Multiple sequence alignment - TraesCS1B01G085600

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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 TraesCS1B01G085600 chr1B 100.000 3725 0 0 1 3725 70232060 70235784 0.000000e+00 6879.0
1 TraesCS1B01G085600 chr1B 90.537 2029 156 21 723 2734 4954469 4952460 0.000000e+00 2651.0
2 TraesCS1B01G085600 chr1B 90.050 2010 161 22 743 2734 4597570 4595582 0.000000e+00 2567.0
3 TraesCS1B01G085600 chr1B 89.586 2055 166 20 723 2747 46830353 46828317 0.000000e+00 2566.0
4 TraesCS1B01G085600 chr1B 81.677 322 14 17 570 859 4543325 4543017 3.740000e-55 226.0
5 TraesCS1B01G085600 chr1B 76.652 227 26 10 244 462 4955410 4955203 2.370000e-17 100.0
6 TraesCS1B01G085600 chr1D 94.865 1928 66 10 808 2732 49764434 49766331 0.000000e+00 2981.0
7 TraesCS1B01G085600 chr1D 94.250 800 32 8 2730 3519 49766598 49767393 0.000000e+00 1210.0
8 TraesCS1B01G085600 chr1D 93.196 485 25 3 330 810 49745890 49746370 0.000000e+00 706.0
9 TraesCS1B01G085600 chr1D 93.662 142 8 1 24 165 49739083 49739223 1.050000e-50 211.0
10 TraesCS1B01G085600 chr1D 89.535 86 6 3 3534 3618 49734881 49734964 5.090000e-19 106.0
11 TraesCS1B01G085600 chr6D 87.327 2675 241 53 732 3376 53176004 53173398 0.000000e+00 2972.0
12 TraesCS1B01G085600 chr6D 88.912 2354 189 34 729 3050 51342922 51345235 0.000000e+00 2835.0
13 TraesCS1B01G085600 chr6D 88.426 2350 200 34 732 3050 51068203 51070511 0.000000e+00 2767.0
14 TraesCS1B01G085600 chr6D 87.326 2225 205 32 732 2934 50956360 50958529 0.000000e+00 2475.0
15 TraesCS1B01G085600 chr6D 85.270 2349 235 57 732 3046 51348818 51351089 0.000000e+00 2318.0
16 TraesCS1B01G085600 chr6D 86.150 361 31 10 2935 3281 50958572 50958927 4.540000e-99 372.0
17 TraesCS1B01G085600 chr6D 82.779 331 29 13 3060 3374 51345352 51345670 1.710000e-68 270.0
18 TraesCS1B01G085600 chr6D 82.175 331 31 13 3060 3374 51070628 51070946 3.690000e-65 259.0
19 TraesCS1B01G085600 chr6D 80.738 244 26 12 392 631 51342535 51342761 1.780000e-38 171.0
20 TraesCS1B01G085600 chr5D 92.648 2013 106 16 723 2723 57819531 57821513 0.000000e+00 2859.0
21 TraesCS1B01G085600 chr5D 91.837 882 44 8 2650 3505 535495201 535494322 0.000000e+00 1205.0
22 TraesCS1B01G085600 chr5D 98.305 59 1 0 3455 3513 535494346 535494288 1.830000e-18 104.0
23 TraesCS1B01G085600 chr5D 89.062 64 6 1 3375 3438 535494516 535494454 1.110000e-10 78.7
24 TraesCS1B01G085600 chr5B 92.548 2013 111 14 723 2723 60825993 60824008 0.000000e+00 2850.0
25 TraesCS1B01G085600 chr5B 99.138 116 1 0 3610 3725 225116285 225116400 3.770000e-50 209.0
26 TraesCS1B01G085600 chr5B 93.284 134 5 3 3595 3725 267758015 267758147 1.060000e-45 195.0
27 TraesCS1B01G085600 chr5B 83.951 162 15 5 486 637 60826357 60826197 1.080000e-30 145.0
28 TraesCS1B01G085600 chr5B 84.286 70 7 1 3126 3191 617173138 617173207 8.640000e-07 65.8
29 TraesCS1B01G085600 chr6B 88.478 2352 198 31 728 3050 120355096 120352789 0.000000e+00 2774.0
30 TraesCS1B01G085600 chr6B 81.846 325 30 15 3063 3374 120352699 120352391 2.870000e-61 246.0
31 TraesCS1B01G085600 chr6B 98.291 117 2 0 3609 3725 1160120 1160004 4.880000e-49 206.0
32 TraesCS1B01G085600 chr6B 99.123 114 1 0 3612 3725 643217458 643217345 4.880000e-49 206.0
33 TraesCS1B01G085600 chr6B 98.276 116 2 0 3610 3725 422696826 422696941 1.750000e-48 204.0
34 TraesCS1B01G085600 chr6B 79.757 247 29 12 392 634 120595818 120595589 3.850000e-35 159.0
35 TraesCS1B01G085600 chr6B 84.076 157 18 3 478 634 120355401 120355252 1.080000e-30 145.0
36 TraesCS1B01G085600 chr6A 89.347 2037 166 20 723 2746 613493630 613495628 0.000000e+00 2512.0
37 TraesCS1B01G085600 chr6A 85.920 2081 222 34 994 3046 64174538 64172501 0.000000e+00 2154.0
38 TraesCS1B01G085600 chr1A 89.513 1993 175 19 769 2746 2943269 2945242 0.000000e+00 2492.0
39 TraesCS1B01G085600 chr1A 89.948 1920 170 13 828 2735 3533038 3531130 0.000000e+00 2455.0
40 TraesCS1B01G085600 chr1A 93.023 86 6 0 636 721 32545453 32545538 3.910000e-25 126.0
41 TraesCS1B01G085600 chr1A 78.414 227 16 8 572 780 3012855 3013066 2.350000e-22 117.0
42 TraesCS1B01G085600 chr1A 80.864 162 15 12 486 631 2942936 2943097 3.040000e-21 113.0
43 TraesCS1B01G085600 chr1A 86.667 60 3 2 221 275 2942228 2942287 1.120000e-05 62.1
44 TraesCS1B01G085600 chrUn 93.713 334 21 0 2065 2398 382963962 382964295 5.550000e-138 501.0
45 TraesCS1B01G085600 chrUn 80.864 162 15 12 486 631 361631341 361631502 3.040000e-21 113.0
46 TraesCS1B01G085600 chr2A 99.138 116 1 0 3610 3725 569281657 569281772 3.770000e-50 209.0
47 TraesCS1B01G085600 chr7B 96.694 121 4 0 3605 3725 413255452 413255332 6.310000e-48 202.0
48 TraesCS1B01G085600 chr7B 85.484 124 11 2 511 631 591461315 591461434 5.050000e-24 122.0
49 TraesCS1B01G085600 chr3D 93.478 138 5 4 3592 3725 66523597 66523734 6.310000e-48 202.0
50 TraesCS1B01G085600 chr5A 94.030 134 5 3 3595 3725 489674152 489674019 2.270000e-47 200.0
51 TraesCS1B01G085600 chr4B 88.112 143 16 1 2589 2731 630238443 630238584 6.400000e-38 169.0
52 TraesCS1B01G085600 chr7D 80.412 194 17 9 447 631 548230707 548230888 1.090000e-25 128.0


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 TraesCS1B01G085600 chr1B 70232060 70235784 3724 False 6879.000000 6879 100.000000 1 3725 1 chr1B.!!$F1 3724
1 TraesCS1B01G085600 chr1B 4595582 4597570 1988 True 2567.000000 2567 90.050000 743 2734 1 chr1B.!!$R2 1991
