Multiple sequence alignment - TraesCS6A01G390600

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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 TraesCS6A01G390600 chr6A 100.000 7708 0 0 1 7708 605382628 605374921 0.000000e+00 14235.0
1 TraesCS6A01G390600 chr6A 92.982 57 3 1 5762 5818 496014557 496014502 1.780000e-11 82.4
2 TraesCS6A01G390600 chr6B 92.244 6666 330 84 171 6764 699010077 699003527 0.000000e+00 9273.0
3 TraesCS6A01G390600 chr6B 87.214 743 55 20 7006 7708 698994186 698993444 0.000000e+00 809.0
4 TraesCS6A01G390600 chr6B 91.195 159 13 1 6758 6915 698995443 698995285 1.680000e-51 215.0
5 TraesCS6A01G390600 chr6D 91.159 6888 404 100 1 6752 459700801 459693983 0.000000e+00 9156.0
6 TraesCS6A01G390600 chr6D 84.182 373 38 8 7295 7666 459271524 459271172 7.410000e-90 342.0
7 TraesCS6A01G390600 chr6D 92.982 57 3 1 5762 5818 152191801 152191746 1.780000e-11 82.4
8 TraesCS6A01G390600 chr2A 79.783 277 36 14 2978 3245 501320045 501320310 4.750000e-42 183.0
9 TraesCS6A01G390600 chr2A 94.000 50 3 0 5410 5459 112593904 112593953 8.290000e-10 76.8
10 TraesCS6A01G390600 chr2B 79.562 274 41 11 2978 3245 439770270 439770534 1.710000e-41 182.0
11 TraesCS6A01G390600 chr2D 79.422 277 37 14 2978 3245 370240079 370240344 2.210000e-40 178.0
12 TraesCS6A01G390600 chr1B 83.871 93 9 3 5762 5854 184036214 184036128 4.960000e-12 84.2
13 TraesCS6A01G390600 chr1B 96.000 50 2 0 5410 5459 437592527 437592576 1.780000e-11 82.4
14 TraesCS6A01G390600 chr1B 92.982 57 3 1 5762 5818 488747874 488747819 1.780000e-11 82.4
15 TraesCS6A01G390600 chr1B 90.476 63 5 1 5756 5818 499502456 499502517 1.780000e-11 82.4
16 TraesCS6A01G390600 chr5A 96.000 50 2 0 5410 5459 59629023 59629072 1.780000e-11 82.4
17 TraesCS6A01G390600 chr5A 90.476 63 5 1 5756 5818 473462551 473462612 1.780000e-11 82.4
18 TraesCS6A01G390600 chr3B 92.982 57 3 1 5762 5818 13372777 13372722 1.780000e-11 82.4
19 TraesCS6A01G390600 chr4B 95.833 48 2 0 5412 5459 79296289 79296242 2.310000e-10 78.7
20 TraesCS6A01G390600 chr7A 94.000 50 3 0 5410 5459 487704539 487704490 8.290000e-10 76.8
21 TraesCS6A01G390600 chr1A 94.000 50 3 0 5410 5459 509025361 509025312 8.290000e-10 76.8
22 TraesCS6A01G390600 chr3A 92.000 50 4 0 5410 5459 25405836 25405787 3.860000e-08 71.3


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 TraesCS6A01G390600 chr6A 605374921 605382628 7707 True 14235 14235 100.0000 1 7708 1 chr6A.!!$R2 7707
1 TraesCS6A01G390600 chr6B 699003527 699010077 6550 True 9273 9273 92.2440 171 6764 1 chr6B.!!$R1 6593
2 TraesCS6A01G390600 chr6B 698993444 698995443 1999 True 512 809 89.2045 6758 7708 2 chr6B.!!$R2 950
3 TraesCS6A01G390600 chr6D 459693983 459700801 6818 True 9156 9156 91.1590 1 6752 1 chr6D.!!$R3 6751

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
302 335 0.348370 ATGAAGGAGGATGGTCCCCT 59.652 55.000 0.00 0.00 38.38 4.79 F
487 523 1.004745 ACATCACGGCCTGAAAAGGAT 59.995 47.619 0.00 0.00 30.60 3.24 F
1333 1394 0.169009 TCGATCGCTCGCTCCATATG 59.831 55.000 11.09 0.00 44.65 1.78 F
2305 2379 0.698818 ATCCTGGTTGGTCCTGTTCC 59.301 55.000 0.00 0.00 37.07 3.62 F
3069 3152 1.006102 GTACACGAGTGGCAGCACT 60.006 57.895 8.19 0.00 38.26 4.40 F
3375 3461 1.524621 GTGCACTGCAGACTGTGGT 60.525 57.895 23.35 0.00 43.75 4.16 F
3799 3886 2.502130 TGTGGACAAGTACAAGGTGTCA 59.498 45.455 16.10 5.06 42.81 3.58 F
5052 5145 1.944024 TCTTTGGTGTGCAGGTAAACG 59.056 47.619 0.00 0.00 0.00 3.60 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1330 1391 0.036483 TTGACAGCAAGCGAGCCATA 60.036 50.0 0.00 0.00 34.23 2.74 R
1437 1498 0.107508 ATCAGCAATGTCCCTGTCCG 60.108 55.0 0.00 0.00 0.00 4.79 R
2830 2911 0.251787 GCCACCAAACATCCCTTCCT 60.252 55.0 0.00 0.00 0.00 3.36 R
3814 3901 0.529119 GTGAACGGACGAGTGTTGGT 60.529 55.0 0.00 0.00 0.00 3.67 R
4288 4376 1.464734 ACGGCTCGAGAATCTTCTGA 58.535 50.0 18.75 0.00 37.73 3.27 R
4525 4618 5.079643 AGAGTGGCCACTATGAATGTTTTT 58.920 37.5 37.87 12.05 42.66 1.94 R
5577 5678 1.314534 TGCCAATTCGATGCCCACTG 61.315 55.0 0.00 0.00 0.00 3.66 R
6886 7072 0.180406 CGGTTGTATGGGAGGAAGGG 59.820 60.0 0.00 0.00 0.00 3.95 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
23 24 4.511454 TCTCTGCCGTTATTATGTGCAATC 59.489 41.667 0.00 0.00 0.00 2.67
24 25 4.195416 TCTGCCGTTATTATGTGCAATCA 58.805 39.130 0.00 0.00 0.00 2.57
27 28 5.518812 TGCCGTTATTATGTGCAATCATTC 58.481 37.500 0.00 0.00 0.00 2.67
28 29 4.917415 GCCGTTATTATGTGCAATCATTCC 59.083 41.667 0.00 0.00 0.00 3.01
29 30 5.507149 GCCGTTATTATGTGCAATCATTCCA 60.507 40.000 0.00 0.00 0.00 3.53
30 31 5.914635 CCGTTATTATGTGCAATCATTCCAC 59.085 40.000 0.00 0.00 0.00 4.02
32 33 6.971756 CGTTATTATGTGCAATCATTCCACAA 59.028 34.615 0.00 0.00 42.10 3.33
35 36 4.877378 ATGTGCAATCATTCCACAACTT 57.123 36.364 0.00 0.00 42.10 2.66
41 42 6.036953 GTGCAATCATTCCACAACTTTTCAAA 59.963 34.615 0.00 0.00 0.00 2.69
62 63 8.002433 TCAAATTTAAATAAGTGAAAGCGTGC 57.998 30.769 0.01 0.00 0.00 5.34
87 88 5.379732 TTTTCAGACCAACGACACTTTTT 57.620 34.783 0.00 0.00 0.00 1.94
