Multiple sequence alignment - TraesCS1D01G108500

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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 TraesCS1D01G108500 chr1D 100.000 5139 0 0 839 5977 101142282 101137144 0.000000e+00 9491.0
1 TraesCS1D01G108500 chr1D 98.322 894 15 0 5084 5977 98546632 98547525 0.000000e+00 1568.0
2 TraesCS1D01G108500 chr1D 97.770 897 18 1 5081 5977 440667228 440668122 0.000000e+00 1544.0
3 TraesCS1D01G108500 chr1D 97.315 894 24 0 5084 5977 236977839 236976946 0.000000e+00 1519.0
4 TraesCS1D01G108500 chr1D 100.000 581 0 0 1 581 101143120 101142540 0.000000e+00 1074.0
5 TraesCS1D01G108500 chr1B 94.539 2948 116 27 875 3805 150538510 150541429 0.000000e+00 4510.0
6 TraesCS1D01G108500 chr1B 95.004 1261 50 9 3829 5083 150541592 150542845 0.000000e+00 1967.0
7 TraesCS1D01G108500 chr1B 100.000 28 0 0 847 874 150538467 150538494 1.100000e-02 52.8
8 TraesCS1D01G108500 chr1A 94.194 1688 63 14 2143 3806 104226937 104228613 0.000000e+00 2542.0
9 TraesCS1D01G108500 chr1A 94.774 1282 54 9 3810 5083 104228667 104229943 0.000000e+00 1984.0
10 TraesCS1D01G108500 chr1A 93.100 1029 40 10 839 1858 104225542 104226548 0.000000e+00 1478.0
11 TraesCS1D01G108500 chr1A 91.429 490 37 2 10 496 104224875 104225362 0.000000e+00 667.0
12 TraesCS1D01G108500 chr1A 93.709 302 13 5 1859 2158 104226580 104226877 1.180000e-121 448.0
13 TraesCS1D01G108500 chr4D 97.433 896 23 0 5082 5977 402661629 402660734 0.000000e+00 1528.0
14 TraesCS1D01G108500 chr7D 97.427 894 23 0 5084 5977 4692932 4692039 0.000000e+00 1524.0
15 TraesCS1D01G108500 chr6D 97.430 895 22 1 5084 5977 111985706 111986600 0.000000e+00 1524.0
16 TraesCS1D01G108500 chr2D 97.204 894 25 0 5084 5977 400133152 400134045 0.000000e+00 1513.0
17 TraesCS1D01G108500 chr5D 97.204 894 24 1 5084 5977 348863875 348862983 0.000000e+00 1511.0
18 TraesCS1D01G108500 chr3D 96.980 894 27 0 5084 5977 16771172 16772065 0.000000e+00 1502.0
19 TraesCS1D01G108500 chr3D 90.667 75 7 0 5007 5081 402341402 402341328 3.810000e-17 100.0


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 TraesCS1D01G108500 chr1D 101137144 101143120 5976 True 5282.5 9491 100.000000 1 5977 2 chr1D.!!$R2 5976
1 TraesCS1D01G108500 chr1D 98546632 98547525 893 False 1568.0 1568 98.322000 5084 5977 1 chr1D.!!$F1 893
2 TraesCS1D01G108500 chr1D 440667228 440668122 894 False 1544.0 1544 97.770000 5081 5977 1 chr1D.!!$F2 896
3 TraesCS1D01G108500 chr1D 236976946 236977839 893 True 1519.0 1519 97.315000 5084 5977 1 chr1D.!!$R1 893
4 TraesCS1D01G108500 chr1B 150538467 150542845 4378 False 2176.6 4510 96.514333 847 5083 3 chr1B.!!$F1 4236
5 TraesCS1D01G108500 chr1A 104224875 104229943 5068 False 1423.8 2542 93.441200 10 5083 5 chr1A.!!$F1 5073
6 TraesCS1D01G108500 chr4D 402660734 402661629 895 True 1528.0 1528 97.433000 5082 5977 1 chr4D.!!$R1 895
7 TraesCS1D01G108500 chr7D 4692039 4692932 893 True 1524.0 1524 97.427000 5084 5977 1 chr7D.!!$R1 893
8 TraesCS1D01G108500 chr6D 111985706 111986600 894 False 1524.0 1524 97.430000 5084 5977 1 chr6D.!!$F1 893
9 TraesCS1D01G108500 chr2D 400133152 400134045 893 False 1513.0 1513 97.204000 5084 5977 1 chr2D.!!$F1 893
10 TraesCS1D01G108500 chr5D 348862983 348863875 892 True 1511.0 1511 97.204000 5084 5977 1 chr5D.!!$R1 893
