Multiple sequence alignment - TraesCS6D01G037300

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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 TraesCS6D01G037300 chr6D 100.000 3527 0 0 1 3527 15420612 15417086 0.000000e+00 6514.0
1 TraesCS6D01G037300 chr6D 93.825 1927 100 9 805 2715 15385353 15383430 0.000000e+00 2881.0
2 TraesCS6D01G037300 chr6D 85.273 1779 245 11 782 2551 15809068 15807298 0.000000e+00 1818.0
3 TraesCS6D01G037300 chr6D 85.216 1779 246 12 782 2551 15799488 15797718 0.000000e+00 1812.0
4 TraesCS6D01G037300 chr6D 85.932 590 56 10 2903 3476 15383101 15382523 3.890000e-169 604.0
5 TraesCS6D01G037300 chr6D 81.461 356 39 14 421 765 15385696 15385357 2.090000e-67 267.0
6 TraesCS6D01G037300 chr6D 82.888 187 21 6 2728 2903 15383324 15383138 1.310000e-34 158.0
7 TraesCS6D01G037300 chr6D 85.507 69 10 0 353 421 34988015 34987947 4.880000e-09 73.1
8 TraesCS6D01G037300 chr6D 85.507 69 10 0 353 421 34994018 34993950 4.880000e-09 73.1
9 TraesCS6D01G037300 chr6B 94.600 2426 104 10 304 2722 27171938 27169533 0.000000e+00 3729.0
10 TraesCS6D01G037300 chr6B 93.711 1924 105 9 805 2715 27124582 27122662 0.000000e+00 2868.0
11 TraesCS6D01G037300 chr6B 91.227 1459 125 3 1071 2528 27181753 27180297 0.000000e+00 1982.0
12 TraesCS6D01G037300 chr6B 94.175 824 32 9 2718 3527 27169499 27168678 0.000000e+00 1242.0
13 TraesCS6D01G037300 chr6B 82.609 828 93 22 2718 3523 27122592 27121794 0.000000e+00 684.0
14 TraesCS6D01G037300 chr6B 96.321 299 11 0 9 307 538067739 538068037 3.160000e-135 492.0
15 TraesCS6D01G037300 chr6B 90.066 151 12 3 617 765 27124735 27124586 3.590000e-45 193.0
16 TraesCS6D01G037300 chr6B 78.680 197 26 9 421 616 27125016 27124835 2.220000e-22 117.0
17 TraesCS6D01G037300 chr6A 95.435 2300 89 10 427 2715 16100740 16098446 0.000000e+00 3651.0
18 TraesCS6D01G037300 chr6A 94.821 1931 77 12 805 2715 15953608 15951681 0.000000e+00 2990.0
19 TraesCS6D01G037300 chr6A 85.405 1754 242 9 786 2530 16400916 16399168 0.000000e+00 1808.0
20 TraesCS6D01G037300 chr6A 96.320 625 18 3 2903 3527 16088839 16088220 0.000000e+00 1022.0
21 TraesCS6D01G037300 chr6A 99.465 187 1 0 2718 2904 16098377 16098191 1.210000e-89 340.0
22 TraesCS6D01G037300 chr6A 81.726 197 18 9 2726 2904 15951577 15951381 7.890000e-32 148.0
23 TraesCS6D01G037300 chr7B 96.990 299 9 0 9 307 121051698 121051996 1.460000e-138 503.0
24 TraesCS6D01G037300 chr7B 96.000 300 12 0 8 307 483393037 483392738 4.090000e-134 488.0
25 TraesCS6D01G037300 chr2D 96.656 299 10 0 9 307 555068302 555068004 6.800000e-137 497.0
26 TraesCS6D01G037300 chr3B 96.321 299 11 0 9 307 73260681 73260979 3.160000e-135 492.0
27 TraesCS6D01G037300 chr3B 96.026 302 12 0 7 308 107529137 107529438 3.160000e-135 492.0
28 TraesCS6D01G037300 chr7D 96.296 297 11 0 11 307 264420771 264421067 4.090000e-134 488.0
29 TraesCS6D01G037300 chr1D 96.296 297 11 0 11 307 388144322 388144618 4.090000e-134 488.0
30 TraesCS6D01G037300 chr4B 95.667 300 13 0 8 307 645069494 645069793 1.900000e-132 483.0
31 TraesCS6D01G037300 chr2A 100.000 31 0 0 353 383 37033743 37033713 1.370000e-04 58.4


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 TraesCS6D01G037300 chr6D 15417086 15420612 3526 True 6514.0 6514 100.0000 1 3527 1 chr6D.!!$R1 3526
1 TraesCS6D01G037300 chr6D 15807298 15809068 1770 True 1818.0 1818 85.2730 782 2551 1 chr6D.!!$R3 1769
2 TraesCS6D01G037300 chr6D 15797718 15799488 1770 True 1812.0 1812 85.2160 782 2551 1 chr6D.!!$R2 1769
3 TraesCS6D01G037300 chr6D 15382523 15385696 3173 True 977.5 2881 86.0265 421 3476 4 chr6D.!!$R6 3055
4 TraesCS6D01G037300 chr6B 27168678 27171938 3260 True 2485.5 3729 94.3875 304 3527 2 chr6B.!!$R3 3223
5 TraesCS6D01G037300 chr6B 27180297 27181753 1456 True 1982.0 1982 91.2270 1071 2528 1 chr6B.!!$R1 1457
6 TraesCS6D01G037300 chr6B 27121794 27125016 3222 True 965.5 2868 86.2665 421 3523 4 chr6B.!!$R2 3102
7 TraesCS6D01G037300 chr6A 16098191 16100740 2549 True 1995.5 3651 97.4500 427 2904 2 chr6A.!!$R4 2477
8 TraesCS6D01G037300 chr6A 16399168 16400916 1748 True 1808.0 1808 85.4050 786 2530 1 chr6A.!!$R2 1744
9 TraesCS6D01G037300 chr6A 15951381 15953608 2227 True 1569.0 2990 88.2735 805 2904 2 chr6A.!!$R3 2099
10 TraesCS6D01G037300 chr6A 16088220 16088839 619 True 1022.0 1022 96.3200 2903 3527 1 chr6A.!!$R1 624

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
150 151 0.040157 CCACTGCATGTCGTGTTTGG 60.040 55.000 13.12 0.00 0.00 3.28 F
245 246 0.100503 AGAATTTAATGCACCGCGCC 59.899 50.000 0.00 0.00 41.33 6.53 F
250 251 0.391927 TTAATGCACCGCGCCTAAGT 60.392 50.000 0.00 0.00 41.33 2.24 F
527 530 0.613012 GGCAGCTCCATGGAAAACCT 60.613 55.000 17.00 6.96 34.01 3.50 F
2076 2200 1.492176 CTTCCCACCTCCATAGCATGT 59.508 52.381 0.00 0.00 0.00 3.21 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1257 1381 0.324614 TTGAGAAGATGGCGCCAGAA 59.675 50.000 35.36 12.12 0.00 3.02 R
1323 1447 1.005097 AGCATGATGAGGAAAGCACCA 59.995 47.619 0.00 0.00 0.00 4.17 R
