Multiple sequence alignment - TraesCS7A01G193300

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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 TraesCS7A01G193300 chr7A 100.000 3596 0 0 1 3596 150986471 150990066 0.000000e+00 6641
1 TraesCS7A01G193300 chr7A 96.517 689 21 3 1 688 720918270 720918956 0.000000e+00 1136
2 TraesCS7A01G193300 chr7A 95.369 691 29 3 5 693 671308607 671307918 0.000000e+00 1096
3 TraesCS7A01G193300 chr7B 88.163 1377 76 37 691 2027 113195330 113196659 0.000000e+00 1559
4 TraesCS7A01G193300 chr7B 88.000 925 67 23 2030 2935 113196706 113197605 0.000000e+00 1053
5 TraesCS7A01G193300 chr7B 86.018 565 54 13 3049 3594 113197891 113198449 1.860000e-162 582
6 TraesCS7A01G193300 chr7D 91.922 978 36 17 727 1686 151314162 151315114 0.000000e+00 1328
7 TraesCS7A01G193300 chr7D 87.267 966 64 23 2097 3030 151316774 151317712 0.000000e+00 1048
8 TraesCS7A01G193300 chr7D 92.174 460 34 2 3138 3596 151317887 151318345 0.000000e+00 649
9 TraesCS7A01G193300 chr7D 85.507 138 12 4 3033 3168 151317745 151317876 1.740000e-28 137
10 TraesCS7A01G193300 chr6A 96.237 691 24 2 1 689 80883315 80884005 0.000000e+00 1131
11 TraesCS7A01G193300 chr6A 85.417 288 24 13 1689 1968 118182081 118182358 2.110000e-72 283
12 TraesCS7A01G193300 chr3A 96.221 688 22 2 4 691 658885498 658884815 0.000000e+00 1123
13 TraesCS7A01G193300 chr3A 95.259 696 30 3 4 697 638934193 638933499 0.000000e+00 1099
14 TraesCS7A01G193300 chr3A 95.620 685 29 1 4 688 456750486 456749803 0.000000e+00 1098
15 TraesCS7A01G193300 chr5A 95.924 687 27 1 4 690 394751545 394750860 0.000000e+00 1112
16 TraesCS7A01G193300 chr5A 86.972 284 23 11 1689 1968 660302417 660302690 1.250000e-79 307
17 TraesCS7A01G193300 chr6B 95.520 692 28 3 4 693 642910578 642909888 0.000000e+00 1103
18 TraesCS7A01G193300 chr6B 87.566 378 31 14 1597 1968 608274775 608275142 1.190000e-114 424
19 TraesCS7A01G193300 chr4A 95.494 688 27 4 4 690 97263106 97262422 0.000000e+00 1096
20 TraesCS7A01G193300 chr4A 86.268 284 25 9 1689 1968 216407043 216406770 2.710000e-76 296
21 TraesCS7A01G193300 chr5D 87.324 284 22 11 1689 1968 326029879 326030152 2.700000e-81 313
22 TraesCS7A01G193300 chr3D 87.324 284 22 11 1689 1968 63801507 63801780 2.700000e-81 313
23 TraesCS7A01G193300 chr1D 87.324 284 22 13 1689 1968 330031289 330031016 2.700000e-81 313
24 TraesCS7A01G193300 chr6D 86.972 284 23 11 1689 1968 42972113 42972386 1.250000e-79 307
25 TraesCS7A01G193300 chr1A 86.620 284 24 11 1689 1968 412575628 412575355 5.830000e-78 302


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 TraesCS7A01G193300 chr7A 150986471 150990066 3595 False 6641.000000 6641 100.000000 1 3596 1 chr7A.!!$F1 3595
1 TraesCS7A01G193300 chr7A 720918270 720918956 686 False 1136.000000 1136 96.517000 1 688 1 chr7A.!!$F2 687
