Multiple sequence alignment - TraesCS5B01G041700

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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 TraesCS5B01G041700 chr5B 100.000 4286 0 0 1 4286 45846950 45842665 0.000000e+00 7915.0
1 TraesCS5B01G041700 chr5B 91.743 109 7 2 583 691 45865647 45865541 2.670000e-32 150.0
2 TraesCS5B01G041700 chr5B 77.091 275 33 17 3452 3724 641396770 641397016 9.670000e-27 132.0
3 TraesCS5B01G041700 chr5B 91.667 60 5 0 4091 4150 508786212 508786153 2.750000e-12 84.2
4 TraesCS5B01G041700 chr5D 89.866 3138 175 57 1187 4286 45665828 45662796 0.000000e+00 3901.0
5 TraesCS5B01G041700 chr5D 91.068 459 36 5 3713 4168 45648733 45648277 2.190000e-172 616.0
6 TraesCS5B01G041700 chr5D 88.380 284 15 7 580 853 45666345 45666070 4.130000e-85 326.0
7 TraesCS5B01G041700 chr5D 96.875 128 4 0 4159 4286 45636934 45636807 9.330000e-52 215.0
8 TraesCS5B01G041700 chr5D 93.220 118 8 0 960 1077 45666030 45665913 1.580000e-39 174.0
9 TraesCS5B01G041700 chr5A 88.505 3071 180 56 1272 4286 36484565 36481612 0.000000e+00 3555.0
10 TraesCS5B01G041700 chr5A 92.939 524 22 6 1 510 535615986 535615464 0.000000e+00 749.0
11 TraesCS5B01G041700 chr5A 83.163 196 10 6 580 752 36485475 36485280 1.600000e-34 158.0
12 TraesCS5B01G041700 chr5A 77.387 199 22 16 218 412 666810104 666809925 3.530000e-16 97.1
13 TraesCS5B01G041700 chr1B 96.477 511 16 2 1 510 605977040 605976531 0.000000e+00 843.0
14 TraesCS5B01G041700 chr1B 93.333 60 4 0 4091 4150 619390614 619390673 5.900000e-14 89.8
15 TraesCS5B01G041700 chr2B 84.041 683 85 14 3053 3734 514324312 514323653 1.680000e-178 636.0
16 TraesCS5B01G041700 chr2B 83.240 537 62 13 3053 3589 651320727 651320219 6.490000e-128 468.0
17 TraesCS5B01G041700 chr2B 84.906 265 36 1 3208 3472 435341779 435342039 9.140000e-67 265.0
18 TraesCS5B01G041700 chr2B 90.196 153 15 0 2862 3014 435343417 435343569 2.610000e-47 200.0
19 TraesCS5B01G041700 chr2B 90.152 132 8 2 2828 2959 514324481 514324355 2.650000e-37 167.0
20 TraesCS5B01G041700 chr2B 90.476 84 8 0 3096 3179 435343599 435343682 1.260000e-20 111.0
21 TraesCS5B01G041700 chr2D 83.260 681 83 13 2344 3009 454716519 454717183 7.930000e-167 597.0
22 TraesCS5B01G041700 chr2D 93.617 47 1 2 3854 3899 252169498 252169543 7.690000e-08 69.4
23 TraesCS5B01G041700 chr7A 80.939 703 90 17 3177 3863 2875490 2876164 2.290000e-142 516.0
24 TraesCS5B01G041700 chr4B 83.985 537 57 17 3053 3589 349114037 349113530 4.980000e-134 488.0
25 TraesCS5B01G041700 chr6D 83.829 538 58 9 3055 3591 203752360 203751851 6.440000e-133 484.0
26 TraesCS5B01G041700 chr6D 81.548 168 20 6 159 323 26247659 26247818 1.250000e-25 128.0
27 TraesCS5B01G041700 chr6D 93.333 60 4 0 4091 4150 368369664 368369723 5.900000e-14 89.8
28 TraesCS5B01G041700 chr6B 83.708 534 58 17 3053 3586 95584219 95584723 1.080000e-130 477.0
29 TraesCS5B01G041700 chr6B 89.542 153 16 0 2862 3014 208898540 208898388 1.220000e-45 195.0
30 TraesCS5B01G041700 chr1D 79.259 540 51 21 3053 3591 453229307 453228828 1.920000e-83 320.0
31 TraesCS5B01G041700 chr7B 80.992 242 27 15 210 444 705012461 705012690 1.580000e-39 174.0
32 TraesCS5B01G041700 chr7B 80.579 242 27 14 210 444 704969673 704969901 7.370000e-38 169.0
33 TraesCS5B01G041700 chr7B 80.498 241 29 14 210 444 705051207 705051435 7.370000e-38 169.0
34 TraesCS5B01G041700 chr7B 78.065 310 36 22 210 500 704895602 704895898 2.650000e-37 167.0
35 TraesCS5B01G041700 chr7B 77.246 167 22 12 210 371 705096616 705096771 2.750000e-12 84.2
36 TraesCS5B01G041700 chr7B 97.059 34 1 0 3870 3903 719444452 719444419 1.660000e-04 58.4
37 TraesCS5B01G041700 chr1A 89.394 132 9 2 2828 2959 7296302 7296176 1.230000e-35 161.0
38 TraesCS5B01G041700 chr2A 88.800 125 11 1 2828 2952 32761817 32761938 2.670000e-32 150.0
39 TraesCS5B01G041700 chr2A 93.333 60 4 0 4091 4150 221300882 221300941 5.900000e-14 89.8
40 TraesCS5B01G041700 chr2A 93.333 60 4 0 4091 4150 568849838 568849779 5.900000e-14 89.8
41 TraesCS5B01G041700 chr3A 93.333 60 4 0 4091 4150 579138538 579138479 5.900000e-14 89.8
42 TraesCS5B01G041700 chr3A 90.244 41 4 0 2974 3014 693458396 693458436 2.000000e-03 54.7


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 TraesCS5B01G041700 chr5B 45842665 45846950 4285 True 7915.0 7915 100.000000 1 4286 1 chr5B.!!$R1 4285
1 TraesCS5B01G041700 chr5D 45662796 45666345 3549 True 1467.0 3901 90.488667 580 4286 3 chr5D.!!$R3 3706
2 TraesCS5B01G041700 chr5A 36481612 36485475 3863 True 1856.5 3555 85.834000 580 4286 2 chr5A.!!$R3 3706
