Multiple sequence alignment - TraesCS5A01G429600

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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 TraesCS5A01G429600 chr5A 100.000 3561 0 0 1 3561 613699240 613702800 0.000000e+00 6577.0
1 TraesCS5A01G429600 chr5A 79.526 1055 192 19 1425 2461 36330853 36331901 0.000000e+00 730.0
2 TraesCS5A01G429600 chr5B 89.839 3287 154 80 87 3298 606300294 606303475 0.000000e+00 4054.0
3 TraesCS5A01G429600 chr5B 79.186 1057 195 19 1425 2461 45393548 45394599 0.000000e+00 710.0
4 TraesCS5A01G429600 chr5B 93.651 126 4 3 3439 3561 606303485 606303609 6.070000e-43 185.0
5 TraesCS5A01G429600 chr5D 90.912 2806 125 54 83 2821 491526412 491529154 0.000000e+00 3650.0
6 TraesCS5A01G429600 chr5D 93.696 349 11 4 2863 3205 491529158 491529501 2.450000e-141 512.0
7 TraesCS5A01G429600 chr5D 95.588 204 7 2 3359 3561 491529545 491529747 3.430000e-85 326.0
8 TraesCS5A01G429600 chr5D 100.000 36 0 0 3286 3321 491529499 491529534 2.290000e-07 67.6
9 TraesCS5A01G429600 chr2B 93.860 798 36 3 1621 2418 298515211 298514427 0.000000e+00 1190.0
10 TraesCS5A01G429600 chr2B 93.217 457 31 0 1958 2414 105742910 105743366 0.000000e+00 673.0
11 TraesCS5A01G429600 chr4A 79.541 1046 185 21 1425 2454 597014698 597015730 0.000000e+00 719.0
12 TraesCS5A01G429600 chr4D 79.559 1042 182 23 1425 2449 6424424 6425451 0.000000e+00 715.0
13 TraesCS5A01G429600 chr4B 79.271 1042 195 16 1425 2454 11657230 11656198 0.000000e+00 708.0
14 TraesCS5A01G429600 chr3B 93.886 458 28 0 1958 2415 130115237 130115694 0.000000e+00 691.0
15 TraesCS5A01G429600 chr3B 76.714 992 192 30 1434 2401 795839887 795840863 1.900000e-142 516.0
16 TraesCS5A01G429600 chr3B 85.567 97 6 3 3170 3258 147718500 147718596 1.050000e-15 95.3
17 TraesCS5A01G429600 chr3D 74.690 1371 283 50 1065 2399 593235776 593237118 5.200000e-153 551.0
18 TraesCS5A01G429600 chr3A 77.149 989 186 32 1434 2399 724515611 724516582 4.050000e-149 538.0
19 TraesCS5A01G429600 chr6A 74.774 995 196 36 1431 2399 609157824 609158789 2.580000e-106 396.0
20 TraesCS5A01G429600 chr6B 74.472 995 193 42 1434 2399 704852628 704851666 1.210000e-99 374.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS5A01G429600 chr5A 613699240 613702800 3560 False 6577.0 6577 100.000 1 3561 1 chr5A.!!$F2 3560
1 TraesCS5A01G429600 chr5A 36330853 36331901 1048 False 730.0 730 79.526 1425 2461 1 chr5A.!!$F1 1036
2 TraesCS5A01G429600 chr5B 606300294 606303609 3315 False 2119.5 4054 91.745 87 3561 2 chr5B.!!$F2 3474
3 TraesCS5A01G429600 chr5B 45393548 45394599 1051 False 710.0 710 79.186 1425 2461 1 chr5B.!!$F1 1036
4 TraesCS5A01G429600 chr5D 491526412 491529747 3335 False 1138.9 3650 95.049 83 3561 4 chr5D.!!$F1 3478
5 TraesCS5A01G429600 chr2B 298514427 298515211 784 True 1190.0 1190 93.860 1621 2418 1 chr2B.!!$R1 797
6 TraesCS5A01G429600 chr4A 597014698 597015730 1032 False 719.0 719 79.541 1425 2454 1 chr4A.!!$F1 1029
7 TraesCS5A01G429600 chr4D 6424424 6425451 1027 False 715.0 715 79.559 1425 2449 1 chr4D.!!$F1 1024
8 TraesCS5A01G429600 chr4B 11656198 11657230 1032 True 708.0 708 79.271 1425 2454 1 chr4B.!!$R1 1029
9 TraesCS5A01G429600 chr3B 795839887 795840863 976 False 516.0 516 76.714 1434 2401 1 chr3B.!!$F3 967
10 TraesCS5A01G429600 chr3D 593235776 593237118 1342 False 551.0 551 74.690 1065 2399 1 chr3D.!!$F1 1334
11 TraesCS5A01G429600 chr3A 724515611 724516582 971 False 538.0 538 77.149 1434 2399 1 chr3A.!!$F1 965
12 TraesCS5A01G429600 chr6A 609157824 609158789 965 False 396.0 396 74.774 1431 2399 1 chr6A.!!$F1 968
13 TraesCS5A01G429600 chr6B 704851666 704852628 962 True 374.0 374 74.472 1434 2399 1 chr6B.!!$R1 965

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
563 610 0.038159 ACTCGACTCAAAAGCCTCCG 60.038 55.0 0.0 0.0 0.0 4.63 F
982 1041 0.039798 TTTCGTCAGTTCGTCGGAGG 60.040 55.0 0.0 0.0 0.0 4.30 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1441 1551 0.040204 CCAGGAAGGGTTCATTGCCT 59.960 55.0 0.0 0.0 0.00 4.75 R
2968 3113 0.745486 TCCAGGATTCATGTGCTGCG 60.745 55.0 0.0 0.0 36.37 5.18 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
18 19 3.865700 CGCGCTTCCCTTTTCTTTT 57.134 47.368 5.56 0.00 0.00 2.27
19 20 1.686464 CGCGCTTCCCTTTTCTTTTC 58.314 50.000 5.56 0.00 0.00 2.29
