Multiple sequence alignment - TraesCS6A01G394200

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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 TraesCS6A01G394200 chr6A 100.000 3990 0 0 1 3990 607930244 607934233 0.000000e+00 7369
1 TraesCS6A01G394200 chr6D 94.100 3576 163 21 1 3563 461332141 461335681 0.000000e+00 5391
2 TraesCS6A01G394200 chr6D 93.204 309 9 4 3570 3870 461335727 461336031 1.020000e-120 444
3 TraesCS6A01G394200 chr6B 93.628 3343 145 24 1 3317 702814275 702817575 0.000000e+00 4931
4 TraesCS6A01G394200 chr6B 94.249 313 9 3 3570 3874 702819654 702819965 1.680000e-128 470
5 TraesCS6A01G394200 chr6B 95.506 178 5 2 3388 3563 702819438 702819614 8.440000e-72 281
6 TraesCS6A01G394200 chr6B 90.909 110 9 1 3864 3973 702820124 702820232 3.210000e-31 147
7 TraesCS6A01G394200 chr6B 95.402 87 1 1 3319 3402 702817740 702817826 6.960000e-28 135
8 TraesCS6A01G394200 chr5B 88.835 206 20 3 2392 2595 55520094 55520298 2.380000e-62 250


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 TraesCS6A01G394200 chr6A 607930244 607934233 3989 False 7369.0 7369 100.0000 1 3990 1 chr6A.!!$F1 3989
1 TraesCS6A01G394200 chr6D 461332141 461336031 3890 False 2917.5 5391 93.6520 1 3870 2 chr6D.!!$F1 3869
2 TraesCS6A01G394200 chr6B 702814275 702820232 5957 False 1192.8 4931 93.9388 1 3973 5 chr6B.!!$F1 3972

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
322 323 0.034896 ATGTGCCGACGTTCCTCTTT 59.965 50.0 0.0 0.0 0.0 2.52 F
1358 1361 0.625849 ACCTGCCTCCCTATGGTTTG 59.374 55.0 0.0 0.0 0.0 2.93 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1589 1592 0.162933 CACACGACAACGCGCTTTAT 59.837 50.0 5.73 0.0 43.96 1.40 R
3169 3197 0.978146 TAGAGAGGACCCCAGCAAGC 60.978 60.0 0.00 0.0 0.00 4.01 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
25 26 0.182061 CCATGTCCCTGGTCTCCATG 59.818 60.000 0.00 0.00 30.82 3.66
67 68 1.454847 TTCAACCAGCCCGCACTTT 60.455 52.632 0.00 0.00 0.00 2.66
94 95 3.833650 ACATGTTCATCAGGGAATTGCAA 59.166 39.130 0.00 0.00 31.56 4.08
211 212 0.383590 TCGTGAACGTGAACGGGTTA 59.616 50.000 19.44 1.85 44.95 2.85
304 305 0.667487 CAGTGAGCAACGACGTCCAT 60.667 55.000 10.58 0.00 0.00 3.41
321 322 0.670546 CATGTGCCGACGTTCCTCTT 60.671 55.000 0.00 0.00 0.00 2.85
322 323 0.034896 ATGTGCCGACGTTCCTCTTT 59.965 50.000 0.00 0.00 0.00 2.52
346 347 2.266055 CCCTCGAACACCAGCCTC 59.734 66.667 0.00 0.00 0.00 4.70
458 459 3.720601 AATGCAGCTGCTCCCCGA 61.721 61.111 36.61 18.16 42.66 5.14
