Multiple sequence alignment - TraesCS3D01G027300

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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 TraesCS3D01G027300 chr3D 100.000 2564 0 0 1 2564 9290556 9293119 0.000000e+00 4735.0
1 TraesCS3D01G027300 chr3D 100.000 375 0 0 2851 3225 9293406 9293780 0.000000e+00 693.0
2 TraesCS3D01G027300 chr3D 83.422 187 25 5 1054 1237 1608465 1608282 5.530000e-38 169.0
3 TraesCS3D01G027300 chr3D 95.122 41 2 0 2853 2893 172019415 172019455 7.470000e-07 65.8
4 TraesCS3D01G027300 chr3A 95.814 1075 35 8 992 2057 11839371 11838298 0.000000e+00 1727.0
5 TraesCS3D01G027300 chr3A 90.095 525 19 11 2056 2564 11838207 11837700 0.000000e+00 651.0
6 TraesCS3D01G027300 chr3A 90.107 374 26 6 2851 3224 11837658 11837296 2.910000e-130 475.0
7 TraesCS3D01G027300 chr3A 85.672 335 26 11 136 465 11840025 11839708 1.850000e-87 333.0
8 TraesCS3D01G027300 chr3A 82.540 252 17 9 720 961 11839596 11839362 2.540000e-46 196.0
9 TraesCS3D01G027300 chr3A 80.150 267 33 11 2969 3224 11833688 11833431 7.110000e-42 182.0
10 TraesCS3D01G027300 chr3A 84.571 175 21 5 1054 1225 7438714 7438543 5.530000e-38 169.0
11 TraesCS3D01G027300 chr3A 82.759 116 13 5 15 126 11840104 11839992 2.650000e-16 97.1
12 TraesCS3D01G027300 chr3A 93.478 46 1 2 2853 2896 554021989 554021944 2.080000e-07 67.6
13 TraesCS3D01G027300 chr3B 96.324 789 26 2 1272 2057 11602034 11602822 0.000000e+00 1293.0
14 TraesCS3D01G027300 chr3B 90.095 525 26 11 2056 2558 11602914 11603434 0.000000e+00 658.0
15 TraesCS3D01G027300 chr3B 85.265 604 31 23 674 1273 11601450 11601999 1.300000e-158 569.0
16 TraesCS3D01G027300 chr3B 86.535 505 35 11 127 625 11600605 11601082 2.850000e-145 525.0
17 TraesCS3D01G027300 chr3B 77.815 302 41 10 2851 3142 11603475 11603760 2.570000e-36 163.0
18 TraesCS3D01G027300 chr3B 80.328 122 21 3 7 126 11600527 11600647 4.430000e-14 89.8
19 TraesCS3D01G027300 chr3B 82.432 74 10 1 2418 2491 775551053 775550983 9.660000e-06 62.1
20 TraesCS3D01G027300 chr7A 82.301 113 18 2 1072 1182 306220888 306221000 2.650000e-16 97.1
21 TraesCS3D01G027300 chr5A 97.561 41 1 0 2853 2893 596084043 596084083 1.610000e-08 71.3
22 TraesCS3D01G027300 chr6B 79.612 103 16 4 2418 2518 716921527 716921626 5.770000e-08 69.4
23 TraesCS3D01G027300 chr1A 95.238 42 2 0 2856 2897 568548814 568548773 2.080000e-07 67.6
24 TraesCS3D01G027300 chr1A 95.238 42 2 0 2856 2897 568549377 568549336 2.080000e-07 67.6
25 TraesCS3D01G027300 chr6D 95.238 42 1 1 2853 2893 456581575 456581534 7.470000e-07 65.8
26 TraesCS3D01G027300 chr6A 95.122 41 2 0 2853 2893 127572033 127571993 7.470000e-07 65.8
27 TraesCS3D01G027300 chr4A 82.432 74 11 2 2418 2491 675529561 675529490 2.690000e-06 63.9
28 TraesCS3D01G027300 chr5B 88.462 52 3 2 2854 2903 542675587 542675537 3.470000e-05 60.2


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 TraesCS3D01G027300 chr3D 9290556 9293780 3224 False 2714.000000 4735 100.000000 1 3225 2 chr3D.!!$F2 3224
1 TraesCS3D01G027300 chr3A 11833431 11840104 6673 True 523.014286 1727 86.733857 15 3224 7 chr3A.!!$R3 3209
2 TraesCS3D01G027300 chr3B 11600527 11603760 3233 False 549.633333 1293 86.060333 7 3142 6 chr3B.!!$F1 3135

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
767 1114 0.109086 CCTGTGTCCGTCTACTGCTG 60.109 60.0 0.0 0.0 0.0 4.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2501 3038 1.243902 TCAAAATCGTTCACCCAGCC 58.756 50.0 0.0 0.0 0.0 4.85 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
113 125 6.549736 TCTGATTCAGAATGTAGACCGGATTA 59.450 38.462 13.96 0.00 37.57 1.75
114 126 7.069455 TCTGATTCAGAATGTAGACCGGATTAA 59.931 37.037 13.96 0.00 37.57 1.40
115 127 6.984474 TGATTCAGAATGTAGACCGGATTAAC 59.016 38.462 9.46 0.70 37.40 2.01
116 128 6.540438 TTCAGAATGTAGACCGGATTAACT 57.460 37.500 9.46 1.66 37.40 2.24
117 129 6.540438 TCAGAATGTAGACCGGATTAACTT 57.460 37.500 9.46 0.00 37.40 2.66
118 130 6.942976 TCAGAATGTAGACCGGATTAACTTT 58.057 36.000 9.46 5.20 37.40 2.66
119 131 6.816640 TCAGAATGTAGACCGGATTAACTTTG 59.183 38.462 9.46 0.00 37.40 2.77
120 132 6.816640 CAGAATGTAGACCGGATTAACTTTGA 59.183 38.462 9.46 0.00 0.00 2.69
121 133 7.495934 CAGAATGTAGACCGGATTAACTTTGAT 59.504 37.037 9.46 0.00 0.00 2.57
