Multiple sequence alignment - TraesCS5A01G176000

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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 TraesCS5A01G176000 chr5A 100.000 3625 0 0 1 3625 370193218 370189594 0.000000e+00 6695.0
1 TraesCS5A01G176000 chr5B 90.397 2114 146 29 1545 3624 316378946 316381036 0.000000e+00 2726.0
2 TraesCS5A01G176000 chr5B 88.467 763 29 21 513 1236 316377877 316378619 0.000000e+00 867.0
3 TraesCS5A01G176000 chr5B 91.628 215 13 5 272 484 316377169 316377380 3.540000e-75 292.0
4 TraesCS5A01G176000 chr5D 92.177 1713 113 8 1920 3625 278311604 278313302 0.000000e+00 2401.0
5 TraesCS5A01G176000 chr5D 87.894 1173 58 36 513 1664 278310099 278311208 0.000000e+00 1303.0
6 TraesCS5A01G176000 chr5D 91.184 397 23 5 1 394 278309502 278309889 2.480000e-146 529.0
7 TraesCS5A01G176000 chr5D 88.177 203 23 1 1679 1880 278311388 278311590 1.300000e-59 241.0
8 TraesCS5A01G176000 chr1B 86.538 208 27 1 1030 1237 242248735 242248529 1.010000e-55 228.0
9 TraesCS5A01G176000 chr1A 86.538 208 27 1 1030 1237 175178822 175178616 1.010000e-55 228.0
10 TraesCS5A01G176000 chr1D 86.341 205 27 1 1030 1234 184470882 184471085 4.710000e-54 222.0
11 TraesCS5A01G176000 chr4D 93.478 46 2 1 1052 1097 476865642 476865686 2.340000e-07 67.6
12 TraesCS5A01G176000 chr4B 93.478 46 2 1 1052 1097 600917296 600917340 2.340000e-07 67.6
13 TraesCS5A01G176000 chr4A 93.478 46 2 1 1052 1097 683606227 683606271 2.340000e-07 67.6


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 TraesCS5A01G176000 chr5A 370189594 370193218 3624 True 6695.0 6695 100.000 1 3625 1 chr5A.!!$R1 3624
1 TraesCS5A01G176000 chr5B 316377169 316381036 3867 False 1295.0 2726 90.164 272 3624 3 chr5B.!!$F1 3352
2 TraesCS5A01G176000 chr5D 278309502 278313302 3800 False 1118.5 2401 89.858 1 3625 4 chr5D.!!$F1 3624

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
227 231 0.036765 CCGTGAACGATGGGAGGAAA 60.037 55.0 4.03 0.0 43.02 3.13 F
2086 3054 0.031994 GCAAATGAACGGTGGCAGTT 59.968 50.0 0.00 0.0 34.07 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2104 3072 0.178964 AAGCAAGCAAAGCTGGGGTA 60.179 50.0 0.0 0.0 42.53 3.69 R
3176 4147 0.038892 GTTCATGCCACCTGTGCTTG 60.039 55.0 0.0 0.0 35.77 4.01 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
48 49 3.160679 ACTGCTTGCTCCATTAAAGGT 57.839 42.857 0.00 0.00 0.00 3.50
131 132 2.337879 TTTCCTTGCCTCGCTGTGGT 62.338 55.000 0.00 0.00 0.00 4.16
148 149 3.248418 TAGCACCAGCAGGCACCA 61.248 61.111 0.00 0.00 45.49 4.17
161 165 1.006922 GCACCAAAAGCCACTCTGC 60.007 57.895 0.00 0.00 0.00 4.26
191 195 5.487433 CACAATGATGAGTGTAGGTAACCA 58.513 41.667 0.00 0.00 37.17 3.67
192 196 6.115446 CACAATGATGAGTGTAGGTAACCAT 58.885 40.000 0.00 0.00 37.17 3.55
193 197 6.037500 CACAATGATGAGTGTAGGTAACCATG 59.962 42.308 0.00 0.00 37.17 3.66
194 198 6.070251 ACAATGATGAGTGTAGGTAACCATGA 60.070 38.462 0.00 0.00 37.17 3.07
195 199 6.560003 ATGATGAGTGTAGGTAACCATGAA 57.440 37.500 0.00 0.00 37.17 2.57
196 200 5.977635 TGATGAGTGTAGGTAACCATGAAG 58.022 41.667 0.00 0.00 37.17 3.02
197 201 4.202245 TGAGTGTAGGTAACCATGAAGC 57.798 45.455 0.00 0.00 37.17 3.86
198 202 3.055385 TGAGTGTAGGTAACCATGAAGCC 60.055 47.826 0.00 0.00 37.17 4.35
199 203 2.910319 AGTGTAGGTAACCATGAAGCCA 59.090 45.455 0.00 0.00 37.17 4.75
204 208 1.824230 GGTAACCATGAAGCCATGCAA 59.176 47.619 0.00 0.00 46.73 4.08
220 224 1.714899 GCAATCCCCGTGAACGATGG 61.715 60.000 4.03 4.83 43.02 3.51
227 231 0.036765 CCGTGAACGATGGGAGGAAA 60.037 55.000 4.03 0.00 43.02 3.13
228 232 1.609580 CCGTGAACGATGGGAGGAAAA 60.610 52.381 4.03 0.00 43.02 2.29
252 256 0.937441 AGGAGGTAGGAGATGGCAGA 59.063 55.000 0.00 0.00 0.00 4.26
273 277 0.765510 AGGAACGGCCTCAAGAAGTT 59.234 50.000 0.00 0.00 46.97 2.66
281 285 3.120060 CGGCCTCAAGAAGTTGAATGAAG 60.120 47.826 0.00 0.00 42.27 3.02
289 293 5.796424 AGAAGTTGAATGAAGGCAACAAT 57.204 34.783 0.00 0.00 45.08 2.71
294 298 6.815089 AGTTGAATGAAGGCAACAATGTTAA 58.185 32.000 0.00 0.00 45.08 2.01