459 460 3.052909 AATGCAGCTGCTCCCCGAT 62.053 57.895 36.61 19.64 42.66 4.18
823 824 2.792599 CTACCTCGCTTCGTCGCT 59.207 61.111 0.00 0.00 0.00 4.93
828 829 3.329688 CTCGCTTCGTCGCTGGAGT 62.330 63.158 0.00 0.00 0.00 3.85
958 961 2.658593 CGATAGGAGTTGGCGCGG 60.659 66.667 8.83 0.00 0.00 6.46
1337 1340 2.410730 CCATCGTCGTGTTCTGGTAAAC 59.589 50.000 0.00 0.00 0.00 2.01
1338 1341 3.314553 CATCGTCGTGTTCTGGTAAACT 58.685 45.455 0.00 0.00 0.00 2.66
1339 1342 4.478699 CATCGTCGTGTTCTGGTAAACTA 58.521 43.478 0.00 0.00 0.00 2.24
1340 1343 3.888934 TCGTCGTGTTCTGGTAAACTAC 58.111 45.455 0.00 0.00 0.00 2.73
1350 1353 1.581223 GGTAAACTACCTGCCTCCCT 58.419 55.000 0.00 0.00 45.52 4.20
1351 1354 2.755686 GGTAAACTACCTGCCTCCCTA 58.244 52.381 0.00 0.00 45.52 3.53
1352 1355 3.315596 GGTAAACTACCTGCCTCCCTAT 58.684 50.000 0.00 0.00 45.52 2.57
1358 1361 0.625849 ACCTGCCTCCCTATGGTTTG 59.374 55.000 0.00 0.00 0.00 2.93
1420 1423 6.989155 AATGGGTTATCATGAATCATGCTT 57.011 33.333 17.81 10.37 41.18 3.91
1481 1484 3.396611 GTGGCCTTATGGGGGTAGAAATA 59.603 47.826 3.32 0.00 35.12 1.40
1522 1525 2.103263 GGGCTCATCTAGTTACCCTGTG 59.897 54.545 0.00 0.00 34.34 3.66
1525 1528 4.589374 GGCTCATCTAGTTACCCTGTGTAT 59.411 45.833 0.00 0.00 0.00 2.29
1589 1592 2.441750 AGCTCACCTTCAGTTTTACCCA 59.558 45.455 0.00 0.00 0.00 4.51
1590 1593 3.074538 AGCTCACCTTCAGTTTTACCCAT 59.925 43.478 0.00 0.00 0.00 4.00
1623 1627 1.974875 TGTGCGACCCTTCTAGCGA 60.975 57.895 0.00 0.00 0.00 4.93
1678 1698 2.296792 TCTTGGTGGTTGTGTGATGTG 58.703 47.619 0.00 0.00 0.00 3.21
1692 1712 6.061441 TGTGTGATGTGTATTTGGAAGACTT 58.939 36.000 0.00 0.00 0.00 3.01
1698 1718 8.474025 TGATGTGTATTTGGAAGACTTGTTTTT 58.526 29.630 0.00 0.00 0.00 1.94
1705 1725 5.845391 TGGAAGACTTGTTTTTCCGAAAT 57.155 34.783 0.00 0.00 42.60 2.17
1775 1795 3.258622 AGCCAGTAGTTAGGTTCAGTGTC 59.741 47.826 0.00 0.00 0.00 3.67
1838 1858 7.764901 TCGCTTACATGTATTATGTTTACCACA 59.235 33.333 6.36 0.00 40.71 4.17
1888 1910 9.178427 GGTGTTTCGTCATATATACTCTTGTAC 57.822 37.037 0.00 0.00 0.00 2.90
2002 2024 7.315890 TCAAGTAGTTGTCTGACATAGTGATG 58.684 38.462 11.86 7.83 35.71 3.07
2009 2031 4.766891 TGTCTGACATAGTGATGACTGTCA 59.233 41.667 13.60 13.60 34.40 3.58
2045 2067 3.321111 GTGTCTTACAGTCTGGGTTGAGA 59.679 47.826 4.53 0.00 0.00 3.27
2070 2092 7.894376 ATAAATACCAGCATTTGCAATATGC 57.106 32.000 25.90 25.90 46.78 3.14
2097 2119 1.069049 GCAAGTTGGTGCAGGAAATGT 59.931 47.619 4.75 0.00 44.29 2.71
2130 2152 1.200020 CCTAAGCTGGAAAAGTTGGCG 59.800 52.381 0.00 0.00 0.00 5.69
