Multiple sequence alignment - TraesCS6B01G455100

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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 TraesCS6B01G455100 chr6B 100.000 3485 0 0 958 4442 712241121 712244605 0.000000e+00 6436.0
1 TraesCS6B01G455100 chr6B 100.000 687 0 0 1 687 712240164 712240850 0.000000e+00 1269.0
2 TraesCS6B01G455100 chr6B 88.293 205 15 5 1003 1198 699123049 699123253 2.070000e-58 237.0
3 TraesCS6B01G455100 chr6D 91.809 1697 98 23 1508 3191 467037567 467039235 0.000000e+00 2326.0
4 TraesCS6B01G455100 chr6D 89.739 1033 70 14 3427 4442 467039754 467040767 0.000000e+00 1288.0
5 TraesCS6B01G455100 chr6D 94.268 314 15 2 3180 3493 467039329 467039639 1.120000e-130 477.0
6 TraesCS6B01G455100 chr6D 92.759 290 12 6 969 1258 467036726 467037006 1.150000e-110 411.0
7 TraesCS6B01G455100 chr6D 100.000 32 0 0 3394 3425 467039640 467039671 4.800000e-05 60.2
8 TraesCS6B01G455100 chr6A 89.658 1112 72 12 3180 4281 613335277 613336355 0.000000e+00 1376.0
9 TraesCS6B01G455100 chr6A 93.579 841 44 5 2351 3191 613334353 613335183 0.000000e+00 1245.0
10 TraesCS6B01G455100 chr6A 82.169 830 70 25 1508 2280 613333535 613334343 3.750000e-180 641.0
11 TraesCS6B01G455100 chr6A 79.893 746 55 46 1 685 613331973 613332684 4.050000e-125 459.0
12 TraesCS6B01G455100 chr6A 88.554 332 23 12 958 1283 613332698 613333020 5.390000e-104 388.0
13 TraesCS6B01G455100 chr1B 91.822 966 61 8 3183 4148 286299866 286298919 0.000000e+00 1330.0
14 TraesCS6B01G455100 chr1B 89.462 446 31 8 3703 4148 223862608 223863037 2.340000e-152 549.0
15 TraesCS6B01G455100 chr1B 84.211 190 21 6 1018 1198 665782812 665782623 4.570000e-40 176.0
16 TraesCS6B01G455100 chr1B 85.039 127 10 3 1009 1126 85713685 85713559 2.170000e-23 121.0
17 TraesCS6B01G455100 chr4D 91.919 693 46 7 2300 2990 51866278 51865594 0.000000e+00 961.0
18 TraesCS6B01G455100 chr4D 91.003 289 17 5 1990 2270 51866557 51866270 9.020000e-102 381.0
19 TraesCS6B01G455100 chr3A 90.794 315 26 2 2877 3191 648181990 648182301 6.870000e-113 418.0
20 TraesCS6B01G455100 chr3A 88.599 307 26 4 3189 3492 648182403 648182703 9.080000e-97 364.0
21 TraesCS6B01G455100 chr3B 85.944 249 24 4 1018 1256 807586310 807586063 5.700000e-64 255.0
22 TraesCS6B01G455100 chr3B 94.366 71 4 0 1009 1079 456360223 456360293 4.700000e-20 110.0
23 TraesCS6B01G455100 chr2B 84.211 266 31 4 1003 1258 780742706 780742970 9.540000e-62 248.0
24 TraesCS6B01G455100 chr7A 78.753 433 39 29 1 421 579219359 579218968 1.600000e-59 241.0
25 TraesCS6B01G455100 chr4A 85.593 236 23 4 1018 1243 111068273 111068039 2.070000e-58 237.0
26 TraesCS6B01G455100 chr4A 85.870 92 4 3 1044 1126 738692738 738692829 6.120000e-14 89.8
27 TraesCS6B01G455100 chr7B 86.829 205 18 3 1003 1198 616528741 616528945 2.080000e-53 220.0
28 TraesCS6B01G455100 chr3D 83.784 185 17 6 2626 2810 608597996 608598167 3.560000e-36 163.0


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 TraesCS6B01G455100 chr6B 712240164 712244605 4441 False 3852.50 6436 100.0000 1 4442 2 chr6B.!!$F2 4441
1 TraesCS6B01G455100 chr6D 467036726 467040767 4041 False 912.44 2326 93.7150 969 4442 5 chr6D.!!$F1 3473
2 TraesCS6B01G455100 chr6A 613331973 613336355 4382 False 821.80 1376 86.7706 1 4281 5 chr6A.!!$F1 4280
3 TraesCS6B01G455100 chr1B 286298919 286299866 947 True 1330.00 1330 91.8220 3183 4148 1 chr1B.!!$R2 965
4 TraesCS6B01G455100 chr4D 51865594 51866557 963 True 671.00 961 91.4610 1990 2990 2 chr4D.!!$R1 1000
5 TraesCS6B01G455100 chr3A 648181990 648182703 713 False 391.00 418 89.6965 2877 3492 2 chr3A.!!$F1 615

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
596 658 0.107459 GGGTGATTGGACTCTGGCTC 60.107 60.0 0.0 0.0 0.00 4.70 F
1384 1786 0.038618 GAAATGTTTGCCCACCCGTC 60.039 55.0 0.0 0.0 0.00 4.79 F
1444 1857 0.036732 AGAATCCGGCTGACTGCAAA 59.963 50.0 0.0 0.0 45.15 3.68 F
1493 1913 0.109319 CACGGTGCTGTAAAATGGCC 60.109 55.0 0.0 0.0 0.00 5.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1424 1837 0.036732 TTGCAGTCAGCCGGATTCTT 59.963 50.000 5.05 0.0 44.83 2.52 R
3207 3797 0.899717 GGCAATCAGGCTGGAAACCA 60.900 55.000 15.73 0.0 40.24 3.67 R
3359 3950 1.226717 CCGAGCGTCTGAGTTAGCC 60.227 63.158 0.00 0.0 0.00 3.93 R
3483 4076 1.947456 GGGGTTCTTTGTGTCACACTC 59.053 52.381 9.90 0.0 35.11 3.51 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
24 25 7.369803 CTAATTGACTGTAAAGCACTGATGT 57.630 36.000 0.00 0.00 0.00 3.06
26 27 4.071961 TGACTGTAAAGCACTGATGTGT 57.928 40.909 0.00 0.00 45.44 3.72
27 28 5.208463 TGACTGTAAAGCACTGATGTGTA 57.792 39.130 0.00 0.00 45.44 2.90
28 29 4.988540 TGACTGTAAAGCACTGATGTGTAC 59.011 41.667 0.00 0.00 45.44 2.90
43 44 6.492254 TGATGTGTACTACTACTACATTGCG 58.508 40.000 0.00 0.00 30.85 4.85
68 69 5.277345 CGGTAATTCAACGATCATTCCCTTC 60.277 44.000 0.00 0.00 0.00 3.46
78 79 4.574013 CGATCATTCCCTTCTTCAAAGGAG 59.426 45.833 5.39 0.00 39.81 3.69
105 106 4.393990 TCAGTTATGAATGAAGCAGTGCAG 59.606 41.667 19.20 0.00 30.61 4.41
107 108 5.005740 AGTTATGAATGAAGCAGTGCAGAA 58.994 37.500 19.20 1.59 0.00 3.02
128 129 7.966753 GCAGAAATAATGGCATCATACATACAG 59.033 37.037 0.00 0.00 32.44 2.74
