Multiple sequence alignment - TraesCS6B01G386400

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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 TraesCS6B01G386400 chr6B 100.000 3837 0 0 1 3837 661337251 661341087 0.000000e+00 7086.0
1 TraesCS6B01G386400 chr6B 89.100 211 14 3 1148 1355 464518007 464518211 1.770000e-63 254.0
2 TraesCS6B01G386400 chr6D 93.614 2396 106 30 1473 3837 437164219 437166598 0.000000e+00 3533.0
3 TraesCS6B01G386400 chr6D 90.124 1367 95 17 72 1410 437162720 437164074 0.000000e+00 1740.0
4 TraesCS6B01G386400 chr6A 93.249 2385 96 24 1503 3837 585427757 585430126 0.000000e+00 3452.0
5 TraesCS6B01G386400 chr6A 89.592 759 45 16 683 1416 585426780 585427529 0.000000e+00 933.0
6 TraesCS6B01G386400 chr6A 88.462 208 18 1 1148 1355 1327074 1327275 2.960000e-61 246.0
7 TraesCS6B01G386400 chr6A 94.737 57 3 0 1 57 585423824 585423880 5.280000e-14 89.8
8 TraesCS6B01G386400 chr4B 93.850 1187 42 21 1528 2713 429268965 429270121 0.000000e+00 1759.0
9 TraesCS6B01G386400 chr3A 94.394 999 50 3 1715 2713 681625860 681626852 0.000000e+00 1530.0
10 TraesCS6B01G386400 chr3A 95.000 140 7 0 1528 1667 681616874 681617013 1.790000e-53 220.0
11 TraesCS6B01G386400 chr3A 81.227 277 19 6 1085 1355 189304023 189304272 3.910000e-45 193.0
12 TraesCS6B01G386400 chr7A 92.260 801 32 11 1528 2328 130189204 130189974 0.000000e+00 1109.0
13 TraesCS6B01G386400 chr7A 96.377 276 10 0 2364 2639 130189973 130190248 4.520000e-124 455.0
14 TraesCS6B01G386400 chr7A 91.720 157 10 1 2483 2639 130190395 130190548 8.350000e-52 215.0
15 TraesCS6B01G386400 chr4A 93.080 289 20 0 2422 2710 589150266 589150554 1.270000e-114 424.0
16 TraesCS6B01G386400 chr3D 86.628 344 28 7 1020 1355 3897080 3896747 7.830000e-97 364.0
17 TraesCS6B01G386400 chr3D 96.341 82 2 1 1539 1619 139731815 139731896 2.400000e-27 134.0
18 TraesCS6B01G386400 chr1B 88.153 287 19 7 1075 1355 683657192 683657469 1.030000e-85 327.0
19 TraesCS6B01G386400 chr1B 88.321 274 20 5 1088 1355 143667532 143667265 6.190000e-83 318.0
20 TraesCS6B01G386400 chr5B 90.816 196 12 1 1160 1355 676286794 676286605 1.370000e-64 257.0
21 TraesCS6B01G386400 chr5B 81.279 219 14 5 1137 1355 699305037 699304846 6.640000e-33 152.0
22 TraesCS6B01G386400 chr2A 81.882 287 16 15 1075 1355 5155781 5156037 3.880000e-50 209.0
23 TraesCS6B01G386400 chr2B 96.341 82 2 1 1539 1619 632573621 632573540 2.400000e-27 134.0
24 TraesCS6B01G386400 chr1A 96.341 82 2 1 1539 1619 31697887 31697968 2.400000e-27 134.0
25 TraesCS6B01G386400 chr1A 97.403 77 2 0 1543 1619 300591178 300591102 8.650000e-27 132.0


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 TraesCS6B01G386400 chr6B 661337251 661341087 3836 False 7086.0 7086 100.000000 1 3837 1 chr6B.!!$F2 3836
1 TraesCS6B01G386400 chr6D 437162720 437166598 3878 False 2636.5 3533 91.869000 72 3837 2 chr6D.!!$F1 3765
2 TraesCS6B01G386400 chr6A 585423824 585430126 6302 False 1491.6 3452 92.526000 1 3837 3 chr6A.!!$F2 3836
3 TraesCS6B01G386400 chr4B 429268965 429270121 1156 False 1759.0 1759 93.850000 1528 2713 1 chr4B.!!$F1 1185
