Multiple sequence alignment - TraesCS2A01G316700

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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 TraesCS2A01G316700 chr2A 100.000 3955 0 0 1 3955 542554884 542550930 0.000000e+00 7304.0
1 TraesCS2A01G316700 chr2B 92.658 1580 78 19 1933 3493 478189488 478187928 0.000000e+00 2241.0
2 TraesCS2A01G316700 chr2B 90.379 738 30 13 989 1714 478190514 478189806 0.000000e+00 931.0
3 TraesCS2A01G316700 chr2B 95.183 436 21 0 3512 3947 478185722 478185287 0.000000e+00 689.0
4 TraesCS2A01G316700 chr2B 84.600 487 38 17 416 870 478191041 478190560 2.170000e-122 449.0
5 TraesCS2A01G316700 chr2B 85.714 315 30 7 3120 3431 478186087 478185785 6.380000e-83 318.0
6 TraesCS2A01G316700 chr2B 86.909 275 30 5 458 731 90713727 90713458 1.790000e-78 303.0
7 TraesCS2A01G316700 chr2B 99.355 155 1 0 1718 1872 478189640 478189486 8.370000e-72 281.0
8 TraesCS2A01G316700 chr2B 89.630 135 6 5 1 135 478191256 478191130 8.790000e-37 165.0
9 TraesCS2A01G316700 chr2B 80.804 224 20 7 2857 3057 478187919 478187696 1.900000e-33 154.0
10 TraesCS2A01G316700 chr2B 89.189 111 11 1 139 248 723434349 723434239 1.920000e-28 137.0
11 TraesCS2A01G316700 chr2B 92.188 64 3 2 1882 1944 774081664 774081602 5.440000e-14 89.8
12 TraesCS2A01G316700 chr2B 84.146 82 11 2 1882 1961 790112973 790113054 1.180000e-10 78.7
13 TraesCS2A01G316700 chr2D 90.551 1524 101 17 2450 3955 404122476 404120978 0.000000e+00 1977.0
14 TraesCS2A01G316700 chr2D 89.138 580 24 21 892 1454 404124259 404123702 0.000000e+00 686.0
15 TraesCS2A01G316700 chr2D 89.896 386 29 4 2051 2427 404122926 404122542 4.590000e-134 488.0
16 TraesCS2A01G316700 chr2D 91.468 293 22 3 433 723 404124703 404124412 2.210000e-107 399.0
17 TraesCS2A01G316700 chr2D 87.681 276 27 6 458 732 57331190 57330921 8.250000e-82 315.0
18 TraesCS2A01G316700 chr2D 86.594 276 29 7 458 732 57273032 57272764 8.310000e-77 298.0
19 TraesCS2A01G316700 chr2D 87.398 246 20 5 1626 1864 404123318 404123077 5.040000e-69 272.0
20 TraesCS2A01G316700 chr2D 89.781 137 6 5 3 136 404124954 404124823 6.800000e-38 169.0
21 TraesCS2A01G316700 chr2D 93.617 94 6 0 1974 2067 404123042 404122949 1.480000e-29 141.0
22 TraesCS2A01G316700 chr2D 89.189 111 11 1 139 248 155730889 155730999 1.920000e-28 137.0
23 TraesCS2A01G316700 chr2D 93.902 82 4 1 790 870 404124327 404124246 5.370000e-24 122.0
24 TraesCS2A01G316700 chr6D 86.940 268 26 8 467 729 434444155 434443892 3.870000e-75 292.0
25 TraesCS2A01G316700 chr6D 87.698 252 28 3 482 732 429353488 429353737 1.390000e-74 291.0
26 TraesCS2A01G316700 chr6D 86.296 270 28 8 467 731 434450350 434450085 6.470000e-73 285.0
27 TraesCS2A01G316700 chr6D 89.744 117 11 1 133 248 379335480 379335364 8.850000e-32 148.0
28 TraesCS2A01G316700 chr6A 85.821 268 31 7 468 731 581743971 581743707 1.080000e-70 278.0
29 TraesCS2A01G316700 chr1D 91.892 111 8 1 139 248 469813517 469813407 1.900000e-33 154.0
30 TraesCS2A01G316700 chr1D 96.429 56 2 0 1882 1937 463576559 463576614 4.210000e-15 93.5
31 TraesCS2A01G316700 chr3D 90.517 116 10 1 134 248 65452441 65452556 6.850000e-33 152.0
32 TraesCS2A01G316700 chr7D 88.000 125 9 2 139 258 461389754 461389631 4.120000e-30 143.0
33 TraesCS2A01G316700 chr5D 90.741 108 8 2 137 243 582637 582531 4.120000e-30 143.0
34 TraesCS2A01G316700 chr5D 96.429 56 2 0 1882 1937 329763613 329763668 4.210000e-15 93.5
35 TraesCS2A01G316700 chr7B 89.286 112 11 1 138 248 747429216 747429105 5.330000e-29 139.0
36 TraesCS2A01G316700 chr7B 92.424 66 5 0 1882 1947 694802535 694802470 1.170000e-15 95.3
37 TraesCS2A01G316700 chr7B 90.909 66 6 0 1882 1947 696616079 696616014 5.440000e-14 89.8
38 TraesCS2A01G316700 chr3A 84.848 132 17 3 138 267 106611179 106611049 3.210000e-26 130.0
39 TraesCS2A01G316700 chr4B 98.148 54 1 0 1882 1935 237904366 237904419 1.170000e-15 95.3
40 TraesCS2A01G316700 chr5B 95.000 60 2 1 1882 1941 609840345 609840403 4.210000e-15 93.5
41 TraesCS2A01G316700 chr5B 100.000 28 0 0 990 1017 466630023 466630050 7.000000e-03 52.8
42 TraesCS2A01G316700 chr1B 90.625 64 6 0 1882 1945 535908053 535908116 7.040000e-13 86.1


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 TraesCS2A01G316700 chr2A 542550930 542554884 3954 True 7304.00 7304 100.000000 1 3955 1 chr2A.!!$R1 3954
1 TraesCS2A01G316700 chr2B 478185287 478191256 5969 True 653.50 2241 89.790375 1 3947 8 chr2B.!!$R4 3946
2 TraesCS2A01G316700 chr2D 404120978 404124954 3976 True 531.75 1977 90.718875 3 3955 8 chr2D.!!$R3 3952

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
153 157 0.033796 TGAATACTCCCTCCGTCCGT 60.034 55.0 0.00 0.0 0.0 4.69 F
603 623 0.106167 ATGCGGACCACTAGCCTAGA 60.106 55.0 5.58 0.0 0.0 2.43 F
983 1074 0.413832 AGCAAGTGAGGGGAGGTAGA 59.586 55.0 0.00 0.0 0.0 2.59 F
2245 2845 0.535335 TACTGCCCTTGATCGGTGTC 59.465 55.0 0.00 0.0 0.0 3.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1393 1498 2.221055 GTGGTCAATGACACGAACAGTC 59.779 50.000 15.86 0.0 33.68 3.51 R
1539 1809 2.411069 CACTCACTGATCTTGCTTGACG 59.589 50.000 0.00 0.0 0.00 4.35 R
2866 3514 3.129113 TGCCATGAACACATAACTGATGC 59.871 43.478 0.00 0.0 39.39 3.91 R
3684 6539 0.107752 GCTCAAGCTGGAGAAGGAGG 60.108 60.000 22.98 0.0 37.05 4.30 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
76 80 6.003950 TCCTGAATGCTACTTTTGCTTAGTT 58.996 36.000 0.00 0.00 0.00 2.24