129 130 7.966753 CAGAAATAATGGCATCATACATACAGC 59.033 37.037 0.00 0.00 32.44 4.40
130 131 7.886970 AGAAATAATGGCATCATACATACAGCT 59.113 33.333 0.00 0.00 32.44 4.24
131 132 8.413309 AAATAATGGCATCATACATACAGCTT 57.587 30.769 0.00 0.00 32.44 3.74
132 133 5.954296 AATGGCATCATACATACAGCTTC 57.046 39.130 0.00 0.00 32.44 3.86
133 134 4.420522 TGGCATCATACATACAGCTTCA 57.579 40.909 0.00 0.00 0.00 3.02
174 175 9.209048 AGATGGACCATACAAAATAGTACTACA 57.791 33.333 7.05 0.00 0.00 2.74
175 176 9.826574 GATGGACCATACAAAATAGTACTACAA 57.173 33.333 7.05 0.00 0.00 2.41
198 199 8.686334 ACAACATAATCCCAACAAATCATCTAC 58.314 33.333 0.00 0.00 0.00 2.59
248 252 1.070758 AGACGAGTGCAGTTGGTTCAT 59.929 47.619 13.47 0.00 0.00 2.57
249 253 2.299013 AGACGAGTGCAGTTGGTTCATA 59.701 45.455 13.47 0.00 0.00 2.15
250 254 2.412089 GACGAGTGCAGTTGGTTCATAC 59.588 50.000 13.47 0.00 0.00 2.39
251 255 2.224185 ACGAGTGCAGTTGGTTCATACA 60.224 45.455 13.47 0.00 0.00 2.29
252 256 2.805671 CGAGTGCAGTTGGTTCATACAA 59.194 45.455 0.20 0.00 0.00 2.41
253 257 3.249799 CGAGTGCAGTTGGTTCATACAAA 59.750 43.478 0.20 0.00 0.00 2.83
254 258 4.537015 GAGTGCAGTTGGTTCATACAAAC 58.463 43.478 0.00 0.00 38.30 2.93
274 278 8.687824 ACAAACTACAAAGAATTTCACACAAG 57.312 30.769 0.00 0.00 35.03 3.16
294 298 3.521560 AGCACGTACTGACCAATACATG 58.478 45.455 0.00 0.00 0.00 3.21
322 326 8.240883 ACAAGAGTTTGTTAATCGTATCAGAC 57.759 34.615 0.00 0.00 45.01 3.51
323 327 7.870954 ACAAGAGTTTGTTAATCGTATCAGACA 59.129 33.333 0.00 0.00 45.01 3.41
324 328 8.708742 CAAGAGTTTGTTAATCGTATCAGACAA 58.291 33.333 0.00 0.00 0.00 3.18
330 334 8.556517 TTGTTAATCGTATCAGACAATAGACG 57.443 34.615 0.00 0.00 0.00 4.18
332 336 8.068380 TGTTAATCGTATCAGACAATAGACGAG 58.932 37.037 0.00 0.00 41.96 4.18
339 355 1.134965 AGACAATAGACGAGTGCAGCC 60.135 52.381 0.00 0.00 0.00 4.85
406 422 1.221021 GAGAAAGTAGGGCCCGGTG 59.779 63.158 18.44 0.00 0.00 4.94
407 423 2.437895 GAAAGTAGGGCCCGGTGC 60.438 66.667 18.44 2.98 40.16 5.01
439 462 1.925455 CTGGCAGAAGGGGAGGGAA 60.925 63.158 9.42 0.00 0.00 3.97
447 470 1.772561 AAGGGGAGGGAAGGAGGGAA 61.773 60.000 0.00 0.00 0.00 3.97
448 471 1.006227 GGGGAGGGAAGGAGGGAAT 59.994 63.158 0.00 0.00 0.00 3.01
456 508 1.309102 AAGGAGGGAATGGGGAGGG 60.309 63.158 0.00 0.00 0.00 4.30
462 514 1.318380 GGAATGGGGAGGGAGGAGA 59.682 63.158 0.00 0.00 0.00 3.71
472 524 1.762858 GGGAGGAGAGGTACCTGGC 60.763 68.421 22.10 10.71 37.93 4.85
549 611 1.490910 GAACCCTATTCCCTCCACCTG 59.509 57.143 0.00 0.00 0.00 4.00
582 644 4.651008 GTTCGGTCGTGCGGGTGA 62.651 66.667 0.00 0.00 0.00 4.02
583 645 3.687102 TTCGGTCGTGCGGGTGAT 61.687 61.111 0.00 0.00 0.00 3.06
584 646 3.229156 TTCGGTCGTGCGGGTGATT 62.229 57.895 0.00 0.00 0.00 2.57
585 647 3.487202 CGGTCGTGCGGGTGATTG 61.487 66.667 0.00 0.00 0.00 2.67
586 648 3.124921 GGTCGTGCGGGTGATTGG 61.125 66.667 0.00 0.00 0.00 3.16
587 649 2.047655 GTCGTGCGGGTGATTGGA 60.048 61.111 0.00 0.00 0.00 3.53
588 650 2.047655 TCGTGCGGGTGATTGGAC 60.048 61.111 0.00 0.00 0.00 4.02
589 651 2.047274 CGTGCGGGTGATTGGACT 60.047 61.111 0.00 0.00 0.00 3.85
590 652 2.100631 CGTGCGGGTGATTGGACTC 61.101 63.158 0.00 0.00 0.00 3.36
596 658 0.107459 GGGTGATTGGACTCTGGCTC 60.107 60.000 0.00 0.00 0.00 4.70
607 669 4.200283 CTGGCTCCGGACTCGCTC 62.200 72.222 13.28 5.22 34.56 5.03
609 671 3.760035 GGCTCCGGACTCGCTCAA 61.760 66.667 13.28 0.00 34.56 3.02
610 672 2.261671 GCTCCGGACTCGCTCAAA 59.738 61.111 0.00 0.00 34.56 2.69
611 673 1.807573 GCTCCGGACTCGCTCAAAG 60.808 63.158 0.00 0.00 34.56 2.77
613 675 2.125512 CCGGACTCGCTCAAAGGG 60.126 66.667 0.00 0.00 34.56 3.95
614 676 2.815647 CGGACTCGCTCAAAGGGC 60.816 66.667 0.00 0.00 0.00 5.19
622 684 4.082523 CTCAAAGGGCGGCCGAGA 62.083 66.667 33.48 19.53 0.00 4.04
623 685 3.391665 CTCAAAGGGCGGCCGAGAT 62.392 63.158 33.48 10.44 0.00 2.75
625 687 4.489771 AAAGGGCGGCCGAGATGG 62.490 66.667 33.48 0.00 42.50 3.51
659 729 2.445438 CGACCGCGCCTCTTTCTTC 61.445 63.158 0.00 0.00 0.00 2.87
1259 1338 4.472310 CCCCCTCCCCCATTCCCT 62.472 72.222 0.00 0.00 0.00 4.20
1260 1339 2.778717 CCCCTCCCCCATTCCCTC 60.779 72.222 0.00 0.00 0.00 4.30
1261 1340 2.778717 CCCTCCCCCATTCCCTCC 60.779 72.222 0.00 0.00 0.00 4.30
1262 1341 2.044450 CCTCCCCCATTCCCTCCA 59.956 66.667 0.00 0.00 0.00 3.86
1263 1342 1.387926 CCTCCCCCATTCCCTCCAT 60.388 63.158 0.00 0.00 0.00 3.41
1267 1346 1.701024 CCCCATTCCCTCCATCCCA 60.701 63.158 0.00 0.00 0.00 4.37
1271 1350 2.360638 CCCATTCCCTCCATCCCAATTT 60.361 50.000 0.00 0.00 0.00 1.82
1283 1362 3.791953 TCCCAATTTCGTCCTGGTTAA 57.208 42.857 0.00 0.00 0.00 2.01
1284 1363 4.310022 TCCCAATTTCGTCCTGGTTAAT 57.690 40.909 0.00 0.00 0.00 1.40
1287 1366 3.428862 CCAATTTCGTCCTGGTTAATGCC 60.429 47.826 0.00 0.00 0.00 4.40
1288 1367 2.570415 TTTCGTCCTGGTTAATGCCA 57.430 45.000 0.00 0.00 36.97 4.92
1294 1373 1.322538 CCTGGTTAATGCCACTGCCC 61.323 60.000 0.00 0.00 36.33 5.36
1297 1376 3.130819 TTAATGCCACTGCCCGCG 61.131 61.111 0.00 0.00 36.33 6.46
1312 1406 2.255252 GCGCACTGGCATTTCGTT 59.745 55.556 0.30 0.00 41.24 3.85
1313 1407 1.371635 GCGCACTGGCATTTCGTTT 60.372 52.632 0.30 0.00 41.24 3.60
1314 1408 0.939106 GCGCACTGGCATTTCGTTTT 60.939 50.000 0.30 0.00 41.24 2.43
