Multiple sequence alignment - TraesCS5A01G055100

Loading Multiple Alignment...

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 TraesCS5A01G055100 chr5A 100.000 3310 0 0 1 3310 51739052 51735743 0.000000e+00 6113.0
1 TraesCS5A01G055100 chrUn 89.183 1701 108 32 879 2551 65962434 65960782 0.000000e+00 2052.0
2 TraesCS5A01G055100 chrUn 83.688 846 67 28 2506 3310 65960772 65959957 0.000000e+00 732.0
3 TraesCS5A01G055100 chrUn 88.866 494 34 10 2833 3310 65956556 65956068 3.680000e-164 588.0
4 TraesCS5A01G055100 chrUn 88.889 243 16 6 523 765 65962736 65962505 4.180000e-74 289.0
5 TraesCS5A01G055100 chrUn 83.550 231 12 9 120 344 65963014 65962804 3.370000e-45 193.0
6 TraesCS5A01G055100 chrUn 90.678 118 2 4 4 117 65963767 65963655 7.400000e-32 148.0
7 TraesCS5A01G055100 chr5D 91.884 1035 70 7 2282 3310 61785311 61784285 0.000000e+00 1434.0
8 TraesCS5A01G055100 chr5D 93.684 760 34 8 1479 2224 61786066 61785307 0.000000e+00 1125.0
9 TraesCS5A01G055100 chr5D 88.914 875 40 23 522 1379 61786899 61786065 0.000000e+00 1026.0
10 TraesCS5A01G055100 chr5D 84.167 360 10 20 4 344 61787305 61786974 4.150000e-79 305.0
11 TraesCS5A01G055100 chr5D 92.982 57 4 0 462 518 61786988 61786932 2.120000e-12 84.2
12 TraesCS5A01G055100 chr2B 95.205 146 6 1 337 481 103257393 103257538 2.570000e-56 230.0
13 TraesCS5A01G055100 chr2B 99.194 124 1 0 341 464 437818877 437819000 1.200000e-54 224.0
14 TraesCS5A01G055100 chr3B 99.200 125 1 0 341 465 654654213 654654337 3.320000e-55 226.0
15 TraesCS5A01G055100 chr7A 96.350 137 3 2 337 472 511950735 511950870 1.200000e-54 224.0
16 TraesCS5A01G055100 chr7A 99.187 123 1 0 341 463 717822976 717823098 4.300000e-54 222.0
17 TraesCS5A01G055100 chr7A 98.400 125 2 0 340 464 620199858 620199734 1.550000e-53 220.0
18 TraesCS5A01G055100 chr1B 99.187 123 1 0 341 463 299981584 299981706 4.300000e-54 222.0
19 TraesCS5A01G055100 chr1A 98.400 125 2 0 340 464 64852410 64852534 1.550000e-53 220.0
20 TraesCS5A01G055100 chr1A 98.374 123 2 0 341 463 56914476 56914598 2.000000e-52 217.0
21 TraesCS5A01G055100 chr6D 77.619 210 33 8 2564 2761 446899904 446900111 7.510000e-22 115.0


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 TraesCS5A01G055100 chr5A 51735743 51739052 3309 True 6113.00 6113 100.000000 1 3310 1 chr5A.!!$R1 3309
1 TraesCS5A01G055100 chrUn 65956068 65963767 7699 True 667.00 2052 87.475667 4 3310 6 chrUn.!!$R1 3306
2 TraesCS5A01G055100 chr5D 61784285 61787305 3020 True 794.84 1434 90.326200 4 3310 5 chr5D.!!$R1 3306

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
336 986 0.027194 CATGAGCAATCGCCGTCTTG 59.973 55.0 0.00 0.00 39.83 3.02 F
362 1012 0.099082 GGAAGCTCCTCTGACGTACG 59.901 60.0 15.01 15.01 32.53 3.67 F
408 1058 0.107831 TGGGTCAAGTTTCAGTCGGG 59.892 55.0 0.00 0.00 0.00 5.14 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1423 2145 0.032815 TGCAGCACAAGCACGTAGTA 59.967 50.0 0.0 0.0 41.61 1.82 R
1731 2456 0.176680 CTGTCCATCTCCCCGTTCTG 59.823 60.0 0.0 0.0 0.00 3.02 R
2310 3044 0.179100 CGGTGCGGAGAGTCATCATT 60.179 55.0 0.0 0.0 0.00 2.57 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
30 31 3.553511 GCGACAGCATATCATATGGTAGC 59.446 47.826 9.05 11.07 44.35 3.58
31 32 4.747810 CGACAGCATATCATATGGTAGCA 58.252 43.478 9.05 0.00 0.00 3.49
32 33 4.802563 CGACAGCATATCATATGGTAGCAG 59.197 45.833 9.05 11.54 0.00 4.24
33 34 4.511527 ACAGCATATCATATGGTAGCAGC 58.488 43.478 9.05 12.32 0.00 5.25
34 35 4.019950 ACAGCATATCATATGGTAGCAGCA 60.020 41.667 9.05 0.00 0.00 4.41
35 36 4.571176 CAGCATATCATATGGTAGCAGCAG 59.429 45.833 9.05 7.75 0.00 4.24
36 37 4.224594 AGCATATCATATGGTAGCAGCAGT 59.775 41.667 7.62 0.00 0.00 4.40
117 122 2.871096 GTGTCCACCACCCTCATAAA 57.129 50.000 0.00 0.00 38.18 1.40
118 123 3.149005 GTGTCCACCACCCTCATAAAA 57.851 47.619 0.00 0.00 38.18 1.52
119 124 2.817844 GTGTCCACCACCCTCATAAAAC 59.182 50.000 0.00 0.00 38.18 2.43
122 764 1.357761 CCACCACCCTCATAAAACCCT 59.642 52.381 0.00 0.00 0.00 4.34
125 767 3.009695 CACCACCCTCATAAAACCCTACA 59.990 47.826 0.00 0.00 0.00 2.74
168 816 4.005650 CTGCACCTACACAGATCAACAAT 58.994 43.478 0.00 0.00 35.90 2.71
259 909 6.333416 TCTTGTGCATCATTCAGAGTACTAC 58.667 40.000 0.00 0.00 0.00 2.73
260 910 5.011090 TGTGCATCATTCAGAGTACTACC 57.989 43.478 0.00 0.00 0.00 3.18
261 911 4.711846 TGTGCATCATTCAGAGTACTACCT 59.288 41.667 0.00 0.00 0.00 3.08
262 912 5.891551 TGTGCATCATTCAGAGTACTACCTA 59.108 40.000 0.00 0.00 0.00 3.08
263 913 6.039829 TGTGCATCATTCAGAGTACTACCTAG 59.960 42.308 0.00 0.00 0.00 3.02
264 914 6.039941 GTGCATCATTCAGAGTACTACCTAGT 59.960 42.308 0.00 0.00 40.24 2.57