20 21 1.666023 CGCGCTTCCCTTTTCTTTTCC 60.666 52.381 5.56 0.00 0.00 3.13
21 22 1.339929 GCGCTTCCCTTTTCTTTTCCA 59.660 47.619 0.00 0.00 0.00 3.53
22 23 2.223947 GCGCTTCCCTTTTCTTTTCCAA 60.224 45.455 0.00 0.00 0.00 3.53
23 24 3.642705 CGCTTCCCTTTTCTTTTCCAAG 58.357 45.455 0.00 0.00 0.00 3.61
24 25 3.317993 CGCTTCCCTTTTCTTTTCCAAGA 59.682 43.478 0.00 0.00 37.24 3.02
25 26 4.202111 CGCTTCCCTTTTCTTTTCCAAGAA 60.202 41.667 0.00 0.00 45.63 2.52
54 55 5.717038 AAAAACTTTCATTTTCCAGCGTG 57.283 34.783 0.00 0.00 31.35 5.34
55 56 3.369546 AACTTTCATTTTCCAGCGTGG 57.630 42.857 0.00 0.00 39.43 4.94
56 57 1.000274 ACTTTCATTTTCCAGCGTGGC 60.000 47.619 0.00 0.00 37.47 5.01
57 58 0.316841 TTTCATTTTCCAGCGTGGCC 59.683 50.000 0.00 0.00 37.47 5.36
58 59 0.539438 TTCATTTTCCAGCGTGGCCT 60.539 50.000 3.32 0.00 37.47 5.19
59 60 1.213537 CATTTTCCAGCGTGGCCTG 59.786 57.895 3.32 0.00 37.47 4.85
60 61 1.074775 ATTTTCCAGCGTGGCCTGA 59.925 52.632 3.32 0.00 37.47 3.86
61 62 0.962356 ATTTTCCAGCGTGGCCTGAG 60.962 55.000 3.32 0.00 37.47 3.35
62 63 3.551496 TTTCCAGCGTGGCCTGAGG 62.551 63.158 3.32 0.00 37.47 3.86
64 65 4.767255 CCAGCGTGGCCTGAGGAC 62.767 72.222 0.65 0.00 34.77 3.85
73 74 4.492160 CCTGAGGACGCGCGCTAA 62.492 66.667 32.58 12.32 0.00 3.09
74 75 2.506217 CTGAGGACGCGCGCTAAA 60.506 61.111 32.58 11.30 0.00 1.85
75 76 2.048970 TGAGGACGCGCGCTAAAA 60.049 55.556 32.58 10.71 0.00 1.52
76 77 2.279937 CTGAGGACGCGCGCTAAAAC 62.280 60.000 32.58 16.74 0.00 2.43
77 78 3.401846 GAGGACGCGCGCTAAAACG 62.402 63.158 32.58 14.95 0.00 3.60
78 79 4.494400 GGACGCGCGCTAAAACGG 62.494 66.667 32.58 14.15 0.00 4.44
79 80 3.472298 GACGCGCGCTAAAACGGA 61.472 61.111 32.58 0.00 0.00 4.69
80 81 3.401846 GACGCGCGCTAAAACGGAG 62.402 63.158 32.58 12.54 0.00 4.63
81 82 3.176578 CGCGCGCTAAAACGGAGA 61.177 61.111 30.48 0.00 0.00 3.71
82 83 2.695646 GCGCGCTAAAACGGAGAG 59.304 61.111 26.67 0.00 0.00 3.20
83 84 1.804326 GCGCGCTAAAACGGAGAGA 60.804 57.895 26.67 0.00 0.00 3.10
84 85 1.349259 GCGCGCTAAAACGGAGAGAA 61.349 55.000 26.67 0.00 0.00 2.87
85 86 0.640768 CGCGCTAAAACGGAGAGAAG 59.359 55.000 5.56 0.00 0.00 2.85
203 205 2.750350 CTCTCCACCACCACCACC 59.250 66.667 0.00 0.00 0.00 4.61
204 206 2.040359 TCTCCACCACCACCACCA 60.040 61.111 0.00 0.00 0.00 4.17
205 207 2.113139 CTCCACCACCACCACCAC 59.887 66.667 0.00 0.00 0.00 4.16
206 208 3.491598 CTCCACCACCACCACCACC 62.492 68.421 0.00 0.00 0.00 4.61
207 209 3.814906 CCACCACCACCACCACCA 61.815 66.667 0.00 0.00 0.00 4.17
208 210 2.518349 CACCACCACCACCACCAC 60.518 66.667 0.00 0.00 0.00 4.16
283 299 3.238497 TGACCAGTCCACACCCCG 61.238 66.667 0.00 0.00 0.00 5.73
411 458 2.127758 CCAACGAAGCAACGCGTC 60.128 61.111 14.44 0.00 40.23 5.19
502 549 3.869272 GCGTCGCCATTGCCTCTG 61.869 66.667 5.75 0.00 0.00 3.35
504 551 3.512516 GTCGCCATTGCCTCTGCC 61.513 66.667 0.00 0.00 36.33 4.85
505 552 3.720601 TCGCCATTGCCTCTGCCT 61.721 61.111 0.00 0.00 36.33 4.75
506 553 3.207669 CGCCATTGCCTCTGCCTC 61.208 66.667 0.00 0.00 36.33 4.70
507 554 3.207669 GCCATTGCCTCTGCCTCG 61.208 66.667 0.00 0.00 36.33 4.63
520 567 2.091541 CTGCCTCGACTCTCTCTTTCT 58.908 52.381 0.00 0.00 0.00 2.52
521 568 2.088423 TGCCTCGACTCTCTCTTTCTC 58.912 52.381 0.00 0.00 0.00 2.87
522 569 2.290641 TGCCTCGACTCTCTCTTTCTCT 60.291 50.000 0.00 0.00 0.00 3.10
523 570 2.354821 GCCTCGACTCTCTCTTTCTCTC 59.645 54.545 0.00 0.00 0.00 3.20
524 571 2.943033 CCTCGACTCTCTCTTTCTCTCC 59.057 54.545 0.00 0.00 0.00 3.71
525 572 3.370527 CCTCGACTCTCTCTTTCTCTCCT 60.371 52.174 0.00 0.00 0.00 3.69
562 609 1.801178 CAACTCGACTCAAAAGCCTCC 59.199 52.381 0.00 0.00 0.00 4.30
563 610 0.038159 ACTCGACTCAAAAGCCTCCG 60.038 55.000 0.00 0.00 0.00 4.63
565 612 2.391389 CGACTCAAAAGCCTCCGCC 61.391 63.158 0.00 0.00 34.57 6.13
578 625 0.546598 CTCCGCCCTTTCCATACCTT 59.453 55.000 0.00 0.00 0.00 3.50
641 688 1.167851 CCGGCATTCACATGTGAGTT 58.832 50.000 26.48 16.46 41.13 3.01
780 832 2.776670 CTTGCAGCTCTCGCAGTCCA 62.777 60.000 0.00 0.00 41.18 4.02
801 853 0.682852 CCCCCGATTTATACTCCGCA 59.317 55.000 0.00 0.00 0.00 5.69
802 854 1.607251 CCCCCGATTTATACTCCGCAC 60.607 57.143 0.00 0.00 0.00 5.34
803 855 1.415374 CCCGATTTATACTCCGCACG 58.585 55.000 0.00 0.00 0.00 5.34
804 856 1.415374 CCGATTTATACTCCGCACGG 58.585 55.000 1.73 1.73 0.00 4.94
805 857 1.415374 CGATTTATACTCCGCACGGG 58.585 55.000 9.58 2.66 35.59 5.28