122 134 7.495934 AGAATGTAGACCGGATTAACTTTGATG 59.504 37.037 9.46 0.00 0.00 3.07
123 135 6.045072 TGTAGACCGGATTAACTTTGATGT 57.955 37.500 9.46 0.00 0.00 3.06
124 136 6.469410 TGTAGACCGGATTAACTTTGATGTT 58.531 36.000 9.46 0.00 0.00 2.71
125 137 6.592607 TGTAGACCGGATTAACTTTGATGTTC 59.407 38.462 9.46 0.00 0.00 3.18
126 138 5.805728 AGACCGGATTAACTTTGATGTTCT 58.194 37.500 9.46 0.00 0.00 3.01
127 139 5.643777 AGACCGGATTAACTTTGATGTTCTG 59.356 40.000 9.46 0.00 0.00 3.02
128 140 4.700213 ACCGGATTAACTTTGATGTTCTGG 59.300 41.667 9.46 0.00 0.00 3.86
129 141 4.700213 CCGGATTAACTTTGATGTTCTGGT 59.300 41.667 0.00 0.00 0.00 4.00
130 142 5.183140 CCGGATTAACTTTGATGTTCTGGTT 59.817 40.000 0.00 0.00 0.00 3.67
131 143 6.314784 CGGATTAACTTTGATGTTCTGGTTC 58.685 40.000 0.00 0.00 0.00 3.62
132 144 6.072728 CGGATTAACTTTGATGTTCTGGTTCA 60.073 38.462 0.00 0.00 0.00 3.18
133 145 7.308435 GGATTAACTTTGATGTTCTGGTTCAG 58.692 38.462 0.00 0.00 0.00 3.02
134 146 7.174946 GGATTAACTTTGATGTTCTGGTTCAGA 59.825 37.037 0.00 0.00 38.87 3.27
135 147 7.873719 TTAACTTTGATGTTCTGGTTCAGAA 57.126 32.000 6.28 6.28 46.50 3.02
144 156 4.685169 TTCTGGTTCAGAATTCGAATGC 57.315 40.909 12.25 10.16 44.27 3.56
145 157 3.673902 TCTGGTTCAGAATTCGAATGCA 58.326 40.909 18.45 0.00 37.57 3.96
146 158 3.686241 TCTGGTTCAGAATTCGAATGCAG 59.314 43.478 18.45 10.50 37.57 4.41
147 159 3.673902 TGGTTCAGAATTCGAATGCAGA 58.326 40.909 18.45 12.82 0.00 4.26
148 160 3.436704 TGGTTCAGAATTCGAATGCAGAC 59.563 43.478 18.45 12.22 0.00 3.51
149 161 3.686726 GGTTCAGAATTCGAATGCAGACT 59.313 43.478 18.45 7.40 0.00 3.24
150 162 4.436584 GGTTCAGAATTCGAATGCAGACTG 60.437 45.833 18.45 17.03 0.00 3.51
151 163 3.264947 TCAGAATTCGAATGCAGACTGG 58.735 45.455 18.45 1.04 0.00 4.00
152 164 3.055891 TCAGAATTCGAATGCAGACTGGA 60.056 43.478 18.45 0.73 0.00 3.86
153 165 3.875727 CAGAATTCGAATGCAGACTGGAT 59.124 43.478 18.45 3.21 0.00 3.41
154 166 4.025061 CAGAATTCGAATGCAGACTGGATC 60.025 45.833 18.45 5.10 0.00 3.36
155 167 1.926561 TTCGAATGCAGACTGGATCG 58.073 50.000 10.16 14.29 0.00 3.69
158 170 1.576356 GAATGCAGACTGGATCGACC 58.424 55.000 10.16 0.00 39.54 4.79
169 181 2.371306 TGGATCGACCAGTATGTTCGA 58.629 47.619 1.91 1.91 44.64 3.71
179 191 5.437060 ACCAGTATGTTCGAGCCATAAATT 58.563 37.500 8.05 0.00 0.00 1.82
189 201 2.760092 GAGCCATAAATTTGCACCCTGA 59.240 45.455 0.00 0.00 0.00 3.86
190 202 3.172339 AGCCATAAATTTGCACCCTGAA 58.828 40.909 0.00 0.00 0.00 3.02
212 224 1.831736 GCCTACATGGACAGGTGTACT 59.168 52.381 10.80 0.00 38.35 2.73
213 225 2.418746 GCCTACATGGACAGGTGTACTG 60.419 54.545 10.80 0.00 44.06 2.74
214 226 4.692309 GCCTACATGGACAGGTGTACTGA 61.692 52.174 10.80 0.00 43.89 3.41
316 328 5.605534 CAGGTGTATCTGGTCAAGGAATAG 58.394 45.833 0.00 0.00 0.00 1.73
354 366 1.278699 TGCATGTCTGTGTGGATGCTA 59.721 47.619 0.00 0.00 41.49 3.49
397 414 6.400568 CAATGCATTCCCTTAACATTTCTGT 58.599 36.000 9.53 0.00 37.12 3.41
399 416 5.782047 TGCATTCCCTTAACATTTCTGTTG 58.218 37.500 1.39 0.00 45.16 3.33
400 417 5.304101 TGCATTCCCTTAACATTTCTGTTGT 59.696 36.000 1.39 0.00 45.16 3.32
401 418 5.634859 GCATTCCCTTAACATTTCTGTTGTG 59.365 40.000 1.39 0.00 45.16 3.33
402 419 4.846779 TCCCTTAACATTTCTGTTGTGC 57.153 40.909 1.39 0.00 45.16 4.57
403 420 4.469657 TCCCTTAACATTTCTGTTGTGCT 58.530 39.130 1.39 0.00 45.16 4.40
404 421 4.278170 TCCCTTAACATTTCTGTTGTGCTG 59.722 41.667 1.39 0.00 45.16 4.41
405 422 3.983344 CCTTAACATTTCTGTTGTGCTGC 59.017 43.478 1.39 0.00 45.16 5.25
406 423 4.261741 CCTTAACATTTCTGTTGTGCTGCT 60.262 41.667 0.00 0.00 45.16 4.24
407 424 2.787601 ACATTTCTGTTGTGCTGCTG 57.212 45.000 0.00 0.00 28.70 4.41
408 425 1.269413 ACATTTCTGTTGTGCTGCTGC 60.269 47.619 8.89 8.89 33.64 5.25
409 426 1.000607 CATTTCTGTTGTGCTGCTGCT 60.001 47.619 17.00 0.00 40.48 4.24
410 427 0.382873 TTTCTGTTGTGCTGCTGCTG 59.617 50.000 17.00 0.77 40.48 4.41
411 428 2.050351 CTGTTGTGCTGCTGCTGC 60.050 61.111 22.51 22.51 40.48 5.25
412 429 2.517638 TGTTGTGCTGCTGCTGCT 60.518 55.556 27.67 0.00 40.48 4.24
487 508 1.062525 GCGGCGAGCGATCAATTTT 59.937 52.632 12.98 0.00 35.41 1.82
488 509 0.925721 GCGGCGAGCGATCAATTTTC 60.926 55.000 12.98 0.00 35.41 2.29
489 510 0.373370 CGGCGAGCGATCAATTTTCA 59.627 50.000 0.00 0.00 0.00 2.69
490 511 1.593070 CGGCGAGCGATCAATTTTCAG 60.593 52.381 0.00 0.00 0.00 3.02