11 TraesCS1D01G108500 chr3D 16771172 16772065 893 False 1502.0 1502 96.980000 5084 5977 1 chr3D.!!$F1 893

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
908 997 0.460284 ATCGTGGCCGTTGATCTCAC 60.460 55.000 0.0 0.0 35.01 3.51 F
1494 1585 0.113190 TCCTGTGGCTCTCACTCTCA 59.887 55.000 0.0 0.0 46.20 3.27 F
1715 1817 0.606944 TTCCGGGTGCGCAAGTTTAT 60.607 50.000 14.0 0.0 41.68 1.40 F
3454 3694 1.273606 GCAGTAAGCCTCACACTCTGA 59.726 52.381 0.0 0.0 37.23 3.27 F
3504 3744 1.541588 GAAGTGCCACCATGTTCCTTC 59.458 52.381 0.0 0.0 0.00 3.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1715 1817 0.251916 CCGCTGTAGGTGGGAAATGA 59.748 55.000 0.00 0.0 41.64 2.57 R
3388 3628 0.397941 CACCCAAGCTGTTCCAGAGA 59.602 55.000 0.00 0.0 32.44 3.10 R
3627 3867 1.938577 CCTTCCAGATTCGACTGCATG 59.061 52.381 0.00 0.0 36.67 4.06 R
4881 5268 0.683412 CCTGGATGATCCTCGATGCA 59.317 55.000 13.44 0.0 37.46 3.96 R
5306 5694 1.965754 GCGGCTCTCAGAGTCCCAAT 61.966 60.000 0.00 0.0 29.32 3.16 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
58 59 1.340248 GACGGAAGGCAATCGATAGGA 59.660 52.381 0.00 0.00 40.66 2.94
60 61 2.289072 ACGGAAGGCAATCGATAGGATG 60.289 50.000 0.00 0.00 34.93 3.51
75 76 5.574740 CGATAGGATGGAGGTAGAGGAGAAT 60.575 48.000 0.00 0.00 0.00 2.40
117 118 8.824159 AACGTAGATTCCAATATTGATGAGAG 57.176 34.615 17.23 0.00 0.00 3.20
119 120 8.303156 ACGTAGATTCCAATATTGATGAGAGAG 58.697 37.037 17.23 5.38 0.00 3.20
133 134 4.757799 TGAGAGAGAGTCAAACGAGAAG 57.242 45.455 0.00 0.00 0.00 2.85
179 180 7.707893 CAAAATATCTTTTGTGGGACATGATCC 59.292 37.037 0.00 2.48 44.49 3.36
223 227 5.482175 CCTAATTACTGTCTATGAGGAGGGG 59.518 48.000 1.61 0.00 0.00 4.79
240 244 2.626743 AGGGGTCGATGTAATAACTCCG 59.373 50.000 0.00 0.00 37.69 4.63
251 255 6.005583 TGTAATAACTCCGTCTTATAGCCG 57.994 41.667 0.00 0.00 0.00 5.52
252 256 5.764686 TGTAATAACTCCGTCTTATAGCCGA 59.235 40.000 0.00 0.00 0.00 5.54
277 281 9.152595 GACGATAACCTCTTTCTTTTAGTTCAT 57.847 33.333 0.00 0.00 0.00 2.57
325 329 1.298340 CCGTAGGCATTGGTGGTGA 59.702 57.895 0.00 0.00 46.14 4.02
396 400 8.928270 ACTAAGTATATGAGTTGTTCCTTTCG 57.072 34.615 0.00 0.00 0.00 3.46
403 407 5.728351 TGAGTTGTTCCTTTCGTTTACTG 57.272 39.130 0.00 0.00 0.00 2.74
404 408 5.180271 TGAGTTGTTCCTTTCGTTTACTGT 58.820 37.500 0.00 0.00 0.00 3.55
411 415 5.534207 TCCTTTCGTTTACTGTAGGTTCA 57.466 39.130 0.00 0.00 0.00 3.18
428 432 4.070716 GGTTCATGCCATATTCTGAGAGG 58.929 47.826 0.00 0.00 0.00 3.69
438 442 1.827681 TTCTGAGAGGTGGAGACTCG 58.172 55.000 0.00 0.00 39.90 4.18
441 445 2.772515 TCTGAGAGGTGGAGACTCGATA 59.227 50.000 0.00 0.00 39.90 2.92
476 480 7.236007 ATCTGTTTGATGTTGGCTTGACCAC 62.236 44.000 0.00 0.00 40.48 4.16
485 489 2.507484 TGGCTTGACCACTTGAGATTG 58.493 47.619 0.00 0.00 46.36 2.67
498 502 9.857656 ACCACTTGAGATTGATCAATAATATGT 57.142 29.630 20.75 13.70 38.47 2.29
519 590 9.956720 ATATGTTGCAATAGCTTTGTATTCTTC 57.043 29.630 0.59 0.00 42.74 2.87
520 591 6.620678 TGTTGCAATAGCTTTGTATTCTTCC 58.379 36.000 0.59 0.00 42.74 3.46
521 592 5.835113 TGCAATAGCTTTGTATTCTTCCC 57.165 39.130 0.00 0.00 42.74 3.97
522 593 4.335315 TGCAATAGCTTTGTATTCTTCCCG 59.665 41.667 0.00 0.00 42.74 5.14
523 594 4.574828 GCAATAGCTTTGTATTCTTCCCGA 59.425 41.667 0.00 0.00 37.91 5.14
524 595 5.065988 GCAATAGCTTTGTATTCTTCCCGAA 59.934 40.000 0.00 0.00 37.91 4.30
525 596 6.404293 GCAATAGCTTTGTATTCTTCCCGAAA 60.404 38.462 0.00 0.00 37.91 3.46
