Multiple sequence alignment - TraesCS5D01G156300

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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 TraesCS5D01G156300 chr5D 100.000 5925 0 0 1 5925 244616814 244622738 0.000000e+00 10942.0
1 TraesCS5D01G156300 chr5D 86.402 478 44 13 253 718 420593744 420593276 2.460000e-138 503.0
2 TraesCS5D01G156300 chr5D 97.368 228 5 1 1 227 529345612 529345839 2.590000e-103 387.0
3 TraesCS5D01G156300 chr5D 96.943 229 6 1 1 228 25218951 25218723 3.350000e-102 383.0
4 TraesCS5D01G156300 chr5B 95.848 4769 147 20 218 4964 278004780 278009519 0.000000e+00 7662.0
5 TraesCS5D01G156300 chr5B 86.228 973 83 24 4977 5922 278009505 278010453 0.000000e+00 1007.0
6 TraesCS5D01G156300 chr5B 100.000 43 0 0 215 257 278001065 278001107 4.920000e-11 80.5
7 TraesCS5D01G156300 chr5B 97.826 46 1 0 212 257 278002424 278002469 4.920000e-11 80.5
8 TraesCS5D01G156300 chr5A 95.160 4029 130 29 958 4967 328798382 328802364 0.000000e+00 6300.0
9 TraesCS5D01G156300 chr5A 90.387 957 68 13 4977 5925 328802348 328803288 0.000000e+00 1236.0
10 TraesCS5D01G156300 chr5A 87.675 357 36 8 3095 3446 667026865 667027218 5.530000e-110 409.0
11 TraesCS5D01G156300 chr5A 94.583 240 13 0 1 240 320893964 320893725 7.250000e-99 372.0
12 TraesCS5D01G156300 chr5A 87.705 244 25 4 5209 5452 503771660 503771422 4.520000e-71 279.0
13 TraesCS5D01G156300 chr5A 87.444 223 23 5 3228 3447 531217297 531217077 9.860000e-63 252.0
14 TraesCS5D01G156300 chr5A 90.210 143 11 2 3098 3239 531218778 531218638 3.650000e-42 183.0
15 TraesCS5D01G156300 chr6D 88.166 507 43 13 256 749 428398997 428399499 6.610000e-164 588.0
16 TraesCS5D01G156300 chr6D 85.294 510 56 14 253 749 428311269 428311772 5.300000e-140 508.0
17 TraesCS5D01G156300 chr6D 84.105 497 57 15 266 749 100457258 100457745 1.500000e-125 460.0
18 TraesCS5D01G156300 chr6D 97.758 223 4 1 1 222 56235193 56234971 3.350000e-102 383.0
19 TraesCS5D01G156300 chr6D 91.803 61 2 2 2383 2442 417390662 417390604 1.370000e-11 82.4
20 TraesCS5D01G156300 chr6A 85.631 515 58 13 245 746 572973772 572974283 1.460000e-145 527.0
21 TraesCS5D01G156300 chr6A 97.778 45 1 0 213 257 572964936 572964980 1.770000e-10 78.7
22 TraesCS5D01G156300 chr6B 86.385 426 41 12 245 657 644359965 644360386 3.260000e-122 449.0
23 TraesCS5D01G156300 chr6B 90.426 94 8 1 245 337 465663461 465663554 8.060000e-24 122.0
24 TraesCS5D01G156300 chr6B 100.000 43 0 0 215 257 202745660 202745702 4.920000e-11 80.5
25 TraesCS5D01G156300 chr4B 88.451 355 33 7 3097 3447 75737997 75737647 7.100000e-114 422.0
26 TraesCS5D01G156300 chr4B 93.023 86 5 1 253 337 649035715 649035630 2.240000e-24 124.0
27 TraesCS5D01G156300 chr7D 95.385 260 8 3 1 257 182837790 182837532 1.540000e-110 411.0
28 TraesCS5D01G156300 chr7D 97.758 223 3 1 1 221 112034347 112034125 3.350000e-102 383.0
29 TraesCS5D01G156300 chr7D 85.588 340 44 5 414 751 63019259 63018923 9.450000e-93 351.0
30 TraesCS5D01G156300 chr7D 96.774 31 1 0 5568 5598 598023132 598023162 1.100000e-02 52.8
31 TraesCS5D01G156300 chr1A 87.324 355 37 7 3097 3447 65759836 65760186 3.330000e-107 399.0
32 TraesCS5D01G156300 chr1A 82.266 203 33 3 3094 3294 267262320 267262521 7.890000e-39 172.0
33 TraesCS5D01G156300 chr2D 98.182 220 4 0 1 220 457683291 457683072 9.310000e-103 385.0
34 TraesCS5D01G156300 chr2D 97.297 222 5 1 1 221 599883368 599883589 5.610000e-100 375.0
35 TraesCS5D01G156300 chr2D 84.071 339 47 7 414 750 533657214 533657547 2.660000e-83 320.0
36 TraesCS5D01G156300 chr3D 96.552 232 5 3 1 230 487305794 487305564 1.200000e-101 381.0
37 TraesCS5D01G156300 chr3B 80.897 513 70 17 250 750 248131632 248132128 4.330000e-101 379.0
38 TraesCS5D01G156300 chr3B 83.974 312 47 3 3573 3881 216873664 216873353 4.490000e-76 296.0
39 TraesCS5D01G156300 chr1D 85.882 340 40 7 426 761 70451664 70451999 7.300000e-94 355.0
40 TraesCS5D01G156300 chrUn 84.211 342 38 10 414 750 97480682 97480352 9.580000e-83 318.0
41 TraesCS5D01G156300 chrUn 83.841 328 45 8 426 749 92648904 92648581 7.460000e-79 305.0
42 TraesCS5D01G156300 chrUn 97.778 45 1 0 212 256 66732126 66732170 1.770000e-10 78.7
43 TraesCS5D01G156300 chrUn 95.652 46 2 0 212 257 66726527 66726572 2.290000e-09 75.0
44 TraesCS5D01G156300 chrUn 95.652 46 2 0 212 257 66728646 66728691 2.290000e-09 75.0
45 TraesCS5D01G156300 chr2B 80.000 210 28 4 5248 5457 202269867 202270062 6.190000e-30 143.0
46 TraesCS5D01G156300 chr4A 80.606 165 18 13 3095 3252 277904942 277905099 1.350000e-21 115.0
47 TraesCS5D01G156300 chr4D 82.727 110 19 0 3095 3204 375718315 375718206 1.360000e-16 99.0


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 TraesCS5D01G156300 chr5D 244616814 244622738 5924 False 10942.0 10942 100.0000 1 5925 1 chr5D.!!$F1 5924