4 TraesCS6B01G386400 chr3A 681625860 681626852 992 False 1530.0 1530 94.394000 1715 2713 1 chr3A.!!$F3 998
5 TraesCS6B01G386400 chr7A 130189204 130190548 1344 False 593.0 1109 93.452333 1528 2639 3 chr7A.!!$F1 1111

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
146 972 0.187117 TTCACCCCAACTGGCATCAA 59.813 50.0 0.00 0.00 0.00 2.57 F
892 3278 0.235926 GGAAGCAAAGAGTCGTGTGC 59.764 55.0 7.43 7.43 37.26 4.57 F
1939 4587 0.119155 TGGAGAACCTCATGGACCCT 59.881 55.0 0.00 0.00 37.04 4.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1432 3840 0.888619 GATGATGATGGCTGGCATGG 59.111 55.000 22.23 0.0 0.0 3.66 R
2148 4796 1.004440 GCCGAGAAGCACTGTTCCT 60.004 57.895 0.00 0.0 0.0 3.36 R
3763 6585 0.322008 CCTTCTCTGGCCACTGAACC 60.322 60.000 0.00 0.0 0.0 3.62 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
29 30 0.609406 GCCTCAACCCACCTTCTTCC 60.609 60.000 0.00 0.00 0.00 3.46
44 45 2.804828 CTTCCGCACCCTTGTCTCCC 62.805 65.000 0.00 0.00 0.00 4.30
53 54 1.141858 CCCTTGTCTCCCTTAGATGGC 59.858 57.143 0.00 0.00 36.36 4.40
57 58 2.398588 TGTCTCCCTTAGATGGCGATT 58.601 47.619 0.00 0.00 36.36 3.34
58 59 2.103094 TGTCTCCCTTAGATGGCGATTG 59.897 50.000 0.00 0.00 36.36 2.67
59 60 1.694150 TCTCCCTTAGATGGCGATTGG 59.306 52.381 0.00 0.00 0.00 3.16
60 61 1.417890 CTCCCTTAGATGGCGATTGGT 59.582 52.381 0.00 0.00 0.00 3.67
61 62 1.843851 TCCCTTAGATGGCGATTGGTT 59.156 47.619 0.00 0.00 0.00 3.67
63 64 3.456644 TCCCTTAGATGGCGATTGGTTTA 59.543 43.478 0.00 0.00 0.00 2.01
64 65 3.815401 CCCTTAGATGGCGATTGGTTTAG 59.185 47.826 0.00 0.00 0.00 1.85
65 66 3.251004 CCTTAGATGGCGATTGGTTTAGC 59.749 47.826 0.00 0.00 0.00 3.09
67 68 3.838244 AGATGGCGATTGGTTTAGCTA 57.162 42.857 0.00 0.00 0.00 3.32
68 69 4.150897 AGATGGCGATTGGTTTAGCTAA 57.849 40.909 0.86 0.86 0.00 3.09
84 909 9.302345 GGTTTAGCTAAATTTAGGATGAAAAGC 57.698 33.333 21.28 10.75 0.00 3.51
91 916 9.918630 CTAAATTTAGGATGAAAAGCATATGGG 57.081 33.333 16.19 0.00 37.34 4.00
140 966 3.165071 AGCTAAATTTCACCCCAACTGG 58.835 45.455 0.00 0.00 0.00 4.00
146 972 0.187117 TTCACCCCAACTGGCATCAA 59.813 50.000 0.00 0.00 0.00 2.57
249 1085 0.531974 ACGTGCAACTGTAGGTGTGG 60.532 55.000 0.00 0.00 31.75 4.17
255 1091 2.038033 GCAACTGTAGGTGTGGGACTAA 59.962 50.000 0.00 0.00 0.00 2.24
264 1100 5.815233 AGGTGTGGGACTAATGAGATATG 57.185 43.478 0.00 0.00 0.00 1.78
270 1106 7.438459 GTGTGGGACTAATGAGATATGTGTAAC 59.562 40.741 0.00 0.00 37.35 2.50
285 1121 2.112998 TGTAACTATAGTTGCGGGGCT 58.887 47.619 25.27 1.78 42.39 5.19
316 1152 1.136565 CAATTGTAGTTGCGCCCGG 59.863 57.895 4.18 0.00 0.00 5.73
352 1189 1.538047 AATGTAGTTGGTGCCAGCAG 58.462 50.000 7.76 0.00 0.00 4.24
381 1218 4.637483 TGAGTGGAAAAGAGCAAAACTG 57.363 40.909 0.00 0.00 0.00 3.16
390 1227 4.799564 AAGAGCAAAACTGGAACACAAA 57.200 36.364 0.00 0.00 0.00 2.83
437 1274 8.297470 AGGTGCACTATGAAATGATAAAATGT 57.703 30.769 17.98 0.00 0.00 2.71
474 1311 6.436843 AATCCGAAAGAATATCCACACAAC 57.563 37.500 0.00 0.00 0.00 3.32
497 1335 7.956420 ACTGACGAGTGTAATGTTAATCAAA 57.044 32.000 0.00 0.00 0.00 2.69
