Multiple sequence alignment - TraesCS6D01G068500

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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 TraesCS6D01G068500 chr6D 100.000 3911 0 0 932 4842 34394912 34398822 0.000000e+00 7223.0
1 TraesCS6D01G068500 chr6D 100.000 656 0 0 1 656 34393981 34394636 0.000000e+00 1212.0
2 TraesCS6D01G068500 chr6D 91.379 58 5 0 2164 2221 34396076 34396133 4.020000e-11 80.5
3 TraesCS6D01G068500 chr6D 91.379 58 5 0 2096 2153 34396144 34396201 4.020000e-11 80.5
4 TraesCS6D01G068500 chr6B 95.575 3819 109 36 936 4726 71148011 71151797 0.000000e+00 6061.0
5 TraesCS6D01G068500 chr6B 91.770 243 4 9 384 619 71147003 71147236 1.680000e-84 324.0
6 TraesCS6D01G068500 chr6B 87.591 137 17 0 154 290 71145656 71145792 5.020000e-35 159.0
7 TraesCS6D01G068500 chr6B 83.206 131 19 1 1 131 71146751 71146878 3.060000e-22 117.0
8 TraesCS6D01G068500 chr6B 93.220 59 4 0 2164 2222 71149167 71149225 2.400000e-13 87.9
9 TraesCS6D01G068500 chr6A 94.609 3821 132 39 933 4731 38550513 38554281 0.000000e+00 5847.0
10 TraesCS6D01G068500 chr6A 96.020 201 5 2 383 582 38549852 38550050 1.680000e-84 324.0
11 TraesCS6D01G068500 chr1B 91.262 103 9 0 1000 1102 564165507 564165405 1.820000e-29 141.0
12 TraesCS6D01G068500 chr1A 91.262 103 9 0 1000 1102 514553874 514553772 1.820000e-29 141.0


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 TraesCS6D01G068500 chr6D 34393981 34398822 4841 False 2149.00 7223 95.6895 1 4842 4 chr6D.!!$F1 4841
1 TraesCS6D01G068500 chr6B 71145656 71151797 6141 False 1349.78 6061 90.2724 1 4726 5 chr6B.!!$F1 4725
2 TraesCS6D01G068500 chr6A 38549852 38554281 4429 False 3085.50 5847 95.3145 383 4731 2 chr6A.!!$F1 4348

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
308 1248 0.249120 CTGCCAAGGATACACGGTGA 59.751 55.0 16.29 0.0 41.41 4.02 F
1710 3175 0.178984 TACCTCGACCACTCACACCA 60.179 55.0 0.00 0.0 0.00 4.17 F
2412 3879 0.033601 TGCCTGGTCTGTTGTTGGTT 60.034 50.0 0.00 0.0 0.00 3.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1960 3425 0.252479 ATTCTACTGCTGCTGCTGCT 59.748 50.0 27.67 14.24 41.07 4.24 R
2609 4076 0.400213 TTCTGGAACCAGGAACGCAT 59.600 50.0 18.99 0.00 43.75 4.73 R
4315 5793 0.107897 AGCAATCATACACCGGCGAA 60.108 50.0 9.30 0.00 0.00 4.70 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
18 19 1.517832 ATTCTTCCTGTCCGCCTCG 59.482 57.895 0.00 0.00 0.00 4.63
19 20 2.579684 ATTCTTCCTGTCCGCCTCGC 62.580 60.000 0.00 0.00 0.00 5.03
20 21 4.069232 CTTCCTGTCCGCCTCGCA 62.069 66.667 0.00 0.00 0.00 5.10
21 22 4.373116 TTCCTGTCCGCCTCGCAC 62.373 66.667 0.00 0.00 0.00 5.34
24 25 2.571757 CTGTCCGCCTCGCACTAA 59.428 61.111 0.00 0.00 0.00 2.24
25 26 1.517257 CTGTCCGCCTCGCACTAAG 60.517 63.158 0.00 0.00 0.00 2.18
30 31 1.446099 CGCCTCGCACTAAGAAGCA 60.446 57.895 0.00 0.00 0.00 3.91
33 34 2.550978 GCCTCGCACTAAGAAGCATTA 58.449 47.619 0.00 0.00 0.00 1.90
34 35 2.285488 GCCTCGCACTAAGAAGCATTAC 59.715 50.000 0.00 0.00 0.00 1.89
50 51 4.082787 AGCATTACAACCTTTTCGACCATG 60.083 41.667 0.00 0.00 0.00 3.66
52 53 1.686355 ACAACCTTTTCGACCATGCA 58.314 45.000 0.00 0.00 0.00 3.96
56 57 2.726821 ACCTTTTCGACCATGCATGAT 58.273 42.857 28.31 11.89 0.00 2.45
59 60 4.516698 ACCTTTTCGACCATGCATGATATC 59.483 41.667 28.31 19.23 0.00 1.63
64 65 3.575687 TCGACCATGCATGATATCTCTGT 59.424 43.478 28.31 14.02 0.00 3.41
70 71 5.710567 CCATGCATGATATCTCTGTCCAATT 59.289 40.000 28.31 0.00 0.00 2.32
73 74 8.789762 CATGCATGATATCTCTGTCCAATTAAA 58.210 33.333 22.59 0.00 0.00 1.52
84 85 4.083565 TGTCCAATTAAACTGGCCTTACC 58.916 43.478 3.32 0.00 39.84 2.85
85 86 3.128068 GTCCAATTAAACTGGCCTTACCG 59.872 47.826 3.32 0.00 43.94 4.02
95 96 3.463585 CCTTACCGGCGGCCAGTA 61.464 66.667 28.71 15.71 0.00 2.74
119 120 9.216117 GTATATCACAACCCCTACATTTATGAC 57.784 37.037 0.00 0.00 0.00 3.06
130 131 7.030165 CCCTACATTTATGACGATACAGCTAG 58.970 42.308 0.00 0.00 0.00 3.42
136 137 3.000684 TGACGATACAGCTAGTCCTGT 57.999 47.619 7.94 7.94 46.98 4.00
137 138 2.683362 TGACGATACAGCTAGTCCTGTG 59.317 50.000 11.91 0.66 45.17 3.66
139 140 2.946329 ACGATACAGCTAGTCCTGTGAG 59.054 50.000 11.91 6.68 45.17 3.51
140 141 2.946329 CGATACAGCTAGTCCTGTGAGT 59.054 50.000 11.91 0.74 45.17 3.41
141 142 3.378742 CGATACAGCTAGTCCTGTGAGTT 59.621 47.826 11.91 0.00 45.17 3.01
142 143 4.575236 CGATACAGCTAGTCCTGTGAGTTA 59.425 45.833 11.91 0.00 45.17 2.24
144 145 3.497332 ACAGCTAGTCCTGTGAGTTACA 58.503 45.455 2.57 0.00 44.00 2.41