2136 2158 1.172180 TGGAAAAGTTGGCGGCAGAG 61.172 55.000 12.87 0.00 0.00 3.35
2225 2248 8.722480 TCGACAAATTTATGATCTCTGTCATT 57.278 30.769 0.00 0.00 39.45 2.57
2266 2289 2.054687 TTTACTGCGTCGACGTCAAT 57.945 45.000 35.48 25.54 42.22 2.57
2323 2346 1.556564 CGGTAAGTATCTGCCGTGTG 58.443 55.000 0.00 0.00 39.41 3.82
2339 2362 2.017049 GTGTGTTGAGTTGGTTCTGCT 58.983 47.619 0.00 0.00 0.00 4.24
2342 2365 3.202906 GTGTTGAGTTGGTTCTGCTGTA 58.797 45.455 0.00 0.00 0.00 2.74
2385 2409 8.868522 ACAATGATATCAGAACCTTTTCTTGA 57.131 30.769 11.78 0.00 40.34 3.02
2417 2441 3.705604 TGCTTTCTTGTTAGCAAACAGC 58.294 40.909 9.02 9.02 45.99 4.40
2692 2717 8.121305 TCTTGTCCTGCAACAATTAAATACAT 57.879 30.769 4.49 0.00 38.41 2.29
2859 2884 0.670546 CTCCATCTCGGCGTTGTGTT 60.671 55.000 6.85 0.00 33.14 3.32
2959 2984 0.676184 CGTGGATGGTGATCGAGGAT 59.324 55.000 0.00 0.00 0.00 3.24
2962 2987 2.118679 TGGATGGTGATCGAGGATGTT 58.881 47.619 0.00 0.00 0.00 2.71
3012 3037 3.732892 CCAACGCGGCGATGGTTT 61.733 61.111 34.66 15.36 43.21 3.27
3018 3043 3.496131 CGGCGATGGTTTCCGTGG 61.496 66.667 0.00 0.00 38.47 4.94
3021 3046 2.867472 CGATGGTTTCCGTGGCAC 59.133 61.111 7.79 7.79 0.00 5.01
3022 3047 2.867472 GATGGTTTCCGTGGCACG 59.133 61.111 31.78 31.78 42.11 5.34
3053 3078 0.675522 ACACCGCGGTAAAATGGAGG 60.676 55.000 33.70 17.84 0.00 4.30
3073 3098 3.118592 AGGAAACAAGATAAGAGGCGGAG 60.119 47.826 0.00 0.00 0.00 4.63
3103 3128 8.417106 AGAAAACAAGATCGAGATTGAGCTATA 58.583 33.333 16.73 0.00 32.47 1.31
3105 3130 8.531622 AAACAAGATCGAGATTGAGCTATATG 57.468 34.615 16.73 0.00 32.47 1.78
3128 3153 7.302350 TGTGTCCAGTTTTGTATAATCATCG 57.698 36.000 0.00 0.00 0.00 3.84
3129 3154 6.183360 TGTGTCCAGTTTTGTATAATCATCGC 60.183 38.462 0.00 0.00 0.00 4.58
3133 3161 3.059868 AGTTTTGTATAATCATCGCCGCG 60.060 43.478 6.39 6.39 0.00 6.46
3153 3181 1.449778 GGACGCCTAGGGTTCTTGC 60.450 63.158 11.72 0.00 0.00 4.01
3154 3182 1.597461 GACGCCTAGGGTTCTTGCT 59.403 57.895 11.72 0.00 0.00 3.91
3156 3184 1.450312 CGCCTAGGGTTCTTGCTGG 60.450 63.158 11.72 0.00 0.00 4.85
3157 3185 1.077429 GCCTAGGGTTCTTGCTGGG 60.077 63.158 11.72 0.00 0.00 4.45
3159 3187 1.216990 CCTAGGGTTCTTGCTGGGAT 58.783 55.000 0.00 0.00 0.00 3.85
3169 3197 4.883354 GCTGGGATGGGGGCTTCG 62.883 72.222 0.00 0.00 0.00 3.79
3209 3237 4.302004 AGGATTTAGAGGATTGGAGGGA 57.698 45.455 0.00 0.00 0.00 4.20
3215 3243 0.842635 GAGGATTGGAGGGACATGCT 59.157 55.000 0.00 0.00 0.00 3.79
3273 3302 4.272018 CAGAAGGCTTTCCATTAGTCATCG 59.728 45.833 4.73 0.00 33.64 3.84