328 332 1.469423 GCCGAACGAAAACCAAAACCA 60.469 47.619 0.00 0.00 0.00 3.67
408 439 2.594529 AATGCGTTGTAAGCTCGTTG 57.405 45.000 0.00 0.00 35.28 4.10
449 481 1.593006 GTGATACGTGTGCCATACTGC 59.407 52.381 0.00 0.00 0.00 4.40
473 505 2.000447 GGTCAATTTCTCCCGAGAACG 59.000 52.381 6.65 0.02 46.13 3.95
476 508 2.561419 TCAATTTCTCCCGAGAACGAGT 59.439 45.455 6.65 0.00 46.13 4.18
479 511 2.486472 TTCTCCCGAGAACGAGTACT 57.514 50.000 2.98 0.00 42.06 2.73
480 512 2.021355 TCTCCCGAGAACGAGTACTC 57.979 55.000 13.18 13.18 42.66 2.59
489 521 4.832767 CGAGTACTCGTTGCGTGA 57.167 55.556 32.24 0.00 46.99 4.35
490 522 2.337101 CGAGTACTCGTTGCGTGAC 58.663 57.895 32.24 0.00 46.99 3.67
491 523 0.385098 CGAGTACTCGTTGCGTGACA 60.385 55.000 32.24 0.00 46.99 3.58
495 563 1.191647 GTACTCGTTGCGTGACAAAGG 59.808 52.381 0.00 0.00 40.82 3.11
497 565 1.153329 TCGTTGCGTGACAAAGGGT 60.153 52.632 0.00 0.00 40.82 4.34
508 576 1.754226 GACAAAGGGTGAAGGCAACAA 59.246 47.619 0.00 0.00 41.41 2.83
511 579 2.086610 AAGGGTGAAGGCAACAACAT 57.913 45.000 1.91 0.00 41.41 2.71
514 1021 2.108250 AGGGTGAAGGCAACAACATAGT 59.892 45.455 1.91 0.00 41.41 2.12
518 1025 4.069304 GTGAAGGCAACAACATAGTACCA 58.931 43.478 0.00 0.00 41.41 3.25
602 1109 2.097825 AGCTGATTTTCCACCTCATGC 58.902 47.619 0.00 0.00 0.00 4.06
606 1113 0.527565 ATTTTCCACCTCATGCGCAC 59.472 50.000 14.90 0.00 0.00 5.34
646 1153 1.598924 GCTTCAACACAACTCTGCTGC 60.599 52.381 0.00 0.00 0.00 5.25
647 1154 1.945394 CTTCAACACAACTCTGCTGCT 59.055 47.619 0.00 0.00 0.00 4.24
653 1160 1.078567 CAACTCTGCTGCTCCTCCC 60.079 63.158 0.00 0.00 0.00 4.30
688 1200 7.893658 TCTAACACTAAACAAACCAAACCAAA 58.106 30.769 0.00 0.00 0.00 3.28
689 1201 6.788684 AACACTAAACAAACCAAACCAAAC 57.211 33.333 0.00 0.00 0.00 2.93
692 1204 5.701290 CACTAAACAAACCAAACCAAACCAA 59.299 36.000 0.00 0.00 0.00 3.67
693 1205 6.204882 CACTAAACAAACCAAACCAAACCAAA 59.795 34.615 0.00 0.00 0.00 3.28
694 1206 5.440234 AAACAAACCAAACCAAACCAAAC 57.560 34.783 0.00 0.00 0.00 2.93
695 1207 3.413327 ACAAACCAAACCAAACCAAACC 58.587 40.909 0.00 0.00 0.00 3.27
696 1208 3.181443 ACAAACCAAACCAAACCAAACCA 60.181 39.130 0.00 0.00 0.00 3.67
697 1209 3.790089 AACCAAACCAAACCAAACCAA 57.210 38.095 0.00 0.00 0.00 3.67
698 1210 4.308526 AACCAAACCAAACCAAACCAAT 57.691 36.364 0.00 0.00 0.00 3.16
737 1249 1.064537 CCACCACCACCATCATCATCA 60.065 52.381 0.00 0.00 0.00 3.07
738 1250 2.423803 CCACCACCACCATCATCATCAT 60.424 50.000 0.00 0.00 0.00 2.45
739 1251 2.882761 CACCACCACCATCATCATCATC 59.117 50.000 0.00 0.00 0.00 2.92
740 1252 2.510800 ACCACCACCATCATCATCATCA 59.489 45.455 0.00 0.00 0.00 3.07
758 1270 8.105197 TCATCATCATCTTCTTCTTCTCCAAAA 58.895 33.333 0.00 0.00 0.00 2.44
889 1402 0.037326 CTGCGGTTTCAGTAGCCAGA 60.037 55.000 0.00 0.00 0.00 3.86
890 1403 0.037326 TGCGGTTTCAGTAGCCAGAG 60.037 55.000 0.00 0.00 0.00 3.35
905 1418 1.555765 CCAGAGGAAGGAGAAAGGGGA 60.556 57.143 0.00 0.00 0.00 4.81
946 1489 4.390341 AGGAGATCCTGCTGGTCC 57.610 61.111 9.73 9.38 46.55 4.46
974 1517 1.815003 GTTGTTGAGGCAGGGAGATTG 59.185 52.381 0.00 0.00 0.00 2.67
975 1518 1.067295 TGTTGAGGCAGGGAGATTGT 58.933 50.000 0.00 0.00 0.00 2.71
976 1519 2.265367 TGTTGAGGCAGGGAGATTGTA 58.735 47.619 0.00 0.00 0.00 2.41
979 1522 1.839994 TGAGGCAGGGAGATTGTAAGG 59.160 52.381 0.00 0.00 0.00 2.69
980 1523 1.141858 GAGGCAGGGAGATTGTAAGGG 59.858 57.143 0.00 0.00 0.00 3.95
981 1524 0.466372 GGCAGGGAGATTGTAAGGGC 60.466 60.000 0.00 0.00 0.00 5.19
982 1525 0.466372 GCAGGGAGATTGTAAGGGCC 60.466 60.000 0.00 0.00 0.00 5.80
990 1541 1.069358 GATTGTAAGGGCCGAGAGAGG 59.931 57.143 0.00 0.00 0.00 3.69
1047 1598 2.088104 TGGGGCAGAAGATCGACTAT 57.912 50.000 0.00 0.00 0.00 2.12
1238 1789 1.337447 CGCGGGACAAGAGAGGTAAAA 60.337 52.381 0.00 0.00 0.00 1.52
1239 1790 2.677037 CGCGGGACAAGAGAGGTAAAAT 60.677 50.000 0.00 0.00 0.00 1.82
1270 1821 1.816224 CACTAATCCAACCCCAAACCG 59.184 52.381 0.00 0.00 0.00 4.44
1290 1841 2.287909 CGACCCTGCTAGCTGTATCTTC 60.288 54.545 17.23 5.83 0.00 2.87
1291 1842 2.962421 GACCCTGCTAGCTGTATCTTCT 59.038 50.000 17.23 0.00 0.00 2.85