2 TraesCS1B01G085600 chr1B 46828317 46830353 2036 True 2566.000000 2566 89.586000 723 2747 1 chr1B.!!$R3 2024
3 TraesCS1B01G085600 chr1B 4952460 4955410 2950 True 1375.500000 2651 83.594500 244 2734 2 chr1B.!!$R4 2490
4 TraesCS1B01G085600 chr1D 49764434 49767393 2959 False 2095.500000 2981 94.557500 808 3519 2 chr1D.!!$F4 2711
5 TraesCS1B01G085600 chr6D 53173398 53176004 2606 True 2972.000000 2972 87.327000 732 3376 1 chr6D.!!$R1 2644
6 TraesCS1B01G085600 chr6D 51068203 51070946 2743 False 1513.000000 2767 85.300500 732 3374 2 chr6D.!!$F2 2642
7 TraesCS1B01G085600 chr6D 50956360 50958927 2567 False 1423.500000 2475 86.738000 732 3281 2 chr6D.!!$F1 2549
8 TraesCS1B01G085600 chr6D 51342535 51351089 8554 False 1398.500000 2835 84.424750 392 3374 4 chr6D.!!$F3 2982
9 TraesCS1B01G085600 chr5D 57819531 57821513 1982 False 2859.000000 2859 92.648000 723 2723 1 chr5D.!!$F1 2000
10 TraesCS1B01G085600 chr5D 535494288 535495201 913 True 462.566667 1205 93.068000 2650 3513 3 chr5D.!!$R1 863
11 TraesCS1B01G085600 chr5B 60824008 60826357 2349 True 1497.500000 2850 88.249500 486 2723 2 chr5B.!!$R1 2237
12 TraesCS1B01G085600 chr6B 120352391 120355401 3010 True 1055.000000 2774 84.800000 478 3374 3 chr6B.!!$R4 2896
13 TraesCS1B01G085600 chr6A 613493630 613495628 1998 False 2512.000000 2512 89.347000 723 2746 1 chr6A.!!$F1 2023
14 TraesCS1B01G085600 chr6A 64172501 64174538 2037 True 2154.000000 2154 85.920000 994 3046 1 chr6A.!!$R1 2052
15 TraesCS1B01G085600 chr1A 3531130 3533038 1908 True 2455.000000 2455 89.948000 828 2735 1 chr1A.!!$R1 1907
16 TraesCS1B01G085600 chr1A 2942228 2945242 3014 False 889.033333 2492 85.681333 221 2746 3 chr1A.!!$F3 2525

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
232 233 0.102663 GGTCGTGCTCTAGGTAAGGC 59.897 60.0 0.00 0.0 0.00 4.35 F
502 528 0.253044 TAGCCTAGGGTTGCAGCAAG 59.747 55.0 20.59 0.0 0.00 4.01 F
1225 2391 0.257328 TGGTTCTGGTCTTTGCACCA 59.743 50.0 0.00 0.0 44.69 4.17 F
2148 3328 2.435372 TCACACAGCAGGGTTTTCTT 57.565 45.0 0.00 0.0 0.00 2.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1198 2364 0.106149 AGACCAGAACCAACACGGAC 59.894 55.0 0.0 0.0 38.63 4.79 R
2148 3328 0.321919 GGCAGGACTGAATGAGCACA 60.322 55.0 3.0 0.0 0.00 4.57 R
2604 3788 0.752658 TAGGTCGGATGATGCACAGG 59.247 55.0 0.0 0.0 0.00 4.00 R
3648 7500 0.037303 ACCTCATGGTCACAAGGCAG 59.963 55.0 0.0 0.0 44.78 4.85 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
19 20 1.635844 TAGGTATTTCTGTGCGTGCG 58.364 50.000 0.00 0.00 0.00 5.34
20 21 0.320421 AGGTATTTCTGTGCGTGCGT 60.320 50.000 0.00 0.00 0.00 5.24
21 22 1.067425 AGGTATTTCTGTGCGTGCGTA 60.067 47.619 0.00 0.00 0.00 4.42
22 23 1.323534 GGTATTTCTGTGCGTGCGTAG 59.676 52.381 0.00 0.00 0.00 3.51
23 24 1.323534 GTATTTCTGTGCGTGCGTAGG 59.676 52.381 0.00 0.00 0.00 3.18
24 25 1.635663 ATTTCTGTGCGTGCGTAGGC 61.636 55.000 11.41 11.41 38.16 3.93
25 26 4.735132 TCTGTGCGTGCGTAGGCC 62.735 66.667 15.48 0.00 38.85 5.19
31 32 2.739287 CGTGCGTAGGCCCGAAAA 60.739 61.111 6.42 0.00 42.97 2.29
32 33 2.104253 CGTGCGTAGGCCCGAAAAT 61.104 57.895 6.42 0.00 42.97 1.82
33 34 0.806884 CGTGCGTAGGCCCGAAAATA 60.807 55.000 6.42 0.00 42.97 1.40
34 35 0.935196 GTGCGTAGGCCCGAAAATAG 59.065 55.000 5.51 0.00 38.85 1.73
35 36 0.812412 TGCGTAGGCCCGAAAATAGC 60.812 55.000 5.51 0.00 38.85 2.97
36 37 1.828331 GCGTAGGCCCGAAAATAGCG 61.828 60.000 5.51 0.00 0.00 4.26
37 38 0.529119 CGTAGGCCCGAAAATAGCGT 60.529 55.000 0.00 0.00 0.00 5.07
38 39 0.935196 GTAGGCCCGAAAATAGCGTG 59.065 55.000 0.00 0.00 0.00 5.34
39 40 0.812412 TAGGCCCGAAAATAGCGTGC 60.812 55.000 0.00 0.00 0.00 5.34
40 41 2.022762 GCCCGAAAATAGCGTGCG 59.977 61.111 0.00 0.00 0.00 5.34
41 42 2.746803 GCCCGAAAATAGCGTGCGT 61.747 57.895 0.00 0.00 0.00 5.24
42 43 1.347221 CCCGAAAATAGCGTGCGTC 59.653 57.895 0.00 0.00 0.00 5.19
43 44 1.013755 CCGAAAATAGCGTGCGTCG 60.014 57.895 0.00 0.00 43.12 5.12
44 45 1.013755 CGAAAATAGCGTGCGTCGG 60.014 57.895 0.00 0.00 40.26 4.79
45 46 1.296649 GAAAATAGCGTGCGTCGGC 60.297 57.895 0.00 0.00 40.26 5.54
46 47 2.627201 GAAAATAGCGTGCGTCGGCC 62.627 60.000 0.00 0.00 40.26 6.13
57 58 4.179579 GTCGGCCCGCAGCAATTC 62.180 66.667 0.00 0.00 46.50 2.17
65 66 4.481112 GCAGCAATTCCGGGCGTG 62.481 66.667 0.00 0.00 34.54 5.34
66 67 3.814268 CAGCAATTCCGGGCGTGG 61.814 66.667 0.00 0.00 34.54 4.94
69 70 2.360600 CAATTCCGGGCGTGGGAA 60.361 61.111 0.00 5.88 46.86 3.97
70 71 2.045340 AATTCCGGGCGTGGGAAG 60.045 61.111 0.00 0.00 46.08 3.46
71 72 4.796495 ATTCCGGGCGTGGGAAGC 62.796 66.667 0.00 0.00 46.08 3.86
83 84 4.838152 GGAAGCCCATGCGAGCGA 62.838 66.667 0.00 0.00 44.33 4.93
84 85 3.267860 GAAGCCCATGCGAGCGAG 61.268 66.667 0.00 0.00 44.33 5.03
85 86 4.845580 AAGCCCATGCGAGCGAGG 62.846 66.667 0.00 0.00 44.33 4.63
113 114 4.759205 GAAGGCCCGCCCCACATT 62.759 66.667 0.00 0.00 36.58 2.71
114 115 4.759205 AAGGCCCGCCCCACATTC 62.759 66.667 0.00 0.00 36.58 2.67
116 117 4.839706 GGCCCGCCCCACATTCAT 62.840 66.667 0.00 0.00 0.00 2.57
117 118 3.219198 GCCCGCCCCACATTCATC 61.219 66.667 0.00 0.00 0.00 2.92
118 119 2.597340 CCCGCCCCACATTCATCT 59.403 61.111 0.00 0.00 0.00 2.90
119 120 1.076777 CCCGCCCCACATTCATCTT 60.077 57.895 0.00 0.00 0.00 2.40
120 121 1.103398 CCCGCCCCACATTCATCTTC 61.103 60.000 0.00 0.00 0.00 2.87