3 TraesCS5B01G041700 chr5A 535615464 535615986 522 True 749.0 749 92.939000 1 510 1 chr5A.!!$R1 509
4 TraesCS5B01G041700 chr1B 605976531 605977040 509 True 843.0 843 96.477000 1 510 1 chr1B.!!$R1 509
5 TraesCS5B01G041700 chr2B 651320219 651320727 508 True 468.0 468 83.240000 3053 3589 1 chr2B.!!$R1 536
6 TraesCS5B01G041700 chr2B 514323653 514324481 828 True 401.5 636 87.096500 2828 3734 2 chr2B.!!$R2 906
7 TraesCS5B01G041700 chr2D 454716519 454717183 664 False 597.0 597 83.260000 2344 3009 1 chr2D.!!$F2 665
8 TraesCS5B01G041700 chr7A 2875490 2876164 674 False 516.0 516 80.939000 3177 3863 1 chr7A.!!$F1 686
9 TraesCS5B01G041700 chr4B 349113530 349114037 507 True 488.0 488 83.985000 3053 3589 1 chr4B.!!$R1 536
10 TraesCS5B01G041700 chr6D 203751851 203752360 509 True 484.0 484 83.829000 3055 3591 1 chr6D.!!$R1 536
11 TraesCS5B01G041700 chr6B 95584219 95584723 504 False 477.0 477 83.708000 3053 3586 1 chr6B.!!$F1 533

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
514 530 0.104120 AAAAAGGACTTTGCGGGCAC 59.896 50.0 0.00 0.0 32.36 5.01 F
565 581 0.179000 ACCCAATCGGCTTCAGCTAG 59.821 55.0 0.00 0.0 41.70 3.42 F
1428 1824 0.250513 GGCTCGGTTCATTCTCCAGT 59.749 55.0 0.00 0.0 0.00 4.00 F
1698 2117 0.663153 GGATCAATGTGTTAGCGCCC 59.337 55.0 2.29 0.0 0.00 6.13 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1427 1823 0.030773 TCACTCACTCACTCGCACAC 59.969 55.000 0.00 0.0 0.0 3.82 R
1681 2082 0.255890 AGGGGCGCTAACACATTGAT 59.744 50.000 7.64 0.0 0.0 2.57 R
2656 3105 1.080705 CTTCGTCTTCTTCGCCGGT 60.081 57.895 1.90 0.0 0.0 5.28 R
3634 4139 0.108945 GCAAGCAAGCCAGATTCCAC 60.109 55.000 0.00 0.0 0.0 4.02 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
301 307 3.446310 ACATGTGTGAAGTGTACGTGA 57.554 42.857 0.00 0.00 35.76 4.35
309 315 1.000607 GAAGTGTACGTGACTCAGGCA 60.001 52.381 0.00 0.00 0.00 4.75
353 359 2.742372 GAATCACGTGCGTGGCCT 60.742 61.111 22.06 8.88 45.43 5.19
358 364 4.308458 ACGTGCGTGGCCTAGCAA 62.308 61.111 23.48 8.64 45.61 3.91
413 419 7.121315 GTGAAATACAGAGGCTTAAATGAAGGT 59.879 37.037 0.00 0.00 35.49 3.50
485 501 2.288025 GGAACCACCGGTAGCTCCA 61.288 63.158 16.46 0.00 33.12 3.86
510 526 1.068816 CCGGTAAAAAGGACTTTGCGG 60.069 52.381 0.00 0.00 32.36 5.69
511 527 1.068816 CGGTAAAAAGGACTTTGCGGG 60.069 52.381 0.00 0.00 32.36 6.13
512 528 1.336517 GGTAAAAAGGACTTTGCGGGC 60.337 52.381 0.00 0.00 32.36 6.13
513 529 1.338655 GTAAAAAGGACTTTGCGGGCA 59.661 47.619 0.00 0.00 32.36 5.36
514 530 0.104120 AAAAAGGACTTTGCGGGCAC 59.896 50.000 0.00 0.00 32.36 5.01
515 531 1.744320 AAAAGGACTTTGCGGGCACC 61.744 55.000 0.00 0.00 37.85 5.01
539 555 3.136123 CCTTGCCATGGCCGACTG 61.136 66.667 33.44 17.48 41.09 3.51
540 556 3.136123 CTTGCCATGGCCGACTGG 61.136 66.667 33.44 12.91 41.09 4.00
550 566 3.636231 CCGACTGGCCAGAACCCA 61.636 66.667 39.19 0.00 0.00 4.51
551 567 2.429930 CGACTGGCCAGAACCCAA 59.570 61.111 39.19 0.00 30.66 4.12
552 568 1.002134 CGACTGGCCAGAACCCAAT 60.002 57.895 39.19 15.22 30.66 3.16
553 569 1.026718 CGACTGGCCAGAACCCAATC 61.027 60.000 39.19 21.95 30.66 2.67
554 570 1.002134 ACTGGCCAGAACCCAATCG 60.002 57.895 39.19 9.95 30.66 3.34
555 571 1.750399 CTGGCCAGAACCCAATCGG 60.750 63.158 29.88 0.00 37.81 4.18
556 572 3.140814 GGCCAGAACCCAATCGGC 61.141 66.667 0.00 0.00 37.89 5.54
557 573 2.044946 GCCAGAACCCAATCGGCT 60.045 61.111 0.00 0.00 36.63 5.52
558 574 1.678970 GCCAGAACCCAATCGGCTT 60.679 57.895 0.00 0.00 36.63 4.35
559 575 1.657751 GCCAGAACCCAATCGGCTTC 61.658 60.000 0.00 0.00 36.63 3.86
560 576 0.322456 CCAGAACCCAATCGGCTTCA 60.322 55.000 0.00 0.00 33.26 3.02
561 577 1.089920 CAGAACCCAATCGGCTTCAG 58.910 55.000 0.00 0.00 33.26 3.02
562 578 0.678048 AGAACCCAATCGGCTTCAGC 60.678 55.000 0.00 0.00 41.14 4.26
563 579 0.678048 GAACCCAATCGGCTTCAGCT 60.678 55.000 0.00 0.00 41.70 4.24
564 580 0.618458 AACCCAATCGGCTTCAGCTA 59.382 50.000 0.00 0.00 41.70 3.32
565 581 0.179000 ACCCAATCGGCTTCAGCTAG 59.821 55.000 0.00 0.00 41.70 3.42
566 582 0.533755 CCCAATCGGCTTCAGCTAGG 60.534 60.000 0.00 0.00 41.70 3.02
567 583 1.162800 CCAATCGGCTTCAGCTAGGC 61.163 60.000 0.00 0.00 41.70 3.93
571 587 2.202946 GGCTTCAGCTAGGCGGAC 60.203 66.667 0.00 0.00 41.70 4.79
572 588 2.726351 GGCTTCAGCTAGGCGGACT 61.726 63.158 0.00 0.00 41.70 3.85
573 589 1.520342 GCTTCAGCTAGGCGGACTG 60.520 63.158 0.00 0.00 38.21 3.51
574 590 1.520342 CTTCAGCTAGGCGGACTGC 60.520 63.158 0.00 0.00 45.38 4.40
588 604 2.049156 CTGCAGACGCTCGGTTCA 60.049 61.111 8.42 0.00 39.64 3.18