1292 1843 2.962421 ACCCTGCTAGCTGTATCTTCTC 59.038 50.000 17.23 0.00 0.00 2.87
1293 1844 3.230134 CCCTGCTAGCTGTATCTTCTCT 58.770 50.000 17.23 0.00 0.00 3.10
1294 1845 3.255642 CCCTGCTAGCTGTATCTTCTCTC 59.744 52.174 17.23 0.00 0.00 3.20
1295 1846 3.255642 CCTGCTAGCTGTATCTTCTCTCC 59.744 52.174 17.23 0.00 0.00 3.71
1296 1847 2.881513 TGCTAGCTGTATCTTCTCTCCG 59.118 50.000 17.23 0.00 0.00 4.63
1297 1848 2.882137 GCTAGCTGTATCTTCTCTCCGT 59.118 50.000 7.70 0.00 0.00 4.69
1298 1849 3.304391 GCTAGCTGTATCTTCTCTCCGTG 60.304 52.174 7.70 0.00 0.00 4.94
1299 1850 1.407258 AGCTGTATCTTCTCTCCGTGC 59.593 52.381 0.00 0.00 0.00 5.34
1300 1851 1.407258 GCTGTATCTTCTCTCCGTGCT 59.593 52.381 0.00 0.00 0.00 4.40
1319 1870 2.354821 GCTGGCCTCGATCGTTTTATTT 59.645 45.455 15.94 0.00 0.00 1.40
1321 1872 4.342772 CTGGCCTCGATCGTTTTATTTTG 58.657 43.478 15.94 0.00 0.00 2.44
1325 1876 4.557301 GCCTCGATCGTTTTATTTTGTTGG 59.443 41.667 15.94 1.80 0.00 3.77
1328 1897 6.128391 CCTCGATCGTTTTATTTTGTTGGAGA 60.128 38.462 15.94 0.00 0.00 3.71
1331 1900 7.960738 TCGATCGTTTTATTTTGTTGGAGAATC 59.039 33.333 15.94 0.00 0.00 2.52
1332 1901 7.748683 CGATCGTTTTATTTTGTTGGAGAATCA 59.251 33.333 7.03 0.00 36.25 2.57
1353 1922 8.645814 AATCATATTATGCATATAGGCCATGG 57.354 34.615 7.63 7.63 0.00 3.66
1354 1923 6.005823 TCATATTATGCATATAGGCCATGGC 58.994 40.000 29.47 29.47 41.06 4.40
1371 1940 3.521605 CCTGATGGCCATGCACTG 58.478 61.111 26.56 12.69 0.00 3.66
1385 1954 1.416813 GCACTGCAGCACTACTAGCG 61.417 60.000 15.27 0.00 37.01 4.26
1400 1969 1.974680 CTAGCGCGCGGTAGTAATTAC 59.025 52.381 44.17 21.74 40.24 1.89
1422 1996 9.877178 ATTACCTTGTCTGTTTCTCTAGTTATG 57.123 33.333 0.00 0.00 0.00 1.90
1423 1997 7.540474 ACCTTGTCTGTTTCTCTAGTTATGA 57.460 36.000 0.00 0.00 0.00 2.15
1458 2040 1.131126 GATTGTCGTGTGGAATGCAGG 59.869 52.381 0.00 0.00 0.00 4.85
1459 2041 1.514678 TTGTCGTGTGGAATGCAGGC 61.515 55.000 0.00 0.00 0.00 4.85
1461 2043 1.228094 TCGTGTGGAATGCAGGCAA 60.228 52.632 0.00 0.00 0.00 4.52
1466 2048 0.389426 GTGGAATGCAGGCAAGCTTG 60.389 55.000 22.44 22.44 34.99 4.01
1470 2052 2.086869 GAATGCAGGCAAGCTTGTAGA 58.913 47.619 26.55 8.09 34.99 2.59
1471 2053 1.747709 ATGCAGGCAAGCTTGTAGAG 58.252 50.000 26.55 15.27 34.99 2.43
1473 2055 1.202806 TGCAGGCAAGCTTGTAGAGTT 60.203 47.619 26.55 4.75 34.99 3.01
1474 2056 1.882623 GCAGGCAAGCTTGTAGAGTTT 59.117 47.619 26.55 3.42 0.00 2.66
1475 2057 2.095516 GCAGGCAAGCTTGTAGAGTTTC 60.096 50.000 26.55 8.00 0.00 2.78
1478 2060 2.744741 GGCAAGCTTGTAGAGTTTCCTC 59.255 50.000 26.55 6.08 38.04 3.71
1502 2084 1.112315 TTGGTTTTGCGCATGGTCCT 61.112 50.000 12.75 0.00 0.00 3.85
1520 2102 1.233019 CTGTCCTTGGTCAGTGCAAG 58.767 55.000 5.88 4.09 0.00 4.01
1546 2128 3.133141 TGGATTTGTCATTGTCCGTGA 57.867 42.857 0.00 0.00 33.39 4.35
1547 2129 2.811431 TGGATTTGTCATTGTCCGTGAC 59.189 45.455 0.00 0.00 44.77 3.67
1548 2130 2.161609 GGATTTGTCATTGTCCGTGACC 59.838 50.000 4.06 0.00 44.10 4.02
1549 2131 2.631160 TTTGTCATTGTCCGTGACCT 57.369 45.000 4.06 0.00 44.10 3.85
1550 2132 2.631160 TTGTCATTGTCCGTGACCTT 57.369 45.000 4.06 0.00 44.10 3.50
1559 2153 4.074627 TGTCCGTGACCTTATTGTTTGA 57.925 40.909 2.23 0.00 0.00 2.69
1563 2157 4.935205 TCCGTGACCTTATTGTTTGATCTG 59.065 41.667 0.00 0.00 0.00 2.90
1629 2397 7.441836 GGAATTATTGTTCCTTGTGTTCCTTT 58.558 34.615 0.00 0.00 43.49 3.11
1665 2433 5.008217 TGTCCTCAACCGAAAGTTATGTTTG 59.992 40.000 0.00 0.00 36.18 2.93
1670 2438 6.674066 TCAACCGAAAGTTATGTTTGGAATC 58.326 36.000 0.00 0.00 36.18 2.52
1698 2631 5.491070 TGCTACAGATGTTAAGCATGTTCT 58.509 37.500 6.37 0.00 39.92 3.01
1767 2701 6.493458 TGTTCCATCATAATCTAGATCGGACA 59.507 38.462 5.51 4.76 0.00 4.02
1768 2702 6.516739 TCCATCATAATCTAGATCGGACAC 57.483 41.667 5.51 0.00 0.00 3.67
1786 2720 5.755375 CGGACACTTACATCAGAATAGCATT 59.245 40.000 0.00 0.00 0.00 3.56
1792 2726 9.499479 CACTTACATCAGAATAGCATTCCTTAT 57.501 33.333 5.57 0.00 0.00 1.73
1868 2811 2.766263 ACGGTGAGATTAGAATCTGCCA 59.234 45.455 9.49 0.14 45.39 4.92
