Multiple sequence alignment - TraesCS3B01G419000

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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 TraesCS3B01G419000 chr3B 100.000 3951 0 0 1 3951 655633667 655637617 0.000000e+00 7297.0
1 TraesCS3B01G419000 chr3B 90.299 134 12 1 1318 1450 118507269 118507402 1.460000e-39 174.0
2 TraesCS3B01G419000 chr3B 100.000 73 0 0 1 73 405945460 405945388 6.890000e-28 135.0
3 TraesCS3B01G419000 chr3B 100.000 72 0 0 1 72 405938044 405937973 2.480000e-27 134.0
4 TraesCS3B01G419000 chr3A 91.190 2395 136 40 1575 3923 638204298 638201933 0.000000e+00 3184.0
5 TraesCS3B01G419000 chr3A 88.166 1014 64 22 75 1067 638205648 638204670 0.000000e+00 1157.0
6 TraesCS3B01G419000 chr3A 90.991 222 16 2 1069 1286 638204633 638204412 2.990000e-76 296.0
7 TraesCS3B01G419000 chr3A 80.556 144 23 2 1315 1453 530173394 530173537 5.400000e-19 106.0
8 TraesCS3B01G419000 chr3A 100.000 30 0 0 3922 3951 638201851 638201822 5.520000e-04 56.5
9 TraesCS3B01G419000 chr3D 85.465 1548 132 54 2454 3951 496680295 496681799 0.000000e+00 1526.0
10 TraesCS3B01G419000 chr3D 91.037 993 61 12 1446 2425 496679318 496680295 0.000000e+00 1315.0
11 TraesCS3B01G419000 chr3D 91.024 791 46 10 302 1070 496678275 496679062 0.000000e+00 1044.0
12 TraesCS3B01G419000 chr3D 91.791 134 10 1 1318 1450 73206871 73207004 6.740000e-43 185.0
13 TraesCS3B01G419000 chr3D 82.870 216 21 9 3721 3921 496681097 496681311 3.140000e-41 180.0
14 TraesCS3B01G419000 chr7A 93.151 146 9 1 1309 1453 637915691 637915546 3.090000e-51 213.0
15 TraesCS3B01G419000 chr7B 91.429 140 11 1 1316 1454 106804097 106804236 1.450000e-44 191.0
16 TraesCS3B01G419000 chr4B 90.370 135 12 1 1320 1453 184302741 184302607 4.060000e-40 176.0
17 TraesCS3B01G419000 chr6A 100.000 73 0 0 1 73 65559538 65559610 6.890000e-28 135.0
18 TraesCS3B01G419000 chr6A 100.000 73 0 0 1 73 65566293 65566365 6.890000e-28 135.0
19 TraesCS3B01G419000 chr6B 83.688 141 21 2 1314 1453 183308242 183308381 8.910000e-27 132.0
20 TraesCS3B01G419000 chr4A 90.426 94 8 1 1318 1410 449398431 449398524 5.360000e-24 122.0
21 TraesCS3B01G419000 chr4A 94.444 72 3 1 3 73 659137153 659137224 4.170000e-20 110.0
22 TraesCS3B01G419000 chr2D 94.444 72 3 1 3 73 575965151 575965080 4.170000e-20 110.0
23 TraesCS3B01G419000 chr2D 90.909 77 5 2 3 77 575949223 575949147 6.980000e-18 102.0
24 TraesCS3B01G419000 chr2A 94.444 72 3 1 3 73 762400164 762400235 4.170000e-20 110.0
25 TraesCS3B01G419000 chr2A 91.667 72 3 1 3 74 565613541 565613473 3.250000e-16 97.1
26 TraesCS3B01G419000 chr5D 81.022 137 25 1 1318 1453 416418567 416418431 1.500000e-19 108.0


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 TraesCS3B01G419000 chr3B 655633667 655637617 3950 False 7297.000 7297 100.00000 1 3951 1 chr3B.!!$F2 3950
1 TraesCS3B01G419000 chr3A 638201822 638205648 3826 True 1173.375 3184 92.58675 75 3951 4 chr3A.!!$R1 3876
2 TraesCS3B01G419000 chr3D 496678275 496681799 3524 False 1016.250 1526 87.59900 302 3951 4 chr3D.!!$F2 3649

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
33 34 0.183492 ATGGCCACCGACATTAGCAT 59.817 50.0 8.16 0.00 0.0 3.79 F
703 722 0.251386 TCCTCTTCAGCTGTCGACCT 60.251 55.0 14.67 0.01 0.0 3.85 F
1590 1692 0.105593 ATAGAGCCATGACACTGCCG 59.894 55.0 0.00 0.00 0.0 5.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1220 1317 0.895559 AGCAGCCACTAAACAAGCCC 60.896 55.000 0.00 0.00 0.00 5.19 R
2175 2297 0.539669 AGCAAAACCTTTAGGGCGCT 60.540 50.000 7.64 8.86 40.27 5.92 R
3556 3732 1.007721 AGGAGATGTACTGGGCAGAGT 59.992 52.381 0.00 0.00 0.00 3.24 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
17 18 4.963815 GACGGTTGCCAAACATGG 57.036 55.556 0.00 0.00 38.10 3.66
25 26 2.961768 CCAAACATGGCCACCGAC 59.038 61.111 8.16 0.00 0.00 4.79
26 27 1.900981 CCAAACATGGCCACCGACA 60.901 57.895 8.16 0.00 0.00 4.35
27 28 1.250154 CCAAACATGGCCACCGACAT 61.250 55.000 8.16 0.00 0.00 3.06
28 29 0.602562 CAAACATGGCCACCGACATT 59.397 50.000 8.16 0.00 0.00 2.71
29 30 1.815613 CAAACATGGCCACCGACATTA 59.184 47.619 8.16 0.00 0.00 1.90
30 31 1.750193 AACATGGCCACCGACATTAG 58.250 50.000 8.16 0.00 0.00 1.73
31 32 0.748005 ACATGGCCACCGACATTAGC 60.748 55.000 8.16 0.00 0.00 3.09
32 33 0.747644 CATGGCCACCGACATTAGCA 60.748 55.000 8.16 0.00 0.00 3.49
33 34 0.183492 ATGGCCACCGACATTAGCAT 59.817 50.000 8.16 0.00 0.00 3.79