1 TraesCS5D01G156300 chr5B 278001065 278010453 9388 False 2207.5 7662 94.9755 212 5922 4 chr5B.!!$F1 5710
2 TraesCS5D01G156300 chr5A 328798382 328803288 4906 False 3768.0 6300 92.7735 958 5925 2 chr5A.!!$F2 4967
3 TraesCS5D01G156300 chr5A 531217077 531218778 1701 True 217.5 252 88.8270 3098 3447 2 chr5A.!!$R3 349
4 TraesCS5D01G156300 chr6D 428398997 428399499 502 False 588.0 588 88.1660 256 749 1 chr6D.!!$F3 493
5 TraesCS5D01G156300 chr6D 428311269 428311772 503 False 508.0 508 85.2940 253 749 1 chr6D.!!$F2 496
6 TraesCS5D01G156300 chr6A 572973772 572974283 511 False 527.0 527 85.6310 245 746 1 chr6A.!!$F2 501

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
820 4333 0.387929 TGCCGAGTCACGTTTTCTCT 59.612 50.000 8.90 0.00 40.78 3.10 F
1727 5250 1.138859 CACGGACAATCCTATGCCTCA 59.861 52.381 0.00 0.00 33.30 3.86 F
2477 6000 0.742281 CAGACTTGGGGACAGATGCG 60.742 60.000 0.00 0.00 44.54 4.73 F
3420 8300 1.077915 TACACACTGCGCATCACATG 58.922 50.000 12.24 8.15 0.00 3.21 F
4504 9395 0.182061 CACTGGAGCTGGCATATGGT 59.818 55.000 4.56 0.00 0.00 3.55 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1872 5395 1.067060 GTTTGGCAGTTGTCCCTTGAC 59.933 52.381 0.00 0.00 42.12 3.18 R
3420 8300 3.006940 TCAGCATTATTTCCACGGACAC 58.993 45.455 0.00 0.00 0.00 3.67 R
4267 9149 0.318955 GTTGACCCTGCATGCAACAC 60.319 55.000 22.88 13.37 40.11 3.32 R
4733 9624 0.104120 TCACCACCACGAGACAACAG 59.896 55.000 0.00 0.00 0.00 3.16 R
5583 10529 2.069273 CTATTCCCTATTTGCCGCTCG 58.931 52.381 0.00 0.00 0.00 5.03 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
19 20 1.667595 TCCAATGTCCATGGTCAGGA 58.332 50.000 16.79 15.06 39.09 3.86
20 21 1.991813 TCCAATGTCCATGGTCAGGAA 59.008 47.619 16.79 0.75 39.09 3.36
22 23 2.493278 CCAATGTCCATGGTCAGGAAAC 59.507 50.000 16.79 4.30 36.80 2.78
23 24 2.493278 CAATGTCCATGGTCAGGAAACC 59.507 50.000 16.79 0.00 36.80 3.27
32 33 3.963129 TGGTCAGGAAACCATAACCATC 58.037 45.455 0.00 0.00 44.40 3.51
33 34 3.591527 TGGTCAGGAAACCATAACCATCT 59.408 43.478 0.00 0.00 44.40 2.90
34 35 4.785914 TGGTCAGGAAACCATAACCATCTA 59.214 41.667 0.00 0.00 44.40 1.98
35 36 5.431731 TGGTCAGGAAACCATAACCATCTAT 59.568 40.000 0.00 0.00 44.40 1.98
36 37 6.069088 TGGTCAGGAAACCATAACCATCTATT 60.069 38.462 0.00 0.00 44.40 1.73
37 38 6.263168 GGTCAGGAAACCATAACCATCTATTG 59.737 42.308 0.00 0.00 39.27 1.90
39 40 7.721399 GTCAGGAAACCATAACCATCTATTGAT 59.279 37.037 0.00 0.00 0.00 2.57
40 41 7.939039 TCAGGAAACCATAACCATCTATTGATC 59.061 37.037 0.00 0.00 0.00 2.92
41 42 7.720957 CAGGAAACCATAACCATCTATTGATCA 59.279 37.037 0.00 0.00 0.00 2.92
42 43 8.281531 AGGAAACCATAACCATCTATTGATCAA 58.718 33.333 11.26 11.26 0.00 2.57
43 44 8.352942 GGAAACCATAACCATCTATTGATCAAC 58.647 37.037 11.07 0.00 0.00 3.18
46 47 6.931281 ACCATAACCATCTATTGATCAACGAG 59.069 38.462 11.07 11.28 0.00 4.18
47 48 6.128445 CCATAACCATCTATTGATCAACGAGC 60.128 42.308 11.07 0.00 0.00 5.03
48 49 4.679373 ACCATCTATTGATCAACGAGCT 57.321 40.909 11.07 0.00 0.00 4.09
51 52 5.303078 ACCATCTATTGATCAACGAGCTAGT 59.697 40.000 11.07 6.23 0.00 2.57
52 53 5.861251 CCATCTATTGATCAACGAGCTAGTC 59.139 44.000 11.07 0.00 0.00 2.59
53 54 6.442112 CATCTATTGATCAACGAGCTAGTCA 58.558 40.000 11.07 0.00 0.00 3.41
54 55 6.451064 TCTATTGATCAACGAGCTAGTCAA 57.549 37.500 11.07 0.55 0.00 3.18
56 57 4.521130 TTGATCAACGAGCTAGTCAACT 57.479 40.909 3.38 0.00 0.00 3.16
57 58 5.638596 TTGATCAACGAGCTAGTCAACTA 57.361 39.130 3.38 0.00 0.00 2.24
58 59 5.236655 TGATCAACGAGCTAGTCAACTAG 57.763 43.478 11.99 11.99 46.63 2.57
59 60 4.941873 TGATCAACGAGCTAGTCAACTAGA 59.058 41.667 19.03 0.00 46.80 2.43
60 61 4.948608 TCAACGAGCTAGTCAACTAGAG 57.051 45.455 19.03 11.89 46.80 2.43
63 64 2.294074 CGAGCTAGTCAACTAGAGGCT 58.706 52.381 19.03 10.84 46.80 4.58
64 65 2.685897 CGAGCTAGTCAACTAGAGGCTT 59.314 50.000 19.03 1.20 46.80 4.35
65 66 3.878103 CGAGCTAGTCAACTAGAGGCTTA 59.122 47.826 19.03 0.00 46.80 3.09
66 67 4.260866 CGAGCTAGTCAACTAGAGGCTTAC 60.261 50.000 19.03 1.96 46.80 2.34
67 68 4.862371 AGCTAGTCAACTAGAGGCTTACT 58.138 43.478 19.03 3.99 46.80 2.24
68 69 6.003859 AGCTAGTCAACTAGAGGCTTACTA 57.996 41.667 19.03 0.00 46.80 1.82
69 70 6.059484 AGCTAGTCAACTAGAGGCTTACTAG 58.941 44.000 19.03 8.32 46.80 2.57
71 72 4.538738 AGTCAACTAGAGGCTTACTAGGG 58.461 47.826 13.13 6.54 40.86 3.53
72 73 4.230041 AGTCAACTAGAGGCTTACTAGGGA 59.770 45.833 13.13 8.30 40.86 4.20
73 74 4.338964 GTCAACTAGAGGCTTACTAGGGAC 59.661 50.000 13.13 14.30 40.86 4.46
74 75 4.017775 TCAACTAGAGGCTTACTAGGGACA 60.018 45.833 13.13 0.00 40.86 4.02
75 76 4.817874 ACTAGAGGCTTACTAGGGACAT 57.182 45.455 13.13 0.00 40.86 3.06
76 77 4.475345 ACTAGAGGCTTACTAGGGACATG 58.525 47.826 13.13 0.00 40.86 3.21
77 78 3.406512 AGAGGCTTACTAGGGACATGT 57.593 47.619 0.00 0.00 0.00 3.21
