Multiple sequence alignment - TraesCS3D01G279700

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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 TraesCS3D01G279700 chr3D 100.000 3407 0 0 1 3407 388314588 388311182 0.000000e+00 6292.0
1 TraesCS3D01G279700 chr3D 87.642 1497 165 11 963 2441 388325884 388324390 0.000000e+00 1722.0
2 TraesCS3D01G279700 chr3D 96.958 263 8 0 1 263 288675267 288675529 3.120000e-120 442.0
3 TraesCS3D01G279700 chr3D 96.538 260 9 0 1 260 83890872 83890613 6.750000e-117 431.0
4 TraesCS3D01G279700 chr3D 74.695 573 120 19 1741 2296 17342357 17341793 7.350000e-57 231.0
5 TraesCS3D01G279700 chr3D 73.022 771 160 37 1622 2362 17698915 17699667 9.510000e-56 228.0
6 TraesCS3D01G279700 chr3A 94.151 1915 73 16 728 2634 509251960 509250077 0.000000e+00 2880.0
7 TraesCS3D01G279700 chr3A 88.630 1460 155 7 992 2441 509377726 509376268 0.000000e+00 1766.0
8 TraesCS3D01G279700 chr3A 85.451 488 51 5 2757 3242 509249967 509249498 1.100000e-134 490.0
9 TraesCS3D01G279700 chr3A 92.245 245 9 8 319 561 509252365 509252129 4.210000e-89 339.0
10 TraesCS3D01G279700 chr3B 93.908 1740 78 14 861 2588 503968559 503970282 0.000000e+00 2601.0
11 TraesCS3D01G279700 chr3B 87.588 1418 143 11 992 2376 504962043 504960626 0.000000e+00 1613.0
12 TraesCS3D01G279700 chr3B 88.860 386 25 10 256 637 503967962 503968333 3.100000e-125 459.0
13 TraesCS3D01G279700 chr3B 86.957 92 5 3 728 819 503968462 503968546 2.800000e-16 97.1
14 TraesCS3D01G279700 chr1D 97.701 261 4 2 1 260 405382416 405382675 6.710000e-122 448.0
15 TraesCS3D01G279700 chr1D 96.241 266 10 0 1 266 405172004 405172269 1.450000e-118 436.0
16 TraesCS3D01G279700 chr5D 97.328 262 7 0 1 262 416871389 416871650 2.410000e-121 446.0
17 TraesCS3D01G279700 chr5D 95.911 269 11 0 1 269 487560149 487559881 1.450000e-118 436.0
18 TraesCS3D01G279700 chr7D 96.958 263 8 0 1 263 38661931 38661669 3.120000e-120 442.0
19 TraesCS3D01G279700 chr7D 76.951 820 129 34 2617 3407 631470849 631470061 2.450000e-111 412.0
20 TraesCS3D01G279700 chr2D 97.308 260 7 0 1 260 648643090 648643349 3.120000e-120 442.0
21 TraesCS3D01G279700 chr2D 80.182 439 66 10 2988 3407 317584179 317584615 3.300000e-80 309.0
22 TraesCS3D01G279700 chr2D 78.035 346 61 14 3073 3407 20355370 20355711 1.600000e-48 204.0
23 TraesCS3D01G279700 chrUn 96.198 263 10 0 1 263 68214706 68214444 6.750000e-117 431.0
24 TraesCS3D01G279700 chr6B 78.275 603 104 15 2810 3407 12112773 12113353 2.500000e-96 363.0
25 TraesCS3D01G279700 chr7A 84.488 303 39 5 2617 2911 410498453 410498151 3.330000e-75 292.0
26 TraesCS3D01G279700 chr1B 75.699 572 122 16 1741 2304 589897729 589897167 1.560000e-68 270.0
27 TraesCS3D01G279700 chr6D 84.307 274 43 0 3122 3395 369666058 369665785 5.600000e-68 268.0
28 TraesCS3D01G279700 chr4D 84.677 248 37 1 3161 3407 25362597 25362350 2.630000e-61 246.0
29 TraesCS3D01G279700 chr4D 79.937 319 48 14 3101 3407 488963845 488964159 1.590000e-53 220.0
30 TraesCS3D01G279700 chr1A 77.176 425 82 10 1743 2155 110283560 110283139 2.040000e-57 233.0
31 TraesCS3D01G279700 chr5A 79.027 329 53 15 3091 3407 404014781 404015105 9.580000e-51 211.0


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 TraesCS3D01G279700 chr3D 388311182 388314588 3406 True 6292.000000 6292 100.000000 1 3407 1 chr3D.!!$R3 3406
1 TraesCS3D01G279700 chr3D 388324390 388325884 1494 True 1722.000000 1722 87.642000 963 2441 1 chr3D.!!$R4 1478
2 TraesCS3D01G279700 chr3D 17341793 17342357 564 True 231.000000 231 74.695000 1741 2296 1 chr3D.!!$R1 555
3 TraesCS3D01G279700 chr3D 17698915 17699667 752 False 228.000000 228 73.022000 1622 2362 1 chr3D.!!$F1 740
4 TraesCS3D01G279700 chr3A 509376268 509377726 1458 True 1766.000000 1766 88.630000 992 2441 1 chr3A.!!$R1 1449
5 TraesCS3D01G279700 chr3A 509249498 509252365 2867 True 1236.333333 2880 90.615667 319 3242 3 chr3A.!!$R2 2923
6 TraesCS3D01G279700 chr3B 504960626 504962043 1417 True 1613.000000 1613 87.588000 992 2376 1 chr3B.!!$R1 1384
7 TraesCS3D01G279700 chr3B 503967962 503970282 2320 False 1052.366667 2601 89.908333 256 2588 3 chr3B.!!$F1 2332
8 TraesCS3D01G279700 chr7D 631470061 631470849 788 True 412.000000 412 76.951000 2617 3407 1 chr7D.!!$R2 790
9 TraesCS3D01G279700 chr6B 12112773 12113353 580 False 363.000000 363 78.275000 2810 3407 1 chr6B.!!$F1 597
10 TraesCS3D01G279700 chr1B 589897167 589897729 562 True 270.000000 270 75.699000 1741 2304 1 chr1B.!!$R1 563

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
651 705 0.034059 GCTATCTCCACGGACCCATG 59.966 60.0 0.00 0.0 0.0 3.66 F
708 763 0.109551 CGTGACATGTCGACTCAGCT 60.110 55.0 20.54 0.0 0.0 4.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1571 1667 0.374758 CATTCGGTCGAACATGCCTG 59.625 55.0 8.0 0.0 36.91 4.85 R
2495 2611 0.396811 ACAGTAGCTGCGAAAGGGTT 59.603 50.0 0.0 0.0 34.37 4.11 R

All possible primers

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

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
23 24 5.269313 GGAGTAACTTCGGTAGTAACATCG 58.731 45.833 0.00 0.00 35.54 3.84
24 25 5.065218 GGAGTAACTTCGGTAGTAACATCGA 59.935 44.000 0.00 0.00 35.54 3.59
25 26 6.116680 AGTAACTTCGGTAGTAACATCGAG 57.883 41.667 0.00 0.00 35.54 4.04
26 27 5.645497 AGTAACTTCGGTAGTAACATCGAGT 59.355 40.000 0.00 0.00 35.54 4.18
27 28 4.612932 ACTTCGGTAGTAACATCGAGTC 57.387 45.455 0.00 0.00 34.56 3.36