526 597 7.535139 CAATAGCTTTGTATTCTTCCCGAAAA 58.465 34.615 0.00 0.00 34.79 2.29
527 598 7.696992 ATAGCTTTGTATTCTTCCCGAAAAA 57.303 32.000 0.00 0.00 34.79 1.94
882 971 1.482593 CAGGTTTCTCGGCACCTAGAT 59.517 52.381 0.00 0.00 41.86 1.98
883 972 2.093447 CAGGTTTCTCGGCACCTAGATT 60.093 50.000 0.00 0.00 41.86 2.40
884 973 3.132289 CAGGTTTCTCGGCACCTAGATTA 59.868 47.826 0.00 0.00 41.86 1.75
908 997 0.460284 ATCGTGGCCGTTGATCTCAC 60.460 55.000 0.00 0.00 35.01 3.51
948 1037 1.664649 CAGTCGTTCGCTCAAGGCA 60.665 57.895 0.00 0.00 41.91 4.75
979 1068 2.305343 AGCAGGGGAAGCAGATATCATC 59.695 50.000 5.32 0.00 0.00 2.92
1006 1095 2.190313 CGCCTGAAGCTATGGCCA 59.810 61.111 8.56 8.56 43.42 5.36
1280 1369 7.135089 TGCGAAGTTGTGTTATTGCTTATTA 57.865 32.000 0.00 0.00 0.00 0.98
1281 1370 7.018826 TGCGAAGTTGTGTTATTGCTTATTAC 58.981 34.615 0.00 0.00 0.00 1.89
1282 1371 7.094975 TGCGAAGTTGTGTTATTGCTTATTACT 60.095 33.333 0.00 0.00 0.00 2.24
1283 1372 7.749126 GCGAAGTTGTGTTATTGCTTATTACTT 59.251 33.333 0.00 0.00 0.00 2.24
1354 1443 0.915364 CTTTAGAGGAAGGGGCTGCT 59.085 55.000 0.00 0.00 0.00 4.24
1356 1445 1.330655 TTAGAGGAAGGGGCTGCTCG 61.331 60.000 0.00 0.00 38.70 5.03
1368 1457 1.146637 GCTGCTCGTGATGATGGATC 58.853 55.000 0.00 0.00 0.00 3.36
1481 1572 4.083110 GGATGTTGTTCATGTCTTCCTGTG 60.083 45.833 0.00 0.00 36.83 3.66
1482 1573 3.213506 TGTTGTTCATGTCTTCCTGTGG 58.786 45.455 0.00 0.00 0.00 4.17
1483 1574 1.896220 TGTTCATGTCTTCCTGTGGC 58.104 50.000 0.00 0.00 0.00 5.01
1484 1575 1.421268 TGTTCATGTCTTCCTGTGGCT 59.579 47.619 0.00 0.00 0.00 4.75
1485 1576 2.079925 GTTCATGTCTTCCTGTGGCTC 58.920 52.381 0.00 0.00 0.00 4.70
1486 1577 1.649321 TCATGTCTTCCTGTGGCTCT 58.351 50.000 0.00 0.00 0.00 4.09
1487 1578 1.552337 TCATGTCTTCCTGTGGCTCTC 59.448 52.381 0.00 0.00 0.00 3.20
1488 1579 1.277273 CATGTCTTCCTGTGGCTCTCA 59.723 52.381 0.00 0.00 0.00 3.27
1489 1580 0.681733 TGTCTTCCTGTGGCTCTCAC 59.318 55.000 0.00 0.00 46.23 3.51
1490 1581 0.972883 GTCTTCCTGTGGCTCTCACT 59.027 55.000 0.00 0.00 46.20 3.41
1491 1582 1.067213 GTCTTCCTGTGGCTCTCACTC 60.067 57.143 0.00 0.00 46.20 3.51
1492 1583 1.203112 TCTTCCTGTGGCTCTCACTCT 60.203 52.381 0.00 0.00 46.20 3.24
1493 1584 1.204467 CTTCCTGTGGCTCTCACTCTC 59.796 57.143 0.00 0.00 46.20 3.20
1494 1585 0.113190 TCCTGTGGCTCTCACTCTCA 59.887 55.000 0.00 0.00 46.20 3.27
1660 1762 1.546476 CTCTCCCTTGTCTACACGCTT 59.454 52.381 0.00 0.00 0.00 4.68
1705 1807 5.570234 TGAAAAGTAATAATTCCGGGTGC 57.430 39.130 0.00 0.00 0.00 5.01
1715 1817 0.606944 TTCCGGGTGCGCAAGTTTAT 60.607 50.000 14.00 0.00 41.68 1.40
1722 1824 3.179048 GGTGCGCAAGTTTATCATTTCC 58.821 45.455 14.00 0.00 41.68 3.13
1723 1825 3.179048 GTGCGCAAGTTTATCATTTCCC 58.821 45.455 14.00 0.00 41.68 3.97
1727 1829 3.443681 CGCAAGTTTATCATTTCCCACCT 59.556 43.478 0.00 0.00 0.00 4.00
1956 2090 9.933723 AACTCATTTAATTTCCCTCTTCATTTG 57.066 29.630 0.00 0.00 0.00 2.32
1976 2110 9.913310 TCATTTGAATAATGGGTACATTCTACA 57.087 29.630 0.00 0.00 43.67 2.74
1980 2114 8.601845 TGAATAATGGGTACATTCTACATTCG 57.398 34.615 0.00 0.00 43.67 3.34
2031 2165 8.039538 GGGCTTAGAACTTTGTGTTACTATAGT 58.960 37.037 10.87 10.87 39.30 2.12
2266 2495 6.880484 ACATCAATGTACGAGGGTTTATACA 58.120 36.000 0.00 0.00 39.68 2.29
2341 2570 2.158986 AGATGCATCTGTAGTCAGTGCC 60.159 50.000 28.21 0.00 42.33 5.01