78 79 3.725634 AGAGGCTTACTAGGGACATGTT 58.274 45.455 0.00 0.00 0.00 2.71
79 80 3.452627 AGAGGCTTACTAGGGACATGTTG 59.547 47.826 0.00 0.00 0.00 3.33
80 81 3.182152 AGGCTTACTAGGGACATGTTGT 58.818 45.455 0.00 0.00 0.00 3.32
81 82 3.055094 AGGCTTACTAGGGACATGTTGTG 60.055 47.826 0.00 0.00 0.00 3.33
82 83 3.270877 GCTTACTAGGGACATGTTGTGG 58.729 50.000 0.00 0.00 0.00 4.17
83 84 3.307480 GCTTACTAGGGACATGTTGTGGT 60.307 47.826 0.00 0.00 0.00 4.16
84 85 4.504858 CTTACTAGGGACATGTTGTGGTC 58.495 47.826 0.00 0.00 0.00 4.02
85 86 2.621070 ACTAGGGACATGTTGTGGTCT 58.379 47.619 0.00 0.00 34.49 3.85
87 88 4.362677 ACTAGGGACATGTTGTGGTCTAT 58.637 43.478 0.00 0.00 34.49 1.98
89 90 2.912956 AGGGACATGTTGTGGTCTATGT 59.087 45.455 0.00 0.00 36.54 2.29
90 91 4.101114 AGGGACATGTTGTGGTCTATGTA 58.899 43.478 0.00 0.00 34.18 2.29
91 92 4.721776 AGGGACATGTTGTGGTCTATGTAT 59.278 41.667 0.00 0.00 34.18 2.29
92 93 5.191722 AGGGACATGTTGTGGTCTATGTATT 59.808 40.000 0.00 0.00 34.18 1.89
93 94 5.527582 GGGACATGTTGTGGTCTATGTATTC 59.472 44.000 0.00 0.00 34.18 1.75
94 95 6.112734 GGACATGTTGTGGTCTATGTATTCA 58.887 40.000 0.00 0.00 34.18 2.57
95 96 6.037172 GGACATGTTGTGGTCTATGTATTCAC 59.963 42.308 0.00 0.00 34.18 3.18
96 97 6.472016 ACATGTTGTGGTCTATGTATTCACA 58.528 36.000 0.00 0.00 39.52 3.58
97 98 6.371548 ACATGTTGTGGTCTATGTATTCACAC 59.628 38.462 0.00 0.00 37.96 3.82
98 99 5.859495 TGTTGTGGTCTATGTATTCACACA 58.141 37.500 0.00 0.00 37.96 3.72
99 100 6.472016 TGTTGTGGTCTATGTATTCACACAT 58.528 36.000 0.00 0.00 41.88 3.21
100 101 6.371271 TGTTGTGGTCTATGTATTCACACATG 59.629 38.462 0.00 0.00 39.46 3.21
101 102 6.048732 TGTGGTCTATGTATTCACACATGT 57.951 37.500 0.00 0.00 39.46 3.21
103 104 7.791029 TGTGGTCTATGTATTCACACATGTAT 58.209 34.615 0.00 0.00 39.46 2.29
104 105 8.264347 TGTGGTCTATGTATTCACACATGTATT 58.736 33.333 0.00 0.00 39.46 1.89
105 106 9.758651 GTGGTCTATGTATTCACACATGTATTA 57.241 33.333 0.00 0.00 39.46 0.98
106 107 9.758651 TGGTCTATGTATTCACACATGTATTAC 57.241 33.333 0.00 0.00 39.46 1.89
107 108 8.912658 GGTCTATGTATTCACACATGTATTACG 58.087 37.037 0.00 0.00 39.46 3.18
108 109 8.912658 GTCTATGTATTCACACATGTATTACGG 58.087 37.037 0.00 0.00 39.46 4.02
109 110 8.635328 TCTATGTATTCACACATGTATTACGGT 58.365 33.333 0.00 0.00 39.46 4.83
110 111 9.256477 CTATGTATTCACACATGTATTACGGTT 57.744 33.333 0.00 0.00 39.46 4.44
111 112 7.908827 TGTATTCACACATGTATTACGGTTT 57.091 32.000 0.00 0.00 0.00 3.27
112 113 7.966111 TGTATTCACACATGTATTACGGTTTC 58.034 34.615 0.00 0.00 0.00 2.78
113 114 5.866335 TTCACACATGTATTACGGTTTCC 57.134 39.130 0.00 0.00 0.00 3.13
114 115 4.895961 TCACACATGTATTACGGTTTCCA 58.104 39.130 0.00 0.00 0.00 3.53
115 116 4.932799 TCACACATGTATTACGGTTTCCAG 59.067 41.667 0.00 0.00 0.00 3.86
117 118 5.180492 CACACATGTATTACGGTTTCCAGTT 59.820 40.000 0.00 0.00 0.00 3.16
118 119 6.369340 CACACATGTATTACGGTTTCCAGTTA 59.631 38.462 0.00 0.00 0.00 2.24
120 121 7.608761 ACACATGTATTACGGTTTCCAGTTAAT 59.391 33.333 0.00 0.00 0.00 1.40
121 122 9.100554 CACATGTATTACGGTTTCCAGTTAATA 57.899 33.333 0.00 0.00 0.00 0.98
122 123 9.101655 ACATGTATTACGGTTTCCAGTTAATAC 57.898 33.333 0.00 0.00 32.58 1.89
123 124 9.100554 CATGTATTACGGTTTCCAGTTAATACA 57.899 33.333 17.27 17.27 40.70 2.29
124 125 9.669887 ATGTATTACGGTTTCCAGTTAATACAA 57.330 29.630 18.06 9.65 40.20 2.41
125 126 9.669887 TGTATTACGGTTTCCAGTTAATACAAT 57.330 29.630 14.94 0.00 36.55 2.71
155 156 9.346005 AGCATGAACAATAGACAATTATCATGA 57.654 29.630 19.46 0.00 44.39 3.07
156 157 9.955208 GCATGAACAATAGACAATTATCATGAA 57.045 29.630 19.46 0.00 44.39 2.57
162 163 9.685276 ACAATAGACAATTATCATGAACAAGGA 57.315 29.630 0.00 0.00 0.00 3.36
214 215 4.935352 TTAGGGCATATTTCCAACATGC 57.065 40.909 0.00 0.00 43.43 4.06
361 3860 0.835941 AGAGGATTGAGCGATGCCTT 59.164 50.000 0.00 0.00 0.00 4.35
394 3893 1.098712 ACCGTGCGTCAAACCATGTT 61.099 50.000 0.00 0.00 0.00 2.71
473 3975 0.981277 ATAGTGTTGGTAGCCCCGCT 60.981 55.000 0.00 0.00 43.41 5.52
482 3984 0.740737 GTAGCCCCGCTCGTAACTAA 59.259 55.000 0.00 0.00 40.44 2.24
518 4020 3.328382 TCGCCGGAAATATAATGGGAG 57.672 47.619 5.05 0.00 0.00 4.30
543 4056 2.721425 AGGGAAACAAAGAACCGACA 57.279 45.000 0.00 0.00 0.00 4.35
661 4174 4.691216 CACAAACCGAAAAGGAAAAACCAA 59.309 37.500 0.00 0.00 45.00 3.67
695 4208 1.964373 GCTGGTTTTTCCTCGCGGA 60.964 57.895 6.13 0.00 37.60 5.54
762 4275 3.243336 CGCTCGTTAACTAGTTGCTCTT 58.757 45.455 18.56 0.00 0.00 2.85
817 4330 1.390463 GAGATGCCGAGTCACGTTTTC 59.610 52.381 0.00 0.00 40.78 2.29
820 4333 0.387929 TGCCGAGTCACGTTTTCTCT 59.612 50.000 8.90 0.00 40.78 3.10
826 4339 4.211374 CCGAGTCACGTTTTCTCTGAAAAT 59.789 41.667 8.43 0.00 40.78 1.82
828 4341 6.073980 CCGAGTCACGTTTTCTCTGAAAATTA 60.074 38.462 8.43 0.00 40.78 1.40
