Multiple sequence alignment - TraesCS3D01G054100

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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 TraesCS3D01G054100 chr3D 100.000 6428 0 0 1 6428 22275352 22281779 0.000000e+00 11871
1 TraesCS3D01G054100 chr3D 84.828 290 37 4 1292 1575 295885976 295886264 1.050000e-72 285
2 TraesCS3D01G054100 chr3D 80.303 330 42 7 1827 2134 295886516 295886844 1.800000e-55 228
3 TraesCS3D01G054100 chr3D 82.902 193 27 5 3124 3313 258276501 258276690 1.110000e-37 169
4 TraesCS3D01G054100 chr3D 90.179 112 11 0 1572 1683 295886292 295886403 5.190000e-31 147
5 TraesCS3D01G054100 chr3A 92.113 3829 208 48 1720 5515 31956174 31952407 0.000000e+00 5312
6 TraesCS3D01G054100 chr3A 95.983 921 25 5 5515 6428 31952438 31951523 0.000000e+00 1485
7 TraesCS3D01G054100 chr3A 97.044 406 11 1 909 1314 31957016 31956612 0.000000e+00 682
8 TraesCS3D01G054100 chr3A 92.771 249 16 1 1329 1575 31956560 31956312 6.130000e-95 359
9 TraesCS3D01G054100 chr3A 96.581 117 4 0 1572 1688 31956284 31956168 1.830000e-45 195
10 TraesCS3D01G054100 chr3B 93.291 2191 114 17 4268 6428 39458768 39460955 0.000000e+00 3201
11 TraesCS3D01G054100 chr3B 94.195 1292 60 8 1685 2966 39455968 39457254 0.000000e+00 1956
12 TraesCS3D01G054100 chr3B 93.667 1279 62 11 3001 4269 39457258 39458527 0.000000e+00 1895
13 TraesCS3D01G054100 chr3B 90.000 790 35 13 814 1575 39455003 39455776 0.000000e+00 981
14 TraesCS3D01G054100 chr3B 87.563 788 48 15 1 748 39454004 39454781 0.000000e+00 867
15 TraesCS3D01G054100 chr3B 97.368 114 3 0 1572 1685 39455809 39455922 1.830000e-45 195
16 TraesCS3D01G054100 chr1B 92.015 526 33 2 1685 2208 649317065 649317583 0.000000e+00 730
17 TraesCS3D01G054100 chr1B 90.710 549 32 6 1030 1574 649316345 649316878 0.000000e+00 713
18 TraesCS3D01G054100 chr1B 94.737 114 6 0 1572 1685 649316907 649317020 1.840000e-40 178
19 TraesCS3D01G054100 chr5B 82.997 347 45 9 1691 2036 528731404 528731071 1.050000e-77 302
20 TraesCS3D01G054100 chr5B 83.420 193 26 5 3124 3313 700926178 700925989 2.380000e-39 174
21 TraesCS3D01G054100 chr5B 89.474 114 11 1 1572 1685 528738971 528738859 6.720000e-30 143
22 TraesCS3D01G054100 chr6D 87.817 197 24 0 1379 1575 69910482 69910678 1.390000e-56 231
23 TraesCS3D01G054100 chr1A 84.456 193 24 5 3124 3313 13965714 13965903 1.100000e-42 185
24 TraesCS3D01G054100 chr7D 83.938 193 25 5 3124 3313 578159328 578159517 5.120000e-41 180
25 TraesCS3D01G054100 chr5A 83.938 193 25 5 3124 3313 425484169 425483980 5.120000e-41 180
26 TraesCS3D01G054100 chr6B 82.902 193 27 5 3124 3313 21848046 21848235 1.110000e-37 169


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 TraesCS3D01G054100 chr3D 22275352 22281779 6427 False 11871.000000 11871 100.000000 1 6428 1 chr3D.!!$F1 6427
1 TraesCS3D01G054100 chr3D 295885976 295886844 868 False 220.000000 285 85.103333 1292 2134 3 chr3D.!!$F3 842
2 TraesCS3D01G054100 chr3A 31951523 31957016 5493 True 1606.600000 5312 94.898400 909 6428 5 chr3A.!!$R1 5519
3 TraesCS3D01G054100 chr3B 39454004 39460955 6951 False 1515.833333 3201 92.680667 1 6428 6 chr3B.!!$F1 6427
4 TraesCS3D01G054100 chr1B 649316345 649317583 1238 False 540.333333 730 92.487333 1030 2208 3 chr1B.!!$F1 1178

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
468 496 0.033601 AAGTTGGCACAGGGAACACA 60.034 50.000 0.00 0.0 42.39 3.72 F
799 1024 0.102481 TTCTCGCGAGGAAGCATACC 59.898 55.000 33.98 0.0 36.85 2.73 F
809 1034 0.252197 GAAGCATACCCAGGGAACGT 59.748 55.000 14.54 0.0 0.00 3.99 F
810 1035 0.696501 AAGCATACCCAGGGAACGTT 59.303 50.000 14.54 0.0 0.00 3.99 F
1327 1572 0.753262 AATCCAATAGCTCGCCGTCT 59.247 50.000 0.00 0.0 0.00 4.18 F
1329 1574 1.617322 TCCAATAGCTCGCCGTCTAT 58.383 50.000 0.00 0.0 0.00 1.98 F
2912 3333 1.933765 ACCACTCCTCTCTATCCTGGT 59.066 52.381 0.00 0.0 0.00 4.00 F
3254 3678 1.003223 GCAGAAAAACGGTACTTGCGT 60.003 47.619 0.00 0.0 0.00 5.24 F
4485 5161 0.251077 CCAGCTGCAAACTTCTCCCT 60.251 55.000 8.66 0.0 0.00 4.20 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2009 2400 0.106708 TATCAGGCCATCGTTCCAGC 59.893 55.000 5.01 0.00 0.00 4.85 R
2013 2404 3.393089 AGATGTATCAGGCCATCGTTC 57.607 47.619 5.01 0.00 41.81 3.95 R
2539 2958 5.011635 TCAGCACAGACAAAGTAGGTGATTA 59.988 40.000 0.00 0.00 0.00 1.75 R
2555 2974 5.293814 CAGAAGAGGATTTACATCAGCACAG 59.706 44.000 0.00 0.00 0.00 3.66 R
2921 3342 0.703488 TCCCCAATGATGCAAGTGGA 59.297 50.000 6.45 0.00 32.54 4.02 R
3224 3648 2.520979 CGTTTTTCTGCGGTTTCACAA 58.479 42.857 0.00 0.00 0.00 3.33 R
4369 5044 0.250209 ATCGATGCCAGTGCCTCATC 60.250 55.000 0.00 7.69 36.33 2.92 R
4601 5308 1.364901 CAAGGCAACCACCAGCAAG 59.635 57.895 0.00 0.00 37.17 4.01 R