2 TraesCS7A01G193300 chr7A 671307918 671308607 689 True 1096.000000 1096 95.369000 5 693 1 chr7A.!!$R1 688
3 TraesCS7A01G193300 chr7B 113195330 113198449 3119 False 1064.666667 1559 87.393667 691 3594 3 chr7B.!!$F1 2903
4 TraesCS7A01G193300 chr7D 151314162 151318345 4183 False 790.500000 1328 89.217500 727 3596 4 chr7D.!!$F1 2869
5 TraesCS7A01G193300 chr6A 80883315 80884005 690 False 1131.000000 1131 96.237000 1 689 1 chr6A.!!$F1 688
6 TraesCS7A01G193300 chr3A 658884815 658885498 683 True 1123.000000 1123 96.221000 4 691 1 chr3A.!!$R3 687
7 TraesCS7A01G193300 chr3A 638933499 638934193 694 True 1099.000000 1099 95.259000 4 697 1 chr3A.!!$R2 693
8 TraesCS7A01G193300 chr3A 456749803 456750486 683 True 1098.000000 1098 95.620000 4 688 1 chr3A.!!$R1 684
9 TraesCS7A01G193300 chr5A 394750860 394751545 685 True 1112.000000 1112 95.924000 4 690 1 chr5A.!!$R1 686
10 TraesCS7A01G193300 chr6B 642909888 642910578 690 True 1103.000000 1103 95.520000 4 693 1 chr6B.!!$R1 689
11 TraesCS7A01G193300 chr4A 97262422 97263106 684 True 1096.000000 1096 95.494000 4 690 1 chr4A.!!$R1 686

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
930 950 0.693049 TGAAGCAGAGGGGAAGGAAC 59.307 55.0 0.00 0.0 0.0 3.62 F
1372 1425 0.163146 GTTCGACGGTACTGCTTTGC 59.837 55.0 0.23 0.0 0.0 3.68 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2445 3795 0.812549 TGTAATCGTAGGCTGCGTCA 59.187 50.0 23.83 15.41 0.0 4.35 R
3117 4648 0.670546 AGCTGGAATGTTCGTCGTGG 60.671 55.0 0.00 0.00 0.0 4.94 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
184 186 7.332678 GTGGTAATCTTAGTTAACGTTGACCAT 59.667 37.037 18.49 5.03 34.79 3.55
315 319 3.264104 CATGAATGGTCATTGGTTTGGC 58.736 45.455 0.43 0.00 42.03 4.52
338 343 4.654915 GGTTGTTAACCCAAGCCTAGTAA 58.345 43.478 2.48 0.00 46.12 2.24
341 346 8.437517 GGTTGTTAACCCAAGCCTAGTAAGGA 62.438 46.154 2.48 0.00 45.02 3.36
562 571 4.779489 ACATAGGCCATAGATACATCTGCA 59.221 41.667 5.01 0.00 37.76 4.41
626 635 7.915293 TGATGACCAGAAACACGTATTTTAT 57.085 32.000 0.00 0.00 0.00 1.40
693 702 7.981142 ACTCCTGGTGTATTTACCTCTTAAAA 58.019 34.615 0.00 0.00 41.43 1.52
694 703 8.442374 ACTCCTGGTGTATTTACCTCTTAAAAA 58.558 33.333 0.00 0.00 41.43 1.94
715 724 5.700722 AAAACCCCAAAGTCGAGTTATTC 57.299 39.130 5.80 0.00 0.00 1.75
716 725 3.345508 ACCCCAAAGTCGAGTTATTCC 57.654 47.619 5.80 0.00 0.00 3.01
872 887 0.882927 TCAGCGTTGAAAAGGGGACG 60.883 55.000 0.00 0.00 31.15 4.79
908 928 4.517285 ACAGAAGAGAAAGTGTTCAGCAA 58.483 39.130 0.00 0.00 36.09 3.91
928 948 0.911525 CCTGAAGCAGAGGGGAAGGA 60.912 60.000 0.00 0.00 32.44 3.36
929 949 0.987294 CTGAAGCAGAGGGGAAGGAA 59.013 55.000 0.00 0.00 32.44 3.36
930 950 0.693049 TGAAGCAGAGGGGAAGGAAC 59.307 55.000 0.00 0.00 0.00 3.62
955 975 4.081050 GGAAACCCAGACCTGTGC 57.919 61.111 0.00 0.00 0.00 4.57
1274 1327 4.514577 CACGCGGCCCAGACCTAG 62.515 72.222 12.47 0.00 0.00 3.02