145 146 3.256136 ACAGCTAGTCCTGTGAGTTACAC 59.744 47.826 2.57 0.00 44.00 2.90
165 505 4.037565 ACACGATGCGATGGATTCTTACTA 59.962 41.667 0.00 0.00 0.00 1.82
166 506 5.164233 CACGATGCGATGGATTCTTACTAT 58.836 41.667 0.00 0.00 0.00 2.12
174 514 3.572642 TGGATTCTTACTATCCGCCTCA 58.427 45.455 0.00 0.00 43.72 3.86
183 523 4.155462 TTACTATCCGCCTCATAGTAAGCG 59.845 45.833 10.61 0.00 41.36 4.68
190 530 3.242248 CGCCTCATAGTAAGCGTTACAAC 59.758 47.826 9.51 0.00 43.45 3.32
196 536 7.355332 TCATAGTAAGCGTTACAACCTTTTC 57.645 36.000 9.51 0.00 38.60 2.29
197 537 6.930164 TCATAGTAAGCGTTACAACCTTTTCA 59.070 34.615 9.51 0.00 38.60 2.69
198 538 7.441760 TCATAGTAAGCGTTACAACCTTTTCAA 59.558 33.333 9.51 0.00 38.60 2.69
238 578 2.843730 TCCAATCAAGCTGGCCTTACTA 59.156 45.455 3.32 0.00 33.63 1.82
274 1214 4.127171 CAGAACCCCTACATTTATGACGG 58.873 47.826 0.00 0.00 0.00 4.79
286 1226 1.325355 TATGACGGTACAGCTAGCCC 58.675 55.000 12.13 4.21 0.00 5.19
288 1228 1.320344 TGACGGTACAGCTAGCCCTG 61.320 60.000 12.13 6.78 38.78 4.45
290 1230 2.427245 CGGTACAGCTAGCCCTGCT 61.427 63.158 12.13 0.00 43.41 4.24
295 1235 3.333219 AGCTAGCCCTGCTGCCAA 61.333 61.111 12.13 0.00 40.10 4.52
302 1242 1.609239 CCCTGCTGCCAAGGATACA 59.391 57.895 7.55 0.00 41.41 2.29
308 1248 0.249120 CTGCCAAGGATACACGGTGA 59.751 55.000 16.29 0.00 41.41 4.02
310 1250 1.084289 GCCAAGGATACACGGTGAAC 58.916 55.000 16.29 5.39 41.41 3.18
317 1257 4.342359 AGGATACACGGTGAACTCTTACT 58.658 43.478 16.29 0.00 41.41 2.24
328 1268 0.322277 ACTCTTACTGTCCGCCTCGA 60.322 55.000 0.00 0.00 0.00 4.04
368 1308 3.510719 ACACACAATCAACTGTTTGCAC 58.489 40.909 0.00 0.00 31.49 4.57
370 1310 3.548668 CACACAATCAACTGTTTGCACTG 59.451 43.478 0.00 0.00 32.17 3.66
371 1311 3.193267 ACACAATCAACTGTTTGCACTGT 59.807 39.130 0.00 0.00 36.68 3.55
372 1312 3.792956 CACAATCAACTGTTTGCACTGTC 59.207 43.478 0.00 0.00 34.16 3.51
377 1317 2.613595 CAACTGTTTGCACTGTCTAGCA 59.386 45.455 0.00 0.00 39.32 3.49
378 1318 3.131709 ACTGTTTGCACTGTCTAGCAT 57.868 42.857 0.00 0.00 40.94 3.79
381 1321 2.549329 TGTTTGCACTGTCTAGCATGTG 59.451 45.455 0.00 5.02 40.94 3.21
392 1332 6.203723 ACTGTCTAGCATGTGAAGAAGTTTTC 59.796 38.462 0.00 0.00 0.00 2.29
399 1368 8.807667 AGCATGTGAAGAAGTTTTCTATTTTG 57.192 30.769 0.00 0.00 39.61 2.44
401 1370 8.694394 GCATGTGAAGAAGTTTTCTATTTTGTC 58.306 33.333 0.00 0.00 39.61 3.18
600 1574 4.653888 CCACCCCACCCACCGTTC 62.654 72.222 0.00 0.00 0.00 3.95
601 1575 3.566210 CACCCCACCCACCGTTCT 61.566 66.667 0.00 0.00 0.00 3.01
602 1576 3.246880 ACCCCACCCACCGTTCTC 61.247 66.667 0.00 0.00 0.00 2.87
603 1577 2.928396 CCCCACCCACCGTTCTCT 60.928 66.667 0.00 0.00 0.00 3.10
604 1578 2.663196 CCCACCCACCGTTCTCTC 59.337 66.667 0.00 0.00 0.00 3.20
605 1579 1.913762 CCCACCCACCGTTCTCTCT 60.914 63.158 0.00 0.00 0.00 3.10
606 1580 1.592223 CCACCCACCGTTCTCTCTC 59.408 63.158 0.00 0.00 0.00 3.20
607 1581 0.900647 CCACCCACCGTTCTCTCTCT 60.901 60.000 0.00 0.00 0.00 3.10
608 1582 0.528470 CACCCACCGTTCTCTCTCTC 59.472 60.000 0.00 0.00 0.00 3.20
609 1583 0.612453 ACCCACCGTTCTCTCTCTCC 60.612 60.000 0.00 0.00 0.00 3.71
610 1584 1.324005 CCCACCGTTCTCTCTCTCCC 61.324 65.000 0.00 0.00 0.00 4.30
611 1585 0.323908 CCACCGTTCTCTCTCTCCCT 60.324 60.000 0.00 0.00 0.00 4.20
612 1586 1.099689 CACCGTTCTCTCTCTCCCTC 58.900 60.000 0.00 0.00 0.00 4.30
613 1587 0.996583 ACCGTTCTCTCTCTCCCTCT 59.003 55.000 0.00 0.00 0.00 3.69
614 1588 1.064979 ACCGTTCTCTCTCTCCCTCTC 60.065 57.143 0.00 0.00 0.00 3.20
615 1589 1.675552 CGTTCTCTCTCTCCCTCTCC 58.324 60.000 0.00 0.00 0.00 3.71
1109 2560 2.999063 CCCCACCGTACGTCCCTT 60.999 66.667 15.21 0.00 0.00 3.95
1111 2562 1.372307 CCCACCGTACGTCCCTTTT 59.628 57.895 15.21 0.00 0.00 2.27
1112 2563 0.671472 CCCACCGTACGTCCCTTTTC 60.671 60.000 15.21 0.00 0.00 2.29
1113 2564 0.319405 CCACCGTACGTCCCTTTTCT 59.681 55.000 15.21 0.00 0.00 2.52
1117 2568 2.029560 ACCGTACGTCCCTTTTCTTCTC 60.030 50.000 15.21 0.00 0.00 2.87
1118 2569 2.230750 CCGTACGTCCCTTTTCTTCTCT 59.769 50.000 15.21 0.00 0.00 3.10
1129 2584 6.483640 TCCCTTTTCTTCTCTCTTTCTTTTCG 59.516 38.462 0.00 0.00 0.00 3.46
1137 2592 8.414778 TCTTCTCTCTTTCTTTTCGTACTTCTT 58.585 33.333 0.00 0.00 0.00 2.52
1138 2593 7.932120 TCTCTCTTTCTTTTCGTACTTCTTG 57.068 36.000 0.00 0.00 0.00 3.02
1143 2599 8.706492 TCTTTCTTTTCGTACTTCTTGTGTTA 57.294 30.769 0.00 0.00 0.00 2.41
1176 2632 3.489738 CCAGGTTGCTTCTTGTTCTTGTG 60.490 47.826 0.00 0.00 0.00 3.33
1177 2633 3.129287 CAGGTTGCTTCTTGTTCTTGTGT 59.871 43.478 0.00 0.00 0.00 3.72
