Multiple sequence alignment - TraesCS1D01G161900

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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 TraesCS1D01G161900 chr1D 100.000 7631 0 0 1 7631 229490392 229482762 0.000000e+00 14092.0
1 TraesCS1D01G161900 chr1A 92.770 4122 171 48 2921 7003 297748834 297744801 0.000000e+00 5843.0
2 TraesCS1D01G161900 chr1A 88.226 1860 185 19 5086 6937 99658335 99660168 0.000000e+00 2191.0
3 TraesCS1D01G161900 chr1A 89.295 1588 145 14 5096 6668 99699669 99698092 0.000000e+00 1967.0
4 TraesCS1D01G161900 chr1A 87.802 992 57 27 378 1322 297751564 297750590 0.000000e+00 1103.0
5 TraesCS1D01G161900 chr1A 83.232 823 67 37 1709 2490 297750216 297749424 0.000000e+00 689.0
6 TraesCS1D01G161900 chr1A 91.075 493 22 5 2447 2917 297749433 297748941 0.000000e+00 647.0
7 TraesCS1D01G161900 chr1A 87.892 446 45 5 4616 5055 99657894 99658336 4.080000e-142 516.0
8 TraesCS1D01G161900 chr1A 87.727 440 45 7 4623 5056 99700118 99699682 8.840000e-139 505.0
9 TraesCS1D01G161900 chr1A 89.783 323 11 8 1407 1720 297750550 297750241 2.000000e-105 394.0
10 TraesCS1D01G161900 chr1A 86.890 328 28 8 1 327 297751890 297751577 3.390000e-93 353.0
11 TraesCS1D01G161900 chr1A 87.619 315 24 8 4237 4542 99700473 99700165 1.220000e-92 351.0
12 TraesCS1D01G161900 chr1A 80.060 336 33 16 7329 7631 297740833 297740499 1.290000e-52 219.0
13 TraesCS1D01G161900 chr1A 90.184 163 13 2 7170 7332 297741047 297740888 7.760000e-50 209.0
14 TraesCS1D01G161900 chr1A 83.043 230 25 7 2452 2668 99622324 99622552 6.040000e-46 196.0
15 TraesCS1D01G161900 chr1A 83.810 210 19 6 2453 2651 99701085 99700880 1.310000e-42 185.0
16 TraesCS1D01G161900 chr1A 79.094 287 40 11 846 1121 99621631 99621908 6.080000e-41 180.0
17 TraesCS1D01G161900 chr1A 76.825 315 30 20 1738 2041 99622013 99622295 3.710000e-28 137.0
18 TraesCS1D01G161900 chr1A 85.950 121 11 4 7057 7171 297743615 297743495 2.890000e-24 124.0
19 TraesCS1D01G161900 chr1A 100.000 32 0 0 5055 5086 154075455 154075424 8.270000e-05 60.2
20 TraesCS1D01G161900 chr1B 89.197 2666 132 62 1901 4499 328825402 328822826 0.000000e+00 3184.0
21 TraesCS1D01G161900 chr1B 94.164 1919 90 13 5085 6991 328822368 328820460 0.000000e+00 2904.0
22 TraesCS1D01G161900 chr1B 91.206 1012 39 16 736 1707 328826719 328825718 0.000000e+00 1330.0
23 TraesCS1D01G161900 chr1B 85.845 763 68 24 1 745 328832136 328831396 0.000000e+00 774.0
24 TraesCS1D01G161900 chr1B 92.547 483 33 3 4576 5056 328822848 328822367 0.000000e+00 689.0
25 TraesCS1D01G161900 chr1B 84.245 603 45 25 7057 7631 328820375 328819795 6.740000e-150 542.0
26 TraesCS1D01G161900 chr1B 89.474 114 6 3 1795 1902 328825625 328825512 1.030000e-28 139.0
27 TraesCS1D01G161900 chr5D 88.746 1866 172 25 5086 6937 11433771 11435612 0.000000e+00 2248.0
28 TraesCS1D01G161900 chr5D 89.579 902 76 12 5771 6668 11530321 11529434 0.000000e+00 1129.0
29 TraesCS1D01G161900 chr5D 88.412 699 66 10 5096 5780 11531037 11530340 0.000000e+00 828.0
30 TraesCS1D01G161900 chr5D 86.824 425 47 6 4639 5056 11433351 11433773 4.170000e-127 466.0
31 TraesCS1D01G161900 chr5D 85.874 446 54 5 4618 5056 11531493 11531050 4.170000e-127 466.0
32 TraesCS1D01G161900 chr5D 87.580 314 26 6 4237 4542 11531844 11531536 1.220000e-92 351.0
33 TraesCS1D01G161900 chr5D 86.585 246 24 4 4232 4473 388408295 388408055 5.870000e-66 263.0
34 TraesCS1D01G161900 chr5D 84.733 262 27 6 4216 4473 462800501 462800753 4.570000e-62 250.0
35 TraesCS1D01G161900 chr5D 78.116 361 47 19 2452 2785 11432355 11432710 4.670000e-47 200.0
36 TraesCS1D01G161900 chr5D 84.762 210 17 11 2453 2651 11532462 11532257 6.040000e-46 196.0
37 TraesCS1D01G161900 chr5D 80.070 286 38 10 846 1121 11431665 11431941 2.170000e-45 195.0
38 TraesCS1D01G161900 chr5D 83.333 192 13 10 1869 2047 11432150 11432335 7.930000e-35 159.0
39 TraesCS1D01G161900 chr5B 88.889 1584 144 18 5096 6662 11515613 11517181 0.000000e+00 1921.0
40 TraesCS1D01G161900 chr5B 86.038 1812 175 36 5086 6873 11552226 11550469 0.000000e+00 1873.0
41 TraesCS1D01G161900 chr5B 85.941 441 53 7 4623 5056 11515163 11515601 5.390000e-126 462.0
42 TraesCS1D01G161900 chr5B 86.751 317 25 7 4237 4541 11514802 11515113 3.410000e-88 337.0
43 TraesCS1D01G161900 chr5B 79.879 497 56 23 4060 4545 11555394 11554931 2.660000e-84 324.0
44 TraesCS1D01G161900 chr5B 88.123 261 26 3 4616 4873 11554897 11554639 9.620000e-79 305.0
45 TraesCS1D01G161900 chr5B 84.722 216 23 5 2452 2657 11555711 11555496 2.790000e-49 207.0
46 TraesCS1D01G161900 chr5B 81.435 237 30 4 2453 2679 11514191 11514423 1.690000e-41 182.0