573 1411 2.645838 ATTCAGGCGCAAGGATGTAT 57.354 45.000 10.83 0.00 38.28 2.29
575 1413 1.667236 TCAGGCGCAAGGATGTATTG 58.333 50.000 10.83 0.00 38.28 1.90
580 1418 4.754618 CAGGCGCAAGGATGTATTGTATTA 59.245 41.667 10.83 0.00 38.28 0.98
650 2933 3.149196 AGTACAAGGCACCTCAAACATG 58.851 45.455 0.00 0.00 0.00 3.21
665 2948 6.094048 CCTCAAACATGGACGTTTATCTCAAT 59.906 38.462 0.00 0.00 36.98 2.57
669 2952 8.331022 CAAACATGGACGTTTATCTCAATAGAG 58.669 37.037 0.00 0.00 38.87 2.43
676 2959 6.810911 ACGTTTATCTCAATAGAGTGCTGAT 58.189 36.000 0.00 0.00 42.66 2.90
680 2963 8.341173 GTTTATCTCAATAGAGTGCTGATTTGG 58.659 37.037 0.00 0.00 42.66 3.28
692 3063 3.759086 TGCTGATTTGGCCGTAAATGTTA 59.241 39.130 5.80 0.00 30.78 2.41
693 3064 4.102649 GCTGATTTGGCCGTAAATGTTAC 58.897 43.478 5.80 0.00 30.78 2.50
733 3104 3.003275 TCGCTCTTTGTTTGGTCATTCAC 59.997 43.478 0.00 0.00 0.00 3.18
734 3105 3.300009 GCTCTTTGTTTGGTCATTCACG 58.700 45.455 0.00 0.00 0.00 4.35
753 3124 3.084039 ACGTACTCTGTCCGTGGAATAA 58.916 45.455 0.00 0.00 32.86 1.40
845 3225 0.452184 TAACTCGCCAGAAGCTCTCG 59.548 55.000 0.00 0.00 40.39 4.04
846 3226 2.103934 CTCGCCAGAAGCTCTCGG 59.896 66.667 0.00 0.00 40.39 4.63
892 3278 0.235926 GGAAGCAAAGAGTCGTGTGC 59.764 55.000 7.43 7.43 37.26 4.57
975 3364 4.639171 GCGCCAACCAAACCACCG 62.639 66.667 0.00 0.00 0.00 4.94
979 3368 2.415426 CAACCAAACCACCGCCAC 59.585 61.111 0.00 0.00 0.00 5.01
980 3369 2.835895 AACCAAACCACCGCCACC 60.836 61.111 0.00 0.00 0.00 4.61
981 3370 3.663815 AACCAAACCACCGCCACCA 62.664 57.895 0.00 0.00 0.00 4.17
982 3371 3.601685 CCAAACCACCGCCACCAC 61.602 66.667 0.00 0.00 0.00 4.16
983 3372 3.601685 CAAACCACCGCCACCACC 61.602 66.667 0.00 0.00 0.00 4.61
984 3373 4.130554 AAACCACCGCCACCACCA 62.131 61.111 0.00 0.00 0.00 4.17
1137 3533 4.344865 CAGGGGGTCGGTGTTGGG 62.345 72.222 0.00 0.00 0.00 4.12
1143 3545 3.246880 GTCGGTGTTGGGAGGGGT 61.247 66.667 0.00 0.00 0.00 4.95
1147 3549 2.675371 GTGTTGGGAGGGGTAGGC 59.325 66.667 0.00 0.00 0.00 3.93
1278 3686 1.762460 CTGGCGGGAGGAGTGGTAT 60.762 63.158 0.00 0.00 0.00 2.73
1411 3819 1.956170 CGATGCCCGCACAGGTATC 60.956 63.158 5.68 5.68 43.45 2.24
1413 3821 2.324014 GATGCCCGCACAGGTATCCA 62.324 60.000 4.69 0.00 41.68 3.41
1414 3822 1.708993 ATGCCCGCACAGGTATCCAT 61.709 55.000 0.00 0.00 38.74 3.41
1415 3823 1.598130 GCCCGCACAGGTATCCATC 60.598 63.158 0.00 0.00 38.74 3.51
1416 3824 1.829456 CCCGCACAGGTATCCATCA 59.171 57.895 0.00 0.00 38.74 3.07
1417 3825 0.532862 CCCGCACAGGTATCCATCAC 60.533 60.000 0.00 0.00 38.74 3.06
1418 3826 0.532862 CCGCACAGGTATCCATCACC 60.533 60.000 0.00 0.00 36.22 4.02
1423 3831 1.447643 AGGTATCCATCACCTGCGC 59.552 57.895 0.00 0.00 44.89 6.09
1425 3833 0.882042 GGTATCCATCACCTGCGCTG 60.882 60.000 9.73 8.47 32.98 5.18
1427 3835 2.976692 TATCCATCACCTGCGCTGCG 62.977 60.000 19.17 19.17 0.00 5.18
1445 3853 3.224324 CCTGCCATGCCAGCCATC 61.224 66.667 0.00 0.00 29.71 3.51
1446 3854 2.441348 CTGCCATGCCAGCCATCA 60.441 61.111 0.00 0.00 29.71 3.07
1448 3856 1.806461 CTGCCATGCCAGCCATCATC 61.806 60.000 0.00 0.00 29.71 2.92