6102 6818 0.249073 GTGACATCGATCCCACGGAG 60.249 60.000 9.96 0.00 34.05 4.63 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
34 35 1.180029 AACTTGCAGCTAGCCCAATG 58.820 50.000 12.13 4.00 44.83 2.82
68 69 1.003233 GGTTCCTCACGTCCTTGGAAT 59.997 52.381 10.08 0.00 40.20 3.01
77 78 5.601662 TCACGTCCTTGGAATCATCTTATC 58.398 41.667 0.00 0.00 0.00 1.75
100 101 7.177498 TCATATGACGAAATTGACACATAGC 57.823 36.000 0.00 0.00 0.00 2.97
101 102 6.760770 TCATATGACGAAATTGACACATAGCA 59.239 34.615 0.00 0.00 0.00 3.49
102 103 4.661993 TGACGAAATTGACACATAGCAC 57.338 40.909 0.00 0.00 0.00 4.40
103 104 3.435327 TGACGAAATTGACACATAGCACC 59.565 43.478 0.00 0.00 0.00 5.01
137 147 1.154413 GTTGTGCCGCATCGTTCTG 60.154 57.895 0.00 0.00 0.00 3.02
138 148 2.324330 TTGTGCCGCATCGTTCTGG 61.324 57.895 0.00 0.00 0.00 3.86
141 151 3.127533 GCCGCATCGTTCTGGCTT 61.128 61.111 4.65 0.00 44.16 4.35
149 176 3.375299 GCATCGTTCTGGCTTTCAATACT 59.625 43.478 0.00 0.00 0.00 2.12
265 293 4.632538 AGTTTTGCTAATATTCCACCGC 57.367 40.909 0.00 0.00 0.00 5.68
285 313 7.860872 CCACCGCAAACCTATTTTCTAATATTC 59.139 37.037 0.00 0.00 0.00 1.75
321 349 3.086282 GGTACCCAAACAACCATAGTGG 58.914 50.000 0.00 0.00 45.02 4.00
338 366 3.123273 AGTGGTAGAGGTATGCCCAATT 58.877 45.455 0.00 0.00 34.66 2.32
339 367 3.527665 AGTGGTAGAGGTATGCCCAATTT 59.472 43.478 0.00 0.00 34.66 1.82
340 368 4.724798 AGTGGTAGAGGTATGCCCAATTTA 59.275 41.667 0.00 0.00 34.66 1.40
341 369 5.192923 AGTGGTAGAGGTATGCCCAATTTAA 59.807 40.000 0.00 0.00 34.66 1.52
342 370 6.068670 GTGGTAGAGGTATGCCCAATTTAAT 58.931 40.000 0.00 0.00 34.66 1.40
379 407 0.667993 TGCTGCAACACCACTTAAGC 59.332 50.000 0.00 0.00 0.00 3.09
380 408 0.039165 GCTGCAACACCACTTAAGCC 60.039 55.000 1.29 0.00 0.00 4.35
388 416 3.778265 ACACCACTTAAGCCAATTGGAT 58.222 40.909 29.02 20.48 38.88 3.41
405 433 6.661304 ATTGGATTTTCCCATCTAAGCATC 57.339 37.500 0.00 0.00 35.03 3.91
406 434 4.473444 TGGATTTTCCCATCTAAGCATCC 58.527 43.478 0.00 0.00 35.03 3.51
411 439 1.494721 TCCCATCTAAGCATCCCCAAC 59.505 52.381 0.00 0.00 0.00 3.77
422 450 0.039180 ATCCCCAACGGTTTCCCTTC 59.961 55.000 0.00 0.00 0.00 3.46
423 451 1.151908 CCCCAACGGTTTCCCTTCA 59.848 57.895 0.00 0.00 0.00 3.02
428 456 0.109913 AACGGTTTCCCTTCACCCTC 59.890 55.000 0.00 0.00 0.00 4.30
462 490 2.286365 TAGGAAAAGTTGGCACAGGG 57.714 50.000 0.00 0.00 42.39 4.45
468 496 0.033601 AAGTTGGCACAGGGAACACA 60.034 50.000 0.00 0.00 42.39 3.72
501 529 7.179269 AGCTCCTGTATACCCAAAATGTTTTA 58.821 34.615 0.00 0.00 0.00 1.52
525 554 2.095213 TGATCACTAAAAATCACCGCGC 59.905 45.455 0.00 0.00 0.00 6.86
534 563 2.535485 AATCACCGCGCCCATCTTCA 62.535 55.000 0.00 0.00 0.00 3.02
569 598 1.661463 ATGTTGAGCTCCCTTCCTCA 58.339 50.000 12.15 0.54 36.38 3.86
579 608 1.199615 CCCTTCCTCACCTCTTCCTC 58.800 60.000 0.00 0.00 0.00 3.71
580 609 1.199615 CCTTCCTCACCTCTTCCTCC 58.800 60.000 0.00 0.00 0.00 4.30
581 610 1.273552 CCTTCCTCACCTCTTCCTCCT 60.274 57.143 0.00 0.00 0.00 3.69
582 611 2.023888 CCTTCCTCACCTCTTCCTCCTA 60.024 54.545 0.00 0.00 0.00 2.94
588 617 3.699038 CTCACCTCTTCCTCCTAGTTGAG 59.301 52.174 0.00 0.00 0.00 3.02
606 635 2.276740 CTCCCCATGGAAGCCACC 59.723 66.667 15.22 0.00 41.17 4.61
613 642 2.003548 ATGGAAGCCACCCCTCCTC 61.004 63.158 0.00 0.00 35.80 3.71
622 651 1.869452 ACCCCTCCTCCTCCTCCTT 60.869 63.158 0.00 0.00 0.00 3.36
650 691 2.364186 TGCTCGAGCTCCCCATGA 60.364 61.111 35.27 12.31 42.66 3.07
661 702 0.695924 TCCCCATGAACCAACGTGAT 59.304 50.000 0.00 0.00 0.00 3.06
667 708 2.631160 TGAACCAACGTGATGACCTT 57.369 45.000 0.00 0.00 0.00 3.50
668 709 2.217750 TGAACCAACGTGATGACCTTG 58.782 47.619 0.00 0.00 0.00 3.61
677 718 2.009774 GTGATGACCTTGTTGGATCCG 58.990 52.381 7.39 0.00 39.71 4.18
679 720 0.744414 ATGACCTTGTTGGATCCGCG 60.744 55.000 7.39 0.00 39.71 6.46
716 757 2.971413 GCGCATGCTGGCTCTAGG 60.971 66.667 17.13 0.00 38.39 3.02
748 789 1.629043 GGTAGCCACCGATGAGGATA 58.371 55.000 0.00 0.00 45.00 2.59
775 1000 3.193691 GGATATATGGTCCTGTCGGTGAG 59.806 52.174 0.00 0.00 32.85 3.51
776 1001 1.414158 ATATGGTCCTGTCGGTGAGG 58.586 55.000 0.00 0.00 0.00 3.86
777 1002 0.333652 TATGGTCCTGTCGGTGAGGA 59.666 55.000 0.00 0.00 37.27 3.71
780 1005 4.865629 TCCTGTCGGTGAGGACAT 57.134 55.556 0.00 0.00 45.23 3.06
781 1006 3.067011 TCCTGTCGGTGAGGACATT 57.933 52.632 0.00 0.00 45.23 2.71
782 1007 0.895530 TCCTGTCGGTGAGGACATTC 59.104 55.000 0.00 0.00 45.23 2.67
783 1008 0.898320 CCTGTCGGTGAGGACATTCT 59.102 55.000 0.00 0.00 45.23 2.40
786 1011 0.802607 GTCGGTGAGGACATTCTCGC 60.803 60.000 0.00 0.00 41.95 5.03
788 1013 1.511305 GGTGAGGACATTCTCGCGA 59.489 57.895 9.26 9.26 43.17 5.87
789 1014 0.526524 GGTGAGGACATTCTCGCGAG 60.527 60.000 30.03 30.03 43.17 5.03
790 1015 0.526524 GTGAGGACATTCTCGCGAGG 60.527 60.000 33.98 21.22 36.61 4.63
