Multiple sequence alignment - TraesCS4D01G176700

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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 TraesCS4D01G176700 chr4D 100.000 3047 0 0 1 3047 307239021 307235975 0.000000e+00 5627.0
1 TraesCS4D01G176700 chr4D 92.430 251 15 3 2236 2483 95179453 95179204 3.740000e-94 355.0
2 TraesCS4D01G176700 chr4D 92.430 251 16 2 2236 2483 456275958 456276208 3.740000e-94 355.0
3 TraesCS4D01G176700 chr4D 97.273 110 3 0 2938 3047 456276634 456276743 1.440000e-43 187.0
4 TraesCS4D01G176700 chr4A 91.822 2152 90 35 71 2192 170156133 170158228 0.000000e+00 2920.0
5 TraesCS4D01G176700 chr4A 93.103 87 6 0 1 87 170156027 170156113 8.870000e-26 128.0
6 TraesCS4D01G176700 chr4B 91.830 2093 94 33 41 2110 383147102 383145064 0.000000e+00 2846.0
7 TraesCS4D01G176700 chr3A 90.026 391 27 6 2524 2910 613171785 613171403 2.110000e-136 496.0
8 TraesCS4D01G176700 chr3B 89.620 395 31 7 2524 2914 625333411 625333023 7.590000e-136 494.0
9 TraesCS4D01G176700 chr3B 86.667 90 6 2 2964 3047 817317429 817317518 8.990000e-16 95.3
10 TraesCS4D01G176700 chr3D 88.586 403 29 6 2524 2914 470889149 470888752 9.890000e-130 473.0
11 TraesCS4D01G176700 chr3D 92.400 250 16 3 2236 2482 558707327 558707078 1.340000e-93 353.0
12 TraesCS4D01G176700 chr3D 91.700 253 16 5 2238 2487 561098459 561098709 2.250000e-91 346.0
13 TraesCS4D01G176700 chr3D 94.545 110 6 0 2938 3047 301853659 301853768 1.450000e-38 171.0
14 TraesCS4D01G176700 chr3D 87.931 116 8 1 2938 3047 607552421 607552536 6.850000e-27 132.0
15 TraesCS4D01G176700 chr1D 92.430 251 16 2 2236 2483 38791167 38791417 3.740000e-94 355.0
16 TraesCS4D01G176700 chr1D 94.690 113 3 1 2938 3047 38791822 38791934 4.040000e-39 172.0
17 TraesCS4D01G176700 chr5D 92.000 250 18 2 2236 2483 436603862 436603613 1.740000e-92 350.0
18 TraesCS4D01G176700 chr5D 96.907 97 3 0 2938 3034 436603208 436603112 2.430000e-36 163.0
19 TraesCS4D01G176700 chr2A 92.032 251 14 3 2236 2483 18292865 18292618 6.250000e-92 348.0
20 TraesCS4D01G176700 chr7D 91.051 257 18 5 2236 2489 610560381 610560635 2.910000e-90 342.0
21 TraesCS4D01G176700 chr7B 90.769 260 18 5 2229 2483 545987595 545987853 2.910000e-90 342.0
22 TraesCS4D01G176700 chr7A 93.636 110 7 0 2938 3047 112979218 112979109 6.760000e-37 165.0
23 TraesCS4D01G176700 chr5A 96.667 60 2 0 2938 2997 13527366 13527425 1.930000e-17 100.0


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 TraesCS4D01G176700 chr4D 307235975 307239021 3046 True 5627.0 5627 100.0000 1 3047 1 chr4D.!!$R2 3046
1 TraesCS4D01G176700 chr4D 456275958 456276743 785 False 271.0 355 94.8515 2236 3047 2 chr4D.!!$F1 811
2 TraesCS4D01G176700 chr4A 170156027 170158228 2201 False 1524.0 2920 92.4625 1 2192 2 chr4A.!!$F1 2191
3 TraesCS4D01G176700 chr4B 383145064 383147102 2038 True 2846.0 2846 91.8300 41 2110 1 chr4B.!!$R1 2069
4 TraesCS4D01G176700 chr1D 38791167 38791934 767 False 263.5 355 93.5600 2236 3047 2 chr1D.!!$F1 811
5 TraesCS4D01G176700 chr5D 436603112 436603862 750 True 256.5 350 94.4535 2236 3034 2 chr5D.!!$R1 798

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
838 921 0.039527 AGGATTTCGTGCGGTTTTGC 60.04 50.0 0.0 0.0 0.0 3.68 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2810 2978 0.108615 AGGAAACGACCGAGCATCAG 60.109 55.0 0.0 0.0 33.17 2.9 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
46 47 2.628194 GCATGTGTGCGAGTTATACG 57.372 50.000 0.00 0.00 42.28 3.06
174 212 3.308035 TTATCCTTCAGTCCCTCGCTA 57.692 47.619 0.00 0.00 0.00 4.26
175 213 2.390225 ATCCTTCAGTCCCTCGCTAT 57.610 50.000 0.00 0.00 0.00 2.97
186 224 9.642343 TTCAGTCCCTCGCTATATATATATGTT 57.358 33.333 14.42 0.00 0.00 2.71
242 280 3.248266 ACGTCAACTATCACGGCTTTAC 58.752 45.455 0.00 0.00 40.43 2.01
244 282 3.303495 CGTCAACTATCACGGCTTTACAG 59.697 47.826 0.00 0.00 32.19 2.74
245 283 4.491676 GTCAACTATCACGGCTTTACAGA 58.508 43.478 0.00 0.00 0.00 3.41
246 284 5.109903 GTCAACTATCACGGCTTTACAGAT 58.890 41.667 0.00 0.00 0.00 2.90
248 286 5.580691 TCAACTATCACGGCTTTACAGATTG 59.419 40.000 0.00 0.00 0.00 2.67
249 287 5.086104 ACTATCACGGCTTTACAGATTGT 57.914 39.130 0.00 0.00 0.00 2.71
250 288 5.109903 ACTATCACGGCTTTACAGATTGTC 58.890 41.667 0.00 0.00 0.00 3.18
302 348 1.303561 ATGGCGCCAATGTCACTGT 60.304 52.632 36.33 11.02 0.00 3.55
328 374 1.144057 AGGGATACGCCAGCGAAAG 59.856 57.895 20.32 0.00 42.83 2.62
329 375 1.887707 GGGATACGCCAGCGAAAGG 60.888 63.158 20.32 0.00 42.83 3.11
330 376 1.143183 GGATACGCCAGCGAAAGGA 59.857 57.895 20.32 0.00 42.83 3.36
331 377 0.461339 GGATACGCCAGCGAAAGGAA 60.461 55.000 20.32 0.00 42.83 3.36
332 378 0.651031 GATACGCCAGCGAAAGGAAC 59.349 55.000 20.32 0.00 42.83 3.62
425 473 1.525941 CACACCATGACATGACAGCA 58.474 50.000 17.24 0.00 0.00 4.41
457 505 6.143919 GCTATCAATACAAATTTTTAGCCGGC 59.856 38.462 21.89 21.89 32.10 6.13
500 548 0.101579 GACTAGAACTCTCCGCTGCC 59.898 60.000 0.00 0.00 0.00 4.85
501 549 0.323908 ACTAGAACTCTCCGCTGCCT 60.324 55.000 0.00 0.00 0.00 4.75
502 550 1.064611 ACTAGAACTCTCCGCTGCCTA 60.065 52.381 0.00 0.00 0.00 3.93
503 551 2.025155 CTAGAACTCTCCGCTGCCTAA 58.975 52.381 0.00 0.00 0.00 2.69
504 552 0.820871 AGAACTCTCCGCTGCCTAAG 59.179 55.000 0.00 0.00 0.00 2.18
605 666 3.313526 GCGTTGGCATCAAACATATCTCT 59.686 43.478 0.00 0.00 39.62 3.10
