Multiple sequence alignment - TraesCS5B01G226600

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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 TraesCS5B01G226600 chr5B 100.000 3407 0 0 1 3407 403695344 403698750 0.000000e+00 6292.0
1 TraesCS5B01G226600 chr5A 90.402 2761 196 33 1 2730 444521426 444524148 0.000000e+00 3567.0
2 TraesCS5B01G226600 chr5A 95.614 114 5 0 3294 3407 444525031 444525144 2.090000e-42 183.0
3 TraesCS5B01G226600 chr5D 86.641 1280 98 41 519 1774 347484526 347483296 0.000000e+00 1349.0
4 TraesCS5B01G226600 chr5D 92.266 931 55 8 1808 2736 347483298 347482383 0.000000e+00 1304.0
5 TraesCS5B01G226600 chr5D 87.912 182 17 1 3229 3405 347481643 347481462 3.450000e-50 209.0
6 TraesCS5B01G226600 chr5D 93.023 43 2 1 2954 2995 347482073 347482031 1.020000e-05 62.1
7 TraesCS5B01G226600 chr1A 81.092 238 42 2 160 394 414639224 414638987 1.610000e-43 187.0
8 TraesCS5B01G226600 chr1A 80.672 238 43 2 160 394 414644600 414644363 7.510000e-42 182.0
9 TraesCS5B01G226600 chr2D 83.246 191 32 0 186 376 551418977 551419167 3.490000e-40 176.0
10 TraesCS5B01G226600 chr2D 87.209 86 11 0 1194 1279 416932488 416932573 7.780000e-17 99.0
11 TraesCS5B01G226600 chr7D 89.209 139 14 1 2099 2236 437645745 437645607 4.520000e-39 172.0
12 TraesCS5B01G226600 chr6D 79.435 248 47 3 154 397 106076692 106076939 4.520000e-39 172.0
13 TraesCS5B01G226600 chr3A 79.668 241 46 2 154 391 722659240 722659480 1.630000e-38 171.0
14 TraesCS5B01G226600 chr1D 79.508 244 47 2 160 400 292273983 292273740 1.630000e-38 171.0
15 TraesCS5B01G226600 chr7B 90.152 132 10 1 2105 2236 456487963 456488091 5.850000e-38 169.0
16 TraesCS5B01G226600 chr6A 79.253 241 46 3 154 391 33904640 33904879 7.560000e-37 165.0
17 TraesCS5B01G226600 chr4D 79.339 242 45 4 154 391 43490107 43490347 7.560000e-37 165.0
18 TraesCS5B01G226600 chr2A 74.658 292 56 14 1000 1282 573337691 573337409 2.780000e-21 113.0
19 TraesCS5B01G226600 chr4B 96.970 33 1 0 538 570 486257649 486257617 4.750000e-04 56.5


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 TraesCS5B01G226600 chr5B 403695344 403698750 3406 False 6292.000 6292 100.0000 1 3407 1 chr5B.!!$F1 3406
1 TraesCS5B01G226600 chr5A 444521426 444525144 3718 False 1875.000 3567 93.0080 1 3407 2 chr5A.!!$F1 3406
2 TraesCS5B01G226600 chr5D 347481462 347484526 3064 True 731.025 1349 89.9605 519 3405 4 chr5D.!!$R1 2886

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
962 998 0.108424 CTCTCTCCCCACTCTTTGCG 60.108 60.0 0.0 0.0 0.00 4.85 F
1543 1589 0.173935 TGCCGATTTGACCGTATCGT 59.826 50.0 0.0 0.0 41.44 3.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2214 2265 0.110486 TTGCTCACCTTTCCCTCACC 59.890 55.0 0.0 0.0 0.00 4.02 R
3215 4064 0.035056 AATCACCCAGTAGCACCTGC 60.035 55.0 0.0 0.0 42.49 4.85 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
28 29 2.854424 GCACAACACACAAATGGAGTCG 60.854 50.000 0.00 0.00 0.00 4.18
29 30 2.354510 CACAACACACAAATGGAGTCGT 59.645 45.455 0.00 0.00 0.00 4.34
33 34 6.092122 CACAACACACAAATGGAGTCGTATAT 59.908 38.462 0.00 0.00 0.00 0.86
37 38 3.184379 CACAAATGGAGTCGTATATGCCG 59.816 47.826 0.00 0.00 0.00 5.69
41 42 3.570926 TGGAGTCGTATATGCCGAATC 57.429 47.619 14.74 14.74 45.58 2.52
46 47 3.191581 AGTCGTATATGCCGAATCTCCAG 59.808 47.826 1.47 0.00 35.89 3.86
48 49 2.263077 GTATATGCCGAATCTCCAGCG 58.737 52.381 0.00 0.00 0.00 5.18
49 50 0.681733 ATATGCCGAATCTCCAGCGT 59.318 50.000 0.00 0.00 0.00 5.07
65 66 0.882042 GCGTGGCCACCATAGATCTG 60.882 60.000 29.95 13.43 35.28 2.90
73 74 3.071602 GCCACCATAGATCTGGAGCTTTA 59.928 47.826 5.18 0.00 39.73 1.85
80 81 6.407412 CCATAGATCTGGAGCTTTACTTGTCA 60.407 42.308 5.18 0.00 38.69 3.58
91 92 4.391830 GCTTTACTTGTCATGGATCGAACA 59.608 41.667 0.00 0.00 0.00 3.18
110 111 3.953201 CGCTAGGGTTAGGGTTACG 57.047 57.895 0.00 0.00 35.67 3.18
112 113 0.249197 GCTAGGGTTAGGGTTACGCG 60.249 60.000 3.53 3.53 34.06 6.01
114 115 0.324275 TAGGGTTAGGGTTACGCGGT 60.324 55.000 12.47 0.00 34.06 5.68
134 135 2.123251 GGCGATCTGGGGGAGAGA 60.123 66.667 0.00 0.00 32.80 3.10
142 143 1.306141 TGGGGGAGAGAATGCGAGT 60.306 57.895 0.00 0.00 0.00 4.18
156 157 4.357947 GAGTGTGCGGGTCGAGCA 62.358 66.667 17.59 5.21 42.99 4.26
177 178 7.161773 AGCAAGAGAATGAGAGAGATATAGC 57.838 40.000 0.00 0.00 0.00 2.97
181 182 7.377766 AGAGAATGAGAGAGATATAGCGAAC 57.622 40.000 0.00 0.00 0.00 3.95
183 184 6.007076 AGAATGAGAGAGATATAGCGAACCA 58.993 40.000 0.00 0.00 0.00 3.67
184 185 6.491745 AGAATGAGAGAGATATAGCGAACCAA 59.508 38.462 0.00 0.00 0.00 3.67
221 222 0.255033 GTAAGGACGGAGGGGCAAAT 59.745 55.000 0.00 0.00 0.00 2.32
231 232 2.101415 GGAGGGGCAAATATGTCAAAGC 59.899 50.000 0.00 0.00 30.82 3.51
235 236 3.306641 GGGGCAAATATGTCAAAGCAACA 60.307 43.478 0.00 0.00 30.82 3.33
236 237 4.314121 GGGCAAATATGTCAAAGCAACAA 58.686 39.130 0.00 0.00 30.82 2.83
242 243 3.715628 ATGTCAAAGCAACAACCAGTC 57.284 42.857 0.00 0.00 0.00 3.51
243 244 1.748493 TGTCAAAGCAACAACCAGTCC 59.252 47.619 0.00 0.00 0.00 3.85
249 250 0.951558 GCAACAACCAGTCCGTGATT 59.048 50.000 0.00 0.00 0.00 2.57
267 268 5.181245 CGTGATTAAACAACCTTGACTGGAT 59.819 40.000 0.00 0.00 0.00 3.41
