Multiple sequence alignment - TraesCS6B01G044000

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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 TraesCS6B01G044000 chr6B 100.000 3530 0 0 1 3530 26590111 26593640 0.000000e+00 6519.0
1 TraesCS6B01G044000 chr6B 85.530 1707 224 12 867 2563 26597908 26596215 0.000000e+00 1762.0
2 TraesCS6B01G044000 chr6D 92.121 3503 170 34 1 3429 14617716 14621186 0.000000e+00 4843.0
3 TraesCS6B01G044000 chr6D 85.806 1705 219 12 867 2562 14626116 14624426 0.000000e+00 1786.0
4 TraesCS6B01G044000 chr6D 87.095 1480 189 2 1045 2523 14632947 14631469 0.000000e+00 1674.0
5 TraesCS6B01G044000 chr6D 85.651 1582 214 13 1046 2622 14680736 14679163 0.000000e+00 1652.0
6 TraesCS6B01G044000 chr6D 86.133 1536 204 6 997 2531 14656592 14655065 0.000000e+00 1648.0
7 TraesCS6B01G044000 chr6D 98.039 51 1 0 3427 3477 14621880 14621930 4.850000e-14 89.8
8 TraesCS6B01G044000 chr6A 93.128 2270 120 9 654 2898 15782991 15780733 0.000000e+00 3295.0
9 TraesCS6B01G044000 chr6A 85.567 1746 222 16 867 2596 15765850 15767581 0.000000e+00 1801.0
10 TraesCS6B01G044000 chr6A 86.224 1626 207 15 1001 2622 15727844 15729456 0.000000e+00 1746.0
11 TraesCS6B01G044000 chr6A 89.984 629 51 7 2 621 15783610 15782985 0.000000e+00 802.0
12 TraesCS6B01G044000 chr3B 88.136 118 13 1 3316 3432 585835059 585835176 4.750000e-29 139.0
13 TraesCS6B01G044000 chr1A 90.000 100 10 0 3333 3432 53671045 53670946 2.860000e-26 130.0
14 TraesCS6B01G044000 chr2A 89.320 103 10 1 3332 3433 758430494 758430392 1.030000e-25 128.0
15 TraesCS6B01G044000 chr2A 87.629 97 12 0 3333 3429 207335554 207335650 2.880000e-21 113.0
16 TraesCS6B01G044000 chr7D 91.860 86 7 0 3344 3429 58136144 58136229 1.720000e-23 121.0
17 TraesCS6B01G044000 chr5D 84.685 111 17 0 3317 3427 377173545 377173435 1.040000e-20 111.0
18 TraesCS6B01G044000 chr5D 86.869 99 12 1 3335 3432 414106729 414106631 3.730000e-20 110.0
19 TraesCS6B01G044000 chr2D 84.694 98 15 0 3332 3429 537928103 537928200 8.060000e-17 99.0


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 TraesCS6B01G044000 chr6B 26590111 26593640 3529 False 6519.0 6519 100.000 1 3530 1 chr6B.!!$F1 3529
1 TraesCS6B01G044000 chr6B 26596215 26597908 1693 True 1762.0 1762 85.530 867 2563 1 chr6B.!!$R1 1696
2 TraesCS6B01G044000 chr6D 14617716 14621930 4214 False 2466.4 4843 95.080 1 3477 2 chr6D.!!$F1 3476
3 TraesCS6B01G044000 chr6D 14624426 14626116 1690 True 1786.0 1786 85.806 867 2562 1 chr6D.!!$R1 1695
4 TraesCS6B01G044000 chr6D 14631469 14632947 1478 True 1674.0 1674 87.095 1045 2523 1 chr6D.!!$R2 1478
5 TraesCS6B01G044000 chr6D 14679163 14680736 1573 True 1652.0 1652 85.651 1046 2622 1 chr6D.!!$R4 1576
