Multiple sequence alignment - TraesCS7B01G176500

Loading Multiple Alignment...

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 TraesCS7B01G176500 chr7B 100.000 4976 0 0 1 4976 248550334 248545359 0.000000e+00 9190.0
1 TraesCS7B01G176500 chr7D 93.501 3493 99 45 1554 4976 268554538 268551104 0.000000e+00 5075.0
2 TraesCS7B01G176500 chr7D 90.330 910 50 14 580 1465 268555432 268554537 0.000000e+00 1158.0
3 TraesCS7B01G176500 chr7D 90.152 396 24 4 168 563 268555935 268555555 7.440000e-138 501.0
4 TraesCS7B01G176500 chr7D 95.455 44 2 0 564 607 268555475 268555432 2.490000e-08 71.3
5 TraesCS7B01G176500 chr7A 94.038 3321 96 34 1709 4976 294412970 294409699 0.000000e+00 4942.0
6 TraesCS7B01G176500 chr7A 87.374 895 61 29 590 1465 294414018 294413157 0.000000e+00 979.0
7 TraesCS7B01G176500 chr3B 100.000 90 0 0 1470 1559 689693536 689693625 3.080000e-37 167.0
8 TraesCS7B01G176500 chr3B 100.000 86 0 0 1470 1555 435816891 435816976 5.160000e-35 159.0
9 TraesCS7B01G176500 chr2B 100.000 86 0 0 1471 1556 601079227 601079312 5.160000e-35 159.0
10 TraesCS7B01G176500 chrUn 96.739 92 3 0 1464 1555 287061834 287061743 2.400000e-33 154.0
11 TraesCS7B01G176500 chr3D 96.739 92 3 0 1464 1555 570116480 570116389 2.400000e-33 154.0
12 TraesCS7B01G176500 chr5A 95.604 91 3 1 1470 1559 450750793 450750703 1.440000e-30 145.0
13 TraesCS7B01G176500 chr2D 94.681 94 4 1 1470 1563 128890638 128890730 1.440000e-30 145.0
14 TraesCS7B01G176500 chr6D 92.929 99 5 2 1465 1563 41237296 41237200 5.190000e-30 143.0
15 TraesCS7B01G176500 chr6A 92.929 99 5 2 1465 1563 51882717 51882621 5.190000e-30 143.0
16 TraesCS7B01G176500 chr4A 82.955 88 10 5 1425 1511 546062156 546062239 1.920000e-09 75.0


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 TraesCS7B01G176500 chr7B 248545359 248550334 4975 True 9190.000 9190 100.0000 1 4976 1 chr7B.!!$R1 4975
1 TraesCS7B01G176500 chr7D 268551104 268555935 4831 True 1701.325 5075 92.3595 168 4976 4 chr7D.!!$R1 4808
2 TraesCS7B01G176500 chr7A 294409699 294414018 4319 True 2960.500 4942 90.7060 590 4976 2 chr7A.!!$R1 4386

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
804 922 0.036875 CTCCTGACACCCAACCTTCC 59.963 60.0 0.00 0.0 0.00 3.46 F
1374 1523 0.037605 ATCGTCACCACGGTTTCTCC 60.038 55.0 0.00 0.0 46.70 3.71 F
1896 2096 0.454957 GCATGCGCAACTCAAACGAT 60.455 50.0 17.11 0.0 38.36 3.73 F
2476 2691 0.808453 TCGTATTTGCACTAGCGGGC 60.808 55.0 0.00 0.0 46.23 6.13 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2131 2346 0.594796 CAAAACTCAACAGTGCCCGC 60.595 55.000 0.00 0.00 31.06 6.13 R
2628 2843 1.142667 TGTCATTCAGCTGACCAACCA 59.857 47.619 18.03 7.04 43.99 3.67 R
3616 3836 2.676121 CCGGTGCAAATGCCCTGA 60.676 61.111 2.46 0.00 41.18 3.86 R
4325 4549 0.035739 GGTCAGGTTTAGCCCGACAA 59.964 55.000 3.99 0.00 38.26 3.18 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
39 40 3.799755 GGCAACCGTGGCGTCATC 61.800 66.667 0.00 0.00 40.97 2.92
40 41 4.147322 GCAACCGTGGCGTCATCG 62.147 66.667 0.00 0.00 40.37 3.84
45 46 4.129737 CGTGGCGTCATCGGGACT 62.130 66.667 0.00 0.00 44.68 3.85
46 47 2.202756 GTGGCGTCATCGGGACTC 60.203 66.667 0.00 0.00 44.68 3.36
49 50 2.202756 GCGTCATCGGGACTCCAC 60.203 66.667 0.00 0.00 44.68 4.02
50 51 2.494918 CGTCATCGGGACTCCACC 59.505 66.667 0.00 0.00 44.68 4.61
51 52 2.901042 GTCATCGGGACTCCACCC 59.099 66.667 0.00 0.00 43.46 4.61
52 53 2.365105 TCATCGGGACTCCACCCC 60.365 66.667 0.00 0.00 46.62 4.95
53 54 2.365635 CATCGGGACTCCACCCCT 60.366 66.667 0.00 0.00 46.62 4.79
54 55 2.041819 ATCGGGACTCCACCCCTC 60.042 66.667 0.00 0.00 46.62 4.30
55 56 2.637640 ATCGGGACTCCACCCCTCT 61.638 63.158 0.00 0.00 46.62 3.69
56 57 2.591193 ATCGGGACTCCACCCCTCTC 62.591 65.000 0.00 0.00 46.62 3.20
57 58 2.365768 GGGACTCCACCCCTCTCC 60.366 72.222 0.00 0.00 43.81 3.71
58 59 2.365768 GGACTCCACCCCTCTCCC 60.366 72.222 0.00 0.00 0.00 4.30
59 60 2.450243 GACTCCACCCCTCTCCCA 59.550 66.667 0.00 0.00 0.00 4.37
60 61 1.990614 GACTCCACCCCTCTCCCAC 60.991 68.421 0.00 0.00 0.00 4.61
61 62 3.077556 CTCCACCCCTCTCCCACG 61.078 72.222 0.00 0.00 0.00 4.94
62 63 3.907027 CTCCACCCCTCTCCCACGT 62.907 68.421 0.00 0.00 0.00 4.49
63 64 3.391382 CCACCCCTCTCCCACGTC 61.391 72.222 0.00 0.00 0.00 4.34
64 65 3.391382 CACCCCTCTCCCACGTCC 61.391 72.222 0.00 0.00 0.00 4.79
65 66 3.602030 ACCCCTCTCCCACGTCCT 61.602 66.667 0.00 0.00 0.00 3.85
66 67 2.760385 CCCCTCTCCCACGTCCTC 60.760 72.222 0.00 0.00 0.00 3.71
67 68 2.760385 CCCTCTCCCACGTCCTCC 60.760 72.222 0.00 0.00 0.00 4.30
68 69 2.760385 CCTCTCCCACGTCCTCCC 60.760 72.222 0.00 0.00 0.00 4.30
69 70 2.760385 CTCTCCCACGTCCTCCCC 60.760 72.222 0.00 0.00 0.00 4.81
70 71 3.273654 TCTCCCACGTCCTCCCCT 61.274 66.667 0.00 0.00 0.00 4.79
71 72 2.284699 CTCCCACGTCCTCCCCTT 60.285 66.667 0.00 0.00 0.00 3.95
72 73 2.606519 TCCCACGTCCTCCCCTTG 60.607 66.667 0.00 0.00 0.00 3.61
73 74 2.928396 CCCACGTCCTCCCCTTGT 60.928 66.667 0.00 0.00 0.00 3.16
74 75 2.663196 CCACGTCCTCCCCTTGTC 59.337 66.667 0.00 0.00 0.00 3.18
75 76 2.261671 CACGTCCTCCCCTTGTCG 59.738 66.667 0.00 0.00 0.00 4.35
76 77 3.692406 ACGTCCTCCCCTTGTCGC 61.692 66.667 0.00 0.00 0.00 5.19
77 78 4.452733 CGTCCTCCCCTTGTCGCC 62.453 72.222 0.00 0.00 0.00 5.54