791 1016 0.679960 TGAGGACATTCTCGCGAGGA 60.680 55.000 33.98 28.47 36.61 3.71
792 1017 0.456221 GAGGACATTCTCGCGAGGAA 59.544 55.000 33.98 25.34 0.00 3.36
793 1018 0.457851 AGGACATTCTCGCGAGGAAG 59.542 55.000 33.98 26.07 0.00 3.46
794 1019 1.148759 GGACATTCTCGCGAGGAAGC 61.149 60.000 33.98 19.13 0.00 3.86
795 1020 0.458543 GACATTCTCGCGAGGAAGCA 60.459 55.000 33.98 13.46 36.85 3.91
796 1021 0.176680 ACATTCTCGCGAGGAAGCAT 59.823 50.000 33.98 16.14 36.85 3.79
797 1022 1.409064 ACATTCTCGCGAGGAAGCATA 59.591 47.619 33.98 11.88 36.85 3.14
798 1023 1.789464 CATTCTCGCGAGGAAGCATAC 59.211 52.381 33.98 0.00 36.85 2.39
799 1024 0.102481 TTCTCGCGAGGAAGCATACC 59.898 55.000 33.98 0.00 36.85 2.73
800 1025 1.300233 CTCGCGAGGAAGCATACCC 60.300 63.158 28.40 0.00 36.85 3.69
801 1026 2.016393 CTCGCGAGGAAGCATACCCA 62.016 60.000 28.40 0.00 36.85 4.51
802 1027 1.592669 CGCGAGGAAGCATACCCAG 60.593 63.158 0.00 0.00 36.85 4.45
803 1028 1.227674 GCGAGGAAGCATACCCAGG 60.228 63.158 0.00 0.00 37.05 4.45
804 1029 1.447643 CGAGGAAGCATACCCAGGG 59.552 63.158 2.85 2.85 0.00 4.45
805 1030 1.048724 CGAGGAAGCATACCCAGGGA 61.049 60.000 14.54 0.00 0.00 4.20
806 1031 1.213296 GAGGAAGCATACCCAGGGAA 58.787 55.000 14.54 0.00 0.00 3.97
807 1032 0.919710 AGGAAGCATACCCAGGGAAC 59.080 55.000 14.54 0.00 0.00 3.62
808 1033 0.463833 GGAAGCATACCCAGGGAACG 60.464 60.000 14.54 0.00 0.00 3.95
809 1034 0.252197 GAAGCATACCCAGGGAACGT 59.748 55.000 14.54 0.00 0.00 3.99
810 1035 0.696501 AAGCATACCCAGGGAACGTT 59.303 50.000 14.54 0.00 0.00 3.99
811 1036 0.696501 AGCATACCCAGGGAACGTTT 59.303 50.000 14.54 0.00 0.00 3.60
812 1037 0.808755 GCATACCCAGGGAACGTTTG 59.191 55.000 14.54 0.00 0.00 2.93
813 1038 1.459450 CATACCCAGGGAACGTTTGG 58.541 55.000 14.54 10.05 0.00 3.28
814 1039 1.069775 ATACCCAGGGAACGTTTGGT 58.930 50.000 14.54 12.54 33.99 3.67
815 1040 0.845337 TACCCAGGGAACGTTTGGTT 59.155 50.000 14.54 4.99 42.96 3.67
852 1077 0.940126 CCGGCCTGATTCAAGATTCG 59.060 55.000 0.00 0.00 0.00 3.34
869 1094 7.170151 TCAAGATTCGTGTTTTCTATTTGACGA 59.830 33.333 0.00 0.00 34.27 4.20
879 1104 2.066262 CTATTTGACGACTGTTGGCGT 58.934 47.619 0.00 0.00 44.33 5.68
884 1109 2.142418 GACGACTGTTGGCGTGTTCG 62.142 60.000 0.37 0.00 41.34 3.95
931 1165 7.479150 ACGTAACATTTCCGTTTTTAAAAGGA 58.521 30.769 11.11 5.88 43.29 3.36
999 1237 1.522092 CGCTGCCTATCCTTCCACA 59.478 57.895 0.00 0.00 0.00 4.17
1025 1263 2.722201 CCTACCCACCGGTCAGCTC 61.722 68.421 2.59 0.00 43.29 4.09
1026 1264 3.064987 CTACCCACCGGTCAGCTCG 62.065 68.421 2.59 0.00 43.29 5.03
1050 1291 4.783621 GGCACCGGAGCATGCTCA 62.784 66.667 40.37 0.00 44.40 4.26
1221 1466 4.802039 CCGCAATTTCTCATTTTGATGGAG 59.198 41.667 0.00 0.00 0.00 3.86
1320 1565 7.271511 TCTTCTCTTCTGAAATCCAATAGCTC 58.728 38.462 0.00 0.00 0.00 4.09
1321 1566 5.595885 TCTCTTCTGAAATCCAATAGCTCG 58.404 41.667 0.00 0.00 0.00 5.03
1322 1567 4.122776 TCTTCTGAAATCCAATAGCTCGC 58.877 43.478 0.00 0.00 0.00 5.03
1323 1568 2.838736 TCTGAAATCCAATAGCTCGCC 58.161 47.619 0.00 0.00 0.00 5.54
1327 1572 0.753262 AATCCAATAGCTCGCCGTCT 59.247 50.000 0.00 0.00 0.00 4.18
1329 1574 1.617322 TCCAATAGCTCGCCGTCTAT 58.383 50.000 0.00 0.00 0.00 1.98
1332 1577 3.570975 TCCAATAGCTCGCCGTCTATTTA 59.429 43.478 10.13 2.63 34.33 1.40
1381 1680 6.782082 AGAGTTATCAAGTCTGTATCTGCA 57.218 37.500 0.00 0.00 39.66 4.41
1384 1684 6.701340 AGTTATCAAGTCTGTATCTGCAACA 58.299 36.000 0.00 0.00 0.00 3.33
1478 1782 4.080186 TGGGAGAAGCATGATGAATCTTCA 60.080 41.667 11.88 1.23 42.14 3.02
1480 1784 5.221009 GGGAGAAGCATGATGAATCTTCAAC 60.221 44.000 11.88 0.00 41.13 3.18
1502 1806 4.750098 ACGAACACTGTCGAAGATGAAAAT 59.250 37.500 1.02 0.00 43.86 1.82
1505 1809 3.814842 ACACTGTCGAAGATGAAAATGCA 59.185 39.130 0.00 0.00 40.67 3.96
1707 2093 3.944015 ACTGCCAAATGTAGAGCTTGATC 59.056 43.478 0.00 0.00 0.00 2.92
1710 2096 5.012239 TGCCAAATGTAGAGCTTGATCTTT 58.988 37.500 0.00 0.00 0.00 2.52
1752 2138 4.597404 TCTCTCAGTATGCTGCATAAGG 57.403 45.455 22.82 17.20 42.29 2.69
1879 2267 3.680490 TGTTTCGGATGATTACCTGCAA 58.320 40.909 0.00 0.00 0.00 4.08
1930 2318 2.259917 ACAGGATGGATCTGTCACACA 58.740 47.619 0.00 0.00 41.10 3.72
1960 2348 4.593206 ACATCAAGTCTTCTGAAGGTACCA 59.407 41.667 15.94 0.00 0.00 3.25
1963 2351 4.058817 CAAGTCTTCTGAAGGTACCACAC 58.941 47.826 15.94 5.38 0.00 3.82
2003 2394 9.846248 AGATGTTTGCAGAAGTAAATAATGTTC 57.154 29.630 0.00 0.00 32.00 3.18
2013 2404 9.125026 AGAAGTAAATAATGTTCTATTGGCTGG 57.875 33.333 0.00 0.00 0.00 4.85
2106 2519 2.084610 GGCTTCAAGATTTTGCCACC 57.915 50.000 0.00 0.00 42.79 4.61
2122 2535 2.787994 CCACCTGCTCTCAAACAATCT 58.212 47.619 0.00 0.00 0.00 2.40
2313 2727 5.882000 GGCTATTAGAAACCCGGAACTTTAA 59.118 40.000 0.73 0.00 0.00 1.52
2390 2806 9.905713 TTAGCTACTATGTTTCATCCTGATTTT 57.094 29.630 0.00 0.00 0.00 1.82