6 TraesCS6B01G044000 chr6D 14655065 14656592 1527 True 1648.0 1648 86.133 997 2531 1 chr6D.!!$R3 1534
7 TraesCS6B01G044000 chr6A 15780733 15783610 2877 True 2048.5 3295 91.556 2 2898 2 chr6A.!!$R1 2896
8 TraesCS6B01G044000 chr6A 15765850 15767581 1731 False 1801.0 1801 85.567 867 2596 1 chr6A.!!$F2 1729
9 TraesCS6B01G044000 chr6A 15727844 15729456 1612 False 1746.0 1746 86.224 1001 2622 1 chr6A.!!$F1 1621

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
916 965 0.457166 CATCAACACCAGCGCCATTG 60.457 55.0 2.29 0.0 0.0 2.82 F
1314 1363 0.467384 CCATCTGCGATCTCCTTGGT 59.533 55.0 0.00 0.0 0.0 3.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2250 2299 3.015145 TACTCAAGCCCCCTGCCC 61.015 66.667 0.0 0.0 42.71 5.36 R
3312 3434 2.614057 CCGTTGGTGATGAATAGAAGGC 59.386 50.000 0.0 0.0 0.00 4.35 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
55 56 6.515272 AGTCATTTCGCCATAGTTGAATTT 57.485 33.333 0.00 0.00 0.00 1.82
108 109 7.573710 ACCACCACATTCAACTATATACACAT 58.426 34.615 0.00 0.00 0.00 3.21
112 113 8.439971 ACCACATTCAACTATATACACATGGAT 58.560 33.333 0.00 0.00 0.00 3.41
143 144 4.142780 GCTAGGCGGAATTCACCC 57.857 61.111 7.93 6.65 0.00 4.61
193 194 7.479916 CGCAGACTCAAATCTAACTCAAATTTC 59.520 37.037 0.00 0.00 0.00 2.17
219 220 8.985694 CGCTACTAACTGAATTTCGTAAAAATG 58.014 33.333 0.00 0.00 0.00 2.32
227 228 8.564574 ACTGAATTTCGTAAAAATGTGCTTAGA 58.435 29.630 0.00 0.00 0.00 2.10
272 278 3.587061 TCAACCCATGTGAACAGTATCCT 59.413 43.478 0.00 0.00 0.00 3.24
273 279 3.634397 ACCCATGTGAACAGTATCCTG 57.366 47.619 0.00 0.00 44.68 3.86
283 289 7.112122 TGTGAACAGTATCCTGCATTAATTCT 58.888 34.615 0.00 0.00 42.81 2.40
395 404 0.893270 CCGGCACCCAAGTCAATGAA 60.893 55.000 0.00 0.00 0.00 2.57
405 414 2.029838 AGTCAATGAACGCTGGATCC 57.970 50.000 4.20 4.20 0.00 3.36
406 415 1.278985 AGTCAATGAACGCTGGATCCA 59.721 47.619 15.27 15.27 0.00 3.41
512 522 4.708968 CGGCGGCGAGGATCTAGC 62.709 72.222 29.19 0.00 0.00 3.42
578 588 2.859165 TTCAACGCTCTCCAAAGGAT 57.141 45.000 0.00 0.00 0.00 3.24
605 615 3.119352 CCAGATTAAGCCAAAACTGGAGC 60.119 47.826 15.87 0.00 42.44 4.70
652 662 4.488770 TCCCTCCCTTAATTGCTTTGTTT 58.511 39.130 0.00 0.00 0.00 2.83
697 707 4.635765 TGCAATGCACAGGACTAGTTTATC 59.364 41.667 2.72 0.00 31.71 1.75
717 727 1.668337 CGAATCTGCGCTGCTAGCTAT 60.668 52.381 17.23 0.00 39.60 2.97
770 780 1.532604 GGCCAGGTTGCTGGTTAACC 61.533 60.000 18.27 18.27 45.87 2.85
907 956 2.821378 CAGATCCAAAGCATCAACACCA 59.179 45.455 0.00 0.00 0.00 4.17
908 957 3.087031 AGATCCAAAGCATCAACACCAG 58.913 45.455 0.00 0.00 0.00 4.00
909 958 0.961019 TCCAAAGCATCAACACCAGC 59.039 50.000 0.00 0.00 0.00 4.85
