Multiple sequence alignment - TraesCS6D01G260100

Loading Multiple Alignment...

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 TraesCS6D01G260100 chr6D 100.000 2546 0 0 1 2546 366683562 366686107 0.000000e+00 4702.0
1 TraesCS6D01G260100 chr6B 88.024 2288 130 78 330 2546 552404783 552406997 0.000000e+00 2575.0
2 TraesCS6D01G260100 chr6B 90.650 246 12 4 88 326 552404256 552404497 1.470000e-82 316.0
3 TraesCS6D01G260100 chr6B 85.759 323 17 6 1143 1460 495540764 495541062 5.290000e-82 315.0
4 TraesCS6D01G260100 chr6B 98.473 131 2 0 1143 1273 657261015 657261145 5.480000e-57 231.0
5 TraesCS6D01G260100 chr6A 82.112 2348 192 112 88 2319 507121841 507124076 0.000000e+00 1799.0
6 TraesCS6D01G260100 chr6A 87.940 199 10 2 1143 1341 220742675 220742859 3.300000e-54 222.0
7 TraesCS6D01G260100 chr6A 86.628 172 15 5 2380 2544 507124086 507124256 1.560000e-42 183.0
8 TraesCS6D01G260100 chr5A 88.356 584 40 17 1777 2348 49964388 49963821 0.000000e+00 676.0
9 TraesCS6D01G260100 chr5A 89.674 184 5 2 1143 1326 600293964 600294133 3.300000e-54 222.0
10 TraesCS6D01G260100 chr5A 86.911 191 13 7 1383 1561 49965691 49965501 1.190000e-48 204.0
11 TraesCS6D01G260100 chrUn 87.102 597 40 17 1777 2348 311244764 311244180 2.140000e-180 641.0
12 TraesCS6D01G260100 chrUn 87.102 597 40 17 1777 2348 410091035 410091619 2.140000e-180 641.0
13 TraesCS6D01G260100 chrUn 91.026 156 8 2 1613 1763 287696617 287696771 3.320000e-49 206.0
14 TraesCS6D01G260100 chrUn 91.026 156 8 2 1613 1763 287708821 287708975 3.320000e-49 206.0
15 TraesCS6D01G260100 chrUn 91.026 156 8 2 1613 1763 294704834 294704988 3.320000e-49 206.0
16 TraesCS6D01G260100 chrUn 85.276 163 7 7 1408 1561 287696463 287696617 4.390000e-33 152.0
17 TraesCS6D01G260100 chrUn 85.276 163 7 7 1408 1561 287708667 287708821 4.390000e-33 152.0
18 TraesCS6D01G260100 chrUn 85.276 163 7 7 1408 1561 294704680 294704834 4.390000e-33 152.0
19 TraesCS6D01G260100 chr2B 87.081 596 39 18 1777 2346 239860856 239861439 7.680000e-180 640.0
20 TraesCS6D01G260100 chr2B 89.500 200 6 2 1143 1341 5028976 5029161 3.270000e-59 239.0
21 TraesCS6D01G260100 chr2B 91.525 177 8 3 1613 1783 239858837 239859012 1.180000e-58 237.0
22 TraesCS6D01G260100 chr2B 84.663 163 8 7 1408 1561 239858683 239858837 2.040000e-31 147.0
23 TraesCS6D01G260100 chr1B 86.767 597 42 16 1777 2348 605568264 605568848 4.620000e-177 630.0
24 TraesCS6D01G260100 chr1B 85.714 322 19 4 1143 1460 32787996 32787698 5.290000e-82 315.0
25 TraesCS6D01G260100 chr1B 90.960 177 9 3 1613 1783 605566248 605566423 5.480000e-57 231.0
26 TraesCS6D01G260100 chr1B 92.632 95 7 0 1467 1561 605566154 605566248 1.230000e-28 137.0
27 TraesCS6D01G260100 chr1D 86.520 319 17 5 1143 1458 35863005 35863300 6.790000e-86 327.0
28 TraesCS6D01G260100 chr1D 95.098 102 5 0 1262 1363 9855363 9855464 7.290000e-36 161.0
29 TraesCS6D01G260100 chr3B 86.250 320 18 4 1144 1460 654436487 654436191 8.790000e-85 324.0
30 TraesCS6D01G260100 chr3B 90.244 41 3 1 987 1027 654436517 654436478 5.000000e-03 52.8
31 TraesCS6D01G260100 chr1A 89.617 183 5 2 1144 1326 96740289 96740457 1.190000e-53 220.0
32 TraesCS6D01G260100 chr7A 89.130 184 6 2 1143 1326 717181726 717181557 1.530000e-52 217.0
33 TraesCS6D01G260100 chr7D 93.985 133 8 0 1231 1363 138313035 138313167 4.300000e-48 202.0
34 TraesCS6D01G260100 chr4B 100.000 30 0 0 1312 1341 37175641 37175612 3.540000e-04 56.5


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 TraesCS6D01G260100 chr6D 366683562 366686107 2545 False 4702.000000 4702 100.000000 1 2546 1 chr6D.!!$F1 2545
1 TraesCS6D01G260100 chr6B 552404256 552406997 2741 False 1445.500000 2575 89.337000 88 2546 2 chr6B.!!$F3 2458
2 TraesCS6D01G260100 chr6A 507121841 507124256 2415 False 991.000000 1799 84.370000 88 2544 2 chr6A.!!$F2 2456
3 TraesCS6D01G260100 chr5A 49963821 49965691 1870 True 440.000000 676 87.633500 1383 2348 2 chr5A.!!$R1 965
4 TraesCS6D01G260100 chrUn 311244180 311244764 584 True 641.000000 641 87.102000 1777 2348 1 chrUn.!!$R1 571
5 TraesCS6D01G260100 chrUn 410091035 410091619 584 False 641.000000 641 87.102000 1777 2348 1 chrUn.!!$F1 571
6 TraesCS6D01G260100 chr2B 239858683 239861439 2756 False 341.333333 640 87.756333 1408 2346 3 chr2B.!!$F2 938
7 TraesCS6D01G260100 chr1B 605566154 605568848 2694 False 332.666667 630 90.119667 1467 2348 3 chr1B.!!$F1 881

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
