302 4.560000e-128 468.0
13 TraesCS7D01G525200 chr7A 92.157 306 23 1 1058 1363 715787712 715787408 5.980000e-117 431.0
14 TraesCS7D01G525200 chr7A 86.432 398 30 12 990 1363 715925996 715925599 6.030000e-112 414.0
15 TraesCS7D01G525200 chr7A 87.460 311 30 7 72 378 715946175 715945870 1.720000e-92 350.0
16 TraesCS7D01G525200 chr7A 83.895 267 21 6 188 435 715787213 715786950 5.040000e-58 235.0
17 TraesCS7D01G525200 chr7A 97.059 34 1 0 644 677 643520369 643520402 1.170000e-04 58.4
18 TraesCS7D01G525200 chr2D 78.484 1873 324 46 1058 2895 560865896 560864068 0.000000e+00 1153.0
19 TraesCS7D01G525200 chr2B 80.838 1456 223 35 1473 2892 669191526 669192961 0.000000e+00 1092.0
20 TraesCS7D01G525200 chr2A 80.191 1464 233 33 1473 2895 700672854 700671407 0.000000e+00 1044.0
21 TraesCS7D01G525200 chr2A 90.196 306 30 0 1058 1363 375770984 375771289 1.690000e-107 399.0
22 TraesCS7D01G525200 chr7B 81.135 1357 173 45 1354 2673 717226285 717224975 0.000000e+00 1011.0
23 TraesCS7D01G525200 chr7B 80.914 1357 176 45 1354 2673 717150813 717149503 0.000000e+00 994.0
24 TraesCS7D01G525200 chr7B 95.000 320 14 2 2669 2987 717149248 717148930 4.500000e-138 501.0
25 TraesCS7D01G525200 chr7B 95.000 320 14 2 2669 2987 717224720 717224402 4.500000e-138 501.0
26 TraesCS7D01G525200 chr7B 91.503 306 24 1 1058 1363 717226528 717226225 1.300000e-113 420.0
27 TraesCS7D01G525200 chr7B 90.850 306 26 1 1058 1363 717151056 717150753 2.800000e-110 409.0
28 TraesCS7D01G525200 chr7B 83.465 381 40 11 3 378 717178728 717178366 1.740000e-87 333.0
29 TraesCS7D01G525200 chr7B 83.465 381 40 11 3 378 717253381 717253019 1.740000e-87 333.0
30 TraesCS7D01G525200 chr7B 92.105 38 3 0 257 294 505453415 505453378 2.000000e-03 54.7
31 TraesCS7D01G525200 chr3D 92.182 307 22 2 1058 1363 12941279 12941584 1.660000e-117 433.0
32 TraesCS7D01G525200 chr5D 91.205 307 27 0 1058 1364 541266296 541266602 4.660000e-113 418.0
33 TraesCS7D01G525200 chr5D 82.883 222 26 6 1356 1565 541266543 541266764 3.980000e-44 189.0
34 TraesCS7D01G525200 chr5D 87.912 91 11 0 586 676 226946482 226946392 1.150000e-19 108.0
35 TraesCS7D01G525200 chr5D 95.833 48 2 0 630 677 426459051 426459004 8.980000e-11 78.7
36 TraesCS7D01G525200 chr3A 88.462 104 11 1 680 782 191835211 191835108 1.140000e-24 124.0
37 TraesCS7D01G525200 chr1B 90.526 95 8 1 680 773 533745943 533746037 1.140000e-24 124.0
38 TraesCS7D01G525200 chr4B 86.486 111 13 2 680 788 37318767 37318877 1.470000e-23 121.0
39 TraesCS7D01G525200 chr4A 86.486 111 13 2 680 788 577978081 577977971 1.470000e-23 121.0
40 TraesCS7D01G525200 chr4D 85.586 111 14 2 680 788 25379150 25379260 6.840000e-22 115.0
41 TraesCS7D01G525200 chr6A 85.088 114 13 4 680 791 66426519 66426408 2.460000e-21 113.0
42 TraesCS7D01G525200 chr3B 89.583 48 5 0 634 681 44236469 44236422 9.040000e-06 62.1


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS7D01G525200 chr7D 621157546 621160566 3020 False 2844.500000 5579 99.193500 1 3021 2 chr7D.!!$F2 3020
1 TraesCS7D01G525200 chr7D 621202798 621204892 2094 False 987.000000 1563 88.664500 1058 3021 2 chr7D.!!$F3 1963
2 TraesCS7D01G525200 chr7D 621212523 621213283 760 False 568.500000 970 96.332500 986 2987 2 chr7D.!!$F4 2001
3 TraesCS7D01G525200 chr7A 715924415 715925996 1581 True 881.500000 1349 87.847500 990 2706 2 chr7A.!!$R3 1716
4 TraesCS7D01G525200 chr7A 715780836 715787712 6876 True 619.000000 1133 88.278500 188 3015 6 chr7A.!!$R2 2827
5 TraesCS7D01G525200 chr2D 560864068 560865896 1828 True 1153.000000 1153 78.484000 1058 2895 1 chr2D.!!$R1 1837
6 TraesCS7D01G525200 chr2B 669191526 669192961 1435 False 1092.000000 1092 80.838000 1473 2892 1 chr2B.!!$F1 1419
7 TraesCS7D01G525200 chr2A 700671407 700672854 1447 True 1044.000000 1044 80.191000 1473 2895 1 chr2A.!!$R1 1422
8 TraesCS7D01G525200 chr7B 717224402 717226528 2126 True 644.000000 1011 89.212667 1058 2987 3 chr7B.!!$R5 1929
9 TraesCS7D01G525200 chr7B 717148930 717151056 2126 True 634.666667 994 88.921333 1058 2987 3 chr7B.!!$R4 1929

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
464 1375 0.034337 TGCAAACACTCCCCGTACTC 59.966 55.0 0.0 0.0 0.00 2.59 F
852 1776 0.108138 GACGGAGAAGGTCATGGTGG 60.108 60.0 0.0 0.0 34.56 4.61 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1827 3144 0.179084 CGCCGGGCAGATAGAAGAAA 60.179 55.000 20.71 0.0 0.00 2.52 R
2203 3573 1.526917 CACCCATCTTGGCCGATCC 60.527 63.158 0.00 0.0 35.79 3.36 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
27 28 4.716003 GGTGGAAGCCGCTTAGTT 57.284 55.556 5.38 0.00 33.98 2.24
