Multiple sequence alignment - TraesCS5A01G486500

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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 TraesCS5A01G486500 chr5A 100.000 3228 0 0 1 3228 657246878 657243651 0.000000e+00 5962.0
1 TraesCS5A01G486500 chr5A 88.095 588 37 12 115 682 33103285 33103859 0.000000e+00 667.0
2 TraesCS5A01G486500 chr2B 96.008 977 32 2 2259 3228 187163564 187164540 0.000000e+00 1581.0
3 TraesCS5A01G486500 chr2B 95.599 977 36 2 2259 3228 231623766 231624742 0.000000e+00 1559.0
4 TraesCS5A01G486500 chr7B 96.004 976 31 3 2259 3227 336652622 336651648 0.000000e+00 1580.0
5 TraesCS5A01G486500 chr7B 91.392 941 67 5 2295 3228 720035248 720036181 0.000000e+00 1277.0
6 TraesCS5A01G486500 chr7B 83.698 503 67 10 731 1225 28307821 28308316 8.160000e-126 460.0
7 TraesCS5A01G486500 chr7B 80.208 96 11 6 1510 1601 532654090 532654181 7.480000e-07 65.8
8 TraesCS5A01G486500 chr1A 96.839 949 21 2 2259 3200 394595922 394596868 0.000000e+00 1578.0
9 TraesCS5A01G486500 chr1A 88.065 553 32 11 115 646 580934707 580934168 2.730000e-175 625.0
10 TraesCS5A01G486500 chr7A 95.906 977 33 2 2259 3228 5424578 5425554 0.000000e+00 1576.0
11 TraesCS5A01G486500 chr7A 95.292 977 39 3 2259 3228 118149217 118150193 0.000000e+00 1543.0
12 TraesCS5A01G486500 chr7A 91.923 941 69 2 2295 3228 15114339 15115279 0.000000e+00 1310.0
13 TraesCS5A01G486500 chr7A 91.817 941 69 3 2295 3228 731582141 731581202 0.000000e+00 1304.0
14 TraesCS5A01G486500 chr7A 77.679 112 17 6 1510 1617 572322992 572323099 9.670000e-06 62.1
15 TraesCS5A01G486500 chr4A 95.496 977 37 2 2259 3228 610280526 610279550 0.000000e+00 1554.0
16 TraesCS5A01G486500 chr3A 94.882 977 43 2 2259 3228 165326496 165325520 0.000000e+00 1520.0
17 TraesCS5A01G486500 chr3A 91.711 941 71 2 2295 3228 42686764 42685824 0.000000e+00 1299.0
18 TraesCS5A01G486500 chr3A 87.267 589 38 11 115 679 686546413 686546988 3.510000e-179 638.0
19 TraesCS5A01G486500 chr2A 94.780 977 44 2 2259 3228 499770325 499769349 0.000000e+00 1515.0
20 TraesCS5A01G486500 chr6A 92.242 941 64 4 2295 3228 604566940 604567878 0.000000e+00 1325.0
21 TraesCS5A01G486500 chr6A 91.923 941 69 2 2295 3228 450101035 450101975 0.000000e+00 1310.0
22 TraesCS5A01G486500 chr6A 91.605 941 72 2 2295 3228 6707960 6707020 0.000000e+00 1293.0
23 TraesCS5A01G486500 chrUn 91.605 941 72 2 2295 3228 345608900 345609840 0.000000e+00 1293.0
24 TraesCS5A01G486500 chrUn 91.073 941 71 4 2295 3228 185799268 185800202 0.000000e+00 1260.0
25 TraesCS5A01G486500 chr5D 91.480 939 60 9 1312 2237 529155995 529155064 0.000000e+00 1273.0
26 TraesCS5A01G486500 chr5D 91.211 933 70 8 1312 2237 529087052 529086125 0.000000e+00 1258.0
27 TraesCS5A01G486500 chr5D 91.200 875 70 5 1367 2237 529084028 529083157 0.000000e+00 1182.0
28 TraesCS5A01G486500 chr5D 87.552 723 66 11 1367 2085 529125312 529124610 0.000000e+00 815.0
29 TraesCS5A01G486500 chr5D 89.537 497 46 1 1741 2237 529062428 529061938 2.730000e-175 625.0
30 TraesCS5A01G486500 chr5D 78.825 647 112 15 1409 2034 528985710 528985068 2.320000e-111 412.0
31 TraesCS5A01G486500 chr5D 97.561 41 1 0 2197 2237 529115847 529115807 1.610000e-08 71.3
32 TraesCS5A01G486500 chr2D 93.191 514 19 9 723 1227 36661418 36661924 0.000000e+00 741.0
33 TraesCS5A01G486500 chr1B 84.129 649 68 21 1 633 3045253 3045882 2.140000e-166 595.0
34 TraesCS5A01G486500 chr5B 79.343 639 115 11 1409 2034 666372095 666371461 1.780000e-117 433.0
35 TraesCS5A01G486500 chr6B 82.470 502 68 12 726 1219 431804311 431804800 3.850000e-114 422.0
36 TraesCS5A01G486500 chr7D 94.737 38 2 0 1510 1547 504766343 504766380 3.480000e-05 60.2


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 TraesCS5A01G486500 chr5A 657243651 657246878 3227 True 5962 5962 100.0000 1 3228 1 chr5A.!!$R1 3227
1 TraesCS5A01G486500 chr5A 33103285 33103859 574 False 667 667 88.0950 115 682 1 chr5A.!!$F1 567
2 TraesCS5A01G486500 chr2B 187163564 187164540 976 False 1581 1581 96.0080 2259 3228 1 chr2B.!!$F1 969
3 TraesCS5A01G486500 chr2B 231623766 231624742 976 False 1559 1559 95.5990 2259 3228 1 chr2B.!!$F2 969
4 TraesCS5A01G486500 chr7B 336651648 336652622 974 True 1580 1580 96.0040 2259 3227 1 chr7B.!!$R1 968
5 TraesCS5A01G486500 chr7B 720035248 720036181 933 False 1277 1277 91.3920 2295 3228 1 chr7B.!!$F3 933
6 TraesCS5A01G486500 chr1A 394595922 394596868 946 False 1578 1578 96.8390 2259 3200 1 chr1A.!!$F1 941