1277 1330 3.851128 GCGGCCCAGACCTAGGAC 61.851 72.222 17.98 9.98 0.00 3.85
1278 1331 2.363795 CGGCCCAGACCTAGGACA 60.364 66.667 17.98 0.00 0.00 4.02
1279 1332 2.722201 CGGCCCAGACCTAGGACAC 61.722 68.421 17.98 6.53 0.00 3.67
1280 1333 1.612442 GGCCCAGACCTAGGACACA 60.612 63.158 17.98 0.00 0.00 3.72
1281 1334 1.597461 GCCCAGACCTAGGACACAC 59.403 63.158 17.98 1.33 0.00 3.82
1282 1335 1.890894 CCCAGACCTAGGACACACG 59.109 63.158 17.98 0.00 0.00 4.49
1283 1336 1.215647 CCAGACCTAGGACACACGC 59.784 63.158 17.98 0.00 0.00 5.34
1284 1337 1.251527 CCAGACCTAGGACACACGCT 61.252 60.000 17.98 0.00 0.00 5.07
1285 1338 0.171455 CAGACCTAGGACACACGCTC 59.829 60.000 17.98 0.00 0.00 5.03
1286 1339 0.966370 AGACCTAGGACACACGCTCC 60.966 60.000 17.98 0.00 0.00 4.70
1287 1340 0.966370 GACCTAGGACACACGCTCCT 60.966 60.000 17.98 0.00 41.36 3.69
1372 1425 0.163146 GTTCGACGGTACTGCTTTGC 59.837 55.000 0.23 0.00 0.00 3.68
1397 1450 1.679944 CCTGGGAATCGCTTGTGATGT 60.680 52.381 0.00 0.00 0.00 3.06
1398 1451 2.086869 CTGGGAATCGCTTGTGATGTT 58.913 47.619 0.00 0.00 0.00 2.71
1402 1455 3.492313 GGAATCGCTTGTGATGTTGAAC 58.508 45.455 0.00 0.00 0.00 3.18
1565 1618 1.148759 GCGTTCTCTTCATCGAGGGC 61.149 60.000 0.00 0.00 0.00 5.19
1611 1669 4.290942 CACTGGTTAGTATCCTCCTCCTT 58.709 47.826 0.00 0.00 34.74 3.36
1629 1687 2.355920 CCTTCAGATTCAGAGCAGGCTT 60.356 50.000 0.00 0.00 0.00 4.35
1725 2998 2.359214 TCGGTGCTGAGAATAGTAGCAG 59.641 50.000 0.00 0.00 46.91 4.24
1825 3099 6.072452 CCACTTGAATCCTTAGAGTTGGTTTC 60.072 42.308 0.00 0.00 34.41 2.78
1835 3109 8.437575 TCCTTAGAGTTGGTTTCTATTTCAGTT 58.562 33.333 0.00 0.00 0.00 3.16
1836 3110 9.720769 CCTTAGAGTTGGTTTCTATTTCAGTTA 57.279 33.333 0.00 0.00 0.00 2.24
1894 3168 8.206126 TGTCATATCTAATGAATTAGGAGCCA 57.794 34.615 9.60 0.00 40.06 4.75
1913 3190 2.632512 CCAATTACCTTGCCCTTGTTGT 59.367 45.455 0.00 0.00 33.20 3.32
1929 3206 5.182001 CCTTGTTGTTTCTTATGAGTCAGGG 59.818 44.000 0.00 0.00 0.00 4.45
1932 3209 3.674997 TGTTTCTTATGAGTCAGGGCAC 58.325 45.455 0.00 0.00 0.00 5.01
1939 3216 1.372683 GAGTCAGGGCACTTGCAGA 59.627 57.895 3.15 0.00 44.36 4.26
1943 3220 2.040278 AGTCAGGGCACTTGCAGAATTA 59.960 45.455 3.15 0.00 44.36 1.40
1950 3227 5.105063 GGGCACTTGCAGAATTAATCTTTC 58.895 41.667 3.15 0.00 44.36 2.62
1952 3229 5.391950 GGCACTTGCAGAATTAATCTTTCGA 60.392 40.000 3.15 0.00 44.36 3.71
1972 3256 3.306364 CGATAGGCTTGTGAAGGATAGGG 60.306 52.174 0.00 0.00 0.00 3.53
1984 3268 2.409570 AGGATAGGGAAGCACCTTACC 58.590 52.381 0.00 0.00 44.51 2.85
1996 3280 4.781934 AGCACCTTACCTATCATTGAACC 58.218 43.478 0.00 0.00 0.00 3.62
2011 3295 6.291377 TCATTGAACCCATCTATACTTCAGC 58.709 40.000 0.00 0.00 0.00 4.26
2057 3385 0.835543 TTGTTTGGCCCATCCCTTGG 60.836 55.000 0.00 0.00 46.00 3.61
2077 3405 3.243234 TGGTCAACCAAACGTTATTGCAG 60.243 43.478 0.00 0.00 44.35 4.41
2082 3410 5.066117 TCAACCAAACGTTATTGCAGTGTTA 59.934 36.000 0.00 0.00 31.77 2.41