3275 3304 4.222124 AGGCTTTCCATTAGTCATCGTT 57.778 40.909 0.00 0.00 33.74 3.85
3276 3305 3.941483 AGGCTTTCCATTAGTCATCGTTG 59.059 43.478 0.00 0.00 33.74 4.10
3277 3306 3.689649 GGCTTTCCATTAGTCATCGTTGT 59.310 43.478 0.00 0.00 0.00 3.32
3278 3307 4.873827 GGCTTTCCATTAGTCATCGTTGTA 59.126 41.667 0.00 0.00 0.00 2.41
3279 3308 5.006746 GGCTTTCCATTAGTCATCGTTGTAG 59.993 44.000 0.00 0.00 0.00 2.74
3280 3309 5.502544 GCTTTCCATTAGTCATCGTTGTAGC 60.503 44.000 0.00 0.00 0.00 3.58
3281 3310 4.729227 TCCATTAGTCATCGTTGTAGCA 57.271 40.909 0.00 0.00 0.00 3.49
3282 3311 5.079689 TCCATTAGTCATCGTTGTAGCAA 57.920 39.130 0.00 0.00 0.00 3.91
3283 3312 5.670485 TCCATTAGTCATCGTTGTAGCAAT 58.330 37.500 0.00 0.00 0.00 3.56
3286 3315 7.766738 TCCATTAGTCATCGTTGTAGCAATAAA 59.233 33.333 0.00 0.00 0.00 1.40
3288 3317 9.935682 CATTAGTCATCGTTGTAGCAATAAAAT 57.064 29.630 0.00 0.00 0.00 1.82
3532 5355 3.118261 TGCTTGCTAATTAGAGAGGGGTG 60.118 47.826 16.85 0.00 0.00 4.61
3559 5385 5.931724 AGTATTTTAATTTGCAAGTGGTGGC 59.068 36.000 0.00 0.00 0.00 5.01
3563 5389 2.103339 ATTTGCAAGTGGTGGCAGCC 62.103 55.000 14.97 3.66 41.68 4.85
3564 5390 3.736996 TTGCAAGTGGTGGCAGCCT 62.737 57.895 14.15 8.01 41.68 4.58
3565 5391 2.914097 GCAAGTGGTGGCAGCCTT 60.914 61.111 14.15 13.56 0.00 4.35
3566 5392 3.045142 CAAGTGGTGGCAGCCTTG 58.955 61.111 23.52 23.52 0.00 3.61
3567 5393 1.829533 CAAGTGGTGGCAGCCTTGT 60.830 57.895 26.08 6.60 31.79 3.16
3568 5394 0.537143 CAAGTGGTGGCAGCCTTGTA 60.537 55.000 26.08 4.99 31.79 2.41
3747 5624 1.486310 TCAGCACCTTCTTGTGTCTGT 59.514 47.619 12.10 0.00 39.37 3.41
3853 5730 2.614057 GACTGTCTGTCTGTTGGTTTGG 59.386 50.000 0.00 0.00 42.21 3.28
3871 5916 8.871629 TGGTTTGGCTTTTCTTTGACTATATA 57.128 30.769 0.00 0.00 0.00 0.86
3973 6018 7.666804 TCAGAAGGTCATGATTTTTCTTCATCA 59.333 33.333 18.58 0.00 34.70 3.07
3974 6019 7.968956 CAGAAGGTCATGATTTTTCTTCATCAG 59.031 37.037 18.58 6.74 32.91 2.90
3975 6020 7.886970 AGAAGGTCATGATTTTTCTTCATCAGA 59.113 33.333 18.58 0.00 32.91 3.27
3976 6021 8.591114 AAGGTCATGATTTTTCTTCATCAGAT 57.409 30.769 0.00 0.00 32.91 2.90
3977 6022 7.997482 AGGTCATGATTTTTCTTCATCAGATG 58.003 34.615 3.71 3.71 32.91 2.90
3978 6023 7.068348 AGGTCATGATTTTTCTTCATCAGATGG 59.932 37.037 10.67 0.00 32.91 3.51
3979 6024 7.067859 GGTCATGATTTTTCTTCATCAGATGGA 59.932 37.037 10.67 0.16 32.91 3.41
3980 6025 7.914346 GTCATGATTTTTCTTCATCAGATGGAC 59.086 37.037 10.67 1.86 32.91 4.02
3981 6026 6.426980 TGATTTTTCTTCATCAGATGGACG 57.573 37.500 10.67 0.02 0.00 4.79
