Multiple sequence alignment - TraesCS3B01G174500

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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 TraesCS3B01G174500 chr3B 100.000 5293 0 0 1 5293 175781564 175776272 0.000000e+00 9775.0
1 TraesCS3B01G174500 chr3A 95.106 3494 148 16 1641 5123 130854353 130850872 0.000000e+00 5483.0
2 TraesCS3B01G174500 chr3A 89.582 1219 79 10 304 1521 130855650 130854479 0.000000e+00 1504.0
3 TraesCS3B01G174500 chr3A 87.902 529 39 6 121 647 130856506 130856001 2.730000e-167 599.0
4 TraesCS3B01G174500 chr3A 88.966 145 11 2 5152 5293 130849673 130849531 1.960000e-39 174.0
5 TraesCS3B01G174500 chr3A 89.583 96 2 1 1520 1615 130854441 130854354 1.200000e-21 115.0
6 TraesCS3B01G174500 chr3D 96.411 1978 52 5 2462 4437 123316446 123314486 0.000000e+00 3241.0
7 TraesCS3B01G174500 chr3D 95.842 914 35 3 1520 2432 123317359 123316448 0.000000e+00 1474.0
8 TraesCS3B01G174500 chr3D 90.110 1001 62 14 527 1518 123318371 123317399 0.000000e+00 1266.0
9 TraesCS3B01G174500 chr3D 90.126 476 26 7 4472 4944 123314489 123314032 2.730000e-167 599.0
10 TraesCS3B01G174500 chr3D 90.000 340 18 6 4960 5293 123314044 123313715 4.900000e-115 425.0
11 TraesCS3B01G174500 chr3D 84.512 297 39 7 3256 3546 169336781 169336486 2.410000e-73 287.0
12 TraesCS3B01G174500 chr4B 86.879 282 30 6 3260 3535 14121457 14121177 5.150000e-80 309.0
13 TraesCS3B01G174500 chr2A 85.818 275 36 3 3264 3535 195350777 195350503 6.710000e-74 289.0
14 TraesCS3B01G174500 chr2A 85.093 161 24 0 94 254 121056811 121056651 1.180000e-36 165.0
15 TraesCS3B01G174500 chr2B 85.560 277 34 6 3264 3535 237581897 237581622 8.680000e-73 285.0
16 TraesCS3B01G174500 chr2D 84.946 279 38 4 3268 3543 212925849 212926126 4.040000e-71 279.0
17 TraesCS3B01G174500 chr2D 84.014 294 40 7 3256 3543 289684327 289684619 5.220000e-70 276.0
18 TraesCS3B01G174500 chr2D 75.646 271 57 6 99 368 118929582 118929320 5.560000e-25 126.0
19 TraesCS3B01G174500 chr4D 84.892 278 38 4 3268 3542 141578219 141577943 1.450000e-70 278.0
20 TraesCS3B01G174500 chr7D 87.692 65 8 0 94 158 31635375 31635439 5.680000e-10 76.8


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 TraesCS3B01G174500 chr3B 175776272 175781564 5292 True 9775 9775 100.0000 1 5293 1 chr3B.!!$R1 5292
1 TraesCS3B01G174500 chr3A 130849531 130856506 6975 True 1575 5483 90.2278 121 5293 5 chr3A.!!$R1 5172
2 TraesCS3B01G174500 chr3D 123313715 123318371 4656 True 1401 3241 92.4978 527 5293 5 chr3D.!!$R2 4766

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
105 106 0.108585 GGGGGCATGTCGTATGTGAT 59.891 55.000 0.00 0.00 0.00 3.06 F
992 1675 0.249238 CCAGAGGAGCTCCGAATTCG 60.249 60.000 26.95 20.92 42.08 3.34 F
1990 2719 0.179137 TCATGTTCGAGGCAGTAGCG 60.179 55.000 0.00 0.00 43.41 4.26 F
1992 2721 0.246635 ATGTTCGAGGCAGTAGCGTT 59.753 50.000 0.00 0.00 43.41 4.84 F
1993 2722 0.666274 TGTTCGAGGCAGTAGCGTTG 60.666 55.000 0.00 0.00 43.41 4.10 F
3095 3830 1.612442 GGGTCCTACAGCCAGGTCA 60.612 63.158 0.00 0.00 42.97 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1505 2188 0.831711 GCCACACCAATTTCACCCCT 60.832 55.000 0.00 0.00 0.00 4.79 R
2913 3646 1.141185 ATTTAGCTAGCCTCACCCCC 58.859 55.000 12.13 0.00 0.00 5.40 R
3691 4428 0.106819 ATGGAAGACAGATGCAGGCC 60.107 55.000 0.00 0.00 0.00 5.19 R
3791 4528 5.946377 ACAGAATTAGGGAAAGACCAATGAC 59.054 40.000 0.00 0.00 41.20 3.06 R
3804 4541 6.311200 GCAAATAGCAACAAACAGAATTAGGG 59.689 38.462 0.00 0.00 44.79 3.53 R
4516 5253 0.606401 AGACCGTTGCAATGTCCAGG 60.606 55.000 21.57 12.85 0.00 4.45 R

All possible primers

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

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
39 40 3.761897 CCTTTAGGGTTTGGTGTGATCA 58.238 45.455 0.00 0.00 0.00 2.92
40 41 4.344104 CCTTTAGGGTTTGGTGTGATCAT 58.656 43.478 0.00 0.00 0.00 2.45
41 42 4.772100 CCTTTAGGGTTTGGTGTGATCATT 59.228 41.667 0.00 0.00 0.00 2.57
42 43 5.105756 CCTTTAGGGTTTGGTGTGATCATTC 60.106 44.000 0.00 0.00 0.00 2.67
43 44 2.807676 AGGGTTTGGTGTGATCATTCC 58.192 47.619 0.00 5.43 0.00 3.01
44 45 1.824852 GGGTTTGGTGTGATCATTCCC 59.175 52.381 13.93 8.45 0.00 3.97
45 46 2.524306 GGTTTGGTGTGATCATTCCCA 58.476 47.619 13.93 10.55 0.00 4.37
46 47 2.231235 GGTTTGGTGTGATCATTCCCAC 59.769 50.000 13.93 10.17 0.00 4.61
47 48 1.819928 TTGGTGTGATCATTCCCACG 58.180 50.000 13.93 0.00 36.15 4.94
48 49 0.690192 TGGTGTGATCATTCCCACGT 59.310 50.000 13.93 0.00 36.15 4.49
49 50 1.073125 TGGTGTGATCATTCCCACGTT 59.927 47.619 13.93 0.00 36.15 3.99