269 270 5.476599 TGATTAAACAACCTTGACTGGATGG 59.523 40.000 0.00 0.00 34.67 3.51
282 283 3.283751 ACTGGATGGAAACGACACAAAA 58.716 40.909 0.00 0.00 0.00 2.44
291 292 1.523758 ACGACACAAAAGGGCATCTC 58.476 50.000 0.00 0.00 0.00 2.75
307 308 6.995091 AGGGCATCTCTATAAGTGAAATTGAC 59.005 38.462 0.00 0.00 0.00 3.18
312 313 6.403049 TCTCTATAAGTGAAATTGACGGCAA 58.597 36.000 5.94 5.94 38.60 4.52
317 318 2.554032 AGTGAAATTGACGGCAAAGAGG 59.446 45.455 8.31 0.00 37.59 3.69
318 319 2.293399 GTGAAATTGACGGCAAAGAGGT 59.707 45.455 8.31 0.00 37.59 3.85
335 336 5.573337 AGAGGTAAATTTGAGCATGCTTC 57.427 39.130 23.61 15.22 0.00 3.86
336 337 5.012239 AGAGGTAAATTTGAGCATGCTTCA 58.988 37.500 23.61 17.66 0.00 3.02
341 342 7.662669 AGGTAAATTTGAGCATGCTTCAAAATT 59.337 29.630 30.86 29.62 37.00 1.82
342 343 8.934825 GGTAAATTTGAGCATGCTTCAAAATTA 58.065 29.630 30.86 28.97 37.00 1.40
352 353 5.240013 TGCTTCAAAATTAGGGGCAAATT 57.760 34.783 0.00 0.00 0.00 1.82
358 359 6.229733 TCAAAATTAGGGGCAAATTTGAGTG 58.770 36.000 22.31 0.00 36.81 3.51
359 360 6.042552 TCAAAATTAGGGGCAAATTTGAGTGA 59.957 34.615 22.31 6.10 36.81 3.41
375 376 3.009033 TGAGTGATGGGTTTGAGTTAGGG 59.991 47.826 0.00 0.00 0.00 3.53
376 377 3.256704 AGTGATGGGTTTGAGTTAGGGA 58.743 45.455 0.00 0.00 0.00 4.20
379 380 2.943036 TGGGTTTGAGTTAGGGACAC 57.057 50.000 0.00 0.00 0.00 3.67
400 401 5.761234 ACACACGTGTAAATGTCCTTACATT 59.239 36.000 22.90 0.00 45.59 2.71
434 436 6.777213 AAAAAGGTGTTTGTGTGTATGGTA 57.223 33.333 0.00 0.00 0.00 3.25
469 473 5.595952 GTCAATGCCTCTTTTCCCATTCTAT 59.404 40.000 0.00 0.00 0.00 1.98
518 522 4.402155 TCAGTGGCAAACTCAATCAAAAGT 59.598 37.500 0.00 0.00 36.83 2.66
521 525 6.756074 CAGTGGCAAACTCAATCAAAAGTTTA 59.244 34.615 0.00 0.00 42.31 2.01
575 580 5.407084 TCACAACCATTACATGTACGTTGAG 59.593 40.000 28.99 24.36 35.16 3.02
596 601 7.587037 TGAGTTGAATCCAAGATTCAAAACT 57.413 32.000 26.11 21.91 45.88 2.66
685 711 3.305398 AGGAGAGCCGAAATATTAGCG 57.695 47.619 4.22 4.22 39.96 4.26
737 763 4.545610 CCTTGCTATTTGCGTTCTTTGAA 58.454 39.130 0.00 0.00 46.63 2.69
948 984 0.179045 GCTCGCTCTCCTCTCTCTCT 60.179 60.000 0.00 0.00 0.00 3.10
962 998 0.108424 CTCTCTCCCCACTCTTTGCG 60.108 60.000 0.00 0.00 0.00 4.85
1094 1131 1.768077 CAGGTCTGGATCCCCTCCC 60.768 68.421 9.90 3.99 44.23 4.30
1101 1141 1.006227 GGATCCCCTCCCCCTCTTT 59.994 63.158 0.00 0.00 38.19 2.52
1104 1144 0.427685 ATCCCCTCCCCCTCTTTTCT 59.572 55.000 0.00 0.00 0.00 2.52
1105 1145 0.550147 TCCCCTCCCCCTCTTTTCTG 60.550 60.000 0.00 0.00 0.00 3.02
1118 1158 4.393371 CCTCTTTTCTGGACGATTTTCTCC 59.607 45.833 0.00 0.00 0.00 3.71
1122 1162 5.429681 TTTCTGGACGATTTTCTCCCATA 57.570 39.130 0.00 0.00 0.00 2.74
1123 1163 5.429681 TTCTGGACGATTTTCTCCCATAA 57.570 39.130 0.00 0.00 0.00 1.90
1303 1345 2.099062 CGCGTGGCTTTGCATCTC 59.901 61.111 0.00 0.00 0.00 2.75
1308 1350 2.554142 CGTGGCTTTGCATCTCTATGA 58.446 47.619 0.00 0.00 34.84 2.15
1332 1374 7.277539 TGAAAATTCTTGATTGTTTCGCTTTGT 59.722 29.630 0.00 0.00 0.00 2.83
1341 1383 4.340894 TGTTTCGCTTTGTCATGATAGC 57.659 40.909 14.13 14.13 0.00 2.97
1342 1384 3.750652 TGTTTCGCTTTGTCATGATAGCA 59.249 39.130 20.39 4.70 33.29 3.49
1357 1399 8.401709 GTCATGATAGCAGTATTCGATATCTCA 58.598 37.037 0.00 0.00 0.00 3.27
1389 1431 4.074970 GTGGATGAGTTGGATTCTTGTGT 58.925 43.478 0.00 0.00 0.00 3.72
1390 1432 4.154918 GTGGATGAGTTGGATTCTTGTGTC 59.845 45.833 0.00 0.00 0.00 3.67
1393 1435 4.422073 TGAGTTGGATTCTTGTGTCTGT 57.578 40.909 0.00 0.00 0.00 3.41
1394 1436 5.545063 TGAGTTGGATTCTTGTGTCTGTA 57.455 39.130 0.00 0.00 0.00 2.74
1396 1438 5.934043 TGAGTTGGATTCTTGTGTCTGTATG 59.066 40.000 0.00 0.00 0.00 2.39
1397 1439 6.114187 AGTTGGATTCTTGTGTCTGTATGA 57.886 37.500 0.00 0.00 0.00 2.15
1399 1441 7.170965 AGTTGGATTCTTGTGTCTGTATGATT 58.829 34.615 0.00 0.00 0.00 2.57
1400 1442 8.321353 AGTTGGATTCTTGTGTCTGTATGATTA 58.679 33.333 0.00 0.00 0.00 1.75
1402 1444 8.667076 TGGATTCTTGTGTCTGTATGATTATG 57.333 34.615 0.00 0.00 0.00 1.90
1403 1445 8.267183 TGGATTCTTGTGTCTGTATGATTATGT 58.733 33.333 0.00 0.00 0.00 2.29
1404 1446 8.554528 GGATTCTTGTGTCTGTATGATTATGTG 58.445 37.037 0.00 0.00 0.00 3.21
1405 1447 6.908870 TCTTGTGTCTGTATGATTATGTGC 57.091 37.500 0.00 0.00 0.00 4.57
1406 1448 5.817296 TCTTGTGTCTGTATGATTATGTGCC 59.183 40.000 0.00 0.00 0.00 5.01
1408 1450 3.059597 GTGTCTGTATGATTATGTGCCGC 60.060 47.826 0.00 0.00 0.00 6.53
1439 1483 4.872691 GGATTATCTCCATCTTACGCATGG 59.127 45.833 0.00 0.00 44.26 3.66
1481 1527 5.425630 AGTATCTTTTAGGCCTTTACCACG 58.574 41.667 12.58 0.00 0.00 4.94
1484 1530 1.816074 TTTAGGCCTTTACCACGCAG 58.184 50.000 12.58 0.00 0.00 5.18
1495 1541 0.606604 ACCACGCAGATTACCGACTT 59.393 50.000 0.00 0.00 0.00 3.01
1501 1547 2.285220 CGCAGATTACCGACTTGATTGG 59.715 50.000 0.00 0.00 37.97 3.16
1506 1552 0.616371 TACCGACTTGATTGGGGTGG 59.384 55.000 0.00 0.00 35.88 4.61
1537 1583 2.225068 AGTAGATGCCGATTTGACCG 57.775 50.000 0.00 0.00 0.00 4.79
1543 1589 0.173935 TGCCGATTTGACCGTATCGT 59.826 50.000 0.00 0.00 41.44 3.73
1544 1590 0.850856 GCCGATTTGACCGTATCGTC 59.149 55.000 0.00 0.00 41.44 4.20
