Multiple sequence alignment - TraesCS4D01G120100

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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 TraesCS4D01G120100 chr4D 100.000 4206 0 0 2758 6963 101029412 101033617 0.000000e+00 7768.0
1 TraesCS4D01G120100 chr4D 100.000 2420 0 0 1 2420 101026655 101029074 0.000000e+00 4470.0
2 TraesCS4D01G120100 chr4D 85.802 324 35 5 305 619 231979230 231978909 4.020000e-87 333.0
3 TraesCS4D01G120100 chr4B 94.537 3240 121 15 2974 6173 144753107 144756330 0.000000e+00 4951.0
4 TraesCS4D01G120100 chr4B 94.252 2453 87 19 1 2420 144750458 144752889 0.000000e+00 3699.0
5 TraesCS4D01G120100 chr4B 91.211 421 22 3 6297 6716 144758155 144758561 6.100000e-155 558.0
6 TraesCS4D01G120100 chr4B 88.066 243 12 10 6703 6945 144758579 144758804 8.900000e-69 272.0
7 TraesCS4D01G120100 chr4B 90.551 127 6 4 6173 6299 144757922 144758042 5.590000e-36 163.0
8 TraesCS4D01G120100 chr4A 93.979 1993 72 20 1 1960 474738881 474736904 0.000000e+00 2972.0
9 TraesCS4D01G120100 chr4A 95.035 1591 43 9 2758 4340 474735566 474734004 0.000000e+00 2468.0
10 TraesCS4D01G120100 chr4A 96.581 1170 30 6 4325 5487 474728537 474727371 0.000000e+00 1930.0
11 TraesCS4D01G120100 chr4A 91.226 946 35 13 5442 6359 474727372 474726447 0.000000e+00 1243.0
12 TraesCS4D01G120100 chr4A 93.986 582 32 3 6382 6961 474726463 474725883 0.000000e+00 878.0
13 TraesCS4D01G120100 chr4A 97.655 469 10 1 1952 2420 474736052 474735585 0.000000e+00 804.0
14 TraesCS4D01G120100 chr3D 89.198 324 23 6 305 618 251689741 251690062 1.820000e-105 394.0
15 TraesCS4D01G120100 chrUn 88.957 326 24 6 305 620 108422796 108422473 6.550000e-105 392.0
16 TraesCS4D01G120100 chr5A 87.234 329 29 8 305 623 74706598 74706923 5.130000e-96 363.0
17 TraesCS4D01G120100 chr5A 87.097 62 7 1 6445 6505 489872644 489872705 1.250000e-07 69.4
18 TraesCS4D01G120100 chr5D 86.769 325 31 6 305 619 156586172 156586494 1.110000e-92 351.0
19 TraesCS4D01G120100 chr5D 87.097 62 7 1 6445 6505 387109767 387109828 1.250000e-07 69.4
20 TraesCS4D01G120100 chr3A 86.728 324 30 7 305 618 691062158 691062478 1.440000e-91 348.0
21 TraesCS4D01G120100 chr3B 85.672 335 34 8 295 619 263803007 263803337 2.410000e-89 340.0
22 TraesCS4D01G120100 chr1B 95.455 44 2 0 6441 6484 338014762 338014805 3.480000e-08 71.3
23 TraesCS4D01G120100 chr1B 91.489 47 4 0 6432 6478 645555427 645555381 1.620000e-06 65.8
24 TraesCS4D01G120100 chr6B 91.489 47 4 0 6432 6478 44462310 44462356 1.620000e-06 65.8
25 TraesCS4D01G120100 chr6A 91.489 47 4 0 6432 6478 479409165 479409211 1.620000e-06 65.8
26 TraesCS4D01G120100 chr2D 93.182 44 3 0 6436 6479 213702935 213702978 1.620000e-06 65.8
27 TraesCS4D01G120100 chr6D 76.230 122 25 2 4615 4732 342025428 342025549 2.100000e-05 62.1


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 TraesCS4D01G120100 chr4D 101026655 101033617 6962 False 6119.000000 7768 100.000000 1 6963 2 chr4D.!!$F1 6962