491 512 1.460766 GCGAGCGATCAATTTTCAGC 58.539 50.000 0.00 0.00 0.00 4.26
494 515 2.094894 CGAGCGATCAATTTTCAGCTGT 59.905 45.455 14.67 0.00 34.85 4.40
496 517 1.916000 GCGATCAATTTTCAGCTGTGC 59.084 47.619 14.67 0.25 0.00 4.57
516 537 1.293963 TGTTGATCACTCGCTGCTGC 61.294 55.000 5.34 5.34 0.00 5.25
582 603 1.116308 CATCATGGGCCTTGATGCAA 58.884 50.000 35.40 13.33 42.73 4.08
583 604 1.691976 CATCATGGGCCTTGATGCAAT 59.308 47.619 35.40 15.70 42.73 3.56
584 605 1.116308 TCATGGGCCTTGATGCAATG 58.884 50.000 17.45 4.03 0.00 2.82
585 606 0.531974 CATGGGCCTTGATGCAATGC 60.532 55.000 13.94 0.00 34.98 3.56
586 607 0.978667 ATGGGCCTTGATGCAATGCA 60.979 50.000 11.44 11.44 44.86 3.96
606 627 3.365832 CAACGCAATTATGTGAGGCATC 58.634 45.455 0.00 0.00 39.48 3.91
634 655 3.093717 GGATCAATTCCATTGCTGCTG 57.906 47.619 0.00 0.00 44.74 4.41
635 656 2.470821 GATCAATTCCATTGCTGCTGC 58.529 47.619 8.89 8.89 40.05 5.25
636 657 1.552578 TCAATTCCATTGCTGCTGCT 58.447 45.000 17.00 0.00 40.05 4.24
637 658 1.203758 TCAATTCCATTGCTGCTGCTG 59.796 47.619 17.00 7.44 40.05 4.41
638 659 1.067142 CAATTCCATTGCTGCTGCTGT 60.067 47.619 17.00 2.41 40.48 4.40
639 660 1.263356 ATTCCATTGCTGCTGCTGTT 58.737 45.000 17.00 0.00 40.48 3.16
640 661 0.315886 TTCCATTGCTGCTGCTGTTG 59.684 50.000 17.00 10.73 40.48 3.33
641 662 1.736645 CCATTGCTGCTGCTGTTGC 60.737 57.895 17.00 4.76 40.48 4.17
642 663 1.289066 CATTGCTGCTGCTGTTGCT 59.711 52.632 17.00 0.00 40.48 3.91
643 664 1.008875 CATTGCTGCTGCTGTTGCTG 61.009 55.000 17.00 1.98 40.48 4.41
649 670 2.561885 CTGCTGTTGCTGCTGCTC 59.438 61.111 17.00 10.19 40.48 4.26
652 999 2.979197 GCTGTTGCTGCTGCTCAGG 61.979 63.158 27.23 16.83 43.06 3.86
667 1014 2.844654 TCAGGGAGAGAGAGAGCATT 57.155 50.000 0.00 0.00 0.00 3.56
668 1015 2.665165 TCAGGGAGAGAGAGAGCATTC 58.335 52.381 0.00 0.00 0.00 2.67
669 1016 2.024560 TCAGGGAGAGAGAGAGCATTCA 60.025 50.000 0.00 0.00 0.00 2.57
670 1017 2.967201 CAGGGAGAGAGAGAGCATTCAT 59.033 50.000 0.00 0.00 0.00 2.57
671 1018 4.141065 TCAGGGAGAGAGAGAGCATTCATA 60.141 45.833 0.00 0.00 0.00 2.15
672 1019 4.773674 CAGGGAGAGAGAGAGCATTCATAT 59.226 45.833 0.00 0.00 0.00 1.78
673 1020 5.246656 CAGGGAGAGAGAGAGCATTCATATT 59.753 44.000 0.00 0.00 0.00 1.28
705 1052 0.403271 ATGCACTTGCCAGGTCTCTT 59.597 50.000 0.00 0.00 41.18 2.85
717 1064 1.751924 AGGTCTCTTTAGCTAGCGGTG 59.248 52.381 9.55 1.43 0.00 4.94
737 1084 1.212935 GGAGTTACCAGGACCATGCAT 59.787 52.381 0.00 0.00 38.79 3.96
738 1085 2.292267 GAGTTACCAGGACCATGCATG 58.708 52.381 20.19 20.19 0.00 4.06
739 1086 0.740737 GTTACCAGGACCATGCATGC 59.259 55.000 21.69 11.82 0.00 4.06
740 1087 0.330941 TTACCAGGACCATGCATGCA 59.669 50.000 25.04 25.04 0.00 3.96
767 1114 0.109086 CCTGTGTCCGTCTACTGCTG 60.109 60.000 0.00 0.00 0.00 4.41
805 1152 1.073931 CCGGGATAGGTAGGAGAGGA 58.926 60.000 0.00 0.00 0.00 3.71
812 1165 1.152715 GGTAGGAGAGGACGGAGGG 60.153 68.421 0.00 0.00 0.00 4.30
838 1191 2.596923 TGGCAGCAACAATGGCGA 60.597 55.556 0.00 0.00 45.63 5.54
848 1201 0.748005 ACAATGGCGACCACTATGGC 60.748 55.000 0.50 0.00 42.67 4.40
849 1202 0.747644 CAATGGCGACCACTATGGCA 60.748 55.000 0.50 0.00 42.67 4.92
850 1203 0.464373 AATGGCGACCACTATGGCAG 60.464 55.000 0.50 0.00 42.67 4.85
851 1204 1.626356 ATGGCGACCACTATGGCAGT 61.626 55.000 0.50 0.00 42.67 4.40
852 1205 0.973496 TGGCGACCACTATGGCAGTA 60.973 55.000 0.00 0.00 42.67 2.74
889 1242 1.407989 GCACCCTCCAATTCCTCTCAG 60.408 57.143 0.00 0.00 0.00 3.35
892 1245 1.134159 CCCTCCAATTCCTCTCAGCAG 60.134 57.143 0.00 0.00 0.00 4.24
909 1262 1.068954 GCAGAACCACAAGCAGTTAGC 60.069 52.381 0.00 0.00 46.19 3.09
920 1273 1.802636 CAGTTAGCACCCCGCATTG 59.197 57.895 0.00 0.00 46.13 2.82
938 1295 6.036470 CGCATTGTTTCTCTGTAGATCACTA 58.964 40.000 0.00 0.00 0.00 2.74
942 1299 8.867935 CATTGTTTCTCTGTAGATCACTAACAG 58.132 37.037 9.85 9.85 32.10 3.16
951 1308 7.337184 TCTGTAGATCACTAACAGGTTGTAGAG 59.663 40.741 13.95 0.00 33.22 2.43
952 1309 7.173032 TGTAGATCACTAACAGGTTGTAGAGA 58.827 38.462 0.00 0.00 0.00 3.10
953 1310 6.767524 AGATCACTAACAGGTTGTAGAGAG 57.232 41.667 0.00 0.00 0.00 3.20
954 1311 6.486056 AGATCACTAACAGGTTGTAGAGAGA 58.514 40.000 0.00 0.00 0.00 3.10
955 1312 6.601613 AGATCACTAACAGGTTGTAGAGAGAG 59.398 42.308 0.00 0.00 0.00 3.20