78 79 3.319198 GTCCTCCCCTTGTCGCCA 61.319 66.667 0.00 0.00 0.00 5.69
79 80 3.319198 TCCTCCCCTTGTCGCCAC 61.319 66.667 0.00 0.00 0.00 5.01
80 81 4.410400 CCTCCCCTTGTCGCCACC 62.410 72.222 0.00 0.00 0.00 4.61
81 82 4.760047 CTCCCCTTGTCGCCACCG 62.760 72.222 0.00 0.00 0.00 4.94
83 84 4.760047 CCCCTTGTCGCCACCGAG 62.760 72.222 0.00 0.00 45.38 4.63
84 85 4.760047 CCCTTGTCGCCACCGAGG 62.760 72.222 0.00 0.00 45.38 4.63
112 113 4.038080 GGCAAAGCCCGGTCAACG 62.038 66.667 0.00 0.00 44.06 4.10
113 114 3.284449 GCAAAGCCCGGTCAACGT 61.284 61.111 0.00 0.00 42.24 3.99
114 115 2.943653 CAAAGCCCGGTCAACGTC 59.056 61.111 0.00 0.00 42.24 4.34
115 116 2.663852 AAAGCCCGGTCAACGTCG 60.664 61.111 0.00 0.00 42.24 5.12
116 117 4.675029 AAGCCCGGTCAACGTCGG 62.675 66.667 6.44 6.44 45.29 4.79
119 120 3.980989 CCCGGTCAACGTCGGTGA 61.981 66.667 9.38 9.38 44.32 4.02
120 121 2.732094 CCGGTCAACGTCGGTGAC 60.732 66.667 30.87 30.87 42.24 3.67
132 133 3.197614 GGTGACGGCGAGATCTCA 58.802 61.111 22.31 2.81 0.00 3.27
133 134 1.736586 GGTGACGGCGAGATCTCAT 59.263 57.895 22.31 4.61 0.00 2.90
134 135 0.318275 GGTGACGGCGAGATCTCATC 60.318 60.000 22.31 12.66 0.00 2.92
135 136 0.665835 GTGACGGCGAGATCTCATCT 59.334 55.000 22.31 1.39 43.70 2.90
144 145 2.014010 AGATCTCATCTCCCCTCAGC 57.986 55.000 0.00 0.00 33.42 4.26
145 146 1.504660 AGATCTCATCTCCCCTCAGCT 59.495 52.381 0.00 0.00 33.42 4.24
146 147 1.619827 GATCTCATCTCCCCTCAGCTG 59.380 57.143 7.63 7.63 0.00 4.24
147 148 0.398239 TCTCATCTCCCCTCAGCTGG 60.398 60.000 15.13 4.45 0.00 4.85
148 149 0.690411 CTCATCTCCCCTCAGCTGGT 60.690 60.000 15.13 0.00 0.00 4.00
149 150 0.979709 TCATCTCCCCTCAGCTGGTG 60.980 60.000 15.13 7.27 0.00 4.17
150 151 1.692042 ATCTCCCCTCAGCTGGTGG 60.692 63.158 15.13 15.96 0.00 4.61
151 152 2.186873 ATCTCCCCTCAGCTGGTGGA 62.187 60.000 22.54 19.12 31.57 4.02
152 153 2.284921 TCCCCTCAGCTGGTGGAG 60.285 66.667 22.54 13.20 31.57 3.86
153 154 2.608988 CCCCTCAGCTGGTGGAGT 60.609 66.667 22.54 0.00 31.57 3.85
154 155 2.227036 CCCCTCAGCTGGTGGAGTT 61.227 63.158 22.54 0.00 31.57 3.01
155 156 1.763770 CCCTCAGCTGGTGGAGTTT 59.236 57.895 22.54 0.00 31.57 2.66
156 157 0.607489 CCCTCAGCTGGTGGAGTTTG 60.607 60.000 22.54 6.80 31.57 2.93
157 158 0.607489 CCTCAGCTGGTGGAGTTTGG 60.607 60.000 15.13 0.00 31.57 3.28
158 159 1.228245 TCAGCTGGTGGAGTTTGGC 60.228 57.895 15.13 0.00 0.00 4.52
159 160 2.281761 AGCTGGTGGAGTTTGGCG 60.282 61.111 0.00 0.00 0.00 5.69
160 161 4.043200 GCTGGTGGAGTTTGGCGC 62.043 66.667 0.00 0.00 0.00 6.53
161 162 3.726517 CTGGTGGAGTTTGGCGCG 61.727 66.667 0.00 0.00 0.00 6.86
162 163 4.243008 TGGTGGAGTTTGGCGCGA 62.243 61.111 12.10 0.00 0.00 5.87
163 164 3.423154 GGTGGAGTTTGGCGCGAG 61.423 66.667 12.10 0.00 0.00 5.03
164 165 3.423154 GTGGAGTTTGGCGCGAGG 61.423 66.667 12.10 0.00 0.00 4.63
165 166 3.621805 TGGAGTTTGGCGCGAGGA 61.622 61.111 12.10 0.00 0.00 3.71
166 167 2.358247 GGAGTTTGGCGCGAGGAA 60.358 61.111 12.10 0.00 0.00 3.36
170 171 4.634703 TTTGGCGCGAGGAAGGCA 62.635 61.111 12.10 0.00 41.25 4.75
190 191 2.840753 GGGGCTCCCTTCCACAACA 61.841 63.158 4.74 0.00 41.34 3.33
196 197 4.532834 GGCTCCCTTCCACAACATTTATA 58.467 43.478 0.00 0.00 0.00 0.98
248 249 1.954362 CTCCCTTCTCCTGGAGTGCG 61.954 65.000 22.50 11.97 42.67 5.34
251 252 2.203788 TTCTCCTGGAGTGCGGGT 60.204 61.111 22.50 0.00 0.00 5.28
254 255 2.997315 TCCTGGAGTGCGGGTCAG 60.997 66.667 9.64 0.00 0.00 3.51
255 256 3.314331 CCTGGAGTGCGGGTCAGT 61.314 66.667 0.25 0.00 0.00 3.41
266 267 0.744414 CGGGTCAGTGGAATTGCGAT 60.744 55.000 0.00 0.00 0.00 4.58
284 285 3.555139 GCGATCAATTCTCTCACCTCTTG 59.445 47.826 0.00 0.00 0.00 3.02
298 299 8.362464 TCTCACCTCTTGTTAAATAGCTTAGA 57.638 34.615 0.00 0.00 0.00 2.10
303 304 8.035984 ACCTCTTGTTAAATAGCTTAGACACTC 58.964 37.037 0.00 0.00 0.00 3.51
305 306 8.758633 TCTTGTTAAATAGCTTAGACACTCAC 57.241 34.615 0.00 0.00 0.00 3.51
424 425 8.259194 GTGAGACAAAAACAACATTATTTCACG 58.741 33.333 0.00 0.00 0.00 4.35
443 444 1.589716 GCCAATTGCGACAGAGGCTT 61.590 55.000 0.00 0.00 39.02 4.35
456 457 1.625818 AGAGGCTTTTCTGACCGACAT 59.374 47.619 0.00 0.00 0.00 3.06
478 479 3.191581 TCTCGAGAAGGCACTGAACTAAG 59.808 47.826 14.01 0.00 40.86 2.18
486 487 3.118738 AGGCACTGAACTAAGATTACCCG 60.119 47.826 0.00 0.00 37.18 5.28
487 488 3.195661 GCACTGAACTAAGATTACCCGG 58.804 50.000 0.00 0.00 0.00 5.73
488 489 3.195661 CACTGAACTAAGATTACCCGGC 58.804 50.000 0.00 0.00 0.00 6.13
489 490 2.169978 ACTGAACTAAGATTACCCGGCC 59.830 50.000 0.00 0.00 0.00 6.13
490 491 1.487558 TGAACTAAGATTACCCGGCCC 59.512 52.381 0.00 0.00 0.00 5.80
491 492 1.487558 GAACTAAGATTACCCGGCCCA 59.512 52.381 0.00 0.00 0.00 5.36
492 493 0.835276 ACTAAGATTACCCGGCCCAC 59.165 55.000 0.00 0.00 0.00 4.61
494 495 1.420138 CTAAGATTACCCGGCCCACAT 59.580 52.381 0.00 0.00 0.00 3.21
495 496 0.106719 AAGATTACCCGGCCCACATG 60.107 55.000 0.00 0.00 0.00 3.21
496 497 1.226262 GATTACCCGGCCCACATGT 59.774 57.895 0.00 0.00 0.00 3.21
497 498 0.470766 GATTACCCGGCCCACATGTA 59.529 55.000 0.00 0.00 0.00 2.29
498 499 0.920438 ATTACCCGGCCCACATGTAA 59.080 50.000 0.00 0.00 0.00 2.41
499 500 0.253610 TTACCCGGCCCACATGTAAG 59.746 55.000 0.00 0.00 0.00 2.34
500 501 0.618107 TACCCGGCCCACATGTAAGA 60.618 55.000 0.00 0.00 0.00 2.10
501 502 1.153168 CCCGGCCCACATGTAAGAG 60.153 63.158 0.00 0.00 0.00 2.85