2094 2218 1.888018 GCATGCAGCCTCAACACAT 59.112 52.632 14.21 0.00 37.23 3.21 R
2169 2293 4.415150 CCTGCACCGGTCATGCCT 62.415 66.667 2.59 0.00 42.69 4.75 R
3014 3314 1.203523 GCCCAGGCTATAGATCACTCG 59.796 57.143 3.21 0.00 38.26 4.18 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
21 22 2.490115 GCTGATCATAGTACTCCCTCCG 59.510 54.545 0.00 0.00 0.00 4.63
22 23 3.757270 CTGATCATAGTACTCCCTCCGT 58.243 50.000 0.00 0.00 0.00 4.69
23 24 3.752665 TGATCATAGTACTCCCTCCGTC 58.247 50.000 0.00 0.00 0.00 4.79
24 25 3.394940 TGATCATAGTACTCCCTCCGTCT 59.605 47.826 0.00 0.00 0.00 4.18
25 26 4.596212 TGATCATAGTACTCCCTCCGTCTA 59.404 45.833 0.00 0.00 0.00 2.59
26 27 4.620589 TCATAGTACTCCCTCCGTCTAG 57.379 50.000 0.00 0.00 0.00 2.43
27 28 3.327172 TCATAGTACTCCCTCCGTCTAGG 59.673 52.174 0.00 0.00 42.97 3.02
28 29 1.594129 AGTACTCCCTCCGTCTAGGT 58.406 55.000 0.00 0.00 41.99 3.08
29 30 1.212441 AGTACTCCCTCCGTCTAGGTG 59.788 57.143 0.00 0.00 41.99 4.00
30 31 1.211457 GTACTCCCTCCGTCTAGGTGA 59.789 57.143 0.00 0.00 41.99 4.02
31 32 0.256464 ACTCCCTCCGTCTAGGTGAG 59.744 60.000 0.00 0.00 41.99 3.51
32 33 0.256464 CTCCCTCCGTCTAGGTGAGT 59.744 60.000 0.00 0.00 41.99 3.41
33 34 1.489649 CTCCCTCCGTCTAGGTGAGTA 59.510 57.143 0.00 0.00 41.99 2.59
34 35 1.918262 TCCCTCCGTCTAGGTGAGTAA 59.082 52.381 0.00 0.00 41.99 2.24
35 36 2.092538 TCCCTCCGTCTAGGTGAGTAAG 60.093 54.545 0.00 0.00 41.99 2.34
36 37 2.356947 CCCTCCGTCTAGGTGAGTAAGT 60.357 54.545 0.00 0.00 41.99 2.24
37 38 2.944349 CCTCCGTCTAGGTGAGTAAGTC 59.056 54.545 0.00 0.00 41.99 3.01
38 39 3.607741 CTCCGTCTAGGTGAGTAAGTCA 58.392 50.000 0.00 0.00 41.99 3.41
39 40 4.200874 CTCCGTCTAGGTGAGTAAGTCAT 58.799 47.826 0.00 0.00 41.99 3.06
40 41 4.197750 TCCGTCTAGGTGAGTAAGTCATC 58.802 47.826 0.00 0.00 41.99 2.92
42 43 4.641094 CCGTCTAGGTGAGTAAGTCATCTT 59.359 45.833 0.00 0.00 45.09 2.40
43 44 5.821470 CCGTCTAGGTGAGTAAGTCATCTTA 59.179 44.000 0.00 0.00 45.09 2.10
44 45 6.017770 CCGTCTAGGTGAGTAAGTCATCTTAG 60.018 46.154 0.00 0.00 45.09 2.18
45 46 6.017770 CGTCTAGGTGAGTAAGTCATCTTAGG 60.018 46.154 0.00 0.00 45.09 2.69
46 47 6.829811 GTCTAGGTGAGTAAGTCATCTTAGGT 59.170 42.308 0.00 0.00 45.09 3.08
47 48 7.339976 GTCTAGGTGAGTAAGTCATCTTAGGTT 59.660 40.741 0.00 0.00 45.09 3.50
48 49 6.287589 AGGTGAGTAAGTCATCTTAGGTTG 57.712 41.667 0.00 0.00 45.09 3.77
49 50 5.780793 AGGTGAGTAAGTCATCTTAGGTTGT 59.219 40.000 0.00 0.00 45.09 3.32
50 51 5.869888 GGTGAGTAAGTCATCTTAGGTTGTG 59.130 44.000 0.00 0.00 37.56 3.33
51 52 5.348997 GTGAGTAAGTCATCTTAGGTTGTGC 59.651 44.000 0.00 0.00 37.56 4.57
52 53 5.011635 TGAGTAAGTCATCTTAGGTTGTGCA 59.988 40.000 0.00 0.00 36.90 4.57
53 54 5.238583 AGTAAGTCATCTTAGGTTGTGCAC 58.761 41.667 10.75 10.75 36.90 4.57
54 55 4.392138 GTAAGTCATCTTAGGTTGTGCACC 59.608 45.833 15.69 0.00 39.22 5.01
55 56 4.858007 TAAGTCATCTTAGGTTGTGCACCG 60.858 45.833 15.69 0.00 41.54 4.94
56 57 7.249927 TAAGTCATCTTAGGTTGTGCACCGT 62.250 44.000 15.69 3.89 41.54 4.83
61 62 2.515057 GGTTGTGCACCGTGACCA 60.515 61.111 15.69 0.00 35.12 4.02
62 63 2.115911 GGTTGTGCACCGTGACCAA 61.116 57.895 15.69 1.00 35.12 3.67
63 64 1.355210 GTTGTGCACCGTGACCAAG 59.645 57.895 15.69 0.00 0.00 3.61
64 65 1.821759 TTGTGCACCGTGACCAAGG 60.822 57.895 15.69 0.44 35.99 3.61
65 66 2.110213 GTGCACCGTGACCAAGGA 59.890 61.111 5.22 0.00 33.97 3.36
66 67 1.961277 GTGCACCGTGACCAAGGAG 60.961 63.158 5.22 2.30 33.97 3.69
67 68 2.358737 GCACCGTGACCAAGGAGG 60.359 66.667 8.91 2.33 45.67 4.30
68 69 2.879233 GCACCGTGACCAAGGAGGA 61.879 63.158 8.91 0.00 41.22 3.71
69 70 1.293498 CACCGTGACCAAGGAGGAG 59.707 63.158 8.91 0.00 41.22 3.69
70 71 1.913762 ACCGTGACCAAGGAGGAGG 60.914 63.158 8.91 0.00 41.22 4.30
71 72 2.660064 CCGTGACCAAGGAGGAGGG 61.660 68.421 0.00 0.00 41.22 4.30
72 73 1.609501 CGTGACCAAGGAGGAGGGA 60.610 63.158 0.00 0.00 41.22 4.20
73 74 1.192146 CGTGACCAAGGAGGAGGGAA 61.192 60.000 0.00 0.00 41.22 3.97
74 75 1.064825 GTGACCAAGGAGGAGGGAAA 58.935 55.000 0.00 0.00 41.22 3.13
75 76 1.423921 GTGACCAAGGAGGAGGGAAAA 59.576 52.381 0.00 0.00 41.22 2.29
76 77 2.140224 TGACCAAGGAGGAGGGAAAAA 58.860 47.619 0.00 0.00 41.22 1.94
77 78 2.158519 TGACCAAGGAGGAGGGAAAAAC 60.159 50.000 0.00 0.00 41.22 2.43
78 79 1.202891 ACCAAGGAGGAGGGAAAAACG 60.203 52.381 0.00 0.00 41.22 3.60
79 80 1.073284 CCAAGGAGGAGGGAAAAACGA 59.927 52.381 0.00 0.00 41.22 3.85
80 81 2.427506 CAAGGAGGAGGGAAAAACGAG 58.572 52.381 0.00 0.00 0.00 4.18
81 82 2.025636 AGGAGGAGGGAAAAACGAGA 57.974 50.000 0.00 0.00 0.00 4.04
82 83 1.903183 AGGAGGAGGGAAAAACGAGAG 59.097 52.381 0.00 0.00 0.00 3.20
83 84 1.900486 GGAGGAGGGAAAAACGAGAGA 59.100 52.381 0.00 0.00 0.00 3.10
84 85 2.353903 GGAGGAGGGAAAAACGAGAGAC 60.354 54.545 0.00 0.00 0.00 3.36
85 86 1.624312 AGGAGGGAAAAACGAGAGACC 59.376 52.381 0.00 0.00 0.00 3.85
86 87 1.624312 GGAGGGAAAAACGAGAGACCT 59.376 52.381 0.00 0.00 0.00 3.85
87 88 2.038689 GGAGGGAAAAACGAGAGACCTT 59.961 50.000 0.00 0.00 0.00 3.50
