Multiple sequence alignment - TraesCS7D01G268700

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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 TraesCS7D01G268700 chr7D 100.000 3321 0 0 1 3321 252543435 252546755 0.000000e+00 6133
1 TraesCS7D01G268700 chr7B 93.624 2478 107 31 1 2452 229824883 229827335 0.000000e+00 3653
2 TraesCS7D01G268700 chr7B 87.635 833 61 24 2518 3321 229827467 229828286 0.000000e+00 929
3 TraesCS7D01G268700 chr7A 92.436 1613 102 11 853 2452 267570777 267569172 0.000000e+00 2285
4 TraesCS7D01G268700 chr7A 85.139 794 46 26 2577 3321 267569009 267568239 0.000000e+00 747
5 TraesCS7D01G268700 chr7A 86.341 410 26 9 437 821 267571183 267570779 1.420000e-113 420
6 TraesCS7D01G268700 chr7A 90.411 219 13 5 167 381 267571834 267571620 7.010000e-72 281
7 TraesCS7D01G268700 chr7A 87.117 163 13 3 9 169 267572020 267571864 9.470000e-41 178
8 TraesCS7D01G268700 chr1D 91.531 980 67 9 968 1940 168798731 168799701 0.000000e+00 1336
9 TraesCS7D01G268700 chr3A 89.481 694 57 11 1249 1935 327916402 327917086 0.000000e+00 863
10 TraesCS7D01G268700 chr3A 88.075 696 66 12 1252 1940 162275705 162275020 0.000000e+00 809
11 TraesCS7D01G268700 chr3A 87.840 699 68 12 1249 1940 367859246 367859934 0.000000e+00 804
12 TraesCS7D01G268700 chr6D 87.649 502 31 5 1444 1940 934124 933649 3.740000e-154 555
13 TraesCS7D01G268700 chr3B 78.205 234 27 11 169 383 814705898 814706126 9.670000e-26 128


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 TraesCS7D01G268700 chr7D 252543435 252546755 3320 False 6133.0 6133 100.0000 1 3321 1 chr7D.!!$F1 3320
1 TraesCS7D01G268700 chr7B 229824883 229828286 3403 False 2291.0 3653 90.6295 1 3321 2 chr7B.!!$F1 3320
2 TraesCS7D01G268700 chr7A 267568239 267572020 3781 True 782.2 2285 88.2888 9 3321 5 chr7A.!!$R1 3312
3 TraesCS7D01G268700 chr1D 168798731 168799701 970 False 1336.0 1336 91.5310 968 1940 1 chr1D.!!$F1 972
4 TraesCS7D01G268700 chr3A 327916402 327917086 684 False 863.0 863 89.4810 1249 1935 1 chr3A.!!$F1 686
5 TraesCS7D01G268700 chr3A 162275020 162275705 685 True 809.0 809 88.0750 1252 1940 1 chr3A.!!$R1 688
6 TraesCS7D01G268700 chr3A 367859246 367859934 688 False 804.0 804 87.8400 1249 1940 1 chr3A.!!$F2 691

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
474 898 0.109319 CCCGCAGCACCAACATAAAC 60.109 55.0 0.00 0.0 0.0 2.01 F