28 29 3.376546 ACTTCGGTAGTAACATCGAGTCC 59.623 47.826 0.00 0.00 34.56 3.85
29 30 2.989909 TCGGTAGTAACATCGAGTCCA 58.010 47.619 0.00 0.00 0.00 4.02
30 31 3.346315 TCGGTAGTAACATCGAGTCCAA 58.654 45.455 0.00 0.00 0.00 3.53
31 32 3.127548 TCGGTAGTAACATCGAGTCCAAC 59.872 47.826 0.00 0.00 0.00 3.77
32 33 3.128242 CGGTAGTAACATCGAGTCCAACT 59.872 47.826 0.00 0.00 0.00 3.16
33 34 4.670347 GGTAGTAACATCGAGTCCAACTC 58.330 47.826 0.00 0.00 41.71 3.01
34 35 4.157289 GGTAGTAACATCGAGTCCAACTCA 59.843 45.833 7.78 0.00 45.30 3.41
35 36 4.442375 AGTAACATCGAGTCCAACTCAG 57.558 45.455 7.78 1.37 45.30 3.35
36 37 2.086054 AACATCGAGTCCAACTCAGC 57.914 50.000 7.78 0.00 45.30 4.26
37 38 0.969149 ACATCGAGTCCAACTCAGCA 59.031 50.000 7.78 0.00 45.30 4.41
38 39 1.344438 ACATCGAGTCCAACTCAGCAA 59.656 47.619 7.78 0.00 45.30 3.91
39 40 2.027745 ACATCGAGTCCAACTCAGCAAT 60.028 45.455 7.78 0.00 45.30 3.56
40 41 2.839486 TCGAGTCCAACTCAGCAATT 57.161 45.000 7.78 0.00 45.30 2.32
41 42 3.126001 TCGAGTCCAACTCAGCAATTT 57.874 42.857 7.78 0.00 45.30 1.82
42 43 3.476552 TCGAGTCCAACTCAGCAATTTT 58.523 40.909 7.78 0.00 45.30 1.82
43 44 3.250762 TCGAGTCCAACTCAGCAATTTTG 59.749 43.478 7.78 0.00 45.30 2.44
44 45 3.311966 GAGTCCAACTCAGCAATTTTGC 58.688 45.455 7.19 7.19 44.45 3.68
59 60 6.102006 CAATTTTGCTTATGTGGCAATGAG 57.898 37.500 2.01 0.00 46.81 2.90
60 61 4.870123 TTTTGCTTATGTGGCAATGAGT 57.130 36.364 2.01 0.00 46.81 3.41
61 62 4.439305 TTTGCTTATGTGGCAATGAGTC 57.561 40.909 2.01 0.00 46.81 3.36
62 63 3.070476 TGCTTATGTGGCAATGAGTCA 57.930 42.857 0.00 0.00 36.71 3.41
63 64 3.419943 TGCTTATGTGGCAATGAGTCAA 58.580 40.909 0.00 0.00 36.71 3.18
64 65 4.018490 TGCTTATGTGGCAATGAGTCAAT 58.982 39.130 0.00 0.00 36.71 2.57
65 66 4.142337 TGCTTATGTGGCAATGAGTCAATG 60.142 41.667 3.67 3.67 36.71 2.82
66 67 4.142315 GCTTATGTGGCAATGAGTCAATGT 60.142 41.667 9.87 0.00 30.62 2.71
67 68 3.861276 ATGTGGCAATGAGTCAATGTG 57.139 42.857 9.87 4.08 30.62 3.21
68 69 1.887854 TGTGGCAATGAGTCAATGTGG 59.112 47.619 9.87 0.00 30.62 4.17
69 70 2.161855 GTGGCAATGAGTCAATGTGGA 58.838 47.619 9.87 0.00 30.62 4.02
70 71 2.163010 GTGGCAATGAGTCAATGTGGAG 59.837 50.000 9.87 0.00 30.62 3.86
71 72 2.040145 TGGCAATGAGTCAATGTGGAGA 59.960 45.455 9.87 0.00 0.00 3.71
72 73 2.681848 GGCAATGAGTCAATGTGGAGAG 59.318 50.000 9.87 0.00 0.00 3.20
73 74 3.603532 GCAATGAGTCAATGTGGAGAGA 58.396 45.455 9.87 0.00 0.00 3.10
74 75 4.197750 GCAATGAGTCAATGTGGAGAGAT 58.802 43.478 9.87 0.00 0.00 2.75
75 76 4.035324 GCAATGAGTCAATGTGGAGAGATG 59.965 45.833 9.87 0.00 0.00 2.90
76 77 5.183969 CAATGAGTCAATGTGGAGAGATGT 58.816 41.667 0.00 0.00 0.00 3.06
77 78 6.343703 CAATGAGTCAATGTGGAGAGATGTA 58.656 40.000 0.00 0.00 0.00 2.29
78 79 5.588958 TGAGTCAATGTGGAGAGATGTAG 57.411 43.478 0.00 0.00 0.00 2.74
79 80 5.019470 TGAGTCAATGTGGAGAGATGTAGT 58.981 41.667 0.00 0.00 0.00 2.73
80 81 6.187682 TGAGTCAATGTGGAGAGATGTAGTA 58.812 40.000 0.00 0.00 0.00 1.82
81 82 6.095580 TGAGTCAATGTGGAGAGATGTAGTAC 59.904 42.308 0.00 0.00 0.00 2.73
82 83 6.191315 AGTCAATGTGGAGAGATGTAGTACT 58.809 40.000 0.00 0.00 0.00 2.73
83 84 7.347252 AGTCAATGTGGAGAGATGTAGTACTA 58.653 38.462 0.00 0.00 0.00 1.82
84 85 7.500892 AGTCAATGTGGAGAGATGTAGTACTAG 59.499 40.741 1.87 0.00 0.00 2.57
85 86 7.283580 GTCAATGTGGAGAGATGTAGTACTAGT 59.716 40.741 1.87 0.00 0.00 2.57
86 87 8.491958 TCAATGTGGAGAGATGTAGTACTAGTA 58.508 37.037 1.87 0.00 0.00 1.82
87 88 9.121658 CAATGTGGAGAGATGTAGTACTAGTAA 57.878 37.037 3.61 0.00 0.00 2.24
88 89 8.680039 ATGTGGAGAGATGTAGTACTAGTAAC 57.320 38.462 3.61 0.77 0.00 2.50
89 90 7.859540 TGTGGAGAGATGTAGTACTAGTAACT 58.140 38.462 3.61 7.14 0.00 2.24
90 91 8.327271 TGTGGAGAGATGTAGTACTAGTAACTT 58.673 37.037 3.61 0.00 0.00 2.66
91 92 9.829507 GTGGAGAGATGTAGTACTAGTAACTTA 57.170 37.037 3.61 0.00 0.00 2.24
93 94 8.992073 GGAGAGATGTAGTACTAGTAACTTAGC 58.008 40.741 3.61 0.00 0.00 3.09
94 95 9.768662 GAGAGATGTAGTACTAGTAACTTAGCT 57.231 37.037 3.61 0.33 0.00 3.32
111 112 8.983307 AACTTAGCTAGTTACTGTAACATCAC 57.017 34.615 27.12 15.70 45.22 3.06
112 113 8.118976 ACTTAGCTAGTTACTGTAACATCACA 57.881 34.615 27.12 10.61 41.07 3.58
113 114 8.750298 ACTTAGCTAGTTACTGTAACATCACAT 58.250 33.333 27.12 11.85 41.07 3.21
114 115 8.926715 TTAGCTAGTTACTGTAACATCACATG 57.073 34.615 27.12 12.57 41.07 3.21
116 117 7.036220 AGCTAGTTACTGTAACATCACATGTC 58.964 38.462 27.12 9.51 44.07 3.06
117 118 6.255887 GCTAGTTACTGTAACATCACATGTCC 59.744 42.308 27.12 1.73 44.07 4.02
118 119 5.488341 AGTTACTGTAACATCACATGTCCC 58.512 41.667 27.12 1.55 44.07 4.46
119 120 5.012664 AGTTACTGTAACATCACATGTCCCA 59.987 40.000 27.12 0.00 44.07 4.37
120 121 4.365514 ACTGTAACATCACATGTCCCAA 57.634 40.909 0.00 0.00 44.07 4.12
121 122 4.922206 ACTGTAACATCACATGTCCCAAT 58.078 39.130 0.00 0.00 44.07 3.16
122 123 4.701651 ACTGTAACATCACATGTCCCAATG 59.298 41.667 0.00 0.45 44.07 2.82
123 124 3.443329 TGTAACATCACATGTCCCAATGC 59.557 43.478 0.00 0.00 44.07 3.56
124 125 2.219080 ACATCACATGTCCCAATGCA 57.781 45.000 0.00 0.00 39.92 3.96
125 126 2.527497 ACATCACATGTCCCAATGCAA 58.473 42.857 0.00 0.00 39.92 4.08
126 127 3.101437 ACATCACATGTCCCAATGCAAT 58.899 40.909 0.00 0.00 39.92 3.56
127 128 4.279982 ACATCACATGTCCCAATGCAATA 58.720 39.130 0.00 0.00 39.92 1.90
128 129 4.897076 ACATCACATGTCCCAATGCAATAT 59.103 37.500 0.00 0.00 39.92 1.28
129 130 4.922471 TCACATGTCCCAATGCAATATG 57.078 40.909 0.00 0.00 0.00 1.78
130 131 4.534797 TCACATGTCCCAATGCAATATGA 58.465 39.130 0.00 0.00 0.00 2.15