47 TraesCS1D01G161900 chr5B 78.261 322 28 22 1738 2047 11556022 11555731 1.320000e-37 169.0
48 TraesCS1D01G161900 chr5B 83.152 184 18 7 4878 5056 11552399 11552224 1.030000e-33 156.0
49 TraesCS1D01G161900 chr3D 83.206 262 31 5 4216 4473 22229059 22229311 2.140000e-55 228.0
50 TraesCS1D01G161900 chr4B 81.119 143 23 3 174 313 615248407 615248548 2.250000e-20 111.0
51 TraesCS1D01G161900 chr7B 90.361 83 6 2 4921 5003 547966533 547966613 2.910000e-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 TraesCS1D01G161900 chr1D 229482762 229490392 7630 True 14092.000000 14092 100.000000 1 7631 1 chr1D.!!$R1 7630
1 TraesCS1D01G161900 chr1A 99657894 99660168 2274 False 1353.500000 2191 88.059000 4616 6937 2 chr1A.!!$F2 2321
2 TraesCS1D01G161900 chr1A 297740499 297751890 11391 True 1064.555556 5843 87.527333 1 7631 9 chr1A.!!$R3 7630
3 TraesCS1D01G161900 chr1A 99698092 99701085 2993 True 752.000000 1967 87.112750 2453 6668 4 chr1A.!!$R2 4215
4 TraesCS1D01G161900 chr1B 328819795 328826719 6924 True 1464.666667 3184 90.138833 736 7631 6 chr1B.!!$R2 6895
5 TraesCS1D01G161900 chr1B 328831396 328832136 740 True 774.000000 774 85.845000 1 745 1 chr1B.!!$R1 744
6 TraesCS1D01G161900 chr5D 11431665 11435612 3947 False 653.600000 2248 83.417800 846 6937 5 chr5D.!!$F2 6091
7 TraesCS1D01G161900 chr5D 11529434 11532462 3028 True 594.000000 1129 87.241400 2453 6668 5 chr5D.!!$R2 4215
8 TraesCS1D01G161900 chr5B 11514191 11517181 2990 False 725.500000 1921 85.754000 2453 6662 4 chr5B.!!$F1 4209
9 TraesCS1D01G161900 chr5B 11550469 11556022 5553 True 505.666667 1873 83.362500 1738 6873 6 chr5B.!!$R1 5135

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
612 634 0.535102 CTGGGGCATATCCGGTGTTC 60.535 60.000 0.00 0.00 34.94 3.18 F
1281 1351 0.314302 CGATTCGTATCCTCCGCCTT 59.686 55.000 0.00 0.00 0.00 4.35 F
1634 1738 0.113190 CACTTTGGCCTCCTTCCCTT 59.887 55.000 3.32 0.00 0.00 3.95 F
2788 3487 0.327924 ATTCGGCCCAATCACTGTGA 59.672 50.000 13.60 13.60 0.00 3.58 F
3392 4218 0.964358 ATTCCTTGAGCAGCACCAGC 60.964 55.000 0.00 0.00 42.56 4.85 F
3854 4709 1.068588 TCTTTGCGGTCCGATGGATAG 59.931 52.381 17.49 2.85 32.73 2.08 F
4433 5302 1.134189 TCAGATGATTGCTGGGCAGAG 60.134 52.381 0.00 0.00 40.61 3.35 F
4482 5355 1.815003 GCACTTGAGCATTGCTAACCT 59.185 47.619 11.96 0.00 39.88 3.50 F
6271 9482 0.171455 AGCGACTTCCACGATGAGAC 59.829 55.000 0.00 0.00 0.00 3.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1628 1732 0.041090 GGGAATGGAAGGCAAGGGAA 59.959 55.000 0.00 0.00 0.00 3.97 R
2277 2589 1.211743 CGTGATGATGACCCATGACG 58.788 55.000 0.00 0.00 44.65 4.35 R
3384 4210 0.469070 GATCTGATCTGGCTGGTGCT 59.531 55.000 10.37 0.00 39.59 4.40 R
3795 4650 0.321653 GTCCACATGCCGACCTTTCT 60.322 55.000 0.00 0.00 0.00 2.52 R
5257 8389 1.210155 GGTCATGCCGCAGTTTGAC 59.790 57.895 14.61 14.61 38.17 3.18 R
5297 8434 2.030363 TGGCAATTTAGTTCGCAACCTG 60.030 45.455 0.00 0.00 0.00 4.00 R
5769 8917 2.097629 TCGATCAGTCCGAAGCTAACAG 59.902 50.000 0.00 0.00 32.64 3.16 R
6431 9642 2.340078 GCCCATAGATCGCGAGCA 59.660 61.111 27.74 12.95 0.00 4.26 R
7134 11487 1.064946 CAGCGGAGTCTCGTCCATC 59.935 63.158 0.00 0.00 36.23 3.51 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
44 45 6.113411 AGGGTGACGTAATATTCTTTTCCTG 58.887 40.000 0.00 0.00 0.00 3.86
152 158 5.739752 TGGATCTCAATGTGAAATTAGCG 57.260 39.130 0.00 0.00 0.00 4.26
171 177 2.483188 GCGGTCCTTGGTTTCGAGATAT 60.483 50.000 0.00 0.00 0.00 1.63
218 224 4.346709 TGAGACTTGGTTATGTCTTGGTCA 59.653 41.667 0.00 0.00 40.30 4.02
226 232 5.589855 TGGTTATGTCTTGGTCAATGCTATG 59.410 40.000 0.00 0.00 0.00 2.23
248 254 9.994432 CTATGTTCCTGAGATTTTACATTGAAC 57.006 33.333 0.00 0.00 32.98 3.18
267 273 8.690840 CATTGAACTCCGTGTAAAATTTTCTTC 58.309 33.333 6.72 0.66 0.00 2.87
269 275 7.992008 TGAACTCCGTGTAAAATTTTCTTCTT 58.008 30.769 6.72 0.00 0.00 2.52
272 278 8.897872 ACTCCGTGTAAAATTTTCTTCTTAGA 57.102 30.769 6.72 0.00 0.00 2.10
273 279 9.503399 ACTCCGTGTAAAATTTTCTTCTTAGAT 57.497 29.630 6.72 0.00 0.00 1.98
303 312 7.972832 TTTCCTTTCTTACATGTTACGTCAT 57.027 32.000 2.30 0.00 0.00 3.06
317 326 7.490962 TGTTACGTCATTTGATTGAGACTTT 57.509 32.000 0.00 0.00 0.00 2.66
318 327 7.572759 TGTTACGTCATTTGATTGAGACTTTC 58.427 34.615 0.00 0.00 0.00 2.62
332 341 5.529791 TGAGACTTTCCTAAGTTTCAGTCG 58.470 41.667 7.05 0.00 45.37 4.18
334 343 3.400255 ACTTTCCTAAGTTTCAGTCGCC 58.600 45.455 0.00 0.00 41.85 5.54
348 357 1.889829 AGTCGCCTGATATCTAGCCAC 59.110 52.381 3.98 5.83 0.00 5.01
353 362 0.969149 CTGATATCTAGCCACGCCCA 59.031 55.000 3.98 0.00 0.00 5.36
354 363 0.969149 TGATATCTAGCCACGCCCAG 59.031 55.000 3.98 0.00 0.00 4.45