1545 1591 1.799917 GCCGATTTGACCGTATCGTCA 60.800 52.381 0.00 0.00 41.44 4.35
1554 1600 4.359706 TGACCGTATCGTCAATCTGATTG 58.640 43.478 21.51 21.51 39.78 2.67
1573 1619 8.265055 TCTGATTGATATTTAGACCGTTTCCTT 58.735 33.333 0.00 0.00 0.00 3.36
1574 1620 8.208718 TGATTGATATTTAGACCGTTTCCTTG 57.791 34.615 0.00 0.00 0.00 3.61
1612 1658 4.407296 AGTTATTCCTTTTGGTGGTTTGCA 59.593 37.500 0.00 0.00 41.38 4.08
1614 1660 3.467374 TTCCTTTTGGTGGTTTGCATC 57.533 42.857 0.00 0.00 41.38 3.91
1724 1770 7.966111 TGCTGCATTTCAACAATATTTCAATC 58.034 30.769 0.00 0.00 0.00 2.67
1750 1796 9.849166 CGTAGTATTTATTTTGGTGGTTCAATT 57.151 29.630 0.00 0.00 0.00 2.32
1849 1898 7.529158 TGCTCAGTTGTGTTGATTGTATTATG 58.471 34.615 0.00 0.00 0.00 1.90
1866 1915 2.336945 ATGCGATCAGATTGGAAGCA 57.663 45.000 0.00 0.00 38.32 3.91
1873 1922 4.499188 CGATCAGATTGGAAGCAATGCATT 60.499 41.667 5.99 5.99 0.00 3.56
1876 1925 7.361457 CGATCAGATTGGAAGCAATGCATTATA 60.361 37.037 12.53 0.00 0.00 0.98
1903 1952 2.295349 ACCAGCAAAGCAAACTCTCATG 59.705 45.455 0.00 0.00 0.00 3.07
1905 1954 3.005050 CCAGCAAAGCAAACTCTCATGAA 59.995 43.478 0.00 0.00 0.00 2.57
1912 1961 4.670765 AGCAAACTCTCATGAAGGGAATT 58.329 39.130 0.00 0.00 0.00 2.17
1926 1975 4.851639 AGGGAATTAATGTCACAGCTCT 57.148 40.909 0.00 0.00 0.00 4.09
1937 1986 2.291741 GTCACAGCTCTTTTGGTCCTTG 59.708 50.000 0.00 0.00 0.00 3.61
1944 1995 3.381590 GCTCTTTTGGTCCTTGTGACTTT 59.618 43.478 0.00 0.00 43.89 2.66
1945 1996 4.142160 GCTCTTTTGGTCCTTGTGACTTTT 60.142 41.667 0.00 0.00 43.89 2.27
1949 2000 5.828299 TTTGGTCCTTGTGACTTTTACAG 57.172 39.130 0.00 0.00 43.89 2.74
1953 2004 4.381411 GTCCTTGTGACTTTTACAGCTCT 58.619 43.478 0.00 0.00 41.03 4.09
2011 2062 3.192844 AGATGCTTCTTCCATGCTTGTTG 59.807 43.478 0.00 0.00 0.00 3.33
2012 2063 1.000060 TGCTTCTTCCATGCTTGTTGC 60.000 47.619 0.00 0.00 43.25 4.17
2043 2094 6.074356 CGGAGGACATTTTTGTGTTTGAATTC 60.074 38.462 0.00 0.00 31.16 2.17
2051 2102 6.660887 TTTTGTGTTTGAATTCTGCCTTTC 57.339 33.333 7.05 0.00 0.00 2.62
2055 2106 6.913170 TGTGTTTGAATTCTGCCTTTCTATC 58.087 36.000 7.05 0.00 0.00 2.08
2069 2120 5.649831 GCCTTTCTATCTGTCTTTGGTTGAT 59.350 40.000 0.00 0.00 0.00 2.57
2102 2153 3.244596 ACCAGATGGCTCATGATCTGATG 60.245 47.826 20.69 10.61 45.80 3.07
2103 2154 3.244596 CCAGATGGCTCATGATCTGATGT 60.245 47.826 20.69 0.69 45.80 3.06
2214 2265 0.735632 GAGTGCTCTCTGGAACTGCG 60.736 60.000 8.54 0.00 37.68 5.18
2264 2315 8.271458 TGCCTTACAACCATCTAATCTCATTAA 58.729 33.333 0.00 0.00 0.00 1.40
2265 2316 9.120538 GCCTTACAACCATCTAATCTCATTAAA 57.879 33.333 0.00 0.00 0.00 1.52
2611 2662 7.080353 TCTGAATGCATGTTGAATCTACTTG 57.920 36.000 0.00 6.41 0.00 3.16
2631 2682 6.337356 ACTTGTGTTAATTTGGTTTCACCTG 58.663 36.000 0.00 0.00 39.58 4.00
2656 2707 7.882791 TGGCATTCGTGGTTATTGATCTATAAT 59.117 33.333 11.87 0.00 0.00 1.28
2686 2737 1.134551 GTTCCTCACTCTCATGCCCTC 60.135 57.143 0.00 0.00 0.00 4.30
2690 2741 1.220206 CACTCTCATGCCCTCGCTT 59.780 57.895 0.00 0.00 35.36 4.68
2700 2751 3.080121 CCTCGCTTCCCTGCTCCT 61.080 66.667 0.00 0.00 0.00 3.69
2736 2787 3.644966 ACACTTGAGAAACTTCACCCA 57.355 42.857 0.00 0.00 0.00 4.51
2737 2788 4.170468 ACACTTGAGAAACTTCACCCAT 57.830 40.909 0.00 0.00 0.00 4.00
2739 2790 4.339247 ACACTTGAGAAACTTCACCCATTG 59.661 41.667 0.00 0.00 0.00 2.82
2740 2791 3.319122 ACTTGAGAAACTTCACCCATTGC 59.681 43.478 0.00 0.00 0.00 3.56
2743 2794 1.963515 AGAAACTTCACCCATTGCACC 59.036 47.619 0.00 0.00 0.00 5.01
2744 2795 1.686052 GAAACTTCACCCATTGCACCA 59.314 47.619 0.00 0.00 0.00 4.17
2746 2797 0.185901 ACTTCACCCATTGCACCACT 59.814 50.000 0.00 0.00 0.00 4.00
2747 2798 1.423541 ACTTCACCCATTGCACCACTA 59.576 47.619 0.00 0.00 0.00 2.74
2749 2800 1.357137 TCACCCATTGCACCACTAGA 58.643 50.000 0.00 0.00 0.00 2.43
2750 2801 1.915489 TCACCCATTGCACCACTAGAT 59.085 47.619 0.00 0.00 0.00 1.98
2751 2802 2.308570 TCACCCATTGCACCACTAGATT 59.691 45.455 0.00 0.00 0.00 2.40
2752 2803 2.424601 CACCCATTGCACCACTAGATTG 59.575 50.000 0.00 0.00 0.00 2.67
2754 2805 3.091545 CCCATTGCACCACTAGATTGTT 58.908 45.455 0.00 0.00 0.00 2.83
2755 2806 3.511146 CCCATTGCACCACTAGATTGTTT 59.489 43.478 0.00 0.00 0.00 2.83
2756 2807 4.021192 CCCATTGCACCACTAGATTGTTTT 60.021 41.667 0.00 0.00 0.00 2.43
2757 2808 5.184864 CCCATTGCACCACTAGATTGTTTTA 59.815 40.000 0.00 0.00 0.00 1.52
2759 2810 5.699097 TTGCACCACTAGATTGTTTTACC 57.301 39.130 0.00 0.00 0.00 2.85
2760 2811 4.720046 TGCACCACTAGATTGTTTTACCA 58.280 39.130 0.00 0.00 0.00 3.25
2761 2812 5.321102 TGCACCACTAGATTGTTTTACCAT 58.679 37.500 0.00 0.00 0.00 3.55
2762 2813 5.182950 TGCACCACTAGATTGTTTTACCATG 59.817 40.000 0.00 0.00 0.00 3.66
2763 2814 5.640732 CACCACTAGATTGTTTTACCATGC 58.359 41.667 0.00 0.00 0.00 4.06
2765 2816 4.949856 CCACTAGATTGTTTTACCATGCCT 59.050 41.667 0.00 0.00 0.00 4.75
2769 2820 7.120579 CACTAGATTGTTTTACCATGCCTGTTA 59.879 37.037 0.00 0.00 0.00 2.41
2772 3317 7.547227 AGATTGTTTTACCATGCCTGTTAATC 58.453 34.615 0.00 0.00 0.00 1.75
2811 3356 2.079158 TCTGCGAAGGCTGAAAGATTG 58.921 47.619 0.00 0.00 43.10 2.67
2839 3433 8.921670 GGTTAATAGTGCATTTGTTTTAGGTTG 58.078 33.333 0.00 0.00 0.00 3.77
2849 3443 8.655970 GCATTTGTTTTAGGTTGATTATTGTCC 58.344 33.333 0.00 0.00 0.00 4.02