2115 3455 9.755804 TGTTGCAATTGTGTAAAATTTGAGATA 57.244 25.926 0.59 0.00 30.59 1.98
2167 3508 2.322355 AATCAGTCCTTGAGGCATCG 57.678 50.000 0.00 0.00 39.68 3.84
2171 3512 0.984230 AGTCCTTGAGGCATCGGAAA 59.016 50.000 0.00 0.00 34.44 3.13
2248 3590 7.380423 AACAAGAGCTATGTGGGATATTACT 57.620 36.000 5.46 0.00 0.00 2.24
2254 3600 4.692625 GCTATGTGGGATATTACTGCACTG 59.307 45.833 0.00 0.00 0.00 3.66
2290 3638 7.649306 ACATACTCAGTTCAGCAAAAACAATTC 59.351 33.333 0.00 0.00 0.00 2.17
2308 3656 9.787532 AAACAATTCGAGTACAATTATTCCATG 57.212 29.630 0.00 0.00 0.00 3.66
2322 3671 3.726557 TTCCATGGCAGTTGATCTCTT 57.273 42.857 6.96 0.00 0.00 2.85
2359 3709 7.566709 CACTGAACATTCTTAACATTTTTGGC 58.433 34.615 0.00 0.00 0.00 4.52
2503 3853 1.202758 ACTGGTTCGGCAAAGATGACA 60.203 47.619 0.00 0.00 32.33 3.58
2508 3858 0.874390 TCGGCAAAGATGACAAGTGC 59.126 50.000 0.00 0.00 32.33 4.40
2516 3866 1.632409 AGATGACAAGTGCCTGGTGAT 59.368 47.619 0.00 0.00 0.00 3.06
2556 3906 0.108615 AGCGTTTCATCGACAGGGAG 60.109 55.000 0.00 0.00 0.00 4.30
2596 3946 4.702131 GTCCCAGCAACAGTTCTTATTGAT 59.298 41.667 0.00 0.00 0.00 2.57
2599 3949 5.392380 CCCAGCAACAGTTCTTATTGATCAC 60.392 44.000 0.00 0.00 0.00 3.06
2600 3950 5.181811 CCAGCAACAGTTCTTATTGATCACA 59.818 40.000 0.00 0.00 0.00 3.58
2601 3951 6.312487 CAGCAACAGTTCTTATTGATCACAG 58.688 40.000 0.00 0.00 0.00 3.66
2602 3952 5.091431 GCAACAGTTCTTATTGATCACAGC 58.909 41.667 0.00 0.00 0.00 4.40
2603 3953 5.106396 GCAACAGTTCTTATTGATCACAGCT 60.106 40.000 0.00 0.00 0.00 4.24
2604 3954 6.312487 CAACAGTTCTTATTGATCACAGCTG 58.688 40.000 13.48 13.48 0.00 4.24
2605 3955 5.555017 ACAGTTCTTATTGATCACAGCTGT 58.445 37.500 15.25 15.25 0.00 4.40
2606 3956 6.000219 ACAGTTCTTATTGATCACAGCTGTT 59.000 36.000 18.94 2.95 30.50 3.16
2607 3957 6.072838 ACAGTTCTTATTGATCACAGCTGTTG 60.073 38.462 18.94 13.06 30.50 3.33
2608 3958 4.952262 TCTTATTGATCACAGCTGTTGC 57.048 40.909 18.94 9.99 40.05 4.17
2639 3989 1.272313 TGCTTCTCGGTAGGTGTAGGT 60.272 52.381 0.00 0.00 0.00 3.08
2662 4012 8.282982 AGGTAGAGGAGATGTAAGTAATCTTCA 58.717 37.037 0.00 0.00 34.50 3.02
2666 4016 8.986991 AGAGGAGATGTAAGTAATCTTCACAAT 58.013 33.333 0.00 0.00 34.50 2.71
2749 4099 0.401738 AGCTAAAAGTGCTGGCTGGA 59.598 50.000 0.00 0.00 39.56 3.86
2856 4208 9.579932 GGATAGTTTTTGGATCTGGATTATCTT 57.420 33.333 0.00 0.00 0.00 2.40
2874 4226 2.878406 TCTTACAGTGCAACAGGCTTTC 59.122 45.455 0.00 0.00 45.15 2.62
2896 4249 2.203480 GCCCTGGGCTTGTCAACA 60.203 61.111 30.42 0.00 46.69 3.33
2903 4256 2.227388 CTGGGCTTGTCAACATTCTCAC 59.773 50.000 0.00 0.00 0.00 3.51
2911 4264 2.738846 GTCAACATTCTCACGATGTGCT 59.261 45.455 0.00 0.00 32.98 4.40
2936 4312 4.209080 GTGACATTTTGCCTGCAACTTTAC 59.791 41.667 3.64 0.00 35.46 2.01
2947 4323 6.371548 TGCCTGCAACTTTACTCTGTATTAAG 59.628 38.462 0.00 0.00 0.00 1.85
3004 4381 5.278660 CCAGAAAAGCACCATCTTATATGGC 60.279 44.000 3.93 0.00 42.82 4.40