34 35 0.833949 TGGCCACCGACATTAGCATA 59.166 50.000 0.00 0.00 0.00 3.14
35 36 1.202639 TGGCCACCGACATTAGCATAG 60.203 52.381 0.00 0.00 0.00 2.23
36 37 1.070134 GGCCACCGACATTAGCATAGA 59.930 52.381 0.00 0.00 0.00 1.98
37 38 2.289694 GGCCACCGACATTAGCATAGAT 60.290 50.000 0.00 0.00 0.00 1.98
38 39 3.403038 GCCACCGACATTAGCATAGATT 58.597 45.455 0.00 0.00 0.00 2.40
39 40 4.562757 GGCCACCGACATTAGCATAGATTA 60.563 45.833 0.00 0.00 0.00 1.75
40 41 4.994852 GCCACCGACATTAGCATAGATTAA 59.005 41.667 0.00 0.00 0.00 1.40
41 42 5.107065 GCCACCGACATTAGCATAGATTAAC 60.107 44.000 0.00 0.00 0.00 2.01
42 43 5.989168 CCACCGACATTAGCATAGATTAACA 59.011 40.000 0.00 0.00 0.00 2.41
43 44 6.481976 CCACCGACATTAGCATAGATTAACAA 59.518 38.462 0.00 0.00 0.00 2.83
44 45 7.173218 CCACCGACATTAGCATAGATTAACAAT 59.827 37.037 0.00 0.00 0.00 2.71
45 46 8.559536 CACCGACATTAGCATAGATTAACAATT 58.440 33.333 0.00 0.00 0.00 2.32
46 47 9.772973 ACCGACATTAGCATAGATTAACAATTA 57.227 29.630 0.00 0.00 0.00 1.40
108 109 3.563808 TGTAGTGTCCATTGCAACAGTTC 59.436 43.478 0.00 0.00 31.68 3.01
123 124 0.836400 AGTTCCATGTCGACCACCCT 60.836 55.000 14.12 0.00 0.00 4.34
124 125 0.899720 GTTCCATGTCGACCACCCTA 59.100 55.000 14.12 0.00 0.00 3.53
125 126 1.485066 GTTCCATGTCGACCACCCTAT 59.515 52.381 14.12 0.00 0.00 2.57
126 127 2.696707 GTTCCATGTCGACCACCCTATA 59.303 50.000 14.12 0.00 0.00 1.31
176 184 1.750399 ATGTCGGCCATGCTGAACC 60.750 57.895 2.24 0.00 46.01 3.62
183 191 0.889994 GCCATGCTGAACCAACATCA 59.110 50.000 0.00 0.00 0.00 3.07
185 193 2.480759 GCCATGCTGAACCAACATCATC 60.481 50.000 0.00 0.00 0.00 2.92
195 203 5.827267 TGAACCAACATCATCAAAAGTCTGA 59.173 36.000 0.00 0.00 0.00 3.27
199 207 7.555087 ACCAACATCATCAAAAGTCTGAAAAA 58.445 30.769 0.00 0.00 0.00 1.94
235 243 8.871629 AAATATACACACCAATGTTAAGTCCA 57.128 30.769 0.00 0.00 36.72 4.02
236 244 9.474313 AAATATACACACCAATGTTAAGTCCAT 57.526 29.630 0.00 0.00 36.72 3.41
237 245 8.677148 ATATACACACCAATGTTAAGTCCATC 57.323 34.615 0.00 0.00 36.72 3.51
239 247 6.121776 ACACACCAATGTTAAGTCCATCTA 57.878 37.500 0.00 0.00 36.72 1.98
240 248 6.721318 ACACACCAATGTTAAGTCCATCTAT 58.279 36.000 0.00 0.00 36.72 1.98
241 249 7.857456 ACACACCAATGTTAAGTCCATCTATA 58.143 34.615 0.00 0.00 36.72 1.31
242 250 8.325787 ACACACCAATGTTAAGTCCATCTATAA 58.674 33.333 0.00 0.00 36.72 0.98
243 251 8.612619 CACACCAATGTTAAGTCCATCTATAAC 58.387 37.037 0.00 0.00 36.72 1.89
244 252 8.548877 ACACCAATGTTAAGTCCATCTATAACT 58.451 33.333 0.00 0.00 34.46 2.24
245 253 9.396022 CACCAATGTTAAGTCCATCTATAACTT 57.604 33.333 0.00 0.00 37.10 2.66
246 254 9.396022 ACCAATGTTAAGTCCATCTATAACTTG 57.604 33.333 0.00 0.00 35.08 3.16
247 255 9.613428 CCAATGTTAAGTCCATCTATAACTTGA 57.387 33.333 0.00 0.00 35.08 3.02
250 258 8.718102 TGTTAAGTCCATCTATAACTTGAAGC 57.282 34.615 0.00 0.00 35.08 3.86
253 261 5.923204 AGTCCATCTATAACTTGAAGCCTG 58.077 41.667 0.00 0.00 0.00 4.85
259 267 4.777896 TCTATAACTTGAAGCCTGGTGAGT 59.222 41.667 0.00 0.00 0.00 3.41
268 276 1.145738 AGCCTGGTGAGTTGGTTTCAT 59.854 47.619 0.00 0.00 0.00 2.57
270 278 2.862541 CCTGGTGAGTTGGTTTCATCA 58.137 47.619 0.00 0.00 34.66 3.07
271 279 2.554032 CCTGGTGAGTTGGTTTCATCAC 59.446 50.000 0.00 0.00 41.03 3.06
283 291 6.870971 TGGTTTCATCACAAAGTACCTAAC 57.129 37.500 0.00 0.00 0.00 2.34
288 296 6.620877 TCATCACAAAGTACCTAACCATCT 57.379 37.500 0.00 0.00 0.00 2.90
291 299 5.790593 TCACAAAGTACCTAACCATCTGAC 58.209 41.667 0.00 0.00 0.00 3.51
294 302 3.097342 AGTACCTAACCATCTGACGGT 57.903 47.619 0.00 0.00 38.85 4.83
296 304 3.446516 AGTACCTAACCATCTGACGGTTC 59.553 47.826 11.92 0.00 43.36 3.62
297 305 1.203994 ACCTAACCATCTGACGGTTCG 59.796 52.381 11.92 5.80 43.36 3.95
304 312 0.677288 ATCTGACGGTTCGGTGTCAA 59.323 50.000 0.00 0.00 43.91 3.18
340 348 4.880759 TGTTTTTCATTGTCCATTGCGAT 58.119 34.783 0.00 0.00 0.00 4.58
372 380 2.591753 CATGCCGACCACCCTGAT 59.408 61.111 0.00 0.00 0.00 2.90
375 383 0.398522 ATGCCGACCACCCTGATAGA 60.399 55.000 0.00 0.00 0.00 1.98
376 384 1.043116 TGCCGACCACCCTGATAGAG 61.043 60.000 0.00 0.00 0.00 2.43
377 385 1.043673 GCCGACCACCCTGATAGAGT 61.044 60.000 0.00 0.00 0.00 3.24
378 386 1.753141 GCCGACCACCCTGATAGAGTA 60.753 57.143 0.00 0.00 0.00 2.59
379 387 2.662866 CCGACCACCCTGATAGAGTAA 58.337 52.381 0.00 0.00 0.00 2.24
383 391 5.396436 CCGACCACCCTGATAGAGTAAATTT 60.396 44.000 0.00 0.00 0.00 1.82
384 393 6.183360 CCGACCACCCTGATAGAGTAAATTTA 60.183 42.308 0.00 0.00 0.00 1.40