817 869 4.308458 CACGGGGCACTTCGTCCA 62.308 66.667 0.00 0.00 43.46 4.02
834 886 3.370231 ACCGCCCGGCATTGTTTC 61.370 61.111 10.77 0.00 39.32 2.78
835 887 4.128388 CCGCCCGGCATTGTTTCC 62.128 66.667 10.77 0.00 0.00 3.13
837 889 4.128388 GCCCGGCATTGTTTCCCG 62.128 66.667 3.91 0.00 41.60 5.14
838 890 2.675075 CCCGGCATTGTTTCCCGT 60.675 61.111 0.00 0.00 40.38 5.28
839 891 2.272447 CCCGGCATTGTTTCCCGTT 61.272 57.895 0.00 0.00 40.38 4.44
840 892 1.663173 CCGGCATTGTTTCCCGTTT 59.337 52.632 0.00 0.00 40.38 3.60
843 899 1.000717 CGGCATTGTTTCCCGTTTTCT 60.001 47.619 0.00 0.00 37.36 2.52
885 941 1.605232 TCGATTCGATTCGATTCCCGA 59.395 47.619 24.07 16.76 42.81 5.14
920 976 1.098050 CAAATCTTGAGCCTTCCCCG 58.902 55.000 0.00 0.00 0.00 5.73
937 993 0.679960 CCGGTTCCTGGATTCCCAAC 60.680 60.000 0.00 0.89 42.98 3.77
962 1021 1.693627 GCGTCCAGAGATCTCCCTTA 58.306 55.000 19.30 0.00 0.00 2.69
976 1035 3.508793 TCTCCCTTATTTCGTCAGTTCGT 59.491 43.478 0.00 0.00 0.00 3.85
982 1041 0.039798 TTTCGTCAGTTCGTCGGAGG 60.040 55.000 0.00 0.00 0.00 4.30
984 1043 2.623915 CGTCAGTTCGTCGGAGGGT 61.624 63.158 0.00 0.00 0.00 4.34
1010 1069 4.481112 CTGAACAATGGCGGCGGC 62.481 66.667 27.76 27.76 38.90 6.53
1043 1102 4.803426 GCTCTGCGCGCTGGTAGT 62.803 66.667 33.04 0.00 0.00 2.73
1046 1105 4.742201 CTGCGCGCTGGTAGTGGT 62.742 66.667 33.29 0.00 0.00 4.16
1050 1109 4.697756 GCGCTGGTAGTGGTGGCA 62.698 66.667 0.00 0.00 0.00 4.92
1051 1110 2.742372 CGCTGGTAGTGGTGGCAC 60.742 66.667 9.70 9.70 0.00 5.01
1052 1111 2.750350 GCTGGTAGTGGTGGCACT 59.250 61.111 18.45 0.00 39.08 4.40
1138 1197 2.573869 CCAGGATCGTCGTGCAGT 59.426 61.111 0.00 0.00 31.43 4.40
1145 1204 1.010935 ATCGTCGTGCAGTTGCTCAG 61.011 55.000 5.62 0.00 42.66 3.35
1170 1229 2.270352 ACGGCATCAAGAAGGTGAAA 57.730 45.000 0.00 0.00 0.00 2.69
1173 1232 2.095567 CGGCATCAAGAAGGTGAAACTG 60.096 50.000 0.00 0.00 36.74 3.16
1350 1421 2.427506 GTCAACATCAAGTGAGTCCCC 58.572 52.381 0.00 0.00 0.00 4.81
1362 1433 0.912006 GAGTCCCCCTTCCTCTTGCT 60.912 60.000 0.00 0.00 0.00 3.91
1363 1434 0.912006 AGTCCCCCTTCCTCTTGCTC 60.912 60.000 0.00 0.00 0.00 4.26
1367 1438 1.449246 CCCTTCCTCTTGCTCGCTG 60.449 63.158 0.00 0.00 0.00 5.18
1370 1441 0.673022 CTTCCTCTTGCTCGCTGCTT 60.673 55.000 0.00 0.00 43.37 3.91
1371 1442 0.952497 TTCCTCTTGCTCGCTGCTTG 60.952 55.000 0.00 0.00 43.37 4.01
1372 1443 2.479650 CTCTTGCTCGCTGCTTGC 59.520 61.111 0.00 2.32 43.37 4.01
1373 1444 2.031616 TCTTGCTCGCTGCTTGCT 59.968 55.556 13.19 0.00 43.37 3.91
1380 1472 1.642952 CTCGCTGCTTGCTCTTTCCC 61.643 60.000 0.00 0.00 40.11 3.97
1389 1481 0.960364 TGCTCTTTCCCGTTCATGGC 60.960 55.000 0.00 0.00 0.00 4.40
1390 1482 1.982073 GCTCTTTCCCGTTCATGGCG 61.982 60.000 0.00 0.00 0.00 5.69
1392 1484 3.051392 CTTTCCCGTTCATGGCGCC 62.051 63.158 22.73 22.73 0.00 6.53
1408 1500 4.823419 CCCGCCGCGGTTGTATGA 62.823 66.667 29.21 0.00 46.80 2.15
1409 1501 3.560278 CCGCCGCGGTTGTATGAC 61.560 66.667 28.70 5.98 42.73 3.06
1410 1502 3.560278 CGCCGCGGTTGTATGACC 61.560 66.667 28.70 5.16 36.31 4.02
1411 1503 3.199891 GCCGCGGTTGTATGACCC 61.200 66.667 28.70 0.93 36.28 4.46
1412 1504 2.888534 CCGCGGTTGTATGACCCG 60.889 66.667 19.50 0.00 44.46 5.28
1413 1505 2.125832 CGCGGTTGTATGACCCGT 60.126 61.111 0.00 0.00 43.56 5.28
1418 1520 2.198406 CGGTTGTATGACCCGTATGTG 58.802 52.381 0.00 0.00 36.28 3.21
1419 1521 2.417651 CGGTTGTATGACCCGTATGTGT 60.418 50.000 0.00 0.00 36.28 3.72
1441 1551 0.325272 TTTGCAGGTATGTGGCCGTA 59.675 50.000 0.00 0.00 0.00 4.02
2527 2667 2.883253 GCCGCTCTGCTCGTTCTC 60.883 66.667 0.00 0.00 0.00 2.87
2641 2784 6.852420 TTTGGATCAGCAGTAGTTACTAGT 57.148 37.500 0.00 0.00 34.13 2.57
2642 2785 5.836821 TGGATCAGCAGTAGTTACTAGTG 57.163 43.478 19.70 19.70 39.58 2.74
2717 2860 5.887035 TGTTCAGATGGCATTTCACATGATA 59.113 36.000 0.00 0.00 0.00 2.15
2727 2870 6.256321 GGCATTTCACATGATATTCAAACACC 59.744 38.462 0.00 0.00 0.00 4.16
2766 2909 6.634805 ACTATGGTGTACAGTTCATTCAGAG 58.365 40.000 0.00 0.00 0.00 3.35
2769 2912 4.588951 TGGTGTACAGTTCATTCAGAGTCT 59.411 41.667 0.00 0.00 0.00 3.24
2880 3023 7.040494 ACTACTGATGAGTGATGACTGAAATG 58.960 38.462 0.00 0.00 33.21 2.32
2911 3054 3.986435 TGATTCAGAGTCCCAGATCTCA 58.014 45.455 0.00 0.00 33.63 3.27
2968 3113 6.016276 CAGGATTTGGTTGGCAATATAGTACC 60.016 42.308 1.92 0.00 0.00 3.34