121 122 1.103398 CCGCCCCACATTCATCTTCC 61.103 60.000 0.00 0.00 0.00 3.46
122 123 0.107017 CGCCCCACATTCATCTTCCT 60.107 55.000 0.00 0.00 0.00 3.36
123 124 1.685148 GCCCCACATTCATCTTCCTC 58.315 55.000 0.00 0.00 0.00 3.71
124 125 1.752084 GCCCCACATTCATCTTCCTCC 60.752 57.143 0.00 0.00 0.00 4.30
125 126 1.475751 CCCCACATTCATCTTCCTCCG 60.476 57.143 0.00 0.00 0.00 4.63
126 127 1.303309 CCACATTCATCTTCCTCCGC 58.697 55.000 0.00 0.00 0.00 5.54
127 128 1.134280 CCACATTCATCTTCCTCCGCT 60.134 52.381 0.00 0.00 0.00 5.52
128 129 2.208431 CACATTCATCTTCCTCCGCTC 58.792 52.381 0.00 0.00 0.00 5.03
129 130 1.202463 ACATTCATCTTCCTCCGCTCG 60.202 52.381 0.00 0.00 0.00 5.03
130 131 0.249657 ATTCATCTTCCTCCGCTCGC 60.250 55.000 0.00 0.00 0.00 5.03
131 132 2.613739 TTCATCTTCCTCCGCTCGCG 62.614 60.000 0.00 0.00 39.44 5.87
132 133 2.829003 ATCTTCCTCCGCTCGCGA 60.829 61.111 9.26 9.26 42.83 5.87
133 134 2.840066 ATCTTCCTCCGCTCGCGAG 61.840 63.158 31.37 31.37 42.83 5.03
134 135 3.509757 CTTCCTCCGCTCGCGAGA 61.510 66.667 38.74 18.11 42.83 4.04
135 136 3.743091 CTTCCTCCGCTCGCGAGAC 62.743 68.421 38.74 26.70 42.83 3.36
136 137 4.779966 TCCTCCGCTCGCGAGACT 62.780 66.667 38.74 0.00 42.83 3.24
137 138 2.864378 TTCCTCCGCTCGCGAGACTA 62.864 60.000 38.74 20.54 42.83 2.59
138 139 2.325166 CTCCGCTCGCGAGACTAC 59.675 66.667 38.74 19.92 42.83 2.73
139 140 2.125229 TCCGCTCGCGAGACTACT 60.125 61.111 38.74 0.00 42.83 2.57
140 141 0.875040 CTCCGCTCGCGAGACTACTA 60.875 60.000 38.74 15.68 42.83 1.82
141 142 0.875040 TCCGCTCGCGAGACTACTAG 60.875 60.000 38.74 18.15 42.83 2.57
142 143 1.565591 CGCTCGCGAGACTACTAGG 59.434 63.158 38.74 11.21 42.83 3.02
143 144 1.833434 CGCTCGCGAGACTACTAGGG 61.833 65.000 38.74 14.99 42.83 3.53
144 145 0.814812 GCTCGCGAGACTACTAGGGT 60.815 60.000 38.74 0.00 34.47 4.34
145 146 1.666054 CTCGCGAGACTACTAGGGTT 58.334 55.000 32.06 0.00 34.47 4.11
146 147 2.015587 CTCGCGAGACTACTAGGGTTT 58.984 52.381 32.06 0.00 34.47 3.27
147 148 3.201290 CTCGCGAGACTACTAGGGTTTA 58.799 50.000 32.06 0.00 34.47 2.01
148 149 2.939103 TCGCGAGACTACTAGGGTTTAC 59.061 50.000 3.71 0.00 34.47 2.01
149 150 2.941720 CGCGAGACTACTAGGGTTTACT 59.058 50.000 0.00 0.00 0.00 2.24
150 151 4.122776 CGCGAGACTACTAGGGTTTACTA 58.877 47.826 0.00 0.00 0.00 1.82
151 152 4.025313 CGCGAGACTACTAGGGTTTACTAC 60.025 50.000 0.00 0.00 0.00 2.73
152 153 4.878397 GCGAGACTACTAGGGTTTACTACA 59.122 45.833 0.00 0.00 0.00 2.74
153 154 5.220758 GCGAGACTACTAGGGTTTACTACAC 60.221 48.000 0.00 0.00 0.00 2.90
154 155 6.112058 CGAGACTACTAGGGTTTACTACACT 58.888 44.000 0.00 0.00 44.62 3.55
155 156 7.268586 CGAGACTACTAGGGTTTACTACACTA 58.731 42.308 0.00 0.00 39.26 2.74
156 157 7.930865 CGAGACTACTAGGGTTTACTACACTAT 59.069 40.741 0.00 0.00 41.83 2.12
157 158 9.271828 GAGACTACTAGGGTTTACTACACTATC 57.728 40.741 0.00 0.00 41.83 2.08
158 159 7.930865 AGACTACTAGGGTTTACTACACTATCG 59.069 40.741 0.00 0.00 41.83 2.92
159 160 7.569240 ACTACTAGGGTTTACTACACTATCGT 58.431 38.462 0.00 0.00 41.83 3.73
160 161 6.934048 ACTAGGGTTTACTACACTATCGTC 57.066 41.667 0.00 0.00 41.83 4.20
161 162 6.657875 ACTAGGGTTTACTACACTATCGTCT 58.342 40.000 0.00 0.00 41.83 4.18
162 163 6.765512 ACTAGGGTTTACTACACTATCGTCTC 59.234 42.308 0.00 0.00 41.83 3.36
163 164 4.886489 AGGGTTTACTACACTATCGTCTCC 59.114 45.833 0.00 0.00 39.26 3.71
164 165 4.886489 GGGTTTACTACACTATCGTCTCCT 59.114 45.833 0.00 0.00 0.00 3.69
165 166 5.008514 GGGTTTACTACACTATCGTCTCCTC 59.991 48.000 0.00 0.00 0.00 3.71
166 167 5.821995 GGTTTACTACACTATCGTCTCCTCT 59.178 44.000 0.00 0.00 0.00 3.69
167 168 6.018016 GGTTTACTACACTATCGTCTCCTCTC 60.018 46.154 0.00 0.00 0.00 3.20
168 169 4.075963 ACTACACTATCGTCTCCTCTCC 57.924 50.000 0.00 0.00 0.00 3.71
169 170 3.712733 ACTACACTATCGTCTCCTCTCCT 59.287 47.826 0.00 0.00 0.00 3.69
170 171 3.202829 ACACTATCGTCTCCTCTCCTC 57.797 52.381 0.00 0.00 0.00 3.71
171 172 2.158726 ACACTATCGTCTCCTCTCCTCC 60.159 54.545 0.00 0.00 0.00 4.30
172 173 1.071071 ACTATCGTCTCCTCTCCTCCG 59.929 57.143 0.00 0.00 0.00 4.63
173 174 0.250381 TATCGTCTCCTCTCCTCCGC 60.250 60.000 0.00 0.00 0.00 5.54
174 175 3.578272 CGTCTCCTCTCCTCCGCG 61.578 72.222 0.00 0.00 0.00 6.46
175 176 3.213402 GTCTCCTCTCCTCCGCGG 61.213 72.222 22.12 22.12 0.00 6.46
194 195 4.237445 GGACATCTCCGAGGTCGA 57.763 61.111 0.00 0.00 43.16 4.20
195 196 2.026522 GGACATCTCCGAGGTCGAG 58.973 63.158 0.00 0.00 43.16 4.04
196 197 1.357334 GACATCTCCGAGGTCGAGC 59.643 63.158 6.48 6.48 43.02 5.03
197 198 2.329690 CATCTCCGAGGTCGAGCG 59.670 66.667 9.28 2.00 43.02 5.03
216 217 4.977126 CGGCGGCTACGATCGGTC 62.977 72.222 20.98 7.49 44.60 4.79
232 233 0.102663 GGTCGTGCTCTAGGTAAGGC 59.897 60.000 0.00 0.00 0.00 4.35
275 281 1.382420 CCTGAGAGACCCCTCCCTG 60.382 68.421 0.00 0.00 40.30 4.45
279 293 1.305381 AGAGACCCCTCCCTGTTCG 60.305 63.158 0.00 0.00 40.30 3.95
281 295 1.889530 GAGACCCCTCCCTGTTCGTG 61.890 65.000 0.00 0.00 33.30 4.35
283 297 4.760047 CCCCTCCCTGTTCGTGCG 62.760 72.222 0.00 0.00 0.00 5.34
284 298 3.691342 CCCTCCCTGTTCGTGCGA 61.691 66.667 0.00 0.00 0.00 5.10
287 301 1.811266 CTCCCTGTTCGTGCGATGG 60.811 63.158 0.00 0.00 0.00 3.51
288 302 2.047274 CCCTGTTCGTGCGATGGT 60.047 61.111 0.00 0.00 0.00 3.55
290 304 1.635663 CCCTGTTCGTGCGATGGTTC 61.636 60.000 0.00 0.00 0.00 3.62
291 305 0.670546 CCTGTTCGTGCGATGGTTCT 60.671 55.000 0.00 0.00 0.00 3.01
292 306 0.716108 CTGTTCGTGCGATGGTTCTC 59.284 55.000 0.00 0.00 0.00 2.87