1676 2156 0.393820 TTTACAAGAAGGGTCGCGGT 59.606 50.0 6.13 0.0 0.0 5.68 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2006 2490 0.179137 CTGCTGCAGGAATGCACATG 60.179 55.0 21.71 0.0 40.23 3.21 R
3109 3739 0.036732 AGCTGAAATCCCGCAGACAA 59.963 50.0 0.00 0.0 34.06 3.18 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
319 358 6.539826 TGAATGAGCAGAACGAACATCATAAT 59.460 34.615 0.00 0.00 0.00 1.28
471 895 1.673993 CACCCGCAGCACCAACATA 60.674 57.895 0.00 0.00 0.00 2.29
472 896 1.074072 ACCCGCAGCACCAACATAA 59.926 52.632 0.00 0.00 0.00 1.90
473 897 0.538516 ACCCGCAGCACCAACATAAA 60.539 50.000 0.00 0.00 0.00 1.40
474 898 0.109319 CCCGCAGCACCAACATAAAC 60.109 55.000 0.00 0.00 0.00 2.01
583 1011 3.191539 GGAGAGCGCGCAAGAAGG 61.192 66.667 35.10 0.00 43.02 3.46
660 1113 0.685458 GGGTGACGGCTAGGGTTAGA 60.685 60.000 0.00 0.00 0.00 2.10
824 1281 4.345859 TGTAATGGTCGGCCCTTATAAG 57.654 45.455 2.12 5.43 29.73 1.73
826 1283 3.487120 AATGGTCGGCCCTTATAAGAC 57.513 47.619 14.28 5.58 0.00 3.01
827 1284 2.170012 TGGTCGGCCCTTATAAGACT 57.830 50.000 14.28 0.00 32.86 3.24
828 1285 2.474112 TGGTCGGCCCTTATAAGACTT 58.526 47.619 14.28 0.00 32.86 3.01
829 1286 3.645434 TGGTCGGCCCTTATAAGACTTA 58.355 45.455 14.28 0.00 32.86 2.24
830 1287 3.385755 TGGTCGGCCCTTATAAGACTTAC 59.614 47.826 14.28 5.46 32.86 2.34
1276 1741 3.494336 CCAAGCTGCTCTTCGCCG 61.494 66.667 1.00 0.00 38.05 6.46
1293 1758 4.176752 GTCCGCATCCCAGGGTCC 62.177 72.222 5.01 0.00 0.00 4.46
1308 1778 2.056223 GTCCGTGCCTGCCTACCTA 61.056 63.158 0.00 0.00 0.00 3.08
1311 1783 0.743345 CCGTGCCTGCCTACCTAAAC 60.743 60.000 0.00 0.00 0.00 2.01
1313 1785 0.618981 GTGCCTGCCTACCTAAACCT 59.381 55.000 0.00 0.00 0.00 3.50
1314 1786 1.835531 GTGCCTGCCTACCTAAACCTA 59.164 52.381 0.00 0.00 0.00 3.08
1315 1787 2.237893 GTGCCTGCCTACCTAAACCTAA 59.762 50.000 0.00 0.00 0.00 2.69
1316 1788 2.914278 TGCCTGCCTACCTAAACCTAAA 59.086 45.455 0.00 0.00 0.00 1.85
1317 1789 3.054655 TGCCTGCCTACCTAAACCTAAAG 60.055 47.826 0.00 0.00 0.00 1.85
1318 1790 3.542648 CCTGCCTACCTAAACCTAAAGC 58.457 50.000 0.00 0.00 0.00 3.51
1319 1791 3.054655 CCTGCCTACCTAAACCTAAAGCA 60.055 47.826 0.00 0.00 0.00 3.91
1320 1792 4.385310 CCTGCCTACCTAAACCTAAAGCAT 60.385 45.833 0.00 0.00 0.00 3.79
1344 1816 1.467734 CTTGTCTGACTTGCTGATGGC 59.532 52.381 9.51 0.00 42.22 4.40
1367 1839 2.724690 CCTCGCGGTTATTAACATCGAG 59.275 50.000 25.96 25.96 45.60 4.04
1393 1866 3.364441 TGTGATTGCAGCACCGCC 61.364 61.111 16.22 0.00 35.43 6.13