7 TraesCS5A01G486500 chr1A 580934168 580934707 539 True 625 625 88.0650 115 646 1 chr1A.!!$R1 531
8 TraesCS5A01G486500 chr7A 5424578 5425554 976 False 1576 1576 95.9060 2259 3228 1 chr7A.!!$F1 969
9 TraesCS5A01G486500 chr7A 118149217 118150193 976 False 1543 1543 95.2920 2259 3228 1 chr7A.!!$F3 969
10 TraesCS5A01G486500 chr7A 15114339 15115279 940 False 1310 1310 91.9230 2295 3228 1 chr7A.!!$F2 933
11 TraesCS5A01G486500 chr7A 731581202 731582141 939 True 1304 1304 91.8170 2295 3228 1 chr7A.!!$R1 933
12 TraesCS5A01G486500 chr4A 610279550 610280526 976 True 1554 1554 95.4960 2259 3228 1 chr4A.!!$R1 969
13 TraesCS5A01G486500 chr3A 165325520 165326496 976 True 1520 1520 94.8820 2259 3228 1 chr3A.!!$R2 969
14 TraesCS5A01G486500 chr3A 42685824 42686764 940 True 1299 1299 91.7110 2295 3228 1 chr3A.!!$R1 933
15 TraesCS5A01G486500 chr3A 686546413 686546988 575 False 638 638 87.2670 115 679 1 chr3A.!!$F1 564
16 TraesCS5A01G486500 chr2A 499769349 499770325 976 True 1515 1515 94.7800 2259 3228 1 chr2A.!!$R1 969
17 TraesCS5A01G486500 chr6A 604566940 604567878 938 False 1325 1325 92.2420 2295 3228 1 chr6A.!!$F2 933
18 TraesCS5A01G486500 chr6A 450101035 450101975 940 False 1310 1310 91.9230 2295 3228 1 chr6A.!!$F1 933
19 TraesCS5A01G486500 chr6A 6707020 6707960 940 True 1293 1293 91.6050 2295 3228 1 chr6A.!!$R1 933
20 TraesCS5A01G486500 chrUn 345608900 345609840 940 False 1293 1293 91.6050 2295 3228 1 chrUn.!!$F2 933
21 TraesCS5A01G486500 chrUn 185799268 185800202 934 False 1260 1260 91.0730 2295 3228 1 chrUn.!!$F1 933
22 TraesCS5A01G486500 chr5D 529155064 529155995 931 True 1273 1273 91.4800 1312 2237 1 chr5D.!!$R5 925
23 TraesCS5A01G486500 chr5D 529083157 529087052 3895 True 1220 1258 91.2055 1312 2237 2 chr5D.!!$R6 925
24 TraesCS5A01G486500 chr5D 529124610 529125312 702 True 815 815 87.5520 1367 2085 1 chr5D.!!$R4 718
25 TraesCS5A01G486500 chr5D 528985068 528985710 642 True 412 412 78.8250 1409 2034 1 chr5D.!!$R1 625
26 TraesCS5A01G486500 chr2D 36661418 36661924 506 False 741 741 93.1910 723 1227 1 chr2D.!!$F1 504
27 TraesCS5A01G486500 chr1B 3045253 3045882 629 False 595 595 84.1290 1 633 1 chr1B.!!$F1 632
28 TraesCS5A01G486500 chr5B 666371461 666372095 634 True 433 433 79.3430 1409 2034 1 chr5B.!!$R1 625

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
547 579 0.107456 AAATGGAGCGATGGAGCGAT 59.893 50.0 0.0 0.0 43.0 4.58 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2253 5323 0.179108 ACGAACTGCGGAATCCTAGC 60.179 55.0 0.0 0.0 46.49 3.42 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
33 34 8.594881 TTTTGTAAACTTGCAGTTTTCTTCAA 57.405 26.923 16.02 13.44 45.38 2.69
46 47 9.853921 GCAGTTTTCTTCAAATTTGTGATTTAG 57.146 29.630 17.47 7.26 0.00 1.85
63 64 9.730705 TGTGATTTAGAAATTCATGAACTCTCT 57.269 29.630 20.04 17.93 0.00 3.10
85 87 9.528018 TCTCTTCAAATTAAAACACCATTTCAC 57.472 29.630 0.00 0.00 0.00 3.18
146 148 9.645059 TTAATTTCATGAACATTTTTATCCGCA 57.355 25.926 7.89 0.00 0.00 5.69
328 336 5.786264 TTTAAATAAAACAGGCGGTGGAA 57.214 34.783 0.00 0.00 0.00 3.53
337 345 1.681264 CAGGCGGTGGAAAGAAAAACT 59.319 47.619 0.00 0.00 0.00 2.66
542 574 1.453745 GCCCAAATGGAGCGATGGA 60.454 57.895 0.00 0.00 37.39 3.41
543 575 1.450531 GCCCAAATGGAGCGATGGAG 61.451 60.000 0.00 0.00 37.39 3.86
544 576 1.450531 CCCAAATGGAGCGATGGAGC 61.451 60.000 0.00 0.00 37.39 4.70
546 578 0.811219 CAAATGGAGCGATGGAGCGA 60.811 55.000 0.00 0.00 43.00 4.93
547 579 0.107456 AAATGGAGCGATGGAGCGAT 59.893 50.000 0.00 0.00 43.00 4.58
548 580 0.602106 AATGGAGCGATGGAGCGATG 60.602 55.000 0.00 0.00 43.00 3.84
565 597 2.049063 GACCTGCTTGAGCGACGT 60.049 61.111 0.00 0.00 45.83 4.34
599 634 1.638529 CCTCTGGAGTCTGGTCAACT 58.361 55.000 0.00 0.00 0.00 3.16
694 750 9.856488 TGTCACATCTAAATTAGACTTAGACAC 57.144 33.333 17.53 6.74 38.02 3.67
695 751 9.856488 GTCACATCTAAATTAGACTTAGACACA 57.144 33.333 4.66 0.00 38.02 3.72
696 752 9.856488 TCACATCTAAATTAGACTTAGACACAC 57.144 33.333 4.66 0.00 38.02 3.82
697 753 9.862371 CACATCTAAATTAGACTTAGACACACT 57.138 33.333 4.66 0.00 38.02 3.55
704 760 8.467402 AATTAGACTTAGACACACTCATTTCG 57.533 34.615 0.00 0.00 0.00 3.46
705 761 4.810790 AGACTTAGACACACTCATTTCGG 58.189 43.478 0.00 0.00 0.00 4.30
706 762 4.523173 AGACTTAGACACACTCATTTCGGA 59.477 41.667 0.00 0.00 0.00 4.55
707 763 5.010719 AGACTTAGACACACTCATTTCGGAA 59.989 40.000 0.00 0.00 0.00 4.30
708 764 5.607477 ACTTAGACACACTCATTTCGGAAA 58.393 37.500 5.52 5.52 0.00 3.13
709 765 5.696724 ACTTAGACACACTCATTTCGGAAAG 59.303 40.000 9.30 0.00 0.00 2.62