2993 3138 2.228059 CACATGAATCCTGGATCCAGC 58.772 52.381 32.97 20.73 42.35 4.85
2996 3141 2.945080 TGAATCCTGGATCCAGCATC 57.055 50.000 32.97 27.03 42.35 3.91
3001 3146 1.848388 TCCTGGATCCAGCATCACATT 59.152 47.619 32.97 0.00 42.35 2.71
3002 3147 2.242965 TCCTGGATCCAGCATCACATTT 59.757 45.455 32.97 0.00 42.35 2.32
3003 3148 3.459227 TCCTGGATCCAGCATCACATTTA 59.541 43.478 32.97 7.23 42.35 1.40
3004 3149 3.819337 CCTGGATCCAGCATCACATTTAG 59.181 47.826 32.97 13.16 42.35 1.85
3005 3150 3.819337 CTGGATCCAGCATCACATTTAGG 59.181 47.826 28.45 0.93 37.24 2.69
3006 3151 3.152341 GGATCCAGCATCACATTTAGGG 58.848 50.000 6.95 0.00 32.33 3.53
3007 3152 3.181440 GGATCCAGCATCACATTTAGGGA 60.181 47.826 6.95 0.00 32.33 4.20
3025 3170 4.775236 AGGGATCTAGATGCACAACTTTC 58.225 43.478 23.71 5.79 0.00 2.62
3030 3175 5.947228 TCTAGATGCACAACTTTCCTTTG 57.053 39.130 0.00 0.00 0.00 2.77
3163 3312 9.017669 CATTATCTGCTGCTATTTTCAGTTTTC 57.982 33.333 0.00 0.00 34.21 2.29
3167 3316 6.039717 TCTGCTGCTATTTTCAGTTTTCAACT 59.960 34.615 0.00 0.00 44.06 3.16
3209 3372 4.697514 GCCTCTGCTGTTGATCAATACTA 58.302 43.478 12.12 0.00 33.53 1.82
3210 3373 4.509600 GCCTCTGCTGTTGATCAATACTAC 59.490 45.833 12.12 0.00 33.53 2.73
3211 3374 5.683509 GCCTCTGCTGTTGATCAATACTACT 60.684 44.000 12.12 0.00 33.53 2.57
3212 3375 5.752472 CCTCTGCTGTTGATCAATACTACTG 59.248 44.000 12.12 4.32 0.00 2.74
3214 3377 6.101997 TCTGCTGTTGATCAATACTACTGTG 58.898 40.000 12.12 0.00 0.00 3.66
3216 3379 6.643388 TGCTGTTGATCAATACTACTGTGAT 58.357 36.000 12.12 0.00 34.71 3.06
3217 3380 6.536224 TGCTGTTGATCAATACTACTGTGATG 59.464 38.462 12.12 0.00 32.18 3.07
3218 3381 6.536582 GCTGTTGATCAATACTACTGTGATGT 59.463 38.462 12.12 0.00 32.18 3.06
3219 3382 7.706607 GCTGTTGATCAATACTACTGTGATGTA 59.293 37.037 12.12 0.00 32.18 2.29
3220 3383 8.926715 TGTTGATCAATACTACTGTGATGTAC 57.073 34.615 12.12 0.00 32.18 2.90
3221 3384 8.749354 TGTTGATCAATACTACTGTGATGTACT 58.251 33.333 12.12 0.00 32.18 2.73
3222 3385 9.239002 GTTGATCAATACTACTGTGATGTACTC 57.761 37.037 12.12 0.00 32.18 2.59
3223 3386 7.941919 TGATCAATACTACTGTGATGTACTCC 58.058 38.462 0.00 0.00 32.18 3.85
3224 3387 7.559897 TGATCAATACTACTGTGATGTACTCCA 59.440 37.037 0.00 0.00 32.18 3.86
3225 3388 7.334844 TCAATACTACTGTGATGTACTCCAG 57.665 40.000 0.00 0.00 0.00 3.86
3226 3389 6.321435 TCAATACTACTGTGATGTACTCCAGG 59.679 42.308 0.00 0.00 30.65 4.45
3227 3390 3.366396 ACTACTGTGATGTACTCCAGGG 58.634 50.000 0.00 0.00 30.65 4.45
3228 3391 1.573108 ACTGTGATGTACTCCAGGGG 58.427 55.000 0.00 0.00 30.65 4.79
3250 3413 9.301430 AGGGGAATGGAGATTATATCATTGTAT 57.699 33.333 0.00 0.00 30.97 2.29
3265 3428 5.255687 TCATTGTATTGATCAACAGGCACT 58.744 37.500 11.07 0.00 43.88 4.40
3273 3436 4.758688 TGATCAACAGGCACTACTATGTG 58.241 43.478 0.00 0.00 36.02 3.21
3279 3442 3.386078 ACAGGCACTACTATGTGATCTGG 59.614 47.826 16.25 5.61 40.96 3.86
3280 3443 3.386078 CAGGCACTACTATGTGATCTGGT 59.614 47.826 0.00 0.00 40.12 4.00
3321 3484 0.954452 GGCACCTTGGACAAGTTCTG 59.046 55.000 10.81 4.77 36.72 3.02
3324 3487 1.605710 CACCTTGGACAAGTTCTGCTG 59.394 52.381 10.81 0.00 36.72 4.41
3325 3488 1.242076 CCTTGGACAAGTTCTGCTGG 58.758 55.000 10.81 0.00 36.72 4.85
3326 3489 1.477558 CCTTGGACAAGTTCTGCTGGT 60.478 52.381 10.81 0.00 36.72 4.00
3327 3490 2.224523 CCTTGGACAAGTTCTGCTGGTA 60.225 50.000 10.81 0.00 36.72 3.25
3328 3491 2.543777 TGGACAAGTTCTGCTGGTAC 57.456 50.000 0.00 0.00 32.29 3.34
3330 3493 2.224281 TGGACAAGTTCTGCTGGTACTG 60.224 50.000 0.00 0.00 32.91 2.74
3331 3494 2.037251 GGACAAGTTCTGCTGGTACTGA 59.963 50.000 0.00 0.00 29.75 3.41
3332 3495 3.494398 GGACAAGTTCTGCTGGTACTGAA 60.494 47.826 0.00 0.00 29.75 3.02
3333 3496 3.733337 ACAAGTTCTGCTGGTACTGAAG 58.267 45.455 0.00 0.00 33.83 3.02
3334 3497 3.134804 ACAAGTTCTGCTGGTACTGAAGT 59.865 43.478 0.00 0.00 34.25 3.01
3335 3498 3.393089 AGTTCTGCTGGTACTGAAGTG 57.607 47.619 0.00 0.00 34.25 3.16
3336 3499 2.037772 AGTTCTGCTGGTACTGAAGTGG 59.962 50.000 0.00 0.00 34.25 4.00
3337 3500 2.009681 TCTGCTGGTACTGAAGTGGA 57.990 50.000 0.00 0.00 34.25 4.02
3338 3501 1.895798 TCTGCTGGTACTGAAGTGGAG 59.104 52.381 0.00 0.00 34.25 3.86
3339 3502 0.976641 TGCTGGTACTGAAGTGGAGG 59.023 55.000 0.00 0.00 0.00 4.30
3340 3503 0.391793 GCTGGTACTGAAGTGGAGGC 60.392 60.000 0.00 0.00 0.00 4.70
3341 3504 0.976641 CTGGTACTGAAGTGGAGGCA 59.023 55.000 0.00 0.00 0.00 4.75
