Multiple sequence alignment - TraesCS1A01G059300

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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 TraesCS1A01G059300 chr1A 100.000 5841 0 0 1 5841 40152798 40146958 0.000000e+00 10787.0
1 TraesCS1A01G059300 chr1D 96.432 2242 61 9 1983 4212 40878778 40876544 0.000000e+00 3679.0
2 TraesCS1A01G059300 chr1D 96.194 1997 60 7 1 1984 40880809 40878816 0.000000e+00 3253.0
3 TraesCS1A01G059300 chr1D 94.767 1586 43 9 4259 5841 40876529 40874981 0.000000e+00 2433.0
4 TraesCS1A01G059300 chr5B 91.850 319 23 3 5434 5750 697520588 697520271 5.370000e-120 442.0
5 TraesCS1A01G059300 chr4D 90.683 322 26 3 5433 5750 131105466 131105145 5.410000e-115 425.0
6 TraesCS1A01G059300 chr4D 97.059 34 1 0 627 660 474686518 474686485 2.270000e-04 58.4
7 TraesCS1A01G059300 chr4D 100.000 29 0 0 632 660 100563881 100563909 3.000000e-03 54.7
8 TraesCS1A01G059300 chr6B 90.909 319 24 5 5434 5750 487207076 487207391 1.950000e-114 424.0
9 TraesCS1A01G059300 chr6B 90.282 319 27 4 5434 5750 487203826 487204142 1.170000e-111 414.0
10 TraesCS1A01G059300 chr6D 89.697 330 29 5 5424 5750 18859835 18859508 3.260000e-112 416.0
11 TraesCS1A01G059300 chr4A 90.282 319 29 2 5434 5750 716103970 716103652 3.260000e-112 416.0
12 TraesCS1A01G059300 chr4A 90.282 319 29 2 5434 5750 716352554 716352872 3.260000e-112 416.0
13 TraesCS1A01G059300 chr4A 90.252 318 30 1 5434 5750 716118954 716118637 1.170000e-111 414.0
14 TraesCS1A01G059300 chr4A 100.000 30 0 0 631 660 45839424 45839453 8.180000e-04 56.5
15 TraesCS1A01G059300 chr4A 100.000 30 0 0 631 660 473290017 473289988 8.180000e-04 56.5
16 TraesCS1A01G059300 chr5A 90.282 319 25 5 5434 5750 169798843 169799157 4.210000e-111 412.0
17 TraesCS1A01G059300 chr3D 92.208 77 6 0 5756 5832 419929431 419929355 6.190000e-20 110.0
18 TraesCS1A01G059300 chr7A 90.411 73 7 0 5756 5828 63764156 63764228 4.820000e-16 97.1
19 TraesCS1A01G059300 chr3A 96.296 54 2 0 5756 5809 83525634 83525581 8.060000e-14 89.8
20 TraesCS1A01G059300 chr2D 92.593 54 2 2 608 660 640180170 640180222 6.280000e-10 76.8
21 TraesCS1A01G059300 chr2B 89.091 55 3 3 608 660 801249300 801249247 1.360000e-06 65.8
22 TraesCS1A01G059300 chr4B 100.000 30 0 0 631 660 516959378 516959349 8.180000e-04 56.5
23 TraesCS1A01G059300 chr4B 100.000 29 0 0 632 660 142915539 142915567 3.000000e-03 54.7


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 TraesCS1A01G059300 chr1A 40146958 40152798 5840 True 10787.000000 10787 100.000000 1 5841 1 chr1A.!!$R1 5840