123 124 7.545265 CACATTTTGAATTTCATATCCAACGGT 59.455 33.333 0.00 0.00 0.00 4.83
124 125 8.093927 ACATTTTGAATTTCATATCCAACGGTT 58.906 29.630 0.00 0.00 0.00 4.44
130 131 2.828877 TCATATCCAACGGTTTAGGCG 58.171 47.619 0.00 0.00 0.00 5.52
151 152 3.739209 CGGAGCATGATAAGTGAGAGCAA 60.739 47.826 0.00 0.00 0.00 3.91
154 155 5.032327 AGCATGATAAGTGAGAGCAATGA 57.968 39.130 0.00 0.00 0.00 2.57
165 166 1.228367 AGCAATGATGATCCCGGCC 60.228 57.895 0.00 0.00 0.00 6.13
166 167 2.620112 GCAATGATGATCCCGGCCG 61.620 63.158 21.04 21.04 0.00 6.13
167 168 2.281761 AATGATGATCCCGGCCGC 60.282 61.111 22.85 6.58 0.00 6.53
168 169 3.850098 AATGATGATCCCGGCCGCC 62.850 63.158 22.85 8.92 0.00 6.13
194 216 1.821061 CTCCAACGACAGAGCAGGGT 61.821 60.000 0.00 0.00 0.00 4.34
197 219 1.270625 CCAACGACAGAGCAGGGTAAA 60.271 52.381 0.00 0.00 0.00 2.01
217 242 1.688187 CCCTTACCTACCGGCCAGT 60.688 63.158 0.00 0.00 0.00 4.00
219 244 1.713297 CCTTACCTACCGGCCAGTAT 58.287 55.000 0.00 0.00 0.00 2.12
220 245 1.343465 CCTTACCTACCGGCCAGTATG 59.657 57.143 0.00 1.04 0.00 2.39
221 246 0.754472 TTACCTACCGGCCAGTATGC 59.246 55.000 0.00 0.00 31.97 3.14
231 257 2.300433 GGCCAGTATGCAACATCATCA 58.700 47.619 0.00 0.00 31.97 3.07
252 282 0.949105 GCTCCGTCGTTGTTGGTCAT 60.949 55.000 0.00 0.00 0.00 3.06
261 291 4.092968 GTCGTTGTTGGTCATCCAGATAAC 59.907 45.833 0.00 0.00 45.22 1.89
262 292 4.020573 TCGTTGTTGGTCATCCAGATAACT 60.021 41.667 0.00 0.00 45.22 2.24
273 303 6.538742 GTCATCCAGATAACTTTCCATTTCGA 59.461 38.462 0.00 0.00 0.00 3.71
279 309 6.020281 CAGATAACTTTCCATTTCGAGTCTCG 60.020 42.308 16.33 16.33 42.10 4.04
290 320 1.007580 CGAGTCTCGACGATGAAGGA 58.992 55.000 17.52 0.00 43.74 3.36
291 321 1.004398 CGAGTCTCGACGATGAAGGAG 60.004 57.143 17.52 0.00 43.74 3.69
294 324 1.950909 GTCTCGACGATGAAGGAGGAT 59.049 52.381 0.00 0.00 0.00 3.24
302 335 0.348370 ATGAAGGAGGATGGTCCCCT 59.652 55.000 0.00 0.00 38.38 4.79
304 337 1.368203 TGAAGGAGGATGGTCCCCTTA 59.632 52.381 14.68 5.64 43.02 2.69
305 338 1.769465 GAAGGAGGATGGTCCCCTTAC 59.231 57.143 14.68 8.25 43.02 2.34
309 342 2.449450 GGATGGTCCCCTTACCCCG 61.449 68.421 0.00 0.00 38.90 5.73
310 343 1.383525 GATGGTCCCCTTACCCCGA 60.384 63.158 0.00 0.00 38.90 5.14
338 374 4.778143 CGTAGCGCCCCCAAGCTT 62.778 66.667 2.29 0.00 44.15 3.74
418 454 2.880890 CGAGGGGATTGATTCATGAACC 59.119 50.000 11.07 0.14 0.00 3.62
424 460 6.723052 AGGGGATTGATTCATGAACCAATATC 59.277 38.462 24.98 19.34 30.29 1.63
487 523 1.004745 ACATCACGGCCTGAAAAGGAT 59.995 47.619 0.00 0.00 30.60 3.24
565 608 4.688419 CGCGCAGTTGCAACCCAG 62.688 66.667 25.62 17.04 42.21 4.45
572 615 3.222855 TTGCAACCCAGCCCAACG 61.223 61.111 0.00 0.00 0.00 4.10
586 629 4.722700 AACGCAAGCCGCCCATCT 62.723 61.111 0.00 0.00 45.62 2.90
736 779 3.566742 CCCGTACCTGCCAATATTTTACC 59.433 47.826 0.00 0.00 0.00 2.85
747 790 4.339429 CAATATTTTACCAGTCGCGGTTG 58.661 43.478 6.13 4.90 40.67 3.77
786 834 2.527624 TGGCTGGCAGTGGAGAGT 60.528 61.111 17.16 0.00 0.00 3.24
896 944 4.257510 GCTCGCGCTCGGAGATCA 62.258 66.667 14.03 0.00 33.89 2.92
943 998 8.537223 TCGCTCAAAGATCGTTTATTTATACAC 58.463 33.333 0.00 0.00 0.00 2.90
995 1050 1.537776 CGGATCTGGATCTCACTGCAC 60.538 57.143 9.96 0.00 37.92 4.57
1004 1059 3.249189 TCACTGCACCTCCCACCC 61.249 66.667 0.00 0.00 0.00 4.61
1005 1060 4.704833 CACTGCACCTCCCACCCG 62.705 72.222 0.00 0.00 0.00 5.28
1140 1201 2.278206 CGAGTCCATGTCCGAGCG 60.278 66.667 0.00 0.00 0.00 5.03
1186 1247 4.498520 ATCAGCGCCGTCGTCCTG 62.499 66.667 2.29 0.00 38.14 3.86
1216 1277 4.415332 GCCGACGAGGAGCACGAA 62.415 66.667 0.00 0.00 45.00 3.85
1252 1313 4.373116 GAGTTCTCCGCCACCGCA 62.373 66.667 0.00 0.00 34.03 5.69
1288 1349 5.903010 CCCCCAGCAGGTACATACATATATA 59.097 44.000 0.00 0.00 0.00 0.86
1289 1350 6.183360 CCCCCAGCAGGTACATACATATATAC 60.183 46.154 0.00 0.00 0.00 1.47
1290 1351 6.461092 CCCCAGCAGGTACATACATATATACG 60.461 46.154 0.00 0.00 0.00 3.06
1323 1384 1.282570 CTCTGCTCCTCGATCGCTC 59.717 63.158 11.09 0.00 0.00 5.03
1325 1386 4.257510 TGCTCCTCGATCGCTCGC 62.258 66.667 11.09 10.54 44.65 5.03
1327 1388 2.251075 CTCCTCGATCGCTCGCTC 59.749 66.667 11.09 0.00 44.65 5.03
1329 1390 3.586961 CCTCGATCGCTCGCTCCA 61.587 66.667 11.09 0.00 44.65 3.86
1330 1391 2.642129 CTCGATCGCTCGCTCCAT 59.358 61.111 11.09 0.00 44.65 3.41
1331 1392 1.578206 CCTCGATCGCTCGCTCCATA 61.578 60.000 11.09 0.00 44.65 2.74
1333 1394 0.169009 TCGATCGCTCGCTCCATATG 59.831 55.000 11.09 0.00 44.65 1.78
1414 1475 4.449131 TCCTGATCATGATCAAGACAAGC 58.551 43.478 32.38 8.75 46.10 4.01
1416 1477 3.548770 TGATCATGATCAAGACAAGCCC 58.451 45.455 31.46 5.87 44.14 5.19
1421 1482 1.648467 GATCAAGACAAGCCCGGTGC 61.648 60.000 0.00 3.33 41.71 5.01
1437 1498 1.727335 GGTGCTCGCTAAAAGTCAGTC 59.273 52.381 0.00 0.00 0.00 3.51
1438 1499 1.387084 GTGCTCGCTAAAAGTCAGTCG 59.613 52.381 0.00 0.00 0.00 4.18
1513 1585 1.945387 ACAGTGCTAGGATGCATTCG 58.055 50.000 0.00 0.00 45.23 3.34
1523 1595 5.220931 GCTAGGATGCATTCGTCTTGATTTT 60.221 40.000 0.00 0.00 0.00 1.82
1559 1631 1.205064 CTTGCTGCGTTTCGGTCTG 59.795 57.895 0.00 0.00 0.00 3.51
1590 1662 5.412594 GTGATGCCTTAAAGTTGTGATCTCA 59.587 40.000 0.00 0.00 0.00 3.27
