Multiple sequence alignment - TraesCS5B01G166800

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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 TraesCS5B01G166800 chr5B 100.000 7076 0 0 1 7076 308929723 308922648 0.000000e+00 13068
1 TraesCS5B01G166800 chr5A 91.487 2643 143 33 4496 7076 362417462 362414840 0.000000e+00 3559
2 TraesCS5B01G166800 chr5A 86.063 1844 110 43 1639 3373 362420368 362418563 0.000000e+00 1845
3 TraesCS5B01G166800 chr5A 95.713 1073 37 6 3374 4443 362418528 362417462 0.000000e+00 1718
4 TraesCS5B01G166800 chr5A 86.944 1034 68 33 632 1627 362421430 362420426 0.000000e+00 1099
5 TraesCS5B01G166800 chr5A 89.474 171 12 4 141 311 362421593 362421429 2.000000e-50 211
6 TraesCS5B01G166800 chr5A 84.337 166 18 7 4 164 206730372 206730534 9.500000e-34 156
7 TraesCS5B01G166800 chr5D 88.388 2859 171 58 632 3373 273121087 273118273 0.000000e+00 3291
8 TraesCS5B01G166800 chr5D 92.086 1908 79 23 5197 7057 273116314 273114432 0.000000e+00 2621
9 TraesCS5B01G166800 chr5D 95.168 1573 40 11 3669 5214 273117888 273116325 0.000000e+00 2451
10 TraesCS5B01G166800 chr5D 93.645 299 19 0 3374 3672 273118238 273117940 1.400000e-121 448
11 TraesCS5B01G166800 chr5D 91.279 172 10 3 141 312 273121255 273121089 5.520000e-56 230
12 TraesCS5B01G166800 chr3B 95.399 326 15 0 309 634 245527865 245527540 2.930000e-143 520
13 TraesCS5B01G166800 chr1B 95.062 324 16 0 307 630 425483744 425483421 1.760000e-140 510
14 TraesCS5B01G166800 chr1B 83.529 170 22 5 4 167 637909292 637909461 3.420000e-33 154
15 TraesCS5B01G166800 chr2B 95.031 322 16 0 309 630 551493103 551493424 2.280000e-139 507
16 TraesCS5B01G166800 chr2B 93.114 334 19 4 315 644 373485608 373485275 2.970000e-133 486
17 TraesCS5B01G166800 chr6B 95.016 321 15 1 311 630 703274114 703273794 2.950000e-138 503
18 TraesCS5B01G166800 chr4A 93.958 331 15 4 305 633 110087738 110087411 4.930000e-136 496
19 TraesCS5B01G166800 chr4A 93.939 330 16 3 305 633 110088266 110087940 4.930000e-136 496
20 TraesCS5B01G166800 chr4A 83.237 173 26 2 4 173 581461232 581461060 9.500000e-34 156
21 TraesCS5B01G166800 chr2D 94.118 323 19 0 311 633 21616115 21615793 6.380000e-135 492
22 TraesCS5B01G166800 chr7B 93.865 326 18 2 309 633 435675956 435675632 2.290000e-134 490
23 TraesCS5B01G166800 chr7A 83.146 178 26 4 1 175 641988745 641988921 7.350000e-35 159
24 TraesCS5B01G166800 chr7A 82.840 169 21 8 4 167 138505551 138505716 2.060000e-30 145
25 TraesCS5B01G166800 chr6D 84.242 165 21 4 4 163 276135317 276135481 9.500000e-34 156
26 TraesCS5B01G166800 chr2A 83.626 171 18 9 2 167 764676849 764676684 1.230000e-32 152
27 TraesCS5B01G166800 chr4B 83.636 165 19 7 4 163 517751059 517751220 1.590000e-31 148
28 TraesCS5B01G166800 chr4B 82.286 175 22 9 4 173 532435162 532434992 7.400000e-30 143


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 TraesCS5B01G166800 chr5B 308922648 308929723 7075 True 13068.0 13068 100.0000 1 7076 1 chr5B.!!$R1 7075
1 TraesCS5B01G166800 chr5A 362414840 362421593 6753 True 1686.4 3559 89.9362 141 7076 5 chr5A.!!$R1 6935
2 TraesCS5B01G166800 chr5D 273114432 273121255 6823 True 1808.2 3291 92.1132 141 7057 5 chr5D.!!$R1 6916
3 TraesCS5B01G166800 chr4A 110087411 110088266 855 True 496.0 496 93.9485 305 633 2 chr4A.!!$R2 328

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
399 401 0.396695 AGGTTCGGATAGGGAAGCGA 60.397 55.000 0.00 0.00 44.35 4.93 F
1320 1376 0.036765 GGTGCTGTCATCGTTGGGTA 60.037 55.000 0.00 0.00 0.00 3.69 F
1328 1384 0.177141 CATCGTTGGGTATGGTCGGT 59.823 55.000 0.00 0.00 0.00 4.69 F
2500 2676 0.317938 ACGAGTATGATCGCCTTCGC 60.318 55.000 8.73 0.00 46.60 4.70 F
3018 3276 1.193874 GTGCTTTTTACCGTCGACCAG 59.806 52.381 10.58 4.18 0.00 4.00 F
4725 5128 1.227383 GGCCAGGGATAGTGTTGGG 59.773 63.158 0.00 0.00 0.00 4.12 F
5417 5851 2.634453 TGGAGTTTCTGCTCACTGATGA 59.366 45.455 0.00 0.00 37.24 2.92 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2005 2129 0.693622 TTCTTCCCAACCACGGCATA 59.306 50.000 0.00 0.0 0.00 3.14 R
2592 2778 0.596083 CCACCGCGCAGAAGAGATAG 60.596 60.000 8.75 0.0 0.00 2.08 R
2676 2862 1.202698 ACAGTGCCAGAAACTGACTCC 60.203 52.381 10.35 0.0 46.55 3.85 R
3708 4088 2.498167 AGTAGTTCACCTGCAGCAAAG 58.502 47.619 8.66 0.0 0.00 2.77 R
4981 5385 2.216046 CACATATGGCATCTTCAGCGT 58.784 47.619 1.65 0.0 0.00 5.07 R
5528 5962 0.320771 GTGCCCACTACCACACAGAG 60.321 60.000 0.00 0.0 33.23 3.35 R
6284 6753 1.398390 CCGATGTTTTGCTGCTCCTAC 59.602 52.381 0.00 0.0 0.00 3.18 R

All possible primers

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

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
30 31 9.508721 ACTCCCTCCTTTTCTAAATATAAGTCT 57.491 33.333 0.00 0.00 0.00 3.24
106 107 8.375608 AGATTATGAATTCACTCATTCCTTCG 57.624 34.615 11.07 0.00 37.27 3.79
107 108 7.989741 AGATTATGAATTCACTCATTCCTTCGT 59.010 33.333 11.07 0.00 37.27 3.85
108 109 9.261180 GATTATGAATTCACTCATTCCTTCGTA 57.739 33.333 11.07 0.00 37.27 3.43
109 110 9.784531 ATTATGAATTCACTCATTCCTTCGTAT 57.215 29.630 11.07 0.00 37.27 3.06
110 111 6.908870 TGAATTCACTCATTCCTTCGTATG 57.091 37.500 3.38 0.00 32.86 2.39
111 112 6.406370 TGAATTCACTCATTCCTTCGTATGT 58.594 36.000 3.38 0.00 32.86 2.29