131 132 4.581409 TCACATGTCCCAATGCAATATGAG 59.419 41.667 0.00 0.00 0.00 2.90
132 133 4.340097 CACATGTCCCAATGCAATATGAGT 59.660 41.667 0.00 0.00 0.00 3.41
133 134 4.340097 ACATGTCCCAATGCAATATGAGTG 59.660 41.667 0.00 0.00 0.00 3.51
134 135 3.966979 TGTCCCAATGCAATATGAGTGT 58.033 40.909 0.00 0.00 0.00 3.55
135 136 5.109500 TGTCCCAATGCAATATGAGTGTA 57.891 39.130 0.00 0.00 0.00 2.90
136 137 5.693961 TGTCCCAATGCAATATGAGTGTAT 58.306 37.500 0.00 0.00 0.00 2.29
137 138 6.836242 TGTCCCAATGCAATATGAGTGTATA 58.164 36.000 0.00 0.00 0.00 1.47
138 139 7.286313 TGTCCCAATGCAATATGAGTGTATAA 58.714 34.615 0.00 0.00 0.00 0.98
139 140 7.228507 TGTCCCAATGCAATATGAGTGTATAAC 59.771 37.037 0.00 0.00 0.00 1.89
140 141 6.426633 TCCCAATGCAATATGAGTGTATAACG 59.573 38.462 0.00 0.00 0.00 3.18
141 142 6.204688 CCCAATGCAATATGAGTGTATAACGT 59.795 38.462 0.00 0.00 0.00 3.99
142 143 7.386573 CCCAATGCAATATGAGTGTATAACGTA 59.613 37.037 0.00 0.00 0.00 3.57
143 144 8.769891 CCAATGCAATATGAGTGTATAACGTAA 58.230 33.333 0.00 0.00 0.00 3.18
154 155 9.811995 TGAGTGTATAACGTAATAAATGAAGCT 57.188 29.630 0.00 0.00 0.00 3.74
168 169 9.855021 AATAAATGAAGCTTTGTATGTTACCAC 57.145 29.630 0.00 0.00 0.00 4.16
169 170 6.892658 AATGAAGCTTTGTATGTTACCACA 57.107 33.333 0.00 0.00 37.31 4.17
170 171 5.682943 TGAAGCTTTGTATGTTACCACAC 57.317 39.130 0.00 0.00 35.03 3.82
171 172 5.373222 TGAAGCTTTGTATGTTACCACACT 58.627 37.500 0.00 0.00 35.03 3.55
172 173 5.825679 TGAAGCTTTGTATGTTACCACACTT 59.174 36.000 0.00 0.00 35.03 3.16
173 174 6.993308 TGAAGCTTTGTATGTTACCACACTTA 59.007 34.615 0.00 0.00 35.03 2.24
174 175 7.663905 TGAAGCTTTGTATGTTACCACACTTAT 59.336 33.333 0.00 0.00 35.03 1.73
175 176 7.377766 AGCTTTGTATGTTACCACACTTATG 57.622 36.000 0.00 0.00 35.03 1.90
176 177 6.940298 AGCTTTGTATGTTACCACACTTATGT 59.060 34.615 0.00 0.00 40.80 2.29
177 178 7.447238 AGCTTTGTATGTTACCACACTTATGTT 59.553 33.333 0.00 0.00 36.72 2.71
178 179 8.723311 GCTTTGTATGTTACCACACTTATGTTA 58.277 33.333 0.00 0.00 36.72 2.41
180 181 9.781633 TTTGTATGTTACCACACTTATGTTACT 57.218 29.630 0.00 0.00 36.72 2.24
182 183 9.859427 TGTATGTTACCACACTTATGTTACTAC 57.141 33.333 0.00 0.00 36.72 2.73
183 184 9.305925 GTATGTTACCACACTTATGTTACTACC 57.694 37.037 0.00 0.00 36.72 3.18
184 185 6.700352 TGTTACCACACTTATGTTACTACCC 58.300 40.000 0.00 0.00 36.72 3.69
185 186 6.269538 TGTTACCACACTTATGTTACTACCCA 59.730 38.462 0.00 0.00 36.72 4.51
186 187 5.156608 ACCACACTTATGTTACTACCCAC 57.843 43.478 0.00 0.00 36.72 4.61
187 188 4.842380 ACCACACTTATGTTACTACCCACT 59.158 41.667 0.00 0.00 36.72 4.00
188 189 6.018469 ACCACACTTATGTTACTACCCACTA 58.982 40.000 0.00 0.00 36.72 2.74
189 190 6.670902 ACCACACTTATGTTACTACCCACTAT 59.329 38.462 0.00 0.00 36.72 2.12
190 191 7.181485 ACCACACTTATGTTACTACCCACTATT 59.819 37.037 0.00 0.00 36.72 1.73
191 192 7.494625 CCACACTTATGTTACTACCCACTATTG 59.505 40.741 0.00 0.00 36.72 1.90
192 193 8.255206 CACACTTATGTTACTACCCACTATTGA 58.745 37.037 0.00 0.00 36.72 2.57
193 194 8.475639 ACACTTATGTTACTACCCACTATTGAG 58.524 37.037 0.00 0.00 34.46 3.02
194 195 7.926555 CACTTATGTTACTACCCACTATTGAGG 59.073 40.741 0.00 0.00 0.00 3.86
195 196 7.622479 ACTTATGTTACTACCCACTATTGAGGT 59.378 37.037 0.00 0.00 37.69 3.85
196 197 9.139734 CTTATGTTACTACCCACTATTGAGGTA 57.860 37.037 0.00 0.00 35.02 3.08
203 204 7.598759 CTACCCACTATTGAGGTAGTAACAT 57.401 40.000 14.91 0.00 45.39 2.71
204 205 8.701908 CTACCCACTATTGAGGTAGTAACATA 57.298 38.462 14.91 0.00 45.39 2.29
205 206 7.598759 ACCCACTATTGAGGTAGTAACATAG 57.401 40.000 0.00 0.00 33.29 2.23
206 207 7.359849 ACCCACTATTGAGGTAGTAACATAGA 58.640 38.462 0.00 0.00 33.29 1.98
207 208 7.506261 ACCCACTATTGAGGTAGTAACATAGAG 59.494 40.741 0.00 0.00 33.29 2.43
208 209 7.506261 CCCACTATTGAGGTAGTAACATAGAGT 59.494 40.741 0.00 0.00 33.29 3.24
209 210 9.570468 CCACTATTGAGGTAGTAACATAGAGTA 57.430 37.037 0.00 0.00 33.29 2.59
215 216 9.964354 TTGAGGTAGTAACATAGAGTAGTAACA 57.036 33.333 0.00 0.00 0.00 2.41
218 219 9.917887 AGGTAGTAACATAGAGTAGTAACATGT 57.082 33.333 0.00 0.00 0.00 3.21
245 246 9.571816 AGATGTTACTACTCTATGTTACTACCC 57.428 37.037 0.00 0.00 0.00 3.69
246 247 9.347240 GATGTTACTACTCTATGTTACTACCCA 57.653 37.037 0.00 0.00 0.00 4.51
247 248 9.878737 ATGTTACTACTCTATGTTACTACCCAT 57.121 33.333 0.00 0.00 0.00 4.00
248 249 9.705103 TGTTACTACTCTATGTTACTACCCATT 57.295 33.333 0.00 0.00 0.00 3.16
249 250 9.962783 GTTACTACTCTATGTTACTACCCATTG 57.037 37.037 0.00 0.00 0.00 2.82
250 251 9.705103 TTACTACTCTATGTTACTACCCATTGT 57.295 33.333 0.00 0.00 0.00 2.71
251 252 8.008513 ACTACTCTATGTTACTACCCATTGTG 57.991 38.462 0.00 0.00 0.00 3.33
252 253 6.235231 ACTCTATGTTACTACCCATTGTGG 57.765 41.667 0.00 0.00 37.25 4.17
253 254 5.031066 TCTATGTTACTACCCATTGTGGC 57.969 43.478 0.00 0.00 35.79 5.01
254 255 4.719773 TCTATGTTACTACCCATTGTGGCT 59.280 41.667 0.00 0.00 35.79 4.75
255 256 5.900699 TCTATGTTACTACCCATTGTGGCTA 59.099 40.000 0.00 0.00 35.79 3.93
256 257 4.481368 TGTTACTACCCATTGTGGCTAG 57.519 45.455 0.00 0.00 35.79 3.42
257 258 3.841845 TGTTACTACCCATTGTGGCTAGT 59.158 43.478 8.55 8.55 35.79 2.57
258 259 4.081309 TGTTACTACCCATTGTGGCTAGTC 60.081 45.833 7.13 0.00 35.79 2.59
259 260 2.834113 ACTACCCATTGTGGCTAGTCT 58.166 47.619 0.00 0.00 35.79 3.24
260 261 3.990369 ACTACCCATTGTGGCTAGTCTA 58.010 45.455 0.00 0.00 35.79 2.59
261 262 4.359105 ACTACCCATTGTGGCTAGTCTAA 58.641 43.478 0.00 0.00 35.79 2.10
