Multiple sequence alignment - TraesCS2A01G356300

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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 TraesCS2A01G356300 chr2A 100.000 7940 0 0 1 7940 600917780 600909841 0.000000e+00 14663.0
1 TraesCS2A01G356300 chr2A 96.429 56 2 0 491 546 600917233 600917178 8.480000e-15 93.5
2 TraesCS2A01G356300 chr2A 96.429 56 2 0 548 603 600917290 600917235 8.480000e-15 93.5
3 TraesCS2A01G356300 chr2B 94.000 4183 171 23 1281 5424 538239568 538235427 0.000000e+00 6261.0
4 TraesCS2A01G356300 chr2B 94.500 2018 60 14 5423 7430 538235345 538233369 0.000000e+00 3064.0
5 TraesCS2A01G356300 chr2B 92.438 648 23 13 642 1280 538240227 538239597 0.000000e+00 902.0
6 TraesCS2A01G356300 chr2B 93.289 298 14 3 7645 7940 538232219 538231926 1.220000e-117 435.0
7 TraesCS2A01G356300 chr2B 94.667 150 5 3 7427 7576 538232487 538232341 6.200000e-56 230.0
8 TraesCS2A01G356300 chr2B 94.118 51 3 0 1975 2025 538238908 538238858 2.380000e-10 78.7
9 TraesCS2A01G356300 chr2D 96.482 3297 73 14 4043 7318 457410264 457406990 0.000000e+00 5406.0
10 TraesCS2A01G356300 chr2D 93.623 1976 58 21 579 2505 457413802 457411846 0.000000e+00 2889.0
11 TraesCS2A01G356300 chr2D 96.488 1509 44 7 2539 4044 457411846 457410344 0.000000e+00 2484.0
12 TraesCS2A01G356300 chr2D 93.521 355 20 2 176 530 457414733 457414382 7.060000e-145 525.0
13 TraesCS2A01G356300 chr2D 95.882 170 6 1 12 180 560959483 560959652 2.820000e-69 274.0
14 TraesCS2A01G356300 chr2D 92.810 153 10 1 7424 7576 457406594 457406443 3.730000e-53 220.0
15 TraesCS2A01G356300 chr2D 96.000 50 2 0 1975 2024 457412434 457412385 1.840000e-11 82.4
16 TraesCS2A01G356300 chr2D 95.556 45 2 0 1947 1991 457412374 457412330 1.110000e-08 73.1
17 TraesCS2A01G356300 chr5A 95.930 172 6 1 15 185 290391860 290391689 2.180000e-70 278.0
18 TraesCS2A01G356300 chr7A 95.906 171 6 1 15 184 115807686 115807516 7.850000e-70 276.0
19 TraesCS2A01G356300 chr4D 95.882 170 6 1 15 183 93338205 93338036 2.820000e-69 274.0
20 TraesCS2A01G356300 chr4B 95.882 170 5 2 15 182 80990650 80990819 2.820000e-69 274.0
21 TraesCS2A01G356300 chr1D 96.407 167 5 1 15 180 178466307 178466473 2.820000e-69 274.0
22 TraesCS2A01G356300 chr5B 95.349 172 6 2 15 185 663232166 663232336 1.020000e-68 272.0
23 TraesCS2A01G356300 chr5B 92.896 183 10 3 12 193 177644124 177644304 6.110000e-66 263.0
24 TraesCS2A01G356300 chr5D 93.855 179 8 3 2 177 560061525 560061347 4.720000e-67 267.0


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 TraesCS2A01G356300 chr2A 600909841 600917780 7939 True 4950.00 14663 97.619333 1 7940 3 chr2A.!!$R1 7939
1 TraesCS2A01G356300 chr2B 538231926 538240227 8301 True 1828.45 6261 93.835333 642 7940 6 chr2B.!!$R1 7298
2 TraesCS2A01G356300 chr2D 457406443 457414733 8290 True 1668.50 5406 94.925714 176 7576 7 chr2D.!!$R1 7400

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
484 485 0.253044 ATCTCACATCACAACCCCCG 59.747 55.000 0.0 0.0 0.00 5.73 F
1306 1941 0.108520 GGACCGAATTACCTGTGCGA 60.109 55.000 0.0 0.0 0.00 5.10 F
1782 2420 1.949525 CTGGATGATACCAAAAGCCCG 59.050 52.381 0.0 0.0 39.59 6.13 F
2783 3458 0.453282 CGGCATGTCAGTGCTTTTCG 60.453 55.000 0.0 0.0 44.45 3.46 F
2797 3472 2.093783 GCTTTTCGTTATGGACTGACGG 59.906 50.000 0.0 0.0 37.45 4.79 F
4498 5270 0.251297 CTGTCACCAGGGGCAAATGA 60.251 55.000 0.0 0.0 34.90 2.57 F
4725 5497 1.446966 GAAGTCCGCTCAGGCAGTC 60.447 63.158 0.0 0.0 40.77 3.51 F
5497 6364 1.067516 CGCCTTTTCCATGCTATTGGG 59.932 52.381 0.0 0.0 37.37 4.12 F
5647 6514 2.637382 TGTTCCTCTGCCATTGTCAGTA 59.363 45.455 0.0 0.0 33.48 2.74 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1682 2317 0.321830 GGTAAGCCGCCAGGTACAAA 60.322 55.000 0.00 0.00 40.50 2.83 R
2195 2866 1.083489 CAACGTCACCACAACTGTGT 58.917 50.000 8.93 0.00 44.21 3.72 R
3489 4176 2.368221 CTGGAAGAAAATTTGCACCCCA 59.632 45.455 0.00 1.92 34.07 4.96 R
4291 5063 1.134995 TCTGCTTGTCATCAGTAGGCG 60.135 52.381 3.47 0.00 0.00 5.52 R
4516 5288 2.229792 CTTTGTTGCAAGCCTCTACCA 58.770 47.619 0.00 0.00 0.00 3.25 R
5318 6100 1.886542 GCTTTTTCCCGTCTTGGTCAT 59.113 47.619 0.00 0.00 35.15 3.06 R
6424 7293 1.942776 TGAGAGCCATCCAGACAAGA 58.057 50.000 0.00 0.00 0.00 3.02 R
6894 7763 0.329261 TCTTCCCTGTGGATGCCTTG 59.671 55.000 0.00 0.00 41.40 3.61 R
7359 8575 0.820074 AACGATCCGGGCAACAAACA 60.820 50.000 0.00 0.00 39.74 2.83 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
22 23 3.840124 AATATTTCGTCCACTCCCTCC 57.160 47.619 0.00 0.00 0.00 4.30
23 24 1.108776 TATTTCGTCCACTCCCTCCG 58.891 55.000 0.00 0.00 0.00 4.63
24 25 0.903454 ATTTCGTCCACTCCCTCCGT 60.903 55.000 0.00 0.00 0.00 4.69
25 26 1.117142 TTTCGTCCACTCCCTCCGTT 61.117 55.000 0.00 0.00 0.00 4.44
26 27 1.530013 TTCGTCCACTCCCTCCGTTC 61.530 60.000 0.00 0.00 0.00 3.95
27 28 2.979649 GTCCACTCCCTCCGTTCC 59.020 66.667 0.00 0.00 0.00 3.62