29 30 2.103537 GGTGGAAGCCGCTTAGTTTA 57.896 50.000 5.38 0.00 33.98 2.01
30 31 2.640184 GGTGGAAGCCGCTTAGTTTAT 58.360 47.619 5.38 0.00 33.98 1.40
31 32 2.354821 GGTGGAAGCCGCTTAGTTTATG 59.645 50.000 5.38 0.00 33.98 1.90
32 33 2.014128 TGGAAGCCGCTTAGTTTATGC 58.986 47.619 5.38 0.00 0.00 3.14
34 35 2.014128 GAAGCCGCTTAGTTTATGCCA 58.986 47.619 5.38 0.00 0.00 4.92
35 36 2.122783 AGCCGCTTAGTTTATGCCAA 57.877 45.000 0.00 0.00 0.00 4.52
36 37 2.442413 AGCCGCTTAGTTTATGCCAAA 58.558 42.857 0.00 0.00 0.00 3.28
38 39 2.163613 GCCGCTTAGTTTATGCCAAAGT 59.836 45.455 0.00 0.00 0.00 2.66
39 40 3.730963 GCCGCTTAGTTTATGCCAAAGTC 60.731 47.826 0.00 0.00 0.00 3.01
40 41 3.438781 CCGCTTAGTTTATGCCAAAGTCA 59.561 43.478 0.00 0.00 0.00 3.41
42 43 4.083537 CGCTTAGTTTATGCCAAAGTCACA 60.084 41.667 0.00 0.00 0.00 3.58
44 45 5.801947 GCTTAGTTTATGCCAAAGTCACATG 59.198 40.000 0.00 0.00 0.00 3.21
45 46 6.349280 GCTTAGTTTATGCCAAAGTCACATGA 60.349 38.462 0.00 0.00 0.00 3.07
46 47 7.629222 GCTTAGTTTATGCCAAAGTCACATGAT 60.629 37.037 0.00 0.00 0.00 2.45
47 48 6.594788 AGTTTATGCCAAAGTCACATGATT 57.405 33.333 0.00 0.00 0.00 2.57
48 49 7.701539 AGTTTATGCCAAAGTCACATGATTA 57.298 32.000 0.00 0.00 0.00 1.75
49 50 7.538575 AGTTTATGCCAAAGTCACATGATTAC 58.461 34.615 0.00 0.00 0.00 1.89
50 51 7.176515 AGTTTATGCCAAAGTCACATGATTACA 59.823 33.333 0.00 0.00 0.00 2.41
51 52 5.981088 ATGCCAAAGTCACATGATTACAA 57.019 34.783 0.00 0.00 0.00 2.41
54 55 5.030295 GCCAAAGTCACATGATTACAATCG 58.970 41.667 0.00 0.00 38.26 3.34
55 56 5.572211 CCAAAGTCACATGATTACAATCGG 58.428 41.667 0.00 0.00 38.26 4.18
56 57 4.882671 AAGTCACATGATTACAATCGGC 57.117 40.909 0.00 0.00 38.26 5.54
57 58 3.872696 AGTCACATGATTACAATCGGCA 58.127 40.909 0.00 0.00 38.26 5.69
58 59 3.873361 AGTCACATGATTACAATCGGCAG 59.127 43.478 0.00 0.00 38.26 4.85
59 60 2.613595 TCACATGATTACAATCGGCAGC 59.386 45.455 0.00 0.00 38.26 5.25
61 62 3.016031 ACATGATTACAATCGGCAGCAA 58.984 40.909 0.00 0.00 38.26 3.91
62 63 3.181497 ACATGATTACAATCGGCAGCAAC 60.181 43.478 0.00 0.00 38.26 4.17
64 65 3.867857 TGATTACAATCGGCAGCAACTA 58.132 40.909 0.00 0.00 38.26 2.24
65 66 3.871006 TGATTACAATCGGCAGCAACTAG 59.129 43.478 0.00 0.00 38.26 2.57
66 67 3.328382 TTACAATCGGCAGCAACTAGT 57.672 42.857 0.00 0.00 0.00 2.57
67 68 2.185004 ACAATCGGCAGCAACTAGTT 57.815 45.000 1.12 1.12 0.00 2.24
69 70 1.061131 CAATCGGCAGCAACTAGTTCG 59.939 52.381 4.77 6.23 0.00 3.95
70 71 0.530744 ATCGGCAGCAACTAGTTCGA 59.469 50.000 15.88 15.88 0.00 3.71
72 73 1.746787 TCGGCAGCAACTAGTTCGATA 59.253 47.619 4.77 0.00 0.00 2.92
73 74 1.852895 CGGCAGCAACTAGTTCGATAC 59.147 52.381 4.77 0.00 0.00 2.24
74 75 2.734175 CGGCAGCAACTAGTTCGATACA 60.734 50.000 4.77 0.00 0.00 2.29
75 76 3.259064 GGCAGCAACTAGTTCGATACAA 58.741 45.455 4.77 0.00 0.00 2.41
76 77 3.307242 GGCAGCAACTAGTTCGATACAAG 59.693 47.826 4.77 0.00 0.00 3.16
77 78 3.927142 GCAGCAACTAGTTCGATACAAGT 59.073 43.478 4.77 0.00 0.00 3.16
78 79 5.100259 GCAGCAACTAGTTCGATACAAGTA 58.900 41.667 4.77 0.00 0.00 2.24
81 82 5.122869 AGCAACTAGTTCGATACAAGTACGA 59.877 40.000 4.77 0.00 0.00 3.43
82 83 5.451662 GCAACTAGTTCGATACAAGTACGAG 59.548 44.000 4.77 0.00 37.36 4.18
83 84 5.731599 ACTAGTTCGATACAAGTACGAGG 57.268 43.478 0.00 0.00 37.36 4.63
84 85 5.423015 ACTAGTTCGATACAAGTACGAGGA 58.577 41.667 0.00 0.00 37.36 3.71
86 87 5.171147 AGTTCGATACAAGTACGAGGATG 57.829 43.478 0.00 0.00 37.36 3.51
87 88 4.880120 AGTTCGATACAAGTACGAGGATGA 59.120 41.667 0.00 0.00 37.36 2.92
88 89 5.531659 AGTTCGATACAAGTACGAGGATGAT 59.468 40.000 0.00 0.00 37.36 2.45
89 90 6.039493 AGTTCGATACAAGTACGAGGATGATT 59.961 38.462 0.00 0.00 37.36 2.57
90 91 7.228108 AGTTCGATACAAGTACGAGGATGATTA 59.772 37.037 0.00 0.00 37.36 1.75
91 92 7.500720 TCGATACAAGTACGAGGATGATTAA 57.499 36.000 0.00 0.00 0.00 1.40
92 93 7.582352 TCGATACAAGTACGAGGATGATTAAG 58.418 38.462 0.00 0.00 0.00 1.85
93 94 6.305877 CGATACAAGTACGAGGATGATTAAGC 59.694 42.308 0.00 0.00 0.00 3.09
94 95 5.599999 ACAAGTACGAGGATGATTAAGCT 57.400 39.130 0.00 0.00 0.00 3.74
95 96 6.710597 ACAAGTACGAGGATGATTAAGCTA 57.289 37.500 0.00 0.00 0.00 3.32
96 97 6.740110 ACAAGTACGAGGATGATTAAGCTAG 58.260 40.000 0.00 0.00 0.00 3.42
97 98 5.379732 AGTACGAGGATGATTAAGCTAGC 57.620 43.478 6.62 6.62 0.00 3.42
98 99 4.827835 AGTACGAGGATGATTAAGCTAGCA 59.172 41.667 18.83 0.00 0.00 3.49
100 101 2.983136 CGAGGATGATTAAGCTAGCACG 59.017 50.000 18.83 1.53 0.00 5.34
102 103 2.103094 AGGATGATTAAGCTAGCACGCA 59.897 45.455 18.83 7.81 0.00 5.24
116 117 3.199290 ACGCAGTGCTATCTCCTCT 57.801 52.632 14.33 0.00 42.51 3.69
117 118 1.479709 ACGCAGTGCTATCTCCTCTT 58.520 50.000 14.33 0.00 42.51 2.85