502 503 1.153168 CCGGCCCACATGTAAGAGG 60.153 63.158 0.00 0.00 0.00 3.69
503 504 1.819632 CGGCCCACATGTAAGAGGC 60.820 63.158 16.19 16.19 43.09 4.70
504 505 1.302949 GGCCCACATGTAAGAGGCA 59.697 57.895 22.47 0.00 45.72 4.75
508 509 2.298729 GCCCACATGTAAGAGGCAAAAA 59.701 45.455 18.45 0.00 43.32 1.94
531 532 3.775661 AAAATTACGCACATGTAGCCC 57.224 42.857 0.00 0.00 0.00 5.19
532 533 1.675552 AATTACGCACATGTAGCCCC 58.324 50.000 0.00 0.00 0.00 5.80
533 534 0.531974 ATTACGCACATGTAGCCCCG 60.532 55.000 0.00 0.00 0.00 5.73
534 535 1.890625 TTACGCACATGTAGCCCCGT 61.891 55.000 0.00 5.55 0.00 5.28
535 536 2.566057 TACGCACATGTAGCCCCGTG 62.566 60.000 0.00 0.00 0.00 4.94
536 537 2.824041 GCACATGTAGCCCCGTGG 60.824 66.667 0.00 0.00 0.00 4.94
600 680 4.219070 CCTTTGCTTTCTGGACATGATTCA 59.781 41.667 0.00 0.00 0.00 2.57
646 753 0.397941 TGGAAGCTCCTCCACTTGTG 59.602 55.000 2.82 0.00 40.71 3.33
659 766 0.543749 ACTTGTGCTGCTCTATCCCC 59.456 55.000 0.00 0.00 0.00 4.81
742 849 4.397417 CGCCAAGATCTCATCTTCCTTTTT 59.603 41.667 0.00 0.00 46.17 1.94
744 851 5.448360 GCCAAGATCTCATCTTCCTTTTTCG 60.448 44.000 0.00 0.00 46.17 3.46
748 855 7.751768 AGATCTCATCTTCCTTTTTCGTTTT 57.248 32.000 0.00 0.00 35.76 2.43
774 881 1.676967 CCCCAGCAGCAAGAGGAAC 60.677 63.158 0.00 0.00 0.00 3.62
793 911 1.301716 GAACTTGGCGCTCCTGACA 60.302 57.895 7.64 0.00 0.00 3.58
804 922 0.036875 CTCCTGACACCCAACCTTCC 59.963 60.000 0.00 0.00 0.00 3.46
805 923 1.302511 CCTGACACCCAACCTTCCG 60.303 63.158 0.00 0.00 0.00 4.30
806 924 1.450211 CTGACACCCAACCTTCCGT 59.550 57.895 0.00 0.00 0.00 4.69
807 925 0.884704 CTGACACCCAACCTTCCGTG 60.885 60.000 0.00 0.00 0.00 4.94
826 945 2.882324 TGCGTGTTTGCATCGTCTATA 58.118 42.857 0.00 0.00 40.62 1.31
1011 1139 1.833049 GACGACGATGGGGGAGGAT 60.833 63.158 0.00 0.00 0.00 3.24
1110 1238 4.512484 CCTTCTCCATTGTTTCTCTCTCC 58.488 47.826 0.00 0.00 0.00 3.71
1132 1264 4.323562 CCCTTCGATTCCCTGTTACTTCTT 60.324 45.833 0.00 0.00 0.00 2.52
1154 1292 1.915141 CTTTCCCACCTGTTGCTGAT 58.085 50.000 0.00 0.00 0.00 2.90
1161 1299 6.508030 TCCCACCTGTTGCTGATATTAATA 57.492 37.500 0.00 0.00 0.00 0.98
1186 1324 2.947652 GGAATGGATGGATGAGTGTGTG 59.052 50.000 0.00 0.00 0.00 3.82
1187 1325 3.370846 GGAATGGATGGATGAGTGTGTGA 60.371 47.826 0.00 0.00 0.00 3.58
1189 1327 2.259917 TGGATGGATGAGTGTGTGAGT 58.740 47.619 0.00 0.00 0.00 3.41
1191 1329 3.837731 TGGATGGATGAGTGTGTGAGTTA 59.162 43.478 0.00 0.00 0.00 2.24
1212 1351 6.653740 AGTTAGCTAGGCAGAAATTACGTTTT 59.346 34.615 0.00 0.00 0.00 2.43
1244 1383 4.970662 TCTAACATCACGTACTACCACC 57.029 45.455 0.00 0.00 0.00 4.61
1247 1386 3.587797 ACATCACGTACTACCACCAAG 57.412 47.619 0.00 0.00 0.00 3.61
1275 1419 5.049267 CCGGTTTGCTTTTACTTTACTGCTA 60.049 40.000 0.00 0.00 0.00 3.49
1291 1435 1.999051 CTATGCTCGCACGTGGTTC 59.001 57.895 18.88 0.00 0.00 3.62
1292 1436 1.421410 CTATGCTCGCACGTGGTTCC 61.421 60.000 18.88 0.00 0.00 3.62
1354 1503 4.408821 TGCCGTGCCACCATCTCC 62.409 66.667 0.00 0.00 0.00 3.71
1358 1507 1.884464 CGTGCCACCATCTCCATCG 60.884 63.158 0.00 0.00 0.00 3.84
1374 1523 0.037605 ATCGTCACCACGGTTTCTCC 60.038 55.000 0.00 0.00 46.70 3.71
1415 1564 0.605589 AGTGGAGTCGAGCAGGAAAG 59.394 55.000 0.00 0.00 0.00 2.62
1418 1567 2.029290 GTGGAGTCGAGCAGGAAAGTTA 60.029 50.000 0.00 0.00 0.00 2.24
1465 1614 7.661536 TCTTCTGCAAGTGGAGTAATACTAT 57.338 36.000 0.00 0.00 34.87 2.12
1466 1615 8.762481 TCTTCTGCAAGTGGAGTAATACTATA 57.238 34.615 0.00 0.00 34.87 1.31
1467 1616 8.630917 TCTTCTGCAAGTGGAGTAATACTATAC 58.369 37.037 0.00 0.00 34.87 1.47
1468 1617 8.534954 TTCTGCAAGTGGAGTAATACTATACT 57.465 34.615 0.00 0.00 35.36 2.12
1469 1618 7.941919 TCTGCAAGTGGAGTAATACTATACTG 58.058 38.462 9.01 6.03 33.78 2.74
1470 1619 7.560262 TCTGCAAGTGGAGTAATACTATACTGT 59.440 37.037 9.01 0.00 33.78 3.55
1471 1620 8.756486 TGCAAGTGGAGTAATACTATACTGTA 57.244 34.615 9.01 0.00 36.28 2.74
1472 1621 8.627403 TGCAAGTGGAGTAATACTATACTGTAC 58.373 37.037 9.01 0.00 36.28 2.90
1473 1622 8.848182 GCAAGTGGAGTAATACTATACTGTACT 58.152 37.037 9.01 0.00 36.28 2.73
1480 1629 9.439500 GAGTAATACTATACTGTACTCCCTCTG 57.561 40.741 0.00 0.00 36.28 3.35
1481 1630 8.947305 AGTAATACTATACTGTACTCCCTCTGT 58.053 37.037 0.00 0.00 34.86 3.41
1485 1634 9.796180 ATACTATACTGTACTCCCTCTGTAAAG 57.204 37.037 0.00 0.00 32.89 1.85
1486 1635 7.870027 ACTATACTGTACTCCCTCTGTAAAGA 58.130 38.462 0.00 0.00 31.53 2.52
1487 1636 8.334734 ACTATACTGTACTCCCTCTGTAAAGAA 58.665 37.037 0.00 0.00 31.53 2.52
1488 1637 9.186837 CTATACTGTACTCCCTCTGTAAAGAAA 57.813 37.037 0.00 0.00 31.53 2.52
1489 1638 6.936968 ACTGTACTCCCTCTGTAAAGAAAT 57.063 37.500 0.00 0.00 31.53 2.17
1490 1639 9.710818 ATACTGTACTCCCTCTGTAAAGAAATA 57.289 33.333 0.00 0.00 31.53 1.40
1491 1640 8.611051 ACTGTACTCCCTCTGTAAAGAAATAT 57.389 34.615 0.00 0.00 31.53 1.28
1492 1641 9.710818 ACTGTACTCCCTCTGTAAAGAAATATA 57.289 33.333 0.00 0.00 31.53 0.86
1497 1646 8.425703 ACTCCCTCTGTAAAGAAATATAAGAGC 58.574 37.037 0.00 0.00 0.00 4.09
1498 1647 7.434492 TCCCTCTGTAAAGAAATATAAGAGCG 58.566 38.462 0.00 0.00 0.00 5.03
1499 1648 7.069578 TCCCTCTGTAAAGAAATATAAGAGCGT 59.930 37.037 0.00 0.00 0.00 5.07
1500 1649 7.711339 CCCTCTGTAAAGAAATATAAGAGCGTT 59.289 37.037 0.00 0.00 0.00 4.84
