Multiple sequence alignment - TraesCS1A01G144300

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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 TraesCS1A01G144300 chr1A 100.000 6626 0 0 1 6626 250192068 250198693 0.000000e+00 12237.0
1 TraesCS1A01G144300 chr1A 100.000 118 0 0 6957 7074 250199024 250199141 1.190000e-52 219.0
2 TraesCS1A01G144300 chr1D 95.971 6651 172 43 3 6597 199062536 199069146 0.000000e+00 10709.0
3 TraesCS1A01G144300 chr1B 97.444 1682 38 4 3530 5211 279179971 279178295 0.000000e+00 2863.0
4 TraesCS1A01G144300 chr1B 95.595 1521 50 9 2018 3528 279176226 279177739 0.000000e+00 2422.0
5 TraesCS1A01G144300 chr1B 97.098 1413 36 5 4322 5732 279181202 279182611 0.000000e+00 2377.0
6 TraesCS1A01G144300 chr1B 95.626 846 21 8 331 1166 279175388 279176227 0.000000e+00 1343.0
7 TraesCS1A01G144300 chr1B 97.458 472 12 0 5858 6329 279182612 279183083 0.000000e+00 806.0
8 TraesCS1A01G144300 chr1B 90.535 243 18 4 97 336 279175112 279175352 4.120000e-82 316.0
9 TraesCS1A01G144300 chr1B 90.909 198 16 2 6398 6593 279188094 279188291 1.510000e-66 265.0
10 TraesCS1A01G144300 chr1B 95.833 120 3 2 6957 7074 279188716 279188835 7.240000e-45 193.0
11 TraesCS1A01G144300 chr6B 94.382 89 2 2 5722 5807 520230349 520230437 4.450000e-27 134.0
12 TraesCS1A01G144300 chr6B 91.304 92 4 3 5719 5807 520230440 520230350 9.640000e-24 122.0
13 TraesCS1A01G144300 chr7A 93.023 86 3 2 5724 5807 290616050 290616134 9.640000e-24 122.0
14 TraesCS1A01G144300 chr7A 85.075 67 9 1 3453 3519 247068331 247068396 4.580000e-07 67.6
15 TraesCS1A01G144300 chr4D 92.941 85 4 1 5724 5806 303843469 303843553 9.640000e-24 122.0
16 TraesCS1A01G144300 chr4D 92.157 51 2 2 3472 3522 505427044 505426996 3.540000e-08 71.3
17 TraesCS1A01G144300 chr4B 93.023 86 3 2 5723 5806 364668488 364668404 9.640000e-24 122.0
18 TraesCS1A01G144300 chr4A 92.135 89 2 4 5724 5811 625758306 625758222 3.470000e-23 121.0
19 TraesCS1A01G144300 chr2D 92.045 88 4 3 5723 5807 24451834 24451747 3.470000e-23 121.0
20 TraesCS1A01G144300 chr3D 91.011 89 7 1 5720 5807 523900135 523900047 1.250000e-22 119.0
21 TraesCS1A01G144300 chr3D 95.652 46 1 1 3474 3519 306344529 306344485 9.840000e-09 73.1
22 TraesCS1A01G144300 chr7D 95.833 48 2 0 3475 3522 100311382 100311335 2.120000e-10 78.7
23 TraesCS1A01G144300 chr7D 92.157 51 2 2 3462 3512 358560557 358560605 3.540000e-08 71.3
24 TraesCS1A01G144300 chr5B 97.727 44 1 0 3474 3517 526116377 526116334 7.610000e-10 76.8
25 TraesCS1A01G144300 chr5D 97.674 43 1 0 3475 3517 558966911 558966869 2.740000e-09 75.0