118 119 1.407258 ACGCAGTGCTATCTCCTCTTC 59.593 52.381 14.33 0.00 42.51 2.87
119 120 1.599171 CGCAGTGCTATCTCCTCTTCG 60.599 57.143 14.33 0.00 0.00 3.79
120 121 1.678627 GCAGTGCTATCTCCTCTTCGA 59.321 52.381 8.18 0.00 0.00 3.71
121 122 2.099921 GCAGTGCTATCTCCTCTTCGAA 59.900 50.000 8.18 0.00 0.00 3.71
122 123 3.701241 CAGTGCTATCTCCTCTTCGAAC 58.299 50.000 0.00 0.00 0.00 3.95
123 124 3.129462 CAGTGCTATCTCCTCTTCGAACA 59.871 47.826 0.00 0.00 0.00 3.18
125 126 4.220821 AGTGCTATCTCCTCTTCGAACAAA 59.779 41.667 0.00 0.00 0.00 2.83
126 127 4.929808 GTGCTATCTCCTCTTCGAACAAAA 59.070 41.667 0.00 0.00 0.00 2.44
127 128 5.582665 GTGCTATCTCCTCTTCGAACAAAAT 59.417 40.000 0.00 0.00 0.00 1.82
128 129 6.092807 GTGCTATCTCCTCTTCGAACAAAATT 59.907 38.462 0.00 0.00 0.00 1.82
129 130 6.313905 TGCTATCTCCTCTTCGAACAAAATTC 59.686 38.462 0.00 0.00 0.00 2.17
130 131 5.786401 ATCTCCTCTTCGAACAAAATTCG 57.214 39.130 0.00 2.70 42.74 3.34
132 133 3.399330 TCCTCTTCGAACAAAATTCGCT 58.601 40.909 4.22 0.00 41.30 4.93
133 134 4.562082 TCCTCTTCGAACAAAATTCGCTA 58.438 39.130 4.22 0.00 41.30 4.26
134 135 4.992319 TCCTCTTCGAACAAAATTCGCTAA 59.008 37.500 4.22 0.00 41.30 3.09
135 136 5.080068 CCTCTTCGAACAAAATTCGCTAAC 58.920 41.667 4.22 0.00 41.30 2.34
137 138 6.050454 TCTTCGAACAAAATTCGCTAACAA 57.950 33.333 4.22 0.00 41.30 2.83
143 144 5.705609 ACAAAATTCGCTAACAACCATCT 57.294 34.783 0.00 0.00 0.00 2.90
144 145 6.084326 ACAAAATTCGCTAACAACCATCTT 57.916 33.333 0.00 0.00 0.00 2.40
145 146 5.920273 ACAAAATTCGCTAACAACCATCTTG 59.080 36.000 0.00 0.00 0.00 3.02
146 147 5.957842 AAATTCGCTAACAACCATCTTGA 57.042 34.783 0.00 0.00 0.00 3.02
147 148 5.957842 AATTCGCTAACAACCATCTTGAA 57.042 34.783 0.00 0.00 0.00 2.69
148 149 6.515272 AATTCGCTAACAACCATCTTGAAT 57.485 33.333 0.00 0.00 0.00 2.57
149 150 5.957842 TTCGCTAACAACCATCTTGAATT 57.042 34.783 0.00 0.00 0.00 2.17
150 151 5.957842 TCGCTAACAACCATCTTGAATTT 57.042 34.783 0.00 0.00 0.00 1.82
153 154 6.206634 TCGCTAACAACCATCTTGAATTTTCT 59.793 34.615 0.00 0.00 0.00 2.52
154 155 6.524586 CGCTAACAACCATCTTGAATTTTCTC 59.475 38.462 0.00 0.00 0.00 2.87
155 156 7.573843 CGCTAACAACCATCTTGAATTTTCTCT 60.574 37.037 0.00 0.00 0.00 3.10
156 157 7.540055 GCTAACAACCATCTTGAATTTTCTCTG 59.460 37.037 0.00 0.00 0.00 3.35
157 158 6.966534 ACAACCATCTTGAATTTTCTCTGT 57.033 33.333 0.00 0.00 0.00 3.41
158 159 8.463930 AACAACCATCTTGAATTTTCTCTGTA 57.536 30.769 0.00 0.00 0.00 2.74
160 161 6.727824 ACCATCTTGAATTTTCTCTGTACG 57.272 37.500 0.00 0.00 0.00 3.67
161 162 6.231211 ACCATCTTGAATTTTCTCTGTACGT 58.769 36.000 0.00 0.00 0.00 3.57
162 163 7.383687 ACCATCTTGAATTTTCTCTGTACGTA 58.616 34.615 0.00 0.00 0.00 3.57
165 166 9.087424 CATCTTGAATTTTCTCTGTACGTATCA 57.913 33.333 0.00 0.00 0.00 2.15
166 167 9.653287 ATCTTGAATTTTCTCTGTACGTATCAA 57.347 29.630 0.00 0.00 0.00 2.57
167 168 9.653287 TCTTGAATTTTCTCTGTACGTATCAAT 57.347 29.630 0.00 0.00 0.00 2.57
177 178 9.784680 TCTCTGTACGTATCAATTTTCTAGTTC 57.215 33.333 0.00 0.00 0.00 3.01
179 180 8.525316 TCTGTACGTATCAATTTTCTAGTTCCA 58.475 33.333 0.00 0.00 0.00 3.53
180 181 9.314321 CTGTACGTATCAATTTTCTAGTTCCAT 57.686 33.333 0.00 0.00 0.00 3.41
181 182 9.661563 TGTACGTATCAATTTTCTAGTTCCATT 57.338 29.630 0.00 0.00 0.00 3.16
182 183 9.916397 GTACGTATCAATTTTCTAGTTCCATTG 57.084 33.333 0.00 0.00 0.00 2.82
183 184 8.786826 ACGTATCAATTTTCTAGTTCCATTGA 57.213 30.769 9.98 9.98 38.04 2.57
184 185 9.226606 ACGTATCAATTTTCTAGTTCCATTGAA 57.773 29.630 11.01 0.00 37.40 2.69
185 186 9.708222 CGTATCAATTTTCTAGTTCCATTGAAG 57.292 33.333 11.01 5.46 37.40 3.02
196 509 9.113838 TCTAGTTCCATTGAAGATAAAGAATGC 57.886 33.333 0.00 0.00 0.00 3.56
198 511 5.173774 TCCATTGAAGATAAAGAATGCGC 57.826 39.130 0.00 0.00 0.00 6.09
203 516 0.657840 AGATAAAGAATGCGCGCACC 59.342 50.000 39.05 29.63 0.00 5.01
205 518 0.808125 ATAAAGAATGCGCGCACCAA 59.192 45.000 39.05 18.85 0.00 3.67
220 533 4.496507 GCGCACCAAGAGATAAAAGAATCC 60.497 45.833 0.30 0.00 0.00 3.01
231 544 6.116126 AGATAAAAGAATCCGTGCTAGCTTT 58.884 36.000 17.23 7.12 0.00 3.51
232 545 6.599638 AGATAAAAGAATCCGTGCTAGCTTTT 59.400 34.615 17.23 13.22 38.59 2.27
233 546 4.425577 AAAGAATCCGTGCTAGCTTTTG 57.574 40.909 17.23 2.77 0.00 2.44
234 547 3.059352 AGAATCCGTGCTAGCTTTTGT 57.941 42.857 17.23 0.00 0.00 2.83
273 586 6.895782 TCTAAAATGGATCGGGTTTCACTAT 58.104 36.000 0.00 0.00 0.00 2.12
274 587 6.990349 TCTAAAATGGATCGGGTTTCACTATC 59.010 38.462 0.00 0.00 0.00 2.08
279 592 4.941263 TGGATCGGGTTTCACTATCAAAAG 59.059 41.667 0.00 0.00 0.00 2.27
281 594 5.823045 GGATCGGGTTTCACTATCAAAAGAT 59.177 40.000 0.00 0.00 0.00 2.40
