Multiple sequence alignment - TraesCS5A01G171600

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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 TraesCS5A01G171600 chr5A 100.000 2693 0 0 1 2693 364963204 364960512 0.000000e+00 4974.0
1 TraesCS5A01G171600 chr5A 75.920 652 80 38 1082 1692 364970525 364969910 2.060000e-66 263.0
2 TraesCS5A01G171600 chr5A 88.406 207 18 2 1304 1510 364978544 364978344 7.450000e-61 244.0
3 TraesCS5A01G171600 chr5A 84.028 144 17 3 1555 1692 364978215 364978072 1.680000e-27 134.0
4 TraesCS5A01G171600 chr5A 85.345 116 15 1 1088 1203 364978661 364978548 4.710000e-23 119.0
5 TraesCS5A01G171600 chr5D 87.280 1934 117 42 67 1952 276469028 276467176 0.000000e+00 2089.0
6 TraesCS5A01G171600 chr5D 77.626 657 87 30 1082 1692 276546955 276546313 7.140000e-91 344.0
7 TraesCS5A01G171600 chr5D 91.403 221 19 0 2473 2693 276455756 276455536 1.210000e-78 303.0
8 TraesCS5A01G171600 chr5D 88.406 207 18 2 1302 1508 276553708 276553508 7.450000e-61 244.0
9 TraesCS5A01G171600 chr5D 96.809 94 1 2 1946 2037 276456380 276456287 3.590000e-34 156.0
10 TraesCS5A01G171600 chr5B 85.866 1316 120 25 1070 2362 313213048 313211776 0.000000e+00 1339.0
11 TraesCS5A01G171600 chr5B 93.350 391 18 3 67 454 313214134 313213749 3.010000e-159 571.0
12 TraesCS5A01G171600 chr5B 85.751 393 22 12 676 1034 313213439 313213047 4.210000e-103 385.0
13 TraesCS5A01G171600 chr5B 77.439 656 86 34 1082 1692 313311577 313310939 4.300000e-88 335.0
14 TraesCS5A01G171600 chr5B 95.238 168 5 1 454 621 313213619 313213455 2.060000e-66 263.0
15 TraesCS5A01G171600 chr5B 90.083 121 11 1 2361 2481 313211742 313211623 3.590000e-34 156.0
16 TraesCS5A01G171600 chr5B 100.000 28 0 0 2335 2362 618151779 618151806 5.000000e-03 52.8
17 TraesCS5A01G171600 chr1B 77.820 266 50 8 2025 2283 677280182 677279919 3.590000e-34 156.0
18 TraesCS5A01G171600 chr7D 80.882 204 32 6 2025 2223 19582108 19581907 1.290000e-33 154.0
19 TraesCS5A01G171600 chr7D 82.390 159 22 5 2122 2276 111067505 111067349 1.680000e-27 134.0
20 TraesCS5A01G171600 chr1D 78.210 257 45 7 2033 2282 365736333 365736081 1.290000e-33 154.0
21 TraesCS5A01G171600 chrUn 78.175 252 43 10 2035 2277 97969768 97969520 1.670000e-32 150.0
22 TraesCS5A01G171600 chr3A 77.099 262 55 4 2025 2281 709121920 709121659 2.160000e-31 147.0
23 TraesCS5A01G171600 chr3A 76.233 223 38 14 2076 2289 506430650 506430866 1.320000e-18 104.0
24 TraesCS5A01G171600 chr2B 78.189 243 36 10 2060 2289 760952585 760952823 3.620000e-29 139.0
25 TraesCS5A01G171600 chr2B 77.778 198 38 6 2025 2218 381524352 381524547 1.690000e-22 117.0
26 TraesCS5A01G171600 chr2B 80.488 82 15 1 2281 2362 667870497 667870417 8.050000e-06 62.1
27 TraesCS5A01G171600 chr6B 79.747 158 25 6 2025 2179 35062000 35062153 1.020000e-19 108.0


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 TraesCS5A01G171600 chr5A 364960512 364963204 2692 True 4974.0 4974 100.0000 1 2693 1 chr5A.!!$R1 2692
1 TraesCS5A01G171600 chr5A 364969910 364970525 615 True 263.0 263 75.9200 1082 1692 1 chr5A.!!$R2 610
2 TraesCS5A01G171600 chr5D 276467176 276469028 1852 True 2089.0 2089 87.2800 67 1952 1 chr5D.!!$R1 1885
3 TraesCS5A01G171600 chr5D 276546313 276546955 642 True 344.0 344 77.6260 1082 1692 1 chr5D.!!$R2 610
4 TraesCS5A01G171600 chr5D 276455536 276456380 844 True 229.5 303 94.1060 1946 2693 2 chr5D.!!$R4 747
5 TraesCS5A01G171600 chr5B 313211623 313214134 2511 True 542.8 1339 90.0576 67 2481 5 chr5B.!!$R2 2414
6 TraesCS5A01G171600 chr5B 313310939 313311577 638 True 335.0 335 77.4390 1082 1692 1 chr5B.!!$R1 610

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
229 230 0.036577 CACCTTGAGTGCCAGAGGAG 60.037 60.0 0.0 0.0 40.28 3.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2059 2326 0.037605 GGTCTCCGGACGTGAATGTT 60.038 55.0 0.0 0.0 42.97 2.71 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
25 26 7.807977 TTGTCTTCTTCTTTTTGTATGCTCT 57.192 32.000 0.00 0.00 0.00 4.09
26 27 7.426929 TGTCTTCTTCTTTTTGTATGCTCTC 57.573 36.000 0.00 0.00 0.00 3.20
27 28 7.220030 TGTCTTCTTCTTTTTGTATGCTCTCT 58.780 34.615 0.00 0.00 0.00 3.10
28 29 7.172190 TGTCTTCTTCTTTTTGTATGCTCTCTG 59.828 37.037 0.00 0.00 0.00 3.35
29 30 7.386299 GTCTTCTTCTTTTTGTATGCTCTCTGA 59.614 37.037 0.00 0.00 0.00 3.27
30 31 7.933577 TCTTCTTCTTTTTGTATGCTCTCTGAA 59.066 33.333 0.00 0.00 0.00 3.02
31 32 8.627208 TTCTTCTTTTTGTATGCTCTCTGAAT 57.373 30.769 0.00 0.00 0.00 2.57
32 33 8.261492 TCTTCTTTTTGTATGCTCTCTGAATC 57.739 34.615 0.00 0.00 0.00 2.52
33 34 8.099537 TCTTCTTTTTGTATGCTCTCTGAATCT 58.900 33.333 0.00 0.00 0.00 2.40
34 35 8.627208 TTCTTTTTGTATGCTCTCTGAATCTT 57.373 30.769 0.00 0.00 0.00 2.40
35 36 8.261492 TCTTTTTGTATGCTCTCTGAATCTTC 57.739 34.615 0.00 0.00 0.00 2.87
36 37 7.879677 TCTTTTTGTATGCTCTCTGAATCTTCA 59.120 33.333 0.00 0.00 35.57 3.02
37 38 6.974932 TTTGTATGCTCTCTGAATCTTCAC 57.025 37.500 0.00 0.00 32.90 3.18