1602 1674 2.170397 TGTGATCTCACTTGGTGTGTGT 59.830 45.455 11.35 0.00 46.55 3.72
1603 1675 3.206150 GTGATCTCACTTGGTGTGTGTT 58.794 45.455 3.07 0.00 46.27 3.32
1604 1676 3.627577 GTGATCTCACTTGGTGTGTGTTT 59.372 43.478 3.07 0.00 46.27 2.83
1718 1790 2.676822 AGCGAGGTCTGCTCCGAA 60.677 61.111 0.00 0.00 38.62 4.30
1782 1854 1.421268 TCTTCTGGTGATGGCTGTTGT 59.579 47.619 0.00 0.00 0.00 3.32
1802 1875 6.265196 TGTTGTCTGAATTTAGCATTTCTGGT 59.735 34.615 0.00 0.00 36.89 4.00
1805 1878 6.660521 TGTCTGAATTTAGCATTTCTGGTGAT 59.339 34.615 0.00 0.00 34.31 3.06
1808 1881 6.101332 TGAATTTAGCATTTCTGGTGATTGC 58.899 36.000 0.00 0.00 34.31 3.56
1827 1900 2.884012 TGCGAATCATGTGTTGGTTCTT 59.116 40.909 0.00 0.00 42.35 2.52
1836 1909 2.894126 TGTGTTGGTTCTTTGGTGTTGT 59.106 40.909 0.00 0.00 0.00 3.32
2002 2075 3.181423 TGGAGAAGGTTTGCCAGGTAATT 60.181 43.478 0.00 0.00 37.19 1.40
2022 2095 9.224267 GGTAATTATGCATATGCCTATATCTGG 57.776 37.037 24.54 0.00 41.18 3.86
2049 2122 8.226819 TGTTTTGTGAATGGACAGTAAATGTA 57.773 30.769 0.00 0.00 44.17 2.29
2053 2126 6.299922 TGTGAATGGACAGTAAATGTACCAA 58.700 36.000 0.00 0.00 42.78 3.67
2058 2131 4.538490 TGGACAGTAAATGTACCAAGGGAT 59.462 41.667 0.00 0.00 42.78 3.85
2061 2134 6.352394 GGACAGTAAATGTACCAAGGGATGTA 60.352 42.308 0.00 0.00 44.17 2.29
2071 2144 5.450818 ACCAAGGGATGTAAATGCTCTTA 57.549 39.130 0.00 0.00 0.00 2.10
2074 2147 6.157994 ACCAAGGGATGTAAATGCTCTTAGTA 59.842 38.462 0.00 0.00 0.00 1.82
2077 2150 9.778741 CAAGGGATGTAAATGCTCTTAGTATTA 57.221 33.333 0.00 0.00 30.27 0.98
2138 2211 1.830279 ATGCTTTCTGCTAGCTTGCA 58.170 45.000 21.46 21.46 43.37 4.08
2304 2378 3.244770 TGTTATCCTGGTTGGTCCTGTTC 60.245 47.826 0.00 0.00 37.07 3.18
2305 2379 0.698818 ATCCTGGTTGGTCCTGTTCC 59.301 55.000 0.00 0.00 37.07 3.62
2461 2535 3.192212 CCAAGCCCATTCTTCTCAAAGAC 59.808 47.826 0.00 0.00 41.23 3.01
2531 2605 7.285566 TGTAGGTATGTACTAGGATCGACTTT 58.714 38.462 0.00 0.00 0.00 2.66
2533 2607 9.277783 GTAGGTATGTACTAGGATCGACTTTTA 57.722 37.037 0.00 0.00 0.00 1.52
2576 2650 3.365265 GTTGGGCTTCCGTGGCAG 61.365 66.667 0.00 0.00 0.00 4.85
2593 2669 2.037136 AGCACTCACGCTTGCCATC 61.037 57.895 0.00 0.00 39.99 3.51
2830 2911 2.823984 CAAGACACAAAATGGCAAGCA 58.176 42.857 0.00 0.00 39.81 3.91
2972 3055 8.310382 CAATTAACCATTGTTCCTTGGACATAA 58.690 33.333 0.00 0.00 38.01 1.90
3069 3152 1.006102 GTACACGAGTGGCAGCACT 60.006 57.895 8.19 0.00 38.26 4.40
3114 3199 7.124298 AGCTACACTAGATTATCCTGTTGTCAA 59.876 37.037 0.00 0.00 0.00 3.18
3120 3205 8.258708 ACTAGATTATCCTGTTGTCAAGTTACC 58.741 37.037 0.00 0.00 0.00 2.85
3339 3425 3.626217 GCTGTTTTCCCTTATACCTTCCG 59.374 47.826 0.00 0.00 0.00 4.30
3375 3461 1.524621 GTGCACTGCAGACTGTGGT 60.525 57.895 23.35 0.00 43.75 4.16
3505 3591 9.836864 ATATTGTGAAGTTATGTCAGCTCAATA 57.163 29.630 0.00 0.00 31.51 1.90
3521 3607 8.741841 TCAGCTCAATACAAATTTGATGAATGA 58.258 29.630 24.64 22.02 32.94 2.57
3568 3655 4.594970 TCGGGGTTGTCATTATGTTTGAT 58.405 39.130 0.00 0.00 0.00 2.57
3581 3668 8.420222 TCATTATGTTTGATGTGTCCTTTTGTT 58.580 29.630 0.00 0.00 0.00 2.83
3594 3681 8.253810 TGTGTCCTTTTGTTTGACAATTCATAA 58.746 29.630 0.00 0.00 40.41 1.90
3595 3682 8.539674 GTGTCCTTTTGTTTGACAATTCATAAC 58.460 33.333 0.00 0.00 40.41 1.89
3697 3784 8.791327 ATAATTTTTGTGGGGCTTGATTTTAG 57.209 30.769 0.00 0.00 0.00 1.85
3755 3842 4.080129 ACATGTAGACTCCGAACTACCCTA 60.080 45.833 0.00 0.00 38.40 3.53
3799 3886 2.502130 TGTGGACAAGTACAAGGTGTCA 59.498 45.455 16.10 5.06 42.81 3.58
3814 3901 6.600032 ACAAGGTGTCAATATTTTATACCGCA 59.400 34.615 7.46 0.00 0.00 5.69
4055 4143 8.868522 TCAACCATCAAGTTCAATATTCTCTT 57.131 30.769 0.00 0.00 0.00 2.85
4056 4144 8.733458 TCAACCATCAAGTTCAATATTCTCTTG 58.267 33.333 13.29 13.29 37.44 3.02
4091 4179 4.701956 ACTAAATCTCAACATTTGCCGG 57.298 40.909 0.00 0.00 0.00 6.13
4171 4259 5.776744 CTTTGGAGCTTGTCTGCTTTTATT 58.223 37.500 0.00 0.00 44.17 1.40
4223 4311 9.832445 AGTCAACCTAACATAACATACCAATAG 57.168 33.333 0.00 0.00 0.00 1.73
4288 4376 9.050601 GCTAAGAAGCTCATATGACTTAACAAT 57.949 33.333 15.87 7.51 45.85 2.71
4305 4393 3.791245 ACAATCAGAAGATTCTCGAGCC 58.209 45.455 7.81 0.00 42.46 4.70
4477 4569 5.817816 CCAACCAGGAGACTACAAATATGAC 59.182 44.000 0.00 0.00 40.21 3.06
4484 4576 5.812642 GGAGACTACAAATATGACACACTGG 59.187 44.000 0.00 0.00 0.00 4.00
4525 4618 9.177608 GGCTGTAATATGATTTGGATAGCATAA 57.822 33.333 0.00 0.00 0.00 1.90
4711 4804 4.999469 TGCATGGAGGTACATGGATAAT 57.001 40.909 4.33 0.00 46.40 1.28
4715 4808 7.469343 TGCATGGAGGTACATGGATAATTTAT 58.531 34.615 4.33 0.00 46.40 1.40
4919 5012 6.996509 TCTTCTCAATTTCTTTTTCATGGGG 58.003 36.000 0.00 0.00 0.00 4.96
5052 5145 1.944024 TCTTTGGTGTGCAGGTAAACG 59.056 47.619 0.00 0.00 0.00 3.60
5173 5267 5.055812 CAGGAGATTGAAGGAGAATGTAGC 58.944 45.833 0.00 0.00 0.00 3.58
5497 5598 4.987912 GCTGCTTATTTGGTTTGTTTGCTA 59.012 37.500 0.00 0.00 0.00 3.49
5532 5633 3.769739 AGTTCAGTATGTGGCTGTTGA 57.230 42.857 0.00 0.00 37.40 3.18
5547 5648 6.308766 GTGGCTGTTGAAAATTGTTATGCTAG 59.691 38.462 0.00 0.00 0.00 3.42