1896 2859 9.901172 AAAACTTTAACTAACTCTTCTCAGGAA 57.099 29.630 0.00 0.00 0.00 3.36
1905 2868 8.652290 ACTAACTCTTCTCAGGAATAAAACACT 58.348 33.333 0.00 0.00 0.00 3.55
1910 2873 7.735917 TCTTCTCAGGAATAAAACACTGAAGA 58.264 34.615 0.00 0.00 39.26 2.87
1912 2875 8.746052 TTCTCAGGAATAAAACACTGAAGAAA 57.254 30.769 0.00 0.00 39.26 2.52
1913 2876 8.924511 TCTCAGGAATAAAACACTGAAGAAAT 57.075 30.769 0.00 0.00 39.26 2.17
1916 2879 9.231297 TCAGGAATAAAACACTGAAGAAATAGG 57.769 33.333 0.00 0.00 37.06 2.57
1936 2899 5.041191 AGGTAGCACATTAAGCAGCTTAT 57.959 39.130 15.81 2.47 38.47 1.73
1937 2900 5.440610 AGGTAGCACATTAAGCAGCTTATT 58.559 37.500 15.81 9.56 38.47 1.40
1938 2901 6.591935 AGGTAGCACATTAAGCAGCTTATTA 58.408 36.000 15.81 2.26 38.47 0.98
1997 2963 5.959618 AGTAATGTCTTTTGGCACCTAAC 57.040 39.130 0.00 0.00 36.59 2.34
2018 2984 7.921745 CCTAACAGTAATAGGTCTAGCAGTTTC 59.078 40.741 0.00 0.00 36.06 2.78
2080 3048 1.202348 TGGTGTTGCAAATGAACGGTG 60.202 47.619 0.00 0.00 0.00 4.94
2081 3049 1.486439 GTGTTGCAAATGAACGGTGG 58.514 50.000 0.00 0.00 0.00 4.61
2086 3054 0.031994 GCAAATGAACGGTGGCAGTT 59.968 50.000 0.00 0.00 34.07 3.16
2102 3070 5.087391 GGCAGTTATAATAGCCTACCTCC 57.913 47.826 18.65 0.00 43.70 4.30
2103 3071 4.081031 GGCAGTTATAATAGCCTACCTCCC 60.081 50.000 18.65 0.00 43.70 4.30
2104 3072 4.778427 GCAGTTATAATAGCCTACCTCCCT 59.222 45.833 0.00 0.00 0.00 4.20
2105 3073 5.956563 GCAGTTATAATAGCCTACCTCCCTA 59.043 44.000 0.00 0.00 0.00 3.53
2106 3074 6.127394 GCAGTTATAATAGCCTACCTCCCTAC 60.127 46.154 0.00 0.00 0.00 3.18
2107 3075 6.380560 CAGTTATAATAGCCTACCTCCCTACC 59.619 46.154 0.00 0.00 0.00 3.18
2108 3076 2.717701 AATAGCCTACCTCCCTACCC 57.282 55.000 0.00 0.00 0.00 3.69
2109 3077 0.791648 ATAGCCTACCTCCCTACCCC 59.208 60.000 0.00 0.00 0.00 4.95
2110 3078 0.631389 TAGCCTACCTCCCTACCCCA 60.631 60.000 0.00 0.00 0.00 4.96
2111 3079 1.459730 GCCTACCTCCCTACCCCAG 60.460 68.421 0.00 0.00 0.00 4.45
2112 3080 1.459730 CCTACCTCCCTACCCCAGC 60.460 68.421 0.00 0.00 0.00 4.85
2113 3081 1.627019 CTACCTCCCTACCCCAGCT 59.373 63.158 0.00 0.00 0.00 4.24
2201 3169 2.418746 CCGAGCAGTAACAAGTGCCTAT 60.419 50.000 1.69 0.00 40.81 2.57
2210 3178 4.910458 AACAAGTGCCTATTACAGAGGT 57.090 40.909 0.00 0.00 36.37 3.85
2258 3226 1.600916 GACCAAGCGCCAGTCCTTT 60.601 57.895 2.29 0.00 0.00 3.11
2270 3238 3.824133 CCAGTCCTTTGATCATATGGCA 58.176 45.455 2.13 0.00 0.00 4.92
2312 3280 2.522185 AGCCATGCTGACAAGAACATT 58.478 42.857 0.00 0.00 37.57 2.71
2405 3373 4.443266 GCCGAGCGTGAGAGCCTT 62.443 66.667 0.00 0.00 38.01 4.35
2435 3403 2.992114 ACGTCCGCTCTTGAGGCT 60.992 61.111 0.00 0.00 32.90 4.58
2441 3409 0.741221 CCGCTCTTGAGGCTACCAAC 60.741 60.000 0.00 0.00 0.00 3.77
2462 3430 0.620556 TGGAGAAGGCCTTCATGACC 59.379 55.000 39.84 33.04 41.84 4.02
2471 3439 1.218047 CTTCATGACCGGCCTCGAA 59.782 57.895 0.00 0.00 39.00 3.71
2531 3499 2.404995 CGACGAGGCTAACTCCGGT 61.405 63.158 0.00 0.00 43.57 5.28
2638 3606 5.598830 TGTCCTCCTAGATACCATCTTGTTC 59.401 44.000 0.00 0.00 40.76 3.18
2645 3613 3.266772 AGATACCATCTTGTTCCTGGCAA 59.733 43.478 0.00 0.00 35.76 4.52
2670 3638 7.152645 AGTAAAGTTTCTAAGTTGATCTCGCA 58.847 34.615 0.00 0.00 0.00 5.10
2673 3641 4.926238 AGTTTCTAAGTTGATCTCGCAGTG 59.074 41.667 0.00 0.00 0.00 3.66
2802 3770 1.479323 ACGGTGGCGTACAGTTATCAT 59.521 47.619 0.00 0.00 33.79 2.45
2923 3891 2.866156 GCTGCTGCGTATATCTGTCAAA 59.134 45.455 0.00 0.00 0.00 2.69
3016 3987 5.641155 TGCATCCTAGTTGTATAGAGCCTA 58.359 41.667 0.00 0.00 0.00 3.93
3062 4033 3.346315 TCCGCTTGATATGGCATTATGG 58.654 45.455 4.78 0.00 0.00 2.74
3066 4037 4.379813 CGCTTGATATGGCATTATGGGTTC 60.380 45.833 4.78 0.00 0.00 3.62
3146 4117 3.576982 TGTTGGTACTCCGTTCATCTCTT 59.423 43.478 0.00 0.00 36.30 2.85
3176 4147 0.807667 CGTCAGGAGTACAGCATGGC 60.808 60.000 0.00 0.00 43.62 4.40
3201 4172 2.359848 CACAGGTGGCATGAACCATATG 59.640 50.000 17.48 10.87 43.01 1.78
3219 4190 6.259167 ACCATATGATGCATTGTTTGAATTGC 59.741 34.615 3.65 0.00 0.00 3.56
3236 4207 6.862209 TGAATTGCACAGACTAAAAACAACT 58.138 32.000 0.00 0.00 0.00 3.16