88 89 3.260128 GGAGGGAAAAACGAGAGACCTTA 59.740 47.826 0.00 0.00 0.00 2.69
89 90 4.262765 GGAGGGAAAAACGAGAGACCTTAA 60.263 45.833 0.00 0.00 0.00 1.85
90 91 5.489249 GAGGGAAAAACGAGAGACCTTAAT 58.511 41.667 0.00 0.00 0.00 1.40
91 92 5.246307 AGGGAAAAACGAGAGACCTTAATG 58.754 41.667 0.00 0.00 0.00 1.90
92 93 5.001874 GGGAAAAACGAGAGACCTTAATGT 58.998 41.667 0.00 0.00 0.00 2.71
93 94 5.472478 GGGAAAAACGAGAGACCTTAATGTT 59.528 40.000 0.00 0.00 0.00 2.71
94 95 6.016527 GGGAAAAACGAGAGACCTTAATGTTT 60.017 38.462 0.00 0.00 0.00 2.83
95 96 7.173735 GGGAAAAACGAGAGACCTTAATGTTTA 59.826 37.037 0.00 0.00 0.00 2.01
96 97 8.727910 GGAAAAACGAGAGACCTTAATGTTTAT 58.272 33.333 0.00 0.00 0.00 1.40
99 100 9.893305 AAAACGAGAGACCTTAATGTTTATTTG 57.107 29.630 0.00 0.00 0.00 2.32
100 101 7.073342 ACGAGAGACCTTAATGTTTATTTGC 57.927 36.000 0.00 0.00 0.00 3.68
101 102 6.879458 ACGAGAGACCTTAATGTTTATTTGCT 59.121 34.615 0.00 0.00 0.00 3.91
102 103 8.038944 ACGAGAGACCTTAATGTTTATTTGCTA 58.961 33.333 0.00 0.00 0.00 3.49
103 104 8.879759 CGAGAGACCTTAATGTTTATTTGCTAA 58.120 33.333 0.00 0.00 0.00 3.09
137 138 3.855689 ATGCAATGAACTAACCACTGC 57.144 42.857 0.00 0.00 0.00 4.40
138 139 2.580962 TGCAATGAACTAACCACTGCA 58.419 42.857 0.00 0.00 36.06 4.41
139 140 3.156293 TGCAATGAACTAACCACTGCAT 58.844 40.909 0.00 0.00 33.65 3.96
140 141 3.057386 TGCAATGAACTAACCACTGCATG 60.057 43.478 0.00 0.00 33.65 4.06
141 142 3.057315 GCAATGAACTAACCACTGCATGT 60.057 43.478 0.00 0.00 0.00 3.21
142 143 4.726416 CAATGAACTAACCACTGCATGTC 58.274 43.478 0.00 0.00 0.00 3.06
143 144 2.412870 TGAACTAACCACTGCATGTCG 58.587 47.619 0.00 0.00 0.00 4.35
144 145 2.224185 TGAACTAACCACTGCATGTCGT 60.224 45.455 0.00 0.00 0.00 4.34
145 146 1.795768 ACTAACCACTGCATGTCGTG 58.204 50.000 8.87 8.87 0.00 4.35
146 147 1.070134 ACTAACCACTGCATGTCGTGT 59.930 47.619 13.12 2.00 0.00 4.49
147 148 2.143122 CTAACCACTGCATGTCGTGTT 58.857 47.619 13.12 10.39 0.00 3.32
148 149 1.388547 AACCACTGCATGTCGTGTTT 58.611 45.000 13.12 5.09 0.00 2.83
149 150 0.662619 ACCACTGCATGTCGTGTTTG 59.337 50.000 13.12 3.87 0.00 2.93
150 151 0.040157 CCACTGCATGTCGTGTTTGG 60.040 55.000 13.12 0.00 0.00 3.28
151 152 0.662619 CACTGCATGTCGTGTTTGGT 59.337 50.000 7.95 0.00 0.00 3.67
152 153 1.870402 CACTGCATGTCGTGTTTGGTA 59.130 47.619 7.95 0.00 0.00 3.25
153 154 2.096268 CACTGCATGTCGTGTTTGGTAG 60.096 50.000 7.95 0.00 0.00 3.18
154 155 2.143122 CTGCATGTCGTGTTTGGTAGT 58.857 47.619 0.00 0.00 0.00 2.73
155 156 2.139917 TGCATGTCGTGTTTGGTAGTC 58.860 47.619 0.00 0.00 0.00 2.59
156 157 2.224185 TGCATGTCGTGTTTGGTAGTCT 60.224 45.455 0.00 0.00 0.00 3.24
157 158 2.412089 GCATGTCGTGTTTGGTAGTCTC 59.588 50.000 0.00 0.00 0.00 3.36
158 159 3.649073 CATGTCGTGTTTGGTAGTCTCA 58.351 45.455 0.00 0.00 0.00 3.27
159 160 3.804786 TGTCGTGTTTGGTAGTCTCAA 57.195 42.857 0.00 0.00 0.00 3.02
160 161 4.330944 TGTCGTGTTTGGTAGTCTCAAT 57.669 40.909 0.00 0.00 0.00 2.57
161 162 4.699637 TGTCGTGTTTGGTAGTCTCAATT 58.300 39.130 0.00 0.00 0.00 2.32
162 163 4.748102 TGTCGTGTTTGGTAGTCTCAATTC 59.252 41.667 0.00 0.00 0.00 2.17
163 164 4.748102 GTCGTGTTTGGTAGTCTCAATTCA 59.252 41.667 0.00 0.00 0.00 2.57
164 165 5.408604 GTCGTGTTTGGTAGTCTCAATTCAT 59.591 40.000 0.00 0.00 0.00 2.57
165 166 5.995282 TCGTGTTTGGTAGTCTCAATTCATT 59.005 36.000 0.00 0.00 0.00 2.57
166 167 7.117236 GTCGTGTTTGGTAGTCTCAATTCATTA 59.883 37.037 0.00 0.00 0.00 1.90
167 168 7.658167 TCGTGTTTGGTAGTCTCAATTCATTAA 59.342 33.333 0.00 0.00 0.00 1.40
168 169 8.286800 CGTGTTTGGTAGTCTCAATTCATTAAA 58.713 33.333 0.00 0.00 0.00 1.52
169 170 9.959749 GTGTTTGGTAGTCTCAATTCATTAAAA 57.040 29.630 0.00 0.00 0.00 1.52
171 172 9.129209 GTTTGGTAGTCTCAATTCATTAAAAGC 57.871 33.333 0.00 0.00 0.00 3.51
172 173 7.994425 TGGTAGTCTCAATTCATTAAAAGCA 57.006 32.000 0.00 0.00 0.00 3.91
173 174 8.579850 TGGTAGTCTCAATTCATTAAAAGCAT 57.420 30.769 0.00 0.00 0.00 3.79
174 175 8.461222 TGGTAGTCTCAATTCATTAAAAGCATG 58.539 33.333 0.00 0.00 0.00 4.06
175 176 7.433425 GGTAGTCTCAATTCATTAAAAGCATGC 59.567 37.037 10.51 10.51 0.00 4.06
176 177 6.927416 AGTCTCAATTCATTAAAAGCATGCA 58.073 32.000 21.98 0.00 0.00 3.96
177 178 6.810182 AGTCTCAATTCATTAAAAGCATGCAC 59.190 34.615 21.98 2.48 0.00 4.57
178 179 6.587226 GTCTCAATTCATTAAAAGCATGCACA 59.413 34.615 21.98 0.00 0.00 4.57
179 180 6.587226 TCTCAATTCATTAAAAGCATGCACAC 59.413 34.615 21.98 0.00 0.00 3.82
180 181 5.638657 TCAATTCATTAAAAGCATGCACACC 59.361 36.000 21.98 0.00 0.00 4.16
181 182 3.591196 TCATTAAAAGCATGCACACCC 57.409 42.857 21.98 0.00 0.00 4.61
182 183 2.233431 TCATTAAAAGCATGCACACCCC 59.767 45.455 21.98 0.00 0.00 4.95
183 184 2.008242 TTAAAAGCATGCACACCCCT 57.992 45.000 21.98 0.00 0.00 4.79
184 185 1.544724 TAAAAGCATGCACACCCCTC 58.455 50.000 21.98 0.00 0.00 4.30
185 186 0.469705 AAAAGCATGCACACCCCTCA 60.470 50.000 21.98 0.00 0.00 3.86
186 187 0.251922 AAAGCATGCACACCCCTCAT 60.252 50.000 21.98 0.00 0.00 2.90
187 188 0.682209 AAGCATGCACACCCCTCATC 60.682 55.000 21.98 0.00 0.00 2.92
188 189 1.077212 GCATGCACACCCCTCATCT 60.077 57.895 14.21 0.00 0.00 2.90