293 307 0.669318 TGTTCGTGCGATGGTTCTCC 60.669 55.000 0.00 0.00 0.00 3.71
313 332 2.470821 CTTCCCCGATTCGACATGTAC 58.529 52.381 7.83 0.00 0.00 2.90
314 333 0.382873 TCCCCGATTCGACATGTACG 59.617 55.000 7.83 4.78 0.00 3.67
358 377 4.685169 TGGATTCGCTTTCTTGATTGAC 57.315 40.909 0.00 0.00 0.00 3.18
382 401 2.940158 GGAAACCAAACCTGTACCAGT 58.060 47.619 0.00 0.00 0.00 4.00
383 402 4.089408 GGAAACCAAACCTGTACCAGTA 57.911 45.455 0.00 0.00 0.00 2.74
384 403 4.659115 GGAAACCAAACCTGTACCAGTAT 58.341 43.478 0.00 0.00 0.00 2.12
385 404 5.807909 GGAAACCAAACCTGTACCAGTATA 58.192 41.667 0.00 0.00 0.00 1.47
386 405 6.420638 GGAAACCAAACCTGTACCAGTATAT 58.579 40.000 0.00 0.00 0.00 0.86
387 406 7.567458 GGAAACCAAACCTGTACCAGTATATA 58.433 38.462 0.00 0.00 0.00 0.86
397 420 9.132923 ACCTGTACCAGTATATAATATCATCCG 57.867 37.037 0.00 0.00 0.00 4.18
429 452 7.759489 TGTTAATGTTGTAAAGCCATTCTCT 57.241 32.000 0.00 0.00 31.63 3.10
433 456 7.396540 AATGTTGTAAAGCCATTCTCTTAGG 57.603 36.000 0.00 0.00 0.00 2.69
434 457 5.876357 TGTTGTAAAGCCATTCTCTTAGGT 58.124 37.500 0.00 0.00 0.00 3.08
435 458 5.705441 TGTTGTAAAGCCATTCTCTTAGGTG 59.295 40.000 0.00 0.00 0.00 4.00
445 468 6.238981 GCCATTCTCTTAGGTGGTAGTAGTAC 60.239 46.154 0.00 0.00 34.23 2.73
473 499 9.034544 AGAAAGTAAGCTTTTAATTTGCAACTG 57.965 29.630 3.20 0.00 44.25 3.16
474 500 8.940768 AAAGTAAGCTTTTAATTTGCAACTGA 57.059 26.923 3.20 0.00 41.78 3.41
475 501 9.546428 AAAGTAAGCTTTTAATTTGCAACTGAT 57.454 25.926 3.20 0.00 41.78 2.90
476 502 8.748380 AGTAAGCTTTTAATTTGCAACTGATC 57.252 30.769 3.20 0.00 0.00 2.92
502 528 0.253044 TAGCCTAGGGTTGCAGCAAG 59.747 55.000 20.59 0.00 0.00 4.01
524 560 3.008330 CTGCTGCATTTCTAGTTGAGCT 58.992 45.455 1.31 0.00 0.00 4.09
547 583 8.194104 AGCTGATATTAGATTGGCGTTATCTAG 58.806 37.037 0.00 0.00 36.32 2.43
548 584 7.043059 GCTGATATTAGATTGGCGTTATCTAGC 60.043 40.741 0.00 0.00 36.32 3.42
624 1166 1.681264 ACTTTCTTTCTTGCCCAACCG 59.319 47.619 0.00 0.00 0.00 4.44
662 1297 4.161333 GGTTTTCATGTTCAGATTCAGCG 58.839 43.478 0.00 0.00 0.00 5.18
668 1303 3.057969 TGTTCAGATTCAGCGATTGGT 57.942 42.857 0.00 0.00 0.00 3.67
678 1313 6.703607 AGATTCAGCGATTGGTAGTAATTCTG 59.296 38.462 0.00 0.00 0.00 3.02
688 1323 5.312895 TGGTAGTAATTCTGCTTGCAGAAA 58.687 37.500 32.56 19.74 43.44 2.52
691 1326 5.972107 AGTAATTCTGCTTGCAGAAATGT 57.028 34.783 32.56 24.17 43.44 2.71
699 1334 1.710249 CTTGCAGAAATGTTTGCGTCG 59.290 47.619 0.00 0.00 43.13 5.12
714 1349 2.096335 TGCGTCGATTCTAGCTCGTTTA 59.904 45.455 12.38 0.00 37.40 2.01
717 1352 4.908156 GCGTCGATTCTAGCTCGTTTATTA 59.092 41.667 12.38 0.00 37.40 0.98
764 1875 7.330262 AGTTTAATTTAATGATGTTGGCCTGG 58.670 34.615 3.32 0.00 0.00 4.45
772 1885 2.281484 GTTGGCCTGGAGCGTCAA 60.281 61.111 3.32 0.00 45.17 3.18
865 1994 6.751888 GCTTATGAAGAACACACAAGTTTTGT 59.248 34.615 0.00 0.00 46.75 2.83
937 2085 0.879839 TGTGTGTCGCCAGTGTGATG 60.880 55.000 0.00 0.00 32.72 3.07
938 2086 0.599991 GTGTGTCGCCAGTGTGATGA 60.600 55.000 0.00 0.00 32.72 2.92
939 2087 0.321346 TGTGTCGCCAGTGTGATGAT 59.679 50.000 0.00 0.00 32.72 2.45
940 2088 0.723414 GTGTCGCCAGTGTGATGATG 59.277 55.000 0.00 0.00 32.72 3.07
1033 2193 7.858052 GTTGTTTTCTCAACCTTGATGTATG 57.142 36.000 0.00 0.00 40.97 2.39
1198 2364 0.972471 GGGGAATCAAAGGGGTGCTG 60.972 60.000 0.00 0.00 0.00 4.41
1225 2391 0.257328 TGGTTCTGGTCTTTGCACCA 59.743 50.000 0.00 0.00 44.69 4.17
1486 2652 3.662186 CGCACCAAAAATAACGTCAGTTC 59.338 43.478 0.00 0.00 41.49 3.01
1641 2808 4.724074 TTGCCAAGGAATCAATCATCAC 57.276 40.909 0.00 0.00 0.00 3.06
1743 2920 3.449918 TCCAGGTGATGTGGTCTATGAA 58.550 45.455 0.00 0.00 36.37 2.57
2148 3328 2.435372 TCACACAGCAGGGTTTTCTT 57.565 45.000 0.00 0.00 0.00 2.52
2473 3654 3.202906 GTTGCCAAGTCAGTTCACTACA 58.797 45.455 0.00 0.00 0.00 2.74
2584 3768 3.058293 TGCTGAAGCCATTAAGTTGTTCG 60.058 43.478 0.00 0.00 41.18 3.95
2648 3836 7.327214 AGATTCACTTGTCTGGACTTTCTATC 58.673 38.462 2.38 0.00 0.00 2.08
2848 4343 5.472137 TGCCTGTTTGGTAGTATTGTTTCTC 59.528 40.000 0.00 0.00 38.35 2.87
2849 4344 5.705905 GCCTGTTTGGTAGTATTGTTTCTCT 59.294 40.000 0.00 0.00 38.35 3.10
2851 4346 7.389607 GCCTGTTTGGTAGTATTGTTTCTCTAA 59.610 37.037 0.00 0.00 38.35 2.10
2852 4347 8.936864 CCTGTTTGGTAGTATTGTTTCTCTAAG 58.063 37.037 0.00 0.00 0.00 2.18
2901 4403 6.207417 CGCAGGGGATTTTGAAGACATATATT 59.793 38.462 0.00 0.00 0.00 1.28
2924 4426 2.557924 CTGCCTGCTATTTTTGTGTGGA 59.442 45.455 0.00 0.00 0.00 4.02
2976 4530 3.569277 TCAATGTTTCACATGGACCTGTG 59.431 43.478 14.48 14.48 46.34 3.66
3095 4760 9.822185 AGCATAATTTGGATTTTTAGATTCCAC 57.178 29.630 0.00 0.00 37.48 4.02
3202 4881 7.693951 GTGTGCTAATTACATGCTTGAAACTAG 59.306 37.037 6.60 0.00 0.00 2.57
3214 4893 1.423541 TGAAACTAGAAGGGGCTTGCA 59.576 47.619 0.00 0.00 0.00 4.08
3225 4904 3.444029 AGGGGCTTGCATTTCTGTTTAT 58.556 40.909 0.00 0.00 0.00 1.40
3226 4905 4.609301 AGGGGCTTGCATTTCTGTTTATA 58.391 39.130 0.00 0.00 0.00 0.98
3230 4909 5.105351 GGGCTTGCATTTCTGTTTATACCTT 60.105 40.000 0.00 0.00 0.00 3.50
3522 7269 2.552367 AGGCTAAAGGTCCTACTTGCT 58.448 47.619 0.00 0.00 0.00 3.91
3523 7270 2.502130 AGGCTAAAGGTCCTACTTGCTC 59.498 50.000 0.00 0.00 0.00 4.26
3524 7271 2.236395 GGCTAAAGGTCCTACTTGCTCA 59.764 50.000 0.00 0.00 0.00 4.26
3525 7272 3.263261 GCTAAAGGTCCTACTTGCTCAC 58.737 50.000 0.00 0.00 0.00 3.51
3526 7273 3.306780 GCTAAAGGTCCTACTTGCTCACA 60.307 47.826 0.00 0.00 0.00 3.58