87 91 7.640597 ACTTTTGCTTAGTTTTTGTAGGAGT 57.359 32.000 0.00 0.00 0.00 3.85
88 92 8.741603 ACTTTTGCTTAGTTTTTGTAGGAGTA 57.258 30.769 0.00 0.00 0.00 2.59
89 93 8.837389 ACTTTTGCTTAGTTTTTGTAGGAGTAG 58.163 33.333 0.00 0.00 0.00 2.57
90 94 8.967664 TTTTGCTTAGTTTTTGTAGGAGTAGA 57.032 30.769 0.00 0.00 0.00 2.59
91 95 8.603242 TTTGCTTAGTTTTTGTAGGAGTAGAG 57.397 34.615 0.00 0.00 0.00 2.43
108 112 6.882678 GGAGTAGAGTAAAAATGTTGGCCTTA 59.117 38.462 3.32 0.00 0.00 2.69
109 113 7.148289 GGAGTAGAGTAAAAATGTTGGCCTTAC 60.148 40.741 3.32 2.21 0.00 2.34
136 140 1.953686 GTTTGGTAGGTGCTGCTTTGA 59.046 47.619 0.00 0.00 0.00 2.69
137 141 2.356665 TTGGTAGGTGCTGCTTTGAA 57.643 45.000 0.00 0.00 0.00 2.69
138 142 2.584835 TGGTAGGTGCTGCTTTGAAT 57.415 45.000 0.00 0.00 0.00 2.57
139 143 3.712016 TGGTAGGTGCTGCTTTGAATA 57.288 42.857 0.00 0.00 0.00 1.75
140 144 3.343617 TGGTAGGTGCTGCTTTGAATAC 58.656 45.455 0.00 0.00 0.00 1.89
141 145 3.009033 TGGTAGGTGCTGCTTTGAATACT 59.991 43.478 0.00 0.00 0.00 2.12
142 146 3.623510 GGTAGGTGCTGCTTTGAATACTC 59.376 47.826 0.00 0.00 0.00 2.59
143 147 2.716217 AGGTGCTGCTTTGAATACTCC 58.284 47.619 0.00 0.00 0.00 3.85
144 148 1.745653 GGTGCTGCTTTGAATACTCCC 59.254 52.381 0.00 0.00 0.00 4.30
145 149 2.619074 GGTGCTGCTTTGAATACTCCCT 60.619 50.000 0.00 0.00 0.00 4.20
146 150 2.680339 GTGCTGCTTTGAATACTCCCTC 59.320 50.000 0.00 0.00 0.00 4.30
147 151 2.293170 GCTGCTTTGAATACTCCCTCC 58.707 52.381 0.00 0.00 0.00 4.30
148 152 2.555199 CTGCTTTGAATACTCCCTCCG 58.445 52.381 0.00 0.00 0.00 4.63
149 153 1.906574 TGCTTTGAATACTCCCTCCGT 59.093 47.619 0.00 0.00 0.00 4.69
150 154 2.093658 TGCTTTGAATACTCCCTCCGTC 60.094 50.000 0.00 0.00 0.00 4.79
151 155 2.742204 GCTTTGAATACTCCCTCCGTCC 60.742 54.545 0.00 0.00 0.00 4.79
152 156 1.108776 TTGAATACTCCCTCCGTCCG 58.891 55.000 0.00 0.00 0.00 4.79
153 157 0.033796 TGAATACTCCCTCCGTCCGT 60.034 55.000 0.00 0.00 0.00 4.69
154 158 1.212688 TGAATACTCCCTCCGTCCGTA 59.787 52.381 0.00 0.00 0.00 4.02
155 159 2.301346 GAATACTCCCTCCGTCCGTAA 58.699 52.381 0.00 0.00 0.00 3.18
156 160 2.442236 ATACTCCCTCCGTCCGTAAA 57.558 50.000 0.00 0.00 0.00 2.01
157 161 2.442236 TACTCCCTCCGTCCGTAAAT 57.558 50.000 0.00 0.00 0.00 1.40
158 162 2.442236 ACTCCCTCCGTCCGTAAATA 57.558 50.000 0.00 0.00 0.00 1.40
159 163 2.027385 ACTCCCTCCGTCCGTAAATAC 58.973 52.381 0.00 0.00 0.00 1.89
160 164 2.305009 CTCCCTCCGTCCGTAAATACT 58.695 52.381 0.00 0.00 0.00 2.12
161 165 2.692041 CTCCCTCCGTCCGTAAATACTT 59.308 50.000 0.00 0.00 0.00 2.24
162 166 2.428171 TCCCTCCGTCCGTAAATACTTG 59.572 50.000 0.00 0.00 0.00 3.16
163 167 2.167075 CCCTCCGTCCGTAAATACTTGT 59.833 50.000 0.00 0.00 0.00 3.16
164 168 3.442100 CCTCCGTCCGTAAATACTTGTC 58.558 50.000 0.00 0.00 0.00 3.18
165 169 3.119388 CCTCCGTCCGTAAATACTTGTCA 60.119 47.826 0.00 0.00 0.00 3.58
166 170 4.441079 CCTCCGTCCGTAAATACTTGTCAT 60.441 45.833 0.00 0.00 0.00 3.06
167 171 5.221106 CCTCCGTCCGTAAATACTTGTCATA 60.221 44.000 0.00 0.00 0.00 2.15
168 172 6.206395 TCCGTCCGTAAATACTTGTCATAA 57.794 37.500 0.00 0.00 0.00 1.90
169 173 6.629128 TCCGTCCGTAAATACTTGTCATAAA 58.371 36.000 0.00 0.00 0.00 1.40
170 174 7.095910 TCCGTCCGTAAATACTTGTCATAAAA 58.904 34.615 0.00 0.00 0.00 1.52
171 175 7.601886 TCCGTCCGTAAATACTTGTCATAAAAA 59.398 33.333 0.00 0.00 0.00 1.94
172 176 8.392612 CCGTCCGTAAATACTTGTCATAAAAAT 58.607 33.333 0.00 0.00 0.00 1.82
173 177 9.205916 CGTCCGTAAATACTTGTCATAAAAATG 57.794 33.333 0.00 0.00 0.00 2.32
228 232 7.953158 ACATCTACATACATTCATTTCTCCG 57.047 36.000 0.00 0.00 0.00 4.63
229 233 7.726216 ACATCTACATACATTCATTTCTCCGA 58.274 34.615 0.00 0.00 0.00 4.55
230 234 7.653713 ACATCTACATACATTCATTTCTCCGAC 59.346 37.037 0.00 0.00 0.00 4.79
231 235 7.107639 TCTACATACATTCATTTCTCCGACA 57.892 36.000 0.00 0.00 0.00 4.35
232 236 7.552459 TCTACATACATTCATTTCTCCGACAA 58.448 34.615 0.00 0.00 0.00 3.18
233 237 6.668541 ACATACATTCATTTCTCCGACAAG 57.331 37.500 0.00 0.00 0.00 3.16
234 238 6.173339 ACATACATTCATTTCTCCGACAAGT 58.827 36.000 0.00 0.00 0.00 3.16
235 239 7.327975 ACATACATTCATTTCTCCGACAAGTA 58.672 34.615 0.00 0.00 0.00 2.24
236 240 7.987458 ACATACATTCATTTCTCCGACAAGTAT 59.013 33.333 0.00 0.00 0.00 2.12
237 241 8.830580 CATACATTCATTTCTCCGACAAGTATT 58.169 33.333 0.00 0.00 0.00 1.89
238 242 7.687941 ACATTCATTTCTCCGACAAGTATTT 57.312 32.000 0.00 0.00 0.00 1.40
239 243 7.752695 ACATTCATTTCTCCGACAAGTATTTC 58.247 34.615 0.00 0.00 0.00 2.17
240 244 6.403333 TTCATTTCTCCGACAAGTATTTCG 57.597 37.500 0.00 0.00 34.93 3.46
246 250 2.953466 CGACAAGTATTTCGGAGGGA 57.047 50.000 0.00 0.00 0.00 4.20
247 251 2.810650 CGACAAGTATTTCGGAGGGAG 58.189 52.381 0.00 0.00 0.00 4.30
248 252 2.165845 CGACAAGTATTTCGGAGGGAGT 59.834 50.000 0.00 0.00 0.00 3.85
249 253 3.379372 CGACAAGTATTTCGGAGGGAGTA 59.621 47.826 0.00 0.00 0.00 2.59
250 254 4.680702 GACAAGTATTTCGGAGGGAGTAC 58.319 47.826 0.00 0.00 0.00 2.73
260 264 2.099427 CGGAGGGAGTACTAGTCAAAGC 59.901 54.545 0.00 0.00 0.00 3.51
278 282 2.389713 GCAGCGGCTAACACATAATG 57.610 50.000 0.26 0.00 36.96 1.90
279 283 1.002468 GCAGCGGCTAACACATAATGG 60.002 52.381 0.26 0.00 36.96 3.16
280 284 1.603802 CAGCGGCTAACACATAATGGG 59.396 52.381 0.26 0.00 0.00 4.00
286 294 5.487433 CGGCTAACACATAATGGGATATGA 58.513 41.667 1.60 0.00 36.87 2.15
323 331 7.777095 ACCAAATGTTTAAGAGCAAGTGTTAA 58.223 30.769 0.00 0.00 0.00 2.01