938 1313 0.032615 TCTGGAGAAGAGAGGAGGCC 60.033 60.0 0.0 0.0 0.0 5.19 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2377 4788 0.17904 AAAAGGGCGAAAGACGGTGA 60.179 50.0 0.0 0.0 43.44 4.02 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
21 22 4.429854 AGAAGAGAAAAAGGAGCAGTGT 57.570 40.909 0.00 0.00 0.00 3.55
22 23 4.384940 AGAAGAGAAAAAGGAGCAGTGTC 58.615 43.478 0.00 0.00 0.00 3.67
23 24 4.102367 AGAAGAGAAAAAGGAGCAGTGTCT 59.898 41.667 0.00 0.00 0.00 3.41
24 25 4.429854 AGAGAAAAAGGAGCAGTGTCTT 57.570 40.909 0.00 0.00 0.00 3.01
25 26 4.786425 AGAGAAAAAGGAGCAGTGTCTTT 58.214 39.130 0.00 0.00 32.77 2.52
26 27 4.578105 AGAGAAAAAGGAGCAGTGTCTTTG 59.422 41.667 8.32 0.00 31.93 2.77
27 28 4.273318 AGAAAAAGGAGCAGTGTCTTTGT 58.727 39.130 8.32 4.41 31.93 2.83
28 29 4.096984 AGAAAAAGGAGCAGTGTCTTTGTG 59.903 41.667 8.32 0.00 31.93 3.33
29 30 1.972872 AAGGAGCAGTGTCTTTGTGG 58.027 50.000 0.00 0.00 0.00 4.17
30 31 1.131638 AGGAGCAGTGTCTTTGTGGA 58.868 50.000 0.00 0.00 0.00 4.02
31 32 1.490490 AGGAGCAGTGTCTTTGTGGAA 59.510 47.619 0.00 0.00 0.00 3.53
32 33 2.092429 AGGAGCAGTGTCTTTGTGGAAA 60.092 45.455 0.00 0.00 0.00 3.13
33 34 2.291741 GGAGCAGTGTCTTTGTGGAAAG 59.708 50.000 0.00 0.00 40.13 2.62
34 35 2.291741 GAGCAGTGTCTTTGTGGAAAGG 59.708 50.000 0.00 0.00 39.36 3.11
35 36 1.269257 GCAGTGTCTTTGTGGAAAGGC 60.269 52.381 0.00 0.00 43.09 4.35
36 37 1.002468 CAGTGTCTTTGTGGAAAGGCG 60.002 52.381 0.00 0.00 45.33 5.52
37 38 1.021968 GTGTCTTTGTGGAAAGGCGT 58.978 50.000 0.00 0.00 45.33 5.68
38 39 1.021202 TGTCTTTGTGGAAAGGCGTG 58.979 50.000 0.00 0.00 45.33 5.34
39 40 0.310854 GTCTTTGTGGAAAGGCGTGG 59.689 55.000 0.00 0.00 39.36 4.94
40 41 0.106918 TCTTTGTGGAAAGGCGTGGT 60.107 50.000 0.00 0.00 39.36 4.16
41 42 1.141254 TCTTTGTGGAAAGGCGTGGTA 59.859 47.619 0.00 0.00 39.36 3.25
42 43 1.265905 CTTTGTGGAAAGGCGTGGTAC 59.734 52.381 0.00 0.00 35.78 3.34
43 44 0.881159 TTGTGGAAAGGCGTGGTACG 60.881 55.000 0.00 0.00 45.88 3.67
44 45 1.301165 GTGGAAAGGCGTGGTACGT 60.301 57.895 0.00 0.00 44.73 3.57
45 46 0.881600 GTGGAAAGGCGTGGTACGTT 60.882 55.000 0.00 0.00 44.73 3.99
46 47 0.881159 TGGAAAGGCGTGGTACGTTG 60.881 55.000 0.00 0.00 44.73 4.10
47 48 0.600782 GGAAAGGCGTGGTACGTTGA 60.601 55.000 0.00 0.00 44.73 3.18
48 49 1.219646 GAAAGGCGTGGTACGTTGAA 58.780 50.000 0.00 0.00 44.73 2.69
49 50 1.193874 GAAAGGCGTGGTACGTTGAAG 59.806 52.381 0.00 0.00 44.73 3.02
50 51 0.105408 AAGGCGTGGTACGTTGAAGT 59.895 50.000 0.00 0.00 44.73 3.01
51 52 0.599204 AGGCGTGGTACGTTGAAGTG 60.599 55.000 0.00 0.00 44.73 3.16
52 53 0.877213 GGCGTGGTACGTTGAAGTGT 60.877 55.000 0.00 0.00 44.73 3.55
53 54 0.231279 GCGTGGTACGTTGAAGTGTG 59.769 55.000 0.00 0.00 44.73 3.82
54 55 1.563111 CGTGGTACGTTGAAGTGTGT 58.437 50.000 0.00 0.00 36.74 3.72
55 56 1.256895 CGTGGTACGTTGAAGTGTGTG 59.743 52.381 0.00 0.00 36.74 3.82
56 57 2.542597 GTGGTACGTTGAAGTGTGTGA 58.457 47.619 0.00 0.00 0.00 3.58
57 58 2.538449 GTGGTACGTTGAAGTGTGTGAG 59.462 50.000 0.00 0.00 0.00 3.51
58 59 1.525619 GGTACGTTGAAGTGTGTGAGC 59.474 52.381 0.00 0.00 0.00 4.26
59 60 2.198406 GTACGTTGAAGTGTGTGAGCA 58.802 47.619 0.00 0.00 0.00 4.26
60 61 1.006832 ACGTTGAAGTGTGTGAGCAC 58.993 50.000 0.00 0.00 45.44 4.40
61 62 0.304705 CGTTGAAGTGTGTGAGCACC 59.695 55.000 0.00 0.00 44.65 5.01
62 63 0.663153 GTTGAAGTGTGTGAGCACCC 59.337 55.000 0.00 0.00 44.65 4.61
63 64 0.813610 TTGAAGTGTGTGAGCACCCG 60.814 55.000 0.00 0.00 44.65 5.28
64 65 1.961277 GAAGTGTGTGAGCACCCGG 60.961 63.158 0.00 0.00 44.65 5.73
65 66 4.626081 AGTGTGTGAGCACCCGGC 62.626 66.667 0.00 0.00 44.65 6.13
74 75 4.424711 GCACCCGGCTGGATGGAA 62.425 66.667 15.09 0.00 40.25 3.53
75 76 2.124570 CACCCGGCTGGATGGAAG 60.125 66.667 15.09 0.00 37.49 3.46
76 77 3.411517 ACCCGGCTGGATGGAAGG 61.412 66.667 15.09 0.00 37.49 3.46
77 78 3.089874 CCCGGCTGGATGGAAGGA 61.090 66.667 15.09 0.00 37.49 3.36
78 79 2.507944 CCGGCTGGATGGAAGGAG 59.492 66.667 5.28 0.00 37.49 3.69
79 80 2.066393 CCGGCTGGATGGAAGGAGA 61.066 63.158 5.28 0.00 37.49 3.71
80 81 1.626356 CCGGCTGGATGGAAGGAGAA 61.626 60.000 5.28 0.00 37.49 2.87
81 82 0.179062 CGGCTGGATGGAAGGAGAAG 60.179 60.000 0.00 0.00 0.00 2.85
82 83 0.182299 GGCTGGATGGAAGGAGAAGG 59.818 60.000 0.00 0.00 0.00 3.46
83 84 0.915364 GCTGGATGGAAGGAGAAGGT 59.085 55.000 0.00 0.00 0.00 3.50
84 85 1.407989 GCTGGATGGAAGGAGAAGGTG 60.408 57.143 0.00 0.00 0.00 4.00
85 86 2.191400 CTGGATGGAAGGAGAAGGTGA 58.809 52.381 0.00 0.00 0.00 4.02
86 87 1.909302 TGGATGGAAGGAGAAGGTGAC 59.091 52.381 0.00 0.00 0.00 3.67
202 204 5.681543 GCGCATTCTTTTGCTTATTACTACC 59.318 40.000 0.30 0.00 40.54 3.18
234 242 1.112315 ACATAGAGCAGCCCCTCTCG 61.112 60.000 6.98 3.75 41.15 4.04