189 190 1.099879 GCATGCACACCCCTCATCTC 61.100 60.000 14.21 0.00 0.00 2.75
190 191 0.545171 CATGCACACCCCTCATCTCT 59.455 55.000 0.00 0.00 0.00 3.10
191 192 1.064906 CATGCACACCCCTCATCTCTT 60.065 52.381 0.00 0.00 0.00 2.85
192 193 1.951209 TGCACACCCCTCATCTCTTA 58.049 50.000 0.00 0.00 0.00 2.10
193 194 2.481441 TGCACACCCCTCATCTCTTAT 58.519 47.619 0.00 0.00 0.00 1.73
194 195 2.846206 TGCACACCCCTCATCTCTTATT 59.154 45.455 0.00 0.00 0.00 1.40
195 196 3.209410 GCACACCCCTCATCTCTTATTG 58.791 50.000 0.00 0.00 0.00 1.90
196 197 3.813443 CACACCCCTCATCTCTTATTGG 58.187 50.000 0.00 0.00 0.00 3.16
197 198 3.200825 CACACCCCTCATCTCTTATTGGT 59.799 47.826 0.00 0.00 0.00 3.67
198 199 3.852578 ACACCCCTCATCTCTTATTGGTT 59.147 43.478 0.00 0.00 0.00 3.67
199 200 4.202441 CACCCCTCATCTCTTATTGGTTG 58.798 47.826 0.00 0.00 0.00 3.77
200 201 4.080356 CACCCCTCATCTCTTATTGGTTGA 60.080 45.833 0.00 0.00 0.00 3.18
201 202 4.728860 ACCCCTCATCTCTTATTGGTTGAT 59.271 41.667 0.00 0.00 0.00 2.57
202 203 5.911178 ACCCCTCATCTCTTATTGGTTGATA 59.089 40.000 0.00 0.00 0.00 2.15
203 204 6.564152 ACCCCTCATCTCTTATTGGTTGATAT 59.436 38.462 0.00 0.00 0.00 1.63
204 205 6.883217 CCCCTCATCTCTTATTGGTTGATATG 59.117 42.308 0.00 0.00 0.00 1.78
205 206 7.456725 CCCTCATCTCTTATTGGTTGATATGT 58.543 38.462 0.00 0.00 0.00 2.29
206 207 7.605691 CCCTCATCTCTTATTGGTTGATATGTC 59.394 40.741 0.00 0.00 0.00 3.06
207 208 8.152898 CCTCATCTCTTATTGGTTGATATGTCA 58.847 37.037 0.00 0.00 0.00 3.58
208 209 9.551734 CTCATCTCTTATTGGTTGATATGTCAA 57.448 33.333 0.03 0.03 41.89 3.18
220 221 9.906660 TGGTTGATATGTCAATAAACAAGAAAC 57.093 29.630 8.23 0.00 45.46 2.78
221 222 9.061610 GGTTGATATGTCAATAAACAAGAAACG 57.938 33.333 8.23 0.00 45.46 3.60
222 223 9.820229 GTTGATATGTCAATAAACAAGAAACGA 57.180 29.630 8.23 0.00 45.46 3.85
224 225 8.664798 TGATATGTCAATAAACAAGAAACGAGG 58.335 33.333 0.00 0.00 31.81 4.63
225 226 6.877611 ATGTCAATAAACAAGAAACGAGGT 57.122 33.333 0.00 0.00 31.81 3.85
226 227 7.972832 ATGTCAATAAACAAGAAACGAGGTA 57.027 32.000 0.00 0.00 31.81 3.08
227 228 7.416154 TGTCAATAAACAAGAAACGAGGTAG 57.584 36.000 0.00 0.00 0.00 3.18
228 229 7.211573 TGTCAATAAACAAGAAACGAGGTAGA 58.788 34.615 0.00 0.00 0.00 2.59
229 230 7.711772 TGTCAATAAACAAGAAACGAGGTAGAA 59.288 33.333 0.00 0.00 0.00 2.10
230 231 8.718734 GTCAATAAACAAGAAACGAGGTAGAAT 58.281 33.333 0.00 0.00 0.00 2.40
231 232 9.280174 TCAATAAACAAGAAACGAGGTAGAATT 57.720 29.630 0.00 0.00 0.00 2.17
232 233 9.893305 CAATAAACAAGAAACGAGGTAGAATTT 57.107 29.630 0.00 0.00 0.00 1.82
236 237 9.893305 AAACAAGAAACGAGGTAGAATTTAATG 57.107 29.630 0.00 0.00 0.00 1.90
237 238 7.527457 ACAAGAAACGAGGTAGAATTTAATGC 58.473 34.615 0.00 0.00 0.00 3.56
238 239 7.174253 ACAAGAAACGAGGTAGAATTTAATGCA 59.826 33.333 0.00 0.00 0.00 3.96
239 240 7.073342 AGAAACGAGGTAGAATTTAATGCAC 57.927 36.000 0.00 0.00 0.00 4.57
240 241 5.813080 AACGAGGTAGAATTTAATGCACC 57.187 39.130 0.00 0.00 0.00 5.01
241 242 3.869246 ACGAGGTAGAATTTAATGCACCG 59.131 43.478 0.00 0.00 0.00 4.94
242 243 3.303132 CGAGGTAGAATTTAATGCACCGC 60.303 47.826 0.00 0.00 0.00 5.68
243 244 2.612212 AGGTAGAATTTAATGCACCGCG 59.388 45.455 0.00 0.00 0.00 6.46
244 245 2.372350 GTAGAATTTAATGCACCGCGC 58.628 47.619 0.00 0.00 42.89 6.86
245 246 0.100503 AGAATTTAATGCACCGCGCC 59.899 50.000 0.00 0.00 41.33 6.53
246 247 0.100503 GAATTTAATGCACCGCGCCT 59.899 50.000 0.00 0.00 41.33 5.52
247 248 1.332375 GAATTTAATGCACCGCGCCTA 59.668 47.619 0.00 0.00 41.33 3.93
248 249 1.384525 ATTTAATGCACCGCGCCTAA 58.615 45.000 0.00 0.00 41.33 2.69
249 250 0.730265 TTTAATGCACCGCGCCTAAG 59.270 50.000 0.00 0.00 41.33 2.18
250 251 0.391927 TTAATGCACCGCGCCTAAGT 60.392 50.000 0.00 0.00 41.33 2.24
251 252 1.087202 TAATGCACCGCGCCTAAGTG 61.087 55.000 0.00 4.02 41.33 3.16
252 253 3.605749 ATGCACCGCGCCTAAGTGT 62.606 57.895 12.83 0.00 41.33 3.55
253 254 3.047877 GCACCGCGCCTAAGTGTT 61.048 61.111 12.83 0.00 33.96 3.32
254 255 2.613506 GCACCGCGCCTAAGTGTTT 61.614 57.895 12.83 0.00 33.96 2.83
255 256 1.946267 CACCGCGCCTAAGTGTTTT 59.054 52.632 0.00 0.00 0.00 2.43
256 257 1.149987 CACCGCGCCTAAGTGTTTTA 58.850 50.000 0.00 0.00 0.00 1.52
257 258 1.127951 CACCGCGCCTAAGTGTTTTAG 59.872 52.381 0.00 0.00 0.00 1.85
258 259 0.725117 CCGCGCCTAAGTGTTTTAGG 59.275 55.000 0.00 8.30 43.38 2.69
259 260 1.673626 CCGCGCCTAAGTGTTTTAGGA 60.674 52.381 15.32 0.00 43.24 2.94
260 261 2.277084 CGCGCCTAAGTGTTTTAGGAT 58.723 47.619 15.32 0.00 43.24 3.24
261 262 2.676342 CGCGCCTAAGTGTTTTAGGATT 59.324 45.455 15.32 0.00 43.24 3.01
262 263 3.866910 CGCGCCTAAGTGTTTTAGGATTA 59.133 43.478 15.32 0.00 43.24 1.75
263 264 4.510340 CGCGCCTAAGTGTTTTAGGATTAT 59.490 41.667 15.32 0.00 43.24 1.28
264 265 5.007332 CGCGCCTAAGTGTTTTAGGATTATT 59.993 40.000 15.32 0.00 43.24 1.40
265 266 6.457799 CGCGCCTAAGTGTTTTAGGATTATTT 60.458 38.462 15.32 0.00 43.24 1.40
266 267 6.691388 GCGCCTAAGTGTTTTAGGATTATTTG 59.309 38.462 15.32 0.00 43.24 2.32
267 268 7.193595 CGCCTAAGTGTTTTAGGATTATTTGG 58.806 38.462 15.32 0.00 43.24 3.28