324 332 8.421002 ACCAAATGTTTAAGAGCAAGTGTTAAT 58.579 29.630 0.00 0.00 0.00 1.40
335 343 7.262048 AGAGCAAGTGTTAATAGAAGACTAGC 58.738 38.462 0.00 0.00 31.78 3.42
337 345 7.386851 AGCAAGTGTTAATAGAAGACTAGCAA 58.613 34.615 0.00 0.00 31.78 3.91
339 347 8.669243 GCAAGTGTTAATAGAAGACTAGCAAAT 58.331 33.333 0.00 0.00 31.78 2.32
340 348 9.979270 CAAGTGTTAATAGAAGACTAGCAAATG 57.021 33.333 0.00 0.00 31.78 2.32
371 380 8.215926 TCAGTTCCGTTTTCAAATTCTAGAAA 57.784 30.769 9.71 0.00 32.34 2.52
372 381 8.846211 TCAGTTCCGTTTTCAAATTCTAGAAAT 58.154 29.630 9.71 0.00 34.10 2.17
404 421 8.655651 AATTCAAAATAAACAAAAAGGAGCGA 57.344 26.923 0.00 0.00 0.00 4.93
405 422 8.655651 ATTCAAAATAAACAAAAAGGAGCGAA 57.344 26.923 0.00 0.00 0.00 4.70
406 423 8.655651 TTCAAAATAAACAAAAAGGAGCGAAT 57.344 26.923 0.00 0.00 0.00 3.34
407 424 9.751542 TTCAAAATAAACAAAAAGGAGCGAATA 57.248 25.926 0.00 0.00 0.00 1.75
408 425 9.921637 TCAAAATAAACAAAAAGGAGCGAATAT 57.078 25.926 0.00 0.00 0.00 1.28
452 471 5.660629 TGATGAACAAAAAGCAGCAAATG 57.339 34.783 0.00 0.00 0.00 2.32
519 539 1.435105 GAACGCGTACCCCCTCTAC 59.565 63.158 14.46 0.00 0.00 2.59
538 558 5.984725 TCTACCACAAATTATGACGTCCAT 58.015 37.500 14.12 9.22 39.25 3.41
587 607 0.738412 GCATCCACCAAGTGCAATGC 60.738 55.000 13.80 13.80 40.78 3.56
603 623 0.106167 ATGCGGACCACTAGCCTAGA 60.106 55.000 5.58 0.00 0.00 2.43
615 635 4.037446 CACTAGCCTAGACCATGACTCTTC 59.963 50.000 5.58 0.00 0.00 2.87
622 642 4.383850 AGACCATGACTCTTCTTGATCG 57.616 45.455 0.00 0.00 26.72 3.69
648 668 1.785647 GACCCCGTCCAGGTAAGTAT 58.214 55.000 0.00 0.00 37.88 2.12
693 713 2.656560 CTATATAGCACAGTCCCCGC 57.343 55.000 0.00 0.00 0.00 6.13
748 769 3.311966 ACAAGTTTAGCGACCTAACGAC 58.688 45.455 0.00 0.00 33.43 4.34
759 780 2.496470 GACCTAACGACCTGACCTGATT 59.504 50.000 0.00 0.00 0.00 2.57
822 911 1.669115 CAGACCCAGCCAGTTGTCG 60.669 63.158 0.00 0.00 33.04 4.35
857 948 4.523512 CCTCGGGAGGGAGGTATC 57.476 66.667 6.84 0.00 46.97 2.24
858 949 1.228925 CCTCGGGAGGGAGGTATCC 60.229 68.421 6.84 0.00 46.97 2.59
871 962 4.954875 GGAGGTATCCAATCAGAGAAGTG 58.045 47.826 0.00 0.00 45.87 3.16
872 963 4.651503 GGAGGTATCCAATCAGAGAAGTGA 59.348 45.833 0.00 0.00 45.87 3.41
873 964 5.306678 GGAGGTATCCAATCAGAGAAGTGAT 59.693 44.000 0.00 0.00 45.87 3.06
874 965 6.183361 GGAGGTATCCAATCAGAGAAGTGATT 60.183 42.308 0.00 0.00 46.09 2.57
875 966 6.825610 AGGTATCCAATCAGAGAAGTGATTC 58.174 40.000 0.00 0.00 43.85 2.52
876 967 6.614906 AGGTATCCAATCAGAGAAGTGATTCT 59.385 38.462 0.00 0.00 43.85 2.40
877 968 6.928492 GGTATCCAATCAGAGAAGTGATTCTC 59.072 42.308 9.47 9.47 43.85 2.87
923 1014 2.985847 GGCAGAGGCACCAACACC 60.986 66.667 0.00 0.00 43.71 4.16
924 1015 2.203337 GCAGAGGCACCAACACCA 60.203 61.111 0.00 0.00 40.72 4.17
932 1023 3.883180 ACCAACACCAACACGCGC 61.883 61.111 5.73 0.00 0.00 6.86
933 1024 4.622456 CCAACACCAACACGCGCC 62.622 66.667 5.73 0.00 0.00 6.53
934 1025 4.954680 CAACACCAACACGCGCCG 62.955 66.667 5.73 0.00 0.00 6.46
947 1038 2.372690 GCGCCGCCGATACACATAG 61.373 63.158 0.00 0.00 36.29 2.23
960 1051 1.762957 ACACATAGGATTCCACCGGAG 59.237 52.381 9.46 0.00 31.21 4.63
980 1071 1.920835 GGAGCAAGTGAGGGGAGGT 60.921 63.158 0.00 0.00 0.00 3.85
981 1072 0.617820 GGAGCAAGTGAGGGGAGGTA 60.618 60.000 0.00 0.00 0.00 3.08
982 1073 0.827368 GAGCAAGTGAGGGGAGGTAG 59.173 60.000 0.00 0.00 0.00 3.18
983 1074 0.413832 AGCAAGTGAGGGGAGGTAGA 59.586 55.000 0.00 0.00 0.00 2.59
984 1075 0.537653 GCAAGTGAGGGGAGGTAGAC 59.462 60.000 0.00 0.00 0.00 2.59
985 1076 0.818296 CAAGTGAGGGGAGGTAGACG 59.182 60.000 0.00 0.00 0.00 4.18
986 1077 0.702902 AAGTGAGGGGAGGTAGACGA 59.297 55.000 0.00 0.00 0.00 4.20
987 1078 0.702902 AGTGAGGGGAGGTAGACGAA 59.297 55.000 0.00 0.00 0.00 3.85
1116 1207 1.829849 GTCTTCTACCAGGGTGGGTAC 59.170 57.143 0.06 0.00 43.37 3.34
1345 1442 5.548573 TCAGATTAGGATAAACCCCTCCTT 58.451 41.667 0.00 0.00 42.03 3.36
1366 1471 7.050377 TCCTTTGATGTTCAGATATCAGTTCC 58.950 38.462 5.32 0.00 35.25 3.62
1405 1510 3.777807 CAGTGAATGACTGTTCGTGTC 57.222 47.619 0.00 0.00 46.30 3.67
1406 1511 3.123050 CAGTGAATGACTGTTCGTGTCA 58.877 45.455 0.00 0.00 46.30 3.58
1414 1519 2.210116 ACTGTTCGTGTCATTGACCAC 58.790 47.619 14.05 10.78 0.00 4.16
1418 1523 3.743911 TGTTCGTGTCATTGACCACATAC 59.256 43.478 14.05 11.72 0.00 2.39
1459 1724 4.953667 TGATCAGATAGGATTGTCTGTGC 58.046 43.478 0.00 0.00 41.69 4.57
1479 1744 2.687935 GCCAGTGGTCTTGAACTTGAAA 59.312 45.455 11.74 0.00 0.00 2.69
1491 1756 5.376854 TGAACTTGAAAATGGAAGCTAGC 57.623 39.130 6.62 6.62 0.00 3.42
1493 1758 6.237901 TGAACTTGAAAATGGAAGCTAGCTA 58.762 36.000 19.70 2.19 0.00 3.32
1494 1759 6.372659 TGAACTTGAAAATGGAAGCTAGCTAG 59.627 38.462 19.70 16.84 0.00 3.42
1529 1794 4.581493 CAGAAACCAATTCATGATCGACG 58.419 43.478 0.00 0.00 40.72 5.12
1539 1809 6.814076 ATTCATGATCGACGACTAAAAGTC 57.186 37.500 0.00 0.00 41.71 3.01
1602 1872 2.690497 CCTGCTCCGAGTTATCTCAGAA 59.310 50.000 0.00 0.00 40.44 3.02
1621 1891 7.563188 TCTCAGAAAACTTATGAGAGCCTAGAT 59.437 37.037 9.13 0.00 43.36 1.98
1622 1892 8.768501 TCAGAAAACTTATGAGAGCCTAGATA 57.231 34.615 0.00 0.00 0.00 1.98
1623 1893 8.855110 TCAGAAAACTTATGAGAGCCTAGATAG 58.145 37.037 0.00 0.00 0.00 2.08
1662 2035 7.759489 TGGGTTAGTAAGTTCGTTAGTTCTA 57.241 36.000 0.00 0.00 0.00 2.10
1664 2037 6.743172 GGGTTAGTAAGTTCGTTAGTTCTACG 59.257 42.308 0.00 0.00 40.23 3.51
1666 2039 4.398247 AGTAAGTTCGTTAGTTCTACGCG 58.602 43.478 3.53 3.53 38.81 6.01