1315 1409 0.777631 CGCACTGGCATTTCGTTTTG 59.222 50.000 0.00 0.00 41.24 2.44
1323 1417 3.454042 GCATTTCGTTTTGCCAAATCC 57.546 42.857 0.00 0.00 32.66 3.01
1324 1418 2.159854 GCATTTCGTTTTGCCAAATCCG 60.160 45.455 0.00 0.00 32.66 4.18
1326 1420 0.385751 TTCGTTTTGCCAAATCCGCA 59.614 45.000 5.24 0.00 0.00 5.69
1329 1488 0.319813 GTTTTGCCAAATCCGCAGCT 60.320 50.000 0.00 0.00 37.57 4.24
1332 1491 2.751436 GCCAAATCCGCAGCTCCA 60.751 61.111 0.00 0.00 0.00 3.86
1346 1505 0.107508 GCTCCAGCAGCCAATCAGTA 60.108 55.000 0.00 0.00 43.17 2.74
1348 1507 1.209019 CTCCAGCAGCCAATCAGTACT 59.791 52.381 0.00 0.00 0.00 2.73
1349 1508 2.432146 CTCCAGCAGCCAATCAGTACTA 59.568 50.000 0.00 0.00 0.00 1.82
1352 1511 1.202463 AGCAGCCAATCAGTACTAGCG 60.202 52.381 0.00 0.00 0.00 4.26
1355 1514 1.414181 AGCCAATCAGTACTAGCGCAT 59.586 47.619 11.47 0.00 0.00 4.73
1356 1515 2.158900 AGCCAATCAGTACTAGCGCATT 60.159 45.455 11.47 0.00 0.00 3.56
1357 1516 2.032549 GCCAATCAGTACTAGCGCATTG 60.033 50.000 11.47 8.03 0.00 2.82
1362 1521 1.146263 GTACTAGCGCATTGGGCCT 59.854 57.895 20.69 11.40 42.59 5.19
1363 1522 1.146041 TACTAGCGCATTGGGCCTG 59.854 57.895 20.69 15.78 42.59 4.85
1364 1523 2.324014 TACTAGCGCATTGGGCCTGG 62.324 60.000 20.69 13.53 42.59 4.45
1365 1524 4.504596 TAGCGCATTGGGCCTGGG 62.505 66.667 20.69 5.16 42.59 4.45
1369 1771 2.059786 CGCATTGGGCCTGGGAAAT 61.060 57.895 4.53 0.00 40.31 2.17
1375 1777 1.296392 GGGCCTGGGAAATGTTTGC 59.704 57.895 0.84 0.00 0.00 3.68
1377 1779 1.296392 GCCTGGGAAATGTTTGCCC 59.704 57.895 12.61 3.91 46.80 5.36
1379 1781 0.321346 CCTGGGAAATGTTTGCCCAC 59.679 55.000 12.61 0.00 46.57 4.61
1380 1782 0.321346 CTGGGAAATGTTTGCCCACC 59.679 55.000 12.61 0.00 46.57 4.61
1384 1786 0.038618 GAAATGTTTGCCCACCCGTC 60.039 55.000 0.00 0.00 0.00 4.79
1421 1834 0.647410 CAGTTGGCTTCGATGTAGCG 59.353 55.000 1.69 0.00 39.54 4.26
1423 1836 1.813753 TTGGCTTCGATGTAGCGGC 60.814 57.895 1.69 0.00 39.54 6.53
1424 1837 2.202878 GGCTTCGATGTAGCGGCA 60.203 61.111 1.45 0.00 39.54 5.69
1429 1842 2.205074 CTTCGATGTAGCGGCAAGAAT 58.795 47.619 1.45 0.00 0.00 2.40
1431 1844 0.861837 CGATGTAGCGGCAAGAATCC 59.138 55.000 1.45 0.00 0.00 3.01
1433 1846 0.532862 ATGTAGCGGCAAGAATCCGG 60.533 55.000 1.45 0.00 46.51 5.14
1434 1847 2.203015 TAGCGGCAAGAATCCGGC 60.203 61.111 1.45 0.00 46.51 6.13
1441 1854 1.986575 GCAAGAATCCGGCTGACTGC 61.987 60.000 0.00 0.00 41.94 4.40
1442 1855 0.674581 CAAGAATCCGGCTGACTGCA 60.675 55.000 0.00 0.00 45.15 4.41
1444 1857 0.036732 AGAATCCGGCTGACTGCAAA 59.963 50.000 0.00 0.00 45.15 3.68
1445 1858 1.098050 GAATCCGGCTGACTGCAAAT 58.902 50.000 0.00 0.00 45.15 2.32
1447 1860 0.254178 ATCCGGCTGACTGCAAATCT 59.746 50.000 0.00 0.00 45.15 2.40
1461 1881 2.512885 CAAATCTGCAATGCACGACTC 58.487 47.619 2.72 0.00 33.79 3.36
1462 1882 2.105006 AATCTGCAATGCACGACTCT 57.895 45.000 2.72 0.00 33.79 3.24
1463 1883 2.967599 ATCTGCAATGCACGACTCTA 57.032 45.000 2.72 0.00 33.79 2.43
1465 1885 1.546029 TCTGCAATGCACGACTCTACT 59.454 47.619 2.72 0.00 33.79 2.57
1466 1886 1.657594 CTGCAATGCACGACTCTACTG 59.342 52.381 2.72 0.00 33.79 2.74
1467 1887 1.272212 TGCAATGCACGACTCTACTGA 59.728 47.619 2.72 0.00 31.71 3.41
1469 1889 2.932614 GCAATGCACGACTCTACTGAAT 59.067 45.455 0.00 0.00 0.00 2.57
1479 1899 4.684703 CGACTCTACTGAATTTTTCACGGT 59.315 41.667 0.00 0.00 35.46 4.83
1480 1900 5.388475 CGACTCTACTGAATTTTTCACGGTG 60.388 44.000 0.56 0.56 35.46 4.94
1481 1901 4.213482 ACTCTACTGAATTTTTCACGGTGC 59.787 41.667 2.51 0.00 35.46 5.01
1483 1903 3.354089 ACTGAATTTTTCACGGTGCTG 57.646 42.857 2.51 0.00 35.46 4.41
1484 1904 2.687935 ACTGAATTTTTCACGGTGCTGT 59.312 40.909 2.51 0.00 35.46 4.40
1486 1906 4.336993 ACTGAATTTTTCACGGTGCTGTAA 59.663 37.500 2.51 0.00 35.46 2.41
1487 1907 5.163602 ACTGAATTTTTCACGGTGCTGTAAA 60.164 36.000 2.51 0.00 35.46 2.01
1488 1908 5.651530 TGAATTTTTCACGGTGCTGTAAAA 58.348 33.333 2.51 7.75 34.08 1.52
1489 1909 6.276847 TGAATTTTTCACGGTGCTGTAAAAT 58.723 32.000 2.51 9.47 34.44 1.82
1491 1911 3.634568 TTTCACGGTGCTGTAAAATGG 57.365 42.857 2.51 0.00 0.00 3.16
1492 1912 0.878416 TCACGGTGCTGTAAAATGGC 59.122 50.000 2.51 0.00 0.00 4.40
1493 1913 0.109319 CACGGTGCTGTAAAATGGCC 60.109 55.000 0.00 0.00 0.00 5.36
1495 1915 0.171007 CGGTGCTGTAAAATGGCCTG 59.829 55.000 3.32 0.00 0.00 4.85
1496 1916 1.544724 GGTGCTGTAAAATGGCCTGA 58.455 50.000 3.32 0.00 0.00 3.86
1497 1917 1.202348 GGTGCTGTAAAATGGCCTGAC 59.798 52.381 3.32 0.00 0.00 3.51
1498 1918 2.162681 GTGCTGTAAAATGGCCTGACT 58.837 47.619 3.32 0.00 0.00 3.41
1499 1919 2.095059 GTGCTGTAAAATGGCCTGACTG 60.095 50.000 3.32 0.22 0.00 3.51
1500 1920 2.162681 GCTGTAAAATGGCCTGACTGT 58.837 47.619 3.32 0.00 0.00 3.55
1501 1921 2.095059 GCTGTAAAATGGCCTGACTGTG 60.095 50.000 3.32 0.00 0.00 3.66
1502 1922 1.885887 TGTAAAATGGCCTGACTGTGC 59.114 47.619 3.32 0.00 0.00 4.57
1521 1941 2.028839 TGCCACAAGAATGCCAAGAATG 60.029 45.455 0.00 0.00 0.00 2.67
1546 1966 1.374631 CTCGCAGTGCCAGCTAACA 60.375 57.895 10.11 0.00 0.00 2.41
1548 1968 1.374631 CGCAGTGCCAGCTAACAGA 60.375 57.895 10.11 0.00 0.00 3.41
1569 1989 1.369625 CCACCGCTAATCTTCCACAC 58.630 55.000 0.00 0.00 0.00 3.82
1582 2002 2.044793 TCCACACTGGATTTCTCCCT 57.955 50.000 0.00 0.00 42.67 4.20