3342 3505 1.556911 CTGGTACTGAAGTGGAGGCAT 59.443 52.381 0.00 0.00 0.00 4.40
3343 3506 1.278985 TGGTACTGAAGTGGAGGCATG 59.721 52.381 0.00 0.00 0.00 4.06
3344 3507 1.407437 GGTACTGAAGTGGAGGCATGG 60.407 57.143 0.00 0.00 0.00 3.66
3345 3508 1.279271 GTACTGAAGTGGAGGCATGGT 59.721 52.381 0.00 0.00 0.00 3.55
3346 3509 0.326264 ACTGAAGTGGAGGCATGGTC 59.674 55.000 0.00 0.00 0.00 4.02
3347 3510 0.325933 CTGAAGTGGAGGCATGGTCA 59.674 55.000 0.00 0.00 0.00 4.02
3348 3511 0.036732 TGAAGTGGAGGCATGGTCAC 59.963 55.000 0.00 0.00 0.00 3.67
3349 3512 0.678048 GAAGTGGAGGCATGGTCACC 60.678 60.000 0.00 0.00 0.00 4.02
3350 3513 1.136329 AAGTGGAGGCATGGTCACCT 61.136 55.000 0.00 0.00 39.65 4.00
3351 3514 1.377725 GTGGAGGCATGGTCACCTG 60.378 63.158 0.00 0.00 36.05 4.00
3352 3515 2.439156 GGAGGCATGGTCACCTGC 60.439 66.667 9.19 9.19 36.05 4.85
3353 3516 2.673523 GAGGCATGGTCACCTGCT 59.326 61.111 15.32 4.73 36.05 4.24
3354 3517 1.626356 GGAGGCATGGTCACCTGCTA 61.626 60.000 15.32 0.00 40.94 3.49
3355 3518 0.179062 GAGGCATGGTCACCTGCTAG 60.179 60.000 15.32 0.00 36.05 3.42
3356 3519 0.911525 AGGCATGGTCACCTGCTAGT 60.912 55.000 15.32 1.96 38.45 2.57
3357 3520 0.745845 GGCATGGTCACCTGCTAGTG 60.746 60.000 15.32 0.74 38.45 2.74
3362 3525 3.396260 TGGTCACCTGCTAGTGTAAAC 57.604 47.619 0.00 0.00 38.91 2.01
3393 3556 0.837691 TGGAGGCATGGACACTCTGT 60.838 55.000 0.00 0.00 0.00 3.41
3435 3598 5.067936 TCAACAAACGAACACCCAACATATT 59.932 36.000 0.00 0.00 0.00 1.28
3436 3599 5.523438 ACAAACGAACACCCAACATATTT 57.477 34.783 0.00 0.00 0.00 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.666023 GGAAAAGAAAAGGGAAGCGCG 60.666 52.381 0.00 0.00 0.00 6.86
1 2 1.339929 TGGAAAAGAAAAGGGAAGCGC 59.660 47.619 0.00 0.00 0.00 5.92
2 3 3.317993 TCTTGGAAAAGAAAAGGGAAGCG 59.682 43.478 0.00 0.00 0.00 4.68
3 4 4.937201 TCTTGGAAAAGAAAAGGGAAGC 57.063 40.909 0.00 0.00 0.00 3.86
32 33 4.570369 CCACGCTGGAAAATGAAAGTTTTT 59.430 37.500 0.00 0.00 40.96 1.94
33 34 4.119136 CCACGCTGGAAAATGAAAGTTTT 58.881 39.130 0.00 0.00 40.96 2.43
34 35 3.716601 CCACGCTGGAAAATGAAAGTTT 58.283 40.909 0.00 0.00 40.96 2.66
35 36 2.545742 GCCACGCTGGAAAATGAAAGTT 60.546 45.455 8.04 0.00 40.96 2.66
36 37 1.000274 GCCACGCTGGAAAATGAAAGT 60.000 47.619 8.04 0.00 40.96 2.66
37 38 1.669795 GGCCACGCTGGAAAATGAAAG 60.670 52.381 0.00 0.00 40.96 2.62
38 39 0.316841 GGCCACGCTGGAAAATGAAA 59.683 50.000 0.00 0.00 40.96 2.69
39 40 0.539438 AGGCCACGCTGGAAAATGAA 60.539 50.000 5.01 0.00 40.96 2.57
40 41 1.074775 AGGCCACGCTGGAAAATGA 59.925 52.632 5.01 0.00 40.96 2.57
41 42 1.213537 CAGGCCACGCTGGAAAATG 59.786 57.895 5.01 0.00 40.96 2.32
42 43 0.962356 CTCAGGCCACGCTGGAAAAT 60.962 55.000 5.01 0.00 40.96 1.82
43 44 1.600636 CTCAGGCCACGCTGGAAAA 60.601 57.895 5.01 0.00 40.96 2.29
44 45 2.032528 CTCAGGCCACGCTGGAAA 59.967 61.111 5.01 0.00 40.96 3.13
45 46 4.020617 CCTCAGGCCACGCTGGAA 62.021 66.667 5.01 0.00 40.96 3.53
47 48 4.767255 GTCCTCAGGCCACGCTGG 62.767 72.222 5.01 0.00 41.55 4.85
56 57 3.982372 TTTAGCGCGCGTCCTCAGG 62.982 63.158 32.35 0.04 0.00 3.86
57 58 2.092291 TTTTAGCGCGCGTCCTCAG 61.092 57.895 32.35 0.92 0.00 3.35
58 59 2.048970 TTTTAGCGCGCGTCCTCA 60.049 55.556 32.35 9.56 0.00 3.86
59 60 2.394524 GTTTTAGCGCGCGTCCTC 59.605 61.111 32.35 14.78 0.00 3.71
60 61 3.475774 CGTTTTAGCGCGCGTCCT 61.476 61.111 32.35 22.64 0.00 3.85
61 62 4.494400 CCGTTTTAGCGCGCGTCC 62.494 66.667 32.35 16.02 0.00 4.79
62 63 3.401846 CTCCGTTTTAGCGCGCGTC 62.402 63.158 32.35 22.88 0.00 5.19
63 64 3.475774 CTCCGTTTTAGCGCGCGT 61.476 61.111 32.35 20.00 0.00 6.01
64 65 3.126722 CTCTCCGTTTTAGCGCGCG 62.127 63.158 28.44 28.44 0.00 6.86
65 66 1.349259 TTCTCTCCGTTTTAGCGCGC 61.349 55.000 26.66 26.66 0.00 6.86
66 67 0.640768 CTTCTCTCCGTTTTAGCGCG 59.359 55.000 0.00 0.00 0.00 6.86
67 68 0.370615 GCTTCTCTCCGTTTTAGCGC 59.629 55.000 0.00 0.00 0.00 5.92
68 69 1.000145 GGCTTCTCTCCGTTTTAGCG 59.000 55.000 0.00 0.00 0.00 4.26
69 70 1.000145 CGGCTTCTCTCCGTTTTAGC 59.000 55.000 0.00 0.00 41.85 3.09
70 71 2.260481 GTCGGCTTCTCTCCGTTTTAG 58.740 52.381 1.22 0.00 46.49 1.85
71 72 1.401931 CGTCGGCTTCTCTCCGTTTTA 60.402 52.381 1.22 0.00 46.49 1.52
72 73 0.666577 CGTCGGCTTCTCTCCGTTTT 60.667 55.000 1.22 0.00 46.49 2.43
73 74 1.080705 CGTCGGCTTCTCTCCGTTT 60.081 57.895 1.22 0.00 46.49 3.60