50 51 2.159382 GGTGTGATCATTCCCACGTTT 58.841 47.619 0.00 0.00 36.15 3.60
51 52 2.161609 GGTGTGATCATTCCCACGTTTC 59.838 50.000 0.00 0.00 36.15 2.78
52 53 2.161609 GTGTGATCATTCCCACGTTTCC 59.838 50.000 0.00 0.00 36.15 3.13
53 54 1.743394 GTGATCATTCCCACGTTTCCC 59.257 52.381 0.00 0.00 0.00 3.97
54 55 1.352687 TGATCATTCCCACGTTTCCCA 59.647 47.619 0.00 0.00 0.00 4.37
55 56 1.743394 GATCATTCCCACGTTTCCCAC 59.257 52.381 0.00 0.00 0.00 4.61
56 57 0.768622 TCATTCCCACGTTTCCCACT 59.231 50.000 0.00 0.00 0.00 4.00
57 58 1.979308 TCATTCCCACGTTTCCCACTA 59.021 47.619 0.00 0.00 0.00 2.74
58 59 2.372504 TCATTCCCACGTTTCCCACTAA 59.627 45.455 0.00 0.00 0.00 2.24
59 60 3.009695 TCATTCCCACGTTTCCCACTAAT 59.990 43.478 0.00 0.00 0.00 1.73
60 61 2.483014 TCCCACGTTTCCCACTAATG 57.517 50.000 0.00 0.00 0.00 1.90
61 62 1.003812 TCCCACGTTTCCCACTAATGG 59.996 52.381 0.00 0.00 46.81 3.16
80 81 3.360296 GCCCTAGGCCTATACGACT 57.640 57.895 14.30 0.00 44.06 4.18
81 82 0.889306 GCCCTAGGCCTATACGACTG 59.111 60.000 14.30 0.00 44.06 3.51
82 83 1.547223 GCCCTAGGCCTATACGACTGA 60.547 57.143 14.30 0.00 44.06 3.41
83 84 2.438411 CCCTAGGCCTATACGACTGAG 58.562 57.143 14.30 0.00 0.00 3.35
84 85 2.438411 CCTAGGCCTATACGACTGAGG 58.562 57.143 14.30 5.37 0.00 3.86
85 86 2.040012 CCTAGGCCTATACGACTGAGGA 59.960 54.545 14.30 0.00 31.45 3.71
86 87 2.279935 AGGCCTATACGACTGAGGAG 57.720 55.000 1.29 0.00 31.45 3.69
87 88 1.202952 AGGCCTATACGACTGAGGAGG 60.203 57.143 1.29 0.00 31.45 4.30
88 89 1.249407 GCCTATACGACTGAGGAGGG 58.751 60.000 0.00 0.00 31.45 4.30
89 90 1.912417 CCTATACGACTGAGGAGGGG 58.088 60.000 0.00 0.00 31.45 4.79
90 91 1.548128 CCTATACGACTGAGGAGGGGG 60.548 61.905 0.00 0.00 31.45 5.40
91 92 0.178970 TATACGACTGAGGAGGGGGC 60.179 60.000 0.00 0.00 0.00 5.80
92 93 2.238319 ATACGACTGAGGAGGGGGCA 62.238 60.000 0.00 0.00 0.00 5.36
93 94 2.238319 TACGACTGAGGAGGGGGCAT 62.238 60.000 0.00 0.00 0.00 4.40
94 95 2.914289 GACTGAGGAGGGGGCATG 59.086 66.667 0.00 0.00 0.00 4.06
95 96 1.997874 GACTGAGGAGGGGGCATGT 60.998 63.158 0.00 0.00 0.00 3.21
96 97 1.977293 GACTGAGGAGGGGGCATGTC 61.977 65.000 0.00 0.00 0.00 3.06
97 98 3.083349 TGAGGAGGGGGCATGTCG 61.083 66.667 0.00 0.00 0.00 4.35
98 99 3.083997 GAGGAGGGGGCATGTCGT 61.084 66.667 0.00 0.00 0.00 4.34
99 100 1.760875 GAGGAGGGGGCATGTCGTA 60.761 63.158 0.00 0.00 0.00 3.43
100 101 1.074471 AGGAGGGGGCATGTCGTAT 60.074 57.895 0.00 0.00 0.00 3.06
101 102 1.071471 GGAGGGGGCATGTCGTATG 59.929 63.158 0.00 0.00 0.00 2.39
102 103 1.696097 GGAGGGGGCATGTCGTATGT 61.696 60.000 0.00 0.00 0.00 2.29
103 104 0.532862 GAGGGGGCATGTCGTATGTG 60.533 60.000 0.00 0.00 0.00 3.21
104 105 0.980754 AGGGGGCATGTCGTATGTGA 60.981 55.000 0.00 0.00 0.00 3.58
105 106 0.108585 GGGGGCATGTCGTATGTGAT 59.891 55.000 0.00 0.00 0.00 3.06
106 107 1.512926 GGGGCATGTCGTATGTGATC 58.487 55.000 0.00 0.00 0.00 2.92
107 108 1.512926 GGGCATGTCGTATGTGATCC 58.487 55.000 0.00 0.00 0.00 3.36
108 109 1.512926 GGCATGTCGTATGTGATCCC 58.487 55.000 0.00 0.00 0.00 3.85
109 110 1.070758 GGCATGTCGTATGTGATCCCT 59.929 52.381 0.00 0.00 0.00 4.20
110 111 2.485479 GGCATGTCGTATGTGATCCCTT 60.485 50.000 0.00 0.00 0.00 3.95
111 112 3.206150 GCATGTCGTATGTGATCCCTTT 58.794 45.455 0.00 0.00 0.00 3.11
112 113 3.002656 GCATGTCGTATGTGATCCCTTTG 59.997 47.826 0.00 0.00 0.00 2.77
113 114 2.627945 TGTCGTATGTGATCCCTTTGC 58.372 47.619 0.00 0.00 0.00 3.68
114 115 1.940613 GTCGTATGTGATCCCTTTGCC 59.059 52.381 0.00 0.00 0.00 4.52
115 116 1.837439 TCGTATGTGATCCCTTTGCCT 59.163 47.619 0.00 0.00 0.00 4.75
116 117 2.158957 TCGTATGTGATCCCTTTGCCTC 60.159 50.000 0.00 0.00 0.00 4.70
117 118 2.213499 GTATGTGATCCCTTTGCCTCG 58.787 52.381 0.00 0.00 0.00 4.63
118 119 0.749454 ATGTGATCCCTTTGCCTCGC 60.749 55.000 0.00 0.00 0.00 5.03
119 120 1.377202 GTGATCCCTTTGCCTCGCA 60.377 57.895 0.00 0.00 36.47 5.10
129 130 1.483316 TTGCCTCGCAATATACGTCG 58.517 50.000 0.00 0.00 43.99 5.12
187 188 1.272147 ACCCCCTTCTCTTTGTCATGC 60.272 52.381 0.00 0.00 0.00 4.06
205 206 5.066375 GTCATGCATAGCACTCCACAAAATA 59.934 40.000 0.00 0.00 43.04 1.40
206 207 5.829391 TCATGCATAGCACTCCACAAAATAT 59.171 36.000 0.00 0.00 43.04 1.28
252 255 2.134346 CCCATGCGTTTCCAAAAACTG 58.866 47.619 0.00 0.00 42.18 3.16
319 322 4.205587 GCAAATCCCATCTTGATCAGTCT 58.794 43.478 0.00 0.00 0.00 3.24
339 342 6.471198 CAGTCTACGATTTACGACATGCTTTA 59.529 38.462 0.00 0.00 45.77 1.85
341 344 6.252015 GTCTACGATTTACGACATGCTTTACA 59.748 38.462 0.00 0.00 45.77 2.41
353 356 6.401688 CGACATGCTTTACAGTAAATCCGAAA 60.402 38.462 6.20 0.00 0.00 3.46
358 1034 6.128117 TGCTTTACAGTAAATCCGAAATCCAC 60.128 38.462 6.20 0.00 0.00 4.02