38 39 5.665916 TGTATGCTCTCTGAATCTTCACA 57.334 39.130 0.00 0.00 32.90 3.58
39 40 5.658468 TGTATGCTCTCTGAATCTTCACAG 58.342 41.667 0.00 0.00 32.90 3.66
40 41 3.606595 TGCTCTCTGAATCTTCACAGG 57.393 47.619 0.00 0.00 35.20 4.00
41 42 2.235650 TGCTCTCTGAATCTTCACAGGG 59.764 50.000 0.00 0.00 36.11 4.45
42 43 2.419851 GCTCTCTGAATCTTCACAGGGG 60.420 54.545 0.00 0.00 35.57 4.79
43 44 2.836981 CTCTCTGAATCTTCACAGGGGT 59.163 50.000 0.00 0.00 35.57 4.95
44 45 3.251484 TCTCTGAATCTTCACAGGGGTT 58.749 45.455 0.00 0.00 35.57 4.11
45 46 3.261897 TCTCTGAATCTTCACAGGGGTTC 59.738 47.826 0.00 0.00 35.57 3.62
46 47 2.028112 TCTGAATCTTCACAGGGGTTCG 60.028 50.000 0.00 0.00 35.20 3.95
47 48 1.087501 GAATCTTCACAGGGGTTCGC 58.912 55.000 0.00 0.00 0.00 4.70
48 49 0.693049 AATCTTCACAGGGGTTCGCT 59.307 50.000 0.00 0.00 0.00 4.93
50 51 1.672356 CTTCACAGGGGTTCGCTGG 60.672 63.158 14.76 5.79 46.52 4.85
51 52 2.397413 CTTCACAGGGGTTCGCTGGT 62.397 60.000 14.76 0.68 46.52 4.00
52 53 2.669569 CACAGGGGTTCGCTGGTG 60.670 66.667 14.76 8.00 46.52 4.17
53 54 2.847234 ACAGGGGTTCGCTGGTGA 60.847 61.111 14.76 0.00 46.52 4.02
54 55 2.358737 CAGGGGTTCGCTGGTGAC 60.359 66.667 4.35 0.00 40.11 3.67
55 56 2.847234 AGGGGTTCGCTGGTGACA 60.847 61.111 0.00 0.00 39.59 3.58
56 57 2.112297 GGGGTTCGCTGGTGACAA 59.888 61.111 0.00 0.00 42.06 3.18
57 58 1.527380 GGGGTTCGCTGGTGACAAA 60.527 57.895 0.00 0.00 42.06 2.83
58 59 1.652563 GGGTTCGCTGGTGACAAAC 59.347 57.895 0.00 0.00 42.06 2.93
59 60 1.278637 GGTTCGCTGGTGACAAACG 59.721 57.895 0.00 0.00 42.06 3.60
60 61 1.433837 GGTTCGCTGGTGACAAACGT 61.434 55.000 0.00 0.00 42.06 3.99
61 62 1.210870 GTTCGCTGGTGACAAACGTA 58.789 50.000 0.00 0.00 42.06 3.57
62 63 1.593933 GTTCGCTGGTGACAAACGTAA 59.406 47.619 0.00 0.00 42.06 3.18
63 64 1.493772 TCGCTGGTGACAAACGTAAG 58.506 50.000 0.00 0.00 42.06 2.34
64 65 1.202440 TCGCTGGTGACAAACGTAAGT 60.202 47.619 0.00 0.00 46.92 2.24
178 179 2.903135 CCTTCACCTCTGACCTCTCTTT 59.097 50.000 0.00 0.00 0.00 2.52
222 223 2.282462 CACCCCACCTTGAGTGCC 60.282 66.667 0.00 0.00 45.83 5.01
229 230 0.036577 CACCTTGAGTGCCAGAGGAG 60.037 60.000 0.00 0.00 40.28 3.69
230 231 1.078567 CCTTGAGTGCCAGAGGAGC 60.079 63.158 0.00 0.00 0.00 4.70
234 238 0.972983 TGAGTGCCAGAGGAGCCTAC 60.973 60.000 0.00 0.00 0.00 3.18
251 255 3.867216 GCCTACCGCTAACCAGAGAAAAA 60.867 47.826 0.00 0.00 0.00 1.94
350 354 6.368791 GTCACTGCACATATCAAACACTTCTA 59.631 38.462 0.00 0.00 0.00 2.10
354 358 7.772292 ACTGCACATATCAAACACTTCTATGAT 59.228 33.333 0.00 0.00 36.54 2.45
356 360 7.042523 TGCACATATCAAACACTTCTATGATCG 60.043 37.037 0.00 0.00 34.54 3.69
365 369 5.837437 ACACTTCTATGATCGATCAAGGAC 58.163 41.667 30.41 2.17 40.69 3.85
444 448 1.066605 ACTAGTCACAACAACGACGCT 59.933 47.619 0.00 0.00 37.23 5.07
452 456 3.184783 CACAACAACGACGCTAACCATTA 59.815 43.478 0.00 0.00 0.00 1.90
473 608 6.748333 TTAAAAGAGTTCCATGATGAGCTG 57.252 37.500 0.00 0.00 0.00 4.24
483 618 3.070734 CCATGATGAGCTGCTAAGTAGGT 59.929 47.826 0.15 0.00 0.00 3.08
573 708 8.466617 TTTTCTGTTTCTCTCTCTACTACACT 57.533 34.615 0.00 0.00 0.00 3.55
621 756 3.305398 AGACATGTCTTTCGTCTGGAC 57.695 47.619 22.89 0.00 38.55 4.02
622 757 2.028930 AGACATGTCTTTCGTCTGGACC 60.029 50.000 22.89 0.00 38.55 4.46
623 758 1.691976 ACATGTCTTTCGTCTGGACCA 59.308 47.619 0.00 0.00 0.00 4.02
624 759 2.104111 ACATGTCTTTCGTCTGGACCAA 59.896 45.455 0.00 0.00 0.00 3.67
625 760 2.526304 TGTCTTTCGTCTGGACCAAG 57.474 50.000 0.00 0.00 0.00 3.61
626 761 1.760613 TGTCTTTCGTCTGGACCAAGT 59.239 47.619 0.00 0.00 0.00 3.16
627 762 2.169769 TGTCTTTCGTCTGGACCAAGTT 59.830 45.455 0.00 0.00 0.00 2.66
628 763 3.385433 TGTCTTTCGTCTGGACCAAGTTA 59.615 43.478 0.00 0.00 0.00 2.24
629 764 4.141892 TGTCTTTCGTCTGGACCAAGTTAA 60.142 41.667 0.00 0.00 0.00 2.01
630 765 4.995487 GTCTTTCGTCTGGACCAAGTTAAT 59.005 41.667 0.00 0.00 0.00 1.40
631 766 4.994852 TCTTTCGTCTGGACCAAGTTAATG 59.005 41.667 0.00 0.00 0.00 1.90
632 767 4.345859 TTCGTCTGGACCAAGTTAATGT 57.654 40.909 0.00 0.00 0.00 2.71
633 768 3.659786 TCGTCTGGACCAAGTTAATGTG 58.340 45.455 0.00 0.00 0.00 3.21
634 769 3.070446 TCGTCTGGACCAAGTTAATGTGT 59.930 43.478 0.00 0.00 0.00 3.72
635 770 3.186409 CGTCTGGACCAAGTTAATGTGTG 59.814 47.826 0.00 0.00 0.00 3.82
636 771 3.502211 GTCTGGACCAAGTTAATGTGTGG 59.498 47.826 0.00 0.00 37.17 4.17
637 772 3.392947 TCTGGACCAAGTTAATGTGTGGA 59.607 43.478 0.00 0.00 35.04 4.02
638 773 4.141287 CTGGACCAAGTTAATGTGTGGAA 58.859 43.478 0.00 0.00 35.04 3.53
639 774 4.537751 TGGACCAAGTTAATGTGTGGAAA 58.462 39.130 0.00 0.00 35.04 3.13
640 775 4.339814 TGGACCAAGTTAATGTGTGGAAAC 59.660 41.667 0.00 0.00 35.04 2.78
641 776 4.583073 GGACCAAGTTAATGTGTGGAAACT 59.417 41.667 0.00 0.00 35.04 2.66
642 777 5.278315 GGACCAAGTTAATGTGTGGAAACTC 60.278 44.000 0.00 0.00 35.04 3.01
643 778 5.445964 ACCAAGTTAATGTGTGGAAACTCT 58.554 37.500 0.00 0.00 35.04 3.24
644 779 5.299279 ACCAAGTTAATGTGTGGAAACTCTG 59.701 40.000 0.00 0.00 35.04 3.35