237 245 0.614979 TAGAGCAGCCCCTCTCGTTT 60.615 55.000 6.98 0.00 41.15 3.60
238 246 0.614979 AGAGCAGCCCCTCTCGTTTA 60.615 55.000 0.00 0.00 37.66 2.01
241 249 2.102588 GAGCAGCCCCTCTCGTTTATTA 59.897 50.000 0.00 0.00 0.00 0.98
243 251 2.808543 GCAGCCCCTCTCGTTTATTATG 59.191 50.000 0.00 0.00 0.00 1.90
247 255 3.139077 CCCCTCTCGTTTATTATGTGCC 58.861 50.000 0.00 0.00 0.00 5.01
248 256 3.181454 CCCCTCTCGTTTATTATGTGCCT 60.181 47.826 0.00 0.00 0.00 4.75
249 257 3.809832 CCCTCTCGTTTATTATGTGCCTG 59.190 47.826 0.00 0.00 0.00 4.85
327 341 3.971894 AGGGGCCGTCCTCTTATG 58.028 61.111 0.00 0.00 41.58 1.90
340 636 5.404968 CGTCCTCTTATGATGATCTGAAAGC 59.595 44.000 0.00 0.00 0.00 3.51
376 677 0.036306 AACCAGGTGTCCGGTTGATC 59.964 55.000 0.00 0.00 38.34 2.92
382 683 0.460311 GTGTCCGGTTGATCGATCCT 59.540 55.000 22.31 0.00 0.00 3.24
389 690 2.030717 CGGTTGATCGATCCTAGGACAG 60.031 54.545 22.31 11.36 0.00 3.51
391 692 2.362397 GTTGATCGATCCTAGGACAGCA 59.638 50.000 22.31 7.36 0.00 4.41
392 693 2.234143 TGATCGATCCTAGGACAGCAG 58.766 52.381 22.31 4.07 0.00 4.24
393 694 0.965439 ATCGATCCTAGGACAGCAGC 59.035 55.000 15.42 0.00 0.00 5.25
408 709 4.870363 ACAGCAGCAACAACGATAATTTT 58.130 34.783 0.00 0.00 0.00 1.82
411 712 5.574055 CAGCAGCAACAACGATAATTTTCAT 59.426 36.000 0.00 0.00 0.00 2.57
478 800 1.949465 AAACTTTCTCGCGTTCCACT 58.051 45.000 5.77 0.00 0.00 4.00
479 801 1.949465 AACTTTCTCGCGTTCCACTT 58.051 45.000 5.77 0.00 0.00 3.16
480 802 1.499049 ACTTTCTCGCGTTCCACTTC 58.501 50.000 5.77 0.00 0.00 3.01
481 803 0.790814 CTTTCTCGCGTTCCACTTCC 59.209 55.000 5.77 0.00 0.00 3.46
482 804 0.105224 TTTCTCGCGTTCCACTTCCA 59.895 50.000 5.77 0.00 0.00 3.53
483 805 0.599204 TTCTCGCGTTCCACTTCCAC 60.599 55.000 5.77 0.00 0.00 4.02
484 806 2.355363 TCGCGTTCCACTTCCACG 60.355 61.111 5.77 0.00 36.98 4.94
485 807 2.660552 CGCGTTCCACTTCCACGT 60.661 61.111 0.00 0.00 36.29 4.49
486 808 1.372004 CGCGTTCCACTTCCACGTA 60.372 57.895 0.00 0.00 36.29 3.57
488 810 1.623973 GCGTTCCACTTCCACGTAGC 61.624 60.000 0.00 0.00 36.29 3.58
490 812 1.429463 GTTCCACTTCCACGTAGCAG 58.571 55.000 0.00 0.00 0.00 4.24
494 816 0.319900 CACTTCCACGTAGCAGCAGT 60.320 55.000 0.00 0.00 0.00 4.40
495 817 0.393077 ACTTCCACGTAGCAGCAGTT 59.607 50.000 0.00 0.00 0.00 3.16
508 830 1.225704 GCAGTTCCTAGGCCAGCAT 59.774 57.895 5.01 0.00 0.00 3.79
586 925 1.152483 AGGTGCAATTGCCAGGTGT 60.152 52.632 26.94 3.65 41.18 4.16
587 926 0.760189 AGGTGCAATTGCCAGGTGTT 60.760 50.000 26.94 3.67 41.18 3.32
588 927 0.319813 GGTGCAATTGCCAGGTGTTC 60.320 55.000 26.94 7.49 41.18 3.18
589 928 0.319813 GTGCAATTGCCAGGTGTTCC 60.320 55.000 26.94 0.00 41.18 3.62
590 929 1.080569 GCAATTGCCAGGTGTTCCG 60.081 57.895 20.06 0.00 35.24 4.30
601 940 3.365976 GTGTTCCGGTACACACACA 57.634 52.632 32.13 9.73 46.00 3.72
602 941 0.932399 GTGTTCCGGTACACACACAC 59.068 55.000 32.13 16.34 46.00 3.82
603 942 0.535797 TGTTCCGGTACACACACACA 59.464 50.000 10.19 0.00 0.00 3.72
675 1027 4.778415 CTGCTCCGTCCGTCCACG 62.778 72.222 0.00 0.00 39.61 4.94
677 1029 4.773117 GCTCCGTCCGTCCACGTC 62.773 72.222 0.00 0.00 38.14 4.34
678 1030 4.112341 CTCCGTCCGTCCACGTCC 62.112 72.222 0.00 0.00 38.14 4.79
679 1031 4.953010 TCCGTCCGTCCACGTCCA 62.953 66.667 0.00 0.00 38.14 4.02
680 1032 4.415332 CCGTCCGTCCACGTCCAG 62.415 72.222 0.00 0.00 38.14 3.86
722 1082 4.988598 CAACACGCAGCCTCCGGT 62.989 66.667 0.00 0.00 0.00 5.28
723 1083 4.681978 AACACGCAGCCTCCGGTC 62.682 66.667 0.00 0.00 0.00 4.79
781 1141 2.751436 GATGCGCAGAGGCCCAAA 60.751 61.111 18.32 0.00 36.38 3.28
894 1269 2.679342 CCCCAATCCTCCTCGCCAA 61.679 63.158 0.00 0.00 0.00 4.52
898 1273 0.250234 CAATCCTCCTCGCCAACTCA 59.750 55.000 0.00 0.00 0.00 3.41
900 1275 1.207791 ATCCTCCTCGCCAACTCATT 58.792 50.000 0.00 0.00 0.00 2.57
903 1278 0.462759 CTCCTCGCCAACTCATTCCC 60.463 60.000 0.00 0.00 0.00 3.97
907 1282 0.250234 TCGCCAACTCATTCCCAGAG 59.750 55.000 0.00 0.00 39.04 3.35
908 1283 1.372087 CGCCAACTCATTCCCAGAGC 61.372 60.000 0.00 0.00 36.58 4.09
909 1284 0.322816 GCCAACTCATTCCCAGAGCA 60.323 55.000 0.00 0.00 36.58 4.26
910 1285 1.457346 CCAACTCATTCCCAGAGCAC 58.543 55.000 0.00 0.00 36.58 4.40
911 1286 1.457346 CAACTCATTCCCAGAGCACC 58.543 55.000 0.00 0.00 36.58 5.01
912 1287 1.067295 AACTCATTCCCAGAGCACCA 58.933 50.000 0.00 0.00 36.58 4.17
913 1288 1.067295 ACTCATTCCCAGAGCACCAA 58.933 50.000 0.00 0.00 36.58 3.67
914 1289 1.004044 ACTCATTCCCAGAGCACCAAG 59.996 52.381 0.00 0.00 36.58 3.61
915 1290 1.280133 CTCATTCCCAGAGCACCAAGA 59.720 52.381 0.00 0.00 0.00 3.02