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 TraesCS1A01G144300 chr1A 250192068 250199141 7073 False 6228.0 12237 100.0000 1 7074 2 chr1A.!!$F1 7073
1 TraesCS1A01G144300 chr1D 199062536 199069146 6610 False 10709.0 10709 95.9710 3 6597 1 chr1D.!!$F1 6594
2 TraesCS1A01G144300 chr1B 279178295 279179971 1676 True 2863.0 2863 97.4440 3530 5211 1 chr1B.!!$R1 1681
3 TraesCS1A01G144300 chr1B 279175112 279183083 7971 False 1452.8 2422 95.2624 97 6329 5 chr1B.!!$F1 6232
4 TraesCS1A01G144300 chr1B 279188094 279188835 741 False 229.0 265 93.3710 6398 7074 2 chr1B.!!$F2 676

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
69 70 0.319555 TTGCTCGACTTCGACAAGGG 60.320 55.000 0.00 0.00 44.22 3.95 F
340 390 0.400594 AAACCTCTTCCCTTCCCACG 59.599 55.000 0.00 0.00 0.00 4.94 F
1404 1465 2.012673 GGGAGATGAACATGTCAGCAC 58.987 52.381 12.61 0.83 45.54 4.40 F
2378 2471 1.886542 CCTGCACTTTCCAGGTAAACC 59.113 52.381 0.00 0.00 43.86 3.27 F
3077 3179 2.692557 TGTTTGGTCATGTTTGGACTGG 59.307 45.455 0.00 0.00 35.61 4.00 F
4105 4775 3.634910 ACTTTGATGGTTGTGTGGTTACC 59.365 43.478 0.00 0.00 0.00 2.85 F
5737 8801 2.792878 AGATAATACTCCCTCCGTCCG 58.207 52.381 0.00 0.00 0.00 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1851 1926 5.414454 TGTAGTGGTTCAACTGGAATTATGC 59.586 40.000 0.00 0.0 37.93 3.14 R
2321 2414 7.036863 ACCCAATAAATCTTCCCTAAGTTCAGA 60.037 37.037 0.00 0.0 34.13 3.27 R
2649 2748 0.962356 GGTTGTGTCCCAGGCTCATG 60.962 60.000 0.00 0.0 0.00 3.07 R
3273 3375 2.677902 GCTATATTGCGCTATCCTGCCA 60.678 50.000 9.73 0.0 0.00 4.92 R
4661 7723 3.541632 TCGCTCTCTTTTTCCAGTTGTT 58.458 40.909 0.00 0.0 0.00 2.83 R
6009 9073 0.863144 GCGTAGTTTGTTCAAGCCGA 59.137 50.000 0.00 0.0 0.00 5.54 R
6987 10189 6.963796 AGAAGAAAAATGTCACAAGCTAGTG 58.036 36.000 0.00 0.0 40.85 2.74 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
24 25 2.224606 TGGAGTCTTAACACGACGACT 58.775 47.619 0.00 0.00 39.27 4.18
27 28 3.667726 GGAGTCTTAACACGACGACTTTC 59.332 47.826 0.00 0.00 36.90 2.62
35 36 2.044860 CACGACGACTTTCAGACTGTC 58.955 52.381 0.00 0.00 0.00 3.51
40 41 4.468643 GACGACTTTCAGACTGTCTACTG 58.531 47.826 10.47 0.00 35.72 2.74
44 45 5.220710 ACTTTCAGACTGTCTACTGCAAT 57.779 39.130 10.47 0.00 34.57 3.56
64 65 4.905412 ATAAGTTTTGCTCGACTTCGAC 57.095 40.909 0.00 0.00 44.22 4.20
65 66 2.218953 AGTTTTGCTCGACTTCGACA 57.781 45.000 0.00 0.00 44.22 4.35
69 70 0.319555 TTGCTCGACTTCGACAAGGG 60.320 55.000 0.00 0.00 44.22 3.95
84 85 2.758737 GGGAGGGACGATGACGGT 60.759 66.667 0.00 0.00 44.46 4.83