912 961 2.146073 AAAGCATCAACACCAGCGCC 62.146 55.000 2.29 0.00 0.00 6.53
913 962 3.364441 GCATCAACACCAGCGCCA 61.364 61.111 2.29 0.00 0.00 5.69
914 963 2.703798 GCATCAACACCAGCGCCAT 61.704 57.895 2.29 0.00 0.00 4.40
915 964 1.885157 CATCAACACCAGCGCCATT 59.115 52.632 2.29 0.00 0.00 3.16
916 965 0.457166 CATCAACACCAGCGCCATTG 60.457 55.000 2.29 0.00 0.00 2.82
917 966 2.216750 ATCAACACCAGCGCCATTGC 62.217 55.000 2.29 0.00 0.00 3.56
918 967 2.911509 AACACCAGCGCCATTGCA 60.912 55.556 2.29 0.00 37.32 4.08
919 968 2.497173 AACACCAGCGCCATTGCAA 61.497 52.632 2.29 0.00 37.32 4.08
920 969 2.126228 CACCAGCGCCATTGCAAG 60.126 61.111 2.29 0.00 37.32 4.01
921 970 4.060038 ACCAGCGCCATTGCAAGC 62.060 61.111 2.29 2.55 37.32 4.01
922 971 3.755628 CCAGCGCCATTGCAAGCT 61.756 61.111 2.29 5.07 41.07 3.74
923 972 2.202570 CAGCGCCATTGCAAGCTC 60.203 61.111 2.29 0.00 37.94 4.09
1314 1363 0.467384 CCATCTGCGATCTCCTTGGT 59.533 55.000 0.00 0.00 0.00 3.67
1389 1438 1.319614 TGTCCCTCATCGACGATGCA 61.320 55.000 28.87 18.96 39.63 3.96
1632 1681 2.750237 GCCTACTTTGTGCCGGGG 60.750 66.667 2.18 0.00 0.00 5.73
1936 1985 3.426117 AACATCGTCGCTAGGCCCG 62.426 63.158 0.00 0.00 0.00 6.13
2199 2248 0.606673 GTGGAGCTGGTGGGAACTTC 60.607 60.000 0.00 0.00 0.00 3.01
2226 2275 1.615392 GGGCTGACACAATTGCTCTTT 59.385 47.619 5.05 0.00 0.00 2.52
2250 2299 1.671850 ACTTCGTCCAAGTATGGCACG 60.672 52.381 11.17 11.17 44.13 5.34
2775 2838 4.212636 ACGTCGGTTCCAAAGTTAAATGAG 59.787 41.667 0.00 0.00 0.00 2.90
2782 2845 6.420903 GGTTCCAAAGTTAAATGAGCAGTTTC 59.579 38.462 0.00 0.00 0.00 2.78
2971 3061 6.014584 ACATGTCCATGACAGTAGTAAAGACA 60.015 38.462 13.93 0.00 46.04 3.41
2996 3086 7.919313 TCGACGAAATGATTTAGTACATACC 57.081 36.000 3.66 0.00 0.00 2.73
3018 3108 6.277605 ACCAGTAAACTGTAAAATGTTTGGC 58.722 36.000 9.17 0.00 42.27 4.52
3029 3140 5.687770 AAAATGTTTGGCTGCAAATAACC 57.312 34.783 0.50 0.00 0.00 2.85
3042 3153 6.682611 GCTGCAAATAACCCAATGCATACTTA 60.683 38.462 0.00 0.00 46.59 2.24
3057 3168 5.053145 GCATACTTAAGGTGGATGTCTCAG 58.947 45.833 7.53 0.00 0.00 3.35
3072 3183 7.343057 TGGATGTCTCAGTGTAAGACTATTCAT 59.657 37.037 11.93 0.00 42.93 2.57
3098 3209 8.196771 TGTACTTGTGCATCTTCAAAATTTCTT 58.803 29.630 0.00 0.00 0.00 2.52
3122 3233 7.664082 TGAAAAGTTTGAAGACATGCAAAAA 57.336 28.000 0.00 0.00 35.95 1.94
3147 3259 9.558396 AATTTGTTCAAATATCCTTGCAGAAAA 57.442 25.926 10.54 0.00 0.00 2.29
3191 3303 7.095695 AGTGTTATTGCAACTAGTTGTGTTT 57.904 32.000 30.90 18.22 42.31 2.83
3231 3343 9.651913 AATTTAACCATCGTTTTGCAAGATAAT 57.348 25.926 0.00 0.00 33.17 1.28
3276 3398 6.015434 GTGTATCTTTTGTCCCTCAACCATTT 60.015 38.462 0.00 0.00 35.61 2.32