1711 2090 7.148171 GCTCCCCAATATTGCTATGTTATTCTC 60.148 40.741 10.11 0.00 0.00 2.87
1715 2094 9.950496 CCCAATATTGCTATGTTATTCTCTACT 57.050 33.333 10.11 0.00 0.00 2.57
1866 2409 4.218635 GCCCTGGAGGTAAAAAGAAGAAAG 59.781 45.833 0.00 0.00 38.26 2.62
1872 2415 8.617290 TGGAGGTAAAAAGAAGAAAGATGTAC 57.383 34.615 0.00 0.00 0.00 2.90
1873 2416 8.437575 TGGAGGTAAAAAGAAGAAAGATGTACT 58.562 33.333 0.00 0.00 0.00 2.73
1874 2417 8.937884 GGAGGTAAAAAGAAGAAAGATGTACTC 58.062 37.037 0.00 0.00 0.00 2.59
1875 2418 8.850007 AGGTAAAAAGAAGAAAGATGTACTCC 57.150 34.615 0.00 0.00 0.00 3.85
1876 2419 7.883833 AGGTAAAAAGAAGAAAGATGTACTCCC 59.116 37.037 0.00 0.00 0.00 4.30
1877 2420 7.883833 GGTAAAAAGAAGAAAGATGTACTCCCT 59.116 37.037 0.00 0.00 0.00 4.20
1878 2421 7.987750 AAAAAGAAGAAAGATGTACTCCCTC 57.012 36.000 0.00 0.00 0.00 4.30
1879 2422 5.685520 AAGAAGAAAGATGTACTCCCTCC 57.314 43.478 0.00 0.00 0.00 4.30
1880 2423 3.702045 AGAAGAAAGATGTACTCCCTCCG 59.298 47.826 0.00 0.00 0.00 4.63
1881 2424 3.103080 AGAAAGATGTACTCCCTCCGT 57.897 47.619 0.00 0.00 0.00 4.69
1882 2425 4.246712 AGAAAGATGTACTCCCTCCGTA 57.753 45.455 0.00 0.00 0.00 4.02
1883 2426 4.208746 AGAAAGATGTACTCCCTCCGTAG 58.791 47.826 0.00 0.00 0.00 3.51
1884 2427 3.947612 AAGATGTACTCCCTCCGTAGA 57.052 47.619 0.00 0.00 0.00 2.59
1885 2428 4.456662 AAGATGTACTCCCTCCGTAGAT 57.543 45.455 0.00 0.00 0.00 1.98
1886 2429 4.023726 AGATGTACTCCCTCCGTAGATC 57.976 50.000 0.00 0.00 37.70 2.75
1887 2430 3.394940 AGATGTACTCCCTCCGTAGATCA 59.605 47.826 9.14 0.00 39.04 2.92
1888 2431 2.928334 TGTACTCCCTCCGTAGATCAC 58.072 52.381 0.00 0.00 0.00 3.06
1889 2432 2.508716 TGTACTCCCTCCGTAGATCACT 59.491 50.000 0.00 0.00 0.00 3.41
1890 2433 3.713248 TGTACTCCCTCCGTAGATCACTA 59.287 47.826 0.00 0.00 0.00 2.74
1891 2434 3.211718 ACTCCCTCCGTAGATCACTAC 57.788 52.381 0.00 0.00 43.74 2.73
1892 2435 2.778850 ACTCCCTCCGTAGATCACTACT 59.221 50.000 0.00 0.00 44.65 2.57
1893 2436 3.202595 ACTCCCTCCGTAGATCACTACTT 59.797 47.826 0.00 0.00 44.65 2.24
1894 2437 4.208746 CTCCCTCCGTAGATCACTACTTT 58.791 47.826 0.00 0.00 44.65 2.66
1895 2438 5.104193 ACTCCCTCCGTAGATCACTACTTTA 60.104 44.000 0.00 0.00 44.65 1.85
1896 2439 5.374921 TCCCTCCGTAGATCACTACTTTAG 58.625 45.833 0.00 0.00 44.65 1.85
1897 2440 5.104193 TCCCTCCGTAGATCACTACTTTAGT 60.104 44.000 0.00 0.00 44.65 2.24
1911 2454 7.393841 ACTACTTTAGTGATCTAAACGCTCT 57.606 36.000 0.00 0.00 40.05 4.09
1912 2455 7.828712 ACTACTTTAGTGATCTAAACGCTCTT 58.171 34.615 0.00 0.00 40.05 2.85
1913 2456 8.954350 ACTACTTTAGTGATCTAAACGCTCTTA 58.046 33.333 0.00 0.00 40.05 2.10
1914 2457 9.953697 CTACTTTAGTGATCTAAACGCTCTTAT 57.046 33.333 0.00 0.00 40.05 1.73
1915 2458 8.859517 ACTTTAGTGATCTAAACGCTCTTATC 57.140 34.615 0.00 0.00 40.05 1.75
1916 2459 8.688151 ACTTTAGTGATCTAAACGCTCTTATCT 58.312 33.333 0.00 0.00 40.05 1.98
1917 2460 9.522804 CTTTAGTGATCTAAACGCTCTTATCTT 57.477 33.333 0.00 0.00 40.05 2.40
1920 2463 8.228035 AGTGATCTAAACGCTCTTATCTTAGT 57.772 34.615 0.00 0.00 0.00 2.24
1921 2464 8.688151 AGTGATCTAAACGCTCTTATCTTAGTT 58.312 33.333 0.00 0.00 0.00 2.24
1922 2465 9.303537 GTGATCTAAACGCTCTTATCTTAGTTT 57.696 33.333 0.00 0.00 36.11 2.66
1926 2469 9.565213 TCTAAACGCTCTTATCTTAGTTTACAC 57.435 33.333 0.00 0.00 34.29 2.90
1927 2470 9.350357 CTAAACGCTCTTATCTTAGTTTACACA 57.650 33.333 0.00 0.00 34.29 3.72
1928 2471 7.813852 AACGCTCTTATCTTAGTTTACACAG 57.186 36.000 0.00 0.00 0.00 3.66
1929 2472 6.331061 ACGCTCTTATCTTAGTTTACACAGG 58.669 40.000 0.00 0.00 0.00 4.00
1930 2473 5.749109 CGCTCTTATCTTAGTTTACACAGGG 59.251 44.000 0.00 0.00 0.00 4.45
1931 2474 6.405508 CGCTCTTATCTTAGTTTACACAGGGA 60.406 42.308 0.00 0.00 0.00 4.20
1932 2475 6.981559 GCTCTTATCTTAGTTTACACAGGGAG 59.018 42.308 0.00 0.00 0.00 4.30
1933 2476 7.363968 GCTCTTATCTTAGTTTACACAGGGAGT 60.364 40.741 0.00 0.00 0.00 3.85
1934 2477 9.186837 CTCTTATCTTAGTTTACACAGGGAGTA 57.813 37.037 0.00 0.00 0.00 2.59
1945 2488 8.404765 GTTTACACAGGGAGTATAGACTAAGTC 58.595 40.741 0.00 0.00 35.45 3.01
1955 2498 2.708386 AGACTAAGTCAGACACGTGC 57.292 50.000 17.22 8.74 34.60 5.34
1957 2500 2.361119 AGACTAAGTCAGACACGTGCAA 59.639 45.455 17.22 0.00 34.60 4.08
1962 2505 1.867233 AGTCAGACACGTGCAATTCAC 59.133 47.619 17.22 5.18 42.23 3.18
1963 2506 1.069906 GTCAGACACGTGCAATTCACC 60.070 52.381 17.22 0.00 42.69 4.02
1970 2513 1.336148 ACGTGCAATTCACCAATGCTG 60.336 47.619 0.00 0.00 42.69 4.41
1971 2514 1.336148 CGTGCAATTCACCAATGCTGT 60.336 47.619 0.00 0.00 42.69 4.40
1972 2515 2.095314 CGTGCAATTCACCAATGCTGTA 60.095 45.455 0.00 0.00 42.69 2.74
2214 2814 1.202770 ACTTCTAGCAGCCCGTTTGTT 60.203 47.619 0.00 0.00 0.00 2.83
2245 2845 0.535335 TACTGCCCTTGATCGGTGTC 59.465 55.000 0.00 0.00 0.00 3.67
2315 2915 4.278419 ACCTTCAACCTTGAATTGCAGTAC 59.722 41.667 0.97 0.00 45.26 2.73
2535 3182 6.599638 GTGGTCTTAAAATGAGCTCTTGGTAT 59.400 38.462 16.19 0.00 33.59 2.73
2541 3188 9.956720 CTTAAAATGAGCTCTTGGTATAATTGG 57.043 33.333 16.19 0.00 0.00 3.16
2547 3194 8.506168 TGAGCTCTTGGTATAATTGGTTAAAG 57.494 34.615 16.19 0.00 0.00 1.85
2550 3197 9.178758 AGCTCTTGGTATAATTGGTTAAAGAAG 57.821 33.333 0.00 0.00 0.00 2.85
2619 3266 3.076032 AGGAGGCCAACCAAAACTATCTT 59.924 43.478 18.84 0.00 39.06 2.40
2695 3343 8.063630 CAGCATTATTTTGTTTGAACTGAAACC 58.936 33.333 0.00 0.00 35.34 3.27
2707 3355 6.210287 TGAACTGAAACCGTGGTTAATTTT 57.790 33.333 4.41 0.00 37.35 1.82