28 29 1.609794 GTCCACTCCCTCCGTTCCT 60.610 63.158 0.00 0.00 0.00 3.36
29 30 0.324091 GTCCACTCCCTCCGTTCCTA 60.324 60.000 0.00 0.00 0.00 2.94
30 31 0.410663 TCCACTCCCTCCGTTCCTAA 59.589 55.000 0.00 0.00 0.00 2.69
31 32 1.007963 TCCACTCCCTCCGTTCCTAAT 59.992 52.381 0.00 0.00 0.00 1.73
32 33 2.245546 TCCACTCCCTCCGTTCCTAATA 59.754 50.000 0.00 0.00 0.00 0.98
33 34 3.116862 TCCACTCCCTCCGTTCCTAATAT 60.117 47.826 0.00 0.00 0.00 1.28
34 35 3.646637 CCACTCCCTCCGTTCCTAATATT 59.353 47.826 0.00 0.00 0.00 1.28
35 36 4.102681 CCACTCCCTCCGTTCCTAATATTT 59.897 45.833 0.00 0.00 0.00 1.40
36 37 5.057149 CACTCCCTCCGTTCCTAATATTTG 58.943 45.833 0.00 0.00 0.00 2.32
37 38 4.720273 ACTCCCTCCGTTCCTAATATTTGT 59.280 41.667 0.00 0.00 0.00 2.83
38 39 5.163332 ACTCCCTCCGTTCCTAATATTTGTC 60.163 44.000 0.00 0.00 0.00 3.18
39 40 4.966805 TCCCTCCGTTCCTAATATTTGTCT 59.033 41.667 0.00 0.00 0.00 3.41
40 41 5.427481 TCCCTCCGTTCCTAATATTTGTCTT 59.573 40.000 0.00 0.00 0.00 3.01
41 42 6.069847 TCCCTCCGTTCCTAATATTTGTCTTT 60.070 38.462 0.00 0.00 0.00 2.52
42 43 6.602009 CCCTCCGTTCCTAATATTTGTCTTTT 59.398 38.462 0.00 0.00 0.00 2.27
43 44 7.122204 CCCTCCGTTCCTAATATTTGTCTTTTT 59.878 37.037 0.00 0.00 0.00 1.94
44 45 9.169592 CCTCCGTTCCTAATATTTGTCTTTTTA 57.830 33.333 0.00 0.00 0.00 1.52
46 47 9.947433 TCCGTTCCTAATATTTGTCTTTTTAGA 57.053 29.630 0.00 0.00 0.00 2.10
60 61 9.965824 TTGTCTTTTTAGAGATTTCAAATGGAC 57.034 29.630 0.00 0.00 0.00 4.02
61 62 9.354673 TGTCTTTTTAGAGATTTCAAATGGACT 57.645 29.630 0.00 0.00 0.00 3.85
75 76 9.923143 TTTCAAATGGACTACTATATACGGATG 57.077 33.333 0.00 0.00 0.00 3.51
76 77 8.645814 TCAAATGGACTACTATATACGGATGT 57.354 34.615 0.00 0.00 0.00 3.06
77 78 9.743581 TCAAATGGACTACTATATACGGATGTA 57.256 33.333 0.00 0.00 34.45 2.29
117 118 6.734104 AGTGTAGATTCACTCATTTTGCTC 57.266 37.500 0.00 0.00 44.07 4.26
118 119 5.645497 AGTGTAGATTCACTCATTTTGCTCC 59.355 40.000 0.00 0.00 44.07 4.70
119 120 4.631377 TGTAGATTCACTCATTTTGCTCCG 59.369 41.667 0.00 0.00 0.00 4.63
120 121 3.679389 AGATTCACTCATTTTGCTCCGT 58.321 40.909 0.00 0.00 0.00 4.69
121 122 4.832248 AGATTCACTCATTTTGCTCCGTA 58.168 39.130 0.00 0.00 0.00 4.02
122 123 5.431765 AGATTCACTCATTTTGCTCCGTAT 58.568 37.500 0.00 0.00 0.00 3.06
123 124 4.944962 TTCACTCATTTTGCTCCGTATG 57.055 40.909 0.00 0.00 0.00 2.39
124 125 3.937814 TCACTCATTTTGCTCCGTATGT 58.062 40.909 0.00 0.00 0.00 2.29
125 126 5.079689 TCACTCATTTTGCTCCGTATGTA 57.920 39.130 0.00 0.00 0.00 2.29
126 127 5.109210 TCACTCATTTTGCTCCGTATGTAG 58.891 41.667 0.00 0.00 0.00 2.74
127 128 4.870426 CACTCATTTTGCTCCGTATGTAGT 59.130 41.667 0.00 0.00 0.00 2.73
128 129 5.005779 CACTCATTTTGCTCCGTATGTAGTC 59.994 44.000 0.00 0.00 0.00 2.59
129 130 5.079689 TCATTTTGCTCCGTATGTAGTCA 57.920 39.130 0.00 0.00 0.00 3.41
130 131 4.868171 TCATTTTGCTCCGTATGTAGTCAC 59.132 41.667 0.00 0.00 0.00 3.67
131 132 4.530710 TTTTGCTCCGTATGTAGTCACT 57.469 40.909 0.00 0.00 0.00 3.41
132 133 4.530710 TTTGCTCCGTATGTAGTCACTT 57.469 40.909 0.00 0.00 0.00 3.16
133 134 3.503827 TGCTCCGTATGTAGTCACTTG 57.496 47.619 0.00 0.00 0.00 3.16
134 135 2.823747 TGCTCCGTATGTAGTCACTTGT 59.176 45.455 0.00 0.00 0.00 3.16
135 136 3.257375 TGCTCCGTATGTAGTCACTTGTT 59.743 43.478 0.00 0.00 0.00 2.83
136 137 3.612860 GCTCCGTATGTAGTCACTTGTTG 59.387 47.826 0.00 0.00 0.00 3.33
137 138 4.617530 GCTCCGTATGTAGTCACTTGTTGA 60.618 45.833 0.00 0.00 0.00 3.18
138 139 5.456548 TCCGTATGTAGTCACTTGTTGAA 57.543 39.130 0.00 0.00 35.39 2.69
139 140 5.845103 TCCGTATGTAGTCACTTGTTGAAA 58.155 37.500 0.00 0.00 35.39 2.69
140 141 6.460781 TCCGTATGTAGTCACTTGTTGAAAT 58.539 36.000 0.00 0.00 35.39 2.17
141 142 6.588756 TCCGTATGTAGTCACTTGTTGAAATC 59.411 38.462 0.00 0.00 35.39 2.17
142 143 6.590292 CCGTATGTAGTCACTTGTTGAAATCT 59.410 38.462 0.00 0.00 35.39 2.40
143 144 7.201444 CCGTATGTAGTCACTTGTTGAAATCTC 60.201 40.741 0.00 0.00 35.39 2.75
144 145 7.542477 CGTATGTAGTCACTTGTTGAAATCTCT 59.458 37.037 0.00 0.00 35.39 3.10
145 146 9.856488 GTATGTAGTCACTTGTTGAAATCTCTA 57.144 33.333 0.00 0.00 35.39 2.43
147 148 9.778741 ATGTAGTCACTTGTTGAAATCTCTAAA 57.221 29.630 0.00 0.00 35.39 1.85
148 149 9.607988 TGTAGTCACTTGTTGAAATCTCTAAAA 57.392 29.630 0.00 0.00 35.39 1.52
151 152 9.396022 AGTCACTTGTTGAAATCTCTAAAAAGA 57.604 29.630 0.00 0.00 35.39 2.52
152 153 9.439537 GTCACTTGTTGAAATCTCTAAAAAGAC 57.560 33.333 0.00 0.00 35.39 3.01
153 154 9.173021 TCACTTGTTGAAATCTCTAAAAAGACA 57.827 29.630 0.00 0.00 0.00 3.41
154 155 9.787532 CACTTGTTGAAATCTCTAAAAAGACAA 57.212 29.630 0.00 0.00 0.00 3.18
171 172 9.908152 AAAAAGACAAATATTTAGAAACGGAGG 57.092 29.630 0.00 0.00 0.00 4.30
172 173 8.857694 AAAGACAAATATTTAGAAACGGAGGA 57.142 30.769 0.00 0.00 0.00 3.71
173 174 8.857694 AAGACAAATATTTAGAAACGGAGGAA 57.142 30.769 0.00 0.00 0.00 3.36
174 175 8.494016 AGACAAATATTTAGAAACGGAGGAAG 57.506 34.615 0.00 0.00 0.00 3.46
254 255 6.619874 GCTTTTATTCTCGTCCATTCGTTCAA 60.620 38.462 0.00 0.00 0.00 2.69