5577 5678 7.916977 TGAGTTATCTTGCACATTTGAATATGC 59.083 33.333 0.20 0.20 39.21 3.14
5901 6006 4.109766 CGCACTCAGGTATTTTCGTGATA 58.890 43.478 0.00 0.00 32.97 2.15
5905 6010 6.092259 GCACTCAGGTATTTTCGTGATACTTT 59.908 38.462 0.00 0.00 32.97 2.66
5944 6049 3.254166 TCCGTTCTAAAGCGAGTTACACT 59.746 43.478 0.00 0.00 0.00 3.55
5959 6064 9.474249 GCGAGTTACACTATCAGAAAATAAAAC 57.526 33.333 0.00 0.00 0.00 2.43
5988 6093 2.550830 ACATGGAAGTATGCGATCCC 57.449 50.000 0.00 0.00 32.01 3.85
6026 6131 5.290158 GTCTATTCAGCATGCCAAAATTGTG 59.710 40.000 15.66 3.26 34.76 3.33
6055 6160 5.349817 ACAAAGTGAGTTCTGATAGATTGCG 59.650 40.000 0.00 0.00 0.00 4.85
6058 6163 5.911752 AGTGAGTTCTGATAGATTGCGAAT 58.088 37.500 0.00 0.00 0.00 3.34
6059 6164 5.752472 AGTGAGTTCTGATAGATTGCGAATG 59.248 40.000 0.00 0.00 0.00 2.67
6060 6165 5.521735 GTGAGTTCTGATAGATTGCGAATGT 59.478 40.000 0.00 0.00 0.00 2.71
6061 6166 6.036517 GTGAGTTCTGATAGATTGCGAATGTT 59.963 38.462 0.00 0.00 0.00 2.71
6062 6167 6.256539 TGAGTTCTGATAGATTGCGAATGTTC 59.743 38.462 0.00 0.00 0.00 3.18
6066 6198 4.522114 TGATAGATTGCGAATGTTCCCAA 58.478 39.130 0.00 0.00 30.48 4.12
6078 6210 2.790433 TGTTCCCAATTCACCAGCTAC 58.210 47.619 0.00 0.00 0.00 3.58
6136 6276 5.376625 ACACTCTTTGTTAGCCAGATGAAA 58.623 37.500 0.00 0.00 33.09 2.69
6148 6288 3.552875 CCAGATGAAACATGCTCCAGAT 58.447 45.455 0.00 0.00 0.00 2.90
6169 6309 7.117523 CCAGATTAGCTACTGTCAATCTTATGC 59.882 40.741 9.74 0.00 35.96 3.14
6250 6422 1.725665 CTGCCTGTCATTCATGCGG 59.274 57.895 0.00 0.00 39.86 5.69
6528 6702 6.379386 GTTGGTAGAAGGTTGATTTTAGTGC 58.621 40.000 0.00 0.00 0.00 4.40
6531 6705 5.063564 GGTAGAAGGTTGATTTTAGTGCTCG 59.936 44.000 0.00 0.00 0.00 5.03
6534 6708 4.202245 AGGTTGATTTTAGTGCTCGCTA 57.798 40.909 0.00 0.00 0.00 4.26
6552 6729 3.000322 CGCTAGTCCTTTTAATCAGTGCG 60.000 47.826 0.00 0.00 0.00 5.34
6574 6751 4.692228 GATTTTCTCCTGAGGCTAGTGAG 58.308 47.826 0.00 0.00 0.00 3.51
6608 6786 6.878923 TGGTGTAATGTAATGTTCTCTCCTTG 59.121 38.462 0.00 0.00 0.00 3.61
6676 6857 4.601019 GTGAATGTATTGATTGGCCGAAG 58.399 43.478 0.00 0.00 0.00 3.79
6713 6894 9.398170 CAATAAAGGAAATGTCAACTGTGTTAG 57.602 33.333 0.00 0.00 0.00 2.34
6755 6940 3.694566 GTGGTGTTTTCTCAAGTCTGGTT 59.305 43.478 0.00 0.00 0.00 3.67
6782 6967 4.546829 AAAGGGAGCGTGTACTGATTAA 57.453 40.909 0.00 0.00 0.00 1.40
6786 6971 2.860735 GGAGCGTGTACTGATTAAGCAG 59.139 50.000 18.88 18.88 41.63 4.24
6807 6992 2.401720 GCTGAAAATGTCTTTTGCGTCG 59.598 45.455 0.00 0.00 34.73 5.12
6808 6993 2.973224 CTGAAAATGTCTTTTGCGTCGG 59.027 45.455 0.00 0.00 34.73 4.79
6840 7026 3.539604 CAGGACCACTTGATCTTGATCC 58.460 50.000 7.99 0.00 0.00 3.36
6886 7072 4.878397 CACTATTCATCTTCAACCTCACCC 59.122 45.833 0.00 0.00 0.00 4.61
6887 7073 2.879103 TTCATCTTCAACCTCACCCC 57.121 50.000 0.00 0.00 0.00 4.95
6894 7080 0.840722 TCAACCTCACCCCCTTCCTC 60.841 60.000 0.00 0.00 0.00 3.71
6900 7086 0.327191 TCACCCCCTTCCTCCCATAC 60.327 60.000 0.00 0.00 0.00 2.39
6907 7093 0.463833 CTTCCTCCCATACAACCGCC 60.464 60.000 0.00 0.00 0.00 6.13
6915 7101 2.971598 ATACAACCGCCTGCCTGCT 61.972 57.895 0.00 0.00 0.00 4.24
6916 7102 2.876368 ATACAACCGCCTGCCTGCTC 62.876 60.000 0.00 0.00 0.00 4.26
6917 7103 4.711949 CAACCGCCTGCCTGCTCT 62.712 66.667 0.00 0.00 0.00 4.09
6918 7104 4.711949 AACCGCCTGCCTGCTCTG 62.712 66.667 0.00 0.00 0.00 3.35
6924 7110 4.486503 CTGCCTGCTCTGCCCCTC 62.487 72.222 0.00 0.00 0.00 4.30
6926 7112 4.486503 GCCTGCTCTGCCCCTCTG 62.487 72.222 0.00 0.00 0.00 3.35
6927 7113 4.486503 CCTGCTCTGCCCCTCTGC 62.487 72.222 0.00 0.00 0.00 4.26
6928 7114 3.400928 CTGCTCTGCCCCTCTGCT 61.401 66.667 0.00 0.00 0.00 4.24
6929 7115 2.932194 TGCTCTGCCCCTCTGCTT 60.932 61.111 0.00 0.00 0.00 3.91
6930 7116 2.438075 GCTCTGCCCCTCTGCTTG 60.438 66.667 0.00 0.00 0.00 4.01
6931 7117 2.271497 CTCTGCCCCTCTGCTTGG 59.729 66.667 0.00 0.00 0.00 3.61
6932 7118 3.991725 CTCTGCCCCTCTGCTTGGC 62.992 68.421 0.00 0.00 45.56 4.52
6936 7122 3.970410 CCCCTCTGCTTGGCACCA 61.970 66.667 0.00 0.00 33.79 4.17
6937 7123 2.674380 CCCTCTGCTTGGCACCAC 60.674 66.667 0.00 0.00 33.79 4.16
6938 7124 2.674380 CCTCTGCTTGGCACCACC 60.674 66.667 0.00 0.00 33.79 4.61
6972 7158 3.088044 GCTCTGCGCATGTCTCAC 58.912 61.111 12.24 0.00 38.92 3.51
6976 7162 4.678499 TGCGCATGTCTCACGGCA 62.678 61.111 5.66 0.00 0.00 5.69
6979 7165 2.316867 CGCATGTCTCACGGCACAA 61.317 57.895 0.00 0.00 0.00 3.33
6980 7166 1.207593 GCATGTCTCACGGCACAAC 59.792 57.895 0.00 0.00 0.00 3.32
6985 7171 2.358737 CTCACGGCACAACCCTCC 60.359 66.667 0.00 0.00 33.26 4.30
7004 7190 2.477104 CCCCCATCCCTTATGCTTTT 57.523 50.000 0.00 0.00 33.92 2.27
7009 8254 5.397360 CCCCATCCCTTATGCTTTTTCTAT 58.603 41.667 0.00 0.00 33.92 1.98
7019 8264 7.756722 CCTTATGCTTTTTCTATGACTTGTTGG 59.243 37.037 0.00 0.00 0.00 3.77
7048 8293 4.180817 GCATTTGGTTATGTAAAGGCCAC 58.819 43.478 5.01 0.00 37.55 5.01
7056 8301 6.320164 TGGTTATGTAAAGGCCACATATTCAC 59.680 38.462 13.54 9.69 38.36 3.18
7057 8302 6.238925 GGTTATGTAAAGGCCACATATTCACC 60.239 42.308 13.54 13.77 38.36 4.02
7061 8306 0.180406 AGGCCACATATTCACCCGTC 59.820 55.000 5.01 0.00 0.00 4.79
