Multiple sequence alignment - TraesCS7A01G276300

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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 TraesCS7A01G276300 chr7A 100.000 5946 0 0 1 5946 288923055 288929000 0.000000e+00 10981.0
1 TraesCS7A01G276300 chr7A 91.803 61 5 0 2687 2747 148483614 148483674 1.060000e-12 86.1
2 TraesCS7A01G276300 chr7D 88.945 2379 121 67 614 2907 264747384 264749705 0.000000e+00 2806.0
3 TraesCS7A01G276300 chr7D 94.143 1400 58 11 3249 4627 264750233 264751629 0.000000e+00 2109.0
4 TraesCS7A01G276300 chr7D 93.647 787 31 7 5168 5946 264752408 264753183 0.000000e+00 1158.0
5 TraesCS7A01G276300 chr7D 94.581 406 19 1 4637 5039 264751679 264752084 5.060000e-175 625.0
6 TraesCS7A01G276300 chr7D 97.898 333 3 2 2908 3239 264749804 264750133 1.860000e-159 573.0
7 TraesCS7A01G276300 chr7D 77.187 583 26 47 1 548 264746061 264746571 2.140000e-59 241.0
8 TraesCS7A01G276300 chr7D 80.597 134 11 5 2629 2747 147003347 147003480 8.210000e-14 89.8
9 TraesCS7A01G276300 chr7B 92.000 1325 50 26 1341 2632 245066528 245067829 0.000000e+00 1808.0
10 TraesCS7A01G276300 chr7B 90.670 1179 61 13 3202 4334 245068372 245069547 0.000000e+00 1522.0
11 TraesCS7A01G276300 chr7B 83.460 1318 57 54 1 1265 245065207 245066416 0.000000e+00 1077.0
12 TraesCS7A01G276300 chr7B 89.467 788 39 9 5168 5946 245070636 245071388 0.000000e+00 955.0
13 TraesCS7A01G276300 chr7B 90.654 642 29 11 4423 5039 245069607 245070242 0.000000e+00 824.0
14 TraesCS7A01G276300 chr7B 94.444 288 15 1 2912 3199 245067925 245068211 5.470000e-120 442.0
15 TraesCS7A01G276300 chr7B 91.803 61 5 0 2687 2747 109928555 109928615 1.060000e-12 86.1
16 TraesCS7A01G276300 chr5B 86.881 404 31 15 5562 5946 532876655 532877055 3.290000e-117 433.0
17 TraesCS7A01G276300 chr5B 90.189 265 26 0 5682 5946 638336803 638336539 4.410000e-91 346.0
18 TraesCS7A01G276300 chr5A 90.881 318 23 3 5635 5946 553420967 553421284 7.120000e-114 422.0
19 TraesCS7A01G276300 chr5A 93.333 60 4 0 2687 2746 548672441 548672500 8.210000e-14 89.8
20 TraesCS7A01G276300 chr1D 90.596 319 22 5 5635 5946 472561000 472561317 3.310000e-112 416.0
21 TraesCS7A01G276300 chr5D 90.645 310 23 3 5643 5946 438360064 438360373 2.000000e-109 407.0
22 TraesCS7A01G276300 chr5D 86.834 319 34 4 5635 5946 507835816 507835499 3.410000e-92 350.0
23 TraesCS7A01G276300 chr1A 89.969 319 24 5 5635 5946 566564257 566564574 7.180000e-109 405.0
24 TraesCS7A01G276300 chr1B 89.655 319 25 5 5635 5946 657272149 657272466 3.340000e-107 399.0
25 TraesCS7A01G276300 chr4B 78.322 286 39 7 2629 2893 404515312 404515595 4.770000e-36 163.0
26 TraesCS7A01G276300 chr2A 94.203 69 4 0 2679 2747 71343032 71343100 8.150000e-19 106.0
27 TraesCS7A01G276300 chr2A 91.803 61 5 0 2687 2747 227833324 227833384 1.060000e-12 86.1
28 TraesCS7A01G276300 chr6B 81.416 113 18 3 2734 2845 101701514 101701404 8.210000e-14 89.8
29 TraesCS7A01G276300 chr2B 91.803 61 5 0 2687 2747 379102349 379102409 1.060000e-12 86.1
30 TraesCS7A01G276300 chr3D 85.294 68 6 2 2804 2867 310713451 310713384 3.850000e-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 TraesCS7A01G276300 chr7A 288923055 288929000 5945 False 10981.000000 10981 100.000000 1 5946 1 chr7A.!!$F2 5945
1 TraesCS7A01G276300 chr7D 264746061 264753183 7122 False 1252.000000 2806 91.066833 1 5946 6 chr7D.!!$F2 5945
2 TraesCS7A01G276300 chr7B 245065207 245071388 6181 False 1104.666667 1808 90.115833 1 5946 6 chr7B.!!$F2 5945

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
359 399 0.101759 GTTACTATCTCACGGCCGCA 59.898 55.0 28.58 11.76 0.00 5.69 F
1337 2197 0.029167 TGCATGTTTCGTGTGTGCTG 59.971 50.0 0.00 0.00 36.78 4.41 F
2293 3240 0.467384 CATACCCTGAGGCTGTCCTG 59.533 60.0 0.00 0.00 44.46 3.86 F
3080 4143 0.039764 ACTCCAGTCAGGACGGATCA 59.960 55.0 11.48 0.00 43.07 2.92 F
3926 5277 0.322008 GTTGCAGCCTGCCTCTAACT 60.322 55.0 15.29 0.00 44.23 2.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1854 2776 0.884514 GAACAGCTTTCCCTTCCTGC 59.115 55.0 0.00 0.00 0.00 4.85 R
2535 3482 0.115152 TCTGCTTCAGAGGTCCTCCA 59.885 55.0 15.72 5.02 35.39 3.86 R
3819 5170 0.320421 CCGGAACCCACGCATATAGG 60.320 60.0 0.00 0.00 0.00 2.57 R
4641 6024 0.107456 ACAGGATGGCGATGATGACC 59.893 55.0 0.00 0.00 43.62 4.02 R
5105 6796 0.468226 ACTTCACCAGAAACCGAGCA 59.532 50.0 0.00 0.00 32.35 4.26 R

All possible primers

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

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
23 24 0.826715 TCCTGGGAGATTCTTGCTCG 59.173 55.000 0.00 0.00 33.19 5.03
49 50 4.737855 TGTCCTTGCCTCTTGTATCTAC 57.262 45.455 0.00 0.00 0.00 2.59
50 51 4.353777 TGTCCTTGCCTCTTGTATCTACT 58.646 43.478 0.00 0.00 0.00 2.57
51 52 4.402793 TGTCCTTGCCTCTTGTATCTACTC 59.597 45.833 0.00 0.00 0.00 2.59