710 766 2.808543 AGACACACTCATTTCGGAAAGC 59.191 45.455 9.30 0.00 0.00 3.51
711 767 2.548057 GACACACTCATTTCGGAAAGCA 59.452 45.455 9.30 0.00 0.00 3.91
712 768 2.549754 ACACACTCATTTCGGAAAGCAG 59.450 45.455 9.30 9.12 0.00 4.24
713 769 2.807967 CACACTCATTTCGGAAAGCAGA 59.192 45.455 14.97 9.49 0.00 4.26
714 770 2.808543 ACACTCATTTCGGAAAGCAGAC 59.191 45.455 14.97 0.00 0.00 3.51
715 771 2.160417 CACTCATTTCGGAAAGCAGACC 59.840 50.000 14.97 0.00 0.00 3.85
721 777 2.269241 GGAAAGCAGACCGAGGGG 59.731 66.667 0.00 0.00 40.11 4.79
722 778 2.291043 GGAAAGCAGACCGAGGGGA 61.291 63.158 0.00 0.00 36.97 4.81
723 779 1.627297 GGAAAGCAGACCGAGGGGAT 61.627 60.000 0.00 0.00 36.97 3.85
724 780 1.120530 GAAAGCAGACCGAGGGGATA 58.879 55.000 0.00 0.00 36.97 2.59
725 781 1.485066 GAAAGCAGACCGAGGGGATAA 59.515 52.381 0.00 0.00 36.97 1.75
726 782 1.807814 AAGCAGACCGAGGGGATAAT 58.192 50.000 0.00 0.00 36.97 1.28
727 783 1.807814 AGCAGACCGAGGGGATAATT 58.192 50.000 0.00 0.00 36.97 1.40
728 784 1.694696 AGCAGACCGAGGGGATAATTC 59.305 52.381 0.00 0.00 36.97 2.17
772 828 3.740832 CGGGAAATTTGAAGGAAAAGTGC 59.259 43.478 0.00 0.00 0.00 4.40
842 898 6.231211 ACGAAGGAATATTGAACAGTGTTCT 58.769 36.000 30.69 17.70 0.00 3.01
863 919 3.758172 GGAAAAGTTCCCGCAGCA 58.242 55.556 0.00 0.00 44.30 4.41
1025 1081 6.144402 AGACAAAAGTAAATCATTGCTTTGCG 59.856 34.615 5.60 3.86 46.51 4.85
1110 1174 1.404315 CCTTCGTACTGTTCCCTCTGC 60.404 57.143 0.00 0.00 0.00 4.26
1126 1190 3.375299 CCTCTGCCGTTTCCTCTATTTTG 59.625 47.826 0.00 0.00 0.00 2.44
1127 1191 4.003648 CTCTGCCGTTTCCTCTATTTTGT 58.996 43.478 0.00 0.00 0.00 2.83
1128 1192 5.155278 TCTGCCGTTTCCTCTATTTTGTA 57.845 39.130 0.00 0.00 0.00 2.41
1129 1193 5.553123 TCTGCCGTTTCCTCTATTTTGTAA 58.447 37.500 0.00 0.00 0.00 2.41
1163 1227 7.023171 AGTATGTTTTACACCCACATTCCTA 57.977 36.000 0.00 0.00 33.19 2.94
1165 1229 7.773690 AGTATGTTTTACACCCACATTCCTATC 59.226 37.037 0.00 0.00 33.19 2.08
1179 1243 7.392673 CCACATTCCTATCCCATTTCTCTATTG 59.607 40.741 0.00 0.00 0.00 1.90
1191 1255 5.965033 TTTCTCTATTGCTCTCCATTCCT 57.035 39.130 0.00 0.00 0.00 3.36
1227 1291 0.323629 TGAACCGAACAGGGCCTAAG 59.676 55.000 5.28 0.00 46.96 2.18
1228 1292 0.611714 GAACCGAACAGGGCCTAAGA 59.388 55.000 5.28 0.00 46.96 2.10
1229 1293 1.209747 GAACCGAACAGGGCCTAAGAT 59.790 52.381 5.28 0.00 46.96 2.40
1230 1294 0.831307 ACCGAACAGGGCCTAAGATC 59.169 55.000 5.28 0.00 46.96 2.75
1231 1295 0.106894 CCGAACAGGGCCTAAGATCC 59.893 60.000 5.28 0.00 35.97 3.36
1232 1296 0.249489 CGAACAGGGCCTAAGATCCG 60.249 60.000 5.28 0.33 0.00 4.18
1233 1297 0.106894 GAACAGGGCCTAAGATCCGG 59.893 60.000 5.28 0.00 0.00 5.14
1234 1298 1.345715 AACAGGGCCTAAGATCCGGG 61.346 60.000 5.28 0.00 0.00 5.73
1235 1299 2.849646 AGGGCCTAAGATCCGGGC 60.850 66.667 2.82 11.36 44.59 6.13
1238 1302 3.168528 GCCTAAGATCCGGGCCCA 61.169 66.667 24.92 2.47 39.96 5.36
1239 1303 2.752807 GCCTAAGATCCGGGCCCAA 61.753 63.158 24.92 9.92 39.96 4.12
1240 1304 1.148498 CCTAAGATCCGGGCCCAAC 59.852 63.158 24.92 9.53 0.00 3.77
1241 1305 1.345715 CCTAAGATCCGGGCCCAACT 61.346 60.000 24.92 11.86 0.00 3.16
1242 1306 0.106894 CTAAGATCCGGGCCCAACTC 59.893 60.000 24.92 14.43 0.00 3.01
1243 1307 1.682451 TAAGATCCGGGCCCAACTCG 61.682 60.000 24.92 7.03 0.00 4.18
1244 1308 4.547367 GATCCGGGCCCAACTCGG 62.547 72.222 24.92 17.19 44.59 4.63
1248 1312 4.016706 CGGGCCCAACTCGGTCTT 62.017 66.667 24.92 0.00 0.00 3.01
1249 1313 2.046217 GGGCCCAACTCGGTCTTC 60.046 66.667 19.95 0.00 0.00 2.87
1250 1314 2.593956 GGGCCCAACTCGGTCTTCT 61.594 63.158 19.95 0.00 0.00 2.85
1251 1315 1.376037 GGCCCAACTCGGTCTTCTG 60.376 63.158 0.00 0.00 0.00 3.02
1252 1316 1.671742 GCCCAACTCGGTCTTCTGA 59.328 57.895 0.00 0.00 0.00 3.27
1253 1317 0.034896 GCCCAACTCGGTCTTCTGAA 59.965 55.000 0.00 0.00 0.00 3.02
1254 1318 1.339151 GCCCAACTCGGTCTTCTGAAT 60.339 52.381 0.00 0.00 0.00 2.57
1255 1319 2.350522 CCCAACTCGGTCTTCTGAATG 58.649 52.381 0.00 0.00 0.00 2.67
1256 1320 2.028112 CCCAACTCGGTCTTCTGAATGA 60.028 50.000 0.00 0.00 0.00 2.57
1257 1321 3.257393 CCAACTCGGTCTTCTGAATGAG 58.743 50.000 0.00 0.00 34.09 2.90
1258 1322 3.257393 CAACTCGGTCTTCTGAATGAGG 58.743 50.000 11.29 0.00 32.94 3.86
1259 1323 1.205893 ACTCGGTCTTCTGAATGAGGC 59.794 52.381 11.29 0.00 32.94 4.70
1260 1324 0.173481 TCGGTCTTCTGAATGAGGCG 59.827 55.000 0.00 0.00 0.00 5.52
1261 1325 0.108615 CGGTCTTCTGAATGAGGCGT 60.109 55.000 0.00 0.00 0.00 5.68
1262 1326 1.673033 CGGTCTTCTGAATGAGGCGTT 60.673 52.381 0.00 0.00 0.00 4.84
1263 1327 2.416836 CGGTCTTCTGAATGAGGCGTTA 60.417 50.000 0.00 0.00 0.00 3.18