654 726 4.190772 CCCTCTGATTCTTCTTCTTGCTC 58.809 47.826 0.00 0.00 0.00 4.26
656 728 4.190772 CTCTGATTCTTCTTCTTGCTCCC 58.809 47.826 0.00 0.00 0.00 4.30
660 732 0.693049 TCTTCTTCTTGCTCCCCACC 59.307 55.000 0.00 0.00 0.00 4.61
671 745 0.469892 CTCCCCACCTGCTTTGGTTT 60.470 55.000 0.00 0.00 38.45 3.27
672 746 0.758685 TCCCCACCTGCTTTGGTTTG 60.759 55.000 0.00 0.00 38.45 2.93
673 747 1.069596 CCCACCTGCTTTGGTTTGC 59.930 57.895 0.00 0.00 38.45 3.68
674 748 1.402107 CCCACCTGCTTTGGTTTGCT 61.402 55.000 0.00 0.00 38.45 3.91
675 749 0.465287 CCACCTGCTTTGGTTTGCTT 59.535 50.000 0.00 0.00 38.45 3.91
676 750 1.538849 CCACCTGCTTTGGTTTGCTTC 60.539 52.381 0.00 0.00 38.45 3.86
677 751 0.752658 ACCTGCTTTGGTTTGCTTCC 59.247 50.000 0.00 0.00 36.89 3.46
678 752 0.318955 CCTGCTTTGGTTTGCTTCCG 60.319 55.000 0.00 0.00 0.00 4.30
679 753 0.385390 CTGCTTTGGTTTGCTTCCGT 59.615 50.000 0.00 0.00 0.00 4.69
680 754 0.102120 TGCTTTGGTTTGCTTCCGTG 59.898 50.000 0.00 0.00 0.00 4.94
681 755 0.597377 GCTTTGGTTTGCTTCCGTGG 60.597 55.000 0.00 0.00 0.00 4.94
682 756 0.597377 CTTTGGTTTGCTTCCGTGGC 60.597 55.000 0.00 0.00 0.00 5.01
683 757 1.323271 TTTGGTTTGCTTCCGTGGCA 61.323 50.000 0.00 0.00 37.97 4.92
684 758 1.112315 TTGGTTTGCTTCCGTGGCAT 61.112 50.000 0.00 0.00 39.54 4.40
685 759 1.212751 GGTTTGCTTCCGTGGCATC 59.787 57.895 0.00 0.00 39.54 3.91
686 760 1.212751 GTTTGCTTCCGTGGCATCC 59.787 57.895 0.00 0.00 39.54 3.51
687 761 1.228398 TTTGCTTCCGTGGCATCCA 60.228 52.632 0.00 0.00 39.54 3.41
688 762 0.825425 TTTGCTTCCGTGGCATCCAA 60.825 50.000 0.00 0.00 39.54 3.53
689 763 0.825425 TTGCTTCCGTGGCATCCAAA 60.825 50.000 0.00 0.00 39.54 3.28
690 764 0.611618 TGCTTCCGTGGCATCCAAAT 60.612 50.000 0.00 0.00 34.18 2.32
691 765 0.101219 GCTTCCGTGGCATCCAAATC 59.899 55.000 0.00 0.00 34.18 2.17
692 766 1.462616 CTTCCGTGGCATCCAAATCA 58.537 50.000 0.00 0.00 34.18 2.57
709 783 0.867746 TCATCCATGCGCGCTAATTC 59.132 50.000 33.29 1.73 0.00 2.17
720 794 1.287425 CGCTAATTCCTCGGGTGTTC 58.713 55.000 0.00 0.00 0.00 3.18
734 808 2.487265 GGGTGTTCTTGAAGAAGCTCCA 60.487 50.000 8.06 0.00 34.42 3.86
750 824 3.511146 AGCTCCATCTCTCTTATAGCTGC 59.489 47.826 0.00 0.00 37.44 5.25
751 825 3.511146 GCTCCATCTCTCTTATAGCTGCT 59.489 47.826 7.57 7.57 0.00 4.24
752 826 4.618927 GCTCCATCTCTCTTATAGCTGCTG 60.619 50.000 13.43 0.00 0.00 4.41
765 839 7.980099 TCTTATAGCTGCTGGTAAGTTCTTAAC 59.020 37.037 23.74 1.15 0.00 2.01
781 855 8.503458 AGTTCTTAACTTCATCCATCTTCATG 57.497 34.615 0.00 0.00 39.04 3.07
782 856 6.932356 TCTTAACTTCATCCATCTTCATGC 57.068 37.500 0.00 0.00 0.00 4.06
785 859 7.930325 TCTTAACTTCATCCATCTTCATGCTAG 59.070 37.037 0.00 0.00 0.00 3.42
786 860 5.627182 ACTTCATCCATCTTCATGCTAGT 57.373 39.130 0.00 0.00 0.00 2.57
787 861 6.737720 ACTTCATCCATCTTCATGCTAGTA 57.262 37.500 0.00 0.00 0.00 1.82
789 863 7.160049 ACTTCATCCATCTTCATGCTAGTATG 58.840 38.462 14.12 14.12 0.00 2.39
790 864 6.676990 TCATCCATCTTCATGCTAGTATGT 57.323 37.500 18.78 0.00 0.00 2.29
792 866 7.512130 TCATCCATCTTCATGCTAGTATGTTT 58.488 34.615 18.78 2.18 0.00 2.83
795 878 9.851686 ATCCATCTTCATGCTAGTATGTTTTTA 57.148 29.630 18.78 0.00 0.00 1.52
832 915 1.948104 TTGGATAGGATTTCGTGCGG 58.052 50.000 0.00 0.00 0.00 5.69
835 918 2.285977 GGATAGGATTTCGTGCGGTTT 58.714 47.619 0.00 0.00 0.00 3.27
838 921 0.039527 AGGATTTCGTGCGGTTTTGC 60.040 50.000 0.00 0.00 0.00 3.68
876 959 4.835199 TTTCAAAGTATCGTTAGCTCGC 57.165 40.909 0.00 0.00 0.00 5.03
881 968 0.703466 GTATCGTTAGCTCGCGCATC 59.297 55.000 8.75 0.00 39.10 3.91
882 969 0.591659 TATCGTTAGCTCGCGCATCT 59.408 50.000 8.75 2.95 39.10 2.90
883 970 0.591659 ATCGTTAGCTCGCGCATCTA 59.408 50.000 8.75 1.84 39.10 1.98
884 971 0.591659 TCGTTAGCTCGCGCATCTAT 59.408 50.000 8.75 0.00 39.10 1.98
885 972 1.001706 TCGTTAGCTCGCGCATCTATT 60.002 47.619 8.75 0.00 39.10 1.73
886 973 1.123217 CGTTAGCTCGCGCATCTATTG 59.877 52.381 8.75 0.00 39.10 1.90
905 992 1.342474 TGTTCTGTTGGAAAAGGGCCA 60.342 47.619 6.18 0.00 35.51 5.36
933 1020 0.468226 TGTTTCAGCCAGGAGAACGT 59.532 50.000 0.00 0.00 0.00 3.99
946 1034 0.515564 AGAACGTGCGCGCTAATTTT 59.484 45.000 33.29 17.28 42.83 1.82
989 1077 1.913403 GCTCGGTGAAATTTTGCATCG 59.087 47.619 6.27 6.27 39.82 3.84
1028 1119 4.404394 TGATGGCGATTCTGTTCCTAACTA 59.596 41.667 0.00 0.00 0.00 2.24
1042 1133 5.762825 TCCTAACTACCTATACGCAGTTG 57.237 43.478 0.00 0.00 37.78 3.16
1062 1153 3.437213 TGTTGGTCGAGGAGATAGGAAA 58.563 45.455 0.00 0.00 0.00 3.13
1320 1414 2.109799 CAGTGGCCGCCTATCCTG 59.890 66.667 14.07 7.65 0.00 3.86
1543 1637 0.030705 AGAGGGAGGAGCCAGCAATA 60.031 55.000 0.00 0.00 38.95 1.90
1638 1735 2.125961 GTACCTGGCCGAGACCGAT 61.126 63.158 0.00 0.00 38.22 4.18
1997 2094 2.127232 GCTCGCACGACCTTTTGC 60.127 61.111 0.00 0.00 35.26 3.68
2118 2215 6.317391 GTCTAGCATCTTGTAAAGCTGGATTT 59.683 38.462 0.00 0.00 45.70 2.17
2147 2244 4.497300 TGGTTGAACCGTAATACACTAGC 58.503 43.478 10.16 0.00 42.58 3.42
2150 2247 5.404946 GTTGAACCGTAATACACTAGCTCA 58.595 41.667 0.00 0.00 0.00 4.26
2166 2263 4.566545 AGCTCATTCGTCTCTATGTCTG 57.433 45.455 0.00 0.00 0.00 3.51
2206 2303 6.910536 GCAAGATGCAGTAATACTAGTGTT 57.089 37.500 9.95 9.95 44.26 3.32
2208 2305 8.066668 GCAAGATGCAGTAATACTAGTGTTAG 57.933 38.462 11.91 3.78 44.26 2.34
2209 2306 7.169982 GCAAGATGCAGTAATACTAGTGTTAGG 59.830 40.741 11.91 8.88 44.26 2.69
2210 2307 7.899648 AGATGCAGTAATACTAGTGTTAGGT 57.100 36.000 11.91 1.11 31.90 3.08
