Multiple sequence alignment - TraesCS6D01G067800

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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 TraesCS6D01G067800 chr6D 100.000 3143 0 0 1 3143 33894053 33897195 0.000000e+00 5805.0
1 TraesCS6D01G067800 chr6D 87.339 1477 175 9 1091 2557 8987334 8988808 0.000000e+00 1681.0
2 TraesCS6D01G067800 chr6D 92.275 699 37 8 2353 3042 8567307 8566617 0.000000e+00 976.0
3 TraesCS6D01G067800 chr6D 78.768 1380 239 33 808 2161 8893879 8895230 0.000000e+00 876.0
4 TraesCS6D01G067800 chr6D 78.448 348 38 22 811 1142 8402592 8402266 3.200000e-45 193.0
5 TraesCS6D01G067800 chr6D 90.541 74 4 2 803 876 34006896 34006966 9.280000e-16 95.3
6 TraesCS6D01G067800 chr5B 86.443 1999 225 27 991 2963 556795758 556793780 0.000000e+00 2148.0
7 TraesCS6D01G067800 chr5B 98.039 51 1 0 2971 3021 556793788 556793738 4.320000e-14 89.8
8 TraesCS6D01G067800 chr5B 89.231 65 5 1 798 862 621238422 621238360 2.600000e-11 80.5
9 TraesCS6D01G067800 chr6A 86.835 1937 231 16 1115 3042 9355310 9357231 0.000000e+00 2143.0
10 TraesCS6D01G067800 chr6A 88.482 1146 124 7 1112 2254 9040184 9039044 0.000000e+00 1378.0
11 TraesCS6D01G067800 chr6B 87.978 1855 164 32 940 2758 15715259 15713428 0.000000e+00 2135.0
12 TraesCS6D01G067800 chr6B 86.164 2002 241 27 984 2963 15397963 15395976 0.000000e+00 2130.0
13 TraesCS6D01G067800 chr6B 90.567 1516 123 10 881 2377 16237181 16238695 0.000000e+00 1989.0
14 TraesCS6D01G067800 chr6B 84.381 2068 237 32 993 3042 670592702 670590703 0.000000e+00 1951.0
15 TraesCS6D01G067800 chr6B 87.054 1653 174 24 943 2557 16320505 16322155 0.000000e+00 1831.0
16 TraesCS6D01G067800 chr6B 84.642 1439 170 30 956 2377 15264324 15262920 0.000000e+00 1386.0
17 TraesCS6D01G067800 chr6B 86.118 1203 151 12 958 2150 15249540 15248344 0.000000e+00 1282.0
18 TraesCS6D01G067800 chr6B 95.402 348 16 0 1 348 16234444 16234791 3.540000e-154 555.0
19 TraesCS6D01G067800 chr6B 80.163 615 72 16 2366 2942 15215462 15214860 6.270000e-112 414.0
20 TraesCS6D01G067800 chr6B 80.065 612 73 17 2366 2939 90940906 90941506 2.920000e-110 409.0
21 TraesCS6D01G067800 chr6B 78.804 184 21 3 2839 3020 16238726 16238893 1.190000e-19 108.0
22 TraesCS6D01G067800 chr6B 98.039 51 1 0 2971 3021 15395984 15395934 4.320000e-14 89.8
23 TraesCS6D01G067800 chr6B 84.211 76 9 3 804 878 52981185 52981112 1.560000e-08 71.3
24 TraesCS6D01G067800 chr6B 100.000 30 0 0 3013 3042 16238910 16238939 4.380000e-04 56.5
25 TraesCS6D01G067800 chr2B 84.379 2087 277 41 984 3042 709569776 709567711 0.000000e+00 2002.0
26 TraesCS6D01G067800 chr2B 80.760 1289 191 21 1703 2957 89491332 89492597 0.000000e+00 953.0
27 TraesCS6D01G067800 chr2B 81.383 752 120 7 1661 2408 709321246 709320511 2.090000e-166 595.0
28 TraesCS6D01G067800 chr3B 84.269 1443 188 23 956 2377 778342946 778341522 0.000000e+00 1371.0
29 TraesCS6D01G067800 chr3D 85.343 1078 130 20 943 1999 582879791 582880861 0.000000e+00 1090.0
30 TraesCS6D01G067800 chr2D 82.686 1184 190 12 944 2122 588162236 588163409 0.000000e+00 1037.0
31 TraesCS6D01G067800 chr4B 94.979 239 12 0 1 239 72886550 72886788 2.960000e-100 375.0
32 TraesCS6D01G067800 chr5D 82.212 416 43 13 2557 2963 42077645 42078038 2.340000e-86 329.0
33 TraesCS6D01G067800 chr5A 89.231 65 5 1 798 862 624205412 624205350 2.600000e-11 80.5


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 TraesCS6D01G067800 chr6D 33894053 33897195 3142 False 5805.000 5805 100.00000 1 3143 1 chr6D.!!$F3 3142
1 TraesCS6D01G067800 chr6D 8987334 8988808 1474 False 1681.000 1681 87.33900 1091 2557 1 chr6D.!!$F2 1466
2 TraesCS6D01G067800 chr6D 8566617 8567307 690 True 976.000 976 92.27500 2353 3042 1 chr6D.!!$R2 689
3 TraesCS6D01G067800 chr6D 8893879 8895230 1351 False 876.000 876 78.76800 808 2161 1 chr6D.!!$F1 1353
4 TraesCS6D01G067800 chr5B 556793738 556795758 2020 True 1118.900 2148 92.24100 991 3021 2 chr5B.!!$R2 2030
5 TraesCS6D01G067800 chr6A 9355310 9357231 1921 False 2143.000 2143 86.83500 1115 3042 1 chr6A.!!$F1 1927
6 TraesCS6D01G067800 chr6A 9039044 9040184 1140 True 1378.000 1378 88.48200 1112 2254 1 chr6A.!!$R1 1142
7 TraesCS6D01G067800 chr6B 15713428 15715259 1831 True 2135.000 2135 87.97800 940 2758 1 chr6B.!!$R4 1818
8 TraesCS6D01G067800 chr6B 670590703 670592702 1999 True 1951.000 1951 84.38100 993 3042 1 chr6B.!!$R6 2049
9 TraesCS6D01G067800 chr6B 16320505 16322155 1650 False 1831.000 1831 87.05400 943 2557 1 chr6B.!!$F1 1614
10 TraesCS6D01G067800 chr6B 15262920 15264324 1404 True 1386.000 1386 84.64200 956 2377 1 chr6B.!!$R3 1421
11 TraesCS6D01G067800 chr6B 15248344 15249540 1196 True 1282.000 1282 86.11800 958 2150 1 chr6B.!!$R2 1192
12 TraesCS6D01G067800 chr6B 15395934 15397963 2029 True 1109.900 2130 92.10150 984 3021 2 chr6B.!!$R7 2037
13 TraesCS6D01G067800 chr6B 16234444 16238939 4495 False 677.125 1989 91.19325 1 3042 4 chr6B.!!$F3 3041
14 TraesCS6D01G067800 chr6B 15214860 15215462 602 True 414.000 414 80.16300 2366 2942 1 chr6B.!!$R1 576
15 TraesCS6D01G067800 chr6B 90940906 90941506 600 False 409.000 409 80.06500 2366 2939 1 chr6B.!!$F2 573
16 TraesCS6D01G067800 chr2B 709567711 709569776 2065 True 2002.000 2002 84.37900 984 3042 1 chr2B.!!$R2 2058