1188 2650 3.211045 TGTTCTTGTGTTTGTAGAGGCC 58.789 45.455 0.00 0.00 0.00 5.19
1215 2677 1.592131 TTGCTGCTTGCGCCTTTTG 60.592 52.632 4.18 0.00 46.63 2.44
1216 2678 2.014064 TTGCTGCTTGCGCCTTTTGA 62.014 50.000 4.18 0.00 46.63 2.69
1252 2715 6.530887 TGATTGATTCTTTTTGTGTGTGTGTG 59.469 34.615 0.00 0.00 0.00 3.82
1253 2716 5.384063 TGATTCTTTTTGTGTGTGTGTGT 57.616 34.783 0.00 0.00 0.00 3.72
1254 2717 5.159925 TGATTCTTTTTGTGTGTGTGTGTG 58.840 37.500 0.00 0.00 0.00 3.82
1255 2718 4.576216 TTCTTTTTGTGTGTGTGTGTGT 57.424 36.364 0.00 0.00 0.00 3.72
1256 2719 3.894920 TCTTTTTGTGTGTGTGTGTGTG 58.105 40.909 0.00 0.00 0.00 3.82
1257 2720 3.316588 TCTTTTTGTGTGTGTGTGTGTGT 59.683 39.130 0.00 0.00 0.00 3.72
1311 2774 5.500234 TGGTTCTTGATCTAGATTTGGGTG 58.500 41.667 6.70 0.00 0.00 4.61
1320 2783 2.871096 AGATTTGGGTGGCGTTTCTA 57.129 45.000 0.00 0.00 0.00 2.10
1375 2838 0.798009 CACAATGCGGTCGCCAATTC 60.798 55.000 12.94 0.00 41.09 2.17
1513 2976 5.803461 TGTCGATTTCGTTACCATTCAGTAG 59.197 40.000 0.00 0.00 40.80 2.57
1514 2977 5.803967 GTCGATTTCGTTACCATTCAGTAGT 59.196 40.000 0.00 0.00 40.80 2.73
1515 2978 6.968904 GTCGATTTCGTTACCATTCAGTAGTA 59.031 38.462 0.00 0.00 40.80 1.82
1710 3175 0.178984 TACCTCGACCACTCACACCA 60.179 55.000 0.00 0.00 0.00 4.17
2088 3553 5.245531 AGAATTTAATTCACCTCGCTGTCA 58.754 37.500 18.37 0.00 41.71 3.58
2097 3562 3.758088 CTCGCTGTCATCCGTCCGG 62.758 68.421 0.00 0.00 0.00 5.14
2153 3618 2.514205 ATTTGGCTGCACTTGTTGTC 57.486 45.000 0.50 0.00 0.00 3.18
2162 3627 4.261155 GCTGCACTTGTTGTCAATTCACTA 60.261 41.667 0.00 0.00 32.82 2.74
2230 3695 4.672801 GCTGCACTTGCTGTTTATCTTACC 60.673 45.833 9.51 0.00 42.66 2.85
2233 3698 4.215399 GCACTTGCTGTTTATCTTACCACA 59.785 41.667 0.00 0.00 38.21 4.17
2344 3809 3.557264 GCTATGGGATACTGCAGGTAACC 60.557 52.174 19.93 14.95 41.06 2.85
2376 3841 0.961019 TGTCTTGGTTTGCTGATGGC 59.039 50.000 0.00 0.00 42.22 4.40
2391 3856 4.082571 GCTGATGGCTACATGTTTGTTCTT 60.083 41.667 2.30 0.00 37.47 2.52
2396 3862 3.740832 GGCTACATGTTTGTTCTTTTGCC 59.259 43.478 2.30 0.00 37.28 4.52
2401 3868 3.518634 TGTTTGTTCTTTTGCCTGGTC 57.481 42.857 0.00 0.00 0.00 4.02
2406 3873 2.426738 TGTTCTTTTGCCTGGTCTGTTG 59.573 45.455 0.00 0.00 0.00 3.33
2412 3879 0.033601 TGCCTGGTCTGTTGTTGGTT 60.034 50.000 0.00 0.00 0.00 3.67
2414 3881 0.944386 CCTGGTCTGTTGTTGGTTCG 59.056 55.000 0.00 0.00 0.00 3.95
2430 3897 6.583050 TGTTGGTTCGAAGTTGTAAAAGTTTG 59.417 34.615 0.00 0.00 0.00 2.93
2440 3907 6.999950 AGTTGTAAAAGTTTGTTCTTTGGGT 58.000 32.000 0.00 0.00 37.65 4.51
2691 4158 7.655328 GGTCACCTTCATGAGTTATCTGATAAG 59.345 40.741 10.26 0.00 0.00 1.73
2830 4300 7.470935 AGTCTCCTATTCATCAGAGATGATG 57.529 40.000 10.20 11.18 45.10 3.07
2839 4309 7.429374 TTCATCAGAGATGATGTAGTTTCCT 57.571 36.000 15.69 0.00 44.33 3.36
3007 4477 3.117888 CACCAGGTGTGCCTATTATCCTT 60.118 47.826 11.99 0.00 44.97 3.36
3051 4521 1.401409 CGTCACATGGCCACATTGTTC 60.401 52.381 8.16 3.78 34.35 3.18
3160 4630 4.950744 GCAATGGCAGTCACACAC 57.049 55.556 0.00 0.00 40.72 3.82
3241 4711 3.577649 TCTAAGCTTCTGTGAACCTCG 57.422 47.619 0.00 0.00 0.00 4.63
3282 4752 5.885230 TTCTGTGCTTGAGAATATTGGTG 57.115 39.130 0.00 0.00 0.00 4.17
3306 4776 8.148351 GTGTATACCTAGATGAATTGTTGGCTA 58.852 37.037 0.00 0.00 0.00 3.93
3317 4787 9.860898 GATGAATTGTTGGCTATTTAGTTCTTT 57.139 29.630 0.00 0.00 0.00 2.52
3372 4842 7.936847 TGATGGTTTAGACTGTCAGTTGTATTT 59.063 33.333 7.00 0.00 0.00 1.40
3559 5029 1.732259 GGAGGCGATGTTGTGTTACTG 59.268 52.381 0.00 0.00 0.00 2.74
3636 5106 2.967599 ACTACATCGAATGCAGCTCA 57.032 45.000 0.00 0.00 0.00 4.26
3736 5206 4.829064 TTTTCTGGTCCTTGTCGATTTG 57.171 40.909 0.00 0.00 0.00 2.32
3945 5415 1.303806 TCATGGTCGTCGTCCCTCA 60.304 57.895 6.05 0.00 0.00 3.86
4265 5740 4.150897 TCTTGTTATGGTCTGTATGCCC 57.849 45.455 0.00 0.00 0.00 5.36
4314 5792 8.343168 TGAATTATGATTCGGTTTGGTTTACT 57.657 30.769 5.81 0.00 43.75 2.24
4315 5793 8.798402 TGAATTATGATTCGGTTTGGTTTACTT 58.202 29.630 5.81 0.00 43.75 2.24
4316 5794 9.634163 GAATTATGATTCGGTTTGGTTTACTTT 57.366 29.630 0.00 0.00 32.96 2.66
4323 5802 1.334556 GTTTGGTTTACTTTCGCCGGT 59.665 47.619 1.90 0.00 0.00 5.28
4472 5951 7.531857 TGTTTTGTATGATATTGGTGTTGGT 57.468 32.000 0.00 0.00 0.00 3.67
4473 5952 7.374272 TGTTTTGTATGATATTGGTGTTGGTG 58.626 34.615 0.00 0.00 0.00 4.17
4508 5989 7.966753 GCTGCAATAGGATATTGTTGATATGTG 59.033 37.037 10.35 0.00 31.00 3.21
4509 5990 8.922931 TGCAATAGGATATTGTTGATATGTGT 57.077 30.769 10.35 0.00 31.00 3.72