3287 3409 1.002251 TCAACCATTTTTCGTCACCGC 60.002 47.619 0.00 0.00 0.00 5.68
3300 3422 2.740580 CGTCACCGCCAACTACCAATAT 60.741 50.000 0.00 0.00 0.00 1.28
3309 3431 5.050091 CGCCAACTACCAATATTGTCTGATC 60.050 44.000 14.25 0.00 0.00 2.92
3310 3432 6.058183 GCCAACTACCAATATTGTCTGATCT 58.942 40.000 14.25 0.00 0.00 2.75
3312 3434 7.386299 GCCAACTACCAATATTGTCTGATCTAG 59.614 40.741 14.25 0.00 0.00 2.43
3313 3435 7.386299 CCAACTACCAATATTGTCTGATCTAGC 59.614 40.741 14.25 0.00 0.00 3.42
3319 3441 7.510685 ACCAATATTGTCTGATCTAGCCTTCTA 59.489 37.037 14.25 0.00 0.00 2.10
3326 3448 6.779539 TGTCTGATCTAGCCTTCTATTCATCA 59.220 38.462 0.00 0.00 0.00 3.07
3327 3449 7.090173 GTCTGATCTAGCCTTCTATTCATCAC 58.910 42.308 0.00 0.00 0.00 3.06
3329 3451 5.840693 TGATCTAGCCTTCTATTCATCACCA 59.159 40.000 0.00 0.00 0.00 4.17
3330 3452 6.327365 TGATCTAGCCTTCTATTCATCACCAA 59.673 38.462 0.00 0.00 0.00 3.67
3334 3456 3.873910 CCTTCTATTCATCACCAACGGT 58.126 45.455 0.00 0.00 35.62 4.83
3343 3465 1.178276 TCACCAACGGTTGCTGTTTT 58.822 45.000 15.31 0.00 31.02 2.43
3345 3467 0.174617 ACCAACGGTTGCTGTTTTGG 59.825 50.000 15.31 2.56 42.15 3.28
3361 3483 0.251634 TTGGTGCGCTGGTCATATGA 59.748 50.000 9.73 0.00 0.00 2.15
3362 3484 0.179076 TGGTGCGCTGGTCATATGAG 60.179 55.000 9.73 0.00 0.00 2.90
3383 3505 0.389948 CCTTAGCACGGCGACTTCTT 60.390 55.000 16.62 0.00 0.00 2.52
3386 3508 0.388134 TAGCACGGCGACTTCTTGAC 60.388 55.000 16.62 0.00 0.00 3.18
3388 3510 0.388134 GCACGGCGACTTCTTGACTA 60.388 55.000 16.62 0.00 0.00 2.59
3395 3517 4.553156 CGGCGACTTCTTGACTATCTACTC 60.553 50.000 0.00 0.00 0.00 2.59
3477 4295 4.935352 ATGTTTGGTGAAGCTAGCAAAA 57.065 36.364 18.83 4.74 45.95 2.44
3478 4296 4.727507 TGTTTGGTGAAGCTAGCAAAAA 57.272 36.364 18.83 7.51 45.95 1.94
3479 4297 5.275067 TGTTTGGTGAAGCTAGCAAAAAT 57.725 34.783 18.83 0.00 45.95 1.82
3480 4298 6.398234 TGTTTGGTGAAGCTAGCAAAAATA 57.602 33.333 18.83 3.73 45.95 1.40
3481 4299 6.991938 TGTTTGGTGAAGCTAGCAAAAATAT 58.008 32.000 18.83 0.00 45.95 1.28
3482 4300 7.090173 TGTTTGGTGAAGCTAGCAAAAATATC 58.910 34.615 18.83 3.97 45.95 1.63
3483 4301 6.832520 TTGGTGAAGCTAGCAAAAATATCA 57.167 33.333 18.83 6.48 35.36 2.15
3484 4302 6.441093 TGGTGAAGCTAGCAAAAATATCAG 57.559 37.500 18.83 0.00 0.00 2.90
3485 4303 5.163622 TGGTGAAGCTAGCAAAAATATCAGC 60.164 40.000 18.83 16.64 35.32 4.26
3486 4304 5.277047 GTGAAGCTAGCAAAAATATCAGCC 58.723 41.667 18.83 0.00 0.00 4.85
3487 4305 5.067023 GTGAAGCTAGCAAAAATATCAGCCT 59.933 40.000 18.83 0.00 0.00 4.58
3488 4306 5.653769 TGAAGCTAGCAAAAATATCAGCCTT 59.346 36.000 18.83 0.00 0.00 4.35
3489 4307 6.828273 TGAAGCTAGCAAAAATATCAGCCTTA 59.172 34.615 18.83 0.00 0.00 2.69
3490 4308 7.503566 TGAAGCTAGCAAAAATATCAGCCTTAT 59.496 33.333 18.83 0.00 0.00 1.73