381 701 4.279671 ACAATCCGTGCCAGATTTAACAAA 59.720 37.500 0.00 0.00 31.56 2.83
382 702 5.221342 ACAATCCGTGCCAGATTTAACAAAA 60.221 36.000 0.00 0.00 31.56 2.44
395 727 6.763610 AGATTTAACAAAATTCAAAACGGCCA 59.236 30.769 2.24 0.00 0.00 5.36
402 734 5.398603 AAATTCAAAACGGCCACATATCA 57.601 34.783 2.24 0.00 0.00 2.15
411 743 2.165234 CGGCCACATATCATCTCGATCT 59.835 50.000 2.24 0.00 35.39 2.75
412 744 3.367806 CGGCCACATATCATCTCGATCTT 60.368 47.826 2.24 0.00 35.39 2.40
420 752 7.440556 CACATATCATCTCGATCTTGGAAAACT 59.559 37.037 0.00 0.00 35.39 2.66
424 756 4.600692 TCTCGATCTTGGAAAACTGACA 57.399 40.909 0.00 0.00 0.00 3.58
426 758 4.991056 TCTCGATCTTGGAAAACTGACAAG 59.009 41.667 0.00 0.00 42.14 3.16
435 1346 6.436843 TGGAAAACTGACAAGAAGAGAAAC 57.563 37.500 0.00 0.00 0.00 2.78
464 1375 0.034337 TGCAAACACTCCCCGTACTC 59.966 55.000 0.00 0.00 0.00 2.59
465 1376 0.320697 GCAAACACTCCCCGTACTCT 59.679 55.000 0.00 0.00 0.00 3.24
523 1434 1.486310 TGGCTCTTTGGCATCGATAGT 59.514 47.619 0.00 0.00 46.76 2.12
555 1466 7.769044 TGTGTAGCTAATTCTGGTTTCCTAATC 59.231 37.037 0.00 0.00 0.00 1.75
556 1467 6.984474 TGTAGCTAATTCTGGTTTCCTAATCG 59.016 38.462 0.00 0.00 0.00 3.34
557 1468 6.235231 AGCTAATTCTGGTTTCCTAATCGA 57.765 37.500 0.00 0.00 0.00 3.59
590 1503 1.398692 TGGAATTTCTATTGCGGCCC 58.601 50.000 0.00 0.00 35.07 5.80
593 1506 1.880027 GAATTTCTATTGCGGCCCGAT 59.120 47.619 7.68 0.00 0.00 4.18
628 1541 0.326927 GACCCGGTCCAGGATTTTCA 59.673 55.000 6.25 0.00 0.00 2.69
674 1591 4.828296 GGGCTGCCCATGACCAGG 62.828 72.222 32.46 0.00 44.65 4.45
675 1592 4.052518 GGCTGCCCATGACCAGGT 62.053 66.667 7.66 0.00 0.00 4.00
676 1593 2.679342 GGCTGCCCATGACCAGGTA 61.679 63.158 7.66 0.00 0.00 3.08
677 1594 1.302949 GCTGCCCATGACCAGGTAA 59.697 57.895 12.52 0.00 0.00 2.85
687 1604 5.932303 CCCATGACCAGGTAAAATATAGACG 59.068 44.000 0.00 0.00 0.00 4.18
784 1708 4.701171 AGAAACGAAGGGTGTACAAAACAA 59.299 37.500 0.00 0.00 40.63 2.83
785 1709 4.359971 AACGAAGGGTGTACAAAACAAC 57.640 40.909 0.00 0.00 45.78 3.32
793 1717 3.490249 GGTGTACAAAACAACTTGAGGCC 60.490 47.826 0.00 0.00 42.96 5.19
814 1738 2.604686 AGGCGGAGAACAGGAGCA 60.605 61.111 0.00 0.00 0.00 4.26
817 1741 2.266055 CGGAGAACAGGAGCACCC 59.734 66.667 0.00 0.00 36.73 4.61
818 1742 2.671682 GGAGAACAGGAGCACCCC 59.328 66.667 0.00 0.00 36.73 4.95
852 1776 0.108138 GACGGAGAAGGTCATGGTGG 60.108 60.000 0.00 0.00 34.56 4.61
880 1815 1.557443 CGCACGACCCTCAACTCAAC 61.557 60.000 0.00 0.00 0.00 3.18
935 2020 5.452356 GGACAAGAAAAGATTATGGCCCATG 60.452 44.000 6.46 0.00 32.80 3.66
939 2024 2.761786 AAGATTATGGCCCATGCTGT 57.238 45.000 6.46 0.00 37.74 4.40
1280 2390 4.749310 CCTCGAGCTGCGCCAGTT 62.749 66.667 6.99 0.00 40.61 3.16
1323 2434 2.403987 CGCTACTCCCTCGTCGTG 59.596 66.667 0.00 0.00 0.00 4.35
1337 2448 4.129737 CGTGGACACCCTCGCGAT 62.130 66.667 10.36 0.00 41.64 4.58
1338 2449 2.509336 GTGGACACCCTCGCGATG 60.509 66.667 10.36 8.16 0.00 3.84
1339 2450 4.451150 TGGACACCCTCGCGATGC 62.451 66.667 10.36 0.00 0.00 3.91
1365 2476 2.720605 GGGCTCGACCGCTACTAC 59.279 66.667 0.00 0.00 40.62 2.73
1366 2477 2.720605 GGCTCGACCGCTACTACC 59.279 66.667 0.00 0.00 0.00 3.18
1367 2478 1.823041 GGCTCGACCGCTACTACCT 60.823 63.158 0.00 0.00 0.00 3.08
1368 2479 1.648174 GCTCGACCGCTACTACCTC 59.352 63.158 0.00 0.00 0.00 3.85
1369 2480 1.933005 CTCGACCGCTACTACCTCG 59.067 63.158 0.00 0.00 0.00 4.63
1370 2481 0.809241 CTCGACCGCTACTACCTCGT 60.809 60.000 0.00 0.00 0.00 4.18
1371 2482 0.807667 TCGACCGCTACTACCTCGTC 60.808 60.000 0.00 0.00 0.00 4.20
1372 2483 1.640604 GACCGCTACTACCTCGTCG 59.359 63.158 0.00 0.00 0.00 5.12
1373 2484 1.078848 ACCGCTACTACCTCGTCGT 60.079 57.895 0.00 0.00 0.00 4.34
1374 2485 1.351012 CCGCTACTACCTCGTCGTG 59.649 63.158 0.00 0.00 0.00 4.35
1375 2486 1.351012 CGCTACTACCTCGTCGTGG 59.649 63.158 11.71 11.71 0.00 4.94
1376 2487 1.086067 CGCTACTACCTCGTCGTGGA 61.086 60.000 19.68 3.29 0.00 4.02
1377 2488 0.376502 GCTACTACCTCGTCGTGGAC 59.623 60.000 19.68 0.00 0.00 4.02
1378 2489 1.730501 CTACTACCTCGTCGTGGACA 58.269 55.000 19.68 6.33 32.09 4.02
1379 2490 1.396301 CTACTACCTCGTCGTGGACAC 59.604 57.143 19.68 0.00 32.09 3.67
1484 2628 3.003173 CACGCCCCTCCTCTTCCA 61.003 66.667 0.00 0.00 0.00 3.53
1496 2640 4.778143 CTTCCACTTCCCGGCGGG 62.778 72.222 38.92 38.92 46.11 6.13
1555 2699 3.787001 GGGTCTCCGGCCTCCAAG 61.787 72.222 0.00 0.00 0.00 3.61
1703 3020 2.261671 GGGCATCAGTCGTGTCGT 59.738 61.111 0.00 0.00 0.00 4.34
1709 3026 0.803117 ATCAGTCGTGTCGTCGTGAT 59.197 50.000 0.00 0.00 0.00 3.06
1715 3032 1.372997 GTGTCGTCGTGATGGCAGT 60.373 57.895 0.00 0.00 31.86 4.40