268 269 7.148137 CGCCTAAGTGTTTTAGGATTATTTGGT 60.148 37.037 15.32 0.00 43.24 3.67
269 270 8.528643 GCCTAAGTGTTTTAGGATTATTTGGTT 58.471 33.333 15.32 0.00 43.24 3.67
297 298 4.966965 AGATGACTTACACACCTAGACG 57.033 45.455 0.00 0.00 0.00 4.18
298 299 3.695060 AGATGACTTACACACCTAGACGG 59.305 47.826 0.00 0.00 39.35 4.79
299 300 3.144657 TGACTTACACACCTAGACGGA 57.855 47.619 0.00 0.00 36.31 4.69
300 301 3.079578 TGACTTACACACCTAGACGGAG 58.920 50.000 0.00 0.00 36.31 4.63
301 302 2.422832 GACTTACACACCTAGACGGAGG 59.577 54.545 0.00 0.00 42.89 4.30
302 303 1.749634 CTTACACACCTAGACGGAGGG 59.250 57.143 5.42 0.00 41.36 4.30
311 312 2.574450 CTAGACGGAGGGAGTAGGAAC 58.426 57.143 0.00 0.00 0.00 3.62
394 396 7.224167 CACGTCGCCTAGTATCTATACATATGA 59.776 40.741 10.38 0.00 35.74 2.15
395 397 7.932491 ACGTCGCCTAGTATCTATACATATGAT 59.068 37.037 10.38 1.47 35.74 2.45
398 400 9.628500 TCGCCTAGTATCTATACATATGATGTT 57.372 33.333 10.38 0.00 41.63 2.71
474 476 6.650427 ATGCACATACCTAAAGATACGAGA 57.350 37.500 0.00 0.00 0.00 4.04
475 477 6.459670 TGCACATACCTAAAGATACGAGAA 57.540 37.500 0.00 0.00 0.00 2.87
504 507 4.825422 TCCAATTGAAAACAAGTTGTGCA 58.175 34.783 9.79 5.86 0.00 4.57
509 512 3.958704 TGAAAACAAGTTGTGCATACGG 58.041 40.909 9.79 0.00 0.00 4.02
527 530 0.613012 GGCAGCTCCATGGAAAACCT 60.613 55.000 17.00 6.96 34.01 3.50
529 532 1.620323 GCAGCTCCATGGAAAACCTTT 59.380 47.619 17.00 0.00 0.00 3.11
573 581 7.167468 GTGCGAACTTGAGAATTTACATGTTTT 59.833 33.333 2.30 0.00 35.57 2.43
627 734 7.612633 ACTTTGTTTTAGAACCTGTTAGAACCA 59.387 33.333 0.00 0.00 34.80 3.67
634 741 8.786826 TTAGAACCTGTTAGAACCAATACATG 57.213 34.615 0.00 0.00 0.00 3.21
748 864 4.516698 AGGTCAAACATGTGACTGATGTTC 59.483 41.667 14.16 1.32 45.98 3.18
801 920 2.548480 GGACAAAAGGAAACGTCAGGAG 59.452 50.000 0.00 0.00 0.00 3.69
803 922 3.467803 ACAAAAGGAAACGTCAGGAGAG 58.532 45.455 0.00 0.00 0.00 3.20
1257 1381 4.021925 GCTGGGGTCGCCTCTGTT 62.022 66.667 7.55 0.00 0.00 3.16
2076 2200 1.492176 CTTCCCACCTCCATAGCATGT 59.508 52.381 0.00 0.00 0.00 3.21
2094 2218 4.283467 GCATGTATGGTCCTGTACTCCATA 59.717 45.833 12.19 12.19 41.45 2.74
2169 2293 3.997400 CTCCCTCGGGCTCGTCTCA 62.997 68.421 5.57 0.00 37.69 3.27
2571 2696 3.677596 TCAATGTATACCATGCGCGTATG 59.322 43.478 27.54 27.54 32.82 2.39
2805 3053 5.996513 AGATGAATATGAGAGCATTGGTCAC 59.003 40.000 17.46 11.87 35.94 3.67
3014 3314 7.393841 AGCGTGAGGAGTACTATAATATTCC 57.606 40.000 0.00 0.00 32.42 3.01
3193 3499 4.122776 CCTTTAGATACATTCAGCACGCT 58.877 43.478 0.00 0.00 0.00 5.07
3198 3504 5.207110 AGATACATTCAGCACGCTAAGAT 57.793 39.130 0.00 0.00 0.00 2.40
3318 3624 3.770666 CAGTCGCTCCGAGATTCTTAAA 58.229 45.455 0.00 0.00 36.23 1.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.490115 CGGAGGGAGTACTATGATCAGC 59.510 54.545 0.09 0.00 0.00 4.26
1 2 3.754323 GACGGAGGGAGTACTATGATCAG 59.246 52.174 0.09 0.00 0.00 2.90
2 3 3.394940 AGACGGAGGGAGTACTATGATCA 59.605 47.826 0.00 0.00 0.00 2.92
3 4 4.023726 AGACGGAGGGAGTACTATGATC 57.976 50.000 0.00 0.00 0.00 2.92
4 5 4.019141 CCTAGACGGAGGGAGTACTATGAT 60.019 50.000 0.00 0.00 32.39 2.45
5 6 3.327172 CCTAGACGGAGGGAGTACTATGA 59.673 52.174 0.00 0.00 32.39 2.15
6 7 3.072768 ACCTAGACGGAGGGAGTACTATG 59.927 52.174 0.00 0.00 41.36 2.23
7 8 3.072768 CACCTAGACGGAGGGAGTACTAT 59.927 52.174 0.00 0.00 41.36 2.12
8 9 2.437281 CACCTAGACGGAGGGAGTACTA 59.563 54.545 0.00 0.00 41.36 1.82
9 10 1.212441 CACCTAGACGGAGGGAGTACT 59.788 57.143 0.00 0.00 41.36 2.73
10 11 1.211457 TCACCTAGACGGAGGGAGTAC 59.789 57.143 5.42 0.00 41.36 2.73
11 12 1.489649 CTCACCTAGACGGAGGGAGTA 59.510 57.143 5.42 0.00 41.36 2.59
12 13 0.256464 CTCACCTAGACGGAGGGAGT 59.744 60.000 5.42 0.00 41.36 3.85
13 14 0.256464 ACTCACCTAGACGGAGGGAG 59.744 60.000 12.80 12.80 41.36 4.30
14 15 1.588239 TACTCACCTAGACGGAGGGA 58.412 55.000 5.42 0.16 41.36 4.20
15 16 2.299521 CTTACTCACCTAGACGGAGGG 58.700 57.143 5.42 0.00 41.36 4.30
16 17 2.944349 GACTTACTCACCTAGACGGAGG 59.056 54.545 0.00 0.00 42.89 4.30
17 18 3.607741 TGACTTACTCACCTAGACGGAG 58.392 50.000 0.00 0.00 36.31 4.63
18 19 3.708403 TGACTTACTCACCTAGACGGA 57.292 47.619 0.00 0.00 36.31 4.69
19 20 4.200874 AGATGACTTACTCACCTAGACGG 58.799 47.826 0.00 0.00 39.35 4.79
20 21 5.821516 AAGATGACTTACTCACCTAGACG 57.178 43.478 0.00 0.00 34.28 4.18
21 22 6.829811 ACCTAAGATGACTTACTCACCTAGAC 59.170 42.308 0.00 0.00 37.53 2.59
22 23 6.971340 ACCTAAGATGACTTACTCACCTAGA 58.029 40.000 0.00 0.00 37.53 2.43
23 24 7.122948 ACAACCTAAGATGACTTACTCACCTAG 59.877 40.741 0.00 0.00 37.53 3.02
24 25 6.952358 ACAACCTAAGATGACTTACTCACCTA 59.048 38.462 0.00 0.00 37.53 3.08
25 26 5.780793 ACAACCTAAGATGACTTACTCACCT 59.219 40.000 0.00 0.00 37.53 4.00
26 27 5.869888 CACAACCTAAGATGACTTACTCACC 59.130 44.000 0.00 0.00 37.53 4.02
27 28 5.348997 GCACAACCTAAGATGACTTACTCAC 59.651 44.000 0.00 0.00 37.53 3.51
28 29 5.011635 TGCACAACCTAAGATGACTTACTCA 59.988 40.000 0.00 0.00 37.53 3.41