112 113 7.552459 TGAATTCACTCATTCCTTCGTATGTA 58.448 34.615 3.38 0.00 32.86 2.29
113 114 7.706607 TGAATTCACTCATTCCTTCGTATGTAG 59.293 37.037 3.38 0.00 32.86 2.74
114 115 6.525578 TTCACTCATTCCTTCGTATGTAGT 57.474 37.500 0.00 0.00 0.00 2.73
115 116 6.132791 TCACTCATTCCTTCGTATGTAGTC 57.867 41.667 0.00 0.00 0.00 2.59
116 117 5.067413 TCACTCATTCCTTCGTATGTAGTCC 59.933 44.000 0.00 0.00 0.00 3.85
117 118 4.341520 ACTCATTCCTTCGTATGTAGTCCC 59.658 45.833 0.00 0.00 0.00 4.46
118 119 4.543689 TCATTCCTTCGTATGTAGTCCCT 58.456 43.478 0.00 0.00 0.00 4.20
119 120 4.583489 TCATTCCTTCGTATGTAGTCCCTC 59.417 45.833 0.00 0.00 0.00 4.30
120 121 3.657398 TCCTTCGTATGTAGTCCCTCA 57.343 47.619 0.00 0.00 0.00 3.86
121 122 4.180377 TCCTTCGTATGTAGTCCCTCAT 57.820 45.455 0.00 0.00 0.00 2.90
122 123 4.543689 TCCTTCGTATGTAGTCCCTCATT 58.456 43.478 0.00 0.00 0.00 2.57
123 124 4.341235 TCCTTCGTATGTAGTCCCTCATTG 59.659 45.833 0.00 0.00 0.00 2.82
124 125 4.501571 CCTTCGTATGTAGTCCCTCATTGG 60.502 50.000 0.00 0.00 0.00 3.16
125 126 3.905968 TCGTATGTAGTCCCTCATTGGA 58.094 45.455 0.00 0.00 38.35 3.53
126 127 4.283337 TCGTATGTAGTCCCTCATTGGAA 58.717 43.478 0.00 0.00 35.80 3.53
127 128 4.899457 TCGTATGTAGTCCCTCATTGGAAT 59.101 41.667 0.00 0.00 35.80 3.01
128 129 6.072649 TCGTATGTAGTCCCTCATTGGAATA 58.927 40.000 0.00 0.00 35.80 1.75
129 130 6.724441 TCGTATGTAGTCCCTCATTGGAATAT 59.276 38.462 0.00 0.00 37.31 1.28
130 131 7.036220 CGTATGTAGTCCCTCATTGGAATATC 58.964 42.308 0.00 0.00 37.31 1.63
131 132 7.093727 CGTATGTAGTCCCTCATTGGAATATCT 60.094 40.741 0.00 0.00 37.31 1.98
132 133 9.256228 GTATGTAGTCCCTCATTGGAATATCTA 57.744 37.037 0.00 0.00 37.31 1.98
133 134 8.742125 ATGTAGTCCCTCATTGGAATATCTAA 57.258 34.615 0.00 0.00 37.31 2.10
134 135 8.561536 TGTAGTCCCTCATTGGAATATCTAAA 57.438 34.615 0.00 0.00 37.31 1.85
135 136 8.651389 TGTAGTCCCTCATTGGAATATCTAAAG 58.349 37.037 0.00 0.00 37.31 1.85
136 137 7.937700 AGTCCCTCATTGGAATATCTAAAGA 57.062 36.000 0.00 0.00 35.80 2.52
137 138 7.972301 AGTCCCTCATTGGAATATCTAAAGAG 58.028 38.462 2.83 2.83 34.07 2.85
138 139 7.791766 AGTCCCTCATTGGAATATCTAAAGAGA 59.208 37.037 9.37 0.00 35.57 3.10
139 140 7.875554 GTCCCTCATTGGAATATCTAAAGAGAC 59.124 40.741 9.37 0.19 35.57 3.36
178 179 4.412528 AGGGAGTATTATCTTGGTCCCAAC 59.587 45.833 7.92 0.00 45.41 3.77
180 181 5.163088 GGGAGTATTATCTTGGTCCCAACAT 60.163 44.000 0.11 0.00 42.91 2.71
193 195 3.314080 GTCCCAACATTCTTGTGACGAAA 59.686 43.478 0.00 0.00 35.83 3.46
294 296 3.074412 GCAGCTGGTACTAGCAGAAAAA 58.926 45.455 29.93 0.00 45.98 1.94
295 297 3.126000 GCAGCTGGTACTAGCAGAAAAAG 59.874 47.826 29.93 12.90 45.98 2.27
296 298 3.126000 CAGCTGGTACTAGCAGAAAAAGC 59.874 47.826 29.93 3.72 45.98 3.51
297 299 3.074412 GCTGGTACTAGCAGAAAAAGCA 58.926 45.455 24.73 0.00 45.98 3.91
299 301 3.408634 TGGTACTAGCAGAAAAAGCACC 58.591 45.455 0.00 0.00 0.00 5.01
300 302 3.181449 TGGTACTAGCAGAAAAAGCACCA 60.181 43.478 0.00 0.00 33.55 4.17
301 303 4.010349 GGTACTAGCAGAAAAAGCACCAT 58.990 43.478 0.00 0.00 0.00 3.55
303 305 3.084786 ACTAGCAGAAAAAGCACCATCC 58.915 45.455 0.00 0.00 0.00 3.51
372 374 4.033009 TGCCATGTAGGATCGGATATGAT 58.967 43.478 0.00 0.00 41.22 2.45
373 375 4.141869 TGCCATGTAGGATCGGATATGATG 60.142 45.833 0.00 0.00 41.22 3.07
399 401 0.396695 AGGTTCGGATAGGGAAGCGA 60.397 55.000 0.00 0.00 44.35 4.93
408 410 2.279935 TAGGGAAGCGAGATCCTCTC 57.720 55.000 0.00 0.00 40.06 3.20
430 432 1.743252 GAGGCGGGTGCTTGAAGAG 60.743 63.158 0.00 0.00 42.25 2.85
466 468 3.447742 GGTGACAAAAGCTGAAAAGGTG 58.552 45.455 0.00 0.00 0.00 4.00
468 470 3.130340 GTGACAAAAGCTGAAAAGGTGGA 59.870 43.478 0.00 0.00 0.00 4.02
469 471 3.381272 TGACAAAAGCTGAAAAGGTGGAG 59.619 43.478 0.00 0.00 0.00 3.86
470 472 3.365472 ACAAAAGCTGAAAAGGTGGAGT 58.635 40.909 0.00 0.00 0.00 3.85
471 473 3.131046 ACAAAAGCTGAAAAGGTGGAGTG 59.869 43.478 0.00 0.00 0.00 3.51
485 487 3.515901 GGTGGAGTGGAAAGTAGAGATGT 59.484 47.826 0.00 0.00 0.00 3.06
550 552 4.823442 CACTAATGATAGCTTGCATTGGGA 59.177 41.667 20.61 6.05 37.31 4.37
551 553 5.300034 CACTAATGATAGCTTGCATTGGGAA 59.700 40.000 20.61 5.79 37.31 3.97
552 554 5.893255 ACTAATGATAGCTTGCATTGGGAAA 59.107 36.000 20.61 5.53 37.31 3.13
555 557 5.680594 TGATAGCTTGCATTGGGAAAAAT 57.319 34.783 0.00 0.00 0.00 1.82
588 590 9.942850 ATGTAAATCCCTCAAATTACTTTTTGG 57.057 29.630 0.00 0.00 37.23 3.28
630 632 1.675720 GCCACCATTGTACATGCCCC 61.676 60.000 0.00 0.00 0.00 5.80
657 659 1.369692 CCCGTGGCAGTAACAGTGA 59.630 57.895 0.00 0.00 0.00 3.41
673 675 3.891366 ACAGTGATTACCAGCAGCTTTTT 59.109 39.130 0.00 0.00 0.00 1.94
674 676 5.070001 ACAGTGATTACCAGCAGCTTTTTA 58.930 37.500 0.00 0.00 0.00 1.52
675 677 5.048713 ACAGTGATTACCAGCAGCTTTTTAC 60.049 40.000 0.00 0.00 0.00 2.01
676 678 5.048782 CAGTGATTACCAGCAGCTTTTTACA 60.049 40.000 0.00 0.00 0.00 2.41
677 679 5.182001 AGTGATTACCAGCAGCTTTTTACAG 59.818 40.000 0.00 0.00 0.00 2.74
681 683 6.458232 TTACCAGCAGCTTTTTACAGAAAA 57.542 33.333 0.00 0.00 32.61 2.29
682 684 4.936891 ACCAGCAGCTTTTTACAGAAAAG 58.063 39.130 0.00 6.84 39.55 2.27
692 698 4.394439 TTTACAGAAAAGCACCAAACCC 57.606 40.909 0.00 0.00 0.00 4.11
703 709 2.616765 GCACCAAACCCAAACCAAGTTT 60.617 45.455 0.00 0.00 36.05 2.66