3237 4208 6.751425 TGAATTGCACAGACTAAAAACAACTG 59.249 34.615 0.00 0.00 35.14 3.16
3334 4305 7.649533 TGGTTGAGATATAGACGGTTTCTTA 57.350 36.000 0.00 0.00 35.55 2.10
3346 4317 9.880157 ATAGACGGTTTCTTAGCTGTAATTTTA 57.120 29.630 0.00 0.00 35.55 1.52
3395 4366 8.148351 TGACTCCGTTAATTCTAAATCATAGGG 58.852 37.037 0.00 0.00 0.00 3.53
3463 4434 6.102663 TGAAAACAAATTTTGTGTCGGTCAT 58.897 32.000 15.17 0.00 44.59 3.06
3464 4435 6.591834 TGAAAACAAATTTTGTGTCGGTCATT 59.408 30.769 15.17 1.25 44.59 2.57
3600 4571 2.375146 GAAACTTGACTGGTGTGGGTT 58.625 47.619 0.00 0.00 0.00 4.11
3610 4581 3.516512 TGTGGGTTGGGGGTGCAT 61.517 61.111 0.00 0.00 0.00 3.96
3618 4589 3.978193 GGGGGTGCATGGTGGTCA 61.978 66.667 0.00 0.00 0.00 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 5.296151 TCACTTCTGTCCTTCTTCATTGT 57.704 39.130 0.00 0.00 0.00 2.71
20 21 1.949525 TGGAGCAAGCAGTTTCACTTC 59.050 47.619 0.00 0.00 0.00 3.01
32 33 3.989817 GCAACAACCTTTAATGGAGCAAG 59.010 43.478 14.04 2.83 0.00 4.01
39 40 1.713404 CGCACGCAACAACCTTTAATG 59.287 47.619 0.00 0.00 0.00 1.90
48 49 0.882484 TCTTCATCCGCACGCAACAA 60.882 50.000 0.00 0.00 0.00 2.83
131 132 2.350511 TTTGGTGCCTGCTGGTGCTA 62.351 55.000 11.69 0.00 40.48 3.49
137 138 2.341176 GGCTTTTGGTGCCTGCTG 59.659 61.111 0.00 0.00 46.38 4.41
148 149 1.615392 GGACAATGCAGAGTGGCTTTT 59.385 47.619 0.00 0.00 34.04 2.27
182 186 2.240921 TGCATGGCTTCATGGTTACCTA 59.759 45.455 2.07 0.00 46.18 3.08
183 187 1.005805 TGCATGGCTTCATGGTTACCT 59.994 47.619 2.07 0.00 46.18 3.08
191 195 1.111116 CGGGGATTGCATGGCTTCAT 61.111 55.000 0.00 0.00 0.00 2.57
192 196 1.753848 CGGGGATTGCATGGCTTCA 60.754 57.895 0.00 0.00 0.00 3.02
193 197 1.754234 ACGGGGATTGCATGGCTTC 60.754 57.895 0.00 0.00 0.00 3.86
194 198 2.053865 CACGGGGATTGCATGGCTT 61.054 57.895 0.00 0.00 0.00 4.35
195 199 2.440796 CACGGGGATTGCATGGCT 60.441 61.111 0.00 0.00 0.00 4.75
196 200 2.051518 TTCACGGGGATTGCATGGC 61.052 57.895 0.00 0.00 0.00 4.40
197 201 1.809207 GTTCACGGGGATTGCATGG 59.191 57.895 0.00 0.00 0.00 3.66
198 202 1.024046 TCGTTCACGGGGATTGCATG 61.024 55.000 0.00 0.00 40.29 4.06
199 203 0.107214 ATCGTTCACGGGGATTGCAT 60.107 50.000 0.00 0.00 40.29 3.96
204 208 1.686325 CTCCCATCGTTCACGGGGAT 61.686 60.000 14.52 0.00 44.75 3.85
227 231 2.507471 CCATCTCCTACCTCCTGCTTTT 59.493 50.000 0.00 0.00 0.00 2.27
228 232 2.122768 CCATCTCCTACCTCCTGCTTT 58.877 52.381 0.00 0.00 0.00 3.51
268 272 5.291971 ACATTGTTGCCTTCATTCAACTTC 58.708 37.500 6.65 0.00 42.11 3.01
273 277 5.982516 GTGTTAACATTGTTGCCTTCATTCA 59.017 36.000 12.26 0.00 0.00 2.57
281 285 2.389998 CCACGTGTTAACATTGTTGCC 58.610 47.619 15.65 3.21 0.00 4.52
289 293 1.532007 GCGAAATCCCACGTGTTAACA 59.468 47.619 15.65 3.59 0.00 2.41
294 298 2.718747 TTCGGCGAAATCCCACGTGT 62.719 55.000 21.53 0.00 0.00 4.49
328 332 3.537206 GACTCGGCACTTGGGCAGT 62.537 63.158 0.00 0.00 43.60 4.40
449 481 2.092968 TCTCGGGAGAAATTGACCATGG 60.093 50.000 11.19 11.19 39.18 3.66
473 505 1.762419 TTGTCACGCAACGAGTACTC 58.238 50.000 13.18 13.18 31.07 2.59
476 508 1.493772 CCTTTGTCACGCAACGAGTA 58.506 50.000 0.00 0.00 36.72 2.59
479 511 1.153329 ACCCTTTGTCACGCAACGA 60.153 52.632 0.00 0.00 36.72 3.85
480 512 1.010125 CACCCTTTGTCACGCAACG 60.010 57.895 0.00 0.00 36.72 4.10
481 513 0.736053 TTCACCCTTTGTCACGCAAC 59.264 50.000 0.00 0.00 36.72 4.17
484 516 1.949257 CCTTCACCCTTTGTCACGC 59.051 57.895 0.00 0.00 0.00 5.34
485 517 0.817634 TGCCTTCACCCTTTGTCACG 60.818 55.000 0.00 0.00 0.00 4.35
486 518 1.067060 GTTGCCTTCACCCTTTGTCAC 59.933 52.381 0.00 0.00 0.00 3.67
487 519 1.341482 TGTTGCCTTCACCCTTTGTCA 60.341 47.619 0.00 0.00 0.00 3.58
488 520 1.398692 TGTTGCCTTCACCCTTTGTC 58.601 50.000 0.00 0.00 0.00 3.18
489 521 1.480545 GTTGTTGCCTTCACCCTTTGT 59.519 47.619 0.00 0.00 0.00 2.83
490 522 1.480137 TGTTGTTGCCTTCACCCTTTG 59.520 47.619 0.00 0.00 0.00 2.77
491 523 1.859302 TGTTGTTGCCTTCACCCTTT 58.141 45.000 0.00 0.00 0.00 3.11
495 563 3.439129 GGTACTATGTTGTTGCCTTCACC 59.561 47.826 0.00 0.00 0.00 4.02
497 565 4.202419 ACTGGTACTATGTTGTTGCCTTCA 60.202 41.667 0.00 0.00 0.00 3.02