159 187 3.258228 GAGCAGCTCAAGGAAAGTCTAC 58.742 50.000 18.17 0.00 0.00 2.59
161 189 1.996191 CAGCTCAAGGAAAGTCTACGC 59.004 52.381 0.00 0.00 0.00 4.42
165 193 2.346803 TCAAGGAAAGTCTACGCATGC 58.653 47.619 7.91 7.91 0.00 4.06
166 194 2.028112 TCAAGGAAAGTCTACGCATGCT 60.028 45.455 17.13 5.50 0.00 3.79
167 195 2.744202 CAAGGAAAGTCTACGCATGCTT 59.256 45.455 17.13 9.37 0.00 3.91
168 196 2.350522 AGGAAAGTCTACGCATGCTTG 58.649 47.619 17.13 3.27 0.00 4.01
169 197 1.398390 GGAAAGTCTACGCATGCTTGG 59.602 52.381 17.13 8.87 0.00 3.61
170 198 2.346803 GAAAGTCTACGCATGCTTGGA 58.653 47.619 17.13 11.47 0.00 3.53
171 199 2.698855 AAGTCTACGCATGCTTGGAT 57.301 45.000 17.13 0.00 0.00 3.41
174 202 0.829990 TCTACGCATGCTTGGATGGA 59.170 50.000 17.13 0.68 0.00 3.41
175 203 1.209261 TCTACGCATGCTTGGATGGAA 59.791 47.619 17.13 0.00 0.00 3.53
177 205 1.027357 ACGCATGCTTGGATGGAATC 58.973 50.000 17.13 0.00 44.55 2.52
179 207 0.313043 GCATGCTTGGATGGAATCGG 59.687 55.000 11.37 0.00 46.86 4.18
182 220 2.260844 TGCTTGGATGGAATCGGATC 57.739 50.000 0.00 0.00 46.86 3.36
218 256 0.950555 TCCGCTACTGCTTGCAGTTG 60.951 55.000 29.37 26.93 36.68 3.16
229 267 2.668212 GCAGTTGCAGTGCCCGTA 60.668 61.111 13.72 0.00 38.58 4.02
230 268 2.966309 GCAGTTGCAGTGCCCGTAC 61.966 63.158 13.72 5.70 38.58 3.67
231 269 1.596752 CAGTTGCAGTGCCCGTACA 60.597 57.895 13.72 0.00 0.00 2.90
248 287 2.134789 ACATGCCCCATCTCAACTTC 57.865 50.000 0.00 0.00 0.00 3.01
320 360 2.893489 CAGGAAAGAAAACCCTCCTTGG 59.107 50.000 0.00 0.00 36.10 3.61
321 361 1.618837 GGAAAGAAAACCCTCCTTGGC 59.381 52.381 0.00 0.00 0.00 4.52
324 364 0.405973 AGAAAACCCTCCTTGGCTCC 59.594 55.000 0.00 0.00 0.00 4.70
327 367 0.405973 AAACCCTCCTTGGCTCCTTC 59.594 55.000 0.00 0.00 0.00 3.46
328 368 0.772124 AACCCTCCTTGGCTCCTTCA 60.772 55.000 0.00 0.00 0.00 3.02
329 369 1.204113 ACCCTCCTTGGCTCCTTCAG 61.204 60.000 0.00 0.00 0.00 3.02
330 370 1.204113 CCCTCCTTGGCTCCTTCAGT 61.204 60.000 0.00 0.00 0.00 3.41
332 372 0.979665 CTCCTTGGCTCCTTCAGTCA 59.020 55.000 0.00 0.00 33.68 3.41
335 375 2.089980 CCTTGGCTCCTTCAGTCATTG 58.910 52.381 0.00 0.00 36.30 2.82
338 378 3.726557 TGGCTCCTTCAGTCATTGATT 57.273 42.857 0.00 0.00 35.27 2.57
339 379 4.038271 TGGCTCCTTCAGTCATTGATTT 57.962 40.909 0.00 0.00 35.27 2.17
340 380 3.760151 TGGCTCCTTCAGTCATTGATTTG 59.240 43.478 0.00 0.00 35.27 2.32
341 381 3.760684 GGCTCCTTCAGTCATTGATTTGT 59.239 43.478 0.00 0.00 35.27 2.83
342 382 4.219288 GGCTCCTTCAGTCATTGATTTGTT 59.781 41.667 0.00 0.00 35.27 2.83
343 383 5.415701 GGCTCCTTCAGTCATTGATTTGTTA 59.584 40.000 0.00 0.00 35.27 2.41
344 384 6.317857 GCTCCTTCAGTCATTGATTTGTTAC 58.682 40.000 0.00 0.00 35.27 2.50
345 385 6.150140 GCTCCTTCAGTCATTGATTTGTTACT 59.850 38.462 0.00 0.00 35.27 2.24
346 386 7.334421 GCTCCTTCAGTCATTGATTTGTTACTA 59.666 37.037 0.00 0.00 35.27 1.82
359 399 0.101759 GTTACTATCTCACGGCCGCA 59.898 55.000 28.58 11.76 0.00 5.69
438 487 0.753262 GGCGGTCCACATCTATCAGT 59.247 55.000 0.00 0.00 0.00 3.41
439 488 1.961394 GGCGGTCCACATCTATCAGTA 59.039 52.381 0.00 0.00 0.00 2.74
483 538 4.909880 GCCACTGTAACGACTTCATTTTTC 59.090 41.667 0.00 0.00 0.00 2.29
502 557 6.828502 TTTTCGTGATAGTGTGAGATATGC 57.171 37.500 0.00 0.00 0.00 3.14
608 1388 2.171079 TTAAAGGAGCCGCGCGATG 61.171 57.895 34.63 17.45 0.00 3.84
616 1396 3.972803 CCGCGCGATGCTCGTTAC 61.973 66.667 34.63 0.00 42.81 2.50
617 1397 2.949678 CGCGCGATGCTCGTTACT 60.950 61.111 28.94 0.00 42.81 2.24
619 1399 2.906719 GCGCGATGCTCGTTACTCG 61.907 63.158 12.10 0.00 42.81 4.18
620 1400 1.297378 CGCGATGCTCGTTACTCGA 60.297 57.895 0.00 0.00 46.83 4.04
749 1569 2.817396 GCCGCACTTGAGAGAGCC 60.817 66.667 0.00 0.00 36.29 4.70
750 1570 2.507992 CCGCACTTGAGAGAGCCG 60.508 66.667 0.00 0.00 36.29 5.52
751 1571 3.184683 CGCACTTGAGAGAGCCGC 61.185 66.667 0.00 0.00 36.29 6.53
752 1572 2.817396 GCACTTGAGAGAGCCGCC 60.817 66.667 0.00 0.00 33.94 6.13
753 1573 2.659016 CACTTGAGAGAGCCGCCA 59.341 61.111 0.00 0.00 0.00 5.69
781 1610 3.510559 TTACCGGCCAACAACCCCC 62.511 63.158 0.00 0.00 0.00 5.40
801 1630 2.159653 CCAAACGAATTGAAGAGAGGCG 60.160 50.000 7.17 0.00 41.85 5.52
833 1662 4.115199 ATTGCCGCACCTCCTCCC 62.115 66.667 0.00 0.00 0.00 4.30
861 1699 1.444119 TTGGCTTCAACTCCACGCAC 61.444 55.000 0.00 0.00 30.97 5.34
866 1705 4.354212 CAACTCCACGCACGCACG 62.354 66.667 0.00 0.00 39.50 5.34
980 1827 1.476007 GGATCGATCAGTGGAGGGGG 61.476 65.000 25.93 0.00 0.00 5.40
997 1844 3.371063 GTCCGTCGCCCTCTCACA 61.371 66.667 0.00 0.00 0.00 3.58
1095 1942 0.308684 TCTTTGCTTGCTGTGCTTCG 59.691 50.000 0.00 0.00 0.00 3.79
1096 1943 1.273455 CTTTGCTTGCTGTGCTTCGC 61.273 55.000 0.00 0.00 0.00 4.70
1097 1944 1.727511 TTTGCTTGCTGTGCTTCGCT 61.728 50.000 0.00 0.00 0.00 4.93
1098 1945 0.884259 TTGCTTGCTGTGCTTCGCTA 60.884 50.000 0.00 0.00 0.00 4.26
1112 1961 1.032657 TCGCTAGCTCCAGTCAGTCC 61.033 60.000 13.93 0.00 0.00 3.85