262 263 3.914426 ACCCATTGTGGCTAGTCTAAG 57.086 47.619 0.00 0.00 35.79 2.18
263 264 2.092914 ACCCATTGTGGCTAGTCTAAGC 60.093 50.000 0.00 0.00 41.99 3.09
264 265 2.092968 CCCATTGTGGCTAGTCTAAGCA 60.093 50.000 0.00 0.00 44.64 3.91
265 266 2.939103 CCATTGTGGCTAGTCTAAGCAC 59.061 50.000 0.00 0.00 44.64 4.40
266 267 3.599343 CATTGTGGCTAGTCTAAGCACA 58.401 45.455 0.00 0.00 44.64 4.57
275 276 7.711339 GTGGCTAGTCTAAGCACATAATTAAGT 59.289 37.037 0.00 0.00 44.64 2.24
297 298 3.064931 GCTTTAGTTGCTAACACCTCGT 58.935 45.455 0.00 0.00 0.00 4.18
305 306 2.260481 GCTAACACCTCGTCTAAGCAC 58.740 52.381 0.00 0.00 31.44 4.40
307 308 1.045407 AACACCTCGTCTAAGCACCA 58.955 50.000 0.00 0.00 0.00 4.17
308 309 1.267121 ACACCTCGTCTAAGCACCAT 58.733 50.000 0.00 0.00 0.00 3.55
309 310 2.453521 ACACCTCGTCTAAGCACCATA 58.546 47.619 0.00 0.00 0.00 2.74
310 311 2.165845 ACACCTCGTCTAAGCACCATAC 59.834 50.000 0.00 0.00 0.00 2.39
312 313 3.097614 ACCTCGTCTAAGCACCATACTT 58.902 45.455 0.00 0.00 0.00 2.24
313 314 3.119101 ACCTCGTCTAAGCACCATACTTG 60.119 47.826 0.00 0.00 0.00 3.16
322 323 1.340017 GCACCATACTTGGAAGAGGCA 60.340 52.381 0.00 0.00 46.92 4.75
326 327 5.192927 CACCATACTTGGAAGAGGCAATTA 58.807 41.667 0.00 0.00 46.92 1.40
329 330 6.322201 ACCATACTTGGAAGAGGCAATTATTG 59.678 38.462 0.00 0.00 46.92 1.90
354 357 4.382386 TTTTCCTCCTTCGATTTTCCCT 57.618 40.909 0.00 0.00 0.00 4.20
393 396 1.070914 TCCATTACGTCAGTGCACCAA 59.929 47.619 14.63 0.00 0.00 3.67
403 406 2.203280 TGCACCAACAAGGGTCGG 60.203 61.111 0.00 0.00 43.89 4.79
651 705 0.034059 GCTATCTCCACGGACCCATG 59.966 60.000 0.00 0.00 0.00 3.66
657 711 2.334946 CCACGGACCCATGCTTGTG 61.335 63.158 0.00 0.00 0.00 3.33
663 717 1.679032 GGACCCATGCTTGTGTCCTAC 60.679 57.143 21.91 1.71 44.41 3.18
680 735 1.192146 TACCTCAACGGCTTCAGGCT 61.192 55.000 0.00 0.00 41.46 4.58
682 737 1.301677 CCTCAACGGCTTCAGGCTTC 61.302 60.000 0.00 0.00 41.46 3.86
683 738 0.603707 CTCAACGGCTTCAGGCTTCA 60.604 55.000 0.00 0.00 41.46 3.02
684 739 0.603707 TCAACGGCTTCAGGCTTCAG 60.604 55.000 0.00 0.00 41.46 3.02
686 741 3.130160 CGGCTTCAGGCTTCAGGC 61.130 66.667 6.25 6.25 41.46 4.85
687 742 2.034687 GGCTTCAGGCTTCAGGCA 59.965 61.111 10.53 0.00 44.01 4.75
689 744 1.382692 GGCTTCAGGCTTCAGGCATC 61.383 60.000 10.53 0.00 44.01 3.91
691 746 0.392193 CTTCAGGCTTCAGGCATCGT 60.392 55.000 2.85 0.00 44.01 3.73
692 747 0.674581 TTCAGGCTTCAGGCATCGTG 60.675 55.000 2.85 0.00 44.01 4.35
693 748 1.078918 CAGGCTTCAGGCATCGTGA 60.079 57.895 2.85 0.00 44.01 4.35
694 749 1.078848 AGGCTTCAGGCATCGTGAC 60.079 57.895 2.85 0.00 44.01 3.67
695 750 1.375908 GGCTTCAGGCATCGTGACA 60.376 57.895 0.00 0.00 44.01 3.58
696 751 0.745845 GGCTTCAGGCATCGTGACAT 60.746 55.000 0.00 0.00 44.01 3.06
697 752 0.376152 GCTTCAGGCATCGTGACATG 59.624 55.000 0.00 0.00 41.35 3.21
698 753 1.730501 CTTCAGGCATCGTGACATGT 58.269 50.000 0.00 0.00 0.00 3.21
699 754 1.662629 CTTCAGGCATCGTGACATGTC 59.337 52.381 19.27 19.27 0.00 3.06
700 755 0.458370 TCAGGCATCGTGACATGTCG 60.458 55.000 20.54 10.83 33.29 4.35
701 756 0.458370 CAGGCATCGTGACATGTCGA 60.458 55.000 20.54 15.89 40.28 4.20
703 758 0.458543 GGCATCGTGACATGTCGACT 60.459 55.000 20.54 3.00 38.85 4.18
704 759 0.917259 GCATCGTGACATGTCGACTC 59.083 55.000 20.54 6.73 38.85 3.36
705 760 1.732405 GCATCGTGACATGTCGACTCA 60.732 52.381 20.54 9.53 38.85 3.41
706 761 2.180397 CATCGTGACATGTCGACTCAG 58.820 52.381 20.54 8.89 38.85 3.35
708 763 0.109551 CGTGACATGTCGACTCAGCT 60.110 55.000 20.54 0.00 0.00 4.24
709 764 1.130561 CGTGACATGTCGACTCAGCTA 59.869 52.381 20.54 0.00 0.00 3.32
710 765 2.520979 GTGACATGTCGACTCAGCTAC 58.479 52.381 20.54 6.41 0.00 3.58
711 766 2.162608 GTGACATGTCGACTCAGCTACT 59.837 50.000 20.54 0.00 0.00 2.57
712 767 2.420372 TGACATGTCGACTCAGCTACTC 59.580 50.000 20.54 1.32 0.00 2.59
713 768 1.746220 ACATGTCGACTCAGCTACTCC 59.254 52.381 17.92 0.00 0.00 3.85
714 769 1.745653 CATGTCGACTCAGCTACTCCA 59.254 52.381 17.92 0.00 0.00 3.86
715 770 1.905637 TGTCGACTCAGCTACTCCAA 58.094 50.000 17.92 0.00 0.00 3.53
716 771 1.813178 TGTCGACTCAGCTACTCCAAG 59.187 52.381 17.92 0.00 0.00 3.61
717 772 0.811915 TCGACTCAGCTACTCCAAGC 59.188 55.000 0.00 0.00 43.11 4.01
718 773 0.528017 CGACTCAGCTACTCCAAGCA 59.472 55.000 0.00 0.00 45.30 3.91
719 774 1.734047 CGACTCAGCTACTCCAAGCAC 60.734 57.143 0.00 0.00 45.30 4.40
720 775 0.610687 ACTCAGCTACTCCAAGCACC 59.389 55.000 0.00 0.00 45.30 5.01
721 776 0.459237 CTCAGCTACTCCAAGCACCG 60.459 60.000 0.00 0.00 45.30 4.94
722 777 1.185618 TCAGCTACTCCAAGCACCGT 61.186 55.000 0.00 0.00 45.30 4.83
723 778 1.016130 CAGCTACTCCAAGCACCGTG 61.016 60.000 0.00 0.00 45.30 4.94
724 779 1.741770 GCTACTCCAAGCACCGTGG 60.742 63.158 0.00 0.00 42.30 4.94
725 780 1.741770 CTACTCCAAGCACCGTGGC 60.742 63.158 0.00 0.00 35.99 5.01
730 785 3.357079 CAAGCACCGTGGCTGGTC 61.357 66.667 0.00 0.00 45.07 4.02
780 835 0.321671 TGGAGCAAGAAAGGACTCGG 59.678 55.000 0.00 0.00 0.00 4.63
789 844 2.760387 AAAGGACTCGGCCGTTCGTC 62.760 60.000 27.15 26.21 0.00 4.20
790 845 4.790861 GGACTCGGCCGTTCGTCC 62.791 72.222 31.90 31.90 39.14 4.79
850 905 3.814268 ACGCGGTCATGCATTGCC 61.814 61.111 12.47 0.75 34.15 4.52
886 941 1.066502 TGGATTGAATTCGACGAGCCA 60.067 47.619 0.00 0.90 35.24 4.75
895 950 4.966965 ATTCGACGAGCCACCTATATAG 57.033 45.455 2.46 2.46 0.00 1.31
930 985 1.582968 GTGGGTCGTTCGTAGAGCA 59.417 57.895 8.40 0.00 37.72 4.26
940 995 1.827681 TCGTAGAGCAGAGCAGAACT 58.172 50.000 0.00 0.00 0.00 3.01