262 263 6.370442 TCTCGTCCATTCGTTCAATACAAAAT 59.630 34.615 0.00 0.00 0.00 1.82
263 264 6.904498 TCGTCCATTCGTTCAATACAAAATT 58.096 32.000 0.00 0.00 0.00 1.82
291 292 9.629878 TTACACTACAACCCAAAATCTTCTTAA 57.370 29.630 0.00 0.00 0.00 1.85
293 294 7.778382 ACACTACAACCCAAAATCTTCTTAAGT 59.222 33.333 1.63 0.00 0.00 2.24
323 324 0.839946 ATAGCCCTAGCCACCAACAG 59.160 55.000 0.00 0.00 41.25 3.16
331 332 3.197766 CCTAGCCACCAACAGAATACTCA 59.802 47.826 0.00 0.00 0.00 3.41
409 410 5.865085 AGGCATTTATAGCATACCTCGAAA 58.135 37.500 0.00 0.00 0.00 3.46
410 411 6.296026 AGGCATTTATAGCATACCTCGAAAA 58.704 36.000 0.00 0.00 0.00 2.29
411 412 6.428159 AGGCATTTATAGCATACCTCGAAAAG 59.572 38.462 0.00 0.00 0.00 2.27
412 413 6.426937 GGCATTTATAGCATACCTCGAAAAGA 59.573 38.462 0.00 0.00 0.00 2.52
459 460 1.076332 CTGGTCCGTCCATTCGAAAC 58.924 55.000 0.00 0.00 46.12 2.78
484 485 0.253044 ATCTCACATCACAACCCCCG 59.747 55.000 0.00 0.00 0.00 5.73
485 486 1.125093 TCTCACATCACAACCCCCGT 61.125 55.000 0.00 0.00 0.00 5.28
488 489 2.150719 ACATCACAACCCCCGTGGA 61.151 57.895 0.00 0.00 38.00 4.02
489 490 1.302949 CATCACAACCCCCGTGGAT 59.697 57.895 0.00 0.00 38.00 3.41
490 491 0.748005 CATCACAACCCCCGTGGATC 60.748 60.000 0.00 0.00 38.00 3.36
491 492 2.252072 ATCACAACCCCCGTGGATCG 62.252 60.000 0.00 0.00 38.00 3.69
492 493 4.404098 ACAACCCCCGTGGATCGC 62.404 66.667 0.00 0.00 38.00 4.58
506 507 2.757868 TGGATCGCCAAAATTACCTTGG 59.242 45.455 3.40 3.40 45.26 3.61
507 508 2.100749 GGATCGCCAAAATTACCTTGGG 59.899 50.000 9.01 1.14 43.11 4.12
508 509 2.296073 TCGCCAAAATTACCTTGGGT 57.704 45.000 9.01 0.00 43.11 4.51
509 510 2.599677 TCGCCAAAATTACCTTGGGTT 58.400 42.857 9.01 0.00 43.11 4.11
510 511 2.559231 TCGCCAAAATTACCTTGGGTTC 59.441 45.455 9.01 0.00 43.11 3.62
511 512 2.297597 CGCCAAAATTACCTTGGGTTCA 59.702 45.455 9.01 0.00 43.11 3.18
512 513 3.659786 GCCAAAATTACCTTGGGTTCAC 58.340 45.455 9.01 0.00 43.11 3.18
513 514 3.859252 GCCAAAATTACCTTGGGTTCACG 60.859 47.826 9.01 0.00 43.11 4.35
514 515 3.319689 CCAAAATTACCTTGGGTTCACGT 59.680 43.478 0.11 0.00 39.82 4.49
515 516 4.202172 CCAAAATTACCTTGGGTTCACGTT 60.202 41.667 0.11 0.00 39.82 3.99
516 517 5.353111 CAAAATTACCTTGGGTTCACGTTT 58.647 37.500 0.00 0.00 37.09 3.60
517 518 6.461231 CCAAAATTACCTTGGGTTCACGTTTA 60.461 38.462 0.11 0.00 39.82 2.01
518 519 5.694231 AATTACCTTGGGTTCACGTTTAC 57.306 39.130 0.00 0.00 37.09 2.01
519 520 2.713863 ACCTTGGGTTCACGTTTACA 57.286 45.000 0.00 0.00 27.29 2.41
520 521 3.002038 ACCTTGGGTTCACGTTTACAA 57.998 42.857 0.00 0.00 27.29 2.41
521 522 2.684374 ACCTTGGGTTCACGTTTACAAC 59.316 45.455 0.00 0.00 27.29 3.32
522 523 2.033675 CCTTGGGTTCACGTTTACAACC 59.966 50.000 6.85 6.85 39.18 3.77
526 527 1.605232 GGTTCACGTTTACAACCCTGG 59.395 52.381 4.73 0.00 34.55 4.45
527 528 1.002142 GTTCACGTTTACAACCCTGGC 60.002 52.381 0.00 0.00 0.00 4.85
528 529 0.535553 TCACGTTTACAACCCTGGCC 60.536 55.000 0.00 0.00 0.00 5.36
529 530 0.820074 CACGTTTACAACCCTGGCCA 60.820 55.000 4.71 4.71 0.00 5.36
530 531 0.820482 ACGTTTACAACCCTGGCCAC 60.820 55.000 0.00 0.00 0.00 5.01
531 532 1.520600 CGTTTACAACCCTGGCCACC 61.521 60.000 0.00 0.00 0.00 4.61
532 533 0.468400 GTTTACAACCCTGGCCACCA 60.468 55.000 0.00 0.00 0.00 4.17
540 541 4.100479 CTGGCCACCAGCAAATCA 57.900 55.556 0.00 0.00 45.13 2.57
541 542 1.588082 CTGGCCACCAGCAAATCAC 59.412 57.895 0.00 0.00 45.13 3.06
542 543 0.896940 CTGGCCACCAGCAAATCACT 60.897 55.000 0.00 0.00 45.13 3.41
543 544 0.895100 TGGCCACCAGCAAATCACTC 60.895 55.000 0.00 0.00 46.50 3.51
544 545 1.598701 GGCCACCAGCAAATCACTCC 61.599 60.000 0.00 0.00 46.50 3.85
564 565 0.613572 ACCGCCAAAATTACCCTGGG 60.614 55.000 12.28 12.28 0.00 4.45
577 578 1.212441 ACCCTGGGTTCACGTTTACAA 59.788 47.619 14.05 0.00 27.29 2.41
586 1175 0.820074 CACGTTTACAACCCTGGCCA 60.820 55.000 4.71 4.71 0.00 5.36
612 1201 5.634859 CAGCAAATTACTCCAATTTCACACC 59.365 40.000 0.00 0.00 43.51 4.16
614 1203 5.279456 GCAAATTACTCCAATTTCACACCCT 60.279 40.000 0.00 0.00 43.51 4.34
737 1326 2.203280 CCAGGCCGAACCACACAA 60.203 61.111 0.00 0.00 43.14 3.33
739 1328 2.203294 AGGCCGAACCACACAACC 60.203 61.111 0.00 0.00 43.14 3.77
740 1329 2.203294 GGCCGAACCACACAACCT 60.203 61.111 0.00 0.00 38.86 3.50
741 1330 1.071814 GGCCGAACCACACAACCTA 59.928 57.895 0.00 0.00 38.86 3.08
742 1331 0.535553 GGCCGAACCACACAACCTAA 60.536 55.000 0.00 0.00 38.86 2.69
765 1354 4.038080 GGGCAAAACCGTCCGCAG 62.038 66.667 0.00 0.00 40.62 5.18
802 1391 2.364324 GAGAGAGAGCGAGAGAGTAGGA 59.636 54.545 0.00 0.00 0.00 2.94
824 1423 3.274690 AGAGGAGAGAGAGGAGGGAAAAT 59.725 47.826 0.00 0.00 0.00 1.82
843 1442 8.900781 GGGAAAATATTGAAGTAGTAGAAACCC 58.099 37.037 0.00 0.00 0.00 4.11
864 1463 0.317103 CCGTTCGTCTCTATCGCCAG 60.317 60.000 0.00 0.00 0.00 4.85
922 1521 4.753662 CGTCTCCCCCTCCCACGA 62.754 72.222 0.00 0.00 32.08 4.35
1077 1685 3.398353 CTTCGTCTCGCTCCCGGAC 62.398 68.421 0.73 0.00 33.90 4.79