388 397 9.628500 ACCACCCTGATAGAGTAAATTTATTTC 57.372 33.333 0.31 3.27 0.00 2.17
451 461 3.502572 GGCTTCAGGATTGCCGAC 58.497 61.111 0.00 0.00 39.96 4.79
494 513 7.261829 AGTGCTAGTACTTGTAGTATAGTGC 57.738 40.000 7.78 0.00 32.65 4.40
692 711 2.943690 CGTATCCGTCTCTTCCTCTTCA 59.056 50.000 0.00 0.00 0.00 3.02
702 721 0.603569 TTCCTCTTCAGCTGTCGACC 59.396 55.000 14.67 0.00 0.00 4.79
703 722 0.251386 TCCTCTTCAGCTGTCGACCT 60.251 55.000 14.67 0.01 0.00 3.85
704 723 0.605589 CCTCTTCAGCTGTCGACCTT 59.394 55.000 14.67 0.00 0.00 3.50
705 724 1.819288 CCTCTTCAGCTGTCGACCTTA 59.181 52.381 14.67 0.00 0.00 2.69
751 771 0.601558 CCTTTCCTCGTCGGTCTTGA 59.398 55.000 0.00 0.00 0.00 3.02
857 886 2.680352 GAGACCCTGCGTCCTCCA 60.680 66.667 0.00 0.00 43.08 3.86
975 1010 0.466555 CTCCTACTCCTCCTCCACGG 60.467 65.000 0.00 0.00 0.00 4.94
979 1014 2.164332 TACTCCTCCTCCACGGCCTT 62.164 60.000 0.00 0.00 0.00 4.35
1003 1038 2.696125 AGATCCGGGCCCCAATGT 60.696 61.111 18.66 5.42 0.00 2.71
1049 1084 3.618855 TAGGTGAGCCCCCTTCGCT 62.619 63.158 0.00 0.00 39.95 4.93
1077 1174 1.452108 CCTCCTGCCCGGATTGAAC 60.452 63.158 0.73 0.00 42.12 3.18
1082 1179 1.473434 CCTGCCCGGATTGAACTAGAC 60.473 57.143 0.73 0.00 33.16 2.59
1115 1212 2.106683 CGAGGGGTTTGGTCGATGC 61.107 63.158 0.00 0.00 35.70 3.91
1145 1242 1.129326 GGTCGATTGATTAGTCGCGG 58.871 55.000 6.13 0.00 37.74 6.46
1174 1271 2.992689 TGCGTGCGGGGAGAAGTA 60.993 61.111 0.00 0.00 0.00 2.24
1175 1272 2.508663 GCGTGCGGGGAGAAGTAC 60.509 66.667 0.00 0.00 0.00 2.73
1199 1296 1.514003 TAGAACGGTGCAATTGCGAA 58.486 45.000 24.58 6.13 45.83 4.70
1245 1342 4.201822 GCTTGTTTAGTGGCTGCTATGTAC 60.202 45.833 0.00 0.00 0.00 2.90
1246 1343 4.819105 TGTTTAGTGGCTGCTATGTACT 57.181 40.909 0.00 0.00 0.00 2.73
1248 1345 5.902681 TGTTTAGTGGCTGCTATGTACTAG 58.097 41.667 0.00 0.00 0.00 2.57
1249 1346 5.421056 TGTTTAGTGGCTGCTATGTACTAGT 59.579 40.000 0.00 0.00 0.00 2.57
1281 1382 2.006888 CTGTTGCCACCGGTTAGTATG 58.993 52.381 2.97 0.00 0.00 2.39
1286 1387 2.691526 TGCCACCGGTTAGTATGAGTAG 59.308 50.000 2.97 0.00 0.00 2.57
1287 1388 2.692041 GCCACCGGTTAGTATGAGTAGT 59.308 50.000 2.97 0.00 0.00 2.73
1289 1390 4.522022 GCCACCGGTTAGTATGAGTAGTAT 59.478 45.833 2.97 0.00 0.00 2.12
1292 1393 6.921857 CCACCGGTTAGTATGAGTAGTATTTG 59.078 42.308 2.97 0.00 0.00 2.32
1293 1394 7.417116 CCACCGGTTAGTATGAGTAGTATTTGT 60.417 40.741 2.97 0.00 0.00 2.83
1313 1414 6.877611 TTGTTTTTCTTCTATGAGGGTGTC 57.122 37.500 0.00 0.00 0.00 3.67
1318 1419 7.733773 TTTTCTTCTATGAGGGTGTCATCTA 57.266 36.000 0.00 0.00 42.80 1.98
1319 1420 6.716934 TTCTTCTATGAGGGTGTCATCTAC 57.283 41.667 0.00 0.00 42.80 2.59
1322 1423 4.730966 TCTATGAGGGTGTCATCTACTCC 58.269 47.826 0.00 0.00 42.80 3.85
1327 1428 1.033574 GGTGTCATCTACTCCCTCCG 58.966 60.000 0.00 0.00 35.99 4.63
1328 1429 1.685491 GGTGTCATCTACTCCCTCCGT 60.685 57.143 0.00 0.00 35.99 4.69
1329 1430 2.100989 GTGTCATCTACTCCCTCCGTT 58.899 52.381 0.00 0.00 0.00 4.44
1330 1431 2.099427 GTGTCATCTACTCCCTCCGTTC 59.901 54.545 0.00 0.00 0.00 3.95
1331 1432 1.334243 GTCATCTACTCCCTCCGTTCG 59.666 57.143 0.00 0.00 0.00 3.95
1332 1433 1.211212 TCATCTACTCCCTCCGTTCGA 59.789 52.381 0.00 0.00 0.00 3.71
1333 1434 2.022195 CATCTACTCCCTCCGTTCGAA 58.978 52.381 0.00 0.00 0.00 3.71
1334 1435 2.205022 TCTACTCCCTCCGTTCGAAA 57.795 50.000 0.00 0.00 0.00 3.46
1335 1436 2.731572 TCTACTCCCTCCGTTCGAAAT 58.268 47.619 0.00 0.00 0.00 2.17
1336 1437 3.889815 TCTACTCCCTCCGTTCGAAATA 58.110 45.455 0.00 0.00 0.00 1.40
1337 1438 4.467769 TCTACTCCCTCCGTTCGAAATAT 58.532 43.478 0.00 0.00 0.00 1.28
1338 1439 5.624159 TCTACTCCCTCCGTTCGAAATATA 58.376 41.667 0.00 0.00 0.00 0.86
1339 1440 6.064060 TCTACTCCCTCCGTTCGAAATATAA 58.936 40.000 0.00 0.00 0.00 0.98
1340 1441 5.197682 ACTCCCTCCGTTCGAAATATAAG 57.802 43.478 0.00 0.00 0.00 1.73
1341 1442 4.891756 ACTCCCTCCGTTCGAAATATAAGA 59.108 41.667 0.00 0.00 0.00 2.10
1342 1443 5.539193 ACTCCCTCCGTTCGAAATATAAGAT 59.461 40.000 0.00 0.00 0.00 2.40
1343 1444 5.779922 TCCCTCCGTTCGAAATATAAGATG 58.220 41.667 0.00 0.00 0.00 2.90
1344 1445 5.303589 TCCCTCCGTTCGAAATATAAGATGT 59.696 40.000 0.00 0.00 0.00 3.06
1345 1446 5.989777 CCCTCCGTTCGAAATATAAGATGTT 59.010 40.000 0.00 0.00 0.00 2.71
1346 1447 6.482308 CCCTCCGTTCGAAATATAAGATGTTT 59.518 38.462 0.00 0.00 0.00 2.83
1347 1448 7.012044 CCCTCCGTTCGAAATATAAGATGTTTT 59.988 37.037 0.00 0.00 0.00 2.43