355 364 1.257743 GATATCTAGCCACGCCCAGA 58.742 55.000 0.00 0.00 0.00 3.86
356 365 0.969894 ATATCTAGCCACGCCCAGAC 59.030 55.000 0.00 0.00 0.00 3.51
357 366 1.452953 TATCTAGCCACGCCCAGACG 61.453 60.000 0.00 0.00 39.50 4.18
371 380 0.738975 CAGACGCCCTCGAGATAACA 59.261 55.000 15.71 0.00 39.41 2.41
374 383 2.128035 GACGCCCTCGAGATAACATTG 58.872 52.381 15.71 0.00 39.41 2.82
391 400 6.859420 AACATTGGCCAGTTAACATTTTTC 57.141 33.333 5.11 0.00 0.00 2.29
431 440 4.386350 TGTAACATGTACACATACACGTGC 59.614 41.667 17.22 0.00 44.11 5.34
443 452 6.752351 ACACATACACGTGCATTTTAACAAAA 59.248 30.769 17.22 0.00 40.73 2.44
463 472 5.621197 AAAAACACTGGCCTTTGAAAAAC 57.379 34.783 3.32 0.00 0.00 2.43
466 478 4.486125 ACACTGGCCTTTGAAAAACAAT 57.514 36.364 3.32 0.00 38.36 2.71
496 508 4.781775 TCCCCTAATTTCGAATTGCCTA 57.218 40.909 0.00 0.00 0.00 3.93
502 514 7.611855 CCCCTAATTTCGAATTGCCTATATCTT 59.388 37.037 0.00 0.00 0.00 2.40
508 520 5.541845 TCGAATTGCCTATATCTTGTGAGG 58.458 41.667 0.00 0.00 0.00 3.86
516 528 5.931146 GCCTATATCTTGTGAGGAATCAGTG 59.069 44.000 0.00 0.00 0.00 3.66
572 591 8.427012 GTTGATATTTTTCTTCACGTACGTACA 58.573 33.333 22.34 7.93 0.00 2.90
573 592 8.692110 TGATATTTTTCTTCACGTACGTACAT 57.308 30.769 22.34 7.61 0.00 2.29
574 593 8.588789 TGATATTTTTCTTCACGTACGTACATG 58.411 33.333 22.34 20.13 0.00 3.21
575 594 4.634349 TTTTCTTCACGTACGTACATGC 57.366 40.909 22.34 0.00 0.00 4.06
576 595 1.886037 TCTTCACGTACGTACATGCG 58.114 50.000 22.34 13.45 37.94 4.73
606 628 2.348998 GGAGCTGGGGCATATCCG 59.651 66.667 0.00 0.00 41.70 4.18
610 632 3.120086 GCTGGGGCATATCCGGTGT 62.120 63.158 0.00 0.00 38.54 4.16
611 633 1.531748 CTGGGGCATATCCGGTGTT 59.468 57.895 0.00 0.00 34.94 3.32
612 634 0.535102 CTGGGGCATATCCGGTGTTC 60.535 60.000 0.00 0.00 34.94 3.18
613 635 1.228154 GGGGCATATCCGGTGTTCC 60.228 63.158 0.00 0.00 34.94 3.62
614 636 1.529796 GGGCATATCCGGTGTTCCA 59.470 57.895 0.00 0.00 34.94 3.53
615 637 0.818040 GGGCATATCCGGTGTTCCAC 60.818 60.000 0.00 0.00 34.94 4.02
671 693 2.030562 GGACACCACCACTCCACG 59.969 66.667 0.00 0.00 0.00 4.94
729 751 3.037833 CGCGAGCACTGCACTGAA 61.038 61.111 0.00 0.00 0.00 3.02
774 796 0.593128 GAGTGCATCCACACAACCAC 59.407 55.000 0.00 0.00 44.53 4.16
776 798 0.961019 GTGCATCCACACAACCACAT 59.039 50.000 0.00 0.00 41.67 3.21
777 799 1.340889 GTGCATCCACACAACCACATT 59.659 47.619 0.00 0.00 41.67 2.71
780 802 3.831333 TGCATCCACACAACCACATTAAT 59.169 39.130 0.00 0.00 0.00 1.40
782 804 5.655974 TGCATCCACACAACCACATTAATAT 59.344 36.000 0.00 0.00 0.00 1.28
784 806 7.340487 TGCATCCACACAACCACATTAATATTA 59.660 33.333 0.00 0.00 0.00 0.98
786 808 8.902806 CATCCACACAACCACATTAATATTACT 58.097 33.333 0.00 0.00 0.00 2.24
788 810 9.607988 TCCACACAACCACATTAATATTACTAG 57.392 33.333 0.00 0.00 0.00 2.57
970 1011 2.858974 CACCCACCCCACCTCCTT 60.859 66.667 0.00 0.00 0.00 3.36
977 1018 1.229984 CCCCACCTCCTTCCTCCTT 60.230 63.158 0.00 0.00 0.00 3.36
1216 1273 4.308458 CGCCACCGTCCCAACTCA 62.308 66.667 0.00 0.00 0.00 3.41
1237 1297 3.386768 TCCTCTTGTCTTTTCCTCGTG 57.613 47.619 0.00 0.00 0.00 4.35
1281 1351 0.314302 CGATTCGTATCCTCCGCCTT 59.686 55.000 0.00 0.00 0.00 4.35
1292 1362 1.779025 CTCCGCCTTACGCTACGCTA 61.779 60.000 0.00 0.00 41.76 4.26
1374 1453 8.567285 AGAACAAATTAGTAAGATGGTTCCAG 57.433 34.615 12.09 0.00 35.27 3.86
1384 1463 2.610859 GGTTCCAGCCCTCCCTCA 60.611 66.667 0.00 0.00 0.00 3.86
1534 1634 1.188863 GAGAGGTGCATGGCCAAATT 58.811 50.000 10.96 0.00 0.00 1.82
1631 1735 4.423231 CCACTTTGGCCTCCTTCC 57.577 61.111 3.32 0.00 0.00 3.46
1632 1736 1.304464 CCACTTTGGCCTCCTTCCC 60.304 63.158 3.32 0.00 0.00 3.97
1633 1737 1.770324 CACTTTGGCCTCCTTCCCT 59.230 57.895 3.32 0.00 0.00 4.20
1634 1738 0.113190 CACTTTGGCCTCCTTCCCTT 59.887 55.000 3.32 0.00 0.00 3.95
1635 1739 0.113190 ACTTTGGCCTCCTTCCCTTG 59.887 55.000 3.32 0.00 0.00 3.61
1636 1740 1.228862 TTTGGCCTCCTTCCCTTGC 60.229 57.895 3.32 0.00 0.00 4.01
1707 1823 3.256558 GCAGGTACGAATTTCCTACGTT 58.743 45.455 0.00 0.00 40.61 3.99
1728 1885 6.207810 ACGTTGTATTTTCTTTTGGCTGGATA 59.792 34.615 0.00 0.00 0.00 2.59
1729 1886 7.093945 ACGTTGTATTTTCTTTTGGCTGGATAT 60.094 33.333 0.00 0.00 0.00 1.63
1761 1918 4.590647 AGAGATTTGGCGATAAGATGAGGA 59.409 41.667 0.00 0.00 0.00 3.71
1763 1920 5.059833 AGATTTGGCGATAAGATGAGGAAC 58.940 41.667 0.00 0.00 0.00 3.62
1802 1965 6.127619 GGAGTAAGATAAATGCTTTGCTTGGT 60.128 38.462 0.00 0.00 0.00 3.67
1805 1968 5.320549 AGATAAATGCTTTGCTTGGTCAG 57.679 39.130 0.00 0.00 0.00 3.51
1955 2237 7.581213 TTTCGCATGGATCCAGTATTTATTT 57.419 32.000 21.33 0.00 0.00 1.40
1961 2255 8.940952 GCATGGATCCAGTATTTATTTCTAGAC 58.059 37.037 21.33 0.00 0.00 2.59