933 1308 4.099881 CCAAGAAGATCTGGAGAAGAGAGG 59.900 50.000 0.00 0.00 38.67 3.69
936 1311 3.600448 AGATCTGGAGAAGAGAGGAGG 57.400 52.381 0.00 0.00 38.67 4.30
937 1312 1.963515 GATCTGGAGAAGAGAGGAGGC 59.036 57.143 0.00 0.00 38.67 4.70
938 1313 0.032615 TCTGGAGAAGAGAGGAGGCC 60.033 60.000 0.00 0.00 0.00 5.19
956 1341 1.609239 CATTGCTAGCTCCCCACCA 59.391 57.895 17.23 0.00 0.00 4.17
959 1344 1.635817 TTGCTAGCTCCCCACCATCC 61.636 60.000 17.23 0.00 0.00 3.51
966 1351 1.307866 TCCCCACCATCCCCTTCTC 60.308 63.158 0.00 0.00 0.00 2.87
972 1357 1.062121 CACCATCCCCTTCTCCCTCTA 60.062 57.143 0.00 0.00 0.00 2.43
974 1359 2.158081 ACCATCCCCTTCTCCCTCTATC 60.158 54.545 0.00 0.00 0.00 2.08
975 1360 2.113414 CCATCCCCTTCTCCCTCTATCT 59.887 54.545 0.00 0.00 0.00 1.98
977 1362 1.133009 TCCCCTTCTCCCTCTATCTGC 60.133 57.143 0.00 0.00 0.00 4.26
978 1363 1.347062 CCCTTCTCCCTCTATCTGCC 58.653 60.000 0.00 0.00 0.00 4.85
979 1364 1.132881 CCCTTCTCCCTCTATCTGCCT 60.133 57.143 0.00 0.00 0.00 4.75
980 1365 2.110899 CCCTTCTCCCTCTATCTGCCTA 59.889 54.545 0.00 0.00 0.00 3.93
981 1366 3.430453 CCTTCTCCCTCTATCTGCCTAG 58.570 54.545 0.00 0.00 0.00 3.02
982 1367 2.595750 TCTCCCTCTATCTGCCTAGC 57.404 55.000 0.00 0.00 0.00 3.42
983 1368 1.173043 CTCCCTCTATCTGCCTAGCG 58.827 60.000 0.00 0.00 0.00 4.26
984 1369 0.478942 TCCCTCTATCTGCCTAGCGT 59.521 55.000 0.00 0.00 0.00 5.07
985 1370 1.133450 TCCCTCTATCTGCCTAGCGTT 60.133 52.381 0.00 0.00 0.00 4.84
1530 1936 1.192146 AGAGCTTCCAGTACGGCCAA 61.192 55.000 2.24 0.00 33.14 4.52
1565 1971 1.068474 GCAGCTTGCTTTGCATCTTG 58.932 50.000 0.00 0.00 40.96 3.02
1572 1997 2.309613 TGCTTTGCATCTTGTTCTGGT 58.690 42.857 0.00 0.00 31.71 4.00
1579 2004 2.154462 CATCTTGTTCTGGTGGTGTCC 58.846 52.381 0.00 0.00 0.00 4.02
1580 2005 0.105964 TCTTGTTCTGGTGGTGTCCG 59.894 55.000 0.00 0.00 0.00 4.79
1581 2006 1.507141 CTTGTTCTGGTGGTGTCCGC 61.507 60.000 0.00 0.00 0.00 5.54
1582 2007 3.041940 GTTCTGGTGGTGTCCGCG 61.042 66.667 0.00 0.00 34.37 6.46
1583 2008 3.228017 TTCTGGTGGTGTCCGCGA 61.228 61.111 8.23 0.00 34.37 5.87
1584 2009 3.220999 TTCTGGTGGTGTCCGCGAG 62.221 63.158 8.23 0.00 40.41 5.03
1585 2010 3.680786 CTGGTGGTGTCCGCGAGA 61.681 66.667 8.23 0.00 41.33 4.04
1586 2011 2.994995 TGGTGGTGTCCGCGAGAT 60.995 61.111 8.23 0.00 34.37 2.75
1587 2012 2.202756 GGTGGTGTCCGCGAGATC 60.203 66.667 8.23 1.23 34.37 2.75
1588 2013 2.202756 GTGGTGTCCGCGAGATCC 60.203 66.667 8.23 10.64 0.00 3.36
1589 2014 2.678580 TGGTGTCCGCGAGATCCA 60.679 61.111 8.23 12.97 0.00 3.41
1590 2015 2.279810 TGGTGTCCGCGAGATCCAA 61.280 57.895 8.23 0.17 31.39 3.53
1591 2016 1.079405 GGTGTCCGCGAGATCCAAA 60.079 57.895 8.23 0.00 0.00 3.28
1592 2017 0.462047 GGTGTCCGCGAGATCCAAAT 60.462 55.000 8.23 0.00 0.00 2.32
1593 2018 1.202486 GGTGTCCGCGAGATCCAAATA 60.202 52.381 8.23 0.00 0.00 1.40
1594 2019 2.128035 GTGTCCGCGAGATCCAAATAG 58.872 52.381 8.23 0.00 0.00 1.73
1595 2020 2.028876 TGTCCGCGAGATCCAAATAGA 58.971 47.619 8.23 0.00 0.00 1.98
1596 2021 2.223735 TGTCCGCGAGATCCAAATAGAC 60.224 50.000 8.23 1.78 0.00 2.59
1597 2022 2.028876 TCCGCGAGATCCAAATAGACA 58.971 47.619 8.23 0.00 0.00 3.41
1598 2023 2.128035 CCGCGAGATCCAAATAGACAC 58.872 52.381 8.23 0.00 0.00 3.67
1599 2024 1.781429 CGCGAGATCCAAATAGACACG 59.219 52.381 0.00 0.00 0.00 4.49
1600 2025 2.540973 CGCGAGATCCAAATAGACACGA 60.541 50.000 0.00 0.00 0.00 4.35
1601 2026 2.789893 GCGAGATCCAAATAGACACGAC 59.210 50.000 0.00 0.00 0.00 4.34
1602 2027 3.036633 CGAGATCCAAATAGACACGACG 58.963 50.000 0.00 0.00 0.00 5.12
1603 2028 3.242641 CGAGATCCAAATAGACACGACGA 60.243 47.826 0.00 0.00 0.00 4.20
1604 2029 4.030134 AGATCCAAATAGACACGACGAC 57.970 45.455 0.00 0.00 0.00 4.34
1605 2030 2.251869 TCCAAATAGACACGACGACG 57.748 50.000 5.58 5.58 45.75 5.12
1606 2031 1.135603 TCCAAATAGACACGACGACGG 60.136 52.381 12.58 3.35 44.46 4.79
1608 2033 1.135603 CAAATAGACACGACGACGGGA 60.136 52.381 17.90 0.00 46.86 5.14
1609 2034 1.167851 AATAGACACGACGACGGGAA 58.832 50.000 17.90 1.37 46.86 3.97
1610 2035 0.731417 ATAGACACGACGACGGGAAG 59.269 55.000 17.90 3.24 46.86 3.46
1611 2036 1.300971 TAGACACGACGACGGGAAGG 61.301 60.000 17.90 0.28 46.86 3.46
1673 2155 2.049627 GATGGGGAAGATGGCTCGCT 62.050 60.000 0.00 0.00 0.00 4.93
1800 4173 4.959210 TGGTGGTTCTTTCCATTCTTTTGA 59.041 37.500 0.00 0.00 39.81 2.69
1802 4175 5.509670 GGTGGTTCTTTCCATTCTTTTGAGG 60.510 44.000 0.00 0.00 39.81 3.86
1825 4198 2.029470 CGTGGGTGCCATGTAAATGTTT 60.029 45.455 0.00 0.00 35.92 2.83
2051 4436 3.813166 TGTTTTCCTTTCGTAGAGGCTTG 59.187 43.478 0.00 0.00 38.43 4.01