1451 3859 0.888619 CCATGCCAGCCATCATCATC 59.111 55.000 0.00 0.00 29.71 2.92
1452 3860 1.616159 CATGCCAGCCATCATCATCA 58.384 50.000 0.00 0.00 29.71 3.07
1453 3861 1.960689 CATGCCAGCCATCATCATCAA 59.039 47.619 0.00 0.00 29.71 2.57
1454 3862 2.375014 TGCCAGCCATCATCATCAAT 57.625 45.000 0.00 0.00 0.00 2.57
1455 3863 2.235891 TGCCAGCCATCATCATCAATC 58.764 47.619 0.00 0.00 0.00 2.67
1456 3864 2.158519 TGCCAGCCATCATCATCAATCT 60.159 45.455 0.00 0.00 0.00 2.40
1457 3865 2.229062 GCCAGCCATCATCATCAATCTG 59.771 50.000 0.00 0.00 0.00 2.90
1458 3866 2.229062 CCAGCCATCATCATCAATCTGC 59.771 50.000 0.00 0.00 0.00 4.26
1461 3869 2.229062 GCCATCATCATCAATCTGCCTG 59.771 50.000 0.00 0.00 0.00 4.85
1462 3870 3.487372 CCATCATCATCAATCTGCCTGT 58.513 45.455 0.00 0.00 0.00 4.00
1465 4084 5.123979 CCATCATCATCAATCTGCCTGTATG 59.876 44.000 0.00 0.00 0.00 2.39
1476 4095 3.131223 TCTGCCTGTATGCTCTAACTGAC 59.869 47.826 0.00 0.00 0.00 3.51
1477 4096 3.099905 TGCCTGTATGCTCTAACTGACT 58.900 45.455 0.00 0.00 0.00 3.41
1480 4099 4.677584 CCTGTATGCTCTAACTGACTGAC 58.322 47.826 0.00 0.00 0.00 3.51
1481 4100 4.400884 CCTGTATGCTCTAACTGACTGACT 59.599 45.833 0.00 0.00 0.00 3.41
1482 4101 5.449862 CCTGTATGCTCTAACTGACTGACTC 60.450 48.000 0.00 0.00 0.00 3.36
1483 4102 5.010282 TGTATGCTCTAACTGACTGACTCA 58.990 41.667 0.00 0.00 0.00 3.41
1505 4124 1.679139 TGATCCAAACATGGCCGATC 58.321 50.000 0.00 2.75 0.00 3.69
1645 4287 4.789012 TCAATTTCATTCTTGGGTCAGC 57.211 40.909 0.00 0.00 0.00 4.26
1696 4344 5.239963 TGATTCATGTATGTGATGATGGTGC 59.760 40.000 0.00 0.00 29.96 5.01
1939 4587 0.119155 TGGAGAACCTCATGGACCCT 59.881 55.000 0.00 0.00 37.04 4.34
2148 4796 2.280524 CGTGGACAAGGACGGCAA 60.281 61.111 0.00 0.00 31.84 4.52
2152 4800 1.072505 GGACAAGGACGGCAAGGAA 59.927 57.895 0.00 0.00 0.00 3.36
2963 5746 4.339872 TTTTGCCATCAGAAGTTGCATT 57.660 36.364 0.00 0.00 0.00 3.56
2986 5769 3.181516 GCAAGACAAGTTCATAAGCCGAG 60.182 47.826 0.00 0.00 0.00 4.63
3008 5791 8.507249 CCGAGACTGAATTTTTAACTTCTCAAT 58.493 33.333 0.00 0.00 0.00 2.57
3028 5811 7.711772 TCTCAATAAACACTTTCTTCCACGTAA 59.288 33.333 0.00 0.00 0.00 3.18
3030 5813 8.286800 TCAATAAACACTTTCTTCCACGTAATG 58.713 33.333 0.00 0.00 0.00 1.90
3031 5814 7.739498 ATAAACACTTTCTTCCACGTAATGT 57.261 32.000 0.00 0.00 0.00 2.71
3032 5815 8.836268 ATAAACACTTTCTTCCACGTAATGTA 57.164 30.769 0.00 0.00 0.00 2.29
3033 5816 6.535274 AACACTTTCTTCCACGTAATGTAC 57.465 37.500 0.00 0.00 0.00 2.90
3074 5857 9.688592 AAATAGCTATGCAATCAAAGAAATAGC 57.311 29.630 7.09 4.68 41.68 2.97
3090 5873 0.448197 TAGCGCGAGTCTGTTCAGAG 59.552 55.000 12.10 0.00 0.00 3.35
3095 5879 1.540267 GCGAGTCTGTTCAGAGTACCA 59.460 52.381 9.73 0.00 0.00 3.25
3098 5882 4.810790 CGAGTCTGTTCAGAGTACCAAAT 58.189 43.478 9.73 0.00 0.00 2.32
3107 5891 7.874940 TGTTCAGAGTACCAAATTCATGAAAG 58.125 34.615 13.09 5.63 0.00 2.62
3137 5921 4.045783 CAGCGCATGCATTTCATTCATTA 58.954 39.130 19.57 0.00 46.23 1.90
3141 5925 4.684242 CGCATGCATTTCATTCATTAGCAT 59.316 37.500 19.57 0.00 41.42 3.79
3145 5929 8.007716 GCATGCATTTCATTCATTAGCATTTAC 58.992 33.333 14.21 0.00 39.00 2.01
