Multiple sequence alignment - TraesCS3B01G504500

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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 TraesCS3B01G504500 chr3B 100.000 3497 0 0 1 3497 748988283 748991779 0.000000e+00 6458
1 TraesCS3B01G504500 chr3B 75.823 972 178 36 2108 3033 820336896 820335936 1.150000e-119 440
2 TraesCS3B01G504500 chr3B 80.784 255 47 2 2618 2872 819304072 819304324 7.660000e-47 198
3 TraesCS3B01G504500 chr3D 94.084 2789 155 4 713 3496 561701073 561703856 0.000000e+00 4228
4 TraesCS3B01G504500 chr3D 92.475 505 38 0 1 505 561700299 561700803 0.000000e+00 723
5 TraesCS3B01G504500 chr3D 81.050 686 114 12 916 1589 609291642 609290961 1.850000e-147 532
6 TraesCS3B01G504500 chr3D 90.310 258 20 4 465 717 561700790 561701047 2.010000e-87 333
7 TraesCS3B01G504500 chr3A 81.832 644 115 2 947 1589 742877007 742876365 1.100000e-149 540
8 TraesCS3B01G504500 chr3A 78.426 394 74 8 2598 2990 742336346 742336729 2.700000e-61 246
9 TraesCS3B01G504500 chr1D 73.494 913 189 42 2140 3020 455749446 455750337 2.640000e-76 296
10 TraesCS3B01G504500 chr2B 78.409 440 90 5 2596 3033 4624471 4624907 7.390000e-72 281


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 TraesCS3B01G504500 chr3B 748988283 748991779 3496 False 6458.000000 6458 100.000000 1 3497 1 chr3B.!!$F1 3496
1 TraesCS3B01G504500 chr3B 820335936 820336896 960 True 440.000000 440 75.823000 2108 3033 1 chr3B.!!$R1 925
2 TraesCS3B01G504500 chr3D 561700299 561703856 3557 False 1761.333333 4228 92.289667 1 3496 3 chr3D.!!$F1 3495
3 TraesCS3B01G504500 chr3D 609290961 609291642 681 True 532.000000 532 81.050000 916 1589 1 chr3D.!!$R1 673
4 TraesCS3B01G504500 chr3A 742876365 742877007 642 True 540.000000 540 81.832000 947 1589 1 chr3A.!!$R1 642
5 TraesCS3B01G504500 chr1D 455749446 455750337 891 False 296.000000 296 73.494000 2140 3020 1 chr1D.!!$F1 880

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
645 678 0.179121 TCTTCGTTGTGTGACTGCGT 60.179 50.0 0.0 0.0 0.0 5.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2546 2663 0.109723 AGTTTCCCGTTGCTTGGCTA 59.89 50.0 0.0 0.0 0.0 3.93 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
75 76 2.333926 TGTTGCTCGTATGGTTCTTCG 58.666 47.619 0.00 0.00 0.00 3.79
79 80 0.529992 CTCGTATGGTTCTTCGGCCC 60.530 60.000 0.00 0.00 0.00 5.80
96 97 1.614850 GCCCGGTTTCCCTCATAAACA 60.615 52.381 0.00 0.00 38.34 2.83
98 99 2.026636 CCCGGTTTCCCTCATAAACAGA 60.027 50.000 0.00 0.00 38.34 3.41
122 123 9.626045 AGAATCAATTTGTTTAGGTTTTCGATC 57.374 29.630 0.00 0.00 0.00 3.69
124 125 6.375377 TCAATTTGTTTAGGTTTTCGATCCG 58.625 36.000 0.00 0.00 0.00 4.18
