Multiple sequence alignment - TraesCS7D01G120400

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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 TraesCS7D01G120400 chr7D 100.000 4325 0 0 1 4325 74597040 74601364 0.000000e+00 7987
1 TraesCS7D01G120400 chr7D 86.147 231 18 6 3092 3322 74867040 74867256 2.010000e-58 237
2 TraesCS7D01G120400 chr7A 92.181 4374 217 58 1 4325 78508277 78512574 0.000000e+00 6067
3 TraesCS7D01G120400 chr7A 80.288 624 62 31 3098 3677 78564791 78565397 8.650000e-112 414
4 TraesCS7D01G120400 chr7B 96.923 2015 50 6 2313 4325 18207430 18209434 0.000000e+00 3367
5 TraesCS7D01G120400 chr7B 90.843 1780 105 31 433 2198 18205583 18207318 0.000000e+00 2331
6 TraesCS7D01G120400 chr7B 90.476 336 31 1 2887 3222 18449161 18449495 3.970000e-120 442
7 TraesCS7D01G120400 chr7B 82.670 352 47 8 1 343 18203582 18203928 2.530000e-77 300
8 TraesCS7D01G120400 chr7B 96.907 97 3 0 2231 2327 18207316 18207412 3.460000e-36 163
9 TraesCS7D01G120400 chr1D 84.839 963 117 22 2374 3324 455114995 455115940 0.000000e+00 942
10 TraesCS7D01G120400 chr1D 77.954 948 153 26 757 1683 455113487 455114399 3.800000e-150 542
11 TraesCS7D01G120400 chr1B 86.269 772 92 8 2531 3298 625809566 625810327 0.000000e+00 826
12 TraesCS7D01G120400 chr1B 77.529 939 166 27 757 1692 625808671 625809567 1.380000e-144 523
13 TraesCS7D01G120400 chr1B 87.019 208 22 4 1478 1684 625777303 625777506 3.360000e-56 230
14 TraesCS7D01G120400 chr1A 78.505 856 126 28 869 1704 549047490 549048307 3.860000e-140 508
15 TraesCS7D01G120400 chr1A 76.826 876 135 40 2786 3614 549054072 549054926 8.590000e-117 431
16 TraesCS7D01G120400 chr1A 84.941 425 48 10 2376 2791 549048853 549049270 2.410000e-112 416


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 TraesCS7D01G120400 chr7D 74597040 74601364 4324 False 7987.00 7987 100.00000 1 4325 1 chr7D.!!$F1 4324
1 TraesCS7D01G120400 chr7A 78508277 78512574 4297 False 6067.00 6067 92.18100 1 4325 1 chr7A.!!$F1 4324
2 TraesCS7D01G120400 chr7A 78564791 78565397 606 False 414.00 414 80.28800 3098 3677 1 chr7A.!!$F2 579
3 TraesCS7D01G120400 chr7B 18203582 18209434 5852 False 1540.25 3367 91.83575 1 4325 4 chr7B.!!$F2 4324
4 TraesCS7D01G120400 chr1D 455113487 455115940 2453 False 742.00 942 81.39650 757 3324 2 chr1D.!!$F1 2567
5 TraesCS7D01G120400 chr1B 625808671 625810327 1656 False 674.50 826 81.89900 757 3298 2 chr1B.!!$F2 2541