17 TraesCS6D01G067800 chr2B 89491332 89492597 1265 False 953.000 953 80.76000 1703 2957 1 chr2B.!!$F1 1254
18 TraesCS6D01G067800 chr2B 709320511 709321246 735 True 595.000 595 81.38300 1661 2408 1 chr2B.!!$R1 747
19 TraesCS6D01G067800 chr3B 778341522 778342946 1424 True 1371.000 1371 84.26900 956 2377 1 chr3B.!!$R1 1421
20 TraesCS6D01G067800 chr3D 582879791 582880861 1070 False 1090.000 1090 85.34300 943 1999 1 chr3D.!!$F1 1056
21 TraesCS6D01G067800 chr2D 588162236 588163409 1173 False 1037.000 1037 82.68600 944 2122 1 chr2D.!!$F1 1178

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
512 513 0.110010 GCTCTCGTGCTTCCTTTTGC 60.110 55.0 0.0 0.0 0.0 3.68 F
528 529 0.111061 TTGCTCAAGACATGCTGGGT 59.889 50.0 0.0 0.0 0.0 4.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1778 3833 0.539438 AAAAGCAATGCCCACCTCGA 60.539 50.000 0.0 0.0 0.0 4.04 R
2176 4231 1.208052 AGACATACAGCAGCGGACAAT 59.792 47.619 0.0 0.0 0.0 2.71 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
42 43 6.982852 AGGTACCAGATATATTCGACACTTG 58.017 40.000 15.94 0.00 0.00 3.16
45 46 6.465439 ACCAGATATATTCGACACTTGTCA 57.535 37.500 9.94 0.00 44.99 3.58
50 51 7.378194 CAGATATATTCGACACTTGTCAGACAG 59.622 40.741 9.94 1.18 44.99 3.51
151 152 7.201767 GGATGGTCCAAGAGAAAATGTGATTAG 60.202 40.741 0.00 0.00 36.28 1.73
152 153 6.778821 TGGTCCAAGAGAAAATGTGATTAGA 58.221 36.000 0.00 0.00 0.00 2.10
169 170 2.745515 AGACTCTAAAAGGTGCGGTC 57.254 50.000 0.00 0.00 0.00 4.79
186 187 6.080406 GTGCGGTCATTTCTTCTTTTTCTAG 58.920 40.000 0.00 0.00 0.00 2.43
218 219 1.451449 ATGTGGTGGTTGGGACCTTA 58.549 50.000 0.00 0.00 46.66 2.69
291 292 8.556194 TGATATGCCATCGTAAGTTTTATTGAC 58.444 33.333 0.00 0.00 39.48 3.18
296 297 6.961554 GCCATCGTAAGTTTTATTGACAGAAG 59.038 38.462 0.00 0.00 39.48 2.85
418 419 5.537300 ACAGAGCGAATACATGTTATCCT 57.463 39.130 2.30 2.85 0.00 3.24
420 421 7.233389 ACAGAGCGAATACATGTTATCCTAT 57.767 36.000 2.30 0.00 0.00 2.57
421 422 8.349568 ACAGAGCGAATACATGTTATCCTATA 57.650 34.615 2.30 0.00 0.00 1.31
422 423 8.972127 ACAGAGCGAATACATGTTATCCTATAT 58.028 33.333 2.30 0.00 0.00 0.86
440 441 7.402054 TCCTATATATTGCAATGTACAAGGGG 58.598 38.462 28.08 20.14 0.00 4.79
441 442 7.238723 TCCTATATATTGCAATGTACAAGGGGA 59.761 37.037 28.08 21.33 0.00 4.81
442 443 7.336931 CCTATATATTGCAATGTACAAGGGGAC 59.663 40.741 24.65 0.00 0.00 4.46
443 444 2.666272 TTGCAATGTACAAGGGGACA 57.334 45.000 0.00 0.00 0.00 4.02
444 445 2.666272 TGCAATGTACAAGGGGACAA 57.334 45.000 0.00 0.00 0.00 3.18
445 446 2.950781 TGCAATGTACAAGGGGACAAA 58.049 42.857 0.00 0.00 0.00 2.83
446 447 2.625790 TGCAATGTACAAGGGGACAAAC 59.374 45.455 0.00 0.00 0.00 2.93
447 448 2.625790 GCAATGTACAAGGGGACAAACA 59.374 45.455 0.00 0.00 0.00 2.83
448 449 3.068873 GCAATGTACAAGGGGACAAACAA 59.931 43.478 0.00 0.00 0.00 2.83
449 450 4.616953 CAATGTACAAGGGGACAAACAAC 58.383 43.478 0.00 0.00 0.00 3.32
450 451 3.367646 TGTACAAGGGGACAAACAACA 57.632 42.857 0.00 0.00 0.00 3.33
451 452 3.698289 TGTACAAGGGGACAAACAACAA 58.302 40.909 0.00 0.00 0.00 2.83
452 453 3.697045 TGTACAAGGGGACAAACAACAAG 59.303 43.478 0.00 0.00 0.00 3.16
455 456 3.056179 ACAAGGGGACAAACAACAAGTTG 60.056 43.478 11.16 11.16 45.58 3.16
456 457 3.094484 AGGGGACAAACAACAAGTTGA 57.906 42.857 18.90 0.00 42.93 3.18
457 458 3.436243 AGGGGACAAACAACAAGTTGAA 58.564 40.909 18.90 0.00 42.93 2.69
458 459 4.030216 AGGGGACAAACAACAAGTTGAAT 58.970 39.130 18.90 5.26 42.93 2.57
459 460 4.119136 GGGGACAAACAACAAGTTGAATG 58.881 43.478 18.90 16.96 42.93 2.67
460 461 4.142049 GGGGACAAACAACAAGTTGAATGA 60.142 41.667 18.90 0.00 42.93 2.57
461 462 5.415221 GGGACAAACAACAAGTTGAATGAA 58.585 37.500 18.90 0.00 42.93 2.57
464 465 6.253512 GGACAAACAACAAGTTGAATGAAGTC 59.746 38.462 18.90 15.42 42.93 3.01
465 466 6.686630 ACAAACAACAAGTTGAATGAAGTCA 58.313 32.000 18.90 0.00 42.93 3.41
466 467 7.151308 ACAAACAACAAGTTGAATGAAGTCAA 58.849 30.769 18.90 0.00 42.93 3.18
475 476 5.362556 TTGAATGAAGTCAACTAAGCTGC 57.637 39.130 0.00 0.00 32.56 5.25
476 477 4.388485 TGAATGAAGTCAACTAAGCTGCA 58.612 39.130 1.02 0.00 0.00 4.41
479 480 4.277515 TGAAGTCAACTAAGCTGCATCT 57.722 40.909 1.02 0.00 0.00 2.90
480 481 3.999001 TGAAGTCAACTAAGCTGCATCTG 59.001 43.478 1.02 0.00 0.00 2.90
481 482 2.983229 AGTCAACTAAGCTGCATCTGG 58.017 47.619 1.02 0.00 0.00 3.86
482 483 2.304180 AGTCAACTAAGCTGCATCTGGT 59.696 45.455 1.02 0.00 0.00 4.00
488 489 3.455910 ACTAAGCTGCATCTGGTGGATTA 59.544 43.478 1.02 0.00 31.27 1.75
489 490 3.370840 AAGCTGCATCTGGTGGATTAA 57.629 42.857 1.02 0.00 31.27 1.40
490 491 3.589951 AGCTGCATCTGGTGGATTAAT 57.410 42.857 1.02 0.00 31.27 1.40
491 492 3.220110 AGCTGCATCTGGTGGATTAATG 58.780 45.455 1.02 0.00 31.27 1.90
493 494 2.889045 CTGCATCTGGTGGATTAATGGG 59.111 50.000 0.00 0.00 31.27 4.00
494 495 1.615392 GCATCTGGTGGATTAATGGGC 59.385 52.381 0.00 0.00 31.27 5.36
495 496 2.754186 GCATCTGGTGGATTAATGGGCT 60.754 50.000 0.00 0.00 31.27 5.19
496 497 3.152341 CATCTGGTGGATTAATGGGCTC 58.848 50.000 0.00 0.00 31.27 4.70
497 498 2.492025 TCTGGTGGATTAATGGGCTCT 58.508 47.619 0.00 0.00 0.00 4.09
498 499 2.439507 TCTGGTGGATTAATGGGCTCTC 59.560 50.000 0.00 0.00 0.00 3.20
499 500 1.140852 TGGTGGATTAATGGGCTCTCG 59.859 52.381 0.00 0.00 0.00 4.04
502 503 1.230324 GGATTAATGGGCTCTCGTGC 58.770 55.000 0.00 0.00 0.00 5.34
503 504 1.202698 GGATTAATGGGCTCTCGTGCT 60.203 52.381 0.00 0.00 0.00 4.40