126 127 3.681593 TGTTTAGGTTTTCGATCCGGA 57.318 42.857 6.61 6.61 0.00 5.14
141 142 6.012113 TCGATCCGGATTCCCTTATAAACTA 58.988 40.000 20.22 0.00 0.00 2.24
147 148 7.039223 TCCGGATTCCCTTATAAACTAGATCAC 60.039 40.741 0.00 0.00 0.00 3.06
176 177 4.980573 AGTGTATGGCCAACTTTGAGTAA 58.019 39.130 10.96 0.00 0.00 2.24
213 214 2.286121 TCCCTCACCCATCACCCC 60.286 66.667 0.00 0.00 0.00 4.95
246 247 5.348179 TCACAAAAATCATTAATGCAAGCGG 59.652 36.000 10.76 2.13 0.00 5.52
248 249 2.514205 AATCATTAATGCAAGCGGCC 57.486 45.000 10.76 0.00 43.89 6.13
343 344 4.142160 CCAATTTAACTTAGGCAGGAAGGC 60.142 45.833 0.00 0.00 44.61 4.35
371 372 6.600350 CATGCATCTTGTGTGCTAGATAATC 58.400 40.000 0.00 0.00 42.92 1.75
400 401 0.888285 GGCTAGCTCCATCACATGCC 60.888 60.000 15.72 0.00 0.00 4.40
420 421 4.105697 TGCCTAATCCTAAAAGGGTATGGG 59.894 45.833 0.00 0.00 35.59 4.00
426 427 6.704056 ATCCTAAAAGGGTATGGGTGATAG 57.296 41.667 0.00 0.00 35.59 2.08
485 486 6.409704 ACTACTTTATAAAGGTTCCCCGTTC 58.590 40.000 25.25 0.00 40.31 3.95
487 488 2.985957 TATAAAGGTTCCCCGTTCCG 57.014 50.000 0.00 0.00 34.12 4.30
506 537 5.334724 TCCGAGGACTTTATCAAAGGTAC 57.665 43.478 3.88 0.00 42.82 3.34
509 540 5.484715 CGAGGACTTTATCAAAGGTACCAA 58.515 41.667 15.94 0.00 42.82 3.67
531 562 6.039605 CCAAATATCACACACATGGCTAATGA 59.960 38.462 0.00 0.00 38.72 2.57
560 591 0.464036 TTGAGCGAGTGAGTTGGTGT 59.536 50.000 0.00 0.00 0.00 4.16
567 598 3.059800 GCGAGTGAGTTGGTGTCTTTTAC 60.060 47.826 0.00 0.00 0.00 2.01
613 644 0.977627 ATCCGATCCAGTGGAGCACA 60.978 55.000 26.25 12.60 38.11 4.57
641 672 0.597637 CCGCTCTTCGTTGTGTGACT 60.598 55.000 0.00 0.00 36.19 3.41
642 673 0.504384 CGCTCTTCGTTGTGTGACTG 59.496 55.000 0.00 0.00 0.00 3.51
645 678 0.179121 TCTTCGTTGTGTGACTGCGT 60.179 50.000 0.00 0.00 0.00 5.24
678 711 2.475187 GCTACTGTGTGAGGTACGTACG 60.475 54.545 18.98 15.01 0.00 3.67
682 715 2.995939 CTGTGTGAGGTACGTACGAGTA 59.004 50.000 24.41 1.17 0.00 2.59
683 716 2.995939 TGTGTGAGGTACGTACGAGTAG 59.004 50.000 24.41 0.00 0.00 2.57
706 739 9.930693 GTAGGAACTATTTCACCTAGATTATGG 57.069 37.037 0.00 0.00 45.60 2.74
741 804 9.426534 TGAGTTTGATCTATCAGGATTCTTCTA 57.573 33.333 0.00 0.00 38.19 2.10
755 818 8.778358 CAGGATTCTTCTATTGTGCCTAATAAC 58.222 37.037 0.00 0.00 0.00 1.89
756 819 8.494433 AGGATTCTTCTATTGTGCCTAATAACA 58.506 33.333 0.00 0.00 0.00 2.41
766 829 4.081807 TGTGCCTAATAACATTGCAATGCA 60.082 37.500 33.94 24.00 40.04 3.96
777 840 0.540133 TGCAATGCATGTGGTGGTCT 60.540 50.000 2.72 0.00 31.71 3.85
796 859 7.339976 GGTGGTCTGTCTAGTCTAGTTTAGATT 59.660 40.741 6.77 0.00 37.13 2.40
797 860 8.400186 GTGGTCTGTCTAGTCTAGTTTAGATTC 58.600 40.741 6.77 6.85 37.13 2.52