956 1313 5.877491 TCACTAACAGGTTGTAGAGAGAGA 58.123 41.667 0.00 0.00 0.00 3.10
957 1314 5.941058 TCACTAACAGGTTGTAGAGAGAGAG 59.059 44.000 0.00 0.00 0.00 3.20
958 1315 5.941058 CACTAACAGGTTGTAGAGAGAGAGA 59.059 44.000 0.00 0.00 0.00 3.10
959 1316 6.093495 CACTAACAGGTTGTAGAGAGAGAGAG 59.907 46.154 0.00 0.00 0.00 3.20
960 1317 4.919774 ACAGGTTGTAGAGAGAGAGAGA 57.080 45.455 0.00 0.00 0.00 3.10
961 1318 4.843728 ACAGGTTGTAGAGAGAGAGAGAG 58.156 47.826 0.00 0.00 0.00 3.20
962 1319 4.534500 ACAGGTTGTAGAGAGAGAGAGAGA 59.466 45.833 0.00 0.00 0.00 3.10
963 1320 5.118990 CAGGTTGTAGAGAGAGAGAGAGAG 58.881 50.000 0.00 0.00 0.00 3.20
964 1321 5.030147 AGGTTGTAGAGAGAGAGAGAGAGA 58.970 45.833 0.00 0.00 0.00 3.10
965 1322 5.129485 AGGTTGTAGAGAGAGAGAGAGAGAG 59.871 48.000 0.00 0.00 0.00 3.20
966 1323 5.128827 GGTTGTAGAGAGAGAGAGAGAGAGA 59.871 48.000 0.00 0.00 0.00 3.10
967 1324 6.276847 GTTGTAGAGAGAGAGAGAGAGAGAG 58.723 48.000 0.00 0.00 0.00 3.20
968 1325 5.766590 TGTAGAGAGAGAGAGAGAGAGAGA 58.233 45.833 0.00 0.00 0.00 3.10
969 1326 5.830457 TGTAGAGAGAGAGAGAGAGAGAGAG 59.170 48.000 0.00 0.00 0.00 3.20
970 1327 5.136068 AGAGAGAGAGAGAGAGAGAGAGA 57.864 47.826 0.00 0.00 0.00 3.10
971 1328 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
972 1329 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
973 1330 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
974 1331 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
975 1332 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
976 1333 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
977 1334 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
978 1335 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
979 1336 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
980 1337 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
981 1338 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
982 1339 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
983 1340 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
984 1341 4.222336 AGAGAGAGAGAGAGAGAGAGAGG 58.778 52.174 0.00 0.00 0.00 3.69
985 1342 4.078922 AGAGAGAGAGAGAGAGAGAGAGGA 60.079 50.000 0.00 0.00 0.00 3.71
986 1343 4.222336 AGAGAGAGAGAGAGAGAGAGGAG 58.778 52.174 0.00 0.00 0.00 3.69
987 1344 3.312890 AGAGAGAGAGAGAGAGAGGAGG 58.687 54.545 0.00 0.00 0.00 4.30
988 1345 3.051803 AGAGAGAGAGAGAGAGAGGAGGA 60.052 52.174 0.00 0.00 0.00 3.71
989 1346 3.711704 GAGAGAGAGAGAGAGAGGAGGAA 59.288 52.174 0.00 0.00 0.00 3.36
990 1347 3.713764 AGAGAGAGAGAGAGAGGAGGAAG 59.286 52.174 0.00 0.00 0.00 3.46
1020 1387 3.092511 GGGAGGGATCAGCAGGCA 61.093 66.667 0.00 0.00 0.00 4.75
1024 1391 2.124403 GGGATCAGCAGGCAGGTG 60.124 66.667 2.33 2.33 46.98 4.00
1026 1393 1.626356 GGGATCAGCAGGCAGGTGTA 61.626 60.000 8.95 0.00 45.77 2.90
1251 1618 1.092345 GCGCCTCCACCATTCTTCTC 61.092 60.000 0.00 0.00 0.00 2.87
1252 1619 0.807667 CGCCTCCACCATTCTTCTCG 60.808 60.000 0.00 0.00 0.00 4.04
1253 1620 0.537188 GCCTCCACCATTCTTCTCGA 59.463 55.000 0.00 0.00 0.00 4.04
1293 1696 2.322830 GGCGGTGGACGGTTTTCTC 61.323 63.158 0.00 0.00 44.51 2.87
1496 1911 2.894257 ATCACCTTCGTGCTGGCCA 61.894 57.895 4.71 4.71 40.04 5.36
1687 2102 2.196595 CCCATCTTCAACTGGACCCTA 58.803 52.381 0.00 0.00 34.24 3.53
1726 2141 2.664081 CCACTGCCTCTCCTGGTCC 61.664 68.421 0.00 0.00 0.00 4.46
2151 2660 2.670148 GCCAAGACCCGGAGATGGT 61.670 63.158 0.73 0.00 39.32 3.55
2157 2666 4.227134 CCCGGAGATGGTGAGGCG 62.227 72.222 0.73 0.00 0.00 5.52
2210 2719 0.689055 AGATCAGCAAGTGAGCACCA 59.311 50.000 0.00 0.00 44.63 4.17
2451 2981 4.889995 ACTATGCTCCCTAATTTTGAAGCC 59.110 41.667 0.00 0.00 0.00 4.35
2509 3046 3.260380 TGGTTTATGATTTTGGCTGGGTG 59.740 43.478 0.00 0.00 0.00 4.61
2893 3431 2.813754 GCTTACCACATGTGTCATGTGT 59.186 45.455 28.73 21.89 45.74 3.72
2915 3453 2.698274 TGTCTCACTGTTGGCACTTAGA 59.302 45.455 0.00 0.00 0.00 2.10
2922 3460 3.070018 CTGTTGGCACTTAGACTTCCTG 58.930 50.000 0.00 0.00 0.00 3.86
2944 3489 5.379187 TGTGAAGTATCCATTGGATGATGG 58.621 41.667 25.47 4.09 43.06 3.51
2994 3539 1.991230 GCCTGGGCCTTTGACTAGA 59.009 57.895 4.53 0.00 34.56 2.43
3006 3551 6.651225 GGCCTTTGACTAGAACATATGTATCC 59.349 42.308 9.21 1.88 0.00 2.59
3016 3561 3.517612 ACATATGTATCCGGGCCTACTT 58.482 45.455 6.56 2.80 0.00 2.24