1584 2004 1.065126 CCACACTGGATTTCTCCCTCC 60.065 57.143 0.00 0.00 40.96 4.30
1587 2007 1.065126 CACTGGATTTCTCCCTCCACC 60.065 57.143 0.00 0.00 41.29 4.61
1588 2008 1.289160 CTGGATTTCTCCCTCCACCA 58.711 55.000 0.00 0.00 41.29 4.17
1589 2009 1.635487 CTGGATTTCTCCCTCCACCAA 59.365 52.381 0.00 0.00 41.29 3.67
1590 2010 2.243221 CTGGATTTCTCCCTCCACCAAT 59.757 50.000 0.00 0.00 41.29 3.16
1591 2011 2.025037 TGGATTTCTCCCTCCACCAATG 60.025 50.000 0.00 0.00 41.29 2.82
1592 2012 2.687914 GGATTTCTCCCTCCACCAATGG 60.688 54.545 0.00 0.00 40.61 3.16
1605 2025 2.754012 CCAATGGTGGTGGGTGATAT 57.246 50.000 0.00 0.00 40.42 1.63
1606 2026 3.874383 CCAATGGTGGTGGGTGATATA 57.126 47.619 0.00 0.00 40.42 0.86
1607 2027 3.486383 CCAATGGTGGTGGGTGATATAC 58.514 50.000 0.00 0.00 40.42 1.47
1608 2028 3.750599 CCAATGGTGGTGGGTGATATACC 60.751 52.174 0.00 0.00 43.60 2.73
1609 2029 5.986577 CCAATGGTGGTGGGTGATATACCT 61.987 50.000 0.00 0.00 43.72 3.08
1610 2030 6.700154 CCAATGGTGGTGGGTGATATACCTA 61.700 48.000 0.00 0.00 43.72 3.08
1611 2031 7.950045 CCAATGGTGGTGGGTGATATACCTAT 61.950 46.154 0.00 0.00 42.42 2.57
1612 2032 8.685253 CCAATGGTGGTGGGTGATATACCTATA 61.685 44.444 0.00 0.00 42.42 1.31
1622 2042 7.490657 GGTGATATACCTATACATGAACCCA 57.509 40.000 0.00 0.00 46.51 4.51
1626 2046 2.132686 ACCTATACATGAACCCACCCC 58.867 52.381 0.00 0.00 0.00 4.95
1630 2050 1.843462 TACATGAACCCACCCCCACG 61.843 60.000 0.00 0.00 0.00 4.94
1633 2053 4.340246 GAACCCACCCCCACGGTC 62.340 72.222 0.00 0.00 43.58 4.79
1642 2062 0.903454 CCCCCACGGTCAAGTACTCT 60.903 60.000 0.00 0.00 0.00 3.24
1682 2105 5.240891 TCAATATCCGGAGATCATTTCTGC 58.759 41.667 12.91 0.00 39.31 4.26
1686 2109 3.393472 GGAGATCATTTCTGCGCCT 57.607 52.632 4.18 0.00 33.74 5.52
1719 2142 4.589216 TCCTTGTTTCTTTCATGCTTGG 57.411 40.909 0.00 0.00 0.00 3.61
1720 2143 3.321682 TCCTTGTTTCTTTCATGCTTGGG 59.678 43.478 0.00 0.00 0.00 4.12
1730 2153 0.523072 CATGCTTGGGTGCAGTGTAC 59.477 55.000 2.25 2.25 46.71 2.90
1732 2156 0.250295 TGCTTGGGTGCAGTGTACTC 60.250 55.000 11.32 7.88 38.12 2.59
1736 2160 3.868369 GCTTGGGTGCAGTGTACTCATTA 60.868 47.826 15.11 0.00 0.00 1.90
1748 2176 8.383619 GCAGTGTACTCATTATAAAGTGTTGAG 58.616 37.037 10.23 10.23 39.70 3.02
1766 2208 5.221362 TGTTGAGACACTTTTCGACTATCCA 60.221 40.000 0.00 0.00 0.00 3.41
1783 2225 6.970484 ACTATCCACAACTGTTTCATCAAAC 58.030 36.000 0.00 0.00 42.16 2.93
1784 2226 4.647424 TCCACAACTGTTTCATCAAACC 57.353 40.909 0.00 0.00 41.25 3.27
1785 2227 4.019858 TCCACAACTGTTTCATCAAACCA 58.980 39.130 0.00 0.00 41.25 3.67
1825 2274 7.716998 TCTCTTGCTCTTTTCATACTTGAGTTT 59.283 33.333 0.00 0.00 32.27 2.66
1860 2309 1.205893 CTGTCCTCTAACTGGGAGTGC 59.794 57.143 0.00 0.00 31.66 4.40
1931 2380 4.735132 TTCCTCGGGCGTGCGAAG 62.735 66.667 0.00 0.00 0.00 3.79
1978 2427 5.009010 CACTAATGTGCCTTCTTCACTTGTT 59.991 40.000 0.00 0.00 37.38 2.83
1987 2436 4.319766 CCTTCTTCACTTGTTGATTGGTCG 60.320 45.833 0.00 0.00 32.84 4.79
2055 2504 3.944055 TCAAGGTAGAGCACTCTTGTC 57.056 47.619 5.33 0.00 40.93 3.18
2122 2578 4.670478 CGTTAATTTACGGACAAGCATGCA 60.670 41.667 21.98 0.00 37.86 3.96
2601 3084 7.037586 AGGTAAGATAACCAATCACTCCAAAGA 60.038 37.037 0.00 0.00 42.40 2.52
2831 3317 9.981114 AAAAAGTTGGTTATCAGGTATGAAAAG 57.019 29.630 0.00 0.00 39.39 2.27
2864 3350 6.209192 TCAATGTGATTTTATGGAGTGCAGTT 59.791 34.615 0.00 0.00 0.00 3.16
3183 3669 4.584743 TGCATCATCGGTATGAACTCTACT 59.415 41.667 0.00 0.00 45.12 2.57
3201 3791 5.665459 TCTACTTCTGCTCTTCCTTTATGC 58.335 41.667 0.00 0.00 0.00 3.14
3206 3796 5.636903 TCTGCTCTTCCTTTATGCCTTAT 57.363 39.130 0.00 0.00 0.00 1.73
3207 3797 6.006275 TCTGCTCTTCCTTTATGCCTTATT 57.994 37.500 0.00 0.00 0.00 1.40
3221 3811 2.883888 GCCTTATTGGTTTCCAGCCTGA 60.884 50.000 0.00 0.00 38.35 3.86
3222 3812 3.635591 CCTTATTGGTTTCCAGCCTGAT 58.364 45.455 0.00 0.00 33.81 2.90
3359 3950 6.346896 CAGACATATCCATGGATATCACCAG 58.653 44.000 34.97 26.89 43.59 4.00
3483 4076 3.555956 CGAGTTCCTCCACAAAATATCCG 59.444 47.826 0.00 0.00 0.00 4.18
3508 4281 3.053544 TGTGACACAAAGAACCCCCTTTA 60.054 43.478 5.62 0.00 34.85 1.85
3530 4303 1.886886 TTACCTGACAAAGAACCCGC 58.113 50.000 0.00 0.00 0.00 6.13
3531 4304 1.053424 TACCTGACAAAGAACCCGCT 58.947 50.000 0.00 0.00 0.00 5.52
3535 4308 2.338500 CTGACAAAGAACCCGCTCTAC 58.662 52.381 0.00 0.00 0.00 2.59
3553 4326 1.864750 CTTTGCCGAAATCGCAGCG 60.865 57.895 9.06 9.06 38.18 5.18
3578 4351 5.220605 GCGGTAGATTTTGTTGGATCTGTAC 60.221 44.000 0.00 0.00 34.60 2.90
3614 4387 1.659098 CTTTGCTACCATCGAACGACC 59.341 52.381 0.00 0.00 0.00 4.79
3668 4442 6.339730 TGAATAAAAATGGCATCCATGTGTC 58.660 36.000 0.00 0.00 44.40 3.67
3719 4493 7.125204 TCTGCCACATATACCCTTACCATATAC 59.875 40.741 0.00 0.00 0.00 1.47
3759 4533 8.632906 AAGAATCTTTTCACTCTGATGAATGT 57.367 30.769 0.00 0.00 38.37 2.71
3807 4582 3.955650 TGTCTTACTGACCAGTTAGGC 57.044 47.619 12.26 12.26 44.75 3.93
3836 4611 7.257790 TGAAATCTTGTTTCTCTGGAGGATA 57.742 36.000 0.00 0.00 0.00 2.59
3837 4612 7.865820 TGAAATCTTGTTTCTCTGGAGGATAT 58.134 34.615 0.00 0.00 0.00 1.63
3874 4650 7.094933 CCCTGTTCTGTGTAAGTGGTATTTTAC 60.095 40.741 0.00 0.00 0.00 2.01
3875 4651 7.660208 CCTGTTCTGTGTAAGTGGTATTTTACT 59.340 37.037 0.00 0.00 32.37 2.24