1 TraesCS4D01G120100 chr4B 144750458 144758804 8346 False 1928.600000 4951 91.723400 1 6945 5 chr4B.!!$F1 6944
2 TraesCS4D01G120100 chr4A 474734004 474738881 4877 True 2081.333333 2972 95.556333 1 4340 3 chr4A.!!$R2 4339
3 TraesCS4D01G120100 chr4A 474725883 474728537 2654 True 1350.333333 1930 93.931000 4325 6961 3 chr4A.!!$R1 2636

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
379 393 0.035152 ATTGAAGCGAGTGGCCATGA 60.035 50.000 9.72 0.00 45.17 3.07 F
764 790 0.474854 TGTAGGGCCCTCCAGAACAA 60.475 55.000 32.80 4.60 38.24 2.83 F
765 791 0.696501 GTAGGGCCCTCCAGAACAAA 59.303 55.000 32.80 3.63 38.24 2.83 F
1568 1602 2.426522 TGCTAGGCTGCTAGTTTTGTG 58.573 47.619 0.00 0.00 0.00 3.33 F
2862 3763 0.179156 GCGTGGCACAAAGATGGATG 60.179 55.000 19.09 0.00 44.16 3.51 F
3934 4845 2.334307 AGAACACCACATGTGCTGC 58.666 52.632 20.81 5.57 46.57 5.25 F
4120 5031 1.063174 CGCTGCCTTACTCTTTCATGC 59.937 52.381 0.00 0.00 0.00 4.06 F
5087 6007 0.753867 TCTCCGTGCCTGTTGTTACA 59.246 50.000 0.00 0.00 0.00 2.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1364 1398 1.072331 ACAGAGGAAATCGTGCAAGGT 59.928 47.619 0.0 0.0 0.00 3.50 R
2156 3053 2.368439 TGCTCGGCAAAAATAGCAGAT 58.632 42.857 0.0 0.0 39.92 2.90 R
2830 3731 0.179225 GCCACGCTTTGACACATACG 60.179 55.000 0.0 0.0 0.00 3.06 R
2963 3865 4.041691 ACCATGCTCACCTACAGTAAAACT 59.958 41.667 0.0 0.0 0.00 2.66 R
4043 4954 0.911769 AGTTGCCAGGATCATCCGAA 59.088 50.000 0.0 0.0 42.75 4.30 R
4806 5725 1.068055 GCCAACAATGTGAAGCAGAGG 60.068 52.381 0.0 0.0 0.00 3.69 R
5599 6583 1.374947 GCCTGGTACTTGCCTCACA 59.625 57.895 0.0 0.0 0.00 3.58 R
6841 9576 0.118144 AGAGGCAGGAAGAGAAGGGT 59.882 55.000 0.0 0.0 0.00 4.34 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
308 322 4.855340 TCCATTTGTTCATAAGAGGGTCC 58.145 43.478 0.00 0.00 0.00 4.46
379 393 0.035152 ATTGAAGCGAGTGGCCATGA 60.035 50.000 9.72 0.00 45.17 3.07
380 394 0.674581 TTGAAGCGAGTGGCCATGAG 60.675 55.000 9.72 4.05 45.17 2.90
382 396 2.527951 GAAGCGAGTGGCCATGAGGT 62.528 60.000 9.72 5.89 45.17 3.85
485 504 3.641436 TCTACTGGTGCCGATATGTCAAT 59.359 43.478 0.00 0.00 0.00 2.57
489 508 4.096382 ACTGGTGCCGATATGTCAATTTTC 59.904 41.667 0.00 0.00 0.00 2.29
491 510 4.096231 TGGTGCCGATATGTCAATTTTCTG 59.904 41.667 0.00 0.00 0.00 3.02
496 515 6.150976 TGCCGATATGTCAATTTTCTGTCTTT 59.849 34.615 0.00 0.00 0.00 2.52
553 572 1.847798 TATGCAGAGGCCGGGTGTTT 61.848 55.000 2.18 0.00 40.13 2.83
611 634 6.945072 AGTTAATAAAAGCGCTCTTTATCGG 58.055 36.000 24.60 0.00 41.40 4.18
612 635 6.759827 AGTTAATAAAAGCGCTCTTTATCGGA 59.240 34.615 24.60 16.19 41.40 4.55
657 681 3.951563 TGGGCTTTTAGCATATCACCT 57.048 42.857 0.67 0.00 44.75 4.00
713 737 8.709386 TGATATAAGTTTCACTCAGCTTTCTC 57.291 34.615 0.00 0.00 0.00 2.87
764 790 0.474854 TGTAGGGCCCTCCAGAACAA 60.475 55.000 32.80 4.60 38.24 2.83