3147 5931 6.696583 TGCATTTCATTCATTAGCATTTACGG 59.303 34.615 0.00 0.00 0.00 4.02
3148 5932 6.144402 GCATTTCATTCATTAGCATTTACGGG 59.856 38.462 0.00 0.00 0.00 5.28
3175 5959 6.019237 CACACCAATGAAACAGAGATAGATCG 60.019 42.308 0.00 0.00 0.00 3.69
3202 5986 9.706691 ACTTCAATATATATACAACCAAGACCG 57.293 33.333 0.00 0.00 0.00 4.79
3203 5987 9.706691 CTTCAATATATATACAACCAAGACCGT 57.293 33.333 0.00 0.00 0.00 4.83
3253 6045 3.747099 GTCACACATTATGCAGACCAC 57.253 47.619 0.00 0.00 32.94 4.16
3496 6308 4.947147 GTTGCCCACTGGGTCGCA 62.947 66.667 16.03 4.71 46.51 5.10
3541 6353 1.879380 CCGACATCAACAAGCTTTCCA 59.121 47.619 0.00 0.00 0.00 3.53
3547 6359 3.558931 TCAACAAGCTTTCCACTCTCA 57.441 42.857 0.00 0.00 0.00 3.27
3550 6362 1.151668 CAAGCTTTCCACTCTCACCG 58.848 55.000 0.00 0.00 0.00 4.94
3571 6383 2.262915 GAGGTCGACCAGCCAGTG 59.737 66.667 35.00 0.00 38.89 3.66
3673 6485 1.555075 TCCTTGGTTTCCTCCTCATCG 59.445 52.381 0.00 0.00 0.00 3.84
3721 6533 0.661020 CGGCACCTGAAGAAAACGTT 59.339 50.000 0.00 0.00 0.00 3.99
3727 6539 1.069906 CCTGAAGAAAACGTTGGCGAG 60.070 52.381 0.00 0.00 42.00 5.03
3738 6550 2.063266 CGTTGGCGAGTTTAGCAAGTA 58.937 47.619 0.00 0.00 41.33 2.24
3755 6577 5.799960 GCAAGTAGCAACACATACTACATG 58.200 41.667 0.00 0.00 44.79 3.21
3764 6586 8.623903 AGCAACACATACTACATGATTAATTGG 58.376 33.333 0.00 0.00 0.00 3.16
3781 6603 0.397941 TGGTTCAGTGGCCAGAGAAG 59.602 55.000 17.66 2.26 0.00 2.85
3782 6604 0.322008 GGTTCAGTGGCCAGAGAAGG 60.322 60.000 17.66 0.21 0.00 3.46
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
29 30 0.108138 CTAAGGGAGACAAGGGTGCG 60.108 60.000 0.00 0.00 0.00 5.34
44 45 4.130118 AGCTAAACCAATCGCCATCTAAG 58.870 43.478 0.00 0.00 0.00 2.18
53 54 8.836413 TCATCCTAAATTTAGCTAAACCAATCG 58.164 33.333 20.85 7.67 0.00 3.34
58 59 9.302345 GCTTTTCATCCTAAATTTAGCTAAACC 57.698 33.333 20.85 6.73 0.00 3.27
59 60 9.855021 TGCTTTTCATCCTAAATTTAGCTAAAC 57.145 29.630 20.85 3.59 0.00 2.01
64 65 9.415544 CCATATGCTTTTCATCCTAAATTTAGC 57.584 33.333 18.18 8.06 36.63 3.09
65 66 9.918630 CCCATATGCTTTTCATCCTAAATTTAG 57.081 33.333 16.90 16.90 36.63 1.85
67 68 8.206189 CACCCATATGCTTTTCATCCTAAATTT 58.794 33.333 0.00 0.00 36.63 1.82
68 69 7.345392 ACACCCATATGCTTTTCATCCTAAATT 59.655 33.333 0.00 0.00 36.63 1.82
84 909 3.580022 TGAGATCTAGCCACACCCATATG 59.420 47.826 0.00 0.00 0.00 1.78
88 913 1.273267 ACTGAGATCTAGCCACACCCA 60.273 52.381 0.00 0.00 0.00 4.51
91 916 3.876274 TCAACTGAGATCTAGCCACAC 57.124 47.619 0.00 0.00 0.00 3.82
173 1005 7.810759 AGAAGTAGAAAACGCAACAAAGAAAAA 59.189 29.630 0.00 0.00 0.00 1.94
176 1008 6.431198 AGAAGTAGAAAACGCAACAAAGAA 57.569 33.333 0.00 0.00 0.00 2.52
184 1016 7.316544 AGAAGAAAAAGAAGTAGAAAACGCA 57.683 32.000 0.00 0.00 0.00 5.24
185 1017 8.616377 AAAGAAGAAAAAGAAGTAGAAAACGC 57.384 30.769 0.00 0.00 0.00 4.84
186 1018 9.769093 TGAAAGAAGAAAAAGAAGTAGAAAACG 57.231 29.630 0.00 0.00 0.00 3.60
188 1020 9.769093 CGTGAAAGAAGAAAAAGAAGTAGAAAA 57.231 29.630 0.00 0.00 0.00 2.29
231 1066 1.227999 CCCACACCTACAGTTGCACG 61.228 60.000 0.00 0.00 0.00 5.34