3876 4652 8.967664 TGTTCTGTGTAAGTGGTATTTTACTT 57.032 30.769 0.00 0.00 40.09 2.24
3877 4653 9.398538 TGTTCTGTGTAAGTGGTATTTTACTTT 57.601 29.630 0.00 0.00 38.11 2.66
3902 4678 4.510038 TTTACAGTCTCGGTGAGTAACC 57.490 45.455 0.00 0.00 46.60 2.85
3955 4736 1.102809 TGCAGGTTCTTGGTGTGCAG 61.103 55.000 0.00 0.00 39.17 4.41
4097 4882 2.100197 GCCTGGGGACAAAGGTAAATC 58.900 52.381 0.00 0.00 42.06 2.17
4103 4888 3.937079 GGGGACAAAGGTAAATCAGTACG 59.063 47.826 0.00 0.00 0.00 3.67
4111 4896 2.618053 GTAAATCAGTACGGCTGCTGT 58.382 47.619 19.28 19.28 44.66 4.40
4196 4986 4.446371 GAGGCTGTAGCATGAGTGTTATT 58.554 43.478 6.18 0.00 44.36 1.40
4212 5002 4.338400 GTGTTATTCCTAATCCCTGTTGCC 59.662 45.833 0.00 0.00 0.00 4.52
4213 5003 4.017958 TGTTATTCCTAATCCCTGTTGCCA 60.018 41.667 0.00 0.00 0.00 4.92
4244 5034 1.746615 CAGGGGAACACAGATGGCG 60.747 63.158 0.00 0.00 0.00 5.69
4283 5073 5.578615 GGTAACACCCATATGCTCCTGCA 62.579 52.174 0.00 0.00 42.55 4.41
4295 5085 1.202734 GCTCCTGCAATGCTAGATCCA 60.203 52.381 6.82 0.00 39.41 3.41
4296 5086 2.552591 GCTCCTGCAATGCTAGATCCAT 60.553 50.000 6.82 0.00 39.41 3.41
4297 5087 3.307269 GCTCCTGCAATGCTAGATCCATA 60.307 47.826 6.82 0.00 39.41 2.74
4432 5224 0.738762 CTGTGGCGATCTGTGTGAGG 60.739 60.000 0.00 0.00 0.00 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
19 20 6.492254 CGCAATGTAGTAGTAGTACACATCA 58.508 40.000 18.08 9.69 36.89 3.07
24 25 3.242837 CCGCGCAATGTAGTAGTAGTACA 60.243 47.826 18.03 18.03 38.28 2.90
26 27 2.945008 ACCGCGCAATGTAGTAGTAGTA 59.055 45.455 8.75 0.00 0.00 1.82
27 28 1.747355 ACCGCGCAATGTAGTAGTAGT 59.253 47.619 8.75 0.00 0.00 2.73
28 29 2.486951 ACCGCGCAATGTAGTAGTAG 57.513 50.000 8.75 0.00 0.00 2.57
43 44 3.303791 GGGAATGATCGTTGAATTACCGC 60.304 47.826 4.51 0.00 0.00 5.68
68 69 6.748333 TCATAACTGAATGCTCCTTTGAAG 57.252 37.500 0.00 0.00 0.00 3.02
105 106 8.048534 AGCTGTATGTATGATGCCATTATTTC 57.951 34.615 0.00 0.00 34.31 2.17
107 108 7.666804 TGAAGCTGTATGTATGATGCCATTATT 59.333 33.333 0.00 0.00 34.31 1.40
128 129 4.815269 TCTTCTTCTACTGAAGCTGAAGC 58.185 43.478 4.72 0.00 46.81 3.86
129 130 5.811613 CCATCTTCTTCTACTGAAGCTGAAG 59.188 44.000 8.35 3.44 46.81 3.02
130 131 5.481824 TCCATCTTCTTCTACTGAAGCTGAA 59.518 40.000 8.35 0.00 46.81 3.02
131 132 5.019470 TCCATCTTCTTCTACTGAAGCTGA 58.981 41.667 8.35 3.03 46.81 4.26
132 133 5.108517 GTCCATCTTCTTCTACTGAAGCTG 58.891 45.833 0.00 0.00 46.81 4.24
133 134 4.161377 GGTCCATCTTCTTCTACTGAAGCT 59.839 45.833 1.31 0.00 46.81 3.74
183 184 9.599866 TGACAGTATTAGTAGATGATTTGTTGG 57.400 33.333 0.00 0.00 0.00 3.77
198 199 6.849588 TGCTTGTATGCATGACAGTATTAG 57.150 37.500 10.16 5.30 38.12 1.73
201 202 4.036027 GCTTGCTTGTATGCATGACAGTAT 59.964 41.667 10.16 0.00 42.96 2.12
203 204 2.163010 GCTTGCTTGTATGCATGACAGT 59.837 45.455 10.16 0.00 42.96 3.55
204 205 2.162809 TGCTTGCTTGTATGCATGACAG 59.837 45.455 10.16 2.95 42.96 3.51
248 252 9.781834 CTTGTGTGAAATTCTTTGTAGTTTGTA 57.218 29.630 0.00 0.00 0.00 2.41
249 253 7.275560 GCTTGTGTGAAATTCTTTGTAGTTTGT 59.724 33.333 0.00 0.00 0.00 2.83
250 254 7.275341 TGCTTGTGTGAAATTCTTTGTAGTTTG 59.725 33.333 0.00 0.00 0.00 2.93
251 255 7.275560 GTGCTTGTGTGAAATTCTTTGTAGTTT 59.724 33.333 0.00 0.00 0.00 2.66
252 256 6.751888 GTGCTTGTGTGAAATTCTTTGTAGTT 59.248 34.615 0.00 0.00 0.00 2.24
253 257 6.265577 GTGCTTGTGTGAAATTCTTTGTAGT 58.734 36.000 0.00 0.00 0.00 2.73
254 258 5.396362 CGTGCTTGTGTGAAATTCTTTGTAG 59.604 40.000 0.00 0.00 0.00 2.74
273 277 3.194755 TCATGTATTGGTCAGTACGTGCT 59.805 43.478 16.18 0.00 39.15 4.40
274 278 3.517602 TCATGTATTGGTCAGTACGTGC 58.482 45.455 16.18 0.00 39.15 5.34
314 318 4.921547 TGCACTCGTCTATTGTCTGATAC 58.078 43.478 0.00 0.00 0.00 2.24
318 322 1.923204 GCTGCACTCGTCTATTGTCTG 59.077 52.381 0.00 0.00 0.00 3.51
319 323 1.134965 GGCTGCACTCGTCTATTGTCT 60.135 52.381 0.50 0.00 0.00 3.41
320 324 1.281899 GGCTGCACTCGTCTATTGTC 58.718 55.000 0.50 0.00 0.00 3.18
321 325 0.108138 GGGCTGCACTCGTCTATTGT 60.108 55.000 0.50 0.00 0.00 2.71
322 326 1.148157 CGGGCTGCACTCGTCTATTG 61.148 60.000 0.00 0.00 0.00 1.90
323 327 1.141881 CGGGCTGCACTCGTCTATT 59.858 57.895 0.00 0.00 0.00 1.73
324 328 1.109920 ATCGGGCTGCACTCGTCTAT 61.110 55.000 0.00 0.00 0.00 1.98
326 330 3.071206 ATCGGGCTGCACTCGTCT 61.071 61.111 0.00 0.00 0.00 4.18
327 331 2.887568 CATCGGGCTGCACTCGTC 60.888 66.667 0.00 0.00 0.00 4.20
352 368 3.451894 CCACCTTGAATGGCCGGC 61.452 66.667 21.18 21.18 0.00 6.13
353 369 1.606313 AACCACCTTGAATGGCCGG 60.606 57.895 0.00 0.00 41.31 6.13
354 370 1.586028 CAACCACCTTGAATGGCCG 59.414 57.895 0.00 0.00 41.31 6.13
355 371 0.541764 TCCAACCACCTTGAATGGCC 60.542 55.000 0.00 0.00 41.31 5.36
356 372 0.890683 CTCCAACCACCTTGAATGGC 59.109 55.000 0.00 0.00 41.31 4.40
357 373 1.075374 TCCTCCAACCACCTTGAATGG 59.925 52.381 0.00 0.00 43.43 3.16
358 374 2.440409 CTCCTCCAACCACCTTGAATG 58.560 52.381 0.00 0.00 30.42 2.67
359 375 1.355720 CCTCCTCCAACCACCTTGAAT 59.644 52.381 0.00 0.00 30.42 2.57
360 376 0.771127 CCTCCTCCAACCACCTTGAA 59.229 55.000 0.00 0.00 30.42 2.69
361 377 1.133809 CCCTCCTCCAACCACCTTGA 61.134 60.000 0.00 0.00 30.42 3.02
362 378 1.380302 CCCTCCTCCAACCACCTTG 59.620 63.158 0.00 0.00 0.00 3.61