765 791 0.696501 GTAGGGCCCTCCAGAACAAA 59.303 55.000 32.80 3.63 38.24 2.83
789 815 8.831715 AAGTTGTTTTATTCAATGTGGATTCC 57.168 30.769 0.00 0.00 0.00 3.01
802 828 3.003897 TGTGGATTCCGTAACTGCAAAAC 59.996 43.478 0.00 0.00 0.00 2.43
846 872 9.878667 TTGGATTCTTTCGTTATTACTATGTCA 57.121 29.630 0.00 0.00 0.00 3.58
948 977 6.351286 GGAACTTGCAGGAATTTGATGGTAAT 60.351 38.462 1.40 0.00 0.00 1.89
1112 1141 9.620660 CTTTATGTCTTAATTGGGTGTTGTAAC 57.379 33.333 0.00 0.00 0.00 2.50
1135 1164 7.744678 ACTGTAAAATACCCACTAGTACCAT 57.255 36.000 0.00 0.00 0.00 3.55
1287 1319 5.622346 AGATTGCCCTTTTACTCTCCTAG 57.378 43.478 0.00 0.00 0.00 3.02
1298 1330 9.369672 CCTTTTACTCTCCTAGTAGGAATATGT 57.630 37.037 19.59 16.08 45.28 2.29
1373 1407 2.842208 TTCACTTTTCACCTTGCACG 57.158 45.000 0.00 0.00 0.00 5.34
1379 1413 3.243401 ACTTTTCACCTTGCACGATTTCC 60.243 43.478 0.00 0.00 0.00 3.13
1568 1602 2.426522 TGCTAGGCTGCTAGTTTTGTG 58.573 47.619 0.00 0.00 0.00 3.33
1727 1761 5.294060 GCAAGAAGGAAAGTTGCAAATTTCA 59.706 36.000 37.97 1.92 44.87 2.69
2795 3696 6.424812 GCAAGTGTAAATGAATGCCTTTCTTT 59.575 34.615 0.00 0.00 35.23 2.52
2830 3731 1.336125 GAGCTAATGCAAGCCATGGAC 59.664 52.381 18.40 7.03 43.86 4.02
2850 3751 0.871722 GTATGTGTCAAAGCGTGGCA 59.128 50.000 0.00 0.00 40.39 4.92
2862 3763 0.179156 GCGTGGCACAAAGATGGATG 60.179 55.000 19.09 0.00 44.16 3.51
2872 3773 5.124457 GCACAAAGATGGATGTCTATTGTGT 59.876 40.000 20.04 1.37 41.98 3.72
2896 3798 7.672660 TGTGGAAGTGGTAGAGTAGAATTAGAA 59.327 37.037 0.00 0.00 0.00 2.10
2950 3852 4.095483 GCAACTCAATTAGCTGCATACACT 59.905 41.667 1.02 0.00 45.02 3.55
2963 3865 4.384940 TGCATACACTTCTGCACTTTGTA 58.615 39.130 0.00 0.00 43.11 2.41
3043 3945 5.385509 TTGTCTCATGATGACGAGTTACA 57.614 39.130 15.80 0.00 37.26 2.41
3092 3997 4.506758 CAAATGTTCAATGGTTGGATCCC 58.493 43.478 9.90 0.00 0.00 3.85
3682 4590 5.071519 AGACAAATCTACATATGCTGAGCCT 59.928 40.000 0.23 0.00 31.46 4.58
3783 4691 8.586273 CAAATTTTGTGAACAAAGACAGTACAG 58.414 33.333 8.49 0.00 45.34 2.74
3890 4798 6.040247 TGTTTCGCAGGTTAGATATGTAGTG 58.960 40.000 0.00 0.00 0.00 2.74
3891 4799 5.847111 TTCGCAGGTTAGATATGTAGTGT 57.153 39.130 0.00 0.00 0.00 3.55
3892 4800 6.947644 TTCGCAGGTTAGATATGTAGTGTA 57.052 37.500 0.00 0.00 0.00 2.90
3893 4801 6.947644 TCGCAGGTTAGATATGTAGTGTAA 57.052 37.500 0.00 0.00 0.00 2.41
3934 4845 2.334307 AGAACACCACATGTGCTGC 58.666 52.632 20.81 5.57 46.57 5.25
4030 4941 7.576403 TGTTATCCCTCTTGATTGATCAATGA 58.424 34.615 25.37 14.86 44.92 2.57
4033 4944 5.188434 TCCCTCTTGATTGATCAATGACAC 58.812 41.667 25.37 11.32 44.92 3.67
4043 4954 1.067295 TCAATGACACTTGCCTCCCT 58.933 50.000 0.00 0.00 0.00 4.20
4120 5031 1.063174 CGCTGCCTTACTCTTTCATGC 59.937 52.381 0.00 0.00 0.00 4.06
4161 5072 1.849976 GAGCTGCTGTCACCACTTGC 61.850 60.000 7.01 0.00 0.00 4.01
4207 5121 2.438075 CTCCTCTTGCAGCCTGCC 60.438 66.667 15.29 0.00 44.23 4.85