362 1038 4.941873 ACAGTAAATCCGAAATCCACCTTC 59.058 41.667 0.00 0.00 0.00 3.46
374 1050 7.387948 CCGAAATCCACCTTCATAATAACCTAG 59.612 40.741 0.00 0.00 0.00 3.02
391 1067 5.167303 ACCTAGTTTAGAAGCAAGGAAGG 57.833 43.478 0.00 0.00 0.00 3.46
410 1086 1.070758 GGCTTCATCCTAATCGCCTCA 59.929 52.381 0.00 0.00 34.80 3.86
443 1119 5.954335 ACTGCAAATTAACCATAGCTTGTC 58.046 37.500 0.00 0.00 0.00 3.18
470 1146 9.271828 TCATAACATTTGCATATTCACGTAGAT 57.728 29.630 0.00 0.00 0.00 1.98
474 1150 8.607441 ACATTTGCATATTCACGTAGATACAT 57.393 30.769 0.00 0.00 0.00 2.29
475 1151 8.712363 ACATTTGCATATTCACGTAGATACATC 58.288 33.333 0.00 0.00 0.00 3.06
476 1152 6.927933 TTGCATATTCACGTAGATACATCG 57.072 37.500 0.00 0.00 0.00 3.84
506 1182 7.173218 TGGTCAAAGTTGTTTATGATCAGAGAC 59.827 37.037 0.09 2.41 29.97 3.36
512 1188 3.046390 GTTTATGATCAGAGACCGCGAG 58.954 50.000 8.23 0.00 0.00 5.03
513 1189 2.256117 TATGATCAGAGACCGCGAGA 57.744 50.000 8.23 0.00 0.00 4.04
514 1190 1.614996 ATGATCAGAGACCGCGAGAT 58.385 50.000 8.23 0.41 0.00 2.75
515 1191 0.947960 TGATCAGAGACCGCGAGATC 59.052 55.000 8.23 10.69 36.51 2.75
516 1192 1.234821 GATCAGAGACCGCGAGATCT 58.765 55.000 8.23 7.55 35.90 2.75
517 1193 2.224305 TGATCAGAGACCGCGAGATCTA 60.224 50.000 8.23 0.00 30.46 1.98
518 1194 1.872388 TCAGAGACCGCGAGATCTAG 58.128 55.000 8.23 0.00 30.46 2.43
519 1195 1.139256 TCAGAGACCGCGAGATCTAGT 59.861 52.381 8.23 0.00 30.46 2.57
520 1196 2.364647 TCAGAGACCGCGAGATCTAGTA 59.635 50.000 8.23 0.00 30.46 1.82
521 1197 3.132160 CAGAGACCGCGAGATCTAGTAA 58.868 50.000 8.23 0.00 30.46 2.24
522 1198 3.560481 CAGAGACCGCGAGATCTAGTAAA 59.440 47.826 8.23 0.00 30.46 2.01
523 1199 4.035324 CAGAGACCGCGAGATCTAGTAAAA 59.965 45.833 8.23 0.00 30.46 1.52
524 1200 4.035441 AGAGACCGCGAGATCTAGTAAAAC 59.965 45.833 8.23 0.00 30.46 2.43
525 1201 3.946558 AGACCGCGAGATCTAGTAAAACT 59.053 43.478 8.23 0.00 26.23 2.66
532 1208 6.467047 CGCGAGATCTAGTAAAACTTAACGAA 59.533 38.462 0.00 0.00 0.00 3.85
590 1269 7.890127 TGGAGGATAATGTTTTGAGAAAGACAT 59.110 33.333 0.00 0.00 34.41 3.06
599 1278 4.610605 TTGAGAAAGACATAACCGGACA 57.389 40.909 9.46 0.00 0.00 4.02
618 1297 4.697352 GGACATGTAGCTTGTTGTTCATCT 59.303 41.667 0.00 0.00 0.00 2.90
631 1310 3.765381 TGTTCATCTTCAGAAATGCCCA 58.235 40.909 0.00 0.00 0.00 5.36
633 1312 2.358957 TCATCTTCAGAAATGCCCACG 58.641 47.619 0.00 0.00 0.00 4.94
691 1371 2.548920 CCCCAGACTCGGCAGATATTTC 60.549 54.545 0.00 0.00 0.00 2.17
692 1372 2.548920 CCCAGACTCGGCAGATATTTCC 60.549 54.545 0.00 0.00 0.00 3.13
693 1373 2.103094 CCAGACTCGGCAGATATTTCCA 59.897 50.000 0.00 0.00 0.00 3.53
699 1379 6.038714 AGACTCGGCAGATATTTCCATTTTTC 59.961 38.462 0.00 0.00 0.00 2.29
700 1380 5.888161 ACTCGGCAGATATTTCCATTTTTCT 59.112 36.000 0.00 0.00 0.00 2.52
702 1382 7.556275 ACTCGGCAGATATTTCCATTTTTCTAA 59.444 33.333 0.00 0.00 0.00 2.10
705 1385 9.023967 CGGCAGATATTTCCATTTTTCTAAAAG 57.976 33.333 0.00 0.00 0.00 2.27
769 1449 2.995939 CTCAAAATAGAGACACGCAGCA 59.004 45.455 0.00 0.00 37.87 4.41
770 1450 3.398406 TCAAAATAGAGACACGCAGCAA 58.602 40.909 0.00 0.00 0.00 3.91
773 1453 0.460987 ATAGAGACACGCAGCAAGCC 60.461 55.000 0.00 0.00 41.38 4.35
844 1524 3.545911 CGAACTGGAAACGGACCG 58.454 61.111 13.61 13.61 41.09 4.79
970 1653 3.386402 CCCACCAAAACCTAAGCAAGAAA 59.614 43.478 0.00 0.00 0.00 2.52
990 1673 1.524482 GCCAGAGGAGCTCCGAATT 59.476 57.895 26.95 9.79 42.08 2.17
992 1675 0.249238 CCAGAGGAGCTCCGAATTCG 60.249 60.000 26.95 20.92 42.08 3.34
1380 2063 2.300152 CAAGGAGCCCAGCTTCGATATA 59.700 50.000 0.00 0.00 39.54 0.86
1414 2097 3.056322 GCCCATGTTTCATTGCTTCTCTT 60.056 43.478 0.00 0.00 0.00 2.85
1431 2114 6.037610 GCTTCTCTTTGTCTTCACTTTGAGAA 59.962 38.462 0.00 0.00 37.10 2.87
1514 2197 4.679331 CCCTGGTAAATTTAGGGGTGAAA 58.321 43.478 14.59 0.00 46.05 2.69
1518 2201 6.351796 CCTGGTAAATTTAGGGGTGAAATTGG 60.352 42.308 0.00 0.00 36.77 3.16
1565 2294 2.271497 GGCAGACTGGCATCAGCT 59.729 61.111 23.18 0.00 44.59 4.24
1566 2295 1.378250 GGCAGACTGGCATCAGCTT 60.378 57.895 23.18 0.00 44.59 3.74
1567 2296 1.375098 GGCAGACTGGCATCAGCTTC 61.375 60.000 23.18 0.00 44.59 3.86
1568 2297 0.392729 GCAGACTGGCATCAGCTTCT 60.393 55.000 4.26 0.00 44.59 2.85
1705 2434 5.972935 TCACAATACCGCATCTCTTCTAAA 58.027 37.500 0.00 0.00 0.00 1.85
1774 2503 5.849510 TCTAGTGTTGGATGTTTTTCGAGA 58.150 37.500 0.00 0.00 0.00 4.04
1927 2656 3.515901 GTGGATGTGAGTAGGACCTCTTT 59.484 47.826 0.00 0.00 32.50 2.52
1937 2666 7.176340 GTGAGTAGGACCTCTTTACTTGTAGAA 59.824 40.741 0.00 0.00 32.50 2.10
1990 2719 0.179137 TCATGTTCGAGGCAGTAGCG 60.179 55.000 0.00 0.00 43.41 4.26