733 770 3.271703 TCCTCCCTCCTCCGGTTATATA 58.728 50.000 0.00 0.00 0.00 0.86
739 776 4.565028 CCCTCCTCCGGTTATATAAAAGCC 60.565 50.000 0.00 0.00 0.00 4.35
759 1050 3.385384 CTCTCCCTCGGCACAGCA 61.385 66.667 0.00 0.00 0.00 4.41
774 1065 2.428071 GCACGCTTGCTGCTTCAC 60.428 61.111 8.12 0.00 46.17 3.18
783 1078 1.081840 GCTGCTTCACGCTTCAACC 60.082 57.895 0.00 0.00 40.11 3.77
871 1174 2.461637 CTCCCTCCCCTCCCCTTT 59.538 66.667 0.00 0.00 0.00 3.11
872 1175 1.694525 CTCCCTCCCCTCCCCTTTC 60.695 68.421 0.00 0.00 0.00 2.62
893 1196 2.333938 CACTTGCAGCACCAGCAC 59.666 61.111 0.00 0.00 45.49 4.40
902 1205 2.697761 GCACCAGCACCAGCATCAG 61.698 63.158 0.00 0.00 45.49 2.90
909 1212 0.746923 GCACCAGCATCAGCATCAGA 60.747 55.000 0.00 0.00 45.49 3.27
910 1213 1.300481 CACCAGCATCAGCATCAGAG 58.700 55.000 0.00 0.00 45.49 3.35
911 1214 1.134491 CACCAGCATCAGCATCAGAGA 60.134 52.381 0.00 0.00 45.49 3.10
912 1215 1.139256 ACCAGCATCAGCATCAGAGAG 59.861 52.381 0.00 0.00 45.49 3.20
915 1218 2.362717 CAGCATCAGCATCAGAGAGAGA 59.637 50.000 0.00 0.00 45.49 3.10
916 1219 2.626266 AGCATCAGCATCAGAGAGAGAG 59.374 50.000 0.00 0.00 45.49 3.20
917 1220 2.624364 GCATCAGCATCAGAGAGAGAGA 59.376 50.000 0.00 0.00 41.58 3.10
918 1221 3.305131 GCATCAGCATCAGAGAGAGAGAG 60.305 52.174 0.00 0.00 41.58 3.20
919 1222 3.929955 TCAGCATCAGAGAGAGAGAGA 57.070 47.619 0.00 0.00 0.00 3.10
920 1223 3.812262 TCAGCATCAGAGAGAGAGAGAG 58.188 50.000 0.00 0.00 0.00 3.20
921 1224 3.455543 TCAGCATCAGAGAGAGAGAGAGA 59.544 47.826 0.00 0.00 0.00 3.10
922 1225 3.813724 CAGCATCAGAGAGAGAGAGAGAG 59.186 52.174 0.00 0.00 0.00 3.20
923 1226 3.713248 AGCATCAGAGAGAGAGAGAGAGA 59.287 47.826 0.00 0.00 0.00 3.10
924 1227 4.063689 GCATCAGAGAGAGAGAGAGAGAG 58.936 52.174 0.00 0.00 0.00 3.20
925 1228 4.202295 GCATCAGAGAGAGAGAGAGAGAGA 60.202 50.000 0.00 0.00 0.00 3.10
926 1229 5.539979 CATCAGAGAGAGAGAGAGAGAGAG 58.460 50.000 0.00 0.00 0.00 3.20
927 1230 4.871822 TCAGAGAGAGAGAGAGAGAGAGA 58.128 47.826 0.00 0.00 0.00 3.10
928 1231 4.892345 TCAGAGAGAGAGAGAGAGAGAGAG 59.108 50.000 0.00 0.00 0.00 3.20
929 1232 4.892345 CAGAGAGAGAGAGAGAGAGAGAGA 59.108 50.000 0.00 0.00 0.00 3.10
930 1233 5.009911 CAGAGAGAGAGAGAGAGAGAGAGAG 59.990 52.000 0.00 0.00 0.00 3.20
931 1234 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
932 1235 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
933 1236 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
934 1237 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
935 1238 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
936 1239 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
937 1240 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
938 1241 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
939 1242 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
940 1243 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
941 1244 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
942 1245 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
943 1246 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
944 1247 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
945 1248 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
946 1249 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
947 1250 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
948 1251 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
949 1252 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
950 1253 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
951 1254 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
952 1255 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
953 1256 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
954 1257 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
955 1258 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
956 1259 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
957 1260 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
958 1261 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
975 1278 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
979 1282 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
982 1285 5.714863 AGAGAGAGAGAGAGAGAGAGAGAT 58.285 45.833 0.00 0.00 0.00 2.75
983 1286 6.142498 AGAGAGAGAGAGAGAGAGAGAGATT 58.858 44.000 0.00 0.00 0.00 2.40
1036 1339 2.256117 ACACAAGGTTCAGGTAGTGC 57.744 50.000 0.00 0.00 0.00 4.40
1053 1359 6.150140 AGGTAGTGCTAATTTTCTTTGCTCTG 59.850 38.462 0.00 0.00 0.00 3.35
1082 1392 1.745115 CGTGTTCATCCATGGCGGT 60.745 57.895 6.96 0.00 35.57 5.68