1538 2016 5.817816 GTCACCTATGGGTAACTGAATGAAG 59.182 44.000 0.00 0.00 45.41 3.02
1676 2156 0.393820 TTTACAAGAAGGGTCGCGGT 59.606 50.000 6.13 0.00 0.00 5.68
1769 2249 1.558756 CTGGAGATTGAGGTTCAGGCT 59.441 52.381 0.00 0.00 0.00 4.58
1826 2307 6.465321 GGCAACCTAGTAATAGGCATAGGAAA 60.465 42.308 16.11 0.00 40.90 3.13
1838 2319 5.320277 AGGCATAGGAAATAATCAGGAAGC 58.680 41.667 0.00 0.00 0.00 3.86
1883 2364 6.889722 TGTTAGCTTTATTTAGCCAGTTCCAT 59.110 34.615 0.00 0.00 42.20 3.41
1912 2393 9.725019 TTGCTAAGAAACTTGAATATCTTCAGA 57.275 29.630 0.00 0.00 42.19 3.27
1951 2432 8.862325 ACCAATAATAATGTGTTTCAGACTCA 57.138 30.769 0.00 0.00 36.31 3.41
1957 2438 2.771089 TGTGTTTCAGACTCAGATGCC 58.229 47.619 0.00 0.00 0.00 4.40
1963 2444 1.003580 TCAGACTCAGATGCCCCAAAC 59.996 52.381 0.00 0.00 0.00 2.93
1964 2445 1.067295 AGACTCAGATGCCCCAAACA 58.933 50.000 0.00 0.00 0.00 2.83
1971 2454 1.203038 AGATGCCCCAAACATGACACA 60.203 47.619 0.00 0.00 0.00 3.72
1972 2455 0.968405 ATGCCCCAAACATGACACAC 59.032 50.000 0.00 0.00 0.00 3.82
1986 2470 4.418013 TGACACACAAACACTTCAGTTG 57.582 40.909 0.00 0.00 0.00 3.16
1995 2479 7.504238 ACACAAACACTTCAGTTGGGATAATTA 59.496 33.333 0.00 0.00 0.00 1.40
1997 2481 8.739972 ACAAACACTTCAGTTGGGATAATTATC 58.260 33.333 15.88 15.88 0.00 1.75
1999 2483 9.533831 AAACACTTCAGTTGGGATAATTATCTT 57.466 29.630 21.80 4.22 33.28 2.40
2000 2484 8.738645 ACACTTCAGTTGGGATAATTATCTTC 57.261 34.615 21.80 15.50 33.28 2.87
2001 2485 8.328758 ACACTTCAGTTGGGATAATTATCTTCA 58.671 33.333 21.80 17.41 33.28 3.02
2002 2486 9.347240 CACTTCAGTTGGGATAATTATCTTCAT 57.653 33.333 21.80 7.27 33.28 2.57
2003 2487 9.927081 ACTTCAGTTGGGATAATTATCTTCATT 57.073 29.630 21.80 11.00 33.28 2.57
2006 2490 9.793259 TCAGTTGGGATAATTATCTTCATTACC 57.207 33.333 21.80 14.11 33.28 2.85
2007 2491 9.573166 CAGTTGGGATAATTATCTTCATTACCA 57.427 33.333 21.80 16.12 33.28 3.25
2033 2522 4.978083 CATTCCTGCAGCAGAACTATTT 57.022 40.909 24.90 0.00 32.44 1.40
2047 2536 9.039870 AGCAGAACTATTTTCTGAATTATCTCG 57.960 33.333 16.41 0.00 46.57 4.04
2059 2548 8.026341 TCTGAATTATCTCGCATGATGATTTC 57.974 34.615 0.00 0.00 34.30 2.17
2066 2555 4.448732 TCTCGCATGATGATTTCGTAATGG 59.551 41.667 0.00 0.00 0.00 3.16
2073 2562 6.421377 TGATGATTTCGTAATGGACACTTG 57.579 37.500 0.00 0.00 0.00 3.16
2122 2611 1.227853 GGCACTTGGAGAACACGGT 60.228 57.895 0.00 0.00 0.00 4.83
2131 2620 1.933853 GGAGAACACGGTGTCATATGC 59.066 52.381 15.09 0.00 0.00 3.14
2248 2737 1.012841 GGCTGCGGATGAAGAAGAAG 58.987 55.000 0.00 0.00 0.00 2.85