6 TraesCS7D01G120400 chr1A 549047490 549049270 1780 False 462.00 508 81.72300 869 2791 2 chr1A.!!$F2 1922
7 TraesCS7D01G120400 chr1A 549054072 549054926 854 False 431.00 431 76.82600 2786 3614 1 chr1A.!!$F1 828

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
481 2063 0.511221 TTGCGTAAACTGCTCGAAGC 59.489 50.0 0.0 0.0 42.82 3.86 F
1177 2791 0.108329 CTACTACCCACAAGGCACCG 60.108 60.0 0.0 0.0 40.58 4.94 F
1515 3148 0.833287 ACTTGCTATCCTGCGATGGT 59.167 50.0 0.0 0.0 35.36 3.55 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2213 4200 0.984230 TTGGCTCACTGGAAGGGTAG 59.016 55.000 0.0 0.0 39.54 3.18 R
2948 4976 1.474077 GTCCTTGGGTGATCATTGTGC 59.526 52.381 0.0 0.0 0.00 4.57 R
3362 5451 5.505780 CCCATAGTAACATCCAAAAGGTCA 58.494 41.667 0.0 0.0 0.00 4.02 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
91 105 2.338984 GCCCCGTAGATACCAGCG 59.661 66.667 0.00 0.00 0.00 5.18
138 152 2.881352 GTACGTGCTGCTCGCTCC 60.881 66.667 22.17 8.02 40.11 4.70
162 176 2.987125 GCCCCAGTTCTTCGGCTA 59.013 61.111 0.00 0.00 38.41 3.93
223 237 5.880164 AAGCTAGTAGATTTCTTCCCCTC 57.120 43.478 0.00 0.00 0.00 4.30
252 266 2.090775 AGGGGTTCCATTTTGTTCCAGT 60.091 45.455 0.00 0.00 34.83 4.00
276 290 1.745653 TGATGGTCTGAGCTCGTAGTG 59.254 52.381 9.64 0.00 0.00 2.74
412 1979 5.234972 CAGAAACAAAGTCTTGCCATTTTCC 59.765 40.000 0.00 0.00 35.84 3.13
414 1981 4.961438 ACAAAGTCTTGCCATTTTCCAT 57.039 36.364 0.00 0.00 35.84 3.41
421 1988 4.567959 GTCTTGCCATTTTCCATAACATGC 59.432 41.667 0.00 0.00 0.00 4.06
423 1990 2.757314 TGCCATTTTCCATAACATGCGA 59.243 40.909 0.00 0.00 0.00 5.10
431 1998 7.566760 TTTTCCATAACATGCGAGTATGATT 57.433 32.000 8.11 2.30 0.00 2.57
433 2000 5.852827 TCCATAACATGCGAGTATGATTGA 58.147 37.500 8.11 0.00 0.00 2.57
434 2001 6.466812 TCCATAACATGCGAGTATGATTGAT 58.533 36.000 8.11 0.00 0.00 2.57
435 2002 6.591448 TCCATAACATGCGAGTATGATTGATC 59.409 38.462 8.11 0.00 0.00 2.92
442 2023 6.161855 TGCGAGTATGATTGATCCTACTTT 57.838 37.500 9.37 0.00 38.03 2.66
456 2037 7.397221 TGATCCTACTTTGACATGAATTCTGT 58.603 34.615 7.05 8.45 0.00 3.41
465 2046 6.486253 TGACATGAATTCTGTACTCTTTGC 57.514 37.500 7.05 0.00 0.00 3.68
467 2048 4.997395 ACATGAATTCTGTACTCTTTGCGT 59.003 37.500 7.05 0.00 0.00 5.24
476 2057 3.739300 TGTACTCTTTGCGTAAACTGCTC 59.261 43.478 0.00 0.00 0.00 4.26