4387 5301 7.038799 AGGAACTGATCAATTGCCAACTAAAAT 60.039 33.333 4.70 0.00 37.18 1.82
4593 5508 5.471456 CACAAATTCATACTAGATCAGGGCC 59.529 44.000 0.00 0.00 0.00 5.80
4806 5725 6.045955 TCCCTTGACAGTTGTTAAAATTTGC 58.954 36.000 0.00 0.00 0.00 3.68
4824 5743 1.610038 TGCCTCTGCTTCACATTGTTG 59.390 47.619 0.00 0.00 38.71 3.33
5079 5999 5.597806 TGTATATTTTAGTCTCCGTGCCTG 58.402 41.667 0.00 0.00 0.00 4.85
5087 6007 0.753867 TCTCCGTGCCTGTTGTTACA 59.246 50.000 0.00 0.00 0.00 2.41
5152 6072 2.159240 TCTATGTAGCGCCTCACTTGTG 60.159 50.000 2.29 0.00 0.00 3.33
5576 6560 6.599244 GGGGTACATCATATGACATATGGTTG 59.401 42.308 27.47 25.25 42.23 3.77
5648 6632 5.605908 AGAGATCTCATTTTCCAGAGGCATA 59.394 40.000 24.39 0.00 32.76 3.14
5685 6669 7.229306 TGTTGACATAGAAAAAGAACTGCTGAT 59.771 33.333 0.00 0.00 0.00 2.90
5721 6705 3.798337 GTCAAATTGCTGTCTTGTTGTGG 59.202 43.478 0.00 0.00 0.00 4.17
5742 6726 6.493115 TGTGGTGGATTTTGTGAAATATGTCT 59.507 34.615 0.00 0.00 35.65 3.41
5743 6727 7.015098 TGTGGTGGATTTTGTGAAATATGTCTT 59.985 33.333 0.00 0.00 35.65 3.01
5881 6865 1.141881 CGCCCGTGCTAGTCTTCAT 59.858 57.895 0.00 0.00 34.43 2.57
5887 6871 4.335594 GCCCGTGCTAGTCTTCATTTTTAT 59.664 41.667 0.00 0.00 33.53 1.40
5935 6919 3.459598 TCATCCATGGGCTAAAAGCTACT 59.540 43.478 13.02 0.00 41.99 2.57
6011 6995 3.752222 TCCTCGTTGTCTCTCACTAGTTC 59.248 47.826 0.00 0.00 0.00 3.01
6133 7126 8.311836 TCTGGAAGTTTCGAGATAAGTATTGTT 58.688 33.333 2.91 0.00 37.17 2.83
6167 7160 1.721664 GGCGGCTCCGTTTATTTCCC 61.722 60.000 10.24 0.00 42.09 3.97
6203 8788 1.279025 ATACCTGGACCGTTGGCCAT 61.279 55.000 6.09 0.00 30.92 4.40
6204 8789 0.618107 TACCTGGACCGTTGGCCATA 60.618 55.000 6.09 0.00 30.92 2.74
6205 8790 1.301623 CCTGGACCGTTGGCCATAA 59.698 57.895 6.09 0.00 30.92 1.90
6206 8791 0.106719 CCTGGACCGTTGGCCATAAT 60.107 55.000 6.09 0.00 30.92 1.28
6208 8793 2.494059 CTGGACCGTTGGCCATAATAG 58.506 52.381 6.09 0.00 30.92 1.73
6209 8794 1.841277 TGGACCGTTGGCCATAATAGT 59.159 47.619 6.09 0.00 0.00 2.12
6210 8795 2.158871 TGGACCGTTGGCCATAATAGTC 60.159 50.000 6.09 9.74 0.00 2.59
6211 8796 2.158871 GGACCGTTGGCCATAATAGTCA 60.159 50.000 6.09 0.00 0.00 3.41
6212 8797 3.537580 GACCGTTGGCCATAATAGTCAA 58.462 45.455 6.09 0.00 0.00 3.18
6213 8798 4.134563 GACCGTTGGCCATAATAGTCAAT 58.865 43.478 6.09 0.00 0.00 2.57
6214 8799 4.134563 ACCGTTGGCCATAATAGTCAATC 58.865 43.478 6.09 0.00 0.00 2.67
6215 8800 4.141482 ACCGTTGGCCATAATAGTCAATCT 60.141 41.667 6.09 0.00 0.00 2.40
6219 8804 6.498304 GTTGGCCATAATAGTCAATCTTGTG 58.502 40.000 6.09 0.00 0.00 3.33
6282 8867 3.429410 GCATACTTGTGATTTTGAGGCCC 60.429 47.826 0.00 0.00 0.00 5.80
6365 9065 3.071479 ACCTTGTGGTTTATAGTGCACG 58.929 45.455 12.01 0.00 46.05 5.34
6366 9066 3.244284 ACCTTGTGGTTTATAGTGCACGA 60.244 43.478 12.01 6.67 46.05 4.35
6367 9067 3.938963 CCTTGTGGTTTATAGTGCACGAT 59.061 43.478 16.88 16.88 0.00 3.73