1086 1396 1.077787 TTCATCCATGGCGGTGTCC 60.078 57.895 6.96 0.00 35.57 4.02
1090 1400 1.852157 ATCCATGGCGGTGTCCAAGT 61.852 55.000 6.96 0.00 39.96 3.16
1095 1405 1.003839 GGCGGTGTCCAAGTCATCA 60.004 57.895 0.00 0.00 0.00 3.07
1098 1408 1.432514 CGGTGTCCAAGTCATCACTG 58.567 55.000 0.00 0.00 31.06 3.66
1099 1409 1.270305 CGGTGTCCAAGTCATCACTGT 60.270 52.381 0.00 0.00 33.94 3.55
1100 1410 2.806745 CGGTGTCCAAGTCATCACTGTT 60.807 50.000 0.00 0.00 33.94 3.16
1101 1411 3.214328 GGTGTCCAAGTCATCACTGTTT 58.786 45.455 0.00 0.00 31.06 2.83
1103 1413 3.251004 GTGTCCAAGTCATCACTGTTTCC 59.749 47.826 0.00 0.00 31.06 3.13
1104 1414 3.118075 TGTCCAAGTCATCACTGTTTCCA 60.118 43.478 0.00 0.00 31.06 3.53
1105 1415 4.074970 GTCCAAGTCATCACTGTTTCCAT 58.925 43.478 0.00 0.00 31.06 3.41
1107 1417 3.441572 CCAAGTCATCACTGTTTCCATCC 59.558 47.826 0.00 0.00 31.06 3.51
1108 1418 4.074259 CAAGTCATCACTGTTTCCATCCA 58.926 43.478 0.00 0.00 31.06 3.41
1109 1419 3.679389 AGTCATCACTGTTTCCATCCAC 58.321 45.455 0.00 0.00 0.00 4.02
1110 1420 3.072915 AGTCATCACTGTTTCCATCCACA 59.927 43.478 0.00 0.00 0.00 4.17
1111 1421 3.820467 GTCATCACTGTTTCCATCCACAA 59.180 43.478 0.00 0.00 0.00 3.33
1113 1423 2.217750 TCACTGTTTCCATCCACAACG 58.782 47.619 0.00 0.00 0.00 4.10
1114 1424 1.946768 CACTGTTTCCATCCACAACGT 59.053 47.619 0.00 0.00 0.00 3.99
1115 1425 2.357637 CACTGTTTCCATCCACAACGTT 59.642 45.455 0.00 0.00 0.00 3.99
1116 1426 2.357637 ACTGTTTCCATCCACAACGTTG 59.642 45.455 26.20 26.20 0.00 4.10
1117 1427 2.357637 CTGTTTCCATCCACAACGTTGT 59.642 45.455 27.70 27.70 43.36 3.32
1143 1456 1.648116 AGCAGCATTTGGGTTTCCAT 58.352 45.000 0.00 0.00 43.63 3.41
1149 1462 2.038295 GCATTTGGGTTTCCATCCACAA 59.962 45.455 0.00 0.00 43.63 3.33
1157 1470 4.770010 GGGTTTCCATCCACAACAAAGATA 59.230 41.667 0.00 0.00 0.00 1.98
1158 1471 5.336451 GGGTTTCCATCCACAACAAAGATAC 60.336 44.000 0.00 0.00 0.00 2.24
1159 1472 5.336451 GGTTTCCATCCACAACAAAGATACC 60.336 44.000 0.00 0.00 0.00 2.73
1160 1473 4.649267 TCCATCCACAACAAAGATACCA 57.351 40.909 0.00 0.00 0.00 3.25
1168 1481 7.458397 TCCACAACAAAGATACCACTAAATCT 58.542 34.615 0.00 0.00 33.87 2.40
1206 1537 5.355596 GGGAGTATCTCTGTTCATGAGTTG 58.644 45.833 0.00 0.00 33.73 3.16
1207 1538 4.808364 GGAGTATCTCTGTTCATGAGTTGC 59.192 45.833 0.00 0.00 33.73 4.17
1254 1606 4.155462 CAGCATTGAGAACTGTAGTGCATT 59.845 41.667 0.00 0.00 33.80 3.56
1257 1609 2.068519 TGAGAACTGTAGTGCATTGCG 58.931 47.619 3.84 0.00 0.00 4.85
1399 1789 1.956629 ATGCTTTGCTGCTCCATGCC 61.957 55.000 0.00 0.00 42.00 4.40
1427 1823 0.462759 GGGCTCGGTTCATTCTCCAG 60.463 60.000 0.00 0.00 0.00 3.86
1428 1824 0.250513 GGCTCGGTTCATTCTCCAGT 59.749 55.000 0.00 0.00 0.00 4.00
1436 1834 0.969149 TCATTCTCCAGTGTGCGAGT 59.031 50.000 0.00 0.00 0.00 4.18
1438 1836 0.969149 ATTCTCCAGTGTGCGAGTGA 59.031 50.000 0.00 0.00 0.00 3.41
1474 1872 2.036475 GAGTGAGCTCAGTGAGGTTTGA 59.964 50.000 28.54 10.35 40.67 2.69
1494 1892 1.217916 TGTTGGTGGGAAGAGGTTCA 58.782 50.000 0.00 0.00 33.93 3.18
1524 1922 2.358615 TGCTCACACCATCGCACC 60.359 61.111 0.00 0.00 0.00 5.01
1641 2042 5.653507 CCACAAATTCCCACACATTCATAG 58.346 41.667 0.00 0.00 0.00 2.23
1642 2043 5.394443 CCACAAATTCCCACACATTCATAGG 60.394 44.000 0.00 0.00 0.00 2.57
1644 2045 6.097270 CACAAATTCCCACACATTCATAGGAT 59.903 38.462 0.00 0.00 0.00 3.24
1645 2046 6.322201 ACAAATTCCCACACATTCATAGGATC 59.678 38.462 0.00 0.00 0.00 3.36
1646 2047 5.651612 ATTCCCACACATTCATAGGATCA 57.348 39.130 0.00 0.00 0.00 2.92
1647 2048 4.694760 TCCCACACATTCATAGGATCAG 57.305 45.455 0.00 0.00 0.00 2.90
1649 2050 4.474651 TCCCACACATTCATAGGATCAGTT 59.525 41.667 0.00 0.00 0.00 3.16
1650 2051 5.044919 TCCCACACATTCATAGGATCAGTTT 60.045 40.000 0.00 0.00 0.00 2.66
1651 2052 5.653769 CCCACACATTCATAGGATCAGTTTT 59.346 40.000 0.00 0.00 0.00 2.43
1680 2081 9.853555 TGAAATTAACAGCACATTTACTTATGG 57.146 29.630 0.00 0.00 0.00 2.74
1694 2113 9.669353 CATTTACTTATGGATCAATGTGTTAGC 57.331 33.333 0.00 0.00 0.00 3.09
1698 2117 0.663153 GGATCAATGTGTTAGCGCCC 59.337 55.000 2.29 0.00 0.00 6.13
1893 2325 2.037136 CAAGAACAGCCTCCTGCCG 61.037 63.158 0.00 0.00 43.02 5.69
1925 2357 2.043248 GGGCTCCTCGGAGTACCA 60.043 66.667 14.08 0.00 43.70 3.25
1944 2376 1.258445 ACAAGGACCGCTCGGATTCT 61.258 55.000 15.95 6.21 38.96 2.40
2139 2571 1.195442 TCGTGCACTCCAACCCCATA 61.195 55.000 16.19 0.00 0.00 2.74
2154 2586 2.498167 CCCATATTCTCCAAGAAGGCG 58.502 52.381 0.00 0.00 37.69 5.52
2308 2740 2.202492 CCTCGTCGTCTTCGCTGG 60.202 66.667 0.00 0.00 36.96 4.85