2850 3444 9.150348 CATTTGTTTTAGGTTGATTATTGTCCC 57.850 33.333 0.00 0.00 0.00 4.46
2856 3462 1.676006 GTTGATTATTGTCCCGGGCTG 59.324 52.381 18.49 0.00 0.00 4.85
2864 3470 2.041430 TCCCGGGCTGGATTGGTA 59.959 61.111 18.49 0.00 42.00 3.25
2873 3479 2.648059 GCTGGATTGGTAGAACATGCT 58.352 47.619 0.00 0.00 0.00 3.79
2883 3489 2.775911 AGAACATGCTGCTTGCTCTA 57.224 45.000 16.81 0.00 43.37 2.43
2898 3614 1.694696 GCTCTACCCTTCGGATTCCAT 59.305 52.381 3.09 0.00 0.00 3.41
2909 3625 6.321181 CCCTTCGGATTCCATGAAAGATAAAA 59.679 38.462 3.09 0.00 0.00 1.52
2910 3626 7.196331 CCTTCGGATTCCATGAAAGATAAAAC 58.804 38.462 3.09 0.00 0.00 2.43
2932 3648 4.854399 CACTTTGCGTGGAAAGTTATTCA 58.146 39.130 15.57 0.00 42.33 2.57
2933 3649 4.675114 CACTTTGCGTGGAAAGTTATTCAC 59.325 41.667 15.57 0.00 42.33 3.18
2952 3668 0.954452 CGGAGTGCTTCCTTGCTTTT 59.046 50.000 6.32 0.00 44.41 2.27
2991 3709 4.733165 CCATATCCCAGATTCACCACAAT 58.267 43.478 0.00 0.00 0.00 2.71
2995 3713 4.860802 TCCCAGATTCACCACAATATGT 57.139 40.909 0.00 0.00 0.00 2.29
2996 3714 5.966853 TCCCAGATTCACCACAATATGTA 57.033 39.130 0.00 0.00 0.00 2.29
2997 3715 5.928976 TCCCAGATTCACCACAATATGTAG 58.071 41.667 0.00 0.00 0.00 2.74
2999 3717 4.516698 CCAGATTCACCACAATATGTAGGC 59.483 45.833 0.00 0.00 0.00 3.93
3000 3718 4.212004 CAGATTCACCACAATATGTAGGCG 59.788 45.833 0.00 0.00 0.00 5.52
3001 3719 3.897141 TTCACCACAATATGTAGGCGA 57.103 42.857 0.00 0.00 0.00 5.54
3002 3720 3.452755 TCACCACAATATGTAGGCGAG 57.547 47.619 0.00 0.00 0.00 5.03
3003 3721 1.867233 CACCACAATATGTAGGCGAGC 59.133 52.381 0.00 0.00 0.00 5.03
3004 3722 1.484653 ACCACAATATGTAGGCGAGCA 59.515 47.619 0.00 0.00 0.00 4.26
3005 3723 2.093181 ACCACAATATGTAGGCGAGCAA 60.093 45.455 0.00 0.00 0.00 3.91
3006 3724 2.942376 CCACAATATGTAGGCGAGCAAA 59.058 45.455 0.00 0.00 0.00 3.68
3009 3727 3.118408 ACAATATGTAGGCGAGCAAAGGA 60.118 43.478 0.00 0.00 0.00 3.36
3010 3728 2.890808 TATGTAGGCGAGCAAAGGAG 57.109 50.000 0.00 0.00 0.00 3.69
3012 3730 1.815840 GTAGGCGAGCAAAGGAGGC 60.816 63.158 0.00 0.00 0.00 4.70
3013 3731 3.031417 TAGGCGAGCAAAGGAGGCC 62.031 63.158 0.00 0.00 44.07 5.19
3014 3732 4.416738 GGCGAGCAAAGGAGGCCT 62.417 66.667 3.86 3.86 40.59 5.19
3015 3733 3.130160 GCGAGCAAAGGAGGCCTG 61.130 66.667 12.00 0.00 32.13 4.85
3016 3734 2.437359 CGAGCAAAGGAGGCCTGG 60.437 66.667 12.00 0.00 32.13 4.45
3018 3736 1.075659 GAGCAAAGGAGGCCTGGTT 59.924 57.895 12.00 0.00 32.13 3.67
3019 3737 1.228675 AGCAAAGGAGGCCTGGTTG 60.229 57.895 12.00 12.76 32.13 3.77
3020 3738 2.935740 GCAAAGGAGGCCTGGTTGC 61.936 63.158 22.20 22.20 39.25 4.17
3021 3739 1.531365 CAAAGGAGGCCTGGTTGCA 60.531 57.895 12.00 0.00 32.13 4.08
3022 3740 0.901580 CAAAGGAGGCCTGGTTGCAT 60.902 55.000 12.00 0.00 32.13 3.96
3023 3741 0.613012 AAAGGAGGCCTGGTTGCATC 60.613 55.000 12.00 0.00 41.12 3.91
3024 3742 1.504275 AAGGAGGCCTGGTTGCATCT 61.504 55.000 12.00 0.00 41.55 2.90
3025 3743 1.000396 GGAGGCCTGGTTGCATCTT 60.000 57.895 12.00 0.00 41.55 2.40
3026 3744 1.318158 GGAGGCCTGGTTGCATCTTG 61.318 60.000 12.00 0.00 41.55 3.02
3027 3745 1.941999 GAGGCCTGGTTGCATCTTGC 61.942 60.000 12.00 0.00 45.29 4.01
3053 3799 2.500098 TGGAAACGAAGATAGGTGAGGG 59.500 50.000 0.00 0.00 0.00 4.30
3080 3826 9.519191 TCTATCACAATGGAGATTCTTTCAAAA 57.481 29.630 0.00 0.00 0.00 2.44
3090 3836 8.786898 TGGAGATTCTTTCAAAAATGAGTACAG 58.213 33.333 0.00 0.00 0.00 2.74
3092 3838 7.597386 AGATTCTTTCAAAAATGAGTACAGCC 58.403 34.615 0.00 0.00 0.00 4.85
3093 3839 6.959639 TTCTTTCAAAAATGAGTACAGCCT 57.040 33.333 0.00 0.00 0.00 4.58
3096 3842 2.819608 TCAAAAATGAGTACAGCCTGGC 59.180 45.455 11.65 11.65 0.00 4.85
3098 3844 0.392998 AAATGAGTACAGCCTGGCGG 60.393 55.000 17.47 17.47 0.00 6.13
3117 3944 2.772287 GGAGCATGAGTAATAGCCACC 58.228 52.381 0.00 0.00 0.00 4.61
3119 3946 3.433598 GGAGCATGAGTAATAGCCACCAA 60.434 47.826 0.00 0.00 0.00 3.67
3120 3947 4.392940 GAGCATGAGTAATAGCCACCAAT 58.607 43.478 0.00 0.00 0.00 3.16
3138 3965 7.548780 GCCACCAATTTTATCAGAGCAAATTTA 59.451 33.333 0.00 0.00 29.49 1.40
3151 3978 3.129287 AGCAAATTTACCGAAGATGCCAG 59.871 43.478 0.00 0.00 0.00 4.85
3155 3982 1.558167 TTACCGAAGATGCCAGCCCA 61.558 55.000 0.00 0.00 0.00 5.36
3165 3992 0.322816 TGCCAGCCCAGAAGATTGAC 60.323 55.000 0.00 0.00 0.00 3.18
3215 4064 2.476619 GTCAAGGTGAACGAGACACATG 59.523 50.000 0.00 0.00 39.65 3.21
3217 4066 0.392706 AGGTGAACGAGACACATGCA 59.607 50.000 0.00 0.00 39.65 3.96
3229 4078 1.028330 CACATGCAGGTGCTACTGGG 61.028 60.000 19.60 0.00 42.66 4.45
3230 4079 1.300963 CATGCAGGTGCTACTGGGT 59.699 57.895 3.18 0.00 42.66 4.51
3231 4080 1.028330 CATGCAGGTGCTACTGGGTG 61.028 60.000 3.18 0.00 42.66 4.61
3237 4109 2.489329 CAGGTGCTACTGGGTGATTTTG 59.511 50.000 0.92 0.00 34.84 2.44
3241 4113 3.689649 GTGCTACTGGGTGATTTTGTAGG 59.310 47.826 0.00 0.00 33.35 3.18
3251 4123 4.278419 GGTGATTTTGTAGGAGCAACAACT 59.722 41.667 0.00 0.00 36.61 3.16
3277 4149 5.488341 GTTCCTACCACATGTTATCACTGT 58.512 41.667 0.00 0.00 0.00 3.55
3285 4157 6.127451 ACCACATGTTATCACTGTCGATTCTA 60.127 38.462 0.00 0.00 0.00 2.10
3300 4172 6.861572 TGTCGATTCTACGGAATTTATAGCAG 59.138 38.462 0.00 0.00 41.68 4.24