2329 2818 0.607620 AGCTGAACTGAGGCAGTCTC 59.392 55.000 0.00 0.00 44.62 3.36
2334 2823 0.398318 AACTGAGGCAGTCTCCAACC 59.602 55.000 0.00 0.00 44.62 3.77
2337 2826 1.376553 GAGGCAGTCTCCAACCTGC 60.377 63.158 3.12 3.12 41.60 4.85
2339 2828 2.031163 GCAGTCTCCAACCTGCGT 59.969 61.111 0.00 0.00 33.04 5.24
2342 2831 2.432628 GTCTCCAACCTGCGTCCG 60.433 66.667 0.00 0.00 0.00 4.79
2424 2913 1.872773 TTGTTTTGGAAACCCTGCCT 58.127 45.000 1.53 0.00 0.00 4.75
2461 2957 6.817396 TCAAATCACGAAATACTGTTCTTCG 58.183 36.000 17.20 17.20 45.65 3.79
2474 2987 3.764466 CTTCGCCCCTCGCTCTGT 61.764 66.667 0.00 0.00 38.27 3.41
2475 2988 3.708220 CTTCGCCCCTCGCTCTGTC 62.708 68.421 0.00 0.00 38.27 3.51
2480 2993 1.984570 CCCCTCGCTCTGTCCTTCA 60.985 63.158 0.00 0.00 0.00 3.02
2504 3017 1.878775 GATCTGCCGTGCTTTGCTT 59.121 52.632 0.00 0.00 0.00 3.91
2505 3018 0.455633 GATCTGCCGTGCTTTGCTTG 60.456 55.000 0.00 0.00 0.00 4.01
2506 3019 2.482296 ATCTGCCGTGCTTTGCTTGC 62.482 55.000 0.00 0.00 0.00 4.01
2507 3020 4.627447 TGCCGTGCTTTGCTTGCG 62.627 61.111 0.00 0.00 0.00 4.85
2510 3023 3.095278 CGTGCTTTGCTTGCGCTG 61.095 61.111 9.73 2.28 38.62 5.18
2511 3024 2.332514 GTGCTTTGCTTGCGCTGA 59.667 55.556 9.73 0.00 37.87 4.26
2514 3072 1.728426 GCTTTGCTTGCGCTGACAG 60.728 57.895 9.73 0.00 36.97 3.51
2518 3076 0.815213 TTGCTTGCGCTGACAGACTT 60.815 50.000 9.73 0.00 36.97 3.01
2519 3077 0.033366 TGCTTGCGCTGACAGACTTA 59.967 50.000 9.73 0.00 36.97 2.24
2569 3127 2.125350 GGTTCTCTGGGCGCTCTG 60.125 66.667 9.62 8.76 0.00 3.35
2603 3161 4.836125 TTTGCCAGATTTGAGAACACTC 57.164 40.909 0.00 0.00 0.00 3.51
2636 3195 4.303086 GCAATTCTTCATGCTGCATACT 57.697 40.909 15.78 0.00 39.46 2.12
2637 3196 4.042398 GCAATTCTTCATGCTGCATACTG 58.958 43.478 15.78 5.01 39.46 2.74
2638 3197 4.201980 GCAATTCTTCATGCTGCATACTGA 60.202 41.667 15.78 7.61 39.46 3.41
2639 3198 5.271625 CAATTCTTCATGCTGCATACTGAC 58.728 41.667 15.78 0.00 0.00 3.51
2640 3199 3.900966 TCTTCATGCTGCATACTGACT 57.099 42.857 15.78 0.00 0.00 3.41
2641 3200 3.528532 TCTTCATGCTGCATACTGACTG 58.471 45.455 15.78 2.61 0.00 3.51
2681 3252 0.537143 AAACAGCGAACCTGCATCCA 60.537 50.000 0.00 0.00 45.78 3.41
2865 3474 2.125512 CTCCACCTACCGCAGCAC 60.126 66.667 0.00 0.00 0.00 4.40
2868 3477 2.434884 CACCTACCGCAGCACCAG 60.435 66.667 0.00 0.00 0.00 4.00
3013 3631 0.803768 CTCCTCACACAGAATCGCCG 60.804 60.000 0.00 0.00 0.00 6.46