6368 9068 4.394920 CCTTGTGGTTTATAGTGCACGATT 59.605 41.667 17.88 6.13 0.00 3.34
6369 9069 5.106317 CCTTGTGGTTTATAGTGCACGATTT 60.106 40.000 17.88 0.00 0.00 2.17
6370 9070 6.092944 CCTTGTGGTTTATAGTGCACGATTTA 59.907 38.462 17.88 1.62 0.00 1.40
6371 9071 7.201696 CCTTGTGGTTTATAGTGCACGATTTAT 60.202 37.037 17.88 9.42 0.00 1.40
6372 9072 8.719560 TTGTGGTTTATAGTGCACGATTTATA 57.280 30.769 17.88 8.43 0.00 0.98
6373 9073 8.360325 TGTGGTTTATAGTGCACGATTTATAG 57.640 34.615 17.88 0.00 0.00 1.31
6374 9074 7.982919 TGTGGTTTATAGTGCACGATTTATAGT 59.017 33.333 17.88 0.00 0.00 2.12
6375 9075 8.273557 GTGGTTTATAGTGCACGATTTATAGTG 58.726 37.037 17.88 0.00 41.01 2.74
6411 9111 4.458989 TGGTTTGATATTTCGCAAGCTTCT 59.541 37.500 0.00 0.00 37.18 2.85
6449 9149 3.077484 AGCAACATTGGCATGTACTCT 57.923 42.857 0.00 0.00 43.34 3.24
6505 9206 5.479027 ACTTTCTTTGAGAGAGGGAGTACTC 59.521 44.000 14.87 14.87 35.37 2.59
6524 9225 1.202758 TCACAGCTGTTCCGTTTGGAT 60.203 47.619 18.94 0.00 45.91 3.41
6528 9229 0.169009 GCTGTTCCGTTTGGATGCTC 59.831 55.000 0.00 0.00 45.91 4.26
6588 9290 2.557924 TGCATCTTGTTTCGGCAGAAAT 59.442 40.909 15.10 0.00 46.64 2.17
6603 9305 3.858503 GCAGAAATGCCTTCAGTTTGGAC 60.859 47.826 0.00 0.00 36.40 4.02
6605 9307 4.021719 CAGAAATGCCTTCAGTTTGGACAT 60.022 41.667 0.00 0.00 36.40 3.06
6642 9344 1.134907 GCCATTGAAGCCCATGACTTG 60.135 52.381 5.77 0.00 0.00 3.16
6653 9355 3.341823 CCCATGACTTGTCTCTCCTTTG 58.658 50.000 0.00 0.00 0.00 2.77
6753 9488 6.315393 TGGCAGAAATCCTAAATACGAAACTC 59.685 38.462 0.00 0.00 0.00 3.01
6754 9489 6.539103 GGCAGAAATCCTAAATACGAAACTCT 59.461 38.462 0.00 0.00 0.00 3.24
6795 9530 3.863400 GCAAAGATCCATGCAGCTTTTGT 60.863 43.478 13.79 0.00 42.12 2.83
6798 9533 4.226427 AGATCCATGCAGCTTTTGTCTA 57.774 40.909 0.00 0.00 0.00 2.59
6841 9576 3.002791 CTGCATGCGTCCTCTCTTTTTA 58.997 45.455 14.09 0.00 0.00 1.52
6845 9580 1.975680 TGCGTCCTCTCTTTTTACCCT 59.024 47.619 0.00 0.00 0.00 4.34
6906 9641 1.028905 GATCAGTCTCCTGTCTCCCG 58.971 60.000 0.00 0.00 39.82 5.14
6910 9645 0.178929 AGTCTCCTGTCTCCCGGTTT 60.179 55.000 0.00 0.00 0.00 3.27
6911 9646 0.246910 GTCTCCTGTCTCCCGGTTTC 59.753 60.000 0.00 0.00 0.00 2.78
6961 9696 2.287069 CGATGACGGACACTCATAGGTC 60.287 54.545 0.00 0.00 35.72 3.85
6962 9697 1.092348 TGACGGACACTCATAGGTCG 58.908 55.000 0.00 0.00 34.87 4.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
161 162 4.094739 TGCGCGACTGTAAATAGTACTGTA 59.905 41.667 12.10 0.00 31.30 2.74
162 163 3.119743 TGCGCGACTGTAAATAGTACTGT 60.120 43.478 12.10 0.00 33.32 3.55
163 164 3.431856 TGCGCGACTGTAAATAGTACTG 58.568 45.455 12.10 0.00 0.00 2.74
164 165 3.770263 TGCGCGACTGTAAATAGTACT 57.230 42.857 12.10 0.00 0.00 2.73
165 166 4.288531 AGATGCGCGACTGTAAATAGTAC 58.711 43.478 12.10 0.00 0.00 2.73
168 169 6.453643 AATTAGATGCGCGACTGTAAATAG 57.546 37.500 12.10 0.00 0.00 1.73
221 222 3.425938 GACGCGCCGCAATCAAGAG 62.426 63.158 10.75 0.00 0.00 2.85