1501 1650 9.099454 CCTCTGTAAAGAAATATAAGAGCGTTT 57.901 33.333 0.00 0.00 0.00 3.60
1502 1651 9.907576 CTCTGTAAAGAAATATAAGAGCGTTTG 57.092 33.333 0.00 0.00 0.00 2.93
1503 1652 8.879759 TCTGTAAAGAAATATAAGAGCGTTTGG 58.120 33.333 0.00 0.00 0.00 3.28
1504 1653 8.780846 TGTAAAGAAATATAAGAGCGTTTGGA 57.219 30.769 0.00 0.00 0.00 3.53
1505 1654 9.391006 TGTAAAGAAATATAAGAGCGTTTGGAT 57.609 29.630 0.00 0.00 0.00 3.41
1506 1655 9.865484 GTAAAGAAATATAAGAGCGTTTGGATC 57.135 33.333 0.00 0.00 0.00 3.36
1507 1656 8.506168 AAAGAAATATAAGAGCGTTTGGATCA 57.494 30.769 0.00 0.00 32.03 2.92
1508 1657 7.484035 AGAAATATAAGAGCGTTTGGATCAC 57.516 36.000 0.00 0.00 32.03 3.06
1509 1658 7.275920 AGAAATATAAGAGCGTTTGGATCACT 58.724 34.615 0.00 0.00 32.03 3.41
1510 1659 8.421784 AGAAATATAAGAGCGTTTGGATCACTA 58.578 33.333 0.00 0.00 32.03 2.74
1511 1660 7.948278 AATATAAGAGCGTTTGGATCACTAC 57.052 36.000 0.00 0.00 32.03 2.73
1512 1661 3.963428 AAGAGCGTTTGGATCACTACT 57.037 42.857 0.00 0.00 32.03 2.57
1513 1662 3.963428 AGAGCGTTTGGATCACTACTT 57.037 42.857 0.00 0.00 32.03 2.24
1514 1663 4.273148 AGAGCGTTTGGATCACTACTTT 57.727 40.909 0.00 0.00 32.03 2.66
1515 1664 5.401531 AGAGCGTTTGGATCACTACTTTA 57.598 39.130 0.00 0.00 32.03 1.85
1516 1665 5.411781 AGAGCGTTTGGATCACTACTTTAG 58.588 41.667 0.00 0.00 32.03 1.85
1517 1666 5.047235 AGAGCGTTTGGATCACTACTTTAGT 60.047 40.000 0.00 0.00 40.28 2.24
1518 1667 5.548406 AGCGTTTGGATCACTACTTTAGTT 58.452 37.500 0.00 0.00 36.76 2.24
1519 1668 6.694447 AGCGTTTGGATCACTACTTTAGTTA 58.306 36.000 0.00 0.00 36.76 2.24
1520 1669 7.328737 AGCGTTTGGATCACTACTTTAGTTAT 58.671 34.615 0.00 0.00 36.76 1.89
1521 1670 7.491696 AGCGTTTGGATCACTACTTTAGTTATC 59.508 37.037 0.00 0.64 38.23 1.75
1522 1671 7.491696 GCGTTTGGATCACTACTTTAGTTATCT 59.508 37.037 0.00 0.00 38.71 1.98
1657 1824 3.845178 TCACACGAACATAGTGACATCC 58.155 45.455 3.20 0.00 41.83 3.51
1706 1873 6.215845 ACTTTCATGACTGGCAAATGTTTAC 58.784 36.000 0.00 0.00 0.00 2.01
1746 1946 3.553508 CCAAGTTCCAGCAATCCAAACTG 60.554 47.826 0.00 0.00 30.95 3.16
1752 1952 6.151144 AGTTCCAGCAATCCAAACTGTATTAC 59.849 38.462 0.00 0.00 0.00 1.89
1793 1993 6.516718 TCACAGCTAAGCTTCCAGTTATATC 58.483 40.000 0.00 0.00 36.40 1.63
1894 2094 3.440267 GCATGCGCAACTCAAACG 58.560 55.556 17.11 0.00 38.36 3.60
1896 2096 0.454957 GCATGCGCAACTCAAACGAT 60.455 50.000 17.11 0.00 38.36 3.73
2002 2217 2.008329 CACTGCCTGCTTTCTCTGATC 58.992 52.381 0.00 0.00 0.00 2.92
2088 2303 2.354510 ACAACCATATTCGGCAATGTCG 59.645 45.455 0.00 0.00 0.00 4.35
2304 2519 7.096065 GCAATTCTGTACATTTCAAACTTCACC 60.096 37.037 0.00 0.00 0.00 4.02
2339 2554 6.391227 ACTGGATGTTTCTTGTTTAGTTGG 57.609 37.500 0.00 0.00 0.00 3.77
2472 2687 3.181501 TGCCATTTCGTATTTGCACTAGC 60.182 43.478 0.00 0.00 42.57 3.42
2476 2691 0.808453 TCGTATTTGCACTAGCGGGC 60.808 55.000 0.00 0.00 46.23 6.13
2512 2727 7.436933 TCCTACTTGCTCTACATGTCATATTG 58.563 38.462 0.00 0.00 37.74 1.90
2871 3086 7.050970 TGGTATGCTTACAGTTACAGGATAG 57.949 40.000 11.47 0.00 0.00 2.08
2894 3109 7.303182 AGAGCTATTTACCATGCTGTGTATA 57.697 36.000 0.00 0.00 35.76 1.47
2896 3111 7.015682 AGAGCTATTTACCATGCTGTGTATACT 59.984 37.037 4.17 0.00 35.76 2.12
2962 3177 2.496899 AAGGGACTCGTCATTTGCAT 57.503 45.000 0.00 0.00 38.49 3.96
3053 3268 6.925718 GCTGAAGCTAATGTATAGTCATGTGA 59.074 38.462 0.00 0.00 38.21 3.58
3111 3326 9.347934 CAGAAACAACAACACAAGTATTAAACA 57.652 29.630 0.00 0.00 0.00 2.83
3300 3520 2.202974 GGTTTACTAGCCCGCCGG 60.203 66.667 0.00 0.00 0.00 6.13
3547 3767 4.141181 CCAGGGATTTTCCTACATGATCCA 60.141 45.833 0.00 0.00 38.38 3.41
3574 3794 3.344515 CTTTACAGCCTTAGTTCACCCC 58.655 50.000 0.00 0.00 0.00 4.95
3616 3836 1.609555 GGTGTTGTGAGAGTCGAGACT 59.390 52.381 5.31 5.31 45.84 3.24
3763 3985 7.934457 ACATATTCATCTGGTGATTTAAGTGC 58.066 34.615 0.00 0.00 36.54 4.40
3798 4020 6.599437 CAGTCCACTGGTTTAAATTCTAACG 58.401 40.000 0.00 0.00 40.20 3.18
3891 4113 5.420104 GTGGAATTCAGAAAATCCATGGTCT 59.580 40.000 19.05 3.99 44.37 3.85
4019 4241 3.461061 TGACTCTTTGAGCTGAAGTGTG 58.539 45.455 15.11 4.47 32.73 3.82
4023 4245 2.810274 TCTTTGAGCTGAAGTGTGATGC 59.190 45.455 0.00 0.00 0.00 3.91
4048 4270 2.042162 AGGTCAACTCTCATGGCCAAAT 59.958 45.455 10.96 0.00 45.17 2.32
4050 4272 3.350833 GTCAACTCTCATGGCCAAATCT 58.649 45.455 10.96 0.00 0.00 2.40
4089 4312 3.110705 AGAAGCAAGCATAGGAGGAAGA 58.889 45.455 0.00 0.00 0.00 2.87
4108 4331 3.936564 AGAGAAGCTTCCTAGTGCAAAG 58.063 45.455 22.81 0.00 0.00 2.77
4135 4358 7.765695 AACTATGGGGTAAATTCTGCATATG 57.234 36.000 0.00 0.00 0.00 1.78
4136 4359 7.090319 ACTATGGGGTAAATTCTGCATATGA 57.910 36.000 6.97 0.00 0.00 2.15
4137 4360 6.942576 ACTATGGGGTAAATTCTGCATATGAC 59.057 38.462 6.97 0.00 0.00 3.06
4138 4361 4.133820 TGGGGTAAATTCTGCATATGACG 58.866 43.478 6.97 0.00 0.00 4.35
4153 4376 0.943835 TGACGGACAGCATTGTGACG 60.944 55.000 0.00 0.00 37.76 4.35
4243 4466 1.148273 TTGCTTTGTGCCCGTCTCT 59.852 52.632 0.00 0.00 42.00 3.10
4244 4467 0.884704 TTGCTTTGTGCCCGTCTCTC 60.885 55.000 0.00 0.00 42.00 3.20
4245 4468 1.004440 GCTTTGTGCCCGTCTCTCT 60.004 57.895 0.00 0.00 35.15 3.10
4246 4469 1.294659 GCTTTGTGCCCGTCTCTCTG 61.295 60.000 0.00 0.00 35.15 3.35
4247 4470 1.294659 CTTTGTGCCCGTCTCTCTGC 61.295 60.000 0.00 0.00 0.00 4.26