4559 6040 4.160439 TCAGACAGGCCACTACTTCTATTG 59.840 45.833 5.01 0.00 0.00 1.90
4675 6156 3.294493 ATTGCAACGCCGCCTGTT 61.294 55.556 0.00 0.00 0.00 3.16
4678 6159 4.264638 GCAACGCCGCCTGTTTGT 62.265 61.111 0.00 0.00 0.00 2.83
4680 6161 1.206578 CAACGCCGCCTGTTTGTAG 59.793 57.895 0.00 0.00 0.00 2.74
4681 6162 1.070105 AACGCCGCCTGTTTGTAGA 59.930 52.632 0.00 0.00 0.00 2.59
4726 6215 3.741344 GTCTGACGCTGTAACTCAAACAT 59.259 43.478 0.00 0.00 0.00 2.71
4727 6216 3.740832 TCTGACGCTGTAACTCAAACATG 59.259 43.478 0.00 0.00 0.00 3.21
4729 6218 4.123506 TGACGCTGTAACTCAAACATGAA 58.876 39.130 0.00 0.00 0.00 2.57
4730 6219 4.754618 TGACGCTGTAACTCAAACATGAAT 59.245 37.500 0.00 0.00 0.00 2.57
4731 6220 5.107104 TGACGCTGTAACTCAAACATGAATC 60.107 40.000 0.00 0.00 0.00 2.52
4732 6221 4.154195 ACGCTGTAACTCAAACATGAATCC 59.846 41.667 0.00 0.00 0.00 3.01
4733 6222 4.437390 CGCTGTAACTCAAACATGAATCCC 60.437 45.833 0.00 0.00 0.00 3.85
4734 6223 4.702131 GCTGTAACTCAAACATGAATCCCT 59.298 41.667 0.00 0.00 0.00 4.20
4735 6224 5.183904 GCTGTAACTCAAACATGAATCCCTT 59.816 40.000 0.00 0.00 0.00 3.95
4736 6225 6.573664 TGTAACTCAAACATGAATCCCTTG 57.426 37.500 0.00 0.00 0.00 3.61
4737 6226 6.303054 TGTAACTCAAACATGAATCCCTTGA 58.697 36.000 0.00 0.00 0.00 3.02
4738 6227 5.712152 AACTCAAACATGAATCCCTTGAC 57.288 39.130 0.00 0.00 0.00 3.18
4739 6228 3.753272 ACTCAAACATGAATCCCTTGACG 59.247 43.478 0.00 0.00 0.00 4.35
4740 6229 2.487762 TCAAACATGAATCCCTTGACGC 59.512 45.455 0.00 0.00 0.00 5.19
4741 6230 1.463674 AACATGAATCCCTTGACGCC 58.536 50.000 0.00 0.00 0.00 5.68
4742 6231 0.620556 ACATGAATCCCTTGACGCCT 59.379 50.000 0.00 0.00 0.00 5.52
4743 6232 1.303309 CATGAATCCCTTGACGCCTC 58.697 55.000 0.00 0.00 0.00 4.70
4744 6233 0.181350 ATGAATCCCTTGACGCCTCC 59.819 55.000 0.00 0.00 0.00 4.30
4745 6234 1.153147 GAATCCCTTGACGCCTCCC 60.153 63.158 0.00 0.00 0.00 4.30
4746 6235 2.610532 GAATCCCTTGACGCCTCCCC 62.611 65.000 0.00 0.00 0.00 4.81
4747 6236 3.642741 ATCCCTTGACGCCTCCCCT 62.643 63.158 0.00 0.00 0.00 4.79
4748 6237 3.787001 CCCTTGACGCCTCCCCTC 61.787 72.222 0.00 0.00 0.00 4.30
4749 6238 2.685380 CCTTGACGCCTCCCCTCT 60.685 66.667 0.00 0.00 0.00 3.69
4750 6239 2.581354 CTTGACGCCTCCCCTCTG 59.419 66.667 0.00 0.00 0.00 3.35
4751 6240 3.672295 CTTGACGCCTCCCCTCTGC 62.672 68.421 0.00 0.00 0.00 4.26
4775 6264 4.969196 CCCCGCCGGTCGATGATG 62.969 72.222 17.96 2.91 41.67 3.07
4776 6265 4.969196 CCCGCCGGTCGATGATGG 62.969 72.222 17.96 7.73 41.67 3.51
4777 6266 4.969196 CCGCCGGTCGATGATGGG 62.969 72.222 17.96 0.00 41.67 4.00
4778 6267 4.969196 CGCCGGTCGATGATGGGG 62.969 72.222 12.11 0.00 41.67 4.96
4779 6268 3.546543 GCCGGTCGATGATGGGGA 61.547 66.667 1.90 0.00 0.00 4.81
4780 6269 2.737180 CCGGTCGATGATGGGGAG 59.263 66.667 0.00 0.00 0.00 4.30
4781 6270 2.737180 CGGTCGATGATGGGGAGG 59.263 66.667 0.00 0.00 0.00 4.30
4782 6271 1.832608 CGGTCGATGATGGGGAGGA 60.833 63.158 0.00 0.00 0.00 3.71
4783 6272 1.810606 CGGTCGATGATGGGGAGGAG 61.811 65.000 0.00 0.00 0.00 3.69
4784 6273 0.470080 GGTCGATGATGGGGAGGAGA 60.470 60.000 0.00 0.00 0.00 3.71
4785 6274 1.414158 GTCGATGATGGGGAGGAGAA 58.586 55.000 0.00 0.00 0.00 2.87
4786 6275 1.974236 GTCGATGATGGGGAGGAGAAT 59.026 52.381 0.00 0.00 0.00 2.40
4787 6276 2.028567 GTCGATGATGGGGAGGAGAATC 60.029 54.545 0.00 0.00 0.00 2.52
4799 6288 1.144936 GAGAATCCCAGTGCCTCCG 59.855 63.158 0.00 0.00 0.00 4.63
4800 6289 2.514824 GAATCCCAGTGCCTCCGC 60.515 66.667 0.00 0.00 0.00 5.54
4801 6290 3.011517 AATCCCAGTGCCTCCGCT 61.012 61.111 0.00 0.00 35.36 5.52
4802 6291 2.932130 GAATCCCAGTGCCTCCGCTC 62.932 65.000 0.00 0.00 35.36 5.03
4806 6295 3.790437 CAGTGCCTCCGCTCCCAT 61.790 66.667 0.00 0.00 35.36 4.00
4807 6296 3.011517 AGTGCCTCCGCTCCCATT 61.012 61.111 0.00 0.00 35.36 3.16
4808 6297 2.825836 GTGCCTCCGCTCCCATTG 60.826 66.667 0.00 0.00 35.36 2.82
4809 6298 4.113815 TGCCTCCGCTCCCATTGG 62.114 66.667 0.00 0.00 35.36 3.16
4810 6299 4.115199 GCCTCCGCTCCCATTGGT 62.115 66.667 1.20 0.00 0.00 3.67
4811 6300 2.742116 GCCTCCGCTCCCATTGGTA 61.742 63.158 1.20 0.00 0.00 3.25
4812 6301 1.447643 CCTCCGCTCCCATTGGTAG 59.552 63.158 1.20 0.00 0.00 3.18
4813 6302 1.338136 CCTCCGCTCCCATTGGTAGT 61.338 60.000 1.20 0.00 0.00 2.73
4814 6303 0.541863 CTCCGCTCCCATTGGTAGTT 59.458 55.000 1.20 0.00 0.00 2.24
4815 6304 0.988832 TCCGCTCCCATTGGTAGTTT 59.011 50.000 1.20 0.00 0.00 2.66
4816 6305 2.169769 CTCCGCTCCCATTGGTAGTTTA 59.830 50.000 1.20 0.00 0.00 2.01