1 TraesCS1A01G059300 chr1D 40874981 40880809 5828 True 3121.666667 3679 95.797667 1 5841 3 chr1D.!!$R1 5840
2 TraesCS1A01G059300 chr6B 487203826 487207391 3565 False 419.000000 424 90.595500 5434 5750 2 chr6B.!!$F1 316

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
661 670 2.916640 TGTGTGCATGTTGAGAGAACA 58.083 42.857 0.0 0.0 34.31 3.18 F
1614 1626 1.406539 CTCAGCGGGATTCAATTTGGG 59.593 52.381 0.0 0.0 0.00 4.12 F
2456 2515 2.158415 AGGGGTGAATTATGGGATGCAG 60.158 50.000 0.0 0.0 0.00 4.41 F
3954 4019 1.362224 TGGTCTCTTGGGAGGAAAGG 58.638 55.000 0.0 0.0 39.86 3.11 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2588 2647 1.760029 GCTCCCCCAAAACAACTGAAA 59.240 47.619 0.00 0.00 0.0 2.69 R
2829 2888 3.006217 CCATAGTCGATCAAGAGGATGCA 59.994 47.826 0.00 0.00 36.0 3.96 R
3967 4032 0.245539 ATGCCATCACAAGCTTGCAC 59.754 50.000 26.27 9.76 0.0 4.57 R
5183 5257 1.268032 CCATTCGAACGCCTAATGTGC 60.268 52.381 0.00 0.00 0.0 4.57 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
68 77 9.965824 GTTCTTTATCACAGGAAAATTTTCTGA 57.034 29.630 25.86 21.79 37.35 3.27
92 101 4.877823 TGATTAGCATGTCCAGCTTTACAG 59.122 41.667 4.37 0.00 43.25 2.74
207 216 7.385205 GGCTATGTGTCTCAACGATTTGTATAT 59.615 37.037 0.00 0.00 34.02 0.86
375 384 8.948631 TCTTTAATTGTACTAGATGCTTCCTG 57.051 34.615 0.00 0.00 0.00 3.86
584 593 5.215252 TGTTGAGGTGAGTTCTTTCCTAG 57.785 43.478 0.00 0.00 0.00 3.02
590 599 3.055094 GGTGAGTTCTTTCCTAGGCATCA 60.055 47.826 2.96 0.00 0.00 3.07
661 670 2.916640 TGTGTGCATGTTGAGAGAACA 58.083 42.857 0.00 0.00 34.31 3.18
907 919 7.330946 CCATTATGATCATGCTTTAAATGCCTG 59.669 37.037 18.72 3.44 0.00 4.85
925 937 3.600388 CCTGTCACTAATTGTCCTCACC 58.400 50.000 0.00 0.00 0.00 4.02
962 974 8.885722 GGAACCACGACATTTCATACTATTAAA 58.114 33.333 0.00 0.00 0.00 1.52
965 977 8.044908 ACCACGACATTTCATACTATTAAAGGT 58.955 33.333 0.00 0.00 30.57 3.50
1001 1013 2.029728 GCACATCGCTACATCAACACTC 59.970 50.000 0.00 0.00 37.77 3.51
1027 1039 3.703001 TCTCCTTTGGCTTTGAGGTAG 57.297 47.619 0.00 0.00 32.33 3.18
1080 1092 6.800543 TGTTTGTTGTATTGCTTCTTGCTAA 58.199 32.000 0.00 0.00 43.37 3.09
1165 1177 8.803235 TCTATTGATAACGCAATACATACCTCT 58.197 33.333 0.00 0.00 39.15 3.69
1173 1185 5.639506 ACGCAATACATACCTCTCATAATGC 59.360 40.000 0.00 0.00 0.00 3.56
1361 1373 3.006537 TCTTAAGTGAACTTAGCGCCTGT 59.993 43.478 2.29 0.00 39.36 4.00
1560 1572 4.794278 ATCAAGTGCAGCAATGATTTCA 57.206 36.364 15.93 0.00 0.00 2.69
1614 1626 1.406539 CTCAGCGGGATTCAATTTGGG 59.593 52.381 0.00 0.00 0.00 4.12