3491 4309 7.446001 AGCTAGCAAAAATATCAGCCTTATC 57.554 36.000 18.83 0.00 0.00 1.75
3492 4310 7.230027 AGCTAGCAAAAATATCAGCCTTATCT 58.770 34.615 18.83 0.00 0.00 1.98
3493 4311 7.723172 AGCTAGCAAAAATATCAGCCTTATCTT 59.277 33.333 18.83 0.00 0.00 2.40
3494 4312 7.806960 GCTAGCAAAAATATCAGCCTTATCTTG 59.193 37.037 10.63 0.00 0.00 3.02
3495 4313 6.510536 AGCAAAAATATCAGCCTTATCTTGC 58.489 36.000 0.00 0.00 36.55 4.01
3496 4314 6.323225 AGCAAAAATATCAGCCTTATCTTGCT 59.677 34.615 0.00 0.00 40.53 3.91
3497 4315 6.640092 GCAAAAATATCAGCCTTATCTTGCTC 59.360 38.462 0.00 0.00 35.12 4.26
3498 4316 6.551385 AAAATATCAGCCTTATCTTGCTCG 57.449 37.500 0.00 0.00 35.12 5.03
3499 4317 2.540265 ATCAGCCTTATCTTGCTCGG 57.460 50.000 0.00 0.00 35.12 4.63
3500 4318 1.485124 TCAGCCTTATCTTGCTCGGA 58.515 50.000 0.00 0.00 35.12 4.55
3501 4319 2.042464 TCAGCCTTATCTTGCTCGGAT 58.958 47.619 0.00 0.00 35.12 4.18
3502 4320 3.230976 TCAGCCTTATCTTGCTCGGATA 58.769 45.455 0.00 0.00 35.12 2.59
3503 4321 3.834813 TCAGCCTTATCTTGCTCGGATAT 59.165 43.478 0.00 0.00 35.12 1.63
3504 4322 5.016831 TCAGCCTTATCTTGCTCGGATATA 58.983 41.667 0.00 0.00 35.12 0.86
3505 4323 5.105716 TCAGCCTTATCTTGCTCGGATATAC 60.106 44.000 0.00 0.00 35.12 1.47
3506 4324 4.772624 AGCCTTATCTTGCTCGGATATACA 59.227 41.667 0.00 0.00 30.33 2.29
3507 4325 5.246203 AGCCTTATCTTGCTCGGATATACAA 59.754 40.000 0.00 0.00 30.33 2.41
3508 4326 6.070538 AGCCTTATCTTGCTCGGATATACAAT 60.071 38.462 0.00 0.00 30.33 2.71
3509 4327 6.256757 GCCTTATCTTGCTCGGATATACAATC 59.743 42.308 0.00 0.00 0.00 2.67
3510 4328 7.323420 CCTTATCTTGCTCGGATATACAATCA 58.677 38.462 0.00 0.00 0.00 2.57
3511 4329 7.984050 CCTTATCTTGCTCGGATATACAATCAT 59.016 37.037 0.00 0.00 0.00 2.45
3513 4331 9.803315 TTATCTTGCTCGGATATACAATCATAC 57.197 33.333 0.00 0.00 0.00 2.39
3514 4332 7.227049 TCTTGCTCGGATATACAATCATACA 57.773 36.000 0.00 0.00 0.00 2.29
3515 4333 7.315890 TCTTGCTCGGATATACAATCATACAG 58.684 38.462 0.00 0.00 0.00 2.74
3516 4334 5.965922 TGCTCGGATATACAATCATACAGG 58.034 41.667 0.00 0.00 0.00 4.00
3517 4335 5.714806 TGCTCGGATATACAATCATACAGGA 59.285 40.000 0.00 0.00 0.00 3.86
3518 4336 6.210584 TGCTCGGATATACAATCATACAGGAA 59.789 38.462 0.00 0.00 0.00 3.36
3519 4337 7.097192 GCTCGGATATACAATCATACAGGAAA 58.903 38.462 0.00 0.00 0.00 3.13
3520 4338 7.063544 GCTCGGATATACAATCATACAGGAAAC 59.936 40.741 0.00 0.00 0.00 2.78
3521 4339 7.088272 TCGGATATACAATCATACAGGAAACG 58.912 38.462 0.00 0.00 0.00 3.60
3522 4340 6.866770 CGGATATACAATCATACAGGAAACGT 59.133 38.462 0.00 0.00 0.00 3.99
3523 4341 8.024865 CGGATATACAATCATACAGGAAACGTA 58.975 37.037 0.00 0.00 0.00 3.57
3524 4342 9.136952 GGATATACAATCATACAGGAAACGTAC 57.863 37.037 0.00 0.00 0.00 3.67