363 379 1.852626 CCCCTCCTCCAACCACCTT 60.853 63.158 0.00 0.00 0.00 3.50
364 380 2.204151 CCCCTCCTCCAACCACCT 60.204 66.667 0.00 0.00 0.00 4.00
365 381 4.048470 GCCCCTCCTCCAACCACC 62.048 72.222 0.00 0.00 0.00 4.61
413 429 2.046892 CTTCTGCCAGTGGTCCGG 60.047 66.667 11.74 0.00 0.00 5.14
414 430 2.046892 CCTTCTGCCAGTGGTCCG 60.047 66.667 11.74 0.00 0.00 4.79
416 432 2.190488 CTCCCCTTCTGCCAGTGGTC 62.190 65.000 11.74 3.74 0.00 4.02
417 433 2.121963 TCCCCTTCTGCCAGTGGT 60.122 61.111 11.74 0.00 0.00 4.16
418 434 2.673523 CTCCCCTTCTGCCAGTGG 59.326 66.667 4.20 4.20 0.00 4.00
421 444 1.919600 CTTCCCTCCCCTTCTGCCAG 61.920 65.000 0.00 0.00 0.00 4.85
427 450 1.694525 CCCTCCTTCCCTCCCCTTC 60.695 68.421 0.00 0.00 0.00 3.46
439 462 2.272170 TCCCTCCCCATTCCCTCCT 61.272 63.158 0.00 0.00 0.00 3.69
447 470 0.633835 TACCTCTCCTCCCTCCCCAT 60.634 60.000 0.00 0.00 0.00 4.00
448 471 1.230853 TACCTCTCCTCCCTCCCCA 60.231 63.158 0.00 0.00 0.00 4.96
456 508 2.128507 CGGCCAGGTACCTCTCCTC 61.129 68.421 12.84 0.00 32.37 3.71
577 639 0.107459 GAGCCAGAGTCCAATCACCC 60.107 60.000 0.00 0.00 0.00 4.61
579 641 0.460987 CGGAGCCAGAGTCCAATCAC 60.461 60.000 0.00 0.00 33.14 3.06
580 642 1.617018 CCGGAGCCAGAGTCCAATCA 61.617 60.000 0.00 0.00 33.14 2.57
581 643 1.144936 CCGGAGCCAGAGTCCAATC 59.855 63.158 0.00 0.00 33.14 2.67
582 644 1.306141 TCCGGAGCCAGAGTCCAAT 60.306 57.895 0.00 0.00 33.14 3.16
583 645 2.119611 TCCGGAGCCAGAGTCCAA 59.880 61.111 0.00 0.00 33.14 3.53
584 646 2.680352 GTCCGGAGCCAGAGTCCA 60.680 66.667 3.06 0.00 33.14 4.02
585 647 2.363147 AGTCCGGAGCCAGAGTCC 60.363 66.667 3.06 0.00 0.00 3.85
586 648 2.766400 CGAGTCCGGAGCCAGAGTC 61.766 68.421 3.06 0.00 0.00 3.36
587 649 2.752238 CGAGTCCGGAGCCAGAGT 60.752 66.667 3.06 0.00 0.00 3.24
588 650 4.200283 GCGAGTCCGGAGCCAGAG 62.200 72.222 3.06 0.00 36.06 3.35
589 651 4.742649 AGCGAGTCCGGAGCCAGA 62.743 66.667 3.06 0.00 36.06 3.86
590 652 4.200283 GAGCGAGTCCGGAGCCAG 62.200 72.222 3.06 0.00 36.06 4.85
596 658 2.125512 CCCTTTGAGCGAGTCCGG 60.126 66.667 0.00 0.00 36.06 5.14
607 669 3.204827 CATCTCGGCCGCCCTTTG 61.205 66.667 23.51 9.60 0.00 2.77
642 705 0.670854 AAGAAGAAAGAGGCGCGGTC 60.671 55.000 8.83 0.00 0.00 4.79
644 707 1.362406 GGAAGAAGAAAGAGGCGCGG 61.362 60.000 8.83 0.00 0.00 6.46
649 712 7.757941 AAAAGAATCAGGAAGAAGAAAGAGG 57.242 36.000 0.00 0.00 0.00 3.69
1245 1324 1.387926 ATGGAGGGAATGGGGGAGG 60.388 63.158 0.00 0.00 0.00 4.30
1252 1331 2.624838 CGAAATTGGGATGGAGGGAATG 59.375 50.000 0.00 0.00 0.00 2.67
1253 1332 2.244769 ACGAAATTGGGATGGAGGGAAT 59.755 45.455 0.00 0.00 0.00 3.01
1255 1334 1.211949 GACGAAATTGGGATGGAGGGA 59.788 52.381 0.00 0.00 0.00 4.20
1257 1336 1.212935 AGGACGAAATTGGGATGGAGG 59.787 52.381 0.00 0.00 0.00 4.30
1259 1338 1.064758 CCAGGACGAAATTGGGATGGA 60.065 52.381 0.00 0.00 0.00 3.41
1260 1339 1.340991 ACCAGGACGAAATTGGGATGG 60.341 52.381 0.00 0.00 36.28 3.51
1261 1340 2.128771 ACCAGGACGAAATTGGGATG 57.871 50.000 0.00 0.00 36.28 3.51
1262 1341 2.899303 AACCAGGACGAAATTGGGAT 57.101 45.000 0.00 0.00 36.28 3.85
1263 1342 3.791953 TTAACCAGGACGAAATTGGGA 57.208 42.857 0.00 0.00 36.28 4.37
1267 1346 3.192633 GTGGCATTAACCAGGACGAAATT 59.807 43.478 0.00 0.00 41.46 1.82
1271 1350 0.981183 AGTGGCATTAACCAGGACGA 59.019 50.000 0.00 0.00 41.46 4.20
1294 1373 3.593551 AACGAAATGCCAGTGCGCG 62.594 57.895 0.00 0.00 41.78 6.86
1297 1376 0.508213 GCAAAACGAAATGCCAGTGC 59.492 50.000 0.00 0.00 36.56 4.40
1312 1406 1.586028 GAGCTGCGGATTTGGCAAA 59.414 52.632 16.01 16.01 40.39 3.68
1313 1407 2.342650 GGAGCTGCGGATTTGGCAA 61.343 57.895 0.00 0.00 40.39 4.52
1314 1408 2.751436 GGAGCTGCGGATTTGGCA 60.751 61.111 0.00 0.00 38.92 4.92
1315 1409 2.751436 TGGAGCTGCGGATTTGGC 60.751 61.111 0.00 0.00 0.00 4.52
1317 1411 1.989966 CTGCTGGAGCTGCGGATTTG 61.990 60.000 19.53 0.03 42.66 2.32
1318 1412 1.748122 CTGCTGGAGCTGCGGATTT 60.748 57.895 19.53 0.00 42.66 2.17
1319 1413 2.124819 CTGCTGGAGCTGCGGATT 60.125 61.111 19.53 0.00 42.66 3.01
1329 1488 1.279496 AGTACTGATTGGCTGCTGGA 58.721 50.000 0.00 0.00 0.00 3.86
1332 1491 1.202463 CGCTAGTACTGATTGGCTGCT 60.202 52.381 5.39 0.00 0.00 4.24
1337 1496 2.545526 CCAATGCGCTAGTACTGATTGG 59.454 50.000 14.92 14.92 35.29 3.16
1339 1498 2.838736 CCCAATGCGCTAGTACTGATT 58.161 47.619 9.73 0.00 0.00 2.57
1343 1502 1.146263 GGCCCAATGCGCTAGTACT 59.854 57.895 9.73 0.00 42.61 2.73
1346 1505 2.124570 CAGGCCCAATGCGCTAGT 60.125 61.111 9.73 0.00 42.61 2.57
1348 1507 4.504596 CCCAGGCCCAATGCGCTA 62.505 66.667 9.73 0.00 42.61 4.26
1352 1511 1.266867 ACATTTCCCAGGCCCAATGC 61.267 55.000 0.00 0.00 40.16 3.56
1355 1514 1.055040 CAAACATTTCCCAGGCCCAA 58.945 50.000 0.00 0.00 0.00 4.12
1356 1515 1.479368 GCAAACATTTCCCAGGCCCA 61.479 55.000 0.00 0.00 0.00 5.36
1357 1516 1.296392 GCAAACATTTCCCAGGCCC 59.704 57.895 0.00 0.00 0.00 5.80
1363 1522 1.676968 GGGTGGGCAAACATTTCCC 59.323 57.895 0.00 0.00 40.47 3.97
1364 1523 1.291906 CGGGTGGGCAAACATTTCC 59.708 57.895 0.00 0.00 0.00 3.13
1365 1524 0.038618 GACGGGTGGGCAAACATTTC 60.039 55.000 0.00 0.00 0.00 2.17
1367 1526 2.265182 CGACGGGTGGGCAAACATT 61.265 57.895 0.00 0.00 0.00 2.71
1375 1777 3.528370 CTAGAGGCGACGGGTGGG 61.528 72.222 0.00 0.00 0.00 4.61