3046 3591 6.602803 GGTATTCCCCCGTAAAGTTTTAATCA 59.397 38.462 0.00 0.00 0.00 2.57
3049 3594 5.817784 TCCCCCGTAAAGTTTTAATCATGA 58.182 37.500 0.00 0.00 0.00 3.07
3052 3597 6.096282 CCCCCGTAAAGTTTTAATCATGACAT 59.904 38.462 0.00 0.00 0.00 3.06
3078 3623 1.128692 GTGAATGCGGAAGAAAGACGG 59.871 52.381 0.00 0.00 0.00 4.79
3079 3624 0.097150 GAATGCGGAAGAAAGACGGC 59.903 55.000 0.00 0.00 0.00 5.68
3080 3625 0.605319 AATGCGGAAGAAAGACGGCA 60.605 50.000 0.00 0.00 43.84 5.69
3112 3657 2.185004 AGGACTTGCGTGTTATTGCT 57.815 45.000 0.00 0.00 0.00 3.91
3162 7571 2.148916 TCTAATATGTGGCTTCGGCG 57.851 50.000 0.00 0.00 42.91 6.46
3182 7591 2.351350 CGTTTCCGAAAAAGGGATGTGG 60.351 50.000 0.00 0.00 35.63 4.17
3184 7593 0.039035 TCCGAAAAAGGGATGTGGGG 59.961 55.000 0.00 0.00 0.00 4.96
3185 7594 1.604147 CCGAAAAAGGGATGTGGGGC 61.604 60.000 0.00 0.00 0.00 5.80
3190 7599 0.846427 AAAGGGATGTGGGGCTGAGA 60.846 55.000 0.00 0.00 0.00 3.27
3191 7600 0.846427 AAGGGATGTGGGGCTGAGAA 60.846 55.000 0.00 0.00 0.00 2.87
3224 7633 3.012518 GAGGACCCTGTTTGATCATGTG 58.987 50.000 0.00 0.00 0.00 3.21
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 7.145985 TCCAATTAAGTCGCAGTCATATCTAC 58.854 38.462 0.00 0.00 0.00 2.59
1 2 7.284919 TCCAATTAAGTCGCAGTCATATCTA 57.715 36.000 0.00 0.00 0.00 1.98
2 3 6.161855 TCCAATTAAGTCGCAGTCATATCT 57.838 37.500 0.00 0.00 0.00 1.98
3 4 6.844696 TTCCAATTAAGTCGCAGTCATATC 57.155 37.500 0.00 0.00 0.00 1.63
4 5 6.767902 ACATTCCAATTAAGTCGCAGTCATAT 59.232 34.615 0.00 0.00 0.00 1.78
5 6 6.112734 ACATTCCAATTAAGTCGCAGTCATA 58.887 36.000 0.00 0.00 0.00 2.15
12 13 7.123830 GTGTACATACATTCCAATTAAGTCGC 58.876 38.462 0.00 0.00 38.63 5.19
13 14 8.192068 TGTGTACATACATTCCAATTAAGTCG 57.808 34.615 0.00 0.00 38.63 4.18
18 19 9.844257 TCATGATGTGTACATACATTCCAATTA 57.156 29.630 0.00 0.00 41.15 1.40
61 73 9.682465 ATCCACACAGACGTATATAGTACATAT 57.318 33.333 0.00 0.00 0.00 1.78
62 74 9.511272 AATCCACACAGACGTATATAGTACATA 57.489 33.333 0.00 0.00 0.00 2.29
63 75 7.997773 ATCCACACAGACGTATATAGTACAT 57.002 36.000 0.00 0.00 0.00 2.29
64 76 7.718314 AGAATCCACACAGACGTATATAGTACA 59.282 37.037 0.00 0.00 0.00 2.90
65 77 8.016229 CAGAATCCACACAGACGTATATAGTAC 58.984 40.741 0.00 0.00 0.00 2.73
66 78 7.935210 TCAGAATCCACACAGACGTATATAGTA 59.065 37.037 0.00 0.00 0.00 1.82
67 79 6.771267 TCAGAATCCACACAGACGTATATAGT 59.229 38.462 0.00 0.00 0.00 2.12
68 80 7.203255 TCAGAATCCACACAGACGTATATAG 57.797 40.000 0.00 0.00 0.00 1.31
69 81 7.761038 ATCAGAATCCACACAGACGTATATA 57.239 36.000 0.00 0.00 0.00 0.86
70 82 6.656632 ATCAGAATCCACACAGACGTATAT 57.343 37.500 0.00 0.00 0.00 0.86
124 136 3.673902 TGCATTCGAATTCTGAACCAGA 58.326 40.909 8.21 0.00 38.87 3.86
125 137 3.686241 TCTGCATTCGAATTCTGAACCAG 59.314 43.478 8.21 20.80 33.10 4.00
126 138 3.436704 GTCTGCATTCGAATTCTGAACCA 59.563 43.478 16.39 11.80 0.00 3.67
127 139 3.686726 AGTCTGCATTCGAATTCTGAACC 59.313 43.478 16.39 7.70 0.00 3.62
128 140 4.436584 CCAGTCTGCATTCGAATTCTGAAC 60.437 45.833 16.39 11.68 0.00 3.18
129 141 3.686241 CCAGTCTGCATTCGAATTCTGAA 59.314 43.478 16.39 12.77 0.00 3.02
130 142 3.055891 TCCAGTCTGCATTCGAATTCTGA 60.056 43.478 8.21 10.52 0.00 3.27
131 143 3.264947 TCCAGTCTGCATTCGAATTCTG 58.735 45.455 8.21 8.13 0.00 3.02
132 144 3.616956 TCCAGTCTGCATTCGAATTCT 57.383 42.857 8.21 0.00 0.00 2.40
133 145 3.060003 CGATCCAGTCTGCATTCGAATTC 60.060 47.826 8.21 4.05 0.00 2.17
134 146 2.868583 CGATCCAGTCTGCATTCGAATT 59.131 45.455 8.21 0.00 0.00 2.17
135 147 2.101415 TCGATCCAGTCTGCATTCGAAT 59.899 45.455 4.39 4.39 33.21 3.34
136 148 1.476488 TCGATCCAGTCTGCATTCGAA 59.524 47.619 14.02 0.00 33.21 3.71
137 149 1.102978 TCGATCCAGTCTGCATTCGA 58.897 50.000 12.95 12.95 33.67 3.71
138 150 1.203928 GTCGATCCAGTCTGCATTCG 58.796 55.000 9.67 9.67 0.00 3.34
139 151 1.134699 TGGTCGATCCAGTCTGCATTC 60.135 52.381 0.00 0.00 41.93 2.67
140 152 0.904649 TGGTCGATCCAGTCTGCATT 59.095 50.000 0.00 0.00 41.93 3.56
141 153 2.595558 TGGTCGATCCAGTCTGCAT 58.404 52.632 0.00 0.00 41.93 3.96
142 154 4.111967 TGGTCGATCCAGTCTGCA 57.888 55.556 0.00 0.00 41.93 4.41
155 167 2.604046 ATGGCTCGAACATACTGGTC 57.396 50.000 0.75 0.00 0.00 4.02
158 170 5.682862 GCAAATTTATGGCTCGAACATACTG 59.317 40.000 8.52 6.20 31.02 2.74