2397 2813 6.435430 TGTTTCATCCTGATTTTATCACCG 57.565 37.500 0.00 0.00 35.06 4.94
2487 2906 4.013728 GGCACATACCAACATCCTAACAA 58.986 43.478 0.00 0.00 0.00 2.83
2492 2911 7.416664 GCACATACCAACATCCTAACAATCAAT 60.417 37.037 0.00 0.00 0.00 2.57
2539 2958 3.758554 AGCTCATTTTATGCTCGTGGTTT 59.241 39.130 0.00 0.00 30.41 3.27
2555 2974 5.697633 TCGTGGTTTAATCACCTACTTTGTC 59.302 40.000 2.49 0.00 37.75 3.18
2662 3081 6.624352 TGCCTGACTATTTATTCAGAATGC 57.376 37.500 5.85 0.00 41.65 3.56
2792 3213 3.674997 TGGAAGGTTCATGCACTAACTC 58.325 45.455 11.57 4.14 0.00 3.01
2794 3215 3.686726 GGAAGGTTCATGCACTAACTCTG 59.313 47.826 11.57 0.00 0.00 3.35
2795 3216 4.319177 GAAGGTTCATGCACTAACTCTGT 58.681 43.478 11.57 0.00 0.00 3.41
2796 3217 4.357918 AGGTTCATGCACTAACTCTGTT 57.642 40.909 11.57 0.00 0.00 3.16
2798 3219 5.865085 AGGTTCATGCACTAACTCTGTTAA 58.135 37.500 11.57 0.00 0.00 2.01
2799 3220 6.296026 AGGTTCATGCACTAACTCTGTTAAA 58.704 36.000 11.57 0.00 0.00 1.52
2800 3221 6.942576 AGGTTCATGCACTAACTCTGTTAAAT 59.057 34.615 11.57 0.00 0.00 1.40
2801 3222 8.100791 AGGTTCATGCACTAACTCTGTTAAATA 58.899 33.333 11.57 0.00 0.00 1.40
2912 3333 1.933765 ACCACTCCTCTCTATCCTGGT 59.066 52.381 0.00 0.00 0.00 4.00
2921 3342 5.043281 TCCTCTCTATCCTGGTTACTTCCTT 60.043 44.000 0.00 0.00 0.00 3.36
2966 3387 7.225784 TCTTGCAAAGGTATATTGAAAGCAA 57.774 32.000 0.00 0.00 46.24 3.91
2967 3388 7.515957 CTTGCAAAGGTATATTGAAAGCAAG 57.484 36.000 0.00 0.00 46.64 4.01
2968 3389 6.832520 TGCAAAGGTATATTGAAAGCAAGA 57.167 33.333 0.00 0.00 37.45 3.02
2969 3390 6.620678 TGCAAAGGTATATTGAAAGCAAGAC 58.379 36.000 0.00 0.00 37.45 3.01
2970 3391 6.208402 TGCAAAGGTATATTGAAAGCAAGACA 59.792 34.615 0.00 0.00 37.45 3.41
2971 3392 7.093814 TGCAAAGGTATATTGAAAGCAAGACAT 60.094 33.333 0.00 0.00 37.45 3.06
2972 3393 8.405531 GCAAAGGTATATTGAAAGCAAGACATA 58.594 33.333 0.00 0.00 37.45 2.29
2984 3405 9.679661 TGAAAGCAAGACATATTAATCCTTACA 57.320 29.630 0.00 0.00 0.00 2.41
3011 3432 9.616156 TTTAGTTTCACATGTGACTAAAACCTA 57.384 29.630 31.11 21.34 39.66 3.08
3016 3437 6.822442 TCACATGTGACTAAAACCTAACTCA 58.178 36.000 24.56 0.00 34.14 3.41
3037 3458 4.021016 TCAAACTTTGTAGAGAGCTCCCTC 60.021 45.833 10.93 1.96 38.42 4.30
3064 3485 7.651808 ACACAAAATAATTGACTCTGGACTTG 58.348 34.615 0.00 0.00 0.00 3.16
3224 3648 6.998074 TCAGTGTCCTATTGTTCAGTCAATTT 59.002 34.615 0.00 0.00 38.68 1.82
3243 3667 4.912528 TTTTGTGAAACCGCAGAAAAAC 57.087 36.364 0.00 0.00 37.86 2.43
3253 3677 1.670326 GCAGAAAAACGGTACTTGCG 58.330 50.000 0.00 0.00 0.00 4.85
3254 3678 1.003223 GCAGAAAAACGGTACTTGCGT 60.003 47.619 0.00 0.00 0.00 5.24
3255 3679 2.221517 GCAGAAAAACGGTACTTGCGTA 59.778 45.455 0.00 0.00 0.00 4.42
3257 3681 3.062042 AGAAAAACGGTACTTGCGTAGG 58.938 45.455 0.00 0.00 0.00 3.18
3259 3683 2.818130 AAACGGTACTTGCGTAGGAA 57.182 45.000 0.00 0.00 35.74 3.36
3306 3733 5.321927 TCCAATAGTTCCTTTGGAGTTTCC 58.678 41.667 0.37 0.00 44.92 3.13
3313 3740 4.292186 TCCTTTGGAGTTTCCTGATCAG 57.708 45.455 16.24 16.24 37.46 2.90
3322 3749 5.096443 AGTTTCCTGATCAGATGGACTTC 57.904 43.478 24.62 6.90 0.00 3.01
3324 3751 4.750021 TTCCTGATCAGATGGACTTCAG 57.250 45.455 24.62 3.19 34.83 3.02
3326 3753 4.356436 TCCTGATCAGATGGACTTCAGAA 58.644 43.478 24.62 0.00 36.25 3.02
3351 3778 9.941325 AATTCTTTCATTATGCACCATTAAACA 57.059 25.926 0.00 0.00 0.00 2.83
3414 3841 5.006386 TGCAAAATTTTCACCAACCAACTT 58.994 33.333 0.00 0.00 0.00 2.66
3422 3849 9.892130 AATTTTCACCAACCAACTTTTATGTAA 57.108 25.926 0.00 0.00 0.00 2.41
3476 3903 3.115390 TCAGCTGGTAGGCCTTTCTATT 58.885 45.455 12.58 0.00 35.27 1.73
3538 3965 9.462606 CTCTTTATTTGTAATAACCAACCTCCT 57.537 33.333 0.00 0.00 0.00 3.69
3625 4054 4.833380 ACGCCAGGTATACAGTCTTCATAT 59.167 41.667 5.01 0.00 0.00 1.78
3782 4211 3.976169 TGTTTGCACTTTTAGACCATGC 58.024 40.909 0.00 0.00 36.81 4.06
3792 4221 5.539955 ACTTTTAGACCATGCATTTTCACCT 59.460 36.000 0.00 0.00 0.00 4.00
3848 4277 7.830739 AGTTTTTGATTCATCGCCTTTATTCT 58.169 30.769 0.00 0.00 0.00 2.40
3859 4288 5.352284 TCGCCTTTATTCTCTCTTCATGTC 58.648 41.667 0.00 0.00 0.00 3.06
3868 4297 9.935241 TTATTCTCTCTTCATGTCTATATTGGC 57.065 33.333 0.00 0.00 0.00 4.52
3961 4390 8.902806 ACATGTTCTTCACTTCTTGATTTTACA 58.097 29.630 0.00 0.00 32.84 2.41
4066 4496 9.408648 GAGGAAGAGAATATTTTAACATGGGAA 57.591 33.333 0.00 0.00 0.00 3.97
4081 4511 3.243359 TGGGAAAGATTCTTGCAACCT 57.757 42.857 6.72 0.00 0.00 3.50
4239 4669 6.749118 GGTTCTTGACTTCATCATTACAATGC 59.251 38.462 0.00 0.00 37.11 3.56
4262 4692 5.221048 GCTTTTTGTAGTTGAGCTTCCTTGA 60.221 40.000 0.00 0.00 0.00 3.02
4290 4962 5.888982 AGTAGAACTGAAGGGACAAAAGA 57.111 39.130 0.00 0.00 0.00 2.52
4350 5025 8.033038 TGTATAGTCATAACAACTGTTGGACTC 58.967 37.037 23.90 15.21 43.75 3.36