834 4347 9.887406 TCACGTTTTCTCTGAAAATTATAAACC 57.113 29.630 8.43 0.00 0.00 3.27
835 4348 8.837059 CACGTTTTCTCTGAAAATTATAAACCG 58.163 33.333 8.43 7.38 0.00 4.44
836 4349 8.776470 ACGTTTTCTCTGAAAATTATAAACCGA 58.224 29.630 8.43 0.00 0.00 4.69
868 4381 4.241590 TCGTTATACGTGTGAGTTTGGT 57.758 40.909 0.00 0.00 43.14 3.67
880 4393 2.495084 GAGTTTGGTCCACCTGAACTC 58.505 52.381 20.24 20.24 44.34 3.01
942 4456 5.500546 TCTAGGTTTTCTTTCCTCTTCCC 57.499 43.478 0.00 0.00 35.51 3.97
1494 5008 9.716507 TCTTTCGTTTCTTCTTTGTTTTATCTG 57.283 29.630 0.00 0.00 0.00 2.90
1545 5063 6.098266 AGTTCATAAGCTGGGTTTCAAGTTTT 59.902 34.615 0.00 0.00 0.00 2.43
1614 5132 7.617041 AGGATTATTAGAAGCTGACAACAAC 57.383 36.000 0.00 0.00 0.00 3.32
1727 5250 1.138859 CACGGACAATCCTATGCCTCA 59.861 52.381 0.00 0.00 33.30 3.86
1746 5269 2.705658 TCATTTCACTGTCCACCAGACT 59.294 45.455 0.00 0.00 46.46 3.24
1872 5395 9.702726 CATAATCGCAATATTATCTTTAACCGG 57.297 33.333 0.00 0.00 31.17 5.28
1934 5457 2.566833 TTGGTCCTTCCTGTCATGTG 57.433 50.000 0.00 0.00 37.07 3.21
2103 5626 3.160269 AGCAGACTAAAAGCTTGCCAAT 58.840 40.909 0.00 0.00 34.37 3.16
2247 5770 4.529897 ACCAGCATGTTCATGTACATCAT 58.470 39.130 14.38 4.03 36.64 2.45
2314 5837 9.739276 ATGTTGACTTAAGTTGATTCTTCCATA 57.261 29.630 10.02 0.00 0.00 2.74
2327 5850 8.347004 TGATTCTTCCATAAACTGTATTTGCA 57.653 30.769 0.00 0.00 0.00 4.08
2347 5870 3.129287 GCATCTTCCATTCGTTGGTGAAT 59.871 43.478 6.97 0.00 46.52 2.57
2477 6000 0.742281 CAGACTTGGGGACAGATGCG 60.742 60.000 0.00 0.00 44.54 4.73
2792 6315 5.061853 AGATGCCTAATCATGTCACACATC 58.938 41.667 0.00 1.40 36.53 3.06
2814 6337 8.774586 ACATCCGTCTCTATACAAATTTAATGC 58.225 33.333 0.00 0.00 0.00 3.56
3226 6749 6.692681 CCATTATACTGACATTTTCTTTGGCG 59.307 38.462 0.00 0.00 0.00 5.69
3420 8300 1.077915 TACACACTGCGCATCACATG 58.922 50.000 12.24 8.15 0.00 3.21
3564 8444 7.042950 GTGTTTGGTACTTTGGGTTGTTATTT 58.957 34.615 0.00 0.00 0.00 1.40
3691 8571 7.389803 CACTAATTGTGTTGGATAATCACCA 57.610 36.000 0.00 0.00 41.53 4.17
3910 8792 6.790282 GTTGTAAACCAAACGTACCCTAAAA 58.210 36.000 0.00 0.00 42.21 1.52
3937 8819 3.137176 AGGCTATTATTCTCTGCCAGCAA 59.863 43.478 0.00 0.00 45.42 3.91
4504 9395 0.182061 CACTGGAGCTGGCATATGGT 59.818 55.000 4.56 0.00 0.00 3.55
4564 9455 4.530857 GTCGAGGGGTCATGGCCG 62.531 72.222 10.95 0.00 0.00 6.13
4585 9476 1.420532 AAGGGTTCCACGGCCAGTTA 61.421 55.000 2.24 0.00 0.00 2.24
4656 9547 2.881352 CGAGAAAGAGGCCGTCGC 60.881 66.667 0.00 0.00 0.00 5.19
4657 9548 2.574399 GAGAAAGAGGCCGTCGCT 59.426 61.111 0.00 0.00 34.44 4.93
4716 9607 0.250295 TCTGTTGAAAGGTCTGGGCG 60.250 55.000 0.00 0.00 0.00 6.13
4721 9612 3.249189 AAAGGTCTGGGCGGCTCA 61.249 61.111 9.56 1.02 0.00 4.26
4733 9624 1.503542 CGGCTCATGGTTTGTGCTC 59.496 57.895 0.00 0.00 42.97 4.26
4798 9689 3.455469 GCACCATTGGAGGCTGGC 61.455 66.667 10.37 0.00 35.88 4.85
4825 9716 0.828022 ATGGCATGCTTGATGTTGGG 59.172 50.000 18.92 0.00 34.14 4.12
4840 9731 2.813908 GGGTCGTGTAAGCTGCGG 60.814 66.667 0.00 0.00 0.00 5.69
4927 9818 1.205893 GAGGCTGTTGCTAGCTAGTGT 59.794 52.381 21.62 3.69 43.22 3.55
4937 9828 3.118992 TGCTAGCTAGTGTGGAGTTCATG 60.119 47.826 21.62 0.00 0.00 3.07
4938 9829 3.118956 GCTAGCTAGTGTGGAGTTCATGT 60.119 47.826 21.62 0.00 0.00 3.21
4939 9830 4.621747 GCTAGCTAGTGTGGAGTTCATGTT 60.622 45.833 21.62 0.00 0.00 2.71
4940 9831 3.931578 AGCTAGTGTGGAGTTCATGTTC 58.068 45.455 0.00 0.00 0.00 3.18
4941 9832 3.324846 AGCTAGTGTGGAGTTCATGTTCA 59.675 43.478 0.00 0.00 0.00 3.18
4942 9833 4.019860 AGCTAGTGTGGAGTTCATGTTCAT 60.020 41.667 0.00 0.00 0.00 2.57
4954 9845 4.801521 TCATGTTCATCCCATGGATCTT 57.198 40.909 15.22 0.00 40.98 2.40
4955 9846 5.910355 TCATGTTCATCCCATGGATCTTA 57.090 39.130 15.22 0.00 40.98 2.10
4956 9847 6.264771 TCATGTTCATCCCATGGATCTTAA 57.735 37.500 15.22 0.00 40.98 1.85
4957 9848 6.855667 TCATGTTCATCCCATGGATCTTAAT 58.144 36.000 15.22 0.00 40.98 1.40
4958 9849 7.987820 TCATGTTCATCCCATGGATCTTAATA 58.012 34.615 15.22 0.00 40.98 0.98
4959 9850 8.105197 TCATGTTCATCCCATGGATCTTAATAG 58.895 37.037 15.22 0.00 40.98 1.73
4960 9851 7.392766 TGTTCATCCCATGGATCTTAATAGT 57.607 36.000 15.22 0.00 40.98 2.12
4961 9852 7.226441 TGTTCATCCCATGGATCTTAATAGTG 58.774 38.462 15.22 0.00 40.98 2.74
4962 9853 5.809001 TCATCCCATGGATCTTAATAGTGC 58.191 41.667 15.22 0.00 40.98 4.40
4963 9854 5.549228 TCATCCCATGGATCTTAATAGTGCT 59.451 40.000 15.22 0.00 40.98 4.40
4964 9855 5.912149 TCCCATGGATCTTAATAGTGCTT 57.088 39.130 15.22 0.00 0.00 3.91
4965 9856 7.237471 TCATCCCATGGATCTTAATAGTGCTTA 59.763 37.037 15.22 0.00 40.98 3.09
4966 9857 7.574021 TCCCATGGATCTTAATAGTGCTTAT 57.426 36.000 15.22 0.00 0.00 1.73
4967 9858 7.988937 TCCCATGGATCTTAATAGTGCTTATT 58.011 34.615 15.22 0.00 36.05 1.40
4968 9859 8.448008 TCCCATGGATCTTAATAGTGCTTATTT 58.552 33.333 15.22 0.00 33.96 1.40