4248 4471 3.573772 TTGTGCCCGTCTCTCTGCG 62.574 63.158 0.00 0.00 0.00 5.18
4251 4474 4.863925 GCCCGTCTCTCTGCGCTC 62.864 72.222 9.73 0.00 0.00 5.03
4252 4475 4.544689 CCCGTCTCTCTGCGCTCG 62.545 72.222 9.73 0.00 0.00 5.03
4260 4483 0.879090 TCTCTGCGCTCGTGTCTTTA 59.121 50.000 9.73 0.00 0.00 1.85
4325 4549 3.700538 TCTATTTGCTCATGTTTGGCCT 58.299 40.909 3.32 0.00 0.00 5.19
4363 4587 0.250234 CTGCCCATGAGAGGTCGAAA 59.750 55.000 0.00 0.00 0.00 3.46
4397 4621 7.783042 AGTTGGCACTACTTCCTACTTATAAG 58.217 38.462 11.05 11.05 35.46 1.73
4535 4787 6.015180 ACATGAGCAAATTACACAAACCTGAT 60.015 34.615 0.00 0.00 0.00 2.90
4536 4788 6.403866 TGAGCAAATTACACAAACCTGATT 57.596 33.333 0.00 0.00 0.00 2.57
4538 4790 7.367285 TGAGCAAATTACACAAACCTGATTAC 58.633 34.615 0.00 0.00 0.00 1.89
4539 4791 6.687604 AGCAAATTACACAAACCTGATTACC 58.312 36.000 0.00 0.00 0.00 2.85
4540 4792 6.493458 AGCAAATTACACAAACCTGATTACCT 59.507 34.615 0.00 0.00 0.00 3.08
4541 4793 6.586082 GCAAATTACACAAACCTGATTACCTG 59.414 38.462 0.00 0.00 0.00 4.00
4542 4794 7.523052 GCAAATTACACAAACCTGATTACCTGA 60.523 37.037 0.00 0.00 0.00 3.86
4543 4795 8.356657 CAAATTACACAAACCTGATTACCTGAA 58.643 33.333 0.00 0.00 0.00 3.02
4544 4796 6.870971 TTACACAAACCTGATTACCTGAAC 57.129 37.500 0.00 0.00 0.00 3.18
4545 4797 4.787551 ACACAAACCTGATTACCTGAACA 58.212 39.130 0.00 0.00 0.00 3.18
4546 4798 5.385198 ACACAAACCTGATTACCTGAACAT 58.615 37.500 0.00 0.00 0.00 2.71
4547 4799 6.539173 ACACAAACCTGATTACCTGAACATA 58.461 36.000 0.00 0.00 0.00 2.29
4548 4800 6.430000 ACACAAACCTGATTACCTGAACATAC 59.570 38.462 0.00 0.00 0.00 2.39
4753 5017 7.816995 TCTTGATAAATTTTGCTGCGGTTTTAT 59.183 29.630 0.00 2.73 0.00 1.40
4802 5066 6.018994 CGGTATGTGGATTTTGTAGAAGTAGC 60.019 42.308 0.00 0.00 0.00 3.58
4813 5077 1.629043 AGAAGTAGCCGTTCCAGTCA 58.371 50.000 0.00 0.00 0.00 3.41
4908 5172 1.126846 GTTGATGTCGTCGAAGCTTGG 59.873 52.381 2.10 1.69 0.00 3.61
4911 5175 2.029739 TGATGTCGTCGAAGCTTGGTTA 60.030 45.455 2.10 0.00 0.00 2.85
4912 5176 2.512485 TGTCGTCGAAGCTTGGTTAA 57.488 45.000 2.10 0.00 0.00 2.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
22 23 3.799755 GATGACGCCACGGTTGCC 61.800 66.667 0.00 0.00 0.00 4.52
23 24 4.147322 CGATGACGCCACGGTTGC 62.147 66.667 0.00 0.00 0.00 4.17
24 25 3.487202 CCGATGACGCCACGGTTG 61.487 66.667 0.00 0.00 41.47 3.77
25 26 4.752879 CCCGATGACGCCACGGTT 62.753 66.667 10.61 0.00 44.34 4.44
34 35 2.901042 GGGTGGAGTCCCGATGAC 59.099 66.667 6.74 0.00 44.82 3.06
40 41 2.365768 GGAGAGGGGTGGAGTCCC 60.366 72.222 6.74 0.00 46.31 4.46
41 42 2.365768 GGGAGAGGGGTGGAGTCC 60.366 72.222 0.73 0.73 0.00 3.85
42 43 1.990614 GTGGGAGAGGGGTGGAGTC 60.991 68.421 0.00 0.00 0.00 3.36
43 44 2.122954 GTGGGAGAGGGGTGGAGT 59.877 66.667 0.00 0.00 0.00 3.85
44 45 3.077556 CGTGGGAGAGGGGTGGAG 61.078 72.222 0.00 0.00 0.00 3.86
45 46 3.899545 GACGTGGGAGAGGGGTGGA 62.900 68.421 0.00 0.00 0.00 4.02
46 47 3.391382 GACGTGGGAGAGGGGTGG 61.391 72.222 0.00 0.00 0.00 4.61
47 48 3.391382 GGACGTGGGAGAGGGGTG 61.391 72.222 0.00 0.00 0.00 4.61
48 49 3.602030 AGGACGTGGGAGAGGGGT 61.602 66.667 0.00 0.00 0.00 4.95
49 50 2.760385 GAGGACGTGGGAGAGGGG 60.760 72.222 0.00 0.00 0.00 4.79
50 51 2.760385 GGAGGACGTGGGAGAGGG 60.760 72.222 0.00 0.00 0.00 4.30
51 52 2.760385 GGGAGGACGTGGGAGAGG 60.760 72.222 0.00 0.00 0.00 3.69
52 53 2.760385 GGGGAGGACGTGGGAGAG 60.760 72.222 0.00 0.00 0.00 3.20
53 54 2.865147 AAGGGGAGGACGTGGGAGA 61.865 63.158 0.00 0.00 0.00 3.71
54 55 2.284699 AAGGGGAGGACGTGGGAG 60.285 66.667 0.00 0.00 0.00 4.30
55 56 2.606519 CAAGGGGAGGACGTGGGA 60.607 66.667 0.00 0.00 0.00 4.37
56 57 2.928396 ACAAGGGGAGGACGTGGG 60.928 66.667 0.00 0.00 0.00 4.61
57 58 2.663196 GACAAGGGGAGGACGTGG 59.337 66.667 0.00 0.00 0.00 4.94
58 59 2.261671 CGACAAGGGGAGGACGTG 59.738 66.667 0.00 0.00 0.00 4.49
59 60 3.692406 GCGACAAGGGGAGGACGT 61.692 66.667 0.00 0.00 0.00 4.34
60 61 4.452733 GGCGACAAGGGGAGGACG 62.453 72.222 0.00 0.00 0.00 4.79
61 62 3.319198 TGGCGACAAGGGGAGGAC 61.319 66.667 0.00 0.00 37.44 3.85
62 63 3.319198 GTGGCGACAAGGGGAGGA 61.319 66.667 0.00 0.00 46.06 3.71
63 64 4.410400 GGTGGCGACAAGGGGAGG 62.410 72.222 0.00 0.00 46.06 4.30
64 65 4.760047 CGGTGGCGACAAGGGGAG 62.760 72.222 0.00 0.00 46.06 4.30
66 67 4.760047 CTCGGTGGCGACAAGGGG 62.760 72.222 0.00 0.00 46.06 4.79
67 68 4.760047 CCTCGGTGGCGACAAGGG 62.760 72.222 0.00 0.00 46.06 3.95
96 97 3.249973 GACGTTGACCGGGCTTTGC 62.250 63.158 9.82 0.00 42.24 3.68
97 98 2.943653 GACGTTGACCGGGCTTTG 59.056 61.111 9.82 0.00 42.24 2.77
98 99 2.663852 CGACGTTGACCGGGCTTT 60.664 61.111 9.82 0.00 42.24 3.51
99 100 4.675029 CCGACGTTGACCGGGCTT 62.675 66.667 9.82 0.00 41.89 4.35
112 113 2.278013 GATCTCGCCGTCACCGAC 60.278 66.667 0.00 0.00 35.63 4.79
113 114 2.437895 AGATCTCGCCGTCACCGA 60.438 61.111 0.00 0.00 35.63 4.69
114 115 2.024871 GAGATCTCGCCGTCACCG 59.975 66.667 7.04 0.00 0.00 4.94
115 116 0.318275 GATGAGATCTCGCCGTCACC 60.318 60.000 17.76 0.00 0.00 4.02
116 117 0.665835 AGATGAGATCTCGCCGTCAC 59.334 55.000 17.76 4.32 33.42 3.67
117 118 0.947960 GAGATGAGATCTCGCCGTCA 59.052 55.000 17.76 0.21 45.50 4.35
118 119 3.765349 GAGATGAGATCTCGCCGTC 57.235 57.895 17.76 12.37 45.50 4.79
125 126 1.504660 AGCTGAGGGGAGATGAGATCT 59.495 52.381 0.00 0.00 43.70 2.75