4817 6306 2.169769 TCCGCTCCCATTGGTAGTTTAG 59.830 50.000 1.20 0.00 0.00 1.85
4818 6307 2.169769 CCGCTCCCATTGGTAGTTTAGA 59.830 50.000 1.20 0.00 0.00 2.10
4819 6308 3.181454 CCGCTCCCATTGGTAGTTTAGAT 60.181 47.826 1.20 0.00 0.00 1.98
4820 6309 4.451900 CGCTCCCATTGGTAGTTTAGATT 58.548 43.478 1.20 0.00 0.00 2.40
4821 6310 5.454187 CCGCTCCCATTGGTAGTTTAGATTA 60.454 44.000 1.20 0.00 0.00 1.75
4822 6311 6.053005 CGCTCCCATTGGTAGTTTAGATTAA 58.947 40.000 1.20 0.00 0.00 1.40
4823 6312 6.202954 CGCTCCCATTGGTAGTTTAGATTAAG 59.797 42.308 1.20 0.00 0.00 1.85
4824 6313 7.280356 GCTCCCATTGGTAGTTTAGATTAAGA 58.720 38.462 1.20 0.00 0.00 2.10
4825 6314 7.939588 GCTCCCATTGGTAGTTTAGATTAAGAT 59.060 37.037 1.20 0.00 0.00 2.40
4826 6315 9.853177 CTCCCATTGGTAGTTTAGATTAAGATT 57.147 33.333 1.20 0.00 0.00 2.40
4840 6329 7.765695 AGATTAAGATTTTTGAGTCCTTGCA 57.234 32.000 0.00 0.00 0.00 4.08
4841 6330 7.824672 AGATTAAGATTTTTGAGTCCTTGCAG 58.175 34.615 0.00 0.00 0.00 4.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.517832 CGAGGCGGACAGGAAGAAT 59.482 57.895 0.00 0.00 0.00 2.40
1 2 2.970639 CGAGGCGGACAGGAAGAA 59.029 61.111 0.00 0.00 0.00 2.52
2 3 3.760035 GCGAGGCGGACAGGAAGA 61.760 66.667 0.00 0.00 0.00 2.87
3 4 4.069232 TGCGAGGCGGACAGGAAG 62.069 66.667 0.00 0.00 0.00 3.46
10 11 1.511305 CTTCTTAGTGCGAGGCGGA 59.489 57.895 0.00 0.00 0.00 5.54
11 12 2.167861 GCTTCTTAGTGCGAGGCGG 61.168 63.158 0.00 0.00 0.00 6.13
12 13 0.807667 ATGCTTCTTAGTGCGAGGCG 60.808 55.000 0.00 0.00 36.41 5.52
13 14 1.373570 AATGCTTCTTAGTGCGAGGC 58.626 50.000 0.00 0.00 34.47 4.70
16 17 3.682858 GGTTGTAATGCTTCTTAGTGCGA 59.317 43.478 0.00 0.00 0.00 5.10
17 18 3.684788 AGGTTGTAATGCTTCTTAGTGCG 59.315 43.478 0.00 0.00 0.00 5.34
18 19 5.629079 AAGGTTGTAATGCTTCTTAGTGC 57.371 39.130 0.00 0.00 0.00 4.40
19 20 6.797033 CGAAAAGGTTGTAATGCTTCTTAGTG 59.203 38.462 0.00 0.00 0.00 2.74
20 21 6.708949 TCGAAAAGGTTGTAATGCTTCTTAGT 59.291 34.615 0.00 0.00 0.00 2.24
21 22 7.015877 GTCGAAAAGGTTGTAATGCTTCTTAG 58.984 38.462 0.00 0.00 0.00 2.18
24 25 4.215613 GGTCGAAAAGGTTGTAATGCTTCT 59.784 41.667 0.00 0.00 0.00 2.85
25 26 4.023536 TGGTCGAAAAGGTTGTAATGCTTC 60.024 41.667 0.00 0.00 0.00 3.86
30 31 3.823873 TGCATGGTCGAAAAGGTTGTAAT 59.176 39.130 0.00 0.00 0.00 1.89
33 34 1.686355 TGCATGGTCGAAAAGGTTGT 58.314 45.000 0.00 0.00 0.00 3.32
34 35 2.228582 TCATGCATGGTCGAAAAGGTTG 59.771 45.455 25.97 0.00 0.00 3.77
50 51 8.288208 CAGTTTAATTGGACAGAGATATCATGC 58.712 37.037 5.32 0.73 0.00 4.06
52 53 7.446625 GCCAGTTTAATTGGACAGAGATATCAT 59.553 37.037 10.77 0.00 37.96 2.45
56 57 5.191722 AGGCCAGTTTAATTGGACAGAGATA 59.808 40.000 14.80 0.00 46.75 1.98
59 60 3.690460 AGGCCAGTTTAATTGGACAGAG 58.310 45.455 14.80 0.00 46.75 3.35
64 65 3.349022 CGGTAAGGCCAGTTTAATTGGA 58.651 45.455 10.77 0.00 37.96 3.53
84 85 0.249699 TTGTGATATACTGGCCGCCG 60.250 55.000 4.58 2.21 0.00 6.46
85 86 1.226746 GTTGTGATATACTGGCCGCC 58.773 55.000 1.04 1.04 0.00 6.13
93 94 9.216117 GTCATAAATGTAGGGGTTGTGATATAC 57.784 37.037 0.00 0.00 0.00 1.47
94 95 8.092068 CGTCATAAATGTAGGGGTTGTGATATA 58.908 37.037 0.00 0.00 0.00 0.86
95 96 6.934645 CGTCATAAATGTAGGGGTTGTGATAT 59.065 38.462 0.00 0.00 0.00 1.63
119 120 2.946329 ACTCACAGGACTAGCTGTATCG 59.054 50.000 0.00 0.00 31.92 2.92
136 137 1.474879 TCCATCGCATCGTGTAACTCA 59.525 47.619 0.00 0.00 31.75 3.41
137 138 2.203800 TCCATCGCATCGTGTAACTC 57.796 50.000 0.00 0.00 31.75 3.01
139 140 3.123804 AGAATCCATCGCATCGTGTAAC 58.876 45.455 0.00 0.00 0.00 2.50
140 141 3.452755 AGAATCCATCGCATCGTGTAA 57.547 42.857 0.00 0.00 0.00 2.41
141 142 3.452755 AAGAATCCATCGCATCGTGTA 57.547 42.857 0.00 0.00 0.00 2.90
142 143 2.315925 AAGAATCCATCGCATCGTGT 57.684 45.000 0.00 0.00 0.00 4.49
144 145 3.735237 AGTAAGAATCCATCGCATCGT 57.265 42.857 0.00 0.00 0.00 3.73
145 146 4.800993 GGATAGTAAGAATCCATCGCATCG 59.199 45.833 0.00 0.00 42.21 3.84
146 147 4.800993 CGGATAGTAAGAATCCATCGCATC 59.199 45.833 3.24 0.00 42.69 3.91
149 150 2.924290 GCGGATAGTAAGAATCCATCGC 59.076 50.000 3.24 0.00 42.69 4.58
152 492 4.160329 TGAGGCGGATAGTAAGAATCCAT 58.840 43.478 3.24 0.00 42.69 3.41
174 514 7.308169 GGTTGAAAAGGTTGTAACGCTTACTAT 60.308 37.037 8.61 0.00 37.06 2.12
183 523 4.099824 CGTGTGGTTGAAAAGGTTGTAAC 58.900 43.478 0.00 0.00 0.00 2.50
190 530 3.936585 CCACGTGTGGTTGAAAAGG 57.063 52.632 15.65 0.00 45.53 3.11
208 548 3.129988 CCAGCTTGATTGGACAAAGATCC 59.870 47.826 0.00 0.00 37.96 3.36