1760 3077 1.630148 GTCACCATCGTAGACTGCAC 58.370 55.000 0.00 0.00 42.51 4.57
1864 3187 4.595538 ACGCCTTGTTCGCCGACA 62.596 61.111 0.00 0.00 0.00 4.35
1954 3315 5.500234 TGGATTCTTCAGAAGTTACCATGG 58.500 41.667 11.19 11.19 37.48 3.66
1957 3318 7.127186 TGGATTCTTCAGAAGTTACCATGGATA 59.873 37.037 21.47 4.21 37.48 2.59
2017 3382 4.153117 GCACTTTATCAGGTGTTCAGTGAG 59.847 45.833 0.00 0.00 33.44 3.51
2020 3385 5.070446 ACTTTATCAGGTGTTCAGTGAGTGA 59.930 40.000 0.00 0.00 0.00 3.41
2032 3397 0.095417 GTGAGTGATTCGAAAGCCGC 59.905 55.000 0.00 1.42 38.37 6.53
2033 3398 0.320334 TGAGTGATTCGAAAGCCGCA 60.320 50.000 0.00 0.00 38.37 5.69
2109 3474 3.479489 TGCATTTCTCAGCTGAACTTCA 58.521 40.909 18.85 8.23 0.00 3.02
2142 3508 4.100529 CGATGTTTGAAATCATGGACTGC 58.899 43.478 0.00 0.00 0.00 4.40
2203 3573 2.789208 CTTAATGCAACCTCACATGCG 58.211 47.619 0.00 0.00 45.47 4.73
2220 3591 2.919043 GGATCGGCCAAGATGGGT 59.081 61.111 2.24 0.00 38.19 4.51
2226 3598 1.076549 GGCCAAGATGGGTGGTGAA 59.923 57.895 0.00 0.00 38.19 3.18
2476 6684 8.833493 CATCATAATGCTTCTAAAGTGATCACA 58.167 33.333 27.02 6.41 0.00 3.58
2665 6880 7.563188 TGAGGAAGACTAGCTCTCTTCATAAAT 59.437 37.037 24.97 12.09 43.79 1.40
2756 7230 1.136147 CAGAAGCTGTGGCGAATGC 59.864 57.895 0.00 0.00 44.37 3.56
2782 7256 5.140747 AGTAATTCTCAGTGTGTCTGACC 57.859 43.478 5.17 0.00 46.77 4.02
2995 7470 6.678878 CAAGCTAATAATGATGCAGCTCATT 58.321 36.000 17.30 17.30 45.44 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 2.609610 TAAGCGGCTTCCACCCCT 60.610 61.111 20.06 0.00 0.00 4.79
8 9 2.124695 CTAAGCGGCTTCCACCCC 60.125 66.667 20.06 0.00 0.00 4.95
9 10 0.608308 AAACTAAGCGGCTTCCACCC 60.608 55.000 20.06 0.00 0.00 4.61
10 11 2.103537 TAAACTAAGCGGCTTCCACC 57.896 50.000 20.06 0.00 0.00 4.61
12 13 2.014128 GCATAAACTAAGCGGCTTCCA 58.986 47.619 20.06 1.24 0.00 3.53
13 14 1.333931 GGCATAAACTAAGCGGCTTCC 59.666 52.381 20.06 7.78 0.00 3.46
15 16 2.122783 TGGCATAAACTAAGCGGCTT 57.877 45.000 20.32 20.32 0.00 4.35
16 17 2.122783 TTGGCATAAACTAAGCGGCT 57.877 45.000 0.00 0.00 0.00 5.52
21 22 7.144722 TCATGTGACTTTGGCATAAACTAAG 57.855 36.000 0.00 0.00 0.00 2.18
22 23 7.701539 ATCATGTGACTTTGGCATAAACTAA 57.298 32.000 0.00 0.00 0.00 2.24
23 24 7.701539 AATCATGTGACTTTGGCATAAACTA 57.298 32.000 0.00 0.00 0.00 2.24
24 25 6.594788 AATCATGTGACTTTGGCATAAACT 57.405 33.333 0.00 0.00 0.00 2.66
25 26 7.312154 TGTAATCATGTGACTTTGGCATAAAC 58.688 34.615 0.00 0.00 0.00 2.01
26 27 7.459795 TGTAATCATGTGACTTTGGCATAAA 57.540 32.000 0.00 0.00 0.00 1.40
27 28 7.459795 TTGTAATCATGTGACTTTGGCATAA 57.540 32.000 0.00 0.00 0.00 1.90
29 30 5.981088 TTGTAATCATGTGACTTTGGCAT 57.019 34.783 0.00 0.00 0.00 4.40
30 31 5.391843 CGATTGTAATCATGTGACTTTGGCA 60.392 40.000 5.55 0.00 35.11 4.92
31 32 5.030295 CGATTGTAATCATGTGACTTTGGC 58.970 41.667 5.55 0.00 35.11 4.52
32 33 5.572211 CCGATTGTAATCATGTGACTTTGG 58.428 41.667 5.55 0.00 35.11 3.28
34 35 4.699735 TGCCGATTGTAATCATGTGACTTT 59.300 37.500 5.55 0.00 35.11 2.66
35 36 4.260985 TGCCGATTGTAATCATGTGACTT 58.739 39.130 5.55 0.00 35.11 3.01
36 37 3.872696 TGCCGATTGTAATCATGTGACT 58.127 40.909 5.55 0.00 35.11 3.41
38 39 2.613595 GCTGCCGATTGTAATCATGTGA 59.386 45.455 5.55 0.00 35.11 3.58
39 40 2.355444 TGCTGCCGATTGTAATCATGTG 59.645 45.455 0.00 0.00 35.11 3.21
40 41 2.642427 TGCTGCCGATTGTAATCATGT 58.358 42.857 0.00 0.00 35.11 3.21
42 43 3.282021 AGTTGCTGCCGATTGTAATCAT 58.718 40.909 0.00 0.00 35.11 2.45
44 45 3.871594 ACTAGTTGCTGCCGATTGTAATC 59.128 43.478 0.00 0.00 0.00 1.75
45 46 3.873910 ACTAGTTGCTGCCGATTGTAAT 58.126 40.909 0.00 0.00 0.00 1.89
46 47 3.328382 ACTAGTTGCTGCCGATTGTAA 57.672 42.857 0.00 0.00 0.00 2.41
47 48 3.259064 GAACTAGTTGCTGCCGATTGTA 58.741 45.455 14.14 0.00 0.00 2.41
48 49 2.076863 GAACTAGTTGCTGCCGATTGT 58.923 47.619 14.14 0.00 0.00 2.71
49 50 1.061131 CGAACTAGTTGCTGCCGATTG 59.939 52.381 14.14 0.00 0.00 2.67
50 51 1.067142 TCGAACTAGTTGCTGCCGATT 60.067 47.619 14.14 0.00 0.00 3.34
51 52 0.530744 TCGAACTAGTTGCTGCCGAT 59.469 50.000 14.14 0.00 0.00 4.18
54 55 2.888594 TGTATCGAACTAGTTGCTGCC 58.111 47.619 14.14 0.00 0.00 4.85
55 56 3.927142 ACTTGTATCGAACTAGTTGCTGC 59.073 43.478 14.14 1.61 40.66 5.25
56 57 5.227391 CGTACTTGTATCGAACTAGTTGCTG 59.773 44.000 14.14 2.77 40.66 4.41
57 58 5.122869 TCGTACTTGTATCGAACTAGTTGCT 59.877 40.000 14.14 0.00 40.66 3.91
58 59 5.327091 TCGTACTTGTATCGAACTAGTTGC 58.673 41.667 14.14 4.02 40.66 4.17
59 60 5.964168 CCTCGTACTTGTATCGAACTAGTTG 59.036 44.000 14.14 5.81 40.66 3.16
61 62 5.423015 TCCTCGTACTTGTATCGAACTAGT 58.577 41.667 14.87 14.87 44.73 2.57