3303 4175 7.594015 TCGATTCTACGGAATTTATAGCAGTTC 59.406 37.037 0.00 0.00 41.68 3.01
3374 4251 2.405357 CGAGTCTGACTGTAGTTTTGCG 59.595 50.000 16.28 5.24 0.00 4.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 4.570772 GCATATACGACTCCATTTGTGTGT 59.429 41.667 0.00 0.00 0.00 3.72
28 29 2.263077 CGCTGGAGATTCGGCATATAC 58.737 52.381 0.00 0.00 38.88 1.47
29 30 1.893137 ACGCTGGAGATTCGGCATATA 59.107 47.619 0.00 0.00 38.88 0.86
33 34 2.125552 CACGCTGGAGATTCGGCA 60.126 61.111 0.00 0.00 38.88 5.69
37 38 2.109126 GTGGCCACGCTGGAGATTC 61.109 63.158 22.49 0.00 40.96 2.52
41 42 2.930385 CTATGGTGGCCACGCTGGAG 62.930 65.000 29.08 16.90 40.96 3.86
46 47 0.882042 CAGATCTATGGTGGCCACGC 60.882 60.000 29.08 21.49 35.80 5.34
48 49 1.071385 CTCCAGATCTATGGTGGCCAC 59.929 57.143 28.57 28.57 41.43 5.01
49 50 1.427809 CTCCAGATCTATGGTGGCCA 58.572 55.000 0.00 0.00 41.43 5.36
65 66 3.557595 CGATCCATGACAAGTAAAGCTCC 59.442 47.826 0.00 0.00 0.00 4.70
73 74 2.337583 CGTGTTCGATCCATGACAAGT 58.662 47.619 0.00 0.00 39.71 3.16
80 81 0.389391 CCCTAGCGTGTTCGATCCAT 59.611 55.000 0.00 0.00 39.71 3.41
91 92 1.106285 CGTAACCCTAACCCTAGCGT 58.894 55.000 0.00 0.00 0.00 5.07
110 111 4.899239 CCCAGATCGCCTCACCGC 62.899 72.222 0.00 0.00 0.00 5.68
112 113 3.866582 CCCCCAGATCGCCTCACC 61.867 72.222 0.00 0.00 0.00 4.02
114 115 2.444706 CTCCCCCAGATCGCCTCA 60.445 66.667 0.00 0.00 0.00 3.86
126 127 0.460987 CACACTCGCATTCTCTCCCC 60.461 60.000 0.00 0.00 0.00 4.81
134 135 2.742372 GACCCGCACACTCGCATT 60.742 61.111 0.00 0.00 0.00 3.56
142 143 3.573772 CTCTTGCTCGACCCGCACA 62.574 63.158 0.00 0.00 37.07 4.57
155 156 7.376435 TCGCTATATCTCTCTCATTCTCTTG 57.624 40.000 0.00 0.00 0.00 3.02
156 157 7.094377 GGTTCGCTATATCTCTCTCATTCTCTT 60.094 40.741 0.00 0.00 0.00 2.85
177 178 1.136110 GGGCCCAAACATATTGGTTCG 59.864 52.381 19.95 0.00 37.88 3.95
181 182 1.566211 TGTGGGCCCAAACATATTGG 58.434 50.000 30.64 0.15 39.25 3.16
183 184 2.831565 ACATGTGGGCCCAAACATATT 58.168 42.857 30.64 13.90 35.28 1.28
184 185 2.548464 ACATGTGGGCCCAAACATAT 57.452 45.000 30.64 13.93 35.28 1.78
221 222 3.568007 GGACTGGTTGTTGCTTTGACATA 59.432 43.478 0.00 0.00 0.00 2.29
231 232 4.035792 TGTTTAATCACGGACTGGTTGTTG 59.964 41.667 0.00 0.00 0.00 3.33
235 236 3.566742 GGTTGTTTAATCACGGACTGGTT 59.433 43.478 0.00 0.00 0.00 3.67
236 237 3.143728 GGTTGTTTAATCACGGACTGGT 58.856 45.455 0.00 0.00 0.00 4.00
242 243 4.320202 CCAGTCAAGGTTGTTTAATCACGG 60.320 45.833 0.00 0.00 0.00 4.94
243 244 4.513692 TCCAGTCAAGGTTGTTTAATCACG 59.486 41.667 0.00 0.00 0.00 4.35
249 250 4.715534 TCCATCCAGTCAAGGTTGTTTA 57.284 40.909 0.00 0.00 0.00 2.01
267 268 0.741915 GCCCTTTTGTGTCGTTTCCA 59.258 50.000 0.00 0.00 0.00 3.53
269 270 2.293399 AGATGCCCTTTTGTGTCGTTTC 59.707 45.455 0.00 0.00 0.00 2.78
282 283 6.995091 GTCAATTTCACTTATAGAGATGCCCT 59.005 38.462 0.00 0.00 0.00 5.19
291 292 7.072177 TCTTTGCCGTCAATTTCACTTATAG 57.928 36.000 0.00 0.00 31.33 1.31
307 308 3.057596 TGCTCAAATTTACCTCTTTGCCG 60.058 43.478 0.00 0.00 33.40 5.69
312 313 5.477984 TGAAGCATGCTCAAATTTACCTCTT 59.522 36.000 22.93 0.00 0.00 2.85
317 318 9.962759 CTAATTTTGAAGCATGCTCAAATTTAC 57.037 29.630 30.56 15.34 34.01 2.01
318 319 9.153721 CCTAATTTTGAAGCATGCTCAAATTTA 57.846 29.630 30.56 29.71 34.01 1.40
335 336 6.229733 TCACTCAAATTTGCCCCTAATTTTG 58.770 36.000 13.54 0.00 34.01 2.44
336 337 6.432403 TCACTCAAATTTGCCCCTAATTTT 57.568 33.333 13.54 0.00 34.01 1.82
341 342 3.364549 CCATCACTCAAATTTGCCCCTA 58.635 45.455 13.54 0.00 0.00 3.53
342 343 2.181975 CCATCACTCAAATTTGCCCCT 58.818 47.619 13.54 0.00 0.00 4.79
352 353 4.506625 CCCTAACTCAAACCCATCACTCAA 60.507 45.833 0.00 0.00 0.00 3.02
358 359 3.244770 TGTGTCCCTAACTCAAACCCATC 60.245 47.826 0.00 0.00 0.00 3.51
359 360 2.714250 TGTGTCCCTAACTCAAACCCAT 59.286 45.455 0.00 0.00 0.00 4.00
375 376 4.746115 TGTAAGGACATTTACACGTGTGTC 59.254 41.667 30.83 25.84 43.74 3.67
376 377 4.695396 TGTAAGGACATTTACACGTGTGT 58.305 39.130 30.83 19.70 46.87 3.72
413 415 5.442391 AGTACCATACACACAAACACCTTT 58.558 37.500 0.00 0.00 0.00 3.11
415 417 4.699925 AGTACCATACACACAAACACCT 57.300 40.909 0.00 0.00 0.00 4.00
480 484 2.810274 CCACTGAGTTGATCAACACCAG 59.190 50.000 34.68 34.68 43.47 4.00
481 485 2.849942 CCACTGAGTTGATCAACACCA 58.150 47.619 33.92 28.03 43.47 4.17
575 580 9.528018 TGTAAAGTTTTGAATCTTGGATTCAAC 57.472 29.630 25.59 19.13 44.67 3.18
624 644 7.801716 TTGGCTAGCTAACATTATGGTTTAG 57.198 36.000 15.72 0.00 32.29 1.85
688 714 6.743172 CCTGTCGAAAGAAAAAGCTTTATAGC 59.257 38.462 13.10 2.43 45.25 2.97
689 715 7.244192 CCCTGTCGAAAGAAAAAGCTTTATAG 58.756 38.462 13.10 1.81 45.01 1.31
690 716 6.349033 GCCCTGTCGAAAGAAAAAGCTTTATA 60.349 38.462 13.10 0.00 45.01 0.98
691 717 5.564848 GCCCTGTCGAAAGAAAAAGCTTTAT 60.565 40.000 13.10 0.00 45.01 1.40
776 803 1.941812 GTTGTCAGTCAACGGCCTG 59.058 57.895 0.00 0.00 45.23 4.85
829 865 0.725117 GTAAATGGGCCAGACGTTCG 59.275 55.000 13.78 0.00 0.00 3.95
935 971 0.923358 GTGGGGAGAGAGAGAGGAGA 59.077 60.000 0.00 0.00 0.00 3.71
948 984 1.600636 CTTGCGCAAAGAGTGGGGA 60.601 57.895 25.01 0.00 40.50 4.81