86 87 2.050350 GGAGGGACGATGACGGTGA 61.050 63.158 0.00 0.00 44.46 4.02
88 89 1.592400 GAGGGACGATGACGGTGACA 61.592 60.000 0.00 0.00 44.46 3.58
126 127 1.068588 AGTGTTTGTGTCGCTGCTAGA 59.931 47.619 0.00 0.00 0.00 2.43
134 135 2.294791 GTGTCGCTGCTAGATGGTCTAT 59.705 50.000 0.00 0.00 0.00 1.98
144 145 5.244851 TGCTAGATGGTCTATGGATCTGAAC 59.755 44.000 0.00 0.00 0.00 3.18
281 290 2.856988 TTGCCTTTCCGGTCCCCT 60.857 61.111 0.00 0.00 34.25 4.79
340 390 0.400594 AAACCTCTTCCCTTCCCACG 59.599 55.000 0.00 0.00 0.00 4.94
516 570 2.282407 CCCCGTCAAATAGGGTTTACG 58.718 52.381 0.00 0.00 46.17 3.18
521 575 3.726782 CGTCAAATAGGGTTTACGCAAGC 60.727 47.826 0.00 0.00 45.62 4.01
594 648 4.659172 CCACACCACATGCCCCGT 62.659 66.667 0.00 0.00 0.00 5.28
706 761 3.674753 GCAATCCATTCGTTGTTTCCTTG 59.325 43.478 0.00 0.00 0.00 3.61
731 786 8.980596 TGGGAATTTGAGTTAATCTTGCATAAT 58.019 29.630 0.00 0.00 0.00 1.28
834 895 9.454585 CATAGGCTATACATTGTTCACATTTTG 57.545 33.333 6.72 0.00 0.00 2.44
1146 1207 4.887655 AGTTAACTTGCTTGCACTTTACCT 59.112 37.500 1.12 0.00 0.00 3.08
1200 1261 7.994911 TGCCATTATCAGAAGTCAGAATTATGT 59.005 33.333 5.22 0.00 0.00 2.29
1232 1293 7.937942 TGTATCAACCCTACTATGACTACTCTC 59.062 40.741 0.00 0.00 0.00 3.20
1404 1465 2.012673 GGGAGATGAACATGTCAGCAC 58.987 52.381 12.61 0.83 45.54 4.40
1459 1520 4.286032 TGTTCCATGCCTTAGTGAAGTAGT 59.714 41.667 0.00 0.00 0.00 2.73
1575 1636 7.509318 TGGTTGGATAGATACATACTGCTAGTT 59.491 37.037 0.00 0.00 0.00 2.24
1851 1926 8.129211 TCATAATATAGCGTATTCATGACTCCG 58.871 37.037 0.00 0.00 0.00 4.63
1869 1944 3.013921 TCCGCATAATTCCAGTTGAACC 58.986 45.455 0.00 0.00 35.31 3.62
1885 1960 7.370383 CAGTTGAACCACTACAATATTGCTTT 58.630 34.615 15.48 0.00 0.00 3.51
2157 2250 2.846206 TCACCAGCTTATCACCATTCCT 59.154 45.455 0.00 0.00 0.00 3.36
2248 2341 2.041081 TGCAAGTGCCTACAAGGGTTAT 59.959 45.455 0.00 0.00 41.18 1.89
2321 2414 4.441792 TGCTTCGTATACAATCAGTGCAT 58.558 39.130 3.32 0.00 0.00 3.96
2378 2471 1.886542 CCTGCACTTTCCAGGTAAACC 59.113 52.381 0.00 0.00 43.86 3.27
2384 2477 3.816523 CACTTTCCAGGTAAACCGCTAAA 59.183 43.478 0.00 0.00 42.08 1.85
2400 2493 5.757808 ACCGCTAAAAATTGCACTTGAATTT 59.242 32.000 0.00 0.00 35.06 1.82
2510 2606 2.762535 TTTGACCTAGTACAGCTGGC 57.237 50.000 19.93 10.58 0.00 4.85
2649 2748 8.353423 ACCTGGCATCCATAATGATATAAAAC 57.647 34.615 0.00 0.00 37.59 2.43
2738 2837 8.587111 CCACTCATAATATCATCAATTACGTCG 58.413 37.037 0.00 0.00 0.00 5.12
2826 2925 4.036380 GCATTTAGTGGGCAGGTATGTAAC 59.964 45.833 0.00 0.00 0.00 2.50