1992 2721 0.246635 ATGTTCGAGGCAGTAGCGTT 59.753 50.000 0.00 0.00 43.41 4.84
1993 2722 0.666274 TGTTCGAGGCAGTAGCGTTG 60.666 55.000 0.00 0.00 43.41 4.10
2081 2810 4.524714 AGTATATGTGCGATAGGCTTGACT 59.475 41.667 0.00 0.00 44.05 3.41
2086 2815 2.099263 GTGCGATAGGCTTGACTCAGTA 59.901 50.000 0.00 0.00 44.05 2.74
2111 2840 5.016831 TGTGAGGCTCTTGTACTAGATTCA 58.983 41.667 16.72 9.14 0.00 2.57
2116 2845 7.342026 TGAGGCTCTTGTACTAGATTCACAATA 59.658 37.037 16.72 0.00 32.14 1.90
2119 2848 7.386299 GGCTCTTGTACTAGATTCACAATATGG 59.614 40.741 7.49 0.00 32.14 2.74
2142 2871 7.402054 TGGTGGCATCTATCTTTTCTTCTTTA 58.598 34.615 0.00 0.00 0.00 1.85
2160 2890 4.573201 TCTTTATTATGCACACGGTTAGCC 59.427 41.667 0.00 0.00 0.00 3.93
2179 2909 8.957466 GGTTAGCCTCTACATTTTATCTGTTTT 58.043 33.333 0.00 0.00 0.00 2.43
2259 2990 8.732746 AATTAGTGTAATAGAAACGCATCCTT 57.267 30.769 0.00 0.00 0.00 3.36
2321 3052 2.479566 TGACCAGGCTGATCAAGTTC 57.520 50.000 17.94 1.19 0.00 3.01
2443 3174 4.829492 GCATTTTATAGAGGGTTCCTGCAT 59.171 41.667 0.00 0.00 31.76 3.96
2473 3206 6.049955 TCCCTATCTTCTGTTACTTGTTGG 57.950 41.667 0.00 0.00 0.00 3.77
2474 3207 5.045869 TCCCTATCTTCTGTTACTTGTTGGG 60.046 44.000 0.00 0.00 0.00 4.12
2495 3228 3.550678 GGAGCTTTTATCCTCGTAACACG 59.449 47.826 0.00 0.00 44.19 4.49
2496 3229 3.518590 AGCTTTTATCCTCGTAACACGG 58.481 45.455 0.00 0.00 42.81 4.94
2586 3319 5.832221 TGGTTTGGTTGGGATGTAATGATA 58.168 37.500 0.00 0.00 0.00 2.15
2852 3585 4.415179 TCATGAGGTTATCCCCTGCAATAA 59.585 41.667 0.00 0.00 34.03 1.40
2913 3646 4.202131 GGGACTCGGGTGTAAAGATTAGAG 60.202 50.000 0.00 0.00 0.00 2.43
2940 3673 6.717084 GGGTGAGGCTAGCTAAATTATTTGAT 59.283 38.462 15.72 0.00 0.00 2.57
2982 3715 7.987458 TGAGGATCGAGTCTAAGCAAATAAAAT 59.013 33.333 0.00 0.00 38.61 1.82
2983 3716 8.147642 AGGATCGAGTCTAAGCAAATAAAATG 57.852 34.615 0.00 0.00 0.00 2.32
2994 3727 9.603921 CTAAGCAAATAAAATGATTGAATGGGT 57.396 29.630 0.00 0.00 0.00 4.51
3071 3806 5.157940 AGAGCTGATTGTCTTTCTGCTAA 57.842 39.130 0.00 0.00 45.02 3.09
3095 3830 1.612442 GGGTCCTACAGCCAGGTCA 60.612 63.158 0.00 0.00 42.97 4.02
3162 3897 5.048504 TGGCAGACTTCATCTCAACAAAATC 60.049 40.000 0.00 0.00 34.41 2.17
3195 3930 2.365293 GCCCATGCCCTAACCATTTAAG 59.635 50.000 0.00 0.00 0.00 1.85
3354 4091 4.533222 CAACTTAGTTGGGCGTTTAGTTG 58.467 43.478 16.62 0.00 39.56 3.16
3464 4201 3.132925 CCAACTTGTGGCTCCAATTTTG 58.867 45.455 0.00 0.00 41.72 2.44
3471 4208 3.130633 GTGGCTCCAATTTTGTTGAACC 58.869 45.455 0.00 0.00 0.00 3.62
3543 4280 2.945456 CCTAGAACCAAATTAGCCCCC 58.055 52.381 0.00 0.00 0.00 5.40
3672 4409 3.148412 TCTAATGCTTTGCAGTTGCTCA 58.852 40.909 5.62 0.00 43.65 4.26
3691 4428 4.153117 GCTCACATGAGTTGAGTAACTTGG 59.847 45.833 10.50 0.00 46.79 3.61
3716 4453 4.815308 CCTGCATCTGTCTTCCATTCTAAG 59.185 45.833 0.00 0.00 0.00 2.18
3791 4528 6.851222 ACAGATTTGTACTGTTGAGTCTTG 57.149 37.500 0.00 0.00 44.69 3.02
3804 4541 5.296780 TGTTGAGTCTTGTCATTGGTCTTTC 59.703 40.000 0.00 0.00 0.00 2.62
3932 4669 4.499758 CGCTTTACTGGACGTATCTTCTTC 59.500 45.833 0.00 0.00 0.00 2.87
4106 4843 7.093992 GGAAGATCTATGAGCATAAGGTACAC 58.906 42.308 0.00 0.00 0.00 2.90
4120 4857 3.997762 AGGTACACAACATTGCTACGAA 58.002 40.909 0.00 0.00 0.00 3.85
4151 4888 4.080526 ACAAAGTACAAGGTCCTGTCTGTT 60.081 41.667 0.00 0.00 0.00 3.16
4238 4975 0.602638 AATCTTTGAGCACGGCGTCA 60.603 50.000 10.85 1.75 0.00 4.35
4247 4984 0.793861 GCACGGCGTCACTTTATTCA 59.206 50.000 10.85 0.00 0.00 2.57
4269 5006 0.745845 GTTGGCATGGATCAGACGCT 60.746 55.000 0.00 0.00 0.00 5.07
4516 5253 1.737008 GTTCCCTGAAGTCGCCGAC 60.737 63.158 9.71 9.71 0.00 4.79
4548 5285 0.179067 ACGGTCTCCAAAACAGCGAA 60.179 50.000 0.00 0.00 35.11 4.70
4550 5287 1.535462 CGGTCTCCAAAACAGCGAATT 59.465 47.619 0.00 0.00 32.84 2.17
4555 5292 3.629855 TCTCCAAAACAGCGAATTTGACA 59.370 39.130 11.19 0.00 38.50 3.58
4853 5592 1.350684 TGCACCAGCCATGTCTAAGAA 59.649 47.619 0.00 0.00 41.13 2.52
4876 5615 1.191944 CTACACTATCACGCGCACAG 58.808 55.000 5.73 0.29 0.00 3.66
4877 5616 0.800683 TACACTATCACGCGCACAGC 60.801 55.000 5.73 0.00 43.95 4.40
4878 5617 1.807165 CACTATCACGCGCACAGCT 60.807 57.895 5.73 0.00 45.59 4.24
4910 5651 0.239347 GCAAAAGCATGACGAGCAGT 59.761 50.000 0.00 0.00 0.00 4.40
4929 5670 4.508124 GCAGTAGCAAAGATGTACGCTAAT 59.492 41.667 0.00 0.00 38.61 1.73
4930 5671 5.690409 GCAGTAGCAAAGATGTACGCTAATA 59.310 40.000 0.00 0.00 38.61 0.98
4931 5672 6.345882 GCAGTAGCAAAGATGTACGCTAATAC 60.346 42.308 0.00 0.00 38.61 1.89
4945 5686 6.638168 ACGCTAATACGTTTAGGAGTTTTC 57.362 37.500 14.90 1.95 45.75 2.29