2628 3076 3.635268 CTGGGCCAGCAAGGAGGAC 62.635 68.421 22.68 0.00 41.22 3.85
2656 3105 4.069232 CCTCGCCGGACAAGAGCA 62.069 66.667 5.05 0.00 33.16 4.26
2679 3128 1.960994 GCGAAGAAGACGAAGCCAGC 61.961 60.000 0.00 0.00 0.00 4.85
2751 3200 3.392431 CTCGCATCAAGGCACGAG 58.608 61.111 0.00 0.00 45.02 4.18
2804 3253 5.049167 TGTGCCTGATTGTTTCATTCAAAC 58.951 37.500 0.00 0.00 44.31 2.93
3010 3464 3.017265 GTGAAACAAATCCCAGCTGTG 57.983 47.619 13.81 6.33 36.32 3.66
3039 3510 8.471609 TCAACAAATTCTGATCATGCATTGTAT 58.528 29.630 13.89 0.00 0.00 2.29
3040 3511 8.752254 CAACAAATTCTGATCATGCATTGTATC 58.248 33.333 13.89 1.33 0.00 2.24
3041 3512 8.002984 ACAAATTCTGATCATGCATTGTATCA 57.997 30.769 12.99 12.99 0.00 2.15
3042 3513 8.471609 ACAAATTCTGATCATGCATTGTATCAA 58.528 29.630 14.05 4.74 0.00 2.57
3043 3514 8.968242 CAAATTCTGATCATGCATTGTATCAAG 58.032 33.333 14.05 9.95 0.00 3.02
3044 3515 7.818997 ATTCTGATCATGCATTGTATCAAGT 57.181 32.000 14.05 4.47 0.00 3.16
3045 3516 7.634671 TTCTGATCATGCATTGTATCAAGTT 57.365 32.000 14.05 0.00 0.00 2.66
3046 3517 8.735692 TTCTGATCATGCATTGTATCAAGTTA 57.264 30.769 14.05 2.59 0.00 2.24
3047 3518 8.146479 TCTGATCATGCATTGTATCAAGTTAC 57.854 34.615 14.05 0.00 0.00 2.50
3048 3519 7.769970 TCTGATCATGCATTGTATCAAGTTACA 59.230 33.333 14.05 0.00 0.00 2.41
3049 3520 7.922837 TGATCATGCATTGTATCAAGTTACAG 58.077 34.615 11.78 0.00 33.81 2.74
3050 3521 7.769970 TGATCATGCATTGTATCAAGTTACAGA 59.230 33.333 11.78 0.00 33.81 3.41
3051 3522 7.920160 TCATGCATTGTATCAAGTTACAGAA 57.080 32.000 0.00 0.00 33.81 3.02
3103 3574 1.095228 GGCCGATCAAATGAAGGCGA 61.095 55.000 19.86 0.00 46.15 5.54
3345 3818 4.565236 CCTGACTGAAAGAAGAAGCCTGAT 60.565 45.833 0.00 0.00 37.43 2.90
3414 3887 1.343142 TCGATGTGCTGTAGGTGTTGT 59.657 47.619 0.00 0.00 0.00 3.32
3495 3980 5.829391 TGCCATTGATAACATGAGCTAATGT 59.171 36.000 11.27 11.27 42.62 2.71
3504 3989 6.780457 AACATGAGCTAATGTTAATTGCCT 57.220 33.333 25.43 1.38 46.41 4.75
3505 3990 6.140303 ACATGAGCTAATGTTAATTGCCTG 57.860 37.500 11.27 0.00 37.50 4.85
3506 3991 4.637483 TGAGCTAATGTTAATTGCCTGC 57.363 40.909 0.00 0.00 0.00 4.85
3507 3992 4.272489 TGAGCTAATGTTAATTGCCTGCT 58.728 39.130 0.00 0.00 0.00 4.24
3508 3993 4.096833 TGAGCTAATGTTAATTGCCTGCTG 59.903 41.667 0.00 0.00 0.00 4.41
3509 3994 4.272489 AGCTAATGTTAATTGCCTGCTGA 58.728 39.130 0.00 0.00 0.00 4.26
3510 3995 4.337555 AGCTAATGTTAATTGCCTGCTGAG 59.662 41.667 0.00 0.00 0.00 3.35
3681 4186 2.760092 GCCATAAGCCATTTTGGTCTGA 59.240 45.455 0.00 0.00 40.46 3.27
3694 4200 1.208052 TGGTCTGAGACTGCATTAGCC 59.792 52.381 12.92 0.00 41.13 3.93
3711 4217 6.618811 CATTAGCCCATGATAGCTCAAAATC 58.381 40.000 7.95 0.00 40.56 2.17
3715 4221 5.068723 AGCCCATGATAGCTCAAAATCAAAG 59.931 40.000 1.14 0.00 35.82 2.77
3762 4268 2.364972 AACCTTCAAGAACCCACCAG 57.635 50.000 0.00 0.00 0.00 4.00
3801 4309 6.424207 AGACACCTTCTCGAACTTGTAAATTC 59.576 38.462 0.00 0.00 0.00 2.17
3802 4310 6.053005 ACACCTTCTCGAACTTGTAAATTCA 58.947 36.000 0.00 0.00 0.00 2.57
3827 4335 2.030274 ACATTTCTGGCCGCAACTTAAC 60.030 45.455 0.00 0.00 0.00 2.01
3888 4396 3.705043 ATCGCAGGATTCTCAAAATGC 57.295 42.857 0.00 0.00 0.00 3.56
3897 4405 6.544931 CAGGATTCTCAAAATGCAGGAATAGA 59.455 38.462 0.00 0.00 0.00 1.98
3899 4407 7.616935 AGGATTCTCAAAATGCAGGAATAGAAA 59.383 33.333 7.43 0.00 0.00 2.52
3954 4462 7.843490 TGAATCCTGTAGAATTAGAAAACCG 57.157 36.000 0.00 0.00 0.00 4.44
4058 4566 8.729805 AATTTCTTCCAAAATAGTGTGCAAAA 57.270 26.923 0.00 0.00 0.00 2.44
4062 4570 6.533367 TCTTCCAAAATAGTGTGCAAAACAAC 59.467 34.615 0.00 0.00 41.57 3.32
4074 4583 4.932799 GTGCAAAACAACCCTTACAAACTT 59.067 37.500 0.00 0.00 0.00 2.66
4240 4749 4.402793 CCTGACAGCATTAGTAGTACCACT 59.597 45.833 0.00 0.00 0.00 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
301 307 1.442769 CTTTACACGCATGCCTGAGT 58.557 50.000 21.37 11.45 35.62 3.41
309 315 0.887387 AACACCCGCTTTACACGCAT 60.887 50.000 0.00 0.00 0.00 4.73
353 359 3.758023 CACCCATGTGATTTGACTTGCTA 59.242 43.478 0.00 0.00 45.76 3.49
358 364 1.428912 ACCCACCCATGTGATTTGACT 59.571 47.619 0.00 0.00 45.76 3.41
440 446 4.463891 ACCAATAAAATCTTGCCACCTCAG 59.536 41.667 0.00 0.00 0.00 3.35
483 499 1.810755 GTCCTTTTTACCGGAGCTTGG 59.189 52.381 9.46 2.89 0.00 3.61
485 501 3.503800 AAGTCCTTTTTACCGGAGCTT 57.496 42.857 9.46 0.00 0.00 3.74
522 538 3.136123 CAGTCGGCCATGGCAAGG 61.136 66.667 36.56 24.44 44.11 3.61
523 539 3.136123 CCAGTCGGCCATGGCAAG 61.136 66.667 36.56 28.37 44.11 4.01
533 549 2.484287 ATTGGGTTCTGGCCAGTCGG 62.484 60.000 31.58 8.15 0.00 4.79