3032 3662 1.201855 CGCTCGTTTTGCTAGCAGAAG 60.202 52.381 20.12 13.86 35.85 2.85
3033 3663 1.801178 GCTCGTTTTGCTAGCAGAAGT 59.199 47.619 20.12 0.00 36.11 3.01
3047 3677 2.035632 CAGAAGTGCTAGGACTAGGGG 58.964 57.143 18.05 4.28 33.87 4.79
3048 3678 0.753867 GAAGTGCTAGGACTAGGGGC 59.246 60.000 18.05 1.80 33.87 5.80
3049 3679 1.043673 AAGTGCTAGGACTAGGGGCG 61.044 60.000 18.05 0.00 33.87 6.13
3050 3680 2.838225 TGCTAGGACTAGGGGCGC 60.838 66.667 0.00 0.00 33.87 6.53
3070 3700 1.176527 CCCATGAATTGGTCTTGCGT 58.823 50.000 0.00 0.00 44.83 5.24
3109 3739 2.435805 AGATCACGCATAGGGTTCATGT 59.564 45.455 0.00 0.00 0.00 3.21
3119 3749 1.586154 GGGTTCATGTTGTCTGCGGG 61.586 60.000 0.00 0.00 0.00 6.13
3121 3751 1.453155 GTTCATGTTGTCTGCGGGAT 58.547 50.000 0.00 0.00 0.00 3.85
3145 3775 4.998051 TCAGCTAGAAATTGGGGAAAAGT 58.002 39.130 0.00 0.00 0.00 2.66
3186 3816 3.687572 TCTGGTCGTTTCTATCGCTAC 57.312 47.619 0.00 0.00 0.00 3.58
3191 3821 3.246226 GGTCGTTTCTATCGCTACGAGTA 59.754 47.826 0.00 0.00 42.83 2.59
3211 3841 3.456380 ACCCATACCATTTGCTTCTGT 57.544 42.857 0.00 0.00 0.00 3.41
3229 3859 5.281693 TCTGTTGCTATGATTTGTTCACG 57.718 39.130 0.00 0.00 37.11 4.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
319 358 2.614481 GGACGGATTGGTGCTTAACTGA 60.614 50.000 0.00 0.00 0.00 3.41
471 895 8.797350 AAAAGGTACAGTACTGTAGTTTGTTT 57.203 30.769 31.32 22.53 45.61 2.83
473 897 9.485206 CATAAAAGGTACAGTACTGTAGTTTGT 57.515 33.333 31.32 24.19 45.61 2.83
474 898 8.932791 CCATAAAAGGTACAGTACTGTAGTTTG 58.067 37.037 31.32 21.15 45.61 2.93
660 1113 0.314302 CTCTCGTTCGTGGTCCAAGT 59.686 55.000 4.63 0.00 0.00 3.16
824 1281 3.582780 CGAACCCACCAGTTAGTAAGTC 58.417 50.000 0.00 0.00 0.00 3.01
826 1283 2.933928 GCCGAACCCACCAGTTAGTAAG 60.934 54.545 0.00 0.00 0.00 2.34
827 1284 1.002315 GCCGAACCCACCAGTTAGTAA 59.998 52.381 0.00 0.00 0.00 2.24
828 1285 0.609662 GCCGAACCCACCAGTTAGTA 59.390 55.000 0.00 0.00 0.00 1.82
829 1286 1.125711 AGCCGAACCCACCAGTTAGT 61.126 55.000 0.00 0.00 0.00 2.24
830 1287 0.036306 AAGCCGAACCCACCAGTTAG 59.964 55.000 0.00 0.00 0.00 2.34
1276 1741 4.176752 GGACCCTGGGATGCGGAC 62.177 72.222 22.23 1.50 0.00 4.79
1293 1758 0.743345 GGTTTAGGTAGGCAGGCACG 60.743 60.000 0.00 0.00 0.00 5.34
1300 1770 3.315470 GCATGCTTTAGGTTTAGGTAGGC 59.685 47.826 11.37 0.00 0.00 3.93
1308 1778 3.891366 AGACAAGTGCATGCTTTAGGTTT 59.109 39.130 20.33 3.51 0.00 3.27
1311 1783 3.076621 TCAGACAAGTGCATGCTTTAGG 58.923 45.455 20.33 7.28 0.00 2.69