1137 1745 0.315382 CGGCGAATTCGAATCACTGC 60.315 55.000 31.01 12.34 43.02 4.40
1138 1746 1.009829 GGCGAATTCGAATCACTGCT 58.990 50.000 31.01 0.00 43.02 4.24
1139 1747 1.398390 GGCGAATTCGAATCACTGCTT 59.602 47.619 31.01 0.00 43.02 3.91
1140 1748 2.159517 GGCGAATTCGAATCACTGCTTT 60.160 45.455 31.01 0.00 43.02 3.51
1141 1749 3.492313 GCGAATTCGAATCACTGCTTTT 58.508 40.909 31.01 0.00 43.02 2.27
1142 1750 3.914364 GCGAATTCGAATCACTGCTTTTT 59.086 39.130 31.01 0.00 43.02 1.94
1213 1821 9.630098 TTGTATCCGTCGATATTTTATACCTTC 57.370 33.333 0.00 0.00 33.54 3.46
1300 1935 3.329929 GTCACAAGGACCGAATTACCT 57.670 47.619 0.00 0.00 40.83 3.08
1306 1941 0.108520 GGACCGAATTACCTGTGCGA 60.109 55.000 0.00 0.00 0.00 5.10
1405 2040 5.711976 AGTGGTTGCTATTTTGATTGCTAGT 59.288 36.000 0.00 0.00 0.00 2.57
1475 2110 2.951813 TCCAGGGTGGACCAGTCT 59.048 61.111 0.00 0.00 42.67 3.24
1664 2299 3.118956 GGGTGAGTCTTCTCGTGATGAAT 60.119 47.826 4.83 4.12 43.09 2.57
1682 2317 8.675504 GTGATGAATTCTTCTCATGATGAAACT 58.324 33.333 18.92 0.00 38.99 2.66
1782 2420 1.949525 CTGGATGATACCAAAAGCCCG 59.050 52.381 0.00 0.00 39.59 6.13
2057 2727 4.574674 TGCCAAATGGACTAGTGAGAAT 57.425 40.909 0.00 0.00 37.39 2.40
2068 2738 6.666113 TGGACTAGTGAGAATACATGGTGTAA 59.334 38.462 0.00 0.00 36.31 2.41
2123 2793 5.532779 GGAATGTCAAATGGATTAGGGAGAC 59.467 44.000 0.00 0.00 0.00 3.36
2195 2866 2.940514 TGGATCAGGGAGAGGTACAA 57.059 50.000 0.00 0.00 0.00 2.41
2228 2899 3.695060 GTGACGTTGAGAGATCCCTAGAA 59.305 47.826 0.00 0.00 0.00 2.10
2258 2929 8.076781 ACTGTCACTCATACGACATGATTATAC 58.923 37.037 0.00 3.77 41.13 1.47
2423 3096 3.780294 TGGCCCTAACACTGAATACATCT 59.220 43.478 0.00 0.00 0.00 2.90
2530 3205 4.944619 TGATCACATCTGCTTACCTAGG 57.055 45.455 7.41 7.41 0.00 3.02
2654 3329 8.877864 ATGATAACTCCATCAAACCTTTGTTA 57.122 30.769 0.00 0.00 38.39 2.41
2766 3441 4.466828 CTGCAAGTTGATAGTTGAAACGG 58.533 43.478 7.16 0.00 36.93 4.44
2767 3442 3.234386 GCAAGTTGATAGTTGAAACGGC 58.766 45.455 7.16 0.00 36.93 5.68
2783 3458 0.453282 CGGCATGTCAGTGCTTTTCG 60.453 55.000 0.00 0.00 44.45 3.46
2791 3466 3.496884 TGTCAGTGCTTTTCGTTATGGAC 59.503 43.478 0.00 0.00 0.00 4.02
2797 3472 2.093783 GCTTTTCGTTATGGACTGACGG 59.906 50.000 0.00 0.00 37.45 4.79
2878 3564 5.414454 TGCGTATTTTCTTGTGCTTATTCCT 59.586 36.000 0.00 0.00 0.00 3.36
3000 3686 2.687935 TCAGCCCAACACTTCAAGAAAC 59.312 45.455 0.00 0.00 0.00 2.78
3144 3830 9.847706 ATCGATACATTGTTAGCATTACTAGAG 57.152 33.333 0.00 0.00 30.79 2.43
3263 3949 3.892588 TGTCCTGAAAAATTAAAGCCGGT 59.107 39.130 1.90 0.00 0.00 5.28
3360 4046 3.817084 CAGATGCTGGAAGAGACAACAAA 59.183 43.478 0.00 0.00 34.07 2.83
3431 4117 7.099764 AGTAACAGTTGATGACACCTATTCAG 58.900 38.462 0.00 0.00 0.00 3.02
3489 4176 2.780924 TGGGGCAAACAGGGTCCT 60.781 61.111 0.00 0.00 0.00 3.85
3508 4195 2.289631 CCTGGGGTGCAAATTTTCTTCC 60.290 50.000 0.00 0.00 0.00 3.46
3517 4204 6.367149 GGTGCAAATTTTCTTCCAGATTCTTC 59.633 38.462 0.00 0.00 0.00 2.87
3599 4286 5.680619 TGTTTATGCTATCTGGGTACTTGG 58.319 41.667 0.00 0.00 0.00 3.61
3604 4291 4.359105 TGCTATCTGGGTACTTGGTAGTT 58.641 43.478 0.00 0.00 35.78 2.24
3785 4473 8.028938 CCAGAATAGGTTTAACTTTGTGATTGG 58.971 37.037 0.00 0.00 0.00 3.16
3818 4506 9.784531 CAGTTTGGTGATTATACTAGATTCCAT 57.215 33.333 0.00 0.00 0.00 3.41
4252 5024 7.399191 ACAAGATGGAAGTCCTACATACAGTAA 59.601 37.037 0.00 0.00 36.82 2.24
4498 5270 0.251297 CTGTCACCAGGGGCAAATGA 60.251 55.000 0.00 0.00 34.90 2.57
4669 5441 4.591072 AGTAAAGTCACAGGAGAAGAAGCT 59.409 41.667 0.00 0.00 0.00 3.74
4725 5497 1.446966 GAAGTCCGCTCAGGCAGTC 60.447 63.158 0.00 0.00 40.77 3.51
4764 5536 2.352960 GCAAGAAGACCCGCTAAAGATG 59.647 50.000 0.00 0.00 0.00 2.90
4848 5620 2.383855 CCGATCTGAGGAAAGAGGACT 58.616 52.381 0.00 0.00 0.00 3.85
4867 5639 4.336433 GGACTCTCTCTCTGATGAAGACAG 59.664 50.000 0.00 0.00 36.80 3.51
4963 5735 2.629137 TCATGCATGGGTATTGATTGCC 59.371 45.455 25.97 0.00 32.39 4.52
4994 5766 6.191315 TGGGTTTCTGCTTTGCCTATTTATA 58.809 36.000 0.00 0.00 0.00 0.98
5163 5935 3.130869 TCTGAATGGTAATGGCATTGTGC 59.869 43.478 22.57 11.92 44.08 4.57
5188 5960 4.703575 ACCATGTACGCTCTAGTTCTGTTA 59.296 41.667 0.00 0.00 0.00 2.41
5275 6057 8.579850 AATGATCTAACTTGGTTATCTGCAAA 57.420 30.769 0.00 0.00 0.00 3.68
5318 6100 3.945285 GGAAATGGCGTCTCCTAAATCAA 59.055 43.478 0.00 0.00 35.26 2.57
5411 6193 5.331876 AGCTGAAGAGGTATACACACTTC 57.668 43.478 19.54 19.54 38.71 3.01
5497 6364 1.067516 CGCCTTTTCCATGCTATTGGG 59.932 52.381 0.00 0.00 37.37 4.12
5647 6514 2.637382 TGTTCCTCTGCCATTGTCAGTA 59.363 45.455 0.00 0.00 33.48 2.74
5682 6549 3.002791 TCTGAGCAAGATTTGTAAGCCG 58.997 45.455 0.00 0.00 0.00 5.52
5693 6560 2.902705 TGTAAGCCGACACTTCTGTT 57.097 45.000 0.00 0.00 0.00 3.16
6171 7038 3.008330 CCTAATGCAGCATCTGATAGGC 58.992 50.000 15.15 0.00 31.97 3.93
6331 7198 3.243336 GTGACTCACTGCGGTTAGTAAG 58.757 50.000 12.46 0.52 30.96 2.34