1114 1963 1.316706 GCTAGCTCCAGTCAGTCCGT 61.317 60.000 7.70 0.00 0.00 4.69
1115 1964 1.178276 CTAGCTCCAGTCAGTCCGTT 58.822 55.000 0.00 0.00 0.00 4.44
1116 1965 1.546476 CTAGCTCCAGTCAGTCCGTTT 59.454 52.381 0.00 0.00 0.00 3.60
1117 1966 0.759346 AGCTCCAGTCAGTCCGTTTT 59.241 50.000 0.00 0.00 0.00 2.43
1118 1967 1.141053 AGCTCCAGTCAGTCCGTTTTT 59.859 47.619 0.00 0.00 0.00 1.94
1143 1992 9.929722 TTTTTCTATATAAACGTAATGCTGCTG 57.070 29.630 0.00 0.00 0.00 4.41
1153 2002 2.866085 AATGCTGCTGCCTCGTCTCC 62.866 60.000 13.47 0.00 38.71 3.71
1293 2149 3.316308 GTGCTTCCTGGCCATGTTTATAG 59.684 47.826 5.51 0.00 0.00 1.31
1337 2197 0.029167 TGCATGTTTCGTGTGTGCTG 59.971 50.000 0.00 0.00 36.78 4.41
1367 2252 8.903570 TGTGCAGGTTATAATTAAAAATGACG 57.096 30.769 0.00 0.00 0.00 4.35
1492 2377 5.283457 GGTACCAATCTTACTCTGCATCT 57.717 43.478 7.15 0.00 0.00 2.90
1496 2381 8.030106 GGTACCAATCTTACTCTGCATCTATAC 58.970 40.741 7.15 0.00 0.00 1.47
1557 2469 6.570672 TCTGTCGATTTGTCTTGTACTACT 57.429 37.500 0.00 0.00 0.00 2.57
1558 2470 7.677454 TCTGTCGATTTGTCTTGTACTACTA 57.323 36.000 0.00 0.00 0.00 1.82
1569 2481 3.413846 TGTACTACTATCCGAGGCGAT 57.586 47.619 0.00 0.00 0.00 4.58
1581 2493 1.469940 CGAGGCGATGTGAGTTAAGCT 60.470 52.381 0.00 0.00 0.00 3.74
1587 2499 3.496130 GCGATGTGAGTTAAGCTATGCAT 59.504 43.478 3.79 3.79 0.00 3.96
1589 2501 4.987285 CGATGTGAGTTAAGCTATGCATCT 59.013 41.667 0.19 0.00 32.49 2.90
1590 2502 5.464722 CGATGTGAGTTAAGCTATGCATCTT 59.535 40.000 0.19 3.93 32.49 2.40
1628 2540 4.526650 GGTACTGGGACATTGTTTGGAATT 59.473 41.667 0.00 0.00 38.20 2.17
1676 2598 4.089361 TGATGTGTAAGAAGAGGAGCTCA 58.911 43.478 17.19 0.00 32.06 4.26
1690 2612 6.715280 AGAGGAGCTCAACTTCATTCATTTA 58.285 36.000 17.19 0.00 32.06 1.40
1700 2622 8.359642 TCAACTTCATTCATTTACCCTCTTTTG 58.640 33.333 0.00 0.00 0.00 2.44
2017 2957 2.885894 CTCCTCGGGATTCTACACCTAC 59.114 54.545 0.00 0.00 0.00 3.18
2029 2969 6.879276 TTCTACACCTACGGAATCTATGAG 57.121 41.667 0.00 0.00 0.00 2.90
2080 3020 1.599576 GGAGACCAGAGTGGCCTTC 59.400 63.158 3.32 1.37 42.67 3.46
2083 3023 1.072331 GAGACCAGAGTGGCCTTCAAA 59.928 52.381 3.32 0.00 42.67 2.69
2101 3041 7.432545 GCCTTCAAACTTAGAAAAGACAAGTTC 59.567 37.037 0.00 0.00 40.63 3.01
2106 3046 6.600246 ACTTAGAAAAGACAAGTTCGTTCC 57.400 37.500 0.00 0.00 36.50 3.62
2108 3048 3.881220 AGAAAAGACAAGTTCGTTCCCA 58.119 40.909 0.00 0.00 0.00 4.37
2121 3067 6.117488 AGTTCGTTCCCAACTTTAAGAAAGA 58.883 36.000 5.98 0.00 41.02 2.52
2122 3068 6.600427 AGTTCGTTCCCAACTTTAAGAAAGAA 59.400 34.615 5.98 0.00 41.02 2.52
2178 3125 4.024048 CACTGAAACTATGTGTTGGTGGAC 60.024 45.833 0.00 0.00 39.13 4.02
2179 3126 4.141482 ACTGAAACTATGTGTTGGTGGACT 60.141 41.667 0.00 0.00 39.13 3.85
2180 3127 4.787551 TGAAACTATGTGTTGGTGGACTT 58.212 39.130 0.00 0.00 39.13 3.01
2181 3128 5.931294 TGAAACTATGTGTTGGTGGACTTA 58.069 37.500 0.00 0.00 39.13 2.24
2182 3129 5.761234 TGAAACTATGTGTTGGTGGACTTAC 59.239 40.000 0.00 0.00 39.13 2.34
2194 3141 1.347707 TGGACTTACTGCAGGTTCCAG 59.652 52.381 19.93 8.36 31.12 3.86
2248 3195 2.280389 CCGATGCCTGATGACCGG 60.280 66.667 0.00 0.00 0.00 5.28
2293 3240 0.467384 CATACCCTGAGGCTGTCCTG 59.533 60.000 0.00 0.00 44.46 3.86
2396 3343 7.912056 TTGACTTCATTCTGAATAACCTCTG 57.088 36.000 1.98 0.00 35.59 3.35
2411 3358 8.839310 AATAACCTCTGCATTACTCATATGTC 57.161 34.615 1.90 0.00 0.00 3.06
2424 3371 4.142359 ACTCATATGTCTGTCAAGGTCGAC 60.142 45.833 7.13 7.13 36.40 4.20
2589 3536 3.866582 GGGCCCACTATGCTCGCT 61.867 66.667 19.95 0.00 0.00 4.93
2605 3552 3.367087 GCTCGCTGTAAGTTCAGACCTTA 60.367 47.826 6.53 0.00 37.61 2.69
2654 3602 5.196695 AGGGCTCATTCTTTTTACAGGATC 58.803 41.667 0.00 0.00 0.00 3.36
2655 3603 5.044550 AGGGCTCATTCTTTTTACAGGATCT 60.045 40.000 0.00 0.00 0.00 2.75
2686 3634 8.158169 TCATAGGAATATGAAAAGTCATGTGC 57.842 34.615 0.00 0.00 44.49 4.57
2741 3704 8.204836 GTCTCACCTAATGCTAAGAATCCTTAA 58.795 37.037 0.00 0.00 34.71 1.85
2757 3720 9.933240 AGAATCCTTAAGAATTTTCCATGAGAT 57.067 29.630 3.36 0.00 0.00 2.75
2763 3726 6.674694 AAGAATTTTCCATGAGATCTCACG 57.325 37.500 27.37 19.67 43.11 4.35
2773 3736 5.985530 CCATGAGATCTCACGTAATGCTAAA 59.014 40.000 27.37 0.03 43.11 1.85
2779 3742 5.712217 TCTCACGTAATGCTAAAAATCCG 57.288 39.130 0.00 0.00 0.00 4.18
2780 3743 5.172934 TCTCACGTAATGCTAAAAATCCGT 58.827 37.500 0.00 0.00 0.00 4.69
2824 3787 4.068599 GCAATCCTTAGGAATCTAGCACC 58.931 47.826 4.56 0.00 34.34 5.01
2826 3789 5.546526 CAATCCTTAGGAATCTAGCACCTC 58.453 45.833 4.56 0.00 34.34 3.85
2841 3804 7.069986 TCTAGCACCTCTATTCCTATGAAACT 58.930 38.462 0.00 0.00 33.32 2.66
2882 3846 5.031066 TCCTGTATAAATCCTCCAAACCG 57.969 43.478 0.00 0.00 0.00 4.44
2945 4008 3.627577 TGCAACAAGTTCTGAAAGGTCTC 59.372 43.478 0.00 0.00 0.00 3.36
2987 4050 2.365293 TCTTAGCGCTCATTATGCTGGA 59.635 45.455 16.34 0.00 39.73 3.86