7070 8315 1.227999 ATTCACCCGTCGCAGTTGTG 61.228 55.000 0.00 0.00 0.00 3.33
7076 8322 0.163788 CCGTCGCAGTTGTGTCATTC 59.836 55.000 0.00 0.00 0.00 2.67
7080 8326 2.921121 GTCGCAGTTGTGTCATTCGATA 59.079 45.455 0.00 0.00 0.00 2.92
7088 8334 7.910162 GCAGTTGTGTCATTCGATATAACATTT 59.090 33.333 0.00 0.00 37.00 2.32
7188 8468 3.067833 GTGCACAAGTTCCTTCCTAGTC 58.932 50.000 13.17 0.00 0.00 2.59
7189 8469 2.972713 TGCACAAGTTCCTTCCTAGTCT 59.027 45.455 0.00 0.00 0.00 3.24
7190 8470 3.006967 TGCACAAGTTCCTTCCTAGTCTC 59.993 47.826 0.00 0.00 0.00 3.36
7199 8479 0.393402 TTCCTAGTCTCGGCGCACTA 60.393 55.000 10.83 15.05 0.00 2.74
7201 8481 0.454600 CCTAGTCTCGGCGCACTAAA 59.545 55.000 10.83 1.92 0.00 1.85
7215 8497 4.725169 GCGCACTAAATCTTAGCTCAACAC 60.725 45.833 0.30 0.00 0.00 3.32
7238 8520 5.643777 ACAAACAAGGAGATATTTCGTGGAG 59.356 40.000 0.00 0.00 0.00 3.86
7273 8555 5.473039 TGAGGAGATAATGTACGCATGATG 58.527 41.667 0.00 0.00 35.15 3.07
7275 8557 5.858381 AGGAGATAATGTACGCATGATGTT 58.142 37.500 0.00 0.00 35.15 2.71
7300 8582 4.790718 AAAGGGAGATAATGTACCACCC 57.209 45.455 0.00 0.00 36.47 4.61
7376 8658 6.313519 AGCTTTCAACTCCATAATGTCCTA 57.686 37.500 0.00 0.00 0.00 2.94
7399 8681 2.705127 ACATTCCCAAGCCAACAAACAT 59.295 40.909 0.00 0.00 0.00 2.71
7436 8718 2.092753 ACTCGATGCCACAAGGATTCAT 60.093 45.455 0.00 0.00 36.89 2.57
7446 8728 2.421073 ACAAGGATTCATGCACATCACG 59.579 45.455 0.00 0.00 0.00 4.35
7533 8815 4.290622 CCTGCCTGGCCACCTTGT 62.291 66.667 17.53 0.00 0.00 3.16
7554 8836 1.006102 CTCGCCGTCACCTTTCTGT 60.006 57.895 0.00 0.00 0.00 3.41
7560 8842 1.308998 CGTCACCTTTCTGTTTGCCT 58.691 50.000 0.00 0.00 0.00 4.75
7581 8863 2.126228 CCGCCACGAAGTCGCTTA 60.126 61.111 0.00 0.00 44.04 3.09
7602 8884 2.124983 CCATGCAGACGGACCAGG 60.125 66.667 0.00 0.00 0.00 4.45
7649 8931 2.728383 GCGCACTGCTGCAAACAG 60.728 61.111 13.46 13.46 44.50 3.16
7656 8938 2.144952 TGCTGCAAACAGGAGGAGA 58.855 52.632 0.00 0.00 44.63 3.71
7688 8973 1.006922 GCCTCAGCTTGTTGTTGGC 60.007 57.895 0.00 7.88 35.50 4.52
7696 8981 2.076863 GCTTGTTGTTGGCGATCTAGT 58.923 47.619 0.00 0.00 0.00 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
18 19 6.601741 TTTGAAAAGTTGTGGAATGATTGC 57.398 33.333 0.00 0.00 0.00 3.56
41 42 5.695818 ACGCACGCTTTCACTTATTTAAAT 58.304 33.333 5.89 5.89 0.00 1.40
51 52 1.512771 CTGAAAAACGCACGCTTTCAC 59.487 47.619 13.68 4.02 34.88 3.18
57 58 0.248296 TTGGTCTGAAAAACGCACGC 60.248 50.000 0.00 0.00 0.00 5.34
60 61 1.062880 GTCGTTGGTCTGAAAAACGCA 59.937 47.619 16.79 7.34 44.70 5.24
62 63 2.350498 AGTGTCGTTGGTCTGAAAAACG 59.650 45.455 15.91 15.91 46.03 3.60
87 88 7.993101 TGAAATTCAAAATGTGCCATTGAAAA 58.007 26.923 4.51 0.00 43.79 2.29
123 124 3.133901 TCACTTATCATGCTCCGCCTAAA 59.866 43.478 0.00 0.00 0.00 1.85
124 125 2.698274 TCACTTATCATGCTCCGCCTAA 59.302 45.455 0.00 0.00 0.00 2.69
130 131 3.465742 TGCTCTCACTTATCATGCTCC 57.534 47.619 0.00 0.00 0.00 4.70
151 152 4.335647 GGCGGCCGGGATCATCAT 62.336 66.667 29.38 0.00 0.00 2.45
165 166 4.891727 CGTTGGAGATCCGGGGCG 62.892 72.222 0.00 0.00 39.43 6.13
166 167 3.467226 TCGTTGGAGATCCGGGGC 61.467 66.667 0.00 0.00 39.43 5.80
167 168 2.298158 CTGTCGTTGGAGATCCGGGG 62.298 65.000 0.00 0.00 39.43 5.73
168 169 1.141881 CTGTCGTTGGAGATCCGGG 59.858 63.158 0.00 0.00 39.43 5.73
169 170 0.101399 CTCTGTCGTTGGAGATCCGG 59.899 60.000 0.00 0.00 39.43 5.14
194 216 1.203237 GCCGGTAGGTAAGGGGTTTA 58.797 55.000 1.90 0.00 40.50 2.01
197 219 2.366034 GGCCGGTAGGTAAGGGGT 60.366 66.667 1.90 0.00 40.50 4.95
217 242 2.874086 CGGAGCTTGATGATGTTGCATA 59.126 45.455 0.00 0.00 0.00 3.14
219 244 1.089112 CGGAGCTTGATGATGTTGCA 58.911 50.000 0.00 0.00 0.00 4.08
220 245 1.063174 GACGGAGCTTGATGATGTTGC 59.937 52.381 0.00 0.00 0.00 4.17
221 246 1.325640 CGACGGAGCTTGATGATGTTG 59.674 52.381 0.00 0.00 0.00 3.33
231 257 0.878961 GACCAACAACGACGGAGCTT 60.879 55.000 0.00 0.00 0.00 3.74
252 282 6.049955 ACTCGAAATGGAAAGTTATCTGGA 57.950 37.500 0.00 0.00 0.00 3.86
273 303 1.065345 TCCTCCTTCATCGTCGAGACT 60.065 52.381 0.00 0.00 0.00 3.24
279 309 1.069358 GGACCATCCTCCTTCATCGTC 59.931 57.143 0.00 0.00 32.53 4.20
281 311 0.394565 GGGACCATCCTCCTTCATCG 59.605 60.000 0.00 0.00 36.57 3.84
302 335 2.650196 CGTTGGTCGTCGGGGTAA 59.350 61.111 0.00 0.00 34.52 2.85
309 342 3.177249 GCTACGCCGTTGGTCGTC 61.177 66.667 0.00 0.00 36.94 4.20
352 388 2.104170 GAATGGAAATTTACCGGGGCA 58.896 47.619 6.32 0.00 0.00 5.36
424 460 7.395190 TGGTCATTTCTTCCTTGATATTGTG 57.605 36.000 0.00 0.00 0.00 3.33
487 523 5.126869 TGATTCAGCAACTCCACAAGAAAAA 59.873 36.000 0.00 0.00 0.00 1.94
494 531 3.507233 GGAATTGATTCAGCAACTCCACA 59.493 43.478 0.51 0.00 42.21 4.17
551 589 3.994853 GGGCTGGGTTGCAACTGC 61.995 66.667 27.64 25.41 42.50 4.40
552 590 2.132996 TTGGGCTGGGTTGCAACTG 61.133 57.895 27.64 18.49 34.04 3.16
572 615 3.512516 GTGAGATGGGCGGCTTGC 61.513 66.667 9.56 0.00 45.38 4.01
586 629 2.047655 GATCGTGCGGGTTGGTGA 60.048 61.111 0.00 0.00 0.00 4.02
706 749 4.446413 CAGGTACGGGGTGGCGAC 62.446 72.222 0.00 0.00 0.00 5.19
786 834 2.313317 AGTCGTGTGTTGACTTCCCTA 58.687 47.619 0.00 0.00 44.00 3.53