1348 1449 9.037737 CCTCCGTTCGAAATATAAGATGTTTTA 57.962 33.333 0.00 0.00 0.00 1.52
1350 1451 8.545420 TCCGTTCGAAATATAAGATGTTTTAGC 58.455 33.333 0.00 0.00 0.00 3.09
1351 1452 8.548721 CCGTTCGAAATATAAGATGTTTTAGCT 58.451 33.333 0.00 0.00 0.00 3.32
1352 1453 9.916397 CGTTCGAAATATAAGATGTTTTAGCTT 57.084 29.630 0.00 0.00 38.77 3.74
1385 1486 8.771920 AATTGAATGTATCTAGACGTGTTTCA 57.228 30.769 0.00 0.00 0.00 2.69
1386 1487 7.812309 TTGAATGTATCTAGACGTGTTTCAG 57.188 36.000 0.00 0.00 0.00 3.02
1387 1488 6.920817 TGAATGTATCTAGACGTGTTTCAGT 58.079 36.000 0.00 0.00 0.00 3.41
1388 1489 6.806739 TGAATGTATCTAGACGTGTTTCAGTG 59.193 38.462 0.00 0.00 0.00 3.66
1389 1490 5.700722 TGTATCTAGACGTGTTTCAGTGT 57.299 39.130 0.00 0.00 0.00 3.55
1390 1491 5.458015 TGTATCTAGACGTGTTTCAGTGTG 58.542 41.667 0.00 0.00 0.00 3.82
1391 1492 4.585955 ATCTAGACGTGTTTCAGTGTGT 57.414 40.909 0.00 0.00 0.00 3.72
1392 1493 5.700722 ATCTAGACGTGTTTCAGTGTGTA 57.299 39.130 0.00 0.00 0.00 2.90
1393 1494 5.104562 TCTAGACGTGTTTCAGTGTGTAG 57.895 43.478 0.00 0.00 31.53 2.74
1394 1495 4.818005 TCTAGACGTGTTTCAGTGTGTAGA 59.182 41.667 0.00 0.00 35.59 2.59
1395 1496 4.585955 AGACGTGTTTCAGTGTGTAGAT 57.414 40.909 0.00 0.00 0.00 1.98
1396 1497 4.945246 AGACGTGTTTCAGTGTGTAGATT 58.055 39.130 0.00 0.00 0.00 2.40
1397 1498 4.982916 AGACGTGTTTCAGTGTGTAGATTC 59.017 41.667 0.00 0.00 0.00 2.52
1398 1499 4.689071 ACGTGTTTCAGTGTGTAGATTCA 58.311 39.130 0.00 0.00 0.00 2.57
1399 1500 5.113383 ACGTGTTTCAGTGTGTAGATTCAA 58.887 37.500 0.00 0.00 0.00 2.69
1400 1501 5.758296 ACGTGTTTCAGTGTGTAGATTCAAT 59.242 36.000 0.00 0.00 0.00 2.57
1401 1502 6.073765 ACGTGTTTCAGTGTGTAGATTCAATC 60.074 38.462 0.00 0.00 0.00 2.67
1402 1503 6.073819 CGTGTTTCAGTGTGTAGATTCAATCA 60.074 38.462 0.00 0.00 0.00 2.57
1403 1504 7.360353 CGTGTTTCAGTGTGTAGATTCAATCAT 60.360 37.037 0.00 0.00 0.00 2.45
1404 1505 8.292448 GTGTTTCAGTGTGTAGATTCAATCATT 58.708 33.333 0.00 0.00 0.00 2.57
1405 1506 8.849168 TGTTTCAGTGTGTAGATTCAATCATTT 58.151 29.630 0.00 0.00 0.00 2.32
1406 1507 9.683069 GTTTCAGTGTGTAGATTCAATCATTTT 57.317 29.630 0.00 0.00 0.00 1.82
1409 1510 9.725019 TCAGTGTGTAGATTCAATCATTTTAGT 57.275 29.630 0.00 0.00 0.00 2.24
1412 1513 9.478019 GTGTGTAGATTCAATCATTTTAGTTCG 57.522 33.333 0.00 0.00 0.00 3.95
1413 1514 9.214957 TGTGTAGATTCAATCATTTTAGTTCGT 57.785 29.630 0.00 0.00 0.00 3.85
1422 1523 9.745880 TCAATCATTTTAGTTCGTATCTAGTCC 57.254 33.333 0.00 0.00 0.00 3.85
1423 1524 9.529325 CAATCATTTTAGTTCGTATCTAGTCCA 57.471 33.333 0.00 0.00 0.00 4.02
1444 1545 9.512588 AGTCCATATTGAAATATCCAAGACATC 57.487 33.333 11.09 0.00 29.35 3.06
1445 1546 9.512588 GTCCATATTGAAATATCCAAGACATCT 57.487 33.333 0.00 0.00 29.35 2.90
1505 1606 6.343703 TGTCAGCATGTGATGGATATATAGC 58.656 40.000 0.00 0.00 37.56 2.97
1590 1692 0.105593 ATAGAGCCATGACACTGCCG 59.894 55.000 0.00 0.00 0.00 5.69
1604 1706 0.603569 CTGCCGTCTGTAGGTTGAGT 59.396 55.000 0.00 0.00 0.00 3.41
1628 1730 8.730680 AGTTTGCTAGTTATGTTGGTTGATAAG 58.269 33.333 0.00 0.00 0.00 1.73
1670 1773 8.715191 TTCAAAGATTTGTTTTATGTTGCTGT 57.285 26.923 5.29 0.00 39.18 4.40
1684 1787 0.602562 TGCTGTAATGTGCTTTGGCC 59.397 50.000 0.00 0.00 37.74 5.36
1746 1849 3.601443 TGGTTGTGTTTTGGACAAAGG 57.399 42.857 0.00 0.00 40.65 3.11
1754 1857 3.198635 TGTTTTGGACAAAGGGCATTTCA 59.801 39.130 0.00 0.00 34.69 2.69
1796 1899 3.458189 GGAATTACCTGACATGGAGACG 58.542 50.000 0.00 0.00 35.41 4.18
1845 1954 2.637382 TCACATAGCTGGGTCTGTTTGA 59.363 45.455 0.00 0.00 0.00 2.69
1873 1982 5.007823 GCGCTCTTCTATCACTGTCTAGTTA 59.992 44.000 0.00 0.00 34.07 2.24
1876 1985 7.041712 CGCTCTTCTATCACTGTCTAGTTATCA 60.042 40.741 0.00 0.00 34.07 2.15
1877 1986 8.792633 GCTCTTCTATCACTGTCTAGTTATCAT 58.207 37.037 0.00 0.00 34.07 2.45
1887 1996 8.993121 CACTGTCTAGTTATCATTGTCACTTTT 58.007 33.333 0.00 0.00 34.07 2.27
1911 2021 4.682778 AGGTTGTTACACTCTGTTGCTA 57.317 40.909 0.00 0.00 0.00 3.49
1948 2066 4.960938 TGTATGCATATGGTGTTCTCTCC 58.039 43.478 10.16 0.00 0.00 3.71
1976 2094 6.015772 GCAATCCTAGTGTTTGGTCCTTTTTA 60.016 38.462 0.00 0.00 0.00 1.52
1980 2098 9.628500 ATCCTAGTGTTTGGTCCTTTTTATATC 57.372 33.333 0.00 0.00 0.00 1.63
2006 2124 8.902806 CATTTATGTAACATCCCTGTACACATT 58.097 33.333 0.00 0.00 39.74 2.71
2131 2253 7.712639 GTCTTGTATGAGATTCTTATTCAGGCA 59.287 37.037 0.00 0.00 0.00 4.75
2175 2297 6.061441 ACATACCATGTGACAAAGAAACTGA 58.939 36.000 0.00 0.00 43.01 3.41