4946 5687 6.393171 ACGCTAATACGTTTAGGAGTTTTCT 58.607 36.000 14.90 0.00 45.75 2.52
4947 5688 6.870439 ACGCTAATACGTTTAGGAGTTTTCTT 59.130 34.615 14.90 0.00 45.75 2.52
4950 5691 9.539139 GCTAATACGTTTAGGAGTTTTCTTTTC 57.461 33.333 14.90 0.00 0.00 2.29
4979 5720 7.812690 ACCGAGTTTAGGAGTTTGTTAAATT 57.187 32.000 0.00 0.00 0.00 1.82
5028 5769 7.479352 ACCATGTTCAAAATCCATGTATCAA 57.521 32.000 0.00 0.00 35.34 2.57
5035 5776 8.956426 GTTCAAAATCCATGTATCAAGGACTAA 58.044 33.333 0.00 0.00 33.98 2.24
5039 5780 4.631131 TCCATGTATCAAGGACTAATGCG 58.369 43.478 0.00 0.00 0.00 4.73
5064 5807 9.009327 CGCATACTTTAAGATAACAAAACATGG 57.991 33.333 0.00 0.00 0.00 3.66
5085 5828 4.461081 TGGTGTTTTATGGTATGGACTTGC 59.539 41.667 0.00 0.00 0.00 4.01
5105 5848 2.744202 GCGACACATCCACATTCTTTCT 59.256 45.455 0.00 0.00 0.00 2.52
5124 5867 8.575565 TCTTTCTGACAGTCATATTATTACGC 57.424 34.615 2.97 0.00 0.00 4.42
5125 5868 6.986424 TTCTGACAGTCATATTATTACGCG 57.014 37.500 3.53 3.53 0.00 6.01
5126 5869 5.458015 TCTGACAGTCATATTATTACGCGG 58.542 41.667 12.47 0.00 0.00 6.46
5129 5872 6.144854 TGACAGTCATATTATTACGCGGTAC 58.855 40.000 12.47 0.00 0.00 3.34
5213 7126 3.260632 GGCACAAATAACCACCAATCCTT 59.739 43.478 0.00 0.00 0.00 3.36
5218 7131 6.589907 CACAAATAACCACCAATCCTTTAAGC 59.410 38.462 0.00 0.00 0.00 3.09
5228 7141 4.650588 CCAATCCTTTAAGCATTGGATGGA 59.349 41.667 19.95 0.00 46.66 3.41
5229 7142 5.306160 CCAATCCTTTAAGCATTGGATGGAT 59.694 40.000 19.95 0.00 46.66 3.41
5269 7185 6.265196 GGATGACAGTAAATATTCATGGCCAA 59.735 38.462 10.96 0.00 0.00 4.52
5274 7190 6.437162 ACAGTAAATATTCATGGCCAACAGTT 59.563 34.615 10.96 1.29 0.00 3.16
5286 7202 4.082081 TGGCCAACAGTTGATTTGATCATC 60.082 41.667 15.36 0.00 39.39 2.92
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
18 19 3.761897 TGATCACACCAAACCCTAAAGG 58.238 45.455 0.00 0.00 43.78 3.11
19 20 5.105756 GGAATGATCACACCAAACCCTAAAG 60.106 44.000 13.17 0.00 0.00 1.85
20 21 4.770010 GGAATGATCACACCAAACCCTAAA 59.230 41.667 13.17 0.00 0.00 1.85
21 22 4.340617 GGAATGATCACACCAAACCCTAA 58.659 43.478 13.17 0.00 0.00 2.69
22 23 3.308832 GGGAATGATCACACCAAACCCTA 60.309 47.826 17.91 0.00 33.40 3.53
23 24 2.557452 GGGAATGATCACACCAAACCCT 60.557 50.000 17.91 0.00 33.40 4.34
24 25 1.824852 GGGAATGATCACACCAAACCC 59.175 52.381 17.91 10.54 0.00 4.11
25 26 2.524306 TGGGAATGATCACACCAAACC 58.476 47.619 17.91 6.83 32.81 3.27
32 33 2.432444 GGAAACGTGGGAATGATCACA 58.568 47.619 0.00 0.00 36.35 3.58
33 34 1.743394 GGGAAACGTGGGAATGATCAC 59.257 52.381 0.00 0.00 0.00 3.06
34 35 1.352687 TGGGAAACGTGGGAATGATCA 59.647 47.619 0.00 0.00 0.00 2.92
35 36 1.743394 GTGGGAAACGTGGGAATGATC 59.257 52.381 0.00 0.00 0.00 2.92
36 37 1.354368 AGTGGGAAACGTGGGAATGAT 59.646 47.619 0.00 0.00 0.00 2.45
37 38 0.768622 AGTGGGAAACGTGGGAATGA 59.231 50.000 0.00 0.00 0.00 2.57
38 39 2.483014 TAGTGGGAAACGTGGGAATG 57.517 50.000 0.00 0.00 0.00 2.67
39 40 3.352648 CATTAGTGGGAAACGTGGGAAT 58.647 45.455 0.00 0.00 0.00 3.01
40 41 2.553466 CCATTAGTGGGAAACGTGGGAA 60.553 50.000 0.00 0.00 42.11 3.97
41 42 1.003812 CCATTAGTGGGAAACGTGGGA 59.996 52.381 0.00 0.00 42.11 4.37
42 43 1.459450 CCATTAGTGGGAAACGTGGG 58.541 55.000 0.00 0.00 42.11 4.61
52 53 1.456287 GCCTAGGGCCCATTAGTGG 59.544 63.158 27.56 16.54 44.06 4.00
63 64 2.438411 CTCAGTCGTATAGGCCTAGGG 58.562 57.143 19.33 9.71 0.00 3.53
64 65 2.040012 TCCTCAGTCGTATAGGCCTAGG 59.960 54.545 19.33 12.25 0.00 3.02
65 66 3.340034 CTCCTCAGTCGTATAGGCCTAG 58.660 54.545 19.33 4.80 0.00 3.02
66 67 2.040012 CCTCCTCAGTCGTATAGGCCTA 59.960 54.545 16.60 16.60 0.00 3.93
67 68 1.202952 CCTCCTCAGTCGTATAGGCCT 60.203 57.143 11.78 11.78 0.00 5.19
68 69 1.249407 CCTCCTCAGTCGTATAGGCC 58.751 60.000 0.00 0.00 0.00 5.19
69 70 1.249407 CCCTCCTCAGTCGTATAGGC 58.751 60.000 0.00 0.00 0.00 3.93
70 71 1.548128 CCCCCTCCTCAGTCGTATAGG 60.548 61.905 0.00 0.00 0.00 2.57
71 72 1.912417 CCCCCTCCTCAGTCGTATAG 58.088 60.000 0.00 0.00 0.00 1.31
72 73 0.178970 GCCCCCTCCTCAGTCGTATA 60.179 60.000 0.00 0.00 0.00 1.47
73 74 1.457831 GCCCCCTCCTCAGTCGTAT 60.458 63.158 0.00 0.00 0.00 3.06
74 75 2.043248 GCCCCCTCCTCAGTCGTA 60.043 66.667 0.00 0.00 0.00 3.43
75 76 3.625632 ATGCCCCCTCCTCAGTCGT 62.626 63.158 0.00 0.00 0.00 4.34
76 77 2.765807 ATGCCCCCTCCTCAGTCG 60.766 66.667 0.00 0.00 0.00 4.18
77 78 1.977293 GACATGCCCCCTCCTCAGTC 61.977 65.000 0.00 0.00 0.00 3.51
78 79 1.997874 GACATGCCCCCTCCTCAGT 60.998 63.158 0.00 0.00 0.00 3.41
79 80 2.914289 GACATGCCCCCTCCTCAG 59.086 66.667 0.00 0.00 0.00 3.35
80 81 2.523740 TACGACATGCCCCCTCCTCA 62.524 60.000 0.00 0.00 0.00 3.86