2021 2321 5.048083 TGACTTCATCAGTAATGCAAAACCC 60.048 40.000 0.00 0.00 35.01 4.11
2052 2354 9.529325 TGATCTTCGTCTATAATTGAACGAAAT 57.471 29.630 15.20 12.45 38.75 2.17
2222 2534 4.806481 CTCGCGCTGCATGCACAC 62.806 66.667 18.46 11.19 43.06 3.82
2239 2551 6.995511 TGCACACATAGGAGTATTTTAACC 57.004 37.500 0.00 0.00 0.00 2.85
2365 2677 2.670905 TCGGTTGCTCAATACGTCAATG 59.329 45.455 0.00 0.00 0.00 2.82
2500 2871 3.568430 AGTCGTGATTTTCCTTTTGACCC 59.432 43.478 0.00 0.00 0.00 4.46
2788 3487 0.327924 ATTCGGCCCAATCACTGTGA 59.672 50.000 13.60 13.60 0.00 3.58
2917 3616 7.116233 CGGATTTTTGCTAAACTGCTGTTTATT 59.884 33.333 23.85 6.84 44.57 1.40
2918 3617 9.418045 GGATTTTTGCTAAACTGCTGTTTATTA 57.582 29.630 23.85 15.30 44.57 0.98
3027 3838 2.077687 CCAGCAGGCCCAATTAATCT 57.922 50.000 0.00 0.00 0.00 2.40
3202 4023 4.144727 GCCTCTCCCTCCCTCCGA 62.145 72.222 0.00 0.00 0.00 4.55
3361 4187 5.372373 CATATTCTCTCCTCCAAAACCTCC 58.628 45.833 0.00 0.00 0.00 4.30
3384 4210 3.181423 ACCCAACCTTTATTCCTTGAGCA 60.181 43.478 0.00 0.00 0.00 4.26
3385 4211 3.445096 CCCAACCTTTATTCCTTGAGCAG 59.555 47.826 0.00 0.00 0.00 4.24
3386 4212 3.119352 CCAACCTTTATTCCTTGAGCAGC 60.119 47.826 0.00 0.00 0.00 5.25
3387 4213 3.439857 ACCTTTATTCCTTGAGCAGCA 57.560 42.857 0.00 0.00 0.00 4.41
3388 4214 3.084786 ACCTTTATTCCTTGAGCAGCAC 58.915 45.455 0.00 0.00 0.00 4.40
3389 4215 2.424956 CCTTTATTCCTTGAGCAGCACC 59.575 50.000 0.00 0.00 0.00 5.01
3390 4216 2.877097 TTATTCCTTGAGCAGCACCA 57.123 45.000 0.00 0.00 0.00 4.17
3391 4217 2.408271 TATTCCTTGAGCAGCACCAG 57.592 50.000 0.00 0.00 0.00 4.00
3392 4218 0.964358 ATTCCTTGAGCAGCACCAGC 60.964 55.000 0.00 0.00 42.56 4.85
3417 4243 5.156649 AGATCAGATCTGGGAATCACTCAT 58.843 41.667 22.42 4.48 38.44 2.90
3436 4270 2.501128 CATCCATCCACGGACGCT 59.499 61.111 0.00 0.00 38.07 5.07
3470 4304 5.830000 TCAATGATTCAGAGATGCCTTTG 57.170 39.130 0.00 0.00 0.00 2.77
3507 4354 6.127619 GCATAAGAAAAACAGGCTAATGGAGT 60.128 38.462 0.00 0.00 0.00 3.85
3619 4467 6.881065 AGCATGTTTCACATCACAACTATACT 59.119 34.615 0.00 0.00 36.53 2.12
3627 4475 6.434340 TCACATCACAACTATACTCACTGAGT 59.566 38.462 16.00 16.00 45.54 3.41
3672 4524 4.872691 CACATGCCCTACAGACTTCTTTAG 59.127 45.833 0.00 0.00 0.00 1.85
3682 4537 4.345257 ACAGACTTCTTTAGTTCTCCAGCA 59.655 41.667 0.00 0.00 37.17 4.41
3795 4650 2.214376 AAGGCCAACCGATCAATTGA 57.786 45.000 11.26 11.26 42.76 2.57
3802 4657 3.758554 CCAACCGATCAATTGAGAAAGGT 59.241 43.478 14.54 15.64 34.31 3.50
3854 4709 1.068588 TCTTTGCGGTCCGATGGATAG 59.931 52.381 17.49 2.85 32.73 2.08
3949 4805 5.424252 ACGTATCAGGATAGGGACTTTTGAA 59.576 40.000 12.15 0.00 41.75 2.69
3976 4832 4.157840 ACAAGTTGGGTCAGACAAGTTTTC 59.842 41.667 7.96 0.00 38.92 2.29
4042 4902 3.023832 CAATTTGTACTGACCCCCATCC 58.976 50.000 0.00 0.00 0.00 3.51
4087 4948 4.918583 GTGCTAGAAACAGTGAGTCACTAC 59.081 45.833 25.04 12.62 43.43 2.73
4104 4967 2.440253 ACTACTTGGGTTGTTGGTGCTA 59.560 45.455 0.00 0.00 0.00 3.49
4200 5063 9.926158 TGATATGCTGTCAAATTGTAAAATTGT 57.074 25.926 0.00 0.00 0.00 2.71
4205 5068 9.891828 TGCTGTCAAATTGTAAAATTGTACTAG 57.108 29.630 7.31 0.00 0.00 2.57
4206 5069 9.893305 GCTGTCAAATTGTAAAATTGTACTAGT 57.107 29.630 7.31 0.00 0.00 2.57
4227 5090 4.573607 AGTACTATCGTAATGACTGCGTCA 59.426 41.667 12.53 12.53 46.90 4.35
4347 5214 5.541101 CCATATTTCCCATGACATGTTGGAT 59.459 40.000 16.72 6.36 34.81 3.41
4433 5302 1.134189 TCAGATGATTGCTGGGCAGAG 60.134 52.381 0.00 0.00 40.61 3.35
4482 5355 1.815003 GCACTTGAGCATTGCTAACCT 59.185 47.619 11.96 0.00 39.88 3.50
4589 5468 5.437060 TGAAATTCAGCTAACCATCCCTAC 58.563 41.667 0.00 0.00 0.00 3.18
4902 8022 4.039245 TGCAGCAACTAACTCTTCACTAGT 59.961 41.667 0.00 0.00 0.00 2.57
4956 8076 5.695851 AACTGGCAATGAACTGAAACTAG 57.304 39.130 0.00 0.00 0.00 2.57
5045 8170 2.223249 GCAAGACGTGAAGACTTTTGCA 60.223 45.455 12.85 0.00 32.78 4.08
5094 8219 8.918202 TGTTTATTGAATCACATATACCCCTC 57.082 34.615 0.00 0.00 0.00 4.30
5167 8297 6.373005 TCCTGATGTTCTTGTAATTCCTGA 57.627 37.500 0.00 0.00 0.00 3.86
5257 8389 3.545078 CGAAAGGTACGGAGAACAATACG 59.455 47.826 0.00 0.00 0.00 3.06
5297 8434 3.127548 CAGTGCATTGGGTCTTATGTGTC 59.872 47.826 0.32 0.00 0.00 3.67
5308 8445 3.064207 TCTTATGTGTCAGGTTGCGAAC 58.936 45.455 0.00 0.00 0.00 3.95
5587 8726 4.288670 CAGGTGCTGCTCATTTCATTAG 57.711 45.455 0.00 0.00 0.00 1.73
5769 8917 4.823989 AGTATTGCTGATTGCCTAATGGTC 59.176 41.667 0.00 0.00 42.00 4.02
5781 8929 3.458189 CCTAATGGTCTGTTAGCTTCGG 58.542 50.000 0.00 0.00 0.00 4.30
6137 9347 6.006449 GCCCATGATACACCTTCTTCATATT 58.994 40.000 0.00 0.00 0.00 1.28
6167 9377 7.520451 TTCAGTGTACTCATACTACAGTTGT 57.480 36.000 0.00 0.00 32.00 3.32