62 63 5.980698 TCCTCGTACTTGTATCGAACTAG 57.019 43.478 0.00 0.00 37.04 2.57
64 65 4.880120 TCATCCTCGTACTTGTATCGAACT 59.120 41.667 0.00 0.00 33.32 3.01
65 66 5.165911 TCATCCTCGTACTTGTATCGAAC 57.834 43.478 0.00 0.00 33.32 3.95
66 67 6.387041 AATCATCCTCGTACTTGTATCGAA 57.613 37.500 0.00 0.00 33.32 3.71
67 68 7.500720 TTAATCATCCTCGTACTTGTATCGA 57.499 36.000 0.00 0.00 0.00 3.59
69 70 7.371936 AGCTTAATCATCCTCGTACTTGTATC 58.628 38.462 0.00 0.00 0.00 2.24
70 71 7.291411 AGCTTAATCATCCTCGTACTTGTAT 57.709 36.000 0.00 0.00 0.00 2.29
72 73 5.599999 AGCTTAATCATCCTCGTACTTGT 57.400 39.130 0.00 0.00 0.00 3.16
73 74 5.631512 GCTAGCTTAATCATCCTCGTACTTG 59.368 44.000 7.70 0.00 0.00 3.16
74 75 5.302059 TGCTAGCTTAATCATCCTCGTACTT 59.698 40.000 17.23 0.00 0.00 2.24
75 76 4.827835 TGCTAGCTTAATCATCCTCGTACT 59.172 41.667 17.23 0.00 0.00 2.73
76 77 4.918583 GTGCTAGCTTAATCATCCTCGTAC 59.081 45.833 17.23 0.00 0.00 3.67
77 78 4.320275 CGTGCTAGCTTAATCATCCTCGTA 60.320 45.833 17.23 0.00 0.00 3.43
78 79 3.551046 CGTGCTAGCTTAATCATCCTCGT 60.551 47.826 17.23 0.00 0.00 4.18
81 82 2.103094 TGCGTGCTAGCTTAATCATCCT 59.897 45.455 17.23 0.00 38.13 3.24
82 83 2.478134 CTGCGTGCTAGCTTAATCATCC 59.522 50.000 17.23 0.00 38.13 3.51
83 84 3.060003 CACTGCGTGCTAGCTTAATCATC 60.060 47.826 17.23 0.00 38.13 2.92
84 85 2.868583 CACTGCGTGCTAGCTTAATCAT 59.131 45.455 17.23 0.00 38.13 2.45
97 98 0.743688 AGAGGAGATAGCACTGCGTG 59.256 55.000 4.61 4.61 36.51 5.34
98 99 1.407258 GAAGAGGAGATAGCACTGCGT 59.593 52.381 0.00 0.00 33.57 5.24
100 101 1.678627 TCGAAGAGGAGATAGCACTGC 59.321 52.381 0.00 0.00 0.00 4.40
102 103 3.357203 TGTTCGAAGAGGAGATAGCACT 58.643 45.455 0.00 0.00 38.43 4.40
104 105 4.801330 TTTGTTCGAAGAGGAGATAGCA 57.199 40.909 0.00 0.00 38.43 3.49
105 106 6.508721 CGAATTTTGTTCGAAGAGGAGATAGC 60.509 42.308 0.00 0.00 43.97 2.97
106 107 6.508721 GCGAATTTTGTTCGAAGAGGAGATAG 60.509 42.308 13.65 0.00 43.97 2.08
107 108 5.291128 GCGAATTTTGTTCGAAGAGGAGATA 59.709 40.000 13.65 0.00 43.97 1.98
108 109 4.093556 GCGAATTTTGTTCGAAGAGGAGAT 59.906 41.667 13.65 0.00 43.97 2.75
109 110 3.432252 GCGAATTTTGTTCGAAGAGGAGA 59.568 43.478 13.65 0.00 43.97 3.71
110 111 3.433615 AGCGAATTTTGTTCGAAGAGGAG 59.566 43.478 13.65 0.00 43.97 3.69
111 112 3.399330 AGCGAATTTTGTTCGAAGAGGA 58.601 40.909 13.65 0.00 43.97 3.71
113 114 5.675970 TGTTAGCGAATTTTGTTCGAAGAG 58.324 37.500 13.65 0.00 43.97 2.85
114 115 5.660629 TGTTAGCGAATTTTGTTCGAAGA 57.339 34.783 13.65 0.00 43.97 2.87
115 116 5.115021 GGTTGTTAGCGAATTTTGTTCGAAG 59.885 40.000 13.65 0.00 43.97 3.79
116 117 4.971220 GGTTGTTAGCGAATTTTGTTCGAA 59.029 37.500 13.65 0.00 43.97 3.71
117 118 4.035324 TGGTTGTTAGCGAATTTTGTTCGA 59.965 37.500 13.65 0.00 43.97 3.71
118 119 4.283678 TGGTTGTTAGCGAATTTTGTTCG 58.716 39.130 5.87 5.87 44.06 3.95
119 120 6.149633 AGATGGTTGTTAGCGAATTTTGTTC 58.850 36.000 0.00 0.00 0.00 3.18
120 121 6.084326 AGATGGTTGTTAGCGAATTTTGTT 57.916 33.333 0.00 0.00 0.00 2.83
121 122 5.705609 AGATGGTTGTTAGCGAATTTTGT 57.294 34.783 0.00 0.00 0.00 2.83
122 123 6.148948 TCAAGATGGTTGTTAGCGAATTTTG 58.851 36.000 0.00 0.00 0.00 2.44
123 124 6.325919 TCAAGATGGTTGTTAGCGAATTTT 57.674 33.333 0.00 0.00 0.00 1.82
125 126 5.957842 TTCAAGATGGTTGTTAGCGAATT 57.042 34.783 0.00 0.00 0.00 2.17
126 127 6.515272 AATTCAAGATGGTTGTTAGCGAAT 57.485 33.333 0.00 0.00 0.00 3.34
127 128 5.957842 AATTCAAGATGGTTGTTAGCGAA 57.042 34.783 0.00 0.00 0.00 4.70
128 129 5.957842 AAATTCAAGATGGTTGTTAGCGA 57.042 34.783 0.00 0.00 0.00 4.93
129 130 6.381801 AGAAAATTCAAGATGGTTGTTAGCG 58.618 36.000 0.00 0.00 0.00 4.26
130 131 7.540055 CAGAGAAAATTCAAGATGGTTGTTAGC 59.460 37.037 0.00 0.00 0.00 3.09
132 133 8.463930 ACAGAGAAAATTCAAGATGGTTGTTA 57.536 30.769 0.00 0.00 0.00 2.41
133 134 7.352079 ACAGAGAAAATTCAAGATGGTTGTT 57.648 32.000 0.00 0.00 0.00 2.83
134 135 6.966534 ACAGAGAAAATTCAAGATGGTTGT 57.033 33.333 0.00 0.00 0.00 3.32
135 136 7.017645 CGTACAGAGAAAATTCAAGATGGTTG 58.982 38.462 0.00 0.00 0.00 3.77
137 138 6.231211 ACGTACAGAGAAAATTCAAGATGGT 58.769 36.000 0.00 0.00 0.00 3.55
153 154 8.525316 TGGAACTAGAAAATTGATACGTACAGA 58.475 33.333 0.00 0.00 0.00 3.41
154 155 8.697846 TGGAACTAGAAAATTGATACGTACAG 57.302 34.615 0.00 0.00 0.00 2.74
155 156 9.661563 AATGGAACTAGAAAATTGATACGTACA 57.338 29.630 0.00 0.00 0.00 2.90
156 157 9.916397 CAATGGAACTAGAAAATTGATACGTAC 57.084 33.333 0.00 0.00 0.00 3.67
157 158 9.878667 TCAATGGAACTAGAAAATTGATACGTA 57.121 29.630 0.00 0.00 0.00 3.57
158 159 8.786826 TCAATGGAACTAGAAAATTGATACGT 57.213 30.769 0.00 0.00 0.00 3.57
170 171 9.113838 GCATTCTTTATCTTCAATGGAACTAGA 57.886 33.333 0.00 0.00 0.00 2.43