645 780 5.278463 CCAAGTTAATGTGTGGAAACTCTGG 60.278 44.000 0.00 0.00 31.15 3.86
651 786 0.823356 TGTGGAAACTCTGGCCAAGC 60.823 55.000 7.01 0.00 32.68 4.01
674 809 3.834799 CCGACCGGAGCCTACCAC 61.835 72.222 9.46 0.00 37.50 4.16
792 933 3.900601 ACCATTTTGTTGGCTGATTGGTA 59.099 39.130 0.00 0.00 40.68 3.25
857 998 1.334384 GCTTCCCTCTGACCCTCTCC 61.334 65.000 0.00 0.00 0.00 3.71
867 1008 0.983905 GACCCTCTCCCCCTCCTTTC 60.984 65.000 0.00 0.00 0.00 2.62
874 1017 1.192146 TCCCCCTCCTTTCTGTGTCG 61.192 60.000 0.00 0.00 0.00 4.35
902 1050 7.238486 ACTCTCTGTCTGCATATAAATAGGG 57.762 40.000 0.00 0.00 0.00 3.53
928 1079 4.061596 GGGTATCTTGCTGCTGATAAGAC 58.938 47.826 14.12 7.72 33.69 3.01
953 1127 4.081752 CAGAAGCTCATCCAACTCTACTGT 60.082 45.833 0.00 0.00 0.00 3.55
967 1141 5.317808 ACTCTACTGTCAAGCTAGACAAGA 58.682 41.667 0.00 0.00 46.90 3.02
971 1145 5.637006 ACTGTCAAGCTAGACAAGACTAG 57.363 43.478 0.00 0.00 46.90 2.57
980 1154 2.785562 AGACAAGACTAGAGCTCGTGT 58.214 47.619 8.37 11.16 33.68 4.49
1005 1179 3.233507 ACATTGTCCAAGCAAGATGGTT 58.766 40.909 0.00 0.00 38.82 3.67
1023 1197 4.993028 TGGTTAAGGTTGGTTGCTAATCT 58.007 39.130 0.00 0.00 0.00 2.40
1037 1212 5.385509 TGCTAATCTGCAAACCTTTTACC 57.614 39.130 0.00 0.00 40.29 2.85
1038 1213 4.830046 TGCTAATCTGCAAACCTTTTACCA 59.170 37.500 0.00 0.00 40.29 3.25
1039 1214 5.303078 TGCTAATCTGCAAACCTTTTACCAA 59.697 36.000 0.00 0.00 40.29 3.67
1040 1215 6.014669 TGCTAATCTGCAAACCTTTTACCAAT 60.015 34.615 0.00 0.00 40.29 3.16
1041 1216 6.873605 GCTAATCTGCAAACCTTTTACCAATT 59.126 34.615 0.00 0.00 0.00 2.32
1042 1217 7.387673 GCTAATCTGCAAACCTTTTACCAATTT 59.612 33.333 0.00 0.00 0.00 1.82
1043 1218 9.921637 CTAATCTGCAAACCTTTTACCAATTTA 57.078 29.630 0.00 0.00 0.00 1.40
1044 1219 8.831715 AATCTGCAAACCTTTTACCAATTTAG 57.168 30.769 0.00 0.00 0.00 1.85
1045 1220 6.220201 TCTGCAAACCTTTTACCAATTTAGC 58.780 36.000 0.00 0.00 0.00 3.09
1046 1221 6.041523 TCTGCAAACCTTTTACCAATTTAGCT 59.958 34.615 0.00 0.00 0.00 3.32
1047 1222 6.220201 TGCAAACCTTTTACCAATTTAGCTC 58.780 36.000 0.00 0.00 0.00 4.09
1048 1223 5.344933 GCAAACCTTTTACCAATTTAGCTCG 59.655 40.000 0.00 0.00 0.00 5.03
1049 1224 6.443792 CAAACCTTTTACCAATTTAGCTCGT 58.556 36.000 0.00 0.00 0.00 4.18
1050 1225 5.874895 ACCTTTTACCAATTTAGCTCGTC 57.125 39.130 0.00 0.00 0.00 4.20
1051 1226 4.390909 ACCTTTTACCAATTTAGCTCGTCG 59.609 41.667 0.00 0.00 0.00 5.12
1052 1227 4.390909 CCTTTTACCAATTTAGCTCGTCGT 59.609 41.667 0.00 0.00 0.00 4.34
1053 1228 4.914312 TTTACCAATTTAGCTCGTCGTG 57.086 40.909 0.00 0.00 0.00 4.35
1054 1229 2.450609 ACCAATTTAGCTCGTCGTGT 57.549 45.000 0.00 0.00 0.00 4.49
1055 1230 2.762745 ACCAATTTAGCTCGTCGTGTT 58.237 42.857 0.00 0.00 0.00 3.32
1056 1231 2.735134 ACCAATTTAGCTCGTCGTGTTC 59.265 45.455 0.00 0.00 0.00 3.18
1057 1232 2.993899 CCAATTTAGCTCGTCGTGTTCT 59.006 45.455 0.00 0.00 0.00 3.01
1058 1233 4.171005 CCAATTTAGCTCGTCGTGTTCTA 58.829 43.478 0.00 0.00 0.00 2.10
1059 1234 4.265556 CCAATTTAGCTCGTCGTGTTCTAG 59.734 45.833 0.00 0.00 0.00 2.43
1060 1235 2.539346 TTAGCTCGTCGTGTTCTAGC 57.461 50.000 0.00 0.00 0.00 3.42
1061 1236 1.735386 TAGCTCGTCGTGTTCTAGCT 58.265 50.000 8.65 8.65 45.14 3.32
1062 1237 1.735386 AGCTCGTCGTGTTCTAGCTA 58.265 50.000 2.33 0.00 41.56 3.32
1063 1238 1.397692 AGCTCGTCGTGTTCTAGCTAC 59.602 52.381 2.33 0.00 41.56 3.58
1064 1239 1.851295 GCTCGTCGTGTTCTAGCTACG 60.851 57.143 0.00 0.00 39.04 3.51
1065 1240 1.657594 CTCGTCGTGTTCTAGCTACGA 59.342 52.381 4.60 4.60 43.63 3.43
1066 1241 1.657594 TCGTCGTGTTCTAGCTACGAG 59.342 52.381 8.85 4.51 46.01 4.18
1067 1242 1.392853 CGTCGTGTTCTAGCTACGAGT 59.607 52.381 8.85 0.00 46.01 4.18
1068 1243 2.771689 GTCGTGTTCTAGCTACGAGTG 58.228 52.381 8.85 0.00 46.01 3.51
1076 1251 5.240183 TGTTCTAGCTACGAGTGTTAGTGTT 59.760 40.000 0.00 0.00 0.00 3.32
1080 1255 7.692088 TCTAGCTACGAGTGTTAGTGTTTATC 58.308 38.462 0.00 0.00 0.00 1.75
1105 1280 1.792949 AGTTTTGTGCGTCGATCTGAC 59.207 47.619 0.00 7.40 44.53 3.51
1113 1288 0.982673 CGTCGATCTGACCGTGTTTC 59.017 55.000 10.66 0.00 45.23 2.78
1157 1333 1.002792 GTTCTCAAGTTGCCGTTGGAC 60.003 52.381 0.00 0.00 0.00 4.02
1210 1386 2.406616 CCGTTGGCATGGCAGGTAC 61.407 63.158 22.17 16.32 0.00 3.34
1235 1413 3.518705 AGAAGAAGCCACTGATCATGACT 59.481 43.478 0.00 0.00 0.00 3.41
1237 1415 4.399004 AGAAGCCACTGATCATGACTAC 57.601 45.455 0.00 0.00 0.00 2.73
1240 1418 2.169352 AGCCACTGATCATGACTACCAC 59.831 50.000 0.00 0.00 0.00 4.16
1277 1478 4.244425 TCTTCTCTTCGTTGGTTCTCAG 57.756 45.455 0.00 0.00 0.00 3.35
1521 1730 2.044650 TACGGCTACGGTGGAGCT 60.045 61.111 0.38 0.00 46.48 4.09
1579 1809 0.604073 TTACCATCAGAACGCGGTGA 59.396 50.000 12.47 10.99 32.81 4.02
1596 1826 3.495352 GACGCCGATTCCCTACCCG 62.495 68.421 0.00 0.00 0.00 5.28
1693 1935 1.265095 CCGGCTGCAGCATAATGTAAG 59.735 52.381 37.63 16.65 44.36 2.34
1694 1936 1.334419 CGGCTGCAGCATAATGTAAGC 60.334 52.381 37.63 16.56 44.36 3.09
1695 1937 1.952296 GGCTGCAGCATAATGTAAGCT 59.048 47.619 37.63 0.00 44.36 3.74