504 505 2.565841 GATTAATGGGCTCTCGTGCTT 58.434 47.619 0.00 0.00 0.00 3.91
505 506 2.024176 TTAATGGGCTCTCGTGCTTC 57.976 50.000 0.00 0.00 0.00 3.86
507 508 1.557269 AATGGGCTCTCGTGCTTCCT 61.557 55.000 0.00 0.00 0.00 3.36
511 512 0.519077 GGCTCTCGTGCTTCCTTTTG 59.481 55.000 0.00 0.00 0.00 2.44
512 513 0.110010 GCTCTCGTGCTTCCTTTTGC 60.110 55.000 0.00 0.00 0.00 3.68
513 514 1.517242 CTCTCGTGCTTCCTTTTGCT 58.483 50.000 0.00 0.00 0.00 3.91
516 517 1.603802 CTCGTGCTTCCTTTTGCTCAA 59.396 47.619 0.00 0.00 0.00 3.02
518 519 1.603802 CGTGCTTCCTTTTGCTCAAGA 59.396 47.619 0.00 0.00 0.00 3.02
519 520 2.603173 CGTGCTTCCTTTTGCTCAAGAC 60.603 50.000 0.00 0.00 0.00 3.01
520 521 2.358898 GTGCTTCCTTTTGCTCAAGACA 59.641 45.455 0.00 0.00 0.00 3.41
521 522 3.005155 GTGCTTCCTTTTGCTCAAGACAT 59.995 43.478 0.00 0.00 0.00 3.06
522 523 3.005050 TGCTTCCTTTTGCTCAAGACATG 59.995 43.478 0.00 0.00 0.00 3.21
523 524 3.572584 CTTCCTTTTGCTCAAGACATGC 58.427 45.455 0.00 0.00 0.00 4.06
526 527 2.352421 CCTTTTGCTCAAGACATGCTGG 60.352 50.000 0.00 0.00 0.00 4.85
528 529 0.111061 TTGCTCAAGACATGCTGGGT 59.889 50.000 0.00 0.00 0.00 4.51
529 530 0.321919 TGCTCAAGACATGCTGGGTC 60.322 55.000 0.00 0.00 35.50 4.46
537 1312 1.003580 GACATGCTGGGTCTTCCTTCA 59.996 52.381 0.00 0.00 36.20 3.02
544 1319 1.425066 TGGGTCTTCCTTCACTTGCAT 59.575 47.619 0.00 0.00 36.20 3.96
548 1323 4.072131 GGTCTTCCTTCACTTGCATGTAA 58.928 43.478 4.73 0.00 0.00 2.41
549 1324 4.518970 GGTCTTCCTTCACTTGCATGTAAA 59.481 41.667 4.73 0.00 0.00 2.01
550 1325 5.452777 GTCTTCCTTCACTTGCATGTAAAC 58.547 41.667 4.73 0.00 0.00 2.01
551 1326 5.008613 GTCTTCCTTCACTTGCATGTAAACA 59.991 40.000 4.73 0.00 0.00 2.83
552 1327 5.592282 TCTTCCTTCACTTGCATGTAAACAA 59.408 36.000 4.73 0.00 0.00 2.83
553 1328 6.265196 TCTTCCTTCACTTGCATGTAAACAAT 59.735 34.615 4.73 0.00 0.00 2.71
554 1329 6.403866 TCCTTCACTTGCATGTAAACAATT 57.596 33.333 4.73 0.00 0.00 2.32
555 1330 6.815089 TCCTTCACTTGCATGTAAACAATTT 58.185 32.000 4.73 0.00 0.00 1.82
556 1331 6.700960 TCCTTCACTTGCATGTAAACAATTTG 59.299 34.615 4.73 0.00 0.00 2.32
557 1332 6.700960 CCTTCACTTGCATGTAAACAATTTGA 59.299 34.615 4.73 0.00 0.00 2.69
559 1334 6.804677 TCACTTGCATGTAAACAATTTGACT 58.195 32.000 4.73 0.00 0.00 3.41
560 1335 6.696583 TCACTTGCATGTAAACAATTTGACTG 59.303 34.615 4.73 0.00 0.00 3.51
561 1336 6.696583 CACTTGCATGTAAACAATTTGACTGA 59.303 34.615 4.73 0.00 0.00 3.41
562 1337 6.919662 ACTTGCATGTAAACAATTTGACTGAG 59.080 34.615 2.92 0.00 0.00 3.35
563 1338 6.389830 TGCATGTAAACAATTTGACTGAGT 57.610 33.333 2.79 0.00 0.00 3.41
564 1339 6.437928 TGCATGTAAACAATTTGACTGAGTC 58.562 36.000 5.47 5.47 0.00 3.36
565 1340 6.039159 TGCATGTAAACAATTTGACTGAGTCA 59.961 34.615 11.93 11.93 41.09 3.41
566 1341 7.086376 GCATGTAAACAATTTGACTGAGTCAT 58.914 34.615 16.98 0.00 42.40 3.06
567 1342 7.061441 GCATGTAAACAATTTGACTGAGTCATG 59.939 37.037 16.98 14.05 42.40 3.07
568 1343 6.437928 TGTAAACAATTTGACTGAGTCATGC 58.562 36.000 16.98 3.78 42.40 4.06
569 1344 3.818961 ACAATTTGACTGAGTCATGCG 57.181 42.857 16.98 8.04 42.40 4.73
570 1345 3.141398 ACAATTTGACTGAGTCATGCGT 58.859 40.909 16.98 8.66 42.40 5.24
572 1347 2.238942 TTTGACTGAGTCATGCGTGT 57.761 45.000 16.98 0.00 42.40 4.49
573 1348 1.783284 TTGACTGAGTCATGCGTGTC 58.217 50.000 16.98 0.00 42.40 3.67
575 1350 1.273327 TGACTGAGTCATGCGTGTCAT 59.727 47.619 11.93 0.00 37.67 3.06
577 1352 1.547820 ACTGAGTCATGCGTGTCATCT 59.452 47.619 5.68 1.03 31.79 2.90
580 1355 1.657594 GAGTCATGCGTGTCATCTGTG 59.342 52.381 5.68 0.00 31.79 3.66
581 1356 1.001293 AGTCATGCGTGTCATCTGTGT 59.999 47.619 5.68 0.00 31.79 3.72
582 1357 2.231235 AGTCATGCGTGTCATCTGTGTA 59.769 45.455 5.68 0.00 31.79 2.90
583 1358 2.993220 GTCATGCGTGTCATCTGTGTAA 59.007 45.455 5.68 0.00 31.79 2.41
584 1359 2.993220 TCATGCGTGTCATCTGTGTAAC 59.007 45.455 5.68 0.00 31.79 2.50
585 1360 2.736192 CATGCGTGTCATCTGTGTAACA 59.264 45.455 0.00 0.00 37.75 2.41
586 1361 3.186205 CATGCGTGTCATCTGTGTAACAA 59.814 43.478 0.00 0.00 39.15 2.83
587 1362 4.142838 CATGCGTGTCATCTGTGTAACAAT 60.143 41.667 0.00 0.00 39.15 2.71
602 1377 7.151999 GTGTAACAATCAAATGGATGTGGTA 57.848 36.000 0.00 0.00 36.02 3.25
603 1378 7.771183 GTGTAACAATCAAATGGATGTGGTAT 58.229 34.615 0.00 0.00 36.02 2.73
606 1381 5.663456 ACAATCAAATGGATGTGGTATTGC 58.337 37.500 0.00 0.00 36.02 3.56
608 1604 6.126997 ACAATCAAATGGATGTGGTATTGCAT 60.127 34.615 0.00 0.00 36.02 3.96
612 1608 6.817641 TCAAATGGATGTGGTATTGCATTTTC 59.182 34.615 0.00 0.00 40.49 2.29
613 1609 6.549433 AATGGATGTGGTATTGCATTTTCT 57.451 33.333 0.00 0.00 30.85 2.52
614 1610 7.658525 AATGGATGTGGTATTGCATTTTCTA 57.341 32.000 0.00 0.00 30.85 2.10
616 1612 6.186957 TGGATGTGGTATTGCATTTTCTACT 58.813 36.000 0.00 0.00 0.00 2.57
622 1618 6.806739 GTGGTATTGCATTTTCTACTCCAAAC 59.193 38.462 0.00 0.00 0.00 2.93
624 1620 7.094377 TGGTATTGCATTTTCTACTCCAAACTC 60.094 37.037 0.00 0.00 0.00 3.01
625 1621 7.121315 GGTATTGCATTTTCTACTCCAAACTCT 59.879 37.037 0.00 0.00 0.00 3.24
645 1641 6.681729 CTCTGGAGGAGTACTAGAGAGTAT 57.318 45.833 12.47 0.00 42.72 2.12
646 1642 7.786046 CTCTGGAGGAGTACTAGAGAGTATA 57.214 44.000 12.47 0.00 42.72 1.47
649 1645 9.000978 TCTGGAGGAGTACTAGAGAGTATAAAA 57.999 37.037 0.00 0.00 40.32 1.52
650 1646 9.280174 CTGGAGGAGTACTAGAGAGTATAAAAG 57.720 40.741 0.00 0.00 40.32 2.27