265 915 7.228906 GTGCATCATTCAGAGTACTACCTAGTA 59.771 40.741 0.00 0.00 37.73 1.82
266 916 7.445707 TGCATCATTCAGAGTACTACCTAGTAG 59.554 40.741 0.00 0.23 39.29 2.57
268 918 9.999660 CATCATTCAGAGTACTACCTAGTAGTA 57.000 37.037 9.93 9.93 45.99 1.82
327 977 3.219176 TCCCTTGGATCATGAGCAATC 57.781 47.619 13.85 0.00 0.00 2.67
336 986 0.027194 CATGAGCAATCGCCGTCTTG 59.973 55.000 0.00 0.00 39.83 3.02
347 997 3.862124 CGTCTTGTGCGGAGGAAG 58.138 61.111 0.00 0.00 0.00 3.46
348 998 2.383527 CGTCTTGTGCGGAGGAAGC 61.384 63.158 0.00 0.00 0.00 3.86
349 999 1.004440 GTCTTGTGCGGAGGAAGCT 60.004 57.895 0.00 0.00 35.28 3.74
350 1000 1.016653 GTCTTGTGCGGAGGAAGCTC 61.017 60.000 0.00 0.00 35.28 4.09
351 1001 1.743252 CTTGTGCGGAGGAAGCTCC 60.743 63.158 0.00 0.00 40.04 4.70
359 1009 4.854587 AGGAAGCTCCTCTGACGT 57.145 55.556 0.00 0.00 45.66 4.34
360 1010 3.981051 AGGAAGCTCCTCTGACGTA 57.019 52.632 0.00 0.00 45.66 3.57
361 1011 1.465794 AGGAAGCTCCTCTGACGTAC 58.534 55.000 0.00 0.00 45.66 3.67
362 1012 0.099082 GGAAGCTCCTCTGACGTACG 59.901 60.000 15.01 15.01 32.53 3.67
363 1013 1.085091 GAAGCTCCTCTGACGTACGA 58.915 55.000 24.41 0.00 0.00 3.43
364 1014 0.803740 AAGCTCCTCTGACGTACGAC 59.196 55.000 24.41 17.22 0.00 4.34
387 1037 4.598257 CCGTTAGGCCACTGACAG 57.402 61.111 5.01 0.00 33.11 3.51
388 1038 1.079127 CCGTTAGGCCACTGACAGG 60.079 63.158 5.01 0.00 33.11 4.00
389 1039 1.671742 CGTTAGGCCACTGACAGGT 59.328 57.895 5.01 0.00 33.11 4.00
390 1040 0.670546 CGTTAGGCCACTGACAGGTG 60.671 60.000 5.01 2.99 33.11 4.00
397 1047 3.312404 CACTGACAGGTGGGTCAAG 57.688 57.895 7.51 0.00 46.36 3.02
398 1048 0.469917 CACTGACAGGTGGGTCAAGT 59.530 55.000 7.51 0.00 46.36 3.16
399 1049 1.134098 CACTGACAGGTGGGTCAAGTT 60.134 52.381 7.51 0.00 46.36 2.66
400 1050 1.564348 ACTGACAGGTGGGTCAAGTTT 59.436 47.619 7.51 0.00 46.36 2.66
401 1051 2.222027 CTGACAGGTGGGTCAAGTTTC 58.778 52.381 0.00 0.00 46.36 2.78
402 1052 1.562008 TGACAGGTGGGTCAAGTTTCA 59.438 47.619 0.00 0.00 44.34 2.69
403 1053 2.222027 GACAGGTGGGTCAAGTTTCAG 58.778 52.381 0.00 0.00 37.73 3.02
404 1054 1.564348 ACAGGTGGGTCAAGTTTCAGT 59.436 47.619 0.00 0.00 0.00 3.41
405 1055 2.222027 CAGGTGGGTCAAGTTTCAGTC 58.778 52.381 0.00 0.00 0.00 3.51
406 1056 1.202651 AGGTGGGTCAAGTTTCAGTCG 60.203 52.381 0.00 0.00 0.00 4.18
407 1057 1.226746 GTGGGTCAAGTTTCAGTCGG 58.773 55.000 0.00 0.00 0.00 4.79
408 1058 0.107831 TGGGTCAAGTTTCAGTCGGG 59.892 55.000 0.00 0.00 0.00 5.14
409 1059 1.235281 GGGTCAAGTTTCAGTCGGGC 61.235 60.000 0.00 0.00 0.00 6.13
410 1060 1.235281 GGTCAAGTTTCAGTCGGGCC 61.235 60.000 0.00 0.00 0.00 5.80
411 1061 1.072505 TCAAGTTTCAGTCGGGCCC 59.927 57.895 13.57 13.57 0.00 5.80
412 1062 1.228124 CAAGTTTCAGTCGGGCCCA 60.228 57.895 24.92 6.15 0.00 5.36
413 1063 0.609131 CAAGTTTCAGTCGGGCCCAT 60.609 55.000 24.92 3.43 0.00 4.00
414 1064 0.609131 AAGTTTCAGTCGGGCCCATG 60.609 55.000 24.92 17.36 0.00 3.66
415 1065 1.002624 GTTTCAGTCGGGCCCATGA 60.003 57.895 24.92 19.54 0.00 3.07
416 1066 1.026718 GTTTCAGTCGGGCCCATGAG 61.027 60.000 24.92 8.91 0.00 2.90
417 1067 1.488705 TTTCAGTCGGGCCCATGAGT 61.489 55.000 24.92 12.20 0.00 3.41
418 1068 1.899437 TTCAGTCGGGCCCATGAGTC 61.899 60.000 24.92 2.74 0.00 3.36
419 1069 2.284625 AGTCGGGCCCATGAGTCA 60.285 61.111 24.92 0.00 0.00 3.41
420 1070 2.187946 GTCGGGCCCATGAGTCAG 59.812 66.667 24.92 1.98 0.00 3.51
421 1071 3.785859 TCGGGCCCATGAGTCAGC 61.786 66.667 24.92 0.00 0.00 4.26
423 1073 3.785859 GGGCCCATGAGTCAGCGA 61.786 66.667 19.95 0.00 0.00 4.93
424 1074 2.512515 GGCCCATGAGTCAGCGAC 60.513 66.667 0.00 1.15 0.00 5.19
425 1075 2.887568 GCCCATGAGTCAGCGACG 60.888 66.667 0.00 0.00 37.67 5.12
426 1076 2.202797 CCCATGAGTCAGCGACGG 60.203 66.667 0.00 0.00 37.67 4.79
427 1077 2.710902 CCCATGAGTCAGCGACGGA 61.711 63.158 0.00 0.00 37.67 4.69
428 1078 1.215382 CCATGAGTCAGCGACGGAA 59.785 57.895 0.00 0.00 37.67 4.30
429 1079 1.078759 CCATGAGTCAGCGACGGAAC 61.079 60.000 0.00 0.00 37.67 3.62
458 1108 4.554036 GCACGGCAGGGGATCCTC 62.554 72.222 12.58 7.90 42.67 3.71
459 1109 4.227134 CACGGCAGGGGATCCTCG 62.227 72.222 12.58 5.37 42.67 4.63
460 1110 4.779733 ACGGCAGGGGATCCTCGT 62.780 66.667 12.58 11.06 42.67 4.18
461 1111 3.917760 CGGCAGGGGATCCTCGTC 61.918 72.222 12.58 4.80 42.67 4.20
462 1112 3.551407 GGCAGGGGATCCTCGTCC 61.551 72.222 12.58 10.58 42.67 4.79
463 1113 3.917760 GCAGGGGATCCTCGTCCG 61.918 72.222 12.58 0.08 42.67 4.79
464 1114 2.442272 CAGGGGATCCTCGTCCGT 60.442 66.667 12.58 0.00 42.67 4.69
465 1115 2.123812 AGGGGATCCTCGTCCGTC 60.124 66.667 12.58 0.00 39.80 4.79