1696 1938 3.141398 GGCTGCAGCATAATGTAAGCTA 58.859 45.455 37.63 0.00 44.36 3.32
1697 1939 3.565482 GGCTGCAGCATAATGTAAGCTAA 59.435 43.478 37.63 0.00 44.36 3.09
1698 1940 4.320057 GGCTGCAGCATAATGTAAGCTAAG 60.320 45.833 37.63 0.00 44.36 2.18
1699 1941 4.781071 CTGCAGCATAATGTAAGCTAAGC 58.219 43.478 0.00 0.00 36.73 3.09
1700 1942 4.454678 TGCAGCATAATGTAAGCTAAGCT 58.545 39.130 0.00 0.00 42.56 3.74
1746 2011 2.637947 GGGGAGACTCAAGCTTTCATC 58.362 52.381 4.53 0.00 0.00 2.92
1772 2037 8.635765 TCAAAATAAGTTCAGGACAAGCTTAT 57.364 30.769 0.00 0.00 34.86 1.73
1795 2060 2.662006 TCCTGAACTGATCAAGCGAG 57.338 50.000 0.00 0.00 37.67 5.03
1867 2132 4.458397 ACATAGCTTGTGGAATCATCTGG 58.542 43.478 0.00 0.00 37.11 3.86
1869 2134 3.726557 AGCTTGTGGAATCATCTGGAA 57.273 42.857 0.00 0.00 0.00 3.53
1891 2156 4.447138 TGGTTGTCTGTAAATTCAGGGT 57.553 40.909 0.00 0.00 36.25 4.34
1933 2198 3.306703 GTGTTGTGGTTTGTGCAAGATTG 59.693 43.478 0.00 0.00 0.00 2.67
1947 2212 3.230134 CAAGATTGGAAAAGGGTGGACA 58.770 45.455 0.00 0.00 0.00 4.02
2045 2312 2.105649 TCATGGCAGTACAAGAACACCA 59.894 45.455 0.00 0.00 33.84 4.17
2057 2324 9.436957 AGTACAAGAACACCAGATGTAATAAAG 57.563 33.333 0.00 0.00 42.31 1.85
2058 2325 9.431887 GTACAAGAACACCAGATGTAATAAAGA 57.568 33.333 0.00 0.00 42.31 2.52
2059 2326 8.918202 ACAAGAACACCAGATGTAATAAAGAA 57.082 30.769 0.00 0.00 42.31 2.52
2060 2327 9.349713 ACAAGAACACCAGATGTAATAAAGAAA 57.650 29.630 0.00 0.00 42.31 2.52
2061 2328 9.612620 CAAGAACACCAGATGTAATAAAGAAAC 57.387 33.333 0.00 0.00 42.31 2.78
2062 2329 8.918202 AGAACACCAGATGTAATAAAGAAACA 57.082 30.769 0.00 0.00 42.31 2.83
2063 2330 9.520515 AGAACACCAGATGTAATAAAGAAACAT 57.479 29.630 0.00 0.00 42.31 2.71
2066 2333 9.295825 ACACCAGATGTAATAAAGAAACATTCA 57.704 29.630 0.00 0.00 40.88 2.57
2067 2334 9.559958 CACCAGATGTAATAAAGAAACATTCAC 57.440 33.333 0.00 0.00 34.09 3.18
2068 2335 8.450964 ACCAGATGTAATAAAGAAACATTCACG 58.549 33.333 0.00 0.00 34.09 4.35
2069 2336 8.450964 CCAGATGTAATAAAGAAACATTCACGT 58.549 33.333 0.00 0.00 34.09 4.49
2070 2337 9.478019 CAGATGTAATAAAGAAACATTCACGTC 57.522 33.333 0.00 0.00 34.09 4.34
2071 2338 8.665685 AGATGTAATAAAGAAACATTCACGTCC 58.334 33.333 0.00 0.00 34.09 4.79
2072 2339 6.823531 TGTAATAAAGAAACATTCACGTCCG 58.176 36.000 0.00 0.00 0.00 4.79
2073 2340 4.939509 ATAAAGAAACATTCACGTCCGG 57.060 40.909 0.00 0.00 0.00 5.14
2085 2352 1.378250 CGTCCGGAGACCACCTAGT 60.378 63.158 3.06 0.00 40.12 2.57
2092 2359 0.810016 GAGACCACCTAGTGACGACC 59.190 60.000 0.00 0.00 35.23 4.79
2105 2372 2.417239 GTGACGACCACAAACACTGAAA 59.583 45.455 7.60 0.00 45.03 2.69
2113 2380 4.142182 ACCACAAACACTGAAATGAGTTGG 60.142 41.667 0.00 0.00 0.00 3.77
2118 2385 1.466167 CACTGAAATGAGTTGGAGGCG 59.534 52.381 0.00 0.00 0.00 5.52
2120 2387 2.301870 ACTGAAATGAGTTGGAGGCGTA 59.698 45.455 0.00 0.00 0.00 4.42
2144 2411 2.143419 GTCATCGCCCCTCCCTCAT 61.143 63.158 0.00 0.00 0.00 2.90
2146 2413 1.840650 CATCGCCCCTCCCTCATCT 60.841 63.158 0.00 0.00 0.00 2.90
2147 2414 0.542938 CATCGCCCCTCCCTCATCTA 60.543 60.000 0.00 0.00 0.00 1.98
2163 2430 5.588648 CCTCATCTAAGCCGGACAAAATTTA 59.411 40.000 5.05 0.00 0.00 1.40
2166 2433 8.740123 TCATCTAAGCCGGACAAAATTTATTA 57.260 30.769 5.05 0.00 0.00 0.98
2175 2442 9.048446 GCCGGACAAAATTTATTATAGTAGACA 57.952 33.333 5.05 0.00 0.00 3.41
2198 2465 2.346803 TGGAAAGTCATCGTGCTAAGC 58.653 47.619 0.00 0.00 0.00 3.09
2201 2468 0.107654 AAGTCATCGTGCTAAGCCCC 60.108 55.000 0.00 0.00 0.00 5.80
2221 2489 1.233019 CAAGACCAGTGCACCAGAAG 58.767 55.000 14.63 0.12 0.00 2.85
2230 2500 0.179043 TGCACCAGAAGCAACCGTTA 60.179 50.000 0.00 0.00 39.39 3.18
2246 2516 5.924475 ACCGTTACTGATGAAGAAAAGTG 57.076 39.130 0.00 0.00 0.00 3.16
2269 2539 5.415701 TGTAGATTGAAAGAATCCAACCTGC 59.584 40.000 0.00 0.00 0.00 4.85
2288 2558 3.402110 TGCAGACACATGAAACGAAGAT 58.598 40.909 0.00 0.00 0.00 2.40
2294 2564 5.352569 AGACACATGAAACGAAGATTGGATC 59.647 40.000 0.00 0.00 0.00 3.36
2301 2571 3.071874 ACGAAGATTGGATCCAAGCAA 57.928 42.857 36.89 15.47 43.87 3.91
2304 2574 4.463891 ACGAAGATTGGATCCAAGCAAATT 59.536 37.500 36.89 25.50 43.87 1.82
2305 2575 5.039333 CGAAGATTGGATCCAAGCAAATTC 58.961 41.667 36.89 29.45 43.87 2.17
2309 2579 5.659525 AGATTGGATCCAAGCAAATTCATCA 59.340 36.000 36.89 10.67 43.87 3.07
2315 2585 5.787953 TCCAAGCAAATTCATCAAAGACA 57.212 34.783 0.00 0.00 0.00 3.41
2321 2591 4.092383 GCAAATTCATCAAAGACATGCACC 59.908 41.667 0.00 0.00 0.00 5.01
2322 2592 3.770263 ATTCATCAAAGACATGCACCG 57.230 42.857 0.00 0.00 0.00 4.94
2324 2594 2.989909 TCATCAAAGACATGCACCGAT 58.010 42.857 0.00 0.00 0.00 4.18
2334 2604 0.526096 ATGCACCGATTGAATTGCGC 60.526 50.000 0.00 0.00 37.82 6.09
2337 2607 0.587242 CACCGATTGAATTGCGCGAG 60.587 55.000 12.10 0.00 0.00 5.03
2352 2622 0.248296 GCGAGATCCGTCAGAGACAC 60.248 60.000 5.66 0.00 41.15 3.67
2384 2689 2.355209 GGGCTAGGTGAGGAGAAACTTG 60.355 54.545 0.00 0.00 0.00 3.16