126 127 1.619827 CAGCTGAGGGGAGATGAGATC 59.380 57.143 8.42 0.00 30.56 2.75
127 128 1.719529 CAGCTGAGGGGAGATGAGAT 58.280 55.000 8.42 0.00 30.56 2.75
128 129 0.398239 CCAGCTGAGGGGAGATGAGA 60.398 60.000 17.39 0.00 30.56 3.27
129 130 0.690411 ACCAGCTGAGGGGAGATGAG 60.690 60.000 17.39 0.00 30.56 2.90
130 131 0.979709 CACCAGCTGAGGGGAGATGA 60.980 60.000 17.39 0.00 32.15 2.92
131 132 1.525923 CACCAGCTGAGGGGAGATG 59.474 63.158 17.39 0.00 32.15 2.90
132 133 1.692042 CCACCAGCTGAGGGGAGAT 60.692 63.158 17.39 0.00 32.15 2.75
133 134 2.284921 CCACCAGCTGAGGGGAGA 60.285 66.667 17.39 0.00 32.15 3.71
134 135 2.284921 TCCACCAGCTGAGGGGAG 60.285 66.667 18.93 3.25 32.15 4.30
135 136 2.284921 CTCCACCAGCTGAGGGGA 60.285 66.667 20.81 20.81 32.15 4.81
136 137 1.783250 AAACTCCACCAGCTGAGGGG 61.783 60.000 17.39 18.88 32.80 4.79
137 138 0.607489 CAAACTCCACCAGCTGAGGG 60.607 60.000 17.39 16.10 32.80 4.30
138 139 0.607489 CCAAACTCCACCAGCTGAGG 60.607 60.000 17.39 16.83 32.80 3.86
139 140 1.239968 GCCAAACTCCACCAGCTGAG 61.240 60.000 17.39 6.98 34.73 3.35
140 141 1.228245 GCCAAACTCCACCAGCTGA 60.228 57.895 17.39 0.00 0.00 4.26
141 142 2.620112 CGCCAAACTCCACCAGCTG 61.620 63.158 6.78 6.78 0.00 4.24
142 143 2.281761 CGCCAAACTCCACCAGCT 60.282 61.111 0.00 0.00 0.00 4.24
143 144 4.043200 GCGCCAAACTCCACCAGC 62.043 66.667 0.00 0.00 0.00 4.85
144 145 3.726517 CGCGCCAAACTCCACCAG 61.727 66.667 0.00 0.00 0.00 4.00
145 146 4.243008 TCGCGCCAAACTCCACCA 62.243 61.111 0.00 0.00 0.00 4.17
146 147 3.423154 CTCGCGCCAAACTCCACC 61.423 66.667 0.00 0.00 0.00 4.61
147 148 3.423154 CCTCGCGCCAAACTCCAC 61.423 66.667 0.00 0.00 0.00 4.02
148 149 3.171828 TTCCTCGCGCCAAACTCCA 62.172 57.895 0.00 0.00 0.00 3.86
149 150 2.358247 TTCCTCGCGCCAAACTCC 60.358 61.111 0.00 0.00 0.00 3.85
150 151 2.391389 CCTTCCTCGCGCCAAACTC 61.391 63.158 0.00 0.00 0.00 3.01
151 152 2.358737 CCTTCCTCGCGCCAAACT 60.359 61.111 0.00 0.00 0.00 2.66
152 153 4.103103 GCCTTCCTCGCGCCAAAC 62.103 66.667 0.00 0.00 0.00 2.93
153 154 4.634703 TGCCTTCCTCGCGCCAAA 62.635 61.111 0.00 0.00 0.00 3.28
161 162 4.475135 GAGCCCCGTGCCTTCCTC 62.475 72.222 0.00 0.00 42.71 3.71
248 249 1.017387 GATCGCAATTCCACTGACCC 58.983 55.000 0.00 0.00 0.00 4.46
266 267 9.658799 CTATTTAACAAGAGGTGAGAGAATTGA 57.341 33.333 0.00 0.00 0.00 2.57
276 277 7.819900 AGTGTCTAAGCTATTTAACAAGAGGTG 59.180 37.037 0.00 0.00 32.28 4.00
325 326 9.567776 TCATTTCATCAACCAGAAAAGTTACTA 57.432 29.630 0.00 0.00 37.30 1.82
326 327 8.463930 TCATTTCATCAACCAGAAAAGTTACT 57.536 30.769 0.00 0.00 37.30 2.24
327 328 9.696917 ATTCATTTCATCAACCAGAAAAGTTAC 57.303 29.630 0.00 0.00 37.30 2.50
336 337 9.806203 TGCTAAAATATTCATTTCATCAACCAG 57.194 29.630 0.00 0.00 33.09 4.00
373 374 7.147897 ACGACAAGAATTATGGATCAGAGTACA 60.148 37.037 0.00 0.00 0.00 2.90
424 425 1.589716 AAGCCTCTGTCGCAATTGGC 61.590 55.000 7.72 0.00 40.54 4.52
436 437 1.048601 TGTCGGTCAGAAAAGCCTCT 58.951 50.000 0.00 0.00 0.00 3.69
443 444 2.433436 TCTCGAGATGTCGGTCAGAAA 58.567 47.619 12.08 0.00 46.80 2.52
456 457 1.621992 AGTTCAGTGCCTTCTCGAGA 58.378 50.000 12.08 12.08 0.00 4.04
478 479 0.470766 TACATGTGGGCCGGGTAATC 59.529 55.000 9.11 0.00 0.00 1.75
486 487 0.323360 TTGCCTCTTACATGTGGGCC 60.323 55.000 22.04 0.00 41.84 5.80
487 488 1.544724 TTTGCCTCTTACATGTGGGC 58.455 50.000 19.77 19.77 42.73 5.36
488 489 3.826157 TCTTTTTGCCTCTTACATGTGGG 59.174 43.478 9.11 6.61 0.00 4.61
489 490 5.452078 TTCTTTTTGCCTCTTACATGTGG 57.548 39.130 9.11 1.56 0.00 4.17
490 491 7.769272 TTTTTCTTTTTGCCTCTTACATGTG 57.231 32.000 9.11 0.00 0.00 3.21
491 492 8.962884 AATTTTTCTTTTTGCCTCTTACATGT 57.037 26.923 2.69 2.69 0.00 3.21
494 495 7.168469 GCGTAATTTTTCTTTTTGCCTCTTACA 59.832 33.333 0.00 0.00 0.00 2.41
495 496 7.168469 TGCGTAATTTTTCTTTTTGCCTCTTAC 59.832 33.333 0.00 0.00 0.00 2.34
496 497 7.168469 GTGCGTAATTTTTCTTTTTGCCTCTTA 59.832 33.333 0.00 0.00 0.00 2.10
497 498 6.019075 GTGCGTAATTTTTCTTTTTGCCTCTT 60.019 34.615 0.00 0.00 0.00 2.85
498 499 5.462068 GTGCGTAATTTTTCTTTTTGCCTCT 59.538 36.000 0.00 0.00 0.00 3.69
499 500 5.233263 TGTGCGTAATTTTTCTTTTTGCCTC 59.767 36.000 0.00 0.00 0.00 4.70
500 501 5.112686 TGTGCGTAATTTTTCTTTTTGCCT 58.887 33.333 0.00 0.00 0.00 4.75
501 502 5.396750 TGTGCGTAATTTTTCTTTTTGCC 57.603 34.783 0.00 0.00 0.00 4.52
502 503 6.418141 ACATGTGCGTAATTTTTCTTTTTGC 58.582 32.000 0.00 0.00 0.00 3.68
503 504 7.735586 GCTACATGTGCGTAATTTTTCTTTTTG 59.264 33.333 9.11 0.00 0.00 2.44
504 505 7.095816 GGCTACATGTGCGTAATTTTTCTTTTT 60.096 33.333 9.11 0.00 0.00 1.94
508 509 4.142469 GGGCTACATGTGCGTAATTTTTCT 60.142 41.667 9.11 0.00 0.00 2.52
531 532 0.386731 GTTTGATTTGACGGCCACGG 60.387 55.000 2.24 0.00 46.48 4.94
533 534 2.500509 TTGTTTGATTTGACGGCCAC 57.499 45.000 2.24 0.00 0.00 5.01
534 535 3.526931 TTTTGTTTGATTTGACGGCCA 57.473 38.095 2.24 0.00 0.00 5.36
535 536 3.303066 GCTTTTTGTTTGATTTGACGGCC 60.303 43.478 0.00 0.00 0.00 6.13
536 537 3.555547 AGCTTTTTGTTTGATTTGACGGC 59.444 39.130 0.00 0.00 0.00 5.68
646 753 2.499693 GGATTAGAGGGGATAGAGCAGC 59.500 54.545 0.00 0.00 0.00 5.25
659 766 2.029470 GGCCGTCAGATCTGGATTAGAG 60.029 54.545 22.42 6.23 39.20 2.43
742 849 2.116556 GGGGCTGGGGAAAAACGA 59.883 61.111 0.00 0.00 0.00 3.85