2179 2301 1.330521 TGTGACAAAGAAACTGAGCGC 59.669 47.619 0.00 0.00 0.00 5.92
2182 2304 0.179018 ACAAAGAAACTGAGCGCCCT 60.179 50.000 2.29 0.00 0.00 5.19
2238 2360 4.142403 GGCAATTGCTCAGTATGCTGTTAA 60.142 41.667 28.42 5.36 39.62 2.01
2443 2569 6.958752 CCGTGTATACATATGTGTGTTTTGTG 59.041 38.462 18.81 0.53 39.39 3.33
2444 2570 6.464519 CGTGTATACATATGTGTGTTTTGTGC 59.535 38.462 18.81 0.00 39.39 4.57
2554 2680 4.396166 CAGTAATGCCTAAACTCAACCCTG 59.604 45.833 0.00 0.00 0.00 4.45
2717 2843 4.170251 AGGTGAGGCTATTTCCTAGGTCTA 59.830 45.833 9.08 0.00 36.38 2.59
2749 2877 9.832445 ACATATTCCAGAATACGTGACTTAAAT 57.168 29.630 0.00 0.45 36.24 1.40
2754 2882 8.922058 TCCAGAATACGTGACTTAAATCTTAC 57.078 34.615 0.00 0.00 0.00 2.34
2800 2928 0.806102 CAGCATTACCACCTCGACCG 60.806 60.000 0.00 0.00 0.00 4.79
2824 2952 2.677836 GCATGAGCACCGAGAATTTGTA 59.322 45.455 0.00 0.00 41.58 2.41
2853 2981 3.682858 ACGTATGGTTACAACAGTCATGC 59.317 43.478 0.00 0.00 0.00 4.06
2881 3009 4.568760 GGTTCTGTTCTGAATGCTAGCTAC 59.431 45.833 17.23 7.77 0.00 3.58
2958 3086 4.621797 ACCCATCCTACTAGGTTGTAGT 57.378 45.455 10.93 6.42 38.49 2.73
3094 3222 8.688222 TGTAAATAGGGCTGGTATATCCATTA 57.312 34.615 0.00 0.00 46.12 1.90
3168 3296 7.894364 ACCCTTTGTACTTGTCTAGAAGATAGA 59.106 37.037 0.00 0.00 0.00 1.98
3211 3349 9.374838 CTTGGAAAATAAAGAAATGCAATAGCT 57.625 29.630 0.00 0.00 42.74 3.32
3238 3378 2.045926 GCAACCCTGCCGACTCAT 60.046 61.111 0.00 0.00 43.26 2.90
3292 3432 4.935808 AGTTATTCCTAAAGTGCCTTGTCG 59.064 41.667 0.00 0.00 0.00 4.35
3319 3459 4.268644 ACTCGAATGATCATTGCTGTTACG 59.731 41.667 25.37 18.80 0.00 3.18
3338 3478 6.153170 TGTTACGTACCCAGAAGATGTTGATA 59.847 38.462 0.00 0.00 0.00 2.15
3353 3493 0.188587 TGATATCTCAGCTCCGGGGT 59.811 55.000 1.62 0.00 0.00 4.95
3401 3541 2.104111 CTGTCCTGTGTTTGTGTCCCTA 59.896 50.000 0.00 0.00 0.00 3.53
3402 3542 2.708861 TGTCCTGTGTTTGTGTCCCTAT 59.291 45.455 0.00 0.00 0.00 2.57
3470 3614 2.026641 CAATAGCACCCACCAATCCTG 58.973 52.381 0.00 0.00 0.00 3.86
3471 3615 0.106519 ATAGCACCCACCAATCCTGC 60.107 55.000 0.00 0.00 0.00 4.85
3521 3697 2.254546 TTGCTTGGCTGGTATATCCG 57.745 50.000 0.00 0.00 39.52 4.18
3522 3698 1.419381 TGCTTGGCTGGTATATCCGA 58.581 50.000 0.00 0.00 39.52 4.55
3523 3699 1.977854 TGCTTGGCTGGTATATCCGAT 59.022 47.619 0.00 0.00 39.52 4.18
3524 3700 2.371841 TGCTTGGCTGGTATATCCGATT 59.628 45.455 0.00 0.00 39.52 3.34
3525 3701 3.181445 TGCTTGGCTGGTATATCCGATTT 60.181 43.478 0.00 0.00 39.52 2.17
3533 3709 7.504238 TGGCTGGTATATCCGATTTGTTTTATT 59.496 33.333 0.00 0.00 39.52 1.40
3556 3732 3.482436 ACGGTAAATTGGCAACTGAAGA 58.518 40.909 0.00 0.00 37.61 2.87
3577 3753 2.245028 ACTCTGCCCAGTACATCTCCTA 59.755 50.000 0.00 0.00 0.00 2.94
3578 3754 2.890311 CTCTGCCCAGTACATCTCCTAG 59.110 54.545 0.00 0.00 0.00 3.02
3624 3800 5.059833 CAGATAGCCTGGTACATCTTTTCC 58.940 45.833 0.00 0.00 39.23 3.13
3634 3816 4.263771 GGTACATCTTTTCCTTTCCTGGGA 60.264 45.833 0.00 0.00 0.00 4.37
3765 3948 4.509230 GCACTCGAATGATCATTGCTCTTA 59.491 41.667 25.37 3.73 0.00 2.10
3776 3959 5.178096 TCATTGCTCTTACCCAGATTTCA 57.822 39.130 0.00 0.00 0.00 2.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.963815 CCATGTTTGGCAACCGTC 57.036 55.556 0.00 0.00 35.85 4.79
8 9 1.250154 ATGTCGGTGGCCATGTTTGG 61.250 55.000 9.72 0.00 46.66 3.28
9 10 0.602562 AATGTCGGTGGCCATGTTTG 59.397 50.000 9.72 0.00 0.00 2.93
10 11 2.091541 CTAATGTCGGTGGCCATGTTT 58.908 47.619 9.72 0.00 0.00 2.83
11 12 1.750193 CTAATGTCGGTGGCCATGTT 58.250 50.000 9.72 0.49 0.00 2.71
12 13 0.748005 GCTAATGTCGGTGGCCATGT 60.748 55.000 9.72 0.00 0.00 3.21
13 14 0.747644 TGCTAATGTCGGTGGCCATG 60.748 55.000 9.72 4.89 0.00 3.66
14 15 0.183492 ATGCTAATGTCGGTGGCCAT 59.817 50.000 9.72 0.00 0.00 4.40
15 16 0.833949 TATGCTAATGTCGGTGGCCA 59.166 50.000 0.00 0.00 0.00 5.36
16 17 1.070134 TCTATGCTAATGTCGGTGGCC 59.930 52.381 0.00 0.00 0.00 5.36
17 18 2.526304 TCTATGCTAATGTCGGTGGC 57.474 50.000 0.00 0.00 0.00 5.01
18 19 5.989168 TGTTAATCTATGCTAATGTCGGTGG 59.011 40.000 0.00 0.00 0.00 4.61
19 20 7.477144 TTGTTAATCTATGCTAATGTCGGTG 57.523 36.000 0.00 0.00 0.00 4.94
20 21 8.677148 AATTGTTAATCTATGCTAATGTCGGT 57.323 30.769 0.00 0.00 0.00 4.69
108 109 5.302059 CCTATATATAGGGTGGTCGACATGG 59.698 48.000 25.73 0.00 44.97 3.66
161 169 1.971167 GTTGGTTCAGCATGGCCGA 60.971 57.895 0.00 0.00 34.99 5.54
164 172 0.889994 TGATGTTGGTTCAGCATGGC 59.110 50.000 2.14 0.00 35.55 4.40