3525 4343 9.687210 GATATACAATCATACAGGAAACGTACA 57.313 33.333 0.00 0.00 0.00 2.90
3527 4345 6.903883 ACAATCATACAGGAAACGTACATC 57.096 37.500 0.00 0.00 0.00 3.06
3528 4346 5.815740 ACAATCATACAGGAAACGTACATCC 59.184 40.000 6.81 6.81 35.88 3.51
3529 4347 5.607939 ATCATACAGGAAACGTACATCCA 57.392 39.130 15.01 0.00 38.23 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
86 87 7.801104 TCCATGTGTATATAGTTGAATGTGGT 58.199 34.615 0.00 0.00 0.00 4.16
90 91 7.413328 CGCCATCCATGTGTATATAGTTGAATG 60.413 40.741 0.00 0.00 0.00 2.67
108 109 0.736053 GCGGTAAAAATCGCCATCCA 59.264 50.000 0.00 0.00 45.42 3.41
166 167 3.849911 TGAGTTAGATTTGAGTCTGCGG 58.150 45.455 0.00 0.00 0.00 5.69
193 194 8.985694 CATTTTTACGAAATTCAGTTAGTAGCG 58.014 33.333 0.00 0.00 0.00 4.26
272 278 6.283544 TCTTGATTTGGCAGAATTAATGCA 57.716 33.333 14.99 0.00 45.68 3.96
273 279 6.257193 CCTTCTTGATTTGGCAGAATTAATGC 59.743 38.462 6.58 6.58 43.09 3.56
283 289 1.269448 GTTCGCCTTCTTGATTTGGCA 59.731 47.619 0.00 0.00 45.13 4.92
341 350 3.411446 CTGATCTTTTGTGTGCCCACTA 58.589 45.455 0.00 0.00 42.34 2.74
405 414 3.450152 CGTGACTCGACGCGTGTG 61.450 66.667 20.70 9.54 42.86 3.82
473 483 4.373116 TCCTGCGTCCGTGCCTTC 62.373 66.667 0.00 0.00 0.00 3.46
512 522 5.291905 ACCGATTGTTAAGGGATTCTAGG 57.708 43.478 0.00 0.00 0.00 3.02
605 615 6.439599 ACCGAGTGAGATAGTTGATTAATCG 58.560 40.000 10.80 0.00 0.00 3.34
652 662 5.364778 CACCCTACGGAATCATTCATGTTA 58.635 41.667 0.00 0.00 0.00 2.41
683 693 4.677378 CGCAGATTCGATAAACTAGTCCTG 59.323 45.833 0.00 0.00 0.00 3.86
684 694 4.793353 GCGCAGATTCGATAAACTAGTCCT 60.793 45.833 0.30 0.00 0.00 3.85
697 707 2.926855 GCTAGCAGCGCAGATTCG 59.073 61.111 11.47 0.00 0.00 3.34
717 727 6.234920 TGTAGAAAAGCAATTACAGGTAGCA 58.765 36.000 0.00 0.00 0.00 3.49
773 783 2.911484 AGCCAGTTTCACAGCTATAGC 58.089 47.619 17.33 17.33 42.49 2.97
859 888 3.673809 CGGCGAGGTATTTATAACTGAGC 59.326 47.826 0.00 0.00 32.71 4.26
863 892 4.081807 GGGATCGGCGAGGTATTTATAACT 60.082 45.833 17.22 0.00 31.77 2.24
907 956 3.446570 GGAGCTTGCAATGGCGCT 61.447 61.111 10.39 10.39 45.35 5.92
908 957 2.948840 GATGGAGCTTGCAATGGCGC 62.949 60.000 0.00 0.00 45.35 6.53
909 958 1.065273 GATGGAGCTTGCAATGGCG 59.935 57.895 0.00 0.00 45.35 5.69
912 961 3.204306 TCCTAGATGGAGCTTGCAATG 57.796 47.619 0.00 0.00 40.56 2.82
922 971 0.688749 TGCTGCTGCTCCTAGATGGA 60.689 55.000 17.00 0.00 43.58 3.41
923 972 0.179702 TTGCTGCTGCTCCTAGATGG 59.820 55.000 17.00 0.00 40.48 3.51
1043 1092 1.669115 GGCAGCGAGAACTTGCTCA 60.669 57.895 12.95 0.00 46.96 4.26
1356 1405 0.741221 GGGACATGCAGAAGACGGTC 60.741 60.000 0.00 0.00 0.00 4.79
1389 1438 1.517832 GACGGTGATGTAGCCAGCT 59.482 57.895 0.00 0.00 0.00 4.24