4369 5044 2.671396 CTCGTCCAACACCTAATTTCCG 59.329 50.000 0.00 0.00 0.00 4.30
4474 5150 4.393155 CCTACCACGCCAGCTGCA 62.393 66.667 8.66 0.00 41.33 4.41
4485 5161 0.251077 CCAGCTGCAAACTTCTCCCT 60.251 55.000 8.66 0.00 0.00 4.20
4486 5162 0.879765 CAGCTGCAAACTTCTCCCTG 59.120 55.000 0.00 0.00 0.00 4.45
4536 5240 6.984740 TTTTTGCATCAAAGATGACGTAAC 57.015 33.333 10.95 0.00 38.69 2.50
4578 5285 3.916035 ACCAGCTGTATCATAGTCTGGA 58.084 45.455 13.81 0.00 39.60 3.86
4585 5292 6.382570 AGCTGTATCATAGTCTGGAAGAGTTT 59.617 38.462 0.00 0.00 46.68 2.66
4601 5308 4.327680 AGAGTTTAAATCACCAGAGCCAC 58.672 43.478 0.00 0.00 0.00 5.01
4621 5328 4.347453 GCTGGTGGTTGCCTTGCG 62.347 66.667 0.00 0.00 0.00 4.85
4691 5400 1.298157 TACCACTTGCTCATGCGTGC 61.298 55.000 0.00 0.00 43.34 5.34
4774 5483 0.395586 TGTGTTGAGCAGCTTGGGTT 60.396 50.000 0.00 0.00 0.00 4.11
4811 5520 5.772393 ACCTGGTTACATTCAAGGTGATA 57.228 39.130 0.00 0.00 0.00 2.15
4847 5557 8.061857 ACATCTGTGTATGAAAATAATTACGCG 58.938 33.333 3.53 3.53 36.63 6.01
4891 5601 1.152860 TTTTCAGGAGGCGGCAACA 60.153 52.632 13.08 0.00 0.00 3.33
4947 5657 1.215382 GGCTTCACCAAAATCGGCC 59.785 57.895 0.00 0.00 38.86 6.13
4965 5675 2.853914 GAAGCAGGACGACGTTGC 59.146 61.111 15.19 15.19 0.00 4.17
5065 5775 5.579047 TGGGATCAAAGCCAAATCTTCTTA 58.421 37.500 0.00 0.00 0.00 2.10
5206 5917 2.075338 CTGAAGCTCAAAGCCTCTGAC 58.925 52.381 0.00 0.00 43.77 3.51
5266 5977 4.035441 GCAAGAAACATTGTTTGGCATGTT 59.965 37.500 19.03 0.00 38.71 2.71
5330 6041 7.359598 GGTTAATCTAGCATTATTCAGCAGTCG 60.360 40.741 0.00 0.00 0.00 4.18
5384 6096 5.461407 CCAGTGACATAATCTCAGTCATTCG 59.539 44.000 0.00 0.00 43.35 3.34
5420 6132 6.003950 ACTGTTGTCCATGTTGCTATAGTTT 58.996 36.000 0.84 0.00 0.00 2.66
5422 6134 4.963276 TGTCCATGTTGCTATAGTTTGC 57.037 40.909 0.84 0.00 0.00 3.68
5435 6147 6.538742 TGCTATAGTTTGCTACTTTGCTTAGG 59.461 38.462 0.84 0.00 38.33 2.69
5440 6152 6.882140 TAGTTTGCTACTTTGCTTAGGCATAA 59.118 34.615 0.00 0.00 42.14 1.90
5489 6201 2.708216 TGGACAAGAAGCAGACAACA 57.292 45.000 0.00 0.00 0.00 3.33
5500 6212 4.782019 AGCAGACAACAAACACTGAAAA 57.218 36.364 0.00 0.00 32.90 2.29
5507 6219 7.220683 CAGACAACAAACACTGAAAAACATAGG 59.779 37.037 0.00 0.00 32.90 2.57
5542 6254 3.439857 ACACTGAAACACATAGGGCAT 57.560 42.857 0.00 0.00 0.00 4.40
5666 6380 6.806739 GGATTCAAAAGCAACACATACCTAAC 59.193 38.462 0.00 0.00 0.00 2.34
5691 6405 9.066892 ACTCTAAATGTTTGTTGCTTAAGATGA 57.933 29.630 6.67 0.00 0.00 2.92
5967 6683 0.739462 TTGCCGTATGAGTGAAGCGG 60.739 55.000 0.00 0.00 44.60 5.52
6102 6818 1.621672 CCTTCTGGCTGGTCCTCTCC 61.622 65.000 0.00 0.00 35.26 3.71
6121 6837 0.249073 CTCCGTGGGATCGATGTCAC 60.249 60.000 0.54 10.01 0.00 3.67
6153 6869 3.006752 TCCAAATGAAAATGGACCTGCAC 59.993 43.478 0.00 0.00 40.74 4.57
6154 6870 3.244146 CCAAATGAAAATGGACCTGCACA 60.244 43.478 0.00 0.00 39.12 4.57
6187 6903 5.752650 TCGTAAGGGTGAAGAAGATCTAGA 58.247 41.667 0.00 0.00 38.47 2.43
6188 6904 6.366340 TCGTAAGGGTGAAGAAGATCTAGAT 58.634 40.000 4.47 4.47 38.47 1.98
6190 6906 6.920758 CGTAAGGGTGAAGAAGATCTAGATTG 59.079 42.308 6.70 0.00 0.00 2.67
6219 6940 4.955811 TGCTGGGTAAATACAGATCGAT 57.044 40.909 0.00 0.00 36.86 3.59
6242 6963 3.097614 GGTCTACCTTGAGCTTCCTGTA 58.902 50.000 0.00 0.00 0.00 2.74
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
34 35 3.652869 TGAGGAACCATGGAGGAATATCC 59.347 47.826 21.47 13.02 41.22 2.59
68 69 9.762933 TGTCAATTTCGTCATATGATAAGATGA 57.237 29.630 9.02 11.02 0.00 2.92
77 78 6.847792 GTGCTATGTGTCAATTTCGTCATATG 59.152 38.462 0.00 0.00 0.00 1.78
99 100 3.408634 ACCACACAAGTAACATAGGTGC 58.591 45.455 0.00 0.00 32.89 5.01
100 101 4.819630 ACAACCACACAAGTAACATAGGTG 59.180 41.667 0.00 0.00 35.66 4.00
101 102 4.819630 CACAACCACACAAGTAACATAGGT 59.180 41.667 0.00 0.00 0.00 3.08
102 103 4.320202 GCACAACCACACAAGTAACATAGG 60.320 45.833 0.00 0.00 0.00 2.57
103 104 4.320202 GGCACAACCACACAAGTAACATAG 60.320 45.833 0.00 0.00 38.86 2.23
250 278 2.949644 AGGTTTGCGGTGGAATATTAGC 59.050 45.455 0.00 0.00 0.00 3.09
255 283 5.258051 AGAAAATAGGTTTGCGGTGGAATA 58.742 37.500 0.00 0.00 0.00 1.75
315 343 3.630625 TGGGCATACCTCTACCACTAT 57.369 47.619 0.00 0.00 41.11 2.12
316 344 3.408157 TTGGGCATACCTCTACCACTA 57.592 47.619 0.00 0.00 41.11 2.74
321 349 7.447238 TGCTAATTAAATTGGGCATACCTCTAC 59.553 37.037 0.00 0.00 41.11 2.59
379 407 5.129155 TGCTTAGATGGGAAAATCCAATTGG 59.871 40.000 19.08 19.08 40.62 3.16
380 408 6.224665 TGCTTAGATGGGAAAATCCAATTG 57.775 37.500 0.00 0.00 40.62 2.32
388 416 2.584965 TGGGGATGCTTAGATGGGAAAA 59.415 45.455 0.00 0.00 0.00 2.29
422 450 2.292828 ATCAGGGTTTGTTGAGGGTG 57.707 50.000 0.00 0.00 0.00 4.61
423 451 4.166144 CCTATATCAGGGTTTGTTGAGGGT 59.834 45.833 0.00 0.00 41.26 4.34