214 554 0.112995 AGGCCAGCTTGATTGGACAA 59.887 50.000 5.01 0.00 46.75 3.18
238 578 2.721167 TTCTGATACGCTGGCCGCT 61.721 57.895 15.78 7.19 41.76 5.52
254 594 4.146745 ACCGTCATAAATGTAGGGGTTC 57.853 45.455 9.84 0.00 32.63 3.62
286 1226 1.091771 CCGTGTATCCTTGGCAGCAG 61.092 60.000 0.00 0.00 0.00 4.24
288 1228 1.078426 ACCGTGTATCCTTGGCAGC 60.078 57.895 0.00 0.00 0.00 5.25
290 1230 0.687920 TTCACCGTGTATCCTTGGCA 59.312 50.000 0.00 0.00 0.00 4.92
291 1231 1.084289 GTTCACCGTGTATCCTTGGC 58.916 55.000 0.00 0.00 0.00 4.52
292 1232 2.233922 AGAGTTCACCGTGTATCCTTGG 59.766 50.000 0.00 0.00 0.00 3.61
293 1233 3.594603 AGAGTTCACCGTGTATCCTTG 57.405 47.619 0.00 0.00 0.00 3.61
294 1234 4.771054 AGTAAGAGTTCACCGTGTATCCTT 59.229 41.667 0.00 2.19 0.00 3.36
295 1235 4.158025 CAGTAAGAGTTCACCGTGTATCCT 59.842 45.833 0.00 0.00 0.00 3.24
302 1242 1.268899 CGGACAGTAAGAGTTCACCGT 59.731 52.381 0.00 0.00 35.40 4.83
308 1248 0.526662 CGAGGCGGACAGTAAGAGTT 59.473 55.000 0.00 0.00 0.00 3.01
310 1250 0.378962 CTCGAGGCGGACAGTAAGAG 59.621 60.000 3.91 0.00 0.00 2.85
317 1257 0.745486 TACGATTCTCGAGGCGGACA 60.745 55.000 13.56 2.20 43.74 4.02
328 1268 7.823665 TGTGTGTAGATTTGTAGTACGATTCT 58.176 34.615 15.85 15.85 0.00 2.40
334 1274 9.204570 AGTTGATTGTGTGTAGATTTGTAGTAC 57.795 33.333 0.00 0.00 0.00 2.73
335 1275 9.203421 CAGTTGATTGTGTGTAGATTTGTAGTA 57.797 33.333 0.00 0.00 0.00 1.82
336 1276 7.715249 ACAGTTGATTGTGTGTAGATTTGTAGT 59.285 33.333 0.00 0.00 0.00 2.73
340 1280 7.306167 GCAAACAGTTGATTGTGTGTAGATTTG 60.306 37.037 4.42 0.00 38.34 2.32
345 1285 4.734854 GTGCAAACAGTTGATTGTGTGTAG 59.265 41.667 0.00 0.00 38.34 2.74
368 1308 6.426328 AGAAAACTTCTTCACATGCTAGACAG 59.574 38.462 0.00 0.00 36.36 3.51
370 1310 6.793492 AGAAAACTTCTTCACATGCTAGAC 57.207 37.500 0.00 0.00 36.36 2.59
371 1311 9.507329 AAATAGAAAACTTCTTCACATGCTAGA 57.493 29.630 0.00 0.00 41.14 2.43
377 1317 9.136323 AGGACAAAATAGAAAACTTCTTCACAT 57.864 29.630 0.00 0.00 41.14 3.21
378 1318 8.519799 AGGACAAAATAGAAAACTTCTTCACA 57.480 30.769 0.00 0.00 41.14 3.58
381 1321 9.057089 TCTGAGGACAAAATAGAAAACTTCTTC 57.943 33.333 0.00 0.00 41.14 2.87
392 1332 7.809806 GGACAAATGTTTCTGAGGACAAAATAG 59.190 37.037 1.01 0.00 0.00 1.73
399 1368 5.514274 TTTGGACAAATGTTTCTGAGGAC 57.486 39.130 0.00 0.00 0.00 3.85
401 1370 5.906073 AGTTTTGGACAAATGTTTCTGAGG 58.094 37.500 0.00 0.00 0.00 3.86
585 1559 3.246880 GAGAACGGTGGGTGGGGT 61.247 66.667 0.00 0.00 0.00 4.95
586 1560 2.928396 AGAGAACGGTGGGTGGGG 60.928 66.667 0.00 0.00 0.00 4.96
587 1561 1.889530 GAGAGAGAACGGTGGGTGGG 61.890 65.000 0.00 0.00 0.00 4.61
600 1574 1.421646 GAGAGGGAGAGGGAGAGAGAG 59.578 61.905 0.00 0.00 0.00 3.20
601 1575 1.518367 GAGAGGGAGAGGGAGAGAGA 58.482 60.000 0.00 0.00 0.00 3.10
602 1576 0.478507 GGAGAGGGAGAGGGAGAGAG 59.521 65.000 0.00 0.00 0.00 3.20
603 1577 0.996762 GGGAGAGGGAGAGGGAGAGA 60.997 65.000 0.00 0.00 0.00 3.10
604 1578 0.998945 AGGGAGAGGGAGAGGGAGAG 60.999 65.000 0.00 0.00 0.00 3.20
605 1579 0.996762 GAGGGAGAGGGAGAGGGAGA 60.997 65.000 0.00 0.00 0.00 3.71
606 1580 0.998945 AGAGGGAGAGGGAGAGGGAG 60.999 65.000 0.00 0.00 0.00 4.30
607 1581 0.556380 AAGAGGGAGAGGGAGAGGGA 60.556 60.000 0.00 0.00 0.00 4.20
608 1582 0.105709 GAAGAGGGAGAGGGAGAGGG 60.106 65.000 0.00 0.00 0.00 4.30
609 1583 0.933700 AGAAGAGGGAGAGGGAGAGG 59.066 60.000 0.00 0.00 0.00 3.69
610 1584 2.244769 AGAAGAAGAGGGAGAGGGAGAG 59.755 54.545 0.00 0.00 0.00 3.20
611 1585 2.243736 GAGAAGAAGAGGGAGAGGGAGA 59.756 54.545 0.00 0.00 0.00 3.71
612 1586 2.666317 GAGAAGAAGAGGGAGAGGGAG 58.334 57.143 0.00 0.00 0.00 4.30
613 1587 1.289530 GGAGAAGAAGAGGGAGAGGGA 59.710 57.143 0.00 0.00 0.00 4.20
614 1588 1.691163 GGGAGAAGAAGAGGGAGAGGG 60.691 61.905 0.00 0.00 0.00 4.30
615 1589 1.290732 AGGGAGAAGAAGAGGGAGAGG 59.709 57.143 0.00 0.00 0.00 3.69
931 1905 1.208706 GGGAGGAGGGGAAGAAGAAG 58.791 60.000 0.00 0.00 0.00 2.85
932 1906 0.253207 GGGGAGGAGGGGAAGAAGAA 60.253 60.000 0.00 0.00 0.00 2.52
933 1907 1.162951 AGGGGAGGAGGGGAAGAAGA 61.163 60.000 0.00 0.00 0.00 2.87
934 1908 0.692756 GAGGGGAGGAGGGGAAGAAG 60.693 65.000 0.00 0.00 0.00 2.85
1109 2560 8.943909 AAGTACGAAAAGAAAGAGAGAAGAAA 57.056 30.769 0.00 0.00 0.00 2.52
1111 2562 7.942990 AGAAGTACGAAAAGAAAGAGAGAAGA 58.057 34.615 0.00 0.00 0.00 2.87
1112 2563 8.484008 CAAGAAGTACGAAAAGAAAGAGAGAAG 58.516 37.037 0.00 0.00 0.00 2.85
1113 2564 7.980099 ACAAGAAGTACGAAAAGAAAGAGAGAA 59.020 33.333 0.00 0.00 0.00 2.87
1117 2568 7.235430 ACACAAGAAGTACGAAAAGAAAGAG 57.765 36.000 0.00 0.00 0.00 2.85