2728 2963 1.750399 CCTGAAGATTGCCCACCGG 60.750 63.158 0.00 0.00 0.00 5.28
2748 2983 2.416431 GGATTGCTCAAAGCCATGTGAC 60.416 50.000 0.00 0.00 44.26 3.67
2907 3143 4.357947 TCGTGTCTCGTGCAGGGC 62.358 66.667 6.56 0.00 40.80 5.19
2934 3170 4.997395 GTCATTATGGAACGATGCTATGGT 59.003 41.667 0.00 0.00 0.00 3.55
3175 3415 7.696992 TCTTATTAAAGCTACCAACTTTGGG 57.303 36.000 12.65 0.00 41.45 4.12
3191 3431 7.441017 CAACTTTGGGTTAAATCATTTCAGGA 58.559 34.615 0.00 0.00 36.23 3.86
3198 3438 6.442112 GGTTAAATCATTTCAGGAGCTATGC 58.558 40.000 0.00 0.00 0.00 3.14
3221 3461 1.485124 ATGTACGAGATCCTGCCACA 58.515 50.000 0.00 0.00 0.00 4.17
3320 3560 5.103290 TGGTGTATCTTTCGTTGCTTTTC 57.897 39.130 0.00 0.00 0.00 2.29
3361 3601 8.403236 ACAGTTGTGACAATACTTTTCCTTTAC 58.597 33.333 0.00 0.00 0.00 2.01
3375 3615 3.985127 TCCTTTACTGTAGGGGAATCGA 58.015 45.455 7.92 0.00 33.41 3.59
3382 3622 5.470047 ACTGTAGGGGAATCGATATGTTC 57.530 43.478 0.00 0.00 0.00 3.18
3384 3624 5.365605 ACTGTAGGGGAATCGATATGTTCAA 59.634 40.000 0.00 0.00 0.00 2.69
3388 3628 6.688073 AGGGGAATCGATATGTTCAATACT 57.312 37.500 0.00 0.00 0.00 2.12
3454 3694 1.273606 GCAGTAAGCCTCACACTCTGA 59.726 52.381 0.00 0.00 37.23 3.27
3504 3744 1.541588 GAAGTGCCACCATGTTCCTTC 59.458 52.381 0.00 0.00 0.00 3.46
3512 3752 4.262592 GCCACCATGTTCCTTCTTTTCATT 60.263 41.667 0.00 0.00 0.00 2.57
3617 3857 8.554835 TCAACAATTGATTTCATGAATGCAAT 57.445 26.923 21.36 21.36 34.08 3.56
3627 3867 9.270576 GATTTCATGAATGCAATATACACGATC 57.729 33.333 9.40 0.38 0.00 3.69
3636 3876 4.433413 GCAATATACACGATCATGCAGTCG 60.433 45.833 14.86 14.86 43.13 4.18
3667 3907 5.206905 AGGGTATAATCTTTGGCAGGTTT 57.793 39.130 0.00 0.00 0.00 3.27
3673 3913 7.338449 GGTATAATCTTTGGCAGGTTTGTTCTA 59.662 37.037 0.00 0.00 0.00 2.10
3710 3950 6.182627 TCCTCAATAGCATCTTTCACATTGT 58.817 36.000 0.00 0.00 0.00 2.71
3797 4040 8.934507 TGTTTTTATTCAAACTGGTAAACTGG 57.065 30.769 0.00 0.00 37.51 4.00
3798 4041 8.532819 TGTTTTTATTCAAACTGGTAAACTGGT 58.467 29.630 0.00 0.00 37.51 4.00
3799 4042 8.813282 GTTTTTATTCAAACTGGTAAACTGGTG 58.187 33.333 0.00 0.00 34.35 4.17
3800 4043 7.883391 TTTATTCAAACTGGTAAACTGGTGA 57.117 32.000 0.00 0.00 0.00 4.02
3801 4044 8.472007 TTTATTCAAACTGGTAAACTGGTGAT 57.528 30.769 0.00 0.00 0.00 3.06
3802 4045 9.575868 TTTATTCAAACTGGTAAACTGGTGATA 57.424 29.630 0.00 0.00 0.00 2.15
3803 4046 7.687941 ATTCAAACTGGTAAACTGGTGATAG 57.312 36.000 0.00 0.00 0.00 2.08
3805 4048 3.629142 ACTGGTAAACTGGTGATAGCC 57.371 47.619 0.00 0.00 0.00 3.93
3807 4050 3.587506 ACTGGTAAACTGGTGATAGCCTT 59.412 43.478 0.00 0.00 0.00 4.35
3903 4284 1.956170 CTCCGCCGTGCATATGGTC 60.956 63.158 4.56 0.00 35.28 4.02
3916 4297 3.130516 GCATATGGTCTATGCTACCGCTA 59.869 47.826 4.56 0.00 44.93 4.26
3922 4303 4.015084 GGTCTATGCTACCGCTAATCCTA 58.985 47.826 0.00 0.00 36.97 2.94
4002 4383 3.570550 AGTTAGATGGTCGTCCTATGAGC 59.429 47.826 0.00 0.00 32.56 4.26
4067 4448 3.929610 GCTGTTGATCTGACTTCAGTACC 59.070 47.826 6.15 0.00 44.12 3.34
4074 4455 5.300539 TGATCTGACTTCAGTACCAGATAGC 59.699 44.000 9.89 2.61 43.88 2.97
4075 4456 4.861196 TCTGACTTCAGTACCAGATAGCT 58.139 43.478 6.15 0.00 44.12 3.32
4092 4475 3.305398 AGCTCTCTTGGTAAACACTCG 57.695 47.619 0.00 0.00 0.00 4.18
4095 4478 3.184581 GCTCTCTTGGTAAACACTCGTTG 59.815 47.826 0.00 0.00 34.86 4.10
4114 4497 8.395633 ACTCGTTGTTGGTAATAATATTTGAGC 58.604 33.333 0.00 0.00 0.00 4.26