169 177 4.874970 ACTTTTGATGATGTTGGTTCAGC 58.125 39.130 0.00 0.00 0.00 4.26
217 225 8.612619 GTTATAGATGGACTTAACATTGGTGTG 58.387 37.037 0.00 0.00 38.92 3.82
221 229 9.613428 TCAAGTTATAGATGGACTTAACATTGG 57.387 33.333 0.00 0.00 32.69 3.16
227 235 7.987458 CAGGCTTCAAGTTATAGATGGACTTAA 59.013 37.037 0.00 0.00 32.69 1.85
228 236 7.419057 CCAGGCTTCAAGTTATAGATGGACTTA 60.419 40.741 0.00 0.00 32.69 2.24
231 239 5.059833 CCAGGCTTCAAGTTATAGATGGAC 58.940 45.833 0.00 0.00 0.00 4.02
233 241 4.818546 CACCAGGCTTCAAGTTATAGATGG 59.181 45.833 0.00 0.00 0.00 3.51
234 242 5.674525 TCACCAGGCTTCAAGTTATAGATG 58.325 41.667 0.00 0.00 0.00 2.90
235 243 5.426833 ACTCACCAGGCTTCAAGTTATAGAT 59.573 40.000 0.00 0.00 0.00 1.98
236 244 4.777896 ACTCACCAGGCTTCAAGTTATAGA 59.222 41.667 0.00 0.00 0.00 1.98
237 245 5.091261 ACTCACCAGGCTTCAAGTTATAG 57.909 43.478 0.00 0.00 0.00 1.31
239 247 4.074970 CAACTCACCAGGCTTCAAGTTAT 58.925 43.478 0.00 0.00 0.00 1.89
240 248 3.476552 CAACTCACCAGGCTTCAAGTTA 58.523 45.455 0.00 0.00 0.00 2.24
241 249 2.301346 CAACTCACCAGGCTTCAAGTT 58.699 47.619 0.00 0.00 0.00 2.66
242 250 1.477558 CCAACTCACCAGGCTTCAAGT 60.478 52.381 0.00 0.00 0.00 3.16
243 251 1.242076 CCAACTCACCAGGCTTCAAG 58.758 55.000 0.00 0.00 0.00 3.02
244 252 0.550914 ACCAACTCACCAGGCTTCAA 59.449 50.000 0.00 0.00 0.00 2.69
245 253 0.550914 AACCAACTCACCAGGCTTCA 59.449 50.000 0.00 0.00 0.00 3.02
246 254 1.609072 GAAACCAACTCACCAGGCTTC 59.391 52.381 0.00 0.00 0.00 3.86
247 255 1.064017 TGAAACCAACTCACCAGGCTT 60.064 47.619 0.00 0.00 0.00 4.35
248 256 0.550914 TGAAACCAACTCACCAGGCT 59.449 50.000 0.00 0.00 0.00 4.58
249 257 1.541588 GATGAAACCAACTCACCAGGC 59.458 52.381 0.00 0.00 0.00 4.85
250 258 2.554032 GTGATGAAACCAACTCACCAGG 59.446 50.000 0.00 0.00 33.51 4.45
253 261 4.097892 ACTTTGTGATGAAACCAACTCACC 59.902 41.667 0.00 0.00 37.74 4.02
259 267 6.263617 GGTTAGGTACTTTGTGATGAAACCAA 59.736 38.462 0.00 0.00 41.75 3.67
268 276 5.566032 CGTCAGATGGTTAGGTACTTTGTGA 60.566 44.000 0.00 0.00 41.75 3.58
270 278 4.322499 CCGTCAGATGGTTAGGTACTTTGT 60.322 45.833 0.00 0.00 41.75 2.83
271 279 4.181578 CCGTCAGATGGTTAGGTACTTTG 58.818 47.826 0.00 0.00 41.75 2.77
283 291 0.736325 GACACCGAACCGTCAGATGG 60.736 60.000 7.18 7.18 32.24 3.51
288 296 1.593209 GCTTGACACCGAACCGTCA 60.593 57.895 0.00 0.00 40.30 4.35
291 299 0.320073 TTAGGCTTGACACCGAACCG 60.320 55.000 0.00 0.00 0.00 4.44
294 302 3.410631 TCATTTAGGCTTGACACCGAA 57.589 42.857 0.00 0.00 0.00 4.30
296 304 5.296780 ACATTATCATTTAGGCTTGACACCG 59.703 40.000 0.00 0.00 0.00 4.94
297 305 6.699575 ACATTATCATTTAGGCTTGACACC 57.300 37.500 0.00 0.00 0.00 4.16
340 348 5.353938 GTCGGCATGGAAATAGTACAAGTA 58.646 41.667 0.00 0.00 0.00 2.24
388 397 7.501559 AGTGGTTGATGATAATCTTGATTGAGG 59.498 37.037 6.15 0.00 0.00 3.86
462 472 4.995124 ACAAGTACTAGCACTAATGACGG 58.005 43.478 0.00 0.00 0.00 4.79
494 513 1.996786 GCATGTCGACAAGGCCATGG 61.997 60.000 26.30 7.63 36.16 3.66
634 653 3.000819 TGGACTACGTGGCAGGGG 61.001 66.667 12.33 6.52 0.00 4.79
692 711 0.900647 AGTGGCTAAGGTCGACAGCT 60.901 55.000 21.41 7.34 35.60 4.24
857 886 3.576356 CGAATTGCGGCGCAGGAT 61.576 61.111 34.19 23.40 40.61 3.24
994 1029 1.749258 GGTTCCTCGACATTGGGGC 60.749 63.158 0.00 0.00 0.00 5.80
1077 1174 1.859080 GAAATTAGGGCACGCGTCTAG 59.141 52.381 9.86 0.00 0.00 2.43
1082 1179 1.636340 CTCGAAATTAGGGCACGCG 59.364 57.895 3.53 3.53 0.00 6.01
1145 1242 1.484356 CGCACGCACTATAACCCTAC 58.516 55.000 0.00 0.00 0.00 3.18
1174 1271 3.119849 GCAATTGCACCGTTCTAATCTGT 60.120 43.478 25.36 0.00 41.59 3.41
1175 1272 3.429085 GCAATTGCACCGTTCTAATCTG 58.571 45.455 25.36 0.00 41.59 2.90
1220 1317 0.895559 AGCAGCCACTAAACAAGCCC 60.896 55.000 0.00 0.00 0.00 5.19
1245 1342 6.112734 TGGCAACAGGATAACATTGTACTAG 58.887 40.000 0.00 0.00 46.17 2.57
1246 1343 6.056090 TGGCAACAGGATAACATTGTACTA 57.944 37.500 0.00 0.00 46.17 1.82
1264 1365 1.903860 ACTCATACTAACCGGTGGCAA 59.096 47.619 8.52 0.00 0.00 4.52
1286 1387 8.793592 ACACCCTCATAGAAGAAAAACAAATAC 58.206 33.333 0.00 0.00 0.00 1.89
1287 1388 8.934023 ACACCCTCATAGAAGAAAAACAAATA 57.066 30.769 0.00 0.00 0.00 1.40
1289 1390 6.831353 TGACACCCTCATAGAAGAAAAACAAA 59.169 34.615 0.00 0.00 0.00 2.83
1292 1393 6.881602 AGATGACACCCTCATAGAAGAAAAAC 59.118 38.462 0.00 0.00 39.96 2.43
1293 1394 7.020827 AGATGACACCCTCATAGAAGAAAAA 57.979 36.000 0.00 0.00 39.96 1.94
1313 1414 1.676746 TCGAACGGAGGGAGTAGATG 58.323 55.000 0.00 0.00 0.00 2.90