1376 1778 3.528370 CCTAGAGGCGACGGGTGG 61.528 72.222 0.00 0.00 0.00 4.61
1389 1791 1.472376 GCCAACTGCTGTAGAGCCTAG 60.472 57.143 9.72 3.51 45.57 3.02
1401 1803 0.375106 GCTACATCGAAGCCAACTGC 59.625 55.000 0.00 0.00 41.71 4.40
1402 1804 0.647410 CGCTACATCGAAGCCAACTG 59.353 55.000 2.10 0.00 36.60 3.16
1408 1821 0.806102 TCTTGCCGCTACATCGAAGC 60.806 55.000 0.00 0.00 36.60 3.86
1411 1824 1.538204 GGATTCTTGCCGCTACATCGA 60.538 52.381 0.00 0.00 0.00 3.59
1412 1825 0.861837 GGATTCTTGCCGCTACATCG 59.138 55.000 0.00 0.00 0.00 3.84
1413 1826 0.861837 CGGATTCTTGCCGCTACATC 59.138 55.000 0.00 0.00 42.55 3.06
1414 1827 2.992089 CGGATTCTTGCCGCTACAT 58.008 52.632 0.00 0.00 42.55 2.29
1421 1834 1.078143 AGTCAGCCGGATTCTTGCC 60.078 57.895 5.05 0.00 0.00 4.52
1423 1836 0.674581 TGCAGTCAGCCGGATTCTTG 60.675 55.000 5.05 0.00 44.83 3.02
1424 1837 0.036732 TTGCAGTCAGCCGGATTCTT 59.963 50.000 5.05 0.00 44.83 2.52
1429 1842 0.674581 CAGATTTGCAGTCAGCCGGA 60.675 55.000 5.05 0.00 44.83 5.14
1441 1854 2.161012 AGAGTCGTGCATTGCAGATTTG 59.839 45.455 12.53 0.21 40.08 2.32
1442 1855 2.430465 AGAGTCGTGCATTGCAGATTT 58.570 42.857 12.53 5.01 40.08 2.17
1444 1857 2.167281 AGTAGAGTCGTGCATTGCAGAT 59.833 45.455 12.53 0.00 40.08 2.90
1445 1858 1.546029 AGTAGAGTCGTGCATTGCAGA 59.454 47.619 12.53 8.96 40.08 4.26
1447 1860 1.272212 TCAGTAGAGTCGTGCATTGCA 59.728 47.619 7.38 7.38 35.60 4.08
1449 1862 5.536554 AAATTCAGTAGAGTCGTGCATTG 57.463 39.130 0.00 0.00 0.00 2.82
1451 1864 5.700832 TGAAAAATTCAGTAGAGTCGTGCAT 59.299 36.000 0.00 0.00 34.08 3.96
1457 1877 5.614887 GCACCGTGAAAAATTCAGTAGAGTC 60.615 44.000 1.65 0.00 41.01 3.36
1461 1881 4.024048 ACAGCACCGTGAAAAATTCAGTAG 60.024 41.667 1.65 0.00 41.01 2.57
1462 1882 3.880490 ACAGCACCGTGAAAAATTCAGTA 59.120 39.130 1.65 0.00 41.01 2.74
1463 1883 2.687935 ACAGCACCGTGAAAAATTCAGT 59.312 40.909 1.65 0.00 41.01 3.41
1465 1885 4.902443 TTACAGCACCGTGAAAAATTCA 57.098 36.364 1.65 0.00 37.33 2.57
1466 1886 6.346518 CCATTTTACAGCACCGTGAAAAATTC 60.347 38.462 1.65 0.00 29.49 2.17
1467 1887 5.465056 CCATTTTACAGCACCGTGAAAAATT 59.535 36.000 1.65 0.00 29.49 1.82
1469 1889 4.363999 CCATTTTACAGCACCGTGAAAAA 58.636 39.130 1.65 3.76 29.49 1.94
1479 1899 2.161855 CAGTCAGGCCATTTTACAGCA 58.838 47.619 5.01 0.00 0.00 4.41
1480 1900 2.095059 CACAGTCAGGCCATTTTACAGC 60.095 50.000 5.01 0.00 0.00 4.40
1481 1901 2.095059 GCACAGTCAGGCCATTTTACAG 60.095 50.000 5.01 0.00 0.00 2.74
1483 1903 2.636768 GCACAGTCAGGCCATTTTAC 57.363 50.000 5.01 0.00 0.00 2.01
1491 1911 0.819259 TTCTTGTGGCACAGTCAGGC 60.819 55.000 20.97 0.00 41.80 4.85
1492 1912 1.538512 CATTCTTGTGGCACAGTCAGG 59.461 52.381 20.97 8.22 41.80 3.86
1493 1913 1.068748 GCATTCTTGTGGCACAGTCAG 60.069 52.381 20.97 15.43 41.80 3.51
1495 1915 0.242017 GGCATTCTTGTGGCACAGTC 59.758 55.000 20.97 6.54 41.80 3.51
1496 1916 2.344535 GGCATTCTTGTGGCACAGT 58.655 52.632 20.97 5.79 41.80 3.55
1501 1921 2.028748 ACATTCTTGGCATTCTTGTGGC 60.029 45.455 0.00 0.00 44.24 5.01
1502 1922 3.581755 CACATTCTTGGCATTCTTGTGG 58.418 45.455 11.20 0.00 31.67 4.17
1503 1923 3.581755 CCACATTCTTGGCATTCTTGTG 58.418 45.455 11.80 11.80 34.30 3.33
1504 1924 3.947910 CCACATTCTTGGCATTCTTGT 57.052 42.857 0.00 0.00 0.00 3.16
1554 1974 2.672961 TCCAGTGTGGAAGATTAGCG 57.327 50.000 0.00 0.00 45.00 4.26
1569 1989 1.289160 TGGTGGAGGGAGAAATCCAG 58.711 55.000 0.00 0.00 46.09 3.86
1587 2007 3.486383 GGTATATCACCCACCACCATTG 58.514 50.000 0.00 0.00 42.07 2.82
1588 2008 3.876309 GGTATATCACCCACCACCATT 57.124 47.619 0.00 0.00 42.07 3.16
1599 2019 7.328737 GGTGGGTTCATGTATAGGTATATCAC 58.671 42.308 0.00 0.00 0.00 3.06
1601 2021 6.126854 GGGGTGGGTTCATGTATAGGTATATC 60.127 46.154 0.00 0.00 0.00 1.63
1602 2022 5.729718 GGGGTGGGTTCATGTATAGGTATAT 59.270 44.000 0.00 0.00 0.00 0.86
1603 2023 5.095809 GGGGTGGGTTCATGTATAGGTATA 58.904 45.833 0.00 0.00 0.00 1.47
1604 2024 3.914435 GGGGTGGGTTCATGTATAGGTAT 59.086 47.826 0.00 0.00 0.00 2.73
1605 2025 3.320129 GGGGTGGGTTCATGTATAGGTA 58.680 50.000 0.00 0.00 0.00 3.08
1606 2026 2.132686 GGGGTGGGTTCATGTATAGGT 58.867 52.381 0.00 0.00 0.00 3.08
1607 2027 1.423921 GGGGGTGGGTTCATGTATAGG 59.576 57.143 0.00 0.00 0.00 2.57
1608 2028 2.131854 TGGGGGTGGGTTCATGTATAG 58.868 52.381 0.00 0.00 0.00 1.31
1609 2029 1.847737 GTGGGGGTGGGTTCATGTATA 59.152 52.381 0.00 0.00 0.00 1.47
1610 2030 0.629058 GTGGGGGTGGGTTCATGTAT 59.371 55.000 0.00 0.00 0.00 2.29
1611 2031 1.843462 CGTGGGGGTGGGTTCATGTA 61.843 60.000 0.00 0.00 0.00 2.29
1612 2032 2.851045 GTGGGGGTGGGTTCATGT 59.149 61.111 0.00 0.00 0.00 3.21
1613 2033 2.361104 CGTGGGGGTGGGTTCATG 60.361 66.667 0.00 0.00 0.00 3.07
1614 2034 3.657350 CCGTGGGGGTGGGTTCAT 61.657 66.667 0.00 0.00 0.00 2.57
1626 2046 2.165167 TGGTAGAGTACTTGACCGTGG 58.835 52.381 17.67 0.00 34.49 4.94
1630 2050 5.508200 CTCTGATGGTAGAGTACTTGACC 57.492 47.826 16.57 16.57 39.45 4.02
1642 2062 8.088365 CGGATATTGATTAACACTCTGATGGTA 58.912 37.037 0.00 0.00 0.00 3.25
1653 2076 9.219603 GAAATGATCTCCGGATATTGATTAACA 57.780 33.333 3.57 0.00 31.46 2.41
1656 2079 7.550551 GCAGAAATGATCTCCGGATATTGATTA 59.449 37.037 3.57 0.91 35.73 1.75