651 1647 9.000978 TGGAGGAGTACTAGAGAGTATAAAAGA 57.999 37.037 0.00 0.00 40.32 2.52
663 1659 9.930158 AGAGAGTATAAAAGATGTACTTCCTCT 57.070 33.333 5.19 7.82 36.23 3.69
664 1660 9.959749 GAGAGTATAAAAGATGTACTTCCTCTG 57.040 37.037 12.81 0.00 36.23 3.35
665 1661 8.417884 AGAGTATAAAAGATGTACTTCCTCTGC 58.582 37.037 5.19 0.00 36.23 4.26
666 1662 7.501844 AGTATAAAAGATGTACTTCCTCTGCC 58.498 38.462 5.19 0.00 37.93 4.85
668 1664 4.479786 AAAGATGTACTTCCTCTGCCTC 57.520 45.455 5.19 0.00 37.93 4.70
677 2615 4.013050 ACTTCCTCTGCCTCAAAATAAGC 58.987 43.478 0.00 0.00 0.00 3.09
679 2617 1.064654 CCTCTGCCTCAAAATAAGCGC 59.935 52.381 0.00 0.00 0.00 5.92
680 2618 1.064654 CTCTGCCTCAAAATAAGCGCC 59.935 52.381 2.29 0.00 0.00 6.53
686 2624 1.130373 CTCAAAATAAGCGCCGCTGAA 59.870 47.619 14.52 4.23 39.62 3.02
691 2629 1.512926 ATAAGCGCCGCTGAATTAGG 58.487 50.000 14.52 0.00 39.62 2.69
699 2637 2.488153 GCCGCTGAATTAGGACAAAGTT 59.512 45.455 0.00 0.00 0.00 2.66
700 2638 3.687698 GCCGCTGAATTAGGACAAAGTTA 59.312 43.478 0.00 0.00 0.00 2.24
702 2640 5.175859 CCGCTGAATTAGGACAAAGTTAGA 58.824 41.667 0.00 0.00 0.00 2.10
775 2713 8.693504 CATGTGAAAGCAGTAAAAATGTTACAG 58.306 33.333 0.00 0.00 0.00 2.74
803 2747 6.071221 TGCATTCTAAGTACGTTTTAGAGGGA 60.071 38.462 16.71 13.30 38.13 4.20
804 2748 6.255237 GCATTCTAAGTACGTTTTAGAGGGAC 59.745 42.308 16.71 8.79 38.13 4.46
806 2750 6.506500 TCTAAGTACGTTTTAGAGGGACTG 57.493 41.667 14.61 0.00 41.55 3.51
809 2753 1.349067 ACGTTTTAGAGGGACTGGCT 58.651 50.000 0.00 0.00 41.55 4.75
843 2787 1.079503 GTCAGCATCAAGGTCGAACC 58.920 55.000 0.00 0.00 38.99 3.62
847 2791 1.066573 AGCATCAAGGTCGAACCAGAG 60.067 52.381 0.00 0.00 41.95 3.35
848 2792 1.338200 GCATCAAGGTCGAACCAGAGT 60.338 52.381 0.00 0.00 41.95 3.24
878 2822 3.272020 AGACCATTCTCTCCCTCTCTCTT 59.728 47.826 0.00 0.00 0.00 2.85
879 2823 3.636764 GACCATTCTCTCCCTCTCTCTTC 59.363 52.174 0.00 0.00 0.00 2.87
1053 3053 2.560119 CCTCTCATCTCCCTCCGCG 61.560 68.421 0.00 0.00 0.00 6.46
1201 3231 1.194781 GCTCTCCCACCTCAAGTCCA 61.195 60.000 0.00 0.00 0.00 4.02
1390 3420 2.430921 CACGCCTCGTCTCGCTTT 60.431 61.111 0.00 0.00 38.32 3.51
1605 3645 0.743097 ACGTACTTAGGCCATCGACC 59.257 55.000 5.01 0.00 0.00 4.79
1778 3833 1.292223 CGTTCAGGTGGTCGGATGT 59.708 57.895 0.00 0.00 0.00 3.06
2176 4231 3.862264 GCTCTGATGTAACTGTGTGCTGA 60.862 47.826 0.00 0.00 0.00 4.26
2223 4279 0.958822 GCTGGGTTGGTGGTTGTTAG 59.041 55.000 0.00 0.00 0.00 2.34
2225 4281 0.259065 TGGGTTGGTGGTTGTTAGCA 59.741 50.000 0.00 0.00 0.00 3.49
2398 4473 7.761249 GCCATTCTGTAATGCACTAAAATTTCT 59.239 33.333 0.00 0.00 41.06 2.52
2460 4541 5.316987 CAAGGTAAGGTCTCCTTCATTGTT 58.683 41.667 4.21 0.00 43.57 2.83
2760 4891 5.221561 ACGATTTGGAACCATCGGTCATATA 60.222 40.000 17.23 0.00 42.54 0.86
2781 4930 2.999331 GGAAATACCTACTGGCTGCAA 58.001 47.619 0.50 0.00 36.63 4.08
2844 5001 4.000988 AGGGATGCACACTTAACTAAACG 58.999 43.478 0.00 0.00 0.00 3.60
2954 5133 5.412594 TGTTATTGAGACAATGGAGAAGCAC 59.587 40.000 7.16 0.00 0.00 4.40
2955 5134 3.777106 TTGAGACAATGGAGAAGCACT 57.223 42.857 0.00 0.00 0.00 4.40
2956 5135 3.777106 TGAGACAATGGAGAAGCACTT 57.223 42.857 0.00 0.00 0.00 3.16
2957 5136 3.405831 TGAGACAATGGAGAAGCACTTG 58.594 45.455 0.00 0.00 0.00 3.16
2958 5137 2.157738 AGACAATGGAGAAGCACTTGC 58.842 47.619 0.00 0.00 42.49 4.01
2959 5138 1.200948 GACAATGGAGAAGCACTTGCC 59.799 52.381 0.00 0.00 43.38 4.52
2960 5139 0.169672 CAATGGAGAAGCACTTGCCG 59.830 55.000 0.00 0.00 43.38 5.69
2961 5140 1.589716 AATGGAGAAGCACTTGCCGC 61.590 55.000 0.00 0.00 43.38 6.53
2962 5141 2.359230 GGAGAAGCACTTGCCGCT 60.359 61.111 0.00 0.00 43.38 5.52
2963 5142 2.394563 GGAGAAGCACTTGCCGCTC 61.395 63.158 10.81 10.81 43.38 5.03
2964 5143 1.375268 GAGAAGCACTTGCCGCTCT 60.375 57.895 11.63 5.93 43.38 4.09
2965 5144 0.952984 GAGAAGCACTTGCCGCTCTT 60.953 55.000 11.63 0.00 43.38 2.85
2966 5145 0.536006 AGAAGCACTTGCCGCTCTTT 60.536 50.000 0.00 0.00 43.38 2.52
2967 5146 0.312102 GAAGCACTTGCCGCTCTTTT 59.688 50.000 0.00 0.00 43.38 2.27
2968 5147 1.535462 GAAGCACTTGCCGCTCTTTTA 59.465 47.619 0.00 0.00 43.38 1.52
2969 5148 0.875059 AGCACTTGCCGCTCTTTTAC 59.125 50.000 0.00 0.00 43.38 2.01
3009 5222 3.312890 AGGTGTATTATCCTGCTCTGCT 58.687 45.455 0.00 0.00 32.29 4.24
3055 5299 3.196040 TGGATTTCCAGCAGATGCC 57.804 52.632 0.14 0.00 42.01 4.40
3056 5300 0.627451 TGGATTTCCAGCAGATGCCT 59.373 50.000 0.14 0.00 42.01 4.75
3057 5301 1.316651 GGATTTCCAGCAGATGCCTC 58.683 55.000 0.14 0.00 43.38 4.70
3058 5302 1.133853 GGATTTCCAGCAGATGCCTCT 60.134 52.381 0.14 0.00 43.38 3.69
3059 5303 2.220313 GATTTCCAGCAGATGCCTCTC 58.780 52.381 0.14 0.00 43.38 3.20
3060 5304 0.254178 TTTCCAGCAGATGCCTCTCC 59.746 55.000 0.14 0.00 43.38 3.71
3061 5305 0.619832 TTCCAGCAGATGCCTCTCCT 60.620 55.000 0.14 0.00 43.38 3.69
3062 5306 0.262876 TCCAGCAGATGCCTCTCCTA 59.737 55.000 0.14 0.00 43.38 2.94
3063 5307 0.392336 CCAGCAGATGCCTCTCCTAC 59.608 60.000 0.14 0.00 43.38 3.18
3064 5308 1.412079 CAGCAGATGCCTCTCCTACT 58.588 55.000 0.14 0.00 43.38 2.57
3065 5309 2.591923 CAGCAGATGCCTCTCCTACTA 58.408 52.381 0.14 0.00 43.38 1.82
3066 5310 3.164268 CAGCAGATGCCTCTCCTACTAT 58.836 50.000 0.14 0.00 43.38 2.12
3067 5311 3.577848 CAGCAGATGCCTCTCCTACTATT 59.422 47.826 0.14 0.00 43.38 1.73
3068 5312 4.040217 CAGCAGATGCCTCTCCTACTATTT 59.960 45.833 0.14 0.00 43.38 1.40