428 456 7.703058 ACTTTTCCTATATCAGGGTTTGTTG 57.297 36.000 0.00 0.00 45.58 3.33
448 476 1.111277 GTGTTCCCTGTGCCAACTTT 58.889 50.000 0.00 0.00 0.00 2.66
517 546 3.700970 TGAAGATGGGCGCGGTGA 61.701 61.111 8.83 0.00 0.00 4.02
522 551 1.941668 GCTATAGGTGAAGATGGGCGC 60.942 57.143 0.00 0.00 0.00 6.53
525 554 4.780021 ACCTATGCTATAGGTGAAGATGGG 59.220 45.833 20.42 1.21 45.56 4.00
569 598 2.043801 AGCTCAACTAGGAGGAAGAGGT 59.956 50.000 0.00 0.00 35.41 3.85
579 608 0.471617 CCATGGGGAGCTCAACTAGG 59.528 60.000 17.19 7.35 35.59 3.02
580 609 1.500474 TCCATGGGGAGCTCAACTAG 58.500 55.000 17.19 1.83 38.64 2.57
581 610 1.839994 CTTCCATGGGGAGCTCAACTA 59.160 52.381 17.19 6.09 46.01 2.24
582 611 0.622665 CTTCCATGGGGAGCTCAACT 59.377 55.000 17.19 0.00 46.01 3.16
588 617 2.440980 GTGGCTTCCATGGGGAGC 60.441 66.667 24.50 24.50 46.01 4.70
606 635 0.398381 CAGAAGGAGGAGGAGGAGGG 60.398 65.000 0.00 0.00 0.00 4.30
613 642 1.221293 CAGCAGCAGAAGGAGGAGG 59.779 63.158 0.00 0.00 0.00 4.30
622 651 3.644399 CTCGAGCAGCAGCAGCAGA 62.644 63.158 12.92 9.81 45.49 4.26
644 685 1.468520 GTCATCACGTTGGTTCATGGG 59.531 52.381 0.00 0.00 0.00 4.00
650 691 2.357637 CAACAAGGTCATCACGTTGGTT 59.642 45.455 7.10 0.00 44.19 3.67
661 702 1.375396 CGCGGATCCAACAAGGTCA 60.375 57.895 13.41 0.00 39.02 4.02
700 741 0.462581 TTTCCTAGAGCCAGCATGCG 60.463 55.000 13.01 7.31 36.02 4.73
703 744 1.211457 CTGGTTTCCTAGAGCCAGCAT 59.789 52.381 2.03 0.00 41.46 3.79
716 757 2.453638 GCTACCGCGAGCTGGTTTC 61.454 63.158 8.23 6.00 40.96 2.78
748 789 3.432378 GACAGGACCATATATCCTCCGT 58.568 50.000 4.96 2.37 45.25 4.69
775 1000 1.148759 GCTTCCTCGCGAGAATGTCC 61.149 60.000 36.59 15.40 41.32 4.02
776 1001 0.458543 TGCTTCCTCGCGAGAATGTC 60.459 55.000 36.59 20.14 41.32 3.06
777 1002 0.176680 ATGCTTCCTCGCGAGAATGT 59.823 50.000 36.59 14.40 41.32 2.71
780 1005 0.102481 GGTATGCTTCCTCGCGAGAA 59.898 55.000 36.59 24.86 41.32 2.87
781 1006 1.734137 GGTATGCTTCCTCGCGAGA 59.266 57.895 36.59 19.76 39.12 4.04
782 1007 1.300233 GGGTATGCTTCCTCGCGAG 60.300 63.158 29.06 29.06 0.00 5.03
783 1008 2.016393 CTGGGTATGCTTCCTCGCGA 62.016 60.000 9.26 9.26 0.00 5.87
786 1011 1.048724 TCCCTGGGTATGCTTCCTCG 61.049 60.000 13.56 0.00 0.00 4.63
788 1013 0.919710 GTTCCCTGGGTATGCTTCCT 59.080 55.000 13.56 0.00 0.00 3.36
789 1014 0.463833 CGTTCCCTGGGTATGCTTCC 60.464 60.000 13.56 0.00 0.00 3.46
790 1015 0.252197 ACGTTCCCTGGGTATGCTTC 59.748 55.000 13.56 0.00 0.00 3.86
791 1016 0.696501 AACGTTCCCTGGGTATGCTT 59.303 50.000 13.56 3.47 0.00 3.91
792 1017 0.696501 AAACGTTCCCTGGGTATGCT 59.303 50.000 13.56 0.00 0.00 3.79
793 1018 0.808755 CAAACGTTCCCTGGGTATGC 59.191 55.000 13.56 0.83 0.00 3.14
794 1019 1.271707 ACCAAACGTTCCCTGGGTATG 60.272 52.381 19.08 11.48 34.31 2.39
795 1020 1.069775 ACCAAACGTTCCCTGGGTAT 58.930 50.000 19.08 0.00 34.31 2.73
796 1021 0.845337 AACCAAACGTTCCCTGGGTA 59.155 50.000 19.08 0.00 34.31 3.69
797 1022 0.032912 AAACCAAACGTTCCCTGGGT 60.033 50.000 19.08 11.72 34.31 4.51
798 1023 0.671796 GAAACCAAACGTTCCCTGGG 59.328 55.000 19.08 6.33 34.31 4.45
799 1024 0.309612 CGAAACCAAACGTTCCCTGG 59.690 55.000 14.56 14.56 31.78 4.45
800 1025 0.309612 CCGAAACCAAACGTTCCCTG 59.690 55.000 0.00 0.00 31.78 4.45
801 1026 1.449726 GCCGAAACCAAACGTTCCCT 61.450 55.000 0.00 0.00 31.78 4.20
802 1027 1.008194 GCCGAAACCAAACGTTCCC 60.008 57.895 0.00 0.00 31.78 3.97
803 1028 0.317519 CAGCCGAAACCAAACGTTCC 60.318 55.000 0.00 0.00 31.78 3.62
804 1029 0.658897 TCAGCCGAAACCAAACGTTC 59.341 50.000 0.00 0.00 31.78 3.95
805 1030 0.379316 GTCAGCCGAAACCAAACGTT 59.621 50.000 0.00 0.00 35.70 3.99
806 1031 1.768112 CGTCAGCCGAAACCAAACGT 61.768 55.000 0.00 0.00 39.56 3.99
807 1032 1.083015 CGTCAGCCGAAACCAAACG 60.083 57.895 0.00 0.00 39.56 3.60
808 1033 0.316689 CACGTCAGCCGAAACCAAAC 60.317 55.000 0.00 0.00 40.70 2.93
809 1034 0.745128 ACACGTCAGCCGAAACCAAA 60.745 50.000 0.00 0.00 40.70 3.28
810 1035 1.153329 ACACGTCAGCCGAAACCAA 60.153 52.632 0.00 0.00 40.70 3.67
811 1036 1.593209 GACACGTCAGCCGAAACCA 60.593 57.895 0.00 0.00 40.70 3.67
812 1037 2.654912 CGACACGTCAGCCGAAACC 61.655 63.158 0.00 0.00 40.70 3.27
813 1038 1.659335 TCGACACGTCAGCCGAAAC 60.659 57.895 0.00 0.00 40.70 2.78
814 1039 1.659335 GTCGACACGTCAGCCGAAA 60.659 57.895 11.55 0.00 40.70 3.46
815 1040 2.050714 GTCGACACGTCAGCCGAA 60.051 61.111 11.55 0.00 40.70 4.30
852 1077 5.907391 CCAACAGTCGTCAAATAGAAAACAC 59.093 40.000 0.00 0.00 0.00 3.32
941 1175 9.799106 ACTGGTTTGTTTCTACTAGTAGTAGTA 57.201 33.333 28.50 20.54 46.31 1.82
952 1190 4.813296 CAGTCCACTGGTTTGTTTCTAC 57.187 45.455 0.00 0.00 40.20 2.59
999 1237 1.486145 CCGGTGGGTAGGTGGAAACT 61.486 60.000 0.00 0.00 0.00 2.66
1221 1466 2.433318 GCAGGAGCCAGACACGTC 60.433 66.667 0.00 0.00 33.58 4.34