748 755 5.893512 AAACGAAAATAAAACGGGCTTTC 57.106 34.783 0.00 0.00 0.00 2.62
763 770 1.443802 CTTTCGCTGTCCCTTTCCTC 58.556 55.000 0.00 0.00 0.00 3.71
788 798 0.686441 TAAGCAGCGCCTTCCTCCTA 60.686 55.000 2.29 0.00 0.00 2.94
789 799 2.202946 GCAGCGCCTTCCTCCTAC 60.203 66.667 2.29 0.00 0.00 3.18
790 800 2.726351 GCAGCGCCTTCCTCCTACT 61.726 63.158 2.29 0.00 0.00 2.57
887 905 3.795041 CTGGCAGGGGGAGCTGAG 61.795 72.222 6.61 0.00 0.00 3.35
912 930 6.064846 TCAAAATGCAAACAAGACTCTCTC 57.935 37.500 0.00 0.00 0.00 3.20
916 934 4.250116 TGCAAACAAGACTCTCTCTCTC 57.750 45.455 0.00 0.00 0.00 3.20
917 935 3.894427 TGCAAACAAGACTCTCTCTCTCT 59.106 43.478 0.00 0.00 0.00 3.10
962 980 2.043450 ACCTCTCCTCCAGCTCCG 60.043 66.667 0.00 0.00 0.00 4.63
989 1010 1.394151 CAAGTCTCCCCCTCCTCCT 59.606 63.158 0.00 0.00 0.00 3.69
1041 1074 1.363744 CCATCAAGCAGTTCTCCGTC 58.636 55.000 0.00 0.00 0.00 4.79
1117 1150 4.021916 AGAAGGGAATGGAATGAAAGCAG 58.978 43.478 0.00 0.00 0.00 4.24
1118 1151 2.743553 AGGGAATGGAATGAAAGCAGG 58.256 47.619 0.00 0.00 0.00 4.85
1151 1184 1.781786 TCTTCTCTGCCGGCTATTCT 58.218 50.000 29.70 0.00 0.00 2.40
1181 1216 0.610232 ATGCGCCCTTGCTTTCTTCT 60.610 50.000 4.18 0.00 35.36 2.85
1241 1276 4.521062 GTGCCGATCTGCTCCGCT 62.521 66.667 10.62 0.00 0.00 5.52
1315 1371 2.020720 TGTTTTGGTGCTGTCATCGTT 58.979 42.857 0.00 0.00 0.00 3.85
1318 1374 0.888736 TTGGTGCTGTCATCGTTGGG 60.889 55.000 0.00 0.00 0.00 4.12
1319 1375 1.302511 GGTGCTGTCATCGTTGGGT 60.303 57.895 0.00 0.00 0.00 4.51
1320 1376 0.036765 GGTGCTGTCATCGTTGGGTA 60.037 55.000 0.00 0.00 0.00 3.69
1321 1377 1.406887 GGTGCTGTCATCGTTGGGTAT 60.407 52.381 0.00 0.00 0.00 2.73
1322 1378 1.665679 GTGCTGTCATCGTTGGGTATG 59.334 52.381 0.00 0.00 0.00 2.39
1323 1379 1.299541 GCTGTCATCGTTGGGTATGG 58.700 55.000 0.00 0.00 0.00 2.74
1324 1380 1.406887 GCTGTCATCGTTGGGTATGGT 60.407 52.381 0.00 0.00 0.00 3.55
1325 1381 2.550978 CTGTCATCGTTGGGTATGGTC 58.449 52.381 0.00 0.00 0.00 4.02
1326 1382 1.134936 TGTCATCGTTGGGTATGGTCG 60.135 52.381 0.00 0.00 0.00 4.79
1327 1383 0.462375 TCATCGTTGGGTATGGTCGG 59.538 55.000 0.00 0.00 0.00 4.79
1328 1384 0.177141 CATCGTTGGGTATGGTCGGT 59.823 55.000 0.00 0.00 0.00 4.69
1378 1434 1.937223 CTGTTGTCGTGTGCTGGTTTA 59.063 47.619 0.00 0.00 0.00 2.01
1389 1445 3.568007 TGTGCTGGTTTACATTTCTGGTC 59.432 43.478 0.00 0.00 0.00 4.02
1390 1446 3.821033 GTGCTGGTTTACATTTCTGGTCT 59.179 43.478 0.00 0.00 0.00 3.85
1391 1447 4.278419 GTGCTGGTTTACATTTCTGGTCTT 59.722 41.667 0.00 0.00 0.00 3.01
1392 1448 4.518970 TGCTGGTTTACATTTCTGGTCTTC 59.481 41.667 0.00 0.00 0.00 2.87
1463 1524 4.537433 GCCCTACCTCGCTGGCTG 62.537 72.222 0.00 0.00 40.77 4.85
1465 1526 4.537433 CCTACCTCGCTGGCTGCC 62.537 72.222 12.87 12.87 40.22 4.85
1494 1555 4.098349 TGATAATGTTTGGATCTTGCAGGC 59.902 41.667 0.00 0.00 0.00 4.85
1544 1605 4.159120 GTTTCGATTAGCCTTGTTCTTGC 58.841 43.478 0.00 0.00 0.00 4.01
1545 1606 3.334583 TCGATTAGCCTTGTTCTTGCT 57.665 42.857 0.00 0.00 39.10 3.91
1551 1612 3.443099 AGCCTTGTTCTTGCTTCAAAC 57.557 42.857 0.00 0.00 29.17 2.93
1553 1614 4.207165 AGCCTTGTTCTTGCTTCAAACTA 58.793 39.130 0.00 0.00 29.17 2.24
1572 1633 8.830580 TCAAACTATGATCAAATCCGAGATTTC 58.169 33.333 0.00 1.29 31.50 2.17
1578 1639 5.945784 TGATCAAATCCGAGATTTCCTTTGT 59.054 36.000 8.38 0.00 0.00 2.83
1603 1665 4.707105 TGTGACTTTCTCTTGCTCATTCA 58.293 39.130 0.00 0.00 0.00 2.57
1606 1668 6.936335 TGTGACTTTCTCTTGCTCATTCATTA 59.064 34.615 0.00 0.00 0.00 1.90
1608 1670 6.372659 TGACTTTCTCTTGCTCATTCATTACC 59.627 38.462 0.00 0.00 0.00 2.85
1696 1813 8.633075 TCTTTTACTTTGTGATTTTGAGCTTG 57.367 30.769 0.00 0.00 0.00 4.01
1709 1826 7.333921 TGATTTTGAGCTTGATTGTTGTTTTGT 59.666 29.630 0.00 0.00 0.00 2.83
1710 1827 8.715191 ATTTTGAGCTTGATTGTTGTTTTGTA 57.285 26.923 0.00 0.00 0.00 2.41
1711 1828 7.518731 TTTGAGCTTGATTGTTGTTTTGTAC 57.481 32.000 0.00 0.00 0.00 2.90
1745 1862 7.642669 TCTTGCTTCAAAGTCTCTTGTTATTG 58.357 34.615 0.00 0.00 0.00 1.90
1747 1864 7.333528 TGCTTCAAAGTCTCTTGTTATTGTT 57.666 32.000 0.00 0.00 0.00 2.83
1769 1887 6.488683 TGTTACTTTGGTGTTCTTAGGAATGG 59.511 38.462 0.00 0.00 33.71 3.16
1775 1893 2.755103 GTGTTCTTAGGAATGGCCCTTG 59.245 50.000 0.00 0.00 37.74 3.61
1811 1929 1.577468 TACAGCTGACGTTTGTGTGG 58.423 50.000 23.35 0.00 0.00 4.17
1813 1931 1.153168 AGCTGACGTTTGTGTGGCT 60.153 52.632 0.00 0.00 0.00 4.75
1938 2062 2.103094 TCTCATTAGATGTTGGAGGCGG 59.897 50.000 0.00 0.00 0.00 6.13
1957 2081 3.181516 GCGGTAGCACTTTCTTTGATCTG 60.182 47.826 0.00 0.00 44.35 2.90
1979 2103 6.826741 TCTGAAAAAGCACTAGTACTTTGGTT 59.173 34.615 19.52 12.18 36.28 3.67
2001 2125 3.697166 AGGTCCTAATTGCAATTTCGGT 58.303 40.909 28.45 7.88 0.00 4.69
2005 2129 5.124936 GGTCCTAATTGCAATTTCGGTACTT 59.875 40.000 28.45 5.70 0.00 2.24
2034 2159 4.517075 GTGGTTGGGAAGAAGAAGAAGAAG 59.483 45.833 0.00 0.00 0.00 2.85
2035 2160 4.412199 TGGTTGGGAAGAAGAAGAAGAAGA 59.588 41.667 0.00 0.00 0.00 2.87
2037 2162 5.471797 GGTTGGGAAGAAGAAGAAGAAGAAG 59.528 44.000 0.00 0.00 0.00 2.85
2043 2168 7.387673 GGGAAGAAGAAGAAGAAGAAGAAGAAG 59.612 40.741 0.00 0.00 0.00 2.85
2044 2169 8.147704 GGAAGAAGAAGAAGAAGAAGAAGAAGA 58.852 37.037 0.00 0.00 0.00 2.87