2393 2698 3.261897 TGAGGAGAAACTTGTCCCATCTC 59.738 47.826 2.14 0.00 41.30 2.75
2396 2701 4.021102 GAGAAACTTGTCCCATCTCCAA 57.979 45.455 0.00 0.00 32.30 3.53
2485 2880 1.209747 ACGGAGCAGGAATCCTAAACC 59.790 52.381 0.00 4.68 34.45 3.27
2496 2891 7.154656 CAGGAATCCTAAACCTTTTTCTTTGG 58.845 38.462 0.00 0.00 29.64 3.28
2503 2898 6.721668 CCTAAACCTTTTTCTTTGGAGAGGAT 59.278 38.462 0.00 0.00 32.44 3.24
2505 2900 5.066913 ACCTTTTTCTTTGGAGAGGATGT 57.933 39.130 0.00 0.00 32.44 3.06
2507 2902 4.219288 CCTTTTTCTTTGGAGAGGATGTGG 59.781 45.833 0.00 0.00 32.44 4.17
2513 2908 2.202987 GAGAGGATGTGGCGGCTG 60.203 66.667 11.43 0.00 0.00 4.85
2537 2932 4.317291 CGTAAAGCGACATGTTAAAAGCAC 59.683 41.667 0.00 0.00 44.77 4.40
2541 2936 5.621197 AGCGACATGTTAAAAGCACATTA 57.379 34.783 0.00 0.00 32.25 1.90
2580 2975 8.571336 AGACATGAAGAACCTAATGAAACTTTG 58.429 33.333 0.00 0.00 0.00 2.77
2645 3040 6.594284 TCTATTTGAGTTGATTGATCTGCG 57.406 37.500 0.00 0.00 0.00 5.18
2682 3077 1.893801 ACCTCGAGACCAAAGACGATT 59.106 47.619 15.71 0.00 34.41 3.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 8.225603 AGAGCATACAAAAAGAAGAAGACAAA 57.774 30.769 0.00 0.00 0.00 2.83
1 2 7.716998 AGAGAGCATACAAAAAGAAGAAGACAA 59.283 33.333 0.00 0.00 0.00 3.18
2 3 7.172190 CAGAGAGCATACAAAAAGAAGAAGACA 59.828 37.037 0.00 0.00 0.00 3.41
4 5 7.445121 TCAGAGAGCATACAAAAAGAAGAAGA 58.555 34.615 0.00 0.00 0.00 2.87
5 6 7.664082 TCAGAGAGCATACAAAAAGAAGAAG 57.336 36.000 0.00 0.00 0.00 2.85
6 7 8.627208 ATTCAGAGAGCATACAAAAAGAAGAA 57.373 30.769 0.00 0.00 0.00 2.52
7 8 8.099537 AGATTCAGAGAGCATACAAAAAGAAGA 58.900 33.333 0.00 0.00 0.00 2.87
8 9 8.266392 AGATTCAGAGAGCATACAAAAAGAAG 57.734 34.615 0.00 0.00 0.00 2.85
9 10 8.627208 AAGATTCAGAGAGCATACAAAAAGAA 57.373 30.769 0.00 0.00 0.00 2.52
10 11 7.879677 TGAAGATTCAGAGAGCATACAAAAAGA 59.120 33.333 0.00 0.00 32.50 2.52
11 12 7.961827 GTGAAGATTCAGAGAGCATACAAAAAG 59.038 37.037 0.00 0.00 37.98 2.27
12 13 7.445096 TGTGAAGATTCAGAGAGCATACAAAAA 59.555 33.333 0.00 0.00 37.98 1.94
13 14 6.936335 TGTGAAGATTCAGAGAGCATACAAAA 59.064 34.615 0.00 0.00 37.98 2.44
14 15 6.466812 TGTGAAGATTCAGAGAGCATACAAA 58.533 36.000 0.00 0.00 37.98 2.83
15 16 6.041423 TGTGAAGATTCAGAGAGCATACAA 57.959 37.500 0.00 0.00 37.98 2.41
16 17 5.665916 TGTGAAGATTCAGAGAGCATACA 57.334 39.130 0.00 0.00 37.98 2.29
24 25 3.604582 GAACCCCTGTGAAGATTCAGAG 58.395 50.000 11.68 11.68 45.26 3.35
25 26 2.028112 CGAACCCCTGTGAAGATTCAGA 60.028 50.000 0.00 0.00 37.98 3.27
26 27 2.350522 CGAACCCCTGTGAAGATTCAG 58.649 52.381 0.00 0.00 37.98 3.02
27 28 1.610624 GCGAACCCCTGTGAAGATTCA 60.611 52.381 0.00 0.00 34.20 2.57
28 29 1.087501 GCGAACCCCTGTGAAGATTC 58.912 55.000 0.00 0.00 0.00 2.52
29 30 0.693049 AGCGAACCCCTGTGAAGATT 59.307 50.000 0.00 0.00 0.00 2.40
30 31 0.036010 CAGCGAACCCCTGTGAAGAT 60.036 55.000 0.00 0.00 0.00 2.40
31 32 1.371183 CAGCGAACCCCTGTGAAGA 59.629 57.895 0.00 0.00 0.00 2.87
32 33 1.672356 CCAGCGAACCCCTGTGAAG 60.672 63.158 0.00 0.00 0.00 3.02
33 34 2.429930 CCAGCGAACCCCTGTGAA 59.570 61.111 0.00 0.00 0.00 3.18
34 35 2.847234 ACCAGCGAACCCCTGTGA 60.847 61.111 0.00 0.00 0.00 3.58
35 36 2.669569 CACCAGCGAACCCCTGTG 60.670 66.667 0.00 0.00 0.00 3.66
36 37 2.847234 TCACCAGCGAACCCCTGT 60.847 61.111 0.00 0.00 0.00 4.00
37 38 2.358737 GTCACCAGCGAACCCCTG 60.359 66.667 0.00 0.00 0.00 4.45
38 39 1.990160 TTTGTCACCAGCGAACCCCT 61.990 55.000 0.00 0.00 0.00 4.79
39 40 1.527380 TTTGTCACCAGCGAACCCC 60.527 57.895 0.00 0.00 0.00 4.95
40 41 1.652563 GTTTGTCACCAGCGAACCC 59.347 57.895 0.00 0.00 0.00 4.11
41 42 1.278637 CGTTTGTCACCAGCGAACC 59.721 57.895 0.00 0.00 0.00 3.62
42 43 1.210870 TACGTTTGTCACCAGCGAAC 58.789 50.000 0.00 0.00 0.00 3.95
43 44 1.862201 CTTACGTTTGTCACCAGCGAA 59.138 47.619 0.00 0.00 0.00 4.70
44 45 1.202440 ACTTACGTTTGTCACCAGCGA 60.202 47.619 0.00 0.00 0.00 4.93
45 46 1.214367 ACTTACGTTTGTCACCAGCG 58.786 50.000 0.00 0.00 0.00 5.18
46 47 3.064271 TGAAACTTACGTTTGTCACCAGC 59.936 43.478 1.53 0.00 43.09 4.85
47 48 4.260620 CCTGAAACTTACGTTTGTCACCAG 60.261 45.833 1.53 3.32 43.09 4.00
48 49 3.623960 CCTGAAACTTACGTTTGTCACCA 59.376 43.478 1.53 0.00 43.09 4.17
49 50 3.547413 GCCTGAAACTTACGTTTGTCACC 60.547 47.826 1.53 0.00 43.09 4.02
50 51 3.614588 GCCTGAAACTTACGTTTGTCAC 58.385 45.455 1.53 0.00 43.09 3.67
51 52 2.285756 CGCCTGAAACTTACGTTTGTCA 59.714 45.455 1.53 0.00 43.09 3.58
52 53 2.286025 ACGCCTGAAACTTACGTTTGTC 59.714 45.455 1.53 0.00 43.09 3.18
53 54 2.031191 CACGCCTGAAACTTACGTTTGT 59.969 45.455 1.53 0.00 43.09 2.83
54 55 2.635444 CACGCCTGAAACTTACGTTTG 58.365 47.619 1.53 0.00 43.09 2.93
55 56 1.003223 GCACGCCTGAAACTTACGTTT 60.003 47.619 0.00 0.00 45.58 3.60
56 57 0.584876 GCACGCCTGAAACTTACGTT 59.415 50.000 0.00 0.00 34.19 3.99
57 58 0.531090 TGCACGCCTGAAACTTACGT 60.531 50.000 0.00 0.00 37.47 3.57
58 59 0.584396 TTGCACGCCTGAAACTTACG 59.416 50.000 0.00 0.00 0.00 3.18
59 60 2.766970 TTTGCACGCCTGAAACTTAC 57.233 45.000 0.00 0.00 0.00 2.34