3527 7274 4.624125 GCTAAAGGTCCTACTTGCTCACAT 60.624 45.833 0.00 0.00 0.00 3.21
3528 7275 3.340814 AAGGTCCTACTTGCTCACATG 57.659 47.619 0.00 0.00 0.00 3.21
3529 7276 2.540383 AGGTCCTACTTGCTCACATGA 58.460 47.619 0.00 0.00 0.00 3.07
3530 7277 2.906389 AGGTCCTACTTGCTCACATGAA 59.094 45.455 0.00 0.00 0.00 2.57
3531 7278 3.003480 GGTCCTACTTGCTCACATGAAC 58.997 50.000 0.00 0.00 0.00 3.18
3532 7279 3.307059 GGTCCTACTTGCTCACATGAACT 60.307 47.826 0.00 0.00 0.00 3.01
3533 7280 4.319177 GTCCTACTTGCTCACATGAACTT 58.681 43.478 0.00 0.00 0.00 2.66
3534 7281 4.757149 GTCCTACTTGCTCACATGAACTTT 59.243 41.667 0.00 0.00 0.00 2.66
3535 7282 5.239525 GTCCTACTTGCTCACATGAACTTTT 59.760 40.000 0.00 0.00 0.00 2.27
3536 7283 5.827797 TCCTACTTGCTCACATGAACTTTTT 59.172 36.000 0.00 0.00 0.00 1.94
3563 7310 7.980742 AAACTGTGAATAGTTTTTCCGAAAC 57.019 32.000 0.00 0.00 45.85 2.78
3564 7311 6.068473 ACTGTGAATAGTTTTTCCGAAACC 57.932 37.500 0.00 0.00 0.00 3.27
3566 7313 4.023878 TGTGAATAGTTTTTCCGAAACCCG 60.024 41.667 0.00 0.00 38.18 5.28
3574 7321 2.835580 TTCCGAAACCCGTGAACATA 57.164 45.000 0.00 0.00 36.31 2.29
3577 7429 3.677190 TCCGAAACCCGTGAACATAATT 58.323 40.909 0.00 0.00 36.31 1.40
3632 7484 0.831711 TTTTGAAGGGGAGCCTTGGC 60.832 55.000 2.97 2.97 0.00 4.52
3633 7485 3.567579 TTGAAGGGGAGCCTTGGCG 62.568 63.158 5.95 0.00 0.00 5.69
3641 7493 3.605749 GAGCCTTGGCGCAGTGGTA 62.606 63.158 10.83 0.00 0.00 3.25
3642 7494 2.671619 GCCTTGGCGCAGTGGTAA 60.672 61.111 10.83 0.00 0.00 2.85
3643 7495 2.265182 GCCTTGGCGCAGTGGTAAA 61.265 57.895 10.83 0.00 0.00 2.01
3645 7497 1.210155 CTTGGCGCAGTGGTAAAGC 59.790 57.895 10.83 0.00 0.00 3.51
3646 7498 1.228124 TTGGCGCAGTGGTAAAGCT 60.228 52.632 10.83 0.00 0.00 3.74
3647 7499 1.514678 TTGGCGCAGTGGTAAAGCTG 61.515 55.000 10.83 0.00 35.93 4.24
3653 7505 0.607489 CAGTGGTAAAGCTGCTGCCT 60.607 55.000 12.44 2.45 40.80 4.75
3655 7507 0.242017 GTGGTAAAGCTGCTGCCTTG 59.758 55.000 12.44 0.00 40.80 3.61
3657 7509 0.242017 GGTAAAGCTGCTGCCTTGTG 59.758 55.000 12.44 0.00 40.80 3.33
3660 9610 1.458639 AAAGCTGCTGCCTTGTGACC 61.459 55.000 12.44 0.00 40.80 4.02
3661 9611 2.595463 GCTGCTGCCTTGTGACCA 60.595 61.111 3.85 0.00 0.00 4.02
3665 9615 0.607217 TGCTGCCTTGTGACCATGAG 60.607 55.000 0.00 0.00 0.00 2.90
3666 9616 1.310933 GCTGCCTTGTGACCATGAGG 61.311 60.000 0.00 0.00 42.21 3.86
3681 9631 2.859165 TGAGGTCATGGGTTCAAGTC 57.141 50.000 0.00 0.00 0.00 3.01
3685 9635 1.614317 GGTCATGGGTTCAAGTCCTGG 60.614 57.143 0.00 0.00 0.00 4.45
3686 9636 1.351017 GTCATGGGTTCAAGTCCTGGA 59.649 52.381 0.00 0.00 0.00 3.86
3705 9655 4.985538 TGGAAACAGCCTCTTACAGAAAT 58.014 39.130 0.00 0.00 35.01 2.17
3706 9656 4.761739 TGGAAACAGCCTCTTACAGAAATG 59.238 41.667 0.00 0.00 35.01 2.32
3707 9657 4.762251 GGAAACAGCCTCTTACAGAAATGT 59.238 41.667 0.00 0.00 0.00 2.71
3708 9658 5.938125 GGAAACAGCCTCTTACAGAAATGTA 59.062 40.000 0.00 0.00 0.00 2.29
3709 9659 6.092807 GGAAACAGCCTCTTACAGAAATGTAG 59.907 42.308 0.00 0.00 0.00 2.74
3710 9660 5.091261 ACAGCCTCTTACAGAAATGTAGG 57.909 43.478 0.00 0.00 0.00 3.18
3711 9661 4.080863 ACAGCCTCTTACAGAAATGTAGGG 60.081 45.833 0.00 0.66 0.00 3.53
3713 9663 4.783227 AGCCTCTTACAGAAATGTAGGGAA 59.217 41.667 0.00 0.00 0.00 3.97
3714 9664 5.250774 AGCCTCTTACAGAAATGTAGGGAAA 59.749 40.000 0.00 0.00 0.00 3.13
3716 9666 6.116126 CCTCTTACAGAAATGTAGGGAAAGG 58.884 44.000 0.00 0.00 0.00 3.11
3718 9668 5.250774 TCTTACAGAAATGTAGGGAAAGGCT 59.749 40.000 0.00 0.00 0.00 4.58
3719 9669 3.690460 ACAGAAATGTAGGGAAAGGCTG 58.310 45.455 0.00 0.00 0.00 4.85
3720 9670 2.424956 CAGAAATGTAGGGAAAGGCTGC 59.575 50.000 0.00 0.00 0.00 5.25
3721 9671 2.041620 AGAAATGTAGGGAAAGGCTGCA 59.958 45.455 0.50 0.00 0.00 4.41
3722 9672 2.834638 AATGTAGGGAAAGGCTGCAT 57.165 45.000 0.50 0.00 0.00 3.96
3723 9673 3.951563 AATGTAGGGAAAGGCTGCATA 57.048 42.857 0.50 0.00 0.00 3.14
3724 9674 2.710096 TGTAGGGAAAGGCTGCATAC 57.290 50.000 0.50 0.00 33.66 2.39
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 0.320421 ACGCACGCACAGAAATACCT 60.320 50.000 0.00 0.00 0.00 3.08
4 5 1.635844 CCTACGCACGCACAGAAATA 58.364 50.000 0.00 0.00 0.00 1.40
5 6 1.635663 GCCTACGCACGCACAGAAAT 61.636 55.000 0.00 0.00 34.03 2.17
6 7 2.314647 GCCTACGCACGCACAGAAA 61.315 57.895 0.00 0.00 34.03 2.52
7 8 2.736995 GCCTACGCACGCACAGAA 60.737 61.111 0.00 0.00 34.03 3.02
8 9 4.735132 GGCCTACGCACGCACAGA 62.735 66.667 0.00 0.00 36.38 3.41
15 16 0.935196 CTATTTTCGGGCCTACGCAC 59.065 55.000 0.84 0.00 36.38 5.34
16 17 0.812412 GCTATTTTCGGGCCTACGCA 60.812 55.000 0.84 0.00 36.38 5.24
17 18 1.828331 CGCTATTTTCGGGCCTACGC 61.828 60.000 0.84 0.00 0.00 4.42
18 19 0.529119 ACGCTATTTTCGGGCCTACG 60.529 55.000 0.84 0.00 0.00 3.51
19 20 0.935196 CACGCTATTTTCGGGCCTAC 59.065 55.000 0.84 0.00 0.00 3.18
20 21 3.372795 CACGCTATTTTCGGGCCTA 57.627 52.632 0.84 0.00 0.00 3.93
21 22 4.218722 CACGCTATTTTCGGGCCT 57.781 55.556 0.84 0.00 0.00 5.19
24 25 1.347221 GACGCACGCTATTTTCGGG 59.653 57.895 0.00 0.00 0.00 5.14
25 26 1.013755 CGACGCACGCTATTTTCGG 60.014 57.895 0.00 0.00 34.51 4.30
26 27 1.013755 CCGACGCACGCTATTTTCG 60.014 57.895 0.00 0.00 41.07 3.46
27 28 1.296649 GCCGACGCACGCTATTTTC 60.297 57.895 0.00 0.00 41.07 2.29
28 29 2.746803 GGCCGACGCACGCTATTTT 61.747 57.895 0.00 0.00 41.07 1.82
29 30 3.192922 GGCCGACGCACGCTATTT 61.193 61.111 0.00 0.00 41.07 1.40