2211 2308 8.991783 AGATGCAGTAATACTAGTGTTAGGTA 57.008 34.615 11.91 7.93 31.90 3.08
2212 2309 8.848182 AGATGCAGTAATACTAGTGTTAGGTAC 58.152 37.037 11.91 3.96 31.90 3.34
2213 2310 7.338800 TGCAGTAATACTAGTGTTAGGTACC 57.661 40.000 11.91 2.73 31.90 3.34
2214 2311 6.322201 TGCAGTAATACTAGTGTTAGGTACCC 59.678 42.308 11.91 0.77 31.90 3.69
2215 2312 6.322201 GCAGTAATACTAGTGTTAGGTACCCA 59.678 42.308 11.91 0.00 31.90 4.51
2216 2313 7.469732 GCAGTAATACTAGTGTTAGGTACCCAG 60.470 44.444 11.91 0.00 31.90 4.45
2217 2314 7.559170 CAGTAATACTAGTGTTAGGTACCCAGT 59.441 40.741 11.91 5.24 0.00 4.00
2218 2315 8.781951 AGTAATACTAGTGTTAGGTACCCAGTA 58.218 37.037 11.91 6.18 0.00 2.74
2219 2316 7.888250 AATACTAGTGTTAGGTACCCAGTAC 57.112 40.000 8.74 3.55 38.19 2.73
2220 2317 5.527026 ACTAGTGTTAGGTACCCAGTACT 57.473 43.478 8.74 11.07 38.85 2.73
2221 2318 6.642733 ACTAGTGTTAGGTACCCAGTACTA 57.357 41.667 8.74 11.60 38.85 1.82
2222 2319 6.418946 ACTAGTGTTAGGTACCCAGTACTAC 58.581 44.000 8.74 0.00 38.85 2.73
2223 2320 5.527026 AGTGTTAGGTACCCAGTACTACT 57.473 43.478 8.74 1.73 38.85 2.57
2224 2321 5.504853 AGTGTTAGGTACCCAGTACTACTC 58.495 45.833 8.74 0.00 38.85 2.59
2225 2322 5.252630 AGTGTTAGGTACCCAGTACTACTCT 59.747 44.000 8.74 0.62 38.85 3.24
2226 2323 5.588246 GTGTTAGGTACCCAGTACTACTCTC 59.412 48.000 8.74 0.00 38.85 3.20
2227 2324 5.490357 TGTTAGGTACCCAGTACTACTCTCT 59.510 44.000 8.74 0.00 38.85 3.10
2228 2325 4.776435 AGGTACCCAGTACTACTCTCTC 57.224 50.000 8.74 0.00 38.85 3.20
2229 2326 4.110072 AGGTACCCAGTACTACTCTCTCA 58.890 47.826 8.74 0.00 38.85 3.27
2230 2327 4.727841 AGGTACCCAGTACTACTCTCTCAT 59.272 45.833 8.74 0.00 38.85 2.90
2231 2328 5.910003 AGGTACCCAGTACTACTCTCTCATA 59.090 44.000 8.74 0.00 38.85 2.15
2232 2329 6.043474 AGGTACCCAGTACTACTCTCTCATAG 59.957 46.154 8.74 0.00 38.85 2.23
2233 2330 6.043012 GGTACCCAGTACTACTCTCTCATAGA 59.957 46.154 0.00 0.00 38.85 1.98
2234 2331 6.773583 ACCCAGTACTACTCTCTCATAGAT 57.226 41.667 0.00 0.00 32.41 1.98
2266 2363 3.003897 GCAAGAAACCACCACATTTACGA 59.996 43.478 0.00 0.00 0.00 3.43
2279 2376 4.000988 ACATTTACGACTAGGTTTGCAGG 58.999 43.478 0.00 0.00 0.00 4.85
2283 2380 3.418684 ACGACTAGGTTTGCAGGAAAT 57.581 42.857 0.00 0.00 0.00 2.17
2287 2384 4.327680 GACTAGGTTTGCAGGAAATCACT 58.672 43.478 0.00 0.00 0.00 3.41
2317 2414 0.462225 TCCGTTGCAGAAAACACCGA 60.462 50.000 0.00 0.00 0.00 4.69
2366 2463 2.242965 ACTGATCAGATGATTTGGCCCA 59.757 45.455 29.27 0.00 34.37 5.36
2383 2480 7.732222 TTGGCCCATTTAATCACTTTCTTAT 57.268 32.000 0.00 0.00 0.00 1.73
2386 2483 9.261035 TGGCCCATTTAATCACTTTCTTATAAA 57.739 29.630 0.00 0.00 0.00 1.40
2411 2508 4.218312 GGGCCAGATTGTAAGGAATTGAT 58.782 43.478 4.39 0.00 0.00 2.57
2491 2591 3.119096 GGAACACCGCTCTTCCGC 61.119 66.667 0.00 0.00 0.00 5.54
2502 2602 4.821589 CTTCCGCCGAGGTGCCTC 62.822 72.222 8.14 8.14 41.99 4.70
2516 2616 2.279985 CCTCTGCATGCTCGCGAT 60.280 61.111 20.33 0.00 33.35 4.58
2517 2617 2.595878 CCTCTGCATGCTCGCGATG 61.596 63.158 20.33 6.54 33.35 3.84
2518 2618 3.224745 CTCTGCATGCTCGCGATGC 62.225 63.158 22.77 22.77 45.45 3.91
2519 2619 3.270092 CTGCATGCTCGCGATGCT 61.270 61.111 27.58 13.12 45.45 3.79
2520 2620 2.820619 CTGCATGCTCGCGATGCTT 61.821 57.895 27.58 19.29 45.45 3.91
2521 2621 2.052414 GCATGCTCGCGATGCTTC 60.052 61.111 22.39 11.65 42.52 3.86
2522 2622 2.532256 GCATGCTCGCGATGCTTCT 61.532 57.895 22.39 9.47 42.52 2.85
2523 2623 1.275953 CATGCTCGCGATGCTTCTG 59.724 57.895 24.04 16.88 0.00 3.02
2524 2624 2.532256 ATGCTCGCGATGCTTCTGC 61.532 57.895 24.04 16.87 40.20 4.26
2571 2671 2.885113 CGGACAGGATGACGCTCA 59.115 61.111 0.00 0.00 39.69 4.26
2572 2672 1.215382 CGGACAGGATGACGCTCAA 59.785 57.895 0.00 0.00 39.69 3.02
2573 2673 0.803768 CGGACAGGATGACGCTCAAG 60.804 60.000 0.00 0.00 39.69 3.02
2574 2674 1.086634 GGACAGGATGACGCTCAAGC 61.087 60.000 0.00 0.00 39.69 4.01
2575 2675 0.108424 GACAGGATGACGCTCAAGCT 60.108 55.000 0.00 0.00 39.69 3.74
2576 2676 0.390866 ACAGGATGACGCTCAAGCTG 60.391 55.000 0.00 0.00 39.69 4.24
2577 2677 1.088340 CAGGATGACGCTCAAGCTGG 61.088 60.000 0.00 0.00 39.69 4.85
2578 2678 2.467826 GGATGACGCTCAAGCTGGC 61.468 63.158 0.00 0.00 39.32 4.85
2579 2679 2.437359 ATGACGCTCAAGCTGGCC 60.437 61.111 0.00 0.00 39.32 5.36
2580 2680 3.984193 ATGACGCTCAAGCTGGCCC 62.984 63.158 0.00 0.00 39.32 5.80
2613 2713 4.659172 CGCAGAACCCCAGGCCAA 62.659 66.667 5.01 0.00 0.00 4.52
2614 2714 2.677875 GCAGAACCCCAGGCCAAG 60.678 66.667 5.01 0.00 0.00 3.61
2615 2715 2.036256 CAGAACCCCAGGCCAAGG 59.964 66.667 5.01 6.36 0.00 3.61
2616 2716 2.452491 AGAACCCCAGGCCAAGGT 60.452 61.111 5.01 5.35 34.60 3.50
2618 2718 2.780924 AACCCCAGGCCAAGGTGA 60.781 61.111 5.01 0.00 33.05 4.02
2649 2770 2.355126 CGCGCAGATACGGAGCAT 60.355 61.111 8.75 0.00 0.00 3.79
2672 2793 4.982701 GCAGCCCCAAGTGCCTGT 62.983 66.667 0.00 0.00 33.29 4.00
2674 2795 4.982701 AGCCCCAAGTGCCTGTGC 62.983 66.667 0.00 0.00 38.26 4.57
2729 2897 4.695993 TCAAGCACGCCATCGCCA 62.696 61.111 0.00 0.00 39.84 5.69
2731 2899 3.511595 AAGCACGCCATCGCCATG 61.512 61.111 0.00 0.00 39.84 3.66
2733 2901 4.241999 GCACGCCATCGCCATGAC 62.242 66.667 0.00 0.00 39.84 3.06
2742 2910 1.644437 ATCGCCATGACCATCCCCAA 61.644 55.000 0.00 0.00 0.00 4.12
2745 2913 1.825191 CCATGACCATCCCCAAGCG 60.825 63.158 0.00 0.00 0.00 4.68
2746 2914 1.077501 CATGACCATCCCCAAGCGT 60.078 57.895 0.00 0.00 0.00 5.07