255 1091 8.029522 CCGCAACTATAGTTACACATATCTCAT 58.970 37.037 17.62 0.00 36.32 2.90
264 1100 2.159000 AGCCCCGCAACTATAGTTACAC 60.159 50.000 17.62 9.55 36.32 2.90
270 1106 0.249911 GGTCAGCCCCGCAACTATAG 60.250 60.000 0.00 0.00 0.00 1.31
285 1121 5.276461 ACTACAATTGCATATCTCGGTCA 57.724 39.130 5.05 0.00 0.00 4.02
310 1146 1.956629 ATATCCTTATCGGCCGGGCG 61.957 60.000 41.57 41.57 0.00 6.13
316 1152 5.643777 ACTACATTTGCATATCCTTATCGGC 59.356 40.000 0.00 0.00 0.00 5.54
352 1189 3.187432 GCTCTTTTCCACTCAAGTACAGC 59.813 47.826 0.00 0.00 0.00 4.40
381 1218 8.001549 CGCTGTTTTTAATACATTTTGTGTTCC 58.998 33.333 0.00 0.00 42.29 3.62
390 1227 9.187455 CACCTTTTACGCTGTTTTTAATACATT 57.813 29.630 0.00 0.00 0.00 2.71
471 1308 7.346208 TGATTAACATTACACTCGTCAGTTG 57.654 36.000 0.00 0.00 0.00 3.16
474 1311 9.825972 AATTTTGATTAACATTACACTCGTCAG 57.174 29.630 0.00 0.00 0.00 3.51
515 1353 9.479549 TCCTCTTGGATTTGCTAATTCTTAATT 57.520 29.630 0.81 0.00 37.46 1.40
524 1362 7.605449 CATTCTTTTCCTCTTGGATTTGCTAA 58.395 34.615 0.00 0.00 42.81 3.09
525 1363 6.350445 GCATTCTTTTCCTCTTGGATTTGCTA 60.350 38.462 0.00 0.00 42.81 3.49
527 1365 4.628766 GCATTCTTTTCCTCTTGGATTTGC 59.371 41.667 0.00 0.00 42.81 3.68
549 1387 0.819259 TCCTTGCGCCTGAATATGGC 60.819 55.000 4.18 0.00 46.42 4.40
616 1456 4.041075 TGCCTTGTACTCTTGGTGAATACA 59.959 41.667 0.00 0.00 35.85 2.29
617 1457 4.392138 GTGCCTTGTACTCTTGGTGAATAC 59.608 45.833 0.00 0.00 0.00 1.89
650 2933 5.460419 CAGCACTCTATTGAGATAAACGTCC 59.540 44.000 11.29 0.00 42.73 4.79
665 2948 0.613260 ACGGCCAAATCAGCACTCTA 59.387 50.000 2.24 0.00 0.00 2.43
669 2952 2.094752 ACATTTACGGCCAAATCAGCAC 60.095 45.455 2.24 0.00 0.00 4.40
692 3063 2.100989 GACCTATCAGGAAGTGACCGT 58.899 52.381 0.00 0.00 37.67 4.83
693 3064 1.065701 CGACCTATCAGGAAGTGACCG 59.934 57.143 0.00 0.00 37.67 4.79
702 3073 2.969628 ACAAAGAGCGACCTATCAGG 57.030 50.000 0.00 0.00 42.49 3.86
733 3104 3.770263 TTATTCCACGGACAGAGTACG 57.230 47.619 0.00 0.00 46.43 3.67
734 3105 6.592607 TCAAAATTATTCCACGGACAGAGTAC 59.407 38.462 0.00 0.00 0.00 2.73
747 3118 8.682128 TTATGCGACAAGTTCAAAATTATTCC 57.318 30.769 0.00 0.00 0.00 3.01
753 3124 6.676950 TGACATTATGCGACAAGTTCAAAAT 58.323 32.000 0.00 0.00 0.00 1.82
839 3219 0.743701 TACGTGAGACTCCCGAGAGC 60.744 60.000 14.47 0.00 44.65 4.09
892 3278 2.203972 CTCGTGGGTTTGCATGCAGG 62.204 60.000 21.50 3.59 0.00 4.85
975 3364 2.281761 CTGGTCTGTGGTGGTGGC 60.282 66.667 0.00 0.00 0.00 5.01
979 3368 1.121407 TCTGGTCTGGTCTGTGGTGG 61.121 60.000 0.00 0.00 0.00 4.61
980 3369 0.034059 GTCTGGTCTGGTCTGTGGTG 59.966 60.000 0.00 0.00 0.00 4.17
981 3370 0.398522 TGTCTGGTCTGGTCTGTGGT 60.399 55.000 0.00 0.00 0.00 4.16
982 3371 0.979665 ATGTCTGGTCTGGTCTGTGG 59.020 55.000 0.00 0.00 0.00 4.17
983 3372 1.620323 TCATGTCTGGTCTGGTCTGTG 59.380 52.381 0.00 0.00 0.00 3.66
984 3373 1.620819 GTCATGTCTGGTCTGGTCTGT 59.379 52.381 0.00 0.00 0.00 3.41
1131 3527 3.006728 CGCCTACCCCTCCCAACA 61.007 66.667 0.00 0.00 0.00 3.33
1222 3630 4.439901 GCTCCCCTCCCCCTCCTT 62.440 72.222 0.00 0.00 0.00 3.36