4411 4794 9.809096 TTACTTTGATTCACAAATGTTTTGCTA 57.191 25.926 0.06 0.00 45.63 3.49
4472 4855 6.399639 TTTGTAAATTCAGGGACAAGAACC 57.600 37.500 0.00 0.00 33.60 3.62
4623 5006 7.872113 AATCTTCAGAAATACCTTGTCATCC 57.128 36.000 0.00 0.00 0.00 3.51
4644 5027 6.155475 TCCCGATTTTCAAGTGATGTTTTT 57.845 33.333 0.00 0.00 0.00 1.94
4760 5145 1.897133 AGAAAAGCATGGCAAGCATCA 59.103 42.857 17.75 0.00 0.00 3.07
4771 5156 1.705256 CAAGCATCATGTTGTGTGCC 58.295 50.000 5.69 0.00 36.28 5.01
4827 5214 6.426328 AGTCACTCACATTTCTTTCTGCTAAG 59.574 38.462 0.00 0.00 0.00 2.18
4881 5268 0.178068 ATCAGAACTTGGGCGCGTAT 59.822 50.000 8.43 0.00 0.00 3.06
4994 5381 6.111768 ACATGAGTAAAAATGTCATCGCTC 57.888 37.500 0.00 0.00 31.33 5.03
5034 5421 2.327343 GGTGCTGCTGCGTGATTCA 61.327 57.895 11.21 0.00 43.34 2.57
5306 5694 1.135527 CCGGACACTGTTATAAGCCGA 59.864 52.381 0.00 0.00 39.62 5.54
5307 5695 2.223971 CCGGACACTGTTATAAGCCGAT 60.224 50.000 0.00 0.00 39.62 4.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 2.440409 ACTCATGGCCAATGAAGACAC 58.560 47.619 10.96 0.00 44.77 3.67
5 6 3.264193 ACACTACTCATGGCCAATGAAGA 59.736 43.478 10.96 2.02 44.77 2.87
7 8 3.719268 ACACTACTCATGGCCAATGAA 57.281 42.857 10.96 0.00 44.77 2.57
8 9 4.835284 TTACACTACTCATGGCCAATGA 57.165 40.909 10.96 13.41 43.24 2.57
9 10 5.185454 TCTTTACACTACTCATGGCCAATG 58.815 41.667 10.96 9.31 37.66 2.82
10 11 5.189736 TCTCTTTACACTACTCATGGCCAAT 59.810 40.000 10.96 0.00 0.00 3.16
11 12 4.530553 TCTCTTTACACTACTCATGGCCAA 59.469 41.667 10.96 0.00 0.00 4.52
12 13 4.093743 TCTCTTTACACTACTCATGGCCA 58.906 43.478 8.56 8.56 0.00 5.36
13 14 4.737855 TCTCTTTACACTACTCATGGCC 57.262 45.455 0.00 0.00 0.00 5.36
14 15 5.112686 CCTTCTCTTTACACTACTCATGGC 58.887 45.833 0.00 0.00 0.00 4.40
15 16 5.422331 TCCCTTCTCTTTACACTACTCATGG 59.578 44.000 0.00 0.00 0.00 3.66
16 17 6.334202 GTCCCTTCTCTTTACACTACTCATG 58.666 44.000 0.00 0.00 0.00 3.07
17 18 5.125739 CGTCCCTTCTCTTTACACTACTCAT 59.874 44.000 0.00 0.00 0.00 2.90
58 59 7.791766 TCTTTTCATATTCTCCTCTACCTCCAT 59.208 37.037 0.00 0.00 0.00 3.41
60 61 7.604657 TCTTTTCATATTCTCCTCTACCTCC 57.395 40.000 0.00 0.00 0.00 4.30
95 96 9.859427 CTCTCTCTCATCAATATTGGAATCTAC 57.141 37.037 15.36 0.00 0.00 2.59
97 98 8.495160 ACTCTCTCTCATCAATATTGGAATCT 57.505 34.615 15.36 0.00 0.00 2.40
117 118 3.243771 TGTTCCCTTCTCGTTTGACTCTC 60.244 47.826 0.00 0.00 0.00 3.20
119 120 2.801111 GTGTTCCCTTCTCGTTTGACTC 59.199 50.000 0.00 0.00 0.00 3.36
133 134 6.380095 TTTGTGTTATGTACTTGTGTTCCC 57.620 37.500 0.00 0.00 0.00 3.97
240 244 4.455190 AGAGGTTATCGTCGGCTATAAGAC 59.545 45.833 0.00 0.00 34.19 3.01
251 255 8.530269 TGAACTAAAAGAAAGAGGTTATCGTC 57.470 34.615 0.00 0.00 0.00 4.20
259 263 8.848474 TTCTGGTATGAACTAAAAGAAAGAGG 57.152 34.615 0.00 0.00 0.00 3.69
307 311 0.107214 ATCACCACCAATGCCTACGG 60.107 55.000 0.00 0.00 0.00 4.02
308 312 1.016627 CATCACCACCAATGCCTACG 58.983 55.000 0.00 0.00 0.00 3.51
350 354 5.010933 AGTTTCATCGACTTCTCCTCTGTA 58.989 41.667 0.00 0.00 0.00 2.74
384 388 5.525012 ACCTACAGTAAACGAAAGGAACAAC 59.475 40.000 0.00 0.00 0.00 3.32
395 399 3.331150 TGGCATGAACCTACAGTAAACG 58.669 45.455 0.00 0.00 0.00 3.60
396 400 7.499232 AGAATATGGCATGAACCTACAGTAAAC 59.501 37.037 10.98 0.00 0.00 2.01
403 407 5.858381 TCTCAGAATATGGCATGAACCTAC 58.142 41.667 10.98 0.00 0.00 3.18
404 408 5.012458 CCTCTCAGAATATGGCATGAACCTA 59.988 44.000 10.98 0.00 0.00 3.08