466 1116 2.123812 GGGGATCCTCGTCCGTCT 60.124 66.667 12.58 0.00 39.26 4.18
467 1117 1.757340 GGGGATCCTCGTCCGTCTT 60.757 63.158 12.58 0.00 39.26 3.01
468 1118 1.437986 GGGATCCTCGTCCGTCTTG 59.562 63.158 12.58 0.00 39.26 3.02
469 1119 1.321074 GGGATCCTCGTCCGTCTTGT 61.321 60.000 12.58 0.00 39.26 3.16
470 1120 0.179134 GGATCCTCGTCCGTCTTGTG 60.179 60.000 3.84 0.00 0.00 3.33
471 1121 0.179134 GATCCTCGTCCGTCTTGTGG 60.179 60.000 0.00 0.00 0.00 4.17
518 1168 0.247460 TCTGCAACACGATGAGGAGG 59.753 55.000 0.00 0.00 0.00 4.30
520 1170 0.247460 TGCAACACGATGAGGAGGAG 59.753 55.000 0.00 0.00 0.00 3.69
579 1258 5.212532 TGACAATTTGGGGTTTCATTCAG 57.787 39.130 0.78 0.00 0.00 3.02
580 1259 3.996363 GACAATTTGGGGTTTCATTCAGC 59.004 43.478 0.78 0.00 0.00 4.26
614 1309 2.094545 CCACATGCAGGCTCCTTTTAAC 60.095 50.000 0.00 0.00 0.00 2.01
647 1342 5.648092 GCAATTAAGCTTATCCGGACCATAT 59.352 40.000 6.12 0.00 0.00 1.78
648 1343 6.403636 GCAATTAAGCTTATCCGGACCATATG 60.404 42.308 6.12 0.00 0.00 1.78
649 1344 5.818678 TTAAGCTTATCCGGACCATATGT 57.181 39.130 6.12 0.00 0.00 2.29
650 1345 6.921486 TTAAGCTTATCCGGACCATATGTA 57.079 37.500 6.12 0.00 0.00 2.29
665 1360 5.538813 ACCATATGTAATTAGCGAGGACAGA 59.461 40.000 1.24 0.00 0.00 3.41
666 1361 5.864474 CCATATGTAATTAGCGAGGACAGAC 59.136 44.000 1.24 0.00 0.00 3.51
667 1362 6.447162 CATATGTAATTAGCGAGGACAGACA 58.553 40.000 0.00 0.00 0.00 3.41
668 1363 4.371855 TGTAATTAGCGAGGACAGACAG 57.628 45.455 0.00 0.00 0.00 3.51
669 1364 2.969628 AATTAGCGAGGACAGACAGG 57.030 50.000 0.00 0.00 0.00 4.00
670 1365 0.461961 ATTAGCGAGGACAGACAGGC 59.538 55.000 0.00 0.00 0.00 4.85
681 1376 0.900182 CAGACAGGCCCCCTTTTTCC 60.900 60.000 0.00 0.00 0.00 3.13
685 1380 3.691342 GGCCCCCTTTTTCCACGC 61.691 66.667 0.00 0.00 0.00 5.34
741 1436 7.733402 TTGTGTTGGGTACAGAAATTACTAC 57.267 36.000 0.00 0.00 37.11 2.73
743 1438 6.932400 TGTGTTGGGTACAGAAATTACTACTG 59.068 38.462 0.00 0.00 37.45 2.74
744 1439 7.156673 GTGTTGGGTACAGAAATTACTACTGA 58.843 38.462 0.00 0.00 37.45 3.41
745 1440 7.822822 GTGTTGGGTACAGAAATTACTACTGAT 59.177 37.037 0.00 0.00 37.45 2.90
772 1467 0.251341 ACTTGACATTGCCCTCCACC 60.251 55.000 0.00 0.00 0.00 4.61
773 1468 0.251297 CTTGACATTGCCCTCCACCA 60.251 55.000 0.00 0.00 0.00 4.17
774 1469 0.539438 TTGACATTGCCCTCCACCAC 60.539 55.000 0.00 0.00 0.00 4.16
775 1470 1.678970 GACATTGCCCTCCACCACC 60.679 63.158 0.00 0.00 0.00 4.61
776 1471 2.424842 GACATTGCCCTCCACCACCA 62.425 60.000 0.00 0.00 0.00 4.17
777 1472 1.978617 CATTGCCCTCCACCACCAC 60.979 63.158 0.00 0.00 0.00 4.16
778 1473 3.224007 ATTGCCCTCCACCACCACC 62.224 63.158 0.00 0.00 0.00 4.61
811 1506 1.801332 CACATGGCAGAAGCAGAGC 59.199 57.895 0.00 0.00 44.61 4.09
812 1507 1.744368 ACATGGCAGAAGCAGAGCG 60.744 57.895 0.00 0.00 44.61 5.03
813 1508 2.823147 ATGGCAGAAGCAGAGCGC 60.823 61.111 0.00 0.00 44.61 5.92
814 1509 3.617143 ATGGCAGAAGCAGAGCGCA 62.617 57.895 11.47 0.00 46.13 6.09
815 1510 3.052082 GGCAGAAGCAGAGCGCAA 61.052 61.111 11.47 0.00 46.13 4.85
816 1511 2.404995 GGCAGAAGCAGAGCGCAAT 61.405 57.895 11.47 0.00 46.13 3.56
817 1512 1.226323 GCAGAAGCAGAGCGCAATG 60.226 57.895 11.47 9.08 46.13 2.82
818 1513 1.642037 GCAGAAGCAGAGCGCAATGA 61.642 55.000 11.47 0.00 46.13 2.57
819 1514 0.374063 CAGAAGCAGAGCGCAATGAG 59.626 55.000 11.47 0.00 46.13 2.90
820 1515 0.248565 AGAAGCAGAGCGCAATGAGA 59.751 50.000 11.47 0.00 46.13 3.27
821 1516 0.651551 GAAGCAGAGCGCAATGAGAG 59.348 55.000 11.47 0.00 46.13 3.20
837 1532 3.095332 TGAGAGTGTGAGAGAATGGGAG 58.905 50.000 0.00 0.00 0.00 4.30
838 1533 3.245407 TGAGAGTGTGAGAGAATGGGAGA 60.245 47.826 0.00 0.00 0.00 3.71
839 1534 3.364549 AGAGTGTGAGAGAATGGGAGAG 58.635 50.000 0.00 0.00 0.00 3.20
840 1535 2.430332 GAGTGTGAGAGAATGGGAGAGG 59.570 54.545 0.00 0.00 0.00 3.69
841 1536 2.043664 AGTGTGAGAGAATGGGAGAGGA 59.956 50.000 0.00 0.00 0.00 3.71
842 1537 2.430332 GTGTGAGAGAATGGGAGAGGAG 59.570 54.545 0.00 0.00 0.00 3.69
853 1548 2.122768 GGGAGAGGAGATCCATTGTGT 58.877 52.381 0.92 0.00 38.70 3.72
854 1549 2.507471 GGGAGAGGAGATCCATTGTGTT 59.493 50.000 0.92 0.00 38.70 3.32
855 1550 3.539604 GGAGAGGAGATCCATTGTGTTG 58.460 50.000 0.92 0.00 38.89 3.33
856 1551 3.198635 GGAGAGGAGATCCATTGTGTTGA 59.801 47.826 0.92 0.00 38.89 3.18
857 1552 4.141528 GGAGAGGAGATCCATTGTGTTGAT 60.142 45.833 0.92 0.00 38.89 2.57
858 1553 5.070981 GGAGAGGAGATCCATTGTGTTGATA 59.929 44.000 0.92 0.00 38.89 2.15
859 1554 6.408548 GGAGAGGAGATCCATTGTGTTGATAA 60.409 42.308 0.92 0.00 38.89 1.75
860 1555 6.352516 AGAGGAGATCCATTGTGTTGATAAC 58.647 40.000 0.92 0.00 38.89 1.89