2164 4549 2.166664 GGCTTCGATGGACTCTAGTGTT 59.833 50.000 0.00 0.00 0.00 3.32
2181 4566 1.803334 GTTGGTGCATCAACGAGGTA 58.197 50.000 25.99 0.00 37.80 3.08
2182 4567 1.463444 GTTGGTGCATCAACGAGGTAC 59.537 52.381 25.99 3.36 37.80 3.34
2183 4568 2.870435 GTTGGTGCATCAACGAGGTACT 60.870 50.000 25.99 0.00 38.62 2.73
2227 4617 4.092968 GTGTCGGTGTATTAGCAAAGAAGG 59.907 45.833 0.00 0.00 0.00 3.46
2308 4718 9.771915 AAAATTTGCACATTTCTTTACAAGTTG 57.228 25.926 11.08 0.00 0.00 3.16
2315 4725 5.475564 ACATTTCTTTACAAGTTGGGCGTAT 59.524 36.000 7.96 0.00 0.00 3.06
2316 4726 5.365403 TTTCTTTACAAGTTGGGCGTATG 57.635 39.130 7.96 0.00 0.00 2.39
2317 4727 4.010667 TCTTTACAAGTTGGGCGTATGT 57.989 40.909 7.96 0.00 0.00 2.29
2333 4744 4.151689 GCGTATGTTGTTTCTCAAGCTACA 59.848 41.667 0.00 0.00 36.66 2.74
2341 4752 6.560253 TGTTTCTCAAGCTACATCTTTTCC 57.440 37.500 0.00 0.00 0.00 3.13
2355 4766 2.289547 TCTTTTCCAAAAAGGCTCGTCG 59.710 45.455 11.18 0.00 37.29 5.12
2377 4788 3.509967 GCCCCGCCTTATAAATAAAGCAT 59.490 43.478 4.64 0.00 30.93 3.79
2383 4794 5.049680 CGCCTTATAAATAAAGCATCACCGT 60.050 40.000 4.64 0.00 30.93 4.83
2466 4882 5.864474 AGTGACATTAGAGCAGAAAGTAACG 59.136 40.000 0.00 0.00 0.00 3.18
2469 4885 6.365247 TGACATTAGAGCAGAAAGTAACGAAC 59.635 38.462 0.00 0.00 0.00 3.95
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.102367 AGACACTGCTCCTTTTTCTCTTCT 59.898 41.667 0.00 0.00 0.00 2.85
1 2 4.384940 AGACACTGCTCCTTTTTCTCTTC 58.615 43.478 0.00 0.00 0.00 2.87
2 3 4.429854 AGACACTGCTCCTTTTTCTCTT 57.570 40.909 0.00 0.00 0.00 2.85
3 4 4.429854 AAGACACTGCTCCTTTTTCTCT 57.570 40.909 0.00 0.00 0.00 3.10
4 5 4.336713 ACAAAGACACTGCTCCTTTTTCTC 59.663 41.667 0.00 0.00 0.00 2.87
5 6 4.096984 CACAAAGACACTGCTCCTTTTTCT 59.903 41.667 0.00 0.00 0.00 2.52
6 7 4.354587 CACAAAGACACTGCTCCTTTTTC 58.645 43.478 0.00 0.00 0.00 2.29
7 8 3.131046 CCACAAAGACACTGCTCCTTTTT 59.869 43.478 0.00 0.00 0.00 1.94
8 9 2.689983 CCACAAAGACACTGCTCCTTTT 59.310 45.455 0.00 0.00 0.00 2.27
9 10 2.092429 TCCACAAAGACACTGCTCCTTT 60.092 45.455 0.00 0.00 0.00 3.11
10 11 1.490490 TCCACAAAGACACTGCTCCTT 59.510 47.619 0.00 0.00 0.00 3.36
11 12 1.131638 TCCACAAAGACACTGCTCCT 58.868 50.000 0.00 0.00 0.00 3.69
12 13 1.967319 TTCCACAAAGACACTGCTCC 58.033 50.000 0.00 0.00 0.00 4.70
13 14 2.291741 CCTTTCCACAAAGACACTGCTC 59.708 50.000 0.00 0.00 41.60 4.26
14 15 2.301346 CCTTTCCACAAAGACACTGCT 58.699 47.619 0.00 0.00 41.60 4.24
15 16 1.269257 GCCTTTCCACAAAGACACTGC 60.269 52.381 0.00 0.00 41.60 4.40
16 17 1.002468 CGCCTTTCCACAAAGACACTG 60.002 52.381 0.00 0.00 41.60 3.66
17 18 1.308998 CGCCTTTCCACAAAGACACT 58.691 50.000 0.00 0.00 41.60 3.55
18 19 1.021968 ACGCCTTTCCACAAAGACAC 58.978 50.000 0.00 0.00 41.60 3.67
19 20 1.021202 CACGCCTTTCCACAAAGACA 58.979 50.000 0.00 0.00 41.60 3.41
20 21 0.310854 CCACGCCTTTCCACAAAGAC 59.689 55.000 0.00 0.00 41.60 3.01
21 22 0.106918 ACCACGCCTTTCCACAAAGA 60.107 50.000 0.00 0.00 41.60 2.52
22 23 1.265905 GTACCACGCCTTTCCACAAAG 59.734 52.381 0.00 0.00 39.11 2.77
23 24 1.310904 GTACCACGCCTTTCCACAAA 58.689 50.000 0.00 0.00 0.00 2.83
24 25 0.881159 CGTACCACGCCTTTCCACAA 60.881 55.000 0.00 0.00 33.65 3.33
25 26 1.301087 CGTACCACGCCTTTCCACA 60.301 57.895 0.00 0.00 33.65 4.17
26 27 3.557824 CGTACCACGCCTTTCCAC 58.442 61.111 0.00 0.00 33.65 4.02
36 37 2.538449 CTCACACACTTCAACGTACCAC 59.462 50.000 0.00 0.00 0.00 4.16
37 38 2.816689 CTCACACACTTCAACGTACCA 58.183 47.619 0.00 0.00 0.00 3.25
38 39 1.525619 GCTCACACACTTCAACGTACC 59.474 52.381 0.00 0.00 0.00 3.34
39 40 2.034001 GTGCTCACACACTTCAACGTAC 60.034 50.000 0.00 0.00 46.61 3.67
40 41 2.198406 GTGCTCACACACTTCAACGTA 58.802 47.619 0.00 0.00 46.61 3.57
41 42 1.006832 GTGCTCACACACTTCAACGT 58.993 50.000 0.00 0.00 46.61 3.99
42 43 3.806257 GTGCTCACACACTTCAACG 57.194 52.632 0.00 0.00 46.61 4.10
57 58 4.424711 TTCCATCCAGCCGGGTGC 62.425 66.667 28.23 0.02 42.74 5.01
58 59 2.124570 CTTCCATCCAGCCGGGTG 60.125 66.667 26.78 26.78 43.84 4.61
59 60 3.411517 CCTTCCATCCAGCCGGGT 61.412 66.667 0.00 0.00 38.11 5.28
60 61 3.089874 TCCTTCCATCCAGCCGGG 61.090 66.667 2.18 0.00 38.37 5.73
61 62 1.626356 TTCTCCTTCCATCCAGCCGG 61.626 60.000 0.00 0.00 0.00 6.13
62 63 0.179062 CTTCTCCTTCCATCCAGCCG 60.179 60.000 0.00 0.00 0.00 5.52
63 64 0.182299 CCTTCTCCTTCCATCCAGCC 59.818 60.000 0.00 0.00 0.00 4.85
64 65 0.915364 ACCTTCTCCTTCCATCCAGC 59.085 55.000 0.00 0.00 0.00 4.85
65 66 2.093235 GTCACCTTCTCCTTCCATCCAG 60.093 54.545 0.00 0.00 0.00 3.86
66 67 1.909302 GTCACCTTCTCCTTCCATCCA 59.091 52.381 0.00 0.00 0.00 3.41
67 68 1.909302 TGTCACCTTCTCCTTCCATCC 59.091 52.381 0.00 0.00 0.00 3.51