2747 3395 3.206964 GTTCAGGCAAATCTACCTAGCC 58.793 50.000 0.00 0.00 45.54 3.93
2770 3418 2.343484 GGCCCAACTGGACCTAATAC 57.657 55.000 0.00 0.00 35.25 1.89
2798 3446 1.939934 CTGTTCAAACTTGAGGACGCA 59.060 47.619 0.00 0.00 38.61 5.24
2825 3473 7.648039 AAACAAAATAGGTAAGGTTGTCACA 57.352 32.000 0.00 0.00 31.41 3.58
2866 3514 8.032952 TCTTATAGAAAATCTGCAAGTGTGTG 57.967 34.615 0.00 0.00 33.76 3.82
2962 3610 3.000078 GCAGACACCGTGTAATAATGTCG 60.000 47.826 3.58 0.00 43.54 4.35
3072 3722 4.492646 TCATGCCCCTCTATAGATGACAA 58.507 43.478 2.11 0.00 0.00 3.18
3109 3760 9.466497 ACATAAAGTGAGATGGTAATGATGTTT 57.534 29.630 0.00 0.00 0.00 2.83
3110 3761 9.941664 CATAAAGTGAGATGGTAATGATGTTTC 57.058 33.333 0.00 0.00 0.00 2.78
3111 3762 7.396540 AAAGTGAGATGGTAATGATGTTTCC 57.603 36.000 0.00 0.00 0.00 3.13
3112 3763 5.118990 AGTGAGATGGTAATGATGTTTCCG 58.881 41.667 0.00 0.00 0.00 4.30
3113 3764 3.876914 TGAGATGGTAATGATGTTTCCGC 59.123 43.478 0.00 0.00 0.00 5.54
3114 3765 3.876914 GAGATGGTAATGATGTTTCCGCA 59.123 43.478 0.00 0.00 0.00 5.69
3115 3766 3.627577 AGATGGTAATGATGTTTCCGCAC 59.372 43.478 0.00 0.00 0.00 5.34
3116 3767 3.066291 TGGTAATGATGTTTCCGCACT 57.934 42.857 0.00 0.00 0.00 4.40
3174 3825 3.294214 CCAATGCAAGGAGCCTAGAAAT 58.706 45.455 2.49 0.00 44.83 2.17
3198 3849 5.711698 AGTAGAATGGGACCCAAAAGAAAA 58.288 37.500 19.58 0.00 36.95 2.29
3296 3947 5.559427 TGCAAAAAGGAAAAGGAAAAAGC 57.441 34.783 0.00 0.00 0.00 3.51
3379 4033 8.836268 ATGTAAAAATGCACTCACAAATTCAT 57.164 26.923 0.00 0.00 0.00 2.57
3456 4123 1.065701 GAAGCAGAGCTCAATGCCATG 59.934 52.381 20.84 8.21 43.60 3.66
3470 4137 1.263356 GCCATGCCGTACCTATCCTA 58.737 55.000 0.00 0.00 0.00 2.94
3473 4140 3.307480 GCCATGCCGTACCTATCCTATTT 60.307 47.826 0.00 0.00 0.00 1.40
3482 6306 7.536855 CCGTACCTATCCTATTTGATGTCTAC 58.463 42.308 0.00 0.00 0.00 2.59
3528 6383 4.100808 AGAGAAATCCTAGTGAGTCATGGC 59.899 45.833 0.00 0.00 0.00 4.40
3666 6521 2.341543 CATCATCCCGCTCTCCCG 59.658 66.667 0.00 0.00 0.00 5.14
3683 6538 2.932234 CGGTCCTCCACGAACAGCT 61.932 63.158 0.00 0.00 0.00 4.24
3684 6539 1.079750 GGTCCTCCACGAACAGCTC 60.080 63.158 0.00 0.00 0.00 4.09
3765 6620 4.554036 GCTCATCGGCACCCCCTC 62.554 72.222 0.00 0.00 0.00 4.30
3797 6652 4.748798 AGAGGTCCAGCCCCAGGG 62.749 72.222 0.00 0.00 38.26 4.45
3911 6766 1.068264 CGATGTCGATGATCATCCCGT 60.068 52.381 26.30 18.83 43.02 5.28
3918 6773 0.039437 ATGATCATCCCGTACGCGTC 60.039 55.000 18.63 6.85 36.15 5.19
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
87 91 6.786122 AGGTAAGGCCAACATTTTTACTCTA 58.214 36.000 5.01 0.00 40.61 2.43
88 92 5.641155 AGGTAAGGCCAACATTTTTACTCT 58.359 37.500 5.01 0.29 40.61 3.24
89 93 5.977489 AGGTAAGGCCAACATTTTTACTC 57.023 39.130 5.01 0.00 40.61 2.59
90 94 7.093509 CCATAAGGTAAGGCCAACATTTTTACT 60.094 37.037 12.52 0.00 40.61 2.24
91 95 7.039270 CCATAAGGTAAGGCCAACATTTTTAC 58.961 38.462 12.52 6.83 40.61 2.01
109 113 3.016736 CAGCACCTACCAAACCATAAGG 58.983 50.000 0.00 0.00 42.21 2.69
136 140 2.442236 TTACGGACGGAGGGAGTATT 57.558 50.000 0.00 0.00 0.00 1.89
137 141 2.442236 TTTACGGACGGAGGGAGTAT 57.558 50.000 0.00 0.00 0.00 2.12
138 142 2.442236 ATTTACGGACGGAGGGAGTA 57.558 50.000 0.00 0.00 0.00 2.59
139 143 2.027385 GTATTTACGGACGGAGGGAGT 58.973 52.381 0.00 0.00 0.00 3.85
140 144 2.305009 AGTATTTACGGACGGAGGGAG 58.695 52.381 0.00 0.00 0.00 4.30
141 145 2.428171 CAAGTATTTACGGACGGAGGGA 59.572 50.000 0.00 0.00 0.00 4.20
142 146 2.167075 ACAAGTATTTACGGACGGAGGG 59.833 50.000 0.00 0.00 0.00 4.30
143 147 3.119388 TGACAAGTATTTACGGACGGAGG 60.119 47.826 0.00 0.00 0.00 4.30
144 148 4.100707 TGACAAGTATTTACGGACGGAG 57.899 45.455 0.00 0.00 0.00 4.63
145 149 4.724074 ATGACAAGTATTTACGGACGGA 57.276 40.909 0.00 0.00 0.00 4.69
146 150 6.890663 TTTATGACAAGTATTTACGGACGG 57.109 37.500 0.00 0.00 0.00 4.79
147 151 9.205916 CATTTTTATGACAAGTATTTACGGACG 57.794 33.333 0.00 0.00 0.00 4.79
202 206 9.645059 CGGAGAAATGAATGTATGTAGATGTAT 57.355 33.333 0.00 0.00 0.00 2.29
203 207 8.856103 TCGGAGAAATGAATGTATGTAGATGTA 58.144 33.333 0.00 0.00 0.00 2.29
204 208 7.653713 GTCGGAGAAATGAATGTATGTAGATGT 59.346 37.037 0.00 0.00 39.69 3.06
205 209 7.653311 TGTCGGAGAAATGAATGTATGTAGATG 59.347 37.037 0.00 0.00 39.69 2.90
206 210 7.726216 TGTCGGAGAAATGAATGTATGTAGAT 58.274 34.615 0.00 0.00 39.69 1.98
207 211 7.107639 TGTCGGAGAAATGAATGTATGTAGA 57.892 36.000 0.00 0.00 39.69 2.59
208 212 7.492669 ACTTGTCGGAGAAATGAATGTATGTAG 59.507 37.037 0.00 0.00 39.69 2.74
209 213 7.327975 ACTTGTCGGAGAAATGAATGTATGTA 58.672 34.615 0.00 0.00 39.69 2.29
210 214 6.173339 ACTTGTCGGAGAAATGAATGTATGT 58.827 36.000 0.00 0.00 39.69 2.29
211 215 6.668541 ACTTGTCGGAGAAATGAATGTATG 57.331 37.500 0.00 0.00 39.69 2.39
212 216 8.964476 AATACTTGTCGGAGAAATGAATGTAT 57.036 30.769 0.00 0.00 39.69 2.29
213 217 8.786826 AAATACTTGTCGGAGAAATGAATGTA 57.213 30.769 0.00 0.00 39.69 2.29
214 218 7.413000 CGAAATACTTGTCGGAGAAATGAATGT 60.413 37.037 0.00 0.00 39.69 2.71
215 219 6.901887 CGAAATACTTGTCGGAGAAATGAATG 59.098 38.462 0.00 0.00 39.69 2.67
216 220 7.005062 CGAAATACTTGTCGGAGAAATGAAT 57.995 36.000 0.00 0.00 39.69 2.57
217 221 6.403333 CGAAATACTTGTCGGAGAAATGAA 57.597 37.500 0.00 0.00 39.69 2.57
227 231 2.165845 ACTCCCTCCGAAATACTTGTCG 59.834 50.000 0.00 0.00 37.01 4.35
228 232 3.889520 ACTCCCTCCGAAATACTTGTC 57.110 47.619 0.00 0.00 0.00 3.18
229 233 4.351127 AGTACTCCCTCCGAAATACTTGT 58.649 43.478 0.00 0.00 0.00 3.16