81 82 1.122019 ATACGACATGCCCCCTCCTC 61.122 60.000 0.00 0.00 0.00 3.71
82 83 1.074471 ATACGACATGCCCCCTCCT 60.074 57.895 0.00 0.00 0.00 3.69
83 84 1.071471 CATACGACATGCCCCCTCC 59.929 63.158 0.00 0.00 0.00 4.30
84 85 0.532862 CACATACGACATGCCCCCTC 60.533 60.000 0.00 0.00 0.00 4.30
85 86 0.980754 TCACATACGACATGCCCCCT 60.981 55.000 0.00 0.00 0.00 4.79
86 87 0.108585 ATCACATACGACATGCCCCC 59.891 55.000 0.00 0.00 0.00 5.40
87 88 1.512926 GATCACATACGACATGCCCC 58.487 55.000 0.00 0.00 0.00 5.80
88 89 1.512926 GGATCACATACGACATGCCC 58.487 55.000 0.00 0.00 0.00 5.36
89 90 1.070758 AGGGATCACATACGACATGCC 59.929 52.381 0.00 0.00 0.00 4.40
90 91 2.533266 AGGGATCACATACGACATGC 57.467 50.000 0.00 0.00 0.00 4.06
91 92 3.002656 GCAAAGGGATCACATACGACATG 59.997 47.826 0.00 0.00 0.00 3.21
92 93 3.206150 GCAAAGGGATCACATACGACAT 58.794 45.455 0.00 0.00 0.00 3.06
93 94 2.627945 GCAAAGGGATCACATACGACA 58.372 47.619 0.00 0.00 0.00 4.35
94 95 1.940613 GGCAAAGGGATCACATACGAC 59.059 52.381 0.00 0.00 0.00 4.34
95 96 1.837439 AGGCAAAGGGATCACATACGA 59.163 47.619 0.00 0.00 0.00 3.43
96 97 2.213499 GAGGCAAAGGGATCACATACG 58.787 52.381 0.00 0.00 0.00 3.06
97 98 2.213499 CGAGGCAAAGGGATCACATAC 58.787 52.381 0.00 0.00 0.00 2.39
98 99 1.475034 GCGAGGCAAAGGGATCACATA 60.475 52.381 0.00 0.00 0.00 2.29
99 100 0.749454 GCGAGGCAAAGGGATCACAT 60.749 55.000 0.00 0.00 0.00 3.21
100 101 1.377202 GCGAGGCAAAGGGATCACA 60.377 57.895 0.00 0.00 0.00 3.58
101 102 0.960364 TTGCGAGGCAAAGGGATCAC 60.960 55.000 0.00 0.00 45.96 3.06
102 103 1.378378 TTGCGAGGCAAAGGGATCA 59.622 52.632 0.00 0.00 45.96 2.92
103 104 4.319133 TTGCGAGGCAAAGGGATC 57.681 55.556 0.00 0.00 45.96 3.36
111 112 0.664224 TCGACGTATATTGCGAGGCA 59.336 50.000 6.41 0.00 36.47 4.75
112 113 1.328439 CTCGACGTATATTGCGAGGC 58.672 55.000 12.72 0.00 44.58 4.70
115 116 1.600485 TGAGCTCGACGTATATTGCGA 59.400 47.619 9.64 0.00 0.00 5.10
116 117 2.032414 TGAGCTCGACGTATATTGCG 57.968 50.000 9.64 0.00 0.00 4.85
117 118 2.726760 CCTTGAGCTCGACGTATATTGC 59.273 50.000 9.64 0.00 0.00 3.56
118 119 2.726760 GCCTTGAGCTCGACGTATATTG 59.273 50.000 9.64 0.00 38.99 1.90
119 120 2.604855 CGCCTTGAGCTCGACGTATATT 60.605 50.000 9.64 0.00 40.39 1.28
120 121 1.069159 CGCCTTGAGCTCGACGTATAT 60.069 52.381 9.64 0.00 40.39 0.86
121 122 0.306840 CGCCTTGAGCTCGACGTATA 59.693 55.000 9.64 0.00 40.39 1.47
122 123 1.064296 CGCCTTGAGCTCGACGTAT 59.936 57.895 9.64 0.00 40.39 3.06
123 124 1.978712 CTCGCCTTGAGCTCGACGTA 61.979 60.000 9.64 0.00 38.03 3.57
124 125 3.329688 CTCGCCTTGAGCTCGACGT 62.330 63.158 9.64 0.00 38.03 4.34
125 126 2.578178 CTCGCCTTGAGCTCGACG 60.578 66.667 9.64 8.41 38.03 5.12
129 130 1.137086 TGATAACCTCGCCTTGAGCTC 59.863 52.381 6.82 6.82 43.82 4.09
187 188 9.669353 GTTAATCATATTTTGTGGAGTGCTATG 57.331 33.333 0.00 0.00 0.00 2.23
228 229 0.037512 TTTGGAAACGCATGGGCATG 60.038 50.000 10.10 0.00 41.24 4.06
313 316 4.095932 AGCATGTCGTAAATCGTAGACTGA 59.904 41.667 0.00 0.00 42.51 3.41
319 322 6.094719 ACTGTAAAGCATGTCGTAAATCGTA 58.905 36.000 0.00 0.00 40.80 3.43
329 332 6.417191 TTCGGATTTACTGTAAAGCATGTC 57.583 37.500 24.60 14.01 35.87 3.06
339 342 4.569719 AGGTGGATTTCGGATTTACTGT 57.430 40.909 0.00 0.00 0.00 3.55
341 344 5.174037 TGAAGGTGGATTTCGGATTTACT 57.826 39.130 0.00 0.00 0.00 2.24
358 1034 9.832445 TGCTTCTAAACTAGGTTATTATGAAGG 57.168 33.333 20.41 9.18 0.00 3.46
362 1038 9.832445 TCCTTGCTTCTAAACTAGGTTATTATG 57.168 33.333 0.00 0.00 31.67 1.90
391 1067 2.139118 GTGAGGCGATTAGGATGAAGC 58.861 52.381 0.00 0.00 0.00 3.86
410 1086 5.116882 GGTTAATTTGCAGTATCCTCTCGT 58.883 41.667 0.00 0.00 0.00 4.18
443 1119 8.764287 TCTACGTGAATATGCAAATGTTATGAG 58.236 33.333 0.00 0.00 0.00 2.90
470 1146 6.627395 AACAACTTTGACCATTTCGATGTA 57.373 33.333 0.00 0.00 0.00 2.29
471 1147 5.514274 AACAACTTTGACCATTTCGATGT 57.486 34.783 0.00 0.00 0.00 3.06
474 1150 7.265647 TCATAAACAACTTTGACCATTTCGA 57.734 32.000 0.00 0.00 0.00 3.71
475 1151 7.807433 TGATCATAAACAACTTTGACCATTTCG 59.193 33.333 0.00 0.00 0.00 3.46
476 1152 9.132521 CTGATCATAAACAACTTTGACCATTTC 57.867 33.333 0.00 0.00 0.00 2.17
506 1182 5.170981 CGTTAAGTTTTACTAGATCTCGCGG 59.829 44.000 6.13 0.00 0.00 6.46
512 1188 9.623350 ACTCACTTCGTTAAGTTTTACTAGATC 57.377 33.333 0.00 0.00 43.60 2.75
517 1193 8.909671 CGAATACTCACTTCGTTAAGTTTTACT 58.090 33.333 0.00 0.00 43.60 2.24
518 1194 7.681650 GCGAATACTCACTTCGTTAAGTTTTAC 59.318 37.037 7.21 0.00 43.60 2.01
519 1195 7.381948 TGCGAATACTCACTTCGTTAAGTTTTA 59.618 33.333 7.21 0.00 43.60 1.52
520 1196 6.201425 TGCGAATACTCACTTCGTTAAGTTTT 59.799 34.615 7.21 0.00 43.60 2.43