60 61 4.047822 CAAATTTGCACGCCTGAAACTTA 58.952 39.130 5.01 0.00 0.00 2.24
61 62 2.865551 CAAATTTGCACGCCTGAAACTT 59.134 40.909 5.01 0.00 0.00 2.66
62 63 2.100584 TCAAATTTGCACGCCTGAAACT 59.899 40.909 13.54 0.00 0.00 2.66
63 64 2.468831 TCAAATTTGCACGCCTGAAAC 58.531 42.857 13.54 0.00 0.00 2.78
64 65 2.879002 TCAAATTTGCACGCCTGAAA 57.121 40.000 13.54 0.00 0.00 2.69
65 66 3.058450 CAATCAAATTTGCACGCCTGAA 58.942 40.909 13.54 0.00 0.00 3.02
129 130 5.006746 CGTGAAATCATGGTTTCCTAGCTAC 59.993 44.000 25.05 15.52 37.31 3.58
130 131 5.116180 CGTGAAATCATGGTTTCCTAGCTA 58.884 41.667 25.05 5.97 37.31 3.32
131 132 3.941483 CGTGAAATCATGGTTTCCTAGCT 59.059 43.478 25.05 0.00 37.31 3.32
185 186 2.224281 TGAAAGAGATGTGCCGTCAAGT 60.224 45.455 0.00 0.00 0.00 3.16
229 230 0.822164 TTCTCTGGTTAGCGGTAGGC 59.178 55.000 0.00 0.00 44.05 3.93
230 231 3.604875 TTTTCTCTGGTTAGCGGTAGG 57.395 47.619 0.00 0.00 0.00 3.18
251 255 0.034756 TGGATACTGCTGTGTGCGTT 59.965 50.000 6.48 0.00 46.63 4.84
255 259 3.752747 TGTGATTTGGATACTGCTGTGTG 59.247 43.478 6.48 0.00 37.61 3.82
350 354 5.586243 ACAATTTTCGTCCTTGATCGATCAT 59.414 36.000 27.75 6.96 36.56 2.45
354 358 4.151689 GTGACAATTTTCGTCCTTGATCGA 59.848 41.667 0.00 0.00 32.15 3.59
356 360 5.385617 CAGTGACAATTTTCGTCCTTGATC 58.614 41.667 0.00 0.00 32.15 2.92
365 369 5.237344 AGAAAGAGACCAGTGACAATTTTCG 59.763 40.000 0.00 0.00 0.00 3.46
444 448 9.177608 CTCATCATGGAACTCTTTTAATGGTTA 57.822 33.333 0.00 0.00 0.00 2.85
452 456 3.442977 GCAGCTCATCATGGAACTCTTTT 59.557 43.478 0.00 0.00 0.00 2.27
473 608 4.765856 TCGAATATGGAGGACCTACTTAGC 59.234 45.833 5.02 0.00 37.04 3.09
573 708 7.148120 GCTTGGTCAGTGACAAGTATACTACTA 60.148 40.741 24.20 0.00 38.26 1.82
621 756 5.278463 CCAGAGTTTCCACACATTAACTTGG 60.278 44.000 0.00 0.00 31.41 3.61
622 757 5.762045 CCAGAGTTTCCACACATTAACTTG 58.238 41.667 0.00 0.00 31.41 3.16
623 758 4.278419 GCCAGAGTTTCCACACATTAACTT 59.722 41.667 0.00 0.00 31.41 2.66
624 759 3.821033 GCCAGAGTTTCCACACATTAACT 59.179 43.478 0.00 0.00 33.78 2.24
625 760 3.057526 GGCCAGAGTTTCCACACATTAAC 60.058 47.826 0.00 0.00 0.00 2.01
626 761 3.153919 GGCCAGAGTTTCCACACATTAA 58.846 45.455 0.00 0.00 0.00 1.40
627 762 2.107378 TGGCCAGAGTTTCCACACATTA 59.893 45.455 0.00 0.00 0.00 1.90
628 763 1.133513 TGGCCAGAGTTTCCACACATT 60.134 47.619 0.00 0.00 0.00 2.71
629 764 0.478072 TGGCCAGAGTTTCCACACAT 59.522 50.000 0.00 0.00 0.00 3.21
630 765 0.257328 TTGGCCAGAGTTTCCACACA 59.743 50.000 5.11 0.00 0.00 3.72
631 766 0.954452 CTTGGCCAGAGTTTCCACAC 59.046 55.000 5.11 0.00 0.00 3.82
632 767 0.823356 GCTTGGCCAGAGTTTCCACA 60.823 55.000 5.11 0.00 0.00 4.17
633 768 0.538287 AGCTTGGCCAGAGTTTCCAC 60.538 55.000 5.11 0.00 0.00 4.02
634 769 1.003580 CTAGCTTGGCCAGAGTTTCCA 59.996 52.381 5.11 0.00 0.00 3.53
635 770 1.743996 CTAGCTTGGCCAGAGTTTCC 58.256 55.000 5.11 0.00 0.00 3.13
636 771 1.090728 GCTAGCTTGGCCAGAGTTTC 58.909 55.000 5.11 0.00 0.00 2.78
637 772 0.401738 TGCTAGCTTGGCCAGAGTTT 59.598 50.000 17.23 2.94 0.00 2.66
638 773 0.322008 GTGCTAGCTTGGCCAGAGTT 60.322 55.000 17.23 7.50 0.00 3.01
639 774 1.298014 GTGCTAGCTTGGCCAGAGT 59.702 57.895 17.23 0.00 0.00 3.24
640 775 1.451028 GGTGCTAGCTTGGCCAGAG 60.451 63.158 17.23 8.07 0.00 3.35
641 776 2.671070 GGTGCTAGCTTGGCCAGA 59.329 61.111 17.23 0.00 0.00 3.86
642 777 2.821366 CGGTGCTAGCTTGGCCAG 60.821 66.667 17.23 1.08 0.00 4.85
643 778 3.318384 TCGGTGCTAGCTTGGCCA 61.318 61.111 17.23 0.00 0.00 5.36
644 779 2.820037 GTCGGTGCTAGCTTGGCC 60.820 66.667 17.23 11.54 0.00 5.36
645 780 2.820037 GGTCGGTGCTAGCTTGGC 60.820 66.667 17.23 6.87 0.00 4.52
674 809 1.350193 CTCAACGTCGAGTGATTGGG 58.650 55.000 0.00 0.00 0.00 4.12
857 998 0.037232 GACGACACAGAAAGGAGGGG 60.037 60.000 0.00 0.00 0.00 4.79
867 1008 3.124466 CAGACAGAGAGTAGACGACACAG 59.876 52.174 0.00 0.00 0.00 3.66
902 1050 2.902343 GCAGCAAGATACCCCGGC 60.902 66.667 0.00 0.00 0.00 6.13
928 1079 1.005340 GAGTTGGATGAGCTTCTGCG 58.995 55.000 0.00 0.00 45.42 5.18
933 1084 3.834813 TGACAGTAGAGTTGGATGAGCTT 59.165 43.478 0.00 0.00 0.00 3.74
953 1127 4.594970 AGCTCTAGTCTTGTCTAGCTTGA 58.405 43.478 0.00 0.00 37.78 3.02
967 1141 3.944055 ATGTTTCACACGAGCTCTAGT 57.056 42.857 12.85 7.13 0.00 2.57
971 1145 2.096218 GGACAATGTTTCACACGAGCTC 60.096 50.000 2.73 2.73 0.00 4.09
980 1154 4.262121 CCATCTTGCTTGGACAATGTTTCA 60.262 41.667 0.00 0.00 36.26 2.69
1005 1179 4.027674 TGCAGATTAGCAACCAACCTTA 57.972 40.909 0.00 0.00 42.46 2.69
1023 1197 6.168270 AGCTAAATTGGTAAAAGGTTTGCA 57.832 33.333 0.00 0.00 0.00 4.08
1029 1204 4.390909 ACGACGAGCTAAATTGGTAAAAGG 59.609 41.667 0.00 0.00 0.00 3.11
1035 1210 2.450609 ACACGACGAGCTAAATTGGT 57.549 45.000 0.00 0.00 0.00 3.67
1036 1211 2.993899 AGAACACGACGAGCTAAATTGG 59.006 45.455 0.00 0.00 0.00 3.16
1037 1212 4.259451 GCTAGAACACGACGAGCTAAATTG 60.259 45.833 0.00 0.00 34.23 2.32
1038 1213 3.858238 GCTAGAACACGACGAGCTAAATT 59.142 43.478 0.00 0.00 34.23 1.82