863 1558 6.600822 AGGAGATCCATTGTGTTGATAACTTG 59.399 38.462 0.92 0.00 38.89 3.16
867 1562 6.801539 TCCATTGTGTTGATAACTTGAGAC 57.198 37.500 0.00 0.00 0.00 3.36
880 1575 7.500227 TGATAACTTGAGACCATTGGATCATTC 59.500 37.037 10.37 0.00 0.00 2.67
882 1577 5.824421 ACTTGAGACCATTGGATCATTCTT 58.176 37.500 10.37 0.00 0.00 2.52
884 1579 5.440207 TGAGACCATTGGATCATTCTTCA 57.560 39.130 10.37 0.85 0.00 3.02
885 1580 6.009908 TGAGACCATTGGATCATTCTTCAT 57.990 37.500 10.37 0.00 0.00 2.57
886 1581 6.060136 TGAGACCATTGGATCATTCTTCATC 58.940 40.000 10.37 0.00 0.00 2.92
887 1582 5.061853 AGACCATTGGATCATTCTTCATCG 58.938 41.667 10.37 0.00 0.00 3.84
895 1614 3.868757 TCATTCTTCATCGTTCCTCGT 57.131 42.857 0.00 0.00 40.80 4.18
938 1657 1.057822 CTGCAAAGATCGACGCGTG 59.942 57.895 20.70 9.70 0.00 5.34
958 1677 2.234661 TGATGGAGTGGAGCAAGTAGTG 59.765 50.000 0.00 0.00 0.00 2.74
967 1686 4.760047 CAAGTAGTGGCGGCGGCT 62.760 66.667 33.21 17.57 39.81 5.52
989 1708 1.060937 GCTGCGGAATTGTAGCGTG 59.939 57.895 0.00 0.00 37.82 5.34
1217 1939 1.373497 CGTCCTCGCACTGCTTCTT 60.373 57.895 0.00 0.00 0.00 2.52
1357 2079 2.464459 GCGGCCGTCAAGATTCAGG 61.464 63.158 28.70 0.00 0.00 3.86
1381 2103 2.236766 CCTTCCGATCGTACCTGGTAT 58.763 52.381 15.09 0.00 0.00 2.73
1386 2108 2.287427 CCGATCGTACCTGGTATGTGAC 60.287 54.545 22.11 14.43 0.00 3.67
1387 2109 2.601504 CGATCGTACCTGGTATGTGACG 60.602 54.545 22.11 17.08 0.00 4.35
1400 2122 1.578618 GTGACGCTCCGTACGTACG 60.579 63.158 35.02 35.02 45.24 3.67
1414 2136 2.937994 CGTACGTACGTCCCTATGAG 57.062 55.000 33.95 7.63 44.13 2.90
1416 2138 3.062763 CGTACGTACGTCCCTATGAGAT 58.937 50.000 33.95 0.00 44.13 2.75
1417 2139 3.120752 CGTACGTACGTCCCTATGAGATG 60.121 52.174 33.95 5.49 44.13 2.90
1419 2141 2.158711 ACGTACGTCCCTATGAGATGGA 60.159 50.000 16.72 0.00 0.00 3.41
1422 2144 1.689273 ACGTCCCTATGAGATGGAAGC 59.311 52.381 0.00 0.00 31.79 3.86
1423 2145 1.967066 CGTCCCTATGAGATGGAAGCT 59.033 52.381 0.00 0.00 30.44 3.74
1424 2146 3.157881 CGTCCCTATGAGATGGAAGCTA 58.842 50.000 0.00 0.00 22.26 3.32
1438 2160 1.429463 AAGCTACTACGTGCTTGTGC 58.571 50.000 9.78 1.67 46.25 4.57
1441 2163 0.716108 CTACTACGTGCTTGTGCTGC 59.284 55.000 0.00 0.00 40.48 5.25
1443 2165 1.224069 ACTACGTGCTTGTGCTGCAG 61.224 55.000 10.11 10.11 41.41 4.41
1458 2180 2.751436 CAGCGTGGTTGATGGGGG 60.751 66.667 0.00 0.00 0.00 5.40
1475 2197 1.666209 GGGGTGGTGAAATCCATGCG 61.666 60.000 0.00 0.00 39.81 4.73
1743 2468 1.984570 CAGGAGCAGAACGGGGAGA 60.985 63.158 0.00 0.00 0.00 3.71
1744 2469 1.002274 AGGAGCAGAACGGGGAGAT 59.998 57.895 0.00 0.00 0.00 2.75
1745 2470 1.144936 GGAGCAGAACGGGGAGATG 59.855 63.158 0.00 0.00 0.00 2.90
1747 2472 1.306141 AGCAGAACGGGGAGATGGA 60.306 57.895 0.00 0.00 0.00 3.41
1749 2474 1.899437 GCAGAACGGGGAGATGGACA 61.899 60.000 0.00 0.00 0.00 4.02
1751 2476 1.153349 GAACGGGGAGATGGACAGC 60.153 63.158 0.00 0.00 0.00 4.40
1753 2478 4.227134 CGGGGAGATGGACAGCGG 62.227 72.222 0.00 0.00 0.00 5.52
1754 2479 4.554036 GGGGAGATGGACAGCGGC 62.554 72.222 0.00 0.00 0.00 6.53
2189 2923 1.743252 GCCAAGGAGCTCCGTTGAG 60.743 63.158 30.66 24.02 42.08 3.02
2331 3072 1.226717 GATGACTCTCCGCACCGAC 60.227 63.158 0.00 0.00 0.00 4.79
2356 3097 3.128589 GGAGCGAATGAAATTTACTGCCA 59.871 43.478 0.00 0.00 36.07 4.92
2367 3108 8.082334 TGAAATTTACTGCCACAATAAAAAGC 57.918 30.769 0.00 0.00 0.00 3.51
2368 3109 7.712639 TGAAATTTACTGCCACAATAAAAAGCA 59.287 29.630 0.00 0.00 0.00 3.91
2407 3148 0.999406 CTGTCCTGCGGTAACAATCG 59.001 55.000 0.00 0.00 0.00 3.34
2425 3166 5.154932 CAATCGTGGACGGTCTATTCTATC 58.845 45.833 8.23 0.00 40.29 2.08
2427 3168 3.562973 TCGTGGACGGTCTATTCTATCAC 59.437 47.826 8.23 4.23 40.29 3.06
2429 3174 3.562973 GTGGACGGTCTATTCTATCACGA 59.437 47.826 8.23 0.00 0.00 4.35
2433 3178 5.359716 ACGGTCTATTCTATCACGACATC 57.640 43.478 0.00 0.00 0.00 3.06
2453 3198 2.162681 CTTCAAAGCGGACCCTCAAAT 58.837 47.619 0.00 0.00 0.00 2.32
2456 3201 0.036306 AAAGCGGACCCTCAAATCGT 59.964 50.000 0.00 0.00 0.00 3.73
2459 3204 0.391263 GCGGACCCTCAAATCGTCTT 60.391 55.000 0.00 0.00 0.00 3.01
2516 3320 5.147330 TGATCAAACGTGATTCTGTACCT 57.853 39.130 0.00 0.00 44.83 3.08
2517 3321 6.275494 TGATCAAACGTGATTCTGTACCTA 57.725 37.500 0.00 0.00 44.83 3.08
2524 3332 3.556513 GTGATTCTGTACCTATCGAGCG 58.443 50.000 0.00 0.00 0.00 5.03
2538 3346 4.148825 AGCGGTCGGGATGCACTC 62.149 66.667 0.00 0.00 0.00 3.51
2552 3360 0.572125 GCACTCTTTTGCGCAAACAC 59.428 50.000 33.73 15.85 31.51 3.32
2555 3363 1.268032 ACTCTTTTGCGCAAACACGAG 60.268 47.619 32.62 32.62 34.06 4.18
2582 3390 0.035439 GGGGATTTGCAGAAGTCCGA 60.035 55.000 0.00 0.00 38.58 4.55