481 2063 0.511221 TTGCGTAAACTGCTCGAAGC 59.489 50.000 0.00 0.00 42.82 3.86
482 2064 1.057361 GCGTAAACTGCTCGAAGCG 59.943 57.895 0.00 0.00 46.26 4.68
495 2077 0.994995 CGAAGCGTCACAGATTCAGG 59.005 55.000 0.00 0.00 36.42 3.86
496 2078 0.723981 GAAGCGTCACAGATTCAGGC 59.276 55.000 0.00 0.00 36.62 4.85
497 2079 1.016130 AAGCGTCACAGATTCAGGCG 61.016 55.000 0.00 0.00 0.00 5.52
503 2085 0.725686 CACAGATTCAGGCGCAGAAG 59.274 55.000 10.83 3.99 0.00 2.85
508 2090 1.332997 GATTCAGGCGCAGAAGGAATG 59.667 52.381 10.83 0.00 0.00 2.67
515 2097 1.009829 CGCAGAAGGAATGTACAGCC 58.990 55.000 0.33 5.55 0.00 4.85
520 2102 4.780815 CAGAAGGAATGTACAGCCCAATA 58.219 43.478 15.97 0.00 0.00 1.90
523 2105 6.016777 CAGAAGGAATGTACAGCCCAATATTC 60.017 42.308 15.97 11.47 0.00 1.75
524 2106 5.653255 AGGAATGTACAGCCCAATATTCT 57.347 39.130 15.97 0.00 0.00 2.40
528 2110 6.204882 GGAATGTACAGCCCAATATTCTACAC 59.795 42.308 0.33 0.00 0.00 2.90
530 2112 6.056090 TGTACAGCCCAATATTCTACACAA 57.944 37.500 0.00 0.00 0.00 3.33
531 2113 6.658849 TGTACAGCCCAATATTCTACACAAT 58.341 36.000 0.00 0.00 0.00 2.71
532 2114 7.116075 TGTACAGCCCAATATTCTACACAATT 58.884 34.615 0.00 0.00 0.00 2.32
533 2115 7.613801 TGTACAGCCCAATATTCTACACAATTT 59.386 33.333 0.00 0.00 0.00 1.82
534 2116 9.116067 GTACAGCCCAATATTCTACACAATTTA 57.884 33.333 0.00 0.00 0.00 1.40
535 2117 8.766994 ACAGCCCAATATTCTACACAATTTAT 57.233 30.769 0.00 0.00 0.00 1.40
536 2118 9.200817 ACAGCCCAATATTCTACACAATTTATT 57.799 29.630 0.00 0.00 0.00 1.40
593 2180 8.758633 TTTTACATCACAAAGGAAAACGAAAA 57.241 26.923 0.00 0.00 0.00 2.29
602 2189 4.489679 AGGAAAACGAAAAGACTGATGC 57.510 40.909 0.00 0.00 0.00 3.91
639 2226 1.301637 CATGCCATGCCATGCCATG 60.302 57.895 13.50 13.50 41.71 3.66
640 2227 3.177194 ATGCCATGCCATGCCATGC 62.177 57.895 11.13 7.49 40.92 4.06
745 2332 7.652909 TGAATAATGCATGCTGCTTAATTAACC 59.347 33.333 20.33 9.40 45.31 2.85
939 2527 0.537188 ATGCAGGTAGACAGGAACCG 59.463 55.000 0.00 0.00 40.88 4.44
1176 2790 0.981943 ACTACTACCCACAAGGCACC 59.018 55.000 0.00 0.00 40.58 5.01
1177 2791 0.108329 CTACTACCCACAAGGCACCG 60.108 60.000 0.00 0.00 40.58 4.94
1189 2803 4.789075 GCACCGCGACGAAGGCTA 62.789 66.667 8.23 0.00 0.00 3.93
1209 2823 2.497092 CGTCGGCGACACTTCATCG 61.497 63.158 35.62 18.13 42.55 3.84
1210 2824 2.158959 GTCGGCGACACTTCATCGG 61.159 63.158 33.07 0.00 39.99 4.18
1211 2825 2.126071 CGGCGACACTTCATCGGT 60.126 61.111 0.00 0.00 39.99 4.69