1784 1796 3.828451 CACATGGGTGGACAATTTTCTCT 59.172 43.478 0.00 0.00 41.45 3.10
1915 1929 8.774890 AGAATTCATCAAGCATATGTAGCTAG 57.225 34.615 8.44 0.00 42.53 3.42
2083 2136 7.669089 TTTTGGGAACTTCTAAACAAAGGAT 57.331 32.000 0.00 0.00 0.00 3.24
2107 2160 7.214467 TGTCTTTCATGGTAAATGAAGTTCC 57.786 36.000 0.00 0.00 38.98 3.62
2131 2184 6.882140 CCTACAATGTAGTTATGTGGTTCCAA 59.118 38.462 18.00 0.00 0.00 3.53
2150 2203 3.081804 CAAACTTCCCACCACATAGACC 58.918 50.000 0.00 0.00 0.00 3.85
2197 2250 8.621532 TGTGTTAATTAGCTCTTCTTTGACAT 57.378 30.769 0.00 0.00 0.00 3.06
2199 2252 8.721478 GTGTTAATTAGCTCTTCTTTGACATCA 58.279 33.333 0.00 0.00 0.00 3.07
2200 2253 9.453572 TGTTAATTAGCTCTTCTTTGACATCAT 57.546 29.630 0.00 0.00 0.00 2.45
2202 2255 9.671279 TTAATTAGCTCTTCTTTGACATCATCA 57.329 29.630 0.00 0.00 34.65 3.07
2222 2275 3.075283 TCATGATCTCTCTCCCTCTACCC 59.925 52.174 0.00 0.00 0.00 3.69
2223 2276 2.503824 TGATCTCTCTCCCTCTACCCA 58.496 52.381 0.00 0.00 0.00 4.51
2232 2291 2.716424 CTCCCTCTACCCATCTCTCTCT 59.284 54.545 0.00 0.00 0.00 3.10
2239 2298 5.722290 TCTACCCATCTCTCTCTCTCTCTA 58.278 45.833 0.00 0.00 0.00 2.43
2246 2305 6.440010 CCATCTCTCTCTCTCTCTATCTCTCT 59.560 46.154 0.00 0.00 0.00 3.10
2288 2347 9.573133 CATCATCGATACACATGTATAGCTTTA 57.427 33.333 0.00 0.00 40.99 1.85
2428 2487 8.451908 ACAATGTGCCTAAAGATTATAGGAAC 57.548 34.615 4.09 4.09 45.81 3.62
2453 2512 7.071071 ACAAAATAAGGGGTGAATTATGGGATG 59.929 37.037 0.00 0.00 0.00 3.51
2456 2515 2.158415 AGGGGTGAATTATGGGATGCAG 60.158 50.000 0.00 0.00 0.00 4.41
2703 2762 4.882671 ACCGCTTGACATGATACATTTC 57.117 40.909 0.00 0.00 0.00 2.17
2714 2773 9.671279 TGACATGATACATTTCTCTTGTACAAT 57.329 29.630 9.13 0.00 32.70 2.71
2829 2888 5.497474 ACCAAGCTTCTTAACGGTTATCAT 58.503 37.500 0.00 0.00 0.00 2.45
2876 2935 9.750125 GGATTTATCTTGAACACTTTTCTTGTT 57.250 29.630 0.00 0.00 39.94 2.83
2899 2958 8.417106 TGTTGATTGTAGTTTTATTTGCAAGGA 58.583 29.630 0.00 0.00 0.00 3.36
2992 3055 9.706691 ACGGTTGAAACATATATATGAGTAAGG 57.293 33.333 26.05 11.77 37.15 2.69
2993 3056 9.923143 CGGTTGAAACATATATATGAGTAAGGA 57.077 33.333 26.05 5.98 37.15 3.36
3060 3123 4.016444 TGTTGTCTAGATTTTCCCATGGC 58.984 43.478 6.09 0.00 0.00 4.40
3376 3440 6.942532 ATAATGCAATCCACTTGTTCGTAT 57.057 33.333 0.00 0.00 37.18 3.06
3409 3473 4.096984 GGTTAGGAATTGCCACATTCTCAG 59.903 45.833 0.00 0.00 40.02 3.35
3597 3661 8.371699 TCATCATTACCATATACCATGAACGAA 58.628 33.333 0.00 0.00 0.00 3.85
3607 3671 4.040445 ACCATGAACGAAAACTTTGTGG 57.960 40.909 0.00 0.00 0.00 4.17