6424 7293 5.726793 ACTTAGGTGGATCCTTAGATGTGTT 59.273 40.000 14.23 0.00 45.67 3.32
6435 7304 5.485353 TCCTTAGATGTGTTCTTGTCTGGAT 59.515 40.000 0.00 0.00 35.79 3.41
6497 7366 3.875727 GCATGACAATCTGAGTATGCTGT 59.124 43.478 0.00 0.00 38.23 4.40
6531 7400 8.472007 TGATTTCCTGGTTTGTACTAACATTT 57.528 30.769 19.45 0.24 34.97 2.32
6645 7514 3.326747 GAAAGTTGTGCGTGAGGATAGT 58.673 45.455 0.00 0.00 0.00 2.12
6894 7763 2.435059 GAAGAGCCGGTGTCTGCC 60.435 66.667 1.90 0.00 0.00 4.85
7026 7895 9.443323 AATGTTTTAGGCTTTACTTTTGTTTGT 57.557 25.926 0.00 0.00 0.00 2.83
7212 8090 4.019174 AGGAGCCCAACTTCATTGTATTG 58.981 43.478 0.00 0.00 36.47 1.90
7226 8104 8.781067 TTCATTGTATTGTCGAGTTCTTTTTG 57.219 30.769 0.00 0.00 0.00 2.44
7238 8116 4.610945 AGTTCTTTTTGCAGTCATTTCCG 58.389 39.130 0.00 0.00 0.00 4.30
7243 8121 5.705441 TCTTTTTGCAGTCATTTCCGTATCT 59.295 36.000 0.00 0.00 0.00 1.98
7273 8157 7.663081 TCATTATGCAAGTTGTCTCTTTTCTCT 59.337 33.333 4.48 0.00 0.00 3.10
7319 8535 2.167693 TCAGGTATCTTGCCCTGTTACG 59.832 50.000 5.66 0.00 46.79 3.18
7434 8650 8.534333 TCGCCTTTTATAGATAGCTTATTGTG 57.466 34.615 0.00 0.00 0.00 3.33
7447 9546 6.530913 AGCTTATTGTGTTATATGCTGTCG 57.469 37.500 0.00 0.00 38.98 4.35
7492 9591 7.513371 ACCCGTAGATTCACATTTAAAAACA 57.487 32.000 0.00 0.00 0.00 2.83
7586 9714 5.830457 TCAACTTTTCACTCTCTCTCTCTCA 59.170 40.000 0.00 0.00 0.00 3.27
7587 9715 6.322456 TCAACTTTTCACTCTCTCTCTCTCAA 59.678 38.462 0.00 0.00 0.00 3.02
7638 9768 6.054941 AGCACGAATATCACCATGAACATTA 58.945 36.000 0.00 0.00 0.00 1.90
7639 9769 6.712095 AGCACGAATATCACCATGAACATTAT 59.288 34.615 0.00 0.00 0.00 1.28
7641 9771 7.862372 GCACGAATATCACCATGAACATTATTT 59.138 33.333 0.00 0.00 0.00 1.40
7643 9773 9.950680 ACGAATATCACCATGAACATTATTTTC 57.049 29.630 0.00 0.00 0.00 2.29
7687 9839 9.656323 ACAGGTAAACTTCTCTGTATATATCCA 57.344 33.333 0.00 0.00 38.52 3.41
7748 9900 9.653287 TCTTAATACATAAGCATACACTATGGC 57.347 33.333 0.00 0.00 40.76 4.40
7752 9904 6.037786 ACATAAGCATACACTATGGCGTAT 57.962 37.500 0.00 0.00 36.68 3.06
7788 9940 4.882842 TCAAAGGGTAAAGGAAAATGGC 57.117 40.909 0.00 0.00 0.00 4.40
7795 9947 4.583073 GGGTAAAGGAAAATGGCGATACAT 59.417 41.667 0.00 0.00 0.00 2.29
7843 9995 3.573538 TGCAAACAACTTCATATGTGCCT 59.426 39.130 1.90 0.00 0.00 4.75
7891 10045 9.546909 GCTTATTTGTTCATATGATTGATACCG 57.453 33.333 6.17 0.00 0.00 4.02
7908 10062 7.224290 TGATACCGTTATTTTGTATGTGTCG 57.776 36.000 0.00 0.00 0.00 4.35
7922 10076 5.584251 TGTATGTGTCGATGTATTGTTGCAT 59.416 36.000 0.00 0.00 0.00 3.96
7931 10085 5.695363 CGATGTATTGTTGCATGATCTCTCT 59.305 40.000 0.00 0.00 0.00 3.10
7932 10086 6.202379 CGATGTATTGTTGCATGATCTCTCTT 59.798 38.462 0.00 0.00 0.00 2.85
7933 10087 6.673154 TGTATTGTTGCATGATCTCTCTTG 57.327 37.500 0.00 0.00 0.00 3.02
7934 10088 5.587443 TGTATTGTTGCATGATCTCTCTTGG 59.413 40.000 0.00 0.00 0.00 3.61
7935 10089 3.708403 TGTTGCATGATCTCTCTTGGT 57.292 42.857 0.00 0.00 0.00 3.67
7937 10091 4.005650 TGTTGCATGATCTCTCTTGGTTC 58.994 43.478 0.00 0.00 0.00 3.62
7938 10092 4.260170 GTTGCATGATCTCTCTTGGTTCT 58.740 43.478 0.00 0.00 0.00 3.01
7939 10093 3.870274 TGCATGATCTCTCTTGGTTCTG 58.130 45.455 0.00 0.00 0.00 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.558898 CGGAGGGAGTGGACGAAATATTAG 60.559 50.000 0.00 0.00 0.00 1.73
1 2 3.319972 CGGAGGGAGTGGACGAAATATTA 59.680 47.826 0.00 0.00 0.00 0.98
2 3 2.102588 CGGAGGGAGTGGACGAAATATT 59.897 50.000 0.00 0.00 0.00 1.28
3 4 1.687123 CGGAGGGAGTGGACGAAATAT 59.313 52.381 0.00 0.00 0.00 1.28
4 5 1.108776 CGGAGGGAGTGGACGAAATA 58.891 55.000 0.00 0.00 0.00 1.40
5 6 0.903454 ACGGAGGGAGTGGACGAAAT 60.903 55.000 0.00 0.00 0.00 2.17
6 7 1.117142 AACGGAGGGAGTGGACGAAA 61.117 55.000 0.00 0.00 0.00 3.46
7 8 1.530013 GAACGGAGGGAGTGGACGAA 61.530 60.000 0.00 0.00 0.00 3.85
8 9 1.975407 GAACGGAGGGAGTGGACGA 60.975 63.158 0.00 0.00 0.00 4.20
9 10 2.572284 GAACGGAGGGAGTGGACG 59.428 66.667 0.00 0.00 0.00 4.79
10 11 0.324091 TAGGAACGGAGGGAGTGGAC 60.324 60.000 0.00 0.00 0.00 4.02
11 12 0.410663 TTAGGAACGGAGGGAGTGGA 59.589 55.000 0.00 0.00 0.00 4.02
12 13 1.497161 ATTAGGAACGGAGGGAGTGG 58.503 55.000 0.00 0.00 0.00 4.00
13 14 4.957684 AATATTAGGAACGGAGGGAGTG 57.042 45.455 0.00 0.00 0.00 3.51
14 15 4.720273 ACAAATATTAGGAACGGAGGGAGT 59.280 41.667 0.00 0.00 0.00 3.85
15 16 5.070580 AGACAAATATTAGGAACGGAGGGAG 59.929 44.000 0.00 0.00 0.00 4.30
16 17 4.966805 AGACAAATATTAGGAACGGAGGGA 59.033 41.667 0.00 0.00 0.00 4.20
17 18 5.291905 AGACAAATATTAGGAACGGAGGG 57.708 43.478 0.00 0.00 0.00 4.30
18 19 7.625828 AAAAGACAAATATTAGGAACGGAGG 57.374 36.000 0.00 0.00 0.00 4.30
20 21 9.947433 TCTAAAAAGACAAATATTAGGAACGGA 57.053 29.630 0.00 0.00 0.00 4.69
34 35 9.965824 GTCCATTTGAAATCTCTAAAAAGACAA 57.034 29.630 0.00 0.00 0.00 3.18
35 36 9.354673 AGTCCATTTGAAATCTCTAAAAAGACA 57.645 29.630 0.00 0.00 0.00 3.41