3069 5313 4.657969 AGCAGATGCCTCTCCTACTATTTT 59.342 41.667 0.14 0.00 43.38 1.82
3070 5314 4.994217 GCAGATGCCTCTCCTACTATTTTC 59.006 45.833 0.00 0.00 34.31 2.29
3071 5315 5.453903 GCAGATGCCTCTCCTACTATTTTCA 60.454 44.000 0.00 0.00 34.31 2.69
3072 5316 6.743773 GCAGATGCCTCTCCTACTATTTTCAT 60.744 42.308 0.00 0.00 34.31 2.57
3073 5317 7.526192 GCAGATGCCTCTCCTACTATTTTCATA 60.526 40.741 0.00 0.00 34.31 2.15
3074 5318 8.538701 CAGATGCCTCTCCTACTATTTTCATAT 58.461 37.037 0.00 0.00 0.00 1.78
3075 5319 8.757877 AGATGCCTCTCCTACTATTTTCATATC 58.242 37.037 0.00 0.00 0.00 1.63
3076 5320 8.677870 ATGCCTCTCCTACTATTTTCATATCT 57.322 34.615 0.00 0.00 0.00 1.98
3077 5321 8.128322 TGCCTCTCCTACTATTTTCATATCTC 57.872 38.462 0.00 0.00 0.00 2.75
3078 5322 7.952930 TGCCTCTCCTACTATTTTCATATCTCT 59.047 37.037 0.00 0.00 0.00 3.10
3079 5323 8.466798 GCCTCTCCTACTATTTTCATATCTCTC 58.533 40.741 0.00 0.00 0.00 3.20
3080 5324 9.527157 CCTCTCCTACTATTTTCATATCTCTCA 57.473 37.037 0.00 0.00 0.00 3.27
3095 5339 9.029368 TCATATCTCTCATAATTCTAGTGTGGG 57.971 37.037 0.00 0.00 0.00 4.61
3096 5340 8.811017 CATATCTCTCATAATTCTAGTGTGGGT 58.189 37.037 0.00 0.00 0.00 4.51
3098 5342 8.964533 ATCTCTCATAATTCTAGTGTGGGTAT 57.035 34.615 0.00 0.00 0.00 2.73
3099 5343 8.783660 TCTCTCATAATTCTAGTGTGGGTATT 57.216 34.615 0.00 0.00 0.00 1.89
3100 5344 9.877222 TCTCTCATAATTCTAGTGTGGGTATTA 57.123 33.333 0.00 0.00 0.00 0.98
3127 5371 9.891828 TGTTCTATAACTAAAATGCACAAGTTG 57.108 29.630 0.00 0.00 36.51 3.16
3130 5374 9.278978 TCTATAACTAAAATGCACAAGTTGACA 57.721 29.630 10.54 7.82 34.23 3.58
3133 5377 9.762933 ATAACTAAAATGCACAAGTTGACATTT 57.237 25.926 23.68 23.68 40.57 2.32
3134 5378 8.491331 AACTAAAATGCACAAGTTGACATTTT 57.509 26.923 32.16 32.16 44.74 1.82
3135 5379 7.908230 ACTAAAATGCACAAGTTGACATTTTG 58.092 30.769 34.18 28.99 43.74 2.44
3136 5380 4.799419 AATGCACAAGTTGACATTTTGC 57.201 36.364 10.54 8.36 31.72 3.68
3137 5381 3.242549 TGCACAAGTTGACATTTTGCA 57.757 38.095 10.54 11.01 36.20 4.08
3138 5382 3.593096 TGCACAAGTTGACATTTTGCAA 58.407 36.364 10.54 0.00 35.65 4.08
3139 5383 4.190001 TGCACAAGTTGACATTTTGCAAT 58.810 34.783 10.54 0.00 35.65 3.56
3140 5384 4.634883 TGCACAAGTTGACATTTTGCAATT 59.365 33.333 10.54 0.00 35.65 2.32
3141 5385 4.965158 GCACAAGTTGACATTTTGCAATTG 59.035 37.500 10.54 0.00 0.00 2.32
3142 5386 5.503498 CACAAGTTGACATTTTGCAATTGG 58.497 37.500 10.54 0.00 0.00 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
15 16 5.014858 TGTCGAATATATCTGGTACCTCCC 58.985 45.833 14.36 0.00 34.77 4.30
42 43 3.406764 AGTTCAGGAATTGCTGTCTGAC 58.593 45.455 24.15 17.75 36.18 3.51
45 46 7.530426 AAATTTAGTTCAGGAATTGCTGTCT 57.470 32.000 24.15 22.80 0.00 3.41
93 94 6.248433 ACATTCAGTAAATCAGTTGGTCCAT 58.752 36.000 0.00 0.00 0.00 3.41
151 152 2.450609 TGACCGCACCTTTTAGAGTC 57.549 50.000 0.00 0.00 0.00 3.36
152 153 3.418684 AATGACCGCACCTTTTAGAGT 57.581 42.857 0.00 0.00 0.00 3.24
169 170 8.672815 GTCCATCTCCTAGAAAAAGAAGAAATG 58.327 37.037 0.00 0.00 0.00 2.32
291 292 3.553105 GCAAAAGTCAAAACAGGCTTCTG 59.447 43.478 0.00 0.00 43.84 3.02
296 297 2.609002 CCTTGCAAAAGTCAAAACAGGC 59.391 45.455 0.00 0.00 0.00 4.85
392 393 7.985184 AGGATAACATGTATTCGCTCTGTAAAA 59.015 33.333 0.00 0.00 0.00 1.52
395 396 6.650427 AGGATAACATGTATTCGCTCTGTA 57.350 37.500 0.00 0.00 0.00 2.74
414 415 8.055181 CCCCTTGTACATTGCAATATATAGGAT 58.945 37.037 21.42 0.00 0.00 3.24
415 416 7.238723 TCCCCTTGTACATTGCAATATATAGGA 59.761 37.037 21.42 11.47 0.00 2.94
416 417 7.336931 GTCCCCTTGTACATTGCAATATATAGG 59.663 40.741 12.53 14.99 0.00 2.57
418 419 7.750655 TGTCCCCTTGTACATTGCAATATATA 58.249 34.615 12.53 0.00 0.00 0.86
420 421 6.007485 TGTCCCCTTGTACATTGCAATATA 57.993 37.500 12.53 1.57 0.00 0.86
421 422 4.865905 TGTCCCCTTGTACATTGCAATAT 58.134 39.130 12.53 2.82 0.00 1.28
422 423 4.308526 TGTCCCCTTGTACATTGCAATA 57.691 40.909 12.53 0.00 0.00 1.90
423 424 3.168035 TGTCCCCTTGTACATTGCAAT 57.832 42.857 5.99 5.99 0.00 3.56
425 426 2.625790 GTTTGTCCCCTTGTACATTGCA 59.374 45.455 0.00 0.00 0.00 4.08
427 428 4.098654 TGTTGTTTGTCCCCTTGTACATTG 59.901 41.667 0.00 0.00 0.00 2.82
428 429 4.282496 TGTTGTTTGTCCCCTTGTACATT 58.718 39.130 0.00 0.00 0.00 2.71
429 430 3.904717 TGTTGTTTGTCCCCTTGTACAT 58.095 40.909 0.00 0.00 0.00 2.29
430 431 3.367646 TGTTGTTTGTCCCCTTGTACA 57.632 42.857 0.00 0.00 0.00 2.90
431 432 3.697542 ACTTGTTGTTTGTCCCCTTGTAC 59.302 43.478 0.00 0.00 0.00 2.90
432 433 3.970842 ACTTGTTGTTTGTCCCCTTGTA 58.029 40.909 0.00 0.00 0.00 2.41
433 434 2.815158 ACTTGTTGTTTGTCCCCTTGT 58.185 42.857 0.00 0.00 0.00 3.16
434 435 3.194542 TCAACTTGTTGTTTGTCCCCTTG 59.805 43.478 12.44 0.00 36.63 3.61
435 436 3.436243 TCAACTTGTTGTTTGTCCCCTT 58.564 40.909 12.44 0.00 36.63 3.95
436 437 3.094484 TCAACTTGTTGTTTGTCCCCT 57.906 42.857 12.44 0.00 36.63 4.79
437 438 3.878160 TTCAACTTGTTGTTTGTCCCC 57.122 42.857 12.44 0.00 36.63 4.81
438 439 5.004922 TCATTCAACTTGTTGTTTGTCCC 57.995 39.130 12.44 0.00 36.63 4.46
439 440 6.099341 ACTTCATTCAACTTGTTGTTTGTCC 58.901 36.000 12.44 0.00 36.63 4.02
440 441 6.806249 TGACTTCATTCAACTTGTTGTTTGTC 59.194 34.615 12.44 12.40 36.63 3.18
441 442 6.686630 TGACTTCATTCAACTTGTTGTTTGT 58.313 32.000 12.44 5.60 36.63 2.83
442 443 7.579589 TTGACTTCATTCAACTTGTTGTTTG 57.420 32.000 12.44 11.07 36.63 2.93