941 996 2.163509 TCGTAGAGCAGAGCAGAACTT 58.836 47.619 0.00 0.00 0.00 2.66
942 997 2.095008 TCGTAGAGCAGAGCAGAACTTG 60.095 50.000 0.00 0.00 0.00 3.16
943 998 2.095008 CGTAGAGCAGAGCAGAACTTGA 60.095 50.000 0.00 0.00 0.00 3.02
944 999 3.612717 CGTAGAGCAGAGCAGAACTTGAA 60.613 47.826 0.00 0.00 0.00 2.69
945 1000 3.042871 AGAGCAGAGCAGAACTTGAAG 57.957 47.619 0.00 0.00 0.00 3.02
946 1001 1.464219 GAGCAGAGCAGAACTTGAAGC 59.536 52.381 0.00 0.00 0.00 3.86
947 1002 1.202734 AGCAGAGCAGAACTTGAAGCA 60.203 47.619 0.00 0.00 0.00 3.91
948 1003 1.197264 GCAGAGCAGAACTTGAAGCAG 59.803 52.381 0.00 0.00 0.00 4.24
949 1004 2.763933 CAGAGCAGAACTTGAAGCAGA 58.236 47.619 0.00 0.00 0.00 4.26
950 1005 3.136763 CAGAGCAGAACTTGAAGCAGAA 58.863 45.455 0.00 0.00 0.00 3.02
951 1006 3.059051 CAGAGCAGAACTTGAAGCAGAAC 60.059 47.826 0.00 0.00 0.00 3.01
952 1007 2.874701 GAGCAGAACTTGAAGCAGAACA 59.125 45.455 0.00 0.00 0.00 3.18
953 1008 2.877168 AGCAGAACTTGAAGCAGAACAG 59.123 45.455 0.00 0.00 0.00 3.16
954 1009 2.874701 GCAGAACTTGAAGCAGAACAGA 59.125 45.455 0.00 0.00 0.00 3.41
955 1010 3.059051 GCAGAACTTGAAGCAGAACAGAG 60.059 47.826 0.00 0.00 0.00 3.35
956 1011 3.059051 CAGAACTTGAAGCAGAACAGAGC 60.059 47.826 0.00 0.00 0.00 4.09
957 1012 1.889545 ACTTGAAGCAGAACAGAGCC 58.110 50.000 0.00 0.00 0.00 4.70
958 1013 1.141657 ACTTGAAGCAGAACAGAGCCA 59.858 47.619 0.00 0.00 0.00 4.75
983 1038 2.543430 CCAACCCAAAAAGCATTTCGTG 59.457 45.455 0.00 0.00 37.28 4.35
1003 1066 1.745141 GCTAGGACAGTGAAGCCATGG 60.745 57.143 7.63 7.63 0.00 3.66
1225 1288 2.267642 CCGCCGATTCCAACTCCA 59.732 61.111 0.00 0.00 0.00 3.86
1284 1371 2.636830 CTCCTGAAATCCATGAACGCT 58.363 47.619 0.00 0.00 0.00 5.07
1432 1519 2.718731 CCGATCTCGCGCTCTTCT 59.281 61.111 5.56 0.00 38.18 2.85
1515 1608 2.285024 CCCGGGTGTTCCTCCGTTA 61.285 63.158 14.18 0.00 44.32 3.18
1571 1667 3.895232 TGAAGTACTCAAGGCCATCTC 57.105 47.619 5.01 0.00 0.00 2.75
1719 1815 4.652131 TGCATCGGGCCGTTGGTT 62.652 61.111 31.54 10.07 43.89 3.67
1847 1955 1.005340 CAGCTCGAGGAGATTGCAAC 58.995 55.000 15.58 0.00 0.00 4.17
2226 2337 0.838987 AGGTGGTTAAGGCCGAGGAA 60.839 55.000 0.00 0.00 0.00 3.36
2421 2535 5.865552 GCAGCATTGATGTGAAACTTGTAAT 59.134 36.000 3.56 0.00 38.04 1.89
2495 2611 4.191033 TGCGGACTAAGTTTATTTCCGA 57.809 40.909 18.84 7.57 41.22 4.55
2559 2678 3.321497 CACTCTGCTTCTTGTGAGTACC 58.679 50.000 0.00 0.00 37.64 3.34
2560 2679 3.006323 CACTCTGCTTCTTGTGAGTACCT 59.994 47.826 0.00 0.00 37.64 3.08
2636 2780 2.040278 CTCCCTCCCAGCCACTCT 59.960 66.667 0.00 0.00 0.00 3.24
2702 2847 4.150454 CTCCGGCCTCTCCTCCCT 62.150 72.222 0.00 0.00 0.00 4.20
2917 3070 2.042762 TAGCTGCCATGGAGGGGT 59.957 61.111 18.40 12.08 38.09 4.95
2945 3098 2.434185 GCGGTTCAGCGTGGATCA 60.434 61.111 0.00 0.00 0.00 2.92
2967 3120 0.896019 CGGCGGATCTGGATCTAGGT 60.896 60.000 6.21 0.00 37.92 3.08
3051 3204 4.324991 GGGTCTTCCCGTTGCGGT 62.325 66.667 6.82 0.00 46.80 5.68
3120 3290 3.706373 GGGTGCTGAGAAGGCGGA 61.706 66.667 0.00 0.00 0.00 5.54
3288 3459 4.308458 CGGGCGGTTGTGGAGACA 62.308 66.667 0.00 0.00 38.70 3.41
3290 3461 3.050275 GGCGGTTGTGGAGACAGC 61.050 66.667 0.00 0.00 44.46 4.40
3292 3463 2.338620 CGGTTGTGGAGACAGCGA 59.661 61.111 0.00 0.00 44.46 4.93
3294 3465 2.022129 GGTTGTGGAGACAGCGACG 61.022 63.158 0.00 0.00 44.46 5.12
3331 3502 3.453070 GATGGGAGCCTCACGAGCC 62.453 68.421 0.00 0.00 0.00 4.70
3337 3508 1.424493 GAGCCTCACGAGCCATTTCG 61.424 60.000 0.00 0.00 45.70 3.46
3346 3517 3.929948 GCCATTTCGAGCTCGGCG 61.930 66.667 33.98 19.48 40.29 6.46
3374 3545 0.747283 GTGCCTGGATTGCTCCTCTG 60.747 60.000 0.00 0.00 42.59 3.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 5.065218 TCGATGTTACTACCGAAGTTACTCC 59.935 44.000 8.00 1.54 39.80 3.85
3 4 5.873732 ACTCGATGTTACTACCGAAGTTAC 58.126 41.667 0.00 0.00 39.80 2.50
4 5 5.065218 GGACTCGATGTTACTACCGAAGTTA 59.935 44.000 0.00 0.00 39.80 2.24
6 7 3.376546 GGACTCGATGTTACTACCGAAGT 59.623 47.826 0.00 0.00 42.62 3.01
8 9 3.346315 TGGACTCGATGTTACTACCGAA 58.654 45.455 0.00 0.00 0.00 4.30
11 12 4.670347 GAGTTGGACTCGATGTTACTACC 58.330 47.826 0.00 0.00 35.28 3.18
42 43 3.070476 TGACTCATTGCCACATAAGCA 57.930 42.857 0.00 0.00 38.81 3.91
43 44 4.142315 ACATTGACTCATTGCCACATAAGC 60.142 41.667 1.55 0.00 0.00 3.09
44 45 5.337554 CACATTGACTCATTGCCACATAAG 58.662 41.667 1.55 0.00 0.00 1.73
45 46 4.158209 CCACATTGACTCATTGCCACATAA 59.842 41.667 1.55 0.00 0.00 1.90
46 47 3.695556 CCACATTGACTCATTGCCACATA 59.304 43.478 1.55 0.00 0.00 2.29
47 48 2.494471 CCACATTGACTCATTGCCACAT 59.506 45.455 1.55 0.00 0.00 3.21
48 49 1.887854 CCACATTGACTCATTGCCACA 59.112 47.619 1.55 0.00 0.00 4.17
49 50 2.161855 TCCACATTGACTCATTGCCAC 58.838 47.619 1.55 0.00 0.00 5.01
50 51 2.040145 TCTCCACATTGACTCATTGCCA 59.960 45.455 1.55 0.00 0.00 4.92
51 52 2.681848 CTCTCCACATTGACTCATTGCC 59.318 50.000 1.55 0.00 0.00 4.52
52 53 3.603532 TCTCTCCACATTGACTCATTGC 58.396 45.455 1.55 0.00 0.00 3.56
53 54 5.183969 ACATCTCTCCACATTGACTCATTG 58.816 41.667 0.00 0.27 0.00 2.82
54 55 5.432680 ACATCTCTCCACATTGACTCATT 57.567 39.130 0.00 0.00 0.00 2.57
55 56 5.660417 ACTACATCTCTCCACATTGACTCAT 59.340 40.000 0.00 0.00 0.00 2.90
56 57 5.019470 ACTACATCTCTCCACATTGACTCA 58.981 41.667 0.00 0.00 0.00 3.41
57 58 5.590530 ACTACATCTCTCCACATTGACTC 57.409 43.478 0.00 0.00 0.00 3.36
58 59 6.191315 AGTACTACATCTCTCCACATTGACT 58.809 40.000 0.00 0.00 0.00 3.41
59 60 6.458232 AGTACTACATCTCTCCACATTGAC 57.542 41.667 0.00 0.00 0.00 3.18