411 415 3.321039 TCCACCTCTCAGAATATGGCAT 58.679 45.455 4.88 4.88 0.00 4.40
428 432 6.903883 TTTAAAAGCATATCGAGTCTCCAC 57.096 37.500 0.00 0.00 0.00 4.02
441 445 8.776470 CCAACATCAAACAGATTTTAAAAGCAT 58.224 29.630 17.74 3.32 33.72 3.79
496 500 6.350110 GGGAAGAATACAAAGCTATTGCAACA 60.350 38.462 0.00 0.00 42.74 3.33
497 501 6.036470 GGGAAGAATACAAAGCTATTGCAAC 58.964 40.000 0.00 0.00 42.74 4.17
498 502 5.163663 CGGGAAGAATACAAAGCTATTGCAA 60.164 40.000 0.00 0.00 42.74 4.08
499 503 4.335315 CGGGAAGAATACAAAGCTATTGCA 59.665 41.667 1.12 0.00 42.74 4.08
500 504 4.574828 TCGGGAAGAATACAAAGCTATTGC 59.425 41.667 8.09 0.00 40.05 3.56
528 599 9.511144 AATTTTCGAGTCGAATACAAAGTTTTT 57.489 25.926 27.26 9.41 45.28 1.94
529 600 9.166126 GAATTTTCGAGTCGAATACAAAGTTTT 57.834 29.630 27.26 12.34 45.28 2.43
530 601 8.339714 TGAATTTTCGAGTCGAATACAAAGTTT 58.660 29.630 27.26 12.99 45.28 2.66
531 602 7.857569 TGAATTTTCGAGTCGAATACAAAGTT 58.142 30.769 27.26 15.10 45.28 2.66
532 603 7.416154 TGAATTTTCGAGTCGAATACAAAGT 57.584 32.000 27.26 17.66 45.28 2.66
533 604 8.009974 ACTTGAATTTTCGAGTCGAATACAAAG 58.990 33.333 27.26 24.47 46.42 2.77
534 605 7.857569 ACTTGAATTTTCGAGTCGAATACAAA 58.142 30.769 27.26 18.70 46.42 2.83
535 606 7.416154 ACTTGAATTTTCGAGTCGAATACAA 57.584 32.000 27.26 24.15 46.42 2.41
838 909 2.530701 AGAGTACTGCCAAGCTACTGT 58.469 47.619 0.00 0.00 0.00 3.55
839 910 3.257393 CAAGAGTACTGCCAAGCTACTG 58.743 50.000 0.00 0.00 0.00 2.74
840 911 2.354203 GCAAGAGTACTGCCAAGCTACT 60.354 50.000 0.00 0.00 0.00 2.57
841 912 2.003301 GCAAGAGTACTGCCAAGCTAC 58.997 52.381 0.00 0.00 0.00 3.58
842 913 2.386661 GCAAGAGTACTGCCAAGCTA 57.613 50.000 0.00 0.00 0.00 3.32
843 914 3.239861 GCAAGAGTACTGCCAAGCT 57.760 52.632 0.00 0.00 0.00 3.74
876 947 3.654414 GGCCACGATCTGTTAATCTAGG 58.346 50.000 0.00 0.00 0.00 3.02
882 971 1.001068 TCAACGGCCACGATCTGTTAA 59.999 47.619 2.24 0.00 44.60 2.01
883 972 0.604073 TCAACGGCCACGATCTGTTA 59.396 50.000 2.24 0.00 44.60 2.41
884 973 0.036388 ATCAACGGCCACGATCTGTT 60.036 50.000 2.24 0.00 44.60 3.16
908 997 1.818959 TTACCTGGACCCGTTCACCG 61.819 60.000 0.00 0.00 0.00 4.94
910 999 1.406477 GGATTACCTGGACCCGTTCAC 60.406 57.143 0.00 0.00 0.00 3.18
948 1037 2.361610 CCCCTGCTTCGCCATTGT 60.362 61.111 0.00 0.00 0.00 2.71
1280 1369 2.093128 CAGCCAACGGGGACTAATAAGT 60.093 50.000 0.00 0.00 40.01 2.24
1281 1370 2.169769 TCAGCCAACGGGGACTAATAAG 59.830 50.000 0.00 0.00 40.01 1.73
1282 1371 2.169769 CTCAGCCAACGGGGACTAATAA 59.830 50.000 0.00 0.00 40.01 1.40
1283 1372 1.760613 CTCAGCCAACGGGGACTAATA 59.239 52.381 0.00 0.00 40.01 0.98
1284 1373 0.541863 CTCAGCCAACGGGGACTAAT 59.458 55.000 0.00 0.00 40.01 1.73
1285 1374 1.550130 CCTCAGCCAACGGGGACTAA 61.550 60.000 0.00 0.00 40.01 2.24
1354 1443 4.525912 AATCATCGATCCATCATCACGA 57.474 40.909 0.00 0.00 37.39 4.35
1356 1445 8.434733 AATCATAATCATCGATCCATCATCAC 57.565 34.615 0.00 0.00 0.00 3.06
1368 1457 6.153510 TCTCCTCCCTGTAATCATAATCATCG 59.846 42.308 0.00 0.00 0.00 3.84
1481 1572 0.684153 AGAGCCTGAGAGTGAGAGCC 60.684 60.000 0.00 0.00 0.00 4.70
1482 1573 0.457035 CAGAGCCTGAGAGTGAGAGC 59.543 60.000 0.00 0.00 32.44 4.09
1483 1574 1.105457 CCAGAGCCTGAGAGTGAGAG 58.895 60.000 4.00 0.00 32.44 3.20
1484 1575 0.324183 CCCAGAGCCTGAGAGTGAGA 60.324 60.000 4.00 0.00 32.44 3.27