2747 2915 0.680921 CATGACCATCCCCAAGCGTT 60.681 55.000 0.00 0.00 0.00 4.84
2749 2917 1.303317 GACCATCCCCAAGCGTTGT 60.303 57.895 0.00 0.00 0.00 3.32
2760 2928 4.036804 GCGTTGTGCCATCGCCAA 62.037 61.111 15.44 0.00 43.81 4.52
2761 2929 2.126888 CGTTGTGCCATCGCCAAC 60.127 61.111 6.60 6.60 40.17 3.77
2762 2930 2.258286 GTTGTGCCATCGCCAACC 59.742 61.111 5.70 0.00 38.86 3.77
2763 2931 3.361158 TTGTGCCATCGCCAACCG 61.361 61.111 0.00 0.00 38.61 4.44
2770 2938 4.875713 ATCGCCAACCGCCCCATC 62.876 66.667 0.00 0.00 36.73 3.51
2785 2953 0.865769 CCATCGGCTACAAATACGGC 59.134 55.000 0.00 0.00 0.00 5.68
2786 2954 0.865769 CATCGGCTACAAATACGGCC 59.134 55.000 0.00 0.00 41.02 6.13
2788 2956 4.526770 GGCTACAAATACGGCCGT 57.473 55.556 36.01 36.01 35.08 5.68
2789 2957 3.665544 GGCTACAAATACGGCCGTA 57.334 52.632 37.91 37.91 35.08 4.02
2792 2960 2.543641 GCTACAAATACGGCCGTAAGT 58.456 47.619 39.14 34.07 33.99 2.24
2793 2961 2.931969 GCTACAAATACGGCCGTAAGTT 59.068 45.455 39.14 30.81 33.99 2.66
2794 2962 3.371898 GCTACAAATACGGCCGTAAGTTT 59.628 43.478 39.14 30.94 33.99 2.66
2795 2963 4.566360 GCTACAAATACGGCCGTAAGTTTA 59.434 41.667 39.14 25.21 33.99 2.01
2796 2964 5.234972 GCTACAAATACGGCCGTAAGTTTAT 59.765 40.000 39.14 26.75 33.99 1.40
2797 2965 6.238184 GCTACAAATACGGCCGTAAGTTTATT 60.238 38.462 39.14 26.26 33.99 1.40
2798 2966 7.042791 GCTACAAATACGGCCGTAAGTTTATTA 60.043 37.037 39.14 24.93 33.99 0.98
2799 2967 7.237920 ACAAATACGGCCGTAAGTTTATTAG 57.762 36.000 39.14 23.92 33.99 1.73
2800 2968 6.818142 ACAAATACGGCCGTAAGTTTATTAGT 59.182 34.615 39.14 24.48 33.99 2.24
2801 2969 7.334171 ACAAATACGGCCGTAAGTTTATTAGTT 59.666 33.333 39.14 22.43 33.99 2.24
2802 2970 7.468922 AATACGGCCGTAAGTTTATTAGTTC 57.531 36.000 39.14 0.00 33.99 3.01
2803 2971 5.077134 ACGGCCGTAAGTTTATTAGTTCT 57.923 39.130 33.34 0.00 0.00 3.01
2804 2972 4.866486 ACGGCCGTAAGTTTATTAGTTCTG 59.134 41.667 33.34 0.00 0.00 3.02
2806 2974 5.577945 CGGCCGTAAGTTTATTAGTTCTGAA 59.422 40.000 19.50 0.00 0.00 3.02
2807 2975 6.454715 CGGCCGTAAGTTTATTAGTTCTGAAC 60.455 42.308 19.50 12.54 0.00 3.18
2808 2976 6.592994 GGCCGTAAGTTTATTAGTTCTGAACT 59.407 38.462 24.80 24.80 45.40 3.01
2809 2977 7.118825 GGCCGTAAGTTTATTAGTTCTGAACTT 59.881 37.037 26.33 13.29 42.81 2.66
2810 2978 8.167345 GCCGTAAGTTTATTAGTTCTGAACTTC 58.833 37.037 26.33 11.28 42.81 3.01
2816 2987 8.940952 AGTTTATTAGTTCTGAACTTCTGATGC 58.059 33.333 26.33 12.53 42.81 3.91
2817 2988 8.940952 GTTTATTAGTTCTGAACTTCTGATGCT 58.059 33.333 26.33 3.63 42.81 3.79
2821 2992 1.895798 TCTGAACTTCTGATGCTCGGT 59.104 47.619 3.60 0.00 0.00 4.69
2822 2993 2.094494 TCTGAACTTCTGATGCTCGGTC 60.094 50.000 3.60 0.00 0.00 4.79
2829 3000 0.108615 CTGATGCTCGGTCGTTTCCT 60.109 55.000 0.00 0.00 0.00 3.36
2830 3001 0.108804 TGATGCTCGGTCGTTTCCTC 60.109 55.000 0.00 0.00 0.00 3.71
2832 3003 0.108615 ATGCTCGGTCGTTTCCTCTG 60.109 55.000 0.00 0.00 0.00 3.35
2833 3004 1.289380 GCTCGGTCGTTTCCTCTGT 59.711 57.895 0.00 0.00 0.00 3.41
2834 3005 0.524862 GCTCGGTCGTTTCCTCTGTA 59.475 55.000 0.00 0.00 0.00 2.74
2835 3006 1.467713 GCTCGGTCGTTTCCTCTGTAG 60.468 57.143 0.00 0.00 0.00 2.74
2836 3007 0.524862 TCGGTCGTTTCCTCTGTAGC 59.475 55.000 0.00 0.00 0.00 3.58
2837 3008 0.242825 CGGTCGTTTCCTCTGTAGCA 59.757 55.000 0.00 0.00 0.00 3.49
2838 3009 1.336517 CGGTCGTTTCCTCTGTAGCAA 60.337 52.381 0.00 0.00 0.00 3.91
2839 3010 2.067013 GGTCGTTTCCTCTGTAGCAAC 58.933 52.381 0.00 0.00 0.00 4.17
2840 3011 2.288886 GGTCGTTTCCTCTGTAGCAACT 60.289 50.000 0.00 0.00 0.00 3.16
2841 3012 2.987821 GTCGTTTCCTCTGTAGCAACTC 59.012 50.000 0.00 0.00 0.00 3.01
2842 3013 2.891580 TCGTTTCCTCTGTAGCAACTCT 59.108 45.455 0.00 0.00 0.00 3.24
2843 3014 2.989840 CGTTTCCTCTGTAGCAACTCTG 59.010 50.000 0.00 0.00 0.00 3.35
2844 3015 3.553096 CGTTTCCTCTGTAGCAACTCTGT 60.553 47.826 0.00 0.00 0.00 3.41
2846 3017 2.171840 TCCTCTGTAGCAACTCTGTCC 58.828 52.381 0.00 0.00 0.00 4.02
2848 3019 2.175202 CTCTGTAGCAACTCTGTCCCT 58.825 52.381 0.00 0.00 0.00 4.20
2850 3021 2.300152 TCTGTAGCAACTCTGTCCCTTG 59.700 50.000 0.00 0.00 0.00 3.61
2853 3024 0.689623 AGCAACTCTGTCCCTTGGAG 59.310 55.000 0.00 0.00 29.39 3.86
2854 3025 0.957888 GCAACTCTGTCCCTTGGAGC 60.958 60.000 0.00 0.00 29.39 4.70
2855 3026 0.322008 CAACTCTGTCCCTTGGAGCC 60.322 60.000 0.00 0.00 29.39 4.70
2857 3028 0.548682 ACTCTGTCCCTTGGAGCCAT 60.549 55.000 0.00 0.00 29.39 4.40
2858 3029 0.179936 CTCTGTCCCTTGGAGCCATC 59.820 60.000 0.00 0.00 29.39 3.51
2860 3031 1.903877 CTGTCCCTTGGAGCCATCGT 61.904 60.000 0.00 0.00 29.39 3.73
2861 3032 1.153349 GTCCCTTGGAGCCATCGTC 60.153 63.158 0.00 0.00 29.39 4.20
2862 3033 1.612146 TCCCTTGGAGCCATCGTCA 60.612 57.895 0.00 0.00 0.00 4.35
2863 3034 0.982852 TCCCTTGGAGCCATCGTCAT 60.983 55.000 0.00 0.00 0.00 3.06
2864 3035 0.107017 CCCTTGGAGCCATCGTCATT 60.107 55.000 0.00 0.00 0.00 2.57
2865 3036 1.683011 CCCTTGGAGCCATCGTCATTT 60.683 52.381 0.00 0.00 0.00 2.32
2866 3037 1.402968 CCTTGGAGCCATCGTCATTTG 59.597 52.381 0.00 0.00 0.00 2.32
2867 3038 0.810648 TTGGAGCCATCGTCATTTGC 59.189 50.000 0.00 0.00 0.00 3.68
2868 3039 0.035152 TGGAGCCATCGTCATTTGCT 60.035 50.000 0.00 0.00 34.40 3.91
2869 3040 1.098050 GGAGCCATCGTCATTTGCTT 58.902 50.000 0.00 0.00 31.23 3.91
2870 3041 1.474077 GGAGCCATCGTCATTTGCTTT 59.526 47.619 0.00 0.00 31.23 3.51
2873 3044 1.403249 GCCATCGTCATTTGCTTTGCT 60.403 47.619 0.00 0.00 0.00 3.91