29 30 5.348997 GTGCACAACCTAAGATGACTTACTC 59.651 44.000 13.17 0.00 37.53 2.59
30 31 5.238583 GTGCACAACCTAAGATGACTTACT 58.761 41.667 13.17 0.00 37.53 2.24
31 32 4.392138 GGTGCACAACCTAAGATGACTTAC 59.608 45.833 20.43 0.00 46.55 2.34
32 33 4.575885 GGTGCACAACCTAAGATGACTTA 58.424 43.478 20.43 0.00 46.55 2.24
33 34 3.412386 GGTGCACAACCTAAGATGACTT 58.588 45.455 20.43 0.00 46.55 3.01
34 35 3.059352 GGTGCACAACCTAAGATGACT 57.941 47.619 20.43 0.00 46.55 3.41
44 45 2.058829 CTTGGTCACGGTGCACAACC 62.059 60.000 20.43 18.91 46.60 3.77
45 46 1.355210 CTTGGTCACGGTGCACAAC 59.645 57.895 20.43 10.47 0.00 3.32
46 47 1.821759 CCTTGGTCACGGTGCACAA 60.822 57.895 20.43 9.76 0.00 3.33
47 48 2.203139 CCTTGGTCACGGTGCACA 60.203 61.111 20.43 1.81 0.00 4.57
48 49 1.961277 CTCCTTGGTCACGGTGCAC 60.961 63.158 8.80 8.80 0.00 4.57
49 50 2.425592 CTCCTTGGTCACGGTGCA 59.574 61.111 2.51 0.00 0.00 4.57
50 51 2.358737 CCTCCTTGGTCACGGTGC 60.359 66.667 2.51 0.00 0.00 5.01
51 52 1.293498 CTCCTCCTTGGTCACGGTG 59.707 63.158 0.56 0.56 37.07 4.94
52 53 1.913762 CCTCCTCCTTGGTCACGGT 60.914 63.158 0.00 0.00 37.07 4.83
53 54 2.660064 CCCTCCTCCTTGGTCACGG 61.660 68.421 0.00 0.00 37.07 4.94
54 55 1.192146 TTCCCTCCTCCTTGGTCACG 61.192 60.000 0.00 0.00 37.07 4.35
55 56 1.064825 TTTCCCTCCTCCTTGGTCAC 58.935 55.000 0.00 0.00 37.07 3.67
56 57 1.827792 TTTTCCCTCCTCCTTGGTCA 58.172 50.000 0.00 0.00 37.07 4.02
57 58 2.515854 GTTTTTCCCTCCTCCTTGGTC 58.484 52.381 0.00 0.00 37.07 4.02
58 59 1.202891 CGTTTTTCCCTCCTCCTTGGT 60.203 52.381 0.00 0.00 37.07 3.67
59 60 1.073284 TCGTTTTTCCCTCCTCCTTGG 59.927 52.381 0.00 0.00 37.10 3.61
60 61 2.038557 TCTCGTTTTTCCCTCCTCCTTG 59.961 50.000 0.00 0.00 0.00 3.61
61 62 2.303311 CTCTCGTTTTTCCCTCCTCCTT 59.697 50.000 0.00 0.00 0.00 3.36
62 63 1.903183 CTCTCGTTTTTCCCTCCTCCT 59.097 52.381 0.00 0.00 0.00 3.69
63 64 1.900486 TCTCTCGTTTTTCCCTCCTCC 59.100 52.381 0.00 0.00 0.00 4.30
64 65 2.353903 GGTCTCTCGTTTTTCCCTCCTC 60.354 54.545 0.00 0.00 0.00 3.71
65 66 1.624312 GGTCTCTCGTTTTTCCCTCCT 59.376 52.381 0.00 0.00 0.00 3.69
66 67 1.624312 AGGTCTCTCGTTTTTCCCTCC 59.376 52.381 0.00 0.00 0.00 4.30
67 68 3.404224 AAGGTCTCTCGTTTTTCCCTC 57.596 47.619 0.00 0.00 0.00 4.30
68 69 4.968971 TTAAGGTCTCTCGTTTTTCCCT 57.031 40.909 0.00 0.00 0.00 4.20
69 70 5.001874 ACATTAAGGTCTCTCGTTTTTCCC 58.998 41.667 0.00 0.00 0.00 3.97
70 71 6.555812 AACATTAAGGTCTCTCGTTTTTCC 57.444 37.500 0.00 0.00 0.00 3.13
73 74 9.893305 CAAATAAACATTAAGGTCTCTCGTTTT 57.107 29.630 0.00 0.00 0.00 2.43
74 75 8.021396 GCAAATAAACATTAAGGTCTCTCGTTT 58.979 33.333 0.00 0.00 0.00 3.60
75 76 7.390718 AGCAAATAAACATTAAGGTCTCTCGTT 59.609 33.333 0.00 0.00 0.00 3.85
76 77 6.879458 AGCAAATAAACATTAAGGTCTCTCGT 59.121 34.615 0.00 0.00 0.00 4.18
77 78 7.308782 AGCAAATAAACATTAAGGTCTCTCG 57.691 36.000 0.00 0.00 0.00 4.04
112 113 4.221262 AGTGGTTAGTTCATTGCATGCAAT 59.779 37.500 34.78 34.78 46.35 3.56
113 114 3.573538 AGTGGTTAGTTCATTGCATGCAA 59.426 39.130 33.57 33.57 40.47 4.08
114 115 3.057386 CAGTGGTTAGTTCATTGCATGCA 60.057 43.478 18.46 18.46 0.00 3.96
115 116 3.504863 CAGTGGTTAGTTCATTGCATGC 58.495 45.455 11.82 11.82 0.00 4.06
116 117 3.504863 GCAGTGGTTAGTTCATTGCATG 58.495 45.455 6.68 0.00 44.01 4.06
117 118 3.855689 GCAGTGGTTAGTTCATTGCAT 57.144 42.857 6.68 0.00 44.01 3.96
119 120 3.057315 ACATGCAGTGGTTAGTTCATTGC 60.057 43.478 0.00 4.92 44.56 3.56
120 121 4.669965 CGACATGCAGTGGTTAGTTCATTG 60.670 45.833 0.00 0.00 0.00 2.82
121 122 3.436704 CGACATGCAGTGGTTAGTTCATT 59.563 43.478 0.00 0.00 0.00 2.57
122 123 3.002791 CGACATGCAGTGGTTAGTTCAT 58.997 45.455 0.00 0.00 0.00 2.57
123 124 2.224185 ACGACATGCAGTGGTTAGTTCA 60.224 45.455 0.00 0.00 35.47 3.18
124 125 2.157668 CACGACATGCAGTGGTTAGTTC 59.842 50.000 11.93 0.00 37.03 3.01
125 126 2.143122 CACGACATGCAGTGGTTAGTT 58.857 47.619 11.93 0.00 37.03 2.24
126 127 1.070134 ACACGACATGCAGTGGTTAGT 59.930 47.619 20.60 1.96 42.25 2.24
127 128 1.795768 ACACGACATGCAGTGGTTAG 58.204 50.000 20.60 1.38 42.25 2.34
128 129 2.248280 AACACGACATGCAGTGGTTA 57.752 45.000 20.60 0.00 42.25 2.85
129 130 1.388547 AAACACGACATGCAGTGGTT 58.611 45.000 20.60 18.36 42.73 3.67
130 131 0.662619 CAAACACGACATGCAGTGGT 59.337 50.000 20.60 14.15 42.25 4.16
131 132 0.040157 CCAAACACGACATGCAGTGG 60.040 55.000 20.60 3.36 42.25 4.00
132 133 0.662619 ACCAAACACGACATGCAGTG 59.337 50.000 16.62 16.62 43.46 3.66
133 134 2.143122 CTACCAAACACGACATGCAGT 58.857 47.619 0.00 0.00 0.00 4.40
134 135 2.143122 ACTACCAAACACGACATGCAG 58.857 47.619 0.00 0.00 0.00 4.41
135 136 2.139917 GACTACCAAACACGACATGCA 58.860 47.619 0.00 0.00 0.00 3.96
136 137 2.412089 GAGACTACCAAACACGACATGC 59.588 50.000 0.00 0.00 0.00 4.06
137 138 3.649073 TGAGACTACCAAACACGACATG 58.351 45.455 0.00 0.00 0.00 3.21
138 139 4.330944 TTGAGACTACCAAACACGACAT 57.669 40.909 0.00 0.00 0.00 3.06
139 140 3.804786 TTGAGACTACCAAACACGACA 57.195 42.857 0.00 0.00 0.00 4.35
140 141 4.748102 TGAATTGAGACTACCAAACACGAC 59.252 41.667 0.00 0.00 0.00 4.34
141 142 4.951254 TGAATTGAGACTACCAAACACGA 58.049 39.130 0.00 0.00 0.00 4.35