834 882 3.657038 TTCTCCGACTCCTCCCCCG 62.657 68.421 0.00 0.00 0.00 5.73
836 884 1.758906 CCTTCTCCGACTCCTCCCC 60.759 68.421 0.00 0.00 0.00 4.81
837 885 1.758906 CCCTTCTCCGACTCCTCCC 60.759 68.421 0.00 0.00 0.00 4.30
1096 1157 4.658786 AGCTTGTCCGGGGTCCCT 62.659 66.667 8.15 0.00 0.00 4.20
1157 1218 2.203082 CGCTGATCCCGGAGATGGA 61.203 63.158 0.73 0.00 34.42 3.41
1216 1277 4.070552 GCGCTGGGGAAGACGAGT 62.071 66.667 0.00 0.00 0.00 4.18
1247 1308 3.063084 GGAGGAGACGAGTGCGGT 61.063 66.667 0.00 0.00 43.17 5.68
1268 1329 6.472486 GTGCGTATATATGTATGTACCTGCTG 59.528 42.308 8.21 0.00 29.62 4.41
1323 1384 1.301244 AAGCGAGCCATATGGAGCG 60.301 57.895 26.47 25.06 36.95 5.03
1325 1386 0.250209 AGCAAGCGAGCCATATGGAG 60.250 55.000 26.47 15.76 37.39 3.86
1327 1388 0.816825 ACAGCAAGCGAGCCATATGG 60.817 55.000 18.07 18.07 38.53 2.74
1329 1390 0.178767 TGACAGCAAGCGAGCCATAT 59.821 50.000 0.00 0.00 34.23 1.78
1330 1391 0.036483 TTGACAGCAAGCGAGCCATA 60.036 50.000 0.00 0.00 34.23 2.74
1331 1392 0.679002 ATTGACAGCAAGCGAGCCAT 60.679 50.000 0.00 0.00 37.45 4.40
1333 1394 1.300971 TGATTGACAGCAAGCGAGCC 61.301 55.000 0.00 0.00 43.12 4.70
1414 1475 1.359459 GACTTTTAGCGAGCACCGGG 61.359 60.000 6.32 0.00 39.04 5.73
1416 1477 0.716108 CTGACTTTTAGCGAGCACCG 59.284 55.000 0.00 0.00 42.21 4.94
1421 1482 2.251893 GTCCGACTGACTTTTAGCGAG 58.748 52.381 0.00 0.00 41.03 5.03
1422 1483 1.610038 TGTCCGACTGACTTTTAGCGA 59.390 47.619 0.00 0.00 44.75 4.93
1423 1484 1.986378 CTGTCCGACTGACTTTTAGCG 59.014 52.381 0.00 0.00 44.75 4.26
1425 1486 2.561419 TCCCTGTCCGACTGACTTTTAG 59.439 50.000 6.97 0.00 44.75 1.85
1437 1498 0.107508 ATCAGCAATGTCCCTGTCCG 60.108 55.000 0.00 0.00 0.00 4.79
1438 1499 2.134789 AATCAGCAATGTCCCTGTCC 57.865 50.000 0.00 0.00 0.00 4.02
1513 1585 7.597386 AGGAAATGAAGCACTAAAATCAAGAC 58.403 34.615 0.00 0.00 0.00 3.01
1523 1595 5.048504 CAGCAAGAAAGGAAATGAAGCACTA 60.049 40.000 0.00 0.00 0.00 2.74
1559 1631 6.529125 CACAACTTTAAGGCATCACAATCATC 59.471 38.462 0.00 0.00 0.00 2.92
1590 1662 3.945346 TGTACTGAAACACACACCAAGT 58.055 40.909 0.00 0.00 0.00 3.16
1602 1674 5.708697 TCTCGTACATCTCCTTGTACTGAAA 59.291 40.000 11.63 0.00 46.32 2.69
1603 1675 5.250982 TCTCGTACATCTCCTTGTACTGAA 58.749 41.667 11.63 0.00 46.32 3.02
1604 1676 4.840271 TCTCGTACATCTCCTTGTACTGA 58.160 43.478 11.63 9.65 46.32 3.41
1718 1790 0.600255 CCTTGCTGACGTCGAGGTTT 60.600 55.000 12.67 0.00 31.74 3.27
1782 1854 7.541162 CAATCACCAGAAATGCTAAATTCAGA 58.459 34.615 0.00 0.00 0.00 3.27
1805 1878 2.884012 AGAACCAACACATGATTCGCAA 59.116 40.909 0.00 0.00 0.00 4.85
1808 1881 4.229096 CCAAAGAACCAACACATGATTCG 58.771 43.478 0.00 0.00 0.00 3.34
1819 1892 2.757868 CTGGACAACACCAAAGAACCAA 59.242 45.455 0.00 0.00 39.59 3.67
1827 1900 1.004862 TGAACCACTGGACAACACCAA 59.995 47.619 0.71 0.00 39.59 3.67
1836 1909 1.850549 CCCCCTTTGAACCACTGGA 59.149 57.895 0.71 0.00 0.00 3.86
1922 1995 0.911769 TCATTGCCCTCCCAGTACAG 59.088 55.000 0.00 0.00 0.00 2.74
1948 2021 1.225704 GGTGAGCTTCCCATCCTGG 59.774 63.158 0.00 0.00 37.25 4.45
1979 2052 0.178990 ACCTGGCAAACCTTCTCCAC 60.179 55.000 0.00 0.00 36.63 4.02
2002 2075 7.199167 ACAACCAGATATAGGCATATGCATA 57.801 36.000 28.07 25.51 44.36 3.14
2022 2095 7.491048 ACATTTACTGTCCATTCACAAAACAAC 59.509 33.333 0.00 0.00 29.94 3.32
2049 2122 4.322057 AAGAGCATTTACATCCCTTGGT 57.678 40.909 0.00 0.00 0.00 3.67
2053 2126 9.381038 TCTAATACTAAGAGCATTTACATCCCT 57.619 33.333 0.00 0.00 0.00 4.20
2061 2134 7.775561 CCCAAACCTCTAATACTAAGAGCATTT 59.224 37.037 0.00 0.00 39.36 2.32
2071 2144 4.227527 CACCTTCCCCAAACCTCTAATACT 59.772 45.833 0.00 0.00 0.00 2.12
2074 2147 2.291605 GCACCTTCCCCAAACCTCTAAT 60.292 50.000 0.00 0.00 0.00 1.73
2077 2150 1.068352 AGCACCTTCCCCAAACCTCT 61.068 55.000 0.00 0.00 0.00 3.69
2138 2211 6.750039 CGACACCAACACTTTTCAAGTAATTT 59.250 34.615 0.00 0.00 40.46 1.82
2304 2378 0.943673 TGCATCGCATCATAAACGGG 59.056 50.000 0.00 0.00 31.71 5.28
2305 2379 1.334059 GGTGCATCGCATCATAAACGG 60.334 52.381 0.00 0.00 41.91 4.44
2419 2493 0.968393 GCCCCCTTTTCACGGCATTA 60.968 55.000 0.00 0.00 41.25 1.90
2461 2535 1.140452 ACCAGAGCAGCATCCACTATG 59.860 52.381 0.00 0.00 38.74 2.23
2531 2605 9.123902 ACAGCTCAAATTGTCTATGCAATATAA 57.876 29.630 0.00 0.00 38.03 0.98
2533 2607 7.578310 ACAGCTCAAATTGTCTATGCAATAT 57.422 32.000 0.00 0.00 38.03 1.28
2536 2610 5.009911 ACAACAGCTCAAATTGTCTATGCAA 59.990 36.000 0.00 0.00 30.82 4.08
2576 2650 2.327343 TGATGGCAAGCGTGAGTGC 61.327 57.895 2.99 0.00 40.14 4.40
2593 2669 3.181485 ACAACACAACATTAAACCCCGTG 60.181 43.478 0.00 0.00 0.00 4.94
2692 2772 7.551974 ACAGCATTCAGTTATATATGGATCTGC 59.448 37.037 0.00 0.00 0.00 4.26
2830 2911 0.251787 GCCACCAAACATCCCTTCCT 60.252 55.000 0.00 0.00 0.00 3.36
2972 3055 3.576078 TGGTCACAACATCCTGAAAGT 57.424 42.857 0.00 0.00 0.00 2.66
2994 3077 3.753272 CCACATCACACTTGGTAGGAAAG 59.247 47.826 0.00 0.00 0.00 2.62
3114 3199 7.657023 AACAGAGATTAATACTCGGGTAACT 57.343 36.000 0.00 0.00 39.12 2.24
3149 3234 4.526970 CCAGAAGTATGCATAACACCCTT 58.473 43.478 8.28 7.10 0.00 3.95