2874 3045 2.523015 CCATCGTCATTTGCTTTGCTC 58.477 47.619 0.00 0.00 0.00 4.26
2875 3046 2.163010 CCATCGTCATTTGCTTTGCTCT 59.837 45.455 0.00 0.00 0.00 4.09
2877 3048 1.069022 TCGTCATTTGCTTTGCTCTGC 60.069 47.619 0.00 0.00 0.00 4.26
2879 3050 2.606308 CGTCATTTGCTTTGCTCTGCTT 60.606 45.455 0.00 0.00 0.00 3.91
2880 3051 3.387397 GTCATTTGCTTTGCTCTGCTTT 58.613 40.909 0.00 0.00 0.00 3.51
2881 3052 3.805971 GTCATTTGCTTTGCTCTGCTTTT 59.194 39.130 0.00 0.00 0.00 2.27
2883 3054 2.965572 TTGCTTTGCTCTGCTTTTGT 57.034 40.000 0.00 0.00 0.00 2.83
2884 3055 2.965572 TGCTTTGCTCTGCTTTTGTT 57.034 40.000 0.00 0.00 0.00 2.83
2885 3056 2.542597 TGCTTTGCTCTGCTTTTGTTG 58.457 42.857 0.00 0.00 0.00 3.33
2886 3057 2.094078 TGCTTTGCTCTGCTTTTGTTGT 60.094 40.909 0.00 0.00 0.00 3.32
2888 3059 1.925229 TTGCTCTGCTTTTGTTGTGC 58.075 45.000 0.00 0.00 0.00 4.57
2889 3060 0.816373 TGCTCTGCTTTTGTTGTGCA 59.184 45.000 0.00 0.00 35.30 4.57
2892 3063 3.349088 CTGCTTTTGTTGTGCAGCA 57.651 47.368 0.00 0.00 45.76 4.41
2893 3064 1.860676 CTGCTTTTGTTGTGCAGCAT 58.139 45.000 0.00 0.00 45.76 3.79
2895 3066 2.727798 CTGCTTTTGTTGTGCAGCATAC 59.272 45.455 0.00 0.54 45.76 2.39
2896 3067 2.100418 TGCTTTTGTTGTGCAGCATACA 59.900 40.909 0.00 3.59 32.55 2.29
2897 3068 2.472488 GCTTTTGTTGTGCAGCATACAC 59.528 45.455 11.64 4.18 38.55 2.90
2900 3080 0.110295 TGTTGTGCAGCATACACCCT 59.890 50.000 0.00 0.00 37.22 4.34
2905 3085 1.454479 GCAGCATACACCCTGCCAT 60.454 57.895 1.38 0.00 46.59 4.40
2912 3092 1.626356 TACACCCTGCCATGAGGAGC 61.626 60.000 1.97 0.00 34.69 4.70
2913 3093 2.611800 ACCCTGCCATGAGGAGCA 60.612 61.111 1.97 0.00 34.69 4.26
2918 3098 2.203181 GCCATGAGGAGCAGAGGC 60.203 66.667 0.00 0.00 42.16 4.70
2926 3106 2.202987 GAGCAGAGGCACCATCCG 60.203 66.667 0.00 0.00 44.61 4.18
2927 3107 4.479993 AGCAGAGGCACCATCCGC 62.480 66.667 0.00 0.00 44.61 5.54
3003 3187 4.810790 TCTTCTTCTTCTTCTTACTGCCG 58.189 43.478 0.00 0.00 0.00 5.69
3034 3218 1.304962 TGCTTGGAGTAGCCGGAGA 60.305 57.895 5.05 0.00 40.49 3.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
46 47 4.689345 ACAAGAACGTTGACTAACTATGCC 59.311 41.667 5.00 0.00 34.60 4.40
139 177 4.657814 AGGATAATTGACCTGTGGTGTT 57.342 40.909 4.78 0.00 35.25 3.32
186 224 8.678199 TGTGTGTATTTTTGTAATTCTGTGACA 58.322 29.630 0.00 0.00 0.00 3.58
221 259 2.450609 AAAGCCGTGATAGTTGACGT 57.549 45.000 0.00 0.00 33.66 4.34
242 280 6.458478 GCATTCAATTGAGGAGAGACAATCTG 60.458 42.308 8.41 0.00 38.84 2.90
244 282 5.356190 TGCATTCAATTGAGGAGAGACAATC 59.644 40.000 8.41 0.00 35.99 2.67
245 283 5.258841 TGCATTCAATTGAGGAGAGACAAT 58.741 37.500 8.41 0.00 38.18 2.71
246 284 4.654915 TGCATTCAATTGAGGAGAGACAA 58.345 39.130 8.41 0.00 0.00 3.18
248 286 5.589452 AGAATGCATTCAATTGAGGAGAGAC 59.411 40.000 34.59 8.57 39.23 3.36
249 287 5.752650 AGAATGCATTCAATTGAGGAGAGA 58.247 37.500 34.59 0.00 39.23 3.10
250 288 5.008811 GGAGAATGCATTCAATTGAGGAGAG 59.991 44.000 34.59 0.00 39.23 3.20
302 348 1.252215 TGGCGTATCCCTGACGAACA 61.252 55.000 0.00 0.00 42.98 3.18
438 486 4.464597 TCCTGCCGGCTAAAAATTTGTATT 59.535 37.500 29.70 0.00 0.00 1.89
446 494 1.241315 GCTGTCCTGCCGGCTAAAAA 61.241 55.000 29.70 5.44 33.80 1.94
457 505 1.204467 GGAGACTCTCAAGCTGTCCTG 59.796 57.143 8.35 0.00 31.08 3.86
500 548 1.449601 ACATCGCCCGGTTGCTTAG 60.450 57.895 0.00 0.00 0.00 2.18
501 549 1.743623 CACATCGCCCGGTTGCTTA 60.744 57.895 0.00 0.00 0.00 3.09
502 550 3.055719 CACATCGCCCGGTTGCTT 61.056 61.111 0.00 0.00 0.00 3.91
505 553 2.413437 TTTTGCACATCGCCCGGTTG 62.413 55.000 0.00 0.00 41.33 3.77
506 554 2.196925 TTTTGCACATCGCCCGGTT 61.197 52.632 0.00 0.00 41.33 4.44
507 555 2.596046 TTTTGCACATCGCCCGGT 60.596 55.556 0.00 0.00 41.33 5.28
508 556 2.126502 GTTTTGCACATCGCCCGG 60.127 61.111 0.00 0.00 41.33 5.73
509 557 1.003262 CTTGTTTTGCACATCGCCCG 61.003 55.000 0.00 0.00 41.33 6.13
510 558 0.313672 TCTTGTTTTGCACATCGCCC 59.686 50.000 0.00 0.00 41.33 6.13
511 559 2.053627 CTTCTTGTTTTGCACATCGCC 58.946 47.619 0.00 0.00 41.33 5.54
512 560 1.453148 GCTTCTTGTTTTGCACATCGC 59.547 47.619 0.00 0.00 42.89 4.58
637 709 2.644299 TGGGGAGCAAGAAGAAGAATCA 59.356 45.455 0.00 0.00 0.00 2.57
654 726 1.747774 CAAACCAAAGCAGGTGGGG 59.252 57.895 5.45 0.00 42.25 4.96
656 728 0.465287 AAGCAAACCAAAGCAGGTGG 59.535 50.000 0.00 0.00 42.25 4.61
660 732 0.385390 ACGGAAGCAAACCAAAGCAG 59.615 50.000 0.00 0.00 0.00 4.24
671 745 0.611618 ATTTGGATGCCACGGAAGCA 60.612 50.000 0.00 0.00 45.94 3.91
672 746 0.101219 GATTTGGATGCCACGGAAGC 59.899 55.000 0.00 0.00 30.78 3.86
673 747 1.462616 TGATTTGGATGCCACGGAAG 58.537 50.000 0.00 0.00 30.78 3.46
674 748 2.023673 GATGATTTGGATGCCACGGAA 58.976 47.619 0.00 0.00 30.78 4.30
675 749 1.679139 GATGATTTGGATGCCACGGA 58.321 50.000 0.00 0.00 30.78 4.69
676 750 0.670162 GGATGATTTGGATGCCACGG 59.330 55.000 0.00 0.00 30.78 4.94
677 751 1.391577 TGGATGATTTGGATGCCACG 58.608 50.000 0.00 0.00 30.78 4.94
678 752 2.547218 GCATGGATGATTTGGATGCCAC 60.547 50.000 0.00 0.00 34.58 5.01
679 753 1.689813 GCATGGATGATTTGGATGCCA 59.310 47.619 0.00 0.00 34.58 4.92
680 754 1.336517 CGCATGGATGATTTGGATGCC 60.337 52.381 0.00 0.00 36.83 4.40
681 755 1.933500 GCGCATGGATGATTTGGATGC 60.934 52.381 0.30 0.00 36.81 3.91
682 756 1.664874 CGCGCATGGATGATTTGGATG 60.665 52.381 8.75 0.00 0.00 3.51
683 757 0.594602 CGCGCATGGATGATTTGGAT 59.405 50.000 8.75 0.00 0.00 3.41