230 234 5.593502 ACTAGTACTCCCTCCGAAATACTTG 59.406 44.000 0.00 0.00 0.00 3.16
231 235 5.764432 ACTAGTACTCCCTCCGAAATACTT 58.236 41.667 0.00 0.00 0.00 2.24
232 236 5.104193 TGACTAGTACTCCCTCCGAAATACT 60.104 44.000 0.00 0.00 0.00 2.12
233 237 5.128919 TGACTAGTACTCCCTCCGAAATAC 58.871 45.833 0.00 0.00 0.00 1.89
234 238 5.378230 TGACTAGTACTCCCTCCGAAATA 57.622 43.478 0.00 0.00 0.00 1.40
235 239 4.246712 TGACTAGTACTCCCTCCGAAAT 57.753 45.455 0.00 0.00 0.00 2.17
236 240 3.726557 TGACTAGTACTCCCTCCGAAA 57.273 47.619 0.00 0.00 0.00 3.46
237 241 3.726557 TTGACTAGTACTCCCTCCGAA 57.273 47.619 0.00 0.00 0.00 4.30
238 242 3.618351 CTTTGACTAGTACTCCCTCCGA 58.382 50.000 0.00 0.00 0.00 4.55
239 243 2.099427 GCTTTGACTAGTACTCCCTCCG 59.901 54.545 0.00 0.00 0.00 4.63
240 244 3.097614 TGCTTTGACTAGTACTCCCTCC 58.902 50.000 0.00 0.00 0.00 4.30
241 245 3.429684 GCTGCTTTGACTAGTACTCCCTC 60.430 52.174 0.00 0.00 0.00 4.30
242 246 2.498078 GCTGCTTTGACTAGTACTCCCT 59.502 50.000 0.00 0.00 0.00 4.20
243 247 2.735762 CGCTGCTTTGACTAGTACTCCC 60.736 54.545 0.00 0.00 0.00 4.30
244 248 2.531206 CGCTGCTTTGACTAGTACTCC 58.469 52.381 0.00 0.00 0.00 3.85
245 249 2.531206 CCGCTGCTTTGACTAGTACTC 58.469 52.381 0.00 0.00 0.00 2.59
246 250 1.404315 GCCGCTGCTTTGACTAGTACT 60.404 52.381 0.00 0.00 33.53 2.73
247 251 1.000145 GCCGCTGCTTTGACTAGTAC 59.000 55.000 0.00 0.00 33.53 2.73
248 252 3.436001 GCCGCTGCTTTGACTAGTA 57.564 52.632 0.00 0.00 33.53 1.82
249 253 4.285851 GCCGCTGCTTTGACTAGT 57.714 55.556 0.00 0.00 33.53 2.57
260 264 1.603802 CCCATTATGTGTTAGCCGCTG 59.396 52.381 2.16 0.00 0.00 5.18
272 276 6.230472 TCCAGAAACGTCATATCCCATTATG 58.770 40.000 0.00 0.00 0.00 1.90
274 278 5.600898 TCTCCAGAAACGTCATATCCCATTA 59.399 40.000 0.00 0.00 0.00 1.90
275 279 4.408921 TCTCCAGAAACGTCATATCCCATT 59.591 41.667 0.00 0.00 0.00 3.16
276 280 3.967326 TCTCCAGAAACGTCATATCCCAT 59.033 43.478 0.00 0.00 0.00 4.00
277 281 3.132289 GTCTCCAGAAACGTCATATCCCA 59.868 47.826 0.00 0.00 0.00 4.37
278 282 3.492829 GGTCTCCAGAAACGTCATATCCC 60.493 52.174 0.00 0.00 0.00 3.85
279 283 3.132289 TGGTCTCCAGAAACGTCATATCC 59.868 47.826 0.00 0.00 0.00 2.59
280 284 4.386867 TGGTCTCCAGAAACGTCATATC 57.613 45.455 0.00 0.00 0.00 1.63
286 294 3.208747 ACATTTGGTCTCCAGAAACGT 57.791 42.857 0.00 0.00 33.81 3.99
323 331 6.126940 TGAGCTTCCATTTGCTAGTCTTCTAT 60.127 38.462 0.00 0.00 39.91 1.98
324 332 5.187772 TGAGCTTCCATTTGCTAGTCTTCTA 59.812 40.000 0.00 0.00 39.91 2.10
335 343 2.154462 ACGGAACTGAGCTTCCATTTG 58.846 47.619 12.17 1.85 39.98 2.32
337 345 2.568623 AACGGAACTGAGCTTCCATT 57.431 45.000 12.17 3.07 39.98 3.16
339 347 2.218603 GAAAACGGAACTGAGCTTCCA 58.781 47.619 12.17 0.00 39.98 3.53
340 348 2.218603 TGAAAACGGAACTGAGCTTCC 58.781 47.619 0.00 4.41 37.01 3.46
419 436 9.878667 TGCTTTTTGTTCATCATGAATTCATAT 57.121 25.926 20.32 11.46 38.79 1.78
420 437 9.361315 CTGCTTTTTGTTCATCATGAATTCATA 57.639 29.630 20.32 9.78 38.79 2.15
421 438 7.148474 GCTGCTTTTTGTTCATCATGAATTCAT 60.148 33.333 15.36 15.36 38.79 2.57
422 439 6.146510 GCTGCTTTTTGTTCATCATGAATTCA 59.853 34.615 11.26 11.26 38.79 2.57
423 440 6.146510 TGCTGCTTTTTGTTCATCATGAATTC 59.853 34.615 2.67 0.00 38.79 2.17
424 441 5.992829 TGCTGCTTTTTGTTCATCATGAATT 59.007 32.000 2.67 0.00 38.79 2.17
425 442 5.543714 TGCTGCTTTTTGTTCATCATGAAT 58.456 33.333 2.67 0.00 38.79 2.57
426 443 4.946445 TGCTGCTTTTTGTTCATCATGAA 58.054 34.783 0.00 0.00 33.32 2.57
427 444 4.587584 TGCTGCTTTTTGTTCATCATGA 57.412 36.364 0.00 0.00 0.00 3.07
428 445 5.660629 TTTGCTGCTTTTTGTTCATCATG 57.339 34.783 0.00 0.00 0.00 3.07
429 446 5.761234 ACATTTGCTGCTTTTTGTTCATCAT 59.239 32.000 0.00 0.00 0.00 2.45
430 447 5.117584 ACATTTGCTGCTTTTTGTTCATCA 58.882 33.333 0.00 0.00 0.00 3.07
431 448 5.662211 ACATTTGCTGCTTTTTGTTCATC 57.338 34.783 0.00 0.00 0.00 2.92
470 489 4.933400 CCCTGCCAATTCTTGAATTGAAAG 59.067 41.667 27.73 23.11 41.44 2.62
519 539 5.220854 GGAGAATGGACGTCATAATTTGTGG 60.221 44.000 18.91 0.00 34.44 4.17
587 607 0.395311 TGGTCTAGGCTAGTGGTCCG 60.395 60.000 20.45 0.00 0.00 4.79
603 623 2.419297 GCCGATCAAGAAGAGTCATGGT 60.419 50.000 0.00 0.00 0.00 3.55
648 668 1.268352 GCATGGTGCGACCTTTAAACA 59.732 47.619 0.00 0.00 39.58 2.83
674 694 2.164624 GAGCGGGGACTGTGCTATATAG 59.835 54.545 5.30 5.30 39.49 1.31
745 766 2.666508 CGTTACAAATCAGGTCAGGTCG 59.333 50.000 0.00 0.00 0.00 4.79
748 769 2.742053 CCACGTTACAAATCAGGTCAGG 59.258 50.000 0.00 0.00 0.00 3.86
759 780 1.074072 ATGGCAGCCCACGTTACAA 59.926 52.632 9.64 0.00 45.77 2.41
787 843 0.034186 CTGCTGGAGGCCCATGTTAA 60.034 55.000 0.00 0.00 42.59 2.01
788 844 0.913934 TCTGCTGGAGGCCCATGTTA 60.914 55.000 0.00 0.00 42.59 2.41
804 860 1.669115 CGACAACTGGCTGGGTCTG 60.669 63.158 13.54 6.47 0.00 3.51
822 911 1.668151 GACGGCTGGACAGTTGGAC 60.668 63.158 0.00 0.00 0.00 4.02
851 942 6.614906 AGAATCACTTCTCTGATTGGATACCT 59.385 38.462 0.00 0.00 40.33 3.08
852 943 6.825610 AGAATCACTTCTCTGATTGGATACC 58.174 40.000 0.00 0.00 40.33 2.73
886 977 4.834496 TGCCACTTCTCTGATTGGATTTTT 59.166 37.500 0.00 0.00 0.00 1.94
887 978 4.410099 TGCCACTTCTCTGATTGGATTTT 58.590 39.130 0.00 0.00 0.00 1.82
888 979 4.015084 CTGCCACTTCTCTGATTGGATTT 58.985 43.478 0.00 0.00 0.00 2.17
889 980 3.265221 TCTGCCACTTCTCTGATTGGATT 59.735 43.478 0.00 0.00 0.00 3.01
905 996 2.203337 GTGTTGGTGCCTCTGCCA 60.203 61.111 0.00 0.00 36.33 4.92