1039 1214 3.128938 AGCTAGAACACGACGAGCTAAAT 59.871 43.478 0.00 0.00 42.54 1.40
1040 1215 2.486982 AGCTAGAACACGACGAGCTAAA 59.513 45.455 0.00 0.00 42.54 1.85
1041 1216 2.082231 AGCTAGAACACGACGAGCTAA 58.918 47.619 0.00 0.00 42.54 3.09
1042 1217 1.735386 AGCTAGAACACGACGAGCTA 58.265 50.000 0.00 0.00 42.54 3.32
1043 1218 1.397692 GTAGCTAGAACACGACGAGCT 59.602 52.381 0.00 6.79 45.22 4.09
1044 1219 1.812662 GTAGCTAGAACACGACGAGC 58.187 55.000 0.00 0.00 36.53 5.03
1045 1220 1.657594 TCGTAGCTAGAACACGACGAG 59.342 52.381 0.00 0.00 39.58 4.18
1046 1221 1.657594 CTCGTAGCTAGAACACGACGA 59.342 52.381 0.00 4.42 39.58 4.20
1047 1222 1.392853 ACTCGTAGCTAGAACACGACG 59.607 52.381 4.60 0.00 39.58 5.12
1048 1223 2.159234 ACACTCGTAGCTAGAACACGAC 59.841 50.000 4.60 0.00 39.58 4.34
1049 1224 2.420642 ACACTCGTAGCTAGAACACGA 58.579 47.619 8.29 8.29 41.98 4.35
1050 1225 2.896243 ACACTCGTAGCTAGAACACG 57.104 50.000 0.00 0.00 37.03 4.49
1051 1226 5.087397 CACTAACACTCGTAGCTAGAACAC 58.913 45.833 0.00 0.00 0.00 3.32
1052 1227 4.758674 ACACTAACACTCGTAGCTAGAACA 59.241 41.667 0.00 0.00 0.00 3.18
1053 1228 5.294050 ACACTAACACTCGTAGCTAGAAC 57.706 43.478 0.00 0.00 0.00 3.01
1054 1229 5.954296 AACACTAACACTCGTAGCTAGAA 57.046 39.130 0.00 0.00 0.00 2.10
1055 1230 5.954296 AAACACTAACACTCGTAGCTAGA 57.046 39.130 0.00 0.00 0.00 2.43
1056 1231 6.628065 CGATAAACACTAACACTCGTAGCTAG 59.372 42.308 0.00 0.00 0.00 3.42
1057 1232 6.481134 CGATAAACACTAACACTCGTAGCTA 58.519 40.000 0.00 0.00 0.00 3.32
1058 1233 5.330295 CGATAAACACTAACACTCGTAGCT 58.670 41.667 0.00 0.00 0.00 3.32
1059 1234 4.027864 GCGATAAACACTAACACTCGTAGC 60.028 45.833 0.00 0.00 0.00 3.58
1060 1235 5.330295 AGCGATAAACACTAACACTCGTAG 58.670 41.667 0.00 0.00 0.00 3.51
1061 1236 5.106594 TGAGCGATAAACACTAACACTCGTA 60.107 40.000 0.00 0.00 0.00 3.43
1062 1237 4.164294 GAGCGATAAACACTAACACTCGT 58.836 43.478 0.00 0.00 0.00 4.18
1063 1238 4.163552 TGAGCGATAAACACTAACACTCG 58.836 43.478 0.00 0.00 0.00 4.18
1064 1239 5.162075 ACTGAGCGATAAACACTAACACTC 58.838 41.667 0.00 0.00 0.00 3.51
1065 1240 5.135508 ACTGAGCGATAAACACTAACACT 57.864 39.130 0.00 0.00 0.00 3.55
1066 1241 5.840940 AACTGAGCGATAAACACTAACAC 57.159 39.130 0.00 0.00 0.00 3.32
1067 1242 6.259167 ACAAAACTGAGCGATAAACACTAACA 59.741 34.615 0.00 0.00 0.00 2.41
1068 1243 6.573725 CACAAAACTGAGCGATAAACACTAAC 59.426 38.462 0.00 0.00 0.00 2.34
1105 1280 0.042188 CAACACAGAGCGAAACACGG 60.042 55.000 0.00 0.00 42.83 4.94
1157 1333 2.492090 CTCCTGTTCCTCTCGCCG 59.508 66.667 0.00 0.00 0.00 6.46
1210 1386 2.964740 TGATCAGTGGCTTCTTCTTCG 58.035 47.619 0.00 0.00 0.00 3.79
1237 1415 9.454859 AGAGAAGAAGATAATTTAAACAGGTGG 57.545 33.333 0.00 0.00 0.00 4.61
1277 1478 3.054065 AGAATTCATTCACCACCTCTCCC 60.054 47.826 8.44 0.00 39.23 4.30
1469 1675 4.625781 CTCCGCCGTAGCCGTAGC 62.626 72.222 0.00 0.00 40.32 3.58
1470 1676 1.996786 TTTCTCCGCCGTAGCCGTAG 61.997 60.000 0.00 0.00 34.57 3.51
1471 1677 1.594194 TTTTCTCCGCCGTAGCCGTA 61.594 55.000 0.00 0.00 34.57 4.02
1472 1678 2.830704 CTTTTCTCCGCCGTAGCCGT 62.831 60.000 0.00 0.00 34.57 5.68
1473 1679 2.125832 TTTTCTCCGCCGTAGCCG 60.126 61.111 0.00 0.00 34.57 5.52
1474 1680 0.390735 TTCTTTTCTCCGCCGTAGCC 60.391 55.000 0.00 0.00 34.57 3.93
1475 1681 1.000145 CTTCTTTTCTCCGCCGTAGC 59.000 55.000 0.00 0.00 0.00 3.58
1476 1682 2.649331 TCTTCTTTTCTCCGCCGTAG 57.351 50.000 0.00 0.00 0.00 3.51
1579 1809 3.534056 CGGGTAGGGAATCGGCGT 61.534 66.667 6.85 0.00 0.00 5.68
1587 1817 4.059304 TGGTACGCCGGGTAGGGA 62.059 66.667 2.18 0.00 41.48 4.20
1590 1820 3.426117 CTGCTGGTACGCCGGGTAG 62.426 68.421 2.18 0.00 41.51 3.18
1693 1935 1.432270 CGGCACCTTAGCAGCTTAGC 61.432 60.000 0.00 0.00 35.83 3.09
1694 1936 0.175760 TCGGCACCTTAGCAGCTTAG 59.824 55.000 0.00 0.00 35.83 2.18
1695 1937 0.108329 GTCGGCACCTTAGCAGCTTA 60.108 55.000 0.00 0.00 35.83 3.09
1696 1938 1.376037 GTCGGCACCTTAGCAGCTT 60.376 57.895 0.00 0.00 35.83 3.74
1697 1939 2.266055 GTCGGCACCTTAGCAGCT 59.734 61.111 0.00 0.00 35.83 4.24
1698 1940 3.188786 CGTCGGCACCTTAGCAGC 61.189 66.667 0.00 0.00 35.83 5.25
1699 1941 1.517257 CTCGTCGGCACCTTAGCAG 60.517 63.158 0.00 0.00 35.83 4.24
1700 1942 1.529152 TTCTCGTCGGCACCTTAGCA 61.529 55.000 0.00 0.00 35.83 3.49
1746 2011 6.566197 AGCTTGTCCTGAACTTATTTTGAG 57.434 37.500 0.00 0.00 0.00 3.02
1772 2037 5.084818 TCGCTTGATCAGTTCAGGATTTA 57.915 39.130 0.00 0.00 33.37 1.40
1867 2132 5.476945 ACCCTGAATTTACAGACAACCATTC 59.523 40.000 0.00 0.00 39.94 2.67
1869 2134 4.998051 ACCCTGAATTTACAGACAACCAT 58.002 39.130 0.00 0.00 39.94 3.55
1891 2156 6.710597 ACACTAGTACACTCTGAACTGAAA 57.289 37.500 0.00 0.00 0.00 2.69
1933 2198 5.105351 CCATTTATTCTGTCCACCCTTTTCC 60.105 44.000 0.00 0.00 0.00 3.13
1947 2212 6.656902 TGCATCTCTCTGTTCCATTTATTCT 58.343 36.000 0.00 0.00 0.00 2.40
2028 2294 2.543777 TCTGGTGTTCTTGTACTGCC 57.456 50.000 0.00 0.00 0.00 4.85
2045 2312 8.665685 GGACGTGAATGTTTCTTTATTACATCT 58.334 33.333 0.00 0.00 31.63 2.90