2846 2945 8.628882 TGTAACATGTCACGACTAAGAATATG 57.371 34.615 0.00 0.00 0.00 1.78
2993 3095 3.267031 CCAAGGTCCTCCAGTTATTCCTT 59.733 47.826 0.00 0.00 34.69 3.36
3077 3179 2.692557 TGTTTGGTCATGTTTGGACTGG 59.307 45.455 0.00 0.00 35.61 4.00
3153 3255 4.633565 ACTTAAGTTCCGTCTAGTAGGTCG 59.366 45.833 1.12 3.35 0.00 4.79
3588 3697 8.982723 ACACTAAAGAGGACATATACAGTCAAT 58.017 33.333 8.83 0.00 37.74 2.57
3887 3998 8.172741 ACATCAGGCCATTAAATTATGAGGTAT 58.827 33.333 5.01 0.00 29.50 2.73
4105 4775 3.634910 ACTTTGATGGTTGTGTGGTTACC 59.365 43.478 0.00 0.00 0.00 2.85
4473 7535 7.164803 GCCTTATCTTAGGACTGAAATATGCT 58.835 38.462 0.00 0.00 37.50 3.79
4661 7723 4.806330 CGGCTAACTGAAACAGTAAGAGA 58.194 43.478 4.84 0.00 44.62 3.10
4681 7743 3.561725 AGAACAACTGGAAAAAGAGAGCG 59.438 43.478 0.00 0.00 0.00 5.03
4888 7950 5.830000 AAACCTGGAACTGTTCTTGTAAC 57.170 39.130 19.05 3.27 0.00 2.50
4931 7993 5.468072 AGAACTTCACTGCACAACTATTGAG 59.532 40.000 0.00 0.00 0.00 3.02
4946 8008 8.030106 ACAACTATTGAGAGTGTAAACTAGAGC 58.970 37.037 0.00 0.00 0.00 4.09
5075 8137 6.992063 TTCTTTTGACAGCCTTCTCATATC 57.008 37.500 0.00 0.00 0.00 1.63
5097 8159 5.535333 TCTCTTAAACAGGTGAAAGGTACG 58.465 41.667 0.00 0.00 0.00 3.67
5220 8282 7.834881 ATTGTACATTCTATTCCTCTCGGTA 57.165 36.000 0.00 0.00 0.00 4.02
5268 8330 4.506288 GTGCTGTTGGTTTGGTAATTTGAC 59.494 41.667 0.00 0.00 0.00 3.18
5272 8334 6.364976 GCTGTTGGTTTGGTAATTTGACATAC 59.635 38.462 0.00 0.00 0.00 2.39
5305 8367 5.904362 AGTGAGGCCACATTATTTTCTTC 57.096 39.130 6.04 0.00 45.54 2.87
5519 8582 6.508777 TGCGGGGAAATATAAAGTAAAATGC 58.491 36.000 0.00 0.00 0.00 3.56
5737 8801 2.792878 AGATAATACTCCCTCCGTCCG 58.207 52.381 0.00 0.00 0.00 4.79
5750 8814 3.368116 CCTCCGTCCGAAAATAAGTGTCT 60.368 47.826 0.00 0.00 0.00 3.41
5796 8860 5.690865 AGTTGAGACACTTATTTTGGGACA 58.309 37.500 0.00 0.00 0.00 4.02
5826 8890 7.011482 GGAGTATGTTTTATGCTTCCTGTACTG 59.989 40.741 0.00 0.00 0.00 2.74
5832 8896 6.588719 TTTATGCTTCCTGTACTGCATTTT 57.411 33.333 4.65 0.00 42.60 1.82
5833 8897 3.921119 TGCTTCCTGTACTGCATTTTG 57.079 42.857 0.00 0.00 0.00 2.44
5834 8898 3.221771 TGCTTCCTGTACTGCATTTTGT 58.778 40.909 0.00 0.00 0.00 2.83
5894 8958 6.479006 TGATCTCTGTCCATTTTCTGAATGT 58.521 36.000 0.00 0.00 0.00 2.71
6009 9073 8.121305 TCATGTGCTTAATCATTTAACCTTGT 57.879 30.769 0.00 0.00 0.00 3.16
6154 9218 8.599055 AGTCTTACCCTAAAAAGAAGTTAACG 57.401 34.615 0.00 0.00 33.70 3.18
6240 9304 3.365666 CCAGTTGAATGTGATGCACTGTC 60.366 47.826 0.00 0.00 35.11 3.51
6268 9332 5.626142 TCCTTGTTGCTTATTACTGGTTGA 58.374 37.500 0.00 0.00 0.00 3.18