3339 3425 2.472816 CACCTGATGCCAACAAACAAC 58.527 47.619 0.00 0.00 0.00 3.32
3366 3452 3.008049 GTCCAGTAATCCAACCACAGTCT 59.992 47.826 0.00 0.00 0.00 3.24
3375 3461 6.326323 TCACATAGCTATGTCCAGTAATCCAA 59.674 38.462 31.90 5.40 44.57 3.53
3568 3655 6.030548 TGAATTGTCAAACAAAAGGACACA 57.969 33.333 0.00 0.00 41.96 3.72
3581 3668 7.523293 AGTGGATTGTGTTATGAATTGTCAA 57.477 32.000 0.00 0.00 37.30 3.18
3594 3681 8.691661 AAACATAAAAGTCTAGTGGATTGTGT 57.308 30.769 0.00 0.00 0.00 3.72
3755 3842 2.360350 CCAGCACCGACCAGCATT 60.360 61.111 0.00 0.00 0.00 3.56
3799 3886 6.238266 CGAGTGTTGGTGCGGTATAAAATATT 60.238 38.462 0.00 0.00 0.00 1.28
3814 3901 0.529119 GTGAACGGACGAGTGTTGGT 60.529 55.000 0.00 0.00 0.00 3.67
4069 4157 5.353123 GTCCGGCAAATGTTGAGATTTAGTA 59.647 40.000 0.00 0.00 0.00 1.82
4074 4162 2.489329 CTGTCCGGCAAATGTTGAGATT 59.511 45.455 0.00 0.00 0.00 2.40
4112 4200 2.925724 ACCAACGGACAGTTCAATTCA 58.074 42.857 0.00 0.00 42.02 2.57
4171 4259 6.159293 GGTTGTCAGATGCAGATATATCGAA 58.841 40.000 7.08 0.00 0.00 3.71
4223 4311 8.425577 ACATATGTAATAAGCAGTGAGTGAAC 57.574 34.615 6.56 0.00 29.06 3.18
4288 4376 1.464734 ACGGCTCGAGAATCTTCTGA 58.535 50.000 18.75 0.00 37.73 3.27
4305 4393 8.014322 TCTAATAGTTTTGCACAGTAGAAACG 57.986 34.615 4.30 0.00 37.15 3.60
4477 4569 5.280945 CCAGTGTGTTTTATTTCCAGTGTG 58.719 41.667 0.00 0.00 0.00 3.82
4484 4576 9.289303 CATATTACAGCCAGTGTGTTTTATTTC 57.711 33.333 0.00 0.00 40.69 2.17
4525 4618 5.079643 AGAGTGGCCACTATGAATGTTTTT 58.920 37.500 37.87 12.05 42.66 1.94
4919 5012 6.408858 TTTCAAGATCAGTCACTTTATCGC 57.591 37.500 0.00 0.00 0.00 4.58
5497 5598 9.726438 ACATACTGAACTTAAACTCTAGCAAAT 57.274 29.630 0.00 0.00 0.00 2.32
5547 5648 6.902341 TCAAATGTGCAAGATAACTCAGTTC 58.098 36.000 0.00 0.00 0.00 3.01
5577 5678 1.314534 TGCCAATTCGATGCCCACTG 61.315 55.000 0.00 0.00 0.00 3.66
5944 6049 7.696992 AAAGGCGGAGTTTTATTTTCTGATA 57.303 32.000 0.00 0.00 0.00 2.15
5959 6064 2.403252 ACTTCCATGTAAAGGCGGAG 57.597 50.000 9.23 0.00 0.00 4.63
5988 6093 8.692110 TGCTGAATAGACAAATTTTAAGCATG 57.308 30.769 0.00 0.00 31.11 4.06
6053 6158 1.543802 TGGTGAATTGGGAACATTCGC 59.456 47.619 1.90 1.90 42.32 4.70
6055 6160 2.827921 AGCTGGTGAATTGGGAACATTC 59.172 45.455 0.00 0.00 42.32 2.67
6058 6163 2.375174 AGTAGCTGGTGAATTGGGAACA 59.625 45.455 0.00 0.00 39.83 3.18
6059 6164 3.073274 AGTAGCTGGTGAATTGGGAAC 57.927 47.619 0.00 0.00 0.00 3.62
6060 6165 6.354130 GTTATAGTAGCTGGTGAATTGGGAA 58.646 40.000 0.00 0.00 0.00 3.97
6061 6166 5.452776 CGTTATAGTAGCTGGTGAATTGGGA 60.453 44.000 0.00 0.00 0.00 4.37
6062 6167 4.750098 CGTTATAGTAGCTGGTGAATTGGG 59.250 45.833 0.00 0.00 0.00 4.12
6066 6198 4.262079 GCCTCGTTATAGTAGCTGGTGAAT 60.262 45.833 0.00 0.00 0.00 2.57
6078 6210 4.861210 CTGAACTACAGGCCTCGTTATAG 58.139 47.826 0.00 2.53 42.39 1.31
6136 6276 3.708631 ACAGTAGCTAATCTGGAGCATGT 59.291 43.478 14.07 0.00 42.69 3.21
6148 6288 6.283694 CCAGCATAAGATTGACAGTAGCTAA 58.716 40.000 0.00 0.00 0.00 3.09
6169 6309 3.827008 TTGCTATGTCTTCCTAGCCAG 57.173 47.619 0.00 0.00 39.68 4.85
6267 6440 2.435938 GCAAACGCCCCGATCTGA 60.436 61.111 0.00 0.00 0.00 3.27
6279 6452 0.250467 TCCTGTCTGGAGCTGCAAAC 60.250 55.000 9.92 7.13 40.56 2.93
6494 6668 3.267483 CCTTCTACCAACCACATAACCG 58.733 50.000 0.00 0.00 0.00 4.44
6528 6702 4.268884 GCACTGATTAAAAGGACTAGCGAG 59.731 45.833 0.00 0.00 0.00 5.03
6531 6705 4.181578 TCGCACTGATTAAAAGGACTAGC 58.818 43.478 0.00 0.00 0.00 3.42
6534 6708 6.431234 AGAAAATCGCACTGATTAAAAGGACT 59.569 34.615 0.00 0.00 46.65 3.85
6552 6729 4.692228 CTCACTAGCCTCAGGAGAAAATC 58.308 47.826 0.00 0.00 0.00 2.17
6574 6751 1.135315 CATTACACCACGCTGCAGC 59.865 57.895 29.12 29.12 37.78 5.25
6578 6756 4.391830 AGAACATTACATTACACCACGCTG 59.608 41.667 0.00 0.00 0.00 5.18
6608 6786 7.631915 ACACAAGTTTACAAAAGTGAAACAC 57.368 32.000 0.00 0.00 41.43 3.32
6733 6918 3.279434 ACCAGACTTGAGAAAACACCAC 58.721 45.455 0.00 0.00 0.00 4.16
6764 6949 2.202566 GCTTAATCAGTACACGCTCCC 58.797 52.381 0.00 0.00 0.00 4.30
6771 6956 6.430925 ACATTTTCAGCTGCTTAATCAGTACA 59.569 34.615 9.47 0.00 36.49 2.90
6772 6957 6.846350 ACATTTTCAGCTGCTTAATCAGTAC 58.154 36.000 9.47 0.00 36.49 2.73
6782 6967 3.387397 GCAAAAGACATTTTCAGCTGCT 58.613 40.909 9.47 0.00 36.47 4.24
6786 6971 2.401720 CGACGCAAAAGACATTTTCAGC 59.598 45.455 0.00 0.00 36.47 4.26
6807 6992 0.476771 TGGTCCTGGGAAAAGTGACC 59.523 55.000 0.00 0.00 44.57 4.02
6808 6993 1.143073 AGTGGTCCTGGGAAAAGTGAC 59.857 52.381 0.00 0.00 0.00 3.67
6840 7026 2.126467 CTGATGTGTTTTTGGCCGTTG 58.874 47.619 0.00 0.00 0.00 4.10
6886 7072 0.180406 CGGTTGTATGGGAGGAAGGG 59.820 60.000 0.00 0.00 0.00 3.95
6887 7073 0.463833 GCGGTTGTATGGGAGGAAGG 60.464 60.000 0.00 0.00 0.00 3.46
6894 7080 2.828549 GGCAGGCGGTTGTATGGG 60.829 66.667 0.00 0.00 0.00 4.00
6900 7086 4.711949 AGAGCAGGCAGGCGGTTG 62.712 66.667 0.00 0.00 39.27 3.77
6907 7093 4.486503 GAGGGGCAGAGCAGGCAG 62.487 72.222 0.00 0.00 35.46 4.85
6915 7101 4.039092 GCCAAGCAGAGGGGCAGA 62.039 66.667 0.00 0.00 46.92 4.26
6919 7105 3.970410 TGGTGCCAAGCAGAGGGG 61.970 66.667 0.00 0.00 40.08 4.79