74 75 2.266627 ACGTCGGCTTCTCTCCGTT 61.267 57.895 0.00 0.00 46.49 4.44
75 76 2.672307 ACGTCGGCTTCTCTCCGT 60.672 61.111 0.00 0.00 46.49 4.69
77 78 2.182030 CCACGTCGGCTTCTCTCC 59.818 66.667 0.00 0.00 0.00 3.71
78 79 2.182030 CCCACGTCGGCTTCTCTC 59.818 66.667 0.00 0.00 0.00 3.20
79 80 4.070552 GCCCACGTCGGCTTCTCT 62.071 66.667 17.69 0.00 46.10 3.10
158 160 4.527157 GTCATTGCGCTCGCTGCC 62.527 66.667 9.73 0.00 42.51 4.85
159 161 4.527157 GGTCATTGCGCTCGCTGC 62.527 66.667 9.73 5.19 42.51 5.25
160 162 3.869272 GGGTCATTGCGCTCGCTG 61.869 66.667 9.73 6.50 42.51 5.18
161 163 2.310327 TATGGGTCATTGCGCTCGCT 62.310 55.000 9.73 0.00 42.51 4.93
162 164 1.887242 TATGGGTCATTGCGCTCGC 60.887 57.895 9.73 7.38 42.35 5.03
163 165 1.821241 CGTATGGGTCATTGCGCTCG 61.821 60.000 9.73 0.00 0.00 5.03
164 166 1.934463 CGTATGGGTCATTGCGCTC 59.066 57.895 9.73 0.00 0.00 5.03
165 167 2.180204 GCGTATGGGTCATTGCGCT 61.180 57.895 9.73 0.00 40.70 5.92
257 265 2.660064 GGACTGGTCAGTGGCGGAT 61.660 63.158 8.49 0.00 42.66 4.18
261 277 1.598130 GTGTGGACTGGTCAGTGGC 60.598 63.158 8.49 0.00 42.66 5.01
283 299 2.280186 GATGACGGATCGTGGGGC 60.280 66.667 0.00 0.00 41.37 5.80
501 548 2.088423 GAGAAAGAGAGAGTCGAGGCA 58.912 52.381 0.00 0.00 0.00 4.75
502 549 2.354821 GAGAGAAAGAGAGAGTCGAGGC 59.645 54.545 0.00 0.00 0.00 4.70
504 551 3.873910 AGGAGAGAAAGAGAGAGTCGAG 58.126 50.000 0.00 0.00 0.00 4.04
505 552 3.992943 AGGAGAGAAAGAGAGAGTCGA 57.007 47.619 0.00 0.00 0.00 4.20
506 553 4.261801 AGAAGGAGAGAAAGAGAGAGTCG 58.738 47.826 0.00 0.00 0.00 4.18
507 554 5.501156 AGAGAAGGAGAGAAAGAGAGAGTC 58.499 45.833 0.00 0.00 0.00 3.36
520 567 0.611062 TCCGGCGAAAGAGAAGGAGA 60.611 55.000 9.30 0.00 0.00 3.71
521 568 0.461961 ATCCGGCGAAAGAGAAGGAG 59.538 55.000 9.30 0.00 0.00 3.69
522 569 0.902531 AATCCGGCGAAAGAGAAGGA 59.097 50.000 9.30 0.00 0.00 3.36
523 570 1.291132 GAATCCGGCGAAAGAGAAGG 58.709 55.000 9.30 0.00 0.00 3.46
524 571 2.010145 TGAATCCGGCGAAAGAGAAG 57.990 50.000 9.30 0.00 0.00 2.85
525 572 2.073816 GTTGAATCCGGCGAAAGAGAA 58.926 47.619 9.30 0.00 0.00 2.87
562 609 0.546598 AGGAAGGTATGGAAAGGGCG 59.453 55.000 0.00 0.00 0.00 6.13
563 610 1.847088 AGAGGAAGGTATGGAAAGGGC 59.153 52.381 0.00 0.00 0.00 5.19
565 612 4.576330 AACAGAGGAAGGTATGGAAAGG 57.424 45.455 0.00 0.00 0.00 3.11
578 625 2.158813 AGGCAAGAAACGAAACAGAGGA 60.159 45.455 0.00 0.00 0.00 3.71
650 702 2.243221 ACAGATGGGGAAGAAAGGGATG 59.757 50.000 0.00 0.00 0.00 3.51
780 832 1.553704 GCGGAGTATAAATCGGGGGAT 59.446 52.381 0.00 0.00 0.00 3.85
817 869 3.370231 GAAACAATGCCGGGCGGT 61.370 61.111 15.40 9.73 37.65 5.68
826 878 3.317993 ACAGGAGAAAACGGGAAACAATG 59.682 43.478 0.00 0.00 0.00 2.82
827 879 3.562182 ACAGGAGAAAACGGGAAACAAT 58.438 40.909 0.00 0.00 0.00 2.71
828 880 3.007473 ACAGGAGAAAACGGGAAACAA 57.993 42.857 0.00 0.00 0.00 2.83
829 881 2.721425 ACAGGAGAAAACGGGAAACA 57.279 45.000 0.00 0.00 0.00 2.83
830 882 2.032290 CGAACAGGAGAAAACGGGAAAC 60.032 50.000 0.00 0.00 0.00 2.78
831 883 2.158928 TCGAACAGGAGAAAACGGGAAA 60.159 45.455 0.00 0.00 0.00 3.13
832 884 1.413445 TCGAACAGGAGAAAACGGGAA 59.587 47.619 0.00 0.00 0.00 3.97
834 886 1.145803 GTCGAACAGGAGAAAACGGG 58.854 55.000 0.00 0.00 0.00 5.28
835 887 1.792949 CAGTCGAACAGGAGAAAACGG 59.207 52.381 0.00 0.00 0.00 4.44
837 889 4.991687 AGATTCAGTCGAACAGGAGAAAAC 59.008 41.667 0.00 0.00 32.81 2.43
838 890 5.215252 AGATTCAGTCGAACAGGAGAAAA 57.785 39.130 0.00 0.00 32.81 2.29
839 891 4.616143 CGAGATTCAGTCGAACAGGAGAAA 60.616 45.833 0.00 0.00 39.92 2.52
840 892 3.119814 CGAGATTCAGTCGAACAGGAGAA 60.120 47.826 0.00 0.00 39.92 2.87
843 899 2.433436 TCGAGATTCAGTCGAACAGGA 58.567 47.619 0.00 0.00 43.26 3.86
878 934 1.679977 TCCGAACGGAGTCGGGAAT 60.680 57.895 20.04 0.00 45.00 3.01
879 935 2.282391 TCCGAACGGAGTCGGGAA 60.282 61.111 20.04 3.83 45.00 3.97
920 976 0.324368 GGGTTGGGAATCCAGGAACC 60.324 60.000 15.06 15.06 45.04 3.62
937 993 3.471244 GATCTCTGGACGCGACGGG 62.471 68.421 15.93 10.72 0.00 5.28
962 1021 1.402456 CCTCCGACGAACTGACGAAAT 60.402 52.381 0.00 0.00 37.99 2.17
976 1035 2.007568 AGGCCTCTCTACCCTCCGA 61.008 63.158 0.00 0.00 0.00 4.55
982 1041 2.420687 CCATTGTTCAGGCCTCTCTACC 60.421 54.545 0.00 0.00 0.00 3.18
984 1043 1.210478 GCCATTGTTCAGGCCTCTCTA 59.790 52.381 0.00 0.00 45.18 2.43
1138 1197 2.281484 GCCGTTGTCCCTGAGCAA 60.281 61.111 0.00 0.00 0.00 3.91