6271 9482 0.171455 AGCGACTTCCACGATGAGAC 59.829 55.000 0.00 0.00 0.00 3.36
6276 9487 3.366476 CGACTTCCACGATGAGACTTCTT 60.366 47.826 0.00 0.00 0.00 2.52
6277 9488 4.170256 GACTTCCACGATGAGACTTCTTC 58.830 47.826 0.00 0.00 0.00 2.87
6311 9522 7.519347 AACTGGGGAGATATTTTTGTAGGTA 57.481 36.000 0.00 0.00 0.00 3.08
6743 9960 3.165071 GGAATGGGGCTTGGTTATATGG 58.835 50.000 0.00 0.00 0.00 2.74
6874 10092 0.029035 CGTAGCGCCGTCTTCTACAT 59.971 55.000 2.29 0.00 34.02 2.29
6881 10099 1.339727 GCCGTCTTCTACATTTGGGGT 60.340 52.381 0.00 0.00 0.00 4.95
6945 10163 2.571548 CCACTGAATGGGTCCTTGC 58.428 57.895 0.00 0.00 45.95 4.01
6946 10164 0.038744 CCACTGAATGGGTCCTTGCT 59.961 55.000 0.00 0.00 45.95 3.91
6948 10166 0.773644 ACTGAATGGGTCCTTGCTGT 59.226 50.000 0.00 0.00 0.00 4.40
6949 10167 1.271597 ACTGAATGGGTCCTTGCTGTC 60.272 52.381 0.00 0.00 0.00 3.51
6951 10169 1.271543 TGAATGGGTCCTTGCTGTCTG 60.272 52.381 0.00 0.00 0.00 3.51
6952 10170 0.610232 AATGGGTCCTTGCTGTCTGC 60.610 55.000 0.00 0.00 43.25 4.26
6966 10187 3.027412 CTGTCTGCCTATCTGTACCTGT 58.973 50.000 0.00 0.00 0.00 4.00
7003 10224 9.106070 AGATTTCTTTGGTACGTTCATAATACC 57.894 33.333 0.00 0.00 39.12 2.73
7004 10225 7.614124 TTTCTTTGGTACGTTCATAATACCC 57.386 36.000 0.00 0.00 38.07 3.69
7005 10226 6.297080 TCTTTGGTACGTTCATAATACCCA 57.703 37.500 0.00 0.00 38.07 4.51
7006 10227 6.342906 TCTTTGGTACGTTCATAATACCCAG 58.657 40.000 0.00 0.00 38.07 4.45
7008 10229 3.181463 TGGTACGTTCATAATACCCAGGC 60.181 47.826 0.00 0.00 38.07 4.85
7010 10231 2.124411 ACGTTCATAATACCCAGGCCT 58.876 47.619 0.00 0.00 0.00 5.19
7012 10233 3.323979 ACGTTCATAATACCCAGGCCTAG 59.676 47.826 3.98 1.76 0.00 3.02
7013 10234 3.676093 GTTCATAATACCCAGGCCTAGC 58.324 50.000 3.98 0.00 0.00 3.42
7015 10236 1.899814 CATAATACCCAGGCCTAGCGA 59.100 52.381 3.98 0.00 0.00 4.93
7016 10237 1.629043 TAATACCCAGGCCTAGCGAG 58.371 55.000 3.98 0.00 0.00 5.03
7017 10238 1.122019 AATACCCAGGCCTAGCGAGG 61.122 60.000 3.98 8.78 46.93 4.63
7020 10241 3.230245 CCAGGCCTAGCGAGGGAG 61.230 72.222 15.29 0.00 43.97 4.30
7021 10242 3.230245 CAGGCCTAGCGAGGGAGG 61.230 72.222 15.29 1.30 43.97 4.30
7022 10243 3.756783 AGGCCTAGCGAGGGAGGT 61.757 66.667 15.29 0.00 43.97 3.85
7023 10244 3.541713 GGCCTAGCGAGGGAGGTG 61.542 72.222 15.29 0.00 43.97 4.00
7025 10246 3.905678 CCTAGCGAGGGAGGTGCG 61.906 72.222 4.68 0.00 39.48 5.34
7026 10247 3.141488 CTAGCGAGGGAGGTGCGT 61.141 66.667 0.00 0.00 0.00 5.24
7027 10248 1.822613 CTAGCGAGGGAGGTGCGTA 60.823 63.158 0.00 0.00 0.00 4.42
7030 10251 3.111939 CGAGGGAGGTGCGTAGAG 58.888 66.667 0.00 0.00 0.00 2.43
7031 10252 1.451567 CGAGGGAGGTGCGTAGAGA 60.452 63.158 0.00 0.00 0.00 3.10
7032 10253 0.820074 CGAGGGAGGTGCGTAGAGAT 60.820 60.000 0.00 0.00 0.00 2.75
7033 10254 1.542767 CGAGGGAGGTGCGTAGAGATA 60.543 57.143 0.00 0.00 0.00 1.98
7034 10255 1.881324 GAGGGAGGTGCGTAGAGATAC 59.119 57.143 0.00 0.00 0.00 2.24
7035 10256 0.960286 GGGAGGTGCGTAGAGATACC 59.040 60.000 0.00 0.00 0.00 2.73
7036 10257 1.688772 GGAGGTGCGTAGAGATACCA 58.311 55.000 0.00 0.00 35.66 3.25
7037 10258 1.609555 GGAGGTGCGTAGAGATACCAG 59.390 57.143 0.00 0.00 35.66 4.00
7039 10260 0.674534 GGTGCGTAGAGATACCAGGG 59.325 60.000 0.00 0.00 33.42 4.45
7040 10261 0.032267 GTGCGTAGAGATACCAGGGC 59.968 60.000 0.00 0.00 0.00 5.19
7043 10264 0.592148 CGTAGAGATACCAGGGCGAC 59.408 60.000 0.00 0.00 0.00 5.19
7044 10265 1.688772 GTAGAGATACCAGGGCGACA 58.311 55.000 0.00 0.00 0.00 4.35
7045 10266 2.240279 GTAGAGATACCAGGGCGACAT 58.760 52.381 0.00 0.00 0.00 3.06
7047 10268 2.240279 AGAGATACCAGGGCGACATAC 58.760 52.381 0.00 0.00 0.00 2.39
7048 10269 1.272769 GAGATACCAGGGCGACATACC 59.727 57.143 0.00 0.00 0.00 2.73
7206 14014 2.124901 CAACCTATCCGCCGCCAA 60.125 61.111 0.00 0.00 0.00 4.52
7245 14053 0.442699 GCTAAACCTGCGTGCTGTAC 59.557 55.000 0.00 0.00 0.00 2.90
7247 14055 0.320946 TAAACCTGCGTGCTGTACCC 60.321 55.000 0.00 0.00 0.00 3.69
7249 14057 4.778143 CCTGCGTGCTGTACCCCC 62.778 72.222 0.00 0.00 0.00 5.40
7406 14279 5.986501 AAATATGAAAACTAAACGGGCCA 57.013 34.783 4.39 0.00 0.00 5.36
7415 14288 0.538516 TAAACGGGCCATGTTGTGCT 60.539 50.000 12.78 1.11 0.00 4.40
7466 14340 1.616994 GGCCCTAAGAAAGCCACATGT 60.617 52.381 0.00 0.00 46.34 3.21
7469 14368 2.009774 CCTAAGAAAGCCACATGTCGG 58.990 52.381 0.00 2.40 0.00 4.79
7510 14409 0.179048 CATGCTGGCTATTGGGTCGA 60.179 55.000 0.00 0.00 0.00 4.20
7533 14432 3.451894 CAGGACCGGCCCATTTGC 61.452 66.667 10.37 0.00 37.37 3.68
7572 14471 1.877680 CGCTCGAAATCATGGCCCATA 60.878 52.381 0.00 0.00 0.00 2.74
7582 14481 8.334632 CGAAATCATGGCCCATAAATTTAAAAC 58.665 33.333 13.42 4.30 0.00 2.43