3080 4143 0.039764 ACTCCAGTCAGGACGGATCA 59.960 55.000 11.48 0.00 43.07 2.92
3201 4424 8.998277 AGAGAGCACTCCATAAGTTAGTATAA 57.002 34.615 7.60 0.00 43.53 0.98
3202 4425 9.594936 AGAGAGCACTCCATAAGTTAGTATAAT 57.405 33.333 7.60 0.00 43.53 1.28
3285 4602 2.573941 ACATAAGTAACTCGGTCGGC 57.426 50.000 0.00 0.00 0.00 5.54
3398 4715 2.038295 CCAGAAGACTGAGCAAAGAGGT 59.962 50.000 0.00 0.00 46.03 3.85
3480 4812 7.642082 ACGACTAGATAAGGTTCACAGTAAT 57.358 36.000 0.00 0.00 0.00 1.89
3542 4890 9.534565 CCATACATATGCATATCTTACTACCAC 57.465 37.037 16.46 0.00 32.40 4.16
3630 4978 0.636647 TACCAGGAGAGGCTGGATCA 59.363 55.000 0.00 0.00 43.08 2.92
3688 5039 8.584919 CTTATAAGCTACAGTATAGCGTTACG 57.415 38.462 0.00 0.00 44.73 3.18
3703 5054 3.423123 GCGTTACGACATGCTTATATGGC 60.423 47.826 9.62 0.00 32.57 4.40
3819 5170 7.927048 AGAACATTGTAACTGGAAACTACAAC 58.073 34.615 0.00 0.00 38.11 3.32
3879 5230 2.157834 TCGACGCCACACTAACAATT 57.842 45.000 0.00 0.00 0.00 2.32
3926 5277 0.322008 GTTGCAGCCTGCCTCTAACT 60.322 55.000 15.29 0.00 44.23 2.24
3934 5285 2.680339 GCCTGCCTCTAACTTGAATGAC 59.320 50.000 0.00 0.00 0.00 3.06
3951 5302 2.115427 TGACTGGTGTCCTGACAAGAA 58.885 47.619 0.75 0.00 43.77 2.52
4110 5461 3.008049 ACCCCAACTATGTCAACAGACTC 59.992 47.826 0.00 0.00 33.41 3.36
4119 5470 7.619050 ACTATGTCAACAGACTCTTCATCAAT 58.381 34.615 0.00 0.00 33.41 2.57
4166 5517 2.744787 CGTCCAGCAGTTAATCATGC 57.255 50.000 2.93 2.93 42.87 4.06
4169 5520 2.019249 TCCAGCAGTTAATCATGCAGC 58.981 47.619 11.38 0.00 45.01 5.25
4182 5533 6.710597 AATCATGCAGCTGTTTCTAATCAT 57.289 33.333 16.64 4.47 0.00 2.45
4226 5587 1.839994 CAGTATGGGCTTTGGGAGAGA 59.160 52.381 0.00 0.00 0.00 3.10
4353 5714 6.127083 TGTTGTTGGCTCACTCAGATATCATA 60.127 38.462 5.32 0.00 0.00 2.15
4354 5715 5.847304 TGTTGGCTCACTCAGATATCATAC 58.153 41.667 5.32 0.00 0.00 2.39
4355 5716 5.363580 TGTTGGCTCACTCAGATATCATACA 59.636 40.000 5.32 0.00 0.00 2.29
4358 5719 5.600069 TGGCTCACTCAGATATCATACAACT 59.400 40.000 5.32 0.00 0.00 3.16
4363 5724 7.298374 TCACTCAGATATCATACAACTACCCT 58.702 38.462 5.32 0.00 0.00 4.34
4364 5725 8.445588 TCACTCAGATATCATACAACTACCCTA 58.554 37.037 5.32 0.00 0.00 3.53
4365 5726 9.078990 CACTCAGATATCATACAACTACCCTAA 57.921 37.037 5.32 0.00 0.00 2.69
4415 5781 2.501723 ACTAACATCTTGCCTGATCCGT 59.498 45.455 0.00 0.00 0.00 4.69
4416 5782 1.742761 AACATCTTGCCTGATCCGTG 58.257 50.000 0.00 0.00 0.00 4.94
4420 5786 2.046023 TTGCCTGATCCGTGCCTG 60.046 61.111 0.00 0.00 0.00 4.85
4424 5790 1.142748 CCTGATCCGTGCCTGTCTC 59.857 63.158 0.00 0.00 0.00 3.36
4641 6024 8.272545 TCATGTTGGTTCTCTTTCTTATCATG 57.727 34.615 0.00 0.00 0.00 3.07
4642 6025 7.337689 TCATGTTGGTTCTCTTTCTTATCATGG 59.662 37.037 0.00 0.00 0.00 3.66
4651 6034 7.150640 TCTCTTTCTTATCATGGTCATCATCG 58.849 38.462 0.00 0.00 32.92 3.84
4792 6199 1.071471 CTGGCTCTTCAACGTGGGT 59.929 57.895 0.00 0.00 0.00 4.51
4798 6205 0.828022 TCTTCAACGTGGGTGTGAGT 59.172 50.000 0.00 0.00 0.00 3.41
4801 6208 1.145156 CAACGTGGGTGTGAGTGGA 59.855 57.895 0.00 0.00 0.00 4.02
4816 6223 3.706373 GGAGCCTGGCTTGTCCGA 61.706 66.667 24.26 0.00 39.88 4.55
4928 6335 2.103042 GTGCCTGCCGCTAACTCAG 61.103 63.158 0.00 0.00 38.78 3.35
4951 6358 6.703165 CAGGCCCAAAAGCTAATTGATTAATC 59.297 38.462 8.60 8.60 0.00 1.75
4979 6394 4.334203 TGCCTTAGCCGTATTGTATTTGTG 59.666 41.667 0.00 0.00 38.69 3.33
4982 6397 6.037391 GCCTTAGCCGTATTGTATTTGTGTAA 59.963 38.462 0.00 0.00 0.00 2.41
5039 6457 2.572290 TGATTCAGCAGAGCATCCATG 58.428 47.619 0.00 0.00 33.66 3.66
5041 6459 2.034104 TTCAGCAGAGCATCCATGTC 57.966 50.000 0.00 0.00 33.66 3.06
5045 6463 2.121948 AGCAGAGCATCCATGTCCTAA 58.878 47.619 0.00 0.00 33.66 2.69
5047 6465 3.137913 AGCAGAGCATCCATGTCCTAATT 59.862 43.478 0.00 0.00 33.66 1.40
5048 6466 4.349048 AGCAGAGCATCCATGTCCTAATTA 59.651 41.667 0.00 0.00 33.66 1.40
5049 6467 5.065914 GCAGAGCATCCATGTCCTAATTAA 58.934 41.667 0.00 0.00 33.66 1.40
5051 6469 6.881065 GCAGAGCATCCATGTCCTAATTAATA 59.119 38.462 0.00 0.00 33.66 0.98
5053 6471 7.335422 CAGAGCATCCATGTCCTAATTAATACC 59.665 40.741 0.00 0.00 33.66 2.73
5056 6659 6.128282 GCATCCATGTCCTAATTAATACCACG 60.128 42.308 0.00 0.00 0.00 4.94
5070 6673 5.929697 AATACCACGTCATGCATAATCTG 57.070 39.130 0.00 0.00 0.00 2.90
5072 6675 4.400529 ACCACGTCATGCATAATCTGTA 57.599 40.909 0.00 0.00 0.00 2.74
5076 6679 6.591448 ACCACGTCATGCATAATCTGTATATG 59.409 38.462 0.00 0.00 34.55 1.78
5098 6789 4.127171 GCCTGTGTTCTCAACTCTGTTTA 58.873 43.478 0.00 0.00 0.00 2.01
5099 6790 4.024809 GCCTGTGTTCTCAACTCTGTTTAC 60.025 45.833 0.00 0.00 0.00 2.01
5100 6791 5.360591 CCTGTGTTCTCAACTCTGTTTACT 58.639 41.667 0.00 0.00 0.00 2.24
5101 6792 6.513180 CCTGTGTTCTCAACTCTGTTTACTA 58.487 40.000 0.00 0.00 0.00 1.82
5102 6793 6.421202 CCTGTGTTCTCAACTCTGTTTACTAC 59.579 42.308 0.00 0.00 0.00 2.73
5104 6795 5.401674 GTGTTCTCAACTCTGTTTACTACCG 59.598 44.000 0.00 0.00 0.00 4.02