49 50 9.923143 CATCCGTATATAGTAGTCCATTTGAAA 57.077 33.333 0.00 0.00 0.00 2.69
50 51 9.085645 ACATCCGTATATAGTAGTCCATTTGAA 57.914 33.333 0.00 0.00 0.00 2.69
51 52 8.645814 ACATCCGTATATAGTAGTCCATTTGA 57.354 34.615 0.00 0.00 0.00 2.69
95 96 5.446473 CGGAGCAAAATGAGTGAATCTACAC 60.446 44.000 0.00 0.00 40.60 2.90
96 97 4.631377 CGGAGCAAAATGAGTGAATCTACA 59.369 41.667 0.00 0.00 0.00 2.74
97 98 4.631813 ACGGAGCAAAATGAGTGAATCTAC 59.368 41.667 0.00 0.00 0.00 2.59
98 99 4.832248 ACGGAGCAAAATGAGTGAATCTA 58.168 39.130 0.00 0.00 0.00 1.98
99 100 3.679389 ACGGAGCAAAATGAGTGAATCT 58.321 40.909 0.00 0.00 0.00 2.40
100 101 5.065218 ACATACGGAGCAAAATGAGTGAATC 59.935 40.000 0.00 0.00 0.00 2.52
101 102 4.943705 ACATACGGAGCAAAATGAGTGAAT 59.056 37.500 0.00 0.00 0.00 2.57
102 103 4.323417 ACATACGGAGCAAAATGAGTGAA 58.677 39.130 0.00 0.00 0.00 3.18
103 104 3.937814 ACATACGGAGCAAAATGAGTGA 58.062 40.909 0.00 0.00 0.00 3.41
104 105 4.870426 ACTACATACGGAGCAAAATGAGTG 59.130 41.667 0.00 0.00 0.00 3.51
105 106 5.086104 ACTACATACGGAGCAAAATGAGT 57.914 39.130 0.00 0.00 0.00 3.41
106 107 5.005779 GTGACTACATACGGAGCAAAATGAG 59.994 44.000 0.00 0.00 0.00 2.90
107 108 4.868171 GTGACTACATACGGAGCAAAATGA 59.132 41.667 0.00 0.00 0.00 2.57
108 109 4.870426 AGTGACTACATACGGAGCAAAATG 59.130 41.667 0.00 0.00 0.00 2.32
109 110 5.086104 AGTGACTACATACGGAGCAAAAT 57.914 39.130 0.00 0.00 0.00 1.82
110 111 4.530710 AGTGACTACATACGGAGCAAAA 57.469 40.909 0.00 0.00 0.00 2.44
111 112 4.242475 CAAGTGACTACATACGGAGCAAA 58.758 43.478 0.00 0.00 0.00 3.68
112 113 3.257375 ACAAGTGACTACATACGGAGCAA 59.743 43.478 0.00 0.00 0.00 3.91
113 114 2.823747 ACAAGTGACTACATACGGAGCA 59.176 45.455 0.00 0.00 0.00 4.26
114 115 3.505464 ACAAGTGACTACATACGGAGC 57.495 47.619 0.00 0.00 0.00 4.70
115 116 5.055642 TCAACAAGTGACTACATACGGAG 57.944 43.478 0.00 0.00 0.00 4.63
116 117 5.456548 TTCAACAAGTGACTACATACGGA 57.543 39.130 0.00 0.00 35.39 4.69
117 118 6.590292 AGATTTCAACAAGTGACTACATACGG 59.410 38.462 0.00 0.00 35.39 4.02
118 119 7.542477 AGAGATTTCAACAAGTGACTACATACG 59.458 37.037 0.00 0.00 35.39 3.06
119 120 8.764524 AGAGATTTCAACAAGTGACTACATAC 57.235 34.615 0.00 0.00 35.39 2.39
121 122 9.778741 TTTAGAGATTTCAACAAGTGACTACAT 57.221 29.630 0.00 0.00 35.39 2.29
122 123 9.607988 TTTTAGAGATTTCAACAAGTGACTACA 57.392 29.630 0.00 0.00 35.39 2.74
125 126 9.396022 TCTTTTTAGAGATTTCAACAAGTGACT 57.604 29.630 0.00 0.00 35.39 3.41
126 127 9.439537 GTCTTTTTAGAGATTTCAACAAGTGAC 57.560 33.333 0.00 0.00 35.39 3.67
127 128 9.173021 TGTCTTTTTAGAGATTTCAACAAGTGA 57.827 29.630 0.00 0.00 0.00 3.41
128 129 9.787532 TTGTCTTTTTAGAGATTTCAACAAGTG 57.212 29.630 0.00 0.00 0.00 3.16
145 146 9.908152 CCTCCGTTTCTAAATATTTGTCTTTTT 57.092 29.630 11.05 0.00 0.00 1.94
146 147 9.292195 TCCTCCGTTTCTAAATATTTGTCTTTT 57.708 29.630 11.05 0.00 0.00 2.27
147 148 8.857694 TCCTCCGTTTCTAAATATTTGTCTTT 57.142 30.769 11.05 0.00 0.00 2.52
148 149 8.857694 TTCCTCCGTTTCTAAATATTTGTCTT 57.142 30.769 11.05 0.00 0.00 3.01
149 150 8.101419 ACTTCCTCCGTTTCTAAATATTTGTCT 58.899 33.333 11.05 0.00 0.00 3.41
150 151 8.265165 ACTTCCTCCGTTTCTAAATATTTGTC 57.735 34.615 11.05 0.00 0.00 3.18
151 152 9.901172 ATACTTCCTCCGTTTCTAAATATTTGT 57.099 29.630 11.05 0.00 0.00 2.83
160 161 9.075678 CCTAAAGATATACTTCCTCCGTTTCTA 57.924 37.037 0.00 0.00 37.93 2.10
161 162 7.783596 TCCTAAAGATATACTTCCTCCGTTTCT 59.216 37.037 0.00 0.00 37.93 2.52
162 163 7.949434 TCCTAAAGATATACTTCCTCCGTTTC 58.051 38.462 0.00 0.00 37.93 2.78
163 164 7.783596 TCTCCTAAAGATATACTTCCTCCGTTT 59.216 37.037 0.00 0.00 37.93 3.60
164 165 7.231115 GTCTCCTAAAGATATACTTCCTCCGTT 59.769 40.741 0.00 0.00 37.93 4.44
165 166 6.716173 GTCTCCTAAAGATATACTTCCTCCGT 59.284 42.308 0.00 0.00 37.93 4.69
166 167 6.715718 TGTCTCCTAAAGATATACTTCCTCCG 59.284 42.308 0.00 0.00 37.93 4.63
167 168 8.658840 ATGTCTCCTAAAGATATACTTCCTCC 57.341 38.462 0.00 0.00 37.93 4.30
262 263 8.973182 AGAAGATTTTGGGTTGTAGTGTAAAAA 58.027 29.630 0.00 0.00 0.00 1.94
263 264 8.528044 AGAAGATTTTGGGTTGTAGTGTAAAA 57.472 30.769 0.00 0.00 0.00 1.52
291 292 8.101419 GTGGCTAGGGCTATATATGTAAAAACT 58.899 37.037 0.00 0.00 38.73 2.66
293 294 7.017750 TGGTGGCTAGGGCTATATATGTAAAAA 59.982 37.037 0.00 0.00 38.73 1.94
323 324 8.613482 GGGCTTAAGTGTAGAATTTGAGTATTC 58.387 37.037 4.02 0.00 35.26 1.75
331 332 4.341487 GGTGGGGCTTAAGTGTAGAATTT 58.659 43.478 4.02 0.00 0.00 1.82
442 443 1.076332 CTGTTTCGAATGGACGGACC 58.924 55.000 0.00 0.00 39.54 4.46
459 460 4.082571 GGGGTTGTGATGTGAGATTTTCTG 60.083 45.833 0.00 0.00 0.00 3.02
484 485 3.428862 CCAAGGTAATTTTGGCGATCCAC 60.429 47.826 0.00 0.00 43.33 4.02
485 486 2.757868 CCAAGGTAATTTTGGCGATCCA 59.242 45.455 0.00 0.00 38.73 3.41
488 489 2.815158 ACCCAAGGTAATTTTGGCGAT 58.185 42.857 2.33 0.00 43.00 4.58
489 490 2.296073 ACCCAAGGTAATTTTGGCGA 57.704 45.000 2.33 0.00 43.00 5.54
490 491 2.297597 TGAACCCAAGGTAATTTTGGCG 59.702 45.455 2.33 0.00 43.00 5.69