1145 1204 0.804989 CTTCTTGATGCCGTTGTCCC 59.195 55.000 0.00 0.00 0.00 4.46
1350 1421 2.105466 GCAGCGAGCAAGAGGAAGG 61.105 63.158 0.00 0.00 44.79 3.46
1367 1438 1.135575 CATGAACGGGAAAGAGCAAGC 60.136 52.381 0.00 0.00 0.00 4.01
1370 1441 0.960364 GCCATGAACGGGAAAGAGCA 60.960 55.000 0.00 0.00 0.00 4.26
1371 1442 1.803289 GCCATGAACGGGAAAGAGC 59.197 57.895 0.00 0.00 0.00 4.09
1372 1443 1.982073 GCGCCATGAACGGGAAAGAG 61.982 60.000 0.00 0.00 0.00 2.85
1373 1444 2.038269 GCGCCATGAACGGGAAAGA 61.038 57.895 0.00 0.00 0.00 2.52
1394 1486 3.199891 GGGTCATACAACCGCGGC 61.200 66.667 28.58 5.70 40.46 6.53
1395 1487 2.888534 CGGGTCATACAACCGCGG 60.889 66.667 26.86 26.86 41.23 6.46
1399 1491 3.255969 ACACATACGGGTCATACAACC 57.744 47.619 0.00 0.00 38.69 3.77
1400 1492 3.998341 ACAACACATACGGGTCATACAAC 59.002 43.478 0.00 0.00 0.00 3.32
1401 1493 4.274602 ACAACACATACGGGTCATACAA 57.725 40.909 0.00 0.00 0.00 2.41
1402 1494 3.965379 ACAACACATACGGGTCATACA 57.035 42.857 0.00 0.00 0.00 2.29
1403 1495 4.670735 GCAAACAACACATACGGGTCATAC 60.671 45.833 0.00 0.00 0.00 2.39
1404 1496 3.437395 GCAAACAACACATACGGGTCATA 59.563 43.478 0.00 0.00 0.00 2.15
1405 1497 2.227865 GCAAACAACACATACGGGTCAT 59.772 45.455 0.00 0.00 0.00 3.06
1406 1498 1.604755 GCAAACAACACATACGGGTCA 59.395 47.619 0.00 0.00 0.00 4.02
1407 1499 1.604755 TGCAAACAACACATACGGGTC 59.395 47.619 0.00 0.00 0.00 4.46
1408 1500 1.606668 CTGCAAACAACACATACGGGT 59.393 47.619 0.00 0.00 0.00 5.28
1409 1501 1.068610 CCTGCAAACAACACATACGGG 60.069 52.381 0.00 0.00 0.00 5.28
1410 1502 1.606668 ACCTGCAAACAACACATACGG 59.393 47.619 0.00 0.00 0.00 4.02
1411 1503 4.083537 ACATACCTGCAAACAACACATACG 60.084 41.667 0.00 0.00 0.00 3.06
1412 1504 5.153513 CACATACCTGCAAACAACACATAC 58.846 41.667 0.00 0.00 0.00 2.39
1413 1505 4.217334 CCACATACCTGCAAACAACACATA 59.783 41.667 0.00 0.00 0.00 2.29
1418 1520 1.336795 GGCCACATACCTGCAAACAAC 60.337 52.381 0.00 0.00 0.00 3.32
1419 1521 0.965439 GGCCACATACCTGCAAACAA 59.035 50.000 0.00 0.00 0.00 2.83
1441 1551 0.040204 CCAGGAAGGGTTCATTGCCT 59.960 55.000 0.00 0.00 0.00 4.75
1450 1560 1.988406 GTAGGACGCCAGGAAGGGT 60.988 63.158 0.00 0.00 38.09 4.34
2524 2664 2.861730 TGGACCAGAGCCAGGAGA 59.138 61.111 0.00 0.00 0.00 3.71
2567 2707 7.140705 TCAACTGATGCAAAATAAGTCTGTTG 58.859 34.615 19.61 19.61 43.76 3.33
2577 2717 7.572353 GCAACAAATGATCAACTGATGCAAAAT 60.572 33.333 25.10 0.00 37.48 1.82
2582 2722 3.615496 GGCAACAAATGATCAACTGATGC 59.385 43.478 23.40 23.40 36.99 3.91
2641 2784 5.481105 ACAAAGAATCGTACCGAATTACCA 58.519 37.500 0.00 0.00 39.99 3.25
2642 2785 6.753744 AGTACAAAGAATCGTACCGAATTACC 59.246 38.462 0.00 0.00 39.99 2.85
2657 2800 7.512746 AGGTATATATGCCTCCAGTACAAAGAA 59.487 37.037 16.02 0.00 38.64 2.52
2727 2870 4.272748 CACCATAGTCATCAAGCACATCAG 59.727 45.833 0.00 0.00 0.00 2.90
2766 2909 3.937706 CACTGGAACATTGGATCTGAGAC 59.062 47.826 0.00 0.00 38.20 3.36
2769 2912 4.849813 ATCACTGGAACATTGGATCTGA 57.150 40.909 0.00 0.00 39.59 3.27
2821 2964 5.409520 TCAGCAAGTACAACACATCAAGATC 59.590 40.000 0.00 0.00 0.00 2.75
2856 2999 6.479331 CCATTTCAGTCATCACTCATCAGTAG 59.521 42.308 0.00 0.00 0.00 2.57
2857 3000 6.155049 TCCATTTCAGTCATCACTCATCAGTA 59.845 38.462 0.00 0.00 0.00 2.74
2858 3001 5.046087 TCCATTTCAGTCATCACTCATCAGT 60.046 40.000 0.00 0.00 0.00 3.41
2859 3002 5.425630 TCCATTTCAGTCATCACTCATCAG 58.574 41.667 0.00 0.00 0.00 2.90
2860 3003 5.046087 ACTCCATTTCAGTCATCACTCATCA 60.046 40.000 0.00 0.00 0.00 3.07
2861 3004 5.426504 ACTCCATTTCAGTCATCACTCATC 58.573 41.667 0.00 0.00 0.00 2.92
2880 3023 4.382147 GGGACTCTGAATCAACTGTACTCC 60.382 50.000 0.00 0.00 0.00 3.85
2911 3054 0.848735 ATACTCCATGGCCATGCTGT 59.151 50.000 36.08 32.91 37.49 4.40
2968 3113 0.745486 TCCAGGATTCATGTGCTGCG 60.745 55.000 0.00 0.00 36.37 5.18
2993 3138 6.370994 GTGCATCTAGATCCCTAAATGTGATG 59.629 42.308 1.03 0.00 28.44 3.07
2996 3141 5.614308 TGTGCATCTAGATCCCTAAATGTG 58.386 41.667 1.03 0.00 28.44 3.21
3001 3146 5.957771 AAGTTGTGCATCTAGATCCCTAA 57.042 39.130 1.03 0.00 0.00 2.69
3002 3147 5.163301 GGAAAGTTGTGCATCTAGATCCCTA 60.163 44.000 1.03 0.00 0.00 3.53
3003 3148 4.384647 GGAAAGTTGTGCATCTAGATCCCT 60.385 45.833 1.03 0.00 0.00 4.20
3004 3149 3.879892 GGAAAGTTGTGCATCTAGATCCC 59.120 47.826 1.03 0.00 0.00 3.85
3005 3150 4.775236 AGGAAAGTTGTGCATCTAGATCC 58.225 43.478 1.03 0.00 0.00 3.36