684 758 2.024117 CGCGCATGGATGATTTGGA 58.976 52.632 8.75 0.00 0.00 3.53
685 759 1.659335 GCGCGCATGGATGATTTGG 60.659 57.895 29.10 0.00 0.00 3.28
686 760 0.587768 TAGCGCGCATGGATGATTTG 59.412 50.000 35.10 0.00 0.00 2.32
687 761 1.308047 TTAGCGCGCATGGATGATTT 58.692 45.000 35.10 10.92 0.00 2.17
688 762 1.527034 ATTAGCGCGCATGGATGATT 58.473 45.000 35.10 11.76 0.00 2.57
689 763 1.466167 GAATTAGCGCGCATGGATGAT 59.534 47.619 35.10 11.52 0.00 2.45
690 764 0.867746 GAATTAGCGCGCATGGATGA 59.132 50.000 35.10 9.31 0.00 2.92
691 765 0.110056 GGAATTAGCGCGCATGGATG 60.110 55.000 35.10 0.00 0.00 3.51
692 766 0.250467 AGGAATTAGCGCGCATGGAT 60.250 50.000 35.10 17.59 0.00 3.41
709 783 2.417719 CTTCTTCAAGAACACCCGAGG 58.582 52.381 0.00 0.00 29.89 4.63
720 794 4.741321 AGAGAGATGGAGCTTCTTCAAG 57.259 45.455 10.37 0.00 0.00 3.02
734 808 6.074648 ACTTACCAGCAGCTATAAGAGAGAT 58.925 40.000 23.54 6.35 0.00 2.75
765 839 7.160049 ACATACTAGCATGAAGATGGATGAAG 58.840 38.462 10.02 0.00 0.00 3.02
768 842 7.741027 AAACATACTAGCATGAAGATGGATG 57.259 36.000 10.02 0.00 0.00 3.51
795 878 8.585018 CCTATCCAAAACATTGAACCTAAAACT 58.415 33.333 0.00 0.00 0.00 2.66
807 890 5.650543 GCACGAAATCCTATCCAAAACATT 58.349 37.500 0.00 0.00 0.00 2.71
811 894 2.680841 CCGCACGAAATCCTATCCAAAA 59.319 45.455 0.00 0.00 0.00 2.44
848 931 7.573627 AGCTAACGATACTTTGAAAACTTCAC 58.426 34.615 0.00 0.00 39.87 3.18
850 933 6.948777 CGAGCTAACGATACTTTGAAAACTTC 59.051 38.462 0.00 0.00 35.09 3.01
858 941 2.886324 CGCGAGCTAACGATACTTTG 57.114 50.000 0.00 0.00 35.09 2.77
876 959 4.944962 TTCCAACAGAACAATAGATGCG 57.055 40.909 0.00 0.00 0.00 4.73
881 968 4.321974 GGCCCTTTTCCAACAGAACAATAG 60.322 45.833 0.00 0.00 32.95 1.73
882 969 3.576550 GGCCCTTTTCCAACAGAACAATA 59.423 43.478 0.00 0.00 32.95 1.90
883 970 2.368548 GGCCCTTTTCCAACAGAACAAT 59.631 45.455 0.00 0.00 32.95 2.71
884 971 1.760029 GGCCCTTTTCCAACAGAACAA 59.240 47.619 0.00 0.00 32.95 2.83
885 972 1.342474 TGGCCCTTTTCCAACAGAACA 60.342 47.619 0.00 0.00 32.95 3.18
886 973 1.341209 CTGGCCCTTTTCCAACAGAAC 59.659 52.381 0.00 0.00 32.95 3.01
905 992 2.310538 CTGGCTGAAACAAAGTTCCCT 58.689 47.619 0.00 0.00 0.00 4.20
933 1020 0.814457 ATTGGGAAAATTAGCGCGCA 59.186 45.000 35.10 14.88 0.00 6.09
964 1052 2.288152 GCAAAATTTCACCGAGCCTCAA 60.288 45.455 0.00 0.00 0.00 3.02
965 1053 1.269448 GCAAAATTTCACCGAGCCTCA 59.731 47.619 0.00 0.00 0.00 3.86
967 1055 1.327303 TGCAAAATTTCACCGAGCCT 58.673 45.000 0.00 0.00 0.00 4.58
989 1077 1.328680 CATCAGGCATAGTTGTGCGAC 59.671 52.381 0.00 0.00 45.97 5.19
1011 1099 7.296660 CGTATAGGTAGTTAGGAACAGAATCG 58.703 42.308 0.00 0.00 0.00 3.34
1028 1119 2.673043 CGACCAACAACTGCGTATAGGT 60.673 50.000 0.00 0.00 0.00 3.08
1042 1133 4.342665 AGATTTCCTATCTCCTCGACCAAC 59.657 45.833 0.00 0.00 0.00 3.77
1062 1153 2.158986 CGCCATGTCTTTCTCCTGAGAT 60.159 50.000 0.00 0.00 37.29 2.75
1304 1398 1.460305 ATCAGGATAGGCGGCCACT 60.460 57.895 23.09 10.62 0.00 4.00
1320 1414 3.140225 GACGCCGAGGAGGTCCATC 62.140 68.421 0.00 0.00 43.70 3.51
1369 1463 1.812686 TACTGTCTTCGCGCCAAGGT 61.813 55.000 14.92 7.55 0.00 3.50
1519 1613 3.791586 GGCTCCTCCCTCTGGCAC 61.792 72.222 0.00 0.00 0.00 5.01
1997 2094 1.128611 CTGCGCGAGAACAAACGAG 59.871 57.895 12.10 0.00 0.00 4.18
2147 2244 4.041049 GCACAGACATAGAGACGAATGAG 58.959 47.826 0.00 0.00 0.00 2.90
2150 2247 3.696548 TGAGCACAGACATAGAGACGAAT 59.303 43.478 0.00 0.00 0.00 3.34
2166 2263 1.527034 TGCAATTCTGTCCTGAGCAC 58.473 50.000 0.00 0.00 0.00 4.40
2208 2305 7.256763 ATCTATGAGAGAGTAGTACTGGGTACC 60.257 44.444 7.76 2.17 44.50 3.34
2209 2306 7.065120 TCTATGAGAGAGTAGTACTGGGTAC 57.935 44.000 7.76 0.00 39.10 3.34
2210 2307 7.513091 TCATCTATGAGAGAGTAGTACTGGGTA 59.487 40.741 7.76 0.00 37.70 3.69
2211 2308 6.330514 TCATCTATGAGAGAGTAGTACTGGGT 59.669 42.308 7.76 0.00 37.70 4.51
2212 2309 6.774673 TCATCTATGAGAGAGTAGTACTGGG 58.225 44.000 7.76 0.00 37.70 4.45
2227 2324 7.148188 GGTTTCTTGCAATTGACTCATCTATGA 60.148 37.037 10.34 0.00 35.16 2.15
2228 2325 6.971184 GGTTTCTTGCAATTGACTCATCTATG 59.029 38.462 10.34 0.00 0.00 2.23
2229 2326 6.660521 TGGTTTCTTGCAATTGACTCATCTAT 59.339 34.615 10.34 0.00 0.00 1.98
2230 2327 6.003326 TGGTTTCTTGCAATTGACTCATCTA 58.997 36.000 10.34 0.00 0.00 1.98
2231 2328 4.828939 TGGTTTCTTGCAATTGACTCATCT 59.171 37.500 10.34 0.00 0.00 2.90
2232 2329 4.919754 GTGGTTTCTTGCAATTGACTCATC 59.080 41.667 10.34 0.00 0.00 2.92
2233 2330 4.262164 GGTGGTTTCTTGCAATTGACTCAT 60.262 41.667 10.34 0.00 0.00 2.90
2234 2331 3.068024 GGTGGTTTCTTGCAATTGACTCA 59.932 43.478 10.34 0.00 0.00 3.41
2266 2363 4.373156 AGTGATTTCCTGCAAACCTAGT 57.627 40.909 0.00 0.00 0.00 2.57
2279 2376 6.882458 ACGGATTAACGAGTTAGTGATTTC 57.118 37.500 0.00 0.00 37.61 2.17
2283 2380 3.922240 GCAACGGATTAACGAGTTAGTGA 59.078 43.478 0.00 0.00 37.61 3.41
2287 2384 4.177165 TCTGCAACGGATTAACGAGTTA 57.823 40.909 0.00 0.00 37.61 2.24
2322 2419 5.635549 GCTTTTTGCAACGACTTAACAAT 57.364 34.783 0.00 0.00 42.31 2.71
2333 2430 8.475132 AATCATCTGATCAGTGCTTTTTGCAAC 61.475 37.037 21.92 0.00 43.18 4.17
2352 2449 5.901276 AGTGATTAAATGGGCCAAATCATCT 59.099 36.000 26.53 22.03 39.70 2.90
2383 2480 3.529734 TCCTTACAATCTGGCCCCATTTA 59.470 43.478 0.00 0.00 0.00 1.40
2386 2483 1.607225 TCCTTACAATCTGGCCCCAT 58.393 50.000 0.00 0.00 0.00 4.00
2464 2563 2.926242 GGTGTTCCACGGGGAGGA 60.926 66.667 6.46 0.00 46.01 3.71