2589 3397 0.179059 TGCAGAAGTCCGAACAGCAA 60.179 50.000 0.00 0.00 0.00 3.91
2593 3401 2.549754 CAGAAGTCCGAACAGCAAACAT 59.450 45.455 0.00 0.00 0.00 2.71
2640 3448 0.321653 CAAAACTCCTCCTGGACCCG 60.322 60.000 0.00 0.00 37.46 5.28
2691 3499 5.137412 TCCCCTTTTCTCTTTTTCCTTCA 57.863 39.130 0.00 0.00 0.00 3.02
2761 3569 1.194781 ACGAGCCAGTCACCTCCAAT 61.195 55.000 0.00 0.00 0.00 3.16
2783 3591 9.947669 CCAATGAGCATTACAAATTTTGAAAAA 57.052 25.926 15.81 7.30 0.00 1.94
2805 3613 8.491331 AAAATGTTTGTTGCCATAACATATCC 57.509 30.769 0.00 0.00 40.54 2.59
2825 3633 8.689972 CATATCCAGATTTACCAAAGAAAGCTT 58.310 33.333 0.00 0.00 30.37 3.74
2896 3730 8.885722 AGTAAATTGCCATGCTATTCAAATTTG 58.114 29.630 12.15 12.15 33.44 2.32
2900 3734 6.483385 TGCCATGCTATTCAAATTTGTTTG 57.517 33.333 17.47 8.92 0.00 2.93
2922 3756 9.649024 GTTTGACATGGTTTGTTGAATAAATTG 57.351 29.630 0.00 0.00 39.18 2.32
2931 3765 5.495926 TGTTGAATAAATTGGCCATGGTT 57.504 34.783 14.67 3.52 0.00 3.67
2948 3782 6.198029 GCCATGGTTTAAAACAAATTTTGCAC 59.802 34.615 14.67 0.00 38.50 4.57
2949 3783 7.253422 CCATGGTTTAAAACAAATTTTGCACA 58.747 30.769 10.54 0.00 38.50 4.57
2956 3790 5.799681 AAACAAATTTTGCACAGTCCAAG 57.200 34.783 9.04 0.00 0.00 3.61
2968 3802 5.123186 TGCACAGTCCAAGAATAATTTACCG 59.877 40.000 0.00 0.00 0.00 4.02
3183 7919 6.775594 AATTCCTAAAGCTTGTAATGGGAC 57.224 37.500 0.00 0.00 0.00 4.46
3262 7999 6.626623 GCCAAGCAATTTGTCATGTCTAGAAT 60.627 38.462 0.00 0.00 34.87 2.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.795877 TGATATGCTGTCGCTCATTCAA 58.204 40.909 0.00 0.00 36.97 2.69
1 2 3.457610 TGATATGCTGTCGCTCATTCA 57.542 42.857 0.00 0.00 36.97 2.57
2 3 5.006455 CCATATGATATGCTGTCGCTCATTC 59.994 44.000 3.65 0.00 32.73 2.67
28 29 1.801332 CGGAGTACGTACTGCTGCT 59.199 57.895 34.65 13.26 41.76 4.24
29 30 4.379221 CGGAGTACGTACTGCTGC 57.621 61.111 34.65 20.61 41.76 5.25
117 122 0.602905 GAGCTGTTGCGTGTAGGGTT 60.603 55.000 0.00 0.00 45.42 4.11
118 123 1.004918 GAGCTGTTGCGTGTAGGGT 60.005 57.895 0.00 0.00 45.42 4.34
119 124 1.741770 GGAGCTGTTGCGTGTAGGG 60.742 63.158 0.00 0.00 45.42 3.53
122 764 1.890876 ATTTGGAGCTGTTGCGTGTA 58.109 45.000 0.00 0.00 45.42 2.90
125 767 2.351738 GCTTAATTTGGAGCTGTTGCGT 60.352 45.455 0.00 0.00 45.42 5.24
151 793 5.375417 TTTGCATTGTTGATCTGTGTAGG 57.625 39.130 0.00 0.00 0.00 3.18
211 859 5.659440 TGTGCTGATGATGAGTACTTGTA 57.341 39.130 0.00 0.00 0.00 2.41
212 860 4.541973 TGTGCTGATGATGAGTACTTGT 57.458 40.909 0.00 0.00 0.00 3.16
213 861 5.816258 AGATTGTGCTGATGATGAGTACTTG 59.184 40.000 0.00 0.00 0.00 3.16
292 942 5.905088 TCCAAGGGAAGCTAGCTAGTATAT 58.095 41.667 19.70 0.00 0.00 0.86
293 943 5.335028 TCCAAGGGAAGCTAGCTAGTATA 57.665 43.478 19.70 0.00 0.00 1.47
294 944 4.200447 TCCAAGGGAAGCTAGCTAGTAT 57.800 45.455 19.70 11.01 0.00 2.12
295 945 3.682592 TCCAAGGGAAGCTAGCTAGTA 57.317 47.619 19.70 0.00 0.00 1.82
343 993 0.099082 CGTACGTCAGAGGAGCTTCC 59.901 60.000 7.22 0.00 36.58 3.46
344 994 1.085091 TCGTACGTCAGAGGAGCTTC 58.915 55.000 16.05 0.00 0.00 3.86
345 995 0.803740 GTCGTACGTCAGAGGAGCTT 59.196 55.000 16.05 0.00 0.00 3.74
346 996 1.360194 CGTCGTACGTCAGAGGAGCT 61.360 60.000 16.05 0.00 36.74 4.09
347 997 1.060622 CGTCGTACGTCAGAGGAGC 59.939 63.158 16.05 0.00 36.74 4.70
348 998 1.060622 GCGTCGTACGTCAGAGGAG 59.939 63.158 16.05 0.00 44.73 3.69
349 999 2.393768 GGCGTCGTACGTCAGAGGA 61.394 63.158 16.05 0.00 46.84 3.71
350 1000 2.099831 GGCGTCGTACGTCAGAGG 59.900 66.667 16.05 2.54 46.84 3.69
370 1020 1.079127 CCTGTCAGTGGCCTAACGG 60.079 63.158 3.32 1.71 0.00 4.44
371 1021 0.670546 CACCTGTCAGTGGCCTAACG 60.671 60.000 3.32 0.00 33.95 3.18
372 1022 3.233355 CACCTGTCAGTGGCCTAAC 57.767 57.895 3.32 0.00 33.95 2.34
379 1029 0.469917 ACTTGACCCACCTGTCAGTG 59.530 55.000 0.00 0.00 45.37 3.66
380 1030 1.213296 AACTTGACCCACCTGTCAGT 58.787 50.000 0.00 0.00 45.37 3.41
381 1031 2.222027 GAAACTTGACCCACCTGTCAG 58.778 52.381 0.00 0.00 45.37 3.51
382 1032 1.562008 TGAAACTTGACCCACCTGTCA 59.438 47.619 0.00 0.00 43.26 3.58
383 1033 2.222027 CTGAAACTTGACCCACCTGTC 58.778 52.381 0.00 0.00 35.77 3.51
384 1034 1.564348 ACTGAAACTTGACCCACCTGT 59.436 47.619 0.00 0.00 0.00 4.00
385 1035 2.222027 GACTGAAACTTGACCCACCTG 58.778 52.381 0.00 0.00 0.00 4.00
386 1036 1.202651 CGACTGAAACTTGACCCACCT 60.203 52.381 0.00 0.00 0.00 4.00
387 1037 1.226746 CGACTGAAACTTGACCCACC 58.773 55.000 0.00 0.00 0.00 4.61
388 1038 1.226746 CCGACTGAAACTTGACCCAC 58.773 55.000 0.00 0.00 0.00 4.61
389 1039 0.107831 CCCGACTGAAACTTGACCCA 59.892 55.000 0.00 0.00 0.00 4.51
390 1040 1.235281 GCCCGACTGAAACTTGACCC 61.235 60.000 0.00 0.00 0.00 4.46