60 61 7.347252 ACTAGTACTACATCTCTCCACATTGA 58.653 38.462 0.00 0.00 0.00 2.57
61 62 7.575414 ACTAGTACTACATCTCTCCACATTG 57.425 40.000 0.00 0.00 0.00 2.82
62 63 9.122779 GTTACTAGTACTACATCTCTCCACATT 57.877 37.037 0.91 0.00 0.00 2.71
63 64 8.496088 AGTTACTAGTACTACATCTCTCCACAT 58.504 37.037 0.91 0.00 0.00 3.21
64 65 7.859540 AGTTACTAGTACTACATCTCTCCACA 58.140 38.462 0.91 0.00 0.00 4.17
65 66 8.735692 AAGTTACTAGTACTACATCTCTCCAC 57.264 38.462 0.91 0.00 0.00 4.02
67 68 8.992073 GCTAAGTTACTAGTACTACATCTCTCC 58.008 40.741 0.91 0.00 0.00 3.71
68 69 9.768662 AGCTAAGTTACTAGTACTACATCTCTC 57.231 37.037 0.91 0.00 0.00 3.20
87 88 8.118976 TGTGATGTTACAGTAACTAGCTAAGT 57.881 34.615 21.56 0.00 41.49 2.24
88 89 9.025020 CATGTGATGTTACAGTAACTAGCTAAG 57.975 37.037 21.56 6.36 39.38 2.18
89 90 8.528643 ACATGTGATGTTACAGTAACTAGCTAA 58.471 33.333 21.56 3.59 41.63 3.09
90 91 8.063200 ACATGTGATGTTACAGTAACTAGCTA 57.937 34.615 21.56 4.25 41.63 3.32
91 92 6.936279 ACATGTGATGTTACAGTAACTAGCT 58.064 36.000 21.56 6.57 41.63 3.32
92 93 6.255887 GGACATGTGATGTTACAGTAACTAGC 59.744 42.308 21.56 12.59 45.03 3.42
93 94 6.757010 GGGACATGTGATGTTACAGTAACTAG 59.243 42.308 21.56 8.25 45.03 2.57
94 95 6.211785 TGGGACATGTGATGTTACAGTAACTA 59.788 38.462 21.56 10.50 45.03 2.24
95 96 5.012664 TGGGACATGTGATGTTACAGTAACT 59.987 40.000 21.56 9.41 45.03 2.24
96 97 5.242434 TGGGACATGTGATGTTACAGTAAC 58.758 41.667 15.58 15.58 45.03 2.50
97 98 5.491323 TGGGACATGTGATGTTACAGTAA 57.509 39.130 1.15 0.00 45.03 2.24
98 99 5.491323 TTGGGACATGTGATGTTACAGTA 57.509 39.130 1.15 0.00 45.03 2.74
99 100 4.365514 TTGGGACATGTGATGTTACAGT 57.634 40.909 1.15 0.00 45.03 3.55
100 101 4.439153 GCATTGGGACATGTGATGTTACAG 60.439 45.833 1.15 0.00 45.03 2.74
101 102 3.443329 GCATTGGGACATGTGATGTTACA 59.557 43.478 1.15 0.00 45.03 2.41
102 103 3.443329 TGCATTGGGACATGTGATGTTAC 59.557 43.478 1.15 0.00 45.03 2.50
103 104 3.694926 TGCATTGGGACATGTGATGTTA 58.305 40.909 1.15 0.00 45.03 2.41
104 105 2.527497 TGCATTGGGACATGTGATGTT 58.473 42.857 1.15 0.00 45.03 2.71
106 107 3.812156 ATTGCATTGGGACATGTGATG 57.188 42.857 1.15 3.48 39.30 3.07
107 108 5.141910 TCATATTGCATTGGGACATGTGAT 58.858 37.500 1.15 0.00 39.30 3.06
108 109 4.534797 TCATATTGCATTGGGACATGTGA 58.465 39.130 1.15 0.00 39.30 3.58
109 110 4.340097 ACTCATATTGCATTGGGACATGTG 59.660 41.667 1.15 0.00 39.30 3.21
110 111 4.340097 CACTCATATTGCATTGGGACATGT 59.660 41.667 0.00 0.00 39.30 3.21
111 112 4.340097 ACACTCATATTGCATTGGGACATG 59.660 41.667 0.00 0.00 39.30 3.21
112 113 4.539726 ACACTCATATTGCATTGGGACAT 58.460 39.130 0.00 0.00 39.30 3.06
113 114 3.966979 ACACTCATATTGCATTGGGACA 58.033 40.909 0.00 0.00 0.00 4.02
114 115 7.571244 CGTTATACACTCATATTGCATTGGGAC 60.571 40.741 0.00 0.00 0.00 4.46
115 116 6.426633 CGTTATACACTCATATTGCATTGGGA 59.573 38.462 0.00 0.00 0.00 4.37
116 117 6.204688 ACGTTATACACTCATATTGCATTGGG 59.795 38.462 0.00 0.00 0.00 4.12
117 118 7.189693 ACGTTATACACTCATATTGCATTGG 57.810 36.000 0.00 0.00 0.00 3.16
128 129 9.811995 AGCTTCATTTATTACGTTATACACTCA 57.188 29.630 0.00 0.00 0.00 3.41
161 162 6.591448 GTGGGTAGTAACATAAGTGTGGTAAC 59.409 42.308 0.00 0.00 38.92 2.50
162 163 6.497954 AGTGGGTAGTAACATAAGTGTGGTAA 59.502 38.462 0.00 0.00 38.92 2.85
163 164 6.018469 AGTGGGTAGTAACATAAGTGTGGTA 58.982 40.000 0.00 0.00 38.92 3.25
164 165 4.842380 AGTGGGTAGTAACATAAGTGTGGT 59.158 41.667 0.00 0.00 38.92 4.16
165 166 5.416271 AGTGGGTAGTAACATAAGTGTGG 57.584 43.478 0.00 0.00 38.92 4.17
166 167 8.255206 TCAATAGTGGGTAGTAACATAAGTGTG 58.745 37.037 0.00 0.00 38.92 3.82
167 168 8.370266 TCAATAGTGGGTAGTAACATAAGTGT 57.630 34.615 0.00 0.00 41.28 3.55
168 169 7.926555 CCTCAATAGTGGGTAGTAACATAAGTG 59.073 40.741 0.00 0.00 0.00 3.16
169 170 7.622479 ACCTCAATAGTGGGTAGTAACATAAGT 59.378 37.037 2.07 0.00 32.64 2.24
170 171 8.019656 ACCTCAATAGTGGGTAGTAACATAAG 57.980 38.462 2.07 0.00 32.64 1.73
171 172 7.983166 ACCTCAATAGTGGGTAGTAACATAA 57.017 36.000 2.07 0.00 32.64 1.90
172 173 8.701908 CTACCTCAATAGTGGGTAGTAACATA 57.298 38.462 20.63 0.31 40.39 2.29
173 174 7.598759 CTACCTCAATAGTGGGTAGTAACAT 57.401 40.000 20.63 0.00 40.39 2.71
179 180 7.598759 ATGTTACTACCTCAATAGTGGGTAG 57.401 40.000 24.28 24.28 45.24 3.18
180 181 8.505246 TCTATGTTACTACCTCAATAGTGGGTA 58.495 37.037 9.29 9.29 36.09 3.69
181 182 7.359849 TCTATGTTACTACCTCAATAGTGGGT 58.640 38.462 8.14 8.14 36.09 4.51
182 183 7.506261 ACTCTATGTTACTACCTCAATAGTGGG 59.494 40.741 0.00 0.00 36.09 4.61
183 184 8.466617 ACTCTATGTTACTACCTCAATAGTGG 57.533 38.462 0.00 0.00 36.09 4.00
189 190 9.964354 TGTTACTACTCTATGTTACTACCTCAA 57.036 33.333 0.00 0.00 0.00 3.02
192 193 9.917887 ACATGTTACTACTCTATGTTACTACCT 57.082 33.333 0.00 0.00 0.00 3.08
219 220 9.571816 GGGTAGTAACATAGAGTAGTAACATCT 57.428 37.037 0.00 0.00 0.00 2.90
220 221 9.347240 TGGGTAGTAACATAGAGTAGTAACATC 57.653 37.037 0.00 0.00 0.00 3.06
221 222 9.878737 ATGGGTAGTAACATAGAGTAGTAACAT 57.121 33.333 0.00 0.00 0.00 2.71
222 223 9.705103 AATGGGTAGTAACATAGAGTAGTAACA 57.295 33.333 0.00 0.00 0.00 2.41
223 224 9.962783 CAATGGGTAGTAACATAGAGTAGTAAC 57.037 37.037 0.00 0.00 0.00 2.50
224 225 9.705103 ACAATGGGTAGTAACATAGAGTAGTAA 57.295 33.333 0.00 0.00 0.00 2.24
225 226 9.128404 CACAATGGGTAGTAACATAGAGTAGTA 57.872 37.037 0.00 0.00 0.00 1.82
226 227 7.069578 CCACAATGGGTAGTAACATAGAGTAGT 59.930 40.741 0.00 0.00 32.67 2.73