2073 2200 2.151202 ACAACTTTGGTACATCAGCCG 58.849 47.619 0.00 0.00 39.30 5.52
2111 2238 3.039202 GCGCCTCCCATGTTCGTTG 62.039 63.158 0.00 0.00 0.00 4.10
2199 2340 1.354040 CAAGCACGCTTCTAGAGTGG 58.646 55.000 11.37 0.00 44.58 4.00
2200 2341 1.067565 CAAGCACGCTTCTAGAGTGGA 60.068 52.381 11.37 0.00 44.58 4.02
2201 2342 0.528470 AGCACGCTTCTAGAGTGGAC 59.472 55.000 11.37 0.00 44.58 4.02
2203 2344 1.734047 GCACGCTTCTAGAGTGGACAG 60.734 57.143 11.37 0.00 44.58 3.51
2211 2352 1.205893 CTAGAGTGGACAGGACCTTGC 59.794 57.143 0.00 0.00 0.00 4.01
2212 2353 1.374758 GAGTGGACAGGACCTTGCG 60.375 63.158 0.00 0.00 0.00 4.85
2322 2476 1.152881 CTTGGGCCACCTATCCAGC 60.153 63.158 5.23 0.00 37.76 4.85
2362 2516 2.522638 CGCGAGTTAATGGCCGGAC 61.523 63.158 5.05 0.56 0.00 4.79
2406 2560 1.976045 CGCACCTTGTTTTTATGTCGC 59.024 47.619 0.00 0.00 0.00 5.19
2438 2606 0.631753 AGGGGAGAGGTCTGAATCGA 59.368 55.000 0.00 0.00 0.00 3.59
2473 2649 2.050350 TCGGTCCATGACGAGTCCC 61.050 63.158 0.00 0.00 34.67 4.46
2500 2676 0.317938 ACGAGTATGATCGCCTTCGC 60.318 55.000 8.73 0.00 46.60 4.70
2569 2755 6.970414 CGCAATTCGACATCTCCACTGAGA 62.970 50.000 0.00 0.00 45.80 3.27
2592 2778 8.534333 AGAAAACAACAGTTCCTTTTCTTTTC 57.466 30.769 16.35 7.55 39.02 2.29
2627 2813 3.052745 CGGTGGAATCACGATATCAGTG 58.947 50.000 16.62 16.62 44.50 3.66
2656 2842 9.575783 GCCTTTTTCATGATTTTTATACCGTAA 57.424 29.630 0.00 0.00 0.00 3.18
2676 2862 1.218875 TACAGTGTTGCGTTGCCGAG 61.219 55.000 0.00 0.00 35.63 4.63
2677 2863 2.972505 AGTGTTGCGTTGCCGAGG 60.973 61.111 0.00 0.00 35.63 4.63
2681 2867 2.357034 TTGCGTTGCCGAGGAGTC 60.357 61.111 0.00 0.00 35.63 3.36
2707 2893 3.141398 TCTGGCACTGTTGTTTGAGATC 58.859 45.455 0.00 0.00 0.00 2.75
2731 2917 3.329277 ACTTCTTGGTAGGGGGTAACAA 58.671 45.455 0.00 0.00 35.86 2.83
2732 2918 3.723154 ACTTCTTGGTAGGGGGTAACAAA 59.277 43.478 0.00 0.00 37.89 2.83
2733 2919 4.355889 ACTTCTTGGTAGGGGGTAACAAAT 59.644 41.667 0.00 0.00 37.89 2.32
2904 3162 4.297299 ACTGTTGATGAAGCAACTTGTG 57.703 40.909 12.19 3.75 46.31 3.33
2990 3248 4.391216 CAGAATGAGATTGACAGCGTTCTT 59.609 41.667 0.00 0.00 39.69 2.52
3002 3260 1.566018 GCGTTCTTGCCGTAAGTGCT 61.566 55.000 0.00 0.00 37.65 4.40
3016 3274 1.505425 AGTGCTTTTTACCGTCGACC 58.495 50.000 10.58 0.00 0.00 4.79
3018 3276 1.193874 GTGCTTTTTACCGTCGACCAG 59.806 52.381 10.58 4.18 0.00 4.00
3071 3355 1.366319 ATTCCTCTGACCAGCAACCT 58.634 50.000 0.00 0.00 0.00 3.50
3188 3472 3.117888 CAGGTACAATAATCAGGCCCAGT 60.118 47.826 0.00 0.00 0.00 4.00
3189 3473 3.527665 AGGTACAATAATCAGGCCCAGTT 59.472 43.478 0.00 0.00 0.00 3.16
3192 3476 4.806640 ACAATAATCAGGCCCAGTTTTG 57.193 40.909 0.00 0.00 0.00 2.44
3197 3481 1.981256 TCAGGCCCAGTTTTGTCTTC 58.019 50.000 0.00 0.00 0.00 2.87
3214 3498 7.481275 TTGTCTTCAAATTTCCATGCTTTTC 57.519 32.000 0.00 0.00 0.00 2.29
3217 3501 8.366401 TGTCTTCAAATTTCCATGCTTTTCATA 58.634 29.630 0.00 0.00 33.19 2.15
3256 3540 3.507233 TCCTGCTGATTCATTTGTTGGAC 59.493 43.478 0.00 0.00 0.00 4.02
3259 3543 3.567585 TGCTGATTCATTTGTTGGACGAA 59.432 39.130 0.00 0.00 0.00 3.85
3266 3550 3.066064 TCATTTGTTGGACGAACTGGTTG 59.934 43.478 1.90 0.00 35.37 3.77
3268 3552 1.658994 TGTTGGACGAACTGGTTGTC 58.341 50.000 4.41 4.41 35.37 3.18
3388 3708 6.530019 TTCCATTTCCTTGCTCTAATTTCC 57.470 37.500 0.00 0.00 0.00 3.13
3470 3790 1.623811 ACAGAGCATCGGTAGGTGTTT 59.376 47.619 0.00 0.00 43.20 2.83
3472 3792 3.259876 ACAGAGCATCGGTAGGTGTTTAA 59.740 43.478 0.00 0.00 43.20 1.52
3473 3793 3.617263 CAGAGCATCGGTAGGTGTTTAAC 59.383 47.826 0.00 0.00 42.67 2.01
3622 3943 4.732285 TTTTTCTTGAGACGCATGACTC 57.268 40.909 0.00 2.43 37.40 3.36
4031 4411 7.172361 GGATAACTTCTGAAGGATATGAACTGC 59.828 40.741 20.61 6.68 0.00 4.40
4033 4413 5.181748 ACTTCTGAAGGATATGAACTGCAC 58.818 41.667 20.61 0.00 0.00 4.57
4042 4422 5.245751 AGGATATGAACTGCACTCTCCATAG 59.754 44.000 0.00 0.00 0.00 2.23
4149 4529 8.881743 CATCAAGCTATCTGAAATAATAGGAGC 58.118 37.037 0.00 0.00 0.00 4.70
4269 4649 4.520492 ACATTAGGCCTCTTGTTTCTGTTG 59.480 41.667 9.68 0.00 0.00 3.33
4344 4724 7.286508 CAAACTGCATAATTACTGAGATAGCG 58.713 38.462 0.00 0.00 0.00 4.26
4524 4906 4.722220 TGGGCCTGATAAAATCTCTCATG 58.278 43.478 4.53 0.00 0.00 3.07
4725 5128 1.227383 GGCCAGGGATAGTGTTGGG 59.773 63.158 0.00 0.00 0.00 4.12
4870 5274 5.050490 ACACAGCCTTATAAGTTATGAGCG 58.950 41.667 11.50 4.61 0.00 5.03
4981 5385 8.568794 CAACCTTAGTACTGATCGAGATTCATA 58.431 37.037 5.39 0.00 0.00 2.15
5020 5424 4.535781 TGTGCATGCCAGAACCTAAATAT 58.464 39.130 16.68 0.00 0.00 1.28
5169 5574 3.658757 TTGCCTTCCAAGTGCATTTAC 57.341 42.857 0.00 0.00 34.04 2.01
5417 5851 2.634453 TGGAGTTTCTGCTCACTGATGA 59.366 45.455 0.00 0.00 37.24 2.92
5558 5994 2.356665 AGTGGGCACAACATTACACA 57.643 45.000 0.00 0.00 0.00 3.72
5579 6015 7.448420 ACACACCCATCTTATATTCTCTGATG 58.552 38.462 0.00 0.00 35.59 3.07
5601 6037 5.361427 TGGAACAGAACACACTTTCGATTA 58.639 37.500 0.00 0.00 0.00 1.75
5625 6061 4.857037 GTGCAAAATCGAATAAACTGACCC 59.143 41.667 0.00 0.00 0.00 4.46
5626 6062 4.082463 TGCAAAATCGAATAAACTGACCCC 60.082 41.667 0.00 0.00 0.00 4.95
5731 6187 3.058016 ACACATTGGCGAGTTTCTGATTG 60.058 43.478 0.00 0.00 0.00 2.67