5105 6796 5.068198 TGTTCTCAACTCTGTTTACTACCGT 59.932 40.000 0.00 0.00 0.00 4.83
5106 6797 5.117355 TCTCAACTCTGTTTACTACCGTG 57.883 43.478 0.00 0.00 0.00 4.94
5107 6798 3.645884 TCAACTCTGTTTACTACCGTGC 58.354 45.455 0.00 0.00 0.00 5.34
5108 6799 3.319972 TCAACTCTGTTTACTACCGTGCT 59.680 43.478 0.00 0.00 0.00 4.40
5109 6800 3.572604 ACTCTGTTTACTACCGTGCTC 57.427 47.619 0.00 0.00 0.00 4.26
5120 6811 3.244105 CGTGCTCGGTTTCTGGTG 58.756 61.111 0.00 0.00 0.00 4.17
5141 6839 5.009210 GGTGAAGTGTTTTGGTGCTGTAATA 59.991 40.000 0.00 0.00 0.00 0.98
5142 6840 6.294508 GGTGAAGTGTTTTGGTGCTGTAATAT 60.295 38.462 0.00 0.00 0.00 1.28
5160 6858 5.999205 AATATGCCAAAATCTCACCACAA 57.001 34.783 0.00 0.00 0.00 3.33
5166 6868 3.191371 CCAAAATCTCACCACAACTAGCC 59.809 47.826 0.00 0.00 0.00 3.93
5189 6931 2.041620 ACAATCCAGGGTGCATGTTACT 59.958 45.455 0.00 0.00 0.00 2.24
5197 6939 4.021192 CAGGGTGCATGTTACTGGAAAAAT 60.021 41.667 0.00 0.00 0.00 1.82
5198 6940 4.021192 AGGGTGCATGTTACTGGAAAAATG 60.021 41.667 0.00 0.00 0.00 2.32
5201 6943 6.165577 GGTGCATGTTACTGGAAAAATGAAT 58.834 36.000 0.00 0.00 0.00 2.57
5202 6944 6.091169 GGTGCATGTTACTGGAAAAATGAATG 59.909 38.462 0.00 0.00 0.00 2.67
5203 6945 6.646240 GTGCATGTTACTGGAAAAATGAATGT 59.354 34.615 0.00 0.00 0.00 2.71
5223 6967 7.611467 TGAATGTATTCTAGTTTTGGATGTGCT 59.389 33.333 6.21 0.00 37.67 4.40
5253 6997 0.179006 GGGGAGGGAGTCATGAATGC 60.179 60.000 6.07 6.07 0.00 3.56
5301 7045 3.593794 GCCGATCGTCCTAGCCGT 61.594 66.667 15.09 0.00 0.00 5.68
5339 7083 2.920912 GTCCGGGTCCAGGTGTCA 60.921 66.667 8.03 0.00 0.00 3.58
5382 7126 2.452937 GCCCCATCCACCCTACTCC 61.453 68.421 0.00 0.00 0.00 3.85
5384 7128 1.056700 CCCCATCCACCCTACTCCAG 61.057 65.000 0.00 0.00 0.00 3.86
5449 7200 4.741239 TGGCCCCCTCCCTCACTC 62.741 72.222 0.00 0.00 0.00 3.51
5491 7242 0.702316 TTTAACCTCCCTCCCTTGCC 59.298 55.000 0.00 0.00 0.00 4.52
5737 7495 4.124943 TACCTCGGCCCGCTCTCT 62.125 66.667 0.00 0.00 0.00 3.10
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
23 24 1.202818 ACAAGAGGCAAGGACAAGGAC 60.203 52.381 0.00 0.00 0.00 3.85
49 50 4.869451 ACTTGGGTAGGAAGTAGTAGGAG 58.131 47.826 0.00 0.00 31.72 3.69
50 51 4.961440 ACTTGGGTAGGAAGTAGTAGGA 57.039 45.455 0.00 0.00 31.72 2.94
51 52 4.405036 GGAACTTGGGTAGGAAGTAGTAGG 59.595 50.000 0.00 0.00 33.20 3.18
95 103 2.360767 GGCTGGCCAATCCATGCAA 61.361 57.895 16.63 0.00 45.50 4.08
96 104 2.760799 GGCTGGCCAATCCATGCA 60.761 61.111 16.63 0.00 45.50 3.96
97 105 3.543641 GGGCTGGCCAATCCATGC 61.544 66.667 21.42 13.81 45.50 4.06
98 106 2.042741 TGGGCTGGCCAATCCATG 60.043 61.111 21.84 2.94 45.50 3.66
159 187 0.040692 CGATTCCATCCAAGCATGCG 60.041 55.000 13.01 0.00 0.00 4.73
161 189 1.971481 TCCGATTCCATCCAAGCATG 58.029 50.000 0.00 0.00 0.00 4.06
165 193 3.198409 TGTGATCCGATTCCATCCAAG 57.802 47.619 0.00 0.00 0.00 3.61
166 194 3.136260 TCATGTGATCCGATTCCATCCAA 59.864 43.478 0.00 0.00 0.00 3.53
167 195 2.705127 TCATGTGATCCGATTCCATCCA 59.295 45.455 0.00 0.00 0.00 3.41
168 196 3.407424 TCATGTGATCCGATTCCATCC 57.593 47.619 0.00 0.00 0.00 3.51
182 220 2.094894 GCGGAGAAACAGTGATCATGTG 59.905 50.000 0.00 2.32 0.00 3.21
218 256 3.508840 GGCATGTACGGGCACTGC 61.509 66.667 10.27 0.00 39.14 4.40
220 258 4.109675 GGGGCATGTACGGGCACT 62.110 66.667 10.21 0.00 32.86 4.40
222 260 3.414136 GATGGGGCATGTACGGGCA 62.414 63.158 12.00 0.00 0.00 5.36
223 261 2.594592 GATGGGGCATGTACGGGC 60.595 66.667 0.00 2.71 0.00 6.13
224 262 1.071471 GAGATGGGGCATGTACGGG 59.929 63.158 0.00 0.00 0.00 5.28
225 263 0.180171 TTGAGATGGGGCATGTACGG 59.820 55.000 0.00 0.00 0.00 4.02
226 264 1.134401 AGTTGAGATGGGGCATGTACG 60.134 52.381 0.00 0.00 0.00 3.67
227 265 2.717639 AGTTGAGATGGGGCATGTAC 57.282 50.000 0.00 0.00 0.00 2.90
228 266 2.846206 AGAAGTTGAGATGGGGCATGTA 59.154 45.455 0.00 0.00 0.00 2.29
229 267 1.637553 AGAAGTTGAGATGGGGCATGT 59.362 47.619 0.00 0.00 0.00 3.21
230 268 2.295885 GAGAAGTTGAGATGGGGCATG 58.704 52.381 0.00 0.00 0.00 4.06
231 269 1.918262 TGAGAAGTTGAGATGGGGCAT 59.082 47.619 0.00 0.00 0.00 4.40
320 360 5.382618 AACAAATCAATGACTGAAGGAGC 57.617 39.130 1.67 0.00 37.67 4.70
321 361 7.678947 AGTAACAAATCAATGACTGAAGGAG 57.321 36.000 1.67 0.00 37.67 3.69
327 367 8.323854 CGTGAGATAGTAACAAATCAATGACTG 58.676 37.037 0.00 0.00 0.00 3.51
328 368 7.492669 CCGTGAGATAGTAACAAATCAATGACT 59.507 37.037 0.00 0.00 0.00 3.41
329 369 7.621991 CCGTGAGATAGTAACAAATCAATGAC 58.378 38.462 0.00 0.00 0.00 3.06
330 370 6.257849 GCCGTGAGATAGTAACAAATCAATGA 59.742 38.462 0.00 0.00 0.00 2.57
332 372 5.527582 GGCCGTGAGATAGTAACAAATCAAT 59.472 40.000 0.00 0.00 0.00 2.57
335 375 3.489785 CGGCCGTGAGATAGTAACAAATC 59.510 47.826 19.50 0.00 0.00 2.17
338 378 1.470285 GCGGCCGTGAGATAGTAACAA 60.470 52.381 28.70 0.00 0.00 2.83
339 379 0.101759 GCGGCCGTGAGATAGTAACA 59.898 55.000 28.70 0.00 0.00 2.41