7583 14482 9.171877 GAAATCATGGCCCATAAATTTAAAACA 57.828 29.630 13.42 0.00 0.00 2.83
7623 14522 5.451659 GCAAGATGAGAGAGTCAGAGCAATA 60.452 44.000 0.00 0.00 39.07 1.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
152 158 5.302313 AGACTATATCTCGAAACCAAGGACC 59.698 44.000 0.00 0.00 28.16 4.46
218 224 8.757982 ATGTAAAATCTCAGGAACATAGCATT 57.242 30.769 0.00 0.00 0.00 3.56
226 232 7.530863 GGAGTTCAATGTAAAATCTCAGGAAC 58.469 38.462 0.00 0.00 34.78 3.62
303 312 8.746052 TGAAACTTAGGAAAGTCTCAATCAAA 57.254 30.769 0.00 0.00 45.37 2.69
332 341 0.390472 GGCGTGGCTAGATATCAGGC 60.390 60.000 16.56 16.56 40.30 4.85
334 343 0.969149 TGGGCGTGGCTAGATATCAG 59.031 55.000 5.32 1.93 0.00 2.90
353 362 1.693627 ATGTTATCTCGAGGGCGTCT 58.306 50.000 13.56 0.00 38.98 4.18
354 363 2.128035 CAATGTTATCTCGAGGGCGTC 58.872 52.381 13.56 0.00 38.98 5.19
355 364 1.202533 CCAATGTTATCTCGAGGGCGT 60.203 52.381 13.56 0.00 38.98 5.68
356 365 1.502231 CCAATGTTATCTCGAGGGCG 58.498 55.000 13.56 0.00 39.35 6.13
357 366 1.230324 GCCAATGTTATCTCGAGGGC 58.770 55.000 13.56 10.89 0.00 5.19
358 367 1.140852 TGGCCAATGTTATCTCGAGGG 59.859 52.381 13.56 4.08 0.00 4.30
359 368 2.158900 ACTGGCCAATGTTATCTCGAGG 60.159 50.000 13.56 0.00 0.00 4.63
360 369 3.185246 ACTGGCCAATGTTATCTCGAG 57.815 47.619 7.01 5.93 0.00 4.04
361 370 3.627395 AACTGGCCAATGTTATCTCGA 57.373 42.857 7.01 0.00 0.00 4.04
362 371 4.634004 TGTTAACTGGCCAATGTTATCTCG 59.366 41.667 16.02 0.00 0.00 4.04
371 380 6.173427 ACAGAAAAATGTTAACTGGCCAAT 57.827 33.333 7.01 0.00 33.57 3.16
374 383 6.981559 TGTAAACAGAAAAATGTTAACTGGCC 59.018 34.615 7.22 0.00 42.49 5.36
391 400 7.748683 ACATGTTACATGCGTATTTGTAAACAG 59.251 33.333 23.43 0.00 39.34 3.16
443 452 4.278975 TGTTTTTCAAAGGCCAGTGTTT 57.721 36.364 5.01 0.00 0.00 2.83
478 490 9.003658 ACAAGATATAGGCAATTCGAAATTAGG 57.996 33.333 0.00 0.00 0.00 2.69
496 508 8.641498 AAAAACACTGATTCCTCACAAGATAT 57.359 30.769 0.00 0.00 0.00 1.63
523 538 4.319766 CCGACTGATTTCTCACAACCTTTG 60.320 45.833 0.00 0.00 0.00 2.77
542 561 5.923665 ACGTGAAGAAAAATATCAACCGAC 58.076 37.500 0.00 0.00 0.00 4.79
575 594 4.354212 CTCCGTGTGTGCGCAACG 62.354 66.667 22.64 22.64 0.00 4.10
576 595 4.666532 GCTCCGTGTGTGCGCAAC 62.667 66.667 14.00 13.70 0.00 4.17
577 596 4.908687 AGCTCCGTGTGTGCGCAA 62.909 61.111 14.00 0.00 38.49 4.85
610 632 3.961414 GGCGGGGTGGAAGTGGAA 61.961 66.667 0.00 0.00 0.00 3.53
656 678 3.138625 CTCGTGGAGTGGTGGTGT 58.861 61.111 0.00 0.00 0.00 4.16
729 751 2.989055 CTTGACTTGTGTCGCCGGGT 62.989 60.000 2.18 0.00 45.70 5.28
970 1011 1.892819 CGAGCAGGAGCAAAGGAGGA 61.893 60.000 0.00 0.00 45.49 3.71
977 1018 4.441695 CCGAGCGAGCAGGAGCAA 62.442 66.667 4.03 0.00 45.49 3.91
1184 1241 1.373748 GGCGGCGTGAGTGAAAGTA 60.374 57.895 9.37 0.00 0.00 2.24
1216 1273 3.325135 ACACGAGGAAAAGACAAGAGGAT 59.675 43.478 0.00 0.00 0.00 3.24
1237 1297 1.263217 CATGCTATACCGGGCGAAAAC 59.737 52.381 6.32 0.00 0.00 2.43
1292 1362 3.009192 TTCGTGCTAATCGGGCGGT 62.009 57.895 0.00 0.00 0.00 5.68
1348 1427 8.934023 TGGAACCATCTTACTAATTTGTTCTT 57.066 30.769 0.00 0.00 33.27 2.52
1369 1448 2.285668 CCTGAGGGAGGGCTGGAA 60.286 66.667 0.00 0.00 38.36 3.53
1384 1463 0.558712 CTACTCCTGCCCCTACTCCT 59.441 60.000 0.00 0.00 0.00 3.69
1393 1472 2.312390 CTCCTACTTCCTACTCCTGCC 58.688 57.143 0.00 0.00 0.00 4.85
1395 1474 4.446600 CCCTACTCCTACTTCCTACTCCTG 60.447 54.167 0.00 0.00 0.00 3.86
1625 1729 1.005924 GAATGGAAGGCAAGGGAAGGA 59.994 52.381 0.00 0.00 0.00 3.36
1626 1730 1.478631 GAATGGAAGGCAAGGGAAGG 58.521 55.000 0.00 0.00 0.00 3.46
1627 1731 1.478631 GGAATGGAAGGCAAGGGAAG 58.521 55.000 0.00 0.00 0.00 3.46
1628 1732 0.041090 GGGAATGGAAGGCAAGGGAA 59.959 55.000 0.00 0.00 0.00 3.97
1629 1733 1.697297 GGGAATGGAAGGCAAGGGA 59.303 57.895 0.00 0.00 0.00 4.20
1630 1734 1.754234 CGGGAATGGAAGGCAAGGG 60.754 63.158 0.00 0.00 0.00 3.95
1631 1735 2.418083 GCGGGAATGGAAGGCAAGG 61.418 63.158 0.00 0.00 0.00 3.61
1632 1736 1.678635 TGCGGGAATGGAAGGCAAG 60.679 57.895 0.00 0.00 0.00 4.01
1633 1737 1.976474 GTGCGGGAATGGAAGGCAA 60.976 57.895 0.00 0.00 35.10 4.52
1634 1738 2.361104 GTGCGGGAATGGAAGGCA 60.361 61.111 0.00 0.00 0.00 4.75
1635 1739 3.508840 CGTGCGGGAATGGAAGGC 61.509 66.667 0.00 0.00 0.00 4.35
1636 1740 3.508840 GCGTGCGGGAATGGAAGG 61.509 66.667 0.00 0.00 0.00 3.46
1695 1809 9.471084 CCAAAAGAAAATACAACGTAGGAAATT 57.529 29.630 0.00 0.00 0.00 1.82
1696 1812 7.597369 GCCAAAAGAAAATACAACGTAGGAAAT 59.403 33.333 0.00 0.00 0.00 2.17
1728 1885 6.805016 ATCGCCAAATCTCTCATCCTATAT 57.195 37.500 0.00 0.00 0.00 0.86
1729 1886 7.615757 TCTTATCGCCAAATCTCTCATCCTATA 59.384 37.037 0.00 0.00 0.00 1.31
1761 1918 0.622665 CTCCCCTCAATGGCTCAGTT 59.377 55.000 0.00 0.00 0.00 3.16