1278 3686 1.541310 CCTTGGACAGGTACAGCGGA 61.541 60.000 0.00 0.00 37.99 5.54
1428 3836 3.224324 GATGGCTGGCATGGCAGG 61.224 66.667 40.21 26.21 45.49 4.85
1429 3837 1.806461 GATGATGGCTGGCATGGCAG 61.806 60.000 37.54 37.54 45.49 4.85
1430 3838 1.830847 GATGATGGCTGGCATGGCA 60.831 57.895 22.23 21.97 46.31 4.92
1431 3839 1.185618 ATGATGATGGCTGGCATGGC 61.186 55.000 22.23 13.29 0.00 4.40
1432 3840 0.888619 GATGATGATGGCTGGCATGG 59.111 55.000 22.23 0.00 0.00 3.66
1433 3841 1.616159 TGATGATGATGGCTGGCATG 58.384 50.000 22.23 0.00 0.00 4.06
1435 3843 2.158519 AGATTGATGATGATGGCTGGCA 60.159 45.455 6.31 6.31 0.00 4.92
1436 3844 2.229062 CAGATTGATGATGATGGCTGGC 59.771 50.000 0.00 0.00 0.00 4.85
1437 3845 2.229062 GCAGATTGATGATGATGGCTGG 59.771 50.000 0.00 0.00 0.00 4.85
1438 3846 2.229062 GGCAGATTGATGATGATGGCTG 59.771 50.000 0.00 0.00 0.00 4.85
1440 3848 2.229062 CAGGCAGATTGATGATGATGGC 59.771 50.000 0.00 0.00 0.00 4.40
1441 3849 3.487372 ACAGGCAGATTGATGATGATGG 58.513 45.455 0.00 0.00 0.00 3.51
1442 3850 5.392057 GCATACAGGCAGATTGATGATGATG 60.392 44.000 0.00 0.00 0.00 3.07
1443 3851 4.700692 GCATACAGGCAGATTGATGATGAT 59.299 41.667 0.00 0.00 0.00 2.45
1444 3852 4.070009 GCATACAGGCAGATTGATGATGA 58.930 43.478 0.00 0.00 0.00 2.92
1445 3853 4.072839 AGCATACAGGCAGATTGATGATG 58.927 43.478 0.00 0.00 35.83 3.07
1446 3854 4.041815 AGAGCATACAGGCAGATTGATGAT 59.958 41.667 0.00 0.00 35.83 2.45
1448 3856 3.741249 AGAGCATACAGGCAGATTGATG 58.259 45.455 0.00 0.00 35.83 3.07
1451 3859 4.510711 CAGTTAGAGCATACAGGCAGATTG 59.489 45.833 0.00 0.00 35.83 2.67
1452 3860 4.406972 TCAGTTAGAGCATACAGGCAGATT 59.593 41.667 0.00 0.00 35.83 2.40
1453 3861 3.963374 TCAGTTAGAGCATACAGGCAGAT 59.037 43.478 0.00 0.00 35.83 2.90
1454 3862 3.131223 GTCAGTTAGAGCATACAGGCAGA 59.869 47.826 0.00 0.00 35.83 4.26
1455 3863 3.131933 AGTCAGTTAGAGCATACAGGCAG 59.868 47.826 0.00 0.00 35.83 4.85
1456 3864 3.099905 AGTCAGTTAGAGCATACAGGCA 58.900 45.455 0.00 0.00 35.83 4.75
1457 3865 3.131223 TCAGTCAGTTAGAGCATACAGGC 59.869 47.826 0.00 0.00 0.00 4.85
1458 3866 4.400884 AGTCAGTCAGTTAGAGCATACAGG 59.599 45.833 0.00 0.00 0.00 4.00
1461 3869 5.106118 TGTGAGTCAGTCAGTTAGAGCATAC 60.106 44.000 0.00 0.00 35.13 2.39
1462 3870 5.010282 TGTGAGTCAGTCAGTTAGAGCATA 58.990 41.667 0.00 0.00 35.13 3.14
1465 4084 3.924918 TGTGAGTCAGTCAGTTAGAGC 57.075 47.619 0.00 0.00 35.13 4.09
1476 4095 4.095932 CCATGTTTGGATCATGTGAGTCAG 59.904 45.833 0.00 0.00 46.92 3.51
1477 4096 4.011698 CCATGTTTGGATCATGTGAGTCA 58.988 43.478 0.00 0.00 46.92 3.41
1480 4099 2.100252 GGCCATGTTTGGATCATGTGAG 59.900 50.000 0.00 0.00 46.92 3.51
1481 4100 2.101783 GGCCATGTTTGGATCATGTGA 58.898 47.619 0.00 0.00 46.92 3.58
1482 4101 1.202325 CGGCCATGTTTGGATCATGTG 60.202 52.381 2.24 0.00 46.92 3.21
1483 4102 1.105457 CGGCCATGTTTGGATCATGT 58.895 50.000 2.24 0.00 46.92 3.21
1505 4124 1.639298 GCTTGGCTAACCTGCAGACG 61.639 60.000 17.39 1.02 36.54 4.18
2148 4796 1.004440 GCCGAGAAGCACTGTTCCT 60.004 57.895 0.00 0.00 0.00 3.36
2152 4800 4.299547 TGCGCCGAGAAGCACTGT 62.300 61.111 4.18 0.00 38.59 3.55