340 380 0.101759 TGCGGCCGTGAGATAGTAAC 59.898 55.000 28.70 5.44 0.00 2.50
341 381 0.818938 TTGCGGCCGTGAGATAGTAA 59.181 50.000 28.70 5.52 0.00 2.24
342 382 0.384309 CTTGCGGCCGTGAGATAGTA 59.616 55.000 28.70 0.78 0.00 1.82
343 383 1.141881 CTTGCGGCCGTGAGATAGT 59.858 57.895 28.70 0.00 0.00 2.12
344 384 2.240500 GCTTGCGGCCGTGAGATAG 61.241 63.158 28.70 15.18 34.27 2.08
345 385 2.202878 GCTTGCGGCCGTGAGATA 60.203 61.111 28.70 3.57 34.27 1.98
346 386 4.087892 AGCTTGCGGCCGTGAGAT 62.088 61.111 28.70 20.25 43.05 2.75
359 399 2.281761 CCGCCCAAGTCACAGCTT 60.282 61.111 0.00 0.00 0.00 3.74
438 487 2.202336 CGGTGAAGCGCGTACGTA 60.202 61.111 17.90 0.00 42.83 3.57
439 488 4.332637 ACGGTGAAGCGCGTACGT 62.333 61.111 17.90 12.70 42.83 3.57
483 538 4.511617 AGGCATATCTCACACTATCACG 57.488 45.455 0.00 0.00 0.00 4.35
502 557 2.433436 GTGCCTAACCTAACCACAAGG 58.567 52.381 0.00 0.00 40.20 3.61
534 589 9.935682 ACTCGTTGAATTATTGTATAGCATTTG 57.064 29.630 0.00 0.00 0.00 2.32
580 1360 4.023365 CGCGGCTCCTTTAACTACTAGTAT 60.023 45.833 2.33 0.00 0.00 2.12
581 1361 3.313526 CGCGGCTCCTTTAACTACTAGTA 59.686 47.826 0.00 1.89 0.00 1.82
586 1366 1.749609 CGCGCGGCTCCTTTAACTAC 61.750 60.000 24.84 0.00 0.00 2.73
613 1393 4.669318 GATCATCCGTGTCTTTCGAGTAA 58.331 43.478 0.00 0.00 0.00 2.24
614 1394 3.242641 CGATCATCCGTGTCTTTCGAGTA 60.243 47.826 0.00 0.00 0.00 2.59
616 1396 2.112522 CGATCATCCGTGTCTTTCGAG 58.887 52.381 0.00 0.00 0.00 4.04
617 1397 1.741145 TCGATCATCCGTGTCTTTCGA 59.259 47.619 0.00 0.00 0.00 3.71
619 1399 5.174035 CACTAATCGATCATCCGTGTCTTTC 59.826 44.000 0.00 0.00 0.00 2.62
620 1400 5.043903 CACTAATCGATCATCCGTGTCTTT 58.956 41.667 0.00 0.00 0.00 2.52
623 1434 3.309388 CCACTAATCGATCATCCGTGTC 58.691 50.000 0.00 0.00 0.00 3.67
625 1436 2.677199 CCCACTAATCGATCATCCGTG 58.323 52.381 0.00 2.25 0.00 4.94
701 1518 4.379603 CGAGGAGACGATGGAATATGTACC 60.380 50.000 0.00 0.00 35.09 3.34
749 1569 1.579429 GGTAACAGTTGGCTTGGCG 59.421 57.895 0.00 0.00 0.00 5.69
750 1570 1.579429 CGGTAACAGTTGGCTTGGC 59.421 57.895 0.00 0.00 0.00 4.52
751 1571 1.862602 GCCGGTAACAGTTGGCTTGG 61.863 60.000 1.90 2.85 44.16 3.61
752 1572 1.579429 GCCGGTAACAGTTGGCTTG 59.421 57.895 1.90 0.00 44.16 4.01
753 1573 1.602605 GGCCGGTAACAGTTGGCTT 60.603 57.895 11.82 0.00 46.72 4.35
781 1610 2.159653 CCGCCTCTCTTCAATTCGTTTG 60.160 50.000 0.00 0.00 36.61 2.93
782 1611 2.076863 CCGCCTCTCTTCAATTCGTTT 58.923 47.619 0.00 0.00 0.00 3.60
833 1662 0.322906 GTTGAAGCCAAGGAGGAGGG 60.323 60.000 0.00 0.00 41.22 4.30
980 1827 3.371063 TGTGAGAGGGCGACGGAC 61.371 66.667 0.00 0.00 0.00 4.79
988 1835 2.124983 CGCCATGGTGTGAGAGGG 60.125 66.667 17.59 0.00 0.00 4.30
997 1844 2.570302 AGTACCTAAGTTTCGCCATGGT 59.430 45.455 14.67 0.00 0.00 3.55
1061 1908 1.002468 CAAAGATTAATGGCGGCTCGG 60.002 52.381 11.43 0.00 0.00 4.63
1062 1909 1.597937 GCAAAGATTAATGGCGGCTCG 60.598 52.381 11.43 0.00 0.00 5.03
1063 1910 1.678101 AGCAAAGATTAATGGCGGCTC 59.322 47.619 11.43 0.00 0.00 4.70
1064 1911 1.767759 AGCAAAGATTAATGGCGGCT 58.232 45.000 11.43 0.00 0.00 5.52
1065 1912 2.195922 CAAGCAAAGATTAATGGCGGC 58.804 47.619 0.00 0.00 0.00 6.53
1066 1913 2.159198 AGCAAGCAAAGATTAATGGCGG 60.159 45.455 0.00 0.00 0.00 6.13
1067 1914 2.855963 CAGCAAGCAAAGATTAATGGCG 59.144 45.455 0.00 0.00 0.00 5.69
1095 1942 1.316706 ACGGACTGACTGGAGCTAGC 61.317 60.000 6.62 6.62 0.00 3.42
1096 1943 1.178276 AACGGACTGACTGGAGCTAG 58.822 55.000 0.00 0.00 0.00 3.42
1097 1944 1.629043 AAACGGACTGACTGGAGCTA 58.371 50.000 0.00 0.00 0.00 3.32
1098 1945 0.759346 AAAACGGACTGACTGGAGCT 59.241 50.000 0.00 0.00 0.00 4.09
1117 1966 9.929722 CAGCAGCATTACGTTTATATAGAAAAA 57.070 29.630 0.00 0.00 0.00 1.94
1118 1967 8.067784 GCAGCAGCATTACGTTTATATAGAAAA 58.932 33.333 0.00 0.00 41.58 2.29
1143 1992 3.462678 GGTCCAGGGAGACGAGGC 61.463 72.222 0.00 0.00 37.66 4.70
1153 2002 3.324930 TCCTGCAGCTGGTCCAGG 61.325 66.667 25.07 25.07 45.88 4.45
1271 2120 1.544724 TAAACATGGCCAGGAAGCAC 58.455 50.000 26.87 0.00 0.00 4.40
1486 2371 8.698973 AGCTCTAACTAGAAAGTATAGATGCA 57.301 34.615 0.00 0.00 33.75 3.96
1525 2429 8.360390 ACAAGACAAATCGACAGATATAGCATA 58.640 33.333 0.00 0.00 35.74 3.14
1526 2430 7.212976 ACAAGACAAATCGACAGATATAGCAT 58.787 34.615 0.00 0.00 35.74 3.79
1556 2468 0.955178 ACTCACATCGCCTCGGATAG 59.045 55.000 0.00 0.00 0.00 2.08
1557 2469 1.399714 AACTCACATCGCCTCGGATA 58.600 50.000 0.00 0.00 0.00 2.59
1558 2470 1.399714 TAACTCACATCGCCTCGGAT 58.600 50.000 0.00 0.00 0.00 4.18
1569 2481 6.654582 TGAAAAGATGCATAGCTTAACTCACA 59.345 34.615 0.00 0.00 31.11 3.58
1581 2493 6.541278 CCTGACAGAAGATGAAAAGATGCATA 59.459 38.462 3.32 0.00 0.00 3.14
1587 2499 6.459066 CAGTACCTGACAGAAGATGAAAAGA 58.541 40.000 3.32 0.00 32.44 2.52
1589 2501 5.513094 CCCAGTACCTGACAGAAGATGAAAA 60.513 44.000 3.32 0.00 32.44 2.29
1590 2502 4.020218 CCCAGTACCTGACAGAAGATGAAA 60.020 45.833 3.32 0.00 32.44 2.69