1212 2826 2.158959 CGGCGACACTTCATCGGTC 61.159 63.158 0.00 0.00 39.99 4.79
1215 2829 3.782042 GACACTTCATCGGTCGGC 58.218 61.111 0.00 0.00 0.00 5.54
1216 2830 2.126071 ACACTTCATCGGTCGGCG 60.126 61.111 0.00 0.00 0.00 6.46
1217 2831 2.180769 CACTTCATCGGTCGGCGA 59.819 61.111 4.99 4.99 0.00 5.54
1218 2832 2.158959 CACTTCATCGGTCGGCGAC 61.159 63.158 30.72 30.72 0.00 5.19
1219 2833 2.180769 CTTCATCGGTCGGCGACA 59.819 61.111 37.13 21.39 33.68 4.35
1228 2842 2.158959 GTCGGCGACACTTCATCGG 61.159 63.158 33.07 0.00 39.99 4.18
1254 2868 3.366396 TCATAGTTCTGGACCTCACCTC 58.634 50.000 0.00 0.00 0.00 3.85
1269 2883 4.504916 CTCCCTCTGCTGACGCCG 62.505 72.222 0.00 0.00 34.43 6.46
1272 2886 2.507992 CCTCTGCTGACGCCGAAG 60.508 66.667 0.00 0.00 34.43 3.79
1365 2979 1.172175 CAAGAAAGAAGGCCTCCAGC 58.828 55.000 5.23 0.00 42.60 4.85
1407 3021 0.958091 TTGTCAAAGGGCAATGGACG 59.042 50.000 0.00 0.00 0.00 4.79
1507 3140 7.425224 AGTCTGTGTTATTACTTGCTATCCT 57.575 36.000 0.00 0.00 0.00 3.24
1508 3141 7.268586 AGTCTGTGTTATTACTTGCTATCCTG 58.731 38.462 0.00 0.00 0.00 3.86
1509 3142 6.018669 GTCTGTGTTATTACTTGCTATCCTGC 60.019 42.308 0.00 0.00 0.00 4.85
1510 3143 4.808895 TGTGTTATTACTTGCTATCCTGCG 59.191 41.667 0.00 0.00 35.36 5.18
1511 3144 5.047847 GTGTTATTACTTGCTATCCTGCGA 58.952 41.667 0.00 0.00 35.36 5.10
1512 3145 5.696724 GTGTTATTACTTGCTATCCTGCGAT 59.303 40.000 0.00 0.00 35.36 4.58
1513 3146 5.696270 TGTTATTACTTGCTATCCTGCGATG 59.304 40.000 0.00 0.00 35.36 3.84
1514 3147 2.820059 TACTTGCTATCCTGCGATGG 57.180 50.000 0.00 0.00 35.36 3.51
1515 3148 0.833287 ACTTGCTATCCTGCGATGGT 59.167 50.000 0.00 0.00 35.36 3.55
1516 3149 2.039418 ACTTGCTATCCTGCGATGGTA 58.961 47.619 0.00 0.00 35.36 3.25
1517 3150 2.634940 ACTTGCTATCCTGCGATGGTAT 59.365 45.455 0.00 0.00 35.36 2.73
1518 3151 3.257393 CTTGCTATCCTGCGATGGTATC 58.743 50.000 0.00 0.00 35.36 2.24
1519 3152 2.247358 TGCTATCCTGCGATGGTATCA 58.753 47.619 0.00 0.00 35.36 2.15
1520 3153 2.632512 TGCTATCCTGCGATGGTATCAA 59.367 45.455 0.00 0.00 35.36 2.57
1521 3154 3.257393 GCTATCCTGCGATGGTATCAAG 58.743 50.000 0.00 0.00 29.93 3.02
1598 3235 4.080638 GGATTGAGGAAGTGGTCTCAGATT 60.081 45.833 0.00 0.00 40.55 2.40
1693 3330 2.777692 AGGTTTGTCTCTCCAACTTCCA 59.222 45.455 0.00 0.00 0.00 3.53
1699 3336 4.645535 TGTCTCTCCAACTTCCATTTGAG 58.354 43.478 0.00 0.00 0.00 3.02