534 550 1.002134 ATTGGGTTCTGGCCAGTCG 60.002 57.895 31.58 8.56 0.00 4.18
535 551 1.026718 CGATTGGGTTCTGGCCAGTC 61.027 60.000 31.58 23.69 0.00 3.51
536 552 1.002134 CGATTGGGTTCTGGCCAGT 60.002 57.895 31.58 11.33 0.00 4.00
537 553 1.750399 CCGATTGGGTTCTGGCCAG 60.750 63.158 27.87 27.87 0.00 4.85
538 554 2.354729 CCGATTGGGTTCTGGCCA 59.645 61.111 4.71 4.71 0.00 5.36
539 555 3.140814 GCCGATTGGGTTCTGGCC 61.141 66.667 0.00 0.00 39.83 5.36
540 556 2.044946 AGCCGATTGGGTTCTGGC 60.045 61.111 0.00 0.00 45.97 4.85
547 563 0.533755 CCTAGCTGAAGCCGATTGGG 60.534 60.000 0.00 0.00 43.38 4.12
548 564 1.162800 GCCTAGCTGAAGCCGATTGG 61.163 60.000 0.00 0.00 43.38 3.16
549 565 1.493950 CGCCTAGCTGAAGCCGATTG 61.494 60.000 0.00 0.00 43.38 2.67
550 566 1.227380 CGCCTAGCTGAAGCCGATT 60.227 57.895 0.00 0.00 43.38 3.34
551 567 2.419198 CGCCTAGCTGAAGCCGAT 59.581 61.111 0.00 0.00 43.38 4.18
552 568 3.838271 CCGCCTAGCTGAAGCCGA 61.838 66.667 0.00 0.00 43.38 5.54
553 569 3.838271 TCCGCCTAGCTGAAGCCG 61.838 66.667 0.00 0.00 43.38 5.52
554 570 2.202946 GTCCGCCTAGCTGAAGCC 60.203 66.667 0.00 0.00 43.38 4.35
555 571 1.520342 CAGTCCGCCTAGCTGAAGC 60.520 63.158 0.00 0.00 42.49 3.86
556 572 1.520342 GCAGTCCGCCTAGCTGAAG 60.520 63.158 0.00 0.00 32.39 3.02
557 573 2.230994 CTGCAGTCCGCCTAGCTGAA 62.231 60.000 5.25 0.00 41.33 3.02
558 574 2.679996 TGCAGTCCGCCTAGCTGA 60.680 61.111 0.00 0.00 41.33 4.26
559 575 2.202851 CTGCAGTCCGCCTAGCTG 60.203 66.667 5.25 0.00 41.33 4.24
560 576 2.363018 TCTGCAGTCCGCCTAGCT 60.363 61.111 14.67 0.00 41.33 3.32
561 577 2.202810 GTCTGCAGTCCGCCTAGC 60.203 66.667 14.67 0.00 41.33 3.42
562 578 2.103143 CGTCTGCAGTCCGCCTAG 59.897 66.667 14.67 0.00 41.33 3.02
563 579 4.129737 GCGTCTGCAGTCCGCCTA 62.130 66.667 30.02 3.84 41.50 3.93
568 584 3.575351 AACCGAGCGTCTGCAGTCC 62.575 63.158 14.67 4.83 46.23 3.85
569 585 2.049063 AACCGAGCGTCTGCAGTC 60.049 61.111 14.67 7.33 46.23 3.51
570 586 2.049063 GAACCGAGCGTCTGCAGT 60.049 61.111 14.67 0.00 46.23 4.40
571 587 2.049156 TGAACCGAGCGTCTGCAG 60.049 61.111 7.63 7.63 46.23 4.41
572 588 2.049156 CTGAACCGAGCGTCTGCA 60.049 61.111 0.00 0.00 46.23 4.41
573 589 3.482783 GCTGAACCGAGCGTCTGC 61.483 66.667 0.00 0.00 43.24 4.26
618 638 4.351938 CGGACGCTGTCGGGACAA 62.352 66.667 2.81 0.00 41.33 3.18
707 736 2.041265 GGAGGAGGGAGGAAGGCA 59.959 66.667 0.00 0.00 0.00 4.75
733 770 2.671682 GAGGGAGAGCGGGCTTTT 59.328 61.111 0.00 0.00 0.00 2.27
769 1060 1.021202 TTGGTGGTTGAAGCGTGAAG 58.979 50.000 0.00 0.00 0.00 3.02
770 1061 0.736053 GTTGGTGGTTGAAGCGTGAA 59.264 50.000 0.00 0.00 0.00 3.18
771 1062 0.393132 TGTTGGTGGTTGAAGCGTGA 60.393 50.000 0.00 0.00 0.00 4.35
772 1063 0.248458 GTGTTGGTGGTTGAAGCGTG 60.248 55.000 0.00 0.00 0.00 5.34
773 1064 1.381165 GGTGTTGGTGGTTGAAGCGT 61.381 55.000 0.00 0.00 0.00 5.07
774 1065 1.101049 AGGTGTTGGTGGTTGAAGCG 61.101 55.000 0.00 0.00 0.00 4.68
783 1078 2.263741 GGCAGAGCAGGTGTTGGTG 61.264 63.158 0.00 0.00 37.72 4.17
819 1114 9.727627 CAGGATAAGATTGCTTTGTTAATTCTC 57.272 33.333 0.00 0.00 35.56 2.87
871 1174 2.401699 CTGGTGCTGCAAGTGGAGGA 62.402 60.000 2.77 0.00 35.30 3.71
872 1175 1.970114 CTGGTGCTGCAAGTGGAGG 60.970 63.158 2.77 0.00 35.30 4.30
893 1196 1.413077 TCTCTCTGATGCTGATGCTGG 59.587 52.381 0.00 0.00 40.48 4.85
902 1205 4.063689 CTCTCTCTCTCTCTCTCTGATGC 58.936 52.174 0.00 0.00 0.00 3.91
909 1212 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
910 1213 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
911 1214 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
912 1215 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
915 1218 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
916 1219 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
917 1220 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
918 1221 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
919 1222 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
920 1223 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
921 1224 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
922 1225 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
923 1226 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
924 1227 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
925 1228 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
926 1229 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
927 1230 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
928 1231 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
929 1232 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