391 1041 1.235281 GGCCCGACTGAAACTTGACC 61.235 60.000 0.00 0.00 0.00 4.02
392 1042 1.235281 GGGCCCGACTGAAACTTGAC 61.235 60.000 5.69 0.00 0.00 3.18
393 1043 1.072505 GGGCCCGACTGAAACTTGA 59.927 57.895 5.69 0.00 0.00 3.02
394 1044 0.609131 ATGGGCCCGACTGAAACTTG 60.609 55.000 19.37 0.00 0.00 3.16
395 1045 0.609131 CATGGGCCCGACTGAAACTT 60.609 55.000 19.37 0.00 0.00 2.66
396 1046 1.002134 CATGGGCCCGACTGAAACT 60.002 57.895 19.37 0.00 0.00 2.66
397 1047 1.002624 TCATGGGCCCGACTGAAAC 60.003 57.895 19.37 0.00 0.00 2.78
398 1048 1.299648 CTCATGGGCCCGACTGAAA 59.700 57.895 19.37 0.00 0.00 2.69
399 1049 1.899437 GACTCATGGGCCCGACTGAA 61.899 60.000 19.37 0.00 0.00 3.02
400 1050 2.284625 ACTCATGGGCCCGACTGA 60.285 61.111 19.37 18.36 0.00 3.41
401 1051 2.187946 GACTCATGGGCCCGACTG 59.812 66.667 19.37 14.85 0.00 3.51
402 1052 2.284625 TGACTCATGGGCCCGACT 60.285 61.111 19.37 0.33 0.00 4.18
403 1053 2.187946 CTGACTCATGGGCCCGAC 59.812 66.667 19.37 3.37 0.00 4.79
404 1054 3.785859 GCTGACTCATGGGCCCGA 61.786 66.667 19.37 8.43 0.00 5.14
406 1056 3.785859 TCGCTGACTCATGGGCCC 61.786 66.667 17.59 17.59 0.00 5.80
407 1057 2.512515 GTCGCTGACTCATGGGCC 60.513 66.667 0.00 0.00 0.00 5.80
408 1058 2.887568 CGTCGCTGACTCATGGGC 60.888 66.667 0.00 0.00 0.00 5.36
409 1059 2.202797 CCGTCGCTGACTCATGGG 60.203 66.667 0.00 0.00 0.00 4.00
410 1060 1.078759 GTTCCGTCGCTGACTCATGG 61.079 60.000 0.00 2.01 0.00 3.66
411 1061 1.406219 CGTTCCGTCGCTGACTCATG 61.406 60.000 7.03 0.00 0.00 3.07
412 1062 1.154016 CGTTCCGTCGCTGACTCAT 60.154 57.895 7.03 0.00 0.00 2.90
413 1063 2.254350 CGTTCCGTCGCTGACTCA 59.746 61.111 7.03 0.00 0.00 3.41
414 1064 2.504244 CCGTTCCGTCGCTGACTC 60.504 66.667 7.03 0.00 0.00 3.36
415 1065 4.719369 GCCGTTCCGTCGCTGACT 62.719 66.667 7.03 0.00 0.00 3.41
441 1091 4.554036 GAGGATCCCCTGCCGTGC 62.554 72.222 8.55 0.00 44.53 5.34
442 1092 4.227134 CGAGGATCCCCTGCCGTG 62.227 72.222 8.55 0.00 44.53 4.94
443 1093 4.779733 ACGAGGATCCCCTGCCGT 62.780 66.667 8.55 7.95 44.53 5.68
444 1094 3.917760 GACGAGGATCCCCTGCCG 61.918 72.222 8.55 7.30 44.53 5.69
445 1095 3.551407 GGACGAGGATCCCCTGCC 61.551 72.222 8.55 1.52 44.53 4.85
446 1096 3.917760 CGGACGAGGATCCCCTGC 61.918 72.222 8.55 0.00 44.53 4.85
447 1097 2.442272 ACGGACGAGGATCCCCTG 60.442 66.667 8.55 0.45 44.53 4.45
449 1099 1.757340 AAGACGGACGAGGATCCCC 60.757 63.158 8.55 0.79 35.03 4.81
450 1100 1.321074 ACAAGACGGACGAGGATCCC 61.321 60.000 8.55 0.00 35.03 3.85
451 1101 0.179134 CACAAGACGGACGAGGATCC 60.179 60.000 2.48 2.48 35.16 3.36
452 1102 0.179134 CCACAAGACGGACGAGGATC 60.179 60.000 0.00 0.00 0.00 3.36
453 1103 0.898789 ACCACAAGACGGACGAGGAT 60.899 55.000 0.00 0.00 0.00 3.24
454 1104 1.529948 ACCACAAGACGGACGAGGA 60.530 57.895 0.00 0.00 0.00 3.71
455 1105 1.372997 CACCACAAGACGGACGAGG 60.373 63.158 0.00 0.00 0.00 4.63
456 1106 0.387367 CTCACCACAAGACGGACGAG 60.387 60.000 0.00 0.00 0.00 4.18
457 1107 1.105167 ACTCACCACAAGACGGACGA 61.105 55.000 0.00 0.00 0.00 4.20
458 1108 0.249322 AACTCACCACAAGACGGACG 60.249 55.000 0.00 0.00 0.00 4.79
459 1109 1.217882 CAACTCACCACAAGACGGAC 58.782 55.000 0.00 0.00 0.00 4.79
460 1110 0.828022 ACAACTCACCACAAGACGGA 59.172 50.000 0.00 0.00 0.00 4.69
461 1111 0.937304 CACAACTCACCACAAGACGG 59.063 55.000 0.00 0.00 0.00 4.79
462 1112 0.304705 GCACAACTCACCACAAGACG 59.695 55.000 0.00 0.00 0.00 4.18
463 1113 0.663153 GGCACAACTCACCACAAGAC 59.337 55.000 0.00 0.00 0.00 3.01
464 1114 0.254462 TGGCACAACTCACCACAAGA 59.746 50.000 0.00 0.00 31.92 3.02
465 1115 2.792500 TGGCACAACTCACCACAAG 58.208 52.632 0.00 0.00 31.92 3.16
506 1156 0.663688 CGGTACTCCTCCTCATCGTG 59.336 60.000 0.00 0.00 0.00 4.35
518 1168 2.550978 CATTGATGGTCCACGGTACTC 58.449 52.381 0.00 0.00 0.00 2.59
520 1170 1.663695 CCATTGATGGTCCACGGTAC 58.336 55.000 0.00 0.00 43.05 3.34
579 1258 2.798680 CATGTGGTGAGTAGAGTACGC 58.201 52.381 0.00 0.00 0.00 4.42
580 1259 2.163613 TGCATGTGGTGAGTAGAGTACG 59.836 50.000 0.00 0.00 0.00 3.67
614 1309 6.077838 GGATAAGCTTAATTGCGATTTACGG 58.922 40.000 10.85 0.00 42.83 4.02
647 1342 3.130516 CCTGTCTGTCCTCGCTAATTACA 59.869 47.826 0.00 0.00 0.00 2.41
648 1343 3.707793 CCTGTCTGTCCTCGCTAATTAC 58.292 50.000 0.00 0.00 0.00 1.89
649 1344 2.100916 GCCTGTCTGTCCTCGCTAATTA 59.899 50.000 0.00 0.00 0.00 1.40
650 1345 1.134670 GCCTGTCTGTCCTCGCTAATT 60.135 52.381 0.00 0.00 0.00 1.40
665 1360 1.152333 GTGGAAAAAGGGGGCCTGT 60.152 57.895 0.84 0.00 32.13 4.00
666 1361 2.275380 CGTGGAAAAAGGGGGCCTG 61.275 63.158 0.84 0.00 32.13 4.85
667 1362 2.117423 CGTGGAAAAAGGGGGCCT 59.883 61.111 0.84 0.00 33.87 5.19