1726 3363 7.617225 TGAACCGAGGAGTCAAATCTATTTTA 58.383 34.615 0.00 0.00 0.00 1.52
1891 3806 3.804786 TGCAATTCATTATGGGTGCAG 57.195 42.857 12.02 0.00 37.09 4.41
1959 3938 1.496001 TCAGATTCATGGGTGGGGATG 59.504 52.381 0.00 0.00 0.00 3.51
2022 4009 8.635765 AAAAACTAGCTTGAATACATTCAGGA 57.364 30.769 15.84 0.00 46.34 3.86
2146 4133 1.703513 GGGTGGGGAATGGGTATAGTC 59.296 57.143 0.00 0.00 0.00 2.59
2208 4195 3.695060 TCAAACCGGCACTCAAAAACTAA 59.305 39.130 0.00 0.00 0.00 2.24
2213 4200 5.286438 ACCGGCACTCAAAAACTAATTTTC 58.714 37.500 0.00 0.00 39.20 2.29
2222 4209 8.857098 ACTCAAAAACTAATTTTCTACCCTTCC 58.143 33.333 0.00 0.00 39.20 3.46
2327 4314 6.381801 AGGAAAAACTAGAAACAATGCATCG 58.618 36.000 0.00 0.00 0.00 3.84
2478 4497 1.113788 AATGGGGCATGGATGTTTCG 58.886 50.000 0.00 0.00 0.00 3.46
2527 4553 9.670719 GTTCTTTTTCCTGAAAACTTCTCATAG 57.329 33.333 4.61 0.00 39.70 2.23
2948 4976 2.648059 GTCAGAATCCAACCCATCCAG 58.352 52.381 0.00 0.00 0.00 3.86
3021 5049 4.849810 TCTTGGGAAGAAATTCTAGTCCCA 59.150 41.667 24.46 24.46 46.57 4.37
3747 5857 4.124910 CACTGACACGGTGCACTT 57.875 55.556 17.98 0.61 33.85 3.16
3748 5858 3.282557 CACTGACACGGTGCACTTA 57.717 52.632 17.98 0.00 33.85 2.24
3749 5859 1.795768 CACTGACACGGTGCACTTAT 58.204 50.000 17.98 0.00 33.85 1.73
4039 6149 5.622856 GCACACGATCGTAATAGGTAGTTAC 59.377 44.000 22.26 3.12 0.00 2.50
4080 6193 8.603181 CAAAGACATGTTTAAAAAGGAAACCTG 58.397 33.333 0.00 0.00 37.99 4.00
4100 6213 5.536161 ACCTGTTTATTGATTCTGCACAAGT 59.464 36.000 0.00 0.00 0.00 3.16
4153 6266 8.611757 GTTGGTAATGCAAATTGGGATTTTATC 58.388 33.333 4.75 0.00 33.25 1.75
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
77 90 0.318784 GGAAGCGCTGGTATCTACGG 60.319 60.000 12.58 0.00 0.00 4.02
79 92 0.318784 CGGGAAGCGCTGGTATCTAC 60.319 60.000 12.58 0.00 0.00 2.59
80 93 0.754217 ACGGGAAGCGCTGGTATCTA 60.754 55.000 12.58 0.00 0.00 1.98
81 94 2.058595 ACGGGAAGCGCTGGTATCT 61.059 57.895 12.58 0.00 0.00 1.98
82 95 1.883084 CACGGGAAGCGCTGGTATC 60.883 63.158 12.58 4.01 0.00 2.24
83 96 2.186903 CACGGGAAGCGCTGGTAT 59.813 61.111 12.58 0.00 0.00 2.73
84 97 4.077184 CCACGGGAAGCGCTGGTA 62.077 66.667 12.58 0.00 0.00 3.25
117 131 3.463505 CGAGCAGCACGTACCTTG 58.536 61.111 3.79 0.00 0.00 3.61
138 152 2.245438 GAAGAACTGGGGCGGAGGAG 62.245 65.000 0.00 0.00 0.00 3.69
205 219 4.955335 TGTGGAGGGGAAGAAATCTACTA 58.045 43.478 0.00 0.00 0.00 1.82