1763 1920 1.500474 TACTCCCCTCAATGGCTCAG 58.500 55.000 0.00 0.00 0.00 3.35
1955 2237 5.248477 AGAAACAAATACTGCTGGGTCTAGA 59.752 40.000 0.00 0.00 0.00 2.43
2052 2354 1.819288 TGTTCCGCAGTTTTTGTTCCA 59.181 42.857 0.00 0.00 0.00 3.53
2108 2413 5.701290 TCGTCAAATCTTTTCCCTCTTCTTC 59.299 40.000 0.00 0.00 0.00 2.87
2222 2534 3.805422 TGCGCGGTTAAAATACTCCTATG 59.195 43.478 8.83 0.00 0.00 2.23
2223 2535 4.062677 TGCGCGGTTAAAATACTCCTAT 57.937 40.909 8.83 0.00 0.00 2.57
2239 2551 2.735478 TACGGTTCAGGTTGCGCG 60.735 61.111 0.00 0.00 0.00 6.86
2277 2589 1.211743 CGTGATGATGACCCATGACG 58.788 55.000 0.00 0.00 44.65 4.35
2317 2629 5.936956 CACACAGAGAGGAATAAAAGAAGCT 59.063 40.000 0.00 0.00 0.00 3.74
2324 2636 4.556233 CGACACACACAGAGAGGAATAAA 58.444 43.478 0.00 0.00 0.00 1.40
2389 2728 1.941377 ATTTGCTTCCAGGCCAATGA 58.059 45.000 5.01 0.00 0.00 2.57
2396 2735 3.549423 CGCATGACATATTTGCTTCCAGG 60.549 47.826 0.00 0.00 34.23 4.45
2500 2871 2.100631 GGCGACCCATGACGAACTG 61.101 63.158 0.00 0.00 0.00 3.16
2566 2981 5.079406 CCTAACACACGAAATGTTTCATCG 58.921 41.667 8.53 0.00 40.64 3.84
2669 3084 2.258109 GGAGTGGTTGTAGGAAGGAGT 58.742 52.381 0.00 0.00 0.00 3.85
2879 3578 3.123959 GCAAAAATCCGTGAAGCGTACTA 59.876 43.478 0.00 0.00 39.32 1.82
3027 3838 2.427453 GGAATCTAGTCTGTTGGCGAGA 59.573 50.000 0.00 0.00 0.00 4.04
3331 4157 2.564947 GGAGGAGAGAATATGGCGATGT 59.435 50.000 0.00 0.00 0.00 3.06
3361 4187 3.193479 GCTCAAGGAATAAAGGTTGGGTG 59.807 47.826 0.00 0.00 0.00 4.61
3384 4210 0.469070 GATCTGATCTGGCTGGTGCT 59.531 55.000 10.37 0.00 39.59 4.40
3385 4211 0.469070 AGATCTGATCTGGCTGGTGC 59.531 55.000 18.93 0.00 38.44 5.01
3417 4243 3.088941 GCGTCCGTGGATGGATGGA 62.089 63.158 10.03 0.00 43.89 3.41
3436 4270 9.135189 TCTCTGAATCATTGAAAAGGAGAAAAA 57.865 29.630 9.00 0.00 41.32 1.94
3470 4304 4.989279 TTTCTTATGCAGATTTCTGGGC 57.011 40.909 9.49 0.00 43.94 5.36
3507 4354 4.081862 AGCCTACAAAGTAGTAACGCATGA 60.082 41.667 0.00 0.00 0.00 3.07
3619 4467 1.609072 CGTGTTCCTCTCACTCAGTGA 59.391 52.381 7.44 7.44 40.50 3.41
3627 4475 0.969149 ATGTGAGCGTGTTCCTCTCA 59.031 50.000 0.00 0.00 37.27 3.27
3672 4524 7.093992 GGTCTACATATCTTATGCTGGAGAAC 58.906 42.308 0.00 0.00 0.00 3.01
3682 4537 6.554982 TCTGCACAAGGGTCTACATATCTTAT 59.445 38.462 0.00 0.00 0.00 1.73
3795 4650 0.321653 GTCCACATGCCGACCTTTCT 60.322 55.000 0.00 0.00 0.00 2.52
3802 4657 4.758251 CTGCCGTCCACATGCCGA 62.758 66.667 0.00 0.00 0.00 5.54
3854 4709 3.689649 ACGCTAGGGTCAATTGATTTGTC 59.310 43.478 12.12 0.00 36.65 3.18
3949 4805 4.080526 ACTTGTCTGACCCAACTTGTTAGT 60.081 41.667 5.17 0.00 35.68 2.24
3999 4859 1.077285 CATGGGAGCAGGTGCATGA 60.077 57.895 4.48 0.00 45.16 3.07
4073 4934 2.679082 ACCCAAGTAGTGACTCACTGT 58.321 47.619 20.19 6.83 45.01 3.55
4087 4948 1.880027 GTCTAGCACCAACAACCCAAG 59.120 52.381 0.00 0.00 0.00 3.61
4104 4967 2.203294 GGGTGTTGGCGTTGGTCT 60.203 61.111 0.00 0.00 0.00 3.85
4126 4989 7.882791 TGCAGTAAATAAAGACAAGGAGATCAA 59.117 33.333 0.00 0.00 0.00 2.57
4227 5090 4.895297 TCAGCTGAAGGAAAGGAAAACAAT 59.105 37.500 15.67 0.00 0.00 2.71
4433 5302 5.884232 CCTTACCTGGTAATCCCTGTTTAAC 59.116 44.000 19.02 0.00 0.00 2.01
4589 5468 6.025749 TCATACTACAGTTGTCTGAACAGG 57.974 41.667 1.53 0.00 43.76 4.00
4861 5745 7.251704 TGCTGCAGTATAAGAAGAAATTAGC 57.748 36.000 16.64 0.00 0.00 3.09
4925 8045 9.625747 TTCAGTTCATTGCCAGTTTATCATATA 57.374 29.630 0.00 0.00 0.00 0.86
4956 8076 1.413767 CTGCGATACACGGTGACAGC 61.414 60.000 16.29 14.02 42.83 4.40
5045 8170 9.343994 ACAGAATATAGATTCCATACCCAAGAT 57.656 33.333 6.47 0.00 42.25 2.40
5094 8219 5.763204 ACCAGCCGTCAGGTAAATAATTATG 59.237 40.000 0.00 0.00 40.50 1.90
5167 8297 2.370189 CAACTCCCTGGAGACAAGAAGT 59.630 50.000 19.85 0.00 44.53 3.01
5257 8389 1.210155 GGTCATGCCGCAGTTTGAC 59.790 57.895 14.61 14.61 38.17 3.18
5297 8434 2.030363 TGGCAATTTAGTTCGCAACCTG 60.030 45.455 0.00 0.00 0.00 4.00
5308 8445 5.001237 TCTGCATCAACATGGCAATTTAG 57.999 39.130 0.00 0.00 37.06 1.85
5417 8555 6.659242 TGATGTTTCTCCTTTCCATCCTAAAC 59.341 38.462 0.00 0.00 32.78 2.01
5587 8726 4.440145 TGGCCAAAATCCCAGAGC 57.560 55.556 0.61 0.00 0.00 4.09
5767 8915 3.440228 GATCAGTCCGAAGCTAACAGAC 58.560 50.000 0.00 0.00 0.00 3.51
5769 8917 2.097629 TCGATCAGTCCGAAGCTAACAG 59.902 50.000 0.00 0.00 32.64 3.16
5781 8929 5.572511 GCAGAACATCATCTATCGATCAGTC 59.427 44.000 0.00 0.00 0.00 3.51
5795 8971 3.516700 TCTGAGATTGGAGCAGAACATCA 59.483 43.478 0.00 0.00 35.87 3.07
6137 9347 8.129496 TGTAGTATGAGTACACTGAAAATCCA 57.871 34.615 0.00 0.00 29.62 3.41
6167 9377 2.500098 ACGCCTAGGCTATCTGTTCAAA 59.500 45.455 30.55 0.00 39.32 2.69