5829 6287 3.254014 TTCGGGTTCGTCGTCGGAC 62.254 63.158 4.81 4.81 44.07 4.79
5859 6317 1.307097 GCTACTCGTACGACCATCCT 58.693 55.000 15.28 0.00 0.00 3.24
6078 6536 2.031870 ACGATCGAAGGTCCATGATGA 58.968 47.619 24.34 0.00 0.00 2.92
6099 6557 3.535561 ACCTTGTTTCCTGCTCATATCG 58.464 45.455 0.00 0.00 0.00 2.92
6115 6573 6.458888 GCTCATATCGAAGATCGTCATGGATA 60.459 42.308 9.37 8.00 45.12 2.59
6137 6595 2.301009 TGATCCATGATGATCGGAGTGG 59.699 50.000 0.00 1.73 43.34 4.00
6239 6702 0.680921 ATTGTAACCGCTGGCTGCAT 60.681 50.000 16.76 4.55 43.06 3.96
6252 6715 0.955178 GCTGCATAGCTCGAGTAGGA 59.045 55.000 15.13 2.17 46.57 2.94
6253 6716 1.543802 GCTGCATAGCTCGAGTAGGAT 59.456 52.381 15.13 0.00 46.57 3.24
6254 6717 2.415357 GCTGCATAGCTCGAGTAGGATC 60.415 54.545 15.13 0.00 46.57 3.36
6255 6718 2.816672 CTGCATAGCTCGAGTAGGATCA 59.183 50.000 15.13 4.96 0.00 2.92
6256 6719 3.425659 TGCATAGCTCGAGTAGGATCAT 58.574 45.455 15.13 0.00 0.00 2.45
6284 6753 8.530311 TCATATCGGTAGAGGAAGTAGTAGTAG 58.470 40.741 0.00 0.00 0.00 2.57
6288 6757 6.266558 TCGGTAGAGGAAGTAGTAGTAGTAGG 59.733 46.154 0.00 0.00 0.00 3.18
6291 6760 6.178607 AGAGGAAGTAGTAGTAGTAGGAGC 57.821 45.833 0.00 0.00 0.00 4.70
6294 6763 4.516321 GGAAGTAGTAGTAGTAGGAGCAGC 59.484 50.000 0.00 0.00 0.00 5.25
6350 6823 4.322804 CGTGTTGTCGAAGATGGTAGTAAC 59.677 45.833 0.00 0.00 40.67 2.50
6354 6827 5.496133 TGTCGAAGATGGTAGTAACTAGC 57.504 43.478 0.00 0.00 40.67 3.42
6356 6829 5.296283 TGTCGAAGATGGTAGTAACTAGCTC 59.704 44.000 0.00 0.00 40.67 4.09
6379 6852 4.728772 TGATTAACCTGGCTAATGGATGG 58.271 43.478 7.07 0.00 0.00 3.51
6380 6853 4.415179 TGATTAACCTGGCTAATGGATGGA 59.585 41.667 7.07 0.00 0.00 3.41
6381 6854 5.074929 TGATTAACCTGGCTAATGGATGGAT 59.925 40.000 7.07 0.00 0.00 3.41
6382 6855 2.965671 ACCTGGCTAATGGATGGATG 57.034 50.000 0.00 0.00 0.00 3.51
6433 6910 1.949525 CTCATGGCAGGGAAATTACCG 59.050 52.381 0.00 0.00 0.00 4.02
6456 6933 2.104859 CCCAGACATGAGCAGCACG 61.105 63.158 0.00 0.00 0.00 5.34
6480 6957 8.458052 ACGAGCTCTATGTATCTTATCAATCAG 58.542 37.037 12.85 0.00 0.00 2.90
6481 6958 8.458052 CGAGCTCTATGTATCTTATCAATCAGT 58.542 37.037 12.85 0.00 0.00 3.41
6515 6993 9.635520 GTATATGTATGTATATGTAATCGCCCC 57.364 37.037 0.00 0.00 0.00 5.80
6571 7055 2.828877 TGTTACCTGAACCACGACTTG 58.171 47.619 0.00 0.00 37.22 3.16
6582 7067 5.236478 TGAACCACGACTTGAAAGAAATCTC 59.764 40.000 0.00 0.00 0.00 2.75
6584 7069 3.437049 CCACGACTTGAAAGAAATCTCCC 59.563 47.826 0.00 0.00 0.00 4.30
6587 7072 4.021719 ACGACTTGAAAGAAATCTCCCGTA 60.022 41.667 0.00 0.00 0.00 4.02
6977 7478 1.290955 CCGTGGAAACGTCAGGCTA 59.709 57.895 0.00 0.00 0.00 3.93
7034 7536 7.819900 TGTTCTAACAGAAAGAAAGAGATAGGC 59.180 37.037 0.00 0.00 35.75 3.93
7062 7564 4.079615 ACTGTGGATGGATGGATGATTGAA 60.080 41.667 0.00 0.00 0.00 2.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 9.508721 AGACTTATATTTAGAAAAGGAGGGAGT 57.491 33.333 0.00 0.00 0.00 3.85
80 81 9.481340 CGAAGGAATGAGTGAATTCATAATCTA 57.519 33.333 12.12 3.01 38.14 1.98
81 82 7.989741 ACGAAGGAATGAGTGAATTCATAATCT 59.010 33.333 12.12 3.56 38.14 2.40
82 83 8.147642 ACGAAGGAATGAGTGAATTCATAATC 57.852 34.615 12.12 10.78 38.14 1.75
83 84 9.784531 ATACGAAGGAATGAGTGAATTCATAAT 57.215 29.630 12.12 3.20 38.14 1.28
84 85 9.045223 CATACGAAGGAATGAGTGAATTCATAA 57.955 33.333 12.12 0.73 38.14 1.90
85 86 8.204160 ACATACGAAGGAATGAGTGAATTCATA 58.796 33.333 12.12 1.99 38.14 2.15
86 87 7.050377 ACATACGAAGGAATGAGTGAATTCAT 58.950 34.615 12.12 0.66 38.14 2.57
87 88 6.406370 ACATACGAAGGAATGAGTGAATTCA 58.594 36.000 3.38 3.38 38.14 2.57
88 89 6.910536 ACATACGAAGGAATGAGTGAATTC 57.089 37.500 0.00 0.00 36.08 2.17
89 90 7.556844 ACTACATACGAAGGAATGAGTGAATT 58.443 34.615 0.00 0.00 0.00 2.17
90 91 7.113658 ACTACATACGAAGGAATGAGTGAAT 57.886 36.000 0.00 0.00 0.00 2.57
91 92 6.405508 GGACTACATACGAAGGAATGAGTGAA 60.406 42.308 0.00 0.00 0.00 3.18
92 93 5.067413 GGACTACATACGAAGGAATGAGTGA 59.933 44.000 0.00 0.00 0.00 3.41
93 94 5.282510 GGACTACATACGAAGGAATGAGTG 58.717 45.833 0.00 0.00 0.00 3.51
94 95 4.341520 GGGACTACATACGAAGGAATGAGT 59.658 45.833 0.00 0.00 0.00 3.41
95 96 4.585162 AGGGACTACATACGAAGGAATGAG 59.415 45.833 0.00 0.00 36.02 2.90
96 97 4.543689 AGGGACTACATACGAAGGAATGA 58.456 43.478 0.00 0.00 36.02 2.57
97 98 4.341235 TGAGGGACTACATACGAAGGAATG 59.659 45.833 0.00 0.00 41.55 2.67
98 99 4.543689 TGAGGGACTACATACGAAGGAAT 58.456 43.478 0.00 0.00 41.55 3.01
99 100 3.972133 TGAGGGACTACATACGAAGGAA 58.028 45.455 0.00 0.00 41.55 3.36
100 101 3.657398 TGAGGGACTACATACGAAGGA 57.343 47.619 0.00 0.00 41.55 3.36
101 102 4.501571 CCAATGAGGGACTACATACGAAGG 60.502 50.000 0.00 0.00 41.55 3.46
102 103 4.341235 TCCAATGAGGGACTACATACGAAG 59.659 45.833 0.00 0.00 41.55 3.79
103 104 4.283337 TCCAATGAGGGACTACATACGAA 58.717 43.478 0.00 0.00 41.55 3.85
104 105 3.905968 TCCAATGAGGGACTACATACGA 58.094 45.455 0.00 0.00 41.55 3.43
105 106 4.665833 TTCCAATGAGGGACTACATACG 57.334 45.455 0.00 0.00 41.55 3.06
106 107 8.140112 AGATATTCCAATGAGGGACTACATAC 57.860 38.462 0.00 0.00 41.55 2.39
107 108 9.837681 TTAGATATTCCAATGAGGGACTACATA 57.162 33.333 0.00 0.00 41.55 2.29
108 109 8.742125 TTAGATATTCCAATGAGGGACTACAT 57.258 34.615 0.00 0.00 41.55 2.29