1485 1576 0.324183 TCCCAGAGCCTGAGAGTGAG 60.324 60.000 4.00 0.00 32.44 3.51
1486 1577 0.324183 CTCCCAGAGCCTGAGAGTGA 60.324 60.000 4.00 0.00 32.77 3.41
1487 1578 0.324183 TCTCCCAGAGCCTGAGAGTG 60.324 60.000 11.54 0.85 37.55 3.51
1488 1579 0.636101 ATCTCCCAGAGCCTGAGAGT 59.364 55.000 11.54 0.85 37.55 3.24
1489 1580 1.133388 AGATCTCCCAGAGCCTGAGAG 60.133 57.143 7.20 7.20 37.62 3.20
1490 1581 0.932955 AGATCTCCCAGAGCCTGAGA 59.067 55.000 4.00 0.00 39.31 3.27
1491 1582 1.792115 AAGATCTCCCAGAGCCTGAG 58.208 55.000 0.00 0.00 29.18 3.35
1492 1583 2.260639 AAAGATCTCCCAGAGCCTGA 57.739 50.000 0.00 0.00 29.18 3.86
1493 1584 3.454082 ACTAAAAGATCTCCCAGAGCCTG 59.546 47.826 0.00 0.00 29.18 4.85
1494 1585 3.730269 ACTAAAAGATCTCCCAGAGCCT 58.270 45.455 0.00 0.00 29.18 4.58
1689 1791 1.301423 TGCGCACCCGGAATTATTAC 58.699 50.000 5.66 0.00 34.32 1.89
1704 1806 3.179048 GTGGGAAATGATAAACTTGCGC 58.821 45.455 0.00 0.00 0.00 6.09
1705 1807 3.443681 AGGTGGGAAATGATAAACTTGCG 59.556 43.478 0.00 0.00 0.00 4.85
1715 1817 0.251916 CCGCTGTAGGTGGGAAATGA 59.748 55.000 0.00 0.00 41.64 2.57
1722 1824 4.602340 AGTATTATTCCGCTGTAGGTGG 57.398 45.455 0.00 0.00 46.40 4.61
1723 1825 6.920569 AAAAGTATTATTCCGCTGTAGGTG 57.079 37.500 0.00 0.00 0.00 4.00
1727 1829 7.767198 AGTTGCTAAAAGTATTATTCCGCTGTA 59.233 33.333 0.00 0.00 0.00 2.74
1801 1903 6.912051 CGTCTGTTCAGAAAATGTTGAATTCA 59.088 34.615 3.38 3.38 35.91 2.57
1808 1910 7.703328 ACATTAACGTCTGTTCAGAAAATGTT 58.297 30.769 17.88 15.16 38.30 2.71
1955 2089 7.659799 CCGAATGTAGAATGTACCCATTATTCA 59.340 37.037 5.86 0.00 41.37 2.57
1956 2090 7.660208 ACCGAATGTAGAATGTACCCATTATTC 59.340 37.037 0.00 0.00 41.37 1.75
1975 2109 8.450964 ACATTTCACTTAGTAATCAACCGAATG 58.549 33.333 0.00 0.00 0.00 2.67
1976 2110 8.561738 ACATTTCACTTAGTAATCAACCGAAT 57.438 30.769 0.00 0.00 0.00 3.34
1977 2111 7.972832 ACATTTCACTTAGTAATCAACCGAA 57.027 32.000 0.00 0.00 0.00 4.30
2200 2410 7.010460 GCAAATATAACAATTTCCCAAGCAGAC 59.990 37.037 0.00 0.00 0.00 3.51
2210 2439 9.848172 CGCCAAATAAGCAAATATAACAATTTC 57.152 29.630 0.00 0.00 0.00 2.17
2266 2495 5.413833 CACAAAACTGAGCCATGACTTCTAT 59.586 40.000 0.00 0.00 0.00 1.98
2341 2570 5.523552 TGCTACATCAATACCTTCATTCACG 59.476 40.000 0.00 0.00 0.00 4.35
2480 2712 5.119931 AGTAGCACATTCGCAAATCAAAA 57.880 34.783 0.00 0.00 0.00 2.44
2538 2770 9.562583 GTAATTTACGAATTCAAGCAACCATAA 57.437 29.630 6.22 0.00 36.82 1.90
2728 2963 2.229543 TGTCACATGGCTTTGAGCAATC 59.770 45.455 0.00 0.00 44.75 2.67
2748 2983 2.669364 GCATCAGCAGGACAAACTTTG 58.331 47.619 0.00 0.00 41.58 2.77
2778 3013 2.196595 CCTCCAACCATGACCCTCTTA 58.803 52.381 0.00 0.00 0.00 2.10
2907 3143 2.032894 GCATCGTTCCATAATGACACCG 60.033 50.000 0.00 0.00 33.49 4.94
2934 3170 3.819564 ACTGATAAGCATCTACCGCAA 57.180 42.857 0.00 0.00 31.93 4.85
3018 3254 6.505048 AGATCATGTAAACCATCCTGATGA 57.495 37.500 8.69 0.00 41.20 2.92
3066 3306 3.565902 GCATGTAAAGAGGGTTATCTGGC 59.434 47.826 0.00 0.00 0.00 4.85
3175 3415 6.442112 GGCATAGCTCCTGAAATGATTTAAC 58.558 40.000 0.00 0.00 0.00 2.01
3191 3431 3.156288 TCTCGTACATAGGGCATAGCT 57.844 47.619 0.00 0.00 0.00 3.32
3198 3438 1.546476 GGCAGGATCTCGTACATAGGG 59.454 57.143 0.00 0.00 0.00 3.53
3320 3560 4.389992 CACAACTGTGCTACATAACAGAGG 59.610 45.833 9.63 3.98 45.43 3.69
3343 3583 7.336176 CCCCTACAGTAAAGGAAAAGTATTGTC 59.664 40.741 0.00 0.00 36.08 3.18