1632 1681 1.534163 CCCATCACGATGTGCATCATC 59.466 52.381 15.25 15.25 46.68 2.92
2250 2299 3.015145 TACTCAAGCCCCCTGCCC 61.015 66.667 0.00 0.00 42.71 5.36
2637 2700 7.506599 TCACTACCCATATATACTCACGGAAAA 59.493 37.037 0.00 0.00 0.00 2.29
2775 2838 3.456280 TGGCAAAACAGATTGAAACTGC 58.544 40.909 2.12 0.00 38.74 4.40
2782 2845 5.984926 ACAAGTACAATGGCAAAACAGATTG 59.015 36.000 0.00 0.00 32.99 2.67
2971 3061 8.139350 TGGTATGTACTAAATCATTTCGTCGAT 58.861 33.333 0.00 0.00 0.00 3.59
3029 3140 4.889409 ACATCCACCTTAAGTATGCATTGG 59.111 41.667 3.54 3.69 0.00 3.16
3042 3153 4.021016 GTCTTACACTGAGACATCCACCTT 60.021 45.833 0.00 0.00 42.38 3.50
3057 3168 7.330946 TGCACAAGTACATGAATAGTCTTACAC 59.669 37.037 4.87 0.00 0.00 2.90
3072 3183 7.715657 AGAAATTTTGAAGATGCACAAGTACA 58.284 30.769 0.00 0.00 0.00 2.90
3098 3209 7.664082 TTTTTGCATGTCTTCAAACTTTTCA 57.336 28.000 0.00 0.00 32.58 2.69
3122 3233 9.558396 TTTTTCTGCAAGGATATTTGAACAAAT 57.442 25.926 15.41 15.41 42.95 2.32
3134 3245 8.358582 AGATAAGTTGATTTTTCTGCAAGGAT 57.641 30.769 0.00 0.00 0.00 3.24
3212 3324 8.633075 AATACAATTATCTTGCAAAACGATGG 57.367 30.769 0.00 0.00 0.00 3.51
3231 3343 8.911918 ATACACTACACTGGACAAAAATACAA 57.088 30.769 0.00 0.00 0.00 2.41
3242 3354 5.279809 GGGACAAAAGATACACTACACTGGA 60.280 44.000 0.00 0.00 0.00 3.86
3287 3409 7.386299 GCTAGATCAGACAATATTGGTAGTTGG 59.614 40.741 19.37 2.53 0.00 3.77
3300 3422 7.288621 TGATGAATAGAAGGCTAGATCAGACAA 59.711 37.037 0.00 0.00 32.94 3.18
3309 3431 4.747108 CGTTGGTGATGAATAGAAGGCTAG 59.253 45.833 0.00 0.00 0.00 3.42
3310 3432 4.442893 CCGTTGGTGATGAATAGAAGGCTA 60.443 45.833 0.00 0.00 0.00 3.93
3312 3434 2.614057 CCGTTGGTGATGAATAGAAGGC 59.386 50.000 0.00 0.00 0.00 4.35
3313 3435 3.873910 ACCGTTGGTGATGAATAGAAGG 58.126 45.455 0.00 0.00 32.98 3.46
3319 3441 1.909700 AGCAACCGTTGGTGATGAAT 58.090 45.000 14.99 0.00 40.37 2.57
3326 3448 0.174617 CCAAAACAGCAACCGTTGGT 59.825 50.000 10.18 10.18 43.12 3.67
3327 3449 0.174617 ACCAAAACAGCAACCGTTGG 59.825 50.000 13.12 0.00 43.60 3.77
3329 3451 0.459411 GCACCAAAACAGCAACCGTT 60.459 50.000 0.00 0.00 0.00 4.44
3330 3452 1.140804 GCACCAAAACAGCAACCGT 59.859 52.632 0.00 0.00 0.00 4.83
3334 3456 1.226916 CAGCGCACCAAAACAGCAA 60.227 52.632 11.47 0.00 0.00 3.91
3343 3465 0.179076 CTCATATGACCAGCGCACCA 60.179 55.000 11.47 1.29 0.00 4.17
3345 3467 1.502163 GCCTCATATGACCAGCGCAC 61.502 60.000 11.47 0.00 0.00 5.34
3376 3498 7.159322 TGTTGGAGTAGATAGTCAAGAAGTC 57.841 40.000 0.00 0.00 0.00 3.01
3383 3505 6.371548 GCAAACATTGTTGGAGTAGATAGTCA 59.628 38.462 8.14 0.00 0.00 3.41
3386 3508 5.066505 GGGCAAACATTGTTGGAGTAGATAG 59.933 44.000 8.14 0.00 0.00 2.08