6345 9409 7.032580 GCCTTTAATTTTGGTTTGCTTTGTTT 58.967 30.769 0.00 0.00 0.00 2.83
6373 9438 7.116805 CCTCTTCACAATTATTTTGGCAGAAAC 59.883 37.037 0.00 0.00 0.00 2.78
6375 9440 7.652909 TCTTCACAATTATTTTGGCAGAAACAG 59.347 33.333 0.00 0.00 0.00 3.16
6390 9456 3.450096 AGAAACAGTAGTATTCCCCCGTC 59.550 47.826 0.00 0.00 0.00 4.79
6399 9465 3.720002 AGTATTCCCCCGTCCACAAATAT 59.280 43.478 0.00 0.00 0.00 1.28
6481 9549 7.436673 TGTTTTTGTTCATTCATTTTAGTCCGG 59.563 33.333 0.00 0.00 0.00 5.14
6578 9646 1.671328 GCTTTGCGATTTACTCCCTCC 59.329 52.381 0.00 0.00 0.00 4.30
6597 9799 5.451520 CCCTCCGTTCCTAAGTACAATGTAG 60.452 48.000 0.00 0.00 0.00 2.74
6622 9824 9.778741 AGAGAGATTGTTTGATAAAGTGTTACA 57.221 29.630 0.00 0.00 0.00 2.41
6624 9826 9.003658 AGAGATTGTTTGATAAAGTGTTACAGG 57.996 33.333 0.00 0.00 0.00 4.00
6625 9827 8.110860 AGATTGTTTGATAAAGTGTTACAGGG 57.889 34.615 0.00 0.00 0.00 4.45
6987 10189 4.695217 TTATTCATGGCCGAGTGAAAAC 57.305 40.909 18.23 0.00 37.82 2.43
6990 10192 1.202758 TCATGGCCGAGTGAAAACACT 60.203 47.619 0.00 2.45 38.26 3.55
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.376234 TCGTCGTGTTAAGACTCCATAGG 59.624 47.826 0.86 0.00 36.53 2.57
1 2 4.094590 AGTCGTCGTGTTAAGACTCCATAG 59.905 45.833 0.86 0.00 39.49 2.23
9 10 4.036027 AGTCTGAAAGTCGTCGTGTTAAGA 59.964 41.667 0.00 0.00 33.76 2.10
20 21 3.238441 GCAGTAGACAGTCTGAAAGTCG 58.762 50.000 13.84 0.00 37.36 4.18
24 25 6.759272 ACTTATTGCAGTAGACAGTCTGAAA 58.241 36.000 13.84 0.00 34.28 2.69
27 28 7.293745 CAAAACTTATTGCAGTAGACAGTCTG 58.706 38.462 13.84 0.00 35.12 3.51
40 41 4.377022 TCGAAGTCGAGCAAAACTTATTGC 60.377 41.667 0.00 3.92 44.87 3.56
57 58 1.533469 CGTCCCTCCCTTGTCGAAGT 61.533 60.000 0.00 0.00 0.00 3.01
64 65 1.141881 CGTCATCGTCCCTCCCTTG 59.858 63.158 0.00 0.00 0.00 3.61
65 66 2.058595 CCGTCATCGTCCCTCCCTT 61.059 63.158 0.00 0.00 35.01 3.95
69 70 1.139095 GTCACCGTCATCGTCCCTC 59.861 63.158 0.00 0.00 35.01 4.30
84 85 1.610363 AGAGAGCTGAAGACGTGTCA 58.390 50.000 0.00 0.00 0.00 3.58
86 87 1.957177 TGAAGAGAGCTGAAGACGTGT 59.043 47.619 0.00 0.00 0.00 4.49
88 89 2.030363 CACTGAAGAGAGCTGAAGACGT 60.030 50.000 0.00 0.00 0.00 4.34
91 92 4.141846 ACAAACACTGAAGAGAGCTGAAGA 60.142 41.667 0.00 0.00 0.00 2.87
126 127 9.872684 AAAATTATGTTCAGATCCATAGACCAT 57.127 29.630 0.00 0.00 0.00 3.55
231 238 0.804989 CCCAGTCTCAAACCAATCGC 59.195 55.000 0.00 0.00 0.00 4.58
232 239 1.271379 ACCCCAGTCTCAAACCAATCG 60.271 52.381 0.00 0.00 0.00 3.34
263 272 2.361230 GGGGACCGGAAAGGCAAG 60.361 66.667 9.46 0.00 46.52 4.01
281 290 3.379445 GGCCGACGGAGGTGAAGA 61.379 66.667 20.50 0.00 0.00 2.87