834 897 5.763698 AGATCACATCAGCCTTGATTGTATG 59.236 40.000 0.00 0.00 42.12 2.39
967 1038 7.537715 CAACAGATAGATGGCAAACAATACAA 58.462 34.615 0.00 0.00 0.00 2.41
1030 1101 0.249657 GATCCTAGAAGCAGCCACCG 60.250 60.000 0.00 0.00 0.00 4.94
1031 1102 0.687757 ATCCTAGAAGCAGCCACCGA 60.688 55.000 0.00 0.00 0.00 4.69
1058 1129 7.337689 TGGTGATTCCTCATCAATTAAAGAGTG 59.662 37.037 0.00 0.00 43.93 3.51
1066 1137 3.430453 TCAATTAAAGAGTGGGCCAAGG 58.570 45.455 8.40 0.00 0.00 3.61
1175 1246 1.474143 GGATGTGCTGGAACTAGAGCC 60.474 57.143 0.00 0.00 34.04 4.70
1186 1257 2.517998 ACTAGAGCCGTCTCTCCTTT 57.482 50.000 0.00 0.00 46.32 3.11
1219 1290 3.678717 GAGCACGAGACGCCGCTTA 62.679 63.158 9.31 0.00 38.64 3.09
1230 1301 0.663269 CGCCGCTTATCATCGCTGTA 60.663 55.000 0.00 0.00 0.00 2.74
1245 1316 1.246649 CTGTAACACTTGGCCATGCA 58.753 50.000 18.17 6.23 0.00 3.96
1253 1324 0.899720 CTTGGCCATGCATCTTTGGT 59.100 50.000 6.09 0.00 35.34 3.67
1258 1329 2.093341 GGCCATGCATCTTTGGTTTCAT 60.093 45.455 0.00 0.00 35.34 2.57
1267 1338 7.471721 TGCATCTTTGGTTTCATATTTACTCG 58.528 34.615 0.00 0.00 0.00 4.18
1276 1347 3.717707 TCATATTTACTCGAGTGCTGCC 58.282 45.455 28.12 0.00 0.00 4.85
1338 1409 3.009723 CAGGTATGGATTCAACGCACTT 58.990 45.455 0.00 0.00 0.00 3.16
1368 1439 0.669318 TTCGCAACGGCTACCAGAAG 60.669 55.000 0.00 0.00 38.10 2.85
1387 1458 0.806102 GCTCGCGCTGGAGTTGATAA 60.806 55.000 5.56 0.00 36.41 1.75
1398 1469 2.685388 GGAGTTGATAAAAGCAGAGCCC 59.315 50.000 0.00 0.00 0.00 5.19
1506 1577 6.264067 AGCTATTAGCCATTGTTGATTCTTCC 59.736 38.462 12.05 0.00 43.77 3.46
1561 1632 3.129813 TGCTGCAGCTAGAAATGGAAATG 59.870 43.478 36.61 0.00 42.66 2.32
1630 1701 2.275318 GTGCAGCAAACTAGCTCTAGG 58.725 52.381 0.00 0.00 44.54 3.02
1678 1749 7.815068 AGAGCTAGTGTAGTTCATGTGTTTTAG 59.185 37.037 0.00 0.00 38.34 1.85
1765 1836 7.562454 TTTTTGTACCAAAGACTTGTCCTAG 57.438 36.000 0.00 0.00 0.00 3.02
1773 1844 3.724508 AGACTTGTCCTAGCATCATCG 57.275 47.619 0.00 0.00 0.00 3.84
1794 1865 2.699954 CTGTGCTCTTAACCCATCGTT 58.300 47.619 0.00 0.00 38.57 3.85
1813 1884 3.240069 GTTCATGCATGTCTTGACTTGC 58.760 45.455 25.43 25.08 40.04 4.01
1829 1900 3.609853 ACTTGCTTTCAGATATTGCGGA 58.390 40.909 0.00 0.00 0.00 5.54
1837 1908 5.811399 TTCAGATATTGCGGACGAAATTT 57.189 34.783 2.90 0.00 0.00 1.82
1842 1913 2.697431 TTGCGGACGAAATTTTGGAG 57.303 45.000 10.22 2.23 0.00 3.86
1849 1920 4.603985 GGACGAAATTTTGGAGAAACGTT 58.396 39.130 10.22 0.00 33.10 3.99
1894 1965 4.283722 ACTCGGATGGGATTACTCCAATAC 59.716 45.833 1.05 0.00 44.08 1.89
1903 1974 4.452455 GGATTACTCCAATACGAATGGCTG 59.548 45.833 0.00 0.00 41.64 4.85