3006 3151 6.372659 TCAAAGGAAAGTTGTGCATCTAGATC 59.627 38.462 1.03 0.00 0.00 2.75
3007 3152 6.240894 TCAAAGGAAAGTTGTGCATCTAGAT 58.759 36.000 0.00 0.00 0.00 1.98
3025 3170 1.243342 TGCCGACCTGCATTCAAAGG 61.243 55.000 0.00 0.00 36.04 3.11
3030 3175 3.883997 TTTTTGCCGACCTGCATTC 57.116 47.368 0.00 0.00 41.70 2.67
3163 3312 6.807230 GCGTATAATCATCTGGTAGGTAGTTG 59.193 42.308 0.00 0.00 0.00 3.16
3167 3316 5.577100 AGGCGTATAATCATCTGGTAGGTA 58.423 41.667 0.00 0.00 0.00 3.08
3209 3372 1.078823 TCCCCTGGAGTACATCACAGT 59.921 52.381 0.00 0.00 0.00 3.55
3210 3373 1.866015 TCCCCTGGAGTACATCACAG 58.134 55.000 0.00 0.00 0.00 3.66
3211 3374 2.335681 TTCCCCTGGAGTACATCACA 57.664 50.000 0.00 0.00 31.21 3.58
3212 3375 2.158755 CCATTCCCCTGGAGTACATCAC 60.159 54.545 0.00 0.00 38.69 3.06
3214 3377 2.408565 TCCATTCCCCTGGAGTACATC 58.591 52.381 0.00 0.00 40.43 3.06
3221 3384 5.675077 TGATATAATCTCCATTCCCCTGGA 58.325 41.667 0.00 0.00 43.09 3.86
3222 3385 6.587560 ATGATATAATCTCCATTCCCCTGG 57.412 41.667 0.00 0.00 37.66 4.45
3223 3386 7.408543 ACAATGATATAATCTCCATTCCCCTG 58.591 38.462 0.00 0.00 0.00 4.45
3224 3387 7.594849 ACAATGATATAATCTCCATTCCCCT 57.405 36.000 0.00 0.00 0.00 4.79
3225 3388 9.927081 AATACAATGATATAATCTCCATTCCCC 57.073 33.333 0.00 0.00 0.00 4.81
3250 3413 5.046663 TCACATAGTAGTGCCTGTTGATCAA 60.047 40.000 3.38 3.38 39.35 2.57
3252 3415 5.011090 TCACATAGTAGTGCCTGTTGATC 57.989 43.478 0.00 0.00 39.35 2.92
3260 3423 3.384789 TCACCAGATCACATAGTAGTGCC 59.615 47.826 0.00 0.00 39.35 5.01
3262 3425 6.398095 TGTTTCACCAGATCACATAGTAGTG 58.602 40.000 0.00 0.00 40.85 2.74
3265 3428 7.717436 TGTTTTGTTTCACCAGATCACATAGTA 59.283 33.333 0.00 0.00 0.00 1.82
3273 3436 7.769272 TGATTTTGTTTTGTTTCACCAGATC 57.231 32.000 0.00 0.00 0.00 2.75
3279 3442 6.906678 GCCTGATTGATTTTGTTTTGTTTCAC 59.093 34.615 0.00 0.00 0.00 3.18
3280 3443 6.596888 TGCCTGATTGATTTTGTTTTGTTTCA 59.403 30.769 0.00 0.00 0.00 2.69
3321 3484 0.391793 GCCTCCACTTCAGTACCAGC 60.392 60.000 0.00 0.00 0.00 4.85
3324 3487 1.407437 CCATGCCTCCACTTCAGTACC 60.407 57.143 0.00 0.00 0.00 3.34
3325 3488 1.279271 ACCATGCCTCCACTTCAGTAC 59.721 52.381 0.00 0.00 0.00 2.73
3326 3489 1.555075 GACCATGCCTCCACTTCAGTA 59.445 52.381 0.00 0.00 0.00 2.74
3327 3490 0.326264 GACCATGCCTCCACTTCAGT 59.674 55.000 0.00 0.00 0.00 3.41
3328 3491 0.325933 TGACCATGCCTCCACTTCAG 59.674 55.000 0.00 0.00 0.00 3.02
3330 3493 0.678048 GGTGACCATGCCTCCACTTC 60.678 60.000 0.00 0.00 0.00 3.01
3331 3494 1.136329 AGGTGACCATGCCTCCACTT 61.136 55.000 3.63 0.00 0.00 3.16
3332 3495 1.539869 AGGTGACCATGCCTCCACT 60.540 57.895 3.63 0.00 0.00 4.00
3333 3496 1.377725 CAGGTGACCATGCCTCCAC 60.378 63.158 3.63 0.00 31.73 4.02
3334 3497 3.080641 CAGGTGACCATGCCTCCA 58.919 61.111 3.63 0.00 31.73 3.86
3335 3498 1.626356 TAGCAGGTGACCATGCCTCC 61.626 60.000 18.16 0.00 43.60 4.30
3336 3499 0.179062 CTAGCAGGTGACCATGCCTC 60.179 60.000 18.16 0.00 43.60 4.70
3337 3500 0.911525 ACTAGCAGGTGACCATGCCT 60.912 55.000 18.16 10.77 43.60 4.75
3338 3501 0.745845 CACTAGCAGGTGACCATGCC 60.746 60.000 18.16 5.39 43.60 4.40
3339 3502 0.036010 ACACTAGCAGGTGACCATGC 60.036 55.000 15.28 15.28 42.87 4.06
3340 3503 3.610040 TTACACTAGCAGGTGACCATG 57.390 47.619 3.63 0.14 40.13 3.66
3341 3504 3.326588 TGTTTACACTAGCAGGTGACCAT 59.673 43.478 3.63 0.00 40.13 3.55
3342 3505 2.701423 TGTTTACACTAGCAGGTGACCA 59.299 45.455 3.63 4.27 40.13 4.02
3343 3506 3.396260 TGTTTACACTAGCAGGTGACC 57.604 47.619 14.45 0.00 40.13 4.02
3344 3507 4.992381 CTTGTTTACACTAGCAGGTGAC 57.008 45.455 14.45 4.79 40.13 3.67
3352 3515 5.050091 CCACTTCAGTGCTTGTTTACACTAG 60.050 44.000 1.01 0.00 45.15 2.57
3353 3516 4.814234 CCACTTCAGTGCTTGTTTACACTA 59.186 41.667 1.01 0.00 45.15 2.74
3355 3518 3.625764 TCCACTTCAGTGCTTGTTTACAC 59.374 43.478 1.01 0.00 44.34 2.90
3356 3519 3.876914 CTCCACTTCAGTGCTTGTTTACA 59.123 43.478 1.01 0.00 44.34 2.41
3357 3520 3.251004 CCTCCACTTCAGTGCTTGTTTAC 59.749 47.826 1.01 0.00 44.34 2.01
3362 3525 0.535780 TGCCTCCACTTCAGTGCTTG 60.536 55.000 1.01 0.00 44.34 4.01
3393 3556 1.699083 TGAGGGTGATGCAGAGACAAA 59.301 47.619 0.00 0.00 0.00 2.83
3493 3659 8.880991 TTATACTATGAGTTGGAGAGGGATAC 57.119 38.462 0.00 0.00 0.00 2.24


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

AutoCloner maintained by Alex Coulton.