3388 3510 3.763897 GGGCAAACATTGTTGGAGTAGAT 59.236 43.478 8.14 0.00 0.00 1.98
3395 3517 0.673437 AGTCGGGCAAACATTGTTGG 59.327 50.000 2.13 0.54 0.00 3.77
3477 4295 4.284490 TCCGAGCAAGATAAGGCTGATATT 59.716 41.667 0.00 0.00 41.22 1.28
3478 4296 3.834813 TCCGAGCAAGATAAGGCTGATAT 59.165 43.478 0.00 0.00 41.22 1.63
3479 4297 3.230976 TCCGAGCAAGATAAGGCTGATA 58.769 45.455 0.00 0.00 41.22 2.15
3480 4298 2.042464 TCCGAGCAAGATAAGGCTGAT 58.958 47.619 0.00 0.00 41.22 2.90
3481 4299 1.485124 TCCGAGCAAGATAAGGCTGA 58.515 50.000 0.00 0.00 41.22 4.26
3482 4300 2.540265 ATCCGAGCAAGATAAGGCTG 57.460 50.000 0.00 0.00 41.22 4.85
3483 4301 4.772624 TGTATATCCGAGCAAGATAAGGCT 59.227 41.667 0.00 0.00 44.48 4.58
3484 4302 5.073311 TGTATATCCGAGCAAGATAAGGC 57.927 43.478 0.00 0.00 30.31 4.35
3485 4303 7.323420 TGATTGTATATCCGAGCAAGATAAGG 58.677 38.462 0.00 0.00 30.31 2.69
3486 4304 8.939201 ATGATTGTATATCCGAGCAAGATAAG 57.061 34.615 0.00 0.00 30.31 1.73
3487 4305 9.803315 GTATGATTGTATATCCGAGCAAGATAA 57.197 33.333 0.00 0.00 30.31 1.75
3488 4306 8.966868 TGTATGATTGTATATCCGAGCAAGATA 58.033 33.333 0.00 0.00 0.00 1.98
3489 4307 7.840931 TGTATGATTGTATATCCGAGCAAGAT 58.159 34.615 0.00 0.00 0.00 2.40
3490 4308 7.227049 TGTATGATTGTATATCCGAGCAAGA 57.773 36.000 0.00 0.00 0.00 3.02
3491 4309 6.533012 CCTGTATGATTGTATATCCGAGCAAG 59.467 42.308 0.00 0.00 0.00 4.01
3492 4310 6.210584 TCCTGTATGATTGTATATCCGAGCAA 59.789 38.462 0.00 0.00 0.00 3.91
3493 4311 5.714806 TCCTGTATGATTGTATATCCGAGCA 59.285 40.000 0.00 0.00 0.00 4.26
3494 4312 6.208988 TCCTGTATGATTGTATATCCGAGC 57.791 41.667 0.00 0.00 0.00 5.03
3495 4313 7.273598 CGTTTCCTGTATGATTGTATATCCGAG 59.726 40.741 0.00 0.00 0.00 4.63
3496 4314 7.088272 CGTTTCCTGTATGATTGTATATCCGA 58.912 38.462 0.00 0.00 0.00 4.55
3497 4315 6.866770 ACGTTTCCTGTATGATTGTATATCCG 59.133 38.462 0.00 0.00 0.00 4.18
3498 4316 9.136952 GTACGTTTCCTGTATGATTGTATATCC 57.863 37.037 0.00 0.00 0.00 2.59
3499 4317 9.687210 TGTACGTTTCCTGTATGATTGTATATC 57.313 33.333 0.00 0.00 0.00 1.63
3501 4319 9.687210 GATGTACGTTTCCTGTATGATTGTATA 57.313 33.333 0.00 0.00 0.00 1.47
3502 4320 7.656137 GGATGTACGTTTCCTGTATGATTGTAT 59.344 37.037 0.00 0.00 0.00 2.29
3503 4321 6.982141 GGATGTACGTTTCCTGTATGATTGTA 59.018 38.462 0.00 0.00 0.00 2.41
3504 4322 5.815740 GGATGTACGTTTCCTGTATGATTGT 59.184 40.000 0.00 0.00 0.00 2.71
3505 4323 5.815222 TGGATGTACGTTTCCTGTATGATTG 59.185 40.000 0.00 0.00 32.95 2.67
3506 4324 5.984725 TGGATGTACGTTTCCTGTATGATT 58.015 37.500 0.00 0.00 32.95 2.57
3507 4325 5.607939 TGGATGTACGTTTCCTGTATGAT 57.392 39.130 0.00 0.00 32.95 2.45


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

AutoCloner maintained by Alex Coulton.