1906 1977 4.689612 ACTCCAATACGAATGGCTGTAT 57.310 40.909 0.00 0.00 37.88 2.29
1909 1980 4.883083 TCCAATACGAATGGCTGTATCTC 58.117 43.478 0.00 0.00 37.88 2.75
1911 1982 5.012046 TCCAATACGAATGGCTGTATCTCAT 59.988 40.000 0.00 0.00 37.88 2.90
1930 2001 0.744281 TGACAAGTCTGACGTGCTGA 59.256 50.000 21.00 5.03 30.59 4.26
1931 2002 1.341209 TGACAAGTCTGACGTGCTGAT 59.659 47.619 21.00 4.21 30.59 2.90
1934 2005 1.723542 CAAGTCTGACGTGCTGATCAC 59.276 52.381 10.64 0.00 42.23 3.06
1942 2013 0.522705 CGTGCTGATCACATTGCTGC 60.523 55.000 6.27 0.00 45.92 5.25
1945 2016 1.068125 TGCTGATCACATTGCTGCAAC 60.068 47.619 18.51 4.31 34.32 4.17
1952 2023 3.840468 TCACATTGCTGCAACATGATTC 58.160 40.909 18.51 0.00 0.00 2.52
1979 2050 6.312918 TCTTTAGCATATGAAACCGACAAGAC 59.687 38.462 6.97 0.00 0.00 3.01
2001 2072 3.024547 TGGTTATCCTCTCCTCTGTTCG 58.975 50.000 0.00 0.00 34.23 3.95
2033 2104 2.161609 GGGGTCAAGTTAATGTTGCTCG 59.838 50.000 0.00 0.00 0.00 5.03
2054 2125 3.202097 GAGTGCTTCTTCTCTATTGCCC 58.798 50.000 0.00 0.00 0.00 5.36
2055 2126 1.936547 GTGCTTCTTCTCTATTGCCCG 59.063 52.381 0.00 0.00 0.00 6.13
2072 2143 1.202521 CCCGGATGCTTTTTATTGCCC 60.203 52.381 0.73 0.00 0.00 5.36
2099 2170 1.942657 CAGAGATGGTACGGCAATTGG 59.057 52.381 7.72 0.00 0.00 3.16
2280 2351 1.747355 GTTGCTGCATTACTGGCTCAT 59.253 47.619 1.84 0.00 0.00 2.90
2298 2369 6.434340 TGGCTCATGACGATATAATAGACACT 59.566 38.462 0.00 0.00 0.00 3.55
2322 2393 4.454504 ACAATTCTCGACAACCATGGTAAC 59.545 41.667 20.12 11.49 0.00 2.50
2349 2420 2.031682 GGCTTCGCAATTATCGAGCATT 60.032 45.455 16.88 0.00 37.26 3.56
2358 2429 6.346838 CGCAATTATCGAGCATTACTGATGAA 60.347 38.462 0.00 0.00 38.03 2.57
2381 2452 2.976882 ACAAGCCTTTAGACTGGGTACA 59.023 45.455 0.00 0.00 33.27 2.90
2495 2612 1.135972 GGAAGTGCACGTGCTTATGTG 60.136 52.381 37.59 1.03 42.66 3.21
2497 2614 1.432514 AGTGCACGTGCTTATGTGAG 58.567 50.000 37.59 0.00 42.66 3.51
2498 2615 0.443869 GTGCACGTGCTTATGTGAGG 59.556 55.000 37.59 0.00 42.66 3.86
2546 2663 9.499479 CATCTCATTGTATAATCTAAGCAAGGT 57.501 33.333 0.00 0.00 0.00 3.50
2592 2733 2.555664 TCAAGGAAGGAGAGGCAATCT 58.444 47.619 0.00 0.00 42.61 2.40
2612 2753 8.816144 GCAATCTCAAACTCAAAAATACACAAA 58.184 29.630 0.00 0.00 0.00 2.83
2619 2760 6.862944 ACTCAAAAATACACAAACAACACG 57.137 33.333 0.00 0.00 0.00 4.49
2625 2766 7.820044 AAAATACACAAACAACACGTCATTT 57.180 28.000 0.00 0.00 0.00 2.32
2703 2844 4.262808 GGATATAGCAGTGATGCTGGAAGT 60.263 45.833 12.81 0.00 45.81 3.01
2789 2930 3.120786 GCAATGTGCTCTTCATTTGTTGC 60.121 43.478 0.00 0.00 40.96 4.17
2825 2966 1.649271 ATGGGAAGGTGGGAGGATGC 61.649 60.000 0.00 0.00 0.00 3.91
2829 2970 1.134068 GGAAGGTGGGAGGATGCTAAC 60.134 57.143 0.00 0.00 0.00 2.34