206 220 3.803340 TGTGGAGGGGAAGAAATCTACT 58.197 45.455 0.00 0.00 0.00 2.57
207 221 4.569719 TTGTGGAGGGGAAGAAATCTAC 57.430 45.455 0.00 0.00 0.00 2.59
223 237 3.855255 AAATGGAACCCCTTTTTGTGG 57.145 42.857 0.00 0.00 36.69 4.17
252 266 1.216444 GAGCTCAGACCATCACGCA 59.784 57.895 9.40 0.00 0.00 5.24
276 290 6.982852 TCGGTATAGATTGAAGATGAAGGAC 58.017 40.000 0.00 0.00 0.00 3.85
371 387 1.925285 CTGGCTGGGGCATGGAAGTA 61.925 60.000 0.00 0.00 40.87 2.24
376 392 2.037687 TTTCTGGCTGGGGCATGG 59.962 61.111 0.00 0.00 40.87 3.66
412 1979 6.592994 AGGATCAATCATACTCGCATGTTATG 59.407 38.462 0.00 0.00 0.00 1.90
414 1981 6.101650 AGGATCAATCATACTCGCATGTTA 57.898 37.500 0.00 0.00 0.00 2.41
431 1998 7.397221 ACAGAATTCATGTCAAAGTAGGATCA 58.603 34.615 8.44 0.00 0.00 2.92
433 2000 8.543774 AGTACAGAATTCATGTCAAAGTAGGAT 58.456 33.333 8.44 0.00 32.02 3.24
434 2001 7.907389 AGTACAGAATTCATGTCAAAGTAGGA 58.093 34.615 8.44 0.00 32.02 2.94
435 2002 8.037758 AGAGTACAGAATTCATGTCAAAGTAGG 58.962 37.037 8.44 0.00 32.02 3.18
442 2023 5.120674 CGCAAAGAGTACAGAATTCATGTCA 59.879 40.000 8.44 0.00 32.02 3.58
456 2037 2.984471 CGAGCAGTTTACGCAAAGAGTA 59.016 45.455 0.00 0.00 0.00 2.59
465 2046 0.362512 GACGCTTCGAGCAGTTTACG 59.637 55.000 7.47 0.00 42.58 3.18
467 2048 1.269361 TGTGACGCTTCGAGCAGTTTA 60.269 47.619 7.47 0.00 42.58 2.01
476 2057 0.994995 CCTGAATCTGTGACGCTTCG 59.005 55.000 0.00 0.00 0.00 3.79
481 2063 1.690283 CTGCGCCTGAATCTGTGACG 61.690 60.000 4.18 0.00 0.00 4.35
482 2064 0.390340 TCTGCGCCTGAATCTGTGAC 60.390 55.000 4.18 0.00 0.00 3.67
495 2077 0.375106 GCTGTACATTCCTTCTGCGC 59.625 55.000 0.00 0.00 0.00 6.09
496 2078 1.009829 GGCTGTACATTCCTTCTGCG 58.990 55.000 0.00 0.00 0.00 5.18
497 2079 1.340017 TGGGCTGTACATTCCTTCTGC 60.340 52.381 13.57 4.06 0.00 4.26
503 2085 6.204882 GTGTAGAATATTGGGCTGTACATTCC 59.795 42.308 0.00 1.61 0.00 3.01
508 2090 7.568199 AATTGTGTAGAATATTGGGCTGTAC 57.432 36.000 0.00 0.00 0.00 2.90
533 2115 9.820229 CACGAACTCTGCTAAAACAAAATAATA 57.180 29.630 0.00 0.00 0.00 0.98
534 2116 8.349983 ACACGAACTCTGCTAAAACAAAATAAT 58.650 29.630 0.00 0.00 0.00 1.28
535 2117 7.642194 CACACGAACTCTGCTAAAACAAAATAA 59.358 33.333 0.00 0.00 0.00 1.40
536 2118 7.129622 CACACGAACTCTGCTAAAACAAAATA 58.870 34.615 0.00 0.00 0.00 1.40
537 2119 5.971202 CACACGAACTCTGCTAAAACAAAAT 59.029 36.000 0.00 0.00 0.00 1.82
542 2124 2.544267 AGCACACGAACTCTGCTAAAAC 59.456 45.455 0.00 0.00 39.52 2.43