518 1025 9.032624 ACACCAGATGTACTAGTAAAATGTACT 57.967 33.333 3.61 0.00 40.88 2.73
529 1036 2.168521 CCACCCACACCAGATGTACTAG 59.831 54.545 0.00 0.00 40.64 2.57
567 1074 3.782244 GCTGCCAAGACGTGCTCG 61.782 66.667 6.63 6.63 43.34 5.03
602 1109 3.726517 CAGGAAAGCGGGTGTGCG 61.727 66.667 0.00 0.00 40.67 5.34
606 1113 0.804989 GATCAACAGGAAAGCGGGTG 59.195 55.000 0.00 0.00 0.00 4.61
653 1160 9.687210 GTTTGTTTAGTGTTAGAAAATTAGGGG 57.313 33.333 0.00 0.00 0.00 4.79
688 1200 4.440525 GCGATGATGATGAATTGGTTTGGT 60.441 41.667 0.00 0.00 0.00 3.67
689 1201 4.046462 GCGATGATGATGAATTGGTTTGG 58.954 43.478 0.00 0.00 0.00 3.28
692 1204 2.291465 CGGCGATGATGATGAATTGGTT 59.709 45.455 0.00 0.00 0.00 3.67
693 1205 1.875514 CGGCGATGATGATGAATTGGT 59.124 47.619 0.00 0.00 0.00 3.67
694 1206 1.400629 GCGGCGATGATGATGAATTGG 60.401 52.381 12.98 0.00 0.00 3.16
695 1207 1.400629 GGCGGCGATGATGATGAATTG 60.401 52.381 12.98 0.00 0.00 2.32
696 1208 0.877071 GGCGGCGATGATGATGAATT 59.123 50.000 12.98 0.00 0.00 2.17
697 1209 1.293963 CGGCGGCGATGATGATGAAT 61.294 55.000 29.19 0.00 0.00 2.57
698 1210 1.955663 CGGCGGCGATGATGATGAA 60.956 57.895 29.19 0.00 0.00 2.57
805 1318 2.101582 TGCGATTTAGGAGAAGGAGAGC 59.898 50.000 0.00 0.00 0.00 4.09
806 1319 4.367450 CTTGCGATTTAGGAGAAGGAGAG 58.633 47.826 0.00 0.00 0.00 3.20
807 1320 3.430929 GCTTGCGATTTAGGAGAAGGAGA 60.431 47.826 0.00 0.00 0.00 3.71
808 1321 2.869192 GCTTGCGATTTAGGAGAAGGAG 59.131 50.000 0.00 0.00 0.00 3.69
809 1322 2.236146 TGCTTGCGATTTAGGAGAAGGA 59.764 45.455 0.00 0.00 0.00 3.36
852 1365 2.074576 CAGGACTGTCTGTTGCATCAG 58.925 52.381 17.14 17.14 36.85 2.90
889 1402 1.662686 CTGTCCCCTTTCTCCTTCCT 58.337 55.000 0.00 0.00 0.00 3.36
890 1403 0.621082 CCTGTCCCCTTTCTCCTTCC 59.379 60.000 0.00 0.00 0.00 3.46
905 1418 2.203153 ACAGAAAACGGCGCCTGT 60.203 55.556 26.68 20.95 35.28 4.00
946 1489 1.605710 CTGCCTCAACAACCAAGACTG 59.394 52.381 0.00 0.00 0.00 3.51
974 1517 2.134933 CCCCTCTCTCGGCCCTTAC 61.135 68.421 0.00 0.00 0.00 2.34
975 1518 2.282446 CCCCTCTCTCGGCCCTTA 59.718 66.667 0.00 0.00 0.00 2.69
976 1519 4.806339 CCCCCTCTCTCGGCCCTT 62.806 72.222 0.00 0.00 0.00 3.95
981 1524 3.430497 TCCCTCCCCCTCTCTCGG 61.430 72.222 0.00 0.00 0.00 4.63
982 1525 1.725169 ATCTCCCTCCCCCTCTCTCG 61.725 65.000 0.00 0.00 0.00 4.04
990 1541 1.075896 ACGAGACATCTCCCTCCCC 60.076 63.158 3.30 0.00 39.79 4.81
1047 1598 0.254462 TGAGCACCACCTTGAACACA 59.746 50.000 0.00 0.00 0.00 3.72
1238 1789 7.342026 GGGGTTGGATTAGTGATTAGTGAAAAT 59.658 37.037 0.00 0.00 0.00 1.82
1239 1790 6.661805 GGGGTTGGATTAGTGATTAGTGAAAA 59.338 38.462 0.00 0.00 0.00 2.29
1258 1809 1.901464 CAGGGTCGGTTTGGGGTTG 60.901 63.158 0.00 0.00 0.00 3.77
1270 1821 2.962421 AGAAGATACAGCTAGCAGGGTC 59.038 50.000 18.83 11.25 0.00 4.46
1290 1841 4.504916 CGAGGCCAGCACGGAGAG 62.505 72.222 5.01 0.00 36.56 3.20
1292 1843 3.781770 GATCGAGGCCAGCACGGAG 62.782 68.421 5.01 0.00 36.56 4.63
1293 1844 3.838271 GATCGAGGCCAGCACGGA 61.838 66.667 5.01 0.00 36.56 4.69
1295 1846 3.989698 AACGATCGAGGCCAGCACG 62.990 63.158 24.34 10.00 0.00 5.34
1296 1847 1.298859 AAAACGATCGAGGCCAGCAC 61.299 55.000 24.34 0.00 0.00 4.40
1297 1848 0.248012 TAAAACGATCGAGGCCAGCA 59.752 50.000 24.34 0.00 0.00 4.41
1298 1849 1.583054 ATAAAACGATCGAGGCCAGC 58.417 50.000 24.34 0.00 0.00 4.85
1299 1850 4.142687 ACAAAATAAAACGATCGAGGCCAG 60.143 41.667 24.34 0.00 0.00 4.85
1300 1851 3.754323 ACAAAATAAAACGATCGAGGCCA 59.246 39.130 24.34 2.82 0.00 5.36
1325 1876 9.736414 ATGGCCTATATGCATAATATGATTCTC 57.264 33.333 11.13 0.00 33.35 2.87
1328 1897 7.177921 GCCATGGCCTATATGCATAATATGATT 59.822 37.037 27.24 0.00 32.54 2.57
1331 1900 6.263516 GCCATGGCCTATATGCATAATATG 57.736 41.667 27.24 8.80 32.54 1.78
1354 1923 2.782222 GCAGTGCATGGCCATCAGG 61.782 63.158 17.61 6.17 38.23 3.86
1355 1924 2.004808 CTGCAGTGCATGGCCATCAG 62.005 60.000 20.10 15.17 38.13 2.90
1356 1925 2.035940 TGCAGTGCATGGCCATCA 59.964 55.556 17.61 14.27 31.71 3.07
1357 1926 2.805546 CTGCAGTGCATGGCCATC 59.194 61.111 20.10 11.64 38.13 3.51