2830 2971 1.559682 GAAGGTGGGAGGATGCTAACA 59.440 52.381 0.00 0.00 0.00 2.41
2926 3067 2.288666 CTGGTTTGTACACAGTGCTGT 58.711 47.619 0.00 0.00 46.17 4.40
2929 3070 1.260561 GTTTGTACACAGTGCTGTCCG 59.739 52.381 0.00 0.00 42.83 4.79
3101 3242 3.934579 GGCAAATCCAAATCCAATGACAC 59.065 43.478 0.00 0.00 34.01 3.67
3185 3326 8.628630 TCTGTAATGAACATTGTTTGGATACA 57.371 30.769 3.08 9.81 41.25 2.29
3186 3327 9.241919 TCTGTAATGAACATTGTTTGGATACAT 57.758 29.630 3.08 0.00 42.21 2.29
3218 3359 9.762933 CAATATTACTTGTTAATTCATTGGGGG 57.237 33.333 0.00 0.00 32.31 5.40
3242 3383 7.382218 GGGAAAACATTGTACAGTTCATTCTTG 59.618 37.037 0.00 0.00 0.00 3.02
3252 3393 4.161333 CAGTTCATTCTTGCATTCCGTTC 58.839 43.478 0.00 0.00 0.00 3.95
3260 3401 1.802069 TGCATTCCGTTCGATGTTCA 58.198 45.000 0.00 0.00 0.00 3.18
3261 3402 2.355197 TGCATTCCGTTCGATGTTCAT 58.645 42.857 0.00 0.00 0.00 2.57
3262 3403 2.746904 TGCATTCCGTTCGATGTTCATT 59.253 40.909 0.00 0.00 0.00 2.57
3263 3404 3.935828 TGCATTCCGTTCGATGTTCATTA 59.064 39.130 0.00 0.00 0.00 1.90
3276 3417 9.611284 TTCGATGTTCATTAATTTGAAAGACAG 57.389 29.630 0.00 0.00 37.36 3.51
3293 3434 6.552445 AAGACAGCTCTAATGGTGATTAGT 57.448 37.500 0.00 0.00 41.33 2.24
3325 3466 3.380637 ACGAGAATGGACGTAGCTACAAT 59.619 43.478 23.21 10.86 40.92 2.71
3432 3573 3.941483 CACCAGGACAACACATAATCCTC 59.059 47.826 0.00 0.00 39.66 3.71
3487 3630 7.849804 AACATGATAGGTCTTACAATCACAC 57.150 36.000 0.00 0.00 31.56 3.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
58 59 0.459585 GCCGAAGAACCATACGAGCA 60.460 55.000 0.00 0.00 0.00 4.26
62 63 1.881252 CGGGCCGAAGAACCATACG 60.881 63.158 24.41 0.00 0.00 3.06
96 97 9.626045 GATCGAAAACCTAAACAAATTGATTCT 57.374 29.630 0.00 0.00 0.00 2.40
98 99 7.540745 CGGATCGAAAACCTAAACAAATTGATT 59.459 33.333 0.00 0.00 0.00 2.57
118 119 5.148651 AGTTTATAAGGGAATCCGGATCG 57.851 43.478 19.43 0.00 38.33 3.69
122 123 7.038941 AGTGATCTAGTTTATAAGGGAATCCGG 60.039 40.741 0.00 0.00 38.33 5.14
124 125 9.095700 AGAGTGATCTAGTTTATAAGGGAATCC 57.904 37.037 0.00 0.00 0.00 3.01
126 127 9.890915 AGAGAGTGATCTAGTTTATAAGGGAAT 57.109 33.333 0.00 0.00 0.00 3.01
147 148 4.744795 AGTTGGCCATACACTAAGAGAG 57.255 45.455 6.09 0.00 0.00 3.20
176 177 3.910627 GGAGTTCCCCCACATGAGTATAT 59.089 47.826 0.00 0.00 0.00 0.86
192 193 0.253327 GGTGATGGGTGAGGGAGTTC 59.747 60.000 0.00 0.00 0.00 3.01
213 214 8.800972 CATTAATGATTTTTGTGAGGAATCACG 58.199 33.333 10.04 0.00 41.14 4.35
229 230 2.034124 AGGCCGCTTGCATTAATGATT 58.966 42.857 19.73 0.00 43.89 2.57
235 236 1.024271 GATCAAGGCCGCTTGCATTA 58.976 50.000 0.00 0.00 43.22 1.90
236 237 0.682209 AGATCAAGGCCGCTTGCATT 60.682 50.000 0.00 0.00 46.67 3.56