1264 1328 3.596214 GGTCTTCTGAATGAGGCGTTAA 58.404 45.455 0.00 0.00 0.00 2.01
1265 1329 4.192317 GGTCTTCTGAATGAGGCGTTAAT 58.808 43.478 0.00 0.00 0.00 1.40
1266 1330 4.034510 GGTCTTCTGAATGAGGCGTTAATG 59.965 45.833 0.00 0.00 0.00 1.90
1267 1331 4.034510 GTCTTCTGAATGAGGCGTTAATGG 59.965 45.833 0.00 0.00 0.00 3.16
1268 1332 2.917933 TCTGAATGAGGCGTTAATGGG 58.082 47.619 0.00 0.00 0.00 4.00
1269 1333 1.334869 CTGAATGAGGCGTTAATGGGC 59.665 52.381 0.00 0.00 0.00 5.36
1270 1334 1.064758 TGAATGAGGCGTTAATGGGCT 60.065 47.619 5.43 5.43 43.73 5.19
1271 1335 1.334869 GAATGAGGCGTTAATGGGCTG 59.665 52.381 9.76 0.00 40.78 4.85
1272 1336 0.466189 ATGAGGCGTTAATGGGCTGG 60.466 55.000 9.76 0.00 40.78 4.85
1273 1337 2.440247 AGGCGTTAATGGGCTGGC 60.440 61.111 5.01 0.00 39.05 4.85
1274 1338 3.527427 GGCGTTAATGGGCTGGCC 61.527 66.667 14.23 14.23 0.00 5.36
1275 1339 2.440247 GCGTTAATGGGCTGGCCT 60.440 61.111 21.72 4.42 36.10 5.19
1276 1340 1.153046 GCGTTAATGGGCTGGCCTA 60.153 57.895 21.72 7.88 36.10 3.93
1277 1341 1.166531 GCGTTAATGGGCTGGCCTAG 61.167 60.000 21.72 0.34 36.10 3.02
1278 1342 0.180406 CGTTAATGGGCTGGCCTAGT 59.820 55.000 21.72 9.25 36.10 2.57
1279 1343 1.408266 CGTTAATGGGCTGGCCTAGTT 60.408 52.381 21.72 14.86 36.10 2.24
1280 1344 2.158871 CGTTAATGGGCTGGCCTAGTTA 60.159 50.000 21.72 13.94 36.10 2.24
1281 1345 3.477530 GTTAATGGGCTGGCCTAGTTAG 58.522 50.000 21.72 0.00 36.10 2.34
1282 1346 1.893315 AATGGGCTGGCCTAGTTAGA 58.107 50.000 21.72 0.00 36.10 2.10
1283 1347 1.428869 ATGGGCTGGCCTAGTTAGAG 58.571 55.000 21.72 0.00 36.10 2.43
1284 1348 0.691078 TGGGCTGGCCTAGTTAGAGG 60.691 60.000 21.72 0.00 39.88 3.69
1285 1349 1.411651 GGGCTGGCCTAGTTAGAGGG 61.412 65.000 13.80 0.00 37.06 4.30
1286 1350 1.411651 GGCTGGCCTAGTTAGAGGGG 61.412 65.000 3.32 0.00 37.06 4.79
1287 1351 0.691413 GCTGGCCTAGTTAGAGGGGT 60.691 60.000 3.32 0.00 37.06 4.95
1288 1352 1.123928 CTGGCCTAGTTAGAGGGGTG 58.876 60.000 3.32 0.00 37.06 4.61
1289 1353 0.326238 TGGCCTAGTTAGAGGGGTGG 60.326 60.000 3.32 0.00 37.06 4.61
1290 1354 1.697082 GGCCTAGTTAGAGGGGTGGC 61.697 65.000 0.00 0.00 37.06 5.01
1291 1355 1.697082 GCCTAGTTAGAGGGGTGGCC 61.697 65.000 0.00 0.00 37.06 5.36
1292 1356 1.054978 CCTAGTTAGAGGGGTGGCCC 61.055 65.000 0.00 0.00 44.51 5.80
1293 1357 1.382146 TAGTTAGAGGGGTGGCCCG 60.382 63.158 0.00 0.00 46.66 6.13
1294 1358 4.484872 GTTAGAGGGGTGGCCCGC 62.485 72.222 0.00 0.00 46.66 6.13
1309 1373 2.047655 CGCCGCACTGAACCCTTA 60.048 61.111 0.00 0.00 0.00 2.69
1310 1374 1.449601 CGCCGCACTGAACCCTTAT 60.450 57.895 0.00 0.00 0.00 1.73
1324 1392 1.068194 CCCTTATCAGTCGCCGATCTC 60.068 57.143 0.00 0.00 0.00 2.75
1335 1403 1.138883 CCGATCTCGTTGCCTCGAA 59.861 57.895 0.00 0.00 39.34 3.71
1340 1408 3.180584 CGATCTCGTTGCCTCGAAAATAG 59.819 47.826 2.33 0.00 39.34 1.73
1343 1411 4.755411 TCTCGTTGCCTCGAAAATAGAAT 58.245 39.130 2.33 0.00 39.34 2.40
1344 1412 4.804139 TCTCGTTGCCTCGAAAATAGAATC 59.196 41.667 2.33 0.00 39.34 2.52
1345 1413 3.550275 TCGTTGCCTCGAAAATAGAATCG 59.450 43.478 0.00 0.00 40.31 3.34
1346 1414 3.550275 CGTTGCCTCGAAAATAGAATCGA 59.450 43.478 0.00 0.00 45.01 3.59
1349 1417 5.464965 TGCCTCGAAAATAGAATCGAAAC 57.535 39.130 0.00 0.00 46.26 2.78
1371 1441 3.888930 CCCAACTCCAAACTGTACACATT 59.111 43.478 0.00 0.00 0.00 2.71
1387 1457 1.932338 ACATTGGTGAGGATGGGGATT 59.068 47.619 0.00 0.00 0.00 3.01
1398 1468 4.643387 GGGGATTATGGCGCCGCT 62.643 66.667 23.90 14.61 0.00 5.52
1401 1471 2.591715 GATTATGGCGCCGCTGGT 60.592 61.111 23.90 6.39 0.00 4.00
1459 1529 1.964223 GTGCCCGGATCTCATCTTCTA 59.036 52.381 0.73 0.00 0.00 2.10
1489 1567 2.793585 CGGCTACTCGATCGCTAAACAA 60.794 50.000 11.09 0.00 0.00 2.83
1574 1652 2.920912 TCTTCCCCAACGGCGACT 60.921 61.111 16.62 0.00 0.00 4.18
1606 1684 1.914634 CCGACTTCATCTCCGTCTTG 58.085 55.000 0.00 0.00 0.00 3.02
1691 1769 1.330655 GGTCGAGAAGCAGGATCCCA 61.331 60.000 8.55 0.00 0.00 4.37
1692 1770 0.103937 GTCGAGAAGCAGGATCCCAG 59.896 60.000 8.55 2.31 0.00 4.45
1696 4748 0.992431 AGAAGCAGGATCCCAGGCAT 60.992 55.000 19.31 10.06 0.00 4.40
1699 4751 1.076485 GCAGGATCCCAGGCATGTT 60.076 57.895 8.55 0.00 0.00 2.71
1700 4752 0.685458 GCAGGATCCCAGGCATGTTT 60.685 55.000 8.55 0.00 0.00 2.83
1851 4903 1.511850 CTGAAGCACGTCATTGTCCA 58.488 50.000 0.00 0.00 0.00 4.02
1898 4950 2.694628 AGAAAATGTGAGGCTTGCAACA 59.305 40.909 0.00 0.00 0.00 3.33
1925 4977 4.271816 CGACGATGGGAGGGCGAG 62.272 72.222 0.00 0.00 0.00 5.03
1926 4978 3.148279 GACGATGGGAGGGCGAGT 61.148 66.667 0.00 0.00 0.00 4.18