1118 2569 7.605410 AACACAAGAAGTACGAAAAGAAAGA 57.395 32.000 0.00 0.00 0.00 2.52
1129 2584 7.248437 GCATTACCCAATAACACAAGAAGTAC 58.752 38.462 0.00 0.00 0.00 2.73
1137 2592 3.245443 ACCTGGCATTACCCAATAACACA 60.245 43.478 0.00 0.00 37.83 3.72
1138 2593 3.361786 ACCTGGCATTACCCAATAACAC 58.638 45.455 0.00 0.00 37.83 3.32
1143 2599 1.194218 GCAACCTGGCATTACCCAAT 58.806 50.000 0.00 0.00 37.83 3.16
1176 2632 2.812011 ACATTTGTCGGCCTCTACAAAC 59.188 45.455 22.50 3.25 45.47 2.93
1177 2633 3.134574 ACATTTGTCGGCCTCTACAAA 57.865 42.857 22.37 22.37 46.37 2.83
1188 2650 0.780002 GCAAGCAGCAACATTTGTCG 59.220 50.000 0.00 0.00 44.79 4.35
1215 2677 3.629398 AGAATCAATCAACCAATCCGCTC 59.371 43.478 0.00 0.00 0.00 5.03
1216 2678 3.624777 AGAATCAATCAACCAATCCGCT 58.375 40.909 0.00 0.00 0.00 5.52
1252 2715 3.617284 CACCCCCTAATTAGGAACACAC 58.383 50.000 29.75 0.00 46.63 3.82
1253 2716 2.578940 CCACCCCCTAATTAGGAACACA 59.421 50.000 29.75 0.00 46.63 3.72
1254 2717 2.092049 CCCACCCCCTAATTAGGAACAC 60.092 54.545 29.75 0.00 46.63 3.32
1255 2718 2.210644 CCCACCCCCTAATTAGGAACA 58.789 52.381 29.75 0.00 46.63 3.18
1256 2719 1.497716 CCCCACCCCCTAATTAGGAAC 59.502 57.143 29.75 0.00 46.63 3.62
1257 2720 1.632622 CCCCCACCCCCTAATTAGGAA 60.633 57.143 29.75 0.00 46.63 3.36
1375 2838 2.688958 ACCCTAGACGAGAAAAGATCGG 59.311 50.000 0.00 0.00 44.36 4.18
1710 3175 0.254747 CACCCACCAACCATACGGAT 59.745 55.000 0.00 0.00 35.59 4.18
1960 3425 0.252479 ATTCTACTGCTGCTGCTGCT 59.748 50.000 27.67 14.24 41.07 4.24
1962 3427 3.065655 GGATATTCTACTGCTGCTGCTG 58.934 50.000 18.66 18.66 42.70 4.41
2153 3618 1.327460 CATGGCCGTCGTAGTGAATTG 59.673 52.381 0.00 0.00 0.00 2.32
2230 3695 2.480073 CCTGCCAAGAACAACAGTTGTG 60.480 50.000 19.84 7.92 44.59 3.33
2233 3698 2.024414 GTCCTGCCAAGAACAACAGTT 58.976 47.619 0.00 0.00 0.00 3.16
2344 3809 2.072298 CCAAGACAGAAAGAAGAGCCG 58.928 52.381 0.00 0.00 0.00 5.52
2376 3841 4.984161 CCAGGCAAAAGAACAAACATGTAG 59.016 41.667 0.00 0.00 0.00 2.74
2391 3856 1.110442 CCAACAACAGACCAGGCAAA 58.890 50.000 0.00 0.00 0.00 3.68
2396 3862 1.948104 TCGAACCAACAACAGACCAG 58.052 50.000 0.00 0.00 0.00 4.00
2401 3868 3.757745 ACAACTTCGAACCAACAACAG 57.242 42.857 0.00 0.00 0.00 3.16
2406 3873 6.583427 ACAAACTTTTACAACTTCGAACCAAC 59.417 34.615 0.00 0.00 0.00 3.77
2412 3879 7.539366 CCAAAGAACAAACTTTTACAACTTCGA 59.461 33.333 0.00 0.00 37.91 3.71
2414 3881 7.601130 ACCCAAAGAACAAACTTTTACAACTTC 59.399 33.333 0.00 0.00 37.91 3.01
2430 3897 1.338020 CCTGTTGCAGACCCAAAGAAC 59.662 52.381 0.00 0.00 32.44 3.01
2440 3907 0.471780 TCCTCCTGACCTGTTGCAGA 60.472 55.000 0.00 0.00 34.06 4.26
2609 4076 0.400213 TTCTGGAACCAGGAACGCAT 59.600 50.000 18.99 0.00 43.75 4.73
2613 4080 3.071747 AGAGAACTTCTGGAACCAGGAAC 59.928 47.826 18.99 6.74 43.75 3.62
2691 4158 6.646240 ACATACATGCCAGAAACACAAAAATC 59.354 34.615 0.00 0.00 0.00 2.17
2763 4233 7.796054 AGAGTGCATTAAAGCCTATTTCTAGA 58.204 34.615 0.00 0.00 0.00 2.43
2830 4300 8.722394 CAAGGAACAGAAATTAGAGGAAACTAC 58.278 37.037 0.00 0.00 44.43 2.73
2839 4309 9.396022 GATAATGACCAAGGAACAGAAATTAGA 57.604 33.333 0.00 0.00 0.00 2.10
3007 4477 2.738587 TACCAAGCTTTGTTCCCACA 57.261 45.000 8.67 0.00 0.00 4.17
3160 4630 1.351017 TCCCCTGCTTTCACTTGTAGG 59.649 52.381 0.00 0.00 36.11 3.18
3241 4711 5.701290 ACAGAAAGCAGTGGTGAAATACTAC 59.299 40.000 0.00 0.00 40.75 2.73
3282 4752 9.726438 AATAGCCAACAATTCATCTAGGTATAC 57.274 33.333 0.00 0.00 0.00 1.47
3306 4776 7.100458 AGAACACAAGCACAAAGAACTAAAT 57.900 32.000 0.00 0.00 0.00 1.40
3317 4787 3.290948 AGGGTAAAGAACACAAGCACA 57.709 42.857 0.00 0.00 31.97 4.57
3372 4842 5.304101 AGGGCAATGTACAAAGTGAAAATGA 59.696 36.000 0.00 0.00 0.00 2.57
3559 5029 6.038714 CCCTACAGAATTTGGCATCTAAAGTC 59.961 42.308 0.00 0.00 33.65 3.01
3636 5106 8.785184 AAGATAGCTATACTAGTTGGGTCTTT 57.215 34.615 6.13 0.00 33.29 2.52
3736 5206 4.458989 TCAAATACACCCTTGACATTCTGC 59.541 41.667 0.00 0.00 0.00 4.26
3796 5266 3.632145 TCTGCGCCTTTTTCTTCTTCTTT 59.368 39.130 4.18 0.00 0.00 2.52
3945 5415 1.466937 AACCTAGGGTGGGGTAGGGT 61.467 60.000 14.81 0.00 40.32 4.34
4153 5624 6.384015 ACATCATGTCTCTACTTATGGAACCA 59.616 38.462 0.00 0.00 0.00 3.67
4295 5773 5.695818 CGAAAGTAAACCAAACCGAATCAT 58.304 37.500 0.00 0.00 0.00 2.45
4307 5785 1.794512 TACACCGGCGAAAGTAAACC 58.205 50.000 9.30 0.00 0.00 3.27
4312 5790 2.006888 CAATCATACACCGGCGAAAGT 58.993 47.619 9.30 6.25 0.00 2.66
4313 5791 1.268032 GCAATCATACACCGGCGAAAG 60.268 52.381 9.30 0.00 0.00 2.62