248 249 4.205065 AGAGCTCCTTGTGAAGATCAAG 57.795 45.455 10.93 0.00 41.06 3.02
332 333 3.345028 ATGCCTGCCTTCCTGCCT 61.345 61.111 0.00 0.00 0.00 4.75
343 344 0.457853 GCACACAAGATGCATGCCTG 60.458 55.000 16.68 9.75 42.88 4.85
371 372 5.238214 GTGATGGAGCTAGCCTTTAAGATTG 59.762 44.000 12.13 0.00 0.00 2.67
400 401 6.509523 TCACCCATACCCTTTTAGGATTAG 57.490 41.667 0.00 0.00 37.67 1.73
479 480 5.445088 CTTTGATAAAGTCCTCGGAACGGG 61.445 50.000 0.00 0.00 42.52 5.28
485 486 4.081309 TGGTACCTTTGATAAAGTCCTCGG 60.081 45.833 14.36 0.00 36.77 4.63
487 488 7.939784 ATTTGGTACCTTTGATAAAGTCCTC 57.060 36.000 14.36 0.00 36.77 3.71
506 537 5.833406 TTAGCCATGTGTGTGATATTTGG 57.167 39.130 0.00 0.00 0.00 3.28
509 540 7.828508 ATTCATTAGCCATGTGTGTGATATT 57.171 32.000 0.00 0.00 34.06 1.28
531 562 6.992063 ACTCACTCGCTCAATTTGATTATT 57.008 33.333 0.00 0.00 0.00 1.40
560 591 1.344065 TGGACGCTGGAGGTAAAAGA 58.656 50.000 0.00 0.00 0.00 2.52
567 598 2.403252 ACTTTTATGGACGCTGGAGG 57.597 50.000 0.00 0.00 0.00 4.30
622 653 0.597637 AGTCACACAACGAAGAGCGG 60.598 55.000 0.00 0.00 46.49 5.52
633 664 2.296190 AGATCAAGTACGCAGTCACACA 59.704 45.455 0.00 0.00 43.93 3.72
641 672 3.017442 AGTAGCAGAGATCAAGTACGCA 58.983 45.455 0.00 0.00 0.00 5.24
642 673 3.181495 ACAGTAGCAGAGATCAAGTACGC 60.181 47.826 0.00 0.00 0.00 4.42
645 678 5.010282 TCACACAGTAGCAGAGATCAAGTA 58.990 41.667 0.00 0.00 0.00 2.24
682 715 7.454225 GCCATAATCTAGGTGAAATAGTTCCT 58.546 38.462 0.00 0.00 32.28 3.36
683 716 6.655425 GGCCATAATCTAGGTGAAATAGTTCC 59.345 42.308 0.00 0.00 32.28 3.62
706 739 6.855836 TGATAGATCAAACTCAAAACATGGC 58.144 36.000 0.00 0.00 33.08 4.40
741 804 5.524646 GCATTGCAATGTTATTAGGCACAAT 59.475 36.000 33.67 0.00 38.65 2.71
755 818 1.338294 ACCACCACATGCATTGCAATG 60.338 47.619 30.92 30.92 43.62 2.82
756 819 0.978151 ACCACCACATGCATTGCAAT 59.022 45.000 16.46 5.99 43.62 3.56
766 829 3.176924 AGACTAGACAGACCACCACAT 57.823 47.619 0.00 0.00 0.00 3.21
796 859 4.066646 TGTGATCTTCGAACCAAACAGA 57.933 40.909 0.00 0.00 0.00 3.41
797 860 4.452114 TGATGTGATCTTCGAACCAAACAG 59.548 41.667 0.00 0.00 0.00 3.16
834 897 6.265577 AGAAATAATGGCAATCGTAAGCAAC 58.734 36.000 0.00 0.00 37.18 4.17
899 962 4.708726 AAGAAAGGTGATACTTGCATGC 57.291 40.909 11.82 11.82 0.00 4.06
1030 1101 8.455903 TCTTTAATTGATGAGGAATCACCATC 57.544 34.615 7.01 7.01 45.17 3.51
1031 1102 8.057623 ACTCTTTAATTGATGAGGAATCACCAT 58.942 33.333 14.96 0.00 45.17 3.55
1044 1115 4.026052 CCTTGGCCCACTCTTTAATTGAT 58.974 43.478 0.00 0.00 0.00 2.57
1058 1129 1.228510 CCTGGATTCTCCTTGGCCC 59.771 63.158 0.00 0.00 37.46 5.80
1175 1246 3.857549 TGACATCTGAAAGGAGAGACG 57.142 47.619 0.00 0.00 0.00 4.18