930 1233 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
931 1234 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
932 1235 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
933 1236 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
934 1237 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
935 1238 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
936 1239 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
937 1240 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
938 1241 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
939 1242 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
940 1243 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
941 1244 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
942 1245 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
943 1246 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
944 1247 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
945 1248 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
946 1249 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
947 1250 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
948 1251 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
949 1252 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
950 1253 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
951 1254 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
952 1255 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
953 1256 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
954 1257 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
955 1258 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
956 1259 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
957 1260 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
958 1261 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
975 1278 1.202330 CAGTGCCCCTCAATCTCTCT 58.798 55.000 0.00 0.00 0.00 3.10
979 1282 0.326264 GTGACAGTGCCCCTCAATCT 59.674 55.000 0.00 0.00 0.00 2.40
982 1285 2.075566 TGGTGACAGTGCCCCTCAA 61.076 57.895 0.00 0.00 35.01 3.02
983 1286 2.447572 TGGTGACAGTGCCCCTCA 60.448 61.111 0.00 0.00 35.01 3.86
1053 1359 6.293407 CCATGGATGAACACGGATAAATACAC 60.293 42.308 5.56 0.00 0.00 2.90
1082 1392 3.118075 TGGAAACAGTGATGACTTGGACA 60.118 43.478 0.00 0.00 35.01 4.02
1095 1405 4.183780 ACAACGTTGTGGATGGAAACAGT 61.184 43.478 31.87 2.69 41.93 3.55
1118 1428 2.044123 ACCCAAATGCTGCTAGTAGC 57.956 50.000 24.26 24.26 43.95 3.58
1119 1429 3.378427 GGAAACCCAAATGCTGCTAGTAG 59.622 47.826 3.05 3.05 0.00 2.57
1120 1430 3.245087 TGGAAACCCAAATGCTGCTAGTA 60.245 43.478 0.00 0.00 0.00 1.82
1121 1431 2.171003 GGAAACCCAAATGCTGCTAGT 58.829 47.619 0.00 0.00 0.00 2.57
1143 1456 7.458397 AGATTTAGTGGTATCTTTGTTGTGGA 58.542 34.615 0.00 0.00 0.00 4.02
1206 1537 1.196354 CAGCTTTGACACAGTGCTAGC 59.804 52.381 8.10 8.10 32.29 3.42
1207 1538 2.487934 ACAGCTTTGACACAGTGCTAG 58.512 47.619 0.00 0.00 32.29 3.42
1241 1584 1.227999 ACGCGCAATGCACTACAGTT 61.228 50.000 5.73 0.00 46.97 3.16
1254 1606 1.974343 AAAGCCCCATAAACGCGCA 60.974 52.632 5.73 0.00 0.00 6.09
1257 1609 1.111277 ATCCAAAGCCCCATAAACGC 58.889 50.000 0.00 0.00 0.00 4.84
1347 1714 5.835819 AGGGAAAGGGAAAGAAGAAGAAAAG 59.164 40.000 0.00 0.00 0.00 2.27
1352 1719 4.105754 ACAGGGAAAGGGAAAGAAGAAG 57.894 45.455 0.00 0.00 0.00 2.85
1427 1823 0.030773 TCACTCACTCACTCGCACAC 59.969 55.000 0.00 0.00 0.00 3.82
1428 1824 0.312102 CTCACTCACTCACTCGCACA 59.688 55.000 0.00 0.00 0.00 4.57
1436 1834 2.620585 CACTCACTCACTCACTCACTCA 59.379 50.000 0.00 0.00 0.00 3.41
1438 1836 2.884012 CTCACTCACTCACTCACTCACT 59.116 50.000 0.00 0.00 0.00 3.41
1474 1872 1.780309 TGAACCTCTTCCCACCAACAT 59.220 47.619 0.00 0.00 0.00 2.71
1494 1892 1.176527 GTGAGCAGAGAGAGCAGAGT 58.823 55.000 0.00 0.00 0.00 3.24
1499 1897 0.536260 ATGGTGTGAGCAGAGAGAGC 59.464 55.000 0.00 0.00 0.00 4.09
1500 1898 1.202279 CGATGGTGTGAGCAGAGAGAG 60.202 57.143 0.00 0.00 0.00 3.20
1503 1901 1.216444 GCGATGGTGTGAGCAGAGA 59.784 57.895 0.00 0.00 0.00 3.10
1646 2047 9.816354 AAATGTGCTGTTAATTTCAGTAAAACT 57.184 25.926 10.52 0.00 35.60 2.66
1668 2069 9.669353 GCTAACACATTGATCCATAAGTAAATG 57.331 33.333 0.00 0.00 0.00 2.32
1680 2081 0.663153 GGGGCGCTAACACATTGATC 59.337 55.000 7.64 0.00 0.00 2.92
1681 2082 0.255890 AGGGGCGCTAACACATTGAT 59.744 50.000 7.64 0.00 0.00 2.57
1683 2084 0.676466 TCAGGGGCGCTAACACATTG 60.676 55.000 7.64 0.00 0.00 2.82
1692 2111 1.205417 CAAATCAAAATCAGGGGCGCT 59.795 47.619 7.64 0.00 0.00 5.92