227 228 7.434492 CCACAATGGGTAGTAACATAGAGTAG 58.566 42.308 0.00 0.00 32.67 2.57
228 229 6.183360 GCCACAATGGGTAGTAACATAGAGTA 60.183 42.308 0.00 0.00 38.19 2.59
229 230 5.396436 GCCACAATGGGTAGTAACATAGAGT 60.396 44.000 0.00 0.00 38.19 3.24
230 231 5.057149 GCCACAATGGGTAGTAACATAGAG 58.943 45.833 0.00 0.00 38.19 2.43
231 232 5.031066 GCCACAATGGGTAGTAACATAGA 57.969 43.478 0.00 0.00 38.19 1.98
243 244 2.092968 TGCTTAGACTAGCCACAATGGG 60.093 50.000 0.00 0.00 40.49 4.00
244 245 2.939103 GTGCTTAGACTAGCCACAATGG 59.061 50.000 8.78 0.00 40.49 3.16
245 246 3.599343 TGTGCTTAGACTAGCCACAATG 58.401 45.455 12.30 0.00 40.49 2.82
246 247 3.981071 TGTGCTTAGACTAGCCACAAT 57.019 42.857 12.30 0.00 40.49 2.71
247 248 3.981071 ATGTGCTTAGACTAGCCACAA 57.019 42.857 16.41 5.76 40.49 3.33
248 249 5.614324 ATTATGTGCTTAGACTAGCCACA 57.386 39.130 15.38 15.38 40.49 4.17
249 250 7.711339 ACTTAATTATGTGCTTAGACTAGCCAC 59.289 37.037 3.35 7.34 40.49 5.01
250 251 7.710907 CACTTAATTATGTGCTTAGACTAGCCA 59.289 37.037 16.01 0.00 40.49 4.75
251 252 8.077836 CACTTAATTATGTGCTTAGACTAGCC 57.922 38.462 16.01 0.00 40.49 3.93
275 276 3.064207 CGAGGTGTTAGCAACTAAAGCA 58.936 45.455 0.00 0.00 43.85 3.91
277 278 4.557205 AGACGAGGTGTTAGCAACTAAAG 58.443 43.478 0.00 0.00 43.85 1.85
286 287 2.230508 TGGTGCTTAGACGAGGTGTTAG 59.769 50.000 0.00 0.00 0.00 2.34
322 323 7.169158 TCGAAGGAGGAAAAATGCAATAATT 57.831 32.000 0.00 0.00 0.00 1.40
326 327 5.665916 AATCGAAGGAGGAAAAATGCAAT 57.334 34.783 0.00 0.00 0.00 3.56
329 330 4.864806 GGAAAATCGAAGGAGGAAAAATGC 59.135 41.667 0.00 0.00 0.00 3.56
330 331 5.185828 AGGGAAAATCGAAGGAGGAAAAATG 59.814 40.000 0.00 0.00 0.00 2.32
331 332 5.333581 AGGGAAAATCGAAGGAGGAAAAAT 58.666 37.500 0.00 0.00 0.00 1.82
332 333 4.736473 AGGGAAAATCGAAGGAGGAAAAA 58.264 39.130 0.00 0.00 0.00 1.94
337 340 2.485657 GCCTAGGGAAAATCGAAGGAGG 60.486 54.545 11.72 0.00 0.00 4.30
340 343 2.092914 ACTGCCTAGGGAAAATCGAAGG 60.093 50.000 11.72 0.00 0.00 3.46
354 357 1.039785 ATGAGCGAGCAGACTGCCTA 61.040 55.000 23.74 4.75 46.52 3.93
430 433 7.984422 ATCGTCTGGCATTATTTATTGATCA 57.016 32.000 0.00 0.00 0.00 2.92
575 578 1.574428 CGTGACGGGAGCCTTTTTG 59.426 57.895 0.00 0.00 0.00 2.44
624 627 1.884926 GTGGAGATAGCTGTGGCGC 60.885 63.158 0.00 0.00 44.37 6.53
626 629 1.227380 CCGTGGAGATAGCTGTGGC 60.227 63.158 0.00 0.00 39.06 5.01
633 636 0.034059 GCATGGGTCCGTGGAGATAG 59.966 60.000 10.82 0.00 33.81 2.08
637 640 1.746615 CAAGCATGGGTCCGTGGAG 60.747 63.158 10.82 0.00 33.81 3.86
638 641 2.350895 CAAGCATGGGTCCGTGGA 59.649 61.111 10.82 0.00 33.81 4.02
651 705 1.429463 CGTTGAGGTAGGACACAAGC 58.571 55.000 0.00 0.00 0.00 4.01
657 711 0.606604 TGAAGCCGTTGAGGTAGGAC 59.393 55.000 0.00 0.00 43.70 3.85
663 717 1.301677 GAAGCCTGAAGCCGTTGAGG 61.302 60.000 0.00 0.00 45.47 3.86
680 735 1.725641 GACATGTCACGATGCCTGAA 58.274 50.000 21.07 0.00 0.00 3.02
682 737 0.458370 TCGACATGTCACGATGCCTG 60.458 55.000 24.93 6.00 33.62 4.85
683 738 0.458543 GTCGACATGTCACGATGCCT 60.459 55.000 24.93 0.00 40.50 4.75
684 739 0.458543 AGTCGACATGTCACGATGCC 60.459 55.000 24.93 7.20 40.50 4.40
686 741 2.180397 CTGAGTCGACATGTCACGATG 58.820 52.381 24.93 8.85 40.50 3.84
687 742 1.468224 GCTGAGTCGACATGTCACGAT 60.468 52.381 24.93 8.01 40.50 3.73
689 744 0.109551 AGCTGAGTCGACATGTCACG 60.110 55.000 24.93 13.27 0.00 4.35
691 746 2.420372 GAGTAGCTGAGTCGACATGTCA 59.580 50.000 24.93 11.89 0.00 3.58
692 747 2.223386 GGAGTAGCTGAGTCGACATGTC 60.223 54.545 19.50 16.21 0.00 3.06
693 748 1.746220 GGAGTAGCTGAGTCGACATGT 59.254 52.381 19.50 0.00 0.00 3.21
694 749 1.745653 TGGAGTAGCTGAGTCGACATG 59.254 52.381 19.50 8.16 0.00 3.21
695 750 2.130272 TGGAGTAGCTGAGTCGACAT 57.870 50.000 19.50 2.45 0.00 3.06
696 751 1.813178 CTTGGAGTAGCTGAGTCGACA 59.187 52.381 19.50 0.00 0.00 4.35
697 752 1.468395 GCTTGGAGTAGCTGAGTCGAC 60.468 57.143 7.70 7.70 38.15 4.20
698 753 0.811915 GCTTGGAGTAGCTGAGTCGA 59.188 55.000 0.00 0.00 38.15 4.20
699 754 0.528017 TGCTTGGAGTAGCTGAGTCG 59.472 55.000 0.00 0.00 41.76 4.18
700 755 1.404851 GGTGCTTGGAGTAGCTGAGTC 60.405 57.143 0.00 0.00 41.76 3.36
701 756 0.610687 GGTGCTTGGAGTAGCTGAGT 59.389 55.000 0.00 0.00 41.76 3.41
703 758 1.185618 ACGGTGCTTGGAGTAGCTGA 61.186 55.000 0.00 0.00 41.76 4.26
704 759 1.016130 CACGGTGCTTGGAGTAGCTG 61.016 60.000 0.00 0.00 41.76 4.24
705 760 1.293498 CACGGTGCTTGGAGTAGCT 59.707 57.895 0.00 0.00 41.76 3.32
706 761 1.741770 CCACGGTGCTTGGAGTAGC 60.742 63.158 1.68 0.00 41.59 3.58
708 763 2.214216 AGCCACGGTGCTTGGAGTA 61.214 57.895 1.68 0.00 38.85 2.59
709 764 3.560251 AGCCACGGTGCTTGGAGT 61.560 61.111 1.68 0.00 38.85 3.85
710 765 3.052082 CAGCCACGGTGCTTGGAG 61.052 66.667 1.68 0.00 40.32 3.86
711 766 4.641645 CCAGCCACGGTGCTTGGA 62.642 66.667 18.74 0.00 40.32 3.53
712 767 4.954970 ACCAGCCACGGTGCTTGG 62.955 66.667 20.71 20.71 40.32 3.61
713 768 3.357079 GACCAGCCACGGTGCTTG 61.357 66.667 1.68 3.02 40.32 4.01
714 769 3.196207 ATGACCAGCCACGGTGCTT 62.196 57.895 1.68 0.00 40.32 3.91
715 770 3.640407 ATGACCAGCCACGGTGCT 61.640 61.111 1.68 0.82 44.00 4.40
716 771 3.434319 CATGACCAGCCACGGTGC 61.434 66.667 1.68 0.00 40.22 5.01
717 772 2.032528 ACATGACCAGCCACGGTG 59.967 61.111 0.00 0.00 40.22 4.94
718 773 2.032528 CACATGACCAGCCACGGT 59.967 61.111 0.00 0.00 43.91 4.83
719 774 3.434319 GCACATGACCAGCCACGG 61.434 66.667 0.00 0.00 0.00 4.94
723 778 3.434319 CACGGCACATGACCAGCC 61.434 66.667 0.00 6.44 44.89 4.85
724 779 3.434319 CCACGGCACATGACCAGC 61.434 66.667 0.00 0.00 0.00 4.85