1320 1565 4.732285 ATCAGCAAATAAATAGACGGCG 57.268 40.909 4.80 4.80 0.00 6.46
1321 1566 5.609088 CGTATCAGCAAATAAATAGACGGC 58.391 41.667 0.00 0.00 0.00 5.68
1322 1567 5.389516 GGCGTATCAGCAAATAAATAGACGG 60.390 44.000 0.00 0.00 39.27 4.79
1323 1568 5.405571 AGGCGTATCAGCAAATAAATAGACG 59.594 40.000 0.00 0.00 39.27 4.18
1327 1572 6.202762 CAGTCAGGCGTATCAGCAAATAAATA 59.797 38.462 0.00 0.00 39.27 1.40
1329 1574 4.332543 CAGTCAGGCGTATCAGCAAATAAA 59.667 41.667 0.00 0.00 39.27 1.40
1332 1577 2.283298 CAGTCAGGCGTATCAGCAAAT 58.717 47.619 0.00 0.00 39.27 2.32
1381 1680 5.991606 TCAATCAGACGATGAGAAACTTGTT 59.008 36.000 0.00 0.00 42.53 2.83
1384 1684 6.091849 CACATCAATCAGACGATGAGAAACTT 59.908 38.462 15.60 0.00 42.53 2.66
1478 1782 3.364889 TCATCTTCGACAGTGTTCGTT 57.635 42.857 0.00 0.00 40.07 3.85
1480 1784 4.708868 TTTTCATCTTCGACAGTGTTCG 57.291 40.909 0.00 2.94 40.53 3.95
1502 1806 1.742831 CGGGGAATCGAAGAATTTGCA 59.257 47.619 0.00 0.00 43.58 4.08
1505 1809 2.022238 GCCCGGGGAATCGAAGAATTT 61.022 52.381 25.28 0.00 43.58 1.82
1593 1933 1.825474 ACCTCCACAGTTCATACTCCG 59.175 52.381 0.00 0.00 30.26 4.63
1710 2096 9.113838 GAGAGAAACTGAGGAAAATGCATATAA 57.886 33.333 0.00 0.00 0.00 0.98
1888 2276 1.202475 ACGTTTGTGGGGAATTGCAAC 60.202 47.619 0.00 0.00 0.00 4.17
1930 2318 6.656693 CCTTCAGAAGACTTGATGTAACCAAT 59.343 38.462 12.14 0.00 0.00 3.16
1960 2348 9.793252 GCAAACATCTTGATTAATAGATTGTGT 57.207 29.630 0.00 0.00 0.00 3.72
2003 2394 0.947244 GCCATCGTTCCAGCCAATAG 59.053 55.000 0.00 0.00 0.00 1.73
2006 2397 2.361104 GGCCATCGTTCCAGCCAA 60.361 61.111 0.00 0.00 45.07 4.52
2009 2400 0.106708 TATCAGGCCATCGTTCCAGC 59.893 55.000 5.01 0.00 0.00 4.85
2013 2404 3.393089 AGATGTATCAGGCCATCGTTC 57.607 47.619 5.01 0.00 41.81 3.95
2106 2519 6.162079 TCAGACTAAGATTGTTTGAGAGCAG 58.838 40.000 0.00 0.00 0.00 4.24
2411 2827 6.913873 TTGGTAAAGACTTGAGTTGTGTAC 57.086 37.500 0.00 0.00 0.00 2.90
2487 2906 7.709182 CCACTTGCATTCATGTTTCATATTGAT 59.291 33.333 0.00 0.00 0.00 2.57
2492 2911 6.377712 TGATCCACTTGCATTCATGTTTCATA 59.622 34.615 0.00 0.00 0.00 2.15
2539 2958 5.011635 TCAGCACAGACAAAGTAGGTGATTA 59.988 40.000 0.00 0.00 0.00 1.75
2555 2974 5.293814 CAGAAGAGGATTTACATCAGCACAG 59.706 44.000 0.00 0.00 0.00 3.66
2863 3284 2.380941 AGATGCTGCCATATTGCACAA 58.619 42.857 0.00 0.00 39.63 3.33
2912 3333 4.365514 TGATGCAAGTGGAAGGAAGTAA 57.634 40.909 0.00 0.00 0.00 2.24
2921 3342 0.703488 TCCCCAATGATGCAAGTGGA 59.297 50.000 6.45 0.00 32.54 4.02
2975 3396 9.295825 TCACATGTGAAACTAAATGTAAGGATT 57.704 29.630 26.02 0.00 38.04 3.01
2976 3397 8.730680 GTCACATGTGAAACTAAATGTAAGGAT 58.269 33.333 29.42 0.00 41.85 3.24
2977 3398 7.936847 AGTCACATGTGAAACTAAATGTAAGGA 59.063 33.333 29.42 0.00 41.85 3.36
2978 3399 8.099364 AGTCACATGTGAAACTAAATGTAAGG 57.901 34.615 29.42 0.00 41.85 2.69
2982 3403 9.730420 GTTTTAGTCACATGTGAAACTAAATGT 57.270 29.630 32.30 15.41 41.85 2.71
2983 3404 9.180678 GGTTTTAGTCACATGTGAAACTAAATG 57.819 33.333 32.30 9.16 41.85 2.32
2984 3405 9.131791 AGGTTTTAGTCACATGTGAAACTAAAT 57.868 29.630 32.30 23.19 41.85 1.40
2985 3406 8.514330 AGGTTTTAGTCACATGTGAAACTAAA 57.486 30.769 30.32 30.32 41.85 1.85
2986 3407 9.616156 TTAGGTTTTAGTCACATGTGAAACTAA 57.384 29.630 29.42 26.85 41.85 2.24
2987 3408 9.048446 GTTAGGTTTTAGTCACATGTGAAACTA 57.952 33.333 29.42 23.21 41.85 2.24
2988 3409 7.773690 AGTTAGGTTTTAGTCACATGTGAAACT 59.226 33.333 29.42 25.03 41.85 2.66
2989 3410 7.927048 AGTTAGGTTTTAGTCACATGTGAAAC 58.073 34.615 29.42 26.09 41.85 2.78
2990 3411 7.771361 TGAGTTAGGTTTTAGTCACATGTGAAA 59.229 33.333 29.42 18.40 41.85 2.69
2991 3412 7.276658 TGAGTTAGGTTTTAGTCACATGTGAA 58.723 34.615 29.42 13.15 41.85 3.18
2992 3413 6.822442 TGAGTTAGGTTTTAGTCACATGTGA 58.178 36.000 24.56 24.56 37.24 3.58
3007 3428 6.042208 AGCTCTCTACAAAGTTTGAGTTAGGT 59.958 38.462 22.23 15.72 0.00 3.08
3011 3432 5.301555 GGAGCTCTCTACAAAGTTTGAGTT 58.698 41.667 22.23 6.47 0.00 3.01
3016 3437 4.164204 AGAGGGAGCTCTCTACAAAGTTT 58.836 43.478 18.31 0.00 41.86 2.66
3037 3458 8.553459 AGTCCAGAGTCAATTATTTTGTGTAG 57.447 34.615 0.00 0.00 0.00 2.74
3038 3459 8.783093 CAAGTCCAGAGTCAATTATTTTGTGTA 58.217 33.333 0.00 0.00 0.00 2.90
3039 3460 7.285401 ACAAGTCCAGAGTCAATTATTTTGTGT 59.715 33.333 0.00 0.00 0.00 3.72
3040 3461 7.651808 ACAAGTCCAGAGTCAATTATTTTGTG 58.348 34.615 0.00 0.00 0.00 3.33
3044 3465 8.515414 GCTTAACAAGTCCAGAGTCAATTATTT 58.485 33.333 0.00 0.00 0.00 1.40
3045 3466 7.665559 TGCTTAACAAGTCCAGAGTCAATTATT 59.334 33.333 0.00 0.00 0.00 1.40
3048 3469 5.376625 TGCTTAACAAGTCCAGAGTCAATT 58.623 37.500 0.00 0.00 0.00 2.32
3064 3485 3.526534 CTCTTCCTACAGCCTGCTTAAC 58.473 50.000 0.00 0.00 0.00 2.01
3224 3648 2.520979 CGTTTTTCTGCGGTTTCACAA 58.479 42.857 0.00 0.00 0.00 3.33