2483 2583 4.821589 GGCACCTCGGCGGAAGAG 62.822 72.222 7.21 0.00 36.31 2.85
2499 2599 2.279985 ATCGCGAGCATGCAGAGG 60.280 61.111 21.98 6.48 34.15 3.69
2501 2601 3.267118 GCATCGCGAGCATGCAGA 61.267 61.111 24.15 13.57 41.26 4.26
2502 2602 2.697250 GAAGCATCGCGAGCATGCAG 62.697 60.000 28.81 14.56 42.83 4.41
2503 2603 2.816360 GAAGCATCGCGAGCATGCA 61.816 57.895 28.81 0.00 42.83 3.96
2506 2606 2.532256 GCAGAAGCATCGCGAGCAT 61.532 57.895 25.12 17.24 41.58 3.79
2507 2607 3.190849 GCAGAAGCATCGCGAGCA 61.191 61.111 25.12 0.88 41.58 4.26
2508 2608 4.276739 CGCAGAAGCATCGCGAGC 62.277 66.667 16.66 17.94 45.06 5.03
2509 2609 4.276739 GCGCAGAAGCATCGCGAG 62.277 66.667 24.37 8.11 45.06 5.03
2551 2651 2.887568 GCGTCATCCTGTCCGCAG 60.888 66.667 0.00 0.00 45.12 5.18
2553 2653 2.583593 GAGCGTCATCCTGTCCGC 60.584 66.667 0.00 0.00 46.07 5.54
2554 2654 0.803768 CTTGAGCGTCATCCTGTCCG 60.804 60.000 0.00 0.00 0.00 4.79
2555 2655 1.086634 GCTTGAGCGTCATCCTGTCC 61.087 60.000 0.00 0.00 0.00 4.02
2556 2656 2.378028 GCTTGAGCGTCATCCTGTC 58.622 57.895 0.00 0.00 0.00 3.51
2557 2657 4.606071 GCTTGAGCGTCATCCTGT 57.394 55.556 0.00 0.00 0.00 4.00
2596 2696 4.659172 TTGGCCTGGGGTTCTGCG 62.659 66.667 3.32 0.00 0.00 5.18
2597 2697 2.677875 CTTGGCCTGGGGTTCTGC 60.678 66.667 3.32 0.00 0.00 4.26
2598 2698 2.036256 CCTTGGCCTGGGGTTCTG 59.964 66.667 3.32 0.00 0.00 3.02
2599 2699 2.452491 ACCTTGGCCTGGGGTTCT 60.452 61.111 17.49 0.00 0.00 3.01
2600 2700 2.283173 CACCTTGGCCTGGGGTTC 60.283 66.667 17.49 0.00 0.00 3.62
2601 2701 2.780924 TCACCTTGGCCTGGGGTT 60.781 61.111 15.53 0.00 0.00 4.11
2602 2702 3.580319 GTCACCTTGGCCTGGGGT 61.580 66.667 15.53 12.13 0.00 4.95
2603 2703 4.722700 CGTCACCTTGGCCTGGGG 62.723 72.222 17.49 14.36 0.00 4.96
2632 2753 2.355126 ATGCTCCGTATCTGCGCG 60.355 61.111 0.00 0.00 0.00 6.86
2633 2754 2.368105 CGATGCTCCGTATCTGCGC 61.368 63.158 0.00 0.00 0.00 6.09
2637 2758 2.920645 CGCCCGATGCTCCGTATCT 61.921 63.158 0.00 0.00 38.05 1.98
2639 2760 4.664677 GCGCCCGATGCTCCGTAT 62.665 66.667 0.00 0.00 38.05 3.06
2657 2778 4.982701 GCACAGGCACTTGGGGCT 62.983 66.667 0.00 0.00 45.66 5.19
2676 2797 4.758251 TGCTGGACGGCATGACGG 62.758 66.667 27.41 8.39 37.29 4.79
2677 2798 3.490759 GTGCTGGACGGCATGACG 61.491 66.667 21.98 21.98 44.34 4.35
2678 2799 3.127533 GGTGCTGGACGGCATGAC 61.128 66.667 9.28 0.00 44.34 3.06
2679 2800 4.758251 CGGTGCTGGACGGCATGA 62.758 66.667 9.28 0.00 44.34 3.07
2702 2823 3.730761 GTGCTTGACGCCAGCCTG 61.731 66.667 0.00 0.00 38.05 4.85
2711 2832 4.166011 GGCGATGGCGTGCTTGAC 62.166 66.667 0.00 0.00 41.24 3.18
2712 2833 3.974835 ATGGCGATGGCGTGCTTGA 62.975 57.895 0.00 0.00 41.24 3.02
2714 2835 3.511595 CATGGCGATGGCGTGCTT 61.512 61.111 0.00 0.00 38.22 3.91
2716 2884 4.241999 GTCATGGCGATGGCGTGC 62.242 66.667 8.98 0.56 43.44 5.34
2718 2886 3.405093 ATGGTCATGGCGATGGCGT 62.405 57.895 8.98 0.00 41.24 5.68
2720 2888 2.263741 GGATGGTCATGGCGATGGC 61.264 63.158 8.98 6.83 38.90 4.40
2723 2891 1.644437 TTGGGGATGGTCATGGCGAT 61.644 55.000 0.00 0.00 0.00 4.58
2724 2892 2.269520 CTTGGGGATGGTCATGGCGA 62.270 60.000 0.00 0.00 0.00 5.54
2729 2897 0.680921 CAACGCTTGGGGATGGTCAT 60.681 55.000 0.00 0.00 0.00 3.06
2731 2899 1.303317 ACAACGCTTGGGGATGGTC 60.303 57.895 3.42 0.00 34.12 4.02
2733 2901 2.993471 GCACAACGCTTGGGGATGG 61.993 63.158 2.87 0.00 37.77 3.51
2753 2921 4.875713 GATGGGGCGGTTGGCGAT 62.876 66.667 0.00 0.00 44.92 4.58
2764 2932 1.508632 CGTATTTGTAGCCGATGGGG 58.491 55.000 0.00 0.00 39.58 4.96
2765 2933 1.508632 CCGTATTTGTAGCCGATGGG 58.491 55.000 0.00 0.00 0.00 4.00
2766 2934 0.865769 GCCGTATTTGTAGCCGATGG 59.134 55.000 0.00 0.00 0.00 3.51
2768 2936 3.300711 GGCCGTATTTGTAGCCGAT 57.699 52.632 0.00 0.00 35.30 4.18
2772 2940 2.543641 ACTTACGGCCGTATTTGTAGC 58.456 47.619 36.67 0.00 0.00 3.58
2773 2941 6.833342 ATAAACTTACGGCCGTATTTGTAG 57.167 37.500 36.67 30.24 0.00 2.74
2774 2942 7.978975 ACTAATAAACTTACGGCCGTATTTGTA 59.021 33.333 36.67 24.64 0.00 2.41
2776 2944 7.237920 ACTAATAAACTTACGGCCGTATTTG 57.762 36.000 36.67 27.53 0.00 2.32
2777 2945 7.765819 AGAACTAATAAACTTACGGCCGTATTT 59.234 33.333 36.67 32.52 0.00 1.40
2780 2948 6.035843 CAGAACTAATAAACTTACGGCCGTA 58.964 40.000 33.45 33.45 0.00 4.02
2781 2949 4.866486 CAGAACTAATAAACTTACGGCCGT 59.134 41.667 36.01 36.01 0.00 5.68
2782 2950 5.104374 TCAGAACTAATAAACTTACGGCCG 58.896 41.667 26.86 26.86 0.00 6.13
2785 2953 9.420551 AGAAGTTCAGAACTAATAAACTTACGG 57.579 33.333 16.46 0.00 41.91 4.02
2792 2960 9.155975 GAGCATCAGAAGTTCAGAACTAATAAA 57.844 33.333 16.46 2.47 36.22 1.40
2793 2961 7.489435 CGAGCATCAGAAGTTCAGAACTAATAA 59.511 37.037 16.46 3.83 36.22 1.40
2794 2962 6.975197 CGAGCATCAGAAGTTCAGAACTAATA 59.025 38.462 16.46 3.46 36.22 0.98
2795 2963 5.809562 CGAGCATCAGAAGTTCAGAACTAAT 59.190 40.000 16.46 5.37 36.22 1.73
2796 2964 5.164233 CGAGCATCAGAAGTTCAGAACTAA 58.836 41.667 16.46 3.49 36.22 2.24
2797 2965 4.380973 CCGAGCATCAGAAGTTCAGAACTA 60.381 45.833 16.46 0.93 36.22 2.24
2798 2966 3.583806 CGAGCATCAGAAGTTCAGAACT 58.416 45.455 10.27 10.27 38.21 3.01
2799 2967 2.670414 CCGAGCATCAGAAGTTCAGAAC 59.330 50.000 5.00 5.00 33.17 3.01
2800 2968 2.300152 ACCGAGCATCAGAAGTTCAGAA 59.700 45.455 5.50 0.00 33.17 3.02
2801 2969 1.895798 ACCGAGCATCAGAAGTTCAGA 59.104 47.619 5.50 2.64 33.17 3.27
2802 2970 2.266554 GACCGAGCATCAGAAGTTCAG 58.733 52.381 5.50 0.00 33.17 3.02