725 780 1.302431 TTCCACGGCACATGACCAG 60.302 57.895 0.00 0.17 0.00 4.00
726 781 1.599518 GTTCCACGGCACATGACCA 60.600 57.895 0.00 0.00 0.00 4.02
730 785 2.198906 ATTGCGTTCCACGGCACATG 62.199 55.000 0.00 0.00 42.82 3.21
780 835 2.991993 GAACGAACGGACGAACGGC 61.992 63.158 10.16 0.00 38.39 5.68
789 844 0.631745 CACATACGACGAACGAACGG 59.368 55.000 0.00 7.25 45.77 4.44
790 845 0.631745 CCACATACGACGAACGAACG 59.368 55.000 0.00 8.74 45.77 3.95
791 846 0.364515 GCCACATACGACGAACGAAC 59.635 55.000 0.00 0.00 45.77 3.95
792 847 1.066656 CGCCACATACGACGAACGAA 61.067 55.000 0.00 0.00 45.77 3.85
839 894 2.760799 GGCCAGGGCAATGCATGA 60.761 61.111 13.10 0.00 44.11 3.07
886 941 4.567327 GGACCGTGCTACTCCTATATAGGT 60.567 50.000 25.06 12.02 44.02 3.08
895 950 3.834799 CCGGGACCGTGCTACTCC 61.835 72.222 10.17 0.00 37.81 3.85
896 951 3.066814 ACCGGGACCGTGCTACTC 61.067 66.667 6.32 0.00 37.81 2.59
930 985 3.137533 GTTCTGCTTCAAGTTCTGCTCT 58.862 45.455 0.00 0.00 0.00 4.09
940 995 2.346766 TTGGCTCTGTTCTGCTTCAA 57.653 45.000 0.00 0.00 0.00 2.69
941 996 2.346766 TTTGGCTCTGTTCTGCTTCA 57.653 45.000 0.00 0.00 0.00 3.02
942 997 2.287849 GGTTTTGGCTCTGTTCTGCTTC 60.288 50.000 0.00 0.00 0.00 3.86
943 998 1.683385 GGTTTTGGCTCTGTTCTGCTT 59.317 47.619 0.00 0.00 0.00 3.91
944 999 1.322442 GGTTTTGGCTCTGTTCTGCT 58.678 50.000 0.00 0.00 0.00 4.24
945 1000 1.032014 TGGTTTTGGCTCTGTTCTGC 58.968 50.000 0.00 0.00 0.00 4.26
946 1001 2.223805 GGTTGGTTTTGGCTCTGTTCTG 60.224 50.000 0.00 0.00 0.00 3.02
947 1002 2.031870 GGTTGGTTTTGGCTCTGTTCT 58.968 47.619 0.00 0.00 0.00 3.01
948 1003 1.068588 GGGTTGGTTTTGGCTCTGTTC 59.931 52.381 0.00 0.00 0.00 3.18
949 1004 1.119684 GGGTTGGTTTTGGCTCTGTT 58.880 50.000 0.00 0.00 0.00 3.16
950 1005 0.032615 TGGGTTGGTTTTGGCTCTGT 60.033 50.000 0.00 0.00 0.00 3.41
951 1006 1.118838 TTGGGTTGGTTTTGGCTCTG 58.881 50.000 0.00 0.00 0.00 3.35
952 1007 1.872773 TTTGGGTTGGTTTTGGCTCT 58.127 45.000 0.00 0.00 0.00 4.09
953 1008 2.700722 TTTTGGGTTGGTTTTGGCTC 57.299 45.000 0.00 0.00 0.00 4.70
954 1009 2.943646 GCTTTTTGGGTTGGTTTTGGCT 60.944 45.455 0.00 0.00 0.00 4.75
955 1010 1.403679 GCTTTTTGGGTTGGTTTTGGC 59.596 47.619 0.00 0.00 0.00 4.52
956 1011 2.716217 TGCTTTTTGGGTTGGTTTTGG 58.284 42.857 0.00 0.00 0.00 3.28
957 1012 4.979943 AATGCTTTTTGGGTTGGTTTTG 57.020 36.364 0.00 0.00 0.00 2.44
958 1013 4.095632 CGAAATGCTTTTTGGGTTGGTTTT 59.904 37.500 4.70 0.00 0.00 2.43
983 1038 1.661341 CATGGCTTCACTGTCCTAGC 58.339 55.000 0.00 0.00 0.00 3.42
1003 1066 2.352519 GGTACAGGACAACGGTCTTCTC 60.353 54.545 0.00 0.00 43.77 2.87
1284 1371 1.306970 GAGGAAGTCGAGGAGGGGA 59.693 63.158 0.00 0.00 0.00 4.81
1419 1506 0.388649 GGTTGAAGAAGAGCGCGAGA 60.389 55.000 12.10 0.00 0.00 4.04
1432 1519 2.260869 GCTTGCTCGGCAGGTTGAA 61.261 57.895 9.14 0.00 40.61 2.69
1515 1608 3.950869 GGGTAAGTCCGAAGCCTTT 57.049 52.632 0.00 0.00 37.00 3.11
1539 1635 2.993899 GAGTACTTCATCGTTGTGGGTG 59.006 50.000 0.00 0.00 0.00 4.61
1571 1667 0.374758 CATTCGGTCGAACATGCCTG 59.625 55.000 8.00 0.00 36.91 4.85
1719 1815 2.602267 TTGTCTCCGCCTCCCGAA 60.602 61.111 0.00 0.00 40.02 4.30
1847 1955 4.471386 TCTCCCCTGACTTTTCTAATCCAG 59.529 45.833 0.00 0.00 0.00 3.86
2226 2337 0.489567 ACCTGACCTTCTCCTCCACT 59.510 55.000 0.00 0.00 0.00 4.00
2441 2555 1.520494 TGAGATAGCCCGCTACTACG 58.480 55.000 0.00 0.00 0.00 3.51
2495 2611 0.396811 ACAGTAGCTGCGAAAGGGTT 59.603 50.000 0.00 0.00 34.37 4.11
2596 2715 2.544359 CGGTTGTCGCACAGTTCG 59.456 61.111 0.00 0.00 0.00 3.95
2619 2738 2.040278 AGAGTGGCTGGGAGGGAG 59.960 66.667 0.00 0.00 0.00 4.30
2620 2739 2.039624 GAGAGTGGCTGGGAGGGA 59.960 66.667 0.00 0.00 0.00 4.20
2621 2740 3.465403 CGAGAGTGGCTGGGAGGG 61.465 72.222 0.00 0.00 0.00 4.30
2756 2908 3.471806 GCGAGGAGGGGAAGGGTC 61.472 72.222 0.00 0.00 0.00 4.46
2865 3017 3.054503 CCACCGAGACGACGACCT 61.055 66.667 0.00 0.00 35.09 3.85
2895 3048 3.390183 CTCCATGGCAGCTACCGCA 62.390 63.158 6.96 0.00 39.10 5.69
2901 3054 3.736224 CACCCCTCCATGGCAGCT 61.736 66.667 6.96 0.00 0.00 4.24
2940 3093 3.620785 AGATCCGCCGCCTGATCC 61.621 66.667 11.92 0.00 38.50 3.36
2942 3095 3.933722 CCAGATCCGCCGCCTGAT 61.934 66.667 0.00 0.00 0.00 2.90
2945 3098 2.715181 TAGATCCAGATCCGCCGCCT 62.715 60.000 4.01 0.00 38.58 5.52
3046 3199 3.902162 GAACTACCGCACGACCGCA 62.902 63.158 0.00 0.00 0.00 5.69
3051 3204 1.642037 CGAGGAGAACTACCGCACGA 61.642 60.000 0.00 0.00 0.00 4.35
3059 3212 2.110967 CGTCGCCCGAGGAGAACTA 61.111 63.158 4.53 0.00 39.56 2.24
3093 3246 2.666190 CAGCACCCGGATATGCGG 60.666 66.667 27.14 27.14 46.74 5.69
3098 3251 1.686325 GCCTTCTCAGCACCCGGATA 61.686 60.000 0.73 0.00 0.00 2.59
3120 3290 2.356313 CGTCAAGTGACTGCGCCT 60.356 61.111 4.18 0.00 42.66 5.52
3126 3296 1.185618 TAGCCTGCCGTCAAGTGACT 61.186 55.000 9.63 0.00 42.66 3.41
3272 3443 2.358737 CTGTCTCCACAACCGCCC 60.359 66.667 0.00 0.00 29.82 6.13
3275 3446 2.022129 GTCGCTGTCTCCACAACCG 61.022 63.158 0.00 0.00 29.82 4.44
3322 3493 0.459237 AGCTCGAAATGGCTCGTGAG 60.459 55.000 1.57 0.00 39.84 3.51
3331 3502 3.264897 CCCGCCGAGCTCGAAATG 61.265 66.667 36.59 20.69 43.02 2.32
3354 3525 1.203441 AGAGGAGCAATCCAGGCACA 61.203 55.000 0.00 0.00 0.00 4.57
3363 3534 2.124819 CGCAGCCAGAGGAGCAAT 60.125 61.111 0.00 0.00 0.00 3.56
3364 3535 3.596066 GACGCAGCCAGAGGAGCAA 62.596 63.158 0.00 0.00 0.00 3.91


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

AutoCloner maintained by Alex Coulton.