3632 3696 1.407712 GGTCTCTGTCTCTAGGCTCGT 60.408 57.143 0.00 0.00 0.00 4.18
3716 3780 1.497991 CCTGTGTGGTACTGTGAACG 58.502 55.000 0.00 0.00 0.00 3.95
3954 4019 1.362224 TGGTCTCTTGGGAGGAAAGG 58.638 55.000 0.00 0.00 39.86 3.11
3956 4021 1.363246 GTCTCTTGGGAGGAAAGGGT 58.637 55.000 0.00 0.00 39.86 4.34
3957 4022 1.705745 GTCTCTTGGGAGGAAAGGGTT 59.294 52.381 0.00 0.00 39.86 4.11
3967 4032 5.369699 TGGGAGGAAAGGGTTTATCTAGATG 59.630 44.000 15.79 0.00 0.00 2.90
3972 4037 5.885912 GGAAAGGGTTTATCTAGATGTGCAA 59.114 40.000 15.79 0.00 0.00 4.08
3987 4052 1.473677 GTGCAAGCTTGTGATGGCATA 59.526 47.619 26.55 0.00 33.43 3.14
3990 4055 2.945008 GCAAGCTTGTGATGGCATAGTA 59.055 45.455 26.55 0.00 0.00 1.82
4073 4138 7.812690 ATCGTATATAATATACGGTGCAGGA 57.187 36.000 5.35 0.00 45.13 3.86
4211 4284 5.207354 TGCCATTGTTATCTCTCTCTCTCT 58.793 41.667 0.00 0.00 0.00 3.10
4212 4285 5.068855 TGCCATTGTTATCTCTCTCTCTCTG 59.931 44.000 0.00 0.00 0.00 3.35
4218 4291 5.414144 TGTTATCTCTCTCTCTCTGTGTGTG 59.586 44.000 0.00 0.00 0.00 3.82
4219 4292 2.158559 TCTCTCTCTCTCTGTGTGTGC 58.841 52.381 0.00 0.00 0.00 4.57
4220 4293 0.877743 TCTCTCTCTCTGTGTGTGCG 59.122 55.000 0.00 0.00 0.00 5.34
4221 4294 0.595588 CTCTCTCTCTGTGTGTGCGT 59.404 55.000 0.00 0.00 0.00 5.24
4222 4295 0.312102 TCTCTCTCTGTGTGTGCGTG 59.688 55.000 0.00 0.00 0.00 5.34
4223 4296 0.031314 CTCTCTCTGTGTGTGCGTGT 59.969 55.000 0.00 0.00 0.00 4.49
4224 4297 0.249031 TCTCTCTGTGTGTGCGTGTG 60.249 55.000 0.00 0.00 0.00 3.82
4225 4298 1.825285 CTCTCTGTGTGTGCGTGTGC 61.825 60.000 0.00 0.00 43.20 4.57
4251 4324 2.395690 GTGCATACACGTGCTCGC 59.604 61.111 17.22 15.69 45.27 5.03
4252 4325 3.178592 TGCATACACGTGCTCGCG 61.179 61.111 17.22 0.00 45.27 5.87
4253 4326 4.559386 GCATACACGTGCTCGCGC 62.559 66.667 17.22 7.87 41.82 6.86
4254 4327 3.178592 CATACACGTGCTCGCGCA 61.179 61.111 17.22 0.00 45.60 6.09
4282 4355 7.464710 GCGCATAATTAGGAGACTATATTGTGC 60.465 40.741 0.30 0.00 43.96 4.57
4429 4503 6.382087 TGTATGTGGGATGGTAGAAGTATCT 58.618 40.000 0.00 0.00 39.82 1.98
4439 4513 9.482175 GGATGGTAGAAGTATCTCCTATACATT 57.518 37.037 0.00 0.00 37.10 2.71
4488 4562 6.215495 TGTCGATCAATACATGTAGGAACA 57.785 37.500 11.91 9.65 40.69 3.18
4542 4616 3.068165 GCTAATAGTGGGCATCCAAAACC 59.932 47.826 0.00 0.00 46.04 3.27
4650 4724 0.391597 TCACGACCAAGTCCTCCAAC 59.608 55.000 0.00 0.00 0.00 3.77
4734 4808 4.996758 CGATGCACAGGGTATTGATCATAA 59.003 41.667 0.00 0.00 0.00 1.90
5050 5124 1.269051 CGGAGGCAAACACAAAAGGTC 60.269 52.381 0.00 0.00 0.00 3.85
5051 5125 1.754226 GGAGGCAAACACAAAAGGTCA 59.246 47.619 0.00 0.00 0.00 4.02