6920 7106 2.674380 GTGGTGCCAAGCAGAGGG 60.674 66.667 0.00 0.00 40.08 4.30
6921 7107 2.674380 GGTGGTGCCAAGCAGAGG 60.674 66.667 0.00 0.00 40.08 3.69
6922 7108 2.113774 TGGTGGTGCCAAGCAGAG 59.886 61.111 0.00 0.00 45.94 3.35
6956 7142 2.163390 CCGTGAGACATGCGCAGAG 61.163 63.158 18.32 13.98 0.00 3.35
6957 7143 2.125952 CCGTGAGACATGCGCAGA 60.126 61.111 18.32 0.00 0.00 4.26
6958 7144 3.857854 GCCGTGAGACATGCGCAG 61.858 66.667 18.32 10.85 0.00 5.18
6959 7145 4.678499 TGCCGTGAGACATGCGCA 62.678 61.111 14.96 14.96 0.00 6.09
6960 7146 4.152625 GTGCCGTGAGACATGCGC 62.153 66.667 0.00 0.00 0.00 6.09
6961 7147 2.316867 TTGTGCCGTGAGACATGCG 61.317 57.895 0.00 0.00 0.00 4.73
6962 7148 1.207593 GTTGTGCCGTGAGACATGC 59.792 57.895 0.00 0.00 0.00 4.06
6963 7149 1.577328 GGGTTGTGCCGTGAGACATG 61.577 60.000 0.00 0.00 38.44 3.21
6964 7150 1.302511 GGGTTGTGCCGTGAGACAT 60.303 57.895 0.00 0.00 38.44 3.06
6965 7151 2.110213 GGGTTGTGCCGTGAGACA 59.890 61.111 0.00 0.00 38.44 3.41
6966 7152 1.668151 GAGGGTTGTGCCGTGAGAC 60.668 63.158 0.00 0.00 38.44 3.36
6967 7153 2.741092 GAGGGTTGTGCCGTGAGA 59.259 61.111 0.00 0.00 38.44 3.27
6968 7154 2.358737 GGAGGGTTGTGCCGTGAG 60.359 66.667 0.00 0.00 38.44 3.51
6969 7155 3.948719 GGGAGGGTTGTGCCGTGA 61.949 66.667 0.00 0.00 38.44 4.35
6985 7171 2.477104 AAAAGCATAAGGGATGGGGG 57.523 50.000 0.00 0.00 35.91 5.40
6990 7176 7.836183 ACAAGTCATAGAAAAAGCATAAGGGAT 59.164 33.333 0.00 0.00 0.00 3.85
6995 7181 7.039784 AGCCAACAAGTCATAGAAAAAGCATAA 60.040 33.333 0.00 0.00 0.00 1.90
6996 7182 6.434028 AGCCAACAAGTCATAGAAAAAGCATA 59.566 34.615 0.00 0.00 0.00 3.14
6997 7183 5.244626 AGCCAACAAGTCATAGAAAAAGCAT 59.755 36.000 0.00 0.00 0.00 3.79
6998 7184 4.584325 AGCCAACAAGTCATAGAAAAAGCA 59.416 37.500 0.00 0.00 0.00 3.91
6999 7185 5.126396 AGCCAACAAGTCATAGAAAAAGC 57.874 39.130 0.00 0.00 0.00 3.51
7000 7186 7.752239 CACATAGCCAACAAGTCATAGAAAAAG 59.248 37.037 0.00 0.00 0.00 2.27
7001 7187 7.592938 CACATAGCCAACAAGTCATAGAAAAA 58.407 34.615 0.00 0.00 0.00 1.94
7002 7188 6.349280 GCACATAGCCAACAAGTCATAGAAAA 60.349 38.462 0.00 0.00 37.23 2.29
7004 7190 4.635765 GCACATAGCCAACAAGTCATAGAA 59.364 41.667 0.00 0.00 37.23 2.10
7009 8254 2.268762 TGCACATAGCCAACAAGTCA 57.731 45.000 0.00 0.00 44.83 3.41
7019 8264 6.697019 CCTTTACATAACCAAATGCACATAGC 59.303 38.462 0.00 0.00 45.96 2.97
7048 8293 1.327460 CAACTGCGACGGGTGAATATG 59.673 52.381 0.00 0.00 26.80 1.78
7056 8301 1.227999 AATGACACAACTGCGACGGG 61.228 55.000 0.00 0.00 0.00 5.28
7057 8302 0.163788 GAATGACACAACTGCGACGG 59.836 55.000 0.00 0.00 0.00 4.79
7061 8306 5.005299 TGTTATATCGAATGACACAACTGCG 59.995 40.000 0.00 0.00 0.00 5.18
7121 8372 9.881649 ACCATGATGCTCATATAGTATAAACTG 57.118 33.333 0.00 0.00 34.28 3.16
7136 8388 2.542411 GCGATTTTCCACCATGATGCTC 60.542 50.000 0.00 0.00 0.00 4.26
7138 8390 1.134753 TGCGATTTTCCACCATGATGC 59.865 47.619 0.00 0.00 0.00 3.91
7188 8468 1.523095 GCTAAGATTTAGTGCGCCGAG 59.477 52.381 4.18 0.00 0.00 4.63
7189 8469 1.136305 AGCTAAGATTTAGTGCGCCGA 59.864 47.619 4.18 0.00 0.00 5.54
7190 8470 1.523095 GAGCTAAGATTTAGTGCGCCG 59.477 52.381 4.18 0.00 0.00 6.46
7199 8479 6.321181 TCCTTGTTTGTGTTGAGCTAAGATTT 59.679 34.615 0.00 0.00 0.00 2.17
7201 8481 5.376625 TCCTTGTTTGTGTTGAGCTAAGAT 58.623 37.500 0.00 0.00 0.00 2.40
7215 8497 5.065218 CCTCCACGAAATATCTCCTTGTTTG 59.935 44.000 0.00 0.00 0.00 2.93
7282 8564 2.299297 CTCGGGTGGTACATTATCTCCC 59.701 54.545 0.00 0.00 44.52 4.30
7315 8597 4.414337 TGGTTTGGTTTTCATTGGAAGG 57.586 40.909 0.00 0.00 33.82 3.46
7319 8601 2.286563 GCGTTGGTTTGGTTTTCATTGG 59.713 45.455 0.00 0.00 0.00 3.16
7376 8658 1.786937 TTGTTGGCTTGGGAATGTGT 58.213 45.000 0.00 0.00 0.00 3.72
7428 8710 1.065199 ACCGTGATGTGCATGAATCCT 60.065 47.619 0.00 0.00 35.44 3.24
7436 8718 2.177394 AACATACACCGTGATGTGCA 57.823 45.000 5.28 0.00 39.93 4.57
7446 8728 5.560183 GCGTTGGCAATATCTAACATACACC 60.560 44.000 1.92 0.00 39.62 4.16
7490 8772 1.372872 GCGCCCCATTTGTGTGTTC 60.373 57.895 0.00 0.00 0.00 3.18
7515 8797 4.290622 CAAGGTGGCCAGGCAGGT 62.291 66.667 15.19 0.00 40.61 4.00
7527 8809 2.665185 GACGGCGAGCAACAAGGT 60.665 61.111 16.62 0.00 0.00 3.50
7533 8815 1.959226 GAAAGGTGACGGCGAGCAA 60.959 57.895 16.62 0.00 0.00 3.91
7572 8854 2.106683 GCATGGCCGTAAGCGACTT 61.107 57.895 0.00 0.00 45.17 3.01
7580 8862 3.071837 TCCGTCTGCATGGCCGTA 61.072 61.111 0.00 0.00 0.00 4.02
7581 8863 4.760047 GTCCGTCTGCATGGCCGT 62.760 66.667 0.00 0.00 0.00 5.68
7587 8869 4.457496 CGCCTGGTCCGTCTGCAT 62.457 66.667 0.00 0.00 0.00 3.96
7602 8884 4.222847 CCCGCTCTTAGTCCCCGC 62.223 72.222 0.00 0.00 0.00 6.13
7605 8887 3.218227 GGACCCGCTCTTAGTCCC 58.782 66.667 0.00 0.00 43.60 4.46
7607 8889 1.516423 GGTGGACCCGCTCTTAGTC 59.484 63.158 0.00 0.00 0.00 2.59
7647 8929 1.078848 CCACCGCTTTCTCCTCCTG 60.079 63.158 0.00 0.00 0.00 3.86
7649 8931 2.436824 GCCACCGCTTTCTCCTCC 60.437 66.667 0.00 0.00 0.00 4.30
7688 8973 2.898729 ATGCCAAGTCCACTAGATCG 57.101 50.000 0.00 0.00 0.00 3.69


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

AutoCloner maintained by Alex Coulton.