40 41 4.179579 GAATTGCTGCGGGCCGAC 62.180 66.667 33.44 21.47 40.92 4.79
48 49 4.481112 CACGCCCGGAATTGCTGC 62.481 66.667 0.73 0.00 0.00 5.25
49 50 3.814268 CCACGCCCGGAATTGCTG 61.814 66.667 0.73 0.00 0.00 4.41
52 53 2.360600 TTCCCACGCCCGGAATTG 60.361 61.111 0.73 0.00 34.40 2.32
53 54 2.045340 CTTCCCACGCCCGGAATT 60.045 61.111 0.73 0.00 38.69 2.17
54 55 4.796495 GCTTCCCACGCCCGGAAT 62.796 66.667 0.73 0.00 38.69 3.01
66 67 4.838152 TCGCTCGCATGGGCTTCC 62.838 66.667 4.59 0.00 38.10 3.46
67 68 3.267860 CTCGCTCGCATGGGCTTC 61.268 66.667 4.59 0.00 38.10 3.86
68 69 4.845580 CCTCGCTCGCATGGGCTT 62.846 66.667 4.59 0.00 38.10 4.35
96 97 4.759205 AATGTGGGGCGGGCCTTC 62.759 66.667 20.88 13.56 36.10 3.46
97 98 4.759205 GAATGTGGGGCGGGCCTT 62.759 66.667 20.88 6.53 36.10 4.35
99 100 4.839706 ATGAATGTGGGGCGGGCC 62.840 66.667 13.01 13.01 0.00 5.80
100 101 3.219198 GATGAATGTGGGGCGGGC 61.219 66.667 0.00 0.00 0.00 6.13
101 102 1.076777 AAGATGAATGTGGGGCGGG 60.077 57.895 0.00 0.00 0.00 6.13
102 103 1.103398 GGAAGATGAATGTGGGGCGG 61.103 60.000 0.00 0.00 0.00 6.13
103 104 0.107017 AGGAAGATGAATGTGGGGCG 60.107 55.000 0.00 0.00 0.00 6.13
104 105 1.685148 GAGGAAGATGAATGTGGGGC 58.315 55.000 0.00 0.00 0.00 5.80
105 106 1.475751 CGGAGGAAGATGAATGTGGGG 60.476 57.143 0.00 0.00 0.00 4.96
106 107 1.959042 CGGAGGAAGATGAATGTGGG 58.041 55.000 0.00 0.00 0.00 4.61
107 108 1.134280 AGCGGAGGAAGATGAATGTGG 60.134 52.381 0.00 0.00 0.00 4.17
108 109 2.208431 GAGCGGAGGAAGATGAATGTG 58.792 52.381 0.00 0.00 0.00 3.21
109 110 1.202463 CGAGCGGAGGAAGATGAATGT 60.202 52.381 0.00 0.00 0.00 2.71
110 111 1.495878 CGAGCGGAGGAAGATGAATG 58.504 55.000 0.00 0.00 0.00 2.67
111 112 0.249657 GCGAGCGGAGGAAGATGAAT 60.250 55.000 0.00 0.00 0.00 2.57
112 113 1.141881 GCGAGCGGAGGAAGATGAA 59.858 57.895 0.00 0.00 0.00 2.57
113 114 2.808315 GCGAGCGGAGGAAGATGA 59.192 61.111 0.00 0.00 0.00 2.92
114 115 2.656651 CGCGAGCGGAGGAAGATG 60.657 66.667 9.90 0.00 35.56 2.90
115 116 2.829003 TCGCGAGCGGAGGAAGAT 60.829 61.111 17.68 0.00 40.25 2.40
116 117 3.509757 CTCGCGAGCGGAGGAAGA 61.510 66.667 25.07 0.00 40.25 2.87
117 118 3.509757 TCTCGCGAGCGGAGGAAG 61.510 66.667 30.97 5.49 40.25 3.46
118 119 2.864378 TAGTCTCGCGAGCGGAGGAA 62.864 60.000 30.97 9.43 40.25 3.36
119 120 3.381333 TAGTCTCGCGAGCGGAGGA 62.381 63.158 30.97 10.51 40.25 3.71
120 121 2.895865 TAGTCTCGCGAGCGGAGG 60.896 66.667 30.97 7.94 40.25 4.30
121 122 0.875040 TAGTAGTCTCGCGAGCGGAG 60.875 60.000 30.97 8.76 40.25 4.63
122 123 0.875040 CTAGTAGTCTCGCGAGCGGA 60.875 60.000 30.97 12.15 40.25 5.54
123 124 1.565591 CTAGTAGTCTCGCGAGCGG 59.434 63.158 30.97 9.60 40.25 5.52
124 125 1.565591 CCTAGTAGTCTCGCGAGCG 59.434 63.158 30.97 10.43 41.35 5.03
125 126 0.814812 ACCCTAGTAGTCTCGCGAGC 60.815 60.000 30.97 24.09 0.00 5.03
126 127 1.666054 AACCCTAGTAGTCTCGCGAG 58.334 55.000 30.03 30.03 0.00 5.03
127 128 2.119801 AAACCCTAGTAGTCTCGCGA 57.880 50.000 9.26 9.26 0.00 5.87
128 129 2.941720 AGTAAACCCTAGTAGTCTCGCG 59.058 50.000 0.00 0.00 0.00 5.87
129 130 4.878397 TGTAGTAAACCCTAGTAGTCTCGC 59.122 45.833 0.00 0.00 0.00 5.03
130 131 6.112058 AGTGTAGTAAACCCTAGTAGTCTCG 58.888 44.000 0.00 0.00 0.00 4.04
131 132 9.271828 GATAGTGTAGTAAACCCTAGTAGTCTC 57.728 40.741 0.00 0.00 0.00 3.36
132 133 7.930865 CGATAGTGTAGTAAACCCTAGTAGTCT 59.069 40.741 0.00 0.00 0.00 3.24
133 134 8.082334 CGATAGTGTAGTAAACCCTAGTAGTC 57.918 42.308 0.00 0.00 0.00 2.59
153 154 1.803334 CGGAGGAGAGGAGACGATAG 58.197 60.000 0.00 0.00 46.19 2.08
154 155 0.250381 GCGGAGGAGAGGAGACGATA 60.250 60.000 0.00 0.00 0.00 2.92
155 156 1.527380 GCGGAGGAGAGGAGACGAT 60.527 63.158 0.00 0.00 0.00 3.73
156 157 2.124653 GCGGAGGAGAGGAGACGA 60.125 66.667 0.00 0.00 0.00 4.20
157 158 3.578272 CGCGGAGGAGAGGAGACG 61.578 72.222 0.00 0.00 0.00 4.18
158 159 3.213402 CCGCGGAGGAGAGGAGAC 61.213 72.222 24.07 0.00 45.00 3.36
177 178 2.026522 CTCGACCTCGGAGATGTCC 58.973 63.158 6.58 0.00 40.57 4.02
178 179 1.357334 GCTCGACCTCGGAGATGTC 59.643 63.158 6.58 5.51 40.57 3.06
179 180 2.473760 CGCTCGACCTCGGAGATGT 61.474 63.158 6.58 0.00 38.30 3.06
180 181 2.329690 CGCTCGACCTCGGAGATG 59.670 66.667 6.58 0.00 40.29 2.90
199 200 4.977126 GACCGATCGTAGCCGCCG 62.977 72.222 15.09 0.00 0.00 6.46
200 201 4.977126 CGACCGATCGTAGCCGCC 62.977 72.222 15.09 0.00 43.66 6.13
209 210 1.590932 TACCTAGAGCACGACCGATC 58.409 55.000 0.00 0.00 0.00 3.69
210 211 1.948145 CTTACCTAGAGCACGACCGAT 59.052 52.381 0.00 0.00 0.00 4.18
211 212 1.376543 CTTACCTAGAGCACGACCGA 58.623 55.000 0.00 0.00 0.00 4.69
212 213 0.381089 CCTTACCTAGAGCACGACCG 59.619 60.000 0.00 0.00 0.00 4.79
213 214 0.102663 GCCTTACCTAGAGCACGACC 59.897 60.000 0.00 0.00 0.00 4.79
214 215 0.815734 TGCCTTACCTAGAGCACGAC 59.184 55.000 0.00 0.00 0.00 4.34
215 216 0.815734 GTGCCTTACCTAGAGCACGA 59.184 55.000 0.00 0.00 39.52 4.35
216 217 0.179108 GGTGCCTTACCTAGAGCACG 60.179 60.000 7.78 0.00 46.51 5.34
217 218 3.762674 GGTGCCTTACCTAGAGCAC 57.237 57.895 5.44 5.44 46.51 4.40
275 281 0.389948 AGGAGAACCATCGCACGAAC 60.390 55.000 0.00 0.00 38.94 3.95
279 293 0.744771 GGGAAGGAGAACCATCGCAC 60.745 60.000 0.00 0.00 43.23 5.34
281 295 1.153147 GGGGAAGGAGAACCATCGC 60.153 63.158 0.00 0.00 43.09 4.58
283 297 1.132500 ATCGGGGAAGGAGAACCATC 58.868 55.000 0.00 0.00 38.94 3.51
284 298 1.490910 GAATCGGGGAAGGAGAACCAT 59.509 52.381 0.00 0.00 38.94 3.55