3982 6027 5.355071 TGATTTTTCTTCATCAGATGGACGG 59.645 40.000 10.67 0.00 0.00 4.79
3983 6028 2.315925 TTCTTCATCAGATGGACGGC 57.684 50.000 10.67 0.00 0.00 5.68
3984 6029 0.103026 TCTTCATCAGATGGACGGCG 59.897 55.000 10.67 4.80 0.00 6.46
3985 6030 0.877649 CTTCATCAGATGGACGGCGG 60.878 60.000 13.24 0.00 0.00 6.13
3986 6031 2.923426 TTCATCAGATGGACGGCGGC 62.923 60.000 13.24 8.60 0.00 6.53
3987 6032 4.592192 ATCAGATGGACGGCGGCG 62.592 66.667 31.06 31.06 0.00 6.46
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
25 26 1.656441 CAAGGCTGTGTTCTGTGGC 59.344 57.895 0.00 0.00 0.00 5.01
67 68 1.552792 TCCCTGATGAACATGTACGCA 59.447 47.619 0.00 0.00 0.00 5.24
94 95 2.728383 CGCTCGACCGTGTTCGTT 60.728 61.111 0.00 0.00 40.07 3.85
124 125 2.447887 CGTGCATGCTCAGTCGGTC 61.448 63.158 20.33 0.00 0.00 4.79
280 281 1.000506 ACGTCGTTGCTCACTGGTTAT 59.999 47.619 0.00 0.00 0.00 1.89
286 287 0.667487 CATGGACGTCGTTGCTCACT 60.667 55.000 9.92 0.00 0.00 3.41
304 305 0.878523 CAAAGAGGAACGTCGGCACA 60.879 55.000 0.00 0.00 0.00 4.57
321 322 1.002624 GTGTTCGAGGGGATGCCAA 60.003 57.895 5.30 0.00 0.00 4.52
322 323 2.668632 GTGTTCGAGGGGATGCCA 59.331 61.111 5.30 0.00 0.00 4.92
436 437 2.772691 GGAGCAGCTGCATTGCCTC 61.773 63.158 38.24 25.27 45.16 4.70
703 704 3.473647 CTGGAGGAGGATGGCGCA 61.474 66.667 10.83 0.00 0.00 6.09
940 942 2.658593 CGCGCCAACTCCTATCGG 60.659 66.667 0.00 0.00 0.00 4.18
979 982 3.047877 GTTTGGGCTCGTCCGGTG 61.048 66.667 0.00 0.00 34.94 4.94
1098 1101 3.141488 GAGAGGAAGGCGAGGCGA 61.141 66.667 0.00 0.00 0.00 5.54
1337 1340 1.807814 AACCATAGGGAGGCAGGTAG 58.192 55.000 0.00 0.00 38.05 3.18
1338 1341 1.843851 CAAACCATAGGGAGGCAGGTA 59.156 52.381 0.00 0.00 38.05 3.08
1339 1342 0.625849 CAAACCATAGGGAGGCAGGT 59.374 55.000 0.00 0.00 38.05 4.00
1340 1343 0.753111 GCAAACCATAGGGAGGCAGG 60.753 60.000 0.00 0.00 38.05 4.85
1341 1344 0.257039 AGCAAACCATAGGGAGGCAG 59.743 55.000 0.00 0.00 38.05 4.85
1342 1345 0.255890 GAGCAAACCATAGGGAGGCA 59.744 55.000 0.00 0.00 38.05 4.75
1343 1346 0.548510 AGAGCAAACCATAGGGAGGC 59.451 55.000 0.00 0.02 38.05 4.70
1344 1347 1.839994 TCAGAGCAAACCATAGGGAGG 59.160 52.381 0.00 0.00 38.05 4.30
1345 1348 3.634397 TTCAGAGCAAACCATAGGGAG 57.366 47.619 0.00 0.00 38.05 4.30
1346 1349 4.591321 AATTCAGAGCAAACCATAGGGA 57.409 40.909 0.00 0.00 38.05 4.20
1347 1350 5.665916 AAAATTCAGAGCAAACCATAGGG 57.334 39.130 0.00 0.00 41.29 3.53
1348 1351 7.830739 AGTTAAAATTCAGAGCAAACCATAGG 58.169 34.615 0.00 0.00 0.00 2.57