1186 1257 0.318120 TGCTCGCAGTTGACATCTGA 59.682 50.000 16.15 0.00 35.20 3.27
1219 1290 2.009774 GCCAAGTGTTACAGCGATGAT 58.990 47.619 8.12 0.00 0.00 2.45
1230 1301 1.636148 AAGATGCATGGCCAAGTGTT 58.364 45.000 10.96 0.00 0.00 3.32
1245 1316 8.883731 CACTCGAGTAAATATGAAACCAAAGAT 58.116 33.333 19.57 0.00 0.00 2.40
1253 1324 4.570772 GGCAGCACTCGAGTAAATATGAAA 59.429 41.667 19.57 0.00 0.00 2.69
1258 1329 1.801395 GCGGCAGCACTCGAGTAAATA 60.801 52.381 19.57 0.00 44.35 1.40
1276 1347 3.496155 GCCTCAATTCTTCTTCTTTGCG 58.504 45.455 0.00 0.00 0.00 4.85
1387 1458 4.729918 CAGGGCGGGCTCTGCTTT 62.730 66.667 7.73 0.00 37.76 3.51
1407 1478 1.340088 TGTACCTGGTCACGGCTTTA 58.660 50.000 0.63 0.00 0.00 1.85
1506 1577 1.402787 GGCCATACTTTCCCACATGG 58.597 55.000 0.00 0.00 40.80 3.66
1600 1671 7.164122 AGCTAGTTTGCTGCACATACATATAT 58.836 34.615 0.00 0.00 42.33 0.86
1745 1816 3.644265 TGCTAGGACAAGTCTTTGGTACA 59.356 43.478 0.00 0.00 38.66 2.90
1765 1836 1.575244 TAAGAGCACAGCGATGATGC 58.425 50.000 8.12 13.78 39.74 3.91
1773 1844 1.009829 CGATGGGTTAAGAGCACAGC 58.990 55.000 0.00 0.00 0.00 4.40
1813 1884 4.857871 TTTCGTCCGCAATATCTGAAAG 57.142 40.909 0.00 0.00 0.00 2.62
1829 1900 5.494632 AGAACGTTTCTCCAAAATTTCGT 57.505 34.783 0.46 0.00 34.07 3.85
1842 1913 0.534203 TGGCCAGGTGAGAACGTTTC 60.534 55.000 0.00 2.90 0.00 2.78
1849 1920 1.548357 GCTTCTCTGGCCAGGTGAGA 61.548 60.000 32.23 24.02 35.36 3.27
1853 1924 1.537397 TCAGCTTCTCTGGCCAGGT 60.537 57.895 32.23 10.60 43.06 4.00
1894 1965 3.721035 TGTCATGAGATACAGCCATTCG 58.279 45.455 0.00 0.00 0.00 3.34
1903 1974 4.795795 CACGTCAGACTTGTCATGAGATAC 59.204 45.833 0.00 0.00 0.00 2.24
1906 1977 2.608016 GCACGTCAGACTTGTCATGAGA 60.608 50.000 8.72 0.00 0.00 3.27
1909 1980 1.458445 CAGCACGTCAGACTTGTCATG 59.542 52.381 8.72 2.67 0.00 3.07
1911 1982 0.744281 TCAGCACGTCAGACTTGTCA 59.256 50.000 8.72 0.00 0.00 3.58
1930 2001 4.159693 AGAATCATGTTGCAGCAATGTGAT 59.840 37.500 22.77 22.77 34.37 3.06
1931 2002 3.508402 AGAATCATGTTGCAGCAATGTGA 59.492 39.130 20.97 20.97 0.00 3.58
1934 2005 4.744570 AGAAGAATCATGTTGCAGCAATG 58.255 39.130 11.96 6.76 0.00 2.82
1945 2016 9.674824 GGTTTCATATGCTAAAGAAGAATCATG 57.325 33.333 0.00 0.00 0.00 3.07
1952 2023 6.662414 TGTCGGTTTCATATGCTAAAGAAG 57.338 37.500 0.00 0.00 0.00 2.85
1979 2050 3.067461 CGAACAGAGGAGAGGATAACCAG 59.933 52.174 0.00 0.00 38.94 4.00
2033 2104 3.202097 GGGCAATAGAGAAGAAGCACTC 58.798 50.000 0.00 0.00 0.00 3.51
2054 2125 1.535860 CCGGGCAATAAAAAGCATCCG 60.536 52.381 0.00 0.00 36.00 4.18
2055 2126 1.480545 ACCGGGCAATAAAAAGCATCC 59.519 47.619 6.32 0.00 0.00 3.51