161 173 5.449862 GGTGCAAATTTATGGCTCGAACATA 60.450 40.000 5.61 5.61 0.00 2.29
169 181 2.818921 TCAGGGTGCAAATTTATGGCT 58.181 42.857 0.00 0.00 0.00 4.75
179 191 0.403655 TGTAGGCATTCAGGGTGCAA 59.596 50.000 0.00 0.00 44.25 4.08
189 201 1.635487 ACACCTGTCCATGTAGGCATT 59.365 47.619 7.58 0.00 37.61 3.56
190 202 1.289160 ACACCTGTCCATGTAGGCAT 58.711 50.000 7.58 0.00 37.61 4.40
299 311 4.968719 TGCCTTCTATTCCTTGACCAGATA 59.031 41.667 0.00 0.00 0.00 1.98
303 315 4.380843 TTTGCCTTCTATTCCTTGACCA 57.619 40.909 0.00 0.00 0.00 4.02
316 328 7.173907 AGACATGCACATATACTATTTGCCTTC 59.826 37.037 0.00 0.00 31.94 3.46
354 366 1.915489 TGGTGCCATGTTCTATCACCT 59.085 47.619 10.53 0.00 45.43 4.00
381 398 4.278170 CAGCACAACAGAAATGTTAAGGGA 59.722 41.667 0.00 0.00 0.00 4.20
386 403 3.550639 GCAGCAGCACAACAGAAATGTTA 60.551 43.478 0.00 0.00 41.58 2.41
397 414 2.112507 AGAGCAGCAGCAGCACAA 59.887 55.556 12.92 0.00 45.49 3.33
398 415 2.668550 CAGAGCAGCAGCAGCACA 60.669 61.111 12.92 0.00 45.49 4.57
399 416 4.104417 GCAGAGCAGCAGCAGCAC 62.104 66.667 12.92 5.78 45.49 4.40
400 417 4.331067 AGCAGAGCAGCAGCAGCA 62.331 61.111 12.92 0.00 45.49 4.41
401 418 3.805307 CAGCAGAGCAGCAGCAGC 61.805 66.667 3.17 0.46 45.49 5.25
402 419 2.047179 TCAGCAGAGCAGCAGCAG 60.047 61.111 3.17 0.00 45.49 4.24
403 420 2.047179 CTCAGCAGAGCAGCAGCA 60.047 61.111 3.17 0.00 45.49 4.41
404 421 0.745128 ATTCTCAGCAGAGCAGCAGC 60.745 55.000 0.32 0.00 41.81 5.25
405 422 1.292061 GATTCTCAGCAGAGCAGCAG 58.708 55.000 0.32 0.00 41.81 4.24
406 423 0.611714 TGATTCTCAGCAGAGCAGCA 59.388 50.000 0.32 0.00 41.81 4.41
407 424 1.735386 TTGATTCTCAGCAGAGCAGC 58.265 50.000 0.32 0.00 41.81 5.25
408 425 4.966965 AATTTGATTCTCAGCAGAGCAG 57.033 40.909 0.32 0.00 41.81 4.24
409 426 5.356190 CCTTAATTTGATTCTCAGCAGAGCA 59.644 40.000 0.32 0.00 41.81 4.26
410 427 5.732810 GCCTTAATTTGATTCTCAGCAGAGC 60.733 44.000 0.32 0.00 41.81 4.09
411 428 5.503683 CGCCTTAATTTGATTCTCAGCAGAG 60.504 44.000 0.00 0.00 43.48 3.35
412 429 4.333649 CGCCTTAATTTGATTCTCAGCAGA 59.666 41.667 0.00 0.00 0.00 4.26
456 473 3.140141 GCCGCCTGCCTAATTGCA 61.140 61.111 0.00 0.00 39.37 4.08
489 510 1.805869 GAGTGATCAACAGCACAGCT 58.194 50.000 0.00 0.00 41.74 4.24
490 511 0.441533 CGAGTGATCAACAGCACAGC 59.558 55.000 0.00 0.00 41.74 4.40
491 512 0.441533 GCGAGTGATCAACAGCACAG 59.558 55.000 0.00 0.00 41.74 3.66
494 515 1.293963 GCAGCGAGTGATCAACAGCA 61.294 55.000 16.47 0.00 37.22 4.41
496 517 0.720027 CAGCAGCGAGTGATCAACAG 59.280 55.000 0.00 0.00 0.00 3.16
516 537 2.508439 ACGTGCACGCCGGATTAG 60.508 61.111 37.35 10.10 44.43 1.73
538 559 4.868450 TCGCTTTAACCCATTCATTACG 57.132 40.909 0.00 0.00 0.00 3.18
582 603 2.480073 GCCTCACATAATTGCGTTGCAT 60.480 45.455 0.00 0.00 38.76 3.96
583 604 1.135431 GCCTCACATAATTGCGTTGCA 60.135 47.619 0.00 0.00 36.47 4.08
584 605 1.135431 TGCCTCACATAATTGCGTTGC 60.135 47.619 0.00 0.00 0.00 4.17
585 606 2.917701 TGCCTCACATAATTGCGTTG 57.082 45.000 0.00 0.00 0.00 4.10
586 607 3.016031 TGATGCCTCACATAATTGCGTT 58.984 40.909 0.00 0.00 39.84 4.84
625 646 1.289066 CAGCAACAGCAGCAGCAAT 59.711 52.632 3.17 0.00 45.49 3.56
626 647 2.725641 CAGCAACAGCAGCAGCAA 59.274 55.556 3.17 0.00 45.49 3.91
627 648 3.973516 GCAGCAACAGCAGCAGCA 61.974 61.111 3.17 0.00 43.05 4.41
628 649 3.671411 AGCAGCAACAGCAGCAGC 61.671 61.111 7.56 0.00 42.49 5.25
629 650 2.255554 CAGCAGCAACAGCAGCAG 59.744 61.111 7.56 0.00 42.49 4.24
630 651 3.973516 GCAGCAGCAACAGCAGCA 61.974 61.111 7.56 0.00 42.49 4.41
631 652 3.612371 GAGCAGCAGCAACAGCAGC 62.612 63.158 3.17 0.00 45.49 5.25
632 653 2.188849 CTGAGCAGCAGCAACAGCAG 62.189 60.000 13.16 4.98 45.49 4.24
633 654 2.203238 TGAGCAGCAGCAACAGCA 60.203 55.556 3.17 0.00 45.49 4.41
634 655 2.561885 CTGAGCAGCAGCAACAGC 59.438 61.111 13.16 0.00 45.49 4.40
635 656 2.333417 CCCTGAGCAGCAGCAACAG 61.333 63.158 16.81 16.81 45.49 3.16
636 657 2.281970 CCCTGAGCAGCAGCAACA 60.282 61.111 3.17 2.35 45.49 3.33
637 658 2.033141 TCCCTGAGCAGCAGCAAC 59.967 61.111 3.17 0.00 45.49 4.17
638 659 2.181445 CTCTCCCTGAGCAGCAGCAA 62.181 60.000 3.17 0.00 45.49 3.91
639 660 2.605601 TCTCCCTGAGCAGCAGCA 60.606 61.111 3.17 0.00 45.49 4.41
640 661 2.187424 CTCTCCCTGAGCAGCAGC 59.813 66.667 0.00 0.00 43.50 5.25
641 662 0.683828 TCTCTCTCCCTGAGCAGCAG 60.684 60.000 0.00 0.00 42.38 4.24