68 69 3.703001 TTGTCACCTTCTCCTTCCATC 57.297 47.619 0.00 0.00 0.00 3.51
69 70 3.138283 TGTTTGTCACCTTCTCCTTCCAT 59.862 43.478 0.00 0.00 0.00 3.41
70 71 2.507886 TGTTTGTCACCTTCTCCTTCCA 59.492 45.455 0.00 0.00 0.00 3.53
71 72 3.142174 CTGTTTGTCACCTTCTCCTTCC 58.858 50.000 0.00 0.00 0.00 3.46
72 73 3.809905 ACTGTTTGTCACCTTCTCCTTC 58.190 45.455 0.00 0.00 0.00 3.46
73 74 3.933861 ACTGTTTGTCACCTTCTCCTT 57.066 42.857 0.00 0.00 0.00 3.36
74 75 3.545703 CAACTGTTTGTCACCTTCTCCT 58.454 45.455 0.00 0.00 0.00 3.69
75 76 2.618709 CCAACTGTTTGTCACCTTCTCC 59.381 50.000 0.00 0.00 0.00 3.71
76 77 3.279434 ACCAACTGTTTGTCACCTTCTC 58.721 45.455 0.00 0.00 0.00 2.87
77 78 3.366052 ACCAACTGTTTGTCACCTTCT 57.634 42.857 0.00 0.00 0.00 2.85
78 79 3.192633 ACAACCAACTGTTTGTCACCTTC 59.807 43.478 0.00 0.00 34.00 3.46
79 80 3.161866 ACAACCAACTGTTTGTCACCTT 58.838 40.909 0.00 0.00 34.00 3.50
80 81 2.802719 ACAACCAACTGTTTGTCACCT 58.197 42.857 0.00 0.00 34.00 4.00
81 82 3.192633 AGAACAACCAACTGTTTGTCACC 59.807 43.478 0.00 0.00 39.63 4.02
82 83 4.165779 CAGAACAACCAACTGTTTGTCAC 58.834 43.478 0.00 0.00 39.63 3.67
83 84 3.823873 ACAGAACAACCAACTGTTTGTCA 59.176 39.130 0.00 0.00 41.21 3.58
84 85 4.156008 AGACAGAACAACCAACTGTTTGTC 59.844 41.667 15.85 15.85 43.49 3.18
85 86 4.079253 AGACAGAACAACCAACTGTTTGT 58.921 39.130 0.00 0.00 43.49 2.83
86 87 4.414852 CAGACAGAACAACCAACTGTTTG 58.585 43.478 0.00 0.00 43.49 2.93
168 169 1.442769 AAGAATGCGCATGAGAACGT 58.557 45.000 26.09 5.81 0.00 3.99
169 170 2.532531 AAAGAATGCGCATGAGAACG 57.467 45.000 26.09 0.00 0.00 3.95
202 204 4.309933 TGCTCTATGTCTGTGTTTGAGTG 58.690 43.478 0.00 0.00 0.00 3.51
234 242 5.221244 GGATGGTTCCAGGCACATAATAAAC 60.221 44.000 0.00 0.00 42.12 2.01
237 245 4.098914 GGATGGTTCCAGGCACATAATA 57.901 45.455 0.00 0.00 42.12 0.98
238 246 2.949447 GGATGGTTCCAGGCACATAAT 58.051 47.619 0.00 0.00 42.12 1.28
249 257 3.137176 TCCTCTCAATGATGGATGGTTCC 59.863 47.826 1.82 0.00 42.94 3.62
310 324 0.104934 ATCATAAGAGGACGGCCCCT 60.105 55.000 1.76 0.00 39.77 4.79
327 341 1.003759 CTGCGCTGCTTTCAGATCATC 60.004 52.381 9.73 0.00 42.95 2.92
376 677 0.461548 TTGCTGCTGTCCTAGGATCG 59.538 55.000 16.27 10.23 0.00 3.69
382 683 0.391228 TCGTTGTTGCTGCTGTCCTA 59.609 50.000 0.00 0.00 0.00 2.94
389 690 5.004726 GGATGAAAATTATCGTTGTTGCTGC 59.995 40.000 0.00 0.00 0.00 5.25
391 692 6.266168 TGGATGAAAATTATCGTTGTTGCT 57.734 33.333 0.00 0.00 0.00 3.91
392 693 7.524294 AATGGATGAAAATTATCGTTGTTGC 57.476 32.000 0.00 0.00 0.00 4.17
408 709 3.835478 TTGGGGTGGTAAAATGGATGA 57.165 42.857 0.00 0.00 0.00 2.92
411 712 2.896039 CCTTTGGGGTGGTAAAATGGA 58.104 47.619 0.00 0.00 0.00 3.41
446 751 4.265320 CGAGAAAGTTTTTGTGCAGGAAAC 59.735 41.667 10.10 10.10 34.37 2.78
448 753 3.733684 GCGAGAAAGTTTTTGTGCAGGAA 60.734 43.478 0.00 0.00 0.00 3.36
478 800 0.320421 GGAACTGCTGCTACGTGGAA 60.320 55.000 1.81 0.00 0.00 3.53
479 801 1.185618 AGGAACTGCTGCTACGTGGA 61.186 55.000 1.81 0.00 37.18 4.02
480 802 0.530744 TAGGAACTGCTGCTACGTGG 59.469 55.000 0.00 0.00 41.52 4.94
481 803 1.469940 CCTAGGAACTGCTGCTACGTG 60.470 57.143 1.05 0.00 41.52 4.49
482 804 0.818296 CCTAGGAACTGCTGCTACGT 59.182 55.000 1.05 0.00 41.52 3.57
483 805 0.528684 GCCTAGGAACTGCTGCTACG 60.529 60.000 14.75 0.00 41.52 3.51
484 806 0.179070 GGCCTAGGAACTGCTGCTAC 60.179 60.000 14.75 0.00 41.52 3.58
485 807 0.617535 TGGCCTAGGAACTGCTGCTA 60.618 55.000 14.75 0.00 41.52 3.49
486 808 1.908340 CTGGCCTAGGAACTGCTGCT 61.908 60.000 14.75 0.00 41.52 4.24
488 810 1.451028 GCTGGCCTAGGAACTGCTG 60.451 63.158 14.75 0.00 41.52 4.41
490 812 1.099879 CATGCTGGCCTAGGAACTGC 61.100 60.000 14.75 19.01 41.52 4.40
494 816 0.913934 TGTCCATGCTGGCCTAGGAA 60.914 55.000 14.75 0.00 37.47 3.36
495 817 1.306911 TGTCCATGCTGGCCTAGGA 60.307 57.895 14.75 0.91 37.47 2.94
508 830 1.597854 CTTTGCTGGCGTCTGTCCA 60.598 57.895 0.00 0.00 0.00 4.02
511 833 0.882042 CTGACTTTGCTGGCGTCTGT 60.882 55.000 0.00 0.00 0.00 3.41
512 834 0.601046 TCTGACTTTGCTGGCGTCTG 60.601 55.000 0.00 0.00 0.00 3.51
513 835 0.601311 GTCTGACTTTGCTGGCGTCT 60.601 55.000 0.00 0.00 0.00 4.18
514 836 0.880278 TGTCTGACTTTGCTGGCGTC 60.880 55.000 9.51 0.00 0.00 5.19
515 837 0.882042 CTGTCTGACTTTGCTGGCGT 60.882 55.000 9.51 0.00 0.00 5.68
516 838 1.864862 CTGTCTGACTTTGCTGGCG 59.135 57.895 9.51 0.00 0.00 5.69
517 839 0.888285 AGCTGTCTGACTTTGCTGGC 60.888 55.000 17.52 7.97 32.32 4.85
518 840 1.155042 GAGCTGTCTGACTTTGCTGG 58.845 55.000 21.12 2.44 33.83 4.85
586 925 0.535797 TGTGTGTGTGTGTACCGGAA 59.464 50.000 9.46 0.00 0.00 4.30