4969 9860 9.082313 CCCATGGATCTTAATAGTGCTTATTTT 57.918 33.333 15.22 0.00 33.96 1.82
5068 9959 3.461946 GCAGATGCTGTATATTTCCGC 57.538 47.619 0.00 0.00 38.21 5.54
5081 9972 4.896829 TCCGCCCCGCAAAACCAA 62.897 61.111 0.00 0.00 0.00 3.67
5102 9993 2.949177 TTGCAGCTCTCCCTAAAACA 57.051 45.000 0.00 0.00 0.00 2.83
5109 10000 5.006386 CAGCTCTCCCTAAAACAGATTTGT 58.994 41.667 0.00 0.00 39.87 2.83
5117 10008 7.410174 TCCCTAAAACAGATTTGTGGTATCAT 58.590 34.615 0.00 0.00 37.67 2.45
5127 10018 7.335171 CAGATTTGTGGTATCATGAGACTTCAA 59.665 37.037 19.26 19.01 36.78 2.69
5129 10020 5.745312 TGTGGTATCATGAGACTTCAAGT 57.255 39.130 19.26 0.00 36.78 3.16
5149 10040 1.212751 GAACAGATGCCGCAAACCC 59.787 57.895 0.00 0.00 0.00 4.11
5158 10049 2.677003 CCGCAAACCCGTACTGCAG 61.677 63.158 13.48 13.48 35.78 4.41
5159 10050 1.959226 CGCAAACCCGTACTGCAGT 60.959 57.895 25.12 25.12 35.78 4.40
5160 10051 0.668096 CGCAAACCCGTACTGCAGTA 60.668 55.000 22.67 22.67 35.78 2.74
5161 10052 0.794473 GCAAACCCGTACTGCAGTAC 59.206 55.000 36.64 36.64 45.47 2.73
5163 10054 2.334838 CAAACCCGTACTGCAGTACTC 58.665 52.381 39.83 24.25 46.43 2.59
5164 10055 0.893447 AACCCGTACTGCAGTACTCC 59.107 55.000 39.83 23.64 46.43 3.85
5167 10058 1.654954 CCGTACTGCAGTACTCCGCT 61.655 60.000 39.83 13.86 46.43 5.52
5168 10059 0.170561 CGTACTGCAGTACTCCGCTT 59.829 55.000 39.83 13.18 46.43 4.68
5171 10089 0.038159 ACTGCAGTACTCCGCTTGAC 60.038 55.000 20.16 0.00 0.00 3.18
5192 10110 1.587088 CGCGCGGTACCGTAAATCT 60.587 57.895 33.34 0.00 42.09 2.40
5208 10126 9.813446 ACCGTAAATCTGTTTTAGTTAGATAGG 57.187 33.333 0.00 0.00 30.46 2.57
5209 10127 8.762426 CCGTAAATCTGTTTTAGTTAGATAGGC 58.238 37.037 0.00 0.00 30.46 3.93
5210 10128 9.309516 CGTAAATCTGTTTTAGTTAGATAGGCA 57.690 33.333 0.00 0.00 30.46 4.75
5216 10134 9.733556 TCTGTTTTAGTTAGATAGGCAAAATCA 57.266 29.630 0.00 0.00 0.00 2.57
5221 10139 8.827177 TTAGTTAGATAGGCAAAATCATACCG 57.173 34.615 0.00 0.00 0.00 4.02
5222 10140 6.827727 AGTTAGATAGGCAAAATCATACCGT 58.172 36.000 0.00 0.00 0.00 4.83
5223 10141 7.959175 AGTTAGATAGGCAAAATCATACCGTA 58.041 34.615 0.00 0.00 0.00 4.02
5224 10142 8.426489 AGTTAGATAGGCAAAATCATACCGTAA 58.574 33.333 0.00 0.00 0.00 3.18
5225 10143 9.048446 GTTAGATAGGCAAAATCATACCGTAAA 57.952 33.333 0.00 0.00 0.00 2.01
5226 10144 9.787435 TTAGATAGGCAAAATCATACCGTAAAT 57.213 29.630 0.00 0.00 0.00 1.40
5227 10145 8.324163 AGATAGGCAAAATCATACCGTAAATC 57.676 34.615 0.00 0.00 0.00 2.17
5228 10146 5.767816 AGGCAAAATCATACCGTAAATCC 57.232 39.130 0.00 0.00 0.00 3.01
5489 10412 2.556559 GGCAGGAACAAGGTTCCCATTA 60.557 50.000 21.22 0.00 39.39 1.90
5602 10548 1.414919 ACGAGCGGCAAATAGGGAATA 59.585 47.619 1.45 0.00 0.00 1.75
5765 10714 1.000612 GACGGGGAGGAGGAGAACT 59.999 63.158 0.00 0.00 0.00 3.01
5886 10835 3.267031 CCTACCTCCTTGGATTCCACTTT 59.733 47.826 4.45 0.00 39.71 2.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 2.109834 TGGTTTCCTGACCATGGACATT 59.890 45.455 21.47 0.00 44.53 2.71
4 5 1.710244 TGGTTTCCTGACCATGGACAT 59.290 47.619 21.47 0.00 44.53 3.06
5 6 1.144691 TGGTTTCCTGACCATGGACA 58.855 50.000 21.47 18.47 44.53 4.02
12 13 4.236527 AGATGGTTATGGTTTCCTGACC 57.763 45.455 0.00 0.00 40.23 4.02
13 14 7.054124 TCAATAGATGGTTATGGTTTCCTGAC 58.946 38.462 0.00 0.00 0.00 3.51
14 15 7.206789 TCAATAGATGGTTATGGTTTCCTGA 57.793 36.000 0.00 0.00 0.00 3.86
15 16 7.720957 TGATCAATAGATGGTTATGGTTTCCTG 59.279 37.037 0.00 0.00 33.72 3.86
16 17 7.815383 TGATCAATAGATGGTTATGGTTTCCT 58.185 34.615 0.00 0.00 33.72 3.36
17 18 8.352942 GTTGATCAATAGATGGTTATGGTTTCC 58.647 37.037 12.12 0.00 33.72 3.13
18 19 8.070171 CGTTGATCAATAGATGGTTATGGTTTC 58.930 37.037 12.12 0.00 33.72 2.78
19 20 7.773224 TCGTTGATCAATAGATGGTTATGGTTT 59.227 33.333 12.12 0.00 33.72 3.27
20 21 7.279615 TCGTTGATCAATAGATGGTTATGGTT 58.720 34.615 12.12 0.00 33.72 3.67
22 23 6.128445 GCTCGTTGATCAATAGATGGTTATGG 60.128 42.308 19.51 7.58 33.72 2.74
23 24 6.648310 AGCTCGTTGATCAATAGATGGTTATG 59.352 38.462 19.51 8.11 33.72 1.90
26 27 5.028549 AGCTCGTTGATCAATAGATGGTT 57.971 39.130 19.51 6.05 33.72 3.67
28 29 5.777802 ACTAGCTCGTTGATCAATAGATGG 58.222 41.667 19.51 17.62 33.72 3.51
29 30 6.442112 TGACTAGCTCGTTGATCAATAGATG 58.558 40.000 19.51 12.48 33.72 2.90
30 31 6.641169 TGACTAGCTCGTTGATCAATAGAT 57.359 37.500 19.51 16.66 37.13 1.98
31 32 6.095580 AGTTGACTAGCTCGTTGATCAATAGA 59.904 38.462 19.51 16.55 0.00 1.98
32 33 6.269315 AGTTGACTAGCTCGTTGATCAATAG 58.731 40.000 12.12 13.07 0.00 1.73
33 34 6.208988 AGTTGACTAGCTCGTTGATCAATA 57.791 37.500 12.12 2.38 0.00 1.90
34 35 5.078411 AGTTGACTAGCTCGTTGATCAAT 57.922 39.130 12.12 0.00 0.00 2.57
35 36 4.521130 AGTTGACTAGCTCGTTGATCAA 57.479 40.909 3.38 3.38 0.00 2.57
36 37 4.941873 TCTAGTTGACTAGCTCGTTGATCA 59.058 41.667 12.30 0.00 44.24 2.92