642 663 0.683828 CTCTCTCTCCCTGAGCAGCA 60.684 60.000 0.00 0.00 42.38 4.41
643 664 0.395586 TCTCTCTCTCCCTGAGCAGC 60.396 60.000 0.00 0.00 42.38 5.25
644 665 1.683943 CTCTCTCTCTCCCTGAGCAG 58.316 60.000 0.00 0.00 42.38 4.24
645 666 0.395586 GCTCTCTCTCTCCCTGAGCA 60.396 60.000 8.19 0.00 46.41 4.26
646 667 2.419057 GCTCTCTCTCTCCCTGAGC 58.581 63.158 0.00 0.00 42.38 4.26
647 668 2.369983 ATGCTCTCTCTCTCCCTGAG 57.630 55.000 0.00 0.00 43.96 3.35
648 669 2.024560 TGAATGCTCTCTCTCTCCCTGA 60.025 50.000 0.00 0.00 0.00 3.86
649 670 2.386779 TGAATGCTCTCTCTCTCCCTG 58.613 52.381 0.00 0.00 0.00 4.45
652 999 6.757237 TGAAATATGAATGCTCTCTCTCTCC 58.243 40.000 0.00 0.00 0.00 3.71
667 1014 8.117813 AGTGCATGCATGATTATGAAATATGA 57.882 30.769 30.64 0.00 36.36 2.15
668 1015 8.647226 CAAGTGCATGCATGATTATGAAATATG 58.353 33.333 30.64 8.58 36.36 1.78
669 1016 7.330946 GCAAGTGCATGCATGATTATGAAATAT 59.669 33.333 30.64 0.14 45.70 1.28
670 1017 6.643360 GCAAGTGCATGCATGATTATGAAATA 59.357 34.615 30.64 0.00 45.70 1.40
671 1018 5.465390 GCAAGTGCATGCATGATTATGAAAT 59.535 36.000 30.64 0.00 45.70 2.17
672 1019 4.806775 GCAAGTGCATGCATGATTATGAAA 59.193 37.500 30.64 1.64 45.70 2.69
673 1020 4.364860 GCAAGTGCATGCATGATTATGAA 58.635 39.130 30.64 0.00 45.70 2.57
705 1052 1.753073 GGTAACTCCACCGCTAGCTAA 59.247 52.381 13.93 0.00 35.97 3.09
717 1064 0.618458 TGCATGGTCCTGGTAACTCC 59.382 55.000 0.00 0.00 37.61 3.85
737 1084 0.035317 GGACACAGGACAGACATGCA 59.965 55.000 0.00 0.00 33.22 3.96
738 1085 1.016130 CGGACACAGGACAGACATGC 61.016 60.000 0.00 0.00 33.22 4.06
739 1086 0.318441 ACGGACACAGGACAGACATG 59.682 55.000 0.00 0.00 36.29 3.21
740 1087 0.603569 GACGGACACAGGACAGACAT 59.396 55.000 0.00 0.00 0.00 3.06
767 1114 1.148273 TGTGGTTGTCCTGTCCTGC 59.852 57.895 0.00 0.00 34.23 4.85
805 1152 3.760035 CACTAGCGCACCCTCCGT 61.760 66.667 11.47 0.00 0.00 4.69
812 1165 3.049674 TTGCTGCCACTAGCGCAC 61.050 61.111 11.47 0.94 45.88 5.34
838 1191 9.186837 GTATATATAGTGTACTGCCATAGTGGT 57.813 37.037 0.00 0.00 40.46 4.16
848 1201 6.127423 GGTGCAGGGGTATATATAGTGTACTG 60.127 46.154 0.00 0.24 0.00 2.74
849 1202 5.956563 GGTGCAGGGGTATATATAGTGTACT 59.043 44.000 0.00 0.00 0.00 2.73
850 1203 5.128335 GGGTGCAGGGGTATATATAGTGTAC 59.872 48.000 0.00 0.00 0.00 2.90
851 1204 5.016998 AGGGTGCAGGGGTATATATAGTGTA 59.983 44.000 0.00 0.00 0.00 2.90
852 1205 4.101856 GGGTGCAGGGGTATATATAGTGT 58.898 47.826 0.00 0.00 0.00 3.55
889 1242 1.068954 GCTAACTGCTTGTGGTTCTGC 60.069 52.381 0.00 0.00 38.95 4.26
892 1245 1.266989 GGTGCTAACTGCTTGTGGTTC 59.733 52.381 0.00 0.00 43.37 3.62
909 1262 0.523072 CAGAGAAACAATGCGGGGTG 59.477 55.000 0.00 0.00 0.00 4.61
911 1264 2.009774 CTACAGAGAAACAATGCGGGG 58.990 52.381 0.00 0.00 0.00 5.73
912 1265 2.972625 TCTACAGAGAAACAATGCGGG 58.027 47.619 0.00 0.00 0.00 6.13
914 1267 4.867047 AGTGATCTACAGAGAAACAATGCG 59.133 41.667 0.00 0.00 34.61 4.73
920 1273 6.926313 ACCTGTTAGTGATCTACAGAGAAAC 58.074 40.000 14.95 0.00 34.61 2.78
938 1295 5.013704 TCTCTCTCTCTCTCTACAACCTGTT 59.986 44.000 0.00 0.00 0.00 3.16
942 1299 5.128827 TCTCTCTCTCTCTCTCTCTACAACC 59.871 48.000 0.00 0.00 0.00 3.77
951 1308 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
952 1309 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
953 1310 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
954 1311 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
955 1312 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
956 1313 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
957 1314 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
958 1315 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
959 1316 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
960 1317 5.136068 TCTCTCTCTCTCTCTCTCTCTCT 57.864 47.826 0.00 0.00 0.00 3.10
961 1318 4.280677 CCTCTCTCTCTCTCTCTCTCTCTC 59.719 54.167 0.00 0.00 0.00 3.20
962 1319 4.078922 TCCTCTCTCTCTCTCTCTCTCTCT 60.079 50.000 0.00 0.00 0.00 3.10
963 1320 4.219115 TCCTCTCTCTCTCTCTCTCTCTC 58.781 52.174 0.00 0.00 0.00 3.20
964 1321 4.222336 CTCCTCTCTCTCTCTCTCTCTCT 58.778 52.174 0.00 0.00 0.00 3.10
965 1322 3.323403 CCTCCTCTCTCTCTCTCTCTCTC 59.677 56.522 0.00 0.00 0.00 3.20
966 1323 3.051803 TCCTCCTCTCTCTCTCTCTCTCT 60.052 52.174 0.00 0.00 0.00 3.10