1358 1927 3.458163 GCTGCAGTGCATGGCCAT 61.458 61.111 20.10 14.09 38.13 4.40
1359 1928 4.978705 TGCTGCAGTGCATGGCCA 62.979 61.111 20.10 8.56 38.13 5.36
1360 1929 4.430765 GTGCTGCAGTGCATGGCC 62.431 66.667 20.10 9.76 45.23 5.36
1361 1930 2.042259 TAGTGCTGCAGTGCATGGC 61.042 57.895 20.10 19.75 45.23 4.40
1362 1931 0.675837 AGTAGTGCTGCAGTGCATGG 60.676 55.000 24.13 9.29 45.23 3.66
1363 1932 1.931841 CTAGTAGTGCTGCAGTGCATG 59.068 52.381 24.13 13.72 45.23 4.06
1367 1936 2.658538 CGCTAGTAGTGCTGCAGTG 58.341 57.895 19.81 4.29 0.00 3.66
1422 1996 8.554528 ACACGACAATCTTCATTCATTCATATC 58.445 33.333 0.00 0.00 0.00 1.63
1423 1997 8.340443 CACACGACAATCTTCATTCATTCATAT 58.660 33.333 0.00 0.00 0.00 1.78
1444 2018 1.210931 CTTGCCTGCATTCCACACG 59.789 57.895 0.00 0.00 0.00 4.49
1471 2053 4.226761 CGCAAAACCAATACAGAGGAAAC 58.773 43.478 0.00 0.00 0.00 2.78
1473 2055 2.227865 GCGCAAAACCAATACAGAGGAA 59.772 45.455 0.30 0.00 0.00 3.36
1474 2056 1.810151 GCGCAAAACCAATACAGAGGA 59.190 47.619 0.30 0.00 0.00 3.71
1475 2057 1.539388 TGCGCAAAACCAATACAGAGG 59.461 47.619 8.16 0.00 0.00 3.69
1478 2060 2.261345 CCATGCGCAAAACCAATACAG 58.739 47.619 17.11 0.00 0.00 2.74
1480 2062 2.258755 GACCATGCGCAAAACCAATAC 58.741 47.619 17.11 0.00 0.00 1.89
1490 2072 2.894257 AAGGACAGGACCATGCGCA 61.894 57.895 14.96 14.96 0.00 6.09
1502 2084 0.836606 TCTTGCACTGACCAAGGACA 59.163 50.000 10.45 0.00 40.00 4.02
1520 2102 4.201851 CGGACAATGACAAATCCATCACTC 60.202 45.833 0.00 0.00 0.00 3.51
1546 2128 6.594788 ATTGCACAGATCAAACAATAAGGT 57.405 33.333 0.00 0.00 0.00 3.50
1547 2129 9.027129 CATAATTGCACAGATCAAACAATAAGG 57.973 33.333 0.00 0.00 31.05 2.69
1574 2168 6.992063 AAGCAGACAGTGTATTAATTCCAG 57.008 37.500 0.00 0.00 0.00 3.86
1656 2424 5.235305 AGCATGTCGATTCCAAACATAAC 57.765 39.130 0.00 0.00 32.54 1.89
1665 2433 3.722147 ACATCTGTAGCATGTCGATTCC 58.278 45.455 0.00 0.00 27.49 3.01
1670 2438 3.865164 TGCTTAACATCTGTAGCATGTCG 59.135 43.478 4.13 0.00 35.43 4.35
1747 2680 8.515414 TGTAAGTGTCCGATCTAGATTATGATG 58.485 37.037 6.70 0.00 0.00 3.07
1756 2689 6.378710 TTCTGATGTAAGTGTCCGATCTAG 57.621 41.667 0.00 0.00 0.00 2.43
1848 2790 3.459232 TGGCAGATTCTAATCTCACCG 57.541 47.619 2.17 0.00 43.65 4.94
1881 2824 8.647796 TCAGTGTTTTATTCCTGAGAAGAGTTA 58.352 33.333 0.00 0.00 34.86 2.24
1890 2853 9.231297 CCTATTTCTTCAGTGTTTTATTCCTGA 57.769 33.333 0.00 0.00 32.38 3.86
1894 2857 9.989869 GCTACCTATTTCTTCAGTGTTTTATTC 57.010 33.333 0.00 0.00 0.00 1.75
1896 2859 8.947115 GTGCTACCTATTTCTTCAGTGTTTTAT 58.053 33.333 0.00 0.00 0.00 1.40
1905 2868 7.109501 TGCTTAATGTGCTACCTATTTCTTCA 58.890 34.615 0.00 0.00 0.00 3.02
1910 2873 5.440610 AGCTGCTTAATGTGCTACCTATTT 58.559 37.500 0.00 0.00 33.64 1.40
1912 2875 4.696479 AGCTGCTTAATGTGCTACCTAT 57.304 40.909 0.00 0.00 33.64 2.57
1913 2876 4.487714 AAGCTGCTTAATGTGCTACCTA 57.512 40.909 14.24 0.00 35.09 3.08
1914 2877 3.356529 AAGCTGCTTAATGTGCTACCT 57.643 42.857 14.24 0.00 35.09 3.08
1915 2878 5.757850 AATAAGCTGCTTAATGTGCTACC 57.242 39.130 24.34 0.00 35.09 3.18
1916 2879 7.224753 TGTCTAATAAGCTGCTTAATGTGCTAC 59.775 37.037 24.34 15.77 35.09 3.58
1936 2899 6.055588 GCTAATGCTGGGACTTATTGTCTAA 58.944 40.000 0.00 0.00 39.73 2.10
1937 2900 5.611374 GCTAATGCTGGGACTTATTGTCTA 58.389 41.667 0.00 0.00 39.73 2.59
1938 2901 4.455606 GCTAATGCTGGGACTTATTGTCT 58.544 43.478 0.00 0.00 39.73 3.41
1957 2920 8.202461 ACATTACTATTAGGTGCCATAAGCTA 57.798 34.615 0.00 0.00 44.23 3.32
1997 2963 7.548097 TGAAGAAACTGCTAGACCTATTACTG 58.452 38.462 0.00 0.00 0.00 2.74
2051 3019 4.022416 TCATTTGCAACACCAATCAGTACC 60.022 41.667 0.00 0.00 0.00 3.34
2080 3048 4.081031 GGGAGGTAGGCTATTATAACTGCC 60.081 50.000 17.95 17.95 39.60 4.85
2081 3049 4.778427 AGGGAGGTAGGCTATTATAACTGC 59.222 45.833 0.00 3.66 0.00 4.40
2086 3054 4.233755 GGGGTAGGGAGGTAGGCTATTATA 59.766 50.000 0.00 0.00 0.00 0.98
2100 3068 1.140134 AAGCAAAGCTGGGGTAGGGA 61.140 55.000 0.00 0.00 39.62 4.20
2102 3070 1.598701 GCAAGCAAAGCTGGGGTAGG 61.599 60.000 0.00 0.00 39.62 3.18