455 456 5.353678 AGATGCAGCTTAGTTGACTTCATTC 59.646 40.000 0.00 0.00 0.00 2.67
456 457 5.123502 CAGATGCAGCTTAGTTGACTTCATT 59.876 40.000 0.00 0.00 0.00 2.57
457 458 4.634883 CAGATGCAGCTTAGTTGACTTCAT 59.365 41.667 0.00 0.00 0.00 2.57
458 459 3.999001 CAGATGCAGCTTAGTTGACTTCA 59.001 43.478 0.00 0.00 0.00 3.02
459 460 3.373439 CCAGATGCAGCTTAGTTGACTTC 59.627 47.826 0.00 0.33 0.00 3.01
460 461 3.244700 ACCAGATGCAGCTTAGTTGACTT 60.245 43.478 0.00 0.00 0.00 3.01
461 462 2.304180 ACCAGATGCAGCTTAGTTGACT 59.696 45.455 0.00 0.00 0.00 3.41
464 465 1.741706 CCACCAGATGCAGCTTAGTTG 59.258 52.381 0.00 0.00 0.00 3.16
465 466 1.630369 TCCACCAGATGCAGCTTAGTT 59.370 47.619 0.00 0.00 0.00 2.24
466 467 1.279496 TCCACCAGATGCAGCTTAGT 58.721 50.000 0.00 0.00 0.00 2.24
467 468 2.634815 ATCCACCAGATGCAGCTTAG 57.365 50.000 0.00 0.00 32.41 2.18
468 469 4.502105 TTAATCCACCAGATGCAGCTTA 57.498 40.909 0.00 0.00 34.56 3.09
470 471 3.220110 CATTAATCCACCAGATGCAGCT 58.780 45.455 0.00 0.00 34.56 4.24
471 472 2.295349 CCATTAATCCACCAGATGCAGC 59.705 50.000 0.00 0.00 34.56 5.25
472 473 2.889045 CCCATTAATCCACCAGATGCAG 59.111 50.000 0.00 0.00 34.56 4.41
474 475 1.615392 GCCCATTAATCCACCAGATGC 59.385 52.381 0.00 0.00 34.56 3.91
475 476 3.152341 GAGCCCATTAATCCACCAGATG 58.848 50.000 0.00 0.00 34.56 2.90
476 477 3.059097 AGAGCCCATTAATCCACCAGAT 58.941 45.455 0.00 0.00 36.48 2.90
479 480 1.140852 CGAGAGCCCATTAATCCACCA 59.859 52.381 0.00 0.00 0.00 4.17
480 481 1.141053 ACGAGAGCCCATTAATCCACC 59.859 52.381 0.00 0.00 0.00 4.61
481 482 2.213499 CACGAGAGCCCATTAATCCAC 58.787 52.381 0.00 0.00 0.00 4.02
482 483 1.475034 GCACGAGAGCCCATTAATCCA 60.475 52.381 0.00 0.00 0.00 3.41
488 489 1.078143 GGAAGCACGAGAGCCCATT 60.078 57.895 0.00 0.00 34.23 3.16
489 490 1.557269 AAGGAAGCACGAGAGCCCAT 61.557 55.000 0.00 0.00 34.23 4.00
490 491 1.768684 AAAGGAAGCACGAGAGCCCA 61.769 55.000 0.00 0.00 34.23 5.36
491 492 0.606673 AAAAGGAAGCACGAGAGCCC 60.607 55.000 0.00 0.00 34.23 5.19
493 494 0.110010 GCAAAAGGAAGCACGAGAGC 60.110 55.000 0.00 0.00 0.00 4.09
494 495 1.462670 GAGCAAAAGGAAGCACGAGAG 59.537 52.381 0.00 0.00 0.00 3.20
495 496 1.202639 TGAGCAAAAGGAAGCACGAGA 60.203 47.619 0.00 0.00 0.00 4.04
496 497 1.229428 TGAGCAAAAGGAAGCACGAG 58.771 50.000 0.00 0.00 0.00 4.18
497 498 1.603802 CTTGAGCAAAAGGAAGCACGA 59.396 47.619 0.00 0.00 0.00 4.35
498 499 1.603802 TCTTGAGCAAAAGGAAGCACG 59.396 47.619 0.00 0.00 0.00 5.34
499 500 2.358898 TGTCTTGAGCAAAAGGAAGCAC 59.641 45.455 0.00 0.00 0.00 4.40
502 503 3.255149 AGCATGTCTTGAGCAAAAGGAAG 59.745 43.478 0.00 0.00 0.00 3.46
503 504 3.005050 CAGCATGTCTTGAGCAAAAGGAA 59.995 43.478 0.00 0.00 0.00 3.36
504 505 2.555325 CAGCATGTCTTGAGCAAAAGGA 59.445 45.455 0.00 0.00 0.00 3.36
505 506 2.352421 CCAGCATGTCTTGAGCAAAAGG 60.352 50.000 0.00 0.00 0.00 3.11
507 508 1.614903 CCCAGCATGTCTTGAGCAAAA 59.385 47.619 0.00 0.00 0.00 2.44
511 512 0.035630 AGACCCAGCATGTCTTGAGC 60.036 55.000 0.00 0.00 40.06 4.26
516 517 1.280421 GAAGGAAGACCCAGCATGTCT 59.720 52.381 0.00 0.00 44.75 3.41
518 519 1.067295 TGAAGGAAGACCCAGCATGT 58.933 50.000 0.00 0.00 37.41 3.21
519 520 1.004044 AGTGAAGGAAGACCCAGCATG 59.996 52.381 0.00 0.00 37.41 4.06
520 521 1.366319 AGTGAAGGAAGACCCAGCAT 58.634 50.000 0.00 0.00 37.41 3.79
521 522 1.140312 AAGTGAAGGAAGACCCAGCA 58.860 50.000 0.00 0.00 37.41 4.41
522 523 1.528129 CAAGTGAAGGAAGACCCAGC 58.472 55.000 0.00 0.00 37.41 4.85
523 524 1.202806 TGCAAGTGAAGGAAGACCCAG 60.203 52.381 0.00 0.00 37.41 4.45
526 527 2.508526 ACATGCAAGTGAAGGAAGACC 58.491 47.619 0.00 0.00 0.00 3.85
528 529 5.129634 TGTTTACATGCAAGTGAAGGAAGA 58.870 37.500 4.51 0.00 0.00 2.87
529 530 5.437289 TGTTTACATGCAAGTGAAGGAAG 57.563 39.130 4.51 0.00 0.00 3.46
530 531 5.843673 TTGTTTACATGCAAGTGAAGGAA 57.156 34.783 4.51 0.00 0.00 3.36
537 1312 6.804677 TCAGTCAAATTGTTTACATGCAAGT 58.195 32.000 0.00 0.00 0.00 3.16
544 1319 6.437928 GCATGACTCAGTCAAATTGTTTACA 58.562 36.000 12.63 0.00 45.96 2.41
548 1323 3.565482 ACGCATGACTCAGTCAAATTGTT 59.435 39.130 12.63 0.00 45.96 2.83
549 1324 3.058708 CACGCATGACTCAGTCAAATTGT 60.059 43.478 12.63 5.59 45.96 2.71
550 1325 3.058708 ACACGCATGACTCAGTCAAATTG 60.059 43.478 12.63 7.07 45.96 2.32
551 1326 3.141398 ACACGCATGACTCAGTCAAATT 58.859 40.909 12.63 0.00 45.96 1.82
552 1327 2.738846 GACACGCATGACTCAGTCAAAT 59.261 45.455 12.63 0.00 45.96 2.32
553 1328 2.135139 GACACGCATGACTCAGTCAAA 58.865 47.619 12.63 0.00 45.96 2.69
554 1329 1.068434 TGACACGCATGACTCAGTCAA 59.932 47.619 12.63 0.00 45.96 3.18
555 1330 0.673437 TGACACGCATGACTCAGTCA 59.327 50.000 10.71 10.71 46.90 3.41
556 1331 1.923204 GATGACACGCATGACTCAGTC 59.077 52.381 0.00 0.00 37.34 3.51
557 1332 1.547820 AGATGACACGCATGACTCAGT 59.452 47.619 0.00 0.00 37.34 3.41
559 1334 1.273327 ACAGATGACACGCATGACTCA 59.727 47.619 0.00 0.00 37.34 3.41
560 1335 1.657594 CACAGATGACACGCATGACTC 59.342 52.381 0.00 0.00 37.34 3.36
561 1336 1.001293 ACACAGATGACACGCATGACT 59.999 47.619 0.00 0.00 37.34 3.41
562 1337 1.432514 ACACAGATGACACGCATGAC 58.567 50.000 0.00 0.00 37.34 3.06
563 1338 2.993220 GTTACACAGATGACACGCATGA 59.007 45.455 0.00 0.00 37.34 3.07
564 1339 2.736192 TGTTACACAGATGACACGCATG 59.264 45.455 0.00 0.00 37.34 4.06
565 1340 3.038788 TGTTACACAGATGACACGCAT 57.961 42.857 0.00 0.00 40.77 4.73