491 492 3.659786 GTGAACCCAAGGTAATTTTGGC 58.340 45.455 2.33 0.00 43.00 4.52
492 493 3.319689 ACGTGAACCCAAGGTAATTTTGG 59.680 43.478 1.01 1.01 43.77 3.28
493 494 4.577834 ACGTGAACCCAAGGTAATTTTG 57.422 40.909 0.00 0.00 33.12 2.44
494 495 5.601583 AAACGTGAACCCAAGGTAATTTT 57.398 34.783 0.00 0.00 33.12 1.82
495 496 5.593502 TGTAAACGTGAACCCAAGGTAATTT 59.406 36.000 0.00 0.00 33.12 1.82
496 497 5.131784 TGTAAACGTGAACCCAAGGTAATT 58.868 37.500 0.00 0.00 33.12 1.40
497 498 4.716794 TGTAAACGTGAACCCAAGGTAAT 58.283 39.130 0.00 0.00 33.12 1.89
498 499 4.148128 TGTAAACGTGAACCCAAGGTAA 57.852 40.909 0.00 0.00 33.12 2.85
499 500 3.834489 TGTAAACGTGAACCCAAGGTA 57.166 42.857 0.00 0.00 33.12 3.08
500 501 2.684374 GTTGTAAACGTGAACCCAAGGT 59.316 45.455 0.00 0.00 36.92 3.50
501 502 3.343380 GTTGTAAACGTGAACCCAAGG 57.657 47.619 0.00 0.00 36.92 3.61
514 515 1.931296 TGGTGGCCAGGGTTGTAAA 59.069 52.632 5.11 0.00 0.00 2.01
515 516 3.675644 TGGTGGCCAGGGTTGTAA 58.324 55.556 5.11 0.00 0.00 2.41
524 525 0.895100 GAGTGATTTGCTGGTGGCCA 60.895 55.000 0.00 0.00 40.92 5.36
525 526 1.598701 GGAGTGATTTGCTGGTGGCC 61.599 60.000 0.00 0.00 40.92 5.36
526 527 0.895100 TGGAGTGATTTGCTGGTGGC 60.895 55.000 0.00 0.00 42.22 5.01
527 528 0.883833 GTGGAGTGATTTGCTGGTGG 59.116 55.000 0.00 0.00 0.00 4.61
528 529 0.883833 GGTGGAGTGATTTGCTGGTG 59.116 55.000 0.00 0.00 0.00 4.17
529 530 0.606401 CGGTGGAGTGATTTGCTGGT 60.606 55.000 0.00 0.00 0.00 4.00
530 531 1.926511 GCGGTGGAGTGATTTGCTGG 61.927 60.000 0.00 0.00 0.00 4.85
531 532 1.503542 GCGGTGGAGTGATTTGCTG 59.496 57.895 0.00 0.00 0.00 4.41
532 533 1.675641 GGCGGTGGAGTGATTTGCT 60.676 57.895 0.00 0.00 0.00 3.91
533 534 1.523154 TTGGCGGTGGAGTGATTTGC 61.523 55.000 0.00 0.00 0.00 3.68
534 535 0.958091 TTTGGCGGTGGAGTGATTTG 59.042 50.000 0.00 0.00 0.00 2.32
535 536 1.698506 TTTTGGCGGTGGAGTGATTT 58.301 45.000 0.00 0.00 0.00 2.17
536 537 1.923356 ATTTTGGCGGTGGAGTGATT 58.077 45.000 0.00 0.00 0.00 2.57
537 538 1.923356 AATTTTGGCGGTGGAGTGAT 58.077 45.000 0.00 0.00 0.00 3.06
538 539 2.156098 GTAATTTTGGCGGTGGAGTGA 58.844 47.619 0.00 0.00 0.00 3.41
539 540 1.201414 GGTAATTTTGGCGGTGGAGTG 59.799 52.381 0.00 0.00 0.00 3.51
540 541 1.541379 GGTAATTTTGGCGGTGGAGT 58.459 50.000 0.00 0.00 0.00 3.85
541 542 0.815095 GGGTAATTTTGGCGGTGGAG 59.185 55.000 0.00 0.00 0.00 3.86
542 543 0.406361 AGGGTAATTTTGGCGGTGGA 59.594 50.000 0.00 0.00 0.00 4.02
543 544 0.530288 CAGGGTAATTTTGGCGGTGG 59.470 55.000 0.00 0.00 0.00 4.61
544 545 0.530288 CCAGGGTAATTTTGGCGGTG 59.470 55.000 0.00 0.00 0.00 4.94
582 1171 0.817654 GGAGTAATTTGCTGGTGGCC 59.182 55.000 0.00 0.00 40.92 5.36
586 1175 5.304101 TGTGAAATTGGAGTAATTTGCTGGT 59.696 36.000 2.67 0.00 46.27 4.00
596 1185 2.107378 TGCAGGGTGTGAAATTGGAGTA 59.893 45.455 0.00 0.00 0.00 2.59
732 1321 0.671796 GCCCGCTTTTTAGGTTGTGT 59.328 50.000 0.00 0.00 0.00 3.72
733 1322 0.671251 TGCCCGCTTTTTAGGTTGTG 59.329 50.000 0.00 0.00 0.00 3.33
734 1323 1.404843 TTGCCCGCTTTTTAGGTTGT 58.595 45.000 0.00 0.00 0.00 3.32
735 1324 2.517650 TTTGCCCGCTTTTTAGGTTG 57.482 45.000 0.00 0.00 0.00 3.77
737 1326 1.069513 GGTTTTGCCCGCTTTTTAGGT 59.930 47.619 0.00 0.00 0.00 3.08
739 1328 1.414378 CGGTTTTGCCCGCTTTTTAG 58.586 50.000 0.00 0.00 41.78 1.85
740 1329 3.571741 CGGTTTTGCCCGCTTTTTA 57.428 47.368 0.00 0.00 41.78 1.52
741 1330 4.429213 CGGTTTTGCCCGCTTTTT 57.571 50.000 0.00 0.00 41.78 1.94
765 1354 4.492160 TCCATCCGCGAGTCGTGC 62.492 66.667 20.47 0.00 35.94 5.34
802 1391 1.994399 TTCCCTCCTCTCTCTCCTCT 58.006 55.000 0.00 0.00 0.00 3.69
843 1442 1.008767 GCGATAGAGACGAACGGGG 60.009 63.158 0.00 0.00 39.76 5.73
1014 1622 1.153765 CTCGACTTCCATCTGCGCA 60.154 57.895 10.98 10.98 0.00 6.09
1213 1821 6.814146 GGCGATAAATCTCCAACCTTATCTAG 59.186 42.308 0.00 0.00 32.04 2.43
1494 2129 0.607489 ATCATGGGCCGAATAGCAGC 60.607 55.000 0.00 0.00 0.00 5.25
1664 2299 7.939039 AGGTACAAAGTTTCATCATGAGAAGAA 59.061 33.333 0.09 2.79 30.28 2.52
1682 2317 0.321830 GGTAAGCCGCCAGGTACAAA 60.322 55.000 0.00 0.00 40.50 2.83
1782 2420 2.281498 GGAAACTCGCTTTGCAAACAAC 59.719 45.455 8.05 0.00 34.87 3.32
2057 2727 8.911918 AGTAAAGACAACAATTACACCATGTA 57.088 30.769 0.00 0.00 33.10 2.29
2195 2866 1.083489 CAACGTCACCACAACTGTGT 58.917 50.000 8.93 0.00 44.21 3.72
2258 2929 9.557338 GAAAAGTAGTACAGTGTACTCTACATG 57.443 37.037 33.69 0.00 41.34 3.21
2766 3441 2.405892 AACGAAAAGCACTGACATGC 57.594 45.000 0.00 2.70 46.50 4.06
2767 3442 4.154015 TCCATAACGAAAAGCACTGACATG 59.846 41.667 0.00 0.00 0.00 3.21
2783 3458 7.019418 GTGAAAATAAACCGTCAGTCCATAAC 58.981 38.462 0.00 0.00 0.00 1.89
2791 3466 3.059188 ACTGCGTGAAAATAAACCGTCAG 60.059 43.478 0.00 0.00 0.00 3.51
2797 3472 3.664025 GCTGTGACTGCGTGAAAATAAAC 59.336 43.478 0.00 0.00 0.00 2.01
2878 3564 2.710377 GCGCCCATGTCATATATGGAA 58.290 47.619 12.78 2.11 46.42 3.53
3000 3686 3.193691 AGTTTCCATAGAGGTGACGACAG 59.806 47.826 0.00 0.00 39.02 3.51