5065 5139 7.660208 ACACAAAAGGTCAACGAGATAAGTAAT 59.340 33.333 0.00 0.00 0.00 1.89
5100 5174 0.623723 TTGTAGGCCCACCAAGGATC 59.376 55.000 0.00 0.00 41.22 3.36
5183 5257 3.814842 TGCAGTCACCAGTGAAAGTATTG 59.185 43.478 1.23 0.00 41.85 1.90
5242 5316 1.550524 GGGGAAGGACAAATTCTTGCC 59.449 52.381 6.61 6.61 46.46 4.52
5275 5350 2.508867 CTCAACAATCGAATGGTTGCG 58.491 47.619 17.37 10.83 41.17 4.85
5286 5361 0.597568 ATGGTTGCGTGATGTGGTTG 59.402 50.000 0.00 0.00 0.00 3.77
5291 5366 2.177394 TGCGTGATGTGGTTGTATGT 57.823 45.000 0.00 0.00 0.00 2.29
5332 5407 6.154021 ACATTCTTGGATTTCTCTCATTTGGG 59.846 38.462 0.00 0.00 0.00 4.12
5357 5432 6.196538 GTCTTCGTGTTTGAATCTTTTTGTCC 59.803 38.462 0.00 0.00 0.00 4.02
5423 5498 7.067615 TGACTTGACTTTGGCAATTTTACTACA 59.932 33.333 0.00 0.00 0.00 2.74
5558 8883 8.267620 TGTTCACAATGAATATGACTACAAGG 57.732 34.615 0.00 0.00 38.79 3.61
5570 8895 9.700831 AATATGACTACAAGGCCTAGAAATTTT 57.299 29.630 5.16 0.00 0.00 1.82
5602 8927 4.634004 ACTCGAAACACACATTGAGAAACA 59.366 37.500 0.00 0.00 0.00 2.83
5656 8982 6.645790 AGAAGAGACAAAAGCAACATTGAT 57.354 33.333 0.00 0.00 0.00 2.57
5728 9055 8.589701 GATTTTGGACCTAAAATCTTTAGGGA 57.410 34.615 22.89 8.96 46.23 4.20
5733 9060 6.889722 TGGACCTAAAATCTTTAGGGAATGTG 59.110 38.462 22.89 3.57 44.47 3.21
5750 9077 4.836125 ATGTGGTGACATTCTTTGTGAC 57.164 40.909 0.00 0.00 46.14 3.67
5751 9078 3.884895 TGTGGTGACATTCTTTGTGACT 58.115 40.909 0.00 0.00 46.14 3.41
5767 9094 7.933577 TCTTTGTGACTTTGTGAGACTTATCAT 59.066 33.333 0.00 0.00 0.00 2.45
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 9.676861 ATTAGTTTTATTACCCTAGTTGTGTCC 57.323 33.333 0.00 0.00 0.00 4.02
61 70 5.066893 GCTGGACATGCTAATCATCAGAAAA 59.933 40.000 0.00 0.00 31.79 2.29
68 77 5.439721 TGTAAAGCTGGACATGCTAATCAT 58.560 37.500 0.00 0.00 40.22 2.45
74 83 2.304180 ACTCTGTAAAGCTGGACATGCT 59.696 45.455 1.65 0.00 43.32 3.79
92 101 4.394729 TGGTTTTGGATCACCACTAACTC 58.605 43.478 0.00 0.00 46.80 3.01
419 428 9.651913 AAACCAATATTCATGTTCAATACAACC 57.348 29.630 0.00 0.00 40.89 3.77
584 593 1.171308 ACATCAACTGCAGTGATGCC 58.829 50.000 34.52 0.00 42.10 4.40
590 599 4.989279 AAAGACAAACATCAACTGCAGT 57.011 36.364 15.25 15.25 0.00 4.40
661 670 2.887151 AGCTAGCCCTCACAAATGTT 57.113 45.000 12.13 0.00 0.00 2.71
826 838 5.964758 ACACAATCTTGCTTGAAAGTCAAA 58.035 33.333 0.00 0.00 35.73 2.69
907 919 5.123979 GGATTTGGTGAGGACAATTAGTGAC 59.876 44.000 0.00 0.00 0.00 3.67
925 937 5.018539 TGTCGTGGTTCCTATAGGATTTG 57.981 43.478 22.30 10.71 44.98 2.32