287 301 0.822164 TCGAATCGGGGAAGGAGAAC 59.178 55.000 1.76 0.00 0.00 3.01
288 302 0.822164 GTCGAATCGGGGAAGGAGAA 59.178 55.000 1.76 0.00 0.00 2.87
290 304 0.753262 ATGTCGAATCGGGGAAGGAG 59.247 55.000 1.76 0.00 0.00 3.69
291 305 0.464036 CATGTCGAATCGGGGAAGGA 59.536 55.000 1.76 0.00 0.00 3.36
292 306 0.178068 ACATGTCGAATCGGGGAAGG 59.822 55.000 1.76 0.00 0.00 3.46
293 307 2.470821 GTACATGTCGAATCGGGGAAG 58.529 52.381 0.00 0.00 0.00 3.46
334 353 5.920273 GTCAATCAAGAAAGCGAATCCAAAA 59.080 36.000 0.00 0.00 0.00 2.44
335 354 5.009510 TGTCAATCAAGAAAGCGAATCCAAA 59.990 36.000 0.00 0.00 0.00 3.28
336 355 4.518590 TGTCAATCAAGAAAGCGAATCCAA 59.481 37.500 0.00 0.00 0.00 3.53
338 357 4.437930 CCTGTCAATCAAGAAAGCGAATCC 60.438 45.833 0.00 0.00 0.00 3.01
339 358 4.437930 CCCTGTCAATCAAGAAAGCGAATC 60.438 45.833 0.00 0.00 0.00 2.52
340 359 3.441572 CCCTGTCAATCAAGAAAGCGAAT 59.558 43.478 0.00 0.00 0.00 3.34
343 362 1.470098 CCCCTGTCAATCAAGAAAGCG 59.530 52.381 0.00 0.00 0.00 4.68
344 363 2.795329 TCCCCTGTCAATCAAGAAAGC 58.205 47.619 0.00 0.00 0.00 3.51
345 364 4.021981 GGTTTCCCCTGTCAATCAAGAAAG 60.022 45.833 0.00 0.00 0.00 2.62
346 365 3.895041 GGTTTCCCCTGTCAATCAAGAAA 59.105 43.478 0.00 0.00 0.00 2.52
397 420 9.303537 TGGCTTTACAACATTAACAAACTTTAC 57.696 29.630 0.00 0.00 0.00 2.01
433 456 8.504812 AGCTTACTTTCTAGTACTACTACCAC 57.495 38.462 0.00 0.00 36.61 4.16
434 457 9.525826 AAAGCTTACTTTCTAGTACTACTACCA 57.474 33.333 0.00 0.00 42.59 3.25
462 488 5.292101 GCTAGTACTCGATCAGTTGCAAATT 59.708 40.000 0.00 0.00 36.43 1.82
463 489 4.806247 GCTAGTACTCGATCAGTTGCAAAT 59.194 41.667 0.00 0.00 36.43 2.32
464 490 4.174009 GCTAGTACTCGATCAGTTGCAAA 58.826 43.478 0.00 0.00 36.43 3.68
465 491 3.428999 GGCTAGTACTCGATCAGTTGCAA 60.429 47.826 0.00 0.00 36.43 4.08
466 492 2.099263 GGCTAGTACTCGATCAGTTGCA 59.901 50.000 0.00 0.00 36.43 4.08
467 493 2.359531 AGGCTAGTACTCGATCAGTTGC 59.640 50.000 0.00 0.00 36.43 4.17
468 494 4.214545 CCTAGGCTAGTACTCGATCAGTTG 59.785 50.000 19.68 0.00 36.43 3.16
470 496 3.244630 CCCTAGGCTAGTACTCGATCAGT 60.245 52.174 19.68 0.00 39.41 3.41
471 497 3.244630 ACCCTAGGCTAGTACTCGATCAG 60.245 52.174 19.68 0.97 0.00 2.90
473 499 3.421919 ACCCTAGGCTAGTACTCGATC 57.578 52.381 19.68 0.00 0.00 3.69
474 500 3.488363 CAACCCTAGGCTAGTACTCGAT 58.512 50.000 19.68 0.00 0.00 3.59
475 501 2.928334 CAACCCTAGGCTAGTACTCGA 58.072 52.381 19.68 0.00 0.00 4.04
476 502 1.337387 GCAACCCTAGGCTAGTACTCG 59.663 57.143 19.68 4.44 0.00 4.18
502 528 2.477525 GCTCAACTAGAAATGCAGCAGC 60.478 50.000 0.00 0.00 42.57 5.25
506 542 7.493743 AATATCAGCTCAACTAGAAATGCAG 57.506 36.000 0.00 0.00 0.00 4.41
507 543 8.424133 TCTAATATCAGCTCAACTAGAAATGCA 58.576 33.333 0.00 0.00 0.00 3.96
524 560 7.836842 TGCTAGATAACGCCAATCTAATATCA 58.163 34.615 0.00 0.00 35.93 2.15
547 583 5.309323 TCACAAGGTGCACTTATTATTGC 57.691 39.130 17.98 0.00 37.29 3.56
548 584 6.913170 AGTTCACAAGGTGCACTTATTATTG 58.087 36.000 17.98 13.63 36.73 1.90
564 1096 1.511850 CACAGCCGATGAGTTCACAA 58.488 50.000 0.00 0.00 0.00 3.33
662 1297 5.814783 CTGCAAGCAGAATTACTACCAATC 58.185 41.667 16.75 0.00 46.30 2.67
678 1313 1.453148 GACGCAAACATTTCTGCAAGC 59.547 47.619 0.00 0.00 38.52 4.01
688 1323 2.860735 GAGCTAGAATCGACGCAAACAT 59.139 45.455 0.00 0.00 0.00 2.71
691 1326 1.135489 ACGAGCTAGAATCGACGCAAA 60.135 47.619 20.52 0.00 42.76 3.68
714 1349 7.857404 AGCTACCACCATGATTACTACTAAT 57.143 36.000 0.00 0.00 0.00 1.73
717 1352 6.374588 ACTAGCTACCACCATGATTACTACT 58.625 40.000 0.00 0.00 0.00 2.57
764 1875 5.997385 TGTTAGGAAGAAAAATTGACGCTC 58.003 37.500 0.00 0.00 0.00 5.03
772 1885 9.793259 TGTGTCTAGATTGTTAGGAAGAAAAAT 57.207 29.630 0.00 0.00 0.00 1.82
824 1949 9.803507 TCTTCATAAGCATGGAGATTGATTTAT 57.196 29.630 0.00 0.00 41.17 1.40
825 1950 9.631257 TTCTTCATAAGCATGGAGATTGATTTA 57.369 29.630 0.00 0.00 44.69 1.40
830 1955 6.094464 TGTGTTCTTCATAAGCATGGAGATTG 59.906 38.462 0.00 0.00 44.69 2.67
865 1994 9.547753 GAAGTTTTAGCATCTTCTGTATCCATA 57.452 33.333 0.00 0.00 35.92 2.74
908 2053 1.415374 GCGACACACACTCATTACGT 58.585 50.000 0.00 0.00 0.00 3.57
921 2069 0.723414 CATCATCACACTGGCGACAC 59.277 55.000 0.00 0.00 35.60 3.67
938 2086 6.013639 TGCATGTGAAGATAGATGGAGATCAT 60.014 38.462 0.00 0.00 39.13 2.45
939 2087 5.306160 TGCATGTGAAGATAGATGGAGATCA 59.694 40.000 0.00 0.00 0.00 2.92
940 2088 5.791666 TGCATGTGAAGATAGATGGAGATC 58.208 41.667 0.00 0.00 0.00 2.75
1029 2189 6.202954 GCTGTACCAATCATCAGGTAACATAC 59.797 42.308 0.00 0.00 41.71 2.39
1033 2193 4.572389 CAGCTGTACCAATCATCAGGTAAC 59.428 45.833 5.25 0.00 41.71 2.50
1198 2364 0.106149 AGACCAGAACCAACACGGAC 59.894 55.000 0.00 0.00 38.63 4.79
1225 2391 3.728845 ACGATGTCAGTGCTTTTGTAGT 58.271 40.909 0.00 0.00 0.00 2.73
1486 2652 1.207593 CTGCAACCGAGAAAAGCCG 59.792 57.895 0.00 0.00 0.00 5.52
1641 2808 4.213482 CCAGAACCAAACTTTAGGAAGTCG 59.787 45.833 0.00 0.00 45.18 4.18
2148 3328 0.321919 GGCAGGACTGAATGAGCACA 60.322 55.000 3.00 0.00 0.00 4.57
2473 3654 2.237392 GGGCATCTGAAGAGTACTTGGT 59.763 50.000 0.00 0.00 36.39 3.67
2504 3685 7.514784 CATCAATAGATGCCAAGACCAATTA 57.485 36.000 0.00 0.00 44.61 1.40
2604 3788 0.752658 TAGGTCGGATGATGCACAGG 59.247 55.000 0.00 0.00 0.00 4.00
2648 3836 2.674796 AGCAGTAAAGGTAGAAGGCG 57.325 50.000 0.00 0.00 0.00 5.52
2848 4343 8.630037 AGTAAAAAGGGTTCACAACATTCTTAG 58.370 33.333 0.00 0.00 0.00 2.18