171 172 8.066595 CGCATTCTTTATCTTCAATGGAACTAG 58.933 37.037 0.00 0.00 0.00 2.57
172 173 7.467267 GCGCATTCTTTATCTTCAATGGAACTA 60.467 37.037 0.30 0.00 0.00 2.24
173 174 6.678900 GCGCATTCTTTATCTTCAATGGAACT 60.679 38.462 0.30 0.00 0.00 3.01
174 175 5.456822 GCGCATTCTTTATCTTCAATGGAAC 59.543 40.000 0.30 0.00 0.00 3.62
175 176 5.581605 GCGCATTCTTTATCTTCAATGGAA 58.418 37.500 0.30 0.00 0.00 3.53
176 177 4.260743 CGCGCATTCTTTATCTTCAATGGA 60.261 41.667 8.75 0.00 0.00 3.41
177 178 3.970610 CGCGCATTCTTTATCTTCAATGG 59.029 43.478 8.75 0.00 0.00 3.16
179 180 3.065233 TGCGCGCATTCTTTATCTTCAAT 59.935 39.130 33.09 0.00 0.00 2.57
180 181 2.418280 TGCGCGCATTCTTTATCTTCAA 59.582 40.909 33.09 0.00 0.00 2.69
181 182 2.006169 TGCGCGCATTCTTTATCTTCA 58.994 42.857 33.09 0.66 0.00 3.02
182 183 2.366859 GTGCGCGCATTCTTTATCTTC 58.633 47.619 38.62 15.85 0.00 2.87
183 184 1.064060 GGTGCGCGCATTCTTTATCTT 59.936 47.619 38.62 0.00 0.00 2.40
184 185 0.657840 GGTGCGCGCATTCTTTATCT 59.342 50.000 38.62 0.00 0.00 1.98
185 186 0.376852 TGGTGCGCGCATTCTTTATC 59.623 50.000 38.62 21.09 0.00 1.75
186 187 0.808125 TTGGTGCGCGCATTCTTTAT 59.192 45.000 38.62 0.00 0.00 1.40
187 188 0.167908 CTTGGTGCGCGCATTCTTTA 59.832 50.000 38.62 17.69 0.00 1.85
188 189 1.081242 CTTGGTGCGCGCATTCTTT 60.081 52.632 38.62 0.00 0.00 2.52
191 192 1.709147 ATCTCTTGGTGCGCGCATTC 61.709 55.000 38.62 30.07 0.00 2.67
196 509 1.999735 TCTTTTATCTCTTGGTGCGCG 59.000 47.619 0.00 0.00 0.00 6.86
198 511 4.260375 CGGATTCTTTTATCTCTTGGTGCG 60.260 45.833 0.00 0.00 0.00 5.34
203 516 6.292596 GCTAGCACGGATTCTTTTATCTCTTG 60.293 42.308 10.63 0.00 0.00 3.02
205 518 5.069781 AGCTAGCACGGATTCTTTTATCTCT 59.930 40.000 18.83 0.00 0.00 3.10
267 580 7.658167 TGTTGTTCCGTTATCTTTTGATAGTGA 59.342 33.333 0.00 0.00 41.84 3.41
273 586 9.834628 GATATTTGTTGTTCCGTTATCTTTTGA 57.165 29.630 0.00 0.00 0.00 2.69
274 587 9.840427 AGATATTTGTTGTTCCGTTATCTTTTG 57.160 29.630 0.00 0.00 0.00 2.44
305 618 6.900568 TCGTTTTTGCATTGAATGTTCTTT 57.099 29.167 7.05 0.00 0.00 2.52
381 701 5.360714 AGATGATATGTGGCCGTTTTGAATT 59.639 36.000 0.00 0.00 0.00 2.17
382 702 4.889409 AGATGATATGTGGCCGTTTTGAAT 59.111 37.500 0.00 0.00 0.00 2.57
395 727 7.440556 CAGTTTTCCAAGATCGAGATGATATGT 59.559 37.037 0.00 0.00 37.47 2.29
402 734 5.152623 TGTCAGTTTTCCAAGATCGAGAT 57.847 39.130 0.00 0.00 0.00 2.75
411 743 6.432783 TGTTTCTCTTCTTGTCAGTTTTCCAA 59.567 34.615 0.00 0.00 0.00 3.53
412 744 5.943416 TGTTTCTCTTCTTGTCAGTTTTCCA 59.057 36.000 0.00 0.00 0.00 3.53
420 752 5.833406 TTGCAATGTTTCTCTTCTTGTCA 57.167 34.783 0.00 0.00 0.00 3.58
424 756 6.535274 GCAATTTGCAATGTTTCTCTTCTT 57.465 33.333 16.35 0.00 44.26 2.52
484 1395 2.409975 CAGCGGAGAGTAACGGAAAAA 58.590 47.619 0.00 0.00 0.00 1.94
485 1396 1.337447 CCAGCGGAGAGTAACGGAAAA 60.337 52.381 0.00 0.00 0.00 2.29
520 1431 7.124298 ACCAGAATTAGCTACACATTCTCACTA 59.876 37.037 13.82 0.00 35.48 2.74
523 1434 6.299805 ACCAGAATTAGCTACACATTCTCA 57.700 37.500 13.82 0.00 35.48 3.27
555 1466 2.738521 CAAGTGTGGGAGCGGTCG 60.739 66.667 8.77 0.00 0.00 4.79
556 1467 2.358737 CCAAGTGTGGGAGCGGTC 60.359 66.667 5.93 5.93 41.77 4.79
557 1468 1.779061 ATTCCAAGTGTGGGAGCGGT 61.779 55.000 0.00 0.00 46.01 5.68
610 1523 0.328258 CTGAAAATCCTGGACCGGGT 59.672 55.000 19.40 0.00 0.00 5.28
613 1526 1.032114 GGCCTGAAAATCCTGGACCG 61.032 60.000 0.00 0.00 0.00 4.79
614 1527 1.032114 CGGCCTGAAAATCCTGGACC 61.032 60.000 0.00 0.00 30.15 4.46
615 1528 1.032114 CCGGCCTGAAAATCCTGGAC 61.032 60.000 0.00 0.00 0.00 4.02
616 1529 1.302949 CCGGCCTGAAAATCCTGGA 59.697 57.895 0.00 0.00 0.00 3.86
618 1531 1.000896 ACCCGGCCTGAAAATCCTG 60.001 57.895 0.00 0.00 0.00 3.86
619 1532 1.303282 GACCCGGCCTGAAAATCCT 59.697 57.895 0.00 0.00 0.00 3.24
695 1612 9.846248 ACAAGCAAAATAAATGAATCTACACTC 57.154 29.630 0.00 0.00 0.00 3.51
749 1666 7.767659 ACACCCTTCGTTTCTAAATATAAGACC 59.232 37.037 0.00 0.00 0.00 3.85
763 1680 4.460034 AGTTGTTTTGTACACCCTTCGTTT 59.540 37.500 0.00 0.00 36.21 3.60
766 1683 4.095185 TCAAGTTGTTTTGTACACCCTTCG 59.905 41.667 2.11 0.00 36.21 3.79
768 1685 4.401202 CCTCAAGTTGTTTTGTACACCCTT 59.599 41.667 2.11 0.00 36.21 3.95
793 1717 2.125912 CCTGTTCTCCGCCTCGTG 60.126 66.667 0.00 0.00 0.00 4.35
827 1751 1.737008 GACCTTCTCCGTCGGCAAC 60.737 63.158 6.34 0.00 0.00 4.17
832 1756 0.458543 CACCATGACCTTCTCCGTCG 60.459 60.000 0.00 0.00 32.68 5.12
864 1788 1.366366 CGGTTGAGTTGAGGGTCGT 59.634 57.895 0.00 0.00 0.00 4.34
868 1792 2.359975 GCCCGGTTGAGTTGAGGG 60.360 66.667 0.00 0.00 44.72 4.30
869 1793 2.359975 GGCCCGGTTGAGTTGAGG 60.360 66.667 0.00 0.00 0.00 3.86