1318 1419 4.891756 TCTTATATTTCGAACGGAGGGAGT 59.108 41.667 0.00 0.00 0.00 3.85
1319 1420 5.449107 TCTTATATTTCGAACGGAGGGAG 57.551 43.478 0.00 0.00 0.00 4.30
1322 1423 7.478520 AAACATCTTATATTTCGAACGGAGG 57.521 36.000 0.00 0.00 0.00 4.30
1324 1425 8.545420 GCTAAAACATCTTATATTTCGAACGGA 58.455 33.333 0.00 0.00 0.00 4.69
1325 1426 8.548721 AGCTAAAACATCTTATATTTCGAACGG 58.451 33.333 0.00 0.00 0.00 4.44
1326 1427 9.916397 AAGCTAAAACATCTTATATTTCGAACG 57.084 29.630 0.00 0.00 0.00 3.95
1359 1460 9.214957 TGAAACACGTCTAGATACATTCAATTT 57.785 29.630 0.00 0.00 0.00 1.82
1360 1461 8.771920 TGAAACACGTCTAGATACATTCAATT 57.228 30.769 0.00 0.00 0.00 2.32
1361 1462 8.035394 ACTGAAACACGTCTAGATACATTCAAT 58.965 33.333 0.00 0.00 0.00 2.57
1362 1463 7.328493 CACTGAAACACGTCTAGATACATTCAA 59.672 37.037 0.00 0.00 0.00 2.69
1363 1464 6.806739 CACTGAAACACGTCTAGATACATTCA 59.193 38.462 0.00 3.61 0.00 2.57
1364 1465 6.807230 ACACTGAAACACGTCTAGATACATTC 59.193 38.462 0.00 0.00 0.00 2.67
1365 1466 6.586463 CACACTGAAACACGTCTAGATACATT 59.414 38.462 0.00 0.00 0.00 2.71
1366 1467 6.093404 CACACTGAAACACGTCTAGATACAT 58.907 40.000 0.00 0.00 0.00 2.29
1367 1468 5.009310 ACACACTGAAACACGTCTAGATACA 59.991 40.000 0.00 0.00 0.00 2.29
1368 1469 5.458891 ACACACTGAAACACGTCTAGATAC 58.541 41.667 0.00 0.00 0.00 2.24
1369 1470 5.700722 ACACACTGAAACACGTCTAGATA 57.299 39.130 0.00 0.00 0.00 1.98
1370 1471 4.585955 ACACACTGAAACACGTCTAGAT 57.414 40.909 0.00 0.00 0.00 1.98
1371 1472 4.818005 TCTACACACTGAAACACGTCTAGA 59.182 41.667 0.00 0.00 0.00 2.43
1372 1473 5.104562 TCTACACACTGAAACACGTCTAG 57.895 43.478 0.00 0.00 0.00 2.43
1373 1474 5.700722 ATCTACACACTGAAACACGTCTA 57.299 39.130 0.00 0.00 0.00 2.59
1374 1475 4.585955 ATCTACACACTGAAACACGTCT 57.414 40.909 0.00 0.00 0.00 4.18
1375 1476 4.743151 TGAATCTACACACTGAAACACGTC 59.257 41.667 0.00 0.00 0.00 4.34
1376 1477 4.689071 TGAATCTACACACTGAAACACGT 58.311 39.130 0.00 0.00 0.00 4.49
1377 1478 5.651172 TTGAATCTACACACTGAAACACG 57.349 39.130 0.00 0.00 0.00 4.49
1378 1479 7.189693 TGATTGAATCTACACACTGAAACAC 57.810 36.000 6.73 0.00 0.00 3.32
1379 1480 7.984422 ATGATTGAATCTACACACTGAAACA 57.016 32.000 6.73 0.00 0.00 2.83
1380 1481 9.683069 AAAATGATTGAATCTACACACTGAAAC 57.317 29.630 6.73 0.00 0.00 2.78
1383 1484 9.725019 ACTAAAATGATTGAATCTACACACTGA 57.275 29.630 6.73 0.00 0.00 3.41
1386 1487 9.478019 CGAACTAAAATGATTGAATCTACACAC 57.522 33.333 6.73 0.00 0.00 3.82
1387 1488 9.214957 ACGAACTAAAATGATTGAATCTACACA 57.785 29.630 6.73 0.00 0.00 3.72
1396 1497 9.745880 GGACTAGATACGAACTAAAATGATTGA 57.254 33.333 0.00 0.00 0.00 2.57
1397 1498 9.529325 TGGACTAGATACGAACTAAAATGATTG 57.471 33.333 0.00 0.00 0.00 2.67
1418 1519 9.512588 GATGTCTTGGATATTTCAATATGGACT 57.487 33.333 0.00 0.00 31.96 3.85
1419 1520 9.512588 AGATGTCTTGGATATTTCAATATGGAC 57.487 33.333 0.00 0.00 31.96 4.02
1440 1541 9.528489 ACCACAAGTACCAAAAATATAAGATGT 57.472 29.630 0.00 0.00 0.00 3.06
1443 1544 9.357161 ACAACCACAAGTACCAAAAATATAAGA 57.643 29.630 0.00 0.00 0.00 2.10
1444 1545 9.620660 GACAACCACAAGTACCAAAAATATAAG 57.379 33.333 0.00 0.00 0.00 1.73
1445 1546 8.291032 CGACAACCACAAGTACCAAAAATATAA 58.709 33.333 0.00 0.00 0.00 0.98
1446 1547 7.444792 ACGACAACCACAAGTACCAAAAATATA 59.555 33.333 0.00 0.00 0.00 0.86
1447 1548 6.263617 ACGACAACCACAAGTACCAAAAATAT 59.736 34.615 0.00 0.00 0.00 1.28
1448 1549 5.589452 ACGACAACCACAAGTACCAAAAATA 59.411 36.000 0.00 0.00 0.00 1.40
1449 1550 4.399934 ACGACAACCACAAGTACCAAAAAT 59.600 37.500 0.00 0.00 0.00 1.82
1450 1551 3.757493 ACGACAACCACAAGTACCAAAAA 59.243 39.130 0.00 0.00 0.00 1.94
1451 1552 3.345414 ACGACAACCACAAGTACCAAAA 58.655 40.909 0.00 0.00 0.00 2.44
1452 1553 2.988570 ACGACAACCACAAGTACCAAA 58.011 42.857 0.00 0.00 0.00 3.28
1453 1554 2.695127 ACGACAACCACAAGTACCAA 57.305 45.000 0.00 0.00 0.00 3.67
1491 1592 7.928167 CGGCAAATTAGAGCTATATATCCATCA 59.072 37.037 0.00 0.00 0.00 3.07
1505 1606 2.426738 TCATTTGGCCGGCAAATTAGAG 59.573 45.455 30.85 17.63 30.66 2.43
1590 1692 4.884247 ACTAGCAAACTCAACCTACAGAC 58.116 43.478 0.00 0.00 0.00 3.51
1604 1706 8.856153 TCTTATCAACCAACATAACTAGCAAA 57.144 30.769 0.00 0.00 0.00 3.68
1660 1763 4.617995 GCCAAAGCACATTACAGCAACATA 60.618 41.667 0.00 0.00 39.53 2.29
1825 1928 3.005554 CTCAAACAGACCCAGCTATGTG 58.994 50.000 0.00 0.00 0.00 3.21
1845 1954 3.283751 ACAGTGATAGAAGAGCGCTACT 58.716 45.455 11.50 13.16 30.86 2.57