3008 4385 3.693807 AGCACCATCTTATATGGCCATG 58.306 45.455 29.04 11.63 42.82 3.66
3030 4407 4.515191 TGTAGTTGCAGAAAACCATGTCTC 59.485 41.667 0.00 0.00 0.00 3.36
3031 4408 3.554934 AGTTGCAGAAAACCATGTCTCA 58.445 40.909 0.00 0.00 0.00 3.27
3037 4566 4.036734 GCAGAAAACCATGTCTCACAAAGA 59.963 41.667 0.00 0.00 0.00 2.52
3038 4567 5.755813 CAGAAAACCATGTCTCACAAAGAG 58.244 41.667 0.00 0.00 46.14 2.85
3079 4610 1.539827 GAAGGCAAAGCGGTTGTGTAT 59.460 47.619 0.00 0.00 39.63 2.29
3104 4635 7.506328 AACAAAATAGTTACAGACTTGTCCC 57.494 36.000 0.00 0.00 39.86 4.46
3115 4646 4.780021 ACAGACTTGTCCCTAGATTCATGT 59.220 41.667 0.00 0.00 29.46 3.21
3117 4648 3.873952 GACTTGTCCCTAGATTCATGTGC 59.126 47.826 0.00 0.00 0.00 4.57
3132 4664 1.225376 TGTGCCACGACGAACATTCC 61.225 55.000 0.00 0.00 0.00 3.01
3133 4665 1.069935 TGCCACGACGAACATTCCA 59.930 52.632 0.00 0.00 0.00 3.53
3134 4666 0.948623 TGCCACGACGAACATTCCAG 60.949 55.000 0.00 0.00 0.00 3.86
3141 4715 2.415491 CGACGAACATTCCAGCTACTGA 60.415 50.000 0.00 0.00 32.44 3.41
3156 4730 6.477033 CCAGCTACTGATCTACAATACAACAC 59.523 42.308 0.00 0.00 32.44 3.32
3165 4739 7.713073 TGATCTACAATACAACACAGAACAACA 59.287 33.333 0.00 0.00 0.00 3.33
3184 4758 5.992829 ACAACAAAATATATACGATCCCGCA 59.007 36.000 0.00 0.00 39.95 5.69
3187 4761 7.681939 ACAAAATATATACGATCCCGCAAAT 57.318 32.000 0.00 0.00 39.95 2.32
3226 4812 2.174854 AGGTTTGGAAACAGCTACCAGT 59.825 45.455 4.71 0.00 44.54 4.00
3234 4820 2.203998 AGCTACCAGTGGGCCTGT 60.204 61.111 15.21 0.00 39.74 4.00
3268 4854 3.208747 ACAAAACTACACAGGTCTGGG 57.791 47.619 0.00 0.00 40.54 4.45
3282 4868 3.589288 AGGTCTGGGAAAGCTACATTCTT 59.411 43.478 0.00 0.00 0.00 2.52
3312 4898 5.233988 AGCTATAGATTTCGTTCATGAGGC 58.766 41.667 3.21 0.00 0.00 4.70
3321 4907 2.094182 TCGTTCATGAGGCTCCAAGTAC 60.094 50.000 12.86 5.02 0.00 2.73
3393 4979 1.306141 TTCTGATCTCCCCGCCTGT 60.306 57.895 0.00 0.00 0.00 4.00
3519 5105 5.222079 TCTGTGTAGCAAGATACAAACCA 57.778 39.130 0.00 0.00 37.41 3.67
3570 5156 5.595885 TCTGCTAGTATTCTCAATCTGCAC 58.404 41.667 0.00 0.00 0.00 4.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
184 186 1.103803 GGCTCGACTATGTGACCTCA 58.896 55.000 0.00 0.00 0.00 3.86
285 289 7.982252 ACCAATGACCATTCATGTCTAGATAT 58.018 34.615 0.00 0.00 42.00 1.63
341 346 3.068024 TCGGTTACAAACTAGGAACGTGT 59.932 43.478 0.00 0.00 0.00 4.49
347 352 4.322953 GGATGGTTCGGTTACAAACTAGGA 60.323 45.833 0.00 0.00 0.00 2.94
472 480 7.500992 CATGGTAGATCTGTAGGCTTTTTCTA 58.499 38.462 5.18 0.00 0.00 2.10
550 559 5.646793 GCATTCCATGTATGCAGATGTATCT 59.353 40.000 19.53 0.00 45.93 1.98
562 571 3.678056 ATACGGTCGCATTCCATGTAT 57.322 42.857 0.00 0.00 0.00 2.29
693 702 4.521639 GGAATAACTCGACTTTGGGGTTTT 59.478 41.667 0.00 0.00 0.00 2.43
694 703 4.077108 GGAATAACTCGACTTTGGGGTTT 58.923 43.478 0.00 0.00 0.00 3.27
695 704 3.073356 TGGAATAACTCGACTTTGGGGTT 59.927 43.478 0.00 0.00 0.00 4.11