1694 2113 2.029110 ACACAAATCAAAATCAGGGGCG 60.029 45.455 0.00 0.00 0.00 6.13
1698 2117 4.202243 ACACCCACACAAATCAAAATCAGG 60.202 41.667 0.00 0.00 0.00 3.86
1893 2325 4.200283 CCCTCGTCGAGCTCCTGC 62.200 72.222 17.02 0.00 40.05 4.85
1925 2357 1.218316 GAATCCGAGCGGTCCTTGT 59.782 57.895 9.39 0.00 36.47 3.16
1944 2376 4.430765 GAGCGCGACCGGGAAGAA 62.431 66.667 12.10 0.00 34.32 2.52
2049 2481 2.586792 CTGAAGAAGGGCCCGAGG 59.413 66.667 18.44 0.00 0.00 4.63
2139 2571 1.077429 GGCCGCCTTCTTGGAGAAT 60.077 57.895 0.71 0.00 37.90 2.40
2228 2660 1.605710 TCGTCTTCTTCGTTTCCGACT 59.394 47.619 0.00 0.00 44.13 4.18
2235 2667 1.733399 GCCGCTCGTCTTCTTCGTT 60.733 57.895 0.00 0.00 0.00 3.85
2236 2668 2.126424 GCCGCTCGTCTTCTTCGT 60.126 61.111 0.00 0.00 0.00 3.85
2286 2718 2.100603 GAAGACGACGAGGGCGAG 59.899 66.667 0.00 0.00 41.64 5.03
2291 2723 2.202492 CCAGCGAAGACGACGAGG 60.202 66.667 0.00 0.00 42.66 4.63
2292 2724 2.876645 GCCAGCGAAGACGACGAG 60.877 66.667 0.00 0.00 42.66 4.18
2293 2725 4.753877 CGCCAGCGAAGACGACGA 62.754 66.667 6.06 0.00 42.83 4.20
2532 2980 4.218578 ATCTGCAGCTCCCGCTCG 62.219 66.667 9.47 0.00 45.15 5.03
2649 3098 1.630244 CTTCTTCGCCGGTGCTCTTG 61.630 60.000 11.05 0.00 34.43 3.02
2656 3105 1.080705 CTTCGTCTTCTTCGCCGGT 60.081 57.895 1.90 0.00 0.00 5.28
2679 3128 1.734047 CGAGCTTCGAACTCCTCCTTG 60.734 57.143 16.79 0.00 43.74 3.61
2751 3200 6.319658 TCAGGATTAAAATGTGGAGATTCTGC 59.680 38.462 0.00 0.00 0.00 4.26
2804 3253 8.675504 AGATAAGATTCAGAAGAAAATGCTGTG 58.324 33.333 0.00 0.00 37.29 3.66
2832 3282 6.590068 TGAACCATCATGACCAAAACAAAAT 58.410 32.000 0.00 0.00 0.00 1.82
2834 3284 5.362143 TCTGAACCATCATGACCAAAACAAA 59.638 36.000 0.00 0.00 34.37 2.83
3010 3464 5.463286 TGCATGATCAGAATTTGTTGACAC 58.537 37.500 0.09 0.00 0.00 3.67
3039 3510 7.503521 TGCACAATTACATTCTGTAACTTGA 57.496 32.000 18.35 4.95 44.54 3.02
3040 3511 8.572828 TTTGCACAATTACATTCTGTAACTTG 57.427 30.769 2.06 9.78 44.54 3.16
3041 3512 9.593134 TTTTTGCACAATTACATTCTGTAACTT 57.407 25.926 2.06 0.00 44.54 2.66
3068 3539 1.188863 GGCCTGCACCTGAAATGAAT 58.811 50.000 0.00 0.00 0.00 2.57
3159 3630 3.302347 CTCGACCCTCGCCTGCTTT 62.302 63.158 0.00 0.00 40.21 3.51
3332 3805 2.544721 TGAGACCATCAGGCTTCTTCT 58.455 47.619 0.00 0.00 39.06 2.85
3345 3818 1.123861 AGAGGCTTGCACTGAGACCA 61.124 55.000 0.00 0.00 0.00 4.02
3414 3887 6.646653 CAGATTGTACAGACTACAGAGCAAAA 59.353 38.462 0.00 0.00 0.00 2.44
3505 3990 3.862267 CAGTACATTAGTCAGCACTCAGC 59.138 47.826 0.00 0.00 46.19 4.26
3506 3991 5.124617 TCTCAGTACATTAGTCAGCACTCAG 59.875 44.000 0.00 0.00 33.62 3.35
3507 3992 5.010282 TCTCAGTACATTAGTCAGCACTCA 58.990 41.667 0.00 0.00 33.62 3.41
3508 3993 5.568685 TCTCAGTACATTAGTCAGCACTC 57.431 43.478 0.00 0.00 33.62 3.51
3509 3994 5.478679 AGTTCTCAGTACATTAGTCAGCACT 59.521 40.000 0.00 0.00 36.55 4.40
3510 3995 5.715070 AGTTCTCAGTACATTAGTCAGCAC 58.285 41.667 0.00 0.00 0.00 4.40
3630 4135 1.353694 AGCAAGCCAGATTCCACTCTT 59.646 47.619 0.00 0.00 0.00 2.85
3633 4138 1.542492 CAAGCAAGCCAGATTCCACT 58.458 50.000 0.00 0.00 0.00 4.00
3634 4139 0.108945 GCAAGCAAGCCAGATTCCAC 60.109 55.000 0.00 0.00 0.00 4.02
3681 4186 3.558746 GCTATCATGGGCTAATGCAGTCT 60.559 47.826 0.00 0.00 41.91 3.24
3694 4200 6.704289 TCCTTTGATTTTGAGCTATCATGG 57.296 37.500 0.00 4.65 34.73 3.66
3762 4268 7.646130 CGAGAAGGTGTCTTAGTCTGAATATTC 59.354 40.741 8.60 8.60 36.41 1.75
3801 4309 1.314534 TGCGGCCAGAAATGTGGATG 61.315 55.000 2.24 0.00 40.44 3.51
3802 4310 0.611618 TTGCGGCCAGAAATGTGGAT 60.612 50.000 2.24 0.00 40.44 3.41
3899 4407 9.218440 GACATTCCATTTCAACCATGTATTTTT 57.782 29.630 0.00 0.00 0.00 1.94
3902 4410 6.669154 AGGACATTCCATTTCAACCATGTATT 59.331 34.615 0.00 0.00 39.61 1.89
3910 4418 7.118245 GGATTCAAAAGGACATTCCATTTCAAC 59.882 37.037 0.00 0.00 35.49 3.18
3919 4427 7.687941 TTCTACAGGATTCAAAAGGACATTC 57.312 36.000 0.00 0.00 0.00 2.67
3920 4428 8.655935 AATTCTACAGGATTCAAAAGGACATT 57.344 30.769 0.00 0.00 0.00 2.71
3966 4474 5.437946 TGTGGTATCAAACACTGTTTGGTA 58.562 37.500 26.99 23.35 38.39 3.25
3986 4494 6.698329 TGCTCAATTTCTTTGTTTCTCATGTG 59.302 34.615 0.00 0.00 36.65 3.21
4121 4630 7.704047 GCTCCTTTGATTCAAAGTAATTCCATC 59.296 37.037 28.50 10.30 46.40 3.51
4194 4703 2.902486 TCCTGCTTAGGATGCCTATGAG 59.098 50.000 9.75 0.46 35.87 2.90
4217 4726 4.402793 AGTGGTACTACTAATGCTGTCAGG 59.597 45.833 10.57 0.00 0.00 3.86
4219 4728 6.446781 GTAGTGGTACTACTAATGCTGTCA 57.553 41.667 19.42 0.00 45.70 3.58


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

AutoCloner maintained by Alex Coulton.