308 322 0.108804 ACTCCGTACGGTGAAGCATG 60.109 55.000 35.67 17.99 36.47 4.06
330 344 2.084546 ACCGCCTTAGAACAGCAATTC 58.915 47.619 0.00 0.00 0.00 2.17
333 347 0.107831 ACACCGCCTTAGAACAGCAA 59.892 50.000 0.00 0.00 0.00 3.91
364 378 2.129555 AACCTCATGGCCACTCGCTT 62.130 55.000 8.16 0.00 37.74 4.68
399 413 4.885426 CGGAGGTTATGCTGCCAT 57.115 55.556 0.00 0.00 35.44 4.40
496 515 4.021544 AGCCAAACACAAACAGTCTGAAAA 60.022 37.500 6.91 0.00 0.00 2.29
631 654 7.182749 AGGTGATATGCTAAAAGCCCATATCTA 59.817 37.037 16.30 5.34 43.93 1.98
713 737 1.078709 ACACGCATGACCGAATCAAG 58.921 50.000 0.00 0.00 41.93 3.02
764 790 7.598493 CGGAATCCACATTGAATAAAACAACTT 59.402 33.333 0.00 0.00 0.00 2.66
765 791 7.090173 CGGAATCCACATTGAATAAAACAACT 58.910 34.615 0.00 0.00 0.00 3.16
789 815 5.516090 ACCAACAATAGTTTTGCAGTTACG 58.484 37.500 0.00 0.00 35.28 3.18
802 828 8.522830 AGAATCCAACATGTAAACCAACAATAG 58.477 33.333 0.00 0.00 32.02 1.73
877 904 3.244422 ACCTCACTCGAATGCCAAAAGTA 60.244 43.478 0.00 0.00 0.00 2.24
948 977 8.231837 GCACCATTGTCGAAGTAAACTAATTTA 58.768 33.333 0.00 0.00 0.00 1.40
1078 1107 9.100197 ACCCAATTAAGACATAAAGGACAAATT 57.900 29.630 0.00 0.00 0.00 1.82
1112 1141 7.788026 TCATGGTACTAGTGGGTATTTTACAG 58.212 38.462 5.39 0.00 0.00 2.74
1135 1164 9.445878 GAGATAGAGAATATGCATCCAAATTCA 57.554 33.333 17.88 2.99 32.04 2.57
1256 1285 3.532641 AAAGGGCAATCTTCTGTTCCT 57.467 42.857 0.00 0.00 0.00 3.36
1257 1286 4.767409 AGTAAAAGGGCAATCTTCTGTTCC 59.233 41.667 0.00 0.00 0.00 3.62
1270 1302 4.544683 TCCTACTAGGAGAGTAAAAGGGC 58.455 47.826 2.52 0.00 40.06 5.19
1287 1319 7.931407 TGTGGTGATTCACATACATATTCCTAC 59.069 37.037 18.09 0.00 42.05 3.18
1298 1330 4.323417 GGTGTTCTGTGGTGATTCACATA 58.677 43.478 18.09 4.21 45.26 2.29
1364 1398 1.072331 ACAGAGGAAATCGTGCAAGGT 59.928 47.619 0.00 0.00 0.00 3.50
1373 1407 3.291584 GGGGGAAATCACAGAGGAAATC 58.708 50.000 0.00 0.00 0.00 2.17
1379 1413 6.013032 AGTCATATATGGGGGAAATCACAGAG 60.013 42.308 12.78 0.00 0.00 3.35
1568 1602 6.268825 TGATAACCTACTTGACTGAGTGAC 57.731 41.667 0.00 0.00 0.00 3.67
1640 1674 4.623932 AGAAAACATGTCAGTAGGAGCA 57.376 40.909 0.00 0.00 0.00 4.26
1727 1761 3.829026 TCTCTACTATCAGCCGCATTGAT 59.171 43.478 0.00 0.00 38.70 2.57
2017 2914 7.148340 GGCAGGTTATGAATCACTATATGAAGC 60.148 40.741 0.00 0.00 41.93 3.86
2156 3053 2.368439 TGCTCGGCAAAAATAGCAGAT 58.632 42.857 0.00 0.00 39.92 2.90
2830 3731 0.179225 GCCACGCTTTGACACATACG 60.179 55.000 0.00 0.00 0.00 3.06
2850 3751 5.649395 CCACACAATAGACATCCATCTTTGT 59.351 40.000 0.00 0.00 33.78 2.83
2862 3763 5.047235 ACTCTACCACTTCCACACAATAGAC 60.047 44.000 0.00 0.00 0.00 2.59
2872 3773 8.840200 ATTCTAATTCTACTCTACCACTTCCA 57.160 34.615 0.00 0.00 0.00 3.53
2906 3808 9.632638 AGTTGCCATTCTGTTATTTACTATGAT 57.367 29.630 0.00 0.00 0.00 2.45
2950 3852 6.995511 ACAGTAAAACTACAAAGTGCAGAA 57.004 33.333 0.00 0.00 35.62 3.02