1873 1982 6.959639 ACAACCTACAAAAGTGACAATGAT 57.040 33.333 0.00 0.00 0.00 2.45
1876 1985 7.338449 AGTGTAACAACCTACAAAAGTGACAAT 59.662 33.333 0.00 0.00 41.43 2.71
1877 1986 6.655848 AGTGTAACAACCTACAAAAGTGACAA 59.344 34.615 0.00 0.00 41.43 3.18
1878 1987 6.174760 AGTGTAACAACCTACAAAAGTGACA 58.825 36.000 0.00 0.00 41.43 3.58
1887 1996 4.124238 GCAACAGAGTGTAACAACCTACA 58.876 43.478 0.00 0.00 41.43 2.74
1911 2021 5.349061 TGCATACAGTGATGTCTCAGAAT 57.651 39.130 0.00 0.00 30.18 2.40
1948 2066 1.094785 CCAAACACTAGGATTGCCCG 58.905 55.000 0.00 0.00 40.87 6.13
1980 2098 7.857734 TGTGTACAGGGATGTTACATAAATG 57.142 36.000 0.00 0.00 0.00 2.32
2006 2124 8.389779 TGCTGAAGTAATACAACAGAATGAAA 57.610 30.769 16.46 0.00 39.69 2.69
2068 2190 2.227388 CTCATCCAAGTTGCCTGTTGAC 59.773 50.000 0.00 0.00 0.00 3.18
2150 2272 7.220740 TCAGTTTCTTTGTCACATGGTATGTA 58.779 34.615 0.00 0.00 42.70 2.29
2175 2297 0.539669 AGCAAAACCTTTAGGGCGCT 60.540 50.000 7.64 8.86 40.27 5.92
2179 2301 3.809279 CAGCAAAAGCAAAACCTTTAGGG 59.191 43.478 0.10 0.00 40.27 3.53
2182 2304 5.337578 ACTCAGCAAAAGCAAAACCTTTA 57.662 34.783 0.00 0.00 34.12 1.85
2328 2450 6.048732 TGCAAGGTAATGATAGTTCAGACA 57.951 37.500 0.00 0.00 34.73 3.41
2357 2479 7.650834 GCAAACTGCAATTTATAACCAGAAA 57.349 32.000 0.00 0.00 44.26 2.52
2376 2498 1.537202 CTGTGCTCCAACTAGGCAAAC 59.463 52.381 0.00 0.00 37.73 2.93
2443 2569 8.465273 AGGGATTTGACCTTGTTTATATTAGC 57.535 34.615 0.00 0.00 33.64 3.09
2453 2579 5.321927 ACGAATTTAGGGATTTGACCTTGT 58.678 37.500 0.00 0.00 39.54 3.16
2554 2680 2.683362 GAGGCTGCTTTGGTAATGGTAC 59.317 50.000 0.00 0.00 0.00 3.34
2655 2781 6.599244 TGTAAGGATGATAGCCTTGTGAAAAG 59.401 38.462 8.51 0.00 45.05 2.27
2734 2860 9.498176 AACAAGGTAAGATTTAAGTCACGTATT 57.502 29.630 0.44 0.00 0.00 1.89
2749 2877 9.847224 AAGAGAAAACAATAGAACAAGGTAAGA 57.153 29.630 0.00 0.00 0.00 2.10
2753 2881 8.966868 TGAAAAGAGAAAACAATAGAACAAGGT 58.033 29.630 0.00 0.00 0.00 3.50
2754 2882 9.237846 GTGAAAAGAGAAAACAATAGAACAAGG 57.762 33.333 0.00 0.00 0.00 3.61
2818 2946 7.329499 TGTAACCATACGTACCATGTACAAAT 58.671 34.615 0.00 0.00 34.60 2.32
2824 2952 5.149973 TGTTGTAACCATACGTACCATGT 57.850 39.130 0.00 0.00 34.60 3.21
2853 2981 6.293298 GCTAGCATTCAGAACAGAACCATATG 60.293 42.308 10.63 0.00 0.00 1.78
2881 3009 3.009723 AGCATTCACAACATAACCTCCG 58.990 45.455 0.00 0.00 0.00 4.63
2958 3086 2.347490 GCTCCCGCTCTTTGGTGA 59.653 61.111 0.00 0.00 0.00 4.02
3168 3296 4.348486 TCCAAGAGAACAGATCTAGCAGT 58.652 43.478 0.00 0.00 38.96 4.40
3224 3364 1.204146 AATACATGAGTCGGCAGGGT 58.796 50.000 0.00 0.00 0.00 4.34
3231 3371 8.264632 CGCATATGATCATTAATACATGAGTCG 58.735 37.037 14.65 5.89 36.60 4.18
3238 3378 8.040132 TCATCCACGCATATGATCATTAATACA 58.960 33.333 14.65 0.00 0.00 2.29
3292 3432 4.568359 ACAGCAATGATCATTCGAGTACAC 59.432 41.667 18.16 1.49 0.00 2.90
3319 3459 7.055667 TGAGATATCAACATCTTCTGGGTAC 57.944 40.000 5.32 0.00 35.37 3.34
3338 3478 2.444895 GGACCCCGGAGCTGAGAT 60.445 66.667 0.73 0.00 0.00 2.75
3401 3541 7.815383 TGATGGGGTTAAATTCTGTGATAGAT 58.185 34.615 0.00 0.00 34.80 1.98
3402 3542 7.206789 TGATGGGGTTAAATTCTGTGATAGA 57.793 36.000 0.00 0.00 0.00 1.98
3470 3614 4.114794 AGCACAGAAATCACAAACAAAGC 58.885 39.130 0.00 0.00 0.00 3.51
3471 3615 6.418819 CCTAAGCACAGAAATCACAAACAAAG 59.581 38.462 0.00 0.00 0.00 2.77
3521 3697 8.166066 GCCAATTTACCGTCAATAAAACAAATC 58.834 33.333 0.00 0.00 0.00 2.17
3522 3698 7.657761 TGCCAATTTACCGTCAATAAAACAAAT 59.342 29.630 0.00 0.00 0.00 2.32
3523 3699 6.984474 TGCCAATTTACCGTCAATAAAACAAA 59.016 30.769 0.00 0.00 0.00 2.83
3524 3700 6.513180 TGCCAATTTACCGTCAATAAAACAA 58.487 32.000 0.00 0.00 0.00 2.83
3525 3701 6.085555 TGCCAATTTACCGTCAATAAAACA 57.914 33.333 0.00 0.00 0.00 2.83
3533 3709 2.852449 TCAGTTGCCAATTTACCGTCA 58.148 42.857 0.00 0.00 0.00 4.35
3556 3732 1.007721 AGGAGATGTACTGGGCAGAGT 59.992 52.381 0.00 0.00 0.00 3.24
3577 3753 8.691661 TGTTAGACAAGGATTAAAGAAAAGCT 57.308 30.769 0.00 0.00 0.00 3.74
3578 3754 8.784043 TCTGTTAGACAAGGATTAAAGAAAAGC 58.216 33.333 0.00 0.00 0.00 3.51
3624 3800 5.640783 GCATTTCTTTGATTTCCCAGGAAAG 59.359 40.000 16.50 3.73 45.66 2.62
3765 3948 2.486472 CAGAGCTGTGAAATCTGGGT 57.514 50.000 4.50 0.00 37.41 4.51
3776 3959 8.011795 CATAATTATATGTGGCTCCAGAGCTGT 61.012 40.741 18.54 5.89 42.39 4.40


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

AutoCloner maintained by Alex Coulton.