4314 5792 0.730265 GCAATCATACACCGGCGAAA 59.270 50.000 9.30 0.00 0.00 3.46
4315 5793 0.107897 AGCAATCATACACCGGCGAA 60.108 50.000 9.30 0.00 0.00 4.70
4316 5794 0.809636 CAGCAATCATACACCGGCGA 60.810 55.000 9.30 0.00 0.00 5.54
4323 5802 3.363627 TCCATTTGCCAGCAATCATACA 58.636 40.909 5.80 0.00 35.70 2.29
4472 5951 2.771372 TCCTATTGCAGCAGATACCACA 59.229 45.455 0.00 0.00 0.00 4.17
4473 5952 3.475566 TCCTATTGCAGCAGATACCAC 57.524 47.619 0.00 0.00 0.00 4.16
4508 5989 5.482908 CAGATATTGTACCCAGCCAGATAC 58.517 45.833 0.00 0.00 0.00 2.24
4509 5990 4.020218 GCAGATATTGTACCCAGCCAGATA 60.020 45.833 0.00 0.00 0.00 1.98
4559 6040 7.816995 TGGCATGTGTATCCAAGTTTTAAAATC 59.183 33.333 3.52 0.00 0.00 2.17
4602 6083 6.607198 ACCATATCCACCCAAAAGATTTAGTG 59.393 38.462 0.00 0.00 0.00 2.74
4675 6156 2.298729 GTTGGCTGGCCATTTTCTACAA 59.701 45.455 15.41 1.24 46.64 2.41
4678 6159 2.170166 CAGTTGGCTGGCCATTTTCTA 58.830 47.619 15.41 0.00 46.64 2.10
4680 6161 0.968405 TCAGTTGGCTGGCCATTTTC 59.032 50.000 15.41 6.79 46.64 2.29
4681 6162 1.422531 TTCAGTTGGCTGGCCATTTT 58.577 45.000 15.41 1.51 46.64 1.82
4726 6215 1.602237 GGAGGCGTCAAGGGATTCA 59.398 57.895 8.91 0.00 0.00 2.57
4727 6216 1.153147 GGGAGGCGTCAAGGGATTC 60.153 63.158 8.91 0.00 0.00 2.52
4729 6218 3.090532 GGGGAGGCGTCAAGGGAT 61.091 66.667 8.91 0.00 0.00 3.85
4730 6219 4.332543 AGGGGAGGCGTCAAGGGA 62.333 66.667 8.91 0.00 0.00 4.20
4731 6220 3.787001 GAGGGGAGGCGTCAAGGG 61.787 72.222 8.91 0.00 0.00 3.95
4732 6221 2.685380 AGAGGGGAGGCGTCAAGG 60.685 66.667 8.91 0.00 0.00 3.61
4733 6222 2.581354 CAGAGGGGAGGCGTCAAG 59.419 66.667 8.91 0.00 0.00 3.02
4734 6223 3.706373 GCAGAGGGGAGGCGTCAA 61.706 66.667 8.91 0.00 0.00 3.18
4758 6247 4.969196 CATCATCGACCGGCGGGG 62.969 72.222 31.78 21.46 41.33 5.73
4759 6248 4.969196 CCATCATCGACCGGCGGG 62.969 72.222 31.78 13.85 41.33 6.13
4760 6249 4.969196 CCCATCATCGACCGGCGG 62.969 72.222 27.06 27.06 41.33 6.13
4761 6250 4.969196 CCCCATCATCGACCGGCG 62.969 72.222 0.00 6.66 42.69 6.46
4762 6251 3.521529 CTCCCCATCATCGACCGGC 62.522 68.421 0.00 0.00 0.00 6.13
4763 6252 2.737180 CTCCCCATCATCGACCGG 59.263 66.667 0.00 0.00 0.00 5.28
4764 6253 1.810606 CTCCTCCCCATCATCGACCG 61.811 65.000 0.00 0.00 0.00 4.79
4765 6254 0.470080 TCTCCTCCCCATCATCGACC 60.470 60.000 0.00 0.00 0.00 4.79
4766 6255 1.414158 TTCTCCTCCCCATCATCGAC 58.586 55.000 0.00 0.00 0.00 4.20
4767 6256 2.251818 GATTCTCCTCCCCATCATCGA 58.748 52.381 0.00 0.00 0.00 3.59
4768 6257 1.277557 GGATTCTCCTCCCCATCATCG 59.722 57.143 0.00 0.00 32.53 3.84
4777 6266 0.985490 AGGCACTGGGATTCTCCTCC 60.985 60.000 0.00 0.00 37.18 4.30
4778 6267 0.467804 GAGGCACTGGGATTCTCCTC 59.532 60.000 0.00 0.00 41.55 3.71
4779 6268 0.985490 GGAGGCACTGGGATTCTCCT 60.985 60.000 0.00 0.00 41.55 3.69
4780 6269 1.529309 GGAGGCACTGGGATTCTCC 59.471 63.158 0.00 0.00 41.55 3.71
4781 6270 1.144936 CGGAGGCACTGGGATTCTC 59.855 63.158 0.00 0.00 41.55 2.87
4782 6271 3.036429 GCGGAGGCACTGGGATTCT 62.036 63.158 0.00 0.00 41.55 2.40
4783 6272 2.514824 GCGGAGGCACTGGGATTC 60.515 66.667 0.00 0.00 41.55 2.52
4784 6273 3.011517 AGCGGAGGCACTGGGATT 61.012 61.111 0.00 0.00 41.55 3.01
4785 6274 3.474570 GAGCGGAGGCACTGGGAT 61.475 66.667 0.00 0.00 41.55 3.85
4789 6278 3.335356 AATGGGAGCGGAGGCACTG 62.335 63.158 0.00 0.00 41.55 3.66
4791 6280 2.825836 CAATGGGAGCGGAGGCAC 60.826 66.667 0.00 0.00 43.41 5.01
4792 6281 4.113815 CCAATGGGAGCGGAGGCA 62.114 66.667 0.00 0.00 43.41 4.75
4793 6282 2.666596 CTACCAATGGGAGCGGAGGC 62.667 65.000 0.00 0.00 38.05 4.70
4794 6283 1.338136 ACTACCAATGGGAGCGGAGG 61.338 60.000 12.34 0.00 38.05 4.30
4795 6284 0.541863 AACTACCAATGGGAGCGGAG 59.458 55.000 12.34 0.00 38.05 4.63
4796 6285 0.988832 AAACTACCAATGGGAGCGGA 59.011 50.000 12.34 0.00 38.05 5.54
4797 6286 2.169769 TCTAAACTACCAATGGGAGCGG 59.830 50.000 12.34 0.00 38.05 5.52
4798 6287 3.536956 TCTAAACTACCAATGGGAGCG 57.463 47.619 12.34 0.00 38.05 5.03
4799 6288 7.280356 TCTTAATCTAAACTACCAATGGGAGC 58.720 38.462 12.34 0.00 38.05 4.70
4800 6289 9.853177 AATCTTAATCTAAACTACCAATGGGAG 57.147 33.333 10.61 10.61 38.05 4.30
4814 6303 9.295825 TGCAAGGACTCAAAAATCTTAATCTAA 57.704 29.630 0.00 0.00 0.00 2.10
4815 6304 8.862325 TGCAAGGACTCAAAAATCTTAATCTA 57.138 30.769 0.00 0.00 0.00 1.98
4816 6305 7.765695 TGCAAGGACTCAAAAATCTTAATCT 57.234 32.000 0.00 0.00 0.00 2.40


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

AutoCloner maintained by Alex Coulton.