2100 5156 6.775629 CCCTCTCTAGAGCTAGTTTAATGTCT 59.224 42.308 15.35 0.00 40.75 3.41
2113 5169 4.577687 TTAATGTCTAGCGCAAGTTTCG 57.422 40.909 11.47 0.00 41.68 3.46
2128 5184 4.160736 AGTTTCGTTTTTATGCTGCCTC 57.839 40.909 0.00 0.00 0.00 4.70
2143 5199 3.611057 GCTGCCTCTTGTGAACTTTGATG 60.611 47.826 0.00 0.00 0.00 3.07
2148 5209 4.823989 CCTCTTGTGAACTTTGATGGTTCT 59.176 41.667 7.85 0.00 42.27 3.01
2149 5210 5.049129 CCTCTTGTGAACTTTGATGGTTCTC 60.049 44.000 7.85 5.29 42.27 2.87
2189 5259 2.494888 TCCTATGAAGGGATCTGCCA 57.505 50.000 0.00 0.00 43.84 4.92
2190 5260 2.333069 TCCTATGAAGGGATCTGCCAG 58.667 52.381 0.00 0.00 43.84 4.85
2191 5261 2.090550 TCCTATGAAGGGATCTGCCAGA 60.091 50.000 0.00 0.00 43.84 3.86
2192 5262 2.707791 CCTATGAAGGGATCTGCCAGAA 59.292 50.000 0.00 0.00 39.48 3.02
2193 5263 2.725221 ATGAAGGGATCTGCCAGAAC 57.275 50.000 0.00 0.00 38.95 3.01
2194 5264 0.620556 TGAAGGGATCTGCCAGAACC 59.379 55.000 12.35 12.35 36.54 3.62
2237 5307 5.985530 CAGGTTTGGAAGAAAAGAACATTCC 59.014 40.000 0.00 0.00 41.34 3.01
2238 5308 4.982295 GGTTTGGAAGAAAAGAACATTCCG 59.018 41.667 0.00 0.00 43.43 4.30
2239 5309 3.915437 TGGAAGAAAAGAACATTCCGC 57.085 42.857 0.00 0.00 43.43 5.54
2240 5310 3.218453 TGGAAGAAAAGAACATTCCGCA 58.782 40.909 0.00 0.00 43.43 5.69
2241 5311 3.253188 TGGAAGAAAAGAACATTCCGCAG 59.747 43.478 0.00 0.00 43.43 5.18
2242 5312 3.253432 GGAAGAAAAGAACATTCCGCAGT 59.747 43.478 0.00 0.00 32.50 4.40
2243 5313 4.261614 GGAAGAAAAGAACATTCCGCAGTT 60.262 41.667 0.00 0.00 32.50 3.16
2244 5314 4.489679 AGAAAAGAACATTCCGCAGTTC 57.510 40.909 0.00 0.00 43.33 3.01
2245 5315 2.969443 AAAGAACATTCCGCAGTTCG 57.031 45.000 0.00 0.00 46.54 3.95
2246 5316 1.878953 AAGAACATTCCGCAGTTCGT 58.121 45.000 0.00 0.00 46.54 3.85
2247 5317 2.736144 AGAACATTCCGCAGTTCGTA 57.264 45.000 0.00 0.00 46.54 3.43
2248 5318 2.607187 AGAACATTCCGCAGTTCGTAG 58.393 47.619 0.00 0.00 46.54 3.51
2249 5319 1.659098 GAACATTCCGCAGTTCGTAGG 59.341 52.381 0.00 0.00 35.34 3.18
2250 5320 0.892755 ACATTCCGCAGTTCGTAGGA 59.107 50.000 0.00 0.00 36.19 2.94
2251 5321 1.135083 ACATTCCGCAGTTCGTAGGAG 60.135 52.381 0.00 0.00 36.19 3.69
2252 5322 1.135083 CATTCCGCAGTTCGTAGGAGT 60.135 52.381 0.00 0.00 36.19 3.85
2253 5323 0.242825 TTCCGCAGTTCGTAGGAGTG 59.757 55.000 0.00 0.00 36.19 3.51
2254 5324 1.805945 CCGCAGTTCGTAGGAGTGC 60.806 63.158 10.34 10.34 36.19 4.40
2255 5325 1.213013 CGCAGTTCGTAGGAGTGCT 59.787 57.895 15.66 0.00 33.82 4.40
2256 5326 0.450583 CGCAGTTCGTAGGAGTGCTA 59.549 55.000 15.66 0.00 33.82 3.49
2257 5327 1.532090 CGCAGTTCGTAGGAGTGCTAG 60.532 57.143 15.66 0.00 33.82 3.42
2284 5354 1.743958 GCAGTTCGTAGGAGTGCTAGA 59.256 52.381 12.27 0.00 33.43 2.43
2366 5437 4.141251 AGGTCTGAAGGACTTGGCTAAAAA 60.141 41.667 0.00 0.00 43.97 1.94
2530 5602 4.153411 AGGAAGATCGGGTGGTATCTTAG 58.847 47.826 0.00 0.00 41.40 2.18
2926 6005 1.372997 TTCTTGCGAGCGTGGAGTC 60.373 57.895 0.00 0.00 0.00 3.36
3066 6146 5.939883 TCTTTCGAGATGTCATGGTTCAAAT 59.060 36.000 0.00 0.00 0.00 2.32
3174 6254 9.692325 AGATTAGGCATTTGAGAAGTTTCTTAT 57.308 29.630 0.00 0.00 37.73 1.73
3182 6262 5.576563 TGAGAAGTTTCTTATGGGGTTGA 57.423 39.130 0.00 0.00 37.73 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
19 20 7.846644 AATCACAAATTTGAAGAAAACTGCA 57.153 28.000 24.64 0.00 0.00 4.41
60 61 9.311916 TGTGAAATGGTGTTTTAATTTGAAGAG 57.688 29.630 0.00 0.00 0.00 2.85
106 108 6.812656 TCATGAAATTAAAACTGCGCATGAAT 59.187 30.769 12.24 0.00 38.23 2.57
110 112 5.925397 TGTTCATGAAATTAAAACTGCGCAT 59.075 32.000 12.24 0.00 0.00 4.73
112 114 5.820926 TGTTCATGAAATTAAAACTGCGC 57.179 34.783 10.35 0.00 0.00 6.09
113 115 9.649024 AAAAATGTTCATGAAATTAAAACTGCG 57.351 25.926 10.35 0.00 0.00 5.18
152 158 7.979444 AAAAATCGAAGGTATTGAAGAGTCA 57.021 32.000 0.00 0.00 0.00 3.41
153 159 9.922305 CATAAAAATCGAAGGTATTGAAGAGTC 57.078 33.333 0.00 0.00 0.00 3.36
477 489 4.979815 TCAATGAGTGTGTACGTGTGTTAG 59.020 41.667 0.00 0.00 0.00 2.34
542 574 1.449246 GCTCAAGCAGGTCATCGCT 60.449 57.895 0.00 0.00 41.20 4.93
543 575 2.806856 CGCTCAAGCAGGTCATCGC 61.807 63.158 2.50 0.00 42.21 4.58
544 576 1.153765 TCGCTCAAGCAGGTCATCG 60.154 57.895 2.50 0.00 42.21 3.84
546 578 1.446792 CGTCGCTCAAGCAGGTCAT 60.447 57.895 2.50 0.00 42.21 3.06
547 579 2.049156 CGTCGCTCAAGCAGGTCA 60.049 61.111 2.50 0.00 42.21 4.02
548 580 1.664965 AACGTCGCTCAAGCAGGTC 60.665 57.895 2.50 0.00 42.21 3.85
682 738 5.708697 TCCGAAATGAGTGTGTCTAAGTCTA 59.291 40.000 0.00 0.00 0.00 2.59
683 739 4.523173 TCCGAAATGAGTGTGTCTAAGTCT 59.477 41.667 0.00 0.00 0.00 3.24