1628 2540 1.367471 CAGTTCGCTGTCCTGGTGA 59.633 57.895 0.00 0.00 40.26 4.02
1676 2598 8.250143 ACAAAAGAGGGTAAATGAATGAAGTT 57.750 30.769 0.00 0.00 0.00 2.66
1690 2612 9.817809 GAAGAAAATAGAAAAACAAAAGAGGGT 57.182 29.630 0.00 0.00 0.00 4.34
1732 2654 3.284793 TCAACCTCCTTTCCGAAACAA 57.715 42.857 0.00 0.00 0.00 2.83
1733 2655 3.284793 TTCAACCTCCTTTCCGAAACA 57.715 42.857 0.00 0.00 0.00 2.83
1734 2656 3.630769 ACTTTCAACCTCCTTTCCGAAAC 59.369 43.478 0.00 0.00 0.00 2.78
1740 2662 3.548214 GCGTTCACTTTCAACCTCCTTTC 60.548 47.826 0.00 0.00 0.00 2.62
1854 2776 0.884514 GAACAGCTTTCCCTTCCTGC 59.115 55.000 0.00 0.00 0.00 4.85
2017 2957 3.459232 TCCTTGTGCTCATAGATTCCG 57.541 47.619 0.00 0.00 0.00 4.30
2029 2969 2.991540 GGCCACCCTTCCTTGTGC 60.992 66.667 0.00 0.00 0.00 4.57
2080 3020 7.428472 GGAACGAACTTGTCTTTTCTAAGTTTG 59.572 37.037 12.41 12.41 45.11 2.93
2083 3023 5.526479 GGGAACGAACTTGTCTTTTCTAAGT 59.474 40.000 0.00 0.00 36.29 2.24
2101 3041 8.642908 AATTTTCTTTCTTAAAGTTGGGAACG 57.357 30.769 0.00 0.00 39.52 3.95
2194 3141 1.462616 TGTCAGCCATTGCCATGTAC 58.537 50.000 0.00 0.00 38.69 2.90
2275 3222 1.341156 GCAGGACAGCCTCAGGGTAT 61.341 60.000 0.00 0.00 44.80 2.73
2293 3240 3.365472 AGGATTAATTGGGTCCACAAGC 58.635 45.455 7.91 0.00 34.42 4.01
2396 3343 6.051717 ACCTTGACAGACATATGAGTAATGC 58.948 40.000 10.38 0.00 0.00 3.56
2411 3358 1.269102 ACTTGTCGTCGACCTTGACAG 60.269 52.381 22.05 16.44 42.93 3.51
2535 3482 0.115152 TCTGCTTCAGAGGTCCTCCA 59.885 55.000 15.72 5.02 35.39 3.86
2666 3614 6.199937 AGTGCACATGACTTTTCATATTCC 57.800 37.500 21.04 0.00 40.79 3.01
2680 3628 2.947652 CCTAAGGATTGGAGTGCACATG 59.052 50.000 21.04 0.00 0.00 3.21
2682 3630 2.265367 TCCTAAGGATTGGAGTGCACA 58.735 47.619 21.04 0.00 0.00 4.57
2684 3632 4.591321 AATTCCTAAGGATTGGAGTGCA 57.409 40.909 0.00 0.00 33.46 4.57
2685 3633 5.163509 GGAAAATTCCTAAGGATTGGAGTGC 60.164 44.000 4.91 0.00 44.11 4.40
2686 3634 6.456795 GGAAAATTCCTAAGGATTGGAGTG 57.543 41.667 4.91 0.00 44.11 3.51
2741 3704 7.331026 TTACGTGAGATCTCATGGAAAATTCT 58.669 34.615 36.44 21.58 44.12 2.40
2757 3720 5.172934 ACGGATTTTTAGCATTACGTGAGA 58.827 37.500 0.00 0.00 31.60 3.27
2773 3736 4.513406 TTGGCCTAATTCCTACGGATTT 57.487 40.909 3.32 0.00 0.00 2.17
2802 3765 4.068599 GGTGCTAGATTCCTAAGGATTGC 58.931 47.826 0.00 0.00 0.00 3.56
2824 3787 9.941325 ATGAGCATTAGTTTCATAGGAATAGAG 57.059 33.333 0.00 0.00 31.93 2.43
2857 3820 6.546034 CGGTTTGGAGGATTTATACAGGATTT 59.454 38.462 0.00 0.00 0.00 2.17
2860 3823 4.717778 TCGGTTTGGAGGATTTATACAGGA 59.282 41.667 0.00 0.00 0.00 3.86
2861 3824 5.031066 TCGGTTTGGAGGATTTATACAGG 57.969 43.478 0.00 0.00 0.00 4.00
2863 3826 7.227910 GCTTATTCGGTTTGGAGGATTTATACA 59.772 37.037 0.00 0.00 0.00 2.29
2864 3827 7.308408 GGCTTATTCGGTTTGGAGGATTTATAC 60.308 40.741 0.00 0.00 0.00 1.47
2865 3828 6.713450 GGCTTATTCGGTTTGGAGGATTTATA 59.287 38.462 0.00 0.00 0.00 0.98
2987 4050 0.693049 ACTTGGGCGAAAGGTCATCT 59.307 50.000 3.94 0.00 0.00 2.90
3203 4426 9.048446 GCCATAATTGCTGTCATTTGATAAATT 57.952 29.630 0.00 0.00 0.00 1.82
3285 4602 7.062605 GGCAAACATTAAAGATGACATCAAGTG 59.937 37.037 17.57 11.05 0.00 3.16
3398 4715 6.299805 ACAAGCAATCTACCAGAGATACAA 57.700 37.500 0.00 0.00 44.68 2.41
3630 4978 1.202976 ACCTTGCACTCTCTTTGCCAT 60.203 47.619 0.00 0.00 39.39 4.40
3674 5022 3.629058 AGCATGTCGTAACGCTATACTG 58.371 45.455 0.00 0.00 31.60 2.74
3675 5023 3.984508 AGCATGTCGTAACGCTATACT 57.015 42.857 0.00 0.00 31.60 2.12
3681 5032 3.423123 GCCATATAAGCATGTCGTAACGC 60.423 47.826 0.00 0.00 0.00 4.84
3683 5034 4.152402 CAGGCCATATAAGCATGTCGTAAC 59.848 45.833 5.01 0.00 37.26 2.50
3703 5054 8.924511 AACTCCATTATCCACAATAATACAGG 57.075 34.615 0.00 0.00 38.28 4.00
3819 5170 0.320421 CCGGAACCCACGCATATAGG 60.320 60.000 0.00 0.00 0.00 2.57
3926 5277 2.437651 TGTCAGGACACCAGTCATTCAA 59.562 45.455 0.00 0.00 46.80 2.69
3934 5285 3.304928 GCAATTTCTTGTCAGGACACCAG 60.305 47.826 0.77 0.00 41.67 4.00
4026 5377 2.168458 TTCCGATCTCCCACATGGTA 57.832 50.000 0.00 0.00 34.77 3.25
4119 5470 6.930433 AGGTTTCTTTCACCTGTCAGGATGA 61.930 44.000 26.18 20.08 43.17 2.92
4163 5514 4.512944 CCGTATGATTAGAAACAGCTGCAT 59.487 41.667 15.27 8.94 0.00 3.96
4165 5516 3.871594 ACCGTATGATTAGAAACAGCTGC 59.128 43.478 15.27 0.00 0.00 5.25
4166 5517 4.870426 ACACCGTATGATTAGAAACAGCTG 59.130 41.667 13.48 13.48 0.00 4.24
4169 5520 7.821595 TGTAACACCGTATGATTAGAAACAG 57.178 36.000 0.00 0.00 0.00 3.16
4182 5533 4.082081 CCTGAACCTGTATGTAACACCGTA 60.082 45.833 0.00 0.00 33.45 4.02
4226 5587 0.598562 CCGGATACAGCTCTGCGTAT 59.401 55.000 0.00 0.00 33.63 3.06
4369 5730 6.663093 TGCAAAAACACTTGTATGATATCCCT 59.337 34.615 0.00 0.00 0.00 4.20
4370 5731 6.751888 GTGCAAAAACACTTGTATGATATCCC 59.248 38.462 0.00 0.00 37.58 3.85
4371 5732 7.740519 GTGCAAAAACACTTGTATGATATCC 57.259 36.000 0.00 0.00 37.58 2.59