2072 2143 1.602851 CCGTACCATCTCTGAGTACCG 59.397 57.143 4.32 0.75 34.22 4.02
2099 2170 5.108517 TGTGAAGGCATGTCAAACTTTTTC 58.891 37.500 0.00 0.00 0.00 2.29
2226 2297 0.734889 ACTGCTGGATTGCGTAATGC 59.265 50.000 10.72 10.72 46.70 3.56
2298 2369 4.280436 ACCATGGTTGTCGAGAATTGTA 57.720 40.909 13.00 0.00 0.00 2.41
2349 2420 6.211584 AGTCTAAAGGCTTGTCTTCATCAGTA 59.788 38.462 0.00 0.00 0.00 2.74
2358 2429 2.339769 ACCCAGTCTAAAGGCTTGTCT 58.660 47.619 0.00 0.00 0.00 3.41
2440 2520 9.103861 GGATTCAATTAAAAACAAGGAACACAA 57.896 29.630 0.00 0.00 0.00 3.33
2442 2522 8.655651 TGGATTCAATTAAAAACAAGGAACAC 57.344 30.769 0.00 0.00 0.00 3.32
2444 2524 8.229811 GCATGGATTCAATTAAAAACAAGGAAC 58.770 33.333 0.00 0.00 0.00 3.62
2495 2612 2.371179 TCATCATTGGGATCAGCTCCTC 59.629 50.000 0.00 0.00 44.28 3.71
2497 2614 2.945080 TCATCATTGGGATCAGCTCC 57.055 50.000 0.00 0.00 44.11 4.70
2498 2615 3.752222 GTCATCATCATTGGGATCAGCTC 59.248 47.826 0.00 0.00 32.57 4.09
2546 2663 0.109723 AGTTTCCCGTTGCTTGGCTA 59.890 50.000 0.00 0.00 0.00 3.93
2592 2733 8.704234 GTGTTGTTTGTGTATTTTTGAGTTTGA 58.296 29.630 0.00 0.00 0.00 2.69
2594 2735 7.382759 ACGTGTTGTTTGTGTATTTTTGAGTTT 59.617 29.630 0.00 0.00 0.00 2.66
2612 2753 1.098869 TGCCACAAATGACGTGTTGT 58.901 45.000 0.00 0.00 38.49 3.32
2619 2760 4.737054 CAAGTAGGATTGCCACAAATGAC 58.263 43.478 0.00 0.00 36.29 3.06
2926 3067 4.293648 CCAGTGGACACGTGCGGA 62.294 66.667 17.22 0.00 36.20 5.54
2929 3070 3.022287 CAACCAGTGGACACGTGC 58.978 61.111 18.40 8.51 36.20 5.34
3196 3337 8.442660 TTTCCCCCAATGAATTAACAAGTAAT 57.557 30.769 0.00 0.00 33.58 1.89
3218 3359 7.434897 TGCAAGAATGAACTGTACAATGTTTTC 59.565 33.333 0.00 1.31 0.00 2.29
3242 3383 3.405170 AATGAACATCGAACGGAATGC 57.595 42.857 0.00 0.00 0.00 3.56
3252 3393 7.752239 AGCTGTCTTTCAAATTAATGAACATCG 59.248 33.333 0.00 0.00 38.95 3.84
3260 3401 9.247861 ACCATTAGAGCTGTCTTTCAAATTAAT 57.752 29.630 0.00 0.00 33.84 1.40
3261 3402 8.514594 CACCATTAGAGCTGTCTTTCAAATTAA 58.485 33.333 0.00 0.00 33.84 1.40
3262 3403 7.882791 TCACCATTAGAGCTGTCTTTCAAATTA 59.117 33.333 0.00 0.00 33.84 1.40
3263 3404 6.716628 TCACCATTAGAGCTGTCTTTCAAATT 59.283 34.615 0.00 0.00 33.84 1.82
3293 3434 5.475719 ACGTCCATTCTCGTCTTTCAAATA 58.524 37.500 0.00 0.00 35.30 1.40
3303 3444 2.362736 TGTAGCTACGTCCATTCTCGT 58.637 47.619 18.74 0.00 42.82 4.18
3344 3485 6.973843 TGTAGCTATGTTAAACCGTATCGAT 58.026 36.000 2.16 2.16 0.00 3.59
3347 3488 5.404667 GGCTGTAGCTATGTTAAACCGTATC 59.595 44.000 0.00 0.00 41.70 2.24
3432 3573 6.170506 TGTTTACCTAGCCTGTTGTATCTTG 58.829 40.000 0.00 0.00 0.00 3.02


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

AutoCloner maintained by Alex Coulton.