938 950 8.889717 CCTTTAATAGTATGAAATGTCGTGGTT 58.110 33.333 0.00 0.00 0.00 3.67
943 955 7.352739 GCCACCTTTAATAGTATGAAATGTCG 58.647 38.462 0.00 0.00 0.00 4.35
962 974 3.677963 CCTTTCATTGAGGCCACCT 57.322 52.632 5.01 0.00 36.03 4.00
1001 1013 2.357637 TCAAAGCCAAAGGAGAAACACG 59.642 45.455 0.00 0.00 0.00 4.49
1027 1039 7.770897 ACAATATGTTGAAGAGAACTACCCATC 59.229 37.037 9.40 0.00 38.71 3.51
1069 1081 5.179368 TGTTGTGAGTGTATTAGCAAGAAGC 59.821 40.000 0.00 0.00 46.19 3.86
1080 1092 5.278463 GGAAAGCATTGTGTTGTGAGTGTAT 60.278 40.000 0.00 0.00 0.00 2.29
1150 1162 5.871524 AGCATTATGAGAGGTATGTATTGCG 59.128 40.000 0.00 0.00 30.95 4.85
1161 1173 6.690194 AAGCAAGTAAAGCATTATGAGAGG 57.310 37.500 0.00 0.00 0.00 3.69
1165 1177 7.829725 ACATGAAAGCAAGTAAAGCATTATGA 58.170 30.769 0.00 0.00 0.00 2.15
1560 1572 9.190317 GGTTTTCCATCTCCTCTATTTACAATT 57.810 33.333 0.00 0.00 40.31 2.32
1744 1756 6.032094 CCATGTGGAATTTGAAAGAGAATCG 58.968 40.000 0.00 0.00 37.59 3.34
2083 2136 7.004086 AGGAACTTCATTTACCATGAAAGACA 58.996 34.615 0.00 0.00 37.55 3.41
2107 2160 7.915293 TTGGAACCACATAACTACATTGTAG 57.085 36.000 19.90 19.90 0.00 2.74
2131 2184 2.344592 TGGTCTATGTGGTGGGAAGTT 58.655 47.619 0.00 0.00 0.00 2.66
2171 2224 8.621532 TGTCAAAGAAGAGCTAATTAACACAT 57.378 30.769 0.00 0.00 0.00 3.21
2174 2227 8.846943 TGATGTCAAAGAAGAGCTAATTAACA 57.153 30.769 0.00 0.00 0.00 2.41
2176 2229 9.671279 TGATGATGTCAAAGAAGAGCTAATTAA 57.329 29.630 0.00 0.00 32.78 1.40
2197 2250 4.745484 AGAGGGAGAGAGATCATGATGA 57.255 45.455 14.30 0.00 0.00 2.92
2199 2252 4.264352 GGGTAGAGGGAGAGAGATCATGAT 60.264 50.000 8.25 8.25 0.00 2.45
2200 2253 3.075283 GGGTAGAGGGAGAGAGATCATGA 59.925 52.174 0.00 0.00 0.00 3.07
2202 2255 3.067470 TGGGTAGAGGGAGAGAGATCAT 58.933 50.000 0.00 0.00 0.00 2.45
2222 2275 7.396907 AGAGAGAGATAGAGAGAGAGAGAGATG 59.603 44.444 0.00 0.00 0.00 2.90
2223 2276 7.477864 AGAGAGAGATAGAGAGAGAGAGAGAT 58.522 42.308 0.00 0.00 0.00 2.75
2232 2291 9.607333 AATTAGAGAGAGAGAGAGATAGAGAGA 57.393 37.037 0.00 0.00 0.00 3.10
2374 2433 8.154856 TCTTAACTTGCTACTTAACATGGAACT 58.845 33.333 0.00 0.00 0.00 3.01
2428 2487 7.444299 CATCCCATAATTCACCCCTTATTTTG 58.556 38.462 0.00 0.00 0.00 2.44
2435 2494 1.858910 TGCATCCCATAATTCACCCCT 59.141 47.619 0.00 0.00 0.00 4.79
2453 2512 5.512788 CCATGATACGATGTTTGAAAACTGC 59.487 40.000 7.39 0.00 39.59 4.40
2456 2515 8.394877 TGTATCCATGATACGATGTTTGAAAAC 58.605 33.333 9.09 0.00 45.41 2.43
2588 2647 1.760029 GCTCCCCCAAAACAACTGAAA 59.240 47.619 0.00 0.00 0.00 2.69