668 1363 3.691342 GCGTGGAAAAAGGGGGCC 61.691 66.667 0.00 0.00 0.00 5.80
669 1364 2.207229 AAGCGTGGAAAAAGGGGGC 61.207 57.895 0.00 0.00 0.00 5.80
670 1365 0.825840 TCAAGCGTGGAAAAAGGGGG 60.826 55.000 0.00 0.00 0.00 5.40
681 1376 2.193306 ACTGCAAAACTTCAAGCGTG 57.807 45.000 0.00 0.00 0.00 5.34
685 1380 6.035843 TCAGCTTTTACTGCAAAACTTCAAG 58.964 36.000 0.00 0.00 37.59 3.02
740 1435 7.362920 GGGCAATGTCAAGTGTTAAATATCAGT 60.363 37.037 0.00 0.00 0.00 3.41
741 1436 6.974622 GGGCAATGTCAAGTGTTAAATATCAG 59.025 38.462 0.00 0.00 0.00 2.90
743 1438 7.100458 AGGGCAATGTCAAGTGTTAAATATC 57.900 36.000 0.00 0.00 0.00 1.63
744 1439 6.096846 GGAGGGCAATGTCAAGTGTTAAATAT 59.903 38.462 0.00 0.00 0.00 1.28
745 1440 5.417580 GGAGGGCAATGTCAAGTGTTAAATA 59.582 40.000 0.00 0.00 0.00 1.40
757 1452 1.678970 GGTGGTGGAGGGCAATGTC 60.679 63.158 0.00 0.00 0.00 3.06
772 1467 0.911525 AGGGAGATGGTCTGGTGGTG 60.912 60.000 0.00 0.00 0.00 4.17
773 1468 0.911525 CAGGGAGATGGTCTGGTGGT 60.912 60.000 0.00 0.00 0.00 4.16
774 1469 1.910722 CAGGGAGATGGTCTGGTGG 59.089 63.158 0.00 0.00 0.00 4.61
775 1470 1.222936 GCAGGGAGATGGTCTGGTG 59.777 63.158 0.00 0.00 0.00 4.17
776 1471 1.229625 TGCAGGGAGATGGTCTGGT 60.230 57.895 0.00 0.00 0.00 4.00
777 1472 1.222936 GTGCAGGGAGATGGTCTGG 59.777 63.158 0.00 0.00 0.00 3.86
778 1473 0.545171 ATGTGCAGGGAGATGGTCTG 59.455 55.000 0.00 0.00 0.00 3.51
811 1506 2.643933 TCTCTCACACTCTCATTGCG 57.356 50.000 0.00 0.00 0.00 4.85
812 1507 3.622163 CCATTCTCTCACACTCTCATTGC 59.378 47.826 0.00 0.00 0.00 3.56
813 1508 4.081254 TCCCATTCTCTCACACTCTCATTG 60.081 45.833 0.00 0.00 0.00 2.82
814 1509 4.099633 TCCCATTCTCTCACACTCTCATT 58.900 43.478 0.00 0.00 0.00 2.57
815 1510 3.705579 CTCCCATTCTCTCACACTCTCAT 59.294 47.826 0.00 0.00 0.00 2.90
816 1511 3.095332 CTCCCATTCTCTCACACTCTCA 58.905 50.000 0.00 0.00 0.00 3.27
817 1512 3.360867 TCTCCCATTCTCTCACACTCTC 58.639 50.000 0.00 0.00 0.00 3.20
818 1513 3.364549 CTCTCCCATTCTCTCACACTCT 58.635 50.000 0.00 0.00 0.00 3.24
819 1514 2.430332 CCTCTCCCATTCTCTCACACTC 59.570 54.545 0.00 0.00 0.00 3.51
820 1515 2.043664 TCCTCTCCCATTCTCTCACACT 59.956 50.000 0.00 0.00 0.00 3.55
821 1516 2.430332 CTCCTCTCCCATTCTCTCACAC 59.570 54.545 0.00 0.00 0.00 3.82
837 1532 6.352516 AGTTATCAACACAATGGATCTCCTC 58.647 40.000 0.00 0.00 36.82 3.71
838 1533 6.319048 AGTTATCAACACAATGGATCTCCT 57.681 37.500 0.00 0.00 36.82 3.69
839 1534 6.599244 TCAAGTTATCAACACAATGGATCTCC 59.401 38.462 0.00 0.00 0.00 3.71
840 1535 7.550551 TCTCAAGTTATCAACACAATGGATCTC 59.449 37.037 0.00 0.00 0.00 2.75
841 1536 7.335422 GTCTCAAGTTATCAACACAATGGATCT 59.665 37.037 0.00 0.00 0.00 2.75
842 1537 7.414540 GGTCTCAAGTTATCAACACAATGGATC 60.415 40.741 0.00 0.00 0.00 3.36
853 1548 6.720309 TGATCCAATGGTCTCAAGTTATCAA 58.280 36.000 0.00 0.00 0.00 2.57
854 1549 6.312141 TGATCCAATGGTCTCAAGTTATCA 57.688 37.500 0.00 0.00 0.00 2.15
855 1550 7.718753 AGAATGATCCAATGGTCTCAAGTTATC 59.281 37.037 10.35 0.00 0.00 1.75
856 1551 7.580910 AGAATGATCCAATGGTCTCAAGTTAT 58.419 34.615 10.35 0.00 0.00 1.89
857 1552 6.962182 AGAATGATCCAATGGTCTCAAGTTA 58.038 36.000 10.35 0.00 0.00 2.24
858 1553 5.824421 AGAATGATCCAATGGTCTCAAGTT 58.176 37.500 10.35 3.35 0.00 2.66
859 1554 5.447778 AGAATGATCCAATGGTCTCAAGT 57.552 39.130 10.35 3.67 0.00 3.16
860 1555 5.884232 TGAAGAATGATCCAATGGTCTCAAG 59.116 40.000 10.35 0.00 0.00 3.02
863 1558 5.178996 CGATGAAGAATGATCCAATGGTCTC 59.821 44.000 0.00 0.00 0.00 3.36
867 1562 5.278169 GGAACGATGAAGAATGATCCAATGG 60.278 44.000 0.00 0.00 0.00 3.16
880 1575 1.656095 GCAGAACGAGGAACGATGAAG 59.344 52.381 0.00 0.00 45.77 3.02
882 1577 0.888619 AGCAGAACGAGGAACGATGA 59.111 50.000 0.00 0.00 45.77 2.92
884 1579 2.093106 AGTAGCAGAACGAGGAACGAT 58.907 47.619 0.00 0.00 45.77 3.73
885 1580 1.531423 AGTAGCAGAACGAGGAACGA 58.469 50.000 0.00 0.00 45.77 3.85
886 1581 3.795272 GCAAGTAGCAGAACGAGGAACG 61.795 54.545 0.00 0.00 45.26 3.95
887 1582 1.727335 GCAAGTAGCAGAACGAGGAAC 59.273 52.381 0.00 0.00 44.79 3.62
938 1657 2.419297 CCACTACTTGCTCCACTCCATC 60.419 54.545 0.00 0.00 0.00 3.51
967 1686 1.647545 GCTACAATTCCGCAGCTGCA 61.648 55.000 36.03 19.38 42.21 4.41
976 1695 2.094417 GCAGAGAACACGCTACAATTCC 59.906 50.000 0.00 0.00 0.00 3.01
989 1708 1.093159 CTTGCCCATCTGCAGAGAAC 58.907 55.000 22.96 11.70 43.21 3.01
1100 1822 2.185608 GGAAGCTCCAGCGTCTCC 59.814 66.667 13.22 7.77 46.34 3.71
1203 1925 1.018226 CCTCCAAGAAGCAGTGCGAG 61.018 60.000 10.00 8.86 0.00 5.03
1217 1939 3.635191 TCACCGCATGCACCTCCA 61.635 61.111 19.57 0.00 0.00 3.86
1357 2079 2.657620 GTACGATCGGAAGGCGGC 60.658 66.667 20.98 0.00 34.50 6.53