142 143 5.862924 ATGAATTGAGACTACCAAACACG 57.137 39.130 0.00 0.00 0.00 4.49
143 144 9.959749 TTTTAATGAATTGAGACTACCAAACAC 57.040 29.630 0.00 0.00 0.00 3.32
145 146 9.129209 GCTTTTAATGAATTGAGACTACCAAAC 57.871 33.333 0.00 0.00 0.00 2.93
146 147 8.855110 TGCTTTTAATGAATTGAGACTACCAAA 58.145 29.630 0.00 0.00 0.00 3.28
147 148 8.402798 TGCTTTTAATGAATTGAGACTACCAA 57.597 30.769 0.00 0.00 0.00 3.67
148 149 7.994425 TGCTTTTAATGAATTGAGACTACCA 57.006 32.000 0.00 0.00 0.00 3.25
149 150 7.433425 GCATGCTTTTAATGAATTGAGACTACC 59.567 37.037 11.37 0.00 0.00 3.18
150 151 7.970061 TGCATGCTTTTAATGAATTGAGACTAC 59.030 33.333 20.33 0.00 0.00 2.73
151 152 7.970061 GTGCATGCTTTTAATGAATTGAGACTA 59.030 33.333 20.33 0.00 0.00 2.59
152 153 6.810182 GTGCATGCTTTTAATGAATTGAGACT 59.190 34.615 20.33 0.00 0.00 3.24
153 154 6.587226 TGTGCATGCTTTTAATGAATTGAGAC 59.413 34.615 20.33 2.56 0.00 3.36
154 155 6.587226 GTGTGCATGCTTTTAATGAATTGAGA 59.413 34.615 20.33 0.00 0.00 3.27
155 156 6.183360 GGTGTGCATGCTTTTAATGAATTGAG 60.183 38.462 20.33 0.00 0.00 3.02
156 157 5.638657 GGTGTGCATGCTTTTAATGAATTGA 59.361 36.000 20.33 0.00 0.00 2.57
157 158 5.163834 GGGTGTGCATGCTTTTAATGAATTG 60.164 40.000 20.33 0.00 0.00 2.32
158 159 4.937015 GGGTGTGCATGCTTTTAATGAATT 59.063 37.500 20.33 0.00 0.00 2.17
159 160 4.506758 GGGTGTGCATGCTTTTAATGAAT 58.493 39.130 20.33 0.00 0.00 2.57
160 161 3.306641 GGGGTGTGCATGCTTTTAATGAA 60.307 43.478 20.33 0.00 0.00 2.57
161 162 2.233431 GGGGTGTGCATGCTTTTAATGA 59.767 45.455 20.33 0.00 0.00 2.57
162 163 2.234414 AGGGGTGTGCATGCTTTTAATG 59.766 45.455 20.33 0.00 0.00 1.90
163 164 2.497273 GAGGGGTGTGCATGCTTTTAAT 59.503 45.455 20.33 0.00 0.00 1.40
164 165 1.892474 GAGGGGTGTGCATGCTTTTAA 59.108 47.619 20.33 0.00 0.00 1.52
165 166 1.202989 TGAGGGGTGTGCATGCTTTTA 60.203 47.619 20.33 0.00 0.00 1.52
166 167 0.469705 TGAGGGGTGTGCATGCTTTT 60.470 50.000 20.33 0.00 0.00 2.27
167 168 0.251922 ATGAGGGGTGTGCATGCTTT 60.252 50.000 20.33 0.00 0.00 3.51
168 169 0.682209 GATGAGGGGTGTGCATGCTT 60.682 55.000 20.33 0.00 0.00 3.91
169 170 1.077212 GATGAGGGGTGTGCATGCT 60.077 57.895 20.33 0.00 0.00 3.79
170 171 1.077212 AGATGAGGGGTGTGCATGC 60.077 57.895 11.82 11.82 0.00 4.06
171 172 0.545171 AGAGATGAGGGGTGTGCATG 59.455 55.000 0.00 0.00 0.00 4.06
172 173 1.293062 AAGAGATGAGGGGTGTGCAT 58.707 50.000 0.00 0.00 0.00 3.96
173 174 1.951209 TAAGAGATGAGGGGTGTGCA 58.049 50.000 0.00 0.00 0.00 4.57
174 175 3.209410 CAATAAGAGATGAGGGGTGTGC 58.791 50.000 0.00 0.00 0.00 4.57
175 176 3.200825 ACCAATAAGAGATGAGGGGTGTG 59.799 47.826 0.00 0.00 0.00 3.82
176 177 3.464828 ACCAATAAGAGATGAGGGGTGT 58.535 45.455 0.00 0.00 0.00 4.16
177 178 4.080356 TCAACCAATAAGAGATGAGGGGTG 60.080 45.833 0.00 0.00 32.98 4.61
178 179 4.111577 TCAACCAATAAGAGATGAGGGGT 58.888 43.478 0.00 0.00 0.00 4.95
179 180 4.778213 TCAACCAATAAGAGATGAGGGG 57.222 45.455 0.00 0.00 0.00 4.79
180 181 7.456725 ACATATCAACCAATAAGAGATGAGGG 58.543 38.462 0.00 0.00 35.26 4.30
181 182 8.152898 TGACATATCAACCAATAAGAGATGAGG 58.847 37.037 0.00 0.00 35.26 3.86
182 183 9.551734 TTGACATATCAACCAATAAGAGATGAG 57.448 33.333 0.00 0.00 40.01 2.90
198 199 8.664798 CCTCGTTTCTTGTTTATTGACATATCA 58.335 33.333 0.00 0.00 0.00 2.15
199 200 8.665685 ACCTCGTTTCTTGTTTATTGACATATC 58.334 33.333 0.00 0.00 0.00 1.63
200 201 8.561738 ACCTCGTTTCTTGTTTATTGACATAT 57.438 30.769 0.00 0.00 0.00 1.78
201 202 7.972832 ACCTCGTTTCTTGTTTATTGACATA 57.027 32.000 0.00 0.00 0.00 2.29
202 203 6.877611 ACCTCGTTTCTTGTTTATTGACAT 57.122 33.333 0.00 0.00 0.00 3.06
203 204 7.211573 TCTACCTCGTTTCTTGTTTATTGACA 58.788 34.615 0.00 0.00 0.00 3.58
204 205 7.647907 TCTACCTCGTTTCTTGTTTATTGAC 57.352 36.000 0.00 0.00 0.00 3.18
205 206 8.842358 ATTCTACCTCGTTTCTTGTTTATTGA 57.158 30.769 0.00 0.00 0.00 2.57
206 207 9.893305 AAATTCTACCTCGTTTCTTGTTTATTG 57.107 29.630 0.00 0.00 0.00 1.90
210 211 9.893305 CATTAAATTCTACCTCGTTTCTTGTTT 57.107 29.630 0.00 0.00 0.00 2.83
211 212 8.021396 GCATTAAATTCTACCTCGTTTCTTGTT 58.979 33.333 0.00 0.00 0.00 2.83
212 213 7.174253 TGCATTAAATTCTACCTCGTTTCTTGT 59.826 33.333 0.00 0.00 0.00 3.16
213 214 7.481798 GTGCATTAAATTCTACCTCGTTTCTTG 59.518 37.037 0.00 0.00 0.00 3.02
214 215 7.361799 GGTGCATTAAATTCTACCTCGTTTCTT 60.362 37.037 0.00 0.00 0.00 2.52
215 216 6.093633 GGTGCATTAAATTCTACCTCGTTTCT 59.906 38.462 0.00 0.00 0.00 2.52
216 217 6.255950 GGTGCATTAAATTCTACCTCGTTTC 58.744 40.000 0.00 0.00 0.00 2.78
217 218 5.163794 CGGTGCATTAAATTCTACCTCGTTT 60.164 40.000 0.00 0.00 0.00 3.60
218 219 4.331717 CGGTGCATTAAATTCTACCTCGTT 59.668 41.667 0.00 0.00 0.00 3.85
219 220 3.869246 CGGTGCATTAAATTCTACCTCGT 59.131 43.478 0.00 0.00 0.00 4.18
220 221 3.303132 GCGGTGCATTAAATTCTACCTCG 60.303 47.826 0.00 0.00 0.00 4.63
221 222 3.303132 CGCGGTGCATTAAATTCTACCTC 60.303 47.826 0.00 0.00 0.00 3.85
222 223 2.612212 CGCGGTGCATTAAATTCTACCT 59.388 45.455 0.00 0.00 0.00 3.08
223 224 2.853281 GCGCGGTGCATTAAATTCTACC 60.853 50.000 8.83 0.00 45.45 3.18