1349 1352 9.994432 CTAGTTAAAATTCAGAGCAAACCATAG 57.006 33.333 0.00 0.00 0.00 2.23
1350 1353 8.956426 CCTAGTTAAAATTCAGAGCAAACCATA 58.044 33.333 0.00 0.00 0.00 2.74
1351 1354 7.451566 ACCTAGTTAAAATTCAGAGCAAACCAT 59.548 33.333 0.00 0.00 0.00 3.55
1352 1355 6.775629 ACCTAGTTAAAATTCAGAGCAAACCA 59.224 34.615 0.00 0.00 0.00 3.67
1358 1361 4.571176 CGGGACCTAGTTAAAATTCAGAGC 59.429 45.833 0.00 0.00 0.00 4.09
1420 1423 4.225042 TGAAGCCTAATCCAAGTTAGCTGA 59.775 41.667 0.00 0.00 31.72 4.26
1481 1484 2.954318 CCCTTTTCATCCAAGATGCGAT 59.046 45.455 0.00 0.00 0.00 4.58
1522 1525 3.462021 CAAGAGCTACCAAGAGCCATAC 58.538 50.000 0.00 0.00 43.97 2.39
1525 1528 0.615331 CCAAGAGCTACCAAGAGCCA 59.385 55.000 0.00 0.00 43.97 4.75
1589 1592 0.162933 CACACGACAACGCGCTTTAT 59.837 50.000 5.73 0.00 43.96 1.40
1590 1593 1.560770 CACACGACAACGCGCTTTA 59.439 52.632 5.73 0.00 43.96 1.85
1612 1616 1.993370 CGAAACAAGTCGCTAGAAGGG 59.007 52.381 0.00 0.00 33.66 3.95
1623 1627 1.665599 CGCCGGTACCGAAACAAGT 60.666 57.895 35.41 0.00 42.83 3.16
1678 1698 6.731164 TCGGAAAAACAAGTCTTCCAAATAC 58.269 36.000 12.05 0.00 38.88 1.89
1692 1712 6.292596 GCTTATTGTTGCATTTCGGAAAAACA 60.293 34.615 12.71 12.71 0.00 2.83
1698 1718 3.673052 GCTGCTTATTGTTGCATTTCGGA 60.673 43.478 0.00 0.00 38.59 4.55
1705 1725 1.541147 GGTGAGCTGCTTATTGTTGCA 59.459 47.619 2.53 0.00 37.63 4.08
1775 1795 6.518200 GCCTAAGATATGAACCAGGAGAAGAG 60.518 46.154 0.00 0.00 0.00 2.85
1810 1830 7.764901 TGGTAAACATAATACATGTAAGCGACA 59.235 33.333 10.14 0.00 43.97 4.35
1888 1910 9.546909 CTGCACATTAGTATTGAAGTACTTTTG 57.453 33.333 10.02 0.46 36.39 2.44
1942 1964 3.255969 TCCATTTACGGAACCTACTGC 57.744 47.619 0.00 0.00 29.93 4.40
2002 2024 4.007659 ACCGTGGGATAATTTTGACAGTC 58.992 43.478 0.00 0.00 0.00 3.51
2009 2031 5.562635 TGTAAGACACCGTGGGATAATTTT 58.437 37.500 3.03 0.00 0.00 1.82
2045 2067 8.314143 GCATATTGCAAATGCTGGTATTTATT 57.686 30.769 25.93 2.37 45.05 1.40
2070 2092 2.908073 GCACCAACTTGCCGTCCTG 61.908 63.158 0.00 0.00 36.42 3.86
2079 2101 8.220559 AGATATATACATTTCCTGCACCAACTT 58.779 33.333 0.00 0.00 0.00 2.66
2130 2152 1.984066 ACCTCGGATAGTACTCTGCC 58.016 55.000 0.00 0.00 0.00 4.85
2136 2158 5.507650 CCAAAGCTCTAACCTCGGATAGTAC 60.508 48.000 0.00 0.00 0.00 2.73
2208 2231 9.842775 AGAGCAAATAATGACAGAGATCATAAA 57.157 29.630 0.00 0.00 38.40 1.40
2210 2233 7.387122 GCAGAGCAAATAATGACAGAGATCATA 59.613 37.037 0.00 0.00 38.40 2.15
2225 2248 2.092968 ACCGGATTCTGCAGAGCAAATA 60.093 45.455 17.43 0.54 38.41 1.40
2319 2342 2.017049 AGCAGAACCAACTCAACACAC 58.983 47.619 0.00 0.00 0.00 3.82