1657 2080 6.373774 GCAGAAATGATCTCCGGATATTGATT 59.626 38.462 3.57 3.52 35.73 2.57
1658 2081 5.879223 GCAGAAATGATCTCCGGATATTGAT 59.121 40.000 3.57 3.65 35.73 2.57
1659 2082 5.240891 GCAGAAATGATCTCCGGATATTGA 58.759 41.667 3.57 0.00 35.73 2.57
1660 2083 4.092529 CGCAGAAATGATCTCCGGATATTG 59.907 45.833 3.57 0.00 35.63 1.90
1698 2121 3.321682 CCCAAGCATGAAAGAAACAAGGA 59.678 43.478 0.00 0.00 0.00 3.36
1714 2137 0.250295 TGAGTACACTGCACCCAAGC 60.250 55.000 0.00 0.00 0.00 4.01
1719 2142 6.594159 ACACTTTATAATGAGTACACTGCACC 59.406 38.462 5.43 0.00 0.00 5.01
1720 2143 7.596749 ACACTTTATAATGAGTACACTGCAC 57.403 36.000 5.43 0.00 0.00 4.57
1748 2176 4.989168 AGTTGTGGATAGTCGAAAAGTGTC 59.011 41.667 0.00 0.00 0.00 3.67
1756 2184 4.594123 TGAAACAGTTGTGGATAGTCGA 57.406 40.909 0.00 0.00 0.00 4.20
1757 2185 4.929211 TGATGAAACAGTTGTGGATAGTCG 59.071 41.667 0.00 0.00 0.00 4.18
1759 2187 6.016276 GGTTTGATGAAACAGTTGTGGATAGT 60.016 38.462 10.02 0.00 42.95 2.12
1760 2188 6.016360 TGGTTTGATGAAACAGTTGTGGATAG 60.016 38.462 10.02 0.00 42.95 2.08
1761 2189 5.830457 TGGTTTGATGAAACAGTTGTGGATA 59.170 36.000 10.02 0.00 42.95 2.59
1766 2208 5.105392 ACACATGGTTTGATGAAACAGTTGT 60.105 36.000 10.02 6.84 42.95 3.32
1783 2225 6.286758 AGCAAGAGATGAGTAATACACATGG 58.713 40.000 8.02 0.00 29.65 3.66
1784 2226 7.208777 AGAGCAAGAGATGAGTAATACACATG 58.791 38.462 8.02 0.00 29.65 3.21
1785 2227 7.358770 AGAGCAAGAGATGAGTAATACACAT 57.641 36.000 3.05 3.05 32.15 3.21
1825 2274 2.375174 AGGACAGCAATGGGAGTTTACA 59.625 45.455 0.00 0.00 0.00 2.41
1860 2309 2.421424 GGCTGAACAGGACAAGCATTAG 59.579 50.000 3.99 0.00 0.00 1.73
1954 2403 9.066637 TCAACAAGTGAAGAAGGCACATTAGTG 62.067 40.741 0.00 0.00 40.16 2.74
1978 2427 0.737367 CGAAGCTCAGCGACCAATCA 60.737 55.000 0.00 0.00 0.00 2.57
1987 2436 0.391661 TGTCATTCCCGAAGCTCAGC 60.392 55.000 0.00 0.00 0.00 4.26
2111 2567 1.734707 GCAAGTGGATGCATGCTTGTC 60.735 52.381 20.33 13.70 45.70 3.18
2112 2568 0.245539 GCAAGTGGATGCATGCTTGT 59.754 50.000 20.33 4.79 45.70 3.16
2122 2578 5.933463 CCAACAAATACAAATGCAAGTGGAT 59.067 36.000 0.00 0.00 0.00 3.41
2349 2832 4.112634 AGATTAGGTTTGGAGTTGGCAA 57.887 40.909 0.00 0.00 0.00 4.52
2831 3317 7.555087 TCCATAAAATCACATTGAATTCACCC 58.445 34.615 7.89 0.00 0.00 4.61
3070 3556 2.197465 GAAACCCTATCTGGTCCACCT 58.803 52.381 0.00 0.00 37.76 4.00
3183 3669 4.307032 AAGGCATAAAGGAAGAGCAGAA 57.693 40.909 0.00 0.00 0.00 3.02
3201 3791 3.085952 TCAGGCTGGAAACCAATAAGG 57.914 47.619 15.73 0.00 45.67 2.69
3206 3796 0.968405 GCAATCAGGCTGGAAACCAA 59.032 50.000 15.73 0.00 30.80 3.67
3207 3797 0.899717 GGCAATCAGGCTGGAAACCA 60.900 55.000 15.73 0.00 40.24 3.67
3359 3950 1.226717 CCGAGCGTCTGAGTTAGCC 60.227 63.158 0.00 0.00 0.00 3.93
3396 3987 2.024941 TGTAGCTCTGACTCCATCCAGA 60.025 50.000 0.00 0.00 37.77 3.86
3483 4076 1.947456 GGGGTTCTTTGTGTCACACTC 59.053 52.381 9.90 0.00 35.11 3.51
3508 4281 3.254903 GCGGGTTCTTTGTCAGGTAAAAT 59.745 43.478 0.00 0.00 0.00 1.82
3530 4303 1.999735 TGCGATTTCGGCAAAGTAGAG 59.000 47.619 1.75 0.00 40.23 2.43
3531 4304 1.999735 CTGCGATTTCGGCAAAGTAGA 59.000 47.619 1.75 0.00 40.23 2.59
3535 4308 1.864750 CGCTGCGATTTCGGCAAAG 60.865 57.895 18.66 0.00 40.23 2.77
3553 4326 3.065371 CAGATCCAACAAAATCTACCGCC 59.935 47.826 0.00 0.00 31.10 6.13
3578 4351 2.902484 GCAAAGTTACATCTTTCACGCG 59.098 45.455 3.53 3.53 35.77 6.01
3614 4387 2.554032 CAGACAGTAAAACCAAGGGCAG 59.446 50.000 0.00 0.00 0.00 4.85
3719 4493 7.636150 AAAGATTCTTCATTGGTGATACTGG 57.364 36.000 0.00 0.00 33.56 4.00
3788 4562 3.851098 CAGCCTAACTGGTCAGTAAGAC 58.149 50.000 3.87 0.00 46.83 3.01
3807 4582 4.082895 CCAGAGAAACAAGATTTCAGCCAG 60.083 45.833 2.51 0.00 0.00 4.85
3818 4593 9.921637 GTAAGATATATCCTCCAGAGAAACAAG 57.078 37.037 9.18 0.00 0.00 3.16
3836 4611 5.721960 ACACAGAACAGGGTCAGTAAGATAT 59.278 40.000 0.00 0.00 0.00 1.63
3837 4612 5.084519 ACACAGAACAGGGTCAGTAAGATA 58.915 41.667 0.00 0.00 0.00 1.98
3874 4650 7.653767 ACTCACCGAGACTGTAAAATAAAAG 57.346 36.000 0.00 0.00 33.32 2.27
3875 4651 8.981647 GTTACTCACCGAGACTGTAAAATAAAA 58.018 33.333 0.00 0.00 33.32 1.52
3876 4652 7.599998 GGTTACTCACCGAGACTGTAAAATAAA 59.400 37.037 0.00 0.00 35.12 1.40
3877 4653 7.092716 GGTTACTCACCGAGACTGTAAAATAA 58.907 38.462 0.00 0.00 35.12 1.40
3878 4654 6.624423 GGTTACTCACCGAGACTGTAAAATA 58.376 40.000 0.00 0.00 35.12 1.40
3879 4655 5.476614 GGTTACTCACCGAGACTGTAAAAT 58.523 41.667 0.00 0.00 35.12 1.82
3919 4695 6.360370 ACCTGCACTTCAATCTACTTTAGA 57.640 37.500 0.00 0.00 39.50 2.10
3955 4736 0.595095 CTGCTTGGGTTTGACAGAGC 59.405 55.000 0.00 0.00 0.00 4.09
4025 4810 0.106769 TGTTGCTTCTGCCACAAGGA 60.107 50.000 0.00 0.00 41.06 3.36
4174 4964 2.393271 AACACTCATGCTACAGCCTC 57.607 50.000 0.00 0.00 41.18 4.70
4212 5002 1.246056 CCCCTGCAGTGTGGTCAATG 61.246 60.000 13.81 0.00 41.74 2.82
4213 5003 1.075482 CCCCTGCAGTGTGGTCAAT 59.925 57.895 13.81 0.00 0.00 2.57
4256 5046 1.981256 CATATGGGTGTTACCTGGGC 58.019 55.000 0.00 0.00 38.64 5.36
4336 5126 3.012518 ACATTCACTAACTGGCATGCTC 58.987 45.455 18.92 8.46 0.00 4.26
4420 5212 3.062585 GAGCTGCCTCACACAGATC 57.937 57.895 0.00 0.00 42.63 2.75


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

AutoCloner maintained by Alex Coulton.