932 1023 2.607187 GAATCCTATGTGTATCGGCGG 58.393 52.381 7.21 0.00 0.00 6.13
933 1024 2.029380 TGGAATCCTATGTGTATCGGCG 60.029 50.000 0.00 0.00 0.00 6.46
934 1025 3.326747 GTGGAATCCTATGTGTATCGGC 58.673 50.000 0.00 0.00 0.00 5.54
935 1026 3.614150 CGGTGGAATCCTATGTGTATCGG 60.614 52.174 0.00 0.00 0.00 4.18
960 1051 3.672295 CTCCCCTCACTTGCTCCGC 62.672 68.421 0.00 0.00 0.00 5.54
980 1071 0.106619 GCCTCCTCCTCCTTCGTCTA 60.107 60.000 0.00 0.00 0.00 2.59
981 1072 1.380650 GCCTCCTCCTCCTTCGTCT 60.381 63.158 0.00 0.00 0.00 4.18
982 1073 1.045911 ATGCCTCCTCCTCCTTCGTC 61.046 60.000 0.00 0.00 0.00 4.20
983 1074 1.002274 ATGCCTCCTCCTCCTTCGT 59.998 57.895 0.00 0.00 0.00 3.85
984 1075 1.445095 CATGCCTCCTCCTCCTTCG 59.555 63.158 0.00 0.00 0.00 3.79
985 1076 0.985490 ACCATGCCTCCTCCTCCTTC 60.985 60.000 0.00 0.00 0.00 3.46
986 1077 1.083706 ACCATGCCTCCTCCTCCTT 59.916 57.895 0.00 0.00 0.00 3.36
987 1078 1.692042 CACCATGCCTCCTCCTCCT 60.692 63.158 0.00 0.00 0.00 3.69
1116 1207 5.230942 CCGGAGTAATCAGTTAGCTAATGG 58.769 45.833 9.88 5.28 0.00 3.16
1117 1208 4.686554 GCCGGAGTAATCAGTTAGCTAATG 59.313 45.833 5.05 9.14 0.00 1.90
1345 1442 8.868522 AAAAGGAACTGATATCTGAACATCAA 57.131 30.769 15.75 0.00 40.86 2.57
1366 1471 4.446371 ACTGACAGTGAGGAACAGAAAAG 58.554 43.478 7.47 0.00 33.53 2.27
1393 1498 2.221055 GTGGTCAATGACACGAACAGTC 59.779 50.000 15.86 0.00 33.68 3.51
1397 1502 3.994392 AGTATGTGGTCAATGACACGAAC 59.006 43.478 15.86 12.02 33.68 3.95
1399 1504 3.257127 TCAGTATGTGGTCAATGACACGA 59.743 43.478 15.86 4.06 37.40 4.35
1400 1505 3.584834 TCAGTATGTGGTCAATGACACG 58.415 45.455 15.86 1.96 37.40 4.49
1401 1506 5.674569 GCAATCAGTATGTGGTCAATGACAC 60.675 44.000 15.86 11.49 37.40 3.67
1402 1507 4.395854 GCAATCAGTATGTGGTCAATGACA 59.604 41.667 15.86 0.00 37.40 3.58
1403 1508 4.395854 TGCAATCAGTATGTGGTCAATGAC 59.604 41.667 4.51 4.51 37.40 3.06
1404 1509 4.587891 TGCAATCAGTATGTGGTCAATGA 58.412 39.130 0.00 0.00 37.40 2.57
1405 1510 4.968812 TGCAATCAGTATGTGGTCAATG 57.031 40.909 0.00 0.00 37.40 2.82
1406 1511 5.240183 GCTATGCAATCAGTATGTGGTCAAT 59.760 40.000 0.00 0.00 37.40 2.57
1411 1516 4.142966 CGATGCTATGCAATCAGTATGTGG 60.143 45.833 0.00 0.00 43.62 4.17
1414 1519 3.683340 AGCGATGCTATGCAATCAGTATG 59.317 43.478 0.00 0.00 43.62 2.39
1418 1523 2.546789 TCAAGCGATGCTATGCAATCAG 59.453 45.455 0.00 0.00 43.62 2.90
1459 1724 4.981806 TTTTCAAGTTCAAGACCACTGG 57.018 40.909 0.00 0.00 0.00 4.00
1479 1744 5.934781 AGCATAAACTAGCTAGCTTCCATT 58.065 37.500 24.88 14.98 39.78 3.16
1508 1773 4.330074 GTCGTCGATCATGAATTGGTTTCT 59.670 41.667 0.00 0.00 35.23 2.52
1513 1778 5.966636 TTTAGTCGTCGATCATGAATTGG 57.033 39.130 0.00 0.00 0.00 3.16
1529 1794 5.405571 TGATCTTGCTTGACGACTTTTAGTC 59.594 40.000 0.00 0.00 41.71 2.59
1539 1809 2.411069 CACTCACTGATCTTGCTTGACG 59.589 50.000 0.00 0.00 0.00 4.35
1614 1884 5.624344 TTCGCATGTACTACTATCTAGGC 57.376 43.478 0.00 0.00 0.00 3.93
1621 1891 5.347620 AACCCATTTCGCATGTACTACTA 57.652 39.130 0.00 0.00 0.00 1.82
1622 1892 3.906720 ACCCATTTCGCATGTACTACT 57.093 42.857 0.00 0.00 0.00 2.57
1623 1893 5.114081 ACTAACCCATTTCGCATGTACTAC 58.886 41.667 0.00 0.00 0.00 2.73
1662 2035 5.501715 CATTAGCATAATGAAAAGACGCGT 58.498 37.500 13.85 13.85 0.00 6.01
1664 2037 5.514279 AGCATTAGCATAATGAAAAGACGC 58.486 37.500 12.53 0.00 45.49 5.19
1666 2039 6.442112 GGGAGCATTAGCATAATGAAAAGAC 58.558 40.000 12.53 0.00 45.49 3.01
1711 2090 8.388103 CCACGAGAAATAAACAAATACCAGTAG 58.612 37.037 0.00 0.00 0.00 2.57
1715 2094 5.708230 AGCCACGAGAAATAAACAAATACCA 59.292 36.000 0.00 0.00 0.00 3.25
1866 2409 3.502979 GTGATCTACGGAGGGAGTACATC 59.497 52.174 0.00 0.00 0.00 3.06
1887 2430 7.393841 AGAGCGTTTAGATCACTAAAGTAGT 57.606 36.000 0.00 0.00 45.42 2.73
1888 2431 9.953697 ATAAGAGCGTTTAGATCACTAAAGTAG 57.046 33.333 0.00 0.00 45.42 2.57
1889 2432 9.947669 GATAAGAGCGTTTAGATCACTAAAGTA 57.052 33.333 0.00 0.00 45.42 2.24
1890 2433 8.688151 AGATAAGAGCGTTTAGATCACTAAAGT 58.312 33.333 0.00 0.00 45.42 2.66
1891 2434 9.522804 AAGATAAGAGCGTTTAGATCACTAAAG 57.477 33.333 0.00 0.00 45.42 1.85
1894 2437 9.339850 ACTAAGATAAGAGCGTTTAGATCACTA 57.660 33.333 0.00 0.00 37.82 2.74
1895 2438 8.228035 ACTAAGATAAGAGCGTTTAGATCACT 57.772 34.615 0.00 0.00 37.82 3.41
1896 2439 8.859517 AACTAAGATAAGAGCGTTTAGATCAC 57.140 34.615 0.00 0.00 37.82 3.06
1900 2443 9.565213 GTGTAAACTAAGATAAGAGCGTTTAGA 57.435 33.333 0.00 0.00 30.36 2.10
1901 2444 9.350357 TGTGTAAACTAAGATAAGAGCGTTTAG 57.650 33.333 0.00 0.00 30.36 1.85
1902 2445 9.350357 CTGTGTAAACTAAGATAAGAGCGTTTA 57.650 33.333 0.00 0.00 0.00 2.01
1903 2446 7.331193 CCTGTGTAAACTAAGATAAGAGCGTTT 59.669 37.037 0.00 0.00 0.00 3.60
1904 2447 6.812160 CCTGTGTAAACTAAGATAAGAGCGTT 59.188 38.462 0.00 0.00 0.00 4.84
1905 2448 6.331061 CCTGTGTAAACTAAGATAAGAGCGT 58.669 40.000 0.00 0.00 0.00 5.07
1906 2449 5.749109 CCCTGTGTAAACTAAGATAAGAGCG 59.251 44.000 0.00 0.00 0.00 5.03
1907 2450 6.875076 TCCCTGTGTAAACTAAGATAAGAGC 58.125 40.000 0.00 0.00 0.00 4.09
1908 2451 8.068892 ACTCCCTGTGTAAACTAAGATAAGAG 57.931 38.462 0.00 0.00 0.00 2.85
1909 2452 9.710818 ATACTCCCTGTGTAAACTAAGATAAGA 57.289 33.333 0.00 0.00 0.00 2.10
1913 2456 9.134055 GTCTATACTCCCTGTGTAAACTAAGAT 57.866 37.037 0.00 0.00 0.00 2.40
1914 2457 8.334734 AGTCTATACTCCCTGTGTAAACTAAGA 58.665 37.037 0.00 0.00 0.00 2.10
1915 2458 8.522542 AGTCTATACTCCCTGTGTAAACTAAG 57.477 38.462 0.00 0.00 0.00 2.18