386 440 1.134848 CAGTTGCAGAGTCTAGGGCTC 60.135 57.143 0.00 7.01 0.00 4.70
474 528 3.001736 GCTCAACAGCGATCCATCTTTAC 59.998 47.826 0.00 0.00 35.39 2.01
516 570 2.733593 GCAGCAACAGCAGCTTGC 60.734 61.111 10.67 10.67 45.46 4.01
521 575 2.483745 CGGATGCAGCAACAGCAG 59.516 61.111 3.51 0.00 46.36 4.24
594 648 3.636231 CCAGGGGGCGACTTCACA 61.636 66.667 0.00 0.00 0.00 3.58
706 761 9.822185 AATTATGCAAGATTAACTCAAATTCCC 57.178 29.630 0.00 0.00 0.00 3.97
757 812 8.866956 GCGCTTTCTAGTTTCTACATAAAACTA 58.133 33.333 0.00 7.88 43.33 2.24
758 813 7.148457 GGCGCTTTCTAGTTTCTACATAAAACT 60.148 37.037 7.64 6.50 46.04 2.66
759 814 6.959871 GGCGCTTTCTAGTTTCTACATAAAAC 59.040 38.462 7.64 0.00 36.97 2.43
1200 1261 9.601810 AGTCATAGTAGGGTTGATACATTATGA 57.398 33.333 0.00 0.00 0.00 2.15
1459 1520 6.833041 TGGAAGGAACAATGTTAGTAGTTCA 58.167 36.000 0.00 0.00 41.49 3.18
1837 1912 5.700832 TGGAATTATGCGGAGTCATGAATAC 59.299 40.000 0.00 0.00 0.00 1.89
1851 1926 5.414454 TGTAGTGGTTCAACTGGAATTATGC 59.586 40.000 0.00 0.00 37.93 3.14
1869 1944 9.079833 CAAGGAATTGAAAGCAATATTGTAGTG 57.920 33.333 16.61 0.00 43.71 2.74
2024 2117 9.944663 TTTTCATAGTAAACATGAAGAACACAC 57.055 29.630 0.00 0.00 41.92 3.82
2321 2414 7.036863 ACCCAATAAATCTTCCCTAAGTTCAGA 60.037 37.037 0.00 0.00 34.13 3.27
2378 2471 6.648502 ACAAATTCAAGTGCAATTTTTAGCG 58.351 32.000 0.00 0.00 32.25 4.26
2649 2748 0.962356 GGTTGTGTCCCAGGCTCATG 60.962 60.000 0.00 0.00 0.00 3.07
2738 2837 6.530534 AGCGACACTCTGTAATAACACAATAC 59.469 38.462 0.00 0.00 0.00 1.89
2826 2925 5.332883 GCTGCATATTCTTAGTCGTGACATG 60.333 44.000 2.44 0.00 0.00 3.21
2936 3038 8.970020 CCTGCAATATAAGCCCATCATATAAAA 58.030 33.333 0.00 0.00 0.00 1.52
2937 3039 8.335484 TCCTGCAATATAAGCCCATCATATAAA 58.665 33.333 0.00 0.00 0.00 1.40
2993 3095 4.279671 CAGTGTGGTTAAGGTTATTTGGCA 59.720 41.667 0.00 0.00 0.00 4.92
3077 3179 9.476202 AAACAGATTGGAAAACTTATAAGCAAC 57.524 29.630 12.54 2.32 0.00 4.17
3140 3242 7.187244 TCTTTGATATTCGACCTACTAGACG 57.813 40.000 0.00 0.00 0.00 4.18
3273 3375 2.677902 GCTATATTGCGCTATCCTGCCA 60.678 50.000 9.73 0.00 0.00 4.92
3463 3565 6.017109 GCCTATTTCGAGAGATAATTTTGGCA 60.017 38.462 0.00 0.00 41.60 4.92
3833 3944 9.627123 AGCAGGTTATAAATATACAAGCTTTCA 57.373 29.630 0.00 0.00 0.00 2.69
3887 3998 7.897575 ACAACAAATAAGCACACTTGAAAAA 57.102 28.000 0.00 0.00 36.57 1.94
3898 4009 5.945784 AGCCAAGAGATACAACAAATAAGCA 59.054 36.000 0.00 0.00 0.00 3.91
4105 4775 4.143305 GCAAGTTACGTGCAAGAGAAGTAG 60.143 45.833 17.57 0.00 41.80 2.57