2714 2773 9.409312 CAAAGCACAACATTTCAAACTATGATA 57.591 29.630 0.00 0.00 38.03 2.15
2739 2798 6.758416 CACAATGCTTAACATACTCTAGCTCA 59.242 38.462 0.00 0.00 38.34 4.26
2829 2888 3.006217 CCATAGTCGATCAAGAGGATGCA 59.994 47.826 0.00 0.00 36.00 3.96
2873 2932 8.417106 TCCTTGCAAATAAAACTACAATCAACA 58.583 29.630 0.00 0.00 0.00 3.33
2876 2935 8.250332 GGATCCTTGCAAATAAAACTACAATCA 58.750 33.333 3.84 0.00 0.00 2.57
2991 3054 4.897670 AGAAAACAATCCATCCATCCATCC 59.102 41.667 0.00 0.00 0.00 3.51
2992 3055 6.475596 AAGAAAACAATCCATCCATCCATC 57.524 37.500 0.00 0.00 0.00 3.51
2993 3056 6.879367 AAAGAAAACAATCCATCCATCCAT 57.121 33.333 0.00 0.00 0.00 3.41
2994 3057 7.840716 AGATAAAGAAAACAATCCATCCATCCA 59.159 33.333 0.00 0.00 0.00 3.41
3060 3123 4.631131 TGAGTGTGTGAATCCTTGTACAG 58.369 43.478 0.00 0.00 0.00 2.74
3170 3233 5.714333 ACCACACATAATTCCTTGCATGTAA 59.286 36.000 0.00 0.00 30.66 2.41
3172 3235 4.088634 ACCACACATAATTCCTTGCATGT 58.911 39.130 0.00 0.00 31.91 3.21
3173 3236 4.724074 ACCACACATAATTCCTTGCATG 57.276 40.909 0.00 0.00 0.00 4.06
3174 3237 4.771577 TCAACCACACATAATTCCTTGCAT 59.228 37.500 0.00 0.00 0.00 3.96
3175 3238 4.148079 TCAACCACACATAATTCCTTGCA 58.852 39.130 0.00 0.00 0.00 4.08
3176 3239 4.782019 TCAACCACACATAATTCCTTGC 57.218 40.909 0.00 0.00 0.00 4.01
3376 3440 4.464597 GGCAATTCCTAACCAACACCATTA 59.535 41.667 0.00 0.00 0.00 1.90
3409 3473 7.420184 AAAGTTAATGGTAAAAGTTGCATGC 57.580 32.000 11.82 11.82 0.00 4.06
3597 3661 4.409247 ACAGAGACCTACTCCACAAAGTTT 59.591 41.667 0.00 0.00 45.96 2.66
3607 3671 3.135895 AGCCTAGAGACAGAGACCTACTC 59.864 52.174 0.00 0.00 45.22 2.59
3954 4019 5.355350 ACAAGCTTGCACATCTAGATAAACC 59.645 40.000 26.27 0.00 0.00 3.27
3956 4021 6.172630 TCACAAGCTTGCACATCTAGATAAA 58.827 36.000 26.27 0.00 0.00 1.40
3957 4022 5.733676 TCACAAGCTTGCACATCTAGATAA 58.266 37.500 26.27 0.00 0.00 1.75
3967 4032 0.245539 ATGCCATCACAAGCTTGCAC 59.754 50.000 26.27 9.76 0.00 4.57
3972 4037 2.171237 TGCTACTATGCCATCACAAGCT 59.829 45.455 0.00 0.00 0.00 3.74
3999 4064 1.089123 ATGGTAGGCCCCTTTCCAAA 58.911 50.000 0.00 0.00 34.50 3.28
4071 4136 6.924111 TCCAAACAAAGAATAGCATTCTTCC 58.076 36.000 18.32 0.00 37.75 3.46
4073 4138 9.783081 ATTTTCCAAACAAAGAATAGCATTCTT 57.217 25.926 14.54 14.54 40.20 2.52
4252 4325 1.192534 GTCTCCTAATTATGCGCGTGC 59.807 52.381 15.48 15.48 43.20 5.34
4253 4326 2.743938 AGTCTCCTAATTATGCGCGTG 58.256 47.619 13.61 0.00 0.00 5.34
4254 4327 4.785511 ATAGTCTCCTAATTATGCGCGT 57.214 40.909 8.43 7.55 0.00 6.01
4255 4328 6.752351 ACAATATAGTCTCCTAATTATGCGCG 59.248 38.462 0.00 0.00 0.00 6.86