109 110 8.561536 TTTAGATATTCCAATGAGGGACTACA 57.438 34.615 0.00 0.00 41.55 2.74
110 111 8.871125 TCTTTAGATATTCCAATGAGGGACTAC 58.129 37.037 0.00 0.00 41.55 2.73
111 112 9.094578 CTCTTTAGATATTCCAATGAGGGACTA 57.905 37.037 0.00 0.00 41.55 2.59
113 114 7.875554 GTCTCTTTAGATATTCCAATGAGGGAC 59.124 40.741 0.00 0.00 33.20 4.46
114 115 7.791766 AGTCTCTTTAGATATTCCAATGAGGGA 59.208 37.037 0.00 0.00 33.96 4.20
115 116 7.972301 AGTCTCTTTAGATATTCCAATGAGGG 58.028 38.462 0.00 0.00 33.96 4.30
129 130 9.857656 TCCGGTCTTAAATATAGTCTCTTTAGA 57.142 33.333 0.00 0.00 0.00 2.10
131 132 9.075678 CCTCCGGTCTTAAATATAGTCTCTTTA 57.924 37.037 0.00 0.00 0.00 1.85
132 133 7.015389 CCCTCCGGTCTTAAATATAGTCTCTTT 59.985 40.741 0.00 0.00 0.00 2.52
133 134 6.494146 CCCTCCGGTCTTAAATATAGTCTCTT 59.506 42.308 0.00 0.00 0.00 2.85
134 135 6.011481 CCCTCCGGTCTTAAATATAGTCTCT 58.989 44.000 0.00 0.00 0.00 3.10
135 136 6.008960 TCCCTCCGGTCTTAAATATAGTCTC 58.991 44.000 0.00 0.00 0.00 3.36
136 137 5.961897 TCCCTCCGGTCTTAAATATAGTCT 58.038 41.667 0.00 0.00 0.00 3.24
137 138 5.774184 ACTCCCTCCGGTCTTAAATATAGTC 59.226 44.000 0.00 0.00 0.00 2.59
138 139 5.713807 ACTCCCTCCGGTCTTAAATATAGT 58.286 41.667 0.00 0.00 0.00 2.12
139 140 7.957992 ATACTCCCTCCGGTCTTAAATATAG 57.042 40.000 0.00 0.00 0.00 1.31
148 149 4.153411 CAAGATAATACTCCCTCCGGTCT 58.847 47.826 0.00 0.00 0.00 3.85
151 152 3.240302 ACCAAGATAATACTCCCTCCGG 58.760 50.000 0.00 0.00 0.00 5.14
152 153 3.258622 GGACCAAGATAATACTCCCTCCG 59.741 52.174 0.00 0.00 0.00 4.63
163 164 5.476599 CACAAGAATGTTGGGACCAAGATAA 59.523 40.000 13.34 0.00 38.69 1.75
164 165 5.009631 CACAAGAATGTTGGGACCAAGATA 58.990 41.667 13.34 0.38 38.69 1.98
165 166 3.828451 CACAAGAATGTTGGGACCAAGAT 59.172 43.478 7.82 7.82 40.88 2.40
166 167 3.117701 TCACAAGAATGTTGGGACCAAGA 60.118 43.478 3.57 3.39 37.82 3.02
178 179 4.766007 CACACTCTTTCGTCACAAGAATG 58.234 43.478 0.00 0.00 34.39 2.67
180 181 2.607635 GCACACTCTTTCGTCACAAGAA 59.392 45.455 0.00 0.00 29.74 2.52
193 195 1.963338 GCCGAAAGCTGCACACTCT 60.963 57.895 1.02 0.00 38.99 3.24
299 301 9.121161 GCATTGTACATGCCCTTACTTAGGATG 62.121 44.444 15.31 4.48 44.43 3.51
300 302 7.191933 GCATTGTACATGCCCTTACTTAGGAT 61.192 42.308 15.31 0.00 44.43 3.24
301 303 5.918567 GCATTGTACATGCCCTTACTTAGGA 60.919 44.000 15.31 0.00 44.43 2.94
303 305 4.881273 TGCATTGTACATGCCCTTACTTAG 59.119 41.667 20.37 0.00 43.94 2.18
372 374 4.870636 TCCCTATCCGAACCTACTTTACA 58.129 43.478 0.00 0.00 0.00 2.41
373 375 5.738495 GCTTCCCTATCCGAACCTACTTTAC 60.738 48.000 0.00 0.00 0.00 2.01
430 432 1.332686 GTCACCGGACCACACTTTTTC 59.667 52.381 9.46 0.00 38.12 2.29
466 468 6.127310 ACACATACATCTCTACTTTCCACTCC 60.127 42.308 0.00 0.00 0.00 3.85
468 470 6.859112 ACACATACATCTCTACTTTCCACT 57.141 37.500 0.00 0.00 0.00 4.00
469 471 7.773149 AGTACACATACATCTCTACTTTCCAC 58.227 38.462 0.00 0.00 33.30 4.02
470 472 7.956328 AGTACACATACATCTCTACTTTCCA 57.044 36.000 0.00 0.00 33.30 3.53
471 473 9.339850 TCTAGTACACATACATCTCTACTTTCC 57.660 37.037 0.00 0.00 33.30 3.13
515 517 6.003950 GCTATCATTAGTGGGGCTCATTAAA 58.996 40.000 6.41 0.00 32.53 1.52
524 526 3.213206 TGCAAGCTATCATTAGTGGGG 57.787 47.619 0.00 0.00 0.00 4.96
533 535 5.680594 ATTTTTCCCAATGCAAGCTATCA 57.319 34.783 0.00 0.00 0.00 2.15
568 570 6.408869 CATGCCAAAAAGTAATTTGAGGGAT 58.591 36.000 7.50 7.50 41.73 3.85
570 572 4.937015 CCATGCCAAAAAGTAATTTGAGGG 59.063 41.667 8.22 3.39 41.73 4.30
588 590 2.512692 TGGATACATATGCCCCATGC 57.487 50.000 1.58 0.00 46.17 4.06
630 632 4.308458 TGCCACGGGGTCTCGTTG 62.308 66.667 5.12 0.00 41.86 4.10
657 659 6.648879 TTTCTGTAAAAAGCTGCTGGTAAT 57.351 33.333 1.35 0.00 0.00 1.89
673 675 3.019799 TGGGTTTGGTGCTTTTCTGTA 57.980 42.857 0.00 0.00 0.00 2.74
674 676 1.859302 TGGGTTTGGTGCTTTTCTGT 58.141 45.000 0.00 0.00 0.00 3.41
675 677 2.935849 GTTTGGGTTTGGTGCTTTTCTG 59.064 45.455 0.00 0.00 0.00 3.02
676 678 2.093181 GGTTTGGGTTTGGTGCTTTTCT 60.093 45.455 0.00 0.00 0.00 2.52
677 679 2.285083 GGTTTGGGTTTGGTGCTTTTC 58.715 47.619 0.00 0.00 0.00 2.29
681 683 0.829990 CTTGGTTTGGGTTTGGTGCT 59.170 50.000 0.00 0.00 0.00 4.40
682 684 0.539518 ACTTGGTTTGGGTTTGGTGC 59.460 50.000 0.00 0.00 0.00 5.01
683 685 3.342377 AAACTTGGTTTGGGTTTGGTG 57.658 42.857 0.00 0.00 34.23 4.17
692 698 4.594123 ATTCGGGGTTAAACTTGGTTTG 57.406 40.909 5.99 0.00 36.37 2.93
703 709 4.892433 TCTCGTTTGTTTATTCGGGGTTA 58.108 39.130 0.00 0.00 0.00 2.85
748 755 0.391793 GAAGGAGGAAAGGGACAGCG 60.392 60.000 0.00 0.00 0.00 5.18
763 770 0.729690 GAAGGCGCTGCTTAAGAAGG 59.270 55.000 12.62 3.84 0.00 3.46
788 798 4.026357 GGTGAGGGGGAGGGGAGT 62.026 72.222 0.00 0.00 0.00 3.85
789 799 4.825679 GGGTGAGGGGGAGGGGAG 62.826 77.778 0.00 0.00 0.00 4.30
885 903 4.614946 AGTCTTGTTTGCATTTTGAGCTC 58.385 39.130 6.82 6.82 0.00 4.09
886 904 4.340381 AGAGTCTTGTTTGCATTTTGAGCT 59.660 37.500 0.00 0.00 0.00 4.09
887 905 4.614946 AGAGTCTTGTTTGCATTTTGAGC 58.385 39.130 0.00 0.00 0.00 4.26
888 906 6.017275 AGAGAGAGTCTTGTTTGCATTTTGAG 60.017 38.462 0.00 0.00 27.07 3.02
889 907 5.824624 AGAGAGAGTCTTGTTTGCATTTTGA 59.175 36.000 0.00 0.00 27.07 2.69
895 913 3.894427 AGAGAGAGAGAGTCTTGTTTGCA 59.106 43.478 0.00 0.00 34.71 4.08
912 930 1.756538 GGGGAGAAAGCAGAGAGAGAG 59.243 57.143 0.00 0.00 0.00 3.20