1313 1785 3.743521 AGTCAGACAAGTGCATGCTTTA 58.256 40.909 20.33 0.00 0.00 1.85
1314 1786 2.579873 AGTCAGACAAGTGCATGCTTT 58.420 42.857 20.33 10.62 0.00 3.51
1315 1787 2.267174 AGTCAGACAAGTGCATGCTT 57.733 45.000 20.33 2.28 0.00 3.91
1316 1788 1.878088 CAAGTCAGACAAGTGCATGCT 59.122 47.619 20.33 0.00 0.00 3.79
1317 1789 1.665161 GCAAGTCAGACAAGTGCATGC 60.665 52.381 11.82 11.82 35.28 4.06
1318 1790 1.878088 AGCAAGTCAGACAAGTGCATG 59.122 47.619 20.09 0.00 37.68 4.06
1319 1791 1.878088 CAGCAAGTCAGACAAGTGCAT 59.122 47.619 20.09 7.77 37.68 3.96
1320 1792 1.134431 TCAGCAAGTCAGACAAGTGCA 60.134 47.619 20.09 4.14 37.68 4.57
1353 1825 5.443763 CACGCGAAAACTCGATGTTAATAAC 59.556 40.000 15.93 0.00 38.03 1.89
1367 1839 1.044725 CTGCAATCACACGCGAAAAC 58.955 50.000 15.93 0.00 0.00 2.43
1498 1972 3.264866 GACGAACGGTCCGACAGCT 62.265 63.158 20.51 0.00 39.90 4.24
1676 2156 4.007659 GGAAAGGCTCCTTGTCGAAATAA 58.992 43.478 1.33 0.00 41.61 1.40
1769 2249 5.219633 GCCAAAGCTTTACTTGAATCGAAA 58.780 37.500 12.25 0.00 39.09 3.46
1826 2307 4.164796 TCACTGACATGGCTTCCTGATTAT 59.835 41.667 0.00 0.00 0.00 1.28
1834 2315 2.676839 CACAGATCACTGACATGGCTTC 59.323 50.000 0.00 0.00 46.03 3.86
1838 2319 1.065636 AGGCACAGATCACTGACATGG 60.066 52.381 0.00 0.00 46.03 3.66
1905 2386 5.163205 TGGTCCAGAATTTGAACTCTGAAGA 60.163 40.000 3.94 0.00 41.38 2.87
1919 2400 9.253832 TGAAACACATTATTATTGGTCCAGAAT 57.746 29.630 6.39 6.39 0.00 2.40
1940 2421 1.003580 TGGGGCATCTGAGTCTGAAAC 59.996 52.381 3.62 0.00 0.00 2.78
1943 2424 1.003580 GTTTGGGGCATCTGAGTCTGA 59.996 52.381 1.83 1.83 0.00 3.27
1951 2432 1.203038 TGTGTCATGTTTGGGGCATCT 60.203 47.619 0.00 0.00 0.00 2.90
1957 2438 3.119173 AGTGTTTGTGTGTCATGTTTGGG 60.119 43.478 0.00 0.00 0.00 4.12
1963 2444 4.621068 ACTGAAGTGTTTGTGTGTCATG 57.379 40.909 0.00 0.00 0.00 3.07
1964 2445 4.142403 CCAACTGAAGTGTTTGTGTGTCAT 60.142 41.667 0.00 0.00 0.00 3.06
1971 2454 6.976934 AATTATCCCAACTGAAGTGTTTGT 57.023 33.333 0.00 0.00 0.00 2.83
1972 2455 8.960591 AGATAATTATCCCAACTGAAGTGTTTG 58.039 33.333 19.67 0.00 33.17 2.93
1986 2470 8.462016 GCACATGGTAATGAAGATAATTATCCC 58.538 37.037 19.67 12.94 37.24 3.85
1995 2479 5.301045 CAGGAATGCACATGGTAATGAAGAT 59.699 40.000 0.00 0.00 37.24 2.40
1997 2481 4.735578 GCAGGAATGCACATGGTAATGAAG 60.736 45.833 0.00 0.00 37.24 3.02
1999 2483 2.689471 GCAGGAATGCACATGGTAATGA 59.311 45.455 0.00 0.00 37.24 2.57
2000 2484 2.427812 TGCAGGAATGCACATGGTAATG 59.572 45.455 0.00 0.00 40.23 1.90