697 706 3.343941 TGGAATAACTCGACTTTGGGG 57.656 47.619 0.00 0.00 0.00 4.96
725 736 5.412640 TGTAAGTCTTCACGTGAACTTGAA 58.587 37.500 31.71 21.79 33.83 2.69
777 788 6.646653 GCCTTTTCCTTTCTGTCCTTTTTATG 59.353 38.462 0.00 0.00 0.00 1.90
908 928 1.204113 CCTTCCCCTCTGCTTCAGGT 61.204 60.000 0.00 0.00 31.51 4.00
928 948 3.296854 GTCTGGGTTTCCCTTTCTTGTT 58.703 45.455 6.38 0.00 45.70 2.83
929 949 2.424379 GGTCTGGGTTTCCCTTTCTTGT 60.424 50.000 6.38 0.00 45.70 3.16
930 950 2.158460 AGGTCTGGGTTTCCCTTTCTTG 60.158 50.000 6.38 0.00 45.70 3.02
1260 1313 3.851128 GTCCTAGGTCTGGGCCGC 61.851 72.222 9.08 0.00 0.00 6.53
1261 1314 2.363795 TGTCCTAGGTCTGGGCCG 60.364 66.667 9.08 0.00 0.00 6.13
1262 1315 1.612442 TGTGTCCTAGGTCTGGGCC 60.612 63.158 9.08 0.00 0.00 5.80
1263 1316 1.597461 GTGTGTCCTAGGTCTGGGC 59.403 63.158 9.08 0.00 0.00 5.36
1264 1317 1.890894 CGTGTGTCCTAGGTCTGGG 59.109 63.158 9.08 0.00 0.00 4.45
1265 1318 1.215647 GCGTGTGTCCTAGGTCTGG 59.784 63.158 9.08 0.00 0.00 3.86
1266 1319 0.171455 GAGCGTGTGTCCTAGGTCTG 59.829 60.000 9.08 0.00 0.00 3.51
1267 1320 0.966370 GGAGCGTGTGTCCTAGGTCT 60.966 60.000 9.08 0.00 0.00 3.85
1268 1321 0.966370 AGGAGCGTGTGTCCTAGGTC 60.966 60.000 9.08 3.43 43.05 3.85
1269 1322 0.966370 GAGGAGCGTGTGTCCTAGGT 60.966 60.000 9.08 0.00 45.00 3.08
1270 1323 1.810532 GAGGAGCGTGTGTCCTAGG 59.189 63.158 0.82 0.82 45.00 3.02
1271 1324 1.025113 TCGAGGAGCGTGTGTCCTAG 61.025 60.000 0.00 0.00 45.00 3.02
1272 1325 0.393944 ATCGAGGAGCGTGTGTCCTA 60.394 55.000 0.00 0.00 45.00 2.94
1274 1327 0.802607 GAATCGAGGAGCGTGTGTCC 60.803 60.000 0.00 0.00 41.80 4.02
1275 1328 0.802607 GGAATCGAGGAGCGTGTGTC 60.803 60.000 0.00 0.00 41.80 3.67
1276 1329 1.215647 GGAATCGAGGAGCGTGTGT 59.784 57.895 0.00 0.00 41.80 3.72
1277 1330 0.526524 GAGGAATCGAGGAGCGTGTG 60.527 60.000 0.00 0.00 41.80 3.82
1278 1331 0.965866 TGAGGAATCGAGGAGCGTGT 60.966 55.000 0.00 0.00 41.80 4.49
1279 1332 0.387202 ATGAGGAATCGAGGAGCGTG 59.613 55.000 0.00 0.00 41.80 5.34
1280 1333 1.067821 GAATGAGGAATCGAGGAGCGT 59.932 52.381 0.00 0.00 41.80 5.07
1281 1334 1.604185 GGAATGAGGAATCGAGGAGCG 60.604 57.143 0.00 0.00 42.69 5.03
1282 1335 1.691434 AGGAATGAGGAATCGAGGAGC 59.309 52.381 0.00 0.00 0.00 4.70
1283 1336 2.036992 CCAGGAATGAGGAATCGAGGAG 59.963 54.545 0.00 0.00 0.00 3.69
1284 1337 2.042464 CCAGGAATGAGGAATCGAGGA 58.958 52.381 0.00 0.00 0.00 3.71
1285 1338 1.071385 CCCAGGAATGAGGAATCGAGG 59.929 57.143 0.00 0.00 0.00 4.63
1286 1339 1.542108 GCCCAGGAATGAGGAATCGAG 60.542 57.143 0.00 0.00 0.00 4.04
1287 1340 0.469917 GCCCAGGAATGAGGAATCGA 59.530 55.000 0.00 0.00 0.00 3.59
1316 1369 3.665675 ATCAGGCCACGGTTCGAGC 62.666 63.158 5.01 0.00 0.00 5.03
1332 1385 1.649267 GAATCGCTCGGCCCAAATC 59.351 57.895 0.00 0.00 0.00 2.17
1397 1450 2.520979 CAAAAACCGCGAACAGTTCAA 58.479 42.857 8.23 0.00 0.00 2.69