2963 3865 4.041691 ACCATGCTCACCTACAGTAAAACT 59.958 41.667 0.00 0.00 0.00 2.66
3023 3925 6.893958 ATTTGTAACTCGTCATCATGAGAC 57.106 37.500 0.09 8.22 37.83 3.36
3682 4590 2.623418 TGCTTCCTCACCTAGAAGGA 57.377 50.000 0.00 4.82 39.91 3.36
3857 4765 4.789012 AACCTGCGAAACATCATCATTT 57.211 36.364 0.00 0.00 0.00 2.32
3892 4800 9.330220 TCTTTAAGGATACCTAAACAGGTACTT 57.670 33.333 5.70 8.33 46.02 2.24
3893 4801 8.906238 TCTTTAAGGATACCTAAACAGGTACT 57.094 34.615 5.70 0.00 46.02 2.73
4043 4954 0.911769 AGTTGCCAGGATCATCCGAA 59.088 50.000 0.00 0.00 42.75 4.30
4161 5072 1.067071 GTTGTCCCAGTCCTACGGAAG 60.067 57.143 0.00 0.00 31.38 3.46
4207 5121 4.704833 CAGGGTGGCTGTGTCCCG 62.705 72.222 0.00 0.00 45.27 5.14
4213 5127 4.208403 TGCTTGCAGGGTGGCTGT 62.208 61.111 0.00 0.00 34.04 4.40
4387 5301 9.739276 AGTTATCTTGTGATATTCTTGTTCCAA 57.261 29.630 0.00 0.00 35.36 3.53
4593 5508 8.209869 CACTCACTTAAATTCATTTCGCAAAAG 58.790 33.333 0.00 0.00 0.00 2.27
4664 5579 1.000506 GCTCTAAGGTCACACGAACCA 59.999 52.381 0.00 0.00 39.39 3.67
4806 5725 1.068055 GCCAACAATGTGAAGCAGAGG 60.068 52.381 0.00 0.00 0.00 3.69
4824 5743 1.680249 CCTTTCTCAGTTGCCCTAGCC 60.680 57.143 0.00 0.00 38.69 3.93
5079 5999 7.308435 AGCAGAATAAGCAGAATTGTAACAAC 58.692 34.615 0.00 0.00 0.00 3.32
5087 6007 5.108187 TGGAGAGCAGAATAAGCAGAATT 57.892 39.130 0.00 0.00 0.00 2.17
5131 6051 2.100197 ACAAGTGAGGCGCTACATAGA 58.900 47.619 7.64 0.00 0.00 1.98
5173 6093 2.905085 TCATAAAGGTACGACCCCAACA 59.095 45.455 0.00 0.00 39.75 3.33
5456 6378 6.075415 CGAAAACGCATATGCTGGAAAATTAG 60.075 38.462 24.56 8.08 39.32 1.73
5599 6583 1.374947 GCCTGGTACTTGCCTCACA 59.625 57.895 0.00 0.00 0.00 3.58
5648 6632 2.086610 ATGTCAACAAGGGGCAACTT 57.913 45.000 0.00 0.00 0.00 2.66
5685 6669 7.092079 CAGCAATTTGACCAAACAATCTATCA 58.908 34.615 0.00 0.00 32.51 2.15
5721 6705 9.994432 CTAGAAGACATATTTCACAAAATCCAC 57.006 33.333 0.00 0.00 36.49 4.02
5742 6726 8.803397 TCAGTTCTACATTGCTAGTACTAGAA 57.197 34.615 30.09 19.75 35.21 2.10
5743 6727 8.982091 ATCAGTTCTACATTGCTAGTACTAGA 57.018 34.615 30.09 13.20 35.21 2.43
5881 6865 7.780745 TCCACCTCCTCTTTTGTGTTATAAAAA 59.219 33.333 0.00 0.00 0.00 1.94
5887 6871 4.651778 CATCCACCTCCTCTTTTGTGTTA 58.348 43.478 0.00 0.00 0.00 2.41
5935 6919 6.011981 AGTGGTGGGAAGTAAGGAAATCAATA 60.012 38.462 0.00 0.00 0.00 1.90
6011 6995 3.393089 AGGCCTTCTATATCGCACTTG 57.607 47.619 0.00 0.00 0.00 3.16
6204 8789 9.823647 AGATCGTAAATCACAAGATTGACTATT 57.176 29.630 0.00 0.00 43.52 1.73
6205 8790 9.254133 CAGATCGTAAATCACAAGATTGACTAT 57.746 33.333 0.00 0.00 43.52 2.12
6206 8791 8.251026 ACAGATCGTAAATCACAAGATTGACTA 58.749 33.333 0.00 0.00 43.52 2.59
6208 8793 7.063426 TGACAGATCGTAAATCACAAGATTGAC 59.937 37.037 0.00 0.00 43.52 3.18
6209 8794 7.096551 TGACAGATCGTAAATCACAAGATTGA 58.903 34.615 0.00 0.00 43.52 2.57
6210 8795 7.294676 TGACAGATCGTAAATCACAAGATTG 57.705 36.000 0.00 0.00 43.52 2.67