871 1795 1.228124 CTTGGCCCGGTTGAGTTGA 60.228 57.895 0.00 0.00 0.00 3.18
872 1796 2.268076 CCTTGGCCCGGTTGAGTTG 61.268 63.158 0.00 0.00 0.00 3.16
911 1846 4.023291 TGGGCCATAATCTTTTCTTGTCC 58.977 43.478 0.00 0.00 0.00 4.02
912 1847 5.594926 CATGGGCCATAATCTTTTCTTGTC 58.405 41.667 20.73 0.00 0.00 3.18
913 1848 4.141869 GCATGGGCCATAATCTTTTCTTGT 60.142 41.667 20.73 0.00 0.00 3.16
914 1849 4.100498 AGCATGGGCCATAATCTTTTCTTG 59.900 41.667 20.73 4.72 42.56 3.02
915 1850 4.100498 CAGCATGGGCCATAATCTTTTCTT 59.900 41.667 20.73 0.00 42.56 2.52
916 1851 3.640029 CAGCATGGGCCATAATCTTTTCT 59.360 43.478 20.73 3.61 42.56 2.52
959 2044 4.742201 TCCGCTCTGCTTGTCCGC 62.742 66.667 0.00 0.00 0.00 5.54
960 2045 2.507992 CTCCGCTCTGCTTGTCCG 60.508 66.667 0.00 0.00 0.00 4.79
962 2047 0.735632 CTCACTCCGCTCTGCTTGTC 60.736 60.000 0.00 0.00 0.00 3.18
963 2048 1.181741 TCTCACTCCGCTCTGCTTGT 61.182 55.000 0.00 0.00 0.00 3.16
964 2049 0.458197 CTCTCACTCCGCTCTGCTTG 60.458 60.000 0.00 0.00 0.00 4.01
974 2061 1.548269 CCCACTTCAGTCTCTCACTCC 59.452 57.143 0.00 0.00 30.26 3.85
1348 2459 2.720605 GTAGTAGCGGTCGAGCCC 59.279 66.667 9.39 0.00 38.01 5.19
1349 2460 1.784036 GAGGTAGTAGCGGTCGAGCC 61.784 65.000 9.39 1.89 38.01 4.70
1350 2461 1.648174 GAGGTAGTAGCGGTCGAGC 59.352 63.158 4.06 4.06 37.41 5.03
1351 2462 0.809241 ACGAGGTAGTAGCGGTCGAG 60.809 60.000 15.37 0.00 34.72 4.04
1352 2463 0.807667 GACGAGGTAGTAGCGGTCGA 60.808 60.000 15.37 0.00 34.72 4.20
1353 2464 1.640604 GACGAGGTAGTAGCGGTCG 59.359 63.158 8.86 8.86 36.71 4.79
1354 2465 1.086634 ACGACGAGGTAGTAGCGGTC 61.087 60.000 0.00 13.36 0.00 4.79
1355 2466 1.078848 ACGACGAGGTAGTAGCGGT 60.079 57.895 0.00 0.00 0.00 5.68
1356 2467 1.351012 CACGACGAGGTAGTAGCGG 59.649 63.158 0.00 0.00 0.00 5.52
1357 2468 1.086067 TCCACGACGAGGTAGTAGCG 61.086 60.000 11.21 0.00 0.00 4.26
1358 2469 0.376502 GTCCACGACGAGGTAGTAGC 59.623 60.000 11.21 0.00 0.00 3.58
1359 2470 1.396301 GTGTCCACGACGAGGTAGTAG 59.604 57.143 11.21 0.00 34.95 2.57
1360 2471 1.442769 GTGTCCACGACGAGGTAGTA 58.557 55.000 11.21 0.00 34.95 1.82
1361 2472 1.239968 GGTGTCCACGACGAGGTAGT 61.240 60.000 11.21 0.00 34.95 2.73
1362 2473 1.505353 GGTGTCCACGACGAGGTAG 59.495 63.158 11.21 0.00 34.95 3.18
1363 2474 1.973281 GGGTGTCCACGACGAGGTA 60.973 63.158 11.21 0.00 34.95 3.08
1364 2475 3.300765 GGGTGTCCACGACGAGGT 61.301 66.667 11.21 0.00 34.95 3.85
1365 2476 2.989824 AGGGTGTCCACGACGAGG 60.990 66.667 4.78 4.78 34.95 4.63
1366 2477 2.567049 GAGGGTGTCCACGACGAG 59.433 66.667 0.00 0.00 34.95 4.18
1372 2483 2.509336 CATCGCGAGGGTGTCCAC 60.509 66.667 16.66 0.00 34.83 4.02
1373 2484 4.451150 GCATCGCGAGGGTGTCCA 62.451 66.667 23.38 0.00 34.83 4.02
1590 2892 2.851801 ACGGAGTGGAGGAGGACA 59.148 61.111 0.00 0.00 42.51 4.02
1620 2922 1.457643 CATCCTCGCCAGGTCCCTA 60.458 63.158 0.00 0.00 41.28 3.53
1703 3020 1.221566 CCCATCACTGCCATCACGA 59.778 57.895 0.00 0.00 0.00 4.35
1709 3026 2.934932 TGAGCCCCATCACTGCCA 60.935 61.111 0.00 0.00 0.00 4.92
1760 3077 4.181010 CCACCCCGATGAGGCAGG 62.181 72.222 0.00 0.00 39.21 4.85
1826 3143 1.300481 GCCGGGCAGATAGAAGAAAC 58.700 55.000 15.62 0.00 0.00 2.78
1827 3144 0.179084 CGCCGGGCAGATAGAAGAAA 60.179 55.000 20.71 0.00 0.00 2.52
1989 3353 1.806542 ACACCTGATAAAGTGCAAGCG 59.193 47.619 0.00 0.00 37.51 4.68
1990 3354 3.253188 TGAACACCTGATAAAGTGCAAGC 59.747 43.478 0.00 0.00 37.51 4.01
2017 3382 1.913403 CAAATGCGGCTTTCGAATCAC 59.087 47.619 0.00 0.00 35.75 3.06
2020 3385 3.034569 GCAAATGCGGCTTTCGAAT 57.965 47.368 0.00 0.00 39.19 3.34
2032 3397 3.492313 GGTAGCGAGTTTTGAGCAAATG 58.508 45.455 0.00 0.00 0.00 2.32
2033 3398 2.488153 GGGTAGCGAGTTTTGAGCAAAT 59.512 45.455 0.00 0.00 0.00 2.32
2109 3474 7.199766 TGATTTCAAACATCGCAAACTAAACT 58.800 30.769 0.00 0.00 0.00 2.66
2142 3508 5.649782 AGATGGCATTCAAGGTTAACAAG 57.350 39.130 8.10 0.00 0.00 3.16
2203 3573 1.526917 CACCCATCTTGGCCGATCC 60.527 63.158 0.00 0.00 35.79 3.36
2220 3591 2.559698 TGCTCCGAAAGAATTCACCA 57.440 45.000 8.44 0.00 35.15 4.17
2226 3598 3.616956 TCTGTCATGCTCCGAAAGAAT 57.383 42.857 0.00 0.00 0.00 2.40
2315 3687 3.181467 CCTCTCCAGATTAGAACAGCCTG 60.181 52.174 0.00 0.00 0.00 4.85
2316 3688 3.037549 CCTCTCCAGATTAGAACAGCCT 58.962 50.000 0.00 0.00 0.00 4.58
2402 3778 4.350368 TGCACTAAAATGACAGACTGGA 57.650 40.909 7.51 0.00 0.00 3.86
2403 3779 5.181811 TCAATGCACTAAAATGACAGACTGG 59.818 40.000 7.51 0.00 0.00 4.00
2665 6880 5.514136 CCAAACTGGGAGTAATCAGTACCAA 60.514 44.000 0.00 0.00 42.67 3.67


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

AutoCloner maintained by Alex Coulton.