1094 1131 4.327680 AGAAAATCGTCCAGAAAAGAGGG 58.672 43.478 0.00 0.00 0.00 4.30
1101 1141 5.429681 TTATGGGAGAAAATCGTCCAGAA 57.570 39.130 0.00 0.00 34.14 3.02
1104 1144 5.359576 CCAAATTATGGGAGAAAATCGTCCA 59.640 40.000 0.00 0.00 46.27 4.02
1105 1145 5.831997 CCAAATTATGGGAGAAAATCGTCC 58.168 41.667 0.23 0.00 46.27 4.79
1122 1162 4.961438 ACAAATCAGAAGCCACCAAATT 57.039 36.364 0.00 0.00 0.00 1.82
1123 1163 4.559300 CGAACAAATCAGAAGCCACCAAAT 60.559 41.667 0.00 0.00 0.00 2.32
1289 1329 4.970662 TTTCATAGAGATGCAAAGCCAC 57.029 40.909 0.00 0.00 32.62 5.01
1291 1331 6.803642 AGAATTTTCATAGAGATGCAAAGCC 58.196 36.000 0.00 0.00 32.74 4.35
1303 1345 8.679288 AGCGAAACAATCAAGAATTTTCATAG 57.321 30.769 0.00 0.00 0.00 2.23
1308 1350 7.277539 TGACAAAGCGAAACAATCAAGAATTTT 59.722 29.630 0.00 0.00 0.00 1.82
1332 1374 8.511604 TGAGATATCGAATACTGCTATCATGA 57.488 34.615 0.00 0.00 0.00 3.07
1341 1383 9.133627 CCATACAAACTGAGATATCGAATACTG 57.866 37.037 0.00 0.00 0.00 2.74
1342 1384 8.861086 ACCATACAAACTGAGATATCGAATACT 58.139 33.333 0.00 0.00 0.00 2.12
1357 1399 4.042809 TCCAACTCATCCACCATACAAACT 59.957 41.667 0.00 0.00 0.00 2.66
1389 1431 3.751479 AGCGGCACATAATCATACAGA 57.249 42.857 1.45 0.00 0.00 3.41
1390 1432 5.922739 TTTAGCGGCACATAATCATACAG 57.077 39.130 1.45 0.00 0.00 2.74
1393 1435 5.181056 CCACATTTAGCGGCACATAATCATA 59.819 40.000 1.45 0.00 0.00 2.15
1394 1436 4.022935 CCACATTTAGCGGCACATAATCAT 60.023 41.667 1.45 0.00 0.00 2.45
1396 1438 3.563808 TCCACATTTAGCGGCACATAATC 59.436 43.478 1.45 0.00 0.00 1.75
1397 1439 3.550820 TCCACATTTAGCGGCACATAAT 58.449 40.909 1.45 0.00 0.00 1.28
1399 1441 2.700722 TCCACATTTAGCGGCACATA 57.299 45.000 1.45 0.00 0.00 2.29
1400 1442 2.057137 ATCCACATTTAGCGGCACAT 57.943 45.000 1.45 0.00 0.00 3.21
1402 1444 3.815401 AGATAATCCACATTTAGCGGCAC 59.185 43.478 1.45 0.00 0.00 5.01
1403 1445 4.065088 GAGATAATCCACATTTAGCGGCA 58.935 43.478 1.45 0.00 0.00 5.69
1404 1446 4.670227 GAGATAATCCACATTTAGCGGC 57.330 45.455 0.00 0.00 0.00 6.53
1418 1462 5.745312 TCCATGCGTAAGATGGAGATAAT 57.255 39.130 0.00 0.00 43.93 1.28
1434 1478 4.660789 AAAAGTTGATAGCCATCCATGC 57.339 40.909 0.00 0.00 0.00 4.06
1439 1483 9.771534 AAGATACTCTAAAAGTTGATAGCCATC 57.228 33.333 0.00 0.00 39.55 3.51
1472 1518 2.601763 GTCGGTAATCTGCGTGGTAAAG 59.398 50.000 0.00 0.00 0.00 1.85
1479 1525 2.930040 CAATCAAGTCGGTAATCTGCGT 59.070 45.455 0.00 0.00 0.00 5.24
1481 1527 2.614057 CCCAATCAAGTCGGTAATCTGC 59.386 50.000 0.00 0.00 0.00 4.26
1484 1530 2.943033 CACCCCAATCAAGTCGGTAATC 59.057 50.000 0.00 0.00 0.00 1.75
1495 1541 1.000233 GTGCATCCCACCCCAATCA 60.000 57.895 0.00 0.00 38.55 2.57
1501 1547 2.143876 ACTAATTGTGCATCCCACCC 57.856 50.000 0.00 0.00 44.01 4.61
1506 1552 3.187227 CGGCATCTACTAATTGTGCATCC 59.813 47.826 0.00 0.00 37.53 3.51
1544 1590 9.869844 GAAACGGTCTAAATATCAATCAGATTG 57.130 33.333 16.12 16.12 41.57 2.67
1545 1591 9.057089 GGAAACGGTCTAAATATCAATCAGATT 57.943 33.333 0.00 0.00 38.19 2.40
1549 1595 7.827236 ACAAGGAAACGGTCTAAATATCAATCA 59.173 33.333 0.00 0.00 0.00 2.57
1554 1600 8.882415 TGATACAAGGAAACGGTCTAAATATC 57.118 34.615 0.00 0.00 0.00 1.63
1557 1603 7.282450 GGAATGATACAAGGAAACGGTCTAAAT 59.718 37.037 0.00 0.00 0.00 1.40
1612 1658 6.604396 TCCAAATTTGATACTCATGCACTGAT 59.396 34.615 19.86 0.00 32.10 2.90
1614 1660 6.127814 ACTCCAAATTTGATACTCATGCACTG 60.128 38.462 19.86 0.00 0.00 3.66
1634 1680 0.105964 CTGTCGGACAACCAACTCCA 59.894 55.000 12.54 0.00 35.59 3.86
1635 1681 0.106149 ACTGTCGGACAACCAACTCC 59.894 55.000 12.54 0.00 35.59 3.85
1724 1770 9.849166 AATTGAACCACCAAAATAAATACTACG 57.151 29.630 0.00 0.00 0.00 3.51
1750 1796 8.545472 AGGCACCACTAGAAACAAATAAGTATA 58.455 33.333 0.00 0.00 0.00 1.47
1753 1799 5.631119 AGGCACCACTAGAAACAAATAAGT 58.369 37.500 0.00 0.00 0.00 2.24
1812 1861 3.627577 ACAACTGAGCAACCTAGTGTTTG 59.372 43.478 0.00 0.00 34.00 2.93
1820 1869 2.418368 TCAACACAACTGAGCAACCT 57.582 45.000 0.00 0.00 0.00 3.50
1849 1898 2.857489 GCATTGCTTCCAATCTGATCGC 60.857 50.000 0.16 0.00 39.60 4.58
1866 1915 8.299570 GCTTTGCTGGTAGTAATATAATGCATT 58.700 33.333 17.56 17.56 0.00 3.56
1873 1922 8.265055 AGAGTTTGCTTTGCTGGTAGTAATATA 58.735 33.333 0.00 0.00 0.00 0.86
1876 1925 5.316987 AGAGTTTGCTTTGCTGGTAGTAAT 58.683 37.500 0.00 0.00 0.00 1.89
1903 1952 5.189180 AGAGCTGTGACATTAATTCCCTTC 58.811 41.667 0.00 0.00 0.00 3.46
1905 1954 4.851639 AGAGCTGTGACATTAATTCCCT 57.148 40.909 0.00 0.00 0.00 4.20
1912 1961 4.072131 GGACCAAAAGAGCTGTGACATTA 58.928 43.478 0.00 0.00 0.00 1.90
1937 1986 6.147821 TGAGCAAATAGAGCTGTAAAAGTCAC 59.852 38.462 0.00 0.00 43.58 3.67
1944 1995 5.405935 TGAGTGAGCAAATAGAGCTGTAA 57.594 39.130 0.00 0.00 43.58 2.41
1945 1996 5.003692 CTGAGTGAGCAAATAGAGCTGTA 57.996 43.478 0.00 0.00 43.58 2.74
1993 2044 1.706443 GCAACAAGCATGGAAGAAGC 58.294 50.000 0.00 0.00 44.79 3.86
2011 2062 3.243401 ACAAAAATGTCCTCCGAACTTGC 60.243 43.478 0.00 0.00 0.00 4.01
2012 2063 4.202010 ACACAAAAATGTCCTCCGAACTTG 60.202 41.667 0.00 0.00 0.00 3.16
2018 2069 4.300189 TCAAACACAAAAATGTCCTCCG 57.700 40.909 0.00 0.00 30.55 4.63
2019 2070 6.986231 AGAATTCAAACACAAAAATGTCCTCC 59.014 34.615 8.44 0.00 30.55 4.30