521 1197 5.693104 TGCGAATACTCACTTCGTTAAGTTT 59.307 36.000 7.21 0.00 43.60 2.66
522 1198 5.224888 TGCGAATACTCACTTCGTTAAGTT 58.775 37.500 7.21 0.00 43.60 2.66
524 1200 5.756950 TTGCGAATACTCACTTCGTTAAG 57.243 39.130 7.21 0.00 45.46 1.85
525 1201 6.018913 TGTTTTGCGAATACTCACTTCGTTAA 60.019 34.615 7.21 1.62 45.46 2.01
532 1208 5.008613 ACAACATGTTTTGCGAATACTCACT 59.991 36.000 8.77 0.00 0.00 3.41
534 1210 5.431420 ACAACATGTTTTGCGAATACTCA 57.569 34.783 8.77 0.00 0.00 3.41
590 1269 3.244284 ACAACAAGCTACATGTCCGGTTA 60.244 43.478 0.00 0.00 0.00 2.85
599 1278 6.233434 TCTGAAGATGAACAACAAGCTACAT 58.767 36.000 0.00 0.00 0.00 2.29
618 1297 0.109532 TGTCCGTGGGCATTTCTGAA 59.890 50.000 0.00 0.00 0.00 3.02
631 1310 3.681835 GCCGGTGTCTCTGTCCGT 61.682 66.667 1.90 0.00 42.30 4.69
633 1312 2.262915 CTGCCGGTGTCTCTGTCC 59.737 66.667 1.90 0.00 0.00 4.02
674 1354 4.696479 AATGGAAATATCTGCCGAGTCT 57.304 40.909 0.00 0.00 0.00 3.24
712 1392 0.543174 ATATCTGCCGAGTCTCCCCC 60.543 60.000 0.00 0.00 0.00 5.40
713 1393 1.273886 GAATATCTGCCGAGTCTCCCC 59.726 57.143 0.00 0.00 0.00 4.81
714 1394 2.029470 CAGAATATCTGCCGAGTCTCCC 60.029 54.545 0.00 0.00 37.72 4.30
715 1395 3.296322 CAGAATATCTGCCGAGTCTCC 57.704 52.381 0.00 0.00 37.72 3.71
773 1453 3.490759 AGATGGCGCGCTCGTTTG 61.491 61.111 32.29 0.00 38.14 2.93
808 1488 5.414765 AGTTCGGTTTTGGATATTCTGTTCC 59.585 40.000 0.00 0.00 0.00 3.62
810 1490 5.183140 CCAGTTCGGTTTTGGATATTCTGTT 59.817 40.000 0.00 0.00 33.76 3.16
811 1491 4.700213 CCAGTTCGGTTTTGGATATTCTGT 59.300 41.667 0.00 0.00 33.76 3.41
812 1492 4.941263 TCCAGTTCGGTTTTGGATATTCTG 59.059 41.667 0.00 0.00 36.13 3.02
813 1493 5.174037 TCCAGTTCGGTTTTGGATATTCT 57.826 39.130 0.00 0.00 36.13 2.40
844 1524 8.711457 CATTTCATTTGACTTGGGTATTTGTTC 58.289 33.333 0.00 0.00 0.00 3.18
970 1653 2.887738 ATTCGGAGCTCCTCTGGCCT 62.888 60.000 29.73 5.21 37.46 5.19
999 1682 1.607467 GTGCAGGAGGTTGGCCATT 60.607 57.895 6.09 0.00 37.19 3.16
1068 1751 4.698625 ACGACCCTCGCCTCCCTT 62.699 66.667 0.00 0.00 45.12 3.95
1380 2063 1.271840 ACATGGGCACGGACCTGTAT 61.272 55.000 0.00 0.00 0.00 2.29
1414 2097 5.943416 TGAAAGGTTCTCAAAGTGAAGACAA 59.057 36.000 0.00 0.00 0.00 3.18
1499 2182 5.221823 CCACACCAATTTCACCCCTAAATTT 60.222 40.000 0.00 0.00 35.00 1.82
1505 2188 0.831711 GCCACACCAATTTCACCCCT 60.832 55.000 0.00 0.00 0.00 4.79
1509 2192 3.568007 TGAAGTAGCCACACCAATTTCAC 59.432 43.478 0.00 0.00 0.00 3.18
1510 2193 3.826524 TGAAGTAGCCACACCAATTTCA 58.173 40.909 0.00 0.00 0.00 2.69
1514 2197 4.526970 CCTTATGAAGTAGCCACACCAAT 58.473 43.478 0.00 0.00 0.00 3.16
1518 2201 3.906720 TCCCTTATGAAGTAGCCACAC 57.093 47.619 0.00 0.00 0.00 3.82
1561 2290 7.776933 TGTAGCATGTTCTAATTAGAAGCTG 57.223 36.000 31.29 26.65 42.48 4.24
1562 2291 7.041508 GCATGTAGCATGTTCTAATTAGAAGCT 60.042 37.037 28.86 28.86 42.05 3.74
1563 2292 7.074502 GCATGTAGCATGTTCTAATTAGAAGC 58.925 38.462 24.92 23.05 42.05 3.86
1774 2503 1.723128 GCCCAGGTCATCCATCCCAT 61.723 60.000 0.00 0.00 35.89 4.00
1927 2656 5.748670 TGCATTGGGTAGTTCTACAAGTA 57.251 39.130 11.34 0.00 0.00 2.24
1937 2666 3.266772 TCTTGAGGAATGCATTGGGTAGT 59.733 43.478 18.59 0.00 0.00 2.73
1990 2719 2.789409 ATCAACACTAGAGGGCCAAC 57.211 50.000 6.18 0.00 0.00 3.77
1992 2721 2.237143 CAGAATCAACACTAGAGGGCCA 59.763 50.000 6.18 0.00 0.00 5.36
1993 2722 2.501723 TCAGAATCAACACTAGAGGGCC 59.498 50.000 0.00 0.00 0.00 5.80
2081 2810 2.598565 ACAAGAGCCTCACACTACTGA 58.401 47.619 0.00 0.00 0.00 3.41
2086 2815 4.035612 TCTAGTACAAGAGCCTCACACT 57.964 45.455 0.00 0.00 0.00 3.55
2111 2840 7.293073 AGAAAAGATAGATGCCACCATATTGT 58.707 34.615 0.00 0.00 0.00 2.71
2116 2845 6.011122 AGAAGAAAAGATAGATGCCACCAT 57.989 37.500 0.00 0.00 0.00 3.55
2142 2871 2.170607 AGAGGCTAACCGTGTGCATAAT 59.829 45.455 0.00 0.00 42.76 1.28
2152 2881 6.281405 ACAGATAAAATGTAGAGGCTAACCG 58.719 40.000 0.00 0.00 42.76 4.44
2179 2909 5.659440 AAACTCTGCAACAGAAGGAAAAA 57.341 34.783 0.00 0.00 40.18 1.94
2184 2914 4.376340 AACAAAACTCTGCAACAGAAGG 57.624 40.909 0.00 0.00 40.18 3.46
2264 2995 3.057315 CCATGCACCACTGGTTCTTTTAG 60.057 47.826 0.00 0.00 31.02 1.85
2288 3019 2.091055 CCTGGTCATCTCTTCCTCCCTA 60.091 54.545 0.00 0.00 0.00 3.53
2321 3052 6.851330 CGCAAACAAGAAAGAACCTACTTTAG 59.149 38.462 0.00 0.00 39.71 1.85
2443 3174 7.510675 AGTAACAGAAGATAGGGAAAATGGA 57.489 36.000 0.00 0.00 0.00 3.41
2473 3206 3.550678 CGTGTTACGAGGATAAAAGCTCC 59.449 47.826 0.00 0.00 46.05 4.70
2474 3207 3.550678 CCGTGTTACGAGGATAAAAGCTC 59.449 47.826 2.52 0.00 46.05 4.09
2553 3286 3.258228 CCAACCAAACCAGAAAACACAC 58.742 45.455 0.00 0.00 0.00 3.82