566 1341 2.517650 TGTTACACAGATGACACGCA 57.482 45.000 0.00 0.00 0.00 5.24
567 1342 3.431912 TGATTGTTACACAGATGACACGC 59.568 43.478 0.00 0.00 0.00 5.34
568 1343 5.590104 TTGATTGTTACACAGATGACACG 57.410 39.130 0.00 0.00 0.00 4.49
569 1344 6.803320 CCATTTGATTGTTACACAGATGACAC 59.197 38.462 7.66 0.00 30.99 3.67
570 1345 6.714356 TCCATTTGATTGTTACACAGATGACA 59.286 34.615 7.66 0.00 30.99 3.58
572 1347 7.394077 ACATCCATTTGATTGTTACACAGATGA 59.606 33.333 7.66 0.00 30.99 2.92
573 1348 7.486870 CACATCCATTTGATTGTTACACAGATG 59.513 37.037 0.00 0.00 34.01 2.90
575 1350 6.072008 CCACATCCATTTGATTGTTACACAGA 60.072 38.462 0.00 0.00 0.00 3.41
577 1352 5.538053 ACCACATCCATTTGATTGTTACACA 59.462 36.000 0.00 0.00 0.00 3.72
580 1355 7.222611 GCAATACCACATCCATTTGATTGTTAC 59.777 37.037 0.00 0.00 0.00 2.50
581 1356 7.093596 TGCAATACCACATCCATTTGATTGTTA 60.094 33.333 0.00 0.00 0.00 2.41
582 1357 6.108015 GCAATACCACATCCATTTGATTGTT 58.892 36.000 0.00 0.00 0.00 2.83
583 1358 5.187381 TGCAATACCACATCCATTTGATTGT 59.813 36.000 0.00 0.00 0.00 2.71
584 1359 5.662456 TGCAATACCACATCCATTTGATTG 58.338 37.500 0.00 0.00 0.00 2.67
585 1360 5.936187 TGCAATACCACATCCATTTGATT 57.064 34.783 0.00 0.00 0.00 2.57
586 1361 6.488769 AATGCAATACCACATCCATTTGAT 57.511 33.333 0.00 0.00 0.00 2.57
587 1362 5.936187 AATGCAATACCACATCCATTTGA 57.064 34.783 0.00 0.00 0.00 2.69
591 1366 6.835488 AGTAGAAAATGCAATACCACATCCAT 59.165 34.615 0.00 0.00 0.00 3.41
593 1368 6.238759 GGAGTAGAAAATGCAATACCACATCC 60.239 42.308 0.00 0.00 0.00 3.51
594 1369 6.318648 TGGAGTAGAAAATGCAATACCACATC 59.681 38.462 0.00 0.00 0.00 3.06
595 1370 6.186957 TGGAGTAGAAAATGCAATACCACAT 58.813 36.000 0.00 0.00 0.00 3.21
597 1372 6.509418 TTGGAGTAGAAAATGCAATACCAC 57.491 37.500 0.00 0.00 0.00 4.16
598 1373 6.719370 AGTTTGGAGTAGAAAATGCAATACCA 59.281 34.615 0.00 0.00 0.00 3.25
599 1374 7.121315 AGAGTTTGGAGTAGAAAATGCAATACC 59.879 37.037 0.00 0.00 0.00 2.73
600 1375 7.965107 CAGAGTTTGGAGTAGAAAATGCAATAC 59.035 37.037 0.00 0.00 0.00 1.89
602 1377 6.917533 CAGAGTTTGGAGTAGAAAATGCAAT 58.082 36.000 0.00 0.00 0.00 3.56
603 1378 6.317789 CAGAGTTTGGAGTAGAAAATGCAA 57.682 37.500 0.00 0.00 0.00 4.08
622 1618 6.681729 ATACTCTCTAGTACTCCTCCAGAG 57.318 45.833 11.81 11.81 40.98 3.35
624 1620 9.280174 CTTTTATACTCTCTAGTACTCCTCCAG 57.720 40.741 0.00 0.00 40.98 3.86
625 1621 9.000978 TCTTTTATACTCTCTAGTACTCCTCCA 57.999 37.037 0.00 0.00 40.98 3.86
637 1633 9.930158 AGAGGAAGTACATCTTTTATACTCTCT 57.070 33.333 0.00 0.00 36.13 3.10
639 1635 8.417884 GCAGAGGAAGTACATCTTTTATACTCT 58.582 37.037 0.00 0.00 37.56 3.24
640 1636 7.654116 GGCAGAGGAAGTACATCTTTTATACTC 59.346 40.741 0.00 0.00 37.56 2.59
642 1638 7.501844 AGGCAGAGGAAGTACATCTTTTATAC 58.498 38.462 0.00 0.00 37.56 1.47
643 1639 7.344612 TGAGGCAGAGGAAGTACATCTTTTATA 59.655 37.037 0.00 0.00 37.56 0.98
644 1640 6.156949 TGAGGCAGAGGAAGTACATCTTTTAT 59.843 38.462 0.00 0.00 37.56 1.40
645 1641 5.483937 TGAGGCAGAGGAAGTACATCTTTTA 59.516 40.000 0.00 0.00 37.56 1.52
646 1642 4.287067 TGAGGCAGAGGAAGTACATCTTTT 59.713 41.667 0.00 0.00 37.56 2.27
649 1645 3.107402 TGAGGCAGAGGAAGTACATCT 57.893 47.619 0.00 0.00 40.43 2.90
650 1646 3.895232 TTGAGGCAGAGGAAGTACATC 57.105 47.619 0.00 0.00 0.00 3.06
651 1647 4.640771 TTTTGAGGCAGAGGAAGTACAT 57.359 40.909 0.00 0.00 0.00 2.29
652 1648 4.640771 ATTTTGAGGCAGAGGAAGTACA 57.359 40.909 0.00 0.00 0.00 2.90
653 1649 5.065346 GCTTATTTTGAGGCAGAGGAAGTAC 59.935 44.000 0.00 0.00 0.00 2.73
654 1650 5.186198 GCTTATTTTGAGGCAGAGGAAGTA 58.814 41.667 0.00 0.00 0.00 2.24
655 1651 4.013050 GCTTATTTTGAGGCAGAGGAAGT 58.987 43.478 0.00 0.00 0.00 3.01
656 1652 3.064545 CGCTTATTTTGAGGCAGAGGAAG 59.935 47.826 0.00 0.00 0.00 3.46
657 1653 3.009723 CGCTTATTTTGAGGCAGAGGAA 58.990 45.455 0.00 0.00 0.00 3.36
658 1654 2.632377 CGCTTATTTTGAGGCAGAGGA 58.368 47.619 0.00 0.00 0.00 3.71
660 1656 1.064654 GGCGCTTATTTTGAGGCAGAG 59.935 52.381 7.64 0.00 0.00 3.35
661 1657 1.094785 GGCGCTTATTTTGAGGCAGA 58.905 50.000 7.64 0.00 0.00 4.26
662 1658 0.248215 CGGCGCTTATTTTGAGGCAG 60.248 55.000 7.64 0.00 0.00 4.85
663 1659 1.800032 CGGCGCTTATTTTGAGGCA 59.200 52.632 7.64 0.00 0.00 4.75
664 1660 1.586303 GCGGCGCTTATTTTGAGGC 60.586 57.895 26.86 0.00 0.00 4.70
665 1661 0.248215 CAGCGGCGCTTATTTTGAGG 60.248 55.000 34.51 14.03 36.40 3.86
666 1662 0.726827 TCAGCGGCGCTTATTTTGAG 59.273 50.000 34.51 18.52 36.40 3.02
668 1664 2.193306 ATTCAGCGGCGCTTATTTTG 57.807 45.000 34.51 20.98 36.40 2.44
677 2615 1.062587 CTTTGTCCTAATTCAGCGGCG 59.937 52.381 0.51 0.51 0.00 6.46
679 2617 5.175859 TCTAACTTTGTCCTAATTCAGCGG 58.824 41.667 0.00 0.00 0.00 5.52
680 2618 6.100004 TCTCTAACTTTGTCCTAATTCAGCG 58.900 40.000 0.00 0.00 0.00 5.18
718 2656 9.260002 GTGATTTTAAACAACATCCAGATTTGT 57.740 29.630 0.00 3.76 34.92 2.83
754 2692 8.427774 GCATTCTGTAACATTTTTACTGCTTTC 58.572 33.333 0.00 0.00 0.00 2.62
775 2713 8.328864 CCTCTAAAACGTACTTAGAATGCATTC 58.671 37.037 28.44 28.44 35.50 2.67
803 2747 3.626924 GTGACCCCACGAGCCAGT 61.627 66.667 0.00 0.00 33.10 4.00
804 2748 4.394712 GGTGACCCCACGAGCCAG 62.395 72.222 0.00 0.00 44.09 4.85
805 2749 4.954118 AGGTGACCCCACGAGCCA 62.954 66.667 0.00 0.00 44.09 4.75
806 2750 3.637273 AAGGTGACCCCACGAGCC 61.637 66.667 0.00 0.00 44.09 4.70
809 2753 1.754380 CTGACAAGGTGACCCCACGA 61.754 60.000 0.00 0.00 44.09 4.35