2323 2346 3.467803 AGTACAGCAGAACCAACTCAAC 58.532 45.455 0.00 0.00 0.00 3.18
2339 2362 2.949142 TCGTTAATGAGCGCAAGTACA 58.051 42.857 11.47 1.65 41.68 2.90
2342 2365 2.139917 TGTTCGTTAATGAGCGCAAGT 58.860 42.857 11.47 0.00 41.68 3.16
2385 2409 1.331756 CAAGAAAGCACACTTGAGCGT 59.668 47.619 9.94 0.00 43.98 5.07
2417 2441 3.536570 ACAAAAATGAAACGGGTTTGGG 58.463 40.909 0.82 0.00 34.28 4.12
2692 2717 3.980022 TGAGATCCCAATATAGGCCAACA 59.020 43.478 5.01 0.00 0.00 3.33
2859 2884 1.302511 GAAACAGCGGCCTCAGGAA 60.303 57.895 0.00 0.00 0.00 3.36
2959 2984 1.945354 GCTCGACCATCCTCCGAACA 61.945 60.000 0.00 0.00 31.59 3.18
2962 2987 2.044352 TGCTCGACCATCCTCCGA 60.044 61.111 0.00 0.00 0.00 4.55
3018 3043 3.723348 GTGAAAGGCCGGTCGTGC 61.723 66.667 1.90 0.00 0.00 5.34
3021 3046 3.047877 GGTGTGAAAGGCCGGTCG 61.048 66.667 1.90 0.00 0.00 4.79
3022 3047 3.047877 CGGTGTGAAAGGCCGGTC 61.048 66.667 0.00 0.00 41.60 4.79
3053 3078 3.619038 CACTCCGCCTCTTATCTTGTTTC 59.381 47.826 0.00 0.00 0.00 2.78
3073 3098 5.639506 TCAATCTCGATCTTGTTTTCTCCAC 59.360 40.000 6.91 0.00 0.00 4.02
3103 3128 7.467267 GCGATGATTATACAAAACTGGACACAT 60.467 37.037 0.00 0.00 0.00 3.21
3105 3130 6.192360 GCGATGATTATACAAAACTGGACAC 58.808 40.000 0.00 0.00 0.00 3.67
3133 3161 3.015312 AAGAACCCTAGGCGTCCGC 62.015 63.158 2.05 2.45 41.06 5.54
3169 3197 0.978146 TAGAGAGGACCCCAGCAAGC 60.978 60.000 0.00 0.00 0.00 4.01
3246 3274 5.190528 TGACTAATGGAAAGCCTTCTGATCT 59.809 40.000 0.00 0.00 34.31 2.75
3286 3315 8.481492 TGCAAGGTCATTGATTGGATATTATT 57.519 30.769 0.42 0.00 41.83 1.40
3288 3317 7.289310 TCTGCAAGGTCATTGATTGGATATTA 58.711 34.615 0.42 0.00 41.83 0.98
3297 3326 6.656902 TCTAATTCTCTGCAAGGTCATTGAT 58.343 36.000 0.42 0.00 41.83 2.57
3532 5355 6.589907 CACCACTTGCAAATTAAAATACTCCC 59.410 38.462 0.00 0.00 0.00 4.30
3559 5385 2.048444 AGCATCCATGTACAAGGCTG 57.952 50.000 14.98 14.98 0.00 4.85
3563 5389 7.716998 ACTCCTATTAAAGCATCCATGTACAAG 59.283 37.037 0.00 0.00 0.00 3.16
3564 5390 7.573710 ACTCCTATTAAAGCATCCATGTACAA 58.426 34.615 0.00 0.00 0.00 2.41
3565 5391 7.136822 ACTCCTATTAAAGCATCCATGTACA 57.863 36.000 0.00 0.00 0.00 2.90
3566 5392 9.726438 AATACTCCTATTAAAGCATCCATGTAC 57.274 33.333 0.00 0.00 0.00 2.90
3668 5541 3.769739 ACATCCAGCTACTGTTTGTGA 57.230 42.857 0.00 0.00 0.00 3.58
3941 5986 7.668886 AGAAAAATCATGACCTTCTGATGTTCT 59.331 33.333 12.63 5.81 34.94 3.01


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

AutoCloner maintained by Alex Coulton.