550 2132 5.813672 TGTAAAAGTAAAGCACACGAACTCT 59.186 36.000 0.00 0.00 0.00 3.24
551 2133 6.039781 TGTAAAAGTAAAGCACACGAACTC 57.960 37.500 0.00 0.00 0.00 3.01
555 2137 5.524281 TGTGATGTAAAAGTAAAGCACACGA 59.476 36.000 0.00 0.00 30.93 4.35
556 2138 5.743467 TGTGATGTAAAAGTAAAGCACACG 58.257 37.500 0.00 0.00 30.93 4.49
557 2139 7.167468 CCTTTGTGATGTAAAAGTAAAGCACAC 59.833 37.037 0.00 0.00 35.09 3.82
602 2189 3.236632 TGCGATGCTATATGCCTGTAG 57.763 47.619 0.00 0.00 42.00 2.74
640 2227 4.433615 AGTCATTAACATCCGCAGTAGTG 58.566 43.478 0.00 0.00 0.00 2.74
745 2332 8.295288 ACTTCATGCAAGAGAAAGAAAACTATG 58.705 33.333 10.61 0.00 35.82 2.23
1200 2814 2.180769 TCGCCGACCGATGAAGTG 59.819 61.111 0.00 0.00 41.89 3.16
1209 2823 2.158959 CGATGAAGTGTCGCCGACC 61.159 63.158 15.60 6.20 31.85 4.79
1210 2824 2.158959 CCGATGAAGTGTCGCCGAC 61.159 63.158 10.96 10.96 37.75 4.79
1211 2825 2.180769 CCGATGAAGTGTCGCCGA 59.819 61.111 0.00 0.00 37.75 5.54
1212 2826 2.126071 ACCGATGAAGTGTCGCCG 60.126 61.111 0.00 0.00 37.75 6.46
1213 2827 2.158959 CGACCGATGAAGTGTCGCC 61.159 63.158 0.00 0.00 44.29 5.54
1214 2828 3.374330 CGACCGATGAAGTGTCGC 58.626 61.111 0.00 0.00 44.29 5.19
1216 2830 2.060326 TGAACGACCGATGAAGTGTC 57.940 50.000 0.00 0.00 0.00 3.67
1217 2831 2.743636 ATGAACGACCGATGAAGTGT 57.256 45.000 0.00 0.00 0.00 3.55
1218 2832 3.770666 ACTATGAACGACCGATGAAGTG 58.229 45.455 0.00 0.00 0.00 3.16
1219 2833 4.158025 AGAACTATGAACGACCGATGAAGT 59.842 41.667 0.00 0.00 0.00 3.01
1228 2842 3.192844 TGAGGTCCAGAACTATGAACGAC 59.807 47.826 0.00 0.00 0.00 4.34
1269 2883 4.067896 TGAGATGTGAAACCTCAAGCTTC 58.932 43.478 0.00 0.00 33.58 3.86
1272 2886 4.574013 CCTATGAGATGTGAAACCTCAAGC 59.426 45.833 0.00 0.00 39.94 4.01
1365 2979 1.198713 TAGCCCTCTTGAGAGCCTTG 58.801 55.000 2.42 0.00 40.75 3.61
1407 3021 3.963428 TCTTACCTGTCTTCTTCCAGC 57.037 47.619 0.00 0.00 0.00 4.85
1451 3065 6.942532 TGCAAACAGAGAAAATACTGAACT 57.057 33.333 0.00 0.00 37.54 3.01
1507 3140 3.186909 CGAACTTCTTGATACCATCGCA 58.813 45.455 0.00 0.00 0.00 5.10
1508 3141 3.187700 ACGAACTTCTTGATACCATCGC 58.812 45.455 0.00 0.00 32.68 4.58
1509 3142 5.103000 AGAACGAACTTCTTGATACCATCG 58.897 41.667 0.00 0.00 35.49 3.84
1510 3143 6.969828 AAGAACGAACTTCTTGATACCATC 57.030 37.500 0.00 0.00 45.90 3.51
1520 3153 7.254852 TGTAAAATTTGCAAGAACGAACTTCT 58.745 30.769 0.00 0.00 41.39 2.85