1916 2459 9.979897 TTAGTCTATACTCCCTGTGTAAACTAA 57.020 33.333 0.00 0.00 37.15 2.24
1917 2460 9.624373 CTTAGTCTATACTCCCTGTGTAAACTA 57.376 37.037 0.00 0.00 37.15 2.24
1918 2461 8.114743 ACTTAGTCTATACTCCCTGTGTAAACT 58.885 37.037 0.00 0.00 37.15 2.66
1919 2462 8.291191 ACTTAGTCTATACTCCCTGTGTAAAC 57.709 38.462 0.00 0.00 37.15 2.01
1920 2463 8.111545 TGACTTAGTCTATACTCCCTGTGTAAA 58.888 37.037 13.86 0.00 37.15 2.01
1921 2464 7.636579 TGACTTAGTCTATACTCCCTGTGTAA 58.363 38.462 13.86 0.00 37.15 2.41
1922 2465 7.126879 TCTGACTTAGTCTATACTCCCTGTGTA 59.873 40.741 13.86 0.00 37.15 2.90
1923 2466 6.069556 TCTGACTTAGTCTATACTCCCTGTGT 60.070 42.308 13.86 0.00 37.15 3.72
1924 2467 6.261381 GTCTGACTTAGTCTATACTCCCTGTG 59.739 46.154 13.86 0.00 37.15 3.66
1925 2468 6.069556 TGTCTGACTTAGTCTATACTCCCTGT 60.070 42.308 13.86 0.00 37.15 4.00
1926 2469 6.261381 GTGTCTGACTTAGTCTATACTCCCTG 59.739 46.154 13.86 0.00 37.15 4.45
1927 2470 6.358991 GTGTCTGACTTAGTCTATACTCCCT 58.641 44.000 13.86 0.00 37.15 4.20
1928 2471 5.236911 CGTGTCTGACTTAGTCTATACTCCC 59.763 48.000 13.86 2.14 37.15 4.30
1929 2472 5.816777 ACGTGTCTGACTTAGTCTATACTCC 59.183 44.000 13.86 4.09 37.15 3.85
1930 2473 6.707711 CACGTGTCTGACTTAGTCTATACTC 58.292 44.000 13.86 8.54 37.15 2.59
1931 2474 5.064962 GCACGTGTCTGACTTAGTCTATACT 59.935 44.000 18.38 0.00 39.91 2.12
1932 2475 5.163784 TGCACGTGTCTGACTTAGTCTATAC 60.164 44.000 18.38 9.13 33.15 1.47
1933 2476 4.939439 TGCACGTGTCTGACTTAGTCTATA 59.061 41.667 18.38 0.00 33.15 1.31
1934 2477 3.756963 TGCACGTGTCTGACTTAGTCTAT 59.243 43.478 18.38 0.00 33.15 1.98
1955 2498 6.500684 AAGTACTACAGCATTGGTGAATTG 57.499 37.500 21.85 10.59 34.87 2.32
1957 2500 6.003950 ACAAAGTACTACAGCATTGGTGAAT 58.996 36.000 21.85 9.15 34.87 2.57
1962 2505 8.039603 TCATTTACAAAGTACTACAGCATTGG 57.960 34.615 0.00 0.00 0.00 3.16
2164 2759 9.646427 ATCTAGACAAAGTATCTGAGTTCAAAC 57.354 33.333 0.00 0.00 0.00 2.93
2214 2814 6.061022 TCAAGGGCAGTATTACTTTGATGA 57.939 37.500 5.10 0.52 0.00 2.92
2245 2845 6.963796 AGCAACTCAAAGTCAGTTTATGAAG 58.036 36.000 0.00 0.00 40.43 3.02
2315 2915 4.543590 TTGCTTCTCTCTTACTTCCAGG 57.456 45.455 0.00 0.00 0.00 4.45
2535 3182 7.669722 AGTTCCATCAGCTTCTTTAACCAATTA 59.330 33.333 0.00 0.00 0.00 1.40
2541 3188 6.560253 TTCAGTTCCATCAGCTTCTTTAAC 57.440 37.500 0.00 0.00 0.00 2.01
2547 3194 5.295540 GGTAGAATTCAGTTCCATCAGCTTC 59.704 44.000 8.44 0.00 37.56 3.86
2550 3197 4.517285 TGGTAGAATTCAGTTCCATCAGC 58.483 43.478 8.44 0.00 37.56 4.26
2707 3355 9.440773 GCCTGAACATAACATAGATTATCATCA 57.559 33.333 0.00 0.00 0.00 3.07
2770 3418 6.367422 GTCCTCAAGTTTGAACAGATACTCTG 59.633 42.308 2.65 2.65 40.39 3.35
2839 3487 9.066892 ACACACTTGCAGATTTTCTATAAGAAA 57.933 29.630 0.00 0.00 42.00 2.52
2866 3514 3.129113 TGCCATGAACACATAACTGATGC 59.871 43.478 0.00 0.00 39.39 3.91
2935 3583 6.257849 ACATTATTACACGGTGTCTGCATAAG 59.742 38.462 18.43 11.36 0.00 1.73
2949 3597 9.687210 TGTGATCCTATAACGACATTATTACAC 57.313 33.333 0.00 0.00 35.08 2.90
2962 3610 6.174720 TCCACCTTCATGTGATCCTATAAC 57.825 41.667 0.00 0.00 38.55 1.89
3028 3677 9.264719 CATGATATATTCACAACTCACAAGCTA 57.735 33.333 0.00 0.00 37.11 3.32
3087 3738 6.094048 CGGAAACATCATTACCATCTCACTTT 59.906 38.462 0.00 0.00 0.00 2.66
3105 3756 2.851263 ACCAATAGAGTGCGGAAACA 57.149 45.000 0.00 0.00 0.00 2.83
3106 3757 3.335579 AGAACCAATAGAGTGCGGAAAC 58.664 45.455 0.00 0.00 0.00 2.78
3107 3758 3.596214 GAGAACCAATAGAGTGCGGAAA 58.404 45.455 0.00 0.00 0.00 3.13
3108 3759 2.093658 GGAGAACCAATAGAGTGCGGAA 60.094 50.000 0.00 0.00 35.97 4.30
3109 3760 1.480954 GGAGAACCAATAGAGTGCGGA 59.519 52.381 0.00 0.00 35.97 5.54
3110 3761 1.482593 AGGAGAACCAATAGAGTGCGG 59.517 52.381 0.00 0.00 38.94 5.69
3111 3762 2.969628 AGGAGAACCAATAGAGTGCG 57.030 50.000 0.00 0.00 38.94 5.34
3112 3763 3.055094 TGGAAGGAGAACCAATAGAGTGC 60.055 47.826 0.00 0.00 38.94 4.40
3113 3764 4.826274 TGGAAGGAGAACCAATAGAGTG 57.174 45.455 0.00 0.00 38.94 3.51
3114 3765 6.394345 AAATGGAAGGAGAACCAATAGAGT 57.606 37.500 0.00 0.00 39.69 3.24
3115 3766 8.049721 AGTAAAATGGAAGGAGAACCAATAGAG 58.950 37.037 0.00 0.00 39.69 2.43
3116 3767 7.928873 AGTAAAATGGAAGGAGAACCAATAGA 58.071 34.615 0.00 0.00 39.69 1.98
3174 3825 6.457159 TTTCTTTTGGGTCCCATTCTACTA 57.543 37.500 12.68 0.00 31.53 1.82
3296 3947 4.717877 TGATACAATGGTCTAAGGGCATG 58.282 43.478 0.00 0.00 0.00 4.06
3354 4008 8.836268 ATGAATTTGTGAGTGCATTTTTACAT 57.164 26.923 0.00 0.00 0.00 2.29
3456 4123 5.047235 AGACATCAAATAGGATAGGTACGGC 60.047 44.000 0.00 0.00 0.00 5.68
3470 4137 8.593945 ACCCATAACAAATGTAGACATCAAAT 57.406 30.769 0.00 0.00 35.10 2.32
3473 4140 9.693739 ATTTACCCATAACAAATGTAGACATCA 57.306 29.630 0.00 0.00 35.10 3.07
3506 6331 4.100808 AGCCATGACTCACTAGGATTTCTC 59.899 45.833 0.00 0.00 0.00 2.87
3528 6383 0.508641 CGTCAAGACCAACTGCGAAG 59.491 55.000 0.00 0.00 0.00 3.79
3666 6521 1.079750 GAGCTGTTCGTGGAGGACC 60.080 63.158 0.00 0.00 0.00 4.46
3683 6538 1.566211 CTCAAGCTGGAGAAGGAGGA 58.434 55.000 13.35 0.00 37.05 3.71
3684 6539 0.107752 GCTCAAGCTGGAGAAGGAGG 60.108 60.000 22.98 0.00 37.05 4.30
3763 6618 1.523258 CTGCTTCATCCTGCCGGAG 60.523 63.158 5.05 0.00 44.06 4.63
3765 6620 1.523258 CTCTGCTTCATCCTGCCGG 60.523 63.158 0.00 0.00 0.00 6.13
3886 6741 0.317854 TGATCATCGACATCGCGTCC 60.318 55.000 5.77 0.00 42.07 4.79


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

AutoCloner maintained by Alex Coulton.