684 740 4.806330 TCCGAAATGAGTGTGTCTAAGTC 58.194 43.478 0.00 0.00 0.00 3.01
685 741 4.866508 TCCGAAATGAGTGTGTCTAAGT 57.133 40.909 0.00 0.00 0.00 2.24
686 742 5.389935 GCTTTCCGAAATGAGTGTGTCTAAG 60.390 44.000 0.00 0.00 0.00 2.18
687 743 4.451096 GCTTTCCGAAATGAGTGTGTCTAA 59.549 41.667 0.00 0.00 0.00 2.10
688 744 3.994392 GCTTTCCGAAATGAGTGTGTCTA 59.006 43.478 0.00 0.00 0.00 2.59
689 745 2.808543 GCTTTCCGAAATGAGTGTGTCT 59.191 45.455 0.00 0.00 0.00 3.41
690 746 2.548057 TGCTTTCCGAAATGAGTGTGTC 59.452 45.455 0.00 0.00 0.00 3.67
691 747 2.549754 CTGCTTTCCGAAATGAGTGTGT 59.450 45.455 0.00 0.00 0.00 3.72
692 748 2.807967 TCTGCTTTCCGAAATGAGTGTG 59.192 45.455 0.00 0.00 0.00 3.82
693 749 2.808543 GTCTGCTTTCCGAAATGAGTGT 59.191 45.455 0.00 0.00 0.00 3.55
694 750 2.160417 GGTCTGCTTTCCGAAATGAGTG 59.840 50.000 0.00 0.00 0.00 3.51
695 751 2.427506 GGTCTGCTTTCCGAAATGAGT 58.572 47.619 0.00 0.00 0.00 3.41
703 759 2.125512 CCCTCGGTCTGCTTTCCG 60.126 66.667 7.49 7.49 46.93 4.30
704 760 1.627297 ATCCCCTCGGTCTGCTTTCC 61.627 60.000 0.00 0.00 0.00 3.13
705 761 1.120530 TATCCCCTCGGTCTGCTTTC 58.879 55.000 0.00 0.00 0.00 2.62
706 762 1.580059 TTATCCCCTCGGTCTGCTTT 58.420 50.000 0.00 0.00 0.00 3.51
707 763 1.807814 ATTATCCCCTCGGTCTGCTT 58.192 50.000 0.00 0.00 0.00 3.91
708 764 1.694696 GAATTATCCCCTCGGTCTGCT 59.305 52.381 0.00 0.00 0.00 4.24
709 765 1.694696 AGAATTATCCCCTCGGTCTGC 59.305 52.381 0.00 0.00 0.00 4.26
710 766 3.235200 AGAGAATTATCCCCTCGGTCTG 58.765 50.000 0.00 0.00 32.52 3.51
711 767 3.621682 AGAGAATTATCCCCTCGGTCT 57.378 47.619 0.00 0.00 32.52 3.85
712 768 4.221041 CCTTAGAGAATTATCCCCTCGGTC 59.779 50.000 0.00 0.00 32.52 4.79
713 769 4.161102 CCTTAGAGAATTATCCCCTCGGT 58.839 47.826 0.00 0.00 32.52 4.69
714 770 3.055747 GCCTTAGAGAATTATCCCCTCGG 60.056 52.174 0.00 0.00 32.52 4.63
715 771 3.055747 GGCCTTAGAGAATTATCCCCTCG 60.056 52.174 0.00 0.00 32.52 4.63
716 772 3.264706 GGGCCTTAGAGAATTATCCCCTC 59.735 52.174 0.84 0.00 0.00 4.30
717 773 3.261083 GGGCCTTAGAGAATTATCCCCT 58.739 50.000 0.84 0.00 0.00 4.79
718 774 2.309162 GGGGCCTTAGAGAATTATCCCC 59.691 54.545 0.84 0.00 44.53 4.81
719 775 2.027100 CGGGGCCTTAGAGAATTATCCC 60.027 54.545 0.84 0.00 0.00 3.85
720 776 2.638363 ACGGGGCCTTAGAGAATTATCC 59.362 50.000 0.84 0.00 0.00 2.59
721 777 4.316645 GAACGGGGCCTTAGAGAATTATC 58.683 47.826 0.84 0.00 0.00 1.75
722 778 3.244112 CGAACGGGGCCTTAGAGAATTAT 60.244 47.826 0.84 0.00 0.00 1.28
723 779 2.101917 CGAACGGGGCCTTAGAGAATTA 59.898 50.000 0.84 0.00 0.00 1.40
724 780 1.134491 CGAACGGGGCCTTAGAGAATT 60.134 52.381 0.84 0.00 0.00 2.17
725 781 0.464452 CGAACGGGGCCTTAGAGAAT 59.536 55.000 0.84 0.00 0.00 2.40
726 782 1.610554 CCGAACGGGGCCTTAGAGAA 61.611 60.000 0.84 0.00 0.00 2.87
727 783 2.056223 CCGAACGGGGCCTTAGAGA 61.056 63.158 0.84 0.00 0.00 3.10
728 784 2.499685 CCGAACGGGGCCTTAGAG 59.500 66.667 0.84 0.00 0.00 2.43
748 804 4.982295 CACTTTTCCTTCAAATTTCCCGTC 59.018 41.667 0.00 0.00 0.00 4.79
751 807 4.702831 TGCACTTTTCCTTCAAATTTCCC 58.297 39.130 0.00 0.00 0.00 3.97
772 828 0.035630 CCAGAGGAACAGCTTCCCTG 60.036 60.000 12.54 12.54 46.79 4.45
820 876 6.655003 TCCAGAACACTGTTCAATATTCCTTC 59.345 38.462 21.39 0.00 0.00 3.46
975 1031 7.509546 TGTACCTCAAAGAACTCTTCTCATTT 58.490 34.615 0.00 0.00 39.61 2.32
1038 1094 4.354587 GAAAGCACCATCGATTCCAAATC 58.645 43.478 0.00 0.00 0.00 2.17
1039 1095 3.131046 GGAAAGCACCATCGATTCCAAAT 59.869 43.478 0.00 0.00 39.45 2.32
1040 1096 2.491693 GGAAAGCACCATCGATTCCAAA 59.508 45.455 0.00 0.00 39.45 3.28
1041 1097 2.091541 GGAAAGCACCATCGATTCCAA 58.908 47.619 0.00 0.00 39.45 3.53
1042 1098 1.281867 AGGAAAGCACCATCGATTCCA 59.718 47.619 12.83 0.00 41.58 3.53
1043 1099 1.672881 CAGGAAAGCACCATCGATTCC 59.327 52.381 0.00 0.00 39.85 3.01
1044 1100 2.359900 ACAGGAAAGCACCATCGATTC 58.640 47.619 0.00 0.00 0.00 2.52
1110 1174 9.983804 GAATTACTTACAAAATAGAGGAAACGG 57.016 33.333 0.00 0.00 0.00 4.44
1128 1192 9.676861 GGGTGTAAAACATACTAGGAATTACTT 57.323 33.333 0.00 0.00 0.00 2.24
1129 1193 8.828751 TGGGTGTAAAACATACTAGGAATTACT 58.171 33.333 0.00 0.00 0.00 2.24
1138 1202 7.023171 AGGAATGTGGGTGTAAAACATACTA 57.977 36.000 0.00 0.00 33.48 1.82
1139 1203 5.887754 AGGAATGTGGGTGTAAAACATACT 58.112 37.500 0.00 0.00 33.48 2.12
1140 1204 7.012989 GGATAGGAATGTGGGTGTAAAACATAC 59.987 40.741 0.00 0.00 33.48 2.39
1151 1215 3.793827 AGAAATGGGATAGGAATGTGGGT 59.206 43.478 0.00 0.00 0.00 4.51
1163 1227 4.662179 TGGAGAGCAATAGAGAAATGGGAT 59.338 41.667 0.00 0.00 0.00 3.85