1398 1451 1.795889 GCAAAAACCGCGAACAGTTCA 60.796 47.619 8.23 0.00 0.00 3.18
1402 1455 1.189884 CATTGCAAAAACCGCGAACAG 59.810 47.619 8.23 0.00 0.00 3.16
1565 1618 0.824182 CCTCGTAGTAGGCCTCAGGG 60.824 65.000 9.68 0.00 0.00 4.45
1611 1669 3.008813 AGAAAAGCCTGCTCTGAATCTGA 59.991 43.478 0.00 0.00 0.00 3.27
1629 1687 4.080807 TGACAGGACACACTTACCAAGAAA 60.081 41.667 0.00 0.00 0.00 2.52
1725 2998 2.111384 TCCATCTCAGGTGAAGCTACC 58.889 52.381 0.00 0.00 41.17 3.18
1731 3004 4.012374 GCAAGAATTCCATCTCAGGTGAA 58.988 43.478 0.65 0.00 0.00 3.18
1795 3068 4.158764 ACTCTAAGGATTCAAGTGGACTCG 59.841 45.833 0.00 0.00 0.00 4.18
1876 3150 8.045720 AGGTAATTGGCTCCTAATTCATTAGA 57.954 34.615 7.97 0.00 41.72 2.10
1877 3151 8.571336 CAAGGTAATTGGCTCCTAATTCATTAG 58.429 37.037 0.16 0.16 36.49 1.73
1879 3153 6.183360 GCAAGGTAATTGGCTCCTAATTCATT 60.183 38.462 0.00 0.00 39.47 2.57
1894 3168 4.653801 AGAAACAACAAGGGCAAGGTAATT 59.346 37.500 0.00 0.00 0.00 1.40
1913 3190 4.326826 CAAGTGCCCTGACTCATAAGAAA 58.673 43.478 0.00 0.00 0.00 2.52
1929 3206 5.631026 TCGAAAGATTAATTCTGCAAGTGC 58.369 37.500 0.00 0.00 33.93 4.40
1950 3227 3.306364 CCCTATCCTTCACAAGCCTATCG 60.306 52.174 0.00 0.00 0.00 2.92
1952 3229 3.941629 TCCCTATCCTTCACAAGCCTAT 58.058 45.455 0.00 0.00 0.00 2.57
1972 3256 5.297029 GGTTCAATGATAGGTAAGGTGCTTC 59.703 44.000 0.00 0.00 0.00 3.86
1984 3268 9.650539 CTGAAGTATAGATGGGTTCAATGATAG 57.349 37.037 0.00 0.00 0.00 2.08
1996 3280 6.094603 AGCAAAACAAGCTGAAGTATAGATGG 59.905 38.462 0.00 0.00 41.61 3.51
2011 3295 8.524870 AGCATAAATAAGTTCAGCAAAACAAG 57.475 30.769 4.34 0.00 0.00 3.16
2057 3385 3.728718 CACTGCAATAACGTTTGGTTGAC 59.271 43.478 5.91 7.06 39.75 3.18
2077 3405 6.128688 ACACAATTGCAACAACAGTTTAACAC 60.129 34.615 0.00 0.00 0.00 3.32
2082 3410 7.426929 TTTTACACAATTGCAACAACAGTTT 57.573 28.000 0.00 0.00 0.00 2.66
2141 3482 5.488341 TGCCTCAAGGACTGATTAAACTAC 58.512 41.667 0.00 0.00 37.39 2.73
2245 3587 6.765989 AGTATGTTTTTCAGTTCAGTGCAGTA 59.234 34.615 0.00 0.00 0.00 2.74
2248 3590 5.588246 TGAGTATGTTTTTCAGTTCAGTGCA 59.412 36.000 0.00 0.00 0.00 4.57
2290 3638 4.816385 ACTGCCATGGAATAATTGTACTCG 59.184 41.667 18.40 0.00 0.00 4.18
2308 3656 2.485814 GACAACCAAGAGATCAACTGCC 59.514 50.000 0.00 0.00 0.00 4.85
2322 3671 1.317613 GTTCAGTGCCATGACAACCA 58.682 50.000 0.00 0.00 0.00 3.67
2445 3795 0.812549 TGTAATCGTAGGCTGCGTCA 59.187 50.000 23.83 15.41 0.00 4.35
2503 3853 1.067295 TCCTTGATCACCAGGCACTT 58.933 50.000 8.39 0.00 34.60 3.16
2508 3858 1.221840 CCGGTCCTTGATCACCAGG 59.778 63.158 7.07 7.07 32.33 4.45
2516 3866 1.229209 AGAAGCTCCCGGTCCTTGA 60.229 57.895 0.00 0.00 0.00 3.02
2541 3891 3.609853 CATTTCCTCCCTGTCGATGAAA 58.390 45.455 0.00 0.00 33.01 2.69
2556 3906 3.508840 CCGCCACCGAGCATTTCC 61.509 66.667 0.00 0.00 36.29 3.13
2639 3989 9.475620 TTGTGAAGATTACTTACATCTCCTCTA 57.524 33.333 0.00 0.00 36.39 2.43
2662 4012 8.107095 ACTAACCACAATCACCTACATAATTGT 58.893 33.333 0.00 0.00 41.67 2.71