2849 4344 8.528044 AGTAAAAAGGGTTCACAACATTCTTA 57.472 30.769 0.00 0.00 0.00 2.10
2851 4346 7.255001 CGTAGTAAAAAGGGTTCACAACATTCT 60.255 37.037 0.00 0.00 0.00 2.40
2852 4347 6.854381 CGTAGTAAAAAGGGTTCACAACATTC 59.146 38.462 0.00 0.00 0.00 2.67
2901 4403 3.005684 CCACACAAAAATAGCAGGCAGAA 59.994 43.478 0.00 0.00 0.00 3.02
2924 4426 5.779771 ACCACACTGATCCATACCAAAATTT 59.220 36.000 0.00 0.00 0.00 1.82
2976 4530 1.595093 AAGCATGCCGCCTTTGTACC 61.595 55.000 15.66 0.00 44.04 3.34
3095 4760 5.778161 TGACTACACTGCATTTGTAATCG 57.222 39.130 10.67 3.54 30.04 3.34
3202 4881 1.260544 ACAGAAATGCAAGCCCCTTC 58.739 50.000 0.00 0.00 0.00 3.46
3225 4904 7.620880 AGTACTCATCATACTTTTGCAAGGTA 58.379 34.615 13.92 13.92 33.82 3.08
3226 4905 6.476378 AGTACTCATCATACTTTTGCAAGGT 58.524 36.000 0.00 5.82 33.82 3.50
3230 4909 6.935167 TCTGAGTACTCATCATACTTTTGCA 58.065 36.000 25.35 0.00 39.13 4.08
3442 5132 8.276325 CGTTCTACATATATTTTGGAACAGAGC 58.724 37.037 15.32 0.00 42.39 4.09
3475 7222 7.988599 ACCAAAACGTTCTACATATATTGCCTA 59.011 33.333 0.00 0.00 0.00 3.93
3533 7280 8.865001 CGGAAAAACTATTCACAGTTTCAAAAA 58.135 29.630 2.01 0.00 45.68 1.94
3534 7281 8.244802 TCGGAAAAACTATTCACAGTTTCAAAA 58.755 29.630 2.01 0.00 45.68 2.44
3535 7282 7.763356 TCGGAAAAACTATTCACAGTTTCAAA 58.237 30.769 2.01 0.00 45.68 2.69
3536 7283 7.323049 TCGGAAAAACTATTCACAGTTTCAA 57.677 32.000 2.01 0.00 45.68 2.69
3537 7284 6.928979 TCGGAAAAACTATTCACAGTTTCA 57.071 33.333 2.01 0.00 45.68 2.69
3538 7285 7.166970 GGTTTCGGAAAAACTATTCACAGTTTC 59.833 37.037 4.46 0.00 45.68 2.78
3540 7287 6.460537 GGGTTTCGGAAAAACTATTCACAGTT 60.461 38.462 4.46 0.00 40.49 3.16
3541 7288 5.009310 GGGTTTCGGAAAAACTATTCACAGT 59.991 40.000 4.46 0.00 32.39 3.55
3542 7289 5.458015 GGGTTTCGGAAAAACTATTCACAG 58.542 41.667 4.46 0.00 32.39 3.66
3543 7290 4.023878 CGGGTTTCGGAAAAACTATTCACA 60.024 41.667 4.46 0.00 32.39 3.58
3544 7291 4.023792 ACGGGTTTCGGAAAAACTATTCAC 60.024 41.667 4.46 0.00 44.45 3.18
3545 7292 4.023878 CACGGGTTTCGGAAAAACTATTCA 60.024 41.667 4.46 0.00 44.45 2.57
3546 7293 4.213906 TCACGGGTTTCGGAAAAACTATTC 59.786 41.667 4.46 0.00 44.45 1.75
3549 7296 3.191078 TCACGGGTTTCGGAAAAACTA 57.809 42.857 4.46 0.00 44.45 2.24
3551 7298 2.159407 TGTTCACGGGTTTCGGAAAAAC 60.159 45.455 4.46 5.74 44.45 2.43
3554 7301 1.970092 ATGTTCACGGGTTTCGGAAA 58.030 45.000 0.00 0.00 44.45 3.13
3623 7475 3.605749 TACCACTGCGCCAAGGCTC 62.606 63.158 4.18 1.20 39.32 4.70
3627 7479 1.210155 GCTTTACCACTGCGCCAAG 59.790 57.895 4.18 0.00 0.00 3.61
3628 7480 1.228124 AGCTTTACCACTGCGCCAA 60.228 52.632 4.18 0.00 0.00 4.52
3629 7481 1.965930 CAGCTTTACCACTGCGCCA 60.966 57.895 4.18 0.00 0.00 5.69
3630 7482 2.870372 CAGCTTTACCACTGCGCC 59.130 61.111 4.18 0.00 0.00 6.53
3634 7486 0.607489 AGGCAGCAGCTTTACCACTG 60.607 55.000 0.00 0.00 41.70 3.66
3635 7487 0.111253 AAGGCAGCAGCTTTACCACT 59.889 50.000 0.00 0.00 38.40 4.00
3636 7488 0.242017 CAAGGCAGCAGCTTTACCAC 59.758 55.000 0.00 0.00 38.07 4.16
3638 7490 0.242017 CACAAGGCAGCAGCTTTACC 59.758 55.000 0.00 0.00 38.07 2.85
3639 7491 1.068954 GTCACAAGGCAGCAGCTTTAC 60.069 52.381 0.00 0.00 38.07 2.01
3640 7492 1.238439 GTCACAAGGCAGCAGCTTTA 58.762 50.000 0.00 0.00 38.07 1.85
3641 7493 1.458639 GGTCACAAGGCAGCAGCTTT 61.459 55.000 0.00 0.00 41.17 3.51
3642 7494 1.900498 GGTCACAAGGCAGCAGCTT 60.900 57.895 0.00 0.00 41.70 3.74
3643 7495 2.282040 GGTCACAAGGCAGCAGCT 60.282 61.111 0.00 0.00 41.70 4.24
3645 7497 0.607217 TCATGGTCACAAGGCAGCAG 60.607 55.000 0.00 0.00 0.00 4.24
3646 7498 0.607217 CTCATGGTCACAAGGCAGCA 60.607 55.000 0.00 0.00 0.00 4.41
3647 7499 1.310933 CCTCATGGTCACAAGGCAGC 61.311 60.000 0.00 0.00 0.00 5.25
3648 7500 0.037303 ACCTCATGGTCACAAGGCAG 59.963 55.000 0.00 0.00 44.78 4.85
3649 7501 2.154139 ACCTCATGGTCACAAGGCA 58.846 52.632 0.00 0.00 44.78 4.75
3661 9611 2.025887 GGACTTGAACCCATGACCTCAT 60.026 50.000 0.00 0.00 36.96 2.90
3665 9615 1.614317 CCAGGACTTGAACCCATGACC 60.614 57.143 0.00 0.00 34.29 4.02
3666 9616 1.351017 TCCAGGACTTGAACCCATGAC 59.649 52.381 0.00 0.00 0.00 3.06
3667 9617 1.741028 TCCAGGACTTGAACCCATGA 58.259 50.000 0.00 0.00 0.00 3.07
3670 9620 1.566703 TGTTTCCAGGACTTGAACCCA 59.433 47.619 0.00 0.00 0.00 4.51
3672 9622 1.609072 GCTGTTTCCAGGACTTGAACC 59.391 52.381 0.00 0.00 39.22 3.62
3673 9623 1.609072 GGCTGTTTCCAGGACTTGAAC 59.391 52.381 0.00 0.00 39.22 3.18
3674 9624 1.494721 AGGCTGTTTCCAGGACTTGAA 59.505 47.619 0.00 0.00 39.22 2.69
3678 9628 1.439543 AAGAGGCTGTTTCCAGGACT 58.560 50.000 0.00 0.00 39.22 3.85
3679 9629 2.038557 TGTAAGAGGCTGTTTCCAGGAC 59.961 50.000 0.90 0.00 39.22 3.85
3681 9631 2.303022 TCTGTAAGAGGCTGTTTCCAGG 59.697 50.000 17.71 5.83 38.67 4.45
3695 9645 5.355350 CAGCCTTTCCCTACATTTCTGTAAG 59.645 44.000 0.00 0.00 37.41 2.34
3697 9647 4.843728 CAGCCTTTCCCTACATTTCTGTA 58.156 43.478 0.00 0.00 36.79 2.74
3698 9648 3.690460 CAGCCTTTCCCTACATTTCTGT 58.310 45.455 0.00 0.00 39.49 3.41
3699 9649 2.424956 GCAGCCTTTCCCTACATTTCTG 59.575 50.000 0.00 0.00 0.00 3.02
3700 9650 2.041620 TGCAGCCTTTCCCTACATTTCT 59.958 45.455 0.00 0.00 0.00 2.52
3701 9651 2.446435 TGCAGCCTTTCCCTACATTTC 58.554 47.619 0.00 0.00 0.00 2.17
3703 9653 2.834638 ATGCAGCCTTTCCCTACATT 57.165 45.000 0.00 0.00 0.00 2.71
3705 9655 2.710096 GTATGCAGCCTTTCCCTACA 57.290 50.000 0.00 0.00 0.00 2.74


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

AutoCloner maintained by Alex Coulton.