843 2787 1.566211 ATGGTCTGGTCTGGACTCTG 58.434 55.000 0.67 0.00 34.47 3.35
847 2791 2.167487 GAGAGAATGGTCTGGTCTGGAC 59.833 54.545 0.00 0.00 32.80 4.02
848 2792 2.461695 GAGAGAATGGTCTGGTCTGGA 58.538 52.381 0.00 0.00 32.80 3.86
892 2844 1.300931 CGTGGTGGTGTCTGGTCTG 60.301 63.158 0.00 0.00 0.00 3.51
1097 3115 2.830370 CGAAGGCAGGATTGGGGC 60.830 66.667 0.00 0.00 0.00 5.80
1350 3380 2.989253 TCAGAACGCGAGAGGCCA 60.989 61.111 15.93 0.00 38.94 5.36
1390 3420 1.673009 GACGGAATTTGTCGGGGCA 60.673 57.895 0.00 0.00 0.00 5.36
1584 3624 2.555757 GGTCGATGGCCTAAGTACGTAT 59.444 50.000 3.32 0.00 0.00 3.06
1605 3645 3.664025 TTCCGTGCTGATGCCGAGG 62.664 63.158 0.00 0.00 38.71 4.63
1778 3833 0.539438 AAAAGCAATGCCCACCTCGA 60.539 50.000 0.00 0.00 0.00 4.04
2176 4231 1.208052 AGACATACAGCAGCGGACAAT 59.792 47.619 0.00 0.00 0.00 2.71
2223 4279 6.558009 TCAAATTATCAGCTTCATCACTTGC 58.442 36.000 0.00 0.00 0.00 4.01
2225 4281 7.014038 GGGATCAAATTATCAGCTTCATCACTT 59.986 37.037 0.00 0.00 0.00 3.16
2460 4541 8.849168 CAATAGAACATTAGGAATGCATTACCA 58.151 33.333 18.34 0.97 42.69 3.25
2781 4930 2.812011 GTGAGCCCTGTACATTTCGTTT 59.188 45.455 0.00 0.00 0.00 3.60
2844 5001 4.407296 ACCTCCTCCATATGAGAGTTTGAC 59.593 45.833 3.65 0.00 44.42 3.18
2892 5065 5.818678 TGGACAGACACACCTAAGTTTAT 57.181 39.130 0.00 0.00 0.00 1.40
2954 5133 1.401539 GCAAGGTAAAAGAGCGGCAAG 60.402 52.381 1.45 0.00 32.90 4.01
2955 5134 0.596082 GCAAGGTAAAAGAGCGGCAA 59.404 50.000 1.45 0.00 32.90 4.52
2956 5135 1.241315 GGCAAGGTAAAAGAGCGGCA 61.241 55.000 1.45 0.00 33.89 5.69
2957 5136 1.506718 GGCAAGGTAAAAGAGCGGC 59.493 57.895 0.00 0.00 0.00 6.53
2958 5137 1.794222 CGGCAAGGTAAAAGAGCGG 59.206 57.895 0.00 0.00 0.00 5.52
2959 5138 1.134694 GCGGCAAGGTAAAAGAGCG 59.865 57.895 0.00 0.00 0.00 5.03
2960 5139 1.666189 CTAGCGGCAAGGTAAAAGAGC 59.334 52.381 1.45 0.00 31.75 4.09
2961 5140 2.973945 ACTAGCGGCAAGGTAAAAGAG 58.026 47.619 1.45 0.00 31.75 2.85
2962 5141 4.540359 TTACTAGCGGCAAGGTAAAAGA 57.460 40.909 1.45 0.00 31.75 2.52
2963 5142 4.694037 AGTTTACTAGCGGCAAGGTAAAAG 59.306 41.667 18.88 2.24 36.39 2.27
2964 5143 4.644498 AGTTTACTAGCGGCAAGGTAAAA 58.356 39.130 18.88 4.71 36.39 1.52
2965 5144 4.276058 AGTTTACTAGCGGCAAGGTAAA 57.724 40.909 15.63 15.63 33.55 2.01
2966 5145 3.967332 AGTTTACTAGCGGCAAGGTAA 57.033 42.857 1.45 5.63 31.75 2.85
2967 5146 3.967332 AAGTTTACTAGCGGCAAGGTA 57.033 42.857 1.45 0.00 0.00 3.08
2968 5147 2.853235 AAGTTTACTAGCGGCAAGGT 57.147 45.000 1.45 0.07 0.00 3.50
2969 5148 3.195661 CCTAAGTTTACTAGCGGCAAGG 58.804 50.000 1.45 0.00 0.00 3.61
3009 5222 6.707440 AAACACATAATTTATGGCCATCGA 57.293 33.333 24.80 12.77 40.47 3.59
3042 5286 1.910722 GGAGAGGCATCTGCTGGAA 59.089 57.895 13.01 0.00 40.55 3.53
3043 5287 3.639445 GGAGAGGCATCTGCTGGA 58.361 61.111 13.01 0.00 40.55 3.86
3047 5291 4.615588 AAATAGTAGGAGAGGCATCTGC 57.384 45.455 12.36 12.36 43.85 4.26
3048 5292 6.166984 TGAAAATAGTAGGAGAGGCATCTG 57.833 41.667 5.17 0.00 35.30 2.90
3049 5293 8.677870 ATATGAAAATAGTAGGAGAGGCATCT 57.322 34.615 0.00 0.00 38.98 2.90
3050 5294 8.757877 AGATATGAAAATAGTAGGAGAGGCATC 58.242 37.037 0.00 0.00 0.00 3.91
3051 5295 8.677870 AGATATGAAAATAGTAGGAGAGGCAT 57.322 34.615 0.00 0.00 0.00 4.40
3052 5296 7.952930 AGAGATATGAAAATAGTAGGAGAGGCA 59.047 37.037 0.00 0.00 0.00 4.75
3053 5297 8.361169 AGAGATATGAAAATAGTAGGAGAGGC 57.639 38.462 0.00 0.00 0.00 4.70
3054 5298 9.527157 TGAGAGATATGAAAATAGTAGGAGAGG 57.473 37.037 0.00 0.00 0.00 3.69
3069 5313 9.029368 CCCACACTAGAATTATGAGAGATATGA 57.971 37.037 0.00 0.00 0.00 2.15
3070 5314 8.811017 ACCCACACTAGAATTATGAGAGATATG 58.189 37.037 0.00 0.00 0.00 1.78
3071 5315 8.964533 ACCCACACTAGAATTATGAGAGATAT 57.035 34.615 0.00 0.00 0.00 1.63
3073 5317 8.964533 ATACCCACACTAGAATTATGAGAGAT 57.035 34.615 0.00 0.00 0.00 2.75
3074 5318 8.783660 AATACCCACACTAGAATTATGAGAGA 57.216 34.615 0.00 0.00 0.00 3.10
3101 5345 9.891828 CAACTTGTGCATTTTAGTTATAGAACA 57.108 29.630 2.62 0.00 38.10 3.18
3104 5348 9.278978 TGTCAACTTGTGCATTTTAGTTATAGA 57.721 29.630 0.00 0.00 30.19 1.98
3107 5351 9.762933 AAATGTCAACTTGTGCATTTTAGTTAT 57.237 25.926 15.06 0.00 39.13 1.89
3108 5352 9.593134 AAAATGTCAACTTGTGCATTTTAGTTA 57.407 25.926 22.86 0.00 43.83 2.24
3109 5353 8.389603 CAAAATGTCAACTTGTGCATTTTAGTT 58.610 29.630 23.25 11.20 43.83 2.24
3110 5354 7.465781 GCAAAATGTCAACTTGTGCATTTTAGT 60.466 33.333 23.25 11.41 43.83 2.24
3111 5355 6.847289 GCAAAATGTCAACTTGTGCATTTTAG 59.153 34.615 23.25 19.98 43.83 1.85
3112 5356 6.314648 TGCAAAATGTCAACTTGTGCATTTTA 59.685 30.769 23.25 14.86 43.83 1.52
3113 5357 5.123502 TGCAAAATGTCAACTTGTGCATTTT 59.876 32.000 20.82 20.82 45.01 1.82
3114 5358 4.634883 TGCAAAATGTCAACTTGTGCATTT 59.365 33.333 15.06 15.06 41.55 2.32
3115 5359 4.190001 TGCAAAATGTCAACTTGTGCATT 58.810 34.783 0.66 4.30 35.72 3.56
3116 5360 3.794717 TGCAAAATGTCAACTTGTGCAT 58.205 36.364 0.66 0.00 35.72 3.96
3117 5361 3.242549 TGCAAAATGTCAACTTGTGCA 57.757 38.095 0.66 0.66 38.13 4.57
3118 5362 4.799419 ATTGCAAAATGTCAACTTGTGC 57.201 36.364 1.71 0.00 0.00 4.57
3119 5363 5.503498 CCAATTGCAAAATGTCAACTTGTG 58.497 37.500 1.71 0.00 0.00 3.33
3120 5364 5.738118 CCAATTGCAAAATGTCAACTTGT 57.262 34.783 1.71 0.00 0.00 3.16


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

AutoCloner maintained by Alex Coulton.