1521 3154 7.305993 CCTGTAAAATTTGCAAGAACGAACTTC 60.306 37.037 0.00 0.00 0.00 3.01
1693 3330 1.625818 ACTCCTCGGTTCAGCTCAAAT 59.374 47.619 0.00 0.00 0.00 2.32
1699 3336 2.003301 GATTTGACTCCTCGGTTCAGC 58.997 52.381 0.00 0.00 0.00 4.26
1761 3398 4.681483 GGTCAAAGCAAAAGACATAACTGC 59.319 41.667 0.00 0.00 34.04 4.40
1917 3896 6.148948 TGATCTAAGCAAACCAAAAATGACG 58.851 36.000 0.00 0.00 0.00 4.35
1996 3975 9.733556 TCCTGAATGTATTCAAGCTAGTTTTTA 57.266 29.630 8.48 0.00 45.26 1.52
2022 4009 3.839490 TGGCCCAATGACATTCAAATCTT 59.161 39.130 0.00 0.00 0.00 2.40
2064 4051 9.878599 CTTATATTACTCCCAAAATTTAGTGCG 57.121 33.333 2.25 0.00 0.00 5.34
2146 4133 9.144298 TGGATAAGAACCATTCTAGTACTAAGG 57.856 37.037 3.76 6.45 39.61 2.69
2208 4195 3.308473 GGCTCACTGGAAGGGTAGAAAAT 60.308 47.826 0.00 0.00 39.54 1.82
2213 4200 0.984230 TTGGCTCACTGGAAGGGTAG 59.016 55.000 0.00 0.00 39.54 3.18
2222 4209 5.702349 ATTTTCTTCTCTTTGGCTCACTG 57.298 39.130 0.00 0.00 0.00 3.66
2327 4314 5.634859 GGTCAACAACATGATTTTCCATGAC 59.365 40.000 10.42 3.09 44.98 3.06
2453 4471 1.838715 CATCCATGCCCCATTTTTGGA 59.161 47.619 0.00 0.00 40.54 3.53
2527 4553 8.648557 TTCAAGCATGAATACTACACAGATAC 57.351 34.615 0.00 0.00 40.59 2.24
2948 4976 1.474077 GTCCTTGGGTGATCATTGTGC 59.526 52.381 0.00 0.00 0.00 4.57
3003 5031 5.946377 ACATGTTGGGACTAGAATTTCTTCC 59.054 40.000 3.86 6.42 31.27 3.46
3021 5049 7.490840 TGTCAACAGAAAAATCATCACATGTT 58.509 30.769 0.00 0.00 0.00 2.71
3362 5451 5.505780 CCCATAGTAACATCCAAAAGGTCA 58.494 41.667 0.00 0.00 0.00 4.02
3697 5807 4.617253 ACAATAAGTCACCACTGCACTA 57.383 40.909 0.00 0.00 31.06 2.74
3747 5857 7.514721 AGTTTGAACTGAGGGTACTGAAAATA 58.485 34.615 0.00 0.00 37.98 1.40
3748 5858 6.365520 AGTTTGAACTGAGGGTACTGAAAAT 58.634 36.000 0.00 0.00 37.98 1.82
3749 5859 5.751586 AGTTTGAACTGAGGGTACTGAAAA 58.248 37.500 0.00 0.00 37.98 2.29
3878 5988 6.603201 TGCTTTCTTTTATCCATGGGTTCTAG 59.397 38.462 13.02 2.76 0.00 2.43
3926 6036 2.171448 GCAGATGTCCTATGTTGGGTCT 59.829 50.000 0.00 0.00 0.00 3.85
4050 6163 9.936759 TTTCCTTTTTAAACATGTCTTTGTCTT 57.063 25.926 0.00 0.00 0.00 3.01
4080 6193 7.649306 AGAACAACTTGTGCAGAATCAATAAAC 59.351 33.333 0.00 0.00 0.00 2.01
4100 6213 8.421784 AGAAACTGAAGTATCACACTAGAACAA 58.578 33.333 0.00 0.00 36.04 2.83


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

AutoCloner maintained by Alex Coulton.