1165 1229 4.428294 TGGAGAGCAATAGAGAAATGGG 57.572 45.455 0.00 0.00 0.00 4.00
1179 1243 8.686334 TGAATTTAAAACATAGGAATGGAGAGC 58.314 33.333 0.00 0.00 37.43 4.09
1191 1255 9.400638 GTTCGGTTCACATGAATTTAAAACATA 57.599 29.630 0.00 0.00 36.33 2.29
1227 1291 4.547367 CCGAGTTGGGCCCGGATC 62.547 72.222 19.37 13.52 45.58 3.36
1235 1299 2.028112 TCATTCAGAAGACCGAGTTGGG 60.028 50.000 0.24 0.00 44.64 4.12
1236 1300 3.257393 CTCATTCAGAAGACCGAGTTGG 58.743 50.000 0.00 0.00 46.41 3.77
1237 1301 3.257393 CCTCATTCAGAAGACCGAGTTG 58.743 50.000 0.00 0.00 0.00 3.16
1238 1302 2.354203 GCCTCATTCAGAAGACCGAGTT 60.354 50.000 0.00 0.00 0.00 3.01
1239 1303 1.205893 GCCTCATTCAGAAGACCGAGT 59.794 52.381 0.00 0.00 0.00 4.18
1240 1304 1.800655 CGCCTCATTCAGAAGACCGAG 60.801 57.143 0.00 0.00 0.00 4.63
1241 1305 0.173481 CGCCTCATTCAGAAGACCGA 59.827 55.000 0.00 0.00 0.00 4.69
1242 1306 0.108615 ACGCCTCATTCAGAAGACCG 60.109 55.000 0.00 0.00 0.00 4.79
1243 1307 2.100605 AACGCCTCATTCAGAAGACC 57.899 50.000 0.00 0.00 0.00 3.85
1244 1308 4.034510 CCATTAACGCCTCATTCAGAAGAC 59.965 45.833 0.00 0.00 0.00 3.01
1245 1309 4.191544 CCATTAACGCCTCATTCAGAAGA 58.808 43.478 0.00 0.00 0.00 2.87
1246 1310 3.313526 CCCATTAACGCCTCATTCAGAAG 59.686 47.826 0.00 0.00 0.00 2.85
1247 1311 3.278574 CCCATTAACGCCTCATTCAGAA 58.721 45.455 0.00 0.00 0.00 3.02
1248 1312 2.917933 CCCATTAACGCCTCATTCAGA 58.082 47.619 0.00 0.00 0.00 3.27
1249 1313 1.334869 GCCCATTAACGCCTCATTCAG 59.665 52.381 0.00 0.00 0.00 3.02
1250 1314 1.064758 AGCCCATTAACGCCTCATTCA 60.065 47.619 0.00 0.00 0.00 2.57
1251 1315 1.334869 CAGCCCATTAACGCCTCATTC 59.665 52.381 0.00 0.00 0.00 2.67
1252 1316 1.392589 CAGCCCATTAACGCCTCATT 58.607 50.000 0.00 0.00 0.00 2.57
1253 1317 0.466189 CCAGCCCATTAACGCCTCAT 60.466 55.000 0.00 0.00 0.00 2.90
1254 1318 1.077787 CCAGCCCATTAACGCCTCA 60.078 57.895 0.00 0.00 0.00 3.86
1255 1319 2.481471 GCCAGCCCATTAACGCCTC 61.481 63.158 0.00 0.00 0.00 4.70
1256 1320 2.440247 GCCAGCCCATTAACGCCT 60.440 61.111 0.00 0.00 0.00 5.52
1257 1321 2.618368 TAGGCCAGCCCATTAACGCC 62.618 60.000 5.01 0.00 36.58 5.68
1258 1322 1.153046 TAGGCCAGCCCATTAACGC 60.153 57.895 5.01 0.00 36.58 4.84
1259 1323 0.180406 ACTAGGCCAGCCCATTAACG 59.820 55.000 5.01 0.00 36.58 3.18
1260 1324 2.437085 AACTAGGCCAGCCCATTAAC 57.563 50.000 5.01 0.00 36.58 2.01
1261 1325 3.389866 TCTAACTAGGCCAGCCCATTAA 58.610 45.455 5.01 0.00 36.58 1.40
1262 1326 2.972713 CTCTAACTAGGCCAGCCCATTA 59.027 50.000 5.01 1.20 36.58 1.90
1263 1327 1.771255 CTCTAACTAGGCCAGCCCATT 59.229 52.381 5.01 0.00 36.58 3.16
1264 1328 1.428869 CTCTAACTAGGCCAGCCCAT 58.571 55.000 5.01 0.00 36.58 4.00
1265 1329 0.691078 CCTCTAACTAGGCCAGCCCA 60.691 60.000 5.01 0.00 36.58 5.36
1266 1330 1.411651 CCCTCTAACTAGGCCAGCCC 61.412 65.000 5.01 0.00 35.09 5.19
1267 1331 1.411651 CCCCTCTAACTAGGCCAGCC 61.412 65.000 5.01 0.00 35.09 4.85
1268 1332 0.691413 ACCCCTCTAACTAGGCCAGC 60.691 60.000 5.01 0.00 35.09 4.85
1269 1333 1.123928 CACCCCTCTAACTAGGCCAG 58.876 60.000 5.01 2.64 35.09 4.85
1270 1334 0.326238 CCACCCCTCTAACTAGGCCA 60.326 60.000 5.01 0.00 35.09 5.36
1271 1335 1.697082 GCCACCCCTCTAACTAGGCC 61.697 65.000 0.00 0.00 35.09 5.19
1272 1336 1.697082 GGCCACCCCTCTAACTAGGC 61.697 65.000 0.00 0.00 39.86 3.93
1273 1337 2.529312 GGCCACCCCTCTAACTAGG 58.471 63.158 0.00 0.00 36.30 3.02
1291 1355 2.869503 ATAAGGGTTCAGTGCGGCGG 62.870 60.000 9.78 0.00 0.00 6.13
1292 1356 1.429148 GATAAGGGTTCAGTGCGGCG 61.429 60.000 0.51 0.51 0.00 6.46
1293 1357 0.392461 TGATAAGGGTTCAGTGCGGC 60.392 55.000 0.00 0.00 0.00 6.53
1294 1358 1.656652 CTGATAAGGGTTCAGTGCGG 58.343 55.000 0.00 0.00 36.64 5.69
1299 1363 1.802880 CGGCGACTGATAAGGGTTCAG 60.803 57.143 0.00 0.00 44.95 3.02
1300 1364 0.174845 CGGCGACTGATAAGGGTTCA 59.825 55.000 0.00 0.00 0.00 3.18
1301 1365 0.458669 TCGGCGACTGATAAGGGTTC 59.541 55.000 4.99 0.00 0.00 3.62
1302 1366 1.068741 GATCGGCGACTGATAAGGGTT 59.931 52.381 13.76 0.00 0.00 4.11
1303 1367 0.674534 GATCGGCGACTGATAAGGGT 59.325 55.000 13.76 0.00 0.00 4.34
1304 1368 0.962489 AGATCGGCGACTGATAAGGG 59.038 55.000 13.76 0.00 0.00 3.95
1305 1369 1.400371 CGAGATCGGCGACTGATAAGG 60.400 57.143 13.76 0.00 35.37 2.69
1306 1370 1.264557 ACGAGATCGGCGACTGATAAG 59.735 52.381 13.76 2.74 44.95 1.73
1307 1371 1.306148 ACGAGATCGGCGACTGATAA 58.694 50.000 13.76 0.00 44.95 1.75
1308 1372 1.002792 CAACGAGATCGGCGACTGATA 60.003 52.381 13.76 0.00 44.95 2.15
1309 1373 0.248661 CAACGAGATCGGCGACTGAT 60.249 55.000 13.76 0.00 44.95 2.90