916 934 0.610687 AACGGGGAGAAAGCAGAGAG 59.389 55.000 0.00 0.00 0.00 3.20
917 935 1.056660 AAACGGGGAGAAAGCAGAGA 58.943 50.000 0.00 0.00 0.00 3.10
962 980 4.475135 GGAGACTTGCGGGGCTCC 62.475 72.222 13.73 13.73 40.04 4.70
1041 1074 1.521010 CTCACGCTGCTCCATGAGG 60.521 63.158 0.00 0.00 35.87 3.86
1125 1158 1.078143 CGGCAGAGAAGAAAGGGGG 60.078 63.158 0.00 0.00 0.00 5.40
1140 1173 2.352960 CTCAGAAACAAGAATAGCCGGC 59.647 50.000 21.89 21.89 0.00 6.13
1151 1184 0.036732 AGGGCGCATCTCAGAAACAA 59.963 50.000 10.83 0.00 0.00 2.83
1315 1371 2.680707 TGCGACCGACCATACCCA 60.681 61.111 0.00 0.00 0.00 4.51
1318 1374 1.878522 CAGCTGCGACCGACCATAC 60.879 63.158 0.00 0.00 0.00 2.39
1319 1375 1.600511 TTCAGCTGCGACCGACCATA 61.601 55.000 9.47 0.00 0.00 2.74
1320 1376 2.244117 ATTCAGCTGCGACCGACCAT 62.244 55.000 9.47 0.00 0.00 3.55
1321 1377 2.449031 AATTCAGCTGCGACCGACCA 62.449 55.000 9.47 0.00 0.00 4.02
1322 1378 1.741770 AATTCAGCTGCGACCGACC 60.742 57.895 9.47 0.00 0.00 4.79
1323 1379 1.421485 CAATTCAGCTGCGACCGAC 59.579 57.895 9.47 0.00 0.00 4.79
1324 1380 2.390599 GCAATTCAGCTGCGACCGA 61.391 57.895 9.47 0.00 0.00 4.69
1325 1381 2.099062 GCAATTCAGCTGCGACCG 59.901 61.111 9.47 0.00 0.00 4.79
1378 1434 3.500343 CCCCAAAGAAGACCAGAAATGT 58.500 45.455 0.00 0.00 0.00 2.71
1401 1457 5.060940 CGAGCAAAATAAAAGGCTTAGCAAC 59.939 40.000 6.53 0.00 36.59 4.17
1463 1524 5.767168 AGATCCAAACATTATCAAGCTAGGC 59.233 40.000 0.00 0.00 0.00 3.93
1465 1526 7.137426 GCAAGATCCAAACATTATCAAGCTAG 58.863 38.462 0.00 0.00 0.00 3.42
1494 1555 1.676006 GAGCTCGGGAGAAGAAGAGAG 59.324 57.143 0.00 0.00 39.18 3.20
1544 1605 7.776933 TCTCGGATTTGATCATAGTTTGAAG 57.223 36.000 0.00 0.00 38.03 3.02
1545 1606 8.737168 AATCTCGGATTTGATCATAGTTTGAA 57.263 30.769 0.00 0.00 38.03 2.69
1551 1612 7.976135 AAGGAAATCTCGGATTTGATCATAG 57.024 36.000 14.15 0.00 0.00 2.23
1553 1614 6.604795 ACAAAGGAAATCTCGGATTTGATCAT 59.395 34.615 14.15 0.00 33.14 2.45
1578 1639 4.341366 TGAGCAAGAGAAAGTCACATGA 57.659 40.909 0.00 0.00 0.00 3.07
1634 1742 3.197766 TCATCTGCTAACAAGTAGTGGGG 59.802 47.826 0.00 0.00 31.78 4.96
1709 1826 8.150945 AGACTTTGAAGCAAGAAACAGATAGTA 58.849 33.333 0.00 0.00 0.00 1.82
1710 1827 6.995091 AGACTTTGAAGCAAGAAACAGATAGT 59.005 34.615 0.00 0.00 0.00 2.12
1711 1828 7.387397 AGAGACTTTGAAGCAAGAAACAGATAG 59.613 37.037 0.00 0.00 0.00 2.08
1745 1862 6.569801 GCCATTCCTAAGAACACCAAAGTAAC 60.570 42.308 0.00 0.00 33.97 2.50
1747 1864 5.007682 GCCATTCCTAAGAACACCAAAGTA 58.992 41.667 0.00 0.00 33.97 2.24
1752 1869 1.005450 GGGCCATTCCTAAGAACACCA 59.995 52.381 4.39 0.00 33.97 4.17
1775 1893 3.310035 TATGGGTGGGGGCAAAGGC 62.310 63.158 0.00 0.00 40.13 4.35
1781 1899 3.420482 AGCTGTATGGGTGGGGGC 61.420 66.667 0.00 0.00 0.00 5.80
1938 2062 7.114106 GCTTTTTCAGATCAAAGAAAGTGCTAC 59.886 37.037 7.29 0.00 35.41 3.58
1957 2081 7.228108 ACCTAACCAAAGTACTAGTGCTTTTTC 59.772 37.037 29.45 3.02 41.58 2.29
1979 2103 4.850680 ACCGAAATTGCAATTAGGACCTA 58.149 39.130 34.49 0.00 33.34 3.08
2001 2125 1.277579 TCCCAACCACGGCATAAGTA 58.722 50.000 0.00 0.00 0.00 2.24
2005 2129 0.693622 TTCTTCCCAACCACGGCATA 59.306 50.000 0.00 0.00 0.00 3.14
2053 2180 2.151202 CGGCTGATGTACCAAAGTTGT 58.849 47.619 0.00 0.00 0.00 3.32
2073 2200 2.292916 GCGCCGACAAAACAGTTGC 61.293 57.895 0.00 0.00 0.00 4.17
2211 2352 2.434884 ATGGCGTGCTTGACCTCG 60.435 61.111 0.00 0.00 0.00 4.63
2212 2353 1.364626 CTCATGGCGTGCTTGACCTC 61.365 60.000 0.65 0.00 0.00 3.85
2289 2443 4.017126 GGCCCAAGTTCAGCTTAGTTTAT 58.983 43.478 0.00 0.00 35.27 1.40
2322 2476 2.433838 CTGAGCTCCACACGCTGG 60.434 66.667 12.15 0.00 42.29 4.85
2338 2492 1.878522 CCATTAACTCGCGCTCGCT 60.879 57.895 5.56 0.00 39.32 4.93
2362 2516 1.531149 AGATCAAACGACGGCAACTTG 59.469 47.619 0.00 0.00 0.00 3.16
2406 2560 2.763448 CTCTCCCCTAGAACAGTCAAGG 59.237 54.545 0.00 0.00 32.46 3.61
2438 2606 4.569719 ACCGAGTAAAGGTCCAAATCAT 57.430 40.909 0.00 0.00 37.44 2.45
2473 2649 2.603412 GCGATCATACTCGTCAGGACAG 60.603 54.545 0.00 0.00 40.73 3.51
2533 2719 2.412455 CGAATTGCGATCCATCATCAGC 60.412 50.000 0.00 0.00 44.57 4.26
2556 2742 6.512415 GAACTGTTGTTTTCTCAGTGGAGATG 60.512 42.308 0.00 0.00 42.06 2.90
2558 2744 4.876107 GAACTGTTGTTTTCTCAGTGGAGA 59.124 41.667 0.00 0.00 41.41 3.71
2592 2778 0.596083 CCACCGCGCAGAAGAGATAG 60.596 60.000 8.75 0.00 0.00 2.08
2627 2813 6.019075 GGTATAAAAATCATGAAAAAGGCGCC 60.019 38.462 21.89 21.89 0.00 6.53
2676 2862 1.202698 ACAGTGCCAGAAACTGACTCC 60.203 52.381 10.35 0.00 46.55 3.85
2677 2863 2.246719 ACAGTGCCAGAAACTGACTC 57.753 50.000 10.35 0.00 46.55 3.36
2707 2893 2.971901 ACCCCCTACCAAGAAGTTTG 57.028 50.000 0.00 0.00 0.00 2.93
2867 3057 9.529325 TCATCAACAGTACATTGTACTATAAGC 57.471 33.333 25.06 0.34 0.00 3.09
2948 3206 4.012374 TCTGAAGCCTCCAATTTAAGCAG 58.988 43.478 0.00 0.00 0.00 4.24
2954 3212 4.927049 TCTCATTCTGAAGCCTCCAATTT 58.073 39.130 0.00 0.00 0.00 1.82
2990 3248 1.532007 CGGTAAAAAGCACTTACGGCA 59.468 47.619 0.00 0.00 31.26 5.69
3002 3260 1.688197 AGTCCTGGTCGACGGTAAAAA 59.312 47.619 9.92 0.00 37.85 1.94
3018 3276 9.513727 GCTAAAACAATAGTAGTACTACAGTCC 57.486 37.037 29.87 7.49 38.48 3.85
3071 3355 6.071672 TGGTTTCTGCATCGAAATAAAATGGA 60.072 34.615 4.62 0.00 35.56 3.41