4256 4329 7.464710 GCACAATATAGTCTCCTAATTATGCGC 60.465 40.741 0.00 0.00 0.00 6.09
4257 4330 7.253783 CGCACAATATAGTCTCCTAATTATGCG 60.254 40.741 4.88 4.88 38.94 4.73
4366 4440 9.807921 ATCCCAGAAAACTTAATCAAACTTCTA 57.192 29.630 0.00 0.00 0.00 2.10
4480 4554 5.355350 CCAATCACCTGAAGATTGTTCCTAC 59.645 44.000 13.05 0.00 46.81 3.18
4488 4562 3.726557 TCTGCCAATCACCTGAAGATT 57.273 42.857 0.00 0.00 36.19 2.40
4505 4579 3.784511 ATTAGCTCCCACATGGATCTG 57.215 47.619 0.00 0.00 44.07 2.90
4525 4599 0.322997 CGGGTTTTGGATGCCCACTA 60.323 55.000 0.00 0.00 43.41 2.74
4527 4601 1.906333 ACGGGTTTTGGATGCCCAC 60.906 57.895 0.00 0.00 43.41 4.61
4650 4724 1.396996 CGAAAACATAGCCACTTCCCG 59.603 52.381 0.00 0.00 0.00 5.14
4734 4808 2.768253 TGGAAGATCTGCAACGATGT 57.232 45.000 2.29 0.00 0.00 3.06
4768 4842 7.833285 TTTTGAAGGAGTATAGCAACCTTTT 57.167 32.000 0.00 0.00 41.90 2.27
5100 5174 4.280677 ACCCAAACAACATGTGAATACAGG 59.719 41.667 0.00 0.00 43.83 4.00
5183 5257 1.268032 CCATTCGAACGCCTAATGTGC 60.268 52.381 0.00 0.00 0.00 4.57
5242 5316 3.681593 TTGTTGAGGGCATGGATTTTG 57.318 42.857 0.00 0.00 0.00 2.44
5307 5382 6.154021 CCCAAATGAGAGAAATCCAAGAATGT 59.846 38.462 0.00 0.00 0.00 2.71
5332 5407 6.196538 GGACAAAAAGATTCAAACACGAAGAC 59.803 38.462 0.00 0.00 0.00 3.01
5423 5498 4.101119 CCGGATACTTTCCCTTGTGACTAT 59.899 45.833 0.00 0.00 42.06 2.12
5558 8883 6.403309 CGAGTTTGGACCTAAAATTTCTAGGC 60.403 42.308 18.59 13.75 39.78 3.93
5570 8895 3.118702 TGTGTGTTTCGAGTTTGGACCTA 60.119 43.478 0.00 0.00 0.00 3.08
5733 9060 5.036737 CACAAAGTCACAAAGAATGTCACC 58.963 41.667 0.00 0.00 41.46 4.02
5743 9070 7.498900 ACATGATAAGTCTCACAAAGTCACAAA 59.501 33.333 0.00 0.00 0.00 2.83
5744 9071 6.992123 ACATGATAAGTCTCACAAAGTCACAA 59.008 34.615 0.00 0.00 0.00 3.33
5745 9072 6.524734 ACATGATAAGTCTCACAAAGTCACA 58.475 36.000 0.00 0.00 0.00 3.58
5746 9073 7.426929 AACATGATAAGTCTCACAAAGTCAC 57.573 36.000 0.00 0.00 0.00 3.67
5747 9074 7.498900 ACAAACATGATAAGTCTCACAAAGTCA 59.501 33.333 0.00 0.00 0.00 3.41
5748 9075 7.865707 ACAAACATGATAAGTCTCACAAAGTC 58.134 34.615 0.00 0.00 0.00 3.01
5749 9076 7.307396 CGACAAACATGATAAGTCTCACAAAGT 60.307 37.037 0.00 0.00 0.00 2.66
5750 9077 7.011773 CGACAAACATGATAAGTCTCACAAAG 58.988 38.462 0.00 0.00 0.00 2.77
5751 9078 6.481976 ACGACAAACATGATAAGTCTCACAAA 59.518 34.615 0.00 0.00 0.00 2.83
5767 9094 7.915293 ATTGTCCATCTATTTACGACAAACA 57.085 32.000 5.17 0.00 44.16 2.83


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

AutoCloner maintained by Alex Coulton.