3288 3715 5.309543 TGATCAGGAAACTCCAAAGGAACTA 59.690 40.000 0.00 0.00 36.78 2.24
3306 3733 6.584488 AGAATTCTGAAGTCCATCTGATCAG 58.416 40.000 17.07 17.07 39.04 2.90
3313 3740 9.947669 CATAATGAAAGAATTCTGAAGTCCATC 57.052 33.333 9.17 12.30 36.48 3.51
3322 3749 9.806203 TTAATGGTGCATAATGAAAGAATTCTG 57.194 29.630 9.17 0.00 36.48 3.02
3380 3807 9.727627 TGGTGAAAATTTTGCAAAATTATTCAC 57.272 25.926 41.28 41.28 45.16 3.18
3538 3965 9.856162 AGGAAAGTTAAAGTTGTTATACTGGAA 57.144 29.630 0.00 0.00 0.00 3.53
3625 4054 6.166279 CAGCCATGTCAGAGTAAGAGTTAAA 58.834 40.000 0.00 0.00 0.00 1.52
3837 4266 5.355596 AGACATGAAGAGAGAATAAAGGCG 58.644 41.667 0.00 0.00 0.00 5.52
3848 4277 5.604231 ACCTGCCAATATAGACATGAAGAGA 59.396 40.000 0.00 0.00 0.00 3.10
4066 4496 5.474876 AGAAATTCGAGGTTGCAAGAATCTT 59.525 36.000 10.92 8.33 32.79 2.40
4081 4511 2.035321 GGGCACACCAAAAGAAATTCGA 59.965 45.455 0.00 0.00 39.85 3.71
4239 4669 6.377327 TCAAGGAAGCTCAACTACAAAAAG 57.623 37.500 0.00 0.00 0.00 2.27
4262 4692 8.431910 TTTGTCCCTTCAGTTCTACTAGTTAT 57.568 34.615 0.00 0.00 0.00 1.89
4350 5025 2.690786 TCGGAAATTAGGTGTTGGACG 58.309 47.619 0.00 0.00 0.00 4.79
4369 5044 0.250209 ATCGATGCCAGTGCCTCATC 60.250 55.000 0.00 7.69 36.33 2.92
4474 5150 7.230712 CCACACTAAATTAACAGGGAGAAGTTT 59.769 37.037 0.00 0.00 0.00 2.66
4514 5218 6.066054 TGTTACGTCATCTTTGATGCAAAA 57.934 33.333 0.00 0.00 41.74 2.44
4515 5219 5.681337 TGTTACGTCATCTTTGATGCAAA 57.319 34.783 0.00 0.00 41.74 3.68
4528 5232 5.860182 GCTAACACTGACTAATGTTACGTCA 59.140 40.000 0.00 0.00 39.67 4.35
4529 5233 5.860182 TGCTAACACTGACTAATGTTACGTC 59.140 40.000 0.00 0.00 39.67 4.34
4531 5235 6.887376 ATGCTAACACTGACTAATGTTACG 57.113 37.500 0.00 0.00 39.67 3.18
4536 5240 7.609760 TGGTTTATGCTAACACTGACTAATG 57.390 36.000 0.00 0.00 0.00 1.90
4578 5285 4.762251 GTGGCTCTGGTGATTTAAACTCTT 59.238 41.667 0.00 0.00 0.00 2.85
4585 5292 2.436417 GCAAGTGGCTCTGGTGATTTA 58.564 47.619 0.00 0.00 40.25 1.40
4601 5308 1.364901 CAAGGCAACCACCAGCAAG 59.635 57.895 0.00 0.00 37.17 4.01
4621 5328 1.534163 GTTGCAAGTACCTCGGAAACC 59.466 52.381 0.00 0.00 0.00 3.27
4691 5400 2.880890 CACCTGTTTTGGGAGTTCAGAG 59.119 50.000 0.00 0.00 0.00 3.35
4774 5483 3.450904 ACCAGGTATGTTGCCTCTTCTA 58.549 45.455 0.00 0.00 33.31 2.10
4811 5520 9.448438 TTTTCATACACAGATGTTTAGCAGTAT 57.552 29.630 0.00 0.00 40.48 2.12
4844 5554 2.777845 GCATTTGTTGATACATGACGCG 59.222 45.455 3.53 3.53 33.44 6.01
4847 5557 3.543494 GCACGCATTTGTTGATACATGAC 59.457 43.478 0.00 0.00 33.44 3.06
4891 5601 2.678190 GCTTCTTAGGACCGACATGCTT 60.678 50.000 0.00 0.00 0.00 3.91
4947 5657 3.000080 GCAACGTCGTCCTGCTTCG 62.000 63.158 13.50 0.00 33.20 3.79
4965 5675 1.739049 CTCTCTTCTAGCCAGGCGG 59.261 63.158 5.55 3.22 0.00 6.13
4988 5698 3.293337 CAAATCCATCCTCCAATGCAGA 58.707 45.455 0.00 0.00 0.00 4.26
5065 5775 2.430694 GACAGGTTCTTTTGGCACCTTT 59.569 45.455 0.00 0.00 39.01 3.11
5235 5946 6.073657 CCAAACAATGTTTCTTGCAATGTAGG 60.074 38.462 8.59 2.18 30.69 3.18
5266 5977 4.203226 TGACAGTACAAAACATTGAGCCA 58.797 39.130 0.00 0.00 0.00 4.75
5330 6041 4.634012 TCCACCAATATGCCACTATACC 57.366 45.455 0.00 0.00 0.00 2.73
5384 6096 2.420022 GGACAACAGTGTACCATCATGC 59.580 50.000 0.00 0.00 38.41 4.06
5407 6119 5.705441 AGCAAAGTAGCAAACTATAGCAACA 59.295 36.000 0.00 0.00 37.50 3.33
5448 6160 8.623903 GTCCATGAAGTGAAGCAATTAATATGA 58.376 33.333 0.00 0.00 0.00 2.15
5489 6201 4.892934 TCTGCCCTATGTTTTTCAGTGTTT 59.107 37.500 0.00 0.00 0.00 2.83
5500 6212 3.719268 TGTTGTCATCTGCCCTATGTT 57.281 42.857 0.00 0.00 0.00 2.71
5507 6219 2.618241 TCAGTGTTTGTTGTCATCTGCC 59.382 45.455 0.00 0.00 0.00 4.85
5542 6254 9.337396 AGTTTCAAACACAAGTTACTGATCATA 57.663 29.630 2.41 0.00 36.84 2.15
5622 6336 3.942829 TCCTGATGTGCTTTAGGAGTTG 58.057 45.455 0.00 0.00 34.54 3.16
5626 6340 4.842531 TGAATCCTGATGTGCTTTAGGA 57.157 40.909 0.00 0.00 43.01 2.94
5666 6380 9.334693 GTCATCTTAAGCAACAAACATTTAGAG 57.665 33.333 0.00 0.00 0.00 2.43
5874 6588 6.319911 AGCTATTTTGGCAGAAAGAACCTATC 59.680 38.462 0.00 0.00 0.00 2.08
5967 6683 0.799393 GCAAGAAGGCGAAGAAGACC 59.201 55.000 0.00 0.00 0.00 3.85
6102 6818 0.249073 GTGACATCGATCCCACGGAG 60.249 60.000 9.96 0.00 34.05 4.63
6153 6869 1.893801 ACCCTTACGAGGTTCTGTCTG 59.106 52.381 0.00 0.00 41.85 3.51
6154 6870 1.893801 CACCCTTACGAGGTTCTGTCT 59.106 52.381 0.00 0.00 41.85 3.41
6187 6903 7.984475 TGTATTTACCCAGCATATCTACCAAT 58.016 34.615 0.00 0.00 0.00 3.16
6188 6904 7.291416 TCTGTATTTACCCAGCATATCTACCAA 59.709 37.037 0.00 0.00 0.00 3.67
6190 6906 7.241042 TCTGTATTTACCCAGCATATCTACC 57.759 40.000 0.00 0.00 0.00 3.18
6219 6940 2.303022 CAGGAAGCTCAAGGTAGACCAA 59.697 50.000 0.66 0.00 38.89 3.67


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

AutoCloner maintained by Alex Coulton.