2057 2324 1.725164 GTCTCCGGACGTGAATGTTTC 59.275 52.381 0.00 0.00 32.47 2.78
2058 2325 1.607251 GGTCTCCGGACGTGAATGTTT 60.607 52.381 0.00 0.00 42.97 2.83
2059 2326 0.037605 GGTCTCCGGACGTGAATGTT 60.038 55.000 0.00 0.00 42.97 2.71
2060 2327 1.183030 TGGTCTCCGGACGTGAATGT 61.183 55.000 0.00 0.00 42.97 2.71
2061 2328 0.736325 GTGGTCTCCGGACGTGAATG 60.736 60.000 0.00 0.00 42.97 2.67
2062 2329 1.590147 GTGGTCTCCGGACGTGAAT 59.410 57.895 0.00 0.00 42.97 2.57
2063 2330 2.567497 GGTGGTCTCCGGACGTGAA 61.567 63.158 0.00 0.00 42.97 3.18
2064 2331 2.128290 TAGGTGGTCTCCGGACGTGA 62.128 60.000 0.00 0.00 42.97 4.35
2065 2332 1.654954 CTAGGTGGTCTCCGGACGTG 61.655 65.000 0.00 0.00 42.97 4.49
2066 2333 1.378250 CTAGGTGGTCTCCGGACGT 60.378 63.158 0.00 0.00 42.97 4.34
2067 2334 1.378250 ACTAGGTGGTCTCCGGACG 60.378 63.158 0.00 0.00 42.97 4.79
2068 2335 0.323178 TCACTAGGTGGTCTCCGGAC 60.323 60.000 0.00 0.00 41.43 4.79
2069 2336 0.323178 GTCACTAGGTGGTCTCCGGA 60.323 60.000 2.93 2.93 33.87 5.14
2070 2337 1.654954 CGTCACTAGGTGGTCTCCGG 61.655 65.000 0.00 0.00 33.87 5.14
2071 2338 0.675837 TCGTCACTAGGTGGTCTCCG 60.676 60.000 0.00 0.00 33.87 4.63
2072 2339 0.810016 GTCGTCACTAGGTGGTCTCC 59.190 60.000 0.00 0.00 33.87 3.71
2073 2340 0.810016 GGTCGTCACTAGGTGGTCTC 59.190 60.000 0.00 0.00 33.87 3.36
2085 2352 2.388310 TTCAGTGTTTGTGGTCGTCA 57.612 45.000 0.00 0.00 0.00 4.35
2092 2359 5.247507 TCCAACTCATTTCAGTGTTTGTG 57.752 39.130 0.00 0.00 0.00 3.33
2096 2363 2.887152 GCCTCCAACTCATTTCAGTGTT 59.113 45.455 0.00 0.00 0.00 3.32
2097 2364 2.508526 GCCTCCAACTCATTTCAGTGT 58.491 47.619 0.00 0.00 0.00 3.55
2102 2369 2.007608 GGTACGCCTCCAACTCATTTC 58.992 52.381 0.00 0.00 0.00 2.17
2125 2392 3.917760 GAGGGAGGGGCGATGACG 61.918 72.222 0.00 0.00 42.93 4.35
2129 2396 0.191064 TTAGATGAGGGAGGGGCGAT 59.809 55.000 0.00 0.00 0.00 4.58
2144 2411 9.841295 ACTATAATAAATTTTGTCCGGCTTAGA 57.159 29.630 0.00 0.00 0.00 2.10
2147 2414 9.841295 TCTACTATAATAAATTTTGTCCGGCTT 57.159 29.630 0.00 0.00 0.00 4.35
2166 2433 6.153000 ACGATGACTTTCCAACTGTCTACTAT 59.847 38.462 0.00 0.00 0.00 2.12
2175 2442 2.550830 AGCACGATGACTTTCCAACT 57.449 45.000 0.00 0.00 0.00 3.16
2187 2454 1.224592 CTTGGGGGCTTAGCACGAT 59.775 57.895 6.53 0.00 29.41 3.73
2198 2465 2.282462 GTGCACTGGTCTTGGGGG 60.282 66.667 10.32 0.00 0.00 5.40
2201 2468 0.179020 TTCTGGTGCACTGGTCTTGG 60.179 55.000 17.98 0.00 0.00 3.61
2221 2489 4.742438 TTTCTTCATCAGTAACGGTTGC 57.258 40.909 3.07 1.62 0.00 4.17
2230 2500 8.908786 TTCAATCTACACTTTTCTTCATCAGT 57.091 30.769 0.00 0.00 0.00 3.41
2246 2516 5.415701 TGCAGGTTGGATTCTTTCAATCTAC 59.584 40.000 0.00 0.00 33.10 2.59
2253 2523 3.057946 GTGTCTGCAGGTTGGATTCTTTC 60.058 47.826 15.13 0.00 0.00 2.62
2269 2539 4.452114 TCCAATCTTCGTTTCATGTGTCTG 59.548 41.667 0.00 0.00 0.00 3.51
2288 2558 5.741962 TTGATGAATTTGCTTGGATCCAA 57.258 34.783 25.53 25.53 0.00 3.53
2294 2564 5.163893 GCATGTCTTTGATGAATTTGCTTGG 60.164 40.000 0.00 0.00 0.00 3.61
2301 2571 3.758023 TCGGTGCATGTCTTTGATGAATT 59.242 39.130 0.00 0.00 0.00 2.17
2304 2574 2.470983 TCGGTGCATGTCTTTGATGA 57.529 45.000 0.00 0.00 0.00 2.92
2305 2575 3.127376 TCAATCGGTGCATGTCTTTGATG 59.873 43.478 0.00 0.00 0.00 3.07
2309 2579 4.487948 CAATTCAATCGGTGCATGTCTTT 58.512 39.130 0.00 0.00 0.00 2.52
2315 2585 0.526096 GCGCAATTCAATCGGTGCAT 60.526 50.000 0.30 0.00 36.80 3.96
2321 2591 1.397693 GGATCTCGCGCAATTCAATCG 60.398 52.381 8.75 0.00 0.00 3.34
2322 2592 1.397693 CGGATCTCGCGCAATTCAATC 60.398 52.381 8.75 0.91 0.00 2.67
2324 2594 0.739462 ACGGATCTCGCGCAATTCAA 60.739 50.000 8.75 0.00 43.89 2.69
2334 2604 1.087501 TGTGTCTCTGACGGATCTCG 58.912 55.000 0.00 0.00 45.88 4.04
2337 2607 1.133407 GAGGTGTGTCTCTGACGGATC 59.867 57.143 0.00 0.00 34.95 3.36
2352 2622 1.201429 ACCTAGCCCTTGTGGAGGTG 61.201 60.000 0.00 0.00 44.71 4.00
2384 2689 0.985490 AGGCTCCTTGGAGATGGGAC 60.985 60.000 19.85 1.51 0.00 4.46
2425 2736 6.896883 AGTTTATTTAGGGTATGGTGTCCTC 58.103 40.000 0.00 0.00 32.46 3.71
2485 2880 4.321527 GCCACATCCTCTCCAAAGAAAAAG 60.322 45.833 0.00 0.00 0.00 2.27
2496 2891 2.202987 CAGCCGCCACATCCTCTC 60.203 66.667 0.00 0.00 0.00 3.20
2503 2898 3.047280 CTTTACGCAGCCGCCACA 61.047 61.111 0.00 0.00 38.22 4.17
2507 2902 4.500568 GTCGCTTTACGCAGCCGC 62.501 66.667 0.00 0.00 43.23 6.53
2513 2908 3.297202 GCTTTTAACATGTCGCTTTACGC 59.703 43.478 0.00 0.00 43.23 4.42
2557 2952 9.831737 CTACAAAGTTTCATTAGGTTCTTCATG 57.168 33.333 0.00 0.00 0.00 3.07
2580 2975 0.307146 GCTAATGCTGCAGCTGCTAC 59.693 55.000 36.61 27.91 42.66 3.58
2609 3004 9.624697 TCAACTCAAATAGATAAAACATGCAAC 57.375 29.630 0.00 0.00 0.00 4.17
2633 3028 4.192429 TGTCTTCTTCGCAGATCAATCA 57.808 40.909 0.00 0.00 35.04 2.57
2642 3037 1.497278 GCGCATTGTCTTCTTCGCA 59.503 52.632 0.30 0.00 41.84 5.10
2645 3040 1.537202 AGGTTGCGCATTGTCTTCTTC 59.463 47.619 12.75 0.00 0.00 2.87


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

AutoCloner maintained by Alex Coulton.