224 225 2.372350 GCGCGGTGCATTAAATTCTAC 58.628 47.619 8.83 0.00 45.45 2.59
225 226 2.748461 GCGCGGTGCATTAAATTCTA 57.252 45.000 8.83 0.00 45.45 2.10
226 227 3.622459 GCGCGGTGCATTAAATTCT 57.378 47.368 8.83 0.00 45.45 2.40
236 237 2.125202 AAAACACTTAGGCGCGGTGC 62.125 55.000 8.83 4.64 45.38 5.01
237 238 1.127951 CTAAAACACTTAGGCGCGGTG 59.872 52.381 8.83 9.75 37.05 4.94
238 239 1.435577 CTAAAACACTTAGGCGCGGT 58.564 50.000 8.83 0.00 0.00 5.68
239 240 0.725117 CCTAAAACACTTAGGCGCGG 59.275 55.000 8.83 0.00 35.60 6.46
240 241 1.717194 TCCTAAAACACTTAGGCGCG 58.283 50.000 0.00 0.00 40.97 6.86
241 242 6.373186 AATAATCCTAAAACACTTAGGCGC 57.627 37.500 0.00 0.00 40.97 6.53
242 243 7.148137 ACCAAATAATCCTAAAACACTTAGGCG 60.148 37.037 5.79 0.00 40.97 5.52
243 244 8.063200 ACCAAATAATCCTAAAACACTTAGGC 57.937 34.615 5.79 0.00 40.97 3.93
272 273 8.965480 CCGTCTAGGTGTGTAAGTCATCTTACA 61.965 44.444 14.25 14.25 46.55 2.41
273 274 6.677431 CCGTCTAGGTGTGTAAGTCATCTTAC 60.677 46.154 10.12 10.12 43.75 2.34
274 275 5.356190 CCGTCTAGGTGTGTAAGTCATCTTA 59.644 44.000 0.00 0.00 33.66 2.10
275 276 4.158025 CCGTCTAGGTGTGTAAGTCATCTT 59.842 45.833 0.00 0.00 35.02 2.40
276 277 3.695060 CCGTCTAGGTGTGTAAGTCATCT 59.305 47.826 0.00 0.00 34.51 2.90
277 278 3.693085 TCCGTCTAGGTGTGTAAGTCATC 59.307 47.826 0.00 0.00 41.99 2.92
278 279 3.693807 TCCGTCTAGGTGTGTAAGTCAT 58.306 45.455 0.00 0.00 41.99 3.06
279 280 3.079578 CTCCGTCTAGGTGTGTAAGTCA 58.920 50.000 0.00 0.00 41.99 3.41
280 281 2.422832 CCTCCGTCTAGGTGTGTAAGTC 59.577 54.545 0.00 0.00 41.99 3.01
281 282 2.444421 CCTCCGTCTAGGTGTGTAAGT 58.556 52.381 0.00 0.00 41.99 2.24
282 283 1.749634 CCCTCCGTCTAGGTGTGTAAG 59.250 57.143 0.00 0.00 41.99 2.34
283 284 1.355381 TCCCTCCGTCTAGGTGTGTAA 59.645 52.381 0.00 0.00 41.99 2.41
284 285 0.994247 TCCCTCCGTCTAGGTGTGTA 59.006 55.000 0.00 0.00 41.99 2.90
285 286 0.323542 CTCCCTCCGTCTAGGTGTGT 60.324 60.000 0.00 0.00 41.99 3.72
286 287 0.323542 ACTCCCTCCGTCTAGGTGTG 60.324 60.000 0.00 0.00 41.99 3.82
287 288 1.212441 CTACTCCCTCCGTCTAGGTGT 59.788 57.143 0.00 0.00 41.99 4.16
288 289 1.477195 CCTACTCCCTCCGTCTAGGTG 60.477 61.905 0.00 0.00 41.99 4.00
289 290 0.845337 CCTACTCCCTCCGTCTAGGT 59.155 60.000 0.00 0.00 41.99 3.08
290 291 1.138568 TCCTACTCCCTCCGTCTAGG 58.861 60.000 0.00 0.00 42.97 3.02
291 292 2.173143 AGTTCCTACTCCCTCCGTCTAG 59.827 54.545 0.00 0.00 0.00 2.43
292 293 2.203584 AGTTCCTACTCCCTCCGTCTA 58.796 52.381 0.00 0.00 0.00 2.59
293 294 1.001282 AGTTCCTACTCCCTCCGTCT 58.999 55.000 0.00 0.00 0.00 4.18
294 295 2.725221 TAGTTCCTACTCCCTCCGTC 57.275 55.000 0.00 0.00 35.78 4.79
295 296 2.512896 TGATAGTTCCTACTCCCTCCGT 59.487 50.000 0.00 0.00 35.78 4.69
296 297 3.225177 TGATAGTTCCTACTCCCTCCG 57.775 52.381 0.00 0.00 35.78 4.63
297 298 5.477637 GTGTATGATAGTTCCTACTCCCTCC 59.522 48.000 0.00 0.00 35.78 4.30
298 299 5.477637 GGTGTATGATAGTTCCTACTCCCTC 59.522 48.000 0.00 0.00 33.77 4.30
299 300 5.103215 TGGTGTATGATAGTTCCTACTCCCT 60.103 44.000 6.91 0.00 36.54 4.20
300 301 5.145564 TGGTGTATGATAGTTCCTACTCCC 58.854 45.833 6.91 0.00 36.54 4.30
301 302 5.279056 GCTGGTGTATGATAGTTCCTACTCC 60.279 48.000 0.00 0.00 37.24 3.85
302 303 5.302059 TGCTGGTGTATGATAGTTCCTACTC 59.698 44.000 0.00 0.00 35.78 2.59
398 400 3.491104 GCCGTGAACCCATGTTTTAACAA 60.491 43.478 0.00 0.00 43.03 2.83
409 411 1.195442 TGATACTGGCCGTGAACCCA 61.195 55.000 10.01 0.00 0.00 4.51
504 507 0.546122 TTTCCATGGAGCTGCCGTAT 59.454 50.000 15.53 0.00 40.66 3.06
509 512 1.260544 AAGGTTTTCCATGGAGCTGC 58.739 50.000 15.53 0.00 43.73 5.25
573 581 4.385478 TGATGGGAATGCCATGCTATAA 57.615 40.909 12.04 0.00 35.15 0.98
627 734 2.520069 TGCCGGTGAAAACCATGTATT 58.480 42.857 1.90 0.00 0.00 1.89
634 741 1.830847 AGGGTTGCCGGTGAAAACC 60.831 57.895 17.18 17.18 42.21 3.27
801 920 2.795175 TTGACACGTTCTCTGTCCTC 57.205 50.000 1.19 0.00 37.79 3.71
803 922 2.540101 CAGTTTGACACGTTCTCTGTCC 59.460 50.000 1.19 0.00 37.79 4.02
1257 1381 0.324614 TTGAGAAGATGGCGCCAGAA 59.675 50.000 35.36 12.12 0.00 3.02
1323 1447 1.005097 AGCATGATGAGGAAAGCACCA 59.995 47.619 0.00 0.00 0.00 4.17
2076 2200 5.464069 ACACATATGGAGTACAGGACCATA 58.536 41.667 17.02 17.02 46.21 2.74
2094 2218 1.888018 GCATGCAGCCTCAACACAT 59.112 52.632 14.21 0.00 37.23 3.21
2169 2293 4.415150 CCTGCACCGGTCATGCCT 62.415 66.667 2.59 0.00 42.69 4.75
3014 3314 1.203523 GCCCAGGCTATAGATCACTCG 59.796 57.143 3.21 0.00 38.26 4.18
3107 3411 3.096092 TGTTCTTTTGGCAAACCTGACT 58.904 40.909 13.10 0.00 36.63 3.41
3141 3447 3.268023 GGATCACCGACTCCTTTGATT 57.732 47.619 0.00 0.00 0.00 2.57
3142 3448 2.990066 GGATCACCGACTCCTTTGAT 57.010 50.000 0.00 0.00 0.00 2.57
3193 3499 4.537135 ACTCTCGCAGGTCAAAATCTTA 57.463 40.909 0.00 0.00 0.00 2.10
3198 3504 1.336517 CCGTACTCTCGCAGGTCAAAA 60.337 52.381 0.00 0.00 0.00 2.44
3318 3624 9.703892 CTGTAATATATAAAGAGCTGCTCAAGT 57.296 33.333 29.49 16.72 32.06 3.16


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

AutoCloner maintained by Alex Coulton.