6211 8796 7.905604 TTGACAGATCGTAAATCACAAGATT 57.094 32.000 0.00 0.00 46.20 2.40
6212 8797 9.599866 TTATTGACAGATCGTAAATCACAAGAT 57.400 29.630 4.25 0.00 30.65 2.40
6213 8798 8.869897 GTTATTGACAGATCGTAAATCACAAGA 58.130 33.333 4.25 0.00 30.65 3.02
6214 8799 8.873830 AGTTATTGACAGATCGTAAATCACAAG 58.126 33.333 11.40 0.00 30.65 3.16
6215 8800 8.771920 AGTTATTGACAGATCGTAAATCACAA 57.228 30.769 11.40 0.00 30.65 3.33
6219 8804 8.594881 ATGGAGTTATTGACAGATCGTAAATC 57.405 34.615 4.25 0.00 30.65 2.17
6282 8867 9.849607 CTCTTATTATTACATGTGTAAAGTGCG 57.150 33.333 9.11 0.00 42.93 5.34
6363 9063 5.086104 AGGTCAACAGCACTATAAATCGT 57.914 39.130 0.00 0.00 0.00 3.73
6364 9064 5.351465 ACAAGGTCAACAGCACTATAAATCG 59.649 40.000 0.00 0.00 0.00 3.34
6365 9065 6.403636 CCACAAGGTCAACAGCACTATAAATC 60.404 42.308 0.00 0.00 0.00 2.17
6366 9066 5.415701 CCACAAGGTCAACAGCACTATAAAT 59.584 40.000 0.00 0.00 0.00 1.40
6367 9067 4.759693 CCACAAGGTCAACAGCACTATAAA 59.240 41.667 0.00 0.00 0.00 1.40
6368 9068 4.323417 CCACAAGGTCAACAGCACTATAA 58.677 43.478 0.00 0.00 0.00 0.98
6369 9069 3.937814 CCACAAGGTCAACAGCACTATA 58.062 45.455 0.00 0.00 0.00 1.31
6370 9070 2.783135 CCACAAGGTCAACAGCACTAT 58.217 47.619 0.00 0.00 0.00 2.12
6371 9071 2.254546 CCACAAGGTCAACAGCACTA 57.745 50.000 0.00 0.00 0.00 2.74
6372 9072 3.100545 CCACAAGGTCAACAGCACT 57.899 52.632 0.00 0.00 0.00 4.40
6383 9083 4.433186 TGCGAAATATCAAACCACAAGG 57.567 40.909 0.00 0.00 42.21 3.61
6401 9101 5.530519 TTGAGTAATACAAGAAGCTTGCG 57.469 39.130 2.10 0.00 0.00 4.85
6411 9111 7.428282 TGTTGCTTTCGATTGAGTAATACAA 57.572 32.000 0.00 0.00 0.00 2.41
6449 9149 6.085555 ACGTCTTACATTTTGAGACAGAGA 57.914 37.500 0.00 0.00 39.74 3.10
6479 9179 3.244387 ACTCCCTCTCTCAAAGAAAGTGC 60.244 47.826 0.00 0.00 32.23 4.40
6505 9206 1.069022 CATCCAAACGGAACAGCTGTG 60.069 52.381 22.49 10.86 35.74 3.66
6524 9225 1.751351 CTCTTCAGGATGTACGGAGCA 59.249 52.381 0.00 0.00 37.40 4.26
6528 9229 3.488721 CGTTACCTCTTCAGGATGTACGG 60.489 52.174 0.00 0.00 43.65 4.02
6588 9290 3.420893 CCTAATGTCCAAACTGAAGGCA 58.579 45.455 0.00 0.00 0.00 4.75
6653 9355 5.410924 ACAAAGAAAACTTCAGAACCTTGC 58.589 37.500 0.00 0.00 0.00 4.01
6753 9488 4.566266 GCCATTTGGTTTCGGACACGAG 62.566 54.545 0.00 0.00 43.45 4.18
6754 9489 2.742507 GCCATTTGGTTTCGGACACGA 61.743 52.381 0.00 0.00 41.98 4.35
6795 9530 3.147595 ATGCTGCGCCCGAGTAGA 61.148 61.111 4.18 0.00 0.00 2.59
6841 9576 0.118144 AGAGGCAGGAAGAGAAGGGT 59.882 55.000 0.00 0.00 0.00 4.34
6845 9580 5.965033 AATCATTAGAGGCAGGAAGAGAA 57.035 39.130 0.00 0.00 0.00 2.87
6906 9641 0.955919 CAACCGAGCCTCCAGAAACC 60.956 60.000 0.00 0.00 0.00 3.27
6910 9645 2.203788 ACCAACCGAGCCTCCAGA 60.204 61.111 0.00 0.00 0.00 3.86
6911 9646 2.046892 CACCAACCGAGCCTCCAG 60.047 66.667 0.00 0.00 0.00 3.86


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

AutoCloner maintained by Alex Coulton.