4617 7679 6.293626 GCCGCATGACTTGTGATTTAGATTAT 60.294 38.462 0.00 0.00 38.12 1.28
4618 7680 5.007626 GCCGCATGACTTGTGATTTAGATTA 59.992 40.000 0.00 0.00 38.12 1.75
4619 7681 4.201950 GCCGCATGACTTGTGATTTAGATT 60.202 41.667 0.00 0.00 38.12 2.40
4661 7723 3.541632 TCGCTCTCTTTTTCCAGTTGTT 58.458 40.909 0.00 0.00 0.00 2.83
4888 7950 4.424061 TCTCAAAGAAAATGCACGATGG 57.576 40.909 0.00 0.00 0.00 3.51
4931 7993 5.047235 TCCTCCTTTGCTCTAGTTTACACTC 60.047 44.000 0.00 0.00 34.06 3.51
4946 8008 5.334879 CGTTTGTCCTGTTTATCCTCCTTTG 60.335 44.000 0.00 0.00 0.00 2.77
5058 8120 7.093333 TGTTTAAGAGATATGAGAAGGCTGTCA 60.093 37.037 2.54 2.54 0.00 3.58
5075 8137 5.176958 CACGTACCTTTCACCTGTTTAAGAG 59.823 44.000 0.00 0.00 0.00 2.85
5097 8159 3.181487 TGTTCTCTTTCTTTGCTTGCCAC 60.181 43.478 0.00 0.00 0.00 5.01
5220 8282 7.996644 ACGTTGGAATTATTAGGACACCAATAT 59.003 33.333 0.00 0.00 38.03 1.28
5268 8330 3.072211 CCTCACTATGCATGCCTGTATG 58.928 50.000 16.68 7.45 0.00 2.39
5272 8334 1.170919 GGCCTCACTATGCATGCCTG 61.171 60.000 16.68 7.68 35.99 4.85
5363 8425 5.239306 TCTTTCTCAAATGCACAGTTACCAG 59.761 40.000 0.00 0.00 0.00 4.00
5374 8436 6.833342 AACAACACAATCTTTCTCAAATGC 57.167 33.333 0.00 0.00 0.00 3.56
5376 8438 6.857964 CGCTAACAACACAATCTTTCTCAAAT 59.142 34.615 0.00 0.00 0.00 2.32
5772 8836 6.126409 TGTCCCAAAATAAGTGTCTCAACTT 58.874 36.000 0.00 0.00 42.89 2.66
5796 8860 5.430089 AGGAAGCATAAAACATACTCCCTCT 59.570 40.000 0.00 0.00 0.00 3.69
5826 8890 3.047796 CTGAAGCAGACACACAAAATGC 58.952 45.455 0.00 0.00 37.15 3.56
5894 8958 2.168521 CGCCTCAGAGTTCCATTCCTTA 59.831 50.000 0.00 0.00 0.00 2.69
6009 9073 0.863144 GCGTAGTTTGTTCAAGCCGA 59.137 50.000 0.00 0.00 0.00 5.54
6154 9218 1.692519 ACCACTCCAACACAGACTACC 59.307 52.381 0.00 0.00 0.00 3.18
6240 9304 5.355350 CCAGTAATAAGCAACAAGGAGAAGG 59.645 44.000 0.00 0.00 0.00 3.46
6268 9332 2.108952 ACCTGATTGTCCAAAAGAGGCT 59.891 45.455 0.00 0.00 0.00 4.58
6345 9409 4.282957 TGCCAAAATAATTGTGAAGAGGCA 59.717 37.500 0.00 0.00 45.20 4.75
6373 9438 1.411612 GTGGACGGGGGAATACTACTG 59.588 57.143 0.00 0.00 0.00 2.74
6375 9440 1.488390 TGTGGACGGGGGAATACTAC 58.512 55.000 0.00 0.00 0.00 2.73
6458 9526 7.278461 TCCGGACTAAAATGAATGAACAAAA 57.722 32.000 0.00 0.00 0.00 2.44
6578 9646 7.317842 TCTCTCTACATTGTACTTAGGAACG 57.682 40.000 0.00 0.00 0.00 3.95
6987 10189 6.963796 AGAAGAAAAATGTCACAAGCTAGTG 58.036 36.000 0.00 0.00 40.85 2.74
6990 10192 8.445275 TGTAAGAAGAAAAATGTCACAAGCTA 57.555 30.769 0.00 0.00 0.00 3.32


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

AutoCloner maintained by Alex Coulton.