3361 3601 5.468540 TGAACATATCGATTCCCCTACAG 57.531 43.478 1.71 0.00 0.00 2.74
3375 3615 6.989169 GCTGTTCCAGAGAGTATTGAACATAT 59.011 38.462 0.00 0.00 42.91 1.78
3382 3622 3.937706 CCAAGCTGTTCCAGAGAGTATTG 59.062 47.826 0.00 0.00 32.44 1.90
3384 3624 2.503356 CCCAAGCTGTTCCAGAGAGTAT 59.497 50.000 0.00 0.00 32.44 2.12
3388 3628 0.397941 CACCCAAGCTGTTCCAGAGA 59.602 55.000 0.00 0.00 32.44 3.10
3504 3744 8.981659 ACAGAGGGGGATATTTAAAATGAAAAG 58.018 33.333 0.00 0.00 0.00 2.27
3512 3752 6.384886 ACGAGTAACAGAGGGGGATATTTAAA 59.615 38.462 0.00 0.00 0.00 1.52
3518 3758 4.736611 ATACGAGTAACAGAGGGGGATA 57.263 45.455 0.00 0.00 0.00 2.59
3550 3790 7.158099 GGCTTACCTGAAATGTATGAACTTT 57.842 36.000 0.00 0.00 0.00 2.66
3617 3857 4.561735 TTCGACTGCATGATCGTGTATA 57.438 40.909 16.18 3.15 39.38 1.47
3627 3867 1.938577 CCTTCCAGATTCGACTGCATG 59.061 52.381 0.00 0.00 36.67 4.06
3636 3876 6.207614 GCCAAAGATTATACCCTTCCAGATTC 59.792 42.308 0.00 0.00 0.00 2.52
3673 3913 7.765695 TGCTATTGAGGAATTTGTTCTCTTT 57.234 32.000 0.00 0.00 0.00 2.52
3690 3930 6.317088 ACGAACAATGTGAAAGATGCTATTG 58.683 36.000 0.00 0.00 0.00 1.90
3694 3934 6.500684 AATACGAACAATGTGAAAGATGCT 57.499 33.333 0.00 0.00 0.00 3.79
3750 3992 7.660030 ACATAACCTAGGAAATCCCAAATTG 57.340 36.000 17.98 0.00 37.41 2.32
3763 4006 9.855021 CCAGTTTGAATAAAAACATAACCTAGG 57.145 33.333 7.41 7.41 41.56 3.02
3859 4240 7.878621 TCCTATCACATTAAGAGGATTGGAT 57.121 36.000 10.15 0.00 36.96 3.41
3912 4293 7.649370 CATGGATATGCTTATAGGATTAGCG 57.351 40.000 0.00 0.00 37.73 4.26
4002 4383 2.102357 CCTCGACCGATGTCACCG 59.898 66.667 0.00 0.00 41.85 4.94
4035 4416 4.672413 GTCAGATCAACAGCAAAAGAAACG 59.328 41.667 0.00 0.00 0.00 3.60
4067 4448 5.971763 AGTGTTTACCAAGAGAGCTATCTG 58.028 41.667 12.49 2.67 35.30 2.90
4074 4455 4.369182 ACAACGAGTGTTTACCAAGAGAG 58.631 43.478 0.00 0.00 37.01 3.20
4075 4456 4.395959 ACAACGAGTGTTTACCAAGAGA 57.604 40.909 0.00 0.00 37.01 3.10
4155 4538 6.375455 CCTTCCAGACAATAGTACAGCAAAAT 59.625 38.462 0.00 0.00 0.00 1.82
4157 4540 5.245531 CCTTCCAGACAATAGTACAGCAAA 58.754 41.667 0.00 0.00 0.00 3.68
4158 4541 4.832248 CCTTCCAGACAATAGTACAGCAA 58.168 43.478 0.00 0.00 0.00 3.91
4161 4544 4.744795 AGCCTTCCAGACAATAGTACAG 57.255 45.455 0.00 0.00 0.00 2.74
4162 4545 5.499004 AAAGCCTTCCAGACAATAGTACA 57.501 39.130 0.00 0.00 0.00 2.90
4163 4546 7.769044 TGATAAAAGCCTTCCAGACAATAGTAC 59.231 37.037 0.00 0.00 0.00 2.73
4170 4553 3.009473 AGCTGATAAAAGCCTTCCAGACA 59.991 43.478 0.00 0.00 44.68 3.41
4309 4692 6.815089 ACCAACTGAGCACAAATTTCATAAA 58.185 32.000 0.00 0.00 0.00 1.40
4827 5214 3.817647 AGAACTCTTCCAACAATCTGCAC 59.182 43.478 0.00 0.00 0.00 4.57
4881 5268 0.683412 CCTGGATGATCCTCGATGCA 59.317 55.000 13.44 0.00 37.46 3.96
4994 5381 2.939103 CCTGTTAATCGGGAAAGAGCTG 59.061 50.000 0.00 0.00 45.09 4.24
5128 5515 9.492973 TTCACGTGATGATCATTATGACATAAT 57.507 29.630 20.80 13.86 37.11 1.28
5306 5694 1.965754 GCGGCTCTCAGAGTCCCAAT 61.966 60.000 0.00 0.00 29.32 3.16
5307 5695 2.650116 GCGGCTCTCAGAGTCCCAA 61.650 63.158 0.00 0.00 29.32 4.12
5707 6097 0.647410 CGTTGATGTAGAGCTTGCCG 59.353 55.000 0.00 0.00 0.00 5.69
5708 6098 2.010145 TCGTTGATGTAGAGCTTGCC 57.990 50.000 0.00 0.00 0.00 4.52
5937 6327 1.139654 CGCCAGATCCAGATCCTTCAA 59.860 52.381 4.01 0.00 38.58 2.69


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

AutoCloner maintained by Alex Coulton.