2103 3071 0.610232 AGCAAGCAAAGCTGGGGTAG 60.610 55.000 0.00 0.00 41.61 3.18
2104 3072 0.178964 AAGCAAGCAAAGCTGGGGTA 60.179 50.000 0.00 0.00 42.53 3.69
2105 3073 0.178964 TAAGCAAGCAAAGCTGGGGT 60.179 50.000 0.00 0.00 42.53 4.95
2106 3074 1.188863 ATAAGCAAGCAAAGCTGGGG 58.811 50.000 0.00 0.00 42.53 4.96
2107 3075 2.997986 CAAATAAGCAAGCAAAGCTGGG 59.002 45.455 0.00 0.00 42.53 4.45
2108 3076 3.916761 TCAAATAAGCAAGCAAAGCTGG 58.083 40.909 0.00 0.00 42.53 4.85
2109 3077 5.407387 ACAATCAAATAAGCAAGCAAAGCTG 59.593 36.000 0.00 0.00 42.53 4.24
2110 3078 5.544650 ACAATCAAATAAGCAAGCAAAGCT 58.455 33.333 0.00 0.00 45.97 3.74
2111 3079 5.851047 ACAATCAAATAAGCAAGCAAAGC 57.149 34.783 0.00 0.00 0.00 3.51
2112 3080 7.170320 AGTGAACAATCAAATAAGCAAGCAAAG 59.830 33.333 0.00 0.00 37.30 2.77
2113 3081 6.985645 AGTGAACAATCAAATAAGCAAGCAAA 59.014 30.769 0.00 0.00 37.30 3.68
2201 3169 1.825474 GCTCCTACTGCACCTCTGTAA 59.175 52.381 0.00 0.00 0.00 2.41
2210 3178 2.625314 CACTAGCATAGCTCCTACTGCA 59.375 50.000 0.00 0.00 44.39 4.41
2231 3199 0.657840 GGCGCTTGGTCATGTCATAC 59.342 55.000 7.64 0.00 0.00 2.39
2258 3226 0.534877 GCCACCGTGCCATATGATCA 60.535 55.000 3.65 0.00 0.00 2.92
2270 3238 1.079127 CAATTCCTCGAGCCACCGT 60.079 57.895 6.99 0.00 0.00 4.83
2312 3280 3.118445 TGTTCCCGATGAGCATGATAACA 60.118 43.478 0.00 0.00 0.00 2.41
2366 3334 1.122019 ACTCCTTGGCGTCCTCTGTT 61.122 55.000 0.00 0.00 0.00 3.16
2396 3364 3.584406 TCTCCATGAAGAAAAGGCTCTCA 59.416 43.478 0.00 0.00 0.00 3.27
2405 3373 1.671850 GCGGACGTCTCCATGAAGAAA 60.672 52.381 16.46 0.00 36.12 2.52
2429 3397 0.541063 TCTCCACGTTGGTAGCCTCA 60.541 55.000 0.00 0.00 39.03 3.86
2435 3403 0.834687 AGGCCTTCTCCACGTTGGTA 60.835 55.000 0.00 0.00 39.03 3.25
2441 3409 0.250234 TCATGAAGGCCTTCTCCACG 59.750 55.000 38.38 23.99 40.14 4.94
2462 3430 1.130749 CGGTATATCTCTTCGAGGCCG 59.869 57.143 0.00 0.00 37.07 6.13
2471 3439 1.880675 CTGACGGTGCGGTATATCTCT 59.119 52.381 0.00 0.00 0.00 3.10
2486 3454 3.363178 GACAAGGTTTTTCTTGCTGACG 58.637 45.455 4.71 0.00 45.77 4.35
2531 3499 1.004560 CAGCAAGCTCGAGTTCCCA 60.005 57.895 15.13 0.00 0.00 4.37
2638 3606 6.262273 TCAACTTAGAAACTTTACTTGCCAGG 59.738 38.462 0.00 0.00 0.00 4.45
2645 3613 7.152645 TGCGAGATCAACTTAGAAACTTTACT 58.847 34.615 0.00 0.00 0.00 2.24
2670 3638 0.667487 CCATTCAGCGTGTCGACACT 60.667 55.000 37.63 22.99 44.34 3.55
2673 3641 1.374252 ACCCATTCAGCGTGTCGAC 60.374 57.895 9.11 9.11 0.00 4.20
2816 3784 2.158667 AGGTTGGGCTAATTACATCCCG 60.159 50.000 7.72 0.00 41.65 5.14
2850 3818 0.961753 CAAAGGGGGAAGAACAGCAC 59.038 55.000 0.00 0.00 0.00 4.40
2907 3875 6.859017 TGTAGTTCTTTGACAGATATACGCA 58.141 36.000 0.00 0.00 30.40 5.24
2923 3891 5.707242 TTCTCATGTCGTTCTGTAGTTCT 57.293 39.130 0.00 0.00 0.00 3.01
2991 3959 5.545723 AGGCTCTATACAACTAGGATGCATT 59.454 40.000 0.00 0.00 0.00 3.56
3016 3987 2.038387 AACAAAACGAGCTCACACCT 57.962 45.000 15.40 0.00 0.00 4.00
3027 3998 8.891928 CATATCAAGCGGATATAAAACAAAACG 58.108 33.333 11.89 0.00 45.40 3.60
3062 4033 7.571025 TCTCAATAAGGGGTACTTTATGAACC 58.429 38.462 0.00 0.00 40.64 3.62
3108 4079 4.389374 ACCAACATTGACAGTACTCTTGG 58.611 43.478 0.00 0.00 0.00 3.61
3146 4117 2.233271 ACTCCTGACGAACGGTAAGAA 58.767 47.619 0.00 0.00 0.00 2.52
3176 4147 0.038892 GTTCATGCCACCTGTGCTTG 60.039 55.000 0.00 0.00 35.77 4.01
3219 4190 8.391106 GCTATATCCAGTTGTTTTTAGTCTGTG 58.609 37.037 0.00 0.00 0.00 3.66
3236 4207 9.667107 GCAATACCTAAATAGTTGCTATATCCA 57.333 33.333 0.00 0.00 41.30 3.41
3293 4264 4.536090 TCAACCAAAGGATCCTCATAGTGT 59.464 41.667 16.52 4.19 0.00 3.55
3395 4366 4.217550 TGCGAAAATATAATGGCTTAGGGC 59.782 41.667 0.00 0.00 40.90 5.19
3497 4468 2.124983 CATGGAGTCCACGGCCTG 60.125 66.667 15.86 4.45 35.80 4.85
3517 4488 1.340657 CTCGTTCACAGCTCGCACTC 61.341 60.000 0.00 0.00 0.00 3.51
3546 4517 0.457509 CTTCGACTCTGCAGCGTCAT 60.458 55.000 30.37 6.23 30.65 3.06
3600 4571 3.978193 GACCACCATGCACCCCCA 61.978 66.667 0.00 0.00 0.00 4.96


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

AutoCloner maintained by Alex Coulton.