2666 4016 8.158132 TCAAACTAACCACAATCACCTACATAA 58.842 33.333 0.00 0.00 0.00 1.90
2675 4025 6.459573 GCTTCAAGTCAAACTAACCACAATCA 60.460 38.462 0.00 0.00 0.00 2.57
2680 4030 3.883489 AGGCTTCAAGTCAAACTAACCAC 59.117 43.478 0.00 0.00 0.00 4.16
2749 4099 4.436451 CGATGTTGCGATATATGCTGCATT 60.436 41.667 21.56 10.97 37.17 3.56
2856 4208 2.340210 TGAAAGCCTGTTGCACTGTA 57.660 45.000 0.00 0.00 44.83 2.74
2903 4256 2.406024 GCAAAATGTCACAAGCACATCG 59.594 45.455 0.00 0.00 33.12 3.84
2911 4264 2.168106 AGTTGCAGGCAAAATGTCACAA 59.832 40.909 8.47 0.00 37.70 3.33
2947 4323 9.034544 ACAAGAAAGAAATGCATTTCAAAGTAC 57.965 29.630 39.58 26.82 46.50 2.73
2988 4365 3.424703 ACATGGCCATATAAGATGGTGC 58.575 45.455 20.30 0.00 41.17 5.01
3004 4381 4.022068 ACATGGTTTTCTGCAACTACATGG 60.022 41.667 15.52 0.00 38.89 3.66
3008 4385 4.515191 TGAGACATGGTTTTCTGCAACTAC 59.485 41.667 0.00 0.00 0.00 2.73
3030 4407 5.066375 TGGACACTTGTGATTTCTCTTTGTG 59.934 40.000 7.83 0.00 0.00 3.33
3031 4408 5.192927 TGGACACTTGTGATTTCTCTTTGT 58.807 37.500 7.83 0.00 0.00 2.83
3079 4610 8.434392 AGGGACAAGTCTGTAACTATTTTGTTA 58.566 33.333 0.00 0.00 37.17 2.41
3115 4646 0.948623 CTGGAATGTTCGTCGTGGCA 60.949 55.000 0.00 0.00 0.00 4.92
3117 4648 0.670546 AGCTGGAATGTTCGTCGTGG 60.671 55.000 0.00 0.00 0.00 4.94
3132 4664 7.035612 TGTGTTGTATTGTAGATCAGTAGCTG 58.964 38.462 0.00 0.00 0.00 4.24
3133 4665 7.122799 TCTGTGTTGTATTGTAGATCAGTAGCT 59.877 37.037 0.00 0.00 0.00 3.32
3134 4666 7.258441 TCTGTGTTGTATTGTAGATCAGTAGC 58.742 38.462 0.00 0.00 0.00 3.58
3141 4715 8.445275 TTGTTGTTCTGTGTTGTATTGTAGAT 57.555 30.769 0.00 0.00 0.00 1.98
3156 4730 8.221100 CGGGATCGTATATATTTTGTTGTTCTG 58.779 37.037 0.00 0.00 0.00 3.02
3165 4739 9.095065 GTAGATTTGCGGGATCGTATATATTTT 57.905 33.333 0.00 0.00 38.89 1.82
3184 4758 2.616376 TGTGTGCAGCAAACGTAGATTT 59.384 40.909 11.28 0.00 0.00 2.17
3187 4761 1.217001 CTGTGTGCAGCAAACGTAGA 58.783 50.000 11.28 0.00 35.77 2.59
3199 4773 1.802508 GCTGTTTCCAAACCTGTGTGC 60.803 52.381 0.00 0.00 38.11 4.57
3226 4812 1.063070 TCCTTTGTACCACAGGCCCA 61.063 55.000 0.00 0.00 31.92 5.36
3234 4820 6.316890 GTGTAGTTTTGTTCTCCTTTGTACCA 59.683 38.462 0.00 0.00 0.00 3.25
3268 4854 5.874261 AGCTCTGAAGAAGAATGTAGCTTTC 59.126 40.000 0.00 0.00 29.57 2.62
3282 4868 7.334844 TGAACGAAATCTATAGCTCTGAAGA 57.665 36.000 0.00 0.00 0.00 2.87
3312 4898 1.217244 CGGGTTCCCGTACTTGGAG 59.783 63.158 20.65 0.00 43.86 3.86
3393 4979 7.218014 GCATTTCATCGTTTATCGTGAATTTCA 59.782 33.333 0.00 0.00 38.36 2.69
3409 4995 1.926561 TCTCTGTCGGCATTTCATCG 58.073 50.000 0.00 0.00 0.00 3.84
3519 5105 1.673033 GGCTACGTGCTTGATGACACT 60.673 52.381 0.00 0.00 42.39 3.55
3540 5126 8.149647 AGATTGAGAATACTAGCAGAATCCAAG 58.850 37.037 0.00 0.00 0.00 3.61


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

AutoCloner maintained by Alex Coulton.