6271 9482 4.276926 CCCCAGTTTCAGTTTCAGAAGAAG 59.723 45.833 0.00 0.00 34.71 2.85
6276 9487 3.045634 TCTCCCCAGTTTCAGTTTCAGA 58.954 45.455 0.00 0.00 0.00 3.27
6277 9488 3.492102 TCTCCCCAGTTTCAGTTTCAG 57.508 47.619 0.00 0.00 0.00 3.02
6431 9642 2.340078 GCCCATAGATCGCGAGCA 59.660 61.111 27.74 12.95 0.00 4.26
6743 9960 4.156739 ACAGTTGCAGCTTATTTCTAAGGC 59.843 41.667 0.00 0.00 35.79 4.35
6944 10162 2.035632 AGGTACAGATAGGCAGACAGC 58.964 52.381 0.00 0.00 44.65 4.40
6945 10163 3.027412 ACAGGTACAGATAGGCAGACAG 58.973 50.000 0.00 0.00 0.00 3.51
6946 10164 3.101643 ACAGGTACAGATAGGCAGACA 57.898 47.619 0.00 0.00 0.00 3.41
6948 10166 4.079958 TCAGTACAGGTACAGATAGGCAGA 60.080 45.833 11.78 0.00 38.48 4.26
6949 10167 4.207955 TCAGTACAGGTACAGATAGGCAG 58.792 47.826 11.78 0.00 38.48 4.85
6951 10169 4.462133 TCTCAGTACAGGTACAGATAGGC 58.538 47.826 11.78 0.00 38.48 3.93
6952 10170 6.358178 TCTTCTCAGTACAGGTACAGATAGG 58.642 44.000 11.78 3.50 38.48 2.57
6991 10212 2.930826 AGGCCTGGGTATTATGAACG 57.069 50.000 3.11 0.00 0.00 3.95
7003 10224 3.230245 CTCCCTCGCTAGGCCTGG 61.230 72.222 17.99 15.23 42.14 4.45
7004 10225 3.230245 CCTCCCTCGCTAGGCCTG 61.230 72.222 17.99 6.68 42.14 4.85
7005 10226 3.756783 ACCTCCCTCGCTAGGCCT 61.757 66.667 11.78 11.78 42.14 5.19
7006 10227 3.541713 CACCTCCCTCGCTAGGCC 61.542 72.222 0.00 0.00 42.14 5.19
7008 10229 3.905678 CGCACCTCCCTCGCTAGG 61.906 72.222 0.00 0.00 43.25 3.02
7010 10231 1.822613 CTACGCACCTCCCTCGCTA 60.823 63.158 0.00 0.00 0.00 4.26
7012 10233 3.127352 CTCTACGCACCTCCCTCGC 62.127 68.421 0.00 0.00 0.00 5.03
7013 10234 0.820074 ATCTCTACGCACCTCCCTCG 60.820 60.000 0.00 0.00 0.00 4.63
7015 10236 1.479021 GGTATCTCTACGCACCTCCCT 60.479 57.143 0.00 0.00 0.00 4.20
7016 10237 0.960286 GGTATCTCTACGCACCTCCC 59.040 60.000 0.00 0.00 0.00 4.30
7017 10238 1.609555 CTGGTATCTCTACGCACCTCC 59.390 57.143 0.00 0.00 32.04 4.30
7020 10241 0.674534 CCCTGGTATCTCTACGCACC 59.325 60.000 0.00 0.00 0.00 5.01
7021 10242 0.032267 GCCCTGGTATCTCTACGCAC 59.968 60.000 0.00 0.00 0.00 5.34
7022 10243 1.452953 CGCCCTGGTATCTCTACGCA 61.453 60.000 0.00 0.00 0.00 5.24
7023 10244 1.170919 TCGCCCTGGTATCTCTACGC 61.171 60.000 0.00 0.00 0.00 4.42
7025 10246 1.688772 TGTCGCCCTGGTATCTCTAC 58.311 55.000 0.00 0.00 0.00 2.59
7026 10247 2.677542 ATGTCGCCCTGGTATCTCTA 57.322 50.000 0.00 0.00 0.00 2.43
7027 10248 2.240279 GTATGTCGCCCTGGTATCTCT 58.760 52.381 0.00 0.00 0.00 3.10
7030 10251 0.320697 GGGTATGTCGCCCTGGTATC 59.679 60.000 0.00 0.00 42.81 2.24
7031 10252 0.399376 TGGGTATGTCGCCCTGGTAT 60.399 55.000 1.85 0.00 46.22 2.73
7032 10253 1.001888 TGGGTATGTCGCCCTGGTA 59.998 57.895 1.85 0.00 46.22 3.25
7033 10254 2.285069 TGGGTATGTCGCCCTGGT 60.285 61.111 1.85 0.00 46.22 4.00
7034 10255 2.505982 CTGGGTATGTCGCCCTGG 59.494 66.667 1.85 0.00 46.22 4.45
7035 10256 2.505982 CCTGGGTATGTCGCCCTG 59.494 66.667 1.85 1.37 46.22 4.45
7036 10257 3.480133 GCCTGGGTATGTCGCCCT 61.480 66.667 0.00 0.00 46.22 5.19
7037 10258 4.910585 CGCCTGGGTATGTCGCCC 62.911 72.222 0.00 0.00 46.26 6.13
7040 10261 4.910585 GGCCGCCTGGGTATGTCG 62.911 72.222 0.71 0.00 38.44 4.35
7043 10264 4.569180 CCTGGCCGCCTGGGTATG 62.569 72.222 24.40 1.68 38.71 2.39
7134 11487 1.064946 CAGCGGAGTCTCGTCCATC 59.935 63.158 0.00 0.00 36.23 3.51
7178 13986 1.339727 GGATAGGTTGGTTTCGTGGCT 60.340 52.381 0.00 0.00 0.00 4.75
7247 14055 2.822255 CGTACATGGGTTGCGGGG 60.822 66.667 0.00 0.00 0.00 5.73
7249 14057 3.505184 GCCGTACATGGGTTGCGG 61.505 66.667 6.92 6.92 43.00 5.69
7250 14058 3.505184 GGCCGTACATGGGTTGCG 61.505 66.667 0.00 0.00 0.00 4.85
7252 14060 2.439519 GGGGCCGTACATGGGTTG 60.440 66.667 0.00 0.00 0.00 3.77
7253 14061 2.235761 AAGGGGCCGTACATGGGTT 61.236 57.895 0.00 0.00 0.00 4.11
7254 14062 2.612746 AAGGGGCCGTACATGGGT 60.613 61.111 0.00 0.00 0.00 4.51
7389 14262 2.588620 ACATGGCCCGTTTAGTTTTCA 58.411 42.857 0.00 0.00 0.00 2.69
7406 14279 2.270257 ACGCATGCCAGCACAACAT 61.270 52.632 13.15 0.00 0.00 2.71
7447 14321 1.745653 GACATGTGGCTTTCTTAGGGC 59.254 52.381 1.15 0.00 0.00 5.19
7463 14337 4.101448 GTGAGCCTGGCCCGACAT 62.101 66.667 16.57 0.00 0.00 3.06
7469 14368 2.883267 GATCTGTGGTGAGCCTGGCC 62.883 65.000 16.57 7.66 35.27 5.36
7484 14383 2.549563 CCAATAGCCAGCATGACGATCT 60.550 50.000 0.00 0.00 39.69 2.75
7533 14432 2.983592 GTGGCGGACAAACCTGGG 60.984 66.667 0.00 0.00 36.31 4.45
7572 14471 3.243805 CGACCCCGGGTTGTTTTAAATTT 60.244 43.478 21.85 0.00 35.25 1.82
7582 14481 4.404098 CCCTTCGACCCCGGGTTG 62.404 72.222 21.85 17.22 35.25 3.77
7599 14498 2.166050 TGCTCTGACTCTCTCATCTTGC 59.834 50.000 0.00 0.00 0.00 4.01


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

AutoCloner maintained by Alex Coulton.