3263 3949 3.476552 CCCTGAAGTAACTCAGCAAACA 58.523 45.455 0.00 0.00 41.36 2.83
3360 4046 5.403166 CGTGTCATTTTCAACAGCATCAATT 59.597 36.000 0.00 0.00 0.00 2.32
3489 4176 2.368221 CTGGAAGAAAATTTGCACCCCA 59.632 45.455 0.00 1.92 34.07 4.96
3599 4286 6.380560 AGTTTATGTCCCTCTCCTACAACTAC 59.619 42.308 0.00 0.00 0.00 2.73
3604 4291 4.684724 ACAGTTTATGTCCCTCTCCTACA 58.315 43.478 0.00 0.00 37.75 2.74
3866 4554 3.692791 AGCAGAAACCAAAACGTCTTC 57.307 42.857 0.00 0.00 0.00 2.87
4163 4933 6.624352 AACATGCACAGTTATGATACATCC 57.376 37.500 4.66 0.00 0.00 3.51
4291 5063 1.134995 TCTGCTTGTCATCAGTAGGCG 60.135 52.381 3.47 0.00 0.00 5.52
4343 5115 2.359230 GGCTCTGTGGTGACTGGC 60.359 66.667 0.00 0.00 0.00 4.85
4516 5288 2.229792 CTTTGTTGCAAGCCTCTACCA 58.770 47.619 0.00 0.00 0.00 3.25
4602 5374 4.081309 TGGTTTATCTACAGCAGGTGTACC 60.081 45.833 8.45 10.30 40.94 3.34
4669 5441 3.394274 TGATCCTTGACTCTTCCCAACAA 59.606 43.478 0.00 0.00 0.00 2.83
4764 5536 8.734386 ACTGGACTTTCTTGATGATAATTTGTC 58.266 33.333 0.00 0.00 0.00 3.18
4811 5583 2.203294 GGACTGGCCGTTGGTTGT 60.203 61.111 0.00 0.00 0.00 3.32
4848 5620 4.916183 TCACTGTCTTCATCAGAGAGAGA 58.084 43.478 3.19 0.00 44.35 3.10
4867 5639 5.936956 ACCTTCAAACTGAGATCTTCATCAC 59.063 40.000 0.00 0.00 34.68 3.06
4963 5735 1.318576 AAGCAGAAACCCAACCTTCG 58.681 50.000 0.00 0.00 0.00 3.79
5163 5935 3.859961 CAGAACTAGAGCGTACATGGTTG 59.140 47.826 0.00 0.00 0.00 3.77
5188 5960 9.466497 TGATGGAACTGAAGCTCTATAAATTTT 57.534 29.630 0.00 0.00 0.00 1.82
5318 6100 1.886542 GCTTTTTCCCGTCTTGGTCAT 59.113 47.619 0.00 0.00 35.15 3.06
5497 6364 2.550830 TCTTTGACTGAGGAACCTGC 57.449 50.000 0.00 0.00 0.00 4.85
5633 6500 6.500684 AAAACTACATACTGACAATGGCAG 57.499 37.500 15.66 15.66 39.26 4.85
5634 6501 6.892658 AAAAACTACATACTGACAATGGCA 57.107 33.333 0.00 0.00 0.00 4.92
5682 6549 5.399858 TGTATAGCTCGAAACAGAAGTGTC 58.600 41.667 0.00 0.00 35.08 3.67
6171 7038 6.540189 AGGTGCAGAGTACAATATTAAGCTTG 59.460 38.462 9.86 0.00 0.00 4.01
6331 7198 4.021191 GCTACAGCACCTTATTTTGAGC 57.979 45.455 0.00 0.00 41.59 4.26
6424 7293 1.942776 TGAGAGCCATCCAGACAAGA 58.057 50.000 0.00 0.00 0.00 3.02
6435 7304 4.922206 AGATTAACAACCAATGAGAGCCA 58.078 39.130 0.00 0.00 0.00 4.75
6645 7514 2.783135 GATTTGGCTGAAGACACAGGA 58.217 47.619 0.00 0.00 38.22 3.86
6864 7733 1.484653 GGCTCTTCTTCTTCCTCCTCC 59.515 57.143 0.00 0.00 0.00 4.30
6894 7763 0.329261 TCTTCCCTGTGGATGCCTTG 59.671 55.000 0.00 0.00 41.40 3.61
7026 7895 1.449778 TTTCAACGCCGACCACACA 60.450 52.632 0.00 0.00 0.00 3.72
7212 8090 3.944422 TGACTGCAAAAAGAACTCGAC 57.056 42.857 0.00 0.00 0.00 4.20
7226 8104 5.348986 TGAAGTAGATACGGAAATGACTGC 58.651 41.667 0.00 0.00 0.00 4.40
7238 8116 9.319143 AGACAACTTGCATAATGAAGTAGATAC 57.681 33.333 0.00 0.00 32.03 2.24
7243 8121 8.621532 AAAGAGACAACTTGCATAATGAAGTA 57.378 30.769 0.00 0.00 32.03 2.24
7273 8157 1.604755 AGCAAAATTTCACCGCACGTA 59.395 42.857 0.00 0.00 0.00 3.57
7358 8574 1.209127 CGATCCGGGCAACAAACAC 59.791 57.895 0.00 0.00 39.74 3.32
7359 8575 0.820074 AACGATCCGGGCAACAAACA 60.820 50.000 0.00 0.00 39.74 2.83
7398 8614 6.837992 TCTATAAAAGGCGATCAACAACAAC 58.162 36.000 0.00 0.00 0.00 3.32
7434 8650 2.480419 GGCCACATCGACAGCATATAAC 59.520 50.000 0.00 0.00 0.00 1.89
7447 9546 4.278419 GGTATCTTTTATGGTGGCCACATC 59.722 45.833 35.78 20.74 35.80 3.06
7492 9591 2.224305 GGATAGTTTCGGTGGCAGCTAT 60.224 50.000 15.48 5.15 0.00 2.97
7603 9731 8.181573 TGGTGATATTCGTGCTTTTCTATTTTC 58.818 33.333 0.00 0.00 0.00 2.29
7604 9732 8.050778 TGGTGATATTCGTGCTTTTCTATTTT 57.949 30.769 0.00 0.00 0.00 1.82
7608 9736 6.345298 TCATGGTGATATTCGTGCTTTTCTA 58.655 36.000 0.00 0.00 0.00 2.10
7610 9738 5.484173 TCATGGTGATATTCGTGCTTTTC 57.516 39.130 0.00 0.00 0.00 2.29
7638 9768 4.764823 TCTCCGCCAACATACAAAGAAAAT 59.235 37.500 0.00 0.00 0.00 1.82
7639 9769 4.023536 GTCTCCGCCAACATACAAAGAAAA 60.024 41.667 0.00 0.00 0.00 2.29
7641 9771 3.071479 GTCTCCGCCAACATACAAAGAA 58.929 45.455 0.00 0.00 0.00 2.52
7643 9773 2.416547 CTGTCTCCGCCAACATACAAAG 59.583 50.000 0.00 0.00 0.00 2.77
7696 9848 6.934645 TGTAAGGAGAATGTTAAGGACAAGTG 59.065 38.462 0.00 0.00 42.62 3.16
7764 9916 5.874810 GCCATTTTCCTTTACCCTTTGATTC 59.125 40.000 0.00 0.00 0.00 2.52
7769 9921 3.502356 TCGCCATTTTCCTTTACCCTTT 58.498 40.909 0.00 0.00 0.00 3.11
7774 9926 6.413818 CGAAATGTATCGCCATTTTCCTTTAC 59.586 38.462 8.32 0.00 43.28 2.01
7781 9933 4.712122 AACCGAAATGTATCGCCATTTT 57.288 36.364 8.32 0.00 43.28 1.82
7788 9940 9.716507 AGATGATTTTAAAACCGAAATGTATCG 57.283 29.630 1.97 0.00 42.37 2.92
7795 9947 8.172352 TGGAAGAGATGATTTTAAAACCGAAA 57.828 30.769 1.97 0.00 0.00 3.46
7891 10045 9.982291 ACAATACATCGACACATACAAAATAAC 57.018 29.630 0.00 0.00 0.00 1.89
7908 10062 7.353497 CAAGAGAGATCATGCAACAATACATC 58.647 38.462 0.00 0.00 0.00 3.06


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

AutoCloner maintained by Alex Coulton.