587 926 0.179105 GTGTGTGTGTGTGTACCGGA 60.179 55.000 9.46 0.00 0.00 5.14
588 927 0.460459 TGTGTGTGTGTGTGTACCGG 60.460 55.000 0.00 0.00 0.00 5.28
589 928 0.927537 CTGTGTGTGTGTGTGTACCG 59.072 55.000 0.00 0.00 0.00 4.02
590 929 1.931172 GTCTGTGTGTGTGTGTGTACC 59.069 52.381 0.00 0.00 0.00 3.34
600 939 1.775039 CGGTTGCCTGTCTGTGTGTG 61.775 60.000 0.00 0.00 0.00 3.82
601 940 1.523711 CGGTTGCCTGTCTGTGTGT 60.524 57.895 0.00 0.00 0.00 3.72
602 941 2.896801 GCGGTTGCCTGTCTGTGTG 61.897 63.158 0.00 0.00 33.98 3.82
603 942 2.591715 GCGGTTGCCTGTCTGTGT 60.592 61.111 0.00 0.00 33.98 3.72
669 1021 2.430921 CGTGAGCTGGACGTGGAC 60.431 66.667 0.00 0.00 32.06 4.02
675 1027 3.973267 GAGGCGACGTGAGCTGGAC 62.973 68.421 11.66 0.00 34.52 4.02
676 1028 3.749064 GAGGCGACGTGAGCTGGA 61.749 66.667 11.66 0.00 34.52 3.86
677 1029 4.803426 GGAGGCGACGTGAGCTGG 62.803 72.222 11.66 0.00 34.52 4.85
678 1030 4.803426 GGGAGGCGACGTGAGCTG 62.803 72.222 11.66 0.00 34.52 4.24
680 1032 4.803426 CAGGGAGGCGACGTGAGC 62.803 72.222 0.00 0.00 0.00 4.26
681 1033 4.135153 CCAGGGAGGCGACGTGAG 62.135 72.222 0.00 0.00 0.00 3.51
722 1082 4.424566 GCTTCGTACACCGCCGGA 62.425 66.667 11.71 0.00 36.19 5.14
723 1083 3.927163 AAGCTTCGTACACCGCCGG 62.927 63.158 0.00 0.00 36.19 6.13
724 1084 1.952266 GAAAGCTTCGTACACCGCCG 61.952 60.000 0.00 0.00 36.19 6.46
725 1085 0.947180 TGAAAGCTTCGTACACCGCC 60.947 55.000 0.00 0.00 36.19 6.13
726 1086 0.863144 TTGAAAGCTTCGTACACCGC 59.137 50.000 0.00 0.00 36.19 5.68
880 1255 1.207791 ATGAGTTGGCGAGGAGGATT 58.792 50.000 0.00 0.00 0.00 3.01
881 1256 1.139853 GAATGAGTTGGCGAGGAGGAT 59.860 52.381 0.00 0.00 0.00 3.24
882 1257 0.537188 GAATGAGTTGGCGAGGAGGA 59.463 55.000 0.00 0.00 0.00 3.71
883 1258 0.462759 GGAATGAGTTGGCGAGGAGG 60.463 60.000 0.00 0.00 0.00 4.30
884 1259 0.462759 GGGAATGAGTTGGCGAGGAG 60.463 60.000 0.00 0.00 0.00 3.69
894 1269 1.004044 CTTGGTGCTCTGGGAATGAGT 59.996 52.381 0.00 0.00 34.30 3.41
898 1273 1.988107 TCTTCTTGGTGCTCTGGGAAT 59.012 47.619 0.00 0.00 0.00 3.01
900 1275 1.556911 GATCTTCTTGGTGCTCTGGGA 59.443 52.381 0.00 0.00 0.00 4.37
903 1278 2.235650 TCCAGATCTTCTTGGTGCTCTG 59.764 50.000 0.00 0.00 0.00 3.35
907 1282 3.055530 TCTTCTCCAGATCTTCTTGGTGC 60.056 47.826 0.00 0.00 0.00 5.01
908 1283 4.465660 TCTCTTCTCCAGATCTTCTTGGTG 59.534 45.833 0.00 0.00 0.00 4.17
909 1284 4.682563 TCTCTTCTCCAGATCTTCTTGGT 58.317 43.478 0.00 0.00 0.00 3.67
910 1285 4.099881 CCTCTCTTCTCCAGATCTTCTTGG 59.900 50.000 0.00 0.00 0.00 3.61
911 1286 4.955450 TCCTCTCTTCTCCAGATCTTCTTG 59.045 45.833 0.00 0.00 0.00 3.02
912 1287 5.203528 CTCCTCTCTTCTCCAGATCTTCTT 58.796 45.833 0.00 0.00 0.00 2.52
913 1288 4.386761 CCTCCTCTCTTCTCCAGATCTTCT 60.387 50.000 0.00 0.00 0.00 2.85
914 1289 3.891366 CCTCCTCTCTTCTCCAGATCTTC 59.109 52.174 0.00 0.00 0.00 2.87
915 1290 3.914771 CCTCCTCTCTTCTCCAGATCTT 58.085 50.000 0.00 0.00 0.00 2.40
933 1308 1.228094 GGGAGCTAGCAATGGCCTC 60.228 63.158 18.83 3.23 42.56 4.70
936 1311 1.825622 GTGGGGAGCTAGCAATGGC 60.826 63.158 18.83 0.23 41.61 4.40
937 1312 1.152881 GGTGGGGAGCTAGCAATGG 60.153 63.158 18.83 0.00 0.00 3.16
938 1313 0.184451 ATGGTGGGGAGCTAGCAATG 59.816 55.000 18.83 0.00 0.00 2.82
956 1341 2.494439 GCAGATAGAGGGAGAAGGGGAT 60.494 54.545 0.00 0.00 0.00 3.85
959 1344 1.132881 AGGCAGATAGAGGGAGAAGGG 60.133 57.143 0.00 0.00 0.00 3.95
966 1351 1.271102 GAACGCTAGGCAGATAGAGGG 59.729 57.143 0.00 0.00 0.00 4.30
972 1357 0.539051 AGCAAGAACGCTAGGCAGAT 59.461 50.000 0.00 0.00 41.55 2.90
974 1359 0.445436 CAAGCAAGAACGCTAGGCAG 59.555 55.000 0.00 0.00 42.89 4.85
975 1360 0.955428 CCAAGCAAGAACGCTAGGCA 60.955 55.000 0.00 0.00 42.89 4.75
977 1362 1.079503 GACCAAGCAAGAACGCTAGG 58.920 55.000 0.00 0.00 42.89 3.02
978 1363 0.716108 CGACCAAGCAAGAACGCTAG 59.284 55.000 0.00 0.00 42.89 3.42
979 1364 1.289109 GCGACCAAGCAAGAACGCTA 61.289 55.000 0.00 0.00 42.89 4.26
980 1365 2.607892 GCGACCAAGCAAGAACGCT 61.608 57.895 0.00 0.00 46.67 5.07
981 1366 2.127232 GCGACCAAGCAAGAACGC 60.127 61.111 0.00 0.00 39.33 4.84
982 1367 1.577328 ATGGCGACCAAGCAAGAACG 61.577 55.000 2.68 0.00 36.95 3.95
983 1368 0.109597 CATGGCGACCAAGCAAGAAC 60.110 55.000 2.68 0.00 36.95 3.01
984 1369 1.243342 CCATGGCGACCAAGCAAGAA 61.243 55.000 0.00 0.00 36.95 2.52
985 1370 1.675310 CCATGGCGACCAAGCAAGA 60.675 57.895 0.00 0.00 36.95 3.02
1530 1936 1.651240 CTGCTTAGTGCGCCATTGCT 61.651 55.000 4.18 0.00 46.63 3.91
1560 1966 1.270839 CGGACACCACCAGAACAAGAT 60.271 52.381 0.00 0.00 0.00 2.40
1562 1968 1.507141 GCGGACACCACCAGAACAAG 61.507 60.000 0.00 0.00 0.00 3.16