37 38 5.487153 TCTAGTTGACTAGCTCGTTGATC 57.513 43.478 12.30 0.00 44.24 2.92
39 40 3.690139 CCTCTAGTTGACTAGCTCGTTGA 59.310 47.826 12.30 0.00 44.24 3.18
40 41 3.732471 GCCTCTAGTTGACTAGCTCGTTG 60.732 52.174 12.30 0.75 44.24 4.10
41 42 2.424246 GCCTCTAGTTGACTAGCTCGTT 59.576 50.000 12.30 0.00 44.24 3.85
42 43 2.018515 GCCTCTAGTTGACTAGCTCGT 58.981 52.381 12.30 0.00 44.24 4.18
43 44 2.294074 AGCCTCTAGTTGACTAGCTCG 58.706 52.381 12.30 0.00 44.24 5.03
46 47 5.239963 CCTAGTAAGCCTCTAGTTGACTAGC 59.760 48.000 12.30 3.61 44.24 3.42
47 48 5.766174 CCCTAGTAAGCCTCTAGTTGACTAG 59.234 48.000 11.14 11.14 45.57 2.57
48 49 5.431073 TCCCTAGTAAGCCTCTAGTTGACTA 59.569 44.000 0.00 0.00 34.72 2.59
51 52 4.017775 TGTCCCTAGTAAGCCTCTAGTTGA 60.018 45.833 0.00 1.98 34.72 3.18
52 53 4.279145 TGTCCCTAGTAAGCCTCTAGTTG 58.721 47.826 0.00 0.00 34.72 3.16
53 54 4.604784 TGTCCCTAGTAAGCCTCTAGTT 57.395 45.455 0.00 0.00 34.72 2.24
54 55 4.079096 ACATGTCCCTAGTAAGCCTCTAGT 60.079 45.833 0.00 0.00 34.72 2.57
56 57 4.537945 ACATGTCCCTAGTAAGCCTCTA 57.462 45.455 0.00 0.00 0.00 2.43
57 58 3.406512 ACATGTCCCTAGTAAGCCTCT 57.593 47.619 0.00 0.00 0.00 3.69
58 59 3.197983 ACAACATGTCCCTAGTAAGCCTC 59.802 47.826 0.00 0.00 0.00 4.70
59 60 3.055094 CACAACATGTCCCTAGTAAGCCT 60.055 47.826 0.00 0.00 0.00 4.58
60 61 3.270877 CACAACATGTCCCTAGTAAGCC 58.729 50.000 0.00 0.00 0.00 4.35
63 64 4.164981 AGACCACAACATGTCCCTAGTAA 58.835 43.478 0.00 0.00 31.76 2.24
64 65 3.786553 AGACCACAACATGTCCCTAGTA 58.213 45.455 0.00 0.00 31.76 1.82
65 66 2.621070 AGACCACAACATGTCCCTAGT 58.379 47.619 0.00 0.00 31.76 2.57
66 67 4.162320 ACATAGACCACAACATGTCCCTAG 59.838 45.833 0.00 0.00 31.76 3.02
67 68 4.101114 ACATAGACCACAACATGTCCCTA 58.899 43.478 0.00 0.00 31.76 3.53
68 69 2.912956 ACATAGACCACAACATGTCCCT 59.087 45.455 0.00 0.00 31.76 4.20
69 70 3.350219 ACATAGACCACAACATGTCCC 57.650 47.619 0.00 0.00 31.76 4.46
71 72 6.593770 TGTGAATACATAGACCACAACATGTC 59.406 38.462 0.00 0.00 35.16 3.06
72 73 6.371548 GTGTGAATACATAGACCACAACATGT 59.628 38.462 0.00 0.00 39.13 3.21
73 74 6.371271 TGTGTGAATACATAGACCACAACATG 59.629 38.462 0.00 0.00 39.13 3.21
74 75 6.472016 TGTGTGAATACATAGACCACAACAT 58.528 36.000 0.00 0.00 39.13 2.71
75 76 5.859495 TGTGTGAATACATAGACCACAACA 58.141 37.500 0.00 0.00 39.13 3.33
76 77 6.371548 ACATGTGTGAATACATAGACCACAAC 59.628 38.462 0.00 0.00 39.17 3.32
77 78 6.472016 ACATGTGTGAATACATAGACCACAA 58.528 36.000 0.00 0.00 39.17 3.33
78 79 6.048732 ACATGTGTGAATACATAGACCACA 57.951 37.500 0.00 0.00 39.17 4.17
79 80 8.662781 AATACATGTGTGAATACATAGACCAC 57.337 34.615 9.11 0.00 39.17 4.16
80 81 9.758651 GTAATACATGTGTGAATACATAGACCA 57.241 33.333 9.11 0.00 39.17 4.02
81 82 8.912658 CGTAATACATGTGTGAATACATAGACC 58.087 37.037 9.11 0.00 39.17 3.85
82 83 8.912658 CCGTAATACATGTGTGAATACATAGAC 58.087 37.037 9.11 0.00 39.17 2.59
83 84 8.635328 ACCGTAATACATGTGTGAATACATAGA 58.365 33.333 9.11 0.00 39.17 1.98
84 85 8.812147 ACCGTAATACATGTGTGAATACATAG 57.188 34.615 9.11 0.00 39.17 2.23
85 86 9.602568 AAACCGTAATACATGTGTGAATACATA 57.397 29.630 9.11 0.00 39.17 2.29
87 88 7.064847 GGAAACCGTAATACATGTGTGAATACA 59.935 37.037 9.11 0.00 34.63 2.29
89 90 7.104290 TGGAAACCGTAATACATGTGTGAATA 58.896 34.615 9.11 0.00 0.00 1.75
90 91 5.941058 TGGAAACCGTAATACATGTGTGAAT 59.059 36.000 9.11 0.00 0.00 2.57
91 92 5.306394 TGGAAACCGTAATACATGTGTGAA 58.694 37.500 9.11 0.00 0.00 3.18
92 93 4.895961 TGGAAACCGTAATACATGTGTGA 58.104 39.130 9.11 0.00 0.00 3.58
93 94 4.693566 ACTGGAAACCGTAATACATGTGTG 59.306 41.667 9.11 0.00 0.00 3.82
94 95 4.901868 ACTGGAAACCGTAATACATGTGT 58.098 39.130 9.11 0.00 0.00 3.72
95 96 5.873179 AACTGGAAACCGTAATACATGTG 57.127 39.130 9.11 0.00 0.00 3.21
96 97 9.101655 GTATTAACTGGAAACCGTAATACATGT 57.898 33.333 2.69 2.69 32.37 3.21
97 98 9.100554 TGTATTAACTGGAAACCGTAATACATG 57.899 33.333 17.47 0.00 35.38 3.21
98 99 9.669887 TTGTATTAACTGGAAACCGTAATACAT 57.330 29.630 19.66 0.00 38.15 2.29
99 100 9.669887 ATTGTATTAACTGGAAACCGTAATACA 57.330 29.630 17.47 17.47 37.23 2.29
105 106 8.833493 GCTATAATTGTATTAACTGGAAACCGT 58.167 33.333 0.00 0.00 0.00 4.83
106 107 8.832521 TGCTATAATTGTATTAACTGGAAACCG 58.167 33.333 0.00 0.00 0.00 4.44
129 130 9.346005 TCATGATAATTGTCTATTGTTCATGCT 57.654 29.630 18.84 0.00 41.74 3.79
130 131 9.955208 TTCATGATAATTGTCTATTGTTCATGC 57.045 29.630 18.84 0.00 41.74 4.06
136 137 9.685276 TCCTTGTTCATGATAATTGTCTATTGT 57.315 29.630 0.00 0.00 0.00 2.71
190 191 5.846203 CATGTTGGAAATATGCCCTAAAGG 58.154 41.667 0.00 0.00 38.58 3.11
215 216 3.370840 TCATGAACATCTTGAAGGGGG 57.629 47.619 0.00 0.00 29.14 5.40
361 3860 4.260194 CGGTCGTGATGACTGCAA 57.740 55.556 4.63 0.00 46.48 4.08
473 3975 6.795144 TGGAGATTTATGGGTTAGTTACGA 57.205 37.500 0.00 0.00 0.00 3.43