2589 5237 2.151049 GACGTGCCGGAAGTACCTGT 62.151 60.000 5.05 0.00 36.31 4.00
2701 5478 4.421479 CTCGTCGCCGCCAAGACT 62.421 66.667 0.00 0.00 35.38 3.24
2840 5617 1.429930 TCCCGGCCTCTAATTATGCA 58.570 50.000 0.00 0.00 0.00 3.96
2935 5716 6.591062 GCAACTTCTGATGGCAAAATGATTTA 59.409 34.615 0.00 0.00 0.00 1.40
2936 5717 5.410439 GCAACTTCTGATGGCAAAATGATTT 59.590 36.000 0.00 0.00 0.00 2.17
2963 5746 2.483877 CGGCTTATGAACTTGTCTTGCA 59.516 45.455 0.00 0.00 0.00 4.08
3008 5791 7.096106 CGTACATTACGTGGAAGAAAGTGTTTA 60.096 37.037 0.00 0.00 46.41 2.01
3074 5857 1.466024 GGTACTCTGAACAGACTCGCG 60.466 57.143 0.00 0.00 33.22 5.87
3095 5879 6.747280 GCGCTGTATGTTACTTTCATGAATTT 59.253 34.615 9.40 1.73 0.00 1.82
3098 5882 4.693095 TGCGCTGTATGTTACTTTCATGAA 59.307 37.500 9.73 3.38 0.00 2.57
3107 5891 3.338818 AATGCATGCGCTGTATGTTAC 57.661 42.857 14.09 0.00 39.64 2.50
3137 5921 0.398696 TGGTGTGTCCCGTAAATGCT 59.601 50.000 0.00 0.00 34.77 3.79
3141 5925 2.932855 TCATTGGTGTGTCCCGTAAA 57.067 45.000 0.00 0.00 34.77 2.01
3145 5929 1.266718 CTGTTTCATTGGTGTGTCCCG 59.733 52.381 0.00 0.00 34.77 5.14
3147 5931 3.476552 TCTCTGTTTCATTGGTGTGTCC 58.523 45.455 0.00 0.00 0.00 4.02
3148 5932 6.166279 TCTATCTCTGTTTCATTGGTGTGTC 58.834 40.000 0.00 0.00 0.00 3.67
3198 5982 4.439057 TGCCAGTATTTCAAGATACGGTC 58.561 43.478 0.00 0.00 37.53 4.79
3199 5983 4.481368 TGCCAGTATTTCAAGATACGGT 57.519 40.909 0.00 0.00 37.53 4.83
3200 5984 4.634004 TGTTGCCAGTATTTCAAGATACGG 59.366 41.667 0.00 0.00 37.53 4.02
3202 5986 6.473455 GCATTGTTGCCAGTATTTCAAGATAC 59.527 38.462 0.00 0.00 43.38 2.24
3203 5987 6.563422 GCATTGTTGCCAGTATTTCAAGATA 58.437 36.000 0.00 0.00 43.38 1.98
3204 5988 5.413499 GCATTGTTGCCAGTATTTCAAGAT 58.587 37.500 0.00 0.00 43.38 2.40
3205 5989 4.808558 GCATTGTTGCCAGTATTTCAAGA 58.191 39.130 0.00 0.00 43.38 3.02
3253 6045 1.273688 TTGTGTGACGTTGTCGAGTG 58.726 50.000 0.00 0.00 40.62 3.51
3496 6308 0.898320 CGTCTGTCTGGGTCAGGATT 59.102 55.000 0.00 0.00 34.15 3.01
3529 6341 2.576615 GGTGAGAGTGGAAAGCTTGTT 58.423 47.619 0.00 0.00 0.00 2.83
3541 6353 1.674980 GACCTCGGTCGGTGAGAGT 60.675 63.158 0.00 0.00 37.42 3.24
3550 6362 4.131088 GGCTGGTCGACCTCGGTC 62.131 72.222 33.39 20.98 41.40 4.79
3571 6383 1.008309 GTACTCGGCGATGCTCCTC 60.008 63.158 11.27 0.00 0.00 3.71
3721 6533 1.001520 TGCTACTTGCTAAACTCGCCA 59.998 47.619 0.00 0.00 43.37 5.69
3727 6539 6.481954 AGTATGTGTTGCTACTTGCTAAAC 57.518 37.500 0.00 0.00 43.37 2.01
3738 6550 8.623903 CCAATTAATCATGTAGTATGTGTTGCT 58.376 33.333 0.00 0.00 0.00 3.91
3747 6559 7.282224 GCCACTGAACCAATTAATCATGTAGTA 59.718 37.037 0.00 0.00 0.00 1.82
3755 6577 4.016444 TCTGGCCACTGAACCAATTAATC 58.984 43.478 0.00 0.00 34.96 1.75
3763 6585 0.322008 CCTTCTCTGGCCACTGAACC 60.322 60.000 0.00 0.00 0.00 3.62
3764 6586 0.687354 TCCTTCTCTGGCCACTGAAC 59.313 55.000 0.00 0.00 0.00 3.18
3781 6603 2.332654 ACGCGCTGGTTGGATTTCC 61.333 57.895 5.73 0.00 0.00 3.13
3782 6604 1.154225 CACGCGCTGGTTGGATTTC 60.154 57.895 5.73 0.00 0.00 2.17


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

AutoCloner maintained by Alex Coulton.