2001 2485 2.691526 CTGCAGGAATGCACATGGTAAT 59.308 45.455 5.57 0.00 40.23 1.89
2002 2486 2.093890 CTGCAGGAATGCACATGGTAA 58.906 47.619 5.57 0.00 40.23 2.85
2003 2487 1.753930 CTGCAGGAATGCACATGGTA 58.246 50.000 5.57 0.00 40.23 3.25
2004 2488 1.601419 GCTGCAGGAATGCACATGGT 61.601 55.000 17.12 0.00 40.23 3.55
2006 2490 0.179137 CTGCTGCAGGAATGCACATG 60.179 55.000 21.71 0.00 40.23 3.21
2007 2491 0.323087 TCTGCTGCAGGAATGCACAT 60.323 50.000 27.79 0.00 40.23 3.21
2016 2505 4.005650 TCAGAAAATAGTTCTGCTGCAGG 58.994 43.478 27.79 10.85 44.08 4.85
2021 2510 9.039870 CGAGATAATTCAGAAAATAGTTCTGCT 57.960 33.333 10.55 2.28 44.08 4.24
2025 2514 9.591404 CATGCGAGATAATTCAGAAAATAGTTC 57.409 33.333 0.00 0.00 0.00 3.01
2033 2522 7.974482 AATCATCATGCGAGATAATTCAGAA 57.026 32.000 0.00 0.00 0.00 3.02
2047 2536 5.008019 AGTGTCCATTACGAAATCATCATGC 59.992 40.000 0.00 0.00 0.00 4.06
2059 2548 6.420903 ACGATGATTATCAAGTGTCCATTACG 59.579 38.462 0.00 0.00 32.67 3.18
2066 2555 5.331607 GCACGTACGATGATTATCAAGTGTC 60.332 44.000 24.41 1.35 32.67 3.67
2073 2562 5.231357 TCACAAAGCACGTACGATGATTATC 59.769 40.000 24.41 3.67 0.00 1.75
2122 2611 3.261580 CACGTCTTCCAAGCATATGACA 58.738 45.455 6.97 0.00 0.00 3.58
2131 2620 1.941812 GTGCACCACGTCTTCCAAG 59.058 57.895 5.22 0.00 0.00 3.61
2170 2659 0.387929 TCGCCGTTTCTCTGAAGTGT 59.612 50.000 0.00 0.00 0.00 3.55
2248 2737 2.054453 GCCACCATCCTTGAAGGGC 61.054 63.158 11.99 1.52 35.59 5.19
2342 2831 0.248215 CGGATCCATCGCTTGTTTGC 60.248 55.000 13.41 0.00 0.00 3.68
2424 2913 3.501828 CGTGATTTGATCCCAAACACTCA 59.498 43.478 11.16 0.00 44.16 3.41
2461 2957 3.378399 GAAGGACAGAGCGAGGGGC 62.378 68.421 0.00 0.00 44.05 5.80
2474 2987 1.000171 CGGCAGATCGATCATGAAGGA 60.000 52.381 26.47 0.00 0.00 3.36
2475 2988 1.269988 ACGGCAGATCGATCATGAAGG 60.270 52.381 26.47 12.65 0.00 3.46
2480 2993 0.105593 AAGCACGGCAGATCGATCAT 59.894 50.000 26.47 9.59 0.00 2.45
2504 3017 0.958822 TCACTAAGTCTGTCAGCGCA 59.041 50.000 11.47 0.00 0.00 6.09
2505 3018 1.623359 CTCACTAAGTCTGTCAGCGC 58.377 55.000 0.00 0.00 0.00 5.92
2506 3019 1.542030 ACCTCACTAAGTCTGTCAGCG 59.458 52.381 0.00 0.00 0.00 5.18
2507 3020 3.321497 CAACCTCACTAAGTCTGTCAGC 58.679 50.000 0.00 0.00 0.00 4.26
2510 3023 4.220821 TCATCCAACCTCACTAAGTCTGTC 59.779 45.833 0.00 0.00 0.00 3.51
2511 3024 4.160329 TCATCCAACCTCACTAAGTCTGT 58.840 43.478 0.00 0.00 0.00 3.41
2514 3072 6.203723 GCAATATCATCCAACCTCACTAAGTC 59.796 42.308 0.00 0.00 0.00 3.01