1381 2103 1.497278 GTACGTACGGAGCGTCACA 59.503 57.895 21.06 0.00 42.85 3.58
1400 2122 3.305471 GCTTCCATCTCATAGGGACGTAC 60.305 52.174 0.00 0.00 37.92 3.67
1401 2123 2.891580 GCTTCCATCTCATAGGGACGTA 59.108 50.000 0.00 0.00 37.92 3.57
1402 2124 1.689273 GCTTCCATCTCATAGGGACGT 59.311 52.381 0.00 0.00 37.92 4.34
1403 2125 1.967066 AGCTTCCATCTCATAGGGACG 59.033 52.381 0.00 0.00 37.92 4.79
1414 2136 2.860735 CAAGCACGTAGTAGCTTCCATC 59.139 50.000 7.80 0.00 46.11 3.51
1416 2138 1.616865 ACAAGCACGTAGTAGCTTCCA 59.383 47.619 7.80 0.00 46.11 3.53
1417 2139 1.993370 CACAAGCACGTAGTAGCTTCC 59.007 52.381 7.80 0.00 46.11 3.46
1422 2144 0.716108 GCAGCACAAGCACGTAGTAG 59.284 55.000 0.00 0.00 41.61 2.57
1423 2145 0.032815 TGCAGCACAAGCACGTAGTA 59.967 50.000 0.00 0.00 41.61 1.82
1438 2160 2.693762 CCCATCAACCACGCTGCAG 61.694 63.158 10.11 10.11 0.00 4.41
1441 2163 2.751436 CCCCCATCAACCACGCTG 60.751 66.667 0.00 0.00 0.00 5.18
1458 2180 1.139520 GCGCATGGATTTCACCACC 59.860 57.895 0.30 0.00 43.03 4.61
1505 2227 2.046023 TGCAGCTTCACCATCCCG 60.046 61.111 0.00 0.00 0.00 5.14
1731 2456 0.176680 CTGTCCATCTCCCCGTTCTG 59.823 60.000 0.00 0.00 0.00 3.02
1888 2619 3.745803 GCTCCTCGTCGAACCGGT 61.746 66.667 0.00 0.00 0.00 5.28
2165 2899 3.077556 GAGCTCCTTGGCGAGGGA 61.078 66.667 20.82 6.83 46.31 4.20
2310 3044 0.179100 CGGTGCGGAGAGTCATCATT 60.179 55.000 0.00 0.00 0.00 2.57
2311 3045 1.037579 TCGGTGCGGAGAGTCATCAT 61.038 55.000 0.00 0.00 0.00 2.45
2312 3046 1.677633 TCGGTGCGGAGAGTCATCA 60.678 57.895 0.00 0.00 0.00 3.07
2313 3047 1.226717 GTCGGTGCGGAGAGTCATC 60.227 63.158 0.00 0.00 0.00 2.92
2314 3048 2.885861 GTCGGTGCGGAGAGTCAT 59.114 61.111 0.00 0.00 0.00 3.06
2356 3097 4.685628 CGGCAGAAACATGCTTTTTATTGT 59.314 37.500 0.00 0.00 45.75 2.71
2367 3108 5.163723 ACAGATAATTCACGGCAGAAACATG 60.164 40.000 0.00 0.00 0.00 3.21
2368 3109 4.943705 ACAGATAATTCACGGCAGAAACAT 59.056 37.500 0.00 0.00 0.00 2.71
2407 3148 3.562973 TCGTGATAGAATAGACCGTCCAC 59.437 47.826 0.00 0.00 0.00 4.02
2425 3166 1.126846 GTCCGCTTTGAAGATGTCGTG 59.873 52.381 0.00 0.00 0.00 4.35
2427 3168 0.721718 GGTCCGCTTTGAAGATGTCG 59.278 55.000 0.00 0.00 0.00 4.35
2429 3174 0.693049 AGGGTCCGCTTTGAAGATGT 59.307 50.000 0.00 0.00 0.00 3.06
2433 3178 1.604604 TTTGAGGGTCCGCTTTGAAG 58.395 50.000 0.00 0.00 0.00 3.02
2453 3198 6.964908 TGTGCAATTTAAATCTTGAAGACGA 58.035 32.000 0.00 0.00 0.00 4.20
2456 3201 7.591057 CGAACTGTGCAATTTAAATCTTGAAGA 59.409 33.333 0.10 0.00 0.00 2.87
2459 3204 6.016693 TCCGAACTGTGCAATTTAAATCTTGA 60.017 34.615 0.10 0.00 0.00 3.02
2494 3239 5.147330 AGGTACAGAATCACGTTTGATCA 57.853 39.130 0.00 0.00 42.00 2.92
2516 3320 2.916052 GCATCCCGACCGCTCGATA 61.916 63.158 0.71 0.00 43.06 2.92
2517 3321 4.286320 GCATCCCGACCGCTCGAT 62.286 66.667 0.71 0.00 43.06 3.59
2524 3332 0.804989 CAAAAGAGTGCATCCCGACC 59.195 55.000 0.00 0.00 0.00 4.79
2538 3346 1.112459 GTCTCGTGTTTGCGCAAAAG 58.888 50.000 35.09 27.24 31.33 2.27
2552 3360 1.453155 CAAATCCCCAGGTTGTCTCG 58.547 55.000 0.00 0.00 0.00 4.04
2555 3363 0.890683 CTGCAAATCCCCAGGTTGTC 59.109 55.000 0.00 0.00 0.00 3.18
2582 3390 3.498397 CGGAGTTCTACATGTTTGCTGTT 59.502 43.478 2.30 0.00 0.00 3.16
2589 3397 3.770666 CGATGTCGGAGTTCTACATGTT 58.229 45.455 2.30 0.00 34.09 2.71
2593 3401 0.454600 GGCGATGTCGGAGTTCTACA 59.545 55.000 4.44 0.00 40.23 2.74
2640 3448 2.262423 AATAGAAGGATGAAGGCGCC 57.738 50.000 21.89 21.89 0.00 6.53
2805 3613 6.642540 GGAACAAGCTTTCTTTGGTAAATCTG 59.357 38.462 0.00 0.00 0.00 2.90
2822 3630 4.393680 TGAACATAATACCACGGAACAAGC 59.606 41.667 0.00 0.00 0.00 4.01
2825 3633 5.306394 TGTTGAACATAATACCACGGAACA 58.694 37.500 0.00 0.00 0.00 3.18
2896 3730 9.649024 CAATTTATTCAACAAACCATGTCAAAC 57.351 29.630 0.00 0.00 42.99 2.93
2900 3734 6.128309 GGCCAATTTATTCAACAAACCATGTC 60.128 38.462 0.00 0.00 42.99 3.06
2922 3756 5.689514 GCAAAATTTGTTTTAAACCATGGCC 59.310 36.000 13.04 0.00 0.00 5.36
2931 3765 7.604164 TCTTGGACTGTGCAAAATTTGTTTTAA 59.396 29.630 15.56 0.00 0.00 1.52
2948 3782 5.646360 ACCACGGTAAATTATTCTTGGACTG 59.354 40.000 8.13 0.00 0.00 3.51
2949 3783 5.812286 ACCACGGTAAATTATTCTTGGACT 58.188 37.500 8.13 0.00 0.00 3.85
2956 3790 9.843334 TTTGAACATAACCACGGTAAATTATTC 57.157 29.630 0.00 0.00 0.00 1.75
3241 7978 7.175467 TGACAATTCTAGACATGACAAATTGCT 59.825 33.333 19.82 12.71 37.53 3.91
3243 7980 8.291740 TGTGACAATTCTAGACATGACAAATTG 58.708 33.333 19.02 19.02 39.07 2.32
3244 7981 8.394971 TGTGACAATTCTAGACATGACAAATT 57.605 30.769 0.00 0.00 0.00 1.82


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

AutoCloner maintained by Alex Coulton.