744 851 2.583441 GCTGGGGCTGGGGAAAAAC 61.583 63.158 0.00 0.00 35.22 2.43
774 881 2.048222 TCAGGAGCGCCAAGTTCG 60.048 61.111 9.88 0.00 36.29 3.95
793 911 3.868985 ACGCACGGAAGGTTGGGT 61.869 61.111 0.00 0.00 0.00 4.51
804 922 1.788203 GACGATGCAAACACGCACG 60.788 57.895 0.00 0.00 46.56 5.34
805 923 0.787787 TAGACGATGCAAACACGCAC 59.212 50.000 0.00 0.00 46.56 5.34
807 925 3.918258 TTATAGACGATGCAAACACGC 57.082 42.857 0.00 0.00 0.00 5.34
826 945 0.605589 CTCGCTTCCCCGGACTTTTT 60.606 55.000 0.73 0.00 0.00 1.94
902 1022 1.817099 GAGCCAAGTGGATGAGCGG 60.817 63.158 0.18 0.00 37.39 5.52
1110 1238 4.473477 AGAAGTAACAGGGAATCGAAGG 57.527 45.455 0.00 0.00 0.00 3.46
1132 1264 1.896660 GCAACAGGTGGGAAAGCGA 60.897 57.895 0.00 0.00 0.00 4.93
1161 1299 4.647853 CACACTCATCCATCCATTCCATTT 59.352 41.667 0.00 0.00 0.00 2.32
1177 1315 2.231478 GCCTAGCTAACTCACACACTCA 59.769 50.000 0.00 0.00 0.00 3.41
1186 1324 5.349809 ACGTAATTTCTGCCTAGCTAACTC 58.650 41.667 0.00 0.00 0.00 3.01
1187 1325 5.340439 ACGTAATTTCTGCCTAGCTAACT 57.660 39.130 0.00 0.00 0.00 2.24
1189 1327 6.428771 ACAAAACGTAATTTCTGCCTAGCTAA 59.571 34.615 0.00 0.00 0.00 3.09
1191 1329 4.760204 ACAAAACGTAATTTCTGCCTAGCT 59.240 37.500 0.00 0.00 0.00 3.32
1237 1376 1.838073 AACCGGAGCCTTGGTGGTAG 61.838 60.000 9.46 0.00 38.82 3.18
1244 1383 0.389025 AAAAGCAAACCGGAGCCTTG 59.611 50.000 9.46 7.22 0.00 3.61
1247 1386 1.244816 AGTAAAAGCAAACCGGAGCC 58.755 50.000 9.46 0.00 0.00 4.70
1275 1419 2.731691 AAGGAACCACGTGCGAGCAT 62.732 55.000 10.91 0.00 0.00 3.79
1291 1435 0.322098 TGACACGCCATAACCCAAGG 60.322 55.000 0.00 0.00 0.00 3.61
1292 1436 1.199097 GTTGACACGCCATAACCCAAG 59.801 52.381 0.00 0.00 0.00 3.61
1358 1507 0.320508 GGAGGAGAAACCGTGGTGAC 60.321 60.000 0.00 0.00 44.74 3.67
1374 1523 1.761271 GAAGGGACGGGGGTAGGAG 60.761 68.421 0.00 0.00 0.00 3.69
1415 1564 8.532977 AAACTGAACCACAATTGCATTATAAC 57.467 30.769 5.05 0.00 0.00 1.89
1418 1567 7.444299 AGAAAACTGAACCACAATTGCATTAT 58.556 30.769 5.05 0.00 0.00 1.28
1465 1614 9.710818 ATATTTCTTTACAGAGGGAGTACAGTA 57.289 33.333 0.00 0.00 0.00 2.74
1466 1615 6.936968 ATTTCTTTACAGAGGGAGTACAGT 57.063 37.500 0.00 0.00 0.00 3.55
1471 1620 8.425703 GCTCTTATATTTCTTTACAGAGGGAGT 58.574 37.037 0.00 0.00 0.00 3.85
1472 1621 7.596995 CGCTCTTATATTTCTTTACAGAGGGAG 59.403 40.741 4.76 0.00 40.49 4.30
1473 1622 7.069578 ACGCTCTTATATTTCTTTACAGAGGGA 59.930 37.037 14.96 0.00 40.49 4.20
1474 1623 7.210873 ACGCTCTTATATTTCTTTACAGAGGG 58.789 38.462 8.36 8.36 42.53 4.30
1475 1624 8.649973 AACGCTCTTATATTTCTTTACAGAGG 57.350 34.615 0.00 0.00 0.00 3.69
1476 1625 9.907576 CAAACGCTCTTATATTTCTTTACAGAG 57.092 33.333 0.00 0.00 0.00 3.35
1477 1626 8.879759 CCAAACGCTCTTATATTTCTTTACAGA 58.120 33.333 0.00 0.00 0.00 3.41
1478 1627 8.879759 TCCAAACGCTCTTATATTTCTTTACAG 58.120 33.333 0.00 0.00 0.00 2.74
1479 1628 8.780846 TCCAAACGCTCTTATATTTCTTTACA 57.219 30.769 0.00 0.00 0.00 2.41
1480 1629 9.865484 GATCCAAACGCTCTTATATTTCTTTAC 57.135 33.333 0.00 0.00 0.00 2.01
1481 1630 9.607988 TGATCCAAACGCTCTTATATTTCTTTA 57.392 29.630 0.00 0.00 0.00 1.85
1482 1631 8.398665 GTGATCCAAACGCTCTTATATTTCTTT 58.601 33.333 0.00 0.00 0.00 2.52
1483 1632 7.770897 AGTGATCCAAACGCTCTTATATTTCTT 59.229 33.333 0.00 0.00 0.00 2.52
1484 1633 7.275920 AGTGATCCAAACGCTCTTATATTTCT 58.724 34.615 0.00 0.00 0.00 2.52
1485 1634 7.484035 AGTGATCCAAACGCTCTTATATTTC 57.516 36.000 0.00 0.00 0.00 2.17
1486 1635 8.204836 AGTAGTGATCCAAACGCTCTTATATTT 58.795 33.333 0.00 0.00 0.00 1.40
1487 1636 7.727181 AGTAGTGATCCAAACGCTCTTATATT 58.273 34.615 0.00 0.00 0.00 1.28
1488 1637 7.291411 AGTAGTGATCCAAACGCTCTTATAT 57.709 36.000 0.00 0.00 0.00 0.86
1489 1638 6.710597 AGTAGTGATCCAAACGCTCTTATA 57.289 37.500 0.00 0.00 0.00 0.98
1490 1639 5.599999 AGTAGTGATCCAAACGCTCTTAT 57.400 39.130 0.00 0.00 0.00 1.73
1491 1640 5.401531 AAGTAGTGATCCAAACGCTCTTA 57.598 39.130 0.00 0.00 0.00 2.10
1492 1641 3.963428 AGTAGTGATCCAAACGCTCTT 57.037 42.857 0.00 0.00 0.00 2.85
1493 1642 3.963428 AAGTAGTGATCCAAACGCTCT 57.037 42.857 0.00 0.00 0.00 4.09
1494 1643 5.169295 ACTAAAGTAGTGATCCAAACGCTC 58.831 41.667 0.00 0.00 37.69 5.03
1495 1644 5.148651 ACTAAAGTAGTGATCCAAACGCT 57.851 39.130 0.00 0.00 37.69 5.07
1496 1645 5.857822 AACTAAAGTAGTGATCCAAACGC 57.142 39.130 0.00 0.00 39.39 4.84
1497 1646 8.928270 AGATAACTAAAGTAGTGATCCAAACG 57.072 34.615 8.56 0.00 44.51 3.60
1539 1688 8.989131 TGCTAATTAAGTACTCCCTCTGTAAAT 58.011 33.333 0.00 0.00 0.00 1.40
1540 1689 8.255905 GTGCTAATTAAGTACTCCCTCTGTAAA 58.744 37.037 0.00 0.00 37.79 2.01
1541 1690 7.147776 GGTGCTAATTAAGTACTCCCTCTGTAA 60.148 40.741 0.00 0.00 40.41 2.41
1542 1691 6.323225 GGTGCTAATTAAGTACTCCCTCTGTA 59.677 42.308 0.00 0.00 40.41 2.74
1543 1692 5.128991 GGTGCTAATTAAGTACTCCCTCTGT 59.871 44.000 0.00 0.00 40.41 3.41
1544 1693 5.453480 GGGTGCTAATTAAGTACTCCCTCTG 60.453 48.000 0.00 0.00 40.41 3.35
1545 1694 4.654724 GGGTGCTAATTAAGTACTCCCTCT 59.345 45.833 0.00 0.00 40.41 3.69
1546 1695 4.407945 TGGGTGCTAATTAAGTACTCCCTC 59.592 45.833 16.37 0.00 40.40 4.30
1547 1696 4.368067 TGGGTGCTAATTAAGTACTCCCT 58.632 43.478 16.37 0.00 40.40 4.20
1548 1697 4.765813 TGGGTGCTAATTAAGTACTCCC 57.234 45.455 0.00 0.00 40.40 4.30
1549 1698 5.585047 CAGTTGGGTGCTAATTAAGTACTCC 59.415 44.000 0.00 0.00 40.40 3.85