2043 2094 4.583871 ACCAAAGACAGATAGAAAGGCAG 58.416 43.478 0.00 0.00 0.00 4.85
2055 2106 6.623486 TGCAATATTCATCAACCAAAGACAG 58.377 36.000 0.00 0.00 0.00 3.51
2069 2120 3.633525 GAGCCATCTGGTTGCAATATTCA 59.366 43.478 0.59 0.00 37.57 2.57
2083 2134 4.708576 AACATCAGATCATGAGCCATCT 57.291 40.909 7.49 0.00 42.53 2.90
2102 2153 3.195610 GTGGGGAATCTGGAAATGGAAAC 59.804 47.826 0.00 0.00 0.00 2.78
2103 2154 3.440127 GTGGGGAATCTGGAAATGGAAA 58.560 45.455 0.00 0.00 0.00 3.13
2214 2265 0.110486 TTGCTCACCTTTCCCTCACC 59.890 55.000 0.00 0.00 0.00 4.02
2264 2315 9.331282 GACTACATAAATGATAGGTTTGAGCTT 57.669 33.333 0.00 0.00 0.00 3.74
2265 2316 8.709308 AGACTACATAAATGATAGGTTTGAGCT 58.291 33.333 0.00 0.00 0.00 4.09
2266 2317 8.894768 AGACTACATAAATGATAGGTTTGAGC 57.105 34.615 0.00 0.00 0.00 4.26
2279 2330 9.383519 ACACGAATCAAATGAGACTACATAAAT 57.616 29.630 0.00 0.00 0.00 1.40
2631 2682 7.667043 TTATAGATCAATAACCACGAATGCC 57.333 36.000 0.00 0.00 0.00 4.40
2686 2737 2.042831 CCAAAGGAGCAGGGAAGCG 61.043 63.158 0.00 0.00 40.15 4.68
2700 2751 5.189928 TCAAGTGTACTTTTCTGCTCCAAA 58.810 37.500 0.00 0.00 33.11 3.28
2736 2787 5.772672 TGGTAAAACAATCTAGTGGTGCAAT 59.227 36.000 0.00 0.00 0.00 3.56
2737 2788 5.133941 TGGTAAAACAATCTAGTGGTGCAA 58.866 37.500 0.00 0.00 0.00 4.08
2739 2790 5.640732 CATGGTAAAACAATCTAGTGGTGC 58.359 41.667 0.00 0.00 0.00 5.01
2740 2791 5.393027 GGCATGGTAAAACAATCTAGTGGTG 60.393 44.000 0.00 0.00 0.00 4.17
2743 2794 5.415701 ACAGGCATGGTAAAACAATCTAGTG 59.584 40.000 2.31 0.00 0.00 2.74
2744 2795 5.570320 ACAGGCATGGTAAAACAATCTAGT 58.430 37.500 2.31 0.00 0.00 2.57
2746 2797 8.588290 ATTAACAGGCATGGTAAAACAATCTA 57.412 30.769 13.51 0.00 41.81 1.98
2747 2798 6.909550 TTAACAGGCATGGTAAAACAATCT 57.090 33.333 6.36 0.00 35.64 2.40
2749 2800 7.480760 AGATTAACAGGCATGGTAAAACAAT 57.519 32.000 13.51 0.00 41.81 2.71
2750 2801 6.909550 AGATTAACAGGCATGGTAAAACAA 57.090 33.333 13.51 0.00 41.81 2.83
2751 2802 6.491745 TGAAGATTAACAGGCATGGTAAAACA 59.508 34.615 13.51 8.13 41.81 2.83
2752 2803 6.919721 TGAAGATTAACAGGCATGGTAAAAC 58.080 36.000 13.51 10.29 41.81 2.43
2754 2805 7.309744 CCTTTGAAGATTAACAGGCATGGTAAA 60.310 37.037 13.51 0.00 41.81 2.01
2755 2806 6.152661 CCTTTGAAGATTAACAGGCATGGTAA 59.847 38.462 11.79 11.79 42.66 2.85
2756 2807 5.652014 CCTTTGAAGATTAACAGGCATGGTA 59.348 40.000 2.31 0.00 0.00 3.25
2757 2808 4.463891 CCTTTGAAGATTAACAGGCATGGT 59.536 41.667 2.31 0.00 0.00 3.55
2759 2810 5.902613 TCCTTTGAAGATTAACAGGCATG 57.097 39.130 0.00 0.00 0.00 4.06
2760 2811 5.774690 TGTTCCTTTGAAGATTAACAGGCAT 59.225 36.000 0.00 0.00 0.00 4.40
2761 2812 5.136828 TGTTCCTTTGAAGATTAACAGGCA 58.863 37.500 0.00 0.00 0.00 4.75
2762 2813 5.705609 TGTTCCTTTGAAGATTAACAGGC 57.294 39.130 0.00 0.00 0.00 4.85
2763 2814 9.546428 AAAAATGTTCCTTTGAAGATTAACAGG 57.454 29.630 0.00 0.00 41.97 4.00
2765 2816 9.883142 ACAAAAATGTTCCTTTGAAGATTAACA 57.117 25.926 1.80 0.00 41.97 2.41
2769 2820 7.225341 GCAGACAAAAATGTTCCTTTGAAGATT 59.775 33.333 1.80 0.00 43.96 2.40
2772 3317 5.051508 CGCAGACAAAAATGTTCCTTTGAAG 60.052 40.000 1.80 0.00 36.30 3.02
2792 3337 1.808945 ACAATCTTTCAGCCTTCGCAG 59.191 47.619 0.00 0.00 37.52 5.18
2811 3356 8.085909 ACCTAAAACAAATGCACTATTAACCAC 58.914 33.333 0.00 0.00 0.00 4.16
2839 3433 0.472471 TCCAGCCCGGGACAATAATC 59.528 55.000 29.31 2.84 34.36 1.75
2842 3436 0.182537 CAATCCAGCCCGGGACAATA 59.817 55.000 29.31 4.83 40.44 1.90
2843 3437 1.076777 CAATCCAGCCCGGGACAAT 60.077 57.895 29.31 8.62 40.44 2.71
2844 3438 2.354729 CAATCCAGCCCGGGACAA 59.645 61.111 29.31 6.15 40.44 3.18
2845 3439 3.727258 CCAATCCAGCCCGGGACA 61.727 66.667 29.31 3.67 40.44 4.02
2849 3443 0.463833 GTTCTACCAATCCAGCCCGG 60.464 60.000 0.00 0.00 0.00 5.73
2850 3444 0.251916 TGTTCTACCAATCCAGCCCG 59.748 55.000 0.00 0.00 0.00 6.13
2856 3462 2.648059 AGCAGCATGTTCTACCAATCC 58.352 47.619 0.00 0.00 39.31 3.01
2873 3479 2.241435 ATCCGAAGGGTAGAGCAAGCA 61.241 52.381 0.00 0.00 43.57 3.91
2910 3626 4.675114 GTGAATAACTTTCCACGCAAAGTG 59.325 41.667 8.13 0.00 44.28 3.16
2948 3664 1.676006 CGCCCAGCTATAACCCAAAAG 59.324 52.381 0.00 0.00 0.00 2.27
2952 3668 2.508928 GCGCCCAGCTATAACCCA 59.491 61.111 0.00 0.00 44.04 4.51
2991 3709 1.412710 CCTCCTTTGCTCGCCTACATA 59.587 52.381 0.00 0.00 0.00 2.29
2995 3713 2.584608 GCCTCCTTTGCTCGCCTA 59.415 61.111 0.00 0.00 0.00 3.93
2996 3714 4.416738 GGCCTCCTTTGCTCGCCT 62.417 66.667 0.00 0.00 36.65 5.52
2997 3715 4.416738 AGGCCTCCTTTGCTCGCC 62.417 66.667 0.00 0.00 40.03 5.54
2999 3717 2.437359 CCAGGCCTCCTTTGCTCG 60.437 66.667 0.00 0.00 0.00 5.03
3000 3718 1.075659 AACCAGGCCTCCTTTGCTC 59.924 57.895 0.00 0.00 0.00 4.26
3001 3719 1.228675 CAACCAGGCCTCCTTTGCT 60.229 57.895 0.00 0.00 0.00 3.91
3002 3720 2.935740 GCAACCAGGCCTCCTTTGC 61.936 63.158 21.05 21.05 39.25 3.68
3003 3721 0.901580 ATGCAACCAGGCCTCCTTTG 60.902 55.000 0.00 7.78 0.00 2.77
3004 3722 0.613012 GATGCAACCAGGCCTCCTTT 60.613 55.000 0.00 0.00 0.00 3.11
3005 3723 1.000396 GATGCAACCAGGCCTCCTT 60.000 57.895 0.00 0.00 0.00 3.36
3006 3724 1.504275 AAGATGCAACCAGGCCTCCT 61.504 55.000 0.00 0.00 0.00 3.69
3009 3727 1.980772 GCAAGATGCAACCAGGCCT 60.981 57.895 0.00 0.00 44.26 5.19