967 1324 3.309296 TCCTCCTCTCTCTCTCTCTCTC 58.691 54.545 0.00 0.00 0.00 3.20
968 1325 3.421394 TCCTCCTCTCTCTCTCTCTCT 57.579 52.381 0.00 0.00 0.00 3.10
969 1326 3.181450 CCTTCCTCCTCTCTCTCTCTCTC 60.181 56.522 0.00 0.00 0.00 3.20
970 1327 2.780010 CCTTCCTCCTCTCTCTCTCTCT 59.220 54.545 0.00 0.00 0.00 3.10
971 1328 2.777692 TCCTTCCTCCTCTCTCTCTCTC 59.222 54.545 0.00 0.00 0.00 3.20
972 1329 2.780010 CTCCTTCCTCCTCTCTCTCTCT 59.220 54.545 0.00 0.00 0.00 3.10
973 1330 2.158608 CCTCCTTCCTCCTCTCTCTCTC 60.159 59.091 0.00 0.00 0.00 3.20
974 1331 1.852965 CCTCCTTCCTCCTCTCTCTCT 59.147 57.143 0.00 0.00 0.00 3.10
975 1332 1.133482 CCCTCCTTCCTCCTCTCTCTC 60.133 61.905 0.00 0.00 0.00 3.20
976 1333 0.933700 CCCTCCTTCCTCCTCTCTCT 59.066 60.000 0.00 0.00 0.00 3.10
977 1334 0.930726 TCCCTCCTTCCTCCTCTCTC 59.069 60.000 0.00 0.00 0.00 3.20
978 1335 0.933700 CTCCCTCCTTCCTCCTCTCT 59.066 60.000 0.00 0.00 0.00 3.10
979 1336 0.930726 TCTCCCTCCTTCCTCCTCTC 59.069 60.000 0.00 0.00 0.00 3.20
980 1337 0.933700 CTCTCCCTCCTTCCTCCTCT 59.066 60.000 0.00 0.00 0.00 3.69
981 1338 0.930726 TCTCTCCCTCCTTCCTCCTC 59.069 60.000 0.00 0.00 0.00 3.71
982 1339 1.220236 CATCTCTCCCTCCTTCCTCCT 59.780 57.143 0.00 0.00 0.00 3.69
983 1340 1.715785 CATCTCTCCCTCCTTCCTCC 58.284 60.000 0.00 0.00 0.00 4.30
984 1341 1.715785 CCATCTCTCCCTCCTTCCTC 58.284 60.000 0.00 0.00 0.00 3.71
985 1342 0.267356 CCCATCTCTCCCTCCTTCCT 59.733 60.000 0.00 0.00 0.00 3.36
986 1343 0.766288 CCCCATCTCTCCCTCCTTCC 60.766 65.000 0.00 0.00 0.00 3.46
987 1344 0.266152 TCCCCATCTCTCCCTCCTTC 59.734 60.000 0.00 0.00 0.00 3.46
988 1345 0.267356 CTCCCCATCTCTCCCTCCTT 59.733 60.000 0.00 0.00 0.00 3.36
989 1346 1.673928 CCTCCCCATCTCTCCCTCCT 61.674 65.000 0.00 0.00 0.00 3.69
990 1347 1.152139 CCTCCCCATCTCTCCCTCC 60.152 68.421 0.00 0.00 0.00 4.30
1020 1387 4.394712 GCGCCTGCACCTACACCT 62.395 66.667 0.00 0.00 42.15 4.00
1251 1618 1.932511 GCTGGAAGAAGAAGCAGATCG 59.067 52.381 0.00 0.00 36.91 3.69
1252 1619 2.983229 TGCTGGAAGAAGAAGCAGATC 58.017 47.619 0.00 0.00 41.83 2.75
1253 1620 3.430042 TTGCTGGAAGAAGAAGCAGAT 57.570 42.857 0.00 0.00 46.82 2.90
1293 1696 4.654091 AAGAACAAACACACCAGGATTG 57.346 40.909 0.00 0.00 0.00 2.67
1726 2141 4.100084 TGGAGCACCATCCAGCCG 62.100 66.667 0.00 0.00 44.56 5.52
1852 2267 4.641645 TGCACCTTCCACCGGCTG 62.642 66.667 0.00 0.00 0.00 4.85
1885 2300 2.959275 CGCGTAGAGGATGGTGAAC 58.041 57.895 0.00 0.00 0.00 3.18
2024 2439 2.105128 CTGGTCGCCGAGGATGAC 59.895 66.667 0.00 6.45 0.00 3.06
2157 2666 4.821589 CGTCTTCCCCGAGCAGGC 62.822 72.222 0.00 0.00 39.21 4.85
2210 2719 1.598130 GCTTTCACGCCAGGACAGT 60.598 57.895 0.00 0.00 0.00 3.55
2215 2724 2.670934 AGCAGCTTTCACGCCAGG 60.671 61.111 0.00 0.00 0.00 4.45
2501 3038 1.243902 TCAAAATCGTTCACCCAGCC 58.756 50.000 0.00 0.00 0.00 4.85
2860 3398 6.531240 CACATGTGGTAAGCAATCCAAATAAC 59.469 38.462 18.51 0.00 35.38 1.89
2863 3401 4.527816 ACACATGTGGTAAGCAATCCAAAT 59.472 37.500 28.64 0.00 35.38 2.32
2893 3431 2.418368 AAGTGCCAACAGTGAGACAA 57.582 45.000 0.00 0.00 0.00 3.18
2994 3539 3.517612 AGTAGGCCCGGATACATATGTT 58.482 45.455 14.77 1.88 0.00 2.71
3016 3561 2.746279 TTACGGGGGAATACCTACGA 57.254 50.000 6.18 0.00 40.39 3.43
3046 3591 2.945008 CCGCATTCACCTAACATGTCAT 59.055 45.455 0.00 0.00 0.00 3.06
3049 3594 2.779755 TCCGCATTCACCTAACATGT 57.220 45.000 0.00 0.00 0.00 3.21
3052 3597 3.410631 TTCTTCCGCATTCACCTAACA 57.589 42.857 0.00 0.00 0.00 2.41
3056 3601 2.427506 GTCTTTCTTCCGCATTCACCT 58.572 47.619 0.00 0.00 0.00 4.00
3128 3673 9.573166 CCACATATTAGATGAAACCAATCCTTA 57.427 33.333 0.00 0.00 0.00 2.69
3162 7571 2.029380 CCCACATCCCTTTTTCGGAAAC 60.029 50.000 1.96 0.00 31.75 2.78
3174 7583 0.259938 AATTCTCAGCCCCACATCCC 59.740 55.000 0.00 0.00 0.00 3.85
3182 7591 5.200368 TCAAAAGTCAAAATTCTCAGCCC 57.800 39.130 0.00 0.00 0.00 5.19
3184 7593 5.917447 GTCCTCAAAAGTCAAAATTCTCAGC 59.083 40.000 0.00 0.00 0.00 4.26
3185 7594 6.442112 GGTCCTCAAAAGTCAAAATTCTCAG 58.558 40.000 0.00 0.00 0.00 3.35
3190 7599 4.962362 ACAGGGTCCTCAAAAGTCAAAATT 59.038 37.500 0.00 0.00 0.00 1.82
3191 7600 4.546674 ACAGGGTCCTCAAAAGTCAAAAT 58.453 39.130 0.00 0.00 0.00 1.82


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

AutoCloner maintained by Alex Coulton.