3188 3472 7.862512 AAAGCATGGAAATTTGAAGACAAAA 57.137 28.000 0.00 0.00 46.77 2.44
3192 3476 7.662604 ATGAAAAGCATGGAAATTTGAAGAC 57.337 32.000 0.00 0.00 35.42 3.01
3197 3481 8.034215 TGGTACTATGAAAAGCATGGAAATTTG 58.966 33.333 0.00 0.00 37.65 2.32
3256 3540 3.479505 TGTTTGTTGACAACCAGTTCG 57.520 42.857 15.59 0.00 35.28 3.95
3259 3543 6.772716 AGATCTAATGTTTGTTGACAACCAGT 59.227 34.615 15.59 8.28 31.88 4.00
3470 3790 7.972832 ATGAATTCCAAGACAGTTAACGTTA 57.027 32.000 3.29 3.29 0.00 3.18
3472 3792 7.159372 ACTATGAATTCCAAGACAGTTAACGT 58.841 34.615 2.27 1.35 0.00 3.99
3473 3793 7.545965 AGACTATGAATTCCAAGACAGTTAACG 59.454 37.037 2.27 0.00 0.00 3.18
3520 3840 8.361139 CAGAACTAGTGGTATAATCCCTTACAG 58.639 40.741 0.00 0.00 0.00 2.74
3708 4088 2.498167 AGTAGTTCACCTGCAGCAAAG 58.502 47.619 8.66 0.00 0.00 2.77
4023 4403 3.110705 ACCTATGGAGAGTGCAGTTCAT 58.889 45.455 0.00 3.57 0.00 2.57
4031 4411 3.942829 TGCAAGAAACCTATGGAGAGTG 58.057 45.455 0.00 0.00 0.00 3.51
4033 4413 4.815308 CAGATGCAAGAAACCTATGGAGAG 59.185 45.833 0.00 0.00 0.00 3.20
4149 4529 5.023533 TCGTGATTCTATTTCCCCTTCAG 57.976 43.478 0.00 0.00 0.00 3.02
4524 4906 3.006247 GACTTGATGGAGGAACAGAAGC 58.994 50.000 0.00 0.00 0.00 3.86
4725 5128 6.018994 CACCTGACGAACAATAATTAGGTAGC 60.019 42.308 0.00 0.00 35.66 3.58
4767 5170 8.339714 TCGTGTTCGAGAAAGAAAAACAATATT 58.660 29.630 0.00 0.00 41.35 1.28
4865 5269 4.751098 ACGTCCTATGTTTTAAAACGCTCA 59.249 37.500 22.57 8.66 41.74 4.26
4870 5274 6.074195 GGCCAAAACGTCCTATGTTTTAAAAC 60.074 38.462 21.66 21.66 43.26 2.43
4981 5385 2.216046 CACATATGGCATCTTCAGCGT 58.784 47.619 1.65 0.00 0.00 5.07
5020 5424 8.159447 CAGGTAATTTCCATCCTAGATTCATGA 58.841 37.037 3.73 0.00 0.00 3.07
5417 5851 0.846693 AAGAGGCTTCACAACCTGGT 59.153 50.000 0.00 0.00 36.05 4.00
5472 5906 2.995746 TCATCTCTTCCAGGGCCATAT 58.004 47.619 6.18 0.00 0.00 1.78
5528 5962 0.320771 GTGCCCACTACCACACAGAG 60.321 60.000 0.00 0.00 33.23 3.35
5534 5968 1.616159 AATGTTGTGCCCACTACCAC 58.384 50.000 9.78 0.00 36.47 4.16
5579 6015 4.813296 AATCGAAAGTGTGTTCTGTTCC 57.187 40.909 0.00 0.00 0.00 3.62
5583 6019 4.211164 TGCACTAATCGAAAGTGTGTTCTG 59.789 41.667 24.11 5.97 45.01 3.02
5597 6033 9.000018 GTCAGTTTATTCGATTTTGCACTAATC 58.000 33.333 9.64 9.64 0.00 1.75
5601 6037 5.335661 GGGTCAGTTTATTCGATTTTGCACT 60.336 40.000 0.00 0.00 0.00 4.40
5625 6061 3.058224 GCCAGTTGTTAGCACTACTTTGG 60.058 47.826 0.00 0.00 36.93 3.28
5626 6062 3.815401 AGCCAGTTGTTAGCACTACTTTG 59.185 43.478 0.00 0.00 36.93 2.77
5731 6187 3.128764 GGCCAGCAAATACAGTAGGTTTC 59.871 47.826 0.00 0.00 0.00 2.78
5829 6287 0.443088 ACGAGTAGCAGTCGACTTCG 59.557 55.000 26.62 26.62 43.33 3.79
5859 6317 1.429930 TGTACAGCTCCTGGTGGAAA 58.570 50.000 0.00 0.00 45.14 3.13
6023 6481 3.508840 GGGAAATGCCGTCGCCTG 61.509 66.667 0.00 0.00 37.63 4.85
6078 6536 3.197766 TCGATATGAGCAGGAAACAAGGT 59.802 43.478 0.00 0.00 0.00 3.50
6080 6538 5.111989 TCTTCGATATGAGCAGGAAACAAG 58.888 41.667 0.00 0.00 0.00 3.16
6083 6541 4.384247 CGATCTTCGATATGAGCAGGAAAC 59.616 45.833 0.00 0.00 43.74 2.78
6115 6573 3.055312 CCACTCCGATCATCATGGATCAT 60.055 47.826 11.15 0.00 43.07 2.45
6164 6622 7.823745 ATTTCCTGGCGTCAAATAAGATAAT 57.176 32.000 0.00 0.00 0.00 1.28
6239 6702 7.600752 CGATATGATATGATCCTACTCGAGCTA 59.399 40.741 13.61 3.50 0.00 3.32
6252 6715 9.567776 CTACTTCCTCTACCGATATGATATGAT 57.432 37.037 0.00 0.00 0.00 2.45
6253 6716 8.549731 ACTACTTCCTCTACCGATATGATATGA 58.450 37.037 0.00 0.00 0.00 2.15
6254 6717 8.740123 ACTACTTCCTCTACCGATATGATATG 57.260 38.462 0.00 0.00 0.00 1.78
6256 6719 9.044646 ACTACTACTTCCTCTACCGATATGATA 57.955 37.037 0.00 0.00 0.00 2.15
6284 6753 1.398390 CCGATGTTTTGCTGCTCCTAC 59.602 52.381 0.00 0.00 0.00 3.18
6288 6757 2.421424 AGAATCCGATGTTTTGCTGCTC 59.579 45.455 0.00 0.00 0.00 4.26
6291 6760 6.912591 GGTTATTAGAATCCGATGTTTTGCTG 59.087 38.462 0.00 0.00 0.00 4.41
6294 6763 7.241663 TCGGTTATTAGAATCCGATGTTTTG 57.758 36.000 0.97 0.00 45.49 2.44
6350 6823 5.537300 TTAGCCAGGTTAATCAGAGCTAG 57.463 43.478 0.00 0.00 33.31 3.42
6354 6827 5.296151 TCCATTAGCCAGGTTAATCAGAG 57.704 43.478 5.58 0.00 0.00 3.35
6356 6829 4.763793 CCATCCATTAGCCAGGTTAATCAG 59.236 45.833 5.58 1.68 0.00 2.90
6382 6855 1.461897 ACAGTAACGCGCAAATGGTAC 59.538 47.619 5.73 3.91 0.00 3.34
6515 6993 5.125356 TGATATACCAGTTGCAACATCAGG 58.875 41.667 30.11 25.02 0.00 3.86
6571 7055 6.737254 TGAAACATACGGGAGATTTCTTTC 57.263 37.500 0.00 0.00 31.86 2.62
6582 7067 3.500982 CATGCAAGTTGAAACATACGGG 58.499 45.455 7.16 0.00 0.00 5.28
6584 7069 3.361644 GTGCATGCAAGTTGAAACATACG 59.638 43.478 24.58 0.00 0.00 3.06
6587 7072 3.068448 TCAGTGCATGCAAGTTGAAACAT 59.932 39.130 24.58 0.00 0.00 2.71
6713 7198 2.030027 TGGAAGGTGACACAGGAGAT 57.970 50.000 8.08 0.00 0.00 2.75
6777 7277 3.120060 CCGCTTCTGGTGAAAGAAAGATG 60.120 47.826 0.00 0.00 35.79 2.90
6977 7478 5.707298 CCACAGAAAAATATCACTCCTGTGT 59.293 40.000 15.51 0.00 44.84 3.72
7024 7526 3.767673 TCCACAGTTAACGCCTATCTCTT 59.232 43.478 0.00 0.00 0.00 2.85
7034 7536 3.260475 TCCATCCATCCACAGTTAACG 57.740 47.619 0.00 0.00 0.00 3.18


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

AutoCloner maintained by Alex Coulton.