3010 3728 2.575461 GCAAGATGCAACCAGGCC 59.425 61.111 0.00 0.00 44.26 5.19
3019 3737 1.987770 CGTTTCCAACATGCAAGATGC 59.012 47.619 0.00 0.00 45.29 3.91
3020 3738 3.557577 TCGTTTCCAACATGCAAGATG 57.442 42.857 0.00 0.00 0.00 2.90
3021 3739 3.820467 TCTTCGTTTCCAACATGCAAGAT 59.180 39.130 0.00 0.00 0.00 2.40
3022 3740 3.210227 TCTTCGTTTCCAACATGCAAGA 58.790 40.909 0.00 0.00 0.00 3.02
3023 3741 3.624326 TCTTCGTTTCCAACATGCAAG 57.376 42.857 0.00 0.00 0.00 4.01
3024 3742 4.155826 CCTATCTTCGTTTCCAACATGCAA 59.844 41.667 0.00 0.00 0.00 4.08
3025 3743 3.689161 CCTATCTTCGTTTCCAACATGCA 59.311 43.478 0.00 0.00 0.00 3.96
3026 3744 3.689649 ACCTATCTTCGTTTCCAACATGC 59.310 43.478 0.00 0.00 0.00 4.06
3027 3745 4.935205 TCACCTATCTTCGTTTCCAACATG 59.065 41.667 0.00 0.00 0.00 3.21
3028 3746 5.160607 TCACCTATCTTCGTTTCCAACAT 57.839 39.130 0.00 0.00 0.00 2.71
3029 3747 4.562757 CCTCACCTATCTTCGTTTCCAACA 60.563 45.833 0.00 0.00 0.00 3.33
3030 3748 3.933332 CCTCACCTATCTTCGTTTCCAAC 59.067 47.826 0.00 0.00 0.00 3.77
3031 3749 3.055385 CCCTCACCTATCTTCGTTTCCAA 60.055 47.826 0.00 0.00 0.00 3.53
3032 3750 2.500098 CCCTCACCTATCTTCGTTTCCA 59.500 50.000 0.00 0.00 0.00 3.53
3033 3751 2.500504 ACCCTCACCTATCTTCGTTTCC 59.499 50.000 0.00 0.00 0.00 3.13
3034 3752 3.447944 AGACCCTCACCTATCTTCGTTTC 59.552 47.826 0.00 0.00 0.00 2.78
3035 3753 3.442076 AGACCCTCACCTATCTTCGTTT 58.558 45.455 0.00 0.00 0.00 3.60
3036 3754 3.103080 AGACCCTCACCTATCTTCGTT 57.897 47.619 0.00 0.00 0.00 3.85
3037 3755 2.830651 AGACCCTCACCTATCTTCGT 57.169 50.000 0.00 0.00 0.00 3.85
3038 3756 4.216687 GTGATAGACCCTCACCTATCTTCG 59.783 50.000 0.00 0.00 40.95 3.79
3039 3757 5.141182 TGTGATAGACCCTCACCTATCTTC 58.859 45.833 0.00 0.00 41.87 2.87
3042 3760 5.279708 CCATTGTGATAGACCCTCACCTATC 60.280 48.000 0.00 0.00 41.87 2.08
3043 3761 4.594920 CCATTGTGATAGACCCTCACCTAT 59.405 45.833 1.37 0.00 41.87 2.57
3049 3795 5.306678 AGAATCTCCATTGTGATAGACCCTC 59.693 44.000 0.00 0.00 0.00 4.30
3053 3799 8.498054 TTGAAAGAATCTCCATTGTGATAGAC 57.502 34.615 0.00 0.00 0.00 2.59
3080 3826 1.221840 CCGCCAGGCTGTACTCATT 59.778 57.895 14.43 0.00 0.00 2.57
3087 3833 4.790962 CATGCTCCGCCAGGCTGT 62.791 66.667 14.43 0.00 37.47 4.40
3090 3836 2.593468 TTACTCATGCTCCGCCAGGC 62.593 60.000 0.00 0.00 37.47 4.85
3092 3838 2.681706 CTATTACTCATGCTCCGCCAG 58.318 52.381 0.00 0.00 0.00 4.85
3093 3839 1.270305 GCTATTACTCATGCTCCGCCA 60.270 52.381 0.00 0.00 0.00 5.69
3096 3842 2.408050 GTGGCTATTACTCATGCTCCG 58.592 52.381 0.00 0.00 0.00 4.63
3098 3844 3.475566 TGGTGGCTATTACTCATGCTC 57.524 47.619 0.00 0.00 0.00 4.26
3101 3847 8.849168 TGATAAAATTGGTGGCTATTACTCATG 58.151 33.333 0.00 0.00 0.00 3.07
3102 3848 8.995027 TGATAAAATTGGTGGCTATTACTCAT 57.005 30.769 0.00 0.00 0.00 2.90
3105 3851 7.229506 GCTCTGATAAAATTGGTGGCTATTACT 59.770 37.037 0.00 0.00 0.00 2.24
3107 3853 7.059788 TGCTCTGATAAAATTGGTGGCTATTA 58.940 34.615 0.00 0.00 0.00 0.98
3108 3854 5.893255 TGCTCTGATAAAATTGGTGGCTATT 59.107 36.000 0.00 0.00 0.00 1.73
3109 3855 5.448654 TGCTCTGATAAAATTGGTGGCTAT 58.551 37.500 0.00 0.00 0.00 2.97
3110 3856 4.854173 TGCTCTGATAAAATTGGTGGCTA 58.146 39.130 0.00 0.00 0.00 3.93
3111 3857 3.700538 TGCTCTGATAAAATTGGTGGCT 58.299 40.909 0.00 0.00 0.00 4.75
3117 3944 8.909708 TCGGTAAATTTGCTCTGATAAAATTG 57.090 30.769 6.23 1.59 34.58 2.32
3119 3946 8.956426 TCTTCGGTAAATTTGCTCTGATAAAAT 58.044 29.630 6.23 0.00 0.00 1.82
3120 3947 8.330466 TCTTCGGTAAATTTGCTCTGATAAAA 57.670 30.769 6.23 0.00 0.00 1.52
3138 3965 3.329889 TGGGCTGGCATCTTCGGT 61.330 61.111 2.88 0.00 0.00 4.69
3151 3978 3.567164 CACATATGGTCAATCTTCTGGGC 59.433 47.826 7.80 0.00 0.00 5.36
3165 3992 4.567537 TGACAGGGTCTTTTCCACATATGG 60.568 45.833 7.80 0.00 39.30 2.74
3180 4007 1.349026 CCTTGACAGTCATGACAGGGT 59.651 52.381 27.02 20.48 41.32 4.34
3183 4010 3.391506 TCACCTTGACAGTCATGACAG 57.608 47.619 27.02 21.51 32.75 3.51
3215 4064 0.035056 AATCACCCAGTAGCACCTGC 60.035 55.000 0.00 0.00 42.49 4.85
3217 4066 2.108250 ACAAAATCACCCAGTAGCACCT 59.892 45.455 0.00 0.00 0.00 4.00
3229 4078 5.438761 AGTTGTTGCTCCTACAAAATCAC 57.561 39.130 0.00 0.00 37.26 3.06
3230 4079 5.221224 CCAAGTTGTTGCTCCTACAAAATCA 60.221 40.000 1.45 0.00 37.26 2.57
3231 4080 5.221244 ACCAAGTTGTTGCTCCTACAAAATC 60.221 40.000 1.45 0.00 37.26 2.17
3237 4109 2.552743 GGAACCAAGTTGTTGCTCCTAC 59.447 50.000 1.45 0.00 33.93 3.18
3241 4113 2.552743 GGTAGGAACCAAGTTGTTGCTC 59.447 50.000 12.82 7.49 42.36 4.26
3271 4143 4.713824 AATTCCGTAGAATCGACAGTGA 57.286 40.909 0.00 0.00 42.03 3.41
3273 4145 6.862090 GCTATAAATTCCGTAGAATCGACAGT 59.138 38.462 0.00 0.00 42.03 3.55
3277 4149 6.978338 ACTGCTATAAATTCCGTAGAATCGA 58.022 36.000 0.00 0.00 42.03 3.59
3285 4157 6.260936 CCATTCTGAACTGCTATAAATTCCGT 59.739 38.462 0.00 0.00 0.00 4.69
3300 4172 4.437390 CGCCAAGAACATACCATTCTGAAC 60.437 45.833 0.00 0.00 36.52 3.18
3303 4175 2.355756 CCGCCAAGAACATACCATTCTG 59.644 50.000 0.00 0.00 36.52 3.02
3374 4251 1.953559 TCAGTTGCACAGAGTTCACC 58.046 50.000 0.00 0.00 0.00 4.02


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

AutoCloner maintained by Alex Coulton.