1310 1374 1.136774 CAACGAGATCGGCGACTGA 59.863 57.895 13.76 0.00 44.95 3.41
1314 1378 3.411418 GAGGCAACGAGATCGGCGA 62.411 63.158 13.87 13.87 44.95 5.54
1324 1392 3.550275 TCGATTCTATTTTCGAGGCAACG 59.450 43.478 0.00 0.00 39.29 4.10
1335 1403 5.566469 TGGAGTTGGGTTTCGATTCTATTT 58.434 37.500 0.00 0.00 0.00 1.40
1340 1408 3.568430 AGTTTGGAGTTGGGTTTCGATTC 59.432 43.478 0.00 0.00 0.00 2.52
1343 1411 2.294074 CAGTTTGGAGTTGGGTTTCGA 58.706 47.619 0.00 0.00 0.00 3.71
1344 1412 2.021457 ACAGTTTGGAGTTGGGTTTCG 58.979 47.619 0.00 0.00 0.00 3.46
1345 1413 3.949113 TGTACAGTTTGGAGTTGGGTTTC 59.051 43.478 0.00 0.00 0.00 2.78
1346 1414 3.697542 GTGTACAGTTTGGAGTTGGGTTT 59.302 43.478 0.00 0.00 0.00 3.27
1349 1417 2.925724 TGTGTACAGTTTGGAGTTGGG 58.074 47.619 0.00 0.00 0.00 4.12
1371 1441 2.065007 CCATAATCCCCATCCTCACCA 58.935 52.381 0.00 0.00 0.00 4.17
1459 1529 0.461516 TCGAGTAGCCGTCGATCTGT 60.462 55.000 0.00 0.00 41.41 3.41
1489 1567 2.906897 CTGGTGCCGTTGGTTGCT 60.907 61.111 0.00 0.00 0.00 3.91
1579 1657 2.125512 ATGAAGTCGGCGCTGTCC 60.126 61.111 17.37 8.34 0.00 4.02
1622 1700 1.094785 CTGATGGGCCCTTTAACGTG 58.905 55.000 25.70 0.00 0.00 4.49
1645 1723 4.008330 CCATGAAGCTGAACTCAAGATGT 58.992 43.478 0.00 0.00 0.00 3.06
1691 1769 2.576832 GCCTGGTGCAAACATGCCT 61.577 57.895 8.20 0.00 40.77 4.75
1692 1770 2.047939 GCCTGGTGCAAACATGCC 60.048 61.111 8.20 0.00 40.77 4.40
1898 4950 2.413351 CATCGTCGCCACTCGGAT 59.587 61.111 0.00 0.00 39.05 4.18
1925 4977 0.523072 AAACATGCATGGACGAGCAC 59.477 50.000 29.41 0.00 44.49 4.40
1926 4978 0.804364 GAAACATGCATGGACGAGCA 59.196 50.000 29.41 0.00 45.92 4.26
2100 5156 3.909574 GCATAAAAACGAAACTTGCGCTA 59.090 39.130 9.73 0.00 0.00 4.26
2105 5161 4.298332 AGGCAGCATAAAAACGAAACTTG 58.702 39.130 0.00 0.00 0.00 3.16
2113 5169 4.503741 TCACAAGAGGCAGCATAAAAAC 57.496 40.909 0.00 0.00 0.00 2.43
2128 5184 4.823989 AGGAGAACCATCAAAGTTCACAAG 59.176 41.667 6.44 0.00 44.91 3.16
2148 5209 4.669866 TCCAAGTACAAGTCTCCTAGGA 57.330 45.455 11.98 11.98 0.00 2.94
2149 5210 4.342665 GGATCCAAGTACAAGTCTCCTAGG 59.657 50.000 6.95 0.82 0.00 3.02
2189 5259 0.846693 AGAAAGGTGTGCCAGGTTCT 59.153 50.000 0.00 0.00 37.19 3.01
2190 5260 1.692411 AAGAAAGGTGTGCCAGGTTC 58.308 50.000 0.00 0.00 37.19 3.62
2191 5261 2.159179 AAAGAAAGGTGTGCCAGGTT 57.841 45.000 0.00 0.00 37.19 3.50
2192 5262 2.159179 AAAAGAAAGGTGTGCCAGGT 57.841 45.000 0.00 0.00 37.19 4.00
2193 5263 2.430332 TGAAAAAGAAAGGTGTGCCAGG 59.570 45.455 0.00 0.00 37.19 4.45
2194 5264 3.491447 CCTGAAAAAGAAAGGTGTGCCAG 60.491 47.826 0.00 0.00 37.19 4.85
2201 5271 5.719563 TCTTCCAAACCTGAAAAAGAAAGGT 59.280 36.000 0.00 0.00 46.40 3.50
2238 5308 1.202313 CCTAGCACTCCTACGAACTGC 60.202 57.143 0.00 0.00 0.00 4.40
2239 5309 2.366533 TCCTAGCACTCCTACGAACTG 58.633 52.381 0.00 0.00 0.00 3.16
2240 5310 2.803030 TCCTAGCACTCCTACGAACT 57.197 50.000 0.00 0.00 0.00 3.01
2241 5311 3.243468 GGAATCCTAGCACTCCTACGAAC 60.243 52.174 0.00 0.00 0.00 3.95
2242 5312 2.957006 GGAATCCTAGCACTCCTACGAA 59.043 50.000 0.00 0.00 0.00 3.85
2243 5313 2.584236 GGAATCCTAGCACTCCTACGA 58.416 52.381 0.00 0.00 0.00 3.43
2244 5314 1.267261 CGGAATCCTAGCACTCCTACG 59.733 57.143 0.00 0.00 0.00 3.51
2245 5315 1.000052 GCGGAATCCTAGCACTCCTAC 60.000 57.143 0.00 0.00 0.00 3.18
2246 5316 1.329256 GCGGAATCCTAGCACTCCTA 58.671 55.000 0.00 0.00 0.00 2.94
2247 5317 0.687757 TGCGGAATCCTAGCACTCCT 60.688 55.000 0.00 0.00 35.81 3.69
2248 5318 0.249657 CTGCGGAATCCTAGCACTCC 60.250 60.000 0.00 0.00 36.79 3.85
2249 5319 0.461961 ACTGCGGAATCCTAGCACTC 59.538 55.000 0.00 0.00 36.79 3.51
2250 5320 0.905357 AACTGCGGAATCCTAGCACT 59.095 50.000 0.00 0.00 36.79 4.40
2251 5321 1.291132 GAACTGCGGAATCCTAGCAC 58.709 55.000 0.00 0.00 36.79 4.40
2252 5322 0.179111 CGAACTGCGGAATCCTAGCA 60.179 55.000 0.00 0.00 39.25 3.49
2253 5323 0.179108 ACGAACTGCGGAATCCTAGC 60.179 55.000 0.00 0.00 46.49 3.42
2254 5324 2.287668 CCTACGAACTGCGGAATCCTAG 60.288 54.545 0.00 0.00 46.49 3.02
2255 5325 1.679680 CCTACGAACTGCGGAATCCTA 59.320 52.381 0.00 0.00 46.49 2.94
2256 5326 0.460311 CCTACGAACTGCGGAATCCT 59.540 55.000 0.00 0.00 46.49 3.24
2257 5327 0.458669 TCCTACGAACTGCGGAATCC 59.541 55.000 0.00 0.00 46.49 3.01
2530 5602 0.924090 GAATCGCATCTCACACCGAC 59.076 55.000 0.00 0.00 32.07 4.79
3066 6146 1.415672 AAGTCCAAGAACCCCTCGCA 61.416 55.000 0.00 0.00 0.00 5.10
3174 6254 1.133809 AGGTGCTTAGCTCAACCCCA 61.134 55.000 5.60 0.00 0.00 4.96


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

AutoCloner maintained by Alex Coulton.