482 3984 2.810400 CGGCGAATGGAGATTTATGGGT 60.810 50.000 0.00 0.00 0.00 4.51
518 4020 3.308595 CGGTTCTTTGTTTCCCTTTTTGC 59.691 43.478 0.00 0.00 0.00 3.68
699 4212 4.280494 AAGTGTCGCGCGTGGAGT 62.280 61.111 30.98 14.35 0.00 3.85
736 4249 2.643933 ACTAGTTAACGAGCGGTTCC 57.356 50.000 14.82 0.00 40.09 3.62
762 4275 2.160205 TGTTGACACCGGAAACAAACA 58.840 42.857 9.46 9.37 31.16 2.83
817 4330 8.251750 TGTGACTCGGTTTATAATTTTCAGAG 57.748 34.615 0.00 0.00 0.00 3.35
826 4339 8.706492 AACGAATTATGTGACTCGGTTTATAA 57.294 30.769 0.00 0.00 35.64 0.98
828 4341 8.882415 ATAACGAATTATGTGACTCGGTTTAT 57.118 30.769 0.00 0.00 35.64 1.40
832 4345 5.911280 CGTATAACGAATTATGTGACTCGGT 59.089 40.000 0.00 0.00 46.05 4.69
834 4347 6.412943 ACACGTATAACGAATTATGTGACTCG 59.587 38.462 16.62 0.00 46.05 4.18
835 4348 7.430211 TCACACGTATAACGAATTATGTGACTC 59.570 37.037 14.75 0.00 43.05 3.36
836 4349 7.252708 TCACACGTATAACGAATTATGTGACT 58.747 34.615 14.75 0.69 43.05 3.41
868 4381 4.500887 CGTTAGTTGAAGAGTTCAGGTGGA 60.501 45.833 0.00 0.00 41.38 4.02
880 4393 2.064014 GGTTCCGTCCGTTAGTTGAAG 58.936 52.381 0.00 0.00 0.00 3.02
942 4456 1.571773 CCCTACTTTCCCCAGGGTGG 61.572 65.000 4.22 0.00 43.58 4.61
1126 4640 2.029728 CGACCATCTTCGCTGAATCAAC 59.970 50.000 0.00 0.00 31.03 3.18
1494 5008 7.072177 TGTAGGAACATCAATCGATCAAAAC 57.928 36.000 0.00 0.00 0.00 2.43
1603 5121 4.065088 TCCAATCTACAGTTGTTGTCAGC 58.935 43.478 0.00 0.00 41.29 4.26
1614 5132 7.330454 CAGGAATCGACATAATCCAATCTACAG 59.670 40.741 0.00 0.00 34.30 2.74
1746 5269 4.026052 TGACTGAGAAGATCTGCATGGTA 58.974 43.478 2.79 0.00 0.00 3.25
1872 5395 1.067060 GTTTGGCAGTTGTCCCTTGAC 59.933 52.381 0.00 0.00 42.12 3.18
2001 5524 2.794910 CCGATATGTGTTCTGCGGTTAG 59.205 50.000 0.00 0.00 34.45 2.34
2049 5572 7.101054 GGTTACTTATATGTGTTCTGTGGTCA 58.899 38.462 1.63 0.00 0.00 4.02
2203 5726 6.041523 TGGTTGCTTGTATTTAGCCTCTTTTT 59.958 34.615 0.00 0.00 37.85 1.94
2204 5727 5.538433 TGGTTGCTTGTATTTAGCCTCTTTT 59.462 36.000 0.00 0.00 37.85 2.27
2205 5728 5.076873 TGGTTGCTTGTATTTAGCCTCTTT 58.923 37.500 0.00 0.00 37.85 2.52
2265 5788 7.491048 ACATACAAAAACAAGGTTGAATGTCAC 59.509 33.333 0.00 0.00 0.00 3.67
2304 5827 9.193806 AGATGCAAATACAGTTTATGGAAGAAT 57.806 29.630 0.00 0.00 0.00 2.40
2314 5837 6.071952 ACGAATGGAAGATGCAAATACAGTTT 60.072 34.615 0.00 0.00 0.00 2.66
2347 5870 6.591062 GCATCCAAAGCATAAATTCAAACTCA 59.409 34.615 0.00 0.00 0.00 3.41
2477 6000 6.550108 TGGATCCCTCTATAACTGAACTACAC 59.450 42.308 9.90 0.00 0.00 2.90
2792 6315 6.485313 TGGGCATTAAATTTGTATAGAGACGG 59.515 38.462 0.00 0.00 0.00 4.79
3219 6742 4.406943 GAAGCTTACTGATTTCGCCAAAG 58.593 43.478 0.00 0.00 0.00 2.77
3226 6749 6.272822 ACCAAATGGAAGCTTACTGATTTC 57.727 37.500 10.74 0.00 38.94 2.17
3420 8300 3.006940 TCAGCATTATTTCCACGGACAC 58.993 45.455 0.00 0.00 0.00 3.67
3564 8444 3.692690 GGTAACCAATCCTGCTTAACCA 58.307 45.455 0.00 0.00 0.00 3.67
3691 8571 3.715495 TCGCATGCTTTTCATTGTGTTT 58.285 36.364 17.13 0.00 31.79 2.83
3910 8792 4.907875 TGGCAGAGAATAATAGCCTAAGGT 59.092 41.667 0.00 0.00 45.42 3.50
3937 8819 6.359804 AGTGCATACCATGAATGATGTTAGT 58.640 36.000 11.03 0.00 0.00 2.24
4002 8884 6.018016 GCCGAAACTAGGTAAACAGTAAACAA 60.018 38.462 0.00 0.00 0.00 2.83
4051 8933 7.254017 GCGTCGACAAGAATATTTAAACTAGCT 60.254 37.037 17.16 0.00 0.00 3.32
4262 9144 1.252215 CCCTGCATGCAACACCATCA 61.252 55.000 22.88 0.00 0.00 3.07
4264 9146 1.228956 ACCCTGCATGCAACACCAT 60.229 52.632 22.88 1.23 0.00 3.55
4265 9147 1.902918 GACCCTGCATGCAACACCA 60.903 57.895 22.88 0.00 0.00 4.17
4266 9148 1.462731 TTGACCCTGCATGCAACACC 61.463 55.000 22.88 11.79 0.00 4.16
4267 9149 0.318955 GTTGACCCTGCATGCAACAC 60.319 55.000 22.88 13.37 40.11 3.32
4268 9150 0.754587 TGTTGACCCTGCATGCAACA 60.755 50.000 22.88 18.42 45.69 3.33
4269 9151 0.604578 ATGTTGACCCTGCATGCAAC 59.395 50.000 22.88 15.91 40.62 4.17
4324 9215 3.461773 ACAGACGGATGCCCCTCG 61.462 66.667 0.00 0.00 0.00 4.63
4536 9427 2.701780 CCCTCGACCACCTCGACTG 61.702 68.421 0.00 0.00 46.75 3.51
4564 9455 4.966787 TGGCCGTGGAACCCTTGC 62.967 66.667 0.00 0.00 0.00 4.01
4565 9456 2.672996 CTGGCCGTGGAACCCTTG 60.673 66.667 0.00 0.00 0.00 3.61
4606 9497 0.244721 GCAAGACTTTCATGTGGGGC 59.755 55.000 0.00 0.00 0.00 5.80
4657 9548 4.393155 ATCTTGCCGCTGTCGCCA 62.393 61.111 0.00 0.00 0.00 5.69
4664 9555 0.107945 GAGAGTTCCATCTTGCCGCT 60.108 55.000 0.00 0.00 0.00 5.52
4716 9607 0.524862 CAGAGCACAAACCATGAGCC 59.475 55.000 0.00 0.00 45.57 4.70
4721 9612 2.880890 GAGACAACAGAGCACAAACCAT 59.119 45.455 0.00 0.00 0.00 3.55
4733 9624 0.104120 TCACCACCACGAGACAACAG 59.896 55.000 0.00 0.00 0.00 3.16
4798 9689 0.179111 CAAGCATGCCATGGCTTCTG 60.179 55.000 35.53 28.01 46.82 3.02
4809 9700 0.179156 CGACCCAACATCAAGCATGC 60.179 55.000 10.51 10.51 35.65 4.06