1563 1969 1.525077 GCGGACACCACCAGAACAA 60.525 57.895 0.00 0.00 0.00 2.83
1565 1971 3.041940 CGCGGACACCACCAGAAC 61.042 66.667 0.00 0.00 0.00 3.01
1572 1997 1.822114 TTTGGATCTCGCGGACACCA 61.822 55.000 6.13 12.71 33.96 4.17
1579 2004 1.781429 CGTGTCTATTTGGATCTCGCG 59.219 52.381 0.00 0.00 0.00 5.87
1580 2005 2.789893 GTCGTGTCTATTTGGATCTCGC 59.210 50.000 0.00 0.00 0.00 5.03
1581 2006 3.036633 CGTCGTGTCTATTTGGATCTCG 58.963 50.000 0.00 0.00 0.00 4.04
1582 2007 4.036352 GTCGTCGTGTCTATTTGGATCTC 58.964 47.826 0.00 0.00 0.00 2.75
1583 2008 3.487042 CGTCGTCGTGTCTATTTGGATCT 60.487 47.826 0.00 0.00 0.00 2.75
1584 2009 2.782192 CGTCGTCGTGTCTATTTGGATC 59.218 50.000 0.00 0.00 0.00 3.36
1585 2010 2.479049 CCGTCGTCGTGTCTATTTGGAT 60.479 50.000 0.71 0.00 35.01 3.41
1586 2011 1.135603 CCGTCGTCGTGTCTATTTGGA 60.136 52.381 0.71 0.00 35.01 3.53
1587 2012 1.265568 CCGTCGTCGTGTCTATTTGG 58.734 55.000 0.71 0.00 35.01 3.28
1588 2013 1.135603 TCCCGTCGTCGTGTCTATTTG 60.136 52.381 0.71 0.00 35.01 2.32
1589 2014 1.167851 TCCCGTCGTCGTGTCTATTT 58.832 50.000 0.71 0.00 35.01 1.40
1590 2015 1.131883 CTTCCCGTCGTCGTGTCTATT 59.868 52.381 0.71 0.00 35.01 1.73
1591 2016 0.731417 CTTCCCGTCGTCGTGTCTAT 59.269 55.000 0.71 0.00 35.01 1.98
1592 2017 1.300971 CCTTCCCGTCGTCGTGTCTA 61.301 60.000 0.71 0.00 35.01 2.59
1593 2018 2.623915 CCTTCCCGTCGTCGTGTCT 61.624 63.158 0.71 0.00 35.01 3.41
1594 2019 2.126580 CCTTCCCGTCGTCGTGTC 60.127 66.667 0.71 0.00 35.01 3.67
1595 2020 2.138656 CTTCCTTCCCGTCGTCGTGT 62.139 60.000 0.71 0.00 35.01 4.49
1596 2021 1.443872 CTTCCTTCCCGTCGTCGTG 60.444 63.158 0.71 0.00 35.01 4.35
1597 2022 2.960170 CTTCCTTCCCGTCGTCGT 59.040 61.111 0.71 0.00 35.01 4.34
1598 2023 2.506438 GCTTCCTTCCCGTCGTCG 60.506 66.667 0.00 0.00 0.00 5.12
1599 2024 1.153804 GAGCTTCCTTCCCGTCGTC 60.154 63.158 0.00 0.00 0.00 4.20
1600 2025 2.971452 GAGCTTCCTTCCCGTCGT 59.029 61.111 0.00 0.00 0.00 4.34
1601 2026 2.202623 CGAGCTTCCTTCCCGTCG 60.203 66.667 0.00 0.00 0.00 5.12
1602 2027 1.446272 CACGAGCTTCCTTCCCGTC 60.446 63.158 0.00 0.00 0.00 4.79
1603 2028 1.469335 TTCACGAGCTTCCTTCCCGT 61.469 55.000 0.00 0.00 0.00 5.28
1604 2029 0.737715 CTTCACGAGCTTCCTTCCCG 60.738 60.000 0.00 0.00 0.00 5.14
1605 2030 0.608640 TCTTCACGAGCTTCCTTCCC 59.391 55.000 0.00 0.00 0.00 3.97
1606 2031 2.342179 CTTCTTCACGAGCTTCCTTCC 58.658 52.381 0.00 0.00 0.00 3.46
1607 2032 2.028930 TCCTTCTTCACGAGCTTCCTTC 60.029 50.000 0.00 0.00 0.00 3.46
1608 2033 1.971357 TCCTTCTTCACGAGCTTCCTT 59.029 47.619 0.00 0.00 0.00 3.36
1609 2034 1.548269 CTCCTTCTTCACGAGCTTCCT 59.452 52.381 0.00 0.00 0.00 3.36
1610 2035 1.546476 TCTCCTTCTTCACGAGCTTCC 59.454 52.381 0.00 0.00 0.00 3.46
1611 2036 3.057174 TCTTCTCCTTCTTCACGAGCTTC 60.057 47.826 0.00 0.00 0.00 3.86
1699 2181 2.546789 AGCAGCACGGTAAACTAACAAC 59.453 45.455 0.00 0.00 0.00 3.32
1742 2238 9.881649 TCGGTATCTATTATACGTAGAGACATT 57.118 33.333 11.07 0.00 40.43 2.71
1800 4173 1.485294 TTACATGGCACCCACGACCT 61.485 55.000 0.00 0.00 35.80 3.85
1802 4175 1.132262 CATTTACATGGCACCCACGAC 59.868 52.381 0.00 0.00 35.80 4.34
1825 4198 4.837860 AGGCAAAAACATAAGGAATCCACA 59.162 37.500 0.61 0.00 0.00 4.17
2051 4436 2.293677 TGCGTGTCATCTGTGGTATC 57.706 50.000 0.00 0.00 0.00 2.24
2110 4495 9.142515 TCATTATTTTATTTGTTTGAGCAGCAG 57.857 29.630 0.00 0.00 0.00 4.24
2143 4528 1.751924 ACACTAGAGTCCATCGAAGCC 59.248 52.381 0.00 0.00 0.00 4.35
2164 4549 0.973632 AGTACCTCGTTGATGCACCA 59.026 50.000 0.00 0.00 0.00 4.17
2247 4638 4.832266 TGTCTCTGCTTCTTCTTCTTCTCT 59.168 41.667 0.00 0.00 0.00 3.10
2263 4661 4.794248 TTTCGTGTGTGAATTGTCTCTG 57.206 40.909 0.00 0.00 0.00 3.35
2308 4718 2.414161 GCTTGAGAAACAACATACGCCC 60.414 50.000 0.00 0.00 34.56 6.13
2315 4725 6.942532 AAAGATGTAGCTTGAGAAACAACA 57.057 33.333 0.00 0.00 34.56 3.33
2316 4726 6.858478 GGAAAAGATGTAGCTTGAGAAACAAC 59.142 38.462 0.00 0.00 34.56 3.32
2317 4727 6.545666 TGGAAAAGATGTAGCTTGAGAAACAA 59.454 34.615 0.00 0.00 36.97 2.83
2333 4744 3.058224 CGACGAGCCTTTTTGGAAAAGAT 60.058 43.478 13.22 3.48 38.35 2.40
2355 4766 2.888414 TGCTTTATTTATAAGGCGGGGC 59.112 45.455 10.69 0.00 45.11 5.80
2358 4769 5.616866 CGGTGATGCTTTATTTATAAGGCGG 60.617 44.000 10.69 0.00 45.11 6.13
2362 4773 9.651718 GAAAGACGGTGATGCTTTATTTATAAG 57.348 33.333 0.00 0.00 32.45 1.73
2377 4788 0.179040 AAAAGGGCGAAAGACGGTGA 60.179 50.000 0.00 0.00 43.44 4.02
2466 4882 2.126189 AACCGCGCCTACTCGTTC 60.126 61.111 0.00 0.00 0.00 3.95


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

AutoCloner maintained by Alex Coulton.