2803 2971 1.402852 CGACCGAGCATCAGAAGTTCA 60.403 52.381 5.50 0.00 33.17 3.18
2804 2972 1.272781 CGACCGAGCATCAGAAGTTC 58.727 55.000 0.00 0.00 33.17 3.01
2806 2974 0.603569 AACGACCGAGCATCAGAAGT 59.396 50.000 0.00 0.00 33.17 3.01
2807 2975 1.656095 GAAACGACCGAGCATCAGAAG 59.344 52.381 0.00 0.00 33.17 2.85
2808 2976 1.671850 GGAAACGACCGAGCATCAGAA 60.672 52.381 0.00 0.00 33.17 3.02
2809 2977 0.108804 GGAAACGACCGAGCATCAGA 60.109 55.000 0.00 0.00 33.17 3.27
2810 2978 0.108615 AGGAAACGACCGAGCATCAG 60.109 55.000 0.00 0.00 33.17 2.90
2814 2985 1.289066 CAGAGGAAACGACCGAGCA 59.711 57.895 0.00 0.00 34.73 4.26
2816 2987 1.467713 GCTACAGAGGAAACGACCGAG 60.468 57.143 0.00 0.00 34.73 4.63
2817 2988 0.524862 GCTACAGAGGAAACGACCGA 59.475 55.000 0.00 0.00 34.73 4.69
2821 2992 2.891580 AGAGTTGCTACAGAGGAAACGA 59.108 45.455 0.13 0.00 34.43 3.85
2822 2993 2.989840 CAGAGTTGCTACAGAGGAAACG 59.010 50.000 0.13 0.00 34.43 3.60
2829 3000 2.300152 CAAGGGACAGAGTTGCTACAGA 59.700 50.000 0.13 0.00 0.00 3.41
2830 3001 2.613977 CCAAGGGACAGAGTTGCTACAG 60.614 54.545 0.13 0.00 0.00 2.74
2832 3003 1.623811 TCCAAGGGACAGAGTTGCTAC 59.376 52.381 0.00 0.00 0.00 3.58
2833 3004 1.902508 CTCCAAGGGACAGAGTTGCTA 59.097 52.381 0.00 0.00 0.00 3.49
2834 3005 0.689623 CTCCAAGGGACAGAGTTGCT 59.310 55.000 0.00 0.00 0.00 3.91
2835 3006 0.957888 GCTCCAAGGGACAGAGTTGC 60.958 60.000 0.00 0.00 0.00 4.17
2836 3007 0.322008 GGCTCCAAGGGACAGAGTTG 60.322 60.000 0.00 0.00 0.00 3.16
2837 3008 0.768221 TGGCTCCAAGGGACAGAGTT 60.768 55.000 0.00 0.00 0.00 3.01
2838 3009 0.548682 ATGGCTCCAAGGGACAGAGT 60.549 55.000 0.00 0.00 0.00 3.24
2839 3010 0.179936 GATGGCTCCAAGGGACAGAG 59.820 60.000 0.00 0.00 0.00 3.35
2840 3011 1.617018 CGATGGCTCCAAGGGACAGA 61.617 60.000 0.00 0.00 0.00 3.41
2841 3012 1.153289 CGATGGCTCCAAGGGACAG 60.153 63.158 0.00 0.00 0.00 3.51
2842 3013 1.899437 GACGATGGCTCCAAGGGACA 61.899 60.000 0.00 0.00 0.00 4.02
2843 3014 1.153349 GACGATGGCTCCAAGGGAC 60.153 63.158 0.00 0.00 0.00 4.46
2844 3015 0.982852 ATGACGATGGCTCCAAGGGA 60.983 55.000 0.00 0.00 0.00 4.20
2846 3017 1.402968 CAAATGACGATGGCTCCAAGG 59.597 52.381 0.00 0.00 0.00 3.61
2848 3019 0.810648 GCAAATGACGATGGCTCCAA 59.189 50.000 0.00 0.00 0.00 3.53
2850 3021 1.098050 AAGCAAATGACGATGGCTCC 58.902 50.000 0.00 0.00 32.84 4.70
2853 3024 0.994263 GCAAAGCAAATGACGATGGC 59.006 50.000 0.00 0.00 0.00 4.40
2854 3025 2.163010 AGAGCAAAGCAAATGACGATGG 59.837 45.455 0.00 0.00 0.00 3.51
2855 3026 3.168963 CAGAGCAAAGCAAATGACGATG 58.831 45.455 0.00 0.00 0.00 3.84
2857 3028 1.069022 GCAGAGCAAAGCAAATGACGA 60.069 47.619 0.00 0.00 0.00 4.20
2858 3029 1.068748 AGCAGAGCAAAGCAAATGACG 60.069 47.619 0.00 0.00 0.00 4.35
2860 3031 3.738830 AAAGCAGAGCAAAGCAAATGA 57.261 38.095 0.00 0.00 0.00 2.57
2861 3032 3.558418 ACAAAAGCAGAGCAAAGCAAATG 59.442 39.130 0.00 0.00 0.00 2.32
2862 3033 3.800531 ACAAAAGCAGAGCAAAGCAAAT 58.199 36.364 0.00 0.00 0.00 2.32
2863 3034 3.249986 ACAAAAGCAGAGCAAAGCAAA 57.750 38.095 0.00 0.00 0.00 3.68
2864 3035 2.931325 CAACAAAAGCAGAGCAAAGCAA 59.069 40.909 0.00 0.00 0.00 3.91
2865 3036 2.094078 ACAACAAAAGCAGAGCAAAGCA 60.094 40.909 0.00 0.00 0.00 3.91
2866 3037 2.283351 CACAACAAAAGCAGAGCAAAGC 59.717 45.455 0.00 0.00 0.00 3.51
2867 3038 2.283351 GCACAACAAAAGCAGAGCAAAG 59.717 45.455 0.00 0.00 0.00 2.77
2868 3039 2.270047 GCACAACAAAAGCAGAGCAAA 58.730 42.857 0.00 0.00 0.00 3.68
2869 3040 1.204231 TGCACAACAAAAGCAGAGCAA 59.796 42.857 0.00 0.00 33.75 3.91
2870 3041 0.816373 TGCACAACAAAAGCAGAGCA 59.184 45.000 0.00 0.00 33.75 4.26
2877 3048 3.052036 GGTGTATGCTGCACAACAAAAG 58.948 45.455 18.00 0.00 38.51 2.27
2879 3050 1.339610 GGGTGTATGCTGCACAACAAA 59.660 47.619 18.00 0.00 35.21 2.83
2880 3051 0.958091 GGGTGTATGCTGCACAACAA 59.042 50.000 18.00 3.96 35.21 2.83
2881 3052 0.110295 AGGGTGTATGCTGCACAACA 59.890 50.000 3.57 10.12 35.21 3.33
2883 3054 1.243342 GCAGGGTGTATGCTGCACAA 61.243 55.000 3.57 0.00 41.89 3.33
2884 3055 1.675310 GCAGGGTGTATGCTGCACA 60.675 57.895 3.57 0.00 41.89 4.57
2885 3056 2.409870 GGCAGGGTGTATGCTGCAC 61.410 63.158 3.57 0.00 43.84 4.57
2886 3057 2.045045 GGCAGGGTGTATGCTGCA 60.045 61.111 4.13 4.13 43.84 4.41
2888 3059 0.107066 TCATGGCAGGGTGTATGCTG 60.107 55.000 0.00 0.00 43.35 4.41
2889 3060 0.182061 CTCATGGCAGGGTGTATGCT 59.818 55.000 0.00 0.00 43.35 3.79
2891 3062 0.839277 TCCTCATGGCAGGGTGTATG 59.161 55.000 0.00 0.00 33.81 2.39
2892 3063 1.135094 CTCCTCATGGCAGGGTGTAT 58.865 55.000 0.00 0.00 33.81 2.29
2893 3064 1.626356 GCTCCTCATGGCAGGGTGTA 61.626 60.000 0.00 0.00 33.81 2.90
2895 3066 2.124403 GCTCCTCATGGCAGGGTG 60.124 66.667 0.00 0.73 33.81 4.61
2896 3067 2.611800 TGCTCCTCATGGCAGGGT 60.612 61.111 0.00 0.00 33.81 4.34
2900 3080 3.040206 GCCTCTGCTCCTCATGGCA 62.040 63.158 0.00 0.00 41.12 4.92
2902 3082 1.153208 GTGCCTCTGCTCCTCATGG 60.153 63.158 0.00 0.00 38.71 3.66
2930 3110 1.639298 GAGGTTGGTAAGCAGCGCAG 61.639 60.000 11.47 1.31 0.00 5.18
2932 3112 0.955919 AAGAGGTTGGTAAGCAGCGC 60.956 55.000 0.00 0.00 0.00 5.92
2933 3113 1.079503 GAAGAGGTTGGTAAGCAGCG 58.920 55.000 0.00 0.00 0.00 5.18
2934 3114 2.027653 AGAGAAGAGGTTGGTAAGCAGC 60.028 50.000 0.00 0.00 0.00 5.25
2936 3116 3.239449 TCAGAGAAGAGGTTGGTAAGCA 58.761 45.455 0.00 0.00 0.00 3.91


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

AutoCloner maintained by Alex Coulton.