4825 9716 2.048503 ACCCGCAGCTTACACGAC 60.049 61.111 0.00 0.00 0.00 4.34
4840 9731 4.699522 GACCAGGCCACCGTGACC 62.700 72.222 5.01 0.00 0.00 4.02
4927 9818 3.623703 CATGGGATGAACATGAACTCCA 58.376 45.455 0.00 0.00 46.60 3.86
4937 9828 6.150140 GCACTATTAAGATCCATGGGATGAAC 59.850 42.308 13.02 0.00 43.27 3.18
4938 9829 6.044754 AGCACTATTAAGATCCATGGGATGAA 59.955 38.462 13.02 0.65 43.27 2.57
4939 9830 5.549228 AGCACTATTAAGATCCATGGGATGA 59.451 40.000 13.02 0.00 43.27 2.92
4940 9831 5.813383 AGCACTATTAAGATCCATGGGATG 58.187 41.667 13.02 0.00 43.27 3.51
4941 9832 6.460103 AAGCACTATTAAGATCCATGGGAT 57.540 37.500 13.02 4.02 46.28 3.85
4942 9833 5.912149 AAGCACTATTAAGATCCATGGGA 57.088 39.130 13.02 0.00 35.55 4.37
4968 9859 3.146066 AGCACTGTTAGATCGCCAAAAA 58.854 40.909 0.00 0.00 0.00 1.94
4969 9860 2.778299 AGCACTGTTAGATCGCCAAAA 58.222 42.857 0.00 0.00 0.00 2.44
4970 9861 2.472695 AGCACTGTTAGATCGCCAAA 57.527 45.000 0.00 0.00 0.00 3.28
4971 9862 3.118775 ACATAGCACTGTTAGATCGCCAA 60.119 43.478 0.00 0.00 0.00 4.52
4972 9863 2.430694 ACATAGCACTGTTAGATCGCCA 59.569 45.455 0.00 0.00 0.00 5.69
4973 9864 3.099267 ACATAGCACTGTTAGATCGCC 57.901 47.619 0.00 0.00 0.00 5.54
4974 9865 6.583912 TTTAACATAGCACTGTTAGATCGC 57.416 37.500 10.00 0.00 41.32 4.58
5005 9896 3.758554 GCTGCTATCCTTTGTTCCAGAAA 59.241 43.478 0.00 0.00 0.00 2.52
5006 9897 3.009473 AGCTGCTATCCTTTGTTCCAGAA 59.991 43.478 0.00 0.00 0.00 3.02
5007 9898 2.573462 AGCTGCTATCCTTTGTTCCAGA 59.427 45.455 0.00 0.00 0.00 3.86
5008 9899 2.996631 AGCTGCTATCCTTTGTTCCAG 58.003 47.619 0.00 0.00 0.00 3.86
5081 9972 3.760684 CTGTTTTAGGGAGAGCTGCAAAT 59.239 43.478 1.02 0.00 0.00 2.32
5087 9978 5.006386 CACAAATCTGTTTTAGGGAGAGCT 58.994 41.667 0.00 0.00 31.64 4.09
5102 9993 6.950842 TGAAGTCTCATGATACCACAAATCT 58.049 36.000 7.56 0.00 0.00 2.40
5109 10000 4.777366 TCCACTTGAAGTCTCATGATACCA 59.223 41.667 7.56 0.00 32.39 3.25
5117 10008 4.635223 CATCTGTTCCACTTGAAGTCTCA 58.365 43.478 0.00 0.00 32.37 3.27
5127 10018 0.537143 TTTGCGGCATCTGTTCCACT 60.537 50.000 2.28 0.00 0.00 4.00
5129 10020 1.523154 GGTTTGCGGCATCTGTTCCA 61.523 55.000 2.28 0.00 0.00 3.53
5158 10049 2.183555 CGGGGTCAAGCGGAGTAC 59.816 66.667 0.00 0.00 0.00 2.73
5159 10050 3.766691 GCGGGGTCAAGCGGAGTA 61.767 66.667 0.00 0.00 0.00 2.59
5177 10095 4.627035 ACTAAAACAGATTTACGGTACCGC 59.373 41.667 33.62 17.07 36.30 5.68
5178 10096 6.710692 AACTAAAACAGATTTACGGTACCG 57.289 37.500 32.22 32.22 37.68 4.02
5208 10126 5.164606 ACGGATTTACGGTATGATTTTGC 57.835 39.130 0.00 0.00 38.39 3.68
5209 10127 9.217223 CTAAAACGGATTTACGGTATGATTTTG 57.783 33.333 0.00 0.00 38.39 2.44
5210 10128 8.949177 ACTAAAACGGATTTACGGTATGATTTT 58.051 29.630 0.00 0.00 38.39 1.82
5211 10129 8.496707 ACTAAAACGGATTTACGGTATGATTT 57.503 30.769 0.00 0.00 38.39 2.17
5212 10130 8.496707 AACTAAAACGGATTTACGGTATGATT 57.503 30.769 0.00 0.00 38.39 2.57
5213 10131 9.252962 CTAACTAAAACGGATTTACGGTATGAT 57.747 33.333 0.00 0.00 38.39 2.45
5214 10132 8.465999 TCTAACTAAAACGGATTTACGGTATGA 58.534 33.333 0.00 0.00 38.39 2.15
5215 10133 8.633075 TCTAACTAAAACGGATTTACGGTATG 57.367 34.615 0.00 0.00 38.39 2.39
5217 10135 9.950680 CTATCTAACTAAAACGGATTTACGGTA 57.049 33.333 0.00 0.00 38.39 4.02
5218 10136 7.922811 CCTATCTAACTAAAACGGATTTACGGT 59.077 37.037 0.00 0.00 38.39 4.83
5219 10137 7.095899 GCCTATCTAACTAAAACGGATTTACGG 60.096 40.741 0.00 0.00 38.39 4.02
5220 10138 7.436080 TGCCTATCTAACTAAAACGGATTTACG 59.564 37.037 0.00 0.00 40.31 3.18
5221 10139 8.652810 TGCCTATCTAACTAAAACGGATTTAC 57.347 34.615 0.00 0.00 32.27 2.01
5222 10140 9.669887 TTTGCCTATCTAACTAAAACGGATTTA 57.330 29.630 0.00 0.00 32.27 1.40
5223 10141 8.570068 TTTGCCTATCTAACTAAAACGGATTT 57.430 30.769 0.00 0.00 34.92 2.17
5224 10142 8.570068 TTTTGCCTATCTAACTAAAACGGATT 57.430 30.769 0.00 0.00 0.00 3.01
5225 10143 8.747538 ATTTTGCCTATCTAACTAAAACGGAT 57.252 30.769 0.00 0.00 0.00 4.18
5226 10144 7.825270 TGATTTTGCCTATCTAACTAAAACGGA 59.175 33.333 0.00 0.00 0.00 4.69
5227 10145 7.981142 TGATTTTGCCTATCTAACTAAAACGG 58.019 34.615 0.00 0.00 0.00 4.44
5228 10146 9.438291 CATGATTTTGCCTATCTAACTAAAACG 57.562 33.333 0.00 0.00 0.00 3.60
5371 10293 9.625747 AATTCCAAACCATGTTGTTATTTCTTT 57.374 25.926 0.00 0.00 0.00 2.52
5456 10378 2.107378 TGTTCCTGCCAGGTTTATGTCA 59.893 45.455 11.27 0.00 36.53 3.58
5513 10444 5.820404 AGGGTTTATATCGGTTTAGGGAG 57.180 43.478 0.00 0.00 0.00 4.30
5583 10529 2.069273 CTATTCCCTATTTGCCGCTCG 58.931 52.381 0.00 0.00 0.00 5.03
5602 10548 3.007920 CCCTCAGTCAGGCAGGCT 61.008 66.667 0.00 0.00 41.80 4.58
5824 10773 4.382541 TCGGAGCTGGAGAGGGCA 62.383 66.667 0.00 0.00 0.00 5.36
5886 10835 2.122769 TGGAGGTTCCACGGGTGA 60.123 61.111 0.00 0.00 42.67 4.02


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

AutoCloner maintained by Alex Coulton.