2518 3076 5.628797 TGCAATATCATCCAACCTCACTA 57.371 39.130 0.00 0.00 0.00 2.74
2519 3077 4.508551 TGCAATATCATCCAACCTCACT 57.491 40.909 0.00 0.00 0.00 3.41
2569 3127 8.458843 TCAAATCTGGCAAAATAGCTAAAGTAC 58.541 33.333 0.00 0.00 34.17 2.73
2634 3193 5.046014 ACATTCTTCTTCCTATGCAGTCAGT 60.046 40.000 0.00 0.00 0.00 3.41
2635 3194 5.426504 ACATTCTTCTTCCTATGCAGTCAG 58.573 41.667 0.00 0.00 0.00 3.51
2636 3195 5.426689 ACATTCTTCTTCCTATGCAGTCA 57.573 39.130 0.00 0.00 0.00 3.41
2637 3196 5.448360 GCAACATTCTTCTTCCTATGCAGTC 60.448 44.000 0.00 0.00 0.00 3.51
2638 3197 4.397417 GCAACATTCTTCTTCCTATGCAGT 59.603 41.667 0.00 0.00 0.00 4.40
2639 3198 4.397103 TGCAACATTCTTCTTCCTATGCAG 59.603 41.667 0.00 0.00 36.46 4.41
2640 3199 4.334552 TGCAACATTCTTCTTCCTATGCA 58.665 39.130 0.00 0.00 38.78 3.96
2641 3200 4.970662 TGCAACATTCTTCTTCCTATGC 57.029 40.909 0.00 0.00 0.00 3.14
2647 3216 3.423206 CGCTGTTTGCAACATTCTTCTTC 59.577 43.478 0.00 0.00 41.26 2.87
2671 3242 1.078214 CGTGGACATGGATGCAGGT 60.078 57.895 3.51 3.51 0.00 4.00
2681 3252 0.461339 GCCATCGTAACCGTGGACAT 60.461 55.000 0.00 0.00 37.41 3.06
2751 3331 3.390521 CTGGGCCGAGTACCAGCA 61.391 66.667 6.60 0.00 46.78 4.41
2774 3354 2.594592 GACGCCAAGCAACCAGGT 60.595 61.111 0.00 0.00 0.00 4.00
2892 3504 2.419198 GCGCCGATGACATCCTCT 59.581 61.111 9.87 0.00 0.00 3.69
2965 3577 1.603455 CGGGGAGCTTGCCTTGAAA 60.603 57.895 0.00 0.00 0.00 2.69
3013 3631 1.801178 ACTTCTGCTAGCAAAACGAGC 59.199 47.619 19.86 0.00 46.33 5.03
3032 3662 3.130227 CGCCCCTAGTCCTAGCAC 58.870 66.667 0.00 0.00 31.95 4.40
3033 3663 2.838225 GCGCCCCTAGTCCTAGCA 60.838 66.667 0.00 0.00 31.95 3.49
3045 3675 3.539791 CCAATTCATGGGGCGCCC 61.540 66.667 38.57 38.57 46.27 6.13
3070 3700 5.690409 GTGATCTCGTTATCCGAATTAGCAA 59.310 40.000 0.00 0.00 46.75 3.91
3089 3719 2.838736 ACATGAACCCTATGCGTGATC 58.161 47.619 0.00 0.00 0.00 2.92
3109 3739 0.036732 AGCTGAAATCCCGCAGACAA 59.963 50.000 0.00 0.00 34.06 3.18
3145 3775 0.255890 GCTATGGGCAGAGGAACCAA 59.744 55.000 0.00 0.00 41.35 3.67
3186 3816 3.194005 AGCAAATGGTATGGGTACTCG 57.806 47.619 0.00 0.00 0.00 4.18
3191 3821 3.456380 ACAGAAGCAAATGGTATGGGT 57.544 42.857 0.00 0.00 0.00 4.51
3211 3841 2.163412 GGCCGTGAACAAATCATAGCAA 59.837 45.455 0.00 0.00 40.97 3.91
3229 3859 2.281484 TGCCAGACAAACTCGGCC 60.281 61.111 0.00 0.00 39.93 6.13


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

AutoCloner maintained by Alex Coulton.