1550 1699 5.585047 CCAGTTGGGTGCTAATTAAGTACTC 59.415 44.000 0.00 0.00 41.43 2.59
1551 1700 5.249852 TCCAGTTGGGTGCTAATTAAGTACT 59.750 40.000 0.00 0.00 40.41 2.73
1552 1701 5.353400 GTCCAGTTGGGTGCTAATTAAGTAC 59.647 44.000 0.00 0.00 39.89 2.73
1625 1774 4.529109 TGTTCGTGTGAAGATACCATCA 57.471 40.909 0.00 0.00 33.98 3.07
1626 1775 6.199154 CACTATGTTCGTGTGAAGATACCATC 59.801 42.308 0.00 0.00 38.82 3.51
1627 1776 6.042777 CACTATGTTCGTGTGAAGATACCAT 58.957 40.000 0.00 0.00 38.82 3.55
1657 1824 1.872952 TCCAACAACGTTGCTGAGATG 59.127 47.619 28.46 16.90 0.00 2.90
1746 1946 3.506067 ACTTGTGGCAAAGGCAGTAATAC 59.494 43.478 12.03 0.00 43.71 1.89
1752 1952 0.746063 TGAACTTGTGGCAAAGGCAG 59.254 50.000 12.03 0.00 43.71 4.85
1793 1993 4.400251 ACCAGCATCCTATTGTTGTTGATG 59.600 41.667 0.00 0.00 36.70 3.07
1894 2094 8.538856 CGTGTAGTAGTAACAGTACAGACTATC 58.461 40.741 0.00 0.00 35.51 2.08
1896 2096 7.602753 TCGTGTAGTAGTAACAGTACAGACTA 58.397 38.462 0.00 0.00 35.51 2.59
1963 2176 6.372937 GGCAGTGAGAATAAATAGGGAATAGC 59.627 42.308 0.00 0.00 0.00 2.97
1964 2177 7.605691 CAGGCAGTGAGAATAAATAGGGAATAG 59.394 40.741 0.00 0.00 0.00 1.73
2002 2217 3.978718 TCGTCATGCTGTCATCTAGAG 57.021 47.619 0.00 0.00 0.00 2.43
2131 2346 0.594796 CAAAACTCAACAGTGCCCGC 60.595 55.000 0.00 0.00 31.06 6.13
2304 2519 1.274167 ACATCCAGTTGCAAAGCCATG 59.726 47.619 0.00 4.47 0.00 3.66
2339 2554 4.228912 ACAAAATGCACACTTCTAGCAC 57.771 40.909 0.00 0.00 41.60 4.40
2431 2646 5.423886 TGGCATCTTGTACAATCGATTACA 58.576 37.500 10.97 9.96 0.00 2.41
2472 2687 2.551032 AGTAGGAAAAAGAAAACGCCCG 59.449 45.455 0.00 0.00 0.00 6.13
2476 2691 6.061231 AGAGCAAGTAGGAAAAAGAAAACG 57.939 37.500 0.00 0.00 0.00 3.60
2512 2727 6.915349 ACCGACTATCTATCAATGAGCTAAC 58.085 40.000 0.00 0.00 0.00 2.34
2628 2843 1.142667 TGTCATTCAGCTGACCAACCA 59.857 47.619 18.03 7.04 43.99 3.67
2871 3086 7.155328 AGTATACACAGCATGGTAAATAGCTC 58.845 38.462 5.50 0.00 43.62 4.09
3053 3268 9.019656 TCATAAATAATGCACCAGTGTTTAGTT 57.980 29.630 0.00 6.61 31.27 2.24
3111 3326 4.071961 TCTGCACAGTTGTACACTCAAT 57.928 40.909 0.00 0.00 30.92 2.57
3300 3520 6.913170 TCATCTGCATAAAAGAAGTTTCACC 58.087 36.000 0.00 0.00 0.00 4.02
3475 3695 4.889409 TGAAACTGGCTTTGAAGATTCAGT 59.111 37.500 0.00 2.74 38.61 3.41
3513 3733 4.279420 GGAAAATCCCTGGATAGAATGCAC 59.721 45.833 0.00 0.00 33.97 4.57
3547 3767 4.040461 TGAACTAAGGCTGTAAAGCTCACT 59.960 41.667 4.54 0.00 34.73 3.41
3574 3794 4.627467 CCCTTCTTGAATGTGAAGTACTCG 59.373 45.833 0.00 0.00 38.30 4.18
3616 3836 2.676121 CCGGTGCAAATGCCCTGA 60.676 61.111 2.46 0.00 41.18 3.86
4019 4241 3.325293 TGAGAGTTGACCTGAAGCATC 57.675 47.619 0.00 0.00 0.00 3.91
4023 4245 2.354259 GCCATGAGAGTTGACCTGAAG 58.646 52.381 0.00 0.00 0.00 3.02
4089 4312 2.224621 TGCTTTGCACTAGGAAGCTTCT 60.225 45.455 25.05 13.83 44.55 2.85
4108 4331 4.159506 TGCAGAATTTACCCCATAGTTTGC 59.840 41.667 0.00 0.00 0.00 3.68
4135 4358 0.666274 TCGTCACAATGCTGTCCGTC 60.666 55.000 0.00 0.00 31.64 4.79
4136 4359 0.249699 TTCGTCACAATGCTGTCCGT 60.250 50.000 0.00 0.00 31.64 4.69
4137 4360 0.163788 GTTCGTCACAATGCTGTCCG 59.836 55.000 0.00 0.00 31.64 4.79
4138 4361 1.225855 TGTTCGTCACAATGCTGTCC 58.774 50.000 0.00 0.00 31.64 4.02
4211 4434 4.218200 CACAAAGCAACAATGAGTATGGGA 59.782 41.667 0.00 0.00 0.00 4.37
4243 4466 2.363788 AATAAAGACACGAGCGCAGA 57.636 45.000 11.47 0.00 0.00 4.26
4244 4467 3.542291 GCTAAATAAAGACACGAGCGCAG 60.542 47.826 11.47 5.62 0.00 5.18
4245 4468 2.347452 GCTAAATAAAGACACGAGCGCA 59.653 45.455 11.47 0.00 0.00 6.09
4246 4469 2.347452 TGCTAAATAAAGACACGAGCGC 59.653 45.455 0.00 0.00 0.00 5.92
4247 4470 3.000322 CCTGCTAAATAAAGACACGAGCG 60.000 47.826 0.00 0.00 0.00 5.03
4248 4471 3.242446 GCCTGCTAAATAAAGACACGAGC 60.242 47.826 0.00 0.00 0.00 5.03
4249 4472 3.932710 TGCCTGCTAAATAAAGACACGAG 59.067 43.478 0.00 0.00 0.00 4.18
4250 4473 3.932822 TGCCTGCTAAATAAAGACACGA 58.067 40.909 0.00 0.00 0.00 4.35
4251 4474 4.882671 ATGCCTGCTAAATAAAGACACG 57.117 40.909 0.00 0.00 0.00 4.49
4252 4475 7.736447 AGATATGCCTGCTAAATAAAGACAC 57.264 36.000 0.00 0.00 0.00 3.67
4260 4483 4.261322 CGTGCAAAGATATGCCTGCTAAAT 60.261 41.667 0.00 0.00 45.83 1.40
4325 4549 0.035739 GGTCAGGTTTAGCCCGACAA 59.964 55.000 3.99 0.00 38.26 3.18
4343 4567 1.617018 TTCGACCTCTCATGGGCAGG 61.617 60.000 8.94 8.94 33.86 4.85
4363 4587 4.292186 AGTAGTGCCAACTCATGTTCAT 57.708 40.909 0.00 0.00 37.88 2.57
4443 4695 4.998671 TTGAAGCACAGGAATTTCACAA 57.001 36.364 0.00 0.00 29.96 3.33
4580 4832 8.812513 AAGGACATCATTGATCAGTGATAAAA 57.187 30.769 27.39 6.24 35.90 1.52
4624 4888 2.887152 GGAAGACTTTTCACATGCCAGT 59.113 45.455 0.00 0.00 0.00 4.00
4626 4890 3.228188 AGGAAGACTTTTCACATGCCA 57.772 42.857 0.00 0.00 0.00 4.92
4753 5017 4.065088 GTGTCCTCAAGTATGTGCTCAAA 58.935 43.478 0.00 0.00 0.00 2.69
4819 5083 5.925397 CGACATGTTCAATTTTGATCCCAAA 59.075 36.000 0.00 0.00 40.24 3.28
4908 5172 7.378181 ACTTGTCCAACCATTGAATGATTAAC 58.622 34.615 6.76 0.00 0.00 2.01
4911 5175 7.537596 TTACTTGTCCAACCATTGAATGATT 57.462 32.000 6.76 0.00 0.00 2.57
4912 5176 7.451255 TCTTTACTTGTCCAACCATTGAATGAT 59.549 33.333 6.76 0.00 0.00 2.45


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

AutoCloner maintained by Alex Coulton.