4384 5745 4.209080 GGCAAGATGTTAGTGCAAAAACAC 59.791 41.667 15.22 10.39 38.35 3.32
4385 5746 4.099266 AGGCAAGATGTTAGTGCAAAAACA 59.901 37.500 15.25 15.25 40.12 2.83
4386 5747 4.445385 CAGGCAAGATGTTAGTGCAAAAAC 59.555 41.667 5.65 5.65 40.12 2.43
4387 5748 4.340666 TCAGGCAAGATGTTAGTGCAAAAA 59.659 37.500 0.00 0.00 40.12 1.94
4388 5749 3.888323 TCAGGCAAGATGTTAGTGCAAAA 59.112 39.130 0.00 0.00 40.12 2.44
4415 5781 1.811558 GCAGTTCAGTTGAGACAGGCA 60.812 52.381 0.00 0.00 0.00 4.75
4416 5782 0.871057 GCAGTTCAGTTGAGACAGGC 59.129 55.000 0.00 0.00 0.00 4.85
4420 5786 3.722147 TCTTCTGCAGTTCAGTTGAGAC 58.278 45.455 14.67 0.00 43.32 3.36
4424 5790 3.873361 TCACTTCTTCTGCAGTTCAGTTG 59.127 43.478 14.67 6.21 43.32 3.16
4641 6024 0.107456 ACAGGATGGCGATGATGACC 59.893 55.000 0.00 0.00 43.62 4.02
4642 6025 1.600957 CAACAGGATGGCGATGATGAC 59.399 52.381 0.00 0.00 43.62 3.06
4651 6034 0.177141 AATGCATGCAACAGGATGGC 59.823 50.000 26.68 0.00 43.62 4.40
4785 6192 3.138625 CTCCACTCACACCCACGT 58.861 61.111 0.00 0.00 0.00 4.49
4792 6199 2.149383 AAGCCAGGCTCCACTCACA 61.149 57.895 16.53 0.00 38.25 3.58
4798 6205 4.020617 CGGACAAGCCAGGCTCCA 62.021 66.667 16.53 0.00 38.25 3.86
4801 6208 3.710722 CCTCGGACAAGCCAGGCT 61.711 66.667 8.70 8.70 42.56 4.58
4816 6223 4.560739 TCAGATAGATGGTGTTGATCCCT 58.439 43.478 0.00 0.00 0.00 4.20
4928 6335 6.581712 TGATTAATCAATTAGCTTTTGGGCC 58.418 36.000 15.82 0.00 33.08 5.80
4979 6394 5.427036 CTAGCTAGCTAGGTGTCACTTAC 57.573 47.826 34.95 7.53 41.58 2.34
5039 6457 5.756347 TGCATGACGTGGTATTAATTAGGAC 59.244 40.000 0.00 0.00 0.00 3.85
5041 6459 6.801539 ATGCATGACGTGGTATTAATTAGG 57.198 37.500 0.00 0.00 0.00 2.69
5045 6463 7.661437 ACAGATTATGCATGACGTGGTATTAAT 59.339 33.333 10.16 0.00 0.00 1.40
5047 6465 6.521162 ACAGATTATGCATGACGTGGTATTA 58.479 36.000 10.16 0.00 0.00 0.98
5048 6466 5.368145 ACAGATTATGCATGACGTGGTATT 58.632 37.500 10.16 0.00 0.00 1.89
5049 6467 4.960938 ACAGATTATGCATGACGTGGTAT 58.039 39.130 10.16 0.00 0.00 2.73
5051 6469 3.266510 ACAGATTATGCATGACGTGGT 57.733 42.857 10.16 0.00 0.00 4.16
5053 6471 6.456047 GGCATATACAGATTATGCATGACGTG 60.456 42.308 10.16 4.92 45.97 4.49
5070 6673 5.521735 CAGAGTTGAGAACACAGGCATATAC 59.478 44.000 0.00 0.00 0.00 1.47
5072 6675 4.019860 ACAGAGTTGAGAACACAGGCATAT 60.020 41.667 0.00 0.00 0.00 1.78
5076 6679 2.246719 ACAGAGTTGAGAACACAGGC 57.753 50.000 0.00 0.00 0.00 4.85
5104 6795 0.868406 CTTCACCAGAAACCGAGCAC 59.132 55.000 0.00 0.00 32.35 4.40
5105 6796 0.468226 ACTTCACCAGAAACCGAGCA 59.532 50.000 0.00 0.00 32.35 4.26
5106 6797 0.868406 CACTTCACCAGAAACCGAGC 59.132 55.000 0.00 0.00 32.35 5.03
5107 6798 2.240493 ACACTTCACCAGAAACCGAG 57.760 50.000 0.00 0.00 32.35 4.63
5108 6799 2.702592 AACACTTCACCAGAAACCGA 57.297 45.000 0.00 0.00 32.35 4.69
5109 6800 3.434637 CAAAACACTTCACCAGAAACCG 58.565 45.455 0.00 0.00 32.35 4.44
5111 6802 4.173256 CACCAAAACACTTCACCAGAAAC 58.827 43.478 0.00 0.00 32.35 2.78
5115 6806 1.750778 AGCACCAAAACACTTCACCAG 59.249 47.619 0.00 0.00 0.00 4.00
5117 6808 1.476488 ACAGCACCAAAACACTTCACC 59.524 47.619 0.00 0.00 0.00 4.02
5120 6811 5.572896 GCATATTACAGCACCAAAACACTTC 59.427 40.000 0.00 0.00 0.00 3.01
5141 6839 3.233507 AGTTGTGGTGAGATTTTGGCAT 58.766 40.909 0.00 0.00 0.00 4.40
5142 6840 2.665165 AGTTGTGGTGAGATTTTGGCA 58.335 42.857 0.00 0.00 0.00 4.92
5160 6858 2.119495 CACCCTGGATTGTAGGCTAGT 58.881 52.381 0.00 0.00 33.86 2.57
5166 6868 2.425143 ACATGCACCCTGGATTGTAG 57.575 50.000 0.00 0.00 0.00 2.74
5197 6939 7.611467 AGCACATCCAAAACTAGAATACATTCA 59.389 33.333 0.00 0.00 39.23 2.57
5198 6940 7.989826 AGCACATCCAAAACTAGAATACATTC 58.010 34.615 0.00 0.00 37.06 2.67
5201 6943 7.168219 AGAAGCACATCCAAAACTAGAATACA 58.832 34.615 0.00 0.00 0.00 2.29
5202 6944 7.617041 AGAAGCACATCCAAAACTAGAATAC 57.383 36.000 0.00 0.00 0.00 1.89
5203 6945 7.336931 GGAAGAAGCACATCCAAAACTAGAATA 59.663 37.037 0.00 0.00 36.50 1.75
5210 6954 3.305608 CCAGGAAGAAGCACATCCAAAAC 60.306 47.826 7.66 0.00 38.67 2.43
5223 6967 3.009115 CCTCCCCGCCAGGAAGAA 61.009 66.667 0.00 0.00 41.02 2.52
5244 6988 1.992667 GTCGTCGAGTTGCATTCATGA 59.007 47.619 0.00 0.00 0.00 3.07
5301 7045 1.549170 GACCTGAAACGGCCTTCTCTA 59.451 52.381 0.00 0.00 0.00 2.43
5364 7108 2.452937 GGAGTAGGGTGGATGGGGC 61.453 68.421 0.00 0.00 0.00 5.80
5400 7144 3.083600 GAAATCACGGTCTGCGGCG 62.084 63.158 0.51 0.51 0.00 6.46
5409 7155 3.381949 GTCCTTATCTCGGAAATCACGG 58.618 50.000 0.00 0.00 31.13 4.94
5443 7194 3.869272 GCGCGCCAATGGAGTGAG 61.869 66.667 23.24 5.91 35.05 3.51
5491 7242 1.515020 CTGCGTGAGGAAGAGAGGG 59.485 63.158 0.00 0.00 0.00 4.30
5584 7339 3.483869 GGGGAGGAGAGCGCCATT 61.484 66.667 2.29 0.00 38.18 3.16
5648 7406 4.120331 GGCCTTGCGCATGGTGAC 62.120 66.667 34.64 24.08 40.31 3.67


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

AutoCloner maintained by Alex Coulton.