2586 3319 6.820656 CCACAGTATGCTAACAAGAAAGAGAT 59.179 38.462 0.00 0.00 42.53 2.75
2823 3556 2.613977 GGGGATAACCTCATGATCGCAG 60.614 54.545 11.14 0.00 40.03 5.18
2852 3585 4.972591 GCAACGGCTCTTTTGCAT 57.027 50.000 1.51 0.00 46.13 3.96
2913 3646 1.141185 ATTTAGCTAGCCTCACCCCC 58.859 55.000 12.13 0.00 0.00 5.40
2940 3673 2.967201 TCCTCAAACTAGAACCGGTTCA 59.033 45.455 40.66 27.50 41.84 3.18
2982 3715 3.163467 TGACATTGCACCCATTCAATCA 58.837 40.909 0.00 0.00 31.15 2.57
2983 3716 3.194116 ACTGACATTGCACCCATTCAATC 59.806 43.478 0.00 0.00 31.15 2.67
3071 3806 0.412244 TGGCTGTAGGACCCACTAGT 59.588 55.000 0.00 0.00 0.00 2.57
3162 3897 1.813859 CATGGGCAATGTGCTGAGG 59.186 57.895 0.00 0.00 44.28 3.86
3350 4087 1.630369 TCCTAAGATGTGGCTGCAACT 59.370 47.619 8.88 0.00 0.00 3.16
3354 4091 4.427312 CATTTTTCCTAAGATGTGGCTGC 58.573 43.478 0.00 0.00 0.00 5.25
3464 4201 2.956333 ACTTGCCTAAGGTTGGTTCAAC 59.044 45.455 2.46 2.46 42.89 3.18
3597 4334 3.119884 TCGAGCAATTAAACATGCAGGTG 60.120 43.478 4.03 0.00 44.95 4.00
3672 4409 3.412386 GCCCAAGTTACTCAACTCATGT 58.588 45.455 0.00 0.00 44.41 3.21
3691 4428 0.106819 ATGGAAGACAGATGCAGGCC 60.107 55.000 0.00 0.00 0.00 5.19
3791 4528 5.946377 ACAGAATTAGGGAAAGACCAATGAC 59.054 40.000 0.00 0.00 41.20 3.06
3804 4541 6.311200 GCAAATAGCAACAAACAGAATTAGGG 59.689 38.462 0.00 0.00 44.79 3.53
4059 4796 4.700213 CCCATTCCTGTCGAGTTTGTAAAT 59.300 41.667 0.00 0.00 0.00 1.40
4106 4843 1.199097 GGTGGGTTCGTAGCAATGTTG 59.801 52.381 0.00 0.00 0.00 3.33
4120 4857 1.202722 CCTTGTACTTTGTCGGTGGGT 60.203 52.381 0.00 0.00 0.00 4.51
4151 4888 5.067153 GCTAAGTGATCTGACTAGCTCTTGA 59.933 44.000 0.00 0.00 0.00 3.02
4238 4975 4.415596 TCCATGCCAACCTTGAATAAAGT 58.584 39.130 0.00 0.00 33.66 2.66
4247 4984 1.679944 CGTCTGATCCATGCCAACCTT 60.680 52.381 0.00 0.00 0.00 3.50
4269 5006 5.541868 CCTATCCTCCTCTGAGATTTGCTAA 59.458 44.000 6.17 0.00 41.42 3.09
4345 5082 4.702612 AGTACTACTCATCAGTGACTGGTG 59.297 45.833 19.45 19.45 43.32 4.17
4516 5253 0.606401 AGACCGTTGCAATGTCCAGG 60.606 55.000 21.57 12.85 0.00 4.45
4659 5398 7.282901 TGGACTTGACATGGTTCACAATATATG 59.717 37.037 0.00 0.00 0.00 1.78
4675 5414 3.316029 CACAAAGAATGCTGGACTTGACA 59.684 43.478 0.00 0.00 0.00 3.58
4676 5415 3.316308 ACACAAAGAATGCTGGACTTGAC 59.684 43.478 0.00 0.00 0.00 3.18
4678 5417 3.567164 AGACACAAAGAATGCTGGACTTG 59.433 43.478 0.00 0.00 0.00 3.16
4853 5592 1.471287 TGCGCGTGATAGTGTAGAAGT 59.529 47.619 8.43 0.00 0.00 3.01
4910 5651 5.824429 ACGTATTAGCGTACATCTTTGCTA 58.176 37.500 0.00 0.00 43.83 3.49
4929 5670 8.721019 TCAAGAAAAGAAAACTCCTAAACGTA 57.279 30.769 0.00 0.00 0.00 3.57
4930 5671 7.619964 TCAAGAAAAGAAAACTCCTAAACGT 57.380 32.000 0.00 0.00 0.00 3.99
4931 5672 7.431376 GGTTCAAGAAAAGAAAACTCCTAAACG 59.569 37.037 0.00 0.00 0.00 3.60
4945 5686 5.758784 ACTCCTAAACTCGGTTCAAGAAAAG 59.241 40.000 0.00 0.00 0.00 2.27
4946 5687 5.677567 ACTCCTAAACTCGGTTCAAGAAAA 58.322 37.500 0.00 0.00 0.00 2.29
4947 5688 5.286267 ACTCCTAAACTCGGTTCAAGAAA 57.714 39.130 0.00 0.00 0.00 2.52
4950 5691 4.814771 ACAAACTCCTAAACTCGGTTCAAG 59.185 41.667 0.00 0.00 0.00 3.02
5002 5743 7.995289 TGATACATGGATTTTGAACATGGTAC 58.005 34.615 8.51 0.00 44.65 3.34
5003 5744 8.586879 TTGATACATGGATTTTGAACATGGTA 57.413 30.769 8.51 0.55 44.65 3.25
5028 5769 5.914033 TCTTAAAGTATGCGCATTAGTCCT 58.086 37.500 30.42 13.54 0.00 3.85
5035 5776 8.240682 TGTTTTGTTATCTTAAAGTATGCGCAT 58.759 29.630 28.23 28.23 0.00 4.73
5039 5780 9.855021 ACCATGTTTTGTTATCTTAAAGTATGC 57.145 29.630 0.00 0.00 0.00 3.14
5064 5807 4.393680 TCGCAAGTCCATACCATAAAACAC 59.606 41.667 0.00 0.00 39.48 3.32
5085 5828 3.996363 TCAGAAAGAATGTGGATGTGTCG 59.004 43.478 0.00 0.00 0.00 4.35
5105 5848 5.190992 ACCGCGTAATAATATGACTGTCA 57.809 39.130 13.60 13.60 0.00 3.58
5123 5866 2.870411 AGAAACTGAACTTGTGTACCGC 59.130 45.455 0.00 0.00 0.00 5.68
5124 5867 4.446719 GGTAGAAACTGAACTTGTGTACCG 59.553 45.833 0.00 0.00 0.00 4.02
5125 5868 5.608449 AGGTAGAAACTGAACTTGTGTACC 58.392 41.667 0.00 0.00 0.00 3.34
5126 5869 6.759827 TGAAGGTAGAAACTGAACTTGTGTAC 59.240 38.462 0.00 0.00 0.00 2.90
5129 5872 5.007724 GGTGAAGGTAGAAACTGAACTTGTG 59.992 44.000 0.00 0.00 0.00 3.33
5213 7126 5.015072 TGCCCTATATCCATCCAATGCTTAA 59.985 40.000 0.00 0.00 0.00 1.85
5218 7131 4.849813 TCTGCCCTATATCCATCCAATG 57.150 45.455 0.00 0.00 0.00 2.82
5228 7141 5.096521 TGTCATCCTGATTCTGCCCTATAT 58.903 41.667 0.00 0.00 0.00 0.86
5229 7142 4.492646 TGTCATCCTGATTCTGCCCTATA 58.507 43.